#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
OR13C5	138799	hgsc.bcm.edu	37	9	107361179	107361182	+	Frame_Shift_Del	DEL	GTTA	GTTA	-	rs202235686	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GTTA	GTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107361179_107361182delGTTA	ENST00000374779.2	-	1	606_609	c.513_516delTAAC	c.(511-516)aataacfs	p.NN171fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	171						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						GATTGATGATGTTATTCCTGCAGA	0.451														276	0.0551118	0.0817	0.0202	5008	,	,		25393	0.0585		0.0089	False		,,,				2504	0.0879				p.172_173del		Atlas-Indel	.											.	OR13C5	60	.	0			c.514_517del						PASS	.																																			SO:0001589	frameshift_variant	138799	exon1			.		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.513_516delTAAC	9.37:g.107361179_107361182delGTTA	ENSP00000363911:p.Asn171fs	Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	467	34	0.0728051	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	CCDS35091.1																																																																																			.	.	weak		0.451	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
NCOA3	8202	hgsc.bcm.edu	37	20	46279815	46279823	+	In_Frame_Del	DEL	GCAGCAGCA	GCAGCAGCA	-	rs3830810		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GCAGCAGCA	GCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:46279815_46279823delGCAGCAGCA	ENST00000371998.3	+	20	3932_3940	c.3741_3749delGCAGCAGCA	c.(3739-3750)atgcagcagcag>atg	p.QQQ1272del	NCOA3_ENST00000371997.3_In_Frame_Del_p.QQQ1263del|NCOA3_ENST00000341724.6_In_Frame_Del_p.QQQ1198del|NCOA3_ENST00000372004.3_In_Frame_Del_p.QQQ1268del			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1272	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CTATGATGATgcagcagcagcagcagcag	0.545																																					p.1247_1250del		Pindel,Atlas-Indel	.											.	NCOA3	156	.	0			c.3740_3748del						PASS	.																																			SO:0001651	inframe_deletion	8202	exon20			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3741_3749delGCAGCAGCA	20.37:g.46279824_46279832delGCAGCAGCA	ENSP00000361066:p.Gln1272_Gln1274del	Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	114	25	0.219	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	In_Frame_Del	DEL	ENST00000371998.3	37	CCDS13407.1																																																																																			.	.	none		0.545	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
EIF4EBP3	8637	hgsc.bcm.edu	37	5	139931628	139931629	+	IGR	INS	-	-	GT	rs5871740|rs3085220|rs368142622|rs202193903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139931628_139931629insGT	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Frame_Shift_Ins_p.V110fs	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCTCCATCACAGCCTCAGAC	0.589														2174	0.434105	0.2194	0.5144	5008	,	,		18017	0.5645		0.4831	False		,,,				2504	0.4826				p.V110fs		Atlas-Indel	.											SRA1,NS,carcinoma,0,2	SRA1	24	2	0			c.329_330insAC						PASS	.																																			SO:0001628	intergenic_variant	10011	exon3			.	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931628_139931629insGT		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	194	38	0.195876	NM_001035235		Frame_Shift_Ins	INS	ENST00000310331.2	37	CCDS4226.1																																																																																			.	.	strong		0.589	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732	
USP40	55230	hgsc.bcm.edu	37	2	234429739	234429740	+	In_Frame_Ins	INS	-	-	TTC	rs141501074|rs59586144|rs397953463	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234429739_234429740insTTC	ENST00000427112.2	-	16	2254_2255	c.2219_2220insGAA	c.(2218-2220)aaa>aaGAAa	p.740_740K>KK	USP40_ENST00000450966.1_In_Frame_Ins_p.752_752K>KK|USP40_ENST00000251722.6_In_Frame_Ins_p.740_740K>KK			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	740					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		TAGTGACCCATTTCTCTTCCTT	0.361														749	0.149561	0.1967	0.1326	5008	,	,		19239	0.0456		0.2425	False		,,,				2504	0.1094				p.K752delinsKK		Pindel,Atlas-Indel	.											.	USP40	174	.	0			c.2256_2257insGAA						PASS	.			676,2890		63,550,1170						-1.6	0.8		dbSNP_130	84	1690,6138		187,1316,2411	no	coding	USP40	NM_018218.2		250,1866,3581	A1A1,A1R,RR		21.5892,18.9568,20.7653				2366,9028				SO:0001652	inframe_insertion	55230	exon16			.	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.2217_2219dupGAA	2.37:g.234429740_234429742dupTTC	ENSP00000387898:p.Lys740dup	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	66	25	0.379	NM_018218	Q6NX38|Q70EL0	In_Frame_Ins	INS	ENST00000427112.2	37	CCDS46547.1																																																																																			-|0.837;TTC|0.163	0.163	strong		0.361	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
HLA-A	3105	hgsc.bcm.edu	37	6	29912395	29912396	+	Frame_Shift_Ins	INS	-	-	GG	rs545184037|rs143166124|rs201507150	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29912395_29912396insGG	ENST00000376806.5	+	5	1323_1324	c.1014_1015insGG	c.(1015-1017)ggafs	p.G339fs	HLA-A_ENST00000396634.1_Splice_Site|HLA-A_ENST00000376809.5_Splice_Site|HLA-A_ENST00000376802.2_Intron			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	337					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGAGCTCAGGTGGAGAAGGGGT	0.574									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)				279	0.0557109	0.0825	0.0677	5008	,	,		18055	0.0179		0.0656	False		,,,				2504	0.0399				.		Atlas-Indel	.											.	HLA-A	89	.	0			c.1012+2->GG						PASS	.																																			SO:0001589	frameshift_variant	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	.	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000376806.5:c.1015_1016dupGG	6.37:g.29912396_29912397dupGG	ENSP00000366002:p.Gly339fs	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	387	41	0.105943	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Splice_Site	INS	ENST00000376806.5	37																																																																																				.	.	weak		0.574	HLA-A-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000252910.1	NM_002116	
USP36	57602	hgsc.bcm.edu	37	17	76798549	76798554	+	In_Frame_Del	DEL	TTTTTC	TTTTTC	-	rs200324254|rs71964596		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TTTTTC	TTTTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76798549_76798554delTTTTTC	ENST00000542802.3	-	17	3317_3322	c.2874_2879delGAAAAA	c.(2872-2880)aagaaaaaa>aaa	p.958_960KKK>K	USP36_ENST00000312010.6_In_Frame_Del_p.958_960KKK>K|USP36_ENST00000449938.2_In_Frame_Del_p.563_565KKK>K			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	956					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)	p.K959_K960delKK(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			CTGCTTTCTTTTTTTCTTTTTCTTTT	0.534														1638	0.327077	0.0454	0.4092	5008	,	,		13018	0.4107		0.5129	False		,,,				2504	0.3722				p.959_960del		Pindel,Atlas-Indel	.											.	USP36	243	.	1	Deletion - In frame(1)	ovary(1)	c.2875_2880del						PASS	.			526,3738		42,442,1648						-4.5	0.0		dbSNP_130	46	4276,3978		1111,2054,962	no	coding	USP36	NM_025090.3		1153,2496,2610	A1A1,A1R,RR		48.1948,12.3358,38.3608				4802,7716				SO:0001651	inframe_deletion	57602	exon17			.	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2874_2879delGAAAAA	17.37:g.76798555_76798560delTTTTTC	ENSP00000441214:p.Lys958_Lys959del	Somatic	65	.	.		WXS	Illumina HiSeq	Phase_I	68	21	0.309	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	In_Frame_Del	DEL	ENST00000542802.3	37	CCDS32755.1																																																																																			TTTTTC|0.636;-|0.364	0.364	strong		0.534	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
KRT2	3849	hgsc.bcm.edu	37	12	53045601	53045603	+	In_Frame_Del	DEL	CTG	CTG	-	rs369691469		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53045601_53045603delCTG	ENST00000309680.3	-	1	345_347	c.324_326delCAG	c.(322-327)ttcagt>ttt	p.S109del		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	109	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		accaccaccactgaagccgctgc	0.635																																					p.109_109del		Atlas-Indel	.											.	KRT2	94	.	0			c.325_327del						PASS	.			45,4193		0,45,2074						-3.5	0.4		dbSNP_126	33	375,7857		0,375,3741	no	coding	KRT2	NM_000423.2		0,420,5815	A1A1,A1R,RR		4.5554,1.0618,3.3681				420,12050				SO:0001651	inframe_deletion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.324_326delCAG	12.37:g.53045601_53045603delCTG	ENSP00000310861:p.Ser109del	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	147	12	0.0816327	NM_000423	Q4VAQ2	In_Frame_Del	DEL	ENST00000309680.3	37	CCDS8835.1																																																																																			.	.	weak		0.635	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	
CCDC37	348807	hgsc.bcm.edu	37	3	126142434	126142436	+	In_Frame_Del	DEL	GGA	GGA	-	rs140223152|rs398102320|rs35657615|rs200815085	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126142434_126142436delGGA	ENST00000352312.1	+	13	1332_1334	c.1233_1235delGGA	c.(1231-1236)acggag>acg	p.E412del	CCDC37_ENST00000393425.1_In_Frame_Del_p.E413del|CCDC37_ENST00000505024.1_In_Frame_Del_p.E413del	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	412				Missing (in Ref. 3; AAI01370/AAI01368). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		GCCAGGAGACGGAGAAGACCCTG	0.611														272	0.0543131	0.0068	0.0605	5008	,	,		17424	0.003		0.1223	False		,,,				2504	0.0971				p.411_412del		Pindel,Atlas-Indel	.											.	CCDC37	69	.	0			c.1232_1234del						PASS	.			125,4141		4,117,2012						2.6	1.0		dbSNP_134	96	1085,7169		63,959,3105	no	coding	CCDC37	NM_182628.2		67,1076,5117	A1A1,A1R,RR		13.1451,2.9301,9.6645				1210,11310				SO:0001651	inframe_deletion	348807	exon13			.	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1233_1235delGGA	3.37:g.126142434_126142436delGGA	ENSP00000344749:p.Glu412del	Somatic	150	.	.		WXS	Illumina HiSeq	Phase_I	146	39	0.267	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	In_Frame_Del	DEL	ENST00000352312.1	37	CCDS3037.1																																																																																			GGA|0.949;-|0.051	0.051	strong		0.611	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
AK5	26289	hgsc.bcm.edu	37	1	78024345	78024346	+	In_Frame_Ins	INS	-	-	TAT	rs77198824|rs71756472|rs79671213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:78024345_78024346insTAT	ENST00000354567.2	+	14	1942_1943	c.1679_1680insTAT	c.(1678-1683)tctatt>tcTATtatt	p.561_562insI	AK5_ENST00000478255.1_In_Frame_Ins_p.76_77insI|AK5_ENST00000344720.5_In_Frame_Ins_p.535_536insI	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	561				Missing (in Ref. 2; AAP97322 and 5; AAH33896/AAH12467). {ECO:0000305}.	ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						GCTATTGACTCTATTTTCTGAA	0.322														3103	0.619609	0.326	0.817	5008	,	,		19811	0.7411		0.7465	False		,,,				2504	0.6207				p.S560delinsSI		Pindel,Atlas-Indel	.											.	AK5	86	.	0			c.1679_1680insTAT						PASS	.		,	1762,2504		378,1006,749					,	5.6	1.0		dbSNP_130	95	6253,2001		2372,1509,246	no	coding,coding	AK5	NM_174858.2,NM_012093.3	,	2750,2515,995	A1A1,A1R,RR		24.2428,41.3033,35.9824	,	,		8015,4505				SO:0001652	inframe_insertion	26289	exon14			.	AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"""Adenylate kinases"""	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.1680_1682dupTAT	1.37:g.78024346_78024348dupTAT	ENSP00000346577:p.Ile561_Ile561dup	Somatic	291	.	.		WXS	Illumina HiSeq	Phase_I	261	54	0.207	NM_174858	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	In_Frame_Ins	INS	ENST00000354567.2	37	CCDS675.1																																																																																			-|0.343;TAT|0.657	0.657	strong		0.322	AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858	
EPHX2	2053	hgsc.bcm.edu	37	8	27394334	27394335	+	In_Frame_Ins	INS	-	-	GTC	rs71868122|rs71220599|rs71553864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27394334_27394335insGTC	ENST00000521400.1	+	13	1634_1635	c.1204_1205insGTC	c.(1204-1206)agt>aGTCgt	p.403_404insR	EPHX2_ENST00000517536.1_In_Frame_Ins_p.220_221insR|EPHX2_ENST00000380476.3_In_Frame_Ins_p.350_351insR|EPHX2_ENST00000521780.1_In_Frame_Ins_p.337_338insR|EPHX2_ENST00000518379.1_In_Frame_Ins_p.371_372insR	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	403	Epoxide hydrolase.		R -> RR. {ECO:0000269|PubMed:10862610, ECO:0000269|PubMed:14702039}.		arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		ACAGAACCTGAGTCGGACTTTC	0.51														116	0.0231629	0.0068	0.0245	5008	,	,		15678	0.005		0.0507	False		,,,				2504	0.0348				p.S402delinsSR		Pindel,Atlas-Indel	.											.	EPHX2	57	.	0			c.1204_1205insGTC						PASS	.			56,4208		0,56,2076						-1.9	0.1		dbSNP_130	92	486,7768		11,464,3652	no	coding	EPHX2	NM_001979.4		11,520,5728	A1A1,A1R,RR		5.8881,1.3133,4.3298				542,11976				SO:0001652	inframe_insertion	2053	exon13			.	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1205_1207dupGTC	8.37:g.27394335_27394337dupGTC	ENSP00000430269:p.Arg403_Arg403dup	Somatic	153	.	.		WXS	Illumina HiSeq	Phase_I	222	64	0.288	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	In_Frame_Ins	INS	ENST00000521400.1	37	CCDS6060.1																																																																																			-|0.973;GTC|0.027	0.027	strong		0.510	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
RPGR	6103	hgsc.bcm.edu	37	X	38147286	38147288	+	In_Frame_Del	DEL	TTG	TTG	-	rs62653033|rs281865305|rs398123335		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:38147286_38147288delTTG	ENST00000339363.3	-	14	1746_1748	c.1579_1581delCAA	c.(1579-1581)caadel	p.Q527del	RPGR_ENST00000309513.3_In_Frame_Del_p.Q465del|RPGR_ENST00000378505.2_In_Frame_Del_p.Q527del|RPGR_ENST00000342811.3_In_Frame_Del_p.Q527del|RPGR_ENST00000318842.7_In_Frame_Del_p.Q527del|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000338898.3_3'UTR			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	527					cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CCCCAATTGTTTGTTGTTTCTGT	0.315														34	0.00900662	0.0008	0.0086	3775	,	,		15760	0.0		0.0268	False		,,,				2504	0.0				p.527_528del		Pindel,Atlas-Indel	.											.	RPGR	175	.	0			c.1580_1582del						PASS	.		,	8,3713		0,8,0,1584,537					,	0.0	0.0			126	191,6292		1,135,54,2221,1715	no	coding,coding	RPGR	NM_001034853.1,NM_000328.2	,	1,143,54,3805,2252	A1A1,A1R,A1,RR,R		2.9462,0.215,1.9502	,	,		199,10005				SO:0001651	inframe_deletion	6103	exon14			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.1579_1581delCAA	X.37:g.38147289_38147291delTTG	ENSP00000343671:p.Gln527del	Somatic	212	.	.		WXS	Illumina HiSeq	Phase_I	82	59	0.720	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.315	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
ZBTB33	10009	hgsc.bcm.edu	37	X	119387833	119387834	+	In_Frame_Ins	INS	-	-	TGA	rs201958171|rs77815464|rs59686094		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:119387833_119387834insTGA	ENST00000326624.2	+	2	791_792	c.563_564insTGA	c.(562-567)tctgat>tcTGAtgat	p.194_195insD	ZBTB33_ENST00000557385.1_In_Frame_Ins_p.194_195insD	NM_006777.3	NP_006768.1	Q86T24	KAISO_HUMAN	zinc finger and BTB domain containing 33	194					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	26						GTTACCGATTCtgatgatgatg	0.396														1942	0.514437	0.2065	0.4078	3775	,	,		15520	0.4494		0.5328	False		,,,				2504	0.4059				p.S188delinsSD		Pindel,Atlas-Indel	.											.	ZBTB33	72	.	0			c.563_564insTGA						PASS	.																																			SO:0001652	inframe_insertion	10009	exon2			.	BC042753	CCDS14596.1	Xq23	2013-01-09			ENSG00000177485	ENSG00000177485		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16682	protein-coding gene	gene with protein product		300329					Standard	NM_001184742		Approved	ZNF-kaiso, kaiso, WUGSC:H_DJ525N14.1, KAISO, ZNF348	uc004esn.1	Q86T24	OTTHUMG00000171159	ENST00000326624.2:c.579_581dupTGA	X.37:g.119387840_119387842dupTGA	ENSP00000314153:p.Asp194_Asp194dup	Somatic	207	.	.		WXS	Illumina HiSeq	Phase_I	96	54	0.562	NM_006777	B2R5U6|O00319|Q7Z361|Q8IVP6|Q8N3P0	In_Frame_Ins	INS	ENST00000326624.2	37	CCDS14596.1																																																																																			-|0.437;TGA|0.563	0.563	strong		0.396	ZBTB33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058085.2	NM_006777	
NXF1	10482	hgsc.bcm.edu	37	11	62569105	62569106	+	Splice_Site	INS	-	-	AC	rs146787397|rs377023070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62569105_62569106insAC	ENST00000532297.1	-	8	1269		c.e8-2		NXF1_ENST00000531131.1_Splice_Site|NXF1_ENST00000294172.2_Splice_Site|NXF1_ENST00000531709.2_Splice_Site|NXF1_ENST00000439713.2_Splice_Site			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1						gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CATGATCAGCTAGAGGAAAAAG	0.5														565	0.112819	0.1634	0.0548	5008	,	,		20474	0.1558		0.0437	False		,,,				2504	0.1125				.		Pindel,Atlas-Indel	.											.	NXF1	67	.	0			c.640-2->GT						PASS	.		,	608,3656		45,518,1569					,	5.5	0.9		dbSNP_134	171	477,7777		18,441,3668	no	splice-3,splice-3	NXF1	NM_006362.4,NM_001081491.1	,	63,959,5237	A1A1,A1R,RR		5.779,14.2589,8.6675	,	,		1085,11433				SO:0001630	splice_region_variant	10482	exon8			.	AF112880	CCDS8037.1, CCDS44629.1	11q12-q13	2008-07-21			ENSG00000162231	ENSG00000162231			8071	protein-coding gene	gene with protein product	"""tip associating protein"""	602647				9175835, 9660949	Standard	NM_001081491		Approved	TAP, Mex67, DKFZp667O0311	uc001nvf.1	Q9UBU9	OTTHUMG00000167612	ENST00000532297.1:c.640-2->GT	11.37:g.62569105_62569106insAC		Somatic	118	.	.		WXS	Illumina HiSeq	Phase_I	114	35	0.307	NM_006362	B4E269|Q99799|Q9UQL2	Splice_Site	INS	ENST00000532297.1	37	CCDS8037.1																																																																																			-|0.907;AC|0.093	0.093	strong		0.500	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362	Intron
BDNF	627	hgsc.bcm.edu	37	11	27681174	27681175	+	5'UTR	INS	-	-	TG	rs71449160		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:27681174_27681175insTG	ENST00000525528.1	-	0	30_31				BDNF_ENST00000356660.4_Intron|BDNF_ENST00000395980.2_Intron|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000439476.2_5'UTR|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000314915.6_Intron|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000395981.3_Intron|BDNF-AS_ENST00000501176.2_RNA|BDNF_ENST00000525950.1_Intron|BDNF_ENST00000532997.1_Intron|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000395978.3_Intron|BDNF_ENST00000395986.2_Intron|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000395983.3_Intron|BDNF-AS_ENST00000500662.2_RNA|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000533131.1_Intron|BDNF_ENST00000438929.1_Intron|BDNF_ENST00000420794.1_Intron|BDNF_ENST00000530861.1_Intron|BDNF_ENST00000418212.1_Intron|BDNF_ENST00000533246.1_Intron|BDNF_ENST00000584049.1_Intron	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor						axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						GAGATGTTCTCTCtgtgtgtgt	0.446																																					.		Atlas-Indel	.											.	BDNF	63	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	627	.			.	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"""Endogenous ligands"""	1033	protein-coding gene	gene with protein product	"""neurotrophin"""	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.-1064->CA	11.37:g.27681174_27681175insTG		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	205	80	0.390244	.	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	RNA	INS	ENST00000525528.1	37	CCDS7866.1																																																																																			-|0.500;CT|0.500	.	strong		0.446	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240782	39240796	+	In_Frame_Del	DEL	CTGCTGCCGCCCCAG	CTGCTGCCGCCCCAG	-	rs9894966|rs9894106|rs199957151|rs11650261|rs541163988|rs553572799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTGCTGCCGCCCCAG	CTGCTGCCGCCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39240782_39240796delCTGCTGCCGCCCCAG	ENST00000391417.4	+	1	324_338	c.324_338delCTGCTGCCGCCCCAG	c.(322-339)acctgctgccgccccagc>acc	p.CCRPS109del		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	134	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.S113C(1)|p.P112P(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						gccagcccacctgctgccgccccagctgctgccgc	0.67														169	0.033746	0.0061	0.0375	5008	,	,		15885	0.0238		0.0775	False		,,,				2504	0.0337				p.108_113del		Atlas-Indel	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-7	49	2	4	Substitution - Missense(1)|Unknown(1)|Substitution - coding silent(1)|Deletion - In frame(1)	NS(2)|prostate(2)	c.323_337del						PASS	.			120,3626		16,88,1769						1.0	0.3		dbSNP_126	14	690,6608		77,536,3036	no	coding	KRTAP4-7	NM_033061.3		93,624,4805	A1A1,A1R,RR		9.4546,3.2034,7.3343				810,10234				SO:0001651	inframe_deletion	100132476	exon1			.	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.324_338delCTGCTGCCGCCCCAG	17.37:g.39240782_39240796delCTGCTGCCGCCCCAG	ENSP00000375236:p.Cys109_Ser113del	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	122	84	0.688525	NM_033061	A0AVM6|A8MQ08|A8MTL4	In_Frame_Del	DEL	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	none		0.670	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803308	43803309	+	Splice_Site	INS	-	-	TA	rs34966432|rs56283966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43803308_43803309insTA	ENST00000291532.3	-	8	1572		c.e8-1		TMPRSS3_ENST00000380399.1_Splice_Site|TMPRSS3_ENST00000433957.2_Splice_Site|TMPRSS3_ENST00000398397.3_Splice_Site|TMPRSS3_ENST00000398405.1_Splice_Site|TMPRSS3_ENST00000474596.1_Splice_Site	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3						cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)	p.?(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TGACCACAGGCTATGGAGGGGA	0.599														870	0.173722	0.118	0.0865	5008	,	,		22290	0.3145		0.0865	False		,,,				2504	0.2556				.		Pindel,Atlas-Indel	.											TMPRSS3,NS,carcinoma,0,2	TMPRSS3	40	2	2	Unknown(2)	ovary(2)	c.617-1->TA						PASS	.		,	532,3732		34,464,1634				http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,	4.8	0.9		dbSNP_129	68	605,7649		19,567,3541	no	splice-3,splice-3	TMPRSS3	NM_032405.1,NM_024022.2	,	53,1031,5175	A1A1,A1R,RR		7.3298,12.4765,9.0829	,	,		1137,11381				SO:0001630	splice_region_variant	64699	exon9			.	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.617-1->TA	21.37:g.43803309_43803310dupTA		Somatic	57	.	.		WXS	Illumina HiSeq	Phase_I	64	17	0.266	NM_024022	D3DSJ6|Q5USC7|Q6ZMC3	Splice_Site	INS	ENST00000291532.3	37	CCDS13686.1																																																																																			-|0.840;TA|0.160	0.160	strong		0.599	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		Intron
ALMS1	7840	hgsc.bcm.edu	37	2	73675227	73675228	+	In_Frame_Ins	INS	-	-	CTC	rs34628045|rs199801824|rs587621330	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:73675227_73675228insCTC	ENST00000264448.6	+	8	1681_1682	c.1570_1571insCTC	c.(1570-1572)tct>tCTCct	p.524_525insP	ALMS1_ENST00000377715.1_In_Frame_Ins_p.524_525insP|ALMS1_ENST00000409009.1_In_Frame_Ins_p.482_483insP	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	524				S -> SP (in Ref. 1; CAD10391). {ECO:0000305}.	endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.S524P(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GGCTGTAAGTTCTCTAGAAACT	0.421														3007	0.600439	0.2912	0.7046	5008	,	,		17151	0.7847		0.6581	False		,,,				2504	0.6953				p.S524delinsSP		Pindel,Atlas-Indel	.											ALMS1,NS,carcinoma,0,1	ALMS1	384	1	1	Substitution - Missense(1)	pancreas(1)	c.1570_1571insCTC						PASS	.			1351,2331		279,793,769						1.4	0.0		dbSNP_134	97	5015,2861		1592,1831,515	no	coding	ALMS1	NM_015120.4		1871,2624,1284	A1A1,A1R,RR		36.3255,36.692,44.9213				6366,5192				SO:0001652	inframe_insertion	7840	exon8			.	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.1571_1573dupCTC	2.37:g.73675228_73675230dupCTC	ENSP00000264448:p.Ser524_Leu525insPro	Somatic	225	.	.		WXS	Illumina HiSeq	Phase_I	195	68	0.349	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Ins	INS	ENST00000264448.6	37	CCDS42697.1																																																																																			CTC|1.000;|0.000	1.000	strong		0.421	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
MAMDC2	256691	hgsc.bcm.edu	37	9	72755129	72755131	+	In_Frame_Del	DEL	AAA	AAA	-	rs61609258|rs79430954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AAA	AAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:72755129_72755131delAAA	ENST00000377182.4	+	8	1680_1682	c.1063_1065delAAA	c.(1063-1065)aaadel	p.K355del	MAMDC2-AS1_ENST00000591368.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	355	MAM 3. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						TTACCAAGATAAAGAAGGTCCAG	0.453														521	0.104034	0.0061	0.0317	5008	,	,		19109	0.2153		0.0855	False		,,,				2504	0.1922				p.354_355del		Pindel,Atlas-Indel	.											.	MAMDC2	55	.	0			c.1062_1064del						PASS	.			71,4193		1,69,2062						-0.2	1.0		dbSNP_129	125	652,7602		24,604,3499	no	coding	MAMDC2	NM_153267.4		25,673,5561	A1A1,A1R,RR		7.8992,1.6651,5.7757				723,11795				SO:0001651	inframe_deletion	256691	exon8			.	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.1063_1065delAAA	9.37:g.72755129_72755131delAAA	ENSP00000366387:p.Lys355del	Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	91	30	0.330	NM_153267	Q5VW47|Q8WX43|Q96BM4	In_Frame_Del	DEL	ENST00000377182.4	37	CCDS6631.1																																																																																			AAA|0.905;-|0.095	0.095	strong		0.453	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267	
PRSS16	10279	hgsc.bcm.edu	37	6	27223065	27223079	+	In_Frame_Del	DEL	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	-	rs199705677|rs201493618|rs144604424|rs140280737|rs371606222|rs147170589|rs143492910|rs200987021|rs141138864|rs142712601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27223065_27223079delAAGGAGAGCCAGATT	ENST00000230582.3	+	12	1531_1545	c.1516_1530delAAGGAGAGCCAGATT	c.(1516-1530)aaggagagccagattdel	p.KESQI506del	PRSS16_ENST00000421826.2_In_Frame_Del_p.KESQI249del|PRSS16_ENST00000377456.2_3'UTR	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	506					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)	p.K506_I510delKESQI(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CAAGCTGGCAAAGGAGAGCCAGATTAAGGGTGAAG	0.479														511	0.102037	0.1135	0.1124	5008	,	,		20927	0.0139		0.174	False		,,,				2504	0.0961				p.505_510del	NSCLC(178;1118 2105 17078 23587 44429)	Pindel,Atlas-Indel	.											.	PRSS16	66	.	1	Deletion - In frame(1)	ovary(1)	c.1515_1529del						PASS	.			514,3748		27,460,1644						-5.7	0.0		dbSNP_113	73	1519,6735		166,1187,2774	no	coding	PRSS16	NM_005865.3		193,1647,4418	A1A1,A1R,RR		18.4032,12.0601,16.2432				2033,10483				SO:0001651	inframe_deletion	10279	exon12			.	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1516_1530delAAGGAGAGCCAGATT	6.37:g.27223065_27223079delAAGGAGAGCCAGATT	ENSP00000230582:p.Lys506_Ile510del	Somatic	130	.	.		WXS	Illumina HiSeq	Phase_I	105	61	0.581	NM_005865	O75416	In_Frame_Del	DEL	ENST00000230582.3	37	CCDS4623.1																																																																																			AAGGAGAGCCAGATT|0.883;-|0.117	0.117	strong		0.479	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		
PBOV1	59351	hgsc.bcm.edu	37	6	138539183	138539184	+	Frame_Shift_Ins	INS	-	-	G	rs397781314|rs3841283|rs397886596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138539183_138539184insG	ENST00000527246.2	-	1	443_444	c.349_350insC	c.(349-351)ctafs	p.L117fs	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	117						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		TTCCAGACCTAGGGTCTGAGTT	0.386													GGGG|GGG|GGGG|deletion	781	0.15595	0.1498	0.1556	5008	,	,		21295	0.3581		0.0616	False		,,,				2504	0.0532				p.L117fs		Pindel,Atlas-Indel	.											PBOV1_ENST00000527246,bladder,carcinoma,-1,2	PBOV1	12	2	0			c.350_351insC						PASS	.		,	649,3615		49,551,1532					,	-0.7	0.0		dbSNP_107	157	566,7688		18,530,3579	no	frameshift,intron	KIAA1244,PBOV1	NM_021635.2,NM_020340.4	,	67,1081,5111	A1A1,A1R,RR		6.8573,15.2205,9.706	,	,		1215,11303				SO:0001589	frameshift_variant	59351	exon1			.	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.350dupC	6.37:g.138539186_138539186dupG	ENSP00000432353:p.Leu117fs	Somatic	253	.	.		WXS	Illumina HiSeq	Phase_I	206	49	0.238	NM_021635		Frame_Shift_Ins	INS	ENST00000527246.2	37	CCDS5190.1																																																																																			-|0.811;G|0.189	0.189	strong		0.386	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635	
DSPP	1834	hgsc.bcm.edu	37	4	88536317	88536319	+	In_Frame_Del	DEL	AGC	AGC	-	rs143008261	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536317_88536319delAGC	ENST00000282478.7	+	4	2536_2538	c.2503_2505delAGC	c.(2503-2505)agcdel	p.S836del	DSPP_ENST00000399271.1_In_Frame_Del_p.S836del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	836	Asp/Ser-rich.			S -> C (in Ref. 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		cagcagcgatagcagcaacagca	0.498														418	0.0834665	0.0537	0.1023	5008	,	,		37195	0.0942		0.1213	False		,,,				2504	0.0603				p.834_835del		Pindel,Atlas-Indel	.											.	DSPP	174	.	0			c.2502_2504del						PASS	.			179,2961		27,125,1418						-0.4	0.0		dbSNP_134	106	716,4848		92,532,2158	no	coding	DSPP	NM_014208.3		119,657,3576	A1A1,A1R,RR		12.8684,5.7006,10.2826				895,7809				SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2503_2505delAGC	4.37:g.88536320_88536322delAGC	ENSP00000282478:p.Ser836del	Somatic	417	.	.		WXS	Illumina HiSeq	Phase_I	397	68	0.171	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	37	CCDS43248.1																																																																																			AGC|0.917;-|0.083	0.083	strong		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
CD200R1L	344807	hgsc.bcm.edu	37	3	112545911	112545911	+	Frame_Shift_Del	DEL	T	T	-	rs58161637|rs200703227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:112545911delT	ENST00000398214.1	-	4	833	c.608delA	c.(607-609)cacfs	p.H203fs	CD200R1L_ENST00000488794.1_Frame_Shift_Del_p.H182fs|CD200R1L_ENST00000448932.1_Frame_Shift_Del_p.H182fs	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	203	Ig-like C2-type.					integral component of membrane (GO:0016021)		p.H203P(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						AGTAGACTTGTGGCCCTCCCA	0.493													T|T|-|deletion	841	0.167931	0.0953	0.2133	5008	,	,		17526	0.0625		0.3231	False		,,,				2504	0.183				p.H203fs		Pindel,Atlas-Indel	.											CD200R1L,NS,carcinoma,-1,1	CD200R1L	47	1	1	Substitution - Missense(1)	lung(1)	c.609delC						PASS	.		,	560,3704		37,486,1609	55.0	49.0	51.0		,	1.4	0.0	3	dbSNP_129	64	2613,5641		429,1755,1943	yes	frameshift,frameshift	CD200R1L	NM_001199215.1,NM_001008784.2	,	466,2241,3552	A1A1,A1R,RR		31.6574,13.1332,25.3475	,	,	112545911	3173,9345	2175	4016	6191	SO:0001589	frameshift_variant	344807	exon4			.	AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"""Immunoglobulin superfamily / C2-set domain containing"""	24665	protein-coding gene	gene with protein product	"""CD200 receptor 2"""						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.608delA	3.37:g.112545911delT	ENSP00000381272:p.His203fs	Somatic	116	.	.		WXS	Illumina HiSeq	Phase_I	159	54	0.340	NM_001008784	Q6WHB7	Frame_Shift_Del	DEL	ENST00000398214.1	37	CCDS43131.1																																																																																			T|0.815;-|0.185	0.185	strong		0.493	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784	
P2RX5	5026	hgsc.bcm.edu	37	17	3594277	3594277	+	Frame_Shift_Del	DEL	G	G	-	rs138772680|rs397743686|rs3215407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3594277delG	ENST00000225328.5	-	3	731	c.333delC	c.(331-333)cccfs	p.P111fs	P2RX5-TAX1BP3_ENST00000550383.1_Frame_Shift_Del_p.P111fs|P2RX5_ENST00000435558.1_Frame_Shift_Del_p.P111fs|P2RX5_ENST00000550772.1_5'Flank|P2RX5_ENST00000547178.1_Frame_Shift_Del_p.P111fs|P2RX5_ENST00000345901.3_Intron|P2RX5_ENST00000551178.1_Intron|P2RX5_ENST00000552050.1_Intron|P2RX5_ENST00000552276.1_Frame_Shift_Del_p.P111fs	NM_001204519.1|NM_002561.3	NP_001191448.1|NP_002552.2	Q93086	P2RX5_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 5	111					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transport (GO:0006810)	integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|ion channel activity (GO:0005216)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						GCCGCTGGTTGGGGGTCACAA	0.597													GGGGG|GGGGG|GGGG|deletion	2872	0.573482	0.1702	0.7767	5008	,	,		18534	0.8145		0.6918	False		,,,				2504	0.6043				p.N112fs		Pindel,Atlas-Indel	.											.	P2RX5	36	.	0			c.334delA	GRCh37	CD054974	P2RX5	D	rs5818907	PASS	.		,,,	1161,3103		165,831,1136	47.0	23.0	32.0		,,,	3.9	1.0	17	dbSNP_114	59	5647,2607		1943,1761,423	yes	intron,frameshift,intron,frameshift	P2RX5	NM_175080.2,NM_002561.3,NM_001204520.1,NM_001204519.1	,,,	2108,2592,1559	A1A1,A1R,RR		31.5847,27.228,45.6143	,,,	,,,	3594277	6808,5710	2191	4147	6338	SO:0001589	frameshift_variant	5026	exon3			.	AF016709	CCDS11034.1, CCDS11035.1, CCDS56014.1, CCDS56015.1	17p13.3	2012-01-17			ENSG00000083454	ENSG00000083454		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8536	protein-coding gene	gene with protein product		602836				9414125	Standard	NM_002561		Approved	P2X5	uc002fwi.3	Q93086	OTTHUMG00000090700	ENST00000225328.5:c.333delC	17.37:g.3594277delG	ENSP00000225328:p.Pro111fs	Somatic	64	.	.		WXS	Illumina HiSeq	Phase_I	60	21	0.350	NM_001204519	G5E981|O43450|O75540|Q308M5|Q59F38|Q8IXW4|Q93087|Q9NZV0	Frame_Shift_Del	DEL	ENST00000225328.5	37	CCDS11034.1																																																																																			G|0.374;-|0.626	0.626	strong		0.597	P2RX5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207388.3	NM_002561, NM_175080, NM_175081	
ZNF527	84503	hgsc.bcm.edu	37	19	37879855	37879855	+	Frame_Shift_Del	DEL	T	T	-	rs373623156|rs200420244|rs386809049|rs200343305|rs3081552		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:37879855delT	ENST00000436120.2	+	5	1011	c.904delT	c.(904-906)tatfs	p.Y302fs	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGAAAAACCATATGCATGCAA	0.393																																					p.P301fs		Atlas-Indel	.											.	ZNF527	78	.	0			c.903delA						PASS	.			51,3991		2,47,1972	104.0	92.0	96.0			-2.3	0.1	19	dbSNP_102	97	580,7526		48,484,3521	no	frameshift	ZNF527	NM_032453.1		50,531,5493	A1A1,A1R,RR		7.1552,1.2618,5.1943			37879855	631,11517	2092	4235	6327	SO:0001589	frameshift_variant	84503	exon5			.	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.904delT	19.37:g.37879855delT	ENSP00000390179:p.Tyr302fs	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	125	45	0.36	NM_032453	B4DVL5	Frame_Shift_Del	DEL	ENST00000436120.2	37	CCDS42559.1																																																																																			T|0.910;-|0.090	0.090	strong		0.393	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577707	+	RNA	DEL	G	G	-	rs527250207|rs202116886	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90577707delG	ENST00000551025.1	+	0	6135									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		ATGAATTATTGACATCTTTGC	0.378													G|G|-|deletion	307	0.0613019	0.0053	0.0749	5008	,	,		22516	0.0387		0.1163	False		,,,				2504	0.0941				p.L1566X	Colon(187;1656 2025 17045 31481 39901)	Atlas-Indel	.											.	CASP8AP2	108	.	0			c.4697delT						PASS	.		,,	49,3627		4,41,1793	175.0	151.0	158.0		,,	2.6	0.1	6		159	660,7220		65,530,3345	no	frameshift,frameshift,frameshift	CASP8AP2	NM_012115.3,NM_001137668.1,NM_001137667.1	,,	69,571,5138	A1A1,A1R,RR		8.3756,1.333,6.1353	,,	,,	90577707	709,10847	1895	4059	5954			9994	exon8			.	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90577707delG		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	67	14	0.208955	NM_001137668		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	alt		0.378	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
C14orf23	387978	hgsc.bcm.edu	37	14	29261305	29261305	+	Frame_Shift_Del	DEL	A	A	-	rs202195469|rs200251419		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:29261305delA	ENST00000399387.4	+	3	446	c.342delA	c.(340-342)ctafs	p.L114fs	C14orf23_ENST00000550266.1_Intron|C14orf23_ENST00000548213.1_Intron					chromosome 14 open reading frame 23											central_nervous_system(1)	1						CTTCAGCACTAAAAAAAACAA	0.378																																					.		Atlas-Indel	.											.	C14orf23	5	.	0			.						PASS	.																																			SO:0001589	frameshift_variant	387978	.			.			14q11.2	2013-01-15			ENSG00000186960	ENSG00000186960			19828	other	unknown							Standard	NR_026731		Approved		uc001wqf.3	Q86U37	OTTHUMG00000029410	ENST00000399387.4:c.342delA	14.37:g.29261305delA	ENSP00000382318:p.Leu114fs	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	119	16	0.134454	.		RNA	DEL	ENST00000399387.4	37																																																																																				A|0.648;-|0.352	0.352	strong		0.378	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000134019.2	NR_026731	
TRIOBP	11078	hgsc.bcm.edu	37	22	38120176	38120178	+	In_Frame_Del	DEL	CCT	CCT	-	rs529080937|rs36219868	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38120176_38120178delCCT	ENST00000406386.3	+	7	1868_1870	c.1613_1615delCCT	c.(1612-1617)gcctcc>gcc	p.S540del		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	540					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.S540delS(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AATCCCAGAGCCTCCTCTCCCAA	0.606														1254	0.250399	0.1362	0.2277	5008	,	,		30273	0.3651		0.2932	False		,,,				2504	0.2587				p.538_538del		Atlas-Indel	.											.	TRIOBP	262	.	1	Deletion - In frame(1)	ovary(1)	c.1612_1614del						PASS	.			598,3166		11,576,1295						-6.6	0.0		dbSNP_126	143	2675,5301		8,2659,1321	no	coding	TRIOBP	NM_001039141.2		19,3235,2616	A1A1,A1R,RR		33.5381,15.8874,27.879				3273,8467				SO:0001651	inframe_deletion	11078	exon7			.	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1613_1615delCCT	22.37:g.38120179_38120181delCCT	ENSP00000384312:p.Ser540del	Somatic	533	0	0		WXS	Illumina HiSeq	Phase_I	639	230	0.359937	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	In_Frame_Del	DEL	ENST00000406386.3	37	CCDS43015.1																																																																																			.	.	strong		0.606	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
TCEB3CL2	100506888	hgsc.bcm.edu	37	18	44543098	44543099	+	Frame_Shift_Ins	INS	-	-	GC	rs373334809		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44543098_44543099insGC	ENST00000591973.2	-	1	1508_1509	c.1273_1274insGC	c.(1273-1275)cagfs	p.Q425fs	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron	NM_001242907.1	NP_001229836.1	A6NLF2	EA3L2_HUMAN	transcription elongation factor B polypeptide 3C-like 2	425	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)										TCGCAGCCGCTGCTCTCGGGCG	0.554																																					p.Q425fs		Atlas-Indel	.											.	.	.	.	0			c.1274_1275insGC						PASS	.																																			SO:0001589	frameshift_variant	100506888	exon1			.		CCDS59316.1	18q21.1	2012-10-25			ENSG00000266996	ENSG00000274744			33511	protein-coding gene	gene with protein product							Standard	NM_001242907		Approved		uc021ujk.1	A6NLF2	OTTHUMG00000180382	ENST00000591973.2:c.1272_1273dupGC	18.37:g.44543099_44543100dupGC	ENSP00000468046:p.Gln425fs	Somatic	621	0	0		WXS	Illumina HiSeq	Phase_I	591	97	0.164129	NM_001242907		Frame_Shift_Ins	INS	ENST00000591973.2	37	CCDS59316.1																																																																																			.	.	weak		0.554	TCEB3CL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451070.1	XM_929328	
LAD1	3898	hgsc.bcm.edu	37	1	201356002	201356004	+	In_Frame_Del	DEL	CCA	CCA	-	rs78190062|rs552300739|rs35119736|rs398053706|rs386638482	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201356002_201356004delCCA	ENST00000391967.2	-	3	786_788	c.485_487delTGG	c.(484-489)gtgggc>ggc	p.V162del	LAD1_ENST00000367313.3_In_Frame_Del_p.V176del	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	162						basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						GGCTCCCTGCCCACCAAGCTCTC	0.586														301	0.0601038	0.0666	0.0504	5008	,	,		15375	0.0575		0.0686	False		,,,				2504	0.0521				p.162_163del		Pindel,Atlas-Indel	.											.	LAD1	42	.	0			c.486_488del						PASS	.			826,3440		92,642,1399						-0.4	0.0		dbSNP_131	54	717,7533		40,637,3448	no	coding	LAD1	NM_005558.3		132,1279,4847	A1A1,A1R,RR		8.6909,19.3624,12.3282				1543,10973				SO:0001651	inframe_deletion	3898	exon3			.	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.485_487delTGG	1.37:g.201356005_201356007delCCA	ENSP00000375829:p.Val162del	Somatic	149	.	.		WXS	Illumina HiSeq	Phase_I	159	50	0.314	NM_005558	O95614|Q96GD8	In_Frame_Del	DEL	ENST00000391967.2	37	CCDS1410.1																																																																																			CCA|0.886;-|0.114	0.114	strong		0.586	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
EIF4EBP3	8637	hgsc.bcm.edu	37	5	139931629	139931630	+	IGR	INS	-	-	G	rs5871740|rs368142622|rs202193903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139931629_139931630insG	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Frame_Shift_Ins_p.V110fs	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTCCATCACAGCCTCAGACT	0.594													-|-|G|insertion	2174	0.434105	0.2194	0.5144	5008	,	,		17103	0.5645		0.4831	False		,,,				2504	0.4826				p.V110fs		Atlas-Indel	.											SRA1,NS,carcinoma,+1,2	SRA1	24	2	0			c.328_329insC						PASS	.																																			SO:0001628	intergenic_variant	10011	exon3			.	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931629_139931630insG		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	190	38	0.2	NM_001035235		Frame_Shift_Ins	INS	ENST00000310331.2	37	CCDS4226.1																																																																																			.	.	weak		0.594	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732	
FAM154B	283726	hgsc.bcm.edu	37	15	82574734	82574735	+	Frame_Shift_Del	DEL	AC	AC	-	rs531481065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:82574734_82574735delAC	ENST00000339465.5	+	3	597_598	c.528_529delAC	c.(526-531)caacgcfs	p.R177fs	FAM154B_ENST00000427381.2_Frame_Shift_Del_p.R162fs|FAM154B_ENST00000565501.1_3'UTR	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	177										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						CAACTGACCAACGCTTTGAGGA	0.441														6	0.00119808	0.0	0.0	5008	,	,		20560	0.0		0.006	False		,,,				2504	0.0				p.176_176del		Pindel,Atlas-Indel	.											.	FAM154B	50	.	0			c.527_528del						PASS	.			11,4253		0,11,2121						1.4	0.0			67	78,8176		1,76,4050	no	frameshift	FAM154B	NM_001008226.1		1,87,6171	A1A1,A1R,RR		0.945,0.258,0.711				89,12429				SO:0001589	frameshift_variant	283726	exon3			.	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.528_529delAC	15.37:g.82574734_82574735delAC	ENSP00000340445:p.Arg177fs	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	91	34	0.374	NM_001008226	B4E2M2	Frame_Shift_Del	DEL	ENST00000339465.5	37	CCDS32310.1																																																																																			.	.	none		0.441	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226	
OR2T12	127064	hgsc.bcm.edu	37	1	248458876	248458876	+	Frame_Shift_Del	DEL	T	T	-	rs11339452	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248458876delT	ENST00000317996.1	-	1	4	c.5delA	c.(4-6)gagfs	p.E2fs		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	2						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E2fs*2(1)|p.E2G(1)		endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			ATTTCTCATCTCCATAATTTC	0.428													|||unknown(ALL_OTHER_Ns)	1075	0.214657	0.0159	0.245	5008	,	,		14731	0.3591		0.174	False		,,,				2504	0.3548				p.E2fs		Atlas-Indel	.											OR2T12,NS,carcinoma,-1,1	OR2T12	113	1	2	Substitution - Missense(1)|Deletion - Frameshift(1)	lung(1)|pancreas(1)	c.6delG						PASS	.			202,4060		4,194,1933	66.0	61.0	62.0			-2.7	0.0	1	dbSNP_120	70	1430,6824		123,1184,2820	no	frameshift	OR2T12	NM_001004692.1		127,1378,4753	A1A1,A1R,RR		17.3249,4.7396,13.0393			248458876	1632,10884	2200	4211	6411	SO:0001589	frameshift_variant	127064	exon1			.	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.5delA	1.37:g.248458876delT	ENSP00000324583:p.Glu2fs	Somatic	444	0	0		WXS	Illumina HiSeq	Phase_I	429	192	0.447552	NM_001004692		Frame_Shift_Del	DEL	ENST00000317996.1	37	CCDS31110.1																																																																																			T|0.803;-|0.197	0.197	strong		0.428	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
RAI1	10743	hgsc.bcm.edu	37	17	17697102	17697102	+	Frame_Shift_Del	DEL	G	G	-	rs398124422|rs34083643|rs398124421|rs587780431		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17697102delG	ENST00000353383.1	+	3	1309	c.840delG	c.(838-840)cagfs	p.Q291fs	RAI1_ENST00000261641.6_Frame_Shift_Del_p.Q291fs	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	291	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)	p.Q280fs*84(1)		breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ACcagcagcagcagcagcagc	0.627																																					p.Q280fs		Atlas-Indel	.											RAI1,colon,carcinoma,-1,3	RAI1	121	3	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.839delA						PASS	.						20.0	25.0	23.0					17																	17697102		2038	4033	6071	SO:0001589	frameshift_variant	10743	exon3			.	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.840delG	17.37:g.17697102delG	ENSP00000323074:p.Gln291fs	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	21	0.259259	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Frame_Shift_Del	DEL	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	weak		0.627	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
C17orf80	55028	hgsc.bcm.edu	37	17	71241322	71241325	+	Intron	DEL	GTAA	GTAA	-	rs150601360|rs202220073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:71241322_71241325delGTAA	ENST00000535032.2	+	5	1842				C17orf80_ENST00000577615.1_Intron|C17orf80_ENST00000268942.8_Intron|C17orf80_ENST00000255557.4_Frame_Shift_Del_p.RK546fs|C17orf80_ENST00000359042.2_Intron|C17orf80_ENST00000426147.2_Frame_Shift_Del_p.RK582fs|C17orf80_ENST00000582793.1_Intron|RP11-661C3.2_ENST00000579037.1_RNA			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			CAGCGGTGGCGTAAGTAGTGTTGA	0.422														21	0.00419329	0.0008	0.0029	5008	,	,		17069	0.0		0.0159	False		,,,				2504	0.002				p.582_583del		Pindel,Atlas-Indel	.											.	C17orf80	37	.	0			c.1744_1747del						PASS	.		,,	10,3874		0,10,1932					,,	4.8	1.0			80	93,7941		2,89,3926	no	intron,frameshift,intron	C17orf80	NM_017941.4,NM_001100622.1,NM_001100621.1	,,	2,99,5858	A1A1,A1R,RR		1.1576,0.2575,0.8642	,,	,,		103,11815				SO:0001627	intron_variant	55028	exon6			.	AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"""sperm-expressed protein 1"", ""migration-inducing protein 3"""					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.1730-2055GTAA>-	17.37:g.71241322_71241325delGTAA		Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	126	47	0.373	NM_001100622	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Frame_Shift_Del	DEL	ENST00000535032.2	37	CCDS11694.1																																																																																			GTAA|0.994;-|0.006	0.006	strong		0.422	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941	
ARSD	414	hgsc.bcm.edu	37	X	2835999	2836007	+	In_Frame_Del	DEL	CCACGCCGG	CCACGCCGG	-	rs113556864|rs190767292		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CCACGCCGG	CCACGCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2835999_2836007delCCACGCCGG	ENST00000381154.1	-	5	776_784	c.701_709delCCGGCGTGG	c.(700-711)gccggcgtgggc>ggc	p.AGV234del	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	234					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AACAGGCAGCCCACGCCGGCCATGCCGGT	0.593																																					p.234_237del		Atlas-Indel	.											.	ARSD	47	.	0			c.702_710del						PASS	.			451,3270		0,2,449,1590,88						-6.3	0.0		dbSNP_132	32	1416,5068		2,4,1408,2351,362	no	coding	ARSD	NM_001669.3		2,6,1857,3941,450	A1A1,A1R,A1,RR,R		21.8384,12.1204,18.295				1867,8338				SO:0001651	inframe_deletion	414	exon5			.	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.701_709delCCGGCGTGG	X.37:g.2835999_2836007delCCACGCCGG	ENSP00000370546:p.Ala234_Val236del	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	109	36	0.330275	NM_001669	Q9UHJ8	In_Frame_Del	DEL	ENST00000381154.1	37	CCDS35196.1																																																																																			CCACGCCGG|0.500;-|0.500	0.500	weak		0.593	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
OR6C1	390321	hgsc.bcm.edu	37	12	55714406	55714407	+	Frame_Shift_Ins	INS	-	-	A	rs5798345|rs74350806|rs80197193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:55714406_55714407insA	ENST00000379668.2	+	1	61_62	c.23_24insA	c.(22-27)acagagfs	p.E9fs		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						ACAGAAATAACAGAGTTTATTC	0.381													A|A|AA|insertion	1647	0.328874	0.1634	0.4496	5008	,	,		18561	0.3413		0.4264	False		,,,				2504	0.3538				p.T8fs		Pindel,Atlas-Indel	.											.	OR6C1	58	.	0			c.23_24insA						PASS	.			785,3479		74,637,1421						0.1	0.0		dbSNP_114	61	3536,4718		747,2042,1338	no	frameshift	OR6C1	NM_001005182.1		821,2679,2759	A1A1,A1R,RR		42.8398,18.4099,34.5183				4321,8197				SO:0001589	frameshift_variant	390321	exon1			.	AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"""GPCR / Class A : Olfactory receptors"""	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.24dupA	12.37:g.55714407_55714407dupA	ENSP00000368990:p.Glu9fs	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	90	47	0.522	NM_001005182	B2RNM0	Frame_Shift_Ins	INS	ENST00000379668.2	37	CCDS31818.1																																																																																			-|0.656;A|0.344	0.344	strong		0.381	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182	
PRSS48	345062	hgsc.bcm.edu	37	4	152201018	152201019	+	Frame_Shift_Ins	INS	-	-	CAGGT	rs148861921|rs71901196|rs77216366	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:152201018_152201019insCAGGT	ENST00000455694.2	+	2	125_126	c.123_124insCAGGT	c.(124-126)cagfs	p.-43fs	SH3D19_ENST00000604030.1_Intron|PRSS48_ENST00000441586.2_Intron	NM_183375.2	NP_899231.2	Q7RTY5	PRS48_HUMAN	protease, serine, 48							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8						GCTGGCCTTGGCAGGTCAGCCT	0.53														1064	0.21246	0.0787	0.2464	5008	,	,		20396	0.1766		0.4205	False		,,,				2504	0.1922				p.W41fs		Pindel,Atlas-Indel	.											.	PRSS48	91	.	0			c.123_124insCAGGT						PASS	.			524,3274		60,404,1435						5.0	1.0		dbSNP_130	113	3418,4526		764,1890,1318	no	frameshift	PRSS48	NM_183375.2		824,2294,2753	A1A1,A1R,RR		43.0262,13.7967,33.5718				3942,7800				SO:0001589	frameshift_variant	345062	exon2			.	BN000134	CCDS47145.1	4q31.3	2010-05-07			ENSG00000189099	ENSG00000189099		"""Serine peptidases / Serine peptidases"""	24635	protein-coding gene	gene with protein product						12838346	Standard	NM_183375		Approved	ESSPL	uc011cif.2	Q7RTY5	OTTHUMG00000161673	ENST00000455694.2:c.124_128dupCAGGT	4.37:g.152201019_152201023dupCAGGT	ENSP00000401328:p.Val43fs	Somatic	127	.	.		WXS	Illumina HiSeq	Phase_I	157	47	0.299	NM_183375	Q08E82|Q0VAD4	Frame_Shift_Ins	INS	ENST00000455694.2	37	CCDS47145.1																																																																																			.	.	strong		0.530	PRSS48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365685.3	NM_183375	
NRD1	4898	hgsc.bcm.edu	37	1	52306064	52306066	+	In_Frame_Del	DEL	TCT	TCT	-	rs397701944|rs35723519|rs72663147|rs60220085	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:52306064_52306066delTCT	ENST00000354831.7	-	2	651_653	c.462_464delAGA	c.(460-465)gaagat>gat	p.E154del	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_In_Frame_Del_p.E22del|NRD1_ENST00000539524.1_In_Frame_Del_p.E22del|NRD1_ENST00000352171.7_In_Frame_Del_p.E154del	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.E154D(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcatcatcatcttcttcttctt	0.384														2813	0.561701	0.3132	0.6888	5008	,	,		19365	0.9256		0.5457	False		,,,				2504	0.4489				p.155_155del		Pindel,Atlas-Indel	.											NRD1,caecum,carcinoma,0,1	NRD1	89	1	1	Substitution - Missense(1)	pancreas(1)	c.463_465del						PASS	.																																			SO:0001651	inframe_deletion	4898	exon2			.	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.462_464delAGA	1.37:g.52306073_52306075delTCT	ENSP00000346890:p.Glu154del	Somatic	374	.	.		WXS	Illumina HiSeq	Phase_I	319	54	0.169	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	In_Frame_Del	DEL	ENST00000354831.7	37	CCDS559.1																																																																																			TCT|0.388;-|0.612	0.612	strong		0.384	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
MIR509-1	574514	hgsc.bcm.edu	37	X	146340339	146340339	+	RNA	DEL	T	T	-	rs36092315		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:146340339delT	ENST00000385265.1	-	0	94				MIR509-3_ENST00000390725.1_RNA|MIR509-2_ENST00000390724.1_RNA	NR_030236.1|NR_030586.1				microRNA 509-1																		TGATTGCCACTGTCTGCAGTA	0.438																																					.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.						82.0	78.0	79.0					X																	146340339		1403	3211	4614			574514	.			.			Xq27.3	2011-09-12	2007-10-23	2008-12-18	ENSG00000208000	ENSG00000208000		"""ncRNAs / Micro RNAs"""	32146	non-coding RNA	RNA, micro		300875	"""microRNA 509"""	MIRN509, MIRN509-1			Standard	NR_030236		Approved	hsa-mir-509, hsa-mir-509-1	uc022cfy.1				X.37:g.146340339delT		Somatic	953	.	.		WXS	Illumina HiSeq	Phase_I	95	56	0.589	.		RNA	DEL	ENST00000385265.1	37																																																																																				T|0.937;-|0.063	0.063	strong		0.438	MIR509-1-201	KNOWN	basic	miRNA	miRNA		NR_030236	
C21orf58	54058	hgsc.bcm.edu	37	21	47721985	47721986	+	In_Frame_Ins	INS	-	-	TGG	rs144178764|rs112899928|rs35902237|rs71318063	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47721985_47721986insTGG	ENST00000291691.7	-	8	2032_2033	c.896_897insCCA	c.(895-897)cat>caCCAt	p.299_299H>HH	C21orf58_ENST00000472607.1_5'UTR|C21orf58_ENST00000397683.1_In_Frame_Ins_p.193_193H>HH|C21orf58_ENST00000397682.3_In_Frame_Ins_p.193_193H>HH|C21orf58_ENST00000397679.1_In_Frame_Ins_p.193_193H>HH|C21orf58_ENST00000397680.1_In_Frame_Ins_p.193_193H>HH	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	299	Poly-His.							p.H299_A300insH(3)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		GCCACACAGCAtggtggtggtg	0.708														1382	0.275958	0.1384	0.4063	5008	,	,		16708	0.3046		0.3091	False		,,,				2504	0.3057				p.H299delinsHH		Pindel,Atlas-Indel	.											.	C21orf58	25	.	3	Insertion - In frame(3)	breast(2)|central_nervous_system(1)	c.897_898insCCA						PASS	.																																			SO:0001652	inframe_insertion	54058	exon8			.		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.894_896dupCCA	21.37:g.47721992_47721994dupTGG	ENSP00000291691:p.His299dup	Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_058180	B3KPI1	In_Frame_Ins	INS	ENST00000291691.7	37	CCDS13735.1																																																																																			-|0.500;TGG|0.500	0.500	strong		0.708	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180	
CA9	768	hgsc.bcm.edu	37	9	35674059	35674059	+	Frame_Shift_Del	DEL	G	G	-	rs565650695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35674059delG	ENST00000378357.4	+	1	207	c.103delG	c.(103-105)gtcfs	p.V35fs	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	35					bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	TCTGGTGCCTGTCCATCCCCA	0.652													G|G|-|deletion	3	0.000599042	0.0	0.0029	5008	,	,		18058	0.0		0.001	False		,,,				2504	0.0				p.P34fs		Pindel,Atlas-Indel	.											.	CA9	48	.	0			c.102delT						PASS	.						61.0	56.0	57.0					9																	35674059		2203	4300	6503	SO:0001589	frameshift_variant	768	exon1			.	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.103delG	9.37:g.35674059delG	ENSP00000367608:p.Val35fs	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	121	37	0.306	NM_001216	Q5T4R1	Frame_Shift_Del	DEL	ENST00000378357.4	37	CCDS6585.1																																																																																			.	.	none		0.652	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
NFKBIE	4794	hgsc.bcm.edu	37	6	44232842	44232845	+	Frame_Shift_Del	DEL	GTGT	GTGT	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GTGT	GTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44232842_44232845delGTGT	ENST00000275015.5	-	1	655_658	c.656_659delACAC	c.(655-660)tacaccfs	p.YT219fs		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	219					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CAAGGACAGGGTGTAGGTGAGCGA	0.681																																					p.219_220del		Pindel,Atlas-Indel	.											.	NFKBIE	31	.	0			c.657_660del						PASS	.																																			SO:0001589	frameshift_variant	4794	exon1			.	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"""Ankyrin repeat domain containing"""	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.656_659delACAC	6.37:g.44232842_44232845delGTGT	ENSP00000275015:p.Tyr219fs	Somatic	112	.	.		WXS	Illumina HiSeq	Phase_I	146	22	0.151	NM_004556	Q5T9V9	Frame_Shift_Del	DEL	ENST00000275015.5	37	CCDS34463.1																																																																																			.	.	none		0.681	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2		
TCEB3CL	728929	hgsc.bcm.edu	37	18	44549025	44549026	+	Frame_Shift_Ins	INS	-	-	GC			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44549025_44549026insGC	ENST00000451265.1	-	1	1508_1509	c.1273_1274insGC	c.(1273-1275)cagfs	p.Q425fs	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron	NM_001100817.1	NP_001094287.1	Q3SY89	EA3L1_HUMAN	transcription elongation factor B polypeptide 3C-like	425	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|lung(1)|prostate(1)	3						TCGCAGCCGCTGCTCTCGGGCG	0.554																																					p.Q425fs		Atlas-Indel	.											.	TCEB3C	49	.	0			c.1274_1275insGC						PASS	.		,	43,255		12,19,118					,	0.4	0.1			2	484,712		161,162,275	no	intron,frameshift	KATNAL2,TCEB3CL	NM_031303.2,NM_001100817.1	,	173,181,393	A1A1,A1R,RR		40.4682,14.4295,35.2744	,	,		527,967				SO:0001589	frameshift_variant	162699	exon1			.			18q21.1	2007-07-10				ENSG00000275553			31007	protein-coding gene	gene with protein product							Standard	NM_001100817		Approved	HsT828		Q3SY89		ENST00000451265.1:c.1272_1273dupGC	18.37:g.44549026_44549027dupGC	ENSP00000409932:p.Gln425fs	Somatic	760	0	0		WXS	Illumina HiSeq	Phase_I	693	132	0.190476	NM_145653	Q3MI93	Frame_Shift_Ins	INS	ENST00000451265.1	37	CCDS42433.1																																																																																			.	.	none		0.554	TCEB3CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451071.1	XM_001132059	
HSP90B1	7184	hgsc.bcm.edu	37	12	104341188	104341190	+	In_Frame_Del	DEL	GAA	GAA	-	rs5800607|rs201427769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:104341188_104341190delGAA	ENST00000299767.5	+	17	2544_2546	c.2362_2364delGAA	c.(2362-2364)gaadel	p.E791del	C12orf73_ENST00000543740.2_5'Flank	NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	791					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	gggaacagatgaagaagaagaaA	0.424														600	0.119808	0.0053	0.111	5008	,	,		20608	0.3254		0.0954	False		,,,				2504	0.0941				p.787_788del		Pindel,Atlas-Indel	.											.	HSP90B1	72	.	0			c.2361_2363del						PASS	.			250,4012		72,106,1953						-7.4	0.4		dbSNP_114	222	1075,7179		156,763,3208	no	coding	HSP90B1	NM_003299.1		228,869,5161	A1A1,A1R,RR		13.024,5.8658,10.5864				1325,11191				SO:0001651	inframe_deletion	7184	exon17			.	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"""Heat shock proteins / HSPC"""	12028	protein-coding gene	gene with protein product		191175	"""tumor rejection antigen (gp96) 1"""	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.2362_2364delGAA	12.37:g.104341197_104341199delGAA	ENSP00000299767:p.Glu791del	Somatic	196	.	.		WXS	Illumina HiSeq	Phase_I	179	57	0.318	NM_003299	Q96A97	In_Frame_Del	DEL	ENST00000299767.5	37	CCDS9094.1																																																																																			GAA|0.865;-|0.135	0.135	strong		0.424	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
HNRNPA1L2	144983	hgsc.bcm.edu	37	13	53216702	53216702	+	Frame_Shift_Del	DEL	A	A	-	rs374312718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:53216702delA	ENST00000357495.2	+	1	135	c.75delA	c.(73-75)acafs	p.T26fs	HNRNPA1L2_ENST00000342657.3_Frame_Shift_Del_p.T26fs|HNRNPA1L2_ENST00000398039.1_Frame_Shift_Del_p.T26fs			Q32P51	RA1L2_HUMAN	heterogeneous nuclear ribonucleoprotein A1-like 2	26	Globular A domain.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|mRNA transport (GO:0051028)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			cervix(1)|large_intestine(1)|lung(5)	7						GCTTTGAAACAACTGATGAGA	0.502													|||unknown(ALL_OTHER_Ns)	51	0.0101837	0.0242	0.0014	5008	,	,		18435	0.0		0.003	False		,,,				2504	0.0153				p.T25fs		Pindel,Atlas-Indel	.											.	HNRNPA1L2	20	.	0			c.74delC						PASS	.		,	87,4173		5,77,2048	43.0	46.0	45.0		,	0.3	0.8	13		46	54,8196		16,22,4087	no	frameshift,frameshift	HNRNPA1L2	NM_001011725.1,NM_001011724.1	,	21,99,6135	A1A1,A1R,RR		0.6545,2.0423,1.1271	,	,	53216702	141,12369	2202	4295	6497	SO:0001589	frameshift_variant	144983	exon6			.		CCDS31980.1	13q14.3	2013-02-12			ENSG00000139675	ENSG00000139675		"""RNA binding motif (RRM) containing"""	27067	protein-coding gene	gene with protein product						12477932	Standard	NM_001011724		Approved	LOC144983	uc001vgy.1	Q32P51	OTTHUMG00000016972	ENST00000357495.2:c.75delA	13.37:g.53216702delA	ENSP00000350090:p.Thr26fs	Somatic	83	.	.		WXS	Illumina HiSeq	Phase_I	80	27	0.338	NM_001011725	Q5TBS2	Frame_Shift_Del	DEL	ENST00000357495.2	37	CCDS31980.1																																																																																			.	.	weak		0.502	HNRNPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045098.1	NM_001011724	
ZNF527	84503	hgsc.bcm.edu	37	19	37879852	37879853	+	Frame_Shift_Ins	INS	-	-	TGTG	rs2385182|rs376931538|rs386809049	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:37879852_37879853insTGTG	ENST00000436120.2	+	5	1008_1009	c.901_902insTGTG	c.(901-903)ccafs	p.P301fs	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGGAGAAAAACCATATGCATGC	0.391																																					p.P301fs		Atlas-Indel	.											.	ZNF527	78	.	0			c.901_902insTGTG						PASS	.			75,3965		3,69,1948						-1.5	0.3		dbSNP_126	99	898,7198		92,714,3242	no	frameshift	ZNF527	NM_032453.1		95,783,5190	A1A1,A1R,RR		11.0919,1.8564,8.0175				973,11163				SO:0001589	frameshift_variant	84503	exon5			.	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	Exception_encountered	19.37:g.37879852_37879853insTGTG	ENSP00000390179:p.Pro301fs	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	130	45	0.346154	NM_032453	B4DVL5	Frame_Shift_Ins	INS	ENST00000436120.2	37	CCDS42559.1																																																																																			.	.	weak		0.391	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
AGAP6	414189	hgsc.bcm.edu	37	10	51768675	51768676	+	Frame_Shift_Del	DEL	AA	AA	-	rs141217862|rs200646112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:51768675_51768676delAA	ENST00000374056.4	+	7	1119_1120	c.721_722delAA	c.(721-723)aaafs	p.K241fs	AGAP6_ENST00000412531.3_Frame_Shift_Del_p.K264fs			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	241					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						TGACCCAGACAAAGAGAGGAAA	0.55														591	0.118011	0.0356	0.1542	5008	,	,		18267	0.0327		0.2694	False		,,,				2504	0.136				p.263_264del		Pindel,Atlas-Indel	.											.	AGAP6	53	.	0			c.789_790del						PASS	.																																			SO:0001589	frameshift_variant	414189	exon8			.		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.721_722delAA	10.37:g.51768675_51768676delAA	ENSP00000363168:p.Lys241fs	Somatic	125	.	.		WXS	Illumina HiSeq	Phase_I	145	26	0.179	NM_001077665		Frame_Shift_Del	DEL	ENST00000374056.4	37																																																																																				AA|0.500;-|0.500	0.500	weak		0.550	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
DNAH14	127602	hgsc.bcm.edu	37	1	225380562	225380565	+	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs191528375|rs144339803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:225380562_225380565delAAAG	ENST00000445597.2	+	25	4554_4557	c.4554_4557delAAAG	c.(4552-4557)acaaagfs	p.TK1518fs	DNAH14_ENST00000439375.2_Frame_Shift_Del_p.TK1923fs|DNAH14_ENST00000430092.1_Frame_Shift_Del_p.TK1923fs			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1518					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CAAAGAACACAAAGAAAGACATTG	0.289														98	0.0195687	0.0038	0.0231	5008	,	,		16043	0.0		0.0636	False		,,,				2504	0.0133				p.1923_1924del		Pindel,Atlas-Indel	.											.	DNAH14	300	.	0			c.5768_5771del						PASS	.			26,1986		3,20,983						3.0	0.0		dbSNP_134	171	216,3860		17,182,1839	no	frameshift	DNAH14	NM_001373.1		20,202,2822	A1A1,A1R,RR		5.2993,1.2922,3.975				242,5846				SO:0001589	frameshift_variant	127602	exon37			.	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.4554_4557delAAAG	1.37:g.225380566_225380569delAAAG	ENSP00000409472:p.Thr1518fs	Somatic	136	.	.		WXS	Illumina HiSeq	Phase_I	176	57	0.324	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Frame_Shift_Del	DEL	ENST00000445597.2	37																																																																																				AAAG|0.968;-|0.032	0.032	strong		0.289	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ZFYVE19	84936	hgsc.bcm.edu	37	15	41099899	41099900	+	Frame_Shift_Ins	INS	-	-	GGGGC	rs371684343|rs200042011|rs142730574|rs369585041	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41099899_41099900insGGGGC	ENST00000355341.4	+	1	613_614	c.112_113insGGGGC	c.(112-114)tggfs	p.-40fs	ZFYVE19_ENST00000336455.5_Intron|ZFYVE19_ENST00000570108.1_Intron|DNAJC17_ENST00000220496.4_5'Flank|ZFYVE19_ENST00000299173.10_Frame_Shift_Ins_p.-40fs|ZFYVE19_ENST00000564258.1_Intron|ZFYVE19_ENST00000563530.1_3'UTR	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19						abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		AGTGGGCGTGTGgggcggggca	0.718														1685	0.336462	0.3411	0.3112	5008	,	,		13821	0.2252		0.3777	False		,,,				2504	0.4202				p.W38fs		Atlas-Indel	.											.	ZFYVE19	31	.	0			c.112_113insGGGGC						PASS	.			1226,2460		247,732,864						2.0	0.3		dbSNP_130	17	2598,5206		494,1610,1798	no	frameshift	ZFYVE19	NM_001077268.1		741,2342,2662	A1A1,A1R,RR		33.2906,33.261,33.2811				3824,7666				SO:0001589	frameshift_variant	84936	exon1			.	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.118_122dupGGGGC	15.37:g.41099905_41099909dupGGGGC	ENSP00000347498:p.Gly40fs	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	86	18	0.209302	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Frame_Shift_Ins	INS	ENST00000355341.4	37	CCDS42025.1																																																																																			-|0.663;GGGGC|0.337	0.337	strong		0.718	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850	
RAI1	10743	hgsc.bcm.edu	37	17	17697099	17697100	+	Frame_Shift_Del	DEL	GC	GC	-	rs35068024|rs587780431|rs587780429|rs398124422|rs11078398|rs144872134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17697099_17697100delGC	ENST00000353383.1	+	3	1306_1307	c.837_838delGC	c.(835-840)cagcagfs	p.QQ279fs	RAI1_ENST00000261641.6_Frame_Shift_Del_p.QQ279fs	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	279	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ATGACcagcagcagcagcagca	0.634																																					p.279_279del		Atlas-Indel	.											.	RAI1	121	.	0			c.836_837del						PASS	.																																			SO:0001589	frameshift_variant	10743	exon3			.	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.837_838delGC	17.37:g.17697099_17697100delGC	ENSP00000323074:p.Gln279fs	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	22	0.282051	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Frame_Shift_Del	DEL	ENST00000353383.1	37	CCDS11188.1																																																																																			GC|0.875;-|0.125	0.125	strong		0.634	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
C21orf62	56245	hgsc.bcm.edu	37	21	34169317	34169318	+	Intron	INS	-	-	T	rs33987705|rs5843567|rs72564613|rs201838656	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:34169317_34169318insT	ENST00000536776.1	-	2	77				C21orf62_ENST00000490358.1_Intron|C21orf49_ENST00000453404.1_Intron|C21orf49_ENST00000382377.3_3'UTR|C21orf62_ENST00000479548.1_Intron|C21orf49_ENST00000477513.1_Frame_Shift_Ins_p.G38fs|C21orf62_ENST00000487113.1_Intron|C21orf49_ENST00000382375.4_Frame_Shift_Ins_p.G68fs|C21orf49_ENST00000382378.1_Frame_Shift_Ins_p.G68fs	NM_001162495.2|NM_001162496.2|NM_019596.5	NP_001155967.2|NP_001155968.2|NP_062542.5	Q9NYP8	CU062_HUMAN	chromosome 21 open reading frame 62											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	6		Myeloproliferative disorder(46;0.0255)				TATTGGTTTGCGGAACATGTGG	0.49													T|-|T|deletion	3665	0.731829	0.5318	0.8213	5008	,	,		19035	0.9157		0.7664	False		,,,				2504	0.7137				.		Pindel,Atlas-Indel	.											.	C21orf49	1	.	0			.						PASS	.																																			SO:0001627	intron_variant	54067	.			.	AF231922	CCDS42919.1, CCDS42919.2	21q22.1	2011-02-24			ENSG00000205929	ENSG00000205929			1305	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 120"""	C21orf120			Standard	NM_001162495		Approved	B37, PRED81	uc011adu.2	Q9NYP8	OTTHUMG00000163477	ENST00000536776.1:c.64-2521->A	21.37:g.34169317_34169318insT		Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	116	36	0.310	.	A8K4L8	RNA	INS	ENST00000536776.1	37	CCDS42919.2																																																																																			T|1.000;|0.000	1.000	weak		0.490	C21orf62-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139598.5	NM_019596	
IL32	9235	hgsc.bcm.edu	37	16	3119297	3119298	+	Frame_Shift_Ins	INS	-	-	G	rs71818662|rs531600758	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3119297_3119298insG	ENST00000534507.1	+	6	857_858	c.646_647insG	c.(646-648)cggfs	p.R216fs	IL32_ENST00000551513.1_Frame_Shift_Ins_p.R207fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.R150fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.R113fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.R161fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.R170fs|IL32_ENST00000528163.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.R216fs|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000444393.3_Frame_Shift_Ins_p.R170fs|IL32_ENST00000525643.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.R170fs|IL32_ENST00000382213.3_Frame_Shift_Ins_p.R161fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.R194fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.R170fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.R130fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.R216fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.R170fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.R113fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.R113fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.R160fs			P24001	IL32_HUMAN	interleukin 32	216					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)		p.D172fs*12(3)		breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CGGAGCCCCACGGGGGGACAAG	0.579																																					p.R170fs		Pindel,Atlas-Indel	.											IL32,NS,carcinoma,0,1	IL32	32	1	3	Insertion - Frameshift(3)	urinary_tract(1)|breast(1)|pancreas(1)	c.508_509insG						PASS	.																																			SO:0001589	frameshift_variant	9235	exon7			.	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.652dupG	16.37:g.3119303_3119303dupG	ENSP00000431775:p.Arg216fs	Somatic	139	.	.		WXS	Illumina HiSeq	Phase_I	217	36	0.166	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Frame_Shift_Ins	INS	ENST00000534507.1	37																																																																																				.	.	strong		0.579	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
FAM90A1	55138	hgsc.bcm.edu	37	12	8374781	8374782	+	In_Frame_Ins	INS	-	-	ACG	rs71265055		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:8374781_8374782insACG	ENST00000538603.1	-	7	1589_1590	c.1031_1032insCGT	c.(1030-1032)acg>acCGTg	p.344_345insV	FAM90A1_ENST00000307435.6_In_Frame_Ins_p.344_345insV	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	344				T -> TV (in Ref. 1; BAA91593). {ECO:0000305}.			nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TCTGGGGTGACGTACGTGGTCC	0.673														2167	0.432708	0.0802	0.5101	5008	,	,		16505	0.5764		0.6968	False		,,,				2504	0.4346				p.T344delinsTV		Pindel,Atlas-Indel	.											.	FAM90A1	68	.	0			c.1032_1033insCGT						PASS	.			758,3506		60,638,1434						0.0	0.0		dbSNP_130	26	5796,2428		1994,1808,310	no	coding	FAM90A1	NM_018088.3		2054,2446,1744	A1A1,A1R,RR		29.5233,17.7767,47.5176				6554,5934				SO:0001652	inframe_insertion	55138	exon7			.	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.1031_1032insCGT	12.37:g.8374781_8374782insACG	ENSP00000445418:p.Thr344_Ser345insVal	Somatic	252	.	.		WXS	Illumina HiSeq	Phase_I	155	62	0.400	NM_018088	D3DUU9|Q9NVZ6	In_Frame_Ins	INS	ENST00000538603.1	37	CCDS31738.1																																																																																			-|0.250;ACG|0.750	0.750	strong		0.673	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577712	90577728	+	RNA	DEL	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	-	rs202101805|rs202111256|rs201189413|rs199515704|rs202116886|rs200213073|rs537929246|rs200862023|rs199694900|rs201534830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90577712_90577728delCTTTGCCCAGACATGGA	ENST00000551025.1	+	0	6140_6156									caspase 8 associated protein 2									p.S1568fs*1(1)		NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TTATTGACATCTTTGCCCAGACATGGAAAGGAAGCTG	0.378														405	0.0808706	0.0061	0.0908	5008	,	,		25479	0.0437		0.1471	False		,,,				2504	0.1452				p.1568_1573del	Colon(187;1656 2025 17045 31481 39901)	Atlas-Indel	.											.	CASP8AP2	108	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4702_4718del						PASS	.		,,	39,3633		3,33,1800					,,	1.7	0.1			158	479,7383		54,371,3506	no	frameshift,frameshift,frameshift	CASP8AP2	NM_012115.3,NM_001137668.1,NM_001137667.1	,,	57,404,5306	A1A1,A1R,RR		6.0926,1.0621,4.4911	,,	,,		518,11016						9994	exon8			.	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90577712_90577728delCTTTGCCCAGACATGGA		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	61	12	0.196721	NM_001137668		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	none		0.378	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
RBM19	9904	hgsc.bcm.edu	37	12	114392971	114392972	+	In_Frame_Ins	INS	-	-	GGT	rs71443069|rs55840068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:114392971_114392972insGGT	ENST00000545145.2	-	7	963_964	c.885_886insACC	c.(883-888)accgtg>accACCgtg	p.295_296insT	RBM19_ENST00000261741.5_In_Frame_Ins_p.295_296insT|RBM19_ENST00000392561.3_In_Frame_Ins_p.295_296insT	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	295	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					CGCAGCTTCACGGTGTGGCAGG	0.569														74	0.0147764	0.0015	0.0231	5008	,	,		20550	0.0		0.0427	False		,,,				2504	0.0133				p.V296delinsTV		Pindel,Atlas-Indel	.											.	RBM19	117	.	0			c.886_887insACC						PASS	.		,,	59,4205		1,57,2074					,,	5.1	0.9		dbSNP_130	133	534,7720		24,486,3617	no	coding,coding,coding	RBM19	NM_016196.3,NM_001146699.1,NM_001146698.1	,,	25,543,5691	A1A1,A1R,RR		6.4696,1.3837,4.7372	,,	,,		593,11925				SO:0001652	inframe_insertion	9904	exon7			.	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.883_885dupACC	12.37:g.114392972_114392974dupGGT	ENSP00000442053:p.Thr295_Thr295dup	Somatic	138	.	.		WXS	Illumina HiSeq	Phase_I	113	38	0.336	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	In_Frame_Ins	INS	ENST00000545145.2	37	CCDS9172.1																																																																																			-|0.983;GGT|0.017	0.017	strong		0.569	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
KRT24	192666	hgsc.bcm.edu	37	17	38858135	38858135	+	Frame_Shift_Del	DEL	A	A	-	rs11309872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38858135delA	ENST00000264651.2	-	2	722	c.666delT	c.(664-666)aatfs	p.N222fs		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	222	Coil 1B.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CCAATCTGGCATTGTCAATGT	0.333													A|A|-|deletion	2328	0.464856	0.1921	0.6282	5008	,	,		13424	0.5952		0.4563	False		,,,				2504	0.592				p.A223fs	GBM(61;380 1051 14702 23642 31441)	Pindel,Atlas-Indel	.											KRT24,NS,lymphoid_neoplasm,0,1	KRT24	60	1	0			c.667delG						PASS	.			1041,3223		135,771,1226	70.0	54.0	60.0			5.1	1.0	17	dbSNP_120	79	3574,4680		756,2062,1309	no	frameshift	KRT24	NM_019016.2		891,2833,2535	A1A1,A1R,RR		43.3002,24.4137,36.8669			38858135	4615,7903	2078	3619	5697	SO:0001589	frameshift_variant	192666	exon2			.		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.666delT	17.37:g.38858135delA	ENSP00000264651:p.Asn222fs	Somatic	302	.	.		WXS	Illumina HiSeq	Phase_I	355	84	0.237	NM_019016	Q9NXG7	Frame_Shift_Del	DEL	ENST00000264651.2	37	CCDS11372.1																																																																																			A|0.541;-|0.459	0.459	strong		0.333	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970760	45970774	+	In_Frame_Del	DEL	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	-	rs113146284|rs371219783|rs200215960|rs67692969|rs76536096|rs76021731|rs71199610	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45970760_45970774delCTTGCAGCAGACAGG	ENST00000391621.1	-	1	614_628	c.568_582delCCTGTCTGCTGCAAG	c.(568-582)cctgtctgctgcaagdel	p.PVCCK190del	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	190	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						AGCAGATGGACTTGCAGCAGACAGGCTTGCAGCAG	0.609														1066	0.212859	0.1664	0.1513	5008	,	,		23256	0.3661		0.2058	False		,,,				2504	0.1687				p.190_195del		Atlas-Indel	.											.	KRTAP10-2	21	.	0			c.569_583del						PASS	.		,	649,3615		35,579,1518					,	0.6	0.0		dbSNP_130	134	1460,6792		93,1274,2759	no	coding,intron	TSPEAR,KRTAP10-2	NM_198693.2,NM_144991.2	,	128,1853,4277	A1A1,A1R,RR		17.6927,15.2205,16.8504	,	,		2109,10407				SO:0001651	inframe_deletion	386679	exon1			.	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.568_582delCCTGTCTGCTGCAAG	21.37:g.45970760_45970774delCTTGCAGCAGACAGG	ENSP00000375479:p.Pro190_Lys194del	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	182	52	0.285714	NM_198693	Q70LJ5	In_Frame_Del	DEL	ENST00000391621.1	37	CCDS42955.1																																																																																			CTTGCAGCAGACAGG|0.758;-|0.242	0.242	strong		0.609	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
PITRM1	10531	hgsc.bcm.edu	37	10	3193558	3193570	+	Intron	DEL	AAAAAAGAAACAA	AAAAAAGAAACAA	-	rs60985673|rs79011862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AAAAAAGAAACAA	AAAAAAGAAACAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:3193558_3193570delAAAAAAGAAACAA	ENST00000224949.4	-	15	1656				PITRM1_ENST00000380994.1_Intron|PITRM1_ENST00000380989.2_Intron|PITRM1_ENST00000451104.2_Intron|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000464395.1_5'Flank|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1						positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TTCTAGACCTAAAAAAGAAACAAGAAAAAGGAA	0.408														931	0.185903	0.084	0.1859	5008	,	,		21309	0.3006		0.16	False		,,,				2504	0.2321				.		Pindel,Atlas-Indel	.											.	PITRM1	109	.	0			.						PASS	.		,,	322,3302		18,286,1508					,,	5.7	0.7		dbSNP_129	43	1062,6812		64,934,2939	no	intron,intron,intron	PITRM1	NM_014889.3,NM_001242309.1,NM_001242307.1	,,	82,1220,4447	A1A1,A1R,RR		13.4874,8.8852,12.0369	,,	,,		1384,10114				SO:0001627	intron_variant	10531	.			.	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1622-3TTGTTTCTTTTTT>-	10.37:g.3193558_3193570delAAAAAAGAAACAA		Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	50	17	0.340	.	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Splice_Site	DEL	ENST00000224949.4	37	CCDS59208.1																																																																																			AAAAAAGAAACAA|0.500;-|0.500	0.500	strong		0.408	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
WDR73	84942	hgsc.bcm.edu	37	15	85186877	85186894	+	In_Frame_Del	DEL	CTTGGCTCCGTGTTCCAT	CTTGGCTCCGTGTTCCAT	-	rs370347033|rs373448317|rs11267906|rs372798651|rs199676984	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTTGGCTCCGTGTTCCAT	CTTGGCTCCGTGTTCCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85186877_85186894delCTTGGCTCCGTGTTCCAT	ENST00000434634.2	-	8	1004_1021	c.944_961delATGGAACACGGAGCCAAG	c.(943-963)gatggaacacggagccaagta>gta	p.DGTRSQ315del	SCAND2P_ENST00000348993.5_RNA|WDR73_ENST00000398528.3_5'UTR	NM_032856.2	NP_116245.2	Q6P4I2	WDR73_HUMAN	WD repeat domain 73	315										cervix(1)|large_intestine(1)|lung(1)	3						AGAGGTTCTACTTGGCTCCGTGTTCCATCTTGGCTCCG	0.509														794	0.158546	0.1399	0.1383	5008	,	,		21272	0.0843		0.2038	False		,,,				2504	0.228				p.315_321del		Pindel,Atlas-Indel	.											.	WDR73	15	.	0			c.945_962del						PASS	.			344,3500		48,248,1626						-0.4	0.0		dbSNP_120	111	1220,6750		177,866,2942	no	coding	WDR73	NM_032856.2		225,1114,4568	A1A1,A1R,RR		15.3074,8.949,13.2385				1564,10250				SO:0001651	inframe_deletion	84942	exon8			.	AK027200	CCDS45339.1	15q25.2	2013-01-09				ENSG00000177082		"""WD repeat domain containing"""	25928	protein-coding gene	gene with protein product						12477932	Standard	NM_032856		Approved	FLJ14888, HSPC264	uc002bkw.2	Q6P4I2		ENST00000434634.2:c.944_961delATGGAACACGGAGCCAAG	15.37:g.85186877_85186894delCTTGGCTCCGTGTTCCAT	ENSP00000387982:p.Asp315_Gln320del	Somatic	143	.	.		WXS	Illumina HiSeq	Phase_I	152	37	0.243	NM_032856	Q96JZ1|Q9P0B7	In_Frame_Del	DEL	ENST00000434634.2	37	CCDS45339.1																																																																																			.	.	strong		0.509	WDR73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418195.1	NM_032856	
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75804262	75804262	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:75804262delT	ENST00000550916.1	+	2	330	c.283delT	c.(283-285)tgtfs	p.C95fs	GLIPR1L2_ENST00000435775.1_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000378692.3_5'UTR|GLIPR1L2_ENST00000547164.1_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000320460.4_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000441218.1_Frame_Shift_Del_p.C30fs	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	95	SCP.					integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						GGGAAAAAAATGTTTGTTTAC	0.323																																					p.K94fs		Pindel,Atlas-Indel	.											.	GLIPR1L2	54	.	0			c.282delA						PASS	.			0,4264		0,0,2132	87.0	87.0	87.0			0.1	1.0	12		87	3,8247		0,3,4122	no	frameshift	GLIPR1L2	NM_152436.1		0,3,6254	A1A1,A1R,RR		0.0364,0.0,0.024			75804262	3,12511	2203	4299	6502	SO:0001589	frameshift_variant	144321	exon2			.	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.283delT	12.37:g.75804262delT	ENSP00000448248:p.Cys95fs	Somatic	134	.	.		WXS	Illumina HiSeq	Phase_I	136	43	0.316	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Frame_Shift_Del	DEL	ENST00000550916.1	37	CCDS58258.1																																																																																			.	.	none		0.323	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
SLC22A1	6580	hgsc.bcm.edu	37	6	160560881	160560883	+	In_Frame_Del	DEL	ATG	ATG	-	rs202220802|rs72552763|rs35191146|rs142448543|rs34305973|rs35167514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:160560881_160560883delATG	ENST00000366963.4	+	7	1405_1407	c.1258_1260delATG	c.(1258-1260)atgdel	p.M420del	SLC22A1_ENST00000324965.4_In_Frame_Del_p.M420del|SLC22A1_ENST00000457470.2_In_Frame_Del_p.M420del	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	420			Missing (no changes in the MPP uptake. No changes in the MPP uptake; when associated with V-408). {ECO:0000269|PubMed:12439218, ECO:0000269|PubMed:12719534, ECO:0000269|PubMed:14702039}.		dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)		SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	CTGCCTCGTCATGATTTTTATCT	0.517														592	0.118211	0.0454	0.2882	5008	,	,		14486	0.005		0.1839	False		,,,				2504	0.1452				p.419_420del		Atlas-Indel	.											SLC22A1,NS,carcinoma,+2,1	SLC22A1	69	1	0			c.1257_1259del	GRCh37	CD072492	SLC22A1	D	rs35191146	PASS	.																																			SO:0001651	inframe_deletion	6580	exon7			.	U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"""Solute carriers"""	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.1258_1260delATG	6.37:g.160560881_160560883delATG	ENSP00000355930:p.Met420del	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	61	19	0.311475	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	In_Frame_Del	DEL	ENST00000366963.4	37	CCDS5274.1																																																																																			ATG|0.880;-|0.120	0.120	strong		0.517	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
HOXB1	3211	hgsc.bcm.edu	37	17	46608184	46608185	+	In_Frame_Ins	INS	-	-	GGGCGCTGT	rs534792734|rs145570960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46608184_46608185insGGGCGCTGT	ENST00000239174.6	-	1	174_175	c.82_83insACAGCGCCC	c.(82-84)cca>cACAGCGCCCca	p.27_28insHSA	HOXB1_ENST00000577092.1_In_Frame_Ins_p.27_28insHSA	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	27			A -> AHSA (in allele HOXB1*B). {ECO:0000269|PubMed:10671062, ECO:0000269|PubMed:11091361}.		anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)	p.A27_P28insHSA(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAAGGAGGTTGGGGCGCTGTGG	0.619														667	0.133187	0.1157	0.1225	5008	,	,		17469	0.0982		0.2008	False		,,,				2504	0.1309				p.P28delinsHSAP		Pindel,Atlas-Indel	.											.	HOXB1	67	.	1	Insertion - In frame(1)	lung(1)	c.83_84insACAGCGCCC						PASS	.			528,3732		33,462,1635						4.2	1.0		dbSNP_134	66	1685,6565		171,1343,2611	no	coding	HOXB1	NM_002144.3		204,1805,4246	A1A1,A1R,RR		20.4242,12.3944,17.6898				2213,10297				SO:0001652	inframe_insertion	3211	exon1			.		CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.74_82dupACAGCGCCC	17.37:g.46608185_46608193dupGGGCGCTGT	ENSP00000355140:p.His25_Ala27dup	Somatic	40	.	.		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_002144	Q4VB03	In_Frame_Ins	INS	ENST00000239174.6	37	CCDS32675.1																																																																																			.	.	strong		0.619	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
STRBP	55342	hgsc.bcm.edu	37	9	125875138	125875139	+	Intron	INS	-	-	AGGGGC	rs140944398|rs71388354	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:125875138_125875139insAGGGGC	ENST00000530364.1	-	2	31				MIR600HG_ENST00000385007.1_RNA			Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein						cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						ATTCTGAAGCAAGGGGCAGTCA	0.53														2494	0.498003	0.0635	0.5836	5008	,	,		20001	0.3214		0.8539	False		,,,				2504	0.8405				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																			SO:0001627	intron_variant	81571	.			.	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000530364.1:c.255-3106->GCCCCT	9.37:g.125875139_125875144dupAGGGGC		Somatic	180	.	.		WXS	Illumina HiSeq	Phase_I	71	47	0.662	.	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	RNA	INS	ENST00000530364.1	37																																																																																				.	.	strong		0.530	STRBP-009	PUTATIVE	basic	processed_transcript	protein_coding	OTTHUMT00000392598.1		
NUCB2	4925	hgsc.bcm.edu	37	11	17352478	17352480	+	In_Frame_Del	DEL	ACA	ACA	-	rs189362726|rs535406012|rs3842269	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:17352478_17352480delACA	ENST00000529010.1	+	13	1422_1424	c.1203_1205delACA	c.(1201-1206)ttacaa>tta	p.Q403del	NUCB2_ENST00000458064.2_In_Frame_Del_p.Q373del|NUCB2_ENST00000323688.6_In_Frame_Del_p.Q403del	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	403	Binds to necdin. {ECO:0000250}.					cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AAAAAAAATTACAACAAGGAATT	0.32														1270	0.253594	0.1127	0.1484	5008	,	,		15929	0.5139		0.2992	False		,,,				2504	0.2035				p.401_402del		Pindel,Atlas-Indel	.											.	NUCB2	31	.	0			c.1202_1204del						PASS	.			466,3024		27,412,1306						5.5	1.0		dbSNP_107	44	2131,5673		291,1549,2062	no	coding	NUCB2	NM_005013.2		318,1961,3368	A1A1,A1R,RR		27.3065,13.3524,22.9945				2597,8697				SO:0001651	inframe_deletion	4925	exon13			.	AF052642	CCDS41623.1	11p15.1	2013-01-10						"""EF-hand domain containing"""	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.1203_1205delACA	11.37:g.17352481_17352483delACA	ENSP00000436455:p.Gln403del	Somatic	167	.	.		WXS	Illumina HiSeq	Phase_I	156	47	0.301	NM_005013	A8K642|D3DQX5|Q8NFT5	In_Frame_Del	DEL	ENST00000529010.1	37	CCDS41623.1																																																																																			ACA|0.718;-|0.282	0.282	strong		0.320	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013	
CARD10	29775	hgsc.bcm.edu	37	22	37906309	37906314	+	In_Frame_Del	DEL	CTCCTT	CTCCTT	-	rs113275238|rs60611523	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTCCTT	CTCCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:37906309_37906314delCTCCTT	ENST00000403299.1	-	5	1030_1035	c.814_819delAAGGAG	c.(814-819)aaggagdel	p.KE272del	CARD10_ENST00000494166.1_5'UTR|CARD10_ENST00000406271.3_5'Flank|CARD10_ENST00000251973.5_In_Frame_Del_p.KE272del			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	272					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CATTGTCTGGctccttctccttctcc	0.631														1551	0.309704	0.4743	0.2536	5008	,	,		16347	0.3036		0.2535	False		,,,				2504	0.1912				p.272_274del		Pindel,Atlas-Indel	.											.	CARD10	55	.	0			c.815_820del						PASS	.																																			SO:0001651	inframe_deletion	29775	exon4			.	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.814_819delAAGGAG	22.37:g.37906315_37906320delCTCCTT	ENSP00000384570:p.Lys272_Glu273del	Somatic	31	.	.		WXS	Illumina HiSeq	Phase_I	25	12	0.480	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	In_Frame_Del	DEL	ENST00000403299.1	37	CCDS13948.1																																																																																			CTCCTT|0.500;-|0.500	0.500	strong		0.631	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
C1orf220	400798	hgsc.bcm.edu	37	1	178514560	178514561	+	Stop_Codon_Ins	INS	-	-	T	rs397723643|rs397943201|rs34632529	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:178514560_178514561insT	ENST00000319387.2	+	0	321_322				C1ORF220_ENST00000367636.4_5'UTR|C1orf220_ENST00000521244.1_3'UTR|C1orf220_ENST00000367638.1_Stop_Codon_Ins			Q5T0J3	CA220_HUMAN	chromosome 1 open reading frame 220											lung(1)	1						TTGAAGGTTGATTTTGACTACT	0.515													TTTT|TTTT|TTTTT|insertion	1918	0.382987	0.118	0.3631	5008	,	,		19991	0.5357		0.4632	False		,,,				2504	0.5153				.		Pindel,Atlas-Indel	.											.	C1orf220	11	.	0			.						PASS	.																																			SO:0001567	stop_retained_variant	400798	.			.			1q25.2	2013-01-15			ENSG00000213057	ENSG00000213057			33805	protein-coding gene	gene with protein product							Standard	NR_033186		Approved	FLJ35530	uc001glx.1	Q5T0J3	OTTHUMG00000035078	ENST00000319387.2:c.322dupT	1.37:g.178514564_178514564dupT		Somatic	126	.	.		WXS	Illumina HiSeq	Phase_I	156	78	0.500	.	B2RN72|Q8NAD3	RNA	INS	ENST00000319387.2	37																																																																																				-|0.599;T|0.401	0.401	strong		0.515	C1orf220-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000098176.1	NR_033186	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230309	23230311	+	In_Frame_Del	DEL	CTG	CTG	-	rs551962377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:23230309_23230311delCTG	ENST00000526893.1	+	1	350_352	c.76_78delCTG	c.(76-78)ctgdel	p.L29del	IGLL5_ENST00000531372.1_In_Frame_Del_p.L29del|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_In_Frame_Del_p.L29del	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	29						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCGCTGGCCCCTGCTGCTGCTGG	0.665																																					p.25_26del		Atlas-Indel	.											.	IGLL5	26	.	0			c.75_77del						PASS	.																																			SO:0001651	inframe_deletion	100423062	exon1			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.76_78delCTG	22.37:g.23230318_23230320delCTG	ENSP00000431254:p.Leu29del	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	146	19	0.130137	NM_001178126		In_Frame_Del	DEL	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.665	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
GLT6D1	360203	hgsc.bcm.edu	37	9	138516347	138516347	+	Frame_Shift_Del	DEL	A	A	-	rs34217442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:138516347delA	ENST00000371763.1	-	5	680	c.427delT	c.(427-429)tggfs	p.W143fs		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	143					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		CCATCGAGCCACCACCTCTCG	0.552													A|A|-|deletion	860	0.171725	0.09	0.1888	5008	,	,		16603	0.2103		0.1839	False		,,,				2504	0.2178				p.W143fs		Pindel,Atlas-Indel	.											.	GLT6D1	56	.	0			c.428delG						PASS	.			334,3488		26,282,1603	39.0	36.0	37.0			-1.0	0.0	9	dbSNP_126	43	1598,6358		173,1252,2553	yes	frameshift	GLT6D1	NM_182974.2		199,1534,4156	A1A1,A1R,RR		20.0855,8.7389,16.4035			138516347	1932,9846	1961	4021	5982	SO:0001589	frameshift_variant	360203	exon5			.	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.427delT	9.37:g.138516347delA	ENSP00000360829:p.Trp143fs	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	98	30	0.306	NM_182974		Frame_Shift_Del	DEL	ENST00000371763.1	37	CCDS43900.1																																																																																			A|0.829;-|0.171	0.171	strong		0.552	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
TGM6	343641	hgsc.bcm.edu	37	20	2411657	2411658	+	In_Frame_Ins	INS	-	-	AAC	rs557817405		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2411657_2411658insAAC	ENST00000202625.2	+	12	2012_2013	c.1951_1952insAAC	c.(1951-1953)gaa>gAACaa	p.652_653insQ	TGM6_ENST00000381423.1_Intron	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	652					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	CCTTCTCCAGGAACAGCTCAGC	0.594																																					p.E651delinsEQ		Pindel,Atlas-Indel	.											.	TGM6	126	.	0			c.1951_1952insAAC						PASS	.			4,4260		0,4,2128						5.2	1.0			81	27,8227		0,27,4100	no	coding	TGM6	NM_198994.2		0,31,6228	A1A1,A1R,RR		0.3271,0.0938,0.2476				31,12487				SO:0001652	inframe_insertion	343641	exon12			.	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1952_1954dupAAC	20.37:g.2411658_2411660dupAAC	ENSP00000202625:p.Gln652_Gln652dup	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	In_Frame_Ins	INS	ENST00000202625.2	37	CCDS13025.1																																																																																			.	.	none		0.594	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
NUP54	53371	hgsc.bcm.edu	37	4	77065318	77065319	+	In_Frame_Ins	INS	-	-	TGT	rs76406406|rs57577548|rs36024409|rs67608403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:77065318_77065319insTGT	ENST00000264883.3	-	3	418_419	c.278_279insACA	c.(277-279)cag>caACAg	p.93_93Q>QQ	NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000515460.1_5'UTR|NUP54_ENST00000514987.1_Intron	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	93	9 X 2 AA repeats of F-G.|Poly-Gln.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)	p.Q93>HK(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						GCTGCTGCTGCTGTGTATTAAA	0.411														776	0.154952	0.0567	0.1282	5008	,	,		16499	0.3512		0.1312	False		,,,				2504	0.1288				p.Q93delinsQQ		Pindel,Atlas-Indel	.											NUP54,NS,carcinoma,0,1	NUP54	48	1	1	Complex - insertion inframe(1)	kidney(1)	c.279_280insACA						PASS	.			300,3966		14,272,1847						5.2	1.0		dbSNP_126	211	1244,7010		96,1052,2979	no	coding	NUP54	NM_017426.2		110,1324,4826	A1A1,A1R,RR		15.0715,7.0323,12.3323				1544,10976				SO:0001652	inframe_insertion	53371	exon3			.	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.276_278dupACA	4.37:g.77065319_77065321dupTGT	ENSP00000264883:p.Gln97dup	Somatic	152	.	.		WXS	Illumina HiSeq	Phase_I	169	46	0.272	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	In_Frame_Ins	INS	ENST00000264883.3	37	CCDS3576.1																																																																																			-|0.827;TGT|0.173	0.173	strong		0.411	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
OR5M1	390168	hgsc.bcm.edu	37	11	56380547	56380550	+	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs71931749|rs72003051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CAGA	CAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56380547_56380550delCAGA	ENST00000526538.1	-	1	428_431	c.429_432delTCTG	c.(427-432)tgtctgfs	p.CL143fs		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						GGATAGTGACCAGACAGACACAGA	0.436														634	0.126597	0.031	0.098	5008	,	,		22572	0.1617		0.2008	False		,,,				2504	0.1636				p.144_145del		Pindel,Atlas-Indel	.											.	OR5M1	92	.	0			c.430_433del						PASS	.			236,3532		12,212,1660						3.7	0.0		dbSNP_130	118	1705,6265		205,1295,2485	no	frameshift	OR5M1	NM_001004740.1		217,1507,4145	A1A1,A1R,RR		21.3927,6.2633,16.536				1941,9797				SO:0001589	frameshift_variant	390168	exon1			.	AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"""GPCR / Class A : Olfactory receptors"""	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.429_432delTCTG	11.37:g.56380551_56380554delCAGA	ENSP00000435416:p.Cys143fs	Somatic	268	.	.		WXS	Illumina HiSeq	Phase_I	207	57	0.275	NM_001004740	Q6IF60|Q96RB6	Frame_Shift_Del	DEL	ENST00000526538.1	37	CCDS53631.1																																																																																			CAGA|0.853;-|0.147	0.147	strong		0.436	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740	
MDFIC	29969	hgsc.bcm.edu	37	7	114562638	114562639	+	In_Frame_Ins	INS	-	-	GAG			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:114562638_114562639insGAG	ENST00000257724.3	+	1	430_431	c.167_168insGAG	c.(166-171)aagagg>aaGAGgagg	p.62_63insR	MDFIC_ENST00000393486.1_5'UTR|MDFIC_ENST00000423503.1_5'Flank|MDFIC_ENST00000448022.1_5'UTR					MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						CCGGGGCggaagaggaggagga	0.703											OREG0003787	type=REGULATORY REGION|Gene=MDFIC|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.K56delinsKR		Pindel,Atlas-Indel	.											.	MDFIC	30	.	0			c.167_168insGAG						PASS	.																																			SO:0001652	inframe_insertion	29969	exon1			.	AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000257724.3:c.183_185dupGAG	7.37:g.114562645_114562647dupGAG	ENSP00000257724:p.Arg62_Arg62dup	Somatic	40	.	.	1459	WXS	Illumina HiSeq	Phase_I	42	13	0.310	NM_001166346		In_Frame_Ins	INS	ENST00000257724.3	37	CCDS34737.1																																																																																			.	.	none		0.703	MDFIC-007	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366397.1	NM_199072	
GAL3ST3	89792	hgsc.bcm.edu	37	11	65811114	65811116	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65811114_65811116delGAG	ENST00000312006.4	-	3	439_441	c.158_160delCTC	c.(157-162)cctctg>ctg	p.P53del	GAL3ST3_ENST00000527878.1_In_Frame_Del_p.P53del	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	53					monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						GAGTTCCGCAGAGGAGGGCAGCT	0.645																																					p.53_54del		Pindel,Atlas-Indel	.											.	GAL3ST3	40	.	0			c.159_161del						PASS	.																																			SO:0001651	inframe_deletion	89792	exon3			.	AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"""Sulfotransferases, membrane-bound"""	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.158_160delCTC	11.37:g.65811117_65811119delGAG	ENSP00000308591:p.Pro53del	Somatic	185	.	.		WXS	Illumina HiSeq	Phase_I	161	55	0.342	NM_033036	Q14D05	In_Frame_Del	DEL	ENST00000312006.4	37	CCDS8128.1																																																																																			.	.	none		0.645	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119755	38119757	+	In_Frame_Del	DEL	CAA	CAA	-	rs201160789|rs71322688|rs55745992|rs67890459|rs77530465|rs199535040	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38119755_38119757delCAA	ENST00000406386.3	+	7	1447_1449	c.1192_1194delCAA	c.(1192-1194)caadel	p.Q398del		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.Q398R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGAACCACTCAACGAGAGAATT	0.552														1684	0.336262	0.1536	0.2853	5008	,	,		18750	0.5863		0.3877	False		,,,				2504	0.3088				p.397_398del		Pindel,Atlas-Indel	.											.	TRIOBP	262	.	1	Substitution - Missense(1)	lung(1)	c.1191_1193del						PASS	.			658,3014		76,506,1254						-4.9	0.1		dbSNP_132	129	3439,4489		755,1929,1280	no	coding	TRIOBP	NM_001039141.2		831,2435,2534	A1A1,A1R,RR		43.3779,17.9194,35.319				4097,7503				SO:0001651	inframe_deletion	11078	exon7			.	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1192_1194delCAA	22.37:g.38119755_38119757delCAA	ENSP00000384312:p.Gln398del	Somatic	183	.	.		WXS	Illumina HiSeq	Phase_I	167	93	0.557	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	In_Frame_Del	DEL	ENST00000406386.3	37	CCDS43015.1																																																																																			-|0.368;CAA|0.632	0.368	strong		0.552	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
PKD1L2	114780	hgsc.bcm.edu	37	16	81242149	81242150	+	RNA	DEL	TT	TT	-	rs55980345|rs75398810|rs532218091|rs548490632|rs386792900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81242149_81242150delTT	ENST00000525539.1	-	0	705_706				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.N236fs*26(6)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CGGACACAGGTTTCCAAAGTAG	0.554																																					p.236_236del		Atlas-Indel	.											.	PKD1L2	361	.	6	Deletion - Frameshift(6)	breast(4)|lung(2)	c.707_708del						PASS	.																																					114780	exon4			.	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242149_81242150delTT		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Frame_Shift_Del	DEL	ENST00000525539.1	37																																																																																				TT|0.500;-|0.500	0.500	strong		0.554	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
CELA1	1990	hgsc.bcm.edu	37	12	51723598	51723599	+	Frame_Shift_Ins	INS	-	-	G	rs398102298|rs76813052|rs17860363|rs75442020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51723598_51723599insG	ENST00000293636.1	-	7	668_669	c.628_629insC	c.(628-630)ctcfs	p.L210fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	210	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.L210fs*24(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						CAAGCAATGGAGGGGGCCCCCA	0.564													GGGGG|GGGGG|GGGGGG|insertion	729	0.145567	0.084	0.1772	5008	,	,		16900	0.0407		0.2863	False		,,,				2504	0.1697				p.L210fs		Pindel,Atlas-Indel	.											.	CELA1	39	.	1	Insertion - Frameshift(1)	ovary(1)	c.629_630insC						PASS	.			562,3700		35,492,1604						5.4	0.2		dbSNP_123	63	2566,5688		406,1754,1967	no	frameshift	CELA1	NM_001971.5		441,2246,3571	A1A1,A1R,RR		31.088,13.1863,24.992				3128,9388				SO:0001589	frameshift_variant	1990	exon7			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.629dupC	12.37:g.51723603_51723603dupG	ENSP00000293636:p.Leu210fs	Somatic	47	.	.		WXS	Illumina HiSeq	Phase_I	62	20	0.323	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Frame_Shift_Ins	INS	ENST00000293636.1	37	CCDS8812.1																																																																																			-|0.851;G|0.149	0.149	strong		0.564	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
ZNF681	148213	hgsc.bcm.edu	37	19	23927742	23927743	+	Frame_Shift_Del	DEL	CA	CA	-	rs61397759	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:23927742_23927743delCA	ENST00000402377.3	-	4	750_751	c.609_610delTG	c.(607-612)tgtggafs	p.CG203fs	ZNF681_ENST00000395385.3_Frame_Shift_Del_p.CG134fs	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	203					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C134fs*5(1)|p.G135R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				AAGGCTTTTCCACAGTCTTCAC	0.292														564	0.11262	0.0106	0.1441	5008	,	,		17190	0.0913		0.1998	False		,,,				2504	0.1605				p.204_204del		Pindel,Atlas-Indel	.											LOC148213,extremity,malignant_melanoma,-1,1	ZNF681	76	1	2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|skin(1)	c.610_611del						PASS	.			179,4075		8,163,1956						-2.8	0.0		dbSNP_129	28	1687,6547		180,1327,2610	yes	frameshift	ZNF681	NM_138286.2		188,1490,4566	A1A1,A1R,RR		20.4882,4.2078,14.9423				1866,10622				SO:0001589	frameshift_variant	148213	exon4			.	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.609_610delTG	19.37:g.23927744_23927745delCA	ENSP00000384000:p.Cys203fs	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_138286	B3KVF7	Frame_Shift_Del	DEL	ENST00000402377.3	37	CCDS12414.2																																																																																			CA|0.870;-|0.130	0.130	strong		0.292	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388504	1388505	+	Frame_Shift_Del	DEL	CG	CG	-	rs568118449|rs528384190|rs115485610	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388504_1388505delCG	ENST00000324803.4	+	1	3165_3166	c.205_206delCG	c.(205-207)cgtfs	p.R69fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	69					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGCTCACACACGTGTCCATGTG	0.629														54	0.0107827	0.0174	0.0043	5008	,	,		20699	0.002		0.0169	False		,,,				2504	0.0092				p.68_69del		Atlas-Indel	.											.	CRIPAK	185	.	0			c.204_205del						PASS	.																																			SO:0001589	frameshift_variant	285464	exon1			.	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.205_206delCG	4.37:g.1388504_1388505delCG	ENSP00000323978:p.Arg69fs	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	289	42	0.145329	NM_175918	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.629	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
HOXD9	3235	hgsc.bcm.edu	37	2	176988290	176988291	+	In_Frame_Ins	INS	-	-	GCA	rs529626130|rs35578003|rs200417886|rs397814627|rs559323002|rs56007470	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:176988290_176988291insGCA	ENST00000249499.6	+	1	1203_1204	c.794_795insGCA	c.(793-798)ccgcag>ccGCAgcag	p.269_270insQ	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	269			Missing. {ECO:0000269|PubMed:11857506}.		adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		CATTCGCAGCCGCAGCAGCAGC	0.554																																					p.P265delinsPQ	GBM(47;924 952 7959 9248 12176)	Pindel,Atlas-Indel	.											.	HOXD9	49	.	0			c.794_795insGCA						PASS	.																																			SO:0001652	inframe_insertion	3235	exon1			.		CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"""Homeoboxes / ANTP class : HOXL subclass"""	5140	protein-coding gene	gene with protein product		142982	"""homeo box D9"""	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.804_806dupGCA	2.37:g.176988297_176988299dupGCA	ENSP00000249499:p.Gln269_Gln269dup	Somatic	22	.	.		WXS	Illumina HiSeq	Phase_I	31	10	0.323	NM_014213	Q86ST1	In_Frame_Ins	INS	ENST00000249499.6	37	CCDS2267.2																																																																																			-|0.685;GCA|0.315	0.315	strong		0.554	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4		
PARD6G	84552	hgsc.bcm.edu	37	18	77926795	77926796	+	Intron	INS	-	-	ACAAATAAC	rs71338092|rs11275834	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:77926795_77926796insACAAATAAC	ENST00000353265.3	-	3	493				AC139100.2_ENST00000586421.1_In_Frame_Ins_p.94_95insITQ|AC139100.2_ENST00000585422.1_3'UTR|AC139100.2_ENST00000589574.1_Intron|AC139100.2_ENST00000587254.1_Intron	NM_032510.3	NP_115899.1	Q9BYG4	PAR6G_HUMAN	par-6 family cell polarity regulator gamma						cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	8		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)		AATATTTTCTTACAAATAACCC	0.401														1083	0.216254	0.4977	0.1643	5008	,	,		17199	0.0595		0.1541	False		,,,				2504	0.0982				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																			SO:0001627	intron_variant	100130522	.			.		CCDS12022.1	18q23	2013-08-28	2013-08-28		ENSG00000178184	ENSG00000178184			16076	protein-coding gene	gene with protein product		608976	"""par-6 (partitioning defective 6, C.elegans) homolog gamma"", ""par-6 partitioning defective 6 homolog gamma (C. elegans)"""			11260256	Standard	NM_032510		Approved	PAR-6G, PAR6gamma	uc002lny.3	Q9BYG4	OTTHUMG00000132922	ENST00000353265.3:c.296-8306->GTTATTTGT	18.37:g.77926796_77926804dupACAAATAAC		Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	63	16	0.254	.	A8QM57	RNA	INS	ENST00000353265.3	37	CCDS12022.1																																																																																			-|0.795;ACAAATAAC|0.205	0.205	strong		0.401	PARD6G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256435.2	NM_032510	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111500816	111500817	+	Splice_Site	INS	-	-	TAAAA	rs145708081|rs369027426		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:111500816_111500817insTAAAA	ENST00000261486.5	-	23	2209		c.e23-1		EPB41L4A_ENST00000507810.1_Intron|EPB41L4A-AS1_ENST00000413221.2_lincRNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		CATTTCTTCTCTAAAATATATT	0.317																																					.		Atlas-Indel	.											.	EPB41L4A	130	.	0			c.1933-1->TTTTA						PASS	.			3408,36		1689,30,3						5.3	1.0		dbSNP_134	59	7446,316		3600,246,35	no	splice-3	EPB41L4A	NM_022140.3		5289,276,38	A1A1,A1R,RR		4.0711,1.0453,3.1412				10854,352				SO:0001630	splice_region_variant	64097	exon24			.	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1933-1->TTTTA	5.37:g.111500817_111500821dupTAAAA		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	38	0.348624	NM_022140	A4FUI6	Splice_Site	INS	ENST00000261486.5	37	CCDS43350.1																																																																																			-|0.025;TAAAA|0.975	0.975	strong		0.317	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		Intron
RPGR	6103	hgsc.bcm.edu	37	X	38145632	38145646	+	Intron	DEL	CTTCCTCCCCTTCTT	CTTCCTCCCCTTCTT	-	rs201131185|rs200824587		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTTCCTCCCCTTCTT	CTTCCTCCCCTTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:38145632_38145646delCTTCCTCCCCTTCTT	ENST00000339363.3	-	14	2688				RPGR_ENST00000309513.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.EEGEE869del|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						tccccttctccttcctccccttcttcctccccttc	0.6																																					p.869_874del		Atlas-Indel	.											.	RPGR	175	.	0			c.2607_2621del	GRCh37	CD033265|CD064604|CI013682|CM074396	orf15	D|I|M		PASS	.		,	43,2971		2,33,6,1315,308					,	-0.2	0.0			10	195,4756		24,97,50,1779,1101	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	26,130,56,3094,1409	A1A1,A1R,A1,RR,R		3.9386,1.4267,2.9881	,	,		238,7727				SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+700AAGAAGGGGAGGAAG>-	X.37:g.38145632_38145646delCTTCCTCCCCTTCTT		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	27	20	0.740741	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				CTTCCTCCCCTTCTT|0.987;-|0.013	0.013	strong		0.600	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129924	175129925	+	In_Frame_Ins	INS	-	-	CTT	rs150137790|rs374766108		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:175129924_175129925insCTT	ENST00000423313.1	-	4	761_762	c.225_226insAAG	c.(223-228)aaggat>aagAAGgat	p.75_76insK	KIAA0040_ENST00000444639.1_In_Frame_Ins_p.75_76insK|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000545251.2_In_Frame_Ins_p.75_76insK	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tcttcttcatccttcttcttct	0.505																																					p.D76delinsKD		Pindel,Atlas-Indel	.											.	KIAA0040	2	.	0			c.226_227insAAG						PASS	.																																			SO:0001652	inframe_insertion	9674	exon5			.	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.223_225dupAAG	1.37:g.175129931_175129933dupCTT	ENSP00000462172:p.Lys75_Lys75dup	Somatic	96	.	.		WXS	Illumina HiSeq	Phase_I	148	45	0.304	NM_001162893	A8K9H6|Q2NKQ0	In_Frame_Ins	INS	ENST00000423313.1	37																																																																																				.	.	alt		0.505	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
PKNOX2	63876	hgsc.bcm.edu	37	11	125301193	125301195	+	In_Frame_Del	DEL	GAG	GAG	-	rs397840770|rs397849304|rs3832749	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:125301193_125301195delGAG	ENST00000298282.9	+	13	1595_1597	c.1324_1326delGAG	c.(1324-1326)gagdel	p.E447del	PKNOX2_ENST00000542175.1_In_Frame_Del_p.E383del|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	447	Asp/Glu-rich (acidic).		Missing. {ECO:0000269|PubMed:15489334}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		tgagatggaagaggaggaggagg	0.571														294	0.0587061	0.0129	0.0576	5008	,	,		20223	0.0744		0.1123	False		,,,				2504	0.0501				p.441_442del		Pindel,Atlas-Indel	.											.	PKNOX2	60	.	0			c.1323_1325del						PASS	.																																			SO:0001651	inframe_deletion	63876	exon13			.	AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"""Homeoboxes / TALE class"""	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.1324_1326delGAG	11.37:g.125301202_125301204delGAG	ENSP00000298282:p.Glu447del	Somatic	62	.	.		WXS	Illumina HiSeq	Phase_I	72	21	0.292	NM_022062	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	In_Frame_Del	DEL	ENST00000298282.9	37	CCDS41730.1																																																																																			GAG|0.918;-|0.082	0.082	strong		0.571	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3		
PDE11A	50940	hgsc.bcm.edu	37	2	178494173	178494174	+	In_Frame_Ins	INS	-	-	GGA	rs397723704|rs67772336|rs3830637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:178494173_178494174insGGA	ENST00000286063.6	-	20	3080_3081	c.2763_2764insTCC	c.(2761-2766)tcccct>tccTCCcct	p.921_922insS	PDE11A_ENST00000389683.3_In_Frame_Ins_p.477_478insS|PDE11A_ENST00000450799.2_In_Frame_Ins_p.112_113insS|PDE11A_ENST00000409504.1_In_Frame_Ins_p.563_564insS|PDE11A_ENST00000449286.2_In_Frame_Ins_p.563_564insS|PDE11A_ENST00000358450.4_In_Frame_Ins_p.671_672insS	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	921				S -> SS (in Ref. 1; BAB16371/BAB16372, 2; CAB82573, 3; AAG32023/CAC15567, 4; BAB62712/BAB62713/BAB62714 and 6; AAI12394/AAI14432). {ECO:0000305}.	blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	ACACTGGCAGGGGAGGATGAGG	0.5									Primary Pigmented Nodular Adrenocortical Disease, Familial					2943	0.58766	0.1982	0.7882	5008	,	,		20873	0.7014		0.7425	False		,,,				2504	0.6953				p.P922delinsSP		Pindel,Atlas-Indel	.											.	PDE11A	283	.	0			c.2764_2765insTCC						PASS	.		,,,	1326,25,2915		216,2,892,0,23,1000					,,,	-0.7	0.0		dbSNP_130	198	6097,62,2095		2237,51,1572,0,11,256	no	codingComplex,codingComplex,codingComplex,codingComplex	PDE11A	NM_016953.3,NM_001077358.1,NM_001077197.1,NM_001077196.1	,,,	2453,53,2464,0,34,1256	A1A1,A1A2,A1R,A2A2,A2R,RR		26.1328,31.669,40.7109	,,,	,,,		7423,87,5010				SO:0001652	inframe_insertion	50940	exon20	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	.	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2761_2763dupTCC	2.37:g.178494177_178494179dupGGA	ENSP00000286063:p.Ser921_Ser921dup	Somatic	197	.	.		WXS	Illumina HiSeq	Phase_I	265	114	0.430	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	In_Frame_Ins	INS	ENST00000286063.6	37	CCDS33334.1																																																																																			GGA|1.000;|0.000	1.000	strong		0.500	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
SLC28A1	9154	hgsc.bcm.edu	37	15	85438311	85438312	+	In_Frame_Ins	INS	-	-	TTG	rs17215836|rs151038463	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85438311_85438312insTTG	ENST00000286749.3	+	5	508_509	c.418_419insTTG	c.(418-420)ctc>cTTGtc	p.140_141insV	SLC28A1_ENST00000537624.1_In_Frame_Ins_p.140_141insV|SLC28A1_ENST00000537216.1_In_Frame_Ins_p.140_141insV|SLC28A1_ENST00000538177.1_In_Frame_Ins_p.140_141insV|SLC28A1_ENST00000394573.1_In_Frame_Ins_p.140_141insV|SLC28A1_ENST00000537703.1_In_Frame_Ins_p.62_63insV|SLC28A1_ENST00000338602.2_In_Frame_Ins_p.140_141insV			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	140			L -> LV (in A). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.L140_K141insV(2)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GAGGAGGTTTCTCAAGCCTCAG	0.639														1294	0.258387	0.3132	0.2651	5008	,	,		16712	0.1925		0.3111	False		,,,				2504	0.1933				p.L140delinsLV		Pindel,Atlas-Indel	.											.	SLC28A1	118	.	2	Insertion - In frame(2)	lung(2)	c.418_419insTTG						PASS	.		,	1267,2997		209,849,1074					,	-2.5	0.0		dbSNP_126	46	2510,5742		383,1744,1999	no	coding,coding	SLC28A1	NM_201651.1,NM_004213.3	,	592,2593,3073	A1A1,A1R,RR		30.4169,29.7139,30.1774	,	,		3777,8739				SO:0001652	inframe_insertion	9154	exon6			.	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	Exception_encountered	15.37:g.85438311_85438312insTTG	ENSP00000286749:p.Leu140_Lys141insVal	Somatic	90	.	.		WXS	Illumina HiSeq	Phase_I	112	33	0.295	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	In_Frame_Ins	INS	ENST00000286749.3	37	CCDS10334.1																																																																																			-|0.732;TTG|0.268	0.268	strong		0.639	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765400	27765411	+	In_Frame_Del	DEL	GAGGAGGAGGAG	GAGGAGGAGGAG	-	rs371896121		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAGGAGGAGGAG	GAGGAGGAGGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:27765400_27765411delGAGGAGGAGGAG	ENST00000451261.2	+	5	787_798	c.388_399delGAGGAGGAGGAG	c.(388-399)gaggaggaggagdel	p.EEEE142del		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	142	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						ggaggaggaagaggaggaggaggaggaggagg	0.561																																					p.129_133del		Pindel,Atlas-Indel	.											.	DCAF8L2	79	.	0			c.387_398del						PASS	.																																			SO:0001651	inframe_deletion	347442	exon1			.		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.388_399delGAGGAGGAGGAG	X.37:g.27765400_27765411delGAGGAGGAGGAG	ENSP00000462745:p.Glu142_Glu145del	Somatic	52	.	.		WXS	Illumina HiSeq	Phase_I	63	12	0.190	NM_001136533	B2RXH9|J3KT06	In_Frame_Del	DEL	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	alt		0.561	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
ZNF284	342909	hgsc.bcm.edu	37	19	44590000	44590002	+	In_Frame_Del	DEL	CTC	CTC	-	rs398121017|rs201737232|rs76566549|rs369411341|rs75164559|rs139900131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44590000_44590002delCTC	ENST00000421176.3	+	5	585_587	c.369_371delCTC	c.(367-372)ttctcc>ttc	p.S124del	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	124					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				GCTCTCAGTTCTCCACACAAGGT	0.453														2258	0.450879	0.2663	0.3703	5008	,	,		21908	0.3313		0.665	False		,,,				2504	0.6605				p.123_124del		Pindel,Atlas-Indel	.											.	ZNF284	38	.	0			c.368_370del						PASS	.			1472,2780		275,922,929						1.1	0.0		dbSNP_134	93	5440,2814		1787,1866,474	no	coding	ZNF284	NM_001037813.2		2062,2788,1403	A1A1,A1R,RR		34.0926,34.619,44.7305				6912,5594				SO:0001651	inframe_deletion	342909	exon5			.	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"""Zinc fingers, C2H2-type"", ""-"""	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.369_371delCTC	19.37:g.44590000_44590002delCTC	ENSP00000411032:p.Ser124del	Somatic	187	.	.		WXS	Illumina HiSeq	Phase_I	166	80	0.482	NM_001037813	Q86WM1	In_Frame_Del	DEL	ENST00000421176.3	37	CCDS46099.1																																																																																			CTC|0.548;-|0.452	0.452	strong		0.453	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813	
ATAD5	79915	hgsc.bcm.edu	37	17	29161956	29161961	+	In_Frame_Del	DEL	CAATGT	CAATGT	-	rs60663953|rs80170526|rs398102309|rs72427574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CAATGT	CAATGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29161956_29161961delCAATGT	ENST00000321990.4	+	2	1235_1240	c.857_862delCAATGT	c.(856-864)acaatgtca>aca	p.MS287del	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	287					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CCAGACTCTACAATGTCAATTTGTGT	0.354														721	0.14397	0.0703	0.1859	5008	,	,		20341	0.1359		0.1074	False		,,,				2504	0.2597				p.286_287del		Pindel,Atlas-Indel	.											ATAD5,NS,carcinoma,0,1	ATAD5	150	1	0			c.856_861del						PASS	.			276,3982		14,248,1867						0.7	0.0		dbSNP_130	43	796,7436		29,738,3349	no	coding	ATAD5	NM_024857.3		43,986,5216	A1A1,A1R,RR		9.6696,6.4819,8.5829				1072,11418				SO:0001651	inframe_deletion	79915	exon2			.		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.857_862delCAATGT	17.37:g.29161956_29161961delCAATGT	ENSP00000313171:p.Met287_Ser288del	Somatic	137	.	.		WXS	Illumina HiSeq	Phase_I	78	58	0.744	NM_024857	Q05DH0|Q69YR6|Q9H9I1	In_Frame_Del	DEL	ENST00000321990.4	37	CCDS11260.1																																																																																			CAATGT|0.874;-|0.126	0.126	strong		0.354	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
ERI1	90459	hgsc.bcm.edu	37	8	8887543	8887545	+	Stop_Codon_Del	DEL	AAC	AAC	-	rs200590562|rs66532380|rs140242735|rs201293350	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:8887543_8887545delAAC	ENST00000523898.1	+	0	1728_1730				ERI1_ENST00000520332.1_Intron|ERI1_ENST00000519292.1_Stop_Codon_Del|ERI1_ENST00000250263.7_Stop_Codon_Del			Q8IV48	ERI1_HUMAN	exoribonuclease 1						gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125)	cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11						TTTAGAAAGTAACAACAGTTTTG	0.409														2197	0.438698	0.1112	0.5648	5008	,	,		20640	0.6944		0.4364	False		,,,				2504	0.5307				p.350_350del		Pindel,Atlas-Indel	.											.	ERI1	20	.	0			c.1048_1050del						PASS	.			724,3540		54,616,1462						4.7	1.0		dbSNP_130	68	3689,4565		828,2033,1266	no	coding	ERI1	NM_153332.3		882,2649,2728	A1A1,A1R,RR		44.6935,16.9794,35.2532				4413,8105				SO:0001567	stop_retained_variant	90459	exon7			.	BC035279	CCDS5972.1	8p23.1	2008-12-16	2008-12-16	2008-12-16	ENSG00000104626	ENSG00000104626		"""Enhanced RNAi three prime mRNA exonucleases"""	23994	protein-coding gene	gene with protein product	"""exoribonuclease 1"", ""enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)"""	608739	"""three prime histone mRNA exonuclease 1"""	THEX1		14536070	Standard	NM_153332		Approved	3'HEXO	uc003wsk.2	Q8IV48	OTTHUMG00000129328	Exception_encountered	8.37:g.8887546_8887548delAAC		Somatic	54	.	.		WXS	Illumina HiSeq	Phase_I	70	24	0.343	NM_153332	A8K4U7|Q9NSX3	In_Frame_Del	DEL	ENST00000523898.1	37	CCDS5972.1																																																																																			AAC|0.548;-|0.452	0.452	strong		0.409	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332	
OR13C2	392376	hgsc.bcm.edu	37	9	107367665	107367666	+	Frame_Shift_Del	DEL	GC	GC	-	rs377668801|rs143760725|rs144815315|rs140970710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107367665_107367666delGC	ENST00000542196.1	-	1	285_286	c.243_244delGC	c.(241-246)acgctafs	p.L82fs		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						AAGCTCACTAGCGTGGAGGGAA	0.515														1574	0.314297	0.4138	0.2003	5008	,	,		20880	0.4097		0.16	False		,,,				2504	0.3211				p.82_82del		Pindel,Atlas-Indel	.											.	OR13C2	46	.	0			c.244_245del						PASS	.			2387,1861		730,927,467						2.2	0.0		dbSNP_134	35	1565,6681		171,1223,2729	no	frameshift	OR13C2	NM_001004481.1		901,2150,3196	A1A1,A1R,RR		18.9789,43.8089,31.6312				3952,8542				SO:0001589	frameshift_variant	392376	exon1			.		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.243_244delGC	9.37:g.107367665_107367666delGC	ENSP00000438815:p.Leu82fs	Somatic	733	.	.		WXS	Illumina HiSeq	Phase_I	683	122	0.179	NM_001004481	B9EGV8|Q6IF54	Frame_Shift_Del	DEL	ENST00000542196.1	37	CCDS35092.1																																																																																			.	.	strong		0.515	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
PI4KB	5298	hgsc.bcm.edu	37	1	151263677	151263678	+	IGR	INS	-	-	ACA	rs145032688	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151263677_151263678insACA	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_3'UTR			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GGCTGTTGGGGACAACTAGTCT	0.584														82	0.0163738	0.0023	0.0144	5008	,	,		16222	0.0		0.0547	False		,,,				2504	0.0143				p.D1236delinsDN	Colon(154;765 1838 9854 28443 37492)	Pindel,Atlas-Indel	.											.	ZNF687	94	.	0			c.3706_3707insACA						PASS	.			59,4025		4,51,1987						4.7	1.0		dbSNP_134	30	528,7434		53,422,3506	no	coding	ZNF687	NM_020832.1		57,473,5493	A1A1,A1R,RR		6.6315,1.4447,4.873				587,11459				SO:0001628	intergenic_variant	57592	exon9			.	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348		1.37:g.151263678_151263680dupACA		Somatic	25	.	.		WXS	Illumina HiSeq	Phase_I	32	14	0.438	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	In_Frame_Ins	INS	ENST00000368873.1	37																																																																																				-|0.977;ACA|0.023	0.023	strong		0.584	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651	
STRC	161497	hgsc.bcm.edu	37	15	43910866	43910867	+	In_Frame_Ins	INS	-	-	CAG			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43910866_43910867insCAG	ENST00000450892.2	-	1	131_132	c.54_55insCTG	c.(52-57)ctgtcc>ctgCTGtcc	p.18_19insL	STRC_ENST00000541030.1_Intron	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	18					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CCTGCAAAGGAcagcagcagca	0.515											OREG0003955	type=REGULATORY REGION|Gene=STRC|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.S19delinsLS		Pindel,Atlas-Indel	.											.	STRC	58	.	0			c.55_56insCTG						PASS	.																																			SO:0001652	inframe_insertion	161497	exon1			.	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.52_54dupCTG	15.37:g.43910873_43910875dupCAG	ENSP00000401513:p.Leu18_Leu18dup	Somatic	254	.	.	920	WXS	Illumina HiSeq	Phase_I	240	52	0.217	NM_153700		In_Frame_Ins	INS	ENST00000450892.2	37	CCDS10098.1																																																																																			.	.	none		0.515	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
BACE2	25825	hgsc.bcm.edu	37	21	42551433	42551433	+	Intron	DEL	G	G	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:42551433delG	ENST00000330333.6	+	1	775				PLAC4_ENST00000536486.1_RNA|PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000440221.2_RNA|PLAC4_ENST00000414699.1_RNA|BACE2_ENST00000347667.5_Intron|BACE2_ENST00000328735.6_Intron|BACE2-IT1_ENST00000433378.1_RNA	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				GACGGTGTCTGGGGTGAGTGA	0.607																																					p.R42fs		Atlas-Indel	.											.	.	.	.	0			c.124delA						PASS	.						124.0	109.0	114.0					21																	42551433		2196	4275	6471	SO:0001627	intron_variant	191585	exon1			.	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10931G>-	21.37:g.42551433delG		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	220	26	0.118182	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Frame_Shift_Del	DEL	ENST00000330333.6	37	CCDS13668.1																																																																																			.	.	none		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
ATXN1	6310	hgsc.bcm.edu	37	6	16327913	16327915	+	In_Frame_Del	DEL	TGA	TGA	-	rs11969612|rs369629396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:16327913_16327915delTGA	ENST00000244769.4	-	8	1563_1565	c.627_629delTCA	c.(625-630)catcag>cag	p.H209del	ATXN1_ENST00000436367.1_In_Frame_Del_p.H209del	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	209	Poly-Gln.		H -> Q (in dbSNP:rs11969612).		adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.H209delH(2)|p.H209_H211delHQH(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				ctgctgatgctgatgctgctgct	0.665																																					p.210_210del		Atlas-Indel	.											ATXN1,colon,carcinoma,0,2	ATXN1	117	2	3	Deletion - In frame(3)	upper_aerodigestive_tract(1)|large_intestine(1)|prostate(1)	c.628_630del						PASS	.		,|,	615,313,2022|637,2259		169,39,238,43,188,798|112,413,923					,|,		0.0|0.0		dbSNP_130	7|7	1006,693,4879|752,5866		252,19,483,15,644,1876|24,704,2581	no|no	codingComplex,codingComplex|coding,coding	ATXN1|ATXN1	NM_001128164.1,NM_000332.3|NM_001128164.1,NM_000332.3	,|,	421,58,721,58,832,2674|136,1117,3504	A1A1,A1A2,A1R,A2A2,A2R,RR|A1A1,A1R,RR		25.8285,31.4576,27.5714|11.3629,21.9959,14.5995	,|,	,|,		1621,1006,6901|1389,8125				SO:0001651	inframe_deletion	6310	exon7			.	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.627_629delTCA	6.37:g.16327913_16327915delTGA	ENSP00000244769:p.His209del	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	91	17	0.186813	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	In_Frame_Del	DEL	ENST00000244769.4	37	CCDS34342.1																																																																																			.	.	weak		0.665	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084943	31084945	+	Intron	DEL	CTT	CTT	-	rs57244323|rs540877039	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31084943_31084945delCTT	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_In_Frame_Del_p.S153del	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGAGCTGCTGCTTCCCGAGTGAG	0.571														939	0.1875	0.2065	0.1527	5008	,	,		17220	0.1637		0.1869	False		,,,				2504	0.2117				p.150_150del		Pindel,Atlas-Indel	.											.	CDSN	48	.	0			c.448_450del						PASS	.		,	950,3314		87,776,1269					,	2.5	0.2		dbSNP_126	37	1846,6398		222,1402,2498	no	intron,coding	CDSN,PSORS1C1	NM_014068.2,NM_001264.4	,	309,2178,3767	A1A1,A1R,RR		22.392,22.2795,22.3537	,	,		2796,9712				SO:0001627	intron_variant	1041	exon2			.	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2275CTT>-	6.37:g.31084943_31084945delCTT		Somatic	72	.	.		WXS	Illumina HiSeq	Phase_I	89	22	0.247	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	In_Frame_Del	DEL	ENST00000259881.9	37	CCDS34390.1																																																																																			CTT|0.500;-|0.500	0.500	strong		0.571	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
Unknown	0	hgsc.bcm.edu	37	9	18075	18075	+	IGR	DEL	G	G	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:18075delG								None (None upstream) : MIR1302-2 (9581 downstream)																							TGGATCCTGTGGCGGGGGCGT	0.662																																					p.H121fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.362delA						PASS	.																																			SO:0001628	intergenic_variant	100287171	exon4			.																													9.37:g.18075delG		Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	66	20	0.303	NM_182905		Frame_Shift_Del	DEL		37																																																																																				G|0.500;-|0.500	0.500	weak	0	0.662								
TNFAIP3	7128	hgsc.bcm.edu	37	6	138192494	138192501	+	Frame_Shift_Del	DEL	CACCGATA	CACCGATA	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CACCGATA	CACCGATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138192494_138192501delCACCGATA	ENST00000237289.4	+	2	196_203	c.130_137delCACCGATA	c.(130-138)caccgatacfs	p.HRY44fs		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	44					apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.M43fs*55(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		TAAAACCATGCACCGATACACACTGGAA	0.438			"""D, N, F"""		"""marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"""																																p.43_46del	GBM(130;153 1739 22295 28918 47987)	Atlas-Indel	.		Rec	yes		6	6q23	7128	"""tumor necrosis factor, alpha-induced protein 3"""		L	.	TNFAIP3	340	.	26	Whole gene deletion(25)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(26)	c.129_136del						PASS	.																																			SO:0001589	frameshift_variant	7128	exon2			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"""OTU domain containing"""	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.130_137delCACCGATA	6.37:g.138192494_138192501delCACCGATA	ENSP00000237289:p.His44fs	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	114	12	0.105263	NM_006290	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Del	DEL	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.438	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		
UBAC1	10422	hgsc.bcm.edu	37	9	138836942	138836944	+	In_Frame_Del	DEL	CCT	CCT	-	rs66767056|rs140946801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:138836942_138836944delCCT	ENST00000371756.3	-	7	1023_1025	c.806_808delAGG	c.(805-810)gaggcc>gcc	p.E269del	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	269				Missing (in Ref. 1; AAD51084). {ECO:0000305}.	protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.E269delE(1)|p.E269fs*6(1)		NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		TCATCTCTGGCCTCCTCATCGGT	0.621														851	0.169928	0.0197	0.2104	5008	,	,		17759	0.2183		0.2465	False		,,,				2504	0.2157				p.269_270del	NSCLC(78;973 1398 27381 29552 42415)	Pindel,Atlas-Indel	.											.	UBAC1	40	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	stomach(1)|kidney(1)	c.807_809del						PASS	.			274,3990		12,250,1870						0.6	0.8		dbSNP_130	124	2296,5958		312,1672,2143	no	coding	UBAC1	NM_016172.2		324,1922,4013	A1A1,A1R,RR		27.8168,6.4259,20.5304				2570,9948				SO:0001651	inframe_deletion	10422	exon7			.	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"""ubiquitin associated domain containing 1"""	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.806_808delAGG	9.37:g.138836945_138836947delCCT	ENSP00000360821:p.Glu269del	Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	92	60	0.652	NM_016172	O75500|Q9UMW7	In_Frame_Del	DEL	ENST00000371756.3	37	CCDS35177.1																																																																																			CCT|0.815;-|0.185	0.185	strong		0.621	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172	
ASPHD1	253982	hgsc.bcm.edu	37	16	29912802	29912803	+	In_Frame_Ins	INS	-	-	GGT	rs35784618|rs140411458|rs375867010	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:29912802_29912803insGGT	ENST00000308748.5	+	1	762_763	c.510_511insGGT	c.(511-513)ggt>GGTggt	p.171_171G>GG	SEZ6L2_ENST00000537485.1_5'Flank|ASPHD1_ENST00000483405.1_Intron|SEZ6L2_ENST00000346932.5_5'Flank|SEZ6L2_ENST00000308713.5_5'Flank|SEZ6L2_ENST00000350527.3_5'Flank	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	171	Gly-rich.				peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)	dioxygenase activity (GO:0051213)			endometrium(4)|large_intestine(2)|lung(1)|prostate(1)	8						GGGCAGCTCAGGGTGGCCCAGG	0.673														1013	0.202276	0.1104	0.2925	5008	,	,		13741	0.0804		0.4563	False		,,,				2504	0.1268				p.Q170delinsQG		Pindel,Atlas-Indel	.											.	ASPHD1	28	.	0			c.510_511insGGT						PASS	.			673,3567		66,541,1513						3.2	1.0		dbSNP_126	30	3768,4432		929,1910,1261	no	coding	ASPHD1	NM_181718.3		995,2451,2774	A1A1,A1R,RR		45.9512,15.8726,35.6994				4441,7999				SO:0001652	inframe_insertion	253982	exon1			.	AF070642	CCDS10660.1	16p11.2	2008-02-05			ENSG00000174939	ENSG00000174939			27380	protein-coding gene	gene with protein product							Standard	NM_181718		Approved		uc002dut.3	Q5U4P2	OTTHUMG00000132121	ENST00000308748.5:c.511_513dupGGT	16.37:g.29912803_29912805dupGGT	ENSP00000311447:p.Gly172dup	Somatic	40	.	.		WXS	Illumina HiSeq	Phase_I	26	12	0.462	NM_181718	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	In_Frame_Ins	INS	ENST00000308748.5	37	CCDS10660.1																																																																																			-|0.756;GGT|0.244	0.244	strong		0.673	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718	
C12orf60	144608	hgsc.bcm.edu	37	12	14976418	14976419	+	Frame_Shift_Del	DEL	TA	TA	-	rs202023163|rs10556010|rs139293175	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:14976418_14976419delTA	ENST00000330828.2	+	2	753_754	c.549_550delTA	c.(547-552)actatgfs	p.M184fs	C12orf60_ENST00000527783.1_Intron	NM_175874.3	NP_787070.2	Q5U649	CL060_HUMAN	chromosome 12 open reading frame 60	184										breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	9						CCAAAACCACTATGATAGACAC	0.401														952	0.190096	0.323	0.0893	5008	,	,		19363	0.0823		0.1431	False		,,,				2504	0.2413				p.183_183del		Pindel,Atlas-Indel	.											.	C12orf60	31	.	0			c.548_549del						PASS	.			1110,3154		144,822,1166						1.4	0.0		dbSNP_119	49	1274,6978		101,1072,2953	no	frameshift	C12orf60	NM_175874.3		245,1894,4119	A1A1,A1R,RR		15.4387,26.0319,19.0476				2384,10132				SO:0001589	frameshift_variant	144608	exon2			.	BC038836	CCDS8667.1	12p12.3	2012-08-16			ENSG00000182993	ENSG00000182993			28726	protein-coding gene	gene with protein product						12477932	Standard	NM_175874		Approved	MGC47869	uc001rcj.4	Q5U649	OTTHUMG00000167473	ENST00000330828.2:c.549_550delTA	12.37:g.14976418_14976419delTA	ENSP00000331691:p.Met184fs	Somatic	105	.	.		WXS	Illumina HiSeq	Phase_I	140	46	0.329	NM_175874	A8K1M7|Q5XKK8|Q8IXY2	Frame_Shift_Del	DEL	ENST00000330828.2	37	CCDS8667.1																																																																																			TA|0.835;-|0.165	0.165	strong		0.401	C12orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394735.1	NM_175874	
ASPN	54829	hgsc.bcm.edu	37	9	95221948	95221949	+	Frame_Shift_Ins	INS	-	-	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:95221948_95221949insT	ENST00000375544.3	-	7	1153_1154	c.910_911insA	c.(910-912)atcfs	p.I304fs	CENPP_ENST00000375587.3_Intron|ASPN_ENST00000375543.1_Intron	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	304					bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						TCCTGAAGGGATTTTTTTTAGT	0.342																																					p.I304fs		Pindel,Atlas-Indel	.											.	ASPN	52	.	0			c.911_912insA						PASS	.		,,	1,4263		0,1,2131					,,	5.5	1.0			109	8,8246		0,8,4119	no	frameshift,intron,intron	ASPN,CENPP	NM_017680.4,NM_001193335.1,NM_001012267.1	,,	0,9,6250	A1A1,A1R,RR		0.0969,0.0235,0.0719	,,	,,		9,12509				SO:0001589	frameshift_variant	54829	exon7			.	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	14872	protein-coding gene	gene with protein product	"""asporin proteoglycan"""	608135	"""asporin (LRR class 1)"""				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.911dupA	9.37:g.95221956_95221956dupT	ENSP00000364694:p.Ile304fs	Somatic	184	.	.		WXS	Illumina HiSeq	Phase_I	178	48	0.270	NM_017680	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Frame_Shift_Ins	INS	ENST00000375544.3	37																																																																																				.	.	none		0.342	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680	
TET2	54790	hgsc.bcm.edu	37	4	106197061	106197061	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106197061delA	ENST00000540549.1	+	11	6254	c.5394delA	c.(5392-5394)tcafs	p.S1798fs	TET2_ENST00000513237.1_Frame_Shift_Del_p.S1819fs|TET2_ENST00000380013.4_Frame_Shift_Del_p.S1798fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1798					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ATGGGTTATCAAAGATGCTTC	0.463			"""Mis N, F"""		MDS																																p.S1798X		Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.5393delC						PASS	.						23.0	21.0	21.0					4																	106197061		692	1591	2283	SO:0001589	frameshift_variant	54790	exon11			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5394delA	4.37:g.106197061delA	ENSP00000442788:p.Ser1798fs	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	130	22	0.169231	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.463	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
EP400	57634	hgsc.bcm.edu	37	12	132547093	132547094	+	In_Frame_Ins	INS	-	-	CAG	rs10902490|rs113304321|rs528214697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:132547093_132547094insCAG	ENST00000333577.4	+	48	8398_8399	c.8289_8290insCAG	c.(8290-8292)cag>CAGcag	p.2764_2764Q>QQ	EP400_ENST00000389561.2_In_Frame_Ins_p.2728_2728Q>QQ|EP400_ENST00000332482.4_In_Frame_Ins_p.2691_2691Q>QQ|EP400_ENST00000330386.6_In_Frame_Ins_p.2647_2647Q>QQ|EP400_ENST00000389562.2_In_Frame_Ins_p.2727_2727Q>QQ			Q96L91	EP400_HUMAN	E1A binding protein p400	2764	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q2726Q(9)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcaacaacagcagcagca	0.564														1869	0.373203	0.3427	0.513	5008	,	,		15674	0.2391		0.4722	False		,,,				2504	0.3517				p.Q2727delinsQQ		Atlas-Indel	.											EP400,NS,carcinoma,0,15	EP400	370	15	9	Substitution - coding silent(9)	lung(3)|kidney(2)|endometrium(2)|central_nervous_system(2)	c.8181_8182insCAG						PASS	.																																			SO:0001652	inframe_insertion	57634	exon47			.	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8329_8331dupCAG	12.37:g.132547100_132547102dupCAG	ENSP00000333602:p.Gln2784dup	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	In_Frame_Ins	INS	ENST00000333577.4	37																																																																																				.	.	weak		0.564	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
SCRN3	79634	hgsc.bcm.edu	37	2	175292581	175292593	+	Frame_Shift_Del	DEL	TCAAATTTATCAG	TCAAATTTATCAG	-	rs145699077|rs79038555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TCAAATTTATCAG	TCAAATTTATCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:175292581_175292593delTCAAATTTATCAG	ENST00000272732.6	+	8	1315_1327	c.1233_1245delTCAAATTTATCAG	c.(1231-1245)attcaaatttatcagfs	p.IQIYQ411fs	SCRN3_ENST00000409673.3_Frame_Shift_Del_p.IQIYQ404fs|SCRN3_ENST00000548921.1_3'UTR	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	411							dipeptidase activity (GO:0016805)	p.I406V(1)|p.I413V(1)|p.N417fs*>4(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			AAGATGAAATTCAAATTTATCAGTCAAATTTAT	0.319														1062	0.212061	0.0832	0.1931	5008	,	,		19634	0.2113		0.3817	False		,,,				2504	0.226				p.411_415del		Pindel,Atlas-Indel	.											.	SCRN3	76	.	3	Substitution - Missense(2)|Deletion - Frameshift(1)	endometrium(2)|urinary_tract(1)	c.1232_1244del						PASS	.		,	515,3749		33,449,1650					,	5.6	1.0		dbSNP_134	72	2708,5524		474,1760,1882	no	frameshift,frameshift	SCRN3	NM_024583.4,NM_001193528.1	,	507,2209,3532	A1A1,A1R,RR		32.896,12.0779,25.7923	,	,		3223,9273				SO:0001589	frameshift_variant	79634	exon8			.	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.1233_1245delTCAAATTTATCAG	2.37:g.175292581_175292593delTCAAATTTATCAG	ENSP00000272732:p.Ile411fs	Somatic	403	.	.		WXS	Illumina HiSeq	Phase_I	296	79	0.267	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Frame_Shift_Del	DEL	ENST00000272732.6	37	CCDS2258.1																																																																																			TCAAATTTATCAG|0.751;-|0.249	0.249	strong		0.319	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583	
TAS2R8	50836	hgsc.bcm.edu	37	12	10958845	10958846	+	Frame_Shift_Ins	INS	-	-	A	rs200711805|rs149008514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10958845_10958846insA	ENST00000240615.2	-	1	1046_1047	c.734_735insT	c.(733-735)ttcfs	p.F245fs		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	245					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TATAGTATAGGAAAAAAAAGAA	0.366													AAAAAAAA|AAAAAAAA|AAAAAAAAA|insertion	40	0.00798722	0.0	0.0216	5008	,	,		15757	0.002		0.0119	False		,,,				2504	0.0112				p.F245fs		Pindel,Atlas-Indel	.											TAS2R8,NS,malignant_melanoma,0,1	TAS2R8	42	1	0			c.735_736insT						PASS	.																																			SO:0001589	frameshift_variant	50836	exon1			.	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.735dupT	12.37:g.10958853_10958853dupA	ENSP00000240615:p.Phe245fs	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	90	33	0.367	NM_023918	Q4KN29|Q645Y2	Frame_Shift_Ins	INS	ENST00000240615.2	37	CCDS8632.1																																																																																			-|0.994;A|0.006	0.006	strong		0.366	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
GPR50	9248	hgsc.bcm.edu	37	X	150349558	150349569	+	In_Frame_Del	DEL	CACCACTGGCCA	CACCACTGGCCA	-	rs377556761|rs199797606|rs68058591|rs200787393		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CACCACTGGCCA	CACCACTGGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:150349558_150349569delCACCACTGGCCA	ENST00000218316.3	+	2	1572_1583	c.1503_1514delCACCACTGGCCA	c.(1501-1515)cccaccactggccac>ccc	p.TTGH502del	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	502	Pro-rich.		Missing (lower fasting circulating triglyceride levels). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8647286, ECO:0000269|Ref.2}.		cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)	p.T502_H505delTTGH(1)		breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					ACCCTAAACCCACCACTGGCCACATCAAGCCA	0.608																																					p.501_505del		Pindel,Atlas-Indel	.											.	GPR50	195	.	1	Deletion - In frame(1)	ovary(1)	c.1502_1513del						PASS	.			1488,2015		315,617,241,554,290						2.6	0.0		dbSNP_130	100	2487,3842		404,1011,668,899,1033	no	coding	GPR50	NM_004224.3		719,1628,909,1453,1323	A1A1,A1R,A1,RR,R		39.2953,42.4779,40.4292				3975,5857				SO:0001651	inframe_deletion	9248	exon2			.	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1503_1514delCACCACTGGCCA	X.37:g.150349558_150349569delCACCACTGGCCA	ENSP00000218316:p.Thr502_His505del	Somatic	200	.	.		WXS	Illumina HiSeq	Phase_I	75	36	0.480	NM_004224	Q0VGG3|Q3ZAR0	In_Frame_Del	DEL	ENST00000218316.3	37	CCDS44012.1																																																																																			CACCACTGGCCA|0.500;-|0.500	0.500	weak		0.608	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
MUC20	200958	hgsc.bcm.edu	37	3	195453018	195453018	+	Frame_Shift_Del	DEL	C	C	-	rs144288174	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195453018delC	ENST00000447234.2	+	2	1670	c.1544delC	c.(1543-1545)gccfs	p.A515fs	MUC20_ENST00000436408.1_Frame_Shift_Del_p.A515fs|MUC20_ENST00000320736.6_Frame_Shift_Del_p.A344fs|MUC20_ENST00000445522.2_Frame_Shift_Del_p.A480fs	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	515	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.T516fs*39(2)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GCACCCGGGGCCACGACCCTC	0.577													cc|CC|C|deletion	439	0.0876597	0.0295	0.1398	5008	,	,		26511	0.0377		0.169	False		,,,				2504	0.0971				p.A344fs		Atlas-Indel	.											.	MUC20	84	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1030delG						PASS	.		,	185,3935		1,183,1876	54.0	47.0	49.0		,	-0.7	0.0	3	dbSNP_134	54	1243,6833		18,1207,2813	no	frameshift,frameshift	MUC20	NM_152673.2,NM_001098516.1	,	19,1390,4689	A1A1,A1R,RR		15.3913,4.4903,11.7088	,	,	195453018	1428,10768	2136	4208	6344	SO:0001589	frameshift_variant	200958	exon3			.	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1544delC	3.37:g.195453018delC	ENSP00000414350:p.Ala515fs	Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	447	154	0.344519	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Frame_Shift_Del	DEL	ENST00000447234.2	37																																																																																				C|0.915;-|0.085	0.085	strong		0.577	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
RFPL1	5988	hgsc.bcm.edu	37	22	29837567	29837569	+	In_Frame_Del	DEL	TCC	TCC	-	rs397745673|rs79401928|rs71324764|rs3842466	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29837567_29837569delTCC	ENST00000354373.2	+	2	619_621	c.410_412delTCC	c.(409-414)ttcctc>ttc	p.L139del	RFPL1S_ENST00000461286.3_RNA|RFPL1S_ENST00000539579.1_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	139	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		Missing (in RFPL1S).				zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						GCCAACAACTTCCTCCTCATTTC	0.502														1336	0.266773	0.149	0.4193	5008	,	,		21601	0.1131		0.4503	False		,,,				2504	0.2873				p.137_137del		Pindel,Atlas-Indel	.											.	RFPL1	43	.	0			c.409_411del						PASS	.			779,3485		64,651,1417						-2.2	0.0		dbSNP_130	107	3633,4621		805,2023,1299	no	coding	RFPL1	NM_021026.2		869,2674,2716	A1A1,A1R,RR		44.015,18.2692,35.2452				4412,8106				SO:0001651	inframe_deletion	5988	exon2			.	AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250		"""RING-type (C3HC4) zinc fingers"""	9977	protein-coding gene	gene with protein product		605968				10508838	Standard	NM_021026		Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.410_412delTCC	22.37:g.29837570_29837572delTCC	ENSP00000346342:p.Leu139del	Somatic	344	.	.		WXS	Illumina HiSeq	Phase_I	345	80	0.232	NM_021026	Q6IC06|Q9UJ97	In_Frame_Del	DEL	ENST00000354373.2	37	CCDS13857.2																																																																																			TCC|0.697;-|0.303	0.303	strong		0.502	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318719.1	NM_021026	
CCDC150	284992	hgsc.bcm.edu	37	2	197521469	197521470	+	Frame_Shift_Del	DEL	TG	TG	-	rs143904259		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:197521469_197521470delTG	ENST00000389175.4	+	3	424_425	c.289_290delTG	c.(289-291)tgtfs	p.C97fs	CCDC150_ENST00000272831.7_Intron|CCDC150_ENST00000472405.2_5'UTR|CCDC150_ENST00000423093.2_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	97										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						ATGGAAGAACTGTGAGTTTCTG	0.411																																					p.96_97del		Pindel,Atlas-Indel	.											.	CCDC150	96	.	0			c.288_289del						PASS	.			9,3541		2,5,1768						5.0	1.0		dbSNP_134	110	123,7711		1,121,3795	no	frameshift	CCDC150	NM_001080539.1		3,126,5563	A1A1,A1R,RR		1.5701,0.2535,1.1595				132,11252				SO:0001589	frameshift_variant	284992	exon3			.		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.289_290delTG	2.37:g.197521471_197521472delTG	ENSP00000373827:p.Cys97fs	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	151	50	0.331	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Frame_Shift_Del	DEL	ENST00000389175.4	37	CCDS46478.1																																																																																			TG|0.989;-|0.011	0.011	strong		0.411	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539	
POLQ	10721	hgsc.bcm.edu	37	3	121208704	121208706	+	In_Frame_Del	DEL	TTT	TTT	-	rs41547220	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121208704_121208706delTTT	ENST00000264233.5	-	16	3200_3202	c.3072_3074delAAA	c.(3070-3075)aaaaag>aag	p.1024_1025KK>K		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1024					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CAAAGGTGCCTTTTTTGTTTTCT	0.399								DNA polymerases (catalytic subunits)						42	0.00838658	0.0008	0.0274	5008	,	,		18465	0.0		0.0199	False		,,,				2504	0.002				p.1025_1025del	Pancreas(152;907 1925 26081 31236 36904)	Pindel,Atlas-Indel	.											.	POLQ	273	.	0			c.3073_3075del						PASS	.			23,4241		0,23,2109						3.8	1.0		dbSNP_127	78	177,8065		4,169,3948	no	coding	POLQ	NM_199420.3		4,192,6057	A1A1,A1R,RR		2.1475,0.5394,1.5992				200,12306				SO:0001651	inframe_deletion	10721	exon16			.	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3072_3074delAAA	3.37:g.121208707_121208709delTTT	ENSP00000264233:p.Lys1025del	Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	77	26	0.338	NM_199420	O95160|Q6VMB5	In_Frame_Del	DEL	ENST00000264233.5	37	CCDS33833.1																																																																																			TTT|0.989;-|0.011	0.011	strong		0.399	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
TCEB3C	162699	hgsc.bcm.edu	37	18	44554940	44554941	+	Frame_Shift_Ins	INS	-	-	GC			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44554940_44554941insGC	ENST00000330682.2	-	1	1508_1509	c.1273_1274insGC	c.(1273-1275)cagfs	p.Q425fs	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron	NM_145653.3	NP_663628.2	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide 3C (elongin A3)	425	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(16)|skin(2)	30						TCGCAGCCGCTGCTCTCGGGCG	0.554																																					p.Q425fs		Atlas-Indel	.											.	TCEB3C	49	.	0			c.1274_1275insGC						PASS	.																																			SO:0001589	frameshift_variant	162699	exon1			.	AB076840	CCDS11931.1	18q21.1	2008-08-13			ENSG00000183791	ENSG00000183791			24617	protein-coding gene	gene with protein product	"""elongin A3"""					11932239, 11994304	Standard	NM_145653		Approved	HsT829, TCEB3L2	uc010xdb.2	Q8NG57	OTTHUMG00000132651	ENST00000330682.2:c.1272_1273dupGC	18.37:g.44554941_44554942dupGC	ENSP00000328232:p.Gln425fs	Somatic	699	0	0		WXS	Illumina HiSeq	Phase_I	623	107	0.17175	NM_145653		Frame_Shift_Ins	INS	ENST00000330682.2	37	CCDS11931.1																																																																																			.	.	none		0.554	TCEB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255902.1	NM_145653	
PRUNE2	158471	hgsc.bcm.edu	37	9	79324135	79324136	+	In_Frame_Ins	INS	-	-	TGACTGTTGCAG	rs2307907|rs11267622	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79324135_79324136insTGACTGTTGCAG	ENST00000376718.3	-	8	3177_3178	c.3054_3055insCTGCAACAGTCA	c.(3052-3057)tcatct>tcaCTGCAACAGTCAtct	p.1017_1018insSLQQ	PRUNE2_ENST00000428286.1_In_Frame_Ins_p.658_659insSLQQ	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1017					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CGATTTCGAGATGACTGTTGCA	0.45														2520	0.503195	0.3427	0.6441	5008	,	,		23395	0.4504		0.5984	False		,,,				2504	0.5767				p.S1019delinsLQQSS		Pindel,Atlas-Indel	.											.	PRUNE2	331	.	0			c.3055_3056insCTGCAACAGTCA						PASS	.			1304,2110		277,750,680						1.3	0.0		dbSNP_120	98	4176,2922		1294,1588,667	no	coding	PRUNE2	NM_015225.2		1571,2338,1347	A1A1,A1R,RR		41.1665,38.1957,47.8691				5480,5032				SO:0001652	inframe_insertion	158471	exon8			.	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.3043_3054dupCTGCAACAGTCA	9.37:g.79324135_79324136insTGACTGTTGCAG	ENSP00000365908:p.Ser1014_Gln1017dup	Somatic	274	.	.		WXS	Illumina HiSeq	Phase_I	264	66	0.250	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	In_Frame_Ins	INS	ENST00000376718.3	37	CCDS47982.1																																																																																			-|0.492;TGACTGTTGCAG|0.508	0.508	strong		0.450	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
ZSCAN21	7589	hgsc.bcm.edu	37	7	99662512	99662515	+	3'UTR	DEL	TAGT	TAGT	-	rs56833874|rs71689664|rs202229615|rs200297846|rs200795752|rs398111646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TAGT	TAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99662512_99662515delTAGT	ENST00000292450.4	+	0	1858_1861				ZSCAN21_ENST00000456748.2_3'UTR|ZSCAN21_ENST00000543588.1_3'UTR|ZNF3_ENST00000413658.2_Frame_Shift_Del_p.TT98fs	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21						positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			ACCTTTTGCGTAGTTAAACAGACG	0.407														1393	0.278155	0.1573	0.232	5008	,	,		19468	0.4067		0.2763	False		,,,				2504	0.3436				p.98_99del		Pindel,Atlas-Indel	.											.	ZNF3	54	.	0			c.293_296del						PASS	.		,	697,3191		89,519,1336					,	-4.0	0.0		dbSNP_130	140	2233,5761		344,1545,2108	yes	utr-3,frameshift	ZNF3,ZSCAN21	NM_145914.2,NM_017715.2	,	433,2064,3444	A1A1,A1R,RR		27.9335,17.927,24.6591	,	,		2930,8952				SO:0001624	3_prime_UTR_variant	7551	exon6			.	AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"""-"", ""Zinc fingers, C2H2-type"""	13104	protein-coding gene	gene with protein product		601261	"""zinc finger protein 38 (KOX 25)"", ""zinc finger protein 38"""	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.*275TAGT>-	7.37:g.99662512_99662515delTAGT		Somatic	126	.	.		WXS	Illumina HiSeq	Phase_I	145	47	0.324	NM_017715	A4D2A6|D6W5T9|Q9H0B5	Frame_Shift_Del	DEL	ENST00000292450.4	37	CCDS5681.1																																																																																			TAGT|0.748;-|0.252	0.252	strong		0.407	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914	
TRPM7	54822	hgsc.bcm.edu	37	15	50884289	50884294	+	In_Frame_Del	DEL	ATTTTT	ATTTTT	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	ATTTTT	ATTTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:50884289_50884294delATTTTT	ENST00000313478.7	-	26	4419_4424	c.4138_4143delAAAAAT	c.(4138-4143)aaaaatdel	p.KN1380del	TRPM7_ENST00000560955.1_In_Frame_Del_p.KN1380del	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1380					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		Ctaatttttgatttttattaaatatt	0.417																																					p.1380_1382del		Pindel,Atlas-Indel	.											.	TRPM7	145	.	0			c.4139_4144del						PASS	.			3,3465		1,1,1732						0.5	0.6			62	3,7803		0,3,3900	no	coding	TRPM7	NM_017672.4		1,4,5632	A1A1,A1R,RR		0.0384,0.0865,0.0532				6,11268				SO:0001651	inframe_deletion	54822	exon26			.	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.4138_4143delAAAAAT	15.37:g.50884289_50884294delATTTTT	ENSP00000320239:p.Lys1380_Asn1381del	Somatic	35	.	.		WXS	Illumina HiSeq	Phase_I	35	10	0.286	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	In_Frame_Del	DEL	ENST00000313478.7	37	CCDS42035.1																																																																																			.	.	none		0.417	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672	
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39411670	39411671	+	In_Frame_Ins	INS	-	-	ACCTGCTGCAGGACC	rs67700678|rs540633489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39411670_39411671insACCTGCTGCAGGACC	ENST00000394008.1	+	1	35_36	c.33_34insACCTGCTGCAGGACC	c.(34-36)acc>ACCTGCTGCAGGACCacc	p.12_12T>TCCRTT		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	12	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GCTGTCAGCCTACCTGCTGCAG	0.604														2488	0.496805	0.298	0.647	5008	,	,		16406	0.4196		0.5805	False		,,,				2504	0.6524				p.P11delinsPTCCRT		Pindel,Atlas-Indel	.											.	KRTAP9-9	24	.	0			c.33_34insACCTGCTGCAGGACC						PASS	.																																			SO:0001652	inframe_insertion	81870	exon1			.	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.34_48dupACCTGCTGCAGGACC	17.37:g.39411670_39411671insACCTGCTGCAGGACC	Exception_encountered	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	48	17	0.354	NM_030975	B5MDD6|Q9BYQ1	In_Frame_Ins	INS	ENST00000394008.1	37	CCDS54127.1																																																																																			.	.	none		0.604	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
BCL6B	255877	hgsc.bcm.edu	37	17	6928019	6928020	+	In_Frame_Ins	INS	-	-	CAG	rs72254884|rs146207245|rs55799550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6928019_6928020insCAG	ENST00000293805.5	+	4	793_794	c.701_702insCAG	c.(700-705)tccagc>tcCAGcagc	p.234_235SS>SSS		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	234	Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			skin(1)	1						GACGAGGCCTCcagcagcagca	0.594														3317	0.66234	0.4939	0.5591	5008	,	,		22809	0.7232		0.8022	False		,,,				2504	0.7566				p.S234delinsSS		Pindel,Atlas-Indel	.											.	BCL6B	85	.	0			c.701_702insCAG						PASS	.																																			SO:0001652	inframe_insertion	255877	exon4			.	AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1002	protein-coding gene	gene with protein product		608992	"""zinc finger protein 62"", ""B-cell CLL/lymphoma 6, member B (zinc finger protein)"""	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.729_731dupCAG	17.37:g.6928026_6928028dupCAG	ENSP00000293805:p.Ser243_Ser244dup	Somatic	80	.	.		WXS	Illumina HiSeq	Phase_I	92	46	0.500	NM_181844	Q6PCB4	In_Frame_Ins	INS	ENST00000293805.5	37	CCDS42248.1																																																																																			.	.	strong		0.594	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844	
OR13C2	392376	hgsc.bcm.edu	37	9	107367393	107367396	+	Frame_Shift_Del	DEL	GTTA	GTTA	-	rs112364120|rs143198170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GTTA	GTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107367393_107367396delGTTA	ENST00000542196.1	-	1	555_558	c.513_516delTAAC	c.(511-516)aataacfs	p.NN171fs		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	171						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GATTGATGATGTTATTCCTGCAGA	0.451														1868	0.373003	0.4304	0.2161	5008	,	,		20908	0.5665		0.1789	False		,,,				2504	0.407				p.172_173del		Atlas-Indel	.											.	OR13C2	46	.	0			c.514_517del						PASS	.			1624,2632		344,936,848						1.3	0.3		dbSNP_129	138	1571,6681		165,1241,2720	no	frameshift	OR13C2	NM_001004481.1		509,2177,3568	A1A1,A1R,RR		19.0378,38.1579,25.5437				3195,9313				SO:0001589	frameshift_variant	392376	exon1			.		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.513_516delTAAC	9.37:g.107367393_107367396delGTTA	ENSP00000438815:p.Asn171fs	Somatic	459	0	0		WXS	Illumina HiSeq	Phase_I	378	137	0.362434	NM_001004481	B9EGV8|Q6IF54	Frame_Shift_Del	DEL	ENST00000542196.1	37	CCDS35092.1																																																																																			.	.	strong		0.451	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
ZNF880	400713	hgsc.bcm.edu	37	19	52887246	52887247	+	In_Frame_Ins	INS	-	-	CAA	rs398071206|rs71836013|rs34678014		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52887246_52887247insCAA	ENST00000422689.2	+	4	428_429	c.413_414insCAA	c.(412-417)atcaac>atCAAcaac	p.140_141insN		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	140					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GAAAAACCTATCAACAATTCCT	0.312																																					p.I138delinsIN		Pindel,Atlas-Indel	.											.	ZNF880	45	.	0			c.413_414insCAA						PASS	.			958,2510		225,508,1001						-0.9	0.0		dbSNP_126	61	2771,4597		695,1381,1608	no	coding	ZNF880	NM_001145434.1		920,1889,2609	A1A1,A1R,RR		37.6086,27.624,34.4131				3729,7107				SO:0001652	inframe_insertion	400713	exon4			.	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.417_419dupCAA	19.37:g.52887250_52887252dupCAA	ENSP00000406318:p.Asn140_Asn140dup	Somatic	156	.	.		WXS	Illumina HiSeq	Phase_I	147	53	0.361	NM_001145434	B4DNA6	In_Frame_Ins	INS	ENST00000422689.2	37	CCDS46164.1																																																																																			-|0.657;CAA|0.343	0.343	strong		0.312	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Frame_Shift_Del	DEL	A	A	-	rs398101268|rs34470614		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52887146delA	ENST00000422689.2	+	4	328	c.313delA	c.(313-315)aaafs	p.K105fs	ZNF880_ENST00000424032.2_3'UTR	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	105					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CAAGTCTCTTAAAAATCAACT	0.368																																					p.L104fs		Pindel,Atlas-Indel	.											.	ZNF880	45	.	0			c.312delT						PASS	.			1094,2682		234,626,1028	61.0	45.0	50.0			-2.8	0.0	19	dbSNP_126	72	3080,4810		677,1726,1542	no	frameshift	ZNF880	NM_001145434.1		911,2352,2570	A1A1,A1R,RR		39.0368,28.9725,35.7792			52887146	4174,7492	690	1569	2259	SO:0001589	frameshift_variant	400713	exon4			.	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.313delA	19.37:g.52887146delA	ENSP00000406318:p.Lys105fs	Somatic	122	.	.		WXS	Illumina HiSeq	Phase_I	126	40	0.317	NM_001145434	B4DNA6	Frame_Shift_Del	DEL	ENST00000422689.2	37	CCDS46164.1																																																																																			A|0.672;-|0.328	0.328	strong		0.368	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388622	1388623	+	Frame_Shift_Ins	INS	-	-	CA	rs79704405|rs540461234|rs558358960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388622_1388623insCA	ENST00000324803.4	+	1	3283_3284	c.323_324insCA	c.(322-327)ctcacgfs	p.LT108fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	108					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCCCGCCTGCTCACGTGCCCAT	0.668														506	0.101038	0.0567	0.1427	5008	,	,		19207	0.0169		0.1759	False		,,,				2504	0.1411				p.L108fs		Atlas-Indel	.											CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	1	Substitution - Missense(1)	pancreas(1)	c.323_324insCA						PASS	.																																			SO:0001589	frameshift_variant	285464	exon1			.	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.324_325dupCA	4.37:g.1388623_1388624dupCA	ENSP00000323978:p.Leu108fs	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	152	115	0.756579	NM_175918	Q8NB03	Frame_Shift_Ins	INS	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.668	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10524657	10524659	+	In_Frame_Del	DEL	GAC	GAC	-	rs56252625|rs75627261|rs571414967|rs113642662	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAC	GAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:10524657_10524659delGAC	ENST00000396560.2	+	3	407_409	c.180_182delGAC	c.(178-183)aggacg>agg	p.T62del	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_In_Frame_Del_p.T62del|ATF7IP2_ENST00000324570.5_In_Frame_Del_p.T62del|ATF7IP2_ENST00000356427.2_In_Frame_Del_p.T62del	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	62					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						TCATAACTAGGACGACTGAAATA	0.374														3021	0.603235	0.5628	0.572	5008	,	,		18516	0.6994		0.5686	False		,,,				2504	0.6166				p.60_61del		Pindel,Atlas-Indel	.											.	ATF7IP2	40	.	0			c.179_181del						PASS	.			2445,1819		712,1021,399							0.1		dbSNP_131	58	4927,3327		1439,2049,639	no	coding	ATF7IP2	NM_024997.2		2151,3070,1038	A1A1,A1R,RR		40.3077,42.6595,41.1088				7372,5146				SO:0001651	inframe_deletion	80063	exon4			.	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.180_182delGAC	16.37:g.10524660_10524662delGAC	ENSP00000379808:p.Thr62del	Somatic	199	.	.		WXS	Illumina HiSeq	Phase_I	199	103	0.518	NM_001256160	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	In_Frame_Del	DEL	ENST00000396560.2	37	CCDS10540.1																																																																																			GAC|0.396;-|0.604	0.604	strong		0.374	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
FERD3L	222894	hgsc.bcm.edu	37	7	19184746	19184747	+	In_Frame_Ins	INS	-	-	TCT	rs34966908|rs199985178|rs71017023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:19184746_19184747insTCT	ENST00000275461.3	-	1	297_298	c.239_240insAGA	c.(238-240)gag>gaAGAg	p.80_80E>EE	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	80	Poly-Glu.				cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E81_R82insE(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						ttccgcgctcctcttcctcctc	0.624														836	0.166933	0.0446	0.1643	5008	,	,		17679	0.1587		0.2654	False		,,,				2504	0.2413				p.E80delinsEE		Pindel,Atlas-Indel	.											.	FERD3L	63	.	1	Insertion - In frame(1)	ovary(1)	c.240_241insAGA						PASS	.			307,0,3957		13,0,281,0,0,1838						0.6	0.7		dbSNP_134	60	2211,1,6042		291,0,1629,0,1,2206	no	codingComplex	FERD3L	NM_152898.2		304,0,1910,0,1,4044	A1A1,A1A2,A1R,A2A2,A2R,RR		26.7991,7.1998,20.123				2518,1,9999				SO:0001652	inframe_insertion	222894	exon1			.	AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"""Basic helix-loop-helix proteins"""	16660	protein-coding gene	gene with protein product			"""Fer3-like (Drosophila)"""			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.237_239dupAGA	7.37:g.19184747_19184749dupTCT	ENSP00000275461:p.Glu81dup	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	62	36	0.581	NM_152898	Q495K0	In_Frame_Ins	INS	ENST00000275461.3	37	CCDS5368.1																																																																																			-|0.500;TCT|0.500	0.500	strong		0.624	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1		
URI1	8725	hgsc.bcm.edu	37	19	30500119	30500121	+	In_Frame_Del	DEL	TGA	TGA	-	rs541497604|rs397841639|rs398059661|rs200466034|rs556897562|rs3840928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:30500119_30500121delTGA	ENST00000542441.2	+	8	1191_1193	c.894_896delTGA	c.(892-897)agtgat>agt	p.D311del	URI1_ENST00000392271.1_In_Frame_Del_p.D235del|URI1_ENST00000360605.4_In_Frame_Del_p.D293del|URI1_ENST00000312051.6_In_Frame_Del_p.D271del			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	311	Poly-Asp.			Missing (in Ref. 1; AAD08679, 2; BAA34781, 3; BAF84859 and 5; AAH26184). {ECO:0000305}.	cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										CTTACCACAGtgatgatgatgat	0.419																																					p.298_299del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.893_895del						PASS	.																																			SO:0001651	inframe_deletion	8725	exon8			.	AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	13236	protein-coding gene	gene with protein product	"""unconventional prefoldin RPB5 interactor"", ""RPB5-mediating protein"", ""protein phosphatase 1, regulatory subunit 19"""	603494	"""chromosome 19 open reading frame 2"""	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.894_896delTGA	19.37:g.30500128_30500130delTGA	ENSP00000442436:p.Asp311del	Somatic	89	.	.		WXS	Illumina HiSeq	Phase_I	73	28	0.384	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	In_Frame_Del	DEL	ENST00000542441.2	37	CCDS12420.1																																																																																			TGA|0.500;-|0.500	0.500	strong		0.419	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447	
ZP3	7784	hgsc.bcm.edu	37	7	76071183	76071184	+	Frame_Shift_Ins	INS	-	-	G	rs375263236		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76071183_76071184insG	ENST00000394857.3	+	8	1143_1144	c.1085_1086insG	c.(1084-1089)gtggggfs	p.VG362fs	ZP3_ENST00000336517.4_Frame_Shift_Ins_p.VG311fs|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Frame_Shift_Ins_p.VG186fs	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	362					binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						GATGTCACCGTGGGGCCACTGA	0.545																																					p.V362fs		Atlas-Indel	.											.	ZP3	32	.	0			c.1085_1086insG						PASS	.																																			SO:0001589	frameshift_variant	7784	exon8			.	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.1089dupG	7.37:g.76071187_76071187dupG	ENSP00000378326:p.Val362fs	Somatic	658	0	0		WXS	Illumina HiSeq	Phase_I	737	50	0.0678426	NM_001110354	Q06633|Q29RW0	Frame_Shift_Ins	INS	ENST00000394857.3	37	CCDS47618.1																																																																																			.	.	weak		0.545	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
WDR60	55112	hgsc.bcm.edu	37	7	158664075	158664077	+	In_Frame_Del	DEL	GAA	GAA	-	rs3833679|rs145233696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:158664075_158664077delGAA	ENST00000407559.3	+	3	470_472	c.312_314delGAA	c.(310-315)ctgaag>ctg	p.K105del		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	105					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K105delK(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		aagaaaagctgaaggagaaacat	0.542														583	0.116414	0.0908	0.0965	5008	,	,		19368	0.0556		0.1889	False		,,,				2504	0.1534				p.104_105del		Pindel,Atlas-Indel	.											.	WDR60	94	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.311_313del						PASS	.			346,3112		52,242,1435						-8.3	0.0		dbSNP_107	66	1313,5999		217,879,2560	no	coding	WDR60	NM_018051.4		269,1121,3995	A1A1,A1R,RR		17.9568,10.0058,15.4039				1659,9111				SO:0001651	inframe_deletion	55112	exon3			.		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.312_314delGAA	7.37:g.158664075_158664077delGAA	ENSP00000384290:p.Lys105del	Somatic	39	.	.		WXS	Illumina HiSeq	Phase_I	53	22	0.415	NM_018051	Q9NW58	In_Frame_Del	DEL	ENST00000407559.3	37	CCDS47757.1																																																																																			GAA|0.880;-|0.120	0.120	strong		0.542	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051	
POC1B	282809	hgsc.bcm.edu	37	12	89866055	89866064	+	Intron	DEL	AGAAAGAAGA	AGAAAGAAGA	-	rs59139895|rs71082492|rs147832668|rs147021755|rs398055805|rs191378952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AGAAAGAAGA	AGAAAGAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:89866055_89866064delAGAAAGAAGA	ENST00000313546.3	-	5	581				POC1B_ENST00000378528.2_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000549035.1_Intron	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B						cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						GTGAAAATCTAGAAAGAAGAAGAAAGAAGA	0.367														2704	0.539936	0.6823	0.4784	5008	,	,		11890	0.5456		0.499	False		,,,				2504	0.4274				.		Pindel,Atlas-Indel	.											.	POC1B	41	.	0			.						PASS	.																																			SO:0001627	intron_variant	282809	.			.	AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"""WD repeat domain containing"""	30836	protein-coding gene	gene with protein product		614784	"""WD repeat domain 51B"", ""POC1 centriolar protein homolog B (Chlamydomonas)"""	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.453-3TCTTCTTTCT>-	12.37:g.89866065_89866074delAGAAAGAAGA		Somatic	70	.	.		WXS	Illumina HiSeq	Phase_I	46	19	0.413	.	G3V1X0	Splice_Site	DEL	ENST00000313546.3	37	CCDS31869.1																																																																																			-|1.000;|0.000	1.000	strong		0.367	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240	
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361452	+	Frame_Shift_Del	DEL	GC	GC	-	rs376107801|rs201540433|rs377523807|rs199665292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107361451_107361452delGC	ENST00000374779.2	-	1	336_337	c.243_244delGC	c.(241-246)acgctafs	p.L82fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AAGCTCACTAGCGTGGAGGGAA	0.51																																					p.82_82del		Atlas-Indel	.											.	OR13C5	60	.	0			c.244_245del						PASS	.																																			SO:0001589	frameshift_variant	138799	exon1			.		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.243_244delGC	9.37:g.107361451_107361452delGC	ENSP00000363911:p.Leu82fs	Somatic	664	0	0		WXS	Illumina HiSeq	Phase_I	532	99	0.18609	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	CCDS35091.1																																																																																			GC|0.500;-|0.500	0.500	strong		0.510	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
SYNPO2	171024	hgsc.bcm.edu	37	4	119947962	119947964	+	In_Frame_Del	DEL	AAG	AAG	-	rs70944826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:119947962_119947964delAAG	ENST00000429713.2	+	3	620_622	c.438_440delAAG	c.(436-441)caaaga>caa	p.R147del	SYNPO2_ENST00000307142.4_In_Frame_Del_p.R147del|SYNPO2_ENST00000434046.2_In_Frame_Del_p.R147del|SYNPO2_ENST00000448416.2_Intron	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	147				Missing (in Ref. 3; AL832031). {ECO:0000305}.		actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CTGAGAACCAAAGAAGTGGTCCC	0.552														1780	0.355431	0.2375	0.4654	5008	,	,		17830	0.496		0.3489	False		,,,				2504	0.2986				p.146_147del		Pindel,Atlas-Indel	.											.	SYNPO2	353	.	0			c.437_439del						PASS	.		,,	1140,3126		155,830,1148					,,	2.9	0.4		dbSNP_130	44	3087,5167		549,1989,1589	no	coding,coding,coding	SYNPO2	NM_133477.2,NM_001128934.1,NM_001128933.1	,,	704,2819,2737	A1A1,A1R,RR		37.4,26.7229,33.762	,,	,,		4227,8293				SO:0001651	inframe_deletion	171024	exon3			.	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.438_440delAAG	4.37:g.119947965_119947967delAAG	ENSP00000395143:p.Arg147del	Somatic	94	.	.		WXS	Illumina HiSeq	Phase_I	127	40	0.315	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	In_Frame_Del	DEL	ENST00000429713.2	37	CCDS47129.1																																																																																			AAG|0.631;-|0.369	0.369	strong		0.552	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
KMT2B	9757	hgsc.bcm.edu	37	19	36211375	36211377	+	In_Frame_Del	DEL	AAG	AAG	-	rs199534880		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36211375_36211377delAAG	ENST00000222270.7	+	3	1126_1128	c.1126_1128delAAG	c.(1126-1128)aagdel	p.K376del	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_In_Frame_Del_p.K376del|KMT2B_ENST00000341701.1_In_Frame_Del_p.K376del	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	376	Asp/Glu-rich (acidic).				chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										agaaaaagacaaggagggagaag	0.512																																					p.375_376del		Pindel,Atlas-Indel	.											.	MLL4	229	.	0			c.1125_1127del						PASS	.			24,3672		2,20,1826						-3.5	0.0			21	274,7182		39,196,3493	no	coding	MLL4	NM_014727.1		41,216,5319	A1A1,A1R,RR		3.6749,0.6494,2.6722				298,10854				SO:0001651	inframe_deletion	8085	exon3			.	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.1126_1128delAAG	19.37:g.36211375_36211377delAAG	ENSP00000222270:p.Lys376del	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	128	39	0.305	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	In_Frame_Del	DEL	ENST00000222270.7	37	CCDS46055.1																																																																																			AAG|0.983;-|0.017	0.017	strong		0.512	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
OR51I2	390064	hgsc.bcm.edu	37	11	5475431	5475432	+	Frame_Shift_Ins	INS	-	-	CA	rs199654892|rs35301588|rs67809969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5475431_5475432insCA	ENST00000341449.2	+	1	794_795	c.713_714insCA	c.(712-717)ctcaacfs	p.N239fs	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	239					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCAAAGCTCTCAACACATGTG	0.495														853	0.170327	0.0416	0.2983	5008	,	,		25029	0.0417		0.3708	False		,,,				2504	0.18				p.L238fs		Pindel,Atlas-Indel	.											.	OR51I2	76	.	0			c.713_714insCA						PASS	.			426,3836		32,362,1737						5.6	1.0		dbSNP_126	252	3078,5176		571,1936,1620	no	frameshift	OR51I2	NM_001004754.2		603,2298,3357	A1A1,A1R,RR		37.291,9.9953,27.9962				3504,9012				SO:0001589	frameshift_variant	390064	exon1			.	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"""GPCR / Class A : Olfactory receptors"""	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.714_715dupCA	11.37:g.5475432_5475433dupCA	ENSP00000341987:p.Asn239fs	Somatic	294	.	.		WXS	Illumina HiSeq	Phase_I	310	121	0.390	NM_001004754	Q6IF81	Frame_Shift_Ins	INS	ENST00000341449.2	37	CCDS31383.1																																																																																			-|0.792;CA|0.208	0.208	strong		0.495	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057613	46057627	+	In_Frame_Del	DEL	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	-	rs66931310|rs375198526|rs56249559|rs55677560|rs77286437	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46057613_46057627delCTGCTGTGTGCCTGT	ENST00000380095.1	+	1	341_355	c.279_293delCTGCTGTGTGCCTGT	c.(277-294)gcctgctgtgtgcctgtc>gcc	p.CCVPV104del	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	104	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						gccagcaggcctgctgtgtgcctgtctgctgtgtg	0.628														2493	0.497804	0.5575	0.6153	5008	,	,		22046	0.37		0.5736	False		,,,				2504	0.3875				p.93_98del		Pindel,Atlas-Indel	.											.	KRTAP10-10	37	.	0			c.278_292del						PASS	.		,	2335,1929		615,1105,412					,	-1.6	0.0		dbSNP_130	113	4575,3679		1191,2193,743	no	coding,intron	TSPEAR,KRTAP10-10	NM_181688.1,NM_144991.2	,	1806,3298,1155	A1A1,A1R,RR		44.5723,45.2392,44.7995	,	,		6910,5608				SO:0001651	inframe_deletion	353333	exon1			.	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.279_293delCTGCTGTGTGCCTGT	21.37:g.46057613_46057627delCTGCTGTGTGCCTGT	ENSP00000369438:p.Cys104_Val108del	Somatic	270	.	.		WXS	Illumina HiSeq	Phase_I	179	29	0.162	NM_181688		In_Frame_Del	DEL	ENST00000380095.1	37	CCDS33585.1																																																																																			CTGCTGTGTGCCTGT|0.469;-|0.531	0.531	strong		0.628	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
RSU1	6251	hgsc.bcm.edu	37	10	16635400	16635402	+	In_Frame_Del	DEL	TTC	TTC	-	rs575845875		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:16635400_16635402delTTC	ENST00000377921.3	-	8	1126_1128	c.825_827delGAA	c.(823-828)aagaac>aac	p.K275del	RSU1_ENST00000464074.2_5'UTR|RSU1_ENST00000602389.1_In_Frame_Del_p.K222del|RSU1_ENST00000345264.5_In_Frame_Del_p.K275del			Q15404	RSU1_HUMAN	Ras suppressor protein 1	275					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		TCCTTATCTGTTCTTGGCTGCCA	0.507																																					p.276_276del		Pindel,Atlas-Indel	.											.	RSU1	31	.	0			c.826_828del						PASS	.																																			SO:0001651	inframe_deletion	6251	exon9			.	AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.825_827delGAA	10.37:g.16635400_16635402delTTC	ENSP00000367154:p.Lys275del	Somatic	205	.	.		WXS	Illumina HiSeq	Phase_I	213	71	0.333	NM_012425	A8KA46|D3DRU3|Q6FI17	In_Frame_Del	DEL	ENST00000377921.3	37	CCDS7112.1																																																																																			.	.	none		0.507	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79059020	79059021	+	Frame_Shift_Ins	INS	-	-	A	rs199873382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79059020_79059021insA	ENST00000388820.4	-	19	3442_3443	c.3232_3233insT	c.(3232-3234)tacfs	p.Y1078fs	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1078					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						AGAGGGCCCGTAGGACAGATCC	0.624																																					p.Y1078fs		Atlas-Indel	.											.	ADAMTS7	142	.	0			c.3233_3234insT						PASS	.			42,4206		0,42,2082						4.4	0.0			24	197,8007		1,195,3906	no	frameshift	ADAMTS7	NM_014272.3		1,237,5988	A1A1,A1R,RR		2.4013,0.9887,1.9194				239,12213				SO:0001589	frameshift_variant	11173	exon19			.	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3233dupT	15.37:g.79059021_79059021dupA	ENSP00000373472:p.Tyr1078fs	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	166	12	0.0722892	NM_014272	Q14F51|Q6P7J9	Frame_Shift_Ins	INS	ENST00000388820.4	37	CCDS32303.1																																																																																			.	.	none		0.624	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
ALPK2	115701	hgsc.bcm.edu	37	18	56204388	56204402	+	In_Frame_Del	DEL	CAGTTGATGTGTCCT	CAGTTGATGTGTCCT	-	rs199745034|rs201560823|rs386803723|rs149103820|rs60644017|rs67925233	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CAGTTGATGTGTCCT	CAGTTGATGTGTCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204388_56204402delCAGTTGATGTGTCCT	ENST00000361673.3	-	5	3230_3244	c.3017_3031delAGGACACATCAACTG	c.(3016-3033)gaggacacatcaactgtt>gtt	p.EDTST1006del	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1006						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GCAATGGTAACAGTTGATGTGTCCTCAGTCTCCCT	0.493														2013	0.401957	0.4274	0.4251	5008	,	,		24283	0.2371		0.5696	False		,,,				2504	0.3487				p.1006_1011del		Pindel,Atlas-Indel	.											.	ALPK2	487	.	0			c.3018_3032del						PASS	.																																			SO:0001651	inframe_deletion	115701	exon5			.	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3017_3031delAGGACACATCAACTG	18.37:g.56204388_56204402delCAGTTGATGTGTCCT	ENSP00000354991:p.Glu1006_Thr1010del	Somatic	221	.	.		WXS	Illumina HiSeq	Phase_I	151	43	0.285	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	In_Frame_Del	DEL	ENST00000361673.3	37	CCDS11966.2																																																																																			.	.	strong		0.493	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
NCL	4691	hgsc.bcm.edu	37	2	232325415	232325417	+	In_Frame_Del	DEL	TCA	TCA	-	rs540030591|rs368566589|rs139777351|rs527711138|rs371359723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:232325415_232325417delTCA	ENST00000322723.4	-	4	1014_1016	c.774_776delTGA	c.(772-777)gatgaa>gaa	p.D258del	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	258	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		Ctcatcatcttcatcatcatcat	0.433																																					p.259_259del		Pindel,Atlas-Indel	.											.	NCL	80	.	0			c.775_777del						PASS	.																																			SO:0001651	inframe_deletion	4691	exon4			.		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.774_776delTGA	2.37:g.232325424_232325426delTCA	ENSP00000318195:p.Asp258del	Somatic	262	.	.		WXS	Illumina HiSeq	Phase_I	273	64	0.234	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	In_Frame_Del	DEL	ENST00000322723.4	37	CCDS33397.1																																																																																			.	.	strong		0.433	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386607	56386608	+	In_Frame_Ins	INS	-	-	TCCTCCTCT	rs148608257|rs200436316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56386607_56386608insTCCTCCTCT	ENST00000343736.4	-	22	4188_4189	c.4025_4026insAGAGGAGGA	c.(4024-4026)gac>gaAGAGGAGGAc	p.1341_1342insEEE	BZRAP1_ENST00000355701.3_In_Frame_Ins_p.1341_1342insEEE|BZRAP1_ENST00000268893.6_In_Frame_Ins_p.1281_1282insEEE			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1341	Poly-Glu.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					cctcctcctcgtcctcctcttc	0.604														88	0.0175719	0.0	0.0331	5008	,	,		17600	0.0		0.0557	False		,,,				2504	0.0092				p.D1342delinsEEED		Pindel,Atlas-Indel	.											BZRAP1_ENST00000355701,rectum,carcinoma,0,2	BZRAP1	287	2	0			c.4026_4027insAGAGGAGGA						PASS	.		,	53,4211		1,51,2080					,	-10.1	0.0			68	480,7774		18,444,3665	no	coding,coding	BZRAP1	NM_024418.1,NM_004758.2	,	19,495,5745	A1A1,A1R,RR		5.8154,1.243,4.2579	,	,		533,11985				SO:0001652	inframe_insertion	9256	exon22			.	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4017_4025dupAGAGGAGGA	17.37:g.56386608_56386616dupTCCTCCTCT	ENSP00000345824:p.Glu1344_Glu1345dup	Somatic	78	.	.		WXS	Illumina HiSeq	Phase_I	78	13	0.167	NM_001261835	O75111|Q8N5W3	In_Frame_Ins	INS	ENST00000343736.4	37	CCDS11605.1																																																																																			-|0.978;TCCTCCTCT|0.022	0.022	strong		0.604	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
OR13C5	138799	hgsc.bcm.edu	37	9	107360769	107360769	+	Frame_Shift_Del	DEL	T	T	-	rs78341003|rs11314210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107360769delT	ENST00000374779.2	-	1	1019	c.926delA	c.(925-927)cacfs	p.H309fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						TCTCAGTAGGTGTTTTACTGC	0.323													T|T|-|deletion	2184	0.436102	0.6475	0.2277	5008	,	,		19983	0.5754		0.1789	False		,,,				2504	0.4192				p.H309fs		Pindel,Atlas-Indel	.											.	OR13C5	60	.	0			c.927delC						PASS	.			2496,1768		742,1012,378	57.0	85.0	77.0			-8.0	0.0	9	dbSNP_120	94	1603,6651		175,1253,2699	no	frameshift	OR13C5	NM_001004482.1		917,2265,3077	A1A1,A1R,RR		19.4209,41.4634,32.7448			107360769	4099,8419	1566	4154	5720	SO:0001589	frameshift_variant	138799	exon1			.		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.926delA	9.37:g.107360769delT	ENSP00000363911:p.His309fs	Somatic	164	.	.		WXS	Illumina HiSeq	Phase_I	152	46	0.303	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	CCDS35091.1																																																																																			T|0.620;-|0.380	0.380	strong		0.323	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
TPTE	7179	hgsc.bcm.edu	37	21	10942925	10942927	+	In_Frame_Del	DEL	CTT	CTT	-	rs113444703|rs386816290|rs3047743|rs558478158		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:10942925_10942927delCTT	ENST00000361285.4	-	12	989_991	c.660_662delAAG	c.(658-663)agaagg>agg	p.220_221RR>R	TPTE_ENST00000298232.7_In_Frame_Del_p.202_203RR>R|TPTE_ENST00000342420.5_In_Frame_Del_p.182_183RR>R|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	220					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ACTTACCCGCCTTCTTATCAGCT	0.32																																					p.221_221del		Atlas-Indel	.											.	TPTE	513	.	0			c.661_663del						PASS	.																																			SO:0001651	inframe_deletion	7179	exon12			.	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.660_662delAAG	21.37:g.10942928_10942930delCTT	ENSP00000355208:p.Arg222del	Somatic	409	0	0		WXS	Illumina HiSeq	Phase_I	844	220	0.260664	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	In_Frame_Del	DEL	ENST00000361285.4	37	CCDS13560.2																																																																																			CTT|0.500;-|0.500	0.500	strong		0.320	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
WWTR1	25937	hgsc.bcm.edu	37	3	149238595	149238596	+	Frame_Shift_Ins	INS	-	-	TTAA	rs112399999|rs71717642|rs34351019	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:149238595_149238596insTTAA	ENST00000465804.1	-	8	1455_1456	c.1199_1200insTTAA	c.(1198-1200)ctgfs	p.-401fs	WWTR1_ENST00000360632.3_Frame_Shift_Ins_p.-401fs|WWTR1_ENST00000467467.1_Frame_Shift_Ins_p.-401fs	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1						cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GTAGTGATTACAGCCAGGTTAG	0.455			T	CAMTA1	epitheliod hemangioendothelioma									573	0.114417	0.1505	0.0576	5008	,	,		18218	0.2004		0.0795	False		,,,				2504	0.0532				p.L400_X401delinsLX		Pindel,Atlas-Indel	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	.	WWTR1	42	.	0			c.1200_1201insTTAA						PASS	.		,,	580,3686		38,504,1591					,,	5.5	1.0		dbSNP_130	132	762,7492		34,694,3399	no	frameshift,frameshift,frameshift	WWTR1	NM_015472.4,NM_001168280.1,NM_001168278.1	,,	72,1198,4990	A1A1,A1R,RR		9.2319,13.5959,10.7188	,,	,,		1342,11178				SO:0001589	frameshift_variant	25937	exon7			.	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.1199_1200insTTAA	3.37:g.149238595_149238596insTTAA	ENSP00000419465:p.*401fs	Somatic	158	.	.		WXS	Illumina HiSeq	Phase_I	167	37	0.222	NM_015472	D3DNH7|Q8N3P2|Q9Y3W6	Frame_Shift_Ins	INS	ENST00000465804.1	37	CCDS3144.1																																																																																			TTAA|1.000;|0.000	1.000	strong		0.455	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472	
CLEC17A	388512	hgsc.bcm.edu	37	19	14694175	14694176	+	In_Frame_Ins	INS	-	-	GGA	rs138602183|rs34295949|rs548360441	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14694175_14694176insGGA	ENST00000417570.1	+	2	88_89	c.50_51insGGA	c.(49-54)atggag>atGGAggag	p.22_23insE	RN7SL337P_ENST00000462468.2_RNA|CLEC17A_ENST00000397439.2_In_Frame_Ins_p.22_23insE|CLEC17A_ENST00000547437.1_In_Frame_Ins_p.22_23insE	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	22	Poly-Glu.					cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)										GAAGGGACCATGGAGGAGGAGG	0.579														414	0.0826677	0.174	0.0346	5008	,	,		19484	0.004		0.0656	False		,,,				2504	0.092				p.M17delinsME		Pindel,Atlas-Indel	.											.	CLEC17A	27	.	0			c.50_51insGGA						PASS	.																																			SO:0001652	inframe_insertion	388512	exon2			.	AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912		"""C-type lectin domain containing"""	34520	protein-coding gene	gene with protein product	"""prolectin"""					19419970	Standard	NM_207390		Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.66_68dupGGA	19.37:g.14694182_14694184dupGGA	ENSP00000393719:p.Glu22_Glu22dup	Somatic	301	.	.		WXS	Illumina HiSeq	Phase_I	361	74	0.205	NM_207390	A8MX68|B2RTX0|B7ZMM4	In_Frame_Ins	INS	ENST00000417570.1	37	CCDS56087.1																																																																																			-|0.500;GGA|0.500	0.500	weak		0.579	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403400.1	NM_207390	
CEMIP	57214	hgsc.bcm.edu	37	15	81241247	81241249	+	In_Frame_Del	DEL	GAA	GAA	-	rs200201338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:81241247_81241249delGAA	ENST00000394685.3	+	30	4487_4489	c.4068_4070delGAA	c.(4066-4071)gtgaag>gtg	p.K1360del	RP11-351M8.2_ENST00000560873.1_RNA|MESDC2_ENST00000560244.1_Intron|KIAA1199_ENST00000220244.3_In_Frame_Del_p.K1360del|KIAA1199_ENST00000356249.5_In_Frame_Del_p.K1360del			Q8WUJ3	CEMIP_HUMAN		1360					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)	p.K1357>?(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TCCCTGTGGTGAAGAAGAAGAAG	0.571														20	0.00399361	0.0008	0.0072	5008	,	,		18528	0.0		0.0129	False		,,,				2504	0.001				p.1356_1357del		Pindel,Atlas-Indel	.											.	KIAA1199	118	.	1	Complex(1)	lung(1)	c.4067_4069del						PASS	.			20,4244		0,20,2112						2.7	1.0			156	167,8087		1,165,3961	no	coding	KIAA1199	NM_018689.1		1,185,6073	A1A1,A1R,RR		2.0233,0.469,1.4938				187,12331				SO:0001651	inframe_deletion	57214	exon29			.																												ENST00000394685.3:c.4068_4070delGAA	15.37:g.81241256_81241258delGAA	ENSP00000378177:p.Lys1360del	Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	80	27	0.338	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	In_Frame_Del	DEL	ENST00000394685.3	37	CCDS10315.1																																																																																			GAA|0.991;-|0.009	0.009	strong		0.571	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
KIAA1841	84542	hgsc.bcm.edu	37	2	61361326	61361326	+	Frame_Shift_Del	DEL	G	G	-	rs142269591	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:61361326delG	ENST00000295031.5	+	21	2460	c.2083delG	c.(2083-2085)ggtfs	p.G695fs		NM_032506.2	NP_115895.2	Q6NSI8	K1841_HUMAN	KIAA1841	0										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			cagaaaaagtggTTTGAGCAG	0.393													GG|GG|G|deletion	119	0.023762	0.0038	0.036	5008	,	,		21790	0.001		0.0736	False		,,,				2504	0.0143				p.S694fs		Pindel,Atlas-Indel	.											.	KIAA1841	95	.	0			c.2082delT						PASS	.			74,4190		0,74,2058	171.0	143.0	152.0			0.8	0.1	2	dbSNP_134	161	685,7569		38,609,3480	no	frameshift	KIAA1841	NM_032506.2		38,683,5538	A1A1,A1R,RR		8.299,1.7355,6.0633			61361326	759,11759	2203	4286	6489	SO:0001589	frameshift_variant	84542	exon21			.	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000295031.5:c.2083delG	2.37:g.61361326delG	ENSP00000295031:p.Gly695fs	Somatic	156	.	.		WXS	Illumina HiSeq	Phase_I	178	96	0.539	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Frame_Shift_Del	DEL	ENST00000295031.5	37	CCDS1867.1																																																																																			G|0.962;-|0.038	0.038	strong		0.393	KIAA1841-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251580.1	NM_032506	
SKA3	221150	hgsc.bcm.edu	37	13	21746601	21746601	+	Frame_Shift_Del	DEL	G	G	-	rs151272242	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:21746601delG	ENST00000314759.5	-	3	332	c.208delC	c.(208-210)caafs	p.Q70fs	SKA3_ENST00000400018.3_Frame_Shift_Del_p.Q70fs	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	70					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						ATGCCTTCTTGATTTTCCAAT	0.259													G|G|-|deletion	696	0.138978	0.0295	0.134	5008	,	,		19850	0.2391		0.1412	False		,,,				2504	0.1851				p.Q70fs		Atlas-Indel	.											.	SKA3	76	.	0			c.209delA						PASS	.		,	159,4085		0,159,1963	42.0	43.0	42.0		,	3.0	0.9	13	dbSNP_134	45	930,7300		2,926,3187	no	frameshift,frameshift	SKA3	NM_145061.5,NM_001166017.1	,	2,1085,5150	A1A1,A1R,RR		11.3001,3.7465,8.7302	,	,	21746601	1089,11385	2195	4287	6482	SO:0001589	frameshift_variant	221150	exon3			.	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.208delC	13.37:g.21746601delG	ENSP00000319417:p.Gln70fs	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	152	36	0.236842	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Frame_Shift_Del	DEL	ENST00000314759.5	37	CCDS31946.1																																																																																			.	.	strong		0.259	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
TRAK1	22906	hgsc.bcm.edu	37	3	42251578	42251580	+	Intron	DEL	GGA	GGA	-	rs35624871		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:42251578_42251580delGGA	ENST00000327628.5	+	14	2363				TRAK1_ENST00000396175.1_Intron|TRAK1_ENST00000341421.3_In_Frame_Del_p.E640del|TRAK1_ENST00000487159.1_Intron	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1						endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.E640delE(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CAGCGGCCACggaggaggaggag	0.621																																					p.688_689del	GBM(44;195 884 22595 31865 41850)	Pindel	.											TRAK1,caecum,carcinoma,0,1	TRAK1	188	1	1	Deletion - In frame(1)	kidney(1)	c.2063_2065del						PASS	.																																			SO:0001627	intron_variant	22906	exon14			.		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1963+101GGA>-	3.37:g.42251587_42251589delGGA		Somatic	96	.	.		WXS	Illumina HiSeq	Phase_I	96	20	0.208	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	In_Frame_Del	DEL	ENST00000327628.5	37	CCDS43072.1																																																																																			.	.	strong		0.621	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
DMKN	93099	hgsc.bcm.edu	37	19	36002362	36002412	+	In_Frame_Del	DEL	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	-	rs112672248|rs142519211|rs144877871|rs544198244|rs199498909|rs11667007|rs12981076|rs146822312|rs148799704|rs138902616|rs56743379|rs140071083|rs371511253|rs117522133|rs59309505|rs113540509|rs111543270|rs58579970|rs201369392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36002362_36002412delCTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	ENST00000339686.3	-	5	995_1045	c.819_869delCAGTGGCAGCAGCAGTGGCGGCAGCAGTGGCGGCAGCAGTGGTGGCAGCAG	c.(817-870)agcagtggcagcagcagtggcggcagcagtggcggcagcagtggtggcagcagt>agt	p.273_290SSGSSSGGSSGGSSGGSS>S	DMKN_ENST00000440396.1_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000424570.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000418261.1_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000451297.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	273	Gly-rich.		G -> S (in dbSNP:rs11667007). {ECO:0000269|PubMed:17380110}.	G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			actgttgccactgctgccaccactgctgccgccactgctgccgccactgctgctgccactgctgctgccac	0.641																																					p.274_290del		Pindel	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.820_870del						PASS	.		,,,,,,	1051,3093		133,785,1154					,,,,,,	-3.2	0.0		dbSNP_130	28	1360,6640		184,992,2824	no	coding,coding,coding,intron,coding,coding,intron	DMKN	NM_033317.4,NM_001190349.1,NM_001190348.1,NM_001190347.1,NM_001126058.2,NM_001126057.2,NM_001126056.2	,,,,,,	317,1777,3978	A1A1,A1R,RR		17.0,25.362,19.8534	,,,,,,	,,,,,,		2411,9733				SO:0001651	inframe_deletion	93099	exon5			.	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.819_869delCAGTGGCAGCAGCAGTGGCGGCAGCAGTGGCGGCAGCAGTGGTGGCAGCAG	19.37:g.36002362_36002412delCTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	ENSP00000342012:p.Ser273_Ser289del	Somatic	78	.	.		WXS	Illumina HiSeq	Phase_I	81	33	0.407	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.641	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
OVGP1	5016	hgsc.bcm.edu	37	1	111957515	111957583	+	In_Frame_Del	DEL	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	-	rs61742558|rs568931117|rs12096782|rs112145355|rs113984808|rs201350653|rs375218077|rs79262073|rs201210901|rs75512011|rs1126656|rs368203827|rs150261549|rs3767609|rs3767608|rs201662631|rs376377993|rs145862799|rs45455292|rs74322126|rs374145757|rs140282461|rs549398942|rs369687480|rs386634633|rs144666939|rs551744565|rs139753199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111957515_111957583delACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ENST00000369732.3	-	11	1595_1663	c.1540_1608delTATCAGTCTGTGACCCCTGGGGAAAAGACCCTGACCCCTGTGGGTCATCAGTCTGTGACCCCTGTGAGT	c.(1540-1608)tatcagtctgtgacccctggggaaaagaccctgacccctgtgggtcatcagtctgtgacccctgtgagtdel	p.YQSVTPGEKTLTPVGHQSVTPVS514del		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	514			Y -> H (in dbSNP:rs1126656). {ECO:0000269|Ref.2}.		binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)	p.T597_V604delTPVSHQSV(2)|p.T533_V540delTPVSHQSV(2)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		CAGACTGATGACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATAACCCACAGAG	0.554																																					p.514_537del		Pindel	.											.	OVGP1	177	.	4	Deletion - In frame(4)	haematopoietic_and_lymphoid_tissue(2)|stomach(2)	c.1541_1609del						PASS	.																																			SO:0001651	inframe_deletion	5016	exon11			.	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1540_1608delTATCAGTCTGTGACCCCTGGGGAAAAGACCCTGACCCCTGTGGGTCATCAGTCTGTGACCCCTGTGAGT	1.37:g.111957515_111957583delACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ENSP00000358747:p.Tyr514_Ser536del	Somatic	177	.	.		WXS	Illumina HiSeq	Phase_I	78	39	0.500	NM_002557	A0AV19|B9EGE1|Q15841	In_Frame_Del	DEL	ENST00000369732.3	37	CCDS834.1																																																																																			.	.	none		0.554	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
CLCA4	22802	hgsc.bcm.edu	37	1	87045897	87045902	+	In_Frame_Del	DEL	CCTACA	CCTACA	-	rs1932809|rs4001061|rs77067122|rs56040873|rs574759485|rs368263974|rs201606404	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CCTACA	CCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:87045897_87045902delCCTACA	ENST00000370563.3	+	14	2671_2676	c.2629_2634delCCTACA	c.(2629-2634)cctacadel	p.PT885del	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	885					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TGACATTGAtcctacacctactccta	0.354														3541	0.707069	0.5363	0.7925	5008	,	,		17981	0.7282		0.7207	False		,,,				2504	0.8415				p.876_878del		Pindel	.											.	CLCA4	131	.	0			c.2628_2633del						PASS	.																																			SO:0001651	inframe_deletion	22802	exon14			.	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2629_2634delCCTACA	1.37:g.87045897_87045902delCCTACA	ENSP00000359594:p.Pro885_Thr886del	Somatic	178	.	.		WXS	Illumina HiSeq	Phase_I	115	64	0.557	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	In_Frame_Del	DEL	ENST00000370563.3	37	CCDS41355.1																																																																																			CCTACA|0.284;-|0.716	0.716	strong		0.354	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
HLA-B	3106	hgsc.bcm.edu	37	6	31324525	31324531	+	Frame_Shift_Del	DEL	CCTGGGC	CCTGGGC	-	rs41546313|rs41548914|rs1140404|rs1131212|rs1131204|rs1131213|rs1071817|rs71533898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CCTGGGC	CCTGGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31324525_31324531delCCTGGGC	ENST00000412585.2	-	2	305_311	c.277_283delGCCCAGG	c.(277-285)gcccaggcafs	p.AQA93fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	93	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TCAGTCTGTGCCTGGGCCTTGTAGATC	0.676									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.93_95del		Pindel	.											.	HLA-B	54	.	0			c.278_284del						PASS	.																																			SO:0001589	frameshift_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	.	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.277_283delGCCCAGG	6.37:g.31324525_31324531delCCTGGGC	ENSP00000399168:p.Ala93fs	Somatic	58	.	.		WXS	Illumina HiSeq	Phase_I	131	45	0.344	NM_005514	Q29764	Frame_Shift_Del	DEL	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	none		0.676	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
RIMBP3B	440804	hgsc.bcm.edu	37	22	21741340	21741341	+	In_Frame_Ins	INS	-	-	TGCAGG	rs555102406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21741340_21741341insTGCAGG	ENST00000434111.1	+	1	3678_3679	c.3193_3194insTGCAGG	c.(3193-3195)ctg>cTGCAGGtg	p.1067_1068insQV	RN7SKP63_ENST00000363187.1_RNA|SCARNA18_ENST00000516505.1_RNA|SCARNA17_ENST00000516211.1_RNA	NM_001128635.1	NP_001122107.1	A6NNM3	RIM3B_HUMAN	RIMS binding protein 3B	1067	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.																ATGGGACTTGCTGCAGGTGTAT	0.663																																					p.L1065delinsLQV		Pindel	.											.	RIMBP3C	6	.	0			c.3193_3194insTGCAGG						PASS	.			6,24		3,0,12						-2.0	0.0			1	7,131		3,1,65	no	coding	RIMBP3B	NM_001128635.1		6,1,77	A1A1,A1R,RR		5.0725,20.0,7.7381				13,155				SO:0001652	inframe_insertion	150221	exon1			.		CCDS46668.1	22q11.21	2008-10-23			ENSG00000196934	ENSG00000274600			33891	protein-coding gene	gene with protein product		612700				17855024	Standard	NM_001128635		Approved			A6NNM3	OTTHUMG00000150819	ENST00000434111.1:c.3194_3199dupTGCAGG	22.37:g.21741341_21741346dupTGCAGG	ENSP00000407925:p.Gln1066_Val1067dup	Somatic	2	.	.		WXS	Illumina HiSeq	Phase_I	15	15	1.000	NM_001128633		In_Frame_Ins	INS	ENST00000434111.1	37	CCDS46668.1																																																																																			.	.	none		0.663	RIMBP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320196.2	XM_036936	
SPATA3	130560	hgsc.bcm.edu	37	2	231861033	231861059	+	In_Frame_Del	DEL	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	-	rs13005918|rs72362780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENST00000452881.1	+	1	193_219	c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	c.(85-111)cagcagcctagccctgaatccacaccadel	p.QQPSPESTP47del	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_In_Frame_Del_p.QQPSPESTP47del|SPATA3_ENST00000455816.1_In_Frame_Del_p.QQPSPESTP47del|SPATA3_ENST00000424440.1_In_Frame_Del_p.QQPSPESTP47del			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	47			Missing.							endometrium(2)|lung(1)	3						TTCCACCTCTCAGCAGCCTAGCCCTGAATCCACACCACAGCAGCCTA	0.564																																					p.28_37del		Pindel	.											.	SPATA3	52	.	0			c.84_110del						PASS	.			924,1842		222,480,681						-8.0	0.0		dbSNP_130	187	2754,2350		871,1012,669	no	coding	SPATA3	NM_139073.3		1093,1492,1350	A1A1,A1R,RR		46.0423,33.4056,46.7344				3678,4192				SO:0001651	inframe_deletion	130560	exon1			.	AY032925	CCDS2481.1	2q37.1	2008-02-05			ENSG00000173699	ENSG00000173699			17884	protein-coding gene	gene with protein product							Standard	NM_139073		Approved	TSARG1	uc010zmd.2	Q8NHX4	OTTHUMG00000133221	ENST00000452881.1:c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	2.37:g.231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENSP00000388895:p.Gln47_Pro55del	Somatic	140	.	.		WXS	Illumina HiSeq	Phase_I	103	30	0.291	NM_139073	Q86WX5|Q8N9Y6	In_Frame_Del	DEL	ENST00000452881.1	37	CCDS2481.1																																																																																			.	.	strong		0.564	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511804	99511805	+	Frame_Shift_Ins	INS	-	-	C	rs398043625|rs5814919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:99511804_99511805insC	ENST00000378919.6	-	5	698_699	c.493_494insG	c.(493-495)gtcfs	p.V165fs	PGPEP1L_ENST00000535714.1_Frame_Shift_Ins_p.V111fs|RP11-654A16.3_ENST00000559468.1_RNA	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	165							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						CTGGATGATGACTCTCAAGGCT	0.574													C|C|CC|insertion	2217	0.442692	0.1558	0.4914	5008	,	,		17754	0.4841		0.5716	False		,,,				2504	0.6207				p.V165fs		Pindel	.											.	PGPEP1L	26	.	0			c.494_495insG						PASS	.		,	816,2946		112,592,1177					,	1.6	0.2		dbSNP_114	44	4130,3796		1081,1968,914	no	frameshift,frameshift	PGPEP1L	NM_001167902.1,NM_001102612.2	,	1193,2560,2091	A1A1,A1R,RR		47.893,21.6906,42.3169	,	,		4946,6742				SO:0001589	frameshift_variant	145814	exon5			.		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.494dupG	15.37:g.99511805_99511805dupC	ENSP00000368199:p.Val165fs	Somatic	218	.	.		WXS	Illumina HiSeq	Phase_I	217	56	0.258	NM_001102612	H0YF86	Frame_Shift_Ins	INS	ENST00000378919.6	37	CCDS53977.1																																																																																			-|0.556;C|0.444	0.444	strong		0.574	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
ZNF271	10778	hgsc.bcm.edu	37	18	32888075	32888075	+	RNA	DEL	A	A	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:32888075delA	ENST00000399070.3	+	0	2469					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(9)	12						ctgtctatttaaaaaaaaaaa	0.388																																					.		Pindel	.											.	ZNF271	16	.	0			.						PASS	.																																					10778	.			.	X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267		"""Zinc fingers, C2H2-type"""	13065	other	unknown		604754				7865130, 11777961	Standard	NR_024565		Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563		18.37:g.32888075delA		Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	60	10	0.167	.	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	DEL	ENST00000399070.3	37																																																																																				.	.	none		0.388	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
COL6A3	1293	hgsc.bcm.edu	37	2	238244864	238244866	+	In_Frame_Del	DEL	GCA	GCA	-	rs35879189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238244864_238244866delGCA	ENST00000295550.4	-	40	9329_9331	c.8877_8879delTGC	c.(8875-8880)gctgca>gca	p.2959_2960AA>A	COL6A3_ENST00000472056.1_In_Frame_Del_p.2352_2353AA>A|COL6A3_ENST00000409809.1_In_Frame_Del_p.2753_2754AA>A|COL6A3_ENST00000346358.4_In_Frame_Del_p.2759_2760AA>A|COL6A3_ENST00000347401.3_In_Frame_Del_p.2758_2759AA>A|COL6A3_ENST00000353578.4_In_Frame_Del_p.2753_2754AA>A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2959	Ala-rich.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CACTGGTTTTGCAGCAGCAGCAG	0.611														256	0.0511182	0.003	0.0591	5008	,	,		19560	0.0089		0.1302	False		,,,				2504	0.0726				p.2960_2960del		Pindel	.											.	COL6A3	608	.	0			c.8878_8880del						PASS	.		,,	96,4160		2,92,2034					,,	2.1	0.0		dbSNP_126	40	977,7259		76,825,3217	no	coding,coding,coding	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	,,	78,917,5251	A1A1,A1R,RR		11.8626,2.2556,8.5895	,,	,,		1073,11419				SO:0001651	inframe_deletion	1293	exon40			.	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8877_8879delTGC	2.37:g.238244873_238244875delGCA	ENSP00000295550:p.Ala2960del	Somatic	43	.	.		WXS	Illumina HiSeq	Phase_I	62	16	0.258	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	In_Frame_Del	DEL	ENST00000295550.4	37	CCDS33412.1																																																																																			GCA|0.935;-|0.065	0.065	strong		0.611	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
PELP1	27043	hgsc.bcm.edu	37	17	4576216	4576217	+	In_Frame_Ins	INS	-	-	GGCATGGGGCCTGCTGAA	rs147763003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576216_4576217insGGCATGGGGCCTGCTGAA	ENST00000574876.1	-	16	2086_2087	c.2069_2070insTTCAGCAGGCCCCATGCC	c.(2068-2070)ccc>ccTTCAGCAGGCCCCATGCCc	p.690_690P>PSAGPMP	PELP1_ENST00000301396.4_In_Frame_Ins_p.834_834P>PSAGPMP|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_In_Frame_Ins_p.600_600P>PSAGPMP|PELP1_ENST00000572293.1_In_Frame_Ins_p.740_740P>PSAGPMP|PELP1_ENST00000436683.2_In_Frame_Ins_p.543_543P>PSAGPMP			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	690	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GGCCTGCTGAGGGCATGGGGCC	0.688																																					p.P690delinsPSAGPMP		Pindel	.											.	PELP1	102	.	0			c.2070_2071insTTCAGCAGGCCCCATGCC						PASS	.																																			SO:0001652	inframe_insertion	27043	exon16			.		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2052_2069dupTTCAGCAGGCCCCATGCC	17.37:g.4576216_4576217insGGCATGGGGCCTGCTGAA	ENSP00000461625:p.SerAlaGlyProMetPro690dup	Somatic	147	.	.		WXS	Illumina HiSeq	Phase_I	146	33	0.226	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	In_Frame_Ins	INS	ENST00000574876.1	37	CCDS58503.1																																																																																			.	.	none		0.688	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																					p.45_45del		Pindel	.											.	KRTAP10-7	41	.	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.134_134del						PASS	.		,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				SO:0001651	inframe_deletion	386675	exon1			.	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	77	35	0.455	NM_198689	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																				.	.	weak		0.698	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
PCDHA4	56144	hgsc.bcm.edu	37	5	140186979	140186990	+	In_Frame_Del	DEL	GGGCCGCGGAGG	GGGCCGCGGAGG	-	rs67934344|rs200172095|rs563991668|rs3822355|rs3822354|rs17844273|rs3822351|rs3822350|rs3822353|rs3822352|rs386692888|rs543774145|rs201303975|rs386692887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GGGCCGCGGAGG	GGGCCGCGGAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140186979_140186990delGGGCCGCGGAGG	ENST00000530339.1	+	1	207_218	c.207_218delGGGCCGCGGAGG	c.(205-219)aagggccgcggaggc>aac	p.69_73KGRGG>N	PCDHA4_ENST00000512229.2_In_Frame_Del_p.69_73KGRGG>N|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_In_Frame_Del_p.69_73KGRGG>N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	69	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.G72R(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCGTCCAAGGGCCGCGGAGGCCTTCTGGAG	0.656																																					p.69_73del		Pindel	.											.	PCDHA4	419	.	2	Substitution - Missense(2)	lung(2)	c.206_217del						PASS	.																																			SO:0001651	inframe_deletion	56144	exon1			.	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.207_218delGGGCCGCGGAGG	5.37:g.140186979_140186990delGGGCCGCGGAGG	ENSP00000435300:p.Lys69_Gly73delinsAsn	Somatic	127	.	.		WXS	Illumina HiSeq	Phase_I	46	14	0.304	NM_031500	O75285|Q2M253	In_Frame_Del	DEL	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.656	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
ZNF280D	54816	hgsc.bcm.edu	37	15	56946704	56946704	+	Intron	DEL	A	A	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:56946704delA	ENST00000267807.7	-	18	2274				ZNF280D_ENST00000559000.1_Intron|ZNF280D_ENST00000559237.1_Intron	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		TAATGCCCCTAAAAAAAAAAG	0.284																																					.		Pindel	.											.	ZNF280D	82	.	0			c.2058-2T>-						PASS	.						45.0	44.0	45.0					15																	56946704		2192	4289	6481	SO:0001627	intron_variant	54816	exon19			.	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.2058-3T>-	15.37:g.56946704delA		Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	108	20	0.185	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Splice_Site	DEL	ENST00000267807.7	37	CCDS32245.1																																																																																			.	.	none		0.284	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
NUPL2	11097	hgsc.bcm.edu	37	7	23221797	23221798	+	In_Frame_Ins	INS	-	-	CGGCAGCAACCG	rs200880793|rs371896223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:23221797_23221798insCGGCAGCAACCG	ENST00000258742.5	+	1	352_353	c.93_94insCGGCAGCAACCG	c.(94-96)cgg>CGGCAGCAACCGcgg	p.32_32R>RQQPR	NUPL2_ENST00000487595.1_3'UTR|NUPL2_ENST00000410002.3_In_Frame_Ins_p.32_32R>RQQPR|AC005082.1_ENST00000366347.4_Intron	NM_007342.2	NP_031368.1	O15504	NUPL2_HUMAN	nucleoporin like 2	32					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclear export signal receptor activity (GO:0005049)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CAGGAGGAGGACGGCAGCAACC	0.649														62	0.0123802	0.0015	0.0303	5008	,	,		15515	0.0		0.0368	False		,,,				2504	0.002				p.G31delinsGRQQP		Pindel	.											.	NUPL2	51	.	0			c.93_94insCGGCAGCAACCG						PASS	.			35,4229		1,33,2098						-0.0	1.0			54	407,7847		9,389,3729	no	coding	NUPL2	NM_007342.2		10,422,5827	A1A1,A1R,RR		4.9309,0.8208,3.5309				442,12076				SO:0001652	inframe_insertion	11097	exon1			.	U97198	CCDS5379.1	7p15	2003-08-07			ENSG00000136243	ENSG00000136243			17010	protein-coding gene	gene with protein product	"""nucleoporin-like protein 1"""					10358091, 9450185	Standard	NM_007342		Approved	NLP_1, CG1, hCG1, H_RG271G13.9	uc003svu.3	O15504	OTTHUMG00000096955	ENST00000258742.5:c.94_105dupCGGCAGCAACCG	7.37:g.23221797_23221798insCGGCAGCAACCG	Exception_encountered	Somatic	65	.	.		WXS	Illumina HiSeq	Phase_I	39	11	0.282	NM_007342	A4D143|B4DP42|Q49AE7|Q9BS49	In_Frame_Ins	INS	ENST00000258742.5	37	CCDS5379.1																																																																																			-|0.989;CGGCAGCAACCG|0.011	0.011	strong		0.649	NUPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214017.2	NM_007342	
MUC4	4585	hgsc.bcm.edu	37	3	195508490	195508537	+	In_Frame_Del	DEL	CTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	CTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	-	rs534369822|rs199896372|rs568102602|rs531526881|rs62282476|rs201195860|rs545603027|rs541132330|rs200820395|rs150322486|rs201164988|rs141064104|rs540026448|rs148923966|rs113686997|rs146135943|rs549350827|rs202097189|rs574066429|rs374619108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	CTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508490_195508537delCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	ENST00000463781.3	-	2	10373_10420	c.9914_9961delTATCCACAGGTCACGCCACTCCTCTTCTTGTCACCGACGCTTCCTCAG	c.(9913-9963)gtatccacaggtcacgccactcctcttcttgtcaccgacgcttcctcagca>gca	p.VSTGHATPLLVTDASS3305del	MUC4_ENST00000475231.1_In_Frame_Del_p.VSTGHATPLLVTDASS3305del|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.D3317E(2)|p.A3310T(2)|p.H3309D(2)|p.V3305A(1)|p.D3317N(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)|p.L3314P(1)|p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.S3317R(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATACTGAGGAAGT	0.565																																					p.3305_3321del		Pindel	.											.	MUC4	1505	.	12	Substitution - Missense(10)|Deletion - In frame(2)	stomach(11)|kidney(1)	c.9915_9962del						PASS	.		,,	1072,1522		327,418,552					,,	-2.0	0.0		dbSNP_130	14	2388,3868		646,1096,1386	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	973,1514,1938	A1A1,A1R,RR		38.1714,41.3261,39.096	,,	,,		3460,5390				SO:0001651	inframe_deletion	4585	exon2			.	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9914_9961delTATCCACAGGTCACGCCACTCCTCTTCTTGTCACCGACGCTTCCTCAG	3.37:g.195508490_195508537delCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	ENSP00000417498:p.Val3305_Ser3320del	Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	112	19	0.170	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.565	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577728	+	RNA	DEL	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	-	rs202101805|rs202111256|rs201189413|rs199515704|rs202116886|rs539529375|rs200213073|rs537929246|rs527250207|rs200862023|rs199694900|rs201534830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90577707_90577728delGACATCTTTGCCCAGACATGGA	ENST00000551025.1	+	0	6135_6156									caspase 8 associated protein 2									p.S1568fs*1(1)		NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		ATGAATTATTGACATCTTTGCCCAGACATGGAAAGGAAGCTG	0.374																																					p.1566_1573del	Colon(187;1656 2025 17045 31481 39901)	Pindel	.											.	CASP8AP2	108	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4697_4718del						PASS	.																																					9994	exon8			.	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90577707_90577728delGACATCTTTGCCCAGACATGGA		Somatic	89	.	.		WXS	Illumina HiSeq	Phase_I	68	16	0.235	NM_012115		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	alt		0.374	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
NADK	65220	hgsc.bcm.edu	37	1	1684347	1684348	+	In_Frame_Ins	INS	-	-	CCT	rs139135464|rs71578334|rs150880809		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1684347_1684348insCCT	ENST00000341426.5	-	12	1557_1558	c.1336_1337insAGG	c.(1336-1338)ggc>gAGGgc	p.445_446insE	NADK_ENST00000378625.1_In_Frame_Ins_p.590_591insE|NADK_ENST00000344463.4_In_Frame_Ins_p.590_591insE|NADK_ENST00000341991.3_In_Frame_Ins_p.445_446insE|NADK_ENST00000342348.5_In_Frame_Ins_p.413_414insE	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	445	Poly-Glu.			E -> EE (in Ref. 2; BAB14412). {ECO:0000305}.|G -> EG (in Ref. 3; BAH12420). {ECO:0000305}.	ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		CTTGACCTAGCcctcctcctcc	0.629																																					p.G591delinsEG		Pindel	.											.	NADK	79	.	0			c.1772_1773insAGG						PASS	.																																			SO:0001652	inframe_insertion	65220	exon14			.	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.1334_1336dupAGG	1.37:g.1684354_1684356dupCCT	ENSP00000341679:p.Glu445_Glu445dup	Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	93	19	0.204	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	In_Frame_Ins	INS	ENST00000341426.5	37	CCDS30565.1																																																																																			.	.	strong		0.629	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
ZNF527	84503	hgsc.bcm.edu	37	19	37879853	37879855	+	In_Frame_Del	DEL	CAT	CAT	-	rs200420244|rs373623156|rs2385182|rs3081552|rs386809049|rs200343305|rs2891700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:37879853_37879855delCAT	ENST00000436120.2	+	5	1009_1011	c.902_904delCAT	c.(901-906)ccatat>cat	p.301_302PY>H	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGAGAAAAACCATATGCATGCAA	0.394																																					p.301_301del		Pindel	.											.	ZNF527	78	.	0			c.901_903del						PASS	.																																			SO:0001651	inframe_deletion	84503	exon5			.	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.902_904delCAT	19.37:g.37879853_37879855delCAT	ENSP00000390179:p.Pro301_Tyr302delinsHis	Somatic	124	.	.		WXS	Illumina HiSeq	Phase_I	129	32	0.248	NM_032453	B4DVL5	In_Frame_Del	DEL	ENST00000436120.2	37	CCDS42559.1																																																																																			.	.	alt		0.394	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388594	1388622	+	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-	rs76374232|rs151313714|rs540461234|rs75969203|rs558358960|rs79704405|rs200174708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENST00000324803.4	+	1	3255_3283	c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	c.(295-324)cacgtgcccatgtggagtgcccgcctgctcfs	p.HVPMWSARLL99fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	99					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CCTGCTCACACACGTGCCCATGTGGAGTGCCCGCCTGCTCACGTGCCCA	0.655																																					p.98_108del		Pindel	.											.	CRIPAK	185	.	1	Substitution - Missense(1)	pancreas(1)	c.294_322del						PASS	.																																			SO:0001589	frameshift_variant	285464	exon1			.	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.295_323delCACGTGCCCATGTGGAGTGCCCGCCTGCT	4.37:g.1388594_1388622delCACGTGCCCATGTGGAGTGCCCGCCTGCT	ENSP00000323978:p.His99fs	Somatic	274	.	.		WXS	Illumina HiSeq	Phase_I	178	42	0.236	NM_175918	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.655	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
KRT2	3849	hgsc.bcm.edu	37	12	53045615	53045616	+	In_Frame_Ins	INS	-	-	CCTCCAAAGCCGCTGCCG	rs150409603|rs532019270|rs75253159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53045615_53045616insCCTCCAAAGCCGCTGCCG	ENST00000309680.3	-	1	332_333	c.311_312insCGGCAGCGGCTTTGGAGG	c.(310-312)ggt>ggCGGCAGCGGCTTTGGAGGt	p.104_104G>GGSGFGG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	104	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		agccgctgccacctccaaagct	0.619														905	0.180711	0.0151	0.1441	5008	,	,		13575	0.3948		0.168	False		,,,				2504	0.2229				p.G104delinsGGSGFGG		Pindel	.											.	KRT2	94	.	0			c.312_313insCGGCAGCGGCTTTGGAGG						PASS	.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.311_312insCGGCAGCGGCTTTGGAGG	12.37:g.53045615_53045616insCCTCCAAAGCCGCTGCCG	Exception_encountered	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	140	26	0.186	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	37	CCDS8835.1																																																																																			.	.	none		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242149	81242151	+	RNA	DEL	TTT	TTT	-	rs532218091|rs55980345|rs75398810|rs5818326|rs548490632|rs386792900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81242149_81242151delTTT	ENST00000525539.1	-	0	704_706				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.N236fs*26(6)|p.G235G(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CGGACACAGGTTTCCAAAGTAGG	0.557														146	0.0291534	0.0038	0.0101	5008	,	,		21632	0.0635		0.0119	False		,,,				2504	0.0593				p.236_236del		Pindel	.											.	PKD1L2	361	.	8	Deletion - Frameshift(6)|Substitution - coding silent(2)	lung(4)|breast(4)	c.706_708del						PASS	.		,	824,61,3211		115,28,566,0,33,1306					,	3.1	1.0		dbSNP_129	86	3173,330,4601		544,214,1871,1,114,1308	yes	codingComplex,codingComplex	PKD1L2	NM_052892.3,NM_001076780.1	,	659,242,2437,1,147,2614	A1A1,A1A2,A1R,A2A2,A2R,RR		43.2256,21.6064,35.9672	,	,		3997,391,7812						114780	exon4			.	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242149_81242151delTTT		Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	42	20	0.476	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	In_Frame_Del	DEL	ENST00000525539.1	37																																																																																				-|0.500;TT|0.500	0.500	alt		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
ASPN	54829	hgsc.bcm.edu	37	9	95237025	95237027	+	In_Frame_Del	DEL	TCA	TCA	-	rs200538582|rs397840756|rs557103556|rs3078372|rs397838876		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:95237025_95237027delTCA	ENST00000375544.3	-	2	396_398	c.153_155delTGA	c.(151-156)gatgag>gag	p.D51del	CENPP_ENST00000375587.3_Intron|ASPN_ENST00000375543.1_In_Frame_Del_p.D51del|ASPN_ENST00000395538.3_In_Frame_Del_p.D51del|ASPN_ENST00000450139.2_In_Frame_Del_p.D23del	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	51	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						AGAGTTGTCCtcatcatcatcat	0.394																																					p.52_52del		Pindel	.											.	ASPN	52	.	0			c.154_156del						PASS	.																																			SO:0001651	inframe_deletion	54829	exon2			.	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	14872	protein-coding gene	gene with protein product	"""asporin proteoglycan"""	608135	"""asporin (LRR class 1)"""				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.153_155delTGA	9.37:g.95237034_95237036delTCA	ENSP00000364694:p.Asp51del	Somatic	89	.	.		WXS	Illumina HiSeq	Phase_I	108	35	0.324	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	In_Frame_Del	DEL	ENST00000375544.3	37																																																																																				TCA|0.500;-|0.500	0.500	strong		0.394	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680	
SLC22A1	6580	hgsc.bcm.edu	37	6	160560883	160560905	+	Splice_Site	DEL	GATTTTTATCTCACCTGGTAAGT	GATTTTTATCTCACCTGGTAAGT	-	rs200234072|rs202220802|rs72552763|rs35191146|rs113569197|rs36056065|rs35854239|rs77297078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GATTTTTATCTCACCTGGTAAGT	GATTTTTATCTCACCTGGTAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:160560883_160560905delGATTTTTATCTCACCTGGTAAGT	ENST00000366963.4	+	7	1407_1423	c.1260_1276delGATTTTTATCTCACCTGGTAAGT	c.(1258-1278)atgatttttatctcacctggt>atgt	p.IFISPG421fs	SLC22A1_ENST00000324965.4_Splice_Site_p.IFISPG421fs|SLC22A1_ENST00000457470.2_Splice_Site_p.IFISPG421fs	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	421					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)		SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	GCCTCGTCATGATTTTTATCTCACCTGGTAAGTTGGTAAGTTG	0.511																																					p.420_426del		Pindel	.											.	SLC22A1	69	.	0			c.1259_1276del	GRCh37	CD072492	SLC22A1	D	rs35191146	PASS	.																																			SO:0001630	splice_region_variant	6580	exon7			.	U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"""Solute carriers"""	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.1276+1GATTTTTATCTCACCTGGTAAGT>-	6.37:g.160560883_160560905delGATTTTTATCTCACCTGGTAAGT		Somatic	46	.	.		WXS	Illumina HiSeq	Phase_I	60	12	0.200	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	In_Frame_Del	DEL	ENST00000366963.4	37	CCDS5274.1																																																																																			-|0.079;G|0.468;GAT|0.453	0.079	strong		0.511	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		Frame_Shift_Del
DNAH5	1767	hgsc.bcm.edu	37	5	13868104	13868104	+	Intron	DEL	A	A	-	rs397769827|rs35398031|rs376631255	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13868104delA	ENST00000265104.4	-	25	3939				CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TAAGATTCCTAAAAAAAAATA	0.363									Kartagener syndrome					1744	0.348243	0.2731	0.3184	5008	,	,		19615	0.2659		0.4433	False		,,,				2504	0.4581				.		Pindel	.											.	DNAH5	868	.	0			c.3835-2T>-						PASS	.			3,1314,2949		0,0,3,214,886,1030	35.0	28.0	30.0			5.1	0.9	5	dbSNP_134	46	5,3668,4581		0,1,4,858,1951,1313	no	intron	DNAH5	NM_001369.2		0,1,7,1072,2837,2343	A1A1,A1A2,A1R,A2A2,A2R,RR		44.4996,30.872,39.8562			13868104	8,4982,7530	2203	4296	6499	SO:0001627	intron_variant	1767	exon26	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	.	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3835-3T>-	5.37:g.13868104delA		Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	112	36	0.321	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Splice_Site	DEL	ENST00000265104.4	37	CCDS3882.1																																																																																			A|0.250;-|0.750	0.750	strong		0.363	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912490	45912492	+	In_Frame_Del	DEL	AAG	AAG	-	rs374686338|rs35729377		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45912490_45912492delAAG	ENST00000309424.3	+	3	1752_1754	c.1264_1266delAAG	c.(1264-1266)aagdel	p.K428del	ERCC1_ENST00000423698.2_3'UTR|CD3EAP_ENST00000589804.1_In_Frame_Del_p.K430del|ERCC1_ENST00000588738.1_5'Flank|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000300853.3_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	428	Poly-Lys.				rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		CACATCCACCaagaagaagaaga	0.557																																					p.421_422del		Pindel	.											.	CD3EAP	27	.	0			c.1263_1265del						PASS	.																																			SO:0001651	inframe_deletion	10849	exon3			.	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"""CD3 epsilon associated protein"", ""antisense to ERCC 1"""	107325	"""CD3e antigen, epsilon polypeptide associated protein"""			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.1264_1266delAAG	19.37:g.45912499_45912501delAAG	ENSP00000310966:p.Lys428del	Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	82	21	0.256	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	In_Frame_Del	DEL	ENST00000309424.3	37	CCDS12661.1																																																																																			.	.	strong		0.557	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
ACSBG2	81616	hgsc.bcm.edu	37	19	6187800	6187800	+	Missense_Mutation	SNP	G	G	A	rs17856650	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6187800G>A	ENST00000586696.1	+	13	2147	c.1871G>A	c.(1870-1872)aGg>aAg	p.R624K	ACSBG2_ENST00000591403.1_Missense_Mutation_p.R624K|RFX2_ENST00000587700.1_5'Flank|ACSBG2_ENST00000252669.5_Missense_Mutation_p.R624K|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000588485.1_Missense_Mutation_p.R437K|ACSBG2_ENST00000588304.1_Missense_Mutation_p.R574K			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	624			R -> K (in dbSNP:rs17856650). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AATGCACAGAGGATTGAAAAG	0.502													A|||	471	0.0940495	0.2284	0.0331	5008	,	,		18563	0.0407		0.0338	False		,,,				2504	0.0726				p.R624K		Atlas-SNP	.											.	ACSBG2	83	.	0			c.G1871A						PASS	.	A	LYS/ARG	803,3603	750.3+/-412.1	76,651,1476	188.0	170.0	176.0		1871	-2.4	0.0	19	dbSNP_123	176	297,8303	805.9+/-407.3	3,291,4006	yes	missense	ACSBG2	NM_030924.3	26	79,942,5482	AA,AG,GG		3.4535,18.2251,8.4576	benign	624/667	6187800	1100,11906	2203	4300	6503	SO:0001583	missense	81616	exon13			CACAGAGGATTGA		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1871G>A	19.37:g.6187800G>A	ENSP00000465589:p.Arg624Lys	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	155	55	0.354839	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	191	0.08745421245421245	128	0.2601626016260163	12	0.03314917127071823	23	0.04020979020979021	28	0.036939313984168866	A	0.056	-1.237525	0.01493	0.182251	0.034535	ENSG00000130377	ENST00000252669	T	0.16324	2.35	5.46	-2.41	0.06562	.	0.819030	0.10394	N	0.680018	T	0.00012	0.0000	N	0.04132	-0.27	0.43559	P	0.004126999999999992	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.46762	-0.9168	9	0.02654	T	1	-18.8489	13.9856	0.64334	0.4057:0.0:0.5943:0.0	rs17856650;rs17856650	596;624	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	K	624	ENSP00000252669:R624K	ENSP00000252669:R624K	R	+	2	0	ACSBG2	6138800	0.497000	0.26067	0.000000	0.03702	0.163000	0.22366	0.470000	0.22084	-1.298000	0.02348	-0.972000	0.02603	AGG	G|0.918;A|0.082	0.082	strong		0.502	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
RBMX	27316	hgsc.bcm.edu	37	X	135956586	135956586	+	Silent	SNP	T	T	C	rs150079822		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:135956586T>C	ENST00000320676.7	-	9	1045	c.891A>G	c.(889-891)acA>acG	p.T297T	RBMX_ENST00000570135.1_Silent_p.T162T|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000496459.2_5'Flank|RBMX_ENST00000565438.1_Silent_p.T169T|RBMX_ENST00000562646.1_3'UTR	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	297					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GGGGCCCTCGTGTAGGTGGAG	0.453																																					p.T297T		Atlas-SNP	.											.	RBMX	149	.	0			c.A891G						PASS	.						82.0	77.0	79.0					X																	135956586		2203	4300	6503	SO:0001819	synonymous_variant	27316	exon9			CCCTCGTGTAGGT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.891A>G	X.37:g.135956586T>C		Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	237	33	0.139241	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Silent	SNP	ENST00000320676.7	37	CCDS14661.1																																																																																			T|0.500;C|0.500	0.500	weak		0.453	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
GRM7	2917	hgsc.bcm.edu	37	3	6903297	6903297	+	Silent	SNP	C	C	T	rs3749380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:6903297C>T	ENST00000357716.4	+	1	496	c.222C>T	c.(220-222)aaC>aaT	p.N74N	GRM7_ENST00000402647.2_Silent_p.N74N|GRM7_ENST00000403881.1_Silent_p.N74N|GRM7_ENST00000486284.1_Silent_p.N74N|GRM7_ENST00000389336.4_Silent_p.N74N	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	74					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						AGAGGGAAAACGGGATCCACA	0.642													C|||	2088	0.416933	0.3593	0.4496	5008	,	,		14695	0.3214		0.4066	False		,,,				2504	0.5808				p.N74N		Atlas-SNP	.											GRM7,caecum,carcinoma,0,1	GRM7	223	1	0			c.C222T	GRCh37	CM085114	GRM7	M	rs3749380	scavenged	.	C	,	1431,2975	431.2+/-342.8	223,985,995	30.0	28.0	29.0	http://www.ncbi.nlm.nih.gov/pubmed?term	222,222	3.6	1.0	3	dbSNP_107	29	3236,5364	451.8+/-362.8	641,1954,1705	yes	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	864,2939,2700	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	37.6279,32.4784,35.8834	,	74/916,74/923	6903297	4667,8339	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon1			GGAAAACGGGATC	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.222C>T	3.37:g.6903297C>T		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			C|0.630;T|0.370	0.370	strong		0.642	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
NEO1	4756	hgsc.bcm.edu	37	15	73564881	73564881	+	Silent	SNP	C	C	T	rs1131854	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:73564881C>T	ENST00000339362.5	+	20	3390	c.2943C>T	c.(2941-2943)tcC>tcT	p.S981S	NEO1_ENST00000558964.1_Silent_p.S981S|NEO1_ENST00000560262.1_Silent_p.S981S|NEO1_ENST00000261908.6_Silent_p.S981S			Q92859	NEO1_HUMAN	neogenin 1	981	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						AGCCTCCCTCCGAAGCCAATG	0.448													c|||	1806	0.360623	0.1256	0.5735	5008	,	,		18909	0.3254		0.4891	False		,,,				2504	0.4315				p.S981S		Atlas-SNP	.											.	NEO1	102	.	0			c.C2943T						PASS	.	A	,,	838,3558	328.5+/-300.6	85,668,1445	76.0	71.0	72.0		2943,2943,2943	-11.8	0.5	15	dbSNP_86	72	4512,4082	591.4+/-392.8	1196,2120,981	no	coding-synonymous,coding-synonymous,coding-synonymous	NEO1	NM_001172623.1,NM_001172624.1,NM_002499.3	,,	1281,2788,2426	TT,TC,CC		47.4983,19.0628,41.1855	,,	981/1409,981/1451,981/1462	73564881	5350,7640	2198	4297	6495	SO:0001819	synonymous_variant	4756	exon19			TCCCTCCGAAGCC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7754	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 2"""	601907	"""neogenin (chicken) homolog 1"""			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.2943C>T	15.37:g.73564881C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Silent	SNP	ENST00000339362.5	37	CCDS10247.1																																																																																			C|0.611;T|0.389	0.389	strong		0.448	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499	
CST9	128822	hgsc.bcm.edu	37	20	23586360	23586360	+	Missense_Mutation	SNP	G	G	A	rs2983640	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23586360G>A	ENST00000376971.3	-	1	153	c.142C>T	c.(142-144)Ctc>Ttc	p.L48F		NM_001008693.2	NP_001008693.2	Q5W186	CST9_HUMAN	cystatin 9 (testatin)	48			L -> F (in dbSNP:rs2983640). {ECO:0000269|PubMed:12535658}.			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			central_nervous_system(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Colorectal(13;0.0993)					ACTGTGGCGAGGAACATAGGA	0.507													G|||	2279	0.455072	0.0915	0.6182	5008	,	,		21096	0.6796		0.6302	False		,,,				2504	0.4192				p.L48F		Atlas-SNP	.											.	CST9	26	.	0			c.C142T						PASS	.	G	PHE/LEU	711,3695	293.8+/-282.8	64,583,1556	267.0	223.0	238.0		142	-1.9	0.0	20	dbSNP_101	238	5219,3381	641.7+/-399.7	1610,1999,691	yes	missense	CST9	NM_001008693.2	22	1674,2582,2247	AA,AG,GG		39.314,16.1371,45.5943	probably-damaging	48/160	23586360	5930,7076	2203	4300	6503	SO:0001583	missense	128822	exon1			TGGCGAGGAACAT	AF494536	CCDS33450.1	20p11.21	2012-08-14			ENSG00000173335	ENSG00000173335			13261	protein-coding gene	gene with protein product						20565543	Standard	NM_001008693		Approved	CLM, CTES7A	uc002wtl.3	Q5W186	OTTHUMG00000032076	ENST00000376971.3:c.142C>T	20.37:g.23586360G>A	ENSP00000366170:p.Leu48Phe	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_001008693	B2RP76|Q8TD53	Missense_Mutation	SNP	ENST00000376971.3	37	CCDS33450.1	1133	0.5187728937728938	45	0.09146341463414634	223	0.6160220994475138	375	0.6555944055944056	490	0.6464379947229552	G	5.925	0.354650	0.11239	0.161371	0.60686	ENSG00000173335	ENST00000376971	T	0.26223	1.75	2.66	-1.91	0.07641	Proteinase inhibitor I25, cystatin (1);	1.320590	0.05565	N	0.570071	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D	0.61080	0.989	P	0.60173	0.87	T	0.48514	-0.9029	9	0.09590	T	0.72	.	2.6821	0.05096	0.405:0.0:0.3833:0.2117	rs2983640;rs17684648;rs52834245;rs59793432;rs2983640	48	Q5W186	CST9_HUMAN	F	48	ENSP00000366170:L48F	ENSP00000366170:L48F	L	-	1	0	CST9	23534360	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.154000	0.10130	-0.396000	0.07703	-0.225000	0.12378	CTC	G|0.526;A|0.474	0.474	strong		0.507	CST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078341.1	NM_001008693.1	
VARS2	57176	hgsc.bcm.edu	37	6	30893428	30893428	+	Missense_Mutation	SNP	G	G	A	rs2252863	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30893428G>A	ENST00000321897.5	+	27	3525	c.2893G>A	c.(2893-2895)Gca>Aca	p.A965T	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Missense_Mutation_p.A825T|VARS2_ENST00000416670.2_Missense_Mutation_p.A965T|VARS2_ENST00000541562.1_Missense_Mutation_p.A995T			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	965			A -> T (in dbSNP:rs2252863). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						ACCCCCAGGCGCAGCAGCTCC	0.672													G|||	1117	0.223043	0.0983	0.2075	5008	,	,		15352	0.247		0.3559	False		,,,				2504	0.2413				p.A995T		Atlas-SNP	.											.	VARS2	60	.	0			c.G2983A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	429,2571		40,349,1111	14.0	16.0	15.0		2473,2983,2893	-2.5	0.0	6	dbSNP_100	15	2001,3397		361,1279,1059	yes	missense,missense,missense	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	58,58,58	401,1628,2170	AA,AG,GG		37.0693,14.3,28.9355	benign,benign,benign	825/924,995/1094,965/1064	30893428	2430,5968	1500	2699	4199	SO:0001583	missense	57176	exon28			CCAGGCGCAGCAG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2893G>A	6.37:g.30893428G>A	ENSP00000316092:p.Ala965Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	161	92	0.571429	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	530	0.24267399267399267	31	0.06300813008130081	74	0.20441988950276244	162	0.28321678321678323	263	0.3469656992084433	G	4.057	0.008232	0.07912	0.143	0.370693	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.74	-2.55	0.06288	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	1.258290	0.05390	N	0.538867	T	0.09291	0.0229	L	0.59436	1.845	0.80722	P	0.0	B;B;B	0.24132	0.098;0.008;0.004	B;B;B	0.14578	0.011;0.003;0.001	T	0.24368	-1.0162	9	0.16896	T	0.51	0.6404	6.7922	0.23705	0.4999:0.1207:0.3793:0.0	rs2252863;rs57153953	403;995;965	Q5ST30-2;F5GXJ0;Q5ST30	.;.;SYVM_HUMAN	T	965;965;825;995	ENSP00000316092:A965T;ENSP00000394802:A965T;ENSP00000438200:A825T;ENSP00000441000:A995T	ENSP00000316092:A965T	A	+	1	0	VARS2	31001407	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	-1.432000	0.02430	-0.547000	0.06207	-0.742000	0.03525	GCA	G|0.761;A|0.239	0.239	strong		0.672	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
ALMS1	7840	hgsc.bcm.edu	37	2	73675844	73675844	+	Silent	SNP	C	C	T	rs397897413|rs7598901	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:73675844C>T	ENST00000264448.6	+	8	2298	c.2187C>T	c.(2185-2187)ttC>ttT	p.F729F	ALMS1_ENST00000377715.1_Silent_p.F729F|ALMS1_ENST00000409009.1_Silent_p.F687F	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	729	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AACAAGAGTTCGCAGACAGTC	0.473													C|||	2636	0.526358	0.1021	0.562	5008	,	,		19280	0.7798		0.6491	False		,,,				2504	0.6871				p.F729F		Atlas-SNP	.											.	ALMS1	384	.	0			c.C2187T						PASS	.	C		779,2947		93,593,1177	129.0	126.0	127.0		2187	-6.6	0.0	2	dbSNP_116	127	5129,3085		1594,1941,572	no	coding-synonymous	ALMS1	NM_015120.4		1687,2534,1749	TT,TC,CC		37.5578,20.9071,49.4807		729/4168	73675844	5908,6032	1863	4107	5970	SO:0001819	synonymous_variant	7840	exon8			AGAGTTCGCAGAC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.2187C>T	2.37:g.73675844C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			C|0.465;T|0.535	0.535	strong		0.473	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
EXOSC2	23404	hgsc.bcm.edu	37	9	133579152	133579152	+	Silent	SNP	G	G	A	rs34680820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133579152G>A	ENST00000372358.5	+	9	944	c.873G>A	c.(871-873)caG>caA	p.Q291Q	EXOSC2_ENST00000372351.3_Silent_p.Q261Q|EXOSC2_ENST00000467138.1_3'UTR|EXOSC2_ENST00000546165.1_Silent_p.Q265Q|EXOSC2_ENST00000372352.3_Silent_p.Q283Q			Q13868	EXOS2_HUMAN	exosome component 2	291					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|7S RNA binding (GO:0008312)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		TTTTGGAACAGGAGGGATAAG	0.478													G|||	22	0.00439297	0.0023	0.0043	5008	,	,		20923	0.0		0.0109	False		,,,				2504	0.0051				p.Q291Q	Pancreas(134;1683 1824 10118 27928 31640)	Atlas-SNP	.											.	EXOSC2	15	.	0			c.G873A						PASS	.	G		24,4382	29.9+/-59.1	0,24,2179	119.0	128.0	125.0		873	4.1	1.0	9	dbSNP_126	125	230,8370	93.8+/-155.7	3,224,4073	no	coding-synonymous	EXOSC2	NM_014285.5		3,248,6252	AA,AG,GG		2.6744,0.5447,1.9529		291/294	133579152	254,12752	2203	4300	6503	SO:0001819	synonymous_variant	23404	exon9			GGAACAGGAGGGA	AK001916	CCDS6935.1, CCDS65160.1, CCDS65161.1	9q34	2008-02-05			ENSG00000130713	ENSG00000130713			17097	protein-coding gene	gene with protein product	"""homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4)"""	602238				8600032, 1538749	Standard	XM_005272176		Approved	hRrp4p, Rrp4p, RRP4, p7	uc004bzu.2	Q13868	OTTHUMG00000020811	ENST00000372358.5:c.873G>A	9.37:g.133579152G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	36	13	0.361111	NM_014285	A3KFL3|B4DKK6|Q9NUY4	Silent	SNP	ENST00000372358.5	37	CCDS6935.1																																																																																			G|0.986;A|0.014	0.014	strong		0.478	EXOSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054673.1	NM_014285	
TMEM63A	9725	hgsc.bcm.edu	37	1	226054333	226054333	+	Missense_Mutation	SNP	G	G	A	rs45492299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:226054333G>A	ENST00000366835.3	-	9	886	c.616C>T	c.(616-618)Ctc>Ttc	p.L206F	TMEM63A_ENST00000537914.1_5'UTR|TMEM63A_ENST00000474478.1_5'Flank	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	206				L -> F (in Ref. 1; BAA34512). {ECO:0000305}.	ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					CCCACAGTGAGGAAGAGGTAA	0.552													G|||	841	0.167931	0.0083	0.2205	5008	,	,		19972	0.2956		0.162	False		,,,				2504	0.2209				p.L206F		Atlas-SNP	.											.	TMEM63A	75	.	0			c.C616T						PASS	.	G	PHE/LEU	156,4250	106.5+/-144.9	5,146,2052	122.0	103.0	109.0		616	4.6	1.0	1	dbSNP_127	109	1507,7093	285.5+/-297.2	150,1207,2943	yes	missense	TMEM63A	NM_014698.2	22	155,1353,4995	AA,AG,GG		17.5233,3.5406,12.7864	possibly-damaging	206/808	226054333	1663,11343	2203	4300	6503	SO:0001583	missense	9725	exon9			CAGTGAGGAAGAG		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.616C>T	1.37:g.226054333G>A	ENSP00000355800:p.Leu206Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	150	86	0.573333	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	37	CCDS31042.1	348	0.15934065934065933	8	0.016260162601626018	76	0.20994475138121546	144	0.2517482517482518	120	0.158311345646438	G	20.5	4.006161	0.74932	0.035406	0.175233	ENSG00000196187	ENST00000366835	T	0.44881	0.91	5.49	4.58	0.56647	.	0.058639	0.64402	D	0.000002	T	0.00039	0.0001	M	0.74389	2.26	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.08166	-1.0735	9	0.33141	T	0.24	-36.3683	10.2329	0.43266	0.1611:0.0:0.8389:0.0	rs45492299;rs61756701	206	O94886	TM63A_HUMAN	F	206	ENSP00000355800:L206F	ENSP00000355800:L206F	L	-	1	0	TMEM63A	224120956	1.000000	0.71417	0.987000	0.45799	0.915000	0.54546	4.475000	0.60210	1.323000	0.45263	0.563000	0.77884	CTC	G|0.862;A|0.138	0.138	strong		0.552	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
ZNF479	90827	hgsc.bcm.edu	37	7	57188148	57188148	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:57188148C>T	ENST00000331162.4	-	5	1244	c.974G>A	c.(973-975)tGc>tAc	p.C325Y		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	325					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			CTCACACCTGCAGGGTTTCTC	0.448																																					p.C325Y		Atlas-SNP	.											ZNF479,NS,carcinoma,+1,1	ZNF479	193	1	0			c.G974A						scavenged	.						9.0	9.0	9.0					7																	57188148		1858	3992	5850	SO:0001583	missense	90827	exon5			CACCTGCAGGGTT	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"""Zinc fingers, C2H2-type"", ""-"""	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.974G>A	7.37:g.57188148C>T	ENSP00000333776:p.Cys325Tyr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	153	17	0.111111	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	37	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	t	0.001	-4.081994	0.00002	.	.	ENSG00000185177	ENST00000331162	T	0.12039	2.72	1.01	-2.03	0.07365	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01387	0.0045	N	0.00027	-2.645	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27262	-1.0079	9	0.02654	T	1	.	2.5235	0.04685	0.336:0.2032:0.0:0.4608	.	325	Q96JC4	ZN479_HUMAN	Y	325	ENSP00000333776:C325Y	ENSP00000333776:C325Y	C	-	2	0	ZNF479	57192090	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.435000	0.02423	-1.647000	0.01511	-1.672000	0.00744	TGC	.	.	none		0.448	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10575824	10575824	+	Silent	SNP	C	C	A	rs1970817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:10575824C>A	ENST00000396560.2	+	12	1994	c.1767C>A	c.(1765-1767)ccC>ccA	p.P589P	ATF7IP2_ENST00000543967.1_Silent_p.P133P|ATF7IP2_ENST00000396559.1_3'UTR|ATF7IP2_ENST00000324570.5_3'UTR|ATF7IP2_ENST00000356427.2_Silent_p.P589P	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	589	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						TTTTCAGACCCAATGGCATTG	0.463													C|||	2334	0.466054	0.2958	0.5173	5008	,	,		17249	0.5704		0.5179	False		,,,				2504	0.499				p.P589P		Atlas-SNP	.											ATF7IP2_ENST00000396560,NS,adenoma,0,1	ATF7IP2	40	1	0			c.C1767A						PASS	.	C		1458,2936	470.2+/-355.7	247,964,986	106.0	104.0	104.0		1767	2.7	0.5	16	dbSNP_92	104	4484,4116	590.1+/-392.6	1132,2220,948	no	coding-synonymous	ATF7IP2	NM_024997.2		1379,3184,1934	AA,AC,CC		47.8605,33.1816,45.7288		589/683	10575824	5942,7052	2197	4300	6497	SO:0001819	synonymous_variant	80063	exon12			CAGACCCAATGGC	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1767C>A	16.37:g.10575824C>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	37	CCDS10540.1																																																																																			C|0.529;A|0.471	0.471	strong		0.463	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
UTS2	10911	hgsc.bcm.edu	37	1	7913029	7913029	+	Missense_Mutation	SNP	A	A	G	rs34305100	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7913029A>G	ENST00000361696.5	-	1	66	c.35T>C	c.(34-36)aTa>aCa	p.I12T	UTS2_ENST00000054668.5_Intron|UTS2_ENST00000377516.2_Missense_Mutation_p.I12T	NM_006786.3	NP_006777.1	O95399	UTS2_HUMAN	urotensin 2	12			I -> T (in dbSNP:rs34305100). {ECO:0000269|PubMed:12975309}.		muscle contraction (GO:0006936)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell differentiation (GO:0045597)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of heart rate (GO:0010460)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to testosterone (GO:0033574)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			kidney(1)|lung(4)|urinary_tract(1)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		TAAGAATCCTATGAAAAGCAA	0.413													A|||	416	0.0830671	0.0635	0.0994	5008	,	,		17758	0.0357		0.1839	False		,,,				2504	0.0429				p.I12T		Atlas-SNP	.											UTS2_ENST00000361696,NS,carcinoma,-1,1	UTS2	18	1	0			c.T35C						PASS	.	A	THR/ILE,	330,4076	169.4+/-200.1	11,308,1884	75.0	81.0	79.0		35,	2.8	0.0	1	dbSNP_126	79	1526,7074	285.9+/-297.4	139,1248,2913	yes	missense,intron	UTS2	NM_006786.3,NM_021995.2	89,	150,1556,4797	GG,GA,AA		17.7442,7.4898,14.2703	,	12/125,	7913029	1856,11150	2203	4300	6503	SO:0001583	missense	10911	exon1			AATCCTATGAAAA	AF104118	CCDS90.1, CCDS91.1	1p36	2013-02-28			ENSG00000049247	ENSG00000049247		"""Endogenous ligands"""	12636	protein-coding gene	gene with protein product	"""prepro U-II"""	604097				9861051, 10499587	Standard	NM_021995		Approved	UII, U-II, UCN2, PRO1068	uc001aos.3	O95399	OTTHUMG00000001218	ENST00000361696.5:c.35T>C	1.37:g.7913029A>G	ENSP00000355163:p.Ile12Thr	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	215	118	0.548837	NM_006786	Q5H8X7|Q6UXF6|Q9UKP7	Missense_Mutation	SNP	ENST00000361696.5	37	CCDS91.1	232	0.10622710622710622	29	0.05894308943089431	45	0.12430939226519337	18	0.03146853146853147	140	0.18469656992084432	A	11.02	1.517424	0.27123	0.074898	0.177442	ENSG00000049247	ENST00000377516;ENST00000400910;ENST00000361696	T;T	0.39592	1.07;1.15	5.2	2.83	0.33086	.	0.467176	0.22376	N	0.060863	T	0.00073	0.0002	L	0.38175	1.15	0.58432	P	1.0000000000287557E-6	B;B	0.23806	0.055;0.091	B;B	0.22386	0.018;0.039	T	0.10064	-1.0646	9	0.39692	T	0.17	-1.1173	4.3418	0.11113	0.6983:0.0:0.1556:0.1461	rs34305100	12;12	O95399;Q5H8X8	UTS2_HUMAN;.	T	12	ENSP00000366738:I12T;ENSP00000355163:I12T	ENSP00000355163:I12T	I	-	2	0	UTS2	7835616	0.003000	0.15002	0.000000	0.03702	0.031000	0.12232	1.875000	0.39578	0.370000	0.24538	0.528000	0.53228	ATA	A|0.874;G|0.126	0.126	strong		0.413	UTS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003612.1	NM_006786	
MRGPRX3	117195	hgsc.bcm.edu	37	11	18158958	18158958	+	Missense_Mutation	SNP	C	C	T	rs61733595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18158958C>T	ENST00000396275.2	+	3	570	c.209C>T	c.(208-210)gCg>gTg	p.A70V		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						AACCTGGTCGCGGCCGACTTC	0.567													c|||	38	0.00758786	0.0015	0.0144	5008	,	,		20868	0.0		0.0249	False		,,,				2504	0.001				p.A70V		Atlas-SNP	.											MRGPRX3,colon,carcinoma,-1,1	MRGPRX3	59	1	0			c.C209T						PASS	.	C	VAL/ALA	16,4384	24.3+/-50.5	0,16,2184	97.0	93.0	94.0		209	-2.9	0.0	11	dbSNP_129	94	205,8381	88.9+/-151.2	6,193,4094	yes	missense	MRGPRX3	NM_054031.3	64	6,209,6278	TT,TC,CC		2.3876,0.3636,1.7018	benign	70/323	18158958	221,12765	2200	4293	6493	SO:0001583	missense	117195	exon3			TGGTCGCGGCCGA		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.209C>T	11.37:g.18158958C>T	ENSP00000379571:p.Ala70Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	154	62	0.402597	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	24	0.01098901098901099	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	19	0.025065963060686015	C	6.482	0.457078	0.12283	0.003636	0.023876	ENSG00000179826	ENST00000396275;ENST00000531264	T;T	0.17691	2.26;2.26	1.46	-2.93	0.05598	GPCR, rhodopsin-like superfamily (1);	1.571520	0.03654	N	0.241532	T	0.02970	0.0088	L	0.29908	0.895	0.09310	N	1	B	0.14805	0.011	B	0.15870	0.014	T	0.25398	-1.0133	10	0.06236	T	0.91	.	4.2118	0.10515	0.0:0.3809:0.2485:0.3706	rs61733595	70	Q96LB0	MRGX3_HUMAN	V	70	ENSP00000379571:A70V;ENSP00000436242:A70V	ENSP00000379571:A70V	A	+	2	0	MRGPRX3	18115534	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.038000	0.12144	-1.289000	0.02375	-0.687000	0.03738	GCG	C|0.987;T|0.013	0.013	strong		0.567	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
CYP11B2	1585	hgsc.bcm.edu	37	8	143995743	143995743	+	Silent	SNP	C	C	T	rs4543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143995743C>T	ENST00000323110.2	-	5	893	c.891G>A	c.(889-891)gcG>gcA	p.A297A		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	297					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	GTGACAGTTCCGCCTTCAACA	0.567									Familial Hyperaldosteronism type I				.|||	518	0.103435	0.2466	0.0648	5008	,	,		18807	0.002		0.0765	False		,,,				2504	0.0695				p.A297A		Atlas-SNP	.											.	CYP11B2	107	.	0			c.G891A						PASS	.	C		950,3456		125,700,1378	158.0	131.0	140.0		891	-7.7	0.0	8	dbSNP_52	140	753,7847		38,677,3585	no	coding-synonymous	CYP11B2	NM_000498.3		163,1377,4963	TT,TC,CC		8.7558,21.5615,13.094		297/504	143995743	1703,11303	2203	4300	6503	SO:0001819	synonymous_variant	1585	exon5	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CAGTTCCGCCTTC	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"""Cytochrome P450s"""	2592	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	124080	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"""	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.891G>A	8.37:g.143995743C>T		Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	316	165	0.522152	NM_000498	B0ZBE4|Q16726	Silent	SNP	ENST00000323110.2	37	CCDS6393.1																																																																																			C|0.880;T|0.120	0.120	strong		0.567	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
MMS22L	253714	hgsc.bcm.edu	37	6	97599674	97599674	+	Missense_Mutation	SNP	G	G	A	rs138146580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:97599674G>A	ENST00000275053.4	-	23	3720	c.3455C>T	c.(3454-3456)cCt>cTt	p.P1152L	MMS22L_ENST00000369251.2_Missense_Mutation_p.P1112L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1152					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						CTGGGAGGAAGGTTCTTCTTC	0.433													G|||	37	0.00738818	0.0023	0.0058	5008	,	,		15425	0.0		0.0239	False		,,,				2504	0.0061				p.P1152L		Atlas-SNP	.											.	MMS22L	102	.	0			c.C3455T						PASS	.	G	LEU/PRO	17,4389	24.3+/-50.5	0,17,2186	204.0	203.0	203.0		3455	3.6	1.0	6	dbSNP_134	203	155,8445	73.5+/-136.2	2,151,4147	yes	missense	MMS22L	NM_198468.2	98	2,168,6333	AA,AG,GG		1.8023,0.3858,1.3225	benign	1152/1244	97599674	172,12834	2203	4300	6503	SO:0001583	missense	253714	exon23			GAGGAAGGTTCTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3455C>T	6.37:g.97599674G>A	ENSP00000275053:p.Pro1152Leu	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	184	109	0.592391	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	9.389	1.074903	0.20227	0.003858	0.018023	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.29655	3.93;1.56	5.44	3.59	0.41128	.	0.290094	0.38492	N	0.001666	T	0.09202	0.0227	L	0.56769	1.78	0.44966	D	0.997984	B;B	0.31548	0.328;0.082	B;B	0.27380	0.079;0.036	T	0.13255	-1.0516	10	0.14252	T	0.57	.	3.4047	0.07336	0.1576:0.1261:0.5698:0.1465	.	1112;1152	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1152;1112	ENSP00000275053:P1152L;ENSP00000358254:P1112L	ENSP00000275053:P1152L	P	-	2	0	MMS22L	97706395	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.175000	0.31944	0.606000	0.29965	0.650000	0.86243	CCT	G|0.987;A|0.013	0.013	strong		0.433	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
SEC16B	89866	hgsc.bcm.edu	37	1	177935050	177935050	+	Silent	SNP	T	T	A	rs1889981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177935050T>A	ENST00000308284.6	-	3	479	c.390A>T	c.(388-390)ccA>ccT	p.P130P	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000464631.2_Silent_p.P130P	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	130	Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)		p.P130P(1)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						GCAGCCACTGTGGGTGTCCAT	0.478													T|||	1039	0.207468	0.0772	0.1988	5008	,	,		18014	0.3284		0.2167	False		,,,				2504	0.2556				p.P130P		Atlas-SNP	.											SEC16B,NS,carcinoma,0,1	SEC16B	92	1	1	Substitution - coding silent(1)	stomach(1)	c.A390T						scavenged	.	T		377,3337		17,343,1497	91.0	83.0	85.0		390	-10.7	0.0	1	dbSNP_92	85	1938,6316		231,1476,2420	no	coding-synonymous	SEC16B	NM_033127.2		248,1819,3917	AA,AT,TT		23.4795,10.1508,19.3432		130/1061	177935050	2315,9653	1857	4127	5984	SO:0001819	synonymous_variant	89866	exon3			CCACTGTGGGTGT	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.390A>T	1.37:g.177935050T>A		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			T|0.786;A|0.214	0.214	strong		0.478	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
FBXW9	84261	hgsc.bcm.edu	37	19	12805424	12805424	+	Missense_Mutation	SNP	C	C	T	rs117566511	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12805424C>T	ENST00000380339.3	-	3	698	c.662G>A	c.(661-663)cGa>cAa	p.R221Q	FBXW9_ENST00000587955.1_Missense_Mutation_p.R211Q|FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Missense_Mutation_p.R221Q			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	221					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GGTACTATTTCGCTTAGTGCC	0.562													C|||	59	0.0117812	0.0023	0.0101	5008	,	,		19271	0.0		0.0268	False		,,,				2504	0.0225				p.R221Q		Atlas-SNP	.											.	FBXW9	30	.	0			c.G662A						PASS	.	C	GLN/ARG	21,4183		0,21,2081	61.0	69.0	66.0		662	-5.6	0.0	19	dbSNP_132	66	208,8236		2,204,4016	yes	missense	FBXW9	NM_032301.2	43	2,225,6097	TT,TC,CC		2.4633,0.4995,1.8106	benign	221/459	12805424	229,12419	2102	4222	6324	SO:0001583	missense	84261	exon3			CTATTTCGCTTAG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.662G>A	19.37:g.12805424C>T	ENSP00000369696:p.Arg221Gln	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	93	36	0.387097	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		21	0.009615384615384616	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	15	0.01978891820580475	C	2.365	-0.345652	0.05208	0.004995	0.024633	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.50813	1.74;0.73	4.29	-5.55	0.02536	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.878110	0.09915	N	0.739321	T	0.10981	0.0268	N	0.13371	0.34	0.09310	N	0.999999	B;B;B	0.26258	0.09;0.037;0.145	B;B;B	0.15870	0.013;0.014;0.009	T	0.21895	-1.0232	10	0.13470	T	0.59	-0.0119	8.4494	0.32862	0.0:0.5114:0.2365:0.2521	.	211;221;221	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	Q	221	ENSP00000376945:R221Q;ENSP00000369696:R221Q	ENSP00000369696:R221Q	R	-	2	0	FBXW9	12666424	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.364000	0.07583	-1.163000	0.02793	-0.502000	0.04539	CGA	C|0.986;T|0.014	0.014	strong		0.562	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
FAM81B	153643	hgsc.bcm.edu	37	5	94749723	94749723	+	Silent	SNP	G	G	A	rs7726891	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94749723G>A	ENST00000283357.5	+	4	412	c.366G>A	c.(364-366)gcG>gcA	p.A122A		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	122						nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		ACAACCAGGCGCGTACCATAG	0.502													G|||	1090	0.217652	0.2428	0.2406	5008	,	,		19920	0.1071		0.334	False		,,,				2504	0.1616				p.A122A		Atlas-SNP	.											.	FAM81B	51	.	0			c.G366A						PASS	.	G		1016,2994		129,758,1118	99.0	105.0	103.0		366	1.8	1.0	5	dbSNP_116	103	2417,5941		365,1687,2127	no	coding-synonymous	FAM81B	NM_152548.2		494,2445,3245	AA,AG,GG		28.9184,25.3367,27.7571		122/453	94749723	3433,8935	2005	4179	6184	SO:0001819	synonymous_variant	153643	exon4			CCAGGCGCGTACC		CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.366G>A	5.37:g.94749723G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_152548		Silent	SNP	ENST00000283357.5	37	CCDS43341.1																																																																																			G|0.759;A|0.241	0.241	strong		0.502	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548	
ABL1	25	hgsc.bcm.edu	37	9	133760029	133760029	+	Silent	SNP	C	C	G	rs2229070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760029C>G	ENST00000318560.5	+	11	2733	c.2352C>G	c.(2350-2352)ccC>ccG	p.P784P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	784	Pro-rich.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CGCCTCCCCCCAGGCTGGTGA	0.592			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	534	0.106629	0.2821	0.0865	5008	,	,		18610	0.001		0.0696	False		,,,				2504	0.0307				p.P803P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2409G						PASS	.	C	,	985,3415		107,771,1322	26.0	30.0	28.0		2352,2409	1.6	0.2	9	dbSNP_98	28	622,7976		27,568,3704	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	134,1339,5026	GG,GC,CC		7.2342,22.3864,12.3634	,	784/1131,803/1150	133760029	1607,11391	2200	4299	6499	SO:0001819	synonymous_variant	25	exon11			TCCCCCCAGGCTG	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2352C>G	9.37:g.133760029C>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			C|0.885;G|0.115	0.115	strong		0.592	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
PLD4	122618	hgsc.bcm.edu	37	14	105393556	105393556	+	Missense_Mutation	SNP	G	G	C	rs2841280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105393556G>C	ENST00000392593.4	+	2	247	c.79G>C	c.(79-81)Gag>Cag	p.E27Q	PLD4_ENST00000540372.1_Missense_Mutation_p.E34Q	NM_138790.2	NP_620145.2	Q96BZ4	PLD4_HUMAN	phospholipase D family, member 4	27			E -> Q (in dbSNP:rs2841280).		glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phagocytosis (GO:0006909)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase D activity (GO:0004630)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	13		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00067)|OV - Ovarian serous cystadenocarcinoma(23;0.00976)|Epithelial(46;0.0201)|GBM - Glioblastoma multiforme(11;0.116)			GTGGGACAGAGAGGCTGGCAC	0.657													G|||	2063	0.411941	0.2201	0.4813	5008	,	,		16805	0.5982		0.4692	False		,,,				2504	0.3712				p.E27Q		Atlas-SNP	.											.	PLD4	46	.	0			c.G79C						PASS	.	G	GLN/GLU	832,2894		111,610,1142	7.0	9.0	8.0		79	1.2	0.0	14	dbSNP_100	8	3591,4533		883,1825,1354	no	missense	PLD4	NM_138790.2	29	994,2435,2496	CC,CG,GG		44.2024,22.3296,37.3249	benign	27/507	105393556	4423,7427	1863	4062	5925	SO:0001583	missense	122618	exon2			GACAGAGAGGCTG		CCDS9995.2	14q32.33	2014-01-28	2005-05-20	2005-05-20	ENSG00000166428	ENSG00000166428			23792	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 175"""	C14orf175			Standard	XM_006720024		Approved		uc001ypu.1	Q96BZ4	OTTHUMG00000144167	ENST00000392593.4:c.79G>C	14.37:g.105393556G>C	ENSP00000376372:p.Glu27Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_138790	Q6UWD2	Missense_Mutation	SNP	ENST00000392593.4	37	CCDS9995.2	982	0.44963369963369965	104	0.21138211382113822	160	0.4419889502762431	358	0.6258741258741258	360	0.47493403693931396	G	3.851	-0.031823	0.07543	0.223296	0.442024	ENSG00000166428	ENST00000540372;ENST00000392593;ENST00000557573	T;T;T	0.24723	1.93;1.93;1.84	3.23	1.17	0.20885	.	2.738770	0.02964	U	0.143486	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B;B	0.26483	0.15;0.092	B;B	0.17098	0.017;0.007	T	0.42361	-0.9456	9	0.15066	T	0.55	-6.5022	9.5387	0.39237	0.0:0.416:0.584:0.0	rs2841280;rs11543933;rs2841280	34;27	F5H2B5;Q96BZ4	.;PLD4_HUMAN	Q	34;27;27	ENSP00000438677:E34Q;ENSP00000376372:E27Q;ENSP00000451278:E27Q	ENSP00000376372:E27Q	E	+	1	0	PLD4	104464601	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.448000	0.06820	0.115000	0.18071	0.511000	0.50034	GAG	G|0.554;C|0.446	0.446	strong		0.657	PLD4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000291348.2	NM_138790	
KDM4E	390245	hgsc.bcm.edu	37	11	94759494	94759494	+	Missense_Mutation	SNP	T	T	C	rs16921260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:94759494T>C	ENST00000450979.2	+	1	1073	c.773T>C	c.(772-774)tTc>tCc	p.F258S		NM_001161630.1	NP_001155102.1	B2RXH2	KDM4E_HUMAN	lysine (K)-specific demethylase 4E	258	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.		F -> S (in dbSNP:rs16921260).		histone H3-K9 demethylation (GO:0033169)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|kidney(1)|lung(3)	12						GGGATTCCCTTCAATTGCATG	0.532													T|||	195	0.0389377	0.0174	0.1023	5008	,	,		21147	0.0357		0.0388	False		,,,				2504	0.0266				p.F258S		Atlas-SNP	.											.	KDM4E	60	.	0			c.T773C						PASS	.	T	SER/PHE	41,1343		1,39,652	26.0	26.0	26.0		773	2.2	0.4	11	dbSNP_123	26	109,3073		1,107,1483	yes	missense	KDM4DL	NM_001161630.1	155	2,146,2135	CC,CT,TT		3.4255,2.9624,3.2852	possibly-damaging	258/507	94759494	150,4416	692	1591	2283	SO:0001583	missense	390245	exon1			TTCCCTTCAATTG	BC157851	CCDS44713.1	11q21	2012-03-30	2012-03-28	2012-03-28		ENSG00000235268		"""Chromatin-modifying enzymes / K-demethylases"""	37098	protein-coding gene	gene with protein product			"""lysine (K)-specific demethylase 4D-like"""	KDM4DL		21076780	Standard	NM_001161630		Approved	JMJD2E	uc010ruf.1	B2RXH2		ENST00000450979.2:c.773T>C	11.37:g.94759494T>C	ENSP00000397239:p.Phe258Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_001161630		Missense_Mutation	SNP	ENST00000450979.2	37	CCDS44713.1	89	0.04075091575091575	12	0.024390243902439025	31	0.0856353591160221	21	0.03671328671328671	25	0.032981530343007916	T	12.01	1.809351	0.31961	0.029624	0.034255	ENSG00000235268	ENST00000450979	T	0.71817	-0.6	2.18	2.18	0.27775	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	.	.	.	.	T	0.18882	0.0453	M	0.86651	2.83	0.33996	D	0.649756	D	0.76494	0.999	D	0.71414	0.973	T	0.68269	-0.5453	9	0.72032	D	0.01	-17.8731	8.2694	0.31836	0.0:0.0:0.0:1.0	rs16921260;rs56513502;rs16921260	258	B2RXH2	KD4DL_HUMAN	S	258	ENSP00000397239:F258S	ENSP00000397239:F258S	F	+	2	0	KDM4DL	94399142	0.996000	0.38824	0.369000	0.25952	0.054000	0.15201	3.151000	0.50670	1.264000	0.44198	0.374000	0.22700	TTC	T|0.965;C|0.035	0.035	strong		0.532	KDM4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396649.1	NM_001161630	
ERAP1	51752	hgsc.bcm.edu	37	5	96118866	96118866	+	Missense_Mutation	SNP	C	C	T	rs17482078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:96118866C>T	ENST00000443439.2	-	15	2240	c.2174G>A	c.(2173-2175)cGa>cAa	p.R725Q	ERAP1_ENST00000296754.3_Missense_Mutation_p.R725Q|ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000602972.1_RNA|CTD-2260A17.1_ENST00000512856.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	725			R -> Q (in dbSNP:rs17482078). {ECO:0000269|PubMed:11481040, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:9628581}.		angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		CCGCAGCATTCGCTCTGAGAC	0.532													C|||	504	0.100639	0.0537	0.1239	5008	,	,		18856	0.0575		0.2237	False		,,,				2504	0.0654				p.R725Q		Atlas-SNP	.											.	ERAP1	59	.	0			c.G2174A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	422,3984	205.8+/-227.6	22,378,1803	184.0	156.0	165.0		2174,2174,2174	5.8	1.0	5	dbSNP_123	165	1762,6838	319.9+/-314.4	191,1380,2729	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	43,43,43	213,1758,4532	TT,TC,CC		20.4884,9.5778,16.7922	probably-damaging,probably-damaging,probably-damaging	725/942,725/942,725/949	96118866	2184,10822	2203	4300	6503	SO:0001583	missense	51752	exon15			AGCATTCGCTCTG	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2174G>A	5.37:g.96118866C>T	ENSP00000406304:p.Arg725Gln	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	285	0.1304945054945055	28	0.056910569105691054	48	0.13259668508287292	40	0.06993006993006994	169	0.22295514511873352	C	18.63	3.664349	0.67700	0.095778	0.204884	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.05258	3.47;3.47	5.78	5.78	0.91487	.	0.065264	0.64402	D	0.000020	T	0.00012	0.0000	M	0.76838	2.35	0.09310	P	0.999999367196	B;P;P	0.41673	0.272;0.587;0.759	B;B;B	0.28305	0.027;0.04;0.088	T	0.52373	-0.8584	9	0.30854	T	0.27	.	19.6088	0.95594	0.0:1.0:0.0:0.0	rs17482078;rs17482078	725;725;725	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	Q	725	ENSP00000296754:R725Q;ENSP00000406304:R725Q	ENSP00000296754:R725Q	R	-	2	0	ERAP1	96144622	1.000000	0.71417	0.990000	0.47175	0.504000	0.33889	4.515000	0.60489	2.734000	0.93682	0.563000	0.77884	CGA	C|0.859;T|0.141	0.141	strong		0.532	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
SPTA1	6708	hgsc.bcm.edu	37	1	158592935	158592935	+	Silent	SNP	G	G	A	rs3753068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158592935G>A	ENST00000368147.4	-	43	6138	c.5958C>T	c.(5956-5958)ccC>ccT	p.P1986P		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1986					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.P1986P(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAGTGATCTCGGGAAGTCTCT	0.498													G|||	1555	0.310503	0.4387	0.2478	5008	,	,		17157	0.2044		0.3091	False		,,,				2504	0.2924				p.P1986P		Atlas-SNP	.											SPTA1,mouth,carcinoma,0,1	SPTA1	720	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C5958T						PASS	.	G		1561,2283		303,955,664	290.0	291.0	291.0		5958	-9.6	0.0	1	dbSNP_107	291	2386,5880		341,1704,2088	no	coding-synonymous	SPTA1	NM_003126.2		644,2659,2752	AA,AG,GG		28.8652,40.6087,32.5929		1986/2420	158592935	3947,8163	1922	4133	6055	SO:0001819	synonymous_variant	6708	exon43			GATCTCGGGAAGT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5958C>T	1.37:g.158592935G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	265	263	0.992453	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.680;A|0.320	0.320	strong		0.498	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
PCDHA9	9752	hgsc.bcm.edu	37	5	140229368	140229368	+	Missense_Mutation	SNP	G	G	C	rs251355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140229368G>C	ENST00000532602.1	+	1	2321	c.1288G>C	c.(1288-1290)Ggg>Cgg	p.G430R	PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.G430R|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	430	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		G -> R (in dbSNP:rs251355).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCGCGGGACGGGGGCTCGCC	0.632													.|||	2264	0.452077	0.2458	0.4481	5008	,	,		17136	0.4563		0.5109	False		,,,				2504	0.6687				p.G430R	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1288C						PASS	.	G	ARG/GLY,,,,,,,,,,,ARG/GLY	1187,3205		207,773,1216	83.0	80.0	81.0		1288,,,,,,,,,,,1288	3.6	0.4	5	dbSNP_79	81	4569,3975		1385,1799,1088	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1	125,,,,,,,,,,,125	1592,2572,2304	CC,CG,GG		46.5239,27.0264,44.496	,,,,,,,,,,,	430/843,,,,,,,,,,,430/951	140229368	5756,7180	2196	4272	6468	SO:0001583	missense	9752	exon1			CGGGACGGGGGCT	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1288G>C	5.37:g.140229368G>C	ENSP00000436042:p.Gly430Arg	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	290	198	0.682759	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	975	0.44642857142857145	132	0.2682926829268293	192	0.5303867403314917	265	0.4632867132867133	386	0.5092348284960422	G	6.223	0.409284	0.11812	0.270264	0.534761	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.51071	0.72;0.72	3.6	3.6	0.41247	Cadherin (5);Cadherin-like (1);	0.272289	0.18265	U	0.146497	T	0.00012	0.0000	L	0.50847	1.595	0.80722	P	0.0	P;B	0.37955	0.612;0.212	B;B	0.37422	0.249;0.068	T	0.50259	-0.8849	9	0.51188	T	0.08	.	12.5672	0.56316	0.0:0.1685:0.8314:0.0	rs251355;rs17844328	430;430	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	R	430	ENSP00000436042:G430R;ENSP00000367362:G430R	ENSP00000367362:G430R	G	+	1	0	PCDHA9	140209552	0.000000	0.05858	0.356000	0.25785	0.073000	0.16967	-1.232000	0.02936	1.977000	0.57605	0.313000	0.20887	GGG	G|0.548;C|0.452	0.452	strong		0.632	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
MUC4	4585	hgsc.bcm.edu	37	3	195508249	195508249	+	Missense_Mutation	SNP	A	A	G	rs201846606		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508249A>G	ENST00000463781.3	-	2	10661	c.10202T>C	c.(10201-10203)gTa>gCa	p.V3401A	MUC4_ENST00000475231.1_Missense_Mutation_p.V3401A|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3401A(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATACTGAGGAAGT	0.577																																					p.V3401A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,7	MUC4	1505	7	3	Substitution - Missense(3)	stomach(2)|kidney(1)	c.T10202C						scavenged	.						33.0	25.0	27.0					3																	195508249		685	1579	2264	SO:0001583	missense	4585	exon2			GTGGATACTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10202T>C	3.37:g.195508249A>G	ENSP00000417498:p.Val3401Ala	Somatic	281	4	0.0142349		WXS	Illumina HiSeq	Phase_I	406	57	0.140394	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	0.030	-1.338402	0.01287	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.54;1.48	0.743	-1.49	0.08718	.	.	.	.	.	T	0.07908	0.0198	N	0.02539	-0.55	0.09310	N	1	B	0.33494	0.414	B	0.19946	0.027	T	0.18366	-1.0339	8	.	.	.	.	2.8398	0.05525	0.2532:0.0:0.4936:0.2531	.	3273	E7ESK3	.	A	3401	ENSP00000417498:V3401A;ENSP00000420243:V3401A	.	V	-	2	0	MUC4	196993028	0.000000	0.05858	0.011000	0.14972	0.012000	0.07955	-0.712000	0.05013	-1.995000	0.00971	-2.001000	0.00444	GTA	A|0.500;G|0.500	0.500	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SEMG2	6407	hgsc.bcm.edu	37	20	43850525	43850525	+	Silent	SNP	A	A	G	rs2233898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43850525A>G	ENST00000372769.3	+	2	342	c.252A>G	c.(250-252)caA>caG	p.Q84Q		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	84	Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				AAAGTCAGCAATATGATTTGA	0.368													A|||	497	0.0992412	0.0885	0.0922	5008	,	,		21932	0.0317		0.161	False		,,,				2504	0.1247				p.Q84Q		Atlas-SNP	.											SEMG2,caecum,carcinoma,0,1	SEMG2	92	1	0			c.A252G						PASS	.	A		476,3930	223.0+/-239.6	30,416,1757	119.0	110.0	113.0		252	1.3	0.0	20	dbSNP_98	113	1520,7080	286.3+/-297.7	123,1274,2903	no	coding-synonymous	SEMG2	NM_003008.2		153,1690,4660	GG,GA,AA		17.6744,10.8034,15.3468		84/583	43850525	1996,11010	2203	4300	6503	SO:0001819	synonymous_variant	6407	exon2			TCAGCAATATGAT		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.252A>G	20.37:g.43850525A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Silent	SNP	ENST00000372769.3	37	CCDS13346.1																																																																																			A|0.863;G|0.137	0.137	strong		0.368	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
GRM6	2916	hgsc.bcm.edu	37	5	178413947	178413947	+	Silent	SNP	T	T	C	rs11746675	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178413947T>C	ENST00000517717.1	-	8	1430	c.1392A>G	c.(1390-1392)ggA>ggG	p.G464G	GRM6_ENST00000231188.5_Silent_p.G464G|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	464					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CGGGCGCATCTCCGTTCTCGT	0.647													T|||	2682	0.535543	0.3971	0.6066	5008	,	,		17555	0.5863		0.6382	False		,,,				2504	0.5143				p.G464G		Atlas-SNP	.											.	GRM6	149	.	0			c.A1392G						PASS	.	T		1911,2495	546.7+/-377.1	419,1073,711	72.0	60.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1392	-2.8	0.8	5	dbSNP_120	64	5482,3118	653.9+/-401.1	1739,2004,557	yes	coding-synonymous	GRM6	NM_000843.3		2158,3077,1268	CC,CT,TT		36.2558,43.3727,43.157		464/878	178413947	7393,5613	2203	4300	6503	SO:0001819	synonymous_variant	2916	exon7			CGCATCTCCGTTC	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1392A>G	5.37:g.178413947T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			T|0.434;C|0.566	0.566	strong		0.647	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
CSNK2A3	283106	hgsc.bcm.edu	37	11	11374269	11374269	+	Missense_Mutation	SNP	A	A	G	rs2071460	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:11374269A>G	ENST00000528848.2	-	1	635	c.398T>C	c.(397-399)aTt>aCt	p.I133T	RP11-567I13.1_ENST00000526867.1_RNA|GALNT18_ENST00000227756.4_Intron	NM_001256686.1	NP_001243615.1	Q8NEV1	CSK23_HUMAN	casein kinase 2, alpha 3 polypeptide	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> T (in a lung carcinoma sample; somatic mutation; shows greater kinase activity, provides a cell growth advantage and increases its interaction with the PML tumor suppressor protein and PML degradation). {ECO:0000269|PubMed:20625391}.		positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)										GTAAAATCGAATATCATAGTC	0.408													-|||	2106	0.420527	0.1906	0.4553	5008	,	,		19710	0.5248		0.4791	False		,,,				2504	0.5389				p.I133T		Atlas-SNP	.											.	.	.	.	0			c.T398C						PASS	.																																			SO:0001583	missense	283106	exon1			AATCGAATATCAT	X64692	CCDS59224.1	11p15.3	2013-01-18	2013-01-17	2013-01-17	ENSG00000254598	ENSG00000254598			2458	protein-coding gene	gene with protein product			"""casein kinase 2, alpha 1 polypeptide pseudogene"""	CSNK2A1P		12102635, 1610905, 20625391	Standard	NM_001256686		Approved		uc001mjp.4	Q8NEV1	OTTHUMG00000165708	ENST00000528848.2:c.398T>C	11.37:g.11374269A>G	ENSP00000473553:p.Ile133Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	139	63	0.453237	NM_001256686		Missense_Mutation	SNP	ENST00000528848.2	37	CCDS59224.1																																																																																			A|0.875;G|0.125	0.125	weak		0.408	CSNK2A3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385850.3	NM_001256686	
GTF3C1	2975	hgsc.bcm.edu	37	16	27472772	27472772	+	Missense_Mutation	SNP	C	C	T	rs2228248	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:27472772C>T	ENST00000356183.4	-	37	6244	c.6229G>A	c.(6229-6231)Gag>Aag	p.E2077K	GTF3C1_ENST00000561623.1_Missense_Mutation_p.E2052K|GTF3C1_ENST00000567806.1_5'Flank	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	2077			E -> K (in dbSNP:rs2228248).		5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						ATGGGGCTCTCGTCCAGGCTG	0.612													C|||	349	0.0696885	0.0098	0.1844	5008	,	,		19233	0.001		0.16	False		,,,				2504	0.047				p.E2077K		Atlas-SNP	.											.	GTF3C1	210	.	0			c.G6229A						PASS	.		LYS/GLU	168,4226	111.6+/-149.8	1,166,2030	97.0	88.0	91.0		6229	5.2	0.0	16	dbSNP_98	91	1299,7301	256.8+/-281.1	91,1117,3092	yes	missense	GTF3C1	NM_001520.3	56	92,1283,5122	TT,TC,CC		15.1047,3.8234,11.2898	possibly-damaging	2077/2110	27472772	1467,11527	2197	4300	6497	SO:0001583	missense	2975	exon37			GGCTCTCGTCCAG	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.6229G>A	16.37:g.27472772C>T	ENSP00000348510:p.Glu2077Lys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	191	0.08745421245421245	7	0.014227642276422764	59	0.16298342541436464	0	0.0	125	0.16490765171503957	C	18.29	3.590500	0.66219	0.038234	0.151047	ENSG00000077235	ENST00000356183	T	0.25579	1.79	5.22	5.22	0.72569	.	0.349225	0.29676	N	0.011495	T	0.00109	0.0003	M	0.63428	1.95	0.80722	P	0.0	P;P	0.51791	0.695;0.948	B;B	0.39840	0.051;0.311	T	0.08046	-1.0741	9	0.66056	D	0.02	-20.8177	15.5443	0.76081	0.0:1.0:0.0:0.0	rs2228248;rs17788232;rs52802181;rs58904899;rs2228248	2077;2052	Q12789;Q12789-3	TF3C1_HUMAN;.	K	2077	ENSP00000348510:E2077K	ENSP00000348510:E2077K	E	-	1	0	GTF3C1	27380273	0.504000	0.26123	0.005000	0.12908	0.028000	0.11728	3.221000	0.51215	2.450000	0.82876	0.556000	0.70494	GAG	C|0.897;T|0.103	0.103	strong		0.612	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
CCDC176	80127	hgsc.bcm.edu	37	14	74523869	74523869	+	Missense_Mutation	SNP	A	A	G	rs3742809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:74523869A>G	ENST00000394009.3	+	11	1609	c.1486A>G	c.(1486-1488)Aaa>Gaa	p.K496E	CCDC176_ENST00000553773.1_Missense_Mutation_p.K221E|CCDC176_ENST00000492247.2_Missense_Mutation_p.K40E|AC005484.5_ENST00000492026.1_RNA|ALDH6A1_ENST00000553458.1_3'UTR	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	496			K -> E (in dbSNP:rs3742809).		motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											GCTTCAAGATAAAATCTTCAT	0.398													A|||	1210	0.241613	0.1566	0.1671	5008	,	,		19313	0.2371		0.1849	False		,,,				2504	0.4724				p.K496E		Atlas-SNP	.											.	.	.	.	0			c.A1486G						PASS	.	A	GLU/LYS	733,3673	301.0+/-286.6	66,601,1536	76.0	76.0	76.0		1486	2.7	0.8	14	dbSNP_107	76	1566,7034	292.6+/-300.9	136,1294,2870	yes	missense	C14orf45	NM_025057.2	56	202,1895,4406	GG,GA,AA		18.2093,16.6364,17.6765	benign	496/530	74523869	2299,10707	2203	4300	6503	SO:0001583	missense	80127	exon11			CAAGATAAAATCT	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 45"""	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.1486A>G	14.37:g.74523869A>G	ENSP00000377577:p.Lys496Glu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_025057	Q0P604|Q9H5P8	Missense_Mutation	SNP	ENST00000394009.3	37	CCDS32119.2	408	0.18681318681318682	70	0.14227642276422764	64	0.17679558011049723	137	0.2395104895104895	137	0.18073878627968337	A	9.915	1.210595	0.22289	0.166364	0.182093	ENSG00000119636	ENST00000394009;ENST00000553773;ENST00000492247	T;T;T	0.49720	2.29;0.94;0.77	4.59	2.71	0.32032	.	0.659026	0.12998	N	0.421864	T	0.00012	0.0000	N	0.22421	0.69	0.29472	P	0.8569869999999999	B	0.02656	0.0	B	0.04013	0.001	T	0.22521	-1.0214	9	0.22109	T	0.4	1.0849	8.9085	0.35539	0.1716:0.6698:0.1585:0.0	rs3742809;rs52797532;rs59742664;rs3742809	496	Q8ND07	CN045_HUMAN	E	496;221;40	ENSP00000377577:K496E;ENSP00000451097:K221E;ENSP00000451020:K40E	ENSP00000377577:K496E	K	+	1	0	C14orf45	73593622	0.912000	0.30974	0.783000	0.31826	0.680000	0.39746	0.991000	0.29654	0.640000	0.30582	-1.290000	0.01357	AAA	G|0.185;N|0.001	0.185	strong		0.398	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
TTN	7273	hgsc.bcm.edu	37	2	179605725	179605725	+	Missense_Mutation	SNP	T	T	C	rs34070843	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179605725T>C	ENST00000591111.1	-	46	11508	c.11284A>G	c.(11284-11286)Att>Gtt	p.I3762V	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I3908V|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I3716V|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I3841V|TTN_ENST00000589042.1_Missense_Mutation_p.I4079V			Q8WZ42	TITIN_HUMAN	titin	33926			I -> V. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTTTCAAAATGGTGTCTTTT	0.433													T|||	81	0.0161741	0.0	0.0202	5008	,	,		21621	0.0		0.0268	False		,,,				2504	0.0409				p.I4079V		Atlas-SNP	.											.	TTN	18412	.	0			c.A12235G						PASS	.	T	VAL/ILE,,VAL/ILE,VAL/ILE	20,3700		0,20,1840	125.0	121.0	122.0		11146,,11521,11722	-1.7	0.0	2	dbSNP_126	122	152,8056		1,150,3953	yes	missense,intron,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,,29,29	1,170,5793	CC,CT,TT		1.8519,0.5376,1.442	,,,	3716/26927,,3841/27052,3908/27119	179605725	172,11756	1860	4104	5964	SO:0001583	missense	7273	exon48			TCAAAATGGTGTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11284A>G	2.37:g.179605725T>C	ENSP00000465570:p.Ile3762Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		20	0.009157509157509158	0	0.0	7	0.019337016574585635	0	0.0	13	0.017150395778364115	T	4.390	0.072015	0.08436	0.005376	0.018519	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.60920	0.23;0.15;0.16	5.37	-1.66	0.08265	.	.	.	.	.	T	0.23572	0.0570	L	0.27053	0.805	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.22243	-1.0222	9	0.87932	D	0	.	5.8073	0.18448	0.0:0.2752:0.2348:0.49	rs34070843	3716;3841;3908	D3DPF9;E7EQE6;E7ET18	.;.;.	V	3716;3908;3841;3716	ENSP00000434586:I3716V;ENSP00000340554:I3908V;ENSP00000352154:I3841V	ENSP00000340554:I3908V	I	-	1	0	TTN	179313970	0.018000	0.18449	0.023000	0.16930	0.061000	0.15899	0.033000	0.13754	-0.441000	0.07201	-0.290000	0.09829	ATT	T|0.989;C|0.011	0.011	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZFP41	286128	hgsc.bcm.edu	37	8	144332045	144332045	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144332045C>T	ENST00000330701.4	+	2	401	c.32C>T	c.(31-33)aCg>aTg	p.T11M	ZFP41_ENST00000522452.1_Missense_Mutation_p.T11M|ZFP41_ENST00000520584.1_Missense_Mutation_p.T11M	NM_173832.4	NP_776193.1	Q8N8Y5	ZFP41_HUMAN	ZFP41 zinc finger protein	11					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|lung(4)|ovary(1)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			AAAAAGAAGACGCCGACCCCA	0.592																																					p.T11M		Atlas-SNP	.											ZFP41,NS,carcinoma,0,1	ZFP41	25	1	0			c.C32T						PASS	.						26.0	29.0	28.0					8																	144332045		2200	4299	6499	SO:0001583	missense	286128	exon2			AGAAGACGCCGAC		CCDS6397.1	8q24.3	2013-01-08	2012-11-27		ENSG00000181638	ENSG00000181638		"""Zinc fingers, C2H2-type"""	26786	protein-coding gene	gene with protein product			"""zinc finger protein 41 homolog (mouse)"""			11214971	Standard	NM_173832		Approved	FLJ38705, FLJ00028, ZNF753	uc003yxw.4	Q8N8Y5	OTTHUMG00000164951	ENST00000330701.4:c.32C>T	8.37:g.144332045C>T	ENSP00000327427:p.Thr11Met	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_173832	D3DWJ5	Missense_Mutation	SNP	ENST00000330701.4	37	CCDS6397.1	.	.	.	.	.	.	.	.	.	.	C	9.340	1.062804	0.19987	.	.	ENSG00000181638	ENST00000520584;ENST00000330701;ENST00000522452	T;T;T	0.06371	3.31;3.31;3.31	2.64	-1.62	0.08372	.	.	.	.	.	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	1	B	0.27013	0.166	B	0.12837	0.008	T	0.42310	-0.9459	9	0.66056	D	0.02	-0.6933	0.4835	0.00552	0.1961:0.3496:0.1927:0.2616	.	11	Q8N8Y5	ZFP41_HUMAN	M	11	ENSP00000430465:T11M;ENSP00000327427:T11M;ENSP00000428966:T11M	ENSP00000327427:T11M	T	+	2	0	ZFP41	144403420	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.428000	0.07339	-0.339000	0.08088	ACG	.	.	none		0.592	ZFP41-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381114.2	NM_173832	
TRPM1	4308	hgsc.bcm.edu	37	15	31330313	31330313	+	Silent	SNP	A	A	G	rs12913672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:31330313A>G	ENST00000256552.6	-	19	2520	c.2373T>C	c.(2371-2373)taT>taC	p.Y791Y	RP11-348B17.1_ENST00000558755.1_RNA|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Silent_p.Y769Y|TRPM1_ENST00000542188.1_Silent_p.Y808Y	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AGAAATCATCATATGTGCGAA	0.388													A|||	914	0.182508	0.2678	0.2219	5008	,	,		18787	0.0079		0.2913	False		,,,				2504	0.1074				p.Y808Y		Atlas-SNP	.											.	TRPM1	183	.	0			c.T2424C						PASS	.	A		919,2787		113,693,1047	97.0	88.0	91.0		2307	-2.7	0.1	15	dbSNP_121	91	2128,6046		278,1572,2237	no	coding-synonymous	TRPM1	NM_002420.4		391,2265,3284	GG,GA,AA		26.0338,24.7976,25.6481		769/1604	31330313	3047,8833	1853	4087	5940	SO:0001819	synonymous_variant	4308	exon18			ATCATCATATGTG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2373T>C	15.37:g.31330313A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			A|0.799;G|0.201	0.201	strong		0.388	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
GPAT2	150763	hgsc.bcm.edu	37	2	96688929	96688929	+	Missense_Mutation	SNP	G	G	A	rs201647131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:96688929G>A	ENST00000434632.1	-	20	2533	c.2074C>T	c.(2074-2076)Cgc>Tgc	p.R692C	GPAT2_ENST00000453542.1_Missense_Mutation_p.R621C|FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000359548.4_Missense_Mutation_p.R692C|GPAT2_ENST00000377137.3_Intron			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	692					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerol-3-phosphate metabolic process (GO:0006072)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.R692C(3)		NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						CTGAGCAGGCGGCAGAGGAAA	0.652																																					p.R692C		Atlas-SNP	.											GPAT2,NS,adenocarcinoma,0,4	GPAT2	46	4	3	Substitution - Missense(3)	large_intestine(1)|NS(1)|skin(1)	c.C2074T						scavenged	.						14.0	17.0	16.0					2																	96688929		1816	4045	5861	SO:0001583	missense	150763	exon19			GCAGGCGGCAGAG	BC042847	CCDS42714.1	2q11.2	2010-05-04			ENSG00000186281	ENSG00000186281			27168	protein-coding gene	gene with protein product	"""cancer/testis antigen 123"""					12477932	Standard	NM_207328		Approved	CT123	uc010yuf.1	Q6NUI2	OTTHUMG00000155208	ENST00000434632.1:c.2074C>T	2.37:g.96688929G>A	ENSP00000389395:p.Arg692Cys	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	385	115	0.298701	NM_207328	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	37	CCDS42714.1	152	0.0695970695970696	8	0.016260162601626018	16	0.04419889502762431	27	0.0472027972027972	101	0.13324538258575197	g	16.45	3.127649	0.56721	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542	T;T;T	0.80480	-1.38;-1.38;-0.41	5.44	5.44	0.79542	.	0.381151	0.27411	N	0.019488	T	0.02727	0.0082	L	0.50333	1.59	0.80722	D	1	P;D;P;B	0.54207	0.584;0.965;0.953;0.354	B;B;B;B	0.42062	0.093;0.374;0.267;0.065	T	0.41840	-0.9486	10	0.66056	D	0.02	-11.9956	16.7485	0.85479	0.0:0.0:1.0:0.0	.	621;698;692;621	E9PE95;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;GPAT2_HUMAN;.	C	692;692;621	ENSP00000352547:R692C;ENSP00000389395:R692C;ENSP00000393770:R621C	ENSP00000352547:R692C	R	-	1	0	GPAT2	96052656	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.041000	0.49807	2.569000	0.86673	0.637000	0.83480	CGC	A|1.000;|0.000	1.000	weak		0.652	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328	
NOD2	64127	hgsc.bcm.edu	37	16	50746228	50746228	+	Silent	SNP	G	G	T	rs104895495		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50746228G>T	ENST00000300589.2	+	4	2511	c.2406G>T	c.(2404-2406)gtG>gtT	p.V802V	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	802					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				ACAACTCTGTGGGTGACATTG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		21477	0.0		0.001	False		,,,				2504	0.0				p.V802V		Atlas-SNP	.											.	NOD2	118	.	0			c.G2406T						PASS	.	G		2,4394	4.2+/-10.8	0,2,2196	113.0	115.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2406	3.3	1.0	16	dbSNP_132	114	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	NOD2	NM_022162.1		0,18,6480	TT,TG,GG		0.186,0.0455,0.1385		802/1041	50746228	18,12978	2198	4300	6498	SO:0001819	synonymous_variant	64127	exon4			CTCTGTGGGTGAC	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2406G>T	16.37:g.50746228G>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	147	66	0.44898	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Silent	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	6.792	0.515223	0.12944	4.55E-4	0.00186	ENSG00000167207	ENST00000534057	.	.	.	5.29	3.28	0.37604	.	.	.	.	.	T	0.54983	0.1892	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47262	-0.9131	4	.	.	.	.	6.42	0.21738	0.0846:0.0:0.5875:0.3279	.	.	.	.	W	42	.	.	G	+	1	0	NOD2	49303729	0.786000	0.28738	0.995000	0.50966	0.966000	0.64601	-0.179000	0.09768	0.575000	0.29434	0.555000	0.69702	GGG	G|0.998;T|0.002	0.002	strong		0.602	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
HRSP12	10247	hgsc.bcm.edu	37	8	99115082	99115082	+	Silent	SNP	C	C	T	rs11537947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:99115082C>T	ENST00000254878.3	-	6	546	c.402G>A	c.(400-402)acG>acA	p.T134T		NM_005836.2	NP_005827.1	P52758	UK114_HUMAN	heat-responsive protein 12	134					regulation of translational termination (GO:0006449)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deaminase activity (GO:0019239)|endonuclease activity (GO:0004519)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	6	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			ATAGTGATGCCGTTGTCAGTG	0.348													T|||	308	0.0615016	0.0877	0.0648	5008	,	,		19758	0.001		0.1034	False		,,,				2504	0.0429				p.T134T		Atlas-SNP	.											.	HRSP12	13	.	0			c.G402A						PASS	.	T		329,4077	796.4+/-415.4	11,307,1885	140.0	136.0	138.0		402	-0.2	0.0	8	dbSNP_120	138	687,7913	788.5+/-407.6	25,637,3638	no	coding-synonymous	HRSP12	NM_005836.2		36,944,5523	TT,TC,CC		7.9884,7.4671,7.8118		134/138	99115082	1016,11990	2203	4300	6503	SO:0001819	synonymous_variant	10247	exon6			TGATGCCGTTGTC	BC008418	CCDS6276.1	8q22	2014-05-09			ENSG00000132541	ENSG00000132541			16897	protein-coding gene	gene with protein product	"""translational inhibitor p14.5"""	602487				8973653, 9405234, 20817725	Standard	NM_005836		Approved	UK114, P14.5, PSP	uc003yii.1	P52758	OTTHUMG00000164670	ENST00000254878.3:c.402G>A	8.37:g.99115082C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_005836	Q6FHU9|Q6IBG0	Silent	SNP	ENST00000254878.3	37	CCDS6276.1	127|127	0.05815018315018315|0.05815018315018315	29|29	0.05894308943089431|0.05894308943089431	25|25	0.06906077348066299|0.06906077348066299	0|0	0.0|0.0	73|73	0.09630606860158311|0.09630606860158311	T|T	5.053|5.053	0.195374|0.195374	0.09599|0.09599	0.074671|0.074671	0.079884|0.079884	ENSG00000132541|ENSG00000132541	ENST00000520507|ENST00000521560	.|.	.|.	.|.	5.49|5.49	-0.158|-0.158	0.13383|0.13383	.|.	.|.	.|.	.|.	.|.	T|T	0.00524|0.00524	0.0017|0.0017	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18147|0.18147	-1.0346|-1.0346	3|3	.|.	.|.	.|.	.|.	1.1412|1.1412	0.01766|0.01766	0.1291:0.2341:0.2659:0.3709|0.1291:0.2341:0.2659:0.3709	rs11537947;rs11537947|rs11537947;rs11537947	.|.	.|.	.|.	S|Q	145|124	.|.	.|.	G|R	-|-	1|2	0|0	HRSP12|HRSP12	99184258|99184258	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.154000|0.154000	0.21943|0.21943	-0.269000|-0.269000	0.08596|0.08596	-0.121000|-0.121000	0.11787|0.11787	-0.254000|-0.254000	0.11334|0.11334	GGC|CGG	C|0.923;T|0.077	0.077	strong		0.348	HRSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379687.1	NM_005836	
NME8	51314	hgsc.bcm.edu	37	7	37896896	37896896	+	Silent	SNP	G	G	A	rs3213976	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:37896896G>A	ENST00000199447.4	+	6	591	c.219G>A	c.(217-219)gtG>gtA	p.V73V	EPDR1_ENST00000476620.1_5'UTR|NME8_ENST00000440017.1_Silent_p.V73V	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	73	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										ACAACATTGTGACTTTGCAGC	0.299													G|||	332	0.0662939	0.0076	0.1268	5008	,	,		16942	0.0764		0.1173	False		,,,				2504	0.0399				p.V73V		Atlas-SNP	.											.	.	.	.	0			c.G219A						PASS	.	G		129,4277	94.4+/-133.1	2,125,2076	110.0	109.0	109.0		219	0.7	0.9	7	dbSNP_106	109	940,7658	206.3+/-248.5	43,854,3402	no	coding-synonymous	TXNDC3	NM_016616.4		45,979,5478	AA,AG,GG		10.9328,2.9278,8.2205		73/589	37896896	1069,11935	2203	4299	6502	SO:0001819	synonymous_variant	51314	exon6			CATTGTGACTTTG	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.219G>A	7.37:g.37896896G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	37	CCDS5452.1																																																																																			G|0.912;A|0.088	0.088	strong		0.299	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
TMEM214	54867	hgsc.bcm.edu	37	2	27260469	27260469	+	Missense_Mutation	SNP	G	G	A	rs1124649	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:27260469G>A	ENST00000238788.9	+	9	1113	c.1051G>A	c.(1051-1053)Gtg>Atg	p.V351M	TMEM214_ENST00000404032.3_Missense_Mutation_p.V306M	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	351			V -> M (in dbSNP:rs1124649).		apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CCGACTGAAAGTGCTGGCATT	0.542													G|||	1518	0.303115	0.4478	0.4006	5008	,	,		18858	0.0655		0.3091	False		,,,				2504	0.2771				p.V351M		Atlas-SNP	.											.	TMEM214	41	.	0			c.G1051A						PASS	.	G	MET/VAL,MET/VAL	1640,2310		333,974,668	111.0	116.0	115.0		916,1051	5.7	1.0	2	dbSNP_86	115	2550,5770		395,1760,2005	yes	missense,missense	TMEM214	NM_001083590.1,NM_017727.4	21,21	728,2734,2673	AA,AG,GG		30.649,41.519,34.1483	probably-damaging,probably-damaging	306/645,351/690	27260469	4190,8080	1975	4160	6135	SO:0001583	missense	54867	exon9			CTGAAAGTGCTGG		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.1051G>A	2.37:g.27260469G>A	ENSP00000238788:p.Val351Met	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	217	99	0.456221	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	37	CCDS42664.1	605	0.27701465201465203	208	0.42276422764227645	141	0.38950276243093923	33	0.057692307692307696	223	0.2941952506596306	G	19.92	3.915582	0.73098	0.41519	0.30649	ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397	T;T	0.55588	0.51;0.51	5.69	5.69	0.88448	.	0.057286	0.64402	D	0.000001	T	0.00012	0.0000	M	0.74258	2.255	0.09310	P	0.999999747868	D;D	0.89917	1.0;0.998	D;D	0.81914	0.995;0.991	T	0.20874	-1.0262	9	0.52906	T	0.07	-21.5626	17.5913	0.87997	0.0:0.0:1.0:0.0	rs1124649;rs17529988;rs60677582;rs1124649	306;351	Q6NUQ4-2;Q6NUQ4	.;TM214_HUMAN	M	351;306;91	ENSP00000238788:V351M;ENSP00000384417:V306M	ENSP00000238788:V351M	V	+	1	0	TMEM214	27113973	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.222000	0.95196	2.700000	0.92200	0.561000	0.74099	GTG	G|0.713;A|0.287	0.287	strong		0.542	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727	
ADAM29	11086	hgsc.bcm.edu	37	4	175899075	175899075	+	Missense_Mutation	SNP	C	C	T	rs140568401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175899075C>T	ENST00000359240.3	+	5	3069	c.2399C>T	c.(2398-2400)aCa>aTa	p.T800I	ADAM29_ENST00000445694.1_Missense_Mutation_p.T800I|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.T800I|ADAM29_ENST00000404450.4_Missense_Mutation_p.T800I	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	800	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCTCCTGTGACACCCTCCCAG	0.562																																					p.T800I	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,NS,carcinoma,-1,1	ADAM29	262	1	0			c.C2399T						PASS	.						140.0	130.0	133.0					4																	175899075		2203	4300	6503	SO:0001583	missense	11086	exon4			CTGTGACACCCTC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2399C>T	4.37:g.175899075C>T	ENSP00000352177:p.Thr800Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	209	67	0.320574	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	5.685	0.311023	0.10733	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01933	4.55;4.55;4.55;4.55	0.727	-1.45	0.08828	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.25351	0.124	B	0.16722	0.016	T	0.47812	-0.9088	8	.	.	.	.	2.9588	0.05886	0.2545:0.5364:0.0:0.2091	.	800	Q9UKF5	ADA29_HUMAN	I	800	ENSP00000352177:T800I;ENSP00000414544:T800I;ENSP00000384229:T800I;ENSP00000423517:T800I	.	T	+	2	0	ADAM29	176135650	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-2.202000	0.01235	-1.087000	0.03081	-0.712000	0.03635	ACA	C|0.991;T|0.008	0.008	strong		0.562	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
ZNF33A	7581	hgsc.bcm.edu	37	10	38343772	38343772	+	Missense_Mutation	SNP	G	G	C	rs41276138	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:38343772G>C	ENST00000458705.2	+	5	875	c.717G>C	c.(715-717)gaG>gaC	p.E239D	ZNF33A_ENST00000307441.9_Missense_Mutation_p.E239D|ZNF33A_ENST00000432900.2_Missense_Mutation_p.E246D|ZNF33A_ENST00000374618.3_Missense_Mutation_p.E240D|ZNF33A_ENST00000469037.2_Intron			Q06730	ZN33A_HUMAN	zinc finger protein 33A	239					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AGAAGAGAGAGAACGCAGAAG	0.383													G|||	42	0.00838658	0.0	0.0058	5008	,	,		20492	0.0		0.0189	False		,,,				2504	0.0194				p.E240D		Atlas-SNP	.											.	ZNF33A	103	.	0			c.G720C						PASS	.	G	ASP/GLU,ASP/GLU	19,4387	24.3+/-50.5	0,19,2184	83.0	78.0	80.0		720,717	-3.3	0.0	10	dbSNP_127	80	205,8395	87.9+/-150.2	1,203,4096	yes	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	45,45	1,222,6280	CC,CG,GG		2.3837,0.4312,1.7223	benign,benign	240/812,239/811	38343772	224,12782	2203	4300	6503	SO:0001583	missense	7581	exon5			GAGAGAGAACGCA	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.717G>C	10.37:g.38343772G>C	ENSP00000387713:p.Glu239Asp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	21	0.009615384615384616	0	0.0	2	0.0055248618784530384	0	0.0	19	0.025065963060686015	G	10.30	1.313109	0.23908	0.004312	0.023837	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.05855	3.4;3.39;3.38;3.38	2.33	-3.27	0.05048	.	0.520434	0.14668	N	0.305548	T	0.01061	0.0035	N	0.22421	0.69	0.09310	N	1	P;P;B	0.40794	0.729;0.61;0.051	B;B;B	0.39027	0.288;0.104;0.009	T	0.34601	-0.9822	10	0.51188	T	0.08	.	2.7746	0.05344	0.4568:0.0:0.3322:0.2109	rs41276138	246;239;240	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	D	240;246;239;239	ENSP00000363747:E240D;ENSP00000402467:E246D;ENSP00000387713:E239D;ENSP00000304268:E239D	ENSP00000304268:E239D	E	+	3	2	ZNF33A	38383778	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.833000	0.04396	-0.488000	0.06726	0.460000	0.39030	GAG	G|0.984;C|0.016	0.016	strong		0.383	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
TPTE2	93492	hgsc.bcm.edu	37	13	20006680	20006680	+	Silent	SNP	G	G	C	rs201767816		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:20006680G>C	ENST00000400230.2	-	16	1199	c.1155C>G	c.(1153-1155)ctC>ctG	p.L385L	TPTE2_ENST00000390680.2_Silent_p.L308L|TPTE2_ENST00000382977.4_Silent_p.L385L|TPTE2_ENST00000382978.1_Silent_p.L345L|TPTE2_ENST00000400103.2_Silent_p.L274L|TPTE2_ENST00000382975.4_Silent_p.L345L|TPTE2_ENST00000457266.2_Silent_p.L274L|TPTE2_ENST00000255310.6_Silent_p.L308L			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	385	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L308L(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TCCAGTTGTAGAGATGTTTCA	0.343																																					p.L385L		Atlas-SNP	.											TPTE2,mouth,carcinoma,0,1	TPTE2	225	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C1155G						scavenged	.						34.0	33.0	34.0					13																	20006680		2202	4291	6493	SO:0001819	synonymous_variant	93492	exon17			GTTGTAGAGATGT	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.1155C>G	13.37:g.20006680G>C		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	206	13	0.0631068	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Silent	SNP	ENST00000400230.2	37	CCDS45014.1																																																																																			G|0.999;C|0.001	0.001	weak		0.343	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
DOK7	285489	hgsc.bcm.edu	37	4	3494600	3494600	+	Missense_Mutation	SNP	A	A	G	rs6811423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:3494600A>G	ENST00000340083.5	+	7	952	c.887A>G	c.(886-888)cAg>cGg	p.Q296R	DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR|DOK7_ENST00000389653.2_Missense_Mutation_p.Q296R	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	296	Ser-rich.		Q -> R (in dbSNP:rs6811423). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:22661499}.		neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		AGCACGTCACAGGAGGGGCCT	0.687													.|||	1092	0.218051	0.0272	0.1398	5008	,	,		13805	0.504		0.2286	False		,,,				2504	0.226				p.Q296R		Atlas-SNP	.											DOK7,NS,carcinoma,0,1	DOK7	44	1	0			c.A887G						scavenged	.	A	,ARG/GLN	244,4150		11,222,1964	22.0	20.0	21.0		,887	1.4	0.5	4	dbSNP_116	21	1775,6813		196,1383,2715	yes	utr-3,missense	DOK7	NM_001164673.1,NM_173660.4	,43	207,1605,4679	GG,GA,AA		20.6684,5.553,15.5523	,benign	,296/505	3494600	2019,10963	2197	4294	6491	SO:0001583	missense	285489	exon7			CGTCACAGGAGGG	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.887A>G	4.37:g.3494600A>G	ENSP00000344432:p.Gln296Arg	Somatic	133	2	0.0150376		WXS	Illumina HiSeq	Phase_I	115	49	0.426087	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Missense_Mutation	SNP	ENST00000340083.5	37	CCDS3370.2	559	0.25595238095238093	16	0.032520325203252036	60	0.16574585635359115	308	0.5384615384615384	175	0.23087071240105542	A	0.215	-1.032992	0.02029	0.05553	0.206684	ENSG00000175920	ENST00000389653;ENST00000340083	T;T	0.65916	-0.18;-0.09	3.93	1.42	0.22433	.	0.685034	0.14082	N	0.342604	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	P;B	0.34724	0.465;0.0	B;B	0.28011	0.085;0.0	T	0.48514	-0.9029	9	0.18276	T	0.48	-18.3256	5.3934	0.16257	0.5641:0.3427:0.0932:0.0	rs6811423;rs57140233;rs6811423	158;296	Q18PE1-2;Q18PE1	.;DOK7_HUMAN	R	296	ENSP00000374304:Q296R;ENSP00000344432:Q296R	ENSP00000344432:Q296R	Q	+	2	0	DOK7	3464398	0.995000	0.38212	0.462000	0.27118	0.151000	0.21798	1.651000	0.37302	0.123000	0.18342	0.402000	0.26972	CAG	A|0.810;G|0.190	0.190	strong		0.687	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
QARS	5859	hgsc.bcm.edu	37	3	49141116	49141116	+	Silent	SNP	G	G	A	rs5030795	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49141116G>A	ENST00000306125.6	-	4	736	c.399C>T	c.(397-399)caC>caT	p.H133H	QARS_ENST00000414533.1_Silent_p.H122H|QARS_ENST00000420147.2_Silent_p.H151H|QARS_ENST00000470225.1_5'Flank			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	133					brain development (GO:0007420)|gene expression (GO:0010467)|glutaminyl-tRNA aminoacylation (GO:0006425)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|glutamine-tRNA ligase activity (GO:0004819)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)	GCTGGGGCCGGTGCCTGTTAA	0.547													G|||	265	0.0529153	0.0076	0.0648	5008	,	,		18745	0.0506		0.1153	False		,,,				2504	0.044				p.H133H		Atlas-SNP	.											.	QARS	55	.	0			c.C399T						PASS	.	G		107,4299	82.9+/-121.4	0,107,2096	30.0	33.0	32.0		399	2.7	0.8	3	dbSNP_113	32	927,7673	202.8+/-246.0	51,825,3424	no	coding-synonymous	QARS	NM_005051.1		51,932,5520	AA,AG,GG		10.7791,2.4285,7.9502		133/776	49141116	1034,11972	2203	4300	6503	SO:0001819	synonymous_variant	5859	exon4			GGGCCGGTGCCTG	X76013	CCDS2788.1, CCDS63633.1	3p21.31	2011-07-01			ENSG00000172053	ENSG00000172053	6.1.1.18	"""Aminoacyl tRNA synthetases / Class I"""	9751	protein-coding gene	gene with protein product	"""glutamine tRNA ligase"""	603727				8078941, 10393422	Standard	NM_005051		Approved		uc003cvx.4	P47897	OTTHUMG00000156774	ENST00000306125.6:c.399C>T	3.37:g.49141116G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_005051	B4DWJ2	Silent	SNP	ENST00000306125.6	37	CCDS2788.1																																																																																			G|0.924;A|0.076	0.076	strong		0.547	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051	
PLRG1	5356	hgsc.bcm.edu	37	4	155461113	155461113	+	Silent	SNP	T	T	C	rs7671792	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155461113T>C	ENST00000499023.2	-	11	1158	c.1032A>G	c.(1030-1032)caA>caG	p.Q344Q	PLRG1_ENST00000393905.2_Silent_p.Q344Q|PLRG1_ENST00000302078.5_Silent_p.Q335Q	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	344					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				CTGTAATAATTTGTGGTTCTG	0.338													T|||	1160	0.231629	0.1536	0.1888	5008	,	,		18870	0.1438		0.325	False		,,,				2504	0.362				p.Q344Q		Atlas-SNP	.											.	PLRG1	43	.	0			c.A1032G						PASS	.	T	,	788,3618	317.4+/-295.1	72,644,1487	201.0	178.0	186.0		1005,1032	-11.7	0.2	4	dbSNP_116	186	2829,5771	445.7+/-361.0	459,1911,1930	no	coding-synonymous,coding-synonymous	PLRG1	NM_001201564.1,NM_002669.3	,	531,2555,3417	CC,CT,TT		32.8953,17.8847,27.8102	,	335/506,344/515	155461113	3617,9389	2203	4300	6503	SO:0001819	synonymous_variant	5356	exon11			AATAATTTGTGGT	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1032A>G	4.37:g.155461113T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	37	CCDS34083.1																																																																																			T|0.738;C|0.262	0.262	strong		0.338	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
TMEM159	57146	hgsc.bcm.edu	37	16	21185384	21185384	+	Missense_Mutation	SNP	G	G	A	rs1046480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:21185384G>A	ENST00000233047.4	+	4	787	c.319G>A	c.(319-321)Ggc>Agc	p.G107S	TMEM159_ENST00000451578.2_Missense_Mutation_p.G131S|TMEM159_ENST00000261388.3_Missense_Mutation_p.G107S|TMEM159_ENST00000572258.1_Intron|TMEM159_ENST00000572599.1_Missense_Mutation_p.G107S			Q96B96	TM159_HUMAN	transmembrane protein 159	107			G -> S (in dbSNP:rs1046480). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				large_intestine(3)|lung(2)|ovary(1)	6				GBM - Glioblastoma multiforme(48;0.0972)		CTGTGGTTTGGGCTTCGTATC	0.502													G|||	474	0.0946486	0.0076	0.1427	5008	,	,		16105	0.001		0.2465	False		,,,				2504	0.1186				p.G107S		Atlas-SNP	.											.	TMEM159	14	.	0			c.G319A						PASS	.	G	SER/GLY	238,4162	137.3+/-173.1	2,234,1964	240.0	178.0	199.0		319	-0.9	0.2	16	dbSNP_86	199	2187,6413	373.8+/-337.2	270,1647,2383	yes	missense	TMEM159	NM_020422.4	56	272,1881,4347	AA,AG,GG		25.4302,5.4091,18.6538	benign	107/162	21185384	2425,10575	2200	4300	6500	SO:0001583	missense	57146	exon4			GGTTTGGGCTTCG	AF070596	CCDS10595.1	16p12.2	2008-02-05			ENSG00000011638	ENSG00000011638			30136	protein-coding gene	gene with protein product		611304				8619474, 9110174, 15589683	Standard	NM_020422		Approved	promethin	uc002dif.4	Q96B96	OTTHUMG00000131559	ENST00000233047.4:c.319G>A	16.37:g.21185384G>A	ENSP00000233047:p.Gly107Ser	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	262	134	0.51145	NM_020422	A6NMA9|B4DEC1|O00323	Missense_Mutation	SNP	ENST00000233047.4	37	CCDS10595.1	251	0.11492673992673992	6	0.012195121951219513	63	0.17403314917127072	1	0.0017482517482517483	181	0.23878627968337732	G	13.53	2.265960	0.40095	0.054091	0.254302	ENSG00000011638	ENST00000233047;ENST00000261388;ENST00000451578	T;T;T	0.18016	2.24;2.24;2.24	6.07	-0.927	0.10451	.	0.596486	0.16623	N	0.206381	T	0.00012	0.0000	L	0.41824	1.3	0.39035	P	0.03997499999999998	B;B	0.20052	0.041;0.041	B;B	0.16722	0.016;0.016	T	0.41106	-0.9527	9	0.32370	T	0.25	-6.7976	4.4753	0.11733	0.2849:0.0:0.4758:0.2393	rs1046480;rs52830007;rs57715043;rs1046480	131;107	B4DEC1;Q96B96	.;TM159_HUMAN	S	107;107;131	ENSP00000233047:G107S;ENSP00000261388:G107S;ENSP00000409879:G131S	ENSP00000233047:G107S	G	+	1	0	TMEM159	21092885	1.000000	0.71417	0.244000	0.24202	0.720000	0.41350	1.291000	0.33330	-0.358000	0.08162	0.650000	0.86243	GGC	G|0.845;A|0.155	0.155	strong		0.502	TMEM159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254421.1	NM_020422	
KIAA2018	205717	hgsc.bcm.edu	37	3	113377361	113377361	+	Silent	SNP	A	A	G	rs9813630	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:113377361A>G	ENST00000478658.1	-	5	3185	c.3168T>C	c.(3166-3168)aaT>aaC	p.N1056N	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.N1056N			Q68DE3	K2018_HUMAN	KIAA2018	1056						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						CTCTATCATCATTGTTCATCA	0.403													G|||	1524	0.304313	0.4387	0.2709	5008	,	,		22325	0.2183		0.3569	False		,,,				2504	0.181				p.N1056N		Atlas-SNP	.											.	KIAA2018	180	.	0			c.T3168C						PASS	.	G		1536,2330		312,912,709	149.0	138.0	142.0		3168	-2.3	0.2	3	dbSNP_119	142	2792,5470		492,1808,1831	no	coding-synonymous	KIAA2018	NM_001009899.2		804,2720,2540	GG,GA,AA		33.7933,39.731,35.686		1056/2246	113377361	4328,7800	1933	4131	6064	SO:0001819	synonymous_variant	205717	exon7			ATCATCATTGTTC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.3168T>C	3.37:g.113377361A>G		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			A|0.657;G|0.343	0.343	strong		0.403	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
MCMBP	79892	hgsc.bcm.edu	37	10	121586827	121586827	+	IGR	SNP	A	A	G	rs56055506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:121586827A>G	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Silent_p.R978R|INPP5F_ENST00000369080.3_Silent_p.R368R	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein						DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.R978R(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						CAGAGACCAGATCTGTGTCTC	0.433													G|||	1062	0.212061	0.1203	0.1254	5008	,	,		22364	0.1915		0.164	False		,,,				2504	0.4683				p.R978R		Atlas-SNP	.											INPP5F,NS,carcinoma,0,1	INPP5F	112	1	1	Substitution - coding silent(1)	stomach(1)	c.A2934G						PASS	.	G		571,3835	773.0+/-413.9	30,511,1662	74.0	70.0	71.0		2934	-5.6	0.0	10	dbSNP_129	71	1509,7091	748.2+/-407.3	142,1225,2933	no	coding-synonymous	INPP5F	NM_014937.3		172,1736,4595	GG,GA,AA		17.5465,12.9596,15.9926		978/1133	121586827	2080,10926	2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			GACCAGATCTGTG	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159		10.37:g.121586827A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																			A|0.835;G|0.165	0.165	strong		0.433	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
MED16	10025	hgsc.bcm.edu	37	19	880066	880066	+	Silent	SNP	G	G	A	rs34799086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:880066G>A	ENST00000589119.1	-	7	1223	c.1224C>T	c.(1222-1224)tcC>tcT	p.S408S	MED16_ENST00000395808.3_Silent_p.S408S|MED16_ENST00000269814.4_Silent_p.S408S|MED16_ENST00000606828.1_Intron|MED16_ENST00000325464.1_Silent_p.S408S|MED16_ENST00000312090.6_Silent_p.S408S			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	408					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGGGGCCGCGGAGCTGTAGA	0.682													G|||	1390	0.277556	0.1551	0.2248	5008	,	,		13045	0.5863		0.1262	False		,,,				2504	0.318				p.S408S		Atlas-SNP	.											MED16,NS,carcinoma,0,1	MED16	61	1	0			c.C1224T						PASS	.	G		579,3755		35,509,1623	18.0	19.0	19.0		1224	-8.5	0.3	19	dbSNP_126	19	1162,7386		81,1000,3193	no	coding-synonymous	MED16	NM_005481.2		116,1509,4816	AA,AG,GG		13.5938,13.3595,13.515		408/878	880066	1741,11141	2167	4274	6441	SO:0001819	synonymous_variant	10025	exon8			GGCCGCGGAGCTG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1224C>T	19.37:g.880066G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	40	14	0.35	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			G|0.821;A|0.179	0.179	strong		0.682	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
GNB1L	54584	hgsc.bcm.edu	37	22	19808874	19808874	+	Missense_Mutation	SNP	G	G	A	rs36070348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:19808874G>A	ENST00000329517.6	-	3	241	c.5C>T	c.(4-6)aCg>aTg	p.T2M	GNB1L_ENST00000405009.1_Missense_Mutation_p.T2M|GNB1L_ENST00000460402.1_Intron|GNB1L_ENST00000403325.1_Missense_Mutation_p.T2M	NM_053004.2	NP_443730.1	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	2					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|social behavior (GO:0035176)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)				breast(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	12	Colorectal(54;0.0993)					GCAGGGGGCCGTCATGCTGGG	0.657													G|||	162	0.0323482	0.0015	0.0115	5008	,	,		17868	0.0139		0.0288	False		,,,				2504	0.1115				p.T2M		Atlas-SNP	.											.	GNB1L	34	.	0			c.C5T						PASS	.	G	MET/THR	31,4373		0,31,2171	39.0	48.0	44.0		5	3.7	0.2	22	dbSNP_126	44	246,8348		3,240,4054	yes	missense	GNB1L	NM_053004.2	81	3,271,6225	AA,AG,GG		2.8625,0.7039,2.1311	benign	2/328	19808874	277,12721	2202	4297	6499	SO:0001583	missense	54584	exon3			GGGGCCGTCATGC	AF238328	CCDS13768.1	22q11.2	2013-05-21			ENSG00000185838	ENSG00000185838		"""WD repeat domain containing"""	4397	protein-coding gene	gene with protein product		610778				11072084	Standard	NM_053004		Approved	GY2, WDR14	uc002zqf.1	Q9BYB4	OTTHUMG00000150279	ENST00000329517.6:c.5C>T	22.37:g.19808874G>A	ENSP00000331313:p.Thr2Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_053004	Q9H2S2|Q9H4M4	Missense_Mutation	SNP	ENST00000329517.6	37	CCDS13768.1	33	0.01510989010989011	0	0.0	2	0.0055248618784530384	11	0.019230769230769232	20	0.026385224274406333	G	15.97	2.990646	0.54041	0.007039	0.028625	ENSG00000185838	ENST00000329517;ENST00000403325;ENST00000405009;ENST00000453108	T;T;T;T	0.62941	1.12;1.12;-0.01;0.47	4.73	3.7	0.42460	.	2.937810	0.03052	N	0.154737	T	0.24160	0.0585	N	0.08118	0	0.09310	N	1	B	0.15473	0.013	B	0.14578	0.011	T	0.34304	-0.9834	10	0.62326	D	0.03	0.5498	11.0733	0.48016	0.0886:0.0:0.9114:0.0	rs36070348;rs61752241	2	Q9BYB4	GNB1L_HUMAN	M	2	ENSP00000331313:T2M;ENSP00000385154:T2M;ENSP00000384626:T2M;ENSP00000389412:T2M	ENSP00000331313:T2M	T	-	2	0	GNB1L	18188874	0.226000	0.23696	0.248000	0.24265	0.378000	0.30076	0.600000	0.24104	1.104000	0.41587	0.313000	0.20887	ACG	G|0.983;A|0.017	0.017	strong		0.657	GNB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075202.1		
ACSBG2	81616	hgsc.bcm.edu	37	19	6187805	6187805	+	Missense_Mutation	SNP	G	G	C	rs17856651	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6187805G>C	ENST00000586696.1	+	13	2152	c.1876G>C	c.(1876-1878)Gaa>Caa	p.E626Q	ACSBG2_ENST00000591403.1_Missense_Mutation_p.E626Q|RFX2_ENST00000587700.1_5'Flank|ACSBG2_ENST00000252669.5_Missense_Mutation_p.E626Q|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000588485.1_Missense_Mutation_p.E439Q|ACSBG2_ENST00000588304.1_Missense_Mutation_p.E576Q			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	626			E -> Q (in dbSNP:rs17856651). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACAGAGGATTGAAAAGTGGGT	0.507													C|||	471	0.0940495	0.2284	0.0331	5008	,	,		18262	0.0407		0.0338	False		,,,				2504	0.0726				p.E626Q		Atlas-SNP	.											.	ACSBG2	83	.	0			c.G1876C						PASS	.	C	GLN/GLU	803,3603	750.4+/-412.1	76,651,1476	189.0	171.0	177.0		1876	4.4	0.0	19	dbSNP_123	177	298,8302	805.9+/-407.3	3,292,4005	yes	missense	ACSBG2	NM_030924.3	29	79,943,5481	CC,CG,GG		3.4651,18.2251,8.4653	benign	626/667	6187805	1101,11905	2203	4300	6503	SO:0001583	missense	81616	exon13			AGGATTGAAAAGT		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1876G>C	19.37:g.6187805G>C	ENSP00000465589:p.Glu626Gln	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	152	59	0.388158	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	191	0.08745421245421245	128	0.2601626016260163	12	0.03314917127071823	23	0.04020979020979021	28	0.036939313984168866	C	1.504	-0.551263	0.03996	0.182251	0.034651	ENSG00000130377	ENST00000252669	T	0.09163	3.01	5.46	4.42	0.53409	.	0.795410	0.10142	N	0.710752	T	0.00012	0.0000	N	0.00002	-3.585	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41520	-0.9504	9	0.02654	T	1	-13.6155	10.1432	0.42747	0.0:0.7875:0.1377:0.0748	rs17856651;rs17856651	598;626	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	Q	626	ENSP00000252669:E626Q	ENSP00000252669:E626Q	E	+	1	0	ACSBG2	6138805	1.000000	0.71417	0.012000	0.15200	0.382000	0.30200	5.759000	0.68785	0.692000	0.31613	-0.120000	0.15030	GAA	G|0.919;C|0.081	0.081	strong		0.507	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
PHKG1	5260	hgsc.bcm.edu	37	7	56149362	56149362	+	Silent	SNP	C	C	T	rs11238393	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:56149362C>T	ENST00000297373.2	-	9	1073	c.879G>A	c.(877-879)gtG>gtA	p.V293V	PHKG1_ENST00000537360.1_Silent_p.V239V|PHKG1_ENST00000452681.2_Silent_p.V325V|PHKG1_ENST00000489604.1_5'Flank	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	293					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321)			endometrium(1)|large_intestine(1)|lung(5)	7	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GCACTTCCTCCACCAAGTACT	0.607													C|||	749	0.149561	0.0613	0.2147	5008	,	,		17366	0.0714		0.2237	False		,,,				2504	0.227				p.V325V	Melanoma(184;580 2064 5329 24177 35303)	Atlas-SNP	.											.	PHKG1	38	.	0			c.G975A						PASS	.	C		350,4056	180.1+/-208.5	18,314,1871	37.0	39.0	38.0		879	-1.4	1.0	7	dbSNP_120	38	1921,6679	332.8+/-320.3	208,1505,2587	no	coding-synonymous	PHKG1	NM_006213.3		226,1819,4458	TT,TC,CC		22.3372,7.9437,17.4612		293/388	56149362	2271,10735	2203	4300	6503	SO:0001819	synonymous_variant	5260	exon10			TTCCTCCACCAAG	X80590	CCDS5525.1, CCDS59057.1	7p11.2	2009-07-10			ENSG00000164776	ENSG00000164776	2.7.11.19		8930	protein-coding gene	gene with protein product		172470		PHKG		8530014	Standard	NM_001258459		Approved		uc011kdb.2	Q16816	OTTHUMG00000023869	ENST00000297373.2:c.879G>A	7.37:g.56149362C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_001258459	B7Z1D0|F5H2S1|Q75LP5	Silent	SNP	ENST00000297373.2	37	CCDS5525.1																																																																																			C|0.839;T|0.161	0.161	strong		0.607	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1	NM_006213	
GLYATL3	389396	hgsc.bcm.edu	37	6	49479775	49479775	+	Silent	SNP	A	A	T	rs1480615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:49479775A>T	ENST00000371197.4	+	2	185	c.72A>T	c.(70-72)tcA>tcT	p.S24S		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	24						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						TTCCTGAATCACTCAAGGTAC	0.313													A|||	2271	0.453474	0.3608	0.3631	5008	,	,		14524	0.378		0.6362	False		,,,				2504	0.5327				p.S24S		Atlas-SNP	.											GLYATL3,trunk,malignant_melanoma,+1,1	GLYATL3	19	1	0			c.A72T						PASS	.	A		562,822		112,338,242	165.0	139.0	147.0		72	1.7	1.0	6	dbSNP_88	147	2062,1120		673,716,202	no	coding-synonymous	GLYATL3	NM_001010904.1		785,1054,444	TT,TA,AA		35.198,40.6069,42.5318		24/289	49479775	2624,1942	692	1591	2283	SO:0001819	synonymous_variant	389396	exon2			TGAATCACTCAAG		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.72A>T	6.37:g.49479775A>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_001010904		Silent	SNP	ENST00000371197.4	37	CCDS47440.1																																																																																			T|0.431;N|0.000	0.431	strong		0.313	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346712	140346712	+	Silent	SNP	T	T	C	rs155808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140346712T>C	ENST00000289269.5	+	1	893	c.361T>C	c.(361-363)Ttg>Ctg	p.L121L	PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	121	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGCTCAGCTTGGAAGTGCT	0.627													T|||	1800	0.359425	0.2239	0.402	5008	,	,		19004	0.5486		0.3419	False		,,,				2504	0.3354				p.L121L	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.T361C						PASS	.	T	,,,,,,,,,,,,,,,,,,	1108,3298	373.4+/-320.8	147,814,1242	36.0	38.0	38.0		,361,,,,,,,,,,,,,,,,,361	0.5	1.0	5	dbSNP_79	38	2917,5683	435.7+/-358.1	487,1943,1870	yes	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	634,2757,3112	CC,CT,TT		33.9186,25.1475,30.9473	,,,,,,,,,,,,,,,,,,	,121/1008,,,,,,,,,,,,,,,,,121/885	140346712	4025,8981	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			CTCAGCTTGGAAG	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.361T>C	5.37:g.140346712T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	59	16	0.271186	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			T|0.675;C|0.325	0.325	strong		0.627	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
DPPA4	55211	hgsc.bcm.edu	37	3	109047928	109047928	+	Silent	SNP	C	C	T	rs1163439	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:109047928C>T	ENST00000335658.6	-	6	741	c.687G>A	c.(685-687)agG>agA	p.R229R	DPPA4_ENST00000478791.1_5'Flank	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	229					lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.R229R(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						CCACACACCACCTGACACCTG	0.512													C|||	782	0.15615	0.2224	0.2061	5008	,	,		18104	0.1429		0.0497	False		,,,				2504	0.1544				p.R229R		Atlas-SNP	.											DPPA4,NS,carcinoma,0,1	DPPA4	56	1	1	Substitution - coding silent(1)	stomach(1)	c.G687A						PASS	.	C		884,3522	340.7+/-306.4	96,692,1415	51.0	49.0	50.0		687	2.1	0.7	3	dbSNP_87	50	421,8179	130.5+/-188.4	8,405,3887	no	coding-synonymous	DPPA4	NM_018189.3		104,1097,5302	TT,TC,CC		4.8953,20.0635,10.0338		229/305	109047928	1305,11701	2203	4300	6503	SO:0001819	synonymous_variant	55211	exon6			ACACCACCTGACA	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.687G>A	3.37:g.109047928C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	169	93	0.550296	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Silent	SNP	ENST00000335658.6	37	CCDS33814.1																																																																																			C|0.885;T|0.115	0.115	strong		0.512	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	
CROCC	9696	hgsc.bcm.edu	37	1	17265601	17265601	+	Silent	SNP	C	C	T	rs146792981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17265601C>T	ENST00000375541.5	+	12	1641	c.1572C>T	c.(1570-1572)atC>atT	p.I524I	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TCGCCCTGATCCACTCCGCCC	0.751													c|||	82	0.0163738	0.0038	0.0303	5008	,	,		10936	0.0		0.0447	False		,,,				2504	0.0112				p.I524I		Atlas-SNP	.											CROCC,NS,haematopoietic_neoplasm,0,1	CROCC	185	1	0			c.C1572T						PASS	.						6.0	6.0	6.0					1																	17265601		2025	3910	5935	SO:0001819	synonymous_variant	9696	exon12			CCTGATCCACTCC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1572C>T	1.37:g.17265601C>T		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			C|0.984;T|0.016	0.016	strong		0.751	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
ZSWIM5	57643	hgsc.bcm.edu	37	1	45500064	45500064	+	Missense_Mutation	SNP	C	C	T	rs182892990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45500064C>T	ENST00000359600.5	-	11	2574	c.2369G>A	c.(2368-2370)cGt>cAt	p.R790H	AL359473.1_ENST00000583502.1_RNA	NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	790						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					GCGAGGATAACGGCTGGGCAC	0.517													C|||	9	0.00179712	0.0	0.0101	5008	,	,		19192	0.0		0.002	False		,,,				2504	0.0				p.R790H		Atlas-SNP	.											.	ZSWIM5	72	.	0			c.G2369A						PASS	.	C	HIS/ARG	0,4164		0,0,2082	123.0	124.0	124.0		2369	4.6	1.0	1		124	6,8430		0,6,4212	yes	missense	ZSWIM5	NM_020883.1	29	0,6,6294	TT,TC,CC		0.0711,0.0,0.0476	possibly-damaging	790/1186	45500064	6,12594	2082	4218	6300	SO:0001583	missense	57643	exon11			GGATAACGGCTGG	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"""Zinc fingers, SWIM-type"""	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.2369G>A	1.37:g.45500064C>T	ENSP00000352614:p.Arg790His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	82	23	0.280488	NM_020883	Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	37	CCDS41319.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	c	35	5.453739	0.96223	0.0	7.11E-4	ENSG00000162415	ENST00000359600	T	0.49432	0.78	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.77103	2.36	0.80722	D	1	D	0.60160	0.987	P	0.50049	0.629	T	0.69281	-0.5186	10	0.66056	D	0.02	-8.8461	18.2179	0.89893	0.0:1.0:0.0:0.0	.	790	Q9P217	ZSWM5_HUMAN	H	790	ENSP00000352614:R790H	ENSP00000352614:R790H	R	-	2	0	ZSWIM5	45272651	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.561000	0.82288	2.479000	0.83701	0.563000	0.77884	CGT	C|0.999;T|0.001	0.001	strong		0.517	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581	
TNRC18	84629	hgsc.bcm.edu	37	7	5396715	5396715	+	Missense_Mutation	SNP	T	T	C	rs35508364	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5396715T>C	ENST00000430969.1	-	16	5374	c.5026A>G	c.(5026-5028)Aac>Gac	p.N1676D	TNRC18_ENST00000399537.4_Missense_Mutation_p.N1676D	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1676							chromatin binding (GO:0003682)	p.N1676D(1)|p.N731D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCCTTCCTGTTCTTCCCCAGC	0.567													C|||	1865	0.372404	0.4939	0.3156	5008	,	,		15116	0.1597		0.4791	False		,,,				2504	0.3579				p.N1676D		Atlas-SNP	.											TNRC18_ENST00000430969,NS,carcinoma,0,2	TNRC18	311	2	2	Substitution - Missense(2)	stomach(2)	c.A5026G						PASS	.	C	ASP/ASN	679,705		183,313,196	57.0	51.0	53.0		5026	4.6	1.0	7	dbSNP_126	53	1477,1705		340,797,454	yes	missense	TNRC18	NM_001080495.2	23	523,1110,650	CC,CT,TT		46.4173,49.0607,47.2186	benign	1676/2969	5396715	2156,2410	692	1591	2283	SO:0001583	missense	84629	exon16			TCCTGTTCTTCCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.5026A>G	7.37:g.5396715T>C	ENSP00000395538:p.Asn1676Asp	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	202	108	0.534653	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	809	0.37042124542124544	235	0.47764227642276424	120	0.3314917127071823	70	0.12237762237762238	384	0.5065963060686016	c	4.760	0.141296	0.09083	0.490607	0.464173	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.39229	2.89;2.89;1.09	5.52	4.64	0.57946	.	0.000000	0.47093	N	0.000245	T	0.00012	0.0000	N	0.00289	-1.7	0.58432	P	8.000000000008E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44982	-0.9292	9	0.07325	T	0.83	.	7.7425	0.28849	0.0:0.7244:0.1333:0.1423	rs35508364;rs59846759;rs61745137	731;1676	A8MSW5;O15417	.;TNC18_HUMAN	D	1676;1676;731;166	ENSP00000382452:N1676D;ENSP00000395538:N1676D;ENSP00000395990:N166D	ENSP00000382452:N1676D	N	-	1	0	TNRC18	5363241	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	1.454000	0.35178	0.724000	0.32296	-0.215000	0.12644	AAC	T|0.609;C|0.391	0.391	strong		0.567	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
LIFR	3977	hgsc.bcm.edu	37	5	38510603	38510603	+	Silent	SNP	G	G	A	rs61748202	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:38510603G>A	ENST00000263409.4	-	7	1116	c.954C>T	c.(952-954)acC>acT	p.T318T	LIFR_ENST00000503088.1_5'UTR|LIFR_ENST00000453190.2_Silent_p.T318T	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	318					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					TGTTATCTTCGGTTGTAAAAA	0.348			T	PLAG1	salivary adenoma								G|||	10	0.00199681	0.0	0.0058	5008	,	,		18085	0.0		0.004	False		,,,				2504	0.002				p.T318T	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.C954T						PASS	.	G	,	6,4400	12.9+/-30.5	0,6,2197	77.0	75.0	75.0		954,954	1.6	0.0	5	dbSNP_129	75	41,8559	27.4+/-76.7	0,41,4259	no	coding-synonymous,coding-synonymous	LIFR	NM_001127671.1,NM_002310.5	,	0,47,6456	AA,AG,GG		0.4767,0.1362,0.3614	,	318/1098,318/1098	38510603	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	3977	exon7			ATCTTCGGTTGTA	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.954C>T	5.37:g.38510603G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	135	52	0.385185	NM_002310	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																			G|0.997;A|0.003	0.003	strong		0.348	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
HDAC9	9734	hgsc.bcm.edu	37	7	18767343	18767343	+	Silent	SNP	A	A	G	rs1178127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:18767343A>G	ENST00000432645.2	+	12	1863	c.1863A>G	c.(1861-1863)ccA>ccG	p.P621P	HDAC9_ENST00000441542.2_Silent_p.P624P|HDAC9_ENST00000401921.1_Silent_p.P580P|HDAC9_ENST00000406451.4_Silent_p.P621P	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	621					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	TACCTCACCCAGCAATGGACC	0.552													A|||	1652	0.329872	0.2133	0.2997	5008	,	,		18396	0.5159		0.2565	False		,,,				2504	0.3926				p.P624P		Atlas-SNP	.											.	HDAC9	560	.	0			c.A1872G						PASS	.	A	,,	806,3178		85,636,1271	45.0	50.0	48.0		1863,1863,1872	2.7	1.0	7	dbSNP_87	48	2083,6223		263,1557,2333	no	coding-synonymous,coding-synonymous,coding-synonymous	HDAC9	NM_058176.2,NM_178423.1,NM_178425.2	,,	348,2193,3604	GG,GA,AA		25.0783,20.2309,23.5069	,,	621/1012,621/1067,624/1070	18767343	2889,9401	1992	4153	6145	SO:0001819	synonymous_variant	9734	exon12			TCACCCAGCAATG	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1863A>G	7.37:g.18767343A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	174	75	0.431034	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			A|0.663;G|0.337	0.337	strong		0.552	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
CHCHD2	51142	hgsc.bcm.edu	37	7	56172086	56172086	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:56172086A>C	ENST00000395422.3	-	2	295	c.133T>G	c.(133-135)Tct>Gct	p.S45A		NM_016139.2	NP_057223.1	Q9Y6H1	CHCH2_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 2	45						mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(3)	5	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GCAGCAGAAGAGCCAACTGCA	0.637																																					p.S45A		Atlas-SNP	.											.	CHCHD2	10	.	0			c.T133G						PASS	.						13.0	16.0	15.0					7																	56172086		2196	4288	6484	SO:0001583	missense	51142	exon2			CAGAAGAGCCAAC	AF078845	CCDS5526.1	7p11.2	2014-07-14	2004-01-19	2004-01-21	ENSG00000106153	ENSG00000106153		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	21645	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 17"""	C7orf17		23303788	Standard	NM_016139		Approved		uc003tsa.3	Q9Y6H1	OTTHUMG00000129429	ENST00000395422.3:c.133T>G	7.37:g.56172086A>C	ENSP00000378812:p.Ser45Ala	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	200	94	0.47	NM_016139	Q498C3|Q6NZ50	Missense_Mutation	SNP	ENST00000395422.3	37	CCDS5526.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.459974	0.26248	.	.	ENSG00000106153	ENST00000395422	T	0.40225	1.04	5.09	2.66	0.31614	.	0.447785	0.23465	N	0.047899	T	0.20047	0.0482	N	0.21194	0.64	0.27295	N	0.957738	B	0.02656	0.0	B	0.01281	0.0	T	0.16988	-1.0384	10	0.07813	T	0.8	.	3.1841	0.06594	0.5928:0.2281:0.1791:0.0	.	45	Q9Y6H1	CHCH2_HUMAN	A	45	ENSP00000378812:S45A	ENSP00000378812:S45A	S	-	1	0	CHCHD2	56139580	0.246000	0.23909	0.544000	0.28141	0.931000	0.56810	0.333000	0.19768	0.936000	0.37367	0.533000	0.62120	TCT	.	.	none		0.637	CHCHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251589.1	NM_016139	
STKLD1	169436	hgsc.bcm.edu	37	9	136269143	136269143	+	Missense_Mutation	SNP	G	G	A	rs17150554	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136269143G>A	ENST00000371957.3	+	16	1810	c.1703G>A	c.(1702-1704)cGg>cAg	p.R568Q	C9orf96_ENST00000371955.1_Missense_Mutation_p.R101Q	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		568			R -> Q (in dbSNP:rs17150554).				ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		AATGCCTACCGGGGACTGGCC	0.607											OREG0019586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	162	0.0323482	0.0045	0.0403	5008	,	,		17509	0.0198		0.0815	False		,,,				2504	0.0266				p.R568Q		Atlas-SNP	.											C9orf96_ENST00000371957,NS,carcinoma,0,2	C9orf96	77	2	0			c.G1703A						PASS	.	G	GLN/ARG	74,4332	66.4+/-103.9	1,72,2130	48.0	49.0	48.0		1703	3.1	1.0	9	dbSNP_123	48	732,7868	175.9+/-225.9	37,658,3605	yes	missense	C9orf96	NM_153710.3	43	38,730,5735	AA,AG,GG		8.5116,1.6795,6.1971	probably-damaging	568/681	136269143	806,12200	2203	4300	6503	SO:0001583	missense	169436	exon16			CCTACCGGGGACT																												ENST00000371957.3:c.1703G>A	9.37:g.136269143G>A	ENSP00000361025:p.Arg568Gln	Somatic	117	0	0	1624	WXS	Illumina HiSeq	Phase_I	124	48	0.387097	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	97	0.044413919413919416	3	0.006097560975609756	16	0.04419889502762431	12	0.02097902097902098	66	0.0870712401055409	G	15.68	2.905428	0.52333	0.016795	0.085116	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.51574	0.7;0.79	5.12	3.07	0.35406	Armadillo-like helical (1);Armadillo-type fold (1);	0.108809	0.39909	N	0.001223	T	0.01156	0.0038	L	0.50333	1.59	0.38264	P	0.05803999999999998	P	0.40250	0.709	B	0.23716	0.048	T	0.16837	-1.0389	9	0.54805	T	0.06	-35.4068	6.0443	0.19752	0.1013:0.0:0.5425:0.3562	rs17150554;rs52833361;rs17150554	568	Q8NE28	SGK71_HUMAN	Q	568;101	ENSP00000361025:R568Q;ENSP00000361023:R101Q	ENSP00000361023:R101Q	R	+	2	0	C9orf96	135258964	0.960000	0.32886	0.983000	0.44433	0.640000	0.38277	1.589000	0.36644	1.116000	0.41820	0.555000	0.69702	CGG	G|0.947;A|0.053	0.053	strong		0.607	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
TST	7263	hgsc.bcm.edu	37	22	37414321	37414321	+	Silent	SNP	G	G	A	rs61743068		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:37414321G>A	ENST00000403892.3	-	1	1187	c.453C>T	c.(451-453)gcC>gcT	p.A151A	MPST_ENST00000397129.1_5'Flank|MPST_ENST00000404802.3_5'Flank|MPST_ENST00000404393.1_5'Flank|MPST_ENST00000401419.3_5'Flank|MPST_ENST00000341116.3_5'Flank|TST_ENST00000249042.3_Silent_p.A151A|MPST_ENST00000429360.2_5'Flank	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	151	Hinge.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						CTTTGAAGACGGCCGGTTCTG	0.592																																					p.A151A		Atlas-SNP	.											.	TST	22	.	0			c.C453T						PASS	.						76.0	67.0	70.0					22																	37414321		2202	4300	6502	SO:0001819	synonymous_variant	7263	exon2			GAAGACGGCCGGT	Z73420	CCDS13938.1	22q13.1	2002-02-05			ENSG00000128311	ENSG00000128311	2.8.1.1		12388	protein-coding gene	gene with protein product		180370				1953758	Standard	NM_003312		Approved	RDS	uc003aqh.4	Q16762	OTTHUMG00000150533	ENST00000403892.3:c.453C>T	22.37:g.37414321G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	167	37	0.221557	NM_003312	B3KRM1|Q6IB06	Silent	SNP	ENST00000403892.3	37	CCDS13938.1																																																																																			G|0.985;T|0.015	.	alt		0.592	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1		
MYO3A	53904	hgsc.bcm.edu	37	10	26463043	26463043	+	Missense_Mutation	SNP	A	A	T	rs3740231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:26463043A>T	ENST00000265944.5	+	30	4016	c.3850A>T	c.(3850-3852)Act>Tct	p.T1284S	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1284			T -> S (in dbSNP:rs3740231). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.T1284S(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CTTTAAAAAAACTTTGGAACC	0.403													A|||	1906	0.380591	0.3003	0.3746	5008	,	,		23264	0.3542		0.4394	False		,,,				2504	0.4601				p.T1284S		Atlas-SNP	.											MYO3A,NS,carcinoma,0,1	MYO3A	371	1	1	Substitution - Missense(1)	stomach(1)	c.A3850T						PASS	.	A	SER/THR	1450,2956	454.4+/-350.6	237,976,990	55.0	59.0	58.0		3850	-3.4	0.0	10	dbSNP_107	58	3694,4906	522.0+/-380.0	805,2084,1411	yes	missense	MYO3A	NM_017433.4	58	1042,3060,2401	TT,TA,AA		42.9535,32.9097,39.551	benign	1284/1617	26463043	5144,7862	2203	4300	6503	SO:0001583	missense	53904	exon30			AAAAAAACTTTGG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3850A>T	10.37:g.26463043A>T	ENSP00000265944:p.Thr1284Ser	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	834	0.38186813186813184	156	0.3170731707317073	124	0.3425414364640884	215	0.3758741258741259	339	0.4472295514511873	A	8.417	0.845530	0.16963	0.329097	0.429535	ENSG00000095777	ENST00000265944	T	0.77620	-1.11	5.22	-3.44	0.04796	.	1.363470	0.04263	N	0.340642	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.22871	-1.0204	9	0.07813	T	0.8	.	2.7165	0.05189	0.2367:0.213:0.0678:0.4825	rs3740231;rs17739656;rs52833109;rs3740231	1284	Q8NEV4	MYO3A_HUMAN	S	1284	ENSP00000265944:T1284S	ENSP00000265944:T1284S	T	+	1	0	MYO3A	26503049	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	0.368000	0.20399	-0.458000	0.07023	0.460000	0.39030	ACT	A|0.603;T|0.397	0.397	strong		0.403	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
SALL2	6297	hgsc.bcm.edu	37	14	21991626	21991626	+	Missense_Mutation	SNP	C	C	G	rs1263810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21991626C>G	ENST00000327430.3	-	2	2530	c.2236G>C	c.(2236-2238)Ggg>Cgg	p.G746R	SALL2_ENST00000450879.2_Missense_Mutation_p.G609R|SALL2_ENST00000538754.1_Intron|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000317492.5_Intron	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	746			G -> R (in dbSNP:rs1263810). {ECO:0000269|PubMed:8975705, ECO:0000269|PubMed:9205841, ECO:0000269|Ref.6}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GGGAAACTCCCTGCCCCGGAG	0.597													C|||	1223	0.244209	0.1059	0.1556	5008	,	,		18594	0.2579		0.3549	False		,,,				2504	0.3661				p.G746R		Atlas-SNP	.											.	SALL2	95	.	0			c.G2236C						PASS	.	C	ARG/GLY	650,3756	277.5+/-273.7	51,548,1604	56.0	49.0	51.0		2236	4.8	1.0	14	dbSNP_87	51	2904,5696	453.1+/-363.1	496,1912,1892	yes	missense	SALL2	NM_005407.1	125	547,2460,3496	GG,GC,CC		33.7674,14.7526,27.3258	probably-damaging	746/1008	21991626	3554,9452	2203	4300	6503	SO:0001583	missense	6297	exon2			AACTCCCTGCCCC	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"""Zinc fingers, C2H2-type"""	10526	protein-coding gene	gene with protein product		602219	"""sal (Drosophila)-like 2"", ""sal-like 2 (Drosophila)"""			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.2236G>C	14.37:g.21991626C>G	ENSP00000333537:p.Gly746Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	125	66	0.528	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Missense_Mutation	SNP	ENST00000327430.3	37	CCDS32045.1	552|552	0.25274725274725274|0.25274725274725274	52|52	0.10569105691056911|0.10569105691056911	70|70	0.19337016574585636|0.19337016574585636	157|157	0.2744755244755245|0.2744755244755245	273|273	0.36015831134564646|0.36015831134564646	C|C	15.46|15.46	2.840915|2.840915	0.51057|0.51057	0.147526|0.147526	0.337674|0.337674	ENSG00000165821|ENSG00000165821	ENST00000327430;ENST00000450879|ENST00000546363	T;T|.	0.04551|.	3.66;3.6|.	4.76|4.76	4.76|4.76	0.60689|0.60689	.|.	0.000000|.	0.39687|.	N|.	0.001296|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.27053|0.27053	0.805|0.805	0.24034|0.24034	P|P	0.99610114|0.99610114	B;B;B|.	0.17667|.	0.023;0.023;0.023|.	B;B;B|.	0.18263|.	0.021;0.021;0.021|.	T|T	0.43861|0.43861	-0.9365|-0.9365	9|4	0.38643|.	T|.	0.18|.	-27.9051|-27.9051	8.8209|8.8209	0.35025|0.35025	0.0:0.8999:0.0:0.1001|0.0:0.8999:0.0:0.1001	rs1263810;rs1754631;rs17792718;rs1263810|rs1263810;rs1754631;rs17792718;rs1263810	609;507;746|.	E7EW59;B4DFD9;Q9Y467|.	.;.;SALL2_HUMAN|.	R|H	746;609|604	ENSP00000333537:G746R;ENSP00000396773:G609R|.	ENSP00000333537:G746R|.	G|Q	-|-	1|3	0|2	SALL2|SALL2	21061466|21061466	0.008000|0.008000	0.16893|0.16893	0.964000|0.964000	0.40570|0.40570	0.128000|0.128000	0.20619|0.20619	0.893000|0.893000	0.28336|0.28336	2.468000|2.468000	0.83385|0.83385	0.563000|0.563000	0.77884|0.77884	GGG|CAG	C|0.711;G|0.289	0.289	strong		0.597	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407	
CUL7	9820	hgsc.bcm.edu	37	6	43006687	43006687	+	Nonsense_Mutation	SNP	G	G	A	rs121918228		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43006687G>A	ENST00000265348.3	-	23	4418	c.4333C>T	c.(4333-4335)Cga>Tga	p.R1445*	CUL7_ENST00000535468.1_Nonsense_Mutation_p.R1529*|RN7SL403P_ENST00000481783.2_RNA			Q14999	CUL7_HUMAN	cullin 7	1445					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CACTGCAGTCGCCTCTGTGAG	0.607													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19760	0.0		0.0	False		,,,				2504	0.0				p.R1529X		Atlas-SNP	.											.	CUL7	133	.	0			c.C4585T	GRCh37	CM053196	CUL7	M	rs121918228	PASS	.	G	stop/ARG,stop/ARG	0,4406		0,0,2203	61.0	54.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4585,4333	3.6	0.0	6	dbSNP_133	56	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	CUL7	NM_001168370.1,NM_014780.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	1529/1783,1445/1699	43006687	1,13005	2203	4300	6503	SO:0001587	stop_gained	9820	exon23			GCAGTCGCCTCTG	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.4333C>T	6.37:g.43006687G>A	ENSP00000265348:p.Arg1445*	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Nonsense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	45	11.398506	0.99556	0.0	1.16E-4	ENSG00000044090	ENST00000265348;ENST00000535468	.	.	.	4.52	3.63	0.41609	.	0.343472	0.30989	N	0.008461	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7945	13.7801	0.63077	0.0:0.0:0.8456:0.1544	.	.	.	.	X	1445;1529	.	ENSP00000265348:R1445X	R	-	1	2	CUL7	43114665	0.819000	0.29175	0.030000	0.17652	0.998000	0.95712	4.557000	0.60782	1.087000	0.41251	0.650000	0.86243	CGA	G|1.000;A|0.000	0.000	strong		0.607	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
ADAM20	8748	hgsc.bcm.edu	37	14	70990410	70990410	+	Missense_Mutation	SNP	C	C	G	rs573164838		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70990410C>G	ENST00000256389.3	-	2	1459	c.1215G>C	c.(1213-1215)caG>caC	p.Q405H	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	355					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		ACACACACCACTGGGTGTCAT	0.428													C|||	1	0.000199681	0.0	0.0	5008	,	,		23061	0.0		0.001	False		,,,				2504	0.0				p.Q405H		Atlas-SNP	.											.	ADAM20	59	.	0			c.G1215C						PASS	.						315.0	160.0	212.0					14																	70990410		2203	4300	6503	SO:0001583	missense	8748	exon2			ACACCACTGGGTG	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1215G>C	14.37:g.70990410C>G	ENSP00000256389:p.Gln405His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_003814	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	C	9.234	1.036560	0.19669	.	.	ENSG00000134007	ENST00000256389	T	0.09538	2.97	4.54	-9.08	0.00720	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	3.250900	0.01722	U	0.028344	T	0.04861	0.0131	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.31280	-0.9949	10	0.48119	T	0.1	.	1.6089	0.02689	0.1825:0.3433:0.1848:0.2894	.	355	O43506	ADA20_HUMAN	H	405	ENSP00000256389:Q405H	ENSP00000256389:Q405H	Q	-	3	2	ADAM20	70060163	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.871000	0.00720	-1.374000	0.02131	-1.644000	0.00765	CAG	.	.	none		0.428	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2		
WDR66	144406	hgsc.bcm.edu	37	12	122386948	122386948	+	Missense_Mutation	SNP	G	G	A	rs78910014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:122386948G>A	ENST00000288912.4	+	8	2104	c.1250G>A	c.(1249-1251)cGg>cAg	p.R417Q	WDR66_ENST00000397454.2_Missense_Mutation_p.R417Q	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	417							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		AGTAAAACACGGGCAATATAT	0.274													G|||	181	0.0361422	0.0098	0.0375	5008	,	,		12978	0.0496		0.0457	False		,,,				2504	0.047				p.R417Q	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	WDR66	143	1	0			c.G1250A						PASS	.	G	GLN/ARG,GLN/ARG	43,3583		2,39,1772	75.0	76.0	76.0		1250,1250	-0.9	0.0	12	dbSNP_131	76	361,7741		14,333,3704	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	43,43	16,372,5476	AA,AG,GG		4.4557,1.1859,3.4447	benign,benign	417/942,417/1150	122386948	404,11324	1813	4051	5864	SO:0001583	missense	144406	exon8			AAACACGGGCAAT	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.1250G>A	12.37:g.122386948G>A	ENSP00000288912:p.Arg417Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	78	0.03571428571428571	12	0.024390243902439025	15	0.04143646408839779	20	0.03496503496503497	31	0.040897097625329816	G	7.855	0.724754	0.15439	0.011859	0.044557	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.05258	3.48;3.47	5.69	-0.905	0.10527	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.302125	0.37669	N	0.002000	T	0.00356	0.0011	N	0.00446	-1.495	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45614	-0.9249	10	0.02654	T	1	.	10.3649	0.44017	0.6673:0.0:0.3327:0.0	.	417	Q8TBY9	WDR66_HUMAN	Q	417	ENSP00000288912:R417Q;ENSP00000380595:R417Q	ENSP00000288912:R417Q	R	+	2	0	WDR66	120871331	0.002000	0.14202	0.011000	0.14972	0.818000	0.46254	0.622000	0.24433	-0.100000	0.12241	-0.247000	0.11927	CGG	G|0.956;A|0.044	0.044	strong		0.274	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
VWA7	80737	hgsc.bcm.edu	37	6	31734345	31734345	+	Silent	SNP	G	G	T	rs3115671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31734345G>T	ENST00000375688.4	-	14	2279	c.2079C>A	c.(2077-2079)tcC>tcA	p.S693S	VWA7_ENST00000375686.3_Silent_p.S693S|VWA7_ENST00000447450.1_Missense_Mutation_p.H687N|VWA7_ENST00000467576.1_5'UTR|SAPCD1-AS1_ENST00000419679.1_RNA			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	693						extracellular region (GO:0005576)											GTCTAGGGGTGGACAGCAGCG	0.692													G|||	170	0.0339457	0.0575	0.0274	5008	,	,		15534	0.0		0.0746	False		,,,				2504	0.0				p.S693S		Atlas-SNP	.											.	.	.	.	0			c.C2079A						PASS	.	G		203,2815		7,189,1313	34.0	34.0	34.0		2079	0.8	0.0	6	dbSNP_103	34	557,4857		33,491,2183	yes	coding-synonymous	C6orf27	NM_025258.2		40,680,3496	TT,TG,GG		10.2881,6.7263,9.0133		693/892	31734345	760,7672	1509	2707	4216	SO:0001819	synonymous_variant	80737	exon14			AGGGGTGGACAGC		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"""chromosome 6 open reading frame 27"""	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.2079C>A	6.37:g.31734345G>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Silent	SNP	ENST00000375688.4	37	CCDS4721.2	96	0.04395604395604396	28	0.056910569105691054	11	0.03038674033149171	0	0.0	57	0.07519788918205805	G	8.875	0.950281	0.18431	0.067263	0.102881	ENSG00000204396	ENST00000447450	T	0.30714	1.52	5.64	0.78	0.18556	.	.	.	.	.	T	0.02970	0.0088	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.44421	-0.9329	6	0.08837	T	0.75	-14.6053	3.73	0.08489	0.237:0.0:0.47:0.2929	rs3115671;rs3115671	.	.	.	N	687	ENSP00000390554:H687N	ENSP00000390554:H687N	H	-	1	0	C6orf27	31842324	0.024000	0.19004	0.007000	0.13788	0.760000	0.43138	0.056000	0.14256	-0.150000	0.11195	-0.261000	0.10672	CAC	G|0.932;T|0.068	0.068	strong		0.692	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258	
D2HGDH	728294	hgsc.bcm.edu	37	2	242690675	242690675	+	Missense_Mutation	SNP	G	G	A	rs1106639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242690675G>A	ENST00000321264.4	+	8	1221	c.1012G>A	c.(1012-1014)Gtc>Atc	p.V338I	D2HGDH_ENST00000486953.1_Intron|D2HGDH_ENST00000403782.1_Missense_Mutation_p.V204I	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	338			V -> I (in dbSNP:rs1106639).		2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TCCGTTTTACGTCCTCATCGA	0.607													G|||	1120	0.223642	0.3003	0.183	5008	,	,		19404	0.122		0.2604	False		,,,				2504	0.2157				p.V338I		Atlas-SNP	.											D2HGDH,caecum,carcinoma,0,1	D2HGDH	39	1	0			c.G1012A						scavenged	.	G	ILE/VAL	1238,3168	426.6+/-341.2	171,896,1136	74.0	69.0	71.0		1012	3.2	0.1	2	dbSNP_86	71	2282,6310	385.3+/-341.4	321,1640,2335	yes	missense	D2HGDH	NM_152783.3	29	492,2536,3471	AA,AG,GG		26.5596,28.098,27.0811	benign	338/522	242690675	3520,9478	2203	4296	6499	SO:0001583	missense	728294	exon8			TTTTACGTCCTCA	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.1012G>A	2.37:g.242690675G>A	ENSP00000315351:p.Val338Ile	Somatic	182	2	0.010989		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	37	CCDS33426.1	462|462	0.21153846153846154|0.21153846153846154	123|123	0.25|0.25	69|69	0.19060773480662985|0.19060773480662985	73|73	0.12762237762237763|0.12762237762237763	197|197	0.2598944591029024|0.2598944591029024	G|G	10.56|10.56	1.384144|1.384144	0.25031|0.25031	0.28098|0.28098	0.265596|0.265596	ENSG00000180902|ENSG00000180902	ENST00000432449|ENST00000321264;ENST00000403782;ENST00000454048	.|D;D;T	.|0.83837	.|-1.77;-1.77;-1.44	5.06|5.06	3.24|3.24	0.37175|0.37175	.|FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	.|0.134831	.|0.50627	.|D	.|0.000114	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.33137|0.33137	0.985|0.985	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.24483	.|0.104	.|B	.|0.27380	.|0.079	T|T	0.04467|0.04467	-1.0949|-1.0949	4|9	.|0.23302	.|T	.|0.38	.|.	6.8186|6.8186	0.23845|0.23845	0.1531:0.1456:0.7014:0.0|0.1531:0.1456:0.7014:0.0	rs1106639|rs1106639	.|338	.|Q8N465	.|D2HDH_HUMAN	H|I	91|338;204;39	.|ENSP00000315351:V338I;ENSP00000384723:V204I;ENSP00000404596:V39I	.|ENSP00000315351:V338I	R|V	+|+	2|1	0|0	D2HGDH|D2HGDH	242339348|242339348	0.941000|0.941000	0.31946|0.31946	0.070000|0.070000	0.20053|0.20053	0.539000|0.539000	0.34962|0.34962	1.731000|1.731000	0.38135|0.38135	0.524000|0.524000	0.28502|0.28502	0.561000|0.561000	0.74099|0.74099	CGT|GTC	G|0.742;A|0.258	0.258	strong		0.607	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
MRPL10	124995	hgsc.bcm.edu	37	17	45904420	45904420	+	Missense_Mutation	SNP	C	C	T	rs11538868	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45904420C>T	ENST00000351111.2	-	3	378	c.373G>A	c.(373-375)Gtc>Atc	p.V125I	MRPL10_ENST00000414011.1_Missense_Mutation_p.V135I|MRPL10_ENST00000290208.7_Missense_Mutation_p.V135I	NM_145255.3	NP_660298.2	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10	125			V -> I (in dbSNP:rs16948568). {ECO:0000269|PubMed:15489334}.		ribosome biogenesis (GO:0042254)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|large_intestine(1)|lung(3)|ovary(1)	8						TTGGGGAAGACCTTCATCAGG	0.577													C|||	795	0.158746	0.0696	0.2161	5008	,	,		20754	0.0139		0.3549	False		,,,				2504	0.1861				p.V135I		Atlas-SNP	.											.	MRPL10	24	.	0			c.G403A						PASS	.	C	ILE/VAL,ILE/VAL	493,3913	228.8+/-243.5	22,449,1732	83.0	71.0	76.0		373,403	-0.1	1.0	17	dbSNP_120	76	3273,5327	491.8+/-373.2	642,1989,1669	yes	missense,missense	MRPL10	NM_145255.3,NM_148887.2	29,29	664,2438,3401	TT,TC,CC		38.0581,11.1893,28.9559	benign,benign	125/262,135/272	45904420	3766,9240	2203	4300	6503	SO:0001583	missense	124995	exon4			GGAAGACCTTCAT	AB051618	CCDS11516.1, CCDS11517.1	17q21.3	2012-09-13			ENSG00000159111	ENSG00000159111		"""Mitochondrial ribosomal proteins / large subunits"""	14055	protein-coding gene	gene with protein product	"""39S ribosomal protein L10, mitochondrial"""	611825				11551941	Standard	NM_148887		Approved	RPML8, MRP-L8, L10MT, MRP-L10, MRPL8, MGC17973	uc002ily.3	Q7Z7H8	OTTHUMG00000156302	ENST00000351111.2:c.373G>A	17.37:g.45904420C>T	ENSP00000324100:p.Val125Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	210	114	0.542857	NM_148887	A6NGJ4|Q96B80|Q96Q55	Missense_Mutation	SNP	ENST00000351111.2	37	CCDS11516.1	425	0.1945970695970696	45	0.09146341463414634	95	0.26243093922651933	7	0.012237762237762238	278	0.36675461741424803	C	10.70	1.425026	0.25639	0.111893	0.380581	ENSG00000159111	ENST00000351111;ENST00000290208;ENST00000414011	T;T;T	0.53857	0.6;0.6;0.6	5.62	-0.131	0.13494	.	0.482175	0.23941	N	0.043052	T	0.00012	0.0000	N	0.21448	0.665	0.48511	P	3.3799999999994945E-4	B;B	0.15930	0.002;0.015	B;B	0.18561	0.015;0.022	T	0.37820	-0.9689	9	0.42905	T	0.14	-2.0015	1.9376	0.03340	0.127:0.3325:0.1243:0.4161	rs16948568;rs17700922;rs17851354;rs52817339;rs16948568	125;135	Q7Z7H8;A6NGJ4	RM10_HUMAN;.	I	125;135;135	ENSP00000324100:V125I;ENSP00000290208:V135I;ENSP00000395870:V135I	ENSP00000290208:V135I	V	-	1	0	MRPL10	43259419	0.779000	0.28652	0.971000	0.41717	0.804000	0.45430	0.048000	0.14078	-0.216000	0.10048	-0.367000	0.07326	GTC	C|0.761;T|0.239	0.239	strong		0.577	MRPL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343764.1	NM_145255	
VRK2	7444	hgsc.bcm.edu	37	2	58316814	58316814	+	Missense_Mutation	SNP	A	A	G	rs1051061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:58316814A>G	ENST00000435505.2	+	10	1244	c.499A>G	c.(499-501)Ata>Gta	p.I167V	VRK2_ENST00000412104.2_Missense_Mutation_p.I167V|VRK2_ENST00000417641.2_Missense_Mutation_p.I167V|VRK2_ENST00000340157.4_Missense_Mutation_p.I167V|VRK2_ENST00000440705.2_Missense_Mutation_p.I144V			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	167	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> V (in dbSNP:rs1051061). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16704422, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9344656}.		cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						TCATGGTGATATAAAAGCAGC	0.279													A|||	1512	0.301917	0.0651	0.3703	5008	,	,		18572	0.4117		0.3966	False		,,,				2504	0.363				p.I167V		Atlas-SNP	.											.	VRK2	46	.	0			c.A499G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	469,3937	220.7+/-238.1	42,385,1776	77.0	83.0	81.0		499,499,430,499,499	5.7	1.0	2	dbSNP_86	81	3473,5113	505.6+/-376.4	708,2057,1528	yes	missense,missense,missense,missense,missense	VRK2	NM_001130480.2,NM_001130481.2,NM_001130482.2,NM_001130483.2,NM_006296.5	29,29,29,29,29	750,2442,3304	GG,GA,AA		40.4496,10.6446,30.3417	benign,benign,benign,benign,benign	167/509,167/509,144/486,167/397,167/509	58316814	3942,9050	2203	4293	6496	SO:0001583	missense	7444	exon7			GGTGATATAAAAG	AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.499A>G	2.37:g.58316814A>G	ENSP00000408002:p.Ile167Val	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	311	309	0.993569	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Missense_Mutation	SNP	ENST00000435505.2	37	CCDS1859.1	742	0.33974358974358976	45	0.09146341463414634	146	0.40331491712707185	247	0.4318181818181818	304	0.40105540897097625	A	20.6	4.021668	0.75275	0.106446	0.404496	ENSG00000028116	ENST00000435505;ENST00000417641;ENST00000423109;ENST00000412104;ENST00000340157;ENST00000394539;ENST00000440705	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.67	5.67	0.87782	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.75615	2.305	0.24250	P	0.99532689	D;D;P;P	0.69078	0.988;0.997;0.927;0.544	D;D;P;P	0.80764	0.994;0.99;0.727;0.569	T	0.43956	-0.9359	9	0.49607	T	0.09	-24.1341	14.8794	0.70519	1.0:0.0:0.0:0.0	rs1051061;rs17845825;rs17858793;rs52838242;rs1051061	171;167;167;167	B7Z2X1;Q86Y07-2;Q86Y07-5;Q86Y07	.;.;.;VRK2_HUMAN	V	167;167;171;167;167;167;144	ENSP00000408002:I167V;ENSP00000402375:I167V;ENSP00000404156:I167V;ENSP00000342381:I167V;ENSP00000398323:I144V	ENSP00000342381:I167V	I	+	1	0	VRK2	58170318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.798000	0.55522	2.150000	0.67090	0.477000	0.44152	ATA	A|0.683;G|0.317	0.317	strong		0.279	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296	
MAST2	23139	hgsc.bcm.edu	37	1	46501359	46501359	+	Missense_Mutation	SNP	A	A	G	rs34070850	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46501359A>G	ENST00000361297.2	+	29	5301	c.5018A>G	c.(5017-5019)aAg>aGg	p.K1673R	MAST2_ENST00000372009.2_Missense_Mutation_p.K1483R	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCAAGCAGAAAGGCAACCATG	0.577													a|||	143	0.0285543	0.0008	0.0375	5008	,	,		19862	0.0		0.0706	False		,,,				2504	0.046				p.K1673R		Atlas-SNP	.											.	MAST2	136	.	0			c.A5018G						PASS	.		ARG/LYS	36,3872		0,36,1918	59.0	64.0	62.0		5018	-1.2	0.7	1	dbSNP_126	62	533,7783		17,499,3642	yes	missense	MAST2	NM_015112.2	26	17,535,5560	GG,GA,AA		6.4093,0.9212,4.6548	benign	1673/1799	46501359	569,11655	1954	4158	6112	SO:0001583	missense	23139	exon29			GCAGAAAGGCAAC	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.5018A>G	1.37:g.46501359A>G	ENSP00000354671:p.Lys1673Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	37	CCDS41326.1	69	0.03159340659340659	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	54	0.0712401055408971	a	8.564	0.878497	0.17395	0.009212	0.064093	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.67698	-0.11;-0.28	5.69	-1.19	0.09585	.	0.586313	0.15633	N	0.252282	T	0.03915	0.0110	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.03148	-1.1067	10	0.10377	T	0.69	-6.6254	4.4622	0.11671	0.4039:0.3224:0.2737:0.0	rs34070850	1483;1673	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	R	1673;1483	ENSP00000354671:K1673R;ENSP00000361079:K1483R	ENSP00000354671:K1673R	K	+	2	0	MAST2	46273946	0.000000	0.05858	0.660000	0.29694	0.375000	0.29983	-0.128000	0.10531	0.081000	0.16988	-0.279000	0.10071	AAG	A|0.956;G|0.044	0.044	strong		0.577	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
RBM47	54502	hgsc.bcm.edu	37	4	40440215	40440215	+	Silent	SNP	T	T	C	rs2291580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:40440215T>C	ENST00000381793.2	-	3	1092	c.696A>G	c.(694-696)gaA>gaG	p.E232E	RBM47_ENST00000515809.1_Intron|RBM47_ENST00000514014.1_Silent_p.E194E|RBM47_ENST00000319592.4_Silent_p.E232E|RBM47_ENST00000381795.6_Silent_p.E232E|RBM47_ENST00000295971.7_Silent_p.E232E			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	232	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						CGATCTCAGGTTCGGCCCAGT	0.627													C|||	3518	0.702476	0.4501	0.781	5008	,	,		17459	0.7331		0.8141	False		,,,				2504	0.8415				p.E232E		Atlas-SNP	.											RBM47_ENST00000381793,NS,carcinoma,0,3	RBM47	146	3	0			c.A696G						PASS	.	C	,	2348,2058	566.7+/-382.0	644,1060,499	99.0	80.0	86.0		696,696	4.7	1.0	4	dbSNP_100	86	7082,1518	285.7+/-297.3	2915,1252,133	no	coding-synonymous,coding-synonymous	RBM47	NM_001098634.1,NM_019027.3	,	3559,2312,632	CC,CT,TT		17.6512,46.709,27.495	,	232/594,232/525	40440215	9430,3576	2203	4300	6503	SO:0001819	synonymous_variant	54502	exon4			CTCAGGTTCGGCC	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"""RNA binding motif (RRM) containing"""	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.696A>G	4.37:g.40440215T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Silent	SNP	ENST00000381793.2	37	CCDS43223.1																																																																																			T|0.267;C|0.733	0.733	strong		0.627	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027	
RRP12	23223	hgsc.bcm.edu	37	10	99125949	99125949	+	Missense_Mutation	SNP	C	C	T	rs2275580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:99125949C>T	ENST00000370992.4	-	29	3544	c.3433G>A	c.(3433-3435)Ggc>Agc	p.G1145S	RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000414986.1_Missense_Mutation_p.G1084S|RRP12_ENST00000536831.1_Missense_Mutation_p.G863S|RRP12_ENST00000315563.6_Missense_Mutation_p.G1045S	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1145			G -> S (in dbSNP:rs2275580). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.			integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		ACCTTGAAGCCGTGGTCCTTC	0.627													C|||	1983	0.395966	0.1271	0.562	5008	,	,		16365	0.3968		0.5934	False		,,,				2504	0.4376				p.G1145S		Atlas-SNP	.											.	RRP12	97	.	0			c.G3433A						PASS	.	C	SER/GLY,SER/GLY	928,3478	354.1+/-312.5	110,708,1385	125.0	99.0	108.0		3250,3433	4.3	1.0	10	dbSNP_100	108	5136,3464	635.4+/-399.0	1550,2036,714	yes	missense,missense	RRP12	NM_001145114.1,NM_015179.3	56,56	1660,2744,2099	TT,TC,CC		40.2791,21.0622,46.6246	possibly-damaging,possibly-damaging	1084/1237,1145/1298	99125949	6064,6942	2203	4300	6503	SO:0001583	missense	23223	exon29			TGAAGCCGTGGTC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3433G>A	10.37:g.99125949C>T	ENSP00000360031:p.Gly1145Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	970	0.4441391941391941	59	0.11991869918699187	208	0.574585635359116	248	0.43356643356643354	455	0.600263852242744	C	19.39	3.819004	0.71028	0.210622	0.597209	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.31510	1.49;1.49;1.5;1.49	5.19	4.28	0.50868	.	0.094109	0.64402	D	0.000001	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.9999928566	D;B;P;P	0.62365	0.991;0.383;0.719;0.943	B;B;B;B	0.41510	0.359;0.114;0.164;0.178	T	0.44620	-0.9316	9	0.16420	T	0.52	-25.5986	12.1406	0.53996	0.0:0.9174:0.0:0.0826	rs2275580;rs17850958;rs60383842;rs2275580	1084;1045;863;1145	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	S	1145;1045;1084;863	ENSP00000360031:G1145S;ENSP00000324315:G1045S;ENSP00000414863:G1084S;ENSP00000446184:G863S	ENSP00000324315:G1045S	G	-	1	0	RRP12	99115939	1.000000	0.71417	0.980000	0.43619	0.974000	0.67602	5.615000	0.67702	2.422000	0.82143	0.555000	0.69702	GGC	C|0.553;T|0.447	0.447	strong		0.627	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
GRIP1	23426	hgsc.bcm.edu	37	12	66773075	66773075	+	Missense_Mutation	SNP	C	C	T	rs145115262	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:66773075C>T	ENST00000398016.3	-	19	2518	c.2450G>A	c.(2449-2451)cGg>cAg	p.R817Q	GRIP1_ENST00000359742.4_Missense_Mutation_p.R869Q|GRIP1_ENST00000286445.7_Missense_Mutation_p.R869Q	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GGCTGTGGACCGGTCCCAGTC	0.517													C|||	15	0.00299521	0.0008	0.0058	5008	,	,		17397	0.003		0.007	False		,,,				2504	0.0				p.R817Q		Atlas-SNP	.											.	GRIP1	106	.	0			c.G2450A						PASS	.	C	GLN/ARG,GLN/ARG	9,3877		0,9,1934	169.0	165.0	166.0		2450,2450	2.0	1.0	12	dbSNP_134	166	69,8193		0,69,4062	yes	missense,missense	GRIP1	NM_001178074.1,NM_021150.3	43,43	0,78,5996	TT,TC,CC		0.8351,0.2316,0.6421	benign,benign	817/1062,817/1077	66773075	78,12070	1943	4131	6074	SO:0001583	missense	23426	exon19			GTGGACCGGTCCC	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.2450G>A	12.37:g.66773075C>T	ENSP00000381098:p.Arg817Gln	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	182	87	0.478022	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	5|5	0.006596306068601583|0.006596306068601583	C|C	13.77|13.77	2.337222|2.337222	0.41398|0.41398	0.002316|0.002316	0.008351|0.008351	ENSG00000155974|ENSG00000155974	ENST00000538164|ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215	.|T;T;T;T;T;T	.|0.81415	.|-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	4.8|4.8	1.95|1.95	0.26073|0.26073	.|.	.|0.233910	.|0.42294	.|N	.|0.000731	T|T	0.69178|0.69178	0.3082|0.3082	M|M	0.62723|0.62723	1.935|1.935	0.44129|0.44129	D|D	0.996911|0.996911	.|P;P;P;D	.|0.54397	.|0.911;0.88;0.956;0.966	.|B;B;B;B	.|0.43018	.|0.173;0.108;0.297;0.405	T|T	0.69124|0.69124	-0.5228|-0.5228	5|9	.|.	.|.	.|.	-5.1095|-5.1095	9.3305|9.3305	0.38018|0.38018	0.0:0.7035:0.0:0.2965|0.0:0.7035:0.0:0.2965	.|.	.|817;869;817;869	.|F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2	.|.;GRIP1_HUMAN;.;.	S|Q	684|817;869;869;817;761;709	.|ENSP00000381098:R817Q;ENSP00000352780:R869Q;ENSP00000286445:R869Q;ENSP00000446047:R817Q;ENSP00000446024:R761Q;ENSP00000446011:R709Q	.|.	G|R	-|-	1|2	0|0	GRIP1|GRIP1	65059342|65059342	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.988000|0.988000	0.76386|0.76386	2.867000|2.867000	0.48428|0.48428	0.317000|0.317000	0.23160|0.23160	-0.258000|-0.258000	0.10820|0.10820	GGT|CGG	C|0.997;T|0.003	0.003	strong		0.517	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2		
MAGEA6	4105	hgsc.bcm.edu	37	X	151869765	151869765	+	Missense_Mutation	SNP	G	G	T	rs7056365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:151869765G>T	ENST00000329342.5	+	3	680	c.455G>T	c.(454-456)aGc>aTc	p.S152I		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	152	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		S -> I (in dbSNP:rs7056365). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20598277}.							breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					GTGATCTTCAGCAAAGCTTCC	0.547													g|||	370	0.0980132	0.1044	0.0476	3775	,	,		15288	0.0258		0.1243	False		,,,				2504	0.0491				p.S152I		Atlas-SNP	.											.	MAGEA6	53	.	0			c.G455T						PASS	.	G	ILE/SER,ILE/SER	541,3293		31,403,76,1198,494	151.0	133.0	139.0		455,455	0.6	0.0	X	dbSNP_116	139	1069,5658		59,649,302,1720,1569	no	missense,missense	MAGEA6	NM_005363.2,NM_175868.1	142,142	90,1052,378,2918,2063	TT,TG,T,GG,G		15.8912,14.1106,15.2448	probably-damaging,probably-damaging	152/315,152/315	151869765	1610,8951	2202	4299	6501	SO:0001583	missense	4105	exon3			TCTTCAGCAAAGC		CCDS76050.1	Xq28	2009-03-13			ENSG00000197172	ENSG00000197172			6804	protein-coding gene	gene with protein product	"""MAGE-6 antigen"", ""melanoma-associated antigen 6"", ""melanoma antigen family A 6"", ""cancer/testis antigen family 1, member 6"""	300176		MAGE6		8575766	Standard	NM_005363		Approved	CT1.6	uc004ffq.1	P43360	OTTHUMG00000022642	ENST00000329342.5:c.455G>T	X.37:g.151869765G>T	ENSP00000329199:p.Ser152Ile	Somatic	671	2	0.00298063		WXS	Illumina HiSeq	Phase_I	274	272	0.992701	NM_005363	A8IF93|Q6NW44	Missense_Mutation	SNP	ENST00000329342.5	37	CCDS14708.1	177	0.10669077757685352	35	0.07478632478632478	16	0.04519774011299435	6	0.010714285714285714	67	0.0968208092485549	g	6.256	0.415311	0.11870	0.141106	0.158912	ENSG00000197172	ENST00000329342;ENST00000412733;ENST00000457643	T;T;T	0.05081	3.5;3.5;3.5	0.605	0.605	0.17553	.	.	.	.	.	T	0.00039	0.0001	M	0.77486	2.375	0.80722	P	0.0	P	0.42973	0.796	B	0.36030	0.216	T	0.28490	-1.0042	7	0.48119	T	0.1	.	.	.	.	rs7056365;rs52803634;rs7056365	152	P43360	MAGA6_HUMAN	I	152	ENSP00000329199:S152I;ENSP00000403303:S152I;ENSP00000401806:S152I	ENSP00000329199:S152I	S	+	2	0	MAGEA6	151620421	0.000000	0.05858	0.013000	0.15412	0.046000	0.14306	0.040000	0.13905	0.573000	0.29400	0.181000	0.17075	AGC	G|0.872;T|0.128	0.128	strong		0.547	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363	
MUC4	4585	hgsc.bcm.edu	37	3	195512531	195512531	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195512531C>T	ENST00000463781.3	-	2	6379	c.5920G>A	c.(5920-5922)Gct>Act	p.A1974T	MUC4_ENST00000475231.1_Missense_Mutation_p.A1974T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A1974T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAGCGTCGGTGACA	0.607																																					p.A1974T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.G5920A						scavenged	.						52.0	43.0	46.0					3																	195512531		690	1590	2280	SO:0001583	missense	4585	exon2			AGGAAGCGTCGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5920G>A	3.37:g.195512531C>T	ENSP00000417498:p.Ala1974Thr	Somatic	282	5	0.0177305		WXS	Illumina HiSeq	Phase_I	602	21	0.0348837	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	C	6.041	0.375968	0.11409	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.45;1.46	.	.	.	.	.	.	.	.	T	0.08802	0.0218	N	0.08118	0	0.09310	N	1	P	0.45986	0.87	B	0.26310	0.068	T	0.27468	-1.0073	7	.	.	.	.	4.7077	0.12858	0.3536:0.6463:0.0:1.0E-4	.	1974	E7ESK3	.	T	1974	ENSP00000417498:A1974T;ENSP00000420243:A1974T	.	A	-	1	0	MUC4	196996926	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-3.284000	0.00527	-0.833000	0.04245	0.064000	0.15345	GCT	.	.	none		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAM186A	121006	hgsc.bcm.edu	37	12	50745857	50745857	+	Missense_Mutation	SNP	T	T	G	rs34602257|rs12297653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745857T>G	ENST00000327337.5	-	4	4757	c.4758A>C	c.(4756-4758)gaA>gaC	p.E1586D	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Missense_Mutation_p.E1586D	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1586																	GGATCCCCAGTTCCTGCGCCT	0.667													t|||	1378	0.27516	0.2247	0.304	5008	,	,		21467	0.3234		0.2982	False		,,,				2504	0.2495				p.E1586D	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,caecum,carcinoma,-1,3	FAM186A	181	3	0			c.A4758C						scavenged	.						6.0	6.0	6.0					12																	50745857		680	1566	2246	SO:0001583	missense	121006	exon4			CCCCAGTTCCTGC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4758A>C	12.37:g.50745857T>G	ENSP00000329995:p.Glu1586Asp	Somatic	231	3	0.012987		WXS	Illumina HiSeq	Phase_I	253	63	0.249012	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	t	0.936	-0.711037	0.03230	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.04406	3.63;3.63	4.11	-8.22	0.01037	.	.	.	.	.	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B;B	0.33477	0.413;0.0	B;B	0.31495	0.131;0.0	T	0.30504	-0.9976	9	0.17832	T	0.49	.	2.244	0.04026	0.3599:0.0663:0.2616:0.3122	rs12297653	1586;1586	F5GYN0;A6NE01	.;F186A_HUMAN	D	1586	ENSP00000441337:E1586D;ENSP00000329995:E1586D	ENSP00000329995:E1586D	E	-	3	2	FAM186A	49032124	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.486000	0.02312	-3.428000	0.00165	-6.680000	0.00000	GAA	.	.	alt		0.667	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
KL	9365	hgsc.bcm.edu	37	13	33634983	33634983	+	Silent	SNP	C	C	T	rs564481	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:33634983C>T	ENST00000380099.3	+	4	1775	c.1767C>T	c.(1765-1767)caC>caT	p.H589H	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	589	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		AGGAAATGCACGTTACACATT	0.517													C|||	1248	0.249201	0.0401	0.5086	5008	,	,		22365	0.1637		0.3618	False		,,,				2504	0.32				p.H589H		Atlas-SNP	.											.	KL	106	.	0			c.C1767T						PASS	.	C		434,3972	208.5+/-229.5	25,384,1794	168.0	142.0	151.0		1767	-3.8	0.0	13	dbSNP_83	151	3520,5080	512.8+/-378.0	748,2024,1528	no	coding-synonymous	KL	NM_004795.3		773,2408,3322	TT,TC,CC		40.9302,9.8502,30.4014		589/1013	33634983	3954,9052	2203	4300	6503	SO:0001819	synonymous_variant	9365	exon4			AATGCACGTTACA	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1767C>T	13.37:g.33634983C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	184	89	0.483696	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																			C|0.704;T|0.296	0.296	strong		0.517	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
SMARCA2	6595	hgsc.bcm.edu	37	9	2073292	2073292	+	Silent	SNP	A	A	G	rs13288443	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:2073292A>G	ENST00000382203.1	+	11	2036	c.1827A>G	c.(1825-1827)ccA>ccG	p.P609P	SMARCA2_ENST00000357248.2_Silent_p.P609P|SMARCA2_ENST00000382194.1_Silent_p.P609P|SMARCA2_ENST00000349721.2_Silent_p.P609P			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	609					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		TGTTCGGACCAGAAGCACCCA	0.483													A|||	538	0.107428	0.1324	0.1527	5008	,	,		19709	0.0427		0.0994	False		,,,				2504	0.1166				p.P609P		Atlas-SNP	.											.	SMARCA2	313	.	0			c.A1827G						PASS	.	A	,	581,3825	256.7+/-261.4	42,497,1664	74.0	72.0	73.0		1827,1827	0.5	1.0	9	dbSNP_121	73	964,7636	209.7+/-250.8	47,870,3383	no	coding-synonymous,coding-synonymous	SMARCA2	NM_003070.3,NM_139045.2	,	89,1367,5047	GG,GA,AA		11.2093,13.1866,11.8791	,	609/1591,609/1573	2073292	1545,11461	2203	4300	6503	SO:0001819	synonymous_variant	6595	exon11			CGGACCAGAAGCA	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.1827A>G	9.37:g.2073292A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	83	53	0.638554	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			A|0.888;G|0.112	0.112	strong		0.483	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
MMP7	4316	hgsc.bcm.edu	37	11	102401411	102401411	+	Missense_Mutation	SNP	A	A	C	rs55701929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:102401411A>C	ENST00000260227.4	-	1	73	c.21T>G	c.(19-21)tgT>tgG	p.C7W		NM_002423.3	NP_002414.1	P09237	MMP7_HUMAN	matrix metallopeptidase 7 (matrilysin, uterine)	7					antibacterial peptide secretion (GO:0002779)|collagen catabolic process (GO:0030574)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)	Marimastat(DB00786)	GGCACACAGCACACAGCACGG	0.552													A|||	33	0.00658946	0.0	0.013	5008	,	,		16462	0.0		0.0239	False		,,,				2504	0.0				p.C7W		Atlas-SNP	.											.	MMP7	27	.	0			c.T21G						PASS	.	A	TRP/CYS	10,4396	14.3+/-33.2	0,10,2193	72.0	61.0	64.0		21	-10.0	0.0	11	dbSNP_129	64	170,8428	74.8+/-137.4	1,168,4130	yes	missense	MMP7	NM_002423.3	215	1,178,6323	CC,CA,AA		1.9772,0.227,1.3842	possibly-damaging	7/268	102401411	180,12824	2203	4299	6502	SO:0001583	missense	4316	exon1			CACAGCACACAGC	Z11887	CCDS8317.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000137673	ENSG00000137673	3.4.24.23		7174	protein-coding gene	gene with protein product		178990	"""matrix metalloproteinase 7 (matrilysin, uterine)"""	MPSL1		8978768	Standard	NM_002423		Approved	PUMP-1	uc001phb.3	P09237	OTTHUMG00000048193	ENST00000260227.4:c.21T>G	11.37:g.102401411A>C	ENSP00000260227:p.Cys7Trp	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_002423	Q9BTK9	Missense_Mutation	SNP	ENST00000260227.4	37	CCDS8317.1	20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	A	11.14	1.549954	0.27652	0.00227	0.019772	ENSG00000137673	ENST00000260227	T	0.23754	1.89	4.98	-9.96	0.00443	.	0.795814	0.11130	N	0.596412	T	0.09818	0.0241	M	0.64997	1.995	0.20074	N	0.999937	B;B;B	0.19706	0.038;0.008;0.002	B;B;B	0.12837	0.008;0.003;0.001	T	0.07908	-1.0748	10	0.49607	T	0.09	-0.8984	9.0726	0.36502	0.4852:0.3526:0.1622:0.0	rs55701929;rs61751461	7;7;7	B4DDW4;Q53GF1;P09237	.;.;MMP7_HUMAN	W	7	ENSP00000260227:C7W	ENSP00000260227:C7W	C	-	3	2	MMP7	101906621	0.000000	0.05858	0.000000	0.03702	0.252000	0.25951	-1.188000	0.03064	-2.917000	0.00306	-0.959000	0.02639	TGT	A|0.988;C|0.012	0.012	strong		0.552	MMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109633.2		
MBD3L3	653657	hgsc.bcm.edu	37	19	7056537	7056537	+	Silent	SNP	G	G	A	rs201991311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7056537G>A	ENST00000333843.4	-	2	457	c.423C>T	c.(421-423)ccC>ccT	p.P141P		NM_001164425.1	NP_001157897.1	A6NE82	MB3L3_HUMAN	methyl-CpG binding domain protein 3-like 3	141					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.P141P(1)		central_nervous_system(1)|lung(5)|stomach(1)	7						GCCCAGGGGTGGGCTCAAGCG	0.632																																					p.P141P		Atlas-SNP	.											MBD3L3,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	MBD3L3	12	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C423T						scavenged	.						15.0	23.0	20.0					19																	7056537		692	1587	2279	SO:0001819	synonymous_variant	653657	exon2			AGGGGTGGGCTCA		CCDS45944.1	19p13.2	2014-04-01			ENSG00000182315	ENSG00000182315			37205	protein-coding gene	gene with protein product							Standard	NM_001164425		Approved		uc021uns.1	A6NE82	OTTHUMG00000181976	ENST00000333843.4:c.423C>T	19.37:g.7056537G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	264	58	0.219697	NM_001164425		Silent	SNP	ENST00000333843.4	37	CCDS45944.1																																																																																			G|0.975;A|0.025	0.025	strong		0.632	MBD3L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458500.1	NM_001164425	
DIS3L	115752	hgsc.bcm.edu	37	15	66618342	66618342	+	Missense_Mutation	SNP	A	A	G	rs3803412	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:66618342A>G	ENST00000319212.4	+	12	1891	c.1841A>G	c.(1840-1842)gAt>gGt	p.D614G	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000319194.5_Missense_Mutation_p.D531G	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	614			D -> G (in dbSNP:rs3803412). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						AAAGACTTGGATGAGAAGAGC	0.453													A|||	1258	0.251198	0.0953	0.3199	5008	,	,		19288	0.3165		0.2952	False		,,,				2504	0.3006				p.D614G		Atlas-SNP	.											.	DIS3L	175	.	0			c.A1841G						PASS	.	A	GLY/ASP,GLY/ASP	608,3794	264.7+/-266.2	35,538,1628	121.0	113.0	116.0		1841,1592	5.3	0.7	15	dbSNP_107	116	2617,5981	423.7+/-354.4	397,1823,2079	yes	missense,missense	DIS3L	NM_001143688.1,NM_133375.3	94,94	432,2361,3707	GG,GA,AA		30.4373,13.8119,24.8077	benign,benign	614/1055,531/972	66618342	3225,9775	2201	4299	6500	SO:0001583	missense	115752	exon12			ACTTGGATGAGAA		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"""DIS3 mitotic control homolog (S. cerevisiae)-like"""			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.1841A>G	15.37:g.66618342A>G	ENSP00000321711:p.Asp614Gly	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Missense_Mutation	SNP	ENST00000319212.4	37	CCDS45286.1	551	0.2522893772893773	46	0.09349593495934959	106	0.292817679558011	172	0.3006993006993007	227	0.2994722955145119	A	9.152	1.016533	0.19355	0.138119	0.304373	ENSG00000166938	ENST00000319194;ENST00000319212	T;T	0.25250	1.81;1.81	5.31	5.31	0.75309	Ribonuclease II/R (2);	0.391663	0.30999	N	0.008458	T	0.00012	0.0000	N	0.04043	-0.29	0.09310	P	1.0	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.11329	0.006;0.003;0.003	T	0.41088	-0.9528	9	0.36615	T	0.2	-17.8793	14.4288	0.67236	1.0:0.0:0.0:0.0	rs3803412;rs52810111;rs3803412	614;480;614	Q8TF46;Q8TF46-2;Q8TF46-3	DI3L1_HUMAN;.;.	G	531;614	ENSP00000321583:D531G;ENSP00000321711:D614G	ENSP00000321583:D531G	D	+	2	0	DIS3L	64405396	1.000000	0.71417	0.712000	0.30502	0.337000	0.28794	4.706000	0.61845	1.991000	0.58162	0.379000	0.24179	GAT	A|0.760;G|0.240	0.240	strong		0.453	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
ARHGEF4	50649	hgsc.bcm.edu	37	2	131688783	131688783	+	Missense_Mutation	SNP	G	G	A	rs61750360	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:131688783G>A	ENST00000326016.5	+	3	772	c.253G>A	c.(253-255)Gtc>Atc	p.V85I	ARHGEF4_ENST00000525839.1_Missense_Mutation_p.V85I|ARHGEF4_ENST00000409303.1_Missense_Mutation_p.V85I|ARHGEF4_ENST00000392953.3_Missense_Mutation_p.V85I|ARHGEF4_ENST00000409359.1_Missense_Mutation_p.V941I|ARHGEF4_ENST00000428230.2_Missense_Mutation_p.V85I|SCARNA4_ENST00000517020.2_RNA	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	85	ABR (APC-binding region) domain.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		GCAGGCCCACGTCGAAAGGAG	0.577													G|||	700	0.139776	0.0378	0.0951	5008	,	,		20620	0.1319		0.175	False		,,,				2504	0.2812				p.V85I		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.G253A						PASS	.	G	ILE/VAL,ILE/VAL	260,4146		14,232,1957	34.0	28.0	30.0		253,253	-6.6	0.0	2	dbSNP_129	30	1482,7118		125,1232,2943	yes	missense,missense	ARHGEF4	NM_032995.1,NM_015320.2	29,29	139,1464,4900	AA,AG,GG		17.2326,5.901,13.3938	benign,benign	85/671,85/691	131688783	1742,11264	2203	4300	6503	SO:0001583	missense	50649	exon3			GCCCACGTCGAAA	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.253G>A	2.37:g.131688783G>A	ENSP00000316845:p.Val85Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_032995	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	37	CCDS2165.1	265	0.12133699633699634	17	0.034552845528455285	41	0.1132596685082873	60	0.1048951048951049	147	0.19393139841688653	G	12.77	2.037539	0.35989	0.05901	0.172326	ENSG00000136002	ENST00000409359;ENST00000326016;ENST00000392953;ENST00000438985;ENST00000428230;ENST00000525839;ENST00000409303	T;T;T;T;T;T;T	0.70164	0.95;-0.18;-0.29;0.95;0.96;-0.29;-0.46	4.72	-6.62	0.01813	.	.	.	.	.	T	0.00073	0.0002	L	0.27053	0.805	0.80722	P	0.0	B;B;B;B	0.28470	0.001;0.213;0.001;0.001	B;B;B;B	0.16722	0.0;0.016;0.001;0.0	T	0.06215	-1.0839	8	0.34782	T	0.22	.	0.0491	0.00011	0.2661:0.2247:0.2034:0.3058	rs61750360	85;941;85;85	E9PEM0;E7EV07;Q9NR80-4;Q9NR80	.;.;.;ARHG4_HUMAN	I	941;85;85;265;85;85;85	ENSP00000386794:V941I;ENSP00000316845:V85I;ENSP00000376680:V85I;ENSP00000389661:V265I;ENSP00000398455:V85I;ENSP00000432267:V85I;ENSP00000387285:V85I	ENSP00000316845:V85I	V	+	1	0	ARHGEF4	131405253	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-1.771000	0.01789	-1.009000	0.03400	0.467000	0.42956	GTC	G|0.866;A|0.134	0.134	strong		0.577	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
LAMA4	3910	hgsc.bcm.edu	37	6	112430675	112430675	+	Missense_Mutation	SNP	C	C	T	rs142048329		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:112430675C>T	ENST00000230538.7	-	39	5834	c.5437G>A	c.(5437-5439)Ggc>Agc	p.G1813S	LAMA4_ENST00000389463.4_Missense_Mutation_p.G1806S|LAMA4_ENST00000424408.2_Missense_Mutation_p.G1806S|LAMA4_ENST00000522006.1_Missense_Mutation_p.G1806S	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1813	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)	p.G1806R(1)		NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		CTTACGGCGCCGCTGACCAGG	0.537																																					p.G1813S		Atlas-SNP	.											LAMA4,bladder,carcinoma,0,1	LAMA4	227	1	1	Substitution - Missense(1)	urinary_tract(1)	c.G5437A						scavenged	.	C	SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	80.0	73.0	76.0		5437,5416,5416	6.2	0.8	6	dbSNP_134	76	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	56,56,56	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	1813/1824,1806/1817,1806/1817	112430675	2,13004	2203	4300	6503	SO:0001583	missense	3910	exon39			CGGCGCCGCTGAC		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.5437G>A	6.37:g.112430675C>T	ENSP00000230538:p.Gly1813Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	127	3	0.023622	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	C	33	5.235966	0.95240	0.0	2.33E-4	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	6.17	6.17	0.99709	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.85682	D	0.000000	D	0.90376	0.6988	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89837	0.4000	10	0.72032	D	0.01	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1813;1806	Q16363;Q16363-2	LAMA4_HUMAN;.	S	1813;1806;1806;1806	ENSP00000230538:G1813S;ENSP00000429488:G1806S;ENSP00000374114:G1806S;ENSP00000416470:G1806S	ENSP00000230538:G1813S	G	-	1	0	LAMA4	112537368	1.000000	0.71417	0.780000	0.31762	0.927000	0.56198	6.848000	0.75409	2.941000	0.99782	0.655000	0.94253	GGC	C|1.000;T|0.000	0.000	weak		0.537	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
ARSD	414	hgsc.bcm.edu	37	X	2835985	2835985	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2835985G>A	ENST00000381154.1	-	5	798	c.723C>T	c.(721-723)ttC>ttT	p.F241F	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	241					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCAAGAGATGAAAAACAGGC	0.582													g|||	14	0.00370861	0.0061	0.0	3775	,	,		18064	0.0		0.001	False		,,,				2504	0.0051				p.F241F		Atlas-SNP	.											.	ARSD	47	.	0			c.C723T						PASS	.						32.0	36.0	35.0					X																	2835985		2203	4300	6503	SO:0001819	synonymous_variant	414	exon5			AGAGATGAAAAAC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.723C>T	X.37:g.2835985G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	131	51	0.389313	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			.	.	none		0.582	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
AP5B1	91056	hgsc.bcm.edu	37	11	65547455	65547455	+	Missense_Mutation	SNP	C	C	A	rs12362011	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65547455C>A	ENST00000532090.2	-	2	719	c.509G>T	c.(508-510)gGg>gTg	p.G170V		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	170	Leu-rich.				endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-type membrane coat adaptor complex (GO:0030119)|lysosomal membrane (GO:0005765)				lung(1)	1						CCGCAGCAACCCCAGGGAGCC	0.692													C|||	702	0.140176	0.18	0.0922	5008	,	,		13977	0.2222		0.1362	False		,,,				2504	0.0399				p.G170V		Atlas-SNP	.											.	AP5B1	40	.	0			c.G509T						PASS	.	C	VAL/GLY	433,3095		25,383,1356	5.0	7.0	6.0		338	4.9	1.0	11	dbSNP_120	6	874,7096		43,788,3154	no	missense	DKFZp761E198	NM_138368.3	109	68,1171,4510	AA,AC,CC		10.9661,12.2732,11.3672	probably-damaging	113/822	65547455	1307,10191	1764	3985	5749	SO:0001583	missense	91056	exon2			AGCAACCCCAGGG	JQ313135	CCDS58146.1	11q13.1	2012-02-29			ENSG00000254470	ENSG00000254470			25104	protein-coding gene	gene with protein product		614367				22022230	Standard	NM_138368		Approved	PP1030, AP-5, DKFZp761E198	uc031qbm.1	Q2VPB7	OTTHUMG00000166593	ENST00000532090.2:c.509G>T	11.37:g.65547455C>A	ENSP00000454303:p.Gly170Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_138368	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Missense_Mutation	SNP	ENST00000532090.2	37	CCDS58146.1																																																																																			C|0.832;A|0.168	0.168	strong		0.692	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368	
RPL36AL	6166	hgsc.bcm.edu	37	14	50085571	50085571	+	Silent	SNP	G	G	A	rs1054427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50085571G>A	ENST00000298289.6	-	2	411	c.252C>T	c.(250-252)gcC>gcT	p.A84A	RP11-649E7.5_ENST00000555043.1_RNA|MGAT2_ENST00000305386.2_5'Flank	NM_001001.4	NP_000992.1	Q969Q0	RL36L_HUMAN	ribosomal protein L36a-like	84					translation (GO:0006412)	ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)					all_epithelial(31;0.0021)|Breast(41;0.0124)					ATCTCTTAATGGCCAGCATCC	0.418													G|||	857	0.171126	0.261	0.3141	5008	,	,		20139	0.0258		0.2286	False		,,,				2504	0.0389				p.Q84H		Atlas-SNP	.											.	RPL36AL	6	.	0			c.A252T						PASS	.	G		1118,3284		139,840,1222	81.0	82.0	82.0		252	2.9	1.0	14	dbSNP_86	82	1868,6730		219,1430,2650	no	coding-synonymous	RPL36AL	NM_001001.3		358,2270,3872	AA,AG,GG		21.726,25.3975,22.9692		84/107	50085571	2986,10014	2201	4299	6500	SO:0001819	synonymous_variant	6166	exon2			CTTAATGGCCAGC	BC000741	CCDS9689.1	14q21	2008-08-29	2002-01-15	2002-01-18	ENSG00000165502	ENSG00000165502		"""L ribosomal proteins"""	10346	protein-coding gene	gene with protein product		180469	"""ribosomal protein L36a"""	RPL36A		1577483	Standard	NM_001001		Approved		uc001wwq.2	Q969Q0	OTTHUMG00000152330	ENST00000298289.6:c.252C>T	14.37:g.50085571G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_001001	Q3B7A5	Missense_Mutation	SNP	ENST00000298289.6	37	CCDS9689.1																																																																																			G|0.250;A|0.750	0.750	weak		0.418	RPL36AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276808.2		
SECISBP2L	9728	hgsc.bcm.edu	37	15	49293194	49293194	+	Missense_Mutation	SNP	C	C	A	rs11854184	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:49293194C>A	ENST00000559471.1	-	15	2391	c.2128G>T	c.(2128-2130)Gta>Tta	p.V710L	SECISBP2L_ENST00000559122.1_5'UTR|SECISBP2L_ENST00000261847.3_Missense_Mutation_p.V665L	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	710							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTTGCTCTTACAGGATCTTTT	0.378													C|||	385	0.076877	0.0408	0.1081	5008	,	,		17414	0.003		0.2018	False		,,,				2504	0.0511				p.V710L		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.G2128T						PASS	.	C	LEU/VAL,LEU/VAL	275,4119	154.8+/-188.1	10,255,1932	123.0	108.0	113.0		2128,1993	4.2	1.0	15	dbSNP_120	113	1897,6693	335.5+/-321.5	195,1507,2593	yes	missense,missense	SECISBP2L	NM_001193489.1,NM_014701.3	32,32	205,1762,4525	AA,AC,CC		22.0838,6.2585,16.7283	benign,benign	710/1102,665/1057	49293194	2172,10812	2197	4295	6492	SO:0001583	missense	9728	exon15			CTCTTACAGGATC	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2128G>T	15.37:g.49293194C>A	ENSP00000453854:p.Val710Leu	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	261	261	1	NM_001193489	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	219	0.10027472527472528	24	0.04878048780487805	42	0.11602209944751381	2	0.0034965034965034965	151	0.19920844327176782	C	14.83	2.651974	0.47362	0.062585	0.220838	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.56611	0.45	5.09	4.17	0.49024	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.361874	0.29046	N	0.013316	T	0.00039	0.0001	N	0.22421	0.69	0.29397	P	0.862182	B;B	0.18610	0.029;0.013	B;B	0.15870	0.014;0.008	T	0.06267	-1.0836	9	0.49607	T	0.09	.	8.8473	0.35179	0.0:0.7802:0.0:0.2198	rs11854184;rs52809376;rs59584512;rs11854184	710;665	Q93073;Q93073-2	SBP2L_HUMAN;.	L	665;710	ENSP00000261847:V665L	ENSP00000261847:V665L	V	-	1	0	SECISBP2L	47080486	1.000000	0.71417	0.956000	0.39512	0.900000	0.52787	3.043000	0.49823	1.282000	0.44496	-0.251000	0.11542	GTA	C|0.860;A|0.140	0.140	strong		0.378	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
UBASH3A	53347	hgsc.bcm.edu	37	21	43852232	43852232	+	Silent	SNP	C	C	T	rs13052676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43852232C>T	ENST00000319294.6	+	9	1222	c.1191C>T	c.(1189-1191)agC>agT	p.S397S	UBASH3A_ENST00000398367.1_Silent_p.S359S|UBASH3A_ENST00000291535.6_Silent_p.S359S	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	397	Phosphatase-like.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						CAAGGAAGAGCGTGCTGGTGG	0.587													C|||	1283	0.25619	0.1921	0.2608	5008	,	,		19823	0.2232		0.331	False		,,,				2504	0.2965				p.S397S		Atlas-SNP	.											.	UBASH3A	72	.	0			c.C1191T						PASS	.	C	,	974,3432	359.4+/-314.8	109,756,1338	132.0	89.0	103.0		1077,1191	-0.1	0.1	21	dbSNP_121	103	2809,5791	436.2+/-358.2	456,1897,1947	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	565,2653,3285	TT,TC,CC		32.6628,22.1062,29.0866	,	359/624,397/662	43852232	3783,9223	2203	4300	6503	SO:0001819	synonymous_variant	53347	exon9			GAAGAGCGTGCTG	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.1191C>T	21.37:g.43852232C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	59	0.578431	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			C|0.722;T|0.278	0.278	strong		0.587	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18829952	18829952	+	Missense_Mutation	SNP	A	A	G	rs41304755	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:18829952A>G	ENST00000380548.4	+	23	4565	c.4226A>G	c.(4225-4227)gAt>gGt	p.D1409G	ADAMTSL1_ENST00000380545.5_Missense_Mutation_p.D110G	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1409	Ig-like C2-type 4.			D -> G (in Ref. 3; BAC03925). {ECO:0000305}.		proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CTGGTCCTGGATCCTGGGAAT	0.552													A|||	548	0.109425	0.0129	0.2003	5008	,	,		19684	0.0139		0.2465	False		,,,				2504	0.1329				p.D1409G		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A4226G						PASS	.	A	GLY/ASP	175,3935		4,167,1884	64.0	64.0	64.0		4226	4.5	1.0	9	dbSNP_127	64	2038,6368		257,1524,2422	yes	missense	ADAMTSL1	NM_001040272.5	94	261,1691,4306	GG,GA,AA		24.2446,4.2579,17.6814	benign	1409/1763	18829952	2213,10303	2055	4203	6258	SO:0001583	missense	92949	exon23			TCCTGGATCCTGG	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.4226A>G	9.37:g.18829952A>G	ENSP00000369921:p.Asp1409Gly	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	111	36	0.324324	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	276	0.12637362637362637	6	0.012195121951219513	73	0.20165745856353592	6	0.01048951048951049	191	0.2519788918205805	A	12.05	1.822179	0.32237	0.042579	0.242446	ENSG00000178031	ENST00000380548;ENST00000380545;ENST00000316239;ENST00000380541;ENST00000380538	T;T;T	0.66995	-0.24;-0.24;-0.24	5.81	4.48	0.54585	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.472937	0.24393	N	0.038912	T	0.00012	0.0000	L	0.39898	1.24	0.36876	P	0.11082199999999998	B;B	0.28128	0.137;0.201	B;B	0.28385	0.085;0.089	T	0.07673	-1.0760	9	0.29301	T	0.29	.	6.0982	0.20033	0.8341:0.0:0.1659:0.0	rs41304755	110;1409	Q8N6G6-6;Q8N6G6	.;ATL1_HUMAN	G	1409;110;113;113;11	ENSP00000369921:D1409G;ENSP00000369918:D110G;ENSP00000369911:D11G	ENSP00000325584:D113G	D	+	2	0	ADAMTSL1	18819952	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.508000	0.45450	2.225000	0.72522	0.533000	0.62120	GAT	A|0.852;G|0.148	0.148	strong		0.552	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
FMO2	2327	hgsc.bcm.edu	37	1	171154959	171154959	+	Missense_Mutation	SNP	A	A	G	rs2020870	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:171154959A>G	ENST00000209929.7	+	2	265	c.107A>G	c.(106-108)gAt>gGt	p.D36G	FMO2_ENST00000529935.1_Intron|FMO2_ENST00000441535.1_Missense_Mutation_p.D36G			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	36					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AGAACTGAAGATATTGGAGGA	0.453													A|||	461	0.0920527	0.0628	0.0447	5008	,	,		18771	0.1508		0.0586	False		,,,				2504	0.1391				p.D36G		Atlas-SNP	.											.	FMO2	66	.	0			c.A107G	GRCh37	CM033897	FMO2	M	rs2020870	PASS	.	A	GLY/ASP	290,4116	160.0+/-192.4	12,266,1925	254.0	244.0	248.0		107	5.7	1.0	1	dbSNP_98	248	583,8017	156.4+/-210.3	32,519,3749	yes	missense	FMO2	NM_001460.2	94	44,785,5674	GG,GA,AA		6.7791,6.5819,6.7123	benign	36/472	171154959	873,12133	2203	4300	6503	SO:0001583	missense	2327	exon2			CTGAAGATATTGG	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.107A>G	1.37:g.171154959A>G	ENSP00000209929:p.Asp36Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	135	78	0.577778	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	178	0.0815018315018315	39	0.07926829268292683	16	0.04419889502762431	76	0.13286713286713286	47	0.06200527704485488	A	28.8	4.948795	0.92660	0.065819	0.067791	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.64085	-0.08;-0.08	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.64527	0.2606	M	0.78223	2.4	0.09310	P	0.99999530272	B	0.33212	0.402	P	0.44772	0.46	T	0.71896	-0.4454	9	0.72032	D	0.01	-28.1586	14.8692	0.70444	1.0:0.0:0.0:0.0	rs2020870;rs2266712;rs52821140;rs58458262;rs2020870	36	Q99518	FMO2_HUMAN	G	36	ENSP00000209929:D36G;ENSP00000405905:D36G	ENSP00000209929:D36G	D	+	2	0	FMO2	169421583	1.000000	0.71417	0.971000	0.41717	0.938000	0.57974	8.869000	0.92326	2.145000	0.66743	0.533000	0.62120	GAT	A|0.919;G|0.081	0.081	strong		0.453	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
TMC7	79905	hgsc.bcm.edu	37	16	19041595	19041595	+	Missense_Mutation	SNP	G	G	A	rs28583298	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19041595G>A	ENST00000304381.5	+	6	891	c.761G>A	c.(760-762)gGg>gAg	p.G254E	TMC7_ENST00000569532.1_Missense_Mutation_p.G254E|TMC7_ENST00000421369.3_Missense_Mutation_p.G144E	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	254			G -> E (in dbSNP:rs28583298). {ECO:0000269|PubMed:12812529, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						ACCATTGATGGGGTGAAATTT	0.478													G|||	2723	0.54373	0.171	0.598	5008	,	,		20258	0.7788		0.6491	False		,,,				2504	0.6585				p.G254E		Atlas-SNP	.											.	TMC7	75	.	0			c.G761A						PASS	.	G	GLU/GLY,GLU/GLY	1084,3310	391.7+/-328.2	124,836,1237	143.0	128.0	133.0		431,761	4.5	1.0	16	dbSNP_125	133	5395,3205	653.2+/-401.0	1717,1961,622	yes	missense,missense	TMC7	NM_001160364.1,NM_024847.3	98,98	1841,2797,1859	AA,AG,GG		37.2674,24.67,49.8615	benign,benign	144/614,254/724	19041595	6479,6515	2197	4300	6497	SO:0001583	missense	79905	exon6			TTGATGGGGTGAA	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.761G>A	16.37:g.19041595G>A	ENSP00000304710:p.Gly254Glu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Missense_Mutation	SNP	ENST00000304381.5	37	CCDS10573.1	1235	0.5654761904761905	96	0.1951219512195122	213	0.5883977900552486	444	0.7762237762237763	482	0.6358839050131926	G	13.07	2.127155	0.37533	0.2467	0.627326	ENSG00000170537	ENST00000304381;ENST00000421369	T;T	0.49432	0.78;0.78	5.52	4.51	0.55191	.	0.357378	0.30076	N	0.010468	T	0.00012	0.0000	N	0.14661	0.345	0.32260	P	0.5702929999999999	B	0.02656	0.0	B	0.12156	0.007	T	0.37197	-0.9716	9	0.02654	T	1	.	13.4685	0.61270	0.0:0.3142:0.6858:0.0	rs4072393;rs5816024;rs17527436	254	Q7Z402	TMC7_HUMAN	E	254;144	ENSP00000304710:G254E;ENSP00000397081:G144E	ENSP00000304710:G254E	G	+	2	0	TMC7	18949096	0.953000	0.32496	0.997000	0.53966	0.974000	0.67602	1.028000	0.30128	2.770000	0.95276	0.655000	0.94253	GGG	G|0.443;A|0.557	0.557	strong		0.478	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847	
CX3CL1	6376	hgsc.bcm.edu	37	16	57413660	57413660	+	Missense_Mutation	SNP	C	C	T	rs62037084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:57413660C>T	ENST00000006053.6	+	2	296	c.185C>T	c.(184-186)gCa>gTa	p.A62V	CX3CL1_ENST00000564948.1_Intron|CX3CL1_ENST00000565912.1_Missense_Mutation_p.A24V|CX3CL1_ENST00000563383.1_Missense_Mutation_p.A68V	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	62	Chemokine.				angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GGCAAACGCGCAATCATGTAG	0.512													C|||	8	0.00159744	0.0008	0.0	5008	,	,		24126	0.0		0.006	False		,,,				2504	0.001				p.A62V		Atlas-SNP	.											CX3CL1,NS,carcinoma,+1,1	CX3CL1	27	1	0			c.C185T						PASS	.	C	VAL/ALA	5,4391	9.9+/-24.2	0,5,2193	160.0	125.0	137.0		185	3.2	0.8	16	dbSNP_129	137	58,8542	36.4+/-91.3	1,56,4243	yes	missense	CX3CL1	NM_002996.3	64	1,61,6436	TT,TC,CC		0.6744,0.1137,0.4848	probably-damaging	62/398	57413660	63,12933	2198	4300	6498	SO:0001583	missense	6376	exon2			AACGCGCAATCAT	U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"""Endogenous ligands"""	10647	protein-coding gene	gene with protein product		601880	"""small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"""	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.185C>T	16.37:g.57413660C>T	ENSP00000006053:p.Ala62Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	126	71	0.563492	NM_002996	O00672	Missense_Mutation	SNP	ENST00000006053.6	37	CCDS10779.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	17.81	3.481779	0.63849	0.001137	0.006744	ENSG00000006210	ENST00000006053	T	0.25250	1.81	3.2	3.2	0.36748	Chemokine interleukin-8-like domain (3);	0.000000	0.64402	D	0.000020	T	0.36608	0.0973	M	0.93898	3.47	0.29244	N	0.872459	P	0.51240	0.943	P	0.48334	0.574	T	0.54596	-0.8270	10	0.87932	D	0	-15.9569	10.2419	0.43316	0.0:1.0:0.0:0.0	rs62037084	62	P78423	X3CL1_HUMAN	V	62	ENSP00000006053:A62V	ENSP00000006053:A62V	A	+	2	0	CX3CL1	55971161	0.376000	0.25098	0.848000	0.33437	0.018000	0.09664	0.962000	0.29280	2.128000	0.65567	0.460000	0.39030	GCA	C|0.996;T|0.004	0.004	strong		0.512	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996	
PLCB1	23236	hgsc.bcm.edu	37	20	8737734	8737734	+	Silent	SNP	G	G	A	rs2076413	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:8737734G>A	ENST00000338037.6	+	24	2592	c.2565G>A	c.(2563-2565)gcG>gcA	p.A855A	PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Silent_p.A855A|PLCB1_ENST00000378641.3_Silent_p.A855A	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	855					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						CAAGTGAAGCGAGAACGACTC	0.473													G|||	1063	0.21226	0.1104	0.2219	5008	,	,		17943	0.13		0.3022	False		,,,				2504	0.3354				p.P855P		Atlas-SNP	.											.	PLCB1	394	.	0			c.T2565A						PASS	.	G	,	588,3818	257.0+/-261.6	43,502,1658	71.0	74.0	73.0		2565,2565	-1.6	0.8	20	dbSNP_96	73	2688,5912	430.6+/-356.6	451,1786,2063	no	coding-synonymous,coding-synonymous	PLCB1	NM_015192.2,NM_182734.1	,	494,2288,3721	AA,AG,GG		31.2558,13.3454,25.1884	,	855/1217,855/1174	8737734	3276,9730	2203	4300	6503	SO:0001819	synonymous_variant	23236	exon24			TGAAGCGAGAACG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2565G>A	20.37:g.8737734G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			G|0.773;A|0.227	0.227	strong		0.473	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
CDC27	996	hgsc.bcm.edu	37	17	45198343	45198343	+	Silent	SNP	C	C	T	rs731790	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45198343C>T	ENST00000066544.3	-	19	2526	c.2433G>A	c.(2431-2433)gcG>gcA	p.A811A	AC002558.1_ENST00000408089.1_RNA|CDC27_ENST00000527547.1_Silent_p.A810A|CDC27_ENST00000446365.2_Silent_p.A750A|CDC27_ENST00000531206.1_Silent_p.A817A	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	811					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						GTGTGTCATCCGCATCTGTCA	0.398													C|||	284	0.0567093	0.1074	0.0576	5008	,	,		19405	0.0089		0.0636	False		,,,				2504	0.0297				p.A817A		Atlas-SNP	.											.	CDC27	337	.	0			c.G2451A						PASS	.	C	,	472,3934	221.3+/-238.5	22,428,1753	126.0	96.0	106.0		2451,2433	-11.5	0.3	17	dbSNP_86	106	584,8016	153.9+/-208.2	19,546,3735	no	coding-synonymous,coding-synonymous	CDC27	NM_001114091.1,NM_001256.3	,	41,974,5488	TT,TC,CC		6.7907,10.7127,8.1193	,	817/831,811/825	45198343	1056,11950	2203	4300	6503	SO:0001819	synonymous_variant	996	exon19			GTCATCCGCATCT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.2433G>A	17.37:g.45198343C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			C|0.925;T|0.075	0.075	strong		0.398	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
MED12	9968	hgsc.bcm.edu	37	X	70349947	70349947	+	Silent	SNP	A	A	C	rs5030619	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:70349947A>C	ENST00000374080.3	+	28	3962	c.3930A>C	c.(3928-3930)ccA>ccC	p.P1310P	MED12_ENST00000333646.6_Silent_p.P1310P|MED12_ENST00000374102.1_Silent_p.P1310P			Q93074	MED12_HUMAN	mediator complex subunit 12	1310					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TGCAAGACCCAGTGTTGAGTA	0.552			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome						.|||	419	0.110993	0.0166	0.1326	3775	,	,		16117	0.001		0.2565	False		,,,				2504	0.047				p.P1310P		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A3930C						PASS	.	A		204,3369		12,145,35,1344,536	57.0	56.0	57.0		3930	-4.0	1.0	X	dbSNP_113	57	2089,4488		225,1046,593,1111,1220	no	coding-synonymous	MED12	NM_005120.2		237,1191,628,2455,1756	CC,CA,C,AA,A		31.7622,5.7095,22.5911		1310/2178	70349947	2293,7857	2072	4195	6267	SO:0001819	synonymous_variant	9968	exon28			AGACCCAGTGTTG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.3930A>C	X.37:g.70349947A>C		Somatic	432	0	0		WXS	Illumina HiSeq	Phase_I	223	221	0.991031	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1																																																																																			A|0.853;0|0.007	.	strong		0.552	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
VSTM1	284415	hgsc.bcm.edu	37	19	54545186	54545186	+	Silent	SNP	C	C	T	rs73058793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54545186C>T	ENST00000338372.2	-	7	712	c.537G>A	c.(535-537)ccG>ccA	p.P179P	VSTM1_ENST00000366170.2_Silent_p.P91P|VSTM1_ENST00000425006.2_3'UTR|VSTM1_ENST00000376626.1_Silent_p.P148P	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	179					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		CCTCCTGCTCCGGAAGTTTGG	0.493													C|||	907	0.18111	0.1384	0.2896	5008	,	,		17447	0.0645		0.331	False		,,,				2504	0.1278				p.P179P		Atlas-SNP	.											.	VSTM1	30	.	0			c.G537A						PASS	.	C		745,3661	304.1+/-288.3	66,613,1524	55.0	56.0	55.0		537	-6.1	0.0	19	dbSNP_130	55	2663,5937	426.5+/-355.3	400,1863,2037	no	coding-synonymous	VSTM1	NM_198481.3		466,2476,3561	TT,TC,CC		30.9651,16.9088,26.2033		179/237	54545186	3408,9598	2203	4300	6503	SO:0001819	synonymous_variant	284415	exon7			CTGCTCCGGAAGT	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.537G>A	19.37:g.54545186C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	55	54	0.981818	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Silent	SNP	ENST00000338372.2	37	CCDS12872.1																																																																																			C|0.755;T|0.245	0.245	strong		0.493	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481	
IL17F	112744	hgsc.bcm.edu	37	6	52101844	52101844	+	Missense_Mutation	SNP	T	T	C	rs2397084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:52101844T>C	ENST00000336123.4	-	3	484	c.377A>G	c.(376-378)gAg>gGg	p.E126G		NM_052872.3	NP_443104.1	Q96PD4	IL17F_HUMAN	interleukin 17F	126			E -> G (in dbSNP:rs2397084).		cartilage development (GO:0051216)|cytokine biosynthetic process (GO:0042089)|inflammatory response (GO:0006954)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045423)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of interleukin-8 biosynthetic process (GO:0045414)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine binding (GO:0019955)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)	14	Lung NSC(77;0.116)					GACCAGGGTCTCTTGCTGGAT	0.547													T|||	166	0.033147	0.003	0.0476	5008	,	,		21490	0.004		0.0785	False		,,,				2504	0.047				p.E126G		Atlas-SNP	.											IL17F,NS,carcinoma,+1,2	IL17F	28	2	0			c.A377G						PASS	.	T	GLY/GLU	95,4311	75.7+/-113.9	0,95,2108	95.0	87.0	90.0		377	5.7	1.0	6	dbSNP_100	90	772,7828	183.5+/-231.7	29,714,3557	yes	missense	IL17F	NM_052872.3	98	29,809,5665	CC,CT,TT		8.9767,2.1562,6.6662	probably-damaging	126/164	52101844	867,12139	2203	4300	6503	SO:0001583	missense	112744	exon3			AGGGTCTCTTGCT	AF384857	CCDS4938.1	6p12	2014-09-17			ENSG00000112116	ENSG00000112116		"""Interleukins and interleukin receptors"""	16404	protein-coding gene	gene with protein product		606496				11591732, 11591768	Standard	NM_052872		Approved	IL-17F, ML-1, ML1	uc003pam.1	Q96PD4	OTTHUMG00000014845	ENST00000336123.4:c.377A>G	6.37:g.52101844T>C	ENSP00000337432:p.Glu126Gly	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	57	0.575758	NM_052872	Q6NSI0|Q7Z6P4|Q96PI8|Q9NUE6	Missense_Mutation	SNP	ENST00000336123.4	37	CCDS4938.1	89	0.04075091575091575	4	0.008130081300813009	22	0.06077348066298342	1	0.0017482517482517483	62	0.08179419525065963	T	21.9	4.216069	0.79352	0.021562	0.089767	ENSG00000112116	ENST00000336123	T	0.57107	0.42	5.72	5.72	0.89469	.	0.056430	0.64402	D	0.000001	T	0.69324	0.3098	M	0.84846	2.72	0.46749	D	0.999186	D	0.89917	1.0	D	0.77557	0.99	T	0.75473	-0.3305	10	0.66056	D	0.02	-37.3585	13.9726	0.64250	0.0:0.0:0.0:1.0	rs2397084;rs2397084	126	Q96PD4	IL17F_HUMAN	G	126	ENSP00000337432:E126G	ENSP00000337432:E126G	E	-	2	0	IL17F	52209803	1.000000	0.71417	0.973000	0.42090	0.860000	0.49131	4.643000	0.61390	2.194000	0.70268	0.533000	0.62120	GAG	T|0.948;C|0.052	0.052	strong		0.547	IL17F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040901.3	NM_052872	
PDLIM5	10611	hgsc.bcm.edu	37	4	95496882	95496882	+	Missense_Mutation	SNP	C	C	T	rs2452600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:95496882C>T	ENST00000317968.4	+	5	543	c.407C>T	c.(406-408)tCt>tTt	p.S136F	PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000542407.1_Missense_Mutation_p.S14F|PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000318007.5_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	136			S -> F (in dbSNP:rs2452600). {ECO:0000269|PubMed:14702039}.		regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		GGTTCTGTGTCTTCACCAAAA	0.527													C|||	1125	0.224641	0.1051	0.2378	5008	,	,		19873	0.378		0.3121	False		,,,				2504	0.1288				p.S136F		Atlas-SNP	.											.	PDLIM5	76	.	0			c.C407T						PASS	.	C	,,,PHE/SER	594,3812	261.9+/-264.6	38,518,1647	296.0	259.0	271.0		,,,407	4.4	1.0	4	dbSNP_100	271	2668,5932	429.7+/-356.3	434,1800,2066	yes	intron,intron,intron,missense	PDLIM5	NM_001011513.2,NM_001011515.1,NM_001011516.1,NM_006457.3	,,,155	472,2318,3713	TT,TC,CC		31.0233,13.4816,25.0807	,,,possibly-damaging	,,,136/597	95496882	3262,9744	2203	4300	6503	SO:0001583	missense	10611	exon5			CTGTGTCTTCACC	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.407C>T	4.37:g.95496882C>T	ENSP00000321746:p.Ser136Phe	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	275	120	0.436364	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	601	0.2751831501831502	43	0.08739837398373984	84	0.23204419889502761	242	0.4230769230769231	232	0.30606860158311344	C	20.8	4.042342	0.75732	0.134816	0.310233	ENSG00000163110	ENST00000317968;ENST00000542407	T;T	0.61627	0.58;0.09	5.25	4.39	0.52855	.	0.343767	0.28865	N	0.013899	T	0.00012	0.0000	L	0.44542	1.39	0.28580	P	0.9101637	P	0.49961	0.93	B	0.42214	0.38	T	0.45086	-0.9285	9	0.56958	D	0.05	.	13.5979	0.62002	0.0:0.9248:0.0:0.0752	rs2452600;rs3792659;rs52807888;rs56704997;rs2452600	136	Q96HC4	PDLI5_HUMAN	F	136;14	ENSP00000321746:S136F;ENSP00000442187:S14F	ENSP00000321746:S136F	S	+	2	0	PDLIM5	95715905	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.262000	0.43285	2.590000	0.87494	0.655000	0.94253	TCT	C|0.737;T|0.263	0.263	strong		0.527	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
DAPK1	1612	hgsc.bcm.edu	37	9	90219920	90219920	+	Silent	SNP	G	G	A	rs36207428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:90219920G>A	ENST00000408954.3	+	3	449	c.114G>A	c.(112-114)caG>caA	p.Q38Q	DAPK1_ENST00000472284.1_Silent_p.Q38Q|DAPK1_ENST00000491893.1_Silent_p.Q38Q|DAPK1_ENST00000469640.2_Silent_p.Q38Q|DAPK1_ENST00000358077.5_Silent_p.Q38Q	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	38	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CCGGCCTCCAGTATGCCGCCA	0.507									Chronic Lymphocytic Leukemia, Familial Clustering of				G|||	433	0.0864617	0.2269	0.0461	5008	,	,		17937	0.0		0.0656	False		,,,				2504	0.0358				p.Q38Q		Atlas-SNP	.											.	DAPK1	329	.	0			c.G114A						PASS	.	G		709,3473		60,589,1442	37.0	40.0	39.0		114	3.1	1.0	9	dbSNP_126	39	425,8057		8,409,3824	no	coding-synonymous	DAPK1	NM_004938.2		68,998,5266	AA,AG,GG		5.0106,16.9536,8.9545		38/1431	90219920	1134,11530	2091	4241	6332	SO:0001819	synonymous_variant	1612	exon3	Familial Cancer Database	Familial CLL	CCTCCAGTATGCC	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.114G>A	9.37:g.90219920G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			G|0.931;A|0.069	0.069	strong		0.507	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
TBX6	6911	hgsc.bcm.edu	37	16	30097630	30097630	+	Silent	SNP	C	C	T	rs2289292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:30097630C>T	ENST00000395224.2	-	9	1286	c.1227G>A	c.(1225-1227)ccG>ccA	p.P409P	TBX6_ENST00000279386.2_Silent_p.P409P	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	409					anatomical structure morphogenesis (GO:0009653)|cell fate specification (GO:0001708)|mesoderm development (GO:0007498)|mesoderm formation (GO:0001707)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P409P(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						GGAGAAAGTGCGGGGCAAAGG	0.677													C|||	1256	0.250799	0.0219	0.3112	5008	,	,		10946	0.4633		0.339	False		,,,				2504	0.2076				p.P409P		Atlas-SNP	.											TBX6,NS,lymphoid_neoplasm,0,2	TBX6	29	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.G1227A						PASS	.	C		356,4038		16,324,1857	26.0	30.0	28.0		1227	-9.5	0.3	16	dbSNP_100	28	2909,5687		502,1905,1891	no	coding-synonymous	TBX6	NM_004608.3		518,2229,3748	TT,TC,CC		33.8413,8.102,25.1347		409/437	30097630	3265,9725	2197	4298	6495	SO:0001819	synonymous_variant	6911	exon9			AAAGTGCGGGGCA	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922		"""T-boxes"""	11605	protein-coding gene	gene with protein product		602427				9888994, 9933572	Standard	NM_004608		Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.1227G>A	16.37:g.30097630C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_004608	Q8TAS4|Q9HA44	Silent	SNP	ENST00000395224.2	37	CCDS10670.1																																																																																			C|0.749;T|0.251	0.251	strong		0.677	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758	
MUC16	94025	hgsc.bcm.edu	37	19	9076950	9076950	+	Missense_Mutation	SNP	C	C	A	rs2547076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9076950C>A	ENST00000397910.4	-	3	10699	c.10496G>T	c.(10495-10497)aGg>aTg	p.R3499M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3500	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TACATTGGCCCTCAGAGTCTC	0.502													A|||	1243	0.248203	0.2005	0.2118	5008	,	,		24394	0.249		0.3121	False		,,,				2504	0.272				p.R3499M		Atlas-SNP	.											.	MUC16	4315	.	0			c.G10496T						PASS	.	A	MET/ARG	886,3278		102,682,1298	127.0	121.0	123.0		10496	0.5	0.0	19	dbSNP_100	123	2432,6002		352,1728,2137	yes	missense	MUC16	NM_024690.2	91	454,2410,3435	AA,AC,CC		28.8357,21.2776,26.3375	benign	3499/14508	9076950	3318,9280	2082	4217	6299	SO:0001583	missense	94025	exon3			TTGGCCCTCAGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10496G>T	19.37:g.9076950C>A	ENSP00000381008:p.Arg3499Met	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	271	135	0.498155	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	a	2.270	-0.367308	0.05069	0.212776	0.288357	ENSG00000181143	ENST00000397910	T	0.02974	4.09	1.51	0.457	0.16661	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.48692	-0.9013	8	0.87932	D	0	.	2.3614	0.04308	0.4966:0.3054:0.198:0.0	rs2547076;rs17418490;rs57816798;rs2547076	3499	B5ME49	.	M	3499	ENSP00000381008:R3499M	ENSP00000381008:R3499M	R	-	2	0	MUC16	8937950	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-0.617000	0.05584	-0.277000	0.09193	-1.032000	0.02404	AGG	C|0.750;A|0.250	0.250	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LRRK2	120892	hgsc.bcm.edu	37	12	40713901	40713901	+	Missense_Mutation	SNP	T	T	A	rs11564148	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:40713901T>A	ENST00000298910.7	+	34	4997	c.4939T>A	c.(4939-4941)Tca>Aca	p.S1647T		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1647			S -> T (in dbSNP:rs11564148). {ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:22415848}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GAACTACATGTCACAGTATTT	0.343											OREG0003827	type=REGULATORY REGION|Gene=LOC486608|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	T|||	1432	0.285942	0.174	0.2349	5008	,	,		15026	0.3373		0.3171	False		,,,				2504	0.3885				p.S1647T		Atlas-SNP	.											.	LRRK2	763	.	0			c.T4939A						PASS	.	T	THR/SER	787,3611	282.8+/-276.7	65,657,1477	48.0	56.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4939	0.4	0.9	12	dbSNP_120	54	2561,6031	400.1+/-346.7	365,1831,2100	yes	missense	LRRK2	NM_198578.3	58	430,2488,3577	AA,AT,TT		29.8068,17.8945,25.7737	benign	1647/2528	40713901	3348,9642	2199	4296	6495	SO:0001583	missense	120892	exon34			TACATGTCACAGT	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4939T>A	12.37:g.40713901T>A	ENSP00000298910:p.Ser1647Thr	Somatic	91	0	0	895	WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	601	0.2751831501831502	84	0.17073170731707318	84	0.23204419889502761	186	0.32517482517482516	247	0.3258575197889182	T	8.769	0.925573	0.18056	0.178945	0.298068	ENSG00000188906	ENST00000298910	T	0.71934	-0.61	5.7	0.447	0.16608	.	0.627416	0.16568	N	0.208778	T	0.00012	0.0000	N	0.20685	0.6	0.28700	P	0.904148	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	9	0.12430	T	0.62	.	2.5413	0.04726	0.1726:0.0729:0.2196:0.5348	rs11564148;rs17443986;rs17461817;rs17583879;rs52790032;rs11564148	1647	Q5S007	LRRK2_HUMAN	T	1647	ENSP00000298910:S1647T	ENSP00000298910:S1647T	S	+	1	0	LRRK2	39000168	0.989000	0.36119	0.936000	0.37596	0.987000	0.75469	0.833000	0.27504	-0.154000	0.11118	0.482000	0.46254	TCA	A|0.266;N|0.000	0.266	strong		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
NME8	51314	hgsc.bcm.edu	37	7	37916455	37916455	+	Silent	SNP	A	A	G	rs62001868	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:37916455A>G	ENST00000199447.4	+	12	1212	c.840A>G	c.(838-840)agA>agG	p.R280R	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Silent_p.R280R	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	280					cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										ATCTGGAAAGACAACATTTAG	0.313													A|||	1005	0.200679	0.2791	0.1254	5008	,	,		14959	0.2222		0.0895	False		,,,				2504	0.2403				p.R280R		Atlas-SNP	.											.	.	.	.	0			c.A840G						PASS	.	A		1011,3395	366.8+/-318.0	128,755,1320	58.0	61.0	60.0		840	0.4	0.3	7	dbSNP_129	60	613,7987	156.6+/-210.4	24,565,3711	no	coding-synonymous	TXNDC3	NM_016616.4		152,1320,5031	GG,GA,AA		7.1279,22.946,12.4865		280/589	37916455	1624,11382	2203	4300	6503	SO:0001819	synonymous_variant	51314	exon12			GGAAAGACAACAT	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.840A>G	7.37:g.37916455A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	37	CCDS5452.1																																																																																			A|0.870;G|0.130	0.130	strong		0.313	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
OR13C5	138799	hgsc.bcm.edu	37	9	107361129	107361129	+	Missense_Mutation	SNP	C	C	T	rs4117966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107361129C>T	ENST00000374779.2	-	1	659	c.566G>A	c.(565-567)tGt>tAt	p.C189Y		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	189			C -> Y (in dbSNP:rs4117966).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						GATGTCAGCACAGGCCAGTTT	0.388													C|||	1820	0.363419	0.3994	0.2133	5008	,	,		24769	0.5645		0.1789	False		,,,				2504	0.4039				p.C189Y		Atlas-SNP	.											.	OR13C5	60	.	0			c.G566A						PASS	.	C	TYR/CYS	1567,2839	492.0+/-362.3	283,1001,919	183.0	169.0	173.0		566	4.2	0.3	9	dbSNP_108	173	1660,6940	306.8+/-308.1	182,1296,2822	no	missense	OR13C5	NM_001004482.1	194	465,2297,3741	TT,TC,CC		19.3023,35.5651,24.8116	probably-damaging	189/319	107361129	3227,9779	2203	4300	6503	SO:0001583	missense	138799	exon1			TCAGCACAGGCCA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.566G>A	9.37:g.107361129C>T	ENSP00000363911:p.Cys189Tyr	Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	401	182	0.453865	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	700	0.32051282051282054	174	0.35365853658536583	72	0.19889502762430938	322	0.5629370629370629	132	0.1741424802110818	C	19.12	3.766581	0.69878	0.355651	0.193023	ENSG00000255800	ENST00000374779	T	0.00462	7.26	4.17	4.17	0.49024	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40469	U	0.001090	T	0.00012	0.0000	H	0.97077	3.935	0.28200	P	0.9273963000000001	D	0.89917	1.0	D	0.97110	1.0	T	0.13124	-1.0521	9	0.87932	D	0	.	14.0519	0.64742	0.0:1.0:0.0:0.0	rs4117966;rs52805780;rs57944987;rs4117966	189	Q8NGS8	O13C5_HUMAN	Y	189	ENSP00000363911:C189Y	ENSP00000363911:C189Y	C	-	2	0	OR13C5	106400950	0.971000	0.33674	0.337000	0.25536	0.483000	0.33249	2.706000	0.47135	2.169000	0.68431	0.531000	0.56144	TGT	C|0.726;T|0.274	0.274	strong		0.388	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
KIAA1755	85449	hgsc.bcm.edu	37	20	36869516	36869516	+	Missense_Mutation	SNP	C	C	A	rs1205434	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:36869516C>A	ENST00000279024.4	-	3	1288	c.1017G>T	c.(1015-1017)aaG>aaT	p.K339N		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	339			K -> N (in dbSNP:rs1205434). {ECO:0000269|PubMed:11214970}.							breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AGCTTTCTGGCTTTGTGCAAG	0.498													C|||	1291	0.257788	0.1808	0.2262	5008	,	,		19642	0.2679		0.3201	False		,,,				2504	0.3098				p.K339N		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G1017T						PASS	.	C	ASN/LYS	886,3520	338.6+/-305.4	94,698,1411	141.0	157.0	151.0		1017	3.1	0.8	20	dbSNP_87	151	2844,5756	439.9+/-359.4	504,1836,1960	yes	missense	KIAA1755	NM_001029864.1	94	598,2534,3371	AA,AC,CC		33.0698,20.1089,28.6791	possibly-damaging	339/1201	36869516	3730,9276	2203	4300	6503	SO:0001583	missense	85449	exon3			TTCTGGCTTTGTG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1017G>T	20.37:g.36869516C>A	ENSP00000279024:p.Lys339Asn	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	592	0.27106227106227104	104	0.21138211382113822	85	0.23480662983425415	149	0.26048951048951047	254	0.33509234828496043	C	15.96	2.985908	0.53934	0.201089	0.330698	ENSG00000149633	ENST00000279024	T	0.63580	-0.05	5.23	3.13	0.36017	.	0.412203	0.20484	N	0.091427	T	0.00012	0.0000	M	0.62723	1.935	0.41623	P	0.011029999999999984	B	0.15473	0.013	B	0.14023	0.01	T	0.15607	-1.0431	9	0.62326	D	0.03	.	7.9862	0.30213	0.0:0.7368:0.167:0.0961	rs1205434;rs52834934;rs61689240;rs1205434	339	Q5JYT7	K1755_HUMAN	N	339	ENSP00000279024:K339N	ENSP00000279024:K339N	K	-	3	2	KIAA1755	36302930	0.003000	0.15002	0.824000	0.32777	0.122000	0.20287	0.488000	0.22371	1.403000	0.46800	0.655000	0.94253	AAG	C|0.710;A|0.290	0.290	strong		0.498	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
PRDM5	11107	hgsc.bcm.edu	37	4	121738049	121738049	+	Silent	SNP	T	T	C	rs343192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:121738049T>C	ENST00000264808.3	-	6	921	c.681A>G	c.(679-681)ctA>ctG	p.L227L	PRDM5_ENST00000428209.2_Intron|PRDM5_ENST00000515109.1_Intron	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	227					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						AAGACTCCTTTAGACTGCTTT	0.363													C|||	1377	0.27496	0.2057	0.3948	5008	,	,		17855	0.3562		0.3191	False		,,,				2504	0.1544				p.L227L		Atlas-SNP	.											PRDM5,NS,carcinoma,-2,1	PRDM5	76	1	0			c.A681G						PASS	.	C		947,3459	735.3+/-410.7	106,735,1362	154.0	159.0	157.0		681	2.4	1.0	4	dbSNP_79	157	2711,5889	682.3+/-403.8	446,1819,2035	no	coding-synonymous	PRDM5	NM_018699.2		552,2554,3397	CC,CT,TT		31.5233,21.4934,28.1255		227/631	121738049	3658,9348	2203	4300	6503	SO:0001819	synonymous_variant	11107	exon6			CTCCTTTAGACTG	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"""Zinc fingers, C2H2-type"""	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.681A>G	4.37:g.121738049T>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	194	92	0.474227	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Silent	SNP	ENST00000264808.3	37	CCDS3716.1																																																																																			T|0.707;C|0.293	0.293	strong		0.363	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
ITPRIP	85450	hgsc.bcm.edu	37	10	106075081	106075081	+	Silent	SNP	G	G	A	rs34043167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:106075081G>A	ENST00000337478.1	-	2	900	c.729C>T	c.(727-729)atC>atT	p.I243I	RP11-127L20.5_ENST00000472915.2_RNA|ITPRIP_ENST00000358187.2_Silent_p.I243I|ITPRIP_ENST00000278071.2_Silent_p.I243I	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	243						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						GGACCACCTTGATCTGGCCGT	0.642													G|||	204	0.0407348	0.0038	0.0591	5008	,	,		19373	0.0		0.1402	False		,,,				2504	0.0174				p.I243I		Atlas-SNP	.											.	ITPRIP	44	.	0			c.C729T						PASS	.	G		142,4264	96.7+/-135.4	0,142,2061	38.0	40.0	39.0		729	5.2	1.0	10	dbSNP_126	39	1300,7300	248.6+/-276.2	109,1082,3109	no	coding-synonymous	ITPRIP	NM_033397.2		109,1224,5170	AA,AG,GG		15.1163,3.2229,11.0872		243/548	106075081	1442,11564	2203	4300	6503	SO:0001819	synonymous_variant	85450	exon2			CACCTTGATCTGG	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"""KIAA1754"", ""inositol 1,4,5-triphosphate receptor interacting protein"""	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.729C>T	10.37:g.106075081G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_001272013	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Silent	SNP	ENST00000337478.1	37	CCDS7557.1																																																																																			G|0.906;A|0.094	0.094	strong		0.642	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397	
FAT3	120114	hgsc.bcm.edu	37	11	92086513	92086513	+	Missense_Mutation	SNP	C	C	T	rs10830902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:92086513C>T	ENST00000298047.6	+	1	1252	c.1235C>T	c.(1234-1236)tCt>tTt	p.S412F	FAT3_ENST00000409404.2_Missense_Mutation_p.S412F|FAT3_ENST00000541502.1_Missense_Mutation_p.S412F|FAT3_ENST00000525166.1_Missense_Mutation_p.S262F			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	412	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> F (in dbSNP:rs10830902).		homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TACAAATTATCTCCTGGTGAG	0.413										TCGA Ovarian(4;0.039)			C|||	274	0.0547125	0.1498	0.0389	5008	,	,		20418	0.001		0.0437	False		,,,				2504	0.0041				p.S412F		Atlas-SNP	.											.	FAT3	1822	.	0			c.C1235T						PASS	.	C	PHE/SER	511,3203		33,445,1379	77.0	72.0	74.0		1235	4.7	0.5	11	dbSNP_120	74	457,7749		16,425,3662	yes	missense	FAT3	NM_001008781.2	155	49,870,5041	TT,TC,CC		5.5691,13.7588,8.1208	benign	412/4558	92086513	968,10952	1857	4103	5960	SO:0001583	missense	120114	exon1			AATTATCTCCTGG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.1235C>T	11.37:g.92086513C>T	ENSP00000298047:p.Ser412Phe	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		112	0.05128205128205128	64	0.13008130081300814	16	0.04419889502762431	0	0.0	32	0.04221635883905013	C	14.19	2.461566	0.43736	0.137588	0.055691	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	5.62	4.7	0.59300	.	.	.	.	.	T	0.00468	0.0015	L	0.44542	1.39	0.51482	P	7.40000000000185E-5	P	0.38922	0.651	B	0.38616	0.277	T	0.16928	-1.0386	8	0.51188	T	0.08	.	8.6092	0.33793	0.0:0.7657:0.1529:0.0814	rs10830902;rs17512294;rs52831462;rs10830902	412	Q8TDW7-3	.	F	412;412;412;262	ENSP00000298047:S412F;ENSP00000387040:S412F;ENSP00000443786:S412F;ENSP00000432586:S262F	ENSP00000298047:S412F	S	+	2	0	FAT3	91726161	0.073000	0.21202	0.454000	0.27019	0.932000	0.56968	2.069000	0.41481	1.342000	0.45619	0.655000	0.94253	TCT	C|0.935;T|0.065	0.065	strong		0.413	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
BUB1	699	hgsc.bcm.edu	37	2	111413444	111413444	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:111413444C>G	ENST00000302759.6	-	16	1866	c.1748G>C	c.(1747-1749)gGt>gCt	p.G583A	BUB1_ENST00000535254.1_Missense_Mutation_p.G563A|BUB1_ENST00000409311.1_Missense_Mutation_p.G583A	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	583					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		GCAGCGAATACCCCATACAGT	0.468																																					p.G583A		Atlas-SNP	.											.	BUB1	91	.	0			c.G1748C						PASS	.						263.0	252.0	256.0					2																	111413444		2203	4300	6503	SO:0001583	missense	699	exon16			CGAATACCCCATA	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"""budding uninhibited by benzimidazoles 1 (yeast homolog)"", ""budding uninhibited by benzimidazoles 1 homolog (yeast)"""	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.1748G>C	2.37:g.111413444C>G	ENSP00000302530:p.Gly583Ala	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	247	119	0.481781	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Missense_Mutation	SNP	ENST00000302759.6	37	CCDS33273.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573710	0.65765	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432	T;T;T	0.52057	1.41;0.68;1.71	5.73	5.73	0.89815	.	0.211524	0.48286	D	0.000188	T	0.58293	0.2112	L	0.49640	1.575	0.36843	D	0.887494	D;D;D	0.76494	0.999;0.997;0.993	D;P;P	0.71870	0.975;0.788;0.725	T	0.55848	-0.8076	10	0.14252	T	0.57	-20.8313	13.0477	0.58937	0.0:0.8385:0.1615:0.0	.	563;583;583	F5GXI5;E9PC26;O43683	.;.;BUB1_HUMAN	A	563;583;583;583	ENSP00000441013:G563A;ENSP00000386701:G583A;ENSP00000302530:G583A	ENSP00000302530:G583A	G	-	2	0	BUB1	111129917	0.928000	0.31464	0.986000	0.45419	0.975000	0.68041	1.580000	0.36547	2.687000	0.91594	0.655000	0.94253	GGT	.	.	none		0.468	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336	
NDUFAF1	51103	hgsc.bcm.edu	37	15	41689166	41689166	+	Missense_Mutation	SNP	C	C	A	rs3204853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41689166C>A	ENST00000260361.4	-	2	473	c.92G>T	c.(91-93)cGc>cTc	p.R31L		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	31			R -> L (in dbSNP:rs3204853). {ECO:0000269|PubMed:11935339}.		mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		CTCTGCAAAGCGAATACCCAA	0.443													C|||	581	0.116014	0.0091	0.1585	5008	,	,		17407	0.0079		0.2714	False		,,,				2504	0.182				p.R31L		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.G92T						PASS	.	C	LEU/ARG	223,4183	128.2+/-165.1	9,205,1989	52.0	53.0	53.0		92	-4.1	0.0	15	dbSNP_105	53	2242,6356	365.7+/-334.0	277,1688,2334	yes	missense	NDUFAF1	NM_016013.2	102	286,1893,4323	AA,AC,CC		26.0758,5.0613,18.9557	benign	31/328	41689166	2465,10539	2203	4299	6502	SO:0001583	missense	51103	exon2			GCAAAGCGAATAC	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"""Mitochondrial respiratory chain complex assembly factors"""	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.92G>T	15.37:g.41689166C>A	ENSP00000260361:p.Arg31Leu	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	192	90	0.46875	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	37	CCDS10075.1	275	0.1259157509157509	6	0.012195121951219513	66	0.18232044198895028	3	0.005244755244755245	200	0.2638522427440633	C	10.60	1.394920	0.25205	0.050613	0.260758	ENSG00000137806	ENST00000260361	T	0.59224	0.28	5.23	-4.12	0.03916	.	1.787450	0.02174	N	0.059935	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11397	-1.0589	9	0.40728	T	0.16	-16.936	6.8289	0.23898	0.146:0.363:0.0:0.491	rs3204853;rs52836078;rs3204853	31	Q9Y375	CIA30_HUMAN	L	31	ENSP00000260361:R31L	ENSP00000260361:R31L	R	-	2	0	NDUFAF1	39476458	0.000000	0.05858	0.000000	0.03702	0.868000	0.49771	-0.952000	0.03881	-0.576000	0.05974	-0.261000	0.10672	CGC	C|0.839;A|0.161	0.161	strong		0.443	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
ZNF772	400720	hgsc.bcm.edu	37	19	57985566	57985566	+	Missense_Mutation	SNP	G	G	C	rs2074060	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57985566G>C	ENST00000343280.4	-	5	806	c.546C>G	c.(544-546)tgC>tgG	p.C182W	AC004076.9_ENST00000596831.1_Intron|ZNF772_ENST00000600175.1_Intron|AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000427512.2_Missense_Mutation_p.C70W|ZNF772_ENST00000425074.3_3'UTR|ZNF772_ENST00000601768.1_Intron|ZNF772_ENST00000356584.3_Missense_Mutation_p.C141W	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	182			C -> W (in dbSNP:rs2074060). {ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		TTGCACTGAAGCAGAACTGTT	0.498													C|||	3390	0.676917	0.6135	0.719	5008	,	,		22251	0.7014		0.6392	False		,,,				2504	0.7464				p.C182W	Melanoma(5;289 436 14293 15924 30817)	Atlas-SNP	.											.	ZNF772	42	.	0			c.C546G						PASS	.	C	TRP/CYS,TRP/CYS	2708,1698	512.6+/-368.1	833,1042,328	118.0	104.0	109.0		546,423	-1.1	0.0	19	dbSNP_96	109	5446,3154	479.5+/-370.1	1679,2088,533	yes	missense,missense	ZNF772	NM_001024596.2,NM_001144068.1	215,215	2512,3130,861	CC,CG,GG		36.6744,38.5384,37.3059	benign,benign	182/490,141/449	57985566	8154,4852	2203	4300	6503	SO:0001583	missense	400720	exon5			ACTGAAGCAGAAC	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"""Zinc fingers, C2H2-type"", ""-"""	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.546C>G	19.37:g.57985566G>C	ENSP00000341165:p.Cys182Trp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_001024596	A6NJK9|B4DH56|B4DYS0	Missense_Mutation	SNP	ENST00000343280.4	37	CCDS33133.1	1449|1449	0.6634615384615384|0.6634615384615384	299|299	0.6077235772357723|0.6077235772357723	255|255	0.7044198895027625|0.7044198895027625	411|411	0.7185314685314685|0.7185314685314685	484|484	0.6385224274406333|0.6385224274406333	C|C	0.004|0.004	-2.310840|-2.310840	0.00237|0.00237	0.614616|0.614616	0.633256|0.633256	ENSG00000197128|ENSG00000197128	ENST00000343280;ENST00000427512;ENST00000319969;ENST00000356584|ENST00000291809	T;T;T|.	0.07567|.	3.18;3.18;3.18|.	3.99|3.99	-1.09|-1.09	0.09904|0.09904	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.27053|0.27053	0.805|0.805	0.52501|0.52501	P|P	4.999999999999449E-5|4.999999999999449E-5	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|T	0.28332|0.28332	-1.0047|-1.0047	8|5	0.34782|0.46703	T|T	0.22|0.11	.|.	1.1261|1.1261	0.01735|0.01735	0.3129:0.2295:0.3079:0.1498|0.3129:0.2295:0.3079:0.1498	rs2074060;rs57900222;rs2074060|rs2074060;rs57900222;rs2074060	70;141;182|.	Q68DY9-2;A6NJK9;Q68DY9|.	.;.;ZN772_HUMAN|.	W|M	182;70;128;141|107	ENSP00000341165:C182W;ENSP00000395967:C70W;ENSP00000348992:C141W|.	ENSP00000321015:C128W|ENSP00000291809:I107M	C|I	-|-	3|3	2|3	ZNF772|ZNF772	62677378|62677378	0.000000|0.000000	0.05858|0.05858	0.018000|0.018000	0.16275|0.16275	0.518000|0.518000	0.34316|0.34316	-1.716000|-1.716000	0.01878|0.01878	0.038000|0.038000	0.15604|0.15604	-0.322000|-0.322000	0.08575|0.08575	TGC|ATC	G|0.353;C|0.646	0.646	strong		0.498	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
MYH3	4621	hgsc.bcm.edu	37	17	10543463	10543463	+	Silent	SNP	T	T	C	rs2285469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10543463T>C	ENST00000583535.1	-	22	2619	c.2532A>G	c.(2530-2532)gcA>gcG	p.A844A	MYH3_ENST00000226209.7_Silent_p.A844A	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	844					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCTCAGTCTCTGCACTCTTGA	0.473													C|||	2336	0.466454	0.2398	0.5346	5008	,	,		17894	0.3839		0.7584	False		,,,				2504	0.5092				p.A844A		Atlas-SNP	.											MYH3,colon,carcinoma,-1,1	MYH3	227	1	0			c.A2532G						PASS	.	C		1302,3104	698.0+/-406.3	198,906,1099	143.0	133.0	137.0		2532	-11.1	0.0	17	dbSNP_100	137	6268,2332	390.0+/-343.1	2260,1748,292	yes	coding-synonymous	MYH3	NM_002470.3		2458,2654,1391	CC,CT,TT		27.1163,29.5506,41.7961		844/1941	10543463	7570,5436	2203	4300	6503	SO:0001819	synonymous_variant	4621	exon22			AGTCTCTGCACTC		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2532A>G	17.37:g.10543463T>C		Somatic	397	0	0		WXS	Illumina HiSeq	Phase_I	424	423	0.997642	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	37	CCDS11157.1																																																																																			T|0.434;C|0.566	0.566	strong		0.473	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
NCOR2	9612	hgsc.bcm.edu	37	12	124826462	124826462	+	Missense_Mutation	SNP	C	C	T	rs2229840	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124826462C>T	ENST00000405201.1	-	34	5095	c.5095G>A	c.(5095-5097)Gcg>Acg	p.A1699T	NCOR2_ENST00000397355.1_Missense_Mutation_p.A1690T|NCOR2_ENST00000429285.2_Missense_Mutation_p.A1689T|NCOR2_ENST00000404621.1_Missense_Mutation_p.A1689T|NCOR2_ENST00000356219.3_Missense_Mutation_p.A1706T|NCOR2_ENST00000404121.2_Missense_Mutation_p.A1260T			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1707					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GCGGTGGCCGCGTTGTGGTGC	0.662													C|||	806	0.160942	0.112	0.2637	5008	,	,		16539	0.1071		0.1551	False		,,,				2504	0.2157				p.A1699T		Atlas-SNP	.											.	NCOR2	475	.	0			c.G5095A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	505,3851		23,459,1696	68.0	87.0	81.0		5065,5065,5095	4.4	0.8	12	dbSNP_98	81	1392,7176		116,1160,3008	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	58,58,58	139,1619,4704	TT,TC,CC		16.2465,11.5932,14.6781	possibly-damaging,possibly-damaging,possibly-damaging	1689/2459,1689/2505,1699/2515	124826462	1897,11027	2178	4284	6462	SO:0001583	missense	9612	exon36			TGGCCGCGTTGTG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5095G>A	12.37:g.124826462C>T	ENSP00000384018:p.Ala1699Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	321|321	0.14697802197802198|0.14697802197802198	48|48	0.0975609756097561|0.0975609756097561	84|84	0.23204419889502761|0.23204419889502761	65|65	0.11363636363636363|0.11363636363636363	124|124	0.16358839050131926|0.16358839050131926	C|C	15.92|15.92	2.976007|2.976007	0.53720|0.53720	0.115932|0.115932	0.162465|0.162465	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285|ENST00000453428	T;T;T;T;T;T|.	0.20069|.	2.1;2.37;2.1;2.37;2.11;2.37|.	4.37|4.37	4.37|4.37	0.52481|0.52481	.|.	0.069881|.	0.56097|.	D|.	0.000027|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.21448|0.21448	0.665|0.665	0.20307|0.20307	P|P	0.9999163375|0.9999163375	P;D;P|.	0.89917|.	0.92;1.0;0.939|.	B;D;B|.	0.77557|.	0.218;0.99;0.315|.	T|T	0.21143|0.21143	-1.0254|-1.0254	9|4	0.25751|.	T|.	0.34|.	-26.8749|-26.8749	10.5892|10.5892	0.45300|0.45300	0.0:0.9103:0.0:0.0897|0.0:0.9103:0.0:0.0897	rs2229840;rs59703581;rs2229840|rs2229840;rs59703581;rs2229840	1689;1690;1699|.	C9J0Q5;C9J239;C9JFD3|.	.;.;.|.	T|H	1699;1689;1706;1690;1698;1260;1689|47	ENSP00000384018:A1699T;ENSP00000384202:A1689T;ENSP00000348551:A1706T;ENSP00000380513:A1690T;ENSP00000385618:A1260T;ENSP00000400281:A1689T|.	ENSP00000348551:A1706T|.	A|R	-|-	1|2	0|0	NCOR2|NCOR2	123392415|123392415	1.000000|1.000000	0.71417|0.71417	0.755000|0.755000	0.31263|0.31263	0.859000|0.859000	0.49053|0.49053	4.646000|4.646000	0.61411|0.61411	1.985000|1.985000	0.57927|0.57927	0.491000|0.491000	0.48974|0.48974	GCG|CGC	C|0.859;T|0.141	0.141	strong		0.662	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114256859	114256859	+	Missense_Mutation	SNP	C	C	T	rs189095552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:114256859C>T	ENST00000306507.5	+	1	199	c.26C>T	c.(25-27)cCt>cTt	p.P9L		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	9					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P9L(2)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GCTGAGCGCCCTCGCTCCACA	0.647																																					p.P9L		Atlas-SNP	.											FOXD4L1,NS,malignant_melanoma,0,2	FOXD4L1	48	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.C26T						scavenged	.						24.0	34.0	31.0					2																	114256859		2142	4164	6306	SO:0001583	missense	200350	exon1			AGCGCCCTCGCTC	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.26C>T	2.37:g.114256859C>T	ENSP00000302756:p.Pro9Leu	Somatic	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	224	69	0.308036	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	265	0.12133699633699634	29	0.05894308943089431	63	0.17403314917127072	122	0.21328671328671328	51	0.06728232189973615	.	0	-2.671754	0.00104	.	.	ENSG00000184492	ENST00000306507	D	0.93307	-3.2	2.57	0.149	0.14863	.	.	.	.	.	T	0.00178	0.0005	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16988	-1.0384	8	0.18276	T	0.48	.	6.9208	0.24387	0.0:0.5889:0.0:0.4111	rs2757969;rs4644326	9	Q9NU39	FX4L1_HUMAN	L	9	ENSP00000302756:P9L	ENSP00000302756:P9L	P	+	2	0	FOXD4L1	113973329	0.000000	0.05858	0.270000	0.24601	0.060000	0.15804	-0.419000	0.07071	-0.116000	0.11893	-1.461000	0.01025	CCT	.	.	weak		0.647	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
FAM183A	440585	hgsc.bcm.edu	37	1	43618596	43618596	+	Silent	SNP	G	G	A	rs12074551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43618596G>A	ENST00000335282.4	+	3	291	c.291G>A	c.(289-291)gaG>gaA	p.E97E	FAM183A_ENST00000409337.1_Intron|FAM183A_ENST00000410048.1_Silent_p.E69E	NM_001101376.2	NP_001094846.2	A6NL82	F183A_HUMAN	family with sequence similarity 183, member A	97										kidney(1)|large_intestine(1)|lung(2)|ovary(3)	7						GGGACTTAGAGCCCTTGGTAA	0.527													G|||	600	0.119808	0.0575	0.1455	5008	,	,		22683	0.0		0.2833	False		,,,				2504	0.1411				p.E97E		Atlas-SNP	.											.	FAM183A	28	.	0			c.G291A						PASS	.	G		280,3796		11,258,1769	64.0	68.0	67.0		291	1.8	1.0	1	dbSNP_120	67	2100,6280		264,1572,2354	no	coding-synonymous	FAM183A	NM_001101376.2		275,1830,4123	AA,AG,GG		25.0597,6.8695,19.1073		97/135	43618596	2380,10076	2038	4190	6228	SO:0001819	synonymous_variant	440585	exon3			CTTAGAGCCCTTG	AI192630, AI375550, AL139138	CCDS44126.1	1p34.2	2008-08-11			ENSG00000186973	ENSG00000186973			34347	protein-coding gene	gene with protein product						11181995	Standard	NM_001101376		Approved	LOC440585, hCG23177	uc009vwo.3	A6NL82	OTTHUMG00000007286	ENST00000335282.4:c.291G>A	1.37:g.43618596G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	136	70	0.514706	NM_001101376	B7ZBL8	Silent	SNP	ENST00000335282.4	37	CCDS44126.1																																																																																			G|0.838;A|0.162	0.162	strong		0.527	FAM183A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019024.3	NM_001101376	
MEN1	4221	hgsc.bcm.edu	37	11	64572018	64572018	+	Missense_Mutation	SNP	T	T	C	rs2959656	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64572018T>C	ENST00000337652.1	-	10	2139	c.1636A>G	c.(1636-1638)Aca>Gca	p.T546A	MEN1_ENST00000312049.6_Missense_Mutation_p.T541A|MEN1_ENST00000377316.2_Missense_Mutation_p.T486A|MAP4K2_ENST00000377350.3_5'Flank|MEN1_ENST00000394374.2_Missense_Mutation_p.T546A|MAP4K2_ENST00000294066.2_5'Flank|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000443283.1_Missense_Mutation_p.T546A|MEN1_ENST00000377321.1_Missense_Mutation_p.T506A|MEN1_ENST00000478548.1_5'UTR|MEN1_ENST00000377313.1_Missense_Mutation_p.T546A|MEN1_ENST00000315422.4_Missense_Mutation_p.T541A|MEN1_ENST00000394376.1_Missense_Mutation_p.T546A|MEN1_ENST00000377326.3_Missense_Mutation_p.T541A	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	546			T -> A (in dbSNP:rs2959656). {ECO:0000269|PubMed:10576763, ECO:0000269|PubMed:12746426, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17555499, ECO:0000269|PubMed:19413330, ECO:0000269|PubMed:19690332, ECO:0000269|PubMed:9103196, ECO:0000269|PubMed:9506756, ECO:0000269|PubMed:9709921, ECO:0000269|PubMed:9888389}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.T541A(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						GGTGATGCTGTGGGTGCTGGC	0.647			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated				C|||	4179	0.834465	0.6664	0.902	5008	,	,		14283	0.6964		0.9911	False		,,,				2504	0.9949				p.T546A	Esophageal Squamous(1;83 158 15500 18603 18803 29295)	Atlas-SNP	.	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	MEN1,NS,carcinoid-endocrine_tumour,0,1	MEN1	442	1	1	Substitution - Missense(1)	lung(1)	c.A1636G	GRCh37	CM085535	MEN1	M	rs2959656	PASS	.	C	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	3247,1155	408.6+/-334.7	1221,805,175	72.0	62.0	65.0		1636,1621,1636,1636,1636,1636,1636	3.3	0.1	11	dbSNP_101	65	8559,35	22.2+/-67.0	4263,33,1	yes	missense,missense,missense,missense,missense,missense,missense	MEN1	NM_000244.3,NM_130799.2,NM_130800.2,NM_130801.2,NM_130802.2,NM_130803.2,NM_130804.2	58,58,58,58,58,58,58	5484,838,176	CC,CT,TT		0.4073,26.2381,9.1567	benign,benign,benign,benign,benign,benign,benign	546/616,541/611,546/616,546/616,546/616,546/616,546/616	64572018	11806,1190	2201	4297	6498	SO:0001583	missense	4221	exon10	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	ATGCTGTGGGTGC	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1636A>G	11.37:g.64572018T>C	ENSP00000337088:p.Thr546Ala	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_130800	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	1847	0.8456959706959707	351	0.7134146341463414	325	0.8977900552486188	418	0.7307692307692307	753	0.9934036939313984	C	0.011	-1.705252	0.00719	0.737619	0.995927	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313	D;D;D;D;D;D;D;D;D;D	0.99298	-5.71;-5.71;-5.71;-5.71;-5.71;-5.71;-5.71;-5.71;-5.71;-5.71	4.35	3.35	0.38373	.	0.623860	0.16072	N	0.230928	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43909	-0.9362	9	0.05959	T	0.93	-9.3871	5.4999	0.16823	0.0:0.6193:0.2637:0.117	rs2959656;rs17856065;rs61237165;rs2959656	541;506;546	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	A	486;506;541;541;541;546;546;546;546;546	ENSP00000366533:T486A;ENSP00000366538:T506A;ENSP00000366543:T541A;ENSP00000308975:T541A;ENSP00000323747:T541A;ENSP00000337088:T546A;ENSP00000377901:T546A;ENSP00000377899:T546A;ENSP00000396940:T546A;ENSP00000366530:T546A	ENSP00000308975:T541A	T	-	1	0	MEN1	64328594	0.006000	0.16342	0.124000	0.21820	0.022000	0.10575	0.131000	0.15870	0.982000	0.38575	-0.366000	0.07423	ACA	T|0.128;C|0.872	0.872	strong		0.647	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1		
OBSL1	23363	hgsc.bcm.edu	37	2	220422126	220422126	+	Silent	SNP	G	G	A	rs375716830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220422126G>A	ENST00000404537.1	-	12	4061	c.4005C>T	c.(4003-4005)gaC>gaT	p.D1335D	OBSL1_ENST00000265317.5_Intron|OBSL1_ENST00000373876.1_Intron|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000603926.1_Silent_p.D1335D|OBSL1_ENST00000265318.4_Silent_p.D1243D	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1335	Ig-like 11.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		ACTCCCCAGCGTCCCCGCTCC	0.692													G|||	6	0.00119808	0.0	0.0014	5008	,	,		14604	0.0		0.005	False		,,,				2504	0.0				p.D1335D		Atlas-SNP	.											.	OBSL1	120	.	0			c.C4005T						PASS	.	G	,	4,4268		0,4,2132	16.0	20.0	19.0		4005,4005	-1.8	1.0	2	dbSNP_134	19	33,8311		0,33,4139	no	coding-synonymous,coding-synonymous	OBSL1	NM_001173431.1,NM_015311.2	,	0,37,6271	AA,AG,GG		0.3955,0.0936,0.2933	,	1335/1544,1335/1897	220422126	37,12579	2136	4172	6308	SO:0001819	synonymous_variant	23363	exon12			CCCAGCGTCCCCG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.4005C>T	2.37:g.220422126G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	25	19	0.76	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1																																																																																			.	.	weak		0.692	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
AMTN	401138	hgsc.bcm.edu	37	4	71396989	71396989	+	Silent	SNP	C	C	T	rs17676820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:71396989C>T	ENST00000339336.4	+	8	721	c.591C>T	c.(589-591)atC>atT	p.I197I	AMTN_ENST00000504451.1_Silent_p.I196I	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	197					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)		p.I197I(1)		NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			CACATGCCATCGAGGAAGCCA	0.522													C|||	1371	0.273762	0.1157	0.4568	5008	,	,		19732	0.1994		0.4453	False		,,,				2504	0.2577				p.I197I		Atlas-SNP	.											AMTN,NS,carcinoma,0,1	AMTN	28	1	1	Substitution - coding silent(1)	prostate(1)	c.C591T						PASS	.	C		801,3605	314.1+/-293.5	65,671,1467	70.0	55.0	60.0		591	-12.3	0.0	4	dbSNP_123	60	3794,4806	526.2+/-380.9	853,2088,1359	no	coding-synonymous	AMTN	NM_212557.2		918,2759,2826	TT,TC,CC		44.1163,18.1798,35.3298		197/210	71396989	4595,8411	2203	4300	6503	SO:0001819	synonymous_variant	401138	exon8			TGCCATCGAGGAA	AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.591C>T	4.37:g.71396989C>T		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	237	236	0.995781	NM_212557	Q0P503|Q0P506	Silent	SNP	ENST00000339336.4	37	CCDS3542.1																																																																																			C|0.684;T|0.316	0.316	strong		0.522	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557	
MGAT5	4249	hgsc.bcm.edu	37	2	135206340	135206340	+	Silent	SNP	C	C	A	rs2230908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:135206340C>A	ENST00000409645.1	+	17	2400	c.2148C>A	c.(2146-2148)gcC>gcA	p.A716A	MGAT5_ENST00000281923.2_Silent_p.A716A			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	716					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		GTGCAGGCGCCCACCCCAGGC	0.597													C|||	251	0.0501198	0.003	0.1095	5008	,	,		19671	0.004		0.0537	False		,,,				2504	0.1155				p.A716A		Atlas-SNP	.											.	MGAT5	84	.	0			c.C2148A						PASS	.	C		49,4357	50.2+/-85.5	0,49,2154	89.0	87.0	88.0		2148	3.1	1.0	2	dbSNP_98	88	539,8061	150.1+/-205.1	18,503,3779	no	coding-synonymous	MGAT5	NM_002410.3		18,552,5933	AA,AC,CC		6.2674,1.1121,4.521		716/742	135206340	588,12418	2203	4300	6503	SO:0001819	synonymous_variant	4249	exon16			AGGCGCCCACCCC	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.2148C>A	2.37:g.135206340C>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	187	99	0.529412	NM_002410	D3DP70	Silent	SNP	ENST00000409645.1	37	CCDS2171.1																																																																																			C|0.959;A|0.041	0.041	strong		0.597	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410	
PLEC	5339	hgsc.bcm.edu	37	8	144993324	144993324	+	Silent	SNP	C	C	T	rs6984820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144993324C>T	ENST00000322810.4	-	32	11245	c.11076G>A	c.(11074-11076)acG>acA	p.T3692T	PLEC_ENST00000354589.3_Silent_p.T3555T|PLEC_ENST00000357649.2_Silent_p.T3559T|PLEC_ENST00000356346.3_Silent_p.T3541T|PLEC_ENST00000398774.2_Silent_p.T3523T|PLEC_ENST00000345136.3_Silent_p.T3555T|PLEC_ENST00000527096.1_Silent_p.T3578T|PLEC_ENST00000436759.2_Silent_p.T3582T|PLEC_ENST00000354958.2_Silent_p.T3533T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3692	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TGTACACCTGCGTGGTCTCCA	0.642													C|||	1172	0.234026	0.0348	0.2983	5008	,	,		17797	0.1349		0.4235	False		,,,				2504	0.365				p.T3692T		Atlas-SNP	.											.	PLEC	1144	.	0			c.G11076A						PASS	.	C	,,,,,,,	378,3836		25,328,1754	105.0	122.0	117.0		10746,10623,10599,11076,10569,10665,10677,10665	-4.8	0.6	8	dbSNP_116	117	3444,4994		721,2002,1496	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	746,2330,3250	TT,TC,CC		40.8154,8.9701,30.2087	,,,,,,,	3582/4575,3541/4534,3533/4526,3692/4685,3523/4516,3555/4548,3559/4552,3555/4548	144993324	3822,8830	2107	4219	6326	SO:0001819	synonymous_variant	5339	exon32			CACCTGCGTGGTC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11076G>A	8.37:g.144993324C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			C|0.730;T|0.270	0.270	strong		0.642	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
OR6A2	8590	hgsc.bcm.edu	37	11	6816875	6816875	+	Missense_Mutation	SNP	G	G	A	rs7122644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6816875G>A	ENST00000332601.3	-	1	253	c.65C>T	c.(64-66)gCg>gTg	p.A22V		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	22			A -> V (in dbSNP:rs7122644).	APLQVL -> VPIQVI (in Ref. 1; AAC70018). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTGTAGTGGCGCAGGAGCAGG	0.498													G|||	1567	0.312899	0.1906	0.2695	5008	,	,		19712	0.4623		0.2932	False		,,,				2504	0.3753				p.A22V		Atlas-SNP	.											.	OR6A2	68	.	0			c.C65T						PASS	.	G	VAL/ALA	978,3424	366.1+/-317.7	111,756,1334	125.0	98.0	107.0		65	-9.9	0.0	11	dbSNP_116	107	2417,6175	399.2+/-346.4	359,1699,2238	yes	missense	OR6A2	NM_003696.2	64	470,2455,3572	AA,AG,GG		28.1308,22.2172,26.1274	benign	22/328	6816875	3395,9599	2201	4296	6497	SO:0001583	missense	8590	exon1			AGTGGCGCAGGAG	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"""GPCR / Class A : Olfactory receptors"""	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.65C>T	11.37:g.6816875G>A	ENSP00000330384:p.Ala22Val	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	218	100	0.458716	NM_003696	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	37	CCDS7772.1	646	0.2957875457875458	93	0.18902439024390244	90	0.24861878453038674	237	0.4143356643356643	226	0.29815303430079154	G	6.981	0.551115	0.13374	0.222172	0.281308	ENSG00000184933	ENST00000332601	T	0.00428	7.44	4.95	-9.9	0.00461	.	1.075410	0.07258	N	0.866968	T	0.00012	0.0000	N	0.20845	0.615	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.35375	-0.9791	9	0.15499	T	0.54	.	15.1035	0.72303	0.2642:0.0969:0.6389:0.0	rs7122644;rs52837330;rs61218993;rs7122644	22	O95222	OR6A2_HUMAN	V	22	ENSP00000330384:A22V	ENSP00000330384:A22V	A	-	2	0	OR6A2	6773451	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.986000	0.01484	-2.137000	0.00809	-2.317000	0.00253	GCG	G|0.722;A|0.278	0.278	strong		0.498	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696	
DLEC1	9940	hgsc.bcm.edu	37	3	38125705	38125705	+	Silent	SNP	G	G	A	rs7652276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38125705G>A	ENST00000308059.6	+	7	1251	c.1230G>A	c.(1228-1230)ccG>ccA	p.P410P	DLEC1_ENST00000469151.1_3'UTR|DLEC1_ENST00000346219.3_Silent_p.P410P|DLEC1_ENST00000452631.2_Silent_p.P410P					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		GAGTCCTCCCGCCTTCCACGC	0.448													g|||	1880	0.375399	0.4145	0.3818	5008	,	,		25644	0.5387		0.3012	False		,,,				2504	0.226				p.P410P		Atlas-SNP	.											.	DLEC1	278	.	0			c.G1230A						PASS	.		,	1644,2520		332,980,770	110.0	120.0	117.0		1230,1230	-10.8	0.0	3	dbSNP_116	117	2535,5901		412,1711,2095	no	coding-synonymous,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	744,2691,2865	AA,AG,GG		30.0498,39.4813,33.1667	,	410/1756,410/1779	38125705	4179,8421	2082	4218	6300	SO:0001819	synonymous_variant	9940	exon7			CCTCCCGCCTTCC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1230G>A	3.37:g.38125705G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	150	58	0.386667	NM_007337		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			G|0.644;A|0.356	0.356	strong		0.448	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
DNAH7	56171	hgsc.bcm.edu	37	2	196738365	196738365	+	Missense_Mutation	SNP	T	T	C	rs75859635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:196738365T>C	ENST00000312428.6	-	39	6440	c.6340A>G	c.(6340-6342)Aca>Gca	p.T2114A		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2114	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TCATTGATTGTTATAATATTG	0.274													T|||	89	0.0177716	0.0144	0.0259	5008	,	,		17472	0.0		0.0447	False		,,,				2504	0.0072				p.T2114A		Atlas-SNP	.											.	DNAH7	512	.	0			c.A6340G						PASS	.	T	ALA/THR	52,3564		0,52,1756	65.0	65.0	65.0		6340	4.8	1.0	2	dbSNP_132	65	353,7783		6,341,3721	yes	missense	DNAH7	NM_018897.2	58	6,393,5477	CC,CT,TT		4.3387,1.4381,3.4462	benign	2114/4025	196738365	405,11347	1808	4068	5876	SO:0001583	missense	56171	exon39			TGATTGTTATAAT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.6340A>G	2.37:g.196738365T>C	ENSP00000311273:p.Thr2114Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	53	0.024267399267399268	9	0.018292682926829267	9	0.024861878453038673	0	0.0	35	0.04617414248021108	T	13.71	2.319196	0.41096	0.014381	0.043387	ENSG00000118997	ENST00000312428	T	0.29917	1.55	4.81	4.81	0.61882	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.02267	0.0070	N	0.04320	-0.23	0.80722	D	1	B	0.16802	0.019	B	0.26864	0.074	T	0.10268	-1.0637	10	0.11794	T	0.64	.	14.4739	0.67535	0.0:0.0:0.0:1.0	.	2114	Q8WXX0	DYH7_HUMAN	A	2114	ENSP00000311273:T2114A	ENSP00000311273:T2114A	T	-	1	0	DNAH7	196446610	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.920000	0.70017	2.137000	0.66172	0.477000	0.44152	ACA	T|0.967;C|0.033	0.033	strong		0.274	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
AKAP11	11215	hgsc.bcm.edu	37	13	42882620	42882620	+	Silent	SNP	C	C	T	rs17521586	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:42882620C>T	ENST00000025301.2	+	9	5323	c.5148C>T	c.(5146-5148)acC>acT	p.T1716T		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1716	Ser-rich.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TTCAGTCAACCGAGTCTGTCA	0.363													C|||	572	0.114217	0.0424	0.1297	5008	,	,		16301	0.123		0.1282	False		,,,				2504	0.1769				p.T1716T		Atlas-SNP	.											.	AKAP11	146	.	0			c.C5148T						PASS	.	C		282,4124	157.0+/-190.0	14,254,1935	102.0	97.0	99.0		5148	-0.9	0.1	13	dbSNP_123	99	1322,7278	259.9+/-283.0	94,1134,3072	no	coding-synonymous	AKAP11	NM_016248.3		108,1388,5007	TT,TC,CC		15.3721,6.4004,12.3328		1716/1902	42882620	1604,11402	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon9			GTCAACCGAGTCT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.5148C>T	13.37:g.42882620C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			C|0.882;T|0.118	0.118	strong		0.363	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
PTPN13	5783	hgsc.bcm.edu	37	4	87685796	87685796	+	Missense_Mutation	SNP	T	T	G	rs10033029	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:87685796T>G	ENST00000411767.2	+	25	4131	c.4068T>G	c.(4066-4068)ttT>ttG	p.F1356L	PTPN13_ENST00000436978.1_Missense_Mutation_p.F1356L|PTPN13_ENST00000316707.6_Missense_Mutation_p.F1165L|PTPN13_ENST00000427191.2_Missense_Mutation_p.F1337L|PTPN13_ENST00000511467.1_Missense_Mutation_p.F1356L			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1356			F -> L (in dbSNP:rs10033029).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TTAAAACTTTTTCTTCATCAC	0.343													T|||	261	0.0521166	0.0318	0.072	5008	,	,		14756	0.0089		0.1203	False		,,,				2504	0.0399				p.F1356L		Atlas-SNP	.											.	PTPN13	203	.	0			c.T4068G						PASS	.	T	LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE	192,3402		7,178,1612	80.0	75.0	76.0		4011,4068,3495,4068	1.2	0.9	4	dbSNP_119	76	974,7170		67,840,3165	yes	missense,missense,missense,missense	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	22,22,22,22	74,1018,4777	GG,GT,TT		11.9597,5.3422,9.9335	benign,benign,benign,benign	1337/2467,1356/2486,1165/2295,1356/2491	87685796	1166,10572	1797	4072	5869	SO:0001583	missense	5783	exon25			AACTTTTTCTTCA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4068T>G	4.37:g.87685796T>G	ENSP00000407249:p.Phe1356Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	136	79	0.580882	NM_080683	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	139	0.06364468864468864	21	0.042682926829268296	27	0.07458563535911603	4	0.006993006993006993	87	0.11477572559366754	T	8.444	0.851464	0.17034	0.053422	0.119597	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18	5.04	1.19	0.21007	PDZ/DHR/GLGF (1);	0.771215	0.11048	N	0.605413	T	0.00271	0.0008	N	0.19112	0.55	0.41615	P	0.011063999999999963	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.10450	0.003;0.005;0.002;0.005	T	0.30880	-0.9963	9	0.10902	T	0.67	.	6.1894	0.20516	0.0:0.1444:0.1361:0.7194	rs10033029;rs52835693;rs59145610;rs10033029	1165;1337;1356;1356	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	L	1337;1356;1165;1356;1356;1305	ENSP00000408368:F1337L;ENSP00000394794:F1356L;ENSP00000322675:F1165L;ENSP00000407249:F1356L;ENSP00000426626:F1356L	ENSP00000322675:F1165L	F	+	3	2	PTPN13	87904820	0.990000	0.36364	0.876000	0.34364	0.859000	0.49053	2.666000	0.46799	0.042000	0.15717	0.528000	0.53228	TTT	T|0.934;G|0.066	0.066	strong		0.343	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
PTBP1	5725	hgsc.bcm.edu	37	19	804396	804396	+	Silent	SNP	C	C	T	rs3180287	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:804396C>T	ENST00000349038.4	+	5	466	c.393C>T	c.(391-393)tcC>tcT	p.S131S	PTBP1_ENST00000394601.4_Silent_p.S131S|PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000356948.6_Silent_p.S131S|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	131	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCAGTTCTCCAACCACAAGG	0.662													C|||	807	0.161142	0.1331	0.268	5008	,	,		14794	0.0228		0.1451	False		,,,				2504	0.2822				p.S131S		Atlas-SNP	.											.	PTBP1	43	.	0			c.C393T						PASS	.	C	,,,	571,3833	251.8+/-258.4	46,479,1677	65.0	56.0	59.0		393,393,393,	1.1	1.0	19	dbSNP_105	59	1274,7326	251.1+/-277.7	86,1102,3112	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	132,1581,4789	TT,TC,CC		14.814,12.9655,14.1879	,,,	131/558,131/551,131/532,	804396	1845,11159	2202	4300	6502	SO:0001819	synonymous_variant	5725	exon5			GTTCTCCAACCAC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.393C>T	19.37:g.804396C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	49	16	0.326531	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.862;G|0.000;T|0.138	0.138	strong		0.662	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
TPTE2	93492	hgsc.bcm.edu	37	13	20006620	20006620	+	Silent	SNP	C	C	T	rs147012324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:20006620C>T	ENST00000400230.2	-	16	1259	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	TPTE2_ENST00000390680.2_Silent_p.S328S|TPTE2_ENST00000382977.4_Silent_p.S405S|TPTE2_ENST00000382978.1_Silent_p.S365S|TPTE2_ENST00000400103.2_Silent_p.S294S|TPTE2_ENST00000382975.4_Silent_p.S365S|TPTE2_ENST00000457266.2_Silent_p.S294S|TPTE2_ENST00000255310.6_Silent_p.S328S			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	405	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S405S(2)|p.S328S(2)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TACCACGAATCGAATAAATAA	0.388																																					p.S405S		Atlas-SNP	.											TPTE2_ENST00000400230,NS,carcinoma,0,6	TPTE2	225	6	4	Substitution - coding silent(4)	prostate(2)|lung(2)	c.G1215A						scavenged	.						32.0	29.0	30.0					13																	20006620		2203	4297	6500	SO:0001819	synonymous_variant	93492	exon17			ACGAATCGAATAA	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.1215G>A	13.37:g.20006620C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	223	29	0.130045	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Silent	SNP	ENST00000400230.2	37	CCDS45014.1																																																																																			.	.	weak		0.388	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
PCDH9	5101	hgsc.bcm.edu	37	13	67800419	67800419	+	Silent	SNP	C	C	G	rs41283952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:67800419C>G	ENST00000377865.2	-	1	2288	c.2154G>C	c.(2152-2154)gtG>gtC	p.V718V	PCDH9_ENST00000456367.1_Silent_p.V718V|PCDH9_ENST00000544246.1_Silent_p.V718V|PCDH9_ENST00000328454.5_Silent_p.V718V|PCDH9_ENST00000377861.3_Silent_p.V718V			Q9HC56	PCDH9_HUMAN	protocadherin 9	718	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		TGTTTCCACTCACTATAGTAT	0.448													C|||	116	0.0231629	0.0023	0.0922	5008	,	,		20791	0.0		0.0417	False		,,,				2504	0.0072				p.V718V		Atlas-SNP	.											.	PCDH9	252	.	0			c.G2154C						PASS	.	C	,	36,4370	41.6+/-74.8	1,34,2168	134.0	134.0	134.0		2154,2154	2.1	1.0	13	dbSNP_127	134	333,8267	115.5+/-175.4	11,311,3978	no	coding-synonymous,coding-synonymous	PCDH9	NM_020403.4,NM_203487.2	,	12,345,6146	GG,GC,CC		3.8721,0.8171,2.8372	,	718/1204,718/1238	67800419	369,12637	2203	4300	6503	SO:0001819	synonymous_variant	5101	exon2			TCCACTCACTATA	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.2154G>C	13.37:g.67800419C>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	CCDS9444.1																																																																																			C|0.970;G|0.030	0.030	strong		0.448	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
NID1	4811	hgsc.bcm.edu	37	1	236141174	236141174	+	Missense_Mutation	SNP	T	T	C	rs3213190	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:236141174T>C	ENST00000264187.6	-	20	3819	c.3737A>G	c.(3736-3738)cAg>cGg	p.Q1246R	NID1_ENST00000366595.3_Missense_Mutation_p.Q1113R	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1246			Q -> R (in dbSNP:rs3213190). {ECO:0000269|PubMed:2471408, ECO:0000269|PubMed:2574658, ECO:0000269|PubMed:7557988}.		basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	TCTTCATTTCTGTTCGATACA	0.502													C|||	1724	0.344249	0.385	0.2608	5008	,	,		21512	0.6131		0.1451	False		,,,				2504	0.2761				p.Q1246R		Atlas-SNP	.											.	NID1	196	.	0			c.A3737G						PASS	.	C	ARG/GLN	1539,2867	671.9+/-402.5	257,1025,921	109.0	106.0	107.0		3737	2.8	1.0	1	dbSNP_106	107	1504,7096	748.1+/-407.3	123,1258,2919	yes	missense	NID1	NM_002508.2	43	380,2283,3840	CC,CT,TT		17.4884,34.9296,23.3969	benign	1246/1248	236141174	3043,9963	2203	4300	6503	SO:0001583	missense	4811	exon20			CATTTCTGTTCGA	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.3737A>G	1.37:g.236141174T>C	ENSP00000264187:p.Gln1246Arg	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	177	86	0.485876	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	712	0.326007326007326	174	0.35365853658536583	86	0.23756906077348067	348	0.6083916083916084	104	0.13720316622691292	C	5.517	0.280385	0.10458	0.349296	0.174884	ENSG00000116962	ENST00000264187;ENST00000366595	T;D	0.86769	-1.48;-2.17	5.67	2.79	0.32731	.	0.054020	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00075	-2.25	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45440	-0.9261	9	0.02654	T	1	.	7.3131	0.26485	0.1194:0.6886:0.0:0.1919	rs3213190;rs3768077;rs60739893;rs3213190	1113;1246	P14543-2;P14543	.;NID1_HUMAN	R	1246;1113	ENSP00000264187:Q1246R;ENSP00000355554:Q1113R	ENSP00000264187:Q1246R	Q	-	2	0	NID1	234207797	0.971000	0.33674	0.953000	0.39169	0.928000	0.56348	0.131000	0.15870	0.072000	0.16694	-0.226000	0.12346	CAG	T|0.706;C|0.293	0.293	strong		0.502	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
ANKRD24	170961	hgsc.bcm.edu	37	19	4216318	4216318	+	Silent	SNP	G	G	T	rs45510899	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4216318G>T	ENST00000600132.1	+	17	1584	c.1308G>T	c.(1306-1308)tcG>tcT	p.S436S	ANKRD24_ENST00000318934.4_Silent_p.S436S|ANKRD24_ENST00000262970.5_Silent_p.S526S|ANKRD24_ENST00000595096.1_3'UTR	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	436										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		TCAGTCCGTCGGCCCAGGAAC	0.657													G|||	268	0.0535144	0.0038	0.0519	5008	,	,		17806	0.0		0.1223	False		,,,				2504	0.1063				p.S436S		Atlas-SNP	.											ANKRD24_ENST00000318934,NS,NS,0,15	ANKRD24	180	15	0			c.G1308T						PASS	.	G		82,3874		0,82,1896	24.0	27.0	26.0		1308	-9.2	0.0	19	dbSNP_127	26	967,7297		58,851,3223	no	coding-synonymous	ANKRD24	NM_133475.1		58,933,5119	TT,TG,GG		11.7014,2.0728,8.5843		436/1147	4216318	1049,11171	1978	4132	6110	SO:0001819	synonymous_variant	170961	exon17			TCCGTCGGCCCAG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1308G>T	19.37:g.4216318G>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_133475	O75268|O95781	Silent	SNP	ENST00000600132.1	37	CCDS45925.1																																																																																			G|0.948;T|0.052	0.052	strong		0.657	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
OR2T3	343173	hgsc.bcm.edu	37	1	248637046	248637046	+	Missense_Mutation	SNP	G	G	A	rs148025314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248637046G>A	ENST00000359594.2	+	1	420	c.395G>A	c.(394-396)tGc>tAc	p.C132Y		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCTGCTGTTTGCAGACCTCTC	0.557																																					p.C132Y		Atlas-SNP	.											.	OR2T3	79	.	0			c.G395A						PASS	.						38.0	36.0	37.0					1																	248637046		2193	4282	6475	SO:0001583	missense	343173	exon1			CTGTTTGCAGACC		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.395G>A	1.37:g.248637046G>A	ENSP00000352604:p.Cys132Tyr	Somatic	490	1	0.00204082		WXS	Illumina HiSeq	Phase_I	623	216	0.346709	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	643	0.2944139194139194	127	0.258130081300813	102	0.281767955801105	241	0.42132867132867136	173	0.22823218997361477	g	15.47	2.843842	0.51164	.	.	ENSG00000196539	ENST00000359594	T	0.02158	4.42	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.90425	3.115	0.33216	P	0.445929	D	0.89917	1.0	D	0.91635	0.999	T	0.43294	-0.9400	8	0.87932	D	0	.	11.721	0.51683	0.0:0.0:1.0:0.0	.	132	Q8NH03	OR2T3_HUMAN	Y	132	ENSP00000352604:C132Y	ENSP00000352604:C132Y	C	+	2	0	OR2T3	246703669	1.000000	0.71417	0.002000	0.10522	0.045000	0.14185	6.128000	0.71650	1.014000	0.39417	0.186000	0.17326	TGC	G|0.744;A|0.256	0.256	strong		0.557	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
OPA1	4976	hgsc.bcm.edu	37	3	193334991	193334991	+	Missense_Mutation	SNP	G	G	A	rs7624750	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:193334991G>A	ENST00000392438.3	+	4	707	c.473G>A	c.(472-474)aGt>aAt	p.S158N	OPA1_ENST00000487986.1_3'UTR|OPA1-AS1_ENST00000444085.1_RNA|OPA1_ENST00000361510.2_Missense_Mutation_p.S158N|OPA1_ENST00000361715.2_Intron|OPA1-AS1_ENST00000433105.1_RNA|OPA1_ENST00000361908.3_Missense_Mutation_p.S158N|OPA1_ENST00000361150.2_Intron|OPA1_ENST00000361828.2_Missense_Mutation_p.S158N	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	158			S -> N (in dbSNP:rs7624750). {ECO:0000269|PubMed:11440988, ECO:0000269|PubMed:11440989, ECO:0000269|PubMed:12036970, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15948788, ECO:0000269|PubMed:16617242, ECO:0000269|PubMed:9628581}.		apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		GCCCTTCCTAGTTCAGAAGAC	0.338													A|||	2344	0.468051	0.5847	0.4683	5008	,	,		16978	0.3681		0.4573	False		,,,				2504	0.4243				p.S158N		Atlas-SNP	.											OPA1,NS,carcinoma,0,1	OPA1	79	1	0			c.G473A						PASS	.	A	ASN/SER,,,,ASN/SER,,ASN/SER,ASN/SER	2474,1930	539.4+/-375.3	696,1082,424	57.0	62.0	60.0		473,,,,473,,473,473	3.6	1.0	3	dbSNP_116	60	3988,4610	596.8+/-393.7	906,2176,1217	yes	missense,intron,intron,intron,missense,intron,missense,missense	OPA1	NM_015560.2,NM_130831.2,NM_130832.2,NM_130833.2,NM_130834.2,NM_130835.2,NM_130836.2,NM_130837.2	46,,,,46,,46,46	1602,3258,1641	AA,AG,GG		46.3829,43.8238,49.7	benign,,,,benign,,benign,benign	158/961,,,,158/979,,158/998,158/1016	193334991	6462,6540	2202	4299	6501	SO:0001583	missense	4976	exon4			TTCCTAGTTCAGA	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"""mitochondrial dynamin-like GTPase"", ""dynamin-like guanosine triphosphatase"", ""Dynamin-like 120 kDa protein, mitochondrial"""	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.473G>A	3.37:g.193334991G>A	ENSP00000376233:p.Ser158Asn	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	238	137	0.57563	NM_130836	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	37	CCDS43186.1	997|997	0.4565018315018315|0.4565018315018315	297|297	0.6036585365853658|0.6036585365853658	157|157	0.43370165745856354|0.43370165745856354	194|194	0.33916083916083917|0.33916083916083917	349|349	0.4604221635883905|0.4604221635883905	A|A	5.124|5.124	0.208417|0.208417	0.09757|0.09757	0.561762|0.561762	0.463829|0.463829	ENSG00000198836|ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361828;ENST00000419435;ENST00000392436|ENST00000434811	D;D;D;D;T;T|.	0.92965|.	-3.1;-3.14;-3.14;-3.13;1.97;-0.86|.	6.05|6.05	3.64|3.64	0.41730|0.41730	.|.	0.424265|.	0.28766|.	N|.	0.014207|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	P|P	0.999999999863361|0.999999999863361	B;B;B;B|.	0.06786|.	0.0;0.0;0.001;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.0;0.001;0.0|.	T|T	0.44907|0.44907	-0.9297|-0.9297	9|4	0.16420|.	T|.	0.52|.	-8.8622|-8.8622	6.4094|6.4094	0.21682|0.21682	0.7267:0.1327:0.1406:0.0|0.7267:0.1327:0.1406:0.0	rs7624750;rs52806158;rs58655170;rs7624750|rs7624750;rs52806158;rs58655170;rs7624750	158;158;158;158|.	O60313;E5KLJ6;E5KLJ7;E5KLJ5|.	OPA1_HUMAN;.;.;.|.	N|I	158;158;158;158;34;158|58	ENSP00000354681:S158N;ENSP00000376233:S158N;ENSP00000355324:S158N;ENSP00000354429:S158N;ENSP00000399877:S34N;ENSP00000376231:S158N|.	ENSP00000355324:S158N|.	S|V	+|+	2|1	0|0	OPA1|OPA1	194817685|194817685	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.993000|0.993000	0.82548|0.82548	3.435000|3.435000	0.52849|0.52849	0.166000|0.166000	0.19597|0.19597	-0.269000|-0.269000	0.10298|0.10298	AGT|GTT	G|0.517;A|0.483	0.483	strong		0.338	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
NUMA1	4926	hgsc.bcm.edu	37	11	71720030	71720030	+	Missense_Mutation	SNP	G	G	A	rs74985106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71720030G>A	ENST00000393695.3	-	19	5372	c.5041C>T	c.(5041-5043)Cgc>Tgc	p.R1681C	NUMA1_ENST00000358965.6_Missense_Mutation_p.R1667C|NUMA1_ENST00000351960.6_Missense_Mutation_p.R545C	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						TCCAGGCTGCGCACCTGGGCA	0.612			T	RARA	APL								G|||	67	0.0133786	0.0008	0.0231	5008	,	,		13503	0.0188		0.0179	False		,,,				2504	0.0133				p.R1681C		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.C5041T						PASS	.	G	CYS/ARG	26,4374	31.7+/-61.6	0,26,2174	63.0	62.0	63.0		5041	5.6	1.0	11	dbSNP_131	63	203,8383	86.3+/-148.7	2,199,4092	yes	missense	NUMA1	NM_006185.2	180	2,225,6266	AA,AG,GG		2.3643,0.5909,1.7634	probably-damaging	1681/2116	71720030	229,12757	2200	4293	6493	SO:0001583	missense	4926	exon19			GGCTGCGCACCTG	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.5041C>T	11.37:g.71720030G>A	ENSP00000377298:p.Arg1681Cys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	36	0.016483516483516484	0	0.0	11	0.03038674033149171	14	0.024475524475524476	11	0.014511873350923483	G	21.4	4.145619	0.77888	0.005909	0.023643	ENSG00000137497	ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	T;T;T	0.50001	2.07;0.76;2.52	5.56	5.56	0.83823	.	0.127189	0.36409	N	0.002604	T	0.31451	0.0797	L	0.32530	0.975	0.46586	D	0.999115	D;D;D;D;D	0.89917	0.998;0.998;0.996;0.998;1.0	P;P;P;P;D	0.65010	0.629;0.819;0.819;0.629;0.931	T	0.48103	-0.9064	10	0.72032	D	0.01	.	14.0441	0.64695	0.0:0.0:0.8489:0.1511	.	1687;1151;1667;1681;545	Q4LE64;Q59HB8;Q14980-2;Q14980;Q9BTE9	.;.;.;NUMA1_HUMAN;.	C	545;1667;1681;1230;636	ENSP00000260051:R545C;ENSP00000351851:R1667C;ENSP00000377298:R1681C	ENSP00000260051:R545C	R	-	1	0	NUMA1	71397678	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.624000	0.46444	2.618000	0.88619	0.561000	0.74099	CGC	G|0.982;A|0.018	0.018	strong		0.612	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
ZC3HC1	51530	hgsc.bcm.edu	37	7	129663496	129663496	+	Missense_Mutation	SNP	C	C	T	rs11556924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:129663496C>T	ENST00000358303.4	-	8	1172	c.1088G>A	c.(1087-1089)cGt>cAt	p.R363H	ZC3HC1_ENST00000311873.5_Missense_Mutation_p.R342H|RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000360708.5_Intron|RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000481503.1_Missense_Mutation_p.R320H	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	363			R -> H (in dbSNP:rs11556924). {ECO:0000269|PubMed:15489334}.		mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					TGGCTCAGGACGGTCAACAGG	0.582													C|||	780	0.155751	0.0265	0.2089	5008	,	,		15956	0.0496		0.3767	False		,,,				2504	0.1748				p.R363H	Melanoma(115;540 1606 16325 28853 48167)	Atlas-SNP	.											.	ZC3HC1	45	.	0			c.G1088A						PASS	.	C	HIS/ARG	359,4047	185.0+/-212.2	15,329,1859	102.0	89.0	93.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1088	5.5	1.0	7	dbSNP_120	93	3290,5310	493.5+/-373.6	651,1988,1661	yes	missense	ZC3HC1	NM_016478.3	29	666,2317,3520	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	38.2558,8.148,28.0563	probably-damaging	363/503	129663496	3649,9357	2203	4300	6503	SO:0001583	missense	51530	exon8			TCAGGACGGTCAA	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1088G>A	7.37:g.129663496C>T	ENSP00000351052:p.Arg363His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	418	0.19139194139194138	23	0.046747967479674794	78	0.2154696132596685	27	0.0472027972027972	290	0.38258575197889183	C	24.1	4.497150	0.85069	0.08148	0.382558	ENSG00000091732	ENST00000358303;ENST00000311873;ENST00000481503	T;T;T	0.51325	1.25;1.28;0.71	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	L	0.57536	1.79	0.25979	P	0.9823921	D;D	0.89917	1.0;1.0	D;D	0.68621	0.959;0.959	T	0.34054	-0.9844	9	0.18276	T	0.48	-14.8822	16.0957	0.81123	0.0:1.0:0.0:0.0	rs11556924;rs12667709;rs17850754;rs11556924	363;320	Q86WB0;C9J0I9	NIPA_HUMAN;.	H	363;342;320	ENSP00000351052:R363H;ENSP00000309301:R342H;ENSP00000418533:R320H	ENSP00000309301:R342H	R	-	2	0	ZC3HC1	129450732	0.994000	0.37717	0.995000	0.50966	0.725000	0.41563	2.567000	0.45956	2.590000	0.87494	0.563000	0.77884	CGT	C|0.777;T|0.223	0.223	strong		0.582	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
CD1D	912	hgsc.bcm.edu	37	1	158151892	158151892	+	Silent	SNP	T	T	C	rs140563679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158151892T>C	ENST00000368171.3	+	4	898	c.399T>C	c.(397-399)caT>caC	p.H133H		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	133					antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					ACTTCTTCCATGTAGCATTTC	0.498													T|||	3	0.000599042	0.0	0.0	5008	,	,		19718	0.0		0.003	False		,,,				2504	0.0				p.H133H		Atlas-SNP	.											.	CD1D	60	.	0			c.T399C						PASS	.	T		0,4406		0,0,2203	130.0	143.0	138.0		399	-9.5	0.0	1	dbSNP_134	138	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	CD1D	NM_001766.3		0,17,6486	CC,CT,TT		0.1977,0.0,0.1307		133/336	158151892	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	912	exon4			CTTCCATGTAGCA	BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1637	protein-coding gene	gene with protein product		188410	"""CD1D antigen, d polypeptide"", ""CD1d antigen"""			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.399T>C	1.37:g.158151892T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	291	160	0.549828	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Silent	SNP	ENST00000368171.3	37	CCDS1173.1																																																																																			T|0.999;C|0.001	0.001	strong		0.498	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766	
CCT7	10574	hgsc.bcm.edu	37	2	73478461	73478461	+	Silent	SNP	A	A	T	rs7851	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:73478461A>T	ENST00000258091.5	+	11	1452	c.1311A>T	c.(1309-1311)gcA>gcT	p.A437A	CCT7_ENST00000398422.2_Silent_p.A233A|CCT7_ENST00000538797.1_Silent_p.A309A|CCT7_ENST00000540468.1_Silent_p.A350A|CCT7_ENST00000539919.1_Silent_p.A393A|CCT7_ENST00000537131.1_Silent_p.A337A	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	437					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)	p.A233A(1)		breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						TGATTGGGGCATATGCCAAGG	0.547													A|||	1273	0.254193	0.118	0.2968	5008	,	,		18007	0.3611		0.3101	False		,,,				2504	0.2403				p.A437A		Atlas-SNP	.											CCT7,NS,carcinoma,0,1	CCT7	60	1	1	Substitution - coding silent(1)	stomach(1)	c.A1311T						PASS	.	A	,,,	585,3279		56,473,1403	115.0	115.0	115.0		699,1050,1179,1311	-9.7	0.4	2	dbSNP_52	115	2538,5738		392,1754,1992	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CCT7	NM_001009570.2,NM_001166284.1,NM_001166285.1,NM_006429.3	,,,	448,2227,3395	TT,TA,AA		30.667,15.1398,25.7249	,,,	233/340,350/457,393/500,437/544	73478461	3123,9017	1932	4138	6070	SO:0001819	synonymous_variant	10574	exon11			TGGGGCATATGCC	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"""Heat Shock Proteins / Chaperonins"""	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.1311A>T	2.37:g.73478461A>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_006429	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Silent	SNP	ENST00000258091.5	37	CCDS46336.1																																																																																			A|0.722;T|0.278	0.278	strong		0.547	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2		
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118368606	118368606	+	Missense_Mutation	SNP	T	T	C	rs1049125	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:118368606T>C	ENST00000528052.1	+	13	1453	c.1382T>C	c.(1381-1383)cTg>cCg	p.L461P	PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.L461P|PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.L461P			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	461	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.		L -> P (in dbSNP:rs1049125).		lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		GAAGACACGCTGCTCACCCTC	0.527													-|||	591	0.118011	0.0083	0.1801	5008	,	,		17779	0.1478		0.1839	False		,,,				2504	0.1237				p.L461P		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.T1382C						PASS	.		PRO/LEU	203,4203		6,191,2006	115.0	104.0	108.0		1382	4.0	1.0	10	dbSNP_86	108	1634,6966		156,1322,2822	yes	missense	PNLIPRP1	NM_006229.2	98	162,1513,4828	CC,CT,TT		19.0,4.6074,14.1243	probably-damaging	461/468	118368606	1837,11169	2203	4300	6503	SO:0001583	missense	5407	exon13			ACACGCTGCTCAC	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.1382T>C	10.37:g.118368606T>C	ENSP00000433933:p.Leu461Pro	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	37	CCDS7595.1	292	0.1336996336996337	6	0.012195121951219513	63	0.17403314917127072	85	0.1486013986013986	138	0.1820580474934037	-	10.43	1.346793	0.24426	0.046074	0.19	ENSG00000187021	ENST00000358834;ENST00000528052;ENST00000534537	T;T;T	0.52295	0.67;0.67;0.67	5.24	3.98	0.46160	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.224339	0.30547	N	0.009398	T	0.00210	0.0006	M	0.84773	2.715	0.24006	P	0.99619404	D	0.89917	1.0	D	0.77557	0.99	T	0.18777	-1.0326	9	0.56958	D	0.05	-7.4848	10.278	0.43521	0.1587:0.0:0.0:0.8413	rs1049125;rs1803927;rs3189217;rs17808821;rs17848298;rs1049125	461	P54315	LIPR1_HUMAN	P	461	ENSP00000351695:L461P;ENSP00000433933:L461P;ENSP00000434159:L461P	ENSP00000351695:L461P	L	+	2	0	PNLIPRP1	118358596	1.000000	0.71417	0.970000	0.41538	0.014000	0.08584	3.464000	0.53057	1.968000	0.57251	0.524000	0.50904	CTG	C|0.139;N|0.000	0.139	strong		0.527	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229	
ZNF780A	284323	hgsc.bcm.edu	37	19	40580545	40580545	+	Nonsense_Mutation	SNP	G	G	A	rs149702621	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40580545G>A	ENST00000595687.2	-	6	2013	c.1804C>T	c.(1804-1806)Cga>Tga	p.R602*	ZNF780A_ENST00000594395.1_Nonsense_Mutation_p.R603*|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000340963.5_Nonsense_Mutation_p.R602*|ZNF780A_ENST00000455521.1_Nonsense_Mutation_p.R603*|ZNF780A_ENST00000450241.2_Nonsense_Mutation_p.R568*|ZNF780A_ENST00000414720.2_Intron	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	602					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TTCTGATGTCGAATAAGTTGC	0.398													g|||	2	0.000399361	0.0	0.0	5008	,	,		23667	0.0		0.002	False		,,,				2504	0.0				p.R603X		Atlas-SNP	.											ZNF780A_ENST00000455521,NS,carcinoma,0,2	ZNF780A	156	2	0			c.C1807T						PASS	.	G	stop/ARG,stop/ARG,stop/ARG,	1,4405	2.1+/-5.4	0,1,2202	140.0	138.0	139.0		1804,1807,1804,	-0.8	0.0	19	dbSNP_134	139	11,8589	7.7+/-29.5	0,11,4289	no	stop-gained,stop-gained,stop-gained,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	,,,	602/642,603/643,602/642,	40580545	12,12994	2203	4300	6503	SO:0001587	stop_gained	284323	exon6			GATGTCGAATAAG	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.1804C>T	19.37:g.40580545G>A	ENSP00000472189:p.Arg602*	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_001142577	E9PB48|Q6ZN87	Nonsense_Mutation	SNP	ENST00000595687.2	37	CCDS33026.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	g	36	5.627543	0.96671	2.27E-4	0.001279	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	.	.	.	1.93	-0.836	0.10770	.	.	.	.	.	.	.	.	.	.	.	0.51482	D	0.999922	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	4.3525	0.11162	0.1631:0.4575:0.3794:0.0	.	.	.	.	X	602;603;602	.	ENSP00000341507:R602X	R	-	1	2	ZNF780A	45272385	0.000000	0.05858	0.000000	0.03702	0.504000	0.33889	-5.163000	0.00145	-0.286000	0.09076	0.313000	0.20887	CGA	G|0.999;A|0.001	0.001	strong		0.398	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880	
MAGEA4	4103	hgsc.bcm.edu	37	X	151092784	151092784	+	Silent	SNP	C	C	T	rs61746135	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:151092784C>T	ENST00000360243.2	+	3	915	c.648C>T	c.(646-648)agC>agT	p.S216S	MAGEA4_ENST00000393920.1_Silent_p.S216S|MAGEA4_ENST00000370337.4_Silent_p.S216S|MAGEA4_ENST00000276344.2_Silent_p.S216S|MAGEA4_ENST00000393921.1_Silent_p.S216S|MAGEA4_ENST00000370340.3_Silent_p.S216S|MAGEA4_ENST00000370335.1_Silent_p.S216S	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	216	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					AGGGCGACAGCGCCTCTGAGG	0.552													C|||	59	0.0156291	0.0023	0.013	3775	,	,		14352	0.001		0.0189	False		,,,				2504	0.0276				p.S216S		Atlas-SNP	.											.	MAGEA4	68	.	0			c.C648T						PASS	.	C	,,,	19,3816		0,18,1,1614,570	105.0	108.0	107.0		648,648,648,648	-4.7	0.0	X	dbSNP_129	107	272,6456		3,199,67,2226,1805	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAGEA4	NM_001011548.1,NM_001011549.1,NM_001011550.1,NM_002362.4	,,,	3,217,68,3840,2375	TT,TC,T,CC,C		4.0428,0.4954,2.7549	,,,	216/318,216/318,216/318,216/318	151092784	291,10272	2203	4300	6503	SO:0001819	synonymous_variant	4103	exon3			CGACAGCGCCTCT		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.648C>T	X.37:g.151092784C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_001011548	Q14798	Silent	SNP	ENST00000360243.2	37	CCDS14702.1																																																																																			C|0.979;T|0.021	0.021	strong		0.552	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362	
PTPRM	5797	hgsc.bcm.edu	37	18	8069868	8069868	+	Silent	SNP	C	C	T	rs2230601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:8069868C>T	ENST00000332175.8	+	8	2354	c.1317C>T	c.(1315-1317)aaC>aaT	p.N439N	PTPRM_ENST00000580170.1_Silent_p.N439N|PTPRM_ENST00000400053.4_Silent_p.N377N|PTPRM_ENST00000444013.1_Silent_p.N226N|PTPRM_ENST00000400060.4_Silent_p.N439N|PTPRM_ENST00000578571.1_3'UTR	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	439	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				ATACAGAAAACTCACACCCTC	0.463													C|||	2376	0.474441	0.5325	0.5159	5008	,	,		18671	0.2946		0.5239	False		,,,				2504	0.501				p.N439N		Atlas-SNP	.											.	PTPRM	185	.	0			c.C1317T						PASS	.	C	,	2506,1900	627.4+/-394.9	708,1090,405	169.0	122.0	138.0		1317,1317	-2.6	0.0	18	dbSNP_98	138	4451,4149	587.6+/-392.2	1167,2117,1016	no	coding-synonymous,coding-synonymous	PTPRM	NM_001105244.1,NM_002845.3	,	1875,3207,1421	TT,TC,CC		48.2442,43.123,46.5093	,	439/1466,439/1453	8069868	6957,6049	2203	4300	6503	SO:0001819	synonymous_variant	5797	exon8			AGAAAACTCACAC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.1317C>T	18.37:g.8069868C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001105244	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	37	CCDS11840.1																																																																																			C|0.517;T|0.483	0.483	strong		0.463	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
HRNR	388697	hgsc.bcm.edu	37	1	152186614	152186614	+	Silent	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152186614C>G	ENST00000368801.2	-	3	7566	c.7491G>C	c.(7489-7491)tcG>tcC	p.S2497S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2497					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCCACAGCTCGATGACTGTC	0.557																																					p.S2497S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.G7491C						scavenged	.						1.0	1.0	1.0					1																	152186614		84	271	355	SO:0001819	synonymous_variant	388697	exon3			ACAGCTCGATGAC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7491G>C	1.37:g.152186614C>G		Somatic	613	1	0.00163132		WXS	Illumina HiSeq	Phase_I	2476	171	0.069063	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			.	.	none		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
PLCB2	5330	hgsc.bcm.edu	37	15	40589002	40589002	+	Silent	SNP	A	A	G	rs2229691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40589002A>G	ENST00000260402.3	-	14	1680	c.1431T>C	c.(1429-1431)acT>acC	p.T477T	PLCB2_ENST00000456256.2_Silent_p.T477T|PLCB2_ENST00000557821.1_Silent_p.T477T	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	477					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		CCTCCCCACCAGTATCCTTAC	0.607													A|||	1779	0.355232	0.1293	0.4755	5008	,	,		19466	0.6736		0.2167	False		,,,				2504	0.3896				p.T477T		Atlas-SNP	.											.	PLCB2	177	.	0			c.T1431C						PASS	.	A		635,3191		58,519,1336	54.0	54.0	54.0		1431	-0.3	0.0	15	dbSNP_98	54	1913,6327		223,1467,2430	no	coding-synonymous	PLCB2	NM_004573.2		281,1986,3766	GG,GA,AA		23.216,16.597,21.1172		477/1186	40589002	2548,9518	1913	4120	6033	SO:0001819	synonymous_variant	5330	exon14			CCCACCAGTATCC		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1431T>C	15.37:g.40589002A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	37	CCDS42020.1																																																																																			A|0.697;G|0.303	0.303	strong		0.607	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
ADAM12	8038	hgsc.bcm.edu	37	10	127753388	127753388	+	Silent	SNP	C	C	T	rs2279091	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:127753388C>T	ENST00000368679.4	-	14	1914	c.1605G>A	c.(1603-1605)acG>acA	p.T535T	ADAM12_ENST00000368676.4_Silent_p.T535T|ADAM12_ENST00000467145.1_5'UTR	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	535	Cys-rich.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		GTCCCCAGAGCGTGACACACT	0.607													C|||	378	0.0754792	0.0651	0.072	5008	,	,		18889	0.0595		0.1243	False		,,,				2504	0.0583				p.T535T		Atlas-SNP	.											.	ADAM12	388	.	0			c.G1605A						PASS	.	C	,	302,4104		6,290,1907	84.0	59.0	67.0		1605,1605	-10.2	0.1	10	dbSNP_100	67	988,7610		62,864,3373	no	coding-synonymous,coding-synonymous	ADAM12	NM_003474.4,NM_021641.3	,	68,1154,5280	TT,TC,CC		11.491,6.8543,9.92	,	535/910,535/739	127753388	1290,11714	2203	4299	6502	SO:0001819	synonymous_variant	8038	exon14			CCAGAGCGTGACA	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"""ADAM metallopeptidase domain containing"""	190	protein-coding gene	gene with protein product	"""meltrin alpha"""	602714	"""a disintegrin and metalloproteinase domain 12 (meltrin alpha)"""			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1605G>A	10.37:g.127753388C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Silent	SNP	ENST00000368679.4	37	CCDS7653.1																																																																																			C|0.908;T|0.092	0.092	strong		0.607	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		
GUCA1C	9626	hgsc.bcm.edu	37	3	108634973	108634973	+	Splice_Site	SNP	C	C	A	rs10933973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108634973C>A	ENST00000261047.3	-	3	575		c.e3+1		GUCA1C_ENST00000471108.1_Missense_Mutation_p.G148V|GUCA1C_ENST00000393963.3_Missense_Mutation_p.G148V	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C						phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(2)|large_intestine(1)|liver(1)|lung(8)|pancreas(1)|skin(1)	14						AGCTCCATTACCATCATTGTT	0.428													C|||	1250	0.249601	0.2519	0.3084	5008	,	,		18757	0.1806		0.3042	False		,,,				2504	0.2198				.	NSCLC(157;1360 1999 30631 40189 44208)	Atlas-SNP	.											.	GUCA1C	39	.	0			c.442+1G>T						PASS	.	C		1193,3213	417.0+/-337.8	156,881,1166	164.0	156.0	159.0			-0.3	0.0	3	dbSNP_120	159	2696,5904	433.1+/-357.3	416,1864,2020	yes	splice-5	GUCA1C	NM_005459.3		572,2745,3186	AA,AC,CC		31.3488,27.0767,29.9016			108634973	3889,9117	2203	4300	6503	SO:0001630	splice_region_variant	9626	exon4			CCATTACCATCAT	AF110002	CCDS2954.1	3q13.1	2013-01-10			ENSG00000138472	ENSG00000138472		"""EF-hand domain containing"""	4680	protein-coding gene	gene with protein product	"""guanylyl cyclase-activating protein 3"""	605128				10037746, 11860507	Standard	NM_005459		Approved	GCAP3	uc003dxj.2	O95843	OTTHUMG00000159204	ENST00000261047.3:c.442+1G>T	3.37:g.108634973C>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	195	83	0.425641	NM_005459	O95844|Q9UNM0	Splice_Site	SNP	ENST00000261047.3	37	CCDS2954.1	562|562	0.2573260073260073|0.2573260073260073	97|97	0.19715447154471544|0.19715447154471544	108|108	0.2983425414364641|0.2983425414364641	127|127	0.22202797202797203|0.22202797202797203	230|230	0.3034300791556728|0.3034300791556728	c|c	14.10|14.10	2.433951|2.433951	0.43224|0.43224	0.270767|0.270767	0.313488|0.313488	ENSG00000138472|ENSG00000138472	ENST00000261047|ENST00000393963;ENST00000471108	.|D;D	.|0.84070	.|-1.8;-1.8	4.2|4.2	-0.274|-0.274	0.12910|0.12910	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999866305|0.9999999866305	.|D	.|0.89917	.|1.0	.|D	.|0.81914	.|0.995	.|T	.|0.07083	.|-1.0791	.|7	.|0.87932	.|D	.|0	.|.	7.7152|7.7152	0.28700|0.28700	0.2868:0.4257:0.2875:0.0|0.2868:0.4257:0.2875:0.0	rs10933973;rs52825108;rs61623352;rs10933973|rs10933973;rs52825108;rs61623352;rs10933973	.|148	.|C9JNI2	.|.	.|V	-1|148	.|ENSP00000377535:G148V;ENSP00000417761:G148V	.|ENSP00000377535:G148V	.|G	-|-	.|2	.|0	GUCA1C|GUCA1C	110117663|110117663	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.970000|0.970000	0.65996|0.65996	1.417000|1.417000	0.34770|0.34770	-0.323000|-0.323000	0.08602|0.08602	0.651000|0.651000	0.88453|0.88453	.|GGT	C|0.727;A|0.273	0.273	strong		0.428	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459	Intron
DNAH14	127602	hgsc.bcm.edu	37	1	225142710	225142710	+	Missense_Mutation	SNP	A	A	T	rs41267347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:225142710A>T	ENST00000445597.2	+	5	658	c.658A>T	c.(658-660)Act>Tct	p.T220S	DNAH14_ENST00000439375.2_Missense_Mutation_p.T43S|DNAH14_ENST00000498360.1_3'UTR|DNAH14_ENST00000366850.3_Missense_Mutation_p.T43S|DNAH14_ENST00000430092.1_Missense_Mutation_p.T43S|DNAH14_ENST00000366849.1_Missense_Mutation_p.T43S|DNAH14_ENST00000400952.3_Missense_Mutation_p.T43S|DNAH14_ENST00000366848.1_Missense_Mutation_p.T43S			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	220			T -> S (in dbSNP:rs41267347). {ECO:0000269|PubMed:15489334}.		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						ACCATTAGAGACTCAACCAGC	0.294													A|||	169	0.033746	0.0045	0.036	5008	,	,		15813	0.0129		0.0736	False		,,,				2504	0.0521				p.T43S		Atlas-SNP	.											.	DNAH14	300	.	0			c.A127T						PASS	.	A	SER/THR,SER/THR,SER/THR	49,3557		0,49,1754	85.0	81.0	82.0		127,127,127	-0.2	0.0	1	dbSNP_127	82	582,7550		24,534,3508	yes	missense,missense,missense	DNAH14	NM_001145154.1,NM_001373.1,NM_144989.2	58,58,58	24,583,5262	TT,TA,AA		7.1569,1.3588,5.3757	benign,benign,benign	43/454,43/4516,43/229	225142710	631,11107	1803	4066	5869	SO:0001583	missense	127602	exon3			TTAGAGACTCAAC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.658A>T	1.37:g.225142710A>T	ENSP00000409472:p.Thr220Ser	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	159	68	0.427673	NM_144989	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		85	0.03891941391941392	4	0.008130081300813009	15	0.04143646408839779	9	0.015734265734265736	57	0.07519788918205805	A	1.431	-0.570318	0.03910	0.013588	0.071569	ENSG00000185842	ENST00000445597;ENST00000413949;ENST00000430092;ENST00000366850;ENST00000400952;ENST00000366849;ENST00000366848;ENST00000439375	T;T;T;T;T;T;T;T	0.56275	2.55;0.47;1.02;1.13;0.96;1.01;1.13;1.02	3.61	-0.167	0.13347	.	2.079080	0.02827	N	0.126330	T	0.01661	0.0053	.	.	.	0.09310	N	1	B;B;B;B	0.10296	0.001;0.003;0.001;0.001	B;B;B;B	0.11329	0.001;0.006;0.001;0.001	T	0.05419	-1.0886	9	0.09590	T	0.72	.	6.1381	0.20245	0.6537:0.0:0.3463:0.0	rs41267347;rs61741648	43;43;43;220	Q0VDD8-4;Q0VDD8-3;Q0VDD8-2;Q0VDD8	.;.;.;DYH14_HUMAN	S	220;43;43;43;43;43;43;43	ENSP00000409472:T220S;ENSP00000412969:T43S;ENSP00000414402:T43S;ENSP00000355815:T43S;ENSP00000383737:T43S;ENSP00000355814:T43S;ENSP00000355813:T43S;ENSP00000392061:T43S	ENSP00000355813:T43S	T	+	1	0	DNAH14	223209333	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.016000	0.13377	-0.044000	0.13491	0.455000	0.32223	ACT	A|0.950;T|0.050	0.050	strong		0.294	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
IL17RC	84818	hgsc.bcm.edu	37	3	9970062	9970062	+	Silent	SNP	C	C	T	rs151110374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:9970062C>T	ENST00000295981.3	+	11	1382	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000413608.1_Silent_p.D317D|IL17RC_ENST00000403601.3_Silent_p.D317D|IL17RC_ENST00000416074.2_Silent_p.D173D|IL17RC_ENST00000455057.1_Silent_p.D302D|IL17RC_ENST00000383812.4_Silent_p.D302D	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	388					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGCTGCTGGACGCACCGTGCT	0.682													C|||	30	0.00599042	0.0	0.0	5008	,	,		15079	0.0		0.0	False		,,,				2504	0.0307				p.D388D		Atlas-SNP	.											.	IL17RC	55	.	0			c.C1164T						PASS	.	C	,,,,,	3,4403	6.2+/-15.9	0,3,2200	30.0	36.0	34.0		951,951,906,906,951,1164	-7.9	0.0	3	dbSNP_134	34	6,8592	5.0+/-18.6	0,6,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	,,,,,	0,9,6493	TT,TC,CC		0.0698,0.0681,0.0692	,,,,,	317/708,317/691,302/689,302/706,317/721,388/792	9970062	9,12995	2203	4299	6502	SO:0001819	synonymous_variant	84818	exon11			GCTGGACGCACCG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1164C>T	3.37:g.9970062C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	30	10	0.333333	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			C|0.999;T|0.001	0.001	strong		0.682	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
PRPS1L1	221823	hgsc.bcm.edu	37	7	18066569	18066569	+	Missense_Mutation	SNP	C	C	A	rs3800962	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:18066569C>A	ENST00000506618.2	-	1	917	c.837G>T	c.(835-837)gaG>gaT	p.E279D		NM_175886.2	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like 1	279			E -> D (in dbSNP:rs3800962). {ECO:0000269|PubMed:15489334}.		5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|nucleotide biosynthetic process (GO:0009165)|ribonucleoside monophosphate biosynthetic process (GO:0009156)		ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)	18	Lung NSC(10;0.0385)|all_lung(11;0.0736)					GCTTCATCTTCTCATCTTGAG	0.433													A|||	1326	0.264776	0.1974	0.3977	5008	,	,		19661	0.1548		0.4165	False		,,,				2504	0.2188				p.E279D		Atlas-SNP	.											.	PRPS1L1	90	.	0			c.G837T						PASS	.	A	ASP/GLU	1003,3399	717.9+/-408.8	108,787,1306	189.0	188.0	189.0		837	-2.1	1.0	7	dbSNP_107	189	3641,4959	622.0+/-397.3	738,2165,1397	yes	missense	PRPS1L1	NM_175886.2	45	846,2952,2703	AA,AC,CC		42.3372,22.7851,35.7176	benign	279/319	18066569	4644,8358	2201	4300	6501	SO:0001583	missense	221823	exon1			CATCTTCTCATCT	M57423	CCDS47552.1	7p21.1	2010-12-10			ENSG00000229937	ENSG00000229937			9463	protein-coding gene	gene with protein product		611566		PRPSL		2168892	Standard	NM_175886		Approved	PRPS3	uc003stz.3	P21108	OTTHUMG00000152742	ENST00000506618.2:c.837G>T	7.37:g.18066569C>A	ENSP00000424595:p.Glu279Asp	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	198	95	0.479798	NM_175886	Q6P5P6	Missense_Mutation	SNP	ENST00000506618.2	37	CCDS47552.1	657	0.3008241758241758	85	0.17276422764227642	154	0.425414364640884	93	0.16258741258741258	325	0.4287598944591029	A	0.593	-0.832338	0.02713	0.227851	0.423372	ENSG00000229937	ENST00000506618	T	0.71934	-0.61	4.44	-2.11	0.07187	.	.	.	.	.	T	0.00012	0.0000	N	0.13198	0.31	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.22138	-1.0225	8	0.02654	T	1	.	7.6097	0.28122	0.2:0.5365:0.2635:0.0	rs3800962;rs11567145;rs12699958;rs17846612;rs17859698;rs3800962	279	P21108	PRPS3_HUMAN	D	279	ENSP00000424595:E279D	ENSP00000424595:E279D	E	-	3	2	PRPS1L1	18033094	0.993000	0.37304	0.965000	0.40720	0.801000	0.45260	0.374000	0.20501	-0.531000	0.06340	-0.264000	0.10439	GAG	C|0.709;A|0.291	0.291	strong		0.433	PRPS1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327667.1	NM_175886	
SEMA3E	9723	hgsc.bcm.edu	37	7	83037751	83037751	+	Silent	SNP	C	C	A	rs2722985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:83037751C>A	ENST00000307792.3	-	6	1070	c.603G>T	c.(601-603)gcG>gcT	p.A201A	SEMA3E_ENST00000427262.1_Silent_p.A141A	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	201	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TGCGGAAGATCGCAGCGTCTC	0.463													C|||	2786	0.55631	0.1339	0.6801	5008	,	,		15839	0.8413		0.5984	False		,,,				2504	0.7025				p.A201A		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G603T						PASS	.	C	,	950,3456	361.6+/-315.8	104,742,1357	62.0	57.0	59.0		423,603	-11.8	0.0	7	dbSNP_100	59	5054,3546	629.2+/-398.2	1501,2052,747	no	coding-synonymous,coding-synonymous	SEMA3E	NM_001178129.1,NM_012431.2	,	1605,2794,2104	AA,AC,CC		41.2326,21.5615,46.1633	,	141/716,201/776	83037751	6004,7002	2203	4300	6503	SO:0001819	synonymous_variant	9723	exon6			GAAGATCGCAGCG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.603G>T	7.37:g.83037751C>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	228	225	0.986842	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																			C|0.504;A|0.496	0.496	strong		0.463	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
SLC35F4	341880	hgsc.bcm.edu	37	14	58060707	58060707	+	Missense_Mutation	SNP	T	T	C	rs145246618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:58060707T>C	ENST00000339762.6	-	2	346	c.347A>G	c.(346-348)cAa>cGa	p.Q116R	SLC35F4_ENST00000556826.1_Missense_Mutation_p.Q80R|SLC35F4_ENST00000557430.1_5'Flank|SLC35F4_ENST00000554729.1_5'UTR			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	116					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TGAGGATCCTTGGTTTTGAAG	0.478													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18702	0.0		0.0	False		,,,				2504	0.0				p.Q80R		Atlas-SNP	.											SLC35F4_ENST00000339762,right_upper_lobe,carcinoma,0,2	SLC35F4	105	2	0			c.A239G						PASS	.	C	ARG/GLN	26,3862		0,26,1918	92.0	92.0	92.0		239	5.8	1.0	14	dbSNP_134	92	4,8274		0,4,4135	yes	missense	SLC35F4	NM_001206920.1	43	0,30,6053	CC,CT,TT		0.0483,0.6687,0.2466	benign	80/485	58060707	30,12136	1944	4139	6083	SO:0001583	missense	341880	exon2			GATCCTTGGTTTT			14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"""Solute carriers"""	19845	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 36"""	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.347A>G	14.37:g.58060707T>C	ENSP00000342518:p.Gln116Arg	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	186	94	0.505376	NM_001206920	A6NDQ3	Missense_Mutation	SNP	ENST00000339762.6	37		7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	7.347	0.622089	0.14193	0.006687	4.83E-4	ENSG00000151812	ENST00000556826;ENST00000339762	T;T	0.38722	1.15;1.12	5.83	5.83	0.93111	.	0.207799	0.41500	N	0.000877	T	0.10337	0.0253	N	0.01048	-1.04	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.16453	-1.0402	10	0.02654	T	1	-3.5905	13.5376	0.61655	0.0:0.928:0.0:0.072	.	116	A4IF30	S35F4_HUMAN	R	80;116	ENSP00000452086:Q80R;ENSP00000342518:Q116R	ENSP00000342518:Q116R	Q	-	2	0	SLC35F4	57130460	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	3.174000	0.50847	1.489000	0.48450	-0.197000	0.12766	CAA	T|0.997;C|0.003	0.003	strong		0.478	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260	
PCDHA9	9752	hgsc.bcm.edu	37	5	140228164	140228164	+	Missense_Mutation	SNP	C	C	A	rs251353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140228164C>A	ENST00000532602.1	+	1	1117	c.84C>A	c.(82-84)agC>agA	p.S28R	PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.S28R|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	28			S -> R (in dbSNP:rs251353).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTGGGGAGCGGCCAGCTCC	0.612													.|||	2256	0.450479	0.2398	0.4496	5008	,	,		14896	0.4554		0.5109	False		,,,				2504	0.6687				p.S28R	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.C84A						PASS	.	C	ARG/SER,,,,,,,,,,,ARG/SER	1153,3241		198,757,1242	63.0	64.0	64.0		84,,,,,,,,,,,84	2.9	0.9	5	dbSNP_79	64	4581,3957		1407,1767,1095	yes	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1	110,,,,,,,,,,,110	1605,2524,2337	AA,AC,CC		46.3457,26.2403,44.3396	,,,,,,,,,,,	28/843,,,,,,,,,,,28/951	140228164	5734,7198	2197	4269	6466	SO:0001583	missense	9752	exon1			GGGGAGCGGCCAG	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.84C>A	5.37:g.140228164C>A	ENSP00000436042:p.Ser28Arg	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	225	137	0.608889	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	974	0.445970695970696	132	0.2682926829268293	194	0.5359116022099447	265	0.4632867132867133	383	0.5052770448548812	C	9.854	1.194548	0.22037	0.262403	0.536543	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53206	0.68;0.63	3.73	2.86	0.33363	Cadherin (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	M	0.85462	2.755	0.49687	P	1.8499999999999073E-4	B;B	0.13594	0.006;0.008	B;B	0.14023	0.009;0.01	T	0.37079	-0.9721	8	0.49607	T	0.09	.	8.1612	0.31201	0.0:0.8136:0.0:0.1864	rs251353;rs17844320;rs56888738	28;28	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	R	28	ENSP00000436042:S28R;ENSP00000367362:S28R	ENSP00000367362:S28R	S	+	3	2	PCDHA9	140208348	0.460000	0.25776	0.907000	0.35723	0.134000	0.20937	0.177000	0.16801	0.889000	0.36185	0.591000	0.81541	AGC	C|0.554;A|0.446	0.446	strong		0.612	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
MORC2	22880	hgsc.bcm.edu	37	22	31342376	31342376	+	Silent	SNP	G	G	C	rs2072132	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:31342376G>C	ENST00000397641.3	-	6	786	c.378C>G	c.(376-378)acC>acG	p.T126T	MORC2_ENST00000215862.4_Silent_p.T64T			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	126						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						GGAAGAGGCAGGTCATGGTGT	0.488													G|||	1765	0.352436	0.2095	0.3271	5008	,	,		20892	0.6498		0.3091	False		,,,				2504	0.3016				p.T64T		Atlas-SNP	.											.	MORC2	78	.	0			c.C192G						PASS	.	G		1086,3320	393.5+/-328.9	131,824,1248	220.0	174.0	189.0		192	1.8	1.0	22	dbSNP_96	189	2730,5870	433.7+/-357.5	444,1842,2014	no	coding-synonymous	MORC2	NM_014941.1		575,2666,3262	CC,CG,GG		31.7442,24.6482,29.3403		64/971	31342376	3816,9190	2203	4300	6503	SO:0001819	synonymous_variant	22880	exon7			GAGGCAGGTCATG	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 1"", ""zinc finger, CW type with coiled-coil domain 1"""	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.378C>G	22.37:g.31342376G>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	194	86	0.443299	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Silent	SNP	ENST00000397641.3	37																																																																																				G|0.676;C|0.324	0.324	strong		0.488	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941	
OVGP1	5016	hgsc.bcm.edu	37	1	111957583	111957583	+	Missense_Mutation	SNP	A	A	G	rs1126656|rs376377993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111957583A>G	ENST00000369732.3	-	11	1595	c.1540T>C	c.(1540-1542)Tat>Cat	p.Y514H		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	514			Y -> H (in dbSNP:rs1126656). {ECO:0000269|Ref.2}.		binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		ACAGACTGATAACCCACAGAG	0.562																																					p.Y514H		Atlas-SNP	.											.	OVGP1	177	.	0			c.T1540C						PASS	.						61.0	57.0	58.0					1																	111957583		2194	4298	6492	SO:0001583	missense	5016	exon11			ACTGATAACCCAC	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1540T>C	1.37:g.111957583A>G	ENSP00000358747:p.Tyr514His	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	409	0.18727106227106227	107	0.21747967479674796	67	0.1850828729281768	72	0.1258741258741259	163	0.21503957783641162	a	1.263	-0.615397	0.03663	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.03717	3.83	2.88	-5.76	0.02376	.	.	.	.	.	T	0.00241	0.0007	N	0.00729	-1.24	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43845	-0.9366	8	0.18710	T	0.47	.	1.6984	0.02867	0.1807:0.1255:0.4461:0.2478	rs1126656	514;578	Q12889;Q59HH5	OVGP1_HUMAN;.	H	514;578;322	ENSP00000358747:Y514H	ENSP00000358743:Y578H	Y	-	1	0	OVGP1	111759106	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-2.105000	0.01339	-3.042000	0.00263	-0.386000	0.06593	TAT	A|0.800;G|0.200	0.200	strong		0.562	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
ARMC4	55130	hgsc.bcm.edu	37	10	28228865	28228865	+	Silent	SNP	A	A	G	rs7893462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:28228865A>G	ENST00000305242.5	-	14	2150	c.2058T>C	c.(2056-2058)aaT>aaC	p.N686N	ARMC4_ENST00000545014.1_Silent_p.N211N|ARMC4_ENST00000537576.1_Silent_p.N378N	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	686					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						GCAGCTGCTCATTCTCACTAT	0.438													G|||	2670	0.533147	0.469	0.5764	5008	,	,		14602	0.5		0.5477	False		,,,				2504	0.6084				p.N686N		Atlas-SNP	.											.	ARMC4	177	.	0			c.T2058C						PASS	.	G		2030,2376	613.0+/-392.1	484,1062,657	104.0	93.0	97.0		2058	-2.7	0.8	10	dbSNP_116	97	4578,4022	556.4+/-386.8	1223,2132,945	yes	coding-synonymous	ARMC4	NM_018076.2		1707,3194,1602	GG,GA,AA		46.7674,46.0735,49.1927		686/1045	28228865	6608,6398	2203	4300	6503	SO:0001819	synonymous_variant	55130	exon14			CTGCTCATTCTCA	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2058T>C	10.37:g.28228865A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	138	60	0.434783	NM_018076	A8K906|B7Z7I1|Q9H0C0	Silent	SNP	ENST00000305242.5	37	CCDS7157.1																																																																																			A|0.488;G|0.512	0.512	strong		0.438	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	
MLIP	90523	hgsc.bcm.edu	37	6	54054686	54054686	+	Missense_Mutation	SNP	T	T	A	rs6934690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:54054686T>A	ENST00000274897.5	+	9	1071	c.958T>A	c.(958-960)Tct>Act	p.S320T	MLIP_ENST00000370877.2_Missense_Mutation_p.S216T|MLIP_ENST00000509997.1_Missense_Mutation_p.S174T|MLIP_ENST00000502396.1_Missense_Mutation_p.S855T|MLIP_ENST00000511744.1_3'UTR|MLIP_ENST00000358276.5_Missense_Mutation_p.S220T|MLIP_ENST00000514921.1_Missense_Mutation_p.S844T|MLIP_ENST00000370876.2_Missense_Mutation_p.S164T	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	320			S -> T (in dbSNP:rs6934690). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						CTCCTCACCATCTTCTACAGT	0.333													T|||	3993	0.797324	0.6104	0.8429	5008	,	,		14843	0.8115		0.9205	False		,,,				2504	0.8763				p.S320T		Atlas-SNP	.											.	MLIP	84	.	0			c.T958A						PASS	.	T	THR/SER	2979,1427	681.4+/-404.0	981,1017,205	99.0	88.0	92.0		958	4.3	0.7	6	dbSNP_116	92	8081,519	794.9+/-407.5	3795,491,14	yes	missense	MLIP	NM_138569.2	58	4776,1508,219	AA,AT,TT		6.0349,32.3877,14.9623	benign	320/459	54054686	11060,1946	2203	4300	6503	SO:0001583	missense	90523	exon9			TCACCATCTTCTA	AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"""muscle-enriched A-type lamin interacting protein"""	614106	"""chromosome 6 open reading frame 142"""	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.958T>A	6.37:g.54054686T>A	ENSP00000274897:p.Ser320Thr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_138569	B7Z2N0|D6RE05|Q96H08|Q96NF7	Missense_Mutation	SNP	ENST00000274897.5	37	CCDS4954.1	1775	0.8127289377289377	293	0.5955284552845529	315	0.8701657458563536	462	0.8076923076923077	705	0.9300791556728232	T	13.23	2.175836	0.38413	0.676123	0.939651	ENSG00000146147	ENST00000274897;ENST00000514921;ENST00000370877;ENST00000509997;ENST00000370876;ENST00000447836;ENST00000502396;ENST00000358276;ENST00000370878;ENST00000514433	T;T;T;T;T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08;1.08	5.52	4.29	0.51040	.	0.335147	0.27600	N	0.018658	T	0.34337	0.0894	L	0.45581	1.43	0.80722	P	0.0	D;P;B;D	0.58268	0.982;0.906;0.42;0.982	P;P;B;P	0.58013	0.831;0.6;0.09;0.831	T	0.20306	-1.0279	9	0.33940	T	0.23	-4.4165	8.0961	0.30829	0.1796:0.0:0.0:0.8204	rs6934690;rs52813986;rs56571777;rs59900170;rs6934690	855;164;320;844	Q5VWP3-3;Q5VWP3-2;Q5VWP3;D6RE05	.;.;MLIP_HUMAN;.	T	320;844;216;174;164;154;855;220;154;249	ENSP00000274897:S320T;ENSP00000425142:S844T;ENSP00000359914:S216T;ENSP00000427584:S174T;ENSP00000359913:S164T;ENSP00000411917:S154T;ENSP00000426290:S855T;ENSP00000351019:S220T;ENSP00000421444:S249T	ENSP00000274897:S320T	S	+	1	0	MLIP	54162645	0.014000	0.17966	0.702000	0.30337	0.599000	0.36880	0.789000	0.26886	2.088000	0.63022	0.482000	0.46254	TCT	T|0.177;A|0.823	0.823	strong		0.333	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569	
QSOX1	5768	hgsc.bcm.edu	37	1	180159654	180159654	+	Silent	SNP	C	C	T	rs7521513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180159654C>T	ENST00000367602.3	+	10	1301	c.1227C>T	c.(1225-1227)gtC>gtT	p.V409V	QSOX1_ENST00000367600.5_Silent_p.V409V			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	409	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						CCCTGTGGGTCCTCTTCCACT	0.592													C|||	630	0.125799	0.0832	0.1556	5008	,	,		18817	0.0744		0.1581	False		,,,				2504	0.182				p.V409V		Atlas-SNP	.											.	QSOX1	79	.	0			c.C1227T						PASS	.	C	,	388,4018		27,334,1842	135.0	121.0	126.0		1227,1227	3.7	1.0	1	dbSNP_116	126	1340,7260		121,1098,3081	no	coding-synonymous,coding-synonymous	QSOX1	NM_001004128.2,NM_002826.4	,	148,1432,4923	TT,TC,CC		15.5814,8.8062,13.2862	,	409/605,409/748	180159654	1728,11278	2203	4300	6503	SO:0001819	synonymous_variant	5768	exon10			GTGGGTCCTCTTC	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1227C>T	1.37:g.180159654C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	170	98	0.576471	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Silent	SNP	ENST00000367602.3	37	CCDS1337.1																																																																																			C|0.863;T|0.137	0.137	strong		0.592	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
TAF4B	6875	hgsc.bcm.edu	37	18	23854692	23854692	+	Silent	SNP	C	C	T	rs17224558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:23854692C>T	ENST00000269142.5	+	4	1661	c.663C>T	c.(661-663)acC>acT	p.T221T	TAF4B_ENST00000578121.1_Silent_p.T221T|TAF4B_ENST00000400466.2_Silent_p.T221T	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	221					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CTGTAACTACCCTGAAGCCTT	0.418													C|||	618	0.123403	0.1415	0.1182	5008	,	,		20318	0.1121		0.1074	False		,,,				2504	0.1309				p.T221T		Atlas-SNP	.											.	TAF4B	71	.	0			c.C663T						PASS	.	C		530,3254		32,466,1394	153.0	146.0	148.0		663	-0.2	0.4	18	dbSNP_123	148	890,7352		48,794,3279	no	coding-synonymous	TAF4B	NM_005640.1		80,1260,4673	TT,TC,CC		10.7983,14.0063,11.8077		221/863	23854692	1420,10606	1892	4121	6013	SO:0001819	synonymous_variant	6875	exon4			AACTACCCTGAAG	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.663C>T	18.37:g.23854692C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	CCDS42421.1																																																																																			C|0.875;T|0.125	0.125	strong		0.418	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
KLC3	147700	hgsc.bcm.edu	37	19	45848869	45848869	+	Missense_Mutation	SNP	G	G	A	rs546355544		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45848869G>A	ENST00000391946.2	+	2	172	c.70G>A	c.(70-72)Gtg>Atg	p.V24M	KLC3_ENST00000470402.1_Missense_Mutation_p.V38M|KLC3_ENST00000585434.1_Missense_Mutation_p.V24M	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	24					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TGAGGAGCTGGTGCGGCAGAC	0.706													G|||	1	0.000199681	0.0	0.0014	5008	,	,		13844	0.0		0.0	False		,,,				2504	0.0				p.V24M		Atlas-SNP	.											.	KLC3	37	.	0			c.G70A						PASS	.						5.0	7.0	7.0					19																	45848869		1932	4073	6005	SO:0001583	missense	147700	exon2			GAGCTGGTGCGGC	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.70G>A	19.37:g.45848869G>A	ENSP00000375810:p.Val24Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Missense_Mutation	SNP	ENST00000391946.2	37	CCDS12660.2	.	.	.	.	.	.	.	.	.	.	G	12.08	1.830370	0.32329	.	.	ENSG00000104892	ENST00000391946;ENST00000470402	D;D	0.85171	-1.93;-1.95	3.4	3.4	0.38934	.	0.110159	0.38272	N	0.001756	T	0.77356	0.4118	N	0.25485	0.75	0.36902	D	0.890437	P;P;P	0.49635	0.926;0.926;0.879	P;P;B	0.46825	0.528;0.528;0.328	T	0.80141	-0.1506	10	0.56958	D	0.05	.	6.7358	0.23409	0.1316:0.0:0.8684:0.0	.	24;38;24	Q6P597-2;Q6P597-3;Q6P597	.;.;KLC3_HUMAN	M	24;38	ENSP00000375810:V24M;ENSP00000436019:V38M	ENSP00000375810:V24M	V	+	1	0	KLC3	50540709	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	2.415000	0.44635	1.918000	0.55548	0.313000	0.20887	GTG	.	.	none		0.706	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
PDIA5	10954	hgsc.bcm.edu	37	3	122880191	122880191	+	Silent	SNP	T	T	C	rs8935	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122880191T>C	ENST00000316218.7	+	16	1463	c.1368T>C	c.(1366-1368)tgT>tgC	p.C456C	PDIA5_ENST00000467157.1_3'UTR	NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	456	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		CTGTTGACTGTGTCAAAGACA	0.537													T|||	1412	0.281949	0.1195	0.281	5008	,	,		19701	0.4613		0.328	False		,,,				2504	0.2699				p.C456C		Atlas-SNP	.											.	PDIA5	66	.	0			c.T1368C						PASS	.	T		748,3658	306.3+/-289.4	72,604,1527	101.0	89.0	93.0		1368	-3.0	0.9	3	dbSNP_52	93	2632,5968	425.7+/-355.0	412,1808,2080	no	coding-synonymous	PDIA5	NM_006810.3		484,2412,3607	CC,CT,TT		30.6047,16.9768,25.988		456/520	122880191	3380,9626	2203	4300	6503	SO:0001819	synonymous_variant	10954	exon16			TGACTGTGTCAAA	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"""Protein disulfide isomerases"""	24811	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 5"""			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.1368T>C	3.37:g.122880191T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	99	61	0.616162	NM_006810	D3DN95|Q9BV43	Silent	SNP	ENST00000316218.7	37	CCDS3020.1																																																																																			C|0.276;T|0.724	0.276	strong		0.537	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810	
EML6	400954	hgsc.bcm.edu	37	2	55189685	55189685	+	Silent	SNP	C	C	T	rs75479836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:55189685C>T	ENST00000356458.6	+	35	5515	c.4995C>T	c.(4993-4995)gaC>gaT	p.D1665D	EML6_ENST00000490828.1_3'UTR	NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	1665						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						GAACCAAAGACGGAGAAATAA	0.413													c|||	152	0.0303514	0.0038	0.0576	5008	,	,		20598	0.0		0.0915	False		,,,				2504	0.0153				p.D1665D		Atlas-SNP	.											EML6,NS,carcinoma,+2,1	EML6	85	1	0			c.C4995T						PASS	.			21,1363		0,21,671	100.0	94.0	96.0		4995	4.4	1.0	2	dbSNP_132	96	230,2952		13,204,1374	no	coding-synonymous	EML6	NM_001039753.2		13,225,2045	TT,TC,CC		7.2282,1.5173,5.4972		1665/1959	55189685	251,4315	692	1591	2283	SO:0001819	synonymous_variant	400954	exon35			CAAAGACGGAGAA		CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595		"""WD repeat domain containing"""	35412	protein-coding gene	gene with protein product							Standard	NM_001039753		Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.4995C>T	2.37:g.55189685C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_001039753	A8MUB5|B6ZDG7	Silent	SNP	ENST00000356458.6	37	CCDS46286.1																																																																																			C|0.952;T|0.048	0.048	strong		0.413	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324997.3	XM_001725002	
NFYC	4802	hgsc.bcm.edu	37	1	41204569	41204569	+	Silent	SNP	C	C	T	rs11546179|rs1057925	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:41204569C>T	ENST00000308733.5	+	1	60	c.54C>T	c.(52-54)agC>agT	p.S18S	NFYC_ENST00000440226.3_Silent_p.S18S|NFYC_ENST00000372654.1_Silent_p.S18S|NFYC_ENST00000372651.1_Silent_p.S18S|NFYC_ENST00000447388.3_Silent_p.S18S|NFYC_ENST00000372652.1_Silent_p.S18S|NFYC_ENST00000456393.2_Silent_p.S18S|NFYC_ENST00000427410.2_Silent_p.S18S|NFYC_ENST00000372653.1_Silent_p.S18S|NFYC_ENST00000425457.2_Silent_p.S18S			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma	18					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription, DNA-templated (GO:0045893)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)|skin(2)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)			CCCAGCAAAGCCTACAGTCGT	0.398													C|||	2414	0.482029	0.4244	0.5115	5008	,	,		18542	0.4692		0.5895	False		,,,				2504	0.4417				p.S18S		Atlas-SNP	.											.	NFYC	39	.	0			c.C54T						PASS	.	C	,,,,	1966,2440	554.3+/-379.0	424,1118,661	108.0	110.0	109.0		54,54,54,54,54	4.1	1.0	1	dbSNP_86	109	5026,3574	628.7+/-398.1	1500,2026,774	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFYC	NM_001142587.1,NM_001142588.1,NM_001142589.1,NM_001142590.1,NM_014223.4	,,,,	1924,3144,1435	TT,TC,CC		41.5581,44.621,46.2402	,,,,	18/335,18/355,18/298,18/302,18/336	41204569	6992,6014	2203	4300	6503	SO:0001819	synonymous_variant	4802	exon2			GCAAAGCCTACAG	U78774	CCDS455.1, CCDS44120.1, CCDS44121.1, CCDS44122.1, CCDS44123.1	1p32	2008-11-11			ENSG00000066136	ENSG00000066136			7806	protein-coding gene	gene with protein product		605344				8921405, 9249075	Standard	NM_014223		Approved	CBF-C, NF-YC	uc009vwd.3	Q13952	OTTHUMG00000007729	ENST00000308733.5:c.54C>T	1.37:g.41204569C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_001142587	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Silent	SNP	ENST00000308733.5	37																																																																																				C|0.485;T|0.515	0.515	strong		0.398	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223	
COL6A2	1292	hgsc.bcm.edu	37	21	47545823	47545823	+	Silent	SNP	G	G	A	rs13052956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47545823G>A	ENST00000300527.4	+	26	2198	c.2094G>A	c.(2092-2094)gcG>gcA	p.A698A	COL6A2_ENST00000357838.4_Silent_p.A698A|COL6A2_ENST00000310645.5_Silent_p.A698A|COL6A2_ENST00000409416.1_Silent_p.A698A|COL6A2_ENST00000397763.1_Silent_p.A698A	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	698	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		AGTGGATTGCGGGCGGCACCT	0.607													G|||	1974	0.394169	0.208	0.6398	5008	,	,		14604	0.4306		0.5109	False		,,,				2504	0.3139				p.A698A		Atlas-SNP	.											.	COL6A2	351	.	0			c.G2094A						PASS	.	G	,,	1065,3341	387.2+/-326.4	148,769,1286	76.0	69.0	72.0		2094,2094,2094	-8.4	0.0	21	dbSNP_121	72	4303,4297	576.5+/-390.4	1047,2209,1044	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	1195,2978,2330	AA,AG,GG		49.9651,24.1716,41.2733	,,	698/1020,698/919,698/829	47545823	5368,7638	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			GATTGCGGGCGGC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2094G>A	21.37:g.47545823G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	182	177	0.972527	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			G|0.578;A|0.422	0.422	strong		0.607	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
LRP4	4038	hgsc.bcm.edu	37	11	46898771	46898771	+	Missense_Mutation	SNP	T	T	C	rs6485702	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:46898771T>C	ENST00000378623.1	-	23	3498	c.3256A>G	c.(3256-3258)Att>Gtt	p.I1086V	LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1086			I -> V (in dbSNP:rs6485702). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9693030, ECO:0000269|Ref.1}.		dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)	p.I1086V(1)		breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		TCTACTCCAATGGCAATGGTG	0.512													T|||	2233	0.445887	0.1256	0.572	5008	,	,		20720	0.2927		0.6769	False		,,,				2504	0.7096				p.I1086V		Atlas-SNP	.											LRP4,NS,carcinoma,0,1	LRP4	160	1	1	Substitution - Missense(1)	stomach(1)	c.A3256G						PASS	.	T	VAL/ILE	977,3425	367.1+/-318.1	126,725,1350	258.0	189.0	212.0		3256	3.9	1.0	11	dbSNP_116	212	5733,2865	674.0+/-403.1	1898,1937,464	yes	missense	LRP4	NM_002334.3	29	2024,2662,1814	CC,CT,TT		33.3217,22.1945,48.3846	benign	1086/1906	46898771	6710,6290	2201	4299	6500	SO:0001583	missense	4038	exon23			CTCCAATGGCAAT	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.3256A>G	11.37:g.46898771T>C	ENSP00000367888:p.Ile1086Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	936	0.42857142857142855	62	0.12601626016260162	193	0.5331491712707183	177	0.3094405594405594	504	0.6649076517150396	T	4.937	0.174078	0.09391	0.221945	0.666783	ENSG00000134569	ENST00000378623	D	0.90955	-2.76	6.17	3.91	0.45181	Six-bladed beta-propeller, TolB-like (1);	0.226336	0.46145	N	0.000309	T	0.00012	0.0000	N	0.08118	0	0.23107	P	0.99828233	B	0.02656	0.0	B	0.06405	0.002	T	0.47649	-0.9101	9	0.19147	T	0.46	.	8.3038	0.32029	0.0:0.2068:0.0:0.7932	rs6485702;rs17790144;rs52801120;rs60959018;rs6485702	1086	O75096	LRP4_HUMAN	V	1086	ENSP00000367888:I1086V	ENSP00000367888:I1086V	I	-	1	0	LRP4	46855347	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.139000	0.42149	1.165000	0.42670	0.533000	0.62120	ATT	T|0.523;C|0.477	0.477	strong		0.512	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
SCD	6319	hgsc.bcm.edu	37	10	102116311	102116311	+	Missense_Mutation	SNP	A	A	C	rs2234970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:102116311A>C	ENST00000370355.2	+	5	1051	c.670A>C	c.(670-672)Atg>Ctg	p.M224L		NM_005063.4	NP_005054.3	O00767	ACOD_HUMAN	stearoyl-CoA desaturase (delta-9-desaturase)	224			M -> L (in dbSNP:rs2234970). {ECO:0000269|PubMed:10229681, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|large_intestine(3)|lung(5)	9		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		TGGCTTGCTGATGATGTGCTT	0.498													C|||	1948	0.388978	0.3631	0.5461	5008	,	,		20017	0.4028		0.4245	False		,,,				2504	0.2618				p.M224L	Colon(67;260 1459 9574 11663)	Atlas-SNP	.											.	SCD	25	.	0			c.A670C						PASS	.	C	LEU/MET	1570,2836	667.9+/-401.9	275,1020,908	183.0	144.0	158.0		670	-8.8	0.0	10	dbSNP_98	158	3627,4973	624.8+/-397.6	737,2153,1410	yes	missense	SCD	NM_005063.4	15	1012,3173,2318	CC,CA,AA		42.1744,35.6332,39.9585	benign	224/360	102116311	5197,7809	2203	4300	6503	SO:0001583	missense	6319	exon5			TTGCTGATGATGT	AF097514	CCDS7493.1	10q23-q24	2013-01-25			ENSG00000099194	ENSG00000099194	1.14.19.1	"""Fatty acid desaturases"""	10571	protein-coding gene	gene with protein product	"""acyl-CoA desaturase"", ""fatty acid desaturase"", ""delta-9-desaturase"""	604031	"""stearoyl-CoA desaturase opposite strand"""	SCDOS		7909540, 10229681	Standard	NM_005063		Approved	FADS5	uc001kqy.3	O00767	OTTHUMG00000018906	ENST00000370355.2:c.670A>C	10.37:g.102116311A>C	ENSP00000359380:p.Met224Leu	Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	209	111	0.5311	NM_005063	B2R5U0|D3DR68|Q16150|Q53GR9|Q5W037|Q5W038|Q6GSS4|Q96KF6|Q9BS07|Q9Y695	Missense_Mutation	SNP	ENST00000370355.2	37	CCDS7493.1	925	0.42353479853479853	182	0.3699186991869919	185	0.511049723756906	230	0.4020979020979021	328	0.43271767810026385	C	0.009	-1.827876	0.00584	0.356332	0.421744	ENSG00000099194	ENST00000423840;ENST00000370355	T	0.15372	2.43	5.53	-8.81	0.00813	Fatty acid desaturase, type 1 (1);	0.506214	0.17853	N	0.159772	T	0.00012	0.0000	N	0.00010	-3.025	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34428	-0.9829	9	0.02654	T	1	-5.4107	4.4685	0.11701	0.1465:0.1341:0.1456:0.5738	rs2234970;rs11598233;rs17855743;rs52813351;rs59706801;rs2234970	224	O00767	ACOD_HUMAN	L	224	ENSP00000359380:M224L	ENSP00000359380:M224L	M	+	1	0	SCD	102106301	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-3.819000	0.00358	-2.211000	0.00737	-1.169000	0.01745	ATG	A|0.604;C|0.396	0.396	strong		0.498	SCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049857.2	NM_005063	
ELOVL3	83401	hgsc.bcm.edu	37	10	103988265	103988265	+	Missense_Mutation	SNP	G	G	A	rs36103207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:103988265G>A	ENST00000370005.3	+	3	546	c.325G>A	c.(325-327)Gat>Aat	p.D109N		NM_152310.1	NP_689523.1	Q9HB03	ELOV3_HUMAN	ELOVL fatty acid elongase 3	109					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			breast(2)|lung(10)|ovary(2)|prostate(1)|skin(1)	16		Colorectal(252;0.207)		Epithelial(162;4.47e-08)|all cancers(201;7.96e-07)		CAACTTCATCGATAATTCCAC	0.493													g|||	89	0.0177716	0.0023	0.0173	5008	,	,		18751	0.0		0.0408	False		,,,				2504	0.0337				p.D109N		Atlas-SNP	.											.	ELOVL3	39	.	0			c.G325A						PASS	.	A	ASN/ASP	39,4367	43.1+/-76.7	0,39,2164	135.0	131.0	132.0		325	-6.6	0.0	10	dbSNP_126	132	365,8235	121.7+/-180.7	13,339,3948	yes	missense	ELOVL3	NM_152310.1	23	13,378,6112	AA,AG,GG		4.2442,0.8852,3.1063	benign	109/271	103988265	404,12602	2203	4300	6503	SO:0001583	missense	83401	exon3			TTCATCGATAATT	AF292387	CCDS7531.1	10q24	2011-05-25	2011-05-25		ENSG00000119915	ENSG00000119915			18047	protein-coding gene	gene with protein product		611815	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3"""				Standard	NM_152310		Approved	CIG-30	uc001kut.3	Q9HB03	OTTHUMG00000018951	ENST00000370005.3:c.325G>A	10.37:g.103988265G>A	ENSP00000359022:p.Asp109Asn	Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	290	138	0.475862	NM_152310	Q5VZL3|Q8N180	Missense_Mutation	SNP	ENST00000370005.3	37	CCDS7531.1	40	0.018315018315018316	3	0.006097560975609756	8	0.022099447513812154	0	0.0	29	0.03825857519788918	g	7.443	0.641134	0.14386	0.008852	0.042442	ENSG00000119915	ENST00000370005	T	0.21361	2.01	4.67	-6.61	0.01818	.	5.486590	0.00166	N	0.000002	T	0.01800	0.0057	N	0.03238	-0.38	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.20075	-1.0286	10	0.24483	T	0.36	-22.5734	8.8107	0.34965	0.6402:0.1009:0.259:0.0	rs36103207;rs36103207	109	Q9HB03	ELOV3_HUMAN	N	109	ENSP00000359022:D109N	ENSP00000359022:D109N	D	+	1	0	ELOVL3	103978255	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.529000	0.06186	-1.596000	0.01611	-0.974000	0.02594	GAT	G|0.970;A|0.030	0.030	strong		0.493	ELOVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050030.1	NM_152310	
PCDHA12	56137	hgsc.bcm.edu	37	5	140255792	140255792	+	Silent	SNP	C	C	A	rs251377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140255792C>A	ENST00000398631.2	+	1	735	c.735C>A	c.(733-735)ccC>ccA	p.P245P	PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	245	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGATAAGCCCAGCTATAAAG	0.433													.|||	2196	0.438498	0.2882	0.415	5008	,	,		18579	0.4256		0.4841	False		,,,				2504	0.6247				p.P245P	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.C735A						PASS	.	C	,,,,,,,,,,,,,,,	1126,2632		163,800,916	103.0	101.0	102.0		,,,735,,,,,,,,,,,,735	-5.0	0.0	5	dbSNP_79	102	4032,4174		973,2086,1044	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,,,,,,,,,,,,,	1136,2886,1960	AA,AC,CC		49.1348,29.9627,43.1127	,,,,,,,,,,,,,,,	,,,245/942,,,,,,,,,,,,245/793	140255792	5158,6806	1879	4103	5982	SO:0001819	synonymous_variant	56137	exon1			TAAGCCCAGCTAT	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.735C>A	5.37:g.140255792C>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	100	64	0.64	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			C|0.560;A|0.440	0.440	strong		0.433	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
APMAP	57136	hgsc.bcm.edu	37	20	24964558	24964558	+	Missense_Mutation	SNP	T	T	C	rs12242	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:24964558T>C	ENST00000217456.2	-	2	483	c.193A>G	c.(193-195)Ata>Gta	p.I65V	APMAP_ENST00000447138.1_Missense_Mutation_p.I65V	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	65			I -> V (in dbSNP:rs17298715).		biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										TGTGGATCTATAGGAGATTCC	0.517													T|||	84	0.0167732	0.0038	0.0245	5008	,	,		17985	0.0		0.0567	False		,,,				2504	0.0051				p.I65V		Atlas-SNP	.											.	APMAP	3	.	0			c.A193G						PASS	.	T	VAL/ILE	38,4368	42.3+/-75.8	0,38,2165	87.0	91.0	90.0		193	5.9	1.0	20	dbSNP_123	90	490,8110	141.9+/-198.1	11,468,3821	yes	missense	C20orf3	NM_020531.2	29	11,506,5986	CC,CT,TT		5.6977,0.8625,4.0597	benign	65/417	24964558	528,12478	2203	4300	6503	SO:0001583	missense	57136	exon2			GATCTATAGGAGA	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.193A>G	20.37:g.24964558T>C	ENSP00000217456:p.Ile65Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	37	CCDS13166.1	55	0.025183150183150184	3	0.006097560975609756	8	0.022099447513812154	0	0.0	44	0.05804749340369393	T	18.64	3.667973	0.67814	0.008625	0.056977	ENSG00000101474	ENST00000217456;ENST00000447138	T;T	0.32272	1.87;1.46	5.93	5.93	0.95920	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.04182	0.0116	L	0.56280	1.765	0.53688	D	0.999973	P;P;D	0.54397	0.947;0.615;0.966	P;B;P	0.45794	0.481;0.1;0.493	T	0.00926	-1.1512	10	0.23891	T	0.37	-29.4431	12.7716	0.57423	0.0:0.0:0.0:1.0	rs17298715	65;49;65	Q9HDC9-2;A2A2F9;Q9HDC9	.;.;APMAP_HUMAN	V	65	ENSP00000217456:I65V;ENSP00000415373:I65V	ENSP00000217456:I65V	I	-	1	0	C20orf3	24912558	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	5.378000	0.66190	2.271000	0.75665	0.533000	0.62120	ATA	T|0.964;C|0.036	0.036	strong		0.517	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
TDG	6996	hgsc.bcm.edu	37	12	104380734	104380734	+	Missense_Mutation	SNP	G	G	A	rs2888805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:104380734G>A	ENST00000392872.3	+	10	1333	c.1099G>A	c.(1099-1101)Gtg>Atg	p.V367M	TDG_ENST00000544861.1_Missense_Mutation_p.V224M|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Missense_Mutation_p.V163M|TDG_ENST00000266775.9_Missense_Mutation_p.V363M|TDG_ENST00000536395.1_3'UTR	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	367			V -> L (in dbSNP:rs2888805).|V -> M (in dbSNP:rs2888805). {ECO:0000269|Ref.2}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		AGTTGAGAGCGTGGAGTTAAG	0.408								Base excision repair (BER), DNA glycosylases					G|||	563	0.11242	0.0053	0.111	5008	,	,		26412	0.2927		0.0944	False		,,,				2504	0.091				p.V367M		Atlas-SNP	.											.	TDG	43	.	0			c.G1099A						PASS	.	G	MET/VAL	97,4309	78.3+/-116.7	0,97,2106	151.0	129.0	136.0		1099	0.2	0.0	12	dbSNP_101	136	836,7764	191.8+/-238.0	26,784,3490	yes	missense	TDG	NM_003211.4	21	26,881,5596	AA,AG,GG		9.7209,2.2015,7.1736	benign	367/411	104380734	933,12073	2203	4300	6503	SO:0001583	missense	6996	exon10			GAGAGCGTGGAGT	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.1099G>A	12.37:g.104380734G>A	ENSP00000376611:p.Val367Met	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_003211	Q8IUZ6|Q8IZM3	Missense_Mutation	SNP	ENST00000392872.3	37	CCDS9095.1	290	0.13278388278388278	4	0.008130081300813009	40	0.11049723756906077	174	0.3041958041958042	72	0.09498680738786279	G	8.454	0.853700	0.17106	0.022015	0.097209	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	T;T;T;T	0.22945	2.27;2.27;2.27;1.93	4.59	0.23	0.15372	.	2.260350	0.01803	N	0.033010	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;B;B	0.44344	0.833;0.074;0.074	B;B;B	0.31191	0.125;0.003;0.004	T	0.27806	-1.0063	9	0.46703	T	0.11	-1.0119	1.0514	0.01581	0.177:0.308:0.2758:0.2392	rs2888805;rs4135140;rs52799886;rs59502858	163;367;367	B4DI29;B2R848;Q13569	.;.;TDG_HUMAN	M	367;363;224;163	ENSP00000376611:V367M;ENSP00000266775:V363M;ENSP00000445899:V224M;ENSP00000439054:V163M	ENSP00000266775:V363M	V	+	1	0	TDG	102904864	0.026000	0.19158	0.001000	0.08648	0.002000	0.02628	0.257000	0.18369	0.022000	0.15160	-0.152000	0.13540	GTG	G|0.908;A|0.092	0.092	strong		0.408	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
ARSD	414	hgsc.bcm.edu	37	X	2833643	2833643	+	Missense_Mutation	SNP	C	C	A	rs115332247		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2833643C>A	ENST00000381154.1	-	6	1029	c.954G>T	c.(952-954)caG>caT	p.Q318H	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	318					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ATAAGCCATGCTGACTTTTCC	0.498																																					p.Q318H		Atlas-SNP	.											.	ARSD	47	.	0			c.G954T						PASS	.						229.0	155.0	180.0					X																	2833643		2203	4300	6503	SO:0001583	missense	414	exon6			GCCATGCTGACTT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.954G>T	X.37:g.2833643C>A	ENSP00000370546:p.Gln318His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	88	22	0.25	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	C	8.150	0.787191	0.16189	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.93659	-3.26	3.68	-6.79	0.01715	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	1.058950	0.07543	N	0.914110	D	0.86351	0.5912	L	0.44542	1.39	0.80722	P	0.0	B;B	0.12013	0.005;0.002	B;B	0.17979	0.02;0.004	T	0.72261	-0.4345	9	0.54805	T	0.06	.	2.4437	0.04500	0.2117:0.2407:0.4073:0.1403	.	318;318	E9PAW5;P51689	.;ARSD_HUMAN	H	318	ENSP00000370546:Q318H	ENSP00000217890:Q318H	Q	-	3	2	ARSD	2843643	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.691000	0.00830	-1.408000	0.02040	-0.363000	0.07495	CAG	.	.	strong		0.498	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
TMEM86A	144110	hgsc.bcm.edu	37	11	18728650	18728650	+	IGR	SNP	T	T	C	rs2289965	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18728650T>C	ENST00000280734.2	+	0	3595				IGSF22_ENST00000513874.1_Missense_Mutation_p.I1131V|IGSF22_ENST00000510673.1_5'Flank|RP11-1081L13.4_ENST00000527285.1_RNA	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A							integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						TTCATGATGATGTAGTGAGCC	0.582													C|||	947	0.189097	0.0166	0.3429	5008	,	,		20413	0.1339		0.3976	False		,,,				2504	0.1554				p.I1131V		Atlas-SNP	.											.	IGSF22	211	.	0			c.A3391G						PASS	.	C	VAL/ILE	104,1280		8,88,596	176.0	140.0	151.0		3391	2.5	0.3	11	dbSNP_100	151	1267,1915		245,777,569	yes	missense	IGSF22	NM_173588.3	29	253,865,1165	CC,CT,TT		39.8177,7.5145,30.0263	benign	1131/1327	18728650	1371,3195	692	1591	2283	SO:0001628	intergenic_variant	283284	exon21			TGATGATGTAGTG	BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4			11.37:g.18728650T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_173588	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	511	0.23397435897435898	13	0.026422764227642278	133	0.3674033149171271	68	0.11888111888111888	297	0.391820580474934	C	8.429	0.848099	0.17034	0.075145	0.398177	ENSG00000179057	ENST00000513874	T	0.56444	0.46	3.57	2.53	0.30540	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	8	0.08179	T	0.78	.	4.9575	0.14050	0.0:0.612:0.1654:0.2226	rs2289965;rs17400035;rs52807214;rs60072054;rs2289965	1131	D6RGV7	.	V	1131	ENSP00000421191:I1131V	ENSP00000421191:I1131V	I	-	1	0	IGSF22	18685226	0.000000	0.05858	0.252000	0.24328	0.490000	0.33462	-0.206000	0.09398	0.218000	0.20820	-0.213000	0.12676	ATC	T|0.800;C|0.200	0.200	strong		0.582	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
BTN2A1	11120	hgsc.bcm.edu	37	6	26468545	26468545	+	Missense_Mutation	SNP	G	G	C	rs3734543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26468545G>C	ENST00000312541.5	+	8	1600	c.1352G>C	c.(1351-1353)gGc>gCc	p.G451A	BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000541522.1_Missense_Mutation_p.G390A|BTN2A1_ENST00000429381.1_3'UTR	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	451	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		G -> A (in dbSNP:rs3734543).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						TGCCGGGTGGGCGTCTTCCTG	0.542													G|||	190	0.0379393	0.0333	0.0346	5008	,	,		20708	0.0099		0.0825	False		,,,				2504	0.0297				p.G451A		Atlas-SNP	.											BTN2A1_ENST00000265424,NS,carcinoma,-1,2	BTN2A1	118	2	0			c.G1352C						PASS	.	G	ALA/GLY,,ALA/GLY,	189,4217	119.2+/-156.9	4,181,2018	128.0	114.0	119.0		1169,,1352,	0.7	0.1	6	dbSNP_107	119	795,7805	185.7+/-233.4	39,717,3544	no	missense,intron,missense,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	60,,60,	43,898,5562	CC,CG,GG		9.2442,4.2896,7.5657	possibly-damaging,,possibly-damaging,	390/467,,451/528,	26468545	984,12022	2203	4300	6503	SO:0001583	missense	11120	exon8			GGGTGGGCGTCTT	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1352G>C	6.37:g.26468545G>C	ENSP00000312158:p.Gly451Ala	Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	508	238	0.468504	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	100	0.045787545787545784	16	0.032520325203252036	11	0.03038674033149171	8	0.013986013986013986	65	0.08575197889182058	G	11.33	1.605979	0.28623	0.042896	0.092442	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000265424	D;D	0.82711	-1.64;-1.64	2.6	0.669	0.17918	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.558553	0.16195	N	0.225196	T	0.74854	0.3771	M	0.85859	2.78	0.80722	P	0.0	P;B	0.39903	0.694;0.189	B;B	0.42361	0.385;0.132	T	0.68534	-0.5383	9	0.56958	D	0.05	.	5.8105	0.18463	0.1453:0.582:0.2726:0.0	rs3734543	390;451	B4DLP9;Q7KYR7	.;BT2A1_HUMAN	A	451;390;437	ENSP00000312158:G451A;ENSP00000443909:G390A	ENSP00000265424:G437A	G	+	2	0	BTN2A1	26576524	0.872000	0.30054	0.075000	0.20258	0.335000	0.28730	3.331000	0.52075	0.127000	0.18452	0.491000	0.48974	GGC	.	.	weak		0.542	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
PRDM7	11105	hgsc.bcm.edu	37	16	90130136	90130136	+	Missense_Mutation	SNP	C	C	T	rs2078478	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:90130136C>T	ENST00000449207.2	-	5	411	c.392G>A	c.(391-393)aGa>aAa	p.R131K	PRDM7_ENST00000407825.1_5'UTR|PRDM7_ENST00000325921.6_5'Flank	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	131			R -> K (in dbSNP:rs2078478).		regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)			lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		TGACAATTCTCTCAAACTAGA	0.418													.|||	1440	0.28754	0.1195	0.2781	5008	,	,		20389	0.7798		0.1571	False		,,,				2504	0.1483				p.R131K		Atlas-SNP	.											.	PRDM7	53	.	0			c.G392A						PASS	.	T	LYS/ARG	460,3272		27,406,1433	93.0	87.0	89.0		392	1.6	0.1	16	dbSNP_96	89	1186,7026		80,1026,3000	yes	missense	PRDM7	NM_001098173.1	26	107,1432,4433	TT,TC,CC		14.4423,12.3258,13.781	benign	131/493	90130136	1646,10298	1866	4106	5972	SO:0001583	missense	11105	exon5			AATTCTCTCAAAC	AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"""Zinc fingers, C2H2-type"", ""-"""	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.392G>A	16.37:g.90130136C>T	ENSP00000396732:p.Arg131Lys	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	276	145	0.525362	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	37	CCDS45557.1	731	0.3347069597069597	76	0.15447154471544716	78	0.2154696132596685	445	0.777972027972028	132	0.1741424802110818	.	0.016	-1.514500	0.00975	0.123258	0.144423	ENSG00000126856	ENST00000449207	T	0.09350	2.99	1.6	1.6	0.23607	.	.	.	.	.	T	0.00012	0.0000	N	0.00186	-1.895	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.13072	-1.0523	7	.	.	.	-7.7225	3.5217	0.07744	0.0:0.2185:0.0:0.7815	rs2078478;rs17784778;rs58861284;rs2078478	131	Q9NQW5	PRDM7_HUMAN	K	131	ENSP00000396732:R131K	.	R	-	2	0	PRDM7	88657637	0.021000	0.18746	0.057000	0.19452	0.003000	0.03518	0.341000	0.19909	0.113000	0.18004	-0.490000	0.04691	AGA	C|0.693;T|0.307	0.307	strong		0.418	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1		
UGT1A9	54600	hgsc.bcm.edu	37	2	234580967	234580967	+	Silent	SNP	A	A	G	rs28946876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234580967A>G	ENST00000354728.4	+	1	469	c.387A>G	c.(385-387)aaA>aaG	p.K129K	UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Silent_p.K129K			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	129					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)			breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	GTTTGTTTAAAGACAAAAAAT	0.313																																					p.K129K		Atlas-SNP	.											UGT1A9,colon,carcinoma,0,1	UGT1A9	79	1	0			c.A387G						scavenged	.						99.0	101.0	101.0					2																	234580967		2203	4300	6503	SO:0001819	synonymous_variant	54600	exon1			GTTTAAAGACAAA	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"""UDP glucuronosyltransferases"""	12541	other	complex locus constituent		606434	"""UDP glycosyltransferase 1 family, polypeptide A9"""			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.387A>G	2.37:g.234580967A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	4	0.0336134	NM_021027	B8K285|P36509|Q9HAX0	Silent	SNP	ENST00000354728.4	37	CCDS2505.1																																																																																			.	.	alt		0.313	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027	
ME3	10873	hgsc.bcm.edu	37	11	86153911	86153911	+	Silent	SNP	G	G	A	rs7548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:86153911G>A	ENST00000393324.3	-	13	1858	c.1605C>T	c.(1603-1605)taC>taT	p.Y535Y	ME3_ENST00000359636.2_Silent_p.Y535Y|RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000543262.1_Silent_p.Y535Y	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	535					aerobic respiration (GO:0009060)|malate metabolic process (GO:0006108)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|pyruvate metabolic process (GO:0006090)	mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)	p.Y535Y(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|skin(3)|stomach(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)				TGAGTGGTGGGTAGAGTCTCC	0.527													G|||	1073	0.214257	0.1384	0.2594	5008	,	,		20219	0.0893		0.341	False		,,,				2504	0.2832				p.Y535Y		Atlas-SNP	.											ME3,NS,carcinoma,0,1	ME3	70	1	1	Substitution - coding silent(1)	stomach(1)	c.C1605T						PASS	.	G	,,	770,3634	314.4+/-293.6	69,632,1501	150.0	131.0	137.0		1605,1605,1605	4.7	1.0	11	dbSNP_52	137	2934,5664	457.3+/-364.3	492,1950,1857	no	coding-synonymous,coding-synonymous,coding-synonymous	ME3	NM_001014811.1,NM_001161586.1,NM_006680.2	,,	561,2582,3358	AA,AG,GG		34.1242,17.4841,28.4879	,,	535/605,535/605,535/605	86153911	3704,9298	2202	4299	6501	SO:0001819	synonymous_variant	10873	exon14			TGGTGGGTAGAGT	X79440	CCDS8277.1	11q14.2	2012-09-20			ENSG00000151376	ENSG00000151376	1.1.1.40		6985	protein-coding gene	gene with protein product		604626				7818469	Standard	NM_001161586		Approved		uc001pbz.3	Q16798	OTTHUMG00000167217	ENST00000393324.3:c.1605C>T	11.37:g.86153911G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_006680	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																			G|0.594;T|0.036	.	strong		0.527	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
OSTN	344901	hgsc.bcm.edu	37	3	190936577	190936577	+	Silent	SNP	A	A	G	rs34687554	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:190936577A>G	ENST00000339051.1	+	2	144	c.144A>G	c.(142-144)acA>acG	p.T48T	OSTN-AS1_ENST00000430375.1_RNA|OSTN_ENST00000445281.1_Silent_p.T48T	NM_198184.1	NP_937827.1	P61366	OSTN_HUMAN	osteocrin	48					cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|endochondral bone growth (GO:0003416)|negative regulation of glucose import (GO:0046325)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of cGMP biosynthetic process (GO:0030828)	extracellular space (GO:0005615)				kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|skin(2)	13	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)		CAACACCCACAGTCAGGGAAG	0.418													A|||	32	0.00638978	0.0	0.0072	5008	,	,		18556	0.0		0.0149	False		,,,				2504	0.0123				p.T48T		Atlas-SNP	.											.	OSTN	25	.	0			c.A144G						PASS	.	A		10,4396	16.8+/-37.8	0,10,2193	140.0	127.0	132.0		144	5.5	0.9	3	dbSNP_126	132	96,8504	54.0+/-114.7	2,92,4206	no	coding-synonymous	OSTN	NM_198184.1		2,102,6399	GG,GA,AA		1.1163,0.227,0.815		48/134	190936577	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	344901	exon2			ACCCACAGTCAGG	AY398681	CCDS3299.1	3q29	2004-01-22			ENSG00000188729	ENSG00000188729			29961	protein-coding gene	gene with protein product		610280				14523025	Standard	NM_198184		Approved		uc011bsn.2	P61366	OTTHUMG00000156190	ENST00000339051.1:c.144A>G	3.37:g.190936577A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_198184	A1A4U3	Silent	SNP	ENST00000339051.1	37	CCDS3299.1																																																																																			A|0.992;G|0.008	0.008	strong		0.418	OSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343350.1	NM_198184	
NPBWR2	2832	hgsc.bcm.edu	37	20	62737568	62737568	+	Missense_Mutation	SNP	T	T	C	rs4809401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62737568T>C	ENST00000369768.1	-	1	956	c.617A>G	c.(616-618)cAg>cGg	p.Q206R		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	206			Q -> R (in dbSNP:rs4809401). {ECO:0000269|PubMed:7590751, ECO:0000269|Ref.7}.		G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					GAACCAGACCTGCTCGGGCCA	0.627													C|||	444	0.0886581	0.0227	0.0937	5008	,	,		20409	0.0863		0.1431	False		,,,				2504	0.1207				p.Q206R		Atlas-SNP	.											NPBWR2,NS,carcinoma,0,1	NPBWR2	36	1	0			c.A617G						PASS	.	C	ARG/GLN	169,4231	791.1+/-415.1	3,163,2034	50.0	44.0	46.0		617	0.7	0.0	20	dbSNP_111	46	1047,7537	759.0+/-407.5	60,927,3305	yes	missense	NPBWR2	NM_005286.2	43	63,1090,5339	CC,CT,TT		12.1971,3.8409,9.3654	benign	206/334	62737568	1216,11768	2200	4292	6492	SO:0001583	missense	2832	exon1			CAGACCTGCTCGG	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4530	protein-coding gene	gene with protein product		600731	"""G protein-coupled receptor 8"""	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.617A>G	20.37:g.62737568T>C	ENSP00000358783:p.Gln206Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_005286	Q6NWQ6|Q9H4K3	Missense_Mutation	SNP	ENST00000369768.1	37	CCDS13557.1	203	0.09294871794871795	17	0.034552845528455285	36	0.09944751381215469	45	0.07867132867132867	105	0.13852242744063326	C	0.815	-0.750803	0.03041	0.038409	0.121971	ENSG00000125522	ENST00000369768	T	0.36520	1.25	3.9	0.669	0.17918	GPCR, rhodopsin-like superfamily (1);	0.299706	0.29417	N	0.012216	T	0.00109	0.0003	N	0.02802	-0.49	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.33007	-0.9885	9	0.09843	T	0.71	.	8.2073	0.31463	0.0:0.5476:0.0:0.4524	rs4809401;rs59506105;rs4809401	206	P48146	NPBW2_HUMAN	R	206	ENSP00000358783:Q206R	ENSP00000358783:Q206R	Q	-	2	0	NPBWR2	62208012	0.000000	0.05858	0.024000	0.17045	0.026000	0.11368	-0.290000	0.08354	-0.505000	0.06568	-1.668000	0.00747	CAG	T|0.908;C|0.092	0.092	strong		0.627	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286	
UGT2B15	7366	hgsc.bcm.edu	37	4	69536084	69536084	+	Missense_Mutation	SNP	A	A	C	rs1902023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69536084A>C	ENST00000338206.5	-	1	262	c.253T>G	c.(253-255)Tat>Gat	p.Y85D		NM_001076.3	NP_001067.2	P54855	UDB15_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B15	85			Y -> D (in dbSNP:rs1902023). {ECO:0000269|PubMed:7835232, ECO:0000269|PubMed:8399210}.		cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)									Acetaminophen(DB00316)|Dabigatran etexilate(DB06695)|Ezetimibe(DB00973)|Lorazepam(DB00186)|Morphine(DB00295)|Oxazepam(DB00842)|Valproic Acid(DB00313)	TCTTCCAAATAATTTTTAGTT	0.308													c|||	2737	0.546526	0.6021	0.6052	5008	,	,		19778	0.5774		0.4871	False		,,,				2504	0.4591				p.Y85D		Atlas-SNP	.											.	UGT2B15	48	.	0			c.T253G	GRCh37	CM004865	UGT2B15	M	rs1902023	PASS	.	C	ASP/TYR	2534,1866		729,1076,395	76.0	90.0	86.0	http://www.ncbi.nlm.nih.gov/omim/600069,601903,606497|http://omim.org/entry/606497|http://omim.org/entry/601903|http://omim.org/entry/600069	253	2.6	0.0	4	dbSNP_92	86	3995,4599		937,2121,1239	no	missense	UGT2B15	NM_001076.2	160	1666,3197,1634	CC,CA,AA		46.4859,42.4091,49.7537	benign	85/531	69536084	6529,6465	2200	4297	6497	SO:0001583	missense	7366	exon1			CCAAATAATTTTT	AF180322	CCDS3524.1	4q13	2008-02-05	2005-07-20		ENSG00000196620	ENSG00000196620		"""UDP glucuronosyltransferases"""	12546	protein-coding gene	gene with protein product		600069	"""UDP glycosyltransferase 2 family, polypeptide B15"""			7835904	Standard	NM_001076		Approved	UGT2B8	uc021xow.1	P54855	OTTHUMG00000161507	ENST00000338206.5:c.253T>G	4.37:g.69536084A>C	ENSP00000341045:p.Tyr85Asp	Somatic	683	1	0.00146413		WXS	Illumina HiSeq	Phase_I	819	817	0.997558	NM_001076	A6NDX0|A6NNJ4|A8K054|P23765|Q9UK63	Missense_Mutation	SNP	ENST00000338206.5	37	CCDS3524.1	1230	0.5631868131868132	315	0.6402439024390244	221	0.6104972375690608	331	0.5786713286713286	363	0.4788918205804749	N	0.004	-2.341011	0.00222	0.575909	0.464859	ENSG00000196620	ENST00000338206	T	0.55588	0.51	2.58	2.58	0.30949	.	1.156670	0.06579	N	0.750000	T	0.00012	0.0000	N	0.00815	-1.16	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43734	-0.9373	9	0.11794	T	0.64	.	3.3319	0.07087	0.259:0.5958:0.0:0.1453	.	85	P54855	UDB15_HUMAN	D	85	ENSP00000341045:Y85D	ENSP00000341045:Y85D	Y	-	1	0	UGT2B15	69218679	0.000000	0.05858	0.005000	0.12908	0.073000	0.16967	-1.341000	0.02647	0.401000	0.25424	-0.407000	0.06327	TAT	A|0.468;C|0.532	0.532	strong		0.308	UGT2B15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365172.1	NM_001076	
KIF26B	55083	hgsc.bcm.edu	37	1	245772692	245772692	+	Silent	SNP	A	A	C	rs61755865	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:245772692A>C	ENST00000407071.2	+	8	2216	c.1776A>C	c.(1774-1776)tcA>tcC	p.S592S	KIF26B_ENST00000366518.4_Silent_p.S211S	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	592	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CCCGTTTCTCAGTCCGGGTTT	0.612													A|||	142	0.0283546	0.0318	0.0648	5008	,	,		16776	0.0278		0.0149	False		,,,				2504	0.0123				p.S592S		Atlas-SNP	.											.	KIF26B	343	.	0			c.A1776C						PASS	.	A		107,3701		1,105,1798	26.0	29.0	28.0		1776	-10.4	0.9	1	dbSNP_129	28	150,8090		2,146,3972	no	coding-synonymous	KIF26B	NM_018012.3		3,251,5770	CC,CA,AA		1.8204,2.8099,2.1331		592/2109	245772692	257,11791	1904	4120	6024	SO:0001819	synonymous_variant	55083	exon8			TTTCTCAGTCCGG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1776A>C	1.37:g.245772692A>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	228	102	0.447368	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			A|0.970;C|0.030	0.030	strong		0.612	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
ITPR3	3710	hgsc.bcm.edu	37	6	33660597	33660597	+	Silent	SNP	C	C	T	rs2229643	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33660597C>T	ENST00000374316.5	+	56	8611	c.7551C>T	c.(7549-7551)atC>atT	p.I2517I	ITPR3_ENST00000605930.1_Silent_p.I2517I			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2517					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GGGTAATCATCGACACCTTCG	0.517													C|||	281	0.0561102	0.115	0.0375	5008	,	,		22917	0.0417		0.0149	False		,,,				2504	0.047				p.I2517I		Atlas-SNP	.											.	ITPR3	409	.	0			c.C7551T						PASS	.	C		537,3869	243.4+/-253.1	39,459,1705	192.0	152.0	166.0		7551	-6.5	0.8	6	dbSNP_98	166	186,8414	83.7+/-146.2	5,176,4119	no	coding-synonymous	ITPR3	NM_002224.3		44,635,5824	TT,TC,CC		2.1628,12.1879,5.559		2517/2672	33660597	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon55			AATCATCGACACC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.7551C>T	6.37:g.33660597C>T		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	373	193	0.517426	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			A|0.000;C|0.953;T|0.047	0.047	strong		0.517	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
PTPRJ	5795	hgsc.bcm.edu	37	11	48145397	48145397	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:48145397C>A	ENST00000418331.2	+	5	1201	c.849C>A	c.(847-849)gaC>gaA	p.D283E	PTPRJ_ENST00000440289.2_Missense_Mutation_p.D283E	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	283	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CAAAGGGAGACCCCTTGGGCA	0.433																																					p.D283E		Atlas-SNP	.											.	PTPRJ	225	.	0			c.C849A						PASS	.						67.0	64.0	65.0					11																	48145397		2201	4298	6499	SO:0001583	missense	5795	exon5			GGGAGACCCCTTG	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.849C>A	11.37:g.48145397C>A	ENSP00000400010:p.Asp283Glu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	131	53	0.40458	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	C	9.966	1.224237	0.22457	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.35236	2.65;1.32	4.27	-1.19	0.09585	Fibronectin, type III (2);	.	.	.	.	T	0.14098	0.0341	N	0.17082	0.46	0.09310	N	1	B;P	0.36874	0.004;0.572	B;B	0.33454	0.003;0.164	T	0.16541	-1.0399	9	0.10902	T	0.67	.	1.6576	0.02785	0.1508:0.3485:0.3127:0.188	.	283;283	Q12913;Q6P4H4	PTPRJ_HUMAN;.	E	283	ENSP00000400010:D283E;ENSP00000409733:D283E	ENSP00000278456:D283E	D	+	3	2	PTPRJ	48101973	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.779000	0.04659	-0.334000	0.08463	0.557000	0.71058	GAC	.	.	none		0.433	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
HS3ST1	9957	hgsc.bcm.edu	37	4	11401012	11401012	+	Silent	SNP	A	A	G	rs1047385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:11401012A>G	ENST00000002596.5	-	2	1792	c.618T>C	c.(616-618)ttT>ttC	p.F206F		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	206					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						GCAGCGGGAAAAAGCGCAGCC	0.602													G|||	1251	0.2498	0.3192	0.1945	5008	,	,		17747	0.1796		0.1978	False		,,,				2504	0.3211				p.F206F		Atlas-SNP	.											.	HS3ST1	41	.	0			c.T618C						PASS	.	G		1288,3118	699.4+/-406.5	196,896,1111	48.0	46.0	47.0		618	3.5	1.0	4	dbSNP_86	47	1817,6783	730.2+/-406.8	188,1441,2671	no	coding-synonymous	HS3ST1	NM_005114.2		384,2337,3782	GG,GA,AA		21.1279,29.2329,23.8736		206/308	11401012	3105,9901	2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			CGGGAAAAAGCGC	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.618T>C	4.37:g.11401012A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	37	CCDS3408.1																																																																																			G|0.240;N|0.000	0.240	strong		0.602	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114	
LVRN	206338	hgsc.bcm.edu	37	5	115298977	115298977	+	Silent	SNP	C	C	T	rs1445708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:115298977C>T	ENST00000357872.4	+	1	787	c.663C>T	c.(661-663)ttC>ttT	p.F221F	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		221						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AGGGACTCTTCCTCAACGTCT	0.667													C|||	1949	0.389177	0.2708	0.4265	5008	,	,		12229	0.4246		0.3917	False		,,,				2504	0.4836				p.F221F		Atlas-SNP	.											FLJ90650,NS,carcinoma,0,1	.	.	1	0			c.C663T						PASS	.	C		1134,3256		174,786,1235	18.0	21.0	20.0		663	3.7	1.0	5	dbSNP_88	20	3333,5213		723,1887,1663	no	coding-synonymous	AQPEP	NM_173800.4		897,2673,2898	TT,TC,CC		39.0007,25.8314,34.5315		221/991	115298977	4467,8469	2195	4273	6468	SO:0001819	synonymous_variant	0	exon1			ACTCTTCCTCAAC																												ENST00000357872.4:c.663C>T	5.37:g.115298977C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			C|0.644;T|0.356	0.356	strong		0.667	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
PCDHA1	56147	hgsc.bcm.edu	37	5	140168070	140168070	+	Missense_Mutation	SNP	A	A	G	rs2240696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140168070A>G	ENST00000504120.2	+	1	2195	c.2195A>G	c.(2194-2196)tAt>tGt	p.Y732C	PCDHA1_ENST00000378133.3_Missense_Mutation_p.Y732C|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	732			Y -> C (in dbSNP:rs2240696).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGGGTGCGTATGTGCCGGGC	0.662													.|||	2631	0.525359	0.4796	0.5879	5008	,	,		16765	0.5317		0.5368	False		,,,				2504	0.5245				p.Y732C		Atlas-SNP	.											PCDHA1_ENST00000504120,colon,carcinoma,0,2	PCDHA1	387	2	0			c.A2195G						PASS	.	G	CYS/TYR,CYS/TYR,	2186,2220		528,1130,545	51.0	45.0	47.0		2195,2195,	2.2	0.0	5	dbSNP_98	47	4539,4061		1192,2155,953	no	missense,missense,intron	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	194,194,	1720,3285,1498	GG,GA,AA		47.2209,49.6142,48.2931	,,	732/951,732/808,	140168070	6725,6281	2203	4300	6503	SO:0001583	missense	56147	exon1			GTGCGTATGTGCC	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.2195A>G	5.37:g.140168070A>G	ENSP00000420840:p.Tyr732Cys	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	254	84	0.330709	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	1158	0.5302197802197802	251	0.5101626016260162	192	0.5303867403314917	311	0.5437062937062938	404	0.5329815303430079	N	0	-2.739289	0.00088	0.496142	0.527791	ENSG00000204970	ENST00000504120;ENST00000378133	T;T	0.08984	3.03;3.03	4.16	2.24	0.28232	.	0.365789	0.19576	N	0.110983	T	0.00012	0.0000	N	0.00025	-2.685	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.34477	-0.9827	9	0.07325	T	0.83	.	3.7944	0.08733	0.2812:0.0:0.5369:0.182	rs2240696;rs17208229;rs17844241;rs52830508;rs2240696	732;732	Q9Y5I3;Q9Y5I3-3	PCDA1_HUMAN;.	C	732	ENSP00000420840:Y732C;ENSP00000367373:Y732C	ENSP00000367373:Y732C	Y	+	2	0	PCDHA1	140148254	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.396000	0.20867	0.322000	0.23283	-0.133000	0.14855	TAT	A|0.482;G|0.518	0.518	strong		0.662	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
LAMTOR2	28956	hgsc.bcm.edu	37	1	156025096	156025096	+	Silent	SNP	C	C	T	rs7541	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156025096C>T	ENST00000368305.4	+	2	249	c.111C>T	c.(109-111)taC>taT	p.Y37Y	UBQLN4_ENST00000368309.3_5'Flank|LAMTOR2_ENST00000368302.3_Silent_p.Y37Y|UBQLN4_ENST00000472638.1_5'Flank|LAMTOR2_ENST00000368304.5_Silent_p.Y37Y|LAMTOR2_ENST00000489664.1_3'UTR	NM_014017.3	NP_054736.1	Q9Y2Q5	LTOR2_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2	37					activation of MAPKK activity (GO:0000186)|cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|Ragulator complex (GO:0071986)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7						ACTCTGGTTACGGGGACACTG	0.582													C|||	359	0.0716853	0.0333	0.1297	5008	,	,		16935	0.001		0.1581	False		,,,				2504	0.0665				p.Y37Y		Atlas-SNP	.											.	LAMTOR2	13	.	0			c.C111T						PASS	.	C	,	252,4154	146.1+/-180.8	6,240,1957	99.0	104.0	102.0		111,111	-4.7	0.9	1	dbSNP_52	102	1400,7200	270.9+/-289.3	128,1144,3028	no	coding-synonymous,coding-synonymous	LAMTOR2	NM_001145264.1,NM_014017.3	,	134,1384,4985	TT,TC,CC		16.2791,5.7195,12.7018	,	37/96,37/126	156025096	1652,11354	2203	4300	6503	SO:0001819	synonymous_variant	28956	exon2			TGGTTACGGGGAC	BC024190	CCDS1128.1, CCDS44243.1	1q22	2014-09-17	2011-02-15	2011-02-15	ENSG00000116586	ENSG00000116586			29796	protein-coding gene	gene with protein product	"""mitogen activated protein binding protein interacting protein"", ""MAPKSP1 adaptor protein"", ""endosomal adaptor protein"""	610389	"""roadblock domain containing 3"""	ROBLD3		11042152	Standard	NM_014017		Approved	MAPBPIP, MAPKSP1AP, p14, ENDAP, Ragulator2	uc001fnb.3	Q9Y2Q5	OTTHUMG00000017462	ENST00000368305.4:c.111C>T	1.37:g.156025096C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	NM_001145264	Q5VY97|Q5VY98|Q5VY99	Silent	SNP	ENST00000368305.4	37	CCDS1128.1																																																																																			C|0.895;T|0.105	0.105	strong		0.582	LAMTOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046197.1	NM_014017	
RGPD3	653489	hgsc.bcm.edu	37	2	107040564	107040564	+	Missense_Mutation	SNP	C	C	T	rs55993306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:107040564C>T	ENST00000409886.3	-	20	3946	c.3859G>A	c.(3859-3861)Gag>Aag	p.E1287K	RGPD3_ENST00000304514.7_Missense_Mutation_p.E1287K	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1287					protein targeting to Golgi (GO:0000042)			p.E1287K(2)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GTTGTTGACTCATCAAAGTGG	0.408													.|||	714	0.142572	0.1021	0.1095	5008	,	,		15360	0.0724		0.2227	False		,,,				2504	0.2106				p.E1287K		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	2	Substitution - Missense(2)	kidney(2)	c.G3859A						PASS	.	C	LYS/GLU	162,1158		31,100,529	162.0	121.0	134.0		3859	2.3	1.0	2	dbSNP_129	134	736,2294		196,344,975	no	missense	RGPD3	NM_001144013.1	56	227,444,1504	TT,TC,CC		24.2904,12.2727,20.6437	possibly-damaging	1287/1759	107040564	898,3452	660	1515	2175	SO:0001583	missense	653489	exon20			TTGACTCATCAAA		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.3859G>A	2.37:g.107040564C>T	ENSP00000386588:p.Glu1287Lys	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	714	611	0.855742	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	326	0.14926739926739926	69	0.1402439024390244	41	0.1132596685082873	37	0.06468531468531469	179	0.23614775725593667	.	9.178	1.022948	0.19433	0.122727	0.242904	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.40756	1.03;1.02	2.35	2.35	0.29111	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.30981	P	0.722513	D	0.54772	0.968	P	0.50405	0.64	T	0.03433	-1.1037	8	0.06236	T	0.91	-28.1101	10.4115	0.44296	0.0:1.0:0.0:0.0	rs55993306	1287	A6NKT7	RGPD3_HUMAN	K	1287	ENSP00000386588:E1287K;ENSP00000303659:E1287K	ENSP00000303659:E1287K	E	-	1	0	RGPD3	106406996	1.000000	0.71417	0.997000	0.53966	0.035000	0.12851	7.578000	0.82498	1.314000	0.45095	0.186000	0.17326	GAG	C|0.847;T|0.153	0.153	strong		0.408	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
PEAK1	79834	hgsc.bcm.edu	37	15	77450964	77450964	+	Missense_Mutation	SNP	C	C	T	rs12909704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:77450964C>T	ENST00000560626.2	-	5	3687	c.3212G>A	c.(3211-3213)aGg>aAg	p.R1071K	PEAK1_ENST00000312493.4_Missense_Mutation_p.R1071K			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1071			R -> K (in dbSNP:rs12909704). {ECO:0000269|PubMed:17344846}.		cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AGTGCAGCCCCTGCCATCTTG	0.468													C|||	992	0.198083	0.0794	0.2622	5008	,	,		21273	0.1121		0.3787	False		,,,				2504	0.2157				p.R1071K		Atlas-SNP	.											.	.	.	.	0			c.G3212A						PASS	.	C	LYS/ARG	415,3481		19,377,1552	130.0	123.0	125.0		3212	2.5	0.0	15	dbSNP_121	125	3003,5269		560,1883,1693	yes	missense	PEAK1	NM_024776.3	26	579,2260,3245	TT,TC,CC		36.3032,10.652,28.0901	benign	1071/1747	77450964	3418,8750	1948	4136	6084	SO:0001583	missense	0	exon6			CAGCCCCTGCCAT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3212G>A	15.37:g.77450964C>T	ENSP00000452796:p.Arg1071Lys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	198	101	0.510101	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	499	0.22847985347985347	48	0.0975609756097561	100	0.27624309392265195	72	0.1258741258741259	279	0.36807387862796836	C	10.46	1.356279	0.24598	0.10652	0.363032	ENSG00000173517	ENST00000312493	T	0.67345	-0.26	4.5	2.54	0.30619	.	0.991955	0.08183	N	0.985190	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.25847	-1.0120	9	0.36615	T	0.2	1.4574	8.0609	0.30633	0.0:0.7527:0.1604:0.0868	rs12909704;rs52835769;rs61009837;rs12909704	1071	Q9H792	PEAK1_HUMAN	K	1071	ENSP00000309230:R1071K	ENSP00000309230:R1071K	R	-	2	0	AC087465.1	75238019	0.005000	0.15991	0.004000	0.12327	0.294000	0.27393	1.412000	0.34714	0.978000	0.38470	0.563000	0.77884	AGG	C|0.760;T|0.240	0.240	strong		0.468	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
LPCAT1	79888	hgsc.bcm.edu	37	5	1494935	1494935	+	Missense_Mutation	SNP	T	T	C	rs28715640	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:1494935T>C	ENST00000283415.3	-	3	505	c.373A>G	c.(373-375)Acc>Gcc	p.T125A		NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	125					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		GCCGCCTCGGTGGGCAGCGCC	0.647													T|||	98	0.0195687	0.003	0.0159	5008	,	,		14699	0.001		0.0746	False		,,,				2504	0.0072				p.T125A		Atlas-SNP	.											.	LPCAT1	70	.	0			c.A373G						PASS	.	T	ALA/THR	73,4333	61.7+/-98.7	5,63,2135	43.0	42.0	42.0		373	-0.6	0.3	5	dbSNP_125	42	692,7908	165.5+/-217.6	26,640,3634	yes	missense	LPCAT1	NM_024830.3	58	31,703,5769	CC,CT,TT		8.0465,1.6568,5.8819	benign	125/535	1494935	765,12241	2203	4300	6503	SO:0001583	missense	79888	exon3			CCTCGGTGGGCAG	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"""EF-hand domain containing"""	25718	protein-coding gene	gene with protein product		610472	"""acyltransferase like 2"""	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.373A>G	5.37:g.1494935T>C	ENSP00000283415:p.Thr125Ala	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Missense_Mutation	SNP	ENST00000283415.3	37	CCDS3864.1	68	0.031135531135531136	2	0.0040650406504065045	7	0.019337016574585635	1	0.0017482517482517483	58	0.07651715039577836	T	1.238	-0.622201	0.03636	0.016568	0.080465	ENSG00000153395	ENST00000283415	D	0.92805	-3.11	4.98	-0.643	0.11482	Phospholipid/glycerol acyltransferase (1);	0.525534	0.21815	N	0.068714	T	0.11580	0.0282	N	0.02011	-0.69	0.27461	N	0.953166	B	0.02656	0.0	B	0.04013	0.001	T	0.51888	-0.8648	10	0.07325	T	0.83	-5.7754	1.7637	0.02998	0.1299:0.3057:0.1337:0.4307	rs28715640	125	Q8NF37	PCAT1_HUMAN	A	125	ENSP00000283415:T125A	ENSP00000283415:T125A	T	-	1	0	LPCAT1	1547935	0.000000	0.05858	0.291000	0.24904	0.498000	0.33706	-1.220000	0.02971	-0.378000	0.07918	-1.114000	0.02060	ACC	T|0.954;C|0.046	0.046	strong		0.647	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	
LY75	4065	hgsc.bcm.edu	37	2	160729005	160729005	+	Missense_Mutation	SNP	C	C	T	rs1397706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160729005C>T	ENST00000263636.4	-	13	2101	c.2074G>A	c.(2074-2076)Gat>Aat	p.D692N	LY75_ENST00000554112.1_Missense_Mutation_p.D692N|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.D692N|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.D692N|LY75_ENST00000553424.1_Missense_Mutation_p.D692N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	692	C-type lectin 4. {ECO:0000255|PROSITE- ProRule:PRU00040}.		D -> N (in dbSNP:rs1397706).		endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		TTTATTTCATCCACATGGCTG	0.388													C|||	491	0.0980431	0.0045	0.0994	5008	,	,		18572	0.2629		0.0775	False		,,,				2504	0.0746				p.D692N		Atlas-SNP	.											.	LY75	151	.	0			c.G2074A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	78,4328	68.7+/-106.4	2,74,2127	123.0	134.0	130.0		2074,2074,2074	-0.8	0.0	2	dbSNP_88	130	671,7929	168.7+/-220.2	24,623,3653	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	23,23,23	26,697,5780	TT,TC,CC		7.8023,1.7703,5.7589	benign,benign,benign	692/1874,692/1818,692/1723	160729005	749,12257	2203	4300	6503	SO:0001583	missense	4065	exon13			TTTCATCCACATG	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.2074G>A	2.37:g.160729005C>T	ENSP00000263636:p.Asp692Asn	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	228	0.1043956043956044	4	0.008130081300813009	26	0.0718232044198895	141	0.2465034965034965	57	0.07519788918205805	C	8.103	0.777188	0.16120	0.017703	0.078023	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15	5.17	-0.818	0.10833	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	2.022460	0.03243	U	0.180745	T	0.00012	0.0000	N	0.17838	0.53	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.12013	0.005;0.003;0.004;0.002	B;B;B;B	0.18561	0.022;0.009;0.015;0.006	T	0.47086	-0.9144	9	0.59425	D	0.04	-2.6917	10.2321	0.43260	0.0:0.5366:0.0:0.4634	rs1397706;rs60798164;rs1397706	310;692;692;692	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	N	692	ENSP00000451511:D692N;ENSP00000451446:D692N;ENSP00000263636:D692N;ENSP00000423463:D692N;ENSP00000421035:D692N	ENSP00000423463:D692N	D	-	1	0	LY75;LY75-CD302	160437251	0.014000	0.17966	0.009000	0.14445	0.169000	0.22640	0.148000	0.16224	-0.374000	0.07967	0.484000	0.47621	GAT	C|0.885;T|0.115	0.115	strong		0.388	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
MUC4	4585	hgsc.bcm.edu	37	3	195505859	195505859	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195505859T>C	ENST00000463781.3	-	2	13051	c.12592A>G	c.(12592-12594)Act>Gct	p.T4198A	MUC4_ENST00000475231.1_Missense_Mutation_p.T4198A|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4198A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGTGTCGGTGACA	0.602																																					p.T4198A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.A12592G						scavenged	.						19.0	15.0	16.0					3																	195505859		689	1576	2265	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12592A>G	3.37:g.195505859T>C	ENSP00000417498:p.Thr4198Ala	Somatic	238	17	0.0714286		WXS	Illumina HiSeq	Phase_I	205	42	0.204878	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	1.310	-0.602470	0.03744	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35789	1.42;1.29	.	.	.	.	.	.	.	.	T	0.15739	0.0379	N	0.14661	0.345	0.18873	N	0.999989	B	0.14438	0.01	B	0.15870	0.014	T	0.21827	-1.0234	7	.	.	.	.	4.4479	0.11606	0.0:0.2715:0.0:0.7285	.	4070	E7ESK3	.	A	4198	ENSP00000417498:T4198A;ENSP00000420243:T4198A	.	T	-	1	0	MUC4	196990638	0.000000	0.05858	0.008000	0.14137	0.030000	0.12068	-0.602000	0.05680	-1.729000	0.01364	-1.976000	0.00459	ACT	.	.	weak		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31085226	31085226	+	Intron	SNP	G	G	A	rs7742033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31085226G>A	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.L56F	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TTCCCAGTGAGGCAGGGGTCG	0.582													G|||	115	0.0229633	0.0598	0.013	5008	,	,		18022	0.003		0.0099	False		,,,				2504	0.0143				p.L56F		Atlas-SNP	.											.	CDSN	48	.	0			c.C166T						PASS	.	G	PHE/LEU,	134,3408		2,130,1639	13.0	10.0	11.0		166,	2.0	0.7	6	dbSNP_116	11	54,6800		0,54,3373	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	22,	2,184,5012	AA,AG,GG		0.7879,3.7832,1.8084	probably-damaging,	56/530,	31085226	188,10208	1771	3427	5198	SO:0001627	intron_variant	1041	exon2			CAGTGAGGCAGGG	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2558G>A	6.37:g.31085226G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	176	107	0.607955	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	31	0.014194139194139194	23	0.046747967479674794	3	0.008287292817679558	2	0.0034965034965034965	3	0.00395778364116095	G	9.818	1.185048	0.21870	0.037832	0.007879	ENSG00000204539	ENST00000376288	T	0.07444	3.19	4.93	1.98	0.26296	.	0.486240	0.16016	N	0.233557	T	0.02649	0.0080	L	0.55990	1.75	0.09310	N	1	B	0.21225	0.053	B	0.21917	0.037	T	0.36407	-0.9749	10	0.44086	T	0.13	-14.2507	3.4184	0.07384	0.2129:0.0:0.5839:0.2031	rs7742033;rs52820068;rs7742033	56	Q15517	CDSN_HUMAN	F	56	ENSP00000365465:L56F	ENSP00000365465:L56F	L	-	1	0	CDSN	31193205	0.039000	0.19947	0.665000	0.29768	0.069000	0.16628	0.060000	0.14342	1.222000	0.43521	0.549000	0.68633	CTC	G|0.979;A|0.021	0.021	strong		0.582	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
ROCK2	9475	hgsc.bcm.edu	37	2	11359120	11359120	+	Missense_Mutation	SNP	G	G	T	rs2230774	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:11359120G>T	ENST00000315872.6	-	10	1740	c.1292C>A	c.(1291-1293)aCt>aAt	p.T431N	ROCK2_ENST00000401753.1_Missense_Mutation_p.T188N	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	431	Interaction with PPP1R12A.		T -> N (in dbSNP:rs2230774). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9734811, ECO:0000269|PubMed:9933571}.		actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)	p.T431N(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TATGGAATCAGTTTCTCTACA	0.284													T|||	2002	0.39976	0.2035	0.5634	5008	,	,		16818	0.3889		0.5268	False		,,,				2504	0.4294				p.T431N		Atlas-SNP	.											ROCK2_ENST00000315872,NS,carcinoma,0,1	ROCK2	224	1	1	Substitution - Missense(1)	stomach(1)	c.C1292A						PASS	.	T	ASN/THR	979,2621		142,695,963	77.0	69.0	72.0		1292	4.4	1.0	2	dbSNP_98	72	4295,3811		1146,2003,904	yes	missense	ROCK2	NM_004850.3	65	1288,2698,1867	TT,TG,GG		47.0146,27.1944,45.0538	benign	431/1389	11359120	5274,6432	1800	4053	5853	SO:0001583	missense	9475	exon10			GAATCAGTTTCTC	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.1292C>A	2.37:g.11359120G>T	ENSP00000317985:p.Thr431Asn	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	288	142	0.493056	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1	931	0.42628205128205127	100	0.2032520325203252	200	0.5524861878453039	234	0.4090909090909091	397	0.5237467018469657	T	3.282	-0.146893	0.06627	0.271944	0.529854	ENSG00000134318	ENST00000315872;ENST00000401753	T;T	0.62498	0.02;1.05	5.54	4.39	0.52855	.	0.397066	0.27172	N	0.020589	T	0.00012	0.0000	N	0.00230	-1.795	0.45837	P	0.0012950000000000461	B	0.02656	0.0	B	0.01281	0.0	T	0.46442	-0.9191	9	0.11794	T	0.64	.	6.4363	0.21825	0.0:0.0809:0.1581:0.761	rs2230774;rs9808232;rs17366763;rs52790024;rs9808232	431	O75116	ROCK2_HUMAN	N	431;188	ENSP00000317985:T431N;ENSP00000385509:T188N	ENSP00000261535:T431N	T	-	2	0	ROCK2	11276571	1.000000	0.71417	0.997000	0.53966	0.807000	0.45602	1.218000	0.32467	0.396000	0.25283	-0.335000	0.08231	ACT	T|0.320;G|0.373;C|0.181;N|0.000;A|0.127	0.320	strong		0.284	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3		
HK1	3098	hgsc.bcm.edu	37	10	71103597	71103597	+	Silent	SNP	C	C	G	rs1133189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71103597C>G	ENST00000359426.6	+	2	182	c.78C>G	c.(76-78)ctC>ctG	p.L26L	HK1_ENST00000494253.1_3'UTR|HK1_ENST00000448642.2_Silent_p.L61L|HK1_ENST00000404387.2_Silent_p.L30L|HK1_ENST00000298649.3_Silent_p.L25L|HK1_ENST00000360289.2_Silent_p.L14L	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	26	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						ACAAGTATCTCTATGCCATGC	0.537													C|||	1419	0.283347	0.3873	0.2334	5008	,	,		20035	0.122		0.3728	False		,,,				2504	0.2526				p.L30L		Atlas-SNP	.											.	HK1	170	.	0			c.C90G						PASS	.	C	,,,,	1734,2672	517.8+/-369.5	352,1030,821	167.0	159.0	162.0		78,75,90,90,42	0.6	1.0	10	dbSNP_86	162	3159,5441	480.7+/-370.5	570,2019,1711	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HK1	NM_000188.2,NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2	,,,,	922,3049,2532	GG,GC,CC		36.7326,39.3554,37.6211	,,,,	26/918,25/917,30/922,30/922,14/906	71103597	4893,8113	2203	4300	6503	SO:0001819	synonymous_variant	3098	exon5			GTATCTCTATGCC	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.78C>G	10.37:g.71103597C>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	113	111	0.982301	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	37	CCDS7292.1																																																																																			C|0.651;G|0.349	0.349	strong		0.537	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
STK36	27148	hgsc.bcm.edu	37	2	219553468	219553468	+	Missense_Mutation	SNP	C	C	T	rs16859180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219553468C>T	ENST00000295709.3	+	12	1708	c.1429C>T	c.(1429-1431)Cgg>Tgg	p.R477W	STK36_ENST00000440309.1_Missense_Mutation_p.R477W|STK36_ENST00000392105.3_Missense_Mutation_p.R477W|STK36_ENST00000392106.2_Missense_Mutation_p.R477W	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		GCCTGCATTCCGGGTCCTGAG	0.532													C|||	239	0.0477236	0.025	0.0259	5008	,	,		21460	0.0863		0.0447	False		,,,				2504	0.0573				p.R477W		Atlas-SNP	.											.	STK36	111	.	0			c.C1429T						PASS	.	C	TRP/ARG	140,4266	98.5+/-137.1	4,132,2067	202.0	185.0	191.0		1429	5.4	1.0	2	dbSNP_123	191	436,8164	133.8+/-191.2	10,416,3874	yes	missense	STK36	NM_015690.4	101	14,548,5941	TT,TC,CC		5.0698,3.1775,4.4287	probably-damaging	477/1316	219553468	576,12430	2203	4300	6503	SO:0001583	missense	27148	exon12			GCATTCCGGGTCC	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.1429C>T	2.37:g.219553468C>T	ENSP00000295709:p.Arg477Trp	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	315	163	0.51746	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	106	0.048534798534798536	12	0.024390243902439025	9	0.024861878453038673	53	0.09265734265734266	32	0.04221635883905013	C	25.6	4.650398	0.87958	0.031775	0.050698	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.76578	-0.37;-0.37;-1.03;-0.37	5.38	5.38	0.77491	Armadillo-like helical (1);	0.000000	0.41938	D	0.000795	T	0.18087	0.0434	L	0.29908	0.895	0.51012	D	0.999904	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.965	T	0.64774	-0.6328	10	0.87932	D	0	-19.144	17.1046	0.86659	0.0:1.0:0.0:0.0	rs16859180;rs52820506;rs56563033;rs16859180	477;477	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	W	477	ENSP00000295709:R477W;ENSP00000375955:R477W;ENSP00000375954:R477W;ENSP00000394095:R477W	ENSP00000295709:R477W	R	+	1	2	STK36	219261712	0.998000	0.40836	0.997000	0.53966	0.905000	0.53344	3.164000	0.50770	2.793000	0.96121	0.655000	0.94253	CGG	C|0.953;T|0.047	0.047	strong		0.532	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
DCAF4L1	285429	hgsc.bcm.edu	37	4	41984118	41984118	+	Silent	SNP	C	C	T	rs2660320	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:41984118C>T	ENST00000333141.5	+	1	406	c.309C>T	c.(307-309)agC>agT	p.S103S		NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN	DDB1 and CUL4 associated factor 4-like 1	103										breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						GCATCATCAGCCTGCGAACTC	0.557													C|||	3300	0.658946	0.1452	0.7983	5008	,	,		22448	0.9593		0.7763	False		,,,				2504	0.8241				p.S103S		Atlas-SNP	.											.	DCAF4L1	70	.	0			c.C309T						PASS	.	C		1080,3326	391.0+/-327.9	130,820,1253	97.0	88.0	91.0		309	0.7	0.3	4	dbSNP_100	91	6679,1921	726.5+/-406.6	2580,1519,201	no	coding-synonymous	DCAF4L1	NM_001029955.3		2710,2339,1454	TT,TC,CC		22.3372,24.512,40.3429		103/397	41984118	7759,5247	2203	4300	6503	SO:0001819	synonymous_variant	285429	exon1			CATCAGCCTGCGA	BC035027	CCDS33978.1	4p13	2013-01-09	2009-07-17	2009-07-17		ENSG00000182308		"""WD repeat domain containing"""	27723	protein-coding gene	gene with protein product			"""WD repeat domain 21B"""	WDR21B			Standard	NM_001029955		Approved		uc003gwk.2	Q3SXM0		ENST00000333141.5:c.309C>T	4.37:g.41984118C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	208	113	0.543269	NM_001029955	B3KVI3|Q3ZCW8|Q499Y5|Q9UFI0	Silent	SNP	ENST00000333141.5	37	CCDS33978.1																																																																																			C|0.375;T|0.625	0.625	strong		0.557	DCAF4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360958.1	NM_001029955	
DGKI	9162	hgsc.bcm.edu	37	7	137150761	137150761	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:137150761C>T	ENST00000288490.5	-	27	2529	c.2529G>A	c.(2527-2529)atG>atA	p.M843I	DGKI_ENST00000453654.2_Missense_Mutation_p.M553I|DGKI_ENST00000446122.1_Missense_Mutation_p.M825I|DGKI_ENST00000424189.2_Missense_Mutation_p.M856I	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	843					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						GGGAAATCTCCATCACAAAGT	0.448																																					p.M843I		Atlas-SNP	.											.	DGKI	335	.	0			c.G2529A						PASS	.						70.0	74.0	72.0					7																	137150761		2203	4300	6503	SO:0001583	missense	9162	exon27			AATCTCCATCACA	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2529G>A	7.37:g.137150761C>T	ENSP00000288490:p.Met843Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.240246	0.39598	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.32023	2.02;1.47;1.67	5.82	5.82	0.92795	.	0.140824	0.64402	D	0.000004	T	0.17959	0.0431	N	0.08118	0	0.38820	D	0.955614	B;B	0.18968	0.004;0.032	B;B	0.17722	0.012;0.019	T	0.11012	-1.0605	10	0.27785	T	0.31	.	14.8811	0.70534	0.1434:0.8566:0.0:0.0	.	553;843	E9PFX6;O75912	.;DGKI_HUMAN	I	553;801;846;843;825	ENSP00000392161:M553I;ENSP00000288490:M843I;ENSP00000399131:M825I	ENSP00000288490:M843I	M	-	3	0	DGKI	136801301	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.836000	0.27545	2.767000	0.95098	0.655000	0.94253	ATG	.	.	none		0.448	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
ARMS2	387715	hgsc.bcm.edu	37	10	124214355	124214355	+	Nonsense_Mutation	SNP	C	C	T	rs2736911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124214355C>T	ENST00000528446.1	+	1	187	c.112C>T	c.(112-114)Cga>Tga	p.R38*		NM_001099667.1	NP_001093137.1	P0C7Q2	ARMS2_HUMAN	age-related maculopathy susceptibility 2	38					retina homeostasis (GO:0001895)	mitochondrion (GO:0005739)|photoreceptor inner segment (GO:0001917)				ovary(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TTCCACTCTGCGAGAGTCTGT	0.542													C|||	573	0.114417	0.056	0.0908	5008	,	,		19861	0.1905		0.173	False		,,,				2504	0.0716				p.R38X		Atlas-SNP	.											ARMS2_ENST00000528446,NS,carcinoma,-1,1	ARMS2	7	1	0			c.C112T	GRCh37	CM083592	ARMS2	M	rs2736911	PASS	.	C	stop/ARG	288,3772		14,260,1756	142.0	147.0	145.0		112	-2.2	0.0	10	dbSNP_100	145	1274,7116		105,1064,3026	yes	stop-gained	ARMS2	NM_001099667.1		119,1324,4782	TT,TC,CC		15.1847,7.0936,12.5462		38/108	124214355	1562,10888	2030	4195	6225	SO:0001587	stop_gained	387715	exon1			ACTCTGCGAGAGT	BC066349	CCDS53585.1	10q26.13	2013-01-23			ENSG00000254636	ENSG00000254636			32685	protein-coding gene	gene with protein product		611313				16080115, 16174643	Standard	NM_001099667		Approved	LOC387715, ARMD8	uc001lgi.3	P0C7Q2	OTTHUMG00000048232	ENST00000528446.1:c.112C>T	10.37:g.124214355C>T	ENSP00000436682:p.Arg38*	Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	211	205	0.971564	NM_001099667	B2Y7I5	Nonsense_Mutation	SNP	ENST00000528446.1	37	CCDS53585.1	283	0.1295787545787546	32	0.06504065040650407	32	0.08839779005524862	101	0.17657342657342656	118	0.15567282321899736	C	12.36	1.914830	0.33815	0.070936	0.151847	ENSG00000254636	ENST00000528446	.	.	.	1.45	-2.21	0.06973	.	.	.	.	.	.	.	.	.	.	.	0.20307	P	0.9999111937	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	0.5279	0.00623	0.1922:0.2562:0.3244:0.2272	rs2736911;rs2736911	.	.	.	X	38	.	ENSP00000436682:R38X	R	+	1	2	ARMS2	124204345	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.426000	0.07008	-0.730000	0.04869	-1.080000	0.02220	CGA	C|0.869;T|0.131	0.131	strong		0.542	ARMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109727.2		
MUC4	4585	hgsc.bcm.edu	37	3	195507365	195507365	+	Missense_Mutation	SNP	G	G	A	rs75737861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507365G>A	ENST00000463781.3	-	2	11545	c.11086C>T	c.(11086-11088)Cct>Tct	p.P3696S	MUC4_ENST00000475231.1_Missense_Mutation_p.P3696S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCCTGA	0.577													.|||	193	0.0385383	0.0613	0.0231	5008	,	,		9654	0.0317		0.0219	False		,,,				2504	0.0429				p.P3696S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11086T						PASS	.						33.0	31.0	32.0					3																	195507365		647	1587	2234	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11086C>T	3.37:g.195507365G>A	ENSP00000417498:p.Pro3696Ser	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	206	168	0.815534	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	1012	0.4633699633699634	233	0.4735772357723577	150	0.4143646408839779	281	0.49125874125874125	348	0.45910290237467016	g	5.502	0.277530	0.10403	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.57436	1.28;0.4	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.47509	-0.9112	6	.	.	.	.	2.6493	0.04994	0.4962:0.0:0.5038:0.0	.	3568	E7ESK3	.	S	3696	ENSP00000417498:P3696S;ENSP00000420243:P3696S	.	P	-	1	0	MUC4	196992144	0.000000	0.05858	0.032000	0.17829	0.032000	0.12392	-2.110000	0.01334	0.064000	0.16427	0.064000	0.15345	CCT	G|0.537;A|0.463	0.463	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SNX13	23161	hgsc.bcm.edu	37	7	17879553	17879553	+	Silent	SNP	G	G	A	rs12720473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:17879553G>A	ENST00000409389.1	-	13	1408	c.1236C>T	c.(1234-1236)acC>acT	p.T412T	SNX13_ENST00000428135.3_Silent_p.T412T			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	412	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					GCTGTTGGGCGGTAACCCGGT	0.398													G|||	107	0.0213658	0.0038	0.0403	5008	,	,		16659	0.0		0.0686	False		,,,				2504	0.0051				p.T412T		Atlas-SNP	.											.	SNX13	113	.	0			c.C1236T						PASS	.	G		68,3700		2,64,1818	123.0	114.0	117.0		1236	4.1	1.0	7	dbSNP_126	117	626,7590		29,568,3511	no	coding-synonymous	SNX13	NM_015132.4		31,632,5329	AA,AG,GG		7.6193,1.8047,5.7911		412/958	17879553	694,11290	1884	4108	5992	SO:0001819	synonymous_variant	23161	exon13			TTGGGCGGTAACC	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.1236C>T	7.37:g.17879553G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Silent	SNP	ENST00000409389.1	37																																																																																				G|0.957;A|0.043	0.043	strong		0.398	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	
GPR116	221395	hgsc.bcm.edu	37	6	46832813	46832813	+	Silent	SNP	G	G	A	rs614826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46832813G>A	ENST00000283296.7	-	14	2244	c.1956C>T	c.(1954-1956)gtC>gtT	p.V652V	GPR116_ENST00000265417.7_Silent_p.V652V|GPR116_ENST00000362015.4_Silent_p.V652V|GPR116_ENST00000456426.2_Silent_p.V510V|GPR116_ENST00000545669.1_Silent_p.V81V	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	652					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			ATGGGCTCCAGACTGAATTAT	0.373													G|||	2504	0.5	0.118	0.6182	5008	,	,		19046	0.628		0.7237	False		,,,				2504	0.5706				p.V652V	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.C1956T						PASS	.	G	,	905,3501	348.2+/-309.8	101,703,1399	179.0	154.0	162.0		1956,1956	2.2	0.2	6	dbSNP_83	162	6230,2370	702.6+/-405.3	2263,1704,333	no	coding-synonymous,coding-synonymous	GPR116	NM_001098518.1,NM_015234.4	,	2364,2407,1732	AA,AG,GG		27.5581,20.5402,45.1407	,	652/1347,652/1347	46832813	7135,5871	2203	4300	6503	SO:0001819	synonymous_variant	221395	exon14			GCTCCAGACTGAA	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.1956C>T	6.37:g.46832813G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	221	89	0.402715	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																			G|0.472;A|0.528	0.528	strong		0.373	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
COL6A2	1292	hgsc.bcm.edu	37	21	47545826	47545826	+	Silent	SNP	C	C	T	rs13046639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47545826C>T	ENST00000300527.4	+	26	2201	c.2097C>T	c.(2095-2097)ggC>ggT	p.G699G	COL6A2_ENST00000357838.4_Silent_p.G699G|COL6A2_ENST00000310645.5_Silent_p.G699G|COL6A2_ENST00000409416.1_Silent_p.G699G|COL6A2_ENST00000397763.1_Silent_p.G699G	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	699	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GGATTGCGGGCGGCACCTGGA	0.612													C|||	1973	0.39397	0.208	0.6383	5008	,	,		14617	0.4306		0.5109	False		,,,				2504	0.3139				p.G699G		Atlas-SNP	.											.	COL6A2	351	.	0			c.C2097T						PASS	.	C	,,	1062,3344	387.2+/-326.4	148,766,1289	76.0	70.0	72.0		2097,2097,2097	-8.4	0.0	21	dbSNP_121	72	4304,4296	576.8+/-390.4	1048,2208,1044	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	1196,2974,2333	TT,TC,CC		49.9535,24.1035,41.2579	,,	699/1020,699/919,699/829	47545826	5366,7640	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			TGCGGGCGGCACC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2097C>T	21.37:g.47545826C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	185	180	0.972973	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			C|0.584;T|0.416	0.416	strong		0.612	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
KMT2C	58508	hgsc.bcm.edu	37	7	151962265	151962265	+	Missense_Mutation	SNP	C	C	T	rs201834857		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151962265C>T	ENST00000262189.6	-	8	1260	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	KMT2C_ENST00000355193.2_Missense_Mutation_p.D348N	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	348					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D348N(2)									CCCGGGCTGTCGCACACTGCA	0.383																																					p.D348N		Atlas-SNP	.											MLL3_ENST00000355193,trunk,malignant_melanoma,0,2	MLL3	1564	2	2	Substitution - Missense(2)	skin(2)	c.G1042A						scavenged	.						112.0	101.0	104.0					7																	151962265		2203	4296	6499	SO:0001583	missense	58508	exon8			GGCTGTCGCACAC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1042G>A	7.37:g.151962265C>T	ENSP00000262189:p.Asp348Asn	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	348	19	0.0545977	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730606	0.48939	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98807	-5.15;-5.15	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.43919	U	0.000512	D	0.98516	0.9505	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.98479	1.0604	10	0.23302	T	0.38	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	348	Q8NEZ4	MLL3_HUMAN	N	348	ENSP00000262189:D348N;ENSP00000347325:D348N	ENSP00000262189:D348N	D	-	1	0	MLL3	151593198	1.000000	0.71417	1.000000	0.80357	0.048000	0.14542	7.772000	0.85439	2.271000	0.75665	0.557000	0.71058	GAC	.	.	weak		0.383	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
PKD1L2	114780	hgsc.bcm.edu	37	16	81249954	81249954	+	RNA	SNP	T	T	A	rs7191351	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81249954T>A	ENST00000525539.1	-	0	358				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGCGGCGGCCTGCCCTCCATG	0.632													T|||	2351	0.469449	0.351	0.5519	5008	,	,		16693	0.4425		0.6541	False		,,,				2504	0.409				p.Q120L		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A359T						PASS	.	T	LEU/GLN,LEU/GLN	1866,2212		433,1000,606	50.0	63.0	59.0		359,359	1.4	0.0	16	dbSNP_116	59	5288,3060		1664,1960,550	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	113,113	2097,2960,1156	AA,AT,TT		36.6555,45.7577,42.4272	probably-damaging,probably-damaging	120/992,120/2460	81249954	7154,5272	2039	4174	6213			114780	exon2			GCGGCCTGCCCTC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81249954T>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1129	0.516941391941392	176	0.35772357723577236	224	0.6187845303867403	234	0.4090909090909091	495	0.6530343007915568	T	13.46	2.245031	0.39697	0.457577	0.633445	ENSG00000166473	ENST00000337114	T	0.20069	2.1	5.09	1.37	0.22104	C-type lectin fold (1);C-type lectin (3);	0.501380	0.20678	N	0.087718	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P;P	0.41848	0.763;0.491	P;B	0.44897	0.463;0.187	T	0.31280	-0.9949	8	0.87932	D	0	-0.6228	7.8882	0.29663	0.0:0.0723:0.3877:0.54	rs7191351;rs7191351	120;120	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	L	120	ENSP00000337397:Q120L	ENSP00000337397:Q120L	Q	-	2	0	PKD1L2	79807455	0.462000	0.25791	0.011000	0.14972	0.008000	0.06430	1.173000	0.31920	0.292000	0.22492	-0.320000	0.08662	CAG	A|0.526;N|0.001	0.526	strong		0.632	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
TMEM132D	121256	hgsc.bcm.edu	37	12	129566406	129566406	+	Silent	SNP	C	C	T	rs79031518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:129566406C>T	ENST00000422113.2	-	7	2147	c.1821G>A	c.(1819-1821)acG>acA	p.T607T	TMEM132D_ENST00000389441.4_Silent_p.T145T	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	607					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TTATCAGCTCCGTGATGTCCA	0.627													C|||	507	0.101238	0.0333	0.0793	5008	,	,		14042	0.1815		0.1143	False		,,,				2504	0.1125				p.T607T		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G1821A						PASS	.	C		195,4211	121.3+/-158.8	3,189,2011	58.0	55.0	56.0		1821	-9.2	0.2	12	dbSNP_131	56	816,7784	189.3+/-236.1	30,756,3514	no	coding-synonymous	TMEM132D	NM_133448.2		33,945,5525	TT,TC,CC		9.4884,4.4258,7.7733		607/1100	129566406	1011,11995	2203	4300	6503	SO:0001819	synonymous_variant	121256	exon7			CAGCTCCGTGATG	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1821G>A	12.37:g.129566406C>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	202	107	0.529703	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																			C|0.912;T|0.088	0.088	strong		0.627	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
TUBB1	81027	hgsc.bcm.edu	37	20	57599402	57599402	+	Missense_Mutation	SNP	G	G	A	rs6070697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57599402G>A	ENST00000217133.1	+	4	1189	c.920G>A	c.(919-921)cGt>cAt	p.R307H		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	307			R -> H (in dbSNP:rs6070697). {ECO:0000269|PubMed:18849486}.		'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	GACCTCCGCCGTGGCCGCTAC	0.637													G|||	721	0.14397	0.1157	0.1527	5008	,	,		19228	0.1042		0.2048	False		,,,				2504	0.1544				p.R307H		Atlas-SNP	.											.	TUBB1	42	.	0			c.G920A						PASS	.	G	HIS/ARG	582,3822	252.4+/-258.8	42,498,1662	52.0	44.0	46.0		920	1.9	0.9	20	dbSNP_114	46	1447,7153	273.8+/-290.9	118,1211,2971	yes	missense	TUBB1	NM_030773.3	29	160,1709,4633	AA,AG,GG		16.8256,13.2153,15.6029	benign	307/452	57599402	2029,10975	2202	4300	6502	SO:0001583	missense	81027	exon4			TCCGCCGTGGCCG	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"""Tubulins"""	16257	protein-coding gene	gene with protein product	"""class VI beta-tubulin"""	612901	"""tubulin, beta 1"""				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.920G>A	20.37:g.57599402G>A	ENSP00000217133:p.Arg307His	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	37	CCDS13475.1	307	0.14056776556776557	48	0.0975609756097561	50	0.13812154696132597	57	0.09965034965034965	152	0.20052770448548812	G	3.164	-0.171452	0.06421	0.132153	0.168256	ENSG00000101162	ENST00000217133	T	0.80909	-1.43	5.41	1.91	0.25777	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.265266	0.44483	N	0.000445	T	0.00039	0.0001	N	0.00108	-2.11	0.22656	P	0.99888428	B	0.14012	0.009	B	0.06405	0.002	T	0.23511	-1.0186	9	0.87932	D	0	.	9.4486	0.38712	0.3292:0.0:0.6708:0.0	rs6070697;rs59113071;rs6070697	307	Q9H4B7	TBB1_HUMAN	H	307	ENSP00000217133:R307H	ENSP00000217133:R307H	R	+	2	0	TUBB1	57032797	0.930000	0.31532	0.868000	0.34077	0.995000	0.86356	1.933000	0.40153	0.656000	0.30886	0.561000	0.74099	CGT	G|0.852;A|0.148	0.148	strong		0.637	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773	
MT-ND6	4541	hgsc.bcm.edu	37	M	14587	14587	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrM:14587A>G	ENST00000361681.2	-	1	86	c.87T>C	c.(85-87)ggT>ggC	p.G29G	MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	29					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						ATCAGTACTAAACCCCCATAA	0.388																																					p.G29G		Atlas-SNP	.											.	.	.	.	0			c.T87C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TACTAAACCCCCA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.87T>C	M.37:g.14587A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	65	0.970149	ENST00000361681	Q34774|Q8HG30	Silent	SNP	ENST00000361681.2	37																																																																																				.	.	none		0.388	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
DCHS2	54798	hgsc.bcm.edu	37	4	155410909	155410909	+	Silent	SNP	A	A	G	rs35172627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155410909A>G	ENST00000339452.1	-	1	1959	c.1599T>C	c.(1597-1599)aaT>aaC	p.N533N	DCHS2_ENST00000443500.1_Silent_p.N533N|DCHS2_ENST00000456341.2_Silent_p.N526N	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1678	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GTGGTTGGTCATTGAGGTCAG	0.637													A|||	568	0.113419	0.0567	0.1571	5008	,	,		16044	0.0109		0.2445	False		,,,				2504	0.1299				p.N533N		Atlas-SNP	.											.	DCHS2	594	.	0			c.T1599C						PASS	.	A	,	135,1249		6,123,563	103.0	106.0	105.0		1599,1599	-4.0	0.8	4	dbSNP_126	105	842,2340		114,614,863	no	coding-synonymous,coding-synonymous	DCHS2	NM_001142552.1,NM_001142553.1	,	120,737,1426	GG,GA,AA		26.4613,9.7543,21.3973	,	533/1370,533/710	155410909	977,3589	692	1591	2283	SO:0001819	synonymous_variant	54798	exon1			TTGGTCATTGAGG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.1599T>C	4.37:g.155410909A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000339452.1	37	CCDS47150.1																																																																																			A|0.843;G|0.157	0.157	strong		0.637	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
ACKR3	57007	hgsc.bcm.edu	37	2	237489904	237489904	+	Silent	SNP	C	C	T	rs1045879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:237489904C>T	ENST00000272928.3	+	2	1106	c.796C>T	c.(796-798)Ctg>Ttg	p.L266L		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	266					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										TGTCTGCTGGCTGCCCTACCA	0.607													c|||	1739	0.347244	0.7398	0.2176	5008	,	,		22079	0.0486		0.2485	False		,,,				2504	0.318				p.L266L		Atlas-SNP	.											CXCR7_ENST00000272928,lower_third,carcinoma,-1,1	CXCR7	72	1	0			c.C796T						PASS	.	T		2915,1491	677.9+/-403.5	987,941,275	161.0	136.0	145.0		796	4.9	1.0	2	dbSNP_86	145	2289,6311	385.5+/-341.5	323,1643,2334	no	coding-synonymous	CXCR7	NM_020311.2		1310,2584,2609	TT,TC,CC		26.6163,33.8402,40.0123		266/363	237489904	5204,7802	2203	4300	6503	SO:0001819	synonymous_variant	57007	exon2			TGCTGGCTGCCCT	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : Atypical"""	23692	protein-coding gene	gene with protein product		610376	"""chemokine orphan receptor 1"", ""chemokine (C-X-C motif) receptor 7"""	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.796C>T	2.37:g.237489904C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	173	92	0.531792	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Silent	SNP	ENST00000272928.3	37	CCDS2516.1																																																																																			C|0.632;T|0.368	0.368	strong		0.607	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057391	46057391	+	Silent	SNP	A	A	G	rs9306108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46057391A>G	ENST00000380095.1	+	1	119	c.57A>G	c.(55-57)gtA>gtG	p.V19V	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	19						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CTTGGCGGGTAGTCGACTGCC	0.667													a|||	1940	0.38738	0.3775	0.2651	5008	,	,		16086	0.3115		0.3827	False		,,,				2504	0.5706				p.V19V		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.A57G						PASS	.	A	,	1497,2909		300,897,1006	89.0	93.0	92.0		,57	0.6	1.0	21	dbSNP_119	92	2965,5635		612,1741,1947	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	912,2638,2953	GG,GA,AA		34.4767,33.9764,34.3072	,	,19/252	46057391	4462,8544	2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			GCGGGTAGTCGAC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.57A>G	21.37:g.46057391A>G		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	170	90	0.529412	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			A|0.648;G|0.352	0.352	strong		0.667	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
FBLN2	2199	hgsc.bcm.edu	37	3	13670508	13670508	+	Silent	SNP	G	G	A	rs41283996	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:13670508G>A	ENST00000295760.7	+	11	2601	c.2532G>A	c.(2530-2532)gcG>gcA	p.A844A	FBLN2_ENST00000404922.3_Silent_p.A891A|FBLN2_ENST00000535798.1_Silent_p.A870A|FBLN2_ENST00000492059.1_Silent_p.A891A	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	844	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			TGATCTGCGCGCGCGGCTACC	0.672													g|||	241	0.048123	0.0023	0.0519	5008	,	,		17097	0.0		0.0974	False		,,,				2504	0.1063				p.A891A		Atlas-SNP	.											FBLN2_ENST00000492059,NS,lymphoid_neoplasm,+2,4	FBLN2	137	4	0			c.G2673A						PASS	.	A	,,	74,4264		2,70,2097	34.0	41.0	38.0		2673,2673,2532	-6.2	0.0	3	dbSNP_127	38	833,7725		34,765,3480	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	,,	36,835,5577	AA,AG,GG		9.7336,1.7059,7.0332	,,	891/1232,891/1232,844/1185	13670508	907,11989	2169	4279	6448	SO:0001819	synonymous_variant	2199	exon12			CTGCGCGCGCGGC	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"""Fibulins"""	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.2532G>A	3.37:g.13670508G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	286	179	0.625874	NM_001004019	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	37	CCDS46762.1																																																																																			G|0.943;A|0.057	0.057	strong		0.672	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
SNX19	399979	hgsc.bcm.edu	37	11	130776613	130776613	+	Silent	SNP	A	A	G	rs4373936	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130776613A>G	ENST00000265909.4	-	6	2738	c.2169T>C	c.(2167-2169)tcT>tcC	p.S723S	SNX19_ENST00000545537.1_5'UTR|SNX19_ENST00000530356.1_Silent_p.S103S|SNX19_ENST00000539184.1_Silent_p.S166S|SNX19_ENST00000534726.1_5'UTR|SNX19_ENST00000533318.1_5'UTR|SNX19_ENST00000533214.1_Silent_p.S723S|SNX19_ENST00000528555.1_Silent_p.S103S	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	723					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		ACCTCAGCCTAGACCTGGTAC	0.413													G|||	3321	0.663139	0.5537	0.6916	5008	,	,		20127	0.6468		0.6372	False		,,,				2504	0.8344				p.S723S		Atlas-SNP	.											.	SNX19	84	.	0			c.T2169C						PASS	.	G		2509,1893	545.1+/-376.7	722,1065,414	73.0	69.0	70.0		2169	2.4	1.0	11	dbSNP_111	70	5697,2897	453.0+/-363.1	1886,1925,486	no	coding-synonymous	SNX19	NM_014758.2		2608,2990,900	GG,GA,AA		33.7096,43.0032,36.8575		723/993	130776613	8206,4790	2201	4297	6498	SO:0001819	synonymous_variant	399979	exon6			CAGCCTAGACCTG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.2169T>C	11.37:g.130776613A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	37	CCDS31721.1																																																																																			A|0.375;G|0.625	0.625	strong		0.413	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
SIGLEC7	27036	hgsc.bcm.edu	37	19	51656454	51656454	+	Silent	SNP	A	A	T	rs273662	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51656454A>T	ENST00000317643.6	+	7	1425	c.1356A>T	c.(1354-1356)ggA>ggT	p.G452G	SIGLEC7_ENST00000305628.7_Silent_p.G359G|SIGLEC7_ENST00000600577.1_3'UTR|CTD-3187F8.14_ENST00000600074.1_RNA	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	452					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.G452G(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		ACCTATCAGGACAAGAAGCCA	0.547													.|||	3586	0.716054	0.5477	0.7493	5008	,	,		18567	0.5744		0.9414	False		,,,				2504	0.8344				p.G452G		Atlas-SNP	.											SIGLEC7,NS,carcinoma,0,1	SIGLEC7	74	1	1	Substitution - coding silent(1)	stomach(1)	c.A1356T						PASS	.	A	,	2630,1776		792,1046,365	89.0	81.0	83.0		1356,1077	-2.8	0.0	19	dbSNP_79	83	8092,508		3819,454,27	no	coding-synonymous,coding-synonymous	SIGLEC7	NM_014385.2,NM_016543.2	,	4611,1500,392	TT,TA,AA		5.907,40.3087,17.5611	,	452/468,359/375	51656454	10722,2284	2203	4300	6503	SO:0001819	synonymous_variant	27036	exon7			ATCAGGACAAGAA	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10876	protein-coding gene	gene with protein product		604410	"""sialic acid binding Ig-like lectin 19, pseudogene"", ""sialic acid binding Ig-like lectin, pseudogene 2"""	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.1356A>T	19.37:g.51656454A>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	37	CCDS12826.1																																																																																			A|0.203;T|0.797	0.797	strong		0.547	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543	
FAM154A	158297	hgsc.bcm.edu	37	9	18950895	18950895	+	Missense_Mutation	SNP	T	T	C	rs7021572	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:18950895T>C	ENST00000380534.4	-	2	358	c.79A>G	c.(79-81)Aaa>Gaa	p.K27E	FAM154A_ENST00000583128.1_5'UTR|FAM154A_ENST00000542071.1_De_novo_Start_InFrame|FAM154A_ENST00000380530.1_Missense_Mutation_p.K27E	NM_153707.2	NP_714918.2	Q8IYX7	F154A_HUMAN	family with sequence similarity 154, member A	27			K -> E (in dbSNP:rs7021572). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|skin(1)	26				GBM - Glioblastoma multiforme(50;6.53e-16)		TTCTCTGTTTTATCATAAATC	0.443													T|||	2394	0.478035	0.1331	0.5865	5008	,	,		19151	0.5169		0.6909	False		,,,				2504	0.6084				p.K27E		Atlas-SNP	.											.	FAM154A	61	.	0			c.A79G						PASS	.	T	GLU/LYS	977,3429	368.8+/-318.8	115,747,1341	168.0	157.0	161.0		79	0.3	1.0	9	dbSNP_116	161	5990,2610	688.1+/-404.3	2080,1830,390	yes	missense	FAM154A	NM_153707.2	56	2195,2577,1731	CC,CT,TT		30.3488,22.1743,46.4324	possibly-damaging	27/475	18950895	6967,6039	2203	4300	6503	SO:0001583	missense	158297	exon2			CTGTTTTATCATA	BC033489	CCDS6487.1, CCDS75819.1, CCDS75820.1	9p22.1	2012-03-23	2008-02-21	2008-02-21	ENSG00000155875	ENSG00000155875			28566	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 138"""	C9orf138		12477932	Standard	NM_153707		Approved	MGC35182	uc003zni.2	Q8IYX7	OTTHUMG00000019609	ENST00000380534.4:c.79A>G	9.37:g.18950895T>C	ENSP00000369907:p.Lys27Glu	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	207	88	0.425121	NM_153707	Q5VY58	Missense_Mutation	SNP	ENST00000380534.4	37	CCDS6487.1	1126	0.5155677655677655	79	0.16056910569105692	225	0.6215469613259669	307	0.5367132867132867	515	0.679419525065963	T	13.49	2.252970	0.39797	0.221743	0.696512	ENSG00000155875	ENST00000380534;ENST00000380530	T;T	0.28255	1.62;1.62	5.54	0.28	0.15682	.	0.480527	0.19245	N	0.119061	T	0.00012	0.0000	L	0.38175	1.15	0.09310	P	0.9999999932157	B	0.23377	0.084	B	0.26416	0.069	T	0.27571	-1.0070	9	0.38643	T	0.18	-11.3227	7.7661	0.28980	0.0:0.0805:0.4239:0.4956	rs7021572;rs17853175;rs52832469;rs57724434;rs7021572	27	Q8IYX7	F154A_HUMAN	E	27	ENSP00000369907:K27E;ENSP00000369902:K27E	ENSP00000369902:K27E	K	-	1	0	FAM154A	18940895	0.999000	0.42202	1.000000	0.80357	0.973000	0.67179	1.033000	0.30191	0.371000	0.24564	-0.291000	0.09656	AAA	T|0.486;C|0.514	0.514	strong		0.443	FAM154A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051811.1	NM_153707	
MARCH2	51257	hgsc.bcm.edu	37	19	8486884	8486884	+	Missense_Mutation	SNP	G	G	A	rs1133893	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8486884G>A	ENST00000602117.1	+	2	615	c.160G>A	c.(160-162)Gcc>Acc	p.A54T	RP11-886P16.6_ENST00000595706.1_RNA|MARCH2_ENST00000601283.1_Intron|MARCH2_ENST00000381035.4_Missense_Mutation_p.A54T|MARCH2_ENST00000393944.1_Missense_Mutation_p.A54T|MARCH2_ENST00000215555.2_Missense_Mutation_p.A54T			Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2, E3 ubiquitin protein ligase	54			A -> T (in dbSNP:rs1133893). {ECO:0000269|PubMed:15489334}.		endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|skin(1)|urinary_tract(1)	10						CGTCATCCGTGCCTTGGACAC	0.607													G|||	996	0.198882	0.0348	0.2723	5008	,	,		18467	0.2381		0.2922	False		,,,				2504	0.2321				p.A54T		Atlas-SNP	.											MARCH2,NS,carcinoma,0,1	MARCH2	17	1	0			c.G160A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	420,3986	204.1+/-226.4	23,374,1806	87.0	69.0	75.0		160,160,160	4.6	1.0	19	dbSNP_86	75	2872,5728	450.7+/-362.5	470,1932,1898	yes	missense,missense,missense	MARCH2	NM_001005415.1,NM_001005416.1,NM_016496.4	58,58,58	493,2306,3704	AA,AG,GG		33.3953,9.5325,25.3114	benign,benign,benign	54/247,54/177,54/247	8486884	3292,9714	2203	4300	6503	SO:0001583	missense	51257	exon2			ATCCGTGCCTTGG	AF151074	CCDS12202.1, CCDS32894.1	19p13.2	2013-01-09	2012-02-23			ENSG00000099785		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	28038	protein-coding gene	gene with protein product		613332	"""membrane-associated ring finger (C3HC4) 2"""			11042152, 14722266	Standard	NM_016496		Approved	HSPC240, MARCH-II, RNF172	uc002mjw.3	Q9P0N8		ENST00000602117.1:c.160G>A	19.37:g.8486884G>A	ENSP00000471536:p.Ala54Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_001005415	A6NP10|Q5H785|Q8N5A3|Q96B78	Missense_Mutation	SNP	ENST00000602117.1	37	CCDS12202.1	476	0.21794871794871795	22	0.044715447154471545	109	0.3011049723756906	124	0.21678321678321677	221	0.29155672823219	G	14.98	2.696507	0.48202	0.095325	0.333953	ENSG00000099785	ENST00000393944;ENST00000215555;ENST00000381035	T;T;T	0.15017	2.46;2.46;2.46	5.65	4.6	0.57074	.	0.109437	0.64402	D	0.000010	T	0.00012	0.0000	L	0.52364	1.645	0.19775	P	0.999951435	B;B	0.30851	0.05;0.297	B;B	0.33890	0.073;0.172	T	0.46233	-0.9206	9	0.13853	T	0.58	-19.541	14.7238	0.69329	0.0:0.0:0.854:0.146	rs1133893;rs3196037;rs11540064;rs11882865;rs17352509;rs17846004;rs17858988;rs58815990;rs11882865	54;54	Q9P0N8-2;Q9P0N8	.;MARH2_HUMAN	T	54	ENSP00000377518:A54T;ENSP00000215555:A54T;ENSP00000370423:A54T	ENSP00000215555:A54T	A	+	1	0	MARCH2	8392884	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.156000	0.58138	1.362000	0.46000	0.555000	0.69702	GCC	T|0.034;G|0.603;C|0.163;A|0.200	0.200	strong		0.607	MARCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460361.2	NM_016496	
SASS6	163786	hgsc.bcm.edu	37	1	100575933	100575933	+	Missense_Mutation	SNP	G	G	A	rs13375867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:100575933G>A	ENST00000287482.5	-	8	916	c.776C>T	c.(775-777)gCg>gTg	p.A259V	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Missense_Mutation_p.A92V	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	259			A -> V (in dbSNP:rs13375867).		centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		TTTATTAGCCGCTTCTAACTC	0.353													G|||	1754	0.35024	0.0658	0.5562	5008	,	,		15563	0.5813		0.3867	False		,,,				2504	0.3129				p.A259V		Atlas-SNP	.											.	SASS6	61	.	0			c.C776T						PASS	.	G	VAL/ALA	576,3830	256.1+/-261.0	43,490,1670	155.0	145.0	148.0		776	3.4	0.8	1	dbSNP_121	148	3410,5190	502.1+/-375.6	671,2068,1561	yes	missense	SASS6	NM_194292.1	64	714,2558,3231	AA,AG,GG		39.6512,13.0731,30.6474	benign	259/658	100575933	3986,9020	2203	4300	6503	SO:0001583	missense	163786	exon8			TTAGCCGCTTCTA	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.776C>T	1.37:g.100575933G>A	ENSP00000287482:p.Ala259Val	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	227	226	0.995595	NM_194292	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	37	CCDS764.1	874	0.4001831501831502	42	0.08536585365853659	190	0.5248618784530387	353	0.6171328671328671	289	0.3812664907651715	G	10.82	1.456932	0.26161	0.130731	0.396512	ENSG00000156876	ENST00000287482;ENST00000539329;ENST00000535161	T;T	0.78246	-1.16;-1.16	5.31	3.41	0.39046	.	0.419300	0.28877	N	0.013853	T	0.36524	0.0970	N	0.10874	0.06	0.80722	P	0.0	B	0.16603	0.018	B	0.13407	0.009	T	0.11131	-1.0600	9	0.27785	T	0.31	-4.242	5.2703	0.15620	0.1664:0.3446:0.489:0.0	rs13375867;rs52830638;rs58236074;rs13375867	259	Q6UVJ0	SAS6_HUMAN	V	259;232;92	ENSP00000287482:A259V;ENSP00000440169:A92V	ENSP00000287482:A259V	A	-	2	0	SASS6	100348521	0.010000	0.17322	0.768000	0.31515	0.785000	0.44390	1.271000	0.33098	2.474000	0.83562	0.655000	0.94253	GCG	G|0.659;A|0.341	0.341	strong		0.353	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292	
ADAM20	8748	hgsc.bcm.edu	37	14	70990398	70990398	+	Silent	SNP	G	G	A	rs10162314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70990398G>A	ENST00000256389.3	-	2	1471	c.1227C>T	c.(1225-1227)tgC>tgT	p.C409C	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	359	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		ACTGTAGCTCGCACACACACC	0.428													g|||	289	0.0577077	0.118	0.0216	5008	,	,		22956	0.0347		0.0348	False		,,,				2504	0.0491				p.C409C		Atlas-SNP	.											.	ADAM20	59	.	0			c.C1227T						PASS	.	G		435,3971	209.5+/-230.2	22,391,1790	317.0	161.0	214.0		1227	-0.9	0.1	14	dbSNP_119	214	200,8400	86.9+/-149.2	1,198,4101	no	coding-synonymous	ADAM20	NM_003814.4		23,589,5891	AA,AG,GG		2.3256,9.8729,4.8824		409/777	70990398	635,12371	2203	4300	6503	SO:0001819	synonymous_variant	8748	exon2			TAGCTCGCACACA	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1227C>T	14.37:g.70990398G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_003814	Q6GTZ1|Q9UKJ9	Silent	SNP	ENST00000256389.3	37	CCDS32111.1																																																																																			G|0.943;A|0.057	0.057	strong		0.428	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2		
HIVEP3	59269	hgsc.bcm.edu	37	1	42046613	42046613	+	Silent	SNP	G	G	T	rs12132697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:42046613G>T	ENST00000372583.1	-	4	4741	c.3856C>A	c.(3856-3858)Cgg>Agg	p.R1286R	HIVEP3_ENST00000372584.1_Silent_p.R1286R|HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000247584.5_Silent_p.R1286R|HIVEP3_ENST00000429157.2_Silent_p.R1286R	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1286					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GGGGGTAGCCGGATGTCACTG	0.617													G|||	607	0.121206	0.0204	0.1311	5008	,	,		17803	0.0446		0.2505	False		,,,				2504	0.1963				p.R1286R		Atlas-SNP	.											HIVEP3,NS,carcinoma,0,1	HIVEP3	235	1	0			c.C3856A						PASS	.	G	,	275,4131	151.8+/-185.6	13,249,1941	44.0	47.0	46.0		3856,3856	5.2	0.4	1	dbSNP_120	46	2176,6424	368.8+/-335.2	297,1582,2421	no	coding-synonymous,coding-synonymous	HIVEP3	NM_001127714.2,NM_024503.4	,	310,1831,4362	TT,TG,GG		25.3023,6.2415,18.8451	,	1286/2406,1286/2407	42046613	2451,10555	2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			GTAGCCGGATGTC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.3856C>A	1.37:g.42046613G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	32	0.313726	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																			G|0.838;T|0.162	0.162	strong		0.617	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
RPE65	6121	hgsc.bcm.edu	37	1	68903942	68903942	+	Silent	SNP	C	C	T	rs12145904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:68903942C>T	ENST00000262340.5	-	10	1109	c.1056G>A	c.(1054-1056)gaG>gaA	p.E352E		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	352					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						TTTTTTTCACCTCTTCCCAGT	0.353													C|||	1121	0.223842	0.2315	0.1729	5008	,	,		17522	0.3641		0.1272	False		,,,				2504	0.2045				p.E352E		Atlas-SNP	.											RPE65,NS,carcinoma,-2,1	RPE65	87	1	0			c.G1056A						PASS	.	C		1017,3389	374.9+/-321.4	122,773,1308	90.0	92.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1056	-0.7	1.0	1	dbSNP_120	91	1012,7588	215.5+/-254.8	55,902,3343	no	coding-synonymous	RPE65	NM_000329.2		177,1675,4651	TT,TC,CC		11.7674,23.0822,15.6005		352/534	68903942	2029,10977	2203	4300	6503	SO:0001819	synonymous_variant	6121	exon10			TTTCACCTCTTCC	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"""retinol isomerase"", ""all-trans-retinyl-palmitate hydrolase"", ""retinoid isomerohydrolase"", ""BCO family, member 3"""	180069	"""retinal pigment epithelium-specific protein (65kD)"""	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.1056G>A	1.37:g.68903942C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	15	0.245902	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			C|0.815;T|0.185	0.185	strong		0.353	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
SULT1A1	6817	hgsc.bcm.edu	37	16	28619911	28619911	+	Silent	SNP	T	T	C	rs1126447	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28619911T>C	ENST00000395607.1	-	3	435	c.162A>G	c.(160-162)gtA>gtG	p.V54V	SULT1A1_ENST00000395609.1_Silent_p.V54V|SULT1A1_ENST00000350842.4_Intron|SULT1A1_ENST00000569554.1_Silent_p.V54V|SULT1A1_ENST00000314752.7_Silent_p.V54V	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	54					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.V54V(1)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	GAATCTGGCTTACCCAGGTAG	0.617													.|||	1455	0.290535	0.2284	0.4769	5008	,	,		24736	0.2669		0.335	False		,,,				2504	0.2209				p.V54V		Atlas-SNP	.											SULT1A1,NS,carcinoma,0,1	SULT1A1	53	1	1	Substitution - coding silent(1)	stomach(1)	c.A162G						scavenged	.	C	,,,,	880,3514		131,618,1448	101.0	72.0	81.0		162,162,162,162,	0.1	1.0	16	dbSNP_86	81	2909,5691		613,1683,2004	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	SULT1A1	NM_001055.3,NM_177529.2,NM_177530.2,NM_177534.2,NM_177536.3	,,,,	744,2301,3452	CC,CT,TT		33.8256,20.0273,29.1596	,,,,	54/296,54/296,54/296,54/296,	28619911	3789,9205	2197	4300	6497	SO:0001819	synonymous_variant	6817	exon2			CTGGCTTACCCAG	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.162A>G	16.37:g.28619911T>C		Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	629	184	0.292528	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Silent	SNP	ENST00000395607.1	37	CCDS32420.1																																																																																			T|0.716;C|0.284	0.284	strong		0.617	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
C7orf71	285941	hgsc.bcm.edu	37	7	26685934	26685934	+	Silent	SNP	T	T	C	rs12671270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:26685934T>C	ENST00000409974.3	+	4	1001	c.285T>C	c.(283-285)tgT>tgC	p.C95C		NM_001145531.1	NP_001139003.1	A4D174	CG071_HUMAN	chromosome 7 open reading frame 71	95																	TCTCCGCATGTGGGACTCTCG	0.423													C|||	1413	0.282149	0.351	0.2176	5008	,	,		18149	0.3264		0.2724	False		,,,				2504	0.1994				p.C95C		Atlas-SNP	.											.	C7orf71	6	.	0			c.T285C						PASS	.	C		483,901		96,291,305	79.0	70.0	73.0		285	-1.3	0.0	7	dbSNP_120	73	967,2215		153,661,777	no	coding-synonymous	C7orf71	NM_001145531.1		249,952,1082	CC,CT,TT		30.3897,34.8988,31.7565		95/170	26685934	1450,3116	692	1591	2283	SO:0001819	synonymous_variant	285941	exon4			CGCATGTGGGACT		CCDS47565.1	7p15.2	2009-09-11			ENSG00000222004	ENSG00000222004			22364	protein-coding gene	gene with protein product							Standard	NM_001145531		Approved		uc003syb.3	A4D174	OTTHUMG00000152860	ENST00000409974.3:c.285T>C	7.37:g.26685934T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_001145531		Silent	SNP	ENST00000409974.3	37	CCDS47565.1																																																																																			C|0.305;N|0.000	0.305	strong		0.423	C7orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328272.1	NM_001145531	
OVGP1	5016	hgsc.bcm.edu	37	1	111957570	111957570	+	Missense_Mutation	SNP	G	G	C	rs376377993|rs45455292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111957570G>C	ENST00000369732.3	-	11	1608	c.1553C>G	c.(1552-1554)aCc>aGc	p.T518S		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	518					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TTCCCCAGGGGTCACAGACTG	0.572													G|||	910	0.181709	0.0643	0.1542	5008	,	,		17214	0.1528		0.2714	False		,,,				2504	0.2975				p.T518S		Atlas-SNP	.											.	OVGP1	177	.	0			c.C1553G						PASS	.						58.0	53.0	55.0					1																	111957570		2194	4297	6491	SO:0001583	missense	5016	exon11			CCAGGGGTCACAG	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1553C>G	1.37:g.111957570G>C	ENSP00000358747:p.Thr518Ser	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	63	53	0.84127	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	284	0.13003663003663005	20	0.04065040650406504	59	0.16298342541436464	62	0.10839160839160839	143	0.18865435356200527	G	12.03	1.816593	0.32145	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04234	3.67	3.36	2.43	0.29744	.	.	.	.	.	T	0.01454	0.0047	L	0.31578	0.945	0.58432	P	5.000000000032756E-6	B;B	0.17038	0.02;0.02	B;B	0.19148	0.024;0.024	T	0.40459	-0.9562	8	0.62326	D	0.03	.	7.157	0.25643	0.1378:0.0:0.8622:0.0	rs45455292	518;582	Q12889;Q59HH5	OVGP1_HUMAN;.	S	518;582;326	ENSP00000358747:T518S	ENSP00000358743:T582S	T	-	2	0	OVGP1	111759093	0.002000	0.14202	0.003000	0.11579	0.242000	0.25591	0.074000	0.14662	0.696000	0.31696	0.454000	0.30748	ACC	G|0.853;C|0.147	0.147	strong		0.572	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
TRIM16	10626	hgsc.bcm.edu	37	17	15554504	15554504	+	Silent	SNP	G	G	A	rs4792642	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:15554504G>A	ENST00000578237.1	-	6	1275	c.420C>T	c.(418-420)gcC>gcT	p.A140A	TRIM16_ENST00000416464.2_Intron|RP11-385D13.1_ENST00000455584.2_Silent_p.A140A|RP11-640I15.1_ENST00000584540.1_RNA|TRIM16_ENST00000336708.7_Silent_p.A140A|TRIM16_ENST00000581224.1_Intron			O95361	TRI16_HUMAN	tripartite motif containing 16	140					histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		GGCAGCAGAAGGCAGACAGTG	0.602													G|||	1384	0.276358	0.2829	0.281	5008	,	,		21480	0.3125		0.2107	False		,,,				2504	0.2945				p.A140A		Atlas-SNP	.											.	TRIM16	45	.	0			c.C420T						PASS	.	G		1318,3088	443.3+/-347.0	205,908,1090	147.0	137.0	140.0		420	4.4	1.0	17	dbSNP_111	140	1949,6651	343.2+/-324.8	214,1521,2565	no	coding-synonymous	TRIM16	NM_006470.3		419,2429,3655	AA,AG,GG		22.6628,29.9138,25.1192		140/565	15554504	3267,9739	2203	4300	6503	SO:0001819	synonymous_variant	10626	exon4			GCAGAAGGCAGAC	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.420C>T	17.37:g.15554504G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	165	87	0.527273	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Silent	SNP	ENST00000578237.1	37	CCDS11171.1	541	0.24771062271062272	134	0.27235772357723576	90	0.24861878453038674	159	0.27797202797202797	158	0.20844327176781002	g	10.27	1.304808	0.23736	0.299138	0.226628	ENSG00000251537	ENST00000455584	.	.	.	5.47	4.44	0.53790	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999375809	.	.	.	.	.	.	T	0.07462	-1.0771	3	.	.	.	.	13.5372	0.61653	0.0:0.2408:0.7592:0.0	rs4792642;rs4792642	.	.	.	L	155	.	.	P	-	2	0	RP11-385D13.1	15495229	0.844000	0.29557	0.998000	0.56505	0.842000	0.47809	0.296000	0.19083	2.563000	0.86464	0.563000	0.77884	CCT	G|0.746;A|0.254	0.254	strong		0.602	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	
PIFO	128344	hgsc.bcm.edu	37	1	111891170	111891170	+	Missense_Mutation	SNP	A	A	C	rs15396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111891170A>C	ENST00000369738.4	+	4	656	c.291A>C	c.(289-291)aaA>aaC	p.K97N	PIFO_ENST00000484512.1_3'UTR|PIFO_ENST00000369737.4_Missense_Mutation_p.K64N	NM_181643.4	NP_857594.2	Q8TCI5	PIFO_HUMAN	primary cilia formation	97			K -> N (in dbSNP:rs15396).		cell projection organization (GO:0030030)|positive regulation of kinase activity (GO:0033674)|regulation of cell projection organization (GO:0031344)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	beta-tubulin binding (GO:0048487)|gamma-tubulin binding (GO:0043015)|kinesin binding (GO:0019894)|protein kinase binding (GO:0019901)|Rab GTPase binding (GO:0017137)										GGTACCAGAAAGTAAGTCCTC	0.383													a|||	104	0.0207668	0.0068	0.0317	5008	,	,		19920	0.0		0.0636	False		,,,				2504	0.0092				p.K97N		Atlas-SNP	.											.	.	.	.	0			c.A291C						PASS	.	C	ASN/LYS	61,4345	57.4+/-93.9	1,59,2143	231.0	251.0	244.0		291	-0.6	0.0	1	dbSNP_52	244	578,8022	155.4+/-209.4	16,546,3738	yes	missense	C1orf88	NM_181643.4	94	17,605,5881	CC,CA,AA		6.7209,1.3845,4.9131	benign	97/192	111891170	639,12367	2203	4300	6503	SO:0001583	missense	128344	exon4			CCAGAAAGTAAGT	BC050319	CCDS833.1, CCDS72836.1	1p13.2	2012-10-10	2012-10-10	2012-10-10	ENSG00000173947	ENSG00000173947			27009	protein-coding gene	gene with protein product		614234	"""chromosome 1 open reading frame 88"""	C1orf88		20643351	Standard	XM_005270472		Approved	FLJ23853, pitchfork	uc001eaw.2	Q8TCI5	OTTHUMG00000011168	ENST00000369738.4:c.291A>C	1.37:g.111891170A>C	ENSP00000358753:p.Lys97Asn	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	97	60	0.618557	NM_181643	D9J0A2|D9J0A3|Q4G0K4|Q52LJ6|Q5T5D5|Q5T5D6|Q8N310	Missense_Mutation	SNP	ENST00000369738.4	37	CCDS833.1	68	0.031135531135531136	4	0.008130081300813009	11	0.03038674033149171	0	0.0	53	0.06992084432717678	a	5.218	0.225661	0.09916	0.013845	0.067209	ENSG00000173947	ENST00000369738;ENST00000369737	T;T	0.33865	1.92;1.39	4.36	-0.598	0.11649	.	1.479250	0.03973	N	0.291991	T	0.07234	0.0183	L	0.29908	0.895	0.09310	N	1	B;B	0.26258	0.145;0.001	B;B	0.24541	0.054;0.002	T	0.18178	-1.0345	10	0.20519	T	0.43	0.1602	0.3038	0.00277	0.4124:0.182:0.2079:0.1977	rs15396;rs1058516;rs3199154;rs60989587;rs15396	64;97	Q8TCI5-3;Q8TCI5	.;PIFO_HUMAN	N	97;64	ENSP00000358753:K97N;ENSP00000358752:K64N	ENSP00000358752:K64N	K	+	3	2	C1orf88	111692693	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.030000	0.12308	-0.003000	0.14444	-0.559000	0.04183	AAA	A|0.957;C|0.043	0.043	strong		0.383	PIFO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030718.1	NM_181643	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549588	32549588	+	Missense_Mutation	SNP	G	G	A	rs201929247	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549588G>A	ENST00000360004.5	-	3	503	c.398C>T	c.(397-399)tCa>tTa	p.S133L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	133	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CTGGGTCTTTGAAGGATATAC	0.512										Multiple Myeloma(14;0.17)																											p.S133L		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C398T						PASS	.						57.0	71.0	66.0					6																	32549588		1511	2709	4220	SO:0001583	missense	3123	exon3			GTCTTTGAAGGAT	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.398C>T	6.37:g.32549588G>A	ENSP00000353099:p.Ser133Leu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	337	32	0.0949555	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	6.973	0.549575	0.13374	.	.	ENSG00000196126	ENST00000360004	T	0.02916	4.11	3.87	2.05	0.26809	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.987485	0.08278	N	0.970401	T	0.01353	0.0044	L	0.48218	1.51	0.09310	N	1	B	0.22541	0.071	B	0.27380	0.079	T	0.47275	-0.9130	10	0.87932	D	0	.	7.8864	0.29653	0.2137:0.0:0.7863:0.0	.	133	P01911	2B1F_HUMAN	L	133	ENSP00000353099:S133L	ENSP00000353099:S133L	S	-	2	0	HLA-DRB1	32657566	0.033000	0.19621	0.179000	0.23059	0.051000	0.14879	2.068000	0.41471	0.252000	0.21531	0.453000	0.30009	TCA	G|0.940;A|0.060	0.060	strong		0.512	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232568041	232568041	+	Missense_Mutation	SNP	G	G	A	rs1547742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:232568041G>A	ENST00000366630.1	-	15	4566	c.4208C>T	c.(4207-4209)tCg>tTg	p.S1403L	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.S1403L|SIPA1L2_ENST00000308942.4_Missense_Mutation_p.S477L			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1403			S -> L (in dbSNP:rs1547742).		regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GCTGCCCTCCGATTTCTTCCA	0.557													G|||	311	0.0621006	0.0129	0.1311	5008	,	,		13952	0.0397		0.0994	False		,,,				2504	0.0644				p.S1403L		Atlas-SNP	.											SIPA1L2,colon,carcinoma,0,1	SIPA1L2	218	1	0			c.C4208T						PASS	.	G	LEU/SER	118,3750		3,112,1819	75.0	73.0	74.0		4208	5.0	0.5	1	dbSNP_88	74	804,7472		33,738,3367	yes	missense	SIPA1L2	NM_020808.3	145	36,850,5186	AA,AG,GG		9.7148,3.0507,7.5922	possibly-damaging	1403/1723	232568041	922,11222	1934	4138	6072	SO:0001583	missense	57568	exon14			CCCTCCGATTTCT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4208C>T	1.37:g.232568041G>A	ENSP00000355589:p.Ser1403Leu	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	155	80	0.516129	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	150	0.06868131868131869	9	0.018292682926829267	47	0.1298342541436464	21	0.03671328671328671	73	0.09630606860158311	G	16.74	3.206872	0.58343	0.030507	0.097148	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.79247	-1.25;-1.25;2.66	5.92	5.01	0.66863	.	0.599107	0.17520	N	0.171294	T	0.02380	0.0073	L	0.51422	1.61	0.30094	P	0.808038	P;D	0.62365	0.93;0.991	B;P	0.44518	0.101;0.452	T	0.52230	-0.8603	9	0.72032	D	0.01	-3.5084	14.9542	0.71098	0.0681:0.0:0.9319:0.0	rs1547742;rs52825369;rs58546657;rs1547742	1403;477	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	L	1403;1403;477	ENSP00000355589:S1403L;ENSP00000262861:S1403L;ENSP00000309102:S477L	ENSP00000262861:S1403L	S	-	2	0	SIPA1L2	230634664	0.996000	0.38824	0.540000	0.28089	0.891000	0.51852	4.530000	0.60595	1.515000	0.48885	0.655000	0.94253	TCG	G|0.931;A|0.069	0.069	strong		0.557	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
PKD1L2	114780	hgsc.bcm.edu	37	16	81249927	81249927	+	RNA	SNP	C	C	T	rs7185774	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81249927C>T	ENST00000525539.1	-	0	385				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CCCGATGTGGCCGCAGGTGTC	0.657													C|||	748	0.149361	0.0598	0.2219	5008	,	,		17980	0.0089		0.3598	False		,,,				2504	0.1472				p.G129D		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G386A						PASS	.	C	ASP/GLY,ASP/GLY	481,3669		32,417,1626	59.0	74.0	69.0		386,386	5.1	0.9	16	dbSNP_116	69	2910,5512		479,1952,1780	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	94,94	511,2369,3406	TT,TC,CC		34.5524,11.5904,26.9726	probably-damaging,probably-damaging	129/992,129/2460	81249927	3391,9181	2075	4211	6286			114780	exon2			ATGTGGCCGCAGG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81249927C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		395	0.18086080586080586	28	0.056910569105691054	105	0.2900552486187845	2	0.0034965034965034965	260	0.34300791556728233	C	17.15	3.316419	0.60524	0.115904	0.345524	ENSG00000166473	ENST00000337114	T	0.18657	2.2	5.09	5.09	0.68999	C-type lectin fold (1);C-type lectin (3);	0.903145	0.09494	N	0.794543	T	0.00012	0.0000	.	.	.	0.29850	P	0.828541	D;D	0.71674	0.998;0.997	D;D	0.66847	0.939;0.947	T	0.28839	-1.0031	8	0.49607	T	0.09	-6.5644	18.5832	0.91180	0.0:1.0:0.0:0.0	rs7185774;rs7185774	129;129	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	D	129	ENSP00000337397:G129D	ENSP00000337397:G129D	G	-	2	0	PKD1L2	79807428	1.000000	0.71417	0.902000	0.35471	0.035000	0.12851	3.983000	0.56916	2.391000	0.81399	0.650000	0.86243	GGC	C|0.772;T|0.228	0.228	strong		0.657	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
NBAS	51594	hgsc.bcm.edu	37	2	15674686	15674686	+	Missense_Mutation	SNP	T	T	C	rs13029846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:15674686T>C	ENST00000281513.5	-	9	752	c.727A>G	c.(727-729)Att>Gtt	p.I243V	NBAS_ENST00000441750.1_Missense_Mutation_p.I243V	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	243			I -> V (in dbSNP:rs13029846). {ECO:0000269|PubMed:15815621}.		negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						GGGTGGTAAATAGCTGTGTTG	0.368													T|||	1949	0.389177	0.2088	0.5807	5008	,	,		18318	0.1617		0.6879	False		,,,				2504	0.4243				p.I243V		Atlas-SNP	.											.	NBAS	246	.	0			c.A727G						PASS	.	T	VAL/ILE	1310,3096	440.6+/-346.1	194,922,1087	227.0	216.0	220.0		727	-4.3	0.0	2	dbSNP_121	220	5857,2743	680.6+/-403.7	1993,1871,436	yes	missense	NBAS	NM_015909.2	29	2187,2793,1523	CC,CT,TT		31.8953,29.7322,44.8947	benign	243/2372	15674686	7167,5839	2203	4300	6503	SO:0001583	missense	51594	exon9			GGTAAATAGCTGT	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.727A>G	2.37:g.15674686T>C	ENSP00000281513:p.Ile243Val	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	167	69	0.413174	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	910	0.4166666666666667	90	0.18292682926829268	211	0.5828729281767956	103	0.18006993006993008	506	0.6675461741424802	T	2.406	-0.336426	0.05278	0.297322	0.681047	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.45276	0.9;0.9	5.82	-4.29	0.03721	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);	0.376573	0.28659	N	0.014571	T	0.00012	0.0000	N	0.21448	0.665	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.44651	-0.9314	9	0.87932	D	0	.	9.3522	0.38145	0.0:0.481:0.1185:0.4006	rs13029846;rs52808679;rs59282131;rs13029846	243	A2RRP1	NBAS_HUMAN	V	243	ENSP00000413201:I243V;ENSP00000281513:I243V	ENSP00000281513:I243V	I	-	1	0	NBAS	15592137	0.001000	0.12720	0.019000	0.16419	0.975000	0.68041	-0.116000	0.10724	-0.749000	0.04747	0.533000	0.62120	ATT	T|0.508;C|0.492	0.492	strong		0.368	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
C3orf17	25871	hgsc.bcm.edu	37	3	112727184	112727184	+	Missense_Mutation	SNP	A	A	T	rs2306857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:112727184A>T	ENST00000314400.5	-	8	1260	c.1069T>A	c.(1069-1071)Ttt>Att	p.F357I	C3orf17_ENST00000383675.2_Missense_Mutation_p.F287I|C3orf17_ENST00000393857.2_Missense_Mutation_p.F221I|C3orf17_ENST00000472762.1_5'UTR	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	357			F -> I (in dbSNP:rs2306857). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of neuron differentiation (GO:0045665)|positive regulation of Notch signaling pathway (GO:0045747)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|lung(6)|prostate(2)|skin(1)	13						CTTTGCACAAAACTTTTGGCA	0.418													A|||	2485	0.496206	0.2065	0.7363	5008	,	,		17372	0.3512		0.7584	False		,,,				2504	0.5971				p.F357I		Atlas-SNP	.											.	C3orf17	37	.	0			c.T1069A						PASS	.	A	ILE/PHE	1315,3091	438.8+/-345.5	203,909,1091	87.0	87.0	87.0		1069	0.2	0.1	3	dbSNP_100	87	6663,1937	725.3+/-406.5	2583,1497,220	yes	missense	C3orf17	NM_015412.3	21	2786,2406,1311	TT,TA,AA		22.5233,29.8457,38.6591	benign	357/568	112727184	7978,5028	2203	4300	6503	SO:0001583	missense	25871	exon8			GCACAAAACTTTT	AL117573	CCDS33824.1	3q13.2	2009-11-06			ENSG00000163608	ENSG00000163608			24496	protein-coding gene	gene with protein product						12477932	Standard	NR_027794		Approved	DKFZP434F2021, NET17	uc003dzr.3	Q6NW34	OTTHUMG00000159286	ENST00000314400.5:c.1069T>A	3.37:g.112727184A>T	ENSP00000320251:p.Phe357Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_015412	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	Missense_Mutation	SNP	ENST00000314400.5	37	CCDS33824.1	1151	0.527014652014652	108	0.21951219512195122	264	0.7292817679558011	201	0.3513986013986014	578	0.762532981530343	A	8.042	0.763993	0.15914	0.298457	0.774767	ENSG00000163608	ENST00000314400;ENST00000383675;ENST00000393857	T;T;T	0.31510	1.49;1.49;1.49	5.55	0.155	0.14906	.	0.395110	0.30850	N	0.008746	T	0.00012	0.0000	L	0.48362	1.52	0.50039	P	1.5699999999996272E-4	B;B;B;B	0.33612	0.419;0.419;0.002;0.005	B;B;B;B	0.37943	0.168;0.261;0.002;0.003	T	0.21449	-1.0245	9	0.23302	T	0.38	-2.1656	4.3654	0.11222	0.5656:0.0:0.2845:0.1499	rs2306857;rs3872608;rs3892310;rs52795272;rs2306857	246;154;287;357	E7EN80;E7EQH6;Q6NW34-2;Q6NW34	.;.;.;CC017_HUMAN	I	357;287;221	ENSP00000320251:F357I;ENSP00000373173:F287I;ENSP00000377438:F221I	ENSP00000320251:F357I	F	-	1	0	C3orf17	114209874	0.090000	0.21635	0.092000	0.20876	0.316000	0.28119	0.291000	0.18994	0.116000	0.18110	0.477000	0.44152	TTT	A|0.415;T|0.585	0.585	strong		0.418	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412	
PRR27	401137	hgsc.bcm.edu	37	4	71024099	71024099	+	Missense_Mutation	SNP	A	A	G	rs1612460	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:71024099A>G	ENST00000344526.5	+	3	319	c.130A>G	c.(130-132)Ata>Gta	p.I44V	C4orf40_ENST00000502441.2_Intron|C4orf40_ENST00000502294.1_Missense_Mutation_p.I44V	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		44	Ala/Pro-rich.		I -> L (in dbSNP:rs1612460).	I -> V (in Ref. 1; CAE45962). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						TCCTTATGGCATACGGAATTT	0.438													A|||	193	0.0385383	0.003	0.0648	5008	,	,		18687	0.002		0.1133	False		,,,				2504	0.0286				p.I44V		Atlas-SNP	.											.	C4orf40	19	.	0			c.A130G						PASS	.	A	VAL/ILE	96,4310	77.8+/-116.1	2,92,2109	179.0	160.0	166.0		130	-3.2	0.0	4	dbSNP_89	166	999,7601	215.5+/-254.8	53,893,3354	yes	missense	C4orf40	NM_214711.3	29	55,985,5463	GG,GA,AA		11.6163,2.1788,8.4192	possibly-damaging	44/220	71024099	1095,11911	2203	4300	6503	SO:0001583	missense	401137	exon3			TATGGCATACGGA																												ENST00000344526.5:c.130A>G	4.37:g.71024099A>G	ENSP00000343172:p.Ile44Val	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	116	0.05311355311355311	0	0.0	25	0.06906077348066299	2	0.0034965034965034965	89	0.11741424802110818	A	2.416	-0.334292	0.05278	0.021788	0.116163	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.32023	1.47;1.47	1.71	-3.16	0.05217	.	.	.	.	.	T	0.00178	0.0005	N	0.14661	0.345	0.80722	P	0.0	B	0.26363	0.147	B	0.31101	0.124	T	0.21075	-1.0256	8	0.02654	T	1	2.5581	2.8972	0.05694	0.2086:0.3859:0.0:0.4055	rs1612460;rs17703358;rs1612460	44	Q6MZM9	CD040_HUMAN	V	44	ENSP00000426249:I44V;ENSP00000343172:I44V	ENSP00000343172:I44V	I	+	1	0	C4orf40	71058688	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.545000	0.02190	-1.081000	0.03105	-0.480000	0.04831	ATA	A|0.927;C|0.007;G|0.066	0.066	strong		0.438	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
ICAM5	7087	hgsc.bcm.edu	37	19	10402938	10402938	+	Missense_Mutation	SNP	G	G	A	rs1056538	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10402938G>A	ENST00000221980.4	+	4	964	c.901G>A	c.(901-903)Gtc>Atc	p.V301I		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	301	Ig-like C2-type 3.		V -> I (in dbSNP:rs1056538). {ECO:0000269|PubMed:8995416}.		phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CAGGCAGCTGGTCTGCAACGT	0.642													G|||	1450	0.289537	0.0439	0.5202	5008	,	,		16487	0.2371		0.4056	False		,,,				2504	0.3926				p.V301I		Atlas-SNP	.											.	ICAM5	53	.	0			c.G901A						PASS	.	G	ILE/VAL	436,3970	202.8+/-225.5	19,398,1786	36.0	29.0	31.0		901	3.3	1.0	19	dbSNP_86	31	3345,5253	473.0+/-368.5	669,2007,1623	no	missense	ICAM5	NM_003259.3	29	688,2405,3409	AA,AG,GG		38.9044,9.8956,29.0757	benign	301/925	10402938	3781,9223	2203	4299	6502	SO:0001583	missense	7087	exon4			CAGCTGGTCTGCA	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.901G>A	19.37:g.10402938G>A	ENSP00000221980:p.Val301Ile	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	45	0.978261	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	641	0.2934981684981685	11	0.022357723577235773	175	0.48342541436464087	145	0.2534965034965035	310	0.40897097625329815	G	16.96	3.265958	0.59540	0.098956	0.389044	ENSG00000105376	ENST00000221980	T	0.05447	3.44	5.54	3.27	0.37495	Immunoglobulin-like fold (1);	0.652062	0.14359	N	0.324603	T	0.00012	0.0000	L	0.60455	1.87	0.45867	P	0.0012799999999999478	B	0.12630	0.006	B	0.11329	0.006	T	0.41395	-0.9511	9	0.30078	T	0.28	-22.8733	5.0439	0.14473	0.3049:0.0:0.6951:0.0	rs1056538;rs2228616;rs11549918;rs17845811;rs17858776;rs61530381	301	Q9UMF0	ICAM5_HUMAN	I	301	ENSP00000221980:V301I	ENSP00000221980:V301I	V	+	1	0	ICAM5	10263938	0.401000	0.25303	1.000000	0.80357	0.884000	0.51177	0.359000	0.20233	1.336000	0.45506	0.485000	0.47835	GTC	G|0.719;A|0.281	0.281	strong		0.642	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
SLCO4C1	353189	hgsc.bcm.edu	37	5	101631790	101631790	+	Silent	SNP	T	T	G	rs10479190	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:101631790T>G	ENST00000310954.6	-	1	463	c.177A>C	c.(175-177)ccA>ccC	p.P59P		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		GAGATGGCTCTGGTGACTTCT	0.582													T|||	711	0.141973	0.0121	0.1398	5008	,	,		15190	0.1558		0.2833	False		,,,				2504	0.1595				p.P59P		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.A177C						PASS	.	T		209,4197	126.1+/-163.2	7,195,2001	76.0	80.0	79.0		177	-2.2	0.0	5	dbSNP_119	79	2096,6504	361.0+/-332.2	262,1572,2466	no	coding-synonymous	SLCO4C1	NM_180991.4		269,1767,4467	GG,GT,TT		24.3721,4.7435,17.7226		59/725	101631790	2305,10701	2203	4300	6503	SO:0001819	synonymous_variant	353189	exon1			TGGCTCTGGTGAC	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.177A>C	5.37:g.101631790T>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_180991		Silent	SNP	ENST00000310954.6	37	CCDS34205.1																																																																																			T|0.830;G|0.170	0.170	strong		0.582	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
GCLC	2729	hgsc.bcm.edu	37	6	53387230	53387230	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:53387230C>T	ENST00000229416.6	-	2	729	c.246G>A	c.(244-246)ggG>ggA	p.G82G	GCLC_ENST00000514004.1_Silent_p.G82G	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	82					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	TTGTCCTTTCCCCCTTCTCTT	0.378																																					p.G82G		Atlas-SNP	.											.	GCLC	58	.	0			c.G246A						PASS	.						115.0	112.0	113.0					6																	53387230		2203	4300	6503	SO:0001819	synonymous_variant	2729	exon2			CCTTTCCCCCTTC	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.246G>A	6.37:g.53387230C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	12	0.131868	NM_001197115	Q14399	Silent	SNP	ENST00000229416.6	37	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	C	9.717	1.158655	0.21454	.	.	ENSG00000001084	ENST00000513939	T	0.72725	-0.68	5.67	1.4	0.22301	.	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34925	-0.9809	7	0.02654	T	1	.	4.0727	0.09889	0.237:0.4463:0.0:0.3167	.	.	.	.	E	70	ENSP00000424211:G70E	ENSP00000424211:G70E	G	-	2	0	GCLC	53495189	0.003000	0.15002	1.000000	0.80357	0.995000	0.86356	-1.302000	0.02746	0.193000	0.20303	0.585000	0.79938	GGG	.	.	none		0.378	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2		
MST1L	11223	hgsc.bcm.edu	37	1	17083782	17083782	+	RNA	SNP	A	A	C	rs200844502	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17083782A>C	ENST00000455405.2	-	0	806							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GACACGCGTGAAGACGGCTGG	0.542																																					p.F672C		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	0			c.T2015G						PASS	.																																					11223	exon15			CGCGTGAAGACGG	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17083782A>C		Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	444	240	0.540541	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	12.47	1.948793	0.34377	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.44483	D	0.000459	T	0.65333	0.2681	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.69903	-0.5019	6	0.87932	D	0	.	5.2253	0.15391	0.9998:0.0:2.0E-4:0.0	.	672;698	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	C	672;698	.	ENSP00000439273:F672C	F	-	2	0	MST1P9	16956369	1.000000	0.71417	0.928000	0.36995	0.000000	0.00434	3.843000	0.55865	0.419000	0.25927	0.000000	0.15137	TTC	A|0.972;C|0.029	0.029	strong		0.542	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
SVEP1	79987	hgsc.bcm.edu	37	9	113212454	113212454	+	Missense_Mutation	SNP	A	A	T	rs10817021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:113212454A>T	ENST00000401783.2	-	24	4324	c.3988T>A	c.(3988-3990)Ttg>Atg	p.L1330M	SVEP1_ENST00000374469.1_Missense_Mutation_p.L1307M|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000302728.8_Missense_Mutation_p.L1330M	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1330	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		L -> M (in dbSNP:rs10817021).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CATTTGCACAAGAATCCCCCA	0.473													A|||	512	0.102236	0.0061	0.0951	5008	,	,		18786	0.0327		0.1531	False		,,,				2504	0.2566				p.L1330M		Atlas-SNP	.											.	SVEP1	326	.	0			c.T3988A						PASS	.	A	MET/LEU	120,3630		1,118,1756	191.0	179.0	183.0		3988	0.5	1.0	9	dbSNP_120	183	1400,6820		125,1150,2835	yes	missense	SVEP1	NM_153366.3	15	126,1268,4591	TT,TA,AA		17.0316,3.2,12.6984	benign	1330/3572	113212454	1520,10450	1875	4110	5985	SO:0001583	missense	79987	exon24			TGCACAAGAATCC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.3988T>A	9.37:g.113212454A>T	ENSP00000384917:p.Leu1330Met	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	206	108	0.524272	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	170	0.07783882783882784	6	0.012195121951219513	34	0.09392265193370165	17	0.02972027972027972	113	0.14907651715039577	A	11.24	1.579014	0.28180	0.032	0.170316	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.61274	0.12;0.12;0.12	5.74	0.456	0.16655	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.102910	0.06717	N	0.774184	T	0.00109	0.0003	N	0.17082	0.46	0.50632	P	1.1799999999995148E-4	B;B	0.19445	0.036;0.012	B;B	0.21360	0.034;0.013	T	0.08086	-1.0739	9	0.46703	T	0.11	.	1.629	0.02729	0.4634:0.1333:0.2752:0.1282	rs10817021;rs52835013;rs10817021	1330;1330	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	M	1330;1307;1330	ENSP00000384917:L1330M;ENSP00000363593:L1307M;ENSP00000304118:L1330M	ENSP00000304118:L1330M	L	-	1	2	SVEP1	112252275	0.003000	0.15002	0.997000	0.53966	0.752000	0.42762	0.033000	0.13754	0.108000	0.17862	-0.334000	0.08254	TTG	A|0.904;T|0.096	0.096	strong		0.473	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PLXNC1	10154	hgsc.bcm.edu	37	12	94543506	94543506	+	Silent	SNP	C	C	T	rs2230754	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:94543506C>T	ENST00000258526.4	+	1	1008	c.759C>T	c.(757-759)taC>taT	p.Y253Y		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	253	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CCTACAACTACACGAGCGGCG	0.682													C|||	2261	0.451478	0.5204	0.4654	5008	,	,		15562	0.4831		0.34	False		,,,				2504	0.4305				p.Y253Y		Atlas-SNP	.											PLXNC1,rectum,carcinoma,0,1	PLXNC1	135	1	0			c.C759T						PASS	.	C		1851,2441		433,985,728	31.0	36.0	34.0		759	4.1	1.0	12	dbSNP_98	34	3103,5439		592,1919,1760	no	coding-synonymous	PLXNC1	NM_005761.2		1025,2904,2488	TT,TC,CC		36.3264,43.1267,38.6006		253/1569	94543506	4954,7880	2146	4271	6417	SO:0001819	synonymous_variant	10154	exon1			CAACTACACGAGC	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.759C>T	12.37:g.94543506C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	29	19	0.655172	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			C|0.560;T|0.440	0.440	strong		0.682	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
DPM2	8818	hgsc.bcm.edu	37	9	130698029	130698029	+	Missense_Mutation	SNP	G	G	C	rs7997	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:130698029G>C	ENST00000314392.8	-	4	890	c.227C>G	c.(226-228)aCc>aGc	p.T76S	RP11-203J24.8_ENST00000608805.1_RNA|RP11-203J24.8_ENST00000587978.1_RNA|RP11-203J24.8_ENST00000592240.1_RNA|RP11-203J24.8_ENST00000587355.1_RNA|RP11-203J24.8_ENST00000590283.1_RNA|RP11-203J24.8_ENST00000588890.1_RNA|RP11-203J24.8_ENST00000586374.1_RNA|RP11-203J24.8_ENST00000591408.1_RNA	NM_003863.3	NP_003854.1	O94777	DPM2_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 2, regulatory subunit	76			T -> S (in dbSNP:rs7997). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19054851, ECO:0000269|Ref.6}.		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|dolichol metabolic process (GO:0019348)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked mannosylation (GO:0035269)|regulation of protein stability (GO:0031647)	dolichol-phosphate-mannose synthase complex (GO:0033185)|endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of endoplasmic reticulum membrane (GO:0030176)|perinuclear region of cytoplasm (GO:0048471)	dolichyl-phosphate beta-D-mannosyltransferase activity (GO:0004582)|enzyme regulator activity (GO:0030234)			lung(1)	1						CACTCTCTTGGTCTTCAGCAT	0.577													C|||	3423	0.683506	0.6467	0.8545	5008	,	,		21281	0.4484		0.8708	False		,,,				2504	0.6616				p.T76S		Atlas-SNP	.											.	DPM2	6	.	0			c.C227G						PASS	.	C	SER/THR	2996,1410	461.7+/-353.0	1022,952,229	138.0	115.0	123.0		227	2.7	0.4	9	dbSNP_52	123	7466,1134	233.5+/-266.7	3251,964,85	yes	missense	DPM2	NM_003863.3	58	4273,1916,314	CC,CG,GG		13.186,32.0018,19.5602	benign	76/85	130698029	10462,2544	2203	4300	6503	SO:0001583	missense	8818	exon4			CTCTTGGTCTTCA	AB013361	CCDS6886.1	9q34.13	2013-02-26			ENSG00000136908	ENSG00000136908			3006	protein-coding gene	gene with protein product	"""DPM synthase complex subunit"""	603564				9724629	Standard	NM_003863		Approved	MGC21559, MGC111193	uc004bsv.2	O94777	OTTHUMG00000020725	ENST00000314392.8:c.227C>G	9.37:g.130698029G>C	ENSP00000322181:p.Thr76Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_003863	Q5XKK9|Q6FGH3	Missense_Mutation	SNP	ENST00000314392.8	37	CCDS6886.1	1541	0.7055860805860806	335	0.6808943089430894	303	0.8370165745856354	248	0.43356643356643354	655	0.8641160949868074	C	0.030	-1.343316	0.01277	0.679982	0.86814	ENSG00000136908	ENST00000314392	T	0.60672	0.17	5.06	2.74	0.32292	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999913218	B	0.02656	0.0	B	0.01281	0.0	T	0.43163	-0.9408	7	0.02654	T	1	.	4.0792	0.09919	0.0:0.1936:0.1787:0.6277	rs7997;rs3209321;rs10760517;rs60872613;rs7997	76	O94777	DPM2_HUMAN	S	76	ENSP00000322181:T76S	ENSP00000322181:T76S	T	-	2	0	DPM2	129737850	0.965000	0.33210	0.392000	0.26245	0.466000	0.32739	0.141000	0.16076	0.058000	0.16222	-1.218000	0.01608	ACC	G|0.241;C|0.759	0.759	strong		0.577	DPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054324.1	NM_003863	
ANK2	287	hgsc.bcm.edu	37	4	114278277	114278277	+	Missense_Mutation	SNP	C	C	T	rs3733617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:114278277C>T	ENST00000357077.4	+	38	8556	c.8503C>T	c.(8503-8505)Cca>Tca	p.P2835S	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.P2802S|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2835					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		AGCAGAATCTCCACAAGCAGA	0.413													C|||	941	0.187899	0.4206	0.1571	5008	,	,		21717	0.1141		0.0447	False		,,,				2504	0.1186				p.P2835S		Atlas-SNP	.											.	ANK2	576	.	0			c.C8503T						PASS	.	C	,SER/PRO,	1509,2897	478.5+/-358.2	254,1001,948	114.0	113.0	113.0		,8503,	2.5	0.0	4	dbSNP_107	113	393,8207	126.3+/-184.8	6,381,3913	yes	intron,missense,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,74,	260,1382,4861	TT,TC,CC		4.5698,34.2488,14.624	,benign,	,2835/3958,	114278277	1902,11104	2203	4300	6503	SO:0001583	missense	287	exon38			GAATCTCCACAAG	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.8503C>T	4.37:g.114278277C>T	ENSP00000349588:p.Pro2835Ser	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	367	0.16804029304029305	222	0.45121951219512196	49	0.13535911602209943	67	0.11713286713286714	29	0.03825857519788918	C	10.80	1.452375	0.26074	0.342488	0.045698	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.66815	-0.21;-0.23	5.61	2.54	0.30619	.	0.666624	0.13666	N	0.371200	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.08055	0.001;0.003	T	0.42999	-0.9418	8	.	.	.	.	4.192	0.10426	0.2746:0.5113:0.13:0.0841	rs3733617;rs61209218;rs3733617	2802;2835	Q01484;Q01484-4	ANK2_HUMAN;.	S	2835;2802	ENSP00000349588:P2835S;ENSP00000264366:P2802S	.	P	+	1	0	ANK2	114497726	0.000000	0.05858	0.038000	0.18304	0.068000	0.16541	-0.389000	0.07342	0.674000	0.31244	0.650000	0.86243	CCA	C|0.831;T|0.169	0.169	strong		0.413	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
STKLD1	169436	hgsc.bcm.edu	37	9	136268084	136268084	+	Missense_Mutation	SNP	A	A	G	rs3124747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136268084A>G	ENST00000371957.3	+	14	1524	c.1417A>G	c.(1417-1419)Aaa>Gaa	p.K473E	C9orf96_ENST00000371955.1_Intron	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		473			K -> E (in dbSNP:rs3124747). {ECO:0000269|PubMed:15489334}.				ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CAGCTCCCTCAAAAGCAGGGA	0.667													G|||	2354	0.470048	0.3533	0.5648	5008	,	,		17050	0.2837		0.6889	False		,,,				2504	0.5276				p.K473E		Atlas-SNP	.											.	C9orf96	77	.	0			c.A1417G						PASS	.	G	GLU/LYS	1810,2574		388,1034,770	33.0	29.0	30.0		1417	-4.6	0.0	9	dbSNP_103	30	5614,2966		1877,1860,553	yes	missense	C9orf96	NM_153710.3	56	2265,2894,1323	GG,GA,AA		34.5688,41.2865,42.7337	benign	473/681	136268084	7424,5540	2192	4290	6482	SO:0001583	missense	169436	exon14			TCCCTCAAAAGCA																												ENST00000371957.3:c.1417A>G	9.37:g.136268084A>G	ENSP00000361025:p.Lys473Glu	Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	1069	0.48946886446886445	178	0.3617886178861789	197	0.5441988950276243	157	0.2744755244755245	537	0.7084432717678101	G	0.426	-0.905737	0.02453	0.412865	0.654312	ENSG00000198870	ENST00000371957	T	0.46063	0.88	4.18	-4.6	0.03390	Armadillo-like helical (1);Armadillo-type fold (1);	1.456700	0.04337	N	0.353447	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37407	-0.9707	9	0.02654	T	1	-0.0051	6.4652	0.21977	0.4299:0.291:0.2791:0.0	rs3124747;rs9411511;rs17150551;rs3124747	473	Q8NE28	SGK71_HUMAN	E	473	ENSP00000361025:K473E	ENSP00000361025:K473E	K	+	1	0	C9orf96	135257905	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.236000	0.02925	-0.960000	0.03613	-1.608000	0.00805	AAA	A|0.479;G|0.521	0.521	strong		0.667	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
PCDHA11	56138	hgsc.bcm.edu	37	5	140250252	140250252	+	Silent	SNP	T	T	C	rs251372	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140250252T>C	ENST00000398640.2	+	1	1564	c.1564T>C	c.(1564-1566)Ttg>Ctg	p.L522L	PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	522	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGCAGCCGTTGGACCACGA	0.682													.|||	2249	0.449081	0.3169	0.4164	5008	,	,		15881	0.4375		0.4841	False		,,,				2504	0.6268				p.L522L		Atlas-SNP	.											.	PCDHA11	209	.	0			c.T1564C						PASS	.	T	,,,,,,,,,,,,,,	1414,2978		253,908,1035	61.0	68.0	65.0		,,1564,,,,,,,,,,,,1564	3.4	1.0	5	dbSNP_79	65	4112,4450		995,2122,1164	no	intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031861.1	,,,,,,,,,,,,,,	1248,3030,2199	CC,CT,TT		48.0262,32.1949,42.6586	,,,,,,,,,,,,,,	,,522/950,,,,,,,,,,,,522/811	140250252	5526,7428	2196	4281	6477	SO:0001819	synonymous_variant	56138	exon1			CAGCCGTTGGACC	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1564T>C	5.37:g.140250252T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_018902	B2RN58|O75279	Silent	SNP	ENST00000398640.2	37	CCDS47284.1																																																																																			T|0.571;C|0.429	0.429	strong		0.682	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902	
ZNF792	126375	hgsc.bcm.edu	37	19	35449082	35449082	+	Silent	SNP	G	G	A	rs3746243	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35449082G>A	ENST00000404801.1	-	4	2063	c.1677C>T	c.(1675-1677)gaC>gaT	p.D559D	ZNF792_ENST00000605484.1_Silent_p.D492D	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	559					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CGTAAGGCCTGTCTGGTTTGT	0.517													A|||	1314	0.26238	0.2277	0.1931	5008	,	,		22050	0.3998		0.1839	False		,,,				2504	0.2975				p.D559D	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											.	ZNF792	46	.	0			c.C1677T						PASS	.	A		967,3439	733.5+/-410.5	102,763,1338	117.0	91.0	100.0		1677	-5.6	0.0	19	dbSNP_107	100	1516,7084	747.6+/-407.3	123,1270,2907	no	coding-synonymous	ZNF792	NM_175872.4		225,2033,4245	AA,AG,GG		17.6279,21.9473,19.0912		559/633	35449082	2483,10523	2203	4300	6503	SO:0001819	synonymous_variant	126375	exon4			AGGCCTGTCTGGT	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1677C>T	19.37:g.35449082G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Silent	SNP	ENST00000404801.1	37	CCDS12440.2																																																																																			G|0.769;A|0.231	0.231	strong		0.517	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
NIN	51199	hgsc.bcm.edu	37	14	51202311	51202311	+	Missense_Mutation	SNP	G	G	C	rs2295847	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:51202311G>C	ENST00000382041.3	-	28	5990	c.5800C>G	c.(5800-5802)Caa>Gaa	p.Q1934E	NIN_ENST00000382043.4_Missense_Mutation_p.Q1221E|NIN_ENST00000245441.5_Missense_Mutation_p.Q1934E|NIN_ENST00000453196.1_Missense_Mutation_p.Q1934E|NIN_ENST00000530997.2_Missense_Mutation_p.Q1934E|NIN_ENST00000324330.9_Missense_Mutation_p.Q1934E|NIN_ENST00000389868.3_Missense_Mutation_p.Q1221E	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1934			Q -> E (in dbSNP:rs2295847).		centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TCTAATTCTTGTTCAAGGGAA	0.338			T	PDGFRB	MPD								G|||	968	0.193291	0.0076	0.2305	5008	,	,		18869	0.5228		0.1153	False		,,,				2504	0.1585				p.Q1934E		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C5800G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN	119,4285	87.8+/-126.4	3,113,2086	113.0	98.0	103.0		3661,5800,5800,5800	3.5	1.0	14	dbSNP_100	103	913,7685	203.1+/-246.2	47,819,3433	yes	missense,missense,missense,missense	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	29,29,29,29	50,932,5519	CC,CG,GG		10.6187,2.7021,7.9372	benign,benign,benign,benign	1221/1378,1934/2134,1934/2047,1934/2091	51202311	1032,11970	2202	4299	6501	SO:0001583	missense	51199	exon28			ATTCTTGTTCAAG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.5800C>G	14.37:g.51202311G>C	ENSP00000371472:p.Gln1934Glu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	470|470	0.21520146520146521|0.21520146520146521	4|4	0.008130081300813009|0.008130081300813009	75|75	0.20718232044198895|0.20718232044198895	295|295	0.5157342657342657|0.5157342657342657	96|96	0.1266490765171504|0.1266490765171504	G|G	15.18|15.18	2.756350|2.756350	0.49362|0.49362	0.027021|0.027021	0.106187|0.106187	ENSG00000100503|ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000389868;ENST00000382043;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196|ENST00000530997;ENST00000389869;ENST00000530853	T;T;T;T;T;T|.	0.10668|.	3.65;2.85;2.89;3.41;3.37;3.38|.	5.45|5.45	3.55|3.55	0.40652|0.40652	.|.	0.674545|.	0.14169|.	N|.	0.336878|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.49915|0.49915	P|P	1.6499999999997073E-4|1.6499999999997073E-4	B;B;B;B;B|.	0.28378|.	0.094;0.047;0.072;0.209;0.033|.	B;B;B;B;B|.	0.30646|.	0.034;0.031;0.054;0.118;0.025|.	T|T	0.48747|0.48747	-0.9008|-0.9008	9|4	0.20046|.	T|.	0.44|.	-0.0051|-0.0051	11.9354|11.9354	0.52870|0.52870	0.0:0.1274:0.728:0.1446|0.0:0.1274:0.728:0.1446	rs2295847;rs52793228;rs58858000|rs2295847;rs52793228;rs58858000	1940;1934;1934;1221;1934|.	Q8N4C6-5;C9J066;Q8N4C6;Q5BKU3;Q8N4C6-7|.	.;.;NIN_HUMAN;.;.|.	E|R	1934;1917;1221;1221;1940;1934;1934;1934|1424	ENSP00000245441:Q1934E;ENSP00000374518:Q1221E;ENSP00000371474:Q1221E;ENSP00000371472:Q1934E;ENSP00000324210:Q1934E;ENSP00000412391:Q1934E|.	ENSP00000245441:Q1934E|.	Q|T	-|-	1|2	0|0	NIN|NIN	50272061|50272061	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.986000|0.986000	0.74619|0.74619	2.766000|2.766000	0.47629|0.47629	0.873000|0.873000	0.35799|0.35799	0.655000|0.655000	0.94253|0.94253	CAA|ACA	G|0.873;C|0.127	0.127	strong		0.338	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
MUC4	4585	hgsc.bcm.edu	37	3	195512118	195512118	+	Silent	SNP	G	G	A	rs199976782		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195512118G>A	ENST00000463781.3	-	2	6792	c.6333C>T	c.(6331-6333)acC>acT	p.T2111T	MUC4_ENST00000475231.1_Silent_p.T2111T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CATGAAGAGCGGTGGCGTGAC	0.572																																					p.T2111T		Atlas-SNP	.											MUC4_ENST00000463781,bladder,carcinoma,0,1	MUC4	1505	1	0			c.C6333T						PASS	.	G	,,	7,1375		0,7,684	72.0	61.0	64.0		,6333,		0.0	3		64	76,3104		0,76,1514	no	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	0,83,2198	AA,AG,GG		2.3899,0.5065,1.8194	,,	,2111/5413,	195512118	83,4479	691	1590	2281	SO:0001819	synonymous_variant	4585	exon2			AAGAGCGGTGGCG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6333C>T	3.37:g.195512118G>A		Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	590	85	0.144068	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.996;A|0.004	0.004	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NRAP	4892	hgsc.bcm.edu	37	10	115389366	115389366	+	Missense_Mutation	SNP	G	G	A	rs2286735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115389366G>A	ENST00000359988.3	-	19	2265	c.2021C>T	c.(2020-2022)gCc>gTc	p.A674V	NRAP_ENST00000369360.3_Missense_Mutation_p.A647V|NRAP_ENST00000360478.3_Missense_Mutation_p.A639V|NRAP_ENST00000369358.4_Missense_Mutation_p.A682V	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GAGCCCATAGGCCTTCTTGGC	0.498													G|||	1376	0.27476	0.1823	0.3948	5008	,	,		20479	0.2817		0.2962	False		,,,				2504	0.2853				p.A674V		Atlas-SNP	.											.	NRAP	208	.	0			c.C2021T						PASS	.	G	VAL/ALA,VAL/ALA	940,3466	354.9+/-312.8	96,748,1359	118.0	100.0	106.0		1916,2021	3.3	1.0	10	dbSNP_100	106	2620,5980	424.4+/-354.6	371,1878,2051	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	64,64	467,2626,3410	AA,AG,GG		30.4651,21.3345,27.372	benign,benign	639/1696,674/1731	115389366	3560,9446	2203	4300	6503	SO:0001583	missense	4892	exon19			CCATAGGCCTTCT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2021C>T	10.37:g.115389366G>A	ENSP00000353078:p.Ala674Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	626	0.2866300366300366	111	0.22560975609756098	132	0.36464088397790057	153	0.2674825174825175	230	0.3034300791556728	G	14.72	2.619352	0.46736	0.213345	0.304651	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.19	3.31	0.37934	.	0.101608	0.64402	N	0.000002	T	0.00012	0.0000	L	0.53617	1.68	0.25327	P	0.9890645	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.18263	0.021;0.015;0.008	T	0.32534	-0.9903	9	0.40728	T	0.16	.	8.5936	0.33701	0.2316:0.0:0.7684:0.0	rs2286735;rs17772920;rs58094688;rs2286735	674;639;674	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	V	682;647;674;639	ENSP00000358365:A682V;ENSP00000358367:A647V;ENSP00000353078:A674V;ENSP00000353666:A639V	ENSP00000353078:A674V	A	-	2	0	NRAP	115379356	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.737000	0.68606	1.319000	0.45190	0.561000	0.74099	GCC	G|0.726;N|0.001	.	strong		0.498	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
GRK6	2870	hgsc.bcm.edu	37	5	176863519	176863519	+	Silent	SNP	G	G	C	rs1130857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176863519G>C	ENST00000355472.5	+	13	1560	c.1392G>C	c.(1390-1392)ccG>ccC	p.P464P	GRK6_ENST00000355958.5_Silent_p.P464P|PRR7-AS1_ENST00000425316.3_RNA|GRK6_ENST00000528793.1_Silent_p.P464P|GRK6_ENST00000507633.1_Silent_p.P464P|GRK6_ENST00000393576.3_Silent_p.P430P	NM_001004106.2|NM_002082.3	NP_001004106.1|NP_002073.2	P43250	GRK6_HUMAN	G protein-coupled receptor kinase 6	464	AGC-kinase C-terminal.				regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)			breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(5)|stomach(1)	25	all_cancers(89;1.15e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGAGCCGCCGTTCAAGCCTG	0.652													C|||	1813	0.362021	0.3941	0.3646	5008	,	,		13271	0.2629		0.5	False		,,,				2504	0.2771				p.P464P		Atlas-SNP	.											.	GRK6	48	.	0			c.G1392C						PASS	.	C	,,	1828,2568		405,1018,775	26.0	30.0	29.0		1392,1392,1392	0.1	1.0	5	dbSNP_86	29	4662,3920		1281,2100,910	no	coding-synonymous,coding-synonymous,coding-synonymous	GRK6	NM_001004105.2,NM_001004106.2,NM_002082.3	,,	1686,3118,1685	CC,CG,GG		45.677,41.5833,49.9923	,,	464/561,464/577,464/590	176863519	6490,6488	2198	4291	6489	SO:0001819	synonymous_variant	2870	exon13			GCCGCCGTTCAAG		CCDS34303.1, CCDS43406.1, CCDS47348.1	5q35	2011-01-14	2004-02-04	2004-02-06	ENSG00000198055	ENSG00000198055			4545	protein-coding gene	gene with protein product		600869		GPRK6		8415712	Standard	NM_002082		Approved		uc021yiu.1	P43250	OTTHUMG00000163401	ENST00000355472.5:c.1392G>C	5.37:g.176863519G>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_002082	O60541|Q13652	Silent	SNP	ENST00000355472.5	37	CCDS34303.1																																																																																			G|0.531;C|0.469	0.469	strong		0.652	GRK6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373204.1	NM_002082	
GIP	2695	hgsc.bcm.edu	37	17	47039132	47039132	+	Missense_Mutation	SNP	T	T	C	rs2291725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:47039132T>C	ENST00000357424.2	-	4	407	c.307A>G	c.(307-309)Agt>Ggt	p.S103G		NM_004123.2	NP_004114.1	P09681	GIP_HUMAN	gastric inhibitory polypeptide	103			S -> G (in dbSNP:rs2291725). {ECO:0000269|PubMed:15489334}.		adult locomotory behavior (GO:0008344)|cellular protein metabolic process (GO:0044267)|digestive system development (GO:0055123)|endocrine pancreas development (GO:0031018)|exploration behavior (GO:0035640)|female pregnancy (GO:0007565)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of glucagon secretion (GO:0070094)|positive regulation of glucose transport (GO:0010828)|positive regulation of insulin secretion (GO:0032024)|regulation of insulin secretion (GO:0050796)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to lipid (GO:0033993)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|response to selenium ion (GO:0010269)|response to starvation (GO:0042594)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|secretory granule lumen (GO:0034774)	hormone activity (GO:0005179)	p.S103G(1)		lung(2)|skin(1)|stomach(1)	4						TTAGCTTGACTGGCCAGCTCC	0.612													T|||	2116	0.422524	0.0651	0.451	5008	,	,		14956	0.6835		0.5497	False		,,,				2504	0.4857				p.S103G		Atlas-SNP	.											GIP,NS,carcinoma,0,1	GIP	15	1	1	Substitution - Missense(1)	stomach(1)	c.A307G						PASS	.	T	GLY/SER	628,3778	268.6+/-268.5	53,522,1628	45.0	36.0	39.0		307	-5.1	0.0	17	dbSNP_100	39	4604,3996	589.1+/-392.5	1220,2164,916	yes	missense	GIP	NM_004123.2	56	1273,2686,2544	CC,CT,TT		46.4651,14.2533,40.2276	benign	103/154	47039132	5232,7774	2203	4300	6503	SO:0001583	missense	2695	exon4			CTTGACTGGCCAG		CCDS11542.1	17q21.3-q22	2013-02-26			ENSG00000159224	ENSG00000159224		"""Endogenous ligands"""	4270	protein-coding gene	gene with protein product	"""glucose-dependent insulinotropic polypeptide"""	137240				2739653	Standard	NM_004123		Approved		uc002iol.1	P09681	OTTHUMG00000161171	ENST00000357424.2:c.307A>G	17.37:g.47039132T>C	ENSP00000350005:p.Ser103Gly	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_004123	Q4VB42|Q6NTD3	Missense_Mutation	SNP	ENST00000357424.2	37	CCDS11542.1	1015	0.46474358974358976	35	0.07113821138211382	157	0.43370165745856354	401	0.701048951048951	422	0.5567282321899736	T	2.629	-0.286910	0.05605	0.142533	0.535349	ENSG00000159224	ENST00000357424	T	0.23950	1.88	5.03	-5.07	0.02938	.	1.314460	0.05040	N	0.476193	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36672	-0.9738	9	0.11485	T	0.65	-3.0984	4.5241	0.11973	0.1114:0.5107:0.1672:0.2106	rs2291725;rs17429827;rs57180664;rs2291725	103	P09681	GIP_HUMAN	G	103	ENSP00000350005:S103G	ENSP00000350005:S103G	S	-	1	0	GIP	44394131	0.007000	0.16637	0.000000	0.03702	0.000000	0.00434	0.042000	0.13949	-1.203000	0.02652	-1.140000	0.01884	AGT	T|0.575;C|0.425	0.425	strong		0.612	GIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364044.1	NM_004123	
CYP1A2	1544	hgsc.bcm.edu	37	15	75047426	75047426	+	Silent	SNP	C	C	T	rs2470890	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75047426C>T	ENST00000343932.4	+	7	1611	c.1548C>T	c.(1546-1548)aaC>aaT	p.N516N		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	515					alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	TCTCCATCAACTGAAGAAGAC	0.577													C|||	1183	0.236222	0.028	0.3271	5008	,	,		14798	0.1637		0.5964	False		,,,				2504	0.1575				p.N516N		Atlas-SNP	.											.	CYP1A2	70	.	0			c.C1548T						PASS	.	C		547,3847	238.0+/-249.6	40,467,1690	30.0	28.0	28.0		1548	0.6	0.3	15	dbSNP_100	28	5619,2973	631.2+/-398.5	1863,1893,540	no	coding-synonymous	CYP1A2	NM_000761.3		1903,2360,2230	TT,TC,CC		34.602,12.4488,47.4819		516/517	75047426	6166,6820	2197	4296	6493	SO:0001819	synonymous_variant	1544	exon7			CATCAACTGAAGA	AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.1548C>T	15.37:g.75047426C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	41	23	0.560976	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Silent	SNP	ENST00000343932.4	37	CCDS32293.1																																																																																			C|0.616;T|0.384	0.384	strong		0.577	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
TSPAN3	10099	hgsc.bcm.edu	37	15	77344793	77344793	+	Silent	SNP	T	T	A	rs11737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:77344793T>A	ENST00000267970.4	-	6	876	c.603A>T	c.(601-603)gtA>gtT	p.V201V	TSPAN3_ENST00000558745.1_5'UTR|TSPAN3_ENST00000561277.1_5'UTR|TSPAN3_ENST00000559494.1_Silent_p.V112V|TSPAN3_ENST00000346495.2_Silent_p.V176V|TSPAN3_ENST00000424443.3_Silent_p.V137V|TSPAN3_ENST00000558394.1_5'Flank	NM_001168412.1|NM_005724.5|NM_198902.2	NP_001161884.1|NP_005715.1|NP_944492.1	O60637	TSN3_HUMAN	tetraspanin 3	201						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	10				all cancers(203;1.14e-19)		GCTTCTTCACTACTAGAGCCT	0.458													A|||	2460	0.491214	0.3858	0.5504	5008	,	,		19688	0.4028		0.6859	False		,,,				2504	0.4826				p.V201V		Atlas-SNP	.											.	TSPAN3	21	.	0			c.A603T						PASS	.	A	,,	1987,2405	616.5+/-392.8	445,1097,654	137.0	110.0	119.0		411,603,528	4.3	1.0	15	dbSNP_52	119	5877,2711	433.0+/-357.3	2032,1813,449	no	coding-synonymous,coding-synonymous,coding-synonymous	TSPAN3	NM_001168412.1,NM_005724.5,NM_198902.2	,,	2477,2910,1103	AA,AT,TT		31.5673,45.2413,39.4145	,,	137/190,201/254,176/229	77344793	7864,5116	2196	4294	6490	SO:0001819	synonymous_variant	10099	exon6			CTTCACTACTAGA		CCDS10292.1, CCDS10293.1, CCDS53963.1	15q23	2013-02-14	2005-03-21	2005-03-21	ENSG00000140391	ENSG00000140391		"""Tetraspanins"""	17752	protein-coding gene	gene with protein product		613134	"""transmembrane 4 superfamily member 8"""	TM4SF8			Standard	NM_005724		Approved	TM4-A, TSPAN-3	uc002bcj.3	O60637	OTTHUMG00000143728	ENST00000267970.4:c.603A>T	15.37:g.77344793T>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_005724	A6NEH4|B3KQQ2|B4DP19|Q9BW22|Q9NVX9	Silent	SNP	ENST00000267970.4	37	CCDS10292.1																																																																																			T|0.433;A|0.567	0.567	strong		0.458	TSPAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289792.3	NM_005724	
SLC25A37	51312	hgsc.bcm.edu	37	8	23423758	23423758	+	Silent	SNP	G	G	A	rs10992	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:23423758G>A	ENST00000519973.1	+	2	546	c.348G>A	c.(346-348)ccG>ccA	p.P116P	SLC25A37_ENST00000517923.1_3'UTR	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	116					iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		GTGCAGGGCCGGCCCATGCCA	0.498													G|||	2031	0.405551	0.1036	0.5317	5008	,	,		18023	0.372		0.6551	False		,,,				2504	0.502				p.P116P		Atlas-SNP	.											SLC25A37,caecum,carcinoma,+2,1	SLC25A37	27	1	0			c.G348A						PASS	.	G		895,2987		117,661,1163	76.0	74.0	75.0		348	-4.7	0.9	8	dbSNP_52	75	5628,2642		1930,1768,437	no	coding-synonymous	SLC25A37	NM_016612.2		2047,2429,1600	AA,AG,GG		31.9468,23.0551,46.3216		116/339	23423758	6523,5629	1941	4135	6076	SO:0001819	synonymous_variant	51312	exon2			AGGGCCGGCCCAT	AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"""Solute carriers"""	29786	protein-coding gene	gene with protein product	"""mitoferrin"""	610387	"""solute carrier family 25, member 37"""			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.348G>A	8.37:g.23423758G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	162	79	0.487654	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Silent	SNP	ENST00000519973.1	37	CCDS47828.1																																																																																			G|0.520;A|0.480	0.480	strong		0.498	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612	
C11orf24	53838	hgsc.bcm.edu	37	11	68030015	68030015	+	Missense_Mutation	SNP	C	C	T	rs901827	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:68030015C>T	ENST00000304271.6	-	4	850	c.448G>A	c.(448-450)Gca>Aca	p.A150T	C11orf24_ENST00000530166.1_5'UTR|C11orf24_ENST00000533310.1_Intron	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	150			A -> T (in dbSNP:rs901827).			Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						CTGGAGGCTGCAGTCGTGGGA	0.642													C|||	1755	0.350439	0.3359	0.2911	5008	,	,		17897	0.4127		0.4473	False		,,,				2504	0.2485				p.A150T	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.G448A						PASS	.	C	THR/ALA	1520,2880	475.7+/-357.4	252,1016,932	39.0	39.0	39.0		448	-1.7	0.0	11	dbSNP_86	39	3732,4856	524.7+/-380.6	816,2100,1378	yes	missense	C11orf24	NM_022338.3	58	1068,3116,2310	TT,TC,CC		43.456,34.5455,40.4373	benign	150/450	68030015	5252,7736	2200	4294	6494	SO:0001583	missense	53838	exon4			AGGCTGCAGTCGT	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.448G>A	11.37:g.68030015C>T	ENSP00000307264:p.Ala150Thr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	204	96	0.470588	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	37	CCDS8180.1	863	0.39514652014652013	195	0.39634146341463417	98	0.27071823204419887	239	0.4178321678321678	331	0.4366754617414248	C	3.202	-0.163472	0.06502	0.345455	0.43456	ENSG00000171067	ENST00000304271	T	0.33865	1.39	3.24	-1.71	0.08133	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15930	0.015	B	0.11329	0.006	T	0.42085	-0.9472	8	0.02654	T	1	.	9.1596	0.37014	0.0:0.3205:0.5829:0.0965	rs901827;rs3187860;rs3802747;rs17415819;rs52836565;rs57250660;rs901827	150	Q96F05	CK024_HUMAN	T	150	ENSP00000307264:A150T	ENSP00000307264:A150T	A	-	1	0	C11orf24	67786591	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.128000	0.10531	-0.761000	0.04670	-0.515000	0.04445	GCA	C|0.589;A|0.002	.	strong		0.642	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338	
FANCI	55215	hgsc.bcm.edu	37	15	89836228	89836228	+	Missense_Mutation	SNP	G	G	C	rs2283432	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89836228G>C	ENST00000310775.7	+	22	2311	c.2225G>C	c.(2224-2226)tGt>tCt	p.C742S	FANCI_ENST00000300027.8_Missense_Mutation_p.C742S	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	742			C -> S (in dbSNP:rs2283432). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					AATAATATCTGTGCTTTTCTT	0.313								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	1327	0.264976	0.0393	0.3473	5008	,	,		18777	0.3135		0.3837	False		,,,				2504	0.3395				p.C742S		Atlas-SNP	.											FANCI_ENST00000310775,NS,adenoma,0,2	FANCI	129	2	0			c.G2225C						PASS	.	G	SER/CYS,SER/CYS	419,3979	203.8+/-226.2	19,381,1799	118.0	119.0	119.0		2225,2225	4.9	1.0	15	dbSNP_100	119	3349,5249	495.5+/-374.1	653,2043,1603	yes	missense,missense	FANCI	NM_001113378.1,NM_018193.2	112,112	672,2424,3402	CC,CG,GG		38.9509,9.5271,28.9935	benign,benign	742/1329,742/1269	89836228	3768,9228	2199	4299	6498	SO:0001583	missense	55215	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ATATCTGTGCTTT	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.2225G>C	15.37:g.89836228G>C	ENSP00000310842:p.Cys742Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	201	96	0.477612	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	635	0.2907509157509158	29	0.05894308943089431	121	0.3342541436464088	179	0.3129370629370629	306	0.40369393139841686	G	12.46	1.945389	0.34377	0.095271	0.389509	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	T;T;T	0.28069	1.63;1.63;1.63	5.9	4.89	0.63831	.	0.102357	0.64402	N	0.000001	T	0.00012	0.0000	L	0.44542	1.39	0.09310	P	1.0	B;P;P	0.39131	0.007;0.46;0.661	B;B;B	0.31869	0.006;0.089;0.137	T	0.48768	-0.9006	9	0.22109	T	0.4	-6.0576	3.9069	0.09186	0.3188:0.0:0.6812:0.0	rs2283432;rs52810132;rs2283432	742;742;742	Q9NVI1;Q9NVI1-2;Q9NVI1-1	FANCI_HUMAN;.;.	S	742	ENSP00000300027:C742S;ENSP00000310842:C742S;ENSP00000413249:C742S	ENSP00000300027:C742S	C	+	2	0	FANCI	87637232	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	4.932000	0.63476	2.793000	0.96121	0.563000	0.77884	TGT	G|0.715;C|0.285	0.285	strong		0.313	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
OR2G3	81469	hgsc.bcm.edu	37	1	247769752	247769752	+	Missense_Mutation	SNP	A	A	G	rs61730407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247769752A>G	ENST00000320002.2	+	1	897	c.865A>G	c.(865-867)Atc>Gtc	p.I289V	RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	289						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			AAATCCTATCATCTATACTTT	0.418													A|||	1693	0.338059	0.2307	0.3127	5008	,	,		19391	0.4325		0.4394	False		,,,				2504	0.2996				p.I289V		Atlas-SNP	.											.	OR2G3	108	.	0			c.A865G						PASS	.	A	VAL/ILE	1057,3349	385.1+/-325.6	140,777,1286	85.0	82.0	83.0		865	3.7	0.5	1	dbSNP_129	83	3646,4954	524.7+/-380.6	790,2066,1444	yes	missense	OR2G3	NM_001001914.1	29	930,2843,2730	GG,GA,AA		42.3953,23.99,36.1602	probably-damaging	289/310	247769752	4703,8303	2203	4300	6503	SO:0001583	missense	81469	exon1			CCTATCATCTATA	BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"""GPCR / Class A : Olfactory receptors"""	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.865A>G	1.37:g.247769752A>G	ENSP00000326301:p.Ile289Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	157	86	0.547771	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Missense_Mutation	SNP	ENST00000320002.2	37	CCDS31093.1	814	0.3727106227106227	104	0.21138211382113822	134	0.3701657458563536	247	0.4318181818181818	329	0.4340369393139842	A	14.76	2.630914	0.46944	0.2399	0.423953	ENSG00000177476	ENST00000320002	T	0.52057	0.68	3.65	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37178	U	0.002213	T	0.00012	0.0000	M	0.86651	2.83	0.49130	P	2.4500000000005073E-4	D	0.63046	0.992	D	0.80764	0.994	T	0.37731	-0.9693	9	0.66056	D	0.02	.	10.5906	0.45308	1.0:0.0:0.0:0.0	rs61730407	289	Q8NGZ4	OR2G3_HUMAN	V	289	ENSP00000326301:I289V	ENSP00000326301:I289V	I	+	1	0	OR2G3	245836375	0.445000	0.25657	0.531000	0.27976	0.988000	0.76386	0.983000	0.29552	1.648000	0.50643	0.403000	0.27427	ATC	A|0.629;G|0.371	0.371	strong		0.418	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1		
COLCA2	120376	hgsc.bcm.edu	37	11	111179054	111179054	+	Silent	SNP	A	A	G	rs3087587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:111179054A>G	ENST00000398035.2	+	5	1115	c.357A>G	c.(355-357)gcA>gcG	p.A119A	COLCA2_ENST00000526216.1_Silent_p.A119A	NM_001136105.2	NP_001129577.1	A8K830	COLC2_HUMAN	colorectal cancer associated 2	119						cytoplasm (GO:0005737)											CTCTCCAGGCAGCAGAGTACT	0.557													G|||	1806	0.360623	0.0545	0.4841	5008	,	,		18587	0.4345		0.5567	False		,,,				2504	0.409				p.A216A		Atlas-SNP	.											.	C11orf93	10	.	0			c.A648G						PASS	.	G		193,1191		18,157,517	95.0	82.0	86.0		357	-12.3	0.0	11	dbSNP_102	86	1779,1403		495,789,307	no	coding-synonymous	C11orf93	NM_001136105.1		513,946,824	GG,GA,AA		44.0918,13.9451,43.1888		119/155	111179054	1972,2594	692	1591	2283	SO:0001819	synonymous_variant	120376	exon5			CCAGGCAGCAGAG	BC042557	CCDS44728.1, CCDS73378.1	11q23.1	2013-10-11	2013-08-22	2013-08-22	ENSG00000214290	ENSG00000214290			26978	protein-coding gene	gene with protein product	"""cancer susceptibility candidate 13"""	615694	"""chromosome 11 open reading frame 93"""	C11orf93		21071539	Standard	NM_001271457		Approved	CASC13	uc031qea.1	A8K830	OTTHUMG00000166657	ENST00000398035.2:c.357A>G	11.37:g.111179054A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001271458	E9PMJ8|Q2TBJ3|V5LD62|V5LDI3|V5LDV1|V5LE09|V5LEU3	Silent	SNP	ENST00000398035.2	37	CCDS44728.1																																																																																			G|0.408;N|0.000	0.408	strong		0.557	COLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390991.1	NM_001136105	
KALRN	8997	hgsc.bcm.edu	37	3	123953756	123953756	+	Silent	SNP	C	C	A	rs144465315	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:123953756C>A	ENST00000240874.3	+	3	380	c.223C>A	c.(223-225)Cgg>Agg	p.R75R	KALRN_ENST00000360013.3_Silent_p.R75R|KALRN_ENST00000460856.1_Silent_p.R75R	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	75	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GGAAGACCTGCGGAAACTCGT	0.582													C|||	4	0.000798722	0.0	0.0	5008	,	,		20662	0.0		0.002	False		,,,				2504	0.002				p.R75R		Atlas-SNP	.											.	KALRN	556	.	0			c.C223A						PASS	.		,	1,4405	2.1+/-5.4	0,1,2202	49.0	41.0	44.0		223,223	2.5	1.0	3	dbSNP_134	44	11,8587	7.1+/-27.0	0,11,4288	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	0,12,6490	AA,AC,CC		0.1279,0.0227,0.0923	,	75/2987,75/1664	123953756	12,12992	2203	4299	6502	SO:0001819	synonymous_variant	8997	exon3			GACCTGCGGAAAC	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.223C>A	3.37:g.123953756C>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	c	10.77	1.444443	0.25987	2.27E-4	0.001279	ENSG00000160145	ENST00000448253;ENST00000354186	.	.	.	5.49	2.54	0.30619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0069	0.64470	0.52:0.48:0.0:0.0	.	.	.	.	X	102;52	.	.	C	+	3	2	KALRN	125436446	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	1.511000	0.35801	0.672000	0.31204	0.651000	0.88453	TGC	C|0.999;A|0.001	0.001	strong		0.582	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
UGGT2	55757	hgsc.bcm.edu	37	13	96638651	96638651	+	Missense_Mutation	SNP	C	C	T	rs12863903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:96638651C>T	ENST00000376747.3	-	9	1037	c.967G>A	c.(967-969)Gct>Act	p.A323T	UGGT2_ENST00000467305.1_5'UTR|UGGT2_ENST00000397618.3_Missense_Mutation_p.A323T|UGGT2_ENST00000376714.3_3'UTR	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	323			A -> T (in dbSNP:rs12863903). {ECO:0000269|PubMed:10694380}.		cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						TAAACTGGAGCGGACATTATT	0.313													c|||	381	0.0760783	0.0166	0.1009	5008	,	,		15082	0.0337		0.1789	False		,,,				2504	0.0767				p.A323T		Atlas-SNP	.											.	UGGT2	127	.	0			c.G967A						PASS	.	C	THR/ALA	196,4210	121.7+/-159.2	4,188,2011	76.0	77.0	77.0		967	2.8	1.0	13	dbSNP_121	77	1389,7201	265.8+/-286.4	127,1135,3033	yes	missense	UGGT2	NM_020121.3	58	131,1323,5044	TT,TC,CC		16.17,4.4485,12.1961	benign	323/1517	96638651	1585,11411	2203	4295	6498	SO:0001583	missense	55757	exon9			CTGGAGCGGACAT	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.967G>A	13.37:g.96638651C>T	ENSP00000365938:p.Ala323Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	208	0.09523809523809523	4	0.008130081300813009	54	0.14917127071823205	17	0.02972027972027972	133	0.17546174142480211	c	9.920	1.212009	0.22289	0.044485	0.1617	ENSG00000102595	ENST00000376747;ENST00000397618	T;T	0.44881	0.91;0.91	5.54	2.79	0.32731	.	0.332788	0.36591	N	0.002512	T	0.00039	0.0001	N	0.05414	-0.055	0.09310	P	0.9999999999876714	B;B;B	0.12630	0.003;0.003;0.006	B;B;B	0.08055	0.003;0.003;0.002	T	0.20075	-1.0286	9	0.16896	T	0.51	-13.5618	8.4809	0.33043	0.0:0.231:0.0:0.769	rs12863903;rs17268651;rs12863903	323;323;323	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	T	323	ENSP00000365938:A323T;ENSP00000380743:A323T	ENSP00000365938:A323T	A	-	1	0	UGGT2	95436652	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.673000	0.25203	0.906000	0.36621	-0.285000	0.09966	GCT	C|0.894;T|0.106	0.106	strong		0.313	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
PTPRH	5794	hgsc.bcm.edu	37	19	55702910	55702910	+	Missense_Mutation	SNP	C	C	A	rs2288523	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55702910C>A	ENST00000376350.3	-	12	2365	c.2343G>T	c.(2341-2343)aaG>aaT	p.K781N	PTPRH_ENST00000263434.5_Missense_Mutation_p.K603N|PTPRH_ENST00000588559.1_5'Flank	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	781			K -> N (in dbSNP:rs2288523).		apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GCTGCTTCTTCTTATTCCTGG	0.552													A|||	1394	0.278355	0.3797	0.3746	5008	,	,		18595	0.2351		0.1193	False		,,,				2504	0.2812				p.K781N		Atlas-SNP	.											.	PTPRH	139	.	0			c.G2343T						PASS	.	A	ASN/LYS,ASN/LYS	1505,2901	674.8+/-403.0	259,987,957	194.0	196.0	195.0		1809,2343	-2.3	0.0	19	dbSNP_100	195	1176,7424	765.2+/-407.6	85,1006,3209	yes	missense,missense	PTPRH	NM_001161440.1,NM_002842.3	94,94	344,1993,4166	AA,AC,CC		13.6744,34.158,20.6136	benign,benign	603/938,781/1116	55702910	2681,10325	2203	4300	6503	SO:0001583	missense	5794	exon12			CTTCTTCTTATTC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2343G>T	19.37:g.55702910C>A	ENSP00000365528:p.Lys781Asn	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	176	87	0.494318	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	529	0.24221611721611722	188	0.3821138211382114	106	0.292817679558011	148	0.25874125874125875	87	0.11477572559366754	A	2.602	-0.292710	0.05568	0.34158	0.136744	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.06768	3.26;4.25	3.69	-2.3	0.06785	.	1.474690	0.04657	N	0.408214	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.15473	0.002;0.013	B;B	0.06405	0.002;0.001	T	0.48603	-0.9021	9	0.15066	T	0.55	.	2.773	0.05340	0.341:0.3552:0.0:0.3038	rs2288523;rs52830953;rs58533782;rs2288523	603;781	C9JCH2;Q9HD43	.;PTPRH_HUMAN	N	781;603	ENSP00000365528:K781N;ENSP00000263434:K603N	ENSP00000263434:K603N	K	-	3	2	PTPRH	60394722	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.665000	0.05286	-0.303000	0.08856	-0.246000	0.11932	AAG	C|0.767;A|0.233	0.233	strong		0.552	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713827	32713827	+	Silent	SNP	C	C	T	rs1129956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32713827C>T	ENST00000374940.3	+	3	693	c.591C>T	c.(589-591)gaC>gaT	p.D197D		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	197	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	GGGGCCTGGACGAGCCTCTTC	0.488																																					p.D197D		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.C591T						PASS	.						190.0	215.0	206.0					6																	32713827		1511	2709	4220	SO:0001819	synonymous_variant	3118	exon3			CCTGGACGAGCCT		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.591C>T	6.37:g.32713827C>T		Somatic	573	0	0		WXS	Illumina HiSeq	Phase_I	783	65	0.083014	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			C|0.730;T|0.270	0.270	strong		0.488	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
PUM2	23369	hgsc.bcm.edu	37	2	20494189	20494189	+	Missense_Mutation	SNP	T	T	C	rs34032508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:20494189T>C	ENST00000361078.2	-	8	1122	c.1100A>G	c.(1099-1101)aAt>aGt	p.N367S	PUM2_ENST00000536417.1_Missense_Mutation_p.N311S|PUM2_ENST00000338086.5_Missense_Mutation_p.N367S|PUM2_ENST00000319801.5_Missense_Mutation_p.N367S|PUM2_ENST00000403432.1_Missense_Mutation_p.N367S			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	367	Ala-rich.|Gln-rich.		N -> S (in dbSNP:rs34032508).		regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCTGTGTTATTTGCCGCAGC	0.488													T|||	11	0.00219649	0.0	0.0014	5008	,	,		16235	0.0		0.0099	False		,,,				2504	0.0				p.N367S		Atlas-SNP	.											.	PUM2	91	.	0			c.A1100G						PASS	.	T	SER/ASN	3,4403	6.2+/-15.9	0,3,2200	117.0	111.0	113.0		1100	3.3	1.0	2	dbSNP_126	113	28,8572	19.8+/-62.0	0,28,4272	yes	missense	PUM2	NM_015317.1	46	0,31,6472	CC,CT,TT		0.3256,0.0681,0.2384	benign	367/1065	20494189	31,12975	2203	4300	6503	SO:0001583	missense	23369	exon8			GTGTTATTTGCCG	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"""pumilio (Drosphila) homolog 2"", ""pumilio homolog 2 (Drosophila)"""			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.1100A>G	2.37:g.20494189T>C	ENSP00000354370:p.Asn367Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	2.595	-0.294380	0.05568	6.81E-4	0.003256	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.17528	2.3;2.54;2.55;2.27;2.3;2.3	5.81	3.32	0.38043	.	0.390535	0.33180	N	0.005192	T	0.03390	0.0098	N	0.01576	-0.805	0.24245	N	0.995342	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.38265	-0.9669	10	0.19147	T	0.46	-4.0477	6.8251	0.23878	0.0:0.1485:0.1398:0.7117	rs34032508	311;367;367	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	S	367;367;367;258;367;311	ENSP00000338173:N367S;ENSP00000354370:N367S;ENSP00000326746:N367S;ENSP00000409905:N258S;ENSP00000385992:N367S;ENSP00000440093:N311S	ENSP00000326746:N367S	N	-	2	0	PUM2	20357670	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	1.260000	0.32968	1.044000	0.40200	0.455000	0.32223	AAT	T|0.996;C|0.004	0.004	strong		0.488	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317	
SNX18	112574	hgsc.bcm.edu	37	5	53815219	53815219	+	Silent	SNP	G	G	A	rs35241631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:53815219G>A	ENST00000326277.3	+	1	1627	c.1437G>A	c.(1435-1437)gaG>gaA	p.E479E	SNX18_ENST00000381410.4_Silent_p.E479E|SNX18_ENST00000343017.6_Silent_p.E479E	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	479	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				AGGCCTTTGAGCTGGACCAGC	0.632													g|||	97	0.019369	0.0045	0.0216	5008	,	,		19624	0.0		0.0497	False		,,,				2504	0.0266				p.E479E		Atlas-SNP	.											.	SNX18	102	.	0			c.G1437A						PASS	.	G	,,	31,4375	37.6+/-69.7	0,31,2172	42.0	41.0	42.0		1437,1437,1437	1.2	1.0	5	dbSNP_126	42	379,8221	123.6+/-182.4	9,361,3930	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX18	NM_001102575.1,NM_001145427.1,NM_052870.2	,,	9,392,6102	AA,AG,GG		4.407,0.7036,3.1524	,,	479/625,479/592,479/629	53815219	410,12596	2203	4300	6503	SO:0001819	synonymous_variant	112574	exon1			CTTTGAGCTGGAC	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1437G>A	5.37:g.53815219G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Silent	SNP	ENST00000326277.3	37	CCDS3962.1																																																																																			G|0.969;A|0.031	0.031	strong		0.632	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
C2orf71	388939	hgsc.bcm.edu	37	2	29295016	29295016	+	Silent	SNP	A	A	G	rs10200693	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29295016A>G	ENST00000331664.5	-	1	2111	c.2112T>C	c.(2110-2112)aaT>aaC	p.N704N		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	704					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						ATGGGATGGCATTTGGAAGCT	0.498													A|||	1672	0.333866	0.4228	0.2579	5008	,	,		21897	0.4444		0.2604	False		,,,				2504	0.229				p.N704N		Atlas-SNP	.											.	C2orf71	146	.	0			c.T2112C						PASS	.	A		1536,2582		305,926,828	116.0	112.0	113.0		2112	-11.5	0.0	2	dbSNP_119	113	2295,6161		309,1677,2242	no	coding-synonymous	C2orf71	NM_001029883.1		614,2603,3070	GG,GA,AA		27.1405,37.2997,30.4676		704/1289	29295016	3831,8743	2059	4228	6287	SO:0001819	synonymous_variant	388939	exon1			GATGGCATTTGGA		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.2112T>C	2.37:g.29295016A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	194	101	0.520619	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			A|0.660;G|0.340	0.340	strong		0.498	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
DNAH5	1767	hgsc.bcm.edu	37	5	13845045	13845045	+	Silent	SNP	G	G	A	rs10041113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13845045G>A	ENST00000265104.4	-	32	5276	c.5172C>T	c.(5170-5172)gcC>gcT	p.A1724A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1724	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCTCTAGAAGGGCAGGATCTG	0.443									Kartagener syndrome				A|||	2277	0.454673	0.5174	0.4092	5008	,	,		18672	0.622		0.3598	False		,,,				2504	0.3272				p.A1724A		Atlas-SNP	.											.	DNAH5	868	.	0			c.C5172T						PASS	.	A		2201,2205	588.0+/-386.8	546,1109,548	84.0	88.0	87.0		5172	-1.3	0.4	5	dbSNP_119	87	2993,5607	664.8+/-402.2	512,1969,1819	no	coding-synonymous	DNAH5	NM_001369.2		1058,3078,2367	AA,AG,GG		34.8023,49.9546,39.9354		1724/4625	13845045	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon32	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TAGAAGGGCAGGA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.5172C>T	5.37:g.13845045G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.574;A|0.426	0.426	strong		0.443	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
MUC16	94025	hgsc.bcm.edu	37	19	9086184	9086184	+	Silent	SNP	G	G	A	rs74999347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9086184G>A	ENST00000397910.4	-	1	5834	c.5631C>T	c.(5629-5631)aaC>aaT	p.N1877N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1877	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TATCAGAGCCGTTTTCCAATC	0.502													g|||	114	0.0227636	0.0053	0.0403	5008	,	,		21306	0.0		0.0686	False		,,,				2504	0.0102				p.N1877N		Atlas-SNP	.											.	MUC16	4315	.	0			c.C5631T						PASS	.	G		69,3773		0,69,1852	62.0	59.0	60.0		5631	0.2	0.0	19	dbSNP_132	60	625,7613		28,569,3522	no	coding-synonymous	MUC16	NM_024690.2		28,638,5374	AA,AG,GG		7.5868,1.7959,5.745		1877/14508	9086184	694,11386	1921	4119	6040	SO:0001819	synonymous_variant	94025	exon1			AGAGCCGTTTTCC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5631C>T	19.37:g.9086184G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.961;A|0.039	0.039	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NAPSA	9476	hgsc.bcm.edu	37	19	50865535	50865535	+	Missense_Mutation	SNP	A	A	G	rs676314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50865535A>G	ENST00000253719.2	-	2	327	c.119T>C	c.(118-120)aTc>aCc	p.I40T	NR1H2_ENST00000600978.1_Intron|NR1H2_ENST00000542413.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	40			I -> T (in dbSNP:rs676314). {ECO:0000269|PubMed:15489334}.		membrane protein proteolysis (GO:0033619)|proteolysis (GO:0006508)|surfactant homeostasis (GO:0043129)	alveolar lamellar body (GO:0097208)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)|peptidase activity (GO:0008233)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		TAGGTTCAGGATCCTGCGTCC	0.547													G|||	1925	0.384385	0.5809	0.428	5008	,	,		18979	0.1706		0.331	False		,,,				2504	0.363				p.I40T		Atlas-SNP	.											NAPSA,tonsil,carcinoma,0,1	NAPSA	38	1	0			c.T119C						PASS	.	G	THR/ILE	2408,1998	560.6+/-380.5	674,1060,469	65.0	61.0	62.0		119	-5.1	0.0	19	dbSNP_83	62	2881,5719	673.0+/-403.0	467,1947,1886	yes	missense	NAPSA	NM_004851.1	89	1141,3007,2355	GG,GA,AA		33.5,45.3473,40.6658	benign	40/421	50865535	5289,7717	2203	4300	6503	SO:0001583	missense	9476	exon2			TTCAGGATCCTGC	AF090386	CCDS12794.1	19q13.33	2011-08-25				ENSG00000131400			13395	protein-coding gene	gene with protein product	"""kidney-derived aspartic protease-like protein"""	605631					Standard	NM_004851		Approved	NAP1, NAPA, Kdap, KAP	uc002prx.3	O96009		ENST00000253719.2:c.119T>C	19.37:g.50865535A>G	ENSP00000253719:p.Ile40Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_004851	Q8WWD9	Missense_Mutation	SNP	ENST00000253719.2	37	CCDS12794.1	800	0.3663003663003663	286	0.5813008130081301	143	0.39502762430939226	117	0.20454545454545456	254	0.33509234828496043	G	0.027	-1.359724	0.01245	0.546527	0.335	ENSG00000131400	ENST00000253719	T	0.29655	1.56	3.9	-5.12	0.02893	Peptidase aspartic (1);	2.362150	0.01398	N	0.013480	T	0.00012	0.0000	N	0.00869	-1.13	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38993	-0.9635	9	0.02654	T	1	.	0.255	0.00210	0.3467:0.1401:0.2293:0.2839	rs676314;rs17856553;rs676314	40	O96009	NAPSA_HUMAN	T	40	ENSP00000253719:I40T	ENSP00000253719:I40T	I	-	2	0	NAPSA	55557347	0.001000	0.12720	0.000000	0.03702	0.029000	0.11900	-0.263000	0.08670	-1.739000	0.01347	-1.238000	0.01547	ATC	A|0.618;G|0.382	0.382	strong		0.547	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	NM_004851	
LGR6	59352	hgsc.bcm.edu	37	1	202287754	202287754	+	Missense_Mutation	SNP	G	G	A	rs75658797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202287754G>A	ENST00000367278.3	+	18	2412	c.2323G>A	c.(2323-2325)Gtg>Atg	p.V775M	LGR6_ENST00000255432.7_Missense_Mutation_p.V723M|LGR6_ENST00000439764.2_Missense_Mutation_p.V636M	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	775					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						GGTGAGGCACGTGGCCTGGCT	0.637													G|||	411	0.0820687	0.059	0.1037	5008	,	,		17778	0.0526		0.1113	False		,,,				2504	0.0982				p.V775M		Atlas-SNP	.											.	LGR6	102	.	0			c.G2323A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	235,4171	138.4+/-174.2	8,219,1976	100.0	79.0	86.0		2323,1906,2167	2.6	1.0	1	dbSNP_131	86	1129,7471	234.6+/-267.5	79,971,3250	yes	missense,missense,missense	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	21,21,21	87,1190,5226	AA,AG,GG		13.1279,5.3336,10.4875	benign,benign,benign	775/968,636/829,723/916	202287754	1364,11642	2203	4300	6503	SO:0001583	missense	59352	exon18			AGGCACGTGGCCT	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2323G>A	1.37:g.202287754G>A	ENSP00000356247:p.Val775Met	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	195	85	0.435897	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	37	CCDS30971.1	190	0.08699633699633699	38	0.07723577235772358	42	0.11602209944751381	32	0.055944055944055944	78	0.10290237467018469	G	13.00	2.107063	0.37145	0.053336	0.131279	ENSG00000133067	ENST00000367278;ENST00000255432;ENST00000439764	T;T;T	0.40225	1.04;1.04;1.04	4.49	2.58	0.30949	.	0.137493	0.48767	N	0.000170	T	0.00271	0.0008	N	0.20530	0.585	0.25761	P	0.9849419	D;P;P	0.54047	0.964;0.941;0.793	B;P;B	0.45881	0.244;0.496;0.409	T	0.06481	-1.0824	9	0.11794	T	0.64	.	6.5745	0.22557	0.1589:0.1488:0.6924:0.0	.	636;723;775	Q9HBX8-1;Q9HBX8-2;Q9HBX8	.;.;LGR6_HUMAN	M	775;723;636	ENSP00000356247:V775M;ENSP00000255432:V723M;ENSP00000387869:V636M	ENSP00000255432:V723M	V	+	1	0	LGR6	200554377	1.000000	0.71417	0.986000	0.45419	0.985000	0.73830	3.339000	0.52135	0.626000	0.30322	0.485000	0.47835	GTG	G|0.899;A|0.101	0.101	strong		0.637	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
ZNF223	7766	hgsc.bcm.edu	37	19	44570393	44570393	+	Missense_Mutation	SNP	C	C	A	rs6509138	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44570393C>A	ENST00000434772.3	+	5	667	c.412C>A	c.(412-414)Cta>Ata	p.L138I	ZNF223_ENST00000591793.1_Missense_Mutation_p.L248I	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	138			L -> I (in dbSNP:rs6509138). {ECO:0000269|PubMed:12743021, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				TGAGGAAGGACTATCTATAAT	0.438													C|||	2011	0.401558	0.1483	0.3516	5008	,	,		21914	0.2996		0.659	False		,,,				2504	0.6196				p.L138I		Atlas-SNP	.											.	ZNF223	61	.	0			c.C412A						PASS	.	C	ILE/LEU	1006,3400	375.1+/-321.5	115,776,1312	110.0	91.0	97.0		412	-0.5	0.0	19	dbSNP_116	97	5558,3042	662.5+/-402.0	1798,1962,540	yes	missense	ZNF223	NM_013361.4	5	1913,2738,1852	AA,AC,CC		35.3721,22.8325,49.531	probably-damaging	138/483	44570393	6564,6442	2203	4300	6503	SO:0001583	missense	7766	exon5			GAAGGACTATCTA	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"""Zinc fingers, C2H2-type"", ""-"""	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.412C>A	19.37:g.44570393C>A	ENSP00000401947:p.Leu138Ile	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	183	81	0.442623	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Missense_Mutation	SNP	ENST00000434772.3	37	CCDS12635.1	907	0.4152930402930403	67	0.13617886178861788	148	0.4088397790055249	187	0.3269230769230769	505	0.6662269129287599	C	7.438	0.640147	0.14386	0.228325	0.646279	ENSG00000178386	ENST00000434772	T	0.04758	3.56	2.18	-0.505	0.11993	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.27594	0.182	B	0.22601	0.04	T	0.11567	-1.0582	8	0.37606	T	0.19	.	2.0444	0.03557	0.3153:0.4775:0.0:0.2072	rs6509138;rs16978657;rs17852035;rs52793953;rs58216538;rs6509138	138	Q9UK11	ZN223_HUMAN	I	138	ENSP00000401947:L138I	ENSP00000401947:L138I	L	+	1	2	ZNF223	49262233	.	.	0.005000	0.12908	0.071000	0.16799	.	.	0.221000	0.20879	0.313000	0.20887	CTA	C|0.542;A|0.458	0.458	strong		0.438	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2		
ENTPD3	956	hgsc.bcm.edu	37	3	40453432	40453432	+	Missense_Mutation	SNP	C	C	T	rs377644776		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:40453432C>T	ENST00000301825.3	+	5	534	c.416C>T	c.(415-417)aCg>aTg	p.T139M	ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3-AS1_ENST00000452768.1_RNA|ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3_ENST00000456402.1_Missense_Mutation_p.T139M|ENTPD3_ENST00000445129.1_Missense_Mutation_p.T139M	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	139					nucleoside diphosphate catabolic process (GO:0009134)|nucleoside triphosphate catabolic process (GO:0009143)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		CTGGGAGCCACGGCTGGGATG	0.517													C|||	1	0.000199681	0.0	0.0	5008	,	,		15474	0.0		0.0	False		,,,				2504	0.001				p.T139M		Atlas-SNP	.											.	ENTPD3	48	.	0			c.C416T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	60.0	49.0	52.0		416	5.6	1.0	3		52	1,8599	1.2+/-3.3	0,1,4299	no	missense	ENTPD3	NM_001248.2	81	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	139/530	40453432	2,13004	2203	4300	6503	SO:0001583	missense	956	exon5			GAGCCACGGCTGG	AF039917	CCDS2691.1, CCDS74919.1	3p21.3	2004-02-26			ENSG00000168032	ENSG00000168032			3365	protein-coding gene	gene with protein product		603161		CD39L3		9676430	Standard	XM_005265605		Approved	NTPDase-3, HB6	uc003ckd.4	O75355	OTTHUMG00000131390	ENST00000301825.3:c.416C>T	3.37:g.40453432C>T	ENSP00000301825:p.Thr139Met	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	38	27	0.710526	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Missense_Mutation	SNP	ENST00000301825.3	37	CCDS2691.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.653329	0.88056	2.27E-4	1.16E-4	ENSG00000168032	ENST00000301825;ENST00000456402;ENST00000445129	T;T;T	0.35421	1.31;1.31;1.31	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.72407	0.3456	H	0.95437	3.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80542	-0.1336	10	0.87932	D	0	-14.6669	17.579	0.87960	0.0:1.0:0.0:0.0	.	139	O75355	ENTP3_HUMAN	M	139	ENSP00000301825:T139M;ENSP00000401565:T139M;ENSP00000404671:T139M	ENSP00000301825:T139M	T	+	2	0	ENTPD3	40428436	1.000000	0.71417	0.984000	0.44739	0.875000	0.50365	6.934000	0.75880	2.832000	0.97577	0.655000	0.94253	ACG	.	.	weak		0.517	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248	
RBMXL2	27288	hgsc.bcm.edu	37	11	7110363	7110363	+	Silent	SNP	G	G	A	rs4758158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7110363G>A	ENST00000306904.5	+	1	199	c.12G>A	c.(10-12)gcG>gcA	p.A4A		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	4						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TGGTTGAAGCGGATCGCCCGG	0.652													G|||	1589	0.317292	0.1437	0.2954	5008	,	,		11303	0.4385		0.3648	False		,,,				2504	0.3937				p.A4A		Atlas-SNP	.											.	RBMXL2	47	.	0			c.G12A						PASS	.	G		670,3732	274.9+/-272.2	61,548,1592	30.0	33.0	32.0		12	-5.6	0.4	11	dbSNP_111	32	2890,5702	447.9+/-361.7	513,1864,1919	no	coding-synonymous	RBMXL2	NM_014469.4		574,2412,3511	AA,AG,GG		33.6359,15.2204,27.3973		4/393	7110363	3560,9434	2201	4296	6497	SO:0001819	synonymous_variant	27288	exon1			TGAAGCGGATCGC	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"""RNA binding motif (RRM) containing"""	17886	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G T"""	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.12G>A	11.37:g.7110363G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_014469	Q6PEZ2|Q9NQU0	Silent	SNP	ENST00000306904.5	37	CCDS7777.1																																																																																			G|0.709;A|0.291	0.291	strong		0.652	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469	
LAMA5	3911	hgsc.bcm.edu	37	20	60899196	60899196	+	Missense_Mutation	SNP	C	C	T	rs116895933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60899196C>T	ENST00000252999.3	-	43	5774	c.5708G>A	c.(5707-5709)aGg>aAg	p.R1903K		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1903	Laminin EGF-like 17. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGGGTCGTCCCTGCTGCTCAC	0.662													.|||	51	0.0101837	0.0023	0.0231	5008	,	,		16348	0.0		0.0268	False		,,,				2504	0.0051				p.R1903K		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5708A						PASS	.	C	LYS/ARG	26,4358		2,22,2168	27.0	30.0	29.0		5708	2.0	0.0	20	dbSNP_132	29	230,8316		3,224,4046	yes	missense	LAMA5	NM_005560.3	26	5,246,6214	TT,TC,CC		2.6913,0.5931,1.9799	benign	1903/3696	60899196	256,12674	2192	4273	6465	SO:0001583	missense	3911	exon43			TCGTCCCTGCTGC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5708G>A	20.37:g.60899196C>T	ENSP00000252999:p.Arg1903Lys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	31	0.014194139194139194	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	19	0.025065963060686015	C	0.057	-1.235018	0.01505	0.005931	0.026913	ENSG00000130702	ENST00000252999	T	0.60672	0.17	4.22	1.95	0.26073	EGF-like, laminin (4);	0.999580	0.08092	U	0.999213	T	0.19846	0.0477	N	0.21508	0.67	0.09310	N	1	B	0.14012	0.009	B	0.18871	0.023	T	0.15521	-1.0434	10	0.27082	T	0.32	.	9.8697	0.41166	0.0:0.6268:0.265:0.1082	.	1903	O15230	LAMA5_HUMAN	K	1903	ENSP00000252999:R1903K	ENSP00000252999:R1903K	R	-	2	0	LAMA5	60332591	0.000000	0.05858	0.001000	0.08648	0.079000	0.17450	-0.785000	0.04628	0.722000	0.32252	0.478000	0.44815	AGG	C|0.983;T|0.017	0.017	strong		0.662	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
KIAA0319	9856	hgsc.bcm.edu	37	6	24570151	24570151	+	Silent	SNP	G	G	A	rs41271797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:24570151G>A	ENST00000378214.3	-	12	2495	c.1971C>T	c.(1969-1971)ttC>ttT	p.F657F	KIAA0319_ENST00000535378.1_Silent_p.F648F|KIAA0319_ENST00000430948.2_Silent_p.F612F|KIAA0319_ENST00000543707.1_Silent_p.F657F|KIAA0319_ENST00000537886.1_Silent_p.F657F	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	657	PKD 4. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						CCCAGTGGTAGAAGACAATGC	0.537													G|||	2	0.000399361	0.0	0.0	5008	,	,		20249	0.0		0.002	False		,,,				2504	0.0				p.F657F		Atlas-SNP	.											KIAA0319,NS,carcinoma,0,1	KIAA0319	117	1	0			c.C1971T						PASS	.	G	,,,,	2,4404	4.2+/-10.8	0,2,2201	118.0	103.0	108.0		1944,1971,1836,1971,1971	2.1	0.8	6	dbSNP_127	108	15,8585	12.6+/-44.7	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIAA0319	NM_001168374.1,NM_001168375.1,NM_001168376.1,NM_001168377.1,NM_014809.3	,,,,	0,17,6486	AA,AG,GG		0.1744,0.0454,0.1307	,,,,	648/1064,657/1073,612/1028,657/1012,657/1073	24570151	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	9856	exon12			GTGGTAGAAGACA	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.1971C>T	6.37:g.24570151G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	250	126	0.504	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Silent	SNP	ENST00000378214.3	37	CCDS34348.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
WDR48	57599	hgsc.bcm.edu	37	3	39111140	39111140	+	Silent	SNP	C	C	A	rs2293312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:39111140C>A	ENST00000302313.5	+	7	605	c.577C>A	c.(577-579)Cgg>Agg	p.R193R	WDR48_ENST00000418020.1_5'UTR|WDR48_ENST00000396258.3_Silent_p.R111R|WDR48_ENST00000544962.1_Intron	NM_020839.2	NP_065890.1	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	193					double-strand break repair via homologous recombination (GO:0000724)|embryonic organ development (GO:0048568)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|positive regulation of epithelial cell proliferation (GO:0050679)|protein deubiquitination (GO:0016579)|regulation of protein monoubiquitination (GO:1902525)|seminiferous tubule development (GO:0072520)|single fertilization (GO:0007338)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		ACAGGTGTTACGGGTATGGGA	0.338													A|||	2239	0.447085	0.8396	0.3242	5008	,	,		17000	0.3403		0.3231	False		,,,				2504	0.2413				p.R193R		Atlas-SNP	.											.	WDR48	41	.	0			c.C577A						PASS	.	A		3318,1088	392.6+/-328.5	1249,820,134	122.0	120.0	121.0		577	3.1	1.0	3	dbSNP_100	121	2785,5815	678.7+/-403.5	470,1845,1985	no	coding-synonymous	WDR48	NM_020839.2		1719,2665,2119	AA,AC,CC		32.3837,24.6936,46.9245		193/678	39111140	6103,6903	2203	4300	6503	SO:0001819	synonymous_variant	57599	exon7			GTGTTACGGGTAT	AF468833	CCDS33738.1	3p21.33	2014-06-16			ENSG00000114742	ENSG00000114742		"""WD repeat domain containing"""	30914	protein-coding gene	gene with protein product		612167				10819331, 12196293, 24482476	Standard	NM_020839		Approved	KIAA1449, P80, SPG60	uc003cit.3	Q8TAF3	OTTHUMG00000155972	ENST00000302313.5:c.577C>A	3.37:g.39111140C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	83	57	0.686747	NM_020839	B4DM86|B4DQI2|B4DY84|Q63HJ2|Q658Y1|Q8N3Z1|Q9NSK8|Q9P279	Silent	SNP	ENST00000302313.5	37	CCDS33738.1																																																																																			C|0.529;N|0.000	.	strong		0.338	WDR48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342529.1	NM_020839	
SLC17A3	10786	hgsc.bcm.edu	37	6	25862466	25862466	+	Missense_Mutation	SNP	C	C	T	rs1165165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:25862466C>T	ENST00000360657.3	-	3	583	c.298G>A	c.(298-300)Gca>Aca	p.A100T	SLC17A3_ENST00000397060.4_Missense_Mutation_p.A100T|SLC17A3_ENST00000361703.6_Missense_Mutation_p.A100T			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	100			A -> T (in dbSNP:rs1165165). {ECO:0000269|PubMed:15489334}.		drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						CTTACCTTTGCAGGAAGACTC	0.378													C|||	1084	0.216454	0.3275	0.1801	5008	,	,		19794	0.131		0.2276	False		,,,				2504	0.1687				p.A100T		Atlas-SNP	.											.	SLC17A3	95	.	0			c.G298A						PASS	.	C	THR/ALA,THR/ALA	1285,3121	434.9+/-344.1	196,893,1114	78.0	69.0	72.0		298,298	2.2	0.0	6	dbSNP_87	72	2014,6586	352.0+/-328.5	225,1564,2511	yes	missense,missense	SLC17A3	NM_001098486.1,NM_006632.3	58,58	421,2457,3625	TT,TC,CC		23.4186,29.1648,25.3652	benign,benign	100/499,100/421	25862466	3299,9707	2203	4300	6503	SO:0001583	missense	10786	exon3			CCTTTGCAGGAAG	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"""Solute carriers"""	10931	protein-coding gene	gene with protein product		611034	"""solute carrier family 17 (sodium phosphate), member 3"""			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.298G>A	6.37:g.25862466C>T	ENSP00000353873:p.Ala100Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	135	67	0.496296	NM_006632	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Missense_Mutation	SNP	ENST00000360657.3	37	CCDS4566.2	499	0.22847985347985347	164	0.3333333333333333	74	0.20441988950276244	83	0.1451048951048951	178	0.23482849604221637	C	9.114	1.007252	0.19199	0.291648	0.234186	ENSG00000124564	ENST00000397060;ENST00000360657;ENST00000361703	T;T;T	0.64260	-0.09;-0.05;-0.05	3.57	2.17	0.27698	.	967.492000	0.00357	N	0.000023	T	0.22781	0.0550	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.31989	0.35;0.1;0.022;0.232	B;B;B;B	0.31547	0.132;0.06;0.06;0.064	T	0.13845	-1.0494	9	0.14656	T	0.56	.	4.9209	0.13869	0.0:0.7415:0.0:0.2585	rs1165165;rs1747544;rs17271037;rs17845568;rs17858467;rs59291168;rs1165165	100;81;100;100	B7Z531;B7Z3L7;B7Z511;O00476	.;.;.;NPT4_HUMAN	T	100	ENSP00000380250:A100T;ENSP00000353873:A100T;ENSP00000355307:A100T	ENSP00000353873:A100T	A	-	1	0	SLC17A3	25970445	0.002000	0.14202	0.008000	0.14137	0.061000	0.15899	0.224000	0.17738	0.612000	0.30071	0.544000	0.68410	GCA	C|0.755;T|0.245	0.245	strong		0.378	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		
PARP4	143	hgsc.bcm.edu	37	13	25074490	25074490	+	Missense_Mutation	SNP	C	C	T	rs9578751	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25074490C>T	ENST00000381989.3	-	4	470	c.365G>A	c.(364-366)aGt>aAt	p.S122N		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	122			S -> N (in dbSNP:rs9578751).		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CTCTGTGGCACTGTCCGGGCA	0.398													.|||	320	0.0638978	0.0772	0.0591	5008	,	,		14701	0.0317		0.0924	False		,,,				2504	0.0532				p.S122N		Atlas-SNP	.											.	PARP4	142	.	0			c.G365A						PASS	.	C	ASN/SER	390,4016	196.7+/-221.0	22,346,1835	121.0	116.0	118.0		365	-3.5	0.0	13	dbSNP_119	118	983,7617	213.4+/-253.3	66,851,3383	yes	missense	PARP4	NM_006437.3	46	88,1197,5218	TT,TC,CC		11.4302,8.8516,10.5567	benign	122/1725	25074490	1373,11633	2203	4300	6503	SO:0001583	missense	143	exon4			GTGGCACTGTCCG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.365G>A	13.37:g.25074490C>T	ENSP00000371419:p.Ser122Asn	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	154	0.07051282051282051	44	0.08943089430894309	24	0.06629834254143646	8	0.013986013986013986	78	0.10290237467018469	C	1.648	-0.514674	0.04200	0.088516	0.114302	ENSG00000102699	ENST00000381989	T	0.44482	0.92	3.38	-3.55	0.04639	.	1.369470	0.04747	N	0.423829	T	0.00328	0.0010	N	0.02736	-0.51	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13522	-1.0506	10	0.10377	T	0.69	-4.6393	9.1088	0.36714	0.0:0.5451:0.0:0.4549	rs9578751;rs17470431;rs52802969;rs9578751	122	Q9UKK3	PARP4_HUMAN	N	122	ENSP00000371419:S122N	ENSP00000371419:S122N	S	-	2	0	PARP4	23972490	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.085000	0.01362	-0.749000	0.04747	-1.427000	0.01099	AGT	C|0.909;T|0.091	0.091	strong		0.398	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
STK38	11329	hgsc.bcm.edu	37	6	36463627	36463627	+	Silent	SNP	C	C	T	rs2071809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:36463627C>T	ENST00000229812.7	-	14	1617	c.1332G>A	c.(1330-1332)acG>acA	p.T444T		NM_007271.2	NP_009202.1			serine/threonine kinase 38											NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGCGCTTGTACGTGTAATTGA	0.463													C|||	586	0.117013	0.0083	0.013	5008	,	,		18204	0.3631		0.0378	False		,,,				2504	0.1656				p.T444T	Colon(180;997 3561 16158)	Atlas-SNP	.											STK38,NS,lymphoid_neoplasm,-1,1	STK38	54	1	0			c.G1332A						PASS	.	C		81,4325	69.2+/-107.0	2,77,2124	245.0	213.0	224.0		1332	-12.3	0.1	6	dbSNP_96	224	392,8208	125.3+/-183.9	14,364,3922	no	coding-synonymous	STK38	NM_007271.2		16,441,6046	TT,TC,CC		4.5581,1.8384,3.6368		444/466	36463627	473,12533	2203	4300	6503	SO:0001819	synonymous_variant	11329	exon14			CTTGTACGTGTAA		CCDS4822.1	6p21	2006-10-06			ENSG00000112079	ENSG00000112079			17847	protein-coding gene	gene with protein product		606964				7761441	Standard	NM_007271		Approved	NDR	uc003omh.3	Q15208	OTTHUMG00000014598	ENST00000229812.7:c.1332G>A	6.37:g.36463627C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	241	97	0.40249	NM_007271		Silent	SNP	ENST00000229812.7	37	CCDS4822.1																																																																																			C|0.930;T|0.070	0.070	strong		0.463	STK38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040346.1	NM_007271	
WDR18	57418	hgsc.bcm.edu	37	19	991129	991129	+	Missense_Mutation	SNP	G	G	A	rs11538683	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:991129G>A	ENST00000251289.5	+	6	813	c.790G>A	c.(790-792)Gtc>Atc	p.V264I	WDR18_ENST00000587001.2_Missense_Mutation_p.V264I	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	264			V -> I (in dbSNP:rs11538683).		multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCCGGGAAGGTCTTCAAAGG	0.682													.|||	772	0.154153	0.0514	0.1081	5008	,	,		11617	0.1964		0.1252	False		,,,				2504	0.3119				p.V264I		Atlas-SNP	.											.	WDR18	20	.	0			c.G790A						PASS	.	G	ILE/VAL	346,4014		14,318,1848	47.0	38.0	41.0		790	1.3	1.0	19	dbSNP_120	41	973,7579		62,849,3365	yes	missense	WDR18	NM_024100.3	29	76,1167,5213	AA,AG,GG		11.3775,7.9358,10.2153	benign	264/433	991129	1319,11593	2180	4276	6456	SO:0001583	missense	57418	exon6			GGGAAGGTCTTCA		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.790G>A	19.37:g.991129G>A	ENSP00000251289:p.Val264Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	30	9	0.3	NM_024100	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	37	CCDS12051.1	275	0.1259157509157509	28	0.056910569105691054	40	0.11049723756906077	108	0.1888111888111888	99	0.13060686015831136	G	9.743	1.165481	0.21538	0.079358	0.113775	ENSG00000065268	ENST00000251289	T	0.61040	0.14	3.62	1.26	0.21427	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.310461	0.28612	N	0.014740	T	0.00039	0.0001	N	0.17082	0.46	0.24767	P	0.99289647	B	0.21606	0.058	B	0.24269	0.052	T	0.08827	-1.0703	9	0.21540	T	0.41	.	7.2122	0.25939	0.1982:0.1575:0.6442:0.0	rs11538683	264	Q9BV38	WDR18_HUMAN	I	264	ENSP00000251289:V264I	ENSP00000251289:V264I	V	+	1	0	WDR18	942129	1.000000	0.71417	0.998000	0.56505	0.883000	0.51084	1.639000	0.37176	0.734000	0.32515	0.591000	0.81541	GTC	G|0.891;A|0.109	0.109	strong		0.682	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
OR2T3	343173	hgsc.bcm.edu	37	1	248637291	248637291	+	Missense_Mutation	SNP	G	G	A	rs1770109	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248637291G>A	ENST00000359594.2	+	1	665	c.640G>A	c.(640-642)Gcc>Acc	p.A214T		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A214T(1)		breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATGCTTCTCGCCCCCATCAT	0.557													.|||	954	0.190495	0.1263	0.1916	5008	,	,		17132	0.2867		0.1064	False		,,,				2504	0.2638				p.A214T		Atlas-SNP	.											OR2T3,trunk,malignant_melanoma,0,1	OR2T3	79	1	1	Substitution - Missense(1)	skin(1)	c.G640A						scavenged	.						211.0	168.0	182.0					1																	248637291		2136	4233	6369	SO:0001583	missense	343173	exon1			CTTCTCGCCCCCA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.640G>A	1.37:g.248637291G>A	ENSP00000352604:p.Ala214Thr	Somatic	615	3	0.00487805		WXS	Illumina HiSeq	Phase_I	267	33	0.123596	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	537	0.24587912087912087	86	0.17479674796747968	71	0.19613259668508287	238	0.4160839160839161	142	0.18733509234828497	g	13.03	2.115628	0.37339	.	.	ENSG00000196539	ENST00000359594	T	0.37235	1.21	2.37	-2.22	0.06952	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.10629	0.01	0.09310	N	1	P	0.39535	0.677	B	0.33568	0.166	T	0.42275	-0.9461	9	0.56958	D	0.05	.	0.5423	0.00647	0.2646:0.2059:0.3262:0.2032	rs1770109	214	Q8NH03	OR2T3_HUMAN	T	214	ENSP00000352604:A214T	ENSP00000352604:A214T	A	+	1	0	OR2T3	246703914	0.000000	0.05858	0.163000	0.22734	0.269000	0.26545	-1.638000	0.02013	0.011000	0.14865	0.186000	0.17326	GCC	G|0.754;A|0.246	0.246	strong		0.557	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20903757	20903757	+	Intron	SNP	T	T	C	rs10841611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:20903757T>C	ENST00000266509.2	+	14	2284				SLCO1C1_ENST00000545102.1_Silent_p.H531H|SLCO1C1_ENST00000545604.1_Silent_p.H649H|SLCO1C1_ENST00000540354.1_Intron|SLCO1C1_ENST00000381552.1_Silent_p.H649H	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1						sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.H649H(1)		NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	CCGCATCTCATTGCTACAGCA	0.378													C|||	2391	0.477436	0.1952	0.5735	5008	,	,		16607	0.5913		0.504	False		,,,				2504	0.6462				p.H649H		Atlas-SNP	.											.	SLCO1C1	216	.	1	Substitution - coding silent(1)	kidney(1)	c.T1947C						PASS	.	C	,,,	1072,3334	722.3+/-409.3	137,798,1268	115.0	105.0	108.0		1593,,1947,	0.4	0.0	12	dbSNP_120	108	4722,3878	544.0+/-384.5	1285,2152,863	no	coding-synonymous,intron,coding-synonymous,intron	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	,,,	1422,2950,2131	CC,CT,TT		45.093,24.3305,44.5487	,,,	531/613,,649/731,	20903757	5794,7212	2203	4300	6503	SO:0001627	intron_variant	53919	exon15			ATCTCATTGCTAC	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1916+31T>C	12.37:g.20903757T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	204	90	0.441176	NM_001145946	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Silent	SNP	ENST00000266509.2	37	CCDS8683.1																																																																																			T|0.496;C|0.504	0.504	strong		0.378	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
CBR3	874	hgsc.bcm.edu	37	21	37507769	37507769	+	Silent	SNP	C	C	T	rs881712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:37507769C>T	ENST00000290354.5	+	1	560	c.279C>T	c.(277-279)gtC>gtT	p.V93V	CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000453159.1_RNA|CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000608622.1_RNA|CBR3-AS1_ENST00000413862.1_RNA	NM_001236.3	NP_001227.1	O75828	CBR3_HUMAN	carbonyl reductase 3	93			V -> I (in dbSNP:rs2835285).		cognition (GO:0050890)|phylloquinone catabolic process (GO:0042376)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	3-keto sterol reductase activity (GO:0000253)|carbonyl reductase (NADPH) activity (GO:0004090)|NADPH binding (GO:0070402)			kidney(1)|large_intestine(1)|lung(1)	3					Doxorubicin(DB00997)	ACGCGGCCGTCGCCTTCAAGA	0.667													C|||	1545	0.308506	0.0673	0.4524	5008	,	,		14412	0.4276		0.4304	False		,,,				2504	0.2843				p.V93V		Atlas-SNP	.											.	CBR3	11	.	0			c.C279T						PASS	.	C		600,3806		50,500,1653	26.0	32.0	30.0		279	4.3	1.0	21	dbSNP_86	30	3809,4789		834,2141,1324	no	coding-synonymous	CBR3	NM_001236.3		884,2641,2977	TT,TC,CC		44.301,13.6178,33.905		93/278	37507769	4409,8595	2203	4299	6502	SO:0001819	synonymous_variant	874	exon1			GGCCGTCGCCTTC	AB004854	CCDS13642.1	21q22.2	2011-09-14			ENSG00000159231	ENSG00000159231	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	1549	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 21C, member 2"""	603608				9740676, 19027726	Standard	NM_001236		Approved	SDR21C2	uc002yve.3	O75828	OTTHUMG00000086617	ENST00000290354.5:c.279C>T	21.37:g.37507769C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_001236	Q6FHP2	Silent	SNP	ENST00000290354.5	37	CCDS13642.1																																																																																			C|0.666;T|0.334	0.334	strong		0.667	CBR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194632.1		
MYH13	8735	hgsc.bcm.edu	37	17	10247199	10247199	+	Silent	SNP	G	G	A	rs12938754	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10247199G>A	ENST00000418404.3	-	15	1975	c.1812C>T	c.(1810-1812)aaC>aaT	p.N604N	RP11-401O9.3_ENST00000577743.1_RNA|MYH13_ENST00000252172.4_Silent_p.N604N			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	604	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CCACAGTCTCGTTCAGGGGGT	0.527													G|||	486	0.0970447	0.0189	0.1527	5008	,	,		19644	0.0		0.3062	False		,,,				2504	0.0481				p.N604N		Atlas-SNP	.											.	MYH13	533	.	0			c.C1812T						PASS	.	G		253,4153	146.5+/-181.1	3,247,1953	81.0	78.0	79.0		1812	-8.7	0.2	17	dbSNP_121	79	2512,6088	411.0+/-350.3	372,1768,2160	no	coding-synonymous	MYH13	NM_003802.2		375,2015,4113	AA,AG,GG		29.2093,5.7422,21.2594		604/1939	10247199	2765,10241	2203	4300	6503	SO:0001819	synonymous_variant	8735	exon16			AGTCTCGTTCAGG	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.1812C>T	17.37:g.10247199G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	203	202	0.995074	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			G|0.817;A|0.183	0.183	strong		0.527	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
OR56A4	120793	hgsc.bcm.edu	37	11	6023581	6023581	+	Silent	SNP	A	A	G	rs11040248	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6023581A>G	ENST00000330728.4	-	1	843	c.798T>C	c.(796-798)ctT>ctC	p.L266L		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAATAAGGATAAGATCAGAGC	0.468													.|||	813	0.16234	0.0582	0.1945	5008	,	,		20590	0.0794		0.2694	False		,,,				2504	0.2556				p.L266L		Atlas-SNP	.											.	OR56A4	66	.	0			c.T798C						PASS	.	A		475,3927	222.6+/-239.4	30,415,1756	35.0	36.0	35.0		798	-0.8	0.2	11	dbSNP_120	35	2563,6029	415.9+/-351.9	399,1765,2132	no	coding-synonymous	OR56A4	NM_001005179.2		429,2180,3888	GG,GA,AA		29.8301,10.7905,23.38		266/366	6023581	3038,9956	2201	4296	6497	SO:0001819	synonymous_variant	120793	exon1			AAGGATAAGATCA	BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"""GPCR / Class A : Olfactory receptors"""	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.798T>C	11.37:g.6023581A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001005179	B9EH17	Silent	SNP	ENST00000330728.4	37	CCDS31404.1																																																																																			A|0.799;G|0.201	0.201	strong		0.468	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
DHX37	57647	hgsc.bcm.edu	37	12	125438712	125438712	+	Silent	SNP	C	C	A	rs11829165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:125438712C>A	ENST00000308736.2	-	19	2597	c.2499G>T	c.(2497-2499)cgG>cgT	p.R833R	DHX37_ENST00000544745.1_Silent_p.R620R	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	833							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CCACCCGGGCCCGCTTGCTCT	0.652													C|||	712	0.142173	0.4728	0.0605	5008	,	,		15886	0.0		0.0338	False		,,,				2504	0.0112				p.R833R		Atlas-SNP	.											DHX37,NS,carcinoma,0,1	DHX37	114	1	0			c.G2499T						PASS	.	C		1886,2520	527.8+/-372.2	401,1084,718	32.0	36.0	35.0		2499	2.4	1.0	12	dbSNP_120	35	342,8258	114.6+/-174.5	3,336,3961	no	coding-synonymous	DHX37	NM_032656.3		404,1420,4679	AA,AC,CC		3.9767,42.8053,17.1306		833/1158	125438712	2228,10778	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon19			CCGGGCCCGCTTG	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.2499G>T	12.37:g.125438712C>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	147	79	0.537415	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																			C|0.852;A|0.148	0.148	strong		0.652	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
FAT4	79633	hgsc.bcm.edu	37	4	126412575	126412575	+	Silent	SNP	A	A	G	rs1014866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:126412575A>G	ENST00000394329.3	+	17	14611	c.14598A>G	c.(14596-14598)agA>agG	p.R4866R	FAT4_ENST00000335110.5_Silent_p.R3107R	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4866					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATACTTCCAGAATGCCCAAAT	0.453													G|||	3709	0.740615	0.652	0.7205	5008	,	,		20986	0.8492		0.7644	False		,,,				2504	0.7382				p.R4866R		Atlas-SNP	.											.	FAT4	1752	.	0			c.A14598G						PASS	.	G		3131,1275	435.7+/-344.4	1114,903,186	68.0	68.0	68.0		14598	3.3	1.0	4	dbSNP_86	68	6548,2052	355.1+/-329.8	2499,1550,251	no	coding-synonymous	FAT4	NM_024582.4		3613,2453,437	GG,GA,AA		23.8605,28.9378,25.5805		4866/4982	126412575	9679,3327	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon17			TTCCAGAATGCCC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.14598A>G	4.37:g.126412575A>G		Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	311	311	1	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			A|0.242;G|0.758	0.758	strong		0.453	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
NCOR2	9612	hgsc.bcm.edu	37	12	124824869	124824869	+	Missense_Mutation	SNP	G	G	A	rs61755988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124824869G>A	ENST00000405201.1	-	36	5459	c.5459C>T	c.(5458-5460)aCg>aTg	p.T1820M	NCOR2_ENST00000397355.1_Missense_Mutation_p.T1811M|NCOR2_ENST00000429285.2_Missense_Mutation_p.T1810M|NCOR2_ENST00000404621.1_Missense_Mutation_p.T1810M|NCOR2_ENST00000356219.3_Missense_Mutation_p.T1827M|NCOR2_ENST00000404121.2_Missense_Mutation_p.T1381M			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1828					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GTGCTCCACCGTCGTGGTGGA	0.672													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		15239	0.0		0.004	False		,,,				2504	0.0				p.T1820M		Atlas-SNP	.											.	NCOR2	475	.	0			c.C5459T						PASS	.	G	MET/THR,MET/THR,MET/THR	7,4175		0,7,2084	54.0	65.0	61.0		5429,5429,5459	4.2	0.2	12	dbSNP_129	61	86,8354		0,86,4134	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	81,81,81	0,93,6218	AA,AG,GG		1.019,0.1674,0.7368	probably-damaging,probably-damaging,probably-damaging	1810/2459,1810/2505,1820/2515	124824869	93,12529	2091	4220	6311	SO:0001583	missense	9612	exon38			TCCACCGTCGTGG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5459C>T	12.37:g.124824869G>A	ENSP00000384018:p.Thr1820Met	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	8.853	0.944957	0.18356	0.001674	0.01019	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285	T;T;T;T;T;T	0.19394	2.15;2.42;2.16;2.42;2.16;2.42	4.18	4.18	0.49190	.	0.204758	0.40554	N	0.001069	T	0.30293	0.0760	L	0.40543	1.245	0.28417	N	0.917932	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.991;0.996;0.994	T	0.14671	-1.0464	10	0.72032	D	0.01	-13.5861	16.4861	0.84184	0.0:0.0:1.0:0.0	rs61755988	1810;1811;1820	C9J0Q5;C9J239;C9JFD3	.;.;.	M	1820;1810;1827;1811;1819;1381;1810	ENSP00000384018:T1820M;ENSP00000384202:T1810M;ENSP00000348551:T1827M;ENSP00000380513:T1811M;ENSP00000385618:T1381M;ENSP00000400281:T1810M	ENSP00000348551:T1827M	T	-	2	0	NCOR2	123390822	1.000000	0.71417	0.195000	0.23364	0.015000	0.08874	6.455000	0.73497	1.858000	0.53909	0.491000	0.48974	ACG	G|0.997;A|0.003	0.003	strong		0.672	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
NBPF14	25832	hgsc.bcm.edu	37	1	148009510	148009510	+	Silent	SNP	G	G	A	rs587690666	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:148009510G>A	ENST00000369219.1	-	16	1813	c.1797C>T	c.(1795-1797)agC>agT	p.S599S				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	599	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.S599S(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					ACAGCTCCCCGCTGAGCCTGG	0.463													-|||	58	0.0115815	0.0015	0.0043	5008	,	,		57574	0.0506		0.001	False		,,,				2504	0.001				p.S599S		Atlas-SNP	.											NBPF14,NS,carcinoma,0,1	NBPF14	107	1	1	Substitution - coding silent(1)	stomach(1)	c.C1797T						PASS	.						110.0	201.0	177.0					1																	148009510		1440	4051	5491	SO:0001819	synonymous_variant	25832	exon16			CTCCCCGCTGAGC	AK092351		1q21.1	2013-01-17			ENSG00000122497			"""neuroblastoma breakpoint family"""	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1797C>T	1.37:g.148009510G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	169	61	0.360947	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Silent	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	g	2.154	-0.393869	0.04899	.	.	ENSG00000122497	ENST00000310701	.	.	.	.	.	.	.	.	.	.	.	T	0.14270	0.0345	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.28808	-1.0032	1	.	.	.	.	.	.	.	rs56160124	.	.	.	V	605	.	.	A	-	2	0	NBPF14	146476134	0.993000	0.37304	.	.	.	.	0.748000	0.26305	.	.	.	.	GCG	G|0.500;A|0.500	0.500	weak		0.463	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383	
SELL	6402	hgsc.bcm.edu	37	1	169677709	169677709	+	Silent	SNP	A	A	G	rs1051091	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169677709A>G	ENST00000236147.4	-	3	520	c.360T>C	c.(358-360)ctT>ctC	p.L120L	SELL_ENST00000463108.1_5'UTR|C1orf112_ENST00000498289.1_Intron	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	107	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					CTTCTTCAGTAAGAGATTTGT	0.463													G|||	1503	0.30012	0.2965	0.3401	5008	,	,		19771	0.2679		0.2724	False		,,,				2504	0.3384				p.L120L		Atlas-SNP	.											.	SELL	43	.	0			c.T360C						PASS	.	G		1070,2948		137,796,1076	89.0	87.0	88.0		360	2.7	0.9	1	dbSNP_86	88	2025,6351		226,1573,2389	no	coding-synonymous	SELL	NM_000655.4		363,2369,3465	GG,GA,AA		24.1762,26.6302,24.9718		120/386	169677709	3095,9299	2009	4188	6197	SO:0001819	synonymous_variant	6402	exon3			TTCAGTAAGAGAT	M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"""CD molecules"""	10720	protein-coding gene	gene with protein product		153240	"""lymphocyte adhesion molecule 1"""	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.360T>C	1.37:g.169677709A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	206	121	0.587379	NM_000655	B2R6Q8|P15023|Q9UJ43	Silent	SNP	ENST00000236147.4	37	CCDS53427.1																																																																																			G|0.290;N|0.000	0.290	strong		0.463	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655	
C6orf89	221477	hgsc.bcm.edu	37	6	36887476	36887476	+	Splice_Site	SNP	C	C	T	rs11542163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:36887476C>T	ENST00000480824.2	+	8	1242	c.948C>T	c.(946-948)atC>atT	p.I316I	C6orf89_ENST00000355190.3_Splice_Site_p.I323I|C6orf89_ENST00000510325.2_Splice_Site_p.I210I|C6orf89_ENST00000373685.1_Splice_Site_p.I316I|C6orf89_ENST00000359359.2_Splice_Site_p.I210I			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	316					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						CAGGGGATATCGGTATGTAGG	0.463													C|||	591	0.118011	0.2753	0.0648	5008	,	,		17753	0.0119		0.0944	False		,,,				2504	0.0767				p.I323I		Atlas-SNP	.											.	C6orf89	39	.	0			c.C969T						PASS	.	C		980,3426	367.1+/-318.1	120,740,1343	84.0	75.0	78.0		969	-6.8	0.1	6	dbSNP_120	78	782,7818	184.9+/-232.8	40,702,3558	yes	coding-synonymous-near-splice	C6orf89	NM_152734.3		160,1442,4901	TT,TC,CC		9.093,22.2424,13.5476		323/355	36887476	1762,11244	2203	4300	6503	SO:0001630	splice_region_variant	221477	exon7			GGATATCGGTATG	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"""bombesin receptor activated protein"""					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.949+1C>T	6.37:g.36887476C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	131	76	0.580153	NM_152734	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Silent	SNP	ENST00000480824.2	37																																																																																				C|0.875;G|0.000;T|0.125	0.125	strong		0.463	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734	Silent
SCNN1A	6337	hgsc.bcm.edu	37	12	6472752	6472752	+	Missense_Mutation	SNP	G	G	A	rs55797039	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6472752G>A	ENST00000228916.2	-	3	639	c.541C>T	c.(541-543)Cgg>Tgg	p.R181W	SCNN1A_ENST00000358945.3_Missense_Mutation_p.R181W|SCNN1A_ENST00000396966.2_Missense_Mutation_p.R181W|SCNN1A_ENST00000538979.1_Intron|SCNN1A_ENST00000543768.1_Missense_Mutation_p.R204W|SCNN1A_ENST00000360168.3_Missense_Mutation_p.R240W|SCNN1A_ENST00000540037.1_5'UTR	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	181			R -> W (functional polymorphism; significant increase of amiloride- sensitive sodium currents; dbSNP:rs55797039). {ECO:0000269|PubMed:16207733, ECO:0000269|PubMed:19462466}.		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	AGAGTCCCCCGCAGGTCGCGA	0.682													G|||	36	0.0071885	0.0	0.0072	5008	,	,		10784	0.0		0.0209	False		,,,				2504	0.0102				p.R240W		Atlas-SNP	.											.	SCNN1A	54	.	0			c.C718T	GRCh37	CM055536	SCNN1A	M	rs55797039	PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	15,4385		0,15,2185	13.0	15.0	14.0		541,610,718	-3.5	0.0	12	dbSNP_129	14	141,8449		4,133,4158	no	missense,missense,missense	SCNN1A	NM_001038.5,NM_001159575.1,NM_001159576.1	101,101,101	4,148,6343	AA,AG,GG		1.6414,0.3409,1.2009	probably-damaging,probably-damaging,probably-damaging	181/670,204/693,240/729	6472752	156,12834	2200	4295	6495	SO:0001583	missense	6337	exon2			TCCCCCGCAGGTC	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.541C>T	12.37:g.6472752G>A	ENSP00000228916:p.Arg181Trp	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	17	11	0.647059	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	14.54	2.565723	0.45694	0.003409	0.016414	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000228916;ENST00000396966;ENST00000543768	T;T;T;T;T	0.70986	-0.49;-0.53;-0.46;-0.13;-0.47	5.46	-3.48	0.04739	.	1.661160	0.03643	N	0.239873	T	0.62974	0.2472	L	0.32530	0.975	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.998	P;P;P	0.59703	0.862;0.809;0.827	T	0.69870	-0.5028	10	0.59425	D	0.04	-31.5772	17.9864	0.89157	0.0:0.7352:0.164:0.1009	rs55797039;rs61759925	204;181;240	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	W	240;181;181;181;204	ENSP00000353292:R240W;ENSP00000351825:R181W;ENSP00000228916:R181W;ENSP00000380166:R181W;ENSP00000438739:R204W	ENSP00000228916:R181W	R	-	1	2	SCNN1A	6343013	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.833000	0.01695	-0.647000	0.05444	0.561000	0.74099	CGG	G|0.986;A|0.014	0.014	strong		0.682	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1		
MFRP	83552	hgsc.bcm.edu	37	11	119215046	119215046	+	Silent	SNP	C	C	T	rs35885438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:119215046C>T	ENST00000530681.1	-	8	1098	c.954G>A	c.(952-954)ctG>ctA	p.L318L	C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000555262.1_Silent_p.L318L|MFRP_ENST00000449574.2_Silent_p.L318L|MFRP_ENST00000360167.4_Intron|MFRP_ENST00000529147.1_5'Flank	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	318	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		GGTACTGCTGCAGGTAGCTGG	0.567													C|||	287	0.0573083	0.0295	0.0187	5008	,	,		19034	0.0357		0.0706	False		,,,				2504	0.1309				p.L318L		Atlas-SNP	.											.	MFRP	63	.	0			c.G954A						PASS	.	C	,	90,4308	76.2+/-114.5	0,90,2109	102.0	87.0	92.0		,954	1.5	0.6	11	dbSNP_126	92	401,8189	127.5+/-185.8	10,381,3904	no	utr-5,coding-synonymous	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,	10,471,6013	TT,TC,CC		4.6682,2.0464,3.7804	,	,318/580	119215046	491,12497	2199	4295	6494	SO:0001819	synonymous_variant	83552	exon8			CTGCTGCAGGTAG	AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"""membrane-type frizzled-related protein"", ""complement C1q tumor necrosis factor-related protein 5 precursor variant 1"""	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.954G>A	11.37:g.119215046C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Silent	SNP	ENST00000530681.1	37	CCDS8421.1																																																																																			C|0.962;T|0.038	0.038	strong		0.567	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433	
DUOX2	50506	hgsc.bcm.edu	37	15	45404066	45404066	+	Missense_Mutation	SNP	G	G	A	rs2001616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45404066G>A	ENST00000603300.1	-	5	615	c.413C>T	c.(412-414)cCc>cTc	p.P138L	DUOXA2_ENST00000323030.5_5'Flank|DUOX2_ENST00000389039.6_Missense_Mutation_p.P138L	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	138	Peroxidase-like; mediates peroxidase activity. {ECO:0000250}.		P -> L (in dbSNP:rs2001616). {ECO:0000269|PubMed:11514595}.		adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GTCGAACACGGGGTCTCCAGG	0.687													G|||	3806	0.759984	0.3555	0.804	5008	,	,		14527	0.9196		0.9115	False		,,,				2504	0.955				p.P138L		Atlas-SNP	.											.	DUOX2	137	.	0			c.C413T						PASS	.	G	LEU/PRO	1892,2504	527.8+/-372.2	424,1044,730	32.0	30.0	31.0		413	1.9	0.9	15	dbSNP_92	31	7763,833	764.3+/-407.6	3512,739,47	yes	missense	DUOX2	NM_014080.4	98	3936,1783,777	AA,AG,GG		9.6906,43.0391,25.685	benign	138/1549	45404066	9655,3337	2198	4298	6496	SO:0001583	missense	50506	exon5			AACACGGGGTCTC	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.413C>T	15.37:g.45404066G>A	ENSP00000475084:p.Pro138Leu	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	1706	0.7811355311355311	190	0.3861788617886179	308	0.850828729281768	514	0.8986013986013986	694	0.9155672823218998	G	15.06	2.721245	0.48728	0.430391	0.903094	ENSG00000140279	ENST00000389039	.	.	.	5.22	1.9	0.25705	.	0.195193	0.45606	D	0.000352	T	0.00012	0.0000	M	0.66506	2.035	0.09310	P	0.99999293406	B	0.18863	0.031	B	0.23852	0.049	T	0.10200	-1.0640	8	0.54805	T	0.06	-22.1546	6.7593	0.23532	0.2274:0.0:0.6385:0.1341	rs2001616;rs2001616	138	Q9NRD8	DUOX2_HUMAN	L	138	.	ENSP00000373691:P138L	P	-	2	0	DUOX2	43191358	0.996000	0.38824	0.859000	0.33776	0.895000	0.52256	2.409000	0.44583	0.603000	0.29913	-0.219000	0.12488	CCC	G|0.234;A|0.766	0.766	strong		0.687	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
TRPC1	7220	hgsc.bcm.edu	37	3	142503605	142503605	+	Silent	SNP	G	G	A	rs7621642	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:142503605G>A	ENST00000476941.1	+	7	1506	c.1020G>A	c.(1018-1020)tcG>tcA	p.S340S	TRPC1_ENST00000273482.6_Silent_p.S306S	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	340					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.S306S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						GACAGATGTCGGGTTACCGAC	0.408													A|||	1989	0.397165	0.7602	0.1873	5008	,	,		18120	0.4077		0.2256	False		,,,				2504	0.2209				p.S340S		Atlas-SNP	.											TRPC1,NS,carcinoma,0,1	TRPC1	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G1020A						PASS	.	A		2947,1459	470.4+/-355.7	989,969,245	121.0	111.0	115.0		918	2.0	1.0	3	dbSNP_116	115	1792,6808	733.4+/-406.9	206,1380,2714	no	coding-synonymous	TRPC1	NM_003304.4		1195,2349,2959	AA,AG,GG		20.8372,33.1139,36.437		306/760	142503605	4739,8267	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon7			GATGTCGGGTTAC	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.1020G>A	3.37:g.142503605G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			G|0.616;A|0.384	0.384	strong		0.408	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
MUC4	4585	hgsc.bcm.edu	37	3	195511268	195511268	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195511268T>A	ENST00000463781.3	-	2	7642	c.7183A>T	c.(7183-7185)Aca>Tca	p.T2395S	MUC4_ENST00000475231.1_Missense_Mutation_p.T2395S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGTCACCTGTGGATGCTGAG	0.592																																					p.T2395S		Atlas-SNP	.											.	MUC4	1505	.	0			c.A7183T						PASS	.						27.0	30.0	29.0					3																	195511268		688	1585	2273	SO:0001583	missense	4585	exon2			CACCTGTGGATGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7183A>T	3.37:g.195511268T>A	ENSP00000417498:p.Thr2395Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	569	27	0.0474517	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	T	5.173	0.217483	0.09810	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.50277	0.75;0.79	.	.	.	.	.	.	.	.	T	0.25680	0.0625	N	0.19112	0.55	0.09310	N	1	P	0.37985	0.613	B	0.35899	0.213	T	0.09952	-1.0651	7	.	.	.	.	2.7352	0.05238	0.0:0.3911:0.0:0.6089	.	2395	E7ESK3	.	S	2395	ENSP00000417498:T2395S;ENSP00000420243:T2395S	.	T	-	1	0	MUC4	196995663	0.004000	0.15560	0.008000	0.14137	0.059000	0.15707	0.962000	0.29280	0.408000	0.25621	0.055000	0.15244	ACA	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GAS2	2620	hgsc.bcm.edu	37	11	22696451	22696451	+	Silent	SNP	A	A	G	rs922571	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:22696451A>G	ENST00000454584.2	+	2	341	c.36A>G	c.(34-36)ggA>ggG	p.G12G	GAS2_ENST00000278187.3_Silent_p.G12G|GAS2_ENST00000533092.1_3'UTR|GAS2_ENST00000433790.1_Silent_p.G12G	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	12					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|regulation of cell shape (GO:0008360)	actin filament (GO:0005884)|cytosol (GO:0005829)|membrane (GO:0016020)		p.G12G(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(4)|stomach(1)	24						TACGCAGTGGACCTGGCCTCT	0.428													A|||	2625	0.524161	0.1747	0.6095	5008	,	,		18535	0.749		0.67	False		,,,				2504	0.5542				p.G12G		Atlas-SNP	.											GAS2,NS,carcinoma,0,1	GAS2	46	1	1	Substitution - coding silent(1)	stomach(1)	c.A36G						PASS	.	A	,,	1132,3274	401.0+/-331.8	144,844,1215	98.0	93.0	95.0		36,36,36	0.2	1.0	11	dbSNP_86	95	5943,2657	685.3+/-404.0	2048,1847,405	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS2	NM_001143830.1,NM_005256.3,NM_177553.2	,,	2192,2691,1620	GG,GA,AA		30.8953,25.6922,45.602	,,	12/314,12/314,12/314	22696451	7075,5931	2203	4300	6503	SO:0001819	synonymous_variant	2620	exon2			CAGTGGACCTGGC	BC040470	CCDS7858.1	11p14.3	2005-10-11			ENSG00000148935	ENSG00000148935			4167	protein-coding gene	gene with protein product		602835				9521882	Standard	NM_005256		Approved		uc001mqo.3	O43903	OTTHUMG00000166071	ENST00000454584.2:c.36A>G	11.37:g.22696451A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_177553	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Silent	SNP	ENST00000454584.2	37	CCDS7858.1																																																																																			A|0.457;G|0.543	0.543	strong		0.428	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553	
LAMA3	3909	hgsc.bcm.edu	37	18	21492734	21492734	+	Silent	SNP	C	C	T	rs62093184		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21492734C>T	ENST00000313654.9	+	56	7459	c.7218C>T	c.(7216-7218)gaC>gaT	p.D2406D	LAMA3_ENST00000399516.3_Silent_p.D2350D|LAMA3_ENST00000269217.6_Silent_p.D797D|LAMA3_ENST00000587184.1_Silent_p.D741D|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2406	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TGCCAAATGACCTGGAAGATT	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		22166	0.0		0.001	False		,,,				2504	0.0				p.D2406D		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7218T						PASS	.	C	,,,	3,4403	6.2+/-15.9	0,3,2200	114.0	113.0	114.0		2391,7050,2223,7218	4.8	1.0	18	dbSNP_129	114	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	0,20,6483	TT,TC,CC		0.1977,0.0681,0.1538	,,,	797/1725,2350/3278,741/1669,2406/3334	21492734	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon56			AAATGACCTGGAA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7218C>T	18.37:g.21492734C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.999;T|0.001	0.001	strong		0.448	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
FRYL	285527	hgsc.bcm.edu	37	4	48582909	48582909	+	Silent	SNP	G	G	A	rs4695391	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:48582909G>A	ENST00000503238.1	-	19	2231	c.2232C>T	c.(2230-2232)agC>agT	p.S744S	FRYL_ENST00000358350.4_Silent_p.S744S|FRYL_ENST00000537810.1_Silent_p.S744S|FRYL_ENST00000506685.1_Silent_p.S450S|FRYL_ENST00000507711.1_Silent_p.S744S|FRYL_ENST00000264319.7_5'UTR			O94915	FRYL_HUMAN	FRY-like	744					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GATGTATGAAGCTCTCAAGAA	0.373													G|||	1940	0.38738	0.171	0.5749	5008	,	,		16054	0.4464		0.5189	False		,,,				2504	0.3507				p.S744S		Atlas-SNP	.											.	FRYL	242	.	0			c.C2232T						PASS	.	G		769,3003		77,615,1194	123.0	113.0	116.0		2232	4.2	1.0	4	dbSNP_111	116	3934,4324		939,2056,1134	no	coding-synonymous	FRYL	NM_015030.1		1016,2671,2328	AA,AG,GG		47.6387,20.3871,39.0939		744/3014	48582909	4703,7327	1886	4129	6015	SO:0001819	synonymous_variant	285527	exon22			TATGAAGCTCTCA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.2232C>T	4.37:g.48582909G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	CCDS43227.1																																																																																			G|0.570;A|0.430	0.430	strong		0.373	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
MCPH1	79648	hgsc.bcm.edu	37	8	6272399	6272399	+	Silent	SNP	G	G	T	rs2305022	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:6272399G>T	ENST00000344683.5	+	3	304	c.228G>T	c.(226-228)gtG>gtT	p.V76V	MCPH1_ENST00000519480.1_Silent_p.V76V|MCPH1_ENST00000522905.1_Silent_p.V76V	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	76	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		TGCTCTGGGTGGAAAAGTAAG	0.393													T|||	3396	0.678115	0.379	0.8256	5008	,	,		19538	0.7808		0.7913	False		,,,				2504	0.7556				p.V76V	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.G228T						PASS	.	T	,,	1714,1954		386,942,506	101.0	91.0	94.0		228,228,228	-7.5	0.7	8	dbSNP_100	94	6543,1619		2596,1351,134	no	coding-synonymous,coding-synonymous,coding-synonymous	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	,,	2982,2293,640	TT,TG,GG		19.8358,46.7285,30.2029	,,	76/611,76/563,76/836	6272399	8257,3573	1834	4081	5915	SO:0001819	synonymous_variant	79648	exon3			CTGGGTGGAAAAG	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.228G>T	8.37:g.6272399G>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_001172575	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	37	CCDS43689.1																																																																																			G|0.306;T|0.694	0.694	strong		0.393	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
MAGEB10	139422	hgsc.bcm.edu	37	X	27839617	27839617	+	Missense_Mutation	SNP	G	G	A	rs12557898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:27839617G>A	ENST00000356790.2	+	3	439	c.194G>A	c.(193-195)cGg>cAg	p.R65Q		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	65			R -> Q (in dbSNP:rs12557898). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						CATGGACTTCGGGAAGCCCAA	0.498													G|||	792	0.209801	0.1112	0.1873	3775	,	,		13898	0.0357		0.3559	False		,,,				2504	0.1237				p.R65Q		Atlas-SNP	.											.	MAGEB10	107	.	0			c.G194A						PASS	.	G	GLN/ARG	678,3155		54,465,105,1112,466	58.0	45.0	49.0		194	-5.0	0.0	X	dbSNP_120	49	3376,3351		620,1200,936,608,935	yes	missense	MAGEB10	NM_182506.3	43	674,1665,1041,1720,1401	AA,AG,A,GG,G		49.8142,17.6885,38.3902	benign	65/348	27839617	4054,6506	2202	4299	6501	SO:0001583	missense	139422	exon3			GACTTCGGGAAGC		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.194G>A	X.37:g.27839617G>A	ENSP00000368304:p.Arg65Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Missense_Mutation	SNP	ENST00000356790.2	37	CCDS35221.1	407	0.24532851115129597	35	0.07608695652173914	52	0.16666666666666666	13	0.022887323943661973	184	0.3076923076923077	g	0.010	-1.757108	0.00657	0.176885	0.501858	ENSG00000177689	ENST00000356790	T	0.02737	4.18	2.52	-5.04	0.02964	Melanoma associated antigen, MAGE, N-terminal (1);	14.954800	0.00166	N	0.000004	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.15141	0.012	B	0.09377	0.004	T	0.43940	-0.9360	9	0.02654	T	1	.	4.2766	0.10811	0.4058:0.3297:0.2645:0.0	rs12557898;rs52801205;rs58263199;rs12557898	65	Q96LZ2	MAGBA_HUMAN	Q	65	ENSP00000368304:R65Q	ENSP00000368304:R65Q	R	+	2	0	MAGEB10	27749538	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.569000	0.05902	-1.585000	0.01634	-2.735000	0.00129	CGG	0|0.012;A|0.299	0.299	strong		0.498	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506	
SEMA5B	54437	hgsc.bcm.edu	37	3	122630372	122630372	+	Silent	SNP	T	T	C	rs61996303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122630372T>C	ENST00000357599.3	-	21	3443	c.3057A>G	c.(3055-3057)ccA>ccG	p.P1019P	SEMA5B_ENST00000195173.4_Silent_p.P1017P|SEMA5B_ENST00000451055.2_Silent_p.P1073P	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	1019					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TGCTGGAGGCTGGCAGGATGA	0.642													T|||	46	0.0091853	0.0008	0.0202	5008	,	,		19167	0.001		0.0199	False		,,,				2504	0.0102				p.P1073P		Atlas-SNP	.											.	SEMA5B	303	.	0			c.A3219G						PASS	.	T		15,4389	22.3+/-47.3	0,15,2187	49.0	45.0	46.0		3057	-0.3	1.0	3	dbSNP_129	46	114,8486	58.3+/-119.8	0,114,4186	no	coding-synonymous	SEMA5B	NM_001031702.2		0,129,6373	CC,CT,TT		1.3256,0.3406,0.992		1019/1152	122630372	129,12875	2202	4300	6502	SO:0001819	synonymous_variant	54437	exon21			GGAGGCTGGCAGG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.3057A>G	3.37:g.122630372T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1	26	0.011904761904761904	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	17	0.022427440633245383	T	10.15	1.270453	0.23221	0.003406	0.013256	ENSG00000082684	ENST00000451541	.	.	.	5.02	-0.328	0.12690	.	.	.	.	.	T	0.26557	0.0649	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.14172	-1.0482	4	.	.	.	.	2.5878	0.04835	0.3049:0.1113:0.0788:0.505	.	.	.	.	R	65	.	.	Q	-	2	0	SEMA5B	124113062	0.812000	0.29077	0.996000	0.52242	0.913000	0.54294	-0.242000	0.08928	-0.189000	0.10482	-0.327000	0.08410	CAG	T|0.990;C|0.010	0.010	strong		0.642	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
HECTD3	79654	hgsc.bcm.edu	37	1	45469176	45469176	+	Silent	SNP	A	A	T	rs12749251	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45469176A>T	ENST00000372172.4	-	21	2645	c.2574T>A	c.(2572-2574)ccT>ccA	p.P858P	HECTD3_ENST00000486132.1_5'UTR|HECTD3_ENST00000372168.3_Silent_p.P468P	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	858					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					ACTCCTCCCAAGGGCTCATGT	0.627													A|||	258	0.0515176	0.0272	0.0591	5008	,	,		21716	0.001		0.1123	False		,,,				2504	0.0685				p.P858P		Atlas-SNP	.											.	HECTD3	158	.	0			c.T2574A						PASS	.	A		205,4127		6,193,1967	66.0	71.0	69.0		2574	2.2	1.0	1	dbSNP_121	69	1238,7276		105,1028,3124	no	coding-synonymous	HECTD3	NM_024602.5		111,1221,5091	TT,TA,AA		14.5408,4.7322,11.2331		858/862	45469176	1443,11403	2166	4257	6423	SO:0001819	synonymous_variant	79654	exon21			CTCCCAAGGGCTC	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"""HECT domain containing 3"""			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2574T>A	1.37:g.45469176A>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	112	75	0.669643	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	37	CCDS41318.1																																																																																			A|0.892;T|0.108	0.108	strong		0.627	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602	
ZDHHC6	64429	hgsc.bcm.edu	37	10	114200355	114200355	+	Silent	SNP	G	G	A	rs2306159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:114200355G>A	ENST00000369405.3	-	5	1041	c.618C>T	c.(616-618)acC>acT	p.T206T	ZDHHC6_ENST00000369404.3_Silent_p.T202T	NM_022494.1	NP_071939.1	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	206					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)		AGGCAAACAAGGTGGTAGCAA	0.443													G|||	2574	0.513978	0.3684	0.5677	5008	,	,		15821	0.4802		0.6014	False		,,,				2504	0.6176				p.T206T		Atlas-SNP	.											.	ZDHHC6	32	.	0			c.C618T						PASS	.	G		1673,2733	509.8+/-367.3	318,1037,848	170.0	154.0	159.0		618	0.5	1.0	10	dbSNP_100	159	4989,3611	625.7+/-397.7	1472,2045,783	no	coding-synonymous	ZDHHC6	NM_022494.1		1790,3082,1631	AA,AG,GG		41.9884,37.9709,48.7775		206/414	114200355	6662,6344	2203	4300	6503	SO:0001819	synonymous_variant	64429	exon5			AAACAAGGTGGTA	AK025605	CCDS7574.1	10q26.11	2008-05-02			ENSG00000023041	ENSG00000023041		"""Zinc fingers, DHHC-type"""	19160	protein-coding gene	gene with protein product							Standard	NM_022494		Approved	ZNF376, FLJ21952	uc001kzv.3	Q9H6R6	OTTHUMG00000019062	ENST00000369405.3:c.618C>T	10.37:g.114200355G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_022494	D3DRB6|Q53G45|Q96IV7|Q9H605	Silent	SNP	ENST00000369405.3	37	CCDS7574.1																																																																																			G|0.496;A|0.504	0.504	strong		0.443	ZDHHC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050393.1	NM_022494	
ACP1	52	hgsc.bcm.edu	37	2	272203	272203	+	Intron	SNP	C	C	T	rs11553746	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:272203C>T	ENST00000272065.5	+	3	324				ACP1_ENST00000484464.1_Intron|ACP1_ENST00000405233.1_Missense_Mutation_p.T53I|ACP1_ENST00000439645.2_Silent_p.D43D|ACP1_ENST00000272067.6_Silent_p.D43D|ACP1_ENST00000407983.3_Missense_Mutation_p.T95I	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble							cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	GGGTCATTGACAGCGGTGCTG	0.542													C|||	1219	0.243411	0.1286	0.232	5008	,	,		16562	0.249		0.334	False		,,,				2504	0.3078				p.T95I		Atlas-SNP	.											ACP1_ENST00000272067,NS,carcinoma,+1,1	ACP1	42	1	0			c.C284T						PASS	.	C	ILE/THR,,	749,3657	306.3+/-289.4	63,623,1517	185.0	149.0	161.0		284,,129	5.9	1.0	2	dbSNP_120	161	2963,5637	459.5+/-364.9	486,1991,1823	yes	missense,intron,coding-synonymous	ACP1	NM_001040649.2,NM_004300.3,NM_007099.3	89,,	549,2614,3340	TT,TC,CC		34.4535,16.9995,28.5407	,,	95/113,,43/159	272203	3712,9294	2203	4300	6503	SO:0001627	intron_variant	52	exon3			CATTGACAGCGGT	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"""Protein tyrosine phosphatases / Class II Cys-based PTPs"""	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.231+53C>T	2.37:g.272203C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	248	124	0.5	NM_001040649	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Missense_Mutation	SNP	ENST00000272065.5	37	CCDS1639.1	520	0.23809523809523808	56	0.11382113821138211	86	0.23756906077348067	126	0.2202797202797203	252	0.3324538258575198	C	17.56	3.419926	0.62622	0.169995	0.344535	ENSG00000143727	ENST00000407983;ENST00000405233;ENST00000449425	T;T	0.47528	0.91;0.84	5.87	5.87	0.94306	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.28039	P	0.9338388	D	0.76494	0.999	D	0.83275	0.996	T	0.01697	-1.1293	7	0.44086	T	0.13	-21.5954	17.6971	0.88285	0.0:1.0:0.0:0.0	rs11553746	95	B5MCC7	.	I	95;53;53	ENSP00000385404:T95I;ENSP00000384307:T53I	ENSP00000384307:T53I	T	+	2	0	ACP1	262203	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.667000	0.68067	2.779000	0.95612	0.655000	0.94253	ACA	C|0.738;T|0.262	0.262	strong		0.542	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3		
TNXB	7148	hgsc.bcm.edu	37	6	32017242	32017242	+	Missense_Mutation	SNP	C	C	T	rs41258944	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32017242C>T	ENST00000375244.3	-	28	9763	c.9562G>A	c.(9562-9564)Gtc>Atc	p.V3188I	TNXB_ENST00000375247.2_Missense_Mutation_p.V3186I			P22105	TENX_HUMAN	tenascin XB	3233	Fibronectin type-III 23. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCCTGGGGGACGGTCCAGGAG	0.677													C|||	364	0.0726837	0.1263	0.0317	5008	,	,		14429	0.0089		0.0686	False		,,,				2504	0.0992				p.V3186I		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,0,2	TNXB	553	2	0			c.G9556A						PASS	.	C	ILE/VAL	283,2221		18,247,987	61.0	67.0	65.0		9556	3.5	0.9	6	dbSNP_127	65	313,4721		14,285,2218	no	missense	TNXB	NM_019105.6	29	32,532,3205	TT,TC,CC		6.2177,11.3019,7.9066	probably-damaging	3186/4243	32017242	596,6942	1252	2517	3769	SO:0001583	missense	7148	exon28			GGGGGACGGTCCA	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9562G>A	6.37:g.32017242C>T	ENSP00000364393:p.Val3188Ile	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	254	150	0.590551	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		154	0.07051282051282051	83	0.16869918699186992	9	0.024861878453038673	6	0.01048951048951049	56	0.07387862796833773	C	16.71	3.199498	0.58126	0.113019	0.062177	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56776	0.44;0.44	4.39	3.51	0.40186	.	0.164586	0.28871	N	0.013875	T	0.53334	0.1790	M	0.64170	1.965	0.43814	P	0.003627000000000047	D	0.61697	0.99	D	0.64595	0.927	T	0.54050	-0.8351	9	0.36615	T	0.2	.	9.9009	0.41346	0.0:0.8985:0.0:0.1015	rs41258944;rs62402695	3186	P22105-3	.	I	3188;3186	ENSP00000364393:V3188I;ENSP00000364396:V3186I	ENSP00000364393:V3188I	V	-	1	0	TNXB	32125220	0.002000	0.14202	0.927000	0.36925	0.813000	0.45954	0.228000	0.17814	2.006000	0.58801	0.306000	0.20318	GTC	C|0.855;T|0.145	0.145	strong		0.677	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
SPATA19	219938	hgsc.bcm.edu	37	11	133714522	133714522	+	Missense_Mutation	SNP	G	G	A	rs2282602	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:133714522G>A	ENST00000299140.3	-	3	203	c.149C>T	c.(148-150)gCt>gTt	p.A50V	SPATA19_ENST00000532889.1_Missense_Mutation_p.A50V	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	50			A -> V (in dbSNP:rs2282602). {ECO:0000269|PubMed:12688595}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		GCCCCGAGAAGCCTCTTCTTC	0.498													G|||	1700	0.339457	0.1044	0.317	5008	,	,		20435	0.6022		0.3926	False		,,,				2504	0.3476				p.A50V		Atlas-SNP	.											.	SPATA19	36	.	0			c.C149T						PASS	.	G	VAL/ALA	741,3661	305.5+/-289.0	65,611,1525	100.0	102.0	101.0		149	5.0	1.0	11	dbSNP_100	101	3216,5378	485.9+/-371.8	616,1984,1697	yes	missense	SPATA19	NM_174927.1	64	681,2595,3222	AA,AG,GG		37.4215,16.8333,30.4478	possibly-damaging	50/168	133714522	3957,9039	2201	4297	6498	SO:0001583	missense	219938	exon3			CGAGAAGCCTCTT	AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"""spergen 1"", ""cancer/testis antigen 132"""	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.149C>T	11.37:g.133714522G>A	ENSP00000299140:p.Ala50Val	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_174927	Q8N7A9	Missense_Mutation	SNP	ENST00000299140.3	37	CCDS8493.1	796	0.36446886446886445	48	0.0975609756097561	120	0.3314917127071823	329	0.5751748251748252	299	0.3944591029023747	G	20.4	3.990884	0.74703	0.168333	0.374215	ENSG00000166118	ENST00000299140;ENST00000532889	T;T	0.56611	0.45;0.45	5.02	5.02	0.67125	.	0.000000	0.56097	D	0.000029	T	0.00012	0.0000	L	0.34521	1.04	0.26466	P	0.9753572	D	0.76494	0.999	D	0.80764	0.994	T	0.50734	-0.8793	9	0.52906	T	0.07	-6.9761	14.1925	0.65646	0.0:0.0:1.0:0.0	rs2282602;rs61530072;rs2282602	50	Q7Z5L4	SPT19_HUMAN	V	50	ENSP00000299140:A50V;ENSP00000435248:A50V	ENSP00000299140:A50V	A	-	2	0	SPATA19	133219732	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	3.306000	0.51881	2.493000	0.84123	0.655000	0.94253	GCT	G|0.673;A|0.327	0.327	strong		0.498	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927	
DOCK8	81704	hgsc.bcm.edu	37	9	421032	421032	+	Silent	SNP	C	C	G	rs2297079	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:421032C>G	ENST00000453981.1	+	32	4219	c.4107C>G	c.(4105-4107)ctC>ctG	p.L1369L	DOCK8_ENST00000493666.2_3'UTR|DOCK8_ENST00000382329.1_Silent_p.L836L|DOCK8_ENST00000469391.1_Silent_p.L1269L|DOCK8_ENST00000432829.2_Silent_p.L1301L			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1369					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		AGGCTTTGCTCCGTGGGGAAG	0.567													C|||	1962	0.391773	0.0809	0.4352	5008	,	,		19327	0.499		0.6203	False		,,,				2504	0.4356				p.L1369L		Atlas-SNP	.											.	DOCK8	401	.	0			c.C4107G						PASS	.	C	,,	742,3664	304.1+/-288.3	67,608,1528	78.0	80.0	79.0		3807,3903,4107	2.8	1.0	9	dbSNP_100	79	5275,3325	644.1+/-400.0	1620,2035,645	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	1687,2643,2173	GG,GC,CC		38.6628,16.8407,46.2633	,,	1269/2000,1301/2032,1369/2100	421032	6017,6989	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon32			TTTGCTCCGTGGG	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.4107C>G	9.37:g.421032C>G		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	197	195	0.989848	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			C|0.538;G|0.462	0.462	strong		0.567	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
COPS3	8533	hgsc.bcm.edu	37	17	17168164	17168164	+	Silent	SNP	G	G	A	rs3182911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17168164G>A	ENST00000268717.5	-	6	679	c.573C>T	c.(571-573)atC>atT	p.I191I	COPS3_ENST00000439936.2_Silent_p.I171I|COPS3_ENST00000539941.2_Silent_p.I171I	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	191					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						GCCCAGTATAGATCATCCCTC	0.358													G|||	2435	0.486222	0.3215	0.5317	5008	,	,		18745	0.6558		0.5119	False		,,,				2504	0.4755				p.I191I		Atlas-SNP	.											.	COPS3	41	.	0			c.C573T						PASS	.	G	,	1436,2970	466.0+/-354.4	239,958,1006	93.0	89.0	90.0		513,573	3.8	1.0	17	dbSNP_105	90	4292,4308	575.5+/-390.2	1062,2168,1070	no	coding-synonymous,coding-synonymous	COPS3	NM_001199125.1,NM_003653.3	,	1301,3126,2076	AA,AG,GG		49.907,32.5919,44.0412	,	171/404,191/424	17168164	5728,7278	2203	4300	6503	SO:0001819	synonymous_variant	8533	exon6			AGTATAGATCATC	AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3"", ""COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"""			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.573C>T	17.37:g.17168164G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	114	66	0.578947	NM_003653	B2R683|B4DY81|O43191|Q7LDR6	Silent	SNP	ENST00000268717.5	37	CCDS11183.1																																																																																			G|0.540;N|0.000	.	strong		0.358	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2		
LYPD2	137797	hgsc.bcm.edu	37	8	143833840	143833840	+	Silent	SNP	C	C	G	rs78400087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143833840C>G	ENST00000359228.3	-	1	112	c.30G>C	c.(28-30)gcG>gcC	p.A10A		NM_205545.1	NP_991108.1	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2	10						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CCAGCACCAGCGCCAGGAGCG	0.687													C|||	46	0.0091853	0.0015	0.0159	5008	,	,		12658	0.0		0.0328	False		,,,				2504	0.0				p.A10A		Atlas-SNP	.											LYPD2,NS,carcinoma,0,1	LYPD2	18	1	0			c.G30C						PASS	.	C		20,4384	24.3+/-50.5	0,20,2182	44.0	50.0	48.0		30	-3.3	0.0	8	dbSNP_133	48	186,8406	78.4+/-141.0	4,178,4114	no	coding-synonymous	LYPD2	NM_205545.1		4,198,6296	GG,GC,CC		2.1648,0.4541,1.5851		10/126	143833840	206,12790	2202	4296	6498	SO:0001819	synonymous_variant	137797	exon1			CACCAGCGCCAGG	AY358432	CCDS6388.1	8q24.3	2005-08-30		2005-08-30	ENSG00000197353	ENSG00000197353			25215	protein-coding gene	gene with protein product				LYPDC2		12975309	Standard	NM_205545		Approved	RGTR430, UNQ430	uc003ywz.3	Q6UXB3	OTTHUMG00000164686	ENST00000359228.3:c.30G>C	8.37:g.143833840C>G		Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	162	82	0.506173	NM_205545	A8K2R6|Q0VD64|Q0VF31	Silent	SNP	ENST00000359228.3	37	CCDS6388.1																																																																																			C|0.985;G|0.015	0.015	strong		0.687	LYPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379742.1	NM_205545	
GSDMD	79792	hgsc.bcm.edu	37	8	144642854	144642854	+	Silent	SNP	G	G	A	rs11551202	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144642854G>A	ENST00000526406.1	+	7	1375	c.492G>A	c.(490-492)ctG>ctA	p.L164L	GSDMD_ENST00000533063.1_Silent_p.L212L|GSDMD_ENST00000262580.4_Silent_p.L164L	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN	gasdermin D	164					cellular response to extracellular stimulus (GO:0031668)					breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						CTGAGGTGCTGCAGACACAGA	0.652													G|||	833	0.166334	0.1263	0.2594	5008	,	,		11973	0.0794		0.1918	False		,,,				2504	0.2178				p.L164L		Atlas-SNP	.											GSDMD,NS,carcinoma,0,1	GSDMD	28	1	0			c.G492A						PASS	.	G	,	628,3730		43,542,1594	34.0	27.0	29.0		492,492	1.6	1.0	8	dbSNP_120	29	1549,7025		140,1269,2878	no	coding-synonymous,coding-synonymous	GSDMD	NM_001166237.1,NM_024736.6	,	183,1811,4472	AA,AG,GG		18.0662,14.4103,16.8342	,	164/485,164/485	144642854	2177,10755	2179	4287	6466	SO:0001819	synonymous_variant	79792	exon7			GGTGCTGCAGACA	AK096216	CCDS34956.1	8q24.3	2008-07-31	2008-07-31	2008-07-31		ENSG00000104518			25697	protein-coding gene	gene with protein product			"""gasdermin domain containing 1"""	GSDMDC1		15289881, 17350798	Standard	NM_024736		Approved	FLJ12150, DF5L	uc003yyg.3	P57764		ENST00000526406.1:c.492G>A	8.37:g.144642854G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_001166237	D3DWJ9|Q96Q98	Silent	SNP	ENST00000526406.1	37	CCDS34956.1																																																																																			G|0.836;A|0.164	0.164	strong		0.652	GSDMD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382046.3	NM_024736	
AIFM2	84883	hgsc.bcm.edu	37	10	71874048	71874048	+	Silent	SNP	G	G	A	rs1053495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71874048G>A	ENST00000307864.1	-	9	1221	c.1008C>T	c.(1006-1008)gaC>gaT	p.D336D	AIFM2_ENST00000373248.1_Silent_p.D336D|AIFM2_ENST00000482166.1_5'Flank	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	336					apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						GGCCCACACCGTCATTTCTCC	0.582													G|||	949	0.189497	0.2859	0.0735	5008	,	,		17271	0.1835		0.1024	False		,,,				2504	0.2372				p.D336D		Atlas-SNP	.											.	AIFM2	33	.	0			c.C1008T						PASS	.	G	,	1052,3354	385.1+/-325.6	122,808,1273	75.0	70.0	72.0		1008,1008	-2.6	1.0	10	dbSNP_86	72	714,7886	174.6+/-224.8	30,654,3616	no	coding-synonymous,coding-synonymous	AIFM2	NM_001198696.1,NM_032797.5	,	152,1462,4889	AA,AG,GG		8.3023,23.8765,13.5783	,	336/374,336/374	71874048	1766,11240	2203	4300	6503	SO:0001819	synonymous_variant	84883	exon9			CACACCGTCATTT	AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"""apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"""	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.1008C>T	10.37:g.71874048G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_001198696	B3KXI0|Q63Z39	Silent	SNP	ENST00000307864.1	37	CCDS7297.1																																																																																			G|0.845;A|0.155	0.155	strong		0.582	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797	
ROBO4	54538	hgsc.bcm.edu	37	11	124767125	124767125	+	Silent	SNP	G	G	A	rs73016370	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124767125G>A	ENST00000306534.3	-	2	588	c.103C>T	c.(103-105)Cta>Tta	p.L35L	ROBO4_ENST00000533054.1_Intron|ROBO4_ENST00000526899.1_5'UTR	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	35	Ig-like C2-type 1.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGGTGGACTAGGATCTGGGGC	0.652													G|||	498	0.0994409	0.003	0.0735	5008	,	,		15800	0.2054		0.0974	False		,,,				2504	0.1411				p.L35L		Atlas-SNP	.											.	ROBO4	130	.	0			c.C103T						PASS	.	G		91,4271		1,89,2091	11.0	10.0	11.0		103	2.6	0.6	11	dbSNP_130	11	797,7743		47,703,3520	no	coding-synonymous	ROBO4	NM_019055.5		48,792,5611	AA,AG,GG		9.3326,2.0862,6.8827		35/1008	124767125	888,12014	2181	4270	6451	SO:0001819	synonymous_variant	54538	exon2			GGACTAGGATCTG	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.103C>T	11.37:g.124767125G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			G|0.919;A|0.081	0.081	strong		0.652	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487174	32487174	+	Missense_Mutation	SNP	C	C	G	rs112872773	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32487174C>G	ENST00000374975.3	-	3	687	c.625G>C	c.(625-627)Gtg>Ctg	p.V209L		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						GGGCTCGTCACGCTTGGGTGC	0.498													C|||	573	0.114417	0.0454	0.2104	5008	,	,		12481	0.121		0.16	False		,,,				2504	0.0859				p.V209L		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	0			c.G625C						scavenged	.	C	LEU/VAL	203,3581		25,153,1714	73.0	83.0	80.0		625	-3.6	0.0	6	dbSNP_132	80	1085,6435		126,833,2801	no	missense	HLA-DRB5	NM_002125.3	32	151,986,4515	GG,GC,CC		14.4282,5.3647,11.3942	benign	209/267	32487174	1288,10016	1892	3760	5652	SO:0001583	missense	3127	exon3			TCGTCACGCTTGG		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.625G>C	6.37:g.32487174C>G	ENSP00000364114:p.Val209Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	215	114	0.530233	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	0.979	-0.697691	0.03279	0.053647	0.144282	ENSG00000198502	ENST00000374975	T	0.01629	4.72	4.36	-3.57	0.04612	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.816604	0.11096	N	0.600213	T	0.00073	0.0002	N	0.00008	-3.11	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.38950	-0.9637	9	0.14656	T	0.56	.	1.4755	0.02425	0.3123:0.2462:0.3234:0.118	.	136;209	Q29973;Q30154	.;DRB5_HUMAN	L	209	ENSP00000364114:V209L	ENSP00000364114:V209L	V	-	1	0	HLA-DRB5	32595152	0.507000	0.26146	0.000000	0.03702	0.022000	0.10575	0.581000	0.23819	-0.961000	0.03609	-0.321000	0.08615	GTG	C|0.859;G|0.120;T|0.021	0.120	strong		0.498	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
ACSM2B	348158	hgsc.bcm.edu	37	16	20576048	20576048	+	Silent	SNP	C	C	A	rs112352583	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20576048C>A	ENST00000329697.6	-	2	288	c.120G>T	c.(118-120)gtG>gtT	p.V40V	ACSM2B_ENST00000567001.1_Silent_p.V40V|ACSM2B_ENST00000414188.2_Silent_p.V40V|ACSM2B_ENST00000565322.1_Intron|ACSM2B_ENST00000565232.1_Silent_p.V40V	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	40					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						ACTTGGCCGGCACTTCCTGGT	0.507													C|||	1328	0.265176	0.0295	0.1686	5008	,	,		18497	0.6845		0.1909	False		,,,				2504	0.2965				p.V40V		Atlas-SNP	.											.	ACSM2B	121	.	0			c.G120T						PASS	.	C	,	248,4154	133.3+/-169.7	7,234,1960	45.0	40.0	42.0		120,120	-6.5	0.1	16	dbSNP_132	42	1675,6919	288.4+/-298.7	159,1357,2781	no	coding-synonymous,coding-synonymous	ACSM2B	NM_001105069.1,NM_182617.3	,	166,1591,4741	AA,AC,CC		19.4903,5.6338,14.7969	,	40/578,40/578	20576048	1923,11073	2201	4297	6498	SO:0001819	synonymous_variant	348158	exon3			GGCCGGCACTTCC	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"""Acyl-CoA synthetase family"""	30931	protein-coding gene	gene with protein product	"""xenobiotic/medium chain fatty acid:CoA ligase"""	614359	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.120G>T	16.37:g.20576048C>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	194	83	0.427835	NM_182617	Q86YT1	Silent	SNP	ENST00000329697.6	37	CCDS10586.1																																																																																			C|0.500;A|0.500	0.500	weak		0.507	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2	NM_182617	
FAT2	2196	hgsc.bcm.edu	37	5	150947719	150947719	+	Silent	SNP	C	C	T	rs3734060	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150947719C>T	ENST00000261800.5	-	1	786	c.774G>A	c.(772-774)tcG>tcA	p.S258S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	258					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCACCACCACCGAAGCAATGG	0.557																																					p.S258S		Atlas-SNP	.											FAT2,colon,carcinoma,0,2	FAT2	465	2	0			c.G774A						PASS	.	C		1956,2450	549.1+/-377.7	420,1116,667	43.0	42.0	43.0		774	-10.1	0.0	5	dbSNP_107	43	4496,4104	585.4+/-391.9	1181,2134,985	no	coding-synonymous	FAT2	NM_001447.2		1601,3250,1652	TT,TC,CC		47.7209,44.394,49.6079		258/4350	150947719	6452,6554	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			CACCACCGAAGCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.774G>A	5.37:g.150947719C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	140	49	0.35	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.527;T|0.473	0.473	strong		0.557	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
PADI4	23569	hgsc.bcm.edu	37	1	17657534	17657534	+	Missense_Mutation	SNP	G	G	A	rs11203366	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17657534G>A	ENST00000375448.4	+	2	189	c.163G>A	c.(163-165)Ggc>Agc	p.G55S	PADI4_ENST00000375453.1_Missense_Mutation_p.G55S|AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	55			G -> S (does not catalytic activity; dbSNP:rs11203366). {ECO:0000269|PubMed:10488123, ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	TATTGCCCACGGCCCTCCAGC	0.602													g|||	2627	0.524561	0.4508	0.5432	5008	,	,		19625	0.5635		0.5755	False		,,,				2504	0.5184				p.G55S		Atlas-SNP	.											.	PADI4	70	.	0			c.G163A						PASS	.	G	SER/GLY	2135,2271	579.1+/-384.8	505,1125,573	72.0	66.0	68.0		163	-10.9	0.0	1	dbSNP_120	68	4958,3642	624.1+/-397.5	1420,2118,762	yes	missense	PADI4	NM_012387.2	56	1925,3243,1335	AA,AG,GG		42.3488,48.4567,45.4636	benign	55/664	17657534	7093,5913	2203	4300	6503	SO:0001583	missense	23569	exon2			GCCCACGGCCCTC	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.163G>A	1.37:g.17657534G>A	ENSP00000364597:p.Gly55Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	37	CCDS180.1	1202	0.5503663003663004	227	0.4613821138211382	191	0.5276243093922652	337	0.5891608391608392	447	0.5897097625329816	g	3.181	-0.167802	0.06461	0.484567	0.576512	ENSG00000159339	ENST00000375453;ENST00000358829;ENST00000375448	T;T	0.06528	3.29;3.29	5.44	-10.9	0.00192	Cupredoxin (1);Protein-arginine deiminase (PAD) N-terminal (1);	1.050470	0.07454	N	0.899595	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.47407	-0.9120	9	0.02654	T	1	-0.0238	4.2913	0.10879	0.2396:0.0922:0.4856:0.1827	rs11203366;rs17845772;rs17858732;rs52837976;rs58026133;rs11203366	55;55	A8K392;Q9UM07	.;PADI4_HUMAN	S	55	ENSP00000364602:G55S;ENSP00000364597:G55S	ENSP00000351690:G55S	G	+	1	0	PADI4	17530121	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-1.530000	0.02221	-1.960000	0.01017	-1.322000	0.01289	GGC	G|0.448;A|0.552	0.552	strong		0.602	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
TBC1D32	221322	hgsc.bcm.edu	37	6	121452897	121452897	+	Splice_Site	SNP	G	G	A	rs150710532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:121452897G>A	ENST00000398212.2	-	25	2824	c.2775C>T	c.(2773-2775)gaC>gaT	p.D925D	TBC1D32_ENST00000275159.6_Splice_Site_p.D966D|TBC1D32_ENST00000398197.2_5'UTR	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	925					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										CAAGATCATTGTCTAATCAGA	0.274													G|||	50	0.00998403	0.0023	0.0187	5008	,	,		16618	0.002		0.0139	False		,,,				2504	0.0184				p.D925D		Atlas-SNP	.											.	C6orf170	146	.	0			c.C2775T						PASS	.	G		14,3576		0,14,1781	65.0	58.0	60.0		2775	1.0	0.2	6	dbSNP_134	60	129,8007		3,123,3942	yes	coding-synonymous-near-splice	C6orf170	NM_152730.4		3,137,5723	AA,AG,GG		1.5855,0.39,1.2195		925/1258	121452897	143,11583	1795	4068	5863	SO:0001630	splice_region_variant	221322	exon25			ATCATTGTCTAAT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.2774-1C>T	6.37:g.121452897G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	14	0.297872	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			G|0.988;A|0.012	0.012	strong		0.274	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	Silent
MLC1	23209	hgsc.bcm.edu	37	22	50502544	50502544	+	Silent	SNP	G	G	A	rs11568186	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50502544G>A	ENST00000311597.5	-	11	1584	c.978C>T	c.(976-978)tgC>tgT	p.C326C	MLC1_ENST00000450140.2_Silent_p.C274C|MLC1_ENST00000395876.2_Silent_p.C326C|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000538737.1_Silent_p.C292C|MLC1_ENST00000535444.1_Silent_p.C247C|MLC1_ENST00000431262.2_Silent_p.C296C	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	326					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		TGAAGCGCACGCACTGGATGG	0.677													g|||	657	0.13119	0.059	0.1758	5008	,	,		14894	0.0923		0.1312	False		,,,				2504	0.2372				p.C326C		Atlas-SNP	.											.	MLC1	48	.	0			c.C978T						PASS	.		,	328,4078	158.9+/-191.5	15,298,1890	45.0	42.0	43.0		978,978	-5.2	0.8	22	dbSNP_120	43	1198,7402	223.4+/-260.2	90,1018,3192	no	coding-synonymous,coding-synonymous	MLC1	NM_015166.3,NM_139202.2	,	105,1316,5082	AA,AG,GG		13.9302,7.4444,11.733	,	326/378,326/378	50502544	1526,11480	2203	4300	6503	SO:0001819	synonymous_variant	23209	exon11			GCGCACGCACTGG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.978C>T	22.37:g.50502544G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			G|0.891;A|0.109	0.109	strong		0.677	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
KDR	3791	hgsc.bcm.edu	37	4	55979558	55979558	+	Missense_Mutation	SNP	C	C	T	rs2305948	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:55979558C>T	ENST00000263923.4	-	7	1184	c.889G>A	c.(889-891)Gta>Ata	p.V297I		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	297	Ig-like C2-type 3.		V -> I (in dbSNP:rs2305948). {ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.V297I(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTCCGGGTTACACCATCTATA	0.443			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			C|||	764	0.152556	0.2436	0.0951	5008	,	,		18659	0.1667		0.0944	False		,,,				2504	0.1155				p.V297I		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	1	Substitution - Missense(1)	prostate(1)	c.G889A	GRCh37	CM074307	KDR	M	rs2305948	PASS	.	C	ILE/VAL	984,3422	368.3+/-318.6	112,760,1331	173.0	162.0	166.0		889	4.6	0.3	4	dbSNP_100	166	872,7728	197.6+/-242.2	46,780,3474	yes	missense	KDR	NM_002253.2	29	158,1540,4805	TT,TC,CC		10.1395,22.3332,14.2703	probably-damaging	297/1357	55979558	1856,11150	2203	4300	6503	SO:0001583	missense	3791	exon7			GGGTTACACCATC	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.889G>A	4.37:g.55979558C>T	ENSP00000263923:p.Val297Ile	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	185	87	0.47027	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	286	0.13095238095238096	107	0.21747967479674796	35	0.09668508287292818	80	0.13986013986013987	64	0.08443271767810026	C	16.90	3.250389	0.59212	0.223332	0.101395	ENSG00000128052	ENST00000263923	T	0.66815	-0.23	5.47	4.63	0.57726	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.00144	0.0004	M	0.67569	2.06	0.20074	P	0.9999359177	D;D	0.89917	0.998;1.0	D;D	0.91635	0.988;0.999	T	0.01528	-1.1332	9	0.49607	T	0.09	.	13.5277	0.61605	0.0:0.9243:0.0:0.0757	rs2305948;rs52830740;rs56532927;rs56973163;rs2305948	297;297	P35968-2;P35968	.;VGFR2_HUMAN	I	297	ENSP00000263923:V297I	ENSP00000263923:V297I	V	-	1	0	KDR	55674315	1.000000	0.71417	0.323000	0.25347	0.279000	0.26890	4.820000	0.62671	1.298000	0.44778	0.563000	0.77884	GTA	C|0.854;A|0.000	.	strong		0.443	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
TREML2	79865	hgsc.bcm.edu	37	6	41166149	41166149	+	Missense_Mutation	SNP	A	A	G	rs62396355|rs71544266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41166149A>G	ENST00000483722.1	-	2	259	c.74T>C	c.(73-75)gTa>gCa	p.V25A		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	25	Ig-like V-type.			V -> A (in Ref. 5; AAI25080). {ECO:0000305}.	T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					TTTTGTGTATACACTGTCAGC	0.478													A|||	414	0.0826677	0.0091	0.0793	5008	,	,		21040	0.0843		0.1173	False		,,,				2504	0.1472				p.V25A		Atlas-SNP	.											.	TREML2	41	.	0			c.T74C						PASS	.	A	ALA/VAL	26,4380		1,24,2178	90.0	89.0	89.0		74	-4.3	0.0	6	dbSNP_129	89	434,8164		53,328,3918	no	missense	TREML2	NM_024807.2	64	54,352,6096	GG,GA,AA		5.0477,0.5901,3.5374	benign	25/322	41166149	460,12544	2203	4299	6502	SO:0001583	missense	79865	exon2			GTGTATACACTGT	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.74T>C	6.37:g.41166149A>G	ENSP00000418767:p.Val25Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	139	0.06364468864468864	5	0.01016260162601626	31	0.0856353591160221	29	0.050699300699300696	74	0.09762532981530343	.	7.549	0.662289	0.14645	0.005901	0.050477	ENSG00000112195	ENST00000483722	T	0.07908	3.15	4.75	-4.27	0.03744	Immunoglobulin-like (1);	1.166620	0.06552	N	0.745132	T	0.02012	0.0063	L	0.50333	1.59	0.80722	P	0.0	B	0.12013	0.005	B	0.16722	0.016	T	0.45293	-0.9271	9	0.19590	T	0.45	-0.4459	6.3814	0.21536	0.4571:0.1392:0.4037:0.0	rs62396355	25	Q5T2D2	TRML2_HUMAN	A	25	ENSP00000418767:V25A	ENSP00000418767:V25A	V	-	2	0	TREML2	41274127	0.001000	0.12720	0.003000	0.11579	0.012000	0.07955	0.184000	0.16939	-1.053000	0.03218	-1.098000	0.02139	GTA	ACACTGT|0.500;GCGCTCC|0.500	.	alt		0.478	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
CIDEA	1149	hgsc.bcm.edu	37	18	12274104	12274104	+	Missense_Mutation	SNP	G	G	T	rs11545881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:12274104G>T	ENST00000320477.9	+	4	408	c.343G>T	c.(343-345)Gtc>Ttc	p.V115F	CIDEA_ENST00000521296.1_3'UTR	NM_001279.3	NP_001270.1	O60543	CIDEA_HUMAN	cell death-inducing DFFA-like effector a	115			V -> F (in dbSNP:rs45619832). {ECO:0000269|Ref.2}.		apoptotic process (GO:0006915)|cell death (GO:0008219)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of execution phase of apoptosis (GO:1900118)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|response to stilbenoid (GO:0035634)|temperature homeostasis (GO:0001659)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|mitochondrial envelope (GO:0005740)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)	13						CAGCCAGCACGTCCCCACTTG	0.582													G|||	1824	0.364217	0.1732	0.402	5008	,	,		19407	0.5278		0.3678	False		,,,				2504	0.4233				p.V115F		Atlas-SNP	.											.	CIDEA	32	.	0			c.G343T	GRCh37	CM053175	CIDEA	M	rs45619832	PASS	.	G	PHE/VAL	863,3543	339.9+/-306.0	96,671,1436	75.0	61.0	66.0		343	-7.5	0.0	18	dbSNP_127	66	3116,5484	475.3+/-369.1	571,1974,1755	yes	missense	CIDEA	NM_001279.3	50	667,2645,3191	TT,TG,GG		36.2326,19.5869,30.5936	benign	115/220	12274104	3979,9027	2203	4300	6503	SO:0001583	missense	1149	exon4			CAGCACGTCCCCA	AF041378	CCDS11856.1	18p11.21	2008-08-01			ENSG00000176194	ENSG00000176194			1976	protein-coding gene	gene with protein product		604440				9564035, 18509062	Standard	NM_001279		Approved	CIDE-A	uc002kqt.4	O60543	OTTHUMG00000131691	ENST00000320477.9:c.343G>T	18.37:g.12274104G>T	ENSP00000320209:p.Val115Phe	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001279	B0YIY7|Q6UPR7	Missense_Mutation	SNP	ENST00000320477.9	37	CCDS11856.1	815	0.3731684981684982	86	0.17479674796747968	138	0.3812154696132597	312	0.5454545454545454	279	0.36807387862796836	G	10.66	1.411750	0.25465	0.195869	0.362326	ENSG00000176194	ENST00000320477	T	0.44083	0.93	5.03	-7.46	0.01369	.	4.069490	0.00732	N	0.000951	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P;B	0.35923	0.528;0.236	B;B	0.28305	0.088;0.081	T	0.27773	-1.0064	9	0.10111	T	0.7	-6.1579	9.7264	0.40335	0.6478:0.1149:0.2373:0.0	rs45619832;rs57700938;rs61758075	149;115	Q8N5P9;O60543	.;CIDEA_HUMAN	F	115	ENSP00000320209:V115F	ENSP00000320209:V115F	V	+	1	0	CIDEA	12264104	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.415000	0.07106	-1.696000	0.01421	-1.731000	0.00696	GTC	C|0.000;G|0.668;T|0.332	0.332	strong		0.582	CIDEA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254599.2	NM_001279	
GLOD4	51031	hgsc.bcm.edu	37	17	663467	663467	+	Silent	SNP	T	T	A	rs74757321	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:663467T>A	ENST00000301328.5	-	10	911	c.888A>T	c.(886-888)gcA>gcT	p.A296A	GLOD4_ENST00000575800.1_5'Flank|GLOD4_ENST00000301329.6_Silent_p.A281A|GLOD4_ENST00000536578.1_Silent_p.A272A			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4	296						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CACTTTTATCTGCTGCCATTG	0.423													T|||	94	0.01877	0.0008	0.0086	5008	,	,		16316	0.0456		0.0179	False		,,,				2504	0.0235				p.A281A		Atlas-SNP	.											.	GLOD4	12	.	0			c.A843T						PASS	.						180.0	149.0	159.0					17																	663467		2203	4300	6503	SO:0001819	synonymous_variant	51031	exon9			TTTATCTGCTGCC	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38		ENST00000301328.5:c.888A>T	17.37:g.663467T>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_016080	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Silent	SNP	ENST00000301328.5	37																																																																																				T|0.978;A|0.022	0.022	strong		0.423	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
PER3	8863	hgsc.bcm.edu	37	1	7890055	7890055	+	Silent	SNP	T	T	A	rs11121034	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7890055T>A	ENST00000361923.2	+	18	3196	c.3021T>A	c.(3019-3021)gcT>gcA	p.A1007A	PER3_ENST00000377532.3_Silent_p.A1016A|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1007	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.		A -> T (in dbSNP:rs1776342).|Missing (associated with eveningness and better cognitive performance during sleep deprivation exepriments; dbSNP:rs57875989).		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CTGCCAGCGCTCTGTCCACAG	0.587																																					p.A1007A		Atlas-SNP	.											PER3,NS,carcinoma,+2,1	PER3	95	1	0			c.T3021A						PASS	.						90.0	71.0	77.0					1																	7890055		1995	3900	5895	SO:0001819	synonymous_variant	8863	exon18			CAGCGCTCTGTCC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3021T>A	1.37:g.7890055T>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	96	25	0.260417	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			T|0.954;A|0.046	0.046	strong		0.587	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
SCN9A	6335	hgsc.bcm.edu	37	2	167145142	167145142	+	Silent	SNP	A	A	G	rs13414203	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:167145142A>G	ENST00000409435.1	-	9	1118	c.1119T>C	c.(1117-1119)gcT>gcC	p.A373A	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.A374A|SCN9A_ENST00000409672.1_Silent_p.A373A|SCN9A_ENST00000375387.4_Silent_p.A374A			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	373					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTTGCCAGCAGCACGCAGCG	0.378													A|||	1775	0.354433	0.357	0.3242	5008	,	,		15731	0.3065		0.4036	False		,,,				2504	0.3712				p.A373A		Atlas-SNP	.											.	SCN9A	296	.	0			c.T1119C						PASS	.	A		1388,2274		279,830,722	62.0	58.0	59.0		1119	4.7	1.0	2	dbSNP_121	59	3180,5018		598,1984,1517	no	coding-synonymous	SCN9A	NM_002977.3		877,2814,2239	GG,GA,AA		38.7899,37.9028,38.516		373/1978	167145142	4568,7292	1831	4099	5930	SO:0001819	synonymous_variant	6335	exon10			GCCAGCAGCACGC	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1119T>C	2.37:g.167145142A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			A|0.652;G|0.348	0.348	strong		0.378	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
MATN4	8785	hgsc.bcm.edu	37	20	43933196	43933196	+	Silent	SNP	C	C	T	rs2233093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43933196C>T	ENST00000372754.1	-	2	323	c.315G>A	c.(313-315)gtG>gtA	p.V105V	RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000537548.1_Silent_p.V105V|MATN4_ENST00000372756.1_Silent_p.V105V|MATN4_ENST00000360607.6_Silent_p.V105V|RBPJL_ENST00000372743.1_5'Flank|MATN4_ENST00000372751.4_Intron|RBPJL_ENST00000343694.3_5'Flank|MATN4_ENST00000342716.4_Silent_p.V105V|MATN4_ENST00000353917.5_Silent_p.V105V			O95460	MATN4_HUMAN	matrilin 4	105	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				GCGCCAGAGGCACCAGGTCGC	0.662													C|||	858	0.171326	0.295	0.1556	5008	,	,		17451	0.0159		0.2087	False		,,,				2504	0.137				p.V105V		Atlas-SNP	.											.	MATN4	57	.	0			c.G315A						PASS	.	C	,,	1213,3187		174,865,1161	22.0	19.0	20.0		315,315,315	2.7	1.0	20	dbSNP_98	20	1913,6671		215,1483,2594	no	coding-synonymous,coding-synonymous,coding-synonymous	MATN4	NM_003833.3,NM_030590.2,NM_030592.2	,,	389,2348,3755	TT,TC,CC		22.2856,27.5682,24.0758	,,	105/582,105/541,105/500	43933196	3126,9858	2200	4292	6492	SO:0001819	synonymous_variant	8785	exon3			CAGAGGCACCAGG	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.315G>A	20.37:g.43933196C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	80	0.97561	NM_030592	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Silent	SNP	ENST00000372754.1	37																																																																																				C|0.801;T|0.199	0.199	strong		0.662	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		
OXNAD1	92106	hgsc.bcm.edu	37	3	16312564	16312564	+	Silent	SNP	C	C	T	rs842259	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:16312564C>T	ENST00000285083.5	+	3	570	c.105C>T	c.(103-105)caC>caT	p.H35H	OXNAD1_ENST00000606098.1_Silent_p.H35H|OXNAD1_ENST00000544043.1_Silent_p.H53H|OXNAD1_ENST00000435829.2_Silent_p.H53H|OXNAD1_ENST00000605932.1_Silent_p.H35H	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	35						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						CTTTGCGCCACCTTACTCTAA	0.483													C|||	2107	0.420727	0.2617	0.4654	5008	,	,		17886	0.4752		0.4324	False		,,,				2504	0.5358				p.H35H		Atlas-SNP	.											OXNAD1,rectum,carcinoma,0,1	OXNAD1	31	1	0			c.C105T						PASS	.	C		1361,3045	450.8+/-349.5	221,919,1063	157.0	146.0	150.0		105	3.0	0.5	3	dbSNP_86	150	3655,4945	526.1+/-380.9	787,2081,1432	no	coding-synonymous	OXNAD1	NM_138381.3		1008,3000,2495	TT,TC,CC		42.5,30.8897,38.5668		35/313	16312564	5016,7990	2203	4300	6503	SO:0001819	synonymous_variant	92106	exon3			GCGCCACCTTACT	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.105C>T	3.37:g.16312564C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	163	74	0.453988	NM_138381	Q2HYC7|Q59FA4	Silent	SNP	ENST00000285083.5	37	CCDS2630.1																																																																																			C|0.609;T|0.391	0.391	strong		0.483	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
MUC4	4585	hgsc.bcm.edu	37	3	195508009	195508009	+	Missense_Mutation	SNP	G	G	A	rs201765368		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508009G>A	ENST00000463781.3	-	2	10901	c.10442C>T	c.(10441-10443)gCa>gTa	p.A3481V	MUC4_ENST00000475231.1_Missense_Mutation_p.A3481V|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTAGATGCTGAGGAAGG	0.577													.|||	1	0.000199681	0.0	0.0	5008	,	,		22173	0.0		0.0	False		,,,				2504	0.001				p.A3481V		Atlas-SNP	.											MUC4_ENST00000463781,colon,carcinoma,-1,1	MUC4	1505	1	0			c.C10442T						scavenged	.						28.0	24.0	25.0					3																	195508009		677	1580	2257	SO:0001583	missense	4585	exon2			GTAGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10442C>T	3.37:g.195508009G>A	ENSP00000417498:p.Ala3481Val	Somatic	84	14	0.166667		WXS	Illumina HiSeq	Phase_I	291	91	0.312715	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	3.129	-0.178800	0.06380	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28666	1.71;1.6	0.743	-1.49	0.08718	.	.	.	.	.	T	0.17662	0.0424	N	0.08118	0	0.09310	N	1	P	0.41008	0.735	P	0.47251	0.542	T	0.18116	-1.0347	8	.	.	.	.	4.9547	0.14033	0.4873:0.0:0.5127:0.0	.	3353	E7ESK3	.	V	3481	ENSP00000417498:A3481V;ENSP00000420243:A3481V	.	A	-	2	0	MUC4	196992788	0.006000	0.16342	0.005000	0.12908	0.005000	0.04900	0.296000	0.19083	-1.764000	0.01305	-1.783000	0.00646	GCA	.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CEP120	153241	hgsc.bcm.edu	37	5	122720648	122720648	+	Missense_Mutation	SNP	T	T	A	rs147430819		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:122720648T>A	ENST00000306467.5	-	11	2064	c.1760A>T	c.(1759-1761)cAa>cTa	p.Q587L	CEP120_ENST00000328236.5_Missense_Mutation_p.Q587L|CEP120_ENST00000306481.6_Missense_Mutation_p.Q561L			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	587					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						GCATTACCCTTGTGCTGCTAT	0.373																																					p.Q587L		Atlas-SNP	.											.	CEP120	72	.	0			c.A1760T						PASS	.	T	LEU/GLN,LEU/GLN	1,4405	2.1+/-5.4	0,1,2202	103.0	95.0	97.0		1682,1760	5.5	1.0	5	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CEP120	NM_001166226.1,NM_153223.3	113,113	0,2,6501	AA,AT,TT		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	561/961,587/987	122720648	2,13004	2203	4300	6503	SO:0001583	missense	153241	exon12			TACCCTTGTGCTG	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.1760A>T	5.37:g.122720648T>A	ENSP00000303058:p.Gln587Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	37	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419777	0.83559	2.27E-4	1.16E-4	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481;ENST00000508442	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.52	5.52	0.82312	.	0.126760	0.53938	D	0.000049	T	0.47838	0.1467	L	0.50333	1.59	0.80722	D	1	P	0.48640	0.913	P	0.44394	0.448	T	0.47100	-0.9143	10	0.41790	T	0.15	.	15.6517	0.77099	0.0:0.0:0.0:1.0	.	587	Q8N960	CE120_HUMAN	L	587;587;561;561	ENSP00000303058:Q587L;ENSP00000327504:Q587L;ENSP00000307419:Q561L;ENSP00000421620:Q561L	ENSP00000303058:Q587L	Q	-	2	0	CEP120	122748547	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.532000	0.81985	2.108000	0.64289	0.477000	0.44152	CAA	T|1.000;A|0.000	0.000	weak		0.373	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
FOXRED2	80020	hgsc.bcm.edu	37	22	36897427	36897427	+	Silent	SNP	T	T	C	rs5756223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:36897427T>C	ENST00000397224.4	-	5	1170	c.1077A>G	c.(1075-1077)gcA>gcG	p.A359A	FOXRED2_ENST00000366463.3_5'Flank|FOXRED2_ENST00000397223.4_Silent_p.A359A|FOXRED2_ENST00000216187.6_Silent_p.A359A	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	359					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						TCTTGCCGAATGCATTTCCCG	0.483													T|||	203	0.0405351	0.0091	0.0403	5008	,	,		18922	0.0536		0.0646	False		,,,				2504	0.045				p.A359A		Atlas-SNP	.											.	FOXRED2	48	.	0			c.A1077G						PASS	.	T	,	111,4295	85.8+/-124.5	0,111,2092	76.0	72.0	73.0		1077,1077	-2.3	0.0	22	dbSNP_114	73	566,8034	153.7+/-208.1	27,512,3761	no	coding-synonymous,coding-synonymous	FOXRED2	NM_001102371.1,NM_024955.5	,	27,623,5853	CC,CT,TT		6.5814,2.5193,5.2053	,	359/685,359/685	36897427	677,12329	2203	4300	6503	SO:0001819	synonymous_variant	80020	exon5			GCCGAATGCATTT	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.1077A>G	22.37:g.36897427T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			T|0.944;C|0.056	0.056	strong		0.483	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
GPR180	160897	hgsc.bcm.edu	37	13	95273447	95273447	+	Silent	SNP	G	G	A	rs12429818	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:95273447G>A	ENST00000376958.4	+	6	877	c.852G>A	c.(850-852)acG>acA	p.T284T		NM_180989.5	NP_851320.1	Q86V85	GP180_HUMAN	G protein-coupled receptor 180	284					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	10	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					GGGATTCTACGCCTGCATCCA	0.423													G|||	830	0.165735	0.0045	0.2839	5008	,	,		15479	0.2728		0.1054	False		,,,				2504	0.2515				p.T284T		Atlas-SNP	.											.	GPR180	24	.	0			c.G852A						PASS	.	G		152,4254	104.3+/-142.8	1,150,2052	151.0	135.0	141.0		852	-6.3	0.3	13	dbSNP_120	141	961,7639	209.7+/-250.8	38,885,3377	no	coding-synonymous	GPR180	NM_180989.5		39,1035,5429	AA,AG,GG		11.1744,3.4498,8.5576		284/441	95273447	1113,11893	2203	4300	6503	SO:0001819	synonymous_variant	160897	exon6			TTCTACGCCTGCA	AF339823	CCDS9472.1	13q32.1	2006-04-05			ENSG00000152749	ENSG00000152749			28899	protein-coding gene	gene with protein product	"""intimal thickness related receptor"""	607787				12538434	Standard	NM_180989		Approved	ITR	uc001vly.3	Q86V85	OTTHUMG00000017207	ENST00000376958.4:c.852G>A	13.37:g.95273447G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_180989	A8K1D5	Silent	SNP	ENST00000376958.4	37	CCDS9472.1																																																																																			G|0.877;A|0.123	0.123	strong		0.423	GPR180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045465.3	NM_180989	
SERPINB3	6317	hgsc.bcm.edu	37	18	61322995	61322995	+	Missense_Mutation	SNP	T	T	C	rs1065205	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:61322995T>C	ENST00000283752.5	-	8	1212	c.1069A>G	c.(1069-1071)Act>Gct	p.T357A	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.T305A	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	357			T -> A (in dbSNP:rs1065205). {ECO:0000269|PubMed:1958219, ECO:0000269|Ref.3, ECO:0000269|Ref.9}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TTAGTTGAAGTAGGTGATGAT	0.473													T|||	964	0.192492	0.0825	0.2017	5008	,	,		20327	0.4405		0.0865	False		,,,				2504	0.1881				p.T357A		Atlas-SNP	.											.	SERPINB3	90	.	0			c.A1069G						PASS	.	T	ALA/THR	375,4031	190.2+/-216.2	32,311,1860	147.0	148.0	148.0		1069	-5.9	0.0	18	dbSNP_86	148	731,7869	177.8+/-227.3	26,679,3595	no	missense	SERPINB3	NM_006919.2	58	58,990,5455	CC,CT,TT		8.5,8.5111,8.5038	benign	357/391	61322995	1106,11900	2203	4300	6503	SO:0001583	missense	6317	exon8			TTGAAGTAGGTGA	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1069A>G	18.37:g.61322995T>C	ENSP00000283752:p.Thr357Ala	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	231	134	0.580087	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	417	0.19093406593406592	50	0.1016260162601626	70	0.19337016574585636	228	0.3986013986013986	69	0.09102902374670185	T	0.531	-0.857900	0.02610	0.085111	0.085	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.82344	-1.6;-1.6	2.96	-5.92	0.02261	Serpin domain (3);	.	.	.	.	T	0.00012	0.0000	N	0.01809	-0.71	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.07947	-1.0746	8	0.05833	T	0.94	.	0.8688	0.01210	0.3065:0.2008:0.1067:0.386	rs1065205;rs3169980;rs52799665;rs56795109;rs1065205	305;357	P29508-2;P29508	.;SPB3_HUMAN	A	357;305	ENSP00000283752:T357A;ENSP00000329498:T305A	ENSP00000283752:T357A	T	-	1	0	SERPINB3	59473975	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.571000	0.00034	-1.670000	0.01468	-1.855000	0.00564	ACT	T|0.864;C|0.136	0.136	strong		0.473	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
PREX2	80243	hgsc.bcm.edu	37	8	69143589	69143589	+	Silent	SNP	A	A	G	rs2280637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:69143589A>G	ENST00000288368.4	+	40	5074	c.4797A>G	c.(4795-4797)ccA>ccG	p.P1599P		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1599					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGTGCGAGCCACCTCCCCCAG	0.443													G|||	1666	0.332668	0.1861	0.3761	5008	,	,		15846	0.3879		0.2992	False		,,,				2504	0.4775				p.P1599P		Atlas-SNP	.											.	PREX2	614	.	0			c.A4797G						PASS	.	G		765,3641	749.6+/-412.0	69,627,1507	64.0	57.0	59.0		4797	-8.5	0.5	8	dbSNP_100	59	2409,6191	693.2+/-404.6	335,1739,2226	no	coding-synonymous	PREX2	NM_024870.2		404,2366,3733	GG,GA,AA		28.0116,17.3627,24.4041		1599/1607	69143589	3174,9832	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon40			CGAGCCACCTCCC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4797A>G	8.37:g.69143589A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			A|0.724;G|0.276	0.276	strong		0.443	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
GRHL2	79977	hgsc.bcm.edu	37	8	102555474	102555474	+	Missense_Mutation	SNP	A	A	G	rs3735709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:102555474A>G	ENST00000251808.3	+	2	364	c.26A>G	c.(25-27)aAa>aGa	p.K9R	GRHL2_ENST00000395927.1_5'UTR	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	9	Transcription activation.				brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			TACAGTAATAAAAGACTAGTG	0.383													A|||	123	0.0245607	0.0008	0.0115	5008	,	,		19402	0.0625		0.0268	False		,,,				2504	0.0245				p.K9R		Atlas-SNP	.											.	GRHL2	68	.	0			c.A26G						PASS	.	A	ARG/LYS	21,4385	28.1+/-56.4	1,19,2183	103.0	105.0	104.0		26	6.0	1.0	8	dbSNP_107	104	231,8369	94.0+/-155.9	1,229,4070	yes	missense	GRHL2	NM_024915.3	26	2,248,6253	GG,GA,AA		2.686,0.4766,1.9376	probably-damaging	9/626	102555474	252,12754	2203	4300	6503	SO:0001583	missense	79977	exon2			GTAATAAAAGACT	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"""deafness, autosomal dominant 28"", ""transcription factor CP2-like 3"""	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.26A>G	8.37:g.102555474A>G	ENSP00000251808:p.Lys9Arg	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	126	69	0.547619	NM_024915	A1L303|Q6NT03|Q9H8B8	Missense_Mutation	SNP	ENST00000251808.3	37	CCDS34931.1	66	0.03021978021978022	0	0.0	6	0.016574585635359115	40	0.06993006993006994	20	0.026385224274406333	A	20.7	4.026092	0.75390	0.004766	0.02686	ENSG00000083307	ENST00000251808;ENST00000395928	T	0.14144	2.53	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.01627	0.0052	M	0.74881	2.28	0.80722	D	1	P;P;P	0.52316	0.952;0.848;0.848	B;P;P	0.48030	0.339;0.564;0.564	T	0.11084	-1.0602	10	0.07325	T	0.83	-27.1139	16.4277	0.83824	1.0:0.0:0.0:0.0	.	9;9;9	B4DL28;Q6ISB3;A8K9Y8	.;GRHL2_HUMAN;.	R	9	ENSP00000251808:K9R	ENSP00000251808:K9R	K	+	2	0	GRHL2	102624650	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.445000	0.90326	2.279000	0.76181	0.533000	0.62120	AAA	A|0.979;G|0.021	0.021	strong		0.383	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	
RARS	5917	hgsc.bcm.edu	37	5	167924260	167924260	+	Silent	SNP	C	C	A	rs11557637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:167924260C>A	ENST00000231572.3	+	7	783	c.729C>A	c.(727-729)acC>acA	p.T243T	RARS_ENST00000520421.1_3'UTR|RARS_ENST00000538719.1_Silent_p.T37T	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	243					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		ACTGGGGGACCCAGTTTGGCA	0.353													C|||	372	0.0742812	0.0091	0.0908	5008	,	,		17277	0.0645		0.1799	False		,,,				2504	0.0521				p.T243T		Atlas-SNP	.											.	RARS	58	.	0			c.C729A						PASS	.	C		161,4245	105.6+/-144.1	2,157,2044	62.0	63.0	63.0		729	-0.1	1.0	5	dbSNP_120	63	1623,6971	292.0+/-300.6	160,1303,2834	yes	coding-synonymous	RARS	NM_002887.3		162,1460,4878	AA,AC,CC		18.8853,3.6541,13.7231		243/661	167924260	1784,11216	2203	4297	6500	SO:0001819	synonymous_variant	5917	exon7			GGGGACCCAGTTT	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.729C>A	5.37:g.167924260C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	37	CCDS4367.1																																																																																			C|0.883;A|0.117	0.117	strong		0.353	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
KLK4	9622	hgsc.bcm.edu	37	19	51412666	51412666	+	Silent	SNP	C	C	A	rs1654552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51412666C>A	ENST00000324041.1	-	2	65	c.66G>T	c.(64-66)tcG>tcT	p.S22S	KLK4_ENST00000431178.2_5'Flank|KLK4_ENST00000597441.1_5'Flank	NM_004917.3	NP_004908.3	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4	22			S -> A (in dbSNP:rs1654551). {ECO:0000269|PubMed:15235027}.		amelogenesis (GO:0097186)|extracellular matrix disassembly (GO:0022617)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(8)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)		CAGAGACGAGCGATCCTGAGG	0.637													C|||	1211	0.241813	0.0666	0.4078	5008	,	,		11864	0.1071		0.4672	False		,,,				2504	0.2679				p.S22S		Atlas-SNP	.											KLK4,colon,carcinoma,0,2	KLK4	46	2	0			c.G66T						PASS	.	C		550,3856	244.3+/-253.7	34,482,1687	89.0	99.0	95.0		66	-1.4	0.0	19	dbSNP_89	95	4082,4518	547.4+/-385.2	959,2164,1177	no	coding-synonymous	KLK4	NM_004917.3		993,2646,2864	AA,AC,CC		47.4651,12.483,35.6143		22/255	51412666	4632,8374	2203	4300	6503	SO:0001819	synonymous_variant	9622	exon2			GACGAGCGATCCT	AF113141	CCDS12809.1	19q13.41	2014-09-04	2006-10-27		ENSG00000167749	ENSG00000167749		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6365	protein-coding gene	gene with protein product		603767	"""kallikrein 4 (prostase, enamel matrix, prostate)"""	PRSS17		10077646, 10438493, 16800724, 10863090, 9465170	Standard	XM_005259441		Approved	EMSP, EMSP1, PSTS, KLK-L1	uc002pua.1	Q9Y5K2	OTTHUMG00000182964	ENST00000324041.1:c.66G>T	19.37:g.51412666C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_004917	Q4VB16|Q96RU5|Q9GZL6|Q9UBJ6	Silent	SNP	ENST00000324041.1	37	CCDS12809.1																																																																																			C|0.685;A|0.315	0.315	strong		0.637	KLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464449.1	NM_004917	
TRIM22	10346	hgsc.bcm.edu	37	11	5719750	5719750	+	Missense_Mutation	SNP	G	G	C	rs1063303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5719750G>C	ENST00000379965.3	+	4	1002	c.725G>C	c.(724-726)aGg>aCg	p.R242T	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	242			R -> T (in dbSNP:rs1063303). {ECO:0000269|PubMed:7797467}.		defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R242T(1)		kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		CGGAGGTTGAGGGGATCGTCA	0.547													G|||	2138	0.426917	0.3722	0.4553	5008	,	,		19187	0.2054		0.5398	False		,,,				2504	0.593				p.R242T	GBM(104;491 2336 5222)	Atlas-SNP	.											TRIM22,NS,carcinoma,0,1	TRIM22	66	1	1	Substitution - Missense(1)	stomach(1)	c.G725C						PASS	.	G	THR/ARG,THR/ARG	1598,2444		337,924,760	54.0	59.0	57.0		713,725	-2.2	0.0	11	dbSNP_86	57	4787,3611		1395,1997,807	yes	missense,missense	TRIM22	NM_001199573.1,NM_006074.4	71,71	1732,2921,1567	CC,CG,GG		42.9983,39.5349,48.6736	benign,benign	238/495,242/499	5719750	6385,6055	2021	4199	6220	SO:0001583	missense	10346	exon4			GGTTGAGGGGATC	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16379	protein-coding gene	gene with protein product		606559	"""tripartite motif-containing 22"""			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.725G>C	11.37:g.5719750G>C	ENSP00000369299:p.Arg242Thr	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	172	171	0.994186	NM_006074	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	848	0.3882783882783883	198	0.4024390243902439	149	0.4116022099447514	90	0.15734265734265734	411	0.5422163588390502	G	10.42	1.345247	0.24426	0.395349	0.570017	ENSG00000132274	ENST00000379965;ENST00000545338;ENST00000454828;ENST00000455293	T;T	0.05025	3.51;3.51	3.53	-2.15	0.07102	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B;B;B	0.14012	0.009;0.0;0.001;0.001	B;B;B;B	0.16722	0.016;0.0;0.009;0.003	T	0.35919	-0.9769	8	0.54805	T	0.06	.	8.0653	0.30657	0.4386:0.0:0.5614:0.0	rs1063303;rs3204345;rs59613853;rs1063303	164;210;238;242	F8WAP8;C9JWC5;Q8IYM9-2;Q8IYM9	.;.;.;TRI22_HUMAN	T	242;53;210;164	ENSP00000369299:R242T;ENSP00000393250:R210T	ENSP00000369299:R242T	R	+	2	0	TRIM22	5676326	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.177000	0.09796	-0.378000	0.07918	-0.384000	0.06662	AGG	G|0.570;C|0.430	0.430	strong		0.547	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
TUBB8	347688	hgsc.bcm.edu	37	10	94004	94004	+	Missense_Mutation	SNP	C	C	T	rs145405488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:94004C>T	ENST00000309812.4	-	4	390	c.328G>A	c.(328-330)Gcg>Acg	p.A110T	TUBB8_ENST00000447903.2_Missense_Mutation_p.A38T|TUBB8_ENST00000332708.5_Silent_p.A73A|TUBB8_ENST00000413237.3_5'UTR	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	110					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A110T(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		ATCAGCTCCGCGCCTTCGGTG	0.607																																					p.A110T	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,colon,carcinoma,+2,2	TUBB8	62	2	1	Substitution - Missense(1)	skin(1)	c.G328A						scavenged	.	C	THR/ALA	55,4351	38.4+/-70.7	0,55,2148	71.0	61.0	64.0		328		0.3	10	dbSNP_134	64	2,8598	1.2+/-3.3	0,2,4298	no	missense	TUBB8	NM_177987.2	58	0,57,6446	TT,TC,CC		0.0233,1.2483,0.4383	probably-damaging	110/445	94004	57,12949	2203	4300	6503	SO:0001583	missense	347688	exon4			GCTCCGCGCCTTC	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.328G>A	10.37:g.94004C>T	ENSP00000311042:p.Ala110Thr	Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	460	7	0.0152174	NM_177987	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.300454	0.23650	0.012483	2.33E-4	ENSG00000173876	ENST00000447903;ENST00000272035;ENST00000440680;ENST00000328974	T	0.69306	-0.39	.	.	.	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	U	0.000011	T	0.67468	0.2896	M	0.83223	2.63	0.36308	D	0.857475	D;P	0.57571	0.98;0.67	P;B	0.56434	0.798;0.13	T	0.73799	-0.3869	9	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	73;110	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	T	38;76;73;110	ENSP00000403895:A38T	ENSP00000272035:A76T	A	-	1	0	RP11-631M21.2	84004	0.998000	0.40836	0.290000	0.24890	0.293000	0.27360	5.268000	0.65536	0.119000	0.18210	0.121000	0.15741	GCG	C|0.991;T|0.009	0.009	strong		0.607	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
KLHL33	123103	hgsc.bcm.edu	37	14	20898308	20898308	+	Missense_Mutation	SNP	C	C	T	rs17242648	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20898308C>T	ENST00000344581.4	-	2	749	c.527G>A	c.(526-528)cGg>cAg	p.R176Q		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	176			R -> Q (in dbSNP:rs17242648).									all_cancers(95;0.00123)		Epithelial(56;7.57e-08)|all cancers(55;8.63e-07)	GBM - Glioblastoma multiforme(265;0.0223)|READ - Rectum adenocarcinoma(17;0.193)		CCCGGCTGCCCGCACCCTCCG	0.652													C|||	625	0.1248	0.1089	0.0576	5008	,	,		19012	0.2143		0.0915	False		,,,				2504	0.136				p.R176Q		Atlas-SNP	.											.	KLHL33	37	.	0			c.G527A						PASS	.	C	GLN/ARG	130,1254		11,108,573	32.0	37.0	36.0		527	3.9	1.0	14	dbSNP_123	36	256,2926		10,236,1345	yes	missense	KLHL33	NM_001109997.2	43	21,344,1918	TT,TC,CC		8.0453,9.3931,8.4538	possibly-damaging	176/534	20898308	386,4180	692	1591	2283	SO:0001583	missense	123103	exon2			GCTGCCCGCACCC		CCDS53882.1	14q11.2	2013-10-15	2013-02-22		ENSG00000185271	ENSG00000185271		"""Kelch-like"""	31952	protein-coding gene	gene with protein product			"""kelch-like 33 (Drosophila)"""				Standard	NM_001109997		Approved		uc010tli.2	A6NCF5	OTTHUMG00000170982	ENST00000344581.4:c.527G>A	14.37:g.20898308C>T	ENSP00000341549:p.Arg176Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	37	CCDS53882.1	270	0.12362637362637363	59	0.11991869918699187	25	0.06906077348066299	113	0.19755244755244755	73	0.09630606860158311	C	13.25	2.179740	0.38511	0.093931	0.080453	ENSG00000185271	ENST00000344581	T	0.72167	-0.63	4.75	3.86	0.44501	BTB/Kelch-associated (1);	0.070861	0.53938	D	0.000042	T	0.00073	0.0002	L	0.27053	0.805	0.40890	P	0.015932999999999975	P	0.44478	0.836	B	0.40782	0.34	T	0.04811	-1.0925	9	0.19590	T	0.45	.	9.8808	0.41231	0.0:0.9041:0.0:0.0959	rs17242648;rs52804888;rs57177627;rs17242648	176	A6NCF5	KLH33_HUMAN	Q	176	ENSP00000341549:R176Q	ENSP00000341549:R176Q	R	-	2	0	KLHL33	19968148	0.302000	0.24454	0.972000	0.41901	0.925000	0.55904	1.494000	0.35616	1.207000	0.43291	0.655000	0.94253	CGG	C|0.873;T|0.127	0.127	strong		0.652	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14779986	14779986	+	Missense_Mutation	SNP	G	G	A	rs76927023		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:14779986G>A	ENST00000358984.4	+	11	1628	c.1448G>A	c.(1447-1449)cGa>cAa	p.R483Q	ANKRD30B_ENST00000447268.2_Missense_Mutation_p.R483Q|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	483										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						GAATCCAAACGAGAGGAAGAT	0.284																																					p.R483Q		Atlas-SNP	.											ANKRD30B_ENST00000358984,bladder,carcinoma,0,2	ANKRD30B	237	2	0			c.G1448A						PASS	.						169.0	160.0	163.0					18																	14779986		692	1591	2283	SO:0001583	missense	374860	exon11			CCAAACGAGAGGA	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.1448G>A	18.37:g.14779986G>A	ENSP00000351875:p.Arg483Gln	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	106	19	0.179245	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	37	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.092170	0.00364	.	.	ENSG00000180777	ENST00000358984;ENST00000447268	T;T	0.36520	1.51;1.25	1.69	0.451	0.16629	.	.	.	.	.	T	0.09905	0.0243	N	0.00926	-1.1	0.09310	N	1	B	0.23854	0.092	B	0.08055	0.003	T	0.28138	-1.0053	9	0.22109	T	0.4	.	3.9288	0.09275	0.7996:0.0:0.2004:0.0	.	483	F8WAG3	.	Q	483	ENSP00000351875:R483Q;ENSP00000399031:R483Q	ENSP00000351875:R483Q	R	+	2	0	ANKRD30B	14769986	0.999000	0.42202	0.002000	0.10522	0.094000	0.18550	1.139000	0.31504	0.127000	0.18452	-1.326000	0.01283	CGA	.	.	weak		0.284	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
PTBP1	5725	hgsc.bcm.edu	37	19	804642	804642	+	Silent	SNP	C	C	T	rs3170451	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:804642C>T	ENST00000349038.4	+	6	619	c.546C>T	c.(544-546)ccC>ccT	p.P182P	PTBP1_ENST00000394601.4_Silent_p.P182P|PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000356948.6_Silent_p.P182P|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	182					alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCAGAGCCCCGTGCTCAGGA	0.682													C|||	806	0.160942	0.1331	0.2666	5008	,	,		14242	0.0228		0.1451	False		,,,				2504	0.2822				p.P182P		Atlas-SNP	.											PTBP1,NS,carcinoma,0,1	PTBP1	43	1	0			c.C546T						PASS	.	C	,,,	571,3835	245.3+/-254.3	46,479,1678	60.0	58.0	59.0		546,546,546,	-9.6	0.0	19	dbSNP_105	59	1273,7327	247.4+/-275.4	85,1103,3112	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	131,1582,4790	TT,TC,CC		14.8023,12.9596,14.1781	,,,	182/558,182/551,182/532,	804642	1844,11162	2203	4300	6503	SO:0001819	synonymous_variant	5725	exon6			GAGCCCCGTGCTC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.546C>T	19.37:g.804642C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.860;T|0.140	0.140	strong		0.682	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
NLRP5	126206	hgsc.bcm.edu	37	19	56572875	56572875	+	Missense_Mutation	SNP	G	G	A	rs36118060	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56572875G>A	ENST00000390649.3	+	15	3584	c.3584G>A	c.(3583-3585)cGg>cAg	p.R1195Q		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	1195			R -> Q (in dbSNP:rs36118060).		cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GAAGATGACCGGTACTGGTGG	0.488													G|||	857	0.171126	0.0749	0.1153	5008	,	,		19788	0.3373		0.1342	False		,,,				2504	0.2076				p.R1195Q		Atlas-SNP	.											.	NLRP5	217	.	0			c.G3584A						PASS	.	G	GLN/ARG	289,3569		10,269,1650	149.0	141.0	143.0		3584	-0.0	0.0	19	dbSNP_126	143	1208,7068		92,1024,3022	yes	missense	NLRP5	NM_153447.4	43	102,1293,4672	AA,AG,GG		14.5964,7.4909,12.3372	probably-damaging	1195/1201	56572875	1497,10637	1929	4138	6067	SO:0001583	missense	126206	exon15			ATGACCGGTACTG	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.3584G>A	19.37:g.56572875G>A	ENSP00000375063:p.Arg1195Gln	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	372	0.17032967032967034	25	0.0508130081300813	40	0.11049723756906077	205	0.3583916083916084	102	0.1345646437994723	G	14.57	2.575088	0.45902	0.074909	0.145964	ENSG00000171487	ENST00000390649	T	0.72394	-0.65	3.43	-0.0225	0.13947	.	.	.	.	.	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	D	0.64830	0.994	P	0.47102	0.537	T	0.11275	-1.0594	8	0.27785	T	0.31	.	3.7389	0.08521	0.2376:0.2052:0.5572:0.0	rs36118060	1195	P59047	NALP5_HUMAN	Q	1195	ENSP00000375063:R1195Q	ENSP00000375063:R1195Q	R	+	2	0	NLRP5	61264687	0.021000	0.18746	0.036000	0.18154	0.927000	0.56198	0.528000	0.23002	0.092000	0.17331	0.655000	0.94253	CGG	G|0.825;A|0.175	0.175	strong		0.488	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
KCNA1	3736	hgsc.bcm.edu	37	12	5021348	5021348	+	Silent	SNP	G	G	C	rs2227910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:5021348G>C	ENST00000382545.3	+	2	1911	c.804G>C	c.(802-804)acG>acC	p.T268T	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	268					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	ATTTCATCACGCTGGGCACCG	0.527													C|||	2671	0.533347	0.4796	0.5764	5008	,	,		20613	0.6627		0.5159	False		,,,				2504	0.4601				p.T268T		Atlas-SNP	.											.	KCNA1	112	.	0			c.G804C						PASS	.	C		2052,2354	607.7+/-391.0	460,1132,611	73.0	74.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	804	-3.2	0.8	12	dbSNP_98	74	4496,4104	561.3+/-387.7	1175,2146,979	no	coding-synonymous	KCNA1	NM_000217.2		1635,3278,1590	CC,CG,GG		47.7209,46.5729,49.654		268/496	5021348	6548,6458	2203	4300	6503	SO:0001819	synonymous_variant	3736	exon2			CATCACGCTGGGC	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.804G>C	12.37:g.5021348G>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_000217	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	37	CCDS8535.1																																																																																			G|0.461;C|0.539	0.539	strong		0.527	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
SAT2	112483	hgsc.bcm.edu	37	17	7530271	7530271	+	Silent	SNP	C	C	T	rs858520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7530271C>T	ENST00000269298.5	-	4	513	c.294G>A	c.(292-294)ccG>ccA	p.P98P	SAT2_ENST00000573566.1_Intron|SHBG_ENST00000576728.1_Intron|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000574539.1_Intron|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000340624.5_5'Flank|SHBG_ENST00000570547.1_Intron|SHBG_ENST00000572262.1_Intron|SHBG_ENST00000575314.1_Intron|SAT2_ENST00000380466.2_5'UTR	NM_133491.3	NP_597998.1	Q96F10	SAT2_HUMAN	spermidine/spermine N1-acetyltransferase family member 2	98	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				nor-spermidine metabolic process (GO:0046204)|putrescine acetylation (GO:0032920)|putrescine catabolic process (GO:0009447)|spermidine acetylation (GO:0032918)|spermine acetylation (GO:0032919)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	diamine N-acetyltransferase activity (GO:0004145)	p.?(1)		kidney(1)|large_intestine(2)	3				READ - Rectum adenocarcinoma(115;0.166)	Spermine(DB00127)	CCCGATATTCCGGCATCACAT	0.557													C|||	1359	0.271366	0.0182	0.2695	5008	,	,		17324	0.3155		0.3887	False		,,,				2504	0.4489				p.P98P		Atlas-SNP	.											.	SAT2	8	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.G294A						PASS	.	C		331,4075	172.7+/-202.6	14,303,1886	71.0	69.0	70.0		294	-11.5	0.0	17	dbSNP_86	70	3338,5262	484.3+/-371.4	671,1996,1633	no	coding-synonymous	SAT2	NM_133491.3		685,2299,3519	TT,TC,CC		38.814,7.5125,28.2101		98/171	7530271	3669,9337	2203	4300	6503	SO:0001819	synonymous_variant	112483	exon4			ATATTCCGGCATC	AF348524	CCDS11116.1	17p13.2	2011-11-16	2008-01-07		ENSG00000141504	ENSG00000141504	2.3.1.57		23160	protein-coding gene	gene with protein product	"""diamine N-acetyltransferase 2"""	611463	"""spermidine/spermine N1-acetyltransferase 2"""			15283699, 17558023	Standard	NM_133491		Approved	SSAT2	uc002gic.2	Q96F10	OTTHUMG00000108152	ENST00000269298.5:c.294G>A	17.37:g.7530271C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_133491		Silent	SNP	ENST00000269298.5	37	CCDS11116.1																																																																																			C|0.723;T|0.277	0.277	strong		0.557	SAT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440078.1	NM_133491	
ARHGEF4	50649	hgsc.bcm.edu	37	2	131688587	131688587	+	Silent	SNP	G	G	A	rs6718816	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:131688587G>A	ENST00000326016.5	+	3	576	c.57G>A	c.(55-57)gcG>gcA	p.A19A	ARHGEF4_ENST00000525839.1_Silent_p.A19A|ARHGEF4_ENST00000409303.1_Silent_p.A19A|ARHGEF4_ENST00000392953.3_Silent_p.A19A|ARHGEF4_ENST00000409359.1_Silent_p.A875A|ARHGEF4_ENST00000428230.2_Silent_p.A19A|SCARNA4_ENST00000517020.2_RNA	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	19					apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		GTCAGAAGGCGTTCCACATGG	0.592													G|||	1289	0.257388	0.4047	0.1297	5008	,	,		18326	0.1607		0.1829	False		,,,				2504	0.3252				p.A19A		Atlas-SNP	.											ARHGEF4,NS,carcinoma,+2,1	ARHGEF4	89	1	0			c.G57A						PASS	.	G	,	1702,2704	513.2+/-368.3	327,1048,828	70.0	64.0	66.0		57,57	-2.4	0.0	2	dbSNP_116	66	1523,7077	287.8+/-298.4	131,1261,2908	no	coding-synonymous,coding-synonymous	ARHGEF4	NM_015320.2,NM_032995.1	,	458,2309,3736	AA,AG,GG		17.7093,38.6291,24.7962	,	19/691,19/671	131688587	3225,9781	2203	4300	6503	SO:0001819	synonymous_variant	50649	exon3			GAAGGCGTTCCAC	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.57G>A	2.37:g.131688587G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_032995	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	37	CCDS2165.1																																																																																			G|0.748;A|0.252	0.252	strong		0.592	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
MUC16	94025	hgsc.bcm.edu	37	19	9006749	9006749	+	Missense_Mutation	SNP	C	C	T	rs75444444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9006749C>T	ENST00000397910.4	-	44	39702	c.39499G>A	c.(39499-39501)Gtg>Atg	p.V13167M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13169	SEA 8. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGAATGGCACCAGGAGAGGG	0.428													c|||	993	0.198283	0.2859	0.1153	5008	,	,		20691	0.1399		0.1889	False		,,,				2504	0.2086				p.V13167M		Atlas-SNP	.											.	MUC16	4315	.	0			c.G39499A						PASS	.	T	MET/VAL	976,2894		134,708,1093	185.0	149.0	160.0		39499	-3.6	0.0	19	dbSNP_131	160	1604,6672		161,1282,2695	yes	missense	MUC16	NM_024690.2	21	295,1990,3788	TT,TC,CC		19.3813,25.2196,21.2416	possibly-damaging	13167/14508	9006749	2580,9566	1935	4138	6073	SO:0001583	missense	94025	exon44			ATGGCACCAGGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.39499G>A	19.37:g.9006749C>T	ENSP00000381008:p.Val13167Met	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	279	275	0.985663	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	381|381	0.17445054945054944|0.17445054945054944	136|136	0.2764227642276423|0.2764227642276423	43|43	0.11878453038674033|0.11878453038674033	56|56	0.0979020979020979|0.0979020979020979	146|146	0.19261213720316622|0.19261213720316622	.|.	6.442|6.442	0.449704|0.449704	0.12223|0.12223	0.252196|0.252196	0.193813|0.193813	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000441155|ENST00000542240	T|.	0.42513|.	0.97|.	2.99|2.99	-3.6|-3.6	0.04570|0.04570	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	L|L	0.49640|0.49640	1.575|1.575	.|.	.|.	.|.	P|.	0.50156|.	0.932|.	P|.	0.47134|.	0.539|.	T|.	0.28870|.	-1.0030|.	8|.	0.87932|.	D|.	0|.	-3.4762|-3.4762	3.4755|3.4755	0.07583|0.07583	0.1856:0.3374:0.0:0.477|0.1856:0.3374:0.0:0.477	.|.	13167|.	B5ME49|.	.|.	M|X	13167;298|6	ENSP00000381008:V13167M|.	ENSP00000381008:V13167M|.	V|W	-|-	1|3	0|0	MUC16|MUC16	8867749|8867749	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-3.453000|-3.453000	0.00465|0.00465	-0.648000|-0.648000	0.05437|0.05437	-1.000000|-1.000000	0.02509|0.02509	GTG|TGG	C|0.824;T|0.176	0.176	strong		0.428	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SH2D3C	10044	hgsc.bcm.edu	37	9	130536717	130536717	+	Missense_Mutation	SNP	G	G	A	rs10760500	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:130536717G>A	ENST00000314830.8	-	2	180	c.67C>T	c.(67-69)Ctc>Ttc	p.L23F	SH2D3C_ENST00000471939.1_5'Flank|SH2D3C_ENST00000373277.4_5'Flank	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	23			L -> F (in dbSNP:rs10760500).		JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AGGTTGGAGAGACTCCCAAAG	0.478													G|||	2686	0.536342	0.208	0.5101	5008	,	,		19251	0.8988		0.5249	False		,,,				2504	0.637				p.L23F		Atlas-SNP	.											.	SH2D3C	102	.	0			c.C67T						PASS	.	G	PHE/LEU	1181,3225	413.9+/-336.6	157,867,1179	56.0	53.0	54.0		67	3.2	1.0	9	dbSNP_120	54	4838,3762	614.2+/-396.2	1335,2168,797	yes	missense	SH2D3C	NM_170600.2	22	1492,3035,1976	AA,AG,GG		43.7442,26.8044,46.2786	probably-damaging	23/861	130536717	6019,6987	2203	4300	6503	SO:0001583	missense	10044	exon2			TGGAGAGACTCCC	AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"""SH2 domain containing"""	16884	protein-coding gene	gene with protein product		604722	"""SH2 domain-containing 3C"""			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.67C>T	9.37:g.130536717G>A	ENSP00000317817:p.Leu23Phe	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_170600	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Missense_Mutation	SNP	ENST00000314830.8	37	CCDS6877.1	1207	0.5526556776556777	117	0.23780487804878048	179	0.494475138121547	518	0.9055944055944056	393	0.5184696569920845	G	17.61	3.432706	0.62844	0.268044	0.562558	ENSG00000095370	ENST00000314830	T	0.23552	1.9	5.03	3.19	0.36642	.	0.195247	0.28187	N	0.016277	T	0.00012	0.0000	N	0.20986	0.625	0.09310	P	0.9999999999994148	B	0.14012	0.009	B	0.15052	0.012	T	0.10847	-1.0612	9	0.87932	D	0	-0.0099	8.8792	0.35365	0.1764:0.0:0.8236:0.0	rs10760500;rs52790152;rs61291828;rs10760500	23	Q8N5H7	SH2D3_HUMAN	F	23	ENSP00000317817:L23F	ENSP00000317817:L23F	L	-	1	0	SH2D3C	129576538	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.487000	0.60293	0.645000	0.30675	0.561000	0.74099	CTC	G|0.503;A|0.497	0.497	strong		0.478	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489	
RAET1E	135250	hgsc.bcm.edu	37	6	150209717	150209717	+	Missense_Mutation	SNP	C	C	G	rs2342767	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:150209717C>G	ENST00000357183.4	-	4	841	c.709G>C	c.(709-711)Gtt>Ctt	p.V237L	RP11-244K5.8_ENST00000606915.1_RNA|RAET1E_ENST00000367363.3_Missense_Mutation_p.V201L|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000532335.1_Intron|RAET1E-AS1_ENST00000605899.1_RNA	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	237			V -> L (in dbSNP:rs2342767).		antigen processing and presentation (GO:0019882)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			cervix(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		CCCATTAAAACTAACAGGATG	0.443													c|||	2735	0.546126	0.4554	0.5043	5008	,	,		19212	0.8859		0.4195	False		,,,				2504	0.4785				p.V237L		Atlas-SNP	.											.	RAET1E	20	.	0			c.G709C						PASS	.	C	LEU/VAL	2015,2391	562.7+/-381.0	458,1099,646	112.0	101.0	105.0		709	-4.2	0.0	6	dbSNP_100	105	3456,5144	507.5+/-376.8	696,2064,1540	yes	missense	RAET1E	NM_139165.2	32	1154,3163,2186	GG,GC,CC		40.186,45.7331,42.0652	benign	237/264	150209717	5471,7535	2203	4300	6503	SO:0001583	missense	135250	exon4			TTAAAACTAACAG	AF359243	CCDS5221.1, CCDS59042.1, CCDS59043.1, CCDS59044.1	6q24.3	2011-02-09			ENSG00000164520	ENSG00000164520			16793	protein-coding gene	gene with protein product		609243				11827464	Standard	NM_139165		Approved	LETAL, bA350J20.7, ULBP4	uc003qnl.1	Q8TD07	OTTHUMG00000015796	ENST00000357183.4:c.709G>C	6.37:g.150209717C>G	ENSP00000349709:p.Val237Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	37	CCDS5221.1	1205	0.5517399267399268	211	0.42886178861788615	186	0.5138121546961326	500	0.8741258741258742	308	0.40633245382585753	C	6.278	0.419345	0.11928	0.457331	0.40186	ENSG00000164520	ENST00000357183;ENST00000367363	T;T	0.01538	5.2;4.79	2.46	-4.24	0.03777	.	3.567220	0.01514	N	0.018041	T	0.00440	0.0014	N	0.19112	0.55	0.53688	P	2.5000000000052758E-5	B;B	0.22211	0.039;0.066	B;B	0.25140	0.014;0.058	T	0.46555	-0.9183	9	0.52906	T	0.07	0.0875	1.4083	0.02286	0.3305:0.2168:0.3276:0.125	rs2342767;rs17674777;rs52801398;rs2342767	237;201	Q8TD07;Q8TD07-2	N2DL4_HUMAN;.	L	237;201	ENSP00000349709:V237L;ENSP00000356332:V201L	ENSP00000349709:V237L	V	-	1	0	RAET1E	150251410	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.787000	0.01764	-1.138000	0.02884	0.404000	0.27445	GTT	C|0.523;G|0.477	0.477	strong		0.443	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
SLC30A9	10463	hgsc.bcm.edu	37	4	42003671	42003671	+	Missense_Mutation	SNP	A	A	G	rs1047626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:42003671A>G	ENST00000264451.7	+	2	328	c.148A>G	c.(148-150)Atg>Gtg	p.M50V		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	50			M -> V (in dbSNP:rs1047626). {ECO:0000269|PubMed:10409434, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CTTTTCAAACATGGTTCCCTG	0.358													A|||	3147	0.628395	0.1051	0.768	5008	,	,		13831	0.9484		0.7565	False		,,,				2504	0.7751				p.M50V		Atlas-SNP	.											.	SLC30A9	58	.	0			c.A148G						PASS	.	A	VAL/MET	939,3467	355.1+/-312.9	105,729,1369	113.0	104.0	107.0		148	-2.8	0.0	4	dbSNP_86	107	6546,2054	716.9+/-406.1	2479,1588,233	yes	missense	SLC30A9	NM_006345.3	21	2584,2317,1602	GG,GA,AA		23.8837,21.3118,42.4496	benign	50/569	42003671	7485,5521	2203	4300	6503	SO:0001583	missense	10463	exon2			TCAAACATGGTTC	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"""Solute carriers"""	1329	protein-coding gene	gene with protein product	"""GRIP1-dependent nuclear receptor coactivator"""	604604	"""chromosome 4 open reading frame 1"""	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.148A>G	4.37:g.42003671A>G	ENSP00000264451:p.Met50Val	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	175	81	0.462857	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	37	CCDS3465.1	1460	0.6684981684981685	57	0.11585365853658537	273	0.7541436464088398	545	0.9527972027972028	585	0.7717678100263852	A	0.007	-2.015140	0.00422	0.213118	0.761163	ENSG00000014824	ENST00000264451	T	0.20598	2.06	4.66	-2.85	0.05734	.	0.711210	0.14166	N	0.337003	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41805	-0.9488	9	0.02654	T	1	0.1043	4.5984	0.12341	0.4612:0.0:0.3868:0.152	rs1047626;rs1801961;rs3187632;rs17412165;rs17530086;rs17845128;rs17856522;rs17857929;rs61370393;rs1047626	50	Q6PML9	ZNT9_HUMAN	V	50	ENSP00000264451:M50V	ENSP00000264451:M50V	M	+	1	0	SLC30A9	41698428	0.000000	0.05858	0.000000	0.03702	0.400000	0.30750	-0.933000	0.03959	-0.527000	0.06374	-0.316000	0.08728	ATG	A|0.395;G|0.605	0.605	strong		0.358	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3		
RARG	5916	hgsc.bcm.edu	37	12	53605545	53605545	+	Missense_Mutation	SNP	G	G	A	rs2229774	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53605545G>A	ENST00000425354.2	-	10	1767	c.1280C>T	c.(1279-1281)tCg>tTg	p.S427L	RARG_ENST00000543762.1_5'UTR|RARG_ENST00000327550.3_Missense_Mutation_p.S355L|RARG_ENST00000394426.1_Missense_Mutation_p.S427L|RARG_ENST00000338561.5_Missense_Mutation_p.S416L|RARG_ENST00000543726.1_Missense_Mutation_p.S405L	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	427			S -> L (in dbSNP:rs2229774).		anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	ACCAGGCTGCGAGGAGTCATC	0.602													G|||	439	0.0876597	0.0991	0.0418	5008	,	,		19278	0.004		0.0636	False		,,,				2504	0.2157				p.S427L		Atlas-SNP	.											.	RARG	53	.	0			c.C1280T						PASS	.	G	LEU/SER,LEU/SER	391,4015	195.0+/-219.7	17,357,1829	72.0	66.0	68.0		1280,1247	4.5	1.0	12	dbSNP_98	68	558,8042	151.9+/-206.6	19,520,3761	yes	missense,missense	RARG	NM_000966.5,NM_001042728.2	145,145	36,877,5590	AA,AG,GG		6.4884,8.8743,7.2966	benign,benign	427/455,416/444	53605545	949,12057	2203	4300	6503	SO:0001583	missense	5916	exon10			GGCTGCGAGGAGT	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"""Nuclear hormone receptors"""	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.1280C>T	12.37:g.53605545G>A	ENSP00000388510:p.Ser427Leu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	37	CCDS8850.1	121	0.0554029304029304	56	0.11382113821138211	19	0.052486187845303865	0	0.0	46	0.06068601583113457	G	12.90	2.077807	0.36662	0.088743	0.064884	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000327550;ENST00000338561;ENST00000543726	D;D;D;D;D	0.92495	-2.89;-2.89;-3.05;-2.85;-2.93	4.53	4.53	0.55603	.	0.554792	0.18339	N	0.144244	T	0.14830	0.0358	L	0.53249	1.67	0.28685	P	0.9049115	B;B;P	0.35872	0.429;0.216;0.525	B;B;B	0.21917	0.028;0.012;0.037	T	0.71728	-0.4505	9	0.59425	D	0.04	.	11.7618	0.51908	0.0:0.0:0.8236:0.1764	rs2229774;rs61642612;rs2229774	405;427;416	B7Z4F1;P13631;F1D8P1	.;RARG_HUMAN;.	L	427;427;355;416;405	ENSP00000388510:S427L;ENSP00000377947:S427L;ENSP00000332695:S355L;ENSP00000343698:S416L;ENSP00000444335:S405L	ENSP00000332695:S355L	S	-	2	0	RARG	51891812	0.259000	0.24043	1.000000	0.80357	0.911000	0.54048	2.736000	0.47385	2.519000	0.84933	0.563000	0.77884	TCG	G|0.927;A|0.073	0.073	strong		0.602	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966	
SORCS1	114815	hgsc.bcm.edu	37	10	108339080	108339080	+	Intron	SNP	G	G	A	rs375056844		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:108339080G>A	ENST00000263054.6	-	25	3379				SORCS1_ENST00000369698.1_Intron|SORCS1_ENST00000344440.6_Intron	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1						neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CTGTCAGGGAGAAGGAAGAGG	0.478																																					p.L1140F		Atlas-SNP	.											.	SORCS1	534	.	0			c.C3418T						PASS	.	G	,,,PHE/LEU,,	2,4404	4.2+/-10.8	0,2,2201	107.0	88.0	94.0		,,,3418,,	-0.0	0.2	10		94	3,8597	3.0+/-9.4	0,3,4297	no	intron,intron,intron,missense,intron,intron	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	,,,22,,	0,5,6498	AA,AG,GG		0.0349,0.0454,0.0384	,,,,,	,,,1140/1160,,	108339080	5,13001	2203	4300	6503	SO:0001627	intron_variant	114815	exon25			CAGGGAGAAGGAA	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3371+46C>T	10.37:g.108339080G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_001206571	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1																																																																																			.	.	none		0.478	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
FAM214B	80256	hgsc.bcm.edu	37	9	35107740	35107740	+	Missense_Mutation	SNP	C	C	T	rs61735988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35107740C>T	ENST00000378561.1	-	2	3587	c.532G>A	c.(532-534)Gcc>Acc	p.A178T	FAM214B_ENST00000605244.1_Missense_Mutation_p.A178T|FAM214B_ENST00000488109.2_Missense_Mutation_p.A178T|FAM214B_ENST00000603301.1_Missense_Mutation_p.A178T|FAM214B_ENST00000605392.1_5'Flank|FAM214B_ENST00000378554.2_Missense_Mutation_p.A178T|FAM214B_ENST00000378557.1_Missense_Mutation_p.A178T|FAM214B_ENST00000378566.1_Intron|FAM214B_ENST00000322813.5_Missense_Mutation_p.A178T			Q7L5A3	F214B_HUMAN	family with sequence similarity 214, member B	178						nucleus (GO:0005634)											CCTGGAGGGGCTGGCCCTGGG	0.617													C|||	59	0.0117812	0.0159	0.0144	5008	,	,		16455	0.0		0.0179	False		,,,				2504	0.0102				p.A178T		Atlas-SNP	.											.	.	.	.	0			c.G532A						PASS	.	C	THR/ALA	58,4332		1,56,2138	37.0	46.0	43.0		532	4.9	1.0	9	dbSNP_129	43	110,8490		1,108,4191	yes	missense	KIAA1539	NM_025182.2	58	2,164,6329	TT,TC,CC		1.2791,1.3212,1.2933	benign	178/539	35107740	168,12822	2195	4300	6495	SO:0001583	missense	80256	exon3			GAGGGGCTGGCCC	AB040972	CCDS6578.1	9p13.2	2011-12-01	2011-12-01	2011-12-01	ENSG00000005238	ENSG00000005238			25666	protein-coding gene	gene with protein product			"""KIAA1539"""	KIAA1539		10819331	Standard	NM_025182		Approved	FLJ11560, bA182N22.6	uc003zwo.3	Q7L5A3	OTTHUMG00000019847	ENST00000378561.1:c.532G>A	9.37:g.35107740C>T	ENSP00000367823:p.Ala178Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	92	54	0.586957	NM_025182	B1AML4|B1AML5|D3DRN5|O60377|Q9BQ60|Q9HAI9|Q9P1Y9	Missense_Mutation	SNP	ENST00000378561.1	37	CCDS6578.1	31	0.014194139194139194	14	0.028455284552845527	6	0.016574585635359115	0	0.0	11	0.014511873350923483	C	13.32	2.201815	0.38905	0.013212	0.012791	ENSG00000005238	ENST00000322813;ENST00000378561;ENST00000378557;ENST00000378554	.	.	.	4.87	4.87	0.63330	.	0.207947	0.33772	N	0.004565	T	0.12347	0.0300	L	0.28115	0.83	0.31954	N	0.60928	B	0.17852	0.024	B	0.12156	0.007	T	0.12889	-1.0530	8	.	.	.	-19.2341	9.3337	0.38038	0.0:0.7761:0.1453:0.0786	.	178	Q7L5A3	K1539_HUMAN	T	178	.	.	A	-	1	0	KIAA1539	35097740	0.995000	0.38212	1.000000	0.80357	0.988000	0.76386	1.281000	0.33214	2.532000	0.85374	0.555000	0.69702	GCC	C|0.988;T|0.012	0.012	strong		0.617	FAM214B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052261.1	NM_025182	
FBXO42	54455	hgsc.bcm.edu	37	1	16641899	16641899	+	Silent	SNP	C	C	T	rs2273311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16641899C>T	ENST00000375592.3	-	2	231	c.15G>A	c.(13-15)tcG>tcA	p.S5S	FBXO42_ENST00000478089.1_5'Flank	NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	5										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		CTTCACTGTCCGAGGAGCTGG	0.463													C|||	1790	0.357428	0.0469	0.3372	5008	,	,		20434	0.6786		0.4235	False		,,,				2504	0.3926				p.S5S		Atlas-SNP	.											.	FBXO42	53	.	0			c.G15A						PASS	.	C		529,3877	241.5+/-251.9	35,459,1709	83.0	70.0	75.0		15	-4.1	0.9	1	dbSNP_100	75	3417,5183	503.5+/-375.9	688,2041,1571	no	coding-synonymous	FBXO42	NM_018994.1		723,2500,3280	TT,TC,CC		39.7326,12.0064,30.3398		5/718	16641899	3946,9060	2203	4300	6503	SO:0001819	synonymous_variant	54455	exon2			ACTGTCCGAGGAG	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.15G>A	1.37:g.16641899C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	ENST00000375592.3	37	CCDS30613.1																																																																																			C|0.658;T|0.342	0.342	strong		0.463	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
EFTUD1	79631	hgsc.bcm.edu	37	15	82456227	82456227	+	Missense_Mutation	SNP	T	T	C	rs1128431	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:82456227T>C	ENST00000268206.7	-	16	2017	c.1849A>G	c.(1849-1851)Att>Gtt	p.I617V	EFTUD1_ENST00000359445.3_Missense_Mutation_p.I566V	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	617			I -> V (in dbSNP:rs1128431).		GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						ACTCTCACAATAGGAGTGGCT	0.378													T|||	875	0.17472	0.3623	0.0692	5008	,	,		19860	0.2143		0.0736	False		,,,				2504	0.0593				p.I617V		Atlas-SNP	.											.	EFTUD1	74	.	0			c.A1849G						PASS	.	T	VAL/ILE,VAL/ILE	1100,2694		164,772,961	91.0	87.0	88.0		1696,1849	5.2	0.8	15	dbSNP_86	88	520,7724		17,486,3619	yes	missense,missense	EFTUD1	NM_001040610.2,NM_024580.5	29,29	181,1258,4580	CC,CT,TT		6.3076,28.9931,13.4574	benign,benign	566/1070,617/1121	82456227	1620,10418	1897	4122	6019	SO:0001583	missense	79631	exon16			TCACAATAGGAGT	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"""ribosome assembly 1 homolog (yeast)"""					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.1849A>G	15.37:g.82456227T>C	ENSP00000268206:p.Ile617Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Missense_Mutation	SNP	ENST00000268206.7	37	CCDS42071.1	353	0.16163003663003664	159	0.3231707317073171	23	0.06353591160220995	114	0.1993006993006993	57	0.07519788918205805	T	24.5	4.539451	0.85917	0.289931	0.063076	ENSG00000140598	ENST00000268206;ENST00000359445	T;T	0.64803	-0.12;-0.12	5.2	5.2	0.72013	Elongation factor G/III/V (1);	0.328424	0.23362	N	0.049019	T	0.00012	0.0000	N	0.05158	-0.105	0.09310	P	0.99999999185105	D;P	0.71674	0.998;0.791	D;P	0.67231	0.95;0.464	T	0.36383	-0.9750	9	0.72032	D	0.01	-1.5349	15.0754	0.72074	0.0:0.0:0.0:1.0	rs1128431;rs2291990;rs3088388;rs3185400;rs11548680;rs17841155;rs52836083;rs59235214;rs1128431	566;617	Q7Z2Z2-2;Q7Z2Z2	.;ETUD1_HUMAN	V	617;566	ENSP00000268206:I617V;ENSP00000352418:I566V	ENSP00000268206:I617V	I	-	1	0	EFTUD1	80243282	1.000000	0.71417	0.782000	0.31804	0.996000	0.88848	7.423000	0.80229	1.972000	0.57404	0.533000	0.62120	ATT	T|0.838;C|0.162	0.162	strong		0.378	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580	
DSP	1832	hgsc.bcm.edu	37	6	7580228	7580228	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:7580228C>T	ENST00000379802.3	+	23	4146	c.3805C>T	c.(3805-3807)Cga>Tga	p.R1269*	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1269	Central fibrous rod domain.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GCAGCGAAGGCGAGCTGAAGA	0.488																																					p.R1269X		Atlas-SNP	.											DSP,NS,carcinoma,-1,2	DSP	306	2	0			c.C3805T						scavenged	.						60.0	61.0	61.0					6																	7580228		2203	4299	6502	SO:0001587	stop_gained	1832	exon23			CGAAGGCGAGCTG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.3805C>T	6.37:g.7580228C>T	ENSP00000369129:p.Arg1269*	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	152	2	0.0131579	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Nonsense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	C	44	10.533054	0.99422	.	.	ENSG00000096696	ENST00000379802	.	.	.	5.17	0.776	0.18532	.	0.000000	0.53938	D	0.000058	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	15.0463	0.71830	0.7552:0.2448:0.0:0.0	.	.	.	.	X	1269	.	ENSP00000369129:R1269X	R	+	1	2	DSP	7525227	0.996000	0.38824	0.969000	0.41365	0.978000	0.69477	0.668000	0.25127	0.125000	0.18397	0.557000	0.71058	CGA	.	.	none		0.488	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
MUT	4594	hgsc.bcm.edu	37	6	49412433	49412433	+	Missense_Mutation	SNP	C	C	T	rs1141321	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:49412433C>T	ENST00000274813.3	-	9	1722	c.1595G>A	c.(1594-1596)cGt>cAt	p.R532H		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	532			R -> H (in dbSNP:rs1141321). {ECO:0000269|PubMed:16281286, ECO:0000269|PubMed:1980486, ECO:0000269|PubMed:2567699, ECO:0000269|PubMed:7912889}.		cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGCAAGACAACGTTCAGCCAA	0.428													C|||	1330	0.265575	0.174	0.2104	5008	,	,		16274	0.2063		0.331	False		,,,				2504	0.4223				p.R532H		Atlas-SNP	.											.	MUT	70	.	0			c.G1595A						PASS	.	C	HIS/ARG	929,3477	352.6+/-311.8	88,753,1362	163.0	155.0	158.0		1595	1.4	0.1	6	dbSNP_86	158	3148,5452	479.1+/-370.0	578,1992,1730	yes	missense	MUT	NM_000255.3	29	666,2745,3092	TT,TC,CC		36.6047,21.0849,31.3471	possibly-damaging	532/751	49412433	4077,8929	2203	4300	6503	SO:0001583	missense	4594	exon9			AGACAACGTTCAG		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"""methylmalonyl Coenzyme A mutase"""			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1595G>A	6.37:g.49412433C>T	ENSP00000274813:p.Arg532His	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	37	CCDS4924.1	573	0.2623626373626374	94	0.1910569105691057	83	0.2292817679558011	112	0.1958041958041958	284	0.37467018469656993	C	8.081	0.772374	0.16051	0.210849	0.366047	ENSG00000146085	ENST00000274813	D	0.98280	-4.84	5.31	1.44	0.22558	Cobalamin (vitamin B12)-dependent enzyme, catalytic (1);Methylmalonyl-CoA mutase, alpha/beta chain, catalytic (1);Methylmalonyl-CoA mutase, alpha chain, catalytic (1);	0.336740	0.30028	N	0.010596	D	0.95739	0.8614	M	0.78916	2.43	0.80722	P	0.0	B	0.28850	0.225	B	0.35931	0.214	D	0.92245	0.5804	9	0.44086	T	0.13	-7.7706	9.9771	0.41791	0.0:0.5716:0.0:0.4284	rs1141321;rs2229386;rs3205245;rs9473558;rs17246003;rs17405002;rs56630024;rs9473558	532	P22033	MUTA_HUMAN	H	532	ENSP00000274813:R532H	ENSP00000274813:R532H	R	-	2	0	MUT	49520392	0.003000	0.15002	0.070000	0.20053	0.139000	0.21198	-0.018000	0.12568	0.310000	0.22990	-0.237000	0.12165	CGT	T|0.242;G|0.135;C|0.582;A|0.041	0.242	strong		0.428	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
MGAM	8972	hgsc.bcm.edu	37	7	141796215	141796215	+	Splice_Site	SNP	T	T	C	rs199885850		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:141796215T>C	ENST00000549489.2	+	42	5099	c.5004T>C	c.(5002-5004)cgT>cgC	p.R1668R	MGAM_ENST00000475668.2_Splice_Site_p.R2564R	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1668	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R1668R(2)|p.R2565R(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCCTGGAGCGTGTGAGTATGG	0.582																																					p.R1668R		Atlas-SNP	.											MGAM_ENST00000549489,NS,carcinoma,+2,6	MGAM	767	6	3	Substitution - coding silent(3)	prostate(3)	c.T5004C						scavenged	.						88.0	83.0	85.0					7																	141796215		1950	4132	6082	SO:0001630	splice_region_variant	8972	exon42			GGAGCGTGTGAGT	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.5004+1T>C	7.37:g.141796215T>C		Somatic	416	1	0.00240385		WXS	Illumina HiSeq	Phase_I	368	7	0.0190217	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			.	.	weak		0.582	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		Silent
NUMA1	4926	hgsc.bcm.edu	37	11	71724784	71724784	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71724784C>T	ENST00000393695.3	-	15	4096	c.3765G>A	c.(3763-3765)gtG>gtA	p.V1255V	NUMA1_ENST00000358965.6_Silent_p.V1255V|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000351960.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						ACTCGGCCATCACCAGCCGCT	0.597			T	RARA	APL																																p.V1255V		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.G3765A						PASS	.						51.0	52.0	52.0					11																	71724784		2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			GGCCATCACCAGC	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.3765G>A	11.37:g.71724784C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			.	.	none		0.597	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
C1orf101	257044	hgsc.bcm.edu	37	1	244724092	244724092	+	Silent	SNP	G	G	A	rs7544794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:244724092G>A	ENST00000366534.4	+	10	1206	c.1152G>A	c.(1150-1152)tcG>tcA	p.S384S	C1orf101_ENST00000366533.4_Silent_p.S384S|C1orf101_ENST00000366531.3_Silent_p.S233S|C1orf101_ENST00000473875.1_3'UTR	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	384						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			TAAGTCTATCGGTGACTGCTA	0.398													A|||	1368	0.273163	0.4334	0.2435	5008	,	,		15481	0.376		0.0775	False		,,,				2504	0.1728				p.S384S		Atlas-SNP	.											.	C1orf101	158	.	0			c.G1152A						PASS	.	A	,,	1680,2726	654.5+/-399.8	318,1044,841	109.0	113.0	111.0		1152,699,1152	-5.6	0.0	1	dbSNP_116	111	764,7836	785.0+/-407.6	26,712,3562	no	coding-synonymous,coding-synonymous,coding-synonymous	C1orf101	NM_001130957.1,NM_001242340.1,NM_173807.4	,,	344,1756,4403	AA,AG,GG		8.8837,38.1298,18.7913	,,	384/952,233/801,384/833	244724092	2444,10562	2203	4300	6503	SO:0001819	synonymous_variant	257044	exon10			TCTATCGGTGACT	BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.1152G>A	1.37:g.244724092G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	188	97	0.515957	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																			G|0.779;A|0.221	0.221	strong		0.398	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807	
ZNF14	7561	hgsc.bcm.edu	37	19	19823270	19823270	+	Missense_Mutation	SNP	T	T	A	rs12973901	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19823270T>A	ENST00000344099.3	-	4	958	c.820A>T	c.(820-822)Act>Tct	p.T274S		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	274			T -> S (in dbSNP:rs12973901). {ECO:0000269|Ref.1}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				TTTTCTCCAGTGTGAGTTCTT	0.403													T|||	915	0.182708	0.0265	0.1657	5008	,	,		19776	0.2649		0.2376	False		,,,				2504	0.2648				p.T274S		Atlas-SNP	.											.	ZNF14	89	.	0			c.A820T						PASS	.	T	SER/THR	245,4161	137.7+/-173.5	4,237,1962	47.0	46.0	46.0		820	1.8	0.0	19	dbSNP_121	46	2206,6392	362.0+/-332.6	297,1612,2390	yes	missense	ZNF14	NM_021030.2	58	301,1849,4352	AA,AT,TT		25.6571,5.5606,18.848	benign	274/643	19823270	2451,10553	2203	4299	6502	SO:0001583	missense	7561	exon4			CTCCAGTGTGAGT	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"""Zinc fingers, C2H2-type"", ""-"""	12924	protein-coding gene	gene with protein product		194556	"""zinc finger protein 14 (KOX 6)"""				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.820A>T	19.37:g.19823270T>A	ENSP00000340514:p.Thr274Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_021030	B9EGA4|Q9ULZ5	Missense_Mutation	SNP	ENST00000344099.3	37	CCDS12409.1	413	0.1891025641025641	6	0.012195121951219513	72	0.19889502762430938	155	0.270979020979021	180	0.23746701846965698	T	17.92	3.505752	0.64410	0.055606	0.256571	ENSG00000105708	ENST00000344099	T	0.24151	1.87	1.8	1.8	0.24995	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.25380	0.74	0.40981	P	0.015221999999999958	B	0.22909	0.077	B	0.19666	0.026	T	0.34153	-0.9840	8	0.54805	T	0.06	.	7.2278	0.26026	0.0:0.0:0.0:1.0	rs12973901;rs52831253;rs12973901	274	P17017	ZNF14_HUMAN	S	274	ENSP00000340514:T274S	ENSP00000340514:T274S	T	-	1	0	ZNF14	19684270	1.000000	0.71417	0.013000	0.15412	0.442000	0.32017	5.501000	0.66950	0.811000	0.34303	0.383000	0.25322	ACT	T|0.808;A|0.192	0.192	strong		0.403	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030	
PDHX	8050	hgsc.bcm.edu	37	11	34937828	34937828	+	5'Flank	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34937828A>G	ENST00000227868.4	+	0	0				APIP_ENST00000527830.1_5'UTR|APIP_ENST00000395787.3_Missense_Mutation_p.S2P|APIP_ENST00000278359.5_5'UTR|PDHX_ENST00000430469.2_5'Flank|PDHX_ENST00000448838.3_5'UTR			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X						cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TCACAGCCAGACATGGCCCAG	0.687																																					p.S2P		Atlas-SNP	.											.	APIP	21	.	0			c.T4C						PASS	.						16.0	18.0	17.0					11																	34937828		2197	4293	6490	SO:0001631	upstream_gene_variant	51074	exon1			AGCCAGACATGGC	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491		11.37:g.34937828A>G	Exception_encountered	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	83	25	0.301205	NM_015957	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	37	CCDS7896.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.018048	0.54576	.	.	ENSG00000149089	ENST00000395787	T	0.19394	2.15	4.68	-0.69	0.11309	.	0.808144	0.11278	N	0.580708	T	0.09024	0.0223	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14117	-1.0484	10	0.54805	T	0.06	.	4.192	0.10426	0.4606:0.3478:0.1917:0.0	.	2	Q96GX9	MTNB_HUMAN	P	2	ENSP00000379133:S2P	ENSP00000379133:S2P	S	-	1	0	APIP	34894404	0.998000	0.40836	0.865000	0.33974	0.003000	0.03518	0.450000	0.21762	0.064000	0.16427	-0.441000	0.05720	TCT	.	.	none		0.687	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
C1QTNF5	114902	hgsc.bcm.edu	37	11	119216504	119216504	+	De_novo_Start_OutOfFrame	SNP	C	C	T	rs3814762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:119216504C>T	ENST00000445041.2	-	0	565				MFRP_ENST00000555262.1_Missense_Mutation_p.V136M|MFRP_ENST00000530681.1_Missense_Mutation_p.V136M|MFRP_ENST00000449574.2_Missense_Mutation_p.V136M|MFRP_ENST00000360167.4_Missense_Mutation_p.V136M|MFRP_ENST00000529147.1_5'UTR	NM_001278431.1|NM_015645.3|NM_031433.2	NP_001265360.1|NP_056460.1|NP_113621.1	Q9BXJ0	C1QT5_HUMAN	C1q and tumor necrosis factor related protein 5							collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(2)	3		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		GAGGGGCTCACGCCTGACTCC	0.652													C|||	912	0.182109	0.0393	0.1657	5008	,	,		15686	0.2004		0.337	False		,,,				2504	0.2086				p.V136M		Atlas-SNP	.											.	MFRP	63	.	0			c.G406A						PASS	.	C	,MET/VAL	429,3969	201.1+/-224.2	17,395,1787	54.0	58.0	57.0		,406	-3.1	0.1	11	dbSNP_107	57	2771,5819	428.3+/-355.9	446,1879,1970	yes	utr-5,missense	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,21	463,2274,3757	TT,TC,CC		32.2584,9.7544,24.6381	,benign	,136/580	119216504	3200,9788	2199	4295	6494			83552	exon4			GGCTCACGCCTGA	AF329841	CCDS8420.1	11q23.3	2013-05-10				ENSG00000223953			14344	protein-coding gene	gene with protein product	"""complement-c1q tumor necrosis factor-related protein 5"", ""complement C1q tumor necrosis factor-related protein 5 precursor variant 3"""	608752				12944416	Standard	NM_015645		Approved	CTRP5, DKFZp586B0621, LORD		Q9BXJ0	OTTHUMG00000166198	ENST00000445041.2:c.-2231G>A	11.37:g.119216504C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	NM_031433	A6NDD3|B0YJ35|Q335M2|Q8N6P2|Q9UFX4	Missense_Mutation	SNP	ENST00000445041.2	37	CCDS8420.1	464	0.21245421245421245	24	0.04878048780487805	80	0.22099447513812154	110	0.19230769230769232	250	0.32981530343007914	C	7.352	0.623059	0.14193	0.097544	0.322584	ENSG00000235718	ENST00000555262;ENST00000449574;ENST00000360167	T;T;T	0.68624	-0.34;-0.34;1.83	3.62	-3.06	0.05379	CUB (1);	0.539616	0.18771	N	0.131620	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B;B	0.23058	0.079;0.008	B;B	0.13407	0.009;0.001	T	0.31420	-0.9944	9	0.34782	T	0.22	-0.9875	6.3566	0.21404	0.0:0.404:0.1485:0.4474	rs3814762;rs3814762	136;136	B4DHN8;Q9BY79	.;MFRP_HUMAN	M	136	ENSP00000450509:V136M;ENSP00000391664:V136M;ENSP00000353291:V136M	ENSP00000353291:V136M	V	-	1	0	MFRP	118721714	0.000000	0.05858	0.140000	0.22221	0.185000	0.23345	-1.868000	0.01644	-0.646000	0.05452	-1.191000	0.01696	GTG	C|0.774;T|0.226	0.226	strong		0.652	C1QTNF5-201	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding		NM_015645	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51920619	51920619	+	Silent	SNP	G	G	C	rs61741679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51920619G>C	ENST00000339313.5	-	2	254	c.138C>G	c.(136-138)ccC>ccG	p.P46P	SIGLEC10_ENST00000441969.3_Silent_p.P46P|SIGLEC10_ENST00000439889.2_Silent_p.P46P|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000442846.3_Silent_p.P46P|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000436984.2_Silent_p.P46P|SIGLEC10_ENST00000432469.2_Silent_p.P46P|SIGLEC10_ENST00000356298.5_Silent_p.P46P|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000353836.5_Silent_p.P46P|SIGLEC10_ENST00000525998.1_Silent_p.P46P			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	46	Ig-like V-type.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.P46P(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		AGTCCTGTCGGGGGTAGGAGA	0.577													g|||	430	0.0858626	0.1558	0.0634	5008	,	,		18068	0.0863		0.0239	False		,,,				2504	0.0706				p.P46P		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,0,2	SIGLEC10	112	2	2	Substitution - coding silent(2)	stomach(2)	c.C138G						PASS	.	G	,,,,,,	628,3778		45,538,1620	65.0	60.0	61.0		138,138,138,138,138,138,138	-5.8	0.0	19	dbSNP_129	61	236,8364		5,226,4069	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	,,,,,,	50,764,5689	CC,CG,GG		2.7442,14.2533,6.6431	,,,,,,	46/640,46/603,46/555,46/545,46/520,46/455,46/698	51920619	864,12142	2203	4300	6503	SO:0001819	synonymous_variant	89790	exon2			CTGTCGGGGGTAG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.138C>G	19.37:g.51920619G>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	164	84	0.512195	NM_001171161	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			G|0.925;C|0.075	0.075	strong		0.577	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
HRCT1	646962	hgsc.bcm.edu	37	9	35906624	35906624	+	Missense_Mutation	SNP	G	G	A	rs75458097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35906624G>A	ENST00000354323.2	+	1	436	c.340G>A	c.(340-342)Gct>Act	p.A114T	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	114						integral component of membrane (GO:0016021)		p.A114T(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						tccccgccacGCTCGCTGAGG	0.667													G|||	286	0.0571086	0.0008	0.0548	5008	,	,		8078	0.1111		0.0358	False		,,,				2504	0.1012				p.A114T		Atlas-SNP	.											HRCT1,NS,haematopoietic_neoplasm,0,1	HRCT1	14	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G340A						PASS	.	G	THR/ALA	21,3127		1,19,1554	7.0	8.0	8.0		340	2.3	0.0	9	dbSNP_132	8	208,5972		5,198,2887	no	missense	HRCT1	NM_001039792.1	58	6,217,4441	AA,AG,GG		3.3657,0.6671,2.455	possibly-damaging	114/116	35906624	229,9099	1574	3090	4664	SO:0001583	missense	646962	exon1			CGCCACGCTCGCT		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.340G>A	9.37:g.35906624G>A	ENSP00000346283:p.Ala114Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	98	0.04487179487179487	5	0.01016260162601626	9	0.024861878453038673	60	0.1048951048951049	24	0.0316622691292876	G	10.94	1.492037	0.26774	0.006671	0.033657	ENSG00000196196	ENST00000354323	.	.	.	3.29	2.29	0.28610	.	.	.	.	.	T	0.00356	0.0011	N	0.14661	0.345	0.09310	N	1	P	0.40144	0.704	B	0.24848	0.056	T	0.13522	-1.0506	8	0.87932	D	0	-27.8878	5.6265	0.17485	0.1741:0.0:0.8259:0.0	.	114	Q6UXD1	HRCT1_HUMAN	T	114	.	ENSP00000346283:A114T	A	+	1	0	HRCT1	35896624	0.006000	0.16342	0.003000	0.11579	0.309000	0.27889	0.849000	0.27723	0.848000	0.35191	0.563000	0.77884	GCT	G|0.954;A|0.046	0.046	strong		0.667	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
SLC44A5	204962	hgsc.bcm.edu	37	1	75672376	75672376	+	Silent	SNP	A	A	G	rs1948874	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:75672376A>G	ENST00000370855.5	-	24	2189	c.2076T>C	c.(2074-2076)tcT>tcC	p.S692S	SLC44A5_ENST00000535611.1_Silent_p.S562S|SLC44A5_ENST00000370859.3_Intron	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	692					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						GTTTTTCTGTAGATCCATCAT	0.403													A|||	2207	0.440695	0.177	0.4669	5008	,	,		18568	0.8323		0.3966	False		,,,				2504	0.4202				p.S692S		Atlas-SNP	.											.	SLC44A5	231	.	0			c.T2076C						PASS	.	A	,	913,3493	352.1+/-311.5	97,719,1387	174.0	166.0	168.0		,2076	-0.5	1.0	1	dbSNP_92	168	3247,5353	486.3+/-371.9	619,2009,1672	no	intron,coding-synonymous	SLC44A5	NM_001130058.1,NM_152697.4	,	716,2728,3059	GG,GA,AA		37.7558,20.7217,31.9852	,	,692/720	75672376	4160,8846	2203	4300	6503	SO:0001819	synonymous_variant	204962	exon24			TTCTGTAGATCCA	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.2076T>C	1.37:g.75672376A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	37	CCDS667.1																																																																																			A|0.619;G|0.381	0.381	strong		0.403	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697	
ZDBF2	57683	hgsc.bcm.edu	37	2	207174316	207174316	+	Silent	SNP	T	T	C	rs3732084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:207174316T>C	ENST00000374423.3	+	5	5450	c.5064T>C	c.(5062-5064)agT>agC	p.S1688S		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1688							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AAGAAGCCAGTCTTCGGAAGG	0.448													C|||	2382	0.475639	0.3812	0.6182	5008	,	,		18961	0.3562		0.5706	False		,,,				2504	0.5276				p.S1688S		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T5064C						PASS	.	C		1796,2074		422,952,561	81.0	82.0	81.0		5064	-3.0	0.0	2	dbSNP_107	81	4977,3249		1512,1953,648	no	coding-synonymous	ZDBF2	NM_020923.1		1934,2905,1209	CC,CT,TT		39.4967,46.4083,44.0063		1688/2355	207174316	6773,5323	1935	4113	6048	SO:0001819	synonymous_variant	57683	exon5			AGCCAGTCTTCGG	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5064T>C	2.37:g.207174316T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	35	0.397727	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			T|0.525;C|0.475	0.475	strong		0.448	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
RNF25	64320	hgsc.bcm.edu	37	2	219529247	219529247	+	Silent	SNP	A	A	C	rs2303562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219529247A>C	ENST00000295704.2	-	10	1253	c.813T>G	c.(811-813)ccT>ccG	p.P271P		NM_022453.2	NP_071898.2	Q96BH1	RNF25_HUMAN	ring finger protein 25	271					positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|NF-kappaB binding (GO:0051059)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGGTTCCGCAGGGGCAGGAG	0.552													A|||	385	0.076877	0.1248	0.0231	5008	,	,		6140	0.123		0.0258	False		,,,				2504	0.0552				p.P271P		Atlas-SNP	.											.	RNF25	40	.	0			c.T813G						PASS	.	A		436,3970	201.1+/-224.2	25,386,1792	56.0	54.0	55.0		813	0.2	0.1	2	dbSNP_100	55	280,8318	102.1+/-163.3	5,270,4024	no	coding-synonymous	RNF25	NM_022453.2		30,656,5816	CC,CA,AA		3.2566,9.8956,5.506		271/460	219529247	716,12288	2203	4299	6502	SO:0001819	synonymous_variant	64320	exon10			TTCCGCAGGGGCA		CCDS2420.1	2q35	2008-02-05			ENSG00000163481	ENSG00000163481		"""RING-type (C3HC4) zinc fingers"""	14662	protein-coding gene	gene with protein product						12748188	Standard	NM_022453		Approved	AO7, FLJ13906	uc002vit.3	Q96BH1	OTTHUMG00000133077	ENST00000295704.2:c.813T>G	2.37:g.219529247A>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_022453	A8K0D6|Q53HQ5|Q9H874	Silent	SNP	ENST00000295704.2	37	CCDS2420.1																																																																																			A|0.937;C|0.063;T|0.000	0.063	strong		0.552	RNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256721.1	NM_022453	
DOCK6	57572	hgsc.bcm.edu	37	19	11326125	11326125	+	Silent	SNP	C	C	T	rs2304154	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11326125C>T	ENST00000294618.7	-	32	4055	c.4044G>A	c.(4042-4044)ccG>ccA	p.P1348P	CTC-510F12.2_ENST00000588634.1_RNA|DOCK6_ENST00000319867.7_Silent_p.P687P	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1348					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCACATTCTCCGGATTCCCAA	0.562													C|||	2267	0.452676	0.2405	0.4899	5008	,	,		18382	0.5109		0.6272	False		,,,				2504	0.4734				p.P1348P		Atlas-SNP	.											.	DOCK6	104	.	0			c.G4044A						PASS	.	C		1325,2701		216,893,904	50.0	49.0	49.0		4044	3.5	1.0	19	dbSNP_100	49	5203,3141		1612,1979,581	no	coding-synonymous	DOCK6	NM_020812.2		1828,2872,1485	TT,TC,CC		37.6438,32.9111,47.2272		1348/2048	11326125	6528,5842	2013	4172	6185	SO:0001819	synonymous_variant	57572	exon32			ATTCTCCGGATTC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4044G>A	19.37:g.11326125C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			C|0.497;T|0.503	0.503	strong		0.562	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
SRRM5	100170229	hgsc.bcm.edu	37	19	44118188	44118188	+	Missense_Mutation	SNP	A	A	C	rs3815422	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44118188A>C	ENST00000607544.1	+	3	2237	c.1915A>C	c.(1915-1917)Agc>Cgc	p.S639R	ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000417606.1_Missense_Mutation_p.S639R|SRRM5_ENST00000526798.1_Missense_Mutation_p.S654R			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	639	Ser-rich.			S -> R (in Ref. 1; BAG60212). {ECO:0000305}.				p.S639R(1)		endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						TAGCAAGGAGAGCGACCCCAG	0.512													A|||	942	0.188099	0.2103	0.2622	5008	,	,		17207	0.2569		0.1461	False		,,,				2504	0.0777				p.S639R		Atlas-SNP	.											SRRM5,NS,carcinoma,0,1	SRRM5	38	1	1	Substitution - Missense(1)	stomach(1)	c.A1915C						PASS	.	A	ARG/SER,	287,1097		29,229,434	75.0	78.0	77.0		1915,	4.3	0.0	19	dbSNP_107	77	479,2703		30,419,1142	yes	missense,intron	ZNF428,SRRM5	NM_001145641.1,NM_182498.3	110,	59,648,1576	CC,CA,AA		15.0534,20.737,16.7762	benign,	639/716,	44118188	766,3800	692	1591	2283	SO:0001583	missense	100170229	exon1			AAGGAGAGCGACC	AK297891	CCDS46095.1	19q13.31	2013-09-20			ENSG00000226763	ENSG00000226763			37248	protein-coding gene	gene with protein product							Standard	NM_001145641		Approved		uc010xwr.2	B3KS81	OTTHUMG00000165480	ENST00000607544.1:c.1915A>C	19.37:g.44118188A>C	ENSP00000476253:p.Ser639Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_001145641	B4DNF0	Missense_Mutation	SNP	ENST00000607544.1	37	CCDS46095.1	434	0.1987179487179487	86	0.17479674796747968	86	0.23756906077348067	143	0.25	119	0.15699208443271767	A	6.411	0.443916	0.12164	0.20737	0.150534	ENSG00000226763	ENST00000526798;ENST00000417606	.	.	.	4.28	4.28	0.50868	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999928164	B	0.02656	0.0	B	0.04013	0.001	T	0.07290	-1.0780	7	0.02654	T	1	.	12.0311	0.53397	1.0:0.0:0.0:0.0	rs3815422;rs17798213	639	B3KS81	SRRM5_HUMAN	R	654;639	.	ENSP00000414512:S639R	S	+	1	0	SRRM5	48810028	0.001000	0.12720	0.003000	0.11579	0.006000	0.05464	0.999000	0.29757	2.161000	0.67846	0.459000	0.35465	AGC	A|0.799;C|0.201	0.201	strong		0.512	SRRM5-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000384398.2	NM_001145641	
DDX52	11056	hgsc.bcm.edu	37	17	35984410	35984410	+	Missense_Mutation	SNP	T	T	C	rs7216445	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:35984410T>C	ENST00000349699.2	-	9	1250	c.1207A>G	c.(1207-1209)Atg>Gtg	p.M403V	DDX52_ENST00000394367.3_Missense_Mutation_p.M295V	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	403	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		M -> V (in dbSNP:rs7216445). {ECO:0000269|PubMed:11124703, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				AGTTCTCTCATGGCCAGAAGT	0.368													T|||	2877	0.574481	0.4002	0.7205	5008	,	,		17075	0.5605		0.7604	False		,,,				2504	0.5297				p.M403V		Atlas-SNP	.											.	DDX52	40	.	0			c.A1207G						PASS	.	T	VAL/MET	2168,2238	582.8+/-385.7	548,1072,583	103.0	102.0	102.0		1207	4.7	1.0	17	dbSNP_116	102	6901,1699	738.1+/-407.0	2768,1365,167	yes	missense	DDX52	NM_007010.3	21	3316,2437,750	CC,CT,TT		19.7558,49.2056,30.2706	benign	403/600	35984410	9069,3937	2203	4300	6503	SO:0001583	missense	11056	exon9			CTCTCATGGCCAG	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.1207A>G	17.37:g.35984410T>C	ENSP00000268854:p.Met403Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	1368	0.6263736263736264	208	0.42276422764227645	265	0.7320441988950276	322	0.5629370629370629	573	0.7559366754617414	T	12.42	1.931580	0.34096	0.492056	0.802442	ENSG00000141141	ENST00000349699;ENST00000394367	T;T	0.04015	3.73;3.73	5.8	4.73	0.59995	Helicase, C-terminal (1);	0.084250	0.85682	D	0.000000	T	0.00012	0.0000	N	0.02296	-0.605	0.22001	P	0.999428028	B	0.11235	0.004	B	0.13407	0.009	T	0.04128	-1.0975	9	0.38643	T	0.18	-18.4889	11.0562	0.47920	0.0:0.0722:0.0:0.9278	rs7216445;rs17854150;rs52820328;rs59452890;rs7216445	403	Q9Y2R4	DDX52_HUMAN	V	403;295	ENSP00000268854:M403V;ENSP00000377893:M295V	ENSP00000268854:M403V	M	-	1	0	DDX52	33058523	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.268000	0.51585	1.027000	0.39758	-0.263000	0.10527	ATG	C|0.654;T|0.346	0.654	strong		0.368	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	
PRSS3	5646	hgsc.bcm.edu	37	9	33797962	33797962	+	Silent	SNP	A	A	G	rs374178684		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:33797962A>G	ENST00000361005.5	+	3	507	c.507A>G	c.(505-507)aaA>aaG	p.K169K	RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000342836.4_Silent_p.K126K|PRSS3_ENST00000429677.3_Silent_p.K105K|PRSS3_ENST00000379405.3_Silent_p.K112K	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	169	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			TGCTGATCAAACTCTCCTCAC	0.567																																					p.K169K		Atlas-SNP	.											PRSS3_ENST00000361005,NS,neuroblastoma,0,3	PRSS3	79	3	0			c.A507G						scavenged	.						266.0	201.0	223.0					9																	33797962		2203	4300	6503	SO:0001819	synonymous_variant	5646	exon3			GATCAAACTCTCC		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.507A>G	9.37:g.33797962A>G		Somatic	287	13	0.0452962		WXS	Illumina HiSeq	Phase_I	319	13	0.0407524	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Silent	SNP	ENST00000361005.5	37	CCDS47958.1																																																																																			.	.	weak		0.567	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
HUS1B	135458	hgsc.bcm.edu	37	6	656343	656343	+	Missense_Mutation	SNP	T	T	C	rs17136239	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:656343T>C	ENST00000380907.2	-	1	620	c.602A>G	c.(601-603)cAa>cGa	p.Q201R	EXOC2_ENST00000448181.3_Intron|EXOC2_ENST00000230449.4_Intron	NM_148959.3	NP_683762.2	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint homolog b (S. pombe)	201			Q -> R (in dbSNP:rs17136239).		DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)	checkpoint clamp complex (GO:0030896)|nucleolus (GO:0005730)				endometrium(3)|large_intestine(1)|lung(7)	11	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)		AAAATAACTTTGAATGGACAC	0.537													T|||	590	0.117812	0.0764	0.0821	5008	,	,		15529	0.1399		0.0825	False		,,,				2504	0.2127				p.Q201R		Atlas-SNP	.											.	HUS1B	26	.	0			c.A602G						PASS	.	T	,ARG/GLN	402,4004	197.7+/-221.8	24,354,1825	95.0	105.0	102.0		,602	-7.2	0.0	6	dbSNP_123	102	668,7932	168.8+/-220.3	21,626,3653	yes	intron,missense	EXOC2,HUS1B	NM_018303.4,NM_148959.3	,43	45,980,5478	CC,CT,TT		7.7674,9.1239,8.227	,benign	,201/279	656343	1070,11936	2203	4300	6503	SO:0001583	missense	135458	exon1			TAACTTTGAATGG	AF508547	CCDS4470.1	6p25.3	2008-08-08	2001-11-28		ENSG00000188996	ENSG00000188996			16485	protein-coding gene	gene with protein product		609713	"""HUS1 (S. pombe) checkpoint homolog b"""			11944979	Standard	NM_148959		Approved		uc003mtg.3	Q8NHY5	OTTHUMG00000090059	ENST00000380907.2:c.602A>G	6.37:g.656343T>C	ENSP00000370293:p.Gln201Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	154	73	0.474026	NM_148959	Q5T4Z2	Missense_Mutation	SNP	ENST00000380907.2	37	CCDS4470.1	207	0.09478021978021978	33	0.06707317073170732	29	0.08011049723756906	88	0.15384615384615385	57	0.07519788918205805	T	9.870	1.198800	0.22121	0.091239	0.077674	ENSG00000188996	ENST00000380907	T	0.11169	2.8	3.73	-7.2	0.01495	.	0.607650	0.14565	N	0.311839	T	0.01092	0.0036	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48210	-0.9055	9	0.16896	T	0.51	.	9.2045	0.37280	0.0:0.1004:0.6757:0.2239	rs17136239;rs17136239	201	Q8NHY5	HUS1B_HUMAN	R	201	ENSP00000370293:Q201R	ENSP00000370293:Q201R	Q	-	2	0	HUS1B	601343	0.405000	0.25336	0.000000	0.03702	0.002000	0.02628	1.547000	0.36190	-1.042000	0.03262	-0.316000	0.08728	CAA	T|0.905;C|0.095	0.095	strong		0.537	HUS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205617.2	NM_148959	
KIAA0226	9711	hgsc.bcm.edu	37	3	197427515	197427515	+	Silent	SNP	C	C	T	rs116791711	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:197427515C>T	ENST00000296343.5	-	7	1229	c.1230G>A	c.(1228-1230)tcG>tcA	p.S410S	KIAA0226_ENST00000449205.1_Silent_p.S410S|KIAA0226_ENST00000389665.5_Silent_p.S410S|KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000273582.5_Silent_p.S350S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	410	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		TGCTGGTATCCGAATGGGAGC	0.547													C|||	33	0.00658946	0.0	0.0058	5008	,	,		18378	0.0		0.0278	False		,,,				2504	0.001				p.S410S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											Q96CK5_HUMAN,NS,carcinoma,-1,6	KIAA0226	136	6	0			c.G1230A						PASS	.	C	,	18,4026		0,18,2004	83.0	84.0	84.0		1050,1230	-10.9	0.1	3	dbSNP_132	84	155,8197		1,153,4022	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	1,171,6026	TT,TC,CC		1.8558,0.4451,1.3956	,	350/928,410/973	197427515	173,12223	2022	4176	6198	SO:0001819	synonymous_variant	9711	exon7			GGTATCCGAATGG	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1230G>A	3.37:g.197427515C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	209	77	0.368421	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	23|23	0.010531135531135532|0.010531135531135532	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	22|22	0.029023746701846966|0.029023746701846966	C|C	5.052|5.052	0.195309|0.195309	0.09599|0.09599	0.004451|0.004451	0.018558|0.018558	ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000415452	.|.	.|.	.|.	5.46|5.46	-10.9|-10.9	0.00192|0.00192	.|.	.|.	.|.	.|.	.|.	T|T	0.21962|0.21962	0.0529|0.0529	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.59616|0.59616	-0.7421|-0.7421	4|4	.|.	.|.	.|.	.|.	8.7159|8.7159	0.34411|0.34411	0.1713:0.5525:0.0677:0.2085|0.1713:0.5525:0.0677:0.2085	.|.	.|.	.|.	.|.	R|Q	389|169	.|.	.|.	G|R	-|-	1|2	0|0	KIAA0226|KIAA0226	198911912|198911912	0.000000|0.000000	0.05858|0.05858	0.145000|0.145000	0.22337|0.22337	0.727000|0.727000	0.41649|0.41649	-3.954000|-3.954000	0.00326|0.00326	-3.421000|-3.421000	0.00166|0.00166	-1.099000|-1.099000	0.02127|0.02127	GGA|CGG	C|0.987;T|0.013	0.013	strong		0.547	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
KCNN3	3782	hgsc.bcm.edu	37	1	154842243	154842243	+	Silent	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154842243A>C	ENST00000271915.4	-	1	513	c.198T>G	c.(196-198)ctT>ctG	p.L66L	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	66	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gctgctgctgaagctgcggag	0.701																																					p.L66L		Atlas-SNP	.											KCNN3,NS,carcinoma,0,3	KCNN3	141	3	0			c.T198G						scavenged	.						6.0	4.0	5.0					1																	154842243		1926	3811	5737	SO:0001819	synonymous_variant	3782	exon1			CTGCTGAAGCTGC	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.198T>G	1.37:g.154842243A>C		Somatic	68	7	0.102941		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	37	CCDS30880.1																																																																																			.	.	none		0.701	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
TTN	7273	hgsc.bcm.edu	37	2	179440029	179440029	+	Silent	SNP	G	G	A	rs12464787	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179440029G>A	ENST00000591111.1	-	276	66131	c.65907C>T	c.(65905-65907)agC>agT	p.S21969S	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.S14737S|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.S14545S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342992.6_Silent_p.S21042S|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.S14670S|TTN_ENST00000589042.1_Silent_p.S23610S|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	21969	Fibronectin type-III 59. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTCCCCGCGCTGTTCACTG	0.502													G|||	734	0.146565	0.0779	0.1167	5008	,	,		20676	0.0417		0.3052	False		,,,				2504	0.2055				p.S23610S		Atlas-SNP	.											.	TTN	18412	.	0			c.C70830T						PASS	.	G	,,,	480,3602		29,422,1590	65.0	66.0	66.0		43635,63126,44010,44211	-2.6	0.8	2	dbSNP_120	66	2497,5897		364,1769,2064	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	393,2191,3654	AA,AG,GG		29.7474,11.7589,23.8618	,,,	14545/26927,21042/33424,14670/27052,14737/27119	179440029	2977,9499	2041	4197	6238	SO:0001819	synonymous_variant	7273	exon326			CCCCGCGCTGTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.65907C>T	2.37:g.179440029G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.832;A|0.168	0.168	strong		0.502	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TOP2A	7153	hgsc.bcm.edu	37	17	38548586	38548586	+	Silent	SNP	T	T	G	rs34270904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38548586T>G	ENST00000423485.1	-	31	4130	c.3972A>C	c.(3970-3972)acA>acC	p.T1324T	Y_RNA_ENST00000410949.1_RNA	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1324			T -> K (in dbSNP:rs28969502).		apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TTGTGAATTTTGTTTTTGCTA	0.299													G|||	171	0.0341454	0.0998	0.0173	5008	,	,		17564	0.0		0.0209	False		,,,				2504	0.0061				p.T1324T		Atlas-SNP	.											.	TOP2A	124	.	0			c.A3972C						PASS	.	G		270,3318		10,250,1534	41.0	35.0	37.0		3972	2.6	1.0	17	dbSNP_126	37	171,7941		3,165,3888	no	coding-synonymous	TOP2A	NM_001067.3		13,415,5422	GG,GT,TT		2.108,7.5251,3.7692		1324/1532	38548586	441,11259	1794	4056	5850	SO:0001819	synonymous_variant	7153	exon31			GAATTTTGTTTTT		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3972A>C	17.37:g.38548586T>G		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	249	92	0.369478	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			T|0.966;G|0.034	0.034	strong		0.299	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509611	195509611	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509611A>T	ENST00000463781.3	-	2	9299	c.8840T>A	c.(8839-8841)gTc>gAc	p.V2947D	MUC4_ENST00000475231.1_Missense_Mutation_p.V2947D|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V2947D(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGTGTCGGTGACAGGAAGAGG	0.592																																					p.V2947D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	skin(2)|endometrium(1)	c.T8840A						scavenged	.						10.0	8.0	9.0					3																	195509611		654	1505	2159	SO:0001583	missense	4585	exon2			TCGGTGACAGGAA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8840T>A	3.37:g.195509611A>T	ENSP00000417498:p.Val2947Asp	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	472	8	0.0169492	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	4.900	0.167345	0.09339	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.5;1.49	.	.	.	.	.	.	.	.	T	0.24509	0.0594	N	0.08118	0	0.09310	N	1	D	0.65815	0.995	D	0.68483	0.958	T	0.10154	-1.0642	7	.	.	.	.	1.3928	0.02254	0.3276:0.0:0.3249:0.3475	.	2819	E7ESK3	.	D	2947	ENSP00000417498:V2947D;ENSP00000420243:V2947D	.	V	-	2	0	MUC4	196994390	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.286000	0.08399	-0.000000	0.14550	0.000000	0.15137	GTC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ADAM29	11086	hgsc.bcm.edu	37	4	175898990	175898990	+	Missense_Mutation	SNP	G	G	T	rs200104149	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175898990G>T	ENST00000359240.3	+	5	2984	c.2314G>T	c.(2314-2316)Gtg>Ttg	p.V772L	ADAM29_ENST00000445694.1_Missense_Mutation_p.V772L|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.V772L|ADAM29_ENST00000404450.4_Missense_Mutation_p.V772L	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	772	9 X 9 AA approximate repeats.			QPRVM -> HPQLT (in Ref. 1; AAF03777). {ECO:0000305}.	spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TCAACCTCGGGTGATGCCTTC	0.572													g|||	340	0.0678914	0.034	0.0663	5008	,	,		18455	0.0615		0.0964	False		,,,				2504	0.092				p.V772L	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,colon,carcinoma,-2,1	ADAM29	262	1	0			c.G2314T						PASS	.																																			SO:0001583	missense	11086	exon4			CCTCGGGTGATGC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2314G>T	4.37:g.175898990G>T	ENSP00000352177:p.Val772Leu	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	210	36	0.171429	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.984431	0.00443	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01854	4.6;4.6;4.6;4.6	0.945	-1.77	0.07982	.	.	.	.	.	T	0.00998	0.0033	N	0.08118	0	0.09310	N	1	B	0.28350	0.208	B	0.15052	0.012	T	0.47509	-0.9112	8	.	.	.	.	1.913	0.03291	0.4213:0.0:0.3113:0.2674	.	772	Q9UKF5	ADA29_HUMAN	L	772	ENSP00000352177:V772L;ENSP00000414544:V772L;ENSP00000384229:V772L;ENSP00000423517:V772L	.	V	+	1	0	ADAM29	176135565	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.689000	0.05144	-0.645000	0.05458	-0.373000	0.07131	GTG	.	.	weak		0.572	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
KCNJ3	3760	hgsc.bcm.edu	37	2	155711357	155711357	+	Silent	SNP	T	T	C	rs17642086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:155711357T>C	ENST00000295101.2	+	3	1515	c.1038T>C	c.(1036-1038)caT>caC	p.H346H	KCNJ3_ENST00000544049.1_3'UTR|KCNJ3_ENST00000493505.1_3'UTR	NM_001260509.1|NM_002239.3	NP_001247438.1|NP_002230.1	P48549	KCNJ3_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 3	346					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to electrical stimulus (GO:0051602)|synaptic transmission (GO:0007268)	external side of plasma membrane (GO:0009897)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)			breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(30)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	54					Halothane(DB01159)	CCCAGTTCCATGCAACATTTG	0.418													T|||	836	0.166933	0.1293	0.2147	5008	,	,		16666	0.0367		0.3549	False		,,,				2504	0.1247				p.H346H		Atlas-SNP	.											.	KCNJ3	126	.	0			c.T1038C						PASS	.	T		692,3714	289.8+/-280.6	54,584,1565	114.0	115.0	114.0		1038	2.0	1.0	2	dbSNP_123	114	2954,5646	459.1+/-364.8	498,1958,1844	no	coding-synonymous	KCNJ3	NM_002239.2		552,2542,3409	CC,CT,TT		34.3488,15.7059,28.0332		346/502	155711357	3646,9360	2203	4300	6503	SO:0001819	synonymous_variant	3760	exon3			GTTCCATGCAACA	U50964	CCDS2200.1, CCDS58733.1	2q24.1	2011-07-05			ENSG00000162989	ENSG00000162989		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6264	protein-coding gene	gene with protein product		601534				8088798, 16382105	Standard	NM_002239		Approved	Kir3.1, GIRK1, KGA	uc002tyv.2	P48549	OTTHUMG00000131937	ENST00000295101.2:c.1038T>C	2.37:g.155711357T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	171	72	0.421053	NM_002239	B4DEW7|Q8TBI0	Silent	SNP	ENST00000295101.2	37	CCDS2200.1																																																																																			T|0.753;C|0.247	0.247	strong		0.418	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239	
ARHGEF38	54848	hgsc.bcm.edu	37	4	106510470	106510470	+	Missense_Mutation	SNP	A	A	G	rs2276970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106510470A>G	ENST00000420470.2	+	2	406	c.262A>G	c.(262-264)Atg>Gtg	p.M88V	ARHGEF38_ENST00000265154.2_Missense_Mutation_p.M88V	NM_001242729.1	NP_001229658.1	Q9NXL2	ARH38_HUMAN	Rho guanine nucleotide exchange factor (GEF) 38	88			M -> V (in dbSNP:rs2276970).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(3)	11						AGAGCATCATATGAAGAGGAT	0.423													A|||	440	0.0878594	0.0915	0.0793	5008	,	,		17891	0.1091		0.1064	False		,,,				2504	0.0481				p.M88V		Atlas-SNP	.											.	ARHGEF38	52	.	0			c.A262G						PASS	.	A	VAL/MET,VAL/MET	470,3936	220.0+/-237.6	33,404,1766	124.0	123.0	123.0		262,262	0.4	0.0	4	dbSNP_100	123	769,7831	182.2+/-230.7	30,709,3561	yes	missense,missense	ARHGEF38	NM_001242729.1,NM_017700.1	21,21	63,1113,5327	GG,GA,AA		8.9419,10.6673,9.5264	benign,benign	88/778,88/220	106510470	1239,11767	2203	4300	6503	SO:0001583	missense	54848	exon2			CATCATATGAAGA	AK000191	CCDS3670.1, CCDS56338.1	4q24	2012-07-24			ENSG00000236699	ENSG00000236699		"""Rho guanine nucleotide exchange factors"""	25968	protein-coding gene	gene with protein product							Standard	NM_001242729		Approved	FLJ20184	uc003hxv.2	Q9NXL2	OTTHUMG00000154752	ENST00000420470.2:c.262A>G	4.37:g.106510470A>G	ENSP00000416125:p.Met88Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_001242729	C9JIB4	Missense_Mutation	SNP	ENST00000420470.2	37	CCDS56338.1	214	0.09798534798534798	54	0.10975609756097561	30	0.08287292817679558	50	0.08741258741258741	80	0.10554089709762533	A	0.007	-2.001471	0.00431	0.106673	0.089419	ENSG00000236699	ENST00000265154;ENST00000420470	T;T	0.28666	1.6;1.61	5.34	0.4	0.16331	Dbl homology (DH) domain (1);	0.908004	0.09725	N	0.763874	T	0.00328	0.0010	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33828	-0.9853	9	0.12766	T	0.61	1.1522	4.8709	0.13631	0.5162:0.2832:0.2005:0.0	rs2276970;rs17258977;rs61636643;rs2276970	88	Q9NXL2	ARH38_HUMAN	V	88	ENSP00000265154:M88V;ENSP00000416125:M88V	ENSP00000265154:M88V	M	+	1	0	ARHGEF38	106729919	0.000000	0.05858	0.000000	0.03702	0.496000	0.33645	-0.031000	0.12287	-0.146000	0.11274	0.533000	0.62120	ATG	A|0.908;G|0.092	0.092	strong		0.423	ARHGEF38-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000336934.3	NM_017700	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125872384	125872384	+	Missense_Mutation	SNP	A	A	G	rs3796191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:125872384A>G	ENST00000393434.2	-	7	1110	c.761T>C	c.(760-762)cTg>cCg	p.L254P	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.L254P|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.L264P|ALDH1L1_ENST00000413612.1_5'UTR|ALDH1L1_ENST00000393431.2_Missense_Mutation_p.L254P|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.L153P|ALDH1L1_ENST00000455064.2_Missense_Mutation_p.L79P	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	254			L -> P (in dbSNP:rs3796191).		10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	CTCGGGCACCAGGCCTGAAGT	0.532													A|||	322	0.0642971	0.0726	0.134	5008	,	,		20332	0.0169		0.0408	False		,,,				2504	0.0767				p.L264P		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.T791C						PASS	.	A	PRO/LEU	304,4102	166.2+/-197.5	7,290,1906	97.0	96.0	96.0		761	2.4	1.0	3	dbSNP_107	96	383,8217	124.1+/-182.9	10,363,3927	yes	missense	ALDH1L1	NM_012190.2	98	17,653,5833	GG,GA,AA		4.4535,6.8997,5.2822	benign	254/903	125872384	687,12319	2203	4300	6503	SO:0001583	missense	10840	exon7			GGCACCAGGCCTG	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"""Aldehyde dehydrogenases"""	3978	protein-coding gene	gene with protein product	"""cytosolic 10-formyltetrahydrofolate dehydrogenase"""	600249	"""formyltetrahydrofolate dehydrogenase"""	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.761T>C	3.37:g.125872384A>G	ENSP00000377083:p.Leu254Pro	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	133	0.060897435897435896	38	0.07723577235772358	42	0.11602209944751381	17	0.02972027972027972	36	0.047493403693931395	A	5.923	0.354437	0.11239	0.068997	0.044535	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434;ENST00000393431;ENST00000455064	T;T;T;T;T;T	0.45668	0.97;0.97;0.97;0.97;0.97;0.89	4.78	2.38	0.29361	Formyl transferase, C-terminal-like (1);Formyl transferase, C-terminal (2);	0.667563	0.14028	N	0.346341	T	0.00210	0.0006	N	0.02539	-0.55	0.20563	P	0.999884906	B;B;B;B;B	0.18968	0.009;0.007;0.0;0.032;0.0	B;B;B;B;B	0.17433	0.006;0.011;0.004;0.018;0.002	T	0.17410	-1.0370	9	0.23302	T	0.38	.	5.562	0.17150	0.641:0.0:0.3589:0.0	rs3796191;rs3796191	79;153;306;159;254	B4DGC8;E9PBX3;Q59G10;Q9UFA9;O75891	.;.;.;.;AL1L1_HUMAN	P	264;254;153;254;254;79	ENSP00000273450:L264P;ENSP00000420293:L254P;ENSP00000395881:L153P;ENSP00000377083:L254P;ENSP00000377081:L254P;ENSP00000414126:L79P	ENSP00000273450:L264P	L	-	2	0	ALDH1L1	127355074	0.008000	0.16893	0.991000	0.47740	0.190000	0.23558	1.488000	0.35551	0.660000	0.30964	0.383000	0.25322	CTG	A|0.945;G|0.055	0.055	strong		0.532	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
KIF1B	23095	hgsc.bcm.edu	37	1	10363664	10363664	+	Intron	SNP	G	G	T	rs41274458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:10363664G>T	ENST00000377086.1	+	22	2317				KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377081.1_Intron|KIF1B_ENST00000377093.4_Missense_Mutation_p.M807I|KIF1B_ENST00000377083.1_Missense_Mutation_p.M807I|RN7SL731P_ENST00000584329.1_RNA			O60333	KIF1B_HUMAN	kinesin family member 1B						anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		AAGACGTCATGGCCACTGGGA	0.493													G|||	33	0.00658946	0.0	0.0101	5008	,	,		18170	0.0		0.0229	False		,,,				2504	0.0031				p.M807I		Atlas-SNP	.											.	KIF1B	242	.	0			c.G2421T						PASS	.	G	,ILE/MET	22,4384	28.1+/-56.4	0,22,2181	65.0	66.0	66.0		,2421	5.6	1.0	1	dbSNP_127	66	221,8379	92.3+/-154.4	3,215,4082	yes	intron,missense	KIF1B	NM_015074.3,NM_183416.3	,10	3,237,6263	TT,TG,GG		2.5698,0.4993,1.8684	,	,807/1154	10363664	243,12763	2203	4300	6503	SO:0001627	intron_variant	23095	exon21			CGTCATGGCCACT	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.2115+6360G>T	1.37:g.10363664G>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	122	81	0.663934	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		14	0.00641025641025641	0	0.0	0	0.0	0	0.0	14	0.018469656992084433	G	0.071	-1.201384	0.01581	0.004993	0.025698	ENSG00000054523	ENST00000377093;ENST00000377083	T;T	0.72051	-0.62;-0.62	5.58	5.58	0.84498	.	.	.	.	.	T	0.37376	0.1001	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47699	-0.9097	8	0.36615	T	0.2	.	14.4174	0.67160	0.0:0.0:0.8526:0.1474	rs41274458	807	O60333-3	.	I	807	ENSP00000366297:M807I;ENSP00000366287:M807I	ENSP00000366287:M807I	M	+	3	0	KIF1B	10286251	1.000000	0.71417	0.998000	0.56505	0.078000	0.17371	2.423000	0.44705	2.611000	0.88343	0.655000	0.94253	ATG	G|0.984;T|0.016	0.016	strong		0.493	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
MAPKBP1	23005	hgsc.bcm.edu	37	15	42115747	42115747	+	Missense_Mutation	SNP	G	G	C	rs3959569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42115747G>C	ENST00000456763.2	+	30	3915	c.3719G>C	c.(3718-3720)cGt>cCt	p.R1240P	RP11-23P13.4_ENST00000510176.1_RNA|RP11-23P13.4_ENST00000512295.1_RNA|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.R1117P|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.R1073P|MAPKBP1_ENST00000514566.1_Intron|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.R1234P	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	1240			R -> P (in dbSNP:rs3959569). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15491607, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9628581}.							breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		GCTGATGGCCGTCCGTCTCGG	0.617													g|||	1172	0.234026	0.0371	0.4121	5008	,	,		19490	0.1796		0.3479	False		,,,				2504	0.3129				p.R1240P		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.G3719C						PASS	.	G	PRO/ARG,PRO/ARG	418,3988		28,362,1813	68.0	63.0	64.0		3719,3701	-0.6	0.0	15	dbSNP_108	64	2858,5742		464,1930,1906	yes	missense,missense	MAPKBP1	NM_001128608.1,NM_014994.2	103,103	492,2292,3719	CC,CG,GG		33.2326,9.4871,25.1884	benign,benign	1240/1515,1234/1509	42115747	3276,9730	2203	4300	6503	SO:0001583	missense	23005	exon30			ATGGCCGTCCGTC	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.3719G>C	15.37:g.42115747G>C	ENSP00000393099:p.Arg1240Pro	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	524	0.23992673992673993	20	0.04065040650406504	140	0.3867403314917127	92	0.16083916083916083	272	0.35883905013192613	.	9.525	1.109421	0.20714	0.094871	0.332326	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763	T;T;T;T	0.42131	1.18;1.32;0.98;1.23	5.82	-0.625	0.11548	.	1.160040	0.05950	N	0.638738	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;P;B;B;B	0.34615	0.0;0.459;0.337;0.002;0.002	B;B;B;B;B	0.38712	0.001;0.28;0.147;0.002;0.004	T	0.39165	-0.9627	9	0.33141	T	0.24	2.2892	7.306	0.26447	0.3584:0.1107:0.5308:0.0	rs3959569;rs56957727	1073;1117;1073;1240;1234	F8WC21;O60336-3;B4DYK7;O60336;O60336-6	.;.;.;MABP1_HUMAN;.	P	1234;1117;1073;1240	ENSP00000397570:R1234P;ENSP00000221214:R1117P;ENSP00000260357:R1073P;ENSP00000393099:R1240P	ENSP00000221214:R1117P	R	+	2	0	MAPKBP1	39903039	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.783000	0.04638	-0.686000	0.05170	-2.487000	0.00196	CGT	G|0.740;C|0.260	0.260	strong		0.617	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994	
AFAP1	60312	hgsc.bcm.edu	37	4	7844953	7844953	+	Silent	SNP	G	G	A	rs28669852	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:7844953G>A	ENST00000360265.4	-	4	693	c.459C>T	c.(457-459)gaC>gaT	p.D153D	AFAP1_ENST00000382543.3_Silent_p.D153D|AFAP1_ENST00000358461.2_Silent_p.D153D|AFAP1_ENST00000420658.1_Silent_p.D153D			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	153	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						AGATTTTGGCGTCCTTGACCA	0.562													G|||	143	0.0285543	0.0129	0.0403	5008	,	,		16377	0.002		0.0755	False		,,,				2504	0.0204				p.D153D		Atlas-SNP	.											.	AFAP1	93	.	0			c.C459T						PASS	.	G	,	93,4313	76.2+/-114.5	0,93,2110	101.0	90.0	94.0		459,459	-4.6	1.0	4	dbSNP_125	94	686,7914	171.0+/-222.0	29,628,3643	no	coding-synonymous,coding-synonymous	AFAP1	NM_001134647.1,NM_198595.2	,	29,721,5753	AA,AG,GG		7.9767,2.1108,5.9895	,	153/815,153/731	7844953	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	60312	exon5			TTTGGCGTCCTTG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.459C>T	4.37:g.7844953G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			G|0.942;A|0.058	0.058	strong		0.562	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
FGD5	152273	hgsc.bcm.edu	37	3	14860968	14860968	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14860968G>A	ENST00000285046.5	+	1	500	c.390G>A	c.(388-390)gcG>gcA	p.A130A	FGD5_ENST00000543601.1_De_novo_Start_InFrame	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	130	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GTGCAGGAGCGCTGAGCAGGG	0.627																																					p.A130A		Atlas-SNP	.											FGD5_ENST00000285046,NS,carcinoma,+1,1	FGD5	248	1	0			c.G390A						PASS	.						19.0	22.0	22.0					3																	14860968		692	1591	2283	SO:0001819	synonymous_variant	152273	exon1			AGGAGCGCTGAGC	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.390G>A	3.37:g.14860968G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	293	126	0.430034	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Silent	SNP	ENST00000285046.5	37	CCDS46767.1																																																																																			.	.	none		0.627	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
ZNF469	84627	hgsc.bcm.edu	37	16	88501971	88501971	+	Missense_Mutation	SNP	T	T	A	rs3812956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88501971T>A	ENST00000437464.1	+	2	8009	c.8009T>A	c.(8008-8010)cTg>cAg	p.L2670Q	ZNF469_ENST00000565624.1_Missense_Mutation_p.L2698Q	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2670			L -> Q (in dbSNP:rs3812956). {ECO:0000269|PubMed:11347906}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						TTGGCCACTCTGGGACCTGGG	0.657													T|||	1474	0.294329	0.1815	0.3473	5008	,	,		15665	0.4028		0.3728	False		,,,				2504	0.2168				p.L2670Q		Atlas-SNP	.											.	ZNF469	121	.	0			c.T8009A						PASS	.	T	GLN/LEU	301,1083		33,235,424	18.0	21.0	20.0		8009	-6.5	0.0	16	dbSNP_107	20	1243,1937		247,749,594	yes	missense	ZNF469	NM_001127464.1	113	280,984,1018	AA,AT,TT		39.0881,21.7486,33.83	benign	2670/3926	88501971	1544,3020	692	1590	2282	SO:0001583	missense	84627	exon2			CCACTCTGGGACC	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.8009T>A	16.37:g.88501971T>A	ENSP00000402343:p.Leu2670Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	695	0.3182234432234432	92	0.18699186991869918	110	0.30386740331491713	209	0.36538461538461536	284	0.37467018469656993	T	4.345	0.063439	0.08388	0.217486	0.390881	ENSG00000225614	ENST00000437464	T	0.05382	3.45	3.23	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48514	-0.9029	8	0.27785	T	0.31	.	0.6077	0.00755	0.1968:0.1814:0.3023:0.3196	rs3812956;rs60168268	2670	Q96JG9	ZN469_HUMAN	Q	2670	ENSP00000402343:L2670Q	ENSP00000402343:L2670Q	L	+	2	0	ZNF469	87029472	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.057000	0.03486	-2.507000	0.00506	-1.156000	0.01807	CTG	T|0.680;A|0.320	0.320	strong		0.657	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
CCL27	10850	hgsc.bcm.edu	37	9	34661994	34661994	+	Missense_Mutation	SNP	G	G	A	rs11575584	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:34661994G>A	ENST00000259631.4	-	3	344	c.286C>T	c.(286-288)Ctc>Ttc	p.L96F	RP11-195F19.30_ENST00000564224.1_RNA|CCL27_ENST00000557161.1_5'UTR	NM_006664.2	NP_006655.1	Q9Y4X3	CCL27_HUMAN	chemokine (C-C motif) ligand 27	96			L -> F (in dbSNP:rs11575584).		cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			kidney(1)|large_intestine(3)|ovary(1)	5	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		GTCCCATGGAGCTTTCTCTCT	0.502													G|||	207	0.0413339	0.003	0.0418	5008	,	,		19142	0.0159		0.0755	False		,,,				2504	0.0838				p.L96F		Atlas-SNP	.											CCL27,lymph_node,lymphoid_neoplasm,0,1	CCL27	6	1	0			c.C286T						PASS	.	G	PHE/LEU	75,4331	68.1+/-105.8	1,73,2129	108.0	116.0	113.0		286	-4.7	0.0	9	dbSNP_120	113	526,8074	147.6+/-202.9	17,492,3791	yes	missense	CCL27	NM_006664.2	22	18,565,5920	AA,AG,GG		6.1163,1.7022,4.6209	probably-damaging	96/113	34661994	601,12405	2203	4300	6503	SO:0001583	missense	10850	exon3			CATGGAGCTTTCT	AJ243542	CCDS6569.1	9p13	2014-05-16	2002-08-22	2002-08-23	ENSG00000213927	ENSG00000213927		"""Chemokine ligands"", ""Endogenous ligands"""	10626	protein-coding gene	gene with protein product	"""CC chemokine ILC"", ""IL-11 Ralpha-locus chemokine"", ""cutaneous T-cell attracting chemokine"""	604833	"""small inducible cytokine subfamily A (Cys-Cys), member 27"""	SCYA27		10556532, 10588729	Standard	NM_006664		Approved	ALP, ILC, CTACK, skinkine, ESkine, PESKY, CTAK	uc003zvm.1	Q9Y4X3	OTTHUMG00000019834	ENST00000259631.4:c.286C>T	9.37:g.34661994G>A	ENSP00000259631:p.Leu96Phe	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_006664		Missense_Mutation	SNP	ENST00000259631.4	37	CCDS6569.1	84	0.038461538461538464	2	0.0040650406504065045	15	0.04143646408839779	8	0.013986013986013986	59	0.07783641160949868	G	8.367	0.834384	0.16820	0.017022	0.061163	ENSG00000213927	ENST00000259631	T	0.32023	1.47	4.99	-4.65	0.03339	Chemokine interleukin-8-like domain (1);	1.572910	0.03568	N	0.228121	T	0.00906	0.0030	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.17592	-1.0364	10	0.48119	T	0.1	-0.009	2.4773	0.04579	0.4822:0.1255:0.2646:0.1277	rs11575584;rs52820755;rs58368429;rs11575584	96	Q9Y4X3	CCL27_HUMAN	F	96	ENSP00000259631:L96F	ENSP00000259631:L96F	L	-	1	0	CCL27	34651994	0.000000	0.05858	0.000000	0.03702	0.465000	0.32709	-0.881000	0.04179	-0.691000	0.05135	0.655000	0.94253	CTC	G|0.957;A|0.043	0.043	strong		0.502	CCL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052228.1	NM_006664	
NES	10763	hgsc.bcm.edu	37	1	156639753	156639753	+	Silent	SNP	G	G	A	rs11582300	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156639753G>A	ENST00000368223.3	-	4	4359	c.4227C>T	c.(4225-4227)tcC>tcT	p.S1409S		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1409	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAAACCCATCGGACTCCCCAT	0.647													G|||	3097	0.618411	0.385	0.6787	5008	,	,		15954	0.8611		0.6312	False		,,,				2504	0.6278				p.S1409S		Atlas-SNP	.											.	NES	196	.	0			c.C4227T						PASS	.	G		1758,2648		355,1048,800	22.0	24.0	23.0		4227	0.8	1.0	1	dbSNP_120	23	5323,3269		1696,1931,669	no	coding-synonymous	NES	NM_006617.1		2051,2979,1469	AA,AG,GG		38.047,39.9001,45.5224		1409/1622	156639753	7081,5917	2203	4296	6499	SO:0001819	synonymous_variant	10763	exon4			CCCATCGGACTCC	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.4227C>T	1.37:g.156639753G>A		Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	300	137	0.456667	NM_006617	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	37	CCDS1151.1																																																																																			G|0.413;A|0.587	0.587	strong		0.647	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
AGO2	27161	hgsc.bcm.edu	37	8	141551407	141551407	+	Silent	SNP	G	G	A	rs2293939	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:141551407G>A	ENST00000220592.5	-	15	2002	c.1890C>T	c.(1888-1890)cgC>cgT	p.R630R	AGO2_ENST00000519980.1_Silent_p.R630R	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	630	Piwi. {ECO:0000255|HAMAP-Rule:MF_03031}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										GCTGCTGCACGCGCACGGTGG	0.617													G|||	1139	0.227436	0.0567	0.281	5008	,	,		17732	0.3581		0.2684	False		,,,				2504	0.2434				p.R630R		Atlas-SNP	.											.	.	.	.	0			c.C1890T						PASS	.	G	,	416,3990	198.4+/-222.2	24,368,1811	83.0	64.0	71.0		1890,1890	-9.1	0.3	8	dbSNP_100	71	2303,6297	379.1+/-339.1	314,1675,2311	no	coding-synonymous,coding-synonymous	EIF2C2	NM_001164623.1,NM_012154.3	,	338,2043,4122	AA,AG,GG		26.7791,9.4417,20.9057	,	630/826,630/860	141551407	2719,10287	2203	4300	6503	SO:0001819	synonymous_variant	27161	exon15			CTGCACGCGCACG	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1890C>T	8.37:g.141551407G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Silent	SNP	ENST00000220592.5	37	CCDS6380.1																																																																																			G|0.783;A|0.217	0.217	strong		0.617	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
BEAN1	146227	hgsc.bcm.edu	37	16	66514549	66514549	+	Silent	SNP	A	A	G	rs141546513		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:66514549A>G	ENST00000536005.2	+	5	718	c.501A>G	c.(499-501)ccA>ccG	p.P167P	BEAN1_ENST00000299694.8_Silent_p.P58P|BEAN1_ENST00000563075.1_Intron|BEAN1_ENST00000561796.1_Intron|RP11-403P17.5_ENST00000561728.1_Intron|CTD-2258A20.5_ENST00000569125.1_RNA|BEAN1_ENST00000564819.1_Intron	NM_001178020.2	NP_001171491.1	Q3B7T3	BEAN1_HUMAN	brain expressed, associated with NEDD4, 1	167					cell death (GO:0008219)	integral component of membrane (GO:0016021)				kidney(1)	1						ACGCACCACCACCCTACTCGC	0.667																																					p.P167P		Atlas-SNP	.											.	BEAN1	6	.	0			c.A501G						PASS	.	A	,,,	0,1384		0,0,692	59.0	66.0	64.0		174,501,,	-9.5	0.1	16	dbSNP_134	64	5,3177		0,5,1586	no	coding-synonymous,coding-synonymous,intron,intron	BEAN1	NM_001136106.3,NM_001178020.1,NM_001197224.1,NM_001197225.1	,,,	0,5,2278	GG,GA,AA		0.1571,0.0,0.1095	,,,	58/151,167/260,,	66514549	5,4561	692	1591	2283	SO:0001819	synonymous_variant	146227	exon5			ACCACCACCCTAC	BC000818	CCDS54015.1, CCDS58469.1, CCDS58470.1	16q21	2014-07-30			ENSG00000166546	ENSG00000166546			24160	protein-coding gene	gene with protein product		612051	"""spinocerebellar ataxia 31"""	SCA31		11042109, 8619474, 23607545	Standard	NM_001178020		Approved		uc021tjl.1	Q3B7T3	OTTHUMG00000173370	ENST00000536005.2:c.501A>G	16.37:g.66514549A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	140	59	0.421429	NM_001178020	B3KPC0|H3BP97	Silent	SNP	ENST00000536005.2	37	CCDS54015.1																																																																																			A|1.000;G|0.000	0.000	strong		0.667	BEAN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422908.1	NM_001136106	
MTCL1	23255	hgsc.bcm.edu	37	18	8783835	8783835	+	Missense_Mutation	SNP	T	T	C	rs35739383	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:8783835T>C	ENST00000306329.11	+	5	1805	c.1805T>C	c.(1804-1806)aTg>aCg	p.M602T	SOGA2_ENST00000359865.3_Missense_Mutation_p.M242T|SOGA2_ENST00000517570.1_Missense_Mutation_p.M242T|SOGA2_ENST00000400050.3_Missense_Mutation_p.M242T|SOGA2_ENST00000306285.7_5'UTR																							ATGGAGGACATGCGGGGCCAG	0.652													T|||	2062	0.411741	0.1467	0.3415	5008	,	,		16309	0.5397		0.5984	False		,,,				2504	0.4959				p.M242T		Atlas-SNP	.											.	.	.	.	0			c.T725C						PASS	.	T	THR/MET	955,3443		105,745,1349	31.0	30.0	30.0		725	5.7	0.4	18	dbSNP_126	30	4975,3619		1491,1993,813	yes	missense	CCDC165	NM_015210.3	81	1596,2738,2162	CC,CT,TT		42.1108,21.7144,45.6435	benign	242/1587	8783835	5930,7062	2199	4297	6496	SO:0001583	missense	23255	exon6			AGGACATGCGGGG																												ENST00000306329.11:c.1805T>C	18.37:g.8783835T>C	ENSP00000305027:p.Met602Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	37		946	0.43315018315018317	81	0.16463414634146342	136	0.3756906077348066	276	0.4825174825174825	453	0.5976253298153035	T	10.08	1.252487	0.22880	0.217144	0.578892	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	T;T;T	0.14893	2.47;2.47;2.47	5.67	5.67	0.87782	.	0.885618	0.09916	N	0.739174	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	1.0	B;B	0.31769	0.339;0.332	B;B	0.29598	0.076;0.104	T	0.38178	-0.9673	9	0.44086	T	0.13	-3.8273	15.9107	0.79470	0.0:0.0:0.0:1.0	rs35739383;rs62086584	263;242	A8MQ54;Q9Y4B5-3	.;.	T	263;242;242;242	ENSP00000429556:M242T;ENSP00000352927:M242T;ENSP00000382924:M242T	ENSP00000305027:M263T	M	+	2	0	CCDC165	8773835	1.000000	0.71417	0.409000	0.26459	0.748000	0.42578	6.305000	0.72805	2.170000	0.68504	0.454000	0.30748	ATG	T|0.555;C|0.445	0.445	strong		0.652	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
PHLDB1	23187	hgsc.bcm.edu	37	11	118516274	118516274	+	Missense_Mutation	SNP	G	G	A	rs149914355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118516274G>A	ENST00000361417.2	+	17	3733	c.3322G>A	c.(3322-3324)Gcc>Acc	p.A1108T	PHLDB1_ENST00000527898.1_Missense_Mutation_p.A159T|PHLDB1_ENST00000524713.1_Missense_Mutation_p.A251T|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000356063.5_Missense_Mutation_p.A1061T	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1108										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		GGGTGAGCACGCCTATGATAC	0.647													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18185	0.0		0.005	False		,,,				2504	0.001				p.A1108T		Atlas-SNP	.											.	PHLDB1	103	.	0			c.G3322A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	3,4397	6.2+/-15.9	0,3,2197	95.0	92.0	93.0		3322,3181,3322	5.5	0.9	11	dbSNP_134	93	12,8578	9.1+/-34.3	0,12,4283	yes	missense,missense,missense	PHLDB1	NM_001144758.1,NM_001144759.1,NM_015157.2	58,58,58	0,15,6480	AA,AG,GG		0.1397,0.0682,0.1155	benign,benign,benign	1108/1378,1061/1320,1108/1378	118516274	15,12975	2200	4295	6495	SO:0001583	missense	23187	exon16			GAGCACGCCTATG		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.3322G>A	11.37:g.118516274G>A	ENSP00000354498:p.Ala1108Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	15.18	2.757205	0.49468	6.82E-4	0.001397	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000356063;ENST00000527898;ENST00000524713	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.52	5.52	0.82312	.	0.223446	0.46758	D	0.000268	T	0.45498	0.1345	L	0.56280	1.765	0.29675	N	0.842181	P;P;P;P;P	0.48016	0.904;0.681;0.898;0.764;0.883	B;B;B;B;B	0.38296	0.23;0.216;0.27;0.151;0.27	T	0.56396	-0.7986	10	0.36615	T	0.2	-19.0047	18.4343	0.90638	0.0:0.0:1.0:0.0	.	251;472;867;1061;1108	B4DK17;B0YJ65;Q5W9G0;Q86UU1-2;Q86UU1	.;.;.;.;PHLB1_HUMAN	T	1108;882;472;1061;159;251	ENSP00000354498:A1108T;ENSP00000348359:A1061T;ENSP00000435388:A159T;ENSP00000434905:A251T	ENSP00000348359:A1061T	A	+	1	0	PHLDB1	118021484	0.998000	0.40836	0.928000	0.36995	0.654000	0.38779	2.954000	0.49113	2.596000	0.87737	0.655000	0.94253	GCC	G|0.998;A|0.002	0.002	strong		0.647	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157	
AP5Z1	9907	hgsc.bcm.edu	37	7	4825314	4825314	+	Splice_Site	SNP	C	C	T	rs11768079	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4825314C>T	ENST00000348624.4	+	9	1225	c.1131C>T	c.(1129-1131)caC>caT	p.H377H	AP5Z1_ENST00000401897.1_Splice_Site_p.H377H|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	377					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											TCCTGAGCCACGGTGAGCCCA	0.582													C|||	359	0.0716853	0.0091	0.0317	5008	,	,		13363	0.0506		0.0676	False		,,,				2504	0.2106				p.H377H		Atlas-SNP	.											.	.	.	.	0			c.C1131T						PASS	.	C		75,4103		0,75,2014	6.0	6.0	6.0		1131	-0.4	0.9	7	dbSNP_120	6	532,7858		19,494,3682	yes	coding-synonymous-near-splice	KIAA0415	NM_014855.2		19,569,5696	TT,TC,CC		6.3409,1.7951,4.8297		377/808	4825314	607,11961	2089	4195	6284	SO:0001630	splice_region_variant	9907	exon9			GAGCCACGGTGAG	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1132+1C>T	7.37:g.4825314C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			C|0.954;T|0.046	0.046	strong		0.582	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		Silent
MUC4	4585	hgsc.bcm.edu	37	3	195506267	195506267	+	Missense_Mutation	SNP	C	C	T	rs370995233	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506267C>T	ENST00000463781.3	-	2	12643	c.12184G>A	c.(12184-12186)Gcc>Acc	p.A4062T	MUC4_ENST00000475231.1_Missense_Mutation_p.A4062T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.582													.|||	33	0.00658946	0.0129	0.0	5008	,	,		10474	0.001		0.001	False		,,,				2504	0.0143				p.A4062T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G12184A						PASS	.						33.0	18.0	23.0					3																	195506267		597	1336	1933	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12184G>A	3.37:g.195506267C>T	ENSP00000417498:p.Ala4062Thr	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	163	118	0.723926	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.160	-1.082303	0.01888	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.39229	1.09;1.1	.	.	.	.	.	.	.	.	T	0.20414	0.0491	N	0.19112	0.55	0.80722	P	0.0	B	0.12013	0.005	B	0.01281	0.0	T	0.22417	-1.0217	6	.	.	.	.	2.1447	0.03784	0.0:0.3304:0.3444:0.3251	.	3934	E7ESK3	.	T	4062	ENSP00000417498:A4062T;ENSP00000420243:A4062T	.	A	-	1	0	MUC4	196991046	0.002000	0.14202	0.003000	0.11579	0.073000	0.16967	-0.026000	0.12392	-0.417000	0.07461	0.064000	0.15345	GCC	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FREM1	158326	hgsc.bcm.edu	37	9	14819370	14819370	+	Missense_Mutation	SNP	G	G	T	rs7023244	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:14819370G>T	ENST00000380880.3	-	14	3191	c.2408C>A	c.(2407-2409)tCt>tAt	p.S803Y	FREM1_ENST00000422223.2_Missense_Mutation_p.S803Y|FREM1_ENST00000380881.4_Missense_Mutation_p.S804Y			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	803			S -> Y (in dbSNP:rs7023244).		cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		ATCTGCATCAGAAATTAGAAT	0.478													G|||	822	0.164137	0.0832	0.255	5008	,	,		18171	0.0794		0.2525	False		,,,				2504	0.2055				p.S803Y		Atlas-SNP	.											.	FREM1	261	.	0			c.C2408A						PASS	.	G	TYR/SER	455,3437		31,393,1522	114.0	109.0	111.0		2408	5.9	1.0	9	dbSNP_116	111	2046,6238		276,1494,2372	yes	missense	FREM1	NM_144966.5	144	307,1887,3894	TT,TG,GG		24.6982,11.6906,20.5404	possibly-damaging	803/2180	14819370	2501,9675	1946	4142	6088	SO:0001583	missense	158326	exon15			GCATCAGAAATTA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.2408C>A	9.37:g.14819370G>T	ENSP00000370262:p.Ser803Tyr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	78	25	0.320513	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	374	0.17124542124542125	37	0.07520325203252033	89	0.24585635359116023	55	0.09615384615384616	193	0.2546174142480211	G	20.5	4.005732	0.74932	0.116906	0.246982	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.27256	1.68;1.68;1.68	5.86	5.86	0.93980	.	0.225793	0.47852	D	0.000210	T	0.00012	0.0000	M	0.85041	2.73	0.09310	P	0.9999956479	D	0.65815	0.995	P	0.62649	0.905	T	0.00071	-1.2130	9	0.87932	D	0	-15.0418	20.1931	0.98233	0.0:0.0:1.0:0.0	rs7023244;rs56569639;rs7023244	803	Q5H8C1	FREM1_HUMAN	Y	804;803;803	ENSP00000370263:S804Y;ENSP00000412940:S803Y;ENSP00000370262:S803Y	ENSP00000370257:S806Y	S	-	2	0	FREM1	14809370	1.000000	0.71417	0.993000	0.49108	0.383000	0.30230	8.582000	0.90791	2.771000	0.95319	0.563000	0.77884	TCT	G|0.830;T|0.170	0.170	strong		0.478	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
TMC3	342125	hgsc.bcm.edu	37	15	81625385	81625385	+	Missense_Mutation	SNP	C	C	T	rs11636318	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:81625385C>T	ENST00000359440.5	-	22	2813	c.2678G>A	c.(2677-2679)tGt>tAt	p.C893Y	RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.C894Y|RP11-761I4.3_ENST00000559781.1_RNA|RP11-761I4.3_ENST00000560973.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						GTAAGAGTCACATTCATTAAT	0.493													C|||	2359	0.471046	0.2277	0.5951	5008	,	,		19670	0.4782		0.7584	False		,,,				2504	0.409				p.C893Y		Atlas-SNP	.											.	TMC3	112	.	0			c.G2678A						PASS	.	C	TYR/CYS	1191,2643		181,829,907	96.0	90.0	92.0		2678	-1.3	0.0	15	dbSNP_120	92	6342,1922		2420,1502,210	yes	missense	TMC3	NM_001080532.1	194	2601,2331,1117	TT,TC,CC		23.2575,31.0642,37.7335	benign	893/1101	81625385	7533,4565	1917	4132	6049	SO:0001583	missense	342125	exon22			GAGTCACATTCAT	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.2678G>A	15.37:g.81625385C>T	ENSP00000352413:p.Cys893Tyr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	1198	0.5485347985347986	118	0.23983739837398374	237	0.6546961325966851	267	0.46678321678321677	576	0.7598944591029023	C	9.839	1.190567	0.21954	0.310642	0.767425	ENSG00000188869	ENST00000359440	T	0.62788	-0.0	5.42	-1.28	0.09318	.	0.784910	0.10051	U	0.722251	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42749	-0.9433	9	0.62326	D	0.03	0.1964	10.804	0.46507	0.0:0.3047:0.0:0.6953	rs11636318;rs52797002;rs11636318	893	Q7Z5M5	TMC3_HUMAN	Y	893	ENSP00000352413:C893Y	ENSP00000352413:C893Y	C	-	2	0	TMC3	79412440	0.038000	0.19896	0.000000	0.03702	0.000000	0.00434	0.726000	0.25984	-0.264000	0.09365	-1.127000	0.01993	TGT	C|0.473;T|0.527	0.527	strong		0.493	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
LVRN	206338	hgsc.bcm.edu	37	5	115336862	115336862	+	Silent	SNP	T	T	C	rs7712021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:115336862T>C	ENST00000357872.4	+	10	1870	c.1746T>C	c.(1744-1746)aaT>aaC	p.N582N	AQPEP_ENST00000395528.2_Silent_p.N99N	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		582						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										TCACTTTAAATGTGTCTACTG	0.398													T|||	1276	0.254792	0.3071	0.2435	5008	,	,		19254	0.2252		0.334	False		,,,				2504	0.1411				p.N582N		Atlas-SNP	.											.	.	.	.	0			c.T1746C						PASS	.	T		1369,3035	454.0+/-350.5	207,955,1040	121.0	119.0	120.0		1746	2.3	1.0	5	dbSNP_116	120	3012,5588	465.0+/-366.4	557,1898,1845	no	coding-synonymous	AQPEP	NM_173800.4		764,2853,2885	CC,CT,TT		35.0233,31.0854,33.6896		582/991	115336862	4381,8623	2202	4300	6502	SO:0001819	synonymous_variant	0	exon10			TTTAAATGTGTCT																												ENST00000357872.4:c.1746T>C	5.37:g.115336862T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	249	111	0.445783	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			C|0.307;N|0.000	0.307	strong		0.398	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29910557	29910557	+	Missense_Mutation	SNP	T	T	A	rs386698549|rs1136659	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29910557T>A	ENST00000396634.1	+	4	438	c.97T>A	c.(97-99)Ttc>Atc	p.F33I	HLA-A_ENST00000376806.5_Missense_Mutation_p.F33I|HLA-A_ENST00000376809.5_Missense_Mutation_p.F33I|HLA-A_ENST00000376802.2_Missense_Mutation_p.F33I			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	33	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GAGGTATTTCTTCACATCCGT	0.721									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	535	0.106829	0.1112	0.1182	5008	,	,		14505	0.12		0.0666	False		,,,				2504	0.1207				p.F33I		Atlas-SNP	.											HLA-A,NS,lymphoid_neoplasm,-1,1	HLA-A	89	1	0			c.T97A						PASS	.						16.0	15.0	15.0					6																	29910557		2182	4266	6448	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TATTTCTTCACAT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.97T>A	6.37:g.29910557T>A	ENSP00000379873:p.Phe33Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	57	11	0.192982	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	207	0.09478021978021978	43	0.08739837398373984	45	0.12430939226519337	74	0.12937062937062938	45	0.059366754617414245	.	4.623	0.115851	0.08831	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.53;9.53;9.53;9.53	3.72	-7.44	0.01379	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	20.031000	0.00447	U	0.000090	T	0.00109	0.0003	H	0.99404	4.55	0.09310	N	1	B;B;B	0.24920	0.106;0.106;0.114	B;B;B	0.39503	0.301;0.103;0.103	T	0.48043	-0.9069	10	0.87932	D	0	.	3.506	0.07691	0.123:0.4384:0.2366:0.202	rs1136659;rs12721668;rs41552214	33;33;33	Q5SRN7;Q5SRN5;P04439	.;.;1A03_HUMAN	I	33	ENSP00000379873:F33I;ENSP00000366002:F33I;ENSP00000366005:F33I;ENSP00000365998:F33I	ENSP00000348012:F33I	F	+	1	0	HLA-A	30018536	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-9.226000	0.00013	-2.974000	0.00285	-0.712000	0.03635	TTC	A|0.086;T|0.914	0.086	strong		0.721	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
REG3A	5068	hgsc.bcm.edu	37	2	79385499	79385499	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:79385499C>T	ENST00000409839.3	-	4	322	c.286G>A	c.(286-288)Ggt>Agt	p.G96S	REG3A_ENST00000393878.1_Missense_Mutation_p.G96S|AC011754.1_ENST00000415201.1_RNA|REG3A_ENST00000305165.2_Missense_Mutation_p.G96S	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	96	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)			breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						TAGCTGTTACCAATGCTCTTC	0.567																																					p.G96S		Atlas-SNP	.											REG3A,NS,carcinoma,+1,1	REG3A	76	1	0			c.G286A						scavenged	.						140.0	113.0	122.0					2																	79385499		2203	4300	6503	SO:0001583	missense	5068	exon3			TGTTACCAATGCT	S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"""pancreatitis-associated protein"""	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.286G>A	2.37:g.79385499C>T	ENSP00000386630:p.Gly96Ser	Somatic	254	3	0.011811		WXS	Illumina HiSeq	Phase_I	321	16	0.0498442	NM_138938		Missense_Mutation	SNP	ENST00000409839.3	37	CCDS1965.1	.	.	.	.	.	.	.	.	.	.	c	1.622	-0.521320	0.04171	.	.	ENSG00000172016	ENST00000409839;ENST00000393878;ENST00000305165	T;T;T	0.15139	2.45;2.45;2.45	4.02	-7.53	0.01336	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	11.951000	0.00166	N	0.000007	T	0.08935	0.0221	N	0.25245	0.725	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.31081	-0.9956	10	0.07325	T	0.83	.	7.5006	0.27516	0.2706:0.5668:0.0:0.1626	.	96	Q06141	REG3A_HUMAN	S	96	ENSP00000386630:G96S;ENSP00000377456:G96S;ENSP00000304311:G96S	ENSP00000304311:G96S	G	-	1	0	REG3A	79239007	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.261000	0.02855	-1.541000	0.01727	-2.019000	0.00433	GGT	.	.	none		0.567	REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580	
KLKB1	3818	hgsc.bcm.edu	37	4	187178437	187178437	+	Missense_Mutation	SNP	G	G	A	rs121964951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187178437G>A	ENST00000264690.6	+	14	1830	c.1643G>A	c.(1642-1644)tGc>tAc	p.C548Y	KLKB1_ENST00000513864.1_Intron	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	548	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		C -> Y (in PKK deficiency). {ECO:0000269|PubMed:14652634}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.C548Y(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		AATGAAGAATGCCAGAAAAGA	0.338																																					p.C548Y		Atlas-SNP	.											KLKB1_ENST00000264690,colon,carcinoma,0,2	KLKB1	155	2	2	Substitution - Missense(2)	large_intestine(2)	c.G1643A	GRCh37	CM033394	KLKB1	M	rs121964951	scavenged	.	G	TYR/CYS	0,4402		0,0,2201	72.0	84.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1643	5.8	1.0	4	dbSNP_133	80	4,8590	3.7+/-12.6	0,4,4293	yes	missense	KLKB1	NM_000892.3	194	0,4,6494	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	548/639	187178437	4,12992	2201	4297	6498	SO:0001583	missense	3818	exon14			AAGAATGCCAGAA	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"""Kallikreins"""	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.1643G>A	4.37:g.187178437G>A	ENSP00000264690:p.Cys548Tyr	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	130	55	0.423077	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.165611|4.165611	0.78339|0.78339	0.0|0.0	4.65E-4|4.65E-4	ENSG00000164344|ENSG00000164344	ENST00000511608|ENST00000264690	.|D	.|0.96992	.|-4.2	5.75|5.75	5.75|5.75	0.90469|0.90469	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99102|0.99102	0.9691|0.9691	H|H	0.99042|0.99042	4.41|4.41	0.80722|0.80722	A|A	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.997	D|D	0.98891|0.98891	1.0773|1.0773	4|9	.|0.87932	.|D	.|0	.|.	19.9525|19.9525	0.97208|0.97208	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|548;548	.|A8K9A9;P03952	.|.;KLKB1_HUMAN	T|Y	596|548	.|ENSP00000264690:C548Y	.|ENSP00000264690:C548Y	A|C	+|+	1|2	0|0	KLKB1|KLKB1	187415431|187415431	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.898000|0.898000	0.52572|0.52572	6.062000|6.062000	0.71155|0.71155	2.719000|2.719000	0.93026|0.93026	0.655000|0.655000	0.94253|0.94253	GCC|TGC	G|1.000;A|0.000	0.000	strong		0.338	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892	
MRO	83876	hgsc.bcm.edu	37	18	48346024	48346024	+	5'UTR	SNP	G	G	T	rs3813089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:48346024G>T	ENST00000428869.2	-	0	142				MRO_ENST00000587291.1_5'Flank|MRO_ENST00000398439.3_5'UTR|MRO_ENST00000431965.2_Missense_Mutation_p.T23N|MRO_ENST00000588444.1_Intron|MRO_ENST00000436348.2_Missense_Mutation_p.T23N|MRO_ENST00000256425.2_5'UTR			Q9BYG7	MSTRO_HUMAN	maestro							nucleolus (GO:0005730)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		GCTTTCCCGGGTAGTAGCCAA	0.572											OREG0024982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	740	0.147764	0.1362	0.1369	5008	,	,		16608	0.0952		0.2157	False		,,,				2504	0.1554				p.T23N		Atlas-SNP	.											.	MRO	36	.	0			c.C68A						PASS	.	G	,ASN/THR,ASN/THR,	194,1190		12,170,510	37.0	39.0	38.0		,68,68,	-0.7	0.0	18	dbSNP_107	38	733,2449		79,575,937	yes	intron,missense,missense,utr-5	MRO	NM_001127174.1,NM_001127175.1,NM_001127176.1,NM_031939.3	,65,65,	91,745,1447	TT,TG,GG		23.0358,14.0173,20.3022	,possibly-damaging,possibly-damaging,	,23/211,23/263,	48346024	927,3639	692	1591	2283	SO:0001623	5_prime_UTR_variant	83876	exon2			TCCCGGGTAGTAG	AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.-117C>A	18.37:g.48346024G>T		Somatic	90	0	0	953	WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_001127175	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Missense_Mutation	SNP	ENST00000428869.2	37	CCDS11947.1	357	0.16346153846153846	84	0.17073170731707318	58	0.16022099447513813	61	0.10664335664335664	154	0.20316622691292877	G	6.659	0.490034	0.12702	0.140173	0.230358	ENSG00000134042	ENST00000436348;ENST00000431965	T;T	0.19105	2.61;2.17	1.57	-0.692	0.11301	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.44825	P	0.0021640000000000548	B;B	0.15719	0.014;0.014	B;B	0.10450	0.005;0.003	T	0.42103	-0.9471	8	0.44086	T	0.13	.	3.2894	0.06944	0.0:0.3072:0.4187:0.2741	rs3813089;rs17663367;rs56429856;rs57952343;rs3813089	23;23	E9PBI3;E9PAT5	.;.	N	23	ENSP00000397900:T23N;ENSP00000392614:T23N	ENSP00000392614:T23N	T	-	2	0	MRO	46600022	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.404000	0.07205	-0.210000	0.10140	0.511000	0.50034	ACC	G|0.849;T|0.151	0.151	strong		0.572	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2	NM_031939	
CASP5	838	hgsc.bcm.edu	37	11	104869708	104869708	+	Missense_Mutation	SNP	G	G	C	rs523104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:104869708G>C	ENST00000260315.3	-	7	999	c.1000C>G	c.(1000-1002)Ctc>Gtc	p.L334V	CASP5_ENST00000393141.2_Missense_Mutation_p.L347V|CASP5_ENST00000531367.1_Missense_Mutation_p.L192V|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000418434.1_Missense_Mutation_p.L192V|CASP5_ENST00000444749.2_Missense_Mutation_p.L276V|CASP5_ENST00000526056.1_Missense_Mutation_p.L347V			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	334			L -> V (in dbSNP:rs523104). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16893518, ECO:0000269|PubMed:7797592, ECO:0000269|Ref.7}.		apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		GAAGAGATGAGTGCCAAGGAT	0.418													C|||	2650	0.529153	0.4644	0.4035	5008	,	,		18397	0.7728		0.4732	False		,,,				2504	0.5123				p.L347V		Atlas-SNP	.											CASP5_ENST00000393141,NS,carcinoma,0,2	CASP5	213	2	0			c.C1039G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	1952,2452	620.7+/-393.6	423,1106,673	117.0	103.0	108.0		826,574,1039,1000	-4.7	0.0	11	dbSNP_83	108	3947,4651	603.5+/-394.7	906,2135,1258	yes	missense,missense,missense,missense	CASP5	NM_001136109.1,NM_001136110.1,NM_001136112.1,NM_004347.3	32,32,32,32	1329,3241,1931	CC,CG,GG		45.906,44.3233,45.3699	benign,benign,benign,benign	276/377,192/293,347/448,334/435	104869708	5899,7103	2202	4299	6501	SO:0001583	missense	838	exon7			AGATGAGTGCCAA		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"""Caspases"""	1506	protein-coding gene	gene with protein product		602665	"""caspase 5, apoptosis-related cysteine protease"""			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.1000C>G	11.37:g.104869708G>C	ENSP00000260315:p.Leu334Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	37	CCDS8328.2	1145	0.5242673992673993	225	0.4573170731707317	150	0.4143646408839779	430	0.7517482517482518	340	0.44854881266490765	C	1.710	-0.499303	0.04291	0.443233	0.45906	ENSG00000137757	ENST00000393141;ENST00000418434;ENST00000260315;ENST00000444749;ENST00000526056;ENST00000531367	T;T;T;T;T;T	0.03181	4.02;4.02;4.02;4.02;4.02;4.02	4.19	-4.68	0.03309	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);	1.643900	0.03386	N	0.201138	T	0.00012	0.0000	N	0.00500	-1.43	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.29427	-1.0012	9	0.16420	T	0.52	.	1.7822	0.03034	0.1254:0.187:0.3485:0.3391	rs523104;rs3824929;rs17222987;rs52796995;rs61281764;rs523104	192;276;334;347	P51878-3;P51878-2;P51878;P51878-5	.;.;CASP5_HUMAN;.	V	347;192;334;276;347;192	ENSP00000376849:L347V;ENSP00000398130:L192V;ENSP00000260315:L334V;ENSP00000388365:L276V;ENSP00000436877:L347V;ENSP00000434471:L192V	ENSP00000260315:L334V	L	-	1	0	CASP5	104374918	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.448000	0.06820	-1.532000	0.01747	-0.968000	0.02614	CTC	G|0.508;C|0.492	0.492	strong		0.418	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	
SUSD2	56241	hgsc.bcm.edu	37	22	24582041	24582041	+	Missense_Mutation	SNP	A	A	G	rs8141797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:24582041A>G	ENST00000358321.3	+	9	1658	c.1397A>G	c.(1396-1398)aAt>aGt	p.N466S		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	466	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.		N -> S (in dbSNP:rs8141797).		immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						TTCACATTCAATGGGCGCGGA	0.667													A|||	577	0.115216	0.1717	0.1167	5008	,	,		20075	0.0764		0.0616	False		,,,				2504	0.1329				p.N466S		Atlas-SNP	.											.	SUSD2	68	.	0			c.A1397G						PASS	.	A	SER/ASN	744,3662	291.8+/-281.7	56,632,1515	32.0	33.0	33.0		1397	4.0	0.8	22	dbSNP_116	33	545,8055	147.7+/-203.1	16,513,3771	yes	missense	SUSD2	NM_019601.3	46	72,1145,5286	GG,GA,AA		6.3372,16.8861,9.9108	benign	466/823	24582041	1289,11717	2203	4300	6503	SO:0001583	missense	56241	exon9			CATTCAATGGGCG	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.1397A>G	22.37:g.24582041A>G	ENSP00000351075:p.Asn466Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_019601	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	37	CCDS13824.1	219	0.10027472527472528	88	0.17886178861788618	30	0.08287292817679558	61	0.10664335664335664	40	0.052770448548812667	A	16.71	3.198632	0.58126	0.168861	0.063372	ENSG00000099994	ENST00000358321	T	0.59638	0.25	5.05	4.01	0.46588	von Willebrand factor, type D domain (3);	0.199114	0.50627	N	0.000114	T	0.00144	0.0004	L	0.60904	1.88	0.32903	P	0.48656900000000003	P	0.36753	0.568	B	0.39068	0.289	T	0.07849	-1.0751	9	0.44086	T	0.13	-18.0237	8.501	0.33159	0.9047:0.0:0.0953:0.0	rs8141797;rs56709043;rs8141797	466	Q9UGT4	SUSD2_HUMAN	S	466	ENSP00000351075:N466S	ENSP00000351075:N466S	N	+	2	0	SUSD2	22912041	1.000000	0.71417	0.818000	0.32626	0.537000	0.34900	4.724000	0.61972	0.913000	0.36797	0.454000	0.30748	AAT	A|0.901;G|0.099	0.099	strong		0.667	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601	
ULK4	54986	hgsc.bcm.edu	37	3	41925398	41925398	+	Missense_Mutation	SNP	C	C	T	rs1052501	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:41925398C>T	ENST00000301831.4	-	17	2086	c.1624G>A	c.(1624-1626)Gct>Act	p.A542T	ULK4_ENST00000420927.1_Missense_Mutation_p.A542T	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	542			A -> T (in dbSNP:rs1052501).		cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGGAGCTCAGCTGTGTGCGAA	0.413													T|||	3448	0.688498	0.3041	0.8184	5008	,	,		19567	0.8532		0.8101	False		,,,				2504	0.8211				p.A542T		Atlas-SNP	.											.	ULK4	150	.	0			c.G1624A						PASS	.	T	THR/ALA	1436,2382		275,886,748	84.0	70.0	74.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1624	0.2	0.0	3	dbSNP_86	74	6779,1429		2803,1173,128	yes	missense	ULK4	NM_017886.2	58	3078,2059,876	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	17.4098,37.6113,31.6897	benign	542/1276	41925398	8215,3811	1909	4104	6013	SO:0001583	missense	54986	exon17			GCTCAGCTGTGTG	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1624G>A	3.37:g.41925398C>T	ENSP00000301831:p.Ala542Thr	Somatic	353	0	0		WXS	Illumina HiSeq	Phase_I	307	306	0.996743	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	1544	0.706959706959707	155	0.3150406504065041	297	0.8204419889502762	483	0.8444055944055944	609	0.8034300791556728	T	0.358	-0.940846	0.02322	0.376113	0.825902	ENSG00000168038	ENST00000301831;ENST00000420927	T;T	0.64260	-0.09;0.71	4.54	0.24	0.15489	Armadillo-like helical (1);Armadillo-type fold (2);	0.765631	0.12488	N	0.464502	T	0.00012	0.0000	N	0.00237	-1.79	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35025	-0.9805	9	0.02654	T	1	.	3.74	0.08526	0.1581:0.3146:0.0:0.5273	rs1052501;rs1716686;rs3192917;rs17081309;rs52805076;rs59312965;rs1052501	542;542	B4E2M4;Q96C45	.;ULK4_HUMAN	T	542	ENSP00000301831:A542T;ENSP00000412187:A542T	ENSP00000301831:A542T	A	-	1	0	ULK4	41900402	0.002000	0.14202	0.006000	0.13384	0.673000	0.39480	-0.120000	0.10660	-0.461000	0.06993	-0.521000	0.04368	GCT	C|0.304;T|0.696	0.696	strong		0.413	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
SEC23IP	11196	hgsc.bcm.edu	37	10	121671651	121671651	+	Silent	SNP	T	T	C	rs17099368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:121671651T>C	ENST00000369075.3	+	6	1359	c.1287T>C	c.(1285-1287)gaT>gaC	p.D429D	SEC23IP_ENST00000543134.1_Silent_p.D218D	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	429					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.D429D(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		GTGGAATTGATGATAACCTTG	0.443													T|||	585	0.116813	0.0023	0.0274	5008	,	,		18490	0.1994		0.0537	False		,,,				2504	0.3149				p.D429D		Atlas-SNP	.											SEC23IP,NS,carcinoma,0,1	SEC23IP	100	1	1	Substitution - coding silent(1)	stomach(1)	c.T1287C						PASS	.	T		38,4368	43.8+/-77.6	0,38,2165	229.0	205.0	213.0		1287	-7.8	0.0	10	dbSNP_123	213	475,8125	139.7+/-196.3	9,457,3834	no	coding-synonymous	SEC23IP	NM_007190.3		9,495,5999	CC,CT,TT		5.5233,0.8625,3.9443		429/1001	121671651	513,12493	2203	4300	6503	SO:0001819	synonymous_variant	11196	exon6			AATTGATGATAAC	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"""Sterile alpha motif (SAM) domain containing"""	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.1287T>C	10.37:g.121671651T>C		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	231	98	0.424242	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Silent	SNP	ENST00000369075.3	37	CCDS7618.1																																																																																			T|0.939;C|0.061	0.061	strong		0.443	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1		
ZCCHC14	23174	hgsc.bcm.edu	37	16	87445270	87445270	+	Silent	SNP	T	T	C	rs3748399	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:87445270T>C	ENST00000268616.4	-	12	2863	c.2646A>G	c.(2644-2646)acA>acG	p.T882T		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	882							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		ACACCCCTGCTGTCCCTGCCA	0.597													T|||	571	0.114018	0.1551	0.0778	5008	,	,		13076	0.1448		0.0497	False		,,,				2504	0.1186				p.T882T		Atlas-SNP	.											ZCCHC14,rectum,carcinoma,-2,1	ZCCHC14	87	1	0			c.A2646G						PASS	.	T		528,3868	235.2+/-247.8	32,464,1702	65.0	53.0	57.0		2646	-10.6	0.0	16	dbSNP_107	57	541,8059	148.5+/-203.7	21,499,3780	no	coding-synonymous	ZCCHC14	NM_015144.2		53,963,5482	CC,CT,TT		6.2907,12.0109,8.2256		882/950	87445270	1069,11927	2198	4300	6498	SO:0001819	synonymous_variant	23174	exon12			CCCTGCTGTCCCT	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2646A>G	16.37:g.87445270T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																			T|0.901;C|0.099	0.099	strong		0.597	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
UGT2B4	7363	hgsc.bcm.edu	37	4	70361163	70361163	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70361163T>C	ENST00000305107.6	-	1	463	c.417A>G	c.(415-417)aaA>aaG	p.K139K	UGT2B4_ENST00000381096.3_Intron|UGT2B4_ENST00000506580.1_5'UTR|UGT2B4_ENST00000512583.1_Silent_p.K139K	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	139					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	ACTCCTGTAGTTTCTTCATAA	0.368																																					p.K139K		Atlas-SNP	.											.	UGT2B4	105	.	0			c.A417G						PASS	.						37.0	38.0	38.0					4																	70361163		2144	4283	6427	SO:0001819	synonymous_variant	7363	exon1			CTGTAGTTTCTTC	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"""UDP glucuronosyltransferases"""	12553	protein-coding gene	gene with protein product		600067	"""UDP glycosyltransferase 2 family, polypeptide B4"""			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.417A>G	4.37:g.70361163T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	157	28	0.178344	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	CCDS43234.1																																																																																			.	.	none		0.368	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
HIST1H1A	3024	hgsc.bcm.edu	37	6	26017542	26017542	+	Missense_Mutation	SNP	T	T	C	rs16891235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26017542T>C	ENST00000244573.3	-	1	498	c.419A>G	c.(418-420)aAa>aGa	p.K140R		NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	140			K -> R (in dbSNP:rs16891235).		nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						CGTGGCCTTTTTGAGCTTTTT	0.493													T|||	369	0.0736821	0.1324	0.0706	5008	,	,		16862	0.0149		0.0944	False		,,,				2504	0.0358				p.K140R		Atlas-SNP	.											.	HIST1H1A	25	.	0			c.A419G						PASS	.	T	ARG/LYS	519,3887		36,447,1720	120.0	128.0	125.0		419	-1.0	0.0	6	dbSNP_123	125	888,7712		45,798,3457	yes	missense	HIST1H1A	NM_005325.3	26	81,1245,5177	CC,CT,TT		10.3256,11.7794,10.8181	benign	140/216	26017542	1407,11599	2203	4300	6503	SO:0001583	missense	3024	exon1			GCCTTTTTGAGCT	AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"""Histones / Replication-dependent"""	4715	protein-coding gene	gene with protein product		142709	"""H1 histone family, member 1"", ""histone 1, H1a"""	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.419A>G	6.37:g.26017542T>C	ENSP00000244573:p.Lys140Arg	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	362	360	0.994475	NM_005325	Q3MJ34	Missense_Mutation	SNP	ENST00000244573.3	37	CCDS4569.1	166	0.076007326007326	52	0.10569105691056911	27	0.07458563535911603	10	0.017482517482517484	77	0.10158311345646438	N	4.085	0.013674	0.07959	0.117794	0.103256	ENSG00000124610	ENST00000244573	T	0.21932	1.98	4.31	-1.02	0.10135	.	0.774546	0.11638	N	0.544065	T	0.02929	0.0087	N	0.08118	0	0.33361	P	0.427677	B	0.13145	0.007	B	0.10450	0.005	T	0.45906	-0.9229	9	0.28530	T	0.3	-21.4092	8.7383	0.34541	0.0:0.3184:0.0:0.6816	rs16891235;rs52798641;rs58813645;rs16891235	140	Q02539	H11_HUMAN	R	140	ENSP00000244573:K140R	ENSP00000244573:K140R	K	-	2	0	HIST1H1A	26125521	0.933000	0.31639	0.003000	0.11579	0.033000	0.12548	1.692000	0.37731	-0.266000	0.09339	-0.315000	0.08773	AAA	T|0.908;C|0.092	0.092	strong		0.493	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1	NM_005325	
TMEM133	83935	hgsc.bcm.edu	37	11	100863354	100863354	+	Silent	SNP	C	C	A	rs471933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100863354C>A	ENST00000303130.2	+	1	544	c.315C>A	c.(313-315)gtC>gtA	p.V105V		NM_032021.2	NP_114410.1	Q9H2Q1	TM133_HUMAN	transmembrane protein 133	105						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(1)|lung(1)|prostate(1)	5		Acute lymphoblastic leukemia(157;0.000869)|all_hematologic(158;0.014)		BRCA - Breast invasive adenocarcinoma(274;0.0675)		CCCTCATTGTCACCGTTATCC	0.418													C|||	1928	0.384984	0.1225	0.3934	5008	,	,		20516	0.756		0.1988	False		,,,				2504	0.5429				p.V105V		Atlas-SNP	.											.	TMEM133	9	.	0			c.C315A						PASS	.	C		585,3821	258.6+/-262.5	43,499,1661	171.0	161.0	164.0		315	-4.4	0.0	11	dbSNP_83	164	1777,6823	321.6+/-315.2	189,1399,2712	no	coding-synonymous	TMEM133	NM_032021.2		232,1898,4373	AA,AC,CC		20.6628,13.2773,18.1608		105/130	100863354	2362,10644	2203	4300	6503	SO:0001819	synonymous_variant	83935	exon1			CATTGTCACCGTT	AF247167	CCDS8309.1	11q22.1	2006-03-09				ENSG00000170647			24033	protein-coding gene	gene with protein product						12477932	Standard	NM_032021		Approved	AD031	uc001pgf.3	Q9H2Q1		ENST00000303130.2:c.315C>A	11.37:g.100863354C>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_032021		Silent	SNP	ENST00000303130.2	37	CCDS8309.1																																																																																			T|0.002;G|0.004	.	strong		0.418	TMEM133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395137.1	NM_032021	
CNOT1	23019	hgsc.bcm.edu	37	16	58616984	58616984	+	Silent	SNP	T	T	C	rs17854029	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:58616984T>C	ENST00000317147.5	-	9	1241	c.909A>G	c.(907-909)ggA>ggG	p.G303G	CNOT1_ENST00000569240.1_Silent_p.G303G|CNOT1_ENST00000441024.2_Silent_p.G303G	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	303					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CATCTGTTAATCCTGAATGAG	0.393													T|||	1012	0.202077	0.1218	0.268	5008	,	,		19053	0.0288		0.4264	False		,,,				2504	0.2117				p.G303G		Atlas-SNP	.											CNOT1_ENST00000441024,NS,carcinoma,0,2	CNOT1	359	2	0			c.A909G						PASS	.	T	,	824,3572	326.7+/-299.7	79,666,1453	104.0	91.0	95.0		909,909	1.3	1.0	16	dbSNP_123	95	3863,4737	542.3+/-384.2	880,2103,1317	no	coding-synonymous,coding-synonymous	CNOT1	NM_016284.3,NM_206999.1	,	959,2769,2770	CC,CT,TT		44.9186,18.7443,36.0649	,	303/2377,303/1552	58616984	4687,8309	2198	4300	6498	SO:0001819	synonymous_variant	23019	exon9			TGTTAATCCTGAA	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.909A>G	16.37:g.58616984T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	194	98	0.505155	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																			T|0.709;C|0.291	0.291	strong		0.393	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
TMED9	54732	hgsc.bcm.edu	37	5	177019262	177019262	+	Missense_Mutation	SNP	C	C	G	rs57960711	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:177019262C>G	ENST00000332598.6	+	1	104	c.47C>G	c.(46-48)aCc>aGc	p.T16S		NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain containing 9	16			T -> S (in dbSNP:rs57960711).		COPI coating of Golgi vesicle (GO:0048205)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network transport vesicle (GO:0030140)	syntaxin binding (GO:0019905)			endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGGCCCGGAACCGGGCTGGGT	0.706													C|||	119	0.023762	0.0386	0.0375	5008	,	,		12574	0.0		0.0398	False		,,,				2504	0.002				p.T16S		Atlas-SNP	.											.	TMED9	18	.	0			c.C47G						PASS	.	C	SER/THR	195,4189		4,187,2001	12.0	16.0	14.0		47	3.0	0.0	5	dbSNP_129	14	335,8247		7,321,3963	yes	missense	TMED9	NM_017510.4	58	11,508,5964	GG,GC,CC		3.9035,4.448,4.0876	benign	16/236	177019262	530,12436	2192	4291	6483	SO:0001583	missense	54732	exon1			CCGGAACCGGGCT	AF441399	CCDS4428.1	5q35.3	2008-02-05			ENSG00000184840	ENSG00000184840			24878	protein-coding gene	gene with protein product						12477932	Standard	NM_017510		Approved	HSGP25L2G	uc003mhx.3	Q9BVK6	OTTHUMG00000130859	ENST00000332598.6:c.47C>G	5.37:g.177019262C>G	ENSP00000330945:p.Thr16Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	91	66	0.725275	NM_017510	Q14437|Q8WZ61	Missense_Mutation	SNP	ENST00000332598.6	37	CCDS4428.1	67	0.030677655677655676	22	0.044715447154471545	13	0.03591160220994475	0	0.0	32	0.04221635883905013	C	0.066	-1.212828	0.01555	0.04448	0.039035	ENSG00000184840	ENST00000332598	T	0.14144	2.53	4.84	3.02	0.34903	.	1.278110	0.05236	N	0.511259	T	0.01287	0.0042	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36986	-0.9725	10	0.07482	T	0.82	-4.0E-4	4.4695	0.11704	0.0:0.6122:0.1872:0.2006	rs57960711	16	Q9BVK6	TMED9_HUMAN	S	16	ENSP00000330945:T16S	ENSP00000330945:T16S	T	+	2	0	TMED9	176951868	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.060000	0.11712	0.605000	0.29947	0.462000	0.41574	ACC	C|0.965;G|0.035	0.035	strong		0.706	TMED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253433.1	NM_017510	
LAMA1	284217	hgsc.bcm.edu	37	18	6986227	6986227	+	Missense_Mutation	SNP	G	G	A	rs12607841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:6986227G>A	ENST00000389658.3	-	37	5381	c.5288C>T	c.(5287-5289)gCg>gTg	p.A1763V		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1763	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CGCCTCAGCCGCCTTTAGTTC	0.478													g|||	709	0.141573	0.1437	0.1052	5008	,	,		17741	0.128		0.1541	False		,,,				2504	0.1656				p.A1763V		Atlas-SNP	.											LAMA1,caecum,carcinoma,+1,1	LAMA1	458	1	0			c.C5288T						PASS	.	G	VAL/ALA	664,3742	282.5+/-276.6	55,554,1594	169.0	146.0	154.0		5288	-6.2	0.0	18	dbSNP_120	154	1320,7280	260.1+/-283.0	97,1126,3077	yes	missense	LAMA1	NM_005559.3	64	152,1680,4671	AA,AG,GG		15.3488,15.0704,15.2545	benign	1763/3076	6986227	1984,11022	2203	4300	6503	SO:0001583	missense	284217	exon37			TCAGCCGCCTTTA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5288C>T	18.37:g.6986227G>A	ENSP00000374309:p.Ala1763Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	188	113	0.601064	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	283	0.1295787545787546	63	0.12804878048780488	43	0.11878453038674033	65	0.11363636363636363	112	0.14775725593667546	g	12.62	1.991699	0.35131	0.150704	0.153488	ENSG00000101680	ENST00000389658	T	0.11712	2.75	5.18	-6.25	0.02039	Laminin I (1);	0.746692	0.12568	N	0.457529	T	0.00039	0.0001	L	0.57536	1.79	0.80722	P	0.0	B	0.17268	0.021	B	0.12837	0.008	T	0.38243	-0.9670	9	0.56958	D	0.05	.	2.5499	0.04746	0.2913:0.0803:0.1245:0.5039	rs12607841	1763	P25391	LAMA1_HUMAN	V	1763	ENSP00000374309:A1763V	ENSP00000374309:A1763V	A	-	2	0	LAMA1	6976227	0.012000	0.17670	0.000000	0.03702	0.001000	0.01503	0.473000	0.22132	-0.884000	0.03976	-1.051000	0.02340	GCG	G|0.855;A|0.145	0.145	strong		0.478	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
IKBKE	9641	hgsc.bcm.edu	37	1	206651107	206651107	+	Silent	SNP	G	G	A	rs2297545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206651107G>A	ENST00000367120.3	+	8	1090	c.717G>A	c.(715-717)acG>acA	p.T239T	IKBKE_ENST00000537984.1_Silent_p.T154T	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GGATCACCACGGAGAAGCCGG	0.652													G|||	1580	0.315495	0.1558	0.402	5008	,	,		15713	0.6131		0.2286	False		,,,				2504	0.2526				p.T239T		Atlas-SNP	.											IKBKE,NS,carcinoma,0,1	IKBKE	77	1	0			c.G717A						PASS	.	G	,,	716,3650		56,604,1523	13.0	14.0	13.0		462,717,717	-9.1	0.1	1	dbSNP_100	13	1791,6755		176,1439,2658	no	coding-synonymous,coding-synonymous,coding-synonymous	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	,,	232,2043,4181	AA,AG,GG		20.9572,16.3995,19.416	,,	154/632,239/658,239/717	206651107	2507,10405	2183	4273	6456	SO:0001819	synonymous_variant	9641	exon8			CACCACGGAGAAG	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.717G>A	1.37:g.206651107G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	154	76	0.493506	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	37	CCDS30996.1																																																																																			G|0.745;A|0.255	0.255	strong		0.652	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
CYP2A13	1553	hgsc.bcm.edu	37	19	41594954	41594954	+	Nonsense_Mutation	SNP	C	C	T	rs72552266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41594954C>T	ENST00000330436.3	+	2	301	c.301C>T	c.(301-303)Cga>Tga	p.R101*		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	101			R -> Q (in allele CYP2A13*4). {ECO:0000269|PubMed:15618722}.		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	GTTCAGCGGGCGAGGCGAGCA	0.637													N|||	19	0.00379393	0.0	0.0058	5008	,	,		17843	0.001		0.0119	False		,,,				2504	0.002				p.R101X		Atlas-SNP	.											CYP2A13,caecum,carcinoma,-1,1	CYP2A13	90	1	0			c.C301T	GRCh37	CM032880	CYP2A13	M	rs72552266	scavenged	.						60.0	57.0	58.0					19																	41594954		2202	4276	6478	SO:0001587	stop_gained	1553	exon2			AGCGGGCGAGGCG	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"""Cytochrome P450s"""	2608	protein-coding gene	gene with protein product		608055	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"""			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.301C>T	19.37:g.41594954C>T	ENSP00000332679:p.Arg101*	Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	418	36	0.0861244	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Nonsense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	50	0.022893772893772892	25	0.0508130081300813	6	0.016574585635359115	1	0.0017482517482517483	18	0.023746701846965697	.	13.66	2.304807	0.40795	.	.	ENSG00000197838	ENST00000330436	.	.	.	3.49	2.42	0.29668	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.9774	0.30164	0.1802:0.6446:0.1752:0.0	.	.	.	.	X	101	.	ENSP00000332679:R101X	R	+	1	2	CYP2A13	46286794	0.081000	0.21417	0.343000	0.25615	0.105000	0.19272	0.470000	0.22084	0.794000	0.33899	-0.572000	0.04151	CGA	C|0.985;T|0.015	0.015	strong		0.637	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766	
SMCR8	140775	hgsc.bcm.edu	37	17	18220674	18220674	+	Missense_Mutation	SNP	C	C	T	rs8080966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18220674C>T	ENST00000406438.3	+	1	2051	c.1571C>T	c.(1570-1572)cCc>cTc	p.P524L	TOP3A_ENST00000542570.1_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	524			P -> L (in dbSNP:rs8080966). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						AGTACCTGCCCCTCTGAGGCC	0.537													C|||	894	0.178514	0.1604	0.2421	5008	,	,		20664	0.0605		0.3062	False		,,,				2504	0.1483				p.P524L		Atlas-SNP	.											.	SMCR8	62	.	0			c.C1571T						PASS	.	C	LEU/PRO	916,3490	349.3+/-310.3	87,742,1374	90.0	89.0	90.0		1571	5.9	1.0	17	dbSNP_116	90	2594,6006	418.1+/-352.7	382,1830,2088	yes	missense	SMCR8	NM_144775.2	98	469,2572,3462	TT,TC,CC		30.1628,20.7898,26.9875	probably-damaging	524/938	18220674	3510,9496	2203	4300	6503	SO:0001583	missense	140775	exon1			CCTGCCCCTCTGA	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1571C>T	17.37:g.18220674C>T	ENSP00000385025:p.Pro524Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	440	0.20146520146520147	79	0.16056910569105692	91	0.2513812154696133	33	0.057692307692307696	237	0.31266490765171506	C	9.135	1.012468	0.19277	0.207898	0.301628	ENSG00000176994	ENST00000406438	T	0.71934	-0.61	5.91	5.91	0.95273	.	0.151452	0.46442	D	0.000294	T	0.00012	0.0000	L	0.32530	0.975	0.09310	P	0.99999898358	D	0.89917	1.0	D	0.85130	0.997	T	0.06935	-1.0799	9	0.14656	T	0.56	-56.313	20.2983	0.98569	0.0:1.0:0.0:0.0	rs8080966;rs52799159;rs59228353;rs8080966	524	Q8TEV9	SMCR8_HUMAN	L	524	ENSP00000385025:P524L	ENSP00000385025:P524L	P	+	2	0	SMCR8	18161399	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.311000	0.65786	2.802000	0.96397	0.655000	0.94253	CCC	C|0.770;T|0.230	0.230	strong		0.537	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
RBM5	10181	hgsc.bcm.edu	37	3	50153356	50153356	+	Silent	SNP	T	T	C	rs1138536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50153356T>C	ENST00000347869.3	+	22	2212	c.2037T>C	c.(2035-2037)taT>taC	p.Y679Y	RP11-493K19.3_ENST00000437204.1_RNA|RP11-493K19.3_ENST00000425674.1_RNA	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	679	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGGACATCTATCGACGATCCA	0.438													C|||	3743	0.747404	0.7458	0.6945	5008	,	,		22551	0.8819		0.5686	False		,,,				2504	0.8323				p.Y679Y		Atlas-SNP	.											.	RBM5	76	.	0			c.T2037C						PASS	.	C		3176,1230	424.0+/-340.3	1145,886,172	108.0	110.0	109.0		2037	2.0	1.0	3	dbSNP_86	109	4904,3696	529.7+/-381.6	1370,2164,766	no	coding-synonymous	RBM5	NM_005778.2		2515,3050,938	CC,CT,TT		42.9767,27.9165,37.8748		679/816	50153356	8080,4926	2203	4300	6503	SO:0001819	synonymous_variant	10181	exon22			CATCTATCGACGA	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.2037T>C	3.37:g.50153356T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	37	CCDS2810.1																																																																																			T|0.328;C|0.672	0.672	strong		0.438	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183108	11183108	+	Missense_Mutation	SNP	G	G	C	rs12318612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:11183108G>C	ENST00000390675.2	-	1	898	c.827C>G	c.(826-828)cCa>cGa	p.P276R	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	276			P -> R (in dbSNP:rs12318612).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						CAGGATGAATGGGTGGATTGA	0.423													.|||	614	0.122604	0.1051	0.2161	5008	,	,		19158	0.0		0.2734	False		,,,				2504	0.0511				p.P276R		Atlas-SNP	.											.	TAS2R31	24	.	0			c.C827G						PASS	.	G	ARG/PRO	499,3503		40,419,1542	192.0	194.0	193.0		827	2.4	0.0	12	dbSNP_120	193	2122,6246		286,1550,2348	no	missense	TAS2R31	NM_176885.2	103	326,1969,3890	CC,CG,GG		25.3585,12.4688,21.1884	possibly-damaging	276/310	11183108	2621,9749	2001	4184	6185	SO:0001583	missense	259290	exon1			ATGAATGGGTGGA	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.827C>G	12.37:g.11183108G>C	ENSP00000375093:p.Pro276Arg	Somatic	506	0	0		WXS	Illumina HiSeq	Phase_I	453	192	0.423841	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	354	0.1620879120879121	71	0.1443089430894309	74	0.20441988950276244	0	0.0	209	0.2757255936675462	.	9.268	1.044890	0.19748	0.124688	0.253585	ENSG00000256436	ENST00000390675	T	0.64085	-0.08	2.41	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	M	0.64404	1.975	0.80722	P	0.0	P	0.41188	0.741	B	0.41412	0.356	T	0.07385	-1.0775	8	0.87932	D	0	.	8.3448	0.32266	0.0:0.0:1.0:0.0	rs12318612	276	P59538	T2R31_HUMAN	R	276	ENSP00000375093:P276R	ENSP00000375093:P276R	P	-	2	0	TAS2R31	11074375	0.007000	0.16637	0.014000	0.15608	0.032000	0.12392	1.677000	0.37576	1.376000	0.46267	0.184000	0.17185	CCA	.	.	weak		0.423	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
OR4L1	122742	hgsc.bcm.edu	37	14	20528528	20528528	+	Missense_Mutation	SNP	G	G	A	rs2775254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20528528G>A	ENST00000315683.1	+	1	325	c.325G>A	c.(325-327)Ggt>Agt	p.G109S		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	109			G -> S (in dbSNP:rs2775254).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		CTTCTTTGGGGGTGCTGAGAT	0.473													G|||	2134	0.426118	0.3623	0.3934	5008	,	,		18993	0.5347		0.3221	False		,,,				2504	0.5307				p.G109S		Atlas-SNP	.											.	OR4L1	98	.	0			c.G325A						PASS	.	G	SER/GLY	1578,2828		284,1010,909	142.0	126.0	132.0		325	4.0	1.0	14	dbSNP_100	132	2761,5839		481,1799,2020	yes	missense	OR4L1	NM_001004717.1	56	765,2809,2929	AA,AG,GG		32.1047,35.8148,33.3615	probably-damaging	109/313	20528528	4339,8667	2203	4300	6503	SO:0001583	missense	122742	exon1			TTTGGGGGTGCTG		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.325G>A	14.37:g.20528528G>A	ENSP00000319217:p.Gly109Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001004717	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	889	0.40705128205128205	184	0.37398373983739835	140	0.3867403314917127	303	0.5297202797202797	262	0.34564643799472294	.	15.15	2.747603	0.49257	0.358148	0.321047	ENSG00000176246	ENST00000315683	T	0.09445	2.98	3.99	3.99	0.46301	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000024	T	0.00012	0.0000	L	0.53780	1.695	0.58432	P	5.000000000032756E-6	D	0.56521	0.976	P	0.49361	0.608	T	0.47861	-0.9084	9	0.72032	D	0.01	.	13.9601	0.64172	0.0:0.0:1.0:0.0	rs2775254;rs2994400;rs52809408;rs57715101;rs2775254	109	Q8NH43	OR4L1_HUMAN	S	109	ENSP00000319217:G109S	ENSP00000319217:G109S	G	+	1	0	OR4L1	19598368	0.000000	0.05858	0.998000	0.56505	0.477000	0.33069	-0.577000	0.05847	2.213000	0.71641	0.650000	0.86243	GGT	G|0.625;A|0.375	0.375	strong		0.473	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
PODN	127435	hgsc.bcm.edu	37	1	53535478	53535478	+	Missense_Mutation	SNP	G	G	A	rs1288386	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:53535478G>A	ENST00000312553.5	+	2	102	c.95G>A	c.(94-96)cGt>cAt	p.R32H	PODN_ENST00000371500.3_Missense_Mutation_p.R13H|PODN_ENST00000395871.2_Missense_Mutation_p.R32H|RP11-334A14.5_ENST00000447867.1_RNA	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	0					negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CACAGGTTCCGTCAGCCCTGG	0.677													G|||	1790	0.357428	0.1241	0.3444	5008	,	,		16566	0.5536		0.4254	False		,,,				2504	0.41				p.R32H		Atlas-SNP	.											PODN,NS,carcinoma,+1,2	PODN	86	2	0			c.G95A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	788,3482		113,562,1460	9.0	11.0	10.0		38,38,95,95	1.0	0.0	1	dbSNP_87	10	3534,4878		798,1938,1470	yes	missense,missense,missense,missense	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	29,29,29,29	911,2500,2930	AA,AG,GG		42.0114,18.4543,34.0798	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	13/643,13/643,32/520,32/662	53535478	4322,8360	2135	4206	6341	SO:0001583	missense	127435	exon2			GGTTCCGTCAGCC	AY313607	CCDS573.1, CCDS55601.1, CCDS55602.1	1p32.3	2008-02-05			ENSG00000174348	ENSG00000174348		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	23174	protein-coding gene	gene with protein product	"""podocan proteoglycan"""	608661					Standard	NM_153703		Approved	PCAN, PODOCAN, MGC24995, SLRR5A	uc010onr.2	Q7Z5L7	OTTHUMG00000008934	ENST00000312553.5:c.95G>A	1.37:g.53535478G>A	ENSP00000308315:p.Arg32His	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Missense_Mutation	SNP	ENST00000312553.5	37	CCDS573.1	830	0.38003663003663	63	0.12804878048780488	129	0.356353591160221	315	0.5506993006993007	323	0.4261213720316623	G	8.949	0.967718	0.18659	0.184543	0.420114	ENSG00000174348	ENST00000371500;ENST00000395871;ENST00000312553	T;T;T	0.62498	0.79;0.02;0.81	1.96	1.03	0.20045	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.31893	0.345;0.345;0.345	B;B;B	0.17979	0.02;0.02;0.02	T	0.48031	-0.9070	7	0.25106	T	0.35	.	4.5042	0.11879	0.1984:0.0:0.8016:0.0	rs1288386;rs1769305;rs17852777;rs61553893;rs1288386	32;13;32	Q7Z5L7-4;Q7Z5L7-2;Q7Z5L7-3	.;.;.	H	13;32;32	ENSP00000360555:R13H;ENSP00000379212:R32H;ENSP00000308315:R32H	ENSP00000308315:R32H	R	+	2	0	PODN	53308066	0.000000	0.05858	0.000000	0.03702	0.204000	0.24138	-0.199000	0.09491	0.403000	0.25479	0.491000	0.48974	CGT	G|0.629;A|0.371	0.371	strong		0.677	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703	
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58335626	58335626	+	Missense_Mutation	SNP	A	A	T	rs3751325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:58335626A>T	ENST00000300145.3	+	1	267	c.142A>T	c.(142-144)Agc>Tgc	p.S48C		NM_033276.2	NP_150592.1	Q9Y6H3	ATP23_HUMAN	XRCC6 binding protein 1	48			S -> C (in dbSNP:rs3751325). {ECO:0000269|PubMed:10219089}.		double-strand break repair via nonhomologous end joining (GO:0006303)|protein phosphorylation (GO:0006468)	DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)	DNA-dependent protein kinase activity (GO:0004677)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	11						CTTCTTCACCAGCAACCAGAA	0.597													A|||	1664	0.332268	0.0794	0.3761	5008	,	,		16918	0.6429		0.3131	False		,,,				2504	0.3425				p.S48C		Atlas-SNP	.											XRCC6BP1,NS,carcinoma,0,1	XRCC6BP1	22	1	0			c.A142T						PASS	.	A	CYS/SER	439,3383		23,393,1495	29.0	34.0	32.0		142	-0.8	0.0	12	dbSNP_107	32	2625,5633		421,1783,1925	yes	missense	XRCC6BP1	NM_033276.2	112	444,2176,3420	TT,TA,AA		31.7874,11.4861,25.3642	benign	48/247	58335626	3064,9016	1911	4129	6040	SO:0001583	missense	91419	exon1			TTCACCAGCAACC	AF078164	CCDS41802.1	12q14.1	2006-01-09				ENSG00000166896			29452	protein-coding gene	gene with protein product	"""Ku70 binding protein 3"""					10219089	Standard	XM_005269223		Approved	KUB3	uc001sqp.3	Q9Y6H3	OTTHUMG00000170493	ENST00000300145.3:c.142A>T	12.37:g.58335626A>T	ENSP00000300145:p.Ser48Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_033276	Q1RLM4|Q96E81	Missense_Mutation	SNP	ENST00000300145.3	37	CCDS41802.1	790	0.3617216117216117	49	0.09959349593495935	126	0.34806629834254144	376	0.6573426573426573	239	0.3153034300791557	A	2.822	-0.244563	0.05906	0.114861	0.317874	ENSG00000166896	ENST00000300145	T	0.45668	0.89	4.84	-0.82	0.10826	Metallopeptidase, catalytic domain (1);	0.632459	0.17512	N	0.171578	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.32396	0.369	B	0.30179	0.112	T	0.38735	-0.9647	9	0.38643	T	0.18	.	7.8058	0.29202	0.23:0.5387:0.0:0.2314	rs3751325;rs17567908;rs17846076;rs17859073;rs52793950;rs58392225;rs3751325	48	Q9Y6H3	ATP23_HUMAN	C	48	ENSP00000300145:S48C	ENSP00000300145:S48C	S	+	1	0	XRCC6BP1	56621893	0.143000	0.22626	0.047000	0.18901	0.010000	0.07245	0.658000	0.24979	0.069000	0.16605	-1.236000	0.01555	AGC	A|0.640;T|0.360	0.360	strong		0.597	XRCC6BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409390.1	NM_033276	
RIOK2	55781	hgsc.bcm.edu	37	5	96503523	96503523	+	Missense_Mutation	SNP	C	C	T	rs160632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:96503523C>T	ENST00000283109.3	-	8	1113	c.1045G>A	c.(1045-1047)Ggg>Agg	p.G349R	RIOK2_ENST00000508447.1_Missense_Mutation_p.G349R|CTD-2215E18.1_ENST00000509481.1_Intron	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	349	Protein kinase.		G -> R (in dbSNP:rs160632). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		TTTTCTGACCCGTAAACCTCT	0.398													T|||	2793	0.557708	0.5159	0.5749	5008	,	,		19203	0.5208		0.5845	False		,,,				2504	0.6125				p.G349R		Atlas-SNP	.											.	RIOK2	82	.	0			c.G1045A						PASS	.	T	ARG/GLY,ARG/GLY	2327,2079	567.8+/-382.2	608,1111,484	154.0	154.0	154.0		1045,1045	-0.0	0.0	5	dbSNP_79	154	5141,3459	505.3+/-376.3	1551,2039,710	yes	missense,missense	RIOK2	NM_001159749.1,NM_018343.2	125,125	2159,3150,1194	TT,TC,CC		40.2209,47.1857,42.5803	benign,benign	349/475,349/553	96503523	7468,5538	2203	4300	6503	SO:0001583	missense	55781	exon8			CTGACCCGTAAAC	AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"""RIO kinase 2 (yeast)"""				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.1045G>A	5.37:g.96503523C>T	ENSP00000283109:p.Gly349Arg	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	212	110	0.518868	NM_001159749	D6RDI3|Q9NUT0	Missense_Mutation	SNP	ENST00000283109.3	37	CCDS4089.1	1205	0.5517399267399268	269	0.5467479674796748	203	0.5607734806629834	288	0.5034965034965035	445	0.5870712401055409	T	4.267	0.048632	0.08243	0.528143	0.597791	ENSG00000058729	ENST00000283109;ENST00000508447	T;T	0.14144	2.53;2.53	5.55	-0.0325	0.13905	.	0.608532	0.17696	N	0.165098	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28870	-1.0030	9	0.15066	T	0.55	-10.8731	1.4885	0.02452	0.116:0.2028:0.24:0.4412	rs160632;rs11566766;rs17697316;rs52833108;rs61352611;rs160632	349;349	D6RDI3;Q9BVS4	.;RIOK2_HUMAN	R	349	ENSP00000283109:G349R;ENSP00000420932:G349R	ENSP00000283109:G349R	G	-	1	0	RIOK2	96529279	0.000000	0.05858	0.005000	0.12908	0.053000	0.15095	-0.249000	0.08842	-0.178000	0.10672	-0.352000	0.07741	GGG	C|0.439;T|0.561	0.561	strong		0.398	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343	
GYG2	8908	hgsc.bcm.edu	37	X	2779749	2779749	+	Missense_Mutation	SNP	C	C	T	rs17330993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2779749C>T	ENST00000381163.3	+	9	1399	c.1117C>T	c.(1117-1119)Cgc>Tgc	p.R373C	GYG2_ENST00000381161.1_3'UTR|GYG2_ENST00000398806.3_Missense_Mutation_p.R342C|GYG2_ENST00000542787.1_Missense_Mutation_p.R373C|GYG2_ENST00000338623.5_Missense_Mutation_p.R373C	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	373			R -> C (in dbSNP:rs17330993).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCTGAAGGACGCCGTTCAGA	0.582													C|||	39	0.0103311	0.0	0.0375	3775	,	,		13746	0.001		0.0099	False		,,,				2504	0.002				p.R373C		Atlas-SNP	.											.	GYG2	39	.	0			c.C1117T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	13,3821		0,9,4,1623,566	45.0	33.0	37.0		1024,1024,1117,559,1117	-4.0	0.0	X	dbSNP_123	37	78,6645		0,58,20,2370,1847	yes	missense,missense,missense,missense,missense	GYG2	NM_001079855.1,NM_001184702.1,NM_001184703.1,NM_001184704.1,NM_003918.2	180,180,180,180,180	0,67,24,3993,2413	TT,TC,T,CC,C		1.1602,0.3391,0.862	benign,benign,benign,benign,benign	342/471,342/470,373/431,187/245,373/502	2779749	91,10466	2202	4295	6497	SO:0001583	missense	8908	exon9			GAAGGACGCCGTT	U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.1117C>T	X.37:g.2779749C>T	ENSP00000370555:p.Arg373Cys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_003918	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	37	CCDS14121.1	17|17	0.010247136829415311|0.010247136829415311	0|0	0.0|0.0	6|6	0.016666666666666666|0.016666666666666666	0|0	0.0|0.0	7|7	0.009358288770053475|0.009358288770053475	C|C	1.304|1.304	-0.604033|-0.604033	0.03717|0.03717	0.003391|0.003391	0.011602|0.011602	ENSG00000056998|ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787|ENST00000381157	T;T;T;T|.	0.44482|.	0.92;1.25;1.25;1.23|.	1.98|1.98	-3.96|-3.96	0.04106|0.04106	.|.	.|.	.|.	.|.	.|.	T|T	0.09069|0.09069	0.0224|0.0224	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.09022|.	0.0;0.002;0.001;0.0;0.0;0.0|.	B;B;B;B;B;B|.	0.04013|.	0.001;0.0;0.0;0.0;0.001;0.0|.	T|T	0.24728|0.24728	-1.0152|-1.0152	8|4	0.52906|.	T|.	0.07|.	.|.	7.4635|7.4635	0.27308|0.27308	0.0:0.1493:0.66:0.1907|0.0:0.1493:0.66:0.1907	rs17330993;rs52834531;rs17330993|rs17330993;rs52834531;rs17330993	373;373;333;342;342;373|.	O15488-6;O15488-4;O15488-3;A8K8Y1;O15488-2;O15488|.	.;.;.;.;.;GLYG2_HUMAN|.	C|M	342;373;373;373|191	ENSP00000381786:R342C;ENSP00000370555:R373C;ENSP00000341273:R373C;ENSP00000446092:R373C|.	ENSP00000341273:R373C|.	R|T	+|+	1|2	0|0	GYG2|GYG2	2789749|2789749	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.404000|-1.404000	0.02494|0.02494	-2.105000|-2.105000	0.00842|0.00842	-1.174000|-1.174000	0.01732|0.01732	CGC|ACG	C|0.987;0|0.003	.	strong		0.582	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918	
ITIH1	3697	hgsc.bcm.edu	37	3	52825912	52825912	+	Silent	SNP	C	C	A	rs7549	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:52825912C>A	ENST00000273283.2	+	22	2745	c.2721C>A	c.(2719-2721)gtC>gtA	p.V907V	ITIH1_ENST00000542827.1_3'UTR|ITIH3_ENST00000416872.2_5'Flank|ITIH1_ENST00000537050.1_Silent_p.V619V|ITIH1_ENST00000540715.1_Silent_p.V765V|ITIH3_ENST00000449956.2_5'Flank|ITIH1_ENST00000405128.3_Silent_p.V273V	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	907	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		ATTATATCGTCCCCGACATCT	0.602													C|||	138	0.0275559	0.0061	0.0432	5008	,	,		21431	0.0		0.0885	False		,,,				2504	0.0112				p.V907V		Atlas-SNP	.											.	ITIH1	108	.	0			c.C2721A						PASS	.	C	,,,	76,4330	65.3+/-102.7	1,74,2128	127.0	114.0	119.0		2295,1857,1857,2721	2.8	0.1	3	dbSNP_52	119	829,7771	191.1+/-237.4	42,745,3513	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	,,,	43,819,5641	AA,AC,CC		9.6395,1.7249,6.9583	,,,	765/770,619/624,619/624,907/912	52825912	905,12101	2203	4300	6503	SO:0001819	synonymous_variant	3697	exon22			TATCGTCCCCGAC		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2721C>A	3.37:g.52825912C>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	195	99	0.507692	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Silent	SNP	ENST00000273283.2	37	CCDS2864.1																																																																																			C|0.941;A|0.059	0.059	strong		0.602	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
CD6	923	hgsc.bcm.edu	37	11	60777073	60777073	+	Missense_Mutation	SNP	G	G	A	rs12360861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60777073G>A	ENST00000313421.7	+	5	997	c.811G>A	c.(811-813)Gct>Act	p.A271T	CD6_ENST00000452451.2_Missense_Mutation_p.A271T|CD6_ENST00000344028.5_Missense_Mutation_p.A271T|CD6_ENST00000352009.5_Missense_Mutation_p.A271T|CD6_ENST00000346437.4_Missense_Mutation_p.A271T|CD6_ENST00000545105.1_Intron	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	271	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.		A -> T (in dbSNP:rs12360861).		cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GACAGGGGGCGCTGACCGCTG	0.637													G|||	384	0.0766773	0.0401	0.121	5008	,	,		19148	0.001		0.1938	False		,,,				2504	0.0521				p.A271T	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											CD6_ENST00000313421,rectum,carcinoma,0,2	CD6	122	2	0			c.G811A						PASS	.	G	THR/ALA	267,4139	145.0+/-179.8	8,251,1944	40.0	38.0	38.0		811	-9.8	0.0	11	dbSNP_120	38	1562,7036	285.1+/-297.0	144,1274,2881	yes	missense	CD6	NM_006725.3	58	152,1525,4825	AA,AG,GG		18.167,6.0599,14.0649	benign	271/669	60777073	1829,11175	2203	4299	6502	SO:0001583	missense	923	exon5			GGGGGCGCTGACC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.811G>A	11.37:g.60777073G>A	ENSP00000323280:p.Ala271Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	221	0.10119047619047619	19	0.03861788617886179	51	0.1408839779005525	1	0.0017482517482517483	150	0.19788918205804748	G	1.521	-0.546883	0.04024	0.060599	0.18167	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000452451;ENST00000352009	T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34	4.9	-9.81	0.00487	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.748670	0.02962	N	0.143237	T	0.00012	0.0000	N	0.11284	0.12	0.80722	P	0.0	B;B;B;B	0.22414	0.055;0.069;0.041;0.054	B;B;B;B	0.15484	0.01;0.01;0.011;0.013	T	0.04495	-1.0947	9	0.12766	T	0.61	.	5.9428	0.19201	0.6054:0.0724:0.1293:0.1929	rs12360861	271;271;271;271	P30203-5;P30203-4;P30203;Q8N4Q7	.;.;CD6_HUMAN;.	T	271	ENSP00000344108:A271T;ENSP00000345566:A271T;ENSP00000323280:A271T;ENSP00000390676:A271T;ENSP00000340628:A271T	ENSP00000323280:A271T	A	+	1	0	CD6	60533649	0.000000	0.05858	0.000000	0.03702	0.346000	0.29079	-7.571000	0.00034	-2.169000	0.00777	-0.266000	0.10368	GCT	G|0.878;A|0.122	0.122	strong		0.637	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1893773	1893773	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:1893773C>A	ENST00000398564.1	+	27	3424	c.3424C>A	c.(3424-3426)Cac>Aac	p.H1142N	ARHGEF10_ENST00000521927.1_3'UTR|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.H1113N|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.H1141N|ARHGEF10_ENST00000520359.1_Missense_Mutation_p.H1079N|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.H1117N			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1142					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		AACTCTCAAGCACCTGCAGGA	0.617																																					p.H1117N		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.C3349A						PASS	.						134.0	106.0	115.0					8																	1893773		2203	4300	6503	SO:0001583	missense	9639	exon27			CTCAAGCACCTGC	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3424C>A	8.37:g.1893773C>A	ENSP00000381571:p.His1142Asn	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		.	.	.	.	.	.	.	.	.	.	c	14.10	2.433766	0.43224	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T	0.62639	1.55;1.55;1.55;1.55;0.01;0.01	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.68668	0.3026	M	0.82823	2.61	0.80722	D	1	B;P	0.34892	0.047;0.474	B;B	0.36335	0.059;0.222	T	0.72757	-0.4197	10	0.48119	T	0.1	-35.744	18.2931	0.90137	0.0:1.0:0.0:0.0	.	1079;1117	O15013-7;O15013-5	.;.	N	1117;1079;1141;1142;1113;761	ENSP00000340297:H1117N;ENSP00000427909:H1079N;ENSP00000431012:H1141N;ENSP00000381571:H1142N;ENSP00000262112:H1113N;ENSP00000427768:H761N	ENSP00000262112:H1113N	H	+	1	0	ARHGEF10	1881180	1.000000	0.71417	0.927000	0.36925	0.343000	0.28985	6.849000	0.75414	2.302000	0.77476	0.431000	0.28591	CAC	.	.	none		0.617	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
MUC4	4585	hgsc.bcm.edu	37	3	195506271	195506271	+	Silent	SNP	A	A	T	rs77023345	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506271A>T	ENST00000463781.3	-	2	12639	c.12180T>A	c.(12178-12180)ggT>ggA	p.G4060G	MUC4_ENST00000475231.1_Silent_p.G4060G|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATA	0.582													.|||	30	0.00599042	0.0113	0.0	5008	,	,		10330	0.001		0.001	False		,,,				2504	0.0133				p.G4060G		Atlas-SNP	.											.	MUC4	1505	.	0			c.T12180A						PASS	.						35.0	19.0	24.0					3																	195506271		599	1336	1935	SO:0001819	synonymous_variant	4585	exon2			GGCGTGACCTGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12180T>A	3.37:g.195506271A>T		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	163	117	0.717791	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.807;T|0.193	0.193	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48595988	48595988	+	Missense_Mutation	SNP	G	G	C	rs8064455	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48595988G>C	ENST00000323776.5	+	5	846	c.684G>C	c.(682-684)gaG>gaC	p.E228D	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.E191D	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			CAAAAGAAGAGAAGAGACCTC	0.542													G|||	1280	0.255591	0.6566	0.1369	5008	,	,		18561	0.0536		0.159	False		,,,				2504	0.1053				p.E228D		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.G684C						PASS	.	G	ASP/GLU	2530,1876	631.8+/-395.7	739,1052,412	112.0	128.0	122.0		684	2.2	0.7	17	dbSNP_116	122	1436,7164	275.2+/-291.6	125,1186,2989	yes	missense	MYCBPAP	NM_032133.4	45	864,2238,3401	CC,CG,GG		16.6977,42.5783,30.4936	benign	228/985	48595988	3966,9040	2203	4300	6503	SO:0001583	missense	84073	exon5			AGAAGAGAAGAGA	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.684G>C	17.37:g.48595988G>C	ENSP00000323184:p.Glu228Asp	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	510	0.23351648351648352	310	0.6300813008130082	55	0.15193370165745856	23	0.04020979020979021	122	0.16094986807387862	G	12.97	2.098796	0.37048	0.574217	0.166977	ENSG00000136449	ENST00000323776;ENST00000452039;ENST00000436259	T;T	0.25250	1.81;1.82	5.37	2.19	0.27852	.	1.163120	0.06304	N	0.701470	T	0.00012	0.0000	L	0.57536	1.79	0.36667	P	0.12172899999999998	B	0.28933	0.228	B	0.27796	0.083	T	0.43163	-0.9408	9	0.22706	T	0.39	-7.293	7.3332	0.26594	0.2003:0.0:0.6813:0.1184	rs8064455;rs52820327;rs58596757;rs8064455	191	Q8TBZ2	MYBPP_HUMAN	D	228;243;191	ENSP00000323184:E228D;ENSP00000397209:E191D	ENSP00000323184:E228D	E	+	3	2	MYCBPAP	45950987	0.091000	0.21658	0.740000	0.30986	0.916000	0.54674	0.197000	0.17197	0.615000	0.30124	0.563000	0.77884	GAG	G|0.721;C|0.279	0.279	strong		0.542	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
ITPR2	3709	hgsc.bcm.edu	37	12	26749831	26749831	+	Silent	SNP	G	G	A	rs2230377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:26749831G>A	ENST00000381340.3	-	31	4655	c.4239C>T	c.(4237-4239)gaC>gaT	p.D1413D		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1413					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGATGCAGTCGTCATGGGTCA	0.458													G|||	898	0.179313	0.0938	0.1599	5008	,	,		18276	0.0476		0.3579	False		,,,				2504	0.2607				p.D1413D		Atlas-SNP	.											.	ITPR2	270	.	0			c.C4239T						PASS	.	G		521,3579		37,447,1566	82.0	82.0	82.0		4239	-5.6	1.0	12	dbSNP_98	82	2873,5519		500,1873,1823	no	coding-synonymous	ITPR2	NM_002223.2		537,2320,3389	AA,AG,GG		34.235,12.7073,27.1694		1413/2702	26749831	3394,9098	2050	4196	6246	SO:0001819	synonymous_variant	3709	exon31			GCAGTCGTCATGG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4239C>T	12.37:g.26749831G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.780;A|0.220	0.220	strong		0.458	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
NRG1	3084	hgsc.bcm.edu	37	8	32505633	32505633	+	Intron	SNP	G	G	C	rs35641374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:32505633G>C	ENST00000405005.3	+	5	502				NRG1_ENST00000519301.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000520502.2_Missense_Mutation_p.V133L|NRG1_ENST00000520407.1_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000287845.5_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TGCCTCAGCTGTGTGGGTGTC	0.502													G|||	151	0.0301518	0.0401	0.0245	5008	,	,		18191	0.0		0.0179	False		,,,				2504	0.0644				p.V133L		Atlas-SNP	.											.	NRG1	260	.	0			c.G397C						PASS	.	G	,,,,,,,,,,,,LEU/VAL,,,	108,4298	84.8+/-123.5	2,104,2097	136.0	120.0	125.0		,,,,,,,,,,,,397,,,	4.3	1.0	8	dbSNP_126	125	160,8440	75.7+/-138.4	0,160,4140	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,intron	NRG1	NM_001159995.1,NM_001159999.1,NM_001160001.1,NM_001160002.1,NM_001160004.1,NM_001160005.1,NM_001160007.1,NM_001160008.1,NM_004495.3,NM_013956.3,NM_013957.3,NM_013958.3,NM_013959.3,NM_013960.3,NM_013962.2,NM_013964.3	,,,,,,,,,,,,32,,,	2,264,6237	CC,CG,GG		1.8605,2.4512,2.0606	,,,,,,,,,,,,,,,	,,,,,,,,,,,,133/297,,,	32505633	268,12738	2203	4300	6503	SO:0001627	intron_variant	3084	exon1			TCAGCTGTGTGGG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.502+31230G>C	8.37:g.32505633G>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_013959	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	47	0.02152014652014652	25	0.0508130081300813	11	0.03038674033149171	0	0.0	11	0.014511873350923483	G	12.29	1.893835	0.33442	0.024512	0.018605	ENSG00000157168	ENST00000520502;ENST00000523041	.	.	.	6.07	4.26	0.50523	.	.	.	.	.	T	0.09818	0.0241	L	0.27053	0.805	0.80722	D	1	B;B	0.18610	0.029;0.012	B;B	0.17979	0.02;0.014	T	0.05305	-1.0893	8	0.34782	T	0.22	.	10.1211	0.42621	0.1604:0.0:0.8396:0.0	rs35641374	133;133	Q53F54;Q02297-10	.;.	L	133;93	.	ENSP00000433289:V133L	V	+	1	0	NRG1	32625175	0.999000	0.42202	0.996000	0.52242	0.945000	0.59286	1.799000	0.38824	1.550000	0.49438	0.655000	0.94253	GTG	G|0.976;C|0.024	0.024	strong		0.502	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
TMEM43	79188	hgsc.bcm.edu	37	3	14174427	14174427	+	Missense_Mutation	SNP	A	A	T	rs4685076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14174427A>T	ENST00000306077.4	+	6	758	c.504A>T	c.(502-504)aaA>aaT	p.K168N	RP11-434D12.1_ENST00000608606.1_5'Flank	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	168			K -> N (in dbSNP:rs4685076). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						TTGGCCACAAAAACCCCAGGT	0.507													A|||	1766	0.352636	0.3026	0.366	5008	,	,		18688	0.4613		0.2545	False		,,,				2504	0.3998				p.K168N		Atlas-SNP	.											.	TMEM43	33	.	0			c.A504T						PASS	.	A	ASN/LYS	1265,3141	431.8+/-343.0	191,883,1129	80.0	86.0	84.0		504	1.6	1.0	3	dbSNP_111	84	2475,6125	407.1+/-349.0	371,1733,2196	yes	missense	TMEM43	NM_024334.2	94	562,2616,3325	TT,TA,AA		28.7791,28.7108,28.756	benign	168/401	14174427	3740,9266	2203	4300	6503	SO:0001583	missense	79188	exon6			CCACAAAAACCCC	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"""arrhythmogenic right ventricular dysplasia 5"""	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.504A>T	3.37:g.14174427A>T	ENSP00000303992:p.Lys168Asn	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	175	98	0.56	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	37	CCDS2618.1	721	0.3301282051282051	165	0.3353658536585366	128	0.35359116022099446	234	0.4090909090909091	194	0.2559366754617414	A	15.44	2.834829	0.50951	0.287108	0.287791	ENSG00000170876	ENST00000306077	T	0.35605	1.3	5.25	1.56	0.23342	.	0.056985	0.64402	D	0.000001	T	0.00012	0.0000	L	0.27053	0.805	0.25967	P	0.9825476	B	0.28208	0.203	B	0.31016	0.123	T	0.49283	-0.8956	9	0.24483	T	0.36	-17.9328	7.8742	0.29584	0.6614:0.0:0.3386:0.0	rs4685076;rs17856367;rs4685076	168	Q9BTV4	TMM43_HUMAN	N	168	ENSP00000303992:K168N	ENSP00000303992:K168N	K	+	3	2	TMEM43	14149428	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.905000	0.28504	0.298000	0.22638	0.482000	0.46254	AAA	A|0.701;T|0.299	0.299	strong		0.507	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334	
ARID4A	5926	hgsc.bcm.edu	37	14	58768333	58768333	+	Silent	SNP	C	C	T	rs45562837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:58768333C>T	ENST00000355431.3	+	3	415	c.42C>T	c.(40-42)acC>acT	p.T14T	ARID4A_ENST00000395168.3_Silent_p.T14T|ARID4A_ENST00000348476.3_Silent_p.T14T|ARID4A_ENST00000431317.2_Silent_p.T14T	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	14					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						CAGTGGGAACCGATGTCAGTG	0.453													C|||	230	0.0459265	0.0045	0.0461	5008	,	,		17442	0.005		0.0825	False		,,,				2504	0.1063				p.T14T		Atlas-SNP	.											ARID4A_ENST00000355431,colon,carcinoma,0,2	ARID4A	222	2	0			c.C42T						PASS	.	C	,,	83,4323	69.8+/-107.6	0,83,2120	82.0	78.0	80.0		42,42,42	-5.0	1.0	14	dbSNP_127	80	641,7959	164.6+/-216.9	19,603,3678	no	coding-synonymous,coding-synonymous,coding-synonymous	ARID4A	NM_002892.3,NM_023000.2,NM_023001.2	,,	19,686,5798	TT,TC,CC		7.4535,1.8838,5.5667	,,	14/1258,14/1204,14/1189	58768333	724,12282	2203	4300	6503	SO:0001819	synonymous_variant	5926	exon3			GGGAACCGATGTC	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.42C>T	14.37:g.58768333C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	117	63	0.538462	NM_002892	Q15991|Q15992|Q15993	Silent	SNP	ENST00000355431.3	37	CCDS9732.1																																																																																			C|0.947;T|0.053	0.053	strong		0.453	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
CPAMD8	27151	hgsc.bcm.edu	37	19	17111297	17111297	+	Missense_Mutation	SNP	A	A	G	rs4808551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17111297A>G	ENST00000443236.1	-	10	966	c.935T>C	c.(934-936)aTg>aCg	p.M312T	CPAMD8_ENST00000388925.4_Missense_Mutation_p.M265T	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	265						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CATGTTGATCATTAAGGCACC	0.522													-|||	3748	0.748403	0.8253	0.7824	5008	,	,		17345	0.6845		0.832	False		,,,				2504	0.6002				p.M312T		Atlas-SNP	.											.	CPAMD8	192	.	0			c.T935C						PASS	.	G	THR/MET	3223,647		1330,563,42	50.0	53.0	52.0		935	-2.0	0.0	19	dbSNP_111	52	6731,1521		2741,1249,136	yes	missense	CPAMD8	NM_015692.2	81	4071,1812,178	GG,GA,AA		18.4319,16.7183,17.8848	benign	312/1933	17111297	9954,2168	1935	4126	6061	SO:0001583	missense	27151	exon10			TTGATCATTAAGG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.935T>C	19.37:g.17111297A>G	ENSP00000402505:p.Met312Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	1621|1621	0.7422161172161172|0.7422161172161172	375|375	0.7621951219512195|0.7621951219512195	281|281	0.7762430939226519|0.7762430939226519	355|355	0.6206293706293706|0.6206293706293706	610|610	0.8047493403693932|0.8047493403693932	-|-	0.001|0.001	-3.651325|-3.651325	0.00006|0.00006	0.832817|0.832817	0.815681|0.815681	ENSG00000160111|ENSG00000160111	ENST00000291440;ENST00000388925|ENST00000443236	T;T|.	0.44482|.	0.92;0.94|.	2.55|2.55	-2.0|-2.0	0.07433|0.07433	.|.	0.644034|.	0.13560|.	N|.	0.378831|.	T|.	0.00012|.	0.0000|.	N|N	0.00275|0.00275	-1.725|-1.725	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|.	0.28808|.	-1.0032|.	9|.	0.06891|.	T|.	0.86|.	.|.	9.7566|9.7566	0.40506|0.40506	0.4724:0.0:0.5276:0.0|0.4724:0.0:0.5276:0.0	rs4808551;rs4808551|rs4808551;rs4808551	265|.	Q8IZJ3|.	CPMD8_HUMAN|.	T|R	312;265|323	ENSP00000291440:M312T;ENSP00000373577:M265T|.	ENSP00000291440:M312T|.	M|X	-|-	2|1	0|0	CPAMD8|CPAMD8	16972297|16972297	0.606000|0.606000	0.26949|0.26949	0.009000|0.009000	0.14445|0.14445	0.001000|0.001000	0.01503|0.01503	0.738000|0.738000	0.26158|0.26158	-0.520000|-0.520000	0.06435|0.06435	-2.912000|-2.912000	0.00091|0.00091	ATG|TGA	A|0.229;G|0.771	0.771	strong		0.522	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
ITLN1	55600	hgsc.bcm.edu	37	1	160851826	160851826	+	Missense_Mutation	SNP	A	A	T	rs2274907	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:160851826A>T	ENST00000326245.3	-	4	441	c.326T>A	c.(325-327)gTc>gAc	p.V109D	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	109	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		V -> D (in dbSNP:rs2274907). {ECO:0000269|PubMed:11313366}.		positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			CTCTGGGTAGACTGCTTTGCT	0.617													T|||	2911	0.58127	0.3275	0.696	5008	,	,		17183	0.6935		0.6779	False		,,,				2504	0.6278				p.V109D		Atlas-SNP	.											.	ITLN1	45	.	0			c.T326A						PASS	.	T	ASP/VAL	1660,2746	658.0+/-400.3	308,1044,851	160.0	136.0	144.0		326	4.2	0.7	1	dbSNP_100	144	5864,2736	437.0+/-358.5	2024,1816,460	no	missense	ITLN1	NM_017625.2	152	2332,2860,1311	TT,TA,AA		31.814,37.6759,42.1498	benign	109/314	160851826	7524,5482	2203	4300	6503	SO:0001583	missense	55600	exon4			GGGTAGACTGCTT	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.326T>A	1.37:g.160851826A>T	ENSP00000323587:p.Val109Asp	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	333	209	0.627628	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Missense_Mutation	SNP	ENST00000326245.3	37	CCDS1211.1	1331	0.6094322344322345	168	0.34146341463414637	240	0.6629834254143646	411	0.7185314685314685	512	0.6754617414248021	T	2.672	-0.277429	0.05679	0.376759	0.68186	ENSG00000179914	ENST00000326245	T	0.10573	2.86	4.17	4.17	0.49024	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.262450	0.30483	N	0.009522	T	0.00412	0.0013	N	0.00027	-2.655	0.40004	P	0.024792999999999954	B	0.02656	0.0	B	0.01281	0.0	T	0.41680	-0.9495	9	0.06757	T	0.87	-13.7648	8.262	0.31790	0.1778:0.0:0.0:0.8222	rs2274907;rs52805845;rs59910824;rs2274907	109	Q8WWA0	ITLN1_HUMAN	D	109	ENSP00000323587:V109D	ENSP00000323587:V109D	V	-	2	0	ITLN1	159118450	0.805000	0.28982	0.685000	0.30070	0.979000	0.70002	1.547000	0.36190	0.638000	0.30545	-0.257000	0.10917	GTC	A|0.411;N|0.001	.	strong		0.617	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
BPI	671	hgsc.bcm.edu	37	20	36932676	36932676	+	Silent	SNP	G	G	C	rs1341024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:36932676G>C	ENST00000262865.4	+	1	152	c.63G>C	c.(61-63)ctG>ctC	p.L21L	CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	21					defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				TGATGGTGCTGGTCGCCATAG	0.627													G|||	2177	0.434704	0.1619	0.5274	5008	,	,		16176	0.5823		0.5447	False		,,,				2504	0.4724				p.L21L		Atlas-SNP	.											.	BPI	67	.	0			c.G63C						PASS	.	G		979,3427	356.6+/-313.6	109,761,1333	72.0	64.0	67.0		63	1.8	1.0	20	dbSNP_88	67	4614,3986	586.2+/-392.0	1241,2132,927	yes	coding-synonymous	BPI	NM_001725.2		1350,2893,2260	CC,CG,GG		46.3488,22.2197,43.0032		21/488	36932676	5593,7413	2203	4300	6503	SO:0001819	synonymous_variant	671	exon1			GGTGCTGGTCGCC	J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"""BPI fold containing"""	1095	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 1"""	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.63G>C	20.37:g.36932676G>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Silent	SNP	ENST00000262865.4	37	CCDS13303.1																																																																																			G|0.549;C|0.451	0.451	strong		0.627	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	
DNAJC2	27000	hgsc.bcm.edu	37	7	102953544	102953544	+	Silent	SNP	T	T	C	rs61749913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:102953544T>C	ENST00000379263.3	-	16	1891	c.1641A>G	c.(1639-1641)ccA>ccG	p.P547P	PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Silent_p.P494P|PMPCB_ENST00000249269.4_3'UTR	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	547					'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						AGTCTGTATATGGACCTGATT	0.368													T|||	73	0.0145767	0.0023	0.0187	5008	,	,		17966	0.0		0.0249	False		,,,				2504	0.0327				p.P547P		Atlas-SNP	.											.	DNAJC2	46	.	0			c.A1641G						PASS	.	T	,,	20,3604		0,20,1792	148.0	135.0	139.0		1482,,1641	0.3	1.0	7	dbSNP_129	139	293,7857		6,281,3788	no	coding-synonymous,utr-3,coding-synonymous	PMPCB,DNAJC2	NM_001129887.1,NM_004279.2,NM_014377.1	,,	6,301,5580	CC,CT,TT		3.5951,0.5519,2.6584	,,	494/569,,547/622	102953544	313,11461	1812	4075	5887	SO:0001819	synonymous_variant	27000	exon16			TGTATATGGACCT	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"""Heat shock proteins / DNAJ (HSP40)"""	13192	protein-coding gene	gene with protein product		605502	"""zuotin related factor 1"""	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1641A>G	7.37:g.102953544T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	54	0.586957	NM_014377	A4VCI0|Q9BVX1	Silent	SNP	ENST00000379263.3	37	CCDS43628.1																																																																																			T|0.982;C|0.018	0.018	strong		0.368	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1		
WLS	79971	hgsc.bcm.edu	37	1	68624878	68624878	+	Silent	SNP	C	C	T	rs3748705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:68624878C>T	ENST00000262348.4	-	3	685	c.432G>A	c.(430-432)gcG>gcA	p.A144A	WLS_ENST00000370976.3_Silent_p.A53A|GNG12-AS1_ENST00000420587.1_RNA|WLS_ENST00000354777.2_Silent_p.A142A|WLS_ENST00000540432.1_Silent_p.A144A|GNG12-AS1_ENST00000413628.1_RNA	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	144	Interacts with Wnt proteins. {ECO:0000250}.				anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						ACTCAGCAAACGCGTCATCAC	0.468													C|||	1751	0.349641	0.2368	0.4524	5008	,	,		19034	0.4127		0.3648	False		,,,				2504	0.3487				p.A144A		Atlas-SNP	.											.	WLS	97	.	0			c.G432A						PASS	.	C	,,	1114,3292	401.3+/-331.9	170,774,1259	161.0	130.0	141.0		426,159,432	2.0	0.0	1	dbSNP_107	141	2961,5639	460.9+/-365.3	524,1913,1863	no	coding-synonymous,coding-synonymous,coding-synonymous	WLS	NM_001002292.3,NM_001193334.1,NM_024911.6	,,	694,2687,3122	TT,TC,CC		34.4302,25.2837,31.3317	,,	142/544,53/451,144/542	68624878	4075,8931	2203	4300	6503	SO:0001819	synonymous_variant	79971	exon3			AGCAAACGCGTCA	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"""wntless homolog"""	611514	"""chromosome 1 open reading frame 139"", ""G protein-coupled receptor 177"", ""wntless homolog (Drosophila)"""	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.432G>A	1.37:g.68624878C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	88	30	0.340909	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Silent	SNP	ENST00000262348.4	37	CCDS642.1	811	0.37133699633699635	131	0.266260162601626	172	0.47513812154696133	238	0.4160839160839161	270	0.3562005277044855	C	0.224	-1.026590	0.02045	0.252837	0.344302	ENSG00000116729	ENST00000534713	.	.	.	5.94	1.98	0.26296	.	.	.	.	.	T	0.30039	0.0752	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.09185	-1.0686	3	.	.	.	-3.2332	8.3848	0.32494	0.0:0.6047:0.2134:0.1818	rs3748705;rs17845107;rs17857898;rs52813654;rs59688613;rs3748705	.	.	.	H	47	.	.	R	-	2	0	WLS	68397466	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	0.049000	0.14099	-0.074000	0.12820	-0.810000	0.03169	CGT	C|0.664;T|0.336	0.336	strong		0.468	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911	
ZNF813	126017	hgsc.bcm.edu	37	19	53990002	53990002	+	Silent	SNP	G	G	A	rs12974996	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53990002G>A	ENST00000396403.4	+	3	260	c.132G>A	c.(130-132)ctG>ctA	p.L44L	ZNF813_ENST00000396421.4_Silent_p.L44L	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	44	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		ATAGGAACCTGGTCTCCCTGG	0.483																																					p.L44L		Atlas-SNP	.											.	ZNF813	81	.	0			c.G132A						PASS	.						60.0	66.0	64.0					19																	53990002		2193	4255	6448	SO:0001819	synonymous_variant	126017	exon3			GAACCTGGTCTCC	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.132G>A	19.37:g.53990002G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			G|0.500;A|0.500	0.500	strong		0.483	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
F13A1	2162	hgsc.bcm.edu	37	6	6222382	6222382	+	Silent	SNP	T	T	G	rs5981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:6222382T>G	ENST00000264870.3	-	8	1261	c.996A>C	c.(994-996)ccA>ccC	p.P332P		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	332					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	CAATTCTTGCTGGTATTCCAA	0.398													T|||	468	0.0934505	0.0522	0.121	5008	,	,		22099	0.006		0.1839	False		,,,				2504	0.1268				p.P332P		Atlas-SNP	.											.	F13A1	135	.	0			c.A996C						PASS	.	T		349,4057	180.5+/-208.7	16,317,1870	109.0	94.0	99.0		996	-1.2	1.0	6	dbSNP_52	99	1704,6896	311.2+/-310.2	179,1346,2775	no	coding-synonymous	F13A1	NM_000129.3		195,1663,4645	GG,GT,TT		19.814,7.921,15.785		332/733	6222382	2053,10953	2203	4300	6503	SO:0001819	synonymous_variant	2162	exon8			TCTTGCTGGTATT	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.996A>C	6.37:g.6222382T>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	175	79	0.451429	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Silent	SNP	ENST00000264870.3	37	CCDS4496.1	224	0.10256410256410256	26	0.052845528455284556	47	0.1298342541436464	3	0.005244755244755245	148	0.19525065963060687	T	10.86	1.470107	0.26423	0.07921	0.19814	ENSG00000124491	ENST00000445223	.	.	.	5.76	-1.18	0.09617	.	.	.	.	.	T	0.13457	0.0326	.	.	.	0.09310	P	0.9999999999984768	.	.	.	.	.	.	T	0.23655	-1.0182	3	.	.	.	.	4.8011	0.13298	0.3692:0.1769:0.0:0.454	rs5981;rs17310756;rs5981	.	.	.	P	49	.	.	Q	-	2	0	F13A1	6167381	0.896000	0.30565	0.996000	0.52242	0.998000	0.95712	-0.022000	0.12480	0.100000	0.17581	0.533000	0.62120	CAG	T|0.868;G|0.132	0.132	strong		0.398	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
ACPP	55	hgsc.bcm.edu	37	3	132075554	132075554	+	Silent	SNP	T	T	C	rs3181784	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:132075554T>C	ENST00000336375.5	+	10	1083	c.993T>C	c.(991-993)taT>taC	p.Y331Y	ACPP_ENST00000351273.7_Silent_p.Y331Y|ACPP_ENST00000475741.1_Silent_p.Y298Y	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	331					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)	p.Y331Y(2)		NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						AGATGTACTATCGGAATGAGA	0.537													T|||	1520	0.303514	0.3245	0.3761	5008	,	,		16201	0.0804		0.3767	False		,,,				2504	0.3783				p.Y331Y		Atlas-SNP	.											ACPP_ENST00000351273,NS,carcinoma,0,4	ACPP	118	4	2	Substitution - coding silent(2)	prostate(2)	c.T993C						scavenged	.	T	,	1430,2976	465.5+/-354.2	235,960,1008	138.0	127.0	131.0		993,993	-4.3	0.9	3	dbSNP_105	131	3304,5296	494.5+/-373.8	634,2036,1630	no	coding-synonymous,coding-synonymous	ACPP	NM_001099.4,NM_001134194.1	,	869,2996,2638	CC,CT,TT		38.4186,32.4557,36.3986	,	331/387,331/419	132075554	4734,8272	2203	4300	6503	SO:0001819	synonymous_variant	55	exon10			GTACTATCGGAAT		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.993T>C	3.37:g.132075554T>C		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Silent	SNP	ENST00000336375.5	37	CCDS3073.1	616	0.28205128205128205	156	0.3170731707317073	141	0.38950276243093923	38	0.06643356643356643	281	0.370712401055409	T	9.892	1.204508	0.22205	0.324557	0.384186	ENSG00000014257	ENST00000507647	.	.	.	5.67	-4.32	0.03688	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999822262	.	.	.	.	.	.	T	0.25813	-1.0121	3	.	.	.	.	12.3643	0.55221	0.0:0.5521:0.0:0.4479	rs3181784;rs17182933;rs17408313	.	.	.	T	16	.	.	I	+	2	0	ACPP	133558244	0.994000	0.37717	0.936000	0.37596	0.939000	0.58152	0.006000	0.13152	-1.077000	0.03121	-0.408000	0.06270	ATC	T|0.657;C|0.343	0.343	strong		0.537	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099	
FAT2	2196	hgsc.bcm.edu	37	5	150943085	150943085	+	Silent	SNP	G	G	A	rs2304054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150943085G>A	ENST00000261800.5	-	2	3387	c.3375C>T	c.(3373-3375)atC>atT	p.I1125I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1125	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCGTAACCTCGATGTAGACTT	0.542													A|||	2060	0.411342	0.4092	0.451	5008	,	,		20232	0.3591		0.4901	False		,,,				2504	0.3589				p.I1125I		Atlas-SNP	.											.	FAT2	465	.	0			c.C3375T						PASS	.	A		1851,2555	634.1+/-396.1	380,1091,732	110.0	96.0	101.0		3375	-4.6	0.9	5	dbSNP_100	101	4498,4102	561.7+/-387.8	1183,2132,985	yes	coding-synonymous	FAT2	NM_001447.2		1563,3223,1717	AA,AG,GG		47.6977,42.0109,48.8159		1125/4350	150943085	6349,6657	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon2			AACCTCGATGTAG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3375C>T	5.37:g.150943085G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	195	67	0.34359	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.540;A|0.460	0.460	strong		0.542	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
IPO4	79711	hgsc.bcm.edu	37	14	24654489	24654489	+	Silent	SNP	T	T	C	rs2025258	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24654489T>C	ENST00000354464.6	-	14	1484	c.1308A>G	c.(1306-1308)gtA>gtG	p.V436V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	436					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		GCAGTGGCATTACCTCCCTTG	0.577													C|||	2312	0.461661	0.3782	0.2939	5008	,	,		19134	0.7897		0.339	False		,,,				2504	0.4816				p.V436V		Atlas-SNP	.											.	IPO4	74	.	0			c.A1308G						PASS	.	C		1560,2650		286,988,831	73.0	75.0	75.0		1308	5.1	1.0	14	dbSNP_94	75	2895,5573		485,1925,1824	no	coding-synonymous	IPO4	NM_024658.3		771,2913,2655	CC,CT,TT		34.1875,37.0546,35.1396		436/1082	24654489	4455,8223	2105	4234	6339	SO:0001819	synonymous_variant	79711	exon14			TGGCATTACCTCC	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1308A>G	14.37:g.24654489T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	175	80	0.457143	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																			T|0.551;C|0.448	0.448	strong		0.577	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
AMER3	205147	hgsc.bcm.edu	37	2	131520178	131520178	+	Missense_Mutation	SNP	C	C	G	rs77687733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:131520178C>G	ENST00000423981.1	+	2	643	c.533C>G	c.(532-534)gCg>gGg	p.A178G	AMER3_ENST00000321420.4_Missense_Mutation_p.A178G	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	178					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										GCCTCGCTGGCGGCCGAGGGG	0.642													C|||	628	0.125399	0.0083	0.2839	5008	,	,		17094	0.1379		0.1879	False		,,,				2504	0.0941				p.A178G		Atlas-SNP	.											FAM123C,caecum,carcinoma,0,1	.	.	1	0			c.C533G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	158,4246		2,154,2046	44.0	49.0	47.0		533,533,533,533	-4.1	0.0	2	dbSNP_131	47	1442,7146		136,1170,2988	yes	missense,missense,missense,missense	FAM123C	NM_001105193.1,NM_001105194.1,NM_001105195.1,NM_152698.2	60,60,60,60	138,1324,5034	GG,GC,CC		16.7909,3.5876,12.3153	benign,benign,benign,benign	178/862,178/862,178/862,178/862	131520178	1600,11392	2202	4294	6496	SO:0001583	missense	205147	exon2			CGCTGGCGGCCGA	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.533C>G	2.37:g.131520178C>G	ENSP00000392700:p.Ala178Gly	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	42	40	0.952381	NM_152698	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	334	0.15293040293040294	4	0.008130081300813009	102	0.281767955801105	84	0.14685314685314685	144	0.18997361477572558	C	5.497	0.276733	0.10403	0.035876	0.167909	ENSG00000178171	ENST00000321420;ENST00000458606;ENST00000423981	T;T	0.47528	0.84;0.84	5.21	-4.14	0.03892	.	1.080390	0.07081	N	0.837120	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.43169	0.8	B	0.39904	0.313	T	0.07028	-1.0794	9	0.27785	T	0.31	.	4.3062	0.10947	0.5233:0.1686:0.0:0.3081	.	178	Q8N944	F123C_HUMAN	G	178	ENSP00000314914:A178G;ENSP00000392700:A178G	ENSP00000314914:A178G	A	+	2	0	FAM123C	131236648	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.164000	0.09983	-0.631000	0.05560	-0.310000	0.09108	GCG	C|0.866;G|0.134	0.134	strong		0.642	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
DRD3	1814	hgsc.bcm.edu	37	3	113890815	113890815	+	Missense_Mutation	SNP	C	C	T	rs6280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:113890815C>T	ENST00000460779.1	-	3	314	c.25G>A	c.(25-27)Ggc>Agc	p.G9S	DRD3_ENST00000467632.1_Missense_Mutation_p.G9S|DRD3_ENST00000383673.2_Missense_Mutation_p.G9S|DRD3_ENST00000295881.7_Missense_Mutation_p.G9S	NM_001282563.1	NP_001269492.1	P35462	DRD3_HUMAN	dopamine receptor D3	9			S -> G (associated with susceptibility to ETM1; gain of function; dbSNP:rs6280). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16641997, ECO:0000269|PubMed:16650084, ECO:0000269|PubMed:16809426, ECO:0000269|PubMed:9034004, ECO:0000269|Ref.11}.		acid secretion (GO:0046717)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|arachidonic acid secretion (GO:0050482)|behavioral response to cocaine (GO:0048148)|cellular calcium ion homeostasis (GO:0006874)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric emptying (GO:0035483)|learning (GO:0007612)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of sodium:proton antiporter activity (GO:0032416)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of mitosis (GO:0045840)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of cAMP metabolic process (GO:0030814)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|regulation of dopamine secretion (GO:0014059)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of lipid metabolic process (GO:0019216)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of multicellular organism growth (GO:0040014)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to morphine (GO:0043278)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)	36					Amisulpride(DB06288)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Domperidone(DB01184)|Dopamine(DB00988)|Haloperidol(DB00502)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pimozide(DB01100)|Pramipexole(DB00413)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sulpiride(DB00391)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TTCAGGTGGCCACTCAGCTGG	0.567													C|||	2572	0.513578	0.1815	0.5735	5008	,	,		16211	0.6935		0.664	False		,,,				2504	0.5798				p.G9S		Atlas-SNP	.											.	DRD3	76	.	0			c.G25A	GRCh37	CM033372	DRD3	M	rs6280	PASS	.	C	SER/GLY,SER/GLY	1216,3188		177,862,1163	27.0	24.0	25.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	25,25	-1.5	0.0	3	dbSNP_52	25	5723,2873		1899,1925,474	yes	missense,missense	DRD3	NM_000796.3,NM_033663.3	56,56	2076,2787,1637	TT,TC,CC		33.4225,27.6113,46.6231	benign,benign	9/401,9/368	113890815	6939,6061	2202	4298	6500	SO:0001583	missense	1814	exon2			GGTGGCCACTCAG		CCDS2978.1, CCDS33829.1	3q13.3	2012-08-08			ENSG00000151577	ENSG00000151577		"""GPCR / Class A : Dopamine receptors"""	3024	protein-coding gene	gene with protein product		126451				1916765	Standard	XM_005247171		Approved		uc003ebc.1	P35462	OTTHUMG00000159334	ENST00000460779.1:c.25G>A	3.37:g.113890815C>T	ENSP00000419402:p.Gly9Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_033663	A1A4V5|Q4VBM8	Missense_Mutation	SNP	ENST00000460779.1	37	CCDS2978.1	1198	0.5485347985347986	89	0.18089430894308944	222	0.6132596685082873	392	0.6853146853146853	495	0.6530343007915568	C	8.616	0.890253	0.17613	0.276113	0.665775	ENSG00000151577	ENST00000460779;ENST00000467632;ENST00000383673;ENST00000281274;ENST00000295881	T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.52	5.0	-1.48	0.08745	.	0.740864	0.13705	N	0.368541	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45071	-0.9286	8	0.15499	T	0.54	.	9.5709	0.39427	0.0:0.2823:0.0:0.7177	rs6280;rs324025;rs52792556;rs59703514;rs6280	9	E9PCM4	.	S	9	ENSP00000419402:G9S;ENSP00000420662:G9S;ENSP00000373169:G9S;ENSP00000295881:G9S	ENSP00000281274:G9S	G	-	1	0	DRD3	115373505	0.000000	0.05858	0.026000	0.17262	0.766000	0.43426	-0.099000	0.11007	-0.171000	0.10797	-0.812000	0.03155	GGC	C|0.492;T|0.508	0.508	strong		0.567	DRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354699.1	NM_000796.3	
E2F7	144455	hgsc.bcm.edu	37	12	77419341	77419341	+	Missense_Mutation	SNP	A	A	T	rs310831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:77419341A>T	ENST00000322886.7	-	12	2797	c.2562T>A	c.(2560-2562)caT>caA	p.H854Q	E2F7_ENST00000416496.2_Intron	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	854			H -> Q (in dbSNP:rs310831).		chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						GCCTCACCTGATGTAATTTTA	0.493													A|||	211	0.0421326	0.0045	0.0677	5008	,	,		19370	0.0		0.1392	False		,,,				2504	0.0184				p.H854Q		Atlas-SNP	.											.	E2F7	201	.	0			c.T2562A						PASS	.	A	GLN/HIS	104,4302	79.9+/-118.3	2,100,2101	145.0	131.0	136.0		2562	-11.8	0.0	12	dbSNP_79	136	1050,7550	222.6+/-259.6	67,916,3317	yes	missense	E2F7	NM_203394.2	24	69,1016,5418	TT,TA,AA		12.2093,2.3604,8.8728	benign	854/912	77419341	1154,11852	2203	4300	6503	SO:0001583	missense	144455	exon12			CACCTGATGTAAT	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.2562T>A	12.37:g.77419341A>T	ENSP00000323246:p.His854Gln	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	146	0.06684981684981685	3	0.006097560975609756	27	0.07458563535911603	0	0.0	116	0.15303430079155672	A	8.626	0.892520	0.17613	0.023604	0.122093	ENSG00000165891	ENST00000322886;ENST00000339887	T	0.11385	2.78	5.88	-11.8	0.00035	.	0.930262	0.09048	N	0.856273	T	0.00012	0.0000	N	0.04203	-0.255	0.26286	P	0.9782084	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	9	0.10377	T	0.69	-2.5349	8.9135	0.35568	0.0848:0.5631:0.091:0.2612	rs310831;rs17759722;rs52796286;rs310831	854	Q96AV8	E2F7_HUMAN	Q	854;325	ENSP00000323246:H854Q	ENSP00000323246:H854Q	H	-	3	2	E2F7	75943472	0.009000	0.17119	0.012000	0.15200	0.697000	0.40408	-1.807000	0.01734	-1.729000	0.01364	-0.472000	0.04984	CAT	A|0.918;T|0.082	0.082	strong		0.493	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
FHOD3	80206	hgsc.bcm.edu	37	18	34289118	34289118	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:34289118G>T	ENST00000359247.4	+	14	1721	c.1721G>T	c.(1720-1722)gGg>gTg	p.G574V	FHOD3_ENST00000590592.1_Missense_Mutation_p.G766V|FHOD3_ENST00000257209.4_Missense_Mutation_p.G591V|FHOD3_ENST00000591635.1_Intron|FHOD3_ENST00000587493.1_3'UTR|FHOD3_ENST00000445677.1_Missense_Mutation_p.G553V	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	574					actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GCAGGGGCGGGGCAGGTTGCT	0.572																																					p.G591V		Atlas-SNP	.											FHOD3,NS,carcinoma,+1,1	FHOD3	210	1	0			c.G1772T						PASS	.						69.0	86.0	80.0					18																	34289118		2203	4300	6503	SO:0001583	missense	80206	exon15			GGGCGGGGCAGGT	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1721G>T	18.37:g.34289118G>T	ENSP00000352186:p.Gly574Val	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	225	89	0.395556	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	14.69	2.609383	0.46527	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.19105	2.2;2.17;2.17	5.84	-2.56	0.06268	.	0.594819	0.18286	N	0.145873	T	0.12860	0.0312	L	0.34521	1.04	0.20489	N	0.999893	B;B;B;B	0.23735	0.078;0.09;0.078;0.047	B;B;B;B	0.23419	0.036;0.046;0.022;0.036	T	0.17379	-1.0371	10	0.49607	T	0.09	.	7.3434	0.26650	0.5464:0.1225:0.3311:0.0	.	553;574;591;766	Q2V2M9-2;Q2V2M9;Q2V2M9-3;E5F5Q0	.;FHOD3_HUMAN;.;.	V	591;574;553	ENSP00000257209:G591V;ENSP00000352186:G574V;ENSP00000411430:G553V	ENSP00000257209:G591V	G	+	2	0	FHOD3	32543116	0.966000	0.33281	0.000000	0.03702	0.001000	0.01503	1.014000	0.29950	-0.327000	0.08551	-1.202000	0.01658	GGG	.	.	none		0.572	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
HCAR1	27198	hgsc.bcm.edu	37	12	123214372	123214372	+	Missense_Mutation	SNP	G	G	A	rs61742326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123214372G>A	ENST00000436083.2	-	1	1018	c.515C>T	c.(514-516)tCg>tTg	p.S172L	HCAR1_ENST00000356987.2_Missense_Mutation_p.S172L|HCAR1_ENST00000432564.1_Missense_Mutation_p.S172L			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	172					response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						GCCATTGGCCGACTCCATGAT	0.532													G|||	12	0.00239617	0.0	0.0072	5008	,	,		20664	0.001		0.006	False		,,,				2504	0.0				p.S172L		Atlas-SNP	.											.	HCAR1	21	.	0			c.C515T						PASS	.	G	LEU/SER	5,4401	9.9+/-24.2	0,5,2198	56.0	57.0	57.0		515	5.5	1.0	12	dbSNP_129	57	31,8569	21.0+/-64.5	0,31,4269	yes	missense	HCAR1	NM_032554.3	145	0,36,6467	AA,AG,GG		0.3605,0.1135,0.2768	benign	172/347	123214372	36,12970	2203	4300	6503	SO:0001583	missense	27198	exon1			TTGGCCGACTCCA	AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	4532	protein-coding gene	gene with protein product	"""lactate receptor 1"""	606923	"""G protein-coupled receptor 104"", ""G protein-coupled receptor 81"""	GPR104, GPR81		11574155, 19047060, 18952058, 21454438	Standard	NM_032554		Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000436083.2:c.515C>T	12.37:g.123214372G>A	ENSP00000409980:p.Ser172Leu	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_032554	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	37	CCDS9236.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	12.54	1.968654	0.34754	0.001135	0.003605	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.28255	1.62;1.62;1.62	5.52	5.52	0.82312	GPCR, rhodopsin-like superfamily (1);	0.194005	0.34802	N	0.003663	T	0.14570	0.0352	L	0.33710	1.025	0.33582	D	0.599988	B	0.32829	0.386	B	0.25884	0.064	T	0.23762	-1.0179	10	0.28530	T	0.3	-8.6437	10.379	0.44099	0.089:0.0:0.911:0.0	.	172	Q9BXC0	HCAR1_HUMAN	L	172	ENSP00000349478:S172L;ENSP00000389255:S172L;ENSP00000409980:S172L	ENSP00000349478:S172L	S	-	2	0	HCAR1	121780325	0.143000	0.22626	0.952000	0.39060	0.774000	0.43823	1.785000	0.38684	2.577000	0.86979	0.655000	0.94253	TCG	G|0.996;A|0.004	0.004	strong		0.532	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1		
PIK3R5	23533	hgsc.bcm.edu	37	17	8792093	8792093	+	Silent	SNP	G	G	A	rs16957702	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8792093G>A	ENST00000447110.1	-	10	1135	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D	PIK3R5_ENST00000581552.1_Silent_p.D337D|PIK3R5_ENST00000584803.1_Silent_p.D337D	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	337				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						CACAGTGCCCGTCAGTTTCCA	0.612													G|||	1017	0.203075	0.2995	0.2839	5008	,	,		18474	0.001		0.2843	False		,,,				2504	0.1401				p.D337D	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.C1011T						PASS	.	G	,	1302,3104	437.8+/-345.1	204,894,1105	106.0	102.0	103.0		1011,1011	-10.5	0.0	17	dbSNP_123	103	2694,5906	430.6+/-356.6	418,1858,2024	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	622,2752,3129	AA,AG,GG		31.3256,29.5506,30.7243	,	337/881,337/881	8792093	3996,9010	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			GTGCCCGTCAGTT	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.1011C>T	17.37:g.8792093G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			G|0.734;A|0.266	0.266	strong		0.612	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
SUSD1	64420	hgsc.bcm.edu	37	9	114804173	114804173	+	Silent	SNP	G	G	A	rs3849117	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:114804173G>A	ENST00000374270.3	-	16	2389	c.2217C>T	c.(2215-2217)ctC>ctT	p.L739L	SUSD1_ENST00000374263.3_3'UTR|SUSD1_ENST00000374264.2_3'UTR	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	739						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGAGGAATGTGAGAATGATCA	0.522													G|||	343	0.0684904	0.0053	0.0346	5008	,	,		22479	0.0625		0.0815	False		,,,				2504	0.1708				p.L739L		Atlas-SNP	.											.	SUSD1	51	.	0			c.C2217T						PASS	.	G		68,4338	61.7+/-98.7	1,66,2136	174.0	153.0	160.0		2217	-5.2	0.0	9	dbSNP_108	160	708,7892	174.5+/-224.7	28,652,3620	no	coding-synonymous	SUSD1	NM_022486.3		29,718,5756	AA,AG,GG		8.2326,1.5433,5.9665		739/748	114804173	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	64420	exon16			GAATGTGAGAATG	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.2217C>T	9.37:g.114804173G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Silent	SNP	ENST00000374270.3	37	CCDS6783.1																																																																																			G|0.943;A|0.057	0.057	strong		0.522	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486	
HELZ2	85441	hgsc.bcm.edu	37	20	62200576	62200576	+	Missense_Mutation	SNP	G	G	A	rs6090457	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62200576G>A	ENST00000467148.1	-	4	1082	c.1013C>T	c.(1012-1014)tCa>tTa	p.S338L	HELZ2_ENST00000479540.1_5'Flank|HELZ2_ENST00000427522.2_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	338					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GTTGGTTGGTGAGATGGGGCC	0.652													G|||	1096	0.21885	0.0091	0.0951	5008	,	,		15531	0.5298		0.1948	False		,,,				2504	0.2945				p.S338L		Atlas-SNP	.											.	.	.	.	0			c.C1013T						PASS	.	G	LEU/SER	203,4197		6,191,2003	34.0	34.0	34.0		1013	4.5	0.0	20	dbSNP_114	34	1626,6974		165,1296,2839	yes	missense	PRIC285	NM_001037335.2	145	171,1487,4842	AA,AG,GG		18.907,4.6136,14.0692	probably-damaging	338/2650	62200576	1829,11171	2200	4300	6500	SO:0001583	missense	85441	exon5			GTTGGTGAGATGG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.1013C>T	20.37:g.62200576G>A	ENSP00000417401:p.Ser338Leu	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	449	0.20558608058608058	6	0.012195121951219513	38	0.10497237569060773	277	0.48426573426573427	128	0.16886543535620052	G	9.400	1.077747	0.20227	0.046136	0.18907	ENSG00000130589	ENST00000467148	T	0.24350	1.86	4.5	4.5	0.54988	.	0.264588	0.35466	N	0.003191	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.30763	0.294	B	0.27887	0.084	T	0.47674	-0.9099	9	0.66056	D	0.02	-21.7885	17.1945	0.86888	0.0:0.0:1.0:0.0	rs6090457	338	Q9BYK8	PR285_HUMAN	L	338	ENSP00000417401:S338L	ENSP00000417401:S338L	S	-	2	0	RP4-697K14.7	61671020	0.992000	0.36948	0.005000	0.12908	0.002000	0.02628	3.690000	0.54713	2.068000	0.61886	0.563000	0.77884	TCA	G|0.840;A|0.160	0.160	strong		0.652	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
MKI67	4288	hgsc.bcm.edu	37	10	129907489	129907489	+	Missense_Mutation	SNP	G	G	A	rs2853344	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:129907489G>A	ENST00000368654.3	-	13	2990	c.2615C>T	c.(2614-2616)gCa>gTa	p.A872V	MKI67_ENST00000484853.1_5'Flank|MKI67_ENST00000368653.3_Missense_Mutation_p.A512V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	872			A -> V (in dbSNP:rs2853344). {ECO:0000269|PubMed:8227122}.		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGACCTGTTTGCAGTGGATAC	0.413													G|||	191	0.038139	0.0008	0.0605	5008	,	,		19589	0.0		0.0944	False		,,,				2504	0.0542				p.A872V		Atlas-SNP	.											.	MKI67	363	.	0			c.C2615T						PASS	.	G	VAL/ALA,VAL/ALA	82,4324	72.0+/-110.0	1,80,2122	226.0	214.0	218.0		1535,2615	-0.8	0.0	10	dbSNP_100	218	843,7757	193.5+/-239.2	46,751,3503	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	64,64	47,831,5625	AA,AG,GG		9.8023,1.8611,7.1121	benign,benign	512/2897,872/3257	129907489	925,12081	2203	4300	6503	SO:0001583	missense	4288	exon13			CTGTTTGCAGTGG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.2615C>T	10.37:g.129907489G>A	ENSP00000357643:p.Ala872Val	Somatic	353	0	0		WXS	Illumina HiSeq	Phase_I	378	195	0.515873	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	93	0.042582417582417584	2	0.0040650406504065045	19	0.052486187845303865	1	0.0017482517482517483	71	0.09366754617414248	G	0.014	-1.571386	0.00895	0.018611	0.098023	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01323	5.07;5.01	3.78	-0.808	0.10868	.	2.181040	0.02551	N	0.095640	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.46414	-0.9193	9	0.10902	T	0.67	.	4.3704	0.11244	0.3515:0.0:0.4909:0.1576	rs2853344;rs52814817;rs60437053;rs2853344	871;512;872	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	872;512;871	ENSP00000357643:A872V;ENSP00000357642:A512V	ENSP00000357642:A512V	A	-	2	0	MKI67	129797479	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.308000	0.19314	-0.602000	0.05775	-1.119000	0.02030	GCA	G|0.941;A|0.059	0.059	strong		0.413	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
APOA4	337	hgsc.bcm.edu	37	11	116693871	116693871	+	Missense_Mutation	SNP	C	C	T	rs12721041	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:116693871C>T	ENST00000357780.3	-	1	151	c.37G>A	c.(37-39)Gtg>Atg	p.V13M		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	13			V -> M (in allele APOA-IV*1D). {ECO:0000269|PubMed:1349197, ECO:0000269|PubMed:15108119}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		GCGACAGCCACCAGGGCCAGG	0.582													C|||	15	0.00299521	0.0	0.0014	5008	,	,		19224	0.0		0.0129	False		,,,				2504	0.001				p.V13M		Atlas-SNP	.											.	APOA4	51	.	0			c.G37A						PASS	.	C	MET/VAL	12,4390	21.2+/-45.6	0,12,2189	138.0	133.0	135.0		37	3.4	1.0	11	dbSNP_126	135	144,8440	71.0+/-133.6	1,142,4149	yes	missense	APOA4	NM_000482.3	21	1,154,6338	TT,TC,CC		1.6775,0.2726,1.2013	benign	13/397	116693871	156,12830	2201	4292	6493	SO:0001583	missense	337	exon1			CAGCCACCAGGGC		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.37G>A	11.37:g.116693871C>T	ENSP00000350425:p.Val13Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	143	77	0.538462	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	37	CCDS31681.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	13.60	2.286795	0.40494	0.002726	0.016775	ENSG00000110244	ENST00000357780	T	0.77098	-1.07	4.33	3.39	0.38822	.	0.512987	0.17527	N	0.171020	T	0.69672	0.3137	M	0.83012	2.62	0.22489	N	0.999052	B	0.29301	0.241	B	0.38880	0.284	T	0.72043	-0.4409	10	0.72032	D	0.01	-28.2212	10.1918	0.43030	0.0:0.798:0.202:0.0	rs12721041;rs45558133	13	P06727	APOA4_HUMAN	M	13	ENSP00000350425:V13M	ENSP00000350425:V13M	V	-	1	0	APOA4	116199081	0.999000	0.42202	1.000000	0.80357	0.774000	0.43823	0.411000	0.21115	1.383000	0.46405	0.655000	0.94253	GTG	C|0.990;T|0.010	0.010	strong		0.582	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
FREM1	158326	hgsc.bcm.edu	37	9	14776140	14776140	+	Missense_Mutation	SNP	C	C	T	rs10961700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:14776140C>T	ENST00000380880.3	-	25	5287	c.4504G>A	c.(4504-4506)Gtg>Atg	p.V1502M	FREM1_ENST00000486223.1_5'Flank|FREM1_ENST00000422223.2_Missense_Mutation_p.V1502M|FREM1_ENST00000380881.4_Missense_Mutation_p.V1503M|FREM1_ENST00000380894.1_Missense_Mutation_p.V38M			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1502			V -> M (in dbSNP:rs10961700).		cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GCTCTGTCCACAGTCTCCAGT	0.582													C|||	408	0.0814696	0.0144	0.062	5008	,	,		20251	0.0625		0.1541	False		,,,				2504	0.1309				p.V1502M		Atlas-SNP	.											FREM1,right_upper_lobe,carcinoma,+2,1	FREM1	261	1	0			c.G4504A						PASS	.	C	MET/VAL,MET/VAL	151,3895		4,143,1876	66.0	74.0	71.0		112,4504	2.7	0.6	9	dbSNP_120	71	1324,7032		103,1118,2957	yes	missense,missense	FREM1	NM_001177704.1,NM_144966.5	21,21	107,1261,4833	TT,TC,CC		15.8449,3.7321,11.8932	benign,benign	38/716,1502/2180	14776140	1475,10927	2023	4178	6201	SO:0001583	missense	158326	exon26			TGTCCACAGTCTC	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.4504G>A	9.37:g.14776140C>T	ENSP00000370262:p.Val1502Met	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	135	54	0.4	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	172	0.07875457875457875	4	0.008130081300813009	26	0.0718232044198895	30	0.05244755244755245	112	0.14775725593667546	C	14.36	2.511555	0.44660	0.037321	0.158449	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380894;ENST00000380880	T;T;T;T	0.57107	0.42;0.42;2.13;0.42	6.05	2.73	0.32206	.	0.459334	0.24497	N	0.038016	T	0.00241	0.0007	M	0.73430	2.235	0.28660	P	0.9061846	B;B	0.34181	0.06;0.44	B;B	0.26770	0.064;0.073	T	0.11108	-1.0601	9	0.56958	D	0.05	-4.0978	10.658	0.45686	0.0:0.7495:0.1133:0.1373	rs10961700;rs52808713;rs56806470;rs10961700	1502;38	Q5H8C1;B7ZBX4	FREM1_HUMAN;.	M	1503;1502;38;1502	ENSP00000370263:V1503M;ENSP00000412940:V1502M;ENSP00000370278:V38M;ENSP00000370262:V1502M	ENSP00000370262:V1502M	V	-	1	0	FREM1	14766140	0.875000	0.30112	0.598000	0.28837	0.821000	0.46438	1.808000	0.38912	0.857000	0.35407	0.650000	0.86243	GTG	C|0.917;T|0.083	0.083	strong		0.582	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
EPHA8	2046	hgsc.bcm.edu	37	1	22902772	22902772	+	Silent	SNP	C	C	T	rs56218493	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22902772C>T	ENST00000166244.3	+	3	294	c.222C>T	c.(220-222)aaC>aaT	p.N74N	EPHA8_ENST00000374644.4_Silent_p.N74N|EPHA8_ENST00000538803.1_Silent_p.N74N	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	74	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGGTTTGCAACGTCATGAGCC	0.607													C|||	514	0.102636	0.0681	0.0821	5008	,	,		18435	0.0516		0.1014	False		,,,				2504	0.2178				p.N74N		Atlas-SNP	.											.	EPHA8	221	.	0			c.C222T						PASS	.	C	,	348,4058	181.2+/-209.3	20,308,1875	103.0	99.0	100.0		222,222	1.5	1.0	1	dbSNP_129	100	783,7817	185.6+/-233.3	42,699,3559	no	coding-synonymous,coding-synonymous	EPHA8	NM_001006943.1,NM_020526.3	,	62,1007,5434	TT,TC,CC		9.1047,7.8983,8.696	,	74/496,74/1006	22902772	1131,11875	2203	4300	6503	SO:0001819	synonymous_variant	2046	exon3			TTGCAACGTCATG	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.222C>T	1.37:g.22902772C>T		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	212	114	0.537736	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																			C|0.911;T|0.089	0.089	strong		0.607	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
HAGHL	84264	hgsc.bcm.edu	37	16	778024	778024	+	Silent	SNP	T	T	C	rs1406814	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:778024T>C	ENST00000341413.4	+	3	446	c.165T>C	c.(163-165)caT>caC	p.H55H	HAGHL_ENST00000549114.1_Silent_p.H55H|HAGHL_ENST00000564537.1_Silent_p.H55H|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000561546.1_Silent_p.H55H|HAGHL_ENST00000389703.3_Silent_p.H55H|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000564545.1_Intron			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	55							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				CCACCCACCATCACTGGTGAG	0.721													t|||	2574	0.513978	0.5862	0.4928	5008	,	,		8072	0.7579		0.2425	False		,,,				2504	0.4591				p.H55H	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											HAGHL,NS,carcinoma,0,1	HAGHL	18	1	0			c.T165C						PASS	.			2208,2150		571,1066,542	22.0	29.0	27.0		165	-1.6	1.0	16	dbSNP_88	27	1792,6782		199,1394,2694	no	coding-synonymous	HAGHL	NM_032304.2		770,2460,3236	CC,CT,TT		20.9004,49.3346,30.931		55/283	778024	4000,8932	2179	4287	6466	SO:0001819	synonymous_variant	84264	exon2			CCACCATCACTGG	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.165T>C	16.37:g.778024T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37																																																																																				T|0.616;C|0.384	0.384	strong		0.721	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
FRMPD2	143162	hgsc.bcm.edu	37	10	49431171	49431171	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:49431171C>T	ENST00000374201.3	-	11	1613	c.1311G>A	c.(1309-1311)ctG>ctA	p.L437L	FRMPD2_ENST00000305531.3_Silent_p.L413L|FRMPD2_ENST00000407470.4_Silent_p.L406L	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	437	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CTCACTGGAGCAGCCCATAGT	0.473																																					p.L437L		Atlas-SNP	.											.	FRMPD2	157	.	0			c.G1311A						PASS	.						85.0	82.0	83.0					10																	49431171		2203	4300	6503	SO:0001819	synonymous_variant	143162	exon11			CTGGAGCAGCCCA	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.1311G>A	10.37:g.49431171C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	51	0.607143	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Silent	SNP	ENST00000374201.3	37	CCDS31195.1																																																																																			.	.	none		0.473	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
NUCB1	4924	hgsc.bcm.edu	37	19	49407660	49407660	+	Silent	SNP	G	G	A	rs1058483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49407660G>A	ENST00000405315.4	+	3	526	c.192G>A	c.(190-192)acG>acA	p.T64T	NUCB1_ENST00000407032.1_Silent_p.T64T|NUCB1_ENST00000263273.5_Silent_p.T64T|NUCB1_ENST00000485798.1_Intron	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	64						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		TACTGGAGACGGATGGGCATT	0.627													g|||	274	0.0547125	0.0076	0.062	5008	,	,		13827	0.001		0.1441	False		,,,				2504	0.0767				p.T64T		Atlas-SNP	.											NUCB1,NS,carcinoma,+1,1	NUCB1	44	1	0			c.G192A						PASS	.			135,4271	95.7+/-134.4	5,125,2073	90.0	67.0	75.0		192	-8.5	0.2	19	dbSNP_86	75	1442,7158	276.4+/-292.3	112,1218,2970	no	coding-synonymous	NUCB1	NM_006184.5		117,1343,5043	AA,AG,GG		16.7674,3.064,12.1252		64/462	49407660	1577,11429	2203	4300	6503	SO:0001819	synonymous_variant	4924	exon3			GGAGACGGATGGG	BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"""EF-hand domain containing"""	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.192G>A	19.37:g.49407660G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_006184	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Silent	SNP	ENST00000405315.4	37	CCDS12740.1	140	0.0641025641025641	7	0.014227642276422764	25	0.06906077348066299	1	0.0017482517482517483	107	0.14116094986807387	g	0.400	-0.918842	0.02396	0.03064	0.167674	ENSG00000104805	ENST00000424608	.	.	.	4.27	-8.54	0.00912	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.999999382115	.	.	.	.	.	.	T	0.11227	-1.0596	3	.	.	.	.	8.5909	0.33686	0.2339:0.0:0.5512:0.2149	rs1058483;rs3199107;rs17272721;rs1058483	.	.	.	Q	64	.	.	R	+	2	0	NUCB1	54099472	0.000000	0.05858	0.239000	0.24122	0.026000	0.11368	-6.299000	0.00071	-1.883000	0.01120	-0.849000	0.03036	CGG	G|0.903;A|0.097	0.097	strong		0.627	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184	
MYH11	4629	hgsc.bcm.edu	37	16	15808876	15808876	+	Missense_Mutation	SNP	C	C	G	rs113964173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15808876C>G	ENST00000300036.5	-	40	5785	c.5676G>C	c.(5674-5676)gaG>gaC	p.E1892D	NDE1_ENST00000396355.1_Intron|MYH11_ENST00000396324.3_Missense_Mutation_p.E1899D|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000576790.2_Missense_Mutation_p.E1892D|MYH11_ENST00000452625.2_Missense_Mutation_p.E1899D|NDE1_ENST00000342673.5_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1892					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGCGCTGGGACTCCTCCTCTG	0.642			T	CBFB	AML								C|||	17	0.00339457	0.0015	0.0029	5008	,	,		13850	0.0		0.0109	False		,,,				2504	0.002				p.E1899D		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G5697C						PASS	.	C	ASP/GLU,ASP/GLU,,ASP/GLU,,ASP/GLU	7,4387	12.9+/-30.5	0,7,2190	128.0	121.0	123.0		5697,5697,,5676,,5676	1.1	1.0	16	dbSNP_132	123	61,8539	37.4+/-92.8	0,61,4239	yes	missense,missense,intron,missense,intron,missense	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	45,45,,45,,45	0,68,6429	GG,GC,CC		0.7093,0.1593,0.5233	possibly-damaging,possibly-damaging,,possibly-damaging,,possibly-damaging	1899/1946,1899/1980,,1892/1973,,1892/1939	15808876	68,12926	2197	4300	6497	SO:0001583	missense	4629	exon41			CTGGGACTCCTCC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5676G>C	16.37:g.15808876C>G	ENSP00000300036:p.Glu1892Asp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	19.31	3.802956	0.70682	0.001593	0.007093	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	4.76	1.09	0.20402	Myosin tail (1);	0.000000	0.85682	D	0.000000	T	0.81992	0.4940	M	0.91140	3.18	0.58432	D	0.999998	P;P;P;P;P	0.46784	0.884;0.884;0.884;0.884;0.884	P;P;P;P;P	0.55011	0.766;0.766;0.766;0.766;0.766	D	0.84056	0.0372	10	0.72032	D	0.01	.	9.1943	0.37217	0.0:0.6481:0.0:0.3519	.	1899;1892;1899;1892;1899	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	D	1892;1892;1899;1899;1899	ENSP00000300036:E1892D;ENSP00000345136:E1892D;ENSP00000379616:E1899D;ENSP00000407821:E1899D	ENSP00000300036:E1892D	E	-	3	2	MYH11	15716377	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.567000	0.45956	0.401000	0.25424	0.455000	0.32223	GAG	C|0.993;G|0.007	0.007	strong		0.642	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549584	32549584	+	Silent	SNP	C	C	T	rs200078051|rs35616319|rs200088269		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549584C>T	ENST00000360004.5	-	3	507	c.402G>A	c.(400-402)aaG>aaA	p.K134K		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	134	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GGGGCTGGGTCTTTGAAGGAT	0.507										Multiple Myeloma(14;0.17)																											p.K134K		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G402A						PASS	.						64.0	80.0	74.0					6																	32549584		1510	2709	4219	SO:0001819	synonymous_variant	3123	exon3			CTGGGTCTTTGAA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.402G>A	6.37:g.32549584C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	368	36	0.0978261	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
LRRCC1	85444	hgsc.bcm.edu	37	8	86057707	86057707	+	Silent	SNP	A	A	G	rs62525428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:86057707A>G	ENST00000360375.3	+	19	3209	c.3060A>G	c.(3058-3060)caA>caG	p.Q1020Q	LRRCC1_ENST00000414626.2_Silent_p.Q1000Q	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	1020					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AAATTAAGCAACTTGCTTTTG	0.299													A|||	286	0.0571086	0.0083	0.0389	5008	,	,		12994	0.0159		0.0905	False		,,,				2504	0.1442				p.Q1020Q		Atlas-SNP	.											.	LRRCC1	212	.	0			c.A3060G						PASS	.	A		71,3547		0,71,1738	55.0	52.0	53.0		3060	4.0	1.0	8	dbSNP_129	53	898,7228		42,814,3207	no	coding-synonymous	LRRCC1	NM_033402.4		42,885,4945	GG,GA,AA		11.0509,1.9624,8.251		1020/1033	86057707	969,10775	1809	4063	5872	SO:0001819	synonymous_variant	85444	exon19			TAAGCAACTTGCT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.3060A>G	8.37:g.86057707A>G		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	237	113	0.476793	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Silent	SNP	ENST00000360375.3	37	CCDS43750.1																																																																																			A|0.926;G|0.074	0.074	strong		0.299	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
OSTF1	26578	hgsc.bcm.edu	37	9	77752510	77752510	+	Silent	SNP	C	C	T	rs2273769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:77752510C>T	ENST00000346234.6	+	8	615	c.465C>T	c.(463-465)atC>atT	p.I155I		NM_012383.4	NP_036515.4	Q92882	OSTF1_HUMAN	osteoclast stimulating factor 1	155					ossification (GO:0001503)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)				endometrium(1)|skin(1)	2						ATGCAGATATCGTCCAGTTGC	0.398													C|||	663	0.132388	0.0144	0.2248	5008	,	,		18956	0.13		0.1829	False		,,,				2504	0.1769				p.I155I		Atlas-SNP	.											OSTF1,colon,carcinoma,+2,1	OSTF1	12	1	0			c.C465T						PASS	.	C		144,4262	100.3+/-138.9	1,142,2060	175.0	149.0	158.0		465	3.0	1.0	9	dbSNP_100	158	1468,7132	280.3+/-294.4	124,1220,2956	no	coding-synonymous	OSTF1	NM_012383.4		125,1362,5016	TT,TC,CC		17.0698,3.2683,12.3943		155/215	77752510	1612,11394	2203	4300	6503	SO:0001819	synonymous_variant	26578	exon8			AGATATCGTCCAG	U63717	CCDS6651.1	9q13-q21.2	2013-01-10			ENSG00000134996	ENSG00000134996		"""Ankyrin repeat domain containing"""	8510	protein-coding gene	gene with protein product		610180				10092216	Standard	NM_012383		Approved	SH3P2, OSF, bA235O14.1	uc004ajv.4	Q92882	OTTHUMG00000020033	ENST00000346234.6:c.465C>T	9.37:g.77752510C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	173	75	0.433526	NM_012383	Q5W126|Q96IJ4	Silent	SNP	ENST00000346234.6	37	CCDS6651.1																																																																																			C|0.861;T|0.139	0.139	strong		0.398	OSTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052704.1	NM_012383	
HIVEP1	3096	hgsc.bcm.edu	37	6	12122174	12122174	+	Missense_Mutation	SNP	A	A	G	rs34746669|rs2228210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:12122174A>G	ENST00000379388.2	+	4	2478	c.2146A>G	c.(2146-2148)Acg>Gcg	p.T716A		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	716			T -> A (in dbSNP:rs2228210).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TCTTGTCACCACGTCAACACC	0.527													A|||	1043	0.208267	0.0204	0.245	5008	,	,		21328	0.2232		0.34	False		,,,				2504	0.2853				p.T716A		Atlas-SNP	.											.	HIVEP1	242	.	0			c.A2146G						PASS	.	A	ALA/THR	274,3896		10,254,1821	65.0	65.0	65.0		2146	-7.6	0.0	6	dbSNP_98	65	2940,5464		518,1904,1780	yes	missense	HIVEP1	NM_002114.2	58	528,2158,3601	GG,GA,AA		34.9833,6.5707,25.5607	benign	716/2719	12122174	3214,9360	2085	4202	6287	SO:0001583	missense	3096	exon4			GTCACCACGTCAA	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.2146A>G	6.37:g.12122174A>G	ENSP00000368698:p.Thr716Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	490	0.22435897435897437	15	0.03048780487804878	88	0.2430939226519337	134	0.23426573426573427	253	0.3337730870712401	A	8.900	0.956058	0.18507	0.065707	0.349833	ENSG00000095951	ENST00000379388	T	0.06849	3.25	5.81	-7.64	0.01286	.	0.486110	0.15530	N	0.257524	T	0.01029	0.0034	N	0.16368	0.405	0.38073	P	0.06356600000000001	B	0.10296	0.003	B	0.04013	0.001	T	0.47799	-0.9089	8	.	.	.	-2.3451	8.1908	0.31368	0.3201:0.3697:0.3102:0.0	rs2228210;rs3800501;rs17609169;rs60098115;rs2228210	716	P15822	ZEP1_HUMAN	A	716	ENSP00000368698:T716A	.	T	+	1	0	HIVEP1	12230160	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.339000	0.07832	-1.190000	0.02698	-1.077000	0.02231	ACG	A|0.754;C|0.002	.	strong		0.527	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
SLC2A11	66035	hgsc.bcm.edu	37	22	24224655	24224655	+	Missense_Mutation	SNP	G	G	A	rs9608213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:24224655G>A	ENST00000345044.6	+	7	963	c.695G>A	c.(694-696)cGg>cAg	p.R232Q	AP000350.10_ENST00000433835.3_Intron|SLC2A11_ENST00000467660.1_3'UTR|RN7SL268P_ENST00000491172.2_RNA|SLC2A11_ENST00000316185.8_Missense_Mutation_p.R235Q|SLC2A11_ENST00000398356.2_Missense_Mutation_p.R239Q			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	232			R -> Q (in dbSNP:rs9608213). {ECO:0000269|PubMed:11741323, ECO:0000269|PubMed:14702039}.		carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						GCACTACGGCGGCTCCGGGGC	0.706													g|||	1721	0.34365	0.1899	0.3689	5008	,	,		13898	0.3194		0.4076	False		,,,				2504	0.4928				p.R239Q		Atlas-SNP	.											.	SLC2A11	32	.	0			c.G716A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	713,2925		129,455,1235	3.0	4.0	3.0		695,704,716	-2.0	0.6	22	dbSNP_119	3	2666,4600		613,1440,1580	yes	missense,missense,missense	SLC2A11	NM_001024938.2,NM_001024939.2,NM_030807.3	43,43,43	742,1895,2815	AA,AG,GG		36.6914,19.5987,30.9886	possibly-damaging,possibly-damaging,possibly-damaging	232/497,235/500,239/504	24224655	3379,7525	1819	3633	5452	SO:0001583	missense	66035	exon8			TACGGCGGCTCCG	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.695G>A	22.37:g.24224655G>A	ENSP00000342542:p.Arg232Gln	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Missense_Mutation	SNP	ENST00000345044.6	37	CCDS46673.1	712|712	0.326007326007326|0.326007326007326	102|102	0.2073170731707317|0.2073170731707317	114|114	0.3149171270718232|0.3149171270718232	183|183	0.31993006993006995|0.31993006993006995	313|313	0.4129287598944591|0.4129287598944591	g|g	9.117|9.117	1.008112|1.008112	0.19199|0.19199	0.195987|0.195987	0.366914|0.366914	ENSG00000251357|ENSG00000133460	ENST00000502845|ENST00000345044;ENST00000398356;ENST00000398359;ENST00000407566;ENST00000316185	.|T;T;T	.|0.75477	.|-0.94;-0.94;-0.94	3.92|3.92	-2.05|-2.05	0.07321|0.07321	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.356230	.|0.28332	.|N	.|0.015729	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.63208|0.63208	1.945|1.945	0.35342|0.35342	P|P	0.21342700000000003|0.21342700000000003	.|B;B;B;B;B	.|0.23937	.|0.04;0.068;0.094;0.047;0.083	.|B;B;B;B;B	.|0.24394	.|0.004;0.006;0.053;0.011;0.016	T|T	0.34179|0.34179	-0.9839|-0.9839	4|8	.|.	.|.	.|.	.|.	9.941|9.941	0.41580|0.41580	0.3218:0.0:0.6782:0.0|0.3218:0.0:0.6782:0.0	rs9608213|rs9608213	.|239;235;232;239;239	.|E7ENI4;Q9BYW1-3;Q9BYW1;E9PH55;Q6P4C1	.|.;.;GTR11_HUMAN;.;.	S|Q	4|232;239;239;239;235	.|ENSP00000342542:R232Q;ENSP00000381399:R239Q;ENSP00000326748:R235Q	.|.	G|R	+|+	1|2	0|0	AP000350.10|SLC2A11	22554655|22554655	0.274000|0.274000	0.24191|0.24191	0.617000|0.617000	0.29091|0.29091	0.001000|0.001000	0.01503|0.01503	0.798000|0.798000	0.27014|0.27014	-0.175000|-0.175000	0.10725|0.10725	-1.188000|-1.188000	0.01700|0.01700	GGC|CGG	G|0.678;A|0.322	0.322	strong		0.706	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
PRKCB	5579	hgsc.bcm.edu	37	16	23847575	23847575	+	Silent	SNP	C	C	A	rs75964872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23847575C>A	ENST00000321728.7	+	1	254	c.79C>A	c.(79-81)Cgg>Agg	p.R27R	PRKCB_ENST00000303531.7_Silent_p.R27R|PRKCB_ENST00000498058.1_Silent_p.R27R	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	27					apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	AGGCGCCCTCCGGCAGAAGAA	0.672													C|||	1084	0.216454	0.3865	0.33	5008	,	,		8484	0.0565		0.1899	False		,,,				2504	0.0982				p.R27R		Atlas-SNP	.											PRKCB_ENST00000321728,NS,carcinoma,0,3	PRKCB	383	3	0			c.C79A						PASS	.	C	,	1603,2791	490.1+/-361.7	293,1017,887	69.0	61.0	64.0		79,79	0.6	1.0	16	dbSNP_131	64	1689,6911	307.6+/-308.5	170,1349,2781	no	coding-synonymous,coding-synonymous	PRKCB	NM_002738.6,NM_212535.2	,	463,2366,3668	AA,AC,CC		19.6395,36.4816,25.3348	,	27/674,27/672	23847575	3292,9702	2197	4300	6497	SO:0001819	synonymous_variant	5579	exon1			GCCCTCCGGCAGA	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.79C>A	16.37:g.23847575C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	48	0.533333	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			C|0.761;A|0.239	0.239	strong		0.672	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
NHSL2	340527	hgsc.bcm.edu	37	X	71363415	71363415	+	IGR	SNP	C	C	T	rs6624597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:71363415C>T	ENST00000373677.1	+	0	3978				NHSL2_ENST00000540800.1_Silent_p.P1223P			Q5HYW2	NHSL2_HUMAN	NHS-like 2											NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					CCGATAACCCCAGTACCTAAG	0.463													C|||	3498	0.926623	0.559	0.7378	3775	,	,		14619	0.7579		0.7604	False		,,,				2504	0.7342				p.P1223P		Atlas-SNP	.											.	NHSL2	148	.	0			c.C3669T						PASS	.	C		924,285		302,187,133,28,42	17.0	14.0	15.0		3669	1.7	0.8	X	dbSNP_116	15	2390,0		800,0,790,0,0	no	coding-synonymous	NHSL2	NM_001013627.2		1102,187,923,28,42	TT,TC,T,CC,C		0.0,23.5732,7.9189		1223/1226	71363415	3314,285	692	1590	2282	SO:0001628	intergenic_variant	340527	exon8			TAACCCCAGTACC			Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807		X.37:g.71363415C>T		Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001013627	B2RN94	Silent	SNP	ENST00000373677.1	37																																																																																				C|0.090;T|0.910	0.910	strong		0.463	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627	
NKAPL	222698	hgsc.bcm.edu	37	6	28228342	28228342	+	Missense_Mutation	SNP	A	A	G	rs1679709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28228342A>G	ENST00000343684.3	+	1	1245	c.1193A>G	c.(1192-1194)gAg>gGg	p.E398G	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	398			E -> G (in dbSNP:rs1679709). {ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						AAGACAAAAGAGAAAGATGAC	0.373													G|||	4257	0.85004	0.7458	0.8732	5008	,	,		18349	0.872		0.8837	False		,,,				2504	0.9172				p.E398G		Atlas-SNP	.											.	NKAPL	72	.	0			c.A1193G						PASS	.	G	GLY/GLU	3268,1138	401.9+/-332.2	1209,850,144	64.0	61.0	62.0		1193	4.6	1.0	6	dbSNP_89	62	7393,1207	243.1+/-272.8	3182,1029,89	yes	missense	NKAPL	NM_001007531.1	98	4391,1879,233	GG,GA,AA		14.0349,25.8284,18.0301	benign	398/403	28228342	10661,2345	2203	4300	6503	SO:0001583	missense	222698	exon1			CAAAAGAGAAAGA	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.1193A>G	6.37:g.28228342A>G	ENSP00000345716:p.Glu398Gly	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	1860	0.8516483516483516	381	0.774390243902439	317	0.8756906077348067	493	0.8618881118881119	669	0.8825857519788918	G	6.557	0.471002	0.12461	0.741716	0.859651	ENSG00000189134	ENST00000343684	T	0.13420	2.59	4.63	4.63	0.57726	.	0.000000	0.85682	N	0.000000	T	0.01320	0.0043	N	0.02539	-0.55	0.51233	P	8.399999999997299E-5	B	0.09022	0.002	B	0.01281	0.0	T	0.43360	-0.9396	9	0.02654	T	1	-8.7747	11.0692	0.47993	0.091:0.0:0.909:0.0	rs1679709;rs52790887;rs61104738;rs1679709	398	Q5M9Q1	NKAPL_HUMAN	G	398	ENSP00000345716:E398G	ENSP00000345716:E398G	E	+	2	0	NKAPL	28336321	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.244000	0.78228	1.322000	0.45245	-0.119000	0.15052	GAG	A|0.162;G|0.838	0.838	strong		0.373	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
ZNF812	729648	hgsc.bcm.edu	37	19	9800982	9800982	+	Silent	SNP	T	T	C	rs145446068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9800982T>C	ENST00000457674.2	-	5	1715	c.1197A>G	c.(1195-1197)ctA>ctG	p.L399L	ZNF812_ENST00000536819.1_5'UTR	NM_001199814.1	NP_001186743.1	P0C7V5	ZN812_HUMAN	zinc finger protein 812	399					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1						GTGAGGAATATAGAAATGCTT	0.403													.|||	36	0.0071885	0.0008	0.0014	5008	,	,		22777	0.0		0.0089	False		,,,				2504	0.0256				p.L399L		Atlas-SNP	.											.	ZNF812	27	.	0			c.A1197G						PASS	.																																			SO:0001819	synonymous_variant	729648	exon6			GGAATATAGAAAT		CCDS54215.1	19p13.2	2014-04-02			ENSG00000224689	ENSG00000224689		"""Zinc fingers, C2H2-type"", ""-"""	33242	protein-coding gene	gene with protein product							Standard	NM_001199814		Approved		uc021uop.1	P0C7V5	OTTHUMG00000167867	ENST00000457674.2:c.1197A>G	19.37:g.9800982T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_001199814		Silent	SNP	ENST00000457674.2	37	CCDS54215.1																																																																																			T|0.998;C|0.002	0.002	strong		0.403	ZNF812-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396726.1		
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331127	28331127	+	Missense_Mutation	SNP	A	A	G	rs13201752|rs371085669	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28331127A>G	ENST00000377255.3	+	5	895	c.598A>G	c.(598-600)Aaa>Gaa	p.K200E	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.K52E|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.K200E	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	200			K -> A (requires 2 nucleotide substitutions; dbSNP:rs13201752). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.|K -> E (in dbSNP:rs45505399). {ECO:0000269|PubMed:14702039}.|K -> T (in dbSNP:rs13201753).		autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						CAGAGAAGATAAAGTGGTAGC	0.542													G|||	1952	0.389776	0.5825	0.3213	5008	,	,		16796	0.2986		0.2843	False		,,,				2504	0.3804				p.K200E		Atlas-SNP	.											ZKSCAN3,NS,other,-2,1	ZKSCAN3	50	1	0			c.A598G						PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS	2170,2236		549,1072,582	97.0	83.0	88.0		598,154,598	-6.0	0.0	6	dbSNP_121	88	2549,6051		401,1747,2152	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	56,56,56	950,2819,2734	GG,GA,AA		29.6395,49.251,36.2833	benign,benign,benign	200/539,52/391,200/539	28331127	4719,8287	2203	4300	6503	SO:0001583	missense	80317	exon4			GAAGATAAAGTGG	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.598A>G	6.37:g.28331127A>G	ENSP00000366465:p.Lys200Glu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	122	48	0.393443	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	584	0.2673992673992674	201	0.40853658536585363	103	0.2845303867403315	128	0.22377622377622378	152	0.20052770448548812	.	0.001	-2.933332	0.00053	0.49251	0.296395	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.13901	2.55;2.55;2.55	2.99	-5.98	0.02220	.	.	.	.	.	T	0.01029	0.0034	N	0.08118	0	0.80722	P	0.0	B	0.21520	0.057	B	0.15870	0.014	T	0.37150	-0.9718	8	0.02654	T	1	.	9.4241	0.38570	0.37:0.1121:0.5179:0.0	rs45505399;rs58188640;rs61741931	200	Q9BRR0	ZKSC3_HUMAN	E	200;52;200	ENSP00000252211:K200E;ENSP00000341883:K52E;ENSP00000366465:K200E	ENSP00000252211:K200E	K	+	1	0	ZKSCAN3	28439106	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.587000	0.02108	-2.492000	0.00516	-2.444000	0.00210	AAA	A|0.648;G|0.352	0.352	alt		0.542	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
FAM214A	56204	hgsc.bcm.edu	37	15	52901638	52901638	+	Silent	SNP	T	T	C	rs3751614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:52901638T>C	ENST00000261844.7	-	6	1625	c.1473A>G	c.(1471-1473)caA>caG	p.Q491Q	FAM214A_ENST00000546305.2_Silent_p.Q498Q	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	491								p.Q491Q(1)									GCTCCAAGTGTTGAGCAATCC	0.428													T|||	2088	0.416933	0.2012	0.6095	5008	,	,		18046	0.1081		0.7445	False		,,,				2504	0.5532				p.Q491Q		Atlas-SNP	.											KIAA1370,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.A1473G						PASS	.	T		1282,2656		201,880,888	163.0	161.0	162.0		1473	-11.6	0.3	15	dbSNP_107	162	6062,2228		2225,1612,308	no	coding-synonymous	KIAA1370	NM_019600.2		2426,2492,1196	CC,CT,TT		26.8758,32.5546,39.9411		491/1077	52901638	7344,4884	1969	4145	6114	SO:0001819	synonymous_variant	56204	exon6			CAAGTGTTGAGCA	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.1473A>G	15.37:g.52901638T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			T|0.560;C|0.440	0.440	strong		0.428	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
LPA	4018	hgsc.bcm.edu	37	6	161026197	161026197	+	Silent	SNP	G	G	A	rs117174672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:161026197G>A	ENST00000316300.5	-	18	2870	c.2826C>T	c.(2824-2826)caC>caT	p.H942H	LPA_ENST00000447678.1_Silent_p.H942H			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3450	Kringle 9. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)	p.H942H(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GTCCATTTCCGTGGTAGCACT	0.463													G|||	164	0.0327476	0.0023	0.0231	5008	,	,		20112	0.0228		0.0447	False		,,,				2504	0.0787				p.H942H		Atlas-SNP	.											LPA,NS,carcinoma,0,1	LPA	237	1	1	Substitution - coding silent(1)	stomach(1)	c.C2826T						PASS	.	G		37,4367	36.8+/-68.6	1,35,2166	278.0	287.0	284.0		2826	-2.2	0.1	6	dbSNP_132	284	309,8291	108.4+/-169.1	6,297,3997	no	coding-synonymous	LPA	NM_005577.2		7,332,6163	AA,AG,GG		3.593,0.8401,2.6607		942/2041	161026197	346,12658	2202	4300	6502	SO:0001819	synonymous_variant	4018	exon19			ATTTCCGTGGTAG	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2826C>T	6.37:g.161026197G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																			G|0.971;A|0.029	0.029	strong		0.463	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
AP3B1	8546	hgsc.bcm.edu	37	5	77423965	77423965	+	Silent	SNP	A	A	C	rs115892142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:77423965A>C	ENST00000255194.6	-	17	2032	c.1857T>G	c.(1855-1857)ctT>ctG	p.L619L	AP3B1_ENST00000519295.1_Silent_p.L570L	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	619					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		ATAAGGTGCCAAGCTGGAAAT	0.373									Hermansky-Pudlak syndrome				A|||	5	0.000998403	0.0	0.0	5008	,	,		16956	0.0		0.005	False		,,,				2504	0.0				p.L619L		Atlas-SNP	.											.	AP3B1	94	.	0			c.T1857G						PASS	.	A		4,4402	4.2+/-10.8	0,4,2199	48.0	48.0	48.0		1857	3.5	1.0	5	dbSNP_132	48	22,8578	8.4+/-32.0	1,20,4279	no	coding-synonymous	AP3B1	NM_003664.3		1,24,6478	CC,CA,AA		0.2558,0.0908,0.1999		619/1095	77423965	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon17	Familial Cancer Database	HPS, HPS1-8	GGTGCCAAGCTGG	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1857T>G	5.37:g.77423965A>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.998;C|0.002	0.002	strong		0.373	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
MUC4	4585	hgsc.bcm.edu	37	3	195513519	195513519	+	Silent	SNP	A	A	T	rs201585392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513519A>T	ENST00000463781.3	-	2	5391	c.4932T>A	c.(4930-4932)ggT>ggA	p.G1644G	MUC4_ENST00000475231.1_Silent_p.G1644G|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.N1637_T1652delNASSLSTGHATPLHVT(2)|p.G1644G(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATA	0.587																																					p.G1644G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	3	Deletion - In frame(2)|Substitution - coding silent(1)	stomach(2)|endometrium(1)	c.T4932A						PASS	.						30.0	37.0	35.0					3																	195513519		690	1580	2270	SO:0001819	synonymous_variant	4585	exon2			GGCGTGACCTGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4932T>A	3.37:g.195513519A>T		Somatic	641	0	0		WXS	Illumina HiSeq	Phase_I	932	168	0.180258	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.964;T|0.036	0.036	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PFKL	5211	hgsc.bcm.edu	37	21	45732116	45732116	+	Silent	SNP	C	C	T	rs1057034	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45732116C>T	ENST00000349048.4	+	4	421	c.366C>T	c.(364-366)ctC>ctT	p.L122L	PFKL_ENST00000403390.1_Silent_p.L169L|PFKL_ENST00000496824.1_3'UTR	NM_002626.4	NP_002617.3	P17858	PFKAL_HUMAN	phosphofructokinase, liver	122	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of insulin secretion (GO:0046676)|protein homotetramerization (GO:0051289)|protein oligomerization (GO:0051259)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|fructose-6-phosphate binding (GO:0070095)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	23				Colorectal(79;0.0811)		ATGGCAGCCTCACAGGTGCCA	0.672													C|||	2296	0.458466	0.2852	0.5231	5008	,	,		14177	0.38		0.5755	False		,,,				2504	0.6074				p.L122L		Atlas-SNP	.											.	PFKL	65	.	0			c.C366T						PASS	.	C		1316,3064		194,928,1068	27.0	21.0	23.0		366	2.1	1.0	21	dbSNP_86	23	4925,3659		1428,2069,795	no	coding-synonymous	PFKL	NM_002626.4		1622,2997,1863	TT,TC,CC		42.6258,30.0457,48.141		122/781	45732116	6241,6723	2190	4292	6482	SO:0001819	synonymous_variant	5211	exon4			CAGCCTCACAGGT		CCDS33582.1	21q22.3	1992-12-17			ENSG00000141959	ENSG00000141959	2.7.1.11		8876	protein-coding gene	gene with protein product		171860					Standard	NR_024108		Approved		uc002zel.3	P17858	OTTHUMG00000086910	ENST00000349048.4:c.366C>T	21.37:g.45732116C>T		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	319	317	0.99373	NM_002626	Q96A64|Q96IH4|Q9BR91	Silent	SNP	ENST00000349048.4	37	CCDS33582.1																																																																																			C|0.555;T|0.445	0.445	strong		0.672	PFKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195805.1		
MYO3A	53904	hgsc.bcm.edu	37	10	26355906	26355906	+	Missense_Mutation	SNP	G	G	A	rs3824700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:26355906G>A	ENST00000265944.5	+	11	1122	c.956G>A	c.(955-957)cGt>cAt	p.R319H	MYO3A_ENST00000543632.1_Missense_Mutation_p.R319H	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	319			R -> H (in dbSNP:rs3824700). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CTCCACAGACGTGAACGTATT	0.363													A|||	1971	0.39357	0.3116	0.3473	5008	,	,		18040	0.2937		0.5527	False		,,,				2504	0.4765				p.R319H		Atlas-SNP	.											.	MYO3A	371	.	0			c.G956A						PASS	.	A	HIS/ARG	1621,2785	661.3+/-400.9	312,997,894	84.0	76.0	79.0		956	5.6	1.0	10	dbSNP_107	79	4731,3869	542.2+/-384.1	1331,2069,900	yes	missense	MYO3A	NM_017433.4	29	1643,3066,1794	AA,AG,GG		44.9884,36.7907,48.839	benign	319/1617	26355906	6352,6654	2203	4300	6503	SO:0001583	missense	53904	exon11			ACAGACGTGAACG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.956G>A	10.37:g.26355906G>A	ENSP00000265944:p.Arg319His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	872	0.3992673992673993	150	0.3048780487804878	124	0.3425414364640884	168	0.2937062937062937	430	0.5672823218997362	A	3.240	-0.155574	0.06544	0.367907	0.550116	ENSG00000095777	ENST00000265944;ENST00000543632	T;T	0.77098	-1.07;-0.87	5.56	5.56	0.83823	Protein kinase-like domain (1);	0.092877	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00061	-2.33	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45687	-0.9244	9	0.02654	T	1	.	6.7392	0.23426	0.7581:0.0:0.0757:0.1662	rs3824700;rs52789678;rs61430642;rs3824700	319;319	F5H0U9;Q8NEV4	.;MYO3A_HUMAN	H	319	ENSP00000265944:R319H;ENSP00000445909:R319H	ENSP00000265944:R319H	R	+	2	0	MYO3A	26395912	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	4.608000	0.61141	0.949000	0.37715	-0.269000	0.10298	CGT	G|0.559;A|0.441	0.441	strong		0.363	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
TMTC1	83857	hgsc.bcm.edu	37	12	29736480	29736480	+	Silent	SNP	A	A	G	rs2113879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:29736480A>G	ENST00000539277.1	-	8	1336	c.1278T>C	c.(1276-1278)caT>caC	p.H426H	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000256062.5_Silent_p.H318H|TMTC1_ENST00000552618.1_Silent_p.H488H|TMTC1_ENST00000381224.2_Silent_p.H380H|TMTC1_ENST00000551659.1_Silent_p.H488H	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	426						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TGCTCAGTCCATGCACAAAAA	0.502													A|||	1854	0.370208	0.5182	0.3112	5008	,	,		16546	0.4623		0.2376	False		,,,				2504	0.2536				p.H426H		Atlas-SNP	.											.	TMTC1	147	.	0			c.T1278C						PASS	.	A	,	2008,2398	560.3+/-380.4	454,1100,649	64.0	62.0	63.0		1278,954	-1.8	1.0	12	dbSNP_96	63	2060,6540	357.0+/-330.6	245,1570,2485	no	coding-synonymous,coding-synonymous	TMTC1	NM_001193451.1,NM_175861.3	,	699,2670,3134	GG,GA,AA		23.9535,45.5742,31.2779	,	426/883,318/775	29736480	4068,8938	2203	4300	6503	SO:0001819	synonymous_variant	83857	exon8			CAGTCCATGCACA		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.1278T>C	12.37:g.29736480A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	202	110	0.544554	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Silent	SNP	ENST00000539277.1	37	CCDS53772.1																																																																																			A|0.662;G|0.338	0.338	strong		0.502	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	
ZNF664	144348	hgsc.bcm.edu	37	12	124496864	124496864	+	Missense_Mutation	SNP	T	T	G	rs80197353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124496864T>G	ENST00000539644.1	+	6	2003	c.173T>G	c.(172-174)gTc>gGc	p.V58G	ZNF664_ENST00000392404.3_Missense_Mutation_p.V58G|ZNF664_ENST00000538932.2_Missense_Mutation_p.V58G|FAM101A_ENST00000545615.1_Intron|ZNF664_ENST00000337815.4_Missense_Mutation_p.V58G			Q8N3J9	ZN664_HUMAN	zinc finger protein 664	58					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(5)|lung(6)|skin(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.000239)|OV - Ovarian serous cystadenocarcinoma(86;0.000247)|all cancers(50;0.00155)|BRCA - Breast invasive adenocarcinoma(302;0.249)		GGAGAGAAGGTCTATAAATGT	0.373													T|||	255	0.0509185	0.0333	0.0447	5008	,	,		21967	0.0		0.0984	False		,,,				2504	0.0828				p.V58G		Atlas-SNP	.											.	ZNF664	27	.	0			c.T173G						PASS	.	T	GLY/VAL,,GLY/VAL	212,4194		0,212,1991	92.0	101.0	98.0		173,,173	3.2	1.0	12	dbSNP_131	98	827,7773		0,827,3473	yes	missense,intron,missense	ZNF664,ZNF664-FAM101A	NM_001204298.1,NM_001204299.1,NM_152437.2	109,,109	0,1039,5464	GG,GT,TT		9.6163,4.8116,7.9886	benign,,benign	58/262,,58/262	124496864	1039,11967	2203	4300	6503	SO:0001583	missense	144348	exon5			AGAAGGTCTATAA		CCDS9257.1	12q24.31	2013-05-10			ENSG00000179195	ENSG00000179195		"""Zinc fingers, C2H2-type"""	25406	protein-coding gene	gene with protein product			"""zinc finger protein 176"""	ZNF176		12477932	Standard	NM_001204298		Approved	ZFOC1, DKFZp761B128	uc001uga.3	Q8N3J9	OTTHUMG00000168596	ENST00000539644.1:c.173T>G	12.37:g.124496864T>G	ENSP00000441405:p.Val58Gly	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	223	78	0.349776	NM_152437	B3KP97|Q15914|Q3ZCQ7	Missense_Mutation	SNP	ENST00000539644.1	37	CCDS9257.1	107	0.04899267399267399	14	0.028455284552845527	18	0.049723756906077346	0	0.0	75	0.09894459102902374	T	15.37	2.814650	0.50527	0.048116	0.096163	ENSG00000179195	ENST00000539644;ENST00000392404;ENST00000538932;ENST00000337815	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.4	3.25	0.37280	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36628	N	0.002500	T	0.00384	0.0012	L	0.33668	1.02	0.54753	D	0.999987	P	0.40083	0.702	P	0.44623	0.455	T	0.28299	-1.0048	9	.	.	.	-24.1678	6.119	0.20142	0.0:0.1965:0.0:0.8035	.	58	Q8N3J9	ZN664_HUMAN	G	58	ENSP00000441405:V58G;ENSP00000376205:V58G;ENSP00000440645:V58G;ENSP00000337320:V58G	.	V	+	2	0	ZNF664	123062817	0.989000	0.36119	0.994000	0.49952	0.992000	0.81027	2.596000	0.46205	1.007000	0.39238	0.533000	0.62120	GTC	T|0.928;G|0.072	0.072	strong		0.373	ZNF664-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400365.1	NM_152437	
RTN3	10313	hgsc.bcm.edu	37	11	63449125	63449125	+	Missense_Mutation	SNP	C	C	A	rs11551944	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:63449125C>A	ENST00000377819.5	+	1	171	c.17C>A	c.(16-18)gCg>gAg	p.A6E	RTN3_ENST00000538995.1_3'UTR|RTN3_ENST00000537981.1_Missense_Mutation_p.A6E|RTN3_ENST00000339997.4_Missense_Mutation_p.A6E|RTN3_ENST00000356000.3_Missense_Mutation_p.A6E|RTN3_ENST00000354497.4_Missense_Mutation_p.A6E|RTN3_ENST00000341307.2_Missense_Mutation_p.A6E|RTN3_ENST00000540798.1_Missense_Mutation_p.A6E	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	6			A -> E (in dbSNP:rs11551944). {ECO:0000269|PubMed:15946766}.		apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						GAGCCGTCGGCGGCCACTCAG	0.687													C|||	380	0.0758786	0.0295	0.0648	5008	,	,		13038	0.003		0.1332	False		,,,				2504	0.1626				p.A6E		Atlas-SNP	.											RTN3_ENST00000356000,NS,carcinoma,0,3	RTN3	104	3	0			c.C17A						PASS	.	C	GLU/ALA,GLU/ALA,GLU/ALA,GLU/ALA	234,4126		8,218,1954	27.0	33.0	31.0		17,17,17,17	3.4	1.0	11	dbSNP_120	31	1271,7283		98,1075,3104	yes	missense,missense,missense,missense	RTN3	NM_006054.2,NM_201428.1,NM_201429.1,NM_201430.1	107,107,107,107	106,1293,5058	AA,AC,CC		14.8585,5.367,11.654	probably-damaging,probably-damaging,probably-damaging,probably-damaging	6/237,6/1014,6/256,6/242	63449125	1505,11409	2180	4277	6457	SO:0001583	missense	10313	exon1			CGTCGGCGGCCAC	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.17C>A	11.37:g.63449125C>A	ENSP00000367050:p.Ala6Glu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_201428	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	143	0.06547619047619048	15	0.03048780487804878	27	0.07458563535911603	1	0.0017482517482517483	100	0.13192612137203166	C	17.49	3.403311	0.62288	0.05367	0.148585	ENSG00000133318	ENST00000341307;ENST00000356000;ENST00000542238;ENST00000377819;ENST00000339997;ENST00000540798;ENST00000545432;ENST00000543552;ENST00000537981;ENST00000354497	T;T;T;T;T;T;T;T;T;T	0.60548	0.55;0.58;0.65;1.1;1.01;0.97;0.22;0.26;0.76;0.18	4.33	3.42	0.39159	.	0.599771	0.13805	N	0.361511	T	0.00524	0.0017	L	0.27053	0.805	0.45930	P	0.0012349999999999861	P;D;D;P;D;D;D	0.65815	0.856;0.992;0.987;0.613;0.995;0.992;0.995	B;P;P;B;D;P;D	0.69142	0.434;0.906;0.807;0.298;0.962;0.906;0.962	T	0.23404	-1.0189	9	0.87932	D	0	-2.6338	8.4535	0.32884	0.0:0.8889:0.0:0.1111	rs11551944;rs17249377;rs11551944	6;6;6;6;6;6;6	B7Z4M0;F5H774;O95197;O95197-5;O95197-3;O95197-2;O95197-4	.;.;RTN3_HUMAN;.;.;.;.	E	6	ENSP00000340903:A6E;ENSP00000348279:A6E;ENSP00000437971:A6E;ENSP00000367050:A6E;ENSP00000344106:A6E;ENSP00000442733:A6E;ENSP00000441614:A6E;ENSP00000442080:A6E;ENSP00000440874:A6E;ENSP00000346492:A6E	ENSP00000344106:A6E	A	+	2	0	RTN3	63205701	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	0.821000	0.27338	0.819000	0.34492	0.462000	0.41574	GCG	C|0.903;A|0.097	0.097	strong		0.687	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054	
ANKZF1	55139	hgsc.bcm.edu	37	2	220100553	220100553	+	Silent	SNP	C	C	A	rs150402081	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220100553C>A	ENST00000323348.5	+	12	2101	c.1927C>A	c.(1927-1929)Cga>Aga	p.R643R	ANKZF1_ENST00000409849.1_Silent_p.R433R|ANKZF1_ENST00000410034.3_Silent_p.R643R|GLB1L_ENST00000497855.1_5'Flank	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	643						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGAGCGTGAACGAGAAGAGCA	0.612													c|||	42	0.00838658	0.0023	0.0144	5008	,	,		19870	0.0		0.0278	False		,,,				2504	0.001				p.R643R		Atlas-SNP	.											.	ANKZF1	45	.	0			c.C1927A						PASS	.	C	,	27,4335		0,27,2154	102.0	118.0	113.0		1927,1927	5.4	1.0	2	dbSNP_134	113	279,8269		5,269,4000	no	coding-synonymous,coding-synonymous	ANKZF1	NM_001042410.1,NM_018089.2	,	5,296,6154	AA,AC,CC		3.2639,0.619,2.3703	,	643/727,643/727	220100553	306,12604	2181	4274	6455	SO:0001819	synonymous_variant	55139	exon12			CGTGAACGAGAAG	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"""Zinc fingers, C2H2-type"", ""Ankyrin repeat domain containing"""	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1927C>A	2.37:g.220100553C>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	199	99	0.497487	NM_001042410	Q9NVZ4	Silent	SNP	ENST00000323348.5	37	CCDS42821.1																																																																																			C|0.982;A|0.018	0.018	strong		0.612	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089	
TYRO3	7301	hgsc.bcm.edu	37	15	41857303	41857303	+	Silent	SNP	T	T	C	rs2277536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41857303T>C	ENST00000263798.3	+	6	971	c.747T>C	c.(745-747)gcT>gcC	p.A249A	TYRO3_ENST00000559066.1_Silent_p.A204A	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	249	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TGCCAGGTGCTGATGGCCGAG	0.592													T|||	1338	0.267173	0.1959	0.4063	5008	,	,		20524	0.1736		0.3082	False		,,,				2504	0.319				p.A249A		Atlas-SNP	.											.	TYRO3	169	.	0			c.T747C						PASS	.	T		890,3516		81,728,1394	94.0	84.0	88.0		747	-0.1	1.0	15	dbSNP_100	88	2455,6145		285,1885,2130	no	coding-synonymous	TYRO3	NM_006293.3		366,2613,3524	CC,CT,TT		28.5465,20.1997,25.7189		249/891	41857303	3345,9661	2203	4300	6503	SO:0001819	synonymous_variant	7301	exon6			AGGTGCTGATGGC	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.747T>C	15.37:g.41857303T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_006293	O14953|Q86VR3	Silent	SNP	ENST00000263798.3	37	CCDS10080.1																																																																																			T|0.736;C|0.264	0.264	strong		0.592	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		
OR5AS1	219447	hgsc.bcm.edu	37	11	55798259	55798259	+	Missense_Mutation	SNP	G	G	T	rs12224086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55798259G>T	ENST00000313555.1	+	1	365	c.365G>T	c.(364-366)cGc>cTc	p.R122L		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	122			R -> L (in dbSNP:rs12224086).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R122L(1)		endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					GCTTATGACCGCTATGCAGCC	0.453													G|||	519	0.103634	0.0477	0.0965	5008	,	,		20013	0.1458		0.1223	False		,,,				2504	0.1217				p.R122L		Atlas-SNP	.											OR5AS1,NS,carcinoma,+1,5	OR5AS1	121	5	1	Substitution - Missense(1)	stomach(1)	c.G365T						PASS	.	G	LEU/ARG	237,4165	139.2+/-174.8	9,219,1973	133.0	109.0	117.0		365	3.6	1.0	11	dbSNP_120	117	1019,7573	218.3+/-256.7	57,905,3334	yes	missense	OR5AS1	NM_001001921.1	102	66,1124,5307	TT,TG,GG		11.8599,5.3839,9.666	probably-damaging	122/325	55798259	1256,11738	2201	4296	6497	SO:0001583	missense	219447	exon1			ATGACCGCTATGC	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.365G>T	11.37:g.55798259G>T	ENSP00000324111:p.Arg122Leu	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	272	153	0.5625	NM_001001921	Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	37	CCDS31516.1	251	0.11492673992673992	29	0.05894308943089431	33	0.09116022099447514	88	0.15384615384615385	101	0.13324538258575197	G	15.37	2.812972	0.50527	0.053839	0.118599	ENSG00000181785	ENST00000313555	T	0.77358	-1.09	5.46	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.224065	0.22821	U	0.055229	T	0.02156	0.0067	M	0.93978	3.48	0.31274	P	0.691424	P	0.47762	0.9	P	0.45538	0.484	T	0.55477	-0.8135	9	0.72032	D	0.01	.	11.0053	0.47631	0.154:0.0:0.846:0.0	rs12224086;rs12224086	122	Q8N127	O5AS1_HUMAN	L	122	ENSP00000324111:R122L	ENSP00000324111:R122L	R	+	2	0	OR5AS1	55554835	0.991000	0.36638	0.997000	0.53966	0.134000	0.20937	6.174000	0.71943	0.680000	0.31366	-0.148000	0.13756	CGC	A|0.000;G|0.900;T|0.099	0.099	strong		0.453	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
PCDHA10	56139	hgsc.bcm.edu	37	5	140236950	140236950	+	Missense_Mutation	SNP	C	C	G	rs251362	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140236950C>G	ENST00000307360.5	+	1	1317	c.1317C>G	c.(1315-1317)agC>agG	p.S439R	PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.S439R|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	439	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> R (in dbSNP:rs251362). {ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGGCCAGCGTGTCTGTGG	0.682													.|||	2354	0.470048	0.3245	0.4582	5008	,	,		17119	0.4355		0.5288	False		,,,				2504	0.6503				p.S439R		Atlas-SNP	.											PCDHA10_ENST00000307360,rectum,carcinoma,0,2	PCDHA10	358	2	0			c.C1317G						PASS	.	C	,ARG/SER,,,,,,,,,,,ARG/SER,ARG/SER	1439,2955		285,869,1043	97.0	93.0	94.0		,1317,,,,,,,,,,,1317,1317	3.1	1.0	5	dbSNP_79	94	4670,3874		1455,1760,1057	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,110,,,,,,,,,,,110,110	1740,2629,2100	GG,GC,CC		45.3418,32.7492,47.2175	,,,,,,,,,,,,,	,439/949,,,,,,,,,,,439/845,439/686	140236950	6109,6829	2197	4272	6469	SO:0001583	missense	56139	exon1			GGCCAGCGTGTCT	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1317C>G	5.37:g.140236950C>G	ENSP00000304234:p.Ser439Arg	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	122	78	0.639344	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	1037	0.4748168498168498	183	0.3719512195121951	193	0.5331491712707183	261	0.4562937062937063	400	0.5277044854881267	C	10.30	1.312597	0.23908	0.327492	0.546582	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.51574	4.64;0.7	3.96	3.09	0.35607	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.41710	1.295	0.80722	P	0.0	B;B;B	0.28258	0.205;0.059;0.001	B;B;B	0.32090	0.14;0.128;0.024	T	0.45659	-0.9246	8	0.36615	T	0.2	.	1.6641	0.02798	0.1571:0.4772:0.1751:0.1907	rs251362;rs3733702;rs17844342;rs56831346	439;439;439	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	R	439	ENSP00000421030:S439R;ENSP00000304234:S439R	ENSP00000304234:S439R	S	+	3	2	PCDHA10	140217134	0.004000	0.15560	1.000000	0.80357	0.985000	0.73830	1.204000	0.32296	1.006000	0.39211	0.556000	0.70494	AGC	C|0.495;G|0.505	0.505	strong		0.682	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
NBPF14	25832	hgsc.bcm.edu	37	1	148010987	148010987	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:148010987T>C	ENST00000369219.1	-	14	1651	c.1635A>G	c.(1633-1635)tcA>tcG	p.S545S				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	545	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.S545S(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					CTGAAGGAGTTGAATAACATC	0.478																																					p.S545S		Atlas-SNP	.											NBPF14,NS,carcinoma,0,3	NBPF14	107	3	1	Substitution - coding silent(1)	kidney(1)	c.A1635G						scavenged	.						2.0	2.0	2.0					1																	148010987		627	1514	2141	SO:0001819	synonymous_variant	25832	exon14			AGGAGTTGAATAA	AK092351		1q21.1	2013-01-17			ENSG00000122497			"""neuroblastoma breakpoint family"""	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1635A>G	1.37:g.148010987T>C		Somatic	500	0	0		WXS	Illumina HiSeq	Phase_I	743	22	0.0296097	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Silent	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	-	0.755	-0.771349	0.02951	.	.	ENSG00000122497	ENST00000310701	.	.	.	.	.	.	.	.	.	.	.	T	0.08714	0.0216	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.36480	-0.9746	2	.	.	.	.	.	.	.	.	.	.	.	R	551	.	.	Q	-	2	0	NBPF14	146477611	0.914000	0.31030	0.004000	0.12327	0.003000	0.03518	-0.265000	0.08644	-0.568000	0.06038	-0.564000	0.04169	CAA	.	.	none		0.478	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383	
EIF4G1	1981	hgsc.bcm.edu	37	3	184037523	184037523	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:184037523C>T	ENST00000346169.2	+	7	742	c.471C>T	c.(469-471)ggC>ggT	p.G157G	EIF4G1_ENST00000319274.6_Silent_p.G157G|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000424196.1_Silent_p.G164G|EIF4G1_ENST00000435046.2_5'Flank|EIF4G1_ENST00000414031.1_Silent_p.G117G|EIF4G1_ENST00000441154.1_5'Flank|EIF4G1_ENST00000342981.4_Silent_p.G157G|EIF4G1_ENST00000427845.1_Silent_p.G70G|EIF4G1_ENST00000411531.1_Silent_p.G117G|EIF4G1_ENST00000382330.3_Silent_p.G164G|EIF4G1_ENST00000392537.2_Silent_p.G70G|EIF4G1_ENST00000352767.3_Silent_p.G164G|EIF4G1_ENST00000350481.5_5'UTR|EIF4G1_ENST00000434061.2_5'Flank	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	157					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TTCCCACTGGCGTGGCCCCCA	0.622																																					p.G164G		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C492T						PASS	.						28.0	24.0	26.0					3																	184037523		2203	4299	6502	SO:0001819	synonymous_variant	1981	exon8			CACTGGCGTGGCC	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.471C>T	3.37:g.184037523C>T		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	392	230	0.586735	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			.	.	none		0.622	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
GPATCH8	23131	hgsc.bcm.edu	37	17	42477385	42477385	+	Missense_Mutation	SNP	T	T	C	rs61744303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42477385T>C	ENST00000591680.1	-	8	2090	c.2060A>G	c.(2059-2061)cAc>cGc	p.H687R	GPATCH8_ENST00000434000.1_Missense_Mutation_p.H609R	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	687	Lys-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		TTTACGTTTGTGTTTGCTGGA	0.443													T|||	18	0.00359425	0.0	0.0058	5008	,	,		20906	0.0		0.0139	False		,,,				2504	0.0				p.H687R		Atlas-SNP	.											.	GPATCH8	114	.	0			c.A2060G						PASS	.	T	ARG/HIS	19,4387	26.2+/-53.5	0,19,2184	240.0	240.0	240.0		2060	5.1	1.0	17	dbSNP_129	240	130,8470	67.0+/-129.4	0,130,4170	yes	missense	GPATCH8	NM_001002909.2	29	0,149,6354	CC,CT,TT		1.5116,0.4312,1.1456	benign	687/1503	42477385	149,12857	2203	4300	6503	SO:0001583	missense	23131	exon8			CGTTTGTGTTTGC	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.2060A>G	17.37:g.42477385T>C	ENSP00000467556:p.His687Arg	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	153	63	0.411765	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	T	6.634	0.485507	0.12641	0.004312	0.015116	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.02258	4.37	5.11	5.11	0.69529	.	0.096415	0.64402	D	0.000001	T	0.00845	0.0028	N	0.17082	0.46	0.39216	D	0.963406	B	0.24920	0.114	B	0.24974	0.057	T	0.60047	-0.7339	10	0.16420	T	0.52	-16.2378	9.5574	0.39348	0.0:0.0782:0.0:0.9218	.	687	Q9UKJ3	GPTC8_HUMAN	R	687;609	ENSP00000395016:H609R	ENSP00000335486:H687R	H	-	2	0	GPATCH8	39832911	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.849000	0.48286	2.156000	0.67533	0.402000	0.26972	CAC	T|0.989;C|0.011	0.011	strong		0.443	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
CCDC108	255101	hgsc.bcm.edu	37	2	219893035	219893035	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219893035C>T	ENST00000341552.5	-	12	1822	c.1739G>A	c.(1738-1740)cGc>cAc	p.R580H	CCDC108_ENST00000441968.1_Missense_Mutation_p.R580H|CCDC108_ENST00000410037.1_Missense_Mutation_p.R515H|CCDC108_ENST00000453220.1_Missense_Mutation_p.R580H|CCDC108_ENST00000409865.3_Missense_Mutation_p.R569H	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	580						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGGTGTGTGCGGTACCAGGT	0.617																																					p.R580H		Atlas-SNP	.											CCDC108,colon,carcinoma,0,1	CCDC108	208	1	0			c.G1739A						scavenged	.						125.0	125.0	125.0					2																	219893035		2203	4300	6503	SO:0001583	missense	255101	exon12			TGTGTGCGGTACC	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.1739G>A	2.37:g.219893035C>T	ENSP00000340776:p.Arg580His	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	301	5	0.0166113	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	C	12.32	1.901162	0.33535	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220;ENST00000545086;ENST00000409865;ENST00000410037;ENST00000441164	T;T;T;T;T	0.11169	3.1;3.1;3.1;2.8;2.8	4.87	4.0	0.46444	.	0.000000	0.45361	D	0.000369	T	0.15132	0.0365	M	0.71581	2.175	0.80722	D	1	P;P;P	0.49185	0.866;0.866;0.92	B;B;B	0.40940	0.277;0.344;0.277	T	0.04242	-1.0966	10	0.54805	T	0.06	-30.8858	13.4595	0.61219	0.0:0.9243:0.0:0.0757	.	569;514;580	E9PG25;B4DYZ8;Q6ZU64	.;.;CC108_HUMAN	H	580;580;580;56;569;515;514	ENSP00000340776:R580H;ENSP00000413377:R580H;ENSP00000409117:R580H;ENSP00000386945:R569H;ENSP00000386258:R515H	ENSP00000340776:R580H	R	-	2	0	CCDC108	219601279	0.995000	0.38212	0.959000	0.39883	0.010000	0.07245	1.200000	0.32247	1.276000	0.44395	-0.137000	0.14449	CGC	.	.	none		0.617	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
LMF1	64788	hgsc.bcm.edu	37	16	1004605	1004605	+	Silent	SNP	A	A	G	rs12448005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1004605A>G	ENST00000262301.11	-	2	273	c.255T>C	c.(253-255)ctT>ctC	p.L85L	LMF1_ENST00000399843.2_Silent_p.L85L|LMF1_ENST00000543238.1_Intron|LMF1_ENST00000539379.1_Silent_p.L78L|LMF1_ENST00000568897.1_5'UTR	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	85					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				CTCTGCAGGGAAGCAGCCCCC	0.522													A|||	187	0.0373403	0.0166	0.062	5008	,	,		21830	0.0109		0.0577	False		,,,				2504	0.0542				p.L85L		Atlas-SNP	.											LMF1,NS,carcinoma,0,4	LMF1	42	4	0			c.T255C						PASS	.	A		113,3937		1,111,1913	59.0	62.0	61.0		255	-1.6	1.0	16	dbSNP_120	61	532,7838		10,512,3663	no	coding-synonymous	LMF1	NM_022773.2		11,623,5576	GG,GA,AA		6.356,2.7901,5.1932		85/568	1004605	645,11775	2025	4185	6210	SO:0001819	synonymous_variant	64788	exon2			GCAGGGAAGCAGC	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.255T>C	16.37:g.1004605A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			A|0.955;G|0.045	0.045	strong		0.522	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
CERS4	79603	hgsc.bcm.edu	37	19	8326866	8326866	+	Missense_Mutation	SNP	C	C	T	rs17160348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8326866C>T	ENST00000251363.5	+	12	1358	c.1058C>T	c.(1057-1059)gCg>gTg	p.A353V	CERS4_ENST00000558331.1_Missense_Mutation_p.A302V|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559336.1_Missense_Mutation_p.A265V|CERS4_ENST00000559450.1_Missense_Mutation_p.A353V	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	353			A -> V (in dbSNP:rs17160348). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGTGAGGAGGCGGCGGCGGCC	0.637													A|||	634	0.126597	0.1271	0.1772	5008	,	,		13525	0.0883		0.161	False		,,,				2504	0.0941				p.A353V		Atlas-SNP	.											LASS4,caecum,carcinoma,0,1	.	.	1	0			c.C1058T						PASS	.	A	VAL/ALA	589,3817		41,507,1655	27.0	29.0	29.0		1058	3.0	0.0	19	dbSNP_123	29	1411,7189		140,1131,3029	yes	missense	CERS4	NM_024552.2	64	181,1638,4684	TT,TC,CC		16.407,13.3681,15.3775	benign	353/395	8326866	2000,11006	2203	4300	6503	SO:0001583	missense	79603	exon12			AGGAGGCGGCGGC		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.1058C>T	19.37:g.8326866C>T	ENSP00000251363:p.Ala353Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	37	CCDS12197.1	316	0.1446886446886447	77	0.1565040650406504	67	0.1850828729281768	42	0.07342657342657342	130	0.17150395778364116	A	19.15	3.772612	0.69992	0.133681	0.16407	ENSG00000090661	ENST00000251363	T	0.06294	3.32	4.06	3.04	0.35103	.	0.667597	0.15133	N	0.278749	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.46261	-0.9204	9	0.36615	T	0.2	-14.8315	4.4314	0.11529	0.691:0.1999:0.1091:0.0	rs17160348;rs17855412;rs58953975;rs17160348	353;353	Q53HF9;Q9HA82	.;CERS4_HUMAN	V	353	ENSP00000251363:A353V	ENSP00000251363:A353V	A	+	2	0	CERS4	8232866	0.981000	0.34729	0.006000	0.13384	0.061000	0.15899	2.819000	0.48049	0.118000	0.18165	-0.494000	0.04653	GCG	C|0.852;N|0.001	.	strong		0.637	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
CCDC61	729440	hgsc.bcm.edu	37	19	46520069	46520069	+	Silent	SNP	C	C	T	rs144277506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46520069C>T	ENST00000595358.1	+	10	1258	c.1209C>T	c.(1207-1209)cgC>cgT	p.R403R	CCDC61_ENST00000263284.2_Silent_p.R422R|CCDC61_ENST00000536603.1_Silent_p.R223R|CCDC61_ENST00000594087.1_Silent_p.R223R|MIR769_ENST00000390225.1_RNA	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	403						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		CCCCTAACCGCTCCCGAAACC	0.726													C|||	37	0.00738818	0.0	0.0101	5008	,	,		8715	0.0		0.0219	False		,,,				2504	0.0082				p.R403R		Atlas-SNP	.											.	CCDC61	32	.	0			c.C1209T						PASS	.			12,3400		0,12,1694	6.0	8.0	7.0		1266	1.8	1.0	19	dbSNP_134	7	132,7592		0,132,3730	no	coding-synonymous	CCDC61	NM_001080402.1		0,144,5424	TT,TC,CC		1.709,0.3517,1.2931		422/532	46520069	144,10992	1706	3862	5568	SO:0001819	synonymous_variant	729440	exon10			TAACCGCTCCCGA		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.1209C>T	19.37:g.46520069C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	77	47	0.61039	NM_001267723	C8CAP4|Q9HDB6	Silent	SNP	ENST00000595358.1	37	CCDS46120.2																																																																																			C|0.989;T|0.011	0.011	strong		0.726	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	
PINX1	54984	hgsc.bcm.edu	37	8	10689212	10689212	+	Silent	SNP	C	C	T	rs12375394	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:10689212C>T	ENST00000314787.3	-	4	383	c.264G>A	c.(262-264)ctG>ctA	p.L88L	PINX1_ENST00000426190.2_Silent_p.L86L|SOX7_ENST00000554914.1_Silent_p.L88L|PINX1_ENST00000519088.1_Silent_p.L88L|PINX1_ENST00000520018.2_5'Flank|SOX7_ENST00000553390.1_Silent_p.L88L	NM_017884.4	NP_060354.4	Q96BK5	PINX1_HUMAN	PIN2/TERF1 interacting, telomerase inhibitor 1	88					mitotic metaphase plate congression (GO:0007080)|negative regulation of cell proliferation (GO:0008285)|negative regulation of telomerase activity (GO:0051974)|regulation of telomerase activity (GO:0051972)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|spindle (GO:0005819)	telomerase inhibitor activity (GO:0010521)|telomeric RNA binding (GO:0070034)			kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)		TCAGTTCGGCCAGAAGCTGGT	0.403													C|||	506	0.101038	0.0416	0.1268	5008	,	,		16577	0.001		0.2048	False		,,,				2504	0.1595				p.L88L		Atlas-SNP	.											.	PINX1	38	.	0			c.G264A						PASS	.	C		245,3481		12,221,1630	79.0	82.0	81.0		264	3.6	1.0	8	dbSNP_120	81	1784,6406		178,1428,2489	no	coding-synonymous	PINX1	NM_017884.4		190,1649,4119	TT,TC,CC		21.7827,6.5754,17.0275		88/329	10689212	2029,9887	1863	4095	5958	SO:0001819	synonymous_variant	54984	exon4			TTCGGCCAGAAGC	AF418553	CCDS47801.1, CCDS64825.1	8p23	2013-01-28				ENSG00000254093		"""G patch domain containing"""	30046	protein-coding gene	gene with protein product	"""PIN2 interacting protein 1"", ""liver-related putative tumor suppressor"""	606505				11003615, 11701125	Standard	NM_001284356		Approved	PinX1, LPTL, LPTS, FLJ20565, MGC8850		Q96BK5		ENST00000314787.3:c.264G>A	8.37:g.10689212C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_017884	B2R9B1|Q548A5|Q6QWG9|Q7Z7J8|Q96QD7|Q9HBU7|Q9NWW2	Silent	SNP	ENST00000314787.3	37	CCDS47801.1																																																																																			C|0.884;T|0.116	0.116	strong		0.403	PINX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375683.1	NM_017884	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42373810	42373810	+	Missense_Mutation	SNP	G	G	C	rs11635685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42373810G>C	ENST00000290472.3	-	11	918	c.824C>G	c.(823-825)cCt>cGt	p.P275R		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	275	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		P -> R (in dbSNP:rs11635685).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		CAGCTCCTCAGGGCTGTGGCA	0.632													G|||	1486	0.296725	0.1316	0.4712	5008	,	,		19169	0.4127		0.3419	False		,,,				2504	0.2301				p.P275R		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.C824G						PASS	.	G	ARG/PRO	774,3632	309.7+/-291.2	65,644,1494	54.0	57.0	56.0		824	3.7	0.6	15	dbSNP_120	56	2981,5617	454.3+/-363.5	520,1941,1838	yes	missense	PLA2G4D	NM_178034.3	103	585,2585,3332	CC,CG,GG		34.6709,17.567,28.8757	benign	275/819	42373810	3755,9249	2203	4299	6502	SO:0001583	missense	283748	exon11			TCCTCAGGGCTGT	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.824C>G	15.37:g.42373810G>C	ENSP00000290472:p.Pro275Arg	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	146	145	0.993151	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	712	0.326007326007326	54	0.10975609756097561	159	0.43922651933701656	231	0.40384615384615385	268	0.35356200527704484	G	10.80	1.451887	0.26074	0.17567	0.346709	ENSG00000159337	ENST00000290472	T	0.01265	5.08	4.58	3.65	0.41850	Lysophospholipase, catalytic domain (2);	0.408988	0.23157	N	0.051293	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	1.0	B	0.18166	0.026	B	0.17433	0.018	T	0.39272	-0.9622	9	0.54805	T	0.06	-4.4823	9.2915	0.37789	0.0:0.1573:0.68:0.1627	rs11635685;rs11635685	275	Q86XP0	PA24D_HUMAN	R	275	ENSP00000290472:P275R	ENSP00000290472:P275R	P	-	2	0	PLA2G4D	40161102	0.961000	0.32948	0.649000	0.29536	0.003000	0.03518	2.683000	0.46943	1.035000	0.39972	0.650000	0.86243	CCT	G|0.713;C|0.287	0.287	strong		0.632	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
ATP8B3	148229	hgsc.bcm.edu	37	19	1808275	1808275	+	Silent	SNP	G	G	A	rs61739534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1808275G>A	ENST00000310127.6	-	5	700	c.462C>T	c.(460-462)taC>taT	p.Y154Y	ATP8B3_ENST00000539485.1_Silent_p.Y154Y|ATP8B3_ENST00000525591.1_Silent_p.Y101Y|ATP8B3_ENST00000526092.2_Silent_p.Y101Y	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	154					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ggaactgctcgtacaggttca	0.602													g|||	89	0.0177716	0.0008	0.0375	5008	,	,		21489	0.0		0.0547	False		,,,				2504	0.0072				p.Y154Y		Atlas-SNP	.											.	ATP8B3	108	.	0			c.C462T						PASS	.	G	,	42,4298		1,40,2129	96.0	108.0	104.0		303,462	-4.2	1.0	19	dbSNP_129	104	568,7974		14,540,3717	no	coding-synonymous,coding-synonymous	ATP8B3	NM_001178002.1,NM_138813.2	,	15,580,5846	AA,AG,GG		6.6495,0.9677,4.7353	,	101/1264,154/1301	1808275	610,12272	2170	4271	6441	SO:0001819	synonymous_variant	148229	exon5			CTGCTCGTACAGG	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.462C>T	19.37:g.1808275G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	210	107	0.509524	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Silent	SNP	ENST00000310127.6	37	CCDS45901.1	58	0.026556776556776556	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	41	0.05408970976253298	g	8.574	0.880809	0.17467	0.009677	0.066495	ENSG00000130270	ENST00000533993	.	.	.	3.89	-4.25	0.03766	.	.	.	.	.	T	0.07279	0.0184	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35968	-0.9767	4	.	.	.	.	9.627	0.39757	0.516:0.0:0.484:0.0	.	.	.	.	M	117	.	.	T	-	2	0	ATP8B3	1759275	0.000000	0.05858	0.976000	0.42696	0.782000	0.44232	-2.722000	0.00810	-0.650000	0.05423	0.456000	0.33151	ACG	G|0.968;A|0.032	0.032	strong		0.602	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
TTN	7273	hgsc.bcm.edu	37	2	179658175	179658175	+	Missense_Mutation	SNP	C	C	T	rs72647851|rs11537855	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179658175C>T	ENST00000591111.1	-	9	1716	c.1492G>A	c.(1492-1494)Gta>Ata	p.V498I	TTN_ENST00000342175.6_Missense_Mutation_p.V498I|TTN_ENST00000360870.5_Missense_Mutation_p.V498I|TTN_ENST00000460472.2_Missense_Mutation_p.V498I|TTN_ENST00000342992.6_Missense_Mutation_p.V498I|TTN_ENST00000359218.5_Missense_Mutation_p.V498I|TTN_ENST00000589042.1_Missense_Mutation_p.V498I			Q8WZ42	TITIN_HUMAN	titin	0			V -> I. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTGGTAATTACTTCTTTGGTT	0.413													C|||	38	0.00758786	0.0015	0.0173	5008	,	,		21111	0.0		0.0149	False		,,,				2504	0.0092				p.V498I		Atlas-SNP	.											TTN_ENST00000360870,right_upper_lobe,carcinoma,+1,6	TTN	18412	6	0			c.G1492A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	28,4378	34.3+/-65.2	0,28,2175	404.0	398.0	400.0		1492,1492,1492,1492,1492	4.7	1.0	2	dbSNP_130	400	200,8400	87.1+/-149.5	6,188,4106	yes	missense,missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133379.3,NM_133378.4,NM_003319.4	29,29,29,29,29	6,216,6281	TT,TC,CC		2.3256,0.6355,1.753	benign,benign,benign,benign,benign	498/27119,498/27052,498/5605,498/33424,498/26927	179658175	228,12778	2203	4300	6503	SO:0001583	missense	7273	exon9			TAATTACTTCTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.1492G>A	2.37:g.179658175C>T	ENSP00000465570:p.Val498Ile	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	191	83	0.434555	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		20	0.009157509157509158	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	12	0.0158311345646438	C	14.37	2.516198	0.44763	0.006355	0.023256	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870;ENST00000436599	T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94	5.61	4.7	0.59300	Titin Z (1);Ribonuclease H-like (1);	.	.	.	.	T	0.16300	0.0392	N	0.16478	0.41	0.23138	N	0.998238	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.08055	0.001;0.001;0.002;0.003;0.003	T	0.17379	-1.0371	9	0.87932	D	0	.	12.3528	0.55157	0.0:0.9118:0.0:0.0882	.	498;498;498;498;498	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	I	498;498;498;498;498;498;94	ENSP00000343764:V498I;ENSP00000434586:V498I;ENSP00000340554:V498I;ENSP00000352154:V498I;ENSP00000354117:V498I;ENSP00000405517:V94I	ENSP00000340554:V498I	V	-	1	0	TTN	179366420	0.996000	0.38824	0.996000	0.52242	0.980000	0.70556	1.242000	0.32755	1.414000	0.47017	0.650000	0.86243	GTA	C|0.985;T|0.015	0.015	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CCDC176	80127	hgsc.bcm.edu	37	14	74523949	74523949	+	Silent	SNP	G	G	A	rs3742808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:74523949G>A	ENST00000394009.3	+	11	1689	c.1566G>A	c.(1564-1566)caG>caA	p.Q522Q	CCDC176_ENST00000553773.1_Silent_p.Q247Q|CCDC176_ENST00000492247.2_Silent_p.Q66Q|AC005484.5_ENST00000492026.1_RNA|ALDH6A1_ENST00000553458.1_3'UTR	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	522					motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											AAGAACCTCAGGAGTCTGACA	0.398													A|||	1505	0.300519	0.3555	0.1801	5008	,	,		20419	0.2381		0.1909	False		,,,				2504	0.4888				p.Q522Q		Atlas-SNP	.											.	.	.	.	0			c.G1566A						PASS	.	A		1483,2923	676.6+/-403.3	263,957,983	63.0	61.0	62.0		1566	-2.0	0.0	14	dbSNP_107	62	1616,6984	741.2+/-407.1	147,1322,2831	no	coding-synonymous	C14orf45	NM_025057.2		410,2279,3814	AA,AG,GG		18.7907,33.6586,23.8275		522/530	74523949	3099,9907	2203	4300	6503	SO:0001819	synonymous_variant	80127	exon11			ACCTCAGGAGTCT	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 45"""	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.1566G>A	14.37:g.74523949G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_025057	Q0P604|Q9H5P8	Silent	SNP	ENST00000394009.3	37	CCDS32119.2																																																																																			G|0.755;A|0.245	0.245	strong		0.398	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
MUC21	394263	hgsc.bcm.edu	37	6	30954754	30954754	+	Missense_Mutation	SNP	G	G	A	rs9262365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30954754G>A	ENST00000376296.3	+	2	1043	c.802G>A	c.(802-804)Ggc>Agc	p.G268S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	268	28 X 15 AA approximate tandem repeats.|Ser-rich.			G -> S (in Ref. 3; AAQ88781 and 4; CAQ08321). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CAGTGGGGCCGGCACAGCCAC	0.632																																					p.G268S		Atlas-SNP	.											MUC21,NS,carcinoma,0,1	MUC21	98	1	0			c.G802A						scavenged	.						154.0	154.0	154.0					6																	30954754		2203	4300	6503	SO:0001583	missense	394263	exon2			GGGGCCGGCACAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.802G>A	6.37:g.30954754G>A	ENSP00000365473:p.Gly268Ser	Somatic	199	8	0.040201		WXS	Illumina HiSeq	Phase_I	249	4	0.0160643	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	2.261	-0.369337	0.05069	.	.	ENSG00000204544	ENST00000376296	T	0.01369	4.97	3.74	-0.338	0.12651	.	.	.	.	.	T	0.00178	0.0005	N	0.01576	-0.805	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.19778	-1.0295	8	.	.	.	-0.7336	4.2134	0.10522	0.5818:0.0:0.2661:0.1521	.	268	Q5SSG8	MUC21_HUMAN	S	268	ENSP00000365473:G268S	.	G	+	1	0	MUC21	31062733	0.003000	0.15002	0.000000	0.03702	0.174000	0.22865	1.375000	0.34295	-0.310000	0.08766	-0.490000	0.04691	GGC	G|0.901;A|0.099	0.099	strong		0.632	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
ATP8B3	148229	hgsc.bcm.edu	37	19	1784944	1784944	+	Splice_Site	SNP	A	A	G	rs3764606	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1784944A>G	ENST00000310127.6	-	28	3772	c.3534T>C	c.(3532-3534)taT>taC	p.Y1178Y	ATP8B3_ENST00000539485.1_Splice_Site_p.Y1188Y|ATP8B3_ENST00000525591.1_Splice_Site_p.Y1141Y	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1178					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGAGGTCGGCATCTGGGGACA	0.622													.|||	2151	0.429513	0.5061	0.3948	5008	,	,		18310	0.3155		0.4563	False		,,,				2504	0.4407				p.Y1178Y		Atlas-SNP	.											.	ATP8B3	108	.	0			c.T3534C						PASS	.	G	,	2125,2227		560,1005,611	48.0	53.0	52.0		3423,3534	-6.8	0.0	19	dbSNP_107	52	4038,4490		970,2098,1196	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ATP8B3	NM_001178002.1,NM_138813.2	,	1530,3103,1807	GG,GA,AA		47.3499,48.8281,47.8494	,	1141/1264,1178/1301	1784944	6163,6717	2176	4264	6440	SO:0001630	splice_region_variant	148229	exon28			GTCGGCATCTGGG	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3533-1T>C	19.37:g.1784944A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Silent	SNP	ENST00000310127.6	37	CCDS45901.1																																																																																			A|0.589;G|0.411	0.411	strong		0.622	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	Silent
CA5A	763	hgsc.bcm.edu	37	16	87938418	87938418	+	Missense_Mutation	SNP	C	C	T	rs138476706		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:87938418C>T	ENST00000309893.2	-	3	498	c.433G>A	c.(433-435)Gtg>Atg	p.V145M		NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	145					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	TGGCCGTCCACTGTGTGCTCT	0.547																																					p.V145M		Atlas-SNP	.											.	CA5A	32	.	0			c.G433A						PASS	.	C	MET/VAL	0,4396		0,0,2198	97.0	88.0	91.0		433	4.2	0.8	16	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	no	missense	CA5A	NM_001739.1	21	0,2,6496	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	145/306	87938418	2,12994	2198	4300	6498	SO:0001583	missense	763	exon3			CGTCCACTGTGTG	L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	4.2.1.1	"""Carbonic anhydrases"""	1377	protein-coding gene	gene with protein product		114761		CA5		8356065, 7490083	Standard	NM_001739		Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.433G>A	16.37:g.87938418C>T	ENSP00000309649:p.Val145Met	Somatic	431	1	0.00232019		WXS	Illumina HiSeq	Phase_I	496	254	0.512097	NM_001739	B2RPF2	Missense_Mutation	SNP	ENST00000309893.2	37	CCDS10965.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.653235	0.47362	0.0	2.33E-4	ENSG00000174990	ENST00000309893	T	0.74947	-0.89	4.22	4.22	0.49857	Carbonic anhydrase, alpha-class, conserved site (1);Carbonic anhydrase, alpha-class, catalytic domain (4);	0.142143	0.46758	D	0.000266	D	0.87621	0.6223	M	0.88377	2.95	0.52099	D	0.99994	D	0.89917	1.0	D	0.87578	0.998	D	0.90265	0.4303	10	0.87932	D	0	-16.7557	14.4554	0.67413	0.0:1.0:0.0:0.0	.	145	P35218	CAH5A_HUMAN	M	145	ENSP00000309649:V145M	ENSP00000309649:V145M	V	-	1	0	CA5A	86495919	0.775000	0.28604	0.801000	0.32222	0.089000	0.18198	1.343000	0.33930	2.034000	0.60081	0.561000	0.74099	GTG	C|1.000;T|0.000	0.000	weak		0.547	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269164.1	NM_001739	
TH	7054	hgsc.bcm.edu	37	11	2188238	2188238	+	Silent	SNP	C	C	T	rs6357	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:2188238C>T	ENST00000381178.1	-	8	831	c.813G>A	c.(811-813)aaG>aaA	p.K271K	TH_ENST00000352909.3_Silent_p.K240K|TH_ENST00000381175.1_Silent_p.K267K|TH_ENST00000333684.5_Intron	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	271					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CGTAGAGGCCCTTCAGCGTGG	0.662													C|||	774	0.154553	0.1165	0.1931	5008	,	,		14280	0.0486		0.3032	False		,,,				2504	0.135				p.K271K		Atlas-SNP	.											.	TH	43	.	0			c.G813A						PASS	.	C	,,	547,3807		33,481,1663	19.0	20.0	20.0		720,813,801	2.2	0.1	11	dbSNP_52	20	2647,5923		433,1781,2071	yes	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	466,2262,3734	TT,TC,CC		30.8868,12.5632,24.7137	,,	240/498,271/529,267/525	2188238	3194,9730	2177	4285	6462	SO:0001819	synonymous_variant	7054	exon8			GAGGCCCTTCAGC	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.813G>A	11.37:g.2188238C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	107	103	0.962617	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			C|0.798;T|0.202	0.202	strong		0.662	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
NAV2	89797	hgsc.bcm.edu	37	11	20112417	20112417	+	Silent	SNP	A	A	C	rs2243624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:20112417A>C	ENST00000396087.3	+	30	5781	c.5682A>C	c.(5680-5682)tcA>tcC	p.S1894S	NAV2_ENST00000533917.1_Silent_p.S899S|NAV2_ENST00000360655.4_Silent_p.S1771S|NAV2_ENST00000540292.1_Silent_p.S1825S|NAV2_ENST00000349880.4_Silent_p.S1835S|NAV2_ENST00000396085.1_Silent_p.S1838S|NAV2_ENST00000527559.2_Silent_p.S1823S|NAV2_ENST00000311043.8_Silent_p.S899S	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1894					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CTAGAATTTCAGAATGCATGG	0.438													A|||	2038	0.406949	0.4592	0.4467	5008	,	,		19772	0.6349		0.3101	False		,,,				2504	0.1728				p.S1894S		Atlas-SNP	.											.	NAV2	255	.	0			c.A5682C						PASS	.	A	,,,	1805,2601	531.5+/-373.2	358,1089,756	85.0	70.0	75.0		5313,2697,5505,5514	-11.1	0.0	11	dbSNP_100	75	2748,5852	439.1+/-359.1	457,1834,2009	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	815,2923,2765	CC,CA,AA		31.9535,40.9669,35.0069	,,,	1771/2366,899/1494,1835/2430,1838/2433	20112417	4553,8453	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon29			AATTTCAGAATGC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.5682A>C	11.37:g.20112417A>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	52	0.65	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			A|0.618;C|0.382	0.382	strong		0.438	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
HERC2	8924	hgsc.bcm.edu	37	15	28412872	28412872	+	Silent	SNP	G	G	A	rs61756152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28412872G>A	ENST00000261609.7	-	68	10623	c.10515C>T	c.(10513-10515)gcC>gcT	p.A3505A		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TGATGCTTGCGGCTCCCAGGT	0.498													G|||	864	0.172524	0.0908	0.2305	5008	,	,		18732	0.2946		0.1074	False		,,,				2504	0.183				p.A3505A		Atlas-SNP	.											.	HERC2	501	.	0			c.C10515T						PASS	.	G		431,3975	209.2+/-230.0	16,399,1788	83.0	88.0	86.0		10515	1.1	1.0	15	dbSNP_129	86	723,7877	175.5+/-225.5	30,663,3607	no	coding-synonymous	HERC2	NM_004667.4		46,1062,5395	AA,AG,GG		8.407,9.7821,8.8728		3505/4835	28412872	1154,11852	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon68			GCTTGCGGCTCCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.10515C>T	15.37:g.28412872G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.885;A|0.115	0.115	strong		0.498	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
CHRNA4	1137	hgsc.bcm.edu	37	20	61981104	61981104	+	Silent	SNP	C	C	T	rs1044397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61981104C>T	ENST00000370263.4	-	5	1880	c.1659G>A	c.(1657-1659)gcG>gcA	p.A553A	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	553					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GCGGGGGCGGCGCTTTGGTGC	0.672													C|||	1762	0.351837	0.0635	0.4899	5008	,	,		13346	0.4008		0.5288	False		,,,				2504	0.411				p.A553A		Atlas-SNP	.											.	CHRNA4	98	.	0			c.G1659A						PASS	.	C		665,3737	272.8+/-271.0	58,549,1594	34.0	40.0	38.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1659	-8.5	0.0	20	dbSNP_86	38	4656,3938	590.3+/-392.6	1279,2098,920	no	coding-synonymous	CHRNA4	NM_000744.5		1337,2647,2514	TT,TC,CC		45.8227,15.1068,40.9434		553/628	61981104	5321,7675	2201	4297	6498	SO:0001819	synonymous_variant	1137	exon5			GGGCGGCGCTTTG		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1958	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 4 (neuronal)"""	118504	"""cholinergic receptor, nicotinic, alpha polypeptide 4"""	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1659G>A	20.37:g.61981104C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	23	14	0.608696	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Silent	SNP	ENST00000370263.4	37	CCDS13517.1																																																																																			C|0.587;T|0.413	0.413	strong		0.672	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
NOC3L	64318	hgsc.bcm.edu	37	10	96114835	96114835	+	Missense_Mutation	SNP	G	G	A	rs12572897	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96114835G>A	ENST00000371361.3	-	6	681	c.581C>T	c.(580-582)cCt>cTt	p.P194L	NOC3L_ENST00000371350.1_Missense_Mutation_p.P194L|NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000543788.1_5'Flank	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	194			P -> L (in dbSNP:rs12572897).		fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				CTCTTGAATAGGATCTTCAAT	0.323													G|||	1032	0.20607	0.1649	0.0908	5008	,	,		17156	0.2917		0.1213	False		,,,				2504	0.3425				p.P194L		Atlas-SNP	.											.	NOC3L	67	.	0			c.C581T						PASS	.	G	LEU/PRO	718,3686	293.6+/-282.7	63,592,1547	154.0	158.0	157.0		581	4.0	0.1	10	dbSNP_120	157	1041,7557	218.7+/-257.0	65,911,3323	yes	missense	NOC3L	NM_022451.9	98	128,1503,4870	AA,AG,GG		12.1075,16.3034,13.5287	benign	194/801	96114835	1759,11243	2202	4299	6501	SO:0001583	missense	64318	exon6			TGAATAGGATCTT	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"""chromosome 10 open reading frame 117"""	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.581C>T	10.37:g.96114835G>A	ENSP00000360412:p.Pro194Leu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_022451	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	399	0.18269230769230768	89	0.18089430894308944	38	0.10497237569060773	181	0.31643356643356646	91	0.12005277044854881	G	11.91	1.779336	0.31502	0.163034	0.121075	ENSG00000173145	ENST00000371361;ENST00000371350	T;T	0.13307	2.6;2.6	5.86	4.02	0.46733	.	0.233884	0.43260	D	0.000584	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.99999465797	B	0.06786	0.001	B	0.06405	0.002	T	0.48547	-0.9026	9	0.30078	T	0.28	-0.03	12.0319	0.53401	0.1383:0.0:0.8617:0.0	rs12572897;rs52833406;rs60029470;rs12572897	194	Q8WTT2	NOC3L_HUMAN	L	194	ENSP00000360412:P194L;ENSP00000360401:P194L	ENSP00000360401:P194L	P	-	2	0	NOC3L	96104825	1.000000	0.71417	0.142000	0.22268	0.601000	0.36947	4.602000	0.61098	1.490000	0.48466	0.655000	0.94253	CCT	G|0.847;A|0.153	0.153	strong		0.323	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	
PMF1	11243	hgsc.bcm.edu	37	1	156206121	156206121	+	Missense_Mutation	SNP	G	G	A	rs1052067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156206121G>A	ENST00000368273.4	+	4	427	c.417G>A	c.(415-417)atG>atA	p.M139I	PMF1_ENST00000565805.1_Intron|PMF1-BGLAP_ENST00000320139.5_Intron|PMF1_ENST00000567140.1_Intron|PMF1_ENST00000368279.3_Intron|PMF1-BGLAP_ENST00000490491.1_Missense_Mutation_p.M137I|PMF1-BGLAP_ENST00000368276.4_Intron|PMF1_ENST00000368277.3_Missense_Mutation_p.M137I	NM_001199654.1	NP_001186583.1			polyamine-modulated factor 1											kidney(1)|large_intestine(2)|lung(3)	6	Hepatocellular(266;0.158)					ACAGTGTTATGGCACCCTACT	0.637													G|||	970	0.19369	0.1127	0.219	5008	,	,		19135	0.2073		0.2773	False		,,,				2504	0.1851				p.M139I	Pancreas(32;764 914 7316 34504 37150)|Ovarian(64;846 1195 21996 34382 40415)	Atlas-SNP	.											PMF1,NS,carcinoma,0,1	PMF1	12	1	0			c.G417A						PASS	.	G	,ILE/MET,,ILE/MET,,ILE/MET,ILE/MET	715,3691	293.6+/-282.7	64,587,1552	85.0	84.0	84.0		,417,,411,,204,411	3.9	0.8	1	dbSNP_86	84	2361,6239	392.1+/-343.9	329,1703,2268	yes	intron,missense,intron,missense,intron,missense,missense	PMF1,PMF1-BGLAP	NM_001199653.1,NM_001199654.1,NM_001199661.1,NM_001199662.1,NM_001199663.1,NM_001199664.1,NM_007221.3	,10,,10,,10,10	393,2290,3820	AA,AG,GG		27.4535,16.2279,23.6506	,possibly-damaging,,possibly-damaging,,possibly-damaging,possibly-damaging	,139/208,,137/212,,68/143,137/206	156206121	3076,9930	2203	4300	6503	SO:0001583	missense	11243	exon4			TGTTATGGCACCC	AF141310	CCDS30886.1, CCDS55648.1, CCDS55649.1	1q22	2013-07-03			ENSG00000160783	ENSG00000160783			9112	protein-coding gene	gene with protein product		609176				10419538	Standard	NM_007221		Approved			Q6P1K2	OTTHUMG00000177123	ENST00000368273.4:c.417G>A	1.37:g.156206121G>A	ENSP00000357256:p.Met139Ile	Somatic	290	1	0.00344828		WXS	Illumina HiSeq	Phase_I	347	208	0.599424	NM_001199654		Missense_Mutation	SNP	ENST00000368273.4	37	CCDS55648.1	462	0.21153846153846154	55	0.11178861788617886	76	0.20994475138121546	113	0.19755244755244755	218	0.287598944591029	G	12.64	1.999039	0.35226	0.162279	0.274535	ENSG00000160783	ENST00000368273;ENST00000368277	T;T	0.26957	1.7;1.7	5.81	3.93	0.45458	.	.	.	.	.	T	0.11110	0.0271	L	0.41236	1.265	0.09310	P	0.9999999999999999	B	0.26002	0.139	B	0.31290	0.127	T	0.05989	-1.0852	8	0.51188	T	0.08	.	10.624	0.45497	0.0723:0.1331:0.7946:0.0	rs1052067;rs17355210;rs17401699;rs17855948;rs58132244;rs1052067	137	Q6P1K2	PMF1_HUMAN	I	139;137	ENSP00000357256:M139I;ENSP00000357260:M137I	ENSP00000357256:M139I	M	+	3	0	PMF1	154472745	0.997000	0.39634	0.831000	0.32960	0.383000	0.30230	2.057000	0.41365	0.802000	0.34089	-0.182000	0.12963	ATG	G|0.788;A|0.212	0.212	strong		0.637	PMF1-005	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040864.2	NM_007221	
IQCB1	9657	hgsc.bcm.edu	37	3	121500697	121500697	+	Missense_Mutation	SNP	G	G	A	rs11920543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121500697G>A	ENST00000310864.6	-	13	1517	c.1303C>T	c.(1303-1305)Cgt>Tgt	p.R435C	IQCB1_ENST00000349820.6_Missense_Mutation_p.R302C	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	435	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.		R -> C (in dbSNP:rs11920543).		cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TTTTTCTTACGGCACTTCGCT	0.408													G|||	20	0.00399361	0.0	0.0014	5008	,	,		19244	0.0		0.0189	False		,,,				2504	0.0				p.R435C		Atlas-SNP	.											IQCB1,caecum,carcinoma,+1,2	IQCB1	50	2	0			c.C1303T						scavenged	.	G	CYS/ARG,CYS/ARG	12,4394	15.5+/-35.6	0,12,2191	115.0	111.0	112.0		1303,904	4.6	1.0	3	dbSNP_120	112	128,8472	65.3+/-127.6	2,124,4174	yes	missense,missense	IQCB1	NM_001023570.2,NM_001023571.2	180,180	2,136,6365	AA,AG,GG		1.4884,0.2724,1.0764	probably-damaging,probably-damaging	435/599,302/466	121500697	140,12866	2203	4300	6503	SO:0001583	missense	9657	exon13			TCTTACGGCACTT	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"""nephrocystin-5"""	609237	"""IQ calmodulin-binding motif containing 1"""			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.1303C>T	3.37:g.121500697G>A	ENSP00000311505:p.Arg435Cys	Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Missense_Mutation	SNP	ENST00000310864.6	37	CCDS33837.1	19	0.0086996336996337	0	0.0	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	G	14.22	2.469545	0.43839	0.002724	0.014884	ENSG00000173226	ENST00000310864;ENST00000349820	T;T	0.80480	-1.38;-1.38	4.61	4.61	0.57282	.	0.226336	0.42420	D	0.000719	T	0.77089	0.4079	L	0.50333	1.59	0.50632	D	0.999888	D;D	0.89917	1.0;1.0	D;P	0.74023	0.982;0.897	T	0.83113	-0.0122	10	0.87932	D	0	0.2165	13.1535	0.59503	0.0:0.0:1.0:0.0	rs11920543;rs52793008;rs11920543	435;302	Q15051;Q15051-2	IQCB1_HUMAN;.	C	435;302	ENSP00000311505:R435C;ENSP00000323756:R302C	ENSP00000311505:R435C	R	-	1	0	IQCB1	122983387	0.656000	0.27385	0.992000	0.48379	0.033000	0.12548	3.375000	0.52410	2.548000	0.85928	0.591000	0.81541	CGT	G|0.990;A|0.010	0.010	strong		0.408	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642	
FUT8	2530	hgsc.bcm.edu	37	14	66136163	66136163	+	Missense_Mutation	SNP	C	C	A	rs35949016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:66136163C>A	ENST00000360689.5	+	7	2527	c.800C>A	c.(799-801)aCa>aAa	p.T267K	FUT8_ENST00000394585.1_Missense_Mutation_p.T267K|FUT8_ENST00000557164.1_Missense_Mutation_p.T104K|FUT8_ENST00000554765.1_3'UTR|FUT8_ENST00000417683.1_Missense_Mutation_p.H2Q|FUT8_ENST00000358307.2_Missense_Mutation_p.T138K|FUT8_ENST00000394586.2_Missense_Mutation_p.T267K	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	267	GT23. {ECO:0000255|PROSITE- ProRule:PRU00992}.		T -> K (in dbSNP:rs35949016).		cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)	p.T267K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		GAGACATGCACAGACAGATCT	0.473													C|||	748	0.149361	0.0136	0.1095	5008	,	,		17709	0.1022		0.2157	False		,,,				2504	0.3415				p.T267K		Atlas-SNP	.											FUT8,NS,carcinoma,0,1	FUT8	101	1	1	Substitution - Missense(1)	stomach(1)	c.C800A						PASS	.	C	LYS/THR,LYS/THR,LYS/THR	143,4263	99.8+/-138.5	2,139,2062	151.0	133.0	139.0		311,800,800	5.8	1.0	14	dbSNP_126	139	1433,7167	274.1+/-291.0	125,1183,2992	yes	missense,missense,missense	FUT8	NM_004480.4,NM_178155.2,NM_178156.2	78,78,78	127,1322,5054	AA,AC,CC		16.6628,3.2456,12.1175	probably-damaging,probably-damaging,probably-damaging	104/413,267/576,267/576	66136163	1576,11430	2203	4300	6503	SO:0001583	missense	2530	exon7			CATGCACAGACAG	AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"""Fucosyltransferases"""	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000360689.5:c.800C>A	14.37:g.66136163C>A	ENSP00000353910:p.Thr267Lys	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	202	107	0.529703	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Missense_Mutation	SNP	ENST00000360689.5	37	CCDS9775.1	287|287	0.13141025641025642|0.13141025641025642	10|10	0.02032520325203252|0.02032520325203252	41|41	0.1132596685082873|0.1132596685082873	64|64	0.11188811188811189|0.11188811188811189	172|172	0.22691292875989447|0.22691292875989447	C|C	6.902|6.902	0.536045|0.536045	0.13188|0.13188	0.032456|0.032456	0.166628|0.166628	ENSG00000033170|ENSG00000033170	ENST00000417683|ENST00000360689;ENST00000394586;ENST00000557164;ENST00000394585;ENST00000358307	T|T;T;T;T;T	0.43294|0.21734	0.95|1.99;1.99;1.99;1.99;1.99	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	.|0.046256	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.62723|0.62723	1.935|1.935	0.40642|0.40642	P|P	0.018046000000000006|0.018046000000000006	B|B;P	0.02656|0.51791	0.0|0.289;0.948	B|B;B	0.01281|0.37267	0.0|0.042;0.245	T|T	0.46569|0.46569	-0.9182|-0.9182	8|9	0.87932|0.19147	D|T	0|0.46	-10.6644|-10.6644	17.6669|17.6669	0.88205|0.88205	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs35949016;rs35949016|rs35949016;rs35949016	2|138;267	Q8IUA5|G3XAD2;Q9BYC5	.|.;FUT8_HUMAN	Q|K	2|267;267;104;267;138	ENSP00000396770:H2Q|ENSP00000353910:T267K;ENSP00000378087:T267K;ENSP00000452433:T104K;ENSP00000378086:T267K;ENSP00000351057:T138K	ENSP00000396770:H2Q|ENSP00000345865:T267K	H|T	+|+	3|2	2|0	FUT8|FUT8	65205916|65205916	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.863000|4.863000	0.62983|0.62983	2.768000|2.768000	0.95171|0.95171	0.655000|0.655000	0.94253|0.94253	CAC|ACA	C|0.875;A|0.125	0.125	strong		0.473	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480	
ZNF665	79788	hgsc.bcm.edu	37	19	53667913	53667913	+	Silent	SNP	A	A	G	rs12459469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53667913A>G	ENST00000600412.1	-	2	1750	c.1635T>C	c.(1633-1635)aaT>aaC	p.N545N	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Silent_p.N610N			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	545					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		CAAGATGTGAATTTTGAGTGA	0.393													A|||	2592	0.517572	0.1543	0.6499	5008	,	,		19812	0.6448		0.5974	False		,,,				2504	0.7014				p.N610N		Atlas-SNP	.											.	ZNF665	136	.	0			c.T1830C						PASS	.	A		1025,3381	371.2+/-319.9	126,773,1304	110.0	114.0	113.0		1830	-4.8	0.0	19	dbSNP_120	113	5250,3350	640.8+/-399.6	1591,2068,641	no	coding-synonymous	ZNF665	NM_024733.3		1717,2841,1945	GG,GA,AA		38.9535,23.2637,48.247		610/679	53667913	6275,6731	2203	4300	6503	SO:0001819	synonymous_variant	79788	exon4			ATGTGAATTTTGA		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1635T>C	19.37:g.53667913A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_024733	A8K5T8	Silent	SNP	ENST00000600412.1	37																																																																																				A|0.488;G|0.512	0.512	strong		0.393	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
ACCS	84680	hgsc.bcm.edu	37	11	44101118	44101118	+	Silent	SNP	C	C	T	rs7950395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:44101118C>T	ENST00000263776.8	+	10	1305	c.871C>T	c.(871-873)Ctg>Ttg	p.L291L		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	291					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						GGTCTACATGCTGTCCGTGTT	0.567													C|||	572	0.114217	0.1203	0.0937	5008	,	,		18903	0.1151		0.1223	False		,,,				2504	0.1115				p.L291L	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.C871T						PASS	.	C	,	580,3826	254.0+/-259.7	51,478,1674	216.0	139.0	165.0		871,871	1.9	1.0	11	dbSNP_116	165	1119,7481	229.8+/-264.4	66,987,3247	no	coding-synonymous,coding-synonymous	ACCS	NM_001127219.1,NM_032592.3	,	117,1465,4921	TT,TC,CC		13.0116,13.1639,13.0632	,	291/502,291/502	44101118	1699,11307	2203	4300	6503	SO:0001819	synonymous_variant	84680	exon10			TACATGCTGTCCG	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.871C>T	11.37:g.44101118C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	209	97	0.464115	NM_032592	B4E219|Q8WUL4|Q96LX5	Silent	SNP	ENST00000263776.8	37	CCDS7907.1																																																																																			C|0.877;T|0.123	0.123	strong		0.567	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592	
KLHDC7B	113730	hgsc.bcm.edu	37	22	50987175	50987175	+	Missense_Mutation	SNP	G	G	T	rs116500907	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50987175G>T	ENST00000395676.2	+	1	714	c.580G>T	c.(580-582)Gtg>Ttg	p.V194L	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	194										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGGTTGGGGGGTGGTGGAGGG	0.756													G|||	268	0.0535144	0.1014	0.0159	5008	,	,		9731	0.0119		0.0328	False		,,,				2504	0.0798				p.V194L		Atlas-SNP	.											.	KLHDC7B	39	.	0			c.G580T						PASS	.	G	LEU/VAL	134,2544		3,128,1208	2.0	3.0	3.0		580	2.9	0.9	22	dbSNP_132	3	127,6159		2,123,3018	no	missense	KLHDC7B	NM_138433.3	32	5,251,4226	TT,TG,GG		2.0204,5.0037,2.9116	benign	194/595	50987175	261,8703	1339	3143	4482	SO:0001583	missense	113730	exon1			TGGGGGGTGGTGG	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.580G>T	22.37:g.50987175G>T	ENSP00000379034:p.Val194Leu	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	11	6	0.545455	NM_138433		Missense_Mutation	SNP	ENST00000395676.2	37	CCDS14097.2	83	0.038003663003663	45	0.09146341463414634	8	0.022099447513812154	4	0.006993006993006993	26	0.03430079155672823	g	10.23	1.291785	0.23564	0.050037	0.020204	ENSG00000130487	ENST00000395676	D	0.82619	-1.63	3.97	2.88	0.33553	.	.	.	.	.	T	0.07188	0.0182	L	0.27053	0.805	0.23168	N	0.998184	P	0.40970	0.734	B	0.32090	0.14	T	0.05289	-1.0894	9	0.31617	T	0.26	.	8.4306	0.32755	0.13:0.0:0.87:0.0	.	194	Q96G42	KLD7B_HUMAN	L	194	ENSP00000379034:V194L	ENSP00000379034:V194L	V	+	1	0	KLHDC7B	49334041	0.231000	0.23751	0.915000	0.36163	0.135000	0.20990	1.505000	0.35736	2.067000	0.61834	0.306000	0.20318	GTG	G|0.958;T|0.042	0.042	strong		0.756	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433	
NBPF10	100132406	hgsc.bcm.edu	37	1	145302775	145302775	+	Missense_Mutation	SNP	T	T	G	rs376014420		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145302775T>G	ENST00000369339.3	+	5	653	c.400T>G	c.(400-402)Tat>Gat	p.Y134D	NBPF10_ENST00000369338.1_Missense_Mutation_p.Y134D|NBPF10_ENST00000342960.5_Missense_Mutation_p.Y405D|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	405						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CCTCACTCCGTATGAGCCGGA	0.577																																					p.Y405D		Atlas-SNP	.											NBPF10_ENST00000369338,NS,carcinoma,0,2	NBPF10	221	2	0			c.T1213G						scavenged	.																																			SO:0001583	missense	100132406	exon8			ACTCCGTATGAGC	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.400T>G	1.37:g.145302775T>G	ENSP00000358345:p.Tyr134Asp	Somatic	183	9	0.0491803		WXS	Illumina HiSeq	Phase_I	223	17	0.0762332	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	0	-2.664813	0.00107	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.46063	0.88;4.33	0.712	-0.91	0.10511	.	.	.	.	.	T	0.03390	0.0098	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33189	-0.9878	7	0.02654	T	1	.	.	.	.	.	134	A8MQ30	.	D	330;134;134;405	ENSP00000358344:Y134D;ENSP00000345684:Y405D	ENSP00000345684:Y405D	Y	+	1	0	NBPF10	144014132	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.464000	0.06688	-1.158000	0.02811	-1.371000	0.01190	TAT	T|0.500;G|0.500	0.500	weak		0.577	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
NPAS4	266743	hgsc.bcm.edu	37	11	66188761	66188761	+	Silent	SNP	G	G	T	rs77600363	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66188761G>T	ENST00000311034.2	+	1	287	c.111G>T	c.(109-111)ctG>ctT	p.L37L		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	37	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						AGGTCCGGCTGTCCTACCTGC	0.652													G|||	850	0.169728	0.0204	0.3963	5008	,	,		16126	0.1696		0.2157	False		,,,				2504	0.1636				p.L37L		Atlas-SNP	.											.	NPAS4	133	.	0			c.G111T						PASS	.	G		225,4175	135.3+/-171.4	6,213,1981	78.0	63.0	68.0		111	3.2	1.0	11	dbSNP_131	68	1854,6736	330.7+/-319.3	199,1456,2640	no	coding-synonymous	NPAS4	NM_178864.3		205,1669,4621	TT,TG,GG		21.5832,5.1136,16.0046		37/803	66188761	2079,10911	2200	4295	6495	SO:0001819	synonymous_variant	266743	exon1			CCGGCTGTCCTAC	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.111G>T	11.37:g.66188761G>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	180	83	0.461111	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Silent	SNP	ENST00000311034.2	37	CCDS8138.1																																																																																			G|0.824;T|0.176	0.176	strong		0.652	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864	
SPTBN5	51332	hgsc.bcm.edu	37	15	42150888	42150888	+	Missense_Mutation	SNP	G	G	A	rs890503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42150888G>A	ENST00000320955.6	-	49	8365	c.8138C>T	c.(8137-8139)aCa>aTa	p.T2713I		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2713					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.T2713I(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CAGCATGGCTGTGTCCAGCAA	0.632													G|||	1133	0.226238	0.295	0.2061	5008	,	,		20335	0.0357		0.325	False		,,,				2504	0.2423				p.T2678I		Atlas-SNP	.											SPTBN5,NS,carcinoma,0,3	SPTBN5	171	3	2	Substitution - Missense(2)	ovary(1)|prostate(1)	c.C8033T						PASS	.	G	ILE/THR	1330,2976		208,914,1031	26.0	29.0	28.0		8033	4.0	0.1	15	dbSNP_86	28	2670,5846		414,1842,2002	yes	missense	SPTBN5	NM_016642.2	89	622,2756,3033	AA,AG,GG		31.3527,30.8871,31.1964	benign	2678/3640	42150888	4000,8822	2153	4258	6411	SO:0001583	missense	51332	exon49			ATGGCTGTGTCCA	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8138C>T	15.37:g.42150888G>A	ENSP00000317790:p.Thr2713Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	141	77	0.546099	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		461	0.21108058608058608	135	0.27439024390243905	76	0.20994475138121546	14	0.024475524475524476	236	0.3113456464379947	.	10.42	1.345440	0.24426	0.308871	0.313527	ENSG00000137877	ENST00000320955	T	0.45668	0.89	4.94	4.03	0.46877	.	0.085238	0.47852	D	0.000214	T	0.00012	0.0000	N	0.12182	0.205	0.41138	P	0.01406099999999999	P	0.35821	0.523	B	0.35859	0.212	T	0.39860	-0.9593	9	0.14656	T	0.56	.	10.4904	0.44748	0.1566:0.0:0.8434:0.0	rs890503;rs890503	2713	Q9NRC6	SPTN5_HUMAN	I	2713	ENSP00000317790:T2713I	ENSP00000317790:T2713I	T	-	2	0	SPTBN5	39938180	1.000000	0.71417	0.094000	0.20943	0.007000	0.05969	5.383000	0.66219	1.067000	0.40740	0.467000	0.42956	ACA	G|0.757;T|0.009	.	strong		0.632	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
CTCFL	140690	hgsc.bcm.edu	37	20	56087800	56087800	+	Missense_Mutation	SNP	T	T	C	rs41305825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:56087800T>C	ENST00000608263.1	-	7	2000	c.1339A>G	c.(1339-1341)Atg>Gtg	p.M447V	CTCFL_ENST00000502686.2_Missense_Mutation_p.M185V|CTCFL_ENST00000608440.1_Missense_Mutation_p.M447V|CTCFL_ENST00000609232.1_Missense_Mutation_p.M447V|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000608858.1_5'Flank|CTCFL_ENST00000429804.3_Missense_Mutation_p.M397V|CTCFL_ENST00000243914.3_Missense_Mutation_p.M447V|CTCFL_ENST00000371196.2_Missense_Mutation_p.M447V|CTCFL_ENST00000423479.3_Missense_Mutation_p.M447V|CTCFL_ENST00000433949.3_Missense_Mutation_p.M242V|CTCFL_ENST00000539382.1_Missense_Mutation_p.M242V|CTCFL_ENST00000608425.1_Missense_Mutation_p.M447V|CTCFL_ENST00000422869.2_Missense_Mutation_p.M447V|CTCFL_ENST00000608903.1_Missense_Mutation_p.M185V	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	447					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			AAGTTGCGCATATGCACACCT	0.473													T|||	107	0.0213658	0.0038	0.0504	5008	,	,		22330	0.0		0.0596	False		,,,				2504	0.0072				p.M447V		Atlas-SNP	.											.	CTCFL	97	.	0			c.A1339G						PASS	.	T	VAL/MET	44,4362	47.5+/-82.1	2,40,2161	75.0	65.0	68.0		1339	-8.5	0.0	20	dbSNP_127	68	600,8000	158.3+/-211.8	23,554,3723	yes	missense	CTCFL	NM_080618.2	21	25,594,5884	CC,CT,TT		6.9767,0.9986,4.9516	benign	447/664	56087800	644,12362	2203	4300	6503	SO:0001583	missense	140690	exon7			TGCGCATATGCAC		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1339A>G	20.37:g.56087800T>C	ENSP00000476783:p.Met447Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	57	0.0260989010989011	0	0.0	17	0.04696132596685083	0	0.0	40	0.052770448548812667	T	4.324	0.059434	0.08339	0.009986	0.069767	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T	0.54479	0.57;0.57;0.57;3.21;0.57;0.57;0.57;0.57	5.35	-8.48	0.00935	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.220744	0.22569	N	0.058365	T	0.01800	0.0057	N	0.25485	0.75	0.80722	D	1	B;B;B;B;B;B	0.06786	0.001;0.001;0.0;0.001;0.001;0.001	B;B;B;B;B;B	0.09377	0.004;0.002;0.001;0.004;0.002;0.001	T	0.02781	-1.1111	10	0.39692	T	0.17	-7.409	2.0976	0.03672	0.5283:0.0988:0.1646:0.2084	rs41305825;rs61749690	447;447;397;447;447;447	A6XGM9;A6XGM2;E7EUE3;A1L4C6;A6XGL8;Q8NI51	.;.;.;.;.;CTCFL_HUMAN	V	447;447;447;397;447;185;242;447	ENSP00000415579:M447V;ENSP00000243914:M447V;ENSP00000360239:M447V;ENSP00000415329:M397V;ENSP00000392034:M447V;ENSP00000437999:M185V;ENSP00000439998:M242V;ENSP00000399061:M447V	ENSP00000243914:M447V	M	-	1	0	CTCFL	55521206	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-1.406000	0.02490	-1.458000	0.01916	-0.213000	0.12676	ATG	T|0.954;C|0.046	0.046	strong		0.473	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
CNTN6	27255	hgsc.bcm.edu	37	3	1424850	1424850	+	Silent	SNP	T	T	G	rs2291100	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:1424850T>G	ENST00000446702.2	+	18	3018	c.2391T>G	c.(2389-2391)tcT>tcG	p.S797S	CNTN6_ENST00000350110.2_Silent_p.S797S|CNTN6_ENST00000539053.1_Silent_p.S725S			Q9UQ52	CNTN6_HUMAN	contactin 6	797	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTGTCTACTCTGGGGAAGATG	0.418													T|||	1325	0.264577	0.0386	0.2781	5008	,	,		20256	0.3452		0.3877	False		,,,				2504	0.3507				p.S797S		Atlas-SNP	.											.	CNTN6	245	.	0			c.T2391G						PASS	.	T		404,4002	200.8+/-224.0	17,370,1816	123.0	109.0	114.0		2391	-12.2	0.2	3	dbSNP_100	114	3216,5384	485.5+/-371.6	597,2022,1681	no	coding-synonymous	CNTN6	NM_014461.2		614,2392,3497	GG,GT,TT		37.3953,9.1693,27.8333		797/1029	1424850	3620,9386	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon18			CTACTCTGGGGAA	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2391T>G	3.37:g.1424850T>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	188	88	0.468085	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			T|0.724;G|0.276	0.276	strong		0.418	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
C9orf131	138724	hgsc.bcm.edu	37	9	35043291	35043291	+	Missense_Mutation	SNP	G	G	T	rs615474	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35043291G>T	ENST00000312292.5	+	2	712	c.665G>T	c.(664-666)tGg>tTg	p.W222L	FLJ00273_ENST00000595331.1_5'Flank|C9orf131_ENST00000354479.5_Missense_Mutation_p.W149L|C9orf131_ENST00000421362.2_Missense_Mutation_p.W174L	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	222			W -> L (in dbSNP:rs615474). {ECO:0000269|PubMed:15489334}.					p.W222L(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			CCTCTGAAGTGGTCTGTTTGT	0.537													T|||	3275	0.653954	0.5991	0.8127	5008	,	,		19415	0.4484		0.7495	False		,,,				2504	0.729				p.W222L		Atlas-SNP	.											C9orf131,NS,carcinoma,0,1	C9orf131	71	1	1	Substitution - Missense(1)	stomach(1)	c.G665T						PASS	.	T	LEU/TRP,LEU/TRP,LEU/TRP,LEU/TRP	2747,1659	505.6+/-366.2	868,1011,324	145.0	131.0	136.0		560,446,521,665	2.8	0.0	9	dbSNP_83	136	6516,2084	360.6+/-332.0	2480,1556,264	yes	missense,missense,missense,missense	C9orf131	NM_001040410.1,NM_001040411.1,NM_001040412.1,NM_203299.2	61,61,61,61	3348,2567,588	TT,TG,GG		24.2326,37.6532,28.779	benign,benign,benign,benign	187/1045,149/1007,174/1032,222/1080	35043291	9263,3743	2203	4300	6503	SO:0001583	missense	138724	exon2			TGAAGTGGTCTGT	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.665G>T	9.37:g.35043291G>T	ENSP00000308279:p.Trp222Leu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	185	97	0.524324	NM_203299	A6NLE6|E9PB26|Q86XC6|Q9UF74	Missense_Mutation	SNP	ENST00000312292.5	37	CCDS6572.2	1446	0.6620879120879121	303	0.6158536585365854	294	0.8121546961325967	279	0.48776223776223776	570	0.7519788918205804	T	0.020	-1.444217	0.01089	0.623468	0.757674	ENSG00000174038	ENST00000421362;ENST00000354479;ENST00000312292;ENST00000378745	T;T;T;T	0.24908	3.05;3.06;3.04;1.83	5.16	2.8	0.32819	.	0.202713	0.24470	N	0.038259	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34229	-0.9837	9	0.02654	T	1	-0.6502	3.6016	0.08027	0.0:0.2034:0.1963:0.6003	rs615474;rs13284410;rs16932162;rs17857307;rs57875944;rs615474	222;149;174	Q5VYM1;A6NLE6;E9PB26	CI131_HUMAN;.;.	L	174;149;222;187	ENSP00000393683:W174L;ENSP00000346472:W149L;ENSP00000308279:W222L;ENSP00000368019:W187L	ENSP00000308279:W222L	W	+	2	0	C9orf131	35033291	0.011000	0.17503	0.009000	0.14445	0.461000	0.32589	0.361000	0.20267	0.448000	0.26722	-0.256000	0.11100	TGG	G|0.380;T|0.620	0.620	strong		0.537	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299	
PRKCQ	5588	hgsc.bcm.edu	37	10	6553071	6553071	+	Silent	SNP	T	T	C	rs17555072	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:6553071T>C	ENST00000263125.5	-	3	303	c.204A>G	c.(202-204)agA>agG	p.R68R	PRKCQ_ENST00000539722.1_5'UTR|PRKCQ_ENST00000397176.2_Silent_p.R68R	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	68	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TCTGCATGACTCTTCCCTTGT	0.498													T|||	121	0.0241613	0.003	0.0259	5008	,	,		20101	0.0		0.0616	False		,,,				2504	0.0378				p.R68R	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.A204G						PASS	.	T	,	65,4341	62.3+/-99.4	0,65,2138	228.0	191.0	204.0		204,204	0.7	0.9	10	dbSNP_123	204	628,7972	162.5+/-215.2	21,586,3693	no	coding-synonymous,coding-synonymous	PRKCQ	NM_001242413.1,NM_006257.3	,	21,651,5831	CC,CT,TT		7.3023,1.4753,5.3283	,	68/644,68/707	6553071	693,12313	2203	4300	6503	SO:0001819	synonymous_variant	5588	exon3			CATGACTCTTCCC	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.204A>G	10.37:g.6553071T>C		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	227	102	0.449339	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	37	CCDS7079.1																																																																																			T|0.958;C|0.042	0.042	strong		0.498	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388378	1388378	+	Missense_Mutation	SNP	T	T	C	rs55884223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388378T>C	ENST00000324803.4	+	1	3039	c.79T>C	c.(79-81)Tgt>Cgt	p.C27R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	27					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGCCTGCTCATGTGCCCATGT	0.637													N|||	782	0.15615	0.1952	0.1412	5008	,	,		16132	0.0278		0.2286	False		,,,				2504	0.1718				p.C27R		Atlas-SNP	.											CRIPAK,NS,carcinoma,-1,1	CRIPAK	185	1	0			c.T79C						scavenged	.						172.0	171.0	171.0					4																	1388378		2203	4300	6503	SO:0001583	missense	285464	exon1			TGCTCATGTGCCC	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.79T>C	4.37:g.1388378T>C	ENSP00000323978:p.Cys27Arg	Somatic	271	8	0.0295203		WXS	Illumina HiSeq	Phase_I	233	77	0.330472	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	T	2.439	-0.329099	0.05314	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.25414	1.8	0.824	-1.65	0.08291	.	.	.	.	.	T	0.08223	0.0205	N	0.08118	0	0.34679	D	0.724554	B	0.20052	0.041	B	0.11329	0.006	T	0.40850	-0.9541	9	0.09338	T	0.73	.	2.0645	0.03600	0.2577:0.2174:0.0:0.5249	rs55884223	27	Q8N1N5	CRPAK_HUMAN	R	27;20	ENSP00000323978:C27R	ENSP00000323978:C27R	C	+	1	0	CRIPAK	1378378	0.017000	0.18338	0.001000	0.08648	0.007000	0.05969	-0.458000	0.06737	-0.973000	0.03555	0.344000	0.21773	TGT	T|0.993;C|0.007	0.007	strong		0.637	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
PPA2	27068	hgsc.bcm.edu	37	4	106317429	106317429	+	Missense_Mutation	SNP	C	C	G	rs13787	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106317429C>G	ENST00000341695.5	-	9	876	c.846G>C	c.(844-846)aaG>aaC	p.K282N	PPA2_ENST00000432483.2_Missense_Mutation_p.K180N|PPA2_ENST00000354147.3_Missense_Mutation_p.K116N|PPA2_ENST00000357415.4_Missense_Mutation_p.K297N|PPA2_ENST00000509426.1_5'Flank|PPA2_ENST00000348706.5_Missense_Mutation_p.K253N|PPA2_ENST00000380004.2_Missense_Mutation_p.K264N	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	282			K -> N (in dbSNP:rs13787). {ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039}.		diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		CTCCATTACACTTCTTCATAA	0.294													C|||	2167	0.432708	0.0923	0.5086	5008	,	,		17915	0.6766		0.4592	False		,,,				2504	0.5603				p.K282N		Atlas-SNP	.											.	PPA2	23	.	0			c.G846C						PASS	.	C	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	585,3821	251.5+/-258.2	40,505,1658	96.0	91.0	93.0		759,540,348,846	0.1	0.7	4	dbSNP_52	93	3925,4669	539.8+/-383.7	890,2145,1262	yes	missense,missense,missense,missense	PPA2	NM_006903.4,NM_176866.2,NM_176867.3,NM_176869.2	94,94,94,94	930,2650,2920	GG,GC,CC		45.6714,13.2773,34.6923	benign,benign,benign,benign	253/306,180/233,116/169,282/335	106317429	4510,8490	2203	4297	6500	SO:0001583	missense	27068	exon9			ATTACACTTCTTC		CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.846G>C	4.37:g.106317429C>G	ENSP00000343885:p.Lys282Asn	Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_176869	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	973	0.44551282051282054	49	0.09959349593495935	163	0.45027624309392267	390	0.6818181818181818	371	0.4894459102902375	C	11.86	1.763782	0.31228	0.132773	0.456714	ENSG00000138777	ENST00000341695;ENST00000348706;ENST00000354147;ENST00000432483;ENST00000357415;ENST00000380004	T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81	5.93	0.105	0.14535	.	0.217385	0.45867	D	0.000321	T	0.00012	0.0000	M	0.73217	2.22	0.21386	P	0.999704449	P;B;B;B;B	0.36789	0.57;0.344;0.033;0.076;0.038	B;B;B;B;B	0.35240	0.198;0.05;0.049;0.011;0.011	T	0.38993	-0.9635	9	0.42905	T	0.14	-22.2528	6.7286	0.23371	0.1115:0.4337:0.0:0.4549	rs13787;rs1127137;rs3182696;rs11267057;rs11566570;rs17256954;rs17839004;rs13787	116;180;253;264;282	Q9H2U2-4;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.;.;.;.;IPYR2_HUMAN	N	282;253;116;180;297;264	ENSP00000343885:K282N;ENSP00000313061:K253N;ENSP00000340352:K116N;ENSP00000389957:K180N;ENSP00000349996:K297N;ENSP00000369340:K264N	ENSP00000343885:K282N	K	-	3	2	PPA2	106536878	0.000000	0.05858	0.742000	0.31022	0.987000	0.75469	-0.843000	0.04350	-0.083000	0.12618	-0.181000	0.13052	AAG	C|0.611;G|0.389	0.389	strong		0.294	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869	
ZFP64	55734	hgsc.bcm.edu	37	20	50769379	50769379	+	Missense_Mutation	SNP	C	C	T	rs3746414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:50769379C>T	ENST00000216923.4	-	6	1701	c.1352G>A	c.(1351-1353)aGt>aAt	p.S451N	ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000371515.4_Missense_Mutation_p.S449N|ZFP64_ENST00000346617.4_Missense_Mutation_p.S397N|ZFP64_ENST00000477786.1_Intron	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	451			S -> N (in dbSNP:rs3746414). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CTTACTCTCACTGTACTCACT	0.582													T|||	848	0.169329	0.1498	0.2781	5008	,	,		20551	0.0843		0.2137	False		,,,				2504	0.1605				p.S451N		Atlas-SNP	.											.	ZFP64	240	.	0			c.G1352A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER,	675,3731	751.0+/-412.2	56,563,1584	73.0	53.0	60.0		1352,1190,1346,	-10.5	0.0	20	dbSNP_107	60	1863,6737	719.1+/-406.2	193,1477,2630	yes	missense,missense,missense,intron	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	46,46,46,	249,2040,4214	TT,TC,CC		21.6628,15.32,19.5141	benign,benign,benign,	451/682,397/628,449/680,	50769379	2538,10468	2203	4300	6503	SO:0001583	missense	55734	exon6			CTCTCACTGTACT	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1352G>A	20.37:g.50769379C>T	ENSP00000216923:p.Ser451Asn	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_018197	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000216923.4	37	CCDS13440.1	385	0.1762820512820513	62	0.12601626016260162	104	0.287292817679558	57	0.09965034965034965	162	0.21372031662269128	T	1.446	-0.566451	0.03910	0.1532	0.216628	ENSG00000020256	ENST00000216923;ENST00000346617;ENST00000371515;ENST00000546083;ENST00000371516	T;T;T	0.07327	3.21;3.25;3.2	5.49	-10.5	0.00291	Zinc finger, C2H2 (1);	1.054690	0.07392	N	0.889223	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.40079	-0.9582	9	0.34782	T	0.22	-0.1662	17.7348	0.88389	0.0741:0.7041:0.0:0.2218	rs3746414;rs17845354;rs17858201;rs17859339;rs58513527;rs3746414	397;449;451	Q9NPA5-2;Q5JWM1;Q9NPA5	.;.;ZF64A_HUMAN	N	451;397;449;293;604	ENSP00000216923:S451N;ENSP00000344615:S397N;ENSP00000360570:S449N	ENSP00000216923:S451N	S	-	2	0	ZFP64	50202786	0.000000	0.05858	0.000000	0.03702	0.149000	0.21700	-2.377000	0.01069	-2.527000	0.00494	-1.178000	0.01721	AGT	C|0.848;T|0.152	0.152	strong		0.582	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
C1orf141	400757	hgsc.bcm.edu	37	1	67558763	67558763	+	Silent	SNP	A	A	G	rs567792598|rs41299551|rs111337099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:67558763A>G	ENST00000371007.2	-	8	1237	c.1128T>C	c.(1126-1128)taT>taC	p.Y376Y	C1orf141_ENST00000544837.1_Silent_p.Y376Y|C1orf141_ENST00000371006.1_Silent_p.Y376Y	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	376										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						GTTCATATATATATTTAAAAG	0.303														536	0.107029	0.2345	0.0821	5008	,	,		15884	0.0635		0.0477	False		,,,				2504	0.0583				p.Y376Y		Atlas-SNP	.											C1orf141,NS,carcinoma,0,1	C1orf141	58	1	0			c.T1128C						PASS	.	A		788,3618		98,592,1513	59.0	63.0	62.0		1128	-0.7	0.0	1	dbSNP_127	62	309,8285		10,289,3998	no	coding-synonymous	C1orf141	NM_001013674.1		108,881,5511	GG,GA,AA		3.5955,17.8847,8.4385		376/401	67558763	1097,11903	2203	4297	6500	SO:0001819	synonymous_variant	400757	exon8			ATATATATATTTA	BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.1128T>C	1.37:g.67558763A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_001276351	Q0P5P5|Q5JVX5	Silent	SNP	ENST00000371007.2	37	CCDS30745.1																																																																																			A|0.901;G|0.099	0.099	strong		0.303	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674	
RPTOR	57521	hgsc.bcm.edu	37	17	78921117	78921117	+	Silent	SNP	C	C	T	rs4969231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:78921117C>T	ENST00000306801.3	+	27	3593	c.3231C>T	c.(3229-3231)aaC>aaT	p.N1077N	RPTOR_ENST00000544334.2_Silent_p.N919N|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1077					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						AGTATCTGAACGGCCAGGACT	0.582													C|||	990	0.197684	0.0219	0.2795	5008	,	,		17535	0.2044		0.3052	False		,,,				2504	0.2597				p.N1077N		Atlas-SNP	.											RPTOR,colon,carcinoma,0,1	RPTOR	122	1	0			c.C3231T						PASS	.	C	,	324,4082	173.0+/-202.9	5,314,1884	71.0	59.0	63.0		2757,3231	-10.5	0.3	17	dbSNP_111	63	2755,5845	438.5+/-358.9	426,1903,1971	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	431,2217,3855	TT,TC,CC		32.0349,7.3536,23.6737	,	919/1178,1077/1336	78921117	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon27			TCTGAACGGCCAG		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.3231C>T	17.37:g.78921117C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	152	88	0.578947	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			C|0.763;T|0.237	0.237	strong		0.582	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
LVRN	206338	hgsc.bcm.edu	37	5	115298475	115298475	+	Missense_Mutation	SNP	T	T	C	rs12520255	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:115298475T>C	ENST00000357872.4	+	1	285	c.161T>C	c.(160-162)tTg>tCg	p.L54S	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		54				L -> S (in Ref. 1; AAS66719, 2; BAF84344, 4; EAW48946 and 5; AAH68560/AAI09023/ AAI09024). {ECO:0000305}.		integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CTCAGGGACTTGGAAGCCGAG	0.692													C|||	3876	0.773962	0.8533	0.804	5008	,	,		12010	0.747		0.7823	False		,,,				2504	0.6646				p.L54S		Atlas-SNP	.											.	.	.	.	0			c.T161C						PASS	.	C	SER/LEU	3696,668		1571,554,57	19.0	22.0	21.0		161	-0.4	0.0	5	dbSNP_120	21	6914,1608		2811,1292,158	yes	missense	AQPEP	NM_173800.4	145	4382,1846,215	CC,CT,TT		18.8688,15.3071,17.6626	benign	54/991	115298475	10610,2276	2182	4261	6443	SO:0001583	missense	0	exon1			GGGACTTGGAAGC																												ENST00000357872.4:c.161T>C	5.37:g.115298475T>C	ENSP00000350541:p.Leu54Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	61	59	0.967213	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	1699	0.7779304029304029	415	0.8434959349593496	292	0.8066298342541437	408	0.7132867132867133	584	0.7704485488126649	C	3.263	-0.150843	0.06585	0.846929	0.811312	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.01234	5.13	3.78	-0.439	0.12264	.	1.678220	0.03753	N	0.256933	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.09596	-1.0667	9	0.06757	T	0.87	.	3.7399	0.08526	0.5123:0.2781:0.0:0.2096	rs12520255;rs12520255	54	Q6Q4G3	AMPQ_HUMAN	S	54	ENSP00000350541:L54S	ENSP00000350541:L54S	L	+	2	0	AC010282.1	115326374	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.553000	0.06012	-0.232000	0.09811	-0.119000	0.15052	TTG	T|0.206;C|0.794	0.794	strong		0.692	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
LILRB4	11006	hgsc.bcm.edu	37	19	55179184	55179184	+	Silent	SNP	T	T	C	rs142100665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55179184T>C	ENST00000391736.1	+	13	1455	c.1140T>C	c.(1138-1140)tcT>tcC	p.S380S	LILRB4_ENST00000430952.2_Silent_p.S379S|LILRB4_ENST00000270452.2_Silent_p.S380S|LILRB4_ENST00000391733.3_Silent_p.S381S|LILRB4_ENST00000391734.3_Intron	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	380					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		CCCCACTGTCTGGGGAATTCC	0.587													T|||	47	0.00938498	0.025	0.0029	5008	,	,		18397	0.0		0.005	False		,,,				2504	0.0072				p.S380S		Atlas-SNP	.											.	LILRB4	86	.	0			c.T1140C						PASS	.						68.0	68.0	68.0					19																	55179184		2201	4297	6498	SO:0001819	synonymous_variant	11006	exon11			ACTGTCTGGGGAA	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1140T>C	19.37:g.55179184T>C		Somatic	468	0	0		WXS	Illumina HiSeq	Phase_I	493	58	0.117647	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Silent	SNP	ENST00000391736.1	37	CCDS12902.1																																																																																			T|0.633;C|0.367	0.367	strong		0.587	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
NRG1	3084	hgsc.bcm.edu	37	8	32453358	32453358	+	Missense_Mutation	SNP	G	G	A	rs3924999	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:32453358G>A	ENST00000405005.3	+	2	113	c.113G>A	c.(112-114)cGa>cAa	p.R38Q	NRG1_ENST00000519301.1_Missense_Mutation_p.R17Q|NRG1_ENST00000341377.5_Missense_Mutation_p.R38Q|NRG1_ENST00000287842.3_Missense_Mutation_p.R38Q|NRG1_ENST00000521670.1_Missense_Mutation_p.R38Q|NRG1_ENST00000338921.4_Missense_Mutation_p.R38Q|NRG1_ENST00000356819.4_Missense_Mutation_p.R38Q|NRG1_ENST00000520407.1_Missense_Mutation_p.R253Q|NRG1_ENST00000523079.1_Missense_Mutation_p.R38Q|NRG1_ENST00000287845.5_Missense_Mutation_p.R38Q			Q02297	NRG1_HUMAN	neuregulin 1	38	Ig-like C2-type.		R -> Q (in dbSNP:rs3924999). {ECO:0000269|PubMed:17565985}.		activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TTGCCTCCCCGATTGAAAGAG	0.423													G|||	1929	0.385184	0.0666	0.3746	5008	,	,		15194	0.7589		0.3767	False		,,,				2504	0.4468				p.R253Q		Atlas-SNP	.											NRG1_ENST00000521670,NS,carcinoma,+1,3	NRG1	260	3	0			c.G758A	GRCh37	CM054795	NRG1	M	rs3924999	PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	586,3820	255.5+/-260.7	40,506,1657	75.0	83.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	50,50,50,113,113,113,113,113,113,113,113,113,113,758,113	5.7	1.0	8	dbSNP_108	80	3404,5196	501.7+/-375.5	655,2094,1551	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	NRG1	NM_001159995.1,NM_001159999.1,NM_001160001.1,NM_001160002.1,NM_001160004.1,NM_001160005.1,NM_001160007.1,NM_001160008.1,NM_004495.3,NM_013956.3,NM_013957.3,NM_013958.3,NM_013960.3,NM_013962.2,NM_013964.3	43,43,43,43,43,43,43,43,43,43,43,43,43,43,43	695,2600,3208	AA,AG,GG		39.5814,13.3,30.6781	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	17/608,17/625,17/591,38/195,38/460,38/208,38/178,38/421,38/212,38/646,38/638,38/242,38/463,253/423,38/641	32453358	3990,9016	2203	4300	6503	SO:0001583	missense	3084	exon2			CTCCCCGATTGAA	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.113G>A	8.37:g.32453358G>A	ENSP00000384620:p.Arg38Gln	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_013962	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	896	0.41025641025641024	45	0.09146341463414634	126	0.34806629834254144	448	0.7832167832167832	277	0.3654353562005277	G	17.68	3.450326	0.63290	0.133	0.395814	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000520407;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000341377;ENST00000287842;ENST00000405005;ENST00000521670	T;T;T;T;T;T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.65	5.65	0.86999	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.370264	0.27266	N	0.020157	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.9999999999999984	B;D;B;P;B;P;B;P;B;B;P;P	0.54397	0.381;0.966;0.251;0.637;0.233;0.58;0.212;0.58;0.212;0.047;0.521;0.698	B;B;B;B;B;B;B;B;B;B;B;B	0.37267	0.081;0.245;0.149;0.188;0.019;0.117;0.048;0.117;0.071;0.022;0.065;0.097	T	0.25012	-1.0144	9	0.51188	T	0.08	.	9.1012	0.36669	0.1236:0.0:0.8764:0.0	rs3924999;rs17665390;rs17845097;rs17857884;rs52817411;rs60068866;rs3924999	38;38;38;37;37;38;38;38;38;38;38;253	E9PHH4;F8W9E3;Q7RTW4;B0FYA9;B0FWZ3;B7Z4Z3;Q02297-7;Q02297;Q02297-6;Q02297-3;Q02297-8;Q02297-9	.;.;.;.;.;.;.;NRG1_HUMAN;.;.;.;.	Q	17;17;253;106;38;38;38;38;38;38;38;38;38	ENSP00000430053:R17Q;ENSP00000429582:R17Q;ENSP00000434640:R253Q;ENSP00000429067:R106Q;ENSP00000430120:R38Q;ENSP00000343395:R38Q;ENSP00000349275:R38Q;ENSP00000287840:R38Q;ENSP00000287845:R38Q;ENSP00000340497:R38Q;ENSP00000287842:R38Q;ENSP00000384620:R38Q;ENSP00000428828:R38Q	ENSP00000287840:R38Q	R	+	2	0	NRG1	32572900	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.343000	0.52167	2.826000	0.97356	0.563000	0.77884	CGA	G|0.635;A|0.365	0.365	strong		0.423	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
SORCS2	57537	hgsc.bcm.edu	37	4	7735111	7735111	+	Silent	SNP	A	A	G	rs79532786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:7735111A>G	ENST00000507866.2	+	24	3280	c.3171A>G	c.(3169-3171)ggA>ggG	p.G1057G	SORCS2_ENST00000329016.9_Silent_p.G885G	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	1057					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						TGCGAGGCGGAGTCCGGGTCC	0.662													A|||	116	0.0231629	0.003	0.0346	5008	,	,		13462	0.0		0.0805	False		,,,				2504	0.0072				p.G1057G		Atlas-SNP	.											SORCS2,NS,carcinoma,0,1	SORCS2	98	1	0			c.A3171G						scavenged	.	A		53,3997		1,51,1973	15.0	18.0	17.0		3171	-1.9	0.3	4	dbSNP_132	17	558,7768		21,516,3626	no	coding-synonymous	SORCS2	NM_020777.2		22,567,5599	GG,GA,AA		6.7019,1.3086,4.937		1057/1160	7735111	611,11765	2025	4163	6188	SO:0001819	synonymous_variant	57537	exon24			AGGCGGAGTCCGG	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.3171A>G	4.37:g.7735111A>G		Somatic	189	10	0.0529101		WXS	Illumina HiSeq	Phase_I	195	97	0.497436	NM_020777	Q9P2L7	Silent	SNP	ENST00000507866.2	37	CCDS47008.1																																																																																			A|0.965;G|0.035	0.035	strong		0.662	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331940	21331940	+	Missense_Mutation	SNP	G	G	A	rs374113543		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:21331940G>A	ENST00000256958.2	+	7	809	c.713G>A	c.(712-714)gGa>gAa	p.G238E		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	238					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	GTGGATATTGGATATGTAGAT	0.333																																					p.G238E		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.G713A						PASS	.	G	GLU/GLY	0,4406		0,0,2203	105.0	105.0	105.0		713	3.8	1.0	12		105	1,8593	1.2+/-3.3	0,1,4296	no	missense	SLCO1B1	NM_006446.4	98	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	238/692	21331940	1,12999	2203	4297	6500	SO:0001583	missense	10599	exon7			ATATTGGATATGT		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.713G>A	12.37:g.21331940G>A	ENSP00000256958:p.Gly238Glu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.747048	0.49257	0.0	1.16E-4	ENSG00000134538	ENST00000256958	T	0.71579	-0.58	3.76	3.76	0.43208	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.83751	0.5322	M	0.80028	2.48	0.53005	D	0.999961	D	0.71674	0.998	D	0.75484	0.986	D	0.85519	0.1202	10	0.46703	T	0.11	.	16.1164	0.81306	0.0:0.0:1.0:0.0	.	238	Q9Y6L6	SO1B1_HUMAN	E	238	ENSP00000256958:G238E	ENSP00000256958:G238E	G	+	2	0	SLCO1B1	21223207	1.000000	0.71417	1.000000	0.80357	0.470000	0.32858	7.186000	0.77722	2.096000	0.63516	0.305000	0.20034	GGA	.	.	weak		0.333	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
TNKS	8658	hgsc.bcm.edu	37	8	9609331	9609331	+	Silent	SNP	G	G	A	rs13265931	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:9609331G>A	ENST00000310430.6	+	19	3071	c.3045G>A	c.(3043-3045)gcG>gcA	p.A1015A	TNKS_ENST00000518281.1_Silent_p.A778A	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	1015					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		ATGGCGCCGCGGGAACAGAAA	0.507													G|||	707	0.141174	0.1369	0.098	5008	,	,		16575	0.1994		0.1561	False		,,,				2504	0.1022				p.A1015A		Atlas-SNP	.											.	TNKS	198	.	0			c.G3045A						PASS	.	G		599,3807	255.2+/-260.5	42,515,1646	60.0	64.0	63.0		3045	-11.5	0.0	8	dbSNP_121	63	1403,7197	254.3+/-279.6	120,1163,3017	no	coding-synonymous	TNKS	NM_003747.2		162,1678,4663	AA,AG,GG		16.314,13.5951,15.3929		1015/1328	9609331	2002,11004	2203	4300	6503	SO:0001819	synonymous_variant	8658	exon19			CGCCGCGGGAACA	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.3045G>A	8.37:g.9609331G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	37	CCDS5974.1																																																																																			G|0.844;A|0.156	0.156	strong		0.507	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	
LMAN2L	81562	hgsc.bcm.edu	37	2	97368800	97368800	+	IGR	SNP	C	C	A	rs373937760		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97368800C>A	ENST00000264963.4	-	0	2397				FER1L5_ENST00000457909.1_RNA	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like						ER to Golgi vesicle-mediated transport (GO:0006888)|protein folding (GO:0006457)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|lung(2)|skin(1)|urinary_tract(1)	7						ATCTTCTCCCCCGACGACTTC	0.557																																					p.P1864H		Atlas-SNP	.											.	FER1L5	113	.	0			c.C5591A						PASS	.	C	HIS/PRO	0,4002		0,0,2001	70.0	66.0	68.0		5591	-2.4	0.0	2		68	1,8327		0,1,4163	no	missense	FER1L5	NM_001113382.1	77	0,1,6164	AA,AC,CC		0.012,0.0,0.0081	benign	1864/2094	97368800	1,12329	2001	4164	6165	SO:0001628	intergenic_variant	90342	exon48			TCTCCCCCGACGA	AL136617	CCDS2023.1, CCDS46365.1	2q11.1	2008-02-05			ENSG00000114988	ENSG00000114988			19263	protein-coding gene	gene with protein product		609552				12609988	Standard	NM_001142292		Approved	DKFZp564L2423, VIPL	uc002swv.3	Q9H0V9	OTTHUMG00000130453		2.37:g.97368800C>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	205	96	0.468293	NM_001113382	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Missense_Mutation	SNP	ENST00000264963.4	37	CCDS2023.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376462	0.24857	0.0	1.2E-4	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.67	-2.36	0.06663	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.693696	0.11893	U	0.519455	T	0.61627	0.2362	L	0.52126	1.63	.	.	.	P;D;P	0.57571	0.954;0.98;0.944	P;P;B	0.54590	0.482;0.756;0.35	T	0.64960	-0.6284	8	0.15499	T	0.54	2.0843	18.405	0.90532	0.0:0.1727:0.7607:0.0667	.	572;1864;573	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	H	1864;1868;573	.	ENSP00000442027:P573H	P	+	2	0	FER1L5	96732527	0.000000	0.05858	0.000000	0.03702	0.987000	0.75469	-0.594000	0.05733	-0.882000	0.03987	0.655000	0.94253	CCC	.	.	weak		0.557	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805	
ZBTB32	27033	hgsc.bcm.edu	37	19	36207510	36207510	+	Silent	SNP	G	G	A	rs1052491	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36207510G>A	ENST00000392197.2	+	7	1638	c.1320G>A	c.(1318-1320)ctG>ctA	p.L440L	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000222270.7_5'Flank|ZBTB32_ENST00000262630.3_Silent_p.L440L|KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000341701.1_5'Flank			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	440					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTCCCAGCCTGGCCTCCATGC	0.701											OREG0025433	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	209	0.0417332	0.0068	0.0591	5008	,	,		16742	0.0		0.1272	False		,,,				2504	0.0317				p.L440L		Atlas-SNP	.											.	ZBTB32	33	.	0			c.G1320A						PASS	.	G		144,4262	101.2+/-139.8	4,136,2063	59.0	56.0	57.0		1320	2.6	1.0	19	dbSNP_86	57	1235,7363	246.7+/-275.0	95,1045,3159	no	coding-synonymous	ZBTB32	NM_014383.1		99,1181,5222	AA,AG,GG		14.3638,3.2683,10.6044		440/488	36207510	1379,11625	2203	4299	6502	SO:0001819	synonymous_variant	27033	exon6			CAGCCTGGCCTCC	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16763	protein-coding gene	gene with protein product	"""repressor of GATA"""	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.1320G>A	19.37:g.36207510G>A		Somatic	49	0	0	861	WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_014383	Q8WVP2	Silent	SNP	ENST00000392197.2	37	CCDS12471.1																																																																																			G|0.910;A|0.090	0.090	strong		0.701	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383	
USP32	84669	hgsc.bcm.edu	37	17	58285542	58285542	+	Missense_Mutation	SNP	G	G	A	rs147413172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:58285542G>A	ENST00000300896.4	-	24	2997	c.2803C>T	c.(2803-2805)Cgg>Tgg	p.R935W	USP32_ENST00000592339.1_Missense_Mutation_p.R605W	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	935	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R935W(2)		NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AGTCCATACCGTACAGGGGTA	0.353																																					p.R935W		Atlas-SNP	.											USP32,NS,malignant_melanoma,0,2	USP32	128	2	2	Substitution - Missense(2)	NS(1)|pancreas(1)	c.C2803T						scavenged	.						37.0	43.0	41.0					17																	58285542		2202	4289	6491	SO:0001583	missense	84669	exon24			CATACCGTACAGG	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"""Ubiquitin-specific peptidases"", ""EF-hand domain containing"""	19143	protein-coding gene	gene with protein product		607740	"""ubiquitin specific protease 32"""			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.2803C>T	17.37:g.58285542G>A	ENSP00000300896:p.Arg935Trp	Somatic	590	1	0.00169492		WXS	Illumina HiSeq	Phase_I	562	167	0.297153	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294566	0.81025	.	.	ENSG00000170832	ENST00000300896	T	0.53206	0.63	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.72550	0.3474	M	0.82433	2.59	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.77376	-0.2611	10	0.87932	D	0	.	18.7745	0.91904	0.0:0.0:1.0:0.0	.	935	Q8NFA0	UBP32_HUMAN	W	935	ENSP00000300896:R935W	ENSP00000300896:R935W	R	-	1	2	USP32	55640324	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	5.540000	0.67205	2.436000	0.82500	0.563000	0.77884	CGG	.	.	weak		0.353	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582	
RND1	27289	hgsc.bcm.edu	37	12	49255798	49255798	+	Silent	SNP	G	G	C	rs1565933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49255798G>C	ENST00000309739.5	-	3	442	c.312C>G	c.(310-312)ctC>ctG	p.L104L		NM_014470.3	NP_055285.1	Q92730	RND1_HUMAN	Rho family GTPase 1	104					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|GTP catabolic process (GO:0006184)|negative regulation of cell adhesion (GO:0007162)|neuron remodeling (GO:0016322)|small GTPase mediated signal transduction (GO:0007264)	adherens junction (GO:0005912)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(2)|skin(1)|urinary_tract(1)	10						TTACCTTCTTGAGTGCGCTGT	0.468													G|||	2057	0.410743	0.2821	0.5432	5008	,	,		22196	0.3869		0.4722	False		,,,				2504	0.4519				p.L104L		Atlas-SNP	.											.	RND1	26	.	0			c.C312G						PASS	.	G		1467,2939	473.7+/-356.8	250,967,986	126.0	105.0	112.0		312	2.3	1.0	12	dbSNP_88	112	4041,4559	556.0+/-386.8	941,2159,1200	no	coding-synonymous	RND1	NM_014470.3		1191,3126,2186	CC,CG,GG		46.9884,33.2955,42.3497		104/233	49255798	5508,7498	2203	4300	6503	SO:0001819	synonymous_variant	27289	exon3			CTTCTTGAGTGCG	Y07923	CCDS8771.1	12q12	2008-01-23				ENSG00000172602			18314	protein-coding gene	gene with protein product	"""ras homolog gene family, member S"""	609038				9531558	Standard	NM_014470		Approved	Rho6, ARHS, RHOS	uc001rsn.3	Q92730	OTTHUMG00000170400	ENST00000309739.5:c.312C>G	12.37:g.49255798G>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	138	67	0.485507	NM_014470	A8K9P7	Silent	SNP	ENST00000309739.5	37	CCDS8771.1																																																																																			G|0.576;C|0.424	0.424	strong		0.468	RND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408915.1	NM_014470	
BTLA	151888	hgsc.bcm.edu	37	3	112185025	112185025	+	Missense_Mutation	SNP	G	G	A	rs9288952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:112185025G>A	ENST00000334529.5	-	5	1002	c.800C>T	c.(799-801)cCg>cTg	p.P267L	BTLA_ENST00000383680.4_Missense_Mutation_p.P219L|BTLA_ENST00000474965.1_5'UTR	NM_181780.3	NP_861445	Q7Z6A9	BTLA_HUMAN	B and T lymphocyte associated	267			P -> L (in dbSNP:rs9288952). {ECO:0000269|PubMed:12796776, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		immune response-regulating cell surface receptor signaling pathway (GO:0002768)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of B cell proliferation (GO:0030889)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|cervix(2)|large_intestine(1)|lung(5)|prostate(1)	11		Acute lymphoblastic leukemia(4;1.34e-07)|all_hematologic(4;0.000361)				TCTTGAGTTCGGTCCAATGAC	0.428													G|||	3228	0.644569	0.1838	0.745	5008	,	,		20917	0.7212		0.9563	False		,,,				2504	0.7965				p.P267L		Atlas-SNP	.											.	BTLA	22	.	0			c.C800T						PASS	.	G	LEU/PRO,LEU/PRO	1302,3104	439.2+/-345.6	192,918,1093	184.0	177.0	179.0		656,800	-0.7	0.0	3	dbSNP_119	179	8240,360	803.4+/-407.3	3947,346,7	yes	missense,missense	BTLA	NM_001085357.1,NM_181780.3	98,98	4139,1264,1100	AA,AG,GG		4.186,29.5506,26.6339	benign,benign	219/242,267/290	112185025	9542,3464	2203	4300	6503	SO:0001583	missense	151888	exon5			GAGTTCGGTCCAA	AY293286	CCDS33819.1, CCDS43130.1	3q13.2	2013-01-11			ENSG00000186265	ENSG00000186265		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21087	protein-coding gene	gene with protein product		607925				12796776	Standard	NM_001085357		Approved	BTLA1, CD272	uc003dza.4	Q7Z6A9	OTTHUMG00000159255	ENST00000334529.5:c.800C>T	3.37:g.112185025G>A	ENSP00000333919:p.Pro267Leu	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_181780	Q3B831|Q3HS85|Q6ZNH9	Missense_Mutation	SNP	ENST00000334529.5	37	CCDS33819.1	1508	0.6904761904761905	85	0.17276422764227642	271	0.7486187845303868	428	0.7482517482517482	724	0.9551451187335093	G	0	-2.602620	0.00123	0.295506	0.95814	ENSG00000186265	ENST00000334529;ENST00000383680	T;T	0.28069	2.05;1.63	4.93	-0.709	0.11237	.	1.638350	0.03415	N	0.205342	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21449	-1.0245	9	0.14656	T	0.56	0.4069	5.0751	0.14626	0.3938:0.4195:0.1868:0.0	rs9288952;rs52829875;rs59894548;rs9288952	219;267	Q7Z6A9-2;Q7Z6A9	.;BTLA_HUMAN	L	267;219	ENSP00000333919:P267L;ENSP00000373178:P219L	ENSP00000333919:P267L	P	-	2	0	BTLA	113667715	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.120000	0.15647	-0.251000	0.09542	-1.130000	0.01982	CCG	G|0.301;A|0.699	0.699	strong		0.428	BTLA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354101.1	NM_181780	
C2orf42	54980	hgsc.bcm.edu	37	2	70377653	70377653	+	Silent	SNP	G	G	A	rs12989348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:70377653G>A	ENST00000264434.2	-	10	1939	c.1560C>T	c.(1558-1560)atC>atT	p.I520I	C2orf42_ENST00000420306.1_Silent_p.I520I	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	520										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						GGATCCACTCGATGATGAAAG	0.478													G|||	172	0.034345	0.0053	0.0447	5008	,	,		18358	0.001		0.1243	False		,,,				2504	0.0082				p.I520I		Atlas-SNP	.											.	C2orf42	30	.	0			c.C1560T						PASS	.	G		122,4284	92.5+/-131.2	1,120,2082	136.0	120.0	126.0		1560	-7.9	0.7	2	dbSNP_121	126	1151,7449	236.9+/-269.0	80,991,3229	no	coding-synonymous	C2orf42	NM_017880.1		81,1111,5311	AA,AG,GG		13.3837,2.769,9.7878		520/575	70377653	1273,11733	2203	4300	6503	SO:0001819	synonymous_variant	54980	exon10			CCACTCGATGATG	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.1560C>T	2.37:g.70377653G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_017880	D6W5G3|Q9H629	Silent	SNP	ENST00000264434.2	37	CCDS1899.1																																																																																			G|0.920;A|0.080	0.080	strong		0.478	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880	
ENTPD4	9583	hgsc.bcm.edu	37	8	23292985	23292985	+	Silent	SNP	A	A	G	rs3736652	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:23292985A>G	ENST00000358689.4	-	11	1615	c.1380T>C	c.(1378-1380)taT>taC	p.Y460Y	ENTPD4_ENST00000521321.1_5'UTR|ENTPD4_ENST00000417069.2_Silent_p.Y452Y|ENTPD4_ENST00000356206.6_Silent_p.Y452Y	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	460					UDP catabolic process (GO:0006256)	cytoplasmic vesicle (GO:0031410)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)	uridine-diphosphatase activity (GO:0045134)	p.Y460Y(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	25		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		TTGTTGCACAATAATCCTGAA	0.373													A|||	679	0.135583	0.1694	0.0706	5008	,	,		21672	0.123		0.0984	False		,,,				2504	0.1871				p.Y460Y		Atlas-SNP	.											ENTPD4,NS,carcinoma,0,1	ENTPD4	56	1	1	Substitution - coding silent(1)	stomach(1)	c.T1380C						PASS	.	A	,	712,3694	294.4+/-283.1	60,592,1551	92.0	82.0	85.0		1356,1380	-4.3	1.0	8	dbSNP_107	85	754,7846	181.8+/-230.4	33,688,3579	no	coding-synonymous,coding-synonymous	ENTPD4	NM_001128930.2,NM_004901.4	,	93,1280,5130	GG,GA,AA		8.7674,16.1598,11.2717	,	452/609,460/617	23292985	1466,11540	2203	4300	6503	SO:0001819	synonymous_variant	9583	exon11			TGCACAATAATCC	AJ131358	CCDS6041.1, CCDS47827.1	8p21.3	2014-05-16	2004-09-22	2004-09-22	ENSG00000197217	ENSG00000197217			14573	protein-coding gene	gene with protein product		607577	"""lysosomal apyrase-like 1"""	LYSAL1		10393803, 9205841	Standard	NM_001128930		Approved	LALP70, LAP70, KIAA0392, NTPDase-4, UDPase	uc003xdl.3	Q9Y227	OTTHUMG00000097852	ENST00000358689.4:c.1380T>C	8.37:g.23292985A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_004901	D3DSS3|O15092	Silent	SNP	ENST00000358689.4	37	CCDS6041.1																																																																																			A|0.884;G|0.116	0.116	strong		0.373	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901	
FBXO36	130888	hgsc.bcm.edu	37	2	230861519	230861519	+	Missense_Mutation	SNP	G	G	T	rs1035834	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:230861519G>T	ENST00000283946.3	+	3	276	c.258G>T	c.(256-258)ttG>ttT	p.L86F	FBXO36_ENST00000373652.3_Missense_Mutation_p.L55F|FBXO36_ENST00000409992.1_Intron	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	86			L -> F (in dbSNP:rs1035834). {ECO:0000269|PubMed:15489334}.					p.L86F(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		TCATCAATTTGTGCAAAGGTA	0.358													G|||	900	0.179712	0.1959	0.268	5008	,	,		20240	0.1042		0.2654	False		,,,				2504	0.0849				p.L86F		Atlas-SNP	.											FBXO36_ENST00000283946,NS,carcinoma,0,1	FBXO36	22	1	1	Substitution - Missense(1)	stomach(1)	c.G258T						PASS	.	G	PHE/LEU	833,3573	326.9+/-299.8	69,695,1439	172.0	166.0	168.0		258	1.0	1.0	2	dbSNP_86	168	2064,6536	358.1+/-331.0	275,1514,2511	no	missense	FBXO36	NM_174899.4	22	344,2209,3950	TT,TG,GG		24.0,18.906,22.2743	probably-damaging	86/189	230861519	2897,10109	2203	4300	6503	SO:0001583	missense	130888	exon3			CAATTTGTGCAAA	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"""F-boxes /  ""other"""""	27020	protein-coding gene	gene with protein product		609105	"""F-box only protein 36"""			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.258G>T	2.37:g.230861519G>T	ENSP00000283946:p.Leu86Phe	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	237	103	0.434599	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	Missense_Mutation	SNP	ENST00000283946.3	37	CCDS2472.1	465	0.2129120879120879	97	0.19715447154471544	106	0.292817679558011	61	0.10664335664335664	201	0.26517150395778366	G	13.49	2.254163	0.39896	0.18906	0.24	ENSG00000153832	ENST00000373652;ENST00000283946	T;T	0.57907	0.37;0.44	5.37	0.962	0.19643	.	0.000000	0.64402	D	0.000008	T	0.00012	0.0000	M	0.81682	2.555	0.09310	P	0.9999999999885822	D;D	0.60160	0.987;0.987	P;P	0.59825	0.864;0.864	T	0.11203	-1.0597	9	0.56958	D	0.05	-18.3118	12.425	0.55542	0.1911:0.0:0.8089:0.0	rs1035834;rs17846077;rs17859075;rs52834785;rs1035834	55;86	B3KVQ6;Q8NEA4	.;FBX36_HUMAN	F	55;86	ENSP00000362756:L55F;ENSP00000283946:L86F	ENSP00000283946:L86F	L	+	3	2	FBXO36	230569763	1.000000	0.71417	0.959000	0.39883	0.083000	0.17756	0.765000	0.26546	0.125000	0.18397	0.561000	0.74099	TTG	G|0.789;T|0.211	0.211	strong		0.358	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899	
OR10P1	121130	hgsc.bcm.edu	37	12	56031318	56031318	+	Missense_Mutation	SNP	A	A	T	rs76940436	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56031318A>T	ENST00000309675.2	+	1	675	c.643A>T	c.(643-645)Att>Ttt	p.I215F	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26						CTTCTCTCTGATTGTCACCTC	0.567													A|||	53	0.0105831	0.0386	0.0029	5008	,	,		18931	0.0		0.0	False		,,,				2504	0.0				p.I215F		Atlas-SNP	.											.	OR10P1	48	.	0			c.A643T						PASS	.	A	PHE/ILE	209,4197	130.2+/-166.9	3,203,1997	133.0	112.0	119.0		643	4.4	0.2	12	dbSNP_131	119	3,8597	2.2+/-6.3	0,3,4297	yes	missense	OR10P1	NM_206899.1	21	3,206,6294	TT,TA,AA		0.0349,4.7435,1.63	probably-damaging	215/314	56031318	212,12794	2203	4300	6503	SO:0001583	missense	121130	exon1			TCTCTGATTGTCA	BK004259	CCDS31828.1	12q13.13	2012-08-09		2004-03-10		ENSG00000175398		"""GPCR / Class A : Olfactory receptors"""	15378	protein-coding gene	gene with protein product				OR10P1P, OR10P2P, OR10P3P			Standard	NM_206899		Approved	OST701	uc010spq.2	Q8NGE3	OTTHUMG00000169961	ENST00000309675.2:c.643A>T	12.37:g.56031318A>T	ENSP00000308082:p.Ile215Phe	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_206899	B9EGY4	Missense_Mutation	SNP	ENST00000309675.2	37	CCDS31828.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	A	12.41	1.929041	0.34002	0.047435	3.49E-4	ENSG00000175398	ENST00000309675	T	0.00333	8.07	4.44	4.44	0.53790	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000194	T	0.00241	0.0007	H	0.97564	4.03	0.37082	D	0.899042	D	0.76494	0.999	D	0.75484	0.986	T	0.08452	-1.0721	10	0.87932	D	0	.	6.7619	0.23546	0.8955:0.0:0.1045:0.0	.	215	Q8NGE3	O10P1_HUMAN	F	215	ENSP00000308082:I215F	ENSP00000308082:I215F	I	+	1	0	OR10P1	54317585	0.728000	0.28080	0.178000	0.23040	0.033000	0.12548	2.073000	0.41519	1.999000	0.58509	0.459000	0.35465	ATT	A|0.985;T|0.015	0.015	strong		0.567	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1		
RNF207	388591	hgsc.bcm.edu	37	1	6279370	6279370	+	Missense_Mutation	SNP	G	G	C	rs846111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:6279370G>C	ENST00000377939.4	+	18	1935	c.1808G>C	c.(1807-1809)gGc>gCc	p.G603A	RNF207_ENST00000377948.2_3'UTR|RNF207_ENST00000483336.1_3'UTR|ICMT_ENST00000495791.1_5'Flank	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	603			G -> A (in dbSNP:rs846111). {ECO:0000269|PubMed:19305409}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		GCTCCGAACGGCCTCTCAGAA	0.498													G|||	864	0.172524	0.0227	0.1758	5008	,	,		16230	0.1756		0.2604	False		,,,				2504	0.2791				p.G603A		Atlas-SNP	.											RNF207,caecum,carcinoma,0,2	RNF207	45	2	0			c.G1808C						PASS	.	G	ALA/GLY	219,3517		9,201,1658	54.0	56.0	55.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1808	1.0	0.0	1	dbSNP_86	55	2163,6045		285,1593,2226	yes	missense	RNF207	NM_207396.2	60	294,1794,3884	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	26.3523,5.8619,19.9431	benign	603/635	6279370	2382,9562	1868	4104	5972	SO:0001583	missense	388591	exon18			CGAACGGCCTCTC	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1808G>C	1.37:g.6279370G>C	ENSP00000367173:p.Gly603Ala	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	206	127	0.616505	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	380	0.17399267399267399	13	0.026422764227642278	70	0.19337016574585636	101	0.17657342657342656	196	0.25857519788918204	G	7.864	0.726640	0.15439	0.058619	0.263523	ENSG00000158286	ENST00000377939	T	0.15952	2.38	5.33	1.01	0.19927	.	0.326684	0.20268	U	0.095722	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.45264	-0.9273	9	0.13470	T	0.59	-0.5354	1.7254	0.02921	0.1818:0.1635:0.4863:0.1684	rs846111;rs3765570;rs17437807;rs846111	603	Q6ZRF8	RN207_HUMAN	A	603	ENSP00000367173:G603A	ENSP00000367173:G603A	G	+	2	0	RNF207	6201957	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.127000	0.10547	0.314000	0.23086	-0.140000	0.14226	GGC	G|0.803;C|0.197	0.197	strong		0.498	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
TNFRSF8	943	hgsc.bcm.edu	37	1	12164437	12164437	+	Splice_Site	SNP	C	C	T	rs2230622	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12164437C>T	ENST00000263932.2	+	4	492	c.270C>T	c.(268-270)gaC>gaT	p.D90D	TNFRSF8_ENST00000417814.2_5'UTR	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	90					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	GTCCCTTAGACGACCTCGTGG	0.597													C|||	1466	0.292732	0.2118	0.379	5008	,	,		16676	0.3264		0.2296	False		,,,				2504	0.3712				p.D90D		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.C270T						PASS	.	C		956,3450		101,754,1348	109.0	89.0	96.0		270	-8.1	0.0	1	dbSNP_98	96	2082,6518		247,1588,2465	yes	coding-synonymous-near-splice	TNFRSF8	NM_001243.3		348,2342,3813	TT,TC,CC		24.2093,21.6977,23.3584		90/596	12164437	3038,9968	2203	4300	6503	SO:0001630	splice_region_variant	943	exon4			CTTAGACGACCTC	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.269-1C>T	1.37:g.12164437C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Silent	SNP	ENST00000263932.2	37	CCDS144.1																																																																																			C|0.611;A|0.050	.	strong		0.597	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1		Silent
HRNR	388697	hgsc.bcm.edu	37	1	152187437	152187437	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152187437A>G	ENST00000368801.2	-	3	6743	c.6668T>C	c.(6667-6669)gTc>gCc	p.V2223A	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2223					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGACCAAAGACAGAAGAGTG	0.567																																					p.V2223A		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.T6668C						scavenged	.						2.0	1.0	1.0					1																	152187437		896	1896	2792	SO:0001583	missense	388697	exon3			CCAAAGACAGAAG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6668T>C	1.37:g.152187437A>G	ENSP00000357791:p.Val2223Ala	Somatic	366	1	0.00273224		WXS	Illumina HiSeq	Phase_I	1275	110	0.0862745	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	12.54	1.967822	0.34754	.	.	ENSG00000197915	ENST00000368801	T	0.15834	2.39	2.79	-1.81	0.07882	.	.	.	.	.	T	0.01905	0.0060	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46345	-0.9198	9	0.08381	T	0.77	.	0.7951	0.01065	0.1625:0.2182:0.3221:0.2972	.	2223	Q86YZ3	HORN_HUMAN	A	2223	ENSP00000357791:V2223A	ENSP00000357791:V2223A	V	-	2	0	HRNR	150454061	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.394000	0.07296	-0.638000	0.05509	-2.011000	0.00436	GTC	.	.	none		0.567	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458598	4458598	+	Missense_Mutation	SNP	G	G	C	rs3809849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4458598G>C	ENST00000254718.4	-	1	328	c.22C>G	c.(22-24)Cag>Gag	p.Q8E	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.Q8E			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	8	Interaction with MYB. {ECO:0000250}.		Q -> E (in dbSNP:rs3809849).		cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						GACATCGGCTGGGCGGGATCC	0.652													C|||	1061	0.211861	0.2496	0.1772	5008	,	,		14645	0.1488		0.2078	False		,,,				2504	0.2546				p.Q8E		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C22G						PASS	.	C	GLU/GLN,GLU/GLN	1012,3384		139,734,1325	13.0	15.0	14.0		22,22	4.1	0.0	17	dbSNP_107	14	1775,6811		198,1379,2716	yes	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	29,29	337,2113,4041	CC,CG,GG		20.6732,23.0209,21.4682	benign,benign	8/1333,8/1329	4458598	2787,10195	2198	4293	6491	SO:0001583	missense	10514	exon1			TCGGCTGGGCGGG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.22C>G	17.37:g.4458598G>C	ENSP00000254718:p.Gln8Glu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	468	0.21428571428571427	118	0.23983739837398374	73	0.20165745856353592	110	0.19230769230769232	167	0.22031662269129287	C	5.998	0.368018	0.11352	0.230209	0.206732	ENSG00000132382	ENST00000381556;ENST00000254718;ENST00000426435	T;T	0.15718	2.4;2.41	4.08	4.08	0.47627	.	0.340848	0.26927	N	0.021789	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37641	-0.9697	9	0.02654	T	1	-25.8904	13.5965	0.61994	0.0:0.842:0.158:0.0	rs3809849;rs3809849	8;8	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	E	8	ENSP00000370968:Q8E;ENSP00000254718:Q8E	ENSP00000254718:Q8E	Q	-	1	0	MYBBP1A	4405347	0.001000	0.12720	0.003000	0.11579	0.001000	0.01503	0.812000	0.27211	1.325000	0.45301	-0.187000	0.12897	CAG	G|0.795;C|0.205	0.205	strong		0.652	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
ASIC2	40	hgsc.bcm.edu	37	17	31618732	31618732	+	Intron	SNP	A	A	G	rs9893935	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:31618732A>G	ENST00000359872.6	-	2	1317				ASIC2_ENST00000448983.1_5'Flank|ASIC2_ENST00000225823.2_Silent_p.T134T	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2						central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	TGTTGCACACAGTGACGGCGG	0.672													G|||	2804	0.559904	0.5673	0.5922	5008	,	,		12047	0.7649		0.4851	False		,,,				2504	0.3926				p.T134T		Atlas-SNP	.											ACCN1,NS,carcinoma,0,2	.	.	2	0			c.T402C						PASS	.	G	,	2418,1942		705,1008,467	31.0	30.0	30.0		,402	-1.1	1.0	17	dbSNP_119	30	4241,4311		1081,2079,1116	no	intron,coding-synonymous	ACCN1	NM_001094.4,NM_183377.1	,	1786,3087,1583	GG,GA,AA		49.5907,44.5413,48.4278	,	,134/564	31618732	6659,6253	2180	4276	6456	SO:0001627	intron_variant	40	exon1			GCACACAGTGACG	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	99	protein-coding gene	gene with protein product	"""degenerin"""	601784	"""amiloride-sensitive cation channel 1, neuronal"""	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.556-179647T>C	17.37:g.31618732A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_183377	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	37	CCDS42296.1																																																																																			A|0.468;G|0.532	0.532	strong		0.672	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094	
DDR1	780	hgsc.bcm.edu	37	6	30864829	30864829	+	Silent	SNP	T	T	C	rs1049623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30864829T>C	ENST00000324771.8	+	16	2456	c.1908T>C	c.(1906-1908)gtT>gtC	p.V636V	DDR1_ENST00000376567.2_Silent_p.V599V|DDR1_ENST00000376570.4_Silent_p.V599V|DDR1_ENST00000361741.4_Silent_p.V303V|DDR1_ENST00000376569.3_Silent_p.V599V|DDR1_ENST00000376568.3_Silent_p.V636V|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000454612.2_Silent_p.V599V|DDR1_ENST00000513240.1_Silent_p.V636V|DDR1_ENST00000452441.1_Silent_p.V636V|DDR1_ENST00000508312.1_Silent_p.V617V|DDR1_ENST00000376575.3_Silent_p.V636V|DDR1_ENST00000418800.2_Silent_p.V599V			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	636	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	AAGATCTGGTTAGTCTTGATT	0.512													C|||	2683	0.535743	0.4531	0.5245	5008	,	,		14894	0.6667		0.3847	False		,,,				2504	0.6759				p.V636V		Atlas-SNP	.											DDR1_ENST00000376575,NS,adenoma,0,3	DDR1	213	3	0			c.T1908C	GRCh37	CM076148	DDR1	M	rs1049623	PASS	.	C	,,,,,	2008,2398	615.9+/-392.7	473,1062,668	203.0	181.0	189.0		,1470,1851,1797,1908,1908	5.3	1.0	6	dbSNP_86	189	3287,5313	648.3+/-400.5	620,2047,1633	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,,,,,	1093,3109,2301	CC,CT,TT		38.2209,45.5742,40.712	,,,,,	,490/768,617/895,599/877,636/914,636/920	30864829	5295,7711	2203	4300	6503	SO:0001819	synonymous_variant	780	exon13			TCTGGTTAGTCTT	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1908T>C	6.37:g.30864829T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	252	99	0.392857	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	37	CCDS34385.1	1109	0.5077838827838828	252	0.5121951219512195	189	0.5220994475138122	349	0.6101398601398601	319	0.420844327176781	C	10.41	1.343892	0.24339	0.455742	0.382209	ENSG00000204580	ENST00000514434	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.79	0.29114	0.0:0.7501:0.1626:0.0873	rs1049623;rs1264316;rs2228636;rs3173380;rs17413087;rs58133601;rs1049623	.	.	.	Q	128	.	.	X	+	1	0	DDR1	30972808	0.012000	0.17670	1.000000	0.80357	0.871000	0.50021	0.586000	0.23894	1.250000	0.43966	-0.215000	0.12644	TAG	T|0.539;C|0.461	0.461	strong		0.512	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907843	12907843	+	Silent	SNP	T	T	G	rs2982093		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12907843T>G	ENST00000317869.6	-	2	525	c.300A>C	c.(298-300)tcA>tcC	p.S100S		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	100						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						TCTCCGCTGCTGATCGTTTCA	0.488																																					p.S100S		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,-1,1	HNRNPCL1	68	1	0			c.A300C						scavenged	.						133.0	126.0	129.0					1																	12907843		2203	4300	6503	SO:0001819	synonymous_variant	343069	exon2			CGCTGCTGATCGT	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.300A>C	1.37:g.12907843T>G		Somatic	414	1	0.00241546		WXS	Illumina HiSeq	Phase_I	357	16	0.0448179	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	37	CCDS30591.1																																																																																			T|1.000;|0.000	.	weak		0.488	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
ZMYM6	9204	hgsc.bcm.edu	37	1	35453651	35453651	+	Missense_Mutation	SNP	A	A	C	rs61744853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:35453651A>C	ENST00000357182.4	-	16	3259	c.3032T>G	c.(3031-3033)tTt>tGt	p.F1011C	ZMYM6_ENST00000493328.1_5'UTR|RP11-244H3.1_ENST00000417456.1_RNA|ZMYM6NB_ENST00000373337.3_5'Flank|ZMYM6_ENST00000487874.1_Intron|ZMYM6_ENST00000373340.2_Intron	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	1011					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				acggtgaataaaacaatgtgt	0.378													A|||	8	0.00159744	0.0	0.0	5008	,	,		17725	0.0		0.008	False		,,,				2504	0.0				p.F1011C		Atlas-SNP	.											.	ZMYM6	110	.	0			c.T3032G						PASS	.						17.0	16.0	16.0					1																	35453651		1207	2574	3781	SO:0001583	missense	9204	exon16			TGAATAAAACAAT	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.3032T>G	1.37:g.35453651A>C	ENSP00000349708:p.Phe1011Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	37	CCDS387.2	.	.	.	.	.	.	.	.	.	.	A	15.49	2.847834	0.51164	.	.	ENSG00000163867	ENST00000357182	T	0.22945	1.93	4.73	4.73	0.59995	Ribonuclease H-like (1);	0.801728	0.11086	N	0.601298	T	0.28699	0.0711	L	0.42686	1.345	0.80722	D	1	D	0.58620	0.983	P	0.46975	0.533	T	0.02398	-1.1165	10	0.49607	T	0.09	-8.2726	10.8072	0.46524	1.0:0.0:0.0:0.0	.	1011	O95789	ZMYM6_HUMAN	C	1011	ENSP00000349708:F1011C	ENSP00000349708:F1011C	F	-	2	0	ZMYM6	35226238	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.834000	0.62774	2.129000	0.65627	0.528000	0.53228	TTT	A|0.986;C|0.014	0.014	weak		0.378	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167	
CC2D2A	57545	hgsc.bcm.edu	37	4	15569018	15569018	+	Silent	SNP	G	G	A	rs73125627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:15569018G>A	ENST00000503292.1	+	26	3381	c.3201G>A	c.(3199-3201)tcG>tcA	p.S1067S	CC2D2A_ENST00000389652.5_Silent_p.S1018S|CC2D2A_ENST00000413206.1_Silent_p.S1067S|CC2D2A_ENST00000424120.1_Silent_p.S1067S	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	1067	C2.				cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)		p.S1018S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						AGCAGCCGTCGAGGTCTTCAA	0.433													G|||	760	0.151757	0.1051	0.1873	5008	,	,		19807	0.0724		0.2475	False		,,,				2504	0.1728				p.S1067S		Atlas-SNP	.											CC2D2A,NS,carcinoma,0,1	CC2D2A	158	1	1	Substitution - coding silent(1)	prostate(1)	c.G3201A						PASS	.	G		483,3519		27,429,1545	63.0	61.0	62.0		3201	-10.8	0.0	4	dbSNP_130	62	2063,6275		267,1529,2373	no	coding-synonymous	CC2D2A	NM_001080522.2		294,1958,3918	AA,AG,GG		24.7421,12.069,20.6321		1067/1621	15569018	2546,9794	2001	4169	6170	SO:0001819	synonymous_variant	57545	exon26			GCCGTCGAGGTCT	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"""Meckel syndrome, type 6"""	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.3201G>A	4.37:g.15569018G>A		Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	435	218	0.501149	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	37	CCDS47026.1																																																																																			G|0.819;A|0.181	0.181	strong		0.433	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522	
RIPK4	54101	hgsc.bcm.edu	37	21	43161805	43161805	+	Silent	SNP	G	G	A	rs2838113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43161805G>A	ENST00000352483.2	-	9	1756	c.1692C>T	c.(1690-1692)gaC>gaT	p.D564D	RIPK4_ENST00000542057.1_Silent_p.D453D|RIPK4_ENST00000544709.1_Silent_p.D453D|RIPK4_ENST00000332512.3_Silent_p.D516D|AP001615.9_ENST00000423276.1_RNA			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	564					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TGCTAGACTCGTCCCCGTTCT	0.642													G|||	2659	0.53095	0.2496	0.5764	5008	,	,		20888	0.6071		0.659	False		,,,				2504	0.6687				p.D516D		Atlas-SNP	.											.	RIPK4	151	.	0			c.C1548T						PASS	.	G		1366,3040	453.6+/-350.4	207,952,1044	99.0	79.0	86.0		1548	0.4	0.8	21	dbSNP_100	86	5324,3276	648.3+/-400.5	1621,2082,597	no	coding-synonymous	RIPK4	NM_020639.2		1828,3034,1641	AA,AG,GG		38.093,31.0032,48.5622		516/785	43161805	6690,6316	2203	4300	6503	SO:0001819	synonymous_variant	54101	exon8			AGACTCGTCCCCG	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1692C>T	21.37:g.43161805G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				G|0.473;A|0.527	0.527	strong		0.642	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
CBLB	868	hgsc.bcm.edu	37	3	105389153	105389153	+	Silent	SNP	A	A	G	rs11713094	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:105389153A>G	ENST00000264122.4	-	18	2934	c.2613T>C	c.(2611-2613)ccT>ccC	p.P871P	CBLB_ENST00000394027.3_Silent_p.P849P|CBLB_ENST00000407712.1_Silent_p.P86P	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	871	Pro-rich.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						ACCTTCTAGCAGGAGGCAAAG	0.388			Mis S		AML								G|||	1057	0.211062	0.2231	0.2983	5008	,	,		15888	0.1915		0.2306	False		,,,				2504	0.1329				p.P871P	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.T2613C						PASS	.	G		922,3484	737.6+/-410.9	91,740,1372	131.0	115.0	121.0		2613	2.0	1.0	3	dbSNP_120	121	1789,6811	732.2+/-406.8	201,1387,2712	no	coding-synonymous	CBLB	NM_170662.3		292,2127,4084	GG,GA,AA		20.8023,20.926,20.8442		871/983	105389153	2711,10295	2203	4300	6503	SO:0001819	synonymous_variant	868	exon18			TCTAGCAGGAGGC	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.2613T>C	3.37:g.105389153A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	147	81	0.55102	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	37	CCDS2948.1																																																																																			A|0.789;G|0.211	0.211	strong		0.388	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
DCHS2	54798	hgsc.bcm.edu	37	4	155219382	155219382	+	Silent	SNP	G	G	C	rs116029479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155219382G>C	ENST00000357232.4	-	18	4718	c.4719C>G	c.(4717-4719)gtC>gtG	p.V1573V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1573	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TAACATCAGTGACATATACTT	0.443													G|||	98	0.0195687	0.0023	0.0288	5008	,	,		20282	0.0		0.0706	False		,,,				2504	0.0041				p.V1573V		Atlas-SNP	.											.	DCHS2	594	.	0			c.C4719G						PASS	.	G		52,4354	52.3+/-87.9	1,50,2152	100.0	100.0	100.0		4719	2.8	1.0	4	dbSNP_132	100	557,8043	151.9+/-206.6	16,525,3759	no	coding-synonymous	DCHS2	NM_017639.3		17,575,5911	CC,CG,GG		6.4767,1.1802,4.6825		1573/2917	155219382	609,12397	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon18			ATCAGTGACATAT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4719C>G	4.37:g.155219382G>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	211	210	0.995261	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			G|0.959;C|0.041	0.041	strong		0.443	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
OVCH1	341350	hgsc.bcm.edu	37	12	29617550	29617550	+	Missense_Mutation	SNP	G	G	A	rs11050243	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:29617550G>A	ENST00000318184.5	-	18	2014	c.2015C>T	c.(2014-2016)tCt>tTt	p.S672F	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	672	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.		S -> F (in dbSNP:rs11050243).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.S672F(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CTCCAGAGGAGAGCTTAGTTG	0.493													G|||	912	0.182109	0.3585	0.1023	5008	,	,		18329	0.0853		0.1352	False		,,,				2504	0.1483				p.S672F		Atlas-SNP	.											OVCH1,NS,carcinoma,0,1	OVCH1	195	1	1	Substitution - Missense(1)	stomach(1)	c.C2015T						scavenged	.	G	PHE/SER	1315,2565		217,881,842	125.0	125.0	125.0		2015	2.7	0.6	12	dbSNP_120	125	1174,7148		90,994,3077	yes	missense	OVCH1	NM_183378.2	155	307,1875,3919	AA,AG,GG		14.1072,33.8918,20.3983	probably-damaging	672/1135	29617550	2489,9713	1940	4161	6101	SO:0001583	missense	341350	exon18			AGAGGAGAGCTTA	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2015C>T	12.37:g.29617550G>A	ENSP00000326708:p.Ser672Phe	Somatic	212	2	0.00943396		WXS	Illumina HiSeq	Phase_I	221	110	0.497738	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		355	0.16254578754578755	164	0.3333333333333333	29	0.08011049723756906	59	0.10314685314685315	103	0.1358839050131926	G	16.70	3.194855	0.58017	0.338918	0.141072	ENSG00000187950	ENST00000318184	T	0.61859	0.07	2.73	2.73	0.32206	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	M	0.71920	2.185	0.41092	P	0.014395999999999964	D	0.89917	1.0	D	0.81914	0.995	T	0.13818	-1.0495	8	0.45353	T	0.12	.	7.0766	0.25207	0.0:0.0:0.7311:0.2689	rs11050243;rs60892337;rs11050243	672	Q7RTY7	OVCH1_HUMAN	F	672	ENSP00000326708:S672F	ENSP00000326708:S672F	S	-	2	0	OVCH1	29508817	0.587000	0.26791	0.559000	0.28332	0.394000	0.30568	1.776000	0.38594	1.836000	0.53414	0.655000	0.94253	TCT	G|0.825;A|0.175	0.175	strong		0.493	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
PDZD2	23037	hgsc.bcm.edu	37	5	32074462	32074462	+	Missense_Mutation	SNP	G	G	A	rs115304584	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:32074462G>A	ENST00000438447.1	+	18	3638	c.3250G>A	c.(3250-3252)Gca>Aca	p.A1084T	PDZD2_ENST00000282493.3_Missense_Mutation_p.A1084T			O15018	PDZD2_HUMAN	PDZ domain containing 2	1084					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						ATCAAGTAGCGCACCCAAATT	0.592													G|||	34	0.00678914	0.0015	0.0144	5008	,	,		19454	0.0		0.0199	False		,,,				2504	0.002				p.A1084T		Atlas-SNP	.											.	PDZD2	306	.	0			c.G3250A						PASS	.	G	THR/ALA	12,4394	20.2+/-43.8	0,12,2191	129.0	144.0	139.0		3250	4.5	0.1	5	dbSNP_132	139	161,8439	76.9+/-139.5	2,157,4141	yes	missense	PDZD2	NM_178140.2	58	2,169,6332	AA,AG,GG		1.8721,0.2724,1.3302	benign	1084/2840	32074462	173,12833	2203	4300	6503	SO:0001583	missense	23037	exon17			AGTAGCGCACCCA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3250G>A	5.37:g.32074462G>A	ENSP00000402033:p.Ala1084Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	19	0.0086996336996337	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	13	0.017150395778364115	G	10.27	1.303238	0.23736	0.002724	0.018721	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06294	3.32;3.32	5.67	4.52	0.55395	.	0.591504	0.14285	N	0.329250	T	0.02418	0.0074	L	0.36672	1.1	0.09310	N	1	B;P	0.35226	0.226;0.491	B;B	0.19391	0.011;0.025	T	0.32877	-0.9890	10	0.48119	T	0.1	.	11.086	0.48086	0.0:0.0:0.1635:0.8365	.	910;1084	B4E3P2;O15018	.;PDZD2_HUMAN	T	1084;886;1084	ENSP00000402033:A1084T;ENSP00000282493:A1084T	ENSP00000282493:A1084T	A	+	1	0	PDZD2	32110219	0.999000	0.42202	0.054000	0.19295	0.001000	0.01503	2.917000	0.48821	0.984000	0.38629	-0.457000	0.05445	GCA	G|0.987;A|0.013	0.013	strong		0.592	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
EML2	24139	hgsc.bcm.edu	37	19	46137712	46137712	+	Missense_Mutation	SNP	C	C	T	rs144104945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46137712C>T	ENST00000245925.3	-	4	247	c.197G>A	c.(196-198)cGa>cAa	p.R66Q	EML2_ENST00000587152.1_Missense_Mutation_p.R267Q|EML2_ENST00000536630.1_Missense_Mutation_p.R213Q|EML2_ENST00000586902.1_5'Flank|EML2_ENST00000589876.1_Missense_Mutation_p.R66Q	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	66	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CCGGCAGTCTCGGCCACGGTA	0.488													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		14049	0.0		0.008	False		,,,				2504	0.001				p.R267Q		Atlas-SNP	.											.	EML2	64	.	0			c.G800A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	9,4397	15.5+/-35.6	0,9,2194	35.0	27.0	30.0		800,638,197	4.7	1.0	19	dbSNP_134	30	50,8550	26.3+/-74.7	1,48,4251	yes	missense,missense,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	43,43,43	1,57,6445	TT,TC,CC		0.5814,0.2043,0.4536	probably-damaging,probably-damaging,probably-damaging	267/851,213/797,66/650	46137712	59,12947	2203	4300	6503	SO:0001583	missense	24139	exon7			CAGTCTCGGCCAC	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.197G>A	19.37:g.46137712C>T	ENSP00000245925:p.Arg66Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	9	0.004120879120879121	1	0.0020325203252032522	0	0.0	0	0.0	8	0.010554089709762533	C	26.6	4.755325	0.89843	0.002043	0.005814	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.32515	1.45;1.45;5.06	4.74	4.74	0.60224	HELP (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.45418	0.1341	M	0.66378	2.025	0.51012	D	0.999905	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.998;0.999;1.0	T	0.49969	-0.8882	10	0.51188	T	0.08	-8.2435	15.2541	0.73571	0.0:1.0:0.0:0.0	.	66;232;213;224;66	B7Z918;B7Z3Q9;B7Z3I2;B7Z872;O95834	.;.;.;.;EMAL2_HUMAN	Q	213;66;267;224	ENSP00000442365:R213Q;ENSP00000245925:R66Q;ENSP00000382503:R224Q	ENSP00000245925:R66Q	R	-	2	0	EML2	50829552	1.000000	0.71417	0.994000	0.49952	0.924000	0.55760	5.478000	0.66806	2.475000	0.83589	0.462000	0.41574	CGA	C|0.996;T|0.004	0.004	strong		0.488	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
SIX5	147912	hgsc.bcm.edu	37	19	46269076	46269076	+	Missense_Mutation	SNP	G	G	A	rs2014576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46269076G>A	ENST00000317578.6	-	3	2284	c.1903C>T	c.(1903-1905)Ccc>Tcc	p.P635S	AC074212.5_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_3'UTR|AC074212.6_ENST00000590076.1_RNA|AC074212.5_ENST00000592217.2_RNA	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	635			P -> S (in dbSNP:rs2014576).		lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		GGGGAGAAGGGCAGGCTGGTG	0.711													G|||	2509	0.500998	0.3192	0.621	5008	,	,		14771	0.6111		0.4523	False		,,,				2504	0.5982				p.P635S		Atlas-SNP	.											.	SIX5	35	.	0			c.C1903T						PASS	.	G	SER/PRO	1510,2866		283,944,961	14.0	17.0	16.0		1903	-0.8	1.0	19	dbSNP_92	16	3703,4851		853,1997,1427	no	missense	SIX5	NM_175875.4	74	1136,2941,2388	AA,AG,GG		43.2897,34.5064,40.3171	possibly-damaging	635/740	46269076	5213,7717	2188	4277	6465	SO:0001583	missense	147912	exon3			AGAAGGGCAGGCT	L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"""Homeoboxes / SINE class"""	10891	protein-coding gene	gene with protein product		600963	"""sine oculis homeobox (Drosophila) homolog 5"", ""sine oculis homeobox homolog 5 (Drosophila)"""	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.1903C>T	19.37:g.46269076G>A	ENSP00000316842:p.Pro635Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_175875		Missense_Mutation	SNP	ENST00000317578.6	37	CCDS12673.1	1119	0.5123626373626373	173	0.3516260162601626	211	0.5828729281767956	386	0.6748251748251748	349	0.4604221635883905	g	12.37	1.919029	0.33908	0.345064	0.432897	ENSG00000177045	ENST00000317578	D	0.88896	-2.44	4.2	-0.76	0.11041	.	1.194610	0.05919	N	0.633071	T	0.00012	0.0000	N	0.14661	0.345	0.49582	P	1.9499999999994522E-4	B	0.11235	0.004	B	0.06405	0.002	T	0.40850	-0.9541	9	0.33940	T	0.23	-6.713	1.8982	0.03262	0.1077:0.1739:0.3629:0.3556	rs2014576;rs52791013;rs2014576	635	Q8N196	SIX5_HUMAN	S	635	ENSP00000316842:P635S	ENSP00000316842:P635S	P	-	1	0	SIX5	50960916	0.011000	0.17503	0.983000	0.44433	0.942000	0.58702	-0.164000	0.09983	0.388000	0.25054	0.555000	0.69702	CCC	G|0.543;A|0.457	0.457	strong		0.711	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875	
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73929751	73929751	+	Intron	SNP	G	G	A	rs138159923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73929751G>A	ENST00000265755.3	+	4	658				GTF2IRD1_ENST00000489094.1_Intron|GTF2IRD1_ENST00000476977.1_Intron|GTF2IRD1_ENST00000424337.2_Intron|GTF2IRD1_ENST00000455841.2_Silent_p.S114S	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1						multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CTGTGGCCTCGCGTGCTCTGT	0.662													G|||	10	0.00199681	0.0008	0.0	5008	,	,		16211	0.0		0.0089	False		,,,				2504	0.0				p.S114S		Atlas-SNP	.											.	GTF2IRD1	91	.	0			c.G342A						PASS	.	G	,,	2,4388		0,2,2193	32.0	29.0	30.0		342,,	-7.3	0.0	7	dbSNP_134	30	57,8515		0,57,4229	yes	coding-synonymous,intron,intron	GTF2IRD1	NM_001199207.1,NM_005685.3,NM_016328.2	,,	0,59,6422	AA,AG,GG		0.665,0.0456,0.4552	,,	114/977,,	73929751	59,12903	2195	4286	6481	SO:0001627	intron_variant	9569	exon4			GGCCTCGCGTGCT	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.266-20G>A	7.37:g.73929751G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Silent	SNP	ENST00000265755.3	37	CCDS5571.1																																																																																			G|0.996;A|0.004	0.004	strong		0.662	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
NHLRC2	374354	hgsc.bcm.edu	37	10	115614740	115614740	+	Silent	SNP	C	C	T	rs17235038	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115614740C>T	ENST00000369301.3	+	1	321	c.109C>T	c.(109-111)Ctg>Ttg	p.L37L	DCLRE1A_ENST00000369305.1_5'Flank|DCLRE1A_ENST00000361384.2_5'Flank|DCLRE1A_ENST00000476112.1_5'Flank	NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	37										breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		GAAGGACAGCCTGGTCTACCA	0.687													C|||	63	0.0125799	0.0023	0.0331	5008	,	,		13673	0.0		0.0308	False		,,,				2504	0.0061				p.L37L		Atlas-SNP	.											.	NHLRC2	56	.	0			c.C109T						PASS	.	C		24,4308		0,24,2142	48.0	41.0	43.0		109	3.2	1.0	10	dbSNP_123	43	193,8253		2,189,4032	no	coding-synonymous	NHLRC2	NM_198514.3		2,213,6174	TT,TC,CC		2.2851,0.554,1.6982		37/727	115614740	217,12561	2166	4223	6389	SO:0001819	synonymous_variant	374354	exon1			GACAGCCTGGTCT	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.109C>T	10.37:g.115614740C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_198514	Q8N1H1|Q8N5A6	Silent	SNP	ENST00000369301.3	37	CCDS7585.1																																																																																			C|0.982;T|0.018	0.018	strong		0.687	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	
LRRCC1	85444	hgsc.bcm.edu	37	8	86027418	86027418	+	Missense_Mutation	SNP	A	A	G	rs3736038	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:86027418A>G	ENST00000360375.3	+	5	777	c.628A>G	c.(628-630)Aca>Gca	p.T210A	LRRCC1_ENST00000414626.2_Missense_Mutation_p.T190A	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	210	LRRCT.		T -> A (in dbSNP:rs3736038).		mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AGTAAATTTGACAGAAATAAA	0.363													G|||	934	0.186502	0.5582	0.072	5008	,	,		15055	0.0685		0.0338	False		,,,				2504	0.044				p.T210A		Atlas-SNP	.											.	LRRCC1	212	.	0			c.A628G						PASS	.	G	ALA/THR	1680,1972		384,912,530	97.0	98.0	98.0		628	-6.7	0.0	8	dbSNP_107	98	453,7723		14,425,3649	yes	missense	LRRCC1	NM_033402.4	58	398,1337,4179	GG,GA,AA		5.5406,46.0022,18.0335	benign	210/1033	86027418	2133,9695	1826	4088	5914	SO:0001583	missense	85444	exon5			AATTTGACAGAAA	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.628A>G	8.37:g.86027418A>G	ENSP00000353538:p.Thr210Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	364	0.16666666666666666	277	0.5630081300813008	30	0.08287292817679558	30	0.05244755244755245	27	0.03562005277044855	G	0.946	-0.708072	0.03230	0.460022	0.055406	ENSG00000133739	ENST00000426019;ENST00000360375;ENST00000414626	T;T	0.28255	1.62;1.62	5.52	-6.65	0.01795	.	1.026620	0.07824	N	0.960303	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.45600	-0.9250	9	0.08599	T	0.76	-0.1444	3.3817	0.07257	0.3481:0.0613:0.3536:0.2369	rs3736038;rs56620689;rs59571386;rs3736038	190;117;210	Q9C099-2;E9PE41;Q9C099	.;.;LRCC1_HUMAN	A	117;210;190	ENSP00000353538:T210A;ENSP00000394695:T190A	ENSP00000353538:T210A	T	+	1	0	LRRCC1	86214670	0.000000	0.05858	0.001000	0.08648	0.836000	0.47400	-0.239000	0.08965	-1.148000	0.02847	-1.473000	0.01005	ACA	A|0.828;G|0.172	0.172	strong		0.363	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
BCL6B	255877	hgsc.bcm.edu	37	17	6929924	6929924	+	Silent	SNP	T	T	C	rs379478	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6929924T>C	ENST00000293805.5	+	6	1130	c.1038T>C	c.(1036-1038)caT>caC	p.H346H		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	346					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			skin(1)	1						TTGCCAGTCATCGTACAGTGC	0.582													C|||	4807	0.959864	0.8638	0.987	5008	,	,		18905	0.996		0.998	False		,,,				2504	0.9939				p.H346H		Atlas-SNP	.											.	BCL6B	85	.	0			c.T1038C						PASS	.	C		3737,465		1664,409,28	98.0	107.0	104.0		1038	5.9	1.0	17	dbSNP_80	104	8446,10		4218,10,0	no	coding-synonymous	BCL6B	NM_181844.3		5882,419,28	CC,CT,TT		0.1183,11.0662,3.7526		346/480	6929924	12183,475	2101	4228	6329	SO:0001819	synonymous_variant	255877	exon6			CAGTCATCGTACA	AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1002	protein-coding gene	gene with protein product		608992	"""zinc finger protein 62"", ""B-cell CLL/lymphoma 6, member B (zinc finger protein)"""	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.1038T>C	17.37:g.6929924T>C		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_181844	Q6PCB4	Silent	SNP	ENST00000293805.5	37	CCDS42248.1																																																																																			T|0.032;C|0.968	0.968	strong		0.582	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844	
MTMR10	54893	hgsc.bcm.edu	37	15	31267147	31267147	+	Silent	SNP	C	C	T	rs1133642	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:31267147C>T	ENST00000435680.1	-	4	415	c.318G>A	c.(316-318)gaG>gaA	p.E106E	MTMR10_ENST00000563714.1_Silent_p.E24E|MTMR10_ENST00000314404.8_5'Flank|MTMR10_ENST00000425768.1_Silent_p.E106E	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	106							phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TGACAATTTGCTCAATACATG	0.323													C|||	2404	0.480032	0.1884	0.4741	5008	,	,		17120	0.8313		0.4453	False		,,,				2504	0.5521				p.E106E		Atlas-SNP	.											.	MTMR10	74	.	0			c.G318A						PASS	.	C		834,2826		112,610,1108	61.0	56.0	58.0		318	0.8	1.0	15	dbSNP_86	58	3577,4575		780,2017,1279	no	coding-synonymous	MTMR10	NM_017762.2		892,2627,2387	TT,TC,CC		43.8788,22.7869,37.3434		106/778	31267147	4411,7401	1830	4076	5906	SO:0001819	synonymous_variant	54893	exon4			AATTTGCTCAATA	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.318G>A	15.37:g.31267147C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_017762	Q6P4Q6	Silent	SNP	ENST00000435680.1	37	CCDS45204.1																																																																																			A|0.000;C|0.421;T|0.579	0.579	strong		0.323	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762	
SEC24D	9871	hgsc.bcm.edu	37	4	119736796	119736796	+	Silent	SNP	A	A	C	rs2389688	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:119736796A>C	ENST00000280551.6	-	5	721	c.483T>G	c.(481-483)ccT>ccG	p.P161P	SEC24D_ENST00000379735.5_Silent_p.P161P|SEC24D_ENST00000419654.2_5'UTR			O94855	SC24D_HUMAN	SEC24 family member D	161	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.P161P(1)		breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						GCAAAATGGAAGGCTGTGGAG	0.562													c|||	2188	0.436901	0.2436	0.5807	5008	,	,		18170	0.5506		0.4354	False		,,,				2504	0.4806				p.P161P		Atlas-SNP	.											SEC24D,NS,carcinoma,0,1	SEC24D	96	1	1	Substitution - coding silent(1)	prostate(1)	c.T483G						PASS	.	T		1283,3123	700.8+/-406.7	192,899,1112	238.0	212.0	221.0		483	-11.4	0.0	4	dbSNP_100	221	3875,4725	608.7+/-395.4	892,2091,1317	no	coding-synonymous	SEC24D	NM_014822.2		1084,2990,2429	CC,CA,AA		45.0581,29.1194,39.6586		161/1033	119736796	5158,7848	2203	4300	6503	SO:0001819	synonymous_variant	9871	exon5			AATGGAAGGCTGT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.483T>G	4.37:g.119736796A>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			T|0.108;G|0.070	.	strong		0.562	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
SORBS1	10580	hgsc.bcm.edu	37	10	97106165	97106165	+	Silent	SNP	T	T	C	rs726176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:97106165T>C	ENST00000361941.3	-	24	2453	c.2427A>G	c.(2425-2427)ctA>ctG	p.L809L	SORBS1_ENST00000371227.4_Silent_p.L763L|SORBS1_ENST00000354106.3_Silent_p.L779L|SORBS1_ENST00000371246.2_Silent_p.L831L|SORBS1_ENST00000371239.1_Silent_p.L586L|SORBS1_ENST00000371247.2_Silent_p.L809L|SORBS1_ENST00000306402.6_Silent_p.L556L|SORBS1_ENST00000347291.4_Silent_p.L621L|SORBS1_ENST00000607232.1_Silent_p.L1069L|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000371245.3_Silent_p.L660L|SORBS1_ENST00000371241.1_Silent_p.L459L|SORBS1_ENST00000353505.5_Silent_p.L660L|SORBS1_ENST00000371249.2_Silent_p.L591L|SORBS1_ENST00000393949.1_Silent_p.L779L|SORBS1_ENST00000277982.5_Silent_p.L831L	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GCACTTACTTTAGTGTCTGAG	0.343													T|||	2043	0.407947	0.205	0.451	5008	,	,		19496	0.6696		0.3241	False		,,,				2504	0.4683				p.L831L		Atlas-SNP	.											.	SORBS1	185	.	0			c.A2493G						PASS	.	T	,,,,,,	915,3491	351.6+/-311.3	95,725,1383	85.0	85.0	85.0		2427,2493,1980,1545,1377,1773,1668	2.1	1.0	10	dbSNP_86	85	2392,6208	398.1+/-346.0	331,1730,2239	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	426,2455,3622	CC,CT,TT		27.814,20.7671,25.4267	,,,,,,	809/1293,831/1152,660/906,515/741,459/685,591/817,556/782	97106165	3307,9699	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon24			TTACTTTAGTGTC	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.2427A>G	10.37:g.97106165T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			A|0.002;C|0.320	0.320	strong		0.343	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
PZP	5858	hgsc.bcm.edu	37	12	9317885	9317885	+	Silent	SNP	G	G	A	rs2277412	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:9317885G>A	ENST00000261336.2	-	19	2365	c.2337C>T	c.(2335-2337)tcC>tcT	p.S779S	PZP_ENST00000381997.2_Silent_p.S648S|PZP_ENST00000539983.1_5'UTR	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	779					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S779S(1)|p.S648S(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CAGCATCTTCGGACAGGCAGA	0.567													G|||	1694	0.338259	0.1558	0.3329	5008	,	,		-128	0.4266		0.3956	False		,,,				2504	0.4387				p.S779S	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,NS,carcinoma,0,2	PZP	422	2	2	Substitution - coding silent(2)	stomach(2)	c.C2337T						PASS	.						96.0	82.0	87.0					12																	9317885		2203	4298	6501	SO:0001819	synonymous_variant	5858	exon19			ATCTTCGGACAGG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2337C>T	12.37:g.9317885G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	142	44	0.309859	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																			G|0.167;A|0.833	0.833	weak		0.567	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
ESRRA	2101	hgsc.bcm.edu	37	11	64081445	64081445	+	Silent	SNP	G	G	A	rs2276014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64081445G>A	ENST00000405666.1	+	3	582	c.348G>A	c.(346-348)ccG>ccA	p.P116P	ESRRA_ENST00000406310.1_Silent_p.P116P|ESRRA_ENST00000000442.6_Silent_p.P116P	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	116					cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						ACAGCTGTCCGGCCTCCAACG	0.672													G|||	447	0.0892572	0.0242	0.1254	5008	,	,		14349	0.1052		0.161	False		,,,				2504	0.0613				p.P116P		Atlas-SNP	.											.	ESRRA	56	.	0			c.G348A						PASS	.	G		202,4146		5,192,1977	12.0	14.0	13.0		348	0.3	1.0	11	dbSNP_100	13	1308,7264		113,1082,3091	no	coding-synonymous	ESRRA	NM_004451.3		118,1274,5068	AA,AG,GG		15.259,4.6458,11.6873		116/424	64081445	1510,11410	2174	4286	6460	SO:0001819	synonymous_variant	2101	exon3			CTGTCCGGCCTCC	X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"""Nuclear hormone receptors"""	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.348G>A	11.37:g.64081445G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	117	65	0.555556	NM_004451	Q14514	Silent	SNP	ENST00000405666.1	37	CCDS41667.1																																																																																			G|0.895;A|0.105	0.105	strong		0.672	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451	
WNK1	65125	hgsc.bcm.edu	37	12	998365	998365	+	Missense_Mutation	SNP	G	G	T	rs12828016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:998365G>T	ENST00000315939.6	+	21	6067	c.5424G>T	c.(5422-5424)atG>atT	p.M1808I	WNK1_ENST00000530271.2_Missense_Mutation_p.M2306I|WNK1_ENST00000340908.4_Missense_Mutation_p.M1401I|WNK1_ENST00000535572.1_Missense_Mutation_p.M1561I|WNK1_ENST00000537687.1_Missense_Mutation_p.M2068I	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1808			M -> I (in dbSNP:rs12828016). {ECO:0000269|PubMed:11571656, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.3}.		intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GTCCAGAGATGATCACAGTGA	0.398													T|||	2091	0.417532	0.5522	0.3213	5008	,	,		19593	0.2808		0.3877	False		,,,				2504	0.4755				p.M2068I	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G6204T						PASS	.	T	ILE/MET,ILE/MET,ILE/MET,ILE/MET	2248,2158	581.2+/-385.3	569,1110,524	177.0	171.0	173.0		6180,5424,4683,6204	2.2	0.2	12	dbSNP_121	173	3363,5237	642.5+/-399.8	675,2013,1612	yes	missense,missense,missense,missense	WNK1	NM_213655.4,NM_018979.3,NM_014823.2,NM_001184985.1	10,10,10,10	1244,3123,2136	TT,TG,GG		39.1047,48.9787,43.1416	benign,benign,benign,benign	2060/2635,1808/2383,1561/2135,2068/2643	998365	5611,7395	2203	4300	6503	SO:0001583	missense	65125	exon21			AGAGATGATCACA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.5424G>T	12.37:g.998365G>T	ENSP00000313059:p.Met1808Ile	Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	843	0.385989010989011	261	0.5304878048780488	127	0.35082872928176795	165	0.28846153846153844	290	0.38258575197889183	T	10.15	1.272499	0.23221	0.510213	0.391047	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	5.77	2.16	0.27623	.	0.262166	0.33346	N	0.005003	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45629	-0.9248	9	0.20046	T	0.44	-1.5706	2.5504	0.04747	0.1087:0.2441:0.1125:0.5346	rs12828016;rs60054820;rs12828016	1561;1561;1808	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	I	1561;1808;2068;981;2306;1401	ENSP00000441972:M1561I;ENSP00000313059:M1808I;ENSP00000444465:M2068I;ENSP00000433548:M2306I;ENSP00000341292:M1401I	ENSP00000252477:M981I	M	+	3	0	WNK1	868626	0.822000	0.29219	0.163000	0.22734	0.446000	0.32137	-0.071000	0.11505	0.183000	0.20059	-0.256000	0.11100	ATG	G|0.585;T|0.415	0.415	strong		0.398	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
DFNB59	494513	hgsc.bcm.edu	37	2	179325735	179325735	+	Missense_Mutation	SNP	C	C	G	rs17304212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179325735C>G	ENST00000409117.3	+	7	1149	c.793C>G	c.(793-795)Cgt>Ggt	p.R265G	DFNB59_ENST00000375129.4_Missense_Mutation_p.R265G	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	265			R -> C (in dbSNP:rs17304212).		sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			TGTCATTTCTCGTTCACAGCT	0.338													C|||	197	0.0393371	0.0371	0.0432	5008	,	,		18996	0.004		0.0567	False		,,,				2504	0.0583				p.R265G		Atlas-SNP	.											DFNB59,lymph_node,lymphoid_neoplasm,0,1	DFNB59	37	1	0			c.C793G	GRCh37	CM074142|CM074143	DFNB59	M	rs17304212	PASS	.						215.0	190.0	198.0					2																	179325735		1860	4102	5962	SO:0001583	missense	494513	exon7			ATTTCTCGTTCAC	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.793C>G	2.37:g.179325735C>G	ENSP00000386647:p.Arg265Gly	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_001042702	A0PK14|B9EJE2	Missense_Mutation	SNP	ENST00000409117.3	37	CCDS42787.1	95	0.043498168498168496	20	0.04065040650406504	24	0.06629834254143646	3	0.005244755244755245	48	0.0633245382585752	C	15.64	2.892539	0.52121	.	.	ENSG00000204311	ENST00000409117;ENST00000375129	T;T	0.60171	0.21;0.21	6.04	6.04	0.98038	.	0.089808	0.45606	U	0.000358	T	0.05410	0.0143	L	0.29908	0.895	0.26970	N	0.965609	B	0.30104	0.268	B	0.26864	0.074	T	0.08371	-1.0725	10	0.49607	T	0.09	-28.2832	14.3944	0.67001	0.2446:0.7554:0.0:0.0	.	265	Q0ZLH3	PJVK_HUMAN	G	265	ENSP00000386647:R265G;ENSP00000364271:R265G	ENSP00000364271:R265G	R	+	1	0	DFNB59	179033981	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.135000	0.42112	2.873000	0.98535	0.563000	0.77884	CGT	C|0.932;G|0.038;T|0.030	0.038	strong		0.338	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1		
ERAP1	51752	hgsc.bcm.edu	37	5	96122210	96122210	+	Missense_Mutation	SNP	C	C	T	rs10050860	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:96122210C>T	ENST00000443439.2	-	12	1789	c.1723G>A	c.(1723-1725)Gac>Aac	p.D575N	ERAP1_ENST00000296754.3_Missense_Mutation_p.D575N|ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000602972.1_RNA|CTD-2260A17.1_ENST00000512856.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	575			D -> G (in dbSNP:rs6863093).|D -> N (in dbSNP:rs10050860). {ECO:0000269|PubMed:11481040, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:9628581}.		angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TGGACCATGTCGGATTTGCTG	0.343													.|||	532	0.10623	0.0651	0.1311	5008	,	,		21138	0.0575		0.2286	False		,,,				2504	0.0685				p.D575N		Atlas-SNP	.											.	ERAP1	59	.	0			c.G1723A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	452,3954	216.1+/-234.9	21,410,1772	114.0	109.0	111.0		1723,1723,1723	5.3	0.9	5	dbSNP_119	111	1831,6769	328.2+/-318.2	202,1427,2671	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	23,23,23	223,1837,4443	TT,TC,CC		21.2907,10.2587,17.5534	benign,benign,benign	575/942,575/942,575/949	96122210	2283,10723	2203	4300	6503	SO:0001583	missense	51752	exon12			CCATGTCGGATTT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.1723G>A	5.37:g.96122210C>T	ENSP00000406304:p.Asp575Asn	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	289	0.13232600732600733	26	0.052845528455284556	50	0.13812154696132597	40	0.06993006993006994	173	0.22823218997361477	C	3.756	-0.050536	0.07407	0.102587	0.212907	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.01422	4.91;4.91	5.33	5.33	0.75918	.	0.810719	0.11919	N	0.516871	T	0.00012	0.0000	N	0.21240	0.645	0.48830	P	2.8799999999995496E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.43956	-0.9359	9	0.05436	T	0.98	.	5.2857	0.15700	0.1717:0.6701:0.0:0.1582	rs10050860;rs17482411;rs52797642;rs59271093;rs10050860	575;575;575	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	N	575	ENSP00000296754:D575N;ENSP00000406304:D575N	ENSP00000296754:D575N	D	-	1	0	ERAP1	96147966	0.386000	0.25180	0.937000	0.37676	0.703000	0.40648	0.514000	0.22786	2.500000	0.84329	0.484000	0.47621	GAC	C|0.855;T|0.145	0.145	strong		0.343	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
MYH15	22989	hgsc.bcm.edu	37	3	108163559	108163559	+	Silent	SNP	C	C	T	rs148022324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108163559C>T	ENST00000273353.3	-	23	2699	c.2643G>A	c.(2641-2643)caG>caA	p.Q881Q		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	881						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GTTCCTCCCTCTGAAACTCTG	0.428													C|||	8	0.00159744	0.0	0.0014	5008	,	,		17597	0.0		0.003	False		,,,				2504	0.0041				p.Q881Q		Atlas-SNP	.											.	MYH15	223	.	0			c.G2643A						PASS	.	C		1,3779		0,1,1889	122.0	114.0	117.0		2643	2.1	0.2	3	dbSNP_134	117	16,8238		0,16,4111	no	coding-synonymous	MYH15	NM_014981.1		0,17,6000	TT,TC,CC		0.1938,0.0265,0.1413		881/1947	108163559	17,12017	1890	4127	6017	SO:0001819	synonymous_variant	22989	exon23			CTCCCTCTGAAAC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.2643G>A	3.37:g.108163559C>T		Somatic	277	1	0.00361011		WXS	Illumina HiSeq	Phase_I	247	106	0.42915	NM_014981		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
FCHO2	115548	hgsc.bcm.edu	37	5	72351905	72351905	+	Silent	SNP	A	A	G	rs57213367	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:72351905A>G	ENST00000430046.2	+	16	1340	c.1224A>G	c.(1222-1224)acA>acG	p.T408T	FCHO2_ENST00000512348.1_Silent_p.T375T|FCHO2_ENST00000341845.6_Silent_p.T408T	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	408					clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		AGGAGTTAACAAAATCAAAGC	0.254													A|||	693	0.138379	0.0144	0.0951	5008	,	,		15762	0.3879		0.169	False		,,,				2504	0.0481				p.T408T		Atlas-SNP	.											.	FCHO2	96	.	0			c.A1224G						PASS	.	A	,	84,3284		1,82,1601	33.0	33.0	33.0		1125,1224	4.2	1.0	5	dbSNP_129	33	885,6655		40,805,2925	no	coding-synonymous,coding-synonymous	FCHO2	NM_001146032.1,NM_138782.2	,	41,887,4526	GG,GA,AA		11.7374,2.4941,8.8834	,	375/778,408/811	72351905	969,9939	1684	3770	5454	SO:0001819	synonymous_variant	115548	exon16			GTTAACAAAATCA	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.1224A>G	5.37:g.72351905A>G		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	221	117	0.529412	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Silent	SNP	ENST00000430046.2	37	CCDS47230.1																																																																																			A|0.828;G|0.172	0.172	strong		0.254	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142	
SLC2A6	11182	hgsc.bcm.edu	37	9	136339181	136339181	+	Silent	SNP	C	C	T	rs28584627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136339181C>T	ENST00000371899.4	-	7	1034	c.957G>A	c.(955-957)ggG>ggA	p.G319G	SLC2A6_ENST00000485978.1_5'UTR|SLC2A6_ENST00000371897.4_Silent_p.G319G	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	319					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		GCCGCACGGCCCCAACGATGG	0.677													C|||	88	0.0175719	0.0045	0.0331	5008	,	,		18876	0.001		0.0437	False		,,,				2504	0.0143				p.G319G		Atlas-SNP	.											.	SLC2A6	31	.	0			c.G957A						PASS	.	C	,	44,4348		1,42,2153	28.0	25.0	26.0		957,957	-10.6	0.0	9	dbSNP_125	26	416,8172		13,390,3891	no	coding-synonymous,coding-synonymous	SLC2A6	NM_001145099.1,NM_017585.3	,	14,432,6044	TT,TC,CC		4.844,1.0018,3.5439	,	319/446,319/508	136339181	460,12520	2196	4294	6490	SO:0001819	synonymous_variant	11182	exon7			CACGGCCCCAACG	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"""Solute carriers"""	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.957G>A	9.37:g.136339181C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Silent	SNP	ENST00000371899.4	37	CCDS6975.1																																																																																			C|0.965;T|0.035	0.035	strong		0.677	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585	
FOXQ1	94234	hgsc.bcm.edu	37	6	1313470	1313470	+	Silent	SNP	C	C	T	rs4435985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:1313470C>T	ENST00000296839.2	+	1	796	c.531C>T	c.(529-531)ttC>ttT	p.F177F		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	177					hair follicle morphogenesis (GO:0031069)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|urinary_tract(1)	2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)		ACGACTGCTTCGTCAAGGTGC	0.622													C|||	956	0.190895	0.1241	0.1167	5008	,	,		7348	0.2986		0.2048	False		,,,				2504	0.2086				p.F177F		Atlas-SNP	.											FOXQ1,NS,carcinoma,0,1	FOXQ1	8	1	0			c.C531T						PASS	.	C		619,3785		37,545,1620	43.0	45.0	44.0		531	3.8	1.0	6	dbSNP_111	44	1699,6897		159,1381,2758	no	coding-synonymous	FOXQ1	NM_033260.3		196,1926,4378	TT,TC,CC		19.765,14.0554,17.8308		177/404	1313470	2318,10682	2202	4298	6500	SO:0001819	synonymous_variant	94234	exon1			CTGCTTCGTCAAG	AF153341	CCDS4471.1	6p25	2008-02-05			ENSG00000164379	ENSG00000164379		"""Forkhead boxes"""	20951	protein-coding gene	gene with protein product		612788				11747606, 12011061	Standard	NM_033260		Approved	HFH1	uc003mtl.4	Q9C009	OTTHUMG00000016160	ENST00000296839.2:c.531C>T	6.37:g.1313470C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	186	183	0.983871	NM_033260	Q9NS06	Silent	SNP	ENST00000296839.2	37	CCDS4471.1																																																																																			C|0.811;T|0.189	0.189	strong		0.622	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	NM_033260	
SEMA3C	10512	hgsc.bcm.edu	37	7	80374342	80374342	+	Silent	SNP	A	A	G	rs1949971	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:80374342A>G	ENST00000265361.3	-	18	2685	c.2124T>C	c.(2122-2124)taT>taC	p.Y708Y	SEMA3C_ENST00000544525.1_Silent_p.Y726Y|SEMA3C_ENST00000419255.2_Silent_p.Y708Y	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	708					axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TGTCTTTGCAATATTGGTTAA	0.498													G|||	4589	0.916334	0.7292	0.9885	5008	,	,		18835	1.0		0.994	False		,,,				2504	0.9519				p.Y708Y		Atlas-SNP	.											.	SEMA3C	106	.	0			c.T2124C						PASS	.	G		3453,953	359.9+/-315.0	1361,731,111	149.0	132.0	137.0		2124	3.6	1.0	7	dbSNP_92	137	8528,72	42.2+/-99.7	4228,72,0	no	coding-synonymous	SEMA3C	NM_006379.3		5589,803,111	GG,GA,AA		0.8372,21.6296,7.881		708/752	80374342	11981,1025	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon18			TTTGCAATATTGG	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.2124T>C	7.37:g.80374342A>G		Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	310	309	0.996774	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			A|0.082;G|0.918	0.918	strong		0.498	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
ZNF648	127665	hgsc.bcm.edu	37	1	182026813	182026813	+	Missense_Mutation	SNP	G	G	C	rs12568050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:182026813G>C	ENST00000339948.3	-	2	540	c.333C>G	c.(331-333)aaC>aaG	p.N111K		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	111			N -> K (in dbSNP:rs12568050).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						CCTGGGTCTCGTTGATCTTTG	0.547													C|||	886	0.176917	0.09	0.121	5008	,	,		18981	0.2837		0.1471	False		,,,				2504	0.2546				p.N111K	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.C333G						PASS	.	C	LYS/ASN	429,3977	787.8+/-414.9	18,393,1792	96.0	92.0	93.0		333	-4.0	0.0	1	dbSNP_120	93	1178,7422	764.8+/-407.6	82,1014,3204	yes	missense	ZNF648	NM_001009992.1	94	100,1407,4996	CC,CG,GG		13.6977,9.7367,12.3558	benign	111/569	182026813	1607,11399	2203	4300	6503	SO:0001583	missense	127665	exon2			GGTCTCGTTGATC	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"""Zinc fingers, C2H2-type"""	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.333C>G	1.37:g.182026813G>C	ENSP00000344129:p.Asn111Lys	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	253	85	0.335968	NM_001009992	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	37	CCDS30952.1	373	0.1707875457875458	57	0.11585365853658537	41	0.1132596685082873	159	0.27797202797202797	116	0.15303430079155672	C	4.957	0.177723	0.09443	0.097367	0.136977	ENSG00000179930	ENST00000339948	T	0.06294	3.32	2.26	-4.0	0.04057	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.43798	-0.9369	8	0.07175	T	0.84	.	6.409	0.21680	0.2096:0.404:0.3864:0.0	rs12568050;rs52805107;rs12568050	111	Q5T619	ZN648_HUMAN	K	111	ENSP00000344129:N111K	ENSP00000344129:N111K	N	-	3	2	ZNF648	180293436	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.038000	0.01419	-1.686000	0.01439	-2.238000	0.00288	AAC	G|0.864;C|0.136	0.136	strong		0.547	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597	
DOCK8	81704	hgsc.bcm.edu	37	9	286593	286593	+	Missense_Mutation	SNP	C	C	A	rs529208	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:286593C>A	ENST00000453981.1	+	3	401	c.289C>A	c.(289-291)Cca>Aca	p.P97T	DOCK8_ENST00000469391.1_Missense_Mutation_p.P29T|DOCK8_ENST00000432829.2_Missense_Mutation_p.P29T			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	97			P -> T (in dbSNP:rs529208). {ECO:0000269|Ref.1}.		blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GGTGTTCACGCCAAAGGAATG	0.468													C|||	2653	0.529752	0.3918	0.5231	5008	,	,		18502	0.7212		0.4841	False		,,,				2504	0.5706				p.P97T		Atlas-SNP	.											.	DOCK8	401	.	0			c.C289A						PASS	.	C	THR/PRO,THR/PRO,THR/PRO	1825,2581	534.8+/-374.1	374,1077,752	142.0	124.0	130.0		85,85,289	4.6	0.4	9	dbSNP_83	130	4213,4387	570.7+/-389.4	1040,2133,1127	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	38,38,38	1414,3210,1879	AA,AC,CC		48.9884,41.4208,46.4247	benign,benign,benign	29/2000,29/2032,97/2100	286593	6038,6968	2203	4300	6503	SO:0001583	missense	81704	exon3			TTCACGCCAAAGG	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.289C>A	9.37:g.286593C>A	ENSP00000408464:p.Pro97Thr	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	206	206	1	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	1145	0.5242673992673993	194	0.3943089430894309	184	0.5082872928176796	414	0.7237762237762237	353	0.4656992084432718	C	18.96	3.734202	0.69189	0.414208	0.489884	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000479404;ENST00000487230;ENST00000469391	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	5.47	4.57	0.56435	.	0.139415	0.49916	D	0.000133	T	0.00012	0.0000	M	0.68593	2.085	0.25048	P	0.99115663	D;D;P	0.67145	0.996;0.964;0.576	D;P;P	0.72625	0.978;0.767;0.457	T	0.39502	-0.9611	9	0.56958	D	0.05	.	9.9931	0.41883	0.0:0.7899:0.1375:0.0726	rs529208;rs3209442;rs17407817;rs17664433;rs52797832;rs59297779;rs529208	29;97;97	E9PH09;A2A349;Q8NF50	.;.;DOCK8_HUMAN	T	97;97;29;29;29;29	ENSP00000408464:P97T;ENSP00000394888:P29T;ENSP00000417082:P29T;ENSP00000418318:P29T;ENSP00000419438:P29T	ENSP00000287364:P97T	P	+	1	0	DOCK8	276593	0.975000	0.34042	0.435000	0.26784	0.990000	0.78478	3.149000	0.50655	1.315000	0.45114	0.563000	0.77884	CCA	C|0.497;A|0.503	0.503	strong		0.468	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
ITPR3	3710	hgsc.bcm.edu	37	6	33653448	33653448	+	Silent	SNP	C	C	T	rs749338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33653448C>T	ENST00000374316.5	+	42	6571	c.5511C>T	c.(5509-5511)ggC>ggT	p.G1837G	ITPR3_ENST00000605930.1_Silent_p.G1837G			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1837					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CGATACCTGGCTCCTCATCCC	0.667													c|||	2556	0.510383	0.0998	0.5692	5008	,	,		19194	0.8621		0.4632	False		,,,				2504	0.7096				p.G1837G		Atlas-SNP	.											.	ITPR3	409	.	0			c.C5511T						PASS	.			821,3585	323.7+/-298.2	69,683,1451	61.0	54.0	56.0		5511	4.0	0.3	6	dbSNP_86	56	3735,4865	526.7+/-381.0	854,2027,1419	no	coding-synonymous	ITPR3	NM_002224.3		923,2710,2870	TT,TC,CC		43.4302,18.6337,35.03		1837/2672	33653448	4556,8450	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon41			ACCTGGCTCCTCA	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.5511C>T	6.37:g.33653448C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	160	61	0.38125	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.600;T|0.400	0.400	strong		0.667	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057958	46057958	+	Silent	SNP	C	C	T	rs4818951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46057958C>T	ENST00000380095.1	+	1	686	c.624C>T	c.(622-624)tcC>tcT	p.S208S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	208	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCGTCCCCTCCTGCGGTGCCT	0.697													C|||	3206	0.640176	0.4092	0.6931	5008	,	,		18953	0.6687		0.7594	False		,,,				2504	0.7628				p.S208S		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C624T						PASS	.	C	,	1952,2454	547.0+/-377.2	407,1138,658	86.0	91.0	89.0		,624	2.3	0.5	21	dbSNP_111	89	6136,2464	691.7+/-404.5	2207,1722,371	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	2614,2860,1029	TT,TC,CC		28.6512,44.3032,37.8133	,	,208/252	46057958	8088,4918	2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CCCCTCCTGCGGT	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.624C>T	21.37:g.46057958C>T		Somatic	409	1	0.00244499		WXS	Illumina HiSeq	Phase_I	300	143	0.476667	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.368;T|0.632	0.632	strong		0.697	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
CCDC171	203238	hgsc.bcm.edu	37	9	15591372	15591372	+	Missense_Mutation	SNP	T	T	A	rs4741510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:15591372T>A	ENST00000380701.3	+	5	689	c.361T>A	c.(361-363)Tca>Aca	p.S121T	CCDC171_ENST00000297641.3_Missense_Mutation_p.S121T|CCDC171_ENST00000535968.1_Missense_Mutation_p.S121T	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	121	Glu-rich.		S -> T (in dbSNP:rs4741510).					p.S121T(1)									AGCACAGAATTCAGAACTTCA	0.348													T|||	1773	0.354034	0.0204	0.4366	5008	,	,		17357	0.5923		0.4503	False		,,,				2504	0.4018				p.S121T		Atlas-SNP	.											C9orf93,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T361A						PASS	.	T	THR/SER	365,4041	176.9+/-206.0	18,329,1856	48.0	47.0	47.0		361	2.0	1.0	9	dbSNP_111	47	3513,5083	501.2+/-375.4	699,2115,1484	yes	missense	C9orf93	NM_173550.2	58	717,2444,3340	AA,AT,TT		40.8678,8.2842,29.8262	benign	121/1327	15591372	3878,9124	2203	4298	6501	SO:0001583	missense	203238	exon5			CAGAATTCAGAAC	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.361T>A	9.37:g.15591372T>A	ENSP00000370077:p.Ser121Thr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	852	0.3901098901098901	16	0.032520325203252036	159	0.43922651933701656	341	0.5961538461538461	336	0.44327176781002636	T	11.37	1.617292	0.28801	0.082842	0.408678	ENSG00000164989	ENST00000535968;ENST00000297641;ENST00000380701	T;T;T	0.47177	0.85;0.85;0.85	5.72	1.95	0.26073	.	1.326280	0.04833	N	0.439153	T	0.00012	0.0000	L	0.27053	0.805	0.52501	P	4.199999999998649E-5	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	T	0.46020	-0.9221	9	0.26408	T	0.33	0.1965	1.8219	0.03112	0.1871:0.0817:0.2548:0.4764	rs4741510;rs52829905;rs4741510	121;121;121;121	B7ZM22;Q6TFL3-3;Q6TFL3;Q7Z3F8	.;.;CI093_HUMAN;.	T	121	ENSP00000438838:S121T;ENSP00000297641:S121T;ENSP00000370077:S121T	ENSP00000297641:S121T	S	+	1	0	C9orf93	15581372	0.985000	0.35326	0.998000	0.56505	0.692000	0.40212	0.079000	0.14782	0.068000	0.16574	0.524000	0.50904	TCA	T|0.666;A|0.334	0.334	strong		0.348	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
LAMA2	3908	hgsc.bcm.edu	37	6	129635920	129635920	+	Missense_Mutation	SNP	G	G	A	rs34505698		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:129635920G>A	ENST00000421865.2	+	24	3581	c.3532G>A	c.(3532-3534)Gca>Aca	p.A1178T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1178	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GTGCTCTGAAGCAAAAGGACT	0.527													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18459	0.0		0.0	False		,,,				2504	0.0				p.A1178T		Atlas-SNP	.											.	LAMA2	481	.	0			c.G3532A						PASS	.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	87.0	83.0	84.0		3532,3532	5.6	1.0	6	dbSNP_126	84	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	58,58	0,13,6490	AA,AG,GG		0.1512,0.0,0.1	benign,benign	1178/3123,1178/3119	129635920	13,12993	2203	4300	6503	SO:0001583	missense	3908	exon24			TCTGAAGCAAAAG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.3532G>A	6.37:g.129635920G>A	ENSP00000400365:p.Ala1178Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.81	3.703093	0.68501	0.0	0.001512	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.36878	1.23	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.46151	0.1378	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.09271	-1.0682	10	0.21540	T	0.41	.	19.5763	0.95446	0.0:0.0:1.0:0.0	rs34505698	1178;1178	A6NF00;P24043	.;LAMA2_HUMAN	T	1178	ENSP00000400365:A1178T	ENSP00000346769:A1178T	A	+	1	0	LAMA2	129677613	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.230000	0.95299	2.646000	0.89796	0.655000	0.94253	GCA	G|0.999;A|0.001	0.001	strong		0.527	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
REG1B	5968	hgsc.bcm.edu	37	2	79313990	79313990	+	Missense_Mutation	SNP	C	C	T	rs62640882	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:79313990C>T	ENST00000305089.3	-	3	211	c.131G>A	c.(130-132)cGc>cAc	p.R44H		NM_006507.3	NP_006498.1	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta	44	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell proliferation (GO:0008283)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						GCAGTAGGAGCGATAGGCATT	0.507													C|||	57	0.0113818	0.0	0.0086	5008	,	,		17949	0.0		0.0437	False		,,,				2504	0.0072				p.R44H		Atlas-SNP	.											.	REG1B	83	.	0			c.G131A						PASS	.	C	HIS/ARG	25,4381	31.7+/-61.6	0,25,2178	156.0	152.0	154.0		131	-0.3	0.0	2	dbSNP_129	154	330,8270	115.2+/-175.0	12,306,3982	yes	missense	REG1B	NM_006507.3	29	12,331,6160	TT,TC,CC		3.8372,0.5674,2.7295	benign	44/167	79313990	355,12651	2203	4300	6503	SO:0001583	missense	5968	exon3			TAGGAGCGATAGG		CCDS1963.1	2p12	2008-06-04	2008-06-04		ENSG00000172023	ENSG00000172023			9952	protein-coding gene	gene with protein product	"""lithostathine 1 beta"", ""secretory pancreatic stone protein 2"""	167771	"""regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)"""			8110835	Standard	NM_006507		Approved	REGL, PSPS2, REGH, REGI-BETA	uc002sny.2	P48304	OTTHUMG00000130019	ENST00000305089.3:c.131G>A	2.37:g.79313990C>T	ENSP00000303206:p.Arg44His	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	193	95	0.492228	NM_006507		Missense_Mutation	SNP	ENST00000305089.3	37	CCDS1963.1	42	0.019230769230769232	0	0.0	5	0.013812154696132596	0	0.0	37	0.048812664907651716	c	10.83	1.459885	0.26248	0.005674	0.038372	ENSG00000172023	ENST00000305089	T	0.08370	3.1	3.74	-0.261	0.12963	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.582077	0.14158	N	0.337555	T	0.00724	0.0024	L	0.45352	1.415	0.09310	N	1	P;P	0.35348	0.496;0.496	B;B	0.15870	0.014;0.014	T	0.37361	-0.9709	10	0.40728	T	0.16	.	3.4587	0.07524	0.0:0.4497:0.1989:0.3515	.	44;44	Q6ICS1;P48304	.;REG1B_HUMAN	H	44	ENSP00000303206:R44H	ENSP00000303206:R44H	R	-	2	0	REG1B	79167498	0.000000	0.05858	0.001000	0.08648	0.778000	0.44026	-0.670000	0.05256	0.044000	0.15775	-0.224000	0.12420	CGC	C|0.975;T|0.025	0.025	strong		0.507	REG1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252292.2	NM_006507	
MUC16	94025	hgsc.bcm.edu	37	19	9071834	9071834	+	Silent	SNP	G	G	C	rs17000803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9071834G>C	ENST00000397910.4	-	3	15815	c.15612C>G	c.(15610-15612)ccC>ccG	p.P5204P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5206	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTGTGTCCGTGGGAAAGCTGG	0.468													G|||	1007	0.201078	0.0946	0.2824	5008	,	,		21218	0.3254		0.167	False		,,,				2504	0.1943				p.P5204P		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	0			c.C15612G						PASS	.	G		399,3425		18,363,1531	188.0	177.0	180.0		15612	-1.2	0.0	19	dbSNP_123	180	1504,6742		136,1232,2755	no	coding-synonymous	MUC16	NM_024690.2		154,1595,4286	CC,CG,GG		18.2391,10.4341,15.7664		5204/14508	9071834	1903,10167	1912	4123	6035	SO:0001819	synonymous_variant	94025	exon3			GTCCGTGGGAAAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15612C>G	19.37:g.9071834G>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.792;C|0.208	0.208	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CLSTN2	64084	hgsc.bcm.edu	37	3	140281723	140281723	+	Silent	SNP	C	C	T	rs11714465	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:140281723C>T	ENST00000458420.3	+	14	2473	c.2283C>T	c.(2281-2283)tcC>tcT	p.S761S		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	761					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GTCCGGCTTCCCTTGAGGCCC	0.562										HNSCC(16;0.037)			C|||	1685	0.336462	0.0666	0.4957	5008	,	,		20945	0.1022		0.6769	False		,,,				2504	0.4796				p.S761S	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.C2283T						PASS	.	C		717,3689	294.1+/-283.0	71,575,1557	54.0	52.0	53.0		2283	-0.8	0.0	3	dbSNP_120	53	6110,2490	694.4+/-404.7	2164,1782,354	no	coding-synonymous	CLSTN2	NM_022131.2		2235,2357,1911	TT,TC,CC		28.9535,16.2733,47.5088		761/956	140281723	6827,6179	2203	4300	6503	SO:0001819	synonymous_variant	64084	exon14			GGCTTCCCTTGAG	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2283C>T	3.37:g.140281723C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																			C|0.555;T|0.445	0.445	strong		0.562	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
CTNND1	1500	hgsc.bcm.edu	37	11	57564451	57564451	+	Missense_Mutation	SNP	C	C	T	rs199813020		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57564451C>T	ENST00000399050.4	+	6	1479	c.943C>T	c.(943-945)Cgt>Tgt	p.R315C	CTNND1_ENST00000528232.1_Missense_Mutation_p.R214C|CTNND1_ENST00000358694.6_Missense_Mutation_p.R315C|CTNND1_ENST00000361332.4_Missense_Mutation_p.R315C|CTNND1_ENST00000534579.1_Missense_Mutation_p.R261C|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000524630.1_Missense_Mutation_p.R315C|CTNND1_ENST00000361391.6_Missense_Mutation_p.R315C|CTNND1_ENST00000532649.1_Missense_Mutation_p.R261C|CTNND1_ENST00000399039.4_Missense_Mutation_p.R315C|CTNND1_ENST00000532463.1_Missense_Mutation_p.R214C|CTNND1_ENST00000426142.2_Missense_Mutation_p.R214C|CTNND1_ENST00000532844.1_Missense_Mutation_p.R261C|CTNND1_ENST00000528621.1_Missense_Mutation_p.R261C|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000526938.1_Missense_Mutation_p.R315C|CTNND1_ENST00000428599.2_Missense_Mutation_p.R315C|CTNND1_ENST00000529873.1_Missense_Mutation_p.R261C|CTNND1_ENST00000530094.1_Missense_Mutation_p.R214C|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000361796.4_Missense_Mutation_p.R315C|CTNND1_ENST00000415361.2_Missense_Mutation_p.R214C|CTNND1_ENST00000529919.1_Missense_Mutation_p.R315C|CTNND1_ENST00000529526.1_Missense_Mutation_p.R261C|CTNND1_ENST00000532787.1_Missense_Mutation_p.R214C|CTNND1_ENST00000526357.1_Missense_Mutation_p.R261C|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000360682.6_Missense_Mutation_p.R315C|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000530748.1_Missense_Mutation_p.R261C|CTNND1_ENST00000529986.1_Missense_Mutation_p.R214C|CTNND1_ENST00000532245.1_Missense_Mutation_p.R214C	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	315					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				CTCTGACCCTCGTCGGCGCCT	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		13710	0.001		0.0	False		,,,				2504	0.0				p.R315C		Atlas-SNP	.											.	CTNND1	203	.	0			c.C943T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1,3955		0,1,1977	60.0	62.0	61.0		943,943,943,943,943,640,640,640,640,640,640,640,781,781,943,781,781,781,781,640,781,943	5.8	1.0	11		61	2,8326		0,2,4162	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	CTNND1	NM_001085458.1,NM_001085459.1,NM_001085460.1,NM_001085461.1,NM_001085462.1,NM_001085463.1,NM_001085464.1,NM_001085465.1,NM_001085466.1,NM_001085467.1,NM_001085468.1,NM_001085469.1,NM_001206883.1,NM_001206884.1,NM_001206885.1,NM_001206886.1,NM_001206887.1,NM_001206888.1,NM_001206889.1,NM_001206890.1,NM_001206891.1,NM_001331.2	180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180	0,3,6139	TT,TC,CC		0.024,0.0253,0.0244	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	315/969,315/963,315/934,315/934,315/934,214/868,214/862,214/841,214/839,214/833,214/833,214/833,261/915,261/886,315/940,261/909,261/888,261/880,261/880,214/833,261/880,315/942	57564451	3,12281	1978	4164	6142	SO:0001583	missense	1500	exon6			GACCCTCGTCGGC	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"""Armadillo repeat containing"""	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.943C>T	11.37:g.57564451C>T	ENSP00000382004:p.Arg315Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Missense_Mutation	SNP	ENST00000399050.4	37	CCDS44604.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.674466	0.67928	2.53E-4	2.4E-4	ENSG00000198561	ENST00000524630;ENST00000529919;ENST00000399039;ENST00000360682;ENST00000361796;ENST00000529526;ENST00000426142;ENST00000399050;ENST00000361391;ENST00000361332;ENST00000532463;ENST00000529986;ENST00000358694;ENST00000532787;ENST00000532649;ENST00000528621;ENST00000530748;ENST00000428599;ENST00000528232;ENST00000529873;ENST00000532844;ENST00000526357;ENST00000530094;ENST00000415361;ENST00000532245;ENST00000534579;ENST00000526938;ENST00000534647	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.73258	-0.36;-0.36;-0.36;-0.73;-0.36;-0.36;-0.27;-0.37;-0.73;-0.37;-0.27;-0.27;-0.36;-0.62;-0.36;-0.36;-0.37;-0.36;-0.28;-0.73;-0.38;-0.37;-0.36;-0.37;-0.27;-0.36;-0.73;2.06	5.82	5.82	0.92795	Armadillo-like helical (1);	0.158729	0.64402	D	0.000018	T	0.79269	0.4417	L	0.43152	1.355	0.53005	D	0.999967	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;P;D;D;D;D;P	0.65010	0.917;0.917;0.828;0.917;0.917;0.931;0.917;0.828	T	0.76556	-0.2916	10	0.39692	T	0.17	-4.6961	19.6883	0.95987	0.0:1.0:0.0:0.0	.	315;315;315;261;261;315;315;315	O60716-3;O60716-2;O60716;O60716-14;O60716-10;O60716-5;F8WA43;C9JZR2	.;.;CTND1_HUMAN;.;.;.;.;.	C	315;315;315;315;315;261;214;315;315;315;214;214;315;214;261;261;261;315;214;261;261;261;214;214;214;261;315;237	ENSP00000436543:R315C;ENSP00000434808:R315C;ENSP00000381996:R315C;ENSP00000353902:R315C;ENSP00000354907:R315C;ENSP00000436323:R261C;ENSP00000409930:R214C;ENSP00000382004:R315C;ENSP00000354785:R315C;ENSP00000354823:R315C;ENSP00000432075:R214C;ENSP00000437156:R214C;ENSP00000351527:R315C;ENSP00000434949:R214C;ENSP00000435379:R261C;ENSP00000432243:R261C;ENSP00000436744:R261C;ENSP00000413586:R315C;ENSP00000435266:R214C;ENSP00000435494:R261C;ENSP00000433276:R261C;ENSP00000433334:R261C;ENSP00000437327:R214C;ENSP00000403518:R214C;ENSP00000434017:R214C;ENSP00000435789:R261C;ENSP00000432041:R315C;ENSP00000434202:R237C	ENSP00000351527:R315C	R	+	1	0	CTNND1	57321027	0.996000	0.38824	1.000000	0.80357	0.974000	0.67602	2.279000	0.43435	2.747000	0.94245	0.655000	0.94253	CGT	.	.	weak		0.527	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331	
KRT2	3849	hgsc.bcm.edu	37	12	53045642	53045642	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53045642A>G	ENST00000309680.3	-	1	306	c.285T>C	c.(283-285)ggT>ggC	p.G95G		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	95	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		cgcctccaaaaccacctcctc	0.617																																					p.G95G		Atlas-SNP	.											KRT2,rectum,carcinoma,0,1	KRT2	94	1	0			c.T285C						PASS	.						53.0	34.0	40.0					12																	53045642		2198	4298	6496	SO:0001819	synonymous_variant	3849	exon1			TCCAAAACCACCT		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.285T>C	12.37:g.53045642A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	142	17	0.119718	NM_000423	Q4VAQ2	Silent	SNP	ENST00000309680.3	37	CCDS8835.1																																																																																			.	.	none		0.617	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	
RBM33	155435	hgsc.bcm.edu	37	7	155503920	155503920	+	Silent	SNP	A	A	T	rs7800753	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:155503920A>T	ENST00000401878.3	+	8	1170	c.972A>T	c.(970-972)ccA>ccT	p.P324P	RBM33_ENST00000486747.1_3'UTR	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	324	Pro-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		CTCCACCGCCACCGCCGCCTC	0.577													A|||	3220	0.642971	0.5015	0.4885	5008	,	,		11116	0.6885		0.7485	False		,,,				2504	0.7883				p.P324P		Atlas-SNP	.											.	RBM33	157	.	0			c.A972T						PASS	.	A		2077,1785		557,963,411	13.0	17.0	16.0		972	-10.5	0.0	7	dbSNP_116	16	5967,2291		2190,1587,352	no	coding-synonymous	RBM33	NM_053043.2		2747,2550,763	TT,TA,AA		27.7428,46.2196,33.6304		324/1171	155503920	8044,4076	1931	4129	6060	SO:0001819	synonymous_variant	155435	exon8			ACCGCCACCGCCG	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.972A>T	7.37:g.155503920A>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	63	58	0.920635	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Silent	SNP	ENST00000401878.3	37	CCDS5941.2	1394	0.6382783882783882	263	0.5345528455284553	192	0.5303867403314917	375	0.6555944055944056	564	0.7440633245382586	A	2.528	-0.309196	0.05458	0.537804	0.722572	ENSG00000184863	ENST00000392761	.	.	.	5.27	-10.5	0.00291	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27614	P	0.9485525	.	.	.	.	.	.	T	0.04178	-1.0971	3	.	.	.	.	9.8494	0.41048	0.2451:0.0:0.4849:0.27	rs7800753;rs61523012	.	.	.	L	96	.	.	H	+	2	0	RBM33	155196681	0.000000	0.05858	0.000000	0.03702	0.237000	0.25408	-3.203000	0.00559	-3.561000	0.00141	-0.379000	0.06801	CAC	A|0.344;T|0.656	0.656	strong		0.577	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
ANKRD36	375248	hgsc.bcm.edu	37	2	97849219	97849219	+	Missense_Mutation	SNP	T	T	C	rs12996352	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97849219T>C	ENST00000461153.2	+	27	2105	c.1861T>C	c.(1861-1863)Tgg>Cgg	p.W621R	ANKRD36_ENST00000420699.2_Missense_Mutation_p.W621R			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	621								p.W621R(1)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						ACAATCGGCCTGGAAGGTAGT	0.289													.|||	1954	0.390176	0.2133	0.4856	5008	,	,		18310	0.2579		0.7932	False		,,,				2504	0.2832				p.W621R		Atlas-SNP	.											ANKRD36_ENST00000420699,NS,carcinoma,0,1	ANKRD36	170	1	1	Substitution - Missense(1)	stomach(1)	c.T1861C						PASS	.																																			SO:0001583	missense	375248	exon27			TCGGCCTGGAAGG	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.1861T>C	2.37:g.97849219T>C	ENSP00000419530:p.Trp621Arg	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	1004	0.4597069597069597	100	0.2032520325203252	179	0.494475138121547	164	0.2867132867132867	561	0.7401055408970977	.	1.944	-0.442827	0.04604	.	.	ENSG00000135976	ENST00000461153;ENST00000420699	T;T	0.29397	1.57;1.57	1.08	-0.18	0.13295	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P;B	0.42993	0.797;0.253	B;B	0.29942	0.088;0.109	T	0.47169	-0.9138	8	0.06625	T	0.88	.	2.9694	0.05918	0.0:0.3053:0.0:0.6947	rs12996352	621;88	A6QL64;Q5JPF3-3	AN36A_HUMAN;.	R	621	ENSP00000419530:W621R;ENSP00000391950:W621R	ENSP00000391950:W621R	W	+	1	0	ANKRD36	97212946	0.244000	0.23889	0.041000	0.18516	0.043000	0.13939	1.815000	0.38981	-0.065000	0.13021	0.155000	0.16302	TGG	T|0.485;C|0.515	0.515	strong		0.289	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
B4GALNT4	338707	hgsc.bcm.edu	37	11	380315	380315	+	Silent	SNP	C	C	T	rs117291242	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:380315C>T	ENST00000329962.6	+	18	2739	c.2739C>T	c.(2737-2739)ctC>ctT	p.L913L		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	913					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCGTGTTCCTCTGCGACCTGC	0.697													.|||	83	0.0165735	0.0008	0.0591	5008	,	,		12431	0.0		0.0368	False		,,,				2504	0.0041				p.L913L		Atlas-SNP	.											B4GALNT4,NS,carcinoma,+2,1	B4GALNT4	83	1	0			c.C2739T						PASS	.	C		43,4363	43.8+/-77.6	0,43,2160	78.0	57.0	64.0		2739	-3.3	1.0	11	dbSNP_132	64	274,8326	103.1+/-164.3	5,264,4031	no	coding-synonymous	B4GALNT4	NM_178537.4		5,307,6191	TT,TC,CC		3.186,0.9759,2.4373		913/1040	380315	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	338707	exon18			GTTCCTCTGCGAC	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2739C>T	11.37:g.380315C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_178537	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																			C|0.978;T|0.022	0.022	strong		0.697	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
CACNA1B	774	hgsc.bcm.edu	37	9	141008876	141008876	+	Silent	SNP	C	C	T	rs2229948	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:141008876C>T	ENST00000371372.1	+	41	5728	c.5583C>T	c.(5581-5583)ttC>ttT	p.F1861F	CACNA1B_ENST00000277549.5_Silent_p.F1055F|CACNA1B_ENST00000371357.1_Silent_p.F1860F|CACNA1B_ENST00000371355.4_Silent_p.F1862F|CACNA1B_ENST00000371363.1_Silent_p.F1859F|CACNA1B_ENST00000277551.2_Silent_p.F1861F	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1861					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TGATGATATTCGACTTCTACA	0.527													C|||	2527	0.504593	0.2269	0.745	5008	,	,		18751	0.2748		0.7773	False		,,,				2504	0.6656				p.F1861F		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C5583T						PASS	.	C		1391,2499		267,857,821	56.0	52.0	53.0		5583	-4.1	0.9	9	dbSNP_98	53	6251,2029		2339,1573,228	no	coding-synonymous	CACNA1B	NM_000718.3		2606,2430,1049	TT,TC,CC		24.5048,35.7584,37.2062		1861/2340	141008876	7642,4528	1945	4140	6085	SO:0001819	synonymous_variant	774	exon40			GATATTCGACTTC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.5583C>T	9.37:g.141008876C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_001243812	B1AQK5	Silent	SNP	ENST00000371372.1	37	CCDS59522.1																																																																																			C|0.503;T|0.497	0.497	strong		0.527	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130830	52130830	+	Silent	SNP	C	C	A	rs8107754	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52130830C>A	ENST00000534261.2	-	7	1566	c.1167G>T	c.(1165-1167)ggG>ggT	p.G389G	SIGLEC5_ENST00000222107.4_Silent_p.G389G|SIGLEC5_ENST00000570106.2_Silent_p.G389G|SIGLEC5_ENST00000429354.3_Silent_p.G389G|SIGLEC5_ENST00000599649.1_Silent_p.G389G			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	389					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGGCCCAGGGCCCAGCTGAGC	0.662													C|||	1646	0.328674	0.382	0.5562	5008	,	,		15906	0.0089		0.4602	False		,,,				2504	0.2894				p.G389G		Atlas-SNP	.											SIGLEC5,NS,carcinoma,-1,1	SIGLEC5	67	1	0			c.G1167T						PASS	.	C		1864,2542	534.0+/-373.9	378,1108,717	47.0	46.0	46.0		1167	3.0	0.9	19	dbSNP_116	46	4136,4464	559.5+/-387.4	996,2144,1160	no	coding-synonymous	SIGLEC5	NM_003830.2		1374,3252,1877	AA,AC,CC		48.093,42.3059,46.1326		389/552	52130830	6000,7006	2203	4300	6503	SO:0001819	synonymous_variant	8778	exon6			CCAGGGCCCAGCT	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1167G>T	19.37:g.52130830C>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_003830		Silent	SNP	ENST00000534261.2	37	CCDS33088.1																																																																																			C|0.575;A|0.425	0.425	strong		0.662	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
CCDC67	159989	hgsc.bcm.edu	37	11	93129484	93129484	+	Missense_Mutation	SNP	A	A	G	rs12282288|rs386756254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:93129484A>G	ENST00000298050.3	+	11	1419	c.1319A>G	c.(1318-1320)gAa>gGa	p.E440G	CCDC67_ENST00000525646.1_Missense_Mutation_p.E182G	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	440			E -> G (in dbSNP:rs12282288).|E -> Q (in dbSNP:rs12288277).	E -> R (in Ref. 3; BAB71673). {ECO:0000305}.	cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				GACCCCGGAGAATACATGGTA	0.353													G|||	1336	0.266773	0.1929	0.1888	5008	,	,		18716	0.3363		0.2843	False		,,,				2504	0.3323				p.E440G		Atlas-SNP	.											.	CCDC67	57	.	0			c.A1319G						PASS	.	G	GLY/GLU	7,3659		1,5,1827	50.0	47.0	48.0		1319	-3.3	0.0	11	dbSNP_120	48	28,8144		2,24,4060	yes	missense	CCDC67	NM_181645.3	98	3,29,5887	GG,GA,AA		0.3426,0.1909,0.2957	benign	440/605	93129484	35,11803	1833	4086	5919	SO:0001583	missense	159989	exon11			CCGGAGAATACAT	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.1319A>G	11.37:g.93129484A>G	ENSP00000298050:p.Glu440Gly	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	130	68	0.523077	NM_181645	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	CCDS44707.1	460	0.21062271062271062	64	0.13008130081300814	66	0.18232044198895028	163	0.28496503496503495	167	0.22031662269129287	G	1.574	-0.533394	0.04082	0.001909	0.003426	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000525646	T;T;T	0.22134	1.97;1.97;1.97	5.26	-3.27	0.05048	.	1.241300	0.05530	N	0.563720	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44236	-0.9341	9	0.25751	T	0.34	.	6.1932	0.20536	0.4217:0.2198:0.3586:0.0	rs12282288;rs58568481;rs12282288	440;440	Q05D60;E9PJR5	CCD67_HUMAN;.	G	440;440;182	ENSP00000432111:E440G;ENSP00000298050:E440G;ENSP00000435079:E182G	ENSP00000298050:E440G	E	+	2	0	CCDC67	92769132	0.000000	0.05858	0.003000	0.11579	0.012000	0.07955	-1.032000	0.03574	-1.184000	0.02720	-1.922000	0.00515	GAA	A|0.801;G|0.199	0.199	strong		0.353	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645	
FASTKD1	79675	hgsc.bcm.edu	37	2	170417031	170417031	+	Silent	SNP	T	T	C	rs35933910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170417031T>C	ENST00000453153.2	-	5	1183	c.837A>G	c.(835-837)caA>caG	p.Q279Q	FASTKD1_ENST00000453929.2_Silent_p.Q279Q	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	279					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						AACTATTAAATTGTAGAAATT	0.284													T|||	175	0.0349441	0.0008	0.0086	5008	,	,		16183	0.1111		0.0288	False		,,,				2504	0.0276				p.Q279Q		Atlas-SNP	.											.	FASTKD1	86	.	0			c.A837G						PASS	.	T		30,4334		0,30,2152	47.0	54.0	51.0		837	-0.8	1.0	2	dbSNP_126	51	297,8277		3,291,3993	no	coding-synonymous	FASTKD1	NM_024622.3		3,321,6145	CC,CT,TT		3.464,0.6874,2.5274		279/848	170417031	327,12611	2182	4287	6469	SO:0001819	synonymous_variant	79675	exon5			ATTAAATTGTAGA	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.837A>G	2.37:g.170417031T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	125	70	0.56	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			T|0.967;C|0.033	0.033	strong		0.284	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
PPIL2	23759	hgsc.bcm.edu	37	22	22039199	22039199	+	Silent	SNP	C	C	T	rs861833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22039199C>T	ENST00000335025.8	+	10	802	c.711C>T	c.(709-711)aaC>aaT	p.N237N	PPIL2_ENST00000406385.1_Silent_p.N237N|PPIL2_ENST00000398831.3_Silent_p.N237N|PPIL2_ENST00000492445.2_Silent_p.N237N|PPIL2_ENST00000456792.2_Silent_p.N216N|PPIL2_ENST00000412327.1_Silent_p.N237N					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					ACAAGCTGAACGCTGTGAGTG	0.617													C|||	347	0.0692891	0.0053	0.0994	5008	,	,		17632	0.001		0.1799	False		,,,				2504	0.091				p.N237N		Atlas-SNP	.											PPIL2,colon,carcinoma,0,1	PPIL2	38	1	0			c.C711T						PASS	.	C	,,	136,4268	97.6+/-136.3	3,130,2069	46.0	48.0	47.0		711,711,711	-5.7	0.5	22	dbSNP_86	47	1394,7206	266.8+/-286.9	115,1164,3021	no	coding-synonymous,coding-synonymous,coding-synonymous	PPIL2	NM_014337.3,NM_148175.2,NM_148176.2	,,	118,1294,5090	TT,TC,CC		16.2093,3.0881,11.7656	,,	237/521,237/521,237/528	22039199	1530,11474	2202	4300	6502	SO:0001819	synonymous_variant	23759	exon10			GCTGAACGCTGTG		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"""U-box domain containing"""	9261	protein-coding gene	gene with protein product	"""U-box domain containing 7"""	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.711C>T	22.37:g.22039199C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_014337		Silent	SNP	ENST00000335025.8	37	CCDS13793.1																																																																																			C|0.901;T|0.099	0.099	strong		0.617	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4		
FAM107A	11170	hgsc.bcm.edu	37	3	58552950	58552950	+	Silent	SNP	C	C	T	rs1139701	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58552950C>T	ENST00000394481.1	-	4	870	c.312G>A	c.(310-312)caG>caA	p.Q104Q	FAM107A_ENST00000464064.1_Silent_p.Q104Q|FAM107A_ENST00000447756.2_Silent_p.Q132Q|FAM107A_ENST00000360997.2_Silent_p.Q104Q|FAM107A_ENST00000474531.1_Silent_p.Q135Q	NM_001282713.1|NM_007177.2	NP_001269642.1|NP_009108.1	O95990	F107A_HUMAN	family with sequence similarity 107, member A	104					regulation of cell growth (GO:0001558)	neuron projection (GO:0043005)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)		TCAGCCTCTGCTGCCGTCTCA	0.627													C|||	87	0.0173722	0.0015	0.0288	5008	,	,		20130	0.001		0.0527	False		,,,				2504	0.0112				p.Q104Q		Atlas-SNP	.											.	FAM107A	33	.	0			c.G312A						PASS	.	C	,	49,4357	50.9+/-86.3	1,47,2155	47.0	39.0	42.0		312,312	3.2	1.0	3	dbSNP_132	42	404,8196	126.0+/-184.5	6,392,3902	no	coding-synonymous,coding-synonymous	FAM107A	NM_001076778.1,NM_007177.2	,	7,439,6057	TT,TC,CC		4.6977,1.1121,3.483	,	104/145,104/145	58552950	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	11170	exon3			CCTCTGCTGCCGT	AF089854	CCDS2892.1, CCDS63672.1, CCDS63673.1	3p14.2	2006-02-03			ENSG00000168309	ENSG00000168309			30827	protein-coding gene	gene with protein product		608295				10564580, 10702698	Standard	XM_005264835		Approved	DRR1, TU3A	uc003dkn.3	O95990	OTTHUMG00000159159	ENST00000394481.1:c.312G>A	3.37:g.58552950C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	211	106	0.50237	NM_001076778	B3KNQ4|B7ZAY5|J3KR61|Q96NH4	Silent	SNP	ENST00000394481.1	37	CCDS2892.1																																																																																			C|0.964;T|0.036	0.036	strong		0.627	FAM107A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353585.1	NM_007177	
KCNH2	3757	hgsc.bcm.edu	37	7	150645534	150645534	+	Missense_Mutation	SNP	T	T	G	rs1805123	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150645534T>G	ENST00000262186.5	-	11	3091	c.2690A>C	c.(2689-2691)aAg>aCg	p.K897T	KCNH2_ENST00000392968.2_Missense_Mutation_p.K801T|KCNH2_ENST00000330883.4_Missense_Mutation_p.K557T	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	897			K -> T (in dbSNP:rs1805123). {ECO:0000269|PubMed:10862094, ECO:0000269|PubMed:11997281}.		cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	cgcctcacccTTGTCCGTGCG	0.667													T|||	682	0.136182	0.0068	0.17	5008	,	,		7620	0.0536		0.2535	False		,,,				2504	0.2515				p.K897T	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											KCNH2,colon,carcinoma,0,1	KCNH2	157	1	0			c.A2690C	GRCh37	CM004877	KCNH2	M	rs1805123	PASS	.	T	THR/LYS,THR/LYS	199,4207	116.7+/-154.6	8,183,2012	27.0	27.0	27.0		2690,1670	-0.0	1.0	7	dbSNP_89	27	2000,6600	322.6+/-315.6	248,1504,2548	yes	missense,missense	KCNH2	NM_000238.3,NM_172057.2	78,78	256,1687,4560	GG,GT,TT		23.2558,4.5166,16.9076	benign,benign	897/1160,557/820	150645534	2199,10807	2203	4300	6503	SO:0001583	missense	3757	exon11			TCACCCTTGTCCG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.2690A>C	7.37:g.150645534T>G	ENSP00000262186:p.Lys897Thr	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	23	15	0.652174	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	282	0.12912087912087913	8	0.016260162601626018	72	0.19889502762430938	20	0.03496503496503497	182	0.24010554089709762	T	14.87	2.663067	0.47572	0.045166	0.232558	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186	D;D;D	0.98747	-4.79;-4.89;-5.11	3.87	-0.036	0.13890	.	0.265285	0.34223	N	0.004151	T	0.00552	0.0018	M	0.62723	1.935	0.09310	P	0.9999999999999913	P;B;B	0.52316	0.952;0.0;0.248	B;B;B	0.39617	0.305;0.001;0.067	T	0.07616	-1.0763	9	0.46703	T	0.11	.	7.2061	0.25907	0.0:0.2987:0.0:0.7013	rs1805123;rs2968861;rs8179016;rs1805123	801;897;557	C4PFH9;Q12809;Q12809-2	.;KCNH2_HUMAN;.	T	557;801;897	ENSP00000328531:K557T;ENSP00000376695:K801T;ENSP00000262186:K897T	ENSP00000262186:K897T	K	-	2	0	KCNH2	150276467	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	2.069000	0.41481	-0.079000	0.12707	0.402000	0.26972	AAG	T|0.855;G|0.145	0.145	strong		0.667	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
COL6A3	1293	hgsc.bcm.edu	37	2	238244923	238244923	+	Silent	SNP	C	C	T	rs11683438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238244923C>T	ENST00000295550.4	-	40	9272	c.8820G>A	c.(8818-8820)acG>acA	p.T2940T	COL6A3_ENST00000472056.1_Silent_p.T2333T|COL6A3_ENST00000409809.1_Silent_p.T2734T|COL6A3_ENST00000346358.4_Silent_p.T2740T|COL6A3_ENST00000347401.3_Silent_p.T2739T|COL6A3_ENST00000353578.4_Silent_p.T2734T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2940	Ala-rich.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GCTTCGCTGCCGTTGCTGGCT	0.637													C|||	216	0.043131	0.003	0.0432	5008	,	,		17309	0.0089		0.1113	False		,,,				2504	0.0624				p.T2940T		Atlas-SNP	.											.	COL6A3	608	.	0			c.G8820A						PASS	.	C	,,	80,4320		1,78,2121	42.0	51.0	48.0		8820,6999,8202	-4.5	0.0	2	dbSNP_120	48	843,7757		43,757,3500	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	44,835,5621	TT,TC,CC		9.8023,1.8182,7.1	,,	2940/3178,2333/2571,2734/2972	238244923	923,12077	2200	4300	6500	SO:0001819	synonymous_variant	1293	exon40			CGCTGCCGTTGCT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8820G>A	2.37:g.238244923C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.933;G|0.000;T|0.067	0.067	strong		0.637	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
ZNF763	284390	hgsc.bcm.edu	37	19	12087921	12087921	+	Silent	SNP	G	G	C	rs376310072	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12087921G>C	ENST00000358987.3	+	2	199	c.72G>C	c.(70-72)tcG>tcC	p.S24S	ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000591944.1_Silent_p.S93S|ZNF763_ENST00000592625.1_Silent_p.S24S|ZNF763_ENST00000343949.5_Silent_p.S27S|ZNF763_ENST00000590798.1_Silent_p.S44S|ZNF763_ENST00000538752.1_Silent_p.S44S			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TGGATATTTCGCAGAGGAAAC	0.493													N|||	4	0.000798722	0.0023	0.0	5008	,	,		18630	0.0		0.001	False		,,,				2504	0.0				p.S27S		Atlas-SNP	.											ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	0			c.G81C						scavenged	.						150.0	152.0	151.0					19																	12087921		2203	4300	6503	SO:0001819	synonymous_variant	284390	exon2			TATTTCGCAGAGG	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"""Zinc fingers, C2H2-type"", ""-"""	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.72G>C	19.37:g.12087921G>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	256	12	0.046875	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				.	.	alt		0.493	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	
WDR81	124997	hgsc.bcm.edu	37	17	1629969	1629969	+	Silent	SNP	C	C	T	rs80035274|rs587780499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1629969C>T	ENST00000409644.1	+	1	1716	c.1716C>T	c.(1714-1716)caC>caT	p.H572H	WDR81_ENST00000419248.1_Intron|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000437219.2_Intron|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	572	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TGGACGCCCACACTCACCTGG	0.622													C|||	681	0.135982	0.0507	0.2147	5008	,	,		17737	0.1647		0.2078	False		,,,				2504	0.092				p.H572H		Atlas-SNP	.											WDR81_ENST00000409644,NS,carcinoma,0,1	WDR81	180	1	0			c.C1716T						PASS	.						12.0	15.0	14.0					17																	1629969		692	1589	2281	SO:0001819	synonymous_variant	124997	exon1			CGCCCACACTCAC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.1716C>T	17.37:g.1629969C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.833;T|0.167	0.167	strong		0.622	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
GAS2L2	246176	hgsc.bcm.edu	37	17	34072031	34072031	+	Missense_Mutation	SNP	G	G	A	rs56386706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34072031G>A	ENST00000254466.6	-	6	2512	c.2485C>T	c.(2485-2487)Cgg>Tgg	p.R829W	GAS2L2_ENST00000587565.1_Missense_Mutation_p.R813W	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	829			R -> W (in dbSNP:rs56386706).		cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCATCCACCCGGGATGCCTCC	0.642													G|||	130	0.0259585	0.0045	0.0375	5008	,	,		17817	0.0		0.0626	False		,,,				2504	0.0358				p.R829W		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C2485T						PASS	.	G	TRP/ARG	56,4350	54.9+/-90.9	0,56,2147	56.0	60.0	59.0		2485	0.3	0.0	17	dbSNP_129	59	471,8129	138.3+/-195.1	9,453,3838	yes	missense	GAS2L2	NM_139285.3	101	9,509,5985	AA,AG,GG		5.4767,1.271,4.052	possibly-damaging	829/881	34072031	527,12479	2203	4300	6503	SO:0001583	missense	246176	exon6			CCACCCGGGATGC	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.2485C>T	17.37:g.34072031G>A	ENSP00000254466:p.Arg829Trp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	57	0.0260989010989011	5	0.01016260162601626	11	0.03038674033149171	0	0.0	41	0.05408970976253298	G	11.13	1.547655	0.27652	0.01271	0.054767	ENSG00000132139	ENST00000254466;ENST00000359507	T	0.18810	2.19	3.57	0.351	0.16042	.	3.764050	0.01567	N	0.020407	T	0.01287	0.0042	N	0.08118	0	0.09310	N	1	D	0.53885	0.963	B	0.34452	0.183	T	0.14200	-1.0481	10	0.66056	D	0.02	6.0647	4.358	0.11188	0.2131:0.3724:0.4144:0.0	rs56386706	829	Q8NHY3	GA2L2_HUMAN	W	829;243	ENSP00000254466:R829W	ENSP00000254466:R829W	R	-	1	2	GAS2L2	31096144	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.218000	0.17622	0.131000	0.18576	-0.304000	0.09214	CGG	G|0.964;A|0.036	0.036	strong		0.642	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285	
SON	6651	hgsc.bcm.edu	37	21	34926043	34926043	+	Missense_Mutation	SNP	G	G	A	rs61743204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:34926043G>A	ENST00000356577.4	+	3	4981	c.4506G>A	c.(4504-4506)atG>atA	p.M1502I	SON_ENST00000300278.4_Missense_Mutation_p.M1502I|SON_ENST00000381692.2_Intron|SON_ENST00000290239.6_Missense_Mutation_p.M1502I|SON_ENST00000381679.4_Missense_Mutation_p.M1502I	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1502					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						AGATTGGCATGCAGGAGATTG	0.388													G|||	769	0.153554	0.118	0.1816	5008	,	,		23665	0.2351		0.1054	False		,,,				2504	0.1472				p.M1502I		Atlas-SNP	.											.	SON	343	.	0			c.G4506A						PASS	.	G	ILE/MET,ILE/MET	540,3864	240.9+/-251.5	35,470,1697	47.0	44.0	45.0		4506,4506	2.0	1.0	21	dbSNP_129	45	759,7841	181.3+/-230.0	41,677,3582	yes	missense,missense	SON	NM_032195.1,NM_138927.1	10,10	76,1147,5279	AA,AG,GG		8.8256,12.2616,9.9892	benign,benign	1502/2304,1502/2427	34926043	1299,11705	2202	4300	6502	SO:0001583	missense	6651	exon3			TGGCATGCAGGAG	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.4506G>A	21.37:g.34926043G>A	ENSP00000348984:p.Met1502Ile	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	335|335	0.1533882783882784|0.1533882783882784	61|61	0.12398373983739837|0.12398373983739837	49|49	0.13535911602209943|0.13535911602209943	142|142	0.24825174825174826|0.24825174825174826	83|83	0.10949868073878628|0.10949868073878628	G|G	0.099|0.099	-1.155417|-1.155417	0.01700|0.01700	0.122616|0.122616	0.088256|0.088256	ENSG00000159140|ENSG00000159140	ENST00000436227|ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	.|T;T;T;T	.|0.10960	.|3.03;3.02;3.0;2.82	5.03|5.03	2.02|2.02	0.26589|0.26589	.|.	.|0.501171	.|0.20410	.|N	.|0.092872	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.39007|0.39007	P|P	0.04052800000000001|0.04052800000000001	.|B;B;B;B;B	.|0.06786	.|0.0;0.0;0.0;0.0;0.001	.|B;B;B;B;B	.|0.09377	.|0.001;0.0;0.001;0.001;0.004	T|T	0.44862|0.44862	-0.9300|-0.9300	4|9	.|0.05620	.|T	.|0.96	.|.	5.6576|5.6576	0.17650|0.17650	0.0916:0.0:0.5638:0.3445|0.0916:0.0:0.5638:0.3445	rs61743204|rs61743204	.|1502;1502;1183;1502;1502	.|P18583-10;P18583;P18583-2;P18583-3;P18583-6	.|.;SON_HUMAN;.;.;.	Y|I	497|1502	.|ENSP00000348984:M1502I;ENSP00000290239:M1502I;ENSP00000300278:M1502I;ENSP00000371095:M1502I	.|ENSP00000290239:M1502I	C|M	+|+	2|3	0|0	SON|SON	33847913|33847913	0.063000|0.063000	0.20901|0.20901	0.972000|0.972000	0.41901|0.41901	0.016000|0.016000	0.09150|0.09150	-0.191000|-0.191000	0.09601|0.09601	0.804000|0.804000	0.34136|0.34136	0.591000|0.591000	0.81541|0.81541	TGC|ATG	G|0.884;A|0.116	0.116	strong		0.388	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
TRIM64B	642446	hgsc.bcm.edu	37	11	89608899	89608899	+	Missense_Mutation	SNP	T	T	G	rs201022110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:89608899T>G	ENST00000329862.6	-	1	286	c.287A>C	c.(286-288)gAg>gCg	p.E96A		NM_001136486.1|NM_001164397.1	NP_001129958.1|NP_001157869.1	A6NI03	TR64B_HUMAN	tripartite motif containing 64B	96						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)	2						CTTAGTCTCCTCATGGAGCAC	0.507													t|||	1413	0.282149	0.4433	0.2378	5008	,	,		24915	0.1696		0.2197	False		,,,				2504	0.2761				p.E96A		Atlas-SNP	.											TRIM64B,NS,carcinoma,0,2	TRIM64B	23	2	0			c.A287C						scavenged	.						7.0	7.0	7.0					11																	89608899		495	1394	1889	SO:0001583	missense	642446	exon1			GTCTCCTCATGGA		CCDS53693.1	11q14.3	2014-04-02	2011-01-25		ENSG00000189253	ENSG00000189253		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	37147	protein-coding gene	gene with protein product			"""tripartite motif-containing 64B"""				Standard	NM_001164397		Approved		uc021qoo.1	A6NI03	OTTHUMG00000167638	ENST00000329862.6:c.287A>C	11.37:g.89608899T>G	ENSP00000332969:p.Glu96Ala	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	135	55	0.407407	NM_001164397		Missense_Mutation	SNP	ENST00000329862.6	37	CCDS53693.1	.	.	.	.	.	.	.	.	.	.	.	7.335	0.619740	0.14193	.	.	ENSG00000189253	ENST00000329862	T	0.57436	0.4	2.06	-2.81	0.05805	.	.	.	.	.	T	0.49081	0.1536	M	0.67569	2.06	0.80722	P	0.0	.	.	.	.	.	.	T	0.51733	-0.8668	5	.	.	.	.	3.3853	0.07269	0.0:0.2863:0.2094:0.5043	.	.	.	.	A	96	ENSP00000332969:E96A	.	E	-	2	0	TRIM64B	89248547	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.140000	0.16056	-0.854000	0.04131	0.321000	0.21382	GAG	T|0.500;G|0.500	0.500	strong		0.507	TRIM64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395440.1		
MUC4	4585	hgsc.bcm.edu	37	3	195505960	195505960	+	Missense_Mutation	SNP	G	G	C	rs112020305	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195505960G>C	ENST00000463781.3	-	2	12950	c.12491C>G	c.(12490-12492)aCc>aGc	p.T4164S	MUC4_ENST00000475231.1_Missense_Mutation_p.T4164S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4164S(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGAAGCGTCGGTGACAGGAAG	0.587													.|||	17	0.00339457	0.0129	0.0	5008	,	,		10875	0.0		0.0	False		,,,				2504	0.0				p.T4164S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	kidney(1)|endometrium(1)	c.C12491G						PASS	.						19.0	12.0	14.0					3																	195505960		671	1528	2199	SO:0001583	missense	4585	exon2			GCGTCGGTGACAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12491C>G	3.37:g.195505960G>C	ENSP00000417498:p.Thr4164Ser	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	108	29	0.268519	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.985	0.182849	0.09495	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35789	1.38;1.29	.	.	.	.	.	.	.	.	T	0.19248	0.0462	N	0.19112	0.55	0.09310	N	0.999997	P	0.37985	0.613	B	0.35899	0.213	T	0.14587	-1.0467	7	.	.	.	.	5.8529	0.18704	9.0E-4:0.0:0.9991:0.0	.	4036	E7ESK3	.	S	4164	ENSP00000417498:T4164S;ENSP00000420243:T4164S	.	T	-	2	0	MUC4	196990739	0.002000	0.14202	0.025000	0.17156	0.022000	0.10575	0.413000	0.21148	0.073000	0.16731	0.074000	0.15403	ACC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EIF2AK4	440275	hgsc.bcm.edu	37	15	40313141	40313141	+	Silent	SNP	C	C	T	rs3207297	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40313141C>T	ENST00000263791.5	+	31	4258	c.4215C>T	c.(4213-4215)ggC>ggT	p.G1405G	EIF2AK4_ENST00000382727.2_Silent_p.G1377G	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1405	Histidyl-tRNA synthetase-like.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		TAAGTGTTGGCCAGATGTCTA	0.483													C|||	1528	0.305112	0.292	0.2939	5008	,	,		19039	0.249		0.3569	False		,,,				2504	0.3354				p.G1405G		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.C4215T						PASS	.	C		1346,2670		244,858,906	134.0	126.0	128.0		4215	1.5	1.0	15	dbSNP_105	128	3059,5317		555,1949,1684	no	coding-synonymous	EIF2AK4	NM_001013703.2		799,2807,2590	TT,TC,CC		36.521,33.5159,35.5471		1405/1650	40313141	4405,7987	2008	4188	6196	SO:0001819	synonymous_variant	440275	exon31			TGTTGGCCAGATG	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.4215C>T	15.37:g.40313141C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	180	77	0.427778	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Silent	SNP	ENST00000263791.5	37	CCDS42016.1																																																																																			C|0.683;T|0.317	0.317	strong		0.483	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1		
SLC25A32	81034	hgsc.bcm.edu	37	8	104427578	104427578	+	5'Flank	SNP	T	T	C	rs3134297	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:104427578T>C	ENST00000297578.4	-	0	0				DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000297579.5_Silent_p.S120S|DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|SLC25A32_ENST00000543107.1_5'Flank	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TGACTGGAAGTAGTCTGGGAA	0.632													T|||	1270	0.253594	0.202	0.268	5008	,	,		18261	0.3333		0.2306	False		,,,				2504	0.2546				p.S120S		Atlas-SNP	.											DCAF13,NS,carcinoma,0,1	DCAF13	66	1	0			c.T360C						scavenged	.	T		949,3453		103,743,1355	37.0	45.0	43.0		360	1.9	0.7	8	dbSNP_103	43	1809,6783		189,1431,2676	no	coding-synonymous	DCAF13	NM_015420.6		292,2174,4031	CC,CT,TT		21.0545,21.5584,21.2252		120/598	104427578	2758,10236	2201	4296	6497	SO:0001631	upstream_gene_variant	25879	exon1			TGGAAGTAGTCTG	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		8.37:g.104427578T>C	Exception_encountered	Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_015420	Q96JZ6|Q96SU7	Silent	SNP	ENST00000297578.4	37	CCDS6300.1																																																																																			T|0.764;C|0.236	0.236	strong		0.632	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
NPW	283869	hgsc.bcm.edu	37	16	2070568	2070568	+	Missense_Mutation	SNP	A	A	C	rs2286472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2070568A>C	ENST00000566435.1	+	2	803	c.290A>C	c.(289-291)gAc>gCc	p.D97A	NPW_ENST00000329610.4_Missense_Mutation_p.D149A			Q8N729	NPW_HUMAN	neuropeptide W	149					feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				kidney(1)	1						CCAGCGGTGGACCCCGCAGCA	0.726													C|||	1810	0.361422	0.6218	0.2579	5008	,	,		11024	0.3313		0.329	False		,,,				2504	0.1472				p.D149A		Atlas-SNP	.											NPW,NS,carcinoma,0,2	NPW	4	2	0			c.A446C						PASS	.	C	ALA/ASP	2209,1627		693,823,402	17.0	23.0	21.0		446	-0.2	0.0	16	dbSNP_100	21	2599,5625		402,1795,1915	yes	missense	NPW	NM_001099456.2	126	1095,2618,2317	CC,CA,AA		31.6026,42.414,39.8673	benign	149/166	2070568	4808,7252	1918	4112	6030	SO:0001583	missense	283869	exon2			CGGTGGACCCCGC	AB084276	CCDS42102.1	16p13.3	2013-02-26			ENSG00000183971	ENSG00000183971		"""Endogenous ligands"""	30509	protein-coding gene	gene with protein product	"""prepro-neuropeptide W"""	607997				12118011, 12401809	Standard	NM_001099456		Approved	PPL8	uc002coh.4	Q8N729	OTTHUMG00000176914	ENST00000566435.1:c.290A>C	16.37:g.2070568A>C	ENSP00000456974:p.Asp97Ala	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_001099456		Missense_Mutation	SNP	ENST00000566435.1	37		820	0.37545787545787546	303	0.6158536585365854	105	0.2900552486187845	173	0.30244755244755245	239	0.3153034300791557	N	0.008	-1.886957	0.00527	0.57586	0.316026	ENSG00000183971	ENST00000329610	T	0.54071	0.59	2.21	-0.235	0.13071	.	0.833798	0.10009	N	0.727475	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45338	-0.9268	9	0.09590	T	0.72	.	2.1559	0.03811	0.2384:0.3075:0.0:0.4541	rs2286472;rs56777272;rs2286472	149	Q8N729	NPW_HUMAN	A	149	ENSP00000330070:D149A	ENSP00000330070:D149A	D	+	2	0	NPW	2010569	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	-0.827000	0.04424	-0.424000	0.07382	-2.803000	0.00113	GAC	A|0.624;C|0.376	0.376	strong		0.726	NPW-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000434312.1	NM_001099456	
JMJD4	65094	hgsc.bcm.edu	37	1	227920357	227920357	+	Silent	SNP	C	C	T	rs4837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:227920357C>T	ENST00000366758.3	-	6	1127	c.1128G>A	c.(1126-1128)tcG>tcA	p.S376S	JMJD4_ENST00000438896.2_Silent_p.S360S|JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000480897.1_3'UTR|SNAP47_ENST00000315781.5_5'Flank|SNAP47_ENST00000366759.4_5'Flank|SNAP47_ENST00000366760.1_Intron	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	376										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				AGTTGATGCCCGAGCAGGACC	0.587													C|||	466	0.0930511	0.1157	0.0706	5008	,	,		20417	0.0486		0.1074	False		,,,				2504	0.1094				p.S376S		Atlas-SNP	.											.	JMJD4	28	.	0			c.G1128A						PASS	.	C	,	514,3892	234.6+/-247.4	32,450,1721	62.0	56.0	58.0		1080,1128	-10.0	0.0	1	dbSNP_52	58	939,7661	205.8+/-248.1	56,827,3417	no	coding-synonymous,coding-synonymous	JMJD4	NM_001161465.1,NM_023007.2	,	88,1277,5138	TT,TC,CC		10.9186,11.6659,11.1718	,	360/448,376/464	227920357	1453,11553	2203	4300	6503	SO:0001819	synonymous_variant	65094	exon6			GATGCCCGAGCAG	AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.1128G>A	1.37:g.227920357C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Silent	SNP	ENST00000366758.3	37	CCDS1561.1	202	0.0924908424908425	62	0.12601626016260162	30	0.08287292817679558	30	0.05244755244755245	80	0.10554089709762533	C	6.866	0.529084	0.13127	0.116659	0.109186	ENSG00000081692	ENST00000438896	.	.	.	5.01	-10.0	0.00425	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999484256	.	.	.	.	.	.	T	0.02184	-1.1199	3	.	.	.	-14.3261	4.112	0.10063	0.2681:0.1906:0.4308:0.1105	rs4837;rs17355133	.	.	.	Q	353	.	.	R	-	2	0	JMJD4	225986980	0.000000	0.05858	0.034000	0.17996	0.956000	0.61745	-5.329000	0.00131	-4.649000	0.00038	-1.779000	0.00650	CGG	C|0.892;T|0.108	0.108	strong		0.587	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007	
AKAP12	9590	hgsc.bcm.edu	37	6	151672185	151672185	+	Missense_Mutation	SNP	A	A	T	rs61748676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:151672185A>T	ENST00000253332.1	+	3	2848	c.2659A>T	c.(2659-2661)Agt>Tgt	p.S887C	AKAP12_ENST00000359755.5_Missense_Mutation_p.S782C|AKAP12_ENST00000354675.6_Missense_Mutation_p.S789C|AKAP12_ENST00000402676.2_Missense_Mutation_p.S887C			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	887					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GCTCAGCGAGAGTCAGGTTCA	0.532													A|||	51	0.0101837	0.0015	0.0259	5008	,	,		18286	0.0		0.0308	False		,,,				2504	0.0				p.S887C	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.A2659T						PASS	.	A	CYS/SER,CYS/SER	29,4377	34.3+/-65.2	0,29,2174	73.0	80.0	78.0		2659,2365	3.0	0.2	6	dbSNP_129	78	287,8313	107.0+/-167.8	4,279,4017	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	112,112	4,308,6191	TT,TA,AA		3.3372,0.6582,2.4296	probably-damaging,probably-damaging	887/1783,789/1685	151672185	316,12690	2203	4300	6503	SO:0001583	missense	9590	exon4			AGCGAGAGTCAGG	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.2659A>T	6.37:g.151672185A>T	ENSP00000253332:p.Ser887Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	32	0.014652014652014652	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	23	0.030343007915567283	A	13.05	2.121763	0.37436	0.006582	0.033372	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.08008	3.14;3.14;3.15;3.15	5.4	3.03	0.35002	.	1.136460	0.06613	N	0.755988	T	0.07548	0.0190	L	0.54323	1.7	0.09310	N	1	D;D;D	0.63046	0.992;0.992;0.985	P;P;P	0.56216	0.794;0.794;0.628	T	0.30937	-0.9961	10	0.56958	D	0.05	.	4.6169	0.12432	0.5207:0.0:0.4793:0.0	rs61748676	782;789;887	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	C	887;887;789;782	ENSP00000384537:S887C;ENSP00000253332:S887C;ENSP00000346702:S789C;ENSP00000352794:S782C	ENSP00000253332:S887C	S	+	1	0	AKAP12	151713878	0.348000	0.24861	0.192000	0.23308	0.015000	0.08874	0.815000	0.27253	0.888000	0.36160	0.459000	0.35465	AGT	A|0.978;T|0.022	0.022	strong		0.532	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
ZNF483	158399	hgsc.bcm.edu	37	9	114305075	114305075	+	Silent	SNP	G	G	A	rs142830150		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:114305075G>A	ENST00000309235.5	+	6	2018	c.1860G>A	c.(1858-1860)acG>acA	p.T620T	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	620					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						GCCATTTTACGTCTGTGATTT	0.408																																					p.T620T		Atlas-SNP	.											ZNF483,NS,carcinoma,+1,1	ZNF483	78	1	0			c.G1860A						scavenged	.	G	,	1,4405	2.1+/-5.4	0,1,2202	65.0	67.0	66.0		,1860	-5.3	0.1	9	dbSNP_134	66	0,8600		0,0,4300	no	intron,coding-synonymous	ZNF483	NM_001007169.2,NM_133464.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	,620/745	114305075	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	158399	exon6			TTTTACGTCTGTG	AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.1860G>A	9.37:g.114305075G>A		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	84	5	0.0595238	NM_133464	Q5VZN2|Q8NAE1	Silent	SNP	ENST00000309235.5	37	CCDS35106.1																																																																																			G|1.000;A|0.000	0.000	weak		0.408	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567	
SLCO1B3	28234	hgsc.bcm.edu	37	12	21011480	21011480	+	Missense_Mutation	SNP	T	T	G	rs4149117	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:21011480T>G	ENST00000381545.3	+	5	553	c.334T>G	c.(334-336)Tct>Gct	p.S112A	SLCO1B3_ENST00000553473.1_Missense_Mutation_p.S112A|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.S112A|LST3_ENST00000381541.3_Missense_Mutation_p.S112A|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.S112A|SLCO1B3_ENST00000545880.1_3'UTR|LST3_ENST00000540229.1_Missense_Mutation_p.S112A	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	112			S -> A (in dbSNP:rs4149117).		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TATTTTGACATCTTTACCACA	0.328													.|||	3518	0.702476	0.3563	0.8372	5008	,	,		14932	0.6974		0.8648	False		,,,				2504	0.9131				p.S112A		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.T334G						PASS	.	G	ALA/SER	1974,2432	618.1+/-393.1	466,1042,695	167.0	151.0	157.0		334	4.0	1.0	12	dbSNP_110	157	7427,1171	238.1+/-269.7	3210,1007,82	yes	missense	SLCO1B3	NM_019844.2	99	3676,2049,777	GG,GT,TT		13.6194,44.8025,27.7069	benign	112/703	21011480	9401,3603	2203	4299	6502	SO:0001583	missense	28234	exon5			TTGACATCTTTAC		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.334T>G	12.37:g.21011480T>G	ENSP00000370956:p.Ser112Ala	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	1549	0.7092490842490843	185	0.37601626016260165	310	0.856353591160221	410	0.7167832167832168	644	0.8496042216358839	G	3.999	-0.002855	0.07773	0.448025	0.863806	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046;ENSG00000257046;ENSG00000205754	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000381541;ENST00000540229;ENST00000554957	T;T;T;T;T;T;T	0.79845	0.68;0.68;0.68;0.68;-1.31;0.68;-1.31	3.99	3.99	0.46301	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.106603	0.64402	N	0.000006	T	0.00012	0.0000	N	0.00960	-1.095	0.53688	P	2.599999999997049E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.43653	-0.9378	9	0.02654	T	1	.	13.2898	0.60264	0.0:0.0:0.8399:0.1601	rs4149117;rs52800447;rs58702833;rs4149117	112;112;112	F5H094;Q5JAR4;Q9NPD5	.;.;SO1B3_HUMAN	A	112	ENSP00000442000:S112A;ENSP00000261196:S112A;ENSP00000370956:S112A;ENSP00000451758:S112A;ENSP00000370952:S112A;ENSP00000441269:S112A;ENSP00000452013:S112A	ENSP00000370952:S112A	S	+	1	0	SLCO1B3;SLCO1B7;RP11-545J16.1	20902747	0.998000	0.40836	0.987000	0.45799	0.648000	0.38561	5.297000	0.65704	0.797000	0.33971	-0.366000	0.07423	TCT	G|0.702;N|0.000	0.702	strong		0.328	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
FAM153A	285596	hgsc.bcm.edu	37	5	177163580	177163580	+	Splice_Site	SNP	A	A	G	rs201479484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:177163580A>G	ENST00000440605.3	-	11	716	c.433T>C	c.(433-435)Ttt>Ctt	p.F145L	FAM153A_ENST00000510276.1_Splice_Site_p.F145L|FAM153A_ENST00000393518.3_Intron|FAM153A_ENST00000513554.1_Intron	NM_173663.3	NP_775934.3	Q9UHL3	F153A_HUMAN	family with sequence similarity 153, member A	145				F -> L (in Ref. 1; AAD42863, 2; BAA34472 and 3; BAF82207). {ECO:0000305}.				p.F145L(1)		kidney(6)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|stomach(1)	11	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAATACGTACATTCGGCCAGT	0.458													g|||	1124	0.224441	0.0817	0.2233	5008	,	,		14448	0.37		0.2396	False		,,,				2504	0.2526				p.F145L		Atlas-SNP	.											FAM153A,NS,carcinoma,0,2	FAM153A	23	2	1	Substitution - Missense(1)	stomach(1)	c.T433C						scavenged	.						102.0	80.0	88.0					5																	177163580		2149	4080	6229	SO:0001630	splice_region_variant	285596	exon11			ACGTACATTCGGC	AB018295	CCDS34305.1	5q35.3	2010-05-12			ENSG00000170074	ENSG00000170074			29940	protein-coding gene	gene with protein product	"""NY REN 7 antigen"""					10508479, 9872452	Standard	NM_173663		Approved	NY-REN-7	uc003mic.3	Q9UHL3	OTTHUMG00000163394	ENST00000440605.3:c.433+1T>C	5.37:g.177163580A>G		Somatic	586	1	0.00170648		WXS	Illumina HiSeq	Phase_I	510	119	0.233333	NM_173663	A8K0F3|O94852	Missense_Mutation	SNP	ENST00000440605.3	37	CCDS34305.1	.	.	.	.	.	.	.	.	.	.	.	0.013	-1.616740	0.00828	.	.	ENSG00000170074	ENST00000440977;ENST00000510276;ENST00000440605	.	.	.	0.885	0.885	0.19188	.	.	.	.	.	T	0.18002	0.0432	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26883	-1.0090	6	.	.	.	.	4.0728	0.09891	0.4065:0.5935:0.0:0.0	.	145	Q9UHL3	F153A_HUMAN	L	222;145;145	.	.	F	-	1	0	FAM153A	177096186	0.003000	0.15002	0.002000	0.10522	0.019000	0.09904	-4.771000	0.00188	-0.033000	0.13736	-1.866000	0.00557	TTT	A|0.500;G|0.500	0.500	strong		0.458	FAM153A-022	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417242.1	NM_173663	Missense_Mutation
LPAR3	23566	hgsc.bcm.edu	37	1	85331462	85331462	+	Silent	SNP	A	A	C	rs41289037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:85331462A>C	ENST00000440886.1	-	1	380	c.342T>G	c.(340-342)acT>acG	p.T114T	LPAR3_ENST00000491034.1_5'UTR|LPAR3_ENST00000370611.3_Silent_p.T114T			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	114					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						TGAGGGAAGCAGTCAAGCTAC	0.502													A|||	24	0.00479233	0.0015	0.0086	5008	,	,		18401	0.0		0.0159	False		,,,				2504	0.0				p.T114T		Atlas-SNP	.											.	LPAR3	53	.	0			c.T342G						PASS	.	A		11,4395	19.1+/-41.9	0,11,2192	189.0	195.0	193.0		342	-11.3	0.2	1	dbSNP_127	193	118,8482	62.1+/-124.0	2,114,4184	no	coding-synonymous	LPAR3	NM_012152.2		2,125,6376	CC,CA,AA		1.3721,0.2497,0.9918		114/354	85331462	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	23566	exon2			GGAAGCAGTCAAG	AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	14298	protein-coding gene	gene with protein product		605106	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"""	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.342T>G	1.37:g.85331462A>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	170	104	0.611765	NM_012152	A0AVA3	Silent	SNP	ENST00000440886.1	37	CCDS700.1																																																																																			A|0.991;C|0.009	0.009	strong		0.502	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204396830	204396830	+	Silent	SNP	G	G	A	rs17334387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204396830G>A	ENST00000367187.3	-	32	5089	c.4533C>T	c.(4531-4533)tcC>tcT	p.S1511S	RP11-739N20.2_ENST00000443515.1_RNA|PIK3C2B_ENST00000424712.2_Silent_p.S1483S	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1511					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TGTAGGAGATGGACAGCTTCA	0.488													G|||	688	0.13738	0.2776	0.1023	5008	,	,		19457	0.0774		0.1113	False		,,,				2504	0.0613				p.S1511S		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C4533T						PASS	.	G		1131,3275	405.1+/-333.4	142,847,1214	197.0	189.0	191.0		4533	2.2	1.0	1	dbSNP_123	191	741,7859	178.0+/-227.5	28,685,3587	no	coding-synonymous	PIK3C2B	NM_002646.3		170,1532,4801	AA,AG,GG		8.6163,25.6695,14.3934		1511/1635	204396830	1872,11134	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon32			GGAGATGGACAGC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4533C>T	1.37:g.204396830G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	168	63	0.375	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			G|0.857;A|0.143	0.143	strong		0.488	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
NOL11	25926	hgsc.bcm.edu	37	17	65739627	65739627	+	Silent	SNP	A	A	G	rs10127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:65739627A>G	ENST00000253247.4	+	17	2083	c.1968A>G	c.(1966-1968)gcA>gcG	p.A656A	SNORA38B_ENST00000363524.1_RNA|NOL11_ENST00000535137.1_Silent_p.A474A	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	656					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTCTGGATGCAAATTTTACTG	0.303													A|||	2441	0.48742	0.3623	0.6196	5008	,	,		14755	0.5069		0.5249	False		,,,				2504	0.5041				p.A656A		Atlas-SNP	.											.	NOL11	48	.	0			c.A1968G						PASS	.	A		1796,2610	525.1+/-371.5	347,1102,754	82.0	86.0	85.0		1968	-0.0	1.0	17	dbSNP_52	85	4700,3888	603.0+/-394.6	1286,2128,880	no	coding-synonymous	NOL11	NM_015462.3		1633,3230,1634	GG,GA,AA		45.2725,40.7626,49.9923		656/720	65739627	6496,6498	2203	4294	6497	SO:0001819	synonymous_variant	25926	exon17			GGATGCAAATTTT	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1968A>G	17.37:g.65739627A>G		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	280	120	0.428571	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Silent	SNP	ENST00000253247.4	37	CCDS11671.1																																																																																			A|0.511;G|0.489	0.489	strong		0.303	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462	
Unknown	0	hgsc.bcm.edu	37	13	103402522	103402522	+	IGR	SNP	C	C	T	rs9300760	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103402522C>T								LINC00283 (4948 upstream) : TEX30 (15817 downstream)																							GGCTTAGACACGTTTCCTCTA	0.343													C|||	3473	0.69349	0.5416	0.7493	5008	,	,		19401	0.5873		0.826	False		,,,				2504	0.8323				p.T175T		Atlas-SNP	.											.	.	.	.	0			c.G525A						PASS	.	C		773,611		217,339,136	244.0	179.0	199.0		525	0.1	0.0	13	dbSNP_119	199	2544,638		1024,496,71	no	coding-synonymous	CCDC168	NM_001146197.1		1241,835,207	TT,TC,CC		20.0503,44.1474,27.3544		175/7082	103402522	3317,1249	692	1591	2283	SO:0001628	intergenic_variant	643677	exon4			TAGACACGTTTCC																													13.37:g.103402522C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	195	74	0.379487	NM_001146197		Silent	SNP		37																																																																																				C|0.316;N|0.001	.	strong	0	0.343								
PRUNE2	158471	hgsc.bcm.edu	37	9	79324179	79324179	+	Missense_Mutation	SNP	G	G	A	rs530978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79324179G>A	ENST00000376718.3	-	8	3134	c.3011C>T	c.(3010-3012)aCg>aTg	p.T1004M	PRUNE2_ENST00000428286.1_Missense_Mutation_p.T645M	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1004					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CTCCTCTGCCGTGGAGTTACC	0.463													G|||	2162	0.431709	0.1952	0.634	5008	,	,		21383	0.3591		0.5885	False		,,,				2504	0.5215				p.T1004M		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C3011T						PASS	.	G	MET/THR	854,2282		125,604,839	133.0	106.0	115.0		3011	3.0	0.0	9	dbSNP_83	115	4335,2829		1317,1701,564	yes	missense	PRUNE2	NM_015225.2	81	1442,2305,1403	AA,AG,GG		39.4891,27.2321,49.6214	probably-damaging	1004/3089	79324179	5189,5111	1568	3582	5150	SO:0001583	missense	158471	exon8			TCTGCCGTGGAGT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.3011C>T	9.37:g.79324179G>A	ENSP00000365908:p.Thr1004Met	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	263	129	0.490494	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	983	0.4500915750915751	106	0.21544715447154472	229	0.6325966850828729	212	0.3706293706293706	436	0.575197889182058	G	15.17	2.752540	0.49362	0.272321	0.605109	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.43294	0.95;0.95	5.94	2.98	0.34508	.	1.502020	0.03684	N	0.245955	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	2.9999999999752447E-6	P	0.51240	0.943	B	0.41813	0.367	T	0.42207	-0.9465	9	0.35671	T	0.21	1.5694	5.2005	0.15262	0.1665:0.0:0.5857:0.2477	rs530978;rs17180809;rs52810524;rs530978	1004	Q8WUY3	PRUN2_HUMAN	M	1004;645;1003	ENSP00000365908:T1004M;ENSP00000397425:T645M	ENSP00000365908:T1004M	T	-	2	0	PRUNE2	78513999	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.447000	0.21710	0.857000	0.35407	0.561000	0.74099	ACG	G|0.567;A|0.433	0.433	strong		0.463	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
ATM	472	hgsc.bcm.edu	37	11	108175462	108175462	+	Missense_Mutation	SNP	G	G	A	rs1801516	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108175462G>A	ENST00000452508.2	+	38	5746	c.5557G>A	c.(5557-5559)Gat>Aat	p.D1853N	ATM_ENST00000278616.4_Missense_Mutation_p.D1853N			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1853			D -> N (common polymorphism; dbSNP:rs1801516). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10425038, ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9711876, ECO:0000269|PubMed:9887333}.|D -> V (might contribute to B-cell chronic lymphocytic leukemia; dbSNP:rs1801673). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872980, ECO:0000269|PubMed:9887333}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.D1853N(10)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTTACTCCAAGATACAAATGA	0.388			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			G|||	335	0.066893	0.0083	0.0965	5008	,	,		16727	0.0159		0.162	False		,,,				2504	0.0798				p.D1853N		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,-1,17	ATM	1657	17	10	Substitution - Missense(10)	breast(9)|skin(1)	c.G5557A	GRCh37	CM077896	ATM	M	rs1801516	PASS	.	G	ASN/ASP	125,4277	92.5+/-131.2	3,119,2079	75.0	72.0	73.0	http://www.ncbi.nlm.nih.gov/pubmed?term	5557	5.5	1.0	11	dbSNP_89	73	1205,7391	241.8+/-272.0	99,1007,3192	yes	missense	ATM	NM_000051.3	23	102,1126,5271	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.0181,2.8396,10.2323	possibly-damaging	1853/3057	108175462	1330,11668	2201	4298	6499	SO:0001583	missense	472	exon37	Familial Cancer Database	AT, Louis-Bar syndrome	CTCCAAGATACAA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5557G>A	11.37:g.108175462G>A	ENSP00000388058:p.Asp1853Asn	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	172	0.07875457875457875	5	0.01016260162601626	40	0.11049723756906077	7	0.012237762237762238	120	0.158311345646438	G	17.18	3.324076	0.60634	0.028396	0.140181	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.73152	-0.72;-0.72	5.52	5.52	0.82312	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.61036	1.89	0.19945	P	0.9999491241	B	0.20368	0.044	B	0.16289	0.015	T	0.10730	-1.0617	9	0.33940	T	0.23	.	19.8041	0.96521	0.0:0.0:1.0:0.0	rs1801516;rs17503060;rs52821794;rs60879649;rs1801516	1853	Q13315	ATM_HUMAN	N	1853	ENSP00000278616:D1853N;ENSP00000388058:D1853N	ENSP00000278616:D1853N	D	+	1	0	ATM	107680672	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.342000	0.72982	2.748000	0.94277	0.591000	0.81541	GAT	G|0.910;A|0.090	0.090	strong		0.388	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
SLC7A11	23657	hgsc.bcm.edu	37	4	139140494	139140494	+	Silent	SNP	G	G	C	rs6838248	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:139140494G>C	ENST00000280612.5	-	5	951	c.672C>G	c.(670-672)gcC>gcG	p.A224A		NM_014331.3	NP_055146.1	Q9UPY5	XCT_HUMAN	solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11	224					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|brain development (GO:0007420)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|lens fiber cell differentiation (GO:0070306)|leukocyte migration (GO:0050900)|platelet aggregation (GO:0070527)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	cystine:glutamate antiporter activity (GO:0015327)			breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)	18	all_hematologic(180;0.166)				Acetylcysteine(DB06151)|L-Cystine(DB00138)|Riluzole(DB00740)|Rosuvastatin(DB01098)|Sulfasalazine(DB00795)|Tauroursodeoxycholic acid(DB08834)	TTCCTGAAAAGGCGTCTTTAA	0.388													G|||	1713	0.342053	0.3018	0.366	5008	,	,		18813	0.0764		0.5099	False		,,,				2504	0.4806				p.A224A		Atlas-SNP	.											.	SLC7A11	40	.	0			c.C672G						PASS	.	G		1390,3016	456.1+/-351.2	207,976,1020	145.0	131.0	135.0		672	1.3	1.0	4	dbSNP_116	135	4176,4424	567.1+/-388.8	1016,2144,1140	no	coding-synonymous	SLC7A11	NM_014331.3		1223,3120,2160	CC,CG,GG		48.5581,31.5479,42.7956		224/502	139140494	5566,7440	2203	4300	6503	SO:0001819	synonymous_variant	23657	exon5			TGAAAAGGCGTCT	AB026891	CCDS3742.1	4q28-q32	2013-05-22	2011-07-12		ENSG00000151012	ENSG00000151012		"""Solute carriers"""	11059	protein-coding gene	gene with protein product		607933				10206947, 12763038	Standard	XM_005262875		Approved	xCT	uc021xrw.1	Q9UPY5	OTTHUMG00000133396	ENST00000280612.5:c.672C>G	4.37:g.139140494G>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	185	83	0.448649	NM_014331	A8K2U4	Silent	SNP	ENST00000280612.5	37	CCDS3742.1																																																																																			G|0.601;C|0.399	0.399	strong		0.388	SLC7A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257251.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1266599	1266599	+	Missense_Mutation	SNP	C	C	T	rs139960671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1266599C>T	ENST00000529681.1	+	31	8547	c.8489C>T	c.(8488-8490)cCg>cTg	p.P2830L	MUC5B_ENST00000447027.1_Missense_Mutation_p.P2833L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2830	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACGACCACCCCGGGCCACACC	0.692													-|||	415	0.0828674	0.0083	0.0793	5008	,	,		13344	0.006		0.2137	False		,,,				2504	0.1309				p.P2830L		Atlas-SNP	.											.	MUC5B	473	.	0			c.C8489T						PASS	.	C	LEU/PRO	162,3882		23,116,1883	69.0	93.0	85.0		8489	-0.9	0.0	11	dbSNP_134	85	1706,6460		354,998,2731	no	missense	MUC5B	NM_002458.2	98	377,1114,4614	TT,TC,CC		20.8915,4.0059,15.2989	benign	2830/5763	1266599	1868,10342	2022	4083	6105	SO:0001583	missense	727897	exon31			CCACCCCGGGCCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.8489C>T	11.37:g.1266599C>T	ENSP00000436812:p.Pro2830Leu	Somatic	501	0	0		WXS	Illumina HiSeq	Phase_I	383	196	0.511749	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	198	0.09065934065934066	6	0.012195121951219513	32	0.08839779005524862	2	0.0034965034965034965	158	0.20844327176781002	-	7.110	0.575801	0.13623	0.040059	0.208915	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.22336	1.96;1.96	2.84	-0.897	0.10553	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.30211	0.273;0.168	B;B	0.17722	0.019;0.013	T	0.36407	-0.9749	8	0.87932	D	0	.	5.1841	0.15174	0.3485:0.5427:0.0:0.1089	.	3413;2833	A7Y9J9;E9PBJ0	.;.	L	2830;2833;2802;2790	ENSP00000436812:P2830L;ENSP00000415793:P2833L	ENSP00000343037:P2802L	P	+	2	0	MUC5B	1223175	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.797000	0.04570	0.038000	0.15604	-0.490000	0.04691	CCG	C|0.895;T|0.105	0.105	strong		0.692	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
HAP1	9001	hgsc.bcm.edu	37	17	39883350	39883350	+	Missense_Mutation	SNP	G	G	A	rs4523977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39883350G>A	ENST00000310778.5	-	10	1487	c.1478C>T	c.(1477-1479)aCg>aTg	p.T493M	JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Missense_Mutation_p.T441M|HAP1_ENST00000393939.2_Missense_Mutation_p.T416M|HAP1_ENST00000341193.5_Missense_Mutation_p.T424M			P54257	HAP1_HUMAN	huntingtin-associated protein 1	493	Glu-rich.		T -> M (may influence the age-at-onset of Huntington disease; increases binding to mutated HTT; influences HTT degradation; dbSNP:rs4523977). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18192679}.		anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			CCTTAGAGACGTTCTGAGCTC	0.572													G|||	996	0.198882	0.0121	0.2017	5008	,	,		17882	0.249		0.2346	False		,,,				2504	0.3609				p.T441M		Atlas-SNP	.											.	HAP1	48	.	0			c.C1322T						PASS	.	G	MET/THR,MET/THR,MET/THR	194,4212	116.3+/-154.2	7,180,2016	37.0	38.0	38.0	http://www.ncbi.nlm.nih.gov/omim/143100,600947|http://omim.org/entry/600947|http://omim.org/entry/143100	1271,1247,1322	-4.3	0.0	17	dbSNP_111	38	1896,6704	301.4+/-305.4	213,1470,2617	yes	missense,missense,missense	HAP1	NM_001079870.1,NM_001079871.1,NM_177977.2	81,81,81	220,1650,4633	AA,AG,GG		22.0465,4.4031,16.0695	benign,benign,benign	424/603,416/595,441/620	39883350	2090,10916	2203	4300	6503	SO:0001583	missense	9001	exon9			AGAGACGTTCTGA	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"""neuroan 1"""	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.1478C>T	17.37:g.39883350G>A	ENSP00000309392:p.Thr493Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_177977	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	37		439	0.20100732600732601	14	0.028455284552845527	78	0.2154696132596685	164	0.2867132867132867	183	0.24142480211081793	G	2.601	-0.293044	0.05568	0.044031	0.220465	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.07114	3.22;3.58;3.34;3.23	3.61	-4.26	0.03755	.	1.151170	0.06867	N	0.800198	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B;B;B	0.34181	0.44;0.44;0.44;0.066	B;B;B;B	0.21917	0.037;0.037;0.037;0.006	T	0.48559	-0.9025	9	0.28530	T	0.3	-0.8888	5.3193	0.15872	0.5082:0.1489:0.3429:0.0	rs4523977;rs52821238;rs56495117;rs57455245;rs4523977	416;424;441;493	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	M	416;493;441;424	ENSP00000377513:T416M;ENSP00000309392:T493M;ENSP00000334002:T441M;ENSP00000343170:T424M	ENSP00000309392:T493M	T	-	2	0	HAP1	37136876	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.167000	0.03126	-1.024000	0.03338	-0.224000	0.12420	ACG	G|0.825;A|0.175	0.175	strong		0.572	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949	
DYRK2	8445	hgsc.bcm.edu	37	12	68052178	68052178	+	Silent	SNP	G	G	T	rs3741644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:68052178G>T	ENST00000344096.3	+	3	1904	c.1491G>T	c.(1489-1491)ggG>ggT	p.G497G	RP11-335O4.3_ENST00000425371.2_RNA|DYRK2_ENST00000393555.3_Silent_p.G424G	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	497	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		GAGAGTGGGGGAACGCGCTGA	0.582													G|||	2559	0.510982	0.3192	0.6037	5008	,	,		18694	0.6052		0.5726	False		,,,				2504	0.544				p.G497G		Atlas-SNP	.											.	DYRK2	63	.	0			c.G1491T						PASS	.	G	,	1563,2843	488.1+/-361.1	271,1021,911	59.0	62.0	61.0		1272,1491	1.0	1.0	12	dbSNP_107	61	5031,3569	624.6+/-397.6	1493,2045,762	no	coding-synonymous,coding-synonymous	DYRK2	NM_003583.3,NM_006482.2	,	1764,3066,1673	TT,TG,GG		41.5,35.4744,49.3003	,	424/529,497/602	68052178	6594,6412	2203	4300	6503	SO:0001819	synonymous_variant	8445	exon3			GTGGGGGAACGCG	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.1491G>T	12.37:g.68052178G>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	183	180	0.983607	NM_006482	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	37	CCDS8978.1																																																																																			C|0.000;G|0.472;T|0.528	0.528	strong		0.582	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
OR2T27	403239	hgsc.bcm.edu	37	1	248814052	248814052	+	Missense_Mutation	SNP	T	T	A	rs28533004		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248814052T>A	ENST00000344889.3	-	1	133	c.134A>T	c.(133-135)aAg>aTg	p.K45M		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	45			K -> M (in dbSNP:rs28533004).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAGAATGATCTTGACCACGTT	0.517																																					p.K45M		Atlas-SNP	.											.	OR2T27	52	.	0			c.A134T						PASS	.						51.0	44.0	46.0					1																	248814052		2202	4282	6484	SO:0001583	missense	403239	exon1			ATGATCTTGACCA		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.134A>T	1.37:g.248814052T>A	ENSP00000342008:p.Lys45Met	Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	357	278	0.778711	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	1246	0.5705128205128205	263	0.5345528455284553	219	0.6049723756906077	318	0.5559440559440559	446	0.5883905013192612	.	0.006	-2.110494	0.00353	.	.	ENSG00000187701	ENST00000344889	T	0.00355	7.91	3.3	3.3	0.37823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	N	0.000198	T	0.00012	0.0000	N	0.00004	-3.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26608	-1.0098	9	0.02654	T	1	.	8.1814	0.31313	0.8202:0.0:0.0:0.1798	rs28533004	45	Q8NH04	O2T27_HUMAN	M	45	ENSP00000342008:K45M	ENSP00000342008:K45M	K	-	2	0	OR2T27	246880675	0.022000	0.18835	0.828000	0.32881	0.018000	0.09664	2.940000	0.49003	0.470000	0.27294	-1.235000	0.01560	AAG	T|0.250;A|0.750	0.750	weak		0.517	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
MUC4	4585	hgsc.bcm.edu	37	3	195515008	195515008	+	Missense_Mutation	SNP	C	C	G	rs201451131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515008C>G	ENST00000463781.3	-	2	3902	c.3443G>C	c.(3442-3444)gGt>gCt	p.G1148A	MUC4_ENST00000475231.1_Missense_Mutation_p.G1148A|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	622					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGTGGTGTGACCTGTGGATAC	0.567													.|||	786	0.156949	0.0582	0.147	5008	,	,		12957	0.254		0.1909	False		,,,				2504	0.1626				p.G1148A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G3443C						PASS	.						12.0	6.0	8.0					3																	195515008		679	1519	2198	SO:0001583	missense	4585	exon2			GTGTGACCTGTGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3443G>C	3.37:g.195515008C>G	ENSP00000417498:p.Gly1148Ala	Somatic	418	0	0		WXS	Illumina HiSeq	Phase_I	96	25	0.260417	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	5.956	0.360432	0.11296	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.48;1.48	0.663	-0.689	0.11313	.	.	.	.	.	T	0.12689	0.0308	N	0.19112	0.55	0.09310	N	1	P	0.36222	0.544	B	0.28849	0.095	T	0.16100	-1.0414	8	.	.	.	.	1.5639	0.02600	0.343:0.3881:0.0:0.2689	.	1148	E7ESK3	.	A	1148	ENSP00000417498:G1148A;ENSP00000420243:G1148A	.	G	-	2	0	MUC4	196999403	0.000000	0.05858	0.004000	0.12327	0.096000	0.18686	-1.079000	0.03410	-0.222000	0.09958	0.064000	0.15345	GGT	C|0.952;G|0.048	0.048	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MAP3K6	9064	hgsc.bcm.edu	37	1	27687466	27687466	+	Missense_Mutation	SNP	G	G	T	rs35659744	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:27687466G>T	ENST00000493901.1	-	15	2105	c.1866C>A	c.(1864-1866)aaC>aaA	p.N622K	MAP3K6_ENST00000374040.3_Missense_Mutation_p.N614K|MAP3K6_ENST00000357582.2_Missense_Mutation_p.N622K	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	622			N -> K (in dbSNP:rs35659744). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		TGGAATCCGGGTTCGTCACCC	0.716													G|||	611	0.122005	0.0182	0.1571	5008	,	,		14370	0.0823		0.2684	False		,,,				2504	0.1278				p.N622K		Atlas-SNP	.											MAP3K6_ENST00000493901,brain,glioma,0,16	MAP3K6	134	16	0			c.C1866A						PASS	.	G	LYS/ASN	243,4005		10,223,1891	11.0	15.0	14.0		1866	-0.3	0.6	1	dbSNP_126	14	2513,5979		407,1699,2140	yes	missense	MAP3K6	NM_004672.3	94	417,1922,4031	TT,TG,GG		29.5926,5.7203,21.6327	benign	622/1289	27687466	2756,9984	2124	4246	6370	SO:0001583	missense	9064	exon14			ATCCGGGTTCGTC	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.1866C>A	1.37:g.27687466G>T	ENSP00000419591:p.Asn622Lys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	22	0.354839	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	324|324	0.14835164835164835|0.14835164835164835	7|7	0.014227642276422764|0.014227642276422764	60|60	0.16574585635359115|0.16574585635359115	57|57	0.09965034965034965|0.09965034965034965	200|200	0.2638522427440633|0.2638522427440633	G|G	11.29|11.29	1.595660|1.595660	0.28445|0.28445	0.057203|0.057203	0.295926|0.295926	ENSG00000142733|ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582|ENST00000472410	T;T;T|.	0.65549|.	-0.16;-0.16;-0.16|.	5.2|5.2	-0.342|-0.342	0.12635|0.12635	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.10296|.	0.003;0.001|.	B;B|.	0.09377|.	0.004;0.002|.	T|T	0.35025|0.35025	-0.9805|-0.9805	8|4	0.41790|.	T|.	0.15|.	.|.	4.454|4.454	0.11635|0.11635	0.4176:0.2041:0.3783:0.0|0.4176:0.2041:0.3783:0.0	rs35659744;rs35659744|rs35659744;rs35659744	614;622|.	O95382-3;O95382|.	.;M3K6_HUMAN|.	K|N	614;622;345;622|346	ENSP00000363152:N614K;ENSP00000419591:N622K;ENSP00000350195:N622K|.	ENSP00000350195:N622K|.	N|T	-|-	3|2	2|0	MAP3K6|MAP3K6	27560053|27560053	0.001000|0.001000	0.12720|0.12720	0.648000|0.648000	0.29521|0.29521	0.791000|0.791000	0.44710|0.44710	0.029000|0.029000	0.13666|0.13666	0.246000|0.246000	0.21394|0.21394	-0.345000|-0.345000	0.07892|0.07892	AAC|ACC	G|0.846;T|0.154	0.154	strong		0.716	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
SUCO	51430	hgsc.bcm.edu	37	1	172558524	172558524	+	Silent	SNP	A	A	G	rs41264546	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:172558524A>G	ENST00000263688.3	+	18	2502	c.2283A>G	c.(2281-2283)ccA>ccG	p.P761P	SUCO_ENST00000610051.1_Intron|SUCO_ENST00000608151.1_Silent_p.P913P|SUCO_ENST00000367723.4_Silent_p.P912P	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	761					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											GACATATACCATCACCAGTGA	0.378													A|||	172	0.034345	0.0038	0.0663	5008	,	,		19208	0.001		0.0984	False		,,,				2504	0.0215				p.P761P		Atlas-SNP	.											.	.	.	.	0			c.A2283G						PASS	.	A	,	85,4313		2,81,2116	68.0	68.0	68.0		2283,2151	-0.2	0.1	1	dbSNP_127	68	850,7738		39,772,3483	no	coding-synonymous,coding-synonymous	C1orf9	NM_014283.3,NM_016227.2	,	41,853,5599	GG,GA,AA		9.8975,1.9327,7.2001	,	761/1255,717/1211	172558524	935,12051	2199	4294	6493	SO:0001819	synonymous_variant	51430	exon18			TATACCATCACCA	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.2283A>G	1.37:g.172558524A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	96	54	0.5625	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Silent	SNP	ENST00000263688.3	37	CCDS1303.1																																																																																			A|0.935;G|0.065	0.065	strong		0.378	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
OR2M2	391194	hgsc.bcm.edu	37	1	248343990	248343990	+	Missense_Mutation	SNP	T	T	C	rs4916104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248343990T>C	ENST00000359682.2	+	1	703	c.703T>C	c.(703-705)Tgc>Cgc	p.C235R		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	235			C -> R (in dbSNP:rs4916104).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			AGAGGGTCGTTGCAAAGCTTT	0.478													C|||	2903	0.579673	0.6142	0.6052	5008	,	,		20359	0.4415		0.6382	False		,,,				2504	0.5971				p.C235R		Atlas-SNP	.											OR2M2,NS,carcinoma,-1,1	OR2M2	149	1	0			c.T703C						PASS	.	C	ARG/CYS	2517,1889		810,897,496	176.0	155.0	162.0		703	1.1	0.0	1	dbSNP_111	162	5393,3205		1825,1743,731	no	missense	OR2M2	NM_001004688.1	180	2635,2640,1227	CC,CT,TT		37.2761,42.8734,39.1726	benign	235/348	248343990	7910,5094	2203	4299	6502	SO:0001583	missense	391194	exon1			GGTCGTTGCAAAG	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"""GPCR / Class A : Olfactory receptors"""	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.703T>C	1.37:g.248343990T>C	ENSP00000352710:p.Cys235Arg	Somatic	434	0	0		WXS	Illumina HiSeq	Phase_I	268	265	0.988806	NM_001004688	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	1105	0.5059523809523809	252	0.5121951219512195	202	0.5580110497237569	227	0.3968531468531469	424	0.5593667546174143	N	0.011	-1.736827	0.00681	0.571266	0.627239	ENSG00000198601	ENST00000359682	T	0.00036	8.86	2.03	1.07	0.20283	GPCR, rhodopsin-like superfamily (1);	1.321480	0.05860	N	0.622788	T	0.00012	0.0000	N	0.00132	-2.035	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23013	-1.0200	9	0.25106	T	0.35	.	6.5264	0.22303	0.1664:0.7098:0.0:0.1238	rs4916104	235	Q96R28	OR2M2_HUMAN	R	235	ENSP00000352710:C235R	ENSP00000352710:C235R	C	+	1	0	OR2M2	246410613	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.939000	0.01545	-0.143000	0.11334	-1.498000	0.00962	TGC	T|0.447;C|0.553	0.553	strong		0.478	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688	
PLEKHS1	79949	hgsc.bcm.edu	37	10	115540411	115540411	+	Silent	SNP	T	T	C	rs11196483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115540411T>C	ENST00000354462.3	+	6	626	c.468T>C	c.(466-468)gcT>gcC	p.A156A	PLEKHS1_ENST00000369312.4_Silent_p.A324A|PLEKHS1_ENST00000361048.1_3'UTR|PLEKHS1_ENST00000369309.1_Silent_p.A240A			Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	420																	CATTCCATGCTGCATCCTGTA	0.418													T|||	1782	0.355831	0.2625	0.2968	5008	,	,		21245	0.4187		0.3926	False		,,,				2504	0.4213				p.A324A		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.T972C						PASS	.	T	,,	1260,3146	432.4+/-343.3	194,872,1137	88.0	82.0	84.0		972,972,	-1.5	0.0	10	dbSNP_120	84	3395,5205	501.5+/-375.5	696,2003,1601	no	coding-synonymous,coding-synonymous,utr-3	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4	,,	890,2875,2738	CC,CT,TT		39.4767,28.5974,35.7912	,,	324/367,324/367,	115540411	4655,8351	2203	4300	6503	SO:0001819	synonymous_variant	79949	exon11			CCATGCTGCATCC	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000354462.3:c.468T>C	10.37:g.115540411T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_001193435	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Silent	SNP	ENST00000354462.3	37																																																																																				T|0.631;C|0.369	0.369	strong		0.418	PLEKHS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050431.2	NM_024889	
ABCA5	23461	hgsc.bcm.edu	37	17	67260926	67260926	+	Silent	SNP	A	A	G	rs12449649	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:67260926A>G	ENST00000392676.3	-	24	3329	c.3265T>C	c.(3265-3267)Ttg>Ctg	p.L1089L	ABCA5_ENST00000392677.2_Silent_p.L1090L|ABCA5_ENST00000588877.1_Silent_p.L1089L			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	1089					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TGAAATGCCAATAAGCTTCCT	0.308													A|||	1900	0.379393	0.1823	0.353	5008	,	,		15840	0.4058		0.493	False		,,,				2504	0.5204				p.L1089L		Atlas-SNP	.											.	ABCA5	162	.	0			c.T3265C						PASS	.	A	,	1030,3376	364.9+/-317.2	119,792,1292	53.0	55.0	54.0		3265,3265	4.7	1.0	17	dbSNP_120	54	4054,4538	547.8+/-385.2	947,2160,1189	no	coding-synonymous,coding-synonymous	ABCA5	NM_018672.3,NM_172232.2	,	1066,2952,2481	GG,GA,AA		47.1834,23.3772,39.1137	,	1089/1643,1089/1643	67260926	5084,7914	2203	4296	6499	SO:0001819	synonymous_variant	23461	exon23			ATGCCAATAAGCT	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.3265T>C	17.37:g.67260926A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Silent	SNP	ENST00000392676.3	37	CCDS11685.1																																																																																			A|0.614;G|0.386	0.386	strong		0.308	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
GSDMC	56169	hgsc.bcm.edu	37	8	130774897	130774897	+	Silent	SNP	T	T	C	rs17190932	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:130774897T>C	ENST00000276708.4	-	5	1532	c.651A>G	c.(649-651)agA>agG	p.R217R		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	217						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)		p.R217R(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						CCAGCTGCTTTCTCTTATAAG	0.527													T|||	472	0.0942492	0.0287	0.2003	5008	,	,		20432	0.0268		0.1899	False		,,,				2504	0.0787				p.R217R		Atlas-SNP	.											GSDMC,NS,carcinoma,0,1	GSDMC	71	1	1	Substitution - coding silent(1)	stomach(1)	c.A651G						PASS	.	T		244,4162	141.5+/-176.9	12,220,1971	257.0	230.0	239.0		651	2.9	0.2	8	dbSNP_123	239	1678,6922	306.9+/-308.1	181,1316,2803	no	coding-synonymous	GSDMC	NM_031415.2		193,1536,4774	CC,CT,TT		19.5116,5.5379,14.7778		217/509	130774897	1922,11084	2203	4300	6503	SO:0001819	synonymous_variant	56169	exon5			CTGCTTTCTCTTA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.651A>G	8.37:g.130774897T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_031415	Q5XKF3|Q6P494	Silent	SNP	ENST00000276708.4	37	CCDS6360.1																																																																																			C|0.125;N|0.000	0.125	strong		0.527	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
NUDT5	11164	hgsc.bcm.edu	37	10	12209752	12209752	+	Silent	SNP	T	T	C	rs6686	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:12209752T>C	ENST00000491614.1	-	10	1004	c.609A>G	c.(607-609)gcA>gcG	p.A203A	SEC61A2_ENST00000495368.1_3'UTR|NUDT5_ENST00000537776.1_Silent_p.A203A|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000378937.3_Silent_p.A216A|SEC61A2_ENST00000304267.8_Intron			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	203					D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				CATGTTTCAGTGCTAGAGCGT	0.448													C|||	2315	0.46226	0.4251	0.5245	5008	,	,		20633	0.5575		0.4821	False		,,,				2504	0.3497				p.A203A		Atlas-SNP	.											.	NUDT5	10	.	0			c.A609G						PASS	.	C	,	1985,2421	615.9+/-392.7	459,1067,677	163.0	148.0	153.0		,609	-10.3	0.0	10	dbSNP_52	153	4282,4318	578.9+/-390.8	1067,2148,1085	no	intron,coding-synonymous	NUDT5,SEC61A2	NM_001142627.1,NM_014142.2	,	1526,3215,1762	CC,CT,TT		49.7907,45.0522,48.1855	,	,203/220	12209752	6267,6739	2203	4300	6503	SO:0001819	synonymous_variant	11164	exon10			TTTCAGTGCTAGA	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"""Nudix motif containing"""	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.609A>G	10.37:g.12209752T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_014142	A8K516|Q6IAG0|Q9UH49	Silent	SNP	ENST00000491614.1	37	CCDS7089.1																																																																																			T|0.523;C|0.477	0.477	strong		0.448	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1		
CAMTA1	23261	hgsc.bcm.edu	37	1	7797503	7797503	+	Missense_Mutation	SNP	C	C	G	rs41278952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7797503C>G	ENST00000303635.7	+	15	3738	c.3531C>G	c.(3529-3531)aaC>aaG	p.N1177K	CAMTA1_ENST00000439411.2_Missense_Mutation_p.N1177K	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1177			N -> K (in dbSNP:rs41278952). {ECO:0000269|PubMed:17222547}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TGGGACAGAACCCCAGAATCC	0.572			T	WWTR1	epitheliod hemangioendothelioma								C|||	503	0.100439	0.0136	0.2089	5008	,	,		17819	0.0774		0.1163	False		,,,				2504	0.1483				p.N1177K		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.C3531G						PASS	.	C	LYS/ASN	163,4243	109.5+/-147.8	3,157,2043	59.0	60.0	60.0		3531	5.0	1.0	1	dbSNP_127	60	1132,7468	233.2+/-266.6	71,990,3239	yes	missense	CAMTA1	NM_015215.2	94	74,1147,5282	GG,GC,CC		13.1628,3.6995,9.9569	benign	1177/1674	7797503	1295,11711	2203	4300	6503	SO:0001583	missense	23261	exon15			ACAGAACCCCAGA	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3531C>G	1.37:g.7797503C>G	ENSP00000306522:p.Asn1177Lys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	152	91	0.598684	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	199|199	0.09111721611721611|0.09111721611721611	8|8	0.016260162601626018|0.016260162601626018	65|65	0.17955801104972377|0.17955801104972377	46|46	0.08041958041958042|0.08041958041958042	80|80	0.10554089709762533|0.10554089709762533	C|C	9.325|9.325	1.059113|1.059113	0.19987|0.19987	0.036995|0.036995	0.131628|0.131628	ENSG00000171735|ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646|ENST00000495233	T;T|.	0.18960|.	2.18;2.18|.	5.91|5.91	4.97|4.97	0.65823|0.65823	.|.	0.206906|.	0.50627|.	D|.	0.000113|.	T|T	0.00144|0.00144	0.0004|0.0004	L|L	0.47716|0.47716	1.5|1.5	0.37138|0.37138	P|P	0.09842700000000004|0.09842700000000004	B;B;B;B|.	0.24317|.	0.101;0.02;0.054;0.014|.	B;B;B;B|.	0.22152|.	0.038;0.016;0.034;0.013|.	T|T	0.13361|0.13361	-1.0512|-1.0512	9|4	0.06494|.	T|.	0.89|.	-10.3436|-10.3436	9.4777|9.4777	0.38882|0.38882	0.0:0.8332:0.0:0.1668|0.0:0.8332:0.0:0.1668	rs41278952;rs61739456|rs41278952;rs61739456	1177;264;133;1177|.	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1|.	.;.;.;CMTA1_HUMAN|.	K|S	1177;1177;264;133|134	ENSP00000306522:N1177K;ENSP00000402561:N1177K|.	ENSP00000306522:N1177K|.	N|T	+|+	3|2	2|0	CAMTA1|CAMTA1	7720090|7720090	0.580000|0.580000	0.26733|0.26733	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.595000|0.595000	0.24029|0.24029	1.411000|1.411000	0.46957|0.46957	0.655000|0.655000	0.94253|0.94253	AAC|ACC	C|0.901;G|0.099	0.099	strong		0.572	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
CLCA2	9635	hgsc.bcm.edu	37	1	86900372	86900372	+	Missense_Mutation	SNP	C	C	G	rs17409304	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86900372C>G	ENST00000370565.4	+	6	1078	c.916C>G	c.(916-918)Cag>Gag	p.Q306E		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	306			Q -> E (in dbSNP:rs17409304).		cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CTCGCTTGTACAGGCTGGTGA	0.443													C|||	1176	0.234824	0.1513	0.3228	5008	,	,		20537	0.1796		0.3449	False		,,,				2504	0.229				p.Q306E	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C916G	GRCh37	CM063904	CLCA2	M	rs17409304	PASS	.	C	GLU/GLN	750,3656	308.6+/-290.6	74,602,1527	166.0	139.0	148.0		916	5.2	1.0	1	dbSNP_123	148	2926,5674	456.6+/-364.1	483,1960,1857	yes	missense	CLCA2	NM_006536.5	29	557,2562,3384	GG,GC,CC		34.0233,17.0222,28.2639	possibly-damaging	306/944	86900372	3676,9330	2203	4300	6503	SO:0001583	missense	9635	exon6			CTTGTACAGGCTG		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.916C>G	1.37:g.86900372C>G	ENSP00000359596:p.Gln306Glu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	120	43	0.358333	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	541	0.24771062271062272	73	0.1483739837398374	117	0.32320441988950277	84	0.14685314685314685	267	0.35224274406332456	C	23.7	4.445471	0.84101	0.170222	0.340233	ENSG00000137975	ENST00000370565	T	0.03607	3.87	6.17	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.07188	0.0182	M	0.86420	2.815	0.24732	P	0.99308046	D	0.56521	0.976	P	0.46659	0.523	T	0.04140	-1.0974	9	0.54805	T	0.06	-10.5931	16.0644	0.80861	0.1347:0.8653:0.0:0.0	rs17409304;rs56630334;rs17409304	306	Q9UQC9	CLCA2_HUMAN	E	306	ENSP00000359596:Q306E	ENSP00000359596:Q306E	Q	+	1	0	CLCA2	86672960	0.997000	0.39634	0.973000	0.42090	0.991000	0.79684	3.913000	0.56394	2.941000	0.99782	0.655000	0.94253	CAG	C|0.739;G|0.261	0.261	strong		0.443	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
HFM1	164045	hgsc.bcm.edu	37	1	91784887	91784887	+	Silent	SNP	G	G	A	rs10493845	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:91784887G>A	ENST00000370425.3	-	24	2741	c.2643C>T	c.(2641-2643)acC>acT	p.T881T	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Silent_p.T113T|HFM1_ENST00000370424.3_Silent_p.T560T	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	881	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.T881T(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AAATCTTTGCGGTATCTTGTG	0.338													G|||	1184	0.236422	0.2481	0.2781	5008	,	,		16268	0.1756		0.3072	False		,,,				2504	0.181				p.T881T		Atlas-SNP	.											HFM1,NS,carcinoma,0,1	HFM1	188	1	1	Substitution - coding silent(1)	stomach(1)	c.C2643T						PASS	.	G		1179,3227	413.0+/-336.3	153,873,1177	113.0	108.0	110.0		2643	-10.0	0.0	1	dbSNP_119	110	2875,5725	451.0+/-362.6	479,1917,1904	no	coding-synonymous	HFM1	NM_001017975.3		632,2790,3081	AA,AG,GG		33.4302,26.759,31.1702		881/1436	91784887	4054,8952	2203	4300	6503	SO:0001819	synonymous_variant	164045	exon24			CTTTGCGGTATCT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2643C>T	1.37:g.91784887G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	170	65	0.382353	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2	548	0.2509157509157509	110	0.22357723577235772	118	0.3259668508287293	80	0.13986013986013987	240	0.316622691292876	G	0.178	-1.065163	0.01934	0.26759	0.334302	ENSG00000162669	ENST00000430465	.	.	.	5.0	-10.0	0.00425	.	.	.	.	.	T	0.04998	0.0134	.	.	.	0.40115	P	0.023468999999999962	.	.	.	.	.	.	T	0.08027	-1.0742	3	.	.	.	.	4.3723	0.11253	0.5367:0.0827:0.0881:0.2926	rs10493845;rs10493845	.	.	.	L	137	.	.	P	-	2	0	HFM1	91557475	0.000000	0.05858	0.000000	0.03702	0.240000	0.25518	-1.031000	0.03578	-3.005000	0.00274	-1.223000	0.01593	CCG	G|0.749;A|0.251	0.251	strong		0.338	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
KRT39	390792	hgsc.bcm.edu	37	17	39123013	39123013	+	Silent	SNP	G	G	A	rs17645930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39123013G>A	ENST00000355612.2	-	1	131	c.96C>T	c.(94-96)aaC>aaT	p.N32N	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	32	Head.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				GATGGCAGCCGTTGTTAGAAG	0.493													G|||	587	0.117212	0.1452	0.0576	5008	,	,		21091	0.1399		0.1322	False		,,,				2504	0.0828				p.N32N		Atlas-SNP	.											.	KRT39	53	.	0			c.C96T						PASS	.	G		631,3775	274.3+/-271.8	54,523,1626	161.0	161.0	161.0		96	-2.4	0.0	17	dbSNP_123	161	1134,7458	235.0+/-267.7	71,992,3233	no	coding-synonymous	KRT39	NM_213656.3		125,1515,4859	AA,AG,GG		13.1983,14.3214,13.579		32/492	39123013	1765,11233	2203	4296	6499	SO:0001819	synonymous_variant	390792	exon1			GCAGCCGTTGTTA	AJ786657	CCDS11382.1	17q21.2	2013-01-16			ENSG00000196859	ENSG00000196859		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	32971	protein-coding gene	gene with protein product						16831889	Standard	NM_213656		Approved	KA35	uc002hvo.1	Q6A163	OTTHUMG00000133424	ENST00000355612.2:c.96C>T	17.37:g.39123013G>A		Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	301	300	0.996678	NM_213656	B2RXK6|Q6IFU6	Silent	SNP	ENST00000355612.2	37	CCDS11382.1																																																																																			G|0.868;A|0.132	0.132	strong		0.493	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	
HS3ST5	222537	hgsc.bcm.edu	37	6	114378970	114378970	+	Silent	SNP	C	C	T	rs2282237	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:114378970C>T	ENST00000312719.5	-	5	1680	c.492G>A	c.(490-492)gaG>gaA	p.E164E	RP3-399L15.3_ENST00000523087.1_RNA|HS3ST5_ENST00000411826.1_Silent_p.E164E|RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000519270.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	164					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)	p.E164E(1)		breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		TTTCTGGAACCTCCTCTGTGA	0.398													C|||	1512	0.301917	0.1604	0.4265	5008	,	,		19184	0.3512		0.3032	False		,,,				2504	0.3528				p.E164E		Atlas-SNP	.											HS3ST5,NS,carcinoma,0,1	HS3ST5	80	1	1	Substitution - coding silent(1)	stomach(1)	c.G492A						PASS	.	C		836,3570	324.8+/-298.8	79,678,1446	154.0	157.0	156.0		492	3.3	1.0	6	dbSNP_100	156	2432,6168	401.0+/-347.0	344,1744,2212	no	coding-synonymous	HS3ST5	NM_153612.3		423,2422,3658	TT,TC,CC		28.2791,18.9741,25.1269		164/347	114378970	3268,9738	2203	4300	6503	SO:0001819	synonymous_variant	222537	exon2			TGGAACCTCCTCT	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"""Sulfotransferases, membrane-bound"""	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.492G>A	6.37:g.114378970C>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	209	130	0.62201	NM_153612	A8K1J2|Q52LI2|Q8N285	Silent	SNP	ENST00000312719.5	37	CCDS34517.1																																																																																			C|0.733;T|0.267	0.267	strong		0.398	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612	
HSPBAP1	79663	hgsc.bcm.edu	37	3	122459477	122459477	+	Silent	SNP	A	A	G	rs61732313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122459477A>G	ENST00000306103.2	-	8	1325	c.1182T>C	c.(1180-1182)ccT>ccC	p.P394P	HSPBAP1_ENST00000383659.1_3'UTR	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	394						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		TCTGTGCTACAGGGACCAGAT	0.512													A|||	389	0.0776757	0.0378	0.1066	5008	,	,		17353	0.125		0.0895	False		,,,				2504	0.0501				p.P394P		Atlas-SNP	.											.	HSPBAP1	32	.	0			c.T1182C						PASS	.	A		182,4224	117.5+/-155.4	7,168,2028	142.0	140.0	141.0		1182	2.9	0.9	3	dbSNP_129	141	928,7672	203.4+/-246.4	46,836,3418	no	coding-synonymous	HSPBAP1	NM_024610.5		53,1004,5446	GG,GA,AA		10.7907,4.1307,8.5345		394/489	122459477	1110,11896	2203	4300	6503	SO:0001819	synonymous_variant	79663	exon8			TGCTACAGGGACC	AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"""HSPB (heat shock 27kD) associated protein 1"""			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.1182T>C	3.37:g.122459477A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	180	178	0.988889	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Silent	SNP	ENST00000306103.2	37	CCDS3017.1																																																																																			A|0.914;G|0.086	0.086	strong		0.512	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610	
HOXB1	3211	hgsc.bcm.edu	37	17	46607958	46607958	+	Missense_Mutation	SNP	T	T	A	rs12939811	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46607958T>A	ENST00000239174.6	-	1	401	c.309A>T	c.(307-309)caA>caT	p.Q103H	HOXB1_ENST00000577092.1_Missense_Mutation_p.Q103H	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	103			Q -> H (in dbSNP:rs12939811).		anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CTCCTTCTGATTGACCCAGAG	0.667													T|||	573	0.114417	0.0651	0.1023	5008	,	,		14669	0.0982		0.1928	False		,,,				2504	0.1258				p.Q103H		Atlas-SNP	.											.	HOXB1	67	.	0			c.A309T						PASS	.	T	HIS/GLN	343,4063	170.1+/-200.6	14,315,1874	63.0	66.0	65.0		309	-5.7	0.0	17	dbSNP_121	65	1621,6979	282.0+/-295.3	153,1315,2832	yes	missense	HOXB1	NM_002144.3	24	167,1630,4706	AA,AT,TT		18.8488,7.7848,15.1007	possibly-damaging	103/302	46607958	1964,11042	2203	4300	6503	SO:0001583	missense	3211	exon1			TTCTGATTGACCC		CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.309A>T	17.37:g.46607958T>A	ENSP00000355140:p.Gln103His	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_002144	Q4VB03	Missense_Mutation	SNP	ENST00000239174.6	37	CCDS32675.1	248	0.11355311355311355	27	0.054878048780487805	34	0.09392265193370165	38	0.06643356643356643	149	0.19656992084432717	T	8.428	0.847945	0.17034	0.077848	0.188488	ENSG00000120094	ENST00000239174	D	0.89875	-2.58	4.37	-5.68	0.02436	.	0.000000	0.41712	D	0.000838	T	0.00328	0.0010	L	0.52011	1.625	0.80722	P	0.0	P	0.38642	0.641	B	0.34824	0.19	T	0.48525	-0.9028	9	0.62326	D	0.03	.	11.7967	0.52104	0.0:0.5455:0.3026:0.1518	rs12939811;rs52833084;rs12939811	103	P14653	HXB1_HUMAN	H	103	ENSP00000355140:Q103H	ENSP00000355140:Q103H	Q	-	3	2	HOXB1	43962957	0.003000	0.15002	0.000000	0.03702	0.737000	0.42083	-1.050000	0.03510	-1.633000	0.01539	-0.925000	0.02716	CAA	T|0.866;A|0.134	0.134	strong		0.667	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
GIPC2	54810	hgsc.bcm.edu	37	1	78585086	78585086	+	Missense_Mutation	SNP	T	T	C	rs540742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:78585086T>C	ENST00000370759.3	+	4	810	c.617T>C	c.(616-618)cTg>cCg	p.L206P		NM_017655.4	NP_060125.4	Q8TF65	GIPC2_HUMAN	GIPC PDZ domain containing family, member 2	206			L -> P (in dbSNP:rs540742). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)	20						GAAATAGAGCTGAGGTCAAAG	0.413													C|||	1538	0.307109	0.2186	0.1758	5008	,	,		18381	0.6637		0.2266	False		,,,				2504	0.2352				p.L206P		Atlas-SNP	.											.	GIPC2	37	.	0			c.T617C						PASS	.	C	PRO/LEU	990,3416	731.6+/-410.3	129,732,1342	90.0	89.0	90.0		617	4.7	0.0	1	dbSNP_83	90	1878,6722	726.7+/-406.6	197,1484,2619	yes	missense	GIPC2	NM_017655.4	98	326,2216,3961	CC,CT,TT		21.8372,22.4694,22.0514	benign	206/316	78585086	2868,10138	2203	4300	6503	SO:0001583	missense	54810	exon4			TAGAGCTGAGGTC	AB073737	CCDS685.1	1p31.1	2010-05-28			ENSG00000137960	ENSG00000137960			18177	protein-coding gene	gene with protein product	"""semaphorin cytoplasmic domain associated protein 2"""					11836570	Standard	NM_017655		Approved	FLJ20075, SEMCAP-2	uc001dik.3	Q8TF65	OTTHUMG00000041145	ENST00000370759.3:c.617T>C	1.37:g.78585086T>C	ENSP00000359795:p.Leu206Pro	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_017655	Q8IYD3|Q9NXS7	Missense_Mutation	SNP	ENST00000370759.3	37	CCDS685.1	737	0.3374542124542125	127	0.258130081300813	67	0.1850828729281768	373	0.6520979020979021	170	0.22427440633245382	C	0.003	-2.457311	0.00173	0.224694	0.218372	ENSG00000137960	ENST00000370759	T	0.80566	-1.39	5.59	4.68	0.58851	PDZ/DHR/GLGF (1);	0.098868	0.64402	N	0.000001	T	0.13114	0.0318	N	0.00024	-2.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17077	-1.0381	9	0.02654	T	1	-17.525	9.1027	0.36678	0.0:0.8313:0.0:0.1687	rs540742;rs3748650;rs17846165;rs17859175;rs52792767;rs57550733;rs540742	206	Q8TF65	GIPC2_HUMAN	P	206	ENSP00000359795:L206P	ENSP00000359795:L206P	L	+	2	0	GIPC2	78357674	0.535000	0.26370	0.007000	0.13788	0.001000	0.01503	2.060000	0.41394	0.867000	0.35654	-0.733000	0.03571	CTG	A|0.004;C|0.271	0.271	strong		0.413	GIPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098629.1	NM_017655	
MED13L	23389	hgsc.bcm.edu	37	12	116403920	116403920	+	Silent	SNP	G	G	A	rs3088260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:116403920G>A	ENST00000281928.3	-	29	6560	c.6354C>T	c.(6352-6354)ccC>ccT	p.P2118P		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	2118						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TTTGAGCCTGGGGACACGATG	0.448													G|||	180	0.0359425	0.0129	0.036	5008	,	,		17606	0.0		0.0845	False		,,,				2504	0.0542				p.P2118P		Atlas-SNP	.											.	MED13L	193	.	0			c.C6354T						PASS	.	G		93,4313	75.7+/-113.9	1,91,2111	136.0	142.0	140.0		6354	-3.8	1.0	12	dbSNP_102	140	818,7782	190.7+/-237.1	40,738,3522	no	coding-synonymous	MED13L	NM_015335.4		41,829,5633	AA,AG,GG		9.5116,2.1108,7.0045		2118/2211	116403920	911,12095	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon29			AGCCTGGGGACAC	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.6354C>T	12.37:g.116403920G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																			G|0.936;A|0.064	0.064	strong		0.448	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854479	12854479	+	Missense_Mutation	SNP	C	C	G	rs1063775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12854479C>G	ENST00000332296.7	+	3	806	c.703C>G	c.(703-705)Cgc>Ggc	p.R235G	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	235					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GAAGAATCTTCGCAAACTCGT	0.438													c|||	502	0.10024	0.115	0.0519	5008	,	,		29731	0.0685		0.0785	False		,,,				2504	0.1697				p.R235G		Atlas-SNP	.											PRAMEF1,NS,carcinoma,-1,2	PRAMEF1	78	2	0			c.C703G						scavenged	.						158.0	163.0	161.0					1																	12854479		2203	4300	6503	SO:0001583	missense	65121	exon3			AATCTTCGCAAAC	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.703C>G	1.37:g.12854479C>G	ENSP00000332134:p.Arg235Gly	Somatic	494	11	0.0222672		WXS	Illumina HiSeq	Phase_I	439	65	0.148064	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	6.921	0.539576	0.13250	.	.	ENSG00000116721	ENST00000332296	T	0.21543	2.0	1.61	1.61	0.23674	.	2.269980	0.01911	N	0.039880	T	0.27594	0.0678	M	0.74467	2.265	0.09310	N	0.999992	B	0.09022	0.002	B	0.06405	0.002	T	0.26916	-1.0089	10	0.39692	T	0.17	.	6.6557	0.22986	0.0:1.0:0.0:0.0	.	235	O95521	PRAM1_HUMAN	G	235	ENSP00000332134:R235G	ENSP00000332134:R235G	R	+	1	0	PRAMEF1	12777066	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-0.124000	0.10595	1.196000	0.43129	0.436000	0.28706	CGC	C|0.811;G|0.187;T|0.002	0.187	strong		0.438	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
CDH3	1001	hgsc.bcm.edu	37	16	68721533	68721533	+	Missense_Mutation	SNP	G	G	C	rs1126933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:68721533G>C	ENST00000264012.4	+	12	2233	c.1689G>C	c.(1687-1689)caG>caC	p.Q563H	CDH3_ENST00000429102.2_Missense_Mutation_p.Q563H|CDH3_ENST00000581171.1_Missense_Mutation_p.Q508H	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	563	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> H (in dbSNP:rs1126933). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15805154, ECO:0000269|PubMed:2793940, ECO:0000269|Ref.3}.		adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		CTGTGCGCCAGGTGCTGAACA	0.577													G|||	1552	0.309904	0.0242	0.3991	5008	,	,		20646	0.5139		0.4046	False		,,,				2504	0.3252				p.Q563H		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G1689C						PASS	.	G	HIS/GLN	396,4000	197.7+/-221.8	17,362,1819	163.0	130.0	141.0		1689	-3.3	0.5	16	dbSNP_86	141	3590,5010	519.8+/-379.5	747,2096,1457	yes	missense	CDH3	NM_001793.4	24	764,2458,3276	CC,CG,GG		41.7442,9.0082,30.671	benign	563/830	68721533	3986,9010	2198	4300	6498	SO:0001583	missense	1001	exon12			GCGCCAGGTGCTG	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1689G>C	16.37:g.68721533G>C	ENSP00000264012:p.Gln563His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	165	87	0.527273	NM_001793	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	37	CCDS10868.1	777	0.3557692307692308	14	0.028455284552845527	142	0.39226519337016574	306	0.534965034965035	315	0.4155672823218997	G	6.651	0.488628	0.12641	0.090082	0.417442	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.61158	0.13;0.13	5.05	-3.29	0.05017	Cadherin (1);Cadherin-like (1);	0.000000	0.39475	N	0.001353	T	0.00012	0.0000	L	0.33339	1.005	0.27598	P	0.9490638	B	0.18610	0.029	B	0.12837	0.008	T	0.46400	-0.9194	9	0.20519	T	0.43	.	7.6829	0.28524	0.358:0.1375:0.5045:0.0	rs1126933;rs17689848;rs52790482;rs1126933	563	P22223	CADH3_HUMAN	H	563;563;508	ENSP00000398485:Q563H;ENSP00000264012:Q563H	ENSP00000264012:Q563H	Q	+	3	2	CDH3	67279034	0.001000	0.12720	0.518000	0.27811	0.491000	0.33493	-0.055000	0.11807	-0.578000	0.05959	-0.471000	0.05019	CAG	G|0.672;C|0.328	0.328	strong		0.577	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
TIE1	7075	hgsc.bcm.edu	37	1	43784956	43784956	+	Silent	SNP	A	A	G	rs1199039|rs45475401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43784956A>G	ENST00000372476.3	+	18	3052	c.2973A>G	c.(2971-2973)ctA>ctG	p.L991L	TIE1_ENST00000473014.1_3'UTR|TIE1_ENST00000433781.2_Silent_p.L636L	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	991	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GAGAGAACCTAGCCTCCAAGA	0.567													G|||	1131	0.225839	0.1815	0.3631	5008	,	,		20631	0.1478		0.3777	False		,,,				2504	0.1125				p.L991L		Atlas-SNP	.											.	TIE1	132	.	0			c.A2973G						PASS	.	G		904,3502	740.8+/-411.2	93,718,1392	118.0	110.0	113.0		2973	5.1	1.0	1	dbSNP_87	113	3360,5240	642.3+/-399.8	665,2030,1605	no	coding-synonymous	TIE1	NM_005424.2		758,2748,2997	GG,GA,AA		39.0698,20.5175,32.7849		991/1139	43784956	4264,8742	2203	4300	6503	SO:0001819	synonymous_variant	7075	exon18			GAACCTAGCCTCC	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11809	protein-coding gene	gene with protein product		600222	"""tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"""	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.2973A>G	1.37:g.43784956A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_005424	B5A949|B5A950	Silent	SNP	ENST00000372476.3	37	CCDS482.1																																																																																			A|0.697;G|0.303	0.303	strong		0.567	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424	
GPATCH2	55105	hgsc.bcm.edu	37	1	217793484	217793484	+	Silent	SNP	C	C	T	rs140815718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:217793484C>T	ENST00000366935.3	-	2	524	c.414G>A	c.(412-414)ggG>ggA	p.G138G	GPATCH2_ENST00000366934.3_Silent_p.G138G	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	138					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		GAGGTCTTTTCCCTCGAACAT	0.408													C|||	18	0.00359425	0.0008	0.0043	5008	,	,		20562	0.0		0.0139	False		,,,				2504	0.0				p.G138G		Atlas-SNP	.											.	GPATCH2	53	.	0			c.G414A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	131.0	120.0	124.0		414	-5.8	0.7	1	dbSNP_134	124	93,8507	51.1+/-111.2	0,93,4207	no	coding-synonymous	GPATCH2	NM_018040.2		0,98,6405	TT,TC,CC		1.0814,0.1135,0.7535		138/529	217793484	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	55105	exon2			TCTTTTCCCTCGA	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.414G>A	1.37:g.217793484C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Silent	SNP	ENST00000366935.3	37	CCDS1518.1																																																																																			C|0.994;T|0.006	0.006	strong		0.408	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383027	39383027	+	Missense_Mutation	SNP	G	G	T	rs71371478	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39383027G>T	ENST00000377721.3	+	1	128	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.A41S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	41	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)		p.A41S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGCCAGCCCGCCTGCTGTGT	0.637																																					p.A41S		Atlas-SNP	.											KRTAP9-2,extremity,malignant_melanoma,0,1	KRTAP9-2	24	1	1	Substitution - Missense(1)	skin(1)	c.G121T						scavenged	.						59.0	53.0	55.0					17																	39383027		2203	4300	6503	SO:0001583	missense	83899	exon1			CAGCCCGCCTGCT	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.121G>T	17.37:g.39383027G>T	ENSP00000366950:p.Ala41Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	122	17	0.139344	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.020245	0.00418	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01192	5.2;5.4	2.86	-2.81	0.05805	.	.	.	.	.	T	0.00328	0.0010	N	0.00368	-1.59	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.02654	T	1	.	5.0512	0.14508	0.3642:0.0:0.0934:0.5425	.	41	Q9BYQ4	KRA92_HUMAN	S	41	ENSP00000366950:A41S;ENSP00000398325:A41S	ENSP00000366950:A41S	A	+	1	0	KRTAP9-2	36636553	0.000000	0.05858	0.088000	0.20740	0.203000	0.24098	-1.973000	0.01500	-1.243000	0.02519	-4.519000	0.00005	GCC	G|0.997;T|0.003	0.003	strong		0.637	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
MAP2K2	5605	hgsc.bcm.edu	37	19	4102449	4102449	+	Silent	SNP	G	G	A	rs17851657	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4102449G>A	ENST00000262948.5	-	4	706	c.453C>T	c.(451-453)gaC>gaT	p.D151D	MAP2K2_ENST00000599345.1_5'UTR|MAP2K2_ENST00000394867.4_Silent_p.D54D	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	151	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)	p.D151D(2)					Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	GGGAGCCGCCGTCCTAGAGGG	0.662													.|||	557	0.111222	0.0197	0.0994	5008	,	,		17424	0.0526		0.2038	False		,,,				2504	0.2086				p.D151D		Atlas-SNP	.											MAP2K2_ENST00000262948,NS,carcinoma,0,1	MAP2K2	72	1	2	Substitution - coding silent(2)	prostate(2)	c.C453T						PASS	.	A		193,4207		7,179,2014	44.0	36.0	39.0		453	-8.4	0.1	19	dbSNP_123	39	1662,6932		143,1376,2778	no	coding-synonymous	MAP2K2	NM_030662.3		150,1555,4792	AA,AG,GG		19.3391,4.3864,14.2758		151/401	4102449	1855,11139	2200	4297	6497	SO:0001819	synonymous_variant	5605	exon4			GCCGCCGTCCTAG	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.453C>T	19.37:g.4102449G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			G|0.865;A|0.135	0.135	strong		0.662	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
SUOX	6821	hgsc.bcm.edu	37	12	56398454	56398454	+	Silent	SNP	G	G	C	rs773115	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56398454G>C	ENST00000394109.3	+	3	2005	c.1281G>C	c.(1279-1281)tcG>tcC	p.S427S	SUOX_ENST00000551841.2_3'UTR|SUOX_ENST00000266971.3_Silent_p.S427S|SUOX_ENST00000548274.1_Silent_p.S427S|SUOX_ENST00000394115.2_Silent_p.S427S|IKZF4_ENST00000262032.5_5'Flank|SUOX_ENST00000356124.4_Silent_p.S427S			P51687	SUOX_HUMAN	sulfite oxidase	427	Homodimerization. {ECO:0000250}.		S -> Y (in ISOD). {ECO:0000269|PubMed:10519592, ECO:0000269|PubMed:9428520}.		cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|sulfite oxidase activity (GO:0008482)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)	15			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			CTGTCCAGTCGGCCATCACAG	0.562													G|||	3767	0.752196	0.2617	0.8977	5008	,	,		20291	0.9355		0.9205	False		,,,				2504	0.9499				p.S427S		Atlas-SNP	.											.	SUOX	33	.	0			c.G1281C						PASS	.	G	,,	1660,2746	506.9+/-366.5	332,996,875	99.0	99.0	99.0		1281,1281,1281	-0.2	1.0	12	dbSNP_86	99	7910,690	788.4+/-407.6	3642,626,32	no	coding-synonymous,coding-synonymous,coding-synonymous	SUOX	NM_000456.2,NM_001032386.1,NM_001032387.1	,,	3974,1622,907	CC,CG,GG		8.0233,37.6759,26.4186	,,	427/546,427/546,427/546	56398454	9570,3436	2203	4300	6503	SO:0001819	synonymous_variant	6821	exon6			CCAGTCGGCCATC	BC065193	CCDS8901.2	12q13.13	2011-02-10			ENSG00000139531	ENSG00000139531	1.8.3.1		11460	protein-coding gene	gene with protein product		606887				7599189	Standard	XM_005269112		Approved		uc001siz.3	P51687	OTTHUMG00000128503	ENST00000394109.3:c.1281G>C	12.37:g.56398454G>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	186	102	0.548387	NM_000456		Silent	SNP	ENST00000394109.3	37	CCDS8901.2																																																																																			G|0.246;C|0.754	0.754	strong		0.562	SUOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250309.1	NM_000456	
MYH7	4625	hgsc.bcm.edu	37	14	23884889	23884889	+	Silent	SNP	C	C	T	rs3729830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:23884889C>T	ENST00000355349.3	-	35	5268	c.5106G>A	c.(5104-5106)gcG>gcA	p.A1702A	MIR208B_ENST00000401172.1_RNA|CTD-2201G16.1_ENST00000557368.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1702					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		GCTCCTGCTCCGCCAGCTTCC	0.632													C|||	589	0.117612	0.2239	0.098	5008	,	,		20562	0.0188		0.1262	False		,,,				2504	0.0808				p.A1702A		Atlas-SNP	.											.	MYH7	349	.	0			c.G5106A						PASS	.	C		956,3450	361.4+/-315.7	117,722,1364	67.0	64.0	65.0		5106	-10.6	0.0	14	dbSNP_107	65	1133,7467	233.2+/-266.6	77,979,3244	no	coding-synonymous	MYH7	NM_000257.2		194,1701,4608	TT,TC,CC		13.1744,21.6977,16.0618		1702/1936	23884889	2089,10917	2203	4300	6503	SO:0001819	synonymous_variant	4625	exon35			CTGCTCCGCCAGC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.5106G>A	14.37:g.23884889C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																			C|0.850;T|0.150	0.150	strong		0.632	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
MEGF11	84465	hgsc.bcm.edu	37	15	66214785	66214785	+	Silent	SNP	G	G	A	rs11637551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:66214785G>A	ENST00000409699.2	-	15	2020	c.1848C>T	c.(1846-1848)caC>caT	p.H616H	MEGF11_ENST00000360698.4_Silent_p.H616H|MEGF11_ENST00000395625.2_Silent_p.H541H|MEGF11_ENST00000422354.1_Silent_p.H616H|MEGF11_ENST00000395614.1_De_novo_Start_OutOfFrame|MEGF11_ENST00000288745.3_Silent_p.H541H			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	616					homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						GGGCGCAGCCGTGGCCATAGA	0.637													G|||	156	0.0311502	0.0038	0.0403	5008	,	,		18705	0.001		0.0964	False		,,,				2504	0.0256				p.H616H		Atlas-SNP	.											.	MEGF11	70	.	0			c.C1848T						PASS	.	G		109,4277		8,93,2092	13.0	12.0	13.0		1848	-10.1	0.0	15	dbSNP_120	13	761,7815		48,665,3575	yes	coding-synonymous	MEGF11	NM_032445.2		56,758,5667	AA,AG,GG		8.8736,2.4852,6.7119		616/1045	66214785	870,12092	2193	4288	6481	SO:0001819	synonymous_variant	84465	exon15			GCAGCCGTGGCCA	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.1848C>T	15.37:g.66214785G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Silent	SNP	ENST00000409699.2	37	CCDS10213.2																																																																																			G|0.950;A|0.050	0.050	strong		0.637	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445	
AOC3	8639	hgsc.bcm.edu	37	17	41004637	41004637	+	Missense_Mutation	SNP	G	G	A	rs33986943	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41004637G>A	ENST00000308423.2	+	1	1437	c.1277G>A	c.(1276-1278)cGt>cAt	p.R426H	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	426			R -> H (in dbSNP:rs33986943). {ECO:0000269|Ref.6}.		amine metabolic process (GO:0009308)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			breast(1)|central_nervous_system(4)|endometrium(4)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|skin(8)	41		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	AAGACAATACGTGATGCCTTT	0.587													G|||	242	0.0483227	0.0091	0.0548	5008	,	,		19023	0.0		0.1123	False		,,,				2504	0.0808				p.R426H	NSCLC(3;192 220 10664 11501 16477)	Atlas-SNP	.											.	AOC3	88	.	0			c.G1277A						PASS	.	G	HIS/ARG	95,4311	77.8+/-116.1	0,95,2108	93.0	83.0	86.0		1277	-3.7	0.0	17	dbSNP_126	86	874,7726	197.3+/-242.0	46,782,3472	yes	missense	AOC3	NM_003734.2	29	46,877,5580	AA,AG,GG		10.1628,2.1562,7.4504	benign	426/764	41004637	969,12037	2203	4300	6503	SO:0001583	missense	8639	exon1			CAATACGTGATGC	AF067406	CCDS11444.1, CCDS62198.1, CCDS74071.1	17q21	2013-05-08	2013-05-08			ENSG00000131471	1.4.3.21		550	protein-coding gene	gene with protein product	"""vascular adhesion protein 1"""	603735				9653080, 8972912	Standard	NM_003734		Approved	VAP1, HPAO, VAP-1	uc002ibv.4	Q16853		ENST00000308423.2:c.1277G>A	17.37:g.41004637G>A	ENSP00000312326:p.Arg426His	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	335	149	0.444776	NM_003734	B2RCI5|K7ESB3|L0L8N9|Q45F94	Missense_Mutation	SNP	ENST00000308423.2	37	CCDS11444.1	120	0.054945054945054944	10	0.02032520325203252	23	0.06353591160220995	0	0.0	87	0.11477572559366754	G	7.371	0.626759	0.14257	0.021562	0.101628	ENSG00000131471	ENST00000308423	T	0.04015	3.73	4.64	-3.71	0.04424	Copper amine oxidase, C-terminal (3);	0.701778	0.14252	N	0.331410	T	0.00073	0.0002	N	0.14661	0.345	0.09310	N	1	B	0.17268	0.021	B	0.09377	0.004	T	0.43212	-0.9405	10	0.41790	T	0.15	.	8.4995	0.33150	0.6385:0.1246:0.2368:0.0	rs33986943;rs33986943	426	Q16853	AOC3_HUMAN	H	426	ENSP00000312326:R426H	ENSP00000312326:R426H	R	+	2	0	AOC3	38258163	0.000000	0.05858	0.000000	0.03702	0.643000	0.38383	-0.172000	0.09868	-0.747000	0.04759	0.591000	0.81541	CGT	G|0.930;A|0.070	0.070	strong		0.587	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734	
OR51A7	119687	hgsc.bcm.edu	37	11	4928841	4928841	+	Missense_Mutation	SNP	T	T	C	rs7108225	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4928841T>C	ENST00000359350.4	+	1	242	c.242T>C	c.(241-243)aTg>aCg	p.M81T	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	81			M -> T (in dbSNP:rs7108225).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTTCCTACCATGTTGAGGGTC	0.458													T|||	287	0.0573083	0.0295	0.0663	5008	,	,		22110	0.002		0.1193	False		,,,				2504	0.0818				p.M81T		Atlas-SNP	.											OR51A7,colon,carcinoma,0,4	OR51A7	86	4	0			c.T242C						scavenged	.	T	THR/MET	231,4171	136.1+/-172.1	5,221,1975	155.0	133.0	141.0		242	3.9	1.0	11	dbSNP_116	141	1037,7559	221.5+/-258.9	63,911,3324	yes	missense	OR51A7	NM_001004749.1	81	68,1132,5299	CC,CT,TT		12.0638,5.2476,9.7553	benign	81/313	4928841	1268,11730	2201	4298	6499	SO:0001583	missense	119687	exon1			CTACCATGTTGAG	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"""GPCR / Class A : Olfactory receptors"""	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.242T>C	11.37:g.4928841T>C	ENSP00000352305:p.Met81Thr	Somatic	216	2	0.00925926		WXS	Illumina HiSeq	Phase_I	169	93	0.550296	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	37	CCDS31364.1	126	0.057692307692307696	12	0.024390243902439025	27	0.07458563535911603	1	0.0017482517482517483	86	0.11345646437994723	T	12.31	1.899731	0.33535	0.052476	0.120638	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.05996	3.36	5.02	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000020	T	0.00144	0.0004	L	0.58354	1.805	0.26250	N	0.978736	B	0.24920	0.114	B	0.31869	0.137	T	0.25745	-1.0123	10	0.31617	T	0.26	.	9.9807	0.41811	0.0:0.0826:0.0:0.9173	rs7108225;rs17252300;rs52835214;rs61049276;rs7108225	81	Q8NH64	O51A7_HUMAN	T	81;81;70	ENSP00000352305:M81T	ENSP00000352305:M81T	M	+	2	0	OR51A7	4885417	0.003000	0.15002	0.998000	0.56505	0.856000	0.48823	1.307000	0.33516	2.098000	0.63641	0.533000	0.62120	ATG	T|0.918;C|0.082	0.082	strong		0.458	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
SENP6	26054	hgsc.bcm.edu	37	6	76425288	76425288	+	Missense_Mutation	SNP	A	A	G	rs9250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:76425288A>G	ENST00000447266.2	+	24	3795	c.3317A>G	c.(3316-3318)tAt>tGt	p.Y1106C	SENP6_ENST00000370014.3_Missense_Mutation_p.Y1106C|SENP6_ENST00000541192.1_3'UTR|SENP6_ENST00000370010.2_Missense_Mutation_p.Y1099C	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	1106	Protease.		Y -> C (in dbSNP:rs9250). {ECO:0000269|PubMed:10799485, ECO:0000269|PubMed:9872452}.		protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				ACAGAACAATATGTCAATAGT	0.343													A|||	765	0.152756	0.0121	0.1931	5008	,	,		18105	0.0466		0.328	False		,,,				2504	0.2434				p.Y1106C		Atlas-SNP	.											.	SENP6	189	.	0			c.A3317G						PASS	.	A	CYS/TYR,CYS/TYR	233,3517		13,207,1655	128.0	116.0	120.0		3296,3317	-3.3	0.0	6	dbSNP_52	120	2937,5287		527,1883,1702	yes	missense,missense	SENP6	NM_001100409.1,NM_015571.2	194,194	540,2090,3357	GG,GA,AA		35.7125,6.2133,26.474	benign,benign	1099/1106,1106/1113	76425288	3170,8804	1875	4112	5987	SO:0001583	missense	26054	exon24			AACAATATGTCAA		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.3317A>G	6.37:g.76425288A>G	ENSP00000402527:p.Tyr1106Cys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	74	28	0.378378	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	37	CCDS47454.1	361	0.1652930402930403	5	0.01016260162601626	80	0.22099447513812154	28	0.04895104895104895	248	0.32717678100263853	A	0.965	-0.702136	0.03255	0.062133	0.357125	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000447266	T;T;T	0.12147	2.71;2.71;2.71	5.12	-3.27	0.05048	.	1.716940	0.02303	N	0.071401	T	0.01661	0.0053	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.40813	-0.9543	9	0.35671	T	0.21	0.2115	3.1101	0.06355	0.2072:0.1048:0.4151:0.2729	rs9250;rs17792658;rs52831124;rs9250	1099;1106	Q9GZR1-2;Q9GZR1	.;SENP6_HUMAN	C	1099;1106;1106	ENSP00000359027:Y1099C;ENSP00000359031:Y1106C;ENSP00000402527:Y1106C	ENSP00000359027:Y1099C	Y	+	2	0	SENP6	76482008	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.117000	0.10708	-0.499000	0.06623	0.397000	0.26171	TAT	A|0.806;G|0.194	0.194	strong		0.343	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
NCOA7	135112	hgsc.bcm.edu	37	6	126210797	126210797	+	Missense_Mutation	SNP	G	G	A	rs35223550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:126210797G>A	ENST00000368357.3	+	10	1949	c.1597G>A	c.(1597-1599)Ggg>Agg	p.G533R	NCOA7_ENST00000229634.9_Missense_Mutation_p.G418R|NCOA7_ENST00000392477.2_Missense_Mutation_p.G533R	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	533			G -> R (in dbSNP:rs35223550).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		GAACAAAGAAGGGCCACAGGT	0.373													G|||	6	0.00119808	0.0008	0.0043	5008	,	,		20188	0.0		0.0	False		,,,				2504	0.002				p.G533R		Atlas-SNP	.											.	NCOA7	92	.	0			c.G1597A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3,4401		0,3,2199	39.0	43.0	42.0		1564,1597,1597,1252,1597	3.7	0.5	6	dbSNP_126	42	50,8540		0,50,4245	yes	missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_181782.4	125,125,125,125,125	0,53,6444	AA,AG,GG		0.5821,0.0681,0.4079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	522/932,533/943,533/943,418/828,533/943	126210797	53,12941	2202	4295	6497	SO:0001583	missense	135112	exon10			AAAGAAGGGCCAC	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.1597G>A	6.37:g.126210797G>A	ENSP00000357341:p.Gly533Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	4	0.0018315018315018315	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	0	0.0	G	14.31	2.497726	0.44455	6.81E-4	0.005821	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	5.52	3.73	0.42828	.	0.382752	0.30277	N	0.009999	T	0.25494	0.0620	N	0.24115	0.695	0.24605	N	0.993753	B;D;D	0.76494	0.002;0.999;0.999	B;D;D	0.69479	0.004;0.964;0.922	T	0.09400	-1.0676	10	0.51188	T	0.08	-0.0117	9.3566	0.38171	0.0756:0.1447:0.7796:0.0	rs35223550	522;522;533	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	R	533;533;418;331	ENSP00000357341:G533R;ENSP00000376269:G533R;ENSP00000229634:G418R;ENSP00000389186:G331R	ENSP00000229634:G418R	G	+	1	0	NCOA7	126252490	1.000000	0.71417	0.535000	0.28026	0.811000	0.45836	2.682000	0.46934	0.670000	0.31165	0.655000	0.94253	GGG	G|0.996;A|0.004	0.004	strong		0.373	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
TTC37	9652	hgsc.bcm.edu	37	5	94834122	94834122	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94834122T>C	ENST00000358746.2	-	33	3813	c.3515A>G	c.(3514-3516)cAa>cGa	p.Q1172R		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	1172						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						ACTGCGGCCTTGGAGTGCATA	0.393																																					p.Q1172R		Atlas-SNP	.											.	TTC37	128	.	0			c.A3515G						PASS	.						208.0	199.0	202.0					5																	94834122		2203	4300	6503	SO:0001583	missense	9652	exon33			CGGCCTTGGAGTG	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.3515A>G	5.37:g.94834122T>C	ENSP00000351596:p.Gln1172Arg	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	258	146	0.565891	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.299214	0.60195	.	.	ENSG00000198677	ENST00000358746	T	0.38401	1.14	5.72	5.72	0.89469	Tetratricopeptide-like helical (1);	0.054387	0.85682	D	0.000000	T	0.57140	0.2033	M	0.66939	2.045	0.50467	D	0.99987	D	0.89917	1.0	D	0.74023	0.982	T	0.53019	-0.8497	10	0.26408	T	0.33	.	16.0084	0.80380	0.0:0.0:0.0:1.0	.	1172	Q6PGP7	TTC37_HUMAN	R	1172	ENSP00000351596:Q1172R	ENSP00000351596:Q1172R	Q	-	2	0	TTC37	94859878	1.000000	0.71417	0.946000	0.38457	0.425000	0.31504	5.509000	0.67012	2.180000	0.69256	0.460000	0.39030	CAA	.	.	none		0.393	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
CAPN1	823	hgsc.bcm.edu	37	11	64981837	64981837	+	IGR	SNP	C	C	T	rs12420456	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64981837C>T	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		CGAGACCTGGCGCAGTCCGTC	0.677													C|||	1438	0.287141	0.1377	0.4611	5008	,	,		14418	0.2599		0.3628	False		,,,				2504	0.316				p.A141V		Atlas-SNP	.											SLC22A20,NS,carcinoma,0,2	SLC22A20	36	2	0			c.C422T						PASS	.	C	VAL/ALA	756,3356		67,622,1367	33.0	38.0	36.0		422	4.5	1.0	11	dbSNP_120	36	2861,5523		466,1929,1797	yes	missense	SLC22A20	NM_001004326.4	64	533,2551,3164	TT,TC,CC		34.1245,18.3852,28.9453	possibly-damaging	141/350	64981837	3617,8879	2056	4192	6248	SO:0001628	intergenic_variant	440044	exon2			ACCTGGCGCAGTC	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		11.37:g.64981837C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	86	32	0.372093	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			C|0.705;T|0.295	0.295	strong		0.677	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
PIWIL4	143689	hgsc.bcm.edu	37	11	94326765	94326765	+	Missense_Mutation	SNP	G	G	C	rs57607909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:94326765G>C	ENST00000299001.6	+	9	1319	c.1108G>C	c.(1108-1110)Gct>Cct	p.A370P	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	370	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.		A -> P (in dbSNP:rs57607909). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CAACAGTGAGGCTCAGCTCGC	0.438													G|||	1151	0.229832	0.3071	0.1686	5008	,	,		18030	0.2649		0.2286	False		,,,				2504	0.1339				p.A370P		Atlas-SNP	.											.	PIWIL4	70	.	0			c.G1108C						PASS	.	G	PRO/ALA	1234,3168	426.6+/-341.2	163,908,1130	149.0	148.0	148.0		1108	-1.1	0.0	11	dbSNP_129	148	1922,6674	340.9+/-323.8	225,1472,2601	yes	missense	PIWIL4	NM_152431.2	27	388,2380,3731	CC,CG,GG		22.3592,28.0327,24.2807	benign	370/853	94326765	3156,9842	2201	4298	6499	SO:0001583	missense	143689	exon9			AGTGAGGCTCAGC	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1108G>C	11.37:g.94326765G>C	ENSP00000299001:p.Ala370Pro	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	509	0.23305860805860806	135	0.27439024390243905	69	0.19060773480662985	136	0.23776223776223776	169	0.22295514511873352	G	0.011	-1.692544	0.00731	0.280327	0.223592	ENSG00000134627	ENST00000299001	T	0.09073	3.02	4.77	-1.1	0.09872	Argonaute/Dicer protein, PAZ (4);	0.585427	0.15970	N	0.235824	T	0.00012	0.0000	N	0.13043	0.29	0.54753	P	1.8999999999991246E-5	B	0.02656	0.0	B	0.09377	0.004	T	0.46830	-0.9163	9	0.30078	T	0.28	-0.0363	13.5706	0.61845	0.0775:0.6422:0.2803:0.0	rs57607909	370	Q7Z3Z4	PIWL4_HUMAN	P	370	ENSP00000299001:A370P	ENSP00000299001:A370P	A	+	1	0	PIWIL4	93966413	0.488000	0.25996	0.005000	0.12908	0.009000	0.06853	0.106000	0.15354	-0.073000	0.12842	-0.379000	0.06801	GCT	G|0.768;C|0.232	0.232	strong		0.438	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
CDC27	996	hgsc.bcm.edu	37	17	45214661	45214661	+	Silent	SNP	G	G	A	rs111322439		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45214661G>A	ENST00000066544.3	-	14	1863	c.1770C>T	c.(1768-1770)ttC>ttT	p.F590F	CDC27_ENST00000527547.1_Silent_p.F589F|CDC27_ENST00000446365.2_Silent_p.F529F|CDC27_ENST00000531206.1_Silent_p.F596F	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	590					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAGCTCTCTGGAAGAATTTAA	0.383																																					p.F596F		Atlas-SNP	.											CDC27_ENST00000531206,rectum,carcinoma,0,4	CDC27	337	4	0			c.C1788T						scavenged	.						58.0	61.0	60.0					17																	45214661		2203	4300	6503	SO:0001819	synonymous_variant	996	exon14			TCTCTGGAAGAAT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1770C>T	17.37:g.45214661G>A		Somatic	19	1	0.0526316		WXS	Illumina HiSeq	Phase_I	40	5	0.125	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			G|0.500;A|0.500	0.500	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
PCDH19	57526	hgsc.bcm.edu	37	X	99661969	99661969	+	Silent	SNP	G	G	A	rs1953337	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:99661969G>A	ENST00000373034.4	-	1	3302	c.1627C>T	c.(1627-1629)Ctg>Ttg	p.L543L	PCDH19_ENST00000420881.2_Silent_p.L543L|PCDH19_ENST00000255531.7_Silent_p.L543L	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	543	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		L -> P (in EIEE9; disease features overlapping with Dravet syndrome). {ECO:0000269|PubMed:19214208}.		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						TTGCTTTGCAGTGAGGGAAGG	0.587													G|||	325	0.0860927	0.0204	0.121	3775	,	,		13359	0.001		0.1819	False		,,,				2504	0.0307				p.L543L		Atlas-SNP	.											.	PCDH19	269	.	0			c.C1627T						PASS	.	G	,,	179,3568		4,148,23,1436,548	129.0	126.0	127.0		1627,1627,1627	4.0	0.9	X	dbSNP_92	127	1917,4749		226,956,509,1231,1331	no	coding-synonymous,coding-synonymous,coding-synonymous	PCDH19	NM_001105243.1,NM_001184880.1,NM_020766.2	,,	230,1104,532,2667,1879	AA,AG,A,GG,G		28.7579,4.7772,20.1287	,,	543/1102,543/1149,543/1101	99661969	2096,8317	2159	4253	6412	SO:0001819	synonymous_variant	57526	exon1			TTTGCAGTGAGGG	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.1627C>T	X.37:g.99661969G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	75	72	0.96	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Silent	SNP	ENST00000373034.4	37	CCDS55462.1																																																																																			G|0.881;A|0.119	0.119	strong		0.587	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766	
BRMS1	25855	hgsc.bcm.edu	37	11	66109033	66109033	+	Silent	SNP	T	T	C	rs11537993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66109033T>C	ENST00000359957.3	-	3	361	c.201A>G	c.(199-201)ctA>ctG	p.L67L	BRMS1_ENST00000425825.2_Silent_p.L67L|RP11-867G23.12_ENST00000526655.1_RNA	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1	67					apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						ACTGCTTCTCTAGGTCCAGCA	0.592													T|||	705	0.140775	0.0234	0.17	5008	,	,		21312	0.0327		0.329	False		,,,				2504	0.1963				p.L67L	GBM(7;55 307 2662 20856 28942)	Atlas-SNP	.											.	BRMS1	42	.	0			c.A201G						PASS	.	T	,	297,4103	162.5+/-194.5	13,271,1916	287.0	262.0	270.0		201,201	2.5	1.0	11	dbSNP_120	270	2854,5736	448.6+/-361.9	475,1904,1916	yes	coding-synonymous,coding-synonymous	BRMS1	NM_001024957.1,NM_015399.3	,	488,2175,3832	CC,CT,TT		33.2247,6.75,24.2571	,	67/291,67/247	66109033	3151,9839	2200	4295	6495	SO:0001819	synonymous_variant	25855	exon3			CTTCTCTAGGTCC	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.201A>G	11.37:g.66109033T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_015399	Q6IAI2	Silent	SNP	ENST00000359957.3	37	CCDS8135.1	346	0.15842490842490842	17	0.034552845528455285	75	0.20718232044198895	18	0.03146853146853147	236	0.3113456464379947	T	8.732	0.916870	0.17907	0.0675	0.332247	ENSG00000174744	ENST00000524699	.	.	.	4.44	2.55	0.30701	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.35674	-0.9779	3	.	.	.	-12.9533	8.2431	0.31671	0.0:0.7956:0.0:0.2044	rs11537993;rs11537993	.	.	.	G	30	.	.	R	-	1	2	BRMS1	65865609	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	1.938000	0.40203	0.608000	0.30000	-0.242000	0.12053	AGA	T|0.796;C|0.204	0.204	strong		0.592	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399	
TECTA	7007	hgsc.bcm.edu	37	11	121000774	121000774	+	Missense_Mutation	SNP	T	T	C	rs520805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:121000774T>C	ENST00000392793.1	+	10	3066	c.2795T>C	c.(2794-2796)gTc>gCc	p.V932A	TECTA_ENST00000264037.2_Missense_Mutation_p.V932A			O75443	TECTA_HUMAN	tectorin alpha	932			V -> A (in dbSNP:rs520805). {ECO:0000269|PubMed:10987647, ECO:0000269|PubMed:9590290}.		cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GTGGTGAACGTCACTGCCTAT	0.592													T|||	1080	0.215655	0.2035	0.2205	5008	,	,		18118	0.2381		0.2286	False		,,,				2504	0.1922				p.V932A		Atlas-SNP	.											.	TECTA	329	.	0			c.T2795C						PASS	.	T	ALA/VAL	771,3635	314.1+/-293.5	69,633,1501	71.0	68.0	69.0		2795	4.7	1.0	11	dbSNP_83	69	1809,6789	324.9+/-316.7	195,1419,2685	yes	missense	TECTA	NM_005422.2	64	264,2052,4186	CC,CT,TT		21.0398,17.4989,19.84	possibly-damaging	932/2156	121000774	2580,10424	2203	4299	6502	SO:0001583	missense	7007	exon9			TGAACGTCACTGC	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.2795T>C	11.37:g.121000774T>C	ENSP00000376543:p.Val932Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	507	0.23214285714285715	95	0.19308943089430894	77	0.212707182320442	168	0.2937062937062937	167	0.22031662269129287	T	4.083	0.013330	0.07912	0.174989	0.210398	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.76060	-0.99;-0.99	5.78	4.65	0.58169	Uncharacterised domain, cysteine-rich (2);	0.199756	0.45361	N	0.000361	T	0.00012	0.0000	L	0.37800	1.135	0.30433	P	0.776963	B	0.10296	0.003	B	0.08055	0.003	T	0.07829	-1.0752	9	0.15952	T	0.53	.	11.707	0.51603	0.0:0.0688:0.0:0.9312	rs520805;rs58634707;rs520805	932	O75443	TECTA_HUMAN	A	932	ENSP00000376543:V932A;ENSP00000264037:V932A	ENSP00000264037:V932A	V	+	2	0	TECTA	120505984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.885000	0.48570	1.026000	0.39733	0.528000	0.53228	GTC	T|0.791;C|0.209	0.209	strong		0.592	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959879	157959879	+	Silent	SNP	C	C	T	rs1130497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:157959879C>T	ENST00000389418.4	-	6	663	c.654G>A	c.(652-654)ccG>ccA	p.P218P	PTPRN2_ENST00000389413.3_Silent_p.P218P|PTPRN2_ENST00000389416.4_Silent_p.P201P|PTPRN2_ENST00000409483.1_Silent_p.P180P|PTPRN2_ENST00000404321.2_Silent_p.P241P	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	218					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CGAGGGTCCGCGGCAGGAGGT	0.657													c|||	1698	0.339058	0.1399	0.4179	5008	,	,		16229	0.4087		0.4533	False		,,,				2504	0.363				p.P218P		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G654A						PASS	.		,,	743,3659	298.7+/-285.4	74,595,1532	39.0	39.0	39.0		654,603,654	-0.4	0.0	7	dbSNP_86	39	3730,4870	518.5+/-379.3	790,2150,1360	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	864,2745,2892	TT,TC,CC		43.3721,16.8787,34.4024	,,	218/1016,201/999,218/987	157959879	4473,8529	2201	4300	6501	SO:0001819	synonymous_variant	5799	exon6			GGTCCGCGGCAGG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.654G>A	7.37:g.157959879C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			C|0.659;T|0.341	0.341	strong		0.657	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
NEK10	152110	hgsc.bcm.edu	37	3	27326451	27326451	+	Splice_Site	SNP	A	A	G	rs10510594	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:27326451A>G	ENST00000429845.2	-	22	2153	c.1791T>C	c.(1789-1791)aaT>aaC	p.N597N	NEK10_ENST00000341435.5_Splice_Site_p.N597N|NEK10_ENST00000357467.2_5'UTR			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	597	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.N597N(3)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						ACAACCTATCATCTATATAAA	0.383													A|||	1052	0.210064	0.1067	0.3516	5008	,	,		17244	0.1002		0.2793	False		,,,				2504	0.2914				p.N597N		Atlas-SNP	.											NEK10_ENST00000429845,NS,carcinoma,0,3	NEK10	271	3	3	Substitution - coding silent(3)	kidney(3)	c.T1791C						PASS	.	A		631,3741		55,521,1610	49.0	52.0	51.0		1791	5.7	1.0	3	dbSNP_119	51	2393,6199		365,1663,2268	yes	coding-synonymous-near-splice	NEK10	NM_199347.2		420,2184,3878	GG,GA,AA		27.8515,14.4328,23.3261		597/713	27326451	3024,9940	2186	4296	6482	SO:0001630	splice_region_variant	152110	exon22			CCTATCATCTATA	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1790-1T>C	3.37:g.27326451A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	37		459|459	0.21016483516483517|0.21016483516483517	54|54	0.10975609756097561|0.10975609756097561	133|133	0.3674033149171271|0.3674033149171271	58|58	0.10139860139860139|0.10139860139860139	214|214	0.28232189973614774|0.28232189973614774	A|A	14.32|14.32	2.500023|2.500023	0.44455|0.44455	0.144328|0.144328	0.278515|0.278515	ENSG00000163491|ENSG00000163491	ENST00000424275|ENST00000435584	.|.	.|.	.|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.05386|.	-1.0888|.	3|.	.|.	.|.	.|.	.|.	15.9466|15.9466	0.79799|0.79799	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs10510594;rs17681232;rs10510594|rs10510594;rs17681232;rs10510594	.|.	.|.	.|.	T|R	84|54	.|.	.|.	M|X	-|-	2|1	0|0	NEK10|NEK10	27301455|27301455	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.852000|0.852000	0.48524|0.48524	3.860000|3.860000	0.55995|0.55995	2.175000|2.175000	0.68902|0.68902	0.397000|0.397000	0.26171|0.26171	ATG|TGA	A|0.792;G|0.208	0.208	strong		0.383	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	Silent
IGFN1	91156	hgsc.bcm.edu	37	1	201168499	201168499	+	Silent	SNP	G	G	A	rs1534057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201168499G>A	ENST00000335211.4	+	6	535	c.405G>A	c.(403-405)ccG>ccA	p.P135P	IGFN1_ENST00000451870.2_Silent_p.P135P|IGFN1_ENST00000295591.8_5'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	135						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACAGGGAACCGCAGGAAGGTA	0.547													G|||	994	0.198482	0.1498	0.2075	5008	,	,		20083	0.256		0.1501	False		,,,				2504	0.2485				p.P135P		Atlas-SNP	.											.	IGFN1	220	.	0			c.G405A						PASS	.	G		184,1200		10,164,518	117.0	117.0	117.0		405	-3.7	0.7	1	dbSNP_88	117	457,2725		32,393,1166	no	coding-synonymous	IGFN1	NM_001164586.1		42,557,1684	AA,AG,GG		14.362,13.2948,14.0385		135/3709	201168499	641,3925	692	1591	2283	SO:0001819	synonymous_variant	91156	exon6			GGAACCGCAGGAA	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.405G>A	1.37:g.201168499G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	194	76	0.391753	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1																																																																																			G|0.819;A|0.181	0.181	strong		0.547	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
SCD5	79966	hgsc.bcm.edu	37	4	83582211	83582211	+	Intron	SNP	C	C	G	rs3733227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:83582211C>G	ENST00000319540.4	-	3	889				SCD5_ENST00000273908.4_Missense_Mutation_p.E197Q	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5						fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				GCTCTTCCTTCTTTCTGGATG	0.428													G|||	3047	0.608427	0.4887	0.7435	5008	,	,		20308	0.623		0.6252	False		,,,				2504	0.6421				p.E197Q		Atlas-SNP	.											.	SCD5	58	.	0			c.G589C						PASS	.	G	,GLN/GLU	2231,2175	585.3+/-386.2	565,1101,537	178.0	181.0	180.0		,589	3.7	0.1	4	dbSNP_107	180	5661,2939	458.0+/-364.5	1837,1987,476	yes	intron,missense	SCD5	NM_001037582.2,NM_024906.2	,29	2402,3088,1013	GG,GC,CC		34.1744,49.3645,39.3203	,	,197/257	83582211	7892,5114	2203	4300	6503	SO:0001627	intron_variant	79966	exon4			TTCCTTCTTTCTG	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"""Fatty acid desaturases"""	21088	protein-coding gene	gene with protein product		608370	"""stearoyl-CoA desaturase 4"""	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.569+19648G>C	4.37:g.83582211C>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	37	CCDS34024.1	1345	0.6158424908424909	243	0.49390243902439024	262	0.7237569060773481	363	0.6346153846153846	477	0.6292875989445911	G	11.55	1.673370	0.29693	0.506355	0.658256	ENSG00000145284	ENST00000273908	.	.	.	3.67	3.67	0.42095	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47094	P	6.899999999999684E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.36578	-0.9742	6	0.28530	T	0.3	.	9.3966	0.38406	0.0:0.2176:0.7824:0.0	rs3733227;rs52790700;rs59899175;rs3733227	197	Q86SK9-2	.	Q	197	.	ENSP00000273908:E197Q	E	-	1	0	SCD5	83801235	0.280000	0.24249	0.059000	0.19551	0.007000	0.05969	1.373000	0.34272	1.153000	0.42468	-0.187000	0.12897	GAA	C|0.388;G|0.612	0.612	strong		0.428	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906	
WFDC9	259240	hgsc.bcm.edu	37	20	44238741	44238741	+	Missense_Mutation	SNP	T	T	G	rs2245898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:44238741T>G	ENST00000326000.1	-	3	297	c.80A>C	c.(79-81)aAc>aCc	p.N27T		NM_147198.3	NP_671731.1	Q8NEX5	WFDC9_HUMAN	WAP four-disulfide core domain 9	27			N -> T (in dbSNP:rs2245898).			extracellular region (GO:0005576)		p.N27T(1)		breast(1)|large_intestine(1)|liver(1)|lung(1)|prostate(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				GGGATCTTTGTTCCAGAAGCT	0.522													G|||	1970	0.393371	0.4175	0.3545	5008	,	,		17994	0.4276		0.325	False		,,,				2504	0.4233				p.N27T		Atlas-SNP	.											WFDC9,NS,carcinoma,0,1	WFDC9	10	1	1	Substitution - Missense(1)	stomach(1)	c.A80C						PASS	.	G	THR/ASN	1736,2670	648.1+/-398.7	334,1068,801	111.0	95.0	101.0		80	-6.1	0.0	20	dbSNP_100	101	2822,5778	675.7+/-403.2	487,1848,1965	yes	missense	WFDC9	NM_147198.3	65	821,2916,2766	GG,GT,TT		32.814,39.4008,35.0454	benign	27/90	44238741	4558,8448	2203	4300	6503	SO:0001583	missense	259240	exon3			TCTTTGTTCCAGA	AL031671	CCDS13362.1	20q13.12	2013-01-21			ENSG00000180205	ENSG00000180205		"""WAP four-disulfide core domain containing"""	20380	protein-coding gene	gene with protein product						12206714	Standard	NM_147198		Approved	WAP9, dJ688G8.2	uc002xoy.3	Q8NEX5	OTTHUMG00000046332	ENST00000326000.1:c.80A>C	20.37:g.44238741T>G	ENSP00000320532:p.Asn27Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_147198	Q3MIX6|Q5TGZ8	Missense_Mutation	SNP	ENST00000326000.1	37	CCDS13362.1	857	0.3923992673992674	232	0.4715447154471545	142	0.39226519337016574	245	0.42832167832167833	238	0.31398416886543534	G	1.900	-0.453305	0.04540	0.394008	0.32814	ENSG00000180205	ENST00000326000	T	0.30714	1.52	4.1	-6.08	0.02151	.	3.200970	0.01266	N	0.009333	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37842	-0.9688	8	0.11485	T	0.65	.	4.1965	0.10445	0.0899:0.1742:0.1313:0.6046	rs2245898;rs52837047;rs60275083;rs2245898	27	Q8NEX5	WFDC9_HUMAN	T	27	ENSP00000320532:N27T	ENSP00000320532:N27T	N	-	2	0	WFDC9	43672155	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.986000	0.01484	-1.726000	0.01370	-1.935000	0.00506	AAC	T|0.626;G|0.374	0.374	strong		0.522	WFDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106945.1		
CYP2C19	1557	hgsc.bcm.edu	37	10	96541616	96541616	+	Silent	SNP	G	G	A	rs4244285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96541616G>A	ENST00000371321.3	+	5	763	c.681G>A	c.(679-681)ccG>ccA	p.P227P	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	227			P -> L (in allele CYP2C19*10; dbSNP:rs6413438). {ECO:0000269|PubMed:12464799}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	ATTATTTCCCGGGAACCCATA	0.294													G|||	1109	0.221446	0.1702	0.1052	5008	,	,		13926	0.3125		0.1451	False		,,,				2504	0.3579				p.P227P		Atlas-SNP	.											.	CYP2C19	88	.	0			c.G681A	GRCh37	CS941458	CYP2C19	S	rs4244285	PASS	.	G		728,3676	271.9+/-270.5	63,602,1537	50.0	55.0	53.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	681	-8.3	0.0	10	dbSNP_111	53	1276,7322	246.1+/-274.7	98,1080,3121	no	coding-synonymous	CYP2C19	NM_000769.1		161,1682,4658	AA,AG,GG		14.8407,16.5304,15.413		227/491	96541616	2004,10998	2202	4299	6501	SO:0001819	synonymous_variant	1557	exon5			TTTCCCGGGAACC	M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.681G>A	10.37:g.96541616G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_000769	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Silent	SNP	ENST00000371321.3	37	CCDS7436.1																																																																																			A|0.170;G|0.830	0.170	strong		0.294	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	
MLH1	4292	hgsc.bcm.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	rs1799977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37053568A>G	ENST00000231790.2	+	8	871	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.I121V	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	219			I -> V (common polymorphism; found in 37% of alleles; dbSNP:rs1799977). {ECO:0000269|PubMed:10375096, ECO:0000269|PubMed:10777691, ECO:0000269|PubMed:11754112, ECO:0000269|PubMed:12115348, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12362047, ECO:0000269|PubMed:9032648, ECO:0000269|PubMed:9067757, ECO:0000269|PubMed:9087566, ECO:0000269|PubMed:9218993, ECO:0000269|PubMed:9833759, ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.I219V(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TATTCGCTCCATCTTTGGAAA	0.368		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	649	0.129593	0.0386	0.1686	5008	,	,		18149	0.0258		0.325	False		,,,				2504	0.1309				p.I219V		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,NS,carcinoma,0,1	MLH1	226	1	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|prostate(1)	c.A655G	GRCh37	CM970958	MLH1	M	rs1799977	PASS	.	A	VAL/ILE,VAL/ILE,,	406,4000	199.4+/-223.0	27,352,1824	145.0	129.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	655,361,,	4.6	1.0	3	dbSNP_89	135	2754,5846	438.0+/-358.8	442,1870,1988	yes	missense,missense,utr-5,utr-5	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	29,29,,	469,2222,3812	GG,GA,AA		32.0233,9.2147,24.2965	benign,benign,,	219/757,121/659,,	37053568	3160,9846	2203	4300	6503	SO:0001583	missense	4292	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CGCTCCATCTTTG	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.655A>G	3.37:g.37053568A>G	ENSP00000231790:p.Ile219Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	93	55	0.591398	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	374	0.17124542124542125	28	0.056910569105691054	72	0.19889502762430938	16	0.027972027972027972	258	0.3403693931398417	A	14.01	2.408011	0.42715	0.092147	0.320233	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.83591	-1.74;-1.74	5.76	4.61	0.57282	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.113678	0.64402	D	0.000010	T	0.00012	0.0000	N	0.25992	0.78	0.09310	P	1.0	B;B;B	0.16603	0.018;0.018;0.018	B;B;B	0.26864	0.028;0.074;0.06	T	0.07424	-1.0773	9	0.12430	T	0.62	-17.9526	7.4844	0.27423	0.7886:0.0:0.2114:0.0	rs1799977;rs2229023;rs11541861;rs17809298;rs52803721;rs56722302;rs1799977	121;219;219	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	V	219;185;185;83;121	ENSP00000231790:I219V;ENSP00000402564:I121V	ENSP00000231790:I219V	I	+	1	0	MLH1	37028572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.209000	0.71365	0.533000	0.62120	ATC	A|0.799;G|0.201	0.201	strong		0.368	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
HERC1	8925	hgsc.bcm.edu	37	15	63922752	63922752	+	Silent	SNP	T	T	A	rs10851731	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63922752T>A	ENST00000443617.2	-	69	12966	c.12879A>T	c.(12877-12879)atA>atT	p.I4293I		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4293					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.I4293I(1)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCACATCTTCTATGATTACTC	0.468													A|||	3189	0.636781	0.8744	0.6484	5008	,	,		18519	0.0972		0.8976	False		,,,				2504	0.5951				p.I4293I		Atlas-SNP	.											HERC1_ENST00000443617,NS,carcinoma,0,1	HERC1	624	1	1	Substitution - coding silent(1)	stomach(1)	c.A12879T						PASS	.	A		3365,569		1441,483,43	160.0	161.0	160.0		12879	-0.9	1.0	15	dbSNP_120	160	7320,994		3215,890,52	no	coding-synonymous	HERC1	NM_003922.3		4656,1373,95	AA,AT,TT		11.9557,14.4637,12.7613		4293/4862	63922752	10685,1563	1967	4157	6124	SO:0001819	synonymous_variant	8925	exon69			ATCTTCTATGATT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.12879A>T	15.37:g.63922752T>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																			T|0.342;A|0.658	0.658	strong		0.468	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
BCAT2	587	hgsc.bcm.edu	37	19	49303070	49303070	+	Missense_Mutation	SNP	G	G	C	rs11548193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49303070G>C	ENST00000316273.6	-	6	569	c.557C>G	c.(556-558)aCg>aGg	p.T186R	BCAT2_ENST00000545387.2_Missense_Mutation_p.T94R|BCAT2_ENST00000402551.1_Missense_Mutation_p.T146R|BCAT2_ENST00000598162.1_Missense_Mutation_p.T186R|BCAT2_ENST00000597011.1_Missense_Mutation_p.T146R|BCAT2_ENST00000599246.1_Missense_Mutation_p.T94R	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial	186			T -> R (in dbSNP:rs11548193). {ECO:0000269|PubMed:8702755, ECO:0000269|PubMed:9165094}.		branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|isoleucine catabolic process (GO:0006550)|leucine metabolic process (GO:0006551)|regulation of hormone levels (GO:0010817)|small molecule metabolic process (GO:0044281)|valine metabolic process (GO:0006573)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	12		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Isoleucine(DB00167)|L-Leucine(DB00149)	GAGCGCGCGCGTGGGCTGGCT	0.701													G|||	355	0.0708866	0.0076	0.1037	5008	,	,		14201	0.0		0.2177	False		,,,				2504	0.0552				p.T186R		Atlas-SNP	.											.	BCAT2	35	.	0			c.C557G						PASS	.	G	ARG/THR,ARG/THR	187,4087		11,165,1961	20.0	18.0	19.0		281,557	2.0	0.0	19	dbSNP_120	19	1658,6738		153,1352,2693	no	missense,missense	BCAT2	NM_001164773.1,NM_001190.3	71,71	164,1517,4654	CC,CG,GG		19.7475,4.3753,14.562	benign,benign	94/301,186/393	49303070	1845,10825	2137	4198	6335	SO:0001583	missense	587	exon6			GCGCGCGTGGGCT	U68418	CCDS12735.1, CCDS54290.1, CCDS74416.1	19q13.33	2013-09-20	2010-05-07		ENSG00000105552	ENSG00000105552	2.6.1.42		977	protein-coding gene	gene with protein product		113530	"""branched chain aminotransferase 2, mitochondrial"""	BCT2		9165094	Standard	NM_001190		Approved	BCAM	uc002pkr.3	O15382	OTTHUMG00000183327	ENST00000316273.6:c.557C>G	19.37:g.49303070G>C	ENSP00000322991:p.Thr186Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001190	B2RB87|O00269|Q96KG1|Q9BTB6|Q9BUU6	Missense_Mutation	SNP	ENST00000316273.6	37	CCDS12735.1	208	0.09523809523809523	3	0.006097560975609756	43	0.11878453038674033	0	0.0	162	0.21372031662269128	G	8.463	0.855676	0.17106	0.043753	0.197475	ENSG00000105552	ENST00000316273;ENST00000545387;ENST00000402551	T;T;T	0.16597	2.33;2.33;2.33	4.24	1.97	0.26223	.	0.784748	0.11673	N	0.540689	T	0.00012	0.0000	L	0.39020	1.185	0.80722	P	0.0	B;B;B;B	0.22080	0.064;0.064;0.015;0.064	B;B;B;B	0.29176	0.099;0.099;0.026;0.099	T	0.37407	-0.9707	9	0.15952	T	0.53	-0.0452	12.1372	0.53979	0.0:0.3239:0.6761:0.0	rs11548193	146;186;94;186	B3KSI3;Q53EW7;O15382-2;O15382	.;.;.;BCAT2_HUMAN	R	186;94;146	ENSP00000322991:T186R;ENSP00000440973:T94R;ENSP00000385161:T146R	ENSP00000322991:T186R	T	-	2	0	BCAT2	53994882	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	1.033000	0.30191	0.502000	0.28037	0.561000	0.74099	ACG	G|0.904;C|0.096	0.096	strong		0.701	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1		
C10orf128	170371	hgsc.bcm.edu	37	10	50374930	50374930	+	Silent	SNP	C	C	T	rs45563932	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50374930C>T	ENST00000474718.1	-	3	244	c.222G>A	c.(220-222)acG>acA	p.T74T	C10orf128_ENST00000374153.2_Silent_p.T74T|C10orf128_ENST00000374151.3_Silent_p.T74T|C10orf128_ENST00000470884.1_5'UTR|C10orf128_ENST00000374148.1_Silent_p.T74T	NM_001010863.1	NP_001010863.1	Q5T292	CJ128_HUMAN	chromosome 10 open reading frame 128	74						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)	3						GGCCCCCAGGCGTGCTTTTCA	0.607													C|||	398	0.0794728	0.0635	0.1455	5008	,	,		19879	0.001		0.1899	False		,,,				2504	0.0215				p.T74T		Atlas-SNP	.											.	C10orf128	20	.	0			c.G222A						PASS	.	C		318,3724		9,300,1712	72.0	76.0	75.0		222	-0.8	0.0	10	dbSNP_127	75	1780,6580		207,1366,2607	no	coding-synonymous	C10orf128	NM_001010863.1		216,1666,4319	TT,TC,CC		21.2919,7.8674,16.9166		74/106	50374930	2098,10304	2021	4180	6201	SO:0001819	synonymous_variant	170371	exon3			CCCAGGCGTGCTT	BC031641	CCDS41519.1, CCDS73128.1	10q11.23	2012-06-13			ENSG00000204161	ENSG00000204161			27274	protein-coding gene	gene with protein product						12477932	Standard	NM_001010863		Approved	Em:AC084727.5	uc001jhn.4	Q5T292	OTTHUMG00000018188	ENST00000474718.1:c.222G>A	10.37:g.50374930C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_001010863	A6XND2|Q5T289|Q5T291	Silent	SNP	ENST00000474718.1	37	CCDS41519.1																																																																																			C|0.865;T|0.135	0.135	strong		0.607	C10orf128-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047978.1	NM_001010863	
RYR1	6261	hgsc.bcm.edu	37	19	38946182	38946182	+	Silent	SNP	G	G	A	rs2288888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38946182G>A	ENST00000359596.3	+	15	1668	c.1668G>A	c.(1666-1668)tcG>tcA	p.S556S	RYR1_ENST00000355481.4_Silent_p.S556S|RYR1_ENST00000360985.3_Silent_p.S556S			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	556					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGGAGGCCTCGTCTGGTAGGA	0.612													G|||	2861	0.571286	0.5098	0.683	5008	,	,		13820	0.6052		0.6918	False		,,,				2504	0.4162				p.S556S		Atlas-SNP	.											.	RYR1	708	.	0			c.G1668A						PASS	.	G	,	2441,1965	620.5+/-393.6	666,1109,428	64.0	60.0	61.0		1668,1668	-8.0	0.8	19	dbSNP_100	61	5780,2820	675.6+/-403.2	1937,1906,457	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	2603,3015,885	AA,AG,GG		32.7907,44.5983,36.7907	,	556/5039,556/5034	38946182	8221,4785	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon15			GGCCTCGTCTGGT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.1668G>A	19.37:g.38946182G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			G|0.376;A|0.624	0.624	strong		0.612	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
FCGBP	8857	hgsc.bcm.edu	37	19	40363916	40363916	+	Missense_Mutation	SNP	C	C	T	rs77005739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40363916C>T	ENST00000221347.6	-	31	14733	c.14726G>A	c.(14725-14727)cGc>cAc	p.R4909H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4909	VWFD 12. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.R4909H(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AACCAGGAGGCGTTGGAGATC	0.602													C|||	420	0.0838658	0.0461	0.062	5008	,	,		20808	0.0714		0.0398	False		,,,				2504	0.2086				p.R4909H		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	pancreas(1)	c.G14726A						PASS	.	C	HIS/ARG	229,4177	136.5+/-172.5	7,215,1981	85.0	70.0	75.0		14726	3.2	0.1	19	dbSNP_131	75	338,8262	117.4+/-177.0	7,324,3969	yes	missense	FCGBP	NM_003890.2	29	14,539,5950	TT,TC,CC		3.9302,5.1975,4.3595	probably-damaging	4909/5406	40363916	567,12439	2203	4300	6503	SO:0001583	missense	8857	exon31			AGGAGGCGTTGGA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.14726G>A	19.37:g.40363916C>T	ENSP00000221347:p.Arg4909His	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	129	0.059065934065934064	28	0.056910569105691054	21	0.058011049723756904	46	0.08041958041958042	34	0.044854881266490766	C	9.570	1.120893	0.20877	0.051975	0.039302	ENSG00000090920	ENST00000221347	T	0.60171	0.21	5.34	3.16	0.36331	von Willebrand factor, type D domain (3);	0.595355	0.16196	U	0.225151	T	0.12305	0.0299	M	0.76938	2.355	0.80722	P	0.0	D	0.89917	1.0	D	0.75020	0.985	T	0.57341	-0.7828	9	0.46703	T	0.11	.	5.3938	0.16259	0.0:0.6469:0.1636:0.1895	.	4909	Q9Y6R7	FCGBP_HUMAN	H	4909	ENSP00000221347:R4909H	ENSP00000221347:R4909H	R	-	2	0	FCGBP	45055756	0.000000	0.05858	0.057000	0.19452	0.021000	0.10359	0.063000	0.14410	0.598000	0.29829	0.313000	0.20887	CGC	C|0.949;T|0.051	0.051	strong		0.602	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
KPRP	448834	hgsc.bcm.edu	37	1	152733301	152733301	+	Missense_Mutation	SNP	T	T	A	rs4329520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152733301T>A	ENST00000606109.1	+	1	1265	c.1237T>A	c.(1237-1239)Tgc>Agc	p.C413S	KPRP_ENST00000368773.1_Missense_Mutation_p.C413S			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	413	Pro-rich.		C -> S (in dbSNP:rs4329520).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCAGAACCATGCATAAGTCT	0.577													T|||	2455	0.490216	0.5787	0.4914	5008	,	,		19481	0.4177		0.5159	False		,,,				2504	0.4182				p.C413S		Atlas-SNP	.											.	KPRP	152	.	0			c.T1237A						PASS	.	T	SER/CYS	2439,1967	620.2+/-393.5	676,1087,440	166.0	170.0	168.0		1237	-0.3	0.0	1	dbSNP_111	168	4323,4277	579.2+/-390.9	1097,2129,1074	yes	missense	KPRP	NM_001025231.1	112	1773,3216,1514	AA,AT,TT		49.7326,44.6437,48.0086	benign	413/580	152733301	6762,6244	2203	4300	6503	SO:0001583	missense	448834	exon2			GAACCATGCATAA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1237T>A	1.37:g.152733301T>A	ENSP00000475216:p.Cys413Ser	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	262	262	1	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	1120	0.5128205128205128	294	0.5975609756097561	196	0.5414364640883977	248	0.43356643356643354	382	0.503957783641161	T	13.38	2.220864	0.39201	0.553563	0.502674	ENSG00000203786	ENST00000368773	T	0.24908	1.83	4.88	-0.312	0.12758	.	0.277746	0.26359	N	0.024827	T	0.04452	0.0122	L	0.52573	1.65	0.80722	P	0.0	B	0.16396	0.017	B	0.15484	0.013	T	0.38023	-0.9680	9	0.09590	T	0.72	-8.4552	0.3401	0.00332	0.2846:0.1651:0.1471:0.4032	rs4329520;rs60534699;rs4329520	413	Q5T749	KPRP_HUMAN	S	413	ENSP00000357762:C413S	ENSP00000357762:C413S	C	+	1	0	KPRP	150999925	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.196000	0.09532	-0.142000	0.11354	0.379000	0.24179	TGC	T|0.489;A|0.511	0.511	strong		0.577	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
CHFR	55743	hgsc.bcm.edu	37	12	133423695	133423695	+	Silent	SNP	A	A	G	rs2306537	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133423695A>G	ENST00000432561.2	-	15	1778	c.1705T>C	c.(1705-1707)Ttg>Ctg	p.L569L	CHFR_ENST00000443047.2_Silent_p.L477L|CHFR_ENST00000266880.7_Silent_p.L568L|CHFR_ENST00000541341.1_5'UTR|CHFR_ENST00000315585.7_Silent_p.L528L|CHFR_ENST00000537522.1_Silent_p.L191L|CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000450056.2_Silent_p.L557L			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	569					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		TTCCATGTCAAACCTCTGGTT	0.458													A|||	713	0.142372	0.0106	0.1571	5008	,	,		19964	0.1736		0.2803	False		,,,				2504	0.136				p.L569L		Atlas-SNP	.											.	CHFR	83	.	0			c.T1705C						PASS	.	A	,,,,	223,4183	136.5+/-172.5	9,205,1989	102.0	104.0	103.0		1705,1702,1669,1429,1582	2.2	1.0	12	dbSNP_100	103	2569,6031	416.9+/-352.3	384,1801,2115	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CHFR	NM_001161344.1,NM_001161345.1,NM_001161346.1,NM_001161347.1,NM_018223.2	,,,,	393,2006,4104	GG,GA,AA		29.8721,5.0613,21.467	,,,,	569/665,568/664,557/653,477/573,528/624	133423695	2792,10214	2203	4300	6503	SO:0001819	synonymous_variant	55743	exon15			ATGTCAAACCTCT	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1705T>C	12.37:g.133423695A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Silent	SNP	ENST00000432561.2	37	CCDS53849.1																																																																																			A|0.803;G|0.197	0.197	strong		0.458	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
CD300LB	124599	hgsc.bcm.edu	37	17	72521967	72521967	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72521967T>C	ENST00000392621.1	-	2	405	c.401A>G	c.(400-402)gAt>gGt	p.D134G	CD300LB_ENST00000314401.3_Missense_Mutation_p.D134G	NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	97					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						ATCTGCGTCATCTCGCCTGAG	0.512																																					p.D134G		Atlas-SNP	.											.	CD300LB	38	.	0			c.A401G						PASS	.						247.0	222.0	231.0					17																	72521967		2203	4300	6503	SO:0001583	missense	124599	exon2			GCGTCATCTCGCC	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"""Immunoglobulin superfamily / V-set domain containing"""	30811	protein-coding gene	gene with protein product	"""triggering receptor expressed on myeloid cells 5"""	610705	"""CD300 antigen like family member B"""			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.401A>G	17.37:g.72521967T>C	ENSP00000376397:p.Asp134Gly	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	210	35	0.166667	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Missense_Mutation	SNP	ENST00000392621.1	37	CCDS11700.1	.	.	.	.	.	.	.	.	.	.	T	8.070	0.770010	0.15983	.	.	ENSG00000178789	ENST00000392621;ENST00000314401	T	0.04454	3.62	5.17	2.93	0.34026	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.155110	0.06495	N	0.735307	T	0.08044	0.0201	L	0.58354	1.805	0.09310	N	1	B;B	0.19935	0.003;0.04	B;B	0.24006	0.015;0.05	T	0.35822	-0.9773	10	0.54805	T	0.06	-16.8791	7.7177	0.28715	0.0:0.1769:0.0:0.8231	.	134;97	B4DQ71;A8K4G0	.;CLM7_HUMAN	G	97;134	ENSP00000317337:D134G	ENSP00000317337:D134G	D	-	2	0	CD300LB	70033562	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.348000	0.07740	0.900000	0.36469	0.460000	0.39030	GAT	.	.	none		0.512	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892	
SLC25A23	79085	hgsc.bcm.edu	37	19	6444196	6444196	+	Silent	SNP	C	C	G	rs138598051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6444196C>G	ENST00000301454.4	-	9	1294	c.1188G>C	c.(1186-1188)ccG>ccC	p.P396P	SLC25A23_ENST00000601760.1_5'UTR|SLC25A23_ENST00000334510.5_Silent_p.P396P|SLC25A23_ENST00000414491.2_Silent_p.P157P	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	396					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CCAGGGCCAGCGGGTAACTGG	0.662													G|||	60	0.0119808	0.0083	0.0029	5008	,	,		17368	0.0		0.0099	False		,,,				2504	0.0378				p.P396P		Atlas-SNP	.											.	SLC25A23	43	.	0			c.G1188C						PASS	.	G		39,4367		0,39,2164	26.0	24.0	24.0		1188	0.0	1.0	19	dbSNP_134	24	149,8447		0,149,4149	no	coding-synonymous	SLC25A23	NM_024103.2		0,188,6313	GG,GC,CC		1.7334,0.8852,1.4459		396/469	6444196	188,12814	2203	4298	6501	SO:0001819	synonymous_variant	79085	exon9			GGCCAGCGGGTAA	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.1188G>C	19.37:g.6444196C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Silent	SNP	ENST00000301454.4	37	CCDS32882.1																																																																																			C|0.989;G|0.011	0.011	strong		0.662	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
ZCCHC16	340595	hgsc.bcm.edu	37	X	111698440	111698440	+	Missense_Mutation	SNP	G	G	T	rs7474140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:111698440G>T	ENST00000340433.2	+	1	714	c.484G>T	c.(484-486)Gac>Tac	p.D162Y		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	162			D -> Y (in dbSNP:rs7474140).				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						CTCTCAGCAGGACCCTGCTAC	0.443													G|||	314	0.0831788	0.0272	0.0735	3775	,	,		15500	0.001		0.1551	False		,,,				2504	0.0716				p.D162Y		Atlas-SNP	.											.	ZCCHC16	66	.	0			c.G484T						PASS	.	G	TYR/ASP	259,3576		10,211,28,1411,543	75.0	73.0	73.0		484	-0.3	0.0	X	dbSNP_116	73	1474,5254		119,831,405,1478,1467	yes	missense	ZCCHC16	NM_001004308.2	160	129,1042,433,2889,2010	TT,TG,T,GG,G		21.9084,6.7536,16.4063	probably-damaging	162/311	111698440	1733,8830	2203	4300	6503	SO:0001583	missense	340595	exon3			CAGCAGGACCCTG	AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"""Zinc fingers, CCHC domain containing"""	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.484G>T	X.37:g.111698440G>T	ENSP00000340590:p.Asp162Tyr	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	117	114	0.974359	NM_001004308	B2RPG1	Missense_Mutation	SNP	ENST00000340433.2	37	CCDS35369.1	162	0.09764918625678119	10	0.02109704641350211	25	0.07183908045977011	0	0.0	73	0.10703812316715543	G	0.013	-1.643386	0.00792	0.067536	0.219084	ENSG00000187823	ENST00000340433	T	0.15952	2.38	3.73	-0.266	0.12942	.	0.533187	0.14888	N	0.292551	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.16802	0.019	B	0.15052	0.012	T	0.40175	-0.9577	9	0.02654	T	1	-2.1091	2.7787	0.05355	0.3851:0.0:0.3731:0.2419	rs7474140;rs52792855;rs56925057;rs7474140	162	Q6ZR62	ZCH16_HUMAN	Y	162	ENSP00000340590:D162Y	ENSP00000340590:D162Y	D	+	1	0	ZCCHC16	111585096	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-0.719000	0.04974	-0.205000	0.10219	0.529000	0.55759	GAC	G|0.866;T|0.134	0.134	strong		0.443	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1	NM_001004308	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970812	45970812	+	Missense_Mutation	SNP	G	G	A	rs2329834	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45970812G>A	ENST00000391621.1	-	1	576	c.530C>T	c.(529-531)cCg>cTg	p.P177L	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	177	22 X 5 AA repeats of C-C-X(3).		P -> L (in dbSNP:rs2329834).			keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CTGCTGACACGGGGAGGAGGT	0.607													G|||	2742	0.547524	0.5015	0.5735	5008	,	,		20805	0.371		0.6163	False		,,,				2504	0.7025				p.P177L		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.C530T						PASS	.	G	,LEU/PRO	2134,2272	574.5+/-383.8	503,1128,572	114.0	117.0	116.0		,530	-1.6	0.0	21	dbSNP_100	116	5441,3159	650.5+/-400.7	1729,1983,588	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,98	2232,3111,1160	AA,AG,GG		36.7326,48.434,41.7577	,benign	,177/256	45970812	7575,5431	2203	4300	6503	SO:0001583	missense	386679	exon1			TGACACGGGGAGG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.530C>T	21.37:g.45970812G>A	ENSP00000375479:p.Pro177Leu	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	233	133	0.570815	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	1087	0.4977106227106227	225	0.4573170731707317	226	0.6243093922651933	185	0.32342657342657344	451	0.5949868073878628	g	1.411	-0.575612	0.03882	0.48434	0.632674	ENSG00000205445	ENST00000391621	T	0.01295	5.04	2.98	-1.58	0.08479	.	.	.	.	.	T	0.00012	0.0000	M	0.91818	3.245	0.80722	P	0.0	B	0.16802	0.019	B	0.13407	0.009	T	0.18085	-1.0348	8	0.40728	T	0.16	.	3.9041	0.09174	0.0988:0.2783:0.4817:0.1412	rs2329834;rs2329834	177	P60368	KR102_HUMAN	L	177	ENSP00000375479:P177L	ENSP00000375479:P177L	P	-	2	0	KRTAP10-2	44795240	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.958000	0.03857	-0.221000	0.09973	-4.721000	0.00003	CCG	G|0.491;A|0.509	0.509	strong		0.607	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
CAMK1G	57172	hgsc.bcm.edu	37	1	209782343	209782343	+	Silent	SNP	A	A	G	rs11119314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:209782343A>G	ENST00000009105.1	+	8	899	c.654A>G	c.(652-654)ccA>ccG	p.P218P	CAMK1G_ENST00000361322.2_Silent_p.P218P|CAMK1G_ENST00000494990.1_3'UTR			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	218	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.P218P(1)		breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		GATACCCCCCATTCTATGAAG	0.517													A|||	2732	0.545527	0.7073	0.5476	5008	,	,		20101	0.5714		0.3867	False		,,,				2504	0.4622				p.P218P	Ovarian(163;530 1939 9680 28669 48710)	Atlas-SNP	.											CAMK1G,NS,adenoma,0,2	CAMK1G	49	2	1	Substitution - coding silent(1)	stomach(1)	c.A654G						PASS	.	A		2909,1497	675.5+/-403.1	957,995,251	117.0	112.0	114.0		654	-10.2	0.5	1	dbSNP_120	114	3346,5254	497.4+/-374.5	643,2060,1597	no	coding-synonymous	CAMK1G	NM_020439.2		1600,3055,1848	GG,GA,AA		38.907,33.9764,48.0932		218/477	209782343	6255,6751	2203	4300	6503	SO:0001819	synonymous_variant	57172	exon8			CCCCCCATTCTAT		CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.654A>G	1.37:g.209782343A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_020439	Q86UH5|Q9Y3J7	Silent	SNP	ENST00000009105.1	37	CCDS1486.1	1134	0.5192307692307693	350	0.7113821138211383	179	0.494475138121547	327	0.5716783216783217	278	0.36675461741424803	A	6.373	0.436872	0.12104	0.660236	0.38907	ENSG00000008118	ENST00000423146	T	0.64085	-0.08	5.48	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.38308	-0.9667	5	0.87932	D	0	.	0.8075	0.01086	0.336:0.2448:0.2567:0.1625	rs11119314;rs17846018;rs17859002;rs60747756;rs11119314	.	.	.	R	193	ENSP00000392173:H193R	ENSP00000392173:H193R	H	+	2	0	CAMK1G	207848966	0.000000	0.05858	0.481000	0.27354	0.191000	0.23601	-3.434000	0.00472	-1.907000	0.01087	-2.614000	0.00158	CAT	A|0.485;G|0.515	0.515	strong		0.517	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439	
SLC22A2	6582	hgsc.bcm.edu	37	6	160679400	160679400	+	Silent	SNP	C	C	A	rs624249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:160679400C>A	ENST00000366953.3	-	1	648	c.390G>T	c.(388-390)acG>acT	p.T130T	SLC22A2_ENST00000366952.1_Silent_p.T109T|SLC22A2_ENST00000491092.1_5'UTR	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	130					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	ACGAGCCAGGCGTCTCGTACA	0.627													C|||	1324	0.264377	0.2663	0.268	5008	,	,		15695	0.1498		0.3926	False		,,,				2504	0.2454				p.T130T		Atlas-SNP	.											.	SLC22A2	78	.	0			c.G390T						PASS	.	C		1083,3321	359.4+/-314.8	129,825,1248	59.0	67.0	64.0		390	0.7	1.0	6	dbSNP_83	64	3496,5104	486.5+/-371.9	706,2084,1510	no	coding-synonymous	SLC22A2	NM_003058.3		835,2909,2758	AA,AC,CC		40.6512,24.5913,35.2122		130/556	160679400	4579,8425	2202	4300	6502	SO:0001819	synonymous_variant	6582	exon1			GCCAGGCGTCTCG	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"""Solute carriers"""	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.390G>T	6.37:g.160679400C>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Silent	SNP	ENST00000366953.3	37	CCDS5276.1																																																																																			C|0.673;A|0.327	0.327	strong		0.627	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058	
GOLGA3	2802	hgsc.bcm.edu	37	12	133384864	133384864	+	Missense_Mutation	SNP	G	G	A	rs3741486	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133384864G>A	ENST00000450791.2	-	4	974	c.791C>T	c.(790-792)cCg>cTg	p.P264L	GOLGA3_ENST00000456883.2_Missense_Mutation_p.P264L|GOLGA3_ENST00000545875.1_Missense_Mutation_p.P264L|GOLGA3_ENST00000537452.1_Missense_Mutation_p.P264L|GOLGA3_ENST00000204726.3_Missense_Mutation_p.P264L			Q08378	GOGA3_HUMAN	golgin A3	264			P -> L (in dbSNP:rs3741486).		intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		ATCGGGAGCCGGGACATTTCC	0.527													G|||	711	0.141973	0.0106	0.1571	5008	,	,		15064	0.1736		0.2813	False		,,,				2504	0.1329				p.P264L		Atlas-SNP	.											.	GOLGA3	234	.	0			c.C791T						PASS	.	G	LEU/PRO,LEU/PRO	225,4181	138.0+/-173.8	9,207,1987	134.0	148.0	143.0		791,791	0.8	0.0	12	dbSNP_107	143	2559,6041	416.7+/-352.2	385,1789,2126	yes	missense,missense	GOLGA3	NM_001172557.1,NM_005895.3	98,98	394,1996,4113	AA,AG,GG		29.7558,5.1067,21.4055	benign,benign	264/1135,264/1499	133384864	2784,10222	2203	4300	6503	SO:0001583	missense	2802	exon5			GGAGCCGGGACAT	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.791C>T	12.37:g.133384864G>A	ENSP00000410378:p.Pro264Leu	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	218	105	0.481651	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	394	0.1804029304029304	8	0.016260162601626018	59	0.16298342541436464	105	0.18356643356643357	222	0.2928759894459103	G	1.008	-0.688716	0.03328	0.051067	0.297558	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	5.23	0.791	0.18619	.	1.119980	0.06397	N	0.718094	T	0.00012	0.0000	L	0.38531	1.155	0.80722	P	0.0	B;B;B	0.14805	0.011;0.006;0.006	B;B;B	0.06405	0.002;0.002;0.001	T	0.35919	-0.9769	9	0.66056	D	0.02	.	9.7493	0.40466	0.4088:0.0:0.5912:0.0	rs3741486;rs52796197;rs60613371;rs3741486	264;264;264	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	L	264	ENSP00000204726:P264L;ENSP00000410378:P264L;ENSP00000409303:P264L;ENSP00000442143:P264L;ENSP00000442603:P264L	ENSP00000204726:P264L	P	-	2	0	GOLGA3	131894937	0.000000	0.05858	0.002000	0.10522	0.034000	0.12701	0.439000	0.21575	0.310000	0.22990	0.585000	0.79938	CCG	G|0.802;A|0.198	0.198	strong		0.527	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
KIAA1671	85379	hgsc.bcm.edu	37	22	25577733	25577733	+	Silent	SNP	T	T	C	rs9612887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:25577733T>C	ENST00000406486.4	+	11	5529	c.5142T>C	c.(5140-5142)ccT>ccC	p.P1714P	KIAA1671_ENST00000401395.1_Silent_p.P221P|KIAA1671_ENST00000358431.3_Silent_p.P1714P			Q9BY89	K1671_HUMAN	KIAA1671	1714								p.P1714P(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						AGAGGACCCCTGTCAGCCATC	0.547													C|||	2662	0.53155	0.416	0.6412	5008	,	,		18343	0.7659		0.4801	False		,,,				2504	0.4213				p.P1714P		Atlas-SNP	.											KIAA1671,NS,carcinoma,0,1	KIAA1671	28	1	1	Substitution - coding silent(1)	stomach(1)	c.T5142C						PASS	.	C		593,791		121,351,220	63.0	69.0	67.0		5142	-9.1	0.0	22	dbSNP_119	67	1430,1752		328,774,489	no	coding-synonymous	KIAA1671	NM_001145206.1		449,1125,709	CC,CT,TT		44.9403,42.8468,44.3057		1714/1807	25577733	2023,2543	692	1591	2283	SO:0001819	synonymous_variant	85379	exon8			GACCCCTGTCAGC		CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077			29345	protein-coding gene	gene with protein product						15289310	Standard	NM_001145206		Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.5142T>C	22.37:g.25577733T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			T|0.458;C|0.542	0.542	strong		0.547	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
AK5	26289	hgsc.bcm.edu	37	1	77759578	77759578	+	Silent	SNP	A	A	G	rs2815311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:77759578A>G	ENST00000354567.2	+	3	611	c.348A>G	c.(346-348)gcA>gcG	p.A116A	AK5_ENST00000317704.4_3'UTR|AK5_ENST00000344720.5_Silent_p.A90A	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	116					ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						CTGAGACTGCAGAGTTGATTG	0.428													A|||	576	0.115016	0.0613	0.1023	5008	,	,		14067	0.1359		0.2038	False		,,,				2504	0.0838				p.A116A		Atlas-SNP	.											.	AK5	86	.	0			c.A348G						PASS	.	A	,	333,4073	173.7+/-203.5	12,309,1882	69.0	70.0	69.0		270,348	-7.4	1.0	1	dbSNP_100	69	1806,6794	325.1+/-316.8	178,1450,2672	no	coding-synonymous,coding-synonymous	AK5	NM_012093.3,NM_174858.2	,	190,1759,4554	GG,GA,AA		21.0,7.5579,16.4463	,	90/537,116/563	77759578	2139,10867	2203	4300	6503	SO:0001819	synonymous_variant	26289	exon3			GACTGCAGAGTTG	AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"""Adenylate kinases"""	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.348A>G	1.37:g.77759578A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	188	109	0.579787	NM_174858	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	Silent	SNP	ENST00000354567.2	37	CCDS675.1																																																																																			A|0.843;G|0.157	0.157	strong		0.428	AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858	
MGA	23269	hgsc.bcm.edu	37	15	41989091	41989091	+	Missense_Mutation	SNP	C	C	A	rs61736074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41989091C>A	ENST00000570161.1	+	2	1883	c.1883C>A	c.(1882-1884)cCa>cAa	p.P628Q	MGA_ENST00000545763.1_Missense_Mutation_p.P628Q|MGA_ENST00000389936.4_Missense_Mutation_p.P628Q|MGA_ENST00000219905.7_Missense_Mutation_p.P628Q|MGA_ENST00000566586.1_Missense_Mutation_p.P628Q			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GCAGGACGACCACCTAAGAAC	0.448													C|||	30	0.00599042	0.0008	0.0058	5008	,	,		19971	0.0		0.0209	False		,,,				2504	0.0041				p.P628Q		Atlas-SNP	.											.	MGA	264	.	0			c.C1883A						PASS	.	C	GLN/PRO,GLN/PRO	14,3724		0,14,1855	23.0	21.0	21.0		1883,1883	5.2	1.0	15	dbSNP_129	21	154,8048		2,150,3949	yes	missense,missense	MGA	NM_001080541.2,NM_001164273.1	76,76	2,164,5804	AA,AC,CC		1.8776,0.3745,1.407	probably-damaging,probably-damaging	628/2857,628/3066	41989091	168,11772	1869	4101	5970	SO:0001583	missense	23269	exon3			GACGACCACCTAA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1883C>A	15.37:g.41989091C>A	ENSP00000457035:p.Pro628Gln	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	22	0.010073260073260074	0	0.0	4	0.011049723756906077	0	0.0	18	0.023746701846965697	C	18.09	3.545802	0.65198	0.003745	0.018776	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.47528	0.84;0.84;0.84	5.21	5.21	0.72293	.	2.567660	0.01142	N	0.006237	T	0.44973	0.1319	N	0.24115	0.695	0.31046	N	0.715753	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.973	T	0.51513	-0.8696	10	0.87932	D	0	.	12.162	0.54109	0.0:0.9216:0.0:0.0784	rs61736074	628;628	F5H7K2;E7ENI0	.;.	Q	628	ENSP00000219905:P628Q;ENSP00000374586:P628Q;ENSP00000442467:P628Q	ENSP00000219905:P628Q	P	+	2	0	MGA	39776383	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.086000	0.57664	2.441000	0.82636	0.462000	0.41574	CCA	C|0.987;A|0.013	0.013	strong		0.448	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
EEA1	8411	hgsc.bcm.edu	37	12	93181768	93181768	+	Missense_Mutation	SNP	C	C	A	rs61756482	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:93181768C>A	ENST00000322349.8	-	22	3289	c.3025G>T	c.(3025-3027)Gca>Tca	p.A1009S		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1009	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TCTTTCTCTGCTGCAAGTTCC	0.358													C|||	104	0.0207668	0.0083	0.0144	5008	,	,		15719	0.0407		0.0398	False		,,,				2504	0.002				p.A1009S		Atlas-SNP	.											.	EEA1	104	.	0			c.G3025T						PASS	.	C	SER/ALA	42,4364	45.3+/-79.5	0,42,2161	74.0	71.0	72.0		3025	3.3	1.0	12	dbSNP_129	72	293,8307	107.8+/-168.5	3,287,4010	yes	missense	EEA1	NM_003566.3	99	3,329,6171	AA,AC,CC		3.407,0.9532,2.5757	benign	1009/1412	93181768	335,12671	2203	4300	6503	SO:0001583	missense	8411	exon22			TCTCTGCTGCAAG	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.3025G>T	12.37:g.93181768C>A	ENSP00000317955:p.Ala1009Ser	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	235	101	0.429787	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	53	0.024267399267399268	2	0.0040650406504065045	6	0.016574585635359115	14	0.024475524475524476	31	0.040897097625329816	C	11.19	1.566512	0.28003	0.009532	0.03407	ENSG00000102189	ENST00000322349	T	0.65549	-0.16	6.06	3.27	0.37495	.	0.117788	0.37393	N	0.002103	T	0.10981	0.0268	N	0.14661	0.345	0.32264	N	0.569819	B	0.10296	0.003	B	0.10450	0.005	T	0.16867	-1.0388	10	0.09590	T	0.72	.	6.3	0.21107	0.1306:0.6722:0.0:0.1973	rs61756482	1009	Q15075	EEA1_HUMAN	S	1009	ENSP00000317955:A1009S	ENSP00000317955:A1009S	A	-	1	0	EEA1	91705899	0.997000	0.39634	0.960000	0.40013	0.947000	0.59692	1.352000	0.34033	0.448000	0.26722	-0.188000	0.12872	GCA	C|0.976;A|0.024	0.024	strong		0.358	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
MUS81	80198	hgsc.bcm.edu	37	11	65628334	65628334	+	Missense_Mutation	SNP	G	G	A	rs13817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65628334G>A	ENST00000308110.4	+	1	459	c.110G>A	c.(109-111)cGc>cAc	p.R37H	CFL1_ENST00000531413.1_5'Flank|CFL1_ENST00000308162.5_5'Flank|MUS81_ENST00000533035.1_Intron|CFL1_ENST00000525451.2_5'Flank|CFL1_ENST00000531407.1_5'Flank|CFL1_ENST00000534769.1_Intron	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	37			R -> H (in dbSNP:rs13817). {ECO:0000269|PubMed:11741546, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		CGCAGCAGGCGCCGCACGCGC	0.701								Homologous recombination					G|||	2143	0.427915	0.2012	0.4063	5008	,	,		10955	0.3323		0.667	False		,,,				2504	0.6022				p.R37H		Atlas-SNP	.											.	MUS81	68	.	0			c.G110A						PASS	.	G	HIS/ARG	1273,2965		226,821,1072	7.0	13.0	11.0		110	3.4	1.0	11	dbSNP_52	11	5719,2697		2013,1693,502	yes	missense	MUS81	NM_025128.4	29	2239,2514,1574	AA,AG,GG		32.0461,30.0378,44.7447	probably-damaging	37/552	65628334	6992,5662	2119	4208	6327	SO:0001583	missense	80198	exon1			GCAGGCGCCGCAC		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.110G>A	11.37:g.65628334G>A	ENSP00000307853:p.Arg37His	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_025128	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	37	CCDS8115.1	976	0.4468864468864469	117	0.23780487804878048	176	0.4861878453038674	174	0.3041958041958042	509	0.6715039577836411	G	17.28	3.349232	0.61183	0.300378	0.679539	ENSG00000172732	ENST00000529857;ENST00000308110;ENST00000437855	T;T	0.47528	0.84;0.84	5.39	3.44	0.39384	DNA-directed DNA polymerase, family X, beta-like, N-terminal (2);	0.209202	0.41294	D	0.000913	T	0.00012	0.0000	M	0.61703	1.905	0.37895	P	0.06915300000000002	D	0.76494	0.999	P	0.57101	0.813	T	0.41910	-0.9482	9	0.45353	T	0.12	-15.9145	6.7869	0.23677	0.0918:0.0:0.7347:0.1734	rs13817;rs1054871;rs1204710;rs3178445;rs3195395;rs17845249;rs17858070;rs57204600;rs13817	37	Q96NY9	MUS81_HUMAN	H	102;37;37	ENSP00000431979:R102H;ENSP00000307853:R37H	ENSP00000307853:R37H	R	+	2	0	MUS81	65384910	0.981000	0.34729	1.000000	0.80357	0.211000	0.24417	0.876000	0.28092	1.277000	0.44412	0.491000	0.48974	CGC	G|0.576;A|0.424	0.424	strong		0.701	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
WFDC10B	280664	hgsc.bcm.edu	37	20	44314609	44314609	+	Missense_Mutation	SNP	A	A	G	rs232729	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:44314609A>G	ENST00000330523.5	-	3	253	c.23T>C	c.(22-24)cTt>cCt	p.L8P	WFDC10B_ENST00000335769.2_Intron	NM_172006.2	NP_742003.1	Q8IUB3	WF10B_HUMAN	WAP four-disulfide core domain 10B	8			L -> P (in dbSNP:rs232729). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			lung(2)|ovary(1)|stomach(1)	4		Myeloproliferative disorder(115;0.0122)				AACCAGGACAAGCAGCAGAGT	0.587													G|||	4254	0.849441	0.9697	0.7939	5008	,	,		21003	0.998		0.6113	False		,,,				2504	0.818				p.L8P		Atlas-SNP	.											.	WFDC10B	15	.	0			c.T23C						PASS	.	G	PRO/LEU,	3962,444	212.8+/-232.6	1791,380,32	132.0	106.0	114.0		23,	-0.1	0.0	20	dbSNP_79	114	5181,3419	502.6+/-375.7	1567,2047,686	yes	missense,intron	WFDC10B	NM_172006.2,NM_172131.2	98,	3358,2427,718	GG,GA,AA		39.7558,10.0772,29.7017	benign,	8/74,	44314609	9143,3863	2203	4300	6503	SO:0001583	missense	280664	exon3			AGGACAAGCAGCA	AF454506	CCDS13365.1, CCDS13366.1	20q13.12	2013-01-21			ENSG00000182931	ENSG00000182931		"""WAP four-disulfide core domain containing"""	20479	protein-coding gene	gene with protein product						12206714	Standard	NM_172006		Approved	WAP12	uc002xpb.3	Q8IUB3	OTTHUMG00000130227	ENST00000330523.5:c.23T>C	20.37:g.44314609A>G	ENSP00000327628:p.Leu8Pro	Somatic	312	1	0.00320513		WXS	Illumina HiSeq	Phase_I	323	150	0.464396	NM_172006	A6PVD7|Q0VAG0|Q0VAG1|Q5TGZ5|Q8IUB4	Missense_Mutation	SNP	ENST00000330523.5	37	CCDS13366.1	1791	0.820054945054945	474	0.9634146341463414	285	0.787292817679558	572	1.0	460	0.6068601583113457	G	0.010	-1.757873	0.00657	0.899228	0.602442	ENSG00000182931	ENST00000330523	T	0.36878	1.23	3.12	-0.113	0.13568	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38243	-0.9670	7	0.02654	T	1	.	3.4716	0.07569	0.3654:0.1985:0.4361:0.0	rs232729;rs60177823	8	Q8IUB3	WF10B_HUMAN	P	8	ENSP00000327628:L8P	ENSP00000327628:L8P	L	-	2	0	WFDC10B	43748023	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.403000	0.07214	-0.216000	0.10048	-0.355000	0.07637	CTT	A|0.257;G|0.743	0.743	strong		0.587	WFDC10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252547.1		
EBP	10682	hgsc.bcm.edu	37	X	48382174	48382174	+	Silent	SNP	G	G	T	rs3048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:48382174G>T	ENST00000495186.1	+	2	838	c.15G>T	c.(13-15)gcG>gcT	p.A5A	EBP_ENST00000276096.6_Intron	NM_006579.2	NP_006570.1	Q15125	EBP_HUMAN	emopamil binding protein (sterol isomerase)	5					cholesterol biosynthetic process (GO:0006695)|cholesterol metabolic process (GO:0008203)|drug transmembrane transport (GO:0006855)|hemopoiesis (GO:0030097)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	C-8 sterol isomerase activity (GO:0000247)|cholestenol delta-isomerase activity (GO:0047750)|drug transmembrane transporter activity (GO:0015238)|steroid delta-isomerase activity (GO:0004769)|transmembrane signaling receptor activity (GO:0004888)	p.A5A(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|stomach(1)	11					Tamoxifen(DB00675)	CTACCAACGCGGGCCCCTTGC	0.478													g|||	1190	0.315232	0.1467	0.2305	3775	,	,		10105	0.3155		0.2724	False		,,,				2504	0.2495				p.A5A	Ovarian(41;550 1000 33077 33474 52335)	Atlas-SNP	.											.	EBP	30	.	1	Substitution - coding silent(1)	stomach(1)	c.G15T						PASS	.			786,3049		78,526,104,1028,467	58.0	42.0	47.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	15	-2.7	0.0	X	dbSNP_36	47	2306,4422		326,1040,614,1062,1258	no	coding-synonymous	EBP	NM_006579.2		404,1566,718,2090,1725	TT,TG,T,GG,G		34.2747,20.4954,29.272		5/231	48382174	3092,7471	2203	4300	6503	SO:0001819	synonymous_variant	10682	exon2			CAACGCGGGCCCC	Z37986	CCDS14300.1	Xp11.23-p11.22	2013-05-22	2001-11-28		ENSG00000147155	ENSG00000147155			3133	protein-coding gene	gene with protein product	"""3-beta-hydroxysteroid-delta-8,delta-7-isomerase"", ""Chondrodysplasia punctata-2, X-linked dominant (Happle syndrome)"", ""sterol 8-isomerase"""	300205	"""emopamil-binding protein (sterol isomerase)"""	CDPX2		7706302, 8938429	Standard	NM_006579		Approved	CPX, CPXD, CHO2	uc004djx.4	Q15125	OTTHUMG00000034482	ENST00000495186.1:c.15G>T	X.37:g.48382174G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_006579	Q6FGL3|Q6IBI9	Silent	SNP	ENST00000495186.1	37	CCDS14300.1																																																																																			G|0.693;T|0.307	0.307	strong		0.478	EBP-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083372.1	NM_006579	
IPO13	9670	hgsc.bcm.edu	37	1	44415415	44415415	+	Silent	SNP	C	C	T	rs2240447	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:44415415C>T	ENST00000372343.3	+	2	1073	c.411C>T	c.(409-411)gaC>gaT	p.D137D		NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	137					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				TGATGCCTGACGCTTGGCCAT	0.592													C|||	2530	0.505192	0.0877	0.6167	5008	,	,		20937	0.6161		0.7634	False		,,,				2504	0.6104				p.D137D		Atlas-SNP	.											.	IPO13	86	.	0			c.C411T						PASS	.	C		901,3505	348.0+/-309.7	101,699,1403	79.0	67.0	71.0		411	-9.4	0.6	1	dbSNP_98	71	6752,1848	730.0+/-406.7	2666,1420,214	no	coding-synonymous	IPO13	NM_014652.3		2767,2119,1617	TT,TC,CC		21.4884,20.4494,41.1579		137/964	44415415	7653,5353	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon2			GCCTGACGCTTGG	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"""Importins"""	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.411C>T	1.37:g.44415415C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			C|0.416;T|0.584	0.584	strong		0.592	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
ADAM20	8748	hgsc.bcm.edu	37	14	70989762	70989762	+	Silent	SNP	T	T	C	rs9323540	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70989762T>C	ENST00000256389.3	-	2	2107	c.1863A>G	c.(1861-1863)gtA>gtG	p.V621V	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	571	Cys-rich.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		GATTGGGAATTACTCCCACAT	0.443													T|||	288	0.057508	0.118	0.0231	5008	,	,		25335	0.0347		0.0348	False		,,,				2504	0.047				p.V621V		Atlas-SNP	.											.	ADAM20	59	.	0			c.A1863G						PASS	.	T		441,3965	211.5+/-231.7	23,395,1785	177.0	109.0	132.0		1863	-9.3	0.0	14	dbSNP_119	132	200,8400	86.9+/-149.2	1,198,4101	no	coding-synonymous	ADAM20	NM_003814.4		24,593,5886	CC,CT,TT		2.3256,10.0091,4.9285		621/777	70989762	641,12365	2203	4300	6503	SO:0001819	synonymous_variant	8748	exon2			GGGAATTACTCCC	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1863A>G	14.37:g.70989762T>C		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	214	82	0.383178	NM_003814	Q6GTZ1|Q9UKJ9	Silent	SNP	ENST00000256389.3	37	CCDS32111.1																																																																																			T|0.943;C|0.057	0.057	strong		0.443	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2		
SLCO6A1	133482	hgsc.bcm.edu	37	5	101724448	101724448	+	Missense_Mutation	SNP	G	G	C	rs10055840	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:101724448G>C	ENST00000506729.1	-	12	2132	c.1961C>G	c.(1960-1962)aCa>aGa	p.T654R	SLCO6A1_ENST00000389019.3_Missense_Mutation_p.T592R|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.T401R|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.T401R|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.T654R			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	654			T -> R (in dbSNP:rs10055840). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		ACAACGTCCTGTGTGTCCACA	0.303													G|||	1022	0.204073	0.171	0.1686	5008	,	,		14921	0.1706		0.3022	False		,,,				2504	0.2076				p.T654R		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.C1961G						PASS	.	G	ARG/THR	761,3641	307.2+/-289.9	71,619,1511	72.0	72.0	72.0		1961	-10.1	0.0	5	dbSNP_119	72	2284,6308	382.7+/-340.5	306,1672,2318	yes	missense	SLCO6A1	NM_173488.3	71	377,2291,3829	CC,CG,GG		26.5829,17.2876,23.4339	benign	654/720	101724448	3045,9949	2201	4296	6497	SO:0001583	missense	133482	exon12			CGTCCTGTGTGTC	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1961C>G	5.37:g.101724448G>C	ENSP00000421339:p.Thr654Arg	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	295	157	0.532203	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	487	0.222985347985348	94	0.1910569105691057	71	0.19613259668508287	96	0.16783216783216784	226	0.29815303430079154	G	0.068	-1.208966	0.01568	0.172876	0.265829	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	5.06	-10.1	0.00402	Major facilitator superfamily domain, general substrate transporter (1);	2.166740	0.01881	N	0.037874	T	0.00012	0.0000	N	0.10972	0.075	0.80722	P	0.0	B;B;B	0.18310	0.001;0.027;0.001	B;B;B	0.28385	0.003;0.089;0.008	T	0.04930	-1.0917	9	0.14656	T	0.56	.	2.5457	0.04736	0.1226:0.3074:0.3555:0.2146	rs10055840;rs17273123;rs10055840	592;401;654	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	R	654;654;592;401;401	ENSP00000421339:T654R;ENSP00000369135:T654R;ENSP00000373671:T592R;ENSP00000421990:T401R;ENSP00000369138:T401R	ENSP00000369135:T654R	T	-	2	0	SLCO6A1	101752347	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.032000	0.00309	-5.239000	0.00018	-0.145000	0.13849	ACA	G|0.778;C|0.222	0.222	strong		0.303	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
SLIT3	6586	hgsc.bcm.edu	37	5	168180047	168180047	+	Missense_Mutation	SNP	C	C	T	rs34260167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:168180047C>T	ENST00000519560.1	-	18	2305	c.1886G>A	c.(1885-1887)aGt>aAt	p.S629N	SLIT3_ENST00000404867.3_Missense_Mutation_p.S629N|SLIT3_ENST00000332966.8_Missense_Mutation_p.S629N	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	629					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTCACCGAACTCAGGCCGGC	0.552													C|||	13	0.00259585	0.0008	0.0029	5008	,	,		21030	0.0		0.0089	False		,,,				2504	0.001				p.S629N	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.G1886A						PASS	.	C	ASN/SER	13,4393	20.2+/-43.8	0,13,2190	143.0	100.0	115.0		1886	4.5	0.9	5	dbSNP_126	115	96,8504	53.1+/-113.8	0,96,4204	yes	missense	SLIT3	NM_003062.2	46	0,109,6394	TT,TC,CC		1.1163,0.2951,0.8381	possibly-damaging	629/1524	168180047	109,12897	2203	4300	6503	SO:0001583	missense	6586	exon18			ACCGAACTCAGGC	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.1886G>A	5.37:g.168180047C>T	ENSP00000430333:p.Ser629Asn	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	197	121	0.614213	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	16.11	3.031419	0.54790	0.002951	0.011163	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.58940	0.3;0.3;0.3	5.34	4.46	0.54185	.	0.153798	0.64402	D	0.000001	T	0.45558	0.1348	L	0.53780	1.695	0.58432	D	0.999999	B	0.02656	0.0	B	0.06405	0.002	T	0.45804	-0.9236	10	0.33141	T	0.24	.	15.7623	0.78096	0.0:0.8551:0.1449:0.0	rs34260167	629	O75094	SLIT3_HUMAN	N	629	ENSP00000430333:S629N;ENSP00000332164:S629N;ENSP00000384890:S629N	ENSP00000332164:S629N	S	-	2	0	SLIT3	168112625	1.000000	0.71417	0.866000	0.34008	0.961000	0.63080	4.970000	0.63742	1.240000	0.43803	0.655000	0.94253	AGT	C|0.994;T|0.006	0.006	strong		0.552	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
CARHSP1	23589	hgsc.bcm.edu	37	16	8953081	8953081	+	Silent	SNP	C	C	G	rs8097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:8953081C>G	ENST00000396593.2	-	2	464	c.105G>C	c.(103-105)cgG>cgC	p.R35R	CARHSP1_ENST00000562843.1_Silent_p.R35R|CARHSP1_ENST00000567626.1_5'Flank|RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000567554.1_Silent_p.R35R|CARHSP1_ENST00000311052.5_Silent_p.R35R|CARHSP1_ENST00000561530.1_Silent_p.R35R	NM_001042476.1|NM_001278260.1|NM_001278261.1|NM_001278262.1|NM_001278263.1|NM_001278264.1|NM_001278265.1|NM_001278266.1|NM_014316.3	NP_001035941.1|NP_001265189.1|NP_001265190.1|NP_001265191.1|NP_001265192.1|NP_001265193.1|NP_001265194.1|NP_001265195.1|NP_055131.2	Q9Y2V2	CHSP1_HUMAN	calcium regulated heat stable protein 1, 24kDa	35					intracellular signal transduction (GO:0035556)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|P granule (GO:0043186)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|phosphatase binding (GO:0019902)			endometrium(2)|lung(1)	3						CCACGTTGCCCCGCAGAGGGG	0.667													C|||	2853	0.569688	0.3449	0.5303	5008	,	,		17652	0.6597		0.666	False		,,,				2504	0.7096				p.R35R		Atlas-SNP	.											.	CARHSP1	12	.	0			c.G105C						PASS	.	C	,	1699,2693		319,1061,816	27.0	25.0	26.0		105,105	0.0	0.5	16	dbSNP_52	26	5509,3091		1774,1961,565	no	coding-synonymous,coding-synonymous	CARHSP1	NM_001042476.1,NM_014316.2	,	2093,3022,1381	GG,GC,CC		35.9419,38.684,44.5197	,	35/148,35/148	8953081	7208,5784	2196	4300	6496	SO:0001819	synonymous_variant	23589	exon2			GTTGCCCCGCAGA	AF115345	CCDS10537.1	16p13.2	2008-02-05	2002-08-29		ENSG00000153048	ENSG00000153048			17150	protein-coding gene	gene with protein product			"""calcium regulated heat stable protein 1 (24kD)"""			9712905	Standard	NM_014316		Approved	CRHSP-24, CSDC1	uc031quz.1	Q9Y2V2	OTTHUMG00000129695	ENST00000396593.2:c.105G>C	16.37:g.8953081C>G		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	228	228	1	NM_001042476	B2R4C3|D3DUF5|Q2YDX5|Q9BQ53	Silent	SNP	ENST00000396593.2	37	CCDS10537.1																																																																																			C|0.436;G|0.564	0.564	strong		0.667	CARHSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251902.1	NM_014316	
ARAP1	116985	hgsc.bcm.edu	37	11	72408657	72408657	+	Silent	SNP	C	C	T	rs2291289	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:72408657C>T	ENST00000393609.3	-	20	2977	c.2775G>A	c.(2773-2775)ctG>ctA	p.L925L	ARAP1_ENST00000429686.1_Silent_p.L619L|ARAP1_ENST00000359373.5_Silent_p.L925L|ARAP1_ENST00000426523.1_Silent_p.L680L|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000393605.3_Silent_p.L685L|ARAP1_ENST00000334211.8_Silent_p.L680L|ARAP1-AS2_ENST00000500163.2_RNA|ARAP1_ENST00000455638.2_Silent_p.L925L	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	925					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						TTCGCTCCACCAGCACCAGCA	0.642													C|||	1297	0.258986	0.0393	0.3357	5008	,	,		15799	0.2569		0.4384	False		,,,				2504	0.319				p.L925L	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.G2775A						PASS	.	C	,,	481,3919	224.9+/-240.9	32,417,1751	107.0	93.0	98.0		2775,1857,2040	3.0	1.0	11	dbSNP_100	98	3951,4635	551.5+/-385.9	916,2119,1258	no	coding-synonymous,coding-synonymous,coding-synonymous	ARAP1	NM_001040118.2,NM_001135190.1,NM_015242.4	,,	948,2536,3009	TT,TC,CC		46.0168,10.9318,34.1291	,,	925/1451,619/1134,680/1206	72408657	4432,8554	2200	4293	6493	SO:0001819	synonymous_variant	116985	exon20			CTCCACCAGCACC	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.2775G>A	11.37:g.72408657C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	214	214	1	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Silent	SNP	ENST00000393609.3	37	CCDS41687.1																																																																																			C|0.692;T|0.308	0.308	strong		0.642	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
HMCN1	83872	hgsc.bcm.edu	37	1	185984517	185984517	+	Silent	SNP	T	T	C	rs6665753	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:185984517T>C	ENST00000271588.4	+	31	5086	c.4857T>C	c.(4855-4857)caT>caC	p.H1619H	HMCN1_ENST00000367492.2_Silent_p.H1619H	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1619	Ig-like C2-type 13.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATACGTGTCATGTAGCCAATG	0.383													T|||	1718	0.343051	0.0325	0.4337	5008	,	,		21273	0.4216		0.4781	False		,,,				2504	0.4785				p.H1619H		Atlas-SNP	.											.	HMCN1	797	.	0			c.T4857C						PASS	.	T		455,3951	218.4+/-236.5	24,407,1772	103.0	102.0	102.0		4857	0.5	0.0	1	dbSNP_116	102	4050,4548	557.0+/-387.0	975,2100,1224	no	coding-synonymous	HMCN1	NM_031935.2		999,2507,2996	CC,CT,TT		47.104,10.3268,34.6432		1619/5636	185984517	4505,8499	2203	4299	6502	SO:0001819	synonymous_variant	83872	exon31			GTGTCATGTAGCC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.4857T>C	1.37:g.185984517T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	43	0.34127	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			T|0.661;C|0.339	0.339	strong		0.383	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
CTNNA2	1496	hgsc.bcm.edu	37	2	80801346	80801346	+	Silent	SNP	T	T	C	rs2228460	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:80801346T>C	ENST00000402739.4	+	12	1805	c.1800T>C	c.(1798-1800)gtT>gtC	p.V600V	AC008067.2_ENST00000609950.1_RNA|CTNNA2_ENST00000496558.1_Silent_p.V600V|CTNNA2_ENST00000541047.1_Silent_p.V600V|CTNNA2_ENST00000361291.4_Silent_p.V634V|CTNNA2_ENST00000540488.1_Silent_p.V600V|AC008067.2_ENST00000430876.1_RNA|CTNNA2_ENST00000466387.1_Silent_p.V600V|CTNNA2_ENST00000343114.3_Silent_p.V279V	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	600					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GTGCCAACGTTCCTCAACCGT	0.488													T|||	1187	0.237021	0.0477	0.4236	5008	,	,		19540	0.3403		0.3519	False		,,,				2504	0.136				p.V600V		Atlas-SNP	.											.	CTNNA2	462	.	0			c.T1800C						PASS	.	T	,	373,3891		23,327,1782	188.0	181.0	183.0		1800,1800	1.6	1.0	2	dbSNP_123	183	2879,5647		465,1949,1849	no	coding-synonymous,coding-synonymous	CTNNA2	NM_001164883.1,NM_004389.3	,	488,2276,3631	CC,CT,TT		33.7673,8.7477,25.4261	,	600/861,600/906	80801346	3252,9538	2132	4263	6395	SO:0001819	synonymous_variant	1496	exon13			CAACGTTCCTCAA		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1800T>C	2.37:g.80801346T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	235	138	0.587234	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																				T|0.724;C|0.276	0.276	strong		0.488	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
TRIM4	89122	hgsc.bcm.edu	37	7	99500899	99500899	+	Silent	SNP	T	T	C	rs2247762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99500899T>C	ENST00000355947.2	-	6	990	c.861A>G	c.(859-861)gtA>gtG	p.V287V	TRIM4_ENST00000354241.5_Silent_p.V261V|TRIM4_ENST00000349062.2_Silent_p.V261V	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	287					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				TCTTCACCTTTACAGCTTCAA	0.458													T|||	1612	0.321885	0.1498	0.3357	5008	,	,		21228	0.2937		0.4235	False		,,,				2504	0.4693				p.V287V		Atlas-SNP	.											.	TRIM4	33	.	0			c.A861G						PASS	.	T	,	934,3472	359.4+/-314.8	101,732,1370	135.0	127.0	130.0		861,783	-0.2	0.0	7	dbSNP_100	130	3964,4636	552.3+/-386.1	897,2170,1233	no	coding-synonymous,coding-synonymous	TRIM4	NM_033017.3,NM_033091.2	,	998,2902,2603	CC,CT,TT		46.093,21.1984,37.6595	,	287/501,261/475	99500899	4898,8108	2203	4300	6503	SO:0001819	synonymous_variant	89122	exon6			CACCTTTACAGCT	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16275	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM4"", ""tripartite motif protein 4"""		"""tripartite motif-containing 4"""			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.861A>G	7.37:g.99500899T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Silent	SNP	ENST00000355947.2	37	CCDS5679.1	687	0.31456043956043955	68	0.13821138211382114	133	0.3674033149171271	155	0.270979020979021	331	0.4366754617414248	T	0.026	-1.374714	0.01214	0.211984	0.46093	ENSG00000146833	ENST00000447480	.	.	.	2.16	-0.222	0.13122	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47711	-0.9096	3	.	.	.	.	4.2291	0.10594	0.0:0.3632:0.0:0.6368	rs2247762;rs10373684;rs17277887;rs2247762	.	.	.	E	163	.	.	K	-	1	0	TRIM4	99338835	0.000000	0.05858	0.023000	0.16930	0.054000	0.15201	-2.459000	0.01000	-0.051000	0.13334	0.528000	0.53228	AAA	T|0.658;C|0.342	0.342	strong		0.458	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017	
LRR1	122769	hgsc.bcm.edu	37	14	50074122	50074122	+	Missense_Mutation	SNP	T	T	A	rs17121605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50074122T>A	ENST00000298288.6	+	3	611	c.287T>A	c.(286-288)aTt>aAt	p.I96N	LRR1_ENST00000318317.4_Intron|LRR1_ENST00000557531.1_3'UTR	NM_152329.3	NP_689542.2	Q96L50	LLR1_HUMAN	leucine rich repeat protein 1	96			I -> N (in dbSNP:rs17121605).		protein ubiquitination (GO:0016567)					kidney(2)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						ATTCAGGCCATTTCCAGCAGT	0.363													A|||	943	0.188299	0.323	0.317	5008	,	,		17181	0.0268		0.2296	False		,,,				2504	0.0389				p.I96N		Atlas-SNP	.											.	LRR1	35	.	0			c.T287A						PASS	.	A	ASN/ILE,	1338,3064		204,930,1067	60.0	69.0	66.0		287,	4.4	1.0	14	dbSNP_123	66	1870,6728		219,1432,2648	yes	missense,intron	LRR1	NM_152329.3,NM_203467.1	149,	423,2362,3715	AA,AT,TT		21.7492,30.3953,24.6769	benign,	96/415,	50074122	3208,9792	2201	4299	6500	SO:0001583	missense	122769	exon3			AGGCCATTTCCAG	BC030142	CCDS9686.1, CCDS9687.1	14q21.3	2011-02-02	2011-02-02	2011-02-02	ENSG00000165501	ENSG00000165501			19742	protein-coding gene	gene with protein product	"""LRR-repeat protein 1"""	609193	"""peptidylprolyl isomerase (cyclophilin)-like 5"""	PPIL5		11804328, 21074724	Standard	NR_037792		Approved	MGC20689, LRR-1	uc001wwn.3	Q96L50	OTTHUMG00000140273	ENST00000298288.6:c.287T>A	14.37:g.50074122T>A	ENSP00000298288:p.Ile96Asn	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_152329	A5D6X3|B4DDE0|Q52M24|Q86SZ1|Q8N6H9	Missense_Mutation	SNP	ENST00000298288.6	37	CCDS9686.1	432|432	0.1978021978021978|0.1978021978021978	134|134	0.27235772357723576|0.27235772357723576	107|107	0.2955801104972376|0.2955801104972376	27|27	0.0472027972027972|0.0472027972027972	164|164	0.21635883905013192|0.21635883905013192	A|A	2.002|2.002	-0.429268|-0.429268	0.04701|0.04701	0.303953|0.303953	0.217492|0.217492	ENSG00000165501|ENSG00000165501	ENST00000361579|ENST00000298288	.|T	.|0.37411	.|1.2	5.58|5.58	4.43|4.43	0.53597|0.53597	.|.	.|0.197635	.|0.56097	.|N	.|0.000028	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00413|0.00413	-1.525|-1.525	0.09310|0.09310	P|P	0.9999999999998432|0.9999999999998432	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.37478|0.37478	-0.9704|-0.9704	5|9	0.18710|0.07325	T|T	0.47|0.83	-8.4979|-8.4979	7.8858|7.8858	0.29648|0.29648	0.8097:0.0:0.0668:0.1235|0.8097:0.0:0.0668:0.1235	rs17121605;rs56802702;rs17121605|rs17121605;rs56802702;rs17121605	.|96	.|Q96L50	.|LLR1_HUMAN	Q|N	118|96	.|ENSP00000298288:I96N	ENSP00000354839:H118Q|ENSP00000298288:I96N	H|I	+|+	3|2	2|0	LRR1|LRR1	49143872|49143872	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.966000|0.966000	0.64601|0.64601	3.432000|3.432000	0.52824|0.52824	0.494000|0.494000	0.27859|0.27859	-0.263000|-0.263000	0.10527|0.10527	CAT|ATT	T|0.789;A|0.211	0.211	strong		0.363	LRR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410790.1	NM_203467	
HECW1	23072	hgsc.bcm.edu	37	7	43483981	43483981	+	Missense_Mutation	SNP	G	G	C	rs61756574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43483981G>C	ENST00000395891.2	+	11	1815	c.1210G>C	c.(1210-1212)Ggt>Cgt	p.G404R	HECW1_ENST00000453890.1_Missense_Mutation_p.G404R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	404				G -> R (in Ref. 1; BAA20780, 4; AAI51228 and 5; BAB13352). {ECO:0000305}.	protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TGTCCCCGATGGTCCAGGGAA	0.602													G|||	467	0.0932508	0.0091	0.1081	5008	,	,		20248	0.0089		0.1909	False		,,,				2504	0.183				p.G404R		Atlas-SNP	.											HECW1_ENST00000395891,NS,carcinoma,-2,2	HECW1	540	2	0			c.G1210C						PASS	.	G	ARG/GLY	136,4040		1,134,1953	43.0	47.0	46.0		1210	-3.7	0.0	7	dbSNP_129	46	1641,6813		161,1319,2747	yes	missense	HECW1	NM_015052.3	125	162,1453,4700	CC,CG,GG		19.4109,3.2567,14.0697	benign	404/1607	43483981	1777,10853	2088	4227	6315	SO:0001583	missense	23072	exon11			CCCGATGGTCCAG	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1210G>C	7.37:g.43483981G>C	ENSP00000379228:p.Gly404Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	144	71	0.493056	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	210	0.09615384615384616	6	0.012195121951219513	50	0.13812154696132597	5	0.008741258741258742	149	0.19656992084432717	G	12.52	1.963650	0.34659	0.032567	0.194109	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.30448	1.55;1.53	5.4	-3.65	0.04502	.	4.093410	0.00575	N	0.000304	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.23735	0.09;0.09	B;B	0.20384	0.021;0.029	T	0.13548	-1.0505	9	0.39692	T	0.17	.	4.0835	0.09937	0.4797:0.1008:0.3227:0.0968	rs61756574	404;404	B4DH42;Q76N89	.;HECW1_HUMAN	R	404	ENSP00000379228:G404R;ENSP00000407774:G404R	ENSP00000265522:G404R	G	+	1	0	HECW1	43450506	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.043000	0.12043	-1.119000	0.02958	0.655000	0.94253	GGT	G|0.872;C|0.128	0.128	strong		0.602	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
ITM2C	81618	hgsc.bcm.edu	37	2	231738269	231738269	+	Silent	SNP	G	G	A	rs2289233	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231738269G>A	ENST00000326427.6	+	2	384	c.258G>A	c.(256-258)gcG>gcA	p.A86A	ITM2C_ENST00000409704.2_Silent_p.A24A|ITM2C_ENST00000326407.6_Silent_p.A86A|ITM2C_ENST00000492029.1_3'UTR|ITM2C_ENST00000335005.6_Intron	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	86					negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		TCTTCCTTGCGCAGGTGAGGG	0.617													G|||	2551	0.509385	0.2277	0.5331	5008	,	,		19946	0.8135		0.504	False		,,,				2504	0.5654				p.A86A		Atlas-SNP	.											.	ITM2C	17	.	0			c.G258A						PASS	.	G	,,	1101,3305	384.4+/-325.3	139,823,1241	88.0	61.0	70.0		,258,258	-5.2	0.8	2	dbSNP_100	70	4165,4435	553.2+/-386.3	1027,2111,1162	no	intron,coding-synonymous,coding-synonymous	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,,	1166,2934,2403	AA,AG,GG		48.4302,24.9887,40.489	,,	,86/231,86/268	231738269	5266,7740	2203	4300	6503	SO:0001819	synonymous_variant	81618	exon2			CCTTGCGCAGGTG	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.258G>A	2.37:g.231738269G>A		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	37	CCDS2479.1																																																																																			G|0.534;A|0.466	0.466	strong		0.617	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
TRIM27	5987	hgsc.bcm.edu	37	6	28891176	28891176	+	Silent	SNP	T	T	C	rs2230683	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28891176T>C	ENST00000377199.3	-	1	590	c.234A>G	c.(232-234)gtA>gtG	p.V78V	TRIM27_ENST00000498117.1_5'Flank|TRIM27_ENST00000377194.3_Silent_p.V78V	NM_006510.4	NP_006501.1	P14373	TRI27_HUMAN	tripartite motif containing 27	78					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell proliferation (GO:0008283)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|negative regulation of adaptive immune response (GO:0002820)|negative regulation of calcium ion import (GO:0090281)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						GCAGCTGCTTTACCAGTTGGG	0.687			T	RET	papillary thyroid								T|||	93	0.0185703	0.0045	0.0245	5008	,	,		13739	0.0		0.0696	False		,,,				2504	0.0				p.V78V		Atlas-SNP	.		Dom	yes		6	6p22	5987	tripartite motif-containing 27		E	.	TRIM27	26	.	0			c.A234G						PASS	.	T		101,4299		3,95,2102	27.0	27.0	27.0		234	2.3	1.0	6	dbSNP_98	27	769,7825		40,689,3568	no	coding-synonymous	TRIM27	NM_006510.4		43,784,5670	CC,CT,TT		8.9481,2.2955,6.6954		78/514	28891176	870,12124	2200	4297	6497	SO:0001819	synonymous_variant	5987	exon1			CTGCTTTACCAGT	Z58939	CCDS4654.1	6p22	2013-01-09	2011-01-25	2006-09-26	ENSG00000204713	ENSG00000204713		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9975	protein-coding gene	gene with protein product		602165	"""ret finger protein"", ""tripartite motif-containing 27"""	RFP		8114113	Standard	NM_006510		Approved	RNF76	uc003nlr.3	P14373	OTTHUMG00000031215	ENST00000377199.3:c.234A>G	6.37:g.28891176T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	33	10	0.30303	NM_006510	A2BE15|Q5RJA8|Q5ST26|Q6LA73|Q6NXR9|Q9BZY6|Q9UJL3	Silent	SNP	ENST00000377199.3	37	CCDS4654.1																																																																																			T|0.950;C|0.050	0.050	strong		0.687	TRIM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076442.2	NM_030950	
OGFRL1	79627	hgsc.bcm.edu	37	6	72006512	72006512	+	Silent	SNP	T	T	C	rs2273888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:72006512T>C	ENST00000370435.4	+	6	818	c.684T>C	c.(682-684)caT>caC	p.H228H	RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	228						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						GATTTCAGCATCTGAATGAGT	0.408													C|||	1081	0.215855	0.323	0.2104	5008	,	,		16017	0.2708		0.1044	False		,,,				2504	0.1329				p.H228H		Atlas-SNP	.											.	OGFRL1	44	.	0			c.T684C						PASS	.	C		1178,3212	639.8+/-397.2	150,878,1167	54.0	60.0	58.0		684	1.6	1.0	6	dbSNP_100	58	873,7719	765.6+/-407.6	51,771,3474	no	coding-synonymous	OGFRL1	NM_024576.3		201,1649,4641	CC,CT,TT		10.1606,26.8337,15.7988		228/452	72006512	2051,10931	2195	4296	6491	SO:0001819	synonymous_variant	79627	exon6			TCAGCATCTGAAT		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.684T>C	6.37:g.72006512T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Silent	SNP	ENST00000370435.4	37	CCDS34482.1																																																																																			T|0.820;C|0.180	0.180	strong		0.408	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576	
ZNF607	84775	hgsc.bcm.edu	37	19	38202515	38202515	+	Missense_Mutation	SNP	G	G	A	rs12461753|rs386809063	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38202515G>A	ENST00000355202.4	-	2	600	c.5C>T	c.(4-6)tCc>tTc	p.S2F	CTD-2528L19.4_ENST00000586606.2_Missense_Mutation_p.S2F|ZNF607_ENST00000395835.3_Missense_Mutation_p.S2F	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	2			S -> A (in dbSNP:rs2909097). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			ACTTACATAGGACATGGTTTG	0.413													G|||	739	0.147564	0.0567	0.1455	5008	,	,		21867	0.119		0.2107	False		,,,				2504	0.2362				p.S2F		Atlas-SNP	.											.	ZNF607	82	.	0			c.C5T						PASS	.	G	PHE/SER,PHE/SER	8,4398		2,4,2197	157.0	130.0	139.0		5,5	0.8	0.7	19	dbSNP_120	139	29,8571		3,23,4274	yes	missense,missense	ZNF607	NM_001172677.1,NM_032689.4	155,155	5,27,6471	AA,AG,GG		0.3372,0.1816,0.2845	benign,benign	2/696,2/697	38202515	37,12969	2203	4300	6503	SO:0001583	missense	84775	exon2			ACATAGGACATGG	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"""Zinc fingers, C2H2-type"", ""-"""	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.5C>T	19.37:g.38202515G>A	ENSP00000347338:p.Ser2Phe	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	NM_001172677	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	246	0.11263736263736264	23	0.046747967479674794	46	0.1270718232044199	55	0.09615384615384616	122	0.16094986807387862	G	9.325	1.058997	0.19987	0.001816	0.003372	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.06608	3.3;3.28	1.88	0.836	0.18891	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.02665	-0.54	0.80722	P	0.0	B;B	0.15719	0.001;0.014	B;B	0.20384	0.001;0.029	T	0.44711	-0.9310	8	0.51188	T	0.08	.	4.2432	0.10658	0.2078:0.0:0.7922:0.0	rs12461753;rs59454183	2;2	Q96SK3;F5H141	ZN607_HUMAN;.	F	2	ENSP00000347338:S2F;ENSP00000438015:S2F	ENSP00000347338:S2F	S	-	2	0	ZNF607	42894355	0.359000	0.24955	0.741000	0.31004	0.036000	0.12997	1.169000	0.31871	0.361000	0.24292	0.563000	0.77884	TCC	G|0.848;A|0.152	0.152	strong		0.413	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689	
OR10G8	219869	hgsc.bcm.edu	37	11	123900411	123900411	+	Missense_Mutation	SNP	G	G	A	rs202220125	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123900411G>A	ENST00000431524.1	+	1	115	c.82G>A	c.(82-84)Gtc>Atc	p.V28I		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CCTCTTTGGAGTCTTCCTGGT	0.572													G|||	7	0.00139776	0.0	0.0043	5008	,	,		19799	0.0		0.001	False		,,,				2504	0.0031				p.V28I		Atlas-SNP	.											OR10G8,right_upper_lobe,carcinoma,-2,2	OR10G8	132	2	0			c.G82A						scavenged	.						195.0	177.0	183.0					11																	123900411		2201	4299	6500	SO:0001583	missense	219869	exon1			TTTGGAGTCTTCC	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"""GPCR / Class A : Olfactory receptors"""	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.82G>A	11.37:g.123900411G>A	ENSP00000389072:p.Val28Ile	Somatic	368	0	0		WXS	Illumina HiSeq	Phase_I	457	9	0.0196937	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	G	4.296	0.054107	0.08291	.	.	ENSG00000234560	ENST00000431524	T	0.02916	4.11	2.95	-4.35	0.03656	.	0.824866	0.10366	N	0.683403	T	0.01254	0.0041	N	0.16066	0.365	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48258	-0.9051	10	0.10377	T	0.69	.	1.3401	0.02153	0.2804:0.2787:0.3033:0.1376	.	28	Q8NGN5	O10G8_HUMAN	I	28	ENSP00000389072:V28I	ENSP00000389072:V28I	V	+	1	0	OR10G8	123405621	0.000000	0.05858	0.003000	0.11579	0.022000	0.10575	-3.513000	0.00446	-1.037000	0.03283	-0.324000	0.08512	GTC	G|0.999;A|0.001	0.001	weak		0.572	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
SERPINA10	51156	hgsc.bcm.edu	37	14	94756450	94756450	+	Missense_Mutation	SNP	T	T	A	rs2232700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94756450T>A	ENST00000393096.1	-	2	946	c.481A>T	c.(481-483)Aca>Tca	p.T161S	SERPINA10_ENST00000261994.4_Missense_Mutation_p.T161S|SERPINA10_ENST00000554173.1_Missense_Mutation_p.T161S|SERPINA10_ENST00000554723.1_Missense_Mutation_p.T201S	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	161			T -> S (in dbSNP:rs2232700). {ECO:0000269|PubMed:12975309, ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		CTCCCCTGTGTGAGGCCCAGT	0.517													T|||	1436	0.286741	0.2511	0.134	5008	,	,		18152	0.6042		0.166	False		,,,				2504	0.2403				p.T161S		Atlas-SNP	.											.	SERPINA10	83	.	0			c.A481T						PASS	.	T	SER/THR,SER/THR	993,3413	359.6+/-314.9	110,773,1320	61.0	67.0	65.0		481,481	-9.9	0.0	14	dbSNP_98	65	1413,7187	269.3+/-288.3	125,1163,3012	yes	missense,missense	SERPINA10	NM_001100607.1,NM_016186.2	58,58	235,1936,4332	AA,AT,TT		16.4302,22.5374,18.4992	benign,benign	161/445,161/445	94756450	2406,10600	2203	4300	6503	SO:0001583	missense	51156	exon2			CCTGTGTGAGGCC	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"""Serine (or cysteine) peptidase inhibitors"""	15996	protein-coding gene	gene with protein product		605271	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"""			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.481A>T	14.37:g.94756450T>A	ENSP00000376809:p.Thr161Ser	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Missense_Mutation	SNP	ENST00000393096.1	37	CCDS9923.1	648	0.2967032967032967	130	0.26422764227642276	51	0.1408839779005525	340	0.5944055944055944	127	0.16754617414248021	T	0.270	-0.993593	0.02145	0.225374	0.164302	ENSG00000140093	ENST00000554723;ENST00000393096;ENST00000261994;ENST00000554173	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	4.97	-9.94	0.00449	Serpin domain (3);	1.698980	0.03320	N	0.191763	T	0.00012	0.0000	N	0.01824	-0.7	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.07177	-1.0786	9	0.06891	T	0.86	.	3.7892	0.08713	0.2143:0.1744:0.0749:0.5364	rs2232700;rs52837981;rs2232700	161	Q9UK55	ZPI_HUMAN	S	201;161;161;161	ENSP00000450896:T201S;ENSP00000376809:T161S;ENSP00000261994:T161S;ENSP00000450971:T161S	ENSP00000261994:T161S	T	-	1	0	SERPINA10	93826203	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-1.741000	0.01837	-1.939000	0.01044	-0.736000	0.03550	ACA	T|0.775;N|0.000	.	strong		0.517	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65351074	65351074	+	Silent	SNP	G	G	A	rs10896018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65351074G>A	ENST00000309295.4	+	9	3196	c.2931G>A	c.(2929-2931)gcG>gcA	p.A977A		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	977						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CCCAGGAAGCGGAGGCTGGGG	0.577													G|||	1391	0.277756	0.0658	0.4524	5008	,	,		15972	0.4504		0.2654	False		,,,				2504	0.2751				p.A977A		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G2931A						PASS	.	G		362,3338		27,308,1515	15.0	16.0	16.0		2931	1.6	1.0	11	dbSNP_120	16	2334,5852		344,1646,2103	no	coding-synonymous	EHBP1L1	NM_001099409.1		371,1954,3618	AA,AG,GG		28.5121,9.7838,22.6821		977/1524	65351074	2696,9190	1850	4093	5943	SO:0001819	synonymous_variant	254102	exon9			GGAAGCGGAGGCT	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.2931G>A	11.37:g.65351074G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	121	67	0.553719	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1	645	0.29532967032967034	36	0.07317073170731707	152	0.4198895027624309	256	0.44755244755244755	201	0.26517150395778366	G	4.671	0.124677	0.08931	0.097838	0.285121	ENSG00000173442	ENST00000533465	.	.	.	5.41	1.59	0.23543	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.6000000000016E-5	.	.	.	.	.	.	T	0.47861	-0.9084	3	.	.	.	.	6.7906	0.23697	0.4492:0.465:0.0858:0.0	rs10896018;rs10896018	.	.	.	R	27	.	.	G	+	1	0	EHBP1L1	65107650	0.002000	0.14202	0.994000	0.49952	0.571000	0.35966	0.223000	0.17719	0.017000	0.15025	-0.436000	0.05848	GGA	G|0.705;A|0.295	0.295	strong		0.577	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
AKNA	80709	hgsc.bcm.edu	37	9	117122202	117122202	+	Silent	SNP	C	C	T	rs3748177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:117122202C>T	ENST00000307564.4	-	10	2426	c.2265G>A	c.(2263-2265)gaG>gaA	p.E755E	AKNA_ENST00000223791.3_Silent_p.E215E|AKNA_ENST00000312033.3_Silent_p.E755E|AKNA_ENST00000374075.5_Silent_p.E674E|AKNA_ENST00000374088.3_Silent_p.E755E	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	755					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.E755E(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GGTAAACTTGCTCCATCTGCA	0.612													C|||	1953	0.389976	0.1339	0.4769	5008	,	,		19116	0.3869		0.508	False		,,,				2504	0.5562				p.E755E		Atlas-SNP	.											AKNA,NS,adenoma,0,2	AKNA	119	2	1	Substitution - coding silent(1)	stomach(1)	c.G2265A						PASS	.	C		867,3539	339.9+/-306.0	93,681,1429	99.0	78.0	85.0		2265	2.5	0.8	9	dbSNP_107	85	4578,4022	597.4+/-393.8	1199,2180,921	no	coding-synonymous	AKNA	NM_030767.4		1292,2861,2350	TT,TC,CC		46.7674,19.6777,41.8653		755/1440	117122202	5445,7561	2203	4300	6503	SO:0001819	synonymous_variant	80709	exon10			AACTTGCTCCATC	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.2265G>A	9.37:g.117122202C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	165	71	0.430303	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1																																																																																			C|0.587;T|0.413	0.413	strong		0.612	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
FSD2	123722	hgsc.bcm.edu	37	15	83447631	83447631	+	Missense_Mutation	SNP	T	T	G	rs4779061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:83447631T>G	ENST00000334574.8	-	6	1179	c.998A>C	c.(997-999)aAa>aCa	p.K333T	FSD2_ENST00000541889.1_Missense_Mutation_p.K333T			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	333			K -> T (in dbSNP:rs4779061).							breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						TTTCAGGAATTTCCCGAGTCT	0.438													T|||	907	0.18111	0.0091	0.1902	5008	,	,		16693	0.248		0.16	False		,,,				2504	0.3599				p.K333T		Atlas-SNP	.											.	FSD2	45	.	0			c.A998C						PASS	.	T	THR/LYS	128,3552		3,122,1715	73.0	72.0	73.0		998	4.7	0.2	15	dbSNP_111	73	1352,6848		120,1112,2868	yes	missense	FSD2	NM_001007122.2	78	123,1234,4583	GG,GT,TT		16.4878,3.4783,12.4579	benign	333/750	83447631	1480,10400	1840	4100	5940	SO:0001583	missense	123722	exon6			AGGAATTTCCCGA	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"""Fibronectin type III domain containing"""	18024	protein-coding gene	gene with protein product			"""SPRY domain containing 1"""	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.998A>C	15.37:g.83447631T>G	ENSP00000335651:p.Lys333Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	163	79	0.484663	NM_001007122	B3KVG1|B7ZM02	Missense_Mutation	SNP	ENST00000334574.8	37	CCDS45332.1	336	0.15384615384615385	8	0.016260162601626018	64	0.17679558011049723	140	0.24475524475524477	124	0.16358839050131926	T	7.773	0.707830	0.15239	0.034783	0.164878	ENSG00000186628	ENST00000334574;ENST00000541889	T;T	0.63417	0.33;-0.04	5.8	4.68	0.58851	.	0.396412	0.27673	N	0.018321	T	0.00012	0.0000	N	0.22421	0.69	0.43579	P	0.004086000000000034	B;B	0.29341	0.008;0.242	B;B	0.27380	0.018;0.079	T	0.09228	-1.0684	9	0.29301	T	0.29	-12.4793	11.0617	0.47950	0.0:0.0722:0.0:0.9278	rs4779061;rs58834378;rs4779061	333;333	B7ZM02;A1L4K1	.;FSD2_HUMAN	T	333	ENSP00000335651:K333T;ENSP00000444078:K333T	ENSP00000335651:K333T	K	-	2	0	FSD2	81244685	0.988000	0.35896	0.158000	0.22627	0.350000	0.29205	1.993000	0.40747	1.028000	0.39785	-0.256000	0.11100	AAA	T|0.807;G|0.193	0.193	strong		0.438	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103029516	103029516	+	Missense_Mutation	SNP	A	A	G	rs688906	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:103029516A>G	ENST00000375735.2	+	27	4382	c.4238A>G	c.(4237-4239)aAa>aGa	p.K1413R	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.K1413R	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1413	Stem. {ECO:0000250}.		K -> R (in dbSNP:rs688906). {ECO:0000269|PubMed:8666668}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AGATGTCAGAAATCATTAAAT	0.259													A|||	3347	0.668331	0.4372	0.7464	5008	,	,		12475	0.7827		0.7346	False		,,,				2504	0.7393				p.K1413R		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A4238G						PASS	.	A	ARG/LYS,ARG/LYS	1736,1646		484,768,439	17.0	15.0	16.0		4238,4238	5.8	1.0	11	dbSNP_83	16	5720,1992		2187,1346,323	yes	missense,missense	DYNC2H1	NM_001080463.1,NM_001377.2	26,26	2671,2114,762	GG,GA,AA		25.8299,48.6694,32.7925	benign,benign	1413/4315,1413/4308	103029516	7456,3638	1691	3856	5547	SO:0001583	missense	79659	exon27			GTCAGAAATCATT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.4238A>G	11.37:g.103029516A>G	ENSP00000364887:p.Lys1413Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	129	126	0.976744	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	1497	0.6854395604395604	233	0.4735772357723577	264	0.7292817679558011	443	0.7744755244755245	557	0.7348284960422163	A	13.55	2.269678	0.40095	0.513306	0.741701	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.69806	-0.43;-0.43	5.79	5.79	0.91817	Dynein heavy chain, domain-2 (1);	0.095070	0.38111	U	0.001811	T	0.00012	0.0000	L	0.53617	1.68	0.26152	P	0.9801221	B;P	0.39131	0.329;0.661	B;B	0.39771	0.232;0.309	T	0.44097	-0.9350	9	0.48119	T	0.1	.	12.0109	0.53286	0.9311:0.0:0.0689:0.0	rs688906;rs17099996;rs52820276;rs56690321;rs688906	1413;1413	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	R	1413	ENSP00000364887:K1413R;ENSP00000381167:K1413R	ENSP00000364887:K1413R	K	+	2	0	DYNC2H1	102534726	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.130000	0.57964	2.212000	0.71576	0.533000	0.62120	AAA	A|0.351;G|0.649	0.649	strong		0.259	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
SEC16B	89866	hgsc.bcm.edu	37	1	177905469	177905469	+	Missense_Mutation	SNP	C	C	A	rs7522194	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177905469C>A	ENST00000308284.6	-	20	2624	c.2535G>T	c.(2533-2535)caG>caT	p.Q845H	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	845			Q -> H (in dbSNP:rs7522194). {ECO:0000269|PubMed:17974005}.		COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CATCAGGAGGCTGGGAAGTTT	0.463													C|||	977	0.195088	0.1006	0.2349	5008	,	,		22653	0.1716		0.2624	False		,,,				2504	0.2495				p.Q845H		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2535T						PASS	.	C	HIS/GLN	487,3513		27,433,1540	143.0	138.0	140.0		2535	3.0	0.0	1	dbSNP_116	140	1944,6436		233,1478,2479	yes	missense	SEC16B	NM_033127.2	24	260,1911,4019	AA,AC,CC		23.1981,12.175,19.6365	possibly-damaging	845/1061	177905469	2431,9949	2000	4190	6190	SO:0001583	missense	89866	exon20			AGGAGGCTGGGAA	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2535G>T	1.37:g.177905469C>A	ENSP00000308339:p.Gln845His	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	335	190	0.567164	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	440	0.20146520146520147	48	0.0975609756097561	84	0.23204419889502761	113	0.19755244755244755	195	0.25725593667546176	C	10.30	1.311719	0.23821	0.12175	0.231981	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.15139	2.45	4.88	2.97	0.34412	.	0.682824	0.14155	N	0.337745	T	0.00012	0.0000	M	0.67953	2.075	0.58432	P	1.999999999946489E-6	D;P;P;P	0.67145	0.996;0.93;0.93;0.93	P;P;P;P	0.56700	0.804;0.459;0.459;0.459	T	0.22382	-1.0218	9	0.11485	T	0.65	-1.0168	7.9554	0.30040	0.0:0.8101:0.0:0.1899	rs7522194;rs52799069;rs58699701;rs7522194	400;846;845;542	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	H	845;529;560	ENSP00000308339:Q845H	ENSP00000239472:Q560H	Q	-	3	2	AL359075.1	176172092	0.034000	0.19679	0.005000	0.12908	0.055000	0.15305	1.251000	0.32862	0.744000	0.32741	0.655000	0.94253	CAG	C|0.807;A|0.193	0.193	strong		0.463	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
BAGE2	85319	hgsc.bcm.edu	37	21	11049617	11049617	+	RNA	SNP	C	C	G	rs2740327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:11049617C>G	ENST00000470054.1	-	0	491							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTGCATCTTCCTTCGCTATAA	0.368																																					p.R95T		Atlas-SNP	.											.	.	.	.	0			c.G284C						PASS	.						135.0	96.0	108.0					21																	11049617		692	1591	2283			85318	exon4			ATCTTCCTTCGCT	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11049617C>G		Somatic	482	0	0		WXS	Illumina HiSeq	Phase_I	604	39	0.0645695	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				C|0.994;G|0.006	0.006	strong		0.368	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
MAGEC1	9947	hgsc.bcm.edu	37	X	140993885	140993885	+	Missense_Mutation	SNP	C	C	T	rs74847167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:140993885C>T	ENST00000285879.4	+	4	981	c.695C>T	c.(694-696)cCt>cTt	p.P232L	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	232								p.P232L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					GCCCAGTCTCCTCTCCAGATT	0.488										HNSCC(15;0.026)																											p.P232L		Atlas-SNP	.											.	MAGEC1	317	.	1	Substitution - Missense(1)	skin(1)	c.C695T						PASS	.	C	LEU/PRO	12,3823		0,11,1,1621,570	100.0	96.0	98.0		695		0.1	X	dbSNP_131	98	74,6638		0,69,5,2359,1851	no	missense	MAGEC1	NM_005462.4	98	0,80,6,3980,2421	TT,TC,T,CC,C		1.1025,0.3129,0.8154	benign	232/1143	140993885	86,10461	2203	4284	6487	SO:0001583	missense	9947	exon4			AGTCTCCTCTCCA	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.695C>T	X.37:g.140993885C>T	ENSP00000285879:p.Pro232Leu	Somatic	822	2	0.00243309		WXS	Illumina HiSeq	Phase_I	327	215	0.657492	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	17	0.010247136829415311	0	0.0	5	0.013812154696132596	0	0.0	13	0.017195767195767195	c	5.440	0.266208	0.10294	0.003129	0.011025	ENSG00000155495	ENST00000285879;ENST00000370510	T	0.02216	4.39	.	.	.	.	.	.	.	.	T	0.00637	0.0021	N	0.08118	0	0.23341	N	0.997875	B	0.06786	0.001	B	0.01281	0.0	T	0.47947	-0.9077	8	0.87932	D	0	.	2.6694	0.05063	0.0:0.5025:0.0:0.4974	.	232	O60732	MAGC1_HUMAN	L	232;33	ENSP00000285879:P232L	ENSP00000285879:P232L	P	+	2	0	MAGEC1	140821551	0.002000	0.14202	0.066000	0.19879	0.066000	0.16364	0.991000	0.29654	0.054000	0.16065	0.054000	0.15206	CCT	C|0.989;T|0.011	0.011	strong		0.488	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
INPP5A	3632	hgsc.bcm.edu	37	10	134540400	134540400	+	Silent	SNP	C	C	T	rs945943	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134540400C>T	ENST00000368594.3	+	9	1000	c.723C>T	c.(721-723)tcC>tcT	p.S241S	INPP5A_ENST00000487614.1_3'UTR|INPP5A_ENST00000368593.3_Silent_p.S241S	NM_005539.3	NP_005530.3	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase, 40kDa	241					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|PH domain binding (GO:0042731)			cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		ATTCCAAGTCCGTCGTGGAGG	0.502													C|||	340	0.0678914	0.1316	0.0432	5008	,	,		19605	0.003		0.0775	False		,,,				2504	0.0562				p.S241S	Pancreas(63;823 1267 11107 20380 51626)	Atlas-SNP	.											.	INPP5A	77	.	0			c.C723T						PASS	.	C		535,3871	240.9+/-251.5	39,457,1707	121.0	113.0	116.0		723	-4.2	0.9	10	dbSNP_86	116	745,7855	179.9+/-228.9	27,691,3582	no	coding-synonymous	INPP5A	NM_005539.3		66,1148,5289	TT,TC,CC		8.6628,12.1425,9.8416		241/413	134540400	1280,11726	2203	4300	6503	SO:0001819	synonymous_variant	3632	exon9			CAAGTCCGTCGTG	X77567	CCDS7669.2	10q26.3	2008-08-07	2002-08-29		ENSG00000068383	ENSG00000068383	3.1.3.56		6076	protein-coding gene	gene with protein product	"""CTCL tumor antigen HD-CL-02"", ""43 kDa inositol polyphosphate 5-phophatase"", ""inositol polyphosphate 5-phophatase, 40kDa"", ""InsP3 5-phosphatase"", ""type I inositol-1,4,5-trisphosphate 5-phosphatase"""	600106	"""inositol polyphosphate-5-phosphatase, 40kD"""			8013665	Standard	NM_005539		Approved	5PTASE	uc001llp.3	Q14642	OTTHUMG00000019293	ENST00000368594.3:c.723C>T	10.37:g.134540400C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	106	41	0.386792	NM_005539	D3DXI3|Q14640|Q5JSF1	Silent	SNP	ENST00000368594.3	37	CCDS7669.2	124	0.056776556776556776	48	0.0975609756097561	18	0.049723756906077346	1	0.0017482517482517483	57	0.07519788918205805	C	6.915	0.538493	0.13250	0.121425	0.086628	ENSG00000068383	ENST00000342652	.	.	.	4.17	-4.22	0.03800	.	.	.	.	.	T	0.00384	0.0012	.	.	.	0.09310	P	0.9999999999999446	.	.	.	.	.	.	T	0.21827	-1.0234	3	.	.	.	-8.5713	5.8861	0.18882	0.1336:0.6069:0.0994:0.1601	rs945943;rs2230389;rs60033225;rs945943	.	.	.	C	213	.	.	R	+	1	0	INPP5A	134390390	0.844000	0.29557	0.947000	0.38551	0.718000	0.41266	-0.174000	0.09839	-0.803000	0.04415	-1.513000	0.00942	CGT	C|0.917;T|0.083	0.083	strong		0.502	INPP5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051085.1	NM_005539	
GJD3	125111	hgsc.bcm.edu	37	17	38519831	38519831	+	Silent	SNP	G	G	T	rs141158879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38519831G>T	ENST00000578689.1	-	1	236	c.237C>A	c.(235-237)ctC>ctA	p.L79L	CTD-2267D19.3_ENST00000578774.1_Nonsense_Mutation_p.E215*|GJD3_ENST00000337376.4_Silent_p.L79L	NM_152219.3	NP_689343.3	Q8N144	CXD3_HUMAN	gap junction protein, delta 3, 31.9kDa	79					cell communication (GO:0007154)|gap junction assembly (GO:0016264)	cell surface (GO:0009986)|connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)						Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)			GGATGTGGAAGAGCCAGAAGC	0.682													G|||	29	0.00579073	0.0008	0.0086	5008	,	,		10470	0.0		0.0159	False		,,,				2504	0.0061				p.L79L		Atlas-SNP	.											.	GJD3	2	.	0			c.C237A						PASS	.	G		19,4233		0,19,2107	24.0	34.0	31.0		237	0.9	1.0	17	dbSNP_134	31	170,8320		2,166,4077	no	coding-synonymous	GJD3	NM_152219.3		2,185,6184	TT,TG,GG		2.0024,0.4468,1.4833		79/295	38519831	189,12553	2126	4245	6371	SO:0001819	synonymous_variant	125111	exon1			GTGGAAGAGCCAG	AF514298	CCDS58547.1	17q21.1	2012-04-19	2007-11-06	2007-11-06	ENSG00000183153	ENSG00000183153		"""Ion channels / Gap junction proteins (connexins)"""	19147	protein-coding gene	gene with protein product	"""connexin 31.9"""	607425	"""gap junction protein, chi 1, 31.9kDa"""	GJC1		12176752	Standard	NM_152219		Approved	CX31.9, GJA11, Cx30.2	uc010cwz.3	Q8N144		ENST00000578689.1:c.237C>A	17.37:g.38519831G>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_152219	Q6ZUW6	Silent	SNP	ENST00000578689.1	37	CCDS58547.1																																																																																			G|0.992;T|0.008	0.008	strong		0.682	GJD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447449.1	NM_152219	
CHORDC1	26973	hgsc.bcm.edu	37	11	89935586	89935586	+	Missense_Mutation	SNP	G	G	T	rs1045861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:89935586G>T	ENST00000320585.6	-	11	1395	c.986C>A	c.(985-987)gCc>gAc	p.A329D	CHORDC1_ENST00000529726.1_Missense_Mutation_p.A141D|CHORDC1_ENST00000457199.2_Missense_Mutation_p.A310D|CHORDC1_ENST00000529987.1_Missense_Mutation_p.A141D	NM_012124.2	NP_036256.2	Q9UHD1	CHRD1_HUMAN	cysteine and histidine-rich domain (CHORD) containing 1	329			A -> D (in dbSNP:rs1045861). {ECO:0000269|PubMed:10571178, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2, ECO:0000269|Ref.5}.		chaperone-mediated protein folding (GO:0061077)|negative regulation of Rho-dependent protein serine/threonine kinase activity (GO:2000299)|regulation of cellular response to heat (GO:1900034)|regulation of centrosome duplication (GO:0010824)|response to stress (GO:0006950)		Hsp90 protein binding (GO:0051879)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(1)|lung(6)	11		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.00915)				ATCTGTTGTGGCATCTTTTTG	0.403													T|||	3057	0.610423	0.3714	0.6542	5008	,	,		19227	0.6756		0.6958	False		,,,				2504	0.7474				p.A329D		Atlas-SNP	.											.	CHORDC1	34	.	0			c.C986A						PASS	.	T	ASP/ALA,ASP/ALA	1817,2583	637.6+/-396.8	384,1049,767	126.0	105.0	112.0		929,986	4.1	0.7	11	dbSNP_86	112	5977,2619	422.7+/-354.1	2062,1853,383	yes	missense,missense	CHORDC1	NM_001144073.1,NM_012124.2	126,126	2446,2902,1150	TT,TG,GG		30.4677,41.2955,40.0277	benign,benign	310/314,329/333	89935586	7794,5202	2200	4298	6498	SO:0001583	missense	26973	exon11			GTTGTGGCATCTT	AF192466	CCDS8289.1, CCDS44705.1	11q14.3	2011-01-25	2011-01-25		ENSG00000110172	ENSG00000110172			14525	protein-coding gene	gene with protein product		604353	"""cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"", ""cysteine and histidine-rich domain (CHORD)-containing 1"""			10571178	Standard	NM_012124		Approved	CHP1	uc001pdg.2	Q9UHD1	OTTHUMG00000167305	ENST00000320585.6:c.986C>A	11.37:g.89935586G>T	ENSP00000319255:p.Ala329Asp	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	251	248	0.988048	NM_012124	B2R6P8|Q6IN49|Q8WVL9|Q9H3D6	Missense_Mutation	SNP	ENST00000320585.6	37	CCDS8289.1	1385	0.6341575091575091	203	0.41260162601626016	247	0.6823204419889503	411	0.7185314685314685	524	0.6912928759894459	T	0.115	-1.133751	0.01756	0.412955	0.695323	ENSG00000110172	ENST00000320585;ENST00000529987;ENST00000457199;ENST00000529726	T;T;T;T	0.43294	0.96;0.95;0.95;0.95	5.24	4.08	0.47627	HSP20-like chaperone (1);	1.095060	0.06902	N	0.806057	T	0.00012	0.0000	N	0.02011	-0.69	0.09310	P	0.99999999876564	B;B	0.13145	0.007;0.0	B;B	0.06405	0.002;0.0	T	0.44907	-0.9297	8	.	.	.	0.1129	11.064	0.47964	0.0:0.0:0.2982:0.7018	rs1045861;rs3185831;rs52803502;rs1045861	310;329	Q9UHD1-2;Q9UHD1	.;CHRD1_HUMAN	D	329;141;310;141	ENSP00000319255:A329D;ENSP00000433719:A141D;ENSP00000401080:A310D;ENSP00000436632:A141D	.	A	-	2	0	CHORDC1	89575234	0.036000	0.19791	0.718000	0.30602	0.172000	0.22775	1.500000	0.35682	0.292000	0.22492	-0.262000	0.10625	GCC	G|0.384;T|0.616	0.616	strong		0.403	CHORDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394111.1	NM_012124	
USH2A	7399	hgsc.bcm.edu	37	1	216462662	216462662	+	Missense_Mutation	SNP	T	T	A	rs1805048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:216462662T>A	ENST00000307340.3	-	11	2317	c.1931A>T	c.(1930-1932)gAt>gTt	p.D644V	USH2A_ENST00000366942.3_Missense_Mutation_p.D644V|USH2A_ENST00000366943.2_Missense_Mutation_p.D644V	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	644	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.		D -> V (in dbSNP:rs1805048). {ECO:0000269|PubMed:10738000, ECO:0000269|PubMed:15025721, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GCCAACTGTATCACAGTCACA	0.428										HNSCC(13;0.011)			T|||	173	0.0345447	0.0015	0.0389	5008	,	,		18077	0.001		0.0825	False		,,,				2504	0.0613				p.D644V		Atlas-SNP	.											.	USH2A	1168	.	0			c.A1931T						PASS	.	T	VAL/ASP,VAL/ASP	68,4338	62.3+/-99.4	0,68,2135	171.0	149.0	156.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1931,1931	5.4	0.7	1	dbSNP_89	156	719,7881	176.5+/-226.3	29,661,3610	yes	missense,missense	USH2A	NM_007123.5,NM_206933.2	152,152	29,729,5745	AA,AT,TT		8.3605,1.5433,6.0511	benign,benign	644/1547,644/5203	216462662	787,12219	2203	4300	6503	SO:0001583	missense	7399	exon11			ACTGTATCACAGT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1931A>T	1.37:g.216462662T>A	ENSP00000305941:p.Asp644Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	142	73	0.514085	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	82	0.037545787545787544	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	61	0.08047493403693931	T	14.76	2.630858	0.46944	0.015433	0.083605	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.63913	-0.07;-0.07;-0.07	5.43	5.43	0.79202	EGF-like, laminin (3);	0.350840	0.20317	N	0.094708	T	0.09642	0.0237	M	0.76838	2.35	0.19300	P	0.9999778724	B;P	0.38677	0.171;0.642	B;B	0.40741	0.061;0.339	T	0.53732	-0.8397	9	0.20046	T	0.44	.	15.7848	0.78294	0.0:0.0:0.0:1.0	rs1805048;rs52816485	644;644	O75445-2;O75445	.;USH2A_HUMAN	V	644	ENSP00000305941:D644V;ENSP00000355910:D644V;ENSP00000355909:D644V	ENSP00000305941:D644V	D	-	2	0	USH2A	214529285	0.976000	0.34144	0.664000	0.29753	0.664000	0.39144	7.118000	0.77137	2.190000	0.69967	0.455000	0.32223	GAT	T|0.942;A|0.058	0.058	strong		0.428	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
ASGR2	433	hgsc.bcm.edu	37	17	7012079	7012079	+	Missense_Mutation	SNP	C	C	T	rs2304978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7012079C>T	ENST00000380952.2	-	3	517	c.253G>A	c.(253-255)Ggg>Agg	p.G85R	ASGR2_ENST00000355035.5_Missense_Mutation_p.G85R|ASGR2_ENST00000446679.2_Missense_Mutation_p.G66R|ASGR2_ENST00000254850.7_Intron	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	85			G -> R (in dbSNP:rs2304978). {ECO:0000269|PubMed:1371982, ECO:0000269|PubMed:3863106, ECO:0000269|Ref.4}.		bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)	p.G85R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	TGCTGGCCCCCGTGACCCTCA	0.637													T|||	1277	0.254992	0.0703	0.3689	5008	,	,		14768	0.2887		0.2724	False		,,,				2504	0.3712				p.G85R		Atlas-SNP	.											ASGR2,NS,carcinoma,0,2	ASGR2	38	2	1	Substitution - Missense(1)	stomach(1)	c.G253A						PASS	.	T	ARG/GLY,,ARG/GLY,,ARG/GLY	476,3930	778.9+/-414.3	30,416,1757	67.0	59.0	62.0		253,,253,,196	0.4	0.0	17	dbSNP_100	62	2435,6165	692.5+/-404.6	362,1711,2227	yes	missense,intron,missense,intron,missense	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	125,,125,,125	392,2127,3984	TT,TC,CC		28.314,10.8034,22.382	benign,,benign,,benign	85/312,,85/312,,66/293	7012079	2911,10095	2203	4300	6503	SO:0001583	missense	433	exon3			GGCCCCCGTGACC	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.253G>A	17.37:g.7012079C>T	ENSP00000370339:p.Gly85Arg	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	188	86	0.457447	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Missense_Mutation	SNP	ENST00000380952.2	37	CCDS32544.1	519	0.23763736263736263	30	0.06097560975609756	125	0.3453038674033149	155	0.270979020979021	209	0.2757255936675462	T	0.718	-0.784581	0.02907	0.108034	0.28314	ENSG00000161944	ENST00000355035;ENST00000380952;ENST00000446679	T;T;T	0.00776	5.71;5.71;5.74	1.92	0.39	0.16275	Hepatic lectin, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17258	-1.0375	8	0.15066	T	0.55	.	1.9813	0.03427	0.3715:0.1682:0.0:0.4603	rs2304978	85;66	P07307;P07307-2	ASGR2_HUMAN;.	R	85;85;66	ENSP00000347140:G85R;ENSP00000370339:G85R;ENSP00000405844:G66R	ENSP00000347140:G85R	G	-	1	0	ASGR2	6952803	0.000000	0.05858	0.001000	0.08648	0.543000	0.35085	-0.348000	0.07740	-0.404000	0.07610	-0.326000	0.08463	GGG	C|0.777;T|0.223	0.223	strong		0.637	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	
CD300LB	124599	hgsc.bcm.edu	37	17	72521897	72521897	+	Silent	SNP	G	G	A	rs17553512	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72521897G>A	ENST00000392621.1	-	2	475	c.471C>T	c.(469-471)atC>atT	p.I157I	CD300LB_ENST00000314401.3_Silent_p.I157I	NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	120					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						CTGGGTCAACGATCACTTTCA	0.532													G|||	1534	0.30631	0.0371	0.3818	5008	,	,		17346	0.2242		0.5497	False		,,,				2504	0.4509				p.I157I		Atlas-SNP	.											.	CD300LB	38	.	0			c.C471T						PASS	.	G		533,3873	241.5+/-251.9	37,459,1707	155.0	143.0	147.0		471	-3.6	0.0	17	dbSNP_123	147	4712,3888	607.7+/-395.3	1285,2142,873	no	coding-synonymous	CD300LB	NM_174892.2		1322,2601,2580	AA,AG,GG		45.2093,12.0971,40.3275		157/239	72521897	5245,7761	2203	4300	6503	SO:0001819	synonymous_variant	124599	exon2			GTCAACGATCACT	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"""Immunoglobulin superfamily / V-set domain containing"""	30811	protein-coding gene	gene with protein product	"""triggering receptor expressed on myeloid cells 5"""	610705	"""CD300 antigen like family member B"""			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.471C>T	17.37:g.72521897G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Silent	SNP	ENST00000392621.1	37	CCDS11700.1																																																																																			G|0.609;A|0.391	0.391	strong		0.532	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892	
PRKD2	25865	hgsc.bcm.edu	37	19	47219450	47219450	+	Silent	SNP	A	A	G	rs56034494	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47219450A>G	ENST00000291281.4	-	1	403	c.178T>C	c.(178-180)Ttg>Ctg	p.L60L	PRKD2_ENST00000595515.1_Silent_p.L60L|PRKD2_ENST00000600194.1_5'Flank|PRKD2_ENST00000433867.1_Silent_p.L60L|PRKD2_ENST00000601806.1_5'UTR			Q9BZL6	KPCD2_HUMAN	protein kinase D2	60					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GCGGCGGGCAACAGCACGAAC	0.672													a|||	48	0.00958466	0.0008	0.0259	5008	,	,		12212	0.0		0.0258	False		,,,				2504	0.0031				p.L60L		Atlas-SNP	.											.	PRKD2	94	.	0			c.T178C						PASS	.		,,	19,4375		0,19,2178	28.0	33.0	31.0		178,178,178	-4.3	0.9	19	dbSNP_129	31	244,8336		1,242,4047	no	coding-synonymous,coding-synonymous,coding-synonymous	PRKD2	NM_001079880.1,NM_001079881.1,NM_016457.4	,,	1,261,6225	GG,GA,AA		2.8438,0.4324,2.0271	,,	60/879,60/879,60/879	47219450	263,12711	2197	4290	6487	SO:0001819	synonymous_variant	25865	exon1			CGGGCAACAGCAC	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"""Pleckstrin homology (PH) domain containing"""	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.178T>C	19.37:g.47219450A>G		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	194	76	0.391753	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Silent	SNP	ENST00000291281.4	37	CCDS12689.1																																																																																			A|0.980;G|0.020	0.020	strong		0.672	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457	
FAT4	79633	hgsc.bcm.edu	37	4	126241253	126241253	+	Silent	SNP	G	G	C	rs7657251	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:126241253G>C	ENST00000394329.3	+	1	3700	c.3687G>C	c.(3685-3687)gtG>gtC	p.V1229V		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1229	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TGACACAAGTGTTAAGAGTAT	0.318													G|||	322	0.0642971	0.0688	0.0648	5008	,	,		21164	0.001		0.1322	False		,,,				2504	0.0532				p.V1229V		Atlas-SNP	.											.	FAT4	1752	.	0			c.G3687C						PASS	.	G		288,3390		10,268,1561	46.0	45.0	45.0		3687	-3.9	0.7	4	dbSNP_116	45	1044,7128		66,912,3108	no	coding-synonymous	FAT4	NM_024582.4		76,1180,4669	CC,CG,GG		12.7753,7.8303,11.2405		1229/4982	126241253	1332,10518	1839	4086	5925	SO:0001819	synonymous_variant	79633	exon1			ACAAGTGTTAAGA	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.3687G>C	4.37:g.126241253G>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			G|0.905;C|0.095	0.095	strong		0.318	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
CCDC33	80125	hgsc.bcm.edu	37	15	74622533	74622533	+	Missense_Mutation	SNP	A	A	G	rs2277603	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:74622533A>G	ENST00000398814.3	+	12	1725	c.1294A>G	c.(1294-1296)Atg>Gtg	p.M432V	CCDC33_ENST00000268082.4_Missense_Mutation_p.M25V|CCDC33_ENST00000321288.5_Missense_Mutation_p.M635V|CCDC33_ENST00000558821.1_Missense_Mutation_p.M25V	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	635										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						TCCACAGGAGATGAACAACTA	0.582													A|||	602	0.120208	0.0121	0.0692	5008	,	,		18218	0.2222		0.0875	False		,,,				2504	0.2311				p.M432V		Atlas-SNP	.											.	CCDC33	160	.	0			c.A1294G						PASS	.	A	VAL/MET,VAL/MET	99,3977		2,95,1941	40.0	44.0	42.0		1294,73	-2.5	0.6	15	dbSNP_100	42	791,7553		36,719,3417	yes	missense,missense	CCDC33	NM_025055.3,NM_182791.2	21,21	38,814,5358	GG,GA,AA		9.4799,2.4289,7.1659	benign,benign	432/756,25/368	74622533	890,11530	2038	4172	6210	SO:0001583	missense	80125	exon12			CAGGAGATGAACA	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1294A>G	15.37:g.74622533A>G	ENSP00000381795:p.Met432Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	199	88	0.442211	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	218	0.09981684981684982	9	0.018292682926829267	37	0.10220994475138122	111	0.19405594405594406	61	0.08047493403693931	A	3.593	-0.083181	0.07141	0.024289	0.094799	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.34667	1.35;2.33;1.97;1.95	4.3	-2.45	0.06481	.	0.524699	0.20717	N	0.086996	T	0.00039	0.0001	M	0.70595	2.14	0.58432	P	5.000000000032756E-6	B;B;B;B	0.27351	0.065;0.081;0.176;0.038	B;B;B;B	0.20577	0.022;0.03;0.025;0.015	T	0.10800	-1.0614	9	0.62326	D	0.03	.	0.5572	0.00673	0.249:0.1459:0.1791:0.4261	rs2277603;rs56484983;rs56997916;rs2277603	25;25;635;432	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	V	635;432;25;25	ENSP00000325012:M635V;ENSP00000381795:M432V;ENSP00000325661:M25V;ENSP00000268082:M25V	ENSP00000268082:M25V	M	+	1	0	CCDC33	72409586	0.003000	0.15002	0.612000	0.29024	0.021000	0.10359	-0.893000	0.04127	-0.324000	0.08589	-0.353000	0.07706	ATG	A|0.887;G|0.113;T|0.000	0.113	strong		0.582	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
ANO9	338440	hgsc.bcm.edu	37	11	421036	421036	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:421036C>T	ENST00000332826.6	-	17	1483	c.1399G>A	c.(1399-1401)Gcc>Acc	p.A467T		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	467					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						CAGCCGCTGGCGTGGCACTGC	0.652																																					p.A467T		Atlas-SNP	.											.	ANO9	61	.	0			c.G1399A						PASS	.						24.0	26.0	26.0					11																	421036		2200	4297	6497	SO:0001583	missense	338440	exon17			CGCTGGCGTGGCA	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	20679	protein-coding gene	gene with protein product			"""tumor protein p53 inducible protein 5"", ""transmembrane protein 16J"""	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.1399G>A	11.37:g.421036C>T	ENSP00000332788:p.Ala467Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	37	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532417	0.85812	.	.	ENSG00000185101	ENST00000332826	T	0.63255	-0.03	3.99	3.06	0.35304	.	0.419080	0.22997	N	0.053128	T	0.56949	0.2020	L	0.46157	1.445	0.80722	D	1	P;P	0.49961	0.903;0.93	B;B	0.43194	0.215;0.411	T	0.61242	-0.7102	10	0.62326	D	0.03	.	13.5161	0.61541	0.0:0.1658:0.8342:0.0	.	168;467	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	T	467	ENSP00000332788:A467T	ENSP00000332788:A467T	A	-	1	0	ANO9	411036	1.000000	0.71417	0.971000	0.41717	0.933000	0.57130	6.568000	0.73987	0.789000	0.33779	0.306000	0.20318	GCC	.	.	none		0.652	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302	
UNC13C	440279	hgsc.bcm.edu	37	15	54847677	54847677	+	Silent	SNP	C	C	T	rs11639005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:54847677C>T	ENST00000260323.11	+	28	5925	c.5925C>T	c.(5923-5925)tgC>tgT	p.C1975C	UNC13C_ENST00000537900.1_Silent_p.C1973C|UNC13C_ENST00000545554.1_Silent_p.C1975C	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1975	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CAAGACAATGCGCTATAATGG	0.453													C|||	2050	0.409345	0.1233	0.464	5008	,	,		18348	0.5427		0.4423	False		,,,				2504	0.5859				p.C1975C		Atlas-SNP	.											.	UNC13C	674	.	0			c.C5925T						PASS	.	C		680,3214		57,566,1324	80.0	77.0	78.0		5925	-4.4	0.0	15	dbSNP_120	78	3562,4696		787,1988,1354	no	coding-synonymous	UNC13C	NM_001080534.1		844,2554,2678	TT,TC,CC		43.1339,17.4628,34.9078		1975/2215	54847677	4242,7910	1947	4129	6076	SO:0001819	synonymous_variant	440279	exon27			ACAATGCGCTATA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5925C>T	15.37:g.54847677C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																			C|0.625;T|0.375	0.375	strong		0.453	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
SCAMP2	10066	hgsc.bcm.edu	37	15	75146371	75146371	+	Silent	SNP	C	C	T	rs77456595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75146371C>T	ENST00000268099.9	-	3	325	c.216G>A	c.(214-216)ccG>ccA	p.P72P		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	72					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						CCTGGGGGGTCGGCTGGGTTG	0.572													C|||	74	0.0147764	0.0023	0.0216	5008	,	,		17320	0.001		0.0487	False		,,,				2504	0.0061				p.P72P		Atlas-SNP	.											.	SCAMP2	18	.	0			c.G216A						PASS	.	C		43,4351	45.3+/-79.5	0,43,2154	88.0	85.0	86.0		216	-3.6	0.0	15	dbSNP_131	86	386,8204	125.5+/-184.1	13,360,3922	no	coding-synonymous	SCAMP2	NM_005697.3		13,403,6076	TT,TC,CC		4.4936,0.9786,3.3041		72/330	75146371	429,12555	2197	4295	6492	SO:0001819	synonymous_variant	10066	exon3			GGGGGTCGGCTGG	AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"""Secretory carrier membrane proteins"""	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.216G>A	15.37:g.75146371C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_005697	B2RDF0|Q9BQE8	Silent	SNP	ENST00000268099.9	37	CCDS10271.1																																																																																			C|0.967;T|0.033	0.033	strong		0.572	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697	
PRRC2A	7916	hgsc.bcm.edu	37	6	31598489	31598489	+	Silent	SNP	A	A	G	rs372791429|rs551644506|rs3130626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31598489A>G	ENST00000376033.2	+	15	2610	c.2376A>G	c.(2374-2376)gtA>gtG	p.V792V	PRRC2A_ENST00000376007.4_Silent_p.V792V	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	792	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TGGCCTGGGTAGGAGATGTCT	0.602													A|||	663	0.132388	0.2103	0.0793	5008	,	,		16570	0.0704		0.1451	False		,,,				2504	0.1155				p.V792V		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A2376G						PASS	.						84.0	74.0	77.0					6																	31598489		2203	4300	6503	SO:0001819	synonymous_variant	7916	exon15			CTGGGTAGGAGAT	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.2376A>G	6.37:g.31598489A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	230	114	0.495652	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			A|0.858;G|0.142	0.142	strong		0.602	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
MDN1	23195	hgsc.bcm.edu	37	6	90368380	90368380	+	Silent	SNP	G	G	A	rs34732313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90368380G>A	ENST00000369393.3	-	89	15085	c.14970C>T	c.(14968-14970)gcC>gcT	p.A4990A	MDN1_ENST00000428876.1_Silent_p.A4990A			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4990					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTTCTTCATCGGCTTCCTTGT	0.488													G|||	521	0.104034	0.0605	0.085	5008	,	,		20043	0.0476		0.1581	False		,,,				2504	0.1789				p.A4990A		Atlas-SNP	.											.	MDN1	478	.	0			c.C14970T						PASS	.	G		278,4128	153.3+/-186.9	11,256,1936	235.0	208.0	217.0		14970	-2.2	0.0	6	dbSNP_126	217	1240,7360	248.6+/-276.2	102,1036,3162	no	coding-synonymous	MDN1	NM_014611.1		113,1292,5098	AA,AG,GG		14.4186,6.3096,11.6715		4990/5597	90368380	1518,11488	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon89			TTCATCGGCTTCC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14970C>T	6.37:g.90368380G>A		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	215	101	0.469767	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			G|0.886;A|0.114	0.114	strong		0.488	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
EDA2R	60401	hgsc.bcm.edu	37	X	65822607	65822607	+	Missense_Mutation	SNP	T	T	C	rs1385698	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:65822607T>C	ENST00000374719.3	-	5	441	c.385A>G	c.(385-387)Aca>Gca	p.T129A	EDA2R_ENST00000253392.5_Missense_Mutation_p.T129A|EDA2R_ENST00000451436.2_Missense_Mutation_p.Y35C|EDA2R_ENST00000456230.2_Missense_Mutation_p.T129A|EDA2R_ENST00000450752.1_Missense_Mutation_p.T129A|EDA2R_ENST00000396050.1_Missense_Mutation_p.T129A	NM_021783.3	NP_068555	Q9HAV5	TNR27_HUMAN	ectodysplasin A2 receptor	129			T -> A (in dbSNP:rs1385698). {ECO:0000269|PubMed:11039935, ECO:0000269|PubMed:12270937, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|embryo development (GO:0009790)|epidermis development (GO:0008544)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						ACTGTGGGTGTATCTGCCTCC	0.557													C|||	3507	0.929007	0.5628	0.7421	3775	,	,		12740	0.7579		0.7614	False		,,,				2504	0.7342				p.T129A		Atlas-SNP	.											.	EDA2R	30	.	0			c.A385G						PASS	.	C	ALA/THR,ALA/THR,ALA/THR	2985,850		988,571,438,73,133	47.0	32.0	37.0		385,385,385	3.5	0.3	X	dbSNP_88	37	6723,3		2425,3,1870,0,0	yes	missense,missense,missense	EDA2R	NM_001199687.2,NM_001242310.1,NM_021783.3	58,58,58	3413,574,2308,73,133	CC,CT,C,TT,T		0.0446,22.1643,8.0769	benign,benign,benign	129/298,129/319,129/298	65822607	9708,853	2203	4298	6501	SO:0001583	missense	60401	exon4			TGGGTGTATCTGC	AF298812	CCDS14386.1, CCDS56603.1	Xq11.1	2013-05-22			ENSG00000131080	ENSG00000131080		"""Tumor necrosis factor receptor superfamily"""	17756	protein-coding gene	gene with protein product		300276				11039935	Standard	NM_021783		Approved	XEDAR, EDA-A2R, EDAA2R, TNFRSF27	uc004dwt.2	Q9HAV5	OTTHUMG00000021736	ENST00000374719.3:c.385A>G	X.37:g.65822607T>C	ENSP00000363851:p.Thr129Ala	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_001242310	Q5VYX9|Q5VYY0|Q6UWM2|Q8IZA6	Missense_Mutation	SNP	ENST00000374719.3	37	CCDS14386.1	1579|1579	0.9517781796262809|0.9517781796262809	214|214	0.6772151898734177|0.6772151898734177	183|183	0.9631578947368421|0.9631578947368421	284|284	1.0|1.0	402|402	1.0|1.0	C|C	9.631|9.631	1.136502|1.136502	0.21123|0.21123	0.778357|0.778357	0.999554|0.999554	ENSG00000131080|ENSG00000131080	ENST00000374719;ENST00000396050;ENST00000253392;ENST00000456230;ENST00000450752|ENST00000451436	D;D;D;D;D|.	0.83992|.	-1.77;-1.77;-1.79;-1.77;-1.79|.	4.37|4.37	3.49|3.49	0.39957|0.39957	.|.	1.140990|.	0.06815|.	N|.	0.791176|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	P|P	0.0|0.0	B;B|B	0.02656|0.02656	0.0;0.0|0.0	B;B|B	0.01281|0.01281	0.0;0.0|0.0	T|T	0.23691|0.23691	-1.0181|-1.0181	9|7	0.07325|0.42905	T|T	0.83|0.14	1.5124|1.5124	6.8935|6.8935	0.24243|0.24243	0.0:0.771:0.0:0.229|0.0:0.771:0.0:0.229	rs1385698;rs17846114;rs17859117;rs52809928;rs1385698|rs1385698;rs17846114;rs17859117;rs52809928;rs1385698	129;129|35	Q9HAV5-2;Q9HAV5|E7EUS4	.;TNR27_HUMAN|.	A|C	129|35	ENSP00000363851:T129A;ENSP00000379365:T129A;ENSP00000253392:T129A;ENSP00000393935:T129A;ENSP00000402929:T129A|.	ENSP00000253392:T129A|ENSP00000415242:Y35C	T|Y	-|-	1|2	0|0	EDA2R|EDA2R	65739332|65739332	0.000000|0.000000	0.05858|0.05858	0.301000|0.301000	0.25044|0.25044	0.845000|0.845000	0.48019|0.48019	-0.049000|-0.049000	0.11924|0.11924	0.170000|0.170000	0.19704|0.19704	-0.170000|-0.170000	0.13304|0.13304	ACA|TAC	T|0.073;C|0.927	0.927	strong		0.557	EDA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057002.1	NM_021783	
LAD1	3898	hgsc.bcm.edu	37	1	201355761	201355761	+	Missense_Mutation	SNP	A	A	G	rs12088790	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201355761A>G	ENST00000391967.2	-	3	1029	c.728T>C	c.(727-729)cTg>cCg	p.L243P	LAD1_ENST00000367313.3_Missense_Mutation_p.L257P	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	243	8 X SEK repeats.		L -> P (in dbSNP:rs12088790).			basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						CCCTGGGGCCAGCGACTTCTC	0.498													G|||	607	0.121206	0.3729	0.0447	5008	,	,		15951	0.0387		0.0288	False		,,,				2504	0.0153				p.L243P		Atlas-SNP	.											.	LAD1	42	.	0			c.T728C						PASS	.	G	PRO/LEU	1454,2952	662.5+/-401.1	249,956,998	80.0	92.0	88.0		728	0.8	0.0	1	dbSNP_120	88	251,8349	789.7+/-407.6	4,243,4053	yes	missense	LAD1	NM_005558.3	98	253,1199,5051	GG,GA,AA		2.9186,33.0005,13.1093	benign	243/518	201355761	1705,11301	2203	4300	6503	SO:0001583	missense	3898	exon3			GGGGCCAGCGACT	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.728T>C	1.37:g.201355761A>G	ENSP00000375829:p.Leu243Pro	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	37	CCDS1410.1	264	0.12087912087912088	206	0.4186991869918699	15	0.04143646408839779	20	0.03496503496503497	23	0.030343007915567283	G	7.155	0.584525	0.13749	0.330005	0.029186	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.13420	2.61;2.59	4.68	0.8	0.18672	.	1.153610	0.06298	N	0.700343	T	0.00012	0.0000	N	0.02736	-0.51	0.80722	P	0.0	B;B	0.11235	0.0;0.004	B;B	0.11329	0.0;0.006	T	0.48714	-0.9011	9	0.23891	T	0.37	-2.0073	7.8079	0.29213	0.4656:0.0:0.5344:0.0	rs12088790;rs52800581;rs12088790	257;243	E9PDI4;O00515	.;LAD1_HUMAN	P	243;257	ENSP00000375829:L243P;ENSP00000356282:L257P	ENSP00000356282:L257P	L	-	2	0	LAD1	199622384	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.524000	0.06222	0.012000	0.14892	-0.282000	0.10007	CTG	A|0.884;G|0.116	0.116	strong		0.498	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
MCC	4163	hgsc.bcm.edu	37	5	112384802	112384802	+	Silent	SNP	G	G	A	rs6594664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:112384802G>A	ENST00000302475.4	-	14	2636	c.2073C>T	c.(2071-2073)gaC>gaT	p.D691D	MCC_ENST00000408903.3_Silent_p.D881D|MCC_ENST00000515367.2_Silent_p.D628D|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	691					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		TGCCAGGTTTGTCTTTGCTGC	0.627													G|||	4324	0.863419	0.5923	0.9539	5008	,	,		19336	0.9405		0.9642	False		,,,				2504	0.9826				p.D881D		Atlas-SNP	.											.	MCC	234	.	0			c.C2643T						PASS	.	G	,	2773,1631	658.7+/-400.4	884,1005,313	92.0	84.0	86.0		2643,2073	1.8	0.8	5	dbSNP_116	86	8380,220	808.8+/-407.2	4083,214,3	no	coding-synonymous,coding-synonymous	MCC	NM_001085377.1,NM_002387.2	,	4967,1219,316	AA,AG,GG		2.5581,37.0345,14.2341	,	881/1020,691/830	112384802	11153,1851	2202	4300	6502	SO:0001819	synonymous_variant	4163	exon16			AGGTTTGTCTTTG		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.2073C>T	5.37:g.112384802G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																			G|0.141;A|0.859	0.859	strong		0.627	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
NRG1	3084	hgsc.bcm.edu	37	8	32505822	32505822	+	Intron	SNP	C	C	T	rs201098616		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:32505822C>T	ENST00000405005.3	+	5	502				NRG1_ENST00000519301.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000520502.2_Missense_Mutation_p.R196W|NRG1_ENST00000520407.1_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000287845.5_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TTCACCCACCCGGAACCCTGA	0.493																																					p.R196W		Atlas-SNP	.											NRG1_ENST00000520502,rectum,carcinoma,-1,1	NRG1	260	1	0			c.C586T						scavenged	.						123.0	102.0	109.0					8																	32505822		2203	4300	6503	SO:0001627	intron_variant	3084	exon1			CCCACCCGGAACC	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.502+31419C>T	8.37:g.32505822C>T		Somatic	250	2	0.008		WXS	Illumina HiSeq	Phase_I	261	3	0.0114943	NM_013959	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181146	0.57800	.	.	ENSG00000157168	ENST00000520502;ENST00000523041	.	.	.	5.77	4.88	0.63580	.	.	.	.	.	T	0.48822	0.1521	N	0.19112	0.55	0.80722	D	1	D;D	0.60160	0.987;0.987	P;P	0.50896	0.653;0.653	T	0.56294	-0.8003	8	0.87932	D	0	.	15.3105	0.74028	0.0:0.8606:0.1394:0.0	.	196;196	Q53F54;Q02297-10	.;.	W	196;156	.	ENSP00000433289:R196W	R	+	1	2	NRG1	32625364	0.992000	0.36948	0.762000	0.31397	0.858000	0.48976	3.057000	0.49931	1.537000	0.49254	0.655000	0.94253	CGG	.	.	weak		0.493	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
CYP2A6	1548	hgsc.bcm.edu	37	19	41351211	41351211	+	Silent	SNP	G	G	A	rs150586234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41351211G>A	ENST00000301141.5	-	7	1169	c.1149C>T	c.(1147-1149)ttC>ttT	p.F383F	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	383					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TAGGGAGGAAGAAATCCCGAA	0.552													.|||	8	0.00159744	0.0	0.0029	5008	,	,		16324	0.0		0.006	False		,,,				2504	0.0				p.F383F		Atlas-SNP	.											.	CYP2A6	69	.	0			c.C1149T						PASS	.						101.0	99.0	100.0					19																	41351211		2203	4300	6503	SO:0001819	synonymous_variant	1548	exon7			GAGGAAGAAATCC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1149C>T	19.37:g.41351211G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	235	18	0.0765957	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Silent	SNP	ENST00000301141.5	37	CCDS12568.1																																																																																			G|0.998;A|0.002	0.002	strong		0.552	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
FAM184A	79632	hgsc.bcm.edu	37	6	119327632	119327632	+	Missense_Mutation	SNP	C	C	T	rs17827619	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:119327632C>T	ENST00000338891.7	-	7	2238	c.1795G>A	c.(1795-1797)Gat>Aat	p.D599N	RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000522284.1_Missense_Mutation_p.D479N|FAM184A_ENST00000368475.4_Missense_Mutation_p.D479N|FAM184A_ENST00000352896.5_Missense_Mutation_p.D479N|FAM184A_ENST00000521531.1_Missense_Mutation_p.D599N	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	599			D -> N (in dbSNP:rs17827619).			extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						AATAGAGCATCCTTGGTCTCC	0.388													C|||	404	0.0806709	0.028	0.0879	5008	,	,		16906	0.0704		0.1014	False		,,,				2504	0.136				p.D599N		Atlas-SNP	.											.	FAM184A	109	.	0			c.G1795A						PASS	.	C	ASN/ASP,ASN/ASP	169,3529		4,161,1684	109.0	103.0	105.0		1435,1795	5.8	1.0	6	dbSNP_123	105	1062,7108		68,926,3091	yes	missense,missense	FAM184A	NM_001100411.1,NM_024581.4	23,23	72,1087,4775	TT,TC,CC		12.9988,4.57,10.3724	benign,benign	479/972,599/1141	119327632	1231,10637	1849	4085	5934	SO:0001583	missense	79632	exon7			GAGCATCCTTGGT	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 60"""	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1795G>A	6.37:g.119327632C>T	ENSP00000342604:p.Asp599Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	107	62	0.579439	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	168	0.07692307692307693	14	0.028455284552845527	39	0.10773480662983426	35	0.06118881118881119	80	0.10554089709762533	C	11.06	1.528683	0.27387	0.0457	0.129988	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	T;T;T;T;T	0.23950	2.5;2.51;1.95;1.94;1.88	5.85	5.85	0.93711	.	0.101830	0.64402	D	0.000003	T	0.10252	0.0251	N	0.17082	0.46	0.22050	P	0.999398441	B;B;B	0.13594	0.006;0.003;0.008	B;B;B	0.17433	0.018;0.005;0.015	T	0.10660	-1.0620	9	0.26408	T	0.33	-14.7958	20.1731	0.98165	0.0:1.0:0.0:0.0	rs17827619;rs52823165;rs17827619	599;479;599	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	N	599;479;479;599;479	ENSP00000342604:D599N;ENSP00000326608:D479N;ENSP00000357460:D479N;ENSP00000430442:D599N;ENSP00000429826:D479N	ENSP00000342604:D599N	D	-	1	0	FAM184A	119369331	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	2.811000	0.47986	2.768000	0.95171	0.655000	0.94253	GAT	C|0.913;T|0.087	0.087	strong		0.388	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581	
LPO	4025	hgsc.bcm.edu	37	17	56332327	56332327	+	Missense_Mutation	SNP	G	G	A	rs2301870	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56332327G>A	ENST00000262290.4	+	9	1577	c.1261G>A	c.(1261-1263)Gtg>Atg	p.V421M	LPO_ENST00000582328.1_Missense_Mutation_p.V338M|LPO_ENST00000543544.1_Missense_Mutation_p.V362M|LPO_ENST00000421678.2_Missense_Mutation_p.V338M	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	421			V -> M (in dbSNP:rs2301870). {ECO:0000269|PubMed:19059195, ECO:0000269|PubMed:2222811, ECO:0000269|Ref.3}.		defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)	p.V421M(1)		breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						GGGAGCCTTCGTGCAGGTAGG	0.612													G|||	808	0.161342	0.2526	0.0821	5008	,	,		14954	0.1151		0.1461	False		,,,				2504	0.1575				p.V421M		Atlas-SNP	.											LPO,NS,carcinoma,0,1	LPO	73	1	1	Substitution - Missense(1)	stomach(1)	c.G1261A						PASS	.	G	MET/VAL,MET/VAL	986,3420	369.1+/-318.9	122,742,1339	68.0	68.0	68.0		1012,1261	-6.8	0.1	17	dbSNP_100	68	1169,7431	238.5+/-269.9	77,1015,3208	yes	missense,missense	LPO	NM_001160102.1,NM_006151.2	21,21	199,1757,4547	AA,AG,GG		13.593,22.3786,16.5693	benign,benign	338/630,421/713	56332327	2155,10851	2203	4300	6503	SO:0001583	missense	4025	exon9			GCCTTCGTGCAGG	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1261G>A	17.37:g.56332327G>A	ENSP00000262290:p.Val421Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	122	72	0.590164	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	37	CCDS32689.1	309	0.14148351648351648	109	0.22154471544715448	36	0.09944751381215469	63	0.11013986013986014	101	0.13324538258575197	G	10.95	1.497075	0.26861	0.223786	0.13593	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.67865	-0.29;-0.29;-0.29	5.44	-6.83	0.01693	.	1.368490	0.04046	N	0.303995	T	0.00039	0.0001	N	0.05050	-0.12	0.80722	P	0.0	B;P	0.38677	0.042;0.642	B;B	0.36378	0.012;0.223	T	0.04090	-1.0978	9	0.07325	T	0.83	.	16.7414	0.85460	0.8059:0.0:0.1941:0.0	rs2301870;rs57193257;rs2301870	338;421	E7EMJ3;P22079	.;PERL_HUMAN	M	421;338;362;166	ENSP00000262290:V421M;ENSP00000400245:V338M;ENSP00000445344:V362M	ENSP00000262290:V421M	V	+	1	0	LPO	53687326	0.000000	0.05858	0.110000	0.21437	0.974000	0.67602	-0.721000	0.04963	-1.086000	0.03084	-0.768000	0.03414	GTG	G|0.838;A|0.162	0.162	strong		0.612	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		
RNF25	64320	hgsc.bcm.edu	37	2	219528995	219528995	+	Silent	SNP	T	T	C	rs13022721	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219528995T>C	ENST00000295704.2	-	10	1505	c.1065A>G	c.(1063-1065)ccA>ccG	p.P355P		NM_022453.2	NP_071898.2	Q96BH1	RNF25_HUMAN	ring finger protein 25	355					positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|NF-kappaB binding (GO:0051059)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCCTCCCTTTGGGTGCCTCC	0.617													C|||	751	0.14996	0.3835	0.0504	5008	,	,		16683	0.124		0.0278	False		,,,				2504	0.0573				p.P355P		Atlas-SNP	.											RNF25,bladder,carcinoma,-1,1	RNF25	40	1	0			c.A1065G						PASS	.	C		1399,3007	682.2+/-404.1	236,927,1040	66.0	77.0	73.0		1065	-3.9	0.5	2	dbSNP_121	73	322,8278	803.3+/-407.3	8,306,3986	no	coding-synonymous	RNF25	NM_022453.2		244,1233,5026	CC,CT,TT		3.7442,31.7522,13.2324		355/460	219528995	1721,11285	2203	4300	6503	SO:0001819	synonymous_variant	64320	exon10			TCCCTTTGGGTGC		CCDS2420.1	2q35	2008-02-05			ENSG00000163481	ENSG00000163481		"""RING-type (C3HC4) zinc fingers"""	14662	protein-coding gene	gene with protein product						12748188	Standard	NM_022453		Approved	AO7, FLJ13906	uc002vit.3	Q96BH1	OTTHUMG00000133077	ENST00000295704.2:c.1065A>G	2.37:g.219528995T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	120	70	0.583333	NM_022453	A8K0D6|Q53HQ5|Q9H874	Silent	SNP	ENST00000295704.2	37	CCDS2420.1																																																																																			T|0.851;C|0.149	0.149	strong		0.617	RNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256721.1	NM_022453	
OR10H5	284433	hgsc.bcm.edu	37	19	15905468	15905468	+	Missense_Mutation	SNP	T	T	G	rs62106065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15905468T>G	ENST00000308940.8	+	1	708	c.610T>G	c.(610-612)Tgt>Ggt	p.C204G		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						GGGCTTGGTGTGTATCACGGC	0.552													.|||	345	0.0688898	0.0567	0.0778	5008	,	,		21276	0.0625		0.0915	False		,,,				2504	0.0624				p.C204G		Atlas-SNP	.											OR10H5,NS,carcinoma,-2,1	OR10H5	49	1	0			c.T610G						PASS	.						125.0	99.0	108.0					19																	15905468		2203	4298	6501	SO:0001583	missense	284433	exon1			TTGGTGTGTATCA	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.610T>G	19.37:g.15905468T>G	ENSP00000310704:p.Cys204Gly	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	228	102	0.447368	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	162	0.07417582417582418	25	0.0508130081300813	35	0.09668508287292818	41	0.07167832167832168	61	0.08047493403693931	.	1.708	-0.499771	0.04291	.	.	ENSG00000172519	ENST00000308940	T	0.35789	1.29	3.36	3.36	0.38483	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000044	T	0.00724	0.0024	N	0.03281	-0.365	0.80722	P	0.0	D	0.71674	0.998	D	0.74674	0.984	T	0.05451	-1.0884	9	0.17369	T	0.5	.	6.7609	0.23540	0.0:0.0:0.2411:0.7589	rs62106065	204	Q8NGA6	O10H5_HUMAN	G	204	ENSP00000310704:C204G	ENSP00000310704:C204G	C	+	1	0	OR10H5	15766468	0.027000	0.19231	0.089000	0.20774	0.079000	0.17450	2.253000	0.43205	1.531000	0.49152	0.477000	0.44152	TGT	T|0.939;G|0.061	0.061	strong		0.552	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
MUC4	4585	hgsc.bcm.edu	37	3	195513812	195513812	+	Missense_Mutation	SNP	T	T	A	rs201142885	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513812T>A	ENST00000463781.3	-	2	5098	c.4639A>T	c.(4639-4641)Aca>Tca	p.T1547S	MUC4_ENST00000475231.1_Missense_Mutation_p.T1547S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.M1535_T1550delMPLPVTSPSSASTGDT(4)|p.T1547S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGTCACCTGTGGATGCTGAG	0.582																																					p.T1547S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	5	Deletion - In frame(4)|Substitution - Missense(1)	stomach(4)|kidney(1)	c.A4639T						scavenged	.																																			SO:0001583	missense	4585	exon2			CACCTGTGGATGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4639A>T	3.37:g.195513812T>A	ENSP00000417498:p.Thr1547Ser	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	176	24	0.136364	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.021	0.372220	0.11409	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.48;1.46	0.844	-0.658	0.11428	.	.	.	.	.	T	0.22437	0.0541	N	0.19112	0.55	0.09310	N	1	P	0.46578	0.88	P	0.50270	0.636	T	0.13764	-1.0497	8	.	.	.	.	3.6421	0.08170	0.0:0.3306:0.0:0.6694	.	1547	E7ESK3	.	S	1547	ENSP00000417498:T1547S;ENSP00000420243:T1547S	.	T	-	1	0	MUC4	196998207	0.034000	0.19679	0.062000	0.19696	0.063000	0.16089	-0.041000	0.12084	0.077000	0.16863	0.076000	0.15429	ACA	T|0.976;A|0.023	0.023	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ACSM1	116285	hgsc.bcm.edu	37	16	20635418	20635418	+	Splice_Site	SNP	C	C	T	rs3743690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20635418C>T	ENST00000307493.4	-	12	1714	c.1647G>A	c.(1645-1647)aaG>aaA	p.K549K	ACSM1_ENST00000520010.1_Splice_Site_p.K549K|ACSM1_ENST00000219151.4_Splice_Site_p.K200K	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	549				K -> N (in Ref. 1; BAB64535/BAB68363). {ECO:0000305}.	benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						CCTCACTCACCTTCCTTGGGT	0.547													C|||	920	0.183706	0.0295	0.1297	5008	,	,		21557	0.499		0.1461	False		,,,				2504	0.1442				p.K549K		Atlas-SNP	.											.	ACSM1	118	.	0			c.G1647A						PASS	.	C		199,4203	125.3+/-162.5	6,187,2008	256.0	199.0	218.0		1647	3.9	1.0	16	dbSNP_107	218	1065,7535	224.4+/-260.8	72,921,3307	yes	coding-synonymous-near-splice	ACSM1	NM_052956.2		78,1108,5315	TT,TC,CC		12.3837,4.5207,9.7216		549/578	20635418	1264,11738	2201	4300	6501	SO:0001630	splice_region_variant	116285	exon12			ACTCACCTTCCTT	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1647+1G>A	16.37:g.20635418C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	177	102	0.576271	NM_052956	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	37	CCDS10587.1	481	0.22023809523809523	20	0.04065040650406504	52	0.143646408839779	305	0.5332167832167832	104	0.13720316622691292	c	5.565	0.289098	0.10513	0.045207	0.123837	ENSG00000166743	ENST00000524149	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.52064	-0.8625	3	.	.	.	.	15.1985	0.73116	0.0:1.0:0.0:0.0	rs3743690;rs3743690	.	.	.	K	221	.	.	R	-	2	0	ACSM1	20542919	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	5.528000	0.67129	2.183000	0.69458	0.609000	0.83330	AGG	C|0.852;T|0.148	0.148	strong		0.547	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	Silent
ANKRD33	341405	hgsc.bcm.edu	37	12	52285086	52285086	+	Missense_Mutation	SNP	G	G	A	rs3180417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52285086G>A	ENST00000340970.4	+	6	1152	c.781G>A	c.(781-783)Gta>Ata	p.V261I	ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Missense_Mutation_p.V192I|ANKRD33_ENST00000301190.6_Silent_p.K452K			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	261			V -> I (in dbSNP:rs3180417).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		TGGCACAGAAGTAGGGGAAGA	0.587													G|||	736	0.146965	0.0318	0.134	5008	,	,		16957	0.2004		0.1918	False		,,,				2504	0.2106				p.V261I		Atlas-SNP	.											.	ANKRD33	33	.	0			c.G781A						PASS	.	G	ILE/VAL,	280,4126	143.5+/-178.5	7,266,1930	24.0	24.0	24.0		781,1356	-6.6	0.0	12	dbSNP_105	24	1745,6855	288.4+/-298.7	194,1357,2749	yes	missense,coding-synonymous	ANKRD33	NM_001130015.1,NM_182608.3	29,	201,1623,4679	AA,AG,GG		20.2907,6.355,15.5697	,	261/273,452/453	52285086	2025,10981	2203	4300	6503	SO:0001583	missense	341405	exon6			ACAGAAGTAGGGG		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"""Ankyrin repeat domain containing"""	13788	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 7"""	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.781G>A	12.37:g.52285086G>A	ENSP00000344690:p.Val261Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_001130015	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	337	0.1543040293040293	24	0.04878048780487805	49	0.13535911602209943	122	0.21328671328671328	142	0.18733509234828497	G	16.88	3.245934	0.59103	0.06355	0.202907	ENSG00000167612	ENST00000538991;ENST00000340970	T;T	0.23950	1.88;2.32	4.32	-6.62	0.01813	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.15141	0.012	B	0.12156	0.007	T	0.38714	-0.9648	7	0.51188	T	0.08	-3.4072	7.0794	0.25223	0.0:0.231:0.3937:0.3752	rs3180417;rs17644218;rs57954374;rs3180417	261	Q7Z3H0	ANR33_HUMAN	I	192;261	ENSP00000443722:V192I;ENSP00000344690:V261I	ENSP00000344690:V261I	V	+	1	0	ANKRD33	50571353	0.000000	0.05858	0.000000	0.03702	0.743000	0.42351	-1.473000	0.02339	-1.026000	0.03330	0.313000	0.20887	GTA	G|0.851;A|0.149	0.149	strong		0.587	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
WNT9B	7484	hgsc.bcm.edu	37	17	44952531	44952531	+	Silent	SNP	G	G	T	rs34072914	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:44952531G>T	ENST00000290015.2	+	3	452	c.399G>T	c.(397-399)cgG>cgT	p.R133R	WNT9B_ENST00000393461.2_Silent_p.R133R	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	133					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			CCCTGGCCCGGGCCTGCAGCG	0.677													G|||	165	0.0329473	0.0499	0.0245	5008	,	,		16790	0.0417		0.0179	False		,,,				2504	0.0225				p.R133R		Atlas-SNP	.											WNT9B,colon,carcinoma,0,3	WNT9B	37	3	0			c.G399T						PASS	.	G		187,4219	117.5+/-155.4	5,177,2021	74.0	87.0	82.0		399	1.5	1.0	17	dbSNP_126	82	251,8347	97.0+/-158.7	7,237,4055	no	coding-synonymous	WNT9B	NM_003396.1		12,414,6076	TT,TG,GG		2.9193,4.2442,3.3682		133/358	44952531	438,12566	2203	4299	6502	SO:0001819	synonymous_variant	7484	exon3			GGCCCGGGCCTGC	AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"""Wingless-type MMTV integration sites"""	12779	protein-coding gene	gene with protein product		602864	"""wingless-type MMTV integration site family, member 15"""	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.399G>T	17.37:g.44952531G>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	129	69	0.534884	NM_003396	Q6UXT4|Q96Q09	Silent	SNP	ENST00000290015.2	37	CCDS11506.1																																																																																			G|0.965;T|0.035	0.035	strong		0.677	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396	
L2HGDH	79944	hgsc.bcm.edu	37	14	50778816	50778816	+	Missense_Mutation	SNP	A	A	C	rs2275591	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50778816A>C	ENST00000267436.4	-	1	450	c.53T>G	c.(52-54)cTt>cGt	p.L18R	L2HGDH_ENST00000261699.4_Missense_Mutation_p.L18R|ATP5S_ENST00000245448.6_5'Flank|ATP5S_ENST00000426751.2_5'Flank|ATP5S_ENST00000311459.7_5'Flank|L2HGDH_ENST00000555610.1_Missense_Mutation_p.L18R|L2HGDH_ENST00000421284.3_Missense_Mutation_p.L18R|L2HGDH_ENST00000555423.1_Missense_Mutation_p.L18R|L2HGDH_ENST00000556393.1_5'UTR			Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase	18			L -> R (in dbSNP:rs2275591). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16134148}.		2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2-hydroxyglutarate dehydrogenase activity (GO:0047545)			kidney(1)|large_intestine(4)|lung(3)|ovary(2)	10	all_epithelial(31;0.000599)|Breast(41;0.0102)					ACCGGCGAAAAGCCCGCGGGC	0.687											OREG0022670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2868	0.572684	0.5696	0.5865	5008	,	,		13616	0.6171		0.5596	False		,,,				2504	0.5348				p.L18R		Atlas-SNP	.											L2HGDH,NS,carcinoma,0,1	L2HGDH	33	1	0			c.T53G						PASS	.	C	ARG/LEU	2465,1913		718,1029,442	18.0	21.0	20.0		53	-2.2	0.0	14	dbSNP_100	20	4826,3742		1405,2016,863	no	missense	L2HGDH	NM_024884.2	102	2123,3045,1305	CC,CA,AA		43.6741,43.6958,43.6814	benign	18/464	50778816	7291,5655	2189	4284	6473	SO:0001583	missense	79944	exon1			GCGAAAAGCCCGC		CCDS9698.1	14q22.1	2006-04-28	2005-05-25	2005-05-25	ENSG00000087299	ENSG00000087299	1.1.99.2		20499	protein-coding gene	gene with protein product	"""2-hydroxyglutarate dehydrogenase"""	609584	"""chromosome 14 open reading frame 160"""	C14orf160		16005139	Standard	NM_024884		Approved	FLJ12618	uc001wxu.3	Q9H9P8	OTTHUMG00000140289	ENST00000267436.4:c.53T>G	14.37:g.50778816A>C	ENSP00000267436:p.Leu18Arg	Somatic	61	0	0	972	WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_024884	Q9BRR1	Missense_Mutation	SNP	ENST00000267436.4	37	CCDS9698.1	1241	0.5682234432234432	268	0.5447154471544715	204	0.56353591160221	344	0.6013986013986014	425	0.5606860158311345	C	8.033	0.762257	0.15914	0.563042	0.563259	ENSG00000087299	ENST00000261699;ENST00000267436;ENST00000421284;ENST00000557131;ENST00000555423;ENST00000555610	D;D;D;D;D	0.92752	-2.95;-3.1;-3.1;-2.39;-2.16	3.97	-2.22	0.06952	.	1.340710	0.04938	N	0.458219	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.17465	0.0;0.022	B;B	0.14023	0.0;0.01	T	0.19582	-1.0301	9	0.10636	T	0.68	6.0095	3.8697	0.09031	0.567:0.206:0.1373:0.0898	rs2275591;rs17845074;rs17857856;rs60990986;rs2275591	18;18	C9JVN9;Q9H9P8	.;L2HDH_HUMAN	R	18	ENSP00000261699:L18R;ENSP00000267436:L18R;ENSP00000405559:L18R;ENSP00000450494:L18R;ENSP00000452483:L18R	ENSP00000261699:L18R	L	-	2	0	L2HGDH	49848566	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.010000	0.00314	-0.779000	0.04560	-0.648000	0.03929	CTT	A|0.430;C|0.570	0.570	strong		0.687	L2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276870.2	NM_024884	
LAMA5	3911	hgsc.bcm.edu	37	20	60905878	60905878	+	Missense_Mutation	SNP	A	A	G	rs3810548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60905878A>G	ENST00000252999.3	-	30	3839	c.3773T>C	c.(3772-3774)aTg>aCg	p.M1258T	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1258	Domain IV 1 (domain IV B).		M -> T (in dbSNP:rs3810548). {ECO:0000269|PubMed:11821406}.		angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGCTGGGGACATGGCTGGAGT	0.687													G|||	3789	0.756589	0.4478	0.8098	5008	,	,		13400	0.9365		0.9175	False		,,,				2504	0.7853				p.M1258T		Atlas-SNP	.											.	LAMA5	268	.	0			c.T3773C						PASS	.	G	THR/MET	2406,1856		684,1038,409	14.0	18.0	16.0		3773	1.8	0.0	20	dbSNP_107	16	7826,598		3653,520,39	no	missense	LAMA5	NM_005560.3	81	4337,1558,448	GG,GA,AA		7.0988,43.5476,19.3442	benign	1258/3696	60905878	10232,2454	2131	4212	6343	SO:0001583	missense	3911	exon30			GGGGACATGGCTG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.3773T>C	20.37:g.60905878A>G	ENSP00000252999:p.Met1258Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	1764	0.8076923076923077	233	0.4735772357723577	294	0.8121546961325967	543	0.9493006993006993	694	0.9155672823218998	G	0.011	-1.703247	0.00719	0.564524	0.929012	ENSG00000130702	ENST00000252999	T	0.17054	2.3	5.15	1.82	0.25136	.	0.772782	0.11890	N	0.519719	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.17137	-1.0379	9	0.11794	T	0.64	.	4.0389	0.09741	0.0873:0.1758:0.5154:0.2214	rs3810548;rs60444386;rs3810548	1258	O15230	LAMA5_HUMAN	T	1258	ENSP00000252999:M1258T	ENSP00000252999:M1258T	M	-	2	0	LAMA5	60339273	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	1.193000	0.32162	0.504000	0.28082	-0.119000	0.15052	ATG	A|0.193;G|0.807	0.807	strong		0.687	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144062632	144062632	+	Nonsense_Mutation	SNP	C	C	G	rs202036368		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:144062632C>G	ENST00000056217.5	+	2	3044	c.2870C>G	c.(2869-2871)tCa>tGa	p.S957*	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	957					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					GCAGGGGTCTCAGAACACCCT	0.597																																					p.S957X		Atlas-SNP	.											ARHGEF5,NS,carcinoma,0,1	ARHGEF5	73	1	0			c.C2870G						scavenged	.						2.0	2.0	2.0					7																	144062632		723	1763	2486	SO:0001587	stop_gained	7984	exon2			GGGTCTCAGAACA	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.2870C>G	7.37:g.144062632C>G	ENSP00000056217:p.Ser957*	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	160	42	0.2625	NM_005435	A6NNJ2|Q6ZML7	Nonsense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.577225|6.577225	0.97676|0.97676	.|.	.|.	ENSG00000050327|ENSG00000050327	ENST00000474817|ENST00000056217	.|.	.|.	.|.	4.06|4.06	2.22|2.22	0.28083|0.28083	.|.	.|0.258318	.|0.20430	.|N	.|0.092497	T|.	0.37237|.	0.0996|.	.|.	.|.	.|.	0.21020|0.21020	N|N	0.99981|0.99981	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.20940|.	-1.0260|.	4|.	.|0.48119	.|T	.|0.1	-0.0888|-0.0888	6.3968|6.3968	0.21616|0.21616	0.0:0.7685:0.0:0.2315|0.0:0.7685:0.0:0.2315	.|.	.|.	.|.	.|.	E|X	211|957	.|.	.|ENSP00000056217:S957X	Q|S	+|+	1|2	0|0	ARHGEF5|ARHGEF5	143693565|143693565	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.014000|0.014000	0.08584|0.08584	0.795000|0.795000	0.26972|0.26972	0.369000|0.369000	0.24510|0.24510	0.555000|0.555000	0.69702|0.69702	CAG|TCA	.	.	weak		0.597	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
NACA2	342538	hgsc.bcm.edu	37	17	59668352	59668352	+	Missense_Mutation	SNP	C	C	T	rs17531723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59668352C>T	ENST00000521764.1	-	1	211	c.190G>A	c.(190-192)Gtc>Atc	p.V64I		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	64			V -> I (in dbSNP:rs17531723).		myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.V64I(1)		large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					GCTTTACCGACTGGTTCTTCA	0.483													C|||	727	0.145168	0.0567	0.1023	5008	,	,		21025	0.1667		0.1421	False		,,,				2504	0.2761				p.V64I		Atlas-SNP	.											NACA2,NS,carcinoma,0,1	NACA2	33	1	1	Substitution - Missense(1)	stomach(1)	c.G190A						PASS	.	C	ILE/VAL	320,4086	168.7+/-199.5	13,294,1896	180.0	164.0	170.0		190	0.8	1.0	17	dbSNP_123	170	1175,7425	238.8+/-270.1	85,1005,3210	yes	missense	NACA2	NM_199290.3	29	98,1299,5106	TT,TC,CC		13.6628,7.2628,11.4947	benign	64/216	59668352	1495,11511	2203	4300	6503	SO:0001583	missense	342538	exon1			TACCGACTGGTTC	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.190G>A	17.37:g.59668352C>T	ENSP00000427802:p.Val64Ile	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	204	104	0.509804	NM_199290	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	248	0.11355311355311355	25	0.0508130081300813	39	0.10773480662983426	73	0.12762237762237763	111	0.14643799472295516	C	15.15	2.747568	0.49257	0.072628	0.136628	ENSG00000253506	ENST00000521764	T	0.44482	0.92	0.753	0.753	0.18404	.	0.000000	0.64402	U	0.000019	T	0.00210	0.0006	M	0.61703	1.905	0.22066	P	0.999383782	B	0.15141	0.012	B	0.11329	0.006	T	0.06752	-1.0809	8	.	.	.	.	7.3227	0.26536	0.0:1.0:0.0:0.0	rs17531723;rs52831210;rs17531723	64	Q9H009	NACA2_HUMAN	I	64	ENSP00000427802:V64I	.	V	-	1	0	NACA2	57023134	1.000000	0.71417	0.985000	0.45067	0.716000	0.41182	3.351000	0.52232	0.702000	0.31825	0.411000	0.27672	GTC	C|0.884;T|0.116	0.116	strong		0.483	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
MAST1	22983	hgsc.bcm.edu	37	19	12978655	12978655	+	Silent	SNP	C	C	T	rs56114354	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12978655C>T	ENST00000251472.4	+	20	2469	c.2430C>T	c.(2428-2430)ccC>ccT	p.P810P		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						TCAGCGCCCCCCAAGAGGACG	0.726													C|||	44	0.00878594	0.0023	0.0101	5008	,	,		12595	0.0		0.0249	False		,,,				2504	0.0092				p.P810P		Atlas-SNP	.											.	MAST1	214	.	0			c.C2430T						PASS	.	C		17,4231		0,17,2107	7.0	9.0	8.0		2430	-2.8	0.8	19	dbSNP_129	8	157,8143		1,155,3994	no	coding-synonymous	MAST1	NM_014975.2		1,172,6101	TT,TC,CC		1.8916,0.4002,1.3867		810/1571	12978655	174,12374	2124	4150	6274	SO:0001819	synonymous_variant	22983	exon20			CGCCCCCCAAGAG	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.2430C>T	19.37:g.12978655C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_014975		Silent	SNP	ENST00000251472.4	37	CCDS32921.1																																																																																			C|0.990;T|0.010	0.010	strong		0.726	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975	
ZSCAN21	7589	hgsc.bcm.edu	37	7	99654689	99654689	+	Silent	SNP	G	G	A	rs11558476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99654689G>A	ENST00000292450.4	+	2	224	c.60G>A	c.(58-60)caG>caA	p.Q20Q	ZSCAN21_ENST00000477297.1_3'UTR|ZSCAN21_ENST00000456748.2_Silent_p.Q20Q|ZSCAN21_ENST00000543588.1_Silent_p.Q20Q	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21	20					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			CACAGGAGCAGGTGGGGCCTC	0.547													G|||	1565	0.3125	0.1157	0.3948	5008	,	,		16203	0.4454		0.326	False		,,,				2504	0.3691				p.Q20Q		Atlas-SNP	.											.	ZSCAN21	29	.	0			c.G60A						PASS	.	G		633,3773	272.8+/-271.0	44,545,1614	133.0	142.0	139.0		60	4.0	0.7	7	dbSNP_120	139	2521,6079	410.7+/-350.2	374,1773,2153	no	coding-synonymous	ZSCAN21	NM_145914.2		418,2318,3767	AA,AG,GG		29.314,14.3668,24.2503		20/474	99654689	3154,9852	2203	4300	6503	SO:0001819	synonymous_variant	7589	exon2			GGAGCAGGTGGGG	AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"""-"", ""Zinc fingers, C2H2-type"""	13104	protein-coding gene	gene with protein product		601261	"""zinc finger protein 38 (KOX 25)"", ""zinc finger protein 38"""	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.60G>A	7.37:g.99654689G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_145914	A4D2A6|D6W5T9|Q9H0B5	Silent	SNP	ENST00000292450.4	37	CCDS5681.1																																																																																			G|0.725;A|0.275	0.275	strong		0.547	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914	
RREB1	6239	hgsc.bcm.edu	37	6	7247344	7247344	+	Missense_Mutation	SNP	C	C	A	rs35742417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:7247344C>A	ENST00000349384.6	+	11	4810	c.4496C>A	c.(4495-4497)tCc>tAc	p.S1499Y	RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379933.3_Missense_Mutation_p.S1499Y|RREB1_ENST00000379938.2_Missense_Mutation_p.S1554Y	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1499			S -> Y (in dbSNP:rs35742417).		multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S1499Y(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				AAGACAGACTCCCCCAAAAGC	0.617													C|||	638	0.127396	0.239	0.0908	5008	,	,		17771	0.0357		0.161	False		,,,				2504	0.0624				p.S1554Y		Atlas-SNP	.											RREB1,NS,carcinoma,0,1	RREB1	242	1	1	Substitution - Missense(1)	stomach(1)	c.C4661A						PASS	.	C	TYR/SER,TYR/SER,,TYR/SER	897,3509	329.3+/-301.0	101,695,1407	74.0	71.0	72.0		4496,4661,,4496	3.4	1.0	6	dbSNP_126	72	1381,7219	251.8+/-278.1	104,1173,3023	yes	missense,missense,intron,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	144,144,,144	205,1868,4430	AA,AC,CC		16.0581,20.3586,17.515	benign,benign,,benign	1499/1688,1554/1743,,1499/1688	7247344	2278,10728	2203	4300	6503	SO:0001583	missense	6239	exon12			CAGACTCCCCCAA	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4496C>A	6.37:g.7247344C>A	ENSP00000305560:p.Ser1499Tyr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	186	79	0.424731	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	297	0.13598901098901098	105	0.21341463414634146	35	0.09668508287292818	25	0.043706293706293704	132	0.1741424802110818	C	11.75	1.731099	0.30684	0.203586	0.160581	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384	T;T;T	0.08193	3.12;3.12;3.12	5.24	3.42	0.39159	.	0.762218	0.11459	N	0.561966	T	0.02727	0.0082	L	0.40543	1.245	0.44798	P	0.0021999999999999797	B;P	0.36315	0.07;0.547	B;B	0.37888	0.123;0.26	T	0.44528	-0.9322	9	0.41790	T	0.15	-28.114	4.3196	0.11011	0.1154:0.4061:0.3851:0.0934	rs35742417;rs61234629	1499;1554	Q92766;Q92766-2	RREB1_HUMAN;.	Y	1499;1554;1499	ENSP00000369265:S1499Y;ENSP00000369270:S1554Y;ENSP00000305560:S1499Y	ENSP00000305560:S1499Y	S	+	2	0	RREB1	7192343	0.999000	0.42202	0.963000	0.40424	0.943000	0.58893	2.107000	0.41844	1.215000	0.43411	-0.254000	0.11334	TCC	C|0.843;A|0.157	0.157	strong		0.617	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
OSBPL6	114880	hgsc.bcm.edu	37	2	179188959	179188959	+	Missense_Mutation	SNP	G	G	A	rs35032920	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179188959G>A	ENST00000190611.4	+	4	534	c.158G>A	c.(157-159)cGg>cAg	p.R53Q	OSBPL6_ENST00000315022.2_Missense_Mutation_p.R32Q|OSBPL6_ENST00000409631.1_Missense_Mutation_p.R53Q|OSBPL6_ENST00000392505.2_Missense_Mutation_p.R53Q|OSBPL6_ENST00000359685.3_Missense_Mutation_p.R53Q|OSBPL6_ENST00000477097.1_3'UTR|OSBPL6_ENST00000357080.4_Missense_Mutation_p.R53Q|OSBPL6_ENST00000409045.3_Missense_Mutation_p.R53Q	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	53			R -> Q (in dbSNP:rs35032920).		lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TCTGTAAGTCGGCAATTGCTA	0.498													G|||	319	0.0636981	0.0303	0.0519	5008	,	,		18960	0.0278		0.0557	False		,,,				2504	0.1626				p.R53Q		Atlas-SNP	.											.	OSBPL6	178	.	0			c.G158A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	138,4268		1,136,2066	76.0	65.0	69.0		158,158,158,158,95	6.0	1.0	2	dbSNP_126	69	367,8233		7,353,3940	yes	missense,missense,missense,missense,missense	OSBPL6	NM_001201480.1,NM_001201481.1,NM_001201482.1,NM_032523.3,NM_145739.2	43,43,43,43,43	8,489,6006	AA,AG,GG		4.2674,3.1321,3.8828	benign,benign,benign,benign,benign	53/960,53/904,53/899,53/935,32/939	179188959	505,12501	2203	4300	6503	SO:0001583	missense	114880	exon4			TAAGTCGGCAATT	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.158G>A	2.37:g.179188959G>A	ENSP00000190611:p.Arg53Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	88	0.040293040293040296	15	0.03048780487804878	22	0.06077348066298342	15	0.026223776223776224	36	0.047493403693931395	G	18.10	3.547563	0.65311	0.031321	0.042674	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98	5.96	5.96	0.96718	.	0.646123	0.16436	N	0.214505	T	0.02083	0.0065	N	0.08118	0	0.35902	D	0.830474	B;B;B;B;B;P	0.35155	0.104;0.379;0.072;0.379;0.098;0.487	B;B;B;B;B;B	0.27262	0.014;0.078;0.026;0.048;0.007;0.042	T	0.13388	-1.0511	10	0.28530	T	0.3	-17.2325	9.2797	0.37720	0.1189:0.0:0.8811:0.0	rs35032920	53;32;53;53;53;53	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	Q	53;53;53;53;53;53;32	ENSP00000376293:R53Q;ENSP00000352713:R53Q;ENSP00000349591:R53Q;ENSP00000387248:R53Q;ENSP00000190611:R53Q;ENSP00000386885:R53Q;ENSP00000318723:R32Q	ENSP00000190611:R53Q	R	+	2	0	OSBPL6	178897205	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.069000	0.57541	2.832000	0.97577	0.655000	0.94253	CGG	G|0.960;A|0.040	0.040	strong		0.498	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
UQCRB	7381	hgsc.bcm.edu	37	8	97243720	97243720	+	Intron	SNP	G	G	A	rs2292835	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:97243720G>A	ENST00000287022.5	-	3	362				UQCRB_ENST00000517523.1_Intron|UQCRB_ENST00000523920.1_Silent_p.H94H|UQCRB_ENST00000518406.1_Silent_p.H94H	NM_001199975.2|NM_006294.4	NP_001186904.1|NP_006285.1	P14927	QCR7_HUMAN	ubiquinol-cytochrome c reductase binding protein						aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)				kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10	Breast(36;5.16e-05)					AGgaagcagagtgcagagctg	0.453													G|||	1169	0.233427	0.1241	0.2594	5008	,	,		17915	0.1806		0.3588	False		,,,				2504	0.2883				p.H94H		Atlas-SNP	.											.	UQCRB	17	.	0			c.C282T						PASS	.																																			SO:0001627	intron_variant	7381	exon4			AGCAGAGTGCAGA	X13585	CCDS6269.1, CCDS59107.1	8q22	2011-07-04			ENSG00000156467	ENSG00000156467		"""Mitochondrial respiratory chain complex / Complex III"""	12582	protein-coding gene	gene with protein product	"""ubiquinol-cytochrome c reductase, complex III subunit VI"", ""cytochrome b-c1 complex subunit 7"""	191330		UQBP		2167087, 2543413, 3056408	Standard	NM_006294		Approved	QP-C, QCR7, UQCR6	uc022ayx.1	P14927	OTTHUMG00000164711	ENST00000287022.5:c.258+281C>T	8.37:g.97243720G>A		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_001254752	E5RJU0|Q6FGD1	Silent	SNP	ENST00000287022.5	37	CCDS6269.1																																																																																			G|0.748;A|0.252	0.252	strong		0.453	UQCRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379863.1	NM_006294	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87446053	87446053	+	Silent	SNP	G	G	A	rs2042395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:87446053G>A	ENST00000268616.4	-	12	2080	c.1863C>T	c.(1861-1863)gcC>gcT	p.A621A		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	621							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)	p.A621A(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		TCCCCGTGGCGGCCGTGCTGG	0.627													G|||	2303	0.459864	0.1127	0.5231	5008	,	,		16463	0.3095		0.7565	False		,,,				2504	0.7342				p.A621A		Atlas-SNP	.											ZCCHC14,NS,lymphoid_neoplasm,0,1	ZCCHC14	87	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1863T						PASS	.	G		1060,3334	366.8+/-318.0	118,824,1255	51.0	61.0	58.0		1863	-11.7	0.0	16	dbSNP_94	58	6496,2102	687.7+/-404.2	2443,1610,246	no	coding-synonymous	ZCCHC14	NM_015144.2		2561,2434,1501	AA,AG,GG		24.4475,24.1238,41.8411		621/950	87446053	7556,5436	2197	4299	6496	SO:0001819	synonymous_variant	23174	exon12			CGTGGCGGCCGTG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.1863C>T	16.37:g.87446053G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																			G|0.485;A|0.515	0.515	strong		0.627	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
ABCA10	10349	hgsc.bcm.edu	37	17	67210992	67210992	+	Splice_Site	SNP	T	T	C	rs11657804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:67210992T>C	ENST00000269081.4	-	10	1768	c.859A>G	c.(859-861)Att>Gtt	p.I287V	ABCA10_ENST00000432313.2_Splice_Site_p.I287V|ABCA10_ENST00000416101.2_Splice_Site_p.I287V	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	287			I -> V (in dbSNP:rs11657804). {ECO:0000269|PubMed:12821155, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1}.		transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					AGGTGTGTAATCTGAGATTTA	0.264													T|||	1310	0.261581	0.0166	0.2839	5008	,	,		13738	0.2788		0.4076	False		,,,				2504	0.409				p.I287V		Atlas-SNP	.											.	ABCA10	209	.	0			c.A859G						PASS	.	T	VAL/ILE	364,4006		30,304,1851	32.0	37.0	35.0		859	-0.9	0.0	17	dbSNP_120	35	3496,5050		742,2012,1519	yes	missense-near-splice	ABCA10	NM_080282.3	29	772,2316,3370	CC,CT,TT		40.908,8.3295,29.8854	benign	287/1544	67210992	3860,9056	2185	4273	6458	SO:0001630	splice_region_variant	10349	exon10			GTGTAATCTGAGA	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"""ATP binding cassette transporters / subfamily A"""	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.859-1A>G	17.37:g.67210992T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	562	0.2573260073260073	10	0.02032520325203252	109	0.3011049723756906	136	0.23776223776223776	307	0.4050131926121372	T	0.025	-1.377296	0.01214	0.083295	0.40908	ENSG00000154263	ENST00000269081;ENST00000416101;ENST00000432313	D;D;D	0.88509	-2.39;-2.39;-2.39	3.34	-0.889	0.10580	.	.	.	.	.	T	0.00012	0.0000	N	0.20530	0.585	0.31687	P	0.642327	B;B	0.28026	0.198;0.106	B;B	0.31016	0.123;0.123	T	0.07986	-1.0744	8	0.11485	T	0.65	.	5.0094	0.14304	0.0:0.1089:0.3514:0.5397	rs11657804;rs52817763;rs56691372;rs11657804	287;287	E5RFP5;Q8WWZ4	.;ABCAA_HUMAN	V	287	ENSP00000269081:I287V;ENSP00000407772:I287V;ENSP00000387674:I287V	ENSP00000269081:I287V	I	-	1	0	ABCA10	64722587	0.888000	0.30383	0.040000	0.18447	0.039000	0.13416	0.177000	0.16801	-0.462000	0.06984	0.416000	0.27883	ATT	T|0.719;C|0.281	0.281	strong		0.264	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282	Missense_Mutation
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257266	114257266	+	Missense_Mutation	SNP	C	C	T	rs142136016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:114257266C>T	ENST00000306507.5	+	1	606	c.433C>T	c.(433-435)Cgc>Tgc	p.R145C		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	145					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R145C(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						CCCCTACTACCGCCGCAAGTT	0.642																																					p.R145C		Atlas-SNP	.											FOXD4L1,NS,malignant_melanoma,0,1	FOXD4L1	48	1	1	Substitution - Missense(1)	NS(1)	c.C433T						scavenged	.						23.0	32.0	29.0					2																	114257266		2014	3973	5987	SO:0001583	missense	200350	exon1			TACTACCGCCGCA	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.433C>T	2.37:g.114257266C>T	ENSP00000302756:p.Arg145Cys	Somatic	702	0	0		WXS	Illumina HiSeq	Phase_I	637	183	0.287284	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	100	0.045787545787545784	17	0.034552845528455285	16	0.04419889502762431	27	0.0472027972027972	40	0.052770448548812667	.	12.80	2.046891	0.36085	.	.	ENSG00000184492	ENST00000306507	D	0.96491	-4.03	2.57	2.57	0.30868	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.32161	U	0.006487	D	0.84995	0.5596	H	0.95402	3.665	0.58432	D	0.999998	B	0.28350	0.208	B	0.26969	0.075	D	0.88738	0.3241	10	0.72032	D	0.01	.	6.7523	0.23493	0.2797:0.7203:0.0:0.0	.	145	Q9NU39	FX4L1_HUMAN	C	145	ENSP00000302756:R145C	ENSP00000302756:R145C	R	+	1	0	FOXD4L1	113973736	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	1.151000	0.31651	1.452000	0.47756	0.184000	0.17185	CGC	C|0.947;T|0.053	0.053	strong		0.642	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
DEF6	50619	hgsc.bcm.edu	37	6	35287755	35287755	+	Silent	SNP	G	G	A	rs61734578	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:35287755G>A	ENST00000316637.5	+	9	1547	c.1542G>A	c.(1540-1542)gaG>gaA	p.E514E	DEF6_ENST00000542066.1_Silent_p.E259E	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)	514						cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						AGCTGGAGGAGGTGCGGCAGA	0.662													G|||	103	0.0205671	0.053	0.013	5008	,	,		18858	0.002		0.0199	False		,,,				2504	0.002				p.E514E		Atlas-SNP	.											.	DEF6	36	.	0			c.G1542A						PASS	.	G		189,4159		3,183,1988	21.0	23.0	23.0		1542	2.3	1.0	6	dbSNP_129	23	171,8367		2,167,4100	no	coding-synonymous	DEF6	NM_022047.3		5,350,6088	AA,AG,GG		2.0028,4.3468,2.7937		514/632	35287755	360,12526	2174	4269	6443	SO:0001819	synonymous_variant	50619	exon9			GGAGGAGGTGCGG	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"""Pleckstrin homology (PH) domain containing"""	2760	protein-coding gene	gene with protein product	"""SWAP-70-like adaptor protein of T cells"""	610094	"""differentially expressed in FDCP (mouse homolog) 6"""			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.1542G>A	6.37:g.35287755G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_022047	Q86VF4	Silent	SNP	ENST00000316637.5	37	CCDS4802.1																																																																																			G|0.969;A|0.031	0.031	strong		0.662	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047	
TRIP12	9320	hgsc.bcm.edu	37	2	230723777	230723777	+	Silent	SNP	G	G	C	rs544480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:230723777G>C	ENST00000283943.5	-	3	790	c.612C>G	c.(610-612)tcC>tcG	p.S204S	TRIP12_ENST00000409677.1_Silent_p.S246S|TRIP12_ENST00000389045.3_Intron|TRIP12_ENST00000389044.4_Silent_p.S246S|TRIP12_ENST00000543084.1_Silent_p.S246S	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	204					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CAGAAGACGAGGAGGAAGTAG	0.537													G|||	919	0.183506	0.0976	0.134	5008	,	,		19006	0.25		0.1789	False		,,,				2504	0.271				p.S204S		Atlas-SNP	.											.	TRIP12	207	.	0			c.C612G						PASS	.	G		559,3847	250.6+/-257.6	41,477,1685	67.0	55.0	59.0		612	3.9	1.0	2	dbSNP_83	59	1824,6776	327.1+/-317.7	221,1382,2697	no	coding-synonymous	TRIP12	NM_004238.1		262,1859,4382	CC,CG,GG		21.2093,12.6872,18.3223		204/1993	230723777	2383,10623	2203	4300	6503	SO:0001819	synonymous_variant	9320	exon3			AGACGAGGAGGAA	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.612C>G	2.37:g.230723777G>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	184	92	0.5	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	37	CCDS33391.1																																																																																			G|0.817;C|0.183	0.183	strong		0.537	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	
ZNF215	7762	hgsc.bcm.edu	37	11	6976988	6976988	+	Silent	SNP	A	A	T	rs2239731	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6976988A>T	ENST00000278319.5	+	7	1368	c.780A>T	c.(778-780)ggA>ggT	p.G260G	ZNF215_ENST00000529903.1_Silent_p.G260G|ZNF215_ENST00000414517.2_Silent_p.G260G|ZNF215_ENST00000527171.1_3'UTR	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	260					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		CCGAAAGTGGACACCCTTCTT	0.388													A|||	3386	0.676118	0.4418	0.7911	5008	,	,		17482	0.7133		0.7227	False		,,,				2504	0.8252				p.G260G		Atlas-SNP	.											.	ZNF215	72	.	0			c.A780T						PASS	.	A		2177,2225	576.6+/-384.3	541,1095,565	89.0	90.0	90.0		780	2.4	0.0	11	dbSNP_98	90	6371,2221	706.0+/-405.5	2340,1691,265	no	coding-synonymous	ZNF215	NM_013250.2		2881,2786,830	TT,TA,AA		25.8496,49.4548,34.2158		260/518	6976988	8548,4446	2201	4296	6497	SO:0001819	synonymous_variant	7762	exon7			AAGTGGACACCCT	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.780A>T	11.37:g.6976988A>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_013250	Q96C84	Silent	SNP	ENST00000278319.5	37	CCDS7775.1																																																																																			T|0.656;N|0.000	0.656	strong		0.388	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
SHC1	6464	hgsc.bcm.edu	37	1	154938076	154938076	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154938076G>A	ENST00000368445.5	-	11	1780	c.1566C>T	c.(1564-1566)ctC>ctT	p.L522L	SHC1_ENST00000368453.4_Silent_p.L413L|SHC1_ENST00000490667.1_Intron|SHC1_ENST00000368450.1_Silent_p.L412L|RP11-307C12.12_ENST00000605085.1_RNA|SHC1_ENST00000448116.2_Silent_p.L523L|SHC1_ENST00000368449.4_Silent_p.L293L|SHC1_ENST00000606391.1_Silent_p.L323L|PYGO2_ENST00000483463.1_5'Flank	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	522	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCAAGCCAGTGAGCACATACT	0.607																																					p.L523L	NSCLC(4;32 234 1864 2492 3259 13747 17376)	Atlas-SNP	.											.	SHC1	91	.	0			c.C1569T						PASS	.						110.0	92.0	98.0					1																	154938076		2203	4300	6503	SO:0001819	synonymous_variant	6464	exon11			GCCAGTGAGCACA	U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"""SH2 domain containing"""	10840	protein-coding gene	gene with protein product		600560	"""SHC (Src homology 2 domain-containing) transforming protein 1"""	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.1566C>T	1.37:g.154938076G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	288	37	0.128472	NM_001130040	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Silent	SNP	ENST00000368445.5	37	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	G	8.211	0.800408	0.16397	.	.	ENSG00000160691	ENST00000444664	.	.	.	4.76	2.74	0.32292	.	.	.	.	.	T	0.38506	0.1043	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32455	-0.9906	4	.	.	.	.	5.1264	0.14886	0.2088:0.3259:0.4652:0.0	.	.	.	.	Y	186	.	.	H	-	1	0	SHC1	153204700	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	0.970000	0.29383	1.235000	0.43724	0.557000	0.71058	CAC	.	.	none		0.607	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001	
MUC4	4585	hgsc.bcm.edu	37	3	195510996	195510996	+	Silent	SNP	G	G	A	rs199626832	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195510996G>A	ENST00000463781.3	-	2	7914	c.7455C>T	c.(7453-7455)gaC>gaT	p.D2485D	MUC4_ENST00000475231.1_Silent_p.D2485D|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGACGAAGCGTCGGTGACAA	0.582													.|||	28	0.00559105	0.0008	0.0043	5008	,	,		15785	0.0		0.0219	False		,,,				2504	0.002				p.D2485D		Atlas-SNP	.											MUC4_ENST00000463781,caecum,carcinoma,0,1	MUC4	1505	1	0			c.C7455T						PASS	.						52.0	45.0	47.0					3																	195510996		652	1590	2242	SO:0001819	synonymous_variant	4585	exon2			CGAAGCGTCGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7455C>T	3.37:g.195510996G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	504	70	0.138889	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.994;A|0.006	0.006	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TLE3	7090	hgsc.bcm.edu	37	15	70345626	70345626	+	Silent	SNP	C	C	T	rs1057865	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:70345626C>T	ENST00000558939.1	-	17	3300	c.1923G>A	c.(1921-1923)acG>acA	p.T641T	TLE3_ENST00000560589.1_Silent_p.T585T|TLE3_ENST00000539550.1_Silent_p.T568T|TLE3_ENST00000559191.1_Silent_p.T222T|TLE3_ENST00000557997.1_Silent_p.T633T|TLE3_ENST00000559048.1_Silent_p.T641T|TLE3_ENST00000557907.1_Silent_p.T633T|TLE3_ENST00000442299.2_Silent_p.T633T|TLE3_ENST00000451782.2_Silent_p.T638T|TLE3_ENST00000558379.1_Silent_p.T636T|TLE3_ENST00000440567.3_Silent_p.T631T|TLE3_ENST00000559929.1_Silent_p.T651T|TLE3_ENST00000558201.1_Silent_p.T647T|TLE3_ENST00000560939.1_Silent_p.T643T|TLE3_ENST00000317509.8_Silent_p.T629T	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	641					Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGGAGCGCACCGTGTTGTCCA	0.607													C|||	1818	0.363019	0.2284	0.4726	5008	,	,		18331	0.256		0.4791	False		,,,				2504	0.4581				p.T641T		Atlas-SNP	.											.	TLE3	104	.	0			c.G1923A						PASS	.	C	,,	1175,3125		187,801,1162	61.0	66.0	65.0		1914,1923,1887	-10.1	0.0	15	dbSNP_86	65	4018,4520		965,2088,1216	no	coding-synonymous,coding-synonymous,coding-synonymous	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	,,	1152,2889,2378	TT,TC,CC		47.0602,27.3256,40.4502	,,	638/770,641/773,629/761	70345626	5193,7645	2150	4269	6419	SO:0001819	synonymous_variant	7090	exon17			GCGCACCGTGTTG	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.1923G>A	15.37:g.70345626C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	212	109	0.514151	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Silent	SNP	ENST00000558939.1	37	CCDS45293.1																																																																																			C|0.639;T|0.361	0.361	strong		0.607	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
SEMA3E	9723	hgsc.bcm.edu	37	7	83029438	83029438	+	Silent	SNP	C	C	T	rs2722974	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:83029438C>T	ENST00000307792.3	-	11	1739	c.1272G>A	c.(1270-1272)ttG>ttA	p.L424L	SEMA3E_ENST00000427262.1_Silent_p.L364L	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	424	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				CTGTTTTTACCAATATTGGTT	0.413													C|||	1700	0.339457	0.0605	0.3862	5008	,	,		15230	0.4454		0.4443	False		,,,				2504	0.4663				p.L424L		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G1272A						PASS	.	C	,	567,3839	254.3+/-259.9	43,481,1679	209.0	187.0	194.0		1092,1272	-2.9	0.0	7	dbSNP_100	194	3830,4770	540.0+/-383.7	893,2044,1363	no	coding-synonymous,coding-synonymous	SEMA3E	NM_001178129.1,NM_012431.2	,	936,2525,3042	TT,TC,CC		44.5349,12.8688,33.8075	,	364/716,424/776	83029438	4397,8609	2203	4300	6503	SO:0001819	synonymous_variant	9723	exon11			TTTTACCAATATT	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1272G>A	7.37:g.83029438C>T		Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	328	161	0.490854	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																			C|0.661;N|0.000	.	strong		0.413	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
PLXNA1	5361	hgsc.bcm.edu	37	3	126726705	126726705	+	Silent	SNP	A	A	G	rs9876615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126726705A>G	ENST00000393409.2	+	8	2061	c.2061A>G	c.(2059-2061)acA>acG	p.T687T	PLXNA1_ENST00000251772.4_Silent_p.T664T	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	687					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		ACGTGTGCACACACAACGTGG	0.622													A|||	769	0.153554	0.1036	0.0605	5008	,	,		21337	0.2044		0.1312	False		,,,				2504	0.2577				p.T687T		Atlas-SNP	.											PLXNA1,NS,carcinoma,0,1	PLXNA1	185	1	0			c.A2061G						PASS	.	A		438,3968	208.8+/-229.8	21,396,1786	82.0	73.0	76.0		2061	-7.3	0.1	3	dbSNP_119	76	960,7640	208.2+/-249.7	62,836,3402	no	coding-synonymous	PLXNA1	NM_032242.3		83,1232,5188	GG,GA,AA		11.1628,9.941,10.7489		687/1897	126726705	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	5361	exon8			GTGCACACACAAC	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2061A>G	3.37:g.126726705A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																			A|0.893;G|0.107	0.107	strong		0.622	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
BRD2	6046	hgsc.bcm.edu	37	6	32948426	32948426	+	Silent	SNP	C	C	T	rs2071876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32948426C>T	ENST00000374825.4	+	13	4038	c.2337C>T	c.(2335-2337)tcC>tcT	p.S779S	BRD2_ENST00000395287.1_Silent_p.S814S|BRD2_ENST00000449085.2_Silent_p.S732S|BRD2_ENST00000374831.4_Silent_p.S779S|BRD2_ENST00000443797.2_Silent_p.S659S|BRD2_ENST00000395289.2_Silent_p.S814S	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	779	Poly-Ser.|Ser-rich.				chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CTTCCAGCTCCAGCTCAGATT	0.527													C|||	303	0.0605032	0.028	0.0591	5008	,	,		18054	0.0397		0.0805	False		,,,				2504	0.1063				p.S814S		Atlas-SNP	.											.	BRD2	70	.	0			c.C2442T						PASS	.	C	,,,	103,2919		1,101,1409	110.0	90.0	97.0		2337,2442,2196,2337	4.3	1.0	6	dbSNP_96	97	432,4986		12,408,2289	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	13,509,3698	TT,TC,CC		7.9734,3.4083,6.3389	,,,	779/802,814/837,732/755,779/802	32948426	535,7905	1511	2709	4220	SO:0001819	synonymous_variant	6046	exon13			CAGCTCCAGCTCA	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.2337C>T	6.37:g.32948426C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	125	46	0.368	NM_001199455	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	122	0.055860805860805864	8	0.016260162601626018	22	0.06077348066298342	30	0.05244755244755245	62	0.08179419525065963	C	10.64	1.405612	0.25378	0.034083	0.079734	ENSG00000204256	ENST00000449025	.	.	.	6.15	4.34	0.51931	.	.	.	.	.	T	0.50429	0.1615	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50242	-0.8851	4	.	.	.	-14.4569	11.7392	0.51784	0.1385:0.7281:0.1333:0.0	rs2071876;rs17430814;rs2071876	.	.	.	L	785	.	.	P	+	2	0	BRD2	33056404	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.126000	0.50477	0.871000	0.35750	0.643000	0.83706	CCA	T|0.061;G|0.000;C|0.938	0.061	strong		0.527	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
SLC52A3	113278	hgsc.bcm.edu	37	20	744308	744308	+	Missense_Mutation	SNP	T	T	C	rs3746802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:744308T>C	ENST00000217254.7	-	3	1148	c.907A>G	c.(907-909)Atc>Gtc	p.I303V	SLC52A3_ENST00000473664.1_Intron|SLC52A3_ENST00000381944.3_Missense_Mutation_p.I303V	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	303			I -> V (in dbSNP:rs3746802). {ECO:0000269|PubMed:15489334}.		cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										AGGGTATAGATGAAGGCCAGG	0.627													T|||	466	0.0930511	0.0651	0.0533	5008	,	,		20059	0.0972		0.1083	False		,,,				2504	0.1391				p.I303V		Atlas-SNP	.											.	.	.	.	0			c.A907G						PASS	.	T	VAL/ILE	347,4059	179.4+/-207.9	16,315,1872	94.0	82.0	86.0		907	4.9	1.0	20	dbSNP_107	86	943,7657	207.0+/-248.9	48,847,3405	yes	missense	C20orf54	NM_033409.3	29	64,1162,5277	CC,CT,TT		10.9651,7.8756,9.9185	probably-damaging	303/470	744308	1290,11716	2203	4300	6503	SO:0001583	missense	113278	exon3			TATAGATGAAGGC	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.907A>G	20.37:g.744308T>C	ENSP00000217254:p.Ile303Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	37	CCDS13007.1	210	0.09615384615384616	40	0.08130081300813008	18	0.049723756906077346	64	0.11188811188811189	88	0.11609498680738786	T	17.07	3.296191	0.60086	0.078756	0.109651	ENSG00000101276	ENST00000217254;ENST00000381944	T;T	0.73469	-0.75;-0.75	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.08846	0.0219	M	0.79805	2.47	0.09310	P	0.99999775311	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.61884	-0.6971	9	0.59425	D	0.04	-45.5399	13.4648	0.61247	0.0:0.0:0.0:1.0	rs3746802;rs17773866;rs17855411;rs56784773;rs3746802	303;303	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	V	303	ENSP00000217254:I303V;ENSP00000371370:I303V	ENSP00000217254:I303V	I	-	1	0	C20orf54	692308	1.000000	0.71417	1.000000	0.80357	0.474000	0.32979	7.949000	0.87791	1.864000	0.54056	0.459000	0.35465	ATC	T|0.901;C|0.099	0.099	strong		0.627	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
SLC24A1	9187	hgsc.bcm.edu	37	15	65917220	65917220	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:65917220G>T	ENST00000261892.6	+	2	1089	c.802G>T	c.(802-804)Gtc>Ttc	p.V268F	SLC24A1_ENST00000546330.1_Missense_Mutation_p.V268F|SLC24A1_ENST00000544319.2_Missense_Mutation_p.V268F|SLC24A1_ENST00000399033.4_Missense_Mutation_p.V268F|SLC24A1_ENST00000537259.1_Missense_Mutation_p.V268F|SLC24A1_ENST00000339868.6_Missense_Mutation_p.V268F	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	268					calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						AGAAGCAAACGTCTTGACTTC	0.473																																					p.V268F		Atlas-SNP	.											.	SLC24A1	58	.	0			c.G802T						PASS	.						102.0	94.0	96.0					15																	65917220		1878	4106	5984	SO:0001583	missense	9187	exon2			GCAAACGTCTTGA	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"""Solute carriers"""	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.802G>T	15.37:g.65917220G>T	ENSP00000261892:p.Val268Phe	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	188	25	0.132979	NM_004727	O43485|O75184|Q17RM9	Missense_Mutation	SNP	ENST00000261892.6	37	CCDS45284.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.441223	0.83993	.	.	ENSG00000074621	ENST00000537259;ENST00000261892;ENST00000339868;ENST00000544319;ENST00000399033;ENST00000546330	T;T;T;T;T;T	0.66280	0.02;-0.2;-0.2;-0.2;-0.17;-0.2	5.19	-0.15	0.13416	.	1.232500	0.05722	N	0.597927	T	0.47893	0.1470	N	0.22421	0.69	0.09310	N	1	P;B;B;D;D	0.56746	0.454;0.325;0.325;0.977;0.961	B;B;B;P;B	0.46049	0.132;0.062;0.062;0.502;0.305	T	0.39143	-0.9628	10	0.66056	D	0.02	.	1.7943	0.03058	0.3931:0.3506:0.0977:0.1586	.	268;268;268;268;268	O60721-2;Q17RM9;O60721;F5H127;B4E1W0	.;.;NCKX1_HUMAN;.;.	F	268	ENSP00000439693:V268F;ENSP00000261892:V268F;ENSP00000341837:V268F;ENSP00000445163:V268F;ENSP00000381991:V268F;ENSP00000439190:V268F	ENSP00000261892:V268F	V	+	1	0	SLC24A1	63704273	0.000000	0.05858	0.001000	0.08648	0.977000	0.68977	0.279000	0.18771	-0.180000	0.10637	-0.302000	0.09304	GTC	.	.	none		0.473	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727	
FAM86A	196483	hgsc.bcm.edu	37	16	5140561	5140561	+	Silent	SNP	C	C	T	rs9673770	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:5140561C>T	ENST00000427587.4	-	5	416	c.348G>A	c.(346-348)tcG>tcA	p.S116S	FAM86A_ENST00000458008.4_Silent_p.S82S|FAM86A_ENST00000587133.1_Silent_p.S55S	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	116						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						CCGAGCCTCCCGAGGGCTGCA	0.582													c|||	459	0.0916534	0.0242	0.17	5008	,	,		20650	0.128		0.1402	False		,,,				2504	0.0399				p.S116S		Atlas-SNP	.											FAM86A,NS,carcinoma,0,1	FAM86A	32	1	0			c.G348A						PASS	.	C	,	138,4256	98.5+/-137.1	3,132,2062	62.0	63.0	63.0		348,246	-10.0	0.0	16	dbSNP_119	63	1084,7516	225.2+/-261.4	74,936,3290	no	coding-synonymous,coding-synonymous	FAM86A	NM_201400.2,NM_201598.2	,	77,1068,5352	TT,TC,CC		12.6047,3.1406,9.4043	,	116/331,82/297	5140561	1222,11772	2197	4300	6497	SO:0001819	synonymous_variant	196483	exon5			GCCTCCCGAGGGC	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.348G>A	16.37:g.5140561C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	198	105	0.530303	NM_201400	D3DUF0|Q96S85	Silent	SNP	ENST00000427587.4	37	CCDS10529.1																																																																																			C|0.896;T|0.104	0.104	strong		0.582	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400	
TMEM82	388595	hgsc.bcm.edu	37	1	16069644	16069644	+	Silent	SNP	C	C	T	rs11584945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16069644C>T	ENST00000375782.1	+	3	429	c.291C>T	c.(289-291)ctC>ctT	p.L97L	TMEM82_ENST00000465575.1_3'UTR|RP11-169K16.4_ENST00000418525.1_RNA	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	97	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|lung(5)|prostate(1)|skin(1)	13		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCGTGGTGCTCGAGTTCTCCC	0.711													C|||	928	0.185304	0.23	0.1744	5008	,	,		13275	0.0337		0.2883	False		,,,				2504	0.183				p.L97L		Atlas-SNP	.											.	TMEM82	30	.	0			c.C291T						PASS	.	C		920,3484	345.7+/-308.6	98,724,1380	48.0	46.0	46.0		291	-8.9	0.7	1	dbSNP_120	46	2385,6213	391.8+/-343.8	362,1661,2276	no	coding-synonymous	TMEM82	NM_001013641.1		460,2385,3656	TT,TC,CC		27.739,20.8901,25.4192		97/344	16069644	3305,9697	2202	4299	6501	SO:0001819	synonymous_variant	388595	exon3			GGTGCTCGAGTTC		CCDS30608.1	1p36.13	2008-02-05				ENSG00000162460			32350	protein-coding gene	gene with protein product							Standard	NM_001013641		Approved		uc001axc.4	A0PJX8		ENST00000375782.1:c.291C>T	1.37:g.16069644C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	46	0.638889	NM_001013641	B2RP27|Q5VVD4	Silent	SNP	ENST00000375782.1	37	CCDS30608.1																																																																																			C|0.766;T|0.234	0.234	strong		0.711	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008471.2	NM_001013641	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558315	140558315	+	Missense_Mutation	SNP	G	G	C	rs17844488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140558315G>C	ENST00000239444.2	+	1	945	c.700G>C	c.(700-702)Gtc>Ctc	p.V234L	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	234	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.			V -> L (in Ref. 4; AAG10031). {ECO:0000305}.	homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CATTGAAGTTGTCGATGTCAA	0.512													G|||	673	0.134385	0.0136	0.1441	5008	,	,		24549	0.3333		0.0805	False		,,,				2504	0.1411				p.V234L		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G700C						PASS	.						179.0	226.0	210.0					5																	140558315		2200	4223	6423	SO:0001583	missense	56128	exon1			GAAGTTGTCGATG	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.700G>C	5.37:g.140558315G>C	ENSP00000239444:p.Val234Leu	Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	487	47	0.0965092	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-3.567528	0.00008	.	.	ENSG00000120322	ENST00000239444	T	0.17054	2.3	4.25	-1.67	0.08238	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.04137	0.0115	N	0.00811	-1.165	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.40961	-0.9535	9	0.02654	T	1	.	10.755	0.46232	0.0717:0.6617:0.1685:0.0982	rs17844488	234	Q9UN66	PCDB8_HUMAN	L	234	ENSP00000239444:V234L	ENSP00000239444:V234L	V	+	1	0	PCDHB8	140538499	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.300000	0.01138	-0.925000	0.03775	-3.232000	0.00051	GTC	.	.	weak		0.512	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
MYEOV	26579	hgsc.bcm.edu	37	11	69063510	69063510	+	Missense_Mutation	SNP	G	G	A	rs11539762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:69063510G>A	ENST00000308946.3	+	3	1043	c.593G>A	c.(592-594)cGa>cAa	p.R198Q	MYEOV_ENST00000441339.2_Missense_Mutation_p.R198Q|MYEOV_ENST00000535407.1_Missense_Mutation_p.R140Q	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	198			R -> Q (in dbSNP:rs11539762). {ECO:0000269|PubMed:10753852}.							endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		ATGTGGGCGCGAATGGATGTG	0.612													G|||	806	0.160942	0.1074	0.0893	5008	,	,		17685	0.2163		0.1083	False		,,,				2504	0.2812				p.R198Q		Atlas-SNP	.											MYEOV,colon,carcinoma,0,1	MYEOV	42	1	0			c.G593A						PASS	.	G	GLN/ARG	433,3967	211.2+/-231.4	17,399,1784	132.0	121.0	125.0		593	1.4	0.0	11	dbSNP_120	125	925,7663	204.9+/-247.5	46,833,3415	yes	missense	MYEOV	NM_138768.2	43	63,1232,5199	AA,AG,GG		10.7708,9.8409,10.4558	probably-damaging	198/314	69063510	1358,11630	2200	4294	6494	SO:0001583	missense	26579	exon3			GGGCGCGAATGGA	AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"""myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"""			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.593G>A	11.37:g.69063510G>A	ENSP00000308330:p.Arg198Gln	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	285	0.1304945054945055	54	0.10975609756097561	38	0.10497237569060773	114	0.1993006993006993	79	0.10422163588390501	G	11.19	1.564823	0.27915	0.098409	0.107708	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.24908	1.84;1.84;1.83	1.41	1.41	0.22369	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.57899	0.981	B	0.32762	0.152	T	0.33803	-0.9854	8	0.87932	D	0	.	6.2163	0.20658	0.0:0.0:1.0:0.0	rs11539762;rs60357322;rs11539762	198	Q96EZ4	MYEOV_HUMAN	Q	198;198;140	ENSP00000412482:R198Q;ENSP00000308330:R198Q;ENSP00000438100:R140Q	ENSP00000308330:R198Q	R	+	2	0	MYEOV	68820086	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.346000	0.07760	1.070000	0.40811	0.313000	0.20887	CGA	G|0.878;A|0.122	0.122	strong		0.612	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
SULT1A1	6817	hgsc.bcm.edu	37	16	28620120	28620120	+	Silent	SNP	C	C	T	rs34513973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28620120C>T	ENST00000395607.1	-	2	330	c.57G>A	c.(55-57)ccG>ccA	p.P19P	SULT1A1_ENST00000395609.1_Silent_p.P19P|SULT1A1_ENST00000350842.4_Intron|SULT1A1_ENST00000569554.1_Silent_p.P19P|SULT1A1_ENST00000314752.7_Silent_p.P19P	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	19					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)			endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	ACTTGATGAGCGGGACCCCCT	0.637																																					p.P19P		Atlas-SNP	.											SULT1A1,NS,carcinoma,-1,2	SULT1A1	53	2	0			c.G57A						PASS	.	C	,,,,	63,4331		0,63,2134	37.0	36.0	36.0		57,57,57,57,	-3.8	0.0	16	dbSNP_126	36	406,8178		2,402,3888	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	SULT1A1	NM_001055.3,NM_177529.2,NM_177530.2,NM_177534.2,NM_177536.3	,,,,	2,465,6022	TT,TC,CC		4.7297,1.4338,3.6138	,,,,	19/296,19/296,19/296,19/296,	28620120	469,12509	2197	4292	6489	SO:0001819	synonymous_variant	6817	exon1			GATGAGCGGGACC	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.57G>A	16.37:g.28620120C>T		Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	1164	155	0.133162	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Silent	SNP	ENST00000395607.1	37	CCDS32420.1																																																																																			C|0.965;T|0.035	0.035	strong		0.637	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
HELZ2	85441	hgsc.bcm.edu	37	20	62196033	62196033	+	Missense_Mutation	SNP	C	C	T	rs3810487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62196033C>T	ENST00000467148.1	-	8	4211	c.4142G>A	c.(4141-4143)aGg>aAg	p.R1381K	HELZ2_ENST00000427522.2_Missense_Mutation_p.R812K	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1381			R -> K (in dbSNP:rs3810487).		cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CACCCCGTCCCTGGGCACGAA	0.687													C|||	1099	0.219449	0.0076	0.0994	5008	,	,		16931	0.5317		0.1958	False		,,,				2504	0.2935				p.R1381K		Atlas-SNP	.											.	.	.	.	0			c.G4142A						PASS	.	C	LYS/ARG,LYS/ARG	191,4159		5,181,1989	13.0	11.0	12.0		4142,2435	-0.3	0.1	20	dbSNP_107	12	1595,6957		167,1261,2848	yes	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	26,26	172,1442,4837	TT,TC,CC		18.6506,4.3908,13.8428	benign,benign	1381/2650,812/2081	62196033	1786,11116	2175	4276	6451	SO:0001583	missense	85441	exon9			CCGTCCCTGGGCA	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.4142G>A	20.37:g.62196033C>T	ENSP00000417401:p.Arg1381Lys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	44	29	0.659091	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	523	0.23946886446886448	6	0.012195121951219513	44	0.12154696132596685	317	0.5541958041958042	156	0.20580474934036938	C	0.010	-1.760787	0.00657	0.043908	0.186506	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.33654	1.4;1.4	4.66	-0.274	0.12910	Ribonuclease II/R (2);	0.704916	0.14555	N	0.312409	T	0.00012	0.0000	N	0.02379	-0.575	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.004	T	0.44574	-0.9319	9	0.02654	T	1	-26.0318	4.9363	0.13943	0.0:0.212:0.1822:0.6059	rs3810487;rs3810487	1381;812	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	K	812;1381	ENSP00000393257:R812K;ENSP00000417401:R1381K	ENSP00000393257:R812K	R	-	2	0	RP4-697K14.7	61666477	0.573000	0.26676	0.059000	0.19551	0.015000	0.08874	0.738000	0.26158	0.069000	0.16605	0.491000	0.48974	AGG	C|0.809;T|0.191	0.191	strong		0.687	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39914225	39914225	+	Missense_Mutation	SNP	G	G	C	rs201914405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39914225G>C	ENST00000409794.3	+	18	3381	c.2531G>C	c.(2530-2532)cGc>cCc	p.R844P	CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R785P|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R815P	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	844					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AATGCCCCGCGCCGCCGGCCT	0.697													G|||	3	0.000599042	0.0	0.0	5008	,	,		13101	0.0		0.001	False		,,,				2504	0.002				p.R844P		Atlas-SNP	.											PLEKHG2_ENST00000458508,colon,carcinoma,0,3	PLEKHG2	329	3	0			c.G2531C						PASS	.	G	PRO/ARG	0,4390		0,0,2195	12.0	13.0	13.0		2531	5.7	1.0	19		13	5,8565		0,5,4280	yes	missense	PLEKHG2	NM_022835.2	103	0,5,6475	CC,CG,GG		0.0583,0.0,0.0386	probably-damaging	844/1387	39914225	5,12955	2195	4285	6480	SO:0001583	missense	64857	exon18			CCCCGCGCCGCCG	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.2531G>C	19.37:g.39914225G>C	ENSP00000386733:p.Arg844Pro	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.264441|4.264441	0.80358|0.80358	0.0|0.0	5.83E-4|5.83E-4	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000458508	.|T;T;T	.|0.73575	.|-0.62;-0.67;-0.76	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.000000	.|0.48767	.|D	.|0.000180	T|T	0.77864|0.77864	0.4194|0.4194	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.63880	.|0.993;0.988;0.988	.|P;P;P	.|0.62649	.|0.905;0.806;0.806	T|T	0.75428|0.75428	-0.3321|-0.3321	5|9	.|.	.|.	.|.	.|.	15.3419|15.3419	0.74303|0.74303	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|815;844;785	.|Q9H7P9-3;Q9H7P9;E7ESZ3	.|.;PKHG2_HUMAN;.	P|P	712|844;815;785	.|ENSP00000386733:R844P;ENSP00000392906:R815P;ENSP00000408857:R785P	.|.	A|R	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44606065|44606065	0.911000|0.911000	0.30947|0.30947	1.000000|1.000000	0.80357|0.80357	0.765000|0.765000	0.43378|0.43378	1.287000|1.287000	0.33284|0.33284	2.694000|2.694000	0.91930|0.91930	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.	weak		0.697	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
ZNF845	91664	hgsc.bcm.edu	37	19	53854397	53854397	+	Missense_Mutation	SNP	G	G	C	rs10415799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53854397G>C	ENST00000595091.1	+	5	688	c.469G>C	c.(469-471)Gaa>Caa	p.E157Q	ZNF845_ENST00000458035.1_Missense_Mutation_p.E157Q			Q96IR2	ZN845_HUMAN	zinc finger protein 845	157					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E157Q(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GTTTCAGACCGAAGGGAAAAT	0.408													.|||	1723	0.34405	0.2307	0.2882	5008	,	,		21024	0.4702		0.3738	False		,,,				2504	0.3763				p.E157Q		Atlas-SNP	.											ZNF845,NS,carcinoma,0,6	ZNF845	101	6	3	Substitution - Missense(3)	kidney(2)|stomach(1)	c.G469C						PASS	.	G	GLN/GLU	332,1052		44,244,404	69.0	48.0	54.0		469	-1.4	0.0	19	dbSNP_119	54	1198,1984		230,738,623	no	missense	ZNF845	NM_138374.1	29	274,982,1027	CC,CG,GG		37.6493,23.9884,33.5085	benign	157/971	53854397	1530,3036	692	1591	2283	SO:0001583	missense	91664	exon4			CAGACCGAAGGGA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.469G>C	19.37:g.53854397G>C	ENSP00000470005:p.Glu157Gln	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	241	240	0.995851	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	792	0.3626373626373626	129	0.2621951219512195	114	0.3149171270718232	283	0.49475524475524474	266	0.35092348284960423	G	1.231	-0.624000	0.03636	0.239884	0.376493	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.08282	3.11	1.2	-1.38	0.09027	.	.	.	.	.	T	0.00012	0.0000	L	0.48935	1.535	0.80722	P	0.0	B	0.28933	0.228	B	0.29663	0.105	T	0.42799	-0.9430	8	0.18276	T	0.48	.	3.6513	0.08205	0.1859:0.2581:0.556:0.0	rs10415799	157	Q96IR2	ZN845_HUMAN	Q	157	ENSP00000388311:E157Q	ENSP00000412086:E157Q	E	+	1	0	ZNF845	58546209	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.057000	0.14279	-0.374000	0.07967	0.411000	0.27672	GAA	G|0.643;C|0.357	0.357	strong		0.408	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
USP45	85015	hgsc.bcm.edu	37	6	99956560	99956560	+	Missense_Mutation	SNP	T	T	C	rs7744845	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:99956560T>C	ENST00000327681.6	-	3	731	c.199A>G	c.(199-201)Aaa>Gaa	p.K67E	USP45_ENST00000500704.2_Missense_Mutation_p.K67E|USP45_ENST00000392738.2_5'UTR|USP45_ENST00000369231.3_Missense_Mutation_p.K67E|USP45_ENST00000329966.6_Missense_Mutation_p.K67E|USP45_ENST00000369232.2_5'UTR|USP45_ENST00000369233.2_Missense_Mutation_p.K67E|USP45_ENST00000472914.2_Missense_Mutation_p.K67E	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	67			K -> E (in dbSNP:rs7744845). {ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.K67E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CTTCTTTCTTTTAAACATTCT	0.373													T|||	1652	0.329872	0.0635	0.3501	5008	,	,		18487	0.5546		0.327	False		,,,				2504	0.4468				p.K67E		Atlas-SNP	.											USP45,NS,carcinoma,0,1	USP45	56	1	1	Substitution - Missense(1)	stomach(1)	c.A199G						PASS	.	T	GLU/LYS	483,3921	223.6+/-240.1	33,417,1752	96.0	92.0	93.0		199	5.3	1.0	6	dbSNP_116	93	2502,6098	410.3+/-350.1	365,1772,2163	yes	missense	USP45	NM_001080481.1	56	398,2189,3915	CC,CT,TT		29.093,10.9673,22.9545	possibly-damaging	67/815	99956560	2985,10019	2202	4300	6502	SO:0001583	missense	85015	exon3			TTTCTTTTAAACA	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"""Ubiquitin-specific peptidases"""	20080	protein-coding gene	gene with protein product			"""ubiquitin specific protease 45"""			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.199A>G	6.37:g.99956560T>C	ENSP00000333376:p.Lys67Glu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	77	47	0.61039	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	37	CCDS34501.1	687	0.31456043956043955	39	0.07926829268292683	108	0.2983425414364641	291	0.5087412587412588	249	0.32849604221635886	T	24.0	4.478488	0.84747	0.109673	0.29093	ENSG00000123552	ENST00000500704;ENST00000327681;ENST00000369233;ENST00000329966;ENST00000472914;ENST00000369231	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	5.35	5.35	0.76521	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.150538	0.56097	D	0.000024	T	0.58736	0.2143	M	0.86651	2.83	0.19775	P	0.9999570881	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.62324	-0.6878	9	0.22109	T	0.4	.	14.9824	0.71321	0.0:0.0:0.0:1.0	rs7744845;rs17845068;rs17857850;rs60315569;rs7744845	67;67	D6RBV3;Q70EL2	.;UBP45_HUMAN	E	67	ENSP00000424372:K67E;ENSP00000333376:K67E;ENSP00000358236:K67E;ENSP00000330540:K67E;ENSP00000423993:K67E;ENSP00000358234:K67E	ENSP00000333376:K67E	K	-	1	0	USP45	100063281	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.207000	0.77899	2.036000	0.60181	0.402000	0.26972	AAA	T|0.734;C|0.266	0.266	strong		0.373	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
JAK1	3716	hgsc.bcm.edu	37	1	65303659	65303659	+	Silent	SNP	C	C	T	rs12129819	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:65303659C>T	ENST00000342505.4	-	22	3344	c.3096G>A	c.(3094-3096)aaG>aaA	p.K1032K		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	1032	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TGTAATACTCCTTATCGGTTT	0.423			Mis		ALL								C|||	193	0.0385383	0.0219	0.0548	5008	,	,		19137	0.0		0.1153	False		,,,				2504	0.0102				p.K1032K		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.G3096A						PASS	.	C		134,3634		2,130,1752	84.0	77.0	79.0		3096	2.4	1.0	1	dbSNP_120	79	834,7408		45,744,3332	no	coding-synonymous	JAK1	NM_002227.2		47,874,5084	TT,TC,CC		10.1189,3.5563,8.06		1032/1155	65303659	968,11042	1884	4121	6005	SO:0001819	synonymous_variant	3716	exon22			ATACTCCTTATCG	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.3096G>A	1.37:g.65303659C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			C|0.937;T|0.063	0.063	strong		0.423	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
TRIM9	114088	hgsc.bcm.edu	37	14	51446216	51446216	+	Missense_Mutation	SNP	T	T	G	rs2275462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:51446216T>G	ENST00000298355.3	-	9	3080	c.1959A>C	c.(1957-1959)ttA>ttC	p.L653F	TRIM9_ENST00000338969.5_Missense_Mutation_p.L734F	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	653	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		L -> F (in dbSNP:rs2275462). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9179496}.		negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TTTTTCTATTTAAGTCGAGGA	0.448													T|||	2954	0.589856	0.4372	0.7262	5008	,	,		19323	0.6925		0.5537	False		,,,				2504	0.6309				p.L653F		Atlas-SNP	.											TRIM9_ENST00000338969,NS,carcinoma,-2,2	TRIM9	188	2	0			c.A1959C						PASS	.	T	PHE/LEU	1944,2462	551.4+/-378.3	432,1080,691	198.0	218.0	211.0		1959	3.5	1.0	14	dbSNP_100	211	4883,3717	618.6+/-396.8	1386,2111,803	yes	missense	TRIM9	NM_015163.5	22	1818,3191,1494	GG,GT,TT		43.2209,44.1217,47.5088	benign	653/711	51446216	6827,6179	2203	4300	6503	SO:0001583	missense	114088	exon9			TCTATTTAAGTCG	AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1959A>C	14.37:g.51446216T>G	ENSP00000298355:p.Leu653Phe	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	135	77	0.57037	NM_015163	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	37	CCDS9703.1	1278	0.5851648351648352	207	0.42073170731707316	241	0.6657458563535912	408	0.7132867132867133	422	0.5567282321899736	T	15.58	2.876985	0.51801	0.441217	0.567791	ENSG00000100505	ENST00000298355;ENST00000338969	T;T	0.73363	-0.44;-0.74	5.89	3.54	0.40534	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.122414	0.56097	N	0.000032	T	0.00012	0.0000	L	0.41236	1.265	0.09310	P	1.0	B;B	0.21606	0.058;0.012	B;B	0.29663	0.105;0.077	T	0.48387	-0.9040	9	0.11182	T	0.66	.	1.0846	0.01650	0.1734:0.1282:0.1816:0.5167	rs2275462;rs17795996;rs17855888;rs60258718;rs2275462	734;653	Q9C026-4;Q9C026	.;TRIM9_HUMAN	F	653;734	ENSP00000298355:L653F;ENSP00000342970:L734F	ENSP00000298355:L653F	L	-	3	2	TRIM9	50515966	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	0.502000	0.22594	1.035000	0.39972	0.455000	0.32223	TTA	T|0.451;G|0.549	0.549	strong		0.448	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163	
CASC5	57082	hgsc.bcm.edu	37	15	40916801	40916801	+	Missense_Mutation	SNP	A	A	G	rs16970911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40916801A>G	ENST00000346991.5	+	11	4807	c.4417A>G	c.(4417-4419)Acc>Gcc	p.T1473A	CASC5_ENST00000399668.2_Missense_Mutation_p.T1447A			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1473			T -> A (in dbSNP:rs16970911). {ECO:0000269|PubMed:10980622}.		acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TCATTTCTCAACCGACCAACC	0.318													A|||	155	0.0309505	0.0023	0.049	5008	,	,		21576	0.0		0.0934	False		,,,				2504	0.0245				p.T1473A		Atlas-SNP	.											.	CASC5	269	.	0			c.A4417G						PASS	.	A	ALA/THR,ALA/THR	72,3612		0,72,1770	81.0	76.0	78.0		4339,4417	1.5	0.0	15	dbSNP_123	78	724,7464		36,652,3406	yes	missense,missense	CASC5	NM_144508.3,NM_170589.3	58,58	36,724,5176	GG,GA,AA		8.8422,1.9544,6.7049	benign,benign	1447/2317,1473/2343	40916801	796,11076	1842	4094	5936	SO:0001583	missense	57082	exon11			TTCTCAACCGACC	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.4417A>G	15.37:g.40916801A>G	ENSP00000335463:p.Thr1473Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	105	0.04807692307692308	2	0.0040650406504065045	25	0.06906077348066299	0	0.0	78	0.10290237467018469	A	1.921	-0.448317	0.04572	0.019544	0.088422	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.04706	3.57;3.57	5.12	1.48	0.22813	.	0.641069	0.14008	N	0.347669	T	0.00109	0.0003	L	0.27053	0.805	0.09310	N	1	B;B;B	0.31705	0.04;0.04;0.336	B;B;B	0.23150	0.028;0.028;0.044	T	0.48625	-0.9019	10	0.10636	T	0.68	.	8.2843	0.31920	0.664:0.0:0.336:0.0	rs16970911;rs52817506;rs60813014;rs16970911	1447;1473;1447	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	A	1473;1447;1447	ENSP00000335463:T1473A;ENSP00000382576:T1447A	ENSP00000260369:T1447A	T	+	1	0	CASC5	38704093	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.292000	0.19011	0.056000	0.16144	0.491000	0.48974	ACC	A|0.945;G|0.055	0.055	strong		0.318	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
FRA10AC1	118924	hgsc.bcm.edu	37	10	95454681	95454681	+	Missense_Mutation	SNP	G	G	C	rs2275438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:95454681G>C	ENST00000359204.4	-	5	430	c.233C>G	c.(232-234)aCa>aGa	p.T78R	FRA10AC1_ENST00000371430.2_Missense_Mutation_p.T78R|FRA10AC1_ENST00000536233.1_Missense_Mutation_p.T78R|FRA10AC1_ENST00000394100.2_Missense_Mutation_p.T78R	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1	78			T -> R (in dbSNP:rs2275438). {ECO:0000269|PubMed:15203205, ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						TACGAACTTTGTATGTCTTTG	0.333													G|||	1806	0.360623	0.0696	0.4539	5008	,	,		15001	0.3978		0.5447	False		,,,				2504	0.4601				p.T78R		Atlas-SNP	.											.	FRA10AC1	68	.	0			c.C233G						PASS	.	G	ARG/THR	629,3775	271.9+/-270.5	61,507,1634	144.0	141.0	142.0		233	-0.3	1.0	10	dbSNP_100	142	4440,4160	587.3+/-392.2	1125,2190,985	yes	missense	FRA10AC1	NM_145246.4	71	1186,2697,2619	CC,CG,GG		48.3721,14.2825,38.9803	benign	78/316	95454681	5069,7935	2202	4300	6502	SO:0001583	missense	118924	exon5			AACTTTGTATGTC	AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"""chromosome 10 open reading frame 4"""	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.233C>G	10.37:g.95454681G>C	ENSP00000360488:p.Thr78Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_145246	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Missense_Mutation	SNP	ENST00000359204.4	37	CCDS7430.1	873	0.39972527472527475	51	0.10365853658536585	164	0.4530386740331492	234	0.4090909090909091	424	0.5593667546174143	G	10.96	1.498328	0.26861	0.142825	0.516279	ENSG00000148690	ENST00000359204;ENST00000536233;ENST00000371426;ENST00000371430;ENST00000394100	T;T;T;T	0.21543	2.07;2.02;2.0;2.01	5.01	-0.297	0.12820	.	0.301591	0.37906	N	0.001893	T	0.00012	0.0000	N	0.03115	-0.41	0.37959	P	0.06711	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.42085	-0.9472	9	0.36615	T	0.2	-14.4182	8.5881	0.33670	0.0:0.3705:0.2075:0.422	rs2275438;rs17487318;rs17851587;rs52797420;rs2275438	78;78;78	F8WCS9;Q70Z53-2;Q70Z53	.;.;F10C1_HUMAN	R	78	ENSP00000360488:T78R;ENSP00000438405:T78R;ENSP00000360484:T78R;ENSP00000377660:T78R	ENSP00000360488:T78R	T	-	2	0	FRA10AC1	95444671	1.000000	0.71417	0.986000	0.45419	0.942000	0.58702	2.067000	0.41461	0.130000	0.18549	0.655000	0.94253	ACA	G|0.606;C|0.394	0.394	strong		0.333	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246	
PSG4	5672	hgsc.bcm.edu	37	19	43708245	43708245	+	Missense_Mutation	SNP	G	G	C	rs3170216	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:43708245G>C	ENST00000405312.3	-	2	460	c.223C>G	c.(223-225)Ctc>Gtc	p.L75V	PSG4_ENST00000244295.9_Missense_Mutation_p.L75V|PSG4_ENST00000433626.2_Missense_Mutation_p.L75V	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	75	Ig-like V-type.		L -> V (in dbSNP:rs3170216). {ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2271648, ECO:0000269|PubMed:7794280}.		female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				TAATGGTAGAGGTATGTCATT	0.423													G|||	864	0.172524	0.2791	0.1643	5008	,	,		18097	0.005		0.2893	False		,,,				2504	0.0869				p.T75A		Atlas-SNP	.											.	PSG4	129	.	0			c.A223G						PASS	.	G	VAL/LEU,VAL/LEU	1246,3024		350,546,1239	196.0	207.0	203.0		223,223	-3.3	0.0	19	dbSNP_105	203	2389,6153		487,1415,2369	yes	missense,missense	PSG4	NM_002780.3,NM_213633.1	32,32	837,1961,3608	CC,CG,GG		27.9677,29.1803,28.3718	,	75/420,75/327	43708245	3635,9177	2135	4271	6406	SO:0001583	missense	5672	exon2			GGTAGAGGTATGT		CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9521	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1-glycoprotein 4"""	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.223C>G	19.37:g.43708245G>C	ENSP00000384770:p.Leu75Val	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	262	132	0.503817	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	37	CCDS46093.1	402	0.18406593406593408	114	0.23170731707317074	61	0.1685082872928177	5	0.008741258741258742	222	0.2928759894459103	N	0.023	-1.397258	0.01175	0.291803	0.279677	ENSG00000243137	ENST00000244295;ENST00000405312;ENST00000433626;ENST00000451895	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	1.65	-3.31	0.04988	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	0.80722	P	0.0	P;P;B	0.46706	0.883;0.694;0.058	P;B;B	0.49140	0.601;0.379;0.056	T	0.08472	-1.0720	8	0.12766	T	0.61	.	2.9373	0.05818	0.2951:0.0:0.3242:0.3807	rs3170216;rs17680844	75;75;75	E7EX79;Q00888-2;Q00888	.;.;PSG4_HUMAN	V	75;75;75;91	ENSP00000244295:L75V;ENSP00000384770:L75V;ENSP00000387864:L75V;ENSP00000388134:L91V	ENSP00000244295:L75V	L	-	1	0	PSG4	48400085	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.219000	0.00553	-2.341000	0.00625	0.173000	0.16961	CTC	G|0.800;C|0.200	0.200	strong		0.423	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
NUP153	9972	hgsc.bcm.edu	37	6	17675246	17675246	+	Missense_Mutation	SNP	T	T	C	rs2228375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:17675246T>C	ENST00000262077.2	-	5	741	c.742A>G	c.(742-744)Atc>Gtc	p.I248V	NUP153_ENST00000537253.1_Missense_Mutation_p.I248V	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	248			I -> V (in dbSNP:rs2228375).		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			GTTTTAAGGATTGAAGAATTC	0.423													T|||	605	0.120807	0.0159	0.2839	5008	,	,		13768	0.0456		0.2376	False		,,,				2504	0.1043				p.I248V		Atlas-SNP	.											.	NUP153	116	.	0			c.A742G						PASS	.	T	VAL/ILE	260,4146	148.8+/-183.1	7,246,1950	102.0	98.0	99.0		742	-11.5	0.0	6	dbSNP_98	99	2527,6073	413.8+/-351.3	387,1753,2160	yes	missense	NUP153	NM_005124.2	29	394,1999,4110	CC,CT,TT		29.3837,5.901,21.4286	benign	248/1476	17675246	2787,10219	2203	4300	6503	SO:0001583	missense	9972	exon5			TAAGGATTGAAGA	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"""nucleoporin 153kD"""			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.742A>G	6.37:g.17675246T>C	ENSP00000262077:p.Ile248Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	37	CCDS4541.1	309	0.14148351648351648	9	0.018292682926829267	77	0.212707182320442	28	0.04895104895104895	195	0.25725593667546176	T	0.032	-1.325540	0.01309	0.05901	0.293837	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.29917	1.55;1.55	5.74	-11.5	0.00074	Nucleoporin, Nup153-like (1);	1.663100	0.03322	N	0.192100	T	0.03477	0.0100	N	0.20401	0.57	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.002	T	0.18840	-1.0324	9	0.02654	T	1	4.1496	11.4151	0.49947	0.2386:0.5434:0.0:0.218	rs2228375;rs12195921;rs17332198;rs60813929;rs2228375	248;270;248	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	V	248;270;248	ENSP00000262077:I248V;ENSP00000444029:I248V	ENSP00000262077:I248V	I	-	1	0	NUP153	17783225	0.015000	0.18098	0.001000	0.08648	0.691000	0.40173	-1.085000	0.03390	-2.927000	0.00302	-3.185000	0.00055	ATC	T|0.840;C|0.160	0.160	strong		0.423	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		
ITPR1	3708	hgsc.bcm.edu	37	3	4842231	4842231	+	Silent	SNP	C	C	T	rs2291862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:4842231C>T	ENST00000443694.2	+	51	7009	c.7009C>T	c.(7009-7011)Ctg>Ttg	p.L2337L	ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000423119.2_Silent_p.L2304L|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Silent_p.L2337L|ITPR1_ENST00000302640.8_Silent_p.L2337L|ITPR1_ENST00000357086.4_Silent_p.L2304L|ITPR1_ENST00000456211.2_Silent_p.L2289L			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2352					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AATTCTACGACTGATATTTTC	0.493													T|||	1325	0.264577	0.1165	0.3617	5008	,	,		20031	0.377		0.3062	False		,,,				2504	0.2372				p.L2337L		Atlas-SNP	.											.	ITPR1	659	.	0			c.C7009T						PASS	.	T	,,	524,3364		32,460,1452	105.0	105.0	105.0		6910,7009,6865	-0.9	0.1	3	dbSNP_100	105	2284,5992		320,1644,2174	no	coding-synonymous,coding-synonymous,coding-synonymous	ITPR1	NM_001099952.2,NM_001168272.1,NM_002222.5	,,	352,2104,3626	TT,TC,CC		27.5979,13.4774,23.0845	,,	2304/2711,2337/2744,2289/2696	4842231	2808,9356	1944	4138	6082	SO:0001819	synonymous_variant	3708	exon53			CTACGACTGATAT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7009C>T	3.37:g.4842231C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	164	78	0.47561	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	37	CCDS54551.1																																																																																			C|0.722;T|0.278	0.278	strong		0.493	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
COL6A3	1293	hgsc.bcm.edu	37	2	238253065	238253065	+	Silent	SNP	C	C	T	rs2291795	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238253065C>T	ENST00000295550.4	-	36	8048	c.7596G>A	c.(7594-7596)aaG>aaA	p.K2532K	COL6A3_ENST00000472056.1_Silent_p.K1925K|COL6A3_ENST00000409809.1_Silent_p.K2326K|COL6A3_ENST00000346358.4_Silent_p.K2332K|COL6A3_ENST00000347401.3_Silent_p.K2331K|COL6A3_ENST00000353578.4_Silent_p.K2326K	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2532	Nonhelical region.|VWFA 11. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CATCTGAGAGCTTGAGCACAG	0.537													C|||	775	0.154752	0.1747	0.1182	5008	,	,		21761	0.1865		0.0944	False		,,,				2504	0.183				p.K2532K		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7596A						PASS	.	C	,,	716,3690	296.4+/-284.2	62,592,1549	162.0	159.0	160.0		7596,5775,6978	4.0	1.0	2	dbSNP_100	160	989,7611	213.8+/-253.6	61,867,3372	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	123,1459,4921	TT,TC,CC		11.5,16.2506,13.1093	,,	2532/3178,1925/2571,2326/2972	238253065	1705,11301	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon36			TGAGAGCTTGAGC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7596G>A	2.37:g.238253065C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	204	96	0.470588	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.865;T|0.135	0.135	strong		0.537	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
OR2J2	26707	hgsc.bcm.edu	37	6	29142054	29142054	+	Silent	SNP	C	C	G	rs3129159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29142054C>G	ENST00000377167.2	+	1	744	c.642C>G	c.(640-642)ctC>ctG	p.L214L		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						CTCTCATTCTCATTCTCACTA	0.473													C|||	1893	0.377995	0.112	0.451	5008	,	,		20987	0.378		0.5477	False		,,,				2504	0.5112				p.L214L		Atlas-SNP	.											.	OR2J2	51	.	0			c.C642G						PASS	.	C		733,3157		72,589,1284	155.0	129.0	137.0		642	1.1	0.3	6	dbSNP_103	137	4502,3786		1240,2022,882	no	coding-synonymous	OR2J2	NM_030905.2		1312,2611,2166	GG,GC,CC		45.6805,18.8432,42.9874		214/313	29142054	5235,6943	1945	4144	6089	SO:0001819	synonymous_variant	26707	exon1			CATTCTCATTCTC		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.642C>G	6.37:g.29142054C>G		Somatic	386	1	0.00259067		WXS	Illumina HiSeq	Phase_I	499	297	0.59519	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Silent	SNP	ENST00000377167.2	37	CCDS43434.1																																																																																			C|0.567;G|0.433	0.433	strong		0.473	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2		
ART4	420	hgsc.bcm.edu	37	12	14993854	14993854	+	Silent	SNP	A	A	G	rs1861698	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:14993854A>G	ENST00000228936.4	-	2	759	c.378T>C	c.(376-378)taT>taC	p.Y126Y	RP11-233G1.4_ENST00000444324.2_RNA|C12orf60_ENST00000527783.1_Intron	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	126					arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)	p.Y126Y(1)		large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						TGTTCAATGTATAAAACAAAA	0.423													A|||	1283	0.25619	0.2625	0.3573	5008	,	,		20350	0.0903		0.3549	False		,,,				2504	0.2454				p.Y126Y		Atlas-SNP	.											ART4,NS,carcinoma,0,1	ART4	27	1	1	Substitution - coding silent(1)	stomach(1)	c.T378C						PASS	.	A		1226,3180	424.5+/-340.5	172,882,1149	138.0	132.0	134.0		378	-0.4	0.0	12	dbSNP_92	134	3233,5367	486.5+/-371.9	624,1985,1691	no	coding-synonymous	ART4	NM_021071.2		796,2867,2840	GG,GA,AA		37.593,27.8257,34.2842		126/315	14993854	4459,8547	2203	4300	6503	SO:0001819	synonymous_variant	420	exon2			CAATGTATAAAAC	X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"""CD molecules"", ""Blood group antigens"""	726	protein-coding gene	gene with protein product		110600	"""Dombrock blood group"", ""ADP-ribosyltransferase 4 (DO blood group)"", ""ADP-ribosyltransferase 4"""	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.378T>C	12.37:g.14993854A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	89	58	0.651685	NM_021071	Q9BZ50|Q9BZ51|Q9HB06	Silent	SNP	ENST00000228936.4	37	CCDS8668.1																																																																																			A|0.694;G|0.306	0.306	strong		0.423	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071	
AMPD1	270	hgsc.bcm.edu	37	1	115236057	115236057	+	Splice_Site	SNP	G	G	A	rs17602729	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:115236057G>A	ENST00000520113.2	-	2	148	c.133C>T	c.(133-135)Caa>Taa	p.Q45*	AMPD1_ENST00000353928.6_Splice_Site_p.Q12*|AMPD1_ENST00000369538.3_Intron			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	45					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	CAATACTCACGTTTCTCTTCA	0.323													G|||	191	0.038139	0.0045	0.0576	5008	,	,		12866	0.001		0.1233	False		,,,				2504	0.0204				p.Q45X		Atlas-SNP	.											AMPD1_ENST00000520113,NS,carcinoma,0,2	AMPD1	223	2	0			c.C133T	GRCh37	CM920025	AMPD1	M	rs17602729	PASS	.	G	stop/GLN,	104,4302	81.9+/-120.4	2,100,2101	85.0	90.0	89.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	133,	2.8	1.0	1	dbSNP_123	89	1126,7472	232.6+/-266.2	89,948,3262	yes	stop-gained-near-splice,intron	AMPD1	NM_000036.2,NM_001172626.1	,	91,1048,5363	AA,AG,GG		13.0961,2.3604,9.4586	,	45/781,	115236057	1230,11774	2203	4299	6502	SO:0001630	splice_region_variant	270	exon2			ACTCACGTTTCTC	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.133+1C>T	1.37:g.115236057G>A		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	174	114	0.655172	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Nonsense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	117	0.05357142857142857	3	0.006097560975609756	30	0.08287292817679558	0	0.0	84	0.11081794195250659	G	29.9	5.043403	0.93685	0.023604	0.130961	ENSG00000116748	ENST00000520113;ENST00000353928	.	.	.	4.91	2.84	0.33178	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6038	0.62035	0.0:0.2934:0.7066:0.0	rs17602729;rs52833197;rs17602729	.	.	.	X	45;12	.	.	Q	-	1	0	AMPD1	115037580	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.265000	0.43311	1.143000	0.42306	0.650000	0.86243	CAA	G|0.923;A|0.077	0.077	strong		0.323	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		Nonsense_Mutation
GGTLC2	91227	hgsc.bcm.edu	37	22	22988849	22988849	+	Missense_Mutation	SNP	G	G	T	rs149057858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22988849G>T	ENST00000480559.1	+	1	34	c.34G>T	c.(34-36)Gcc>Tcc	p.A12S	POM121L1P_ENST00000402027.1_RNA|GGTLC2_ENST00000448514.1_Missense_Mutation_p.A12S	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	12					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)	gamma-glutamyltransferase activity (GO:0003840)	p.A12S(1)		endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		CCAGCTCCGGGCCCAGATCTC	0.632																																					p.A12S		Atlas-SNP	.											GGTLC2,NS,carcinoma,0,1	GGTLC2	20	1	1	Substitution - Missense(1)	prostate(1)	c.G34T						scavenged	.	G	SER/ALA	27,4327		1,25,2151	22.0	19.0	20.0		34		0.0	22	dbSNP_134	20	17,8327		0,17,4155	no	missense	GGTLC2	NM_199127.2	99	1,42,6306	TT,TG,GG		0.2037,0.6201,0.3465	benign	12/219	22988849	44,12654	2177	4172	6349	SO:0001583	missense	91227	exon1			CTCCGGGCCCAGA	X98922	CCDS13802.2	22q11.21	2008-03-25	2008-03-10	2008-03-10	ENSG00000100121	ENSG00000100121		"""Gamma-glutamyltransferases"""	18596	protein-coding gene	gene with protein product		612339	"""gamma-glutamyltransferase-like 4"""	GGTL4		9074928, 18357469	Standard	NM_199127		Approved		uc010gtt.2	Q14390	OTTHUMG00000151177	ENST00000480559.1:c.34G>T	22.37:g.22988849G>T	ENSP00000419751:p.Ala12Ser	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	480	18	0.0375	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Missense_Mutation	SNP	ENST00000480559.1	37	CCDS13802.2	.	.	.	.	.	.	.	.	.	.	g	0.173	-1.069376	0.01918	0.006201	0.002037	ENSG00000100121	ENST00000480559;ENST00000448514	T;T	0.07021	3.23;3.23	.	.	.	.	0.662303	0.15023	N	0.284911	T	0.02047	0.0064	N	0.11064	0.09	0.20489	N	0.999896	B;B	0.10296	0.0;0.003	B;B	0.11329	0.001;0.006	T	0.45411	-0.9263	9	0.07990	T	0.79	-4.876	3.5811	0.07954	2.0E-4:0.4998:0.4998:2.0E-4	.	12;12	Q14390;B7WND7	GGTL2_HUMAN;.	S	12	ENSP00000419751:A12S;ENSP00000415676:A12S	ENSP00000415676:A12S	A	+	1	0	GGTLC2	21318849	0.996000	0.38824	0.000000	0.03702	0.000000	0.00434	0.778000	0.26732	-0.000000	0.14550	0.000000	0.15137	GCC	G|0.996;T|0.004	0.004	strong		0.632	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127	
KRT6C	286887	hgsc.bcm.edu	37	12	52863213	52863213	+	Missense_Mutation	SNP	C	C	T	rs412533	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52863213C>T	ENST00000252250.6	-	8	1488	c.1441G>A	c.(1441-1443)Gtt>Att	p.V481I		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	481	Tail.		V -> I (in dbSNP:rs412533). {ECO:0000269|PubMed:7543104}.		intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		ACTTGTCCAACGCCTTCGCCA	0.607													C|||	1250	0.249601	0.0242	0.2637	5008	,	,		21887	0.4812		0.3628	False		,,,				2504	0.1892				p.V481I		Atlas-SNP	.											.	KRT6C	55	.	0			c.G1441A						PASS	.	C	ILE/VAL	316,4090	170.5+/-200.9	15,286,1902	140.0	109.0	119.0		1441	3.6	1.0	12	dbSNP_80	119	3163,5437	480.9+/-370.5	583,1997,1720	no	missense	KRT6C	NM_173086.4	29	598,2283,3622	TT,TC,CC		36.7791,7.172,26.7492	possibly-damaging	481/565	52863213	3479,9527	2203	4300	6503	SO:0001583	missense	286887	exon8			GTCCAACGCCTTC	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.1441G>A	12.37:g.52863213C>T	ENSP00000252250:p.Val481Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	730	0.3342490842490842	19	0.03861788617886179	116	0.32044198895027626	320	0.5594405594405595	275	0.3627968337730871	C	12.01	1.809706	0.31961	0.07172	0.367791	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.92495	-3.05	3.57	3.57	0.40892	.	0.000000	0.49305	D	0.000143	T	0.00012	0.0000	L	0.54323	1.7	0.40382	P	0.020545000000000035	P	0.44006	0.824	B	0.27500	0.08	T	0.42766	-0.9432	9	0.39692	T	0.17	.	11.8038	0.52143	0.1761:0.8239:0.0:0.0	rs412533	481	P48668	K2C6C_HUMAN	I	481;466	ENSP00000252250:V481I	ENSP00000252250:V481I	V	-	1	0	KRT6C	51149480	0.007000	0.16637	0.994000	0.49952	0.774000	0.43823	0.864000	0.27926	1.983000	0.57843	0.448000	0.29417	GTT	C|0.723;T|0.277	0.277	strong		0.607	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
NHSL1	57224	hgsc.bcm.edu	37	6	138753337	138753337	+	Silent	SNP	C	C	T	rs2039121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138753337C>T	ENST00000427025.2	-	5	2785	c.2157G>A	c.(2155-2157)aaG>aaA	p.K719K	NHSL1_ENST00000343505.5_Silent_p.K715K	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	719										breast(2)|endometrium(4)|kidney(1)	7						AGCTGCCACTCTTGCCTGGGA	0.642													C|||	3690	0.736821	0.5734	0.7219	5008	,	,		15984	0.9008		0.7396	False		,,,				2504	0.7965				p.K719K		Atlas-SNP	.											.	NHSL1	99	.	0			c.G2157A						PASS	.	C	,	847,537		263,321,108	38.0	39.0	38.0		2145,2157	1.9	0.1	6	dbSNP_94	38	2344,838		861,622,108	no	coding-synonymous,coding-synonymous	NHSL1	NM_001144060.1,NM_020464.1	,	1124,943,216	TT,TC,CC		26.3356,38.8006,30.1139	,	715/1607,719/1611	138753337	3191,1375	692	1591	2283	SO:0001819	synonymous_variant	57224	exon5			GCCACTCTTGCCT	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.2157G>A	6.37:g.138753337C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Silent	SNP	ENST00000427025.2	37	CCDS55063.1																																																																																			C|0.236;T|0.764	0.764	strong		0.642	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
FAM179A	165186	hgsc.bcm.edu	37	2	29226498	29226498	+	Silent	SNP	G	G	A	rs12613325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29226498G>A	ENST00000379558.4	+	6	1131	c.780G>A	c.(778-780)ccG>ccA	p.P260P	FAM179A_ENST00000403861.2_Silent_p.P260P	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	260										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TTCCCAGCCCGTTACCTCCAG	0.642													A|||	2971	0.593251	0.3056	0.7089	5008	,	,		18152	0.6677		0.7584	False		,,,				2504	0.6534				p.P260P		Atlas-SNP	.											.	FAM179A	106	.	0			c.G780A						PASS	.	A		1513,2439		294,925,757	28.0	31.0	30.0		780	2.0	0.0	2	dbSNP_120	30	6585,1697		2629,1327,185	no	coding-synonymous	FAM179A	NM_199280.2		2923,2252,942	AA,AG,GG		20.4902,38.2844,33.8074		260/1020	29226498	8098,4136	1976	4141	6117	SO:0001819	synonymous_variant	165186	exon6			CAGCCCGTTACCT	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.780G>A	2.37:g.29226498G>A		Somatic	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	249	248	0.995984	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			G|0.368;A|0.632	0.632	strong		0.642	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418264	105418264	+	Missense_Mutation	SNP	G	G	A	rs55650155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105418264G>A	ENST00000333244.5	-	7	3643	c.3524C>T	c.(3523-3525)gCg>gTg	p.A1175V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1175						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGGGGCTGACGCCCCGAACGA	0.612													.|||	1918	0.382987	0.2474	0.3689	5008	,	,		17745	0.3175		0.5507	False		,,,				2504	0.4714				p.A1175V		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,+1,1	AHNAK2	719	1	0			c.C3524T						PASS	.	G	VAL/ALA	976,2888		190,596,1146	168.0	168.0	168.0		3524	-1.0	0.0	14	dbSNP_129	168	4213,4025		1267,1679,1173	no	missense	AHNAK2	NM_138420.2	64	1457,2275,2319	AA,AG,GG		48.8589,25.2588,42.8772	benign	1175/5796	105418264	5189,6913	1932	4119	6051	SO:0001583	missense	113146	exon7			GCTGACGCCCCGA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3524C>T	14.37:g.105418264G>A	ENSP00000353114:p.Ala1175Val	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	341	205	0.601173	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	753	0.3447802197802198	121	0.2459349593495935	128	0.35359116022099446	151	0.263986013986014	353	0.4656992084432718	a	6.253	0.414800	0.11870	0.252588	0.511411	ENSG00000185567	ENST00000333244	T	0.00669	5.9	4.4	-0.962	0.10333	.	.	.	.	.	T	0.00012	0.0000	N	0.00133	-2.03	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.21518	-1.0243	8	0.02654	T	1	-4.1468	4.5039	0.11878	0.5299:0.0:0.3294:0.1407	rs55650155	1175	Q8IVF2	AHNK2_HUMAN	V	1175	ENSP00000353114:A1175V	ENSP00000353114:A1175V	A	-	2	0	AHNAK2	104489309	0.001000	0.12720	0.002000	0.10522	0.094000	0.18550	1.116000	0.31221	-0.917000	0.03813	-0.490000	0.04691	GCG	G|0.607;A|0.393	0.393	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ALPK2	115701	hgsc.bcm.edu	37	18	56204410	56204410	+	Silent	SNP	C	C	T	rs55910046|rs59392360|rs386803723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204410C>T	ENST00000361673.3	-	5	3222	c.3009G>A	c.(3007-3009)agG>agA	p.R1003R	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1003						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCTCAGTCTCCCTGGTCGCTT	0.483													C|||	2025	0.404353	0.4304	0.4294	5008	,	,		21047	0.2371		0.5736	False		,,,				2504	0.3497				p.R1003R		Atlas-SNP	.											ALPK2_ENST00000361673,colon,carcinoma,0,1	ALPK2	487	1	0			c.G3009A						PASS	.	C		1713,2693		444,825,934	110.0	92.0	98.0		3009	-2.2	0.0	18	dbSNP_129	98	3942,4656		1219,1504,1576	no	coding-synonymous	ALPK2	NM_052947.3		1663,2329,2510	TT,TC,CC		45.8479,38.8788,43.4866		1003/2171	56204410	5655,7349	2203	4299	6502	SO:0001819	synonymous_variant	115701	exon5			AGTCTCCCTGGTC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3009G>A	18.37:g.56204410C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	147	49	0.333333	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.535;T|0.465	0.465	strong		0.483	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
FKBP1A	2280	hgsc.bcm.edu	37	20	1350709	1350709	+	3'UTR	SNP	T	T	C	rs8392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1350709T>C	ENST00000400137.4	-	0	534				SDCBP2-AS1_ENST00000446423.1_RNA|FKBP1A_ENST00000460490.1_5'UTR|SDCBP2-AS1_ENST00000609470.1_RNA|SDCBP2-AS1_ENST00000609285.1_RNA|FKBP1A_ENST00000381724.3_3'UTR	NM_000801.4	NP_000792.1	P62942	FKB1A_HUMAN	FK506 binding protein 1A, 12kDa						'de novo' protein folding (GO:0006458)|amyloid fibril formation (GO:1990000)|calcium ion transmembrane transport (GO:0070588)|chaperone-mediated protein folding (GO:0061077)|extracellular fibril organization (GO:0043206)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|protein peptidyl-prolyl isomerization (GO:0000413)|protein refolding (GO:0042026)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of amyloid precursor protein catabolic process (GO:1902991)|regulation of immune response (GO:0050776)|regulation of protein localization (GO:0032880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|SMAD protein complex assembly (GO:0007183)|T cell activation (GO:0042110)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|terminal cisterna (GO:0014802)|Z disc (GO:0030018)	activin binding (GO:0048185)|FK506 binding (GO:0005528)|ion channel binding (GO:0044325)|macrolide binding (GO:0005527)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|type I transforming growth factor beta receptor binding (GO:0034713)			central_nervous_system(1)|lung(1)|upper_aerodigestive_tract(1)	3					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)	GATCCCTCCATGGCAGATCTG	0.502													T|||	1719	0.343251	0.5129	0.3458	5008	,	,		19072	0.0883		0.4155	False		,,,				2504	0.3006				p.P86P		Atlas-SNP	.											.	FKBP1A	6	.	0			c.A258G						PASS	.																																			SO:0001624	3_prime_UTR_variant	2280	exon4			CCTCCATGGCAGA	M92423	CCDS13014.1, CCDS74688.1	20p13	2013-03-20	2002-08-29		ENSG00000088832	ENSG00000088832			3711	protein-coding gene	gene with protein product	"""calstabin 1"""	186945	"""FK506-binding protein 1A (12kD)"""	FKBP1		1930186	Standard	NM_000801		Approved	FKBP-12, FKBP12, PKC12, PPIASE, FKBP12C	uc002wey.3	P62942	OTTHUMG00000031666	ENST00000400137.4:c.*44A>G	20.37:g.1350709T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_001199786	D3DVW6|P20071|Q4VC47|Q6FGD9|Q6LEU3|Q9H103|Q9H566	Silent	SNP	ENST00000400137.4	37	CCDS13014.1																																																																																			T|0.408;G|0.125;C|0.192;A|0.276	0.192	strong		0.502	FKBP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077534.2		
TANC1	85461	hgsc.bcm.edu	37	2	160086692	160086692	+	Silent	SNP	A	A	G	rs3821296	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160086692A>G	ENST00000263635.6	+	27	4992	c.4755A>G	c.(4753-4755)acA>acG	p.T1585T	TANC1_ENST00000454300.1_Silent_p.T1479T	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1585					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						TAGAGGGAACAGGTACTTTCA	0.567													A|||	2398	0.478834	0.3495	0.6023	5008	,	,		19188	0.6161		0.3718	False		,,,				2504	0.5348				p.T1585T		Atlas-SNP	.											.	TANC1	157	.	0			c.A4755G						PASS	.	A	,	1375,2531		256,863,834	57.0	63.0	61.0		,4755	-8.6	0.0	2	dbSNP_107	61	2869,5395		511,1847,1774	no	utr-3,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	767,2710,2608	GG,GA,AA		34.7168,35.2023,34.8726	,	,1585/1862	160086692	4244,7926	1953	4132	6085	SO:0001819	synonymous_variant	85461	exon27			GGGAACAGGTACT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4755A>G	2.37:g.160086692A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			A|0.569;G|0.431	0.431	strong		0.567	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
DYRK4	8798	hgsc.bcm.edu	37	12	4705317	4705317	+	Silent	SNP	C	C	T	rs3741925|rs17845948	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:4705317C>T	ENST00000540757.2	+	5	445	c.285C>T	c.(283-285)gtC>gtT	p.V95V	DYRK4_ENST00000010132.5_Silent_p.V95V|DYRK4_ENST00000543431.1_Silent_p.V95V	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	95			V -> I. {ECO:0000269|PubMed:11062477}.			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			TTCCACAGGTCCTGCATGATC	0.552													C|||	1183	0.236222	0.1044	0.2867	5008	,	,		19972	0.3135		0.2992	False		,,,				2504	0.2342				p.V95V		Atlas-SNP	.											.	DYRK4	75	.	0			c.C285T						PASS	.	C		518,3888	239.3+/-250.5	32,454,1717	120.0	125.0	123.0		285	1.7	1.0	12	dbSNP_107	123	2440,6160	404.9+/-348.3	366,1708,2226	no	coding-synonymous	DYRK4	NM_003845.1		398,2162,3943	TT,TC,CC		28.3721,11.7567,22.7433		95/521	4705317	2958,10048	2203	4300	6503	SO:0001819	synonymous_variant	8798	exon5			ACAGGTCCTGCAT	Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.285C>T	12.37:g.4705317C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_003845	A8K8F7|Q8NEF2|Q92631	Silent	SNP	ENST00000540757.2	37	CCDS8530.1																																																																																			C|0.758;T|0.242	0.242	strong		0.552	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2		
SNCG	6623	hgsc.bcm.edu	37	10	88719789	88719789	+	Silent	SNP	C	C	G	rs760113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88719789C>G	ENST00000372017.3	+	3	237	c.195C>G	c.(193-195)gcC>gcG	p.A65A	MMRN2_ENST00000372027.5_5'Flank|SNCG_ENST00000348795.4_Missense_Mutation_p.R83G|SNCG_ENST00000483064.1_3'UTR	NM_003087.2	NP_003078.2	O76070	SYUG_HUMAN	synuclein, gamma (breast cancer-specific protein 1)	65	4 X 11 AA tandem repeats of [EGSA]-K-T-K- [EQ]-[GQ]-V-X(4).				adult locomotory behavior (GO:0008344)|aggressive behavior (GO:0002118)|cellular response to hydrostatic pressure (GO:0071464)|protein secretion (GO:0009306)|regulation of dopamine secretion (GO:0014059)|regulation of neurotransmitter secretion (GO:0046928)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				endometrium(1)|skin(1)	2						AGGCCAACGCCGTGAGCGAGG	0.667													c|||	1152	0.230032	0.2693	0.2262	5008	,	,		18394	0.0615		0.2346	False		,,,				2504	0.3487				p.A65A		Atlas-SNP	.											.	SNCG	8	.	0			c.C195G						PASS	.	C		1208,3198	405.1+/-333.4	175,858,1170	87.0	69.0	75.0		195	-8.2	0.2	10	dbSNP_86	75	2140,6460	349.8+/-327.6	246,1648,2406	no	coding-synonymous	SNCG	NM_003087.2		421,2506,3576	GG,GC,CC		24.8837,27.4172,25.742		65/128	88719789	3348,9658	2203	4300	6503	SO:0001819	synonymous_variant	6623	exon3			CAACGCCGTGAGC	AF044311	CCDS7380.1	10q23.2-q23.3	2006-06-28			ENSG00000173267	ENSG00000173267			11141	protein-coding gene	gene with protein product	"""synoretin"""	602998				9044857, 9700196	Standard	NM_003087		Approved	BCSG1, SR, persyn	uc001keb.2	O76070	OTTHUMG00000018656	ENST00000372017.3:c.195C>G	10.37:g.88719789C>G		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	221	99	0.447964	NM_003087	O15104|Q96P61	Silent	SNP	ENST00000372017.3	37	CCDS7380.1	452	0.20695970695970695	133	0.2703252032520325	96	0.26519337016574585	38	0.06643356643356643	185	0.24406332453825857	C	9.818	1.184969	0.21870	0.274172	0.248837	ENSG00000173267	ENST00000348795	D	0.88664	-2.41	4.93	-8.16	0.01061	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.20821	P	0.999841416	.	.	.	.	.	.	T	0.46789	-0.9166	5	0.87932	D	0	-1.3525	1.0486	0.01575	0.1667:0.2461:0.2358:0.3514	rs760113;rs1048609;rs3188622	.	.	.	G	83	ENSP00000344658:R83G	ENSP00000344658:R83G	R	+	1	0	SNCG	88709769	0.000000	0.05858	0.184000	0.23157	0.666000	0.39218	-1.896000	0.01605	-1.414000	0.02025	-1.157000	0.01802	CGT	C|0.759;G|0.241	0.241	strong		0.667	SNCG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049167.1		
PPP1R14D	54866	hgsc.bcm.edu	37	15	41120675	41120675	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41120675G>C	ENST00000299174.5	-	1	232	c.165C>G	c.(163-165)agC>agG	p.S55R	PPP1R14D_ENST00000427255.2_Missense_Mutation_p.S55R	NM_017726.7	NP_060196.1	Q9NXH3	PP14D_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 14D	55					regulation of phosphorylation (GO:0042325)	cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			breast(1)|large_intestine(2)|lung(2)|skin(1)	6		all_cancers(109;6.29e-14)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.88e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CTGTCAGGCGGCTGGGTCTCC	0.597																																					p.S55R		Atlas-SNP	.											.	PPP1R14D	8	.	0			c.C165G						PASS	.						77.0	75.0	76.0					15																	41120675		2203	4300	6503	SO:0001583	missense	54866	exon1			CAGGCGGCTGGGT	AK000258	CCDS10066.1, CCDS45230.1	15q11.2-q14	2012-04-17			ENSG00000166143	ENSG00000166143		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14953	protein-coding gene	gene with protein product	"""gut and brain phosphatase inhibitor 1"", ""PKC-dependent PP1 inhibitory protein"""	613256				11948623	Standard	NM_017726		Approved	CPI17-like, FLJ20251, GBPI-1, MGC119014, MGC119016	uc001zmz.3	Q9NXH3	OTTHUMG00000130064	ENST00000299174.5:c.165C>G	15.37:g.41120675G>C	ENSP00000299174:p.Ser55Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_017726	Q4V773	Missense_Mutation	SNP	ENST00000299174.5	37	CCDS10066.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.682021	0.68042	.	.	ENSG00000166143	ENST00000299174;ENST00000427255	.	.	.	5.82	4.91	0.64330	.	0.067227	0.64402	D	0.000004	T	0.50752	0.1634	N	0.24115	0.695	0.34284	D	0.682531	D;D	0.76494	0.999;0.983	D;P	0.69479	0.964;0.839	T	0.61845	-0.6979	9	0.38643	T	0.18	-11.6822	10.8969	0.47027	0.086:0.0:0.914:0.0	.	55;55	E9PAT1;Q9NXH3	.;PP14D_HUMAN	R	55	.	ENSP00000299174:S55R	S	-	3	2	PPP1R14D	38907967	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.421000	0.44688	1.490000	0.48466	-0.142000	0.14014	AGC	.	.	none		0.597	PPP1R14D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252355.2	NM_017726	
ABCA2	20	hgsc.bcm.edu	37	9	139906359	139906359	+	Silent	SNP	G	G	A	rs2271862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139906359G>A	ENST00000371605.3	-	34	5616	c.5469C>T	c.(5467-5469)caC>caT	p.H1823H	ABCA2_ENST00000265662.5_Silent_p.H1824H|ABCA2_ENST00000341511.6_Silent_p.H1824H			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1823					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CAAACTGCAGGTGCTTGGCCT	0.627													G|||	3442	0.6873	0.6377	0.5403	5008	,	,		12508	0.8175		0.67	False		,,,				2504	0.7423				p.H1854H		Atlas-SNP	.											.	ABCA2	113	.	0			c.C5562T						PASS	.	G	,	2795,1585		898,999,293	43.0	52.0	49.0		5472,5562	2.3	1.0	9	dbSNP_100	49	5973,2585		2090,1793,396	yes	coding-synonymous,coding-synonymous	ABCA2	NM_001606.4,NM_212533.2	,	2988,2792,689	AA,AG,GG		30.2057,36.1872,32.2306	,	1824/2437,1854/2467	139906359	8768,4170	2190	4279	6469	SO:0001819	synonymous_variant	20	exon35			CTGCAGGTGCTTG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.5469C>T	9.37:g.139906359G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				G|0.322;A|0.678	0.678	strong		0.627	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
FAM71B	153745	hgsc.bcm.edu	37	5	156590355	156590355	+	Silent	SNP	A	A	G	rs31220	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:156590355A>G	ENST00000302938.4	-	2	1016	c.921T>C	c.(919-921)ggT>ggC	p.G307G		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	307	Ala-rich.					nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGGTCACTTGACCTGGGCCTG	0.522													G|||	763	0.152356	0.3631	0.1138	5008	,	,		21181	0.0139		0.1372	False		,,,				2504	0.0532				p.G307G		Atlas-SNP	.											.	FAM71B	145	.	0			c.T921C						PASS	.	G		1483,2923	676.6+/-403.3	246,991,966	118.0	113.0	115.0		921	0.8	0.0	5	dbSNP_76	115	1271,7329	760.1+/-407.6	89,1093,3118	no	coding-synonymous	FAM71B	NM_130899.2		335,2084,4084	GG,GA,AA		14.7791,33.6586,21.1748		307/606	156590355	2754,10252	2203	4300	6503	SO:0001819	synonymous_variant	153745	exon2			CACTTGACCTGGG		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.921T>C	5.37:g.156590355A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	40	0.377358	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Silent	SNP	ENST00000302938.4	37	CCDS4335.1																																																																																			A|0.813;G|0.187	0.187	strong		0.522	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
TCEB3	6924	hgsc.bcm.edu	37	1	24083494	24083494	+	Silent	SNP	C	C	T	rs2076345	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:24083494C>T	ENST00000418390.2	+	10	2485	c.2214C>T	c.(2212-2214)agC>agT	p.S738S	TCEB3_ENST00000609199.1_Silent_p.S712S	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	738					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		CCGCCAGTAGCATCAGCTTTA	0.577													C|||	1004	0.200479	0.0885	0.2421	5008	,	,		20319	0.2698		0.3101	False		,,,				2504	0.138				p.S738S		Atlas-SNP	.											.	TCEB3	61	.	0			c.C2214T						PASS	.	C		581,3825	258.0+/-262.2	39,503,1661	176.0	170.0	172.0		2214	3.5	1.0	1	dbSNP_96	172	2655,5945	426.8+/-355.4	400,1855,2045	no	coding-synonymous	TCEB3	NM_003198.2		439,2358,3706	TT,TC,CC		30.8721,13.1866,24.8808		738/799	24083494	3236,9770	2203	4300	6503	SO:0001819	synonymous_variant	6924	exon10			CAGTAGCATCAGC	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"""transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"""			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.2214C>T	1.37:g.24083494C>T		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	164	85	0.518293	NM_003198	B2R7Q8|Q8IXH1	Silent	SNP	ENST00000418390.2	37	CCDS239.2																																																																																			C|0.764;T|0.236	0.236	strong		0.577	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198	
ADCY8	114	hgsc.bcm.edu	37	8	131921956	131921956	+	Silent	SNP	A	A	G	rs12547243	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:131921956A>G	ENST00000286355.5	-	6	3730	c.1638T>C	c.(1636-1638)ccT>ccC	p.P546P	ADCY8_ENST00000377928.3_Silent_p.P546P	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	546					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TATCTTACCCAGGGATTCCTC	0.453										HNSCC(32;0.087)			G|||	2728	0.544728	0.3343	0.6297	5008	,	,		20272	0.6815		0.6958	False		,,,				2504	0.4724				p.P546P		Atlas-SNP	.											.	ADCY8	291	.	0			c.T1638C						PASS	.	G		1581,2825	666.9+/-401.8	286,1009,908	224.0	203.0	210.0		1638	-9.6	0.5	8	dbSNP_120	210	5879,2721	435.9+/-358.1	2034,1811,455	no	coding-synonymous	ADCY8	NM_001115.2		2320,2820,1363	GG,GA,AA		31.6395,35.8829,42.6419		546/1252	131921956	7460,5546	2203	4300	6503	SO:0001819	synonymous_variant	114	exon6			TTACCCAGGGATT	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1638T>C	8.37:g.131921956A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	186	185	0.994624	NM_001115		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																			A|0.424;G|0.576	0.576	strong		0.453	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
GP6	51206	hgsc.bcm.edu	37	19	55525894	55525894	+	3'UTR	SNP	G	G	A	rs1671151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55525894G>A	ENST00000417454.1	-	0	1442				GP6_ENST00000310373.3_Silent_p.P473P|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_3'UTR|CTC-550B14.7_ENST00000586845.1_RNA	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)						blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		AGGGAAGCACGGGAGGATTTT	0.522													G|||	3594	0.717652	0.4992	0.8228	5008	,	,		20144	0.8125		0.8459	False		,,,				2504	0.7086				p.P473P		Atlas-SNP	.											.	GP6	55	.	0			c.C1419T						PASS	.	G	,	2087,1841		568,951,445	71.0	74.0	73.0		1419,	-2.8	0.0	19	dbSNP_89	73	6901,1421		2871,1159,131	no	coding-synonymous,utr-3	GP6	NM_001083899.1,NM_016363.4	,	3439,2110,576	AA,AG,GG		17.0752,46.8686,26.6286	,	473/621,	55525894	8988,3262	1964	4161	6125	SO:0001624	3_prime_UTR_variant	51206	exon8			AAGCACGGGAGGA	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.*395C>T	19.37:g.55525894G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_001083899	Q9HCN7|Q9UIF2	Silent	SNP	ENST00000417454.1	37	CCDS46184.1																																																																																			G|0.231;A|0.769	0.769	strong		0.522	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
ZNF416	55659	hgsc.bcm.edu	37	19	58084034	58084034	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58084034C>T	ENST00000196489.3	-	4	1460	c.1238G>A	c.(1237-1239)gGc>gAc	p.G413D		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		CCCACACTGGCCACACTCATA	0.458																																					p.G413D		Atlas-SNP	.											ZNF416,NS,carcinoma,0,1	ZNF416	50	1	0			c.G1238A						scavenged	.						106.0	96.0	99.0					19																	58084034		2203	4300	6503	SO:0001583	missense	55659	exon4			CACTGGCCACACT	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"""Zinc fingers, C2H2-type"", ""-"""	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.1238G>A	19.37:g.58084034C>T	ENSP00000196489:p.Gly413Asp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	169	3	0.0177515	NM_017879	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	37	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328312	0.60743	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	T	0.16196	2.36	3.86	-6.78	0.01721	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03434	0.0099	N	0.00890	-1.11	0.09310	N	1	B	0.12630	0.006	B	0.12837	0.008	T	0.35101	-0.9802	9	0.40728	T	0.16	.	1.0975	0.01676	0.244:0.1438:0.363:0.2492	.	413	Q9BWM5	ZN416_HUMAN	D	413;372;311	ENSP00000196489:G413D	ENSP00000196489:G413D	G	-	2	0	ZNF416	62775846	0.000000	0.05858	0.000000	0.03702	0.983000	0.72400	-4.249000	0.00266	-1.150000	0.02840	0.655000	0.94253	GGC	.	.	none		0.458	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959895	157959895	+	Missense_Mutation	SNP	C	C	T	rs1130496	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:157959895C>T	ENST00000389418.4	-	6	647	c.638G>A	c.(637-639)cGc>cAc	p.R213H	PTPRN2_ENST00000389413.3_Missense_Mutation_p.R213H|PTPRN2_ENST00000389416.4_Missense_Mutation_p.R196H|PTPRN2_ENST00000409483.1_Missense_Mutation_p.R175H|PTPRN2_ENST00000404321.2_Missense_Mutation_p.R236H	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	213			R -> H (in dbSNP:rs1130496). {ECO:0000269|PubMed:9205841}.		negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GAGGTCCTCGCGGAGCTGGGT	0.652													C|||	1697	0.338858	0.1399	0.4179	5008	,	,		15810	0.4087		0.4543	False		,,,				2504	0.3609				p.R213H		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G638A						PASS	.		HIS/ARG,HIS/ARG,HIS/ARG	746,3658	296.7+/-284.4	74,598,1530	40.0	42.0	41.0		638,587,638	3.7	0.0	7	dbSNP_86	41	3733,4867	519.5+/-379.5	792,2149,1359	no	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	29,29,29	866,2747,2889	TT,TC,CC		43.407,16.9391,34.4432	possibly-damaging,possibly-damaging,possibly-damaging	213/1016,196/999,213/987	157959895	4479,8525	2202	4300	6502	SO:0001583	missense	5799	exon6			TCCTCGCGGAGCT	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.638G>A	7.37:g.157959895C>T	ENSP00000374069:p.Arg213His	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	771	0.35302197802197804	72	0.14634146341463414	160	0.4419889502762431	202	0.3531468531468531	337	0.4445910290237467	C	6.763	0.509606	0.12883	0.169391	0.43407	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03004	4.1;4.08;4.09;4.1;4.09	4.59	3.71	0.42584	.	0.568731	0.13381	N	0.392177	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P;P;P;P	0.49358	0.923;0.733;0.825;0.733;0.733	B;B;B;B;B	0.34722	0.188;0.092;0.188;0.092;0.092	T	0.30650	-0.9971	9	0.33141	T	0.24	.	10.7818	0.46382	0.0:0.1952:0.8048:0.0	rs1130496;rs3189412;rs10385220;rs17847411;rs56726755;rs1130496	236;175;213;196;213	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	H	175;213;196;213;236	ENSP00000387114:R175H;ENSP00000374064:R213H;ENSP00000374067:R196H;ENSP00000374069:R213H;ENSP00000385464:R236H	ENSP00000374064:R213H	R	-	2	0	PTPRN2	157652656	0.601000	0.26907	0.012000	0.15200	0.055000	0.15305	2.538000	0.45710	0.936000	0.37367	-0.244000	0.11960	CGC	C|0.653;T|0.347	0.347	strong		0.652	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
CNN2	1265	hgsc.bcm.edu	37	19	1036444	1036444	+	Silent	SNP	G	G	A	rs930231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1036444G>A	ENST00000263097.4	+	6	900	c.537G>A	c.(535-537)tcG>tcA	p.S179S	CNN2_ENST00000606983.1_3'UTR|CNN2_ENST00000562958.2_Silent_p.S200S|CNN2_ENST00000565096.2_Silent_p.S168S|AC011558.5_ENST00000585757.1_RNA|CNN2_ENST00000348419.3_Silent_p.S140S	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	179					actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGCCAGTCGGGCATGACTG	0.592													G|||	851	0.169928	0.0439	0.3646	5008	,	,		17922	0.0496		0.3002	False		,,,				2504	0.1922				p.S179S		Atlas-SNP	.											.	CNN2	26	.	0			c.G537A						PASS	.	G	,	401,4005	196.4+/-220.7	19,363,1821	65.0	61.0	62.0		537,420	-8.4	0.8	19	dbSNP_86	62	2734,5866	433.9+/-357.6	444,1846,2010	no	coding-synonymous,coding-synonymous	CNN2	NM_004368.2,NM_201277.1	,	463,2209,3831	AA,AG,GG		31.7907,9.1012,24.1043	,	179/310,140/271	1036444	3135,9871	2203	4300	6503	SO:0001819	synonymous_variant	1265	exon6			CCAGTCGGGCATG	D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.537G>A	19.37:g.1036444G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	208	111	0.533654	NM_004368	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			G|0.770;C|0.000;A|0.230	0.230	strong		0.592	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368	
MYBPC2	4606	hgsc.bcm.edu	37	19	50957397	50957397	+	Missense_Mutation	SNP	G	G	A	rs25665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50957397G>A	ENST00000357701.5	+	17	1921	c.1870G>A	c.(1870-1872)Gtc>Atc	p.V624I		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	624	Ig-like C2-type 5.		V -> I (in dbSNP:rs25665).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CACCAACCCCGTCGGCGAGGA	0.632													g|||	1184	0.236422	0.034	0.2824	5008	,	,		18456	0.3829		0.2515	False		,,,				2504	0.3108				p.V624I		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G1870A						PASS	.	G	ILE/VAL	263,3941		7,249,1846	34.0	38.0	37.0		1870	-0.5	0.0	19	dbSNP_72	37	1778,6626		196,1386,2620	yes	missense	MYBPC2	NM_004533.3	29	203,1635,4466	AA,AG,GG		21.1566,6.2559,16.1881	benign	624/1142	50957397	2041,10567	2102	4202	6304	SO:0001583	missense	4606	exon17			AACCCCGTCGGCG		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.1870G>A	19.37:g.50957397G>A	ENSP00000350332:p.Val624Ile	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	220	109	0.495455	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	526	0.24084249084249085	19	0.03861788617886179	91	0.2513812154696133	228	0.3986013986013986	188	0.24802110817941952	g	9.583	1.124179	0.20959	0.062559	0.211566	ENSG00000086967	ENST00000357701	T	0.68181	-0.31	3.26	-0.485	0.12067	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	15.483300	0.02223	U	0.064183	T	0.00012	0.0000	L	0.58810	1.83	0.80722	P	0.0	B	0.20052	0.041	B	0.17098	0.017	T	0.15723	-1.0427	9	0.20519	T	0.43	.	3.9465	0.09350	0.0969:0.1597:0.579:0.1645	rs25665;rs2230838;rs2272322;rs12978290;rs17804237;rs52823468;rs25665	624	Q14324	MYPC2_HUMAN	I	624	ENSP00000350332:V624I	ENSP00000350332:V624I	V	+	1	0	MYBPC2	55649209	0.007000	0.16637	0.010000	0.14722	0.324000	0.28378	1.574000	0.36482	-0.057000	0.13199	-0.555000	0.04198	GTC	G|0.772;A|0.227	0.227	strong		0.632	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
R3HDM2	22864	hgsc.bcm.edu	37	12	57649840	57649840	+	Silent	SNP	C	C	T	rs4075325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57649840C>T	ENST00000347140.3	-	23	2913	c.2523G>A	c.(2521-2523)aaG>aaA	p.K841K	R3HDM2_ENST00000546843.1_5'Flank|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Silent_p.K855K|R3HDM2_ENST00000441731.2_Silent_p.K536K|R3HDM2_ENST00000403821.2_Silent_p.K875K|R3HDM2_ENST00000358907.2_Silent_p.K841K|R3HDM2_ENST00000413953.2_Silent_p.K568K			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	841						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						GGTTTCCATGCTTCAGTCCAC	0.502													C|||	2085	0.416334	0.2284	0.5533	5008	,	,		20612	0.4405		0.4155	False		,,,				2504	0.5491				p.K841K		Atlas-SNP	.											.	R3HDM2	125	.	0			c.G2523A						PASS	.	C		1241,3165	428.7+/-342.0	187,867,1149	198.0	159.0	172.0		2523	3.8	1.0	12	dbSNP_108	172	3992,4608	553.0+/-386.2	947,2098,1255	no	coding-synonymous	R3HDM2	NM_014925.3		1134,2965,2404	TT,TC,CC		46.4186,28.1661,40.2353		841/977	57649840	5233,7773	2203	4300	6503	SO:0001819	synonymous_variant	22864	exon21			TCCATGCTTCAGT	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.2523G>A	12.37:g.57649840C>T		Somatic	365	1	0.00273973		WXS	Illumina HiSeq	Phase_I	339	170	0.501475	NM_014925	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	37	CCDS8937.2																																																																																			C|0.612;T|0.388	0.388	strong		0.502	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	
THSD1	55901	hgsc.bcm.edu	37	13	52971718	52971718	+	Missense_Mutation	SNP	G	G	C	rs9536062	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:52971718G>C	ENST00000258613.4	-	3	848	c.670C>G	c.(670-672)Cga>Gga	p.R224G	THSD1_ENST00000349258.4_Missense_Mutation_p.R224G|RNY4P24_ENST00000362735.1_RNA|THSD1_ENST00000544466.1_Intron	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	224			R -> G (in dbSNP:rs9536062).		hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		ACTGAGTCTCGCCCAAGCAGC	0.537													G|||	267	0.0533147	0.1044	0.0259	5008	,	,		19853	0.0079		0.0388	False		,,,				2504	0.0654				p.R224G		Atlas-SNP	.											.	THSD1	89	.	0			c.C670G						PASS	.	G	GLY/ARG,GLY/ARG	378,4028	190.5+/-216.4	14,350,1839	78.0	68.0	71.0		670,670	2.5	0.3	13	dbSNP_119	71	443,8157	134.7+/-192.1	12,419,3869	yes	missense,missense	THSD1	NM_018676.3,NM_199263.2	125,125	26,769,5708	CC,CG,GG		5.1512,8.5792,6.3125	benign,benign	224/853,224/800	52971718	821,12185	2203	4300	6503	SO:0001583	missense	55901	exon3			AGTCTCGCCCAAG	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.670C>G	13.37:g.52971718G>C	ENSP00000258613:p.Arg224Gly	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	201	93	0.462687	NM_199263	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Missense_Mutation	SNP	ENST00000258613.4	37	CCDS9432.1	95	0.043498168498168496	48	0.0975609756097561	11	0.03038674033149171	7	0.012237762237762238	29	0.03825857519788918	G	10.11	1.260090	0.23051	0.085792	0.051512	ENSG00000136114	ENST00000349258;ENST00000258613;ENST00000378095	T;T	0.17691	2.26;2.44	5.54	2.47	0.30058	.	0.641375	0.14307	N	0.327944	T	0.00328	0.0010	L	0.57536	1.79	0.09310	N	1	P;B	0.40302	0.712;0.422	B;B	0.34536	0.185;0.085	T	0.20571	-1.0271	10	0.22109	T	0.4	-0.1475	4.639	0.12540	0.0797:0.109:0.487:0.3243	rs9536062;rs9536062	224;224	Q9NS62-2;Q9NS62	.;THSD1_HUMAN	G	224	ENSP00000340650:R224G;ENSP00000258613:R224G	ENSP00000258613:R224G	R	-	1	2	THSD1	51869719	0.878000	0.30173	0.279000	0.24732	0.962000	0.63368	0.665000	0.25083	0.675000	0.31264	0.561000	0.74099	CGA	G|0.950;C|0.050	0.050	strong		0.537	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
TBC1D8	11138	hgsc.bcm.edu	37	2	101638888	101638888	+	Silent	SNP	A	A	G	rs3739014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:101638888A>G	ENST00000376840.4	-	16	2570	c.2571T>C	c.(2569-2571)gaT>gaC	p.D857D	TBC1D8_ENST00000409318.1_Silent_p.D872D			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	857					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						ACTGCCGGGCATCTATGCGGT	0.602													G|||	2639	0.526957	0.5227	0.5533	5008	,	,		18012	0.2946		0.6829	False		,,,				2504	0.593				p.D857D		Atlas-SNP	.											.	TBC1D8	169	.	0			c.T2571C						PASS	.	G		2317,1707		683,951,378	42.0	44.0	43.0		2571	-4.2	0.3	2	dbSNP_107	43	5590,2764		1883,1824,470	yes	coding-synonymous	TBC1D8	NM_001102426.1		2566,2775,848	GG,GA,AA		33.0859,42.4205,36.1205		857/1141	101638888	7907,4471	2012	4177	6189	SO:0001819	synonymous_variant	11138	exon16			CCGGGCATCTATG	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.2571T>C	2.37:g.101638888A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	37	CCDS46375.1																																																																																			A|0.446;G|0.554	0.554	strong		0.602	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
ILVBL	10994	hgsc.bcm.edu	37	19	15229993	15229993	+	Silent	SNP	A	A	G	rs1131177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15229993A>G	ENST00000263383.3	-	9	1174	c.1035T>C	c.(1033-1035)gaT>gaC	p.D345D	ILVBL_ENST00000534378.1_Silent_p.D238D|ILVBL_ENST00000531635.1_5'Flank	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	345						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						GGACAATGACATCCGCCTTCT	0.627													A|||	1129	0.225439	0.0265	0.2752	5008	,	,		17072	0.3323		0.1968	False		,,,				2504	0.3783				p.D345D		Atlas-SNP	.											ILVBL,NS,carcinoma,0,1	ILVBL	54	1	0			c.T1035C						PASS	.	A		237,4169	138.8+/-174.5	6,225,1972	74.0	66.0	69.0		1035	-5.4	0.1	19	dbSNP_86	69	1716,6884	313.0+/-311.1	164,1388,2748	no	coding-synonymous	ILVBL	NM_006844.3		170,1613,4720	GG,GA,AA		19.9535,5.379,15.0161		345/633	15229993	1953,11053	2203	4300	6503	SO:0001819	synonymous_variant	10994	exon9			AATGACATCCGCC	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"""acetolactate synthase homolog"""	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1035T>C	19.37:g.15229993A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Silent	SNP	ENST00000263383.3	37	CCDS12325.1																																																																																			A|0.839;G|0.161	0.161	strong		0.627	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844	
GINM1	116254	hgsc.bcm.edu	37	6	149903597	149903597	+	Missense_Mutation	SNP	A	A	G	rs1137086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:149903597A>G	ENST00000367419.5	+	7	860	c.739A>G	c.(739-741)Aag>Gag	p.K247E		NM_138785.3	NP_620140.1	Q9NU53	GINM1_HUMAN	glycoprotein integral membrane 1	247						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											GTGGATGGAAAAGTTTAGAAA	0.348													.|||	78	0.0155751	0.0	0.0216	5008	,	,		15773	0.0		0.0487	False		,,,				2504	0.0143				p.K247E		Atlas-SNP	.											.	.	.	.	0			c.A739G						PASS	.	A	GLU/LYS	42,4364	47.5+/-82.1	0,42,2161	176.0	178.0	177.0		739	-0.1	0.1	6	dbSNP_86	177	394,8206	126.7+/-185.1	9,376,3915	yes	missense	C6orf72	NM_138785.3	56	9,418,6076	GG,GA,AA		4.5814,0.9532,3.3523	benign	247/331	149903597	436,12570	2203	4300	6503	SO:0001583	missense	116254	exon7			ATGGAAAAGTTTA	BC014320	CCDS5216.1	6q24.3	2012-07-20	2012-07-20	2012-07-20	ENSG00000055211	ENSG00000055211			21074	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 72"""	C6orf72			Standard	NM_138785		Approved	dJ12G14.2	uc003qmq.1	Q9NU53	OTTHUMG00000015789	ENST00000367419.5:c.739A>G	6.37:g.149903597A>G	ENSP00000356389:p.Lys247Glu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	187	102	0.545455	NM_138785	B2RDY7|E1P5A2	Missense_Mutation	SNP	ENST00000367419.5	37	CCDS5216.1	54	0.024725274725274724	0	0.0	13	0.03591160220994475	0	0.0	41	0.05408970976253298	A	9.280	1.048023	0.19827	0.009532	0.045814	ENSG00000055211	ENST00000367419	.	.	.	5.59	-0.133	0.13485	.	0.743369	0.13710	N	0.368163	T	0.12263	0.0298	L	0.43152	1.355	0.22873	N	0.998622	B	0.28933	0.228	B	0.30855	0.121	T	0.24154	-1.0168	8	.	.	.	-9.9192	3.8096	0.08791	0.3292:0.3942:0.2766:0.0	rs1137086	247	Q9NU53	CF072_HUMAN	E	247	.	.	K	+	1	0	C6orf72	149945290	0.230000	0.23740	0.132000	0.22025	0.998000	0.95712	0.313000	0.19415	0.116000	0.18110	0.533000	0.62120	AAG	A|0.971;G|0.029	0.029	strong		0.348	GINM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042644.1	NM_138785	
PER3	8863	hgsc.bcm.edu	37	1	7890117	7890117	+	Missense_Mutation	SNP	T	T	C	rs2640909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7890117T>C	ENST00000361923.2	+	18	3258	c.3083T>C	c.(3082-3084)aTg>aCg	p.M1028T	PER3_ENST00000377532.3_Missense_Mutation_p.M1037T|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1028	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.		M -> T (only found in PER3.4 allele; dbSNP:rs2640909). {ECO:0000269|PubMed:11306557}.		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		ACACTGTCCATGGGATTGCCT	0.577													-|||	928	0.185304	0.0968	0.2853	5008	,	,		17789	0.0506		0.2932	False		,,,				2504	0.2618				p.M1028T		Atlas-SNP	.											.	PER3	95	.	0			c.T3083C						PASS	.	T	THR/MET	560,3846		36,488,1679	162.0	130.0	141.0		3083	-1.5	0.0	1	dbSNP_100	141	2539,6061		393,1753,2154	yes	missense	PER3	NM_016831.1	81	429,2241,3833	CC,CT,TT		29.5233,12.7099,23.8275	benign	1028/1202	7890117	3099,9907	2203	4300	6503	SO:0001583	missense	8863	exon18			TGTCCATGGGATT	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3083T>C	1.37:g.7890117T>C	ENSP00000355031:p.Met1028Thr	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	158	88	0.556962	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	406	0.1858974358974359	58	0.11788617886178862	91	0.2513812154696133	38	0.06643356643356643	219	0.28891820580474936	-	0.008	-1.871084	0.00542	0.127099	0.295233	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.13538	2.58;2.58	0.77	-1.54	0.08584	Period circadian-like, C-terminal (1);	2.711880	0.01895	N	0.038848	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B;B;B	0.16396	0.0;0.0;0.0;0.017;0.0	B;B;B;B;B	0.15484	0.001;0.0;0.001;0.013;0.0	T	0.43475	-0.9389	9	0.13108	T	0.6	.	3.4008	0.07323	0.0:0.6486:0.0:0.3514	rs2640909;rs10779690;rs17374481;rs34042617;rs52837510;rs2640909	77;1028;1037;1037;1028	B4DR65;A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;.;PER3_HUMAN	T	1037;1028;221	ENSP00000366755:M1037T;ENSP00000355031:M1028T	ENSP00000355031:M1028T	M	+	2	0	PER3	7812704	0.019000	0.18553	0.002000	0.10522	0.008000	0.06430	0.000000	0.12993	-0.216000	0.10048	-0.736000	0.03550	ATG	T|0.783;C|0.217	0.217	strong		0.577	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
HKDC1	80201	hgsc.bcm.edu	37	10	71026433	71026433	+	Missense_Mutation	SNP	T	T	C	rs148418934	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71026433T>C	ENST00000354624.5	+	18	2807	c.2674T>C	c.(2674-2676)Tca>Cca	p.S892P	RP11-227H15.5_ENST00000413220.1_RNA	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	892	Hexokinase type-2 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						ATTCATGCTGTCAGAAGATGG	0.478													T|||	3	0.000599042	0.0	0.0029	5008	,	,		19517	0.0		0.001	False		,,,				2504	0.0				p.S892P		Atlas-SNP	.											.	HKDC1	98	.	0			c.T2674C						PASS	.	T	PRO/SER	2,4404	4.2+/-10.8	0,2,2201	163.0	145.0	151.0		2674	5.0	1.0	10	dbSNP_134	151	16,8584	11.9+/-42.8	0,16,4284	yes	missense	HKDC1	NM_025130.3	74	0,18,6485	CC,CT,TT		0.186,0.0454,0.1384	probably-damaging	892/918	71026433	18,12988	2203	4300	6503	SO:0001583	missense	80201	exon18			ATGCTGTCAGAAG		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.2674T>C	10.37:g.71026433T>C	ENSP00000346643:p.Ser892Pro	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	20.7	4.030350	0.75504	4.54E-4	0.00186	ENSG00000156510	ENST00000354624	D	0.97279	-4.32	4.96	4.96	0.65561	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98607	0.9534	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96137	0.9097	10	0.87932	D	0	-5.87	15.069	0.72021	0.0:0.0:0.0:1.0	.	892	Q2TB90	HKDC1_HUMAN	P	892	ENSP00000346643:S892P	ENSP00000346643:S892P	S	+	1	0	HKDC1	70696439	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	7.387000	0.79785	2.206000	0.71126	0.533000	0.62120	TCA	T|0.998;C|0.002	0.002	strong		0.478	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
CD163	9332	hgsc.bcm.edu	37	12	7655137	7655137	+	Silent	SNP	A	A	G	rs3210140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7655137A>G	ENST00000359156.4	-	2	272	c.70T>C	c.(70-72)Ttg>Ctg	p.L24L	CD163_ENST00000541972.1_Silent_p.L12L|CD163_ENST00000396620.3_Silent_p.L24L|CD163_ENST00000432237.2_Silent_p.L24L	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	24					acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	aagggactcaagttgacaaaa	0.408													A|||	2314	0.462061	0.1452	0.6931	5008	,	,		-128	0.3829		0.7346	False		,,,				2504	0.5276				p.L24L		Atlas-SNP	.											.	CD163	221	.	0			c.T70C						PASS	.	A	,	999,3403		125,749,1327	71.0	62.0	65.0		70,70	-0.0	0.0	12	dbSNP_105	65	6190,2408		2250,1690,359	no	coding-synonymous,coding-synonymous	CD163	NM_004244.5,NM_203416.3	,	2375,2439,1686	GG,GA,AA		28.0065,22.6942,44.7	,	24/1157,24/1122	7655137	7189,5811	2201	4299	6500	SO:0001819	synonymous_variant	9332	exon2			GACTCAAGTTGAC	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.70T>C	12.37:g.7655137A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1																																																																																			A|0.518;G|0.482	0.482	strong		0.408	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416	
TMBIM1	64114	hgsc.bcm.edu	37	2	219146803	219146803	+	Missense_Mutation	SNP	G	G	A	rs2292553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219146803G>A	ENST00000444881.1	-	3	787	c.62C>T	c.(61-63)cCg>cTg	p.P21L	TMBIM1_ENST00000258412.3_Missense_Mutation_p.P21L|PNKD_ENST00000273077.4_Intron|TMBIM1_ENST00000445635.1_Intron|TMBIM1_ENST00000396809.2_Missense_Mutation_p.P21L|PNKD_ENST00000472650.1_Intron			Q969X1	LFG3_HUMAN	transmembrane BAX inhibitor motif containing 1	21			P -> L (in dbSNP:rs2292553). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15498874, ECO:0000269|PubMed:16303743}.		negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of Fas signaling pathway (GO:1902045)|negative regulation of metalloenzyme activity (GO:0048553)|positive regulation of blood vessel remodeling (GO:2000504)	endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	death receptor binding (GO:0005123)			NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(2)	9		Renal(207;0.0474)		Epithelial(149;8.56e-07)|all cancers(144;0.000154)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCAGGGGGCGGAGGGCCTGG	0.677													G|||	2251	0.449481	0.059	0.5058	5008	,	,		15111	0.6161		0.5835	False		,,,				2504	0.6278				p.P21L		Atlas-SNP	.											.	TMBIM1	20	.	0			c.C62T						PASS	.	G	,LEU/PRO	630,3772		49,532,1620	23.0	28.0	26.0		,62	2.9	0.0	2	dbSNP_100	26	4707,3891		1269,2169,861	yes	intron,missense	PNKD,TMBIM1	NM_015488.4,NM_022152.4	,98	1318,2701,2481	AA,AG,GG		45.2547,14.3117,41.0538	,probably-damaging	,21/312	219146803	5337,7663	2201	4299	6500	SO:0001583	missense	64114	exon2			GGGGGCGGAGGGC	BN000408	CCDS2412.1	2q35	2010-03-18			ENSG00000135926	ENSG00000135926			23410	protein-coding gene	gene with protein product		610364				12477932	Standard	NM_022152		Approved	PP1201, RECS1, LFG3	uc002vhp.1	Q969X1	OTTHUMG00000133105	ENST00000444881.1:c.62C>T	2.37:g.219146803G>A	ENSP00000409738:p.Pro21Leu	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	266	123	0.462406	NM_022152	B3KQY6|Q8N1R3|Q8TAM3|Q96K13	Missense_Mutation	SNP	ENST00000444881.1	37	CCDS2412.1	1036	0.47435897435897434	39	0.07926829268292683	188	0.5193370165745856	363	0.6346153846153846	446	0.5883905013192612	G	5.868	0.344265	0.11126	0.143117	0.547453	ENSG00000135926	ENST00000258412;ENST00000444881;ENST00000396809;ENST00000429501;ENST00000425694;ENST00000418569;ENST00000440422;ENST00000444183;ENST00000453776;ENST00000444000;ENST00000453281;ENST00000451181;ENST00000434015;ENST00000413976	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85	4.75	2.94	0.34122	.	0.807772	0.11282	N	0.580232	T	0.00012	0.0000	M	0.72118	2.19	0.58432	P	1.999999999946489E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.44967	-0.9293	9	0.12766	T	0.61	-6.3566	6.8848	0.24193	0.2835:0.0:0.7165:0.0	rs2292553;rs17850287;rs17851043	21	Q969X1	TMBI1_HUMAN	L	21	ENSP00000258412:P21L;ENSP00000409738:P21L;ENSP00000380025:P21L;ENSP00000399987:P21L;ENSP00000399345:P21L;ENSP00000406744:P21L;ENSP00000412518:P21L;ENSP00000410136:P21L;ENSP00000410771:P21L;ENSP00000403462:P21L;ENSP00000395614:P21L;ENSP00000394946:P21L;ENSP00000405516:P21L;ENSP00000408729:P21L	ENSP00000258412:P21L	P	-	2	0	TMBIM1	218855047	0.995000	0.38212	0.012000	0.15200	0.011000	0.07611	3.078000	0.50096	0.597000	0.29811	-0.140000	0.14226	CCG	G|0.579;A|0.421	0.421	strong		0.677	TMBIM1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338559.1	NM_022152	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116073696	116073696	+	Silent	SNP	C	C	T	rs3813722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:116073696C>T	ENST00000304129.4	-	7	755	c.726G>A	c.(724-726)acG>acA	p.T242T	AFAP1L2_ENST00000369271.3_Silent_p.T242T|AFAP1L2_ENST00000545353.1_Silent_p.T295T			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	242	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		CATTCATCGGCGTGATCTTCA	0.597													C|||	2929	0.584864	0.09	0.8084	5008	,	,		19618	0.8929		0.7614	False		,,,				2504	0.5961				p.T242T		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.G726A						PASS	.	C	,	848,3558	336.0+/-304.2	95,658,1450	213.0	129.0	158.0		726,726	-3.8	0.4	10	dbSNP_107	158	6693,1907	727.4+/-406.6	2613,1467,220	no	coding-synonymous,coding-synonymous	AFAP1L2	NM_001001936.1,NM_032550.2	,	2708,2125,1670	TT,TC,CC		22.1744,19.2465,42.0191	,	242/819,242/815	116073696	7541,5465	2203	4300	6503	SO:0001819	synonymous_variant	84632	exon7			CATCGGCGTGATC	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.726G>A	10.37:g.116073696C>T		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	202	200	0.990099	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			C|0.396;T|0.604	0.604	strong		0.597	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
KDM6B	23135	hgsc.bcm.edu	37	17	7751778	7751778	+	Silent	SNP	G	G	A	rs3744249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7751778G>A	ENST00000448097.2	+	11	2503	c.2172G>A	c.(2170-2172)ccG>ccA	p.P724P	KDM6B_ENST00000254846.5_Silent_p.P724P			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	724	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						CCCAACCCCCGCTGAAGGAGC	0.597													G|||	1263	0.252196	0.3298	0.2867	5008	,	,		8279	0.2758		0.0934	False		,,,				2504	0.2618				p.P724P		Atlas-SNP	.											.	KDM6B	95	.	0			c.G2172A						PASS	.	G		1259,3147	422.3+/-339.7	180,899,1124	75.0	90.0	85.0		2172	-4.0	0.5	17	dbSNP_107	85	962,7638	210.0+/-251.0	48,866,3386	no	coding-synonymous	KDM6B	NM_001080424.1		228,1765,4510	AA,AG,GG		11.186,28.5747,17.0767		724/1683	7751778	2221,10785	2203	4300	6503	SO:0001819	synonymous_variant	23135	exon11			ACCCCCGCTGAAG	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.2172G>A	17.37:g.7751778G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001080424	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																				A|0.168;C|0.000;G|0.832	0.168	strong		0.597	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
DBI	1622	hgsc.bcm.edu	37	2	120125058	120125058	+	Intron	SNP	C	C	T	rs3731607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:120125058C>T	ENST00000355857.3	+	1	140				DBI_ENST00000409094.1_Intron|DBI_ENST00000460901.1_Intron|C2orf76_ENST00000409523.1_5'Flank|DBI_ENST00000311521.4_Intron|C2orf76_ENST00000409466.2_5'Flank|DBI_ENST00000535757.1_Intron|C2orf76_ENST00000334816.7_5'Flank|C2orf76_ENST00000498049.1_5'Flank|DBI_ENST00000542275.1_Missense_Mutation_p.A49V|C2orf76_ENST00000409877.1_5'Flank|DBI_ENST00000393103.2_5'Flank|DBI_ENST00000535617.1_Missense_Mutation_p.A30V	NM_001079862.1|NM_001178043.1	NP_001073331.1|NP_001171514.1	P07108	ACBP_HUMAN	diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein)						hair follicle development (GO:0001942)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|transport (GO:0006810)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear endoplasmic reticulum (GO:0097038)	benzodiazepine receptor binding (GO:0030156)|lipid binding (GO:0008289)|long-chain fatty acyl-CoA binding (GO:0036042)|protein dimerization activity (GO:0046983)			kidney(1)|lung(4)|skin(1)	6						AAGTACGGGGCCGGCTGCTCA	0.677													C|||	811	0.161941	0.121	0.1643	5008	,	,		13898	0.2173		0.1998	False		,,,				2504	0.1196				p.A49V		Atlas-SNP	.											.	DBI	10	.	0			c.C146T						PASS	.																																			SO:0001627	intron_variant	1622	exon1			ACGGGGCCGGCTG	L76366	CCDS2126.1, CCDS42740.1, CCDS42741.1, CCDS74568.1	2q12-q21	2010-10-20	2010-04-30		ENSG00000155368	ENSG00000155368			2690	protein-coding gene	gene with protein product	"""endozepine"""	125950	"""diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein)"""			1440058	Standard	NM_001079863		Approved	ACBP, ACBD1	uc021vnj.1	P07108	OTTHUMG00000131403	ENST00000355857.3:c.9+422C>T	2.37:g.120125058C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_001178017	B8ZWD2|B8ZWD6|B8ZWD7|P08869|Q4VWZ6|Q53SQ7|Q6IB48|Q9UCI8	Missense_Mutation	SNP	ENST00000355857.3	37	CCDS42740.1	396	0.1813186813186813	63	0.12804878048780488	57	0.1574585635359116	131	0.229020979020979	145	0.19129287598944592	C	13.86	2.364455	0.41902	.	.	ENSG00000155368	ENST00000535617;ENST00000542275	T;T	0.19938	2.16;2.11	3.6	0.671	0.17929	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.000000000032756E-6	B	0.14805	0.011	B	0.08055	0.003	T	0.44143	-0.9347	7	0.09843	T	0.71	.	3.2939	0.06958	0.0:0.5159:0.2242:0.2598	rs3731607;rs3731607	30	B8ZWD7	.	V	30;49	ENSP00000442917:A30V;ENSP00000440698:A49V	ENSP00000442917:A30V	A	+	2	0	DBI	119841528	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.430000	0.06973	0.121000	0.18284	0.655000	0.94253	GCC	C|0.815;T|0.185	0.185	strong		0.677	DBI-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330590.1	NM_020548	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5200281	5200281	+	Silent	SNP	C	C	T	rs6555335	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:5200281C>T	ENST00000274181.7	+	9	1488	c.1350C>T	c.(1348-1350)tgC>tgT	p.C450C	ADAMTS16_ENST00000511368.1_Silent_p.C450C	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	450	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						GGAACATGTGCAAAAAGTCCG	0.443													C|||	3632	0.72524	0.5651	0.8314	5008	,	,		19242	0.8026		0.7396	False		,,,				2504	0.772				p.C450C		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C1350T						PASS	.	C		2409,1511		739,931,290	60.0	62.0	61.0		1350	3.2	1.0	5	dbSNP_116	61	6227,2101		2330,1567,267	no	coding-synonymous	ADAMTS16	NM_139056.2		3069,2498,557	TT,TC,CC		25.2281,38.5459,29.4905		450/1225	5200281	8636,3612	1960	4164	6124	SO:0001819	synonymous_variant	170690	exon9			CATGTGCAAAAAG	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17108	protein-coding gene	gene with protein product		607510	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"""			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1350C>T	5.37:g.5200281C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	138	56	0.405797	NM_139056	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	37	CCDS43299.1																																																																																			C|0.270;T|0.730	0.730	strong		0.443	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
AFAP1	60312	hgsc.bcm.edu	37	4	7780582	7780582	+	Missense_Mutation	SNP	C	C	T	rs41264705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:7780582C>T	ENST00000360265.4	-	12	1786	c.1552G>A	c.(1552-1554)Gtg>Atg	p.V518M	AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000382543.3_Missense_Mutation_p.V602M|AFAP1_ENST00000358461.2_Missense_Mutation_p.V518M|AFAP1_ENST00000420658.1_Missense_Mutation_p.V602M|AFAP1-AS1_ENST00000608442.1_RNA			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	518			V -> M (in dbSNP:rs41264705). {ECO:0000269|Ref.5}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TTAGACGCCACGGGGGGCTTT	0.428													C|||	554	0.110623	0.0106	0.1455	5008	,	,		17983	0.0615		0.2992	False		,,,				2504	0.0777				p.V602M		Atlas-SNP	.											.	AFAP1	93	.	0			c.G1804A						PASS	.	C	MET/VAL,MET/VAL	240,4166	141.9+/-177.2	7,226,1970	85.0	93.0	90.0		1804,1552	-0.2	0.0	4	dbSNP_127	90	2578,6022	418.9+/-352.9	409,1760,2131	yes	missense,missense	AFAP1	NM_001134647.1,NM_198595.2	21,21	416,1986,4101	TT,TC,CC		29.9767,5.4471,21.6669	possibly-damaging,possibly-damaging	602/815,518/731	7780582	2818,10188	2203	4300	6503	SO:0001583	missense	60312	exon14			ACGCCACGGGGGG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1552G>A	4.37:g.7780582C>T	ENSP00000353402:p.Val518Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	18	0.346154	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	37	CCDS3397.1	335	0.1533882783882784	12	0.024390243902439025	68	0.1878453038674033	39	0.06818181818181818	216	0.2849604221635884	C	8.194	0.796722	0.16327	0.054471	0.299767	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.15017	2.48;2.46;2.48;2.46	4.66	-0.23	0.13090	.	1.759780	0.02821	N	0.125536	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;P	0.44816	0.832;0.844	B;B	0.26969	0.036;0.075	T	0.42327	-0.9458	9	0.48119	T	0.1	-2.3154	5.8903	0.18909	0.0:0.4928:0.2336:0.2736	rs41264705;rs62289269	602;518	E9PDT7;Q8N556	.;AFAP1_HUMAN	M	518;602;518;602	ENSP00000353402:V518M;ENSP00000410689:V602M;ENSP00000351245:V518M;ENSP00000371983:V602M	ENSP00000351245:V518M	V	-	1	0	AFAP1	7831482	0.000000	0.05858	0.001000	0.08648	0.647000	0.38526	-0.488000	0.06497	-0.038000	0.13624	-0.742000	0.03525	GTG	C|0.800;T|0.200	0.200	strong		0.428	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
DNAJC30	84277	hgsc.bcm.edu	37	7	73097713	73097713	+	Missense_Mutation	SNP	G	G	A	rs61751896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73097713G>A	ENST00000395176.2	-	1	70	c.41C>T	c.(40-42)cCt>cTt	p.P14L	WBSCR22_ENST00000423497.1_5'Flank|WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000464615.1_3'UTR|WBSCR22_ENST00000265758.2_5'Flank	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	14						mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(1)	4						CAACCTCCAAGGTAACAGCCG	0.597													G|||	127	0.0253594	0.0454	0.0202	5008	,	,		13525	0.0		0.0328	False		,,,				2504	0.0204				p.P14L		Atlas-SNP	.											DNAJC30,NS,carcinoma,0,1	DNAJC30	12	1	0			c.C41T						PASS	.	G	LEU/PRO	142,4200		1,140,2030	31.0	38.0	35.0		41	0.7	0.0	7	dbSNP_129	35	293,8189		7,279,3955	yes	missense	DNAJC30	NM_032317.2	98	8,419,5985	AA,AG,GG		3.4544,3.2704,3.3921	possibly-damaging	14/227	73097713	435,12389	2171	4241	6412	SO:0001583	missense	84277	exon1			CTCCAAGGTAACA	AF412025	CCDS5556.1	7q11.23	2011-09-02	2008-06-17	2008-06-17	ENSG00000176410	ENSG00000176410		"""Heat shock proteins / DNAJ (HSP40)"""	16410	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 18"""	WBSCR18		12073013	Standard	NM_032317		Approved		uc003tys.1	Q96LL9	OTTHUMG00000023290	ENST00000395176.2:c.41C>T	7.37:g.73097713G>A	ENSP00000378605:p.Pro14Leu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_032317	Q9BSG8	Missense_Mutation	SNP	ENST00000395176.2	37	CCDS5556.1	71	0.03250915750915751	30	0.06097560975609756	12	0.03314917127071823	0	0.0	29	0.03825857519788918	G	9.242	1.038521	0.19669	0.032704	0.034544	ENSG00000176410	ENST00000395176;ENST00000539255	T	0.54866	0.55	4.96	0.737	0.18314	.	1.007380	0.07997	N	0.988095	T	0.01661	0.0053	N	0.01168	-0.975	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.16335	-1.0406	10	0.02654	T	1	0.0029	1.6009	0.02674	0.4734:0.27:0.0955:0.1611	rs61751896	14	Q96LL9	DJC30_HUMAN	L	14;11	ENSP00000378605:P14L	ENSP00000378605:P14L	P	-	2	0	DNAJC30	72735649	0.013000	0.17824	0.000000	0.03702	0.001000	0.01503	1.122000	0.31295	0.025000	0.15241	-1.053000	0.02334	CCT	G|0.967;A|0.033	0.033	strong		0.597	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2		
C5orf60	285679	hgsc.bcm.edu	37	5	179071893	179071893	+	Silent	SNP	A	A	G	rs4990388	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:179071893A>G	ENST00000448248.2	-	1	154	c.129T>C	c.(127-129)ttT>ttC	p.F43F	C5orf60_ENST00000506142.1_Intron	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	43						integral component of membrane (GO:0016021)		p.F43F(2)		NS(1)|breast(1)|kidney(5)	7						TGAACACAACAAAGAGGACGA	0.517													-|||	83	0.0165735	0.0575	0.0058	5008	,	,		23296	0.0		0.002	False		,,,				2504	0.001				p.F43F		Atlas-SNP	.											C5orf60,NS,carcinoma,0,2	C5orf60	24	2	2	Substitution - coding silent(2)	kidney(2)	c.T129C						scavenged	.						89.0	84.0	86.0					5																	179071893		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			CACAACAAAGAGG	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.129T>C	5.37:g.179071893A>G		Somatic	196	5	0.0255102		WXS	Illumina HiSeq	Phase_I	224	9	0.0401786	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			A|0.993;G|0.007	0.007	strong		0.517	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
SLC30A9	10463	hgsc.bcm.edu	37	4	42022464	42022464	+	Silent	SNP	C	C	A	rs15857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:42022464C>A	ENST00000264451.7	+	4	546	c.366C>A	c.(364-366)ggC>ggA	p.G122G		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	122					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GGGAGTATGGCTCAAAGTACA	0.343													.|||	3341	0.667133	0.1884	0.804	5008	,	,		18317	0.9583		0.7763	False		,,,				2504	0.8047				p.G122G		Atlas-SNP	.											.	SLC30A9	58	.	0			c.C366A						PASS	.	A		1228,3178	706.3+/-407.4	173,882,1148	136.0	126.0	129.0		366	3.7	1.0	4	dbSNP_52	129	6672,1926	340.3+/-323.5	2575,1522,202	no	coding-synonymous	SLC30A9	NM_006345.3		2748,2404,1350	AA,AC,CC		22.4006,27.8711,39.2495		122/569	42022464	7900,5104	2203	4299	6502	SO:0001819	synonymous_variant	10463	exon4			GTATGGCTCAAAG	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"""Solute carriers"""	1329	protein-coding gene	gene with protein product	"""GRIP1-dependent nuclear receptor coactivator"""	604604	"""chromosome 4 open reading frame 1"""	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.366C>A	4.37:g.42022464C>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Silent	SNP	ENST00000264451.7	37	CCDS3465.1																																																																																			C|0.359;A|0.641	0.641	strong		0.343	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3		
KIAA1524	57650	hgsc.bcm.edu	37	3	108303989	108303989	+	Missense_Mutation	SNP	C	C	A	rs34788499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108303989C>A	ENST00000295746.8	-	2	249	c.173G>T	c.(172-174)tGc>tTc	p.C58F	KIAA1524_ENST00000491772.1_5'UTR|KIAA1524_ENST00000487834.1_5'UTR	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	58					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTCTACAAGGCAACTCAAGCA	0.343													C|||	39	0.00778754	0.0008	0.0086	5008	,	,		19289	0.0		0.0278	False		,,,				2504	0.0041				p.C58F		Atlas-SNP	.											.	KIAA1524	82	.	0			c.G173T						PASS	.	C	PHE/CYS	32,4374	37.6+/-69.7	0,32,2171	159.0	153.0	155.0		173	4.7	1.0	3	dbSNP_126	155	213,8387	90.9+/-153.0	2,209,4089	yes	missense	KIAA1524	NM_020890.2	205	2,241,6260	AA,AC,CC		2.4767,0.7263,1.8837	probably-damaging	58/906	108303989	245,12761	2203	4300	6503	SO:0001583	missense	57650	exon2			ACAAGGCAACTCA	AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"""cancerous inhibitor of protein phosphatase 2A"""	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.173G>T	3.37:g.108303989C>A	ENSP00000295746:p.Cys58Phe	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_020890	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Missense_Mutation	SNP	ENST00000295746.8	37	CCDS33812.1	30	0.013736263736263736	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	23	0.030343007915567283	C	18.43	3.622658	0.66787	0.007263	0.024767	ENSG00000163507	ENST00000295746	T	0.33438	1.41	5.53	4.65	0.58169	Armadillo-type fold (1);	0.289012	0.44902	D	0.000417	T	0.23532	0.0569	L	0.54323	1.7	0.42686	D	0.993562	D	0.71674	0.998	P	0.59643	0.861	T	0.33650	-0.9860	10	0.66056	D	0.02	-0.3458	16.0492	0.80744	0.1354:0.8646:0.0:0.0	rs34788499	58	Q8TCG1	CIP2A_HUMAN	F	58	ENSP00000295746:C58F	ENSP00000295746:C58F	C	-	2	0	KIAA1524	109786679	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.816000	0.55658	1.451000	0.47736	-0.188000	0.12872	TGC	C|0.982;A|0.018	0.018	strong		0.343	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890	
HEG1	57493	hgsc.bcm.edu	37	3	124732618	124732618	+	Missense_Mutation	SNP	A	A	G	rs6790837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:124732618A>G	ENST00000311127.4	-	6	1872	c.1805T>C	c.(1804-1806)tTt>tCt	p.F602S	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	602	Ser-rich.		F -> S (in dbSNP:rs6790837).		cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						CTGAGCATGAAAAAAGGAGGA	0.423													A|||	2209	0.441094	0.2269	0.4409	5008	,	,		21906	0.4673		0.5358	False		,,,				2504	0.6063				p.F602S		Atlas-SNP	.											.	HEG1	109	.	0			c.T1805C						PASS	.	A	SER/PHE	1020,2976		122,776,1100	95.0	94.0	95.0		1805	3.3	0.9	3	dbSNP_116	95	4211,4129		1039,2133,998	yes	missense	HEG1	NM_020733.1	155	1161,2909,2098	GG,GA,AA		49.5084,25.5255,42.4043	benign	602/1382	124732618	5231,7105	1998	4170	6168	SO:0001583	missense	57493	exon6			GCATGAAAAAAGG	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1805T>C	3.37:g.124732618A>G	ENSP00000311502:p.Phe602Ser	Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	222	220	0.990991	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	968	0.4432234432234432	112	0.22764227642276422	160	0.4419889502762431	276	0.4825174825174825	420	0.554089709762533	A	0.549	-0.850305	0.02651	0.255255	0.504916	ENSG00000173706	ENST00000311127	D	0.86694	-2.16	5.13	3.35	0.38373	.	.	.	.	.	T	0.00012	0.0000	N	0.00347	-1.61	0.49389	P	2.1700000000002273E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38001	-0.9681	8	0.05833	T	0.94	.	9.2744	0.37690	0.1656:0.0:0.8344:0.0	rs6790837;rs52806541;rs60644473;rs6790837	602;602	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	S	602	ENSP00000311502:F602S	ENSP00000311502:F602S	F	-	2	0	HEG1	126215308	0.998000	0.40836	0.929000	0.37066	0.473000	0.32948	2.578000	0.46051	0.750000	0.32877	-0.132000	0.14878	TTT	A|0.568;G|0.432	0.432	strong		0.423	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
WIPF2	147179	hgsc.bcm.edu	37	17	38416827	38416827	+	Missense_Mutation	SNP	G	G	A	rs142659099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38416827G>A	ENST00000323571.4	+	3	344	c.104G>A	c.(103-105)cGg>cAg	p.R35Q	WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000394103.3_Missense_Mutation_p.R35Q|WIPF2_ENST00000536600.1_Missense_Mutation_p.R35Q|WIPF2_ENST00000583130.1_Missense_Mutation_p.R35Q|WIPF2_ENST00000585043.1_Missense_Mutation_p.R35Q	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	35					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						GATGAGCAGCGGGGTCGAGGC	0.527										HNSCC(43;0.11)			G|||	10	0.00199681	0.0	0.0029	5008	,	,		18945	0.0		0.005	False		,,,				2504	0.0031				p.R35Q		Atlas-SNP	.											.	WIPF2	55	.	0			c.G104A						PASS	.	G	GLN/ARG	5,4401	9.9+/-24.2	0,5,2198	105.0	91.0	96.0		104	5.7	1.0	17	dbSNP_134	96	55,8545	34.3+/-88.2	0,55,4245	yes	missense	WIPF2	NM_133264.4	43	0,60,6443	AA,AG,GG		0.6395,0.1135,0.4613	possibly-damaging	35/441	38416827	60,12946	2203	4300	6503	SO:0001583	missense	147179	exon3			AGCAGCGGGGTCG	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.104G>A	17.37:g.38416827G>A	ENSP00000320924:p.Arg35Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	Missense_Mutation	SNP	ENST00000323571.4	37	CCDS11364.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	23.0	4.362796	0.82353	0.001135	0.006395	ENSG00000171475	ENST00000323571;ENST00000394103;ENST00000536600	T;T;T	0.42131	1.6;0.98;0.98	5.74	5.74	0.90152	.	0.065269	0.64402	D	0.000005	T	0.20170	0.0485	N	0.17082	0.46	0.36982	D	0.894329	P;D	0.59357	0.898;0.985	B;B	0.41299	0.147;0.353	T	0.12502	-1.0545	10	0.30078	T	0.28	-8.5645	13.1603	0.59540	0.0727:0.0:0.9273:0.0	.	35;35	A8MWR2;Q8TF74	.;WIPF2_HUMAN	Q	35	ENSP00000320924:R35Q;ENSP00000377663:R35Q;ENSP00000439175:R35Q	ENSP00000320924:R35Q	R	+	2	0	WIPF2	35670353	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	6.376000	0.73141	2.709000	0.92574	0.555000	0.69702	CGG	G|0.997;A|0.003	0.003	strong		0.527	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264	
GIGYF1	64599	hgsc.bcm.edu	37	7	100279988	100279988	+	Silent	SNP	G	G	A	rs117477530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100279988G>A	ENST00000275732.5	-	21	3927	c.2718C>T	c.(2716-2718)tgC>tgT	p.C906C	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	906					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GCATCTGCTCGCACCACTGGG	0.672													G|||	6	0.00119808	0.0	0.0058	5008	,	,		15974	0.0		0.002	False		,,,				2504	0.0				p.C906C		Atlas-SNP	.											.	GIGYF1	113	.	0			c.C2718T						PASS	.	G		3,4401		0,3,2199	54.0	46.0	49.0		2718	-2.7	0.9	7	dbSNP_132	49	27,8573		0,27,4273	yes	coding-synonymous	GIGYF1	NM_022574.4		0,30,6472	AA,AG,GG		0.314,0.0681,0.2307		906/1036	100279988	30,12974	2202	4300	6502	SO:0001819	synonymous_variant	64599	exon21			CTGCTCGCACCAC	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"""GYF domain containing 1"""	612064	"""PERQ amino acid rich, with GYF domain 1"""	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.2718C>T	7.37:g.100279988G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_022574	Q6Y7W7|Q8WZ38	Silent	SNP	ENST00000275732.5	37	CCDS34708.1																																																																																			G|0.998;A|0.002	0.002	strong		0.672	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574	
OR10H5	284433	hgsc.bcm.edu	37	19	15905431	15905431	+	Silent	SNP	T	T	C	rs4808381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15905431T>C	ENST00000308940.8	+	1	671	c.573T>C	c.(571-573)gaT>gaC	p.D191D		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						CCTGTGGAGATGATGTGCTGG	0.572													.|||	2284	0.45607	0.3359	0.4784	5008	,	,		22330	0.7897		0.3052	False		,,,				2504	0.4141				p.D191D		Atlas-SNP	.											.	OR10H5	49	.	0			c.T573C						PASS	.	T		1488,2918		260,968,975	165.0	130.0	142.0		573	-5.6	0.0	19	dbSNP_111	142	2843,5757		509,1825,1966	no	coding-synonymous	OR10H5	NM_001004466.1		769,2793,2941	CC,CT,TT		33.0581,33.7721,33.3		191/316	15905431	4331,8675	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			TGGAGATGATGTG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.573T>C	19.37:g.15905431T>C		Somatic	359	1	0.00278552		WXS	Illumina HiSeq	Phase_I	245	244	0.995918	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			T|0.623;C|0.377	0.377	strong		0.572	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
SLC52A3	113278	hgsc.bcm.edu	37	20	744415	744415	+	Missense_Mutation	SNP	G	G	A	rs3746804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:744415G>A	ENST00000217254.7	-	3	1041	c.800C>T	c.(799-801)cCg>cTg	p.P267L	SLC52A3_ENST00000473664.1_Intron|SLC52A3_ENST00000381944.3_Missense_Mutation_p.P267L	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	267			P -> L (in dbSNP:rs3746804). {ECO:0000269|PubMed:15489334}.		cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										CTCTTCCCGCGGCCGGATGGA	0.647													G|||	913	0.182308	0.1346	0.1167	5008	,	,		19203	0.255		0.2018	False		,,,				2504	0.1984				p.P267L		Atlas-SNP	.											.	.	.	.	0			c.C800T						PASS	.	G	LEU/PRO	713,3693	296.1+/-284.1	61,591,1551	50.0	50.0	50.0		800	0.1	0.2	20	dbSNP_107	50	1837,6763	329.2+/-318.6	215,1407,2678	yes	missense	C20orf54	NM_033409.3	98	276,1998,4229	AA,AG,GG		21.3605,16.1825,19.6063	benign	267/470	744415	2550,10456	2203	4300	6503	SO:0001583	missense	113278	exon3			TCCCGCGGCCGGA	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.800C>T	20.37:g.744415G>A	ENSP00000217254:p.Pro267Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	116	0.97479	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	37	CCDS13007.1	466	0.21336996336996336	83	0.16869918699186992	42	0.11602209944751381	183	0.31993006993006995	158	0.20844327176781002	G	6.760	0.509184	0.12883	0.161825	0.213605	ENSG00000101276	ENST00000217254;ENST00000381944	T;T	0.72942	-0.63;-0.7	4.95	0.143	0.14820	.	0.889113	0.10011	N	0.727169	T	0.00012	0.0000	N	0.19112	0.55	0.54753	P	1.0999999999983245E-5	B;B	0.16396	0.01;0.017	B;B	0.08055	0.003;0.001	T	0.17018	-1.0383	9	0.25106	T	0.35	-0.336	4.1083	0.10047	0.3612:0.0:0.4742:0.1646	rs3746804;rs17855409;rs61573051;rs3746804	267;267	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	L	267	ENSP00000217254:P267L;ENSP00000371370:P267L	ENSP00000217254:P267L	P	-	2	0	C20orf54	692415	0.000000	0.05858	0.154000	0.22540	0.797000	0.45037	0.461000	0.21940	0.466000	0.27193	0.561000	0.74099	CCG	G|0.794;A|0.206	0.206	strong		0.647	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
GABRA6	2559	hgsc.bcm.edu	37	5	161128627	161128627	+	Missense_Mutation	SNP	C	C	T	rs34907804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:161128627C>T	ENST00000274545.5	+	9	1643	c.1210C>T	c.(1210-1212)Ccc>Tcc	p.P404S	GABRA6_ENST00000523217.1_Missense_Mutation_p.P394S			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	404			P -> S (in dbSNP:rs34907804).		gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	ACCTGTCACACCCCCACCACT	0.473										TCGA Ovarian(5;0.080)			C|||	365	0.0728834	0.1369	0.085	5008	,	,		16777	0.0		0.0765	False		,,,				2504	0.0491				p.P404S		Atlas-SNP	.											GABRA6,lower_third,carcinoma,-2,1	GABRA6	139	1	0			c.C1210T						PASS	.	C	SER/PRO	541,3865	239.6+/-250.7	29,483,1691	109.0	103.0	105.0		1210	5.2	1.0	5	dbSNP_126	105	666,7934	167.1+/-218.9	28,610,3662	yes	missense	GABRA6	NM_000811.2	74	57,1093,5353	TT,TC,CC		7.7442,12.2787,9.2803	benign	404/454	161128627	1207,11799	2203	4300	6503	SO:0001583	missense	2559	exon9			GTCACACCCCCAC		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.1210C>T	5.37:g.161128627C>T	ENSP00000274545:p.Pro404Ser	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	218	81	0.37156	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	158	0.07234432234432235	62	0.12601626016260162	40	0.11049723756906077	0	0.0	56	0.07387862796833773	C	8.391	0.839816	0.16891	0.122787	0.077442	ENSG00000145863	ENST00000274545;ENST00000523217	D;D	0.83335	-1.71;-1.71	5.16	5.16	0.70880	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.345405	0.34484	N	0.003927	T	0.01765	0.0056	L	0.29908	0.895	0.35992	P	0.16322899999999996	B	0.12013	0.005	B	0.06405	0.002	T	0.39014	-0.9634	9	0.20519	T	0.43	.	9.2591	0.37601	0.0:0.7619:0.1583:0.0798	rs34907804;rs52809327;rs61306367	404	Q16445	GBRA6_HUMAN	S	404;394	ENSP00000274545:P404S;ENSP00000430527:P394S	ENSP00000274545:P404S	P	+	1	0	GABRA6	161061205	0.998000	0.40836	0.990000	0.47175	0.451000	0.32288	3.751000	0.55165	2.571000	0.86741	0.655000	0.94253	CCC	C|0.915;T|0.085	0.085	strong		0.473	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
NRAP	4892	hgsc.bcm.edu	37	10	115377290	115377290	+	Missense_Mutation	SNP	T	T	C	rs77678145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115377290T>C	ENST00000359988.3	-	26	3141	c.2897A>G	c.(2896-2898)gAt>gGt	p.D966G	NRAP_ENST00000369360.3_Missense_Mutation_p.D939G|NRAP_ENST00000360478.3_Missense_Mutation_p.D931G|NRAP_ENST00000369358.4_Missense_Mutation_p.D974G	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTTCAAAGCATCTGGATGCTG	0.388													T|||	351	0.0700879	0.0008	0.0677	5008	,	,		19691	0.1528		0.0825	False		,,,				2504	0.0675				p.D966G		Atlas-SNP	.											.	NRAP	208	.	0			c.A2897G						PASS	.	T	GLY/ASP,GLY/ASP	80,4326	69.8+/-107.6	1,78,2124	143.0	137.0	139.0		2792,2897	4.9	1.0	10	dbSNP_131	139	751,7849	180.3+/-229.3	37,677,3586	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	94,94	38,755,5710	CC,CT,TT		8.7326,1.8157,6.3894	benign,benign	931/1696,966/1731	115377290	831,12175	2203	4300	6503	SO:0001583	missense	4892	exon26			AAAGCATCTGGAT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2897A>G	10.37:g.115377290T>C	ENSP00000353078:p.Asp966Gly	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	154	0.07051282051282051	2	0.0040650406504065045	24	0.06629834254143646	65	0.11363636363636363	63	0.08311345646437995	T	13.95	2.390625	0.42410	0.018157	0.087326	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.18174	2.43;2.46;2.32;2.23	6.17	4.86	0.63082	.	0.251467	0.48286	D	0.000187	T	0.00328	0.0010	L	0.43152	1.355	0.33783	P	0.375452	B;B;B	0.25719	0.081;0.132;0.007	B;B;B	0.32624	0.071;0.149;0.011	T	0.07121	-1.0789	9	0.48119	T	0.1	.	8.7616	0.34678	0.0:0.0729:0.1303:0.7969	.	966;931;966	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	G	974;939;966;931	ENSP00000358365:D974G;ENSP00000358367:D939G;ENSP00000353078:D966G;ENSP00000353666:D931G	ENSP00000353078:D966G	D	-	2	0	NRAP	115367280	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.967000	0.29344	2.371000	0.80710	0.533000	0.62120	GAT	A|0.000;C|0.068;T|0.932	0.068	strong		0.388	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
AHNAK	79026	hgsc.bcm.edu	37	11	62293948	62293948	+	Silent	SNP	G	G	A	rs486903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62293948G>A	ENST00000378024.4	-	5	8215	c.7941C>T	c.(7939-7941)agC>agT	p.S2647S	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2647					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.S2647S(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				AGCCAGGCATGCTGAACTTTG	0.532													G|||	2369	0.473043	0.0779	0.6715	5008	,	,		20347	0.3046		0.7366	False		,,,				2504	0.7689				p.S2647S		Atlas-SNP	.											AHNAK,NS,carcinoma,0,1	AHNAK	532	1	1	Substitution - coding silent(1)	stomach(1)	c.C7941T						PASS	.	G	,	854,3550	334.4+/-303.4	102,650,1450	188.0	190.0	189.0		7941,	3.6	1.0	11	dbSNP_83	189	6405,2193	711.8+/-405.9	2384,1637,278	no	coding-synonymous,intron	AHNAK	NM_001620.1,NM_024060.2	,	2486,2287,1728	AA,AG,GG		25.5059,19.3915,44.1701	,	2647/5891,	62293948	7259,5743	2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			AGGCATGCTGAAC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.7941C>T	11.37:g.62293948G>A		Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	233	232	0.995708	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																			G|0.462;A|0.538	0.538	strong		0.532	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
POLR3B	55703	hgsc.bcm.edu	37	12	106903321	106903321	+	Silent	SNP	T	T	C	rs13561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:106903321T>C	ENST00000228347.4	+	28	3618	c.3396T>C	c.(3394-3396)aaT>aaC	p.N1132N	POLR3B_ENST00000539066.1_Silent_p.N1074N|RP11-144F15.1_ENST00000551505.1_Intron	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	1132					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						CCAAGTACAATGAATGAGGAT	0.438													T|||	1627	0.32488	0.0408	0.366	5008	,	,		18100	0.6855		0.2724	False		,,,				2504	0.362				p.N1132N		Atlas-SNP	.											.	POLR3B	123	.	0			c.T3396C						PASS	.	T	,	394,4012	195.3+/-220.0	18,358,1827	92.0	81.0	85.0		3222,3396	-1.6	1.0	12	dbSNP_52	85	2357,6243	394.0+/-344.5	335,1687,2278	no	coding-synonymous,coding-synonymous	POLR3B	NM_001160708.1,NM_018082.5	,	353,2045,4105	CC,CT,TT		27.407,8.9424,21.1518	,	1074/1076,1132/1134	106903321	2751,10255	2203	4300	6503	SO:0001819	synonymous_variant	55703	exon28			GTACAATGAATGA	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.3396T>C	12.37:g.106903321T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_018082	A8K6H0|B3KV73|F5H1E6|Q9NW59	Silent	SNP	ENST00000228347.4	37	CCDS9105.1																																																																																			T|0.734;C|0.266	0.266	strong		0.438	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082	
TCL1B	9623	hgsc.bcm.edu	37	14	96157187	96157187	+	Missense_Mutation	SNP	G	G	A	rs1064017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:96157187G>A	ENST00000340722.7	+	2	328	c.277G>A	c.(277-279)Ggg>Agg	p.G93R	RP11-1070N10.6_ENST00000461160.1_RNA	NM_004918.3	NP_004909.1	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	93			G -> R (in dbSNP:rs1064017). {ECO:0000269|PubMed:10344735, ECO:0000269|PubMed:15489334}.							cervix(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		GCTCTACCCCGGGAGGAAGTA	0.612													G|||	1313	0.262181	0.2413	0.3372	5008	,	,		19471	0.0873		0.4105	False		,,,				2504	0.2648				p.G93R		Atlas-SNP	.											TCL1B,NS,malignant_melanoma,-2,3	TCL1B	30	3	0			c.G277A						scavenged	.	G	ARG/GLY	1294,3112	438.2+/-345.2	194,906,1103	65.0	68.0	67.0		277	0.8	0.0	14	dbSNP_86	67	3832,4768	538.4+/-383.4	851,2130,1319	yes	missense	TCL1B	NM_004918.3	125	1045,3036,2422	AA,AG,GG		44.5581,29.369,39.4126	probably-damaging	93/129	96157187	5126,7880	2203	4300	6503	SO:0001583	missense	9623	exon2			TACCCCGGGAGGA	AB018563	CCDS32151.1	14q32.1	2008-09-05			ENSG00000213231	ENSG00000213231			11649	protein-coding gene	gene with protein product		603769				10077617	Standard	NM_004918		Approved	TML1	uc001yez.3	O95988	OTTHUMG00000028912	ENST00000340722.7:c.277G>A	14.37:g.96157187G>A	ENSP00000343223:p.Gly93Arg	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	141	78	0.553191	NM_004918	A6NEK7|Q6IAR7|Q9UBQ4	Missense_Mutation	SNP	ENST00000340722.7	37	CCDS32151.1	612	0.2802197802197802	127	0.258130081300813	117	0.32320441988950277	62	0.10839160839160839	306	0.40369393139841686	G	13.88	2.369441	0.42003	0.29369	0.445581	ENSG00000213231	ENST00000340722;ENST00000538038	T	0.27402	1.67	3.29	0.758	0.18432	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	P	0.51537	0.946	B	0.41088	0.347	T	0.38735	-0.9647	8	0.06236	T	0.91	-2.7841	2.3513	0.04284	0.232:0.0:0.5016:0.2664	rs1064017;rs1748957;rs3205032;rs17854667;rs52791006;rs58883833;rs1064017	93	O95988	TCL1B_HUMAN	R	93	ENSP00000343223:G93R	ENSP00000343223:G93R	G	+	1	0	TCL1B	95226940	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.137000	0.15995	0.160000	0.19432	0.462000	0.41574	GGG	G|0.658;A|0.342	0.342	strong		0.612	TCL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315123.2		
PFKP	5214	hgsc.bcm.edu	37	10	3172145	3172145	+	Silent	SNP	C	C	T	rs1052337	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:3172145C>T	ENST00000381125.4	+	17	1894	c.1818C>T	c.(1816-1818)ttC>ttT	p.F606F	PFKP_ENST00000381072.1_Silent_p.F24F|PFKP_ENST00000381075.2_Silent_p.F598F	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	606	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		CATACATTTTCGAAGAGCCCT	0.627													C|||	625	0.1248	0.1967	0.0821	5008	,	,		16234	0.0526		0.1292	False		,,,				2504	0.1278				p.F606F		Atlas-SNP	.											PFKP_ENST00000381075,colon,carcinoma,0,2	PFKP	182	2	0			c.C1818T						PASS	.	C	,	828,3578	313.6+/-293.2	76,676,1451	45.0	42.0	43.0		1794,1818	-5.4	0.2	10	dbSNP_86	43	1252,7348	243.5+/-273.1	99,1054,3147	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	175,1730,4598	TT,TC,CC		14.5581,18.7926,15.9926	,	598/777,606/785	3172145	2080,10926	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon17			CATTTTCGAAGAG	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1818C>T	10.37:g.3172145C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																			C|0.856;G|0.000;T|0.144	0.144	strong		0.627	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
TAOK2	9344	hgsc.bcm.edu	37	16	29994922	29994922	+	Silent	SNP	C	C	T	rs3814883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:29994922C>T	ENST00000308893.4	+	13	2402	c.1359C>T	c.(1357-1359)tcC>tcT	p.S453S	TAOK2_ENST00000279394.3_Silent_p.S453S|TAOK2_ENST00000416441.2_Silent_p.S280S|TAOK2_ENST00000543033.1_Silent_p.S453S	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	453					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						CCACCTCTTCCGCCCGCCGCC	0.637													c|||	1840	0.367412	0.1286	0.3804	5008	,	,		14141	0.4444		0.4602	False		,,,				2504	0.5061				p.S453S		Atlas-SNP	.											.	TAOK2	142	.	0			c.C1359T						PASS	.	T	,	731,3663	296.1+/-284.1	74,583,1540	128.0	162.0	151.0		1359,1359	-1.3	1.0	16	dbSNP_107	151	4008,4592	546.4+/-385.0	944,2120,1236	no	coding-synonymous,coding-synonymous	TAOK2	NM_004783.2,NM_016151.2	,	1018,2703,2776	TT,TC,CC		46.6047,16.6363,36.4707	,	453/1050,453/1236	29994922	4739,8255	2197	4300	6497	SO:0001819	synonymous_variant	9344	exon13			CTCTTCCGCCCGC	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.1359C>T	16.37:g.29994922C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_004783	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Silent	SNP	ENST00000308893.4	37	CCDS10663.1																																																																																			C|0.622;T|0.378	0.378	strong		0.637	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151	
MFSD12	126321	hgsc.bcm.edu	37	19	3546264	3546264	+	Missense_Mutation	SNP	C	C	T	rs34878396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:3546264C>T	ENST00000355415.2	-	7	1352	c.1183G>A	c.(1183-1185)Ggt>Agt	p.G395S	MFSD12_ENST00000389395.3_Missense_Mutation_p.G395S|MFSD12_ENST00000591878.1_5'Flank|AC005786.7_ENST00000589360.1_RNA|MFSD12_ENST00000398558.4_Missense_Mutation_p.G395S	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	395			G -> S (in dbSNP:rs34878396).		transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						GTGTGGGGACCGATGAGGTCG	0.682													C|||	10	0.00199681	0.0	0.0029	5008	,	,		13963	0.0		0.007	False		,,,				2504	0.001				p.G395S		Atlas-SNP	.											.	MFSD12	22	.	0			c.G1183A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	6,4266		0,6,2130	17.0	22.0	20.0		1183,1183,1183	4.6	1.0	19	dbSNP_126	20	58,8420		0,58,4181	no	missense,missense,missense	C19orf28	NM_001042680.1,NM_021731.2,NM_174983.3	56,56,56	0,64,6311	TT,TC,CC		0.6841,0.1404,0.502	possibly-damaging,possibly-damaging,possibly-damaging	395/474,395/539,395/481	3546264	64,12686	2136	4239	6375	SO:0001583	missense	126321	exon7			GGGGACCGATGAG	AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 28"""	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.1183G>A	19.37:g.3546264C>T	ENSP00000347583:p.Gly395Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_001042680	A8MXP7|D6W615|E9PAJ8|Q8N459	Missense_Mutation	SNP	ENST00000355415.2	37	CCDS42465.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	32	5.162522	0.94727	0.001404	0.006841	ENSG00000161091	ENST00000389395;ENST00000398558;ENST00000355415	D;D;D	0.87029	-2.2;-2.2;-2.2	4.63	4.63	0.57726	Major facilitator superfamily domain, general substrate transporter (1);	0.053348	0.64402	D	0.000001	D	0.90466	0.7014	M	0.77616	2.38	0.54753	D	0.999988	D;D;D	0.76494	0.992;0.997;0.999	P;P;D	0.65874	0.889;0.828;0.939	D	0.91435	0.5169	10	0.51188	T	0.08	-25.4799	16.4799	0.84155	0.0:1.0:0.0:0.0	rs34878396	395;386;395	Q6NUT3;Q6NUT3-2;A8MXP7	CS028_HUMAN;.;.	S	395	ENSP00000374046:G395S;ENSP00000381566:G395S;ENSP00000347583:G395S	ENSP00000347583:G395S	G	-	1	0	C19orf28	3497264	1.000000	0.71417	0.999000	0.59377	0.923000	0.55619	7.195000	0.77798	2.126000	0.65437	0.561000	0.74099	GGT	C|0.996;T|0.004	0.004	strong		0.682	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983	
AKR1A1	10327	hgsc.bcm.edu	37	1	46032543	46032543	+	Silent	SNP	G	G	A	rs41269113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46032543G>A	ENST00000372070.3	+	5	954	c.207G>A	c.(205-207)gcG>gcA	p.A69A	AKR1A1_ENST00000471651.1_Silent_p.A69A|AKR1A1_ENST00000351829.4_Silent_p.A69A	NM_001202413.1|NM_001202414.1|NM_006066.3	NP_001189342.1|NP_001189343.1|NP_006057.1	P14550	AK1A1_HUMAN	aldo-keto reductase family 1, member A1 (aldehyde reductase)	69					aldehyde catabolic process (GO:0046185)|cellular aldehyde metabolic process (GO:0006081)|D-glucuronate catabolic process (GO:0042840)|glucose metabolic process (GO:0006006)|L-ascorbic acid biosynthetic process (GO:0019853)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|L-glucuronate reductase activity (GO:0047939)			lung(3)|prostate(1)|urinary_tract(1)	5	Acute lymphoblastic leukemia(166;0.155)				Doxorubicin(DB00997)	TGCACTAGGCGGTGCCTCGGG	0.617													G|||	34	0.00678914	0.0015	0.0029	5008	,	,		21072	0.0		0.0268	False		,,,				2504	0.0031				p.A69A		Atlas-SNP	.											.	AKR1A1	25	.	0			c.G207A						PASS	.	G	,,,	29,4377	34.3+/-65.2	0,29,2174	55.0	51.0	52.0		207,207,207,207	-11.7	0.0	1	dbSNP_127	52	263,8337	100.8+/-162.1	6,251,4043	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AKR1A1	NM_001202413.1,NM_001202414.1,NM_006066.3,NM_153326.2	,,,	6,280,6217	AA,AG,GG		3.0581,0.6582,2.2451	,,,	69/326,69/326,69/326,69/326	46032543	292,12714	2203	4300	6503	SO:0001819	synonymous_variant	10327	exon5			CTAGGCGGTGCCT	J04794	CCDS523.1	1p33-p32	2010-04-08			ENSG00000117448	ENSG00000117448	1.1.1.2	"""Aldo-keto reductases"""	380	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 3"""	103830				2498333, 10393438	Standard	NM_001202414		Approved	ALR, DD3	uc001coe.3	P14550	OTTHUMG00000007740	ENST00000372070.3:c.207G>A	1.37:g.46032543G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	NM_001202413	A8KAL8|D3DQ04|Q6IAZ4	Silent	SNP	ENST00000372070.3	37	CCDS523.1																																																																																			G|0.982;A|0.018	0.018	strong		0.617	AKR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020851.1	NM_006066	
MROH2B	133558	hgsc.bcm.edu	37	5	41054934	41054934	+	Silent	SNP	A	A	G	rs325874	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:41054934A>G	ENST00000399564.4	-	11	1492	c.1042T>C	c.(1042-1044)Ttg>Ctg	p.L348L	MROH2B_ENST00000506092.2_Intron	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	348																	TGATCCCTCAACCTGGGCTCT	0.383													A|||	1074	0.214457	0.2095	0.1585	5008	,	,		18279	0.2222		0.2286	False		,,,				2504	0.2382				p.L348L		Atlas-SNP	.											.	.	.	.	0			c.T1042C						PASS	.	A		771,2899		83,605,1147	112.0	105.0	107.0		1042	-0.9	0.0	5	dbSNP_79	107	1831,6327		192,1447,2440	no	coding-synonymous	HEATR7B2	NM_173489.4		275,2052,3587	GG,GA,AA		22.4442,21.0082,21.9986		348/1586	41054934	2602,9226	1835	4079	5914	SO:0001819	synonymous_variant	133558	exon11			CCCTCAACCTGGG		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1042T>C	5.37:g.41054934A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	ENST00000399564.4	37	CCDS47202.1																																																																																			A|0.778;G|0.222	0.222	strong		0.383	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
SHC2	25759	hgsc.bcm.edu	37	19	434718	434718	+	Silent	SNP	G	G	A	rs61749991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:434718G>A	ENST00000264554.6	-	8	1100	c.1101C>T	c.(1099-1101)gcC>gcT	p.A367A		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	367	CH1.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGGTCGAGGGCCGTGAGGG	0.657													G|||	465	0.0928514	0.034	0.0504	5008	,	,		18293	0.1776		0.0199	False		,,,				2504	0.1902				p.A367A		Atlas-SNP	.											.	SHC2	47	.	0			c.C1101T						PASS	.	G		79,3943		1,77,1933	22.0	29.0	27.0		1101	1.9	0.6	19	dbSNP_129	27	106,8214		0,106,4054	no	coding-synonymous	SHC2	NM_012435.2		1,183,5987	AA,AG,GG		1.274,1.9642,1.4989		367/583	434718	185,12157	2011	4160	6171	SO:0001819	synonymous_variant	25759	exon8			GTCGAGGGCCGTG	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"""SH2 domain containing"""	29869	protein-coding gene	gene with protein product	"""neuronal Shc adaptor homolog"""	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1101C>T	19.37:g.434718G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	67	41	0.61194	NM_012435	O60230|Q9NPL5|Q9UCX4	Silent	SNP	ENST00000264554.6	37	CCDS45891.1																																																																																			G|0.934;A|0.066	0.066	strong		0.657	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3		
KLF2	10365	hgsc.bcm.edu	37	19	16436775	16436775	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:16436775G>A	ENST00000248071.5	+	2	931	c.824G>A	c.(823-825)aGc>aAc	p.S275N	KLF2_ENST00000592003.1_Intron|CTD-2562J15.6_ENST00000588799.1_RNA	NM_016270.2	NP_057354.1	Q9Y5W3	KLF2_HUMAN	Kruppel-like factor 2	275					cell morphogenesis (GO:0000902)|cellular response to cycloheximide (GO:0071409)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|cellular response to tumor necrosis factor (GO:0071356)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of interleukin-6 production (GO:0032715)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(3)|lung(1)|skin(1)	5						CACACCTGCAGCTACGCGGGC	0.697																																					p.S275N		Atlas-SNP	.											.	KLF2	10	.	0			c.G824A						PASS	.						8.0	5.0	6.0					19																	16436775		2074	4072	6146	SO:0001583	missense	10365	exon2			CCTGCAGCTACGC	AF123344	CCDS12343.1	19p13.11	2013-10-15	2013-10-15		ENSG00000127528	ENSG00000127528		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6347	protein-coding gene	gene with protein product		602016	"""Kruppel-like factor 2 (lung)"""			10217429, 10458913	Standard	NM_016270		Approved	LKLF	uc002ndw.3	Q9Y5W3	OTTHUMG00000182330	ENST00000248071.5:c.824G>A	19.37:g.16436775G>A	ENSP00000248071:p.Ser275Asn	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	39	5	0.128205	NM_016270	Q6IPC4|Q9UJS5|Q9UKR6	Missense_Mutation	SNP	ENST00000248071.5	37	CCDS12343.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908073	0.33721	.	.	ENSG00000127528	ENST00000248071	T	0.08634	3.07	3.44	2.39	0.29439	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13072	0.0317	L	0.58810	1.83	0.80722	D	1	P	0.50943	0.94	P	0.52159	0.691	T	0.11867	-1.0570	9	0.25751	T	0.34	.	6.8756	0.24145	0.1023:0.3171:0.5806:0.0	.	275	Q9Y5W3	KLF2_HUMAN	N	275	ENSP00000248071:S275N	ENSP00000248071:S275N	S	+	2	0	KLF2	16297775	1.000000	0.71417	0.997000	0.53966	0.014000	0.08584	2.573000	0.46007	0.553000	0.29044	-0.384000	0.06662	AGC	.	.	none		0.697	KLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460562.1		
EPHA8	2046	hgsc.bcm.edu	37	1	22915674	22915674	+	Silent	SNP	G	G	A	rs56044578	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22915674G>A	ENST00000166244.3	+	5	1362	c.1290G>A	c.(1288-1290)gtG>gtA	p.V430V	EPHA8_ENST00000374644.4_Silent_p.V430V|EPHA8_ENST00000538803.1_Silent_p.V430V	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	430	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGGCCGCTGTGGTCAACATCA	0.652													G|||	423	0.0844649	0.0477	0.0504	5008	,	,		17862	0.0486		0.0815	False		,,,				2504	0.1984				p.V430V		Atlas-SNP	.											.	EPHA8	221	.	0			c.G1290A						PASS	.	G	,	224,4182	127.8+/-164.7	6,212,1985	34.0	34.0	34.0		1290,1290	-9.0	0.0	1	dbSNP_129	34	609,7991	155.2+/-209.3	31,547,3722	no	coding-synonymous,coding-synonymous	EPHA8	NM_001006943.1,NM_020526.3	,	37,759,5707	AA,AG,GG		7.0814,5.084,6.4047	,	430/496,430/1006	22915674	833,12173	2203	4300	6503	SO:0001819	synonymous_variant	2046	exon5			CGCTGTGGTCAAC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1290G>A	1.37:g.22915674G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																			G|0.934;A|0.066	0.066	strong		0.652	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48525507	48525507	+	Missense_Mutation	SNP	G	G	A	rs2303690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48525507G>A	ENST00000339841.2	+	6	773	c.595G>A	c.(595-597)Gaa>Aaa	p.E199K	ELSPBP1_ENST00000597519.1_Missense_Mutation_p.E51K	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	199	Fibronectin type-II 4. {ECO:0000255|PROSITE-ProRule:PRU00479}.		E -> K (in dbSNP:rs2303690). {ECO:0000269|PubMed:11144225, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		CTGCACTAACGAAGGATCAAA	0.458													a|||	3432	0.685304	0.6672	0.719	5008	,	,		21670	0.8671		0.5696	False		,,,				2504	0.6176				p.E199K		Atlas-SNP	.											ELSPBP1,NS,adenoma,0,1	ELSPBP1	29	1	0			c.G595A						PASS	.	A	LYS/GLU	2699,1707	514.5+/-368.7	854,991,358	172.0	160.0	164.0		595	1.5	0.0	19	dbSNP_100	164	4879,3721	530.3+/-381.8	1393,2093,814	yes	missense	ELSPBP1	NM_022142.4	56	2247,3084,1172	AA,AG,GG		43.2674,38.7426,41.7346	benign	199/224	48525507	7578,5428	2203	4300	6503	SO:0001583	missense	64100	exon6			ACTAACGAAGGAT	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.595G>A	19.37:g.48525507G>A	ENSP00000340660:p.Glu199Lys	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	205	100	0.487805	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	1512	0.6923076923076923	325	0.6605691056910569	242	0.6685082872928176	497	0.8688811188811189	448	0.5910290237467019	A	1.554	-0.538579	0.04053	0.612574	0.567326	ENSG00000169393	ENST00000339841	T	0.52295	0.67	3.66	1.54	0.23209	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.248846	0.28031	N	0.016863	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	B	0.14805	0.011	B	0.15870	0.014	T	0.44651	-0.9314	9	0.02654	T	1	.	3.8049	0.08773	0.4456:0.2051:0.3493:0.0	rs2303690;rs17845467;rs17858345;rs59769918;rs2303690	199	Q96BH3	ESPB1_HUMAN	K	199	ENSP00000340660:E199K	ENSP00000340660:E199K	E	+	1	0	ELSPBP1	53217319	0.439000	0.25610	0.044000	0.18714	0.012000	0.07955	0.521000	0.22893	0.108000	0.17862	-0.308000	0.09152	GAA	G|0.365;A|0.635	0.635	strong		0.458	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388631	1388631	+	Missense_Mutation	SNP	C	C	G	rs200849975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388631C>G	ENST00000324803.4	+	1	3292	c.332C>G	c.(331-333)cCa>cGa	p.P111R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	111					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P111R(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTCACGTGCCCATGTGGAGTG	0.667													N|||	218	0.0435304	0.0287	0.0548	5008	,	,		18151	0.006		0.0487	False		,,,				2504	0.089				p.P111R		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,2	CRIPAK	185	2	1	Substitution - Missense(1)	skin(1)	c.C332G						PASS	.						193.0	146.0	162.0					4																	1388631		2203	4299	6502	SO:0001583	missense	285464	exon1			CGTGCCCATGTGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.332C>G	4.37:g.1388631C>G	ENSP00000323978:p.Pro111Arg	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	133	88	0.661654	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.610	0.297336	0.10622	.	.	ENSG00000179979	ENST00000324803	T	0.22336	1.96	0.948	-0.0113	0.13993	Post-SET domain (1);	.	.	.	.	T	0.07548	0.0190	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39820	-0.9595	9	0.12103	T	0.63	.	2.6024	0.04869	0.0:0.4564:0.3174:0.2262	.	111	Q8N1N5	CRPAK_HUMAN	R	111	ENSP00000323978:P111R	ENSP00000323978:P111R	P	+	2	0	CRIPAK	1378631	0.005000	0.15991	0.001000	0.08648	0.013000	0.08279	-1.037000	0.03557	-0.011000	0.14247	-1.737000	0.00689	CCA	C|0.935;G|0.065	0.065	strong		0.667	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
TANC1	85461	hgsc.bcm.edu	37	2	160086654	160086654	+	Missense_Mutation	SNP	A	A	G	rs67270488|rs55738533|rs4664277	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160086654A>G	ENST00000263635.6	+	27	4954	c.4717A>G	c.(4717-4719)Act>Gct	p.T1573A	TANC1_ENST00000454300.1_Missense_Mutation_p.T1467A	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1573			T -> A (in dbSNP:rs4664277). {ECO:0000269|PubMed:11214970}.		dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						AATCGCTGCCACTCCTGCTGG	0.562													G|||	2553	0.509784	0.4607	0.6095	5008	,	,		20467	0.6181		0.3728	False		,,,				2504	0.5348				p.T1573A		Atlas-SNP	.											.	TANC1	157	.	0			c.A4717G						PASS	.	G	,ALA/THR	1667,2225		388,891,667	54.0	60.0	58.0		,4717	-3.1	0.0	2	dbSNP_129	58	2739,5545		524,1691,1927	yes	utr-3,missense	TANC1	NM_001145909.1,NM_033394.2	,58	912,2582,2594	GG,GA,AA		33.0637,42.8314,36.1859	,benign	,1573/1862	160086654	4406,7770	1946	4142	6088	SO:0001583	missense	85461	exon27			GCTGCCACTCCTG	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4717A>G	2.37:g.160086654A>G	ENSP00000263635:p.Thr1573Ala	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	900	0.41208791208791207	193	0.39227642276422764	178	0.49171270718232046	306	0.534965034965035	223	0.2941952506596306	G	0.003	-2.544700	0.00142	0.428314	0.330637	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.68331	-0.32;-0.31	5.86	-3.12	0.05282	.	0.971917	0.08544	N	0.930072	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37934	-0.9684	8	.	.	.	.	6.0992	0.20037	0.4496:0.0797:0.3902:0.0805	rs55738533;rs59149467;rs62172669	1573	Q9C0D5	TANC1_HUMAN	A	1467;1573	ENSP00000396339:T1467A;ENSP00000263635:T1573A	.	T	+	1	0	TANC1	159794900	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.704000	0.25661	-1.161000	0.02800	-1.736000	0.00690	ACT	A|0.509;CA|0.001	.	alt		0.562	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
MUC16	94025	hgsc.bcm.edu	37	19	9048320	9048320	+	Missense_Mutation	SNP	C	C	T	rs56334501	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9048320C>T	ENST00000397910.4	-	5	33514	c.33311G>A	c.(33310-33312)aGt>aAt	p.S11104N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11106	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCCCTGGAACTAGTGACCAG	0.527													C|||	927	0.185104	0.062	0.2752	5008	,	,		22994	0.3363		0.167	False		,,,				2504	0.1503				p.S11104N		Atlas-SNP	.											.	MUC16	4315	.	0			c.G33311A						PASS	.		ASN/SER	306,3534		15,276,1629	76.0	69.0	71.0		33311	0.3	0.0	19	dbSNP_129	71	1502,6772		137,1228,2772	yes	missense	MUC16	NM_024690.2	46	152,1504,4401	TT,TC,CC		18.1533,7.9687,14.9249	benign	11104/14508	9048320	1808,10306	1920	4137	6057	SO:0001583	missense	94025	exon5			CTGGAACTAGTGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33311G>A	19.37:g.9048320C>T	ENSP00000381008:p.Ser11104Asn	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	464	0.21245421245421245	34	0.06910569105691057	91	0.2513812154696133	213	0.3723776223776224	126	0.1662269129287599	c	12.98	2.099153	0.37048	0.079687	0.181533	ENSG00000181143	ENST00000397910	T	0.02656	4.21	2.94	0.273	0.15650	.	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	.	.	.	B	0.34226	0.443	B	0.37888	0.26	T	0.45469	-0.9259	8	0.87932	D	0	.	7.801	0.29174	0.5775:0.4225:0.0:0.0	rs56334501;rs61745162	11104	B5ME49	.	N	11104	ENSP00000381008:S11104N	ENSP00000381008:S11104N	S	-	2	0	MUC16	8909320	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.768000	0.01794	0.105000	0.17753	-0.345000	0.07892	AGT	C|0.795;T|0.205	0.205	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CFTR	1080	hgsc.bcm.edu	37	7	117235055	117235055	+	Silent	SNP	T	T	G	rs397508396|rs1042077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:117235055T>G	ENST00000003084.6	+	15	2694	c.2562T>G	c.(2560-2562)acT>acG	p.T854T	CFTR_ENST00000454343.1_Silent_p.T793T	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	854					cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GATATATTACTGTCCACAAGA	0.328									Cystic Fibrosis				T|||	2400	0.479233	0.7065	0.428	5008	,	,		12659	0.3919		0.335	False		,,,				2504	0.4468				p.T854T		Atlas-SNP	.											.	CFTR	171	.	0			c.T2562G	GRCh37	CD003291|CS042144	CFTR	D|S	rs1042077	PASS	.	T		2726,1680	653.8+/-399.6	838,1050,315	158.0	148.0	151.0		2562	0.2	0.0	7	dbSNP_86	151	2513,6087	411.7+/-350.6	373,1767,2160	no	coding-synonymous	CFTR	NM_000492.3		1211,2817,2475	GG,GT,TT		29.2209,38.1298,40.2814		854/1481	117235055	5239,7767	2203	4300	6503	SO:0001819	synonymous_variant	1080	exon15	Familial Cancer Database	CF	TATTACTGTCCAC	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2562T>G	7.37:g.117235055T>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	180	89	0.494444	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	37	CCDS5773.1																																																																																			G|0.425;N|0.000	0.425	strong		0.328	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
LRP2	4036	hgsc.bcm.edu	37	2	170129528	170129528	+	Silent	SNP	G	G	A	rs830994	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170129528G>A	ENST00000263816.3	-	15	2310	c.2025C>T	c.(2023-2025)gtC>gtT	p.V675V	LRP2_ENST00000443831.1_Silent_p.V606V	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	675	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TGTGGCTGAGGACACAGACCT	0.443													G|||	3053	0.609625	0.5045	0.5014	5008	,	,		21510	0.8859		0.661	False		,,,				2504	0.4908				p.V675V		Atlas-SNP	.											.	LRP2	751	.	0			c.C2025T						PASS	.	G		2276,2130	598.6+/-389.1	589,1098,516	164.0	153.0	157.0		2025	1.3	1.0	2	dbSNP_86	157	5723,2877	672.7+/-403.0	1898,1927,475	no	coding-synonymous	LRP2	NM_004525.2		2487,3025,991	AA,AG,GG		33.4535,48.3432,38.4976		675/4656	170129528	7999,5007	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon15			GCTGAGGACACAG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.2025C>T	2.37:g.170129528G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	161	87	0.540373	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.358;A|0.642	0.642	strong		0.443	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
RHBDL3	162494	hgsc.bcm.edu	37	17	30615883	30615883	+	Silent	SNP	C	C	T	rs150485822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:30615883C>T	ENST00000269051.4	+	4	381	c.367C>T	c.(367-369)Ctg>Ttg	p.L123L	RHBDL3_ENST00000536287.1_Silent_p.L25L|RHBDL3_ENST00000538145.1_Silent_p.L115L	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	123						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				CAGCAAGGCCCTGCTGGAGGA	0.597																																					p.L123L		Atlas-SNP	.											.	RHBDL3	49	.	0			c.C367T						PASS	.	C		0,4406		0,0,2203	50.0	46.0	47.0		367	4.9	1.0	17	dbSNP_134	47	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	RHBDL3	NM_138328.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		123/405	30615883	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	162494	exon4			AAGGCCCTGCTGG	AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"""EF-hand domain containing"""	16502	protein-coding gene	gene with protein product			"""rhomboid, veinlet-like 4 (Drosophila)"""	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.367C>T	17.37:g.30615883C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	232	110	0.474138	NM_138328	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Silent	SNP	ENST00000269051.4	37	CCDS32613.1																																																																																			C|1.000;T|0.000	0.000	strong		0.597	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328	
LATS1	9113	hgsc.bcm.edu	37	6	150004779	150004779	+	Silent	SNP	A	A	G	rs3798761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:150004779A>G	ENST00000543571.1	-	4	1993	c.1446T>C	c.(1444-1446)tcT>tcC	p.S482S	LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Silent_p.S482S|LATS1_ENST00000392273.3_Silent_p.S482S	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		CTGTTGTAGCAGAAGGCTGAG	0.413													a|||	2766	0.552316	0.5779	0.6369	5008	,	,		23000	0.8244		0.3579	False		,,,				2504	0.3773				p.S482S		Atlas-SNP	.											.	LATS1	241	.	0			c.T1446C						PASS	.	G		2384,2022	611.8+/-391.8	647,1090,466	137.0	141.0	140.0		1446	-7.1	0.7	6	dbSNP_107	140	3134,5466	477.4+/-369.6	552,2030,1718	no	coding-synonymous	LATS1	NM_004690.2		1199,3120,2184	GG,GA,AA		36.4419,45.892,42.4266		482/1131	150004779	5518,7488	2203	4300	6503	SO:0001819	synonymous_variant	9113	exon4			TGTAGCAGAAGGC	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.1446T>C	6.37:g.150004779A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	161	68	0.42236	NM_001270519		Silent	SNP	ENST00000543571.1	37	CCDS34551.1																																																																																			A|0.510;G|0.490	0.490	strong		0.413	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690	
GOLGA2	2801	hgsc.bcm.edu	37	9	131027963	131027963	+	Silent	SNP	A	A	G	rs12335848	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131027963A>G	ENST00000421699.2	-	11	765	c.753T>C	c.(751-753)tcT>tcC	p.S251S	GOLGA2_ENST00000609374.1_Silent_p.S239S	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	251					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						CCAGATCTTCAGACTCTCCTG	0.597													G|||	584	0.116613	0.0363	0.1239	5008	,	,		17706	0.2431		0.0586	False		,,,				2504	0.1493				p.S251S		Atlas-SNP	.											GOLGA2,NS,carcinoma,0,1	GOLGA2	69	1	0			c.T753C						PASS	.	G		191,4213		7,177,2018	20.0	22.0	21.0		753	-11.4	0.0	9	dbSNP_120	21	472,8128		15,442,3843	no	coding-synonymous	GOLGA2	NM_004486.4		22,619,5861	GG,GA,AA		5.4884,4.337,5.0984		251/1003	131027963	663,12341	2202	4300	6502	SO:0001819	synonymous_variant	2801	exon11			ATCTTCAGACTCT	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.753T>C	9.37:g.131027963A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	ENST00000421699.2	37	CCDS6896.2	246	0.11263736263736264	25	0.0508130081300813	36	0.09944751381215469	142	0.24825174825174826	43	0.05672823218997362	g	1.151	-0.646797	0.03506	0.04337	0.054884	ENSG00000167110	ENST00000458730	.	.	.	5.72	-11.4	0.00090	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999981921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.1026	0.01687	0.4001:0.2328:0.1685:0.1987	rs12335848;rs12335848	.	.	.	R	184	.	.	X	-	1	0	GOLGA2	130067784	0.000000	0.05858	0.000000	0.03702	0.136000	0.21042	-2.309000	0.01130	-3.902000	0.00093	-0.186000	0.12905	TGA	A|0.914;G|0.086	0.086	strong		0.597	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486	
PLAC8L1	153770	hgsc.bcm.edu	37	5	145483844	145483844	+	Missense_Mutation	SNP	A	A	T	rs12187913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145483844A>T	ENST00000311450.4	-	1	88	c.31T>A	c.(31-33)Tgt>Agt	p.C11S	RP11-118M9.3_ENST00000514002.1_RNA	NM_001029869.1	NP_001025040.1	A1L4L8	PL8L1_HUMAN	PLAC8-like 1	11			C -> S (in dbSNP:rs12187913).					p.C11S(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|stomach(2)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCTCAGGACACCTGAAGAAG	0.393													A|||	910	0.181709	0.0076	0.3775	5008	,	,		19898	0.1984		0.2525	False		,,,				2504	0.1881				p.C11S		Atlas-SNP	.											PLAC8L1,NS,carcinoma,0,1	PLAC8L1	17	1	1	Substitution - Missense(1)	stomach(1)	c.T31A						PASS	.	A	SER/CYS	265,4141	149.2+/-183.4	12,241,1950	112.0	108.0	110.0		31	3.5	0.0	5	dbSNP_120	110	2399,6201	399.0+/-346.3	353,1693,2254	yes	missense	PLAC8L1	NM_001029869.1	112	365,1934,4204	TT,TA,AA		27.8953,6.0145,20.4829	benign	11/178	145483844	2664,10342	2203	4300	6503	SO:0001583	missense	153770	exon1			CAGGACACCTGAA		CCDS34264.1	5q32	2008-02-05			ENSG00000173261	ENSG00000173261			31746	protein-coding gene	gene with protein product							Standard	XM_005268381		Approved		uc003lnv.3	A1L4L8	OTTHUMG00000163418	ENST00000311450.4:c.31T>A	5.37:g.145483844A>T	ENSP00000309087:p.Cys11Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	142	52	0.366197	NM_001029869		Missense_Mutation	SNP	ENST00000311450.4	37	CCDS34264.1	428	0.19597069597069597	10	0.02032520325203252	110	0.30386740331491713	117	0.20454545454545456	191	0.2519788918205805	A	1.154	-0.645856	0.03531	0.060145	0.278953	ENSG00000173261	ENST00000311450	T	0.40476	1.03	4.65	3.48	0.39840	.	0.890661	0.09749	N	0.760823	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.19935	0.04	B	0.16722	0.016	T	0.39722	-0.9600	9	0.21014	T	0.42	0.1326	6.0729	0.19899	0.8734:0.0:0.1266:0.0	rs12187913;rs56464188;rs12187913	11	A1L4L8	PL8L1_HUMAN	S	11	ENSP00000309087:C11S	ENSP00000309087:C11S	C	-	1	0	PLAC8L1	145464037	0.000000	0.05858	0.030000	0.17652	0.008000	0.06430	0.477000	0.22196	0.909000	0.36697	0.460000	0.39030	TGT	A|0.797;T|0.203	0.203	strong		0.393	PLAC8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373290.1	XM_087761	
CR1	1378	hgsc.bcm.edu	37	1	207760773	207760773	+	Missense_Mutation	SNP	C	C	T	rs3737002	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207760773C>T	ENST00000367049.4	+	34	5573	c.5573C>T	c.(5572-5574)aCg>aTg	p.T1858M	CR1_ENST00000367052.1_Missense_Mutation_p.T1408M|CR1_ENST00000367053.1_Missense_Mutation_p.T1408M|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367051.1_Missense_Mutation_p.T1408M|CR1_ENST00000400960.2_Missense_Mutation_p.T1408M|RP11-78B10.2_ENST00000596003.1_RNA	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1408	Sushi 29. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						GCCAGTCCTACGATCCCAATT	0.443													C|||	1246	0.248802	0.0446	0.379	5008	,	,		20146	0.3264		0.2873	False		,,,				2504	0.3129				p.T1858M		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,-1,2	CR1	354	2	0			c.C5573T						PASS	.	C	MET/THR,MET/THR	272,3364		11,250,1557	144.0	126.0	132.0		4223,5573	-0.1	0.0	1	dbSNP_107	132	2253,5915		327,1599,2158	yes	missense,missense	CR1	NM_000573.3,NM_000651.4	81,81	338,1849,3715	TT,TC,CC		27.5833,7.4807,21.3911	probably-damaging,probably-damaging	1408/2040,1858/2490	207760773	2525,9279	1818	4084	5902	SO:0001583	missense	1378	exon34			GTCCTACGATCCC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.5573C>T	1.37:g.207760773C>T	ENSP00000356016:p.Thr1858Met	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	293	147	0.501706	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	581	0.266025641025641	34	0.06910569105691057	118	0.3259668508287293	225	0.39335664335664333	204	0.2691292875989446	C	4.828	0.153959	0.09185	0.074807	0.275833	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	3.11	-0.0816	0.13701	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	D;D;D	0.89917	0.987;1.0;1.0	P;D;D	0.81914	0.59;0.995;0.958	T	0.20140	-1.0284	8	0.46703	T	0.11	.	5.3246	0.15898	0.0:0.5385:0.0:0.4615	rs3737002;rs59870088;rs3737002	1408;1408;1858	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	M	1408;1408;1408;1408;958;1858	ENSP00000356019:T1408M;ENSP00000356018:T1408M;ENSP00000356020:T1408M;ENSP00000383744:T1408M;ENSP00000436139:T958M;ENSP00000356016:T1858M	ENSP00000356016:T1858M	T	+	2	0	CR1	205827396	0.000000	0.05858	0.001000	0.08648	0.067000	0.16453	-0.359000	0.07632	-0.027000	0.13873	-0.345000	0.07892	ACG	C|0.751;N|0.000	.	strong		0.443	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
CYP11B2	1585	hgsc.bcm.edu	37	8	143994041	143994041	+	Missense_Mutation	SNP	C	C	T	rs4545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143994041C>T	ENST00000323110.2	-	8	1305	c.1303G>A	c.(1303-1305)Ggc>Agc	p.G435S		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	435			G -> S (in dbSNP:rs4545). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210}.		aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	AAGTTCCTGCCGGAGCCCCTG	0.622									Familial Hyperaldosteronism type I				.|||	814	0.16254	0.0295	0.1009	5008	,	,		13703	0.496		0.0229	False		,,,				2504	0.1861				p.G435S		Atlas-SNP	.											CYP11B2,NS,carcinoma,+2,1	CYP11B2	107	1	0			c.G1303A	GRCh37	CM033362	CYP11B2	M	rs4545	PASS	.	C	SER/GLY	113,4293		3,107,2093	72.0	82.0	79.0		1303	-5.9	0.0	8	dbSNP_52	79	178,8422		6,166,4128	no	missense	CYP11B2	NM_000498.3	56	9,273,6221	TT,TC,CC		2.0698,2.5647,2.2374	benign	435/504	143994041	291,12715	2203	4300	6503	SO:0001583	missense	1585	exon8	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TCCTGCCGGAGCC	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"""Cytochrome P450s"""	2592	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	124080	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"""	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.1303G>A	8.37:g.143994041C>T	ENSP00000325822:p.Gly435Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	37	CCDS6393.1	335	0.1533882783882784	14	0.028455284552845527	30	0.08287292817679558	276	0.4825174825174825	15	0.01978891820580475	.	8.410	0.843957	0.16963	0.025647	0.020698	ENSG00000179142	ENST00000323110	T	0.68331	-0.32	2.96	-5.92	0.02261	.	1.825320	0.02980	N	0.145573	T	0.00012	0.0000	L	0.42008	1.315	0.80722	P	0.0	B	0.24483	0.104	B	0.21708	0.036	T	0.24476	-1.0159	9	0.08837	T	0.75	.	7.4483	0.27223	0.0:0.2907:0.1428:0.5665	rs4545;rs57715984;rs4545	435	P19099	C11B2_HUMAN	S	435	ENSP00000325822:G435S	ENSP00000325822:G435S	G	-	1	0	CYP11B2	143991043	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.484000	0.06528	-2.274000	0.00680	-0.471000	0.05019	GGC	C|0.914;T|0.086	0.086	strong		0.622	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
LAIR2	3904	hgsc.bcm.edu	37	19	55019261	55019261	+	Nonsense_Mutation	SNP	C	C	T	rs61737751	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55019261C>T	ENST00000301202.2	+	3	348	c.226C>T	c.(226-228)Cga>Tga	p.R76*	LAIR2_ENST00000351841.2_Nonsense_Mutation_p.R76*	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	76	Ig-like C2-type.					extracellular region (GO:0005576)				central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		TAATGTGTTTCGACTTGGTCC	0.502													C|||	151	0.0301518	0.0023	0.049	5008	,	,		19721	0.0079		0.0527	False		,,,				2504	0.0542				p.R76X		Atlas-SNP	.											LAIR2,NS,malignant_melanoma,-1,1	LAIR2	30	1	0			c.C226T						PASS	.	C	stop/ARG,stop/ARG	46,4360	49.6+/-84.7	0,46,2157	114.0	105.0	108.0		226,226	0.5	0.0	19	dbSNP_129	108	386,8214	125.1+/-183.8	14,358,3928	yes	stop-gained,stop-gained	LAIR2	NM_002288.4,NM_021270.3	,	14,404,6085	TT,TC,CC		4.4884,1.044,3.3215	,	76/153,76/136	55019261	432,12574	2203	4300	6503	SO:0001587	stop_gained	3904	exon3			GTGTTTCGACTTG	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6478	protein-coding gene	gene with protein product		602993	"""leukocyte-associated Ig-like receptor 2"""			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.226C>T	19.37:g.55019261C>T	ENSP00000301202:p.Arg76*	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	168	92	0.547619	NM_002288	Q6PEZ4	Nonsense_Mutation	SNP	ENST00000301202.2	37	CCDS12897.1	64	0.029304029304029304	0	0.0	25	0.06906077348066299	3	0.005244755244755245	36	0.047493403693931395	C	8.377	0.836584	0.16891	0.01044	0.044884	ENSG00000167618	ENST00000412608;ENST00000452094;ENST00000301202;ENST00000351841	.	.	.	1.8	0.536	0.17138	.	6.594050	0.00397	N	0.000041	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	4.9162	0.13847	0.357:0.643:0.0:0.0	rs61737751	.	.	.	X	70;58;76;76	.	ENSP00000301202:R76X	R	+	1	2	LAIR2	59711073	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.940000	0.03929	0.041000	0.15688	0.313000	0.20887	CGA	C|0.965;T|0.035	0.035	strong		0.502	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1		
OR5H1	26341	hgsc.bcm.edu	37	3	97852291	97852291	+	Silent	SNP	A	A	G	rs112819024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:97852291A>G	ENST00000354565.2	+	1	750	c.750A>G	c.(748-750)ttA>ttG	p.L250L	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	250						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						CTGTCTCTTTATACTATGGAC	0.418													A|||	18	0.00359425	0.0008	0.0029	5008	,	,		17560	0.0		0.0099	False		,,,				2504	0.0051				p.L250L		Atlas-SNP	.											OR5H1,NS,carcinoma,+2,1	OR5H1	71	1	0			c.A750G						PASS	.	A		15,4391	22.3+/-47.3	0,15,2188	123.0	133.0	130.0		750	-0.3	0.8	3	dbSNP_132	130	115,8483	60.2+/-122.0	3,109,4187	no	coding-synonymous	OR5H1	NM_001005338.1		3,124,6375	GG,GA,AA		1.3375,0.3404,0.9997		250/314	97852291	130,12874	2203	4299	6502	SO:0001819	synonymous_variant	26341	exon1			CTCTTTATACTAT	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"""GPCR / Class A : Olfactory receptors"""	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.750A>G	3.37:g.97852291A>G		Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	346	165	0.476879	NM_001005338		Silent	SNP	ENST00000354565.2	37	CCDS33797.1																																																																																			A|0.993;G|0.007	0.007	strong		0.418	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
BMP8A	353500	hgsc.bcm.edu	37	1	39988084	39988084	+	Missense_Mutation	SNP	G	G	A	rs6525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39988084G>A	ENST00000331593.5	+	5	1224	c.878G>A	c.(877-879)cGc>cAc	p.R293H	RP11-69E11.4_ENST00000440190.1_RNA|RP11-69E11.4_ENST00000458207.1_RNA|RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000441741.1_RNA|RP11-69E11.4_ENST00000450157.1_RNA|RP11-69E11.4_ENST00000331856.2_RNA|RP11-69E11.4_ENST00000417869.1_RNA	NM_181809.3	NP_861525.2	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8a	293			R -> H (in dbSNP:rs6525). {ECO:0000269|Ref.1}.		cartilage development (GO:0051216)|cell differentiation (GO:0030154)|diet induced thermogenesis (GO:0002024)|growth (GO:0040007)|negative regulation of insulin secretion (GO:0046676)|ossification (GO:0001503)|regulation of energy homeostasis (GO:2000505)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(1)|skin(1)	5	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GATGACGTCCGCGGCTCCCAC	0.597																																					p.R293H		Atlas-SNP	.											BMP8A,brain,glioma,0,1	BMP8A	24	1	0			c.G878A						PASS	.						74.0	59.0	64.0					1																	39988084		2202	4296	6498	SO:0001583	missense	353500	exon5			ACGTCCGCGGCTC	AY303954	CCDS437.1	1p35-p32	2014-01-30			ENSG00000183682	ENSG00000183682		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	21650	protein-coding gene	gene with protein product							Standard	NM_181809		Approved		uc001cdi.3	Q7Z5Y6	OTTHUMG00000008394	ENST00000331593.5:c.878G>A	1.37:g.39988084G>A	ENSP00000327440:p.Arg293His	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	117	29	0.247863	NM_181809	Q5T3A5	Missense_Mutation	SNP	ENST00000331593.5	37	CCDS437.1	723	0.33104395604395603	64	0.13008130081300814	145	0.4005524861878453	229	0.40034965034965037	285	0.3759894459102902	N	5.501	0.277466	0.10403	.	.	ENSG00000183682	ENST00000331593	T	0.75704	-0.96	4.4	3.27	0.37495	Transforming growth factor-beta, C-terminal (1);	0.398039	0.24841	N	0.035176	T	0.00012	0.0000	N	0.00112	-2.095	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.34004	-0.9846	8	.	.	.	.	8.0955	0.30826	0.8251:0.0:0.1749:0.0	rs6525;rs15525;rs2073023;rs2695323;rs3186975;rs6657903;rs36033681;rs60841611	293	Q7Z5Y6	BMP8A_HUMAN	H	293	ENSP00000327440:R293H	.	R	+	2	0	BMP8A	39760671	0.004000	0.15560	0.905000	0.35620	0.071000	0.16799	0.457000	0.21875	0.192000	0.20272	-0.524000	0.04348	CGC	G|0.333;A|0.667	0.667	strong		0.597	BMP8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023079.1	NM_181809	
FOXI1	2299	hgsc.bcm.edu	37	5	169533240	169533240	+	Silent	SNP	G	G	A	rs2277944	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:169533240G>A	ENST00000306268.6	+	1	340	c.279G>A	c.(277-279)agG>agA	p.R93R	FOXI1_ENST00000449804.2_Silent_p.R93R			Q12951	FOXI1_HUMAN	forkhead box I1	93	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGTGCAGAGGCCGCTGCTGC	0.697									Pendred syndrome				G|||	1813	0.362021	0.5923	0.1888	5008	,	,		11776	0.4821		0.1521	False		,,,				2504	0.2658				p.R93R		Atlas-SNP	.											.	FOXI1	70	.	0			c.G279A						PASS	.	G	,	2227,2139		571,1085,527	9.0	8.0	8.0		279,279	2.4	1.0	5	dbSNP_100	8	1309,7201		143,1023,3089	no	coding-synonymous,coding-synonymous	FOXI1	NM_012188.4,NM_144769.2	,	714,2108,3616	AA,AG,GG		15.3819,48.9922,27.4619	,	93/379,93/284	169533240	3536,9340	2183	4255	6438	SO:0001819	synonymous_variant	2299	exon1	Familial Cancer Database	Goiter-Deafness syndrome	GCAGAGGCCGCTG	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"""Forkhead boxes"""	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.279G>A	5.37:g.169533240G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	66	0.741573	NM_012188	Q14518|Q66SR7|Q8N6L8	Silent	SNP	ENST00000306268.6	37	CCDS4372.1																																																																																			G|0.676;A|0.324	0.324	strong		0.697	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188	
RSPH10B	222967	hgsc.bcm.edu	37	7	5983070	5983070	+	Missense_Mutation	SNP	T	T	C	rs11765019		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5983070T>C	ENST00000405415.1	-	14	2029	c.1643A>G	c.(1642-1644)tAc>tGc	p.Y548C	RSPH10B_ENST00000404406.1_Missense_Mutation_p.Y548C|RSPH10B_ENST00000337579.3_Missense_Mutation_p.Y548C|RSPH10B_ENST00000441023.2_Missense_Mutation_p.Y548C|RSPH10B_ENST00000535104.1_5'UTR|RSPH10B_ENST00000539903.1_3'UTR			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	548										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		ACTCATAGAGTAGAGCGTCCG	0.408																																					p.Y548C		Atlas-SNP	.											.	RSPH10B	28	.	0			c.A1643G						PASS	.						29.0	29.0	29.0					7																	5983070		2159	4265	6424	SO:0001583	missense	222967	exon15			ATAGAGTAGAGCG		CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026			27362	protein-coding gene	gene with protein product						16507594	Standard	NM_173565		Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.1643A>G	7.37:g.5983070T>C	ENSP00000385443:p.Tyr548Cys	Somatic	1070	2	0.00186916		WXS	Illumina HiSeq	Phase_I	1205	289	0.239834	NM_173565	A6NMW7|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000405415.1	37	CCDS34598.1	225	0.10302197802197802	9	0.018292682926829267	86	0.23756906077348067	18	0.03146853146853147	112	0.14775725593667546	T	0.494	-0.874074	0.02550	.	.	ENSG00000155026	ENST00000405415;ENST00000404406;ENST00000337579;ENST00000354951;ENST00000441023	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	3.38	2.2	0.27929	.	0.455544	0.18532	N	0.138477	T	0.00012	0.0000	L	0.43701	1.375	0.52099	P	5.100000000002325E-5	B;B;B	0.26081	0.141;0.013;0.047	B;B;B	0.23419	0.046;0.007;0.021	T	0.11991	-1.0565	9	0.44086	T	0.13	.	4.3495	0.11148	0.1756:0.1077:0.0:0.7167	.	249;548;407	B7Z298;P0C881;F5GXE3	.;R10B1_HUMAN;.	C	548;548;548;407;548	ENSP00000385443:Y548C;ENSP00000384097:Y548C;ENSP00000338556:Y548C;ENSP00000400988:Y548C	ENSP00000338556:Y548C	Y	-	2	0	RSPH10B	5949596	0.001000	0.12720	0.010000	0.14722	0.018000	0.09664	0.336000	0.19823	0.482000	0.27582	0.450000	0.29827	TAC	T|0.891;C|0.109	0.109	strong		0.408	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325465.2	NM_173565	
CORIN	10699	hgsc.bcm.edu	37	4	47682174	47682174	+	Silent	SNP	A	A	G	rs10517195	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:47682174A>G	ENST00000273857.4	-	8	1115	c.1116T>C	c.(1114-1116)tcT>tcC	p.S372S	CORIN_ENST00000508498.1_Silent_p.S233S|CORIN_ENST00000505909.1_Intron|CORIN_ENST00000504584.1_Intron|CORIN_ENST00000502252.1_Silent_p.S305S	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	372	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						TGACCTCGTCAGACTTATCCA	0.507													G|||	1858	0.371006	0.2549	0.5173	5008	,	,		22550	0.1319		0.5785	False		,,,				2504	0.4571				p.S372S		Atlas-SNP	.											.	CORIN	154	.	0			c.T1116C						PASS	.	G		1327,3079	695.5+/-405.9	215,897,1091	136.0	99.0	111.0		1116	-11.3	0.1	4	dbSNP_119	111	5103,3497	512.6+/-378.0	1527,2049,724	yes	coding-synonymous	CORIN	NM_006587.2		1742,2946,1815	GG,GA,AA		40.6628,30.118,49.4387		372/1043	47682174	6430,6576	2203	4300	6503	SO:0001819	synonymous_variant	10699	exon8			CTCGTCAGACTTA	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"""Serine peptidases / Transmembrane"""	19012	protein-coding gene	gene with protein product		605236	"""corin, serine protease"""			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.1116T>C	4.37:g.47682174A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Silent	SNP	ENST00000273857.4	37	CCDS3477.1																																																																																			A|0.562;G|0.438	0.438	strong		0.507	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2		
SECISBP2L	9728	hgsc.bcm.edu	37	15	49325289	49325289	+	Silent	SNP	A	A	C	rs11638215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:49325289A>C	ENST00000559471.1	-	4	800	c.537T>G	c.(535-537)ctT>ctG	p.L179L	SECISBP2L_ENST00000261847.3_Silent_p.L179L	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	179							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						GCTGTTGTAAAAGCTGTTGCT	0.303													A|||	2129	0.42512	0.2292	0.3991	5008	,	,		16480	0.3512		0.6461	False		,,,				2504	0.5573				p.L179L		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.T537G						PASS	.	A	,	1335,3059	441.0+/-346.2	204,927,1066	115.0	105.0	108.0		537,537	5.1	1.0	15	dbSNP_120	108	5381,3209	647.3+/-400.4	1681,2019,595	no	coding-synonymous,coding-synonymous	SECISBP2L	NM_001193489.1,NM_014701.3	,	1885,2946,1661	CC,CA,AA		37.3574,30.3823,48.2748	,	179/1102,179/1057	49325289	6716,6268	2197	4295	6492	SO:0001819	synonymous_variant	9728	exon4			TTGTAAAAGCTGT	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.537T>G	15.37:g.49325289A>C		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_001193489	Q8N767	Silent	SNP	ENST00000559471.1	37	CCDS53942.1																																																																																			A|0.519;C|0.481	0.481	strong		0.303	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
ARF3	377	hgsc.bcm.edu	37	12	49333799	49333799	+	Silent	SNP	G	G	A	rs2228417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49333799G>A	ENST00000256682.4	-	3	574	c.240C>T	c.(238-240)caC>caT	p.H80H	RP11-302B13.5_ENST00000398092.4_Silent_p.H80H|ARF3_ENST00000447318.2_Intron|ARF3_ENST00000541967.1_5'Flank|AC073610.5_ENST00000537495.1_5'Flank|ARF3_ENST00000541959.1_Silent_p.H80H	NM_001659.2	NP_001650.1	P61204	ARF3_HUMAN	ADP-ribosylation factor 3	80					GTP catabolic process (GO:0006184)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|lung(2)|skin(1)	4						TCTGGAAGTAGTGTCTCCAGA	0.507													G|||	310	0.061901	0.0098	0.0288	5008	,	,		20342	0.004		0.0696	False		,,,				2504	0.2076				p.H80H	Pancreas(189;1862 2134 4419 30933 49364)	Atlas-SNP	.											.	ARF3	11	.	0			c.C240T						PASS	.	G		52,4354	54.2+/-90.2	0,52,2151	174.0	136.0	149.0		240	2.7	1.0	12	dbSNP_98	149	614,7986	160.3+/-213.4	23,568,3709	no	coding-synonymous	ARF3	NM_001659.2		23,620,5860	AA,AG,GG		7.1395,1.1802,5.1207		80/182	49333799	666,12340	2203	4300	6503	SO:0001819	synonymous_variant	377	exon3			GAAGTAGTGTCTC	M74491	CCDS8774.1	12q13.12	2013-01-22			ENSG00000134287	ENSG00000134287		"""ADP-ribosylation factors"""	654	protein-coding gene	gene with protein product	"""small GTP binding protein"""	103190				8661066	Standard	NM_001659		Approved		uc001rsr.2	P61204	OTTHUMG00000168080	ENST00000256682.4:c.240C>T	12.37:g.49333799G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	196	89	0.454082	NM_001659	A8K6G8|B7ZB63|P16587	Silent	SNP	ENST00000256682.4	37	CCDS8774.1																																																																																			G|0.954;A|0.046	0.046	strong		0.507	ARF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258242.2	NM_001659	
DSCAM	1826	hgsc.bcm.edu	37	21	41684166	41684166	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:41684166C>T	ENST00000400454.1	-	9	2381	c.1904G>A	c.(1903-1905)cGg>cAg	p.R635Q		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	635	Ig-like C2-type 7.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AGGGATTGGCCGGCCATCCTT	0.522																																					p.R635Q	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											DSCAM,right_upper_lobe,carcinoma,0,1	DSCAM	347	1	0			c.G1904A						scavenged	.						70.0	70.0	70.0					21																	41684166		1914	4144	6058	SO:0001583	missense	1826	exon9			ATTGGCCGGCCAT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.1904G>A	21.37:g.41684166C>T	ENSP00000383303:p.Arg635Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	174	3	0.0172414	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.354362	0.24512	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.64803	-0.12;-0.12	5.55	5.55	0.83447	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.058459	0.64402	D	0.000004	T	0.42223	0.1193	N	0.04355	-0.22	0.44085	D	0.99684	D	0.57571	0.98	B	0.43889	0.435	T	0.44620	-0.9316	10	0.07990	T	0.79	.	19.5017	0.95097	0.0:1.0:0.0:0.0	.	635	O60469	DSCAM_HUMAN	Q	635;387	ENSP00000383303:R635Q;ENSP00000385342:R387Q	ENSP00000383303:R635Q	R	-	2	0	DSCAM	40606036	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.615000	0.46368	2.596000	0.87737	0.563000	0.77884	CGG	.	.	none		0.522	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
PLCG1	5335	hgsc.bcm.edu	37	20	39792063	39792063	+	Missense_Mutation	SNP	A	A	G	rs2228246	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:39792063A>G	ENST00000373271.1	+	9	1240	c.835A>G	c.(835-837)Agc>Ggc	p.S279G	PLCG1_ENST00000244007.3_Missense_Mutation_p.S279G|PLCG1_ENST00000373272.2_Missense_Mutation_p.S279G	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	279			S -> G (in dbSNP:rs2228246). {ECO:0000269|Ref.2}.		activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				GTTCATGCTCAGCTTCCTCCG	0.557													A|||	395	0.0788738	0.0802	0.1167	5008	,	,		18612	0.002		0.162	False		,,,				2504	0.044				p.S279G		Atlas-SNP	.											.	PLCG1	111	.	0			c.A835G						PASS	.	A	GLY/SER,GLY/SER	447,3959	216.1+/-234.9	21,405,1777	72.0	66.0	68.0		835,835	4.6	1.0	20	dbSNP_98	68	1346,7254	263.4+/-285.0	116,1114,3070	yes	missense,missense	PLCG1	NM_002660.2,NM_182811.1	56,56	137,1519,4847	GG,GA,AA		15.6512,10.1453,13.7859	benign,benign	279/1292,279/1291	39792063	1793,11213	2203	4300	6503	SO:0001583	missense	5335	exon9			ATGCTCAGCTTCC	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"", ""SH2 domain containing"""	9065	protein-coding gene	gene with protein product		172420	"""phospholipase C, gamma 1 (formerly subtype 148)"""	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.835A>G	20.37:g.39792063A>G	ENSP00000362368:p.Ser279Gly	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	208	0.09523809523809523	36	0.07317073170731707	34	0.09392265193370165	1	0.0017482517482517483	137	0.18073878627968337	A	12.03	1.816252	0.32145	0.101453	0.156512	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.42513	0.97;0.97;0.97	5.69	4.6	0.57074	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);	0.439299	0.31450	N	0.007636	T	0.00039	0.0001	N	0.24115	0.695	0.30622	P	0.75836	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.09840	-1.0656	9	0.33940	T	0.23	.	7.5861	0.27993	0.7877:0.1412:0.071:0.0	rs2228246;rs8192707;rs52803627;rs57350391;rs2228246	279;279	P19174;A2A284	PLCG1_HUMAN;.	G	279	ENSP00000244007:S279G;ENSP00000362368:S279G;ENSP00000362369:S279G	ENSP00000244007:S279G	S	+	1	0	PLCG1	39225477	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.993000	0.40747	0.998000	0.38996	0.459000	0.35465	AGC	A|0.883;G|0.117	0.117	strong		0.557	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
TEAD1	7003	hgsc.bcm.edu	37	11	12903443	12903443	+	Splice_Site	SNP	C	C	T	rs2304733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:12903443C>T	ENST00000526600.1	+	3	448	c.225C>T	c.(223-225)gaC>gaT	p.D75D	TEAD1_ENST00000361905.4_Splice_Site_p.D156D|TEAD1_ENST00000527575.1_Splice_Site_p.D171D|TEAD1_ENST00000361985.2_Splice_Site_p.D171D|TEAD1_ENST00000527636.1_Splice_Site_p.D171D|TEAD1_ENST00000334310.6_Splice_Site_p.D160D			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	171					gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CTGTTCCCAGCGTCAAGCCTT	0.592													C|||	2172	0.433706	0.2973	0.2925	5008	,	,		20550	0.8393		0.4195	False		,,,				2504	0.3149				p.D171D		Atlas-SNP	.											.	TEAD1	40	.	0			c.C513T						PASS	.	C		1390,3010	457.1+/-351.5	218,954,1028	134.0	119.0	124.0		513	0.2	1.0	11	dbSNP_100	124	3536,5052	514.2+/-378.3	732,2072,1490	yes	coding-synonymous-near-splice	TEAD1	NM_021961.5		950,3026,2518	TT,TC,CC		41.1737,31.5909,37.9273		171/427	12903443	4926,8062	2200	4294	6494	SO:0001630	splice_region_variant	7003	exon8			TCCCAGCGTCAAG	X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079			11714	protein-coding gene	gene with protein product		189967	"""atrophia areata, peripapillary chorioretinal degeneration"""	TCF13, AA		1851669, 9889009, 15016762	Standard	NM_021961		Approved	TEF-1	uc021qdx.1	P28347		ENST00000526600.1:c.225-1C>T	11.37:g.12903443C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_021961	A4FUP2|E7EV65	Silent	SNP	ENST00000526600.1	37																																																																																				C|0.574;T|0.426	0.426	strong		0.592	TEAD1-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000387220.1	NM_021961	Silent
SLC35G5	83650	hgsc.bcm.edu	37	8	11188752	11188752	+	Missense_Mutation	SNP	G	G	A	rs6990563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11188752G>A	ENST00000382435.4	+	1	356	c.137G>A	c.(136-138)gGt>gAt	p.G46D		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	46			G -> D (in dbSNP:rs6990563).			integral component of membrane (GO:0016021)											GCCCTGCTGGGTGGGGGCCTG	0.677													G|||	2136	0.426518	0.1467	0.3718	5008	,	,		16974	0.7351		0.4553	False		,,,				2504	0.4959				p.G46D		Atlas-SNP	.											.	.	.	.	0			c.G137A						PASS	.	G	ASP/GLY	896,3510	343.6+/-307.7	91,714,1398	48.0	55.0	52.0		137	0.3	1.0	8	dbSNP_116	52	4014,4586	552.0+/-386.0	952,2110,1238	no	missense	SLC35G5	NM_054028.1	94	1043,2824,2636	AA,AG,GG		46.6744,20.3359,37.7518	probably-damaging	46/339	11188752	4910,8096	2203	4300	6503	SO:0001583	missense	83650	exon1			TGCTGGGTGGGGG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.137G>A	8.37:g.11188752G>A	ENSP00000371872:p.Gly46Asp	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	139	77	0.553957	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	904	0.4139194139194139	73	0.1483739837398374	134	0.3701657458563536	378	0.6608391608391608	319	0.420844327176781	G	15.55	2.867345	0.51588	0.203359	0.466744	ENSG00000177710	ENST00000382435	T	0.42900	0.96	0.34	0.34	0.15985	.	0.000000	0.45867	D	0.000330	T	0.00012	0.0000	L	0.27053	0.805	0.23391	P	0.99777562	D	0.71674	0.998	D	0.63597	0.916	T	0.42068	-0.9473	9	0.66056	D	0.02	-4.0269	6.5344	0.22344	2.0E-4:0.0:0.9998:0.0	rs6990563;rs58184334	46	Q96KT7	S35G5_HUMAN	D	46	ENSP00000371872:G46D	ENSP00000371872:G46D	G	+	2	0	SLC35G5	11226162	1.000000	0.71417	0.966000	0.40874	0.252000	0.25951	3.390000	0.52523	0.426000	0.26116	0.089000	0.15464	GGT	.	.	weak		0.677	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
PITPNM2	57605	hgsc.bcm.edu	37	12	123471094	123471094	+	Silent	SNP	G	G	A	rs12811109	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123471094G>A	ENST00000542749.1	-	23	3678	c.3615C>T	c.(3613-3615)caC>caT	p.H1205H	PITPNM2_ENST00000320201.4_Silent_p.H1205H|PITPNM2_ENST00000392428.1_Silent_p.H926H|PITPNM2_ENST00000280562.5_Silent_p.H1199H			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	1205					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CATAGGCCGCGTGCACGCGCA	0.682													G|||	613	0.122404	0.0431	0.1873	5008	,	,		15693	0.002		0.2157	False		,,,				2504	0.2117				p.H1205H		Atlas-SNP	.											PITPNM2,colon,carcinoma,0,1	PITPNM2	105	1	0			c.C3615T						PASS	.	G		308,4096		7,294,1901	25.0	22.0	23.0		3615	0.1	1.0	12	dbSNP_121	23	1667,6931		136,1395,2768	no	coding-synonymous	PITPNM2	NM_020845.2		143,1689,4669	AA,AG,GG		19.3882,6.9936,15.19		1205/1350	123471094	1975,11027	2202	4299	6501	SO:0001819	synonymous_variant	57605	exon24			GGCCGCGTGCACG	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.3615C>T	12.37:g.123471094G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	120	70	0.583333	NM_020845	Q9P271	Silent	SNP	ENST00000542749.1	37	CCDS9242.1																																																																																			G|0.860;A|0.140	0.140	strong		0.682	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845	
CSAG1	158511	hgsc.bcm.edu	37	X	151908844	151908844	+	Missense_Mutation	SNP	A	A	T	rs1894359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:151908844A>T	ENST00000370287.3	+	4	411	c.83A>T	c.(82-84)tAc>tTc	p.Y28F	CSAG1_ENST00000370291.2_Missense_Mutation_p.Y28F|CSAG1_ENST00000452779.2_Missense_Mutation_p.Y28F	NM_153478.1	NP_705611.1	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1	28			Y -> F (in dbSNP:rs1894359).	Y -> C (in Ref. 1; AF195880). {ECO:0000305}.						central_nervous_system(1)|kidney(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					AGTAGACTGTACAGAGACACT	0.532													.|||	377	0.0998675	0.0802	0.0533	3775	,	,		11916	0.0238		0.1531	False		,,,				2504	0.0573				p.Y28F		Atlas-SNP	.											.	CSAG1	27	.	0			c.A83T						PASS	.	T	PHE/TYR,PHE/TYR	314,3521		19,223,53,1390,518	232.0	210.0	217.0		83,83	0.8	0.0	X	dbSNP_92	217	1051,5677		80,546,345,1802,1527	no	missense,missense	CSAG1	NM_001102576.1,NM_153478.1	22,22	99,769,398,3192,2045	TT,TA,T,AA,A		15.6213,8.1877,12.9225	benign,benign	28/79,28/79	151908844	1365,9198	2203	4300	6503	SO:0001583	missense	158511	exon4			GACTGTACAGAGA	AF268419	CCDS76047.1	Xq28	2009-08-07			ENSG00000198930	ENSG00000198930			24294	protein-coding gene	gene with protein product	"""cancer/testis antigen family 24, member 1"""					12039054	Standard	XM_006724810		Approved	CSAGE, CT24.1	uc004fgf.3	Q6PB30	OTTHUMG00000022648	ENST00000370287.3:c.83A>T	X.37:g.151908844A>T	ENSP00000359310:p.Tyr28Phe	Somatic	1128	2	0.00177305		WXS	Illumina HiSeq	Phase_I	646	641	0.99226	NM_153478	A6NE22	Missense_Mutation	SNP	ENST00000370287.3	37	CCDS14711.1	146	0.08800482218203737	18	0.0375	16	0.04519774011299435	5	0.008896797153024912	67	0.09544159544159544	T	2.436	-0.329767	0.05314	0.081877	0.156213	ENSG00000198930	ENST00000370287;ENST00000452779;ENST00000370291	T;T;T	0.49432	1.39;1.39;0.78	0.837	0.837	0.18896	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06481	-1.0824	6	0.51188	T	0.08	.	.	.	.	rs1894359;rs52815057;rs61405848;rs1894359	28	Q6PB30	CSAG1_HUMAN	F	28	ENSP00000359310:Y28F;ENSP00000396520:Y28F;ENSP00000359314:Y28F	ENSP00000359310:Y28F	Y	+	2	0	CSAG1	151659500	0.002000	0.14202	0.001000	0.08648	0.003000	0.03518	-0.150000	0.10189	-0.223000	0.09943	-1.340000	0.01251	TAC	.	.	alt		0.532	CSAG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058760.2	NM_153479	
SH3BP1	23616	hgsc.bcm.edu	37	22	38051493	38051493	+	Silent	SNP	G	G	T	rs117382629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38051493G>T	ENST00000357436.4	+	18	2221	c.1908G>T	c.(1906-1908)cgG>cgT	p.R636R	Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000599616.1_Intron	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	636					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					GCCAAAGCCGGCGTTCACCAG	0.711													G|||	40	0.00798722	0.0015	0.0101	5008	,	,		4118	0.0		0.0268	False		,,,				2504	0.0041				p.R636R		Atlas-SNP	.											.	SH3BP1	41	.	0			c.G1908T						PASS	.	G		23,3653		0,23,1815	3.0	4.0	4.0		1908	-1.4	0.5	22	dbSNP_132	4	149,7211		0,149,3531	no	coding-synonymous	SH3BP1	NM_018957.3		0,172,5346	TT,TG,GG		2.0245,0.6257,1.5585		636/702	38051493	172,10864	1838	3680	5518	SO:0001819	synonymous_variant	23616	exon18			AAGCCGGCGTTCA		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.1908G>T	22.37:g.38051493G>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			G|0.987;T|0.013	0.013	strong		0.711	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
SLC22A4	6583	hgsc.bcm.edu	37	5	131671662	131671662	+	Silent	SNP	C	C	G	rs12777	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:131671662C>G	ENST00000200652.3	+	8	1587	c.1413C>G	c.(1411-1413)ggC>ggG	p.G471G	AC034220.3_ENST00000417795.1_RNA|AC034220.3_ENST00000437091.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	471					body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	CCAGAGTGGGCAGCATCATTG	0.478													C|||	92	0.0183706	0.003	0.0403	5008	,	,		17080	0.0		0.0467	False		,,,				2504	0.0133				p.G471G		Atlas-SNP	.											.	SLC22A4	45	.	0			c.C1413G						PASS	.	C		33,4373	38.4+/-70.7	0,33,2170	127.0	123.0	124.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1413	3.5	1.0	5	dbSNP_52	124	349,8251	118.5+/-177.9	6,337,3957	yes	coding-synonymous	SLC22A4	NM_003059.2		6,370,6127	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	4.0581,0.749,2.9371		471/552	131671662	382,12624	2203	4300	6503	SO:0001819	synonymous_variant	6583	exon8			AGTGGGCAGCATC	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.1413C>G	5.37:g.131671662C>G		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	217	146	0.672811	NM_003059	O14546	Silent	SNP	ENST00000200652.3	37	CCDS4153.1																																																																																			C|0.971;G|0.029	0.029	strong		0.478	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059	
PLXNA3	55558	hgsc.bcm.edu	37	X	153695908	153695908	+	Silent	SNP	G	G	T	rs60361517		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153695908G>T	ENST00000369682.3	+	20	3637	c.3462G>T	c.(3460-3462)gcG>gcT	p.A1154A		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1154	IPT/TIG 4.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGATTCCCGCGGCAGCCGGCA	0.662													G|||	1026	0.271788	0.3722	0.0663	3775	,	,		6789	0.126		0.0855	False		,,,				2504	0.2812				p.A1154A		Atlas-SNP	.											.	PLXNA3	156	.	0			c.G3462T						PASS	.	G		1624,2174		303,790,228,534,316	16.0	15.0	15.0		3462	-10.7	0.0	X	dbSNP_129	15	889,5800		53,521,262,1853,1573	no	coding-synonymous	PLXNA3	NM_017514.3		356,1311,490,2387,1889	TT,TG,T,GG,G		13.2905,42.7593,23.963		1154/1872	153695908	2513,7974	2171	4262	6433	SO:0001819	synonymous_variant	55558	exon20			TCCCGCGGCAGCC	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.3462G>T	X.37:g.153695908G>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	105	102	0.971429	NM_017514	Q5HY36	Silent	SNP	ENST00000369682.3	37	CCDS14752.1																																																																																			G|0.810;T|0.190	0.190	strong		0.662	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
OR10R2	343406	hgsc.bcm.edu	37	1	158450238	158450238	+	Missense_Mutation	SNP	G	G	A	rs3820678	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158450238G>A	ENST00000368152.1	+	1	571	c.571G>A	c.(571-573)Gcc>Acc	p.A191T	RP11-144L1.4_ENST00000426251.1_RNA|RP11-144L1.4_ENST00000419738.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	191			A -> T (in dbSNP:rs3820678).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					TTTTTGTAGCGCCAACAAAGT	0.433													G|||	916	0.182907	0.1437	0.147	5008	,	,		22883	0.1935		0.2187	False		,,,				2504	0.2137				p.A191T		Atlas-SNP	.											OR10R2,colon,carcinoma,-1,1	OR10R2	81	1	0			c.G571A						PASS	.	G	THR/ALA	614,3792	268.0+/-268.2	47,520,1636	144.0	137.0	139.0		571	1.2	0.9	1	dbSNP_107	139	1757,6843	318.8+/-313.9	170,1417,2713	yes	missense	OR10R2	NM_001004472.1	58	217,1937,4349	AA,AG,GG		20.4302,13.9355,18.23	benign	191/336	158450238	2371,10635	2203	4300	6503	SO:0001583	missense	343406	exon1			TGTAGCGCCAACA	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"""GPCR / Class A : Olfactory receptors"""	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.571G>A	1.37:g.158450238G>A	ENSP00000357134:p.Ala191Thr	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	218	218	1	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	37	CCDS30898.1	425	0.1945970695970696	64	0.13008130081300814	59	0.16298342541436464	129	0.22552447552447552	173	0.22823218997361477	g	13.56	2.272389	0.40194	0.139355	0.204302	ENSG00000198965	ENST00000368152	T	0.36699	1.24	4.48	1.21	0.21127	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.05868	0.0153	N	0.12527	0.23	0.49915	P	1.6799999999994597E-4	B	0.32829	0.386	B	0.25884	0.064	T	0.29150	-1.0021	8	0.30078	T	0.28	.	5.88	0.18850	0.1009:0.0:0.3717:0.5274	rs3820678;rs17629439;rs56509961;rs57211339;rs3820678	191	Q8NGX6	O10R2_HUMAN	T	191	ENSP00000357134:A191T	ENSP00000357134:A191T	A	+	1	0	OR10R2	156716862	0.000000	0.05858	0.897000	0.35233	0.946000	0.59487	-1.780000	0.01775	0.466000	0.27193	0.655000	0.94253	GCC	G|0.816;A|0.184	0.184	strong		0.433	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472	
PKHD1	5314	hgsc.bcm.edu	37	6	51947237	51947237	+	Silent	SNP	G	G	A	rs9474143	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:51947237G>A	ENST00000371117.3	-	4	509	c.234C>T	c.(232-234)gaC>gaT	p.D78D	PKHD1_ENST00000340994.4_Silent_p.D78D	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	78	IPT/TIG 1; atypical.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.D78D(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CAGGAAAGACGTCACAGGGAA	0.502													G|||	1775	0.354433	0.3949	0.2536	5008	,	,		19417	0.4306		0.2455	False		,,,				2504	0.4049				p.D78D		Atlas-SNP	.											PKHD1,NS,carcinoma,0,1	PKHD1	927	1	1	Substitution - coding silent(1)	stomach(1)	c.C234T						PASS	.	G	,	1748,2658	521.5+/-370.6	334,1080,789	175.0	180.0	178.0		234,234	-6.9	0.0	6	dbSNP_119	178	2098,6502	361.6+/-332.4	268,1562,2470	yes	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	602,2642,3259	AA,AG,GG		24.3953,39.6732,29.571	,	78/4075,78/3397	51947237	3846,9160	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon4			AAAGACGTCACAG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.234C>T	6.37:g.51947237G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			G|0.682;A|0.318	0.318	strong		0.502	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
TRPC6	7225	hgsc.bcm.edu	37	11	101342958	101342958	+	Silent	SNP	G	G	A	rs61743044	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:101342958G>A	ENST00000344327.3	-	8	2539	c.2115C>T	c.(2113-2115)taC>taT	p.Y705Y	TRPC6_ENST00000532133.1_Silent_p.Y627Y|TRPC6_ENST00000360497.4_Silent_p.Y650Y|TRPC6_ENST00000348423.4_Silent_p.Y589Y	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	705					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		CATAAAGAACGTAACCAATGT	0.338													G|||	189	0.0377396	0.1165	0.0202	5008	,	,		17586	0.0		0.0179	False		,,,				2504	0.0031				p.Y705Y	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.C2115T						PASS	.	G		463,3943	214.1+/-233.5	27,409,1767	85.0	86.0	86.0		2115	-2.4	1.0	11	dbSNP_134	86	157,8439	73.5+/-136.2	0,157,4141	no	coding-synonymous	TRPC6	NM_004621.5		27,566,5908	AA,AG,GG		1.8264,10.5084,4.7685		705/932	101342958	620,12382	2203	4298	6501	SO:0001819	synonymous_variant	7225	exon8			AAGAACGTAACCA	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12338	protein-coding gene	gene with protein product		603652	"""focal segmental glomerulosclerosis 2"""	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.2115C>T	11.37:g.101342958G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	37	0.587302	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Silent	SNP	ENST00000344327.3	37	CCDS8311.1																																																																																			G|0.956;A|0.044	0.044	strong		0.338	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621	
MUC4	4585	hgsc.bcm.edu	37	3	195489009	195489009	+	Missense_Mutation	SNP	C	C	A	rs2246901	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195489009C>A	ENST00000346145.4	-	13	1792	c.1753G>T	c.(1753-1755)Gcc>Tcc	p.A585S	MUC4_ENST00000463781.3_Missense_Mutation_p.A4821S|MUC4_ENST00000475231.1_Missense_Mutation_p.A4769S|MUC4_ENST00000349607.4_Missense_Mutation_p.A534S	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1578			S -> A (in dbSNP:rs2246901).		cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGGCGGAGGCGTGGAGGATG	0.716													.|||	3160	0.63099	0.4834	0.5793	5008	,	,		10704	0.8125		0.7147	False		,,,				2504	0.5941				p.A4821S		Atlas-SNP	.											.	MUC4	1505	.	0			c.G14461T	GRCh37	CM066583	MUC4	M	rs2246901	PASS	.	C	SER/ALA,SER/ALA,SER/ALA	2216,2184		562,1092,546	30.0	27.0	28.0		1753,14461,1600	3.0	0.4	3	dbSNP_100	28	6121,2473		2194,1733,370	yes	missense,missense,missense	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	99,99,99	2756,2825,916	AA,AC,CC		28.7759,49.6364,35.8396	probably-damaging,probably-damaging,probably-damaging	585/1177,4821/5413,534/1126	195489009	8337,4657	2200	4297	6497	SO:0001583	missense	4585	exon14			CGGAGGCGTGGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.1753G>T	3.37:g.195489009C>A	ENSP00000304207:p.Ala585Ser	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	37	CCDS3310.1	1429	0.6543040293040293	227	0.4613821138211382	207	0.5718232044198895	448	0.7832167832167832	547	0.7216358839050132	.	11.25	1.583846	0.28268	0.503636	0.712241	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231	T;T;T;T	0.60548	0.18;0.18;0.18;0.18	4.97	3.05	0.35203	.	0.230621	0.30347	N	0.009839	T	0.00012	0.0000	M	0.77486	2.375	0.80722	P	0.0	D;P;D;P;P;P	0.76494	0.999;0.738;0.957;0.897;0.897;0.87	D;P;P;P;P;P	0.83275	0.996;0.477;0.72;0.656;0.656;0.627	T	0.35574	-0.9783	9	0.48119	T	0.1	-21.2177	7.0078	0.24846	0.1702:0.741:0.0:0.0887	rs2246901;rs60461351;rs2246901	4693;534;585;4821;4769;1526	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	S	534;585;4821;4769	ENSP00000338109:A534S;ENSP00000304207:A585S;ENSP00000417498:A4821S;ENSP00000420243:A4769S	ENSP00000304207:A585S	A	-	1	0	MUC4	196974680	0.000000	0.05858	0.439000	0.26833	0.050000	0.14768	-0.496000	0.06436	1.085000	0.41206	0.561000	0.74099	GCC	C|0.374;A|0.626	0.626	strong		0.716	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
ADAMTS8	11095	hgsc.bcm.edu	37	11	130275749	130275749	+	Missense_Mutation	SNP	T	T	C	rs11222085	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130275749T>C	ENST00000257359.6	-	9	3080	c.2374A>G	c.(2374-2376)Aca>Gca	p.T792A		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	792	Spacer.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		CCAGGGACTGTCAGGAGCTGC	0.572													T|||	420	0.0838658	0.0129	0.2464	5008	,	,		19597	0.0		0.175	False		,,,				2504	0.0573				p.T792A		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.A2374G						PASS	.	T	ALA/THR	130,3920		3,124,1898	146.0	153.0	151.0		2374	5.3	0.9	11	dbSNP_120	151	1518,6844		127,1264,2790	yes	missense	ADAMTS8	NM_007037.4	58	130,1388,4688	CC,CT,TT		18.1536,3.2099,13.2775	benign	792/890	130275749	1648,10764	2025	4181	6206	SO:0001583	missense	11095	exon9			GGACTGTCAGGAG	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.2374A>G	11.37:g.130275749T>C	ENSP00000257359:p.Thr792Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	46	0.414414	NM_007037	Q9NZS0	Missense_Mutation	SNP	ENST00000257359.6	37	CCDS41732.1	225	0.10302197802197802	7	0.014227642276422764	75	0.20718232044198895	0	0.0	143	0.18865435356200527	T	8.604	0.887485	0.17540	0.032099	0.181536	ENSG00000134917	ENST00000531752;ENST00000257359;ENST00000414575	T	0.50277	0.75	5.34	5.34	0.76211	ADAM-TS Spacer 1 (1);	0.282192	0.41823	D	0.000807	T	0.00039	0.0001	L	0.37561	1.115	0.29572	P	0.849801	B;B	0.20368	0.009;0.044	B;B	0.24269	0.01;0.052	T	0.14476	-1.0471	9	0.15952	T	0.53	.	9.4078	0.38473	0.2749:0.0:0.0:0.7251	rs11222085;rs52823834;rs11222085	792;273	Q9UP79;B3KVX9	ATS8_HUMAN;.	A	190;792;821	ENSP00000257359:T792A	ENSP00000257359:T792A	T	-	1	0	ADAMTS8	129780959	0.999000	0.42202	0.948000	0.38648	0.204000	0.24138	0.973000	0.29422	2.018000	0.59344	0.377000	0.23210	ACA	T|0.886;C|0.114	0.114	strong		0.572	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	
ARSB	411	hgsc.bcm.edu	37	5	78181423	78181423	+	Missense_Mutation	SNP	C	C	T	rs1071598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:78181423C>T	ENST00000264914.4	-	5	1662	c.1126G>A	c.(1126-1128)Gtg>Atg	p.V376M	ARSB_ENST00000565165.1_Missense_Mutation_p.V376M|ARSB_ENST00000396151.3_Missense_Mutation_p.V376M|ARSB_ENST00000521800.1_5'UTR	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	376			V -> M (in dbSNP:rs17220759). {ECO:0000269|PubMed:14974081, ECO:0000269|PubMed:1718978}.		autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		GTTTTCCACACGTCGAAGCCA	0.532													C|||	544	0.108626	0.0469	0.196	5008	,	,		15642	0.0149		0.1461	False		,,,				2504	0.1881				p.V376M	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											.	ARSB	47	.	0			c.G1126A						PASS	.	C	MET/VAL,MET/VAL	309,4097	166.9+/-198.0	10,289,1904	119.0	108.0	112.0		1126,1126	0.6	1.0	5	dbSNP_123	112	1473,7127	281.7+/-295.2	136,1201,2963	yes	missense,missense	ARSB	NM_000046.3,NM_198709.2	21,21	146,1490,4867	TT,TC,CC		17.1279,7.0132,13.7014	benign,benign	376/534,376/414	78181423	1782,11224	2203	4300	6503	SO:0001583	missense	411	exon6			TCCACACGTCGAA	M32373	CCDS4043.1, CCDS43334.1	5q14.1	2013-02-14			ENSG00000113273	ENSG00000113273	3.1.6.1	"""Arylsulfatase family"""	714	protein-coding gene	gene with protein product		611542				2303452	Standard	NM_000046		Approved		uc003kfq.3	P15848	OTTHUMG00000108129	ENST00000264914.4:c.1126G>A	5.37:g.78181423C>T	ENSP00000264914:p.Val376Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_198709	B2RC20|Q8N322|Q9UDI9	Missense_Mutation	SNP	ENST00000264914.4	37	CCDS4043.1	208	0.09523809523809523	20	0.04065040650406504	70	0.19337016574585636	6	0.01048951048951049	112	0.14775725593667546	C	14.04	2.417132	0.42918	0.070132	0.171279	ENSG00000113273	ENST00000264914;ENST00000396151	D;D	0.96365	-3.99;-3.99	5.46	0.601	0.17529	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.324515	0.32884	N	0.005530	T	0.00875	0.0029	N	0.26162	0.8	0.24694	P	0.99329924	P;P	0.44281	0.779;0.831	B;B	0.32928	0.131;0.155	T	0.47032	-0.9148	9	0.33940	T	0.23	.	9.6382	0.39822	0.0:0.6519:0.0:0.3481	rs17220759;rs17220759	376;376	Q8N322;P15848	.;ARSB_HUMAN	M	376	ENSP00000264914:V376M;ENSP00000379455:V376M	ENSP00000264914:V376M	V	-	1	0	ARSB	78217179	0.977000	0.34250	0.962000	0.40283	0.898000	0.52572	2.189000	0.42621	-0.194000	0.10399	-0.254000	0.11334	GTG	C|0.884;T|0.116	0.116	strong		0.532	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046	
SIN3B	23309	hgsc.bcm.edu	37	19	16976289	16976289	+	Silent	SNP	T	T	C	rs2303091	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:16976289T>C	ENST00000248054.5	+	11	1473	c.1452T>C	c.(1450-1452)tcT>tcC	p.S484S	SIN3B_ENST00000595541.1_Silent_p.S74S|SIN3B_ENST00000379803.1_Silent_p.S516S					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						AGAAGCTATCTCGGATGGCGC	0.582													T|||	792	0.158147	0.0204	0.2104	5008	,	,		12089	0.2778		0.162	False		,,,				2504	0.18				p.S516S		Atlas-SNP	.											.	SIN3B	90	.	0			c.T1548C						PASS	.	T		182,4224	118.0+/-155.7	4,174,2025	90.0	80.0	83.0		1548	-9.6	0.0	19	dbSNP_100	83	1355,7245	263.7+/-285.1	117,1121,3062	no	coding-synonymous	SIN3B	NM_015260.2		121,1295,5087	CC,CT,TT		15.7558,4.1307,11.8176		516/1163	16976289	1537,11469	2203	4300	6503	SO:0001819	synonymous_variant	23309	exon12			GCTATCTCGGATG	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"""SIN3 homolog B, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog B (yeast)"""			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.1452T>C	19.37:g.16976289T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_015260		Silent	SNP	ENST00000248054.5	37																																																																																				T|0.859;C|0.141	0.141	strong		0.582	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260	
NPFFR1	64106	hgsc.bcm.edu	37	10	72014779	72014779	+	Silent	SNP	G	G	A	rs1999624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:72014779G>A	ENST00000277942.6	-	4	1226	c.1227C>T	c.(1225-1227)caC>caT	p.H409H		NM_022146.4	NP_071429.1	Q9GZQ6	NPFF1_HUMAN	neuropeptide FF receptor 1	409					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			endometrium(2)|lung(1)	3						TGGGCAAGCCGTGGTGAGCCA	0.736													G|||	297	0.0593051	0.0469	0.0259	5008	,	,		14059	0.0942		0.0487	False		,,,				2504	0.0746				p.H409H		Atlas-SNP	.											.	NPFFR1	21	.	0			c.C1227T						PASS	.	G		115,3633		0,115,1759	4.0	5.0	5.0		1227	-2.8	0.0	10	dbSNP_92	5	278,7650		0,278,3686	no	coding-synonymous	NPFFR1	NM_022146.4		0,393,5445	AA,AG,GG		3.5066,3.0683,3.3659		409/431	72014779	393,11283	1874	3964	5838	SO:0001819	synonymous_variant	64106	exon4			CAAGCCGTGGTGA	AB040104	CCDS53539.1	10q21-q22	2012-08-10	2006-02-15	2006-02-15	ENSG00000148734	ENSG00000148734		"""GPCR / Class A :  Neuropeptide receptors : FF/AF"", ""GPCR / Class A : RF amide peptide receptors"""	17425	protein-coding gene	gene with protein product	"""neuropeptide FF 1"""	607448	"""G protein-coupled receptor 147"""	GPR147		11024015	Standard	NM_022146		Approved	OT7T022, NPFF1R1	uc021psj.1	Q9GZQ6	OTTHUMG00000018404	ENST00000277942.6:c.1227C>T	10.37:g.72014779G>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_022146	A2RRF0|Q8NGR0|Q96RN3	Silent	SNP	ENST00000277942.6	37	CCDS53539.1																																																																																			G|0.943;A|0.057	0.057	strong		0.736	NPFFR1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048504.2	NM_022146	
SYTL5	94122	hgsc.bcm.edu	37	X	37948832	37948832	+	Missense_Mutation	SNP	A	A	G	rs4827331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:37948832A>G	ENST00000357972.5	+	7	1369	c.823A>G	c.(823-825)Atc>Gtc	p.I275V	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000297875.2_Missense_Mutation_p.I275V|SYTL5_ENST00000456733.2_Missense_Mutation_p.I275V			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	275			I -> V (in dbSNP:rs4827331).		exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						GACCTCAGTCATCAGTAGAGT	0.478													A|||	412	0.109139	0.0991	0.062	3775	,	,		15425	0.0188		0.1213	False		,,,				2504	0.0992				p.I275V		Atlas-SNP	.											.	SYTL5	72	.	0			c.A823G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	515,3318		30,368,87,1233,484	73.0	55.0	61.0		823,823,823	3.9	0.0	X	dbSNP_111	61	1048,5679		65,636,282,1727,1589	yes	missense,missense,missense	SYTL5	NM_001163334.1,NM_001163335.1,NM_138780.2	29,29,29	95,1004,369,2960,2073	GG,GA,G,AA,A		15.579,13.436,14.8011	benign,benign,benign	275/753,275/731,275/731	37948832	1563,8997	2202	4299	6501	SO:0001583	missense	94122	exon6			TCAGTCATCAGTA		CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.823A>G	X.37:g.37948832A>G	ENSP00000350657:p.Ile275Val	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_001163334	A2RRF2	Missense_Mutation	SNP	ENST00000357972.5	37	CCDS14244.1	162	0.09764918625678119	26	0.057777777777777775	14	0.04142011834319527	7	0.01232394366197183	53	0.07528409090909091	A	0.147	-1.095805	0.01858	0.13436	0.15579	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.20200	2.09;2.09;2.44	5.04	3.88	0.44766	.	0.672886	0.13964	N	0.350617	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.12630	0.006;0.0	B;B	0.15052	0.012;0.0	T	0.35624	-0.9781	9	0.26408	T	0.33	-22.3549	3.9262	0.09265	0.7117:0.0:0.102:0.1863	rs4827331;rs58050753;rs4827331	275;275	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	V	275	ENSP00000297875:I275V;ENSP00000350657:I275V;ENSP00000395220:I275V	ENSP00000297875:I275V	I	+	1	0	SYTL5	37833776	0.705000	0.27846	0.007000	0.13788	0.148000	0.21650	2.337000	0.43947	0.597000	0.29811	0.486000	0.48141	ATC	A|0.858;0|0.015	.	strong		0.478	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780	
GRHPR	9380	hgsc.bcm.edu	37	9	37436755	37436755	+	Silent	SNP	G	G	A	rs76299266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37436755G>A	ENST00000318158.6	+	9	1048	c.963G>A	c.(961-963)ccG>ccA	p.P321P		NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	321					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		GAGGGGAGCCGATGCCTAGTG	0.557													G|||	60	0.0119808	0.0272	0.0029	5008	,	,		18599	0.001		0.005	False		,,,				2504	0.0164				p.P321P		Atlas-SNP	.											.	GRHPR	35	.	0			c.G963A						PASS	.	G		103,4303	81.4+/-119.9	2,99,2102	162.0	154.0	157.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	963	-4.3	1.0	9	dbSNP_132	157	45,8555	30.1+/-81.4	0,45,4255	no	coding-synonymous	GRHPR	NM_012203.1		2,144,6357	AA,AG,GG		0.5233,2.3377,1.1379		321/329	37436755	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	9380	exon9			GGAGCCGATGCCT	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"""primary hyperoxaluria type 2"""	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.963G>A	9.37:g.37436755G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Silent	SNP	ENST00000318158.6	37	CCDS6609.1																																																																																			G|0.992;A|0.008	0.008	strong		0.557	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203	
PRUNE2	158471	hgsc.bcm.edu	37	9	79325558	79325558	+	Silent	SNP	G	G	C	rs600859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79325558G>C	ENST00000376718.3	-	8	1755	c.1632C>G	c.(1630-1632)acC>acG	p.T544T	PRUNE2_ENST00000428286.1_Silent_p.T185T	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	544					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TAGACATGTTGGTTCCCATGC	0.502													G|||	2419	0.483027	0.2708	0.6383	5008	,	,		20546	0.4504		0.5974	False		,,,				2504	0.5757				p.T544T		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C1632G						PASS	.	G		1092,2044		226,640,702	37.0	33.0	34.0		1632	2.2	0.0	9	dbSNP_83	34	4416,2748		1366,1684,532	no	coding-synonymous	PRUNE2	NM_015225.2		1592,2324,1234	CC,CG,GG		38.3585,34.8214,46.5243		544/3089	79325558	5508,4792	1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			CATGTTGGTTCCC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.1632C>G	9.37:g.79325558G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1																																																																																			A|0.001;C|0.522;G|0.477	0.522	strong		0.502	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
LILRA4	23547	hgsc.bcm.edu	37	19	54848684	54848684	+	Silent	SNP	G	G	A	rs8105624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54848684G>A	ENST00000291759.4	-	5	995	c.939C>T	c.(937-939)gaC>gaT	p.D313D	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	313	Ig-like C2-type 3.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CGATCAGGATGTCCAGGGGGT	0.677													G|||	986	0.196885	0.1611	0.2075	5008	,	,		13174	0.2609		0.2008	False		,,,				2504	0.1677				p.D313D		Atlas-SNP	.											.	LILRA4	91	.	0			c.C939T						PASS	.	G		715,3681		62,591,1545	24.0	26.0	25.0		939	0.4	0.5	19	dbSNP_116	25	1651,6921		173,1305,2808	no	coding-synonymous	LILRA4	NM_012276.3		235,1896,4353	AA,AG,GG		19.2604,16.2648,18.2449		313/500	54848684	2366,10602	2198	4286	6484	SO:0001819	synonymous_variant	23547	exon5			CAGGATGTCCAGG	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.939C>T	19.37:g.54848684G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	149	85	0.57047	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			G|0.821;A|0.179	0.179	strong		0.677	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
KANK1	23189	hgsc.bcm.edu	37	9	732536	732536	+	Missense_Mutation	SNP	T	T	C	rs34832656	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:732536T>C	ENST00000382303.1	+	10	3816	c.3164T>C	c.(3163-3165)aTt>aCt	p.I1055T	KANK1_ENST00000382293.3_Missense_Mutation_p.I897T|KANK1_ENST00000382297.2_Missense_Mutation_p.I1055T|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1055			I -> T (in dbSNP:rs34832656).		negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GCAGTTAATATTGAAGGTTTG	0.478													T|||	631	0.125998	0.1929	0.2075	5008	,	,		19155	0.004		0.174	False		,,,				2504	0.0542				p.I1055T		Atlas-SNP	.											.	KANK1	231	.	0			c.T3164C						PASS	.	T	THR/ILE,THR/ILE	821,3585	328.0+/-300.3	84,653,1466	191.0	169.0	176.0		3164,2690	0.2	0.1	9	dbSNP_126	176	1521,7079	285.4+/-297.1	151,1219,2930	yes	missense,missense	KANK1	NM_015158.2,NM_153186.3	89,89	235,1872,4396	CC,CT,TT		17.686,18.6337,18.0071	benign,benign	1055/1353,897/1195	732536	2342,10664	2203	4300	6503	SO:0001583	missense	23189	exon10			TTAATATTGAAGG	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.3164T>C	9.37:g.732536T>C	ENSP00000371740:p.Ile1055Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	112	71	0.633929	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	283	0.1295787545787546	83	0.16869918699186992	76	0.20994475138121546	2	0.0034965034965034965	122	0.16094986807387862	T	0.359	-0.940718	0.02322	0.186337	0.17686	ENSG00000107104	ENST00000382303;ENST00000397976;ENST00000382297;ENST00000382293;ENST00000382289	T;T;T	0.44881	0.91;0.91;0.91	5.62	0.228	0.15364	.	1.292170	0.05556	N	0.568328	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.15930	0.004;0.015	B;B	0.17433	0.018;0.014	T	0.18587	-1.0332	9	0.12103	T	0.63	0.1227	0.3629	0.00367	0.3558:0.1491:0.2364:0.2587	rs34832656	78;1055	F5H7I5;Q14678	.;KANK1_HUMAN	T	1055;78;1055;897;10	ENSP00000371740:I1055T;ENSP00000371734:I1055T;ENSP00000371730:I897T	ENSP00000371726:I10T	I	+	2	0	KANK1	722536	0.000000	0.05858	0.097000	0.21041	0.994000	0.84299	0.214000	0.17541	0.080000	0.16959	-0.259000	0.10710	ATT	T|0.838;C|0.162	0.162	strong		0.478	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
ZBTB40	9923	hgsc.bcm.edu	37	1	22852715	22852715	+	Silent	SNP	G	G	C	rs881646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22852715G>C	ENST00000375647.4	+	18	3753	c.3546G>C	c.(3544-3546)ccG>ccC	p.P1182P	ZBTB40_ENST00000374651.4_Silent_p.P1070P|ZBTB40_ENST00000404138.1_Silent_p.P1182P	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	1182					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		CCCCAGAGCCGGTGGCCCCGA	0.557													G|||	1593	0.318091	0.1225	0.2205	5008	,	,		17902	0.4692		0.3936	False		,,,				2504	0.4182				p.P1182P		Atlas-SNP	.											.	ZBTB40	87	.	0			c.G3546C						PASS	.	G	,	704,3702	293.3+/-282.5	61,582,1560	75.0	76.0	76.0		3546,3546	-11.4	0.0	1	dbSNP_86	76	3172,5428	479.8+/-370.2	572,2028,1700	no	coding-synonymous,coding-synonymous	ZBTB40	NM_001083621.1,NM_014870.3	,	633,2610,3260	CC,CG,GG		36.8837,15.9782,29.8016	,	1182/1240,1182/1240	22852715	3876,9130	2203	4300	6503	SO:0001819	synonymous_variant	9923	exon19			AGAGCCGGTGGCC	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.3546G>C	1.37:g.22852715G>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_001083621	O75066|Q5TFU5|Q8N1R1	Silent	SNP	ENST00000375647.4	37	CCDS224.1																																																																																			G|0.692;C|0.308	0.308	strong		0.557	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870	
HERC2	8924	hgsc.bcm.edu	37	15	28419746	28419746	+	Silent	SNP	G	G	A	rs139335991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28419746G>A	ENST00000261609.7	-	65	9960	c.9852C>T	c.(9850-9852)aaC>aaT	p.N3284N		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GGCCGTGGTCGTTGTCACCCC	0.458																																					p.N3284N		Atlas-SNP	.											.	HERC2	501	.	0			c.C9852T						PASS	.						56.0	39.0	45.0					15																	28419746		2202	4279	6481	SO:0001819	synonymous_variant	8924	exon65			GTGGTCGTTGTCA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9852C>T	15.37:g.28419746G>A		Somatic	636	0	0		WXS	Illumina HiSeq	Phase_I	516	46	0.0891473	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.942;A|0.058	0.058	strong		0.458	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
FOXD4	2298	hgsc.bcm.edu	37	9	117696	117696	+	Missense_Mutation	SNP	G	G	A	rs9406415	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:117696G>A	ENST00000382500.2	-	1	721	c.424C>T	c.(424-426)Cgc>Tgc	p.R142C		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	142					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		AACTTGCGGCGGTAGTAGGGG	0.642																																					p.R142C		Atlas-SNP	.											FOXD4_ENST00000382500,brain,glioma,0,1	FOXD4	75	1	0			c.C424T						PASS	.						41.0	68.0	59.0					9																	117696		2097	4163	6260	SO:0001583	missense	2298	exon1			TGCGGCGGTAGTA	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.424C>T	9.37:g.117696G>A	ENSP00000371940:p.Arg142Cys	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	238	151	0.634454	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	477	0.2184065934065934	82	0.16666666666666666	67	0.1850828729281768	135	0.23601398601398602	193	0.2546174142480211	.	15.82	2.945410	0.53079	.	.	ENSG00000170122	ENST00000382500	D	0.96491	-4.03	2.24	2.24	0.28232	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.35870	U	0.002927	T	0.00754	0.0025	M	0.94021	3.485	0.09310	P	0.99999602235	D	0.89917	1.0	D	0.81914	0.995	T	0.00289	-1.1844	9	0.56958	D	0.05	.	4.7852	0.13222	0.0:0.2374:0.5208:0.2418	rs9406415	142	Q12950	FOXD4_HUMAN	C	142	ENSP00000371940:R142C	ENSP00000371940:R142C	R	-	1	0	FOXD4	107696	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	1.314000	0.33597	1.253000	0.44018	0.291000	0.19559	CGC	G|0.778;A|0.222	0.222	strong		0.642	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
TMEM132E	124842	hgsc.bcm.edu	37	17	32962050	32962050	+	Missense_Mutation	SNP	C	C	T	rs75594429	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:32962050C>T	ENST00000321639.5	+	8	1979	c.1651C>T	c.(1651-1653)Cac>Tac	p.H551Y		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	551						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CCGAGTGGCACACATGGTGGA	0.632													C|||	55	0.0109824	0.0008	0.0187	5008	,	,		17260	0.0		0.0358	False		,,,				2504	0.0051				p.H551Y		Atlas-SNP	.											.	TMEM132E	122	.	0			c.C1651T						PASS	.	C	TYR/HIS	21,4385	28.1+/-56.4	0,21,2182	63.0	51.0	55.0		1651	5.2	1.0	17	dbSNP_131	55	273,8327	103.6+/-164.7	3,267,4030	yes	missense	TMEM132E	NM_207313.1	83	3,288,6212	TT,TC,CC		3.1744,0.4766,2.2605	benign	551/985	32962050	294,12712	2203	4300	6503	SO:0001583	missense	124842	exon8			GTGGCACACATGG	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1651C>T	17.37:g.32962050C>T	ENSP00000316532:p.His551Tyr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	33	0.01510989010989011	0	0.0	7	0.019337016574585635	0	0.0	26	0.03430079155672823	C	16.88	3.244653	0.59103	0.004766	0.031744	ENSG00000181291	ENST00000321639	T	0.42131	0.98	5.22	5.22	0.72569	.	0.437153	0.26331	N	0.024989	T	0.12433	0.0302	N	0.22421	0.69	0.42271	D	0.992056	B	0.23540	0.087	B	0.24394	0.053	T	0.04551	-1.0943	10	0.62326	D	0.03	-18.2352	13.6575	0.62346	0.0:0.8452:0.1548:0.0	.	551	Q6IEE7	T132E_HUMAN	Y	551	ENSP00000316532:H551Y	ENSP00000316532:H551Y	H	+	1	0	TMEM132E	29986163	0.068000	0.21057	0.996000	0.52242	0.997000	0.91878	1.410000	0.34691	2.725000	0.93324	0.498000	0.49722	CAC	C|0.979;T|0.021	0.021	strong		0.632	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
MAP4K3	8491	hgsc.bcm.edu	37	2	39583446	39583446	+	Silent	SNP	A	A	G	rs8545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:39583446A>G	ENST00000263881.3	-	3	513	c.189T>C	c.(187-189)atT>atC	p.I63I	MAP4K3_ENST00000341681.5_Silent_p.I63I|MAP4K3_ENST00000484274.1_Silent_p.I63I|MAP4K3_ENST00000437545.1_5'UTR	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	63	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				CTTTCATCATAATAATTTCTT	0.308													A|||	3466	0.692093	0.3169	0.7378	5008	,	,		17698	0.8472		0.9026	False		,,,				2504	0.7904				p.I63I		Atlas-SNP	.											.	MAP4K3	109	.	0			c.T189C						PASS	.	A		1836,2570	533.4+/-373.7	402,1032,769	176.0	190.0	185.0		189	2.9	1.0	2	dbSNP_116	185	7706,888	777.5+/-407.7	3463,780,54	no	coding-synonymous	MAP4K3	NM_003618.2		3865,1812,823	GG,GA,AA		10.3328,41.6704,26.6		63/895	39583446	9542,3458	2203	4297	6500	SO:0001819	synonymous_variant	8491	exon3			CATCATAATAATT	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.189T>C	2.37:g.39583446A>G		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	237	237	1	NM_001270425	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Silent	SNP	ENST00000263881.3	37	CCDS1803.1																																																																																			A|0.276;G|0.724	0.724	strong		0.308	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	
TTN	7273	hgsc.bcm.edu	37	2	179582738	179582738	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179582738C>T	ENST00000591111.1	-	84	24268	c.24044G>A	c.(24043-24045)gGa>gAa	p.G8015E	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.G7088E|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.G8332E			Q8WZ42	TITIN_HUMAN	titin	12207	Ig-like 62.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGAATACTCTCCCACATCACT	0.418																																					p.G8332E		Atlas-SNP	.											.	TTN	18412	.	0			c.G24995A						PASS	.						209.0	199.0	202.0					2																	179582738		2017	4178	6195	SO:0001583	missense	7273	exon86			TACTCTCCCACAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24044G>A	2.37:g.179582738C>T	ENSP00000465570:p.Gly8015Glu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	152	80	0.526316	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	12.42	1.934003	0.34096	.	.	ENSG00000155657	ENST00000342992	D	0.86956	-2.19	6.03	6.03	0.97812	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.97012	0.9024	H	0.99545	4.62	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98008	1.0364	9	0.87932	D	0	.	20.5753	0.99366	0.0:1.0:0.0:0.0	.	8015	Q8WZ42	TITIN_HUMAN	E	7088	ENSP00000343764:G7088E	ENSP00000343764:G7088E	G	-	2	0	TTN	179290983	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	6.027000	0.70881	2.868000	0.98415	0.557000	0.71058	GGA	.	.	none		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511793	99511793	+	Missense_Mutation	SNP	C	C	G	rs1521484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:99511793C>G	ENST00000378919.6	-	5	710	c.505G>C	c.(505-507)Gaa>Caa	p.E169Q	PGPEP1L_ENST00000535714.1_Missense_Mutation_p.E115Q|RP11-654A16.3_ENST00000559468.1_RNA	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	169			E -> Q (in dbSNP:rs1521484).				cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						TCCAGCATTTCCTGGATGATG	0.587													C|||	2220	0.443291	0.1581	0.4914	5008	,	,		17547	0.4841		0.5726	False		,,,				2504	0.6196				p.E169Q		Atlas-SNP	.											.	PGPEP1L	26	.	0			c.G505C						PASS	.	C	GLN/GLU,GLN/GLU	811,3067		85,641,1213	46.0	45.0	45.0		505,343	2.5	0.2	15	dbSNP_88	45	4275,3985		1098,2079,953	yes	missense,missense	PGPEP1L	NM_001102612.2,NM_001167902.1	29,29	1183,2720,2166	GG,GC,CC		48.2446,20.9128,41.9015	probably-damaging,probably-damaging	169/197,115/143	99511793	5086,7052	1939	4130	6069	SO:0001583	missense	145814	exon5			GCATTTCCTGGAT		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.505G>C	15.37:g.99511793C>G	ENSP00000368199:p.Glu169Gln	Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	227	111	0.488987	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	968	0.4432234432234432	83	0.16869918699186992	181	0.5	281	0.49125874125874125	423	0.558047493403694	C	13.24	2.178331	0.38511	0.209128	0.517554	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.30981	1.51	5.39	2.51	0.30379	.	0.377447	0.26704	N	0.022923	T	0.00012	0.0000	N	0.19112	0.55	0.51482	P	7.599999999996498E-5	P	0.39665	0.682	B	0.40199	0.322	T	0.38845	-0.9642	9	0.19147	T	0.46	-10.9564	10.1423	0.42742	0.0:0.786:0.0:0.214	rs1521484;rs1521484	169	A6NFU8	PGPIL_HUMAN	Q	169;162	ENSP00000368199:E169Q	ENSP00000368199:E169Q	E	-	1	0	PGPEP1L	97329316	0.022000	0.18835	0.213000	0.23690	0.357000	0.29423	1.000000	0.29770	0.273000	0.22049	-0.140000	0.14226	GAA	C|0.537;G|0.463	0.463	strong		0.587	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
TMEM8A	58986	hgsc.bcm.edu	37	16	424277	424277	+	Missense_Mutation	SNP	G	G	A	rs3743887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:424277G>A	ENST00000431232.2	-	10	1859	c.1699C>T	c.(1699-1701)Cgg>Tgg	p.R567W	TMEM8A_ENST00000476735.1_5'Flank|TMEM8A_ENST00000250930.3_Missense_Mutation_p.R374W	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	567			R -> W (in dbSNP:rs3743887). {ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						AAGAATCGCCGCACTGAGACG	0.652											OREG0003702	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	717	0.143171	0.1415	0.0879	5008	,	,		17240	0.0903		0.0547	False		,,,				2504	0.3303				p.R567W		Atlas-SNP	.											.	TMEM8A	49	.	0			c.C1699T						PASS	.	G	TRP/ARG	626,3776	262.8+/-265.1	45,536,1620	72.0	73.0	73.0		1699	0.3	0.0	16	dbSNP_107	73	580,8018	153.0+/-207.5	27,526,3746	yes	missense	TMEM8A	NM_021259.2	101	72,1062,5366	AA,AG,GG		6.7458,14.2208,9.2769	possibly-damaging	567/772	424277	1206,11794	2201	4299	6500	SO:0001583	missense	58986	exon10			ATCGCCGCACTGA	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.1699C>T	16.37:g.424277G>A	ENSP00000401338:p.Arg567Trp	Somatic	66	0	0	588	WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	212	0.09706959706959707	78	0.15853658536585366	39	0.10773480662983426	53	0.09265734265734266	42	0.055408970976253295	G	9.543	1.113770	0.20795	0.142208	0.067458	ENSG00000129925	ENST00000431232;ENST00000250930;ENST00000382942;ENST00000448854	T;T;T	0.54479	0.57;0.57;0.57	3.6	0.256	0.15567	.	0.762179	0.11817	N	0.526653	T	0.00271	0.0008	L	0.60455	1.87	0.80722	P	0.0	P	0.51240	0.943	P	0.48030	0.564	T	0.06917	-1.0800	9	0.51188	T	0.08	-3.3777	7.3435	0.26650	0.5326:0.0:0.4674:0.0	rs3743887;rs57468879;rs3743887	567	Q9HCN3	TMM8A_HUMAN	W	567;374;94;115	ENSP00000401338:R567W;ENSP00000250930:R374W;ENSP00000401931:R115W	ENSP00000250930:R374W	R	-	1	2	TMEM8A	364278	0.038000	0.19896	0.003000	0.11579	0.002000	0.02628	1.484000	0.35508	0.243000	0.21327	0.563000	0.77884	CGG	G|0.897;A|0.103	0.103	strong		0.652	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
DLG5	9231	hgsc.bcm.edu	37	10	79579222	79579222	+	Splice_Site	SNP	G	G	A	rs1248634	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:79579222G>A	ENST00000372391.2	-	17	3533	c.3528C>T	c.(3526-3528)ggC>ggT	p.G1176G	DLG5_ENST00000372388.2_Splice_Site_p.G836G|DLG5_ENST00000459739.1_5'UTR	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1176					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GGGGAACAGTGCCTAGAAATG	0.607													G|||	1279	0.255391	0.0908	0.4625	5008	,	,		16812	0.2917		0.2753	False		,,,				2504	0.273				p.G1176G		Atlas-SNP	.											.	DLG5	154	.	0			c.C3528T						PASS	.	G		572,3834	252.1+/-258.6	46,480,1677	43.0	45.0	44.0		3528	2.5	1.0	10	dbSNP_87	44	2379,6221	395.4+/-345.0	322,1735,2243	yes	coding-synonymous-near-splice	DLG5	NM_004747.3		368,2215,3920	AA,AG,GG		27.6628,12.9823,22.6895		1176/1920	79579222	2951,10055	2203	4300	6503	SO:0001630	splice_region_variant	9231	exon17			AACAGTGCCTAGA	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.3527-1C>T	10.37:g.79579222G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			G|0.756;T|0.003	.	strong		0.607	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		Silent
TBX21	30009	hgsc.bcm.edu	37	17	45811210	45811210	+	Silent	SNP	A	A	G	rs2074190	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45811210A>G	ENST00000177694.1	+	1	601	c.390A>G	c.(388-390)ggA>ggG	p.G130G		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	130					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						TACCCGCGGGACTGGAGGTGT	0.672													G|||	1411	0.281749	0.292	0.3429	5008	,	,		11923	0.1121		0.2644	False		,,,				2504	0.4172				p.G130G		Atlas-SNP	.											TBX21,NS,carcinoma,0,1	TBX21	50	1	0			c.A390G						PASS	.	G		1049,2771		151,747,1012	16.0	18.0	18.0		390	3.5	1.0	17	dbSNP_96	18	2149,6061		257,1635,2213	no	coding-synonymous	TBX21	NM_013351.1		408,2382,3225	GG,GA,AA		26.1754,27.4607,26.5835		130/536	45811210	3198,8832	1910	4105	6015	SO:0001819	synonymous_variant	30009	exon1			CGCGGGACTGGAG	AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"""T-boxes"""	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.390A>G	17.37:g.45811210A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_013351		Silent	SNP	ENST00000177694.1	37	CCDS11514.1																																																																																			A|0.750;G|0.250	0.250	strong		0.672	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351	
MADCAM1	8174	hgsc.bcm.edu	37	19	504830	504830	+	Silent	SNP	C	C	G	rs7246543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:504830C>G	ENST00000215637.3	+	5	1060	c.1014C>G	c.(1012-1014)acC>acG	p.T338T	MADCAM1_ENST00000587541.1_Silent_p.T119T|MADCAM1_ENST00000346144.4_Silent_p.T251T|TPGS1_ENST00000359315.5_5'Flank|MADCAM1_ENST00000382683.4_Silent_p.T156T|AC005775.2_ENST00000592413.1_RNA	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	338					aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTTGCCCACCTATCACCTCT	0.662													C|||	1568	0.313099	0.3517	0.4121	5008	,	,		15635	0.2093		0.2763	False		,,,				2504	0.3354				p.T338T		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C1014G						PASS	.	C	,	1435,2971	460.9+/-352.8	222,991,990	46.0	47.0	47.0		1014,753	3.0	0.0	19	dbSNP_116	47	2814,5786	440.1+/-359.4	483,1848,1969	no	coding-synonymous,coding-synonymous	MADCAM1	NM_130760.2,NM_130762.2	,	705,2839,2959	GG,GC,CC		32.7209,32.5692,32.6695	,	338/383,251/296	504830	4249,8757	2203	4300	6503	SO:0001819	synonymous_variant	8174	exon5			GCCCACCTATCAC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.1014C>G	19.37:g.504830C>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	204	71	0.348039	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Silent	SNP	ENST00000215637.3	37	CCDS12028.1																																																																																			C|0.687;G|0.312;T|0.001	0.312	strong		0.662	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32714143	32714143	+	Missense_Mutation	SNP	G	G	A	rs2071800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32714143G>A	ENST00000374940.3	+	4	842	c.740G>A	c.(739-741)gGt>gAt	p.G247D		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	247			G -> D (in dbSNP:rs2071800). {ECO:0000269|PubMed:14574404}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	CGTTCAGTTGGTGCTTCCAGA	0.517													.|||	296	0.0591054	0.0325	0.0375	5008	,	,		21628	0.0546		0.0736	False		,,,				2504	0.1002				p.G247D		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.G740A						PASS	.	G	ASP/GLY	148,2874		1,146,1364	142.0	141.0	142.0		740	-3.1	0.0	6	dbSNP_96	142	386,5032		10,366,2333	yes	missense	HLA-DQA2	NM_020056.4	94	11,512,3697	AA,AG,GG		7.1244,4.8974,6.327	benign	247/256	32714143	534,7906	1511	2709	4220	SO:0001583	missense	3118	exon4			CAGTTGGTGCTTC		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.740G>A	6.37:g.32714143G>A	ENSP00000364076:p.Gly247Asp	Somatic	535	2	0.00373832		WXS	Illumina HiSeq	Phase_I	719	278	0.386648	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	108	0.04945054945054945	16	0.032520325203252036	16	0.04419889502762431	22	0.038461538461538464	54	0.0712401055408971	.	3.059	-0.193674	0.06259	0.048974	0.071244	ENSG00000237541	ENST00000374940	T	0.01933	4.55	3.06	-3.13	0.05266	.	1.442540	0.04321	N	0.350653	T	0.00666	0.0022	L	0.31294	0.92	0.09310	N	1	B	0.18968	0.032	B	0.24394	0.053	T	0.48399	-0.9039	10	0.52906	T	0.07	.	4.2912	0.10879	0.2477:0.352:0.4003:0.0	rs2071800;rs17219764;rs57727560;rs2071800	247	P01906	DQA2_HUMAN	D	247	ENSP00000364076:G247D	ENSP00000364076:G247D	G	+	2	0	HLA-DQA2	32822121	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-1.147000	0.03188	-0.949000	0.03663	0.174000	0.16983	GGT	G|0.944;A|0.056	0.056	strong		0.517	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
GLP1R	2740	hgsc.bcm.edu	37	6	39040654	39040654	+	Silent	SNP	A	A	C	rs2235868	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:39040654A>C	ENST00000373256.4	+	6	569	c.526A>C	c.(526-528)Agg>Cgg	p.R176R		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	176					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.R176R(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	GCACTGCACCAGGAACTACAT	0.547													C|||	2230	0.445288	0.3147	0.536	5008	,	,		23141	0.4444		0.5209	False		,,,				2504	0.4806				p.R176R		Atlas-SNP	.											GLP1R,NS,carcinoma,0,1	GLP1R	64	1	1	Substitution - coding silent(1)	stomach(1)	c.A526C						PASS	.	C		1527,2879	673.6+/-402.8	270,987,946	193.0	155.0	168.0		526	4.7	1.0	6	dbSNP_98	168	4497,4103	562.9+/-388.0	1191,2115,994	no	coding-synonymous	GLP1R	NM_002062.3		1461,3102,1940	CC,CA,AA		47.7093,34.6573,46.3171		176/464	39040654	6024,6982	2203	4300	6503	SO:0001819	synonymous_variant	2740	exon6			TGCACCAGGAACT		CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"""GPCR / Class B : Glucagon receptors"""	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.526A>C	6.37:g.39040654A>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_002062	Q2M229|Q99669	Silent	SNP	ENST00000373256.4	37	CCDS4839.1																																																																																			A|0.542;C|0.458	0.458	strong		0.547	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507251	195507251	+	Missense_Mutation	SNP	G	G	T	rs201456607|rs74187968		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507251G>T	ENST00000463781.3	-	2	11659	c.11200C>A	c.(11200-11202)Cct>Act	p.P3734T	MUC4_ENST00000475231.1_Missense_Mutation_p.P3734T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGGGCTGGTGACA	0.572																																					p.P3734T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C11200A						scavenged	.						47.0	43.0	44.0					3																	195507251		609	1585	2194	SO:0001583	missense	4585	exon2			AGGAAGGGCTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11200C>A	3.37:g.195507251G>T	ENSP00000417498:p.Pro3734Thr	Somatic	57	15	0.263158		WXS	Illumina HiSeq	Phase_I	317	137	0.432177	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.012	-1.684417	0.00745	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27104	1.69;1.8	0.885	-1.77	0.07982	.	0.000000	0.25517	N	0.030134	T	0.08447	0.0210	N	0.14661	0.345	0.09310	N	1	B	0.31931	0.347	B	0.23574	0.047	T	0.28267	-1.0049	9	.	.	.	.	0.0845	0.00034	0.324:0.235:0.2063:0.2347	.	3606	E7ESK3	.	T	3734	ENSP00000417498:P3734T;ENSP00000420243:P3734T	.	P	-	1	0	MUC4	196992030	0.004000	0.15560	0.001000	0.08648	0.004000	0.04260	0.115000	0.15540	-2.731000	0.00384	-2.446000	0.00210	CCT	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SAGE1	55511	hgsc.bcm.edu	37	X	134994054	134994054	+	Silent	SNP	G	G	A	rs4829584	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:134994054G>A	ENST00000370709.3	+	17	2463	c.2463G>A	c.(2461-2463)aaG>aaA	p.K821K	SAGE1_ENST00000535938.1_Silent_p.K821K|SAGE1_ENST00000324447.3_Silent_p.K821K|SAGE1_ENST00000537770.1_Silent_p.K445K			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	821						nucleus (GO:0005634)		p.I823fs*5(1)		breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CCATGGCAAAGAAAATTAATG	0.373													g|||	373	0.0988079	0.0265	0.121	3775	,	,		15260	0.0615		0.1531	False		,,,				2504	0.0389				p.K821K		Atlas-SNP	.											.	SAGE1	160	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.G2463A						PASS	.	G		174,3661		3,146,22,1483,549	54.0	52.0	52.0		2463	-0.5	0.0	X	dbSNP_111	52	1251,5476		92,737,330,1599,1541	no	coding-synonymous	SAGE1	NM_018666.2		95,883,352,3082,2090	AA,AG,A,GG,G		18.5967,4.5372,13.4918		821/905	134994054	1425,9137	2203	4299	6502	SO:0001819	synonymous_variant	55511	exon18			GGCAAAGAAAATT	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.2463G>A	X.37:g.134994054G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			0|0.004;A|0.130	0.130	strong		0.373	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
EPHA8	2046	hgsc.bcm.edu	37	1	22915858	22915858	+	Intron	SNP	C	C	T	rs76452513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22915858C>T	ENST00000166244.3	+	5	1387				EPHA8_ENST00000374644.4_Missense_Mutation_p.L492F|EPHA8_ENST00000538803.1_Missense_Mutation_p.L492F	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.L492F(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCTGGAGGCTCTTCATTGCCT	0.552													C|||	468	0.0934505	0.0779	0.0576	5008	,	,		18884	0.0486		0.0815	False		,,,				2504	0.1984				p.L492F		Atlas-SNP	.											EPHA8_ENST00000374644,NS,carcinoma,0,1	EPHA8	221	1	1	Substitution - Missense(1)	stomach(1)	c.C1474T						scavenged	.	C	PHE/LEU,	352,4046		18,316,1865	41.0	45.0	44.0		1474,	-2.5	0.0	1	dbSNP_131	44	598,7988		28,542,3723	yes	missense,intron	EPHA8	NM_001006943.1,NM_020526.3	22,	46,858,5588	TT,TC,CC		6.9648,8.0036,7.3167	,	492/496,	22915858	950,12034	2199	4293	6492	SO:0001627	intron_variant	2046	exon5			GAGGCTCTTCATT	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1315+159C>T	1.37:g.22915858C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	NM_001006943	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	129	0.059065934065934064	31	0.06300813008130081	24	0.06629834254143646	20	0.03496503496503497	54	0.0712401055408971	C	6.257	0.415574	0.11870	0.080036	0.069648	ENSG00000070886	ENST00000374644;ENST00000538803	T;T	0.01406	4.93;4.93	2.86	-2.54	0.06307	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.45833	-0.9234	7	.	.	.	.	7.8641	0.29526	0.0:0.2774:0.0:0.7226	.	492	P29322-2	.	F	492	ENSP00000363775:L492F;ENSP00000440274:L492F	.	L	+	1	0	EPHA8	22788445	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-1.468000	0.02350	-0.663000	0.05331	0.491000	0.48974	CTT	C|0.929;T|0.071	0.071	strong		0.552	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
FOXJ3	22887	hgsc.bcm.edu	37	1	42657196	42657196	+	Missense_Mutation	SNP	T	T	G	rs1139978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:42657196T>G	ENST00000372572.1	-	11	1440	c.1129A>C	c.(1129-1131)Aca>Cca	p.T377P	FOXJ3_ENST00000545068.1_Missense_Mutation_p.T377P|FOXJ3_ENST00000372571.1_5'Flank|FOXJ3_ENST00000372573.1_Missense_Mutation_p.T377P|FOXJ3_ENST00000361776.1_Missense_Mutation_p.T343P|FOXJ3_ENST00000361346.1_Missense_Mutation_p.T377P	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	377			T -> P (in dbSNP:rs1139978). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:15489334}.		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GATGGCTGTGTGTGCATCTGG	0.587													T|||	248	0.0495208	0.0159	0.0692	5008	,	,		19544	0.001		0.1262	False		,,,				2504	0.0521				p.T377P		Atlas-SNP	.											.	FOXJ3	59	.	0			c.A1129C						PASS	.	T	PRO/THR,PRO/THR,PRO/THR,PRO/THR	139,4267	98.5+/-137.1	0,139,2064	492.0	396.0	429.0		1129,1129,1027,1129	4.2	1.0	1	dbSNP_86	429	1245,7355	250.1+/-277.1	79,1087,3134	yes	missense,missense,missense,missense	FOXJ3	NM_001198850.1,NM_001198851.1,NM_001198852.1,NM_014947.4	38,38,38,38	79,1226,5198	GG,GT,TT		14.4767,3.1548,10.6412	benign,benign,benign,benign	377/623,377/623,343/589,377/623	42657196	1384,11622	2203	4300	6503	SO:0001583	missense	22887	exon11			GCTGTGTGTGCAT	AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"""Forkhead boxes"""	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.1129A>C	1.37:g.42657196T>G	ENSP00000361653:p.Thr377Pro	Somatic	562	2	0.00355872		WXS	Illumina HiSeq	Phase_I	462	177	0.383117	NM_001198851	A7MBL7|A7MD18|D3DPW2|Q9NSS7	Missense_Mutation	SNP	ENST00000372572.1	37	CCDS30689.1	137	0.06272893772893773	9	0.018292682926829267	33	0.09116022099447514	0	0.0	95	0.12532981530343007	T	14.26	2.481602	0.44147	0.031548	0.144767	ENSG00000198815	ENST00000372573;ENST00000372572;ENST00000361346;ENST00000361776;ENST00000545068;ENST00000445886	T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98	5.31	4.16	0.48862	.	14.840200	0.00166	N	0.000011	T	0.00210	0.0006	N	0.08118	0	0.34303	P	0.315465	B;P	0.37466	0.0;0.596	B;B	0.31614	0.0;0.133	T	0.14504	-1.0470	9	0.34782	T	0.22	.	11.0239	0.47734	0.0:0.0:0.1557:0.8443	rs1139978;rs3204084;rs60629335;rs1139978	343;377	Q9UPW0-2;Q9UPW0	.;FOXJ3_HUMAN	P	377;377;377;343;377;343	ENSP00000361654:T377P;ENSP00000361653:T377P;ENSP00000354620:T377P;ENSP00000354449:T343P;ENSP00000439044:T377P;ENSP00000393408:T343P	ENSP00000354620:T377P	T	-	1	0	FOXJ3	42429783	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	0.808000	0.27154	0.925000	0.37094	0.454000	0.30748	ACA	T|0.907;G|0.093	0.093	strong		0.587	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1	NM_014947	
OR8S1	341568	hgsc.bcm.edu	37	12	48919796	48919796	+	Missense_Mutation	SNP	C	C	T	rs12425460	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48919796C>T	ENST00000310194.1	+	1	382	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	128			R -> C (in dbSNP:rs12425460).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						TGCCATCTGCCGCCCACTACT	0.547													C|||	2899	0.578874	0.4879	0.6599	5008	,	,		20053	0.6895		0.5139	False		,,,				2504	0.5971				p.R128C		Atlas-SNP	.											.	OR8S1	47	.	0			c.C382T						PASS	.	C	CYS/ARG	2183,2223	586.1+/-386.4	519,1145,539	133.0	121.0	125.0		382	3.1	1.0	12	dbSNP_120	125	4568,4032	597.4+/-393.8	1210,2148,942	yes	missense	OR8S1	NM_001005203.2	180	1729,3293,1481	TT,TC,CC		46.8837,49.5461,48.0932	benign	128/360	48919796	6751,6255	2203	4300	6503	SO:0001583	missense	341568	exon1			ATCTGCCGCCCAC		CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"""GPCR / Class A : Olfactory receptors"""	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.382C>T	12.37:g.48919796C>T	ENSP00000310632:p.Arg128Cys	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	222	221	0.995495	NM_001005203		Missense_Mutation	SNP	ENST00000310194.1	37	CCDS31789.1	1296	0.5934065934065934	238	0.483739837398374	237	0.6546961325966851	409	0.715034965034965	412	0.5435356200527705	C	11.62	1.691514	0.30052	0.495461	0.531163	ENSG00000197376	ENST00000310194	T	0.01347	4.99	5.03	3.07	0.35406	GPCR, rhodopsin-like superfamily (1);	0.165039	0.29139	N	0.013025	T	0.00012	0.0000	L	0.33485	1.01	0.33610	P	0.396579	B	0.10296	0.003	B	0.08055	0.003	T	0.11372	-1.0590	9	0.72032	D	0.01	-31.9331	8.0558	0.30604	0.1665:0.7433:0.0:0.0902	rs12425460;rs56692529;rs12425460	128	Q8NH09	OR8S1_HUMAN	C	128	ENSP00000310632:R128C	ENSP00000310632:R128C	R	+	1	0	OR8S1	47206063	0.000000	0.05858	1.000000	0.80357	0.771000	0.43674	-0.820000	0.04457	1.345000	0.45676	-0.137000	0.14449	CGC	C|0.456;T|0.544	0.544	strong		0.547	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
SCRIB	23513	hgsc.bcm.edu	37	8	144875242	144875242	+	Silent	SNP	C	C	T	rs11784217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144875242C>T	ENST00000320476.3	-	29	3927	c.3921G>A	c.(3919-3921)ccG>ccA	p.P1307P	RP11-429J17.8_ENST00000532625.1_RNA|SCRIB_ENST00000546337.1_5'UTR|SCRIB_ENST00000377533.3_Silent_p.P1226P|RP11-429J17.8_ENST00000527139.1_RNA|RP11-429J17.8_ENST00000534089.1_RNA|SCRIB_ENST00000356994.2_Silent_p.P1307P	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1307	Pro-rich.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCGGAGAAGGCGGGGAGGGCG	0.692													C|||	45	0.00898562	0.0008	0.0058	5008	,	,		9927	0.001		0.0378	False		,,,				2504	0.001				p.P1307P	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.G3921A						PASS	.	C	,	17,4061		0,17,2022	9.0	10.0	9.0		3921,3921	-4.8	0.8	8	dbSNP_120	9	158,7884		1,156,3864	no	coding-synonymous,coding-synonymous	SCRIB	NM_015356.3,NM_182706.3	,	1,173,5886	TT,TC,CC		1.9647,0.4169,1.4439	,	1307/1631,1307/1656	144875242	175,11945	2039	4021	6060	SO:0001819	synonymous_variant	23513	exon29			AGAAGGCGGGGAG	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.3921G>A	8.37:g.144875242C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1	35	0.016025641025641024	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	32	0.04221635883905013	C	2.044	-0.419390	0.04766	0.004169	0.019647	ENSG00000180900	ENST00000526832	.	.	.	4.1	-4.79	0.03200	.	.	.	.	.	T	0.18509	0.0444	.	.	.	0.52099	D	0.999942	.	.	.	.	.	.	T	0.37150	-0.9718	4	.	.	.	.	7.2565	0.26179	0.1088:0.3813:0.0:0.5099	rs11784217;rs11784217	.	.	.	T	303	.	.	A	-	1	0	SCRIB	144947230	0.000000	0.05858	0.764000	0.31436	0.184000	0.23303	-3.067000	0.00620	-1.243000	0.02519	0.298000	0.19748	GCC	C|0.983;T|0.017	0.017	strong		0.692	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
MGA	23269	hgsc.bcm.edu	37	15	42026764	42026764	+	Silent	SNP	C	C	T	rs1918314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42026764C>T	ENST00000570161.1	+	11	3888	c.3888C>T	c.(3886-3888)gaC>gaT	p.D1296D	MGA_ENST00000545763.1_Silent_p.D1296D|MGA_ENST00000389936.4_Silent_p.D1296D|MGA_ENST00000219905.7_Silent_p.D1296D|MGA_ENST00000566586.1_Silent_p.D1296D			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCACCTGTGACTTGGAGGATG	0.328													C|||	3747	0.748203	0.5386	0.8242	5008	,	,		18640	0.8919		0.8161	False		,,,				2504	0.7597				p.D1296D		Atlas-SNP	.											.	MGA	264	.	0			c.C3888T						PASS	.	C	,	2071,1573		582,907,333	58.0	52.0	54.0		3888,3888	0.9	0.8	15	dbSNP_92	54	6615,1549		2689,1237,156	no	coding-synonymous,coding-synonymous	MGA	NM_001080541.2,NM_001164273.1	,	3271,2144,489	TT,TC,CC		18.9735,43.1668,26.4397	,	1296/2857,1296/3066	42026764	8686,3122	1822	4082	5904	SO:0001819	synonymous_variant	23269	exon12			CTGTGACTTGGAG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.3888C>T	15.37:g.42026764C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																			C|0.228;T|0.772	0.772	strong		0.328	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
TTC21A	199223	hgsc.bcm.edu	37	3	39161464	39161464	+	Missense_Mutation	SNP	G	G	A	rs1274971	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:39161464G>A	ENST00000431162.2	+	8	1011	c.877G>A	c.(877-879)Gaa>Aaa	p.E293K	TTC21A_ENST00000440121.1_Missense_Mutation_p.E244K|TTC21A_ENST00000301819.6_Missense_Mutation_p.E293K			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	293			E -> K (in dbSNP:rs1274971).							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AAGGGAACCCGAAAATCCAAG	0.443													G|||	2282	0.455671	0.8495	0.3429	5008	,	,		18210	0.2738		0.334	False		,,,				2504	0.316				p.E293K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G877A						PASS	.	G	LYS/GLU,LYS/GLU	2790,932		1038,714,109	106.0	114.0	111.0		730,877	3.9	0.9	3	dbSNP_87	111	2786,5410		485,1816,1797	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	56,56	1523,2530,1906	AA,AG,GG		33.9922,25.0403,46.7864	benign,benign	244/1273,293/1321	39161464	5576,6342	1861	4098	5959	SO:0001583	missense	199223	exon8			GAACCCGAAAATC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.877G>A	3.37:g.39161464G>A	ENSP00000398211:p.Glu293Lys	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	152	88	0.578947	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	959	0.4391025641025641	410	0.8333333333333334	133	0.3674033149171271	166	0.2902097902097902	250	0.32981530343007914	G	11.56	1.675769	0.29783	0.749597	0.339922	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.56941	0.43;0.43;2.34	5.67	3.86	0.44501	.	0.701416	0.13630	N	0.373771	T	0.00012	0.0000	N	0.02916	-0.46	0.47094	P	6.859999999999644E-4	B;B;B	0.27498	0.01;0.18;0.113	B;B;B	0.16722	0.004;0.016;0.007	T	0.39781	-0.9597	9	0.02654	T	1	-0.0123	15.4035	0.74861	0.0:0.7314:0.2686:0.0	rs1274971;rs17735053;rs57380373;rs1274971	244;293;293	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	293;285;293;244	ENSP00000301819:E293K;ENSP00000398211:E293K;ENSP00000410882:E244K	ENSP00000301819:E293K	E	+	1	0	TTC21A	39136468	0.956000	0.32656	0.881000	0.34555	0.486000	0.33341	1.922000	0.40045	0.746000	0.32786	-0.147000	0.13772	GAA	G|0.552;A|0.448	0.448	strong		0.443	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
SPG7	6687	hgsc.bcm.edu	37	16	89620328	89620328	+	Missense_Mutation	SNP	G	G	A	rs12960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:89620328G>A	ENST00000268704.2	+	15	2078	c.2063G>A	c.(2062-2064)cGg>cAg	p.R688Q		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	688			R -> Q (neutral polymorphism; dbSNP:rs12960). {ECO:0000269|PubMed:16534102, ECO:0000269|PubMed:20186691}.		anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		GGCATCGGGCGGCGCCCCTTC	0.667													G|||	530	0.105831	0.0098	0.1124	5008	,	,		14832	0.131		0.166	False		,,,				2504	0.1431				p.R688Q		Atlas-SNP	.											.	SPG7	75	.	0			c.G2063A						PASS	.	G	GLN/ARG	165,4231	108.6+/-147.0	3,159,2036	71.0	63.0	65.0		2063	5.2	1.0	16	dbSNP_52	65	1667,6931	299.4+/-304.4	149,1369,2781	yes	missense	SPG7	NM_003119.2	43	152,1528,4817	AA,AG,GG		19.3882,3.7534,14.0988	probably-damaging	688/796	89620328	1832,11162	2198	4299	6497	SO:0001583	missense	6687	exon15			TCGGGCGGCGCCC	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.2063G>A	16.37:g.89620328G>A	ENSP00000268704:p.Arg688Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	37	CCDS10977.1	257	0.11767399267399267	8	0.016260162601626018	43	0.11878453038674033	76	0.13286713286713286	130	0.17150395778364116	G	22.2	4.264034	0.80358	0.037534	0.193882	ENSG00000197912	ENST00000268704	D	0.83163	-1.69	5.21	5.21	0.72293	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	T	0.00241	0.0007	N	0.17631	0.505	0.09310	P	1.0	P	0.43826	0.818	B	0.37780	0.258	T	0.13469	-1.0508	9	0.21014	T	0.42	-17.3655	17.776	0.88508	0.0:0.0:1.0:0.0	rs12960;rs730263;rs1801445;rs16965809;rs17354997;rs12960	688	Q9UQ90	SPG7_HUMAN	Q	688	ENSP00000268704:R688Q	ENSP00000268704:R688Q	R	+	2	0	SPG7	88147829	1.000000	0.71417	0.985000	0.45067	0.586000	0.36452	9.423000	0.97461	2.423000	0.82170	0.563000	0.77884	CGG	G|0.871;A|0.129	0.129	strong		0.667	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14780019	14780019	+	Splice_Site	SNP	G	G	T	rs72873710		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:14780019G>T	ENST00000358984.4	+	11	1661	c.1481G>T	c.(1480-1482)gGg>gTg	p.G494V	ANKRD30B_ENST00000447268.2_Splice_Site_p.G494V|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	494										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						TGGGATTCTGGGGTATTGTGT	0.343																																					p.G494V		Atlas-SNP	.											ANKRD30B_ENST00000358984,caecum,carcinoma,0,4	ANKRD30B	237	4	0			c.G1481T						PASS	.						193.0	177.0	182.0					18																	14780019		692	1591	2283	SO:0001630	splice_region_variant	374860	exon11			ATTCTGGGGTATT	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.1482+1G>T	18.37:g.14780019G>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	19	0.193878	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	37	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	N	3.547	-0.092527	0.07053	.	.	ENSG00000180777	ENST00000358984;ENST00000447268	T;T	0.32988	1.43;1.48	1.69	0.336	0.15958	.	.	.	.	.	T	0.12050	0.0293	N	0.14661	0.345	0.23487	N	0.997578	P	0.50710	0.938	B	0.34931	0.192	T	0.15037	-1.0451	9	0.41790	T	0.15	.	3.5662	0.07900	0.7813:0.0:0.2187:0.0	.	494	F8WAG3	.	V	494	ENSP00000351875:G494V;ENSP00000399031:G494V	ENSP00000351875:G494V	G	+	2	0	ANKRD30B	14770019	1.000000	0.71417	0.341000	0.25589	0.044000	0.14063	0.507000	0.22675	0.156000	0.19299	-0.734000	0.03567	GGG	.	.	strong		0.343	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	Missense_Mutation
HLA-C	3107	hgsc.bcm.edu	37	6	31238931	31238931	+	Silent	SNP	G	G	A	rs697743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31238931G>A	ENST00000376228.5	-	3	552	c.538C>T	c.(538-540)Ctg>Ttg	p.L180L	HLA-C_ENST00000383329.3_Silent_p.L180L	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	180	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.L180L(2)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TAGGCTCTCAGCTGCTCCGCC	0.682													g|||	595	0.11881	0.0749	0.0634	5008	,	,		11367	0.0853		0.1342	False		,,,				2504	0.2362				p.L180L		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,4	HLA-C	92	4	2	Substitution - coding silent(2)	prostate(2)	c.C538T						PASS	.						43.0	30.0	34.0					6																	31238931		2197	4291	6488	SO:0001819	synonymous_variant	3107	exon3			CTCTCAGCTGCTC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.538C>T	6.37:g.31238931G>A		Somatic	411	0	0		WXS	Illumina HiSeq	Phase_I	361	98	0.271468	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	4.195	0.034910	0.08101	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	-5.62	0.02481	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.20638	N	0.999871	.	.	.	.	.	.	T	0.03566	-1.1024	4	.	.	.	.	2.8574	0.05576	0.25:0.4691:0.1066:0.1744	rs697743;rs2308591;rs3176036;rs3179868;rs3200237;rs3204480;rs12721958;rs17839941;rs28732104	.	.	.	V	179	.	.	A	-	2	0	HLA-C	31346910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-12.042000	0.00002	-4.714000	0.00035	-1.872000	0.00552	GCT	G|0.777;C|0.108;A|0.115	0.115	strong		0.682	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SENP6	26054	hgsc.bcm.edu	37	6	76376552	76376552	+	Silent	SNP	G	G	A	rs17414687	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:76376552G>A	ENST00000447266.2	+	10	1597	c.1119G>A	c.(1117-1119)gcG>gcA	p.A373A	SENP6_ENST00000370014.3_Silent_p.A373A|SENP6_ENST00000541192.1_5'Flank|SENP6_ENST00000327284.8_Silent_p.A366A|SENP6_ENST00000370010.2_Silent_p.A366A	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	373					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TAGAAGCAGCGCTAAATGAAA	0.428													G|||	893	0.178315	0.1014	0.2046	5008	,	,		12943	0.0466		0.329	False		,,,				2504	0.2444				p.A373A		Atlas-SNP	.											SENP6_ENST00000447266,NS,carcinoma,0,2	SENP6	189	2	0			c.G1119A						PASS	.	G	,	491,3351		35,421,1465	125.0	121.0	122.0		1098,1119	-1.7	1.0	6	dbSNP_123	122	2944,5302		525,1894,1704	no	coding-synonymous,coding-synonymous	SENP6	NM_001100409.1,NM_015571.2	,	560,2315,3169	AA,AG,GG		35.7022,12.7798,28.4166	,	366/1106,373/1113	76376552	3435,8653	1921	4123	6044	SO:0001819	synonymous_variant	26054	exon10			AGCAGCGCTAAAT		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1119G>A	6.37:g.76376552G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Silent	SNP	ENST00000447266.2	37	CCDS47454.1																																																																																			G|0.773;A|0.227	0.227	strong		0.428	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
DDX60L	91351	hgsc.bcm.edu	37	4	169327191	169327191	+	Silent	SNP	C	C	T	rs3762856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:169327191C>T	ENST00000511577.1	-	24	3370	c.3123G>A	c.(3121-3123)aaG>aaA	p.K1041K	DDX60L_ENST00000505890.1_Silent_p.K1041K|DDX60L_ENST00000260184.7_Silent_p.K1041K			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1041							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TAATGACTATCTTATTCTTAA	0.303													T|||	1636	0.326677	0.1944	0.2867	5008	,	,		17223	0.4048		0.3489	False		,,,				2504	0.4305				p.K1041K		Atlas-SNP	.											.	DDX60L	116	.	0			c.G3123A						PASS	.	T		721,2901		75,571,1165	86.0	73.0	77.0		3123	2.5	0.5	4	dbSNP_107	77	2547,5665		402,1743,1961	no	coding-synonymous	DDX60L	NM_001012967.1		477,2314,3126	TT,TC,CC		31.0156,19.9061,27.6153		1041/1707	169327191	3268,8566	1811	4106	5917	SO:0001819	synonymous_variant	91351	exon24			GACTATCTTATTC	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3123G>A	4.37:g.169327191C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.674;T|0.326	0.326	strong		0.303	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
URGCP	55665	hgsc.bcm.edu	37	7	43917013	43917013	+	Silent	SNP	G	G	A	rs2232105	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43917013G>A	ENST00000453200.1	-	6	2542	c.2049C>T	c.(2047-2049)caC>caT	p.H683H	URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_Silent_p.H640H|URGCP_ENST00000223341.7_Silent_p.H640H|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000402306.3_Silent_p.H674H|URGCP_ENST00000443736.1_Silent_p.H640H|URGCP_ENST00000336086.6_Silent_p.H640H			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	683					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCAGTCGGACGTGCAGCTCCT	0.637													G|||	2466	0.492412	0.326	0.5173	5008	,	,		19545	0.5764		0.4602	False		,,,				2504	0.6462				p.H683H		Atlas-SNP	.											.	URGCP	170	.	0			c.C2049T						PASS	.	G	,,,	1341,2899		221,899,1000	31.0	34.0	33.0		2049,1920,,2022	-6.7	0.0	7	dbSNP_98	33	4003,4463		973,2057,1203	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	,,,	1194,2956,2203	AA,AG,GG		47.2833,31.6274,42.0589	,,,	683/932,640/889,,674/923	43917013	5344,7362	2120	4233	6353	SO:0001819	synonymous_variant	55665	exon6			TCGGACGTGCAGC		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2049C>T	7.37:g.43917013G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Silent	SNP	ENST00000453200.1	37	CCDS47578.1																																																																																			G|0.529;A|0.471	0.471	strong		0.637	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
GRIN3B	116444	hgsc.bcm.edu	37	19	1004724	1004724	+	Silent	SNP	A	A	G	rs11880849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1004724A>G	ENST00000234389.3	+	3	1243	c.1224A>G	c.(1222-1224)ccA>ccG	p.P408P	AC004528.4_ENST00000588380.1_RNA|GRIN3B_ENST00000588335.1_Intron	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	408					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCCCGCCCCCACAGGGTGCCC	0.706													a|||	1334	0.266374	0.3154	0.2392	5008	,	,		12262	0.0893		0.3698	False		,,,				2504	0.2955				p.P408P		Atlas-SNP	.											.	GRIN3B	46	.	0			c.A1224G						PASS	.	A		1417,2963		232,953,1005	21.0	22.0	22.0		1224	-4.3	0.0	19	dbSNP_120	22	3172,5406		603,1966,1720	no	coding-synonymous	GRIN3B	NM_138690.1		835,2919,2725	GG,GA,AA		36.9783,32.3516,35.4144		408/1044	1004724	4589,8369	2190	4289	6479	SO:0001819	synonymous_variant	116444	exon3			GCCCCCACAGGGT		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1224A>G	19.37:g.1004724A>G		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			A|0.692;G|0.308	0.308	strong		0.706	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
CCR8	1237	hgsc.bcm.edu	37	3	39373902	39373902	+	Missense_Mutation	SNP	C	C	G	rs2853699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:39373902C>G	ENST00000326306.4	+	2	218	c.80C>G	c.(79-81)gCg>gGg	p.A27G	CCR8_ENST00000545843.1_Missense_Mutation_p.R2G|CCR8_ENST00000414803.1_Missense_Mutation_p.A27G	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	27			A -> G (in dbSNP:rs2853699). {ECO:0000269|PubMed:12551893}.		cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		CCCTGTGATGCGGAACTTATT	0.478													C|||	649	0.129593	0.1014	0.1628	5008	,	,		19549	0.002		0.2982	False		,,,				2504	0.1022				p.A27G		Atlas-SNP	.											.	CCR8	34	.	0			c.C80G						PASS	.	C	GLY/ALA	635,3771	273.4+/-271.3	57,521,1625	195.0	173.0	181.0		80	-3.2	0.0	3	dbSNP_100	181	2611,5989	422.9+/-354.2	402,1807,2091	yes	missense	CCR8	NM_005201.3	60	459,2328,3716	GG,GC,CC		30.3605,14.4122,24.9577	benign	27/356	39373902	3246,9760	2203	4300	6503	SO:0001583	missense	1237	exon2			GTGATGCGGAACT	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.80C>G	3.37:g.39373902C>G	ENSP00000326432:p.Ala27Gly	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	216	130	0.601852	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Missense_Mutation	SNP	ENST00000326306.4	37	CCDS2684.1	347|347	0.15888278388278387|0.15888278388278387	57|57	0.11585365853658537|0.11585365853658537	73|73	0.20165745856353592|0.20165745856353592	0|0	0.0|0.0	217|217	0.2862796833773087|0.2862796833773087	C|C	9.150|9.150	1.016035|1.016035	0.19355|0.19355	0.144122|0.144122	0.303605|0.303605	ENSG00000179934|ENSG00000179934	ENST00000326306;ENST00000414803|ENST00000545843	T;T|T	0.20200|0.67345	2.09;2.09|-0.26	4.84|4.84	-3.17|-3.17	0.05202|0.05202	.|.	1.810430|.	0.02947|.	N|.	0.141190|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.04013|0.08055	0.001|0.003	T|T	0.18429|0.18429	-1.0337|-1.0337	9|7	0.36615|.	T|.	0.2|.	.|.	2.32|2.32	0.04208|0.04208	0.3225:0.3806:0.1841:0.1127|0.3225:0.3806:0.1841:0.1127	rs2853699;rs52818746;rs61481415;rs2853699|rs2853699;rs52818746;rs61481415;rs2853699	27|2	P51685|Q3KNR3	CCR8_HUMAN|.	G|G	27|2	ENSP00000326432:A27G;ENSP00000390104:A27G|ENSP00000440474:R2G	ENSP00000326432:A27G|.	A|R	+|+	2|1	0|2	CCR8|CCR8	39348906|39348906	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.012000|0.012000	0.07955|0.07955	-1.350000|-1.350000	0.02624|0.02624	-0.487000|-0.487000	0.06735|0.06735	-1.325000|-1.325000	0.01285|0.01285	GCG|CGG	C|0.791;G|0.209	0.209	strong		0.478	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201	
EFTUD1	79631	hgsc.bcm.edu	37	15	82444663	82444663	+	Missense_Mutation	SNP	T	T	C	rs2292071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:82444663T>C	ENST00000268206.7	-	18	2300	c.2132A>G	c.(2131-2133)aAa>aGa	p.K711R	EFTUD1_ENST00000359445.3_Missense_Mutation_p.K660R	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	711			K -> R (in dbSNP:rs2292071).		GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						TTTTTGCTGTTTGCCTATTTC	0.373													T|||	868	0.173323	0.3661	0.0663	5008	,	,		19602	0.2123		0.0676	False		,,,				2504	0.0573				p.K711R		Atlas-SNP	.											.	EFTUD1	74	.	0			c.A2132G						PASS	.	T	ARG/LYS,ARG/LYS	1103,2613		166,771,921	188.0	189.0	189.0		1979,2132	-0.7	0.8	15	dbSNP_100	189	451,7749		13,425,3662	yes	missense,missense	EFTUD1	NM_001040610.2,NM_024580.5	26,26	179,1196,4583	CC,CT,TT		5.5,29.6825,13.0413	benign,benign	660/1070,711/1121	82444663	1554,10362	1858	4100	5958	SO:0001583	missense	79631	exon18			TGCTGTTTGCCTA	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"""ribosome assembly 1 homolog (yeast)"""					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.2132A>G	15.37:g.82444663T>C	ENSP00000268206:p.Lys711Arg	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Missense_Mutation	SNP	ENST00000268206.7	37	CCDS42071.1	349	0.15979853479853479	163	0.3313008130081301	21	0.058011049723756904	114	0.1993006993006993	51	0.06728232189973615	T	13.63	2.295052	0.40594	0.296825	0.055	ENSG00000140598	ENST00000268206;ENST00000359445	T;T	0.26660	1.72;1.72	5.94	-0.711	0.11230	Ribosomal protein S5 domain 2-type fold (1);	0.404113	0.19501	N	0.112734	T	0.00012	0.0000	N	0.25485	0.75	0.21822	P	0.999520864	B;B	0.10296	0.002;0.003	B;B	0.15052	0.012;0.004	T	0.47623	-0.9103	9	0.26408	T	0.33	-1.1557	10.1311	0.42680	0.0:0.3857:0.0:0.6143	rs2292071;rs52810129;rs60840055;rs2292071	660;711	Q7Z2Z2-2;Q7Z2Z2	.;ETUD1_HUMAN	R	711;660	ENSP00000268206:K711R;ENSP00000352418:K660R	ENSP00000268206:K711R	K	-	2	0	EFTUD1	80231718	1.000000	0.71417	0.835000	0.33067	0.974000	0.67602	1.488000	0.35551	-0.371000	0.08004	-0.371000	0.07208	AAA	T|0.844;C|0.156	0.156	strong		0.373	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580	
AKAP11	11215	hgsc.bcm.edu	37	13	42872779	42872779	+	Silent	SNP	C	C	T	rs2273951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:42872779C>T	ENST00000025301.2	+	7	637	c.462C>T	c.(460-462)taC>taT	p.Y154Y		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	154					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		GTATAAGGTACACCTTGGACA	0.403													C|||	570	0.113818	0.0416	0.1297	5008	,	,		16782	0.123		0.1272	False		,,,				2504	0.1769				p.Y154Y		Atlas-SNP	.											.	AKAP11	146	.	0			c.C462T						PASS	.	C		281,4125	157.0+/-190.0	13,255,1935	192.0	164.0	174.0		462	0.9	1.0	13	dbSNP_100	174	1321,7279	259.9+/-283.0	94,1133,3073	no	coding-synonymous	AKAP11	NM_016248.3		107,1388,5008	TT,TC,CC		15.3605,6.3777,12.3174		154/1902	42872779	1602,11404	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon7			AAGGTACACCTTG	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.462C>T	13.37:g.42872779C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	135	67	0.496296	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			C|0.887;T|0.113	0.113	strong		0.403	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
GLOD4	51031	hgsc.bcm.edu	37	17	685752	685752	+	5'Flank	SNP	G	G	A	rs2249542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:685752G>A	ENST00000301328.5	-	0	0				GLOD4_ENST00000301329.6_5'Flank|RNMTL1_ENST00000304478.4_Missense_Mutation_p.G45E|GLOD4_ENST00000536578.1_5'Flank			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TTTCCTTCCGGAGAGGTGGTG	0.657													G|||	763	0.152356	0.0469	0.1787	5008	,	,		16019	0.0923		0.2525	False		,,,				2504	0.2352				p.G45E		Atlas-SNP	.											.	RNMTL1	25	.	0			c.G134A						PASS	.	G	GLU/GLY	377,4029	186.7+/-213.5	21,335,1847	35.0	38.0	37.0		134	5.5	0.6	17	dbSNP_100	37	2255,6345	371.1+/-336.1	316,1623,2361	yes	missense	RNMTL1	NM_018146.2	98	337,1958,4208	AA,AG,GG		26.2209,8.5565,20.2368	benign	45/421	685752	2632,10374	2203	4300	6503	SO:0001631	upstream_gene_variant	55178	exon1			CTTCCGGAGAGGT	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38			17.37:g.685752G>A	Exception_encountered	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_018146	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	37		349|349	0.15979853479853479|0.15979853479853479	30|30	0.06097560975609756|0.06097560975609756	72|72	0.19889502762430938|0.19889502762430938	54|54	0.0944055944055944|0.0944055944055944	193|193	0.2546174142480211|0.2546174142480211	G|G	21.0|21.0	4.081462|4.081462	0.76528|0.76528	0.085565|0.085565	0.262209|0.262209	ENSG00000171861|ENSG00000167699	ENST00000304478|ENST00000397393	T|.	0.17370|.	2.28|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	0.624563|.	0.16419|.	N|.	0.215225|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.42245|0.42245	1.32|1.32	0.27102|0.27102	P|P	0.9625959|0.9625959	B|.	0.29909|.	0.261|.	B|.	0.22880|.	0.042|.	T|T	0.09684|0.09684	-1.0663|-1.0663	9|5	0.02654|0.87932	T|D	1|0	.|.	11.7682|11.7682	0.51943|0.51943	0.0814:0.0:0.9186:0.0|0.0814:0.0:0.9186:0.0	rs2249542;rs17617499;rs28969601;rs52825357;rs2249542|rs2249542;rs17617499;rs28969601;rs52825357;rs2249542	45|.	Q9HC36|.	RMTL1_HUMAN|.	E|S	45|121	ENSP00000306080:G45E|.	ENSP00000306080:G45E|ENSP00000380548:P121S	G|P	+|-	2|1	0|0	RNMTL1|GLOD4	632502|632502	0.433000|0.433000	0.25562|0.25562	0.592000|0.592000	0.28758|0.28758	0.600000|0.600000	0.36913|0.36913	1.415000|1.415000	0.34748|0.34748	2.737000|2.737000	0.93849|0.93849	0.563000|0.563000	0.77884|0.77884	GGA|CCG	G|0.824;A|0.175	0.175	strong		0.657	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
IGF2BP3	10643	hgsc.bcm.edu	37	7	23357321	23357321	+	Silent	SNP	C	C	T	rs156414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:23357321C>T	ENST00000258729.3	-	12	1688	c.1332G>A	c.(1330-1332)gcG>gcA	p.A444A		NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	444	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)	p.A444A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						CTGGTGCTTCCGCTGGAGCAA	0.463													C|||	1225	0.244609	0.0136	0.2435	5008	,	,		20362	0.3671		0.3946	False		,,,				2504	0.2771				p.A444A		Atlas-SNP	.											IGF2BP3,NS,carcinoma,0,1	IGF2BP3	71	1	1	Substitution - coding silent(1)	stomach(1)	c.G1332A						PASS	.	C		364,4042		37,290,1876	203.0	158.0	173.0		1332	-4.7	1.0	7	dbSNP_79	173	3525,5075		727,2071,1502	no	coding-synonymous	IGF2BP3	NM_006547.2		764,2361,3378	TT,TC,CC		40.9884,8.2615,29.9016		444/580	23357321	3889,9117	2203	4300	6503	SO:0001819	synonymous_variant	10643	exon12			TGCTTCCGCTGGA	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"""RNA binding motif (RRM) containing"""	28868	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 3"", ""cancer/testis antigen 98"""	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.1332G>A	7.37:g.23357321C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	199	92	0.462312	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Silent	SNP	ENST00000258729.3	37	CCDS5382.1																																																																																			T|0.301;G|0.001;C|0.698;N|0.000	0.301	strong		0.463	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547	
TAS1R1	80835	hgsc.bcm.edu	37	1	6635306	6635306	+	Missense_Mutation	SNP	G	G	A	rs34160967	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:6635306G>A	ENST00000333172.6	+	3	1307	c.1114G>A	c.(1114-1116)Gca>Aca	p.A372T	TAS1R1_ENST00000328191.4_Missense_Mutation_p.A372T|TAS1R1_ENST00000351136.3_Intron	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	372			A -> T (in dbSNP:rs34160967).		detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		AGCTTTCATGGCACACACGAT	0.592													G|||	678	0.135383	0.0582	0.0648	5008	,	,		20875	0.3204		0.1223	False		,,,				2504	0.1125				p.A372T		Atlas-SNP	.											TAS1R1,caecum,carcinoma,0,1	TAS1R1	76	1	0			c.G1114A						PASS	.	G	THR/ALA,	304,4102	154.8+/-188.1	17,270,1916	65.0	53.0	57.0		1114,	-0.6	0.0	1	dbSNP_126	57	1080,7520	217.7+/-256.3	69,942,3289	yes	missense,intron	TAS1R1	NM_138697.3,NM_177540.2	58,	86,1212,5205	AA,AG,GG		12.5581,6.8997,10.6412	benign,	372/842,	6635306	1384,11622	2203	4300	6503	SO:0001583	missense	80835	exon3			TTCATGGCACACA		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14448	protein-coding gene	gene with protein product		606225	"""G protein-coupled receptor 70"""	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.1114G>A	1.37:g.6635306G>A	ENSP00000331867:p.Ala372Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	144	83	0.576389	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	37	CCDS81.1	334|334	0.15293040293040294|0.15293040293040294	23|23	0.046747967479674794|0.046747967479674794	26|26	0.0718232044198895|0.0718232044198895	197|197	0.34440559440559443|0.34440559440559443	88|88	0.11609498680738786|0.11609498680738786	G|G	1.258|1.258	-0.616607|-0.616607	0.03663|0.03663	0.068997|0.068997	0.125581|0.125581	ENSG00000173662|ENSG00000173662	ENST00000333172;ENST00000328191|ENST00000411823	D;D|.	0.91237|.	-2.43;-2.81|.	5.24|5.24	-0.638|-0.638	0.11500|0.11500	Extracellular ligand-binding receptor (1);|.	1.364240|.	0.04390|.	N|.	0.362231|.	T|.	0.00012|.	0.0000|.	L|L	0.33753|0.33753	1.03|1.03	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.32467|.	0.372;0.158|.	B;B|.	0.28784|.	0.076;0.094|.	T|.	0.43114|.	-0.9411|.	9|.	0.09338|.	T|.	0.73|.	.|.	4.9085|4.9085	0.13811|0.13811	0.3505:0.3088:0.3407:0.0|0.3505:0.3088:0.3407:0.0	rs34160967;rs57648522|rs34160967;rs57648522	372;372|.	Q7RTX1-3;Q7RTX1|.	.;TS1R1_HUMAN|.	T|X	372|297	ENSP00000331867:A372T;ENSP00000327705:A372T|.	ENSP00000327705:A372T|.	A|W	+|+	1|3	0|0	TAS1R1|TAS1R1	6557893|6557893	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	-0.147000|-0.147000	0.10234|0.10234	0.160000|0.160000	0.19432|0.19432	-0.218000|-0.218000	0.12543|0.12543	GCA|TGG	G|0.871;A|0.129	0.129	strong		0.592	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1		
BTN2A1	11120	hgsc.bcm.edu	37	6	26463575	26463575	+	Missense_Mutation	SNP	G	G	T	rs34505465|rs13195402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26463575G>T	ENST00000312541.5	+	4	782	c.534G>T	c.(532-534)tgG>tgT	p.W178C	BTN2A1_ENST00000469185.1_Missense_Mutation_p.W178C|BTN2A1_ENST00000541522.1_Missense_Mutation_p.W117C|BTN2A1_ENST00000429381.1_Missense_Mutation_p.W178C	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	178			W -> C (in dbSNP:rs13195402).|W -> L (in dbSNP:rs13195401).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						TCACAGTGTGGAGGGACCCCT	0.587													G|||	120	0.0239617	0.0227	0.0303	5008	,	,		17982	0.0		0.0686	False		,,,				2504	0.0				p.W178C		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G534T						PASS	.	G	CYS/TRP,CYS/TRP,CYS/TRP,CYS/TRP	136,4270	88.7+/-127.4	3,130,2070	83.0	78.0	79.0		351,534,534,534	2.9	0.4	6	dbSNP_121	79	686,7914	160.0+/-213.2	29,628,3643	yes	missense,missense,missense,missense	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	215,215,215,215	32,758,5713	TT,TG,GG		7.9767,3.0867,6.3202	probably-damaging,probably-damaging,probably-damaging,probably-damaging	117/467,178/331,178/528,178/335	26463575	822,12184	2203	4300	6503	SO:0001583	missense	11120	exon4			AGTGTGGAGGGAC	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.534G>T	6.37:g.26463575G>T	ENSP00000312158:p.Trp178Cys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	61	0.027930402930402932	8	0.016260162601626018	10	0.027624309392265192	0	0.0	43	0.05672823218997362	G	11.93	1.784342	0.31593	0.030867	0.079767	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	2.88	2.88	0.33553	CD80-like, immunoglobulin C2-set (1);	0.000000	0.50627	D	0.000118	T	0.79879	0.4522	M	0.89658	3.05	0.51482	D	0.999928	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.83168	-0.0095	10	0.62326	D	0.03	.	11.9438	0.52915	0.0:0.0:1.0:0.0	rs13195402;rs13195402	178;178	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	C	178;117;178;178;178	ENSP00000312158:W178C;ENSP00000443909:W117C;ENSP00000416945:W178C;ENSP00000419043:W178C	ENSP00000265424:W178C	W	+	3	0	BTN2A1	26571554	1.000000	0.71417	0.394000	0.26270	0.142000	0.21351	5.311000	0.65786	1.896000	0.54893	0.561000	0.74099	TGG	G|0.952;T|0.048	0.048	strong		0.587	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
FAR1	84188	hgsc.bcm.edu	37	11	13734555	13734555	+	Silent	SNP	T	T	C	rs12798176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:13734555T>C	ENST00000354817.3	+	8	1074	c.930T>C	c.(928-930)acT>acC	p.T310T	FAR1_ENST00000527202.1_3'UTR	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	310					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						CAGGCAGCACTAATCCTTTCC	0.343													T|||	77	0.0153754	0.0053	0.0216	5008	,	,		15449	0.0		0.0487	False		,,,				2504	0.0061				p.T310T		Atlas-SNP	.											.	FAR1	40	.	0			c.T930C						PASS	.	T		46,4354	46.7+/-81.2	1,44,2155	242.0	236.0	238.0		930	1.9	1.0	11	dbSNP_121	238	423,8165	131.5+/-189.3	13,397,3884	no	coding-synonymous	FAR1	NM_032228.5		14,441,6039	CC,CT,TT		4.9255,1.0455,3.611		310/516	13734555	469,12519	2200	4294	6494	SO:0001819	synonymous_variant	84188	exon8			CAGCACTAATCCT	AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	26222	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 10E, member 1"""		"""male sterility domain containing 2"""	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.930T>C	11.37:g.13734555T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	177	77	0.435028	NM_032228	D3DQW8|Q5CZA3	Silent	SNP	ENST00000354817.3	37	CCDS7813.1																																																																																			T|0.967;C|0.033	0.033	strong		0.343	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228	
EPDR1	54749	hgsc.bcm.edu	37	7	37988589	37988589	+	Silent	SNP	C	C	T	rs2044831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:37988589C>T	ENST00000199448.4	+	2	796	c.417C>T	c.(415-417)atC>atT	p.I139I	EPDR1_ENST00000476620.1_Silent_p.I37I|EPDR1_ENST00000425345.1_Silent_p.I78I|EPDR1_ENST00000559325.1_Silent_p.I259I|EPDR1_ENST00000423717.1_Intron	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	139					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						AGTACTCCATCGGGGGGCCTC	0.512													C|||	3300	0.658946	0.5098	0.7493	5008	,	,		16813	0.5933		0.7813	False		,,,				2504	0.7382				p.I139I		Atlas-SNP	.											EPDR1,caecum,carcinoma,0,1	EPDR1	48	1	0			c.C417T						PASS	.	C		2486,1920	625.9+/-394.6	710,1066,427	92.0	90.0	91.0		777	-4.3	1.0	7	dbSNP_94	91	6606,1994	722.8+/-406.4	2540,1526,234	no	coding-synonymous	EPDR1	NM_017549.4		3250,2592,661	TT,TC,CC		23.186,43.5769,30.0938		259/345	37988589	9092,3914	2203	4300	6503	SO:0001819	synonymous_variant	54749	exon2			CTCCATCGGGGGG	BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"""ependymin related protein 1 (zebrafish)"""			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.417C>T	7.37:g.37988589C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_017549	A8K4C0|C9JYS3|Q06BL0|Q99M77	Silent	SNP	ENST00000199448.4	37	CCDS5454.2																																																																																			C|0.322;T|0.678	0.678	strong		0.512	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549	
SMG6	23293	hgsc.bcm.edu	37	17	2203453	2203453	+	Silent	SNP	A	A	G	rs216193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:2203453A>G	ENST00000263073.6	-	2	644	c.594T>C	c.(592-594)gcT>gcC	p.A198A	SMG6_ENST00000544865.1_Silent_p.A167A	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	198	Interaction with telomeric DNA.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTTCTATCTCAGCCCTGTCTG	0.512													A|||	2727	0.544529	0.3487	0.6282	5008	,	,		17729	0.6806		0.6133	False		,,,				2504	0.5389				p.A198A	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.T594C						PASS	.	A	,	1825,2581	534.8+/-374.1	375,1075,753	232.0	253.0	246.0		501,594	-3.6	0.0	17	dbSNP_79	246	5364,3236	650.3+/-400.7	1697,1970,633	no	coding-synonymous,coding-synonymous	SMG6	NM_001170957.1,NM_017575.4	,	2072,3045,1386	GG,GA,AA		37.6279,41.4208,44.7255	,	167/1389,198/1420	2203453	7189,5817	2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			TATCTCAGCCCTG	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.594T>C	17.37:g.2203453A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	37	CCDS11016.1																																																																																			A|0.439;G|0.561	0.561	strong		0.512	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
ENTHD2	146705	hgsc.bcm.edu	37	17	79205736	79205736	+	Silent	SNP	G	G	A	rs11655759	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79205736G>A	ENST00000300714.3	-	8	669	c.612C>T	c.(610-612)agC>agT	p.S204S	ENTHD2_ENST00000374769.2_Silent_p.S120S|AC027601.1_ENST00000575922.1_RNA|AC027601.1_ENST00000569559.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	204	Ser-rich.					cytoplasmic vesicle (GO:0031410)											TGCTCAGGTCGCTGTTCTGGG	0.662													G|||	872	0.174121	0.1014	0.2493	5008	,	,		16639	0.0536		0.3857	False		,,,				2504	0.1258				p.S204S		Atlas-SNP	.											.	.	.	.	0			c.C612T						PASS	.	G		661,3745	279.0+/-274.6	55,551,1597	60.0	67.0	65.0		612	-8.4	0.0	17	dbSNP_120	65	3298,5302	487.1+/-372.0	653,1992,1655	no	coding-synonymous	C17orf56	NM_144679.2		708,2543,3252	AA,AG,GG		38.3488,15.0023,30.4398		204/526	79205736	3959,9047	2203	4300	6503	SO:0001819	synonymous_variant	146705	exon8			CAGGTCGCTGTTC	AK056090	CCDS11779.1	17q25.3	2012-07-18	2012-07-18	2012-07-18	ENSG00000167302	ENSG00000167302			26458	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 56"""	C17orf56			Standard	NM_144679		Approved	FLJ31528	uc002jzu.2	Q96N21	OTTHUMG00000177866	ENST00000300714.3:c.612C>T	17.37:g.79205736G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	164	70	0.426829	NM_144679	Q6ZQU0|Q6ZSQ9	Silent	SNP	ENST00000300714.3	37	CCDS11779.1																																																																																			G|0.729;A|0.271	0.271	strong		0.662	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679	
PLEK	5341	hgsc.bcm.edu	37	2	68607984	68607984	+	Missense_Mutation	SNP	G	G	T	rs147263237		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:68607984G>T	ENST00000234313.7	+	3	507	c.328G>T	c.(328-330)Gcc>Tcc	p.A110S		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	110					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)	p.A110T(1)		autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		CCAGAAATTTGCCAGGAAATC	0.478																																					p.A110S		Atlas-SNP	.											PLEK,NS,carcinoma,0,2	PLEK	64	2	1	Substitution - Missense(1)	endometrium(1)	c.G328T						PASS	.	G	SER/ALA	0,4406		0,0,2203	143.0	137.0	139.0		328	2.9	0.9	2	dbSNP_134	139	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PLEK	NM_002664.2	99	0,2,6501	TT,TG,GG		0.0233,0.0,0.0154	benign	110/351	68607984	2,13004	2203	4300	6503	SO:0001583	missense	5341	exon3			AAATTTGCCAGGA	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"""Pleckstrin homology (PH) domain containing"""	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.328G>T	2.37:g.68607984G>T	ENSP00000234313:p.Ala110Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	77	24	0.311688	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187751	0.38609	0.0	2.33E-4	ENSG00000115956	ENST00000234313	T	0.19806	2.12	5.8	2.87	0.33458	.	0.192484	0.56097	N	0.000035	T	0.16599	0.0399	L	0.31065	0.9	0.53005	D	0.999968	B;B	0.13145	0.007;0.003	B;B	0.12156	0.007;0.004	T	0.03212	-1.1060	10	0.28530	T	0.3	.	15.4457	0.75228	0.0:0.0:0.3642:0.6358	.	128;110	Q59GZ2;P08567	.;PLEK_HUMAN	S	110	ENSP00000234313:A110S	ENSP00000234313:A110S	A	+	1	0	PLEK	68461488	1.000000	0.71417	0.941000	0.38009	0.953000	0.61014	3.637000	0.54324	0.295000	0.22570	-0.274000	0.10170	GCC	G|1.000;T|0.000	0.000	weak		0.478	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664	
FLNC	2318	hgsc.bcm.edu	37	7	128477472	128477472	+	Silent	SNP	T	T	C	rs2291560	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128477472T>C	ENST00000325888.8	+	4	981	c.720T>C	c.(718-720)atT>atC	p.I240I	FLNC_ENST00000346177.6_Silent_p.I240I	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	240	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CTGAGGAGATTGTGGACCCCA	0.577													C|||	610	0.121805	0.1248	0.062	5008	,	,		15037	0.121		0.1093	False		,,,				2504	0.1738				p.I240I		Atlas-SNP	.											.	FLNC	339	.	0			c.T720C						PASS	.	C	,	553,3797	223.3+/-239.8	39,475,1661	149.0	157.0	155.0		720,720	-9.7	0.6	7	dbSNP_100	155	952,7628	202.8+/-246.0	49,854,3387	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	88,1329,5048	CC,CT,TT		11.0956,12.7126,11.6396	,	240/2693,240/2726	128477472	1505,11425	2175	4290	6465	SO:0001819	synonymous_variant	2318	exon4			GGAGATTGTGGAC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.720T>C	7.37:g.128477472T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			T|0.879;C|0.121	0.121	strong		0.577	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
PHIP	55023	hgsc.bcm.edu	37	6	79657391	79657391	+	Silent	SNP	G	G	A	rs1984195	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:79657391G>A	ENST00000275034.4	-	36	4322	c.4155C>T	c.(4153-4155)gtC>gtT	p.V1385V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1385	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AAATAAGTCTGACATCTTTAC	0.338													G|||	2545	0.508187	0.3018	0.4611	5008	,	,		17684	0.6835		0.4791	False		,,,				2504	0.6697				p.V1385V		Atlas-SNP	.											.	PHIP	177	.	0			c.C4155T						PASS	.	G		1368,3038	454.0+/-350.5	210,948,1045	145.0	137.0	140.0		4155	4.4	1.0	6	dbSNP_92	140	4234,4366	571.4+/-389.5	1037,2160,1103	no	coding-synonymous	PHIP	NM_017934.5		1247,3108,2148	AA,AG,GG		49.2326,31.0486,43.0724		1385/1822	79657391	5602,7404	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon36			AAGTCTGACATCT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4155C>T	6.37:g.79657391G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	34	0.333333	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			G|0.542;A|0.458	0.458	strong		0.338	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
FAT2	2196	hgsc.bcm.edu	37	5	150945862	150945862	+	Silent	SNP	A	A	G	rs3734057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150945862A>G	ENST00000261800.5	-	1	2643	c.2631T>C	c.(2629-2631)gtT>gtC	p.V877V		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	877	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGTGTCCTGTAACAACCAGTT	0.567													A|||	2102	0.419728	0.441	0.4539	5008	,	,		15603	0.3571		0.4901	False		,,,				2504	0.3589				p.V877V		Atlas-SNP	.											.	FAT2	465	.	0			c.T2631C						PASS	.	A		1960,2446	555.1+/-379.2	423,1114,666	97.0	93.0	94.0		2631	2.7	0.9	5	dbSNP_107	94	4499,4101	592.7+/-393.0	1183,2133,984	no	coding-synonymous	FAT2	NM_001447.2		1606,3247,1650	GG,GA,AA		47.686,44.4848,49.6617		877/4350	150945862	6459,6547	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			TCCTGTAACAACC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2631T>C	5.37:g.150945862A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	190	53	0.278947	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			A|0.526;G|0.474	0.474	strong		0.567	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
AGO1	26523	hgsc.bcm.edu	37	1	36367665	36367665	+	Silent	SNP	C	C	T	rs61751003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36367665C>T	ENST00000373204.4	+	10	1470	c.1257C>T	c.(1255-1257)ggC>ggT	p.G419G	AGO1_ENST00000373206.1_Silent_p.G344G	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	419					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										TGCAGTACGGCGGCCGGGTGA	0.582													C|||	3	0.000599042	0.0	0.0	5008	,	,		17254	0.0		0.002	False		,,,				2504	0.001				p.G419G		Atlas-SNP	.											.	.	.	.	0			c.C1257T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	50.0	56.0	54.0		1257	2.7	1.0	1	dbSNP_129	54	30,8570	21.6+/-65.8	0,30,4270	no	coding-synonymous	EIF2C1	NM_012199.2		0,32,6471	TT,TC,CC		0.3488,0.0454,0.246		419/858	36367665	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	26523	exon10			GTACGGCGGCCGG	AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"""Argonaute/PIWI family"""	3262	protein-coding gene	gene with protein product	"""argonaute 1"""	606228	"""eukaryotic translation initiation factor 2C, 1"""	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.1257C>T	1.37:g.36367665C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	75	0.635593	NM_012199	Q5TA57|Q6P4S0	Silent	SNP	ENST00000373204.4	37	CCDS398.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3		
CEP128	145508	hgsc.bcm.edu	37	14	80971261	80971261	+	Missense_Mutation	SNP	C	C	T	rs61744330	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:80971261C>T	ENST00000555265.1	-	24	3550	c.3175G>A	c.(3175-3177)Gtg>Atg	p.V1059M	CEP128_ENST00000553717.1_5'UTR|CEP128_ENST00000281129.3_Missense_Mutation_p.V1059M			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	1059						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TTACAGTTCACGTATGAAAAT	0.383													T|||	316	0.063099	0.1694	0.0331	5008	,	,		16414	0.002		0.0517	False		,,,				2504	0.0153				p.V1059M		Atlas-SNP	.											.	CEP128	146	.	0			c.G3175A						PASS	.	T	MET/VAL	650,3756	763.6+/-413.2	49,552,1602	54.0	53.0	53.0		3175	1.6	1.0	14	dbSNP_129	53	412,8188	799.5+/-407.4	10,392,3898	yes	missense	CEP128	NM_152446.3	21	59,944,5500	TT,TC,CC		4.7907,14.7526,8.1655	benign	1059/1095	80971261	1062,11944	2203	4300	6503	SO:0001583	missense	145508	exon23			AGTTCACGTATGA	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.3175G>A	14.37:g.80971261C>T	ENSP00000451162:p.Val1059Met	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	127|127	0.05815018315018315|0.05815018315018315	83|83	0.16869918699186992|0.16869918699186992	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	35|35	0.04617414248021108|0.04617414248021108	T|T	9.323|9.323	1.058656|1.058656	0.19987|0.19987	0.147526|0.147526	0.047907|0.047907	ENSG00000100629|ENSG00000100629	ENST00000556061|ENST00000281129;ENST00000555265	.|T;T	.|0.30981	.|1.51;1.51	5.32|5.32	1.57|1.57	0.23409|0.23409	.|.	.|0.274634	.|0.23298	.|N	.|0.049715	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.08118|0.08118	0|0	0.09310|0.09310	P|P	0.99999898117|0.99999898117	.|B	.|0.06786	.|0.001	.|B	.|0.01281	.|0.0	T|T	0.24728|0.24728	-1.0152|-1.0152	4|9	.|0.31617	.|T	.|0.26	.|.	5.2564|5.2564	0.15550|0.15550	0.4005:0.2996:0.0:0.2998|0.4005:0.2996:0.0:0.2998	rs61744330|rs61744330	.|1059	.|Q6ZU80	.|CE128_HUMAN	H|M	124|1059	.|ENSP00000281129:V1059M;ENSP00000451162:V1059M	.|ENSP00000281129:V1059M	R|V	-|-	2|1	0|0	CEP128|CEP128	80041014|80041014	0.917000|0.917000	0.31117|0.31117	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	-0.038000|-0.038000	0.12144|0.12144	0.461000|0.461000	0.27071|0.27071	-1.493000|-1.493000	0.00968|0.00968	CGT|GTG	C|0.923;T|0.077	0.077	strong		0.383	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
CUX1	1523	hgsc.bcm.edu	37	7	101837149	101837149	+	Silent	SNP	G	G	A	rs11540899|rs2230104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:101837149G>A	ENST00000292535.7	+	13	1142	c.1104G>A	c.(1102-1104)ccG>ccA	p.P368P	CUX1_ENST00000437600.4_Silent_p.P377P|CUX1_ENST00000547394.2_Silent_p.P363P|CUX1_ENST00000360264.3_Silent_p.P379P|SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000549414.2_Silent_p.P368P|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000546411.2_Silent_p.P368P|CUX1_ENST00000393824.3_Silent_p.P340P|CUX1_ENST00000425244.2_Silent_p.P333P|CUX1_ENST00000556210.1_Silent_p.P368P|CUX1_ENST00000292538.4_Silent_p.P379P|CUX1_ENST00000550008.2_Silent_p.P368P	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	368					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						AGTTTGCACCGTCCGAGGGCG	0.527													G|||	1495	0.298522	0.3646	0.2738	5008	,	,		19932	0.0675		0.3857	False		,,,				2504	0.3753				p.P379P		Atlas-SNP	.											CUX1_ENST00000292538,rectum,carcinoma,0,2	CUX1	253	2	0			c.G1137A						PASS	.	G	,,,,,,	1667,2739	507.1+/-366.6	331,1005,867	82.0	69.0	73.0		1137,1089,999,1020,1137,1131,1104	-8.6	0.0	7	dbSNP_120	73	3374,5226	499.2+/-374.9	652,2070,1578	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	983,3075,2445	AA,AG,GG		39.2326,37.8348,38.759	,,,,,,	379/1517,363/663,333/633,340/640,379/679,377/677,368/1506	101837149	5041,7965	2203	4300	6503	SO:0001819	synonymous_variant	1523	exon13			TGCACCGTCCGAG	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1104G>A	7.37:g.101837149G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																			G|0.655;A|0.345	0.345	strong		0.527	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
WDR18	57418	hgsc.bcm.edu	37	19	990238	990238	+	Silent	SNP	C	C	T	rs117300378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:990238C>T	ENST00000251289.5	+	4	494	c.471C>T	c.(469-471)gaC>gaT	p.D157D	WDR18_ENST00000587001.2_Silent_p.D157D|WDR18_ENST00000591997.1_3'UTR	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	157					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCAGGCCGACCCCTCCAGGA	0.726													.|||	181	0.0361422	0.003	0.0461	5008	,	,		14076	0.0		0.0646	False		,,,				2504	0.0818				p.D157D		Atlas-SNP	.											.	WDR18	20	.	0			c.C471T						PASS	.			42,4342		0,42,2150	19.0	21.0	20.0		471	1.7	1.0	19	dbSNP_132	20	540,8040		19,502,3769	no	coding-synonymous	WDR18	NM_024100.3		19,544,5919	TT,TC,CC		6.2937,0.958,4.4894		157/433	990238	582,12382	2192	4290	6482	SO:0001819	synonymous_variant	57418	exon4			GGCCGACCCCTCC		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.471C>T	19.37:g.990238C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	27	7	0.259259	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			C|0.961;T|0.039	0.039	strong		0.726	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
TACC2	10579	hgsc.bcm.edu	37	10	123903133	123903133	+	Missense_Mutation	SNP	G	G	A	rs12765679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:123903133G>A	ENST00000369005.1	+	7	6086	c.5746G>A	c.(5746-5748)Gaa>Aaa	p.E1916K	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000369001.1_Intron|TACC2_ENST00000493951.1_3'UTR|TACC2_ENST00000515273.1_Intron|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515603.1_Intron|TACC2_ENST00000334433.3_Missense_Mutation_p.E1916K|TACC2_ENST00000369000.1_Intron|TACC2_ENST00000453444.2_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1916			E -> K (in dbSNP:rs12765679).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CTCGGCTGCAGAACACATAGT	0.577											OREG0020589	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	453	0.0904553	0.0688	0.1138	5008	,	,		14875	0.0		0.2286	False		,,,				2504	0.0542				p.E1916K		Atlas-SNP	.											.	TACC2	271	.	0			c.G5746A						PASS	.	G	,LYS/GLU	361,4045	185.7+/-212.7	15,331,1857	103.0	89.0	94.0		,5746	3.5	0.0	10	dbSNP_121	94	1929,6671	341.6+/-324.1	219,1491,2590	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,56	234,1822,4447	AA,AG,GG		22.4302,8.1934,17.6073	,probably-damaging	,1916/2949	123903133	2290,10716	2203	4300	6503	SO:0001583	missense	10579	exon7			GCTGCAGAACACA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5746G>A	10.37:g.123903133G>A	ENSP00000358001:p.Glu1916Lys	Somatic	65	0	0	1530	WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	268	0.1227106227106227	31	0.06300813008130081	55	0.15193370165745856	0	0.0	182	0.24010554089709762	G	14.03	2.413032	0.42817	0.081934	0.224302	ENSG00000138162	ENST00000369005;ENST00000334433;ENST00000340076	T;T	0.57907	0.37;0.37	4.45	3.53	0.40419	.	0.443678	0.16781	N	0.199795	T	0.00012	0.0000	L	0.32530	0.975	0.48571	P	3.269999999999662E-4	P	0.37061	0.58	B	0.37601	0.254	T	0.11665	-1.0578	9	0.72032	D	0.01	-4.7039	10.6039	0.45384	0.0:0.1948:0.8052:0.0	rs12765679;rs17551488;rs52820192;rs57234473;rs12765679	1916	O95359	TACC2_HUMAN	K	1916;1916;1906	ENSP00000358001:E1916K;ENSP00000334280:E1916K	ENSP00000334280:E1916K	E	+	1	0	TACC2	123893123	0.032000	0.19561	0.003000	0.11579	0.003000	0.03518	2.480000	0.45206	1.209000	0.43321	-0.304000	0.09214	GAA	G|0.854;A|0.146	0.146	strong		0.577	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
SLC7A13	157724	hgsc.bcm.edu	37	8	87229739	87229739	+	Missense_Mutation	SNP	C	C	T	rs4419794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:87229739C>T	ENST00000297524.3	-	3	1242	c.1139G>A	c.(1138-1140)aGg>aAg	p.R380K	SLC7A13_ENST00000520624.1_5'Flank|SLC7A13_ENST00000419776.2_Missense_Mutation_p.R371K	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	380			R -> K (in dbSNP:rs4419794).			integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						GTATCTCCGCCTTAGTATTCC	0.299													C|||	973	0.194289	0.0401	0.1945	5008	,	,		17064	0.3383		0.1372	False		,,,				2504	0.3129				p.R380K		Atlas-SNP	.											SLC7A13,NS,carcinoma,+1,1	SLC7A13	97	1	0			c.G1139A						PASS	.	C	LYS/ARG	248,4140		9,230,1955	29.0	34.0	32.0		1139	-0.8	0.0	8	dbSNP_111	32	1088,7496		80,928,3284	yes	missense	SLC7A13	NM_138817.2	26	89,1158,5239	TT,TC,CC		12.6747,5.6518,10.2991	benign	380/471	87229739	1336,11636	2194	4292	6486	SO:0001583	missense	157724	exon3			CTCCGCCTTAGTA	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1139G>A	8.37:g.87229739C>T	ENSP00000297524:p.Arg380Lys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	120	47	0.391667	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	368	0.1684981684981685	18	0.036585365853658534	56	0.15469613259668508	193	0.3374125874125874	101	0.13324538258575197	C	0.005	-2.129682	0.00338	0.056518	0.126747	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.88818	-2.43;-2.43	5.03	-0.761	0.11038	.	0.592368	0.15885	N	0.239861	T	0.00012	0.0000	N	0.00230	-1.795	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.01281	0.0;0.0	T	0.38478	-0.9659	9	0.27082	T	0.32	.	3.1871	0.06604	0.246:0.2762:0.0:0.4778	rs4419794;rs60737499;rs4419794	371;380	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	K	380;371	ENSP00000297524:R380K;ENSP00000410982:R371K	ENSP00000297524:R380K	R	-	2	0	SLC7A13	87298855	0.931000	0.31567	0.005000	0.12908	0.003000	0.03518	0.841000	0.27613	0.109000	0.17891	-1.124000	0.02001	AGG	C|0.856;T|0.144	0.144	strong		0.299	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
CCDC33	80125	hgsc.bcm.edu	37	15	74622549	74622549	+	Missense_Mutation	SNP	G	G	T	rs2277604	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:74622549G>T	ENST00000398814.3	+	12	1741	c.1310G>T	c.(1309-1311)cGg>cTg	p.R437L	CCDC33_ENST00000268082.4_Missense_Mutation_p.R30L|CCDC33_ENST00000321288.5_Missense_Mutation_p.R640L|CCDC33_ENST00000558821.1_Missense_Mutation_p.R30L	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	640										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						AACTACCGGCGGGCCATGCAG	0.592													g|||	195	0.0389377	0.0023	0.0331	5008	,	,		18149	0.0913		0.0249	False		,,,				2504	0.0532				p.R437L		Atlas-SNP	.											.	CCDC33	160	.	0			c.G1310T						PASS	.	A	LEU/ARG,LEU/ARG	25,4011		0,25,1993	40.0	44.0	43.0		1310,89	-1.0	1.0	15	dbSNP_100	43	321,8015		7,307,3854	yes	missense,missense	CCDC33	NM_025055.3,NM_182791.2	102,102	7,332,5847	TT,TG,GG		3.8508,0.6194,2.7966	probably-damaging,probably-damaging	437/756,30/368	74622549	346,12026	2018	4168	6186	SO:0001583	missense	80125	exon12			ACCGGCGGGCCAT	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1310G>T	15.37:g.74622549G>T	ENSP00000381795:p.Arg437Leu	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	85	0.03891941391941392	0	0.0	17	0.04696132596685083	53	0.09265734265734266	15	0.01978891820580475	G	11.99	1.803458	0.31869	0.006194	0.038508	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.36157	1.27;2.26;1.92;1.92	4.92	-1.03	0.10102	.	0.763485	0.12095	N	0.500017	T	0.00875	0.0029	L	0.55990	1.75	0.21553	N	0.999643	B;B;P;B	0.35714	0.239;0.041;0.517;0.405	B;B;B;B	0.30495	0.051;0.033;0.081;0.116	T	0.05084	-1.0907	10	0.39692	T	0.17	.	3.3433	0.07126	0.3987:0.0:0.3507:0.2506	rs2277604;rs2277604	30;30;640;437	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	L	640;437;30;30	ENSP00000325012:R640L;ENSP00000381795:R437L;ENSP00000325661:R30L;ENSP00000268082:R30L	ENSP00000268082:R30L	R	+	2	0	CCDC33	72409602	0.067000	0.21026	0.999000	0.59377	0.927000	0.56198	0.177000	0.16801	0.147000	0.19030	-0.131000	0.14894	CGG	G|0.958;T|0.042	0.042	strong		0.592	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
MUC4	4585	hgsc.bcm.edu	37	3	195510149	195510149	+	Missense_Mutation	SNP	G	G	A	rs542186658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195510149G>A	ENST00000463781.3	-	2	8761	c.8302C>T	c.(8302-8304)Cct>Tct	p.P2768S	MUC4_ENST00000475231.1_Missense_Mutation_p.P2768S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P2768S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCGTGA	0.577													.|||	2	0.000399361	0.0015	0.0	5008	,	,		5215	0.0		0.0	False		,,,				2504	0.0				p.P2768S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.C8302T						scavenged	.																																			SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8302C>T	3.37:g.195510149G>A	ENSP00000417498:p.Pro2768Ser	Somatic	216	9	0.0416667		WXS	Illumina HiSeq	Phase_I	375	33	0.088	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	5.381	0.255488	0.10185	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27256	1.68;1.68	1.02	-2.03	0.07365	.	.	.	.	.	T	0.09158	0.0226	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.33523	-0.9865	8	.	.	.	.	2.0272	0.03521	0.2702:0.0:0.2738:0.456	.	2640	E7ESK3	.	S	2768	ENSP00000417498:P2768S;ENSP00000420243:P2768S	.	P	-	1	0	MUC4	196994928	0.000000	0.05858	0.010000	0.14722	0.113000	0.19764	-2.060000	0.01392	-0.413000	0.07507	0.074000	0.15403	CCT	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HRNR	388697	hgsc.bcm.edu	37	1	152192397	152192397	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152192397T>C	ENST00000368801.2	-	3	1783	c.1708A>G	c.(1708-1710)Agc>Ggc	p.S570G	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	570					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGGCCACGGCTTGAAGACCTC	0.582																																					p.S570G		Atlas-SNP	.											HRNR,NS,carcinoma,+2,1	HRNR	403	1	0			c.A1708G						scavenged	.						175.0	184.0	181.0					1																	152192397		2203	4300	6503	SO:0001583	missense	388697	exon3			CACGGCTTGAAGA	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1708A>G	1.37:g.152192397T>C	ENSP00000357791:p.Ser570Gly	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	299	5	0.0167224	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	5.546	0.285719	0.10513	.	.	ENSG00000197915	ENST00000368801	T	0.02369	4.32	3.9	-7.8	0.01214	.	.	.	.	.	T	0.00356	0.0011	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47911	-0.9080	9	0.19590	T	0.45	.	11.5235	0.50565	0.0:0.4736:0.4023:0.1241	.	570	Q86YZ3	HORN_HUMAN	G	570	ENSP00000357791:S570G	ENSP00000357791:S570G	S	-	1	0	HRNR	150459021	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.593000	0.00420	-2.388000	0.00588	-0.445000	0.05633	AGC	.	.	none		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
ILDR2	387597	hgsc.bcm.edu	37	1	166905927	166905927	+	Missense_Mutation	SNP	C	C	T	rs33958744	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:166905927C>T	ENST00000271417.3	-	5	659	c.604G>A	c.(604-606)Gtc>Atc	p.V202I	ILDR2_ENST00000529387.1_Intron|ILDR2_ENST00000526687.1_Intron|ILDR2_ENST00000525740.1_Intron|ILDR2_ENST00000529071.1_Missense_Mutation_p.V183I|ILDR2_ENST00000469934.2_Missense_Mutation_p.V202I|ILDR2_ENST00000528703.1_Missense_Mutation_p.V202I	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	202			V -> I (in dbSNP:rs33958744).		cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						CCCACCAGGACGAAGAAGAGG	0.612													C|||	415	0.0828674	0.0658	0.1225	5008	,	,		19504	0.0		0.2068	False		,,,				2504	0.0358				p.V202I		Atlas-SNP	.											.	ILDR2	79	.	0			c.G604A						PASS	.	C	ILE/VAL	350,4056	180.5+/-208.7	15,320,1868	70.0	73.0	72.0		604	3.7	1.0	1	dbSNP_126	72	1641,6959	301.3+/-305.4	152,1337,2811	yes	missense	ILDR2	NM_199351.2	29	167,1657,4679	TT,TC,CC		19.0814,7.9437,15.3083	benign	202/640	166905927	1991,11015	2203	4300	6503	SO:0001583	missense	387597	exon5			CCAGGACGAAGAA	AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"""LISCH-like"""		"""chromosome 1 open reading frame 32"""	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.604G>A	1.37:g.166905927C>T	ENSP00000271417:p.Val202Ile	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	403	192	0.476427	NM_199351		Missense_Mutation	SNP	ENST00000271417.3	37	CCDS1256.1	242	0.1108058608058608	25	0.0508130081300813	61	0.1685082872928177	0	0.0	156	0.20580474934036938	C	19.51	3.841009	0.71488	0.079437	0.190814	ENSG00000143195	ENST00000271417;ENST00000469934;ENST00000529071;ENST00000528703	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.61	3.69	0.42338	LISCH7 (1);	0.074622	0.52532	D	0.000064	T	0.11410	0.0278	N	0.12569	0.235	0.32560	P	0.5311710000000001	B	0.19583	0.037	B	0.15052	0.012	T	0.06954	-1.0798	9	0.54805	T	0.06	.	9.9967	0.41905	0.0:0.6878:0.2233:0.0889	rs33958744	202	Q71H61	ILDR2_HUMAN	I	202;202;183;202	ENSP00000271417:V202I;ENSP00000437008:V202I;ENSP00000436882:V183I;ENSP00000432750:V202I	ENSP00000271417:V202I	V	-	1	0	ILDR2	165172551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.730000	0.55006	1.367000	0.46095	0.563000	0.77884	GTC	C|0.857;T|0.143	0.143	strong		0.612	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351	
ARSE	415	hgsc.bcm.edu	37	X	2852915	2852915	+	Silent	SNP	C	C	T	rs11055	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2852915C>T	ENST00000381134.3	-	11	1794	c.1728G>A	c.(1726-1728)ccG>ccA	p.P576P	ARSE_ENST00000545496.1_Silent_p.P601P|ARSE_ENST00000540563.1_Silent_p.P531P	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	576					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGAGGGGGAACGGGCCACAGC	0.562													C|||	99	0.0262252	0.0015	0.0231	3775	,	,		12902	0.0		0.0765	False		,,,				2504	0.0041				p.P576P		Atlas-SNP	.											.	ARSE	43	.	0			c.G1728A						PASS	.	C		52,3783		1,41,9,1590,562	34.0	30.0	31.0		1728	-6.9	0.0	X	dbSNP_52	31	605,6120		11,408,175,2009,1694	no	coding-synonymous	ARSE	NM_000047.2		12,449,184,3599,2256	TT,TC,T,CC,C		8.9963,1.3559,6.2216		576/590	2852915	657,9903	2203	4297	6500	SO:0001819	synonymous_variant	415	exon11			GGGGAACGGGCCA	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1728G>A	X.37:g.2852915C>T		Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	122	119	0.97541	NM_000047	Q53FT2|Q53FU8	Silent	SNP	ENST00000381134.3	37	CCDS14122.1																																																																																			.	.	weak		0.562	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
EIF2AK3	9451	hgsc.bcm.edu	37	2	88913273	88913273	+	Missense_Mutation	SNP	G	G	C	rs867529	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:88913273G>C	ENST00000303236.3	-	2	708	c.407C>G	c.(406-408)tCc>tGc	p.S136C	EIF2AK3_ENST00000419748.1_5'UTR	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	136			S -> C (in dbSNP:rs867529). {ECO:0000269|PubMed:10932183, ECO:0000269|PubMed:17344846}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						TGACACCAAGGAACCGGATCC	0.383													G|||	1405	0.280551	0.0166	0.3343	5008	,	,		16061	0.4851		0.2982	False		,,,				2504	0.3701				p.S136C	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.C407G						PASS	.	G	CYS/SER	256,4150	145.4+/-180.2	8,240,1955	123.0	109.0	114.0		407	5.4	1.0	2	dbSNP_86	114	2324,6276	389.8+/-343.1	313,1698,2289	yes	missense	EIF2AK3	NM_004836.5	112	321,1938,4244	CC,CG,GG		27.0233,5.8103,19.837	benign	136/1117	88913273	2580,10426	2203	4300	6503	SO:0001583	missense	9451	exon2			ACCAAGGAACCGG	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.407C>G	2.37:g.88913273G>C	ENSP00000307235:p.Ser136Cys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	629	0.288003663003663	10	0.02032520325203252	123	0.3397790055248619	274	0.479020979020979	222	0.2928759894459103	G	14.41	2.527371	0.44969	0.058103	0.270233	ENSG00000172071	ENST00000303236	T	0.30981	1.51	5.38	5.38	0.77491	Quinonprotein alcohol dehydrogenase-like (2);	0.227346	0.46758	D	0.000261	T	0.00012	0.0000	L	0.33245	0.995	0.29294	P	0.8691530000000001	B	0.09022	0.002	B	0.08055	0.003	T	0.49011	-0.8983	9	0.39692	T	0.17	-10.5973	19.1382	0.93436	0.0:0.0:1.0:0.0	rs867529;rs1805163;rs52809782;rs867529	136	Q9NZJ5	E2AK3_HUMAN	C	136	ENSP00000307235:S136C	ENSP00000307235:S136C	S	-	2	0	EIF2AK3	88694388	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	5.704000	0.68347	2.507000	0.84556	0.655000	0.94253	TCC	G|0.764;C|0.236	0.236	strong		0.383	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
ZNF529	57711	hgsc.bcm.edu	37	19	37038584	37038584	+	Silent	SNP	T	T	C	rs183728423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:37038584T>C	ENST00000591340.1	-	5	1034	c.876A>G	c.(874-876)agA>agG	p.R292R	ZNF529_ENST00000334116.7_Silent_p.R187R	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	292					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	Esophageal squamous(110;0.198)					GTGCATGCACTCTAAAGGATT	0.383													T|||	10	0.00199681	0.0	0.0	5008	,	,		20320	0.0		0.007	False		,,,				2504	0.0031				p.R292R		Atlas-SNP	.											.	ZNF529	82	.	0			c.A876G						PASS	.	T	,,	3,4007		0,3,2002	144.0	144.0	144.0		876,822,876	-0.1	0.5	19		144	44,8372		0,44,4164	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF529	NM_001145649.1,NM_001145650.1,NM_020951.4	,,	0,47,6166	CC,CT,TT		0.5228,0.0748,0.3782	,,	292/564,274/546,292/564	37038584	47,12379	2005	4208	6213	SO:0001819	synonymous_variant	57711	exon6			ATGCACTCTAAAG	AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"""Zinc fingers, C2H2-type"", ""-"""	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.876A>G	19.37:g.37038584T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	182	86	0.472527	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Silent	SNP	ENST00000591340.1	37	CCDS54256.1																																																																																			T|0.998;C|0.002	0.002	strong		0.383	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951	
SLC12A7	10723	hgsc.bcm.edu	37	5	1057615	1057615	+	Silent	SNP	A	A	G	rs2241606	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:1057615A>G	ENST00000264930.5	-	22	3040	c.2997T>C	c.(2995-2997)tcT>tcC	p.S999S		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	999					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CTTTGAAACCAGATAGGCTGG	0.602													a|||	2469	0.493011	0.2352	0.6282	5008	,	,		17436	0.4772		0.6372	False		,,,				2504	0.6135				p.S999S		Atlas-SNP	.											SLC12A7,NS,carcinoma,-1,1	SLC12A7	97	1	0			c.T2997C						PASS	.	G		1337,3069	447.5+/-348.4	216,905,1082	167.0	139.0	148.0		2997	-5.7	0.0	5	dbSNP_98	148	5619,2981	666.1+/-402.3	1832,1955,513	no	coding-synonymous	SLC12A7	NM_006598.2		2048,2860,1595	GG,GA,AA		34.6628,30.345,46.517		999/1084	1057615	6956,6050	2203	4300	6503	SO:0001819	synonymous_variant	10723	exon22			GAAACCAGATAGG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2997T>C	5.37:g.1057615A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1																																																																																			A|0.485;G|0.515	0.515	strong		0.602	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
OAT	4942	hgsc.bcm.edu	37	10	126089434	126089434	+	Silent	SNP	G	G	A	rs11461	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:126089434G>A	ENST00000368845.5	-	9	1226	c.1134C>T	c.(1132-1134)aaC>aaT	p.N378N	OAT_ENST00000467675.1_5'Flank|OAT_ENST00000539214.1_Silent_p.N240N	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	378					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	TGACAATAGCGTTTAATAATC	0.308													G|||	2053	0.409944	0.1445	0.5259	5008	,	,		16380	0.6369		0.3648	False		,,,				2504	0.499				p.N378N		Atlas-SNP	.											.	OAT	25	.	0			c.C1134T						PASS	.	G	,	765,3641	309.1+/-290.9	71,623,1509	87.0	80.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1134,720	-4.0	0.5	10	dbSNP_52	82	3334,5262	493.7+/-373.6	620,2094,1584	no	coding-synonymous,coding-synonymous	OAT	NM_000274.3,NM_001171814.1	,	691,2717,3093	AA,AG,GG		38.7855,17.3627,31.5259	,	378/440,240/302	126089434	4099,8903	2203	4298	6501	SO:0001819	synonymous_variant	4942	exon9			AATAGCGTTTAAT	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"""Ornithine aminotransferase"", ""ornithine aminotransferase precursor"", ""gyrate atrophy"""	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.1134C>T	10.37:g.126089434G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	186	86	0.462366	NM_000274	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Silent	SNP	ENST00000368845.5	37	CCDS7639.1																																																																																			G|0.648;A|0.352	0.352	strong		0.308	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274	
ANKLE2	23141	hgsc.bcm.edu	37	12	133331364	133331364	+	Silent	SNP	G	G	A	rs34152718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133331364G>A	ENST00000357997.5	-	2	626	c.537C>T	c.(535-537)ccC>ccT	p.P179P	ANKLE2_ENST00000539605.1_Silent_p.P117P|ANKLE2_ENST00000337516.5_Silent_p.P179P	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	179					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		TGTCACTAGGGGGCACCGAGC	0.557													G|||	172	0.034345	0.0	0.0461	5008	,	,		16904	0.0804		0.0437	False		,,,				2504	0.0153				p.P179P		Atlas-SNP	.											.	ANKLE2	76	.	0			c.C537T						PASS	.	G		24,3894		0,24,1935	68.0	70.0	69.0		537	-2.8	0.0	12	dbSNP_126	69	380,7898		15,350,3774	no	coding-synonymous	ANKLE2	NM_015114.1		15,374,5709	AA,AG,GG		4.5905,0.6126,3.3126		179/939	133331364	404,11792	1959	4139	6098	SO:0001819	synonymous_variant	23141	exon2			ACTAGGGGGCACC	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.537C>T	12.37:g.133331364G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	70	28	0.4	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Silent	SNP	ENST00000357997.5	37	CCDS41869.1																																																																																			G|0.957;A|0.043	0.043	strong		0.557	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
DNAJC18	202052	hgsc.bcm.edu	37	5	138773090	138773090	+	Silent	SNP	A	A	G	rs10900864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:138773090A>G	ENST00000302060.5	-	2	278	c.198T>C	c.(196-198)taT>taC	p.Y66Y		NM_152686.3	NP_689899.1	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	66						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GTTCCTCACTATACGTGGAGT	0.483													a|||	2053	0.409944	0.1225	0.6138	5008	,	,		23337	0.3105		0.6491	False		,,,				2504	0.5102				p.Y66Y		Atlas-SNP	.											.	DNAJC18	30	.	0			c.T198C						PASS	.	A		1004,3402	373.2+/-320.7	102,800,1301	195.0	149.0	165.0		198	-4.6	0.8	5	dbSNP_120	165	5845,2755	679.6+/-403.6	1994,1857,449	no	coding-synonymous	DNAJC18	NM_152686.3		2096,2657,1750	GG,GA,AA		32.0349,22.7871,47.3397		66/359	138773090	6849,6157	2203	4300	6503	SO:0001819	synonymous_variant	202052	exon2			CTCACTATACGTG	AK024054	CCDS4214.1	5q31.2	2011-09-02		2005-08-09	ENSG00000170464	ENSG00000170464		"""Heat shock proteins / DNAJ (HSP40)"""	28429	protein-coding gene	gene with protein product							Standard	NM_152686		Approved	MGC29463	uc003len.3	Q9H819	OTTHUMG00000129225	ENST00000302060.5:c.198T>C	5.37:g.138773090A>G		Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	336	228	0.678571	NM_152686		Silent	SNP	ENST00000302060.5	37	CCDS4214.1																																																																																			A|0.531;G|0.469	0.469	strong		0.483	DNAJC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374191.1	NM_152686	
FGFR2	2263	hgsc.bcm.edu	37	10	123239112	123239112	+	3'UTR	SNP	G	G	A	rs1047057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000356226.4_3'UTR|FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000357555.5_Silent_p.L703L|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000369060.4_3'UTR	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.L703L(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86.0	84.0	85.0		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.*259C>T	10.37:g.123239112G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_001144915	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
VAT1	10493	hgsc.bcm.edu	37	17	41174025	41174025	+	Silent	SNP	A	A	C	rs2070835	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41174025A>C	ENST00000355653.3	-	1	410	c.315T>G	c.(313-315)ccT>ccG	p.P105P	VAT1_ENST00000587173.1_Intron|VAT1_ENST00000420567.3_5'Flank	NM_006373.3	NP_006364.2	P54219	VMAT1_HUMAN	vesicle amine transport 1	0					monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)			endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	TGACAGGCAGAGGCGGGAGAC	0.706													C|||	1716	0.342652	0.2224	0.2939	5008	,	,		10101	0.374		0.3559	False		,,,				2504	0.4939				p.P105P		Atlas-SNP	.											VAT1,NS,carcinoma,0,1	VAT1	19	1	0			c.T315G						PASS	.	C		930,3384		103,724,1330	13.0	13.0	13.0		315	-0.9	1.0	17	dbSNP_96	13	2522,5898		395,1732,2083	no	coding-synonymous	VAT1	NM_006373.3		498,2456,3413	CC,CA,AA		29.9525,21.5577,27.1085		105/394	41174025	3452,9282	2157	4210	6367	SO:0001819	synonymous_variant	10493	exon1			AGGCAGAGGCGGG	U18009	CCDS11451.1	17q21	2013-08-23	2013-08-23			ENSG00000108828			16919	protein-coding gene	gene with protein product		604631	"""vesicle amine transport protein 1 homolog (T. californica)"""			7774926, 8938427	Standard	NM_006373		Approved	VATI, FLJ20230	uc002icm.1	Q99536		ENST00000355653.3:c.315T>G	17.37:g.41174025A>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_006373	E9PDJ5|Q9BRE4	Silent	SNP	ENST00000355653.3	37	CCDS11451.1																																																																																			A|0.711;C|0.289	0.289	strong		0.706	VAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453101.1	NM_006373	
CDH18	1016	hgsc.bcm.edu	37	5	19591174	19591174	+	Silent	SNP	A	A	G	rs17285716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:19591174A>G	ENST00000507958.1	-	9	1981	c.991T>C	c.(991-993)Tta>Cta	p.L331L	CDH18_ENST00000506372.1_Silent_p.L331L|CDH18_ENST00000382275.1_Silent_p.L331L|CDH18_ENST00000274170.4_Silent_p.L331L|CDH18_ENST00000502796.1_Silent_p.L331L|CDH18_ENST00000511273.1_Silent_p.L331L			Q13634	CAD18_HUMAN	cadherin 18, type 2	331	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					ACCTTCTTTAAAGAAAGGATT	0.403													A|||	480	0.0958466	0.0151	0.1945	5008	,	,		16900	0.004		0.1799	False		,,,				2504	0.1431				p.L331L		Atlas-SNP	.											CDH18_ENST00000507958,NS,adenoma,0,4	CDH18	561	4	0			c.T991C						PASS	.	A	,	208,4198	127.8+/-164.7	7,194,2002	88.0	77.0	81.0		991,991	4.1	1.0	5	dbSNP_123	81	1595,7005	295.4+/-302.4	131,1333,2836	no	coding-synonymous,coding-synonymous	CDH18	NM_001167667.1,NM_004934.3	,	138,1527,4838	GG,GA,AA		18.5465,4.7208,13.8628	,	331/575,331/791	19591174	1803,11203	2203	4300	6503	SO:0001819	synonymous_variant	1016	exon7			TCTTTAAAGAAAG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.991T>C	5.37:g.19591174A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	55	0.410448	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	37	CCDS3889.1																																																																																			A|0.879;G|0.121	0.121	strong		0.403	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
UBE2O	63893	hgsc.bcm.edu	37	17	74387455	74387455	+	Missense_Mutation	SNP	C	C	T	rs34070229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74387455C>T	ENST00000319380.7	-	18	3512	c.3448G>A	c.(3448-3450)Gcc>Acc	p.A1150T		NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	1150				A -> T (in Ref. 6; BAB14320). {ECO:0000305}.	positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						TCCAGCAGGGCATGGGTTTCC	0.657													c|||	21	0.00419329	0.0008	0.0043	5008	,	,		14338	0.0		0.0099	False		,,,				2504	0.0072				p.A1150T		Atlas-SNP	.											.	UBE2O	207	.	0			c.G3448A						PASS	.		THR/ALA	9,4395		0,9,2193	32.0	31.0	31.0		3448	3.6	0.6	17	dbSNP_126	31	125,8473		0,125,4174	yes	missense	UBE2O	NM_022066.3	58	0,134,6367	TT,TC,CC		1.4538,0.2044,1.0306	benign	1150/1293	74387455	134,12868	2202	4299	6501	SO:0001583	missense	63893	exon18			GCAGGGCATGGGT	AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.3448G>A	17.37:g.74387455C>T	ENSP00000323687:p.Ala1150Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Missense_Mutation	SNP	ENST00000319380.7	37	CCDS32742.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	c	11.30	1.597943	0.28445	0.002044	0.014538	ENSG00000175931	ENST00000319380	T	0.72615	-0.67	4.58	3.62	0.41486	Ubiquitin-conjugating enzyme/RWD-like (1);	0.271361	0.30085	N	0.010460	T	0.42381	0.1200	N	0.22421	0.69	0.25600	N	0.986606	B	0.06786	0.001	B	0.04013	0.001	T	0.19614	-1.0300	10	0.14656	T	0.56	-14.1712	7.7518	0.28901	0.161:0.7564:0.0:0.0826	rs34070229	1150	Q9C0C9	UBE2O_HUMAN	T	1150	ENSP00000323687:A1150T	ENSP00000323687:A1150T	A	-	1	0	UBE2O	71899050	0.997000	0.39634	0.648000	0.29521	0.911000	0.54048	2.190000	0.42630	1.146000	0.42352	0.556000	0.70494	GCC	C|0.991;T|0.009	0.009	strong		0.657	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066	
PLCE1	51196	hgsc.bcm.edu	37	10	96076495	96076495	+	Silent	SNP	C	C	G	rs942676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96076495C>G	ENST00000371380.3	+	28	6559	c.6324C>G	c.(6322-6324)gtC>gtG	p.V2108V	PLCE1_ENST00000371385.3_Silent_p.V1800V|NOC3L_ENST00000543788.1_Intron|PLCE1_ENST00000260766.3_Silent_p.V2108V|RP11-76P2.4_ENST00000609123.1_RNA|PLCE1_ENST00000371375.1_Silent_p.V1800V			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	2108	Ras-associating 1. {ECO:0000255|PROSITE- ProRule:PRU00166}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				GCAGGATTGTCTTAAAAACCC	0.453													C|||	436	0.0870607	0.0053	0.1873	5008	,	,		15639	0.003		0.1571	False		,,,				2504	0.1411				p.V2108V		Atlas-SNP	.											.	PLCE1	543	.	0			c.C6324G						PASS	.	C	,	108,3688		3,102,1793	71.0	72.0	71.0		5400,6324	2.3	1.0	10	dbSNP_86	71	1319,6897		108,1103,2897	no	coding-synonymous,coding-synonymous	PLCE1	NM_001165979.1,NM_016341.3	,	111,1205,4690	GG,GC,CC		16.054,2.8451,11.8798	,	1800/1995,2108/2303	96076495	1427,10585	1898	4108	6006	SO:0001819	synonymous_variant	51196	exon29			GATTGTCTTAAAA		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.6324C>G	10.37:g.96076495C>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	37	CCDS41552.1																																																																																			C|0.924;G|0.076	0.076	strong		0.453	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
MKI67	4288	hgsc.bcm.edu	37	10	129906674	129906674	+	Missense_Mutation	SNP	T	T	C	rs41300566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:129906674T>C	ENST00000368654.3	-	13	3805	c.3430A>G	c.(3430-3432)Aag>Gag	p.K1144E	MKI67_ENST00000368653.3_Missense_Mutation_p.K784E	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1144	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGCCATTGCTTTGTGCTTGTT	0.468													T|||	199	0.0397364	0.0008	0.0648	5008	,	,		21749	0.0		0.0944	False		,,,				2504	0.0593				p.K1144E		Atlas-SNP	.											.	MKI67	363	.	0			c.A3430G						PASS	.	T	GLU/LYS,GLU/LYS	84,4322	73.1+/-111.1	1,82,2120	339.0	328.0	332.0		2350,3430	2.4	0.0	10	dbSNP_127	332	848,7752	194.2+/-239.7	46,756,3498	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	56,56	47,838,5618	CC,CT,TT		9.8605,1.9065,7.1659	benign,benign	784/2897,1144/3257	129906674	932,12074	2203	4300	6503	SO:0001583	missense	4288	exon13			ATTGCTTTGTGCT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3430A>G	10.37:g.129906674T>C	ENSP00000357643:p.Lys1144Glu	Somatic	475	1	0.00210526		WXS	Illumina HiSeq	Phase_I	463	246	0.531317	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	96	0.04395604395604396	2	0.0040650406504065045	22	0.06077348066298342	1	0.0017482517482517483	71	0.09366754617414248	T	10.78	1.445892	0.25987	0.019065	0.098605	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03982	3.74;3.74	3.62	2.43	0.29744	.	.	.	.	.	T	0.00241	0.0007	M	0.68317	2.08	0.80722	P	0.0	B;P;P	0.47484	0.137;0.804;0.896	B;B;P	0.45660	0.147;0.292;0.489	T	0.31503	-0.9941	8	0.22706	T	0.39	.	8.0898	0.30795	0.18:0.0:0.0:0.82	rs41300566;rs61729194	1143;784;1144	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	E	1144;784;1143	ENSP00000357643:K1144E;ENSP00000357642:K784E	ENSP00000357642:K784E	K	-	1	0	MKI67	129796664	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	0.108000	0.15396	0.548000	0.28955	0.459000	0.35465	AAG	T|0.937;C|0.063	0.063	strong		0.468	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
KIF4B	285643	hgsc.bcm.edu	37	5	154396505	154396505	+	Missense_Mutation	SNP	G	G	A	rs60928118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:154396505G>A	ENST00000435029.4	+	1	3246	c.3086G>A	c.(3085-3087)cGt>cAt	p.R1029H		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	1029	Globular. {ECO:0000250}.|Interaction with PRC1. {ECO:0000250}.			R -> H (in Ref. 3; ABB92415). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AAACCTTCTCGTGTTAAAGAA	0.423													G|||	789	0.157548	0.0885	0.111	5008	,	,		23558	0.1895		0.166	False		,,,				2504	0.2423				p.R1029H		Atlas-SNP	.											.	KIF4B	307	.	0			c.G3086A						PASS	.	G	HIS/ARG	443,3963	211.2+/-231.4	23,397,1783	124.0	126.0	125.0		3086	1.8	1.0	5	dbSNP_129	125	1463,7137	280.1+/-294.3	130,1203,2967	yes	missense	KIF4B	NM_001099293.1	29	153,1600,4750	AA,AG,GG		17.0116,10.0545,14.6548	benign	1029/1235	154396505	1906,11100	2203	4300	6503	SO:0001583	missense	285643	exon1			CTTCTCGTGTTAA	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.3086G>A	5.37:g.154396505G>A	ENSP00000387875:p.Arg1029His	Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	363	222	0.61157	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	309	0.14148351648351648	59	0.11991869918699187	41	0.1132596685082873	88	0.15384615384615385	121	0.15963060686015831	G	10.43	1.349050	0.24426	0.100545	0.170116	ENSG00000226650	ENST00000435029	T	0.69040	-0.37	1.77	1.77	0.24775	.	.	.	.	.	T	0.00271	0.0008	M	0.61703	1.905	0.25967	P	0.9825413	B	0.20887	0.049	B	0.09377	0.004	T	0.22103	-1.0226	8	0.66056	D	0.02	.	7.0054	0.24833	0.0:0.0:1.0:0.0	rs60928118;rs61734294	1029	Q2VIQ3	KIF4B_HUMAN	H	1029	ENSP00000387875:R1029H	ENSP00000387875:R1029H	R	+	2	0	KIF4B	154376698	0.827000	0.29292	0.972000	0.41901	0.950000	0.60333	1.504000	0.35726	1.290000	0.44636	0.563000	0.77884	CGT	G|0.858;A|0.142	0.142	strong		0.423	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
ITM2C	81618	hgsc.bcm.edu	37	2	231742138	231742138	+	Silent	SNP	G	G	A	rs34910213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231742138G>A	ENST00000326427.6	+	5	711	c.585G>A	c.(583-585)acG>acA	p.T195T	ITM2C_ENST00000409704.2_Silent_p.T133T|ITM2C_ENST00000326407.6_Silent_p.T158T|ITM2C_ENST00000335005.6_Silent_p.T148T	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	195	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		TGCCGCAGACGTACATCATCC	0.607													G|||	23	0.00459265	0.0	0.0072	5008	,	,		18458	0.0		0.0179	False		,,,				2504	0.0				p.T195T		Atlas-SNP	.											.	ITM2C	17	.	0			c.G585A						PASS	.	G	,,	24,4382	29.9+/-59.1	0,24,2179	86.0	79.0	81.0		444,474,585	0.3	1.0	2	dbSNP_126	81	140,8460	69.7+/-132.2	1,138,4161	no	coding-synonymous,coding-synonymous,coding-synonymous	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,,	1,162,6340	AA,AG,GG		1.6279,0.5447,1.261	,,	148/221,158/231,195/268	231742138	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	81618	exon5			GCAGACGTACATC	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.585G>A	2.37:g.231742138G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	181	84	0.464088	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	37	CCDS2479.1																																																																																			G|0.988;A|0.012	0.012	strong		0.607	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
MFRP	83552	hgsc.bcm.edu	37	11	119216231	119216231	+	Silent	SNP	A	A	G	rs2510143	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:119216231A>G	ENST00000530681.1	-	5	684	c.540T>C	c.(538-540)caT>caC	p.H180H	C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000555262.1_Silent_p.H180H|MFRP_ENST00000449574.2_Silent_p.H180H|MFRP_ENST00000360167.4_Silent_p.H180H|MFRP_ENST00000529147.1_5'UTR	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	180	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		GCTGTATTGCATGGTCTGTGG	0.577													A|||	4517	0.901957	0.8449	0.8732	5008	,	,		19711	0.875		0.9493	False		,,,				2504	0.9785				p.H180H		Atlas-SNP	.											MFRP,NS,carcinoma,-1,1	MFRP	63	1	0			c.T540C						PASS	.	A	,	3840,558	773.6+/-414.0	1681,478,40	70.0	66.0	67.0		,540	-8.0	0.0	11	dbSNP_100	67	8209,381	801.3+/-407.4	3924,361,10	no	utr-5,coding-synonymous	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,	5605,839,50	GG,GA,AA		4.4354,12.6876,7.2298	,	,180/580	119216231	12049,939	2199	4295	6494	SO:0001819	synonymous_variant	83552	exon5			TATTGCATGGTCT	AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"""membrane-type frizzled-related protein"", ""complement C1q tumor necrosis factor-related protein 5 precursor variant 1"""	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.540T>C	11.37:g.119216231A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Silent	SNP	ENST00000530681.1	37	CCDS8421.1																																																																																			A|0.088;G|0.912	0.912	strong		0.577	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433	
TREML4	285852	hgsc.bcm.edu	37	6	41196727	41196727	+	Silent	SNP	C	C	T	rs2101269	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41196727C>T	ENST00000341495.2	+	2	443	c.339C>T	c.(337-339)aaC>aaT	p.N113N	TREML4_ENST00000448827.2_Silent_p.N113N	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	113	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					GAATCTACAACGCTTCCGAAA	0.478													C|||	3462	0.691294	0.4259	0.8141	5008	,	,		19860	0.8383		0.7734	False		,,,				2504	0.727				p.N113N		Atlas-SNP	.											.	TREML4	25	.	0			c.C339T						PASS	.	C		2167,2239		518,1131,554	86.0	82.0	83.0		339	-1.5	0.0	6	dbSNP_96	83	6802,1798		2687,1428,185	no	coding-synonymous	TREML4	NM_198153.2		3205,2559,739	TT,TC,CC		20.907,49.1829,31.0395		113/201	41196727	8969,4037	2203	4300	6503	SO:0001819	synonymous_variant	285852	exon2			CTACAACGCTTCC	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"""Immunoglobulin superfamily / V-set domain containing"""	30807	protein-coding gene	gene with protein product	"""TREM like transcript 4"""	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.339C>T	6.37:g.41196727C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_198153	B7ZL92	Silent	SNP	ENST00000341495.2	37	CCDS34446.1																																																																																			C|0.306;T|0.694	0.694	strong		0.478	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
DACT2	168002	hgsc.bcm.edu	37	6	168709147	168709147	+	Silent	SNP	G	G	A	rs41266321	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:168709147G>A	ENST00000366795.3	-	4	1378	c.1290C>T	c.(1288-1290)agC>agT	p.S430S	DACT2_ENST00000610183.1_Silent_p.S260S|DACT2_ENST00000366796.3_Intron|DACT2_ENST00000607983.1_Silent_p.S22S	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	430					epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		TGAGGACACAGCTGTTTGAGG	0.627													G|||	221	0.0441294	0.0136	0.0432	5008	,	,		16344	0.004		0.0895	False		,,,				2504	0.0808				p.S430S		Atlas-SNP	.											.	DACT2	46	.	0			c.C1290T						PASS	.	G		29,1355		0,29,663	92.0	83.0	85.0		1290	2.3	0.0	6	dbSNP_127	85	241,2941		9,223,1359	no	coding-synonymous	DACT2	NM_214462.3		9,252,2022	AA,AG,GG		7.5739,2.0954,5.9133		430/775	168709147	270,4296	692	1591	2283	SO:0001819	synonymous_variant	168002	exon4			GACACAGCTGTTT	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1290C>T	6.37:g.168709147G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Silent	SNP	ENST00000366795.3	37	CCDS47519.1																																																																																			G|0.957;A|0.043	0.043	strong		0.627	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
LINC00283	100874057	hgsc.bcm.edu	37	13	103397583	103397583	+	RNA	SNP	C	C	G	rs9582626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103397583C>G	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		TTTAACAATGCCTCCTGTTTC	0.388													C|||	3479	0.694688	0.5424	0.7493	5008	,	,		21547	0.5923		0.826	False		,,,				2504	0.8323				p.A1822P		Atlas-SNP	.											.	.	.	.	0			c.G5464C						PASS	.	C	PRO/ALA	774,610		217,340,135	117.0	102.0	107.0		5464	-0.5	0.0	13	dbSNP_119	107	2544,638		1024,496,71	yes	missense	CCDC168	NM_001146197.1	27	1241,836,206	GG,GC,CC		20.0503,44.0751,27.3325		1822/7082	103397583	3318,1248	692	1591	2283			643677	exon4			ACAATGCCTCCTG			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103397583C>G		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	223	93	0.41704	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.319;G|0.681	0.681	strong		0.388	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
ZCCHC14	23174	hgsc.bcm.edu	37	16	87445363	87445363	+	Silent	SNP	G	G	A	rs1050846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:87445363G>A	ENST00000268616.4	-	12	2770	c.2553C>T	c.(2551-2553)caC>caT	p.H851H		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	851							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		TGTAAGGGGCGTGCACGACGG	0.657													G|||	738	0.147364	0.0545	0.2161	5008	,	,		12294	0.002		0.4453	False		,,,				2504	0.0675				p.H851H		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.C2553T						PASS	.	G		528,3868	229.1+/-243.8	24,480,1694	35.0	32.0	33.0		2553	-0.1	0.2	16	dbSNP_86	33	3787,4813	522.4+/-380.1	828,2131,1341	no	coding-synonymous	ZCCHC14	NM_015144.2		852,2611,3035	AA,AG,GG		44.0349,12.0109,33.2025		851/950	87445363	4315,8681	2198	4300	6498	SO:0001819	synonymous_variant	23174	exon12			AGGGGCGTGCACG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2553C>T	16.37:g.87445363G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																			G|0.719;A|0.281	0.281	strong		0.657	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
TTN	7273	hgsc.bcm.edu	37	2	179498042	179498042	+	Missense_Mutation	SNP	T	T	C	rs6723526	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179498042T>C	ENST00000591111.1	-	183	38259	c.38035A>G	c.(38035-38037)Aaa>Gaa	p.K12679E	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K5447E|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K5255E|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K11752E|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K5380E|TTN_ENST00000589042.1_Missense_Mutation_p.K14320E			Q8WZ42	TITIN_HUMAN	titin	12679			K -> E. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTCCACTTTTATTAGTCGA	0.403													T|||	255	0.0509185	0.0061	0.062	5008	,	,		21983	0.005		0.1004	False		,,,				2504	0.1002				p.K14320E		Atlas-SNP	.											.	TTN	18412	.	0			c.A42958G						PASS	.	T	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	66,3608		2,62,1773	107.0	107.0	107.0		15763,35254,16138,16339	6.2	1.0	2	dbSNP_116	107	898,7282		62,774,3254	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	56,56,56,56	64,836,5027	CC,CT,TT		10.978,1.7964,8.1323	probably-damaging,probably-damaging,probably-damaging,probably-damaging	5255/26927,11752/33424,5380/27052,5447/27119	179498042	964,10890	1837	4090	5927	SO:0001583	missense	7273	exon233			CCACTTTTATTAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.38035A>G	2.37:g.179498042T>C	ENSP00000465570:p.Lys12679Glu	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	290	143	0.493103	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		115	0.052655677655677656	5	0.01016260162601626	25	0.06906077348066299	3	0.005244755244755245	82	0.10817941952506596	T	14.25	2.479880	0.44044	0.017964	0.10978	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65732	-0.17;0.03;0.03;0.01	6.17	6.17	0.99709	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.04318	0.0119	L	0.37800	1.135	0.09310	P	0.99999246212	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	D;D;D;D	0.75020	0.985;0.985;0.985;0.985	T	0.42413	-0.9453	8	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	rs6723526;rs17355040;rs52803857;rs57159952;rs6723526	5255;5380;5447;12679	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	11752;5255;5447;5380;5255	ENSP00000343764:K11752E;ENSP00000434586:K5255E;ENSP00000340554:K5447E;ENSP00000352154:K5380E	ENSP00000340554:K5447E	K	-	1	0	TTN	179206287	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.235000	0.72332	2.371000	0.80710	0.533000	0.62120	AAA	T|0.944;C|0.056	0.056	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TMEM132C	92293	hgsc.bcm.edu	37	12	129181810	129181810	+	Silent	SNP	A	A	G	rs885546	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:129181810A>G	ENST00000435159.2	+	8	1971	c.1971A>G	c.(1969-1971)acA>acG	p.T657T	TMEM132C_ENST00000537538.1_Silent_p.T42T|TMEM132C_ENST00000315208.8_Silent_p.T273T	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	657						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						CAGAGAAGACAATAACCGTGC	0.522													A|||	3990	0.796725	0.5257	0.8833	5008	,	,		21430	0.8472		0.9662	False		,,,				2504	0.8753				p.T657T		Atlas-SNP	.											.	TMEM132C	142	.	0			c.A1971G						PASS	.	A		817,567		240,337,115	31.0	28.0	29.0		1971	-4.2	0.3	12	dbSNP_86	29	3077,105		1490,97,4	no	coding-synonymous	TMEM132C	NM_001136103.2		1730,434,119	GG,GA,AA		3.2998,40.9682,14.7175		657/1109	129181810	3894,672	692	1591	2283	SO:0001819	synonymous_variant	92293	exon8			GAAGACAATAACC	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.1971A>G	12.37:g.129181810A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001136103	Q69YX8	Silent	SNP	ENST00000435159.2	37																																																																																				A|0.186;G|0.814	0.814	strong		0.522	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
PCDH12	51294	hgsc.bcm.edu	37	5	141335498	141335498	+	Missense_Mutation	SNP	C	C	T	rs164515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141335498C>T	ENST00000231484.3	-	1	3129	c.1919G>A	c.(1918-1920)aGt>aAt	p.S640N	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	640	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> N (in dbSNP:rs164515). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039}.		calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCATTTCCACTGCGGATGCT	0.567													C|||	751	0.14996	0.0227	0.196	5008	,	,		19319	0.127		0.2664	False		,,,				2504	0.1933				p.S640N		Atlas-SNP	.											PCDH12,colon,carcinoma,+1,1	PCDH12	133	1	0			c.G1919A						PASS	.	C	ASN/SER	311,4095	165.4+/-196.9	11,289,1903	75.0	68.0	70.0		1919	2.7	0.0	5	dbSNP_79	70	2567,6033	418.0+/-352.6	388,1791,2121	yes	missense	PCDH12	NM_016580.2	46	399,2080,4024	TT,TC,CC		29.8488,7.0586,22.1282	benign	640/1185	141335498	2878,10128	2203	4300	6503	SO:0001583	missense	51294	exon1			TTTCCACTGCGGA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.1919G>A	5.37:g.141335498C>T	ENSP00000231484:p.Ser640Asn	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	55	0.597826	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	370	0.16941391941391942	17	0.034552845528455285	81	0.22375690607734808	71	0.12412587412587413	201	0.26517150395778366	C	0.015	-1.564822	0.00903	0.070586	0.298488	ENSG00000113555	ENST00000231484	D	0.83250	-1.7	5.38	2.7	0.31948	Cadherin (4);Cadherin-like (1);	0.728565	0.14492	N	0.316263	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.04153	-1.0973	9	0.31617	T	0.26	.	4.9107	0.13820	0.0:0.5982:0.1535:0.2483	rs164515;rs3747721;rs17208628;rs58835966;rs164515	640	Q9NPG4	PCD12_HUMAN	N	640	ENSP00000231484:S640N	ENSP00000231484:S640N	S	-	2	0	PCDH12	141315682	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	0.609000	0.24238	0.424000	0.26061	-0.136000	0.14681	AGT	C|0.796;T|0.204	0.204	strong		0.567	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
VPS41	27072	hgsc.bcm.edu	37	7	38829465	38829465	+	Silent	SNP	C	C	T	rs1001476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:38829465C>T	ENST00000310301.4	-	10	774	c.720G>A	c.(718-720)gtG>gtA	p.V240V	VPS41_ENST00000466017.1_5'UTR|VPS41_ENST00000395969.2_Silent_p.V215V	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	240					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TCACTGAGCACACCTGGAAAA	0.363													T|||	592	0.118211	0.3533	0.0576	5008	,	,		20768	0.0		0.0676	False		,,,				2504	0.0174				p.V240V		Atlas-SNP	.											.	VPS41	102	.	0			c.G720A						PASS	.	T	,	1273,3133	702.5+/-406.9	194,885,1124	127.0	117.0	120.0		720,645	-6.5	0.9	7	dbSNP_86	120	607,7993	792.1+/-407.5	21,565,3714	no	coding-synonymous,coding-synonymous	VPS41	NM_014396.3,NM_080631.3	,	215,1450,4838	TT,TC,CC		7.0581,28.8924,14.4549	,	240/855,215/830	38829465	1880,11126	2203	4300	6503	SO:0001819	synonymous_variant	27072	exon10			TGAGCACACCTGG	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.720G>A	7.37:g.38829465C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																			T|0.138;G|0.005	0.138	strong		0.363	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
CYLD	1540	hgsc.bcm.edu	37	16	50810149	50810149	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50810149G>A	ENST00000427738.3	+	6	1187	c.982G>A	c.(982-984)Gac>Aac	p.D328N	CYLD_ENST00000311559.9_Missense_Mutation_p.D328N|CYLD_ENST00000540145.1_Missense_Mutation_p.D328N|CYLD_ENST00000564326.1_Missense_Mutation_p.D325N|CYLD_ENST00000568704.2_Missense_Mutation_p.D325N|CYLD_ENST00000566206.1_Missense_Mutation_p.D325N|CYLD_ENST00000569418.1_Missense_Mutation_p.D325N|CYLD_ENST00000398568.2_Missense_Mutation_p.D325N			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	328	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				AGGTGTTGGGGACAAAGGTTC	0.388			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.D328N		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.G982A						PASS	.						102.0	102.0	102.0					16																	50810149		1861	4094	5955	SO:0001583	missense	1540	exon8	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	GTTGGGGACAAAG	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.982G>A	16.37:g.50810149G>A	ENSP00000392025:p.Asp328Asn	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	13	0.125	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299579	0.81136	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.19669	2.13;2.13;2.13	6.17	6.17	0.99709	.	0.151321	0.64402	D	0.000010	T	0.17365	0.0417	N	0.14661	0.345	0.49582	D	0.999803	B;B;B;B	0.12013	0.003;0.005;0.005;0.003	B;B;B;B	0.11329	0.003;0.006;0.006;0.003	T	0.05937	-1.0855	10	0.48119	T	0.1	-20.1557	20.8794	0.99867	0.0:0.0:1.0:0.0	.	325;328;325;328	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	N	328;328;325;325	ENSP00000445447:D328N;ENSP00000308928:D328N;ENSP00000381574:D325N	ENSP00000308928:D328N	D	+	1	0	CYLD	49367650	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.760000	0.74939	2.941000	0.99782	0.655000	0.94253	GAC	.	.	none		0.388	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
ITM2C	81618	hgsc.bcm.edu	37	2	231738263	231738263	+	Silent	SNP	C	C	T	rs2289234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231738263C>T	ENST00000326427.6	+	2	378	c.252C>T	c.(250-252)ttC>ttT	p.F84F	ITM2C_ENST00000409704.2_Silent_p.F22F|ITM2C_ENST00000326407.6_Silent_p.F84F|ITM2C_ENST00000492029.1_3'UTR|ITM2C_ENST00000335005.6_Intron	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	84					negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GATACTTCTTCCTTGCGCAGG	0.622													C|||	2553	0.509784	0.2277	0.5331	5008	,	,		20020	0.8155		0.504	False		,,,				2504	0.5654				p.F84F		Atlas-SNP	.											.	ITM2C	17	.	0			c.C252T						PASS	.	C	,,	1099,3307	384.2+/-325.2	138,823,1242	96.0	66.0	76.0		,252,252	2.9	1.0	2	dbSNP_100	76	4159,4441	553.8+/-386.4	1025,2109,1166	no	intron,coding-synonymous,coding-synonymous	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,,	1163,2932,2408	TT,TC,CC		48.3605,24.9433,40.4275	,,	,84/231,84/268	231738263	5258,7748	2203	4300	6503	SO:0001819	synonymous_variant	81618	exon2			CTTCTTCCTTGCG	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.252C>T	2.37:g.231738263C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	37	CCDS2479.1																																																																																			C|0.546;T|0.454	0.454	strong		0.622	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
PDHX	8050	hgsc.bcm.edu	37	11	34991727	34991727	+	Silent	SNP	T	T	C	rs497582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34991727T>C	ENST00000227868.4	+	7	942	c.858T>C	c.(856-858)gtT>gtC	p.V286V	PDHX_ENST00000430469.2_Intron|PDHX_ENST00000448838.3_Silent_p.V271V			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	286					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TTCGAAGAGTTATTGCCAAGA	0.403													T|||	2857	0.570487	0.3169	0.5562	5008	,	,		15864	0.7421		0.7058	False		,,,				2504	0.6074				p.V286V		Atlas-SNP	.											.	PDHX	40	.	0			c.T858C						PASS	.	T	,,	1705,2699	513.6+/-368.4	340,1025,837	93.0	84.0	87.0		813,,858	-1.9	1.0	11	dbSNP_83	87	6059,2537	692.5+/-404.6	2150,1759,389	no	coding-synonymous,intron,coding-synonymous	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	,,	2490,2784,1226	CC,CT,TT		29.5137,38.7148,40.2769	,,	271/487,,286/502	34991727	7764,5236	2202	4298	6500	SO:0001819	synonymous_variant	8050	exon7			AAGAGTTATTGCC	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.858T>C	11.37:g.34991727T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	37	CCDS7896.1																																																																																			T|0.407;C|0.593	0.593	strong		0.403	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
LVRN	206338	hgsc.bcm.edu	37	5	115298378	115298378	+	Silent	SNP	C	C	T	rs10062297	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:115298378C>T	ENST00000357872.4	+	1	188	c.64C>T	c.(64-66)Ctg>Ttg	p.L22L	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		22						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.L22L(1)									GCTGGCTGGGCTGGTAGCCGC	0.701													C|||	3881	0.77496	0.8533	0.8069	5008	,	,		13073	0.747		0.7843	False		,,,				2504	0.6656				p.L22L		Atlas-SNP	.											FLJ90650,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	prostate(1)	c.C64T						PASS	.	C		3692,596		1588,516,40	16.0	19.0	18.0		64	1.9	0.0	5	dbSNP_119	18	6950,1482		2857,1236,123	no	coding-synonymous	AQPEP	NM_173800.4		4445,1752,163	TT,TC,CC		17.5759,13.8993,16.3365		22/991	115298378	10642,2078	2144	4216	6360	SO:0001819	synonymous_variant	0	exon1			GCTGGGCTGGTAG																												ENST00000357872.4:c.64C>T	5.37:g.115298378C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			C|0.218;T|0.782	0.782	strong		0.701	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
EIF2A	83939	hgsc.bcm.edu	37	3	150285520	150285520	+	Silent	SNP	T	T	C	rs2293151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:150285520T>C	ENST00000460851.1	+	7	625	c.516T>C	c.(514-516)gaT>gaC	p.D172D	EIF2A_ENST00000273435.5_Silent_p.D167D|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000383043.3_5'Flank|SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000406576.3_Silent_p.D111D|EIF2A_ENST00000487799.1_Silent_p.D147D			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	172					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)			cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			AAATTAATGATTTTGTATTAT	0.279													T|||	597	0.119209	0.1619	0.1441	5008	,	,		20121	0.0208		0.1581	False		,,,				2504	0.1053				p.D172D		Atlas-SNP	.											.	EIF2A	59	.	0			c.T516C						PASS	.	T		531,3049		33,465,1292	72.0	63.0	65.0		516	3.6	1.0	3	dbSNP_100	65	1227,6867		110,1007,2930	no	coding-synonymous	EIF2A	NM_032025.3		143,1472,4222	CC,CT,TT		15.1594,14.8324,15.0591		172/586	150285520	1758,9916	1790	4047	5837	SO:0001819	synonymous_variant	83939	exon7			TAATGATTTTGTA	AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.516T>C	3.37:g.150285520T>C		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	268	119	0.44403	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Silent	SNP	ENST00000460851.1	37	CCDS46935.1																																																																																			T|0.885;C|0.115	0.115	strong		0.279	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025	
OPN4	94233	hgsc.bcm.edu	37	10	88414570	88414570	+	Silent	SNP	G	G	A	rs11202106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88414570G>A	ENST00000241891.5	+	1	197	c.30G>A	c.(28-30)ccG>ccA	p.P10P	OPN4_ENST00000372071.2_Silent_p.P10P	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	10			P -> L (in dbSNP:rs2675703). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CAAGAGTCCCGCCCAGCCCAA	0.642													G|||	1182	0.236022	0.062	0.1758	5008	,	,		15979	0.2778		0.3022	False		,,,				2504	0.4029				p.P10P		Atlas-SNP	.											OPN4,NS,carcinoma,+1,1	OPN4	61	1	0			c.G30A						scavenged	.	G	,	432,3974	207.8+/-229.1	21,390,1792	65.0	66.0	66.0		30,30	-9.3	0.0	10	dbSNP_120	66	2819,5781	443.7+/-360.5	483,1853,1964	no	coding-synonymous,coding-synonymous	OPN4	NM_001030015.2,NM_033282.3	,	504,2243,3756	AA,AG,GG		32.7791,9.8048,24.9962	,	10/490,10/479	88414570	3251,9755	2203	4300	6503	SO:0001819	synonymous_variant	94233	exon1			AGTCCCGCCCAGC	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.30G>A	10.37:g.88414570G>A		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_033282	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Silent	SNP	ENST00000241891.5	37	CCDS7376.1																																																																																			G|0.763;A|0.237	0.237	strong		0.642	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
TOX4	9878	hgsc.bcm.edu	37	14	21960816	21960816	+	Silent	SNP	T	T	C	rs1060722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21960816T>C	ENST00000405508.1	+	8	1317	c.1041T>C	c.(1039-1041)ctT>ctC	p.L347L	TOX4_ENST00000448790.2_Silent_p.L324L|TOX4_ENST00000262709.3_Silent_p.L347L			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	347						chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)			large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		ACTCCACCCTTTCATCCTATG	0.493													T|||	2482	0.495607	0.4281	0.3746	5008	,	,		18322	0.6488		0.503	False		,,,				2504	0.5072				p.L347L		Atlas-SNP	.											.	TOX4	50	.	0			c.T1041C						PASS	.	T		2066,2340	570.7+/-382.9	476,1114,613	114.0	116.0	116.0		1041	1.4	1.0	14	dbSNP_86	116	4318,4282	578.9+/-390.8	1124,2070,1106	no	coding-synonymous	TOX4	NM_014828.2		1600,3184,1719	CC,CT,TT		49.7907,46.8906,49.085		347/622	21960816	6384,6622	2203	4300	6503	SO:0001819	synonymous_variant	9878	exon7			CACCCTTTCATCC	AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"""chromosome 14 open reading frame 92"", ""KIAA0737"""	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.1041T>C	14.37:g.21960816T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_014828	B4DPY8|B4DSM0|E7EV69	Silent	SNP	ENST00000405508.1	37	CCDS32043.1																																																																																			T|0.514;C|0.486	0.486	strong		0.493	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828	
MUC16	94025	hgsc.bcm.edu	37	19	9066874	9066874	+	Missense_Mutation	SNP	G	G	T	rs12609150	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9066874G>T	ENST00000397910.4	-	3	20775	c.20572C>A	c.(20572-20574)Cca>Aca	p.P6858T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6860	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCAAATTTGGAGGTGAACTG	0.493													g|||	1007	0.201078	0.0946	0.2824	5008	,	,		23077	0.3254		0.167	False		,,,				2504	0.1943				p.P6858T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C20572A						PASS	.	G	THR/PRO	425,3671		18,389,1641	163.0	154.0	157.0		20572	-3.0	0.0	19	dbSNP_120	157	1520,6886		138,1244,2821	yes	missense	MUC16	NM_024690.2	38	156,1633,4462	TT,TG,GG		18.0823,10.376,15.5575	probably-damaging	6858/14508	9066874	1945,10557	2048	4203	6251	SO:0001583	missense	94025	exon3			AATTTGGAGGTGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20572C>A	19.37:g.9066874G>T	ENSP00000381008:p.Pro6858Thr	Somatic	440	0	0		WXS	Illumina HiSeq	Phase_I	418	212	0.507177	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	479	0.21932234432234432	56	0.11382113821138211	92	0.2541436464088398	205	0.3583916083916084	126	0.1662269129287599	g	2.557	-0.302824	0.05495	0.10376	0.180823	ENSG00000181143	ENST00000397910	T	0.26067	1.76	2.12	-2.96	0.05547	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	.	.	.	B	0.27351	0.176	B	0.19946	0.027	T	0.45381	-0.9265	8	0.87932	D	0	.	2.1735	0.03856	0.4264:0.0:0.3309:0.2427	rs12609150;rs52836809;rs12609150	6858	B5ME49	.	T	6858	ENSP00000381008:P6858T	ENSP00000381008:P6858T	P	-	1	0	MUC16	8927874	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.960000	0.03849	-0.553000	0.06158	-0.513000	0.04457	CCA	G|0.786;T|0.214	0.214	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FSIP1	161835	hgsc.bcm.edu	37	15	39910052	39910052	+	Missense_Mutation	SNP	C	C	G	rs16969386	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:39910052C>G	ENST00000350221.3	-	11	1792	c.1583G>C	c.(1582-1584)gGc>gCc	p.G528A		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	528			G -> A (in dbSNP:rs16969386).					p.G528A(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCTCCCAATGCCAAGAGTCTT	0.408													C|||	788	0.157348	0.0333	0.1196	5008	,	,		21212	0.2907		0.1471	False		,,,				2504	0.2249				p.G528A		Atlas-SNP	.											FSIP1,NS,carcinoma,0,1	FSIP1	53	1	1	Substitution - Missense(1)	stomach(1)	c.G1583C						PASS	.	C	ALA/GLY	233,4167	136.5+/-172.5	4,225,1971	109.0	102.0	104.0		1583	4.8	1.0	15	dbSNP_123	104	1124,7470	231.9+/-265.7	65,994,3238	yes	missense	FSIP1	NM_152597.4	60	69,1219,5209	GG,GC,CC		13.0789,5.2955,10.4433	probably-damaging	528/582	39910052	1357,11637	2200	4297	6497	SO:0001583	missense	161835	exon11			CCAATGCCAAGAG	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1583G>C	15.37:g.39910052C>G	ENSP00000280236:p.Gly528Ala	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	154	66	0.428571	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	349	0.15979853479853479	16	0.032520325203252036	48	0.13259668508287292	178	0.3111888111888112	107	0.14116094986807387	C	17.76	3.467593	0.63625	0.052955	0.130789	ENSG00000150667	ENST00000350221	T	0.14144	2.53	4.84	4.84	0.62591	.	0.168900	0.38005	N	0.001843	T	0.00012	0.0000	L	0.29908	0.895	0.35187	P	0.22696400000000005	D	0.76494	0.999	D	0.69654	0.965	T	0.46373	-0.9196	8	.	.	.	-7.1189	10.4881	0.44735	0.0:0.9018:0.0:0.0982	rs16969386;rs57363512;rs16969386	528	Q8NA03	FSIP1_HUMAN	A	528	ENSP00000280236:G528A	.	G	-	2	0	FSIP1	37697344	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.819000	0.48049	2.669000	0.90835	0.591000	0.81541	GGC	C|0.858;G|0.142	0.142	strong		0.408	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
ARSD	414	hgsc.bcm.edu	37	X	2836184	2836184	+	Missense_Mutation	SNP	C	C	T	rs73632976		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836184C>T	ENST00000381154.1	-	5	599	c.524G>A	c.(523-525)gGc>gAc	p.G175D	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	175					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GAAGGGCATGCCGTAGAAATA	0.592																																					p.G175D		Atlas-SNP	.											.	ARSD	47	.	0			c.G524A						PASS	.						36.0	22.0	27.0					X																	2836184		2202	4298	6500	SO:0001583	missense	414	exon5			GGCATGCCGTAGA	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.524G>A	X.37:g.2836184C>T	ENSP00000370546:p.Gly175Asp	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	156	68	0.435897	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	140	0.08438818565400844	34	0.07727272727272727	28	0.08187134502923976	34	0.0625	61	0.08333333333333333	c	23.6	4.432561	0.83776	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.95622	-3.76	3.47	3.47	0.39725	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	U	0.000000	D	0.82770	0.5109	H	0.97265	3.97	0.09310	P	0.999999842849	P;D	0.58620	0.931;0.983	P;P	0.61070	0.873;0.883	T	0.80400	-0.1398	9	0.72032	D	0.01	.	14.5312	0.67926	0.0:1.0:0.0:0.0	.	175;175	E9PAW5;P51689	.;ARSD_HUMAN	D	175	ENSP00000370546:G175D	ENSP00000217890:G175D	G	-	2	0	ARSD	2846184	1.000000	0.71417	0.184000	0.23157	0.851000	0.48451	4.701000	0.61810	1.394000	0.46624	0.420000	0.28162	GGC	C|0.915;T|0.085	0.085	strong		0.592	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
ZNF774	342132	hgsc.bcm.edu	37	15	90903502	90903502	+	Missense_Mutation	SNP	G	G	A	rs11854320	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90903502G>A	ENST00000354377.3	+	4	625	c.439G>A	c.(439-441)Gta>Ata	p.V147I	ZNF774_ENST00000379090.5_Intron|ZNF774_ENST00000558115.1_3'UTR	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	147			V -> I (in dbSNP:rs11854320).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V147I(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GGATGGATATGTAGGAGAGAA	0.493													G|||	482	0.096246	0.1694	0.1066	5008	,	,		19912	0.0427		0.1163	False		,,,				2504	0.0245				p.V147I		Atlas-SNP	.											ZNF774,NS,carcinoma,0,1	ZNF774	35	1	1	Substitution - Missense(1)	stomach(1)	c.G439A						scavenged	.	G	ILE/VAL	772,3626	310.8+/-291.8	74,624,1501	74.0	76.0	75.0		439	1.5	0.0	15	dbSNP_120	75	953,7643	207.9+/-249.5	60,833,3405	yes	missense	ZNF774	NM_001004309.2	29	134,1457,4906	AA,AG,GG		11.0866,17.5534,13.2754	benign	147/484	90903502	1725,11269	2199	4298	6497	SO:0001583	missense	342132	exon4			GGATATGTAGGAG	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"""Zinc fingers, C2H2-type"""	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.439G>A	15.37:g.90903502G>A	ENSP00000346348:p.Val147Ile	Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_001004309	A8K020	Missense_Mutation	SNP	ENST00000354377.3	37	CCDS32330.1	245	0.11217948717948718	79	0.16056910569105692	38	0.10497237569060773	35	0.06118881118881119	93	0.12269129287598944	G	9.491	1.100722	0.20552	0.175534	0.110866	ENSG00000196391	ENST00000354377	T	0.05925	3.37	5.51	1.5	0.22942	.	0.528567	0.14024	N	0.346624	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.9999999999047681	B	0.06786	0.001	B	0.04013	0.001	T	0.38067	-0.9678	9	0.66056	D	0.02	.	6.8497	0.24008	0.4968:0.0:0.5032:0.0	rs11854320;rs52813081;rs11854320	147	Q6NX45	ZN774_HUMAN	I	147	ENSP00000346348:V147I	ENSP00000346348:V147I	V	+	1	0	ZNF774	88704506	0.000000	0.05858	0.014000	0.15608	0.205000	0.24178	-0.425000	0.07017	0.270000	0.21984	0.655000	0.94253	GTA	G|0.879;A|0.121	0.121	strong		0.493	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309	
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37730368	37730368	+	Missense_Mutation	SNP	G	G	A	rs12541651	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:37730368G>A	ENST00000330843.4	-	4	1964	c.1952C>T	c.(1951-1953)gCc>gTc	p.A651V	RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000287263.4_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	651			A -> V (in dbSNP:rs12541651). {ECO:0000269|PubMed:16920206}.		protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TGATCCCAGGGCAGAAGAACC	0.512													G|||	3006	0.60024	0.4244	0.6427	5008	,	,		21671	0.7034		0.6889	False		,,,				2504	0.6104				p.A651V		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C1952T						PASS	.	G	VAL/ALA,	2100,2306	575.0+/-383.9	493,1114,596	111.0	106.0	108.0		1952,	4.8	0.1	8	dbSNP_120	108	5839,2761	679.3+/-403.5	1985,1869,446	yes	missense,intron	RAB11FIP1	NM_001002814.2,NM_025151.4	64,	2478,2983,1042	AA,AG,GG		32.1047,47.6623,38.9589	benign,	651/1284,	37730368	7939,5067	2203	4300	6503	SO:0001583	missense	80223	exon4			CCCAGGGCAGAAG	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.1952C>T	8.37:g.37730368G>A	ENSP00000331342:p.Ala651Val	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	190	79	0.415789	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	1381	0.6323260073260073	207	0.42073170731707316	234	0.6464088397790055	416	0.7272727272727273	524	0.6912928759894459	G	17.72	3.458252	0.63401	0.476623	0.678953	ENSG00000156675	ENST00000330843	T	0.15017	2.46	4.84	4.84	0.62591	.	0.299822	0.23702	N	0.045412	T	0.00012	0.0000	.	.	.	0.32824	P	0.49681699999999995	.	.	.	.	.	.	T	0.07908	-1.0748	6	0.31617	T	0.26	-13.2373	9.1369	0.36879	0.0996:0.0:0.9004:0.0	rs12541651;rs52829299;rs59223277;rs12541651	.	.	.	V	651	ENSP00000331342:A651V	ENSP00000331342:A651V	A	-	2	0	RAB11FIP1	37849526	0.000000	0.05858	0.133000	0.22050	0.059000	0.15707	-0.016000	0.12613	2.235000	0.73313	0.655000	0.94253	GCC	G|0.389;A|0.611	0.611	strong		0.512	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151	
OASL	8638	hgsc.bcm.edu	37	12	121471337	121471337	+	Silent	SNP	G	G	A	rs3213545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121471337G>A	ENST00000257570.5	-	2	678	c.408C>T	c.(406-408)ctC>ctT	p.L136L	OASL_ENST00000339275.5_Silent_p.L136L	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	136					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGGTGAAGACGAGAGCATCGG	0.602													G|||	1568	0.313099	0.1293	0.2839	5008	,	,		19668	0.4692		0.3072	False		,,,				2504	0.4274				p.L136L	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.C408T						PASS	.	G	,	645,3761	274.6+/-272.0	46,553,1604	120.0	101.0	108.0	http://www.ncbi.nlm.nih.gov/pubmed?term	408,408	-2.8	0.0	12	dbSNP_106	108	2585,6015	421.5+/-353.7	411,1763,2126	no	coding-synonymous,coding-synonymous	OASL	NM_003733.2,NM_198213.1	,	457,2316,3730	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	30.0581,14.6391,24.8347	,	136/515,136/256	121471337	3230,9776	2203	4300	6503	SO:0001819	synonymous_variant	8638	exon2			GAAGACGAGAGCA	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.408C>T	12.37:g.121471337G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_198213	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Silent	SNP	ENST00000257570.5	37	CCDS9211.1																																																																																			G|0.722;A|0.278	0.278	strong		0.602	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733	
EGFR	1956	hgsc.bcm.edu	37	7	55214348	55214348	+	Silent	SNP	C	C	T	rs2072454	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:55214348C>T	ENST00000275493.2	+	4	651	c.474C>T	c.(472-474)aaC>aaT	p.N158N	EGFR_ENST00000342916.3_Silent_p.N158N|EGFR_ENST00000442591.1_Silent_p.N158N|EGFR_ENST00000420316.2_Silent_p.N158N|EGFR_ENST00000344576.2_Silent_p.N158N|EGFR_ENST00000454757.2_Silent_p.N105N|EGFR_ENST00000455089.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	158			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.N158N(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCCTGTGCAACGTGGAGAGCA	0.547		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	2381	0.475439	0.4932	0.4928	5008	,	,		18168	0.3522		0.4841	False		,,,				2504	0.5573				p.N158N		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	EGFR_ENST00000344576,colon,carcinoma,0,5	EGFR	20426	5	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C474T						PASS	.	C	,,,	2183,2223	586.2+/-386.4	558,1067,578	113.0	95.0	101.0		474,474,474,474	2.0	1.0	7	dbSNP_96	101	4517,4083	592.7+/-393.0	1187,2143,970	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EGFR	NM_005228.3,NM_201282.1,NM_201283.1,NM_201284.1	,,,	1745,3210,1548	TT,TC,CC		47.4767,49.5461,48.4853	,,,	158/1211,158/629,158/406,158/706	55214348	6700,6306	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon4	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTGCAACGTGGAG		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.474C>T	7.37:g.55214348C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	50	0.438596	NM_201283	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1	992	0.4542124542124542	231	0.4695121951219512	169	0.46685082872928174	214	0.3741258741258741	378	0.49868073878627966	C	8.281	0.815468	0.16607	0.495461	0.525233	ENSG00000146648	ENST00000395504	.	.	.	5.6	1.99	0.26369	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999999685169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.7571	0.34652	0.0:0.6122:0.0:0.3878	rs2072454;rs17289679;rs17516844;rs2072454	.	.	.	.	-1	.	.	.	+	.	.	EGFR	55181842	0.692000	0.27719	0.987000	0.45799	0.655000	0.38815	1.216000	0.32443	0.544000	0.28883	-0.136000	0.14681	.	C|0.506;N|0.000	.	strong		0.547	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
KIAA1755	85449	hgsc.bcm.edu	37	20	36870122	36870122	+	Silent	SNP	T	T	G	rs1205435	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:36870122T>G	ENST00000279024.4	-	3	682	c.411A>C	c.(409-411)ccA>ccC	p.P137P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	137										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AGGCTGGCTCTGGAACAGGCT	0.517													G|||	1326	0.264776	0.2027	0.2262	5008	,	,		19761	0.2728		0.3191	False		,,,				2504	0.3119				p.P137P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.A411C						PASS	.	G		910,3496	645.6+/-398.2	148,614,1441	102.0	101.0	102.0		411	-11.7	0.0	20	dbSNP_87	102	2807,5793	656.2+/-401.3	517,1773,2010	no	coding-synonymous	KIAA1755	NM_001029864.1		665,2387,3451	GG,GT,TT		32.6395,20.6537,28.5791		137/1201	36870122	3717,9289	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			TGGCTCTGGAACA	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.411A>C	20.37:g.36870122T>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	184	94	0.51087	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			T|0.674;G|0.319;A|0.007	0.319	strong		0.517	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
NAF1	92345	hgsc.bcm.edu	37	4	164050186	164050186	+	Missense_Mutation	SNP	C	C	T	rs200516616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:164050186C>T	ENST00000274054.2	-	8	1541	c.1348G>A	c.(1348-1350)Ggt>Agt	p.G450S	NAF1_ENST00000422287.2_Intron|NAF1_ENST00000509434.1_Intron	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	450	Pro-rich.				pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				GTAGCCCAACCCATGTTTACA	0.552													C|||	4	0.000798722	0.0	0.0014	5008	,	,		4832	0.0		0.003	False		,,,				2504	0.0				p.G450S		Atlas-SNP	.											.	NAF1	69	.	0			c.G1348A						PASS	.	C	,SER/GLY	4,4130		0,4,2063	7.0	6.0	6.0		,1348	-0.6	0.4	4		6	49,7983		0,49,3967	yes	intron,missense	NAF1	NM_001128931.1,NM_138386.2	,56	0,53,6030	TT,TC,CC		0.6101,0.0968,0.4356	,benign	,450/495	164050186	53,12113	2067	4016	6083	SO:0001583	missense	92345	exon8			CCCAACCCATGTT		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"""nuclear assembly factor 1 homolog (S. cerevisiae)"""			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.1348G>A	4.37:g.164050186C>T	ENSP00000274054:p.Gly450Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_138386	D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	37	CCDS3803.1	.	.	.	.	.	.	.	.	.	.	C	2.898	-0.228083	0.06022	9.68E-4	0.006101	ENSG00000145414	ENST00000274054	T	0.32272	1.46	4.26	-0.646	0.11472	.	1.456920	0.03892	N	0.278939	T	0.12603	0.0306	N	0.19112	0.55	0.21933	N	0.999467	B	0.26081	0.141	B	0.17722	0.019	T	0.13602	-1.0503	10	0.18710	T	0.47	-1.8427	5.522	0.16938	0.0:0.4943:0.1432:0.3625	.	450	Q96HR8	NAF1_HUMAN	S	450	ENSP00000274054:G450S	ENSP00000274054:G450S	G	-	1	0	NAF1	164269636	0.055000	0.20627	0.425000	0.26659	0.250000	0.25880	0.024000	0.13555	-0.312000	0.08741	-2.411000	0.00221	GGT	.	.	weak		0.552	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386	
SPEM1	374768	hgsc.bcm.edu	37	17	7324788	7324788	+	Missense_Mutation	SNP	G	G	A	rs33989543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7324788G>A	ENST00000323675.3	+	3	819	c.794G>A	c.(793-795)cGg>cAg	p.R265Q	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	265					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				TATGATGCCCGGGACATGAGA	0.652													G|||	406	0.0810703	0.0643	0.0836	5008	,	,		17238	0.1151		0.0736	False		,,,				2504	0.0746				p.R265Q		Atlas-SNP	.											.	SPEM1	41	.	0			c.G794A						PASS	.	G	GLN/ARG	253,3645		9,235,1705	30.0	32.0	32.0		794	3.7	0.7	17	dbSNP_126	32	577,7675		34,509,3583	yes	missense	SPEM1	NM_199339.2	43	43,744,5288	AA,AG,GG		6.9922,6.4905,6.8313	benign	265/310	7324788	830,11320	1949	4126	6075	SO:0001583	missense	374768	exon3			ATGCCCGGGACAT	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"""chromosome 17 open reading frame 83"""	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.794G>A	17.37:g.7324788G>A	ENSP00000315554:p.Arg265Gln	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_199339		Missense_Mutation	SNP	ENST00000323675.3	37	CCDS42254.1	189	0.08653846153846154	27	0.054878048780487805	36	0.09944751381215469	70	0.12237762237762238	56	0.07387862796833773	G	20.9	4.063878	0.76187	0.064905	0.069922	ENSG00000181323	ENST00000323675	.	.	.	5.65	3.66	0.41972	.	0.351534	0.20536	N	0.090401	T	0.00440	0.0014	L	0.34521	1.04	0.41581	P	0.011253999999999986	P	0.34462	0.454	B	0.23852	0.049	T	0.06826	-1.0805	8	0.39692	T	0.17	-6.3475	8.5979	0.33727	0.1767:0.0:0.8233:0.0	rs33989543	265	Q8N4L4	SPEM1_HUMAN	Q	265	.	ENSP00000315554:R265Q	R	+	2	0	SPEM1	7265512	0.547000	0.26465	0.653000	0.29593	0.709000	0.40893	1.127000	0.31357	0.732000	0.32470	-0.140000	0.14226	CGG	G|0.924;A|0.076	0.076	strong		0.652	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339	
ITGAX	3687	hgsc.bcm.edu	37	16	31374535	31374535	+	Missense_Mutation	SNP	C	C	G	rs2230429	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31374535C>G	ENST00000268296.4	+	14	1671	c.1550C>G	c.(1549-1551)cCc>cGc	p.P517R	ITGAX_ENST00000562522.1_Missense_Mutation_p.P517R	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	517			P -> R (in dbSNP:rs2230429).		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CAGGGCCACCCCTGGGGTCGC	0.637													C|||	1496	0.298722	0.1014	0.3184	5008	,	,		13794	0.6766		0.339	False		,,,				2504	0.1207				p.P517R		Atlas-SNP	.											.	ITGAX	198	.	0			c.C1550G						PASS	.	C	ARG/PRO	685,3709	284.3+/-277.5	55,575,1567	100.0	109.0	106.0		1550	4.0	1.0	16	dbSNP_98	106	3143,5457	472.8+/-368.4	592,1959,1749	yes	missense	ITGAX	NM_000887.3	103	647,2534,3316	GG,GC,CC		36.5465,15.5894,29.4598	possibly-damaging	517/1164	31374535	3828,9166	2197	4300	6497	SO:0001583	missense	3687	exon14			GCCACCCCTGGGG	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1550C>G	16.37:g.31374535C>G	ENSP00000268296:p.Pro517Arg	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	886	0.4056776556776557	64	0.13008130081300814	130	0.35911602209944754	426	0.7447552447552448	266	0.35092348284960423	C	14.93	2.681501	0.47991	0.155894	0.365465	ENSG00000140678	ENST00000268296	T	0.34667	1.35	4.03	4.03	0.46877	.	.	.	.	.	T	0.00012	0.0000	L	0.60904	1.88	0.37094	P	0.10040199999999999	D	0.67145	0.996	P	0.53490	0.727	T	0.19095	-1.0316	8	0.87932	D	0	.	13.447	0.61146	0.0:1.0:0.0:0.0	rs2230429;rs3087447;rs59868842	517	P20702	ITAX_HUMAN	R	517	ENSP00000268296:P517R	ENSP00000268296:P517R	P	+	2	0	ITGAX	31282036	0.951000	0.32395	1.000000	0.80357	0.965000	0.64279	0.907000	0.28531	1.952000	0.56665	0.460000	0.39030	CCC	C|0.671;G|0.329	0.329	strong		0.637	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
EDA2R	60401	hgsc.bcm.edu	37	X	65824986	65824986	+	Missense_Mutation	SNP	C	C	T	rs1385699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:65824986C>T	ENST00000374719.3	-	3	226	c.170G>A	c.(169-171)aGa>aAa	p.R57K	EDA2R_ENST00000253392.5_Missense_Mutation_p.R57K|EDA2R_ENST00000451436.2_Intron|EDA2R_ENST00000456230.2_Missense_Mutation_p.R57K|EDA2R_ENST00000450752.1_Missense_Mutation_p.R57K|EDA2R_ENST00000396050.1_Missense_Mutation_p.R57K	NM_021783.3	NP_068555	Q9HAV5	TNR27_HUMAN	ectodysplasin A2 receptor	57			R -> K (in dbSNP:rs1385699).		cell differentiation (GO:0030154)|embryo development (GO:0009790)|epidermis development (GO:0008544)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						ACTCTGACATCTGTGGTGGCC	0.542													C|||	2512	0.66543	0.0333	0.6326	3775	,	,		13681	0.7569		0.6123	False		,,,				2504	0.6646				p.R57K		Atlas-SNP	.											.	EDA2R	30	.	0			c.G170A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	547,3288		36,393,82,1203,489	131.0	76.0	95.0		170,170,170	4.0	1.0	X	dbSNP_88	95	5367,1361		1599,731,1438,98,434	yes	missense,missense,missense	EDA2R	NM_001199687.2,NM_001242310.1,NM_021783.3	26,26,26	1635,1124,1520,1301,923	TT,TC,T,CC,C		20.2289,14.2634,44.0121	benign,benign,benign	57/298,57/319,57/298	65824986	5914,4649	2203	4300	6503	SO:0001583	missense	60401	exon2			TGACATCTGTGGT	AF298812	CCDS14386.1, CCDS56603.1	Xq11.1	2013-05-22			ENSG00000131080	ENSG00000131080		"""Tumor necrosis factor receptor superfamily"""	17756	protein-coding gene	gene with protein product		300276				11039935	Standard	NM_021783		Approved	XEDAR, EDA-A2R, EDAA2R, TNFRSF27	uc004dwt.2	Q9HAV5	OTTHUMG00000021736	ENST00000374719.3:c.170G>A	X.37:g.65824986C>T	ENSP00000363851:p.Arg57Lys	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_001242310	Q5VYX9|Q5VYY0|Q6UWM2|Q8IZA6	Missense_Mutation	SNP	ENST00000374719.3	37	CCDS14386.1	1144	0.6895720313441832	26	0.05416666666666667	146	0.6636363636363637	284	1.0	326	0.6877637130801688	C	7.543	0.661064	0.14645	0.142634	0.797711	ENSG00000131080	ENST00000374719;ENST00000396050;ENST00000253392;ENST00000456230;ENST00000450752	T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13	4.04	4.04	0.47022	TNFR/CD27/30/40/95 cysteine-rich region (4);	0.314080	0.26542	N	0.023785	T	0.00012	0.0000	N	0.15975	0.35	0.09310	P	0.9999999999996072	B;B	0.33826	0.001;0.427	B;B	0.31245	0.002;0.126	T	0.51647	-0.8679	9	0.02654	T	1	-10.3612	12.6999	0.57026	0.0:1.0:0.0:0.0	rs1385699;rs52832922;rs61534432;rs1385699	57;57	Q9HAV5-2;Q9HAV5	.;TNR27_HUMAN	K	57	ENSP00000363851:R57K;ENSP00000379365:R57K;ENSP00000253392:R57K;ENSP00000393935:R57K;ENSP00000402929:R57K	ENSP00000253392:R57K	R	-	2	0	EDA2R	65741711	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.661000	0.54503	1.841000	0.53522	0.600000	0.82982	AGA	C|0.436;0|0.005	.	strong		0.542	EDA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057002.1	NM_021783	
CMYA5	202333	hgsc.bcm.edu	37	5	79025503	79025503	+	Silent	SNP	C	C	T	rs76977444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:79025503C>T	ENST00000446378.2	+	2	946	c.915C>T	c.(913-915)ggC>ggT	p.G305G		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	305					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CCTGGAGAGGCGCACTCTCCA	0.408													C|||	27	0.00539137	0.0008	0.0029	5008	,	,		21011	0.0		0.0159	False		,,,				2504	0.0082				p.G305G		Atlas-SNP	.											CMYA5_ENST00000446378,NS,haematopoietic_neoplasm,0,2	CMYA5	643	2	0			c.C915T						PASS	.	C		8,3758		0,8,1875	81.0	75.0	77.0		915	-1.8	0.0	5	dbSNP_132	77	101,8119		0,101,4009	no	coding-synonymous	CMYA5	NM_153610.3		0,109,5884	TT,TC,CC		1.2287,0.2124,0.9094		305/4070	79025503	109,11877	1883	4110	5993	SO:0001819	synonymous_variant	202333	exon2			GAGAGGCGCACTC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.915C>T	5.37:g.79025503C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			C|0.993;T|0.007	0.007	strong		0.408	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
OR10A4	283297	hgsc.bcm.edu	37	11	6898758	6898758	+	Silent	SNP	A	A	C	rs7102808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6898758A>C	ENST00000379829.2	+	1	903	c.880A>C	c.(880-882)Agg>Cgg	p.R294R		NM_207186.2	NP_997069.2	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A, member 4	294					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|liver(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTACAGCTCAAGGAATAAAGA	0.493													A|||	737	0.147165	0.0333	0.2666	5008	,	,		19061	0.1419		0.1889	False		,,,				2504	0.1789				p.R294R		Atlas-SNP	.											.	OR10A4	65	.	0			c.A880C						PASS	.			275,4127	153.3+/-186.9	10,255,1936	110.0	108.0	109.0		880	3.9	1.0	11	dbSNP_116	109	1958,6634	344.4+/-325.3	246,1466,2584	no	coding-synonymous	OR10A4	NM_207186.2		256,1721,4520	CC,CA,AA		22.7886,6.2472,17.1849		294/316	6898758	2233,10761	2201	4296	6497	SO:0001819	synonymous_variant	283297	exon1			AGCTCAAGGAATA	AF209506	CCDS7774.1	11p15.4	2012-08-09	2002-11-13	2004-03-10	ENSG00000170782	ENSG00000170782		"""GPCR / Class A : Olfactory receptors"""	15130	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily A, member 4 pseudogene"""	OR10A4P			Standard	NM_207186		Approved		uc010rat.2	Q9H209	OTTHUMG00000165740	ENST00000379829.2:c.880A>C	11.37:g.6898758A>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_207186	B2RNP5|B9EH36|Q96R20	Silent	SNP	ENST00000379829.2	37	CCDS7774.1																																																																																			A|0.839;C|0.161	0.161	strong		0.493	OR10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385985.1	NM_207186	
CCNT2	905	hgsc.bcm.edu	37	2	135711657	135711657	+	Silent	SNP	G	G	A	rs3814354	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:135711657G>A	ENST00000264157.5	+	9	1662	c.1632G>A	c.(1630-1632)aaG>aaA	p.K544K	CCNT2_ENST00000295238.6_Silent_p.K544K|CCNT2_ENST00000537343.1_Silent_p.K369K	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	544					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		GCAGTGGGAAGAGCAAACATT	0.453													G|||	3516	0.702077	0.6641	0.6225	5008	,	,		20138	0.877		0.5457	False		,,,				2504	0.7904				p.K544K		Atlas-SNP	.											CCNT2_ENST00000264157,colon,carcinoma,0,3	CCNT2	98	3	0			c.G1632A						PASS	.	G	,	2803,1603	653.6+/-399.6	884,1035,284	82.0	82.0	82.0		1632,1632	1.3	1.0	2	dbSNP_107	82	4027,4573	548.0+/-385.3	985,2057,1258	no	coding-synonymous,coding-synonymous	CCNT2	NM_001241.3,NM_058241.2	,	1869,3092,1542	AA,AG,GG		46.8256,36.3822,47.4858	,	544/664,544/731	135711657	6830,6176	2203	4300	6503	SO:0001819	synonymous_variant	905	exon9			TGGGAAGAGCAAA	AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1632G>A	2.37:g.135711657G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	175	78	0.445714	NM_058241	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Silent	SNP	ENST00000264157.5	37	CCDS2174.1																																																																																			G|0.375;A|0.625	0.625	strong		0.453	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241	
LGR6	59352	hgsc.bcm.edu	37	1	202287537	202287537	+	Silent	SNP	G	G	A	rs788794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202287537G>A	ENST00000367278.3	+	18	2195	c.2106G>A	c.(2104-2106)gcG>gcA	p.A702A	LGR6_ENST00000255432.7_Silent_p.A650A|LGR6_ENST00000439764.2_Silent_p.A563A	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	702					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						TGGCCGCCGCGCTGCCCCTGG	0.711													G|||	2644	0.527955	0.2791	0.6182	5008	,	,		14115	0.7163		0.5268	False		,,,				2504	0.6074				p.A702A		Atlas-SNP	.											.	LGR6	102	.	0			c.G2106A						PASS	.	G	,,	1383,3019		216,951,1034	16.0	18.0	18.0		2106,1689,1950	-5.4	0.6	1	dbSNP_86	18	4113,4481		990,2133,1174	no	coding-synonymous,coding-synonymous,coding-synonymous	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	,,	1206,3084,2208	AA,AG,GG		47.859,31.4175,42.2899	,,	702/968,563/829,650/916	202287537	5496,7500	2201	4297	6498	SO:0001819	synonymous_variant	59352	exon18			CGCCGCGCTGCCC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2106G>A	1.37:g.202287537G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	48	35	0.729167	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																			G|0.538;A|0.462	0.462	strong		0.711	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
ANKRD6	22881	hgsc.bcm.edu	37	6	90340446	90340446	+	Missense_Mutation	SNP	C	C	T	rs61739327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90340446C>T	ENST00000522441.1	+	16	2548	c.1907C>T	c.(1906-1908)cCc>cTc	p.P636L	ANKRD6_ENST00000520793.1_Missense_Mutation_p.P572L|ANKRD6_ENST00000339746.4_Missense_Mutation_p.P636L|LYRM2_ENST00000520441.1_Intron|ANKRD6_ENST00000369408.5_Missense_Mutation_p.P601L|ANKRD6_ENST00000447838.2_Missense_Mutation_p.P631L	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	636					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		GCCCAGCAACCCGCAGCCAGC	0.627													C|||	445	0.0888578	0.0053	0.0865	5008	,	,		15655	0.0476		0.1551	False		,,,				2504	0.1779				p.P636L		Atlas-SNP	.											.	ANKRD6	51	.	0			c.C1907T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	102,4106		4,94,2006	26.0	29.0	28.0		1907,1907,1802,1715,1892	1.6	0.0	6	dbSNP_129	28	1177,7277		93,991,3143	yes	missense,missense,missense,missense,missense	ANKRD6	NM_001242809.1,NM_001242811.1,NM_001242813.1,NM_001242814.1,NM_014942.4	98,98,98,98,98	97,1085,5149	TT,TC,CC		13.9224,2.424,10.1011	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	636/728,636/728,601/693,572/664,631/723	90340446	1279,11383	2104	4227	6331	SO:0001583	missense	22881	exon16			AGCAACCCGCAGC	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1907C>T	6.37:g.90340446C>T	ENSP00000430985:p.Pro636Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Missense_Mutation	SNP	ENST00000522441.1	37	CCDS56441.1	165	0.07554945054945054	4	0.008130081300813009	27	0.07458563535911603	25	0.043706293706293704	109	0.1437994722955145	C	7.613	0.675206	0.14841	0.02424	0.139224	ENSG00000135299	ENST00000369408;ENST00000339746;ENST00000447838;ENST00000522441;ENST00000520793	T;T;T;T;T	0.68331	1.15;1.15;1.16;1.15;-0.32	4.67	1.64	0.23874	.	0.437855	0.19735	N	0.107261	T	0.40522	0.1120	L	0.44542	1.39	0.53688	P	2.5000000000052758E-5	P;P;P;P	0.43477	0.808;0.716;0.554;0.716	B;B;B;B	0.42653	0.348;0.394;0.3;0.394	T	0.18461	-1.0336	9	0.41790	T	0.15	-1.6351	7.7072	0.28657	0.3743:0.5397:0.0:0.0861	rs61739327	572;636;601;631	B3KUC3;Q9Y2G4;Q9Y2G4-1;C9JJE8	.;ANKR6_HUMAN;.;.	L	601;636;631;636;572	ENSP00000358416:P601L;ENSP00000345767:P636L;ENSP00000396771:P631L;ENSP00000430985:P636L;ENSP00000429782:P572L	ENSP00000345767:P636L	P	+	2	0	ANKRD6	90397167	0.003000	0.15002	0.001000	0.08648	0.002000	0.02628	1.040000	0.30278	0.668000	0.31126	0.563000	0.77884	CCC	C|0.907;T|0.093	0.093	strong		0.627	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
GPIHBP1	338328	hgsc.bcm.edu	37	8	144295782	144295782	+	Silent	SNP	G	G	T	rs11538388	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144295782G>T	ENST00000330824.2	+	2	213	c.138G>T	c.(136-138)gtG>gtT	p.V46V		NM_178172.3	NP_835466.1	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1	46	Poly-Glu.				cholesterol homeostasis (GO:0042632)|intracellular protein transport (GO:0006886)|positive regulation of chylomicron remnant clearance (GO:0090321)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein import (GO:0017038)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|protein transmembrane transport (GO:0071806)|response to heparin (GO:0071503)|transcytosis (GO:0045056)|triglyceride homeostasis (GO:0070328)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|external side of plasma membrane (GO:0009897)|high-density lipoprotein particle (GO:0034364)	chylomicron binding (GO:0035478)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|protein transmembrane transporter activity (GO:0008320)			lung(2)	2	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					aggatgaggtggaagaggagg	0.632													G|||	1797	0.358826	0.2231	0.4265	5008	,	,		17689	0.4296		0.4473	False		,,,				2504	0.3303				p.V46V		Atlas-SNP	.											.	GPIHBP1	12	.	0			c.G138T						PASS	.	G		999,3329		148,703,1313	181.0	109.0	133.0		138	1.3	0.7	8	dbSNP_120	133	3590,4850		814,1962,1444	no	coding-synonymous	GPIHBP1	NM_178172.3		962,2665,2757	TT,TG,GG		42.5355,23.0823,35.9414		46/185	144295782	4589,8179	2164	4220	6384	SO:0001819	synonymous_variant	338328	exon2			TGAGGTGGAAGAG	AF088057	CCDS34954.1	8q24.3	2014-07-14	2008-02-07						24945	protein-coding gene	gene with protein product	"""endothelial cell LPL transporter"""	612757	"""GPI anchored high density lipoprotein binding protein 1"""			12496272, 17883852, 17620854, 17403372	Standard	NM_178172		Approved	LOC338328, GPI-HBP1	uc003yxu.2	Q8IV16		ENST00000330824.2:c.138G>T	8.37:g.144295782G>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_178172	Q6P3T2|Q86W15	Silent	SNP	ENST00000330824.2	37	CCDS34954.1																																																																																			G|0.641;T|0.359	0.359	strong		0.632	GPIHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381113.1	NM_178172	
ZNF45	7596	hgsc.bcm.edu	37	19	44417575	44417575	+	Silent	SNP	A	A	G	rs417699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44417575A>G	ENST00000269973.5	-	10	3103	c.2013T>C	c.(2011-2013)ttT>ttC	p.F671F	ZNF45_ENST00000589703.1_Silent_p.F671F|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	671					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						CTGATGAAGGAAAGTCCTTGT	0.398													A|||	2712	0.541534	0.388	0.6585	5008	,	,		21581	0.8046		0.5149	False		,,,				2504	0.4223				p.F671F		Atlas-SNP	.											ZNF45,NS,carcinoma,-2,2	ZNF45	51	2	0			c.T2013C						PASS	.	A		1758,2648		357,1044,802	75.0	69.0	71.0		2013	-3.6	0.0	19	dbSNP_80	71	4342,4258		1118,2106,1076	no	coding-synonymous	ZNF45	NM_003425.3		1475,3150,1878	GG,GA,AA		49.5116,39.9001,46.9014		671/683	44417575	6100,6906	2203	4300	6503	SO:0001819	synonymous_variant	7596	exon10			TGAAGGAAAGTCC	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"""Zinc fingers, C2H2-type"", ""-"""	13111	protein-coding gene	gene with protein product		194554	"""zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)"", ""zinc finger protein 13"""	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.2013T>C	19.37:g.44417575A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_003425	P17016|P78472|Q9P1U9	Silent	SNP	ENST00000269973.5	37	CCDS12632.1																																																																																			A|0.474;G|0.526	0.526	strong		0.398	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
CCDC50	152137	hgsc.bcm.edu	37	3	191093175	191093175	+	Intron	SNP	T	T	A	rs2028574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:191093175T>A	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Missense_Mutation_p.I258N	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		GAGACTAAGATTAACCATCAG	0.488													A|||	2512	0.501597	0.7231	0.4683	5008	,	,		23143	0.4702		0.4105	False		,,,				2504	0.3517				p.I258N		Atlas-SNP	.											.	CCDC50	39	.	0			c.T773A						PASS	.	A	,ASN/ILE	2955,1451	470.4+/-355.7	985,985,233	92.0	85.0	87.0		,773	-3.5	0.0	3	dbSNP_94	87	3404,5196	640.0+/-399.5	674,2056,1570	yes	intron,missense	CCDC50	NM_174908.3,NM_178335.2	,149	1659,3041,1803	AA,AT,TT		39.5814,32.9324,48.8928	,benign	,258/483	191093175	6359,6647	2203	4300	6503	SO:0001627	intron_variant	152137	exon6			CTAAGATTAACCA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4773T>A	3.37:g.191093175T>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	66	46	0.69697	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	37	CCDS33913.1	1090	0.4990842490842491	356	0.7235772357723578	165	0.4558011049723757	254	0.44405594405594406	315	0.4155672823218997	A	0.005	-2.181485	0.00308	0.670676	0.395814	ENSG00000152492	ENST00000392456	T	0.27557	1.66	5.48	-3.51	0.04696	.	1.680560	0.03069	N	0.156876	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	8	0.08599	T	0.76	.	0.2695	0.00229	0.3492:0.2346:0.1778:0.2384	rs2028574;rs52816502;rs2028574	258	Q8IVM0-2	.	N	258	ENSP00000376250:I258N	ENSP00000376250:I258N	I	+	2	0	CCDC50	192575869	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.452000	0.06787	-0.512000	0.06505	-0.839000	0.03059	ATT	A|0.494;N|0.000	0.494	strong		0.488	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
ALPK3	57538	hgsc.bcm.edu	37	15	85405995	85405995	+	Missense_Mutation	SNP	T	T	C	rs187316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85405995T>C	ENST00000258888.5	+	10	5032	c.4865T>C	c.(4864-4866)cTt>cCt	p.L1622P		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1622	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.		L -> P (in dbSNP:rs187316). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGGTGTGGCCTTCGGAAGGCC	0.612													T|||	753	0.150359	0.0129	0.2219	5008	,	,		18170	0.1438		0.2714	False		,,,				2504	0.1677				p.L1622P		Atlas-SNP	.											.	ALPK3	289	.	0			c.T4865C						PASS	.	T	PRO/LEU	242,4164	142.3+/-177.5	10,222,1971	79.0	76.0	77.0		4865	3.7	0.5	15	dbSNP_79	77	2353,6245	392.1+/-343.9	316,1721,2262	yes	missense	ALPK3	NM_020778.4	98	326,1943,4233	CC,CT,TT		27.3668,5.4925,19.9554	probably-damaging	1622/1908	85405995	2595,10409	2203	4299	6502	SO:0001583	missense	57538	exon10			GTGGCCTTCGGAA	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4865T>C	15.37:g.85405995T>C	ENSP00000258888:p.Leu1622Pro	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	160	76	0.475	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	400	0.18315018315018314	9	0.018292682926829267	88	0.2430939226519337	88	0.15384615384615385	215	0.2836411609498681	T	15.74	2.923941	0.52653	0.054925	0.273668	ENSG00000136383	ENST00000258888	T	0.08193	3.12	4.86	3.7	0.42460	MHCK/EF2 kinase (3);Protein kinase-like domain (1);	0.418235	0.25050	N	0.033523	T	0.00012	0.0000	L	0.47716	1.5	0.29830	P	0.830098	D	0.62365	0.991	P	0.58172	0.834	T	0.40831	-0.9542	9	0.72032	D	0.01	-4.3524	9.7636	0.40548	0.0:0.0:0.1741:0.8259	rs187316;rs52801929;rs187316	1622	Q96L96	ALPK3_HUMAN	P	1622	ENSP00000258888:L1622P	ENSP00000258888:L1622P	L	+	2	0	ALPK3	83206999	0.094000	0.21725	0.465000	0.27155	0.906000	0.53458	1.711000	0.37930	0.838000	0.34948	0.533000	0.62120	CTT	T|0.815;C|0.185	0.185	strong		0.612	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
NAV2	89797	hgsc.bcm.edu	37	11	20104669	20104669	+	Silent	SNP	G	G	A	rs2028570	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:20104669G>A	ENST00000396087.3	+	29	5718	c.5619G>A	c.(5617-5619)ccG>ccA	p.P1873P	NAV2_ENST00000533917.1_Silent_p.P878P|NAV2_ENST00000360655.4_Silent_p.P1750P|NAV2_ENST00000540292.1_Silent_p.P1804P|NAV2_ENST00000349880.4_Silent_p.P1814P|NAV2_ENST00000396085.1_Silent_p.P1817P|NAV2_ENST00000527559.2_Silent_p.P1802P|NAV2_ENST00000311043.8_Silent_p.P878P	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1873					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CAAAGTTACCGCACAATGGGT	0.483													A|||	2193	0.437899	0.2262	0.4265	5008	,	,		20324	0.3065		0.5765	False		,,,				2504	0.7249				p.P1873P		Atlas-SNP	.											.	NAV2	255	.	0			c.G5619A						PASS	.	A	,,,	1226,3180	706.5+/-407.4	169,888,1146	159.0	140.0	146.0		5250,2634,5442,5451	-2.6	0.9	11	dbSNP_94	146	4817,3783	536.8+/-383.1	1363,2091,846	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	1532,2979,1992	AA,AG,GG		43.9884,27.8257,46.4632	,,,	1750/2366,878/1494,1814/2430,1817/2433	20104669	6043,6963	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon28			GTTACCGCACAAT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.5619G>A	11.37:g.20104669G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			G|0.585;A|0.415	0.415	strong		0.483	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
CHD5	26038	hgsc.bcm.edu	37	1	6185608	6185608	+	Silent	SNP	G	G	A	rs61749270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:6185608G>A	ENST00000262450.3	-	28	4335	c.4236C>T	c.(4234-4236)ctC>ctT	p.L1412L	CHD5_ENST00000378021.1_Silent_p.L269L	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		CAACTCGGGCGAGAAGCGGGG	0.662													G|||	46	0.0091853	0.0008	0.0101	5008	,	,		16550	0.001		0.0249	False		,,,				2504	0.0123				p.L1412L		Atlas-SNP	.											.	CHD5	267	.	0			c.C4236T						PASS	.	G		29,4365		0,29,2168	41.0	43.0	42.0		4236	-9.8	0.2	1	dbSNP_129	42	211,8377		6,199,4089	no	coding-synonymous	CHD5	NM_015557.2		6,228,6257	AA,AG,GG		2.4569,0.66,1.8487		1412/1955	6185608	240,12742	2197	4294	6491	SO:0001819	synonymous_variant	26038	exon28			TCGGGCGAGAAGC	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.4236C>T	1.37:g.6185608G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	52	0.597701	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			G|0.985;A|0.015	0.015	strong		0.662	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
NBAS	51594	hgsc.bcm.edu	37	2	15601441	15601441	+	Silent	SNP	C	C	T	rs7590340	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:15601441C>T	ENST00000281513.5	-	21	2248	c.2223G>A	c.(2221-2223)ctG>ctA	p.L741L	NBAS_ENST00000441750.1_Silent_p.L741L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	741					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						ACAGAATTTCCAGGGCTTGTA	0.378													T|||	2622	0.523562	0.5567	0.6254	5008	,	,		13141	0.2222		0.6938	False		,,,				2504	0.5419				p.L741L		Atlas-SNP	.											.	NBAS	246	.	0			c.G2223A						PASS	.	T		2563,1843	537.0+/-374.6	732,1099,372	97.0	100.0	99.0		2223	-11.3	0.0	2	dbSNP_116	99	5882,2718	434.3+/-357.7	2010,1862,428	no	coding-synonymous	NBAS	NM_015909.2		2742,2961,800	TT,TC,CC		31.6047,41.8293,35.0684		741/2372	15601441	8445,4561	2203	4300	6503	SO:0001819	synonymous_variant	51594	exon21			AATTTCCAGGGCT	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.2223G>A	2.37:g.15601441C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			C|0.410;T|0.590	0.590	strong		0.378	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140774505	140774505	+	Missense_Mutation	SNP	G	G	T	rs367656720		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140774505G>T	ENST00000398604.2	+	1	2125	c.2125G>T	c.(2125-2127)Gct>Tct	p.A709S	PCDHGA7_ENST00000518325.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	709					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCTTTGTCGCTGTGCTTCT	0.602																																					p.A709S		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G2125T						PASS	.	G	,SER/ALA,,,,,,,,,,,SER/ALA	0,4378		0,0,2189	35.0	40.0	38.0		,2125,,,,,,,,,,,2125	0.6	0.0	5		38	1,8587		0,1,4293	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,99,,,,,,,,,,,99	0,1,6482	TT,TG,GG		0.0116,0.0,0.0077	,,,,,,,,,,,,	,709/821,,,,,,,,,,,709/933	140774505	1,12965	2189	4294	6483	SO:0001583	missense	9708	exon1			TTTGTCGCTGTGC	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.2125G>T	5.37:g.140774505G>T	ENSP00000381605:p.Ala709Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	130	89	0.684615	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	6.375	0.437282	0.12104	0.0	1.16E-4	ENSG00000253767	ENST00000398604	T	0.14266	2.52	4.5	0.627	0.17675	.	0.671943	0.11133	U	0.596072	T	0.07908	0.0198	N	0.14661	0.345	0.09310	N	1	B;B	0.22851	0.024;0.076	B;B	0.26310	0.032;0.068	T	0.36383	-0.9750	10	0.87932	D	0	.	4.7807	0.13201	0.4634:0.3303:0.2063:0.0	.	709;709	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	S	709	ENSP00000381605:A709S	ENSP00000381605:A709S	A	+	1	0	PCDHGA8	140754689	0.000000	0.05858	0.008000	0.14137	0.021000	0.10359	-0.022000	0.12480	-0.041000	0.13558	-0.910000	0.02820	GCT	.	.	weak		0.602	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
MLC1	23209	hgsc.bcm.edu	37	22	50518815	50518815	+	Silent	SNP	C	C	T	rs11568172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50518815C>T	ENST00000311597.5	-	4	885	c.279G>A	c.(277-279)tcG>tcA	p.S93S	MLC1_ENST00000450140.2_Intron|MLC1_ENST00000395876.2_Silent_p.S93S|MLC1_ENST00000538737.1_Silent_p.S93S|MLC1_ENST00000535444.1_Silent_p.S14S|MLC1_ENST00000431262.2_Silent_p.S63S	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	93			S -> L (in MLC1; dbSNP:rs80358245). {ECO:0000269|PubMed:11254442}.		caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		TCACAATTGCCGAGGGGATGC	0.552													C|||	21	0.00419329	0.0	0.0058	5008	,	,		18308	0.0		0.005	False		,,,				2504	0.0123				p.S93S		Atlas-SNP	.											.	MLC1	48	.	0			c.G279A						PASS	.	C	,	5,4397	9.9+/-24.2	0,5,2196	64.0	51.0	55.0		279,279	-2.4	0.7	22	dbSNP_120	55	55,8545	29.6+/-80.5	0,55,4245	no	coding-synonymous,coding-synonymous	MLC1	NM_015166.3,NM_139202.2	,	0,60,6441	TT,TC,CC		0.6395,0.1136,0.4615	,	93/378,93/378	50518815	60,12942	2201	4300	6501	SO:0001819	synonymous_variant	23209	exon4			AATTGCCGAGGGG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.279G>A	22.37:g.50518815C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			C|0.995;T|0.005	0.005	strong		0.552	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
MEF2A	4205	hgsc.bcm.edu	37	15	100246936	100246936	+	Silent	SNP	T	T	C	rs325408|rs17854846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:100246936T>C	ENST00000557785.1	+	9	1210	c.861T>C	c.(859-861)aaT>aaC	p.N287N	MEF2A_ENST00000557942.1_Silent_p.N295N|MEF2A_ENST00000338042.6_Silent_p.N296N|MEF2A_ENST00000449277.2_Silent_p.N219N|MEF2A_ENST00000558812.1_Silent_p.N227N|MEF2A_ENST00000453228.2_Silent_p.N287N|MEF2A_ENST00000354410.5_Silent_p.N289N	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	297					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			TCTCACAGAATACCCAGAGGA	0.408													T|||	3067	0.61242	0.2057	0.6369	5008	,	,		16617	0.7103		0.7922	False		,,,				2504	0.8589				p.N289N		Atlas-SNP	.											.	MEF2A	138	.	0			c.T867C						PASS	.	T	,,,,	1234,2640		200,834,903	88.0	78.0	81.0		861,681,657,861,867	-1.8	0.8	15	dbSNP_79	81	6551,1727		2598,1355,186	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MEF2A	NM_001130926.1,NM_001130927.1,NM_001130928.1,NM_001171894.1,NM_005587.2	,,,,	2798,2189,1089	CC,CT,TT		20.8625,31.8534,35.9365	,,,,	287/498,227/438,219/430,287/498,289/500	100246936	7785,4367	1937	4139	6076	SO:0001819	synonymous_variant	4205	exon9			ACAGAATACCCAG		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.861T>C	15.37:g.100246936T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																			T|0.332;C|0.668	0.668	strong		0.408	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
MUC16	94025	hgsc.bcm.edu	37	19	9077581	9077581	+	Missense_Mutation	SNP	G	G	T	rs73011014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9077581G>T	ENST00000397910.4	-	3	10068	c.9865C>A	c.(9865-9867)Cca>Aca	p.P3289T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3290	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCCTCAGGTGGGGATGGGGAG	0.542													G|||	938	0.1873	0.0946	0.2536	5008	,	,		20999	0.3254		0.1322	False		,,,				2504	0.18				p.P3289T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C9865A						PASS	.	G	THR/PRO	392,3698		18,356,1671	101.0	103.0	102.0		9865	-0.8	0.0	19	dbSNP_130	102	1158,7206		72,1014,3096	yes	missense	MUC16	NM_024690.2	38	90,1370,4767	TT,TG,GG		13.8451,9.5844,12.4458	probably-damaging	3289/14508	9077581	1550,10904	2045	4182	6227	SO:0001583	missense	94025	exon3			CAGGTGGGGATGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.9865C>A	19.37:g.9077581G>T	ENSP00000381008:p.Pro3289Thr	Somatic	509	0	0		WXS	Illumina HiSeq	Phase_I	534	266	0.498127	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	439	0.20100732600732601	56	0.11382113821138211	80	0.22099447513812154	205	0.3583916083916084	98	0.12928759894459102	g	8.427	0.847619	0.17034	0.095844	0.138451	ENSG00000181143	ENST00000397910	T	0.03181	4.02	1.67	-0.84	0.10755	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.65815	0.995	P	0.55577	0.779	T	0.53056	-0.8492	8	0.87932	D	0	.	4.138	0.10179	0.4727:0.0:0.5273:0.0	.	3289	B5ME49	.	T	3289	ENSP00000381008:P3289T	ENSP00000381008:P3289T	P	-	1	0	MUC16	8938581	0.001000	0.12720	0.000000	0.03702	0.851000	0.48451	-0.230000	0.09083	-0.166000	0.10890	0.313000	0.20887	CCA	G|0.809;T|0.191	0.191	strong		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DPP3	10072	hgsc.bcm.edu	37	11	66254085	66254085	+	Missense_Mutation	SNP	G	G	T	rs11550299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66254085G>T	ENST00000360510.2	+	4	500	c.435G>T	c.(433-435)caG>caT	p.Q145H	DPP3_ENST00000453114.1_Missense_Mutation_p.Q145H|DPP3_ENST00000530165.1_Missense_Mutation_p.Q115H|DPP3_ENST00000541961.1_Missense_Mutation_p.Q145H|DPP3_ENST00000532677.1_Missense_Mutation_p.Q164H|DPP3_ENST00000531863.1_Missense_Mutation_p.Q165H			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	145			Q -> H (in dbSNP:rs11550299). {ECO:0000269|Ref.1}.		proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Q145H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						GCCTCTGGCAGACCTGCGGGG	0.627													G|||	1083	0.216254	0.1884	0.1599	5008	,	,		18833	0.2887		0.2416	False		,,,				2504	0.1933				p.Q145H		Atlas-SNP	.											DPP3,colon,carcinoma,0,2	DPP3	61	2	1	Substitution - Missense(1)	stomach(1)	c.G435T						PASS	.	G	HIS/GLN,HIS/GLN	742,3658	306.3+/-289.4	57,628,1515	86.0	87.0	86.0		435,435	4.0	1.0	11	dbSNP_120	86	2007,6583	351.3+/-328.2	227,1553,2515	yes	missense,missense	DPP3	NM_005700.3,NM_130443.2	24,24	284,2181,4030	TT,TG,GG		23.3644,16.8636,21.1624	benign,benign	145/738,145/738	66254085	2749,10241	2200	4295	6495	SO:0001583	missense	10072	exon4			CTGGCAGACCTGC	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.435G>T	11.37:g.66254085G>T	ENSP00000353701:p.Gln145His	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	230	99	0.430435	NM_130443	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Missense_Mutation	SNP	ENST00000360510.2	37	CCDS8141.1	519	0.23763736263736263	85	0.17276422764227642	71	0.19613259668508287	167	0.291958041958042	196	0.25857519788918204	G	10.43	1.346721	0.24426	0.168636	0.233644	ENSG00000254986	ENST00000531863;ENST00000532677;ENST00000360510;ENST00000453114;ENST00000541961;ENST00000532019;ENST00000526515;ENST00000530165;ENST00000533725;ENST00000543807;ENST00000347422;ENST00000531354	T;T;T;T;T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93	5.02	4.04	0.47022	.	0.388366	0.26844	N	0.022209	T	0.00012	0.0000	N	0.20986	0.625	0.36036	P	0.16023600000000005	B;B	0.06786	0.001;0.001	B;B	0.14578	0.011;0.006	T	0.29882	-0.9997	9	0.42905	T	0.14	.	6.2999	0.21107	0.0985:0.1891:0.7125:0.0	rs11550299;rs58287157;rs11550299	164;145	G3V1D3;Q9NY33	.;DPP3_HUMAN	H	165;164;145;145;145;43;115;115;43;43;145;145	ENSP00000432782:Q165H;ENSP00000435284:Q164H;ENSP00000353701:Q145H;ENSP00000389943:Q145H;ENSP00000440502:Q145H;ENSP00000437101:Q43H;ENSP00000431606:Q115H;ENSP00000436941:Q115H;ENSP00000434518:Q43H;ENSP00000432618:Q145H	ENSP00000309957:Q145H	Q	+	3	2	DPP3	66010661	0.923000	0.31300	1.000000	0.80357	0.358000	0.29455	0.497000	0.22514	2.323000	0.78572	0.561000	0.74099	CAG	G|0.781;T|0.219	0.219	strong		0.627	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2		
RAI1	10743	hgsc.bcm.edu	37	17	17698023	17698023	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17698023C>T	ENST00000353383.1	+	3	2230	c.1761C>T	c.(1759-1761)ttC>ttT	p.F587F	RAI1_ENST00000261641.6_Silent_p.F587F	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	587					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		TCTCCAAGTTCGTGGCGGGTG	0.632																																					p.F587F		Atlas-SNP	.											.	RAI1	121	.	0			c.C1761T						PASS	.						68.0	70.0	69.0					17																	17698023		2201	4293	6494	SO:0001819	synonymous_variant	10743	exon3			CAAGTTCGTGGCG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.1761C>T	17.37:g.17698023C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	none		0.632	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
FCGBP	8857	hgsc.bcm.edu	37	19	40408821	40408821	+	Missense_Mutation	SNP	C	C	G	rs11083543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40408821C>G	ENST00000221347.6	-	8	4025	c.4018G>C	c.(4018-4020)Gtg>Ctg	p.V1340L		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1340	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.		V -> L (in dbSNP:rs11083543).			extracellular vesicular exosome (GO:0070062)		p.V1340L(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCAGCACCACGGGCAGCTTC	0.577													C|||	1291	0.257788	0.121	0.4092	5008	,	,		19419	0.2173		0.3608	False		,,,				2504	0.271				p.V1340L		Atlas-SNP	.											FCGBP,caecum,carcinoma,0,2	FCGBP	416	2	1	Substitution - Missense(1)	ovary(1)	c.G4018C						PASS	.	C	LEU/VAL	611,3795		45,521,1637	23.0	20.0	21.0		4018	-0.1	0.0	19	dbSNP_120	21	2976,5622		523,1930,1846	yes	missense	FCGBP	NM_003890.2	32	568,2451,3483	GG,GC,CC		34.6127,13.8675,27.5838	probably-damaging	1340/5406	40408821	3587,9417	2203	4299	6502	SO:0001583	missense	8857	exon8			GCACCACGGGCAG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4018G>C	19.37:g.40408821C>G	ENSP00000221347:p.Val1340Leu	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	171	72	0.421053	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	624	0.2857142857142857	76	0.15447154471544716	148	0.4088397790055249	125	0.21853146853146854	275	0.3627968337730871	C	12.27	1.888760	0.33348	0.138675	0.346127	ENSG00000090920	ENST00000221347	T	0.58797	0.31	4.95	-0.14	0.13456	von Willebrand factor, type D domain (3);	0.451564	0.18780	N	0.131345	T	0.00012	0.0000	N	0.25031	0.7	0.80722	P	0.0	B	0.25235	0.121	B	0.21151	0.033	T	0.40232	-0.9574	9	0.11485	T	0.65	.	2.6779	0.05085	0.1375:0.4356:0.268:0.1589	rs11083543;rs11083543	1340	Q9Y6R7	FCGBP_HUMAN	L	1340	ENSP00000221347:V1340L	ENSP00000221347:V1340L	V	-	1	0	FCGBP	45100661	0.000000	0.05858	0.015000	0.15790	0.023000	0.10783	-0.881000	0.04179	0.120000	0.18254	-0.182000	0.12963	GTG	.	.	weak		0.577	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
COL5A2	1290	hgsc.bcm.edu	37	2	189932764	189932764	+	Missense_Mutation	SNP	G	G	A	rs35830636	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:189932764G>A	ENST00000374866.3	-	21	1652	c.1378C>T	c.(1378-1380)Cct>Tct	p.P460S		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	460			P -> S (in dbSNP:rs35830636).		axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			ATTCCCTGAGGACCAGTGCTA	0.502													G|||	58	0.0115815	0.0015	0.0245	5008	,	,		17254	0.001		0.0308	False		,,,				2504	0.0072				p.P460S		Atlas-SNP	.											.	COL5A2	230	.	0			c.C1378T						PASS	.	G	SER/PRO	50,4356	50.9+/-86.3	0,50,2153	77.0	76.0	76.0		1378	5.7	1.0	2	dbSNP_126	76	467,8133	139.0+/-195.8	15,437,3848	yes	missense	COL5A2	NM_000393.3	74	15,487,6001	AA,AG,GG		5.4302,1.1348,3.9751	probably-damaging	460/1500	189932764	517,12489	2203	4300	6503	SO:0001583	missense	1290	exon21			CCTGAGGACCAGT	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.1378C>T	2.37:g.189932764G>A	ENSP00000364000:p.Pro460Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	34	0.015567765567765568	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	19	0.025065963060686015	G	16.31	3.086016	0.55861	0.011348	0.054302	ENSG00000204262	ENST00000374866	D	0.97665	-4.48	5.74	5.74	0.90152	.	0.252743	0.27640	N	0.018475	T	0.80042	0.4551	L	0.43701	1.375	0.41778	D	0.989808	B	0.16802	0.019	B	0.14023	0.01	D	0.84390	0.0554	9	.	.	.	.	15.4173	0.74980	0.0:0.1384:0.8616:0.0	rs35830636	460	P05997	CO5A2_HUMAN	S	460	ENSP00000364000:P460S	.	P	-	1	0	COL5A2	189641009	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.297000	0.72757	2.716000	0.92895	0.591000	0.81541	CCT	G|0.965;A|0.035	0.035	strong		0.502	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
TET2	54790	hgsc.bcm.edu	37	4	106196951	106196951	+	Missense_Mutation	SNP	A	A	G	rs2454206	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106196951A>G	ENST00000540549.1	+	11	6144	c.5284A>G	c.(5284-5286)Ata>Gta	p.I1762V	TET2_ENST00000513237.1_Missense_Mutation_p.I1783V|TET2_ENST00000380013.4_Missense_Mutation_p.I1762V|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1762			I -> V (in dbSNP:rs2454206). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19483684}.		5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.I1762fs*3(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ACCTTCTCACATAATCCATAA	0.458			"""Mis N, F"""		MDS								A|||	1154	0.230431	0.0658	0.2795	5008	,	,		23352	0.1895		0.3718	False		,,,				2504	0.3149				p.I1762V		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.A5284G						PASS	.	A	VAL/ILE	124,1260		11,102,579	19.0	16.0	17.0		5284	-10.3	0.0	4	dbSNP_100	17	1188,1994		223,742,626	yes	missense	TET2	NM_001127208.2	29	234,844,1205	GG,GA,AA		37.335,8.9595,28.7341	benign	1762/2003	106196951	1312,3254	692	1591	2283	SO:0001583	missense	54790	exon11			TCTCACATAATCC	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5284A>G	4.37:g.106196951A>G	ENSP00000442788:p.Ile1762Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	526	0.24084249084249085	33	0.06707317073170732	92	0.2541436464088398	107	0.18706293706293706	294	0.38786279683377306	A	8.920	0.960733	0.18583	0.089595	0.37335	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.01963	4.53;4.53;4.53	5.16	-10.3	0.00346	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.58432	P	1.0000000000287557E-6	B;B	0.15141	0.001;0.012	B;B	0.19666	0.001;0.026	T	0.48340	-0.9044	8	0.13853	T	0.58	0.7576	3.9686	0.09443	0.1159:0.4443:0.2131:0.2267	rs2454206;rs52829850;rs58031039;rs2454206	1783;1762	E7EQS8;Q6N021	.;TET2_HUMAN	V	1762;1783;1762	ENSP00000442788:I1762V;ENSP00000425443:I1783V;ENSP00000369351:I1762V	ENSP00000369351:I1762V	I	+	1	0	TET2	106416400	0.000000	0.05858	0.000000	0.03702	0.738000	0.42128	-0.301000	0.08232	-1.622000	0.01560	-0.456000	0.05471	ATA	A|0.768;G|0.232	0.232	strong		0.458	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
THAP8	199745	hgsc.bcm.edu	37	19	36530343	36530343	+	Missense_Mutation	SNP	C	C	T	rs10421966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36530343C>T	ENST00000292894.1	-	3	1098	c.554G>A	c.(553-555)cGg>cAg	p.R185Q	AC002116.7_ENST00000586962.1_RNA|THAP8_ENST00000524106.1_5'Flank|THAP8_ENST00000538849.1_Missense_Mutation_p.R40Q	NM_152658.2	NP_689871.1	Q8NA92	THAP8_HUMAN	THAP domain containing 8	185			R -> Q (in dbSNP:rs10421966). {ECO:0000269|PubMed:14702039}.				DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TTGCAGCCTCCGCACCCGGCG	0.711													c|||	1294	0.258387	0.2239	0.2233	5008	,	,		15755	0.3274		0.33	False		,,,				2504	0.1851				p.R185Q		Atlas-SNP	.											.	THAP8	11	.	0			c.G554A						PASS	.	C	GLN/ARG	927,3425		105,717,1354	8.0	7.0	7.0		554	-5.1	0.0	19	dbSNP_119	7	2538,5980		398,1742,2119	no	missense	THAP8	NM_152658.2	43	503,2459,3473	TT,TC,CC		29.7957,21.3006,26.9231	benign	185/275	36530343	3465,9405	2176	4259	6435	SO:0001583	missense	199745	exon3			AGCCTCCGCACCC	AK057453	CCDS33000.1	19q13.13	2013-01-25			ENSG00000161277	ENSG00000161277		"""THAP (C2CH-type zinc finger) domain containing"""	23191	protein-coding gene	gene with protein product		612536				12575992	Standard	NM_152658		Approved	FLJ32891	uc002oda.1	Q8NA92	OTTHUMG00000048138	ENST00000292894.1:c.554G>A	19.37:g.36530343C>T	ENSP00000292894:p.Arg185Gln	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_152658	Q0P5Z7|Q96M21	Missense_Mutation	SNP	ENST00000292894.1	37	CCDS33000.1	666	0.30494505494505497	125	0.2540650406504065	90	0.24861878453038674	196	0.34265734265734266	255	0.33641160949868076	c	10.87	1.471684	0.26423	0.213006	0.297957	ENSG00000161277	ENST00000292894;ENST00000392182;ENST00000538849	D;T	0.88354	-2.37;1.87	4.54	-5.09	0.02920	.	0.939552	0.08854	N	0.883987	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02464	-1.1155	9	0.17832	T	0.49	-19.0278	12.6285	0.56644	0.0:0.4052:0.0:0.5948	rs10421966;rs10421966	185	Q8NA92	THAP8_HUMAN	Q	185;185;40	ENSP00000292894:R185Q;ENSP00000445493:R40Q	ENSP00000292894:R185Q	R	-	2	0	THAP8	41222183	0.492000	0.26027	0.006000	0.13384	0.039000	0.13416	-0.273000	0.08548	-1.335000	0.02241	-1.316000	0.01300	CGG	C|0.695;T|0.305	0.305	strong		0.711	THAP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379036.1	NM_152658	
FN3K	64122	hgsc.bcm.edu	37	17	80708601	80708601	+	Silent	SNP	C	C	G	rs1056534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80708601C>G	ENST00000300784.7	+	6	962	c.900C>G	c.(898-900)tcC>tcG	p.S300S	TBCD_ENST00000539345.2_5'Flank|TBCD_ENST00000397466.2_5'Flank|TBCD_ENST00000355528.4_5'Flank	NM_022158.3	NP_071441.1	Q9H479	FN3K_HUMAN	fructosamine 3 kinase	300					epithelial cell differentiation (GO:0030855)|fructoselysine metabolic process (GO:0030393)		fructosamine-3-kinase activity (GO:0030387)			central_nervous_system(1)|kidney(1)|lung(1)|urinary_tract(1)	4	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			GGAGCCCTTCCTTGGGCACCA	0.667													G|||	3281	0.655152	0.68	0.6686	5008	,	,		8801	0.6518		0.6014	False		,,,				2504	0.6708				p.S300S	Melanoma(10;391 597 14592 32548 32749)	Atlas-SNP	.											.	FN3K	17	.	0			c.C900G						PASS	.	G		2831,1575	483.9+/-359.9	918,995,290	56.0	64.0	61.0		900	-2.1	0.1	17	dbSNP_86	61	5214,3386	496.0+/-374.2	1575,2064,661	yes	coding-synonymous	FN3K	NM_022158.3		2493,3059,951	GG,GC,CC		39.3721,35.7467,38.1439		300/310	80708601	8045,4961	2203	4300	6503	SO:0001819	synonymous_variant	64122	exon6			CCCTTCCTTGGGC	AJ404615	CCDS11818.1	17q25	2008-02-05				ENSG00000167363			24822	protein-coding gene	gene with protein product		608425				11522682, 14641062	Standard	NM_022158		Approved		uc010wvs.1	Q9H479		ENST00000300784.7:c.900C>G	17.37:g.80708601C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_022158		Silent	SNP	ENST00000300784.7	37	CCDS11818.1																																																																																			C|0.373;G|0.627	0.627	strong		0.667	FN3K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439229.1	NM_022158	
TAP2	6891	hgsc.bcm.edu	37	6	32797809	32797809	+	Missense_Mutation	SNP	C	C	T	rs2228396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32797809C>T	ENST00000452392.2	-	10	1866	c.1693G>A	c.(1693-1695)Gct>Act	p.A565T	TAP2_ENST00000374899.4_Missense_Mutation_p.A565T|TAP2_ENST00000374897.2_Missense_Mutation_p.A565T|TAP2_ENST00000485701.1_5'Flank			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	AGCCCATAAGCAATGTTGTTC	0.552													C|||	399	0.0796725	0.0923	0.1081	5008	,	,		19997	0.0923		0.0865	False		,,,				2504	0.0225				p.A565T		Atlas-SNP	.											.	TAP2	98	.	0			c.G1693A	GRCh37	CM941307	TAP2	M	rs2228396	PASS	.	C	THR/ALA,THR/ALA	368,2654		29,310,1172	124.0	128.0	127.0		1693,1693	1.5	0.0	6	dbSNP_98	127	460,4958		17,426,2266	yes	missense,missense	TAP2	NM_000544.3,NM_018833.2	58,58	46,736,3438	TT,TC,CC		8.4902,12.1774,9.8104	benign,benign	565/704,565/654	32797809	828,7612	1511	2709	4220	SO:0001583	missense	6891	exon10			CATAAGCAATGTT	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1693G>A	6.37:g.32797809C>T	ENSP00000391806:p.Ala565Thr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	254	108	0.425197	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000452392.2	37		214	0.09798534798534798	62	0.12601626016260162	34	0.09392265193370165	48	0.08391608391608392	70	0.09234828496042216	C	14.39	2.522422	0.44866	0.121774	0.084902	ENSG00000204267;ENSG00000204267;ENSG00000204267;ENSG00000250264	ENST00000556934;ENST00000374899;ENST00000374897;ENST00000452392	D;D;D	0.90732	-2.72;-2.72;-2.72	5.33	1.47	0.22746	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.362459	0.23668	N	0.045755	T	0.68824	0.3043	L	0.28344	0.845	0.37487	D	0.916232	B;B;B;B	0.32918	0.264;0.39;0.39;0.39	B;B;B;B	0.30646	0.118;0.062;0.062;0.062	T	0.55685	-0.8102	9	0.32370	T	0.25	-28.5102	6.9703	0.24644	0.0:0.5109:0.0:0.4891	rs2228396;rs17885149;rs2228396	565;566;565;565	E7ENX8;Q59H06;Q03519;Q9UP03	.;.;TAP2_HUMAN;.	T	565	ENSP00000364034:A565T;ENSP00000364032:A565T;ENSP00000391806:A565T	ENSP00000364032:A565T	A	-	1	0	XXbac-BPG246D15.9;TAP2	32905787	0.000000	0.05858	0.025000	0.17156	0.989000	0.77384	-0.507000	0.06352	0.212000	0.20703	0.501000	0.49751	GCT	C|0.911;T|0.089	0.089	strong		0.552	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34824107	34824107	+	Missense_Mutation	SNP	A	A	C	rs16894945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:34824107A>C	ENST00000192788.5	+	10	1383	c.1212A>C	c.(1210-1212)aaA>aaC	p.K404N	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.K404N	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	404			K -> N (in dbSNP:rs16894945).				histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						TTCAGAGCAAAATGGAGAAGT	0.532													A|||	555	0.110823	0.0333	0.0778	5008	,	,		19096	0.3016		0.0606	False		,,,				2504	0.0941				p.K404N		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.A1212C						PASS	.	A	ASN/LYS	146,3810		2,142,1834	141.0	147.0	145.0		1212	2.4	1.0	6	dbSNP_123	145	483,7845		14,455,3695	yes	missense	UHRF1BP1	NM_017754.3	94	16,597,5529	CC,CA,AA		5.7997,3.6906,5.1205	possibly-damaging	404/1441	34824107	629,11655	1978	4164	6142	SO:0001583	missense	54887	exon10			GAGCAAAATGGAG	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1212A>C	6.37:g.34824107A>C	ENSP00000192788:p.Lys404Asn	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	176	69	0.392045	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	266	0.12179487179487179	9	0.018292682926829267	27	0.07458563535911603	179	0.3129370629370629	51	0.06728232189973615	A	8.795	0.931551	0.18131	0.036906	0.057997	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.08282	3.11;3.11	5.97	2.38	0.29361	.	0.168355	0.52532	D	0.000080	T	0.00815	0.0027	N	0.08118	0	0.31396	P	0.6772210000000001	B	0.21821	0.061	B	0.17979	0.02	T	0.47649	-0.9101	9	0.02654	T	1	-6.3855	5.7378	0.18077	0.5021:0.0:0.4979:0.0	rs16894945;rs59701345;rs16894945	404	Q6BDS2	URFB1_HUMAN	N	404	ENSP00000192788:K404N;ENSP00000400628:K404N	ENSP00000192788:K404N	K	+	3	2	UHRF1BP1	34932085	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	1.941000	0.40233	0.527000	0.28560	0.533000	0.62120	AAA	A|0.884;C|0.116	0.116	strong		0.532	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
MUC16	94025	hgsc.bcm.edu	37	19	9076728	9076728	+	Missense_Mutation	SNP	C	C	T	rs2591594	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9076728C>T	ENST00000397910.4	-	3	10921	c.10718G>A	c.(10717-10719)cGc>cAc	p.R3573H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3574	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGAAGTTGTGCGCCTCTCTGT	0.512													C|||	1243	0.248203	0.2005	0.2118	5008	,	,		21876	0.249		0.3121	False		,,,				2504	0.272				p.R3573H		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-1,4	MUC16	4315	4	0			c.G10718A						PASS	.	C	HIS/ARG	892,3336		102,688,1324	179.0	177.0	178.0		10718	-2.8	0.0	19	dbSNP_100	178	2435,6017		349,1737,2140	yes	missense	MUC16	NM_024690.2	29	451,2425,3464	TT,TC,CC		28.8097,21.0974,26.2382	benign	3573/14508	9076728	3327,9353	2114	4226	6340	SO:0001583	missense	94025	exon3			GTTGTGCGCCTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10718G>A	19.37:g.9076728C>T	ENSP00000381008:p.Arg3573His	Somatic	408	1	0.00245098		WXS	Illumina HiSeq	Phase_I	427	219	0.512881	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	c	1.183	-0.637672	0.03557	0.210974	0.288097	ENSG00000181143	ENST00000397910	T	0.02916	4.11	1.49	-2.79	0.05841	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.46952	-0.9154	8	0.87932	D	0	.	7.7924	0.29127	0.0:0.6856:0.0:0.3144	rs2591594;rs52835104;rs58009126;rs2591594	3573	B5ME49	.	H	3573	ENSP00000381008:R3573H	ENSP00000381008:R3573H	R	-	2	0	MUC16	8937728	0.008000	0.16893	0.000000	0.03702	0.003000	0.03518	-0.053000	0.11846	-1.341000	0.02225	-1.786000	0.00637	CGC	C|0.751;T|0.249	0.249	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CLCNKB	1188	hgsc.bcm.edu	37	1	16382243	16382243	+	Missense_Mutation	SNP	C	C	A	rs375375144		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16382243C>A	ENST00000375679.4	+	18	2030	c.1919C>A	c.(1918-1920)tCc>tAc	p.S640Y	CLCNKB_ENST00000375667.3_Missense_Mutation_p.S470Y|FAM131C_ENST00000494078.1_5'Flank	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	640	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CCAGAGACTTCCCTGCATGAG	0.617											OREG0013133	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S640Y		Atlas-SNP	.											.	CLCNKB	50	.	0			c.C1919A						PASS	.	C	TYR/SER,TYR/SER	0,4406		0,0,2203	70.0	68.0	68.0		1919,1412	4.7	1.0	1		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CLCNKB	NM_000085.3,NM_001165945.1	144,144	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign,benign	640/688,471/519	16382243	1,13005	2203	4300	6503	SO:0001583	missense	1188	exon18			AGACTTCCCTGCA	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1919C>A	1.37:g.16382243C>A	ENSP00000364831:p.Ser640Tyr	Somatic	170	0	0	709	WXS	Illumina HiSeq	Phase_I	135	54	0.4	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Missense_Mutation	SNP	ENST00000375679.4	37	CCDS168.1	.	.	.	.	.	.	.	.	.	.	c	19.03	3.747160	0.69418	0.0	1.16E-4	ENSG00000184908	ENST00000375668;ENST00000375679;ENST00000375667;ENST00000431772	D;D;D	0.95035	-3.59;-3.59;-2.62	4.7	4.7	0.59300	Cystathionine beta-synthase, core (3);	0.067228	0.64402	D	0.000011	D	0.96191	0.8758	M	0.90198	3.095	0.80722	D	1	B;B	0.27380	0.177;0.078	B;B	0.39503	0.301;0.135	D	0.96375	0.9277	10	0.72032	D	0.01	.	15.1589	0.72764	0.0:1.0:0.0:0.0	.	470;640	Q5T5Q7;P51801	.;CLCKB_HUMAN	Y	137;640;470;128	ENSP00000364831:S640Y;ENSP00000364819:S470Y;ENSP00000389344:S128Y	ENSP00000364819:S470Y	S	+	2	0	CLCNKB	16254830	0.957000	0.32711	0.995000	0.50966	0.702000	0.40608	4.220000	0.58567	2.322000	0.78497	0.555000	0.69702	TCC	.	.	none		0.617	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388429	1388429	+	Missense_Mutation	SNP	G	G	A	rs79298048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388429G>A	ENST00000324803.4	+	1	3090	c.130G>A	c.(130-132)Gcc>Acc	p.A44T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	44					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGGAGTGCCCGCCTGCTCACA	0.662													N|||	944	0.188498	0.062	0.2853	5008	,	,		16920	0.0536		0.3797	False		,,,				2504	0.2331				p.A44T		Atlas-SNP	.											CRIPAK,colon,carcinoma,0,2	CRIPAK	185	2	0			c.G130A						PASS	.	G	THR/ALA	508,3898		29,450,1724	219.0	210.0	213.0		130	-1.5	0.0	4	dbSNP_131	213	3442,5158		673,2096,1531	no	missense	CRIPAK	NM_175918.3	58	702,2546,3255	AA,AG,GG		40.0233,11.5297,30.3706	benign	44/447	1388429	3950,9056	2203	4300	6503	SO:0001583	missense	285464	exon1			GTGCCCGCCTGCT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.130G>A	4.37:g.1388429G>A	ENSP00000323978:p.Ala44Thr	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	242	212	0.876033	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	438	0.20054945054945056	28	0.056910569105691054	99	0.27348066298342544	38	0.06643356643356643	273	0.36015831134564646	-	6.138	0.393672	0.11638	0.115297	0.400233	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.24350	1.86	1.11	-1.54	0.08584	Post-SET domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.39748	0.686	B	0.17722	0.019	T	0.47484	-0.9114	8	0.36615	T	0.2	.	3.7735	0.08650	0.1991:0.2527:0.5481:0.0	.	44	Q8N1N5	CRPAK_HUMAN	T	44;37	ENSP00000323978:A44T	ENSP00000323978:A44T	A	+	1	0	CRIPAK	1378429	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.619000	0.05572	-0.466000	0.06943	0.413000	0.27773	GCC	G|0.725;A|0.275	0.275	strong		0.662	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
LILRB1	10859	hgsc.bcm.edu	37	19	55144186	55144186	+	Silent	SNP	C	C	T	rs272423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55144186C>T	ENST00000396331.1	+	7	1290	c.933C>T	c.(931-933)agC>agT	p.S311S	LILRB1_ENST00000418536.2_Silent_p.S311S|LILRB1_ENST00000396315.1_Silent_p.S311S|LILRB1_ENST00000427581.2_Silent_p.S347S|LILRB1_ENST00000396332.4_Silent_p.S311S|LILRB1_ENST00000434867.2_Silent_p.S311S|LILRB1_ENST00000396321.2_Silent_p.S311S|LILRB1_ENST00000324602.7_Silent_p.S311S|LILRB1_ENST00000396317.1_Silent_p.S311S|LILRB1_ENST00000448689.1_Silent_p.S311S|LILRB1_ENST00000396327.3_Silent_p.S311S	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	311	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CGGCCCCCAGCGACCCCCTGG	0.677										HNSCC(37;0.09)			t|||	2973	0.59365	0.6732	0.464	5008	,	,		15698	0.3611		0.7207	False		,,,				2504	0.6871				p.S311S		Atlas-SNP	.											LILRB1,NS,carcinoma,+2,1	LILRB1	140	1	0			c.C933T						PASS	.						28.0	32.0	31.0					19																	55144186		2200	4293	6493	SO:0001819	synonymous_variant	10859	exon6			CCCCAGCGACCCC	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.933C>T	19.37:g.55144186C>T		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	243	226	0.930041	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			C|0.281;T|0.719	0.719	strong		0.677	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
EPHA2	1969	hgsc.bcm.edu	37	1	16464673	16464673	+	Silent	SNP	G	G	A	rs2230597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16464673G>A	ENST00000358432.5	-	5	1141	c.987C>T	c.(985-987)ccC>ccT	p.P329P		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	329	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	GTGGGGCGGAGGGGGGTCCTG	0.662													G|||	1750	0.349441	0.3396	0.4294	5008	,	,		18391	0.1458		0.4215	False		,,,				2504	0.4417				p.P329P		Atlas-SNP	.											.	EPHA2	102	.	0			c.C987T						PASS	.	G		1588,2816		299,990,913	21.0	21.0	21.0		987	1.9	1.0	1	dbSNP_98	21	3467,5131		711,2045,1543	no	coding-synonymous	EPHA2	NM_004431.3		1010,3035,2456	AA,AG,GG		40.3233,36.0581,38.8786		329/977	16464673	5055,7947	2202	4299	6501	SO:0001819	synonymous_variant	1969	exon5			GGCGGAGGGGGGT	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.987C>T	1.37:g.16464673G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	22	7	0.318182	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			G|0.649;A|0.351	0.351	strong		0.662	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
SORT1	6272	hgsc.bcm.edu	37	1	109884775	109884775	+	Silent	SNP	T	T	G	rs2228604	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109884775T>G	ENST00000256637.6	-	9	1027	c.969A>C	c.(967-969)acA>acC	p.T323T	SORT1_ENST00000538502.1_Silent_p.T186T	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	323					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		TCCTTCTTGTTGTATCCTAGA	0.428													T|||	3433	0.685503	0.3593	0.8271	5008	,	,		21426	0.9563		0.7127	False		,,,				2504	0.7188				p.T323T		Atlas-SNP	.											.	SORT1	48	.	0			c.A969C						PASS	.	T	,	1850,2556	535.6+/-374.3	393,1064,746	99.0	80.0	87.0		558,969	-1.1	1.0	1	dbSNP_98	87	6253,2347	702.8+/-405.3	2277,1699,324	no	coding-synonymous,coding-synonymous	SORT1	NM_001205228.1,NM_002959.5	,	2670,2763,1070	GG,GT,TT		27.2907,41.9882,37.698	,	186/695,323/832	109884775	8103,4903	2203	4300	6503	SO:0001819	synonymous_variant	6272	exon9			TCTTGTTGTATCC	BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.969A>C	1.37:g.109884775T>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	154	97	0.62987	NM_002959	B4DWI3|C0JYZ0|Q8IZ49	Silent	SNP	ENST00000256637.6	37	CCDS798.1																																																																																			T|0.284;G|0.716	0.716	strong		0.428	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959	
OR10K2	391107	hgsc.bcm.edu	37	1	158390252	158390252	+	Silent	SNP	T	T	G	rs12239443	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158390252T>G	ENST00000314902.2	-	1	404	c.405A>C	c.(403-405)ctA>ctC	p.L135L		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					CATGTCCCATTAGCACTGAGT	0.502													G|||	1453	0.290136	0.2526	0.2709	5008	,	,		21765	0.1687		0.4592	False		,,,				2504	0.3057				p.L135L		Atlas-SNP	.											.	OR10K2	69	.	0			c.A405C						PASS	.	G		1183,3223	710.9+/-407.9	164,855,1184	185.0	176.0	179.0		405	0.8	0.4	1	dbSNP_120	179	3770,4830	616.0+/-396.4	808,2154,1338	no	coding-synonymous	OR10K2	NM_001004476.1		972,3009,2522	GG,GT,TT		43.8372,26.8498,38.0824		135/313	158390252	4953,8053	2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			TCCCATTAGCACT	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"""GPCR / Class A : Olfactory receptors"""	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.405A>C	1.37:g.158390252T>G		Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	404	403	0.997525	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			T|0.635;G|0.365	0.365	strong		0.502	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476	
RPS6KA4	8986	hgsc.bcm.edu	37	11	64138805	64138805	+	Silent	SNP	T	T	C	rs11542299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64138805T>C	ENST00000334205.4	+	17	2237	c.2172T>C	c.(2170-2172)aaT>aaC	p.N724N	RPS6KA4_ENST00000294261.4_Silent_p.N476N|MIR1237_ENST00000408346.1_RNA|RPS6KA4_ENST00000528057.1_Silent_p.N717N	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	724					axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						GCGTGGAGAATGCACCCCTGG	0.706													C|||	1267	0.252995	0.0514	0.3833	5008	,	,		9149	0.2113		0.3708	False		,,,				2504	0.3548				p.N724N		Atlas-SNP	.											RPS6KA4_ENST00000334205,NS,carcinoma,+1,2	RPS6KA4	85	2	0			c.T2172C						PASS	.	C	,	433,3879		36,361,1759	38.0	43.0	42.0		2154,2172	1.6	1.0	11	dbSNP_120	42	2938,5552		502,1934,1809	no	coding-synonymous,coding-synonymous	RPS6KA4	NM_001006944.1,NM_003942.2	,	538,2295,3568	CC,CT,TT		34.6054,10.0417,26.3318	,	718/767,724/773	64138805	3371,9431	2156	4245	6401	SO:0001819	synonymous_variant	8986	exon17			GGAGAATGCACCC	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"""ribosomal protein S6 kinase, 90kD, polypeptide 4"""			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.2172T>C	11.37:g.64138805T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_003942	A8K7Z8|O75585|Q53ES8	Silent	SNP	ENST00000334205.4	37	CCDS8073.1																																																																																			T|0.729;C|0.271	0.271	strong		0.706	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942	
IL24	11009	hgsc.bcm.edu	37	1	207074905	207074905	+	Missense_Mutation	SNP	T	T	C	rs1150258	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207074905T>C	ENST00000294984.2	+	5	644	c.370T>C	c.(370-372)Tac>Cac	p.Y124H	IL24_ENST00000491169.1_3'UTR|IL24_ENST00000391929.3_Missense_Mutation_p.Y125H|IL24_ENST00000367093.3_Intron	NM_001185156.1|NM_006850.3	NP_001172085.1|NP_006841.1	Q13007	IL24_HUMAN	interleukin 24	124			Y -> H (in dbSNP:rs1150258). {ECO:0000269|PubMed:11704829, ECO:0000269|Ref.5}.		apoptotic process (GO:0006915)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|serine phosphorylation of STAT3 protein (GO:0033136)|wound healing (GO:0042060)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)				endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12	Breast(84;0.201)					TTTCAAAAACTACCACAATAG	0.478													T|||	1581	0.315695	0.2905	0.438	5008	,	,		22780	0.2123		0.4533	False		,,,				2504	0.228				p.Y125H		Atlas-SNP	.											.	IL24	20	.	0			c.T373C						PASS	.	T	HIS/TYR,,,HIS/TYR	1303,3103	441.6+/-346.4	199,905,1099	129.0	118.0	121.0		373,,,370	2.4	0.9	1	dbSNP_87	121	4055,4545	558.8+/-387.3	975,2105,1220	yes	missense,intron,intron,missense	IL24	NM_001185156.1,NM_001185157.1,NM_001185158.1,NM_006850.3	83,,,83	1174,3010,2319	CC,CT,TT		47.1512,29.5733,41.1964	probably-damaging,,,probably-damaging	125/208,,,124/207	207074905	5358,7648	2203	4300	6503	SO:0001583	missense	11009	exon5			AAAAACTACCACA	U16261	CCDS1471.1, CCDS53465.1, CCDS53466.1, CCDS73021.1	1q32	2011-07-15		2001-06-29	ENSG00000162892	ENSG00000162892		"""Interleukins and interleukin receptors"""	11346	protein-coding gene	gene with protein product	"""melanoma differentiation association protein 7"", ""suppression of tumorigenicity 16 (melanoma differentiation)"", ""IL-4-induced secreted protein"""	604136		ST16		8545104, 8799171	Standard	NM_001185156		Approved	mda-7, IL10B, Mob-5, C49A, FISP, IL-24	uc001heu.2	Q13007	OTTHUMG00000036459	ENST00000294984.2:c.370T>C	1.37:g.207074905T>C	ENSP00000294984:p.Tyr124His	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	254	108	0.425197	NM_001185156	Q2YHE5|Q53XZ7|Q5YLN8|Q96DB0|Q96KG4	Missense_Mutation	SNP	ENST00000294984.2	37	CCDS1471.1	796	0.36446886446886445	146	0.2967479674796748	181	0.5	129	0.22552447552447552	340	0.44854881266490765	T	14.19	2.460607	0.43736	0.295733	0.471512	ENSG00000162892	ENST00000391929;ENST00000294984	T;T	0.17854	2.25;2.25	4.72	2.38	0.29361	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.144833	0.47852	D	0.000203	T	0.00012	0.0000	M	0.70595	2.14	0.09310	P	0.999999999449859	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.47045	-0.9147	9	0.44086	T	0.13	.	3.6967	0.08367	0.1904:0.1012:0.0:0.7084	rs1150258;rs17436290;rs52789945;rs61085050;rs1150258	125;124	Q53XZ7;Q13007	.;IL24_HUMAN	H	125;124	ENSP00000375795:Y125H;ENSP00000294984:Y124H	ENSP00000294984:Y124H	Y	+	1	0	IL24	205141528	0.625000	0.27111	0.897000	0.35233	0.388000	0.30384	1.076000	0.30729	0.322000	0.23283	0.454000	0.30748	TAC	T|0.623;G|0.003	.	strong		0.478	IL24-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088680.2	NM_006850	
ENTPD8	377841	hgsc.bcm.edu	37	9	140327663	140327663	+	IGR	SNP	C	C	T	rs34155071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140327663C>T	ENST00000472938.1	-	0	1749				NOXA1_ENST00000392815.2_Missense_Mutation_p.P230L|NOXA1_ENST00000341349.2_Missense_Mutation_p.P286L			Q5MY95	ENTP8_HUMAN	ectonucleoside triphosphate diphosphohydrolase 8						nucleoside diphosphate biosynthetic process (GO:0009133)|nucleoside monophosphate biosynthetic process (GO:0009124)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			biliary_tract(1)|lung(4)|prostate(1)|skin(1)	7	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000224)|Epithelial(140;0.000898)		ACAGGGCTGCCGGCAATGGGG	0.667													c|||	1062	0.212061	0.0779	0.1326	5008	,	,		14280	0.247		0.3151	False		,,,				2504	0.3078				p.P286L		Atlas-SNP	.											NOXA1,colon,carcinoma,0,1	NOXA1	32	1	0			c.C857T						PASS	.	T	LEU/PRO	444,3910		33,378,1766	9.0	11.0	10.0		857	-6.3	0.0	9	dbSNP_126	10	2673,5897		437,1799,2049	yes	missense	NOXA1	NM_006647.1	98	470,2177,3815	TT,TC,CC		31.1902,10.1975,24.1179	benign	286/484	140327663	3117,9807	2177	4285	6462	SO:0001628	intergenic_variant	10811	exon10			GGCTGCCGGCAAT	AY359088	CCDS7043.1, CCDS43913.1	9q34.3	2013-09-20			ENSG00000188833	ENSG00000188833			24860	protein-coding gene	gene with protein product	"""GLSR2492"""					12975309	Standard	NM_198585		Approved	UNQ2492, NTPDase-8	uc004cmw.3	Q5MY95	OTTHUMG00000131831		9.37:g.140327663C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_006647	A2BG17|Q6UVZ0	Missense_Mutation	SNP	ENST00000472938.1	37	CCDS43913.1	479	0.21932234432234432	42	0.08536585365853659	55	0.15193370165745856	141	0.2465034965034965	241	0.3179419525065963	c	5.077	0.199935	0.09652	0.101975	0.311902	ENSG00000188747	ENST00000341349;ENST00000392815	D;D	0.85702	-2.02;-2.01	3.17	-6.34	0.01982	.	3.307570	0.01200	N	0.007549	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.11235	0.003;0.002;0.004	B;B;B	0.06405	0.002;0.001;0.001	T	0.12941	-1.0528	9	0.19147	T	0.46	.	5.8021	0.18420	0.0:0.2326:0.2607:0.5068	rs34155071;rs34155071	230;286;286	Q86UR1-3;Q86UR1;Q86UR1-2	.;NOXA1_HUMAN;.	L	286;230	ENSP00000342848:P286L;ENSP00000376562:P230L	ENSP00000342848:P286L	P	+	2	0	NOXA1	139447484	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.879000	0.00716	-2.169000	0.00777	-0.974000	0.02594	CCG	C|0.795;T|0.205	0.205	strong		0.667	ENTPD8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355991.1	NM_198585	
FBXO7	25793	hgsc.bcm.edu	37	22	32871365	32871365	+	Intron	SNP	G	G	A	rs9621461	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:32871365G>A	ENST00000266087.7	+	1	449				FBXO7_ENST00000382058.3_Missense_Mutation_p.G6E|FBXO7_ENST00000397426.1_5'UTR	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7						cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CGGCCTCCCGGGGGCTCTGGT	0.652													G|||	326	0.0650958	0.0356	0.0922	5008	,	,		11609	0.0615		0.0905	False		,,,				2504	0.0634				p.G6E		Atlas-SNP	.											.	FBXO7	131	.	0			c.G17A						PASS	.	G	GLU/GLY,	139,3501		3,133,1684	24.0	30.0	28.0		17,	-0.5	0.0	22	dbSNP_119	28	782,7350		39,704,3323	yes	missense,intron	FBXO7	NM_001033024.1,NM_012179.3	98,	42,837,5007	AA,AG,GG		9.6163,3.8187,7.8236	,	6/444,	32871365	921,10851	1820	4066	5886	SO:0001627	intron_variant	25793	exon1			CTCCCGGGGGCTC	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.122+254G>A	22.37:g.32871365G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_001033024	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	37	CCDS13907.1	155	0.07097069597069597	14	0.028455284552845527	38	0.10497237569060773	37	0.06468531468531469	66	0.0870712401055409	G	4.989	0.183742	0.09495	0.038187	0.096163	ENSG00000100225	ENST00000452138;ENST00000382058	T;T	0.63744	0.91;-0.06	3.07	-0.468	0.12146	.	.	.	.	.	T	0.01029	0.0034	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.05007	-1.0912	8	0.46703	T	0.11	.	5.1596	0.15054	0.1305:0.4412:0.4283:0.0	rs9621461	6	Q9Y3I1-2	.	E	6	ENSP00000388547:G6E;ENSP00000371490:G6E	ENSP00000371490:G6E	G	+	2	0	FBXO7	31201365	0.006000	0.16342	0.000000	0.03702	0.010000	0.07245	0.718000	0.25866	-0.006000	0.14370	0.561000	0.74099	GGG	G|0.928;A|0.072	0.072	strong		0.652	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
FAM169A	26049	hgsc.bcm.edu	37	5	74077474	74077474	+	Silent	SNP	C	C	T	rs16872269	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:74077474C>T	ENST00000389156.4	-	13	1914	c.1824G>A	c.(1822-1824)aaG>aaA	p.K608K	FAM169A_ENST00000510496.1_Silent_p.K548K|RNU6-1330P_ENST00000362775.1_RNA|FAM169A_ENST00000380515.3_3'UTR	NM_015566.2	NP_056381.1	Q9Y6X4	F169A_HUMAN	family with sequence similarity 169, member A	608						membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	27						CTGACTGATTCTTCTGTCCTG	0.463													C|||	507	0.101238	0.3215	0.0519	5008	,	,		19530	0.0129		0.0169	False		,,,				2504	0.0164				p.K608K		Atlas-SNP	.											.	FAM169A	61	.	0			c.G1824A						PASS	.	C		958,2880		125,708,1086	144.0	135.0	137.0		1824	4.2	1.0	5	dbSNP_123	137	164,8138		1,162,3988	no	coding-synonymous	FAM169A	NM_015566.1		126,870,5074	TT,TC,CC		1.9754,24.9609,9.2422		608/671	74077474	1122,11018	1919	4151	6070	SO:0001819	synonymous_variant	26049	exon13			CTGATTCTTCTGT		CCDS43330.1	5q13.3	2008-08-08			ENSG00000198780	ENSG00000198780			29138	protein-coding gene	gene with protein product		615769				10048485	Standard	NM_015566		Approved	KIAA0888	uc003kdm.4	Q9Y6X4	OTTHUMG00000162930	ENST00000389156.4:c.1824G>A	5.37:g.74077474C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	146	66	0.452055	NM_015566	A8K1T9|Q6MZT0|Q9H989	Silent	SNP	ENST00000389156.4	37	CCDS43330.1																																																																																			C|0.909;T|0.091	0.091	strong		0.463	FAM169A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371092.2		
SPTB	6710	hgsc.bcm.edu	37	14	65263300	65263300	+	Missense_Mutation	SNP	C	C	T	rs229587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:65263300C>T	ENST00000389721.5	-	10	1348	c.1316G>A	c.(1315-1317)aGt>aAt	p.S439N	SPTB_ENST00000556626.1_Missense_Mutation_p.S439N|SPTB_ENST00000542895.1_Missense_Mutation_p.S439N|SPTB_ENST00000389720.3_Missense_Mutation_p.S439N|SPTB_ENST00000389722.3_Missense_Mutation_p.S439N	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	439			S -> N (in dbSNP:rs229587). {ECO:0000269|PubMed:2195026}.		actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CTGGTTTTCACTGAGCCAGGT	0.602													T|||	2338	0.466853	0.6921	0.3429	5008	,	,		18547	0.3532		0.3439	False		,,,				2504	0.4939				p.S439N		Atlas-SNP	.											.	SPTB	378	.	0			c.G1316A						PASS	.	T	ASN/SER,ASN/SER	2796,1610	497.6+/-363.9	883,1030,290	74.0	74.0	74.0		1316,1316	0.8	1.0	14	dbSNP_79	74	2879,5721	672.1+/-402.9	476,1927,1897	yes	missense,missense	SPTB	NM_000347.5,NM_001024858.2	46,46	1359,2957,2187	TT,TC,CC		33.4767,36.5411,43.6337	benign,benign	439/2138,439/2329	65263300	5675,7331	2203	4300	6503	SO:0001583	missense	6710	exon10			TTTTCACTGAGCC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.1316G>A	14.37:g.65263300C>T	ENSP00000374371:p.Ser439Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	904	0.4139194139194139	324	0.6585365853658537	123	0.3397790055248619	197	0.34440559440559443	260	0.34300791556728233	T	10.09	1.256188	0.22965	0.634589	0.334767	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76	5.81	0.765	0.18470	.	0.289195	0.38326	N	0.001739	T	0.00012	0.0000	L	0.46819	1.47	0.53005	P	3.500000000000725E-5	B;B	0.10296	0.003;0.002	B;B	0.17722	0.019;0.007	T	0.43278	-0.9401	9	0.17369	T	0.5	.	10.3943	0.44192	0.0:0.6243:0.0:0.3757	rs229587;rs17180455;rs60734774;rs229587	439;443	P11277;Q59FP5	SPTB1_HUMAN;.	N	443;439;439;439;439;439	ENSP00000374372:S439N;ENSP00000451752:S439N;ENSP00000374371:S439N;ENSP00000443882:S439N;ENSP00000374370:S439N	ENSP00000374370:S439N	S	-	2	0	SPTB	64333053	0.003000	0.15002	0.989000	0.46669	0.933000	0.57130	0.269000	0.18589	-0.081000	0.12662	-0.982000	0.02568	AGT	C|0.569;N|0.000	.	strong		0.602	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
SCN9A	6335	hgsc.bcm.edu	37	2	167144995	167144995	+	Silent	SNP	T	T	C	rs13402180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:167144995T>C	ENST00000409435.1	-	9	1265	c.1266A>G	c.(1264-1266)gaA>gaG	p.E422E	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.E423E|SCN9A_ENST00000409672.1_Silent_p.E422E|SCN9A_ENST00000375387.4_Silent_p.E423E			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	422					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTGTTGAAATTCTAATTCTT	0.363													T|||	1775	0.354433	0.357	0.3242	5008	,	,		14756	0.3065		0.4036	False		,,,				2504	0.3712				p.E422E		Atlas-SNP	.											.	SCN9A	296	.	0			c.A1266G						PASS	.	T		1403,2275		281,841,717	143.0	150.0	148.0		1266	4.6	1.0	2	dbSNP_121	148	3184,5004		600,1984,1510	no	coding-synonymous	SCN9A	NM_002977.3		881,2825,2227	CC,CT,TT		38.8862,38.1457,38.6567		422/1978	167144995	4587,7279	1839	4094	5933	SO:0001819	synonymous_variant	6335	exon10			TTGAAATTCTAAT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1266A>G	2.37:g.167144995T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	56	0.41791	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			C|0.338;T|0.662	0.338	strong		0.363	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
CEACAM20	125931	hgsc.bcm.edu	37	19	45028169	45028169	+	RNA	SNP	C	C	T	rs7260180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45028169C>T	ENST00000454753.1	-	0	600							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				TGGAACACAACGGAGAGGTTG	0.532													C|||	1851	0.369609	0.1377	0.4265	5008	,	,		24882	0.2579		0.6342	False		,,,				2504	0.4857				p.V108I		Atlas-SNP	.											.	CEACAM20	31	.	0			c.G322A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	942,3254		129,684,1285	87.0	87.0	87.0		322,322,322,322	2.3	0.0	19	dbSNP_116	87	5168,3304		1606,1956,674	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	29,29,29,29	1735,2640,1959	TT,TC,CC		38.9991,22.45,48.2318	benign,benign,benign,benign	108/597,108/492,108/504,108/585	45028169	6110,6558	2098	4236	6334			125931	exon3			ACACAACGGAGAG	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45028169C>T		Somatic	232	2	0.00862069		WXS	Illumina HiSeq	Phase_I	248	245	0.987903	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				C|0.629;T|0.371	0.371	strong		0.532	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
MYH7B	57644	hgsc.bcm.edu	37	20	33565480	33565480	+	Silent	SNP	C	C	T	rs6060137	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:33565480C>T	ENST00000262873.7	+	2	143	c.51C>T	c.(49-51)gcC>gcT	p.A17A		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	0						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			ACCGTGGTGCCGAGGTAGGTG	0.622													C|||	1340	0.267572	0.3434	0.1527	5008	,	,		8980	0.2173		0.2396	False		,,,				2504	0.3272				p.A17A		Atlas-SNP	.											.	MYH7B	145	.	0			c.C51T						PASS	.	C		1234,2678		200,834,922	23.0	20.0	21.0		51	-2.8	0.7	20	dbSNP_114	21	2235,6057		310,1615,2221	no	coding-synonymous	MYH7B	NM_020884.3		510,2449,3143	TT,TC,CC		26.9537,31.544,28.4251		17/1984	33565480	3469,8735	1956	4146	6102	SO:0001819	synonymous_variant	57644	exon4			TGGTGCCGAGGTA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.51C>T	20.37:g.33565480C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	157	64	0.407643	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			C|0.748;T|0.252	0.252	strong		0.622	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
XRN1	54464	hgsc.bcm.edu	37	3	142102247	142102247	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:142102247T>C	ENST00000264951.4	-	22	2628	c.2511A>G	c.(2509-2511)cgA>cgG	p.R837R	XRN1_ENST00000392981.2_Silent_p.R837R	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	837					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						AGTCGAAAGCTCGGATGTCCT	0.363																																					p.R837R		Atlas-SNP	.											XRN1,NS,carcinoma,-1,1	XRN1	138	1	0			c.A2511G						scavenged	.						62.0	61.0	62.0					3																	142102247		2203	4300	6503	SO:0001819	synonymous_variant	54464	exon22			GAAAGCTCGGATG	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.2511A>G	3.37:g.142102247T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	152	3	0.0197368	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	CCDS3123.1																																																																																			.	.	none		0.363	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
XKR9	389668	hgsc.bcm.edu	37	8	71646461	71646461	+	Silent	SNP	C	C	T	rs74975207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:71646461C>T	ENST00000408926.3	+	5	1458	c.924C>T	c.(922-924)tgC>tgT	p.C308C	XKR9_ENST00000520273.1_Intron|XKR9_ENST00000520030.1_Silent_p.C308C	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	308						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			TCTGGGTTTGCCCCCTCACTA	0.328													C|||	128	0.0255591	0.0008	0.0216	5008	,	,		16018	0.001		0.0437	False		,,,				2504	0.0685				p.C308C		Atlas-SNP	.											.	XKR9	43	.	0			c.C924T						PASS	.	C		47,4359	47.5+/-82.1	1,45,2157	94.0	92.0	92.0		924	0.1	0.0	8	dbSNP_132	92	438,8160	132.5+/-190.1	16,406,3877	no	coding-synonymous	XKR9	NM_001011720.1		17,451,6034	TT,TC,CC		5.0942,1.0667,3.7296		308/374	71646461	485,12519	2203	4299	6502	SO:0001819	synonymous_variant	389668	exon5			GGTTTGCCCCCTC	AY534247	CCDS34905.1	8q13.3	2006-01-12	2006-01-12			ENSG00000221947			20937	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 9"""				Standard	NM_001287258		Approved		uc003xyq.3	Q5GH70		ENST00000408926.3:c.924C>T	8.37:g.71646461C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	179	83	0.463687	NM_001011720	B2RNS9|B9EH74	Silent	SNP	ENST00000408926.3	37	CCDS34905.1																																																																																			C|0.970;T|0.030	0.030	strong		0.328	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720	
OR4S2	219431	hgsc.bcm.edu	37	11	55419160	55419160	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55419160A>G	ENST00000312422.2	+	1	781	c.781A>G	c.(781-783)Acg>Gcg	p.T261A		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				GCGCCCTGATACGACCTTTTC	0.453																																					p.T261A		Atlas-SNP	.											OR4S2,colon,carcinoma,-1,1	OR4S2	89	1	0			c.A781G						scavenged	.						157.0	136.0	143.0					11																	55419160		2180	4026	6206	SO:0001583	missense	219431	exon1			CCTGATACGACCT	BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"""GPCR / Class A : Olfactory receptors"""	15183	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily S, member 2 pseudogene"""	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.781A>G	11.37:g.55419160A>G	ENSP00000310337:p.Thr261Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	142	4	0.028169	NM_001004059	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	37	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	A	8.439	0.850455	0.17034	.	.	ENSG00000174982	ENST00000312422	T	0.00069	8.77	5.35	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.481200	0.19147	N	0.121552	T	0.00109	0.0003	N	0.21508	0.67	0.09310	N	1	P	0.36483	0.555	B	0.40982	0.345	T	0.12066	-1.0562	10	0.25751	T	0.34	.	7.2169	0.25965	0.7553:0.0:0.2447:0.0	.	261	Q8NH73	OR4S2_HUMAN	A	261	ENSP00000310337:T261A	ENSP00000310337:T261A	T	+	1	0	OR4S2	55175736	0.000000	0.05858	0.030000	0.17652	0.465000	0.32709	0.067000	0.14510	0.878000	0.35920	0.443000	0.29094	ACG	.	.	none		0.453	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059	
PTGFRN	5738	hgsc.bcm.edu	37	1	117529458	117529458	+	Missense_Mutation	SNP	G	G	A	rs10801922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:117529458G>A	ENST00000393203.2	+	9	2656	c.2509G>A	c.(2509-2511)Gtc>Atc	p.V837I		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	837			V -> I (in dbSNP:rs10801922).		lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GCTGATCGGCGTCGGTCTGTC	0.617													G|||	2494	0.498003	0.3018	0.5951	5008	,	,		18613	0.6597		0.4364	False		,,,				2504	0.591				p.V837I		Atlas-SNP	.											PTGFRN,NS,carcinoma,-2,1	PTGFRN	91	1	0			c.G2509A						PASS	.	G	ILE/VAL	1378,3028	454.4+/-350.6	235,908,1060	111.0	96.0	101.0		2509	0.1	0.7	1	dbSNP_120	101	3825,4775	539.9+/-383.7	853,2119,1328	yes	missense	PTGFRN	NM_020440.2	29	1088,3027,2388	AA,AG,GG		44.4767,31.2755,40.0046	benign	837/880	117529458	5203,7803	2203	4300	6503	SO:0001583	missense	5738	exon9			ATCGGCGTCGGTC	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9601	protein-coding gene	gene with protein product		601204	"""prostaglandin F2 receptor negative regulator"""			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.2509G>A	1.37:g.117529458G>A	ENSP00000376899:p.Val837Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_020440	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	1078	0.4935897435897436	159	0.3231707317073171	190	0.5248618784530387	382	0.6678321678321678	347	0.4577836411609499	G	8.889	0.953437	0.18431	0.312755	0.444767	ENSG00000134247	ENST00000393203;ENST00000544471	T	0.04360	3.64	6.17	0.122	0.14702	.	0.456264	0.23245	N	0.050303	T	0.00552	0.0018	N	0.02539	-0.55	0.58432	P	5.000000000032756E-6	B	0.12013	0.005	B	0.08055	0.003	T	0.44436	-0.9328	9	0.07175	T	0.84	-16.8037	11.6594	0.51337	0.3447:0.0:0.6553:0.0	rs10801922;rs17579898;rs52822596;rs61548861;rs10801922	837	Q9P2B2	FPRP_HUMAN	I	837;696	ENSP00000376899:V837I	ENSP00000376899:V837I	V	+	1	0	PTGFRN	117330981	0.796000	0.28864	0.726000	0.30738	0.976000	0.68499	0.593000	0.23999	0.115000	0.18071	-0.137000	0.14449	GTC	G|0.560;A|0.440	0.440	strong		0.617	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
MACROD1	28992	hgsc.bcm.edu	37	11	63885704	63885704	+	Intron	SNP	C	C	T	rs677447	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:63885704C>T	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.Y655Y	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						CCATTGGCTACGGCACCACGC	0.652													C|||	1996	0.398562	0.1309	0.5346	5008	,	,		15285	0.3254		0.6958	False		,,,				2504	0.4335				p.Y655Y		Atlas-SNP	.											.	FLRT1	46	.	0			c.C1965T						PASS	.	C	,	964,3436		109,746,1345	56.0	50.0	52.0		1965,	2.3	1.0	11	dbSNP_83	52	5867,2725		2028,1811,457	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	2137,2557,1802	TT,TC,CC		31.7155,21.9091,47.4215	,	655/675,	63885704	6831,6161	2200	4296	6496	SO:0001627	intron_variant	23769	exon2			TGGCTACGGCACC	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+33006G>A	11.37:g.63885704C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	119	117	0.983193	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			C|0.533;T|0.467	0.467	strong		0.652	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
MUC4	4585	hgsc.bcm.edu	37	3	195515387	195515387	+	Missense_Mutation	SNP	T	T	C	rs13065584	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515387T>C	ENST00000463781.3	-	2	3523	c.3064A>G	c.(3064-3066)Acc>Gcc	p.T1022A	MUC4_ENST00000475231.1_Missense_Mutation_p.T1022A|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	457	Repeat.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.T1022A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGTGTGACCTGTG	0.567													.|||	1418	0.283147	0.2837	0.2478	5008	,	,		17215	0.3472		0.2614	False		,,,				2504	0.2638				p.T1022A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	6	Deletion - In frame(4)|Substitution - Missense(2)	stomach(4)|prostate(2)	c.A3064G						scavenged	.						46.0	25.0	31.0					3																	195515387		692	1590	2282	SO:0001583	missense	4585	exon2			GGGTGGTGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3064A>G	3.37:g.195515387T>C	ENSP00000417498:p.Thr1022Ala	Somatic	602	12	0.0199336		WXS	Illumina HiSeq	Phase_I	177	33	0.186441	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	7.364	0.625483	0.14257	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.5;1.49	1.0	1.0	0.19881	.	.	.	.	.	T	0.14614	0.0353	N	0.14661	0.345	0.09310	N	1	B	0.24426	0.103	B	0.12837	0.008	T	0.25813	-1.0121	8	.	.	.	.	6.2761	0.20981	0.0:0.0:0.0:1.0	rs13065584	1022	E7ESK3	.	A	1022	ENSP00000417498:T1022A;ENSP00000420243:T1022A	.	T	-	1	0	MUC4	196999782	0.000000	0.05858	0.002000	0.10522	0.058000	0.15608	-2.025000	0.01435	0.734000	0.32515	0.055000	0.15244	ACC	T|0.992;C|0.008	0.008	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TMBIM4	51643	hgsc.bcm.edu	37	12	66546100	66546100	+	Missense_Mutation	SNP	A	A	G	rs8793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:66546100A>G	ENST00000358230.3	-	3	383	c.263T>C	c.(262-264)aTt>aCt	p.I88T	TMBIM4_ENST00000398033.4_Missense_Mutation_p.I88T|TMBIM4_ENST00000556010.1_Missense_Mutation_p.I88T|TMBIM4_ENST00000544599.1_5'UTR|TMBIM4_ENST00000286424.7_Missense_Mutation_p.I135T|TMBIM4_ENST00000542724.1_Missense_Mutation_p.I57T|TMBIM4_ENST00000539652.1_Missense_Mutation_p.I88T	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	88			I -> T (in dbSNP:rs8793). {ECO:0000269|PubMed:10810093, ECO:0000269|PubMed:10931946, ECO:0000269|PubMed:16303743}.		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		TCTGTTTAAAATCAACGCAAA	0.338													G|||	2356	0.470447	0.2496	0.245	5008	,	,		13287	0.8839		0.4175	False		,,,				2504	0.5573				p.I88T		Atlas-SNP	.											.	TMBIM4	47	.	0			c.T263C						PASS	.	G	THR/ILE	1064,2606		153,758,924	93.0	91.0	91.0		263	2.6	0.9	12	dbSNP_52	91	3453,4711		736,1981,1365	yes	missense	TMBIM4	NM_016056.2	89	889,2739,2289	GG,GA,AA		42.2954,28.9918,38.1697	benign	88/239	66546100	4517,7317	1835	4082	5917	SO:0001583	missense	51643	exon3			TTTAAAATCAACG	AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.263T>C	12.37:g.66546100A>G	ENSP00000350965:p.Ile88Thr	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	184	95	0.516304	NM_016056	Q542Z6|Q9UHY5|Q9Y3C2	Missense_Mutation	SNP	ENST00000358230.3	37	CCDS41805.1	1029	0.47115384615384615	119	0.241869918699187	99	0.27348066298342544	503	0.8793706293706294	308	0.40633245382585753	G	4.389	0.071874	0.08436	0.289918	0.422954	ENSG00000155957	ENST00000556010;ENST00000358230;ENST00000426857;ENST00000286424;ENST00000398033;ENST00000539043;ENST00000539427;ENST00000542724	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84	5.87	2.64	0.31445	.	0.218305	0.47852	N	0.000212	T	0.00012	0.0000	N	0.02345	-0.59	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0	B;B;B;B;B	0.08055	0.0;0.001;0.0;0.003;0.002	T	0.26744	-1.0094	8	.	.	.	-3.3271	8.1268	0.31003	0.2159:0.0:0.6664:0.1177	rs8793;rs17180104;rs58374222;rs8793	88;135;88;57;88	E7EWY5;G3XAA5;E7EQ00;G3V1M2;Q9HC24	.;.;.;.;TMBI4_HUMAN	T	88;88;88;135;88;88;134;57	ENSP00000451688:I88T;ENSP00000350965:I88T;ENSP00000286424:I135T;ENSP00000381114:I88T;ENSP00000441291:I57T	.	I	-	2	0	TMBIM4	64832367	0.986000	0.35501	0.900000	0.35374	0.336000	0.28762	1.350000	0.34010	0.413000	0.25759	-0.983000	0.02560	ATT	G|0.478;N|0.000	0.478	strong		0.338	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056	
PARP12	64761	hgsc.bcm.edu	37	7	139727135	139727135	+	Silent	SNP	G	G	A	rs2286196	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:139727135G>A	ENST00000263549.3	-	10	2442	c.1569C>T	c.(1567-1569)ttC>ttT	p.F523F		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	523	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					GAACAAAGTAGAAAGGCAGCG	0.507													G|||	1513	0.302117	0.2799	0.3631	5008	,	,		21451	0.5258		0.1998	False		,,,				2504	0.1636				p.F523F		Atlas-SNP	.											.	PARP12	59	.	0			c.C1569T						PASS	.	G		1231,3175	425.7+/-340.9	196,839,1168	103.0	96.0	98.0		1569	3.7	0.3	7	dbSNP_100	98	1731,6869	314.6+/-311.9	165,1401,2734	no	coding-synonymous	PARP12	NM_022750.2		361,2240,3902	AA,AG,GG		20.1279,27.9392,22.7741		523/702	139727135	2962,10044	2203	4300	6503	SO:0001819	synonymous_variant	64761	exon10			AAAGTAGAAAGGC	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1569C>T	7.37:g.139727135G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	166	89	0.536145	NM_022750	Q9H610|Q9NP36|Q9NTI3	Silent	SNP	ENST00000263549.3	37	CCDS5857.1																																																																																			G|0.728;T|0.002	.	strong		0.507	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
TRPM1	4308	hgsc.bcm.edu	37	15	31329944	31329944	+	Silent	SNP	G	G	A	rs12911350	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:31329944G>A	ENST00000256552.6	-	20	2688	c.2541C>T	c.(2539-2541)aaC>aaT	p.N847N	RP11-348B17.1_ENST00000558755.1_RNA|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Silent_p.N825N|TRPM1_ENST00000542188.1_Silent_p.N864N	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CAATGGGCGCGTTATAGAATT	0.408													g|||	446	0.0890575	0.0983	0.1297	5008	,	,		19983	0.0079		0.1362	False		,,,				2504	0.0828				p.N864N		Atlas-SNP	.											.	TRPM1	183	.	0			c.C2592T						PASS	.	A		435,3371		21,393,1489	166.0	151.0	156.0		2475	-5.7	0.5	15	dbSNP_121	156	1099,7153		75,949,3102	no	coding-synonymous	TRPM1	NM_002420.4		96,1342,4591	AA,AG,GG		13.318,11.4293,12.7218		825/1604	31329944	1534,10524	1903	4126	6029	SO:0001819	synonymous_variant	4308	exon19			GGGCGCGTTATAG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2541C>T	15.37:g.31329944G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	194	80	0.412371	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			G|0.909;A|0.091	0.091	strong		0.408	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
SSTR4	6754	hgsc.bcm.edu	37	20	23017044	23017044	+	Silent	SNP	C	C	T	rs3746728	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23017044C>T	ENST00000255008.3	+	1	988	c.924C>T	c.(922-924)ccC>ccT	p.P308P	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	308					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GCGCCAACCCCATTCTCTATG	0.587													C|||	1548	0.309105	0.2315	0.2824	5008	,	,		18308	0.2351		0.3698	False		,,,				2504	0.4468				p.P308P	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,colon,carcinoma,0,2	SSTR4	83	2	0			c.C924T						PASS	.	C		1076,3328	370.0+/-319.4	145,786,1271	151.0	151.0	151.0		924	2.4	0.9	20	dbSNP_107	151	3312,5286	482.4+/-370.9	670,1972,1657	no	coding-synonymous	SSTR4	NM_001052.2		815,2758,2928	TT,TC,CC		38.5206,24.4323,33.7487		308/389	23017044	4388,8614	2202	4299	6501	SO:0001819	synonymous_variant	6754	exon1			CAACCCCATTCTC		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.924C>T	20.37:g.23017044C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Silent	SNP	ENST00000255008.3	37	CCDS42856.1																																																																																			C|0.669;T|0.331	0.331	strong		0.587	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
GPC6	10082	hgsc.bcm.edu	37	13	95034763	95034763	+	Silent	SNP	G	G	A	rs2274020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:95034763G>A	ENST00000377047.4	+	7	1863	c.1248G>A	c.(1246-1248)acG>acA	p.T416T		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	416					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.T416T(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				CAGCGGGCACGTCCAACGAGG	0.532													G|||	799	0.159545	0.1051	0.0908	5008	,	,		21103	0.2897		0.0765	False		,,,				2504	0.2331				p.T416T		Atlas-SNP	.											GPC6,NS,carcinoma,0,1	GPC6	102	1	1	Substitution - coding silent(1)	stomach(1)	c.G1248A						PASS	.	G		456,3950	219.7+/-237.4	24,408,1771	144.0	130.0	135.0		1248	-1.6	1.0	13	dbSNP_100	135	798,7802	187.6+/-234.8	37,724,3539	no	coding-synonymous	GPC6	NM_005708.3		61,1132,5310	AA,AG,GG		9.2791,10.3495,9.6417		416/556	95034763	1254,11752	2203	4300	6503	SO:0001819	synonymous_variant	10082	exon7			GGGCACGTCCAAC	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"""Proteoglycans / Cell Surface : Glypicans"""	4454	protein-coding gene	gene with protein product	"""glypican proteoglycan 6"""	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.1248G>A	13.37:g.95034763G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	159	88	0.553459	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Silent	SNP	ENST00000377047.4	37	CCDS9469.1																																																																																			G|0.881;A|0.119	0.119	strong		0.532	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708	
DENND4A	10260	hgsc.bcm.edu	37	15	65994733	65994733	+	Silent	SNP	C	C	T	rs17810074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:65994733C>T	ENST00000431932.2	-	17	2548	c.2340G>A	c.(2338-2340)gtG>gtA	p.V780V	DENND4A_ENST00000443035.3_Silent_p.V780V	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	780					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GACAGACTTTCACATAAGCTG	0.408													C|||	1234	0.246406	0.0711	0.3977	5008	,	,		18286	0.1935		0.326	False		,,,				2504	0.3487				p.V780V		Atlas-SNP	.											.	DENND4A	217	.	0			c.G2340A						PASS	.	C	,	357,3345		18,321,1512	62.0	54.0	56.0		2340,2340	4.8	1.0	15	dbSNP_123	56	2417,5779		363,1691,2044	no	coding-synonymous,coding-synonymous	DENND4A	NM_001144823.1,NM_005848.3	,	381,2012,3556	TT,TC,CC		29.49,9.6434,23.3148	,	780/1907,780/1864	65994733	2774,9124	1851	4098	5949	SO:0001819	synonymous_variant	10260	exon17			GACTTTCACATAA	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2340G>A	15.37:g.65994733C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	197	99	0.502538	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																			C|0.761;T|0.239	0.239	strong		0.408	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
USP10	9100	hgsc.bcm.edu	37	16	84779248	84779248	+	Silent	SNP	T	T	G	rs7185949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84779248T>G	ENST00000219473.7	+	4	1274	c.1161T>G	c.(1159-1161)gtT>gtG	p.V387V	USP10_ENST00000570191.1_Silent_p.V391V	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	387					autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						TTGTTCCGGTTTCAGAGGATC	0.473													T|||	1163	0.232228	0.0507	0.3948	5008	,	,		20043	0.4038		0.2107	False		,,,				2504	0.2076				p.V391V		Atlas-SNP	.											.	USP10	51	.	0			c.T1173G						PASS	.	T		308,3416		9,290,1563	13.0	14.0	14.0		1161	-4.5	0.7	16	dbSNP_116	14	1783,6445		201,1381,2532	no	coding-synonymous	USP10	NM_005153.2		210,1671,4095	GG,GT,TT		21.6699,8.2707,17.495		387/799	84779248	2091,9861	1862	4114	5976	SO:0001819	synonymous_variant	9100	exon5			TCCGGTTTCAGAG	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.1161T>G	16.37:g.84779248T>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			T|0.769;G|0.231	0.231	strong		0.473	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
EPX	8288	hgsc.bcm.edu	37	17	56272390	56272390	+	Silent	SNP	A	A	G	rs2240815	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56272390A>G	ENST00000225371.5	+	6	770	c.660A>G	c.(658-660)cgA>cgG	p.R220R		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	220					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	ACCGTGGCCGAGCCCTCATGT	0.607													G|||	2511	0.501398	0.8495	0.2968	5008	,	,		18384	0.244		0.4354	False		,,,				2504	0.5092				p.R220R		Atlas-SNP	.											.	EPX	95	.	0			c.A660G						PASS	.	G		3430,976	365.6+/-317.5	1339,752,112	63.0	59.0	60.0		660	2.2	0.0	17	dbSNP_98	60	3795,4805	613.5+/-396.1	842,2111,1347	no	coding-synonymous	EPX	NM_000502.4		2181,2863,1459	GG,GA,AA		44.1279,22.1516,44.4487		220/716	56272390	7225,5781	2203	4300	6503	SO:0001819	synonymous_variant	8288	exon6			TGGCCGAGCCCTC	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.660A>G	17.37:g.56272390A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_000502	Q4TVP3	Silent	SNP	ENST00000225371.5	37	CCDS11602.1																																																																																			A|0.474;G|0.526	0.526	strong		0.607	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
NOD2	64127	hgsc.bcm.edu	37	16	50745583	50745583	+	Silent	SNP	T	T	G	rs1861759	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50745583T>G	ENST00000300589.2	+	4	1866	c.1761T>G	c.(1759-1761)cgT>cgG	p.R587R	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	587	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				TCCTGGTGCGTGCCAAAGGTG	0.587													T|||	1082	0.216054	0.1589	0.2723	5008	,	,		20038	0.0992		0.4165	False		,,,				2504	0.1677				p.R587R		Atlas-SNP	.											.	NOD2	118	.	0			c.T1761G						PASS	.	T		902,3494	346.2+/-308.9	73,756,1369	60.0	40.0	47.0		1761	-4.6	0.1	16	dbSNP_92	47	3462,5138	504.9+/-376.3	716,2030,1554	no	coding-synonymous	NOD2	NM_022162.1		789,2786,2923	GG,GT,TT		40.2558,20.5187,33.5796		587/1041	50745583	4364,8632	2198	4300	6498	SO:0001819	synonymous_variant	64127	exon4			GGTGCGTGCCAAA	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.1761T>G	16.37:g.50745583T>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Silent	SNP	ENST00000300589.2	37	CCDS10746.1																																																																																			T|0.709;G|0.291	0.291	strong		0.587	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
ZNF248	57209	hgsc.bcm.edu	37	10	38120945	38120945	+	Silent	SNP	A	A	G	rs1211708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:38120945A>G	ENST00000395867.3	-	6	1888	c.1338T>C	c.(1336-1338)tgT>tgC	p.C446C	ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000357328.4_Silent_p.C446C|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000494133.1_Intron	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	446					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TTGACTTCACACAGAATGTTT	0.458													G|||	158	0.0315495	0.0015	0.0648	5008	,	,		21357	0.0		0.1024	False		,,,				2504	0.0082				p.C446C		Atlas-SNP	.											.	ZNF248	61	.	0			c.T1338C						PASS	.	G		80,4326	819.0+/-416.3	1,78,2124	162.0	152.0	155.0		1338	1.1	1.0	10	dbSNP_87	155	756,7844	784.7+/-407.6	32,692,3576	no	coding-synonymous	ZNF248	NM_021045.1		33,770,5700	GG,GA,AA		8.7907,1.8157,6.4278		446/580	38120945	836,12170	2203	4300	6503	SO:0001819	synonymous_variant	57209	exon6			CTTCACACAGAAT	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1338T>C	10.37:g.38120945A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_001267597	Q8NDV8|Q9UMP3	Silent	SNP	ENST00000395867.3	37	CCDS7194.1																																																																																			A|0.938;G|0.062	0.062	strong		0.458	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
BMS1	9790	hgsc.bcm.edu	37	10	43316099	43316099	+	Silent	SNP	T	T	C	rs61736599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43316099T>C	ENST00000374518.5	+	17	2976	c.2913T>C	c.(2911-2913)taT>taC	p.Y971Y		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	971					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTCTAAAGTATACCCCACAGC	0.428													T|||	299	0.0597045	0.0961	0.0591	5008	,	,		18769	0.002		0.1044	False		,,,				2504	0.0245				p.Y971Y		Atlas-SNP	.											.	BMS1	132	.	0			c.T2913C						PASS	.	T		496,3900		35,426,1737	47.0	51.0	49.0		2913	-1.5	1.0	10	dbSNP_129	49	772,7818		31,710,3554	no	coding-synonymous	BMS1	NM_014753.3		66,1136,5291	CC,CT,TT		8.9872,11.283,9.7644		971/1283	43316099	1268,11718	2198	4295	6493	SO:0001819	synonymous_variant	9790	exon17			AAAGTATACCCCA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2913T>C	10.37:g.43316099T>C		Somatic	648	0	0		WXS	Illumina HiSeq	Phase_I	628	320	0.509554	NM_014753	Q5QPT5|Q86XJ9	Silent	SNP	ENST00000374518.5	37	CCDS7199.1																																																																																			T|0.913;C|0.087	0.087	strong		0.428	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
SLIT1	6585	hgsc.bcm.edu	37	10	98924600	98924600	+	Missense_Mutation	SNP	G	G	A	rs41307074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:98924600G>A	ENST00000266058.4	-	2	490	c.245C>T	c.(244-246)gCg>gTg	p.A82V	SLIT1_ENST00000371070.4_Missense_Mutation_p.A82V|SLIT1_ENST00000371041.3_Missense_Mutation_p.A82V|SLIT1_ENST00000456008.2_5'UTR|ARHGAP19-SLIT1_ENST00000453547.2_Missense_Mutation_p.R508W	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	82					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CTTGAGCCCCGCAAAGTCATT	0.612													G|||	137	0.0273562	0.0076	0.0519	5008	,	,		16732	0.001		0.0676	False		,,,				2504	0.0225				p.A82V		Atlas-SNP	.											SLIT1,colon,carcinoma,0,1	SLIT1	154	1	0			c.C245T						PASS	.	G	VAL/ALA	68,4338	62.3+/-99.4	0,68,2135	158.0	134.0	142.0		245	0.7	0.9	10	dbSNP_127	142	565,8035	153.9+/-208.2	20,525,3755	yes	missense	SLIT1	NM_003061.2	64	20,593,5890	AA,AG,GG		6.5698,1.5433,4.867	benign	82/1535	98924600	633,12373	2203	4300	6503	SO:0001583	missense	6585	exon2			AGCCCCGCAAAGT	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.245C>T	10.37:g.98924600G>A	ENSP00000266058:p.Ala82Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	37	CCDS7453.1	68|68	0.031135531135531136|0.031135531135531136	9|9	0.018292682926829267|0.018292682926829267	14|14	0.03867403314917127|0.03867403314917127	1|1	0.0017482517482517483|0.0017482517482517483	44|44	0.05804749340369393|0.05804749340369393	G|G	13.63|13.63	2.295937|2.295937	0.40594|0.40594	0.015433|0.015433	0.065698|0.065698	ENSG00000187122|ENSG00000213390	ENST00000266058;ENST00000371057;ENST00000371054;ENST00000371070;ENST00000314867;ENST00000456008;ENST00000371041|ENST00000453547	T;T;T;T|T	0.58060|0.09630	0.36;0.36;0.36;0.36|2.96	4.79|4.79	0.704|0.704	0.18121|0.18121	.|.	0.451135|.	0.25497|.	N|.	0.030262|.	T|T	0.00784|0.00784	0.0026|0.0026	L|L	0.28400|0.28400	0.85|0.85	0.27344|0.27344	N|N	0.95643|0.95643	B;B;B|.	0.15930|.	0.015;0.002;0.002|.	B;B;B|.	0.15484|.	0.013;0.005;0.006|.	T|T	0.28004|0.28004	-1.0057|-1.0057	10|7	0.54805|0.66056	T|D	0.06|0.02	.|.	11.2004|11.2004	0.48739|0.48739	0.2494:0.0:0.7506:0.0|0.2494:0.0:0.7506:0.0	rs41307074|rs41307074	82;82;82|.	E7EWQ8;O75093-2;O75093|.	.;.;SLIT1_HUMAN|.	V|W	82;82;82;82;65;82;82|508	ENSP00000266058:A82V;ENSP00000360109:A82V;ENSP00000315005:A65V;ENSP00000360080:A82V|ENSP00000414774:R508W	ENSP00000266058:A82V|ENSP00000414774:R508W	A|R	-|-	2|1	0|2	SLIT1|ARHGAP19	98914590|98914590	0.029000|0.029000	0.19370|0.19370	0.883000|0.883000	0.34634|0.34634	0.925000|0.925000	0.55904|0.55904	1.666000|1.666000	0.37460|0.37460	-0.039000|-0.039000	0.13602|0.13602	-1.332000|-1.332000	0.01269|0.01269	GCG|CGG	G|0.958;A|0.042	0.042	strong		0.612	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
LMX1A	4009	hgsc.bcm.edu	37	1	165218792	165218792	+	Silent	SNP	G	G	A	rs10753668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:165218792G>A	ENST00000342310.3	-	4	731	c.349C>T	c.(349-351)Ctg>Ttg	p.L117L	LMX1A_ENST00000367893.4_Silent_p.L117L|LMX1A_ENST00000294816.2_Silent_p.L117L	NM_177398.3	NP_796372.1	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	117	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				axon guidance (GO:0007411)|central nervous system neuron differentiation (GO:0021953)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|dopaminergic neuron differentiation (GO:0071542)|midbrain development (GO:0030901)|negative regulation of neuron differentiation (GO:0045665)|regulation of cell growth (GO:0001558)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)	35	all_hematologic(923;0.248)					AAGCAGCTCAGGTGGTATACA	0.552													G|||	1626	0.324681	0.1263	0.3545	5008	,	,		19587	0.5605		0.2406	False		,,,				2504	0.4151				p.L117L		Atlas-SNP	.											.	LMX1A	87	.	0			c.C349T						PASS	.	G	,	709,3697	293.0+/-282.3	50,609,1544	52.0	51.0	51.0		349,349	3.7	1.0	1	dbSNP_120	51	2088,6512	361.6+/-332.4	234,1620,2446	no	coding-synonymous,coding-synonymous	LMX1A	NM_001174069.1,NM_177398.3	,	284,2229,3990	AA,AG,GG		24.2791,16.0917,21.5055	,	117/383,117/383	165218792	2797,10209	2203	4300	6503	SO:0001819	synonymous_variant	4009	exon4			AGCTCAGGTGGTA	AY078391	CCDS1247.1	1q24.1	2011-06-20			ENSG00000162761	ENSG00000162761		"""Homeoboxes / LIM class"""	6653	protein-coding gene	gene with protein product		600298		LMX1		7698771	Standard	NM_177398		Approved	LMX1.1	uc001gcz.2	Q8TE12	OTTHUMG00000034575	ENST00000342310.3:c.349C>T	1.37:g.165218792G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	229	124	0.541485	NM_001174069	B3KXP6|Q0VDB5|Q5VWG4|Q8TE11	Silent	SNP	ENST00000342310.3	37	CCDS1247.1																																																																																			G|0.743;A|0.257	0.257	strong		0.552	LMX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083668.2	NM_177398	
ATRN	8455	hgsc.bcm.edu	37	20	3564672	3564672	+	Silent	SNP	C	C	T	rs235540	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:3564672C>T	ENST00000262919.5	+	17	2960	c.2892C>T	c.(2890-2892)taC>taT	p.Y964Y	ATRN_ENST00000446916.2_Silent_p.Y964Y	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	964	PSI 3.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						CCAATGCCTACGTGGCCTCCT	0.547													C|||	4129	0.824481	0.7088	0.8141	5008	,	,		20160	0.999		0.7187	False		,,,				2504	0.9172				p.Y964Y		Atlas-SNP	.											.	ATRN	118	.	0			c.C2892T						PASS	.	C	,,	3169,1237	705.0+/-407.2	1134,901,168	384.0	310.0	335.0		2544,2892,2892	-3.0	1.0	20	dbSNP_79	335	6339,2261	708.0+/-405.6	2324,1691,285	no	coding-synonymous,coding-synonymous,coding-synonymous	ATRN	NM_001207047.1,NM_139321.2,NM_139322.2	,,	3458,2592,453	TT,TC,CC		26.2907,28.0754,26.8953	,,	848/1157,964/1430,964/1273	3564672	9508,3498	2203	4300	6503	SO:0001819	synonymous_variant	8455	exon17			TGCCTACGTGGCC	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.2892C>T	20.37:g.3564672C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	196	196	1	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Silent	SNP	ENST00000262919.5	37	CCDS13053.1																																																																																			C|0.239;T|0.761	0.761	strong		0.547	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
KLHL6	89857	hgsc.bcm.edu	37	3	183212026	183212026	+	Silent	SNP	C	C	T	rs2256061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183212026C>T	ENST00000341319.3	-	5	1226	c.1191G>A	c.(1189-1191)tcG>tcA	p.S397S		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	397					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			ACTTGTTGATCGAAGAATTAT	0.418													C|||	755	0.150759	0.2436	0.1225	5008	,	,		22548	0.0069		0.1819	False		,,,				2504	0.1616				p.S397S		Atlas-SNP	.											KLHL6,colon,carcinoma,-1,2	KLHL6	100	2	0			c.G1191A						PASS	.	C		995,3411	372.5+/-320.4	114,767,1322	154.0	151.0	152.0		1191	-11.9	0.0	3	dbSNP_100	152	1750,6850	319.2+/-314.1	173,1404,2723	no	coding-synonymous	KLHL6	NM_130446.2		287,2171,4045	TT,TC,CC		20.3488,22.5828,21.1056		397/622	183212026	2745,10261	2203	4300	6503	SO:0001819	synonymous_variant	89857	exon5			GTTGATCGAAGAA	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1191G>A	3.37:g.183212026C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	166	77	0.463855	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	37	CCDS3245.2																																																																																			C|0.818;T|0.182	0.182	strong		0.418	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
WDR24	84219	hgsc.bcm.edu	37	16	735921	735921	+	Silent	SNP	T	T	C	rs763053	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:735921T>C	ENST00000248142.6	-	9	1910	c.1911A>G	c.(1909-1911)gcA>gcG	p.A637A	JMJD8_ENST00000562111.1_5'Flank|JMJD8_ENST00000609261.1_5'Flank|JMJD8_ENST00000454700.1_5'Flank|JMJD8_ENST00000293882.4_5'Flank|JMJD8_ENST00000562824.1_5'Flank|WDR24_ENST00000293883.4_Silent_p.A507A|JMJD8_ENST00000412368.2_5'Flank			Q96S15	WDR24_HUMAN	WD repeat domain 24	637										breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				TGTCGCTCCGTGCATCTCCTT	0.637													t|||	2517	0.502596	0.6278	0.4236	5008	,	,		14641	0.7123		0.2674	False		,,,				2504	0.4151				p.A507A		Atlas-SNP	.											.	WDR24	111	.	0			c.A1521G						PASS	.			2394,2006	609.7+/-391.4	645,1104,451	118.0	114.0	115.0		1521	-6.7	0.5	16	dbSNP_86	115	1958,6640	343.7+/-325.0	214,1530,2555	no	coding-synonymous	WDR24	NM_032259.2		859,2634,3006	CC,CT,TT		22.7727,45.5909,33.4821		507/791	735921	4352,8646	2200	4299	6499	SO:0001819	synonymous_variant	84219	exon5			GCTCCGTGCATCT	AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580		"""WD repeat domain containing"""	20852	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 21"""	C16orf21		11230166	Standard	NM_032259		Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000248142.6:c.1911A>G	16.37:g.735921T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Silent	SNP	ENST00000248142.6	37																																																																																				T|0.601;C|0.399	0.399	strong		0.637	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259	
CES4A	283848	hgsc.bcm.edu	37	16	67037035	67037035	+	Silent	SNP	A	A	G	rs61744392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:67037035A>G	ENST00000326686.5	+	6	753	c.753A>G	c.(751-753)ttA>ttG	p.L251L	CES4A_ENST00000540579.1_Silent_p.L153L|CES4A_ENST00000535696.1_Silent_p.L157L|CES4A_ENST00000338718.4_Silent_p.L274L|CES4A_ENST00000398354.1_Silent_p.L251L|CES4A_ENST00000541479.1_Silent_p.L274L|CES4A_ENST00000540947.2_Silent_p.L251L			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	251						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						GCACCGCGTTATTCAGACTTT	0.557													A|||	172	0.034345	0.034	0.0187	5008	,	,		21915	0.0		0.0298	False		,,,				2504	0.0859				p.L251L		Atlas-SNP	.											.	CES4A	24	.	0			c.A753G						PASS	.	A	,,	127,3861		2,123,1869	102.0	101.0	101.0		459,471,753	-6.1	0.0	16	dbSNP_129	101	273,8077		3,267,3905	no	coding-synonymous,coding-synonymous,coding-synonymous	CES4A	NM_001190201.1,NM_001190202.1,NM_173815.6	,,	5,390,5774	GG,GA,AA		3.2695,3.1846,3.242	,,	153/464,157/375,251/469	67037035	400,11938	1994	4175	6169	SO:0001819	synonymous_variant	283848	exon6			CGCGTTATTCAGA	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"""Carboxylesterases"""	26741	protein-coding gene	gene with protein product			"""carboxylesterase 8 (putative)"""	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.753A>G	16.37:g.67037035A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	139	58	0.417266	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Silent	SNP	ENST00000326686.5	37																																																																																				A|0.974;G|0.026	0.026	strong		0.557	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815	
HLA-C	3107	hgsc.bcm.edu	37	6	31238929	31238929	+	Silent	SNP	C	C	G	rs2308592	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31238929C>G	ENST00000376228.5	-	3	554	c.540G>C	c.(538-540)ctG>ctC	p.L180L	HLA-C_ENST00000383329.3_Silent_p.L180L	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	180	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGTAGGCTCTCAGCTGCTCCG	0.692																																					p.L180L		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,-1,2	HLA-C	92	2	0			c.G540C						scavenged	.						44.0	31.0	36.0					6																	31238929		2196	4292	6488	SO:0001819	synonymous_variant	3107	exon3			GGCTCTCAGCTGC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.540G>C	6.37:g.31238929C>G		Somatic	414	1	0.00241546		WXS	Illumina HiSeq	Phase_I	368	20	0.0543478	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	5.596	0.294742	0.10567	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	-5.62	0.02481	.	.	.	.	.	T	0.06600	0.0169	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.26744	-1.0094	4	.	.	.	.	3.9618	0.09413	0.0987:0.4803:0.1638:0.2572	rs41547419	.	.	.	Q	180	.	.	E	-	1	0	HLA-C	31346908	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.653000	0.00856	-1.717000	0.01385	0.305000	0.20034	GAG	CCG|0.500;GTC|0.500	.	alt		0.692	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SPATS1	221409	hgsc.bcm.edu	37	6	44320548	44320548	+	Silent	SNP	T	T	A	rs4714783	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44320548T>A	ENST00000288390.2	+	2	572	c.225T>A	c.(223-225)tcT>tcA	p.S75S	SPATS1_ENST00000323108.8_Silent_p.S75S|RP11-444E17.6_ENST00000505802.1_3'UTR			Q496A3	SPAS1_HUMAN	spermatogenesis associated, serine-rich 1	75	Poly-Ser.									NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(5)|skin(1)|urinary_tract(1)	14	all_lung(25;0.00469)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCTCATCTTCTGTGGAAACAG	0.502													T|||	3516	0.702077	0.6218	0.8256	5008	,	,		19327	0.7044		0.7714	False		,,,				2504	0.6493				p.S75S		Atlas-SNP	.											.	SPATS1	61	.	0			c.T225A						PASS	.	T		2977,1429	683.9+/-404.3	1013,951,239	106.0	93.0	97.0		225	1.5	0.0	6	dbSNP_111	97	6687,1913	727.0+/-406.6	2596,1495,209	no	coding-synonymous	SPATS1	NM_145026.3		3609,2446,448	AA,AT,TT		22.2442,32.433,25.6958		75/301	44320548	9664,3342	2203	4300	6503	SO:0001819	synonymous_variant	221409	exon3			ATCTTCTGTGGAA	AK058171	CCDS4911.1	6p21.1	2003-08-08			ENSG00000249481	ENSG00000249481			22957	protein-coding gene	gene with protein product							Standard	NM_145026		Approved	SPATA8, FLJ25442, SRSP1	uc021yzz.1	Q496A3	OTTHUMG00000014764	ENST00000288390.2:c.225T>A	6.37:g.44320548T>A		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	202	202	1	NM_145026	Q496A2|Q496A5|Q96LJ0	Silent	SNP	ENST00000288390.2	37	CCDS4911.1	1606	0.7353479853479854	311	0.6321138211382114	303	0.8370165745856354	427	0.7465034965034965	565	0.7453825857519789	T	4.575	0.106806	0.08780	0.67567	0.777558	ENSG00000249481	ENST00000515220	.	.	.	3.92	1.45	0.22620	.	.	.	.	.	T	0.13200	0.0320	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.19063	-1.0317	3	.	.	.	.	3.1895	0.06612	0.2054:0.1122:0.0:0.6824	rs4714783;rs57591389;rs4714783	.	.	.	Q	109	.	.	L	+	2	0	SPATS1	44428526	0.047000	0.20315	0.001000	0.08648	0.008000	0.06430	0.488000	0.22371	0.310000	0.22990	0.533000	0.62120	CTG	T|0.261;A|0.739	0.739	strong		0.502	SPATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040738.2	NM_145026	
LILRB3	11025	hgsc.bcm.edu	37	19	54726226	54726226	+	Silent	SNP	T	T	C	rs75672336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54726226T>C	ENST00000391750.1	-	4	415	c.279A>G	c.(277-279)gcA>gcG	p.A93A	LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000346401.6_Silent_p.A93A|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000424807.1_Silent_p.A93A|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Silent_p.A93A|LILRA6_ENST00000440558.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	93	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGTATCTCCCTGCATGGTGCT	0.562													.|||	4115	0.821685	0.7806	0.8141	5008	,	,		11905	0.7768		0.8996	False		,,,				2504	0.8487				p.A93A		Atlas-SNP	.											.	LILRB3	67	.	0			c.A279G						PASS	.	T	,	3505,499		1592,321,89	65.0	95.0	85.0		279,279	0.8	0.2	19	dbSNP_131	85	7315,701		3433,449,126	no	coding-synonymous,coding-synonymous	LILRB3	NM_001081450.1,NM_006864.2	,	5025,770,215	CC,CT,TT		8.745,12.4625,9.9834	,	93/633,93/632	54726226	10820,1200	2002	4008	6010	SO:0001819	synonymous_variant	11025	exon3			TCTCCCTGCATGG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.279A>G	19.37:g.54726226T>C		Somatic	432	2	0.00462963		WXS	Illumina HiSeq	Phase_I	627	624	0.995215	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			C|1.000;|0.000	1.000	weak		0.562	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
NLRP2	55655	hgsc.bcm.edu	37	19	55512137	55512137	+	Silent	SNP	C	C	A	rs12768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55512137C>A	ENST00000543010.1	+	13	3203	c.3060C>A	c.(3058-3060)atC>atA	p.I1020I	NLRP2_ENST00000537859.1_Silent_p.I998I|NLRP2_ENST00000263437.6_Silent_p.I1017I|NLRP2_ENST00000391721.4_Silent_p.I996I|NLRP2_ENST00000448584.2_Silent_p.I1020I|NLRP2_ENST00000427260.2_Silent_p.I997I|NLRP2_ENST00000339757.7_Silent_p.I998I|NLRP2_ENST00000538819.1_Silent_p.I996I	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	1020					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GGTTGAAAATCGATGACTTTA	0.388													A|||	2757	0.550519	0.4486	0.6686	5008	,	,		16582	0.6815		0.495	False		,,,				2504	0.5266				p.I1020I		Atlas-SNP	.											.	NLRP2	161	.	0			c.C3060A						PASS	.	A	,,,	2044,2362	610.0+/-391.5	478,1088,637	81.0	78.0	79.0		3060,2994,2991,3060	-6.3	0.0	19	dbSNP_52	79	4569,4031	556.8+/-386.9	1206,2157,937	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	1684,3245,1574	AA,AC,CC		46.8721,46.3913,49.1542	,,,	1020/1063,998/1041,997/1040,1020/1063	55512137	6613,6393	2203	4300	6503	SO:0001819	synonymous_variant	55655	exon13			GAAAATCGATGAC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.3060C>A	19.37:g.55512137C>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			T|0.004;G|0.004	.	strong		0.388	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
SFTPB	6439	hgsc.bcm.edu	37	2	85893842	85893842	+	Silent	SNP	C	C	T	rs34682912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85893842C>T	ENST00000519937.2	-	4	310	c.291G>A	c.(289-291)gaG>gaA	p.E97E	SFTPB_ENST00000393822.3_Silent_p.E109E|SFTPB_ENST00000409383.1_Silent_p.E109E|SFTPB_ENST00000342375.3_Silent_p.E97E			P07988	PSPB_HUMAN	surfactant protein B	97	Saposin B-type 1. {ECO:0000255|PROSITE- ProRule:PRU00415}.				organ morphogenesis (GO:0009887)|respiratory gaseous exchange (GO:0007585)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)	16						TGCACTCCTGCTCCAGGAACT	0.612													C|||	14	0.00279553	0.0	0.0014	5008	,	,		18379	0.0		0.001	False		,,,				2504	0.0123				p.E109E		Atlas-SNP	.											.	SFTPB	49	.	0			c.G327A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	163.0	144.0	151.0		327,327	-2.2	0.2	2	dbSNP_126	151	26,8574	19.2+/-60.6	0,26,4274	no	coding-synonymous,coding-synonymous	SFTPB	NM_000542.3,NM_198843.2	,	0,27,6476	TT,TC,CC		0.3023,0.0227,0.2076	,	109/394,109/394	85893842	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	6439	exon5			CTCCTGCTCCAGG	J02761	CCDS1983.1, CCDS1983.2	2p12-p11.2	2008-08-26	2008-08-26		ENSG00000168878	ENSG00000168878			10801	protein-coding gene	gene with protein product		178640	"""surfactant, pulmonary-associated protein B"""	SFTP3		2924687, 1346779	Standard	NM_198843		Approved	SP-B	uc002sqh.3	P07988	OTTHUMG00000130181	ENST00000519937.2:c.291G>A	2.37:g.85893842C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_198843	Q96R04	Silent	SNP	ENST00000519937.2	37		.	.	.	.	.	.	.	.	.	.	C	0.073	-1.197902	0.01594	2.27E-4	0.003023	ENSG00000168878	ENST00000428225	.	.	.	4.47	-2.19	0.07015	.	.	.	.	.	T	0.47930	0.1472	.	.	.	0.35445	D	0.795177	.	.	.	.	.	.	T	0.52003	-0.8633	4	.	.	.	-12.307	9.1563	0.36994	0.0:0.3994:0.0:0.6006	rs34682912	.	.	.	T	94	.	.	A	-	1	0	SFTPB	85747353	0.023000	0.18921	0.170000	0.22879	0.066000	0.16364	-0.258000	0.08733	-0.589000	0.05874	-0.291000	0.09656	GCA	C|0.997;T|0.003	0.003	strong		0.612	SFTPB-001	KNOWN	alternative_3_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252499.3	NM_198843	
SLC22A23	63027	hgsc.bcm.edu	37	6	3273457	3273457	+	Silent	SNP	A	A	G	rs9503518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:3273457A>G	ENST00000406686.3	-	10	1892	c.1893T>C	c.(1891-1893)tcT>tcC	p.S631S	SLC22A23_ENST00000436008.2_Silent_p.S639S|SLC22A23_ENST00000490273.1_Silent_p.S350S|PSMG4_ENST00000451246.2_Intron|SLC22A23_ENST00000380302.4_Silent_p.S350S	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	631					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				GCTCCCCGTTAGAAATGTTCT	0.612													G|||	524	0.104633	0.1362	0.0793	5008	,	,		16721	0.121		0.0606	False		,,,				2504	0.1084				p.S631S		Atlas-SNP	.											.	SLC22A23	89	.	0			c.T1893C						PASS	.	G	,	579,3827	771.2+/-413.8	36,507,1660	89.0	91.0	90.0		1893,1050	4.1	1.0	6	dbSNP_119	90	633,7967	789.5+/-407.6	27,579,3694	no	coding-synonymous,coding-synonymous	SLC22A23	NM_015482.1,NM_021945.5	,	63,1086,5354	GG,GA,AA		7.3605,13.1412,9.3188	,	631/687,350/406	3273457	1212,11794	2203	4300	6503	SO:0001819	synonymous_variant	63027	exon10			CCCGTTAGAAATG	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"""Solute carriers"""	21106	protein-coding gene	gene with protein product		611697	"""chromosome 6 open reading frame 85"""	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.1893T>C	6.37:g.3273457A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Silent	SNP	ENST00000406686.3	37	CCDS47363.1																																																																																			A|0.899;G|0.101	0.101	strong		0.612	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945	
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43632536	43632536	+	Missense_Mutation	SNP	C	C	T	rs7163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43632536C>T	ENST00000236051.2	-	7	809	c.668G>A	c.(667-669)cGc>cAc	p.R223H	EBNA1BP2_ENST00000431635.2_Missense_Mutation_p.R278H	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	223			R -> H (in dbSNP:rs7163).		ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGCCTTCTTGCGCTGTGCCAG	0.488													c|||	708	0.141374	0.1301	0.1513	5008	,	,		17742	0.0		0.2883	False		,,,				2504	0.1442				p.R278H		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.G833A						PASS	.		HIS/ARG,HIS/ARG	518,3888	237.1+/-249.0	29,460,1714	162.0	157.0	158.0		833,668	-1.5	0.0	1	dbSNP_52	158	2216,6384	377.6+/-338.6	292,1632,2376	yes	missense,missense	EBNA1BP2	NM_001159936.1,NM_006824.2	29,29	321,2092,4090	TT,TC,CC		25.7674,11.7567,21.0211	possibly-damaging,possibly-damaging	278/362,223/307	43632536	2734,10272	2203	4300	6503	SO:0001583	missense	10969	exon8			TTCTTGCGCTGTG	U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"""EBNA1-binding protein 2"""			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.668G>A	1.37:g.43632536C>T	ENSP00000236051:p.Arg223His	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_001159936	Q96A66	Missense_Mutation	SNP	ENST00000236051.2	37	CCDS478.1	367	0.16804029304029305	62	0.12601626016260162	67	0.1850828729281768	0	0.0	238	0.31398416886543534	c	9.108	1.005915	0.19199	0.117567	0.257674	ENSG00000117395	ENST00000431635;ENST00000236051	T;T	0.43688	0.94;0.94	5.77	-1.47	0.08772	.	1.470620	0.03747	N	0.255952	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	P;P	0.45672	0.864;0.864	B;B	0.41440	0.357;0.357	T	0.09552	-1.0669	9	0.44086	T	0.13	5.5365	1.3749	0.02218	0.1222:0.3479:0.2379:0.292	rs7163;rs1049316;rs1782373;rs3189460;rs17392458;rs58444052;rs7163	223;223	Q6IB29;Q99848	.;EBP2_HUMAN	H	278;223	ENSP00000407323:R278H;ENSP00000236051:R223H	ENSP00000236051:R223H	R	-	2	0	EBNA1BP2	43405123	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.097000	0.15168	-0.204000	0.10235	-1.219000	0.01604	CGC	C|0.805;T|0.195	0.195	strong		0.488	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1		
ZNF175	7728	hgsc.bcm.edu	37	19	52090100	52090100	+	Silent	SNP	T	T	C	rs45541134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52090100T>C	ENST00000262259.2	+	5	874	c.516T>C	c.(514-516)aaT>aaC	p.N172N	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	172					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		CAGAAAGCAATTGTGAATATA	0.413													T|||	727	0.145168	0.0991	0.1686	5008	,	,		20625	0.0238		0.2684	False		,,,				2504	0.1892				p.N172N		Atlas-SNP	.											.	ZNF175	65	.	0			c.T516C						PASS	.	T		464,3942	218.4+/-236.5	26,412,1765	96.0	92.0	93.0		516	-0.4	0.0	19	dbSNP_127	93	2339,6261	388.9+/-342.7	333,1673,2294	no	coding-synonymous	ZNF175	NM_007147.2		359,2085,4059	CC,CT,TT		27.1977,10.5311,21.5516		172/712	52090100	2803,10203	2203	4300	6503	SO:0001819	synonymous_variant	7728	exon5			AAGCAATTGTGAA	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.516T>C	19.37:g.52090100T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	155	49	0.316129	NM_007147	A8K9H2	Silent	SNP	ENST00000262259.2	37	CCDS12837.1																																																																																			T|0.795;C|0.205	0.205	strong		0.413	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
ICT1	3396	hgsc.bcm.edu	37	17	73016621	73016621	+	Silent	SNP	C	C	T	rs1044228	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73016621C>T	ENST00000301585.5	+	5	418	c.405C>T	c.(403-405)ctC>ctT	p.L135L		NM_001545.1	NP_001536.1	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1	135					mitochondrial translational termination (GO:0070126)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)|translation release factor activity, codon nonspecific (GO:0016150)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)|urinary_tract(1)	6	all_lung(278;0.226)					AGTTGATCCTCACCTCTGAGA	0.473													C|||	1602	0.319888	0.3306	0.4582	5008	,	,		18349	0.1875		0.3618	False		,,,				2504	0.3006				p.L135L		Atlas-SNP	.											.	ICT1	17	.	0			c.C405T						PASS	.	C		1446,2960	457.8+/-351.8	245,956,1002	56.0	58.0	57.0		405	-0.2	1.0	17	dbSNP_86	57	2716,5884	429.3+/-356.2	410,1896,1994	no	coding-synonymous	ICT1	NM_001545.1		655,2852,2996	TT,TC,CC		31.5814,32.8189,32.0006		135/207	73016621	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	3396	exon5			GATCCTCACCTCT	X81788	CCDS11711.1	17q25	2014-02-12				ENSG00000167862			5359	protein-coding gene	gene with protein product		603000				8575443, 20186120	Standard	NM_001545		Approved	DS-1	uc002jmm.3	Q14197		ENST00000301585.5:c.405C>T	17.37:g.73016621C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001545	B2RAD1|Q53HM7|Q53Y11	Silent	SNP	ENST00000301585.5	37	CCDS11711.1																																																																																			C|0.689;T|0.311	0.311	strong		0.473	ICT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445314.1	NM_001545	
OR2B11	127623	hgsc.bcm.edu	37	1	247614896	247614896	+	Missense_Mutation	SNP	A	A	C	rs11583410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247614896A>C	ENST00000318749.6	-	1	412	c.389T>G	c.(388-390)aTc>aGc	p.I130S		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	130			I -> S (in dbSNP:rs11583410).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GGGCTTGCAGATGGCCACGTA	0.617													A|||	1851	0.369609	0.1165	0.3401	5008	,	,		20141	0.4474		0.4742	False		,,,				2504	0.545				p.I130S		Atlas-SNP	.											.	OR2B11	102	.	0			c.T389G						PASS	.	A	SER/ILE	729,3677	302.1+/-287.2	70,589,1544	84.0	69.0	74.0		389	5.0	1.0	1	dbSNP_120	74	3974,4626	551.3+/-385.9	928,2118,1254	yes	missense	OR2B11	NM_001004492.1	142	998,2707,2798	CC,CA,AA		46.2093,16.5456,36.1602	possibly-damaging	130/318	247614896	4703,8303	2203	4300	6503	SO:0001583	missense	127623	exon1			TTGCAGATGGCCA		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"""GPCR / Class A : Olfactory receptors"""	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.389T>G	1.37:g.247614896A>C	ENSP00000325682:p.Ile130Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_001004492	B2RP03	Missense_Mutation	SNP	ENST00000318749.6	37	CCDS31090.1	807	0.3695054945054945	58	0.11788617886178862	119	0.3287292817679558	278	0.486013986013986	352	0.46437994722955145	A	19.21	3.783249	0.70222	0.165456	0.462093	ENSG00000177535	ENST00000318749	T	0.59502	0.26	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000040	T	0.00012	0.0000	H	0.99336	4.52	0.25226	P	0.9898656	D	0.71674	0.998	P	0.62649	0.905	T	0.39981	-0.9587	9	0.87932	D	0	.	12.9237	0.58247	1.0:0.0:0.0:0.0	rs11583410	130	Q5JQS5	OR2BB_HUMAN	S	130	ENSP00000325682:I130S	ENSP00000325682:I130S	I	-	2	0	OR2B11	245681519	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	6.292000	0.72725	2.219000	0.72066	0.450000	0.29827	ATC	A|0.630;C|0.370	0.370	strong		0.617	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
CD200	4345	hgsc.bcm.edu	37	3	112063850	112063850	+	De_novo_Start_OutOfFrame	SNP	C	C	A	rs2272022	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:112063850C>A	ENST00000383681.3	+	0	89				CD200_ENST00000315711.8_Missense_Mutation_p.P46T|CD200_ENST00000473539.1_Missense_Mutation_p.P71T			P41217	OX2G_HUMAN	CD200 molecule						regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				GCTGTACACACCTGCTTCCTT	0.413													C|||	1014	0.202476	0.1188	0.2709	5008	,	,		19654	0.1359		0.3907	False		,,,				2504	0.1421				p.P71T		Atlas-SNP	.											.	CD200	33	.	0			c.C211A						PASS	.	C	THR/PRO,THR/PRO	626,3780	268.3+/-268.4	44,538,1621	66.0	62.0	64.0		211,136	4.2	1.0	3	dbSNP_100	64	3141,5459	473.7+/-368.7	553,2035,1712	yes	missense,missense	CD200	NM_001004196.2,NM_005944.5	38,38	597,2573,3333	AA,AC,CC		36.5233,14.2079,28.9636	benign,benign	71/295,46/270	112063850	3767,9239	2203	4300	6503			4345	exon4			TACACACCTGCTT		CCDS2965.1, CCDS33818.1	3q13.2	2013-09-20	2006-03-28	2004-09-01	ENSG00000091972	ENSG00000091972		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7203	protein-coding gene	gene with protein product		155970	"""antigen identified by monoclonal antibody MRC OX-2"", ""CD200 antigen"""	MOX1, MOX2			Standard	XM_005247482		Approved	MRC, OX-2	uc003dyw.3	P41217	OTTHUMG00000159248	ENST00000383681.3:c.-87C>A	3.37:g.112063850C>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_001004196	B3KQI1|B4DLW9|D3DN65|Q6J2Q6|Q6PIQ4|Q8TB85|Q9H3J3	Missense_Mutation	SNP	ENST00000383681.3	37		517	0.2367216117216117	60	0.12195121951219512	94	0.2596685082872928	65	0.11363636363636363	298	0.39313984168865435	C	4.367	0.067615	0.08436	0.142079	0.365233	ENSG00000091972	ENST00000315711;ENST00000473539	T;T	0.24908	1.83;1.83	6.02	4.19	0.49359	.	0.219660	0.32736	N	0.005710	T	0.00012	0.0000	N	0.16478	0.41	0.09310	P	0.9999999999999996	P;B	0.35628	0.513;0.015	B;B	0.32533	0.147;0.023	T	0.42799	-0.9430	9	0.09338	T	0.73	-4.9917	7.3101	0.26469	0.1736:0.7413:0.0:0.085	rs2272022;rs52832861;rs57361377;rs2272022	46;71	P41217-2;P41217-3	.;.	T	46;71	ENSP00000312766:P46T;ENSP00000420298:P71T	ENSP00000312766:P46T	P	+	1	0	CD200	113546540	0.599000	0.26891	0.994000	0.49952	0.260000	0.26232	0.953000	0.29162	0.831000	0.34780	0.655000	0.94253	CCT	C|0.748;A|0.252	0.252	strong		0.413	CD200-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000354080.1		
CLCA2	9635	hgsc.bcm.edu	37	1	86900332	86900332	+	Silent	SNP	T	T	C	rs17449526	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86900332T>C	ENST00000370565.4	+	6	1038	c.876T>C	c.(874-876)aaT>aaC	p.N292N		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	292					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TTCCCATGAATGGGACTGAGC	0.502													T|||	1176	0.234824	0.1513	0.3228	5008	,	,		18290	0.1796		0.3449	False		,,,				2504	0.229				p.N292N	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.T876C						PASS	.	T		751,3655	308.8+/-290.8	74,603,1526	212.0	177.0	189.0		876	-11.3	0.0	1	dbSNP_123	189	2926,5674	456.6+/-364.1	483,1960,1857	no	coding-synonymous	CLCA2	NM_006536.5		557,2563,3383	CC,CT,TT		34.0233,17.0449,28.2716		292/944	86900332	3677,9329	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon6			CATGAATGGGACT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.876T>C	1.37:g.86900332T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	125	37	0.296	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			T|0.721;C|0.279	0.279	strong		0.502	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
WDFY3	23001	hgsc.bcm.edu	37	4	85762385	85762385	+	Silent	SNP	T	T	C	rs2046402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:85762385T>C	ENST00000295888.4	-	6	743	c.336A>G	c.(334-336)ctA>ctG	p.L112L	WDFY3_ENST00000322366.6_Silent_p.L112L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	112					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GATTAATCTCTAGGAACTGAA	0.403													C|||	2217	0.442692	0.4985	0.4755	5008	,	,		13640	0.4802		0.3817	False		,,,				2504	0.3681				p.L112L		Atlas-SNP	.											.	WDFY3	314	.	0			c.A336G						PASS	.	C		2074,2332	603.9+/-390.2	467,1140,596	66.0	70.0	68.0		336	0.3	1.0	4	dbSNP_94	68	3382,5218	641.4+/-399.7	663,2056,1581	no	coding-synonymous	WDFY3	NM_014991.4		1130,3196,2177	CC,CT,TT		39.3256,47.0722,41.9499		112/3527	85762385	5456,7550	2203	4300	6503	SO:0001819	synonymous_variant	23001	exon6			AATCTCTAGGAAC	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.336A>G	4.37:g.85762385T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	37	CCDS3609.1	965	0.44184981684981683	251	0.5101626016260162	158	0.43646408839779005	282	0.493006993006993	274	0.36147757255936674	C	5.725	0.318186	0.10845	0.470722	0.393256	ENSG00000163625	ENST00000514071	.	.	.	6.08	0.302	0.15786	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2788	0.49181	0.0:0.492:0.0:0.508	rs2046402;rs57706051;rs2046402	.	.	.	W	67	.	.	X	-	2	0	WDFY3	85981409	1.000000	0.71417	0.959000	0.39883	0.567000	0.35839	1.297000	0.33400	-0.550000	0.06183	-0.941000	0.02677	TAG	T|0.572;C|0.428	0.428	strong		0.403	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
AMH	268	hgsc.bcm.edu	37	19	2249583	2249583	+	Silent	SNP	G	G	A	rs61736572	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:2249583G>A	ENST00000221496.4	+	1	274	c.252G>A	c.(250-252)ctG>ctA	p.L84L	MIR4321_ENST00000592276.1_RNA	NM_000479.3	NP_000470	P03971	MIS_HUMAN	anti-Mullerian hormone	84					aging (GO:0007568)|cell-cell signaling (GO:0007267)|gonadal mesoderm development (GO:0007506)|Mullerian duct regression (GO:0001880)|positive regulation of gene expression (GO:0010628)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|preantral ovarian follicle growth (GO:0001546)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|urogenital system development (GO:0001655)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			lung(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGCCTTCCTGGGGGCCGTGC	0.706									Persistant Mullerian Duct Syndrome (type I and II)				G|||	298	0.0595048	0.0015	0.0605	5008	,	,		14406	0.129		0.0457	False		,,,				2504	0.0798				p.L84L		Atlas-SNP	.											.	AMH	12	.	0			c.G252A						PASS	.	G		33,4165		0,33,2066	5.0	7.0	6.0		252	1.6	1.0	19	dbSNP_129	6	276,8102		5,266,3918	no	coding-synonymous	AMH	NM_000479.3		5,299,5984	AA,AG,GG		3.2943,0.7861,2.4571		84/561	2249583	309,12267	2099	4189	6288	SO:0001819	synonymous_variant	268	exon1	Familial Cancer Database	PMDS, Persistent Oviduct Syndrome	CTTCCTGGGGGCC	K03474	CCDS12085.1	19p13.3	2014-01-30				ENSG00000104899		"""Endogenous ligands"""	464	protein-coding gene	gene with protein product		600957				3754790, 18784351	Standard	NM_000479		Approved	MIS	uc002lvh.2	P03971		ENST00000221496.4:c.252G>A	19.37:g.2249583G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_000479	O75246|Q6GTN3	Silent	SNP	ENST00000221496.4	37	CCDS12085.1																																																																																			G|0.944;A|0.056	0.056	strong		0.706	AMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451276.3	NM_000479	
BSPRY	54836	hgsc.bcm.edu	37	9	116132275	116132275	+	Silent	SNP	G	G	A	rs3750529	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:116132275G>A	ENST00000374183.4	+	6	1101	c.1062G>A	c.(1060-1062)ctG>ctA	p.L354L	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	354	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CAGCCCAGCTGGGTGTAGTGC	0.612													G|||	440	0.0878594	0.1293	0.0432	5008	,	,		18726	0.0317		0.0785	False		,,,				2504	0.1309				p.L354L		Atlas-SNP	.											.	BSPRY	21	.	0			c.G1062A						PASS	.	G		384,3506		17,350,1578	36.0	38.0	37.0		1062	3.6	1.0	9	dbSNP_107	37	708,7566		26,656,3455	no	coding-synonymous	BSPRY	NM_017688.2		43,1006,5033	AA,AG,GG		8.5569,9.8715,8.9773		354/403	116132275	1092,11072	1945	4137	6082	SO:0001819	synonymous_variant	54836	exon6			CCAGCTGGGTGTA	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.1062G>A	9.37:g.116132275G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	78	30	0.384615	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Silent	SNP	ENST00000374183.4	37	CCDS43868.1																																																																																			G|0.919;A|0.081	0.081	strong		0.612	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
FCN2	2220	hgsc.bcm.edu	37	9	137775155	137775155	+	Silent	SNP	T	T	C	rs4520243	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:137775155T>C	ENST00000291744.6	+	3	232	c.222T>C	c.(220-222)cgT>cgC	p.R74R	FCN2_ENST00000350339.2_Silent_p.R36R	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	74	Collagen-like.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		CAGGAGAACGTGGCCCCCCTG	0.597													C|||	1880	0.375399	0.3222	0.2997	5008	,	,		16091	0.4097		0.3718	False		,,,				2504	0.4693				p.R74R		Atlas-SNP	.											.	FCN2	55	.	0			c.T222C						PASS	.	C	,	1509,2897	675.0+/-403.0	253,1003,947	85.0	82.0	83.0		222,108	-3.0	0.0	9	dbSNP_111	83	2986,5614	665.3+/-402.3	547,1892,1861	no	coding-synonymous,coding-synonymous	FCN2	NM_004108.2,NM_015837.2	,	800,2895,2808	CC,CT,TT		34.7209,34.2488,34.561	,	74/314,36/276	137775155	4495,8511	2203	4300	6503	SO:0001819	synonymous_variant	2220	exon3			AGAACGTGGCCCC	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.222T>C	9.37:g.137775155T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Silent	SNP	ENST00000291744.6	37	CCDS6983.1																																																																																			T|0.642;C|0.358	0.358	strong		0.597	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
DPCR1	135656	hgsc.bcm.edu	37	6	30918400	30918400	+	Missense_Mutation	SNP	A	A	G	rs2844699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30918400A>G	ENST00000462446.1	+	2	2187	c.2159A>G	c.(2158-2160)gAg>gGg	p.E720G	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	284						integral component of membrane (GO:0016021)		p.E720G(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TCCCCAGCAGAGCCTACAGAA	0.488													-|||	1111	0.221845	0.0983	0.2118	5008	,	,		24807	0.2421		0.3579	False		,,,				2504	0.2352				p.E720G		Atlas-SNP	.											DPCR1_ENST00000462446,NS,carcinoma,0,1	DPCR1	99	1	1	Substitution - Missense(1)	endometrium(1)	c.A2159G						scavenged	.	A	GLY/GLU	173,1211		8,157,527	55.0	63.0	61.0		2159	-4.1	0.0	6	dbSNP_100	61	1159,2023		217,725,649	no	missense	DPCR1	NM_080870.3	98	225,882,1176	GG,GA,AA		36.4236,12.5,29.1721	possibly-damaging	720/1394	30918400	1332,3234	692	1591	2283	SO:0001583	missense	135656	exon2			CAGCAGAGCCTAC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2159A>G	6.37:g.30918400A>G	ENSP00000417182:p.Glu720Gly	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	189	104	0.550265	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	505	0.23122710622710624	31	0.06300813008130081	75	0.20718232044198895	148	0.25874125874125875	251	0.3311345646437995	-	7.598	0.672128	0.14776	0.125	0.364236	ENSG00000168631	ENST00000462446	T	0.47177	0.85	2.04	-4.07	0.03975	.	.	.	.	.	T	0.13415	0.0325	L	0.54908	1.71	0.58432	P	1.999999999946489E-6	B	0.06786	0.001	B	0.08055	0.003	T	0.12426	-1.0548	8	0.33141	T	0.24	.	1.8675	0.03201	0.1759:0.4062:0.2689:0.149	rs2844699	720	E9PEI6	.	G	720	ENSP00000417182:E720G	ENSP00000417182:E720G	E	+	2	0	DPCR1	31026379	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.561000	0.00215	-1.885000	0.01118	0.359000	0.22050	GAG	A|0.768;G|0.232	0.232	strong		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011468	46011468	+	Missense_Mutation	SNP	G	G	A	rs465279	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46011468G>A	ENST00000400368.1	-	1	918	c.898C>T	c.(898-900)Ccc>Tcc	p.P300S	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	300	29 X 5 AA repeats of C-C-X(3).|Poly-Ser.		P -> S (in dbSNP:rs465279). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GAGGAGGAGGGTCTGCAGCAG	0.677													.|||	2514	0.501997	0.236	0.6311	5008	,	,		21656	0.4435		0.7286	False		,,,				2504	0.5971				p.P300S		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C898T						PASS	.	G	,SER/PRO	1320,3086	437.8+/-345.1	203,914,1086	77.0	83.0	81.0		,898	2.7	1.0	21	dbSNP_80	81	5993,2601	682.0+/-403.8	2093,1807,397	no	intron,missense	TSPEAR,KRTAP10-6	NM_144991.2,NM_198688.2	,74	2296,2721,1483	AA,AG,GG		30.2653,29.9591,43.7462	,probably-damaging	,300/366	46011468	7313,5687	2203	4297	6500	SO:0001583	missense	386674	exon1			AGGAGGGTCTGCA	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.898C>T	21.37:g.46011468G>A	ENSP00000383219:p.Pro300Ser	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	278	277	0.996403	NM_198688		Missense_Mutation	SNP	ENST00000400368.1	37	CCDS42959.1	1158	0.5302197802197802	114	0.23170731707317074	235	0.649171270718232	268	0.46853146853146854	541	0.7137203166226913	g	11.98	1.800987	0.31869	0.299591	0.697347	ENSG00000188155	ENST00000400368	T	0.01887	4.58	2.7	2.7	0.31948	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.41122	P	0.01417400000000002	D	0.89917	1.0	D	0.97110	1.0	T	0.01065	-1.1463	8	0.66056	D	0.02	.	11.1673	0.48550	0.0:0.0:1.0:0.0	rs465279;rs57936212	300	P60371	KR106_HUMAN	S	300	ENSP00000383219:P300S	ENSP00000383219:P300S	P	-	1	0	KRTAP10-6	44835896	.	.	0.999000	0.59377	0.184000	0.23303	.	.	1.520000	0.48965	0.194000	0.17425	CCC	G|0.469;A|0.531	0.531	strong		0.677	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
SLC22A14	9389	hgsc.bcm.edu	37	3	38355225	38355225	+	Missense_Mutation	SNP	G	G	A	rs73064822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38355225G>A	ENST00000273173.4	+	7	1262	c.1171G>A	c.(1171-1173)Gtc>Atc	p.V391I	SLC22A14_ENST00000448498.1_Missense_Mutation_p.V391I	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	391					organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		CAGGTTTACCGTCAGTTACAC	0.582													G|||	836	0.166933	0.1626	0.196	5008	,	,		15883	0.2063		0.1859	False		,,,				2504	0.092				p.V391I		Atlas-SNP	.											.	SLC22A14	64	.	0			c.G1171A						PASS	.	G	ILE/VAL	729,3677	300.1+/-286.2	63,603,1537	93.0	86.0	89.0		1171	-6.2	0.0	3	dbSNP_130	89	1434,7166	273.8+/-290.9	127,1180,2993	yes	missense	SLC22A14	NM_004803.3	29	190,1783,4530	AA,AG,GG		16.6744,16.5456,16.6308	benign	391/595	38355225	2163,10843	2203	4300	6503	SO:0001583	missense	9389	exon7			TTTACCGTCAGTT	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"""Solute carriers"""	8495	protein-coding gene	gene with protein product		604048	"""organic cationic transporter-like 4"", ""solute carrier family 22 (organic cation transporter), member 14"""	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.1171G>A	3.37:g.38355225G>A	ENSP00000273173:p.Val391Ile	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	414	0.18956043956043955	86	0.17479674796747968	74	0.20441988950276244	112	0.1958041958041958	142	0.18733509234828497	G	2.686	-0.274360	0.05679	0.165456	0.166744	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.74106	-0.81;-0.81	3.6	-6.15	0.02105	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.740334	0.12590	N	0.455649	T	0.00109	0.0003	L	0.39898	1.24	0.80722	P	0.0	B	0.14805	0.011	B	0.15870	0.014	T	0.01874	-1.1256	9	0.42905	T	0.14	.	11.7661	0.51930	0.3639:0.0:0.6361:0.0	.	391	Q9Y267	S22AE_HUMAN	I	391	ENSP00000396283:V391I;ENSP00000273173:V391I	ENSP00000273173:V391I	V	+	1	0	SLC22A14	38330229	0.000000	0.05858	0.000000	0.03702	0.540000	0.34992	-1.703000	0.01900	-1.385000	0.02101	-0.339000	0.08088	GTC	G|0.825;A|0.175	0.175	strong		0.582	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
SLC4A4	8671	hgsc.bcm.edu	37	4	72433545	72433545	+	3'UTR	SNP	A	A	C	rs1062677	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:72433545A>C	ENST00000264485.5	+	0	3434				SLC4A4_ENST00000351898.6_3'UTR|SLC4A4_ENST00000425175.1_Missense_Mutation_p.I1074L|SLC4A4_ENST00000340595.3_3'UTR	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4						bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	TCAAATTAGAATAGAACTTGA	0.338													A|||	860	0.171725	0.0998	0.3487	5008	,	,		17638	0.1181		0.1849	False		,,,				2504	0.1851				p.I1074L		Atlas-SNP	.											.	SLC4A4	269	.	0			c.A3220C						PASS	.	A	,LEU/ILE,	393,2721		31,331,1195	75.0	66.0	69.0		,3220,	4.4	1.0	4	dbSNP_86	69	1332,5804		132,1068,2368	yes	utr-3,missense,utr-3	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	,5,	163,1399,3563	CC,CA,AA		18.6659,12.6204,16.8293	,benign,	,1074/1095,	72433545	1725,8525	1557	3568	5125	SO:0001624	3_prime_UTR_variant	8671	exon25			ATTAGAATAGAAC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.*77A>C	4.37:g.72433545A>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	217	105	0.483871	NM_001134742	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	346	0.15842490842490842	56	0.11382113821138211	107	0.2955801104972376	54	0.0944055944055944	129	0.17018469656992086	A	13.89	2.371522	0.42003	0.126204	0.186659	ENSG00000080493	ENST00000425175	T	0.78816	-1.21	5.62	4.42	0.53409	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.41340	P	0.012705999999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.05209	-1.0899	8	0.66056	D	0.02	.	13.1225	0.59336	0.8661:0.1339:0.0:0.0	rs1062677;rs1453454;rs3203670;rs17400075;rs59241443;rs1062677	1074	A5JJ20	.	L	1074	ENSP00000393557:I1074L	ENSP00000393557:I1074L	I	+	1	0	SLC4A4	72652409	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.445000	0.52921	1.053000	0.40415	0.477000	0.44152	ATA	A|0.847;C|0.153	0.153	strong		0.338	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
HLA-C	3107	hgsc.bcm.edu	37	6	31239613	31239613	+	Missense_Mutation	SNP	C	C	T	rs2308538	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31239613C>T	ENST00000376228.5	-	2	120	c.106G>A	c.(106-108)Gtg>Atg	p.V36M	HLA-C_ENST00000383329.3_Missense_Mutation_p.V36M	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	36	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.V36M(2)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGCCGGGACACGGCGGTGTCG	0.721																																					p.V36M		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	2	Substitution - Missense(2)	prostate(2)	c.G106A						scavenged	.						19.0	19.0	19.0					6																	31239613		1490	2687	4177	SO:0001583	missense	3107	exon2			GGGACACGGCGGT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.106G>A	6.37:g.31239613C>T	ENSP00000365402:p.Val36Met	Somatic	89	5	0.0561798		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	13.07|13.07	2.127655|2.127655	0.37533|0.37533	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.01092	.|5.35;5.35	2.16|2.16	2.16|2.16	0.27623|0.27623	.|MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.224693	.|0.20953	.|U	.|0.082710	T|T	0.01661|0.01661	0.0053|0.0053	M|M	0.63843|0.63843	1.955|1.955	0.23747|0.23747	N|N	0.996957|0.996957	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.999;0.999;0.999;1.0	T|T	0.53236|0.53236	-0.8467|-0.8467	5|10	.|0.30854	.|T	.|0.27	.|.	7.8706|7.8706	0.29563|0.29563	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|36;36;36;36	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	H|M	35|36;36;36;73	.|ENSP00000365402:V36M;ENSP00000372819:V36M	.|ENSP00000365402:V36M	R|V	-|-	2|1	0|0	HLA-C|HLA-C	31347592|31347592	0.000000|0.000000	0.05858|0.05858	0.780000|0.780000	0.31762|0.31762	0.007000|0.007000	0.05969|0.05969	0.465000|0.465000	0.22004|0.22004	1.524000|1.524000	0.49035|0.49035	0.305000|0.305000	0.20034|0.20034	CGT|GTG	T|0.155;C|0.845	0.155	strong		0.721	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
HS3ST3B1	9953	hgsc.bcm.edu	37	17	14248423	14248423	+	Silent	SNP	T	T	C	rs9906855	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:14248423T>C	ENST00000360954.2	+	2	1069	c.633T>C	c.(631-633)ccT>ccC	p.P211P		NM_006041.1	NP_006032.1	Q9Y662	HS3SB_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	211					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)			large_intestine(3)|lung(3)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		GGGAGGCCCCTGCGCGCATCT	0.617																																					p.P211P		Atlas-SNP	.											.	HS3ST3B1	19	.	0			c.T633C						PASS	.						72.0	43.0	53.0					17																	14248423		2203	4287	6490	SO:0001819	synonymous_variant	9953	exon2			GGCCCCTGCGCGC	AF105377	CCDS11167.1	17p12	2007-04-02			ENSG00000125430	ENSG00000125430	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5198	protein-coding gene	gene with protein product		604058				9988767	Standard	NM_006041		Approved	3OST3B1, 30ST3B1	uc002goh.1	Q9Y662	OTTHUMG00000058810	ENST00000360954.2:c.633T>C	17.37:g.14248423T>C		Somatic	310	1	0.00322581		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_006041	B3KN58|D3DTS6	Silent	SNP	ENST00000360954.2	37	CCDS11167.1																																																																																			T|0.518;C|0.482	0.482	strong		0.617	HS3ST3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129998.1	NM_006041	
MYH7B	57644	hgsc.bcm.edu	37	20	33584289	33584289	+	Silent	SNP	C	C	T	rs3746438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:33584289C>T	ENST00000262873.7	+	27	3302	c.3210C>T	c.(3208-3210)acC>acT	p.T1070T		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1028						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GCGCGCTGACCAAGGCCAAGC	0.701													C|||	2201	0.439497	0.2738	0.6326	5008	,	,		17071	0.5893		0.495	False		,,,				2504	0.3149				p.T1070T		Atlas-SNP	.											.	MYH7B	145	.	0			c.C3210T						PASS	.	C		1395,3007	418.0+/-338.2	225,945,1031	27.0	33.0	31.0		3210	0.6	1.0	20	dbSNP_107	31	3800,4790	512.2+/-377.9	823,2154,1318	no	coding-synonymous	MYH7B	NM_020884.3		1048,3099,2349	TT,TC,CC		44.2375,31.6901,39.9861		1070/1984	33584289	5195,7797	2201	4295	6496	SO:0001819	synonymous_variant	57644	exon29			GCTGACCAAGGCC	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.3210C>T	20.37:g.33584289C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			C|0.542;T|0.458	0.458	strong		0.701	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
HNRNPUL1	11100	hgsc.bcm.edu	37	19	41809995	41809995	+	Silent	SNP	A	A	G	rs1056854	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41809995A>G	ENST00000392006.3	+	13	2264	c.2091A>G	c.(2089-2091)ccA>ccG	p.P697P	HNRNPUL1_ENST00000263367.3_Silent_p.P608P|HNRNPUL1_ENST00000602130.1_Silent_p.P697P|HNRNPUL1_ENST00000593587.1_Silent_p.P597P|HNRNPUL1_ENST00000378215.4_Silent_p.P583P|HNRNPUL1_ENST00000595018.1_Silent_p.P597P|HNRNPUL1_ENST00000352456.3_Silent_p.P597P	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	697	Necessary for interaction with TP53.|Pro-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						AACAgccgccaccacagcagc	0.632													A|||	625	0.1248	0.0673	0.1311	5008	,	,		12076	0.2034		0.171	False		,,,				2504	0.0695				p.P697P		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.A2091G						PASS	.	A	,	388,4018	187.1+/-213.8	22,344,1837	57.0	62.0	60.0		2091,1791	-2.1	0.6	19	dbSNP_86	60	1334,7262	253.0+/-278.9	106,1122,3070	no	coding-synonymous,coding-synonymous	HNRNPUL1	NM_007040.3,NM_144732.2	,	128,1466,4907	GG,GA,AA		15.5188,8.8062,13.2441	,	697/857,597/757	41809995	1722,11280	2203	4298	6501	SO:0001819	synonymous_variant	11100	exon13			GCCGCCACCACAG	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.2091A>G	19.37:g.41809995A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Silent	SNP	ENST00000392006.3	37	CCDS12576.1																																																																																			A|0.867;G|0.133	0.133	strong		0.632	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
PDHB	5162	hgsc.bcm.edu	37	3	58416535	58416535	+	Silent	SNP	C	C	T	rs1126551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58416535C>T	ENST00000302746.6	-	6	480	c.438G>A	c.(436-438)ggG>ggA	p.G146G	PDHB_ENST00000485460.1_Intron|PDHB_ENST00000474765.1_Silent_p.G128G|RP11-802O23.3_ENST00000607214.1_RNA	NM_000925.3|NM_001173468.1	NP_000916.2|NP_001166939.1	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta	146					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	9				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	Pyruvic acid(DB00119)	CACCATTGGGCCCTCTGAAGA	0.532													c|||	1025	0.204673	0.2133	0.2839	5008	,	,		15206	0.001		0.3757	False		,,,				2504	0.1708				p.G146G		Atlas-SNP	.											PDHB,NS,carcinoma,0,1	PDHB	19	1	0			c.G438A						PASS	.	T	,	127,4279		55,17,2131	87.0	88.0	88.0		438,	-5.5	0.8	3	dbSNP_86	88	732,7868		282,168,3850	no	coding-synonymous,intron	PDHB	NM_000925.3,NM_001173468.1	,	337,185,5981	TT,TC,CC		8.5116,2.8824,6.6046	,	146/360,	58416535	859,12147	2203	4300	6503	SO:0001819	synonymous_variant	5162	exon6			ATTGGGCCCTCTG		CCDS2890.1, CCDS54602.1	3p21.1-p14.2	1995-12-20			ENSG00000168291	ENSG00000168291	1.2.4.1		8808	protein-coding gene	gene with protein product		179060					Standard	NR_033384		Approved		uc003dkf.4	P11177	OTTHUMG00000159157	ENST00000302746.6:c.438G>A	3.37:g.58416535C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	169	83	0.491124	NM_000925	B2R7L0|B4DDD7|Q6FH45|Q9BQ27|Q9UFK3	Silent	SNP	ENST00000302746.6	37	CCDS2890.1																																																																																			C|0.695;T|0.305	0.305	strong		0.532	PDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353558.1		
FERMT3	83706	hgsc.bcm.edu	37	11	63988102	63988102	+	Silent	SNP	C	C	T	rs3802933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:63988102C>T	ENST00000279227.5	+	12	1613	c.1518C>T	c.(1516-1518)ctC>ctT	p.L506L	FERMT3_ENST00000345728.5_Silent_p.L502L	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	506	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						CCTACGGCCTCGTTGCCCCCC	0.652													C|||	816	0.162939	0.1278	0.3271	5008	,	,		18008	0.1756		0.17	False		,,,				2504	0.0736				p.L506L		Atlas-SNP	.											.	FERMT3	51	.	0			c.C1518T						PASS	.	C	,	601,3801		36,529,1636	15.0	15.0	15.0		1506,1518	-8.4	0.0	11	dbSNP_107	15	1457,7125		133,1191,2967	no	coding-synonymous,coding-synonymous	FERMT3	NM_031471.5,NM_178443.2	,	169,1720,4603	TT,TC,CC		16.9774,13.6529,15.8503	,	502/664,506/668	63988102	2058,10926	2201	4291	6492	SO:0001819	synonymous_variant	83706	exon12			CGGCCTCGTTGCC	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	23151	protein-coding gene	gene with protein product	"""kindlin-3"""	607901	"""fermitin family homolog 3 (Drosophila)"""				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.1518C>T	11.37:g.63988102C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	101	36	0.356436	NM_178443	Q8IUA1|Q8N207|Q9BT48	Silent	SNP	ENST00000279227.5	37	CCDS8060.1	389	0.17811355311355312	58	0.11788617886178862	105	0.2900552486187845	98	0.17132867132867133	128	0.16886543535620052	C	5.113	0.206446	0.09704	0.136529	0.169774	ENSG00000149781	ENST00000545896	T	0.61274	0.12	4.21	-8.43	0.00953	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999995293	.	.	.	.	.	.	T	0.08848	-1.0702	4	.	.	.	-16.3474	3.2872	0.06936	0.0977:0.3379:0.308:0.2564	rs3802933;rs3802933	.	.	.	L	65	ENSP00000440209:S65L	.	S	+	2	0	FERMT3	63744678	0.004000	0.15560	0.043000	0.18650	0.398000	0.30690	-1.689000	0.01923	-2.298000	0.00660	-1.557000	0.00889	TCG	A|0.000;C|0.843;G|0.000;T|0.156	0.156	strong		0.652	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	
CIDEC	63924	hgsc.bcm.edu	37	3	9908935	9908935	+	Silent	SNP	G	G	A	rs17222536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:9908935G>A	ENST00000336832.2	-	6	739	c.600C>T	c.(598-600)caC>caT	p.H200H	CIDEC_ENST00000383817.1_Missense_Mutation_p.R85C|CIDEC_ENST00000423850.1_Silent_p.H126H|CIDEC_ENST00000430427.1_Silent_p.H210H|CIDEC_ENST00000443115.1_Missense_Mutation_p.R85C|CIDEC_ENST00000455015.1_Silent_p.H126H	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	200					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					CAAGCAGTACGTGGCCTGTGG	0.617													G|||	163	0.0325479	0.003	0.0504	5008	,	,		19995	0.001		0.1034	False		,,,				2504	0.0194				p.H213H		Atlas-SNP	.											.	CIDEC	22	.	0			c.C639T						PASS	.	G	,,,	65,4341	62.3+/-99.4	0,65,2138	68.0	63.0	64.0		630,600,639,600	1.4	0.4	3	dbSNP_123	64	917,7683	204.5+/-247.2	55,807,3438	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIDEC	NM_001199551.1,NM_001199552.1,NM_001199623.1,NM_022094.3	,,,	55,872,5576	AA,AG,GG		10.6628,1.4753,7.5504	,,,	210/249,200/239,213/252,200/239	9908935	982,12024	2203	4300	6503	SO:0001819	synonymous_variant	63924	exon6			CAGTACGTGGCCT		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.600C>T	3.37:g.9908935G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	223	119	0.533632	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Silent	SNP	ENST00000336832.2	37	CCDS2587.1	115	0.052655677655677656	3	0.006097560975609756	28	0.07734806629834254	1	0.0017482517482517483	83	0.10949868073878628	g	5.124	0.208511	0.09757	0.014753	0.106628	ENSG00000187288	ENST00000383817;ENST00000443115	.	.	.	5.31	1.38	0.22167	.	.	.	.	.	T	0.00906	0.0030	.	.	.	0.33143	D	0.544696	B	0.10296	0.003	B	0.08055	0.003	T	0.14090	-1.0485	7	0.87932	D	0	-45.9104	9.0539	0.36394	0.3335:0.0:0.6665:0.0	rs17222536;rs17222536	85	Q96AQ7-3	.	C	85	.	ENSP00000373328:R85C	R	-	1	0	CIDEC	9883935	0.040000	0.19996	0.412000	0.26496	0.017000	0.09413	0.024000	0.13555	0.354000	0.24105	-0.244000	0.11960	CGT	G|0.939;A|0.061	0.061	strong		0.617	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094	
UBR3	130507	hgsc.bcm.edu	37	2	170780657	170780657	+	Silent	SNP	C	C	T	rs61744354	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170780657C>T	ENST00000272793.5	+	13	2046	c.1996C>T	c.(1996-1998)Cta>Tta	p.L666L	UBR3_ENST00000418381.1_Silent_p.L666L			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	666					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						GTTAATGAAACTAATGATTCA	0.294													C|||	136	0.0271565	0.0189	0.0274	5008	,	,		15661	0.0		0.0567	False		,,,				2504	0.0358				p.L666L		Atlas-SNP	.											.	UBR3	182	.	0			c.C1996T						PASS	.	C		39,1345		0,39,653	44.0	39.0	41.0		1996	4.1	1.0	2	dbSNP_129	41	170,2986		5,160,1413	no	coding-synonymous	UBR3	NM_172070.3		5,199,2066	TT,TC,CC		5.3866,2.8179,4.6035		666/1889	170780657	209,4331	692	1578	2270	SO:0001819	synonymous_variant	130507	exon13			ATGAAACTAATGA	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.1996C>T	2.37:g.170780657C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	159	71	0.446541	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				C|0.960;T|0.040	0.040	strong		0.294	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
AXIN2	8313	hgsc.bcm.edu	37	17	63554591	63554591	+	Missense_Mutation	SNP	G	G	A	rs2240308	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:63554591G>A	ENST00000375702.5	-	1	256	c.148C>T	c.(148-150)Cct>Tct	p.P50S	AXIN2_ENST00000307078.5_Missense_Mutation_p.P50S|CTD-2535L24.2_ENST00000577662.1_3'UTR			Q9Y2T1	AXIN2_HUMAN	axin 2	50			S -> P (in polymorphism associated with increased risk of lung cancer; dbSNP:rs2240308). {ECO:0000269|PubMed:16820935}.	QPGVGKGQVTKPMSVSSNTRRNEDGL -> HHGGQGPGHQT HVCLFQHQAERRWV (in Ref. 2; AAF22799). {ECO:0000305}.	bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						GAAGAGACAGGCATGGGTTTG	0.662									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome				G|||	1691	0.33766	0.0666	0.5159	5008	,	,		15989	0.3234		0.4702	False		,,,				2504	0.456				p.P50S		Atlas-SNP	.											.	AXIN2	92	.	0			c.C148T	GRCh37	CM066739	AXIN2	M	rs2240308	PASS	.	G	SER/PRO	596,3810	261.6+/-264.4	46,504,1653	54.0	56.0	55.0		148	2.8	0.8	17	dbSNP_98	55	4539,4061	590.3+/-392.6	1195,2149,956	yes	missense	AXIN2	NM_004655.3	74	1241,2653,2609	AA,AG,GG		47.2209,13.527,39.4818	benign	50/844	63554591	5135,7871	2203	4300	6503	SO:0001583	missense	8313	exon2	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	AGACAGGCATGGG	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.148C>T	17.37:g.63554591G>A	ENSP00000364854:p.Pro50Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37		759	0.3475274725274725	42	0.08536585365853659	171	0.4723756906077348	176	0.3076923076923077	370	0.48812664907651715	G	1.053	-0.675392	0.03378	0.13527	0.527791	ENSG00000168646	ENST00000307078;ENST00000544103;ENST00000375702	T;T;T	0.76578	-0.05;-1.03;-0.04	4.74	2.75	0.32379	.	0.600804	0.16571	N	0.208652	T	0.00012	0.0000	.	.	.	0.22330	P	0.999193277	B	0.02656	0.0	B	0.01281	0.0	T	0.36480	-0.9746	8	0.05620	T	0.96	-7.6866	7.627	0.28218	0.2676:0.0:0.7324:0.0	rs2240308;rs52824132;rs60904566;rs2240308	50	E7ES00	.	S	50	ENSP00000302625:P50S;ENSP00000441151:P50S;ENSP00000364854:P50S	ENSP00000302625:P50S	P	-	1	0	AXIN2	60985053	0.999000	0.42202	0.834000	0.33040	0.020000	0.10135	0.923000	0.28757	0.980000	0.38523	0.561000	0.74099	CCT	G|0.641;A|0.359	0.359	strong		0.662	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	
PHKG1	5260	hgsc.bcm.edu	37	7	56149410	56149410	+	Silent	SNP	G	G	A	rs12538444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:56149410G>A	ENST00000297373.2	-	9	1025	c.831C>T	c.(829-831)taC>taT	p.Y277Y	PHKG1_ENST00000537360.1_Silent_p.Y223Y|PHKG1_ENST00000452681.2_Silent_p.Y309Y|PHKG1_ENST00000489604.1_5'Flank	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	277	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321)			endometrium(1)|large_intestine(1)|lung(5)	7	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CTTCCGCTGTGTAGCGGTTCT	0.597													G|||	749	0.149561	0.0613	0.2147	5008	,	,		17898	0.0714		0.2237	False		,,,				2504	0.227				p.Y309Y	Melanoma(184;580 2064 5329 24177 35303)	Atlas-SNP	.											.	PHKG1	38	.	0			c.C927T						PASS	.	G		349,4057	179.7+/-208.2	18,313,1872	32.0	32.0	32.0		831	1.6	0.6	7	dbSNP_120	32	1923,6677	330.6+/-319.3	207,1509,2584	no	coding-synonymous	PHKG1	NM_006213.3		225,1822,4456	AA,AG,GG		22.3605,7.921,17.4689		277/388	56149410	2272,10734	2203	4300	6503	SO:0001819	synonymous_variant	5260	exon10			CGCTGTGTAGCGG	X80590	CCDS5525.1, CCDS59057.1	7p11.2	2009-07-10			ENSG00000164776	ENSG00000164776	2.7.11.19		8930	protein-coding gene	gene with protein product		172470		PHKG		8530014	Standard	NM_001258459		Approved		uc011kdb.2	Q16816	OTTHUMG00000023869	ENST00000297373.2:c.831C>T	7.37:g.56149410G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	30	0.344828	NM_001258459	B7Z1D0|F5H2S1|Q75LP5	Silent	SNP	ENST00000297373.2	37	CCDS5525.1																																																																																			G|0.840;A|0.160	0.160	strong		0.597	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1	NM_006213	
WBSCR28	135886	hgsc.bcm.edu	37	7	73279482	73279482	+	Missense_Mutation	SNP	T	T	C	rs13227841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73279482T>C	ENST00000320531.2	+	2	268	c.232T>C	c.(232-234)Tgg>Cgg	p.W78R		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	78			W -> R (in dbSNP:rs13227841). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18398435}.			integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				CCAGGCTCTCTGGGCTGGGCT	0.697													C|||	2813	0.561701	0.3336	0.5893	5008	,	,		15345	0.6498		0.6769	False		,,,				2504	0.6411				p.W78R		Atlas-SNP	.											.	WBSCR28	24	.	0			c.T232C						PASS	.	C	ARG/TRP	1628,2146		354,920,613	52.0	58.0	56.0		232	-3.0	0.0	7	dbSNP_121	56	5687,2521		1963,1761,380	yes	missense	WBSCR28	NM_182504.3	101	2317,2681,993	CC,CT,TT		30.7139,43.1373,38.9501	benign	78/266	73279482	7315,4667	1887	4104	5991	SO:0001583	missense	135886	exon2			GCTCTCTGGGCTG	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.232T>C	7.37:g.73279482T>C	ENSP00000316775:p.Trp78Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_182504	Q6UE04|Q8NHP4	Missense_Mutation	SNP	ENST00000320531.2	37	CCDS43597.1	1251	0.5728021978021978	166	0.33739837398373984	203	0.5607734806629834	359	0.6276223776223776	523	0.6899736147757256	C	0.013	-1.639947	0.00799	0.431373	0.692861	ENSG00000175877	ENST00000320531	T	0.12879	2.64	4.51	-3.02	0.05446	.	0.441724	0.17112	N	0.186572	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36040	-0.9764	9	0.02654	T	1	-2.7121	0.1465	0.00089	0.2688:0.2285:0.2447:0.258	rs13227841;rs17856876;rs13227841	78	Q6UE05	WBS28_HUMAN	R	78	ENSP00000316775:W78R	ENSP00000316775:W78R	W	+	1	0	WBSCR28	72917418	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.305000	0.19254	-0.665000	0.05317	-2.015000	0.00435	TGG	T|0.403;C|0.597	0.597	strong		0.697	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
AGTPBP1	23287	hgsc.bcm.edu	37	9	88248239	88248239	+	Silent	SNP	T	T	C	rs144890878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:88248239T>C	ENST00000357081.3	-	14	1497	c.1353A>G	c.(1351-1353)aaA>aaG	p.K451K	AGTPBP1_ENST00000432218.1_Silent_p.K289K|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376109.3_Silent_p.K463K|AGTPBP1_ENST00000376083.3_Silent_p.K411K			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	451					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						GACCACGTACTTTTCCCTCAA	0.328													T|||	31	0.0061901	0.0015	0.0043	5008	,	,		17053	0.0		0.008	False		,,,				2504	0.0184				p.K411K		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.A1233G						PASS	.	T		5,4387		0,5,2191	56.0	60.0	58.0		1233	-3.0	0.0	9	dbSNP_134	58	42,8514		0,42,4236	no	coding-synonymous	AGTPBP1	NM_015239.2		0,47,6427	CC,CT,TT		0.4909,0.1138,0.363		411/1187	88248239	47,12901	2196	4278	6474	SO:0001819	synonymous_variant	23287	exon14			ACGTACTTTTCCC	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 1"", ""tubulinyl-Tyr carboxypeptidase"", ""carboxypeptidase-tubulin"", ""tyrosine carboxypeptidase"", ""soluble carboxypeptidase"""	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1353A>G	9.37:g.88248239T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	37																																																																																				T|0.994;C|0.006	0.006	strong		0.328	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239	
CEL	1056	hgsc.bcm.edu	37	9	135946015	135946015	+	Missense_Mutation	SNP	T	T	C	rs77696629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135946015T>C	ENST00000372080.4	+	10	1479	c.1463T>C	c.(1462-1464)aTc>aCc	p.I488T	CEL_ENST00000351304.7_Intron	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	485					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		AAGGCCATGATCGCCTACTGG	0.612																																					p.I488T		Atlas-SNP	.											.	CEL	71	.	0			c.T1463C						PASS	.						76.0	86.0	83.0					9																	135946015		2018	4177	6195	SO:0001583	missense	1056	exon10			CCATGATCGCCTA	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1463T>C	9.37:g.135946015T>C	ENSP00000361151:p.Ile488Thr	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	313	30	0.0958466	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234627	0.79800	.	.	ENSG00000170835	ENST00000372080;ENST00000303626	T	0.68025	-0.3	5.72	4.57	0.56435	Carboxylesterase, type B (1);	0.094910	0.64402	D	0.000001	T	0.72993	0.3530	L	0.38175	1.15	0.80722	D	1	D	0.54047	0.964	D	0.75020	0.985	T	0.74463	-0.3657	10	0.87932	D	0	.	11.5416	0.50669	0.134:0.0:0.0:0.866	.	485	P19835	CEL_HUMAN	T	488;487	ENSP00000361151:I488T	ENSP00000304021:I487T	I	+	2	0	CEL	134935836	1.000000	0.71417	0.959000	0.39883	0.951000	0.60555	7.622000	0.83099	0.976000	0.38417	0.391000	0.25812	ATC	T|0.980;C|0.020	0.020	strong		0.612	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
VAC14	55697	hgsc.bcm.edu	37	16	70726795	70726795	+	Silent	SNP	C	C	A	rs2278983	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70726795C>A	ENST00000261776.5	-	18	2375	c.2115G>T	c.(2113-2115)ccG>ccT	p.P705P	VAC14_ENST00000536184.2_Silent_p.P137P|VAC14_ENST00000571759.1_5'Flank	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	705					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				CGCTGCTCTGCGGCAGGAGCA	0.667													C|||	1216	0.242812	0.028	0.3401	5008	,	,		18619	0.1657		0.4901	False		,,,				2504	0.2894				p.P705P		Atlas-SNP	.											.	VAC14	65	.	0			c.G2115T						PASS	.	C		412,3980	188.1+/-214.6	22,368,1806	41.0	42.0	42.0		2115	-3.3	1.0	16	dbSNP_100	42	4024,4576	534.8+/-382.7	922,2180,1198	no	coding-synonymous	VAC14	NM_018052.3		944,2548,3004	AA,AC,CC		46.7907,9.3807,34.1441		705/783	70726795	4436,8556	2196	4300	6496	SO:0001819	synonymous_variant	55697	exon18			GCTCTGCGGCAGG	AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"""Tax1 (human T-cell leukemia virus type I) binding protein 2"""	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.2115G>T	16.37:g.70726795C>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	157	87	0.55414	NM_018052	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Silent	SNP	ENST00000261776.5	37	CCDS10896.1																																																																																			A|0.318;C|0.681;T|0.000	0.318	strong		0.667	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052	
GPR98	84059	hgsc.bcm.edu	37	5	90052289	90052289	+	Missense_Mutation	SNP	G	G	A	rs10062026	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:90052289G>A	ENST00000405460.2	+	56	11695	c.11599G>A	c.(11599-11601)Gag>Aag	p.E3867K		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3867	Calx-beta 25. {ECO:0000305|PubMed:11606593}.		E -> A (in dbSNP:rs16869088).		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCCTGAATTGGAGGAAGGATT	0.418													G|||	1483	0.296126	0.0265	0.5144	5008	,	,		16287	0.4871		0.3171	False		,,,				2504	0.2873				p.E3867K		Atlas-SNP	.											.	GPR98	605	.	0			c.G11599A						PASS	.	G	LYS/GLU	317,3491		21,275,1608	143.0	131.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11599	5.8	1.0	5	dbSNP_119	135	2735,5525		456,1823,1851	yes	missense	GPR98	NM_032119.3	56	477,2098,3459	AA,AG,GG		33.1114,8.3246,25.29	benign	3867/6307	90052289	3052,9016	1904	4130	6034	SO:0001583	missense	84059	exon56			GAATTGGAGGAAG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11599G>A	5.37:g.90052289G>A	ENSP00000384582:p.Glu3867Lys	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	120	40	0.333333	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	732|732	0.33516483516483514|0.33516483516483514	25|25	0.0508130081300813|0.0508130081300813	172|172	0.47513812154696133|0.47513812154696133	294|294	0.513986013986014|0.513986013986014	241|241	0.3179419525065963|0.3179419525065963	G|G	10.08|10.08	1.251332|1.251332	0.22880|0.22880	0.083246|0.083246	0.331114|0.331114	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.36699|.	1.24|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.348037|.	0.33419|.	N|.	0.004929|.	T|.	0.00012|.	0.0000|.	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	P|P	0.9999999999998971|0.9999999999998971	P;P|.	0.37781|.	0.608;0.498|.	B;B|.	0.36134|.	0.218;0.164|.	T|.	0.54990|.	-0.8210|.	9|.	0.38643|.	T|.	0.18|.	.|.	10.3117|10.3117	0.43712|0.43712	0.0:0.1832:0.6842:0.1326|0.0:0.1832:0.6842:0.1326	rs10062026;rs59670220;rs10062026|rs10062026;rs59670220;rs10062026	3867;3867|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	K|X	3867|1432	ENSP00000384582:E3867K|.	ENSP00000296619:E3867K|.	E|W	+|+	1|3	0|0	GPR98|GPR98	90088045|90088045	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.124000|0.124000	0.20399|0.20399	3.071000|3.071000	0.50041|0.50041	2.753000|2.753000	0.94483|0.94483	0.467000|0.467000	0.42956|0.42956	GAG|TGG	G|0.664;A|0.336	0.336	strong		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
SART3	9733	hgsc.bcm.edu	37	12	108941700	108941700	+	Silent	SNP	C	C	G	rs11113986	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:108941700C>G	ENST00000228284.3	-	3	741	c.507G>C	c.(505-507)gtG>gtC	p.V169V	SART3_ENST00000431469.2_Silent_p.V169V|SART3_ENST00000552221.1_5'UTR	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	169					cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						AGAGGTCATACACGTGCTCTC	0.468									Porokeratosis				C|||	250	0.0499201	0.0688	0.0303	5008	,	,		19996	0.0169		0.0368	False		,,,				2504	0.0859				p.V169V		Atlas-SNP	.											.	SART3	64	.	0			c.G507C						PASS	.	C		300,4106	165.4+/-196.9	11,278,1914	78.0	73.0	75.0		507	1.8	1.0	12	dbSNP_120	75	327,8273	114.4+/-174.4	5,317,3978	no	coding-synonymous	SART3	NM_014706.3		16,595,5892	GG,GC,CC		3.8023,6.8089,4.8209		169/964	108941700	627,12379	2203	4300	6503	SO:0001819	synonymous_variant	9733	exon3	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	GTCATACACGTGC	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"""RNA binding motif (RRM) containing"""	16860	protein-coding gene	gene with protein product		611684	"""squamous cell carcinoma antigen recognised by T cells 3"""			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.507G>C	12.37:g.108941700C>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_014706	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Silent	SNP	ENST00000228284.3	37	CCDS9117.1																																																																																			C|0.957;G|0.043	0.043	strong		0.468	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1		
MCTP2	55784	hgsc.bcm.edu	37	15	94884108	94884108	+	Silent	SNP	G	G	C	rs8025851	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:94884108G>C	ENST00000357742.4	+	6	924	c.924G>C	c.(922-924)gtG>gtC	p.V308V	MCTP2_ENST00000543482.1_Silent_p.V308V|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Silent_p.V308V	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	308					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)	p.V308V(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			GAGTGATCGTGTTAAATTTGA	0.363													C|||	2410	0.48123	0.587	0.5418	5008	,	,		18919	0.3383		0.5099	False		,,,				2504	0.4131				p.V308V		Atlas-SNP	.											MCTP2,NS,carcinoma,0,2	MCTP2	122	2	1	Substitution - coding silent(1)	stomach(1)	c.G924C						PASS	.	C	,	2483,1911	544.8+/-376.6	705,1073,419	93.0	91.0	92.0		924,924	-6.0	0.6	15	dbSNP_116	92	3895,4701	605.3+/-394.9	902,2091,1305	no	coding-synonymous,coding-synonymous	MCTP2	NM_001159643.1,NM_018349.3	,	1607,3164,1724	CC,CG,GG		45.3118,43.4911,49.0993	,	308/824,308/879	94884108	6378,6612	2197	4298	6495	SO:0001819	synonymous_variant	55784	exon6			GATCGTGTTAAAT	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.924G>C	15.37:g.94884108G>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	44	0.363636	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	37	CCDS32338.1																																																																																			G|0.505;C|0.495	0.495	strong		0.363	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
SLITRK4	139065	hgsc.bcm.edu	37	X	142718181	142718181	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:142718181T>C	ENST00000381779.4	-	2	969	c.744A>G	c.(742-744)ttA>ttG	p.L248L	SLITRK4_ENST00000356928.1_Silent_p.L248L|SLITRK4_ENST00000338017.4_Silent_p.L248L	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	248	LRRCT 1.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					GCCTTCCATATAAGTCACTGG	0.443																																					p.L248L		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A744G						PASS	.						66.0	61.0	63.0					X																	142718181		2203	4300	6503	SO:0001819	synonymous_variant	139065	exon2			TCCATATAAGTCA	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.744A>G	X.37:g.142718181T>C		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	37	CCDS14679.1																																																																																			.	.	none		0.443	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078	
SRPK1	6732	hgsc.bcm.edu	37	6	35803192	35803192	+	Silent	SNP	C	C	A	rs1049649	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:35803192C>A	ENST00000373825.2	-	16	2142	c.1857G>T	c.(1855-1857)tcG>tcT	p.S619S	SRPK1_ENST00000423325.2_Silent_p.S603S|SRPK1_ENST00000373822.1_Silent_p.S511S					SRSF protein kinase 1											endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						CCTCTTCCTGCGACCACTCAT	0.527													A|||	1473	0.294129	0.3071	0.2781	5008	,	,		18125	0.1607		0.3231	False		,,,				2504	0.3957				p.S619S	NSCLC(31;67 978 16289 24856 26454)	Atlas-SNP	.											.	SRPK1	61	.	0			c.G1857T						PASS	.	A		1161,2725		173,815,955	53.0	57.0	56.0		1857	4.3	1.0	6	dbSNP_86	56	2575,5715		422,1731,1992	no	coding-synonymous	SRPK1	NM_003137.4		595,2546,2947	AA,AC,CC		31.0615,29.8765,30.6833		619/656	35803192	3736,8440	1943	4145	6088	SO:0001819	synonymous_variant	6732	exon16			TTCCTGCGACCAC	U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"""SR protein kinase 1"", ""serine/arginine-rich splicing factor kinase 1"""	601939	"""SFRS protein kinase 1"""			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.1857G>T	6.37:g.35803192C>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	182	76	0.417582	NM_003137		Silent	SNP	ENST00000373825.2	37	CCDS47415.1																																																																																			C|0.707;A|0.293	0.293	strong		0.527	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137	
VSX1	30813	hgsc.bcm.edu	37	20	25059546	25059546	+	Silent	SNP	T	T	C	rs12480307	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:25059546T>C	ENST00000376709.4	-	3	809	c.546A>G	c.(544-546)gcA>gcG	p.A182A	VSX1_ENST00000429762.3_Silent_p.A182A|VSX1_ENST00000451258.1_Silent_p.A182A|VSX1_ENST00000424574.1_Silent_p.A182A|VSX1_ENST00000376707.3_Silent_p.A182A|VSX1_ENST00000444511.2_Silent_p.A182A	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1	182					neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(3)|lung(2)	6						CCTCGCTGAATGCCTTCTCCA	0.572													C|||	1454	0.290335	0.4992	0.3501	5008	,	,		17872	0.0268		0.2207	False		,,,				2504	0.3088				p.A182A		Atlas-SNP	.											VSX1_ENST00000376707,caecum,carcinoma,0,2	VSX1	20	2	0			c.A546G						PASS	.	C	,	1908,2498	626.1+/-394.7	405,1098,700	104.0	105.0	104.0		546,546	-10.6	0.0	20	dbSNP_120	104	1987,6613	723.2+/-406.4	238,1511,2551	no	coding-synonymous,coding-synonymous	VSX1	NM_014588.4,NM_199425.1	,	643,2609,3251	CC,CT,TT		23.1047,43.3046,29.9477	,	182/366,182/240	25059546	3895,9111	2203	4300	6503	SO:0001819	synonymous_variant	30813	exon3			GCTGAATGCCTTC	AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"""Homeoboxes / PRD class"""	12723	protein-coding gene	gene with protein product		605020	"""posterior polymorphous corneal dystrophy"", ""visual system homeobox 1 homolog, CHX10-like (zebrafish)"""	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.546A>G	20.37:g.25059546T>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	201	93	0.462687	NM_014588	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Silent	SNP	ENST00000376709.4	37	CCDS13168.1																																																																																			T|0.715;C|0.285	0.285	strong		0.572	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3		
KRT2	3849	hgsc.bcm.edu	37	12	53045615	53045615	+	Silent	SNP	A	A	G	rs532019270|rs75253159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53045615A>G	ENST00000309680.3	-	1	333	c.312T>C	c.(310-312)ggT>ggC	p.G104G		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	104	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		agccgctgccacctccaaagc	0.622																																					p.G104G		Atlas-SNP	.											.	KRT2	94	.	0			c.T312C						PASS	.						48.0	30.0	36.0					12																	53045615		2193	4285	6478	SO:0001819	synonymous_variant	3849	exon1			GCTGCCACCTCCA		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.312T>C	12.37:g.53045615A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	139	28	0.201439	NM_000423	Q4VAQ2	Silent	SNP	ENST00000309680.3	37	CCDS8835.1																																																																																			.	.	weak		0.622	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	
LILRA6	79168	hgsc.bcm.edu	37	19	54744799	54744799	+	Missense_Mutation	SNP	G	G	C	rs1052975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54744799G>C	ENST00000396365.2	-	5	902	c.863C>G	c.(862-864)cCc>cGc	p.P288R	LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000245621.5_Missense_Mutation_p.P288R|LILRA6_ENST00000419410.2_Missense_Mutation_p.P288R|LILRA6_ENST00000440558.2_Missense_Mutation_p.P288R	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	288	Ig-like C2-type 1.		P -> R (in dbSNP:rs1052975).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCCGTGGGAGGGGCTCACAGG	0.657																																					p.P288R		Atlas-SNP	.											.	LILRA6	75	.	0			c.C863G						PASS	.						51.0	62.0	58.0					19																	54744799		2203	4300	6503	SO:0001583	missense	79168	exon5			TGGGAGGGGCTCA	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.863C>G	19.37:g.54744799G>C	ENSP00000379651:p.Pro288Arg	Somatic	474	0	0		WXS	Illumina HiSeq	Phase_I	635	145	0.228346	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	399	0.18269230769230768	67	0.13617886178861788	53	0.1464088397790055	123	0.21503496503496503	156	0.20580474934036938	g	0.021	-1.430762	0.01117	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.13089	2.62;2.62;2.62;2.62	2.38	-4.75	0.03239	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	5.130160	0.00604	N	0.000395	T	0.00012	0.0000	N	0.10618	0.005	0.09310	N	1	B;D;B;B	0.62365	0.001;0.991;0.002;0.001	B;D;B;B	0.65140	0.02;0.932;0.006;0.006	T	0.48514	-0.9029	10	0.06625	T	0.88	.	3.3196	0.07045	0.1141:0.1581:0.4541:0.2736	rs1052975;rs3193457;rs3745417;rs16989284	288;288;288;288	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	R	288	ENSP00000390120:P288R;ENSP00000411227:P288R;ENSP00000379651:P288R;ENSP00000245621:P288R	ENSP00000245621:P288R	P	-	2	0	LILRA6	59436611	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.366000	0.00496	-4.910000	0.00027	-2.001000	0.00444	CCC	G|0.816;C|0.184	0.184	strong		0.657	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
NLGN2	57555	hgsc.bcm.edu	37	17	7319124	7319124	+	Silent	SNP	C	C	T	rs145633225		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7319124C>T	ENST00000302926.2	+	6	1405	c.1332C>T	c.(1330-1332)ggC>ggT	p.G444G	NLGN2_ENST00000575301.1_Silent_p.G444G	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	444					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				GGGACAATGGCGAAATGCGCC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		18788	0.0		0.001	False		,,,				2504	0.0				p.G444G		Atlas-SNP	.											.	NLGN2	61	.	0			c.C1332T						PASS	.	C		0,4406		0,0,2203	85.0	82.0	83.0		1332	-0.8	1.0	17	dbSNP_134	83	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	NLGN2	NM_020795.2		0,14,6489	TT,TC,CC		0.1628,0.0,0.1076		444/836	7319124	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	57555	exon6			CAATGGCGAAATG	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.1332C>T	17.37:g.7319124C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	37	CCDS11103.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
RFX2	5990	hgsc.bcm.edu	37	19	6042059	6042059	+	Missense_Mutation	SNP	C	C	T	rs2288846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6042059C>T	ENST00000303657.5	-	4	405	c.256G>A	c.(256-258)Gcc>Acc	p.A86T	RFX2_ENST00000359161.3_Missense_Mutation_p.A86T|RFX2_ENST00000592546.1_Missense_Mutation_p.A86T	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	86			A -> T (in dbSNP:rs2288846). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8289803}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						ACGCACATGGCTCCATTGGTG	0.607													C|||	1130	0.225639	0.1142	0.2161	5008	,	,		16769	0.2183		0.2783	False		,,,				2504	0.3364				p.A86T	Colon(38;171 817 19800 47433 48051)	Atlas-SNP	.											.	RFX2	60	.	0			c.G256A						PASS	.	C	THR/ALA,THR/ALA	586,3820	259.8+/-263.3	37,512,1654	158.0	128.0	138.0		256,256	4.4	1.0	19	dbSNP_100	138	2345,6255	393.0+/-344.2	324,1697,2279	yes	missense,missense	RFX2	NM_000635.3,NM_134433.2	58,58	361,2209,3933	TT,TC,CC		27.2674,13.3,22.5358	benign,benign	86/724,86/699	6042059	2931,10075	2203	4300	6503	SO:0001583	missense	5990	exon4			ACATGGCTCCATT		CCDS12157.1, CCDS12158.1	19p13.3	2011-11-23			ENSG00000087903	ENSG00000087903			9983	protein-coding gene	gene with protein product	"""trans-acting regulatory factor 2"", ""DNA binding protein RFX2"", ""HLA class II regulatory factor RFX2"""	142765				1505960	Standard	NM_000635		Approved	FLJ14226	uc002meb.3	P48378		ENST00000303657.5:c.256G>A	19.37:g.6042059C>T	ENSP00000306335:p.Ala86Thr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_134433	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	37	CCDS12157.1	443	0.20283882783882784	51	0.10365853658536585	76	0.20994475138121546	106	0.1853146853146853	210	0.2770448548812665	C	11.77	1.737821	0.30774	0.133	0.272674	ENSG00000087903	ENST00000303657;ENST00000359161;ENST00000537791	T;T	0.29397	1.57;1.57	4.37	4.37	0.52481	RFX1 transcription activation region (1);	0.277473	0.41001	D	0.000963	T	0.00012	0.0000	N	0.10874	0.06	0.26672	P	0.9717013	B;B	0.10296	0.002;0.003	B;B	0.17979	0.012;0.02	T	0.37103	-0.9720	9	0.19590	T	0.45	.	10.2743	0.43501	0.0:0.904:0.0:0.096	rs2288846;rs11544239;rs52825735;rs59494381;rs2288846	86;86	P48378-2;P48378	.;RFX2_HUMAN	T	86;86;41	ENSP00000306335:A86T;ENSP00000352076:A86T	ENSP00000306335:A86T	A	-	1	0	RFX2	5993059	1.000000	0.71417	0.995000	0.50966	0.776000	0.43924	2.297000	0.43593	2.268000	0.75426	0.456000	0.33151	GCC	C|0.785;T|0.215	0.215	strong		0.607	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635	
SOS2	6655	hgsc.bcm.edu	37	14	50626657	50626657	+	Silent	SNP	C	C	T	rs35530861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50626657C>T	ENST00000216373.5	-	10	1618	c.1344G>A	c.(1342-1344)ttG>ttA	p.L448L	SOS2_ENST00000555794.1_5'UTR|SOS2_ENST00000543680.1_Silent_p.L415L	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	448	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					CGATTCTTGTCAATGGTCCCT	0.383													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19647	0.0		0.005	False		,,,				2504	0.0				p.L448L		Atlas-SNP	.											.	SOS2	195	.	0			c.G1344A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	197.0	185.0	189.0		1344	3.7	1.0	14	dbSNP_126	189	41,8559	27.9+/-77.7	0,41,4259	no	coding-synonymous	SOS2	NM_006939.2		0,43,6460	TT,TC,CC		0.4767,0.0454,0.3306		448/1333	50626657	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	6655	exon10			TCTTGTCAATGGT	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.1344G>A	14.37:g.50626657C>T		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	281	140	0.498221	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Silent	SNP	ENST00000216373.5	37	CCDS9697.1																																																																																			C|0.997;T|0.003	0.003	strong		0.383	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
OR10A5	144124	hgsc.bcm.edu	37	11	6867462	6867462	+	Silent	SNP	G	G	A	rs543931840		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6867462G>A	ENST00000299454.4	+	1	580	c.549G>A	c.(547-549)ccG>ccA	p.P183P	OR10A5_ENST00000379831.2_Silent_p.P187P			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	183					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P183P(2)		endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GTGACAGCCCGCCTGTGCTGA	0.527													A|||	1	0.000199681	0.0	0.0	5008	,	,		23000	0.001		0.0	False		,,,				2504	0.0				p.P183P	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											OR10A5,NS,carcinoma,0,3	OR10A5	48	3	2	Substitution - coding silent(2)	kidney(2)	c.G549A						scavenged	.						180.0	152.0	161.0					11																	6867462		2201	4296	6497	SO:0001819	synonymous_variant	144124	exon1			CAGCCCGCCTGTG	AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"""GPCR / Class A : Olfactory receptors"""	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.549G>A	11.37:g.6867462G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	281	6	0.0213523	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	37	CCDS7773.1																																																																																			.	.	none		0.527	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168	
OR10H5	284433	hgsc.bcm.edu	37	19	15905206	15905206	+	Silent	SNP	T	T	C	rs4808380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15905206T>C	ENST00000308940.8	+	1	446	c.348T>C	c.(346-348)acT>acC	p.T116T		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						TCCTGCTCACTGTCATGGGCT	0.642													.|||	754	0.150559	0.143	0.1167	5008	,	,		20394	0.1071		0.162	False		,,,				2504	0.2178				p.T116T		Atlas-SNP	.											.	OR10H5	49	.	0			c.T348C						PASS	.	T		636,3770		55,526,1622	146.0	121.0	130.0		348	-6.9	0.0	19	dbSNP_111	130	1451,7149		149,1153,2998	no	coding-synonymous	OR10H5	NM_001004466.1		204,1679,4620	CC,CT,TT		16.8721,14.4349,16.0464		116/316	15905206	2087,10919	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			GCTCACTGTCATG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.348T>C	19.37:g.15905206T>C		Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	283	114	0.402827	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			T|0.250;C|0.750	0.750	strong		0.642	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
PRG3	10394	hgsc.bcm.edu	37	11	57147016	57147016	+	Missense_Mutation	SNP	A	A	G	rs540687	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57147016A>G	ENST00000287143.2	-	3	435	c.326T>C	c.(325-327)aTc>aCc	p.I109T		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						GTAGCGGCAGATCTTGCACCT	0.532													G|||	4800	0.958466	0.8593	0.9841	5008	,	,		19382	0.996		1.0	False		,,,				2504	0.9928				p.I109T	Melanoma(154;1456 2519 19358 45229)	Atlas-SNP	.											PRG3,NS,lymphoid_neoplasm,-1,1	PRG3	35	1	0			c.T326C						PASS	.	G	THR/ILE	3823,579	258.0+/-262.2	1650,523,28	130.0	124.0	126.0		326	-0.4	0.0	11	dbSNP_83	126	8583,9	6.4+/-24.3	4287,9,0	yes	missense	PRG3	NM_006093.3	89	5937,532,28	GG,GA,AA		0.1047,13.1531,4.5252	benign	109/226	57147016	12406,588	2201	4296	6497	SO:0001583	missense	10394	exon3			CGGCAGATCTTGC	AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.326T>C	11.37:g.57147016A>G	ENSP00000287143:p.Ile109Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_006093	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000287143.2	37	CCDS7954.1	2100	0.9615384615384616	416	0.8455284552845529	356	0.9834254143646409	570	0.9965034965034965	758	1.0	G	0.110	-1.140385	0.01728	0.868469	0.998953	ENSG00000156575	ENST00000287143	T	0.40225	1.04	5.1	-0.445	0.12242	C-type lectin (1);	0.937187	0.08984	N	0.865404	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36601	-0.9741	9	0.02654	T	1	-1.5525	3.2035	0.06657	0.1581:0.3997:0.3128:0.1294	rs540687;rs56735691;rs540687	109	Q9Y2Y8	PRG3_HUMAN	T	109	ENSP00000287143:I109T	ENSP00000287143:I109T	I	-	2	0	PRG3	56903592	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.623000	0.05546	-0.543000	0.06240	-0.186000	0.12905	ATC	A|0.046;G|0.954	0.954	strong		0.532	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093	
CDH17	1015	hgsc.bcm.edu	37	8	95186382	95186382	+	Silent	SNP	G	G	A	rs3214050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95186382G>A	ENST00000027335.3	-	6	655	c.531C>T	c.(529-531)gtC>gtT	p.V177V	CDH17_ENST00000450165.2_Silent_p.V177V|CDH17_ENST00000441892.2_Intron	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	177	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)	p.V177V(1)		NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			GAAAGTACATGACATTGTTGA	0.488													G|||	1732	0.345847	0.2307	0.281	5008	,	,		17966	0.3165		0.4384	False		,,,				2504	0.4826				p.V177V		Atlas-SNP	.											CDH17,NS,carcinoma,0,1	CDH17	119	1	1	Substitution - coding silent(1)	stomach(1)	c.C531T						PASS	.	G	,	1045,3361	384.2+/-325.2	103,839,1261	179.0	172.0	174.0		531,531	-2.8	0.5	8	dbSNP_106	174	4029,4571	555.7+/-386.7	933,2163,1204	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	1036,3002,2465	AA,AG,GG		46.8488,23.7177,39.0128	,	177/833,177/833	95186382	5074,7932	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon6			GTACATGACATTG	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.531C>T	8.37:g.95186382G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			G|0.634;A|0.366	0.366	strong		0.488	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
HOXA10	3206	hgsc.bcm.edu	37	7	27211548	27211548	+	Silent	SNP	C	C	T	rs34957925	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:27211548C>T	ENST00000283921.4	-	2	1202	c.1203G>A	c.(1201-1203)cgG>cgA	p.R401R	HOXA-AS4_ENST00000519935.1_RNA|HOXA9_ENST00000497089.1_5'Flank|HOXA10_ENST00000396344.4_Silent_p.R85R|MIR196B_ENST00000384852.1_RNA|HOXA10_ENST00000521421.1_5'UTR|HOXA-AS4_ENST00000523790.1_RNA|HOXA-AS4_ENST00000519694.1_RNA|RP1-170O19.20_ENST00000465941.1_Intron|RP1-170O19.20_ENST00000470747.4_Intron	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	401					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						CTGTGAGCTCCCGGATCCGGT	0.512													C|||	63	0.0125799	0.003	0.0216	5008	,	,		15678	0.0		0.0388	False		,,,				2504	0.0051				p.R401R		Atlas-SNP	.											.	HOXA10	55	.	0			c.G1203A						PASS	.	C		29,4377	35.2+/-66.4	0,29,2174	81.0	91.0	88.0		1203	1.8	1.0	7	dbSNP_126	88	336,8264	116.8+/-176.5	10,316,3974	no	coding-synonymous	HOXA10	NM_018951.3		10,345,6148	TT,TC,CC		3.907,0.6582,2.8064		401/411	27211548	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	3206	exon2			GAGCTCCCGGATC		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"""Homeoboxes / ANTP class : HOXL subclass"""	5100	protein-coding gene	gene with protein product		142957	"""homeo box A10"""	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.1203G>A	7.37:g.27211548C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	212	91	0.429245	NM_018951	O43370|O43605|Q15949|Q504T1	Silent	SNP	ENST00000283921.4	37	CCDS5410.2																																																																																			C|0.959;T|0.041	0.041	strong		0.512	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2		
C2orf78	388960	hgsc.bcm.edu	37	2	74043857	74043857	+	Missense_Mutation	SNP	G	G	A	rs539780072		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74043857G>A	ENST00000409561.1	+	3	2628	c.2507G>A	c.(2506-2508)cGg>cAg	p.R836Q		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	836								p.R806Q(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						ACCAGTCTCCGGTCACTGCCC	0.512													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.R836Q		Atlas-SNP	.											C2orf78,striated_muscle,rhabdoid_tumour,0,1	C2orf78	150	1	1	Substitution - Missense(1)	soft_tissue(1)	c.G2507A						scavenged	.						95.0	91.0	93.0					2																	74043857		1940	4145	6085	SO:0001583	missense	388960	exon3			GTCTCCGGTCACT	AC092653, AC136006, AK125975	CCDS46338.1	2p13.2	2008-07-18			ENSG00000187833	ENSG00000187833			34349	protein-coding gene	gene with protein product							Standard	NM_001080474		Approved	FLJ43987, hCG1989538, COG5373	uc002sjr.1	A6NCI8	OTTHUMG00000152819	ENST00000409561.1:c.2507G>A	2.37:g.74043857G>A	ENSP00000387124:p.Arg836Gln	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	127	16	0.125984	NM_001080474		Missense_Mutation	SNP	ENST00000409561.1	37	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	G	1.645	-0.515425	0.04200	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	T	0.40225	1.04	5.35	-3.06	0.05379	.	1.732830	0.04010	N	0.297965	T	0.08670	0.0215	N	0.00119	-2.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15867	-1.0422	10	0.14252	T	0.57	-2.5945	3.6028	0.08031	0.3735:0.0:0.3371:0.2893	.	836	A6NCI8	CB078_HUMAN	Q	836;806	ENSP00000387124:R836Q	ENSP00000340692:R806Q	R	+	2	0	C2orf78	73897365	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.105000	0.15333	-0.429000	0.07329	-1.440000	0.01072	CGG	.	.	none		0.512	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474	
ZNF667	63934	hgsc.bcm.edu	37	19	56953963	56953963	+	Missense_Mutation	SNP	G	G	A	rs35914474	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56953963G>A	ENST00000504904.3	-	7	1120	c.401C>T	c.(400-402)cCt>cTt	p.P134L	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000292069.6_Missense_Mutation_p.P134L|ZNF667_ENST00000342634.3_Missense_Mutation_p.P262L			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	134			P -> L (in dbSNP:rs35914474). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		CCCTTTCTTAGGTTTTACTAG	0.383													G|||	1536	0.306709	0.2776	0.353	5008	,	,		17812	0.126		0.4662	False		,,,				2504	0.3354				p.P134L		Atlas-SNP	.											.	ZNF667	95	.	0			c.C401T						PASS	.	G	LEU/PRO	1343,3061	439.0+/-345.5	226,891,1085	99.0	105.0	103.0		401	-2.3	0.0	19	dbSNP_126	103	4011,4585	548.7+/-385.4	928,2155,1215	yes	missense	ZNF667	NM_022103.3	98	1154,3046,2300	AA,AG,GG		46.6612,30.495,41.1846	benign	134/611	56953963	5354,7646	2202	4298	6500	SO:0001583	missense	63934	exon5			TTCTTAGGTTTTA		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.401C>T	19.37:g.56953963G>A	ENSP00000439402:p.Pro134Leu	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	165	66	0.4	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	37	CCDS12944.1	695	0.3182234432234432	124	0.25203252032520324	142	0.39226519337016574	82	0.14335664335664336	347	0.4577836411609499	G	5.110	0.205925	0.09704	0.30495	0.466612	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000360227	T;T;T	0.06068	3.35;3.43;3.43	4.98	-2.34	0.06704	.	1.776020	0.03106	N	0.161776	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48559	-0.9025	9	0.66056	D	0.02	2.9345	3.4388	0.07456	0.0866:0.2341:0.4198:0.2595	rs35914474;rs61740744	262;134	E7EPS0;Q5HYK9	.;ZN667_HUMAN	L	262;134;134;8	ENSP00000344699:P262L;ENSP00000439402:P134L;ENSP00000292069:P134L	ENSP00000292069:P134L	P	-	2	0	ZNF667	61645775	0.007000	0.16637	0.000000	0.03702	0.001000	0.01503	-0.079000	0.11357	-0.043000	0.13513	0.585000	0.79938	CCT	G|0.612;A|0.388	0.388	strong		0.383	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
TRIM46	80128	hgsc.bcm.edu	37	1	155149718	155149718	+	Silent	SNP	G	G	A	rs3814316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:155149718G>A	ENST00000334634.4	+	5	861	c.861G>A	c.(859-861)acG>acA	p.T287T	TRIM46_ENST00000543729.1_Silent_p.T294T|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000368383.3_Silent_p.T287T|TRIM46_ENST00000392451.2_Silent_p.T287T|TRIM46_ENST00000545012.1_Silent_p.T161T|TRIM46_ENST00000368385.4_Silent_p.T287T|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000368382.1_Silent_p.T264T	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	287						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			ACCAGGACACGGTACAGACCC	0.617													G|||	2233	0.445887	0.2194	0.5706	5008	,	,		21930	0.7629		0.3579	False		,,,				2504	0.4274				p.T287T		Atlas-SNP	.											TRIM46,colon,carcinoma,0,1	TRIM46	79	1	0			c.G861A						PASS	.	G		1205,3201	421.1+/-339.2	169,867,1167	120.0	110.0	114.0		861	-10.7	0.1	1	dbSNP_107	114	3060,5540	470.6+/-367.9	533,1994,1773	no	coding-synonymous	TRIM46	NM_025058.3		702,2861,2940	AA,AG,GG		35.5814,27.3491,32.7926		287/760	155149718	4265,8741	2203	4300	6503	SO:0001819	synonymous_variant	80128	exon5			GGACACGGTACAG		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19019	protein-coding gene	gene with protein product		600986	"""tripartite motif-containing 46"""				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.861G>A	1.37:g.155149718G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Silent	SNP	ENST00000334634.4	37	CCDS1097.1																																																																																			G|0.609;A|0.391	0.391	strong		0.617	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058	
FKBP15	23307	hgsc.bcm.edu	37	9	115941046	115941046	+	Silent	SNP	T	T	C	rs3810912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:115941046T>C	ENST00000238256.3	-	20	2067	c.1950A>G	c.(1948-1950)gcA>gcG	p.A650A		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	650					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GAGAGACCTGTGCAGTGGCCG	0.458													T|||	427	0.0852636	0.0151	0.0836	5008	,	,		18584	0.0546		0.1789	False		,,,				2504	0.1166				p.A650A		Atlas-SNP	.											.	FKBP15	128	.	0			c.A1950G						PASS	.	T		141,3857		1,139,1859	42.0	40.0	41.0		1950	-1.7	1.0	9	dbSNP_107	41	1462,6866		139,1184,2841	no	coding-synonymous	FKBP15	NM_015258.1		140,1323,4700	CC,CT,TT		17.5552,3.5268,13.005		650/1220	115941046	1603,10723	1999	4164	6163	SO:0001819	synonymous_variant	23307	exon20			GACCTGTGCAGTG	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.1950A>G	9.37:g.115941046T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			T|0.885;C|0.115	0.115	strong		0.458	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
RYR1	6261	hgsc.bcm.edu	37	19	38949904	38949904	+	Silent	SNP	C	C	T	rs3745847	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38949904C>T	ENST00000359596.3	+	19	2286	c.2286C>T	c.(2284-2286)ccC>ccT	p.P762P	RYR1_ENST00000355481.4_Silent_p.P762P|RYR1_ENST00000360985.3_Silent_p.P762P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	762	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACGGCTGCCCCGTGCAGGGTG	0.622													C|||	2775	0.554113	0.497	0.6686	5008	,	,		18731	0.5933		0.6759	False		,,,				2504	0.3845				p.P762P		Atlas-SNP	.											.	RYR1	708	.	0			c.C2286T						PASS	.	C	,	2367,2039	611.7+/-391.8	623,1121,459	111.0	91.0	98.0		2286,2286	-8.7	0.5	19	dbSNP_107	98	5658,2942	668.3+/-402.5	1857,1944,499	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	2480,3065,958	TT,TC,CC		34.2093,46.2778,38.2977	,	762/5039,762/5034	38949904	8025,4981	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon19			CTGCCCCGTGCAG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2286C>T	19.37:g.38949904C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	262	122	0.465649	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.386;T|0.614	0.614	strong		0.622	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552112	32552112	+	Silent	SNP	A	A	G	rs557901512		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32552112A>G	ENST00000360004.5	-	2	249	c.144T>C	c.(142-144)aaT>aaC	p.N48N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	48	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCTCCGTCCCATTGAAGAAAT	0.612										Multiple Myeloma(14;0.17)																											p.N48N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.T144C						PASS	.						21.0	21.0	21.0					6																	32552112		2157	4208	6365	SO:0001819	synonymous_variant	3123	exon2			CGTCCCATTGAAG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.144T>C	6.37:g.32552112A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			A|0.842;G|0.157	0.157	strong		0.612	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
KANSL2	54934	hgsc.bcm.edu	37	12	49048738	49048738	+	Missense_Mutation	SNP	G	G	T	rs3741628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49048738G>T	ENST00000420613.2	-	9	1380	c.1333C>A	c.(1333-1335)Cca>Aca	p.P445T	KANSL2_ENST00000548701.1_5'UTR|KANSL2_ENST00000553086.1_Missense_Mutation_p.P411T|SNORA2A_ENST00000383885.1_RNA|KANSL2_ENST00000550347.1_Missense_Mutation_p.P628T|SNORA34_ENST00000408564.2_RNA	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	445			P -> T (in dbSNP:rs3741628). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)											ATATCCACTGGGTCTTCAGCA	0.478													G|||	2783	0.555711	0.3139	0.5548	5008	,	,		18676	0.7758		0.5437	False		,,,				2504	0.6687				p.P445T		Atlas-SNP	.											.	.	.	.	0			c.C1333A						PASS	.	G	THR/PRO	1188,2620		171,846,887	79.0	80.0	79.0		1333	1.8	1.0	12	dbSNP_107	79	4639,3601		1293,2053,774	yes	missense	C12orf41	NM_017822.3	38	1464,2899,1661	TT,TG,GG		43.7015,31.1975,48.3649	benign	445/493	49048738	5827,6221	1904	4120	6024	SO:0001583	missense	54934	exon9			CCACTGGGTCTTC	AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"""chromosome 12 open reading frame 41"""	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392	ENST00000420613.2:c.1333C>A	12.37:g.49048738G>T	ENSP00000415436:p.Pro445Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_017822	Q8N3B5|Q96CV0|Q9NX51	Missense_Mutation	SNP	ENST00000420613.2	37	CCDS44869.1	1219	0.5581501831501832	165	0.3353658536585366	202	0.5580110497237569	427	0.7465034965034965	425	0.5606860158311345	G	11.00	1.509652	0.27036	0.311975	0.562985	ENSG00000139620	ENST00000550347;ENST00000420613;ENST00000547087;ENST00000553086	T;T;T;T	0.47869	1.25;0.83;0.83;1.28	5.72	1.75	0.24633	.	0.239859	0.42420	N	0.000708	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	1.0	P;B;B;B	0.38078	0.617;0.03;0.02;0.004	B;B;B;B	0.33960	0.173;0.022;0.034;0.006	T	0.32375	-0.9909	9	0.30854	T	0.27	0.0409	1.8743	0.03215	0.2308:0.1378:0.4891:0.1422	rs3741628;rs11547849;rs17238500;rs17850547;rs17851069;rs3741628	628;445;216;411	F8VX10;Q9H9L4;Q9H9L4-2;F8VXI8	.;CL041_HUMAN;.;.	T	628;445;159;411	ENSP00000449747:P628T;ENSP00000415436:P445T;ENSP00000447608:P159T;ENSP00000448833:P411T	ENSP00000415436:P445T	P	-	1	0	C12orf41	47335005	0.995000	0.38212	0.988000	0.46212	0.976000	0.68499	0.199000	0.17237	0.049000	0.15920	0.557000	0.71058	CCA	G|0.447;T|0.553	0.553	strong		0.478	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822	
RUVBL2	10856	hgsc.bcm.edu	37	19	49513273	49513273	+	Silent	SNP	C	C	T	rs1062708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49513273C>T	ENST00000595090.1	+	8	1077	c.613C>T	c.(613-615)Ctg>Ttg	p.L205L	RUVBL2_ENST00000601968.1_Silent_p.L160L|RUVBL2_ENST00000413176.2_Silent_p.L160L	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	205					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)			large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		GATCTCCAAGCTGGGCCGCTC	0.662													C|||	1950	0.389377	0.2027	0.4798	5008	,	,		18420	0.3899		0.503	False		,,,				2504	0.4601				p.L205L		Atlas-SNP	.											.	RUVBL2	31	.	0			c.C613T						PASS	.	C		910,3158		113,684,1237	60.0	62.0	62.0		613	3.0	1.0	19	dbSNP_86	62	3994,4320		968,2058,1131	no	coding-synonymous	RUVBL2	NM_006666.1		1081,2742,2368	TT,TC,CC		48.0395,22.3697,39.6059		205/464	49513273	4904,7478	2034	4157	6191	SO:0001819	synonymous_variant	10856	exon8			TCCAAGCTGGGCC	AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"""INO80 complex subunits"", ""ATPases / AAA-type"""	10475	protein-coding gene	gene with protein product	"""reptin"", ""INO80 complex subunit J"""	604788	"""RuvB (E coli homolog)-like 2"", ""RuvB-like 2 (E. coli)"""			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.613C>T	19.37:g.49513273C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	48	0.421053	NM_006666	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Silent	SNP	ENST00000595090.1	37	CCDS42588.1																																																																																			C|0.579;T|0.421	0.421	strong		0.662	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466235.1		
OR52N4	390072	hgsc.bcm.edu	37	11	5776484	5776484	+	Nonsense_Mutation	SNP	A	A	T	rs4910844	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5776484A>T	ENST00000317254.3	+	1	562	c.514A>T	c.(514-516)Aga>Tga	p.R172*	TRIM5_ENST00000380027.1_Intron	NM_001005175.2	NP_001005175.3	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N, member 4 (gene/pseudogene)	172						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)		GCCCTACTGCAGAGGCAATAT	0.473													A|||	1074	0.214457	0.1498	0.2262	5008	,	,		22836	0.1974		0.2783	False		,,,				2504	0.2454				p.R172X		Atlas-SNP	.											.	OR52N4	55	.	0			c.A514T	GRCh37	CM035853	OR52N4	M	rs4910844	PASS	.	A	stop/ARG	672,3688	253.4+/-259.3	59,554,1567	160.0	151.0	154.0		514	1.9	0.9	11	dbSNP_111	154	2035,6547	344.5+/-325.3	237,1561,2493	yes	stop-gained	OR52N4	NM_001005175.2		296,2115,4060	TT,TA,AA		23.7124,15.4128,20.9164		172/322	5776484	2707,10235	2180	4291	6471	SO:0001587	stop_gained	390072	exon1			TACTGCAGAGGCA	AB065813	CCDS44528.1	11p15.4	2013-10-10	2013-10-10		ENSG00000181074	ENSG00000181074		"""GPCR / Class A : Olfactory receptors"""	15230	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily N, member 4"""				Standard	NM_001005175		Approved		uc001mbu.3	Q8NGI2	OTTHUMG00000066887	ENST00000317254.3:c.514A>T	11.37:g.5776484A>T	ENSP00000323224:p.Arg172*	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	167	70	0.419162	NM_001005175	B2RNP8|Q6IF77	Nonsense_Mutation	SNP	ENST00000317254.3	37	CCDS44528.1	469	0.21474358974358973	80	0.16260162601626016	75	0.20718232044198895	107	0.18706293706293706	207	0.27308707124010556	A	14.18	2.457090	0.43634	0.154128	0.237124	ENSG00000181074	ENST00000317254	.	.	.	5.97	1.94	0.25998	.	0.293923	0.24061	N	0.041914	.	.	.	.	.	.	0.09310	P	0.9999999999957012	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9115	0.24338	0.4539:0.4213:0.1247:0.0	rs4910844;rs52803254;rs4910844	.	.	.	X	172	.	ENSP00000323224:R172X	R	+	1	2	OR52N4	5733060	0.000000	0.05858	0.898000	0.35279	0.037000	0.13140	-0.704000	0.05058	0.451000	0.26802	0.455000	0.32223	AGA	A|0.784;T|0.216	0.216	strong		0.473	OR52N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143350.1	NM_001005175	
TBX10	347853	hgsc.bcm.edu	37	11	67402362	67402362	+	Missense_Mutation	SNP	T	T	G	rs3758938	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67402362T>G	ENST00000335385.3	-	3	389	c.302A>C	c.(301-303)aAg>aCg	p.K101T		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	101			K -> T (in dbSNP:rs3758938).		anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						GCCCAGGATCTTCACCTGGAA	0.677													T|||	1088	0.217252	0.1626	0.4236	5008	,	,		19390	0.131		0.3042	False		,,,				2504	0.1442				p.K101T		Atlas-SNP	.											.	TBX10	25	.	0			c.A302C	GRCh37	CM067720	TBX10	M	rs3758938	PASS	.	T	THR/LYS	765,3635	310.0+/-291.3	61,643,1496	54.0	54.0	54.0		302	1.7	0.9	11	dbSNP_107	54	2520,6068	410.2+/-350.1	399,1722,2173	yes	missense	TBX10	NM_005995.4	78	460,2365,3669	GG,GT,TT		29.3433,17.3864,25.2926	possibly-damaging	101/386	67402362	3285,9703	2200	4294	6494	SO:0001583	missense	347853	exon3			AGGATCTTCACCT	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"""T-boxes"""	11593	protein-coding gene	gene with protein product		604648	"""T-box 7"""	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.302A>C	11.37:g.67402362T>G	ENSP00000335191:p.Lys101Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	128	49	0.382812	NM_005995	Q14D64|Q86XS3	Missense_Mutation	SNP	ENST00000335385.3	37	CCDS31621.1	523	0.23946886446886448	89	0.18089430894308944	141	0.38950276243093923	66	0.11538461538461539	227	0.2994722955145119	T	13.44	2.237093	0.39498	0.173864	0.293433	ENSG00000167800	ENST00000335385	D	0.87809	-2.3	5.3	1.7	0.24286	p53-like transcription factor, DNA-binding (1);	0.078492	0.50627	D	0.000111	T	0.00012	0.0000	L	0.50993	1.605	0.28232	P	0.9260502	D	0.76494	0.999	D	0.75484	0.986	T	0.04191	-1.0970	9	0.87932	D	0	.	8.5722	0.33576	0.0:0.2305:0.0:0.7695	rs3758938;rs17508969;rs58569464;rs3758938	101	O75333	TBX10_HUMAN	T	101	ENSP00000335191:K101T	ENSP00000335191:K101T	K	-	2	0	TBX10	67158938	1.000000	0.71417	0.889000	0.34880	0.007000	0.05969	7.595000	0.82710	0.039000	0.15632	-0.371000	0.07208	AAG	T|0.753;G|0.247	0.247	strong		0.677	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995	
TMEM132C	92293	hgsc.bcm.edu	37	12	128899673	128899673	+	Missense_Mutation	SNP	A	A	G	rs11059681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:128899673A>G	ENST00000435159.2	+	2	482	c.482A>G	c.(481-483)cAc>cGc	p.H161R		NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	161			H -> R (in dbSNP:rs11059681).			integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						TGGGATGACCACGGCGCCGGG	0.597													G|||	1890	0.377396	0.416	0.3487	5008	,	,		16224	0.3998		0.4672	False		,,,				2504	0.2301				p.H161R		Atlas-SNP	.											.	TMEM132C	142	.	0			c.A482G						PASS	.	G	ARG/HIS	590,794		133,324,235	15.0	18.0	17.0		482	-9.1	0.0	12	dbSNP_120	17	1477,1705		340,797,454	yes	missense	TMEM132C	NM_001136103.2	29	473,1121,689	GG,GA,AA		46.4173,42.6301,45.2694	benign	161/1109	128899673	2067,2499	692	1591	2283	SO:0001583	missense	92293	exon2			ATGACCACGGCGC	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.482A>G	12.37:g.128899673A>G	ENSP00000410852:p.His161Arg	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	NM_001136103	Q69YX8	Missense_Mutation	SNP	ENST00000435159.2	37		935	0.4281135531135531	215	0.4369918699186992	138	0.3812154696132597	229	0.40034965034965037	353	0.4656992084432718	G	3.437	-0.114890	0.06881	0.426301	0.464173	ENSG00000181234	ENST00000435159	T	0.10573	2.86	4.96	-9.14	0.00701	.	.	.	.	.	T	0.00012	0.0000	N	0.16903	0.455	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46414	-0.9193	8	0.19147	T	0.46	.	8.8075	0.34948	0.3934:0.2616:0.345:0.0	rs11059681;rs11059681	161	Q8N3T6	T132C_HUMAN	R	161	ENSP00000410852:H161R	ENSP00000410852:H161R	H	+	2	0	TMEM132C	127465626	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	0.354000	0.20146	-2.580000	0.00462	-1.096000	0.02151	CAC	A|0.571;G|0.429	0.429	strong		0.597	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
UNC13D	201294	hgsc.bcm.edu	37	17	73838639	73838639	+	Silent	SNP	C	C	T	rs373551579		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73838639C>T	ENST00000207549.4	-	6	823	c.444G>A	c.(442-444)ggG>ggA	p.G148G	UNC13D_ENST00000587504.1_5'UTR|UNC13D_ENST00000412096.2_Silent_p.G148G	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	148	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGGGGCTGCCCCCTGGCACAC	0.677									Familial Hemophagocytic Lymphohistiocytosis				C|||	1	0.000199681	0.0	0.0014	5008	,	,		16781	0.0		0.0	False		,,,				2504	0.0				p.G148G		Atlas-SNP	.											.	UNC13D	68	.	0			c.G444A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	55.0	56.0	55.0		444	-0.2	0.6	17		55	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	UNC13D	NM_199242.2		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		148/1091	73838639	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	201294	exon6	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCTGCCCCCTGGC	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.444G>A	17.37:g.73838639C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			.	.	weak		0.677	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
TMEM180	79847	hgsc.bcm.edu	37	10	104230437	104230437	+	Silent	SNP	C	C	G	rs3740416	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:104230437C>G	ENST00000238936.4	+	5	504	c.267C>G	c.(265-267)ctC>ctG	p.L89L	TMEM180_ENST00000366277.2_Intron|TMEM180_ENST00000369931.3_Intron	NM_024789.3	NP_079065.2	Q14CX5	TM180_HUMAN	transmembrane protein 180	89						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|skin(1)	13		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GCGCCGGGCTCTCCTCAAGGG	0.697													C|||	1037	0.207069	0.0378	0.2421	5008	,	,		15666	0.4325		0.1302	False		,,,				2504	0.2577				p.L89L		Atlas-SNP	.											.	TMEM180	33	.	0			c.C267G						PASS	.	C		196,4152		4,188,1982	64.0	77.0	72.0		267	1.1	1.0	10	dbSNP_107	72	887,7629		47,793,3418	no	coding-synonymous	TMEM180	NM_024789.3		51,981,5400	GG,GC,CC		10.4157,4.5078,8.4188		89/518	104230437	1083,11781	2174	4258	6432	SO:0001819	synonymous_variant	79847	exon5			CGGGCTCTCCTCA	AK026182	CCDS7535.1	10q24.32	2011-02-09	2006-10-12	2006-10-12	ENSG00000138111	ENSG00000138111			26196	protein-coding gene	gene with protein product				C10orf77		12477932	Standard	XM_006717971		Approved	FLJ22529, bA18I14.8	uc001kvt.3	Q14CX5	OTTHUMG00000018961	ENST00000238936.4:c.267C>G	10.37:g.104230437C>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_024789	Q6NWM8|Q6NWM9|Q6PEZ7|Q9H679	Silent	SNP	ENST00000238936.4	37	CCDS7535.1																																																																																			C|0.872;G|0.128	0.128	strong		0.697	TMEM180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050075.2	NM_024789	
DOCK1	1793	hgsc.bcm.edu	37	10	129245684	129245684	+	Missense_Mutation	SNP	G	G	A	rs869801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:129245684G>A	ENST00000280333.6	+	51	5486	c.5377G>A	c.(5377-5379)Gcg>Acg	p.A1793T		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1793	Interaction with NCK2 second and third SH3 domain (minor).		A -> T (in dbSNP:rs869801).		apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.A1793T(1)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CATGACGGGGGCGGACGTGGC	0.592													G|||	1025	0.204673	0.211	0.2233	5008	,	,		17616	0.12		0.2584	False		,,,				2504	0.2147				p.A1793T		Atlas-SNP	.											DOCK1,NS,carcinoma,0,1	DOCK1	188	1	1	Substitution - Missense(1)	stomach(1)	c.G5377A						PASS	.	G	THR/ALA	769,3209		69,631,1289	32.0	36.0	35.0		5332	-10.4	0.0	10	dbSNP_86	35	2153,6171		278,1597,2287	yes	missense	DOCK1	NM_001380.3	58	347,2228,3576	AA,AG,GG		25.865,19.3313,23.7522	benign	1778/1851	129245684	2922,9380	1989	4162	6151	SO:0001583	missense	1793	exon51			ACGGGGGCGGACG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5377G>A	10.37:g.129245684G>A	ENSP00000280333:p.Ala1793Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		458	0.2097069597069597	99	0.20121951219512196	91	0.2513812154696133	69	0.12062937062937062	199	0.262532981530343	G	6.324	0.427794	0.11987	0.193313	0.25865	ENSG00000150760	ENST00000280333	T	0.03663	3.85	5.22	-10.4	0.00318	.	1.639210	0.04650	U	0.407008	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48536	-0.9027	9	0.21014	T	0.42	.	0.4032	0.00429	0.3463:0.1465:0.2334:0.2738	rs869801;rs2229602;rs17777746;rs869801	1793;1793	B2RUU3;Q14185	.;DOCK1_HUMAN	T	1793	ENSP00000280333:A1793T	ENSP00000280333:A1793T	A	+	1	0	DOCK1	129135674	0.000000	0.05858	0.000000	0.03702	0.340000	0.28889	-0.958000	0.03857	-1.651000	0.01504	0.655000	0.94253	GCG	G|0.786;A|0.214	0.214	strong		0.592	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
AXIN2	8313	hgsc.bcm.edu	37	17	63532528	63532528	+	Missense_Mutation	SNP	G	G	A	rs138287857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:63532528G>A	ENST00000375702.5	-	6	1964	c.1856C>T	c.(1855-1857)gCg>gTg	p.A619V	AXIN2_ENST00000307078.5_Missense_Mutation_p.A684V			Q9Y2T1	AXIN2_HUMAN	axin 2	668				Missing (in Ref. 2; AAF22799). {ECO:0000305}.	bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						GGGAGGCATCGCAGGGTCCTG	0.687									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome				G|||	2	0.000399361	0.0	0.0	5008	,	,		15448	0.0		0.002	False		,,,				2504	0.0				p.A684V		Atlas-SNP	.											.	AXIN2	92	.	0			c.C2051T						PASS	.	G	VAL/ALA	3,4399	6.2+/-15.9	0,3,2198	24.0	26.0	25.0		2051	4.4	0.8	17	dbSNP_134	25	15,8585	10.5+/-38.8	0,15,4285	yes	missense	AXIN2	NM_004655.3	64	0,18,6483	AA,AG,GG		0.1744,0.0682,0.1384	possibly-damaging	684/844	63532528	18,12984	2201	4300	6501	SO:0001583	missense	8313	exon8	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	GGCATCGCAGGGT	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.1856C>T	17.37:g.63532528G>A	ENSP00000364854:p.Ala619Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37		.	.	.	.	.	.	.	.	.	.	G	22.6	4.307951	0.81247	6.82E-4	0.001744	ENSG00000168646	ENST00000307078;ENST00000375702	T;T	0.66280	-0.2;-0.18	5.41	4.37	0.52481	.	0.262657	0.43579	D	0.000560	T	0.57388	0.2050	L	0.48642	1.525	0.46260	D	0.998951	P;P	0.52061	0.95;0.923	B;B	0.40782	0.298;0.34	T	0.66818	-0.5827	10	0.66056	D	0.02	-11.6392	17.7442	0.88415	0.0:0.1327:0.8673:0.0	.	684;619	Q9Y2T1;E7ES00	AXIN2_HUMAN;.	V	684;619	ENSP00000302625:A684V;ENSP00000364854:A619V	ENSP00000302625:A684V	A	-	2	0	AXIN2	60962990	1.000000	0.71417	0.795000	0.32087	0.951000	0.60555	7.302000	0.78861	2.516000	0.84829	0.650000	0.86243	GCG	G|0.998;A|0.002	0.002	strong		0.687	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	
FAM83B	222584	hgsc.bcm.edu	37	6	54735122	54735122	+	Silent	SNP	A	A	G	rs1472679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:54735122A>G	ENST00000306858.7	+	2	194	c.78A>G	c.(76-78)gaA>gaG	p.E26E		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	26										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					ACTACAAGGAATGGTATCGAG	0.423													A|||	1703	0.340056	0.3419	0.317	5008	,	,		20217	0.1488		0.5149	False		,,,				2504	0.3712				p.E26E		Atlas-SNP	.											.	FAM83B	186	.	0			c.A78G						PASS	.	A		1753,2653	523.6+/-371.1	348,1057,798	141.0	129.0	133.0		78	0.8	1.0	6	dbSNP_88	133	4360,4240	581.6+/-391.2	1095,2170,1035	no	coding-synonymous	FAM83B	NM_001010872.1		1443,3227,1833	GG,GA,AA		49.3023,39.7867,47.0014		26/1012	54735122	6113,6893	2203	4300	6503	SO:0001819	synonymous_variant	222584	exon2			CAAGGAATGGTAT	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.78A>G	6.37:g.54735122A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	194	116	0.597938	NM_001010872	Q2M1P3|Q96DQ2	Silent	SNP	ENST00000306858.7	37	CCDS34479.1																																																																																			A|0.584;G|0.416	0.416	strong		0.423	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
SH2D4B	387694	hgsc.bcm.edu	37	10	82363340	82363340	+	Silent	SNP	C	C	A	rs7069048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:82363340C>A	ENST00000470604.2	+	5	646	c.646C>A	c.(646-648)Cgg>Agg	p.R216R	SH2D4B_ENST00000313455.4_Silent_p.R168R|SH2D4B_ENST00000339284.2_Silent_p.R217R			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	216	Glu-rich.									endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			TCCAGTGCGCCGGTCCAAGGC	0.642													C|||	1874	0.374201	0.5151	0.2536	5008	,	,		16741	0.5149		0.2386	False		,,,				2504	0.2638				p.R217R		Atlas-SNP	.											SH2D4B,NS,carcinoma,-1,2	SH2D4B	44	2	0			c.C649A						scavenged	.	C	,	1991,2337		485,1021,658	12.0	14.0	13.0		502,649	0.5	0.2	10	dbSNP_116	13	2087,6401		274,1539,2431	no	coding-synonymous,coding-synonymous	SH2D4B	NM_001145719.1,NM_207372.2	,	759,2560,3089	AA,AC,CC		24.5877,46.0028,31.8196	,	168/310,217/358	82363340	4078,8738	2164	4244	6408	SO:0001819	synonymous_variant	387694	exon5			GTGCGCCGGTCCA		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"""SH2 domain containing"""	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.646C>A	10.37:g.82363340C>A		Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	92	33	0.358696	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Silent	SNP	ENST00000470604.2	37																																																																																				C|0.624;A|0.376	0.376	strong		0.642	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
ABAT	18	hgsc.bcm.edu	37	16	8844389	8844389	+	Silent	SNP	C	C	T	rs2229157	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:8844389C>T	ENST00000396600.2	+	5	1247	c.309C>T	c.(307-309)gtC>gtT	p.V103V	ABAT_ENST00000425191.2_Silent_p.V103V|ABAT_ENST00000268251.8_Silent_p.V103V|ABAT_ENST00000569156.1_Silent_p.V103V|ABAT_ENST00000567812.1_Silent_p.V118V	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	103					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	TCTCCTCTGTCCCCATAGGTA	0.478													C|||	525	0.104832	0.0303	0.0994	5008	,	,		20366	0.1756		0.1034	False		,,,				2504	0.138				p.V103V		Atlas-SNP	.											.	ABAT	46	.	0			c.C309T						PASS	.	C	,,	200,4194	122.5+/-159.9	5,190,2002	173.0	158.0	163.0		309,309,309	-1.8	1.0	16	dbSNP_127	163	968,7632	206.3+/-248.5	51,866,3383	no	coding-synonymous,coding-synonymous,coding-synonymous	ABAT	NM_000663.4,NM_001127448.1,NM_020686.5	,,	56,1056,5385	TT,TC,CC		11.2558,4.5517,8.9888	,,	103/501,103/501,103/501	8844389	1168,11826	2197	4300	6497	SO:0001819	synonymous_variant	18	exon5			CTCTGTCCCCATA	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"""4-aminobutyrate transaminase"""	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.309C>T	16.37:g.8844389C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Silent	SNP	ENST00000396600.2	37	CCDS10534.1																																																																																			C|0.901;T|0.099	0.099	strong		0.478	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686	
TMPRSS11BNL	401136	hgsc.bcm.edu	37	4	69078113	69078113	+	Missense_Mutation	SNP	T	T	C	rs4463136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69078113T>C	ENST00000432593.3	-	2	257	c.91A>G	c.(91-93)Act>Gct	p.T31A	FTLP10_ENST00000503647.1_RNA|RP11-646E20.6_ENST00000510782.1_RNA					TMPRSS11B N-terminal like, pseudogene											autonomic_ganglia(1)	1						AGACCAATAGTTATTCCAAAG	0.348													T|||	3599	0.71865	0.4304	0.6023	5008	,	,		16889	0.9901		0.7306	False		,,,				2504	0.8988				p.T31A		Atlas-SNP	.											.	TMPRSS11BNL	4	.	0			c.A91G						PASS	.	T	ALA/THR	742,642		202,338,152	133.0	102.0	111.0		91	5.2	0.7	4	dbSNP_111	111	2492,690		971,550,70	yes	missense	TMPRSS11BNL	NM_001129907.2	58	1173,888,222	CC,CT,TT		21.6845,46.3873,29.1721	possibly-damaging	31/106	69078113	3234,1332	692	1591	2283	SO:0001583	missense	401136	exon2			CAATAGTTATTCC			4q13.2	2014-05-09	2014-05-08		ENSG00000226894	ENSG00000250026			37262	pseudogene	pseudogene			"""TMPRSS11B N terminal-like"", ""TMPRSS11B N-terminal like"""				Standard	NR_104048		Approved	FLJ41562	uc003hdv.1		OTTHUMG00000160802	ENST00000432593.3:c.91A>G	4.37:g.69078113T>C	ENSP00000391149:p.Thr31Ala	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	240	239	0.995833	NM_001129907		Missense_Mutation	SNP	ENST00000432593.3	37	CCDS47066.1	1567	0.7174908424908425	209	0.4247967479674797	237	0.6546961325966851	567	0.9912587412587412	554	0.7308707124010554	T	12.52	1.963726	0.34659	0.536127	0.783155	ENSG00000226894	ENST00000432593	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	T	0.00012	0.0000	L	0.45422	1.42	0.58432	P	5.000000000032756E-6	P	0.37330	0.59	B	0.35278	0.199	T	0.47711	-0.9096	7	0.09843	T	0.71	.	11.2966	0.49282	0.0:0.0:0.0:1.0	rs4463136;rs52813553;rs58634571;rs4463136	31	B3KVV0	TM11L_HUMAN	A	31	.	ENSP00000391149:T31A	T	-	1	0	TMPRSS11BNL	68760708	0.920000	0.31207	0.740000	0.30986	0.017000	0.09413	3.349000	0.52217	2.178000	0.69098	0.528000	0.53228	ACT	T|0.271;C|0.729	0.729	strong		0.348	TMPRSS11BNL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001129907	
FYCO1	79443	hgsc.bcm.edu	37	3	46009864	46009864	+	Missense_Mutation	SNP	C	C	G	rs3733100|rs200041037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46009864C>G	ENST00000296137.2	-	8	1167	c.962G>C	c.(961-963)gGc>gCc	p.G321A	FYCO1_ENST00000535325.1_Missense_Mutation_p.G321A	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	321			G -> A (in dbSNP:rs3733100). {ECO:0000269|PubMed:11896456, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TAGCTCCAGGCCCTGCAGGCA	0.617													G|||	2669	0.532947	0.2095	0.6427	5008	,	,		19103	0.6667		0.5557	False		,,,				2504	0.7311				p.G321A		Atlas-SNP	.											.	FYCO1	115	.	0			c.G962C						PASS	.	G	ALA/GLY	1086,3320	720.4+/-409.1	143,800,1260	70.0	62.0	65.0		962	3.8	1.0	3	dbSNP_107	65	4678,3922	545.1+/-384.7	1275,2128,897	yes	missense	FYCO1	NM_024513.2	60	1418,2928,2157	GG,GC,CC		45.6047,24.6482,44.318	benign	321/1479	46009864	5764,7242	2203	4300	6503	SO:0001583	missense	79443	exon8			TCCAGGCCCTGCA	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.962G>C	3.37:g.46009864C>G	ENSP00000296137:p.Gly321Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	1137	0.5206043956043956	111	0.22560975609756098	224	0.6187845303867403	366	0.6398601398601399	436	0.575197889182058	G	0.101	-1.151688	0.01700	0.246482	0.543953	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.18338	2.22;2.22	5.66	3.84	0.44239	.	0.179817	0.48767	N	0.000179	T	0.00012	0.0000	N	0.00138	-2.015	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42327	-0.9458	9	0.02654	T	1	-9.0624	7.6507	0.28346	0.1322:0.2524:0.6154:0.0	rs3733100;rs17845108;rs17857899;rs59462026;rs3733100	321;321	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	A	321	ENSP00000296137:G321A;ENSP00000441178:G321A	ENSP00000296137:G321A	G	-	2	0	FYCO1	45984868	0.204000	0.23447	1.000000	0.80357	0.335000	0.28730	1.625000	0.37029	0.750000	0.32877	-0.815000	0.03128	GGC	C|0.537;G|0.463	0.463	strong		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
OPN4	94233	hgsc.bcm.edu	37	10	88422151	88422151	+	Silent	SNP	C	C	A	rs3740337	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88422151C>A	ENST00000241891.5	+	8	1383	c.1216C>A	c.(1216-1218)Cgg>Agg	p.R406R	OPN4_ENST00000372071.2_Silent_p.R417R	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	406					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						GATCTCCATACGGAGGCGCCA	0.672													C|||	1151	0.229832	0.0386	0.1744	5008	,	,		18136	0.2798		0.3012	False		,,,				2504	0.4029				p.R417R		Atlas-SNP	.											.	OPN4	61	.	0			c.C1249A						PASS	.	C	,	359,4017		14,331,1843	36.0	24.0	28.0		1249,1216	2.4	0.2	10	dbSNP_107	28	2751,5813		474,1803,2005	no	coding-synonymous,coding-synonymous	OPN4	NM_001030015.2,NM_033282.3	,	488,2134,3848	AA,AC,CC		32.1228,8.2038,24.034	,	417/490,406/479	88422151	3110,9830	2188	4282	6470	SO:0001819	synonymous_variant	94233	exon9			TCCATACGGAGGC	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.1216C>A	10.37:g.88422151C>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Silent	SNP	ENST00000241891.5	37	CCDS7376.1																																																																																			C|0.794;A|0.206	0.206	strong		0.672	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
SRGAP2	23380	hgsc.bcm.edu	37	1	206566903	206566903	+	Splice_Site	SNP	G	G	A	rs2987927	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206566903G>A	ENST00000414007.1	+	3	284	c.284G>A	c.(283-285)cGt>cAt	p.R95H	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	235	F-BAR domain.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					CCTTTTCAGCGTCAAGCCAAG	0.408													g|||	3	0.000599042	0.0	0.0014	5008	,	,		35930	0.0		0.002	False		,,,				2504	0.0				p.H82H		Atlas-SNP	.											.	.	.	.	0			c.A245A						PASS	.						78.0	67.0	70.0					1																	206566903		1899	4122	6021	SO:0001630	splice_region_variant	100996712	exon3			TTCAGCGTCAAGC	AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"""Rho GTPase activating proteins"""	19751	protein-coding gene	gene with protein product		606524	"""formin binding protein 2"""	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.283-1G>A	1.37:g.206566903G>A		Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	336	52	0.154762	NM_001271887		Silent	SNP	ENST00000414007.1	37		.	.	.	.	.	.	.	.	.	.	g	32	5.192443	0.94960	.	.	ENSG00000163486	ENST00000414359;ENST00000414007	T	0.55930	0.49	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.75925	0.3916	.	.	.	0.80722	D	1.000000	D;D;D	0.89917	1.0;0.996;0.958	D;P;B	0.83275	0.996;0.728;0.425	T	0.78645	-0.2123	8	0.87932	D	0	.	19.5856	0.95488	0.0:0.0:1.0:0.0	rs2987927;rs4844666	82;235;235	B4DDU0;O75044;B7Z3G4	.;FNBP2_HUMAN;.	H	149;95	ENSP00000390898:R95H	ENSP00000390898:R95H	R	+	2	0	SRGAP2	204633526	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.864000	0.99589	2.625000	0.88918	0.555000	0.69702	CGT	G|0.500;A|0.500	0.500	weak		0.408	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	Missense_Mutation
TIMELESS	8914	hgsc.bcm.edu	37	12	56825311	56825311	+	Silent	SNP	C	C	T	rs774033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56825311C>T	ENST00000553532.1	-	8	915	c.765G>A	c.(763-765)gtG>gtA	p.V255V	TIMELESS_ENST00000229201.4_Silent_p.V254V|TIMELESS_ENST00000554616.1_Silent_p.V255V					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GCTGGCGCAACACCTCCAGTT	0.552													C|||	2525	0.504193	0.2526	0.6816	5008	,	,		14831	0.7371		0.4503	False		,,,				2504	0.5337				p.V255V		Atlas-SNP	.											.	TIMELESS	107	.	0			c.G765A						PASS	.	C		1189,3217	413.9+/-336.6	150,889,1164	123.0	104.0	111.0		765	2.4	0.9	12	dbSNP_86	111	3907,4693	547.2+/-385.1	873,2161,1266	no	coding-synonymous	TIMELESS	NM_003920.3		1023,3050,2430	TT,TC,CC		45.4302,26.9859,39.1819		255/1209	56825311	5096,7910	2203	4300	6503	SO:0001819	synonymous_variant	8914	exon8			GCGCAACACCTCC	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.765G>A	12.37:g.56825311C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	112	46	0.410714	NM_003920		Silent	SNP	ENST00000553532.1	37	CCDS8918.1																																																																																			C|0.565;T|0.435	0.435	strong		0.552	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
OR5M10	390167	hgsc.bcm.edu	37	11	56344993	56344993	+	Missense_Mutation	SNP	C	C	A	rs10792043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56344993C>A	ENST00000526812.2	-	1	270	c.205G>T	c.(205-207)Gta>Tta	p.V69L		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	69			V -> L (in dbSNP:rs10792043). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						CAAATGTCTACAAAGGAGAGG	0.458													C|||	3274	0.653754	0.3517	0.719	5008	,	,		22369	0.874		0.6501	False		,,,				2504	0.7924				p.V69L		Atlas-SNP	.											.	OR5M10	56	.	0			c.G205T						PASS	.	C	LEU/VAL	1608,2288		344,920,684	154.0	146.0	148.0		205	4.0	1.0	11	dbSNP_120	148	5511,2771		1843,1825,473	no	missense	OR5M10	NM_001004741.1	32	2187,2745,1157	AA,AC,CC		33.4581,41.2731,41.5421	benign	69/316	56344993	7119,5059	1948	4141	6089	SO:0001583	missense	390167	exon1			TGTCTACAAAGGA	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"""GPCR / Class A : Olfactory receptors"""	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.205G>T	11.37:g.56344993C>A	ENSP00000436004:p.Val69Leu	Somatic	346	1	0.00289017		WXS	Illumina HiSeq	Phase_I	346	159	0.459538	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	37	CCDS53630.1	1387	0.63507326007326	137	0.2784552845528455	267	0.7375690607734806	498	0.8706293706293706	485	0.6398416886543535	C	12.79	2.042699	0.35989	0.412731	0.665419	ENSG00000254834	ENST00000526812	T	0.00832	5.64	4.04	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.25890	0.77	0.45464	P	0.0015610000000000346	B	0.23735	0.09	B	0.25759	0.063	T	0.40156	-0.9578	8	0.44086	T	0.13	.	7.3922	0.26915	0.187:0.6316:0.1814:0.0	rs10792043;rs52791147;rs10792043	69	Q6IEU7	OR5MA_HUMAN	L	69	ENSP00000436004:V69L	ENSP00000436004:V69L	V	-	1	0	OR5M10	56101569	0.000000	0.05858	0.989000	0.46669	0.394000	0.30568	-1.748000	0.01826	2.238000	0.73509	0.632000	0.83419	GTA	C|0.364;A|0.636	0.636	strong		0.458	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741	
DHX57	90957	hgsc.bcm.edu	37	2	39025555	39025555	+	Silent	SNP	G	G	A	rs1530853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:39025555G>A	ENST00000295373.6	-	24	4173	c.4047C>T	c.(4045-4047)tgC>tgT	p.C1349C		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1349							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				GATCAAGTTCGCAACGAAGCT	0.443													G|||	2945	0.588059	0.3139	0.5821	5008	,	,		19068	0.7857		0.6441	False		,,,				2504	0.7014				p.C1349C	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.C4047T						PASS	.	G		1603,2803	496.0+/-363.4	289,1025,889	113.0	103.0	106.0		4047	-10.8	0.0	2	dbSNP_88	106	5436,3164	655.0+/-401.2	1716,2004,580	no	coding-synonymous	DHX57	NM_198963.1		2005,3029,1469	AA,AG,GG		36.7907,36.3822,45.8788		1349/1387	39025555	7039,5967	2203	4300	6503	SO:0001819	synonymous_variant	90957	exon24			AAGTTCGCAACGA	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.4047C>T	2.37:g.39025555G>A		Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Silent	SNP	ENST00000295373.6	37	CCDS1800.1	1326	0.6071428571428571	154	0.3130081300813008	214	0.5911602209944752	456	0.7972027972027972	502	0.662269129287599	G	6.637	0.485909	0.12641	0.363822	0.632093	ENSG00000163214	ENST00000452978	.	.	.	5.42	-10.8	0.00216	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999143102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9687	0.79995	0.744:0.0:0.1799:0.0761	rs1530853;rs17174676;rs57997508;rs1530853	.	.	.	X	628	.	.	R	-	1	2	DHX57	38879059	0.003000	0.15002	0.000000	0.03702	0.808000	0.45660	-1.137000	0.03219	-2.701000	0.00398	-0.312000	0.09012	CGA	G|0.437;A|0.563	0.563	strong		0.443	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
PRKRA	8575	hgsc.bcm.edu	37	2	179300971	179300971	+	Silent	SNP	G	G	A	rs62176107	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179300971G>A	ENST00000325748.4	-	7	885	c.685C>T	c.(685-687)Ctg>Ttg	p.L229L	AC009948.5_ENST00000454488.1_RNA|AC009948.5_ENST00000436616.2_RNA|AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000438687.3_Silent_p.L116L|PRKRA_ENST00000432031.2_Silent_p.L218L|PRKRA_ENST00000487082.1_Silent_p.L204L	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	229	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CTTCTTTTCAGTAAGTTGATC	0.353																																					p.L229L	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											PRKRA,colon,carcinoma,0,1	PRKRA	56	1	0			c.C685T						PASS	.						156.0	180.0	172.0					2																	179300971		2203	4300	6503	SO:0001819	synonymous_variant	8575	exon7			TTTTCAGTAAGTT	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.685C>T	2.37:g.179300971G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	141	59	0.41844	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Silent	SNP	ENST00000325748.4	37	CCDS2279.1																																																																																			G|0.775;A|0.225	0.225	strong		0.353	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	
USP21	27005	hgsc.bcm.edu	37	1	161132777	161132777	+	Missense_Mutation	SNP	G	G	A	rs17356051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161132777G>A	ENST00000289865.8	+	6	1183	c.962G>A	c.(961-963)gGc>gAc	p.G321D	USP21_ENST00000368001.1_Missense_Mutation_p.G321D|USP21_ENST00000368002.3_Missense_Mutation_p.G321D	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	321	USP.		G -> D (in dbSNP:rs17356051).		histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AACCGCCGAGGCCGCCGGGCT	0.582													G|||	107	0.0213658	0.0008	0.0231	5008	,	,		16906	0.0		0.0746	False		,,,				2504	0.0153				p.G321D		Atlas-SNP	.											.	USP21	63	.	0			c.G962A						PASS	.	G	ASP/GLY,ASP/GLY	46,4360	46.7+/-81.2	0,46,2157	56.0	64.0	61.0		962,962	3.8	1.0	1	dbSNP_123	61	504,8096	143.9+/-199.8	11,482,3807	yes	missense,missense	USP21	NM_001014443.2,NM_012475.4	94,94	11,528,5964	AA,AG,GG		5.8605,1.044,4.2288	possibly-damaging,possibly-damaging	321/566,321/566	161132777	550,12456	2203	4300	6503	SO:0001583	missense	27005	exon6			GCCGAGGCCGCCG	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"""Ubiquitin-specific peptidases"""	12620	protein-coding gene	gene with protein product		604729	"""ubiquitin specific protease 21"""	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.962G>A	1.37:g.161132777G>A	ENSP00000289865:p.Gly321Asp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	200	88	0.44	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Missense_Mutation	SNP	ENST00000289865.8	37	CCDS30920.1	66	0.03021978021978022	0	0.0	11	0.03038674033149171	0	0.0	55	0.07255936675461741	G	15.82	2.945230	0.53079	0.01044	0.058605	ENSG00000143258	ENST00000368002;ENST00000289865;ENST00000368001	T;T;T	0.29917	1.55;1.55;1.55	4.72	3.8	0.43715	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	2.377030	0.03429	U	0.207571	T	0.29355	0.0731	L	0.41079	1.255	0.41560	D	0.988622	D	0.76494	0.999	D	0.67231	0.95	T	0.47071	-0.9145	10	0.10111	T	0.7	.	12.152	0.54055	0.0853:0.0:0.9147:0.0	rs17356051	321	Q9UK80	UBP21_HUMAN	D	321	ENSP00000356981:G321D;ENSP00000289865:G321D;ENSP00000356980:G321D	ENSP00000289865:G321D	G	+	2	0	USP21	159399401	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.474000	0.53129	1.202000	0.43218	0.455000	0.32223	GGC	G|0.960;A|0.040	0.040	strong		0.582	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1		
PTPRJ	5795	hgsc.bcm.edu	37	11	48145166	48145166	+	Splice_Site	SNP	G	G	A	rs2270993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:48145166G>A	ENST00000418331.2	+	5	970	c.618G>A	c.(616-618)gaG>gaA	p.E206E	PTPRJ_ENST00000440289.2_Splice_Site_p.E206E	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	206	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.E206E(1)		breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TTAAAATAGAGCCGATCCCAG	0.483													G|||	779	0.155551	0.2337	0.1095	5008	,	,		18337	0.1597		0.1183	False		,,,				2504	0.1166				p.E206E		Atlas-SNP	.											PTPRJ,NS,carcinoma,0,1	PTPRJ	225	1	1	Substitution - coding silent(1)	stomach(1)	c.G618A						PASS	.	G	,	1025,3377	376.6+/-322.1	115,795,1291	60.0	59.0	59.0		618,618	-0.1	0.8	11	dbSNP_100	59	1097,7499	228.7+/-263.7	70,957,3271	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PTPRJ	NM_001098503.1,NM_002843.3	,	185,1752,4562	AA,AG,GG		12.7617,23.2849,16.3256	,	206/540,206/1338	48145166	2122,10876	2201	4298	6499	SO:0001630	splice_region_variant	5795	exon5			AATAGAGCCGATC	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.617-1G>A	11.37:g.48145166G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	CCDS7945.1																																																																																			G|0.843;A|0.157	0.157	strong		0.483	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		Silent
C12orf43	64897	hgsc.bcm.edu	37	12	121454257	121454257	+	Silent	SNP	T	T	A	rs2258227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121454257T>A	ENST00000288757.3	-	1	43	c.21A>T	c.(19-21)acA>acT	p.T7T	C12orf43_ENST00000539736.1_Silent_p.T7T|C12orf43_ENST00000537817.1_5'UTR|C12orf43_ENST00000445832.3_5'UTR|C12orf43_ENST00000536407.2_Silent_p.T7T|C12orf43_ENST00000366211.2_5'UTR	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	7										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AATCGCTCACTGTGCCACTGG	0.622													t|||	3930	0.784744	0.5651	0.9193	5008	,	,		17709	0.8601		0.833	False		,,,				2504	0.8589				p.T7T		Atlas-SNP	.											.	C12orf43	30	.	0			c.A21T						PASS	.	T		2707,1699	651.8+/-399.3	847,1013,343	65.0	61.0	63.0		21	-1.5	0.0	12	dbSNP_100	63	7029,1571	744.2+/-407.2	2861,1307,132	no	coding-synonymous	C12orf43	NM_022895.1		3708,2320,475	AA,AT,TT		18.2674,38.5611,25.1422		7/263	121454257	9736,3270	2203	4300	6503	SO:0001819	synonymous_variant	64897	exon1			GCTCACTGTGCCA	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.21A>T	12.37:g.121454257T>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_022895	Q53HF0|Q9H9Z7	Silent	SNP	ENST00000288757.3	37	CCDS9210.1	1759	0.8054029304029304	298	0.6056910569105691	330	0.9116022099447514	503	0.8793706293706294	628	0.8284960422163589	T	1.483	-0.556644	0.03967	0.614389	0.817326	ENSG00000157895	ENST00000536407	.	.	.	4.95	-1.55	0.08558	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.51482	P	7.900000000005125E-5	.	.	.	.	.	.	T	0.19418	-1.0306	3	.	.	.	-0.0078	0.4743	0.00537	0.256:0.1369:0.3244:0.2828	rs2258227;rs17845434;rs17858306;rs57712993;rs2258227	.	.	.	C	12	.	.	S	-	1	0	C12orf43	119938640	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.147000	0.10234	-0.407000	0.07576	-1.021000	0.02439	AGT	T|0.231;A|0.769	0.769	strong		0.622	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
SPRR1A	6698	hgsc.bcm.edu	37	1	152957832	152957832	+	Missense_Mutation	SNP	C	C	A	rs1611762|rs17882377|rs372951479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152957832C>A	ENST00000368762.1	+	1	126	c.126C>A	c.(124-126)caC>caA	p.H42Q	SPRR1A_ENST00000307122.2_Missense_Mutation_p.H42Q			P35321	SPR1A_HUMAN	small proline-rich protein 1A	42	6 X 8 AA approximate tandem repeats.		H -> Q (in dbSNP:rs1611762). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8325635, ECO:0000269|Ref.3}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCCCTGCCACCCCAAGGTGC	0.647													C|||	2531	0.505391	0.4523	0.4395	5008	,	,		14293	0.5972		0.5348	False		,,,				2504	0.499				p.H42Q		Atlas-SNP	.											.	SPRR1A	17	.	0			c.C126A						PASS	.						122.0	126.0	125.0					1																	152957832		2203	4300	6503	SO:0001583	missense	6698	exon2			CTGCCACCCCAAG	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.126C>A	1.37:g.152957832C>A	ENSP00000357751:p.His42Gln	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	217	134	0.617512	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	37	CCDS1032.1	1174	0.5375457875457875	234	0.47560975609756095	180	0.4972375690607735	358	0.6258741258741258	402	0.5303430079155673	C	9.564	1.119172	0.20877	.	.	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.13657	2.57;2.57	4.77	1.54	0.23209	.	0.648090	0.12758	N	0.441596	T	0.03136	0.0092	.	.	.	0.52099	P	5.3999999999998494E-5	B	0.27013	0.166	B	0.24848	0.056	T	0.40850	-0.9541	8	0.36615	T	0.2	-2.9027	7.3544	0.26711	0.3386:0.4971:0.1643:0.0	rs1611762;rs17884470;rs58509799;rs1611762	42	P35321	SPR1A_HUMAN	Q	42	ENSP00000307340:H42Q;ENSP00000357751:H42Q	ENSP00000307340:H42Q	H	+	3	2	SPRR1A	151224456	0.620000	0.27068	0.970000	0.41538	0.731000	0.41821	0.156000	0.16382	0.397000	0.25310	0.549000	0.68633	CAC	C|0.457;A|0.543	0.543	strong		0.647	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987	
STRN3	29966	hgsc.bcm.edu	37	14	31381351	31381351	+	Missense_Mutation	SNP	T	T	C	rs2273171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:31381351T>C	ENST00000357479.5	-	11	1608	c.1412A>G	c.(1411-1413)aAt>aGt	p.N471S	STRN3_ENST00000366206.2_5'UTR|STRN3_ENST00000355683.5_Missense_Mutation_p.N387S	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	471			N -> S (in dbSNP:rs2273171). {ECO:0000269|PubMed:10748158, ECO:0000269|PubMed:7864889}.		negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N387S(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		ATACTTGGGATTCCATGTCTT	0.423													T|||	1948	0.388978	0.3139	0.4553	5008	,	,		17850	0.4692		0.4632	False		,,,				2504	0.2843				p.N471S		Atlas-SNP	.											STRN3,NS,carcinoma,0,1	STRN3	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1412G						PASS	.	T	SER/ASN,SER/ASN	1515,2891	481.2+/-359.0	271,973,959	130.0	124.0	126.0		1412,1160	5.6	1.0	14	dbSNP_100	126	3983,4617	552.8+/-386.2	904,2175,1221	yes	missense,missense	STRN3	NM_001083893.1,NM_014574.3	46,46	1175,3148,2180	CC,CT,TT		46.314,34.3849,42.2728	possibly-damaging,possibly-damaging	471/798,387/714	31381351	5498,7508	2203	4300	6503	SO:0001583	missense	29966	exon11			TTGGGATTCCATG		CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.1412A>G	14.37:g.31381351T>C	ENSP00000350071:p.Asn471Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	37	CCDS41938.1	941	0.4308608058608059	165	0.3353658536585366	166	0.4585635359116022	250	0.4370629370629371	360	0.47493403693931396	T	24.6	4.544097	0.86022	0.343849	0.46314	ENSG00000196792	ENST00000355683;ENST00000357479	T;T	0.59772	0.24;0.24	5.63	5.63	0.86233	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.083501	0.85682	D	0.000000	T	0.00012	0.0000	L	0.28400	0.85	0.09310	P	0.99999999782838	B;B	0.33135	0.029;0.399	B;B	0.31946	0.037;0.138	T	0.44922	-0.9296	9	0.72032	D	0.01	-10.5307	15.7875	0.78319	0.0:0.0:0.0:1.0	rs2273171;rs57146647;rs2273171	387;471	Q13033-2;Q13033	.;STRN3_HUMAN	S	387;471	ENSP00000347909:N387S;ENSP00000350071:N471S	ENSP00000347909:N387S	N	-	2	0	STRN3	30451102	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.153000	0.71819	2.257000	0.74773	0.533000	0.62120	AAT	C|0.414;N|0.000	0.414	strong		0.423	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
DAAM1	23002	hgsc.bcm.edu	37	14	59789727	59789727	+	Silent	SNP	G	G	A	rs8022614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:59789727G>A	ENST00000395125.1	+	5	581	c.558G>A	c.(556-558)aaG>aaA	p.K186K	DAAM1_ENST00000360909.3_Silent_p.K186K|DAAM1_ENST00000351081.1_Silent_p.K186K	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	186	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		GCTGTATAAAGGCGTTAATGA	0.438													G|||	1685	0.336462	0.0787	0.2406	5008	,	,		20067	0.5883		0.3936	False		,,,				2504	0.4346				p.K186K		Atlas-SNP	.											.	DAAM1	95	.	0			c.G558A						PASS	.	G		526,3880	230.7+/-244.8	38,450,1715	109.0	101.0	104.0		558	3.9	1.0	14	dbSNP_116	104	3354,5246	490.0+/-372.8	668,2018,1614	no	coding-synonymous	DAAM1	NM_014992.1		706,2468,3329	AA,AG,GG		39.0,11.9383,29.8324		186/1079	59789727	3880,9126	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon6			TATAAAGGCGTTA	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.558G>A	14.37:g.59789727G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.684;A|0.316	0.316	strong		0.438	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
CES1	1066	hgsc.bcm.edu	37	16	55862717	55862717	+	Silent	SNP	T	T	C	rs76828834	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55862717T>C	ENST00000361503.4	-	2	349	c.219A>G	c.(217-219)ccA>ccG	p.P73P	CES1_ENST00000422046.2_Silent_p.P73P|CES1_ENST00000566555.1_5'Flank|CES1_ENST00000360526.3_Silent_p.P74P			P23141	EST1_HUMAN	carboxylesterase 1	73					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	CAAAGCTCCATGGTTCTGCAG	0.532																																					p.P74P	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.A222G						PASS	.						110.0	109.0	110.0					16																	55862717		2198	4300	6498	SO:0001819	synonymous_variant	1066	exon2			GCTCCATGGTTCT	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.219A>G	16.37:g.55862717T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	124	30	0.241935	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																			T|0.635;C|0.365	0.365	strong		0.532	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
MBTPS1	8720	hgsc.bcm.edu	37	16	84115483	84115483	+	Silent	SNP	G	G	A	rs3743631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84115483G>A	ENST00000343411.3	-	11	1812	c.1317C>T	c.(1315-1317)ccC>ccT	p.P439P	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	439	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCATACTGGCGGGATTCACCA	0.517													A|||	2650	0.529153	0.5696	0.5159	5008	,	,		5965	0.6974		0.4384	False		,,,				2504	0.4039				p.P439P		Atlas-SNP	.											MBTPS1,NS,carcinoma,0,1	MBTPS1	85	1	0			c.C1317T						PASS	.	A		2310,2090	572.1+/-383.2	604,1102,494	56.0	58.0	57.0		1317	-5.0	0.8	16	dbSNP_107	57	3609,4991	626.1+/-397.8	757,2095,1448	no	coding-synonymous	MBTPS1	NM_003791.2		1361,3197,1942	AA,AG,GG		41.9651,47.5,45.5308		439/1053	84115483	5919,7081	2200	4300	6500	SO:0001819	synonymous_variant	8720	exon11			ACTGGCGGGATTC	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1317C>T	16.37:g.84115483G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																			G|0.504;A|0.496	0.496	strong		0.517	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
BMS1	9790	hgsc.bcm.edu	37	10	43312807	43312807	+	Silent	SNP	C	C	T	rs11239786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43312807C>T	ENST00000374518.5	+	15	2508	c.2445C>T	c.(2443-2445)ccC>ccT	p.P815P		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	815					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AAATTGACCCCGACGAAGAAG	0.313													C|||	1027	0.205072	0.0333	0.1167	5008	,	,		19710	0.4018		0.1988	False		,,,				2504	0.3037				p.P815P		Atlas-SNP	.											BMS1,NS,carcinoma,0,1	BMS1	132	1	0			c.C2445T						PASS	.						18.0	19.0	19.0					10																	43312807		2179	4257	6436	SO:0001819	synonymous_variant	9790	exon15			TGACCCCGACGAA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2445C>T	10.37:g.43312807C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_014753	Q5QPT5|Q86XJ9	Silent	SNP	ENST00000374518.5	37	CCDS7199.1																																																																																			C|0.667;T|0.333	0.333	strong		0.313	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
LOXL4	84171	hgsc.bcm.edu	37	10	100018844	100018844	+	Silent	SNP	G	G	A	rs7077073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:100018844G>A	ENST00000260702.3	-	6	993	c.843C>T	c.(841-843)caC>caT	p.H281H	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	281	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		TGACCACAGCGTGCATGCCAC	0.672													G|||	2512	0.501597	0.23	0.6138	5008	,	,		18007	0.752		0.4473	False		,,,				2504	0.5869				p.H281H		Atlas-SNP	.											.	LOXL4	60	.	0			c.C843T						PASS	.	G		1180,3220		162,856,1182	58.0	41.0	47.0		843	-5.3	0.9	10	dbSNP_116	47	3602,4998		741,2120,1439	no	coding-synonymous	LOXL4	NM_032211.6		903,2976,2621	AA,AG,GG		41.8837,26.8182,36.7846		281/757	100018844	4782,8218	2200	4300	6500	SO:0001819	synonymous_variant	84171	exon6			CACAGCGTGCATG	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.843C>T	10.37:g.100018844G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Silent	SNP	ENST00000260702.3	37	CCDS7473.1																																																																																			G|0.595;A|0.405	0.405	strong		0.672	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
ALPK2	115701	hgsc.bcm.edu	37	18	56204250	56204250	+	Missense_Mutation	SNP	A	A	C	rs3809976	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204250A>C	ENST00000361673.3	-	5	3382	c.3169T>G	c.(3169-3171)Ttg>Gtg	p.L1057V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1057			L -> V (in dbSNP:rs3809976). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						ATATGATCCAACTGCACTTGG	0.507													A|||	3366	0.672125	0.4682	0.6772	5008	,	,		20437	0.7976		0.7674	False		,,,				2504	0.7168				p.L1057V		Atlas-SNP	.											.	ALPK2	487	.	0			c.T3169G						PASS	.	A	VAL/LEU	2278,2128	598.3+/-389.1	597,1084,522	103.0	99.0	100.0		3169	-3.3	0.0	18	dbSNP_107	100	6608,1992	722.6+/-406.4	2551,1506,243	yes	missense	ALPK2	NM_052947.3	32	3148,2590,765	CC,CA,AA		23.1628,48.2978,31.6777	possibly-damaging	1057/2171	56204250	8886,4120	2203	4300	6503	SO:0001583	missense	115701	exon5			GATCCAACTGCAC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3169T>G	18.37:g.56204250A>C	ENSP00000354991:p.Leu1057Val	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	158	156	0.987342	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	1521	0.6964285714285714	212	0.43089430894308944	255	0.7044198895027625	466	0.8146853146853147	588	0.7757255936675461	A	13.12	2.142712	0.37825	0.517022	0.768372	ENSG00000198796	ENST00000361673	T	0.43688	0.94	5.46	-3.32	0.04973	.	4.754610	0.00166	N	0.000005	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P;P	0.42518	0.782;0.675	B;B	0.37888	0.26;0.08	T	0.53464	-0.8435	9	0.02654	T	1	2.9224	5.3655	0.16111	0.4015:0.2743:0.3242:0.0	rs3809976;rs52797820;rs56849248;rs3809976	1052;1057	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	V	1057	ENSP00000354991:L1057V	ENSP00000354991:L1057V	L	-	1	2	ALPK2	54355230	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.229000	0.09098	-0.500000	0.06614	-0.353000	0.07706	TTG	C|0.686;N|0.000	0.686	strong		0.507	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
MCPH1	79648	hgsc.bcm.edu	37	8	6338306	6338306	+	Missense_Mutation	SNP	C	C	A	rs12674488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:6338306C>A	ENST00000344683.5	+	11	2121	c.2045C>A	c.(2044-2046)aCc>aAc	p.T682N		NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	682	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.		T -> N (in dbSNP:rs12674488).		cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GTCTGTGAGACCACGACTCAC	0.488													C|||	733	0.146366	0.0938	0.1153	5008	,	,		18435	0.1806		0.163	False		,,,				2504	0.1871				p.T682N	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.C2045A						PASS	.	C	ASN/THR	335,3637		14,307,1665	126.0	121.0	123.0		2045	0.7	0.0	8	dbSNP_120	123	1301,7031		96,1109,2961	yes	missense	MCPH1	NM_024596.3	65	110,1416,4626	AA,AC,CC		15.6145,8.434,13.2965	probably-damaging	682/836	6338306	1636,10668	1986	4166	6152	SO:0001583	missense	79648	exon11			GTGAGACCACGAC	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.2045C>A	8.37:g.6338306C>A	ENSP00000342924:p.Thr682Asn	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_024596	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	304	0.1391941391941392	41	0.08333333333333333	42	0.11602209944751381	104	0.18181818181818182	117	0.15435356200527706	C	13.12	2.140912	0.37825	0.08434	0.156145	ENSG00000147316	ENST00000344683	T	0.28666	1.6	5.91	0.673	0.17941	BRCT (3);	0.466822	0.27019	N	0.021330	T	0.00109	0.0003	L	0.49126	1.545	0.58432	P	6.999999999979245E-6	D	0.57899	0.981	P	0.60345	0.873	T	0.04140	-1.0974	9	0.44086	T	0.13	-3.8872	18.5762	0.91155	0.0:0.372:0.628:0.0	rs12674488;rs52795475;rs61269664;rs12674488	682	Q8NEM0	MCPH1_HUMAN	N	682	ENSP00000342924:T682N	ENSP00000342924:T682N	T	+	2	0	MCPH1	6325714	0.731000	0.28111	0.000000	0.03702	0.135000	0.20990	1.013000	0.29937	-0.152000	0.11156	0.655000	0.94253	ACC	C|0.850;A|0.150	0.150	strong		0.488	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
KLRC3	3823	hgsc.bcm.edu	37	12	10588530	10588530	+	Missense_Mutation	SNP	C	C	G	rs75545535		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10588530C>G	ENST00000539033.1	-	1	70	c.56G>C	c.(55-57)cGg>cCg	p.R19P	KLRC2_ENST00000536833.2_Intron|KLRC2_ENST00000381902.2_Missense_Mutation_p.R19P|KLRC2_ENST00000381901.1_Missense_Mutation_p.R19P																							CCTTTGCTGCCGCTTTGGGTC	0.433																																					p.R19P		Atlas-SNP	.											KLRC2,NS,carcinoma,0,1	KLRC2	29	1	0			c.G56C						PASS	.						256.0	255.0	255.0					12																	10588530		2203	4300	6503	SO:0001583	missense	3822	exon1			TGCTGCCGCTTTG																												ENST00000539033.1:c.56G>C	12.37:g.10588530C>G	ENSP00000437563:p.Arg19Pro	Somatic	522	0	0		WXS	Illumina HiSeq	Phase_I	642	252	0.392523	NM_002260		Missense_Mutation	SNP	ENST00000539033.1	37		557	0.25503663003663	67	0.13617886178861788	117	0.32320441988950277	145	0.2534965034965035	228	0.3007915567282322	C	11.56	1.674672	0.29693	.	.	ENSG00000255641;ENSG00000205809;ENSG00000205809	ENST00000539033;ENST00000381902;ENST00000381901	T;T;T	0.05996	3.36;3.36;3.36	2.57	-0.0579	0.13799	.	0.475912	0.19666	N	0.108869	T	0.00012	0.0000	L	0.61387	1.9	0.09310	N	1	P;P;D	0.76494	0.932;0.921;0.999	P;P;D	0.70935	0.796;0.88;0.971	T	0.48364	-0.9042	10	0.72032	D	0.01	.	4.9087	0.13811	0.0:0.5158:0.0:0.4842	.	5;19;19	Q3KQS7;P26717;F5H6K3	.;NKG2C_HUMAN;.	P	19	ENSP00000437563:R19P;ENSP00000371327:R19P;ENSP00000371326:R19P	ENSP00000371326:R19P	R	-	2	0	KLRC2;RP11-277P12.6	10479797	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.155000	0.10115	-0.169000	0.10834	0.184000	0.17185	CGG	C|0.745;G|0.255	0.255	strong		0.433	NKG2-E-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000400274.1		
SOCS5	9655	hgsc.bcm.edu	37	2	46987139	46987139	+	Silent	SNP	G	G	A	rs17771838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:46987139G>A	ENST00000306503.5	+	2	1642	c.1470G>A	c.(1468-1470)gcG>gcA	p.A490A	SOCS5_ENST00000394861.2_Silent_p.A490A	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	490	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			TCTGTCGCGCGGTAATCTGCA	0.373													G|||	328	0.0654952	0.031	0.085	5008	,	,		22274	0.0357		0.0885	False		,,,				2504	0.1053				p.A490A		Atlas-SNP	.											.	SOCS5	62	.	0			c.G1470A						PASS	.	G	,	171,4235	112.9+/-151.0	3,165,2035	85.0	81.0	82.0		1470,1470	-4.1	0.9	2	dbSNP_123	82	811,7789	188.7+/-235.6	35,741,3524	no	coding-synonymous,coding-synonymous	SOCS5	NM_014011.4,NM_144949.2	,	38,906,5559	AA,AG,GG		9.4302,3.8811,7.5504	,	490/537,490/537	46987139	982,12024	2203	4300	6503	SO:0001819	synonymous_variant	9655	exon2			TCGCGCGGTAATC	AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.1470G>A	2.37:g.46987139G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_144949	Q53SD4|Q8IYZ4	Silent	SNP	ENST00000306503.5	37	CCDS1830.1																																																																																			G|0.929;A|0.071	0.071	strong		0.373	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2		
DOCK6	57572	hgsc.bcm.edu	37	19	11348960	11348960	+	Missense_Mutation	SNP	G	G	A	rs12609039	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11348960G>A	ENST00000294618.7	-	15	1675	c.1664C>T	c.(1663-1665)cCg>cTg	p.P555L	DOCK6_ENST00000319867.7_5'Flank|C19orf80_ENST00000591200.1_Intron|C19orf80_ENST00000252453.8_5'Flank	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	555	DHR-1.		P -> L (in dbSNP:rs12609039).		blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GAGGCTGTGCGGGTACACGTA	0.647													G|||	196	0.0391374	0.0023	0.0403	5008	,	,		16457	0.0704		0.0517	False		,,,				2504	0.0429				p.P555L		Atlas-SNP	.											.	DOCK6	104	.	0			c.C1664T						PASS	.	G	LEU/PRO	57,4017		0,57,1980	16.0	18.0	17.0		1664	4.8	1.0	19	dbSNP_120	17	615,7701		35,545,3578	yes	missense	DOCK6	NM_020812.2	98	35,602,5558	AA,AG,GG		7.3954,1.3991,5.4237	probably-damaging	555/2048	11348960	672,11718	2037	4158	6195	SO:0001583	missense	57572	exon15			CTGTGCGGGTACA		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.1664C>T	19.37:g.11348960G>A	ENSP00000294618:p.Pro555Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	87	0.03983516483516483	3	0.006097560975609756	15	0.04143646408839779	37	0.06468531468531469	32	0.04221635883905013	G	25.6	4.655909	0.88056	0.013991	0.073954	ENSG00000130158	ENST00000294618	T	0.10763	2.84	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.05547	0.0146	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.47195	-0.9136	10	0.87932	D	0	-28.6951	16.638	0.85064	0.0:0.0:1.0:0.0	rs12609039;rs59939727;rs12609039	555	Q96HP0	DOCK6_HUMAN	L	555	ENSP00000294618:P555L	ENSP00000294618:P555L	P	-	2	0	DOCK6	11209960	1.000000	0.71417	0.987000	0.45799	0.779000	0.44077	9.129000	0.94430	2.211000	0.71520	0.591000	0.81541	CCG	G|0.960;A|0.040	0.040	strong		0.647	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
PDCD11	22984	hgsc.bcm.edu	37	10	105177645	105177645	+	Missense_Mutation	SNP	G	G	T	rs11598673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:105177645G>T	ENST00000369797.3	+	14	1961	c.1867G>T	c.(1867-1869)Gca>Tca	p.A623S		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	623			A -> S (in dbSNP:rs11598673).		mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GAAAGAGCCTGCAGGACACAG	0.478													G|||	134	0.0267572	0.0068	0.0663	5008	,	,		20481	0.0		0.0557	False		,,,				2504	0.0235				p.A623S		Atlas-SNP	.											.	PDCD11	160	.	0			c.G1867T						PASS	.	G	SER/ALA	79,4327	69.2+/-107.0	0,79,2124	154.0	138.0	143.0		1867	2.2	0.0	10	dbSNP_120	143	598,8002	157.7+/-211.4	22,554,3724	yes	missense	PDCD11	NM_014976.1	99	22,633,5848	TT,TG,GG		6.9535,1.793,5.2053	benign	623/1872	105177645	677,12329	2203	4300	6503	SO:0001583	missense	22984	exon14			GAGCCTGCAGGAC	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.1867G>T	10.37:g.105177645G>T	ENSP00000358812:p.Ala623Ser	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	70	0.03205128205128205	3	0.006097560975609756	29	0.08011049723756906	0	0.0	38	0.05013192612137203	G	11.18	1.561328	0.27915	0.01793	0.069535	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.10192	2.9	5.28	2.15	0.27550	Nucleic acid-binding, OB-fold-like (1);	1.245640	0.05180	N	0.501217	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.36237	-0.9756	10	0.09338	T	0.73	0.2355	6.3238	0.21232	0.2411:0.1436:0.6154:0.0	rs11598673;rs52837777;rs57202852;rs11598673	623	Q14690	RRP5_HUMAN	S	623	ENSP00000358812:A623S	ENSP00000358812:A623S	A	+	1	0	PDCD11	105167635	0.000000	0.05858	0.001000	0.08648	0.949000	0.60115	0.046000	0.14035	1.161000	0.42604	0.462000	0.41574	GCA	G|0.954;T|0.046	0.046	strong		0.478	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
ZNF236	7776	hgsc.bcm.edu	37	18	74659494	74659494	+	Silent	SNP	G	G	A	rs9961872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:74659494G>A	ENST00000253159.8	+	27	4992	c.4794G>A	c.(4792-4794)gcG>gcA	p.A1598A	ZNF236_ENST00000320610.9_Silent_p.A1600A	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1598					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		AGTTCCCAGCGCTCCTCACGG	0.493													A|||	251	0.0501198	0.1225	0.0346	5008	,	,		18243	0.0218		0.0258	False		,,,				2504	0.0174				p.A1598A		Atlas-SNP	.											.	ZNF236	325	.	0			c.G4794A						PASS	.	A		472,3814		28,416,1699	74.0	86.0	82.0		4794	-11.4	0.0	18	dbSNP_119	82	171,8355		0,171,4092	no	coding-synonymous	ZNF236	NM_007345.3		28,587,5791	AA,AG,GG		2.0056,11.0126,5.0187		1598/1846	74659494	643,12169	2143	4263	6406	SO:0001819	synonymous_variant	7776	exon27			CCCAGCGCTCCTC	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.4794G>A	18.37:g.74659494G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_007345	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	CCDS42447.1																																																																																			G|0.953;A|0.047	0.047	strong		0.493	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
CLCA2	9635	hgsc.bcm.edu	37	1	86904588	86904588	+	Silent	SNP	C	C	T	rs11161830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86904588C>T	ENST00000370565.4	+	7	1164	c.1002C>T	c.(1000-1002)gcC>gcT	p.A334A		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	334	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TACAACAAGCCGCAGAATTTT	0.398													C|||	546	0.109026	0.1679	0.111	5008	,	,		20635	0.0546		0.0944	False		,,,				2504	0.0992				p.A334A	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C1002T						PASS	.	C		752,3654	307.2+/-289.9	68,616,1519	83.0	85.0	84.0		1002	0.9	1.0	1	dbSNP_120	84	708,7892	174.2+/-224.5	30,648,3622	no	coding-synonymous	CLCA2	NM_006536.5		98,1264,5141	TT,TC,CC		8.2326,17.0676,11.2256		334/944	86904588	1460,11546	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon7			ACAAGCCGCAGAA		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1002C>T	1.37:g.86904588C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	22	0.285714	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			C|0.892;T|0.108	0.108	strong		0.398	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
SORT1	6272	hgsc.bcm.edu	37	1	109897100	109897100	+	Silent	SNP	T	T	C	rs72646560	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109897100T>C	ENST00000256637.6	-	5	655	c.597A>G	c.(595-597)agA>agG	p.R199R	SORT1_ENST00000482236.1_5'Flank|SORT1_ENST00000538502.1_Silent_p.R63R	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	199					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		AATCTGATGATCTAAAGATTC	0.408													.|||	172	0.034345	0.0325	0.0144	5008	,	,		19639	0.002		0.0537	False		,,,				2504	0.0644				p.R199R		Atlas-SNP	.											.	SORT1	48	.	0			c.A597G						PASS	.	T	,	207,4199	127.4+/-164.3	4,199,2000	154.0	145.0	148.0		189,597	-2.3	1.0	1	dbSNP_130	148	475,8125	139.5+/-196.2	11,453,3836	no	coding-synonymous,coding-synonymous	SORT1	NM_001205228.1,NM_002959.5	,	15,652,5836	CC,CT,TT		5.5233,4.6981,5.2437	,	63/695,199/832	109897100	682,12324	2203	4300	6503	SO:0001819	synonymous_variant	6272	exon5			TGATGATCTAAAG	BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.597A>G	1.37:g.109897100T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_002959	B4DWI3|C0JYZ0|Q8IZ49	Silent	SNP	ENST00000256637.6	37	CCDS798.1																																																																																			T|0.955;C|0.045	0.045	strong		0.408	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959	
LARP1B	55132	hgsc.bcm.edu	37	4	129043204	129043204	+	Missense_Mutation	SNP	C	C	G	rs12508837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:129043204C>G	ENST00000326639.6	+	11	1596	c.1385C>G	c.(1384-1386)cCt>cGt	p.P462R	LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000441387.1_Missense_Mutation_p.P462R|LARP1B_ENST00000264584.5_Missense_Mutation_p.P415R|LARP1B_ENST00000512292.1_Missense_Mutation_p.P462R|LARP1B_ENST00000427266.1_Missense_Mutation_p.P462R	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	462			P -> R (in dbSNP:rs12508837). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						AAAAAACATCCTGGAGGAGAT	0.368													C|||	2956	0.590256	0.3941	0.696	5008	,	,		18855	0.5288		0.6759	False		,,,				2504	0.7556				p.P462R		Atlas-SNP	.											.	LARP1B	120	.	0			c.C1385G						PASS	.	C	ARG/PRO,ARG/PRO	2008,2398	562.8+/-381.0	450,1108,645	106.0	101.0	102.0		1385,1385	2.5	1.0	4	dbSNP_120	102	5718,2882	671.3+/-402.8	1917,1884,499	yes	missense,missense	LARP1B	NM_018078.2,NM_178043.1	103,103	2367,2992,1144	GG,GC,CC		33.5116,45.5742,40.5966	probably-damaging,probably-damaging	462/915,462/523	129043204	7726,5280	2203	4300	6503	SO:0001583	missense	55132	exon11			AACATCCTGGAGG		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"""La ribonucleoprotein domain containing"""	24704	protein-coding gene	gene with protein product			"""La ribonucleoprotein domain family, member 2"""	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.1385C>G	4.37:g.129043204C>G	ENSP00000321997:p.Pro462Arg	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	194	193	0.994845	NM_178043	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	37	CCDS3738.1	1219	0.5581501831501832	198	0.4024390243902439	247	0.6823204419889503	261	0.4562937062937063	513	0.6767810026385225	C	12.90	2.077054	0.36662	0.455742	0.664884	ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000264584;ENST00000441387;ENST00000427266	T;T;T;T;T;T	0.32753	1.9;1.44;1.46;1.92;1.89;1.44	5.27	2.54	0.30619	.	0.058961	0.64402	D	0.000001	T	0.00012	0.0000	M	0.64997	1.995	0.09310	P	1.0	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.41052	-0.9530	9	0.49607	T	0.09	.	7.7081	0.28661	0.1367:0.722:0.0:0.1413	rs12508837;rs61183198	415;462;462	D6RJB0;Q659C4;G3XAJ5	.;LAR1B_HUMAN;.	R	462;462;415;415;462;462	ENSP00000321997:P462R;ENSP00000422850:P462R;ENSP00000427281:P415R;ENSP00000264584:P415R;ENSP00000396521:P462R;ENSP00000403586:P462R	ENSP00000264584:P415R	P	+	2	0	LARP1B	129262654	0.996000	0.38824	0.995000	0.50966	0.015000	0.08874	1.486000	0.35530	0.335000	0.23614	-0.157000	0.13467	CCT	C|0.422;G|0.578	0.578	strong		0.368	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078	
DHRS3	9249	hgsc.bcm.edu	37	1	12640650	12640650	+	Silent	SNP	C	C	T	rs11540058	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12640650C>T	ENST00000376223.2	-	2	623	c.240G>A	c.(238-240)acG>acA	p.T80T	DHRS3_ENST00000482265.1_5'UTR	NM_004753.4	NP_004744.2	O75911	DHRS3_HUMAN	dehydrogenase/reductase (SDR family) member 3	80					bone morphogenesis (GO:0060349)|cardiac septum morphogenesis (GO:0060411)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|phototransduction, visible light (GO:0007603)|regulation of ossification (GO:0030278)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|photoreceptor outer segment membrane (GO:0042622)	electron carrier activity (GO:0009055)|NADP-retinol dehydrogenase activity (GO:0052650)|nucleotide binding (GO:0000166)|retinol dehydrogenase activity (GO:0004745)			cervix(1)|large_intestine(4)|lung(2)|prostate(1)|skin(1)	9	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	GGATCTCCTCCGTCGTCTCCT	0.537													C|||	399	0.0796725	0.0446	0.0764	5008	,	,		17584	0.002		0.1918	False		,,,				2504	0.0941				p.T80T		Atlas-SNP	.											.	DHRS3	18	.	0			c.G240A						PASS	.	C		294,4112	161.1+/-193.3	10,274,1919	74.0	71.0	72.0		240	-4.2	0.4	1	dbSNP_120	72	1781,6819	321.8+/-315.3	194,1393,2713	no	coding-synonymous	DHRS3	NM_004753.4		204,1667,4632	TT,TC,CC		20.7093,6.6727,15.9542		80/303	12640650	2075,10931	2203	4300	6503	SO:0001819	synonymous_variant	9249	exon2			CTCCTCCGTCGTC	AF061741	CCDS146.1	1p36.1	2011-09-20			ENSG00000162496	ENSG00000162496	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	17693	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 1"""	612830				9705317, 12226107, 19027726	Standard	XM_005263533		Approved	retSDR1, Rsdr1, SDR1, RDH17, SDR16C1	uc001auc.3	O75911	OTTHUMG00000001885	ENST00000376223.2:c.240G>A	1.37:g.12640650C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	150	53	0.353333	NM_004753	B2R7F3|Q5VUY3|Q6UY38|Q9BUC8	Silent	SNP	ENST00000376223.2	37	CCDS146.1																																																																																			C|0.868;T|0.132	0.132	strong		0.537	DHRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005318.1	NM_004753	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133954011	133954011	+	Silent	SNP	C	C	T	rs2818387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:133954011C>T	ENST00000298622.4	+	9	1539	c.1401C>T	c.(1399-1401)gaC>gaT	p.D467D		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	467						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TGGAATCCGACGGCTCCTCCG	0.592													C|||	2574	0.513978	0.4584	0.5793	5008	,	,		13772	0.5883		0.4841	False		,,,				2504	0.4969				p.D467D		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.C1401T						PASS	.	C		1813,2195		417,979,608	57.0	66.0	63.0		1401	-5.4	0.0	10	dbSNP_100	63	4080,4234		995,2090,1072	yes	coding-synonymous	JAKMIP3	NM_001105521.2		1412,3069,1680	TT,TC,CC		49.0739,45.2345,47.825		467/845	133954011	5893,6429	2004	4157	6161	SO:0001819	synonymous_variant	282973	exon9			ATCCGACGGCTCC	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1401C>T	10.37:g.133954011C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			C|0.497;T|0.503	0.503	strong		0.592	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
ALPK2	115701	hgsc.bcm.edu	37	18	56247567	56247567	+	Silent	SNP	A	A	G	rs9956630	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56247567A>G	ENST00000361673.3	-	4	654	c.441T>C	c.(439-441)taT>taC	p.Y147Y	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	147						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CTTCTTCCTTATAAGGATGTT	0.498													A|||	2418	0.482827	0.3306	0.4755	5008	,	,		20581	0.6022		0.5	False		,,,				2504	0.5532				p.Y147Y		Atlas-SNP	.											.	ALPK2	487	.	0			c.T441C						PASS	.	A		1521,2749		314,893,928	243.0	238.0	239.0		441	-1.0	0.0	18	dbSNP_119	239	4224,4258		1090,2044,1107	no	coding-synonymous	ALPK2	NM_052947.3		1404,2937,2035	GG,GA,AA		49.7996,35.6206,45.0518		147/2171	56247567	5745,7007	2135	4241	6376	SO:0001819	synonymous_variant	115701	exon4			TTCCTTATAAGGA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.441T>C	18.37:g.56247567A>G		Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	300	299	0.996667	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			A|0.515;G|0.485	0.485	strong		0.498	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
HSPA6	3310	hgsc.bcm.edu	37	1	161496134	161496134	+	Missense_Mutation	SNP	C	C	G	rs753856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161496134C>G	ENST00000309758.4	+	1	2099	c.1686C>G	c.(1684-1686)gaC>gaG	p.D562E	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	562			D -> E (in dbSNP:rs753856). {ECO:0000269|Ref.2}.		ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCCTTAGGGACAAGATTCCCG	0.547													C|||	617	0.123203	0.0265	0.1268	5008	,	,		20455	0.2837		0.1143	False		,,,				2504	0.0951				p.D562E		Atlas-SNP	.											.	HSPA6	53	.	0			c.C1686G						PASS	.	C	GLU/ASP	168,4238		2,164,2037	26.0	26.0	26.0		1686	1.6	0.8	1	dbSNP_86	26	889,7709		46,797,3456	no	missense	HSPA6	NM_002155.3	45	48,961,5493	GG,GC,CC		10.3396,3.813,8.1283	benign	562/644	161496134	1057,11947	2203	4299	6502	SO:0001583	missense	3310	exon1			TAGGGACAAGATT		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.1686C>G	1.37:g.161496134C>G	ENSP00000310219:p.Asp562Glu	Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	305	113	0.370492	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	302	0.1382783882783883	19	0.03861788617886179	39	0.10773480662983426	153	0.2674825174825175	91	0.12005277044854881	.	13.45	2.240135	0.39598	0.03813	0.103396	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.15139	2.45	3.6	1.6	0.23607	.	0.237482	0.21074	U	0.080613	T	0.08088	0.0202	L	0.35542	1.07	0.44539	P	0.0025079999999999547	B	0.29115	0.233	P	0.45099	0.469	T	0.25745	-1.0123	9	0.51188	T	0.08	.	5.4576	0.16600	0.1978:0.6893:0.0:0.113	rs753856;rs52815568;rs753856	562	P17066	HSP76_HUMAN	E	562;538	ENSP00000310219:D562E	ENSP00000310219:D562E	D	+	3	2	HSPA6	159762758	0.158000	0.22850	0.770000	0.31555	0.633000	0.38033	0.049000	0.14099	0.167000	0.19631	0.591000	0.81541	GAC	C|0.914;G|0.086	0.086	strong		0.547	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
CKAP2L	150468	hgsc.bcm.edu	37	2	113498566	113498566	+	Missense_Mutation	SNP	A	A	G	rs3811040	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113498566A>G	ENST00000302450.6	-	8	1919	c.1841T>C	c.(1840-1842)tTa>tCa	p.L614S	NT5DC4_ENST00000327581.4_Intron|CKAP2L_ENST00000541405.1_Missense_Mutation_p.L449S	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	614			L -> S (in dbSNP:rs3811040).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						TTCAGCAACTAAAGAGTCAGA	0.368													A|||	2116	0.422524	0.056	0.5519	5008	,	,		22421	0.6895		0.508	False		,,,				2504	0.4632				p.L614S		Atlas-SNP	.											.	CKAP2L	54	.	0			c.T1841C						PASS	.	A	SER/LEU	551,3855	244.7+/-253.9	35,481,1687	149.0	137.0	141.0		1841	-0.5	0.0	2	dbSNP_107	141	4338,4262	579.4+/-390.9	1127,2084,1089	yes	missense	CKAP2L	NM_152515.3	145	1162,2565,2776	GG,GA,AA		49.5581,12.5057,37.5903	benign	614/746	113498566	4889,8117	2203	4300	6503	SO:0001583	missense	150468	exon8			GCAACTAAAGAGT	AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.1841T>C	2.37:g.113498566A>G	ENSP00000305204:p.Leu614Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	158	68	0.43038	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	1006	0.4606227106227106	30	0.06097560975609756	197	0.5441988950276243	400	0.6993006993006993	379	0.5	A	0.014	-1.597170	0.00857	0.125057	0.504419	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.20598	2.06;2.06	4.43	-0.529	0.11901	.	1.678030	0.02972	N	0.144541	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.19331	0.009;0.035	B;B	0.21360	0.007;0.034	T	0.36187	-0.9758	9	0.09338	T	0.73	0.421	7.2134	0.25947	0.5654:0.0:0.4346:0.0	rs3811040;rs17649870;rs56445792;rs58162560;rs3811040	203;614	Q8IYA6-2;Q8IYA6	.;CKP2L_HUMAN	S	449;614	ENSP00000438763:L449S;ENSP00000305204:L614S	ENSP00000305204:L614S	L	-	2	0	CKAP2L	113215037	0.000000	0.05858	0.000000	0.03702	0.368000	0.29767	-0.101000	0.10973	-0.079000	0.12707	0.533000	0.62120	TTA	A|0.592;G|0.408	0.408	strong		0.368	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	
BEST1	7439	hgsc.bcm.edu	37	11	61730183	61730183	+	Silent	SNP	C	C	T	rs1800008	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:61730183C>T	ENST00000378043.4	+	10	2200	c.1557C>T	c.(1555-1557)agC>agT	p.S519S	BEST1_ENST00000301774.9_Silent_p.S147S|FTH1_ENST00000529631.1_Intron|BEST1_ENST00000378042.3_Silent_p.S432S|BEST1_ENST00000449131.2_Silent_p.S459S|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000534553.1_3'UTR	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	519					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						TCTCAGAGAGCGATGGGGCCT	0.473													C|||	508	0.101438	0.0166	0.1239	5008	,	,		21604	0.003		0.2167	False		,,,				2504	0.183				p.S519S		Atlas-SNP	.											BEST1_ENST00000449131,NS,carcinoma,+1,2	BEST1	85	2	0			c.C1557T						PASS	.	C	,	219,4185	132.9+/-169.3	6,207,1989	78.0	74.0	76.0		1377,1557	-6.9	0.0	11	dbSNP_89	76	1998,6600	351.3+/-328.2	229,1540,2530	no	coding-synonymous,coding-synonymous	BEST1	NM_001139443.1,NM_004183.3	,	235,1747,4519	TT,TC,CC		23.238,4.9728,17.0512	,	459/605,519/586	61730183	2217,10785	2202	4299	6501	SO:0001819	synonymous_variant	7439	exon10			AGAGAGCGATGGG	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1557C>T	11.37:g.61730183C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.846;T|0.154	0.154	strong		0.473	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
IGSF10	285313	hgsc.bcm.edu	37	3	151166058	151166058	+	Missense_Mutation	SNP	G	G	A	rs17204557	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:151166058G>A	ENST00000282466.3	-	4	1710	c.1711C>T	c.(1711-1713)Cct>Tct	p.P571S		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	571	Ig-like C2-type 2.		P -> S (in dbSNP:rs17204557).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TCGACCAAAGGTTCTACCACA	0.418													G|||	217	0.0433307	0.0	0.049	5008	,	,		22532	0.0238		0.0328	False		,,,				2504	0.1288				p.P571S		Atlas-SNP	.											.	IGSF10	279	.	0			c.C1711T						PASS	.	G	SER/PRO	29,4377	31.7+/-61.6	0,29,2174	117.0	111.0	113.0		1711	-1.1	0.0	3	dbSNP_123	113	311,8289	112.1+/-172.3	4,303,3993	yes	missense	IGSF10	NM_178822.4	74	4,332,6167	AA,AG,GG		3.6163,0.6582,2.6142	benign	571/2624	151166058	340,12666	2203	4300	6503	SO:0001583	missense	285313	exon4			CCAAAGGTTCTAC	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.1711C>T	3.37:g.151166058G>A	ENSP00000282466:p.Pro571Ser	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	354	159	0.449153	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	49	0.022435897435897436	0	0.0	19	0.052486187845303865	13	0.022727272727272728	17	0.022427440633245383	G	1.507	-0.550529	0.03996	0.006582	0.036163	ENSG00000152580	ENST00000282466	T	0.33654	1.4	5.17	-1.13	0.09775	Immunoglobulin-like (1);	0.521615	0.16136	N	0.227965	T	0.03348	0.0097	L	0.31157	0.91	0.09310	N	1	B	0.12630	0.006	B	0.12837	0.008	T	0.08207	-1.0733	10	0.52906	T	0.07	.	5.214	0.15332	0.1968:0.0:0.3361:0.4671	rs17204557;rs56530914;rs58807081;rs17204557	571	Q6WRI0	IGS10_HUMAN	S	571	ENSP00000282466:P571S	ENSP00000282466:P571S	P	-	1	0	IGSF10	152648748	0.996000	0.38824	0.003000	0.11579	0.027000	0.11550	0.897000	0.28390	-0.621000	0.05633	-0.840000	0.03056	CCT	G|0.971;A|0.029	0.029	strong		0.418	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
FAM186A	121006	hgsc.bcm.edu	37	12	50744753	50744753	+	Silent	SNP	T	T	C	rs10506292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50744753T>C	ENST00000327337.5	-	4	5861	c.5862A>G	c.(5860-5862)aaA>aaG	p.K1954K	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Silent_p.K1954K	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1954								p.K1954K(1)									TTGCCAATCTTTTCTTAGCAA	0.458													T|||	3031	0.605232	0.4985	0.732	5008	,	,		17768	0.7431		0.659	False		,,,				2504	0.4622				p.K1954K	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - coding silent(1)	stomach(1)	c.A5862G						PASS	.						30.0	29.0	29.0					12																	50744753		692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			CAATCTTTTCTTA		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.5862A>G	12.37:g.50744753T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			T|0.351;C|0.649	0.649	strong		0.458	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
BFSP1	631	hgsc.bcm.edu	37	20	17477592	17477592	+	Missense_Mutation	SNP	C	C	T	rs6080719	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:17477592C>T	ENST00000377873.3	-	7	1072	c.1033G>A	c.(1033-1035)Ggt>Agt	p.G345S	BFSP1_ENST00000544874.1_Missense_Mutation_p.G206S|BFSP1_ENST00000536626.1_Missense_Mutation_p.G206S|BFSP1_ENST00000377868.2_Missense_Mutation_p.G220S	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	345	Tail.		G -> S (in dbSNP:rs6080719).		cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						CCTTTCCCACCGGATCCAGTG	0.488													C|||	1339	0.267372	0.0794	0.2925	5008	,	,		16927	0.3998		0.2406	False		,,,				2504	0.3947				p.G345S		Atlas-SNP	.											.	BFSP1	55	.	0			c.G1033A						PASS	.	C	SER/GLY,SER/GLY	362,3984		19,324,1830	42.0	36.0	38.0		658,1033	-5.0	0.0	20	dbSNP_114	38	1781,6631		190,1401,2615	yes	missense,missense	BFSP1	NM_001161705.1,NM_001195.3	56,56	209,1725,4445	TT,TC,CC		21.1721,8.3295,16.7973	benign,benign	220/541,345/666	17477592	2143,10615	2173	4206	6379	SO:0001583	missense	631	exon7			TCCCACCGGATCC	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.1033G>A	20.37:g.17477592C>T	ENSP00000367104:p.Gly345Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001195	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Missense_Mutation	SNP	ENST00000377873.3	37	CCDS13126.1	552	0.25274725274725274	33	0.06707317073170732	104	0.287292817679558	235	0.41083916083916083	180	0.23746701846965698	C	3.787	-0.044410	0.07452	0.083295	0.211721	ENSG00000125864	ENST00000377873;ENST00000377868;ENST00000536626;ENST00000544874	D;T;T;T	0.85773	-2.03;1.66;1.66;1.66	5.95	-5.02	0.02982	.	0.737426	0.13434	N	0.388172	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B;B	0.12630	0.006;0.001	B;B	0.14023	0.01;0.001	T	0.11227	-1.0596	9	0.02654	T	1	-4.3206	13.7019	0.62613	0.0:0.1926:0.0:0.8074	rs6080719;rs52835071;rs59719438;rs6080719	220;345	Q12934-2;Q12934	.;BFSP1_HUMAN	S	345;220;206;206	ENSP00000367104:G345S;ENSP00000367099:G220S;ENSP00000442522:G206S;ENSP00000439870:G206S	ENSP00000367099:G220S	G	-	1	0	BFSP1	17425592	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.577000	0.05847	-0.687000	0.05162	-0.751000	0.03497	GGT	C|0.784;T|0.216	0.216	strong		0.488	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195	
CASC5	57082	hgsc.bcm.edu	37	15	40916237	40916237	+	Missense_Mutation	SNP	A	A	G	rs17747633	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40916237A>G	ENST00000346991.5	+	11	4243	c.3853A>G	c.(3853-3855)Aaa>Gaa	p.K1285E	CASC5_ENST00000399668.2_Missense_Mutation_p.K1259E			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1285			K -> E (in dbSNP:rs17747633). {ECO:0000269|PubMed:10980622}.		acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.K1285E(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GGTCATAGGGAAAGTTGTAGA	0.378													a|||	1019	0.203474	0.0257	0.2565	5008	,	,		20762	0.0992		0.4573	False		,,,				2504	0.2526				p.K1285E		Atlas-SNP	.											CASC5_ENST00000346991,colon,carcinoma,0,3	CASC5	269	3	1	Substitution - Missense(1)	stomach(1)	c.A3853G						PASS	.	C	GLU/LYS,GLU/LYS	357,3341		26,305,1518	86.0	78.0	81.0		3775,3853	3.4	0.2	15	dbSNP_123	81	3546,4648		750,2046,1301	yes	missense,missense	CASC5	NM_144508.3,NM_170589.3	56,56	776,2351,2819	GG,GA,AA		43.2756,9.6539,32.8204	probably-damaging,probably-damaging	1259/2317,1285/2343	40916237	3903,7989	1849	4097	5946	SO:0001583	missense	57082	exon11			ATAGGGAAAGTTG	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.3853A>G	15.37:g.40916237A>G	ENSP00000335463:p.Lys1285Glu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	32	0.380952	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	496	0.2271062271062271	15	0.03048780487804878	108	0.2983425414364641	40	0.06993006993006994	333	0.4393139841688654	a	11.70	1.718008	0.30413	0.096539	0.432756	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.20200	2.09;2.09	4.57	3.44	0.39384	.	0.301070	0.23627	N	0.046177	T	0.00012	0.0000	M	0.63843	1.955	0.44168	P	0.0030210000000000514	D;D;D	0.60160	0.987;0.987;0.974	D;D;P	0.63597	0.916;0.916;0.854	T	0.47471	-0.9115	9	0.37606	T	0.19	.	10.2596	0.43419	0.8335:0.1665:0.0:0.0	rs17747633;rs17747633	1259;1285;1259	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	E	1285;1259;1259	ENSP00000335463:K1285E;ENSP00000382576:K1259E	ENSP00000260369:K1259E	K	+	1	0	CASC5	38703529	0.000000	0.05858	0.158000	0.22627	0.387000	0.30353	0.183000	0.16919	0.877000	0.35895	-0.264000	0.10439	AAA	A|0.758;G|0.242	0.242	strong		0.378	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
ABCF3	55324	hgsc.bcm.edu	37	3	183908982	183908982	+	Missense_Mutation	SNP	C	C	T	rs11706273	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183908982C>T	ENST00000429586.2	+	16	1693	c.1508C>T	c.(1507-1509)cCg>cTg	p.P503L	EIF2B5_ENST00000444495.1_Intron|ABCF3_ENST00000292808.5_Missense_Mutation_p.P497L	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	503	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		P -> L (in dbSNP:rs11706273). {ECO:0000269|PubMed:14702039}.		defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TACTACGATCCGAAGCACGTC	0.547													C|||	128	0.0255591	0.003	0.0403	5008	,	,		19353	0.0		0.0497	False		,,,				2504	0.047				p.P503L		Atlas-SNP	.											.	ABCF3	72	.	0			c.C1508T						PASS	.	C	LEU/PRO	43,4363	46.0+/-80.4	2,39,2162	194.0	171.0	179.0		1508	5.7	0.3	3	dbSNP_120	179	369,8231	121.5+/-180.6	10,349,3941	yes	missense	ABCF3	NM_018358.2	98	12,388,6103	TT,TC,CC		4.2907,0.9759,3.1678	benign	503/710	183908982	412,12594	2203	4300	6503	SO:0001583	missense	55324	exon16			ACGATCCGAAGCA	U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"""ATP binding cassette transporters / subfamily F"""	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.1508C>T	3.37:g.183908982C>T	ENSP00000411471:p.Pro503Leu	Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	248	132	0.532258	NM_018358	A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Missense_Mutation	SNP	ENST00000429586.2	37	CCDS3254.1	56	0.02564102564102564	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	36	0.047493403693931395	C	14.38	2.519024	0.44866	0.009759	0.042907	ENSG00000161204	ENST00000429586;ENST00000292808	D;D	0.92397	-3.02;-3.03	5.74	5.74	0.90152	ABC transporter-like (1);	0.112101	0.64402	D	0.000009	T	0.66752	0.2821	L	0.52206	1.635	0.80722	D	1	B;B	0.27765	0.051;0.188	B;B	0.17098	0.017;0.016	T	0.79191	-0.1905	10	0.56958	D	0.05	-12.6459	18.9233	0.92534	0.0:1.0:0.0:0.0	rs11706273;rs52802929;rs11706273	497;503	Q9NUQ8-2;Q9NUQ8	.;ABCF3_HUMAN	L	503;497	ENSP00000411471:P503L;ENSP00000292808:P497L	ENSP00000292808:P497L	P	+	2	0	ABCF3	185391676	0.931000	0.31567	0.350000	0.25708	0.419000	0.31324	3.692000	0.54727	2.703000	0.92315	0.655000	0.94253	CCG	C|0.968;T|0.032	0.032	strong		0.547	ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358	
EPHA2	1969	hgsc.bcm.edu	37	1	16475123	16475123	+	Silent	SNP	C	C	T	rs6678616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16475123C>T	ENST00000358432.5	-	3	727	c.573G>A	c.(571-573)ctG>ctA	p.L191L	EPHA2_ENST00000461614.1_5'UTR	NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	191	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Mediates interaction with CLDN4.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	GGACGGAGAGCAGCGCCACAC	0.647													C|||	1134	0.226438	0.146	0.366	5008	,	,		19385	0.0308		0.3618	False		,,,				2504	0.2986				p.L191L		Atlas-SNP	.											.	EPHA2	102	.	0			c.G573A						PASS	.	C		733,3673	301.5+/-286.9	67,599,1537	64.0	62.0	62.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	573	3.1	1.0	1	dbSNP_116	62	2973,5627	460.4+/-365.2	510,1953,1837	no	coding-synonymous	EPHA2	NM_004431.3		577,2552,3374	TT,TC,CC		34.5698,16.6364,28.4945		191/977	16475123	3706,9300	2203	4300	6503	SO:0001819	synonymous_variant	1969	exon3			GGAGAGCAGCGCC	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.573G>A	1.37:g.16475123C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			C|0.740;T|0.260	0.260	strong		0.647	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
VWA5B1	127731	hgsc.bcm.edu	37	1	20640906	20640906	+	Silent	SNP	C	C	T	rs61741263	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20640906C>T	ENST00000375079.2	+	4	580	c.384C>T	c.(382-384)ttC>ttT	p.F128F	RP4-745E8.2_ENST00000444923.1_RNA|VWA5B1_ENST00000289825.4_5'UTR|VWA5B1_ENST00000375083.4_Silent_p.F128F|VWA5B1_ENST00000289815.8_Silent_p.F128F	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	128	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GGATCCTGTTCGTGGCCAACC	0.597													C|||	45	0.00898562	0.0008	0.0245	5008	,	,		19180	0.0		0.0209	False		,,,				2504	0.0061				p.F128F		Atlas-SNP	.											.	VWA5B1	44	.	0			c.C384T						PASS	.	C		7,1377		0,7,685	92.0	88.0	89.0		384	-3.0	1.0	1	dbSNP_129	89	56,3126		0,56,1535	no	coding-synonymous	VWA5B1	NM_001039500.2		0,63,2220	TT,TC,CC		1.7599,0.5058,1.3798		128/1216	20640906	63,4503	692	1591	2283	SO:0001819	synonymous_variant	127731	exon4			CCTGTTCGTGGCC	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.384C>T	1.37:g.20640906C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	132	54	0.409091	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Silent	SNP	ENST00000375079.2	37																																																																																				C|0.987;T|0.013	0.013	strong		0.597	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
PEBP4	157310	hgsc.bcm.edu	37	8	22570901	22570901	+	Silent	SNP	C	C	T	rs3087803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:22570901C>T	ENST00000256404.6	-	7	757	c.666G>A	c.(664-666)gcG>gcA	p.A222A	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	222						extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		CAGCTATCTCCGCCTGGTTTT	0.587													C|||	605	0.120807	0.0106	0.2089	5008	,	,		16207	0.2798		0.0805	False		,,,				2504	0.0849				p.A222A		Atlas-SNP	.											PEBP4,NS,adenocarcinoma,-1,1	PEBP4	23	1	0			c.G666A						PASS	.	C		107,3801		1,105,1848	68.0	75.0	73.0		666	-9.7	0.0	8	dbSNP_102	73	762,7534		34,694,3420	no	coding-synonymous	PEBP4	NM_144962.2		35,799,5268	TT,TC,CC		9.1851,2.738,7.1206		222/228	22570901	869,11335	1954	4148	6102	SO:0001819	synonymous_variant	157310	exon7			TATCTCCGCCTGG	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"""cousin-of-RKIP 1 protein"""	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.666G>A	8.37:g.22570901C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	135	67	0.496296	NM_144962	Q5EVA1|Q8WW74	Silent	SNP	ENST00000256404.6	37	CCDS43724.1																																																																																			C|0.888;T|0.112	0.112	strong		0.587	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
L3MBTL4	91133	hgsc.bcm.edu	37	18	6301903	6301903	+	Splice_Site	SNP	G	G	A	rs74645110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:6301903G>A	ENST00000284898.6	-	4	326	c.126C>T	c.(124-126)caC>caT	p.H42H	L3MBTL4_ENST00000317931.7_Splice_Site_p.H42H|L3MBTL4_ENST00000400105.2_Splice_Site_p.H42H|L3MBTL4_ENST00000400104.3_Splice_Site_p.H42H	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	42					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				GATAATTACCGTGACTCAAAG	0.328													G|||	59	0.0117812	0.0	0.0159	5008	,	,		17376	0.001		0.0417	False		,,,				2504	0.0051				p.H42H	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											.	L3MBTL4	87	.	0			c.C126T						PASS	.	G		18,4388		0,18,2185	269.0	255.0	260.0		126	-10.2	0.0	18	dbSNP_131	260	247,8353		2,243,4055	yes	coding-synonymous-near-splice	L3MBTL4	NM_173464.3		2,261,6240	AA,AG,GG		2.8721,0.4085,2.0375		42/624	6301903	265,12741	2203	4300	6503	SO:0001630	splice_region_variant	91133	exon4			ATTACCGTGACTC	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"""Sterile alpha motif (SAM) domain containing"""	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.127+1C>T	18.37:g.6301903G>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	156	62	0.397436	NM_173464	A8MTL8|Q8IXS3	Silent	SNP	ENST00000284898.6	37	CCDS11839.2																																																																																			G|0.981;A|0.019	0.019	strong		0.328	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464	Silent
KRT5	3852	hgsc.bcm.edu	37	12	52912768	52912768	+	Silent	SNP	C	C	T	rs1132948	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52912768C>T	ENST00000252242.4	-	2	1122	c.732G>A	c.(730-732)ctG>ctA	p.L244L		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	244	Coil 1B.|Rod.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCATGTTTCTCAGCTCTGAGT	0.577													C|||	639	0.127596	0.177	0.1844	5008	,	,		19637	0.0377		0.1481	False		,,,				2504	0.092				p.L244L		Atlas-SNP	.											.	KRT5	88	.	0			c.G732A						PASS	.	C		767,3639	311.9+/-292.3	58,651,1494	192.0	169.0	177.0		732	-1.5	1.0	12	dbSNP_86	177	1209,7391	244.3+/-273.6	86,1037,3177	no	coding-synonymous	KRT5	NM_000424.3		144,1688,4671	TT,TC,CC		14.0581,17.4081,15.193		244/591	52912768	1976,11030	2203	4300	6503	SO:0001819	synonymous_variant	3852	exon2			GTTTCTCAGCTCT		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.732G>A	12.37:g.52912768C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	166	62	0.373494	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	37	CCDS8830.1																																																																																			T|0.147;C|0.853	0.147	strong		0.577	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
CELF5	60680	hgsc.bcm.edu	37	19	3224896	3224896	+	Silent	SNP	G	G	C	rs17852497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:3224896G>C	ENST00000292672.2	+	1	196	c.159G>C	c.(157-159)ccG>ccC	p.P53P	CELF5_ENST00000541430.2_Silent_p.P53P	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	53	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						GCCAGATCCCGCGGCACCTGG	0.677													G|||	873	0.174321	0.1104	0.1671	5008	,	,		3684	0.1984		0.2256	False		,,,				2504	0.1881				p.P53P		Atlas-SNP	.											CELF5,NS,carcinoma,0,1	CELF5	32	1	0			c.G159C						scavenged	.	G	,	632,3772		46,540,1616	21.0	20.0	20.0		159,159	-0.6	0.9	19	dbSNP_123	20	1751,6843		186,1379,2732	no	coding-synonymous,coding-synonymous	CELF5	NM_001172673.1,NM_021938.3	,	232,1919,4348	CC,CG,GG		20.3747,14.3506,18.3336	,	53/410,53/486	3224896	2383,10615	2202	4297	6499	SO:0001819	synonymous_variant	60680	exon1			GATCCCGCGGCAC	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"""RNA binding motif (RRM) containing"""	14058	protein-coding gene	gene with protein product		612680	"""Bruno (Drosophila) -like 5, RNA binding protein"", ""bruno-like 5, RNA binding protein (Drosophila)"""	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.159G>C	19.37:g.3224896G>C		Somatic	161	2	0.0124224		WXS	Illumina HiSeq	Phase_I	213	82	0.384977	NM_021938	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Silent	SNP	ENST00000292672.2	37	CCDS12106.1																																																																																			G|0.815;C|0.185	0.185	strong		0.677	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938	
C12orf60	144608	hgsc.bcm.edu	37	12	14976063	14976063	+	Missense_Mutation	SNP	A	A	G	rs7304054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:14976063A>G	ENST00000330828.2	+	2	398	c.194A>G	c.(193-195)aAa>aGa	p.K65R	C12orf60_ENST00000527783.1_Intron	NM_175874.3	NP_787070.2	Q5U649	CL060_HUMAN	chromosome 12 open reading frame 60	65			K -> R (in dbSNP:rs7304054).							breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	9						CAAATGCTCAAAATTTTTAAG	0.363													A|||	953	0.190296	0.3238	0.0893	5008	,	,		20059	0.0823		0.1431	False		,,,				2504	0.2413				p.K65R		Atlas-SNP	.											.	C12orf60	31	.	0			c.A194G						PASS	.	A	ARG/LYS	1147,3259	399.7+/-331.3	149,849,1205	77.0	81.0	79.0		194	-6.9	0.0	12	dbSNP_116	79	1313,7287	258.0+/-281.8	108,1097,3095	yes	missense	C12orf60	NM_175874.3	26	257,1946,4300	GG,GA,AA		15.2674,26.0327,18.9143	benign	65/246	14976063	2460,10546	2203	4300	6503	SO:0001583	missense	144608	exon2			TGCTCAAAATTTT	BC038836	CCDS8667.1	12p12.3	2012-08-16			ENSG00000182993	ENSG00000182993			28726	protein-coding gene	gene with protein product						12477932	Standard	NM_175874		Approved	MGC47869	uc001rcj.4	Q5U649	OTTHUMG00000167473	ENST00000330828.2:c.194A>G	12.37:g.14976063A>G	ENSP00000331691:p.Lys65Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	136	76	0.558824	NM_175874	A8K1M7|Q5XKK8|Q8IXY2	Missense_Mutation	SNP	ENST00000330828.2	37	CCDS8667.1	364	0.16666666666666666	157	0.31910569105691056	44	0.12154696132596685	56	0.0979020979020979	107	0.14116094986807387	A	0.295	-0.977805	0.02197	0.260327	0.152674	ENSG00000182993	ENST00000330828	T	0.12147	2.71	4.95	-6.92	0.01644	.	1.279640	0.05317	N	0.525948	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.47611	-0.9104	9	0.07644	T	0.81	-10.5222	16.4437	0.83909	0.2569:0.0:0.7431:0.0	rs7304054;rs12815267;rs52818247;rs60654136;rs7304054	65	Q5U649	CL060_HUMAN	R	65	ENSP00000331691:K65R	ENSP00000331691:K65R	K	+	2	0	C12orf60	14867330	0.000000	0.05858	0.001000	0.08648	0.122000	0.20287	-0.795000	0.04580	-1.287000	0.02381	-0.441000	0.05720	AAA	A|0.819;G|0.181	0.181	strong		0.363	C12orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394735.1	NM_175874	
FREM1	158326	hgsc.bcm.edu	37	9	14859356	14859356	+	Silent	SNP	T	T	C	rs10961757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:14859356T>C	ENST00000380880.3	-	4	1239	c.456A>G	c.(454-456)caA>caG	p.Q152Q	FREM1_ENST00000422223.2_Silent_p.Q152Q|FREM1_ENST00000380881.4_Silent_p.Q152Q			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	152					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TATCAATCGCTTGGGACAAGC	0.473													T|||	1244	0.248403	0.1483	0.2435	5008	,	,		19125	0.5367		0.164	False		,,,				2504	0.1769				p.Q152Q		Atlas-SNP	.											.	FREM1	261	.	0			c.A456G						PASS	.	T		557,3241		49,459,1391	133.0	131.0	131.0		456	3.4	0.8	9	dbSNP_120	131	1259,6989		117,1025,2982	no	coding-synonymous	FREM1	NM_144966.5		166,1484,4373	CC,CT,TT		15.2643,14.6656,15.0755		152/2180	14859356	1816,10230	1899	4124	6023	SO:0001819	synonymous_variant	158326	exon5			AATCGCTTGGGAC	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.456A>G	9.37:g.14859356T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			T|0.752;C|0.248	0.248	strong		0.473	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
CDC27	996	hgsc.bcm.edu	37	17	45234301	45234301	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45234301C>A	ENST00000066544.3	-	7	913	c.820G>T	c.(820-822)Gct>Tct	p.A274S	CDC27_ENST00000527547.1_Missense_Mutation_p.A274S|CDC27_ENST00000446365.2_Missense_Mutation_p.A213S|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Missense_Mutation_p.A274S	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	274					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.A274S(3)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						GGACTAAGAGCTGCTGGTCCT	0.363																																					p.A274S		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,+1,10	CDC27	337	10	3	Substitution - Missense(3)	prostate(3)	c.G820T						scavenged	.						62.0	65.0	64.0					17																	45234301		2201	4292	6493	SO:0001583	missense	996	exon7			TAAGAGCTGCTGG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.820G>T	17.37:g.45234301C>A	ENSP00000066544:p.Ala274Ser	Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	63	2	0.031746	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.125822	0.37533	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.3;-0.05;-0.31;0.78	5.64	4.68	0.58851	.	0.058237	0.64402	D	0.000002	T	0.46171	0.1379	N	0.11560	0.145	0.50039	D	0.999845	B;B;B;B	0.23442	0.085;0.079;0.073;0.003	B;B;B;B	0.22880	0.013;0.028;0.042;0.004	T	0.36212	-0.9757	10	0.25106	T	0.35	-20.3108	12.4418	0.55629	0.0:0.9186:0.0:0.0814	.	213;274;274;274	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	274;274;213;274;274	ENSP00000066544:A274S;ENSP00000434614:A274S;ENSP00000392802:A213S;ENSP00000437339:A274S;ENSP00000432105:A274S	ENSP00000066544:A274S	A	-	1	0	CDC27	42589300	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.048000	0.41278	1.400000	0.46741	0.460000	0.39030	GCT	.	.	none		0.363	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
ARSD	414	hgsc.bcm.edu	37	X	2835863	2835863	+	Missense_Mutation	SNP	G	G	T	rs78034736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2835863G>T	ENST00000381154.1	-	5	920	c.845C>A	c.(844-846)gCt>gAt	p.A282D	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	282					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ATAGGAAACAGCTTCCTTTAG	0.512																																					p.A282D		Atlas-SNP	.											.	ARSD	47	.	0			c.C845A						PASS	.						47.0	40.0	42.0					X																	2835863		2203	4300	6503	SO:0001583	missense	414	exon5			GAAACAGCTTCCT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.845C>A	X.37:g.2835863G>T	ENSP00000370546:p.Ala282Asp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	131	0.07896323086196504	63	0.13577586206896552	45	0.1271186440677966	28	0.0498220640569395	68	0.0913978494623656	g	15.63	2.889517	0.52014	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.95949	-3.86	3.36	3.36	0.38483	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.199306	0.41294	U	0.000909	T	0.50633	0.1627	H	0.99712	4.72	0.09310	P	0.999999469392	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.971	T	0.55522	-0.8128	9	0.87932	D	0	.	14.3198	0.66479	0.0:0.0:1.0:0.0	.	282;282	E9PAW5;P51689	.;ARSD_HUMAN	D	282	ENSP00000370546:A282D	ENSP00000217890:A282D	A	-	2	0	ARSD	2845863	1.000000	0.71417	0.008000	0.14137	0.274000	0.26718	6.148000	0.71788	1.338000	0.45544	0.281000	0.19383	GCT	G|0.920;T|0.080	0.080	strong		0.512	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
SMC6	79677	hgsc.bcm.edu	37	2	17884495	17884495	+	Missense_Mutation	SNP	C	C	T	rs1065381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:17884495C>T	ENST00000448223.2	-	19	2340	c.2071G>A	c.(2071-2073)Gcc>Acc	p.A691T	SMC6_ENST00000351948.4_Missense_Mutation_p.A691T|SMC6_ENST00000381272.4_Missense_Mutation_p.A717T|SMC6_ENST00000402989.1_Missense_Mutation_p.A691T	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	691			A -> T (in dbSNP:rs1065381). {ECO:0000269|PubMed:11408570, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTTTCAAGGGCAGATAAATGT	0.299													C|||	1034	0.20647	0.3548	0.2161	5008	,	,		14389	0.0119		0.3241	False		,,,				2504	0.0787				p.A691T		Atlas-SNP	.											.	SMC6	102	.	0			c.G2071A						PASS	.	C	THR/ALA,THR/ALA	1395,3009	438.0+/-345.2	215,965,1022	78.0	82.0	81.0		2071,2071	1.5	1.0	2	dbSNP_86	81	2866,5730	447.2+/-361.5	471,1924,1903	yes	missense,missense	SMC6	NM_001142286.1,NM_024624.5	58,58	686,2889,2925	TT,TC,CC		33.3411,31.6757,32.7769	benign,benign	691/1092,691/1092	17884495	4261,8739	2202	4298	6500	SO:0001583	missense	79677	exon19			CAAGGGCAGATAA	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.2071G>A	2.37:g.17884495C>T	ENSP00000404092:p.Ala691Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	91	88	0.967033	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	492	0.22527472527472528	153	0.31097560975609756	89	0.24585635359116023	12	0.02097902097902098	238	0.31398416886543534	C	9.006	0.981245	0.18812	0.316757	0.333411	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.31769	1.57;1.57;1.57;1.57;1.48	5.75	1.55	0.23275	RecF/RecN/SMC (1);	0.528124	0.23204	N	0.050752	T	0.00012	0.0000	N	0.08118	0	0.39475	P	0.032214999999999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.002;0.003;0.002	T	0.46830	-0.9163	9	0.16420	T	0.52	.	4.2671	0.10768	0.2883:0.4449:0.0:0.2668	rs1065381;rs52791607;rs57702280;rs1065381	717;717;691	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	T	691;691;717;691;717	ENSP00000404092:A691T;ENSP00000323439:A691T;ENSP00000370672:A717T;ENSP00000384539:A691T;ENSP00000408644:A717T	ENSP00000323439:A691T	A	-	1	0	SMC6	17747976	1.000000	0.71417	0.990000	0.47175	0.186000	0.23388	0.736000	0.26130	0.371000	0.24564	0.579000	0.79373	GCC	C|0.738;T|0.262	0.262	strong		0.299	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	
NPHS1	4868	hgsc.bcm.edu	37	19	36322270	36322270	+	Silent	SNP	C	C	T	rs2071327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36322270C>T	ENST00000378910.5	-	26	3314	c.3315G>A	c.(3313-3315)tcG>tcA	p.S1105S	NPHS1_ENST00000353632.6_Silent_p.S1065S	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	1105					cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGTCCTCTTCCGACCTTCCAG	0.592													C|||	1841	0.367612	0.0545	0.3919	5008	,	,		16215	0.6716		0.3668	False		,,,				2504	0.4611				p.S1105S		Atlas-SNP	.											.	NPHS1	165	.	0			c.G3315A						PASS	.	C		470,3936	223.0+/-239.6	24,422,1757	102.0	101.0	101.0		3315	-3.4	1.0	19	dbSNP_96	101	3300,5300	494.0+/-373.7	634,2032,1634	no	coding-synonymous	NPHS1	NM_004646.3		658,2454,3391	TT,TC,CC		38.3721,10.6673,28.9866		1105/1242	36322270	3770,9236	2203	4300	6503	SO:0001819	synonymous_variant	4868	exon26			CTCTTCCGACCTT		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.3315G>A	19.37:g.36322270C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_004646	A6NDH2|C3RX61	Silent	SNP	ENST00000378910.5	37	CCDS32996.1																																																																																			C|0.682;T|0.318	0.318	strong		0.592	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
SLC1A7	6512	hgsc.bcm.edu	37	1	53553754	53553754	+	Missense_Mutation	SNP	T	T	C	rs1288401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:53553754T>C	ENST00000371494.4	-	11	1737	c.1610A>G	c.(1609-1611)cAg>cGg	p.Q537R	RP11-334A14.5_ENST00000447867.1_RNA|SLC1A7_ENST00000488036.1_5'UTR	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	537			Q -> R (in dbSNP:rs1288401). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9108121, ECO:0000269|Ref.3}.		dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.Q537R(1)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		CTCCTCATCCTGCTCCACTTG	0.647													T|||	2054	0.410144	0.1498	0.4798	5008	,	,		18341	0.2966		0.7336	False		,,,				2504	0.4969				p.Q537R	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											SLC1A7,NS,carcinoma,-1,2	SLC1A7	65	2	1	Substitution - Missense(1)	stomach(1)	c.A1610G						PASS	.	T	ARG/GLN	1154,3252	406.2+/-333.8	169,816,1218	49.0	49.0	49.0		1610	5.8	1.0	1	dbSNP_87	49	6267,2333	702.1+/-405.3	2295,1677,328	yes	missense	SLC1A7	NM_006671.4	43	2464,2493,1546	CC,CT,TT		27.1279,26.1916,42.9417	benign	537/561	53553754	7421,5585	2203	4300	6503	SO:0001583	missense	6512	exon11			TCATCCTGCTCCA	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"""Solute carriers"""	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.1610A>G	1.37:g.53553754T>C	ENSP00000360549:p.Gln537Arg	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	277	275	0.99278	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Missense_Mutation	SNP	ENST00000371494.4	37	CCDS574.1	995	0.4555860805860806	79	0.16056910569105692	194	0.5359116022099447	161	0.28146853146853146	561	0.7401055408970977	T	12.30	1.896960	0.33535	0.261916	0.728721	ENSG00000162383	ENST00000371494	T	0.49139	0.79	5.76	5.76	0.90799	.	0.214942	0.40222	N	0.001153	T	0.00012	0.0000	N	0.17082	0.46	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29792	-1.0000	9	0.22109	T	0.4	-19.937	16.0916	0.81094	0.0:0.0:0.0:1.0	rs1288401;rs1679919;rs61182428;rs1288401	537	O00341	EAA5_HUMAN	R	537	ENSP00000360549:Q537R	ENSP00000360549:Q537R	Q	-	2	0	SLC1A7	53326342	1.000000	0.71417	0.999000	0.59377	0.586000	0.36452	4.223000	0.58587	2.186000	0.69663	0.533000	0.62120	CAG	T|0.467;C|0.533	0.533	strong		0.647	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671	
LAMA3	3909	hgsc.bcm.edu	37	18	21496533	21496533	+	Silent	SNP	C	C	T	rs61751706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21496533C>T	ENST00000313654.9	+	60	8038	c.7797C>T	c.(7795-7797)gaC>gaT	p.D2599D	LAMA3_ENST00000399516.3_Silent_p.D2543D|LAMA3_ENST00000269217.6_Silent_p.D990D|LAMA3_ENST00000587184.1_Silent_p.D934D|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2599	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AAGAGTCAGACAAAAATTATT	0.423													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18308	0.0		0.004	False		,,,				2504	0.0				p.D2599D		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7797T						PASS	.	C	,,,	5,4401	9.9+/-24.2	0,5,2198	161.0	149.0	153.0		2970,7629,2802,7797	5.2	1.0	18	dbSNP_129	153	60,8540	37.8+/-93.5	1,58,4241	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	1,63,6439	TT,TC,CC		0.6977,0.1135,0.4998	,,,	990/1725,2543/3278,934/1669,2599/3334	21496533	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon60			GTCAGACAAAAAT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7797C>T	18.37:g.21496533C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.995;T|0.005	0.005	strong		0.423	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
PDE4C	5143	hgsc.bcm.edu	37	19	18333062	18333062	+	Missense_Mutation	SNP	C	C	T	rs146818532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18333062C>T	ENST00000355502.3	-	6	1185	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	PDE4C_ENST00000447275.3_5'UTR|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000262805.12_Missense_Mutation_p.R73Q|PDE4C_ENST00000597297.1_5'Flank|PDE4C_ENST00000594465.3_Missense_Mutation_p.R105Q|PDE4C_ENST00000594617.3_Missense_Mutation_p.R105Q|PDE4C_ENST00000598111.2_5'Flank|PDE4C_ENST00000539010.1_5'Flank			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	105					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CTGCATAATCCGGCCCAGGCC	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18538	0.0		0.0	False		,,,				2504	0.0031				p.R105Q		Atlas-SNP	.											.	PDE4C	80	.	0			c.G314A						PASS	.	C	GLN/ARG,GLN/ARG,	4,4402	8.1+/-20.4	0,4,2199	49.0	49.0	49.0		314,218,	-1.8	0.0	19	dbSNP_134	49	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,utr-5	PDE4C	NM_000923.4,NM_001098818.2,NM_001098819.2	43,43,	0,7,6496	TT,TC,CC		0.0349,0.0908,0.0538	benign,benign,	105/713,73/681,	18333062	7,12999	2203	4300	6503	SO:0001583	missense	5143	exon3			ATAATCCGGCCCA		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"""Phosphodiesterases"""	8782	protein-coding gene	gene with protein product	"""phosphodiesterase E1 dunce homolog (Drosophila)"""	600128	"""phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"""	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.314G>A	19.37:g.18333062C>T	ENSP00000347689:p.Arg105Gln	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	37	CCDS12373.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	11.09	1.537093	0.27475	9.08E-4	3.49E-4	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000543547	T;T	0.69926	0.96;-0.44	4.13	-1.8	0.07907	.	0.902683	0.09345	N	0.814920	T	0.48714	0.1515	L	0.33485	1.01	0.80722	D	1	B;B;B	0.21905	0.054;0.062;0.003	B;B;B	0.13407	0.006;0.007;0.009	T	0.41787	-0.9489	10	0.62326	D	0.03	.	3.6337	0.08141	0.3236:0.2868:0.0:0.3896	.	214;105;73	B7Z2S3;Q08493;Q08493-3	.;PDE4C_HUMAN;.	Q	184;105;93;73;214	ENSP00000347689:R105Q;ENSP00000262805:R73Q	ENSP00000262805:R73Q	R	-	2	0	PDE4C	18194062	0.995000	0.38212	0.032000	0.17829	0.140000	0.21249	3.332000	0.52083	-0.112000	0.11979	0.306000	0.20318	CGG	C|0.999;T|0.001	0.001	strong		0.617	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1		
ZNF419	79744	hgsc.bcm.edu	37	19	58003580	58003580	+	Splice_Site	SNP	A	A	G	rs2074071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58003580A>G	ENST00000221735.7	+	4	484		c.e4+1		ZNF419_ENST00000424930.2_Splice_Site|ZNF419_ENST00000354197.4_Splice_Site|ZNF419_ENST00000518999.1_Missense_Mutation_p.D101G|ZNF419_ENST00000415379.2_Intron|ZNF419_ENST00000426954.2_Splice_Site|ZNF419_ENST00000520540.1_Missense_Mutation_p.D88G|ZNF419_ENST00000442920.2_Splice_Site|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000347466.6_Intron			Q96HQ0	ZN419_HUMAN	zinc finger protein 419						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		ATACCGAGAGATAGTTGGTGG	0.512													G|||	3483	0.695487	0.5787	0.7262	5008	,	,		18447	0.6984		0.6839	False		,,,				2504	0.8405				.		Atlas-SNP	.											.	ZNF419	134	.	0			c.298+1A>G						PASS	.	G	,,,,,,	2622,1784	526.0+/-371.8	781,1060,362	128.0	123.0	125.0		,,,,,,	1.0	0.0	19	dbSNP_96	125	5972,2628	425.1+/-354.9	2037,1898,365	yes	splice-5,splice-5,splice-5,intron,intron,intron,splice-5	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	,,,,,,	2818,2958,727	GG,GA,AA		30.5581,40.4902,33.9228	,,,,,,	,,,,,,	58003580	8594,4412	2203	4300	6503	SO:0001630	splice_region_variant	79744	exon4			CGAGAGATAGTTG	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.298+1A>G	19.37:g.58003580A>G		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	286	132	0.461538	NM_024691	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Splice_Site	SNP	ENST00000221735.7	37	CCDS54326.1	1477|1477	0.6762820512820513|0.6762820512820513	290|290	0.5894308943089431|0.5894308943089431	258|258	0.712707182320442|0.712707182320442	410|410	0.7167832167832168|0.7167832167832168	519|519	0.6846965699208444|0.6846965699208444	G|G	4.342|4.342	0.062814|0.062814	0.08388|0.08388	0.595098|0.595098	0.694419|0.694419	ENSG00000105136|ENSG00000105136	ENST00000524372;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000221735|ENST00000520540;ENST00000518999	.|T;T	.|0.00824	.|5.65;5.66	2.05|2.05	0.994|0.994	0.19832|0.19832	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.47698|0.47698	P|P	5.039999999999489E-4|5.039999999999489E-4	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00130	.|-1.2015	.|4	.|.	.|.	.|.	.|.	4.4421|4.4421	0.11579|0.11579	0.3501:0.0:0.6499:0.0|0.3501:0.0:0.6499:0.0	rs2074071;rs52831388;rs58264934;rs2074071|rs2074071;rs52831388;rs58264934;rs2074071	.|.	.|.	.|.	.|G	-1|88;101	.|ENSP00000429471:D88G;ENSP00000427723:D101G	.|.	.|D	+|+	.|2	.|0	ZNF419|ZNF419	62695392|62695392	0.004000|0.004000	0.15560|0.15560	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	0.110000|0.110000	0.15437|0.15437	0.023000|0.023000	0.15187|0.15187	-0.479000|-0.479000	0.04858|0.04858	.|GAT	A|0.324;G|0.676	0.676	strong		0.512	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	Intron
C6orf1	221491	hgsc.bcm.edu	37	6	34214348	34214348	+	Missense_Mutation	SNP	C	C	T	rs34410712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:34214348C>T	ENST00000476320.1	-	5	1105	c.423G>A	c.(421-423)atG>atA	p.M141I	C6orf1_ENST00000413013.2_Missense_Mutation_p.M121I|C6orf1_ENST00000468145.1_Missense_Mutation_p.M141I|C6orf1_ENST00000335352.3_Missense_Mutation_p.M121I|C6orf1_ENST00000481533.1_Missense_Mutation_p.M141I|C6orf1_ENST00000394990.4_Missense_Mutation_p.M141I	NM_001008703.1	NP_001008703.1	Q86T20	CF001_HUMAN	chromosome 6 open reading frame 1	141			M -> I (in dbSNP:rs34410712).			extracellular region (GO:0005576)				endometrium(1)|prostate(1)	2		Ovarian(999;0.0228)		BRCA - Breast invasive adenocarcinoma(397;1.11e-10)		AGCCTCTTCCCATGAGTGCCT	0.612													c|||	186	0.0371406	0.0121	0.0461	5008	,	,		17223	0.0089		0.0795	False		,,,				2504	0.0501				p.M141I		Atlas-SNP	.											.	C6orf1	6	.	0			c.G423A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET	103,4303	80.4+/-118.8	2,99,2102	42.0	44.0	43.0		423,423,423	-2.1	0.0	6	dbSNP_126	43	662,7938	165.8+/-217.9	26,610,3664	yes	missense,missense,missense	C6orf1	NM_178508.3,NM_001008704.1,NM_001008703.1	10,10,10	28,709,5766	TT,TC,CC		7.6977,2.3377,5.8819	benign,benign,benign	141/160,141/160,141/160	34214348	765,12241	2203	4300	6503	SO:0001583	missense	221491	exon5			TCTTCCCATGAGT	AY062936	CCDS4790.1, CCDS75433.1	6p21.3	2011-12-12			ENSG00000186577	ENSG00000186577			1340	protein-coding gene	gene with protein product		611419				10036196	Standard	NM_178508		Approved	LBH, MGC57858	uc003ojh.3	Q86T20	OTTHUMG00000159754	ENST00000476320.1:c.423G>A	6.37:g.34214348C>T	ENSP00000417604:p.Met141Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	71	43	0.605634	NM_001008704	A8K299	Missense_Mutation	SNP	ENST00000476320.1	37	CCDS4790.1	104	0.047619047619047616	10	0.02032520325203252	24	0.06629834254143646	1	0.0017482517482517483	69	0.09102902374670185	C	2.843	-0.240033	0.05944	0.023377	0.076977	ENSG00000186577	ENST00000476320;ENST00000335352;ENST00000394990;ENST00000481533;ENST00000413013;ENST00000468145	T;T;T;T;T;T	0.32988	1.44;1.43;1.44;1.44;1.43;1.44	1.36	-2.1	0.07210	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.80722	P	0.0	B	0.27823	0.19	B	0.17098	0.017	T	0.33752	-0.9856	8	0.87932	D	0	.	2.8005	0.05413	0.4448:0.3238:0.2315:0.0	rs34410712	141	Q86T20	CF001_HUMAN	I	141;121;141;141;121;141	ENSP00000417604:M141I;ENSP00000334260:M121I;ENSP00000378441:M141I;ENSP00000418062:M141I;ENSP00000387460:M121I;ENSP00000418884:M141I	ENSP00000334260:M121I	M	-	3	0	C6orf1	34322326	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.980000	0.03770	-0.599000	0.05798	0.453000	0.30009	ATG	C|0.947;T|0.053	0.053	strong		0.612	C6orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357175.1	NM_178508	
CCT6B	10693	hgsc.bcm.edu	37	17	33288363	33288363	+	Missense_Mutation	SNP	C	C	T	rs9635769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:33288363C>T	ENST00000314144.5	-	1	165	c.50G>A	c.(49-51)cGg>cAg	p.R17Q	CCT6B_ENST00000421975.3_Missense_Mutation_p.R17Q|ZNF830_ENST00000361952.3_5'Flank|CCT6B_ENST00000436961.3_Missense_Mutation_p.R17Q	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	17			R -> Q (in dbSNP:rs9635769). {ECO:0000269|PubMed:15489334}.		chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				CAAAGCTGCCCGGGCCCGCGC	0.557													T|||	2748	0.548722	0.292	0.4813	5008	,	,		18148	0.8353		0.5696	False		,,,				2504	0.6268				p.R17Q		Atlas-SNP	.											CCT6B,caecum,carcinoma,0,3	CCT6B	63	3	0			c.G50A						PASS	.	T	GLN/ARG,GLN/ARG,GLN/ARG	1401,3005	653.7+/-399.6	225,951,1027	37.0	41.0	40.0		50,50,50	0.6	1.0	17	dbSNP_119	40	4973,3627	498.6+/-374.8	1434,2105,761	yes	missense,missense,missense	CCT6B	NM_001193529.1,NM_001193530.1,NM_006584.3	43,43,43	1659,3056,1788	TT,TC,CC		42.1744,31.7975,49.0082	benign,benign,benign	17/494,17/486,17/531	33288363	6374,6632	2203	4300	6503	SO:0001583	missense	10693	exon1			GCTGCCCGGGCCC	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.50G>A	17.37:g.33288363C>T	ENSP00000327191:p.Arg17Gln	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	55	54	0.981818	NM_006584	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	1234	0.565018315018315	155	0.3150406504065041	178	0.49171270718232046	467	0.8164335664335665	434	0.5725593667546174	T	3.321	-0.138708	0.06669	0.317975	0.578256	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.11277	2.79;2.79;2.79	5.23	0.553	0.17235	.	0.173536	0.53938	N	0.000060	T	0.00012	0.0000	N	0.05383	-0.06	0.48975	P	2.6199999999998447E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.07177	-1.0786	9	0.22706	T	0.39	0.002	9.5733	0.39442	0.0:0.3838:0.0:0.6162	rs9635769;rs11552271;rs17856746;rs17856769;rs60052983;rs9635769	17;17;17	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	Q	17	ENSP00000398044:R17Q;ENSP00000327191:R17Q;ENSP00000400917:R17Q	ENSP00000327191:R17Q	R	-	2	0	CCT6B	30312476	1.000000	0.71417	0.994000	0.49952	0.350000	0.29205	1.629000	0.37071	-0.266000	0.09339	-0.254000	0.11334	CGG	C|0.481;T|0.519	0.519	strong		0.557	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584	
ALPK2	115701	hgsc.bcm.edu	37	18	56204671	56204671	+	Missense_Mutation	SNP	A	A	T	rs4940404	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204671A>T	ENST00000361673.3	-	5	2961	c.2748T>A	c.(2746-2748)aaT>aaA	p.N916K	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	916			N -> K (in dbSNP:rs4940404). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GGTAGGTGGAATTCTCCACCT	0.507													A|||	2024	0.404153	0.4312	0.4294	5008	,	,		19055	0.2361		0.5726	False		,,,				2504	0.3497				p.N916K		Atlas-SNP	.											ALPK2_ENST00000361673,NS,carcinoma,-1,2	ALPK2	487	2	0			c.T2748A						PASS	.	A	LYS/ASN	1984,2422	556.3+/-379.5	446,1092,665	75.0	75.0	75.0		2748	2.8	0.1	18	dbSNP_111	75	4592,4008	597.8+/-393.8	1238,2116,946	yes	missense	ALPK2	NM_052947.3	94	1684,3208,1611	TT,TA,AA		46.6047,45.0295,49.4387	probably-damaging	916/2171	56204671	6576,6430	2203	4300	6503	SO:0001583	missense	115701	exon5			GGTGGAATTCTCC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2748T>A	18.37:g.56204671A>T	ENSP00000354991:p.Asn916Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	935	0.4281135531135531	186	0.3780487804878049	184	0.5082872928176796	136	0.23776223776223776	429	0.5659630606860159	A	17.15	3.314820	0.60524	0.450295	0.533953	ENSG00000198796	ENST00000361673	T	0.54279	0.58	5.57	2.8	0.32819	.	0.657975	0.14928	N	0.290234	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P;P	0.46912	0.886;0.59	B;B	0.42245	0.381;0.197	T	0.48186	-0.9057	9	0.54805	T	0.06	-3.5085	5.5695	0.17188	0.724:0.1763:0.0996:0.0	rs4940404;rs52809276;rs56910431;rs4940404	916;916	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	K	916	ENSP00000354991:N916K	ENSP00000354991:N916K	N	-	3	2	ALPK2	54355651	0.000000	0.05858	0.051000	0.19133	0.023000	0.10783	-0.367000	0.07553	0.915000	0.36847	0.482000	0.46254	AAT	A|0.514;T|0.486	0.486	strong		0.507	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
CCDC180	100499483	hgsc.bcm.edu	37	9	100122291	100122291	+	Missense_Mutation	SNP	T	T	C	rs3747495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100122291T>C	ENST00000357054.1	+	37	4371	c.3436T>C	c.(3436-3438)Ttc>Ctc	p.F1146L	CCDC180_ENST00000529487.1_Missense_Mutation_p.F1175L|CCDC180_ENST00000395220.1_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.F1175L			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1146			F -> L (in dbSNP:rs3747495).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.F1146L(1)									ACTCCTCAGCTTCGTCCAAAC	0.507													T|||	1159	0.23143	0.1369	0.3444	5008	,	,		21733	0.2907		0.1879	False		,,,				2504	0.2628				p.F1175L		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T3523C						scavenged	.	T	LEU/PHE	618,3788	267.7+/-268.0	42,534,1627	166.0	166.0	166.0		3523	3.4	0.0	9	dbSNP_107	166	1588,7012	298.5+/-303.9	142,1304,2854	yes	missense	C9orf174	NM_020893.2	22	184,1838,4481	CC,CT,TT		18.4651,14.0263,16.9614	benign	1175/1702	100122291	2206,10800	2203	4300	6503	SO:0001583	missense	0	exon26			CTCAGCTTCGTCC	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.3436T>C	9.37:g.100122291T>C	ENSP00000349562:p.Phe1146Leu	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	178	85	0.477528	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		508	0.2326007326007326	52	0.10569105691056911	128	0.35359116022099446	174	0.3041958041958042	154	0.20316622691292877	T	12.99	2.103262	0.37145	0.140263	0.184651	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.08102	3.13;3.15;3.15	5.71	3.39	0.38822	.	0.472963	0.25919	N	0.027445	T	0.00012	0.0000	L	0.27053	0.805	0.54753	P	1.0999999999983245E-5	B;B	0.33637	0.119;0.42	B;B	0.32090	0.097;0.14	T	0.45366	-0.9266	9	0.10377	T	0.69	-2.0155	6.8103	0.23801	0.0:0.192:0.0:0.808	rs3747495;rs13302501;rs17583370;rs52794397;rs61215609;rs3747495	1314;1146	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	L	1146;1175;1175	ENSP00000349562:F1146L;ENSP00000364348:F1175L;ENSP00000434727:F1175L	ENSP00000349562:F1146L	F	+	1	0	C9orf174	99162112	0.676000	0.27567	0.002000	0.10522	0.031000	0.12232	1.588000	0.36633	0.544000	0.28883	0.459000	0.35465	TTC	T|0.807;C|0.193	0.193	strong		0.507	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416918	105416918	+	Missense_Mutation	SNP	T	T	C	rs71421895	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105416918T>C	ENST00000333244.5	-	7	4989	c.4870A>G	c.(4870-4872)Atg>Gtg	p.M1624V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1624						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TCCACCTCCATGCTGGACAGA	0.617													.|||	105	0.0209665	0.0083	0.0303	5008	,	,		15977	0.0		0.0626	False		,,,				2504	0.0102				p.M1624V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A4870G						PASS	.	C	VAL/MET	68,3616		6,56,1780	98.0	116.0	110.0		4870	-0.3	0.0	14	dbSNP_130	110	520,7558		70,380,3589	no	missense	AHNAK2	NM_138420.2	21	76,436,5369	CC,CT,TT		6.4372,1.8458,4.9991	benign	1624/5796	105416918	588,11174	1842	4039	5881	SO:0001583	missense	113146	exon7			CCTCCATGCTGGA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4870A>G	14.37:g.105416918T>C	ENSP00000353114:p.Met1624Val	Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	409	199	0.486553	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	63	0.028846153846153848	6	0.012195121951219513	14	0.03867403314917127	0	0.0	43	0.05672823218997362	t	0.542	-0.852996	0.02630	0.018458	0.064372	ENSG00000185567	ENST00000333244	T	0.01068	5.38	4.15	-0.264	0.12950	.	.	.	.	.	T	0.00039	0.0001	N	0.00500	-1.43	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.40683	-0.9550	9	0.02654	T	1	.	0.5714	0.00696	0.2481:0.3017:0.1217:0.3285	.	1624	Q8IVF2	AHNK2_HUMAN	V	1624	ENSP00000353114:M1624V	ENSP00000353114:M1624V	M	-	1	0	AHNAK2	104487963	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.972000	0.03802	-0.871000	0.04042	-1.493000	0.00968	ATG	T|0.965;C|0.035	0.035	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SPEM1	374768	hgsc.bcm.edu	37	17	7324852	7324852	+	Silent	SNP	C	C	G	rs34333422	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7324852C>G	ENST00000323675.3	+	3	883	c.858C>G	c.(856-858)ccC>ccG	p.P286P	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	286					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				GCTGCTACCCCCTAGCCTCTG	0.587													C|||	408	0.0814696	0.0643	0.0836	5008	,	,		17635	0.1161		0.0746	False		,,,				2504	0.0746				p.P286P		Atlas-SNP	.											SPEM1,NS,carcinoma,+2,1	SPEM1	41	1	0			c.C858G						PASS	.	C		249,3653		9,231,1711	27.0	31.0	29.0		858	-8.3	0.0	17	dbSNP_126	29	549,7723		33,483,3620	no	coding-synonymous	SPEM1	NM_199339.2		42,714,5331	GG,GC,CC		6.6368,6.3813,6.555		286/310	7324852	798,11376	1951	4136	6087	SO:0001819	synonymous_variant	374768	exon3			CTACCCCCTAGCC	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"""chromosome 17 open reading frame 83"""	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.858C>G	17.37:g.7324852C>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	27	10	0.37037	NM_199339		Silent	SNP	ENST00000323675.3	37	CCDS42254.1																																																																																			C|0.922;G|0.078	0.078	strong		0.587	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339	
OBSCN	84033	hgsc.bcm.edu	37	1	228482010	228482010	+	Silent	SNP	C	C	T	rs449133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228482010C>T	ENST00000422127.1	+	42	11333	c.11289C>T	c.(11287-11289)gaC>gaT	p.D3763D	OBSCN_ENST00000284548.11_Silent_p.D3763D|OBSCN_ENST00000570156.2_Silent_p.D4192D|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000359599.6_Silent_p.D2610D|OBSCN_ENST00000366709.4_Silent_p.D882D|OBSCN_ENST00000366707.4_Silent_p.D882D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3763	Ig-like 38.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGAGGCAGGACGGGTCCAGGT	0.652													C|||	1913	0.381989	0.472	0.4179	5008	,	,		20851	0.247		0.4821	False		,,,				2504	0.271				p.D4192D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C12576T						PASS	.	C	,	1786,2524		398,990,767	144.0	151.0	149.0		11289,11289	-9.9	0.0	1	dbSNP_80	149	4209,4289		1075,2059,1115	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1473,3049,1882	TT,TC,CC		49.5293,41.4385,46.8067	,	3763/7969,3763/6621	228482010	5995,6813	2155	4249	6404	SO:0001819	synonymous_variant	84033	exon47			GCAGGACGGGTCC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11289C>T	1.37:g.228482010C>T		Somatic	332	1	0.00301205		WXS	Illumina HiSeq	Phase_I	370	175	0.472973	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.595;T|0.405	0.405	strong		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
QRICH1	54870	hgsc.bcm.edu	37	3	49067904	49067904	+	Missense_Mutation	SNP	T	T	C	rs61729488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49067904T>C	ENST00000395443.2	-	10	2784	c.2312A>G	c.(2311-2313)aAt>aGt	p.N771S	IMPDH2_ENST00000326739.4_5'Flank|RP13-131K19.6_ENST00000607245.1_RNA|QRICH1_ENST00000424300.1_Missense_Mutation_p.N771S|QRICH1_ENST00000479449.1_5'Flank|QRICH1_ENST00000357496.2_Missense_Mutation_p.N771S	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	771						nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		AGTGCTTGCATTGGCCACTGC	0.498													T|||	226	0.0451278	0.0023	0.0648	5008	,	,		16622	0.0258		0.1123	False		,,,				2504	0.0399				p.N771S		Atlas-SNP	.											.	QRICH1	48	.	0			c.A2312G						PASS	.	T	SER/ASN,SER/ASN	95,4311	78.3+/-116.7	0,95,2108	71.0	66.0	68.0		2312,2312	-7.8	0.0	3	dbSNP_129	68	897,7703	201.8+/-245.2	46,805,3449	yes	missense,missense	QRICH1	NM_017730.2,NM_198880.1	46,46	46,900,5557	CC,CT,TT		10.4302,2.1562,7.6272	benign,benign	771/777,771/777	49067904	992,12014	2203	4300	6503	SO:0001583	missense	54870	exon10			CTTGCATTGGCCA		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.2312A>G	3.37:g.49067904T>C	ENSP00000378830:p.Asn771Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_198880	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	37	CCDS2787.1	136	0.06227106227106227	3	0.006097560975609756	28	0.07734806629834254	21	0.03671328671328671	84	0.11081794195250659	T	8.934	0.964142	0.18583	0.021562	0.104302	ENSG00000198218	ENST00000395443;ENST00000357496;ENST00000424300	.	.	.	5.51	-7.76	0.01232	.	0.621497	0.19226	N	0.119548	T	0.00328	0.0010	N	0.02011	-0.69	0.50813	P	1.0500000000002174E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.10543	-1.0625	8	0.13470	T	0.59	0.0377	18.0993	0.89500	0.0:0.6291:0.0:0.3709	.	771	Q2TAL8	QRIC1_HUMAN	S	771	.	ENSP00000350094:N771S	N	-	2	0	QRICH1	49042908	0.001000	0.12720	0.005000	0.12908	0.987000	0.75469	-0.223000	0.09177	-1.548000	0.01712	-0.256000	0.11100	AAT	T|0.927;C|0.073	0.073	strong		0.498	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730	
ZNF737	100129842	hgsc.bcm.edu	37	19	20736639	20736639	+	Silent	SNP	C	C	T	rs111988999	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20736639C>T	ENST00000427401.4	-	2	100	c.6G>A	c.(4-6)ggG>ggA	p.G2G	ZNF737_ENST00000596797.1_Silent_p.G2G|CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						ATTGCAATGGCCCCTGAAACA	0.408													t|||	295	0.0589058	0.2118	0.0216	5008	,	,		14230	0.0		0.0	False		,,,				2504	0.0				p.G2G		Atlas-SNP	.											.	ZNF737	50	.	0			c.G6A						PASS	.	T		248,1136		23,202,467	30.0	27.0	28.0		6	-1.6	0.0	19	dbSNP_132	28	3,3179		0,3,1588	no	coding-synonymous	ZNF737	NM_001159293.1		23,205,2055	TT,TC,CC		0.0943,17.9191,5.4972		2/537	20736639	251,4315	692	1591	2283	SO:0001819	synonymous_variant	100129842	exon2			CAATGGCCCCTGA	BC015765	CCDS54238.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.6G>A	19.37:g.20736639C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_001159293	C9JHM3	Silent	SNP	ENST00000427401.4	37	CCDS54238.1																																																																																			C|0.940;T|0.060	0.060	strong		0.408	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289	
PCDHGA2	56113	hgsc.bcm.edu	37	5	140720954	140720954	+	Missense_Mutation	SNP	T	T	C	rs66823521	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140720954T>C	ENST00000394576.2	+	1	2416	c.2416T>C	c.(2416-2418)Ttt>Ctt	p.F806L	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_5'Flank	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	806					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAAGAAACGTTTTCTCAGGT	0.393													t|||	223	0.0445288	0.0076	0.085	5008	,	,		21252	0.001		0.1292	False		,,,				2504	0.0235				p.F806L		Atlas-SNP	.											PCDHG_cluster,NS,carcinoma,-2,2	PCDHGA2	205	2	0			c.T2416C						PASS	.	T	,LEU/PHE,LEU/PHE	119,4283		1,117,2083	60.0	64.0	63.0		,2416,2416	-0.9	0.0	5	dbSNP_130	63	1136,7464		65,1006,3229	yes	intron,missense,missense	PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_032009.1	,22,22	66,1123,5312	CC,CT,TT		13.2093,2.7033,9.6524	,,	,806/933,806/824	140720954	1255,11747	2201	4300	6501	SO:0001583	missense	56113	exon1			GAAACGTTTTCTC	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.2416T>C	5.37:g.140720954T>C	ENSP00000378077:p.Phe806Leu	Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	277	174	0.628159	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	37	CCDS47289.1	123	0.05631868131868132	4	0.008130081300813009	29	0.08011049723756906	0	0.0	90	0.11873350923482849	.	0.234	-1.018508	0.02078	0.027033	0.132093	ENSG00000081853	ENST00000394576	T	0.42900	0.96	3.35	-0.876	0.10624	.	1.381570	0.05478	N	0.554274	T	0.00109	0.0003	N	0.00666	-1.275	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.12863	-1.0531	9	0.06099	T	0.92	.	1.4049	0.02279	0.2755:0.0896:0.1576:0.4774	.	806;806	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	L	806	ENSP00000378077:F806L	ENSP00000378077:F806L	F	+	1	0	PCDHGA2	140701138	0.003000	0.15002	0.004000	0.12327	0.030000	0.12068	0.938000	0.28965	-0.250000	0.09555	0.402000	0.26972	TTT	T|0.910;C|0.090	0.090	strong		0.393	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
TRIM65	201292	hgsc.bcm.edu	37	17	73887089	73887089	+	Missense_Mutation	SNP	C	C	T	rs61754864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73887089C>T	ENST00000269383.3	-	6	1390	c.1325G>A	c.(1324-1326)cGc>cAc	p.R442H		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	442	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCCTGGGAGGCGCTGGGCTTC	0.687													C|||	4	0.000798722	0.0	0.0	5008	,	,		15760	0.0		0.004	False		,,,				2504	0.0				p.R442H		Atlas-SNP	.											.	TRIM65	23	.	0			c.G1325A						PASS	.	C	HIS/ARG	11,4369		0,11,2179	17.0	20.0	19.0		1325	3.4	1.0	17	dbSNP_129	19	97,8473		1,95,4189	yes	missense	TRIM65	NM_173547.2	29	1,106,6368	TT,TC,CC		1.1319,0.2511,0.834	benign	442/518	73887089	108,12842	2190	4285	6475	SO:0001583	missense	201292	exon6			GGGAGGCGCTGGG	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.1325G>A	17.37:g.73887089C>T	ENSP00000269383:p.Arg442His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	37	CCDS11732.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	14.58	2.578467	0.46006	0.002511	0.011319	ENSG00000141569	ENST00000269383	T	0.69175	-0.38	5.35	3.36	0.38483	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.248458	0.29113	N	0.013101	T	0.36054	0.0953	N	0.20483	0.58	0.21020	N	0.999809	B	0.18461	0.028	B	0.17098	0.017	T	0.11299	-1.0593	10	0.21014	T	0.42	.	5.3044	0.15795	0.0:0.6089:0.0:0.3911	.	442	Q6PJ69	TRI65_HUMAN	H	442	ENSP00000269383:R442H	ENSP00000269383:R442H	R	-	2	0	TRIM65	71398684	0.014000	0.17966	0.998000	0.56505	0.957000	0.61999	0.102000	0.15272	1.267000	0.44247	0.561000	0.74099	CGC	C|0.997;T|0.003	0.003	strong		0.687	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
PAXIP1	22976	hgsc.bcm.edu	37	7	154760369	154760369	+	Silent	SNP	A	A	G	rs935037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:154760369A>G	ENST00000404141.1	-	7	1696	c.1542T>C	c.(1540-1542)ctT>ctC	p.L514L	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Silent_p.L514L			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	514	Gln-rich.			Missing (in Ref. 4; AAB91434). {ECO:0000305}.	adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		ggagctgggcaagctgctgct	0.637													G|||	3082	0.615415	0.5454	0.7262	5008	,	,		16041	0.6071		0.6292	False		,,,				2504	0.6258				p.L514L		Atlas-SNP	.											.	PAXIP1	150	.	0			c.T1542C						PASS	.	G		1990,1564		577,836,364	16.0	17.0	17.0		1542	-3.0	0.2	7	dbSNP_86	17	4087,2557		1271,1545,506	no	coding-synonymous	PAXIP1	NM_007349.3		1848,2381,870	GG,GA,AA		38.4859,44.0068,40.4099		514/1070	154760369	6077,4121	1777	3322	5099	SO:0001819	synonymous_variant	22976	exon7			CTGGGCAAGCTGC	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1542T>C	7.37:g.154760369A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Silent	SNP	ENST00000404141.1	37	CCDS47753.1																																																																																			A|0.380;G|0.620	0.620	strong		0.637	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
SPINK6	404203	hgsc.bcm.edu	37	5	147593497	147593497	+	Missense_Mutation	SNP	C	C	A	rs12186491	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147593497C>A	ENST00000325630.2	+	3	362	c.106C>A	c.(106-108)Ccc>Acc	p.P36T		NM_001195290.1|NM_205841.3	NP_001182219.1|NP_995313.2	Q6UWN8	ISK6_HUMAN	serine peptidase inhibitor, Kazal type 6	36	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		P -> T (in dbSNP:rs12186491). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20667819}.			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTCCAGGACCCCAAGGTCTA	0.463													C|||	3402	0.679313	0.2489	0.8833	5008	,	,		17174	0.6954		0.9185	False		,,,				2504	0.8538				p.P36T		Atlas-SNP	.											.	SPINK6	8	.	0			c.C106A						PASS	.	C	THR/PRO,THR/PRO	1692,2714	510.6+/-367.6	327,1038,838	135.0	110.0	119.0		106,106	5.8	1.0	5	dbSNP_120	119	7938,662	789.6+/-407.6	3664,610,26	yes	missense,missense	SPINK6	NM_001195290.1,NM_205841.3	38,38	3991,1648,864	AA,AC,CC		7.6977,38.4022,25.9573	probably-damaging,probably-damaging	36/81,36/81	147593497	9630,3376	2203	4300	6503	SO:0001583	missense	404203	exon3			CAGGACCCCAAGG	AY358716	CCDS34268.1	5q32	2011-08-31	2005-08-17		ENSG00000178172	ENSG00000178172		"""Serine peptidase inhibitors, Kazal type"""	29486	protein-coding gene	gene with protein product	"""protease inhibitor H"""	615868	"""serine protease inhibitor, Kazal type 6"""			15060002	Standard	NM_205841		Approved	MGC21394, UNQ844, BUSI2	uc021yff.1	Q6UWN8	OTTHUMG00000163425	ENST00000325630.2:c.106C>A	5.37:g.147593497C>A	ENSP00000324870:p.Pro36Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_205841	E0X656|Q8N5P0	Missense_Mutation	SNP	ENST00000325630.2	37	CCDS34268.1	1522	0.6968864468864469	128	0.2601626016260163	317	0.8756906077348067	384	0.6713286713286714	693	0.9142480211081794	C	12.72	2.023750	0.35701	0.384022	0.923023	ENSG00000178172	ENST00000514389;ENST00000325630	T;T	0.79352	-1.26;-0.84	5.75	5.75	0.90469	Proteinase inhibitor I1, Kazal (2);	0.000000	0.64402	D	0.000004	T	0.00012	0.0000	.	.	.	0.27348	P	0.9563145	D	0.89917	1.0	D	0.91635	0.999	T	0.44251	-0.9340	8	0.59425	D	0.04	-9.9478	15.8177	0.78615	0.0:1.0:0.0:0.0	rs12186491;rs17845980;rs17858962;rs52838371;rs58225460;rs12186491	36	Q6UWN8	ISK6_HUMAN	T	36	ENSP00000421119:P36T;ENSP00000324870:P36T	ENSP00000324870:P36T	P	+	1	0	SPINK6	147573690	0.059000	0.20769	0.994000	0.49952	0.399000	0.30720	1.358000	0.34102	2.885000	0.99019	0.655000	0.94253	CCC	C|0.293;A|0.707	0.707	strong		0.463	SPINK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373332.1	NM_205841	
NTN4	59277	hgsc.bcm.edu	37	12	96131895	96131895	+	Missense_Mutation	SNP	A	A	G	rs17288108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:96131895A>G	ENST00000343702.4	-	3	1061	c.613T>C	c.(613-615)Tac>Cac	p.Y205H	NTN4_ENST00000552603.1_5'UTR|NTN4_ENST00000344911.4_Missense_Mutation_p.Y168H|NTN4_ENST00000538383.1_Missense_Mutation_p.Y168H|NTN4_ENST00000553059.1_Missense_Mutation_p.Y205H	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	205	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.		Y -> H (in dbSNP:rs17288108).		axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)				NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						TCTGTATCGTATGGTGGTGAC	0.458													A|||	367	0.0732827	0.0038	0.0908	5008	,	,		17826	0.0238		0.1849	False		,,,				2504	0.091				p.Y205H		Atlas-SNP	.											NTN4,colon,carcinoma,+2,1	NTN4	67	1	0			c.T613C						PASS	.	A	HIS/TYR	137,4269	97.1+/-135.8	1,135,2067	152.0	142.0	145.0		613	1.6	0.0	12	dbSNP_123	145	1507,7093	285.5+/-297.2	127,1253,2920	yes	missense	NTN4	NM_021229.3	83	128,1388,4987	GG,GA,AA		17.5233,3.1094,12.6403	benign	205/629	96131895	1644,11362	2203	4300	6503	SO:0001583	missense	59277	exon3			TATCGTATGGTGG	AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"""Netrins"""	13658	protein-coding gene	gene with protein product	"""beta-netrin"", ""Netrin-4"""	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.613T>C	12.37:g.96131895A>G	ENSP00000340998:p.Tyr205His	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	37	CCDS9054.1	188	0.08608058608058608	1	0.0020325203252032522	38	0.10497237569060773	7	0.012237762237762238	142	0.18733509234828497	A	4.879	0.163335	0.09287	0.031094	0.175233	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059;ENST00000547980	T;T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9;-0.9	5.51	1.57	0.23409	Laminin, N-terminal (3);	0.390669	0.28436	N	0.015352	T	0.00073	0.0002	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.04041	-1.0982	9	0.15066	T	0.55	.	4.6958	0.12802	0.5194:0.0:0.1166:0.364	rs17288108;rs52829375;rs59573535;rs17288108	205;205	Q9HB63-2;Q9HB63	.;NET4_HUMAN	H	205;168;168;205;168	ENSP00000340998:Y205H;ENSP00000339436:Y168H;ENSP00000444432:Y168H;ENSP00000447292:Y205H;ENSP00000447594:Y168H	ENSP00000340998:Y205H	Y	-	1	0	NTN4	94656026	0.000000	0.05858	0.043000	0.18650	0.748000	0.42578	-0.014000	0.12656	0.895000	0.36342	0.454000	0.30748	TAC	A|0.893;G|0.107	0.107	strong		0.458	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229	
MAU2	23383	hgsc.bcm.edu	37	19	19449686	19449686	+	Silent	SNP	G	G	T	rs2074090	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19449686G>T	ENST00000392313.6	+	5	668	c.489G>T	c.(487-489)tcG>tcT	p.S163S	MAU2_ENST00000586189.3_Intron|MAU2_ENST00000262815.8_Silent_p.S163S	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	163					maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						ACCTGGTGTCGGCCTGTGACC	0.572													G|||	2625	0.524161	0.348	0.5418	5008	,	,		18843	0.6677		0.674	False		,,,				2504	0.4479				p.S163S		Atlas-SNP	.											MAU2,NS,malignant_melanoma,+1,1	MAU2	38	1	0			c.G489T						PASS	.	G		1576,2408		307,962,723	88.0	99.0	95.0		489	-10.8	0.4	19	dbSNP_96	95	5475,2843		1802,1871,486	no	coding-synonymous	MAU2	NM_015329.3		2109,2833,1209	TT,TG,GG		34.1789,39.5582,42.6841		163/614	19449686	7051,5251	1992	4159	6151	SO:0001819	synonymous_variant	23383	exon5			GGTGTCGGCCTGT	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"""sister chromatid cohesion 4"""	614560	"""KIAA0892"", ""MAU2 chromatid cohesion factor homolog (C. elegans)"""	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.489G>T	19.37:g.19449686G>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_015329	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Silent	SNP	ENST00000392313.6	37	CCDS32969.2																																																																																			G|0.437;T|0.563	0.563	strong		0.572	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329	
CDC27	996	hgsc.bcm.edu	37	17	45214685	45214685	+	Silent	SNP	T	T	C	rs11570543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45214685T>C	ENST00000066544.3	-	14	1839	c.1746A>G	c.(1744-1746)gaA>gaG	p.E582E	CDC27_ENST00000527547.1_Silent_p.E581E|CDC27_ENST00000446365.2_Silent_p.E521E|CDC27_ENST00000531206.1_Silent_p.E588E	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	582					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CAATATCATGTTCCCGTTGCA	0.363													T|||	292	0.0583067	0.1127	0.0576	5008	,	,		19515	0.0089		0.0636	False		,,,				2504	0.0307				p.E588E		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,-2,2	CDC27	337	2	0			c.A1764G						PASS	.						55.0	58.0	57.0					17																	45214685		2203	4300	6503	SO:0001819	synonymous_variant	996	exon14			ATCATGTTCCCGT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1746A>G	17.37:g.45214685T>C		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			T|0.932;C|0.068	0.068	strong		0.363	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
UPK3BL	100134938	hgsc.bcm.edu	37	7	102279621	102279621	+	Missense_Mutation	SNP	C	C	T	rs56365279	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:102279621C>T	ENST00000340457.8	-	4	560	c.511G>A	c.(511-513)Gaa>Aaa	p.E171K	POLR2J2_ENST00000591000.1_3'UTR|POLR2J2_ENST00000476151.1_3'UTR|RP11-514P8.6_ENST00000519541.1_Missense_Mutation_p.E171K	NM_001114403.2	NP_001107875.1	B0FP48	UPK3L_HUMAN	uroplakin 3B-like	171						integral component of membrane (GO:0016021)		p.E171K(1)		kidney(2)|stomach(1)	3						ACGGGTCCTTCGTCATTCATC	0.612																																					p.E171K		Atlas-SNP	.											UPK3BL,NS,carcinoma,0,4	UPK3BL	6	4	1	Substitution - Missense(1)	stomach(1)	c.G511A						scavenged	.						85.0	57.0	66.0					7																	102279621		691	1584	2275	SO:0001583	missense	100134938	exon4			GTCCTTCGTCATT	EU341824	CCDS47675.1	7q22.1	2014-02-12	2010-03-03		ENSG00000267368	ENSG00000267368			37278	protein-coding gene	gene with protein product	"""uroplakin-like protein"""						Standard	NM_001114403		Approved	UPLP		B0FP48	OTTHUMG00000165036	ENST00000340457.8:c.511G>A	7.37:g.102279621C>T	ENSP00000342938:p.Glu171Lys	Somatic	846	0	0		WXS	Illumina HiSeq	Phase_I	884	134	0.151584	NM_001114403		Missense_Mutation	SNP	ENST00000340457.8	37	CCDS47675.1	.	.	.	.	.	.	.	.	.	.	c	0.114	-1.134744	0.01742	.	.	ENSG00000205236	ENST00000519541;ENST00000340457	T;T	0.62232	0.04;0.04	1.82	-0.237	0.13061	.	.	.	.	.	T	0.28896	0.0717	N	0.04508	-0.205	0.09310	N	1	.	.	.	.	.	.	T	0.20773	-1.0265	7	0.06891	T	0.86	-0.3179	3.8141	0.08808	0.0:0.4273:0.0:0.5727	rs4729821;rs9648930;rs11557253;rs17358649	.	.	.	K	171	ENSP00000429397:E171K;ENSP00000342938:E171K	ENSP00000342938:E171K	E	-	1	0	UPK3BL	102066857	0.000000	0.05858	0.168000	0.22838	0.095000	0.18619	-0.872000	0.04219	-0.225000	0.09913	0.186000	0.17326	GAA	.	.	weak		0.612	UPK3BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381510.1	NM_001114403	
KCNJ9	3765	hgsc.bcm.edu	37	1	160057522	160057522	+	Missense_Mutation	SNP	C	C	T	rs3001040	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:160057522C>T	ENST00000368088.3	+	3	1339	c.1097C>T	c.(1096-1098)gCg>gTg	p.A366V		NM_004983.2	NP_004974.2	Q92806	KCNJ9_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 9	366			A -> V (in dbSNP:rs3001040). {ECO:0000269|PubMed:10659995, ECO:0000269|PubMed:10913335}.		synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein activated inward rectifier potassium channel activity (GO:0015467)			biliary_tract(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|skin(2)	16	all_cancers(52;5.86e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			gaggagggggcgggggagggg	0.662													c|||	1243	0.248203	0.1475	0.2824	5008	,	,		3073	0.2718		0.3688	False		,,,				2504	0.2117				p.A366V		Atlas-SNP	.											.	KCNJ9	35	.	0			c.C1097T	GRCh37	CM012776	KCNJ9	M	rs3001040	PASS	.		VAL/ALA	421,3293		34,353,1470	5.0	5.0	5.0		1097	3.5	0.0	1	dbSNP_101	5	1609,5435		218,1173,2131	yes	missense	KCNJ9	NM_004983.2	64	252,1526,3601	TT,TC,CC		22.8421,11.3355,18.8697	benign	366/394	160057522	2030,8728	1857	3522	5379	SO:0001583	missense	3765	exon3			AGGGGGCGGGGGA	U52152	CCDS1194.1	1q23.2	2011-07-05			ENSG00000162728	ENSG00000162728		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6270	protein-coding gene	gene with protein product		600932				8575783, 16382105	Standard	NM_004983		Approved	Kir3.3, GIRK3	uc001fuy.1	Q92806	OTTHUMG00000024072	ENST00000368088.3:c.1097C>T	1.37:g.160057522C>T	ENSP00000357067:p.Ala366Val	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	43	7	0.162791	NM_004983	Q5JW75	Missense_Mutation	SNP	ENST00000368088.3	37	CCDS1194.1	635	0.2907509157509158	83	0.16869918699186992	108	0.2983425414364641	160	0.27972027972027974	284	0.37467018469656993	c	11.19	1.564343	0.27915	0.113355	0.228421	ENSG00000162728	ENST00000368088	D	0.88431	-2.38	4.42	3.51	0.40186	.	0.659602	0.12116	U	0.498063	T	0.61961	0.2389	N	0.08118	0	0.80722	P	0.0	B	0.24132	0.098	B	0.12837	0.008	T	0.42137	-0.9469	9	0.33141	T	0.24	.	9.8547	0.41079	0.0:0.901:0.0:0.099	rs3001040;rs3795338	366	Q92806	IRK9_HUMAN	V	366	ENSP00000357067:A366V	ENSP00000357067:A366V	A	+	2	0	KCNJ9	158324146	0.286000	0.24305	0.007000	0.13788	0.815000	0.46073	1.910000	0.39927	0.865000	0.35603	0.550000	0.68814	GCG	C|0.709;T|0.291	0.291	strong		0.662	KCNJ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060628.1	NM_004983	
MVB12B	89853	hgsc.bcm.edu	37	9	129102840	129102840	+	Silent	SNP	G	G	A	rs1888156	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:129102840G>A	ENST00000361171.3	+	2	216	c.135G>A	c.(133-135)acG>acA	p.T45T	MVB12B_ENST00000436593.3_Silent_p.T30T|MVB12B_ENST00000545391.1_Silent_p.T45T	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	45					protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)										TGCCAGAAACGTCAATGGATC	0.478													G|||	1577	0.314896	0.3858	0.3026	5008	,	,		21217	0.2897		0.2903	False		,,,				2504	0.2791				p.T45T		Atlas-SNP	.											.	.	.	.	0			c.G135A						PASS	.	G	,	1566,2840	491.0+/-362.0	267,1032,904	107.0	100.0	103.0		135,135	-3.0	0.0	9	dbSNP_92	103	2762,5838	439.3+/-359.2	447,1868,1985	no	coding-synonymous,coding-synonymous	FAM125B	NM_001011703.2,NM_033446.2	,	714,2900,2889	AA,AG,GG		32.1163,35.5424,33.2769	,	45/222,45/320	129102840	4328,8678	2203	4300	6503	SO:0001819	synonymous_variant	89853	exon2			AGAAACGTCAATG	AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 28"", ""family with sequence similarity 125, member B"""	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.135G>A	9.37:g.129102840G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	NM_001011703	Q8N6S7	Silent	SNP	ENST00000361171.3	37	CCDS35142.1																																																																																			G|0.676;A|0.324	0.324	strong		0.478	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525	
C6orf118	168090	hgsc.bcm.edu	37	6	165703453	165703453	+	Silent	SNP	A	A	C	rs73022263	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:165703453A>C	ENST00000230301.8	-	7	1244	c.1224T>G	c.(1222-1224)gcT>gcG	p.A408A	C6orf118_ENST00000543069.1_3'UTR|C6orf118_ENST00000494696.2_5'UTR	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	408										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		CTTTTTCCAGAGCTTGTATCT	0.328													A|||	101	0.0201677	0.0144	0.0187	5008	,	,		12805	0.0		0.0358	False		,,,				2504	0.0337				p.A408A		Atlas-SNP	.											.	C6orf118	116	.	0			c.T1224G						PASS	.	A		53,4353	54.9+/-90.9	0,53,2150	99.0	101.0	100.0		1224	1.7	0.6	6	dbSNP_130	100	277,8317	104.8+/-165.8	4,269,4024	no	coding-synonymous	C6orf118	NM_144980.3		4,322,6174	CC,CA,AA		3.2232,1.2029,2.5385		408/470	165703453	330,12670	2203	4297	6500	SO:0001819	synonymous_variant	168090	exon7			TTCCAGAGCTTGT		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.1224T>G	6.37:g.165703453A>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	167	86	0.51497	NM_144980	Q8TC11	Silent	SNP	ENST00000230301.8	37	CCDS5288.1																																																																																			A|0.974;C|0.026	0.026	strong		0.328	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
ZNF675	171392	hgsc.bcm.edu	37	19	23837145	23837145	+	Missense_Mutation	SNP	A	A	G	rs11671053	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:23837145A>G	ENST00000359788.4	-	4	758	c.590T>C	c.(589-591)gTg>gCg	p.V197A	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	197			V -> A (in dbSNP:rs11671053).	Missing (in Ref. 2; BAC04216). {ECO:0000305}.	bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GCAGAAATTCACCTTGGTATA	0.303													A|||	1864	0.372204	0.3593	0.4424	5008	,	,		18306	0.125		0.6173	False		,,,				2504	0.3425				p.V197A		Atlas-SNP	.											.	ZNF675	88	.	0			c.T590C						PASS	.	A	ALA/VAL	1689,2713		329,1031,841	42.0	41.0	42.0		590	-2.2	0.0	19	dbSNP_120	42	5328,3268		1655,2018,625	yes	missense	ZNF675	NM_138330.2	64	1984,3049,1466	GG,GA,AA		38.0177,38.3689,46.0148	benign	197/569	23837145	7017,5981	2201	4298	6499	SO:0001583	missense	171392	exon4			AAATTCACCTTGG		CCDS32981.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	30768	protein-coding gene	gene with protein product	"""TRAF6 inhibitory zinc finger"""					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.590T>C	19.37:g.23837145A>G	ENSP00000352836:p.Val197Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_138330	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	37	CCDS32981.1	881	0.4033882783882784	160	0.3252032520325203	167	0.4613259668508287	85	0.1486013986013986	469	0.6187335092348285	.	9.716	1.158276	0.21454	0.383689	0.619823	ENSG00000197372	ENST00000359788	T	0.15139	2.45	1.08	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	L	0.31371	0.925	0.43399	P	0.004471000000000003	B	0.28439	0.212	B	0.29353	0.101	T	0.37244	-0.9714	8	0.66056	D	0.02	.	5.106	0.14785	0.2747:0.0:0.0:0.7252	rs11671053;rs52791469;rs11671053	197	Q8TD23	ZN675_HUMAN	A	197	ENSP00000352836:V197A	ENSP00000352836:V197A	V	-	2	0	ZNF675	23628985	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	-0.105000	0.10907	-0.617000	0.05664	-0.686000	0.03744	GTG	A|0.544;G|0.456	0.456	strong		0.303	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330	
TRIM42	287015	hgsc.bcm.edu	37	3	140406947	140406947	+	Missense_Mutation	SNP	G	G	A	rs28594654	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:140406947G>A	ENST00000286349.3	+	3	1614	c.1423G>A	c.(1423-1425)Gtg>Atg	p.V475M		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	475	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.		V -> M (in dbSNP:rs28594654).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AATAAACTACGTGCCCTTGGA	0.587													A|||	2006	0.400559	0.2655	0.5058	5008	,	,		19201	0.3899		0.5328	False		,,,				2504	0.3834				p.V475M		Atlas-SNP	.											.	TRIM42	143	.	0			c.G1423A						PASS	.	A	MET/VAL	1368,3038	691.2+/-405.4	218,932,1053	77.0	65.0	69.0		1423	1.8	0.9	3	dbSNP_125	69	4983,3617	521.9+/-380.0	1456,2071,773	yes	missense	TRIM42	NM_152616.4	21	1674,3003,1826	AA,AG,GG		42.0581,31.0486,48.8313	benign	475/724	140406947	6351,6655	2203	4300	6503	SO:0001583	missense	287015	exon3			AACTACGTGCCCT	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"""Tripartite motif containing / Tripartite motif containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	19014	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 40"""		"""tripartite motif-containing 42"""				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.1423G>A	3.37:g.140406947G>A	ENSP00000286349:p.Val475Met	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	931	0.42628205128205127	148	0.3008130081300813	179	0.494475138121547	208	0.36363636363636365	396	0.5224274406332454	A	0.139	-1.104067	0.01828	0.310486	0.579419	ENSG00000155890	ENST00000286349	T	0.37752	1.18	5.63	1.79	0.24919	COS domain (1);	0.430834	0.23591	N	0.046556	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44283	-0.9338	9	0.17832	T	0.49	-5.1999	4.4257	0.11501	0.4933:0.3337:0.1731:0.0	rs28594654	475	Q8IWZ5	TRI42_HUMAN	M	475	ENSP00000286349:V475M	ENSP00000286349:V475M	V	+	1	0	TRIM42	141889637	0.030000	0.19436	0.926000	0.36857	0.111000	0.19643	0.379000	0.20585	0.488000	0.27723	-0.254000	0.11334	GTG	G|0.527;A|0.473	0.473	strong		0.587	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	
NOX4	50507	hgsc.bcm.edu	37	11	89060002	89060002	+	Silent	SNP	G	G	A	rs28517716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:89060002G>A	ENST00000263317.4	-	18	1897	c.1659C>T	c.(1657-1659)tcC>tcT	p.S553S	NOX4_ENST00000525196.1_Silent_p.S317S|NOX4_ENST00000527626.1_Silent_p.S366S|NOX4_ENST00000343727.5_Silent_p.S529S|NOX4_ENST00000534731.1_Silent_p.S513S|NOX4_ENST00000528341.1_Silent_p.S528S|NOX4_ENST00000535633.1_Silent_p.S529S|NOX4_ENST00000413594.2_Silent_p.S574S|NOX4_ENST00000542487.1_Silent_p.S529S|NOX4_ENST00000532825.1_Silent_p.S489S|NOX4_ENST00000424319.1_Silent_p.S529S|NOX4_ENST00000531342.1_Silent_p.S206S|NOX4_ENST00000527956.1_Silent_p.S529S|NOX4_ENST00000375979.3_Silent_p.S246S			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	553	Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GAAGAGTCTTGGATAGTGAAT	0.368													G|||	660	0.131789	0.2405	0.0418	5008	,	,		16825	0.1429		0.0507	False		,,,				2504	0.1207				p.S553S		Atlas-SNP	.											NOX4,NS,carcinoma,-1,1	NOX4	101	1	0			c.C1659T						scavenged	.	G	,,	791,3611	299.6+/-285.9	68,655,1478	89.0	89.0	89.0		1539,1587,1659	2.4	1.0	11	dbSNP_125	89	347,8251	115.5+/-175.4	5,337,3957	no	coding-synonymous,coding-synonymous,coding-synonymous	NOX4	NM_001143836.1,NM_001143837.1,NM_016931.3	,,	73,992,5435	AA,AG,GG		4.0358,17.9691,8.7538	,,	513/539,529/555,553/579	89060002	1138,11862	2201	4299	6500	SO:0001819	synonymous_variant	50507	exon18			AGTCTTGGATAGT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1659C>T	11.37:g.89060002G>A		Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	194	89	0.458763	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Silent	SNP	ENST00000263317.4	37	CCDS8285.1																																																																																			G|0.912;A|0.088	0.088	strong		0.368	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
MANBA	4126	hgsc.bcm.edu	37	4	103611845	103611845	+	Missense_Mutation	SNP	C	C	T	rs227368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:103611845C>T	ENST00000226578.4	-	6	856	c.757G>A	c.(757-759)Gta>Ata	p.V253I	MANBA_ENST00000505239.1_Missense_Mutation_p.V196I	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	253			V -> I (in dbSNP:rs227368). {ECO:0000269|PubMed:9384606}.|V -> L (in dbSNP:rs227368).		cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		GGGATGGCTACGATCACTTGA	0.393													C|||	1886	0.376597	0.1195	0.3545	5008	,	,		12527	0.4732		0.497	False		,,,				2504	0.5164				p.V253I		Atlas-SNP	.											.	MANBA	78	.	0			c.G757A						PASS	.	C	ILE/VAL	929,3477	354.1+/-312.5	107,715,1381	271.0	229.0	243.0		757	1.3	0.0	4	dbSNP_79	243	4081,4519	560.9+/-387.7	967,2147,1186	yes	missense	MANBA	NM_005908.3	29	1074,2862,2567	TT,TC,CC		47.4535,21.0849,38.5207	benign	253/880	103611845	5010,7996	2203	4300	6503	SO:0001583	missense	4126	exon6			TGGCTACGATCAC		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.757G>A	4.37:g.103611845C>T	ENSP00000226578:p.Val253Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	161	159	0.987578	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	865	0.39606227106227104	58	0.11788617886178862	137	0.3784530386740331	288	0.5034965034965035	382	0.503957783641161	C	7.365	0.625609	0.14257	0.210849	0.474535	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.55760	0.5;0.5	4.93	1.29	0.21616	.	0.358272	0.29342	N	0.012434	T	0.00012	0.0000	L	0.37800	1.135	0.48830	P	2.8799999999995496E-4	B;B	0.19583	0.037;0.016	B;B	0.08055	0.003;0.003	T	0.48536	-0.9027	9	0.25751	T	0.34	-10.9971	8.9216	0.35615	0.0:0.702:0.0:0.298	rs227368;rs3912789;rs52818263;rs58634559;rs227368	196;253	E9PFW2;O00462	.;MANBA_HUMAN	I	253;196	ENSP00000226578:V253I;ENSP00000427322:V196I	ENSP00000226578:V253I	V	-	1	0	MANBA	103830893	0.000000	0.05858	0.007000	0.13788	0.915000	0.54546	-0.243000	0.08915	0.016000	0.14998	-0.143000	0.13931	GTA	T|0.377;G|0.002;C|0.617;A|0.004	0.377	strong		0.393	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
RPS6KL1	83694	hgsc.bcm.edu	37	14	75388183	75388183	+	Missense_Mutation	SNP	C	C	T	rs7156590	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:75388183C>T	ENST00000555647.1	-	3	349	c.62G>A	c.(61-63)cGa>cAa	p.R21Q	RPS6KL1_ENST00000358328.4_Missense_Mutation_p.R21Q|RPS6KL1_ENST00000557413.1_Missense_Mutation_p.R21Q|RPS6KL1_ENST00000354625.2_Missense_Mutation_p.R21Q|RPS6KL1_ENST00000554900.1_Intron			Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	21			R -> Q (in dbSNP:rs7156590). {ECO:0000269|PubMed:17344846}.			ribosome (GO:0005840)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(234;0.00658)		GGACCGTGCTCGTGAGCAAGG	0.622													C|||	1762	0.351837	0.1846	0.4135	5008	,	,		16733	0.5903		0.3777	False		,,,				2504	0.2618				p.R21Q		Atlas-SNP	.											.	RPS6KL1	35	.	0			c.G62A						PASS	.	C	GLN/ARG	953,3453	361.4+/-315.7	94,765,1344	76.0	73.0	74.0		62	2.6	0.0	14	dbSNP_116	74	3228,5372	486.6+/-371.9	607,2014,1679	yes	missense	RPS6KL1	NM_031464.4	43	701,2779,3023	TT,TC,CC		37.5349,21.6296,32.1467	probably-damaging	21/550	75388183	4181,8825	2203	4300	6503	SO:0001583	missense	83694	exon2			CGTGCTCGTGAGC	BC004540	CCDS9834.1, CCDS9834.2	14q24.2	2011-04-05				ENSG00000198208			20222	protein-coding gene	gene with protein product							Standard	NM_031464		Approved	MGC11287	uc010tux.2	Q9Y6S9		ENST00000555647.1:c.62G>A	14.37:g.75388183C>T	ENSP00000452027:p.Arg21Gln	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	132	74	0.560606	NM_031464	A6NGM9|Q69YT9|Q6ZMQ6|Q96NR9|Q9BSU9	Missense_Mutation	SNP	ENST00000555647.1	37	CCDS9834.2	828	0.3791208791208791	92	0.18699186991869918	146	0.40331491712707185	314	0.548951048951049	276	0.3641160949868074	C	12.83	2.055236	0.36277	0.216296	0.375349	ENSG00000198208	ENST00000555647;ENST00000354625;ENST00000557413;ENST00000358328	T;T;T;T	0.60548	0.26;0.18;0.26;0.26	4.4	2.56	0.30785	.	0.156452	0.28510	N	0.015085	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P;B;P	0.38300	0.462;0.41;0.626	B;B;B	0.24541	0.054;0.031;0.05	T	0.48937	-0.8990	9	0.42905	T	0.14	-6.2096	8.0461	0.30551	0.0:0.8043:0.0:0.1957	rs7156590;rs7156590	21;21;21	Q9Y6S9;Q9Y6S9-4;Q9Y6S9-2	RPKL1_HUMAN;.;.	Q	21	ENSP00000452027:R21Q;ENSP00000346644:R21Q;ENSP00000450567:R21Q;ENSP00000351086:R21Q	ENSP00000346644:R21Q	R	-	2	0	RPS6KL1	74457936	0.039000	0.19947	0.003000	0.11579	0.567000	0.35839	1.323000	0.33701	0.426000	0.26116	0.561000	0.74099	CGA	C|0.654;T|0.346	0.346	strong		0.622	RPS6KL1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413732.1		
ZFP64	55734	hgsc.bcm.edu	37	20	50769183	50769183	+	Silent	SNP	G	G	A	rs3746415	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:50769183G>A	ENST00000216923.4	-	6	1897	c.1548C>T	c.(1546-1548)gcC>gcT	p.A516A	ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000371515.4_Silent_p.A514A|ZFP64_ENST00000346617.4_Silent_p.A462A|ZFP64_ENST00000477786.1_Intron	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	516					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						TCACTGCAGCGGCGGCAGCCT	0.637													G|||	780	0.155751	0.1029	0.2695	5008	,	,		17009	0.0843		0.2137	False		,,,				2504	0.1605				p.A516A		Atlas-SNP	.											.	ZFP64	240	.	0			c.C1548T						PASS	.	G	,,,	459,3947		25,409,1769	22.0	26.0	24.0		1548,1386,1542,	-11.1	0.0	20	dbSNP_107	24	1855,6745		192,1471,2637	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	,,,	217,1880,4406	AA,AG,GG		21.5698,10.4176,17.7918	,,,	516/682,462/628,514/680,	50769183	2314,10692	2203	4300	6503	SO:0001819	synonymous_variant	55734	exon6			TGCAGCGGCGGCA	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1548C>T	20.37:g.50769183G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	34	0.62963	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			G|0.839;A|0.161	0.161	strong		0.637	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
DNAH10	196385	hgsc.bcm.edu	37	12	124298380	124298380	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124298380G>A	ENST00000409039.3	+	20	3372	c.3347G>A	c.(3346-3348)aGa>aAa	p.R1116K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1116	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCAGAAATTAGAAGTAAATCT	0.398																																					p.R1116K		Atlas-SNP	.											.	DNAH10	888	.	0			c.G3347A						PASS	.						73.0	72.0	72.0					12																	124298380		2044	4232	6276	SO:0001583	missense	196385	exon20			AAATTAGAAGTAA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.3347G>A	12.37:g.124298380G>A	ENSP00000386770:p.Arg1116Lys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	14.43	2.531934	0.45073	.	.	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.72	2.94	0.34122	.	.	.	.	.	T	0.18882	0.0453	L	0.54323	1.7	0.36729	D	0.881622	B	0.14805	0.011	B	0.16722	0.016	T	0.11324	-1.0592	9	0.17832	T	0.49	.	9.9842	0.41832	0.2701:0.0:0.7299:0.0	.	1116	Q8IVF4	DYH10_HUMAN	K	1116	ENSP00000386770:R1116K	ENSP00000386770:R1116K	R	+	2	0	DNAH10	122864333	0.988000	0.35896	0.047000	0.18901	0.982000	0.71751	1.629000	0.37071	0.364000	0.24374	-0.136000	0.14681	AGA	.	.	none		0.398	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
CCZ1	51622	hgsc.bcm.edu	37	7	5965288	5965288	+	Silent	SNP	G	G	A	rs1061428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5965288G>A	ENST00000325974.6	+	15	1485	c.1419G>A	c.(1417-1419)acG>acA	p.T473T	CCZ1_ENST00000496860.1_3'UTR|RSPH10B_ENST00000535104.1_5'Flank|RSPH10B_ENST00000539903.1_3'UTR|CCZ1_ENST00000537980.1_Silent_p.T330T	NM_015622.5	NP_056437.4	P86791	CCZ1_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog (S. cerevisiae)	473						lysosome (GO:0005764)|membrane (GO:0016020)				large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	6						TTTGTGCAACGCAGTTCAACA	0.403																																					p.T473T		Atlas-SNP	.											CCZ1,NS,carcinoma,+1,1	CCZ1	21	1	0			c.G1419A						PASS	.	G		132,4270	84.8+/-123.5	3,126,2072	73.0	63.0	67.0		1419	-7.1	0.4	7	dbSNP_134	67	1204,7354	214.3+/-254.0	41,1122,3116	no	coding-synonymous	CCZ1	NM_015622.5		44,1248,5188	AA,AG,GG		14.0687,2.9986,10.3086		473/483	5965288	1336,11624	2201	4279	6480	SO:0001819	synonymous_variant	51622	exon15			TGCAACGCAGTTC	AF151801	CCDS34597.1	7p22.1	2014-02-13	2010-06-29	2010-06-29	ENSG00000122674	ENSG00000122674			21691	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 28A"""	C7orf28A		10810093, 20305638	Standard	NM_015622		Approved	CGI-43, CCZ1A	uc003spf.3	P86791	OTTHUMG00000155502	ENST00000325974.6:c.1419G>A	7.37:g.5965288G>A		Somatic	1437	1	0.000695894		WXS	Illumina HiSeq	Phase_I	1612	751	0.465881	NM_015622	A2RU45|O95766|Q9UG65|Q9Y359	Silent	SNP	ENST00000325974.6	37	CCDS34597.1																																																																																			G|0.922;A|0.078	0.078	strong		0.403	CCZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340391.1	NM_015622	
MAPKAP1	79109	hgsc.bcm.edu	37	9	128246786	128246786	+	Silent	SNP	G	G	A	rs2070113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:128246786G>A	ENST00000373498.1	-	8	1211	c.1143C>T	c.(1141-1143)caC>caT	p.H381H	MAPKAP1_ENST00000350766.3_Silent_p.H345H|MAPKAP1_ENST00000373511.2_Intron|MAPKAP1_ENST00000373503.3_Silent_p.H189H|MAPKAP1_ENST00000373497.5_Silent_p.H94H|MAPKAP1_ENST00000265960.3_Silent_p.H381H|MAPKAP1_ENST00000394063.1_Silent_p.H189H			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	381					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						ACTTGTAATGGTGGCTGCTAA	0.483													G|||	820	0.163738	0.0272	0.1643	5008	,	,		19569	0.2421		0.2256	False		,,,				2504	0.2035				p.H381H		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.C1143T						PASS	.	G	,,,,	288,4118	159.6+/-192.1	13,262,1928	273.0	210.0	231.0		1143,,567,567,1035	5.3	1.0	9	dbSNP_96	231	2030,6570	353.9+/-329.3	231,1568,2501	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	MAPKAP1	NM_001006617.1,NM_001006619.1,NM_001006620.1,NM_001006621.1,NM_024117.3	,,,,	244,1830,4429	AA,AG,GG		23.6047,6.5365,17.8225	,,,,	381/523,,189/331,189/331,345/487	128246786	2318,10688	2203	4300	6503	SO:0001819	synonymous_variant	79109	exon9			GTAATGGTGGCTG	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"""stress-activated protein kinase-interacting 1"""	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.1143C>T	9.37:g.128246786G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	250	123	0.492	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Silent	SNP	ENST00000373498.1	37	CCDS35140.1																																																																																			G|0.819;T|0.001	.	strong		0.483	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1		
ITGAX	3687	hgsc.bcm.edu	37	16	31384648	31384648	+	Silent	SNP	C	C	T	rs12448775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31384648C>T	ENST00000268296.4	+	20	2566	c.2445C>T	c.(2443-2445)taC>taT	p.Y815Y	ITGAX_ENST00000562522.1_Silent_p.Y815Y	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	815					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						AAGACTCCTACGGAACCACCA	0.607													C|||	201	0.0401358	0.0113	0.183	5008	,	,		16004	0.001		0.0388	False		,,,				2504	0.0194				p.Y815Y		Atlas-SNP	.											.	ITGAX	198	.	0			c.C2445T						PASS	.	C		82,4312	69.8+/-107.6	1,80,2116	142.0	99.0	114.0		2445	-4.4	0.4	16	dbSNP_120	114	345,8255	117.9+/-177.5	5,335,3960	no	coding-synonymous	ITGAX	NM_000887.3		6,415,6076	TT,TC,CC		4.0116,1.8662,3.2861		815/1164	31384648	427,12567	2197	4300	6497	SO:0001819	synonymous_variant	3687	exon20			CTCCTACGGAACC	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.2445C>T	16.37:g.31384648C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	48	0.578313	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			C|0.967;T|0.033	0.033	strong		0.607	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
FDXR	2232	hgsc.bcm.edu	37	17	72860654	72860654	+	Silent	SNP	G	G	A	rs2070921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72860654G>A	ENST00000293195.5	-	8	828	c.750C>T	c.(748-750)gcC>gcT	p.A250A	FDXR_ENST00000442102.2_Silent_p.A293A|FDXR_ENST00000413947.2_Silent_p.A281A|FDXR_ENST00000455107.2_Silent_p.A206A|FDXR_ENST00000544854.1_Silent_p.A198A|FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000583917.1_Intron|FDXR_ENST00000582944.1_Silent_p.A242A|FDXR_ENST00000581530.1_Silent_p.A256A|FDXR_ENST00000420580.2_Silent_p.A210A	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	250					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	AAATGGGCCGGGCTCCCGGTA	0.617											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	277	0.0553115	0.0023	0.0663	5008	,	,		14594	0.1458		0.0139	False		,,,				2504	0.0685				p.A293A		Atlas-SNP	.											.	FDXR	68	.	0			c.C879T						PASS	.	G	,	13,4393	19.1+/-41.9	0,13,2190	46.0	51.0	49.0		768,750	-0.2	1.0	17	dbSNP_96	49	81,8519	46.3+/-105.2	0,81,4219	no	coding-synonymous,coding-synonymous	FDXR	NM_004110.3,NM_024417.2	,	0,94,6409	AA,AG,GG		0.9419,0.2951,0.7227	,	256/498,250/492	72860654	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	2232	exon8			GGGCCGGGCTCCC	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"""adrenodoxin-NADP(+) reductase"", ""adrenodoxin reductase"""	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.750C>T	17.37:g.72860654G>A		Somatic	87	0	0	1140	WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Silent	SNP	ENST00000293195.5	37	CCDS58593.1																																																																																			G|0.979;A|0.021	0.021	strong		0.617	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110	
HSD3B7	80270	hgsc.bcm.edu	37	16	30999142	30999142	+	Missense_Mutation	SNP	A	A	G	rs9938550|rs202062612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:30999142A>G	ENST00000297679.5	+	7	841	c.748A>G	c.(748-750)Acc>Gcc	p.T250A	HSD3B7_ENST00000353250.5_Silent_p.Q195Q|AC135048.1_ENST00000602217.1_5'Flank|HSD3B7_ENST00000262520.6_Silent_p.Q195Q	NM_025193.3	NP_079469.2	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	250			T -> A (in dbSNP:rs9938550). {ECO:0000269|PubMed:11067870}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity (GO:0047016)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GCAGCGGGCAACCCTGATGGG	0.632													G|||	2471	0.493411	0.2057	0.5692	5008	,	,		17471	0.9048		0.6362	False		,,,				2504	0.2577				p.T250A		Atlas-SNP	.											.	HSD3B7	33	.	0			c.A748G						PASS	.	G	,,ALA/THR	1271,3121		192,887,1117	80.0	77.0	78.0		585,585,748	0.3	0.0	16	dbSNP_119	78	5518,3078		1807,1904,587	yes	coding-synonymous,coding-synonymous,missense	HSD3B7	NM_001142777.1,NM_001142778.1,NM_025193.3	,,58	1999,2791,1704	GG,GA,AA		35.8074,28.939,47.7287	,,benign	195/197,195/197,250/370	30999142	6789,6199	2196	4298	6494	SO:0001583	missense	80270	exon7			CGGGCAACCCTGA	AF277719	CCDS10698.1, CCDS45466.1	16p11.2	2011-09-14			ENSG00000099377	ENSG00000099377	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	18324	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 3"""	607764				11067870, 19027726	Standard	NM_001142777		Approved	C(27)-3BETA-HSD, SDR11E3	uc002eaf.2	Q9H2F3	OTTHUMG00000132417	ENST00000297679.5:c.748A>G	16.37:g.30999142A>G	ENSP00000297679:p.Thr250Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	27	0.380282	NM_025193	Q96M28|Q9BSN9	Missense_Mutation	SNP	ENST00000297679.5	37	CCDS10698.1	1360	0.6227106227106227	125	0.2540650406504065	219	0.6049723756906077	531	0.9283216783216783	485	0.6398416886543535	G	1.407	-0.576438	0.03854	0.28939	0.641926	ENSG00000099377	ENST00000297679	D	0.84146	-1.81	5.1	0.275	0.15659	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.921721	0.09486	N	0.795663	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.37220	-0.9715	8	0.11794	T	0.64	-2.2092	1.6826	0.02835	0.2421:0.2454:0.3874:0.1251	rs9938550;rs57576950;rs9938550	250	Q9H2F3	3BHS7_HUMAN	A	250	ENSP00000297679:T250A	ENSP00000297679:T250A	T	+	1	0	HSD3B7	30906643	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.060000	0.11712	0.134000	0.18681	-0.119000	0.15052	ACC	A|0.455;G|0.545	0.545	strong		0.632	HSD3B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255554.2		
THADA	63892	hgsc.bcm.edu	37	2	43797619	43797619	+	Missense_Mutation	SNP	C	C	T	rs17031056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:43797619C>T	ENST00000405006.4	-	14	2446	c.2095G>A	c.(2095-2097)Gta>Ata	p.V699I	THADA_ENST00000330266.7_Missense_Mutation_p.V409I|THADA_ENST00000402360.2_Missense_Mutation_p.V699I|THADA_ENST00000405975.2_Missense_Mutation_p.V699I|THADA_ENST00000403856.1_Missense_Mutation_p.V699I|THADA_ENST00000415080.2_Missense_Mutation_p.V409I|THADA_ENST00000404790.1_Missense_Mutation_p.V699I	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	699			V -> I (in dbSNP:rs17031056). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:14702039}.							breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TTATAAAGTACCTGAGAACTT	0.383													C|||	1096	0.21885	0.149	0.147	5008	,	,		16229	0.253		0.2286	False		,,,				2504	0.319				p.V699I		Atlas-SNP	.											.	THADA	131	.	0			c.G2095A						PASS	.	C	ILE/VAL,ILE/VAL	579,3081		47,485,1298	124.0	117.0	119.0		2095,2095	4.5	1.0	2	dbSNP_123	119	1661,6525		168,1325,2600	yes	missense,missense	THADA	NM_001083953.1,NM_022065.4	29,29	215,1810,3898	TT,TC,CC		20.2907,15.8197,18.9093	benign,benign	699/1954,699/1954	43797619	2240,9606	1830	4093	5923	SO:0001583	missense	63892	exon14			AAAGTACCTGAGA	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.2095G>A	2.37:g.43797619C>T	ENSP00000385995:p.Val699Ile	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	155	86	0.554839	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	463	0.211996336996337	76	0.15447154471544716	60	0.16574585635359115	157	0.2744755244755245	170	0.22427440633245382	C	16.35	3.097924	0.56075	0.158197	0.202907	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T;T;T	0.63913	1.51;1.51;2.69;1.51;-0.07;-0.07;1.45	5.41	4.53	0.55603	Armadillo-type fold (1);	0.224028	0.38058	N	0.001824	T	0.00012	0.0000	L	0.57536	1.79	0.35896	P	0.169952	P;P;B;B;P	0.47762	0.9;0.493;0.045;0.124;0.682	B;B;B;B;B	0.43082	0.407;0.178;0.047;0.035;0.197	T	0.17137	-1.0379	9	0.10111	T	0.7	.	14.1442	0.65339	0.0:0.9279:0.0:0.0721	rs17031056;rs52816054;rs56795971;rs17031056	699;699;699;409;699	B5MC89;Q8IY32;Q6YHU6-5;C9JJB1;Q6YHU6	.;.;.;.;THADA_HUMAN	I	409;699;700;409;699;699;699;699	ENSP00000331105:V409I;ENSP00000386088:V699I;ENSP00000416048:V409I;ENSP00000385995:V699I;ENSP00000385441:V699I;ENSP00000384266:V699I;ENSP00000385469:V699I	ENSP00000331105:V409I	V	-	1	0	THADA	43651123	0.998000	0.40836	1.000000	0.80357	0.970000	0.65996	2.527000	0.45615	1.287000	0.44583	0.591000	0.81541	GTA	C|0.781;N|0.000;T|0.219	0.219	strong		0.383	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
PLEC	5339	hgsc.bcm.edu	37	8	145008560	145008560	+	Silent	SNP	A	A	G	rs11783799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145008560A>G	ENST00000322810.4	-	11	1675	c.1506T>C	c.(1504-1506)gaT>gaC	p.D502D	PLEC_ENST00000354589.3_Silent_p.D365D|PLEC_ENST00000357649.2_Silent_p.D369D|PLEC_ENST00000356346.3_Silent_p.D351D|PLEC_ENST00000398774.2_Silent_p.D333D|PLEC_ENST00000345136.3_Silent_p.D365D|PLEC_ENST00000527096.1_Silent_p.D388D|PLEC_ENST00000436759.2_Silent_p.D392D|PLEC_ENST00000354958.2_Silent_p.D343D	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	502	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCTTCTCCACATCCAGCGGGT	0.677													G|||	1159	0.23143	0.0613	0.2867	5008	,	,		16296	0.1409		0.4066	False		,,,				2504	0.3354				p.D502D		Atlas-SNP	.											.	PLEC	1144	.	0			c.T1506C						PASS	.	G	,,,,,,,	440,3688		26,388,1650	32.0	36.0	35.0		1176,1053,1029,1506,999,1095,1107,1095	-5.7	0.6	8	dbSNP_120	35	3220,5166		612,1996,1585	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	638,2384,3235	GG,GA,AA		38.3973,10.6589,29.2472	,,,,,,,	392/4575,351/4534,343/4526,502/4685,333/4516,365/4548,369/4552,365/4548	145008560	3660,8854	2064	4193	6257	SO:0001819	synonymous_variant	5339	exon11			CTCCACATCCAGC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.1506T>C	8.37:g.145008560A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	163	88	0.539877	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.702;G|0.298	0.298	strong		0.677	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
KRT72	140807	hgsc.bcm.edu	37	12	52981512	52981512	+	Missense_Mutation	SNP	G	G	A	rs61740861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52981512G>A	ENST00000537672.2	-	7	1223	c.1213C>T	c.(1213-1215)Cgg>Tgg	p.R405W	KRT72_ENST00000293745.2_Missense_Mutation_p.R405W|KRT72_ENST00000398066.3_Missense_Mutation_p.R217W|KRT72_ENST00000354310.4_Missense_Mutation_p.R363W	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	405	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		CGCAGCATCCGTGCCAGCTCC	0.662													G|||	339	0.0676917	0.0076	0.1484	5008	,	,		18362	0.2123		0.007	False		,,,				2504	0.0051				p.R405W		Atlas-SNP	.											KRT72,NS,malignant_melanoma,+1,1	KRT72	70	1	0			c.C1213T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	39,4367	43.1+/-76.7	0,39,2164	105.0	95.0	99.0		1213,1087,1213	4.0	1.0	12	dbSNP_129	99	26,8574	17.9+/-57.8	0,26,4274	no	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	101,101,101	0,65,6438	AA,AG,GG		0.3023,0.8852,0.4998	probably-damaging,probably-damaging,probably-damaging	405/512,363/470,405/512	52981512	65,12941	2203	4300	6503	SO:0001583	missense	140807	exon7			GCATCCGTGCCAG	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.1213C>T	12.37:g.52981512G>A	ENSP00000441160:p.Arg405Trp	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	222	106	0.477477	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	186	0.08516483516483517	3	0.006097560975609756	47	0.1298342541436464	131	0.229020979020979	5	0.006596306068601583	G	21.2	4.121000	0.77436	0.008852	0.003023	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67	4.92	4.02	0.46733	Filament (1);	0.000000	0.47852	D	0.000207	T	0.00637	0.0021	M	0.82630	2.6	0.25500	P	0.9875634	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00000	-1.3453	9	0.87932	D	0	.	15.3109	0.74031	0.0:0.0:0.8586:0.1414	rs61740861	363;405	B4DEI8;Q14CN4	.;K2C72_HUMAN	W	405;405;363;217	ENSP00000441160:R405W;ENSP00000293745:R405W;ENSP00000346269:R363W;ENSP00000446151:R217W	ENSP00000293745:R405W	R	-	1	2	KRT72	51267779	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	2.184000	0.42575	1.356000	0.45884	0.650000	0.86243	CGG	G|0.973;A|0.027	0.027	strong		0.662	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
BMP4	652	hgsc.bcm.edu	37	14	54417522	54417522	+	Missense_Mutation	SNP	A	A	G	rs17563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:54417522A>G	ENST00000245451.4	-	4	848	c.455T>C	c.(454-456)gTg>gCg	p.V152A	MIR5580_ENST00000580850.1_RNA|BMP4_ENST00000417573.1_Missense_Mutation_p.V152A|BMP4_ENST00000558984.1_Missense_Mutation_p.V152A|BMP4_ENST00000559087.1_Missense_Mutation_p.V152A	NM_001202.3	NP_001193.2	P12644	BMP4_HUMAN	bone morphogenetic protein 4	152			V -> A (in dbSNP:rs17563). {ECO:0000269|PubMed:12404109, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19249007, ECO:0000269|PubMed:9701626}.		activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification (GO:0009948)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|BMP signaling pathway involved in nephric duct formation (GO:0071893)|BMP signaling pathway involved in renal system segmentation (GO:0061151)|BMP signaling pathway involved in ureter morphogenesis (GO:0061149)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchus development (GO:0060433)|bud dilation involved in lung branching (GO:0060503)|bud elongation involved in lung branching (GO:0060449)|cardiac septum development (GO:0003279)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte differentiation (GO:0002062)|cloacal septation (GO:0060197)|common-partner SMAD protein phosphorylation (GO:0007182)|cranial suture morphogenesis (GO:0060363)|deltoid tuberosity development (GO:0035993)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint morphogenesis (GO:0060272)|endocardial cushion development (GO:0003197)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in lung morphogenesis (GO:0060502)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal cell signaling (GO:0060684)|erythrocyte differentiation (GO:0030218)|extracellular matrix organization (GO:0030198)|germ cell development (GO:0007281)|glomerular capillary formation (GO:0072104)|glomerular visceral epithelial cell development (GO:0072015)|hematopoietic progenitor cell differentiation (GO:0002244)|inner ear receptor cell differentiation (GO:0060113)|intermediate mesodermal cell differentiation (GO:0048392)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|mammary gland formation (GO:0060592)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal cell proliferation involved in ureter development (GO:0072198)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate determination (GO:0007500)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway (GO:0072097)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in heart morphogenesis (GO:2000137)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of glomerulus development (GO:0090194)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell proliferation involved in ureter development (GO:0072200)|negative regulation of metanephric comma-shaped body morphogenesis (GO:2000007)|negative regulation of metanephric S-shaped body morphogenesis (GO:2000005)|negative regulation of mitosis (GO:0045839)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of cardiac muscle fiber development (GO:0055020)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell death (GO:0010942)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of kidney development (GO:0090184)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|pulmonary artery endothelial tube morphogenesis (GO:0061155)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|renal system process (GO:0003014)|secondary heart field specification (GO:0003139)|SMAD protein signal transduction (GO:0060395)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|specification of organ position (GO:0010159)|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway (GO:0072101)|steroid hormone mediated signaling pathway (GO:0043401)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|tendon cell differentiation (GO:0035990)|trachea development (GO:0060438)|trachea formation (GO:0060440)|type B pancreatic cell development (GO:0003323)|ureter epithelial cell differentiation (GO:0072192)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	BMP receptor binding (GO:0070700)|chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|heparin binding (GO:0008201)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(3)|urinary_tract(1)	19						AGAGGAGATCACCTCGTTCTC	0.512													A|||	1631	0.325679	0.1831	0.3617	5008	,	,		19089	0.2857		0.5497	False		,,,				2504	0.3037				p.V152A		Atlas-SNP	.											.	BMP4	45	.	0			c.T455C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	1138,3268		145,848,1210	45.0	42.0	43.0		455,455,455	4.1	1.0	14	dbSNP_63	43	4715,3885		1289,2137,874	yes	missense,missense,missense	BMP4	NM_001202.3,NM_130850.2,NM_130851.2	64,64,64	1434,2985,2084	GG,GA,AA		45.1744,25.8284,45.0023	probably-damaging,probably-damaging,probably-damaging	152/409,152/409,152/409	54417522	5853,7153	2203	4300	6503	SO:0001583	missense	652	exon4			GAGATCACCTCGT	AF035427	CCDS9715.1	14q22-q23	2014-01-30			ENSG00000125378	ENSG00000125378		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1071	protein-coding gene	gene with protein product		112262		BMP2B		7558046, 7579580	Standard	NM_001202		Approved		uc010aoh.3	P12644	OTTHUMG00000140303	ENST00000245451.4:c.455T>C	14.37:g.54417522A>G	ENSP00000245451:p.Val152Ala	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_130851	Q9UM80	Missense_Mutation	SNP	ENST00000245451.4	37	CCDS9715.1	812	0.3717948717948718	99	0.20121951219512196	134	0.3701657458563536	152	0.26573426573426573	427	0.5633245382585752	A	12.19	1.864500	0.32977	0.258284	0.548256	ENSG00000125378	ENST00000245451;ENST00000417573	T;T	0.64085	-0.08;-0.08	5.2	4.05	0.47172	Transforming growth factor-beta, N-terminal (1);	0.123114	0.56097	N	0.000032	T	0.00012	0.0000	L	0.44542	1.39	0.22842	P	0.99866552	B	0.09022	0.002	B	0.12156	0.007	T	0.46247	-0.9205	9	0.30078	T	0.28	.	9.1323	0.36852	0.9092:0.0:0.0908:0.0	rs17563;rs1048810;rs3829971;rs17845605;rs17858529;rs52814732;rs17563	152	P12644	BMP4_HUMAN	A	152	ENSP00000245451:V152A;ENSP00000394165:V152A	ENSP00000245451:V152A	V	-	2	0	BMP4	53487272	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.063000	0.64332	0.993000	0.38866	0.533000	0.62120	GTG	A|0.593;G|0.407	0.407	strong		0.512	BMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276894.2	NM_001202	
BARD1	580	hgsc.bcm.edu	37	2	215632255	215632255	+	Missense_Mutation	SNP	C	C	T	rs2070094|rs386654966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:215632255C>T	ENST00000260947.4	-	6	1653	c.1519G>A	c.(1519-1521)Gtg>Atg	p.V507M	BARD1_ENST00000449967.2_Missense_Mutation_p.V363M	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	507			V -> M (in dbSNP:rs2070094). {ECO:0000269|PubMed:9425226}.		cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ACTATATCCACATGCCCATTC	0.408									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	1834	0.366214	0.3608	0.3069	5008	,	,		18664	0.3433		0.3976	False		,,,				2504	0.407				p.V507M		Atlas-SNP	.											.	BARD1	138	.	0			c.G1519A	GRCh37	CM034384	BARD1	M	rs2070094	PASS	.	C	MET/VAL	1278,3128		281,716,1206	127.0	116.0	119.0		1519	-11.3	0.0	2	dbSNP_96	119	2372,6228		550,1272,2478	yes	missense	BARD1	NM_000465.2	21	831,1988,3684	TT,TC,CC		27.5814,29.0059,28.064	benign	507/778	215632255	3650,9356	2203	4300	6503	SO:0001583	missense	580	exon6	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TATCCACATGCCC		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.1519G>A	2.37:g.215632255C>T	ENSP00000260947:p.Val507Met	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	198	104	0.525253	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	622	0.2847985347985348	113	0.22967479674796748	110	0.30386740331491713	169	0.29545454545454547	230	0.3034300791556728	C	9.530	1.110597	0.20714	0.290059	0.275814	ENSG00000138376	ENST00000260947;ENST00000449967	T;T	0.65732	-0.17;-0.17	5.64	-11.3	0.00108	Ankyrin repeat-containing domain (3);	1.450850	0.03685	N	0.246137	T	0.00012	0.0000	L	0.60957	1.885	0.80722	P	0.0	B;B	0.21606	0.001;0.058	B;B	0.17722	0.005;0.019	T	0.04178	-1.0971	9	0.39692	T	0.17	0.2604	2.0607	0.03592	0.1372:0.2469:0.238:0.3779	rs2070094;rs4151064;rs17838599;rs59469134;rs2070094	363;507	E7EUI3;Q99728	.;BARD1_HUMAN	M	507;363	ENSP00000260947:V507M;ENSP00000406752:V363M	ENSP00000260947:V507M	V	-	1	0	BARD1	215340500	0.000000	0.05858	0.001000	0.08648	0.907000	0.53573	-5.264000	0.00136	-3.328000	0.00186	-1.452000	0.01034	GTG	C|0.656;T|0.344	0.344	strong		0.408	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766045	27766045	+	Missense_Mutation	SNP	A	A	G	rs5926895	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:27766045A>G	ENST00000451261.2	+	5	1432	c.1033A>G	c.(1033-1035)Acc>Gcc	p.T345A		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	345			T -> A (in dbSNP:rs5926895).							central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TGTTGTCTTCACCATTGACCT	0.478													A|||	627	0.166093	0.0613	0.1427	3775	,	,		14904	0.0575		0.2714	False		,,,				2504	0.1186				p.T345A		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A1033G						PASS	.	A	ALA/THR	164,1045		7,129,21,381,154	89.0	62.0	70.0		1033	0.1	0.0	X	dbSNP_114	70	886,1505		111,355,309,334,482	yes	missense	DCAF8L2	NM_001136533.1	58	118,484,330,715,636	GG,GA,G,AA,A		37.0556,13.5649,29.1667	benign	345/632	27766045	1050,2550	692	1591	2283	SO:0001583	missense	347442	exon1			GTCTTCACCATTG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1033A>G	X.37:g.27766045A>G	ENSP00000462745:p.Thr345Ala	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	115	112	0.973913	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			A|0.784;0|0.046	.	strong		0.478	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
ZNF780B	163131	hgsc.bcm.edu	37	19	40541066	40541066	+	Missense_Mutation	SNP	C	C	T	rs61730564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40541066C>T	ENST00000434248.1	-	5	1765	c.1700G>A	c.(1699-1701)cGt>cAt	p.R567H	ZNF780B_ENST00000221355.6_Missense_Mutation_p.R419H	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	567					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TGAACCACGACGAAAGAATTT	0.393													C|||	19	0.00379393	0.003	0.0029	5008	,	,		23695	0.0		0.0119	False		,,,				2504	0.001				p.R567H		Atlas-SNP	.											.	ZNF780B	143	.	0			c.G1700A						PASS	.	C	HIS/ARG	18,4388	25.3+/-52.1	0,18,2185	88.0	97.0	94.0		1700	-2.7	0.0	19	dbSNP_129	94	97,8503	51.9+/-112.3	0,97,4203	no	missense	ZNF780B	NM_001005851.2	29	0,115,6388	TT,TC,CC		1.1279,0.4085,0.8842	probably-damaging	567/834	40541066	115,12891	2203	4300	6503	SO:0001583	missense	163131	exon5			CCACGACGAAAGA	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"""Zinc fingers, C2H2-type"", ""-"""	33109	protein-coding gene	gene with protein product			"""zinc finger protein 779"""	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.1700G>A	19.37:g.40541066C>T	ENSP00000391641:p.Arg567His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	C	15.97	2.988762	0.53934	0.004085	0.011279	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.18016	2.24;2.24	2.56	-2.69	0.06022	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17323	0.0416	L	0.35793	1.09	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.15521	-1.0434	9	0.66056	D	0.02	.	4.0862	0.09948	0.3753:0.4847:0.0:0.14	rs61730564	567	Q9Y6R6	Z780B_HUMAN	H	567;419	ENSP00000391641:R567H;ENSP00000221355:R419H	ENSP00000221355:R419H	R	-	2	0	ZNF780B	45232906	0.000000	0.05858	0.000000	0.03702	0.747000	0.42532	-2.166000	0.01273	-0.184000	0.10567	0.462000	0.41574	CGT	C|0.995;T|0.005	0.005	strong		0.393	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851	
GRHPR	9380	hgsc.bcm.edu	37	9	37429814	37429814	+	Silent	SNP	A	A	G	rs309458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37429814A>G	ENST00000318158.6	+	6	664	c.579A>G	c.(577-579)gcA>gcG	p.A193A	GRHPR_ENST00000607784.1_Silent_p.A193A	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	193					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		AGGAAGCAGCAGAATTCCAGG	0.527													G|||	4253	0.849241	0.7141	0.83	5008	,	,		20284	0.9167		0.9205	False		,,,				2504	0.9029				p.A193A		Atlas-SNP	.											.	GRHPR	35	.	0			c.A579G						PASS	.	G		3306,1100	396.0+/-329.9	1237,832,134	80.0	77.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	579	-7.7	0.6	9	dbSNP_79	78	7840,760	181.2+/-229.9	3572,696,32	no	coding-synonymous	GRHPR	NM_012203.1		4809,1528,166	GG,GA,AA		8.8372,24.966,14.3011		193/329	37429814	11146,1860	2203	4300	6503	SO:0001819	synonymous_variant	9380	exon6			AGCAGCAGAATTC	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"""primary hyperoxaluria type 2"""	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.579A>G	9.37:g.37429814A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Silent	SNP	ENST00000318158.6	37	CCDS6609.1																																																																																			A|0.143;G|0.857	0.857	strong		0.527	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203	
DOCK1	1793	hgsc.bcm.edu	37	10	129216658	129216658	+	Silent	SNP	T	T	C	rs2229600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:129216658T>C	ENST00000280333.6	+	45	4591	c.4482T>C	c.(4480-4482)atT>atC	p.I1494I		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1494	DHR-2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AGAATGCCATTGAGACCATGC	0.597													C|||	1597	0.31889	0.2247	0.4222	5008	,	,		15912	0.4296		0.2575	False		,,,				2504	0.3221				p.I1494I		Atlas-SNP	.											.	DOCK1	188	.	0			c.T4482C						PASS	.	C		1055,3329		158,739,1295	52.0	62.0	59.0		4437	-1.7	1.0	10	dbSNP_98	59	2232,6364		304,1624,2370	no	coding-synonymous	DOCK1	NM_001380.3		462,2363,3665	CC,CT,TT		25.9656,24.0648,25.3236		1479/1851	129216658	3287,9693	2192	4298	6490	SO:0001819	synonymous_variant	1793	exon45			TGCCATTGAGACC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.4482T>C	10.37:g.129216658T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				A|0.000;C|0.325;G|0.000;T|0.674	0.325	strong		0.597	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
TREML2	79865	hgsc.bcm.edu	37	6	41166151	41166151	+	Silent	SNP	A	A	G	rs61998254|rs71544266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41166151A>G	ENST00000483722.1	-	2	257	c.72T>C	c.(70-72)agT>agC	p.S24S		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	24	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					TTGTGTATACACTGTCAGCAG	0.478													A|||	413	0.0824681	0.0091	0.0793	5008	,	,		21052	0.0833		0.1173	False		,,,				2504	0.1472				p.S24S		Atlas-SNP	.											.	TREML2	41	.	0			c.T72C						PASS	.	A		7,4399		1,5,2197	87.0	86.0	86.0		72	-4.8	0.0	6	dbSNP_129	86	133,8461		32,69,4196	no	coding-synonymous	TREML2	NM_024807.2		33,74,6393	GG,GA,AA		1.5476,0.1589,1.0769		24/322	41166151	140,12860	2203	4297	6500	SO:0001819	synonymous_variant	79865	exon2			GTATACACTGTCA	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.72T>C	6.37:g.41166151A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Silent	SNP	ENST00000483722.1	37	CCDS4853.2																																																																																			A|0.947;G|0.053	0.053	strong		0.478	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
HCRTR1	3061	hgsc.bcm.edu	37	1	32084904	32084904	+	Silent	SNP	C	C	T	rs1056526	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:32084904C>T	ENST00000373706.5	+	1	264	c.111C>T	c.(109-111)cgC>cgT	p.R37R	HCRTR1_ENST00000468521.1_3'UTR|HCRTR1_ENST00000403528.2_Silent_p.R37R|HCRTR1_ENST00000373705.1_Silent_p.R37R			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1	37					feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|orexin receptor activity (GO:0016499)|peptide hormone binding (GO:0017046)			breast(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		ATCTGTGGCGCGATTATCTGT	0.612													C|||	1767	0.352835	0.0794	0.4654	5008	,	,		21465	0.2371		0.5636	False		,,,				2504	0.545				p.R37R		Atlas-SNP	.											.	HCRTR1	20	.	0			c.C111T						PASS	.	C		718,3688	297.8+/-285.0	70,578,1555	150.0	151.0	151.0		111	-6.0	1.0	1	dbSNP_86	151	4750,3850	610.1+/-395.6	1318,2114,868	no	coding-synonymous	HCRTR1	NM_001525.2		1388,2692,2423	TT,TC,CC		44.7674,16.296,42.0421		37/426	32084904	5468,7538	2203	4300	6503	SO:0001819	synonymous_variant	3061	exon3			GTGGCGCGATTAT	AF041243	CCDS344.1	1p33	2012-08-08			ENSG00000121764	ENSG00000121764		"""GPCR / Class A : Hypocretin (orexin) receptors"""	4848	protein-coding gene	gene with protein product		602392				9491897	Standard	NM_001525		Approved	OX1R	uc009vtx.2	O43613	OTTHUMG00000003876	ENST00000373706.5:c.111C>T	1.37:g.32084904C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	117	73	0.623932	NM_001525	A8K3A6|Q9HBV6	Silent	SNP	ENST00000373706.5	37	CCDS344.1																																																																																			C|0.612;T|0.388	0.388	strong		0.612	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	NM_001525	
TEC	7006	hgsc.bcm.edu	37	4	48147309	48147309	+	Silent	SNP	T	T	C	rs17574371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:48147309T>C	ENST00000381501.3	-	14	1414	c.1257A>G	c.(1255-1257)aaA>aaG	p.K419K	TEC_ENST00000511471.2_5'UTR	NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	419	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						GGTGTGTCAGTTTCCTGGGAA	0.408													T|||	957	0.191094	0.1785	0.3228	5008	,	,		20119	0.0169		0.3748	False		,,,				2504	0.1053				p.K419K		Atlas-SNP	.											.	TEC	81	.	0			c.A1257G						PASS	.	T		947,3459	359.6+/-314.9	112,723,1368	72.0	70.0	71.0		1257	-2.6	1.0	4	dbSNP_123	71	3367,5233	500.3+/-375.2	686,1995,1619	no	coding-synonymous	TEC	NM_003215.2		798,2718,2987	CC,CT,TT		39.1512,21.4934,33.1693		419/632	48147309	4314,8692	2203	4300	6503	SO:0001819	synonymous_variant	7006	exon14			TGTCAGTTTCCTG	D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.1257A>G	4.37:g.48147309T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_003215	B7ZKZ6|Q3MIS5	Silent	SNP	ENST00000381501.3	37	CCDS3481.1																																																																																			T|0.704;C|0.296	0.296	strong		0.408	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3		
GRM6	2916	hgsc.bcm.edu	37	5	178416063	178416063	+	Silent	SNP	G	G	A	rs2645339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178416063G>A	ENST00000517717.1	-	7	1265	c.1227C>T	c.(1225-1227)taC>taT	p.Y409Y	GRM6_ENST00000231188.5_Silent_p.Y409Y|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	409					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		GGGCAATGGCGTACACCGCAT	0.637																																					p.Y409Y		Atlas-SNP	.											GRM6,NS,adenoma,0,1	GRM6	149	1	0			c.C1227T	GRCh37	CM061056	GRM6	M	rs2645339	PASS	.	G		1757,2649	523.5+/-371.1	361,1035,807	143.0	123.0	129.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1227	-0.9	1.0	5	dbSNP_100	129	4593,4007	596.8+/-393.7	1177,2239,884	no	coding-synonymous	GRM6	NM_000843.3		1538,3274,1691	AA,AG,GG		46.593,39.8774,48.8236		409/878	178416063	6350,6656	2203	4300	6503	SO:0001819	synonymous_variant	2916	exon6			AATGGCGTACACC	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1227C>T	5.37:g.178416063G>A		Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	163	162	0.993865	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			G|0.502;A|0.498	0.498	strong		0.637	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
EHMT1	79813	hgsc.bcm.edu	37	9	140611436	140611436	+	Silent	SNP	T	T	C	rs3812497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140611436T>C	ENST00000460843.1	+	3	471	c.444T>C	c.(442-444)ccT>ccC	p.P148P	EHMT1_ENST00000462484.1_Silent_p.P148P|EHMT1_ENST00000334856.6_Silent_p.P117P|EHMT1_ENST00000371394.2_3'UTR	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	148					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		CTTCGCTGCCTGGCCATGCTG	0.607													t|||	1141	0.227835	0.0893	0.4539	5008	,	,		16940	0.1429		0.2634	False		,,,				2504	0.3057				p.P148P		Atlas-SNP	.											.	EHMT1	196	.	0			c.T444C						PASS	.		,	507,3899	229.4+/-244.0	29,449,1725	54.0	56.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	444,444	-0.9	1.0	9	dbSNP_107	56	2364,6234	387.7+/-342.3	321,1722,2256	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	350,2171,3981	CC,CT,TT		27.4948,11.507,22.0778	,	148/809,148/1299	140611436	2871,10133	2203	4299	6502	SO:0001819	synonymous_variant	79813	exon3			GCTGCCTGGCCAT	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.444T>C	9.37:g.140611436T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			T|0.785;C|0.215	0.215	strong		0.607	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
PDPR	55066	hgsc.bcm.edu	37	16	70164334	70164334	+	Missense_Mutation	SNP	A	A	G	rs10852462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70164334A>G	ENST00000288050.4	+	7	1573	c.616A>G	c.(616-618)Atc>Gtc	p.I206V	PDPR_ENST00000398122.3_Missense_Mutation_p.I106V|PDPR_ENST00000568530.1_Missense_Mutation_p.I206V	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	206				I -> V (in Ref. 3; CAH10555). {ECO:0000305}.	cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)	p.I206V(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		AGGTGTTCAGATCTATGACCG	0.428																																					p.I206V		Atlas-SNP	.											PDPR,NS,carcinoma,0,1	PDPR	66	1	1	Substitution - Missense(1)	stomach(1)	c.A616G						PASS	.						108.0	112.0	110.0					16																	70164334		1906	4147	6053	SO:0001583	missense	55066	exon7			GTTCAGATCTATG		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.616A>G	16.37:g.70164334A>G	ENSP00000288050:p.Ile206Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	181	79	0.436464	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	728	0.3333333333333333	183	0.3719512195121951	115	0.31767955801104975	129	0.22552447552447552	301	0.3970976253298153	A	11.67	1.706647	0.30232	.	.	ENSG00000090857	ENST00000288050;ENST00000398122	D;D	0.81579	-1.51;-1.51	4.93	4.93	0.64822	FAD dependent oxidoreductase (1);	0.052601	0.85682	D	0.000000	T	0.00012	0.0000	N	0.11284	0.12	0.80722	D	1	B	0.22541	0.071	B	0.26864	0.074	T	0.15925	-1.0420	10	0.23891	T	0.37	.	8.4788	0.33030	0.912:0.0:0.088:0.0	rs10852462;rs61538560	206	Q8NCN5	PDPR_HUMAN	V	206;106	ENSP00000288050:I206V;ENSP00000381190:I106V	ENSP00000288050:I206V	I	+	1	0	PDPR	68721835	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.916000	0.69981	1.843000	0.53566	0.455000	0.32223	ATC	A|0.665;G|0.335	0.335	strong		0.428	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17914122	17914122	+	Missense_Mutation	SNP	G	G	A	rs35497285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17914122G>A	ENST00000361221.3	+	3	364	c.205G>A	c.(205-207)Gac>Aac	p.D69N	ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.D69N|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.D69N|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.D69N|ARHGEF10L_ENST00000375420.3_5'Flank	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	69			D -> N (in dbSNP:rs35497285).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GATCCACTTGGACTCCATCCC	0.587													G|||	464	0.0926518	0.0038	0.1225	5008	,	,		17367	0.2044		0.0835	False		,,,				2504	0.0859				p.D69N		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.G205A						PASS	.	G	ASN/ASP,ASN/ASP	79,4327	69.2+/-107.0	1,77,2125	130.0	142.0	138.0		205,205	5.3	0.4	1	dbSNP_126	138	727,7873	177.5+/-227.1	44,639,3617	yes	missense,missense	ARHGEF10L	NM_001011722.2,NM_018125.3	23,23	45,716,5742	AA,AG,GG		8.4535,1.793,6.1971	benign,benign	69/1241,69/1280	17914122	806,12200	2203	4300	6503	SO:0001583	missense	55160	exon3			CACTTGGACTCCA	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.205G>A	1.37:g.17914122G>A	ENSP00000355060:p.Asp69Asn	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	221	0.10119047619047619	1	0.0020325203252032522	44	0.12154696132596685	115	0.20104895104895104	61	0.08047493403693931	G	19.11	3.764533	0.69878	0.01793	0.084535	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415	T;T;T;T	0.61274	0.3;0.3;0.12;0.3	5.3	5.3	0.74995	.	0.181464	0.37348	N	0.002128	T	0.00109	0.0003	L	0.27053	0.805	0.09310	P	0.9999999999970101	D;D;D;D	0.69078	0.996;0.969;0.969;0.997	P;P;P;D	0.73380	0.889;0.829;0.766;0.98	T	0.01720	-1.1288	9	0.16420	T	0.52	-37.9281	14.7973	0.69886	0.0:0.0:1.0:0.0	rs35497285;rs61749342	69;69;69;69	Q9HCE6-5;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;ARGAL_HUMAN	N	69	ENSP00000355060:D69N;ENSP00000399401:D69N;ENSP00000394621:D69N;ENSP00000364564:D69N	ENSP00000355060:D69N	D	+	1	0	ARHGEF10L	17786709	0.334000	0.24739	0.387000	0.26183	0.004000	0.04260	2.057000	0.41365	2.649000	0.89929	0.561000	0.74099	GAC	G|0.929;A|0.071	0.071	strong		0.587	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
NLRP1	22861	hgsc.bcm.edu	37	17	5485367	5485367	+	Missense_Mutation	SNP	A	A	T	rs12150220	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5485367A>T	ENST00000572272.1	-	3	463	c.464T>A	c.(463-465)cTc>cAc	p.L155H	NLRP1_ENST00000577119.1_Missense_Mutation_p.L155H|NLRP1_ENST00000354411.3_Missense_Mutation_p.L155H|NLRP1_ENST00000345221.3_Missense_Mutation_p.L155H|NLRP1_ENST00000269280.4_Missense_Mutation_p.L155H|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000262467.5_Missense_Mutation_p.L155H			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	155			L -> H (associated with susceptibility to vitiligo and vitiligo-associated autoimmune diseases; dbSNP:rs12150220). {ECO:0000269|PubMed:11270363, ECO:0000269|PubMed:17377159}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.L155H(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TTGGTAGAGGAGTGAGGCAGA	0.478													A|||	962	0.192093	0.034	0.3674	5008	,	,		18435	0.0308		0.4443	False		,,,				2504	0.1881				p.L155H		Atlas-SNP	.											NLRP1,NS,carcinoma,0,1	NLRP1	358	1	1	Substitution - Missense(1)	prostate(1)	c.T464A	GRCh37	CM074383	NLRP1	M	rs12150220	PASS	.	A	HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU	437,3969	204.8+/-226.9	24,389,1790	34.0	37.0	36.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	464,464,464,464,464	-1.1	0.0	17	dbSNP_120	36	3884,4716	530.3+/-381.8	877,2130,1293	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	99,99,99,99,99	901,2519,3083	TT,TA,AA		45.1628,9.9183,33.2231	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	155/1376,155/1430,155/1474,155/1444,155/1400	5485367	4321,8685	2203	4300	6503	SO:0001583	missense	22861	exon3			TAGAGGAGTGAGG	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.464T>A	17.37:g.5485367A>T	ENSP00000460475:p.Leu155His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	93	0.958763	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	504	0.23076923076923078	20	0.04065040650406504	131	0.36187845303867405	19	0.033216783216783216	334	0.44063324538258575	A	11.80	1.745635	0.30955	0.099183	0.451628	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	2.85	-1.07	0.09968	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;D;D;D;D	0.69078	0.997;0.997;0.994;0.997;0.994	P;P;P;P;P	0.57548	0.823;0.823;0.669;0.823;0.669	T	0.37197	-0.9716	8	0.41790	T	0.15	.	0.4436	0.00490	0.4246:0.2228:0.1358:0.2168	rs12150220;rs52798470;rs12150220	155;155;155;155;155	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	H	155	ENSP00000442029:L155H;ENSP00000262467:L155H;ENSP00000269280:L155H;ENSP00000346390:L155H;ENSP00000324366:L155H	ENSP00000262467:L155H	L	-	2	0	NLRP1	5426091	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.072000	0.03434	-0.277000	0.09193	0.459000	0.35465	CTC	A|0.737;T|0.263	0.263	strong		0.478	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
TNKS	8658	hgsc.bcm.edu	37	8	9414049	9414049	+	Silent	SNP	G	G	A	rs33945943	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:9414049G>A	ENST00000310430.6	+	1	626	c.600G>A	c.(598-600)agG>agA	p.R200R	RP11-375N15.2_ENST00000607598.1_RNA|TNKS_ENST00000522110.1_Silent_p.R200R|TNKS_ENST00000520408.1_Silent_p.R200R	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	200					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		GGGTAAAGAGGCTGGTGGACG	0.597													G|||	1353	0.270168	0.205	0.1772	5008	,	,		16947	0.4048		0.2366	False		,,,				2504	0.32				p.R200R		Atlas-SNP	.											.	TNKS	198	.	0			c.G600A						PASS	.	G		899,3507	318.2+/-295.5	85,729,1389	56.0	63.0	61.0		600	4.5	1.0	8	dbSNP_126	61	2000,6600	322.0+/-315.3	239,1522,2539	no	coding-synonymous	TNKS	NM_003747.2		324,2251,3928	AA,AG,GG		23.2558,20.404,22.2897		200/1328	9414049	2899,10107	2203	4300	6503	SO:0001819	synonymous_variant	8658	exon1			AAAGAGGCTGGTG	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.600G>A	8.37:g.9414049G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	37	CCDS5974.1																																																																																			A|0.233;C|0.000;G|0.767	0.233	strong		0.597	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	
TSSK2	23617	hgsc.bcm.edu	37	22	19119686	19119686	+	Silent	SNP	C	C	T	rs1052756	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:19119686C>T	ENST00000399635.2	+	1	1366	c.774C>T	c.(772-774)agC>agT	p.S258S	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	258	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					CCGACGTCAGCCAGCGGCTCC	0.627													C|||	778	0.155351	0.0938	0.1297	5008	,	,		19325	0.125		0.173	False		,,,				2504	0.2699				p.S258S		Atlas-SNP	.											.	TSSK2	29	.	0			c.C774T						PASS	.	C	,	381,4025	188.8+/-215.1	18,345,1840	70.0	60.0	63.0		,774	5.7	1.0	22	dbSNP_86	63	1589,7011	293.1+/-301.2	165,1259,2876	no	utr-3,coding-synonymous	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,	183,1604,4716	TT,TC,CC		18.4767,8.6473,15.1469	,	,258/359	19119686	1970,11036	2203	4300	6503	SO:0001819	synonymous_variant	23617	exon1			CGTCAGCCAGCGG	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"""serine/threonine kinase 22B (spermiogenesis associated)"""	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.774C>T	22.37:g.19119686C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_053006	Q8IY55	Silent	SNP	ENST00000399635.2	37	CCDS13755.1																																																																																			C|0.851;A|0.001	.	strong		0.627	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
LMBRD2	92255	hgsc.bcm.edu	37	5	36143392	36143392	+	Silent	SNP	C	C	T	rs267766	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:36143392C>T	ENST00000296603.4	-	2	522	c.60G>A	c.(58-60)ctG>ctA	p.L20L		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	20						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.L20L(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATCGATGAAGCAGAAATAATG	0.363													T|||	1681	0.335663	0.4425	0.2752	5008	,	,		16604	0.2192		0.4066	False		,,,				2504	0.2812				p.L20L		Atlas-SNP	.											LMBRD2,NS,carcinoma,0,1	LMBRD2	89	1	1	Substitution - coding silent(1)	stomach(1)	c.G60A						scavenged	.	T		1885,2521	628.9+/-395.2	400,1085,718	117.0	109.0	111.0		60	-0.8	1.0	5	dbSNP_79	111	3502,5098	633.6+/-398.8	717,2068,1515	no	coding-synonymous	LMBRD2	NM_001007527.1		1117,3153,2233	TT,TC,CC		40.7209,42.7826,41.4193		20/696	36143392	5387,7619	2203	4300	6503	SO:0001819	synonymous_variant	92255	exon2			ATGAAGCAGAAAT		CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.60G>A	5.37:g.36143392C>T		Somatic	233	2	0.00858369		WXS	Illumina HiSeq	Phase_I	271	269	0.99262	NM_001007527	B3KRB6|Q9NTC7	Silent	SNP	ENST00000296603.4	37	CCDS34145.1																																																																																			C|0.628;T|0.372	0.372	strong		0.363	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527	
SH3BP2	6452	hgsc.bcm.edu	37	4	2828969	2828969	+	Silent	SNP	G	G	A	rs145235325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2828969G>A	ENST00000356331.5	+	6	702	c.441G>A	c.(439-441)tcG>tcA	p.S147S	SH3BP2_ENST00000503393.2_Silent_p.S204S|SH3BP2_ENST00000515183.1_3'UTR|SH3BP2_ENST00000511747.1_Silent_p.S147S|SH3BP2_ENST00000452765.2_Silent_p.S147S|SH3BP2_ENST00000442312.2_Silent_p.S175S|SH3BP2_ENST00000435136.2_Silent_p.S147S	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	147					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		ACTCCAGCTCGGACACAGACA	0.602									Cherubism				g|||	3	0.000599042	0.0008	0.0	5008	,	,		22783	0.0		0.002	False		,,,				2504	0.0				p.S204S		Atlas-SNP	.											.	SH3BP2	43	.	0			c.G612A						PASS	.		,,,	1,4405	2.1+/-5.4	0,1,2202	133.0	107.0	116.0		441,525,612,441	-9.9	0.9	4	dbSNP_134	116	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	,,,	147/562,175/590,204/619,147/562	2828969	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	6452	exon6	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CAGCTCGGACACA	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	10825	protein-coding gene	gene with protein product		602104	"""Cherubism"""			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.441G>A	4.37:g.2828969G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
SLC25A23	79085	hgsc.bcm.edu	37	19	6452423	6452423	+	Missense_Mutation	SNP	C	C	T	rs61729423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6452423C>T	ENST00000301454.4	-	8	1077	c.971G>A	c.(970-972)cGt>cAt	p.R324H	SLC25A23_ENST00000334510.5_Missense_Mutation_p.R324H|SLC25A23_ENST00000414491.2_Intron	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	324					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CTCCAGGATACGCCTGGCGCA	0.652													C|||	50	0.00998403	0.0008	0.0029	5008	,	,		15658	0.0		0.0099	False		,,,				2504	0.0378				p.R324H		Atlas-SNP	.											.	SLC25A23	43	.	0			c.G971A						PASS	.	C	HIS/ARG	11,4395	17.9+/-39.9	0,11,2192	39.0	35.0	36.0		971	-1.1	0.8	19	dbSNP_129	36	159,8441	75.4+/-138.0	0,159,4141	yes	missense	SLC25A23	NM_024103.2	29	0,170,6333	TT,TC,CC		1.8488,0.2497,1.3071	benign	324/469	6452423	170,12836	2203	4300	6503	SO:0001583	missense	79085	exon8			AGGATACGCCTGG	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.971G>A	19.37:g.6452423C>T	ENSP00000301454:p.Arg324His	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	37	CCDS32882.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	16.49	3.136971	0.56936	0.002497	0.018488	ENSG00000125648	ENST00000264088;ENST00000422102;ENST00000301454;ENST00000334510	T;T;T	0.79653	-1.29;-1.29;-1.29	5.46	-1.06	0.10002	Mitochondrial carrier domain (2);	0.262628	0.38164	N	0.001794	T	0.49626	0.1568	L	0.28274	0.84	0.34903	D	0.746684	B	0.10296	0.003	B	0.10450	0.005	T	0.55256	-0.8169	10	0.48119	T	0.1	-18.2413	9.6813	0.40072	0.0:0.2476:0.0:0.7524	.	324	Q9BV35	SCMC3_HUMAN	H	371;25;324;324	ENSP00000264088:R371H;ENSP00000301454:R324H;ENSP00000334537:R324H	ENSP00000264088:R371H	R	-	2	0	SLC25A23	6403423	1.000000	0.71417	0.843000	0.33291	0.829000	0.46940	1.625000	0.37029	-0.042000	0.13535	0.591000	0.81541	CGT	C|0.990;T|0.010	0.010	strong		0.652	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
SHISA9	729993	hgsc.bcm.edu	37	16	13297348	13297348	+	Silent	SNP	C	C	T	rs12444395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:13297348C>T	ENST00000424107.3	+	3	1234	c.789C>T	c.(787-789)ccC>ccT	p.P263P	SHISA9_ENST00000558583.1_Silent_p.P304P|AC009134.1_ENST00000571939.1_RNA			B4DS77	SHSA9_HUMAN	shisa family member 9	263					regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|dendritic spine membrane (GO:0032591)|ionotropic glutamate receptor complex (GO:0008328)|synapse (GO:0045202)				breast(1)|endometrium(2)|kidney(1)|lung(2)|prostate(1)|skin(2)	9						TCTCCAACCCCTATGAACAGC	0.542													C|||	80	0.0159744	0.0015	0.0173	5008	,	,		18542	0.001		0.0318	False		,,,				2504	0.0337				p.P263P		Atlas-SNP	.											.	SHISA9	33	.	0			c.C789T						PASS	.	C		5,1379		0,5,687	176.0	163.0	167.0		789	1.1	1.0	16	dbSNP_120	167	104,3078		2,100,1489	no	coding-synonymous	SHISA9	NM_001145204.2		2,105,2176	TT,TC,CC		3.2684,0.3613,2.3872		263/425	13297348	109,4457	692	1591	2283	SO:0001819	synonymous_variant	729993	exon3			CAACCCCTATGAA		CCDS45417.1, CCDS45418.1, CCDS45417.2, CCDS45418.2	16p13.12	2013-07-31	2013-07-31		ENSG00000237515	ENSG00000237515		"""Shisa homologs"""	37231	protein-coding gene	gene with protein product		613346	"""shisa homolog 9 (Xenopus laevis)"""				Standard	NM_001145205		Approved		uc010uyy.2	B4DS77	OTTHUMG00000154258	ENST00000424107.3:c.789C>T	16.37:g.13297348C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_001145204	C9J314|C9JCE9	Silent	SNP	ENST00000424107.3	37	CCDS45417.2																																																																																			C|0.980;T|0.020	0.020	strong		0.542	SHISA9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334564.5	NM_001145204	
E2F7	144455	hgsc.bcm.edu	37	12	77438436	77438436	+	Silent	SNP	T	T	C	rs2242384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:77438436T>C	ENST00000322886.7	-	6	1204	c.969A>G	c.(967-969)ccA>ccG	p.P323P	E2F7_ENST00000416496.2_Silent_p.P323P	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	323					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P323P(1)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TACTATGGTCTGGGGCATCTT	0.403													C|||	951	0.189896	0.1036	0.2464	5008	,	,		17986	0.1647		0.2575	False		,,,				2504	0.2229				p.P323P		Atlas-SNP	.											E2F7_ENST00000322886,NS,carcinoma,0,1	E2F7	201	1	1	Substitution - coding silent(1)	stomach(1)	c.A969G						PASS	.	C		586,3820	772.6+/-413.9	50,486,1667	180.0	172.0	174.0		969	-12.1	0.1	12	dbSNP_98	174	2369,6231	702.1+/-405.3	306,1757,2237	no	coding-synonymous	E2F7	NM_203394.2		356,2243,3904	CC,CT,TT		27.5465,13.3,22.7203		323/912	77438436	2955,10051	2203	4300	6503	SO:0001819	synonymous_variant	144455	exon6			ATGGTCTGGGGCA	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.969A>G	12.37:g.77438436T>C		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1	432	0.1978021978021978	51	0.10365853658536585	91	0.2513812154696133	95	0.1660839160839161	195	0.25725593667546176	C	7.117	0.577118	0.13686	0.133	0.275465	ENSG00000165891	ENST00000551058	.	.	.	6.07	-12.1	0.00011	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21627	P	0.999618366	.	.	.	.	.	.	T	0.06698	-1.0812	3	.	.	.	-7.7333	11.7418	0.51796	0.1909:0.5119:0.0:0.2972	rs2242384;rs17760343;rs58868311;rs2242384	.	.	.	R	201	.	.	Q	-	2	0	E2F7	75962567	0.000000	0.05858	0.095000	0.20976	0.924000	0.55760	-4.852000	0.00178	-2.400000	0.00579	-1.874000	0.00550	CAG	T|0.792;C|0.208	0.208	strong		0.403	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
HAPLN3	145864	hgsc.bcm.edu	37	15	89430506	89430506	+	Silent	SNP	C	C	T	rs3743395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89430506C>T	ENST00000359595.3	-	2	238	c.24G>A	c.(22-24)ccG>ccA	p.P8P	HAPLN3_ENST00000562889.1_Silent_p.P70P	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	8					cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	GCAGGAGCAACGGGACCAGGA	0.612													C|||	1020	0.203674	0.1755	0.2248	5008	,	,		18625	0.2222		0.2505	False		,,,				2504	0.1595				p.P8P		Atlas-SNP	.											.	HAPLN3	43	.	0			c.G24A						PASS	.	C		815,3585	322.6+/-297.7	86,643,1471	107.0	95.0	99.0		24	-0.2	0.0	15	dbSNP_107	99	2267,6331	382.7+/-340.5	277,1713,2309	no	coding-synonymous	HAPLN3	NM_178232.2		363,2356,3780	TT,TC,CC		26.3666,18.5227,23.7113		8/361	89430506	3082,9916	2200	4299	6499	SO:0001819	synonymous_variant	145864	exon2			GAGCAACGGGACC	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.24G>A	15.37:g.89430506C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	162	72	0.444444	NM_178232	A8K7P0	Silent	SNP	ENST00000359595.3	37	CCDS10346.1																																																																																			C|0.770;T|0.230	0.230	strong		0.612	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
TOPORS	10210	hgsc.bcm.edu	37	9	32541532	32541532	+	Silent	SNP	A	A	G	rs12348918	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:32541532A>G	ENST00000360538.2	-	3	3107	c.2991T>C	c.(2989-2991)gaT>gaC	p.D997D	TOPORS_ENST00000379858.1_Silent_p.D932D	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	997					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D997D(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		CTTCTCTTACATCGAGAGTTT	0.423													A|||	572	0.114217	0.093	0.1412	5008	,	,		20493	0.0079		0.2545	False		,,,				2504	0.089				p.D997D		Atlas-SNP	.											TOPORS_ENST00000360538,NS,carcinoma,0,2	TOPORS	127	2	1	Substitution - coding silent(1)	prostate(1)	c.T2991C						PASS	.	A	,	551,3855	248.4+/-256.2	34,483,1686	164.0	158.0	160.0		2796,2991	3.1	1.0	9	dbSNP_120	160	2111,6489	363.7+/-333.3	260,1591,2449	no	coding-synonymous,coding-synonymous	TOPORS	NM_001195622.1,NM_005802.4	,	294,2074,4135	GG,GA,AA		24.5465,12.5057,20.4675	,	932/981,997/1046	32541532	2662,10344	2203	4300	6503	SO:0001819	synonymous_variant	10210	exon3			TCTTACATCGAGA	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2991T>C	9.37:g.32541532A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	149	57	0.38255	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Silent	SNP	ENST00000360538.2	37	CCDS6527.1																																																																																			A|0.832;G|0.168	0.168	strong		0.423	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
MTA1	9112	hgsc.bcm.edu	37	14	105930406	105930406	+	Missense_Mutation	SNP	G	G	A	rs4983413	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105930406G>A	ENST00000331320.7	+	13	1328	c.1114G>A	c.(1114-1116)Gtc>Atc	p.V372I	MTA1_ENST00000435036.2_5'UTR|MTA1_ENST00000406191.1_Missense_Mutation_p.V372I|MTA1_ENST00000405646.1_Missense_Mutation_p.V355I	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	372			V -> I (in dbSNP:rs4983413).		circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.V372I(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		CGTCAACAACGTCAAGGCCGG	0.617													G|||	1427	0.284944	0.0121	0.3314	5008	,	,		12491	0.622		0.2366	False		,,,				2504	0.3231				p.V372I		Atlas-SNP	.											MTA1,NS,carcinoma,0,1	MTA1	61	1	1	Substitution - Missense(1)	stomach(1)	c.G1114A						PASS	.	G	ILE/VAL,ILE/VAL	233,4173	138.0+/-173.8	9,215,1979	73.0	76.0	75.0		1114,1114	1.7	1.0	14	dbSNP_111	75	1995,6605	349.7+/-327.5	235,1525,2540	yes	missense,missense	MTA1	NM_001203258.1,NM_004689.3	29,29	244,1740,4519	AA,AG,GG		23.1977,5.2882,17.1306	benign,benign	372/431,372/716	105930406	2228,10778	2203	4300	6503	SO:0001583	missense	9112	exon13			AACAACGTCAAGG	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"""GATA zinc finger domain containing"""	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1114G>A	14.37:g.105930406G>A	ENSP00000333633:p.Val372Ile	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	149	67	0.449664	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	37	CCDS32169.1	655	0.2999084249084249	11	0.022357723577235773	110	0.30386740331491713	360	0.6293706293706294	174	0.22955145118733508	G	12.92	2.082237	0.36758	0.052882	0.231977	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000434050	T;T;T;T	0.30981	1.52;1.52;1.51;1.53	4.61	1.66	0.24008	.	0.396957	0.27080	N	0.021022	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.99999999865637	B;B	0.31274	0.164;0.317	B;B	0.26202	0.036;0.067	T	0.36187	-0.9758	9	0.36615	T	0.2	-21.1079	7.0619	0.25131	0.1661:0.1403:0.6937:0.0	rs4983413;rs60510827;rs4983413	164;372	Q59FW1;Q13330	.;MTA1_HUMAN	I	281;372;372;355;164	ENSP00000333633:V372I;ENSP00000385702:V372I;ENSP00000384180:V355I;ENSP00000394106:V164I	ENSP00000333633:V372I	V	+	1	0	MTA1	105001451	0.813000	0.29090	0.972000	0.41901	0.734000	0.41952	1.456000	0.35201	0.366000	0.24427	0.563000	0.77884	GTC	G|0.782;A|0.218	0.218	strong		0.617	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
PCDHAC1	56135	hgsc.bcm.edu	37	5	140307485	140307485	+	Silent	SNP	T	T	C	rs147219331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140307485T>C	ENST00000253807.2	+	1	1008	c.1008T>C	c.(1006-1008)caT>caC	p.H336H	PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHAC1_ENST00000409700.3_Silent_p.H336H|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	336	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAACGATCATGCCCCCGAAC	0.532													t|||	2	0.000399361	0.0	0.0	5008	,	,		21222	0.0		0.002	False		,,,				2504	0.0				p.H336H		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.T1008C						PASS	.	T	,,,,,,,,,,,,,,,,,	5,4401	9.9+/-24.2	0,5,2198	174.0	160.0	164.0		1008,,,,,,,,,,,,,,,,,1008	-0.5	0.3	5	dbSNP_134	164	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031882.2	,,,,,,,,,,,,,,,,,	0,16,6487	CC,CT,TT		0.1279,0.1135,0.123	,,,,,,,,,,,,,,,,,	336/964,,,,,,,,,,,,,,,,,336/819	140307485	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			CGATCATGCCCCC	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1008T>C	5.37:g.140307485T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	194	61	0.314433	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																			T|0.999;C|0.001	0.001	strong		0.532	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
FAM187A	100528020	hgsc.bcm.edu	37	17	42979026	42979026	+	Intron	SNP	T	T	C	rs74349463	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42979026T>C	ENST00000331733.4	+	3	371				CCDC103_ENST00000417826.2_Intron|EFTUD2_ENST00000402521.3_5'Flank|EFTUD2_ENST00000592576.1_5'Flank|EFTUD2_ENST00000426333.2_5'Flank|CCDC103_ENST00000410006.2_Intron|FAM187A_ENST00000412523.2_Intron|EFTUD2_ENST00000591382.1_5'Flank|CCDC103_ENST00000410027.1_Intron|AC015936.3_ENST00000441312.1_RNA	NM_001258399.1|NM_213607.2	NP_001245328.1|NP_998772.1	A6NFU0	F187A_HUMAN	family with sequence similarity 187, member A							integral component of membrane (GO:0016021)											CCCCGGTAGGTGAGGCCCTGC	0.458													T|||	474	0.0946486	0.0635	0.1037	5008	,	,		21708	0.005		0.166	False		,,,				2504	0.1493				.		Atlas-SNP	.											.	CCDC103	15	.	0			c.280+2T>C						PASS	.	T		309,4097	167.3+/-198.3	7,295,1901	88.0	76.0	80.0			-0.4	0.2	17	dbSNP_132	80	1457,7143	278.4+/-293.4	112,1233,2955	no	intron	CCDC103	NM_213607.1		119,1528,4856	CC,CT,TT		16.9419,7.0132,13.5783			42979026	1766,11240	2203	4300	6503	SO:0001627	intron_variant	388389	exon3			GGTAGGTGAGGCC			17q21.31	2013-01-11			ENSG00000214447	ENSG00000214447		"""Immunoglobulin superfamily / V-set domain containing"""	35153	protein-coding gene	gene with protein product							Standard			Approved		uc002ihp.1	A6NFU0	OTTHUMG00000154266	ENST00000331733.4:c.-1466+6T>C	17.37:g.42979026T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_001258399		Splice_Site	SNP	ENST00000331733.4	37																																																																																				T|0.873;C|0.127	0.127	strong		0.458	FAM187A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334584.1		
DAG1	1605	hgsc.bcm.edu	37	3	49570200	49570200	+	Silent	SNP	C	C	T	rs1801143	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49570200C>T	ENST00000539901.1	+	3	2814	c.2256C>T	c.(2254-2256)caC>caT	p.H752H	DAG1_ENST00000541308.1_Silent_p.H752H|DAG1_ENST00000515359.2_Silent_p.H752H|DAG1_ENST00000545947.1_Silent_p.H752H|DAG1_ENST00000308775.2_Silent_p.H752H|DAG1_ENST00000538711.1_Silent_p.H752H	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	752					basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		TCTACCTGCACACAGTCATTC	0.592													C|||	1081	0.215855	0.2693	0.1744	5008	,	,		19791	0.0724		0.333	False		,,,				2504	0.2004				p.H752H		Atlas-SNP	.											.	DAG1	60	.	0			c.C2256T						PASS	.	C	,,,,,,,,,,,,	1276,3130	434.1+/-343.8	180,916,1107	51.0	45.0	47.0		2256,2256,2256,2256,2256,2256,2256,2256,2256,2256,2256,2256,2256	1.8	1.0	3	dbSNP_89	47	2699,5901	432.2+/-357.0	450,1799,2051	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DAG1	NM_001165928.2,NM_001177634.1,NM_001177635.1,NM_001177636.1,NM_001177637.1,NM_001177638.1,NM_001177639.1,NM_001177640.1,NM_001177641.1,NM_001177642.1,NM_001177643.1,NM_001177644.1,NM_004393.4	,,,,,,,,,,,,	630,2715,3158	TT,TC,CC		31.3837,28.9605,30.5628	,,,,,,,,,,,,	752/896,752/896,752/896,752/896,752/896,752/896,752/896,752/896,752/896,752/896,752/896,752/896,752/896	49570200	3975,9031	2203	4300	6503	SO:0001819	synonymous_variant	1605	exon4			CCTGCACACAGTC	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"""alpha-dystroglycan"", ""dystrophin-associated glycoprotein-1"", ""beta-dystroglycan"""	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.2256C>T	3.37:g.49570200C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	139	63	0.453237	NM_001177642	A8K6M7|Q969J9	Silent	SNP	ENST00000539901.1	37	CCDS2799.1																																																																																			C|0.722;T|0.278	0.278	strong		0.592	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1		
ANKRD33	341405	hgsc.bcm.edu	37	12	52284500	52284500	+	Missense_Mutation	SNP	A	A	G	rs34494292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52284500A>G	ENST00000340970.4	+	5	766	c.395A>G	c.(394-396)cAg>cGg	p.Q132R	ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Missense_Mutation_p.Q63R|ANKRD33_ENST00000301190.6_Missense_Mutation_p.Q257R			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	132			Q -> R (in dbSNP:rs34494292). {ECO:0000269|PubMed:14702039}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		CAGCTTAGCCAGCACTACAAG	0.672													A|||	746	0.148962	0.0318	0.134	5008	,	,		13096	0.2063		0.1918	False		,,,				2504	0.2147				p.Q257R		Atlas-SNP	.											.	ANKRD33	33	.	0			c.A770G						PASS	.	A	ARG/GLN,ARG/GLN	278,4128	142.7+/-177.9	6,266,1931	24.0	26.0	25.0		395,770	-0.6	0.2	12	dbSNP_126	25	1751,6849	290.5+/-299.9	193,1365,2742	yes	missense,missense	ANKRD33	NM_001130015.1,NM_182608.3	43,43	199,1631,4673	GG,GA,AA		20.3605,6.3096,15.6005	possibly-damaging,possibly-damaging	132/273,257/453	52284500	2029,10977	2203	4300	6503	SO:0001583	missense	341405	exon5			TTAGCCAGCACTA		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"""Ankyrin repeat domain containing"""	13788	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 7"""	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.395A>G	12.37:g.52284500A>G	ENSP00000344690:p.Gln132Arg	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	23	6	0.26087	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	340	0.15567765567765568	23	0.046747967479674794	50	0.13812154696132597	126	0.2202797202797203	141	0.18601583113456466	A	11.27	1.588295	0.28357	0.063096	0.203605	ENSG00000167612	ENST00000301190;ENST00000538991;ENST00000340970	T;T;T	0.22539	2.09;1.95;2.4	4.7	-0.552	0.11818	.	0.858027	0.10348	N	0.685403	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;P;B	0.38370	0.146;0.628;0.003	B;B;B	0.28465	0.024;0.09;0.003	T	0.35968	-0.9767	9	0.15066	T	0.55	-3.0E-4	3.2663	0.06867	0.529:0.0:0.1748:0.2962	rs34494292	132;63;257	Q7Z3H0;Q0VAA8;Q7Z3H0-2	ANR33_HUMAN;.;.	R	257;63;132	ENSP00000301190:Q257R;ENSP00000443722:Q63R;ENSP00000344690:Q132R	ENSP00000301190:Q257R	Q	+	2	0	ANKRD33	50570767	0.000000	0.05858	0.201000	0.23476	0.720000	0.41350	0.671000	0.25172	0.026000	0.15269	0.459000	0.35465	CAG	A|0.845;G|0.155	0.155	strong		0.672	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
ARRDC4	91947	hgsc.bcm.edu	37	15	98513845	98513845	+	Missense_Mutation	SNP	T	T	C	rs2130882	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:98513845T>C	ENST00000268042.6	+	7	1236	c.1072T>C	c.(1072-1074)Tca>Cca	p.S358P	ARRDC4_ENST00000538249.1_Missense_Mutation_p.S271P	NM_183376.2	NP_899232.2	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4	358			S -> P (in dbSNP:rs2130882). {ECO:0000269|PubMed:15489334}.		positive regulation of ubiquitin-protein transferase activity (GO:0051443)	endosome (GO:0005768)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|skin(3)	16	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			AGATGTGGTATCAGAGGAAGA	0.403													T|||	2099	0.419129	0.0545	0.5043	5008	,	,		16140	0.5486		0.4811	False		,,,				2504	0.6544				p.S358P		Atlas-SNP	.											ARRDC4,colon,carcinoma,0,1	ARRDC4	30	1	0			c.T1072C						PASS	.	T	PRO/SER	511,3883	233.3+/-246.5	36,439,1722	99.0	87.0	91.0		1072	4.3	1.0	15	dbSNP_96	91	4362,4234	581.6+/-391.2	1096,2170,1032	yes	missense	ARRDC4	NM_183376.2	74	1132,2609,2754	CC,CT,TT		49.2555,11.6295,37.5135	probably-damaging	358/419	98513845	4873,8117	2197	4298	6495	SO:0001583	missense	91947	exon7			GTGGTATCAGAGG	BC028704	CCDS10377.1	15q26.2	2005-08-16			ENSG00000140450	ENSG00000140450			28087	protein-coding gene	gene with protein product						12477932	Standard	NM_183376		Approved	FLJ36045	uc010bom.3	Q8NCT1	OTTHUMG00000149849	ENST00000268042.6:c.1072T>C	15.37:g.98513845T>C	ENSP00000268042:p.Ser358Pro	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	NM_183376	Q6NSI9	Missense_Mutation	SNP	ENST00000268042.6	37	CCDS10377.1	900	0.41208791208791207	38	0.07723577235772358	174	0.48066298342541436	320	0.5594405594405595	368	0.48548812664907653	T	14.26	2.483797	0.44147	0.116295	0.507445	ENSG00000140450	ENST00000538249;ENST00000268042	T;T	0.10382	2.88;3.05	5.49	4.35	0.52113	Immunoglobulin E-set (1);	0.000000	0.64402	D	0.000010	T	0.00012	0.0000	L	0.42686	1.345	0.23162	P	0.99819883	D;D	0.71674	0.998;0.995	P;P	0.60682	0.878;0.876	T	0.30416	-0.9979	9	0.17832	T	0.49	-5.5959	12.0812	0.53671	0.129:0.0:0.0:0.871	rs2130882;rs3759829;rs17852599;rs52814015;rs58570136;rs2130882	358;271	Q8NCT1;F5H824	ARRD4_HUMAN;.	P	271;358	ENSP00000443774:S271P;ENSP00000268042:S358P	ENSP00000268042:S358P	S	+	1	0	ARRDC4	96314849	1.000000	0.71417	0.965000	0.40720	0.753000	0.42808	3.886000	0.56190	0.994000	0.38892	-0.336000	0.08194	TCA	C|0.387;N|0.001	0.387	strong		0.403	ARRDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313535.1	NM_183376	
SSTR4	6754	hgsc.bcm.edu	37	20	23017017	23017017	+	Silent	SNP	T	T	C	rs2567609	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23017017T>C	ENST00000255008.3	+	1	961	c.897T>C	c.(895-897)ctT>ctC	p.L299L	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	299					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					CCCTTATCCTTAGCTATGCCA	0.572													C|||	2415	0.482228	0.4107	0.4669	5008	,	,		18691	0.5258		0.4294	False		,,,				2504	0.5992				p.L299L	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,colon,carcinoma,0,2	SSTR4	83	2	0			c.T897C						PASS	.	C		1770,2636	625.8+/-394.6	379,1012,812	199.0	197.0	197.0		897	2.4	1.0	20	dbSNP_100	197	3925,4675	598.8+/-394.0	922,2081,1297	no	coding-synonymous	SSTR4	NM_001052.2		1301,3093,2109	CC,CT,TT		45.6395,40.1725,43.7875		299/389	23017017	5695,7311	2203	4300	6503	SO:0001819	synonymous_variant	6754	exon1			TATCCTTAGCTAT		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.897T>C	20.37:g.23017017T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	157	71	0.452229	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Silent	SNP	ENST00000255008.3	37	CCDS42856.1																																																																																			T|0.514;C|0.486	0.486	strong		0.572	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
CLIP1	6249	hgsc.bcm.edu	37	12	122812503	122812503	+	Missense_Mutation	SNP	G	G	C	rs1129167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:122812503G>C	ENST00000540338.1	-	16	3281	c.3240C>G	c.(3238-3240)gaC>gaG	p.D1080E	CLIP1_ENST00000302528.7_Missense_Mutation_p.D1069E|CLIP1_ENST00000358808.2_Missense_Mutation_p.D1069E|CLIP1_ENST00000361654.4_Missense_Mutation_p.D958E|CLIP1_ENST00000545889.1_Missense_Mutation_p.D655E|CLIP1_ENST00000537178.1_Missense_Mutation_p.D1034E			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	1080			D -> E (in dbSNP:rs1129167). {ECO:0000269|PubMed:1356075, ECO:0000269|PubMed:15489334}.		microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CTTTGGCTTTGTCGGCTTGCT	0.567													G|||	2036	0.40655	0.0575	0.5159	5008	,	,		20593	0.3889		0.6412	False		,,,				2504	0.5777				p.D1080E		Atlas-SNP	.											.	CLIP1	126	.	0			c.C3240G						PASS	.	G	GLU/ASP,GLU/ASP	701,3705	292.7+/-282.2	54,593,1556	94.0	79.0	84.0		3207,3102	0.7	0.9	12	dbSNP_86	84	5390,3210	640.9+/-399.6	1704,1982,614	yes	missense,missense	CLIP1	NM_002956.2,NM_198240.1	45,45	1758,2575,2170	CC,CG,GG		37.3256,15.9101,46.8322	benign,benign	1069/1428,1034/1393	122812503	6091,6915	2203	4300	6503	SO:0001583	missense	6249	exon17			GGCTTTGTCGGCT		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.3240C>G	12.37:g.122812503G>C	ENSP00000439093:p.Asp1080Glu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_001247997	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	905	0.4143772893772894	38	0.07723577235772358	173	0.47790055248618785	206	0.36013986013986016	488	0.6437994722955145	G	0.068	-1.209154	0.01568	0.159101	0.626744	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000392458;ENST00000537178;ENST00000540338	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26	5.65	0.728	0.18260	.	0.107762	0.64402	N	0.000010	T	0.00012	0.0000	N	0.08118	0	0.39235	P	0.036241999999999996	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.44787	-0.9305	9	0.02654	T	1	-11.3314	1.7014	0.02873	0.2973:0.2949:0.295:0.1128	rs3186758	1034;1069;1080	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	E	655;1069;1069;799;111;1034;1080	ENSP00000438743:D655E;ENSP00000303585:D1069E;ENSP00000351665:D1069E;ENSP00000445531:D1034E;ENSP00000439093:D1080E	ENSP00000303585:D1069E	D	-	3	2	CLIP1	121378456	0.998000	0.40836	0.916000	0.36221	0.028000	0.11728	0.280000	0.18790	0.062000	0.16340	-0.137000	0.14449	GAC	G|0.545;C|0.455	0.455	strong		0.567	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
CEP170	9859	hgsc.bcm.edu	37	1	243329211	243329211	+	Missense_Mutation	SNP	G	G	T	rs2728430		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:243329211G>T	ENST00000366542.1	-	13	2102	c.2051C>A	c.(2050-2052)aCa>aAa	p.T684K	CEP170_ENST00000490813.1_5'Flank|CEP170_ENST00000366543.1_Missense_Mutation_p.T586K|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Missense_Mutation_p.T586K|RP11-261C10.4_ENST00000422938.1_RNA	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	684						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GTATACCTGTGTAGGTGTTTC	0.408																																					p.T684K		Atlas-SNP	.											CEP170,NS,carcinoma,-1,1	CEP170	153	1	0			c.C2051A						scavenged	.						160.0	135.0	143.0					1																	243329211		1845	4100	5945	SO:0001583	missense	9859	exon13			ACCTGTGTAGGTG	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2051C>A	1.37:g.243329211G>T	ENSP00000355500:p.Thr684Lys	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	298	30	0.100671	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.048|4.048	0.006608|0.006608	0.07866|0.07866	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000336415|ENST00000366542;ENST00000366544;ENST00000366543	.|T;T;T	.|0.43294	.|1.0;0.95;0.96	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	.|0.490310	.|0.21930	.|N	.|0.067032	T|T	0.34077|0.34077	0.0885|0.0885	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.30361	.|0.089;0.039;0.277;0.03	.|B;B;B;B	.|0.26969	.|0.075;0.05;0.049;0.045	T|T	0.12553|0.12553	-1.0543|-1.0543	5|10	.|0.11182	.|T	.|0.66	-0.0033|-0.0033	17.8235|17.8235	0.88657|0.88657	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs2728430|rs2728430	.|647;586;586;684	.|B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.|.;.;.;CE170_HUMAN	N|K	648|684;586;586	.|ENSP00000355500:T684K;ENSP00000355502:T586K;ENSP00000355501:T586K	.|ENSP00000355500:T684K	H|T	-|-	1|2	0|0	CEP170|CEP170	241395834|241395834	0.984000|0.984000	0.35163|0.35163	0.007000|0.007000	0.13788|0.13788	0.882000|0.882000	0.50991|0.50991	3.771000|3.771000	0.55318|0.55318	2.445000|2.445000	0.82738|0.82738	0.484000|0.484000	0.47621|0.47621	CAC|ACA	.	.	weak		0.408	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
CLTC	1213	hgsc.bcm.edu	37	17	57759019	57759019	+	Silent	SNP	G	G	A	rs77062632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:57759019G>A	ENST00000269122.3	+	21	3535	c.3261G>A	c.(3259-3261)gaG>gaA	p.E1087E	CLTC_ENST00000393043.1_Silent_p.E1087E|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1087	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TCTTAATTGAGCATATTGGAA	0.393			T	"""ALK, TFE3"""	"""ALCL, renal """								G|||	55	0.0109824	0.0008	0.0144	5008	,	,		20653	0.0		0.0398	False		,,,				2504	0.0041				p.E1087E		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"""clathrin, heavy polypeptide (Hc)"""		L	CLTC_ENST00000269122,caecum,carcinoma,+2,1	CLTC	124	1	0			c.G3261A						PASS	.	G		31,4375	36.8+/-68.6	0,31,2172	101.0	97.0	98.0		3261	3.5	1.0	17	dbSNP_132	98	278,8322	104.6+/-165.6	8,262,4030	no	coding-synonymous	CLTC	NM_004859.3		8,293,6202	AA,AG,GG		3.2326,0.7036,2.3758		1087/1676	57759019	309,12697	2203	4300	6503	SO:0001819	synonymous_variant	1213	exon21			AATTGAGCATATT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"""clathrin, heavy polypeptide (Hc)"", ""clathrin, heavy chain"", ""clathrin, heavy polypeptide-like 2"""	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.3261G>A	17.37:g.57759019G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	139	54	0.388489	NM_004859	D3DU00|Q6N0A0|Q86TF2	Silent	SNP	ENST00000269122.3	37	CCDS32696.1																																																																																			G|0.978;A|0.022	0.022	strong		0.393	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859	
LMF1	64788	hgsc.bcm.edu	37	16	929711	929711	+	Silent	SNP	C	C	T	rs2076425	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:929711C>T	ENST00000262301.11	-	6	774	c.756G>A	c.(754-756)gcG>gcA	p.A252A	LMF1_ENST00000399843.2_Silent_p.A252A|LMF1_ENST00000543238.1_Silent_p.A15A|LMF1_ENST00000568897.1_Silent_p.A35A|LMF1_ENST00000568268.1_5'UTR	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	252					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				GCAGGTAGTACGCCACAGGAT	0.657													C|||	887	0.177117	0.208	0.0735	5008	,	,		14626	0.3026		0.1113	False		,,,				2504	0.1472				p.A252A		Atlas-SNP	.											LMF1,colon,carcinoma,-1,1	LMF1	42	1	0			c.G756A						PASS	.	C		796,3524		69,658,1433	58.0	70.0	66.0		756	3.1	1.0	16	dbSNP_96	66	881,7623		44,793,3415	no	coding-synonymous	LMF1	NM_022773.2		113,1451,4848	TT,TC,CC		10.3598,18.4259,13.077		252/568	929711	1677,11147	2160	4252	6412	SO:0001819	synonymous_variant	64788	exon6			GTAGTACGCCACA	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.756G>A	16.37:g.929711C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	156	63	0.403846	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.827;T|0.173	0.173	strong		0.657	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
WDFY1	57590	hgsc.bcm.edu	37	2	224765956	224765956	+	Silent	SNP	C	C	T	rs2272317	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:224765956C>T	ENST00000233055.4	-	5	531	c.429G>A	c.(427-429)acG>acA	p.T143T		NM_020830.3	NP_065881.1	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	143						cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)	18		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)		TCCCGCTCCGCGTGCACATCC	0.592													C|||	506	0.101038	0.0877	0.1052	5008	,	,		19706	0.248		0.0119	False		,,,				2504	0.0562				p.T143T		Atlas-SNP	.											.	WDFY1	46	.	0			c.G429A						PASS	.	C		357,4049	182.6+/-210.3	13,331,1859	136.0	115.0	122.0		429	-7.9	0.2	2	dbSNP_100	122	101,8499	55.2+/-116.2	0,101,4199	no	coding-synonymous	WDFY1	NM_020830.3		13,432,6058	TT,TC,CC		1.1744,8.1026,3.5215		143/411	224765956	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	57590	exon5			GCTCCGCGTGCAC	AB037856	CCDS33387.1	2q36.2	2013-01-09	2003-03-13		ENSG00000085449	ENSG00000085449		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20451	protein-coding gene	gene with protein product			"""WD40 and FYVE domain containing 1"""			11739631	Standard	NM_020830		Approved	KIAA1435, FENS-1, WDF1, ZFYVE17	uc002vnq.3	Q8IWB7	OTTHUMG00000153370	ENST00000233055.4:c.429G>A	2.37:g.224765956C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_020830	Q53S17|Q9H9D5|Q9P2B3	Silent	SNP	ENST00000233055.4	37	CCDS33387.1																																																																																			C|0.938;T|0.062	0.062	strong		0.592	WDFY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330908.1	NM_020830	
OVCH2	341277	hgsc.bcm.edu	37	11	7727872	7727872	+	lincRNA	SNP	T	T	C	rs12289558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7727872T>C	ENST00000527565.1	-	0	542				OVCH2_ENST00000534193.2_RNA|OVCH2_ENST00000454689.1_RNA|RP11-35J10.4_ENST00000527443.1_RNA																							AGCGAAAGAGTTGCAGATTTA	0.383													T|||	637	0.127196	0.0635	0.1383	5008	,	,		19395	0.0506		0.3181	False		,,,				2504	0.0879				p.T24A		Atlas-SNP	.											OVCH2,colon,carcinoma,0,1	OVCH2	47	1	0			c.A70G						PASS	.	T	ALA/THR	301,3367		16,269,1549	90.0	84.0	86.0		70	2.6	0.7	11	dbSNP_120	86	2645,5529		434,1777,1876	yes	missense	OVCH2	NM_198185.2	58	450,2046,3425	CC,CT,TT		32.3587,8.2061,24.8776	benign	24/565	7727872	2946,8896	1834	4087	5921			341277	exon1			AAAGAGTTGCAGA																													11.37:g.7727872T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_198185		Missense_Mutation	SNP	ENST00000527565.1	37		357	0.16346153846153846	31	0.06300813008130081	62	0.1712707182320442	33	0.057692307692307696	231	0.30474934036939316	T	8.017	0.758841	0.15846	0.082061	0.323587	ENSG00000183378	ENST00000454689	D	0.92495	-3.05	5.03	2.58	0.30949	.	0.506439	0.16701	N	0.203116	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P	0.40083	0.702	B	0.36092	0.217	T	0.24548	-1.0157	9	0.10111	T	0.7	-6.8763	3.5767	0.07937	0.2085:0.1044:0.0:0.6871	rs12289558;rs12289558	24	Q7RTZ1	OVCH2_HUMAN	A	24	ENSP00000407158:T24A	ENSP00000407158:T24A	T	-	1	0	OVCH2	7684448	0.018000	0.18449	0.671000	0.29857	0.016000	0.09150	0.481000	0.22260	0.956000	0.37904	0.459000	0.35465	ACT	T|0.837;C|0.163	0.163	strong		0.383	RP11-35J10.5-001	KNOWN	basic|readthrough_transcript	lincRNA	lincRNA	OTTHUMT00000385692.1		
AIF1	199	hgsc.bcm.edu	37	6	31583312	31583312	+	Missense_Mutation	SNP	G	G	A	rs2736182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31583312G>A	ENST00000376059.3	+	2	186	c.40G>A	c.(40-42)Gga>Aga	p.G14R	AIF1_ENST00000376049.4_5'Flank	NM_001623.3	NP_001614.3	P55008	AIF1_HUMAN	allograft inflammatory factor 1	14			G -> R (in dbSNP:rs2736182). {ECO:0000269|PubMed:14656967, ECO:0000269|PubMed:14702039}.		actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cellular response to interferon-gamma (GO:0071346)|inflammatory response (GO:0006954)|microglial cell activation (GO:0001774)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell proliferation (GO:0048662)|phagocytosis, engulfment (GO:0006911)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell migration (GO:2000406)|positive regulation of T cell proliferation (GO:0042102)|Rac protein signal transduction (GO:0016601)|ruffle assembly (GO:0097178)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|ruffle membrane (GO:0032587)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			lung(2)|ovary(1)	3						AAAAGCTTTCGGACTGCTGAA	0.572													g|||	590	0.117812	0.2209	0.0821	5008	,	,		15284	0.1488		0.0268	False		,,,				2504	0.0654				p.G14R	Ovarian(23;358 734 36938 38933 52312)	Atlas-SNP	.											.	AIF1	13	.	0			c.G40A						PASS	.	A	ARG/GLY,	835,3571	322.3+/-297.6	82,671,1450	51.0	53.0	52.0		40,	3.6	1.0	6	dbSNP_100	52	196,8404	85.3+/-147.7	3,190,4107	yes	missense,utr-5	AIF1	NM_001623.3,NM_004847.3	125,	85,861,5557	AA,AG,GG		2.2791,18.9514,7.9271	benign,	14/148,	31583312	1031,11975	2203	4300	6503	SO:0001583	missense	199	exon2			GCTTTCGGACTGC	U19713	CCDS4706.1, CCDS34398.1	6p21.3	2013-01-10			ENSG00000204472	ENSG00000204472		"""EF-hand domain containing"""	352	protein-coding gene	gene with protein product	"""interferon gamma responsive transcript"", ""ionized calcium-binding adapter molecule 1"""	601833				8912632	Standard	NM_032955		Approved	IRT-1, AIF-1, Em:AF129756.17, IBA1	uc003nuy.3	P55008	OTTHUMG00000031246	ENST00000376059.3:c.40G>A	6.37:g.31583312G>A	ENSP00000365227:p.Gly14Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	110	64	0.581818	NM_001623	A8K406|O43904|Q9UIV4|Q9UKS9	Missense_Mutation	SNP	ENST00000376059.3	37	CCDS4706.1	207	0.09478021978021978	97	0.19715447154471544	27	0.07458563535911603	67	0.11713286713286714	16	0.021108179419525065	g	9.701	1.154377	0.21371	0.189514	0.022791	ENSG00000204472	ENST00000376059;ENST00000337917	T;T	0.74947	-0.79;-0.89	4.43	3.56	0.40772	.	0.079531	0.47852	N	0.000213	T	0.62551	0.2437	M	0.83118	2.625	0.09310	P	1.0	D	0.65815	0.995	B	0.41088	0.347	T	0.68534	-0.5383	9	0.66056	D	0.02	-2.8306	8.7033	0.34338	0.1042:0.0:0.8958:0.0	rs2736182;rs17850514;rs52833368;rs60699614;rs2736182	14	P55008	AIF1_HUMAN	R	14;28	ENSP00000365227:G14R;ENSP00000338776:G28R	ENSP00000338776:G28R	G	+	1	0	AIF1	31691291	1.000000	0.71417	0.974000	0.42286	0.021000	0.10359	3.474000	0.53129	1.260000	0.44134	-0.215000	0.12644	GGA	G|0.914;A|0.086	0.086	strong		0.572	AIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076512.3		
CHRNA5	1138	hgsc.bcm.edu	37	15	78882925	78882925	+	Missense_Mutation	SNP	G	G	A	rs16969968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78882925G>A	ENST00000299565.5	+	5	1392	c.1192G>A	c.(1192-1194)Gat>Aat	p.D398N	CHRNA5_ENST00000559554.1_Intron|RP11-650L12.2_ENST00000567141.1_RNA	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	398			D -> N (associated with susceptibility to lung cancer; dbSNP:rs16969968). {ECO:0000269|PubMed:8906617, ECO:0000269|Ref.4}.		behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	AGCTGCGCTCGATTCTATTCG	0.398													G|||	749	0.149561	0.0234	0.2089	5008	,	,		20833	0.0268		0.3658	False		,,,				2504	0.182				p.D398N		Atlas-SNP	.											.	CHRNA5	48	.	0			c.G1192A	GRCh37	CM081554	CHRNA5	M	rs16969968	PASS	.	G	ASN/ASP	274,4118	151.8+/-185.6	16,242,1938	71.0	68.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1192	3.9	0.0	15	dbSNP_123	69	2993,5593	459.1+/-364.8	550,1893,1850	yes	missense	CHRNA5	NM_000745.3	23	566,2135,3788	AA,AG,GG		34.8591,6.2386,25.1734	benign	398/469	78882925	3267,9711	2196	4293	6489	SO:0001583	missense	1138	exon5			GCGCTCGATTCTA		CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1959	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 5 (neuronal)"""	118505	"""cholinergic receptor, nicotinic, alpha polypeptide 5"""			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.1192G>A	15.37:g.78882925G>A	ENSP00000299565:p.Asp398Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_000745	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	37	CCDS10304.1	383	0.17536630036630035	11	0.022357723577235773	85	0.23480662983425415	16	0.027972027972027972	271	0.3575197889182058	G	10.45	1.352305	0.24512	0.062386	0.348591	ENSG00000169684	ENST00000299565	T	0.69806	-0.43	4.79	3.88	0.44766	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.605324	0.18104	N	0.151590	T	0.00012	0.0000	L	0.60957	1.885	0.09310	P	1.0	B	0.20459	0.045	B	0.14578	0.011	T	0.15607	-1.0431	9	0.38643	T	0.18	.	10.8638	0.46842	0.1543:0.0:0.8457:0.0	rs16969968;rs17486705;rs52821477;rs16969968	398	P30532	ACHA5_HUMAN	N	398	ENSP00000299565:D398N	ENSP00000299565:D398N	D	+	1	0	CHRNA5	76669980	1.000000	0.71417	0.042000	0.18584	0.027000	0.11550	6.622000	0.74233	1.166000	0.42689	-0.229000	0.12294	GAT	G|0.771;A|0.229	0.229	strong		0.398	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1		
PDPR	55066	hgsc.bcm.edu	37	16	70190401	70190401	+	Silent	SNP	C	C	T	rs6499302	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70190401C>T	ENST00000288050.4	+	19	3216	c.2259C>T	c.(2257-2259)gaC>gaT	p.D753D	PDPR_ENST00000542659.1_Silent_p.D98D|RP11-296I10.3_ENST00000502126.1_RNA|RP11-296I10.3_ENST00000566989.1_RNA|PDPR_ENST00000398122.3_Silent_p.D653D|PDPR_ENST00000567046.1_Silent_p.D111D|PDPR_ENST00000568530.1_Silent_p.D753D|PDPR_ENST00000562100.1_3'UTR	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	753					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		TTGGTCGCGACGCCCTCCTGC	0.552																																					p.D753D		Atlas-SNP	.											.	PDPR	66	.	0			c.C2259T						PASS	.	C		1484,2696		12,1460,618	126.0	140.0	135.0		2259	-8.8	0.1	16	dbSNP_116	135	3542,4912		31,3480,716	no	coding-synonymous	PDPR	NM_017990.3		43,4940,1334	TT,TC,CC		41.8973,35.5024,39.7815		753/880	70190401	5026,7608	2090	4227	6317	SO:0001819	synonymous_variant	55066	exon19			TCGCGACGCCCTC		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.2259C>T	16.37:g.70190401C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	196	40	0.204082	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Silent	SNP	ENST00000288050.4	37	CCDS45520.1																																																																																			C|0.645;T|0.355	0.355	strong		0.552	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
CDCA2	157313	hgsc.bcm.edu	37	8	25364834	25364834	+	Missense_Mutation	SNP	A	A	T	rs3829009	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:25364834A>T	ENST00000330560.3	+	15	3129	c.2652A>T	c.(2650-2652)agA>agT	p.R884S	CDCA2_ENST00000380665.3_Missense_Mutation_p.R869S|CDCA2_ENST00000521098.2_3'UTR	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	884			R -> S (in dbSNP:rs3829009). {ECO:0000269|PubMed:15489334}.		mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		TTCAGAGGAGAAATAGTGAAA	0.418													A|||	964	0.192492	0.1687	0.1931	5008	,	,		19130	0.2351		0.2147	False		,,,				2504	0.1575				p.R884S		Atlas-SNP	.											.	CDCA2	78	.	0			c.A2652T						PASS	.	A	SER/ARG	767,3639	303.8+/-288.1	73,621,1509	79.0	84.0	82.0		2652	0.5	0.0	8	dbSNP_107	82	1726,6874	310.0+/-309.6	176,1374,2750	yes	missense	CDCA2	NM_152562.2	110	249,1995,4259	TT,TA,AA		20.0698,17.4081,19.1681	benign	884/1024	25364834	2493,10513	2203	4300	6503	SO:0001583	missense	157313	exon15			GAGGAGAAATAGT	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 81"""					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.2652A>T	8.37:g.25364834A>T	ENSP00000328228:p.Arg884Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	37	CCDS6049.1	457	0.20924908424908426	91	0.18495934959349594	68	0.1878453038674033	135	0.23601398601398602	163	0.21503957783641162	A	1.627	-0.520011	0.04171	0.174081	0.200698	ENSG00000184661	ENST00000330560;ENST00000380665;ENST00000434814	T;T	0.29397	1.57;1.57	5.95	0.538	0.17150	.	1.560230	0.03235	N	0.179576	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.15930	0.015;0.015	B;B	0.15870	0.014;0.014	T	0.21381	-1.0247	9	0.05721	T	0.95	0.2446	8.4248	0.32723	0.5555:0.3775:0.0669:0.0	rs3829009;rs3829009	869;884	E9PEI0;Q69YH5	.;CDCA2_HUMAN	S	884;869;283	ENSP00000328228:R884S;ENSP00000370040:R869S	ENSP00000328228:R884S	R	+	3	2	CDCA2	25420751	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-0.239000	0.08965	-0.118000	0.11851	0.528000	0.53228	AGA	A|0.802;T|0.198	0.198	strong		0.418	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562	
ZNF512B	57473	hgsc.bcm.edu	37	20	62598815	62598815	+	Silent	SNP	C	C	T	rs817330	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62598815C>T	ENST00000450537.1	-	3	243	c.183G>A	c.(181-183)ccG>ccA	p.P61P	ZNF512B_ENST00000217130.3_Silent_p.P61P|ZNF512B_ENST00000369888.1_Silent_p.P61P			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	61					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTGGACTTCCCGGGTCAAAGC	0.617													T|||	1598	0.319089	0.4402	0.2507	5008	,	,		16334	0.0516		0.3767	False		,,,				2504	0.4202				p.P61P		Atlas-SNP	.											ZNF512B,colon,carcinoma,0,1	ZNF512B	72	1	0			c.G183A						PASS	.	T		1970,2436	616.2+/-392.7	444,1082,677	99.0	105.0	103.0		183	-4.0	0.3	20	dbSNP_86	103	3200,5400	652.4+/-400.9	603,1994,1703	no	coding-synonymous	ZNF512B	NM_020713.1		1047,3076,2380	TT,TC,CC		37.2093,44.7118,39.7509		61/893	62598815	5170,7836	2203	4300	6503	SO:0001819	synonymous_variant	57473	exon3			ACTTCCCGGGTCA	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.183G>A	20.37:g.62598815C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_020713	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			C|0.646;T|0.354	0.354	strong		0.617	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
OR2V1	26693	hgsc.bcm.edu	37	5	180551660	180551660	+	Silent	SNP	G	G	T	rs141508488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:180551660G>T	ENST00000329365.2	-	1	644	c.645C>A	c.(643-645)atC>atA	p.I215I		NM_001258283.1	NP_001245212.1	Q8NHB1	OR2V1_HUMAN	olfactory receptor, family 2, subfamily V, member 1	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			lung(4)	4						AGGAGGCCATGATGATGGAGA	0.532													g|||	24	0.00479233	0.0	0.0072	5008	,	,		21397	0.0		0.0099	False		,,,				2504	0.0092				p.I215I		Atlas-SNP	.											.	OR2V1	20	.	0			c.C645A						PASS	.																																			SO:0001819	synonymous_variant	26693	exon1			GGCCATGATGATG	AB065465	CCDS58992.1	5q35.3	2012-08-09		2004-03-10	ENSG00000185372	ENSG00000185372		"""GPCR / Class A : Olfactory receptors"""	8280	protein-coding gene	gene with protein product				OR2V1P			Standard	NM_001258283		Approved	OST265	uc031smg.1	Q8NHB1	OTTHUMG00000162118	ENST00000329365.2:c.645C>A	5.37:g.180551660G>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	98	59	0.602041	NM_001258283		Silent	SNP	ENST00000329365.2	37	CCDS58992.1																																																																																			G|0.994;T|0.006	0.006	strong		0.532	OR2V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367367.1		
SPEG	10290	hgsc.bcm.edu	37	2	220354108	220354108	+	Missense_Mutation	SNP	A	A	G	rs55760516	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220354108A>G	ENST00000312358.7	+	36	8500	c.8368A>G	c.(8368-8370)Agg>Ggg	p.R2790G	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2790	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TGTCACCTCAAGGCCAGCCAG	0.627													G|||	2045	0.408347	0.5333	0.4092	5008	,	,		11102	0.2321		0.334	False		,,,				2504	0.4969				p.R2790G		Atlas-SNP	.											.	SPEG	272	.	0			c.A8368G						PASS	.	G	GLY/ARG	1850,1998		457,936,531	41.0	41.0	41.0		8368	4.3	1.0	2	dbSNP_129	41	2676,5588		426,1824,1882	yes	missense	SPEG	NM_005876.4	125	883,2760,2413	GG,GA,AA		32.3814,48.0769,37.3679	benign	2790/3268	220354108	4526,7586	1924	4132	6056	SO:0001583	missense	10290	exon36			ACCTCAAGGCCAG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8368A>G	2.37:g.220354108A>G	ENSP00000311684:p.Arg2790Gly	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	798	0.36538461538461536	254	0.516260162601626	155	0.4281767955801105	141	0.2465034965034965	248	0.32717678100263853	G	8.848	0.943804	0.18281	0.480769	0.323814	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.63255	-0.03	4.33	4.33	0.51752	.	0.000000	0.37393	N	0.002120	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999956163	B	0.02656	0.0	B	0.01281	0.0	T	0.42120	-0.9470	9	0.02654	T	1	.	6.8063	0.23779	0.2075:0.0:0.7925:0.0	rs55760516;rs61733895	2790	Q15772	SPEG_HUMAN	G	2790	ENSP00000311684:R2790G	ENSP00000265327:R2790G	R	+	1	2	SPEG	220062352	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.890000	0.39728	1.063000	0.40649	-0.366000	0.07423	AGG	A|0.648;G|0.352	0.352	strong		0.627	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
C9orf62	157927	hgsc.bcm.edu	37	9	138236031	138236031	+	Silent	SNP	A	A	G	rs914398	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:138236031A>G	ENST00000320778.2	+	2	387	c.237A>G	c.(235-237)ccA>ccG	p.P79P		NM_173520.2	NP_775791.1	Q8N4C0	CI062_HUMAN	chromosome 9 open reading frame 62	79																	CCGGACGCCCAGTCCTGGGCT	0.622											OREG0019607	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2629	0.52496	0.7383	0.5677	5008	,	,		18306	0.3998		0.4871	False		,,,				2504	0.3742				p.P79P		Atlas-SNP	.											.	C9orf62	1	.	0			c.A237G						PASS	.																																			SO:0001819	synonymous_variant	157927	exon2			ACGCCCAGTCCTG	BC034752	CCDS59154.1	9q34.3	2008-02-05			ENSG00000178243	ENSG00000178243			28581	protein-coding gene	gene with protein product						12477932	Standard	NM_173520		Approved	MGC35463	uc004cfo.3	Q8N4C0	OTTHUMG00000020900	ENST00000320778.2:c.237A>G	9.37:g.138236031A>G		Somatic	45	0	0	1639	WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_173520	Q5T7E2	Silent	SNP	ENST00000320778.2	37	CCDS59154.1																																																																																			A|0.488;G|0.512	0.512	strong		0.622	C9orf62-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000054980.2	NM_173520	
ZNF211	10520	hgsc.bcm.edu	37	19	58152795	58152795	+	Missense_Mutation	SNP	C	C	T	rs11879465	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58152795C>T	ENST00000347302.3	+	3	1120	c.941C>T	c.(940-942)gCg>gTg	p.A314V	ZNF211_ENST00000420680.1_Missense_Mutation_p.A318V|ZNF211_ENST00000240731.4_Missense_Mutation_p.A327V|ZNF211_ENST00000544273.1_Missense_Mutation_p.A326V|ZNF211_ENST00000391703.3_Missense_Mutation_p.A253V|ZNF211_ENST00000541801.1_Missense_Mutation_p.A305V|ZNF211_ENST00000299871.5_Missense_Mutation_p.A379V|ZNF211_ENST00000254182.7_Missense_Mutation_p.A305V	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	314			A -> V (in dbSNP:rs11879465). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AGGCCTTATGCGTGCCCTGAA	0.418													A|||	1072	0.214058	0.2352	0.1297	5008	,	,		22359	0.3214		0.159	False		,,,				2504	0.1912				p.A379V		Atlas-SNP	.											.	ZNF211	78	.	0			c.C1136T						PASS	.	A	VAL/ALA,VAL/ALA	980,3426		117,746,1340	73.0	73.0	73.0		980,941	-2.3	0.0	19	dbSNP_120	73	1345,7255		97,1151,3052	yes	missense,missense	ZNF211	NM_006385.3,NM_198855.2	64,64	214,1897,4392	TT,TC,CC		15.6395,22.2424,17.8764	benign,benign	327/578,314/565	58152795	2325,10681	2203	4300	6503	SO:0001583	missense	10520	exon5			CTTATGCGTGCCC	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.941C>T	19.37:g.58152795C>T	ENSP00000339562:p.Ala314Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	485	0.22206959706959706	135	0.27439024390243905	52	0.143646408839779	180	0.3146853146853147	118	0.15567282321899736	A	10.08	1.251787	0.22880	0.222424	0.156395	ENSG00000121417	ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731	T;T;T;T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29;2.29;2.29;2.29	3.21	-2.34	0.06704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.11651	0.15	0.80722	P	0.0	B;B;B;B;B;B	0.22146	0.065;0.027;0.004;0.027;0.033;0.033	B;B;B;B;B;B	0.10450	0.003;0.002;0.001;0.003;0.005;0.005	T	0.45948	-0.9226	8	0.44086	T	0.13	.	4.3681	0.11233	0.3986:0.4122:0.0837:0.1056	rs11879465;rs52794337;rs59585398;rs11879465	318;326;379;305;314;327	Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1	.;.;.;.;ZN211_HUMAN;.	V	318;314;305;253;305;379;326;327	ENSP00000399193:A318V;ENSP00000339562:A314V;ENSP00000254182:A305V;ENSP00000375584:A253V;ENSP00000442601:A305V;ENSP00000299871:A379V;ENSP00000441386:A326V;ENSP00000240731:A327V	ENSP00000240731:A327V	A	+	2	0	ZNF211	62844607	0.000000	0.05858	0.000000	0.03702	0.533000	0.34776	-2.055000	0.01397	-1.230000	0.02561	-4.775000	0.00003	GCG	C|0.792;T|0.208	0.208	strong		0.418	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
LAMB2	3913	hgsc.bcm.edu	37	3	49168511	49168511	+	Missense_Mutation	SNP	G	G	A	rs200316162		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49168511G>A	ENST00000418109.1	-	8	951	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W	LAMB2_ENST00000305544.4_Missense_Mutation_p.R263W	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	263	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATCTCCCTCCGTGGGTCGAGT	0.582																																					p.R263W		Atlas-SNP	.											LAMB2,colon,carcinoma,0,1	LAMB2	156	1	0			c.C787T						scavenged	.	G	TRP/ARG	0,4406		0,0,2203	133.0	123.0	127.0		787	3.9	1.0	3		127	1,8599	1.2+/-3.3	0,1,4299	yes	missense	LAMB2	NM_002292.3	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	263/1799	49168511	1,13005	2203	4300	6503	SO:0001583	missense	3913	exon7			CCCTCCGTGGGTC		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.787C>T	3.37:g.49168511G>A	ENSP00000388325:p.Arg263Trp	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	150	3	0.02	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.555771	0.65425	0.0	1.16E-4	ENSG00000172037	ENST00000418109;ENST00000305544;ENST00000494831	T;T;T	0.77358	-1.09;-1.09;-1.09	4.76	3.87	0.44632	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89588	0.6758	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.91735	0.5399	10	0.87932	D	0	.	13.5434	0.61688	0.0:0.0:0.8426:0.1574	.	263	P55268	LAMB2_HUMAN	W	263;263;114	ENSP00000388325:R263W;ENSP00000307156:R263W;ENSP00000444751:R114W	ENSP00000307156:R263W	R	-	1	2	LAMB2	49143515	0.979000	0.34478	1.000000	0.80357	0.823000	0.46562	1.799000	0.38824	1.335000	0.45486	0.655000	0.94253	CGG	.	.	weak		0.582	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
OR1A1	8383	hgsc.bcm.edu	37	17	3119673	3119673	+	Silent	SNP	A	A	G	rs769426	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3119673A>G	ENST00000304094.1	+	1	759	c.759A>G	c.(757-759)acA>acG	p.T253T		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						ATTATGGTACAGTCATGGGCA	0.488													A|||	646	0.128994	0.1021	0.1643	5008	,	,		21057	0.004		0.2803	False		,,,				2504	0.1135				p.T253T		Atlas-SNP	.											OR1A1,NS,carcinoma,+1,1	OR1A1	54	1	0			c.A759G						PASS	.	A		556,3850	247.8+/-255.9	40,476,1687	159.0	136.0	143.0		759	-0.0	1.0	17	dbSNP_86	143	2533,6067	413.8+/-351.3	387,1759,2154	yes	coding-synonymous	OR1A1	NM_014565.2		427,2235,3841	GG,GA,AA		29.4535,12.6192,23.7506		253/310	3119673	3089,9917	2203	4300	6503	SO:0001819	synonymous_variant	8383	exon1			TGGTACAGTCATG	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"""GPCR / Class A : Olfactory receptors"""	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.759A>G	17.37:g.3119673A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	187	102	0.545455	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Silent	SNP	ENST00000304094.1	37	CCDS11022.1																																																																																			A|0.801;G|0.199	0.199	strong		0.488	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565	
TG	7038	hgsc.bcm.edu	37	8	133975283	133975283	+	Missense_Mutation	SNP	G	G	A	rs2069561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:133975283G>A	ENST00000220616.4	+	29	5552	c.5512G>A	c.(5512-5514)Gac>Aac	p.D1838N	TG_ENST00000377869.1_Missense_Mutation_p.D1781N|TG_ENST00000542445.1_Missense_Mutation_p.D208N|TG_ENST00000519543.1_5'Flank	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1838			D -> N (in dbSNP:rs2069561). {ECO:0000269|PubMed:10199792}.		hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.D1838N(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ATGTAGAAAAGACACAGTGCC	0.488													G|||	1737	0.346845	0.0333	0.5259	5008	,	,		19744	0.3452		0.5089	False		,,,				2504	0.4785				p.D1838N		Atlas-SNP	.											TG,NS,carcinoma,0,1	TG	416	1	1	Substitution - Missense(1)	stomach(1)	c.G5512A						PASS	.	G	ASN/ASP	530,3876	241.2+/-251.7	37,456,1710	275.0	247.0	257.0		5512	1.7	0.0	8	dbSNP_96	257	4398,4202	585.9+/-391.9	1156,2086,1058	yes	missense	TG	NM_003235.4	23	1193,2542,2768	AA,AG,GG		48.8605,12.0291,37.8902	benign	1838/2769	133975283	4928,8078	2203	4300	6503	SO:0001583	missense	7038	exon29			AGAAAAGACACAG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5512G>A	8.37:g.133975283G>A	ENSP00000220616:p.Asp1838Asn	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	213	97	0.455399	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	803|803	0.3676739926739927|0.3676739926739927	25|25	0.0508130081300813|0.0508130081300813	184|184	0.5082872928176796|0.5082872928176796	201|201	0.3513986013986014|0.3513986013986014	393|393	0.5184696569920845|0.5184696569920845	G|G	9.376|9.376	1.071724|1.071724	0.20147|0.20147	0.120291|0.120291	0.511395|0.511395	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445|ENST00000519178	T;T;T|.	0.66995|.	-0.03;-0.03;-0.24|.	4.41|4.41	1.66|1.66	0.24008|0.24008	.|.	1.854800|.	0.02283|.	N|.	0.069558|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.15930|.	0.015;0.001|.	B;B|.	0.12837|.	0.008;0.003|.	T|T	0.47898|0.47898	-0.9081|-0.9081	9|4	0.54805|.	T|.	0.06|.	.|.	6.41|6.41	0.21686|0.21686	0.3047:0.0:0.6953:0.0|0.3047:0.0:0.6953:0.0	rs2069561;rs2741220;rs3739271;rs17619883;rs52813039;rs59959331;rs2069561|rs2069561;rs2741220;rs3739271;rs17619883;rs52813039;rs59959331;rs2069561	208;1838|.	F5GWW5;P01266|.	.;THYG_HUMAN|.	N|K	1781;644;1838;208|293	ENSP00000367100:D1781N;ENSP00000220616:D1838N;ENSP00000441693:D208N|.	ENSP00000220616:D1838N|.	D|R	+|+	1|2	0|0	TG|TG	134044465|134044465	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.528000|0.528000	0.23002|0.23002	0.374000|0.374000	0.24650|0.24650	-0.251000|-0.251000	0.11542|0.11542	GAC|AGA	G|0.642;A|0.358	0.358	strong		0.488	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
GRIN3B	116444	hgsc.bcm.edu	37	19	1004710	1004710	+	Missense_Mutation	SNP	C	C	T	rs4807399	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1004710C>T	ENST00000234389.3	+	3	1229	c.1210C>T	c.(1210-1212)Cgg>Tgg	p.R404W	AC004528.4_ENST00000588380.1_RNA|GRIN3B_ENST00000588335.1_Intron	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	404			R -> W (in dbSNP:rs4807399).		ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGCCTCTGCACGGCCCCCGCC	0.701													c|||	1811	0.361621	0.3956	0.3573	5008	,	,		11819	0.0933		0.5199	False		,,,				2504	0.4325				p.R404W		Atlas-SNP	.											.	GRIN3B	46	.	0			c.C1210T						PASS	.	C	TRP/ARG	1746,2640		348,1050,795	21.0	21.0	21.0		1210	-3.3	0.0	19	dbSNP_111	21	4461,4115		1183,2095,1010	no	missense	GRIN3B	NM_138690.1	101	1531,3145,1805	TT,TC,CC		47.9827,39.8085,47.8861	probably-damaging	404/1044	1004710	6207,6755	2193	4288	6481	SO:0001583	missense	116444	exon3			TCTGCACGGCCCC		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1210C>T	19.37:g.1004710C>T	ENSP00000234389:p.Arg404Trp	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	766	0.3507326007326007	178	0.3617886178861789	151	0.4171270718232044	41	0.07167832167832168	396	0.5224274406332454	C	1.117	-0.656400	0.03480	0.398085	0.520173	ENSG00000116032	ENST00000234389	T	0.12039	2.72	4.41	-3.29	0.05017	.	19.319700	0.00937	N	0.002782	T	0.00012	0.0000	L	0.35854	1.095	0.80722	P	0.0	B	0.19073	0.033	B	0.08055	0.003	T	0.48559	-0.9025	9	0.38643	T	0.18	.	1.7399	0.02950	0.2459:0.4076:0.1132:0.2333	rs4807399	404	O60391	NMD3B_HUMAN	W	404	ENSP00000234389:R404W	ENSP00000234389:R404W	R	+	1	2	GRIN3B	955710	0.000000	0.05858	0.004000	0.12327	0.024000	0.10985	-1.671000	0.01954	-0.291000	0.09012	-1.976000	0.00459	CGG	C|0.586;T|0.414	0.414	strong		0.701	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
ARRDC2	27106	hgsc.bcm.edu	37	19	18121418	18121418	+	Silent	SNP	G	G	A	rs79985971	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18121418G>A	ENST00000222250.4	+	7	1193	c.1050G>A	c.(1048-1050)gaG>gaA	p.E350E	ARRDC2_ENST00000379656.3_Silent_p.E345E	NM_015683.1	NP_056498.1	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2	350					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)	12						CCGACACTGAGGAGGCAGCCT	0.642													G|||	23	0.00459265	0.0	0.0101	5008	,	,		18192	0.0		0.0159	False		,,,				2504	0.0				p.E350E		Atlas-SNP	.											.	ARRDC2	60	.	0			c.G1050A						PASS	.	G	,	17,4389	25.3+/-52.1	0,17,2186	67.0	69.0	68.0		1035,1050	1.8	0.0	19	dbSNP_132	68	144,8456	68.7+/-131.2	2,140,4158	no	coding-synonymous,coding-synonymous	ARRDC2	NM_001025604.1,NM_015683.1	,	2,157,6344	AA,AG,GG		1.6744,0.3858,1.2379	,	345/403,350/408	18121418	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	27106	exon7			CACTGAGGAGGCA		CCDS12370.1, CCDS32956.1	19p13.12	2008-02-05				ENSG00000105643			25225	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015683		Approved	CLONE24945, PP2703	uc002nhv.3	Q8TBH0		ENST00000222250.4:c.1050G>A	19.37:g.18121418G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_015683	B2RBG9|O95895|Q6ZRV9|Q8WYG6	Silent	SNP	ENST00000222250.4	37	CCDS12370.1																																																																																			G|0.988;A|0.012	0.012	strong		0.642	ARRDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466845.1	NM_015683	
SDK1	221935	hgsc.bcm.edu	37	7	4308362	4308362	+	3'UTR	SNP	C	C	T	rs8514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4308362C>T	ENST00000404826.2	+	0	10127					NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1						cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TGTGGCTCCCCGTGGGTCAGC	0.547													C|||	605	0.120807	0.0431	0.1772	5008	,	,		17932	0.1121		0.2465	False		,,,				2504	0.0654				p.R674C		Atlas-SNP	.											.	SDK1	361	.	0			c.C2020T						PASS	.	C		255,4151	134.1+/-170.4	5,245,1953	180.0	189.0	186.0			-6.1	0.0	7	dbSNP_52	186	1794,6800	316.7+/-312.9	191,1412,2694	no	utr-3	SDK1	NM_152744.3		196,1657,4647	TT,TC,CC		20.875,5.7876,15.7615			4308362	2049,10951	2203	4297	6500	SO:0001624	3_prime_UTR_variant	221935	exon20			GCTCCCCGTGGGT	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.*3346C>T	7.37:g.4308362C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	172	74	0.430233	NM_001079653	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			C|0.819;T|0.181	0.181	strong		0.547	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
GPR132	29933	hgsc.bcm.edu	37	14	105518336	105518336	+	Silent	SNP	G	G	T	rs3803322	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105518336G>T	ENST00000329797.3	-	4	1049	c.138C>A	c.(136-138)gtC>gtA	p.V46V	GPR132_ENST00000539291.2_Silent_p.V46V|GPR132_ENST00000546679.1_5'UTR|GPR132_ENST00000392585.2_Silent_p.V37V	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	46					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		TGTACACCACGACCAGGACTA	0.667													G|||	528	0.105431	0.0045	0.1671	5008	,	,		19174	0.2421		0.0636	False		,,,				2504	0.1002				p.V46V		Atlas-SNP	.											.	GPR132	40	.	0			c.C138A						PASS	.	G		82,4324	69.2+/-107.0	0,82,2121	55.0	56.0	56.0		138	0.2	0.3	14	dbSNP_107	56	653,7947	164.6+/-216.9	20,613,3667	yes	coding-synonymous	GPR132	NM_013345.2		20,695,5788	TT,TG,GG		7.593,1.8611,5.6512		46/381	105518336	735,12271	2203	4300	6503	SO:0001819	synonymous_variant	29933	exon4			CACCACGACCAGG	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"""GPCR / Class A : Orphans"""	17482	protein-coding gene	gene with protein product	"""G2 accumulation"""	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.138C>A	14.37:g.105518336G>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	17	0.320755	NM_013345	A8K7X7|B4E144|Q9BSU2	Silent	SNP	ENST00000329797.3	37	CCDS9997.1																																																																																			G|0.922;T|0.078	0.078	strong		0.667	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345	
KIAA1217	56243	hgsc.bcm.edu	37	10	24832885	24832885	+	Silent	SNP	C	C	T	rs3748218	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:24832885C>T	ENST00000376454.3	+	19	4716	c.4686C>T	c.(4684-4686)acC>acT	p.T1562T	KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000376451.2_Silent_p.T1245T	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1562					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AGGACGCGACCGATGACCAGT	0.483													C|||	1397	0.278954	0.3343	0.2233	5008	,	,		19554	0.3988		0.1521	False		,,,				2504	0.2505				p.T1562T		Atlas-SNP	.											.	KIAA1217	235	.	0			c.C4686T						PASS	.	C	,,	1394,3012	455.5+/-351.0	230,934,1039	90.0	97.0	95.0		,,4686	-10.9	0.0	10	dbSNP_107	95	1245,7355	246.5+/-274.9	85,1075,3140	no	intron,intron,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	315,2009,4179	TT,TC,CC		14.4767,31.6387,20.2906	,,	,,1562/1944	24832885	2639,10367	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon19			CGCGACCGATGAC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.4686C>T	10.37:g.24832885C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			C|0.774;T|0.226	0.226	strong		0.483	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
ST6GALNAC3	256435	hgsc.bcm.edu	37	1	77093180	77093180	+	Missense_Mutation	SNP	C	C	A	rs1184626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:77093180C>A	ENST00000328299.3	+	4	815	c.667C>A	c.(667-669)Ctt>Att	p.L223I		NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	223			L -> I (in dbSNP:rs1184626). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						GTTTACCTTCCTTCTGGCCAT	0.423													A|||	2218	0.442891	0.6407	0.5173	5008	,	,		20065	0.2421		0.3966	False		,,,				2504	0.3773				p.L223I		Atlas-SNP	.											.	ST6GALNAC3	71	.	0			c.C667A						PASS	.	A	ILE/LEU	2693,1713	515.9+/-369.0	847,999,357	221.0	207.0	212.0		667	4.6	1.0	1	dbSNP_87	212	3521,5079	631.8+/-398.5	715,2091,1494	yes	missense	ST6GALNAC3	NM_152996.2	5	1562,3090,1851	AA,AC,CC		40.9419,38.8788,47.7779	benign	223/306	77093180	6214,6792	2203	4300	6503	SO:0001583	missense	256435	exon4			ACCTTCCTTCTGG		CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"""Sialyltransferases"""	19343	protein-coding gene	gene with protein product	"""ST6GALNAC III"""	610133	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"""	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.667C>A	1.37:g.77093180C>A	ENSP00000329214:p.Leu223Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	121	118	0.975207	NM_152996	Q6PCE0|Q6UX29|Q8N259	Missense_Mutation	SNP	ENST00000328299.3	37	CCDS672.1	928	0.4249084249084249	317	0.6443089430894309	180	0.4972375690607735	138	0.24125874125874125	293	0.3865435356200528	A	2.758	-0.258576	0.05791	0.611212	0.409419	ENSG00000184005	ENST00000328299;ENST00000394993	T	0.30981	1.51	5.75	4.61	0.57282	.	0.111259	0.64402	N	0.000013	T	0.02380	0.0073	N	0.00890	-1.11	0.49915	P	1.6300000000002424E-4	B	0.02656	0.0	B	0.06405	0.002	T	0.40850	-0.9541	9	0.02654	T	1	-4.7096	11.8058	0.52155	0.72:0.28:0.0:0.0	rs1184626;rs17857482;rs52834427;rs59601039;rs1184626	223	Q8NDV1	SIA7C_HUMAN	I	223;222	ENSP00000329214:L223I	ENSP00000329214:L223I	L	+	1	0	ST6GALNAC3	76865768	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.866000	0.63005	0.433000	0.26313	-0.264000	0.10439	CTT	C|0.543;A|0.457	0.457	strong		0.423	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996	
MUC4	4585	hgsc.bcm.edu	37	3	195513493	195513493	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513493C>A	ENST00000463781.3	-	2	5417	c.4958G>T	c.(4957-4959)aGc>aTc	p.S1653I	MUC4_ENST00000475231.1_Missense_Mutation_p.S1653I|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1653I(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGCTGGTGACATG	0.592																																					p.S1653I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	endometrium(2)|kidney(1)	c.G4958T						scavenged	.						27.0	30.0	29.0					3																	195513493		690	1576	2266	SO:0001583	missense	4585	exon2			GAAGGGCTGGTGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4958G>T	3.37:g.195513493C>A	ENSP00000417498:p.Ser1653Ile	Somatic	689	7	0.0101597		WXS	Illumina HiSeq	Phase_I	935	75	0.0802139	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	0.027	-1.366531	0.01225	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.43	0.595	-1.19	0.09585	.	.	.	.	.	T	0.08582	0.0213	N	0.08118	0	0.09310	N	1	P	0.42993	0.797	B	0.25884	0.064	T	0.26950	-1.0088	8	.	.	.	.	1.1981	0.01879	0.1873:0.2606:0.3737:0.1784	.	1653	E7ESK3	.	I	1653	ENSP00000417498:S1653I;ENSP00000420243:S1653I	.	S	-	2	0	MUC4	196997888	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.015000	0.03637	-4.523000	0.00044	-4.118000	0.00011	AGC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PKHD1	5314	hgsc.bcm.edu	37	6	51924774	51924774	+	Silent	SNP	A	A	G	rs1896976	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:51924774A>G	ENST00000371117.3	-	15	1460	c.1185T>C	c.(1183-1185)gaT>gaC	p.D395D	PKHD1_ENST00000340994.4_Silent_p.D395D|AL590391.1_ENST00000408630.2_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	395					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AAGCTTGGCTATCTGCCTGAA	0.438													G|||	4799	0.958267	0.8472	0.9914	5008	,	,		19466	1.0		0.999	False		,,,				2504	1.0				p.D395D		Atlas-SNP	.											.	PKHD1	927	.	0			c.T1185C						PASS	.	G	,	3883,523	240.3+/-251.1	1706,471,26	114.0	99.0	104.0		1185,1185	1.1	1.0	6	dbSNP_92	104	8592,8	7.1+/-27.0	4292,8,0	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	5998,479,26	GG,GA,AA		0.093,11.8702,4.0827	,	395/4075,395/3397	51924774	12475,531	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon15			TTGGCTATCTGCC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1185T>C	6.37:g.51924774A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			A|0.039;G|0.961	0.961	strong		0.438	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PNPLA7	375775	hgsc.bcm.edu	37	9	140356422	140356422	+	Silent	SNP	G	G	C	rs28452008	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140356422G>C	ENST00000277531.4	-	31	3828	c.3642C>G	c.(3640-3642)ctC>ctG	p.L1214L	NSMF_ENST00000371474.3_5'Flank|NSMF_ENST00000392812.4_5'Flank|NSMF_ENST00000265663.7_5'Flank|NSMF_ENST00000437259.1_5'Flank|PNPLA7_ENST00000371457.1_Silent_p.L820L|NSMF_ENST00000371475.3_5'Flank|NSMF_ENST00000371472.2_5'Flank|PNPLA7_ENST00000406427.1_Silent_p.L1239L|PNPLA7_ENST00000492278.1_5'UTR|NSMF_ENST00000371473.3_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1214					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		GCTGGTCGCGGAGCATCTTCT	0.706													C|||	2452	0.489617	0.3177	0.3588	5008	,	,		14382	0.8204		0.3847	False		,,,				2504	0.5818				p.L1239L		Atlas-SNP	.											PNPLA7,NS,carcinoma,0,1	PNPLA7	124	1	0			c.C3717G						PASS	.	C	,	1420,2962		231,958,1002	11.0	13.0	13.0		3717,3642	1.1	1.0	9	dbSNP_125	13	3144,5428		623,1898,1765	no	coding-synonymous,coding-synonymous	PNPLA7	NM_001098537.1,NM_152286.3	,	854,2856,2767	CC,CG,GG		36.6776,32.4053,35.2324	,	1239/1343,1214/1318	140356422	4564,8390	2191	4286	6477	SO:0001819	synonymous_variant	375775	exon32			GTCGCGGAGCATC	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.3642C>G	9.37:g.140356422G>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	CCDS7045.1																																																																																			G|0.620;C|0.380	0.380	strong		0.706	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
ACTL8	81569	hgsc.bcm.edu	37	1	18149566	18149566	+	Silent	SNP	C	C	A	rs2296035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:18149566C>A	ENST00000375406.1	+	2	279	c.63C>A	c.(61-63)ggC>ggA	p.G21G		NM_030812.2	NP_110439.2	Q9H568	ACTL8_HUMAN	actin-like 8	21					epithelial cell differentiation (GO:0030855)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	28		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		GCACGGCCGGCTGGAATGAGC	0.602													C|||	2418	0.482827	0.3215	0.5807	5008	,	,		18379	0.6865		0.4732	False		,,,				2504	0.4315				p.G21G		Atlas-SNP	.											.	ACTL8	58	.	0			c.C63A						PASS	.	C		1513,2893	483.2+/-359.6	276,961,966	75.0	63.0	67.0		63	-8.7	0.0	1	dbSNP_100	67	3975,4625	552.6+/-386.1	926,2123,1251	no	coding-synonymous	ACTL8	NM_030812.2		1202,3084,2217	AA,AC,CC		46.2209,34.3395,42.1959		21/367	18149566	5488,7518	2203	4300	6503	SO:0001819	synonymous_variant	81569	exon2			GGCCGGCTGGAAT	AK057339	CCDS183.1	1p36.2-p35	2009-03-25			ENSG00000117148	ENSG00000117148			24018	protein-coding gene	gene with protein product	"""cancer/testis antigen 57"""						Standard	NM_030812		Approved	CT57	uc001bat.3	Q9H568	OTTHUMG00000002512	ENST00000375406.1:c.63C>A	1.37:g.18149566C>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_030812	Q13104|Q96M75	Silent	SNP	ENST00000375406.1	37	CCDS183.1																																																																																			C|0.540;A|0.460	0.460	strong		0.602	ACTL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007143.1	NM_030812	
MUC20	200958	hgsc.bcm.edu	37	3	195453249	195453249	+	Missense_Mutation	SNP	T	T	C	rs3828407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195453249T>C	ENST00000447234.2	+	2	1901	c.1775T>C	c.(1774-1776)aTg>aCg	p.M592T	MUC20_ENST00000436408.1_Missense_Mutation_p.M592T|MUC20_ENST00000320736.6_Missense_Mutation_p.M421T|MUC20_ENST00000445522.2_Missense_Mutation_p.M557T	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	592	Involved in oligomerization.|Thr-rich.			M -> T (in Ref. 5; AAH29267). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ACACCGACCATGGACATCGCA	0.592																																					p.M421T		Atlas-SNP	.											.	MUC20	84	.	0			c.T1262C						PASS	.						64.0	60.0	61.0					3																	195453249		2063	4196	6259	SO:0001583	missense	200958	exon3			CGACCATGGACAT	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1775T>C	3.37:g.195453249T>C	ENSP00000414350:p.Met592Thr	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	106	21	0.198113	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	5.048|5.048	0.194514|0.194514	0.09599|0.09599	.|.	.|.	ENSG00000176945|ENSG00000176945	ENST00000381954|ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	.|T;T;T;T	.|0.08634	.|3.45;3.3;3.62;3.07	4.48|4.48	2.7|2.7	0.31948|0.31948	.|.	.|0.907565	.|0.09232	.|N	.|0.830495	.|T	.|0.02455	.|0.0075	N|N	0.01168|0.01168	-0.975|-0.975	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	.|T	.|0.40831	.|-0.9542	.|10	.|0.02654	.|T	.|1	.|0.077	7.4896|7.4896	0.27454|0.27454	0.0:0.8022:0.0:0.1978|0.0:0.8022:0.0:0.1978	rs3828407;rs4084963|rs3828407;rs4084963	.|421	.|E9PH32	.|.	.|T	-1|592;421;592;557	.|ENSP00000414350:M592T;ENSP00000325431:M421T;ENSP00000396774:M592T;ENSP00000405629:M557T	.|ENSP00000325431:M421T	.|M	+|+	.|2	.|0	MUC20|MUC20	196938920|196938920	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.514000|0.514000	0.22786|0.22786	0.628000|0.628000	0.30357|0.30357	-1.119000|-1.119000	0.02030|0.02030	.|ATG	T|0.982;C|0.018	0.018	strong		0.592	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
CYP39A1	51302	hgsc.bcm.edu	37	6	46620252	46620252	+	Missense_Mutation	SNP	C	C	G	rs12192544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46620252C>G	ENST00000275016.2	-	1	271	c.68G>C	c.(67-69)cGg>cCg	p.R23P	SLC25A27_ENST00000371347.5_5'Flank|SLC25A27_ENST00000411689.2_5'Flank|SLC25A27_ENST00000452689.2_5'Flank	NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	23			R -> P (in dbSNP:rs12192544). {ECO:0000269|PubMed:15489334}.		bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						CAAATTCTTCCGCTGAAGGAG	0.453													C|||	715	0.142772	0.0182	0.1441	5008	,	,		19051	0.1319		0.2087	False		,,,				2504	0.2536				p.R23P		Atlas-SNP	.											.	CYP39A1	41	.	0			c.G68C						PASS	.	C	PRO/ARG	229,4177	135.7+/-171.8	6,217,1980	225.0	237.0	233.0		68	3.4	0.1	6	dbSNP_120	233	1980,6620	347.2+/-326.5	247,1486,2567	yes	missense	CYP39A1	NM_016593.3	103	253,1703,4547	GG,GC,CC		23.0233,5.1975,16.9845	probably-damaging	23/470	46620252	2209,10797	2203	4300	6503	SO:0001583	missense	51302	exon1			TTCTTCCGCTGAA	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.68G>C	6.37:g.46620252C>G	ENSP00000275016:p.Arg23Pro	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	113	70	0.619469	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	303	0.13873626373626374	14	0.028455284552845527	62	0.1712707182320442	69	0.12062937062937062	158	0.20844327176781002	C	16.31	3.087548	0.55968	0.051975	0.230233	ENSG00000146233	ENST00000275016	T	0.76316	-1.01	5.29	3.36	0.38483	.	1.038340	0.07675	N	0.936181	T	0.62624	0.2443	M	0.64997	1.995	0.80722	P	0.0	D;D	0.53619	0.961;0.961	B;B	0.43155	0.41;0.41	T	0.50250	-0.8850	9	0.25751	T	0.34	1.7222	9.7041	0.40205	0.2729:0.5941:0.133:0.0	rs12192544;rs17850639;rs12192544	23;23	B7Z786;Q9NYL5	.;CP39A_HUMAN	P	23	ENSP00000275016:R23P	ENSP00000275016:R23P	R	-	2	0	CYP39A1	46728211	0.007000	0.16637	0.055000	0.19348	0.603000	0.37013	0.391000	0.20784	1.345000	0.45676	0.655000	0.94253	CGG	C|0.846;G|0.154	0.154	strong		0.453	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
RARS	5917	hgsc.bcm.edu	37	5	167933060	167933060	+	Silent	SNP	A	A	G	rs2305733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:167933060A>G	ENST00000231572.3	+	10	1146	c.1092A>G	c.(1090-1092)gtA>gtG	p.V364V	RARS_ENST00000538719.1_Silent_p.V158V	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	364					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		GAAAGATTGTATTTGTCCCAG	0.373													A|||	373	0.0744808	0.0098	0.0908	5008	,	,		16884	0.0645		0.1799	False		,,,				2504	0.0521				p.V364V		Atlas-SNP	.											.	RARS	58	.	0			c.A1092G						PASS	.	A		162,4244	108.6+/-147.0	2,158,2043	145.0	144.0	145.0		1092	0.1	1.0	5	dbSNP_100	145	1628,6972	300.8+/-305.1	162,1304,2834	no	coding-synonymous	RARS	NM_002887.3		164,1462,4877	GG,GA,AA		18.9302,3.6768,13.7629		364/661	167933060	1790,11216	2203	4300	6503	SO:0001819	synonymous_variant	5917	exon10			GATTGTATTTGTC	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1092A>G	5.37:g.167933060A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	37	CCDS4367.1																																																																																			A|0.875;G|0.125	0.125	strong		0.373	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
MAP7D1	55700	hgsc.bcm.edu	37	1	36636774	36636774	+	Silent	SNP	G	G	A	rs139650826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36636774G>A	ENST00000373151.2	+	2	465	c.249G>A	c.(247-249)caG>caA	p.Q83Q	MAP7D1_ENST00000373150.4_Silent_p.Q83Q|MAP7D1_ENST00000316156.4_Silent_p.Q83Q	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	83	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CCCCCCCGCAGGAAGAGTCCC	0.642													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		13296	0.0		0.0179	False		,,,				2504	0.001				p.Q83Q		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G249A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	39.0	43.0	41.0		249	2.2	1.0	1	dbSNP_134	41	125,8475	62.4+/-124.4	1,123,4176	no	coding-synonymous	MAP7D1	NM_018067.3		1,135,6367	AA,AG,GG		1.4535,0.2724,1.0534		83/842	36636774	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	55700	exon2			CCCGCAGGAAGAG	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.249G>A	1.37:g.36636774G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	100	74	0.74	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482989	54482989	+	Silent	SNP	C	C	T	rs6740641	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:54482989C>T	ENST00000317802.7	-	1	420	c.300G>A	c.(298-300)gcG>gcA	p.A100A	ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000607452.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	100					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.A100A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						AGGCAGAGGCCGCTTCTAGGC	0.607													T|||	694	0.138578	0.1263	0.0994	5008	,	,		16663	0.1835		0.1093	False		,,,				2504	0.1667				p.A100A		Atlas-SNP	.											TSPYL6,NS,carcinoma,0,1	TSPYL6	54	1	1	Substitution - coding silent(1)	stomach(1)	c.G300A						PASS	.	T	,	602,3542		69,464,1539	35.0	40.0	38.0		300,	-0.2	0.0	2	dbSNP_116	38	1221,7165		86,1049,3058	no	coding-synonymous,intron	ACYP2,TSPYL6	NM_001003937.2,NM_138448.3	,	155,1513,4597	TT,TC,CC		14.56,14.527,14.5491	,	100/411,	54482989	1823,10707	2072	4193	6265	SO:0001819	synonymous_variant	388951	exon1			AGAGGCCGCTTCT	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.300G>A	2.37:g.54482989C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_001003937	Q6NUJ3	Silent	SNP	ENST00000317802.7	37	CCDS42682.1																																																																																			C|0.869;G|0.001;T|0.130	0.130	strong		0.607	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
RNH1	6050	hgsc.bcm.edu	37	11	494942	494942	+	Silent	SNP	G	G	C	rs7983	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:494942G>C	ENST00000534797.1	-	8	2646	c.1239C>G	c.(1237-1239)gcC>gcG	p.A413A	RNH1_ENST00000397614.1_Silent_p.A413A|RNH1_ENST00000533410.1_Silent_p.A413A|RNH1_ENST00000354420.2_Silent_p.A413A|RNH1_ENST00000356187.5_Silent_p.A413A|RNH1_ENST00000438658.2_Silent_p.A413A|RNH1_ENST00000397604.3_Silent_p.A413A|RNH1_ENST00000397615.2_Silent_p.A413A			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0					mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCAGGATGCCGGCGTCCCCCA	0.692													C|||	1667	0.332867	0.5272	0.366	5008	,	,		15352	0.1865		0.3101	False		,,,				2504	0.2209				p.A413A		Atlas-SNP	.											.	RNH1	24	.	0			c.C1239G						PASS	.	C	,,,,,,,	2181,2223		564,1053,585	26.0	28.0	27.0		1239,1239,1239,1239,1239,1239,1239,1239	-6.5	0.0	11	dbSNP_52	27	2704,5896		430,1844,2026	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNH1	NM_002939.3,NM_203383.1,NM_203384.1,NM_203385.1,NM_203386.1,NM_203387.1,NM_203388.1,NM_203389.1	,,,,,,,	994,2897,2611	CC,CG,GG		31.4419,49.5232,37.5654	,,,,,,,	413/462,413/462,413/462,413/462,413/462,413/462,413/462,413/462	494942	4885,8119	2202	4300	6502	SO:0001819	synonymous_variant	6050	exon9			GATGCCGGCGTCC		CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.1239C>G	11.37:g.494942G>C		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	165	76	0.460606	NM_203384	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Silent	SNP	ENST00000534797.1	37	CCDS7697.1																																																																																			G|0.627;C|0.373	0.373	strong		0.692	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1	NM_203389	
MADD	8567	hgsc.bcm.edu	37	11	47303275	47303275	+	Silent	SNP	T	T	C	rs326217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:47303275T>C	ENST00000311027.5	+	8	1605	c.1440T>C	c.(1438-1440)aaT>aaC	p.N480N	MADD_ENST00000342922.4_Silent_p.N480N|MADD_ENST00000395344.3_Silent_p.N480N|MADD_ENST00000402799.1_Silent_p.N480N|MADD_ENST00000406482.1_Silent_p.N480N|MADD_ENST00000402192.2_Silent_p.N480N|MADD_ENST00000407859.3_Silent_p.N480N|MADD_ENST00000395336.3_Silent_p.N480N|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000349238.3_Silent_p.N480N	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		TCTATGGCAATGATGTGGATT	0.468													T|||	1483	0.296126	0.2481	0.4352	5008	,	,		18300	0.252		0.3042	False		,,,				2504	0.2996				p.N480N		Atlas-SNP	.											.	MADD	172	.	0			c.T1440C						PASS	.	T	,,,,,,,,,	1066,3336	389.1+/-327.2	115,836,1250	80.0	75.0	77.0		1440,1440,1440,1440,1440,1440,1440,1440,1440,1440	-4.1	0.7	11	dbSNP_79	77	2635,5961	426.0+/-355.2	391,1853,2054	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MADD	NM_001135943.1,NM_001135944.1,NM_003682.3,NM_130470.2,NM_130471.2,NM_130472.2,NM_130473.2,NM_130474.2,NM_130475.2,NM_130476.2	,,,,,,,,,	506,2689,3304	CC,CT,TT		30.6538,24.2163,28.4736	,,,,,,,,,	480/1545,480/1542,480/1648,480/1589,480/1566,480/1546,480/1609,480/1480,480/1582,480/1588	47303275	3701,9297	2201	4298	6499	SO:0001819	synonymous_variant	8567	exon8			TGGCAATGATGTG	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1440T>C	11.37:g.47303275T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	111	46	0.414414	NM_130474		Silent	SNP	ENST00000311027.5	37	CCDS7930.1																																																																																			T|0.698;C|0.302	0.302	strong		0.468	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
SMARCC2	6601	hgsc.bcm.edu	37	12	56558483	56558483	+	Missense_Mutation	SNP	G	G	A	rs76701112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56558483G>A	ENST00000267064.4	-	27	3258	c.3172C>T	c.(3172-3174)Ccc>Tcc	p.P1058S	SMARCC2_ENST00000394023.3_Missense_Mutation_p.P1089S|SMARCC2_ENST00000550164.1_Missense_Mutation_p.P1089S|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Missense_Mutation_p.P1089S	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	1058	Pro-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			ATCATTGAGGGAGGAGTTTGT	0.522													G|||	26	0.00519169	0.0159	0.0072	5008	,	,		17586	0.0		0.0	False		,,,				2504	0.0				p.P1089S		Atlas-SNP	.											SMARCC2_ENST00000267064,NS,carcinoma,+1,2	SMARCC2	212	2	0			c.C3265T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	33,4373	36.8+/-68.6	1,31,2171	30.0	29.0	30.0		3265,3172,3265	4.7	1.0	12	dbSNP_131	30	6,8594	3.0+/-9.4	0,6,4294	yes	missense,missense,missense	SMARCC2	NM_139067.2,NM_003075.3,NM_001130420.1	74,74,74	1,37,6465	AA,AG,GG		0.0698,0.749,0.2999	benign,benign,benign	1089/1131,1058/1215,1089/1153	56558483	39,12967	2203	4300	6503	SO:0001583	missense	6601	exon28			TTGAGGGAGGAGT	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.3172C>T	12.37:g.56558483G>A	ENSP00000267064:p.Pro1058Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	102	42	0.411765	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	10.44	1.350723	0.24512	0.00749	6.98E-4	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.55760	1.08;0.57;0.5;0.61	4.67	4.67	0.58626	.	0.000000	0.45126	D	0.000388	T	0.14787	0.0357	N	0.08118	0	0.41798	D	0.989902	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.08973	-1.0696	10	0.27082	T	0.32	-10.7152	6.6581	0.22998	0.0933:0.0:0.7261:0.1806	.	978;1089;1093;1058;1089	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	S	1089;1089;1089;1058	ENSP00000377591:P1089S;ENSP00000449396:P1089S;ENSP00000302919:P1089S;ENSP00000267064:P1058S	ENSP00000267064:P1058S	P	-	1	0	SMARCC2	54844750	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.937000	0.40193	2.528000	0.85240	0.557000	0.71058	CCC	G|0.995;A|0.005	0.005	strong		0.522	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
DCLK1	9201	hgsc.bcm.edu	37	13	36402426	36402426	+	Silent	SNP	A	A	G	rs2296645	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:36402426A>G	ENST00000360631.3	-	9	1459	c.1248T>C	c.(1246-1248)taT>taC	p.Y416Y	DCLK1_ENST00000255448.4_Silent_p.Y416Y|DCLK1_ENST00000379893.1_Silent_p.Y109Y			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	416	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.Y416Y(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TTTTCAGAGCATACTCTCTAG	0.318													A|||	1664	0.332268	0.0968	0.3934	5008	,	,		18258	0.2867		0.504	False		,,,				2504	0.4775				p.Y416Y		Atlas-SNP	.											DCLK1_ENST00000255448,NS,carcinoma,0,1	DCLK1	350	1	1	Substitution - coding silent(1)	stomach(1)	c.T1248C						PASS	.	A	,,	600,3804	263.8+/-265.7	47,506,1649	94.0	88.0	90.0		327,327,1248	4.9	1.0	13	dbSNP_100	90	4095,4499	559.0+/-387.3	988,2119,1190	no	coding-synonymous,coding-synonymous,coding-synonymous	DCLK1	NM_001195415.1,NM_001195416.1,NM_004734.4	,,	1035,2625,2839	GG,GA,AA		47.6495,13.624,36.1209	,,	109/423,109/434,416/730	36402426	4695,8303	2202	4297	6499	SO:0001819	synonymous_variant	9201	exon9			CAGAGCATACTCT	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1248T>C	13.37:g.36402426A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																				A|0.650;G|0.350	0.350	strong		0.318	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
ZNF436	80818	hgsc.bcm.edu	37	1	23688933	23688933	+	Silent	SNP	A	A	G	rs2849028	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:23688933A>G	ENST00000314011.4	-	4	1078	c.942T>C	c.(940-942)aaT>aaC	p.N314N	ZNF436_ENST00000374608.3_Silent_p.N314N	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		TCTGACTGAAATTCTTCCCAC	0.517													A|||	2554	0.509984	0.1861	0.6499	5008	,	,		20985	0.6349		0.7256	False		,,,				2504	0.498				p.N314N		Atlas-SNP	.											.	ZNF436	49	.	0			c.T942C						PASS	.	A	,	1227,3179	425.5+/-340.8	184,859,1160	127.0	116.0	120.0		942,942	1.6	1.0	1	dbSNP_100	120	6290,2310	705.6+/-405.5	2288,1714,298	no	coding-synonymous,coding-synonymous	ZNF436	NM_001077195.1,NM_030634.2	,	2472,2573,1458	GG,GA,AA		26.8605,27.8484,42.2036	,	314/471,314/471	23688933	7517,5489	2203	4300	6503	SO:0001819	synonymous_variant	80818	exon4			ACTGAAATTCTTC	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"""Zinc fingers, C2H2-type"", ""-"""	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.942T>C	1.37:g.23688933A>G		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_001077195	Q658I9	Silent	SNP	ENST00000314011.4	37	CCDS233.1																																																																																			A|0.444;G|0.556	0.556	strong		0.517	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634	
SYTL2	54843	hgsc.bcm.edu	37	11	85435805	85435805	+	Intron	SNP	T	T	C	rs532374094		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:85435805T>C	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000354566.3_Silent_p.T565T|SYTL2_ENST00000359152.5_Silent_p.T1089T|SYTL2_ENST00000525423.1_Silent_p.T565T|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000524452.1_Intron	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TGGGCTCCTCTGTACTACCTA	0.423													T|||	1	0.000199681	0.0	0.0	5008	,	,		16092	0.0		0.001	False		,,,				2504	0.0				p.T565T		Atlas-SNP	.											.	SYTL2	231	.	0			c.A1695G						PASS	.						66.0	67.0	67.0					11																	85435805		2203	4299	6502	SO:0001627	intron_variant	54843	exon1			CTCCTCTGTACTA	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+3133A>G	11.37:g.85435805T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	155	74	0.477419	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			.	.	none		0.423	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
ARSD	414	hgsc.bcm.edu	37	X	2836138	2836138	+	Silent	SNP	G	G	A	rs73632974		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836138G>A	ENST00000381154.1	-	5	645	c.570C>T	c.(568-570)ccC>ccT	p.P190P	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	190					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGTCCACTTCGGGGGGCCTGC	0.642																																					p.P190P		Atlas-SNP	.											.	ARSD	47	.	0			c.C570T						PASS	.						23.0	20.0	21.0					X																	2836138		2201	4297	6498	SO:0001819	synonymous_variant	414	exon5			CACTTCGGGGGGC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.570C>T	X.37:g.2836138G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			G|0.925;A|0.075	0.075	strong		0.642	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
DNASE1L3	1776	hgsc.bcm.edu	37	3	58191242	58191242	+	Silent	SNP	C	C	G	rs17058970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58191242C>G	ENST00000394549.2	-	3	592	c.276G>C	c.(274-276)cgG>cgC	p.R92R	DNASE1L3_ENST00000486455.1_Intron|DNASE1L3_ENST00000318316.3_Silent_p.R92R|DNASE1L3_ENST00000483681.1_Silent_p.R92R	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	92					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		TTCTTCCAAGCCGAGAGCTAA	0.378													C|||	559	0.111621	0.267	0.1239	5008	,	,		22403	0.003		0.0775	False		,,,				2504	0.0399				p.R92R	Esophageal Squamous(96;1069 1424 4841 43466 52325)	Atlas-SNP	.											.	DNASE1L3	36	.	0			c.G276C						PASS	.	C		1101,3303	396.3+/-330.0	128,845,1229	203.0	199.0	200.0		276	-4.7	0.6	3	dbSNP_123	200	805,7795	187.7+/-234.9	32,741,3527	no	coding-synonymous	DNASE1L3	NM_004944.2		160,1586,4756	GG,GC,CC		9.3605,25.0,14.657		92/306	58191242	1906,11098	2202	4300	6502	SO:0001819	synonymous_variant	1776	exon3			TCCAAGCCGAGAG	AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"""DNase gamma"""	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.276G>C	3.37:g.58191242C>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_004944	B2R8B1|B7Z707|O75803	Silent	SNP	ENST00000394549.2	37	CCDS2886.1																																																																																			C|0.863;G|0.137	0.137	strong		0.378	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944	
SLC2A14	144195	hgsc.bcm.edu	37	12	7966958	7966958	+	Missense_Mutation	SNP	C	C	T	rs10845981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7966958C>T	ENST00000543909.1	-	16	2276	c.1517G>A	c.(1516-1518)gGg>gAg	p.G506E	SLC2A14_ENST00000535295.1_Missense_Mutation_p.G397E|SLC2A14_ENST00000542505.1_Missense_Mutation_p.G147E|SLC2A14_ENST00000539924.1_Missense_Mutation_p.G521E|SLC2A14_ENST00000542546.1_Missense_Mutation_p.G397E|SLC2A14_ENST00000431042.2_Missense_Mutation_p.G483E|SLC2A14_ENST00000340749.5_Missense_Mutation_p.G483E|SLC2A14_ENST00000396589.2_Missense_Mutation_p.G506E			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	506			G -> E (in dbSNP:rs10845981).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		GCTGTTCATCCCCATGACGCC	0.572													T|||	1279	0.255391	0.0961	0.2421	5008	,	,		-128	0.4216		0.2674	False		,,,				2504	0.2965				p.G506E		Atlas-SNP	.											SLC2A14,NS,carcinoma,0,1	SLC2A14	78	1	0			c.G1517A						PASS	.	T	GLU/GLY	488,3918		58,372,1773	246.0	160.0	189.0		1517	2.5	0.5	12	dbSNP_120	189	2341,6259		511,1319,2470	no	missense	SLC2A14	NM_153449.2	98	569,1691,4243	TT,TC,CC		27.2209,11.0758,21.7515	benign	506/521	7966958	2829,10177	2203	4300	6503	SO:0001583	missense	144195	exon12			TTCATCCCCATGA	AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"""Solute carriers"""	18301	protein-coding gene	gene with protein product		611039	"""solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"""	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1517G>A	12.37:g.7966958C>T	ENSP00000440480:p.Gly506Glu	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	199	147	0.738693	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	514	0.23534798534798534	33	0.06707317073170732	66	0.18232044198895028	226	0.3951048951048951	189	0.24934036939313983	T	0.029	-1.344877	0.01266	0.110758	0.272209	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000542505;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924	T;D;T;T;D;D;D;T	0.83163	-1.46;-1.5;-1.46;-1.22;-1.5;-1.69;-1.69;-1.49	3.71	2.54	0.30619	.	0.649429	0.15839	N	0.242123	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.13629	-1.0502	9	0.02654	T	1	.	6.9472	0.24526	0.0:0.2098:0.0:0.7902	rs10845981	521;397;483;506	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	E	483;506;483;147;506;397;397;521	ENSP00000340450:G483E;ENSP00000440480:G506E;ENSP00000407287:G483E;ENSP00000438484:G147E;ENSP00000379834:G506E;ENSP00000440492:G397E;ENSP00000443903:G397E;ENSP00000445929:G521E	ENSP00000340450:G483E	G	-	2	0	SLC2A14	7858225	1.000000	0.71417	0.537000	0.28052	0.004000	0.04260	2.648000	0.46647	0.019000	0.15079	-1.777000	0.00654	GGG	C|0.760;T|0.240	0.240	strong		0.572	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	
MCC	4163	hgsc.bcm.edu	37	5	112399791	112399791	+	Silent	SNP	G	G	A	rs2227947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:112399791G>A	ENST00000302475.4	-	12	2096	c.1533C>T	c.(1531-1533)aaC>aaT	p.N511N	MCC_ENST00000408903.3_Silent_p.N701N|MCC_ENST00000515367.2_Silent_p.N448N|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	511					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CCTTGGCAGCGTTCTCAGCTG	0.597													G|||	2571	0.513379	0.1407	0.67	5008	,	,		21510	0.6349		0.6571	False		,,,				2504	0.6329				p.N701N		Atlas-SNP	.											.	MCC	234	.	0			c.C2103T						PASS	.	G	,	941,3463	355.6+/-313.1	112,717,1373	70.0	66.0	68.0		2103,1533	-3.2	1.0	5	dbSNP_98	68	5505,3095	658.1+/-401.5	1761,1983,556	no	coding-synonymous,coding-synonymous	MCC	NM_001085377.1,NM_002387.2	,	1873,2700,1929	AA,AG,GG		35.9884,21.3669,49.5694	,	701/1020,511/830	112399791	6446,6558	2202	4300	6502	SO:0001819	synonymous_variant	4163	exon14			GGCAGCGTTCTCA		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1533C>T	5.37:g.112399791G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																			G|0.494;A|0.506	0.506	strong		0.597	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
STARD13	90627	hgsc.bcm.edu	37	13	33703666	33703666	+	Missense_Mutation	SNP	C	C	G	rs34425674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:33703666C>G	ENST00000336934.5	-	5	1264	c.1148G>C	c.(1147-1149)cGt>cCt	p.R383P	STARD13_ENST00000255486.4_Missense_Mutation_p.R375P|STARD13_ENST00000399365.3_Missense_Mutation_p.R265P	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	383			R -> P (in dbSNP:rs34425674).		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		TTCATGCATACGGCTTTGGTC	0.537													C|||	51	0.0101837	0.0	0.0072	5008	,	,		18202	0.0		0.0268	False		,,,				2504	0.0194				p.R383P		Atlas-SNP	.											STARD13,NS,carcinoma,0,1	STARD13	100	1	0			c.G1148C						PASS	.	C	PRO/ARG,PRO/ARG,PRO/ARG	28,4378	31.7+/-61.6	0,28,2175	74.0	74.0	74.0		794,1148,1124	2.0	0.4	13	dbSNP_126	74	250,8350	97.2+/-158.9	1,248,4051	yes	missense,missense,missense	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	103,103,103	1,276,6226	GG,GC,CC		2.907,0.6355,2.1375	benign,benign,benign	265/996,383/1114,375/1106	33703666	278,12728	2203	4300	6503	SO:0001583	missense	90627	exon5			TGCATACGGCTTT	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.1148G>C	13.37:g.33703666C>G	ENSP00000338785:p.Arg383Pro	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	166	68	0.409639	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	C	11.55	1.671535	0.29693	0.006355	0.02907	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934;ENST00000399364	T;T;T	0.06528	3.3;3.29;3.3	5.82	2.03	0.26663	.	0.215824	0.46442	D	0.000297	T	0.02610	0.0079	L	0.48642	1.525	0.80722	D	1	P;B;B;B	0.45594	0.862;0.451;0.116;0.451	P;B;B;B	0.47941	0.562;0.411;0.154;0.411	T	0.32955	-0.9887	10	0.35671	T	0.21	.	8.9615	0.35849	0.0:0.2181:0.0:0.7819	rs34425674	375;348;383;375	Q9Y3M8-5;Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;.;STA13_HUMAN;.	P	265;375;383;375	ENSP00000382300:R265P;ENSP00000255486:R375P;ENSP00000338785:R383P	ENSP00000255486:R375P	R	-	2	0	STARD13	32601666	0.222000	0.23652	0.427000	0.26684	0.190000	0.23558	0.474000	0.22148	0.963000	0.38082	-0.436000	0.05848	CGT	C|0.981;G|0.019	0.019	strong		0.537	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
PRB4	5545	hgsc.bcm.edu	37	12	11461802	11461802	+	Nonsense_Mutation	SNP	G	G	A	rs12829245	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:11461802G>A	ENST00000535904.1	-	3	148	c.115C>T	c.(115-117)Cga>Tga	p.R39*	PRB4_ENST00000279575.1_Nonsense_Mutation_p.R39*|PRB4_ENST00000445719.2_Nonsense_Mutation_p.R39*			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	39	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.			LISGKPEGR -> IIPPKPPG (in Ref. 5; AA sequence). {ECO:0000305}.		extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TGTGGGCGTCGTCCTTCTGGC	0.547										HNSCC(22;0.051)			G|||	377	0.0752796	0.0113	0.1787	5008	,	,		23181	0.002		0.1839	False		,,,				2504	0.0521				p.R39X		Atlas-SNP	.											.	PRB4	59	.	0			c.C115T						PASS	.	G	stop/ARG	178,4216		2,174,2021	187.0	200.0	196.0		115	-0.7	0.0	12	dbSNP_121	196	1578,7006		48,1482,2762	no	stop-gained	PRB4	NM_002723.3		50,1656,4783	AA,AG,GG		18.383,4.051,13.5306		39/248	11461802	1756,11222	2197	4292	6489	SO:0001587	stop_gained	5545	exon3			GGCGTCGTCCTTC		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.115C>T	12.37:g.11461802G>A	ENSP00000442834:p.Arg39*	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	195	121	0.620513	NM_001261399	A1L439|O00600|P02813|P10161|P10162|P81489	Nonsense_Mutation	SNP	ENST00000535904.1	37	CCDS8641.1	217	0.09935897435897435	9	0.018292682926829267	64	0.17679558011049723	2	0.0034965034965034965	142	0.18733509234828497	.	10.92	1.485680	0.26686	0.04051	0.18383	ENSG00000230657	ENST00000279575;ENST00000535904;ENST00000445719	.	.	.	0.419	-0.661	0.11417	.	.	.	.	.	.	.	.	.	.	.	0.23016	P	0.99842989	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	.	.	.	rs12829245	.	.	.	X	39	.	ENSP00000279575:R39X	R	-	1	2	PRB4	11353069	0.000000	0.05858	0.015000	0.15790	0.098000	0.18820	-1.823000	0.01710	-0.433000	0.07286	0.195000	0.17529	CGA	G|0.900;A|0.100	0.100	strong		0.547	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723	
ANKRD36	375248	hgsc.bcm.edu	37	2	97851069	97851069	+	Silent	SNP	A	A	G	rs62154801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97851069A>G	ENST00000461153.2	+	29	2200	c.1956A>G	c.(1954-1956)caA>caG	p.Q652Q	ANKRD36_ENST00000420699.2_Silent_p.Q652Q			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	652										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						CTCAGAAACAACCAGCCTCAA	0.289													.|||	1955	0.390375	0.2141	0.4856	5008	,	,		19430	0.2579		0.7932	False		,,,				2504	0.2832				p.Q652Q		Atlas-SNP	.											.	ANKRD36	170	.	0			c.A1956G						PASS	.	A		422,962		66,290,336	83.0	81.0	82.0		1956	-2.1	0.0	2	dbSNP_129	82	2388,792		891,606,93	no	coding-synonymous	ANKRD36	NM_001164315.1		957,896,429	GG,GA,AA		24.9057,30.4913,38.4312		652/1942	97851069	2810,1754	692	1590	2282	SO:0001819	synonymous_variant	375248	exon29			GAAACAACCAGCC	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.1956A>G	2.37:g.97851069A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Silent	SNP	ENST00000461153.2	37	CCDS54379.1																																																																																			A|0.558;G|0.442	0.442	strong		0.289	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
DNAH12	201625	hgsc.bcm.edu	37	3	57419497	57419497	+	Missense_Mutation	SNP	C	C	T	rs6773904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:57419497C>T	ENST00000351747.2	-	31	4825	c.4645G>A	c.(4645-4647)Gat>Aat	p.D1549N		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1549	AAA 2. {ECO:0000250}.		D -> N (in dbSNP:rs6773904).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GTTAGCGTATCCGCCAGCACA	0.353													C|||	2024	0.404153	0.1316	0.4611	5008	,	,		16319	0.4177		0.5517	False		,,,				2504	0.5665				p.D1549N		Atlas-SNP	.											.	DNAH12	182	.	0			c.G4645A						PASS	.	C	ASN/ASP	254,1130		23,208,461	165.0	146.0	152.0		4645	4.9	1.0	3	dbSNP_116	152	1582,1600		396,790,405	yes	missense	DNAH12	NM_178504.4	23	419,998,866	TT,TC,CC		49.7172,18.3526,40.2102	probably-damaging	1549/3093	57419497	1836,2730	692	1591	2283	SO:0001583	missense	201625	exon31			GCGTATCCGCCAG	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.4645G>A	3.37:g.57419497C>T	ENSP00000295937:p.Asp1549Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		913	0.41804029304029305	69	0.1402439024390244	172	0.47513812154696133	240	0.4195804195804196	432	0.5699208443271768	C	12.66	2.004007	0.35320	0.183526	0.497172	ENSG00000174844	ENST00000351747;ENST00000495027	T;T	0.54479	0.57;0.57	5.73	4.86	0.63082	ATPase, dynein-related, AAA domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.28649	0.875	0.09310	P	1.0	D	0.63880	0.993	D	0.63113	0.911	T	0.48445	-0.9035	8	0.25751	T	0.34	.	16.9907	0.86353	0.0:0.8725:0.1275:0.0	rs6773904;rs17736942;rs57634010;rs6773904	1549	Q6ZR08	DYH12_HUMAN	N	1549;1572	ENSP00000295937:D1549N;ENSP00000418137:D1572N	ENSP00000295937:D1549N	D	-	1	0	DNAH12	57394537	1.000000	0.71417	0.970000	0.41538	0.021000	0.10359	5.963000	0.70372	1.427000	0.47276	-0.127000	0.14921	GAT	C|0.587;T|0.413	0.413	strong		0.353	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389005	1389005	+	Missense_Mutation	SNP	T	T	C	rs71614970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1389005T>C	ENST00000324803.4	+	1	3666	c.706T>C	c.(706-708)Tgc>Cgc	p.C236R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	236					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACGTGCCGATGCGGAGTGCC	0.672													t|||	859	0.171526	0.1059	0.245	5008	,	,		14444	0.0437		0.2913	False		,,,				2504	0.2168				p.C236R		Atlas-SNP	.											CRIPAK,rectum,NS,0,1	CRIPAK	185	1	0			c.T706C						PASS	.						163.0	133.0	143.0					4																	1389005		2188	4292	6480	SO:0001583	missense	285464	exon1			TGCCGATGCGGAG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.706T>C	4.37:g.1389005T>C	ENSP00000323978:p.Cys236Arg	Somatic	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	1.791	-0.479438	0.04383	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.18338	2.22	1.11	-2.23	0.06930	Post-SET domain (1);	.	.	.	.	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.32214	-0.9915	9	0.46703	T	0.11	.	2.6743	0.05077	0.0:0.3283:0.2597:0.412	.	236	Q8N1N5	CRPAK_HUMAN	R	236;178	ENSP00000323978:C236R	ENSP00000323978:C236R	C	+	1	0	CRIPAK	1379005	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.211000	0.09332	-0.571000	0.06014	-0.530000	0.04314	TGC	C|1.000;|0.000	1.000	weak		0.672	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
OR2T3	343173	hgsc.bcm.edu	37	1	248637362	248637362	+	Silent	SNP	C	C	T	rs77686526	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248637362C>T	ENST00000359594.2	+	1	736	c.711C>T	c.(709-711)gcC>gcT	p.A237A		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATTCTGCCGCCGGCCACAGGA	0.562													.|||	1915	0.382388	0.3124	0.3775	5008	,	,		22676	0.503		0.2604	False		,,,				2504	0.4816				p.A237A		Atlas-SNP	.											.	OR2T3	79	.	0			c.C711T						PASS	.						189.0	159.0	169.0					1																	248637362		2201	4297	6498	SO:0001819	synonymous_variant	343173	exon1			TGCCGCCGGCCAC		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.711C>T	1.37:g.248637362C>T		Somatic	615	0	0		WXS	Illumina HiSeq	Phase_I	543	175	0.322284	NM_001005495	B2RNJ1	Silent	SNP	ENST00000359594.2	37	CCDS31117.1																																																																																			C|0.702;T|0.298	0.298	strong		0.562	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
GOLGB1	2804	hgsc.bcm.edu	37	3	121413239	121413239	+	Missense_Mutation	SNP	T	T	G	rs75383249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121413239T>G	ENST00000340645.5	-	13	6241	c.6116A>C	c.(6115-6117)gAg>gCg	p.E2039A	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2044A	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2039					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AACAGTTCTCTCCAGAGCACT	0.368													T|||	9	0.00179712	0.0	0.0	5008	,	,		19970	0.0		0.0089	False		,,,				2504	0.0				p.E2044A		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A6131C						PASS	.	T	ALA/GLU	6,4400	9.9+/-24.2	0,6,2197	109.0	110.0	110.0		6116	5.5	1.0	3	dbSNP_132	110	38,8560	25.1+/-72.6	0,38,4261	yes	missense	GOLGB1	NM_004487.3	107	0,44,6458	GG,GT,TT		0.442,0.1362,0.3384	probably-damaging	2039/3260	121413239	44,12960	2203	4299	6502	SO:0001583	missense	2804	exon13			GTTCTCTCCAGAG	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6116A>C	3.37:g.121413239T>G	ENSP00000341848:p.Glu2039Ala	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	T	9.851	1.193741	0.22037	0.001362	0.00442	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.20069	2.1;2.1	5.46	5.46	0.80206	.	0.000000	0.53938	D	0.000051	T	0.30885	0.0779	L	0.49640	1.575	0.34058	D	0.656894	D;D;P;D	0.71674	0.998;0.998;0.607;0.977	D;D;B;P	0.81914	0.995;0.995;0.255;0.69	T	0.45381	-0.9265	10	0.37606	T	0.19	.	13.5212	0.61569	0.0:0.0:0.0:1.0	.	1964;2044;2044;2039	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	A	2039;2044	ENSP00000341848:E2039A;ENSP00000377275:E2044A	ENSP00000341848:E2039A	E	-	2	0	GOLGB1	122895929	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.911000	0.48774	2.289000	0.77006	0.482000	0.46254	GAG	T|0.997;G|0.003	0.003	strong		0.368	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
PHRF1	57661	hgsc.bcm.edu	37	11	607680	607680	+	Missense_Mutation	SNP	G	G	A	rs113889171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:607680G>A	ENST00000264555.5	+	14	2352	c.2224G>A	c.(2224-2226)Ggg>Agg	p.G742R	PHRF1_ENST00000533464.1_Missense_Mutation_p.G738R|PHRF1_ENST00000413872.2_Missense_Mutation_p.G740R|PHRF1_ENST00000416188.2_Missense_Mutation_p.G741R	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	742					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CCGGGAGCCCGGGGTGCACAC	0.711													G|||	13	0.00259585	0.0	0.0029	5008	,	,		12943	0.0079		0.002	False		,,,				2504	0.001				p.G741R		Atlas-SNP	.											.	PHRF1	188	.	0			c.G2221A						PASS	.	G	ARG/GLY	4,3762		0,4,1879	11.0	14.0	13.0		2221	-9.1	0.0	11	dbSNP_132	13	36,8126		0,36,4045	no	missense	PHRF1	NM_020901.2	125	0,40,5924	AA,AG,GG		0.4411,0.1062,0.3353	possibly-damaging	741/1649	607680	40,11888	1883	4081	5964	SO:0001583	missense	57661	exon14			GAGCCCGGGGTGC	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.2224G>A	11.37:g.607680G>A	ENSP00000264555:p.Gly742Arg	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	10	6	0.6	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	37		7	0.003205128205128205	0	0.0	0	0.0	4	0.006993006993006993	3	0.00395778364116095	G	5.718	0.316922	0.10845	0.001062	0.004411	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.79247	-1.24;-1.25;-1.24;-1.25	4.56	-9.13	0.00704	.	1.355780	0.05069	N	0.481259	T	0.50905	0.1643	L	0.33485	1.01	0.09310	N	1	B;B;B;B	0.14012	0.005;0.009;0.009;0.005	B;B;B;B	0.12156	0.003;0.007;0.007;0.003	T	0.38908	-0.9639	10	0.20046	T	0.44	-3.3477	5.2969	0.15756	0.6485:0.171:0.0951:0.0854	.	738;740;741;742	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	R	742;740;741;738	ENSP00000264555:G742R;ENSP00000388589:G740R;ENSP00000410626:G741R;ENSP00000431870:G738R	ENSP00000264555:G742R	G	+	1	0	PHRF1	597680	0.065000	0.20965	0.000000	0.03702	0.030000	0.12068	-0.303000	0.08210	-2.559000	0.00474	-0.391000	0.06502	GGG	G|0.996;A|0.004	0.004	strong		0.711	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
ACP6	51205	hgsc.bcm.edu	37	1	147119273	147119273	+	Silent	SNP	G	G	A	rs1344	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:147119273G>A	ENST00000369238.6	-	10	1686	c.1239C>T	c.(1237-1239)caC>caT	p.H413H	ACP6_ENST00000460583.1_5'UTR	NM_016361.3	NP_057445.4	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	413					dephosphorylation (GO:0016311)|lysobisphosphatidic acid metabolic process (GO:2001311)|phospholipid metabolic process (GO:0006644)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	acid phosphatase activity (GO:0003993)|lysophosphatidic acid phosphatase activity (GO:0052642)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(4)|prostate(1)	16	all_hematologic(923;0.0276)					AGCAGAGTGCGTGGTATTTTT	0.438													G|||	2400	0.479233	0.4281	0.6254	5008	,	,		19542	0.4226		0.5765	False		,,,				2504	0.4029				p.H413H		Atlas-SNP	.											.	ACP6	36	.	0			c.C1239T						PASS	.	G		2019,2387	563.5+/-381.2	448,1123,632	163.0	158.0	160.0		1239	2.9	0.9	1	dbSNP_36	160	4889,3711	619.9+/-397.0	1403,2083,814	yes	coding-synonymous	ACP6	NM_016361.3		1851,3206,1446	AA,AG,GG		43.1512,45.8239,46.8861		413/429	147119273	6908,6098	2203	4300	6503	SO:0001819	synonymous_variant	51205	exon10			GAGTGCGTGGTAT	BC009965	CCDS928.1	1q21	2008-02-05			ENSG00000162836	ENSG00000162836			29609	protein-coding gene	gene with protein product		611471				12010880, 10506173	Standard	NM_016361		Approved	LPAP, ACPL1	uc001epr.2	Q9NPH0	OTTHUMG00000014019	ENST00000369238.6:c.1239C>T	1.37:g.147119273G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	235	84	0.357447	NM_016361	Q59G61|Q5T490|Q6IAQ3|Q7LG81|Q9UIG6	Silent	SNP	ENST00000369238.6	37	CCDS928.1																																																																																			G|0.493;A|0.507	0.507	strong		0.438	ACP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039420.2	NM_016361	
GLIS1	148979	hgsc.bcm.edu	37	1	54060016	54060016	+	Missense_Mutation	SNP	G	G	C	rs35227000	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:54060016G>C	ENST00000312233.2	-	3	1126	c.560C>G	c.(559-561)gCa>gGa	p.A187G		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						CACCCTGCCTGCCAGGCCCAG	0.697													G|||	1070	0.213658	0.1104	0.1643	5008	,	,		13194	0.1885		0.2962	False		,,,				2504	0.3292				p.A187G		Atlas-SNP	.											.	GLIS1	52	.	0			c.C560G						PASS	.	G	GLY/ALA	547,3825		59,429,1698	14.0	14.0	14.0		560	-1.2	0.2	1	dbSNP_126	14	2796,5746		502,1792,1977	no	missense	GLIS1	NM_147193.2	60	561,2221,3675	CC,CG,GG		32.7324,12.5114,25.8866	benign	187/621	54060016	3343,9571	2186	4271	6457	SO:0001583	missense	148979	exon3			CTGCCTGCCAGGC	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"""Zinc fingers, C2H2-type"""	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.560C>G	1.37:g.54060016G>C	ENSP00000309653:p.Ala187Gly	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	11	7	0.636364	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	477	0.2184065934065934	66	0.13414634146341464	67	0.1850828729281768	114	0.1993006993006993	230	0.3034300791556728	G	8.908	0.958011	0.18507	0.125114	0.327324	ENSG00000174332	ENST00000312233	T	0.10860	2.83	4.67	-1.17	0.09648	.	0.628717	0.14183	N	0.335887	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.48352	-0.9043	9	0.24483	T	0.36	.	5.9742	0.19369	0.3294:0.1274:0.5432:0.0	rs35227000	187	Q8NBF1	GLIS1_HUMAN	G	187	ENSP00000309653:A187G	ENSP00000309653:A187G	A	-	2	0	GLIS1	53832604	0.000000	0.05858	0.203000	0.23512	0.475000	0.33008	0.042000	0.13949	-0.010000	0.14271	0.462000	0.41574	GCA	G|0.757;C|0.243	0.243	strong		0.697	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
FMN2	56776	hgsc.bcm.edu	37	1	240492734	240492734	+	Missense_Mutation	SNP	G	G	A	rs3795677	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:240492734G>A	ENST00000319653.9	+	10	4633	c.4403G>A	c.(4402-4404)cGt>cAt	p.R1468H	FMN2_ENST00000545751.1_Missense_Mutation_p.R64H	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1468	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.		R -> H (in dbSNP:rs3795677). {ECO:0000269|Ref.3}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TGCTCAATTCGTCGCAAACTG	0.408													G|||	1607	0.320887	0.3381	0.3588	5008	,	,		18670	0.3185		0.2883	False		,,,				2504	0.3067				p.R1468H		Atlas-SNP	.											FMN2,NS,carcinoma,+1,1	FMN2	451	1	0			c.G4403A						PASS	.	G	HIS/ARG	1380,3026	456.3+/-351.3	201,978,1024	144.0	136.0	138.0		4403	1.7	1.0	1	dbSNP_107	138	2363,6237	394.1+/-344.6	308,1747,2245	yes	missense	FMN2	NM_020066.4	29	509,2725,3269	AA,AG,GG		27.4767,31.3209,28.779	possibly-damaging	1468/1723	240492734	3743,9263	2203	4300	6503	SO:0001583	missense	56776	exon10			CAATTCGTCGCAA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.4403G>A	1.37:g.240492734G>A	ENSP00000318884:p.Arg1468His	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	251	251	1	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	705	0.3228021978021978	158	0.32113821138211385	127	0.35082872928176795	196	0.34265734265734266	224	0.2955145118733509	G	7.918	0.737991	0.15574	0.313209	0.274767	ENSG00000155816	ENST00000319653;ENST00000545751;ENST00000537355	T;T	0.18502	2.21;2.21	5.65	1.72	0.24424	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.324081	0.26065	N	0.026552	T	0.00012	0.0000	N	0.25890	0.77	0.09310	P	0.9999999999949641	B;B;B;P	0.34837	0.002;0.005;0.008;0.472	B;B;B;B	0.37780	0.002;0.005;0.008;0.258	T	0.31586	-0.9938	9	0.06365	T	0.9	.	11.8887	0.52616	0.2878:0.0:0.7122:0.0	rs3795677;rs17679152;rs56984583;rs3795677	64;114;97;1468	B4DP05;F5H2C1;B4DN09;Q9NZ56	.;.;.;FMN2_HUMAN	H	1468;64;95	ENSP00000318884:R1468H;ENSP00000437918:R64H	ENSP00000318884:R1468H	R	+	2	0	FMN2	238559357	0.000000	0.05858	0.998000	0.56505	0.979000	0.70002	-0.225000	0.09151	0.059000	0.16252	-0.940000	0.02684	CGT	G|0.684;A|0.316	0.316	strong		0.408	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
SCIMP	388325	hgsc.bcm.edu	37	17	5126674	5126674	+	Silent	SNP	A	A	G	rs2641256	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5126674A>G	ENST00000574081.1	-	2	203	c.99T>C	c.(97-99)ggT>ggC	p.G33G	RP11-333E1.1_ENST00000573772.1_RNA|SCIMP_ENST00000399600.4_Silent_p.G33G|SCIMP_ENST00000574297.1_Silent_p.G33G|RP11-333E1.1_ENST00000575601.1_RNA|RP11-333E1.1_ENST00000571689.1_RNA|SCIMP_ENST00000571800.1_Silent_p.G33G	NM_001271842.1|NM_207103.3	NP_001258771.1|NP_996986.1	Q6UWF3	SCIMP_HUMAN	SLP adaptor and CSK interacting membrane protein	33					positive regulation of ERK1 and ERK2 cascade (GO:0070374)	immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|tetraspanin-enriched microdomain (GO:0097197)|uropod membrane (GO:0031259)											TGAGGCCCAGACCCACAGAGA	0.507													G|||	2193	0.437899	0.3268	0.6354	5008	,	,		20702	0.3542		0.66	False		,,,				2504	0.3057				p.G33G		Atlas-SNP	.											.	.	.	.	0			c.T99C						PASS	.	G		1541,2623		303,935,844	302.0	285.0	291.0		99	3.4	0.6	17	dbSNP_100	291	5852,2586		2026,1800,393	yes	coding-synonymous	C17orf87	NM_207103.2		2329,2735,1237	GG,GA,AA		30.6471,37.0077,41.3347		33/146	5126674	7393,5209	2082	4219	6301	SO:0001819	synonymous_variant	388325	exon2			GCCCAGACCCACA	AY358809	CCDS42242.1, CCDS62044.1	17p13.2	2011-11-24	2011-11-23	2011-11-23	ENSG00000161929	ENSG00000161929			33504	protein-coding gene	gene with protein product	"""SLP65/SLP76, Csk-interacting membrane protein"""	614406	"""chromosome 17 open reading frame 87"""	C17orf87		21930792	Standard	NM_207103		Approved	DTFT5783, UNQ5783, FLJ32580, MGC163426, MGC163428	uc002gbh.3	Q6UWF3	OTTHUMG00000132914	ENST00000574081.1:c.99T>C	17.37:g.5126674A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_207103	A6XGL4|B4DLK1|Q96MD0	Silent	SNP	ENST00000574081.1	37	CCDS42242.1																																																																																			A|0.501;G|0.499	0.499	strong		0.507	SCIMP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256425.2	NM_207103	
LAMC3	10319	hgsc.bcm.edu	37	9	133928345	133928345	+	Silent	SNP	C	C	T	rs12349966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133928345C>T	ENST00000361069.4	+	11	2065	c.1932C>T	c.(1930-1932)agC>agT	p.S644S	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	644	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CCGGCCCCAGCCCTGCCGGTC	0.667											OREG0019556	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2403	0.479832	0.621	0.3271	5008	,	,		14176	0.4226		0.4642	False		,,,				2504	0.4724				p.S644S		Atlas-SNP	.											.	LAMC3	167	.	0			c.C1932T						PASS	.	C		2552,1850		761,1030,410	23.0	23.0	23.0		1932	3.9	0.0	9	dbSNP_120	23	3828,4764		874,2080,1342	no	coding-synonymous	LAMC3	NM_006059.3		1635,3110,1752	TT,TC,CC		44.5531,42.0264,49.0996		644/1576	133928345	6380,6614	2201	4296	6497	SO:0001819	synonymous_variant	10319	exon11			CCCCAGCCCTGCC	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.1932C>T	9.37:g.133928345C>T		Somatic	88	0	0	1606	WXS	Illumina HiSeq	Phase_I	76	76	1	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			C|0.531;T|0.469	0.469	strong		0.667	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
PCDHB16	57717	hgsc.bcm.edu	37	5	140564263	140564263	+	Missense_Mutation	SNP	C	C	T	rs17844666	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140564263C>T	ENST00000361016.2	+	1	3284	c.2129C>T	c.(2128-2130)gCg>gTg	p.A710V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	710				A -> V (in Ref. 3; BAB13447). {ECO:0000305}.	calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGTTCGTGGCGGTGCGGCTG	0.692													C|||	1351	0.269768	0.0477	0.3055	5008	,	,		16208	0.5288		0.2306	False		,,,				2504	0.318				p.A710V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C2129T						PASS	.	C	VAL/ALA	241,4151		11,219,1966	71.0	81.0	78.0		2129	0.9	0.3	5	dbSNP_123	78	1847,6725		206,1435,2645	no	missense	PCDHB16	NM_020957.1	64	217,1654,4611	TT,TC,CC		21.5469,5.4872,16.1061	benign	710/777	140564263	2088,10876	2196	4286	6482	SO:0001583	missense	57717	exon1			TCGTGGCGGTGCG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.2129C>T	5.37:g.140564263C>T	ENSP00000354293:p.Ala710Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	86	57	0.662791	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	571	0.26144688644688646	15	0.03048780487804878	88	0.2430939226519337	300	0.5244755244755245	168	0.22163588390501318	c	14.19	2.461805	0.43736	0.054872	0.215469	ENSG00000196963	ENST00000361016	T	0.15603	2.41	3.91	0.912	0.19349	.	0.524287	0.14313	N	0.327546	T	0.00012	0.0000	M	0.84773	2.715	0.80722	P	0.0	B	0.16396	0.017	B	0.18263	0.021	T	0.32613	-0.9900	9	0.42905	T	0.14	.	7.2915	0.26368	0.0:0.2524:0.5685:0.179	rs61742755	710	Q9NRJ7	PCDBG_HUMAN	V	710	ENSP00000354293:A710V	ENSP00000354293:A710V	A	+	2	0	PCDHB16	140544447	0.000000	0.05858	0.256000	0.24389	0.269000	0.26545	-1.952000	0.01528	0.115000	0.18071	0.479000	0.44913	GCG	C|0.931;T|0.069	0.069	strong		0.692	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
ZNF74	7625	hgsc.bcm.edu	37	22	20761063	20761063	+	Silent	SNP	G	G	A	rs2228236	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20761063G>A	ENST00000400451.2	+	5	2254	c.1740G>A	c.(1738-1740)gaG>gaA	p.E580E	ZNF74_ENST00000356671.5_Silent_p.E580E|ZNF74_ENST00000357502.5_3'UTR|ZNF74_ENST00000405993.1_Silent_p.E548E|ZNF74_ENST00000403682.3_3'UTR	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	580					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			TGCACAGCGAGGGGAAGCCCT	0.572													G|||	547	0.109225	0.1899	0.1066	5008	,	,		20956	0.002		0.164	False		,,,				2504	0.0562				p.E580E		Atlas-SNP	.											.	ZNF74	54	.	0			c.G1740A						PASS	.	G		751,3543		63,625,1459	49.0	55.0	53.0		1740	-8.5	0.0	22	dbSNP_98	53	1315,7225		102,1111,3057	no	coding-synonymous	ZNF74	NM_003426.2		165,1736,4516	AA,AG,GG		15.3981,17.4895,16.0979		580/645	20761063	2066,10768	2147	4270	6417	SO:0001819	synonymous_variant	7625	exon5			CAGCGAGGGGAAG	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"""Zinc fingers, C2H2-type"", ""-"""	13144	protein-coding gene	gene with protein product		194548	"""zinc finger protein 74 (Cos52)"""			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.1740G>A	22.37:g.20761063G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Silent	SNP	ENST00000400451.2	37	CCDS42982.1																																																																																			G|0.859;A|0.141	0.141	strong		0.572	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426	
MFF	56947	hgsc.bcm.edu	37	2	228194481	228194481	+	Missense_Mutation	SNP	G	G	T	rs3211098|rs386655869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228194481G>T	ENST00000353339.3	+	3	461	c.20G>T	c.(19-21)aGt>aTt	p.S7I	MFF_ENST00000409565.1_Intron|MFF_ENST00000392059.1_Missense_Mutation_p.S7I|MFF_ENST00000349901.7_Intron|MFF_ENST00000337110.7_Intron|MFF_ENST00000524634.1_Intron|MFF_ENST00000476924.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000409616.1_5'UTR	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	7			S -> C (in dbSNP:rs3211097).|S -> I (in dbSNP:rs3211098).		mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						GGAACAAGCAGTGACACATCA	0.363													G|||	1364	0.272364	0.0961	0.2493	5008	,	,		17526	0.245		0.3748	False		,,,				2504	0.4499				p.S7I		Atlas-SNP	.											.	MFF	48	.	0			c.G20T						PASS	.	G	ILE/SER	516,3890		31,454,1718	125.0	117.0	120.0		20	3.1	1.0	2	dbSNP_105	120	2985,5615		552,1881,1867	yes	missense	MFF	NM_020194.4	142	583,2335,3585	TT,TG,GG		34.7093,11.7113,26.9183	possibly-damaging	7/343	228194481	3501,9505	2203	4300	6503	SO:0001583	missense	56947	exon3			CAAGCAGTGACAC	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.20G>T	2.37:g.228194481G>T	ENSP00000302037:p.Ser7Ile	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	148	64	0.432432	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	SNP	ENST00000353339.3	37	CCDS2465.1	428	0.19597069597069597	32	0.06504065040650407	88	0.2430939226519337	106	0.1853146853146853	202	0.26649076517150394	G	11.95	1.792561	0.31685	0.117113	0.347093	ENSG00000168958	ENST00000353339;ENST00000436237;ENST00000443428;ENST00000392059	T;T;T;T	0.61859	1.35;0.07;1.34;1.35	5.97	3.1	0.35709	.	0.300115	0.29253	N	0.012695	T	0.00012	0.0000	N	0.22421	0.69	0.39157	P	0.037660999999999945	B	0.23058	0.079	B	0.21546	0.035	T	0.38672	-0.9650	8	.	.	.	-1.6615	7.0809	0.25231	0.0813:0.0:0.6137:0.305	rs3211098;rs10190875;rs60557422;rs3211098	7	Q9GZY8	MFF_HUMAN	I	7	ENSP00000302037:S7I;ENSP00000411386:S7I;ENSP00000391829:S7I;ENSP00000375912:S7I	.	S	+	2	0	MFF	227902725	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.061000	0.41403	0.365000	0.24400	0.650000	0.86243	AGT	G|0.737;T|0.263	0.263	strong		0.363	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194	
SLC12A6	9990	hgsc.bcm.edu	37	15	34528948	34528948	+	Silent	SNP	G	G	A	rs4577050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:34528948G>A	ENST00000354181.3	-	23	3495	c.3003C>T	c.(3001-3003)ctC>ctT	p.L1001L	SLC12A6_ENST00000451844.2_Silent_p.L813L|SLC12A6_ENST00000290209.5_Silent_p.L950L|SLC12A6_ENST00000558667.1_Silent_p.L1001L|SLC12A6_ENST00000397707.2_Silent_p.L986L|SLC12A6_ENST00000560164.1_Silent_p.L813L|SLC12A6_ENST00000397702.2_Silent_p.L942L|SLC12A6_ENST00000560611.1_Silent_p.L1001L|SLC12A6_ENST00000458406.2_Silent_p.L942L|SLC12A6_ENST00000558589.1_Silent_p.L992L			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	1001					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	GCATGTGCCGGAGCATCTGGG	0.458													G|||	2865	0.572085	0.382	0.6643	5008	,	,		20843	0.6657		0.66	False		,,,				2504	0.5767				p.L1001L		Atlas-SNP	.											.	SLC12A6	205	.	0			c.C3003T						PASS	.	G	,,,,,	1911,2491	546.6+/-377.1	432,1047,722	234.0	199.0	211.0		2826,2826,2976,2958,2850,3003	-4.0	1.0	15	dbSNP_111	211	5831,2765	679.1+/-403.5	1999,1833,466	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A6	NM_001042494.1,NM_001042495.1,NM_001042496.1,NM_001042497.1,NM_005135.2,NM_133647.1	,,,,,	2431,2880,1188	AA,AG,GG		32.1661,43.4121,40.437	,,,,,	942/1092,942/1092,992/1142,986/1136,950/1100,1001/1151	34528948	7742,5256	2201	4298	6499	SO:0001819	synonymous_variant	9990	exon22			GTGCCGGAGCATC	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.3003C>T	15.37:g.34528948G>A		Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	357	159	0.445378	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Silent	SNP	ENST00000354181.3	37	CCDS58352.1																																																																																			G|0.406;A|0.594	0.594	strong		0.458	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
PLD2	5338	hgsc.bcm.edu	37	17	4720469	4720469	+	Missense_Mutation	SNP	C	C	T	rs1052748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4720469C>T	ENST00000263088.6	+	17	1861	c.1730C>T	c.(1729-1731)aCa>aTa	p.T577I	PLD2_ENST00000572940.1_Missense_Mutation_p.T577I	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	577	Catalytic.		T -> I (in dbSNP:rs1052748). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9582313}.		cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	AAGACTCCCACATACCCCTAC	0.617													C|||	1251	0.2498	0.1051	0.415	5008	,	,		17674	0.1062		0.4443	False		,,,				2504	0.2761				p.T577I		Atlas-SNP	.											.	PLD2	138	.	0			c.C1730T	GRCh37	CM030489	PLD2	M	rs1052748	PASS	.	C	ILE/THR	735,3671	302.4+/-287.4	67,601,1535	292.0	242.0	259.0		1730	-9.0	0.0	17	dbSNP_86	259	4136,4464	565.5+/-388.5	1006,2124,1170	yes	missense	PLD2	NM_002663.4	89	1073,2725,2705	TT,TC,CC		48.093,16.6818,37.4519	benign	577/934	4720469	4871,8135	2203	4300	6503	SO:0001583	missense	5338	exon17			CTCCCACATACCC	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"""choline phosphatase 2"""	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1730C>T	17.37:g.4720469C>T	ENSP00000263088:p.Thr577Ile	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	193	84	0.435233	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	637	0.2916666666666667	67	0.13617886178861788	158	0.43646408839779005	52	0.09090909090909091	360	0.47493403693931396	C	0.323	-0.960831	0.02249	0.166818	0.48093	ENSG00000129219	ENST00000263088	T	0.21361	2.01	4.48	-8.96	0.00761	.	1.318270	0.04748	N	0.423943	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.38993	-0.9635	9	0.22109	T	0.4	3.9285	5.7643	0.18217	0.0887:0.4622:0.0898:0.3593	rs1052748;rs17856479;rs59776031;rs1052748	434;577;577	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	I	577	ENSP00000263088:T577I	ENSP00000263088:T577I	T	+	2	0	PLD2	4667435	0.000000	0.05858	0.000000	0.03702	0.149000	0.21700	-1.345000	0.02637	-2.558000	0.00475	-1.223000	0.01593	ACA	C|0.670;T|0.330	0.330	strong		0.617	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
OR51S1	119692	hgsc.bcm.edu	37	11	4870139	4870139	+	Silent	SNP	G	G	A	rs11602455	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4870139G>A	ENST00000322101.2	-	1	375	c.300C>T	c.(298-300)gtC>gtT	p.V100V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTGAGGCAGGGACAGTGTGAG	0.527													G|||	1195	0.238618	0.1203	0.2421	5008	,	,		21161	0.0675		0.4046	False		,,,				2504	0.4018				p.V100V		Atlas-SNP	.											.	OR51S1	83	.	0			c.C300T						PASS	.	G		750,3652	305.5+/-289.0	77,596,1528	114.0	97.0	103.0		300	1.5	0.8	11	dbSNP_120	103	3690,4906	527.8+/-381.2	802,2086,1410	no	coding-synonymous	OR51S1	NM_001004758.1		879,2682,2938	AA,AG,GG		42.9269,17.0377,34.1591		100/324	4870139	4440,8558	2201	4298	6499	SO:0001819	synonymous_variant	119692	exon1			GGCAGGGACAGTG	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.300C>T	11.37:g.4870139G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	138	55	0.398551	NM_001004758	B9EGZ1|Q6IFI2	Silent	SNP	ENST00000322101.2	37	CCDS31362.1																																																																																			G|0.691;A|0.309	0.309	strong		0.527	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
COX11	1353	hgsc.bcm.edu	37	17	53038654	53038654	+	3'UTR	SNP	A	A	C	rs1802212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:53038654A>C	ENST00000299335.3	-	0	2409				COX11_ENST00000573912.1_5'Flank|TOM1L1_ENST00000445275.2_3'UTR|TOM1L1_ENST00000540336.1_3'UTR|TOM1L1_ENST00000572158.1_3'UTR|TOM1L1_ENST00000348161.4_3'UTR|TOM1L1_ENST00000575882.1_3'UTR|TOM1L1_ENST00000536554.1_3'UTR	NM_004375.3	NP_004366.1	Q9Y6N1	COX11_HUMAN	cytochrome c oxidase assembly homolog 11 (yeast)						hydrogen ion transmembrane transport (GO:1902600)|negative regulation of glucokinase activity (GO:0033132)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|prostate(1)	9						TAAAACGTAGACTCTGTGCAG	0.398													A|||	759	0.151558	0.0605	0.1585	5008	,	,		20632	0.129		0.2714	False		,,,				2504	0.1697				p.S228A		Atlas-SNP	.											.	COX11	16	.	0			c.T682G						PASS	.						93.0	76.0	81.0					17																	53038654		692	1591	2283	SO:0001624	3_prime_UTR_variant	1353	exon4			ACGTAGACTCTGT	AF044321	CCDS11583.1, CCDS58579.1	17q22	2012-10-15	2012-10-15			ENSG00000166260		"""Mitochondrial respiratory chain complex assembly factors"""	2261	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit 11"", ""cytochrome c oxidase assembly protein COX11"""	603648	"""COX11 (yeast) homolog, cytochrome c oxidase assembly protein"", ""COX11 cytochrome c oxidase assembly homolog (yeast)"""			9878253	Standard	NM_004375		Approved	COX11P	uc010wng.1	Q9Y6N1		ENST00000299335.3:c.*1440T>G	17.37:g.53038654A>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_001162861	D3DTY5|I3L220|Q6FHB7|Q9BRX0|Q9UME8	Missense_Mutation	SNP	ENST00000299335.3	37	CCDS11583.1																																																																																			A|0.835;C|0.165	0.165	strong		0.398	COX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439182.1	NM_004375	
C6orf201	404220	hgsc.bcm.edu	37	6	4087949	4087949	+	Missense_Mutation	SNP	A	A	T	rs13200786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:4087949A>T	ENST00000380175.4	+	2	839	c.74A>T	c.(73-75)gAc>gTc	p.D25V	FAM217A_ENST00000380188.2_5'Flank|C6orf201_ENST00000430835.2_Missense_Mutation_p.D25V|C6orf201_ENST00000333388.5_Intron|C6orf201_ENST00000360378.6_3'UTR	NM_001085401.2	NP_001078870.1	Q7Z4U5	CF201_HUMAN	chromosome 6 open reading frame 201	25			D -> Y (in dbSNP:rs9503910).							central_nervous_system(1)|endometrium(3)|lung(2)	6	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				AGTGAAGAGGACAAGAAAAAA	0.468													A|||	237	0.0473243	0.0794	0.0216	5008	,	,		16756	0.001		0.0626	False		,,,				2504	0.0542				p.D25V		Atlas-SNP	.											.	C6orf201	17	.	0			c.A74T						PASS	.	A	VAL/ASP	293,3525		9,275,1625	151.0	162.0	159.0		74	3.1	0.4	6	dbSNP_121	159	549,7731		19,511,3610	yes	missense	C6orf201	NM_001085401.1	152	28,786,5235	TT,TA,AA		6.6304,7.6742,6.9598	probably-damaging	25/141	4087949	842,11256	1909	4140	6049	SO:0001583	missense	404220	exon2			AAGAGGACAAGAA	BC047663	CCDS43419.1	6p25.2	2012-02-21			ENSG00000185689	ENSG00000185689			21620	protein-coding gene	gene with protein product							Standard	NM_001085401		Approved	dJ1013A10.5	uc003mwa.4	Q7Z4U5	OTTHUMG00000014160	ENST00000380175.4:c.74A>T	6.37:g.4087949A>T	ENSP00000420610:p.Asp25Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	155	61	0.393548	NM_001085401	A6NLI6|Q6NXN5	Missense_Mutation	SNP	ENST00000380175.4	37	CCDS43419.1	91	0.041666666666666664	35	0.07113821138211382	9	0.024861878453038673	0	0.0	47	0.06200527704485488	A	17.22	3.332943	0.60853	0.076742	0.066304	ENSG00000185689	ENST00000541127;ENST00000380175;ENST00000451679;ENST00000436110;ENST00000430835	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	4.28	3.07	0.35406	.	0.000000	0.45126	D	0.000387	T	0.30916	0.0780	L	0.29908	0.895	0.45979	D	0.998791	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.18461	-1.0336	10	0.87932	D	0	.	7.7738	0.29023	0.787:0.213:0.0:0.0	rs13200786	25;25	B4DXB2;Q7Z4U5	.;CF201_HUMAN	V	25	ENSP00000420610:D25V;ENSP00000420763:D25V;ENSP00000417981:D25V;ENSP00000396912:D25V	ENSP00000420610:D25V	D	+	2	0	C6orf201	4032948	0.993000	0.37304	0.351000	0.25721	0.353000	0.29299	3.615000	0.54167	0.757000	0.33036	0.460000	0.39030	GAC	A|0.950;T|0.050	0.050	strong		0.468	C6orf201-001	KNOWN	NMD_exception|basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000314019.2	NM_001085401	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549582	32549582	+	Missense_Mutation	SNP	G	G	T	rs200516145		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549582G>T	ENST00000360004.5	-	3	509	c.404C>A	c.(403-405)aCc>aAc	p.T135N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	135	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CAGGGGCTGGGTCTTTGAAGG	0.507										Multiple Myeloma(14;0.17)																											p.T135N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C404A						PASS	.						67.0	84.0	78.0					6																	32549582		1510	2709	4219	SO:0001583	missense	3123	exon3			GGCTGGGTCTTTG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.404C>A	6.37:g.32549582G>T	ENSP00000353099:p.Thr135Asn	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	375	37	0.0986667	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	11.78	1.740603	0.30865	.	.	ENSG00000196126	ENST00000360004	T	0.02863	4.13	3.87	2.92	0.33932	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.480425	0.24686	N	0.036424	T	0.06781	0.0173	M	0.76574	2.34	0.26397	N	0.97649	D	0.76494	0.999	D	0.87578	0.998	T	0.02632	-1.1131	10	0.87932	D	0	.	10.9743	0.47456	0.0:0.0:0.8139:0.1861	.	135	P01911	2B1F_HUMAN	N	135	ENSP00000353099:T135N	ENSP00000353099:T135N	T	-	2	0	HLA-DRB1	32657560	0.030000	0.19436	0.762000	0.31397	0.139000	0.21198	1.809000	0.38922	1.883000	0.54544	0.453000	0.30009	ACC	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
RAET1E	135250	hgsc.bcm.edu	37	6	150212003	150212003	+	Missense_Mutation	SNP	C	C	T	rs9383583	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:150212003C>T	ENST00000357183.4	-	1	167	c.35G>A	c.(34-36)cGc>cAc	p.R12H	RP11-244K5.8_ENST00000606915.1_RNA|RAET1E_ENST00000367363.3_Missense_Mutation_p.R12H|RAET1E_ENST00000529948.1_Missense_Mutation_p.R12H|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000532335.1_Missense_Mutation_p.R12H|RAET1E-AS1_ENST00000605899.1_RNA	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	12			R -> H (in dbSNP:rs9383583).		antigen processing and presentation (GO:0019882)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			cervix(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		CAAAAGAAGGCGCACAGGGCT	0.498													c|||	1341	0.267772	0.2209	0.1182	5008	,	,		20195	0.5526		0.1581	False		,,,				2504	0.2566				p.R12H		Atlas-SNP	.											.	RAET1E	20	.	0			c.G35A						PASS	.	C	HIS/ARG	979,3427	368.1+/-318.5	103,773,1327	128.0	108.0	115.0		35	-4.4	0.0	6	dbSNP_119	115	1200,7400	243.3+/-273.0	92,1016,3192	yes	missense	RAET1E	NM_139165.2	29	195,1789,4519	TT,TC,CC		13.9535,22.2197,16.7538	benign	12/264	150212003	2179,10827	2203	4300	6503	SO:0001583	missense	135250	exon1			AGAAGGCGCACAG	AF359243	CCDS5221.1, CCDS59042.1, CCDS59043.1, CCDS59044.1	6q24.3	2011-02-09			ENSG00000164520	ENSG00000164520			16793	protein-coding gene	gene with protein product		609243				11827464	Standard	NM_139165		Approved	LETAL, bA350J20.7, ULBP4	uc003qnl.1	Q8TD07	OTTHUMG00000015796	ENST00000357183.4:c.35G>A	6.37:g.150212003C>T	ENSP00000349709:p.Arg12His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	37	CCDS5221.1	568	0.2600732600732601	94	0.1910569105691057	49	0.13535911602209943	316	0.5524475524475524	109	0.1437994722955145	C	5.780	0.328267	0.10956	0.222197	0.139535	ENSG00000164520	ENST00000532335;ENST00000357183;ENST00000367363;ENST00000529948;ENST00000531073	T;T;T;T;T	0.23147	4.87;5.18;3.95;4.81;1.92	2.19	-4.39	0.03611	.	.	.	.	.	T	0.02230	0.0069	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.04013	0.0;0.001;0.0	T	0.38693	-0.9649	8	0.22706	T	0.39	3.5103	7.0463	0.25048	0.0:0.18:0.1453:0.6748	rs9383583;rs52793456;rs60046247;rs9383583	12;12;12	Q8TD07;Q8TD07-2;Q8TD07-3	N2DL4_HUMAN;.;.	H	12	ENSP00000437067:R12H;ENSP00000349709:R12H;ENSP00000356332:R12H;ENSP00000432366:R12H;ENSP00000433489:R12H	ENSP00000349709:R12H	R	-	2	0	RAET1E	150253696	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.057000	0.01395	-2.414000	0.00569	-0.967000	0.02615	CGC	C|0.783;T|0.217	0.217	strong		0.498	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
ALK	238	hgsc.bcm.edu	37	2	29543663	29543663	+	Silent	SNP	T	T	C	rs2293564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29543663T>C	ENST00000389048.3	-	7	2406	c.1500A>G	c.(1498-1500)caA>caG	p.Q500Q	ALK_ENST00000498037.1_5'Flank|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	500	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TGACCTGCCATTGAGGAGTGT	0.547			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				t|||	3889	0.776558	0.4334	0.8847	5008	,	,		17652	0.9206		0.9235	False		,,,				2504	0.864				p.Q500Q		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.A1500G						PASS	.	T		2356,2050	609.3+/-391.3	618,1120,465	184.0	157.0	166.0		1500	1.0	0.1	2	dbSNP_100	166	7931,669	789.2+/-407.6	3657,617,26	no	coding-synonymous	ALK	NM_004304.4		4275,1737,491	CC,CT,TT		7.7791,46.5275,20.9057		500/1621	29543663	10287,2719	2203	4300	6503	SO:0001819	synonymous_variant	238	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CTGCCATTGAGGA	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1500A>G	2.37:g.29543663T>C		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			T|0.203;C|0.797	0.797	strong		0.547	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
GJD2	57369	hgsc.bcm.edu	37	15	35044757	35044757	+	Silent	SNP	C	C	T	rs34964522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:35044757C>T	ENST00000290374.4	-	2	1364	c.888G>A	c.(886-888)gaG>gaA	p.E296E	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	296					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TGTTACGAATCTCATAGATTG	0.527													C|||	189	0.0377396	0.0038	0.0605	5008	,	,		20993	0.0		0.1093	False		,,,				2504	0.0327				p.E296E		Atlas-SNP	.											GJD2,bladder,carcinoma,-2,1	GJD2	49	1	0			c.G888A						PASS	.	C		120,4282	90.2+/-128.9	2,116,2083	90.0	75.0	80.0		888	3.9	1.0	15	dbSNP_126	80	995,7601	214.8+/-254.3	61,873,3364	no	coding-synonymous	GJD2	NM_020660.1		63,989,5447	TT,TC,CC		11.5752,2.726,8.5782		296/322	35044757	1115,11883	2201	4298	6499	SO:0001819	synonymous_variant	57369	exon2			ACGAATCTCATAG	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.888G>A	15.37:g.35044757C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_020660	Q2M241|Q9P2R0	Silent	SNP	ENST00000290374.4	37	CCDS10040.1																																																																																			C|0.925;T|0.075	0.075	strong		0.527	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2		
DHX37	57647	hgsc.bcm.edu	37	12	125453115	125453115	+	Missense_Mutation	SNP	C	C	T	rs11057939	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:125453115C>T	ENST00000308736.2	-	10	1471	c.1373G>A	c.(1372-1374)cGg>cAg	p.R458Q	DHX37_ENST00000544745.1_Missense_Mutation_p.R245Q	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	458			R -> Q (in dbSNP:rs11057939).				ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GCAGACCTTCCGGAAGCACTC	0.602													C|||	269	0.0537141	0.0076	0.0994	5008	,	,		18822	0.0		0.1581	False		,,,				2504	0.0317				p.R458Q		Atlas-SNP	.											.	DHX37	114	.	0			c.G1373A						PASS	.	C	GLN/ARG	117,4289	89.2+/-127.9	1,115,2087	131.0	133.0	132.0		1373	4.6	1.0	12	dbSNP_120	132	1353,7247	265.6+/-286.2	108,1137,3055	yes	missense	DHX37	NM_032656.3	43	109,1252,5142	TT,TC,CC		15.7326,2.6555,11.3025	possibly-damaging	458/1158	125453115	1470,11536	2203	4300	6503	SO:0001583	missense	57647	exon10			ACCTTCCGGAAGC	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1373G>A	12.37:g.125453115C>T	ENSP00000311135:p.Arg458Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	178	0.0815018315018315	7	0.014227642276422764	48	0.13259668508287292	0	0.0	123	0.16226912928759896	C	18.17	3.565362	0.65651	0.026555	0.157326	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.13538	2.58;2.58	4.6	4.6	0.57074	.	0.122536	0.53938	D	0.000043	T	0.00039	0.0001	L	0.54908	1.71	0.19775	P	0.9999506386	P	0.42941	0.794	B	0.32864	0.154	T	0.27571	-1.0070	9	0.52906	T	0.07	-5.5669	17.3773	0.87396	0.0:1.0:0.0:0.0	rs11057939;rs52834302;rs11057939	458	Q8IY37	DHX37_HUMAN	Q	458;245	ENSP00000311135:R458Q;ENSP00000439009:R245Q	ENSP00000311135:R458Q	R	-	2	0	DHX37	124019068	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	4.311000	0.59147	2.263000	0.75096	0.561000	0.74099	CGG	C|0.906;T|0.094	0.094	strong		0.602	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
CLEC19A	728276	hgsc.bcm.edu	37	16	19297219	19297219	+	Missense_Mutation	SNP	T	T	G	rs179196	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19297219T>G	ENST00000465414.1	+	1	119	c.46T>G	c.(46-48)Tct>Gct	p.S16A	CLEC19A_ENST00000493231.1_Missense_Mutation_p.S16A			Q6UXS0	CL19A_HUMAN	C-type lectin domain family 19, member A	16				S -> A (in Ref. 2; BC119018). {ECO:0000305}.		extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)										GACCCTCCACTCTGCACAGGC	0.557													T|||	1058	0.211262	0.0144	0.2378	5008	,	,		19551	0.5228		0.0825	False		,,,				2504	0.2699				p.S16A		Atlas-SNP	.											.	CLEC19A	4	.	0			c.T46G						PASS	.																																			SO:0001583	missense	728276	exon1			CTCCACTCTGCAC			16p12.3	2013-01-07			ENSG00000261210	ENSG00000261210		"""C-type lectin domain containing"""	34522	protein-coding gene	gene with protein product							Standard	NM_001256720		Approved		uc031qvg.1	Q6UXS0	OTTHUMG00000177218	ENST00000465414.1:c.46T>G	16.37:g.19297219T>G	ENSP00000455948:p.Ser16Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001256720	Q0VF32	Missense_Mutation	SNP	ENST00000465414.1	37																																																																																				T|0.805;G|0.195	0.195	strong		0.557	CLEC19A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254277.2	NM_00125672	
KIF17	57576	hgsc.bcm.edu	37	1	21042094	21042094	+	Silent	SNP	G	G	A	rs12046928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:21042094G>A	ENST00000247986.2	-	2	580	c.270C>T	c.(268-270)taC>taT	p.Y90Y	KIF17_ENST00000400463.3_Silent_p.Y90Y|KIF17_ENST00000375044.1_De_novo_Start_OutOfFrame			Q9P2E2	KIF17_HUMAN	kinesin family member 17	90	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CTGTCTGGCCGTAGGCAAAGA	0.647													G|||	1404	0.280351	0.0741	0.1614	5008	,	,		19859	0.7232		0.1451	False		,,,				2504	0.3262				p.Y90Y		Atlas-SNP	.											.	KIF17	130	.	0			c.C270T						PASS	.	G	,	369,4037	187.1+/-213.8	14,341,1848	98.0	83.0	88.0		270,270	-5.7	0.9	1	dbSNP_120	88	1106,7494	230.8+/-265.0	82,942,3276	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	96,1283,5124	AA,AG,GG		12.8605,8.3749,11.3409	,	90/1029,90/1030	21042094	1475,11531	2203	4300	6503	SO:0001819	synonymous_variant	57576	exon2			CTGGCCGTAGGCA	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.270C>T	1.37:g.21042094G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			G|0.810;A|0.190	0.190	strong		0.647	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
CDH6	1004	hgsc.bcm.edu	37	5	31302288	31302288	+	Silent	SNP	C	C	T	rs2287582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:31302288C>T	ENST00000265071.2	+	6	1147	c.882C>T	c.(880-882)gaC>gaT	p.D294D	CDH6_ENST00000514738.1_Silent_p.D239D	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	294	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AAGCCAGCGACGCTGATGTGG	0.463													C|||	2029	0.405152	0.062	0.4986	5008	,	,		17768	0.5238		0.5547	False		,,,				2504	0.5266				p.D294D		Atlas-SNP	.											.	CDH6	175	.	0			c.C882T						PASS	.	C		664,3742	281.1+/-275.7	56,552,1595	127.0	119.0	122.0		882	-5.9	0.3	5	dbSNP_100	122	4545,4055	595.4+/-393.5	1238,2069,993	no	coding-synonymous	CDH6	NM_004932.3		1294,2621,2588	TT,TC,CC		47.1512,15.0704,40.0507		294/791	31302288	5209,7797	2203	4300	6503	SO:0001819	synonymous_variant	1004	exon6			CAGCGACGCTGAT	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.882C>T	5.37:g.31302288C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	238	95	0.39916	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			C|0.591;T|0.409	0.409	strong		0.463	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
ERBB2	2064	hgsc.bcm.edu	37	17	37879588	37879588	+	Missense_Mutation	SNP	A	A	G	rs1136201	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:37879588A>G	ENST00000269571.5	+	17	2122	c.1963A>G	c.(1963-1965)Atc>Gtc	p.I655V	ERBB2_ENST00000445658.2_Missense_Mutation_p.I379V|ERBB2_ENST00000541774.1_Missense_Mutation_p.I640V|ERBB2_ENST00000406381.2_Missense_Mutation_p.I625V|ERBB2_ENST00000540147.1_Missense_Mutation_p.I625V|ERBB2_ENST00000584450.1_Missense_Mutation_p.I655V|ERBB2_ENST00000584601.1_Missense_Mutation_p.I625V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	655			I -> V (in allele B2 and allele B3; dbSNP:rs1136201). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8095488, ECO:0000269|Ref.3}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GACGTCCATCATCTCTGCGGT	0.612		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)			A|||	608	0.121406	0.0098	0.1369	5008	,	,		13960	0.124		0.2455	False		,,,				2504	0.1309				p.I655V		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.A1963G	GRCh37	CM004332	ERBB2	M	rs1136201	PASS	.	A	VAL/ILE,VAL/ILE	212,4194	132.1+/-168.6	5,202,1996	113.0	103.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1873,1963	5.0	1.0	17	dbSNP_86	106	1980,6620	346.8+/-326.3	223,1534,2543	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	29,29	228,1736,4539	GG,GA,AA		23.0233,4.8116,16.8538	benign,benign	625/1226,655/1256	37879588	2192,10814	2203	4300	6503	SO:0001583	missense	2064	exon17			TCCATCATCTCTG	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1963A>G	17.37:g.37879588A>G	ENSP00000269571:p.Ile655Val	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	238	93	0.390756	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	339	0.15521978021978022	5	0.01016260162601626	58	0.16022099447513813	83	0.1451048951048951	193	0.2546174142480211	A	13.67	2.306999	0.40795	0.048116	0.230233	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.76316	-1.01;-1.01;-0.99;-1.01;-1.01	4.97	4.97	0.65823	Cytochrome c1, transmembrane anchor, C-terminal (1);	.	.	.	.	T	0.00039	0.0001	N	0.25485	0.75	0.09310	P	1.0	B;P;B	0.39576	0.406;0.679;0.406	B;B;B	0.37650	0.108;0.255;0.108	T	0.05920	-1.0856	8	0.22706	T	0.39	.	8.987	0.35999	0.9164:0.0:0.0836:0.0	rs1136201;rs1801200;rs2006406;rs2230699;rs17606815;rs59955961;rs1801200	379;640;655	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	625;640;379;655;625	ENSP00000385185:I625V;ENSP00000446466:I640V;ENSP00000404047:I379V;ENSP00000269571:I655V;ENSP00000443562:I625V	ENSP00000269571:I655V	I	+	1	0	ERBB2	35133114	1.000000	0.71417	0.995000	0.50966	0.892000	0.51952	4.008000	0.57103	1.880000	0.54463	0.459000	0.35465	ATC	A|0.845;G|0.155;N|0.000;T|0.000	0.155	strong		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
SIGLEC12	89858	hgsc.bcm.edu	37	19	52000672	52000672	+	Missense_Mutation	SNP	G	G	A	rs3829658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52000672G>A	ENST00000291707.3	-	6	1488	c.1433C>T	c.(1432-1434)aCg>aTg	p.T478M	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.T360M	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	478			T -> M (in dbSNP:rs3829658).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.T478M(1)		NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TGCCCCTAGCGTCACTCCTGA	0.547													N|||	3152	0.629393	0.5756	0.7651	5008	,	,		16318	0.4683		0.6531	False		,,,				2504	0.7474				p.T478M		Atlas-SNP	.											SIGLEC12,NS,carcinoma,-1,2	SIGLEC12	243	2	1	Substitution - Missense(1)	stomach(1)	c.C1433T						PASS	.	A	MET/THR,MET/THR	2640,1766		804,1032,367	144.0	124.0	131.0		1079,1433	-0.0	0.0	19	dbSNP_107	131	5710,2890		1889,1932,479	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	81,81	2693,2964,846	AA,AG,GG		33.6047,40.0817,35.7989	possibly-damaging,possibly-damaging	360/478,478/596	52000672	8350,4656	2203	4300	6503	SO:0001583	missense	89858	exon6			CCTAGCGTCACTC	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1433C>T	19.37:g.52000672G>A	ENSP00000291707:p.Thr478Met	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	226	225	0.995575	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	1317	0.603021978021978	279	0.5670731707317073	269	0.7430939226519337	273	0.4772727272727273	496	0.6543535620052771	.	1.863	-0.462073	0.04508	0.599183	0.663953	ENSG00000254521	ENST00000291707	T	0.04706	3.57	1.52	-0.0378	0.13882	.	1.828130	0.03570	N	0.228517	T	0.00012	0.0000	N	0.16602	0.42	0.80722	P	0.0	B;B	0.31893	0.345;0.212	B;B	0.24848	0.056;0.03	T	0.16100	-1.0414	9	0.29301	T	0.29	.	3.5577	0.07870	0.6556:0.0:0.3444:0.0	rs3829658;rs16982738;rs61360616;rs3829658	478;360	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	M	478	ENSP00000291707:T478M	ENSP00000291707:T478M	T	-	2	0	SIGLEC12	56692484	0.000000	0.05858	0.000000	0.03702	0.117000	0.20001	0.163000	0.16520	-0.055000	0.13244	0.395000	0.25975	ACG	G|0.382;A|0.618	0.618	strong		0.547	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
OBSCN	84033	hgsc.bcm.edu	37	1	228407059	228407059	+	Intron	SNP	G	G	T	rs141906801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228407059G>T	ENST00000422127.1	+	8	2697				OBSCN_ENST00000570156.2_Silent_p.A896A|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000284548.11_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGCAGCCGGCGTGCAGGGAGG	0.647													G|||	68	0.0135783	0.0015	0.0115	5008	,	,		21064	0.0		0.0308	False		,,,				2504	0.0276				p.A896A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2688T						PASS	.																																			SO:0001627	intron_variant	84033	exon9			GCCGGCGTGCAGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2653+2070G>T	1.37:g.228407059G>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	241	123	0.510373	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.989;T|0.011	0.011	strong		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
INMT	11185	hgsc.bcm.edu	37	7	30791848	30791848	+	Missense_Mutation	SNP	G	G	A	rs4723010	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:30791848G>A	ENST00000013222.5	+	1	98	c.82G>A	c.(82-84)Gat>Aat	p.D28N	INMT_ENST00000484180.1_Intron|INMT-FAM188B_ENST00000458257.1_Missense_Mutation_p.D28N|INMT_ENST00000409539.1_Missense_Mutation_p.D28N	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	28			D -> N (in dbSNP:rs4723010). {ECO:0000269|PubMed:15489334}.		amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)			kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						CTACAGCTTCGATGGCAGCCC	0.567													G|||	1296	0.258786	0.2784	0.3314	5008	,	,		19963	0.0367		0.3936	False		,,,				2504	0.271				p.D28N		Atlas-SNP	.											.	INMT	38	.	0			c.G82A						PASS	.	G	ASN/ASP,ASN/ASP	1249,3157	428.9+/-342.0	184,881,1138	118.0	112.0	114.0		82,82	-2.4	0.0	7	dbSNP_111	114	3384,5216	501.6+/-375.5	681,2022,1597	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	23,23	865,2903,2735	AA,AG,GG		39.3488,28.3477,35.622	benign,benign	28/263,28/264	30791848	4633,8373	2203	4300	6503	SO:0001583	missense	11185	exon1			AGCTTCGATGGCA		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.82G>A	7.37:g.30791848G>A	ENSP00000013222:p.Asp28Asn	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_001199219	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	561	0.25686813186813184	126	0.25609756097560976	122	0.3370165745856354	15	0.026223776223776224	298	0.39313984168865435	G	5.964	0.361850	0.11296	0.283477	0.393488	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.09163	3.01;3.01	3.28	-2.41	0.06562	.	1.281540	0.05467	N	0.552416	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.13407	0.009;0.009	T	0.48703	-0.9012	9	0.15499	T	0.54	0.7645	1.7368	0.02944	0.2776:0.1371:0.4455:0.1398	rs4723010;rs17780446;rs4723010	28;28	B8ZZ69;O95050	.;INMT_HUMAN	N	28	ENSP00000013222:D28N;ENSP00000386961:D28N	ENSP00000013222:D28N	D	+	1	0	INMT	30758373	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.185000	0.09684	-0.566000	0.06054	-0.140000	0.14226	GAT	G|0.696;A|0.304	0.304	strong		0.567	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
ATP10D	57205	hgsc.bcm.edu	37	4	47514685	47514685	+	Missense_Mutation	SNP	C	C	T	rs33995001	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:47514685C>T	ENST00000273859.3	+	2	397	c.128C>T	c.(127-129)aCc>aTc	p.T43I	ATP10D_ENST00000504445.1_Missense_Mutation_p.T43I	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	43			T -> I (in dbSNP:rs33995001). {ECO:0000269|PubMed:15489334}.		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TCCTCTCAGACCCCTAAACTG	0.522													C|||	1527	0.304912	0.2958	0.4352	5008	,	,		17210	0.1558		0.4374	False		,,,				2504	0.2423				p.T43I		Atlas-SNP	.											.	ATP10D	168	.	0			c.C128T						PASS	.	C	ILE/THR	1382,3024	455.7+/-351.1	219,944,1040	95.0	89.0	91.0		128	3.3	0.7	4	dbSNP_126	91	3686,4914	527.7+/-381.2	801,2084,1415	yes	missense	ATP10D	NM_020453.3	89	1020,3028,2455	TT,TC,CC		42.8605,31.3663,38.9666	benign	43/1427	47514685	5068,7938	2203	4300	6503	SO:0001583	missense	57205	exon2			CTCAGACCCCTAA	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.128C>T	4.37:g.47514685C>T	ENSP00000273859:p.Thr43Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	751	0.34386446886446886	146	0.2967479674796748	165	0.4558011049723757	109	0.19055944055944055	331	0.4366754617414248	C	5.653	0.305108	0.10678	0.313663	0.428605	ENSG00000145246	ENST00000273859;ENST00000504445	T;T	0.38722	1.12;4.02	5.1	3.3	0.37823	.	0.615971	0.17070	N	0.188207	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	P;B	0.35481	0.504;0.006	B;B	0.28916	0.096;0.008	T	0.47560	-0.9108	9	0.22109	T	0.4	-4.9928	6.758	0.23524	0.0:0.5692:0.2837:0.147	rs33995001	43;43	Q9P241;Q6PEW3	AT10D_HUMAN;.	I	43	ENSP00000273859:T43I;ENSP00000420909:T43I	ENSP00000273859:T43I	T	+	2	0	ATP10D	47209442	0.000000	0.05858	0.689000	0.30133	0.059000	0.15707	0.341000	0.19909	0.604000	0.29930	-0.310000	0.09108	ACC	C|0.623;T|0.377	0.377	strong		0.522	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
TMPPE	643853	hgsc.bcm.edu	37	3	33138549	33138549	+	5'Flank	SNP	G	G	A	rs7637099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:33138549G>A	ENST00000342462.4	-	0	0				GLB1_ENST00000307363.5_Missense_Mutation_p.P10L|GLB1_ENST00000445488.2_Missense_Mutation_p.P10L|GLB1_ENST00000399402.3_5'Flank|TMPPE_ENST00000416695.2_5'Flank|GLB1_ENST00000307377.8_Missense_Mutation_p.P10L	NM_001039770.2	NP_001034859.2	Q6ZT21	TMPPE_HUMAN	transmembrane protein with metallophosphoesterase domain							integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|large_intestine(5)|lung(6)|prostate(1)	13						CAGCAACAGAGGGAGGATGCG	0.682													G|||	2163	0.431909	0.0711	0.572	5008	,	,		12322	0.4891		0.6461	False		,,,				2504	0.5409				p.P10L		Atlas-SNP	.											.	GLB1	51	.	0			c.C29T	GRCh37	CM055955	GLB1	M	rs7637099	PASS	.	G	LEU/PRO,LEU/PRO	641,3363		58,525,1419	43.0	59.0	54.0		29,29	-0.1	0.0	3	dbSNP_116	54	5237,3161		1653,1931,615	yes	missense,missense	GLB1	NM_000404.2,NM_001135602.1	98,98	1711,2456,2034	AA,AG,GG		37.6399,16.009,47.3956	probably-damaging,probably-damaging	10/678,10/547	33138549	5878,6524	2002	4199	6201	SO:0001631	upstream_gene_variant	2720	exon1			AACAGAGGGAGGA	AK126979	CCDS33732.1, CCDS46786.1	3p22.3	2014-02-12	2009-02-24		ENSG00000188167	ENSG00000188167			33865	protein-coding gene	gene with protein product							Standard	NM_001039770		Approved	FLJ45032	uc003cfk.2	Q6ZT21	OTTHUMG00000155779		3.37:g.33138549G>A	Exception_encountered	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	130	127	0.976923	NM_001135602	B2RNG5|Q6ZRG1	Missense_Mutation	SNP	ENST00000342462.4	37	CCDS33732.1	1029	0.47115384615384615	50	0.1016260162601626	225	0.6215469613259669	274	0.479020979020979	480	0.633245382585752	G	10.90	1.482603	0.26598	0.16009	0.623601	ENSG00000170266	ENST00000307363;ENST00000445488;ENST00000307377;ENST00000415454;ENST00000436768	D;D;D;D;D	0.99479	-4.21;-5.16;-4.25;-5.98;-5.07	4.12	-0.128	0.13506	.	2.077820	0.01918	N	0.040312	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.56823	-0.7915	9	0.11485	T	0.65	0.6435	4.8721	0.13639	0.2212:0.3742:0.4046:0.0	rs7637099;rs17551626;rs17850204;rs61323383;rs7637099	10;10	E7EQ29;P16278	.;BGAL_HUMAN	L	10	ENSP00000306920:P10L;ENSP00000393377:P10L;ENSP00000305920:P10L;ENSP00000411813:P10L;ENSP00000387989:P10L	ENSP00000306920:P10L	P	-	2	0	GLB1	33113553	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	0.197000	0.17197	-0.158000	0.11040	0.491000	0.48974	CCT	G|0.527;A|0.473	0.473	strong		0.682	TMPPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341566.1	NM_001039770	
ANGPT2	285	hgsc.bcm.edu	37	8	6377433	6377433	+	Silent	SNP	C	C	T	rs1961222	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:6377433C>T	ENST00000325203.5	-	5	1356	c.882G>A	c.(880-882)acG>acA	p.T294T	ANGPT2_ENST00000523120.1_Silent_p.T293T|ANGPT2_ENST00000338312.6_Silent_p.T242T|MCPH1_ENST00000344683.5_Intron|ANGPT2_ENST00000415216.1_Silent_p.T293T			O15123	ANGP2_HUMAN	angiopoietin 2	294	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		AGATGCCATTCGTGGTGTGTC	0.433													C|||	750	0.14976	0.0121	0.2104	5008	,	,		19696	0.0516		0.3419	False		,,,				2504	0.1963				p.T294T		Atlas-SNP	.											.	ANGPT2	126	.	0			c.G882A						PASS	.	C	,,,	268,4138	151.0+/-185.0	7,254,1942	365.0	313.0	330.0		879,726,882,	-9.7	0.0	8	dbSNP_92	330	2903,5697	455.6+/-363.8	468,1967,1865	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ANGPT2,MCPH1	NM_001118887.1,NM_001118888.1,NM_001147.2,NM_024596.3	,,,	475,2221,3807	TT,TC,CC		33.7558,6.0826,24.3811	,,,	293/496,242/445,294/497,	6377433	3171,9835	2203	4300	6503	SO:0001819	synonymous_variant	285	exon5			GCCATTCGTGGTG	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"""Fibrinogen C domain containing"""	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.882G>A	8.37:g.6377433C>T		Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	256	120	0.46875	NM_001147	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Silent	SNP	ENST00000325203.5	37	CCDS5958.1																																																																																			C|0.786;T|0.214	0.214	strong		0.433	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147	
GLI4	2738	hgsc.bcm.edu	37	8	144358381	144358381	+	Missense_Mutation	SNP	G	G	A	rs1056148	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144358381G>A	ENST00000523522.1	+	3	577	c.538G>A	c.(538-540)Gcc>Acc	p.A180T	GLI4_ENST00000523812.1_3'UTR|ZFP41_ENST00000522452.1_3'UTR|GLI4_ENST00000340042.1_Missense_Mutation_p.A180T			P10075	GLI4_HUMAN	GLI family zinc finger 4	180			A -> T (in dbSNP:rs1056148). {ECO:0000269|PubMed:2850480}.		regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(1)|lung(5)	9	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CGCGCGGGGGGCCAAGCCGCA	0.701													G|||	2352	0.469649	0.0749	0.6628	5008	,	,		11535	0.6577		0.4841	False		,,,				2504	0.6575				p.A180T		Atlas-SNP	.											GLI4,NS,carcinoma,0,1	GLI4	28	1	0			c.G538A						PASS	.	G	THR/ALA	549,3695		70,409,1643	6.0	7.0	7.0		538	1.4	0.0	8	dbSNP_86	7	3701,4669		906,1889,1390	yes	missense	GLI4	NM_138465.3	58	976,2298,3033	AA,AG,GG		44.2174,12.9359,33.6927	benign	180/377	144358381	4250,8364	2122	4185	6307	SO:0001583	missense	2738	exon4			CGGGGGGCCAAGC		CCDS6398.1	8q24.3	2013-01-08	2009-03-05		ENSG00000250571	ENSG00000250571		"""Zinc fingers, C2H2-type"""	4320	protein-coding gene	gene with protein product		165280	"""GLI-Kruppel family member GLI4"", ""glioma-associated oncogene family zinc finger 4"""			2850480	Standard	NM_138465		Approved	HKR4, ZNF928	uc003yxx.3	P10075	OTTHUMG00000164952	ENST00000523522.1:c.538G>A	8.37:g.144358381G>A	ENSP00000430987:p.Ala180Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	46	45	0.978261	NM_138465	Q96CK9	Missense_Mutation	SNP	ENST00000523522.1	37	CCDS6398.1	1032	0.4725274725274725	47	0.09552845528455285	226	0.6243093922651933	388	0.6783216783216783	371	0.4894459102902375	G	12.90	2.077678	0.36662	0.129359	0.442174	ENSG00000250571	ENST00000340042;ENST00000523522	T;T	0.07567	3.18;3.18	3.26	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	N	0.21097	0.63	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13282	-1.0515	8	0.52906	T	0.07	.	7.0503	0.25069	0.2184:0.0:0.7816:0.0	rs1056148;rs3196763;rs1056148	180	P10075	GLI4_HUMAN	T	180	ENSP00000345024:A180T;ENSP00000430987:A180T	ENSP00000345024:A180T	A	+	1	0	GLI4	144429756	0.000000	0.05858	0.004000	0.12327	0.544000	0.35116	0.141000	0.16076	0.201000	0.20466	0.462000	0.41574	GCC	G|0.531;A|0.469	0.469	strong		0.701	GLI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381128.2		
APIP	51074	hgsc.bcm.edu	37	11	34909926	34909926	+	Silent	SNP	T	T	G	rs1571133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34909926T>G	ENST00000395787.3	-	5	589	c.375A>C	c.(373-375)acA>acC	p.T125T	APIP_ENST00000527830.1_5'UTR|APIP_ENST00000278359.5_Silent_p.T142T	NM_015957.2	NP_057041.2			APAF1 interacting protein											kidney(2)|lung(1)|skin(1)	4	all_epithelial(35;0.161)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.000425)			GAAAGAGAAGTGTGGCCATCA	0.408													G|||	2902	0.579473	0.3533	0.5692	5008	,	,		16318	0.7371		0.6839	False		,,,				2504	0.6227				p.T125T		Atlas-SNP	.											.	APIP	21	.	0			c.A375C						PASS	.	G		1824,2580	635.7+/-396.4	378,1068,756	95.0	95.0	95.0		375	4.8	1.0	11	dbSNP_88	95	5952,2644	424.8+/-354.8	2073,1806,419	no	coding-synonymous	APIP	NM_015957.2		2451,2874,1175	GG,GT,TT		30.7585,41.4169,40.1846		125/243	34909926	7776,5224	2202	4298	6500	SO:0001819	synonymous_variant	51074	exon5			GAGAAGTGTGGCC	AF132963	CCDS7895.1	11p13	2014-05-12				ENSG00000149089	4.2.1.109		17581	protein-coding gene	gene with protein product	"""methylthioribulose-1-phosphate dehydratase"""	612491				10810093, 15262985, 24367089	Standard	NM_015957		Approved	CGI-29, Mmrp19, APIP2	uc001mvs.2	Q96GX9		ENST00000395787.3:c.375A>C	11.37:g.34909926T>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_015957		Silent	SNP	ENST00000395787.3	37	CCDS7895.1																																																																																			T|0.394;G|0.606	0.606	strong		0.408	APIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389864.1	NM_015957	
GGCX	2677	hgsc.bcm.edu	37	2	85780107	85780107	+	Silent	SNP	G	G	A	rs10179904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85780107G>A	ENST00000233838.4	-	9	1322	c.1242C>T	c.(1240-1242)acC>acT	p.T414T	GGCX_ENST00000430215.3_Silent_p.T357T|GGCX_ENST00000473665.1_5'UTR	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	414					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	CATCACGGTAGGTGATCTTCA	0.547													G|||	596	0.11901	0.1157	0.098	5008	,	,		19792	0.0704		0.1123	False		,,,				2504	0.1953				p.T414T		Atlas-SNP	.											.	GGCX	44	.	0			c.C1242T						PASS	.	G	,	508,3898	235.2+/-247.8	30,448,1725	189.0	173.0	178.0		1242,1071	5.5	1.0	2	dbSNP_119	178	1009,7591	217.7+/-256.3	56,897,3347	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	86,1345,5072	AA,AG,GG		11.7326,11.5297,11.6638	,	414/759,357/702	85780107	1517,11489	2203	4300	6503	SO:0001819	synonymous_variant	2677	exon9			ACGGTAGGTGATC		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.1242C>T	2.37:g.85780107G>A		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	253	251	0.992095	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			G|0.893;A|0.107	0.107	strong		0.547	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
PLAUR	5329	hgsc.bcm.edu	37	19	44156472	44156472	+	Missense_Mutation	SNP	T	T	C	rs2302524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44156472T>C	ENST00000340093.3	-	6	888	c.659A>G	c.(658-660)aAg>aGg	p.K220R	PLAUR_ENST00000339082.3_Missense_Mutation_p.K220R|PLAUR_ENST00000221264.4_Missense_Mutation_p.K175R|PLAUR_ENST00000601723.1_Intron	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	220	UPAR/Ly6 3.		K -> R (in dbSNP:rs2302524). {ECO:0000269|Ref.8}.		attachment of GPI anchor to protein (GO:0016255)|blood coagulation (GO:0007596)|C-terminal protein lipidation (GO:0006501)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chemotaxis (GO:0006935)|fibrinolysis (GO:0042730)|post-translational protein modification (GO:0043687)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|urokinase plasminogen activator signaling pathway (GO:0038195)	anchored component of membrane (GO:0031225)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)|urokinase plasminogen activator receptor activity (GO:0030377)	p.K220R(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3)	20		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	GCTGTTCCCCTTGCAGCTGTA	0.527											OREG0025532	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	827	0.165136	0.208	0.2666	5008	,	,		18524	0.0833		0.1412	False		,,,				2504	0.1442				p.K220R		Atlas-SNP	.											PLAUR,NS,carcinoma,0,1	PLAUR	71	1	1	Substitution - Missense(1)	stomach(1)	c.A659G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	870,3536	340.5+/-306.2	87,696,1420	93.0	87.0	89.0		659,524,659	4.5	1.0	19	dbSNP_100	89	1432,7168	273.1+/-290.5	109,1214,2977	yes	missense,missense,missense	PLAUR	NM_001005376.2,NM_001005377.2,NM_002659.3	26,26,26	196,1910,4397	CC,CT,TT		16.6512,19.7458,17.6995	benign,benign,benign	220/282,175/291,220/336	44156472	2302,10704	2203	4300	6503	SO:0001583	missense	5329	exon6			TTCCCCTTGCAGC		CCDS12628.1, CCDS33041.1, CCDS33042.1, CCDS74386.1	19q13	2012-03-15			ENSG00000011422	ENSG00000011422		"""CD molecules"""	9053	protein-coding gene	gene with protein product	"""urokinase-type plasminogen activator (uPA) receptor"", ""urokinase plasminogen activator surface receptor"""	173391					Standard	NM_002659		Approved	URKR, UPAR, CD87	uc002oxf.2	Q03405		ENST00000340093.3:c.659A>G	19.37:g.44156472T>C	ENSP00000339328:p.Lys220Arg	Somatic	157	0	0	921	WXS	Illumina HiSeq	Phase_I	161	84	0.521739	NM_001005376	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	Missense_Mutation	SNP	ENST00000340093.3	37	CCDS12628.1	363	0.1662087912087912	122	0.24796747967479674	87	0.24033149171270718	45	0.07867132867132867	109	0.1437994722955145	T	15.77	2.930532	0.52866	0.197458	0.166512	ENSG00000011422	ENST00000339082;ENST00000340093;ENST00000221264	T;T;T	0.69806	-0.43;-0.43;-0.43	4.49	4.49	0.54785	Ly-6 antigen / uPA receptor -like (1);CD59 antigen, conserved site (1);CD59 antigen (1);	0.911534	0.09086	N	0.850673	T	0.00012	0.0000	N	0.19112	0.55	0.33460	P	0.41516299999999995	B;B;B;B	0.26744	0.103;0.067;0.067;0.158	B;B;B;B	0.25614	0.037;0.033;0.033;0.062	T	0.03364	-1.1044	9	0.54805	T	0.06	-13.6979	10.3442	0.43897	0.0:0.0:0.0:1.0	rs2302524;rs59102150;rs2302524	175;220;220;220	Q03405-3;Q03405;Q9UPI5;Q03405-2	.;UPAR_HUMAN;.;.	R	220;220;175	ENSP00000342049:K220R;ENSP00000339328:K220R;ENSP00000221264:K175R	ENSP00000221264:K175R	K	-	2	0	PLAUR	48848312	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	3.565000	0.53798	2.014000	0.59158	0.459000	0.35465	AAG	T|0.832;C|0.168	0.168	strong		0.527	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463571.1	NM_002659	
KDM4C	23081	hgsc.bcm.edu	37	9	6984236	6984236	+	Missense_Mutation	SNP	G	G	A	rs2296067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:6984236G>A	ENST00000381309.3	+	10	1751	c.1186G>A	c.(1186-1188)Gat>Aat	p.D396N	KDM4C_ENST00000535193.1_Missense_Mutation_p.D418N|KDM4C_ENST00000381306.3_Missense_Mutation_p.D396N|KDM4C_ENST00000442236.2_Missense_Mutation_p.D215N|KDM4C_ENST00000428870.2_Missense_Mutation_p.D83N|KDM4C_ENST00000543771.1_Missense_Mutation_p.D396N|KDM4C_ENST00000536108.1_Missense_Mutation_p.D215N	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	396			D -> N (in dbSNP:rs2296067).		histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						AGATGAAGTCGATGGGGCAGA	0.512													G|||	1639	0.327276	0.205	0.3213	5008	,	,		19889	0.4286		0.2227	False		,,,				2504	0.5				p.D418N		Atlas-SNP	.											KDM4C_ENST00000381306,NS,carcinoma,0,4	KDM4C	186	4	0			c.G1252A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	937,3469	357.6+/-314.0	103,731,1369	94.0	84.0	87.0		1186,1186,1252,1186	-0.9	0.0	9	dbSNP_100	87	1886,6714	334.9+/-321.2	200,1486,2614	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	23,23,23,23	303,2217,3983	AA,AG,GG		21.9302,21.2665,21.7054	benign,benign,benign,benign	396/1048,396/814,418/836,396/1057	6984236	2823,10183	2203	4300	6503	SO:0001583	missense	23081	exon10			GAAGTCGATGGGG	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.1186G>A	9.37:g.6984236G>A	ENSP00000370710:p.Asp396Asn	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	620	0.2838827838827839	92	0.18699186991869918	111	0.30662983425414364	236	0.4125874125874126	181	0.23878627968337732	G	10.61	1.398802	0.25291	0.212665	0.219302	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.17370	2.39;2.39;2.56;2.47;2.77;2.28;3.53	5.24	-0.93	0.10441	.	2.473570	0.00904	N	0.002391	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B	0.15719	0.0;0.003;0.008;0.005;0.014	B;B;B;B;B	0.10450	0.0;0.002;0.001;0.003;0.005	T	0.46133	-0.9213	9	0.17369	T	0.5	-29.4604	11.5707	0.50832	0.4732:0.0:0.5268:0.0	rs2296067;rs52808244;rs60515857;rs2296067	215;396;418;396;396	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	N	418;396;396;396;215;215;83	ENSP00000442382:D418N;ENSP00000445427:D396N;ENSP00000370710:D396N;ENSP00000370707:D396N;ENSP00000409353:D215N;ENSP00000440656:D215N;ENSP00000405739:D83N	ENSP00000370707:D396N	D	+	1	0	KDM4C	6974236	0.004000	0.15560	0.000000	0.03702	0.021000	0.10359	0.744000	0.26245	-0.118000	0.11851	-0.137000	0.14449	GAT	G|0.743;A|0.257	0.257	strong		0.512	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
SMCR8	140775	hgsc.bcm.edu	37	17	18219835	18219835	+	Silent	SNP	T	T	C	rs3829956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18219835T>C	ENST00000406438.3	+	1	1212	c.732T>C	c.(730-732)atT>atC	p.I244I	TOP3A_ENST00000542570.1_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	244						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						AGTCCATCATTGAACATCAAG	0.488													T|||	1076	0.214856	0.1452	0.2421	5008	,	,		22242	0.3185		0.2435	False		,,,				2504	0.1534				p.I244I		Atlas-SNP	.											.	SMCR8	62	.	0			c.T732C						PASS	.	T		684,3722	288.4+/-279.8	65,554,1584	69.0	56.0	60.0		732	-0.1	1.0	17	dbSNP_107	60	2196,6404	371.9+/-336.4	284,1628,2388	no	coding-synonymous	SMCR8	NM_144775.2		349,2182,3972	CC,CT,TT		25.5349,15.5243,22.1436		244/938	18219835	2880,10126	2203	4300	6503	SO:0001819	synonymous_variant	140775	exon1			CATCATTGAACAT	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.732T>C	17.37:g.18219835T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			T|0.772;C|0.228	0.228	strong		0.488	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
MYPN	84665	hgsc.bcm.edu	37	10	69926097	69926097	+	Silent	SNP	T	T	C	rs2673794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:69926097T>C	ENST00000358913.5	+	10	2135	c.1647T>C	c.(1645-1647)tcT>tcC	p.S549S	MYPN_ENST00000354393.2_Silent_p.S274S|MYPN_ENST00000540630.1_Silent_p.S549S	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	549					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CAGCCAACTCTACCACCAACC	0.562													C|||	2417	0.482628	0.2769	0.6844	5008	,	,		14543	0.3125		0.6859	False		,,,				2504	0.5838				p.S549S		Atlas-SNP	.											.	MYPN	189	.	0			c.T1647C						PASS	.	C		1540,2866	671.6+/-402.5	267,1006,930	86.0	71.0	76.0		1647	-0.2	0.9	10	dbSNP_100	76	5986,2614	422.5+/-354.0	2084,1818,398	no	coding-synonymous	MYPN	NM_032578.2		2351,2824,1328	CC,CT,TT		30.3953,34.9523,42.1344		549/1321	69926097	7526,5480	2203	4300	6503	SO:0001819	synonymous_variant	84665	exon10			CAACTCTACCACC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1647T>C	10.37:g.69926097T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																			T|0.465;C|0.535	0.535	strong		0.562	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
ITGA9	3680	hgsc.bcm.edu	37	3	37860417	37860417	+	Silent	SNP	C	C	T	rs142961075		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37860417C>T	ENST00000264741.5	+	28	3301	c.3045C>T	c.(3043-3045)atC>atT	p.I1015I	AC093415.2_ENST00000608505.1_RNA|AC093415.2_ENST00000438136.1_RNA|AC093415.2_ENST00000429532.1_RNA|AC093415.2_ENST00000457661.1_RNA|AC093415.2_ENST00000430620.1_RNA|AC093415.2_ENST00000445429.1_RNA|AC093415.2_ENST00000450990.1_RNA|AC093415.2_ENST00000366441.2_RNA|AC093415.2_ENST00000594579.1_RNA|AC093415.2_ENST00000420870.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	1015					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		AAGAAATTATCGAAGCTGAGA	0.473													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18335	0.0		0.0	False		,,,				2504	0.0				p.I1015I		Atlas-SNP	.											.	ITGA9	98	.	0			c.C3045T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	67.0	68.0	68.0		3045	-8.5	0.7	3	dbSNP_134	68	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	ITGA9	NM_002207.2		0,16,6487	TT,TC,CC		0.1628,0.0454,0.123		1015/1036	37860417	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon28			AATTATCGAAGCT	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.3045C>T	3.37:g.37860417C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	144	82	0.569444	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	8.284	0.816181	0.16607	4.54E-4	0.001628	ENSG00000144668	ENST00000411817	.	.	.	6.17	-8.54	0.00912	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	21.0516	0.99944	0.0:0.7126:0.0:0.2874	.	.	.	.	X	49	.	.	R	+	1	2	ITGA9	37835421	0.027000	0.19231	0.654000	0.29608	0.922000	0.55478	-0.950000	0.03889	-1.656000	0.01495	-0.794000	0.03295	CGA	C|0.999;T|0.001	0.001	strong		0.473	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
FAT3	120114	hgsc.bcm.edu	37	11	92086649	92086649	+	Silent	SNP	G	G	A	rs10830903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:92086649G>A	ENST00000298047.6	+	1	1388	c.1371G>A	c.(1369-1371)caG>caA	p.Q457Q	FAT3_ENST00000409404.2_Silent_p.Q457Q|FAT3_ENST00000541502.1_Silent_p.Q457Q|FAT3_ENST00000525166.1_Silent_p.Q307Q			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	457	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TAAAAGCACAGGTCACCATCA	0.458										TCGA Ovarian(4;0.039)			A|||	252	0.0503195	0.1346	0.036	5008	,	,		19091	0.001		0.0437	False		,,,				2504	0.0041				p.Q457Q		Atlas-SNP	.											.	FAT3	1822	.	0			c.G1371A						PASS	.	A		482,3402		33,416,1493	73.0	70.0	71.0		1371	0.8	0.3	11	dbSNP_120	71	461,7827		16,429,3699	no	coding-synonymous	FAT3	NM_001008781.2		49,845,5192	AA,AG,GG		5.5623,12.4099,7.7473		457/4558	92086649	943,11229	1942	4144	6086	SO:0001819	synonymous_variant	120114	exon1			AGCACAGGTCACC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.1371G>A	11.37:g.92086649G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	99	62	0.626263	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				G|0.939;A|0.061	0.061	strong		0.458	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
ENPP7	339221	hgsc.bcm.edu	37	17	77709405	77709405	+	Silent	SNP	C	C	T	rs78553282	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:77709405C>T	ENST00000328313.5	+	3	1184	c.963C>T	c.(961-963)taC>taT	p.Y321Y		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			CCTTCCACTACGCCAACAACC	0.617													C|||	230	0.0459265	0.0469	0.0245	5008	,	,		16412	0.0188		0.0298	False		,,,				2504	0.1043				p.Y321Y		Atlas-SNP	.											.	ENPP7	63	.	0			c.C963T						PASS	.	C		204,4202	126.1+/-163.2	7,190,2006	73.0	68.0	70.0		963	-2.6	1.0	17	dbSNP_131	70	357,8243	119.7+/-179.0	9,339,3952	no	coding-synonymous	ENPP7	NM_178543.3		16,529,5958	TT,TC,CC		4.1512,4.63,4.3134		321/459	77709405	561,12445	2203	4300	6503	SO:0001819	synonymous_variant	339221	exon3			CCACTACGCCAAC	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"""alkaline sphingomyelinase"""					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.963C>T	17.37:g.77709405C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_178543		Silent	SNP	ENST00000328313.5	37	CCDS11763.1																																																																																			C|0.963;T|0.037	0.037	strong		0.617	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
LMNB1	4001	hgsc.bcm.edu	37	5	126140522	126140522	+	Silent	SNP	T	T	C	rs3749830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:126140522T>C	ENST00000261366.5	+	2	775	c.414T>C	c.(412-414)taT>taC	p.Y138Y	LMNB1_ENST00000460265.1_3'UTR|LMNB1_ENST00000395354.1_Silent_p.Y138Y	NM_001198557.1|NM_005573.3	NP_001185486.1|NP_005564.1	P20700	LMNB1_HUMAN	lamin B1	138	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	lamin filament (GO:0005638)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		TTCGAGAATATGAAGCAGCAC	0.418													T|||	217	0.0433307	0.0227	0.0533	5008	,	,		19731	0.0179		0.0646	False		,,,				2504	0.0685				p.Y138Y		Atlas-SNP	.											.	LMNB1	49	.	0			c.T414C						PASS	.	T	,	126,4280	92.5+/-131.2	3,120,2080	120.0	115.0	116.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,414	2.8	1.0	5	dbSNP_107	116	574,8026	154.8+/-208.9	21,532,3747	no	utr-5,coding-synonymous	LMNB1	NM_001198557.1,NM_005573.3	,	24,652,5827	CC,CT,TT		6.6744,2.8597,5.3821	,	,138/587	126140522	700,12306	2203	4300	6503	SO:0001819	synonymous_variant	4001	exon2			AGAATATGAAGCA	L37737	CCDS4140.1	5q23.2	2013-01-16			ENSG00000113368	ENSG00000113368		"""Intermediate filaments type V, lamins"""	6637	protein-coding gene	gene with protein product		150340				7557986, 8838815	Standard	NM_005573		Approved		uc003kud.2	P20700	OTTHUMG00000128969	ENST00000261366.5:c.414T>C	5.37:g.126140522T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_005573	B2R6J6|Q3SYN7|Q96EI6	Silent	SNP	ENST00000261366.5	37	CCDS4140.1																																																																																			T|0.948;C|0.052	0.052	strong		0.418	LMNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250956.2	NM_005573	
DHRS13	147015	hgsc.bcm.edu	37	17	27225586	27225586	+	Missense_Mutation	SNP	A	A	T	rs4795472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:27225586A>T	ENST00000378895.4	-	5	1133	c.1007T>A	c.(1006-1008)cTa>cAa	p.L336Q	FLOT2_ENST00000394908.4_5'Flank|FLOT2_ENST00000394906.2_5'Flank|FLOT2_ENST00000577789.1_5'Flank|DHRS13_ENST00000394901.3_Missense_Mutation_p.L286Q|DHRS13_ENST00000426464.2_Missense_Mutation_p.L255Q|RP11-20B24.4_ENST00000579187.1_RNA|FLOT2_ENST00000585169.1_5'Flank|DHRS13_ENST00000581974.1_5'Flank|RP11-20B24.4_ENST00000580603.1_RNA	NM_144683.3	NP_653284.2	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13	336			L -> Q (in dbSNP:rs4795472).			extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	9	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			GGGGGTGCTTAGAGAAGATGG	0.582													A|||	595	0.11881	0.202	0.1124	5008	,	,		17892	0.0506		0.1282	False		,,,				2504	0.0716				p.L336Q		Atlas-SNP	.											.	DHRS13	22	.	0			c.T1007A						PASS	.	A	GLN/LEU	825,3581	311.1+/-291.9	86,653,1464	25.0	26.0	26.0		1007	-10.1	0.0	17	dbSNP_111	26	1096,7504	223.8+/-260.4	62,972,3266	yes	missense	DHRS13	NM_144683.3	113	148,1625,4730	TT,TA,AA		12.7442,18.7245,14.7701	benign	336/378	27225586	1921,11085	2203	4300	6503	SO:0001583	missense	147015	exon5			GTGCTTAGAGAAG	BC015582	CCDS11246.2	17q11.2	2011-09-14			ENSG00000167536	ENSG00000167536	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	28326	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 5"""					12975309, 19027726	Standard	NM_144683		Approved	MGC23280, SDR7C5	uc002hde.4	Q6UX07	OTTHUMG00000132678	ENST00000378895.4:c.1007T>A	17.37:g.27225586A>T	ENSP00000368173:p.Leu336Gln	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_144683	Q96BH7	Missense_Mutation	SNP	ENST00000378895.4	37	CCDS11246.2	283	0.1295787545787546	107	0.21747967479674796	49	0.13535911602209943	42	0.07342657342657342	85	0.11213720316622691	A	4.298	0.054624	0.08291	0.187245	0.127442	ENSG00000167536	ENST00000378895;ENST00000394901;ENST00000426464	D;T;D	0.84223	-1.53;-1.11;-1.82	5.06	-10.1	0.00402	.	1.964930	0.02486	N	0.088960	T	0.00073	0.0002	N	0.12182	0.205	0.80722	P	0.0	B;B	0.15141	0.012;0.003	B;B	0.10450	0.005;0.002	T	0.14420	-1.0473	9	0.27785	T	0.31	.	5.2366	0.15450	0.1838:0.2923:0.4281:0.0959	rs4795472;rs52795861;rs4795472	255;336	B4DJC5;Q6UX07	.;DHR13_HUMAN	Q	336;286;255	ENSP00000368173:L336Q;ENSP00000378361:L286Q;ENSP00000412826:L255Q	ENSP00000368173:L336Q	L	-	2	0	DHRS13	24249712	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.687000	0.01927	-2.676000	0.00411	-0.379000	0.06801	CTA	A|0.863;T|0.137	0.137	strong		0.582	DHRS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255952.1	NM_144683	
MYO5A	4644	hgsc.bcm.edu	37	15	52611351	52611351	+	Missense_Mutation	SNP	C	C	T	rs143298463	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:52611351C>T	ENST00000399231.3	-	38	5308	c.5065G>A	c.(5065-5067)Gtc>Atc	p.V1689I	MYO5A_ENST00000358212.6_Missense_Mutation_p.V1714I|MYO5A_ENST00000356338.6_Missense_Mutation_p.V1662I|MYO5A_ENST00000553916.1_Missense_Mutation_p.V1687I|MYO5A_ENST00000399233.2_Missense_Mutation_p.V1686I	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1689	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ATCTGCTTGACCACCTGCTTG	0.547													C|||	7	0.00139776	0.0	0.0043	5008	,	,		22370	0.0		0.004	False		,,,				2504	0.0				p.V1689I		Atlas-SNP	.											.	MYO5A	145	.	0			c.G5065A						PASS	.	C	ILE/VAL,ILE/VAL	5,4337		0,5,2166	144.0	145.0	145.0		5065,4984	4.6	1.0	15	dbSNP_134	145	34,8514		0,34,4240	yes	missense,missense	MYO5A	NM_000259.3,NM_001142495.1	29,29	0,39,6406	TT,TC,CC		0.3978,0.1152,0.3026	benign,benign	1689/1856,1662/1829	52611351	39,12851	2171	4274	6445	SO:0001583	missense	4644	exon38			GCTTGACCACCTG		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.5065G>A	15.37:g.52611351C>T	ENSP00000382177:p.Val1689Ile	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	213	114	0.535211	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	16.55	3.153261	0.57259	0.001152	0.003978	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	D;D;D;D;D	0.86097	-2.01;-2.01;-2.05;-2.07;-2.03	5.57	4.63	0.57726	Dilute (1);Dil domain (1);	0.122821	0.56097	N	0.000039	T	0.76744	0.4030	N	0.12961	0.28	0.58432	D	0.999999	B;B;P	0.50443	0.277;0.001;0.935	B;B;P	0.45639	0.206;0.018;0.488	T	0.76898	-0.2789	10	0.36615	T	0.2	.	13.4437	0.61127	0.0:0.9219:0.0:0.0781	.	419;1689;1662	B5LY56;Q9Y4I1;Q9Y4I1-2	.;MYO5A_HUMAN;.	I	1689;1196;1686;1662;1714;1292;1687	ENSP00000382177:V1689I;ENSP00000382179:V1686I;ENSP00000348693:V1662I;ENSP00000350945:V1714I;ENSP00000451109:V1687I	ENSP00000348693:V1662I	V	-	1	0	MYO5A	50398643	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.093000	0.71422	1.311000	0.45024	0.467000	0.42956	GTC	C|0.995;T|0.005	0.005	strong		0.547	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
ATP11A	23250	hgsc.bcm.edu	37	13	113479813	113479813	+	Silent	SNP	G	G	A	rs9549564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:113479813G>A	ENST00000487903.1	+	11	1030	c.942G>A	c.(940-942)ctG>ctA	p.L314L	ATP11A_ENST00000283558.8_Silent_p.L314L|ATP11A_ENST00000375630.2_Silent_p.L314L|ATP11A_ENST00000375645.3_Silent_p.L314L			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	314					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				ACACTGTGCTGAAATACATGT	0.468													G|||	1074	0.214457	0.1225	0.317	5008	,	,		23383	0.1905		0.2903	False		,,,				2504	0.2127				p.L314L		Atlas-SNP	.											.	ATP11A	225	.	0			c.G942A						PASS	.	G	,	639,3767	273.7+/-271.5	55,529,1619	127.0	107.0	114.0		942,942	-2.8	0.2	13	dbSNP_119	114	2376,6224	395.0+/-344.9	319,1738,2243	yes	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	374,2267,3862	AA,AG,GG		27.6279,14.503,23.1816	,	314/1135,314/1192	113479813	3015,9991	2203	4300	6503	SO:0001819	synonymous_variant	23250	exon11			TGTGCTGAAATAC	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.942G>A	13.37:g.113479813G>A		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	217	216	0.995392	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1																																																																																			G|0.774;A|0.226	0.226	strong		0.468	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
CYBA	1535	hgsc.bcm.edu	37	16	88713236	88713236	+	Missense_Mutation	SNP	A	A	G	rs4673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88713236A>G	ENST00000261623.3	-	4	352	c.214T>C	c.(214-216)Tac>Cac	p.Y72H	CYBA_ENST00000567174.1_Missense_Mutation_p.Y72H|CYBA_ENST00000569359.1_Missense_Mutation_p.Y72H|CYBA_ENST00000561972.1_5'Flank	NM_000101.3	NP_000092.2	P13498	CY24A_HUMAN	cytochrome b-245, alpha polypeptide	72			Y -> H (in dbSNP:rs4673). {ECO:0000269|PubMed:19388116, ECO:0000269|PubMed:2469497, ECO:0000269|PubMed:3368442}.		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to amino acid stimulus (GO:0071230)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|cytochrome complex assembly (GO:0017004)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|negative regulation of glomerular filtration by angiotensin (GO:0003106)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of cell growth (GO:0030307)|positive regulation of endothelial cell proliferation (GO:0001938)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|response to nutrient levels (GO:0031667)|smooth muscle hypertrophy (GO:0014895)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|secretory granule (GO:0030141)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			endometrium(1)|liver(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0478)	Dextromethorphan(DB00514)	GCGGTCATGTACTTCTGTCCC	0.652													A|||	3327	0.664337	0.4917	0.6931	5008	,	,		15227	0.9157		0.6581	False		,,,				2504	0.6247				p.Y72H		Atlas-SNP	.											.	CYBA	12	.	0			c.T214C	GRCh37	CM983302	CYBA	M	rs4673	PASS	.	A	HIS/TYR	2432,1964	616.8+/-392.8	661,1110,427	67.0	73.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	214	3.5	1.0	16	dbSNP_52	71	5646,2954	665.9+/-402.3	1876,1894,530	yes	missense	CYBA	NM_000101.2	83	2537,3004,957	GG,GA,AA		34.3488,44.677,37.8424	probably-damaging	72/196	88713236	8078,4918	2198	4300	6498	SO:0001583	missense	1535	exon4			TCATGTACTTCTG		CCDS32504.1	16q24	2014-09-17				ENSG00000051523		"""Cytochrome b genes"""	2577	protein-coding gene	gene with protein product	"""flavocytochrome b-558 alpha polypeptide"""	608508				2243141	Standard	NM_000101		Approved	p22-PHOX	uc002flb.4	P13498		ENST00000261623.3:c.214T>C	16.37:g.88713236A>G	ENSP00000261623:p.Tyr72His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_000101	Q14090|Q9BR72	Missense_Mutation	SNP	ENST00000261623.3	37	CCDS32504.1	1523	0.6973443223443223	245	0.49796747967479676	237	0.6546961325966851	537	0.9388111888111889	504	0.6649076517150396	A	13.40	2.225798	0.39300	0.55323	0.656512	ENSG00000051523	ENST00000261623	D	0.86297	-2.1	4.55	3.46	0.39613	.	0.171366	0.53938	N	0.000050	T	0.00012	0.0000	M	0.79805	2.47	0.27439	P	0.9537626	D	0.89917	1.0	D	0.91635	0.999	T	0.46748	-0.9169	9	0.19590	T	0.45	-6.9848	8.0663	0.30663	0.905:0.0:0.095:0.0	rs4673;rs1130413;rs2228471;rs2242272;rs3189211;rs4782392;rs11266997;rs59455247;rs4673	72	P13498	CY24A_HUMAN	H	72	ENSP00000261623:Y72H	ENSP00000261623:Y72H	Y	-	1	0	CYBA	87240737	1.000000	0.71417	0.970000	0.41538	0.205000	0.24178	4.415000	0.59809	0.616000	0.30141	0.448000	0.29417	TAC	A|0.349;G|0.651	0.651	strong		0.652	CYBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422765.1	NM_000101	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58564863	58564863	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58564863C>T	ENST00000282326.1	+	6	918	c.671C>T	c.(670-672)cCc>cTc	p.P224L		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	224					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CTCGCAGGGCCCTCCTCAGAC	0.622																																					p.P224L		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.C671T						PASS	.						48.0	51.0	50.0					19																	58564863		2203	4300	6503	SO:0001583	missense	284312	exon6			CAGGGCCCTCCTC	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.671C>T	19.37:g.58564863C>T	ENSP00000282326:p.Pro224Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	10	0.15873	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	C	6.071	0.381441	0.11524	.	.	ENSG00000152467	ENST00000282326	T	0.04862	3.54	1.04	-2.09	0.07232	.	.	.	.	.	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	0.999993	B	0.09022	0.002	B	0.06405	0.002	T	0.45934	-0.9227	9	0.23302	T	0.38	.	2.0317	0.03530	0.2546:0.35:0.0:0.3953	.	224	Q8NBB4	ZSCA1_HUMAN	L	224	ENSP00000282326:P224L	ENSP00000282326:P224L	P	+	2	0	ZSCAN1	63256675	0.004000	0.15560	0.005000	0.12908	0.357000	0.29423	0.275000	0.18698	-0.640000	0.05495	0.491000	0.48974	CCC	.	.	none		0.622	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
SLC26A9	115019	hgsc.bcm.edu	37	1	205887981	205887981	+	Missense_Mutation	SNP	T	T	C	rs16856462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205887981T>C	ENST00000367135.3	-	19	2356	c.2243A>G	c.(2242-2244)cAc>cGc	p.H748R	SLC26A9_ENST00000340781.4_Missense_Mutation_p.H748R|SLC26A9_ENST00000367134.2_Missense_Mutation_p.H748R	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	748			H -> R (in dbSNP:rs16856462). {ECO:0000269|PubMed:22544634}.		anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			TTGGAAGTTGTGTCCTGGGGT	0.502											OREG0014164	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	382	0.076278	0.1755	0.0663	5008	,	,		19858	0.0		0.0805	False		,,,				2504	0.0235				p.H748R		Atlas-SNP	.											SLC26A9,upper_leg,malignant_melanoma,-1,1	SLC26A9	176	1	0			c.A2243G						PASS	.	C	ARG/HIS,ARG/HIS	740,3666	757.2+/-412.7	59,622,1522	226.0	214.0	218.0		2243,2243	-10.2	0.0	1	dbSNP_123	218	722,7878	786.5+/-407.6	33,656,3611	yes	missense,missense	SLC26A9	NM_052934.3,NM_134325.2	29,29	92,1278,5133	CC,CT,TT		8.3953,16.7953,11.241	benign,benign	748/792,748/888	205887981	1462,11544	2203	4300	6503	SO:0001583	missense	115019	exon19			AAGTTGTGTCCTG	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"""Solute carriers"""	14469	protein-coding gene	gene with protein product	"""anion transporter/exchanger-9"""	608481	"""solute carrier family 26, member 9"""			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.2243A>G	1.37:g.205887981T>C	ENSP00000356103:p.His748Arg	Somatic	131	0	0	2155	WXS	Illumina HiSeq	Phase_I	144	60	0.416667	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	166	0.076007326007326	85	0.17276422764227642	28	0.07734806629834254	0	0.0	53	0.06992084432717678	C	0.001	-3.212806	0.00024	0.167953	0.083953	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.92099	-2.97;-2.92;-2.97	5.09	-10.2	0.00374	.	1.931050	0.02138	N	0.056944	T	0.00695	0.0023	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.59547	-0.7434	9	0.12766	T	0.61	.	12.1042	0.53803	0.0:0.5159:0.2185:0.2657	rs16856462;rs52804067;rs57411381;rs16856462	748;748	Q7LBE3;B1AVM8	S26A9_HUMAN;.	R	748	ENSP00000341682:H748R;ENSP00000356103:H748R;ENSP00000356102:H748R	ENSP00000341682:H748R	H	-	2	0	SLC26A9	204154604	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.067000	0.00620	-4.527000	0.00044	-2.318000	0.00253	CAC	T|0.899;C|0.101	0.101	strong		0.502	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
PLXNA1	5361	hgsc.bcm.edu	37	3	126708453	126708453	+	Silent	SNP	T	T	C	rs6773789	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126708453T>C	ENST00000393409.2	+	1	1017	c.1017T>C	c.(1015-1017)acT>acC	p.T339T	PLXNA1_ENST00000251772.4_Silent_p.T316T	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	339	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		TGCTGTTCACTGTGTTCGCCC	0.637													C|||	2368	0.472843	0.7088	0.353	5008	,	,		19836	0.4236		0.339	False		,,,				2504	0.4274				p.T339T		Atlas-SNP	.											PLXNA1,NS,carcinoma,0,1	PLXNA1	185	1	0			c.T1017C						PASS	.	C		2860,1546	484.2+/-360.0	904,1052,247	71.0	72.0	72.0		1017	-3.8	0.8	3	dbSNP_116	72	2722,5878	679.7+/-403.6	438,1846,2016	no	coding-synonymous	PLXNA1	NM_032242.3		1342,2898,2263	CC,CT,TT		31.6512,35.0885,42.9187		339/1897	126708453	5582,7424	2203	4300	6503	SO:0001819	synonymous_variant	5361	exon1			GTTCACTGTGTTC	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.1017T>C	3.37:g.126708453T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																			T|0.567;C|0.433	0.433	strong		0.637	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
HMGCLL1	54511	hgsc.bcm.edu	37	6	55406863	55406863	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:55406863C>T	ENST00000398661.2	-	3	405	c.274G>A	c.(274-276)Gaa>Aaa	p.E92K	HMGCLL1_ENST00000370850.2_Missense_Mutation_p.E62K|HMGCLL1_ENST00000428842.1_Missense_Mutation_p.E62K|HMGCLL1_ENST00000308161.4_Missense_Mutation_p.E62K|HMGCLL1_ENST00000508459.1_Missense_Mutation_p.E62K|HMGCLL1_ENST00000274901.4_Missense_Mutation_p.E62K	NM_019036.2	NP_061909.2	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	92					ketone body biosynthetic process (GO:0046951)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|metal ion binding (GO:0046872)	p.E92K(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACTACCTTTTCATTCTGCAAT	0.313																																					p.E92K	Ovarian(35;840 893 7837 15538 42887)	Atlas-SNP	.											HMGCLL1,NS,carcinoma,0,1	HMGCLL1	70	1	1	Substitution - Missense(1)	lung(1)	c.G274A						scavenged	.						102.0	92.0	95.0					6																	55406863		1819	4080	5899	SO:0001583	missense	54511	exon3			CCTTTTCATTCTG	AK055075	CCDS43474.1, CCDS43475.1, CCDS75472.1, CCDS75473.1	6p12.1	2010-04-30	2010-04-30		ENSG00000146151	ENSG00000146151			21359	protein-coding gene	gene with protein product			"""3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1"""			8619474, 9110174	Standard	NM_001042406		Approved	DKFZP434G1411, bA418P12.1	uc003pcn.3	Q8TB92	OTTHUMG00000014902	ENST00000398661.2:c.274G>A	6.37:g.55406863C>T	ENSP00000381654:p.Glu92Lys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	223	3	0.0134529	NM_019036	B1AQ42|B3KNV0|B7Z1S7|F8W793|Q6ZSA9	Missense_Mutation	SNP	ENST00000398661.2	37	CCDS43475.1	.	.	.	.	.	.	.	.	.	.	C	35	5.524307	0.96431	.	.	ENSG00000146151	ENST00000274901;ENST00000398661;ENST00000370850;ENST00000508459;ENST00000308161;ENST00000428842	D;D;D;D;D;D	0.98345	-4.88;-4.88;-4.75;-4.67;-4.88;-4.67	5.97	5.97	0.96955	Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.99363	0.9776	H	0.94503	3.545	0.80722	D	1	D;D;D;D;D;D	0.76494	0.997;0.999;0.963;0.997;0.99;0.996	D;D;P;D;P;D	0.79108	0.948;0.992;0.767;0.919;0.834;0.942	D	0.98948	1.0793	10	0.87932	D	0	-0.071	20.4388	0.99107	0.0:1.0:0.0:0.0	.	62;62;62;62;62;92	B7Z4D4;B7Z212;F8W793;G5E9S9;Q8TB92-2;Q8TB92	.;.;.;.;.;HMGC2_HUMAN	K	62;92;62;62;62;62	ENSP00000274901:E62K;ENSP00000381654:E92K;ENSP00000359887:E62K;ENSP00000424309:E62K;ENSP00000309737:E62K;ENSP00000412924:E62K	ENSP00000274901:E62K	E	-	1	0	HMGCLL1	55514822	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.162000	0.64942	2.836000	0.97738	0.655000	0.94253	GAA	.	.	none		0.313	HMGCLL1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360290.1	XM_166383	
MUS81	80198	hgsc.bcm.edu	37	11	65632262	65632262	+	Silent	SNP	G	G	T	rs558114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65632262G>T	ENST00000308110.4	+	12	1597	c.1248G>T	c.(1246-1248)acG>acT	p.T416T	MUS81_ENST00000533035.1_Silent_p.T341T|EFEMP2_ENST00000532648.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	416					DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		CCCTCTTGACGCGGGGCCTGC	0.597								Homologous recombination					G|||	2145	0.428315	0.202	0.4063	5008	,	,		19357	0.3323		0.668	False		,,,				2504	0.6022				p.T416T		Atlas-SNP	.											.	MUS81	68	.	0			c.G1248T						PASS	.	G		1149,3253	403.5+/-332.8	154,841,1206	51.0	51.0	51.0		1248	-11.8	0.0	11	dbSNP_83	51	5736,2856	668.7+/-402.6	1891,1954,451	no	coding-synonymous	MUS81	NM_025128.4		2045,2795,1657	TT,TG,GG		33.2402,26.1018,47.014		416/552	65632262	6885,6109	2201	4296	6497	SO:0001819	synonymous_variant	80198	exon12			CTTGACGCGGGGC		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.1248G>T	11.37:g.65632262G>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_025128	Q9H7D9	Silent	SNP	ENST00000308110.4	37	CCDS8115.1	976	0.4468864468864469	117	0.23780487804878048	176	0.4861878453038674	174	0.3041958041958042	509	0.6715039577836411	G	5.193	0.221105	0.09863	0.261018	0.667598	ENSG00000172732	ENST00000529374	.	.	.	5.92	-11.8	0.00035	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999963955	.	.	.	.	.	.	T	0.13442	-1.0509	3	.	.	.	-6.0655	4.1591	0.10275	0.0812:0.3495:0.2094:0.3599	rs558114;rs17850601;rs558114	.	.	.	S	342	.	.	A	+	1	0	MUS81	65388838	0.000000	0.05858	0.000000	0.03702	0.776000	0.43924	-7.397000	0.00037	-4.580000	0.00041	-1.433000	0.01084	GCG	G|0.512;T|0.488	0.488	strong		0.597	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
ADH4	127	hgsc.bcm.edu	37	4	100048414	100048414	+	Missense_Mutation	SNP	T	T	C	rs1126671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100048414T>C	ENST00000265512.7	-	7	999	c.925A>G	c.(925-927)Att>Gtt	p.I309V	ADH4_ENST00000505590.1_Missense_Mutation_p.I328V|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000508393.1_Missense_Mutation_p.I328V|ADH4_ENST00000423445.1_Missense_Mutation_p.I328V	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	309			I -> V (in dbSNP:rs1126671). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		TCTGGAAAAATAGTCAATCCT	0.408													T|||	4242	0.847045	0.8608	0.7709	5008	,	,		13467	0.999		0.6968	False		,,,				2504	0.8804				p.I309V		Atlas-SNP	.											.	ADH4	35	.	0			c.A925G	GRCh37	CM025885	ADH4	M	rs1126671	PASS	.	T	VAL/ILE	3626,780	752.9+/-412.3	1487,652,64	89.0	89.0	89.0		925	-7.3	0.0	4	dbSNP_86	89	5880,2720	682.3+/-403.8	1991,1898,411	yes	missense	ADH4	NM_000670.3	29	3478,2550,475	CC,CT,TT		31.6279,17.7031,26.9107	benign	309/381	100048414	9506,3500	2203	4300	6503	SO:0001583	missense	127	exon7			GAAAAATAGTCAA	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"""Alcohol dehydrogenases"""	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.925A>G	4.37:g.100048414T>C	ENSP00000265512:p.Ile309Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	181	181	1	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	37	CCDS34032.1	1791	0.820054945054945	414	0.8414634146341463	274	0.7569060773480663	572	1.0	531	0.7005277044854882	T	0.061	-1.223333	0.01530	0.822969	0.683721	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590	T;T;T;T	0.06142	3.34;3.34;3.34;3.34	3.65	-7.29	0.01451	Alcohol dehydrogenase, C-terminal (1);	0.604873	0.15181	N	0.276103	T	0.00012	0.0000	N	0.21448	0.665	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27773	-1.0064	9	0.59425	D	0.04	-15.3141	3.7678	0.08629	0.0954:0.3913:0.2897:0.2237	rs1126671;rs3181816;rs17407311;rs17845683;rs17858623;rs52793462;rs57095404;rs1126671	328;309	P08319-2;P08319	.;ADH4_HUMAN	V	328;309;328;328	ENSP00000424630:I328V;ENSP00000265512:I309V;ENSP00000397939:I328V;ENSP00000425416:I328V	ENSP00000265512:I309V	I	-	1	0	ADH4	100267437	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.757000	0.04772	-2.687000	0.00405	-1.417000	0.01113	ATT	T|0.213;C|0.787	0.787	strong		0.408	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	
ZNF638	27332	hgsc.bcm.edu	37	2	71633275	71633275	+	Silent	SNP	T	T	C	rs3732233	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71633275T>C	ENST00000409544.1	+	19	3648	c.3018T>C	c.(3016-3018)atT>atC	p.I1006I	ZNF638_ENST00000409407.1_5'Flank|ZNF638_ENST00000264447.4_Silent_p.I1006I|ZNF638_ENST00000355812.3_Silent_p.I1006I	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1006					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TAGATACAATTTATGATCGAT	0.343													T|||	2065	0.41234	0.1649	0.6398	5008	,	,		18894	0.2927		0.5517	False		,,,				2504	0.5654				p.I1006I		Atlas-SNP	.											.	ZNF638	179	.	0			c.T3018C						PASS	.	T	,	1029,3377	377.8+/-322.6	108,813,1282	162.0	150.0	154.0		3018,3018	2.0	0.4	2	dbSNP_107	154	4972,3628	625.2+/-397.7	1432,2108,760	no	coding-synonymous,coding-synonymous	ZNF638	NM_001014972.1,NM_014497.3	,	1540,2921,2042	CC,CT,TT		42.186,23.3545,46.1402	,	1006/1979,1006/1979	71633275	6001,7005	2203	4300	6503	SO:0001819	synonymous_variant	27332	exon19			TACAATTTATGAT	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3018T>C	2.37:g.71633275T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	148	51	0.344595	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	37	CCDS1917.1																																																																																			T|0.560;C|0.440	0.440	strong		0.343	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20852546	20852546	+	Silent	SNP	C	C	T	rs34243130	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:20852546C>T	ENST00000266509.2	+	2	404	c.36C>T	c.(34-36)ttC>ttT	p.F12F	SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000545604.1_Silent_p.F12F|SLCO1C1_ENST00000540354.1_Silent_p.F12F|SLCO1C1_ENST00000381552.1_Silent_p.F12F	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	12					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TCCAGTTGTTCTGCAAAACTT	0.353													C|||	158	0.0315495	0.0061	0.1153	5008	,	,		15937	0.0		0.0586	False		,,,				2504	0.0112				p.F12F		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C36T						PASS	.	C	,,,	79,4327	68.7+/-106.4	1,77,2125	61.0	61.0	61.0		,36,36,36	3.0	1.0	12	dbSNP_126	61	634,7964	162.9+/-215.5	32,570,3697	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	,,,	33,647,5822	TT,TC,CC		7.3738,1.793,5.4829	,,,	,12/664,12/731,12/713	20852546	713,12291	2203	4299	6502	SO:0001819	synonymous_variant	53919	exon2			GTTGTTCTGCAAA	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.36C>T	12.37:g.20852546C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	176	96	0.545455	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Silent	SNP	ENST00000266509.2	37	CCDS8683.1																																																																																			C|0.953;T|0.047	0.047	strong		0.353	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
PLG	5340	hgsc.bcm.edu	37	6	161173946	161173946	+	Silent	SNP	T	T	G	rs11060	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:161173946T>G	ENST00000308192.9	+	19	2349	c.2286T>G	c.(2284-2286)ggT>ggG	p.G762G		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	762	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	ACAGTGGAGGTCCTCTGGTTT	0.468													T|||	3411	0.68111	0.5348	0.7075	5008	,	,		18500	0.9782		0.5249	False		,,,				2504	0.7147				p.G762G		Atlas-SNP	.											.	PLG	150	.	0			c.T2286G						PASS	.						97.0	91.0	93.0					6																	161173946		2203	4300	6503	SO:0001819	synonymous_variant	5340	exon19			TGGAGGTCCTCTG	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.2286T>G	6.37:g.161173946T>G		Somatic	612	2	0.00326797		WXS	Illumina HiSeq	Phase_I	617	272	0.440843	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			T|0.358;G|0.642	0.642	strong		0.468	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
GGT1	2678	hgsc.bcm.edu	37	22	25023459	25023459	+	Missense_Mutation	SNP	G	G	C	rs138813205	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:25023459G>C	ENST00000400382.1	+	12	1836	c.1081G>C	c.(1081-1083)Gac>Cac	p.D361H	GGT1_ENST00000403838.1_Missense_Mutation_p.D17H|GGT1_ENST00000404223.1_Missense_Mutation_p.D17H|GGT1_ENST00000400383.1_Missense_Mutation_p.D361H|GGT1_ENST00000248923.4_Missense_Mutation_p.D361H|GGT1_ENST00000404920.1_Missense_Mutation_p.D17H|GGT1_ENST00000404532.1_Missense_Mutation_p.D17H|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000401885.1_Missense_Mutation_p.D17H|GGT1_ENST00000400380.1_Missense_Mutation_p.D361H|GGT1_ENST00000406383.2_Missense_Mutation_p.D361H			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	361				D -> H (in Ref. 10; AAI28240). {ECO:0000305}.	arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.D361H(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	GATCTCTGACGACACCACTCA	0.642																																					p.D361H		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	prostate(1)	c.G1081C						scavenged	.						37.0	38.0	38.0					22																	25023459		2200	4293	6493	SO:0001583	missense	2678	exon12			TCTGACGACACCA	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1081G>C	22.37:g.25023459G>C	ENSP00000383232:p.Asp361His	Somatic	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	340	26	0.0764706	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	44	0.020146520146520148	3	0.006097560975609756	3	0.008287292817679558	5	0.008741258741258742	33	0.04353562005277045	.	6.591	0.477472	0.12521	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23	3.4	-2.55	0.06288	.	0.371845	0.29046	N	0.013305	T	0.02119	0.0066	M	0.79614	2.46	0.29276	N	0.870324	B	0.17465	0.022	B	0.22152	0.038	T	0.14559	-1.0468	10	0.45353	T	0.12	-4.1646	8.9526	0.35799	0.6006:0.0:0.3994:0.0	.	361	P19440	GGT1_HUMAN	H	361;361;361;361;361;361;17;17;17;17;17	ENSP00000248923:D361H;ENSP00000393537:D361H;ENSP00000383232:D361H;ENSP00000383233:D361H;ENSP00000383231:D361H;ENSP00000385975:D361H;ENSP00000384381:D17H;ENSP00000385445:D17H;ENSP00000384820:D17H;ENSP00000385016:D17H;ENSP00000385001:D17H	ENSP00000248923:D361H	D	+	1	0	GGT1	23353459	0.054000	0.20591	0.000000	0.03702	0.103000	0.19146	0.359000	0.20233	-0.295000	0.08960	0.298000	0.19748	GAC	C|0.014;G|0.986	0.014	strong		0.642	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
SYT16	83851	hgsc.bcm.edu	37	14	62462779	62462779	+	Silent	SNP	C	C	T	rs370890487		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:62462779C>T	ENST00000430451.2	+	1	239	c.42C>T	c.(40-42)ttC>ttT	p.F14F	SYT16_ENST00000446982.2_Silent_p.F14F	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	14					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		AGAACTTCTTCCAGCCTTTCT	0.468													C|||	1	0.000199681	0.0	0.0	5008	,	,		20561	0.0		0.001	False		,,,				2504	0.0				p.F14F		Atlas-SNP	.											.	SYT16	144	.	0			c.C42T						PASS	.	C		1,3785		0,1,1892	79.0	77.0	78.0		42	2.1	1.0	14		78	14,8226		0,14,4106	no	coding-synonymous	SYT16	NM_031914.2		0,15,5998	TT,TC,CC		0.1699,0.0264,0.1247		14/646	62462779	15,12011	1893	4120	6013	SO:0001819	synonymous_variant	83851	exon1			CTTCTTCCAGCCT	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.42C>T	14.37:g.62462779C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	159	72	0.45283	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	37	CCDS45121.1																																																																																			.	.	weak		0.468	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
NUSAP1	51203	hgsc.bcm.edu	37	15	41634587	41634587	+	Missense_Mutation	SNP	A	A	G	rs386783399|rs7178634	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41634587A>G	ENST00000559596.1	+	2	184	c.97A>G	c.(97-99)Acc>Gcc	p.T33A	NUSAP1_ENST00000560177.1_Missense_Mutation_p.T33A|NUSAP1_ENST00000560747.1_Missense_Mutation_p.T33A|NUSAP1_ENST00000558123.1_3'UTR|NUSAP1_ENST00000414849.2_Missense_Mutation_p.T33A|NUSAP1_ENST00000450318.1_Missense_Mutation_p.T33A|NUSAP1_ENST00000260359.6_Missense_Mutation_p.T33A|NUSAP1_ENST00000450592.2_Intron|RP11-16O9.2_ENST00000559959.1_RNA			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	33			T -> A (in dbSNP:rs7178634).|T -> N (in dbSNP:rs7178777).	T -> D (in Ref. 6; AL833611). {ECO:0000305}.	establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.T33A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		CTTGCAGGCAACCAAGTTGTT	0.338													G|||	1714	0.342252	0.5938	0.2781	5008	,	,		23594	0.1548		0.337	False		,,,				2504	0.2464				p.T33A		Atlas-SNP	.											NUSAP1,NS,carcinoma,0,2	NUSAP1	32	2	1	Substitution - Missense(1)	prostate(1)	c.A97G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR	91,3631		12,67,1782	70.0	66.0	67.0		97,97,97	4.6	1.0	15	dbSNP_116	67	59,8135		7,45,4045	yes	missense,missense,missense	NUSAP1	NM_001129897.1,NM_016359.4,NM_018454.7	58,58,58	19,112,5827	GG,GA,AA		0.72,2.4449,1.2588	benign,benign,benign	33/403,33/442,33/441	41634587	150,11766	1861	4097	5958	SO:0001583	missense	51203	exon2			CAGGCAACCAAGT	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.97A>G	15.37:g.41634587A>G	ENSP00000453403:p.Thr33Ala	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	NM_018454	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Missense_Mutation	SNP	ENST00000559596.1	37	CCDS45234.1	577	0.2641941391941392	222	0.45121951219512196	97	0.26795580110497236	72	0.1258741258741259	186	0.24538258575197888	G	12.08	1.830706	0.32329	0.024449	0.0072	ENSG00000137804	ENST00000260359;ENST00000414849;ENST00000450318	T;T;T	0.30981	1.51;1.51;1.51	5.47	4.56	0.56223	.	0.426017	0.27797	N	0.017808	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B;B;B;B	0.12630	0.0;0.006;0.005;0.006;0.005	B;B;B;B;B	0.12837	0.0;0.008;0.006;0.008;0.006	T	0.43048	-0.9415	9	0.72032	D	0.01	.	10.0559	0.42244	0.1593:0.0:0.8407:0.0	rs7178634;rs57619738;rs7178634	33;33;33;33;33	E9PB35;Q9BXS6-3;Q9BXS6-5;Q9BXS6;Q9BXS6-2	.;.;.;NUSAP_HUMAN;.	A	33	ENSP00000260359:T33A;ENSP00000400746:T33A;ENSP00000401351:T33A	ENSP00000260359:T33A	T	+	1	0	NUSAP1	39421879	1.000000	0.71417	0.999000	0.59377	0.229000	0.25112	1.570000	0.36439	0.818000	0.34468	-0.227000	0.12334	ACC	A|0.684;G|0.316	0.316	strong		0.338	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359	
TRMT13	54482	hgsc.bcm.edu	37	1	100598867	100598867	+	Missense_Mutation	SNP	C	C	T	rs35216047|rs687513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:100598867C>T	ENST00000370141.2	+	1	149	c.143C>T	c.(142-144)gCg>gTg	p.A48V	SASS6_ENST00000462159.1_5'Flank|SASS6_ENST00000287482.5_5'Flank|TRMT13_ENST00000370143.1_Missense_Mutation_p.A48V|TRMT13_ENST00000370139.1_Missense_Mutation_p.A17V|SASS6_ENST00000535161.1_5'Flank	NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	48			A -> V (in dbSNP:rs687513).	A -> M (in Ref. 1; BAA92074 and 3; AAH75811). {ECO:0000305}.	tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										GCTGGAGCCGCGGAGGTGTGG	0.552													C|||	3788	0.75639	0.3752	0.8905	5008	,	,		17017	0.9286		0.8519	False		,,,				2504	0.9008				p.A48V		Atlas-SNP	.											.	.	.	.	0			c.C143T						PASS	.	C	VAL/ALA	2009,2397	540.8+/-375.6	478,1053,672	61.0	58.0	59.0		143	5.0	1.0	1	dbSNP_83	59	7268,1332	746.7+/-407.3	3080,1108,112	yes	missense	CCDC76	NM_019083.2	64	3558,2161,784	TT,TC,CC		15.4884,45.5969,28.6714	benign	48/482	100598867	9277,3729	2203	4300	6503	SO:0001583	missense	54482	exon1			GAGCCGCGGAGGT	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"""coiled-coil domain containing 76"""	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.143C>T	1.37:g.100598867C>T	ENSP00000359160:p.Ala48Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_019083	Q5VVL0|Q9NW65	Missense_Mutation	SNP	ENST00000370141.2	37	CCDS765.1	1339	0.6130952380952381	140	0.2845528455284553	267	0.7375690607734806	453	0.791958041958042	479	0.6319261213720316	C	16.75	3.209304	0.58343	0.455969	0.845116	ENSG00000122435	ENST00000370143;ENST00000370141;ENST00000370139	T;T;T	0.48836	0.85;0.85;0.8	4.99	4.99	0.66335	.	0.240042	0.40908	D	0.000994	T	0.19366	0.0465	L	0.42245	1.32	0.35833	P	0.17453399999999997	B;B	0.31519	0.327;0.327	B;B	0.24701	0.055;0.055	T	0.08371	-1.0725	9	0.27785	T	0.31	-6.197	8.4042	0.32605	0.2146:0.6418:0.1436:0.0	rs687513;rs59740257;rs687513	48;48	B4DQS9;Q9NUP7	.;TRM13_HUMAN	V	48;48;17	ENSP00000359162:A48V;ENSP00000359160:A48V;ENSP00000359158:A17V	ENSP00000359158:A17V	A	+	2	0	CCDC76	100371455	0.755000	0.28372	0.984000	0.44739	0.973000	0.67179	1.090000	0.30902	2.588000	0.87417	0.650000	0.86243	GCG	C|0.315;T|0.685	0.685	strong		0.552	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083	
TBC1D32	221322	hgsc.bcm.edu	37	6	121577370	121577370	+	Missense_Mutation	SNP	T	T	C	rs7745023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:121577370T>C	ENST00000398212.2	-	16	1844	c.1795A>G	c.(1795-1797)Ata>Gta	p.I599V	TBC1D32_ENST00000275159.6_Missense_Mutation_p.I599V	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	599			I -> V (in dbSNP:rs7745023).		cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.I599V(1)									CCAGAAAATATAGAAATATCT	0.353													T|||	1306	0.260783	0.0424	0.2954	5008	,	,		18165	0.1111		0.5855	False		,,,				2504	0.3517				p.I599V		Atlas-SNP	.											C6orf170,NS,carcinoma,0,1	C6orf170	146	1	1	Substitution - Missense(1)	prostate(1)	c.A1795G						PASS	.	T	VAL/ILE	468,3146		39,390,1378	62.0	57.0	59.0		1795	-0.5	0.5	6	dbSNP_116	59	4710,3436		1354,2002,717	yes	missense	C6orf170	NM_152730.4	29	1393,2392,2095	CC,CT,TT		42.1802,12.9496,44.0306	benign	599/1258	121577370	5178,6582	1807	4073	5880	SO:0001583	missense	221322	exon16			AAAATATAGAAAT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1795A>G	6.37:g.121577370T>C	ENSP00000381270:p.Ile599Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	90	52	0.577778	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	639	0.2925824175824176	29	0.05894308943089431	121	0.3342541436464088	51	0.08916083916083917	438	0.5778364116094987	T	2.501	-0.315202	0.05422	0.129496	0.578198	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.16073	2.37;2.37	5.21	-0.469	0.12142	.	0.775342	0.12424	N	0.470190	T	0.01695	0.0054	N	0.15975	0.35	0.44261	P	0.0028839999999999977	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.46762	-0.9168	9	0.02654	T	1	-15.6923	5.6919	0.17835	0.0:0.3939:0.3466:0.2596	rs7745023;rs13208594;rs52836518;rs58699322;rs7745023	599;599	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	V	599	ENSP00000275159:I599V;ENSP00000381270:I599V	ENSP00000275159:I599V	I	-	1	0	C6orf170	121619069	0.857000	0.29778	0.468000	0.27192	0.460000	0.32559	0.019000	0.13444	0.057000	0.16193	-1.156000	0.01807	ATA	T|0.674;C|0.326	0.326	strong		0.353	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
FCAMR	83953	hgsc.bcm.edu	37	1	207140447	207140447	+	Missense_Mutation	SNP	C	C	T	rs199884709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207140447C>T	ENST00000324852.4	-	3	593	c.119G>A	c.(118-120)aGg>aAg	p.R40K	FCAMR_ENST00000450945.2_Missense_Mutation_p.R40K|FCAMR_ENST00000400962.3_Missense_Mutation_p.R40K	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	339					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						TCCCGCCCTCCTGCTGGTGAC	0.527													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20112	0.0		0.001	False		,,,				2504	0.001				p.R40K	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.G119A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	2,3134		0,2,1566	61.0	55.0	57.0		119,119,119	-5.3	0.0	1		57	22,7142		0,22,3560	yes	missense,missense,missense	FCAMR	NM_001122979.2,NM_001170631.1,NM_032029.4	26,26,26	0,24,5126	TT,TC,CC		0.3071,0.0638,0.233	,,	40/266,40/578,40/266	207140447	24,10276	1568	3582	5150	SO:0001583	missense	83953	exon3			GCCCTCCTGCTGG	AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.119G>A	1.37:g.207140447C>T	ENSP00000316491:p.Arg40Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	119	42	0.352941	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	37	CCDS53468.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.612	1.131495	0.21041	6.38E-4	0.003071	ENSG00000162897	ENST00000400962;ENST00000324852;ENST00000450945	T;T;T	0.06768	3.26;3.55;3.26	5.35	-5.32	0.02722	.	.	.	.	.	T	0.03011	0.0089	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.47861	-0.9084	6	0.11182	T	0.66	2.788	5.9013	0.18967	0.2988:0.471:0.0:0.2302	.	.	.	.	K	40	ENSP00000383746:R40K;ENSP00000316491:R40K;ENSP00000392707:R40K	ENSP00000316491:R40K	R	-	2	0	FCAMR	205207070	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.129000	0.03244	-0.509000	0.06532	-0.302000	0.09304	AGG	C|0.999;T|0.001	0.001	strong		0.527	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029	
CDHR3	222256	hgsc.bcm.edu	37	7	105615406	105615406	+	Missense_Mutation	SNP	G	G	A	rs35008315	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:105615406G>A	ENST00000317716.9	+	2	243	c.163G>A	c.(163-165)Gtg>Atg	p.V55M	CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000542731.1_Missense_Mutation_p.V55M|CDHR3_ENST00000541203.1_Missense_Mutation_p.V55M|CDHR3_ENST00000478080.1_Intron|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	55	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> M (in dbSNP:rs35008315).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ATTGTCACCTGTGATCCCAGG	0.458													G|||	805	0.160743	0.062	0.2133	5008	,	,		22290	0.2609		0.1789	False		,,,				2504	0.135				p.V55M		Atlas-SNP	.											.	CDHR3	153	.	0			c.G163A						PASS	.	G	MET/VAL	344,3432		18,308,1562	190.0	177.0	181.0		163	4.6	1.0	7	dbSNP_126	181	1637,6615		162,1313,2651	yes	missense	CDHR3	NM_152750.4	21	180,1621,4213	AA,AG,GG		19.8376,9.1102,16.4699	probably-damaging	55/886	105615406	1981,10047	1888	4126	6014	SO:0001583	missense	222256	exon2			TCACCTGTGATCC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.163G>A	7.37:g.105615406G>A	ENSP00000325954:p.Val55Met	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	267	112	0.419476	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	383	0.17536630036630035	36	0.07317073170731707	85	0.23480662983425415	126	0.2202797202797203	136	0.17941952506596306	G	18.28	3.590200	0.66105	0.091102	0.198376	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000541203	T;T;T	0.15487	2.42;2.42;2.42	5.46	4.56	0.56223	Cadherin (2);	0.088554	0.47455	D	0.000221	T	0.00012	0.0000	M	0.68317	2.08	0.09310	P	1.0	D;D	0.53619	0.961;0.961	P;P	0.52646	0.705;0.705	T	0.08597	-1.0714	9	0.56958	D	0.05	-9.0937	15.1633	0.72801	0.0:0.1419:0.8581:0.0	rs35008315;rs58776450;rs62481264	42;55	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	M	55	ENSP00000439766:V55M;ENSP00000325954:V55M;ENSP00000443733:V55M	ENSP00000325954:V55M	V	+	1	0	CDHR3	105402642	1.000000	0.71417	0.997000	0.53966	0.708000	0.40852	2.616000	0.46376	1.491000	0.48482	0.655000	0.94253	GTG	G|0.824;A|0.176	0.176	strong		0.458	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
EFCAB6	64800	hgsc.bcm.edu	37	22	44083442	44083442	+	Missense_Mutation	SNP	T	T	C	rs5764214	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:44083442T>C	ENST00000262726.7	-	11	1304	c.1051A>G	c.(1051-1053)Act>Gct	p.T351A	EFCAB6_ENST00000358439.4_Intron|EFCAB6_ENST00000396231.2_Missense_Mutation_p.T199A	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	351			T -> A (in dbSNP:rs5764214). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TTGATTTTAGTGGTGGCTTTA	0.328													T|||	2082	0.415735	0.5053	0.2867	5008	,	,		14884	0.2669		0.4573	False		,,,				2504	0.4969				p.T351A		Atlas-SNP	.											.	EFCAB6	177	.	0			c.A1051G						PASS	.	T	ALA/THR,ALA/THR	2205,2201	587.5+/-386.7	547,1111,545	59.0	59.0	59.0		1051,595	-3.8	0.0	22	dbSNP_114	59	4081,4519	559.1+/-387.3	944,2193,1163	yes	missense,missense	EFCAB6	NM_022785.3,NM_198856.2	58,58	1491,3304,1708	CC,CT,TT		47.4535,49.9546,48.3315	benign,benign	351/1502,199/1350	44083442	6286,6720	2203	4300	6503	SO:0001583	missense	64800	exon11			TTTTAGTGGTGGC	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1051A>G	22.37:g.44083442T>C	ENSP00000262726:p.Thr351Ala	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	135	85	0.62963	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	830	0.38003663003663	237	0.4817073170731707	118	0.3259668508287293	136	0.23776223776223776	339	0.4472295514511873	T	6.692	0.496279	0.12762	0.500454	0.474535	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.07688	3.17;3.17	4.68	-3.84	0.04256	.	1.984030	0.02128	N	0.056195	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.46190	-0.9209	9	0.18710	T	0.47	0.2565	13.2868	0.60247	0.0:0.6849:0.0:0.3151	rs5764214;rs7284270;rs52791933;rs5764214	351;351	Q5THR3-6;Q5THR3	.;EFCB6_HUMAN	A	199;351	ENSP00000379533:T199A;ENSP00000262726:T351A	ENSP00000262726:T351A	T	-	1	0	EFCAB6	42414775	0.000000	0.05858	0.001000	0.08648	0.958000	0.62258	-1.233000	0.02934	-0.759000	0.04684	0.533000	0.62120	ACT	T|0.603;C|0.397	0.397	strong		0.328	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
RIF1	55183	hgsc.bcm.edu	37	2	152314385	152314385	+	Silent	SNP	G	G	A	rs16830047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:152314385G>A	ENST00000243326.5	+	23	3246	c.2763G>A	c.(2761-2763)ctG>ctA	p.L921L	RIF1_ENST00000444746.2_Silent_p.L921L|RIF1_ENST00000453091.2_Silent_p.L921L|RIF1_ENST00000430328.2_Silent_p.L921L|RIF1_ENST00000428287.2_Silent_p.L921L			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TAATATTTCTGCACAAGAATA	0.378													G|||	1244	0.248403	0.093	0.3631	5008	,	,		15359	0.3224		0.3211	False		,,,				2504	0.226				p.L921L		Atlas-SNP	.											.	RIF1	244	.	0			c.G2763A						PASS	.	G	,,,	557,3849	250.9+/-257.8	38,481,1684	91.0	90.0	90.0		2763,2763,2763,2763	0.4	1.0	2	dbSNP_123	90	2428,6172	400.3+/-346.7	337,1754,2209	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	,,,	375,2235,3893	AA,AG,GG		28.2326,12.6419,22.9509	,,,	921/2447,921/2447,921/2447,921/2473	152314385	2985,10021	2203	4300	6503	SO:0001819	synonymous_variant	55183	exon24			ATTTCTGCACAAG	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.2763G>A	2.37:g.152314385G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	131	52	0.396947	NM_018151	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																			G|0.749;A|0.251	0.251	strong		0.378	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
MS4A4A	51338	hgsc.bcm.edu	37	11	60073626	60073626	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60073626G>A	ENST00000337908.4	+	6	690	c.600G>A	c.(598-600)gtG>gtA	p.V200V	MS4A4A_ENST00000532114.1_Silent_p.V147V|MS4A4A_ENST00000395016.3_Silent_p.V181V|MS4A4A_ENST00000355131.3_Silent_p.V181V	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	200				V -> C (in Ref. 4; AAL56220). {ECO:0000305}.		integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						GCATTGCTGTGTCCCTCTCTG	0.453																																					p.V200V		Atlas-SNP	.											.	MS4A4A	76	.	0			c.G600A						PASS	.						335.0	284.0	301.0					11																	60073626		2203	4300	6503	SO:0001819	synonymous_variant	51338	exon6			TGCTGTGTCCCTC	AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"""membrane-spanning 4-domains, subfamily A, member 4"""	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.600G>A	11.37:g.60073626G>A		Somatic	408	1	0.00245098		WXS	Illumina HiSeq	Phase_I	377	179	0.474801	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Silent	SNP	ENST00000337908.4	37	CCDS7982.1																																																																																			.	.	none		0.453	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2		
TRIM49C	642612	hgsc.bcm.edu	37	11	89774540	89774540	+	Missense_Mutation	SNP	C	C	A	rs75119043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:89774540C>A	ENST00000448984.1	+	8	1510	c.1181C>A	c.(1180-1182)aCc>aAc	p.T394N	TRIM49C_ENST00000432771.1_Intron	NM_001195234.1	NP_001182163.1	P0CI26	TR49C_HUMAN	tripartite motif containing 49C	394	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|lung(4)	8						CTCTTTACCACCTCCCCACTT	0.413																																					p.T394N		Atlas-SNP	.											.	TRIM49C	48	.	0			c.C1181A						PASS	.																																			SO:0001583	missense	642612	exon8			TTACCACCTCCCC	BC126470	CCDS53694.1	11q14.3	2014-02-17	2012-05-18	2012-05-18	ENSG00000204449	ENSG00000204449		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	38877	protein-coding gene	gene with protein product			"""tripartite motif containing 49-like 2"""	TRIM49L2			Standard	NM_001195234		Approved		uc010rua.2	P0CI26		ENST00000448984.1:c.1181C>A	11.37:g.89774540C>A	ENSP00000388299:p.Thr394Asn	Somatic	473	0	0		WXS	Illumina HiSeq	Phase_I	418	112	0.267943	NM_001195234	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	ENST00000448984.1	37	CCDS53694.1	.	.	.	.	.	.	.	.	.	.	C	8.188	0.795366	0.16327	.	.	ENSG00000204449	ENST00000448984	T	0.58797	0.31	0.869	-0.136	0.13473	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.51669	0.1688	L	0.45470	1.425	0.09310	N	1	P	0.40578	0.722	P	0.47941	0.562	T	0.42464	-0.9450	8	.	.	.	.	3.0558	0.06183	0.0:0.6555:0.0:0.3445	.	394	P0CI26	T49L2_HUMAN	N	394	ENSP00000388299:T394N	.	T	+	2	0	TRIM49L2	89414188	0.001000	0.12720	0.001000	0.08648	0.039000	0.13416	0.525000	0.22956	-0.044000	0.13491	0.298000	0.19748	ACC	C|0.946;A|0.054	0.054	strong		0.413	TRIM49C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395455.1	NM_001195234	
THBS1	7057	hgsc.bcm.edu	37	15	39879717	39879717	+	Silent	SNP	G	G	A	rs2229364	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:39879717G>A	ENST00000260356.5	+	8	1455	c.1290G>A	c.(1288-1290)aaG>aaA	p.K430K		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	430					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AGTGTGACAAGAGATGTAAGC	0.547													G|||	818	0.163339	0.0688	0.1167	5008	,	,		21225	0.2897		0.1312	False		,,,				2504	0.227				p.K430K		Atlas-SNP	.											.	THBS1	106	.	0			c.G1290A						PASS	.	G		359,4041	180.1+/-208.5	15,329,1856	37.0	34.0	35.0		1290	3.2	1.0	15	dbSNP_98	35	1111,7483	223.7+/-260.4	62,987,3248	no	coding-synonymous	THBS1	NM_003246.2		77,1316,5104	AA,AG,GG		12.9276,8.1591,11.3129		430/1171	39879717	1470,11524	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon8			TGACAAGAGATGT		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1290G>A	15.37:g.39879717G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			G|0.874;A|0.126	0.126	strong		0.547	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
HELZ2	85441	hgsc.bcm.edu	37	20	62196182	62196182	+	Silent	SNP	G	G	C	rs3810488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62196182G>C	ENST00000467148.1	-	8	4062	c.3993C>G	c.(3991-3993)gcC>gcG	p.A1331A	HELZ2_ENST00000427522.2_Silent_p.A762A	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1331					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CTCGGCGGCCGGCAACCCGGC	0.657													G|||	1052	0.210064	0.0068	0.085	5008	,	,		15542	0.5288		0.1759	False		,,,				2504	0.2802				p.A1331A		Atlas-SNP	.											PRIC285,NS,carcinoma,0,1	.	.	1	0			c.C3993G						PASS	.	G	,	191,4211		6,179,2016	30.0	34.0	33.0		3993,2286	-8.9	0.0	20	dbSNP_107	33	1448,7140		123,1202,2969	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	129,1381,4985	CC,CG,GG		16.8607,4.3389,12.6174	,	1331/2650,762/2081	62196182	1639,11351	2201	4294	6495	SO:0001819	synonymous_variant	85441	exon9			GCGGCCGGCAACC	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.3993C>G	20.37:g.62196182G>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	128	72	0.5625	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			A|0.001;C|0.168;G|0.831	0.168	strong		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
MUC4	4585	hgsc.bcm.edu	37	3	195511273	195511273	+	Missense_Mutation	SNP	G	G	A	rs199533374		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195511273G>A	ENST00000463781.3	-	2	7637	c.7178C>T	c.(7177-7179)gCa>gTa	p.A2393V	MUC4_ENST00000475231.1_Missense_Mutation_p.A2393V|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGC	0.587																																					p.A2393V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	0			c.C7178T						scavenged	.						29.0	31.0	31.0					3																	195511273		685	1586	2271	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7178C>T	3.37:g.195511273G>A	ENSP00000417498:p.Ala2393Val	Somatic	154	13	0.0844156		WXS	Illumina HiSeq	Phase_I	574	95	0.165505	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	6.063	0.379974	0.11466	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.54	.	.	.	.	.	.	.	.	T	0.14442	0.0349	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.25012	-1.0144	7	.	.	.	.	5.4001	0.16291	0.2688:0.0:0.7312:0.0	.	2393	E7ESK3	.	V	2393	ENSP00000417498:A2393V;ENSP00000420243:A2393V	.	A	-	2	0	MUC4	196995668	0.000000	0.05858	0.001000	0.08648	0.043000	0.13939	-2.059000	0.01393	-1.752000	0.01325	-2.092000	0.00371	GCA	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAM209B	388799	hgsc.bcm.edu	37	20	55108507	55108507	+	Missense_Mutation	SNP	C	C	A	rs200150839|rs386815438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55108507C>A	ENST00000371325.1	+	1	206	c.110C>A	c.(109-111)cCg>cAg	p.P37Q		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	37				PC -> QY (in Ref. 2; AAI05793). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)											GGGAAGGTGCCGTGTGGAGAG	0.537													C|||	49	0.00978435	0.0023	0.0086	5008	,	,		20353	0.003		0.0089	False		,,,				2504	0.0286				p.P37Q		Atlas-SNP	.											.	.	.	.	0			c.C110A						PASS	.						167.0	140.0	149.0					20																	55108507		2203	4290	6493	SO:0001583	missense	388799	exon1			AGGTGCCGTGTGG	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.110C>A	20.37:g.55108507C>A	ENSP00000360376:p.Pro37Gln	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	181	26	0.143646	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	C	3.871	-0.027889	0.07589	.	.	ENSG00000213714	ENST00000371325	T	0.08720	3.06	2.8	2.8	0.32819	.	0.000000	0.49305	D	0.000143	T	0.15522	0.0374	L	0.36672	1.1	0.33241	D	0.557293	D	0.89917	1.0	D	0.91635	0.999	T	0.10200	-1.0640	10	0.30854	T	0.27	-19.843	9.141	0.36903	0.0:1.0:0.0:0.0	.	37	Q5JX69	CT107_HUMAN	Q	37	ENSP00000360376:P37Q	ENSP00000360376:P37Q	P	+	2	0	C20orf107	54541914	0.973000	0.33851	0.988000	0.46212	0.019000	0.09904	1.612000	0.36889	1.556000	0.49512	0.393000	0.25936	CCG	.	.	weak		0.537	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
ACAN	176	hgsc.bcm.edu	37	15	89398407	89398407	+	Missense_Mutation	SNP	C	C	T	rs3743398	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89398407C>T	ENST00000561243.1	+	11	2591	c.2591C>T	c.(2590-2592)cCt>cTt	p.P864L	ACAN_ENST00000439576.2_Missense_Mutation_p.P864L|ACAN_ENST00000559004.1_Missense_Mutation_p.P864L|ACAN_ENST00000352105.7_Missense_Mutation_p.P864L			P16112	PGCA_HUMAN	aggrecan	863	CS-1.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TCTGGGGCCCCTGATGTCAGT	0.607													C|||	409	0.0816693	0.0151	0.1081	5008	,	,		19429	0.0952		0.1909	False		,,,				2504	0.0266				p.P864L		Atlas-SNP	.											.	ACAN	220	.	0			c.C2591T						PASS	.	C	LEU/PRO,LEU/PRO	138,3846		4,130,1858	47.0	53.0	51.0		2591,2591	4.9	0.5	15	dbSNP_107	51	1673,6659		152,1369,2645	yes	missense,missense	ACAN	NM_001135.3,NM_013227.3	98,98	156,1499,4503	TT,TC,CC		20.0792,3.4639,14.7044	probably-damaging,probably-damaging	864/2432,864/2531	89398407	1811,10505	1992	4166	6158	SO:0001583	missense	176	exon12			GGGCCCCTGATGT	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2591C>T	15.37:g.89398407C>T	ENSP00000453342:p.Pro864Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	256	0.11721611721611722	11	0.022357723577235773	49	0.13535911602209943	55	0.09615384615384616	141	0.18601583113456466	C	15.30	2.793935	0.50102	0.034639	0.200792	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.03468	4.19;3.92	5.79	4.87	0.63330	.	0.000000	0.32343	N	0.006224	T	0.00012	0.0000	M	0.65975	2.015	0.53005	P	3.799999999998249E-5	P;D	0.76494	0.584;0.999	B;D	0.71184	0.16;0.972	T	0.33599	-0.9862	9	0.09338	T	0.73	-12.1183	9.3039	0.37863	0.1416:0.7849:0.0:0.0735	rs3743398;rs60866336;rs3743398	864;864	E7ENV9;E7EX88	.;.	L	864	ENSP00000387356:P864L;ENSP00000341615:P864L	ENSP00000268134:P864L	P	+	2	0	ACAN	87199411	0.372000	0.25064	0.480000	0.27341	0.521000	0.34408	1.014000	0.29950	2.722000	0.93159	0.655000	0.94253	CCT	C|0.871;T|0.129	0.129	strong		0.607	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
ATG2B	55102	hgsc.bcm.edu	37	14	96800027	96800027	+	Missense_Mutation	SNP	C	C	T	rs183527316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:96800027C>T	ENST00000359933.4	-	8	2098	c.1205G>A	c.(1204-1206)cGt>cAt	p.R402H		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	402					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TTGCTTACCACGGCTAGAAGG	0.363													C|||	2	0.000399361	0.0	0.0	5008	,	,		16337	0.0		0.002	False		,,,				2504	0.0				p.R402H		Atlas-SNP	.											.	ATG2B	169	.	0			c.G1205A						PASS	.	C	HIS/ARG	4,3650		0,4,1823	77.0	70.0	72.0		1205	5.6	1.0	14		72	59,8131		0,59,4036	yes	missense	ATG2B	NM_018036.5	29	0,63,5859	TT,TC,CC		0.7204,0.1095,0.5319	benign	402/2079	96800027	63,11781	1827	4095	5922	SO:0001583	missense	55102	exon8			TTACCACGGCTAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.1205G>A	14.37:g.96800027C>T	ENSP00000353010:p.Arg402His	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.68	3.189548	0.57909	0.001095	0.007204	ENSG00000066739	ENST00000359933	T	0.10382	2.88	5.6	5.6	0.85130	.	0.423584	0.20315	U	0.094755	T	0.05640	0.0148	N	0.19112	0.55	0.47341	D	0.999394	B	0.22211	0.066	B	0.14023	0.01	T	0.24657	-1.0154	10	0.41790	T	0.15	.	13.2187	0.59875	0.0:0.9272:0.0:0.0728	.	402	Q96BY7	ATG2B_HUMAN	H	402	ENSP00000353010:R402H	ENSP00000353010:R402H	R	-	2	0	ATG2B	95869780	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.238000	0.65366	2.793000	0.96121	0.591000	0.81541	CGT	C|0.998;T|0.002	0.002	strong		0.363	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
ARHGAP27	201176	hgsc.bcm.edu	37	17	43472825	43472825	+	Missense_Mutation	SNP	G	G	C	rs117139057|rs11546338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:43472825G>C	ENST00000428638.1	-	17	2666	c.2667C>G	c.(2665-2667)caC>caG	p.H889Q	ARHGAP27_ENST00000442348.1_Missense_Mutation_p.H862Q|ARHGAP27_ENST00000376922.2_Missense_Mutation_p.H548Q|ARHGAP27_ENST00000532038.1_Missense_Mutation_p.H667Q|ARHGAP27_ENST00000532891.2_Missense_Mutation_p.H867Q|ARHGAP27_ENST00000528384.1_Missense_Mutation_p.H521Q|CTB-39G8.3_ENST00000592389.1_RNA|ARHGAP27_ENST00000455881.1_Missense_Mutation_p.H548Q|ARHGAP27_ENST00000582826.1_5'Flank			Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27	889			H -> Q (in dbSNP:rs34793644). {ECO:0000269|PubMed:15489334}.		positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of Rac GTPase activity (GO:0032855)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|SH3 domain binding (GO:0017124)			endometrium(4)|large_intestine(9)|lung(3)|skin(1)	17	Renal(3;0.0405)					CCAGCAGTCAGTGCGGCGGGA	0.682											OREG0024481	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	368	0.0734824	0.0431	0.098	5008	,	,		13456	0.1111		0.0666	False		,,,				2504	0.0654				p.H548Q		Atlas-SNP	.											.	ARHGAP27	37	.	0			c.C1644G						PASS	.	G	GLN/HIS	191,4113		3,185,1964	12.0	11.0	11.0		1644	4.4	1.0	17	dbSNP_126	11	537,7855		21,495,3680	yes	missense	ARHGAP27	NM_199282.2	24	24,680,5644	CC,CG,GG		6.399,4.4377,5.7341	possibly-damaging	548/549	43472825	728,11968	2152	4196	6348	SO:0001583	missense	201176	exon17			CAGTCAGTGCGGC	AK125535	CCDS11498.1, CCDS74082.1	17q21.31	2013-01-10			ENSG00000159314	ENSG00000159314		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	31813	protein-coding gene	gene with protein product		610591	"""SH3 domain containing 20"""	SH3D20		15147912	Standard	NM_199282		Approved	CAMGAP1, FLJ43547, SH3P20	uc002iix.3	Q6ZUM4	OTTHUMG00000166982	ENST00000428638.1:c.2667C>G	17.37:g.43472825G>C	ENSP00000403323:p.His889Gln	Somatic	73	0	0	916	WXS	Illumina HiSeq	Phase_I	72	40	0.555556	NM_199282	A4FU35|A8K3N5|C9JTF3|Q494U0|Q6NWZ8|Q8WY58	Missense_Mutation	SNP	ENST00000428638.1	37		172	0.07875457875457875	22	0.044715447154471545	26	0.0718232044198895	69	0.12062937062937062	55	0.07255936675461741	G	18.08	3.543094	0.65198	0.044377	0.06399	ENSG00000159314	ENST00000532038;ENST00000376922;ENST00000528384;ENST00000532891;ENST00000428638;ENST00000442348;ENST00000455881	T;T;T;T;T;T;T	0.09911	2.93;2.99;3.02;2.97;2.99;3.06;2.99	4.45	4.45	0.53987	.	0.311455	0.28772	N	0.014185	T	0.00271	0.0008	N	0.19112	0.55	0.09310	P	1.0	B;D	0.65815	0.358;0.995	B;D	0.72982	0.081;0.979	T	0.13575	-1.0504	9	0.72032	D	0.01	.	14.6134	0.68531	0.0:0.0:1.0:0.0	rs34793644	862;889	F8WBX1;Q6ZUM4	.;RHG27_HUMAN	Q	667;548;521;867;889;862;548	ENSP00000432762:H667Q;ENSP00000366121:H548Q;ENSP00000431591:H521Q;ENSP00000433942:H867Q;ENSP00000403323:H889Q;ENSP00000409330:H862Q;ENSP00000408235:H548Q	ENSP00000366121:H548Q	H	-	3	2	ARHGAP27	40828608	0.901000	0.30685	1.000000	0.80357	0.096000	0.18686	1.652000	0.37313	2.316000	0.78162	0.542000	0.68232	CAC	G|0.933;C|0.067	0.067	strong		0.682	ARHGAP27-202	KNOWN	basic	protein_coding	protein_coding		NM_199282	
OR10H5	284433	hgsc.bcm.edu	37	19	15905639	15905639	+	Silent	SNP	C	C	T	rs3746151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15905639C>T	ENST00000308940.8	+	1	879	c.781C>T	c.(781-783)Ctg>Ttg	p.L261L		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						CGTCATTTACCTGAAGCCCAA	0.567													.|||	764	0.152556	0.1422	0.1153	5008	,	,		17530	0.122		0.161	False		,,,				2504	0.2157				p.L261L		Atlas-SNP	.											.	OR10H5	49	.	0			c.C781T						PASS	.	C		680,3726		54,572,1577	108.0	86.0	94.0		781	3.9	1.0	19	dbSNP_107	94	1549,7051		150,1249,2901	no	coding-synonymous	OR10H5	NM_001004466.1		204,1821,4478	TT,TC,CC		18.0116,15.4335,17.1382		261/316	15905639	2229,10777	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			ATTTACCTGAAGC	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.781C>T	19.37:g.15905639C>T		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	181	80	0.441989	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			C|0.841;T|0.159	0.159	strong		0.567	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
CTSH	1512	hgsc.bcm.edu	37	15	79237247	79237247	+	Missense_Mutation	SNP	C	C	G	rs1036938	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79237247C>G	ENST00000220166.5	-	1	186	c.77G>C	c.(76-78)tGc>tCc	p.C26S		NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	26			C -> S (in dbSNP:rs1036938). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2587265}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						GGAGTTCACGCACAGTTCGGC	0.706													G|||	1940	0.38738	0.211	0.4179	5008	,	,		12407	0.0952		0.6839	False		,,,				2504	0.6002				p.C26S		Atlas-SNP	.											.	CTSH	23	.	0			c.G77C						PASS	.	G	SER/CYS	1162,2626		219,724,951	12.0	12.0	12.0		77	2.2	0.0	15	dbSNP_86	12	5510,2156		2046,1418,369	yes	missense	CTSH	NM_004390.3	112	2265,2142,1320	GG,GC,CC		28.1242,30.6758,41.7496	benign	26/336	79237247	6672,4782	1894	3833	5727	SO:0001583	missense	1512	exon1			TTCACGCACAGTT	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.77G>C	15.37:g.79237247C>G	ENSP00000220166:p.Cys26Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	848	0.3882783882783883	118	0.23983739837398374	174	0.48066298342541436	50	0.08741258741258741	506	0.6675461741424802	G	7.933	0.741161	0.15642	0.306758	0.718758	ENSG00000103811	ENST00000220166;ENST00000394758;ENST00000444399	T	0.70516	-0.49	3.12	2.16	0.27623	.	9.562280	0.00567	N	0.000297	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12630	0.006;0.0	B;B	0.01281	0.0;0.0	T	0.40720	-0.9548	9	0.06365	T	0.9	.	5.6349	0.17532	0.0:0.222:0.5491:0.2289	rs1036938;rs1130855;rs3177820;rs17856064;rs1036938	26;14	E9PF73;E9PBP2	.;.	S	26;14;26	ENSP00000220166:C26S	ENSP00000220166:C26S	C	-	2	0	CTSH	77024302	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.797000	0.26999	0.317000	0.23160	-0.322000	0.08575	TGC	C|0.624;G|0.376	0.376	strong		0.706	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
TNFSF13	8741	hgsc.bcm.edu	37	17	7462969	7462969	+	Missense_Mutation	SNP	A	A	G	rs3803800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7462969A>G	ENST00000338784.4	+	2	730	c.287A>G	c.(286-288)aAt>aGt	p.N96S	SENP3_ENST00000321337.7_5'Flank|TNFSF13_ENST00000380535.4_Intron|TNFSF12-TNFSF13_ENST00000293826.4_Missense_Mutation_p.N176S|TNFSF12_ENST00000557233.1_Missense_Mutation_p.N176S|SENP3_ENST00000429205.2_5'Flank|TNFSF13_ENST00000396545.4_Missense_Mutation_p.N96S|TNFSF13_ENST00000483039.1_Intron|TNFSF13_ENST00000349228.4_Missense_Mutation_p.N96S|TNFSF13_ENST00000396542.1_Intron	NM_003808.3	NP_003799.1	O75888	TNF13_HUMAN	tumor necrosis factor (ligand) superfamily, member 13	96			N -> S (in dbSNP:rs3803800). {ECO:0000269|PubMed:15489334}.		gene expression (GO:0010467)|immunoglobulin production in mucosal tissue (GO:0002426)|mRNA metabolic process (GO:0016071)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	receptor binding (GO:0005102)			large_intestine(2)|lung(2)|skin(1)	5		Prostate(122;0.157)				GCCTGGGAGAATGGGGAGAGA	0.592													A|||	2803	0.559704	0.2663	0.585	5008	,	,		17686	0.6498		0.7674	False		,,,				2504	0.6319				p.N176S		Atlas-SNP	.											.	TNFSF12-TNFSF13	16	.	0			c.A527G						PASS	.	A	,,,SER/ASN,SER/ASN,SER/ASN,SER/ASN	1663,2743	505.4+/-366.1	311,1041,851	60.0	52.0	55.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,,,287,287,287,527	2.3	1.0	17	dbSNP_107	55	6749,1851	728.8+/-406.7	2643,1463,194	yes	intron,intron,intron,missense,missense,missense,missense	TNFSF13,TNFSF12-TNFSF13	NM_001198622.1,NM_001198623.1,NM_001198624.1,NM_003808.3,NM_172087.2,NM_172088.2,NM_172089.3	,,,46,46,46,46	2954,2504,1045	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	21.5233,37.744,35.3222	,,,benign,benign,benign,benign	,,,96/251,96/235,96/248,176/331	7462969	8412,4594	2203	4300	6503	SO:0001583	missense	407977	exon7			GGGAGAATGGGGA	AF046888	CCDS11111.1, CCDS11112.1, CCDS42256.1, CCDS56019.1, CCDS73957.1	17p13.1	2007-07-23			ENSG00000161955	ENSG00000161955		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11928	protein-coding gene	gene with protein product		604472				9743536	Standard	NM_172088		Approved	APRIL, CD256		O75888	OTTHUMG00000108145	ENST00000338784.4:c.287A>G	17.37:g.7462969A>G	ENSP00000343505:p.Asn96Ser	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_172089	A8MYD5|B4DVT2|Q541E1|Q5U0G8|Q96HV6|Q9P1M8|Q9P1M9	Missense_Mutation	SNP	ENST00000338784.4	37	CCDS11111.1	1370	0.6272893772893773	142	0.2886178861788618	253	0.6988950276243094	386	0.6748251748251748	589	0.7770448548812665	A	10.94	1.491471	0.26774	0.37744	0.784767	ENSG00000239697;ENSG00000248871;ENSG00000161955;ENSG00000161955;ENSG00000161955;ENSG00000161955;ENSG00000161955	ENST00000557233;ENST00000293826;ENST00000438470;ENST00000436057;ENST00000349228;ENST00000338784;ENST00000396545	D;D;T;T;D;D;D	0.97303	-4.33;-4.33;1.47;1.49;-3.83;-3.79;-3.79	4.58	2.35	0.29111	.	0.989634	0.08235	N	0.976927	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.999999964161	B;B;B;B	0.19445	0.002;0.0;0.001;0.036	B;B;B;B	0.20577	0.005;0.001;0.002;0.03	T	0.48559	-0.9025	9	0.02654	T	1	-3.8371	6.0907	0.19993	0.7925:0.0:0.2075:0.0	rs3803800;rs17850296;rs59333674;rs3803800	96;96;96;176	O75888-2;O75888;O75888-3;Q8IZK7	.;TNF13_HUMAN;.;.	S	176;176;79;79;96;96;96	ENSP00000451451:N176S;ENSP00000293826:N176S;ENSP00000390771:N79S;ENSP00000410094:N79S;ENSP00000314455:N96S;ENSP00000343505:N96S;ENSP00000379794:N96S	ENSP00000293826:N176S	N	+	2	0	TNFSF13;TNFSF12-TNFSF13;TNFSF12	7403693	0.997000	0.39634	0.990000	0.47175	0.996000	0.88848	1.119000	0.31258	0.366000	0.24427	0.459000	0.35465	AAT	A|0.373;G|0.627	0.627	strong		0.592	TNFSF13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226948.2	NM_003808	
MAGEB16	139604	hgsc.bcm.edu	37	X	35820696	35820696	+	Missense_Mutation	SNP	G	G	A	rs1410962	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:35820696G>A	ENST00000399989.1	+	2	662	c.383G>A	c.(382-384)tGt>tAt	p.C128Y	MAGEB16_ENST00000399985.1_Missense_Mutation_p.C128Y|MAGEB16_ENST00000399987.1_Missense_Mutation_p.C128Y|MAGEB16_ENST00000399992.1_Missense_Mutation_p.C160Y|MAGEB16_ENST00000399988.1_Missense_Mutation_p.C128Y	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	128	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		C -> Y (in dbSNP:rs1410962).							breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						CTGCACAAGTGTCAGATGAAA	0.458													A|||	2341	0.620132	0.4478	0.4121	3775	,	,		17188	0.5694		0.4185	False		,,,				2504	0.4785				p.C128Y		Atlas-SNP	.											.	MAGEB16	64	.	0			c.G383A						PASS	.	A	TYR/CYS	1943,1385		494,648,307,237,263	59.0	56.0	57.0		383	3.1	0.0	X	dbSNP_88	57	3485,3016		688,1158,951,505,848	yes	missense	MAGEB16	NM_001099921.1	194	1182,1806,1258,742,1111	AA,AG,A,GG,G		46.3929,41.6166,44.7757	benign	128/325	35820696	5428,4401	1949	4150	6099	SO:0001583	missense	139604	exon2			ACAAGTGTCAGAT		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.383G>A	X.37:g.35820696G>A	ENSP00000382871:p.Cys128Tyr	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	1014	0.6112115732368897	151	0.4415204678362573	102	0.4146341463414634	212	0.5792349726775956	230	0.3885135135135135	A	0.007	-1.966782	0.00461	0.583834	0.536071	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04275	3.66;3.66;3.66;3.66;3.66	3.13	3.13	0.36017	.	0.108202	0.64402	N	0.000013	T	0.00012	0.0000	N	0.00009	-3.09	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37009	-0.9724	9	0.02654	T	1	.	4.6321	0.12507	0.8483:0.0:0.1517:0.0	rs1410962;rs17311179;rs61142141;rs1410962	128	A2A368	MAGBG_HUMAN	Y	128;160;128;128;128	ENSP00000382870:C128Y;ENSP00000382874:C160Y;ENSP00000382869:C128Y;ENSP00000382871:C128Y;ENSP00000382867:C128Y	ENSP00000382867:C128Y	C	+	2	0	MAGEB16	35730617	0.327000	0.24678	0.008000	0.14137	0.001000	0.01503	1.389000	0.34453	0.466000	0.27193	-0.426000	0.05927	TGT	0|0.006;A|0.623	0.623	strong		0.458	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
EI24	9538	hgsc.bcm.edu	37	11	125452313	125452313	+	Missense_Mutation	SNP	A	A	G	rs4627097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:125452313A>G	ENST00000343678.4	+	10	985	c.743A>G	c.(742-744)cAt>cGt	p.H248R	EI24_ENST00000278903.6_Silent_p.A285A|EI24_ENST00000530985.1_3'UTR|STT3A-AS1_ENST00000532714.1_RNA|STT3A-AS1_ENST00000530526.1_RNA	NM_001007277.1	NP_001007278.1	O14681	EI24_HUMAN	etoposide induced 2.4	0					apoptotic process (GO:0006915)|autophagy (GO:0006914)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of cell growth (GO:0030308)|neuromuscular process controlling balance (GO:0050885)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|response to drug (GO:0042493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(1)|lung(9)|ovary(1)	11	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		CTGGCAAAGCATAGTAAGTAT	0.343													G|||	1705	0.340455	0.3835	0.2594	5008	,	,		13966	0.2976		0.3658	False		,,,				2504	0.3579				p.I249V		Atlas-SNP	.											.	EI24	33	.	0			c.A745G						PASS	.	G	,ARG/HIS	1334,2298		248,838,730	35.0	34.0	34.0		857,745	-7.7	0.8	11	dbSNP_111	34	2872,5278		483,1906,1686	yes	coding-synonymous,missense	EI24	NM_004879.3,NM_001007277.1	,29	731,2744,2416	GG,GA,AA		35.2393,36.7291,35.6985	,benign	286/341,249/263	125452313	4206,7576	1816	4075	5891	SO:0001583	missense	9538	exon9			CAAAGCATAGTAA	AF010313	CCDS73410.1	11q24.2	2012-11-19	2012-11-16		ENSG00000149547	ENSG00000149547			13276	protein-coding gene	gene with protein product	"""ectopic P-granules autophagy protein 4 homolog (C. elegans)"""	605170	"""etoposide induced 2.4 mRNA"""			10594026, 9305847	Standard	NM_001290135		Approved	PIG8, TP53I8, EPG4	uc001qcb.3	O14681	OTTHUMG00000165851	ENST00000343678.4:c.743A>G	11.37:g.125452313A>G	ENSP00000364081:p.His248Arg	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_001007277	A8K7D6|B4DKL6|Q9BUQ1	Missense_Mutation	SNP	ENST00000343678.4	37		742	0.33974358974358976	199	0.40447154471544716	101	0.27900552486187846	165	0.28846153846153844	277	0.3654353562005277	G	9.401	1.078074	0.20227	0.367291	0.352393	ENSG00000149547	ENST00000343678	.	.	.	4.73	-7.71	0.01254	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41840	-0.9486	6	0.46703	T	0.11	.	6.6214	0.22806	0.3693:0.0:0.381:0.2496	rs4627097;rs17174519;rs59674749;rs4627097	248	A6NES3	.	R	248	.	ENSP00000364081:H248R	H	+	2	0	EI24	124957523	0.001000	0.12720	0.795000	0.32087	0.882000	0.50991	-1.460000	0.02368	-1.390000	0.02087	-1.951000	0.00486	CAT	A|0.658;G|0.342	0.342	strong		0.343	EI24-202	KNOWN	basic	protein_coding	protein_coding		NM_004879	
PRRC2A	7916	hgsc.bcm.edu	37	6	31605016	31605016	+	Missense_Mutation	SNP	T	T	C	rs35595439	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31605016T>C	ENST00000376033.2	+	30	6482	c.6248T>C	c.(6247-6249)tTc>tCc	p.F2083S	PRRC2A_ENST00000376007.4_Missense_Mutation_p.F2083S	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	2083	3 X 50 AA type C repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CTTAGGTCCTTCTCTGGCCTC	0.552													T|||	42	0.00838658	0.0068	0.0072	5008	,	,		17444	0.003		0.0099	False		,,,				2504	0.0153				p.F2083S		Atlas-SNP	.											.	PRRC2A	152	.	0			c.T6248C						PASS	.	T	SER/PHE,SER/PHE	10,3010		0,10,1500	86.0	81.0	83.0		6248,6248	5.6	1.0	6	dbSNP_126	83	41,5375		0,41,2667	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	155,155	0,51,4167	CC,CT,TT		0.757,0.3311,0.6046	probably-damaging,probably-damaging	2083/2158,2083/2158	31605016	51,8385	1510	2708	4218	SO:0001583	missense	7916	exon30			GGTCCTTCTCTGG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.6248T>C	6.37:g.31605016T>C	ENSP00000365201:p.Phe2083Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	T	11.20	1.569725	0.28003	0.003311	0.00757	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01871	4.59;4.59	5.63	5.63	0.86233	.	0.374635	0.24516	N	0.037848	T	0.01800	0.0057	N	0.19112	0.55	0.42923	D	0.994293	D	0.61697	0.99	P	0.51657	0.676	T	0.64193	-0.6465	10	0.87932	D	0	-0.0191	13.6537	0.62325	0.0:0.0:0.0:1.0	rs35595439	2083	P48634	PRC2A_HUMAN	S	2075;2064;2083;2083;1308	ENSP00000365175:F2083S;ENSP00000365201:F2083S	ENSP00000365175:F2083S	F	+	2	0	PRRC2A	31712995	1.000000	0.71417	0.999000	0.59377	0.774000	0.43823	2.456000	0.44997	2.271000	0.75665	0.533000	0.62120	TTC	T|0.993;C|0.007	0.007	strong		0.552	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
NDRG1	10397	hgsc.bcm.edu	37	8	134296524	134296524	+	Missense_Mutation	SNP	C	C	T	rs145871479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:134296524C>T	ENST00000414097.2	-	2	898	c.31G>A	c.(31-33)Gct>Act	p.A11T	NDRG1_ENST00000537882.1_5'UTR|NDRG1_ENST00000323851.7_Missense_Mutation_p.A11T|NDRG1_ENST00000518066.1_Missense_Mutation_p.A11T|NDRG1_ENST00000522476.1_Intron|NDRG1_ENST00000354944.5_Missense_Mutation_p.A11T|NDRG1_ENST00000518176.1_Missense_Mutation_p.A11T	NM_001135242.1	NP_001128714.1	Q92597	NDRG1_HUMAN	N-myc downstream regulated 1	11					cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|mast cell activation (GO:0045576)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of spindle checkpoint (GO:0090232)|response to metal ion (GO:0010038)	cell-cell adherens junction (GO:0005913)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	cadherin binding (GO:0045296)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|Rab GTPase binding (GO:0017137)		NDRG1/ERG(5)	endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(4)|prostate(1)|skin(1)	17	all_epithelial(106;4.26e-24)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			TTCACCTCAGCGAGGTCTACA	0.552			T	ERG	prostate								C|||	3	0.000599042	0.0	0.0014	5008	,	,		20508	0.0		0.002	False		,,,				2504	0.0				p.A11T		Atlas-SNP	.		Dom	yes		8	8q24.3	10397	N-myc downstream regulated 1		E	.	NDRG1	40	.	0			c.G31A						PASS	.	C	THR/ALA,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	234.0	169.0	191.0		31,31	5.0	0.4	8	dbSNP_134	191	15,8585	11.2+/-40.8	0,15,4285	yes	missense,missense	NDRG1	NM_001135242.1,NM_006096.3	58,58	0,18,6485	TT,TC,CC		0.1744,0.0681,0.1384	probably-damaging,probably-damaging	11/395,11/395	134296524	18,12988	2203	4300	6503	SO:0001583	missense	10397	exon2			CCTCAGCGAGGTC	X92845	CCDS34945.1, CCDS59112.1, CCDS59113.1	8q24	2014-09-17	2008-09-12		ENSG00000104419	ENSG00000104419			7679	protein-coding gene	gene with protein product		605262		CAP43		9251681, 8939898, 18455888	Standard	NM_006096		Approved	DRG1, RTP, TDD5, NDR1	uc003yue.2	Q92597	OTTHUMG00000164441	ENST00000414097.2:c.31G>A	8.37:g.134296524C>T	ENSP00000404854:p.Ala11Thr	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	213	117	0.549296	NM_006096	B3KR80|B7Z446|O15207|Q6IBG2|Q9NYR6|Q9UK29	Missense_Mutation	SNP	ENST00000414097.2	37	CCDS34945.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	6.861	0.528153	0.13127	6.81E-4	0.001744	ENSG00000104419	ENST00000323851;ENST00000537144;ENST00000354944;ENST00000414097;ENST00000518176;ENST00000518066;ENST00000520230;ENST00000519228;ENST00000519580;ENST00000522890;ENST00000520943;ENST00000521544;ENST00000522738	T;T;T;T;T;T;T;T;T;T	0.17854	2.44;2.51;2.44;2.35;2.41;2.39;2.39;2.35;2.39;2.25	5.03	5.03	0.67393	.	0.055881	0.64402	D	0.000001	T	0.21387	0.0515	N	0.17800	0.525	0.80722	D	1	D;B	0.76494	0.999;0.027	D;B	0.77004	0.989;0.011	T	0.01791	-1.1273	10	0.02654	T	1	-24.0443	13.7228	0.62737	0.0:1.0:0.0:0.0	.	11;11	E7ESM1;Q92597	.;NDRG1_HUMAN	T	11;11;11;11;11;11;28;11;11;11;22;11;65	ENSP00000319977:A11T;ENSP00000347028:A11T;ENSP00000404854:A11T;ENSP00000428345:A28T;ENSP00000429994:A11T;ENSP00000429272:A11T;ENSP00000428384:A11T;ENSP00000429840:A22T;ENSP00000429524:A11T;ENSP00000428991:A65T	ENSP00000319977:A11T	A	-	1	0	NDRG1	134365706	0.868000	0.29978	0.417000	0.26559	0.896000	0.52359	3.701000	0.54793	2.609000	0.88269	0.650000	0.86243	GCT	C|0.999;T|0.001	0.001	strong		0.552	NDRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378805.1		
CRYZ	1429	hgsc.bcm.edu	37	1	75172001	75172001	+	Silent	SNP	T	T	A	rs7527057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:75172001T>A	ENST00000340866.5	-	9	1056	c.969A>T	c.(967-969)ggA>ggT	p.G323G	CRYZ_ENST00000417775.1_Silent_p.G323G|CRYZ_ENST00000370871.3_Silent_p.G289G|CRYZ_ENST00000370872.3_Silent_p.G186G|CRYZ_ENST00000492102.1_5'UTR	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	323					protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	GAATCATTTTTCCAGTAGCCC	0.388													T|||	1084	0.216454	0.0348	0.3674	5008	,	,		16116	0.1091		0.4592	False		,,,				2504	0.2157				p.G323G		Atlas-SNP	.											.	CRYZ	28	.	0			c.A969T						PASS	.	T	,,,	470,3936	220.4+/-237.8	30,410,1763	94.0	94.0	94.0		969,867,558,969	-8.6	0.3	1	dbSNP_116	94	3966,4632	549.0+/-385.5	920,2126,1253	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRYZ	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001889.3	,,,	950,2536,3016	AA,AT,TT		46.127,10.6673,34.1126	,,,	323/330,289/296,186/193,323/330	75172001	4436,8568	2203	4299	6502	SO:0001819	synonymous_variant	1429	exon9			CATTTTTCCAGTA		CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.969A>T	1.37:g.75172001T>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	206	75	0.364078	NM_001889	A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Silent	SNP	ENST00000340866.5	37	CCDS665.1																																																																																			T|0.678;A|0.322	0.322	strong		0.388	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1		
CELSR2	1952	hgsc.bcm.edu	37	1	109810544	109810544	+	Silent	SNP	C	C	A	rs2281894	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109810544C>A	ENST00000271332.3	+	17	6241	c.6180C>A	c.(6178-6180)cgC>cgA	p.R2060R		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2060					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TGCTCCTGCGCAACGCCACGC	0.677													C|||	1131	0.225839	0.0537	0.2205	5008	,	,		18633	0.4206		0.1928	False		,,,				2504	0.2955				p.R2060R	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C6180A						PASS	.	C		313,4093	152.9+/-186.6	17,279,1907	29.0	29.0	29.0		6180	0.1	1.0	1	dbSNP_100	29	1603,6997	272.4+/-290.1	169,1265,2866	no	coding-synonymous	CELSR2	NM_001408.2		186,1544,4773	AA,AC,CC		18.6395,7.1039,14.7317		2060/2924	109810544	1916,11090	2203	4300	6503	SO:0001819	synonymous_variant	1952	exon17			CCTGCGCAACGCC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6180C>A	1.37:g.109810544C>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			C|0.824;A|0.176	0.176	strong		0.677	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
MAP10	54627	hgsc.bcm.edu	37	1	232941153	232941153	+	Silent	SNP	C	C	T	rs12409898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:232941153C>T	ENST00000418460.1	+	1	511	c.384C>T	c.(382-384)ttC>ttT	p.F128F		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	0					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										GCTTCAGCTTCTCGTTTGCGG	0.662													C|||	2641	0.527356	0.084	0.5879	5008	,	,		14834	0.6607		0.7097	False		,,,				2504	0.7587				p.F128F		Atlas-SNP	.											KIAA1383_ENST00000418460,NS,carcinoma,+2,2	.	.	2	0			c.C384T						PASS	.	C		728,3094		76,576,1259	19.0	21.0	20.0		384	1.8	0.0	1	dbSNP_120	20	5672,2558		1954,1764,397	no	coding-synonymous	KIAA1383	NM_019090.2		2030,2340,1656	TT,TC,CC		31.0814,19.0476,46.8968		128/1048	232941153	6400,5652	1911	4115	6026	SO:0001819	synonymous_variant	54627	exon1			CAGCTTCTCGTTT	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.384C>T	1.37:g.232941153C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	37	CCDS44334.1																																																																																			C|0.474;T|0.526	0.526	strong		0.662	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
MUC4	4585	hgsc.bcm.edu	37	3	195512212	195512212	+	Missense_Mutation	SNP	G	G	T	rs75588776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195512212G>T	ENST00000463781.3	-	2	6698	c.6239C>A	c.(6238-6240)cCt>cAt	p.P2080H	MUC4_ENST00000475231.1_Missense_Mutation_p.P2080H|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P2080H(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GACAAGAAGAGGGGTGGCGTG	0.567																																					p.P2080H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	stomach(2)	c.C6239A						PASS	.						18.0	20.0	19.0					3																	195512212		684	1571	2255	SO:0001583	missense	4585	exon2			AGAAGAGGGGTGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6239C>A	3.37:g.195512212G>T	ENSP00000417498:p.Pro2080His	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	517	137	0.26499	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	3.566	-0.088623	0.07097	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32988	1.43;1.45	.	.	.	.	.	.	.	.	T	0.11495	0.0280	N	0.08118	0	0.09310	N	1	B	0.22909	0.077	B	0.06405	0.002	T	0.28744	-1.0034	7	.	.	.	.	2.8356	0.05513	3.0E-4:2.0E-4:0.5012:0.4983	.	2080	E7ESK3	.	H	2080	ENSP00000417498:P2080H;ENSP00000420243:P2080H	.	P	-	2	0	MUC4	196996607	0.000000	0.05858	0.053000	0.19242	0.070000	0.16714	0.024000	0.13555	0.064000	0.16427	0.064000	0.15345	CCT	G|0.816;T|0.185	0.185	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC24A3	57419	hgsc.bcm.edu	37	20	19565671	19565671	+	Silent	SNP	G	G	A	rs17293432	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:19565671G>A	ENST00000328041.6	+	5	677	c.480G>A	c.(478-480)tcG>tcA	p.S160S		NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	160					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CGGGAAGTTCGGCCCCAGAGC	0.552													G|||	185	0.0369409	0.0454	0.0504	5008	,	,		16242	0.0		0.0716	False		,,,				2504	0.0184				p.S160S		Atlas-SNP	.											.	SLC24A3	92	.	0			c.G480A						PASS	.	G		249,4157	144.2+/-179.2	8,233,1962	97.0	83.0	88.0		480	-8.7	0.9	20	dbSNP_123	88	792,7808	185.7+/-233.4	46,700,3554	no	coding-synonymous	SLC24A3	NM_020689.3		54,933,5516	AA,AG,GG		9.2093,5.6514,8.004		160/645	19565671	1041,11965	2203	4300	6503	SO:0001819	synonymous_variant	57419	exon5			AAGTTCGGCCCCA	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"""Solute carriers"""	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.480G>A	20.37:g.19565671G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Silent	SNP	ENST00000328041.6	37	CCDS13140.1																																																																																			G|0.931;A|0.069	0.069	strong		0.552	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689	
ITIH6	347365	hgsc.bcm.edu	37	X	54781530	54781530	+	Missense_Mutation	SNP	C	C	G	rs17316491	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:54781530C>G	ENST00000218436.6	-	9	3151	c.3122G>C	c.(3121-3123)tGg>tCg	p.W1041S		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1041			W -> S (in dbSNP:rs17316491).		hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										ATTGCCATCCCAGTTTGGACT	0.493													C|||	131	0.034702	0.0045	0.0389	3775	,	,		13733	0.0		0.0875	False		,,,				2504	0.0102				p.W1041S		Atlas-SNP	.											.	.	.	.	0			c.G3122C						PASS	.	C	SER/TRP	48,3787		0,43,5,1589,566	92.0	76.0	81.0		3122	1.6	0.1	X	dbSNP_123	81	639,6089		21,413,184,1994,1688	yes	missense	ITIH5L	NM_198510.2	177	21,456,189,3583,2254	GG,GC,G,CC,C		9.4976,1.2516,6.5038	probably-damaging	1041/1314	54781530	687,9876	2203	4300	6503	SO:0001583	missense	347365	exon9			CCATCCCAGTTTG	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3122G>C	X.37:g.54781530C>G	ENSP00000218436:p.Trp1041Ser	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	97	0.05846895720313442	5	0.010245901639344262	11	0.031073446327683617	0	0.0	54	0.07563025210084033	C	3.999	-0.002876	0.07773	0.012516	0.094976	ENSG00000102313	ENST00000218436	T	0.02323	4.34	1.58	1.58	0.23477	.	0.763532	0.10135	U	0.711568	T	0.00109	0.0003	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	P	0.48694	0.914	B	0.35240	0.198	T	0.48559	-0.9025	9	0.22706	T	0.39	.	6.0319	0.19684	0.0:1.0:0.0:0.0	rs17316491;rs52814299;rs17316491	1041	Q6UXX5	ITH5L_HUMAN	S	1041	ENSP00000218436:W1041S	ENSP00000218436:W1041S	W	-	2	0	ITIH5L	54798255	0.713000	0.27926	0.062000	0.19696	0.473000	0.32948	2.380000	0.44327	1.069000	0.40788	0.287000	0.19450	TGG	C|0.935;0|0.004	.	strong		0.493	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
PLAC8L1	153770	hgsc.bcm.edu	37	5	145477855	145477855	+	Splice_Site	SNP	T	T	C	rs6877277	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145477855T>C	ENST00000311450.4	-	2	177	c.120A>G	c.(118-120)agA>agG	p.R40R	RP11-118M9.3_ENST00000514002.1_RNA	NM_001029869.1	NP_001025040.1	A1L4L8	PL8L1_HUMAN	PLAC8-like 1	40								p.R40R(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|stomach(2)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTACATGGCCTCTGGAGAGTC	0.507													C|||	1090	0.217652	0.1324	0.3991	5008	,	,		17131	0.1984		0.2545	False		,,,				2504	0.1861				p.R40R		Atlas-SNP	.											PLAC8L1,NS,carcinoma,0,1	PLAC8L1	17	1	1	Substitution - coding silent(1)	stomach(1)	c.A120G						PASS	.	C		787,3619	751.2+/-412.2	73,641,1489	64.0	59.0	61.0		120	4.6	0.9	5	dbSNP_116	61	2413,6187	698.3+/-405.0	354,1705,2241	yes	coding-synonymous-near-splice	PLAC8L1	NM_001029869.1		427,2346,3730	CC,CT,TT		28.0581,17.862,24.604		40/178	145477855	3200,9806	2203	4300	6503	SO:0001630	splice_region_variant	153770	exon2			ATGGCCTCTGGAG		CCDS34264.1	5q32	2008-02-05			ENSG00000173261	ENSG00000173261			31746	protein-coding gene	gene with protein product							Standard	XM_005268381		Approved		uc003lnv.3	A1L4L8	OTTHUMG00000163418	ENST00000311450.4:c.120-1A>G	5.37:g.145477855T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_001029869		Silent	SNP	ENST00000311450.4	37	CCDS34264.1																																																																																			T|0.766;C|0.234	0.234	strong		0.507	PLAC8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373290.1	XM_087761	Silent
MUC4	4585	hgsc.bcm.edu	37	3	195508060	195508060	+	Missense_Mutation	SNP	G	G	A	rs200799263		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508060G>A	ENST00000463781.3	-	2	10850	c.10391C>T	c.(10390-10392)tCa>tTa	p.S3464L	MUC4_ENST00000475231.1_Missense_Mutation_p.S3464L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTGGATGCTGAGGAAGTGTC	0.582																																					p.S3464L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C10391T						PASS	.						27.0	23.0	24.0					3																	195508060		680	1581	2261	SO:0001583	missense	4585	exon2			GATGCTGAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10391C>T	3.37:g.195508060G>A	ENSP00000417498:p.Ser3464Leu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	296	21	0.0709459	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.692	0.496377	0.12762	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28069	1.63;1.64	0.743	-1.49	0.08718	.	.	.	.	.	T	0.29389	0.0732	N	0.19112	0.55	0.09310	N	1	D	0.56968	0.978	D	0.65443	0.935	T	0.19712	-1.0297	8	.	.	.	.	3.8921	0.09123	0.0:0.0:0.3778:0.6221	.	3336	E7ESK3	.	L	3464	ENSP00000417498:S3464L;ENSP00000420243:S3464L	.	S	-	2	0	MUC4	196992839	0.001000	0.12720	0.130000	0.21974	0.131000	0.20780	0.570000	0.23653	0.088000	0.17205	0.089000	0.15464	TCA	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CROCC	9696	hgsc.bcm.edu	37	1	17271989	17271989	+	Missense_Mutation	SNP	G	G	A	rs147139590	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17271989G>A	ENST00000375541.5	+	15	2093	c.2024G>A	c.(2023-2025)cGc>cAc	p.R675H	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GAAGGGAAGCGCTCAGTCCTG	0.647																																					p.R675H		Atlas-SNP	.											.	CROCC	185	.	0			c.G2024A						PASS	.						23.0	18.0	20.0					1																	17271989		2201	4284	6485	SO:0001583	missense	9696	exon15			GGAAGCGCTCAGT	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2024G>A	1.37:g.17271989G>A	ENSP00000364691:p.Arg675His	Somatic	583	0	0		WXS	Illumina HiSeq	Phase_I	637	281	0.44113	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	47	0.02152014652014652	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	37	0.048812664907651716	G	11.17	1.560701	0.27827	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.10005	2.92	5.01	4.09	0.47781	.	.	.	.	.	T	0.01156	0.0038	L	0.46157	1.445	0.32904	D	0.513603	B;B	0.34226	0.443;0.41	B;B	0.24701	0.055;0.033	T	0.06899	-1.0801	9	0.27785	T	0.31	.	7.4062	0.26991	0.0874:0.0:0.7426:0.17	.	538;675	A1L0S8;Q5TZA2	.;CROCC_HUMAN	H	675;556	ENSP00000364691:R675H	ENSP00000364691:R675H	R	+	2	0	CROCC	17144576	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.548000	0.36201	2.712000	0.92718	0.561000	0.74099	CGC	G|0.974;A|0.026	0.026	strong		0.647	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
GSTM3	2947	hgsc.bcm.edu	37	1	110279701	110279701	+	Missense_Mutation	SNP	C	C	T	rs7483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110279701C>T	ENST00000540225.1	-	9	980	c.670G>A	c.(670-672)Gta>Ata	p.V224I	GSTM3_ENST00000256594.3_Missense_Mutation_p.V224I|RP4-735C1.4_ENST00000431955.1_RNA|GSTM3_ENST00000361066.2_Missense_Mutation_p.V224I|GSTM3_ENST00000488824.1_5'UTR			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	224			V -> I (in dbSNP:rs7483). {ECO:0000269|PubMed:15489334}.		cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	GCTCAGCATACAGGCTTGTTG	0.478													C|||	1806	0.360623	0.0628	0.4035	5008	,	,		20552	0.7252		0.2962	False		,,,				2504	0.4233				p.V224I		Atlas-SNP	.											.	GSTM3	21	.	0			c.G670A						PASS	.	C	ILE/VAL	493,3913	228.8+/-243.5	29,435,1739	93.0	81.0	85.0		670	-5.2	0.0	1	dbSNP_52	85	2550,6050	416.3+/-352.1	377,1796,2127	yes	missense	GSTM3	NM_000849.4	29	406,2231,3866	TT,TC,CC		29.6512,11.1893,23.3969	benign	224/226	110279701	3043,9963	2203	4300	6503	SO:0001583	missense	2947	exon9			AGCATACAGGCTT	BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4635	protein-coding gene	gene with protein product		138390	"""glutathione S-transferase M3 (brain)"""			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.670G>A	1.37:g.110279701C>T	ENSP00000444978:p.Val224Ile	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	159	99	0.622642	NM_000849	O60550|Q96HA3	Missense_Mutation	SNP	ENST00000540225.1	37	CCDS812.1	829	0.37957875457875456	42	0.08536585365853659	132	0.36464088397790057	420	0.7342657342657343	235	0.3100263852242744	C	0.011	-1.711288	0.00712	0.111893	0.296512	ENSG00000134202	ENST00000540225;ENST00000256594;ENST00000361066	T;T;T	0.01397	4.94;4.94;4.94	5.29	-5.25	0.02781	.	1.179520	0.05914	N	0.632318	T	0.00144	0.0004	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45440	-0.9261	9	0.02654	T	1	-16.1483	1.767	0.03004	0.2593:0.3854:0.1323:0.223	rs7483;rs3167664;rs17845187;rs17857997;rs52802282;rs58618587;rs7483	230;224	Q59EJ5;P21266	.;GSTM3_HUMAN	I	224	ENSP00000444978:V224I;ENSP00000256594:V224I;ENSP00000354357:V224I	ENSP00000256594:V224I	V	-	1	0	GSTM3	110081224	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.859000	0.01657	-0.786000	0.04516	-0.982000	0.02568	GTA	C|0.700;T|0.300	0.300	strong		0.478	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849	
CYP2C9	1559	hgsc.bcm.edu	37	10	96740981	96740981	+	Missense_Mutation	SNP	C	C	T	rs28371685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96740981C>T	ENST00000260682.6	+	7	1015	c.1003C>T	c.(1003-1005)Cgg>Tgg	p.R335W		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	335			R -> W (in allele CYP2C9*11; dbSNP:rs28371685). {ECO:0000269|PubMed:11926893, ECO:0000269|PubMed:15469410}.		arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TGGCAGAAACCGGAGCCCCTG	0.498													C|||	36	0.0071885	0.0242	0.0014	5008	,	,		17934	0.0		0.002	False		,,,				2504	0.001				p.R335W	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											CYP2C9,NS,carcinoma,-1,1	CYP2C9	82	1	0			c.C1003T	GRCh37	CM056574	CYP2C9	M	rs28371685	scavenged	.	C	TRP/ARG	84,4322		0,84,2119	164.0	146.0	152.0		1003	2.8	0.9	10	dbSNP_125	152	16,8584		0,16,4284	no	missense	CYP2C9	NM_000771.3	101	0,100,6403	TT,TC,CC		0.186,1.9065,0.7689	probably-damaging	335/491	96740981	100,12906	2203	4300	6503	SO:0001583	missense	1559	exon7			AGAAACCGGAGCC	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"""Cytochrome P450s"""	2623	protein-coding gene	gene with protein product		601130	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"""	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.1003C>T	10.37:g.96740981C>T	ENSP00000260682:p.Arg335Trp	Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	199	107	0.537688	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	.	12.02	1.813765	0.32053	0.019065	0.00186	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.71698	-0.59	3.78	2.85	0.33270	.	0.293574	0.27035	U	0.021241	T	0.74772	0.3760	H	0.97186	3.955	0.18873	N	0.999988	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.73905	-0.3835	10	0.87932	D	0	.	10.7287	0.46083	0.191:0.809:0.0:0.0	rs28371685;rs60219528	335;335	Q5VX92;P11712	.;CP2C9_HUMAN	W	335	ENSP00000260682:R335W	ENSP00000260682:R335W	R	+	1	2	CYP2C9	96730971	0.615000	0.27026	0.866000	0.34008	0.172000	0.22775	1.328000	0.33758	0.910000	0.36722	0.305000	0.20034	CGG	C|0.986;T|0.014	0.014	strong		0.498	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771	
DNAH9	1770	hgsc.bcm.edu	37	17	11833365	11833365	+	Silent	SNP	G	G	A	rs1859887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11833365G>A	ENST00000262442.4	+	63	12128	c.12060G>A	c.(12058-12060)acG>acA	p.T4020T	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Intron|DNAH9_ENST00000608377.1_Silent_p.T332T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4020	AAA 6. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGCCCCCCACGGGCATGCATG	0.602													G|||	1109	0.221446	0.0779	0.2637	5008	,	,		18928	0.1796		0.34	False		,,,				2504	0.3067				p.T4020T		Atlas-SNP	.											.	DNAH9	695	.	0			c.G12060A						PASS	.	G	,	491,3915	227.5+/-242.7	33,425,1745	67.0	55.0	59.0		12060,996	-10.4	0.1	17	dbSNP_92	59	2855,5745	447.1+/-361.4	482,1891,1927	no	coding-synonymous,coding-synonymous	DNAH9	NM_001372.3,NM_004662.2	,	515,2316,3672	AA,AG,GG		33.1977,11.1439,25.7266	,	4020/4487,332/799	11833365	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon63			CCCCACGGGCATG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.12060G>A	17.37:g.11833365G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	201	80	0.39801	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.743;A|0.257	0.257	strong		0.602	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
AGRN	375790	hgsc.bcm.edu	37	1	990280	990280	+	Silent	SNP	C	C	T	rs4275402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:990280C>T	ENST00000379370.2	+	36	6107	c.6057C>T	c.(6055-6057)gaC>gaT	p.D2019D	RP11-54O7.14_ENST00000418300.1_RNA	NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	2041	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		GCTTGCGGGACGTGGTGGTGG	0.716													C|||	2931	0.585264	0.2617	0.7262	5008	,	,		12314	0.8214		0.6779	False		,,,				2504	0.5838				p.D2019D		Atlas-SNP	.											.	AGRN	110	.	0			c.C6057T						PASS	.	C		1425,2865		267,891,987	12.0	14.0	14.0		6057	-6.2	1.0	1	dbSNP_111	14	5921,2473		2175,1571,451	no	coding-synonymous	AGRN	NM_198576.3		2442,2462,1438	TT,TC,CC		29.4615,33.2168,42.0845		2019/2046	990280	7346,5338	2145	4197	6342	SO:0001819	synonymous_variant	375790	exon36			GCGGGACGTGGTG	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.6057C>T	1.37:g.990280C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			C|0.412;T|0.588	0.588	strong		0.716	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
SMYD1	150572	hgsc.bcm.edu	37	2	88387403	88387403	+	Silent	SNP	C	C	A	rs1542088	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:88387403C>A	ENST00000419482.2	+	3	422	c.337C>A	c.(337-339)Cgg>Agg	p.R113R	SMYD1_ENST00000468008.1_3'UTR|SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.R113R	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	113	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						CATCATGTGGCGGGTGGAGAG	0.607													C|||	2556	0.510383	0.0908	0.6023	5008	,	,		15642	0.9097		0.506	False		,,,				2504	0.6053				p.R113R		Atlas-SNP	.											SMYD1,NS,carcinoma,0,1	SMYD1	95	1	0			c.C337A						PASS	.						37.0	35.0	36.0					2																	88387403		2201	4300	6501	SO:0001819	synonymous_variant	150572	exon3			ATGTGGCGGGTGG	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.337C>A	2.37:g.88387403C>A		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	271	146	0.538745	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			C|0.449;A|0.551	0.551	strong		0.607	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
DPY19L3	147991	hgsc.bcm.edu	37	19	32930069	32930069	+	Silent	SNP	G	G	A	rs6510249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:32930069G>A	ENST00000342179.5	+	7	863	c.648G>A	c.(646-648)gcG>gcA	p.A216A	DPY19L3_ENST00000586987.1_Silent_p.A216A|DPY19L3_ENST00000392250.2_Silent_p.A216A	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	216						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					AGAACTGGGCGCTGCCATTCT	0.358													G|||	2738	0.546725	0.4334	0.4294	5008	,	,		18366	0.6399		0.6402	False		,,,				2504	0.591				p.A216A		Atlas-SNP	.											.	DPY19L3	70	.	0			c.G648A						PASS	.	G	,	2049,2357	568.4+/-382.4	485,1079,639	161.0	159.0	159.0		648,648	-6.8	0.9	19	dbSNP_116	159	5346,3254	649.9+/-400.7	1637,2072,591	no	coding-synonymous,coding-synonymous	DPY19L3	NM_001172774.1,NM_207325.2	,	2122,3151,1230	AA,AG,GG		37.8372,46.5048,43.1416	,	216/717,216/717	32930069	7395,5611	2203	4300	6503	SO:0001819	synonymous_variant	147991	exon7			CTGGGCGCTGCCA		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.648G>A	19.37:g.32930069G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	137	60	0.437956	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	37	CCDS12422.1																																																																																			G|0.425;A|0.575	0.575	strong		0.358	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
SRGN	5552	hgsc.bcm.edu	37	10	70856852	70856852	+	Missense_Mutation	SNP	G	G	A	rs2229498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:70856852G>A	ENST00000242465.3	+	2	132	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	SRGN_ENST00000462445.1_Intron	NM_002727.2	NP_002718.2	P10124	SRGN_HUMAN	serglycin	31			R -> Q (in dbSNP:rs2805910). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2180935, ECO:0000269|PubMed:2798108, ECO:0000269|PubMed:2835370, ECO:0000269|Ref.7}.		biomineral tissue development (GO:0031214)|blood coagulation (GO:0007596)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|maintenance of granzyme B location in T cell secretory granule (GO:0033382)|maintenance of protease location in mast cell secretory granule (GO:0033373)|mast cell secretory granule organization (GO:0033364)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine secretion (GO:0050710)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein processing (GO:0016485)|T cell secretory granule organization (GO:0033371)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|platelet alpha granule lumen (GO:0031093)|zymogen granule (GO:0042588)				large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(3)	7						TATCCTACGCGGAGAGCCAGG	0.423													A|||	2953	0.589657	0.348	0.6066	5008	,	,		16497	0.503		0.8499	False		,,,				2504	0.726				p.R31Q		Atlas-SNP	.											.	SRGN	15	.	0			c.G92A						PASS	.	A	GLN/ARG	1855,2551	632.7+/-395.9	396,1063,744	81.0	70.0	74.0		92	-1.0	0.3	10	dbSNP_100	74	7255,1345	261.3+/-283.8	3067,1121,112	yes	missense	SRGN	NM_002727.2	43	3463,2184,856	AA,AG,GG		15.6395,42.1017,29.9554	benign	31/159	70856852	9110,3896	2203	4300	6503	SO:0001583	missense	5552	exon2			CTACGCGGAGAGC	BC015516	CCDS7285.1	10q22.1	2007-02-16	2007-02-15	2007-02-15	ENSG00000122862	ENSG00000122862		"""Proteoglycans / Extracellular Matrix : Other"""	9361	protein-coding gene	gene with protein product	"""serglycin proteoglycan"""	177040	"""proteoglycan 1, secretory granule"""	PRG, PRG1			Standard	NR_036430		Approved	PPG	uc001joz.3	P10124	OTTHUMG00000018369	ENST00000242465.3:c.92G>A	10.37:g.70856852G>A	ENSP00000242465:p.Arg31Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_002727	B2R4L7|Q5VW06	Missense_Mutation	SNP	ENST00000242465.3	37	CCDS7285.1	1330	0.6089743589743589	153	0.31097560975609756	235	0.649171270718232	300	0.5244755244755245	642	0.8469656992084432	A	3.514	-0.099143	0.07010	0.421017	0.843605	ENSG00000122862	ENST00000242465	T	0.49139	0.79	5.28	-0.986	0.10252	.	0.938118	0.08934	N	0.872598	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.25206	0.12	B	0.21546	0.035	T	0.36065	-0.9763	9	0.05833	T	0.94	-10.4006	10.3335	0.43837	0.4802:0.0:0.5198:0.0	rs41528448	31	P10124	SRGN_HUMAN	Q	31	ENSP00000242465:R31Q	ENSP00000242465:R31Q	R	+	2	0	SRGN	70526858	0.571000	0.26659	0.282000	0.24776	0.143000	0.21401	-0.356000	0.07661	-0.372000	0.07992	-1.282000	0.01380	CGG	G|0.351;A|0.649	0.649	strong		0.423	SRGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048379.1	NM_002727	
CCDC9	26093	hgsc.bcm.edu	37	19	47774772	47774772	+	Missense_Mutation	SNP	T	T	C	rs888836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47774772T>C	ENST00000221922.6	+	12	1655	c.1433T>C	c.(1432-1434)cTg>cCg	p.L478P		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	478			L -> P (in dbSNP:rs888836).				poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		GAGCCCCTGCTGGAGCCCCAG	0.677													C|||	2564	0.511981	0.3396	0.5836	5008	,	,		12240	0.6825		0.4304	False		,,,				2504	0.6022				p.L478P		Atlas-SNP	.											.	CCDC9	37	.	0			c.T1433C						PASS	.	C	PRO/LEU	1400,3006		234,932,1037	49.0	59.0	56.0		1433	0.7	0.0	19	dbSNP_86	56	3759,4841		834,2091,1375	no	missense	CCDC9	NM_015603.2	98	1068,3023,2412	CC,CT,TT		43.7093,31.7749,39.6663	benign	478/532	47774772	5159,7847	2203	4300	6503	SO:0001583	missense	26093	exon12			CCCTGCTGGAGCC	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1433T>C	19.37:g.47774772T>C	ENSP00000221922:p.Leu478Pro	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	1106	0.5064102564102564	190	0.3861788617886179	200	0.5524861878453039	374	0.6538461538461539	342	0.45118733509234826	.	2.454	-0.325757	0.05350	0.317749	0.437093	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.22134	1.97	3.14	0.712	0.18167	.	0.524747	0.16680	N	0.203984	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30238	-0.9985	9	0.10902	T	0.67	-0.2533	2.6765	0.05082	0.3097:0.4044:0.0:0.2859	rs888836;rs58257475;rs888836	478	Q9Y3X0	CCDC9_HUMAN	P	478;460	ENSP00000221922:L478P	ENSP00000221922:L478P	L	+	2	0	CCDC9	52466612	0.000000	0.05858	0.004000	0.12327	0.118000	0.20060	-0.293000	0.08320	0.087000	0.17167	-0.817000	0.03123	CTG	T|0.563;C|0.437	0.437	strong		0.677	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
SPATA9	83890	hgsc.bcm.edu	37	5	94994339	94994339	+	Silent	SNP	A	A	G	rs10705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94994339A>G	ENST00000274432.8	-	5	894	c.753T>C	c.(751-753)aaT>aaC	p.N251N	SPATA9_ENST00000477047.2_Intron|RFESD_ENST00000508206.1_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	251					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		AGATTTGCTCATTCATTTCAG	0.348													A|||	640	0.127796	0.0234	0.1614	5008	,	,		17497	0.127		0.2326	False		,,,				2504	0.138				p.N251N		Atlas-SNP	.											.	SPATA9	17	.	0			c.T753C						PASS	.	A		220,4186	127.8+/-164.7	6,208,1989	74.0	76.0	75.0		753	2.9	0.9	5	dbSNP_52	75	1801,6795	321.8+/-315.3	195,1411,2692	no	coding-synonymous	SPATA9	NM_031952.3		201,1619,4681	GG,GA,AA		20.9516,4.9932,15.5438		251/255	94994339	2021,10981	2203	4298	6501	SO:0001819	synonymous_variant	83890	exon5			TTGCTCATTCATT	AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.753T>C	5.37:g.94994339A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	157	76	0.484076	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Silent	SNP	ENST00000274432.8	37	CCDS4076.1																																																																																			A|0.846;G|0.154	0.154	strong		0.348	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952	
PITRM1	10531	hgsc.bcm.edu	37	10	3191823	3191823	+	Missense_Mutation	SNP	C	C	T	rs2388556	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:3191823C>T	ENST00000224949.4	-	16	1895	c.1861G>A	c.(1861-1863)Gtc>Atc	p.V621I	PITRM1_ENST00000380994.1_Missense_Mutation_p.V179I|PITRM1_ENST00000380989.2_Missense_Mutation_p.V621I|PITRM1_ENST00000451104.2_Missense_Mutation_p.V589I|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000464395.1_5'Flank|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	621			V -> I (in dbSNP:rs2388556). {ECO:0000269|PubMed:10360838}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TTGGTGAGGACGCTGCAGAAG	0.517													C|||	579	0.115615	0.1346	0.0893	5008	,	,		15779	0.0536		0.1571	False		,,,				2504	0.1299				p.V621I		Atlas-SNP	.											.	PITRM1	109	.	0			c.G1861A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	532,3574		45,442,1566	185.0	189.0	188.0		1861,1765,1861	4.5	1.0	10	dbSNP_100	188	1444,6974		128,1188,2893	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	29,29,29	173,1630,4459	TT,TC,CC		17.1537,12.9566,15.7777	possibly-damaging,possibly-damaging,possibly-damaging	621/1039,589/940,621/1038	3191823	1976,10548	2053	4209	6262	SO:0001583	missense	10531	exon16			TGAGGACGCTGCA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1861G>A	10.37:g.3191823C>T	ENSP00000224949:p.Val621Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	245	0.11217948717948718	58	0.11788617886178862	38	0.10497237569060773	30	0.05244755244755245	119	0.15699208443271767	c	23.1	4.376667	0.82682	0.129566	0.171537	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.22336	1.96;1.96;1.96;2.17	5.41	4.51	0.55191	Peptidase M16C associated (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.057779	0.64402	D	0.000001	T	0.00109	0.0003	M	0.71036	2.16	0.09310	P	0.9999943181	P;P;D;D	0.56287	0.792;0.9;0.975;0.975	B;P;P;P	0.55222	0.177;0.459;0.771;0.771	T	0.04115	-1.0976	9	0.33940	T	0.23	.	13.8585	0.63545	0.0:0.9265:0.0:0.0735	rs2388556;rs59691732;rs2388556	614;589;621;621	E9PDX6;E7ES23;C9JSL2;Q5JRX3	.;.;.;PREP_HUMAN	I	621;614;621;179;589	ENSP00000224949:V621I;ENSP00000370377:V621I;ENSP00000370382:V179I;ENSP00000401201:V589I	ENSP00000224949:V621I	V	-	1	0	PITRM1	3181823	1.000000	0.71417	0.982000	0.44146	0.973000	0.67179	5.780000	0.68956	1.294000	0.44707	0.555000	0.69702	GTC	C|0.892;T|0.108	0.108	strong		0.517	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
WNT10A	80326	hgsc.bcm.edu	37	2	219754822	219754822	+	Missense_Mutation	SNP	G	G	A	rs77583146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219754822G>A	ENST00000258411.3	+	3	1126	c.493G>A	c.(493-495)Ggg>Agg	p.G165R		NM_025216.2	NP_079492.2	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family, member 10A	165					cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|epidermis morphogenesis (GO:0048730)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|neural crest cell differentiation (GO:0014033)|neuron differentiation (GO:0030182)|odontogenesis (GO:0042476)|positive regulation of gene expression (GO:0010628)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sebaceous gland development (GO:0048733)|skin development (GO:0043588)|tongue development (GO:0043586)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|cervix(1)|endometrium(2)|lung(6)|skin(2)	12		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCCCGGCGAGGGGACGAGGA	0.642													G|||	11	0.00219649	0.0015	0.0014	5008	,	,		18771	0.0		0.007	False		,,,				2504	0.001				p.G165R		Atlas-SNP	.											.	WNT10A	35	.	0			c.G493A						PASS	.	G	ARG/GLY	10,4396	16.8+/-37.8	0,10,2193	68.0	56.0	60.0		493	4.5	1.0	2	dbSNP_131	60	92,8508	51.1+/-111.2	0,92,4208	yes	missense	WNT10A	NM_025216.2	125	0,102,6401	AA,AG,GG		1.0698,0.227,0.7843	probably-damaging	165/418	219754822	102,12904	2203	4300	6503	SO:0001583	missense	80326	exon3			CGGCGAGGGGACG	AB059569	CCDS2426.1	2q35	2008-05-23			ENSG00000135925	ENSG00000135925		"""Wingless-type MMTV integration sites"""	13829	protein-coding gene	gene with protein product		606268				11350055, 17847007	Standard	NM_025216		Approved		uc002vjd.1	Q9GZT5	OTTHUMG00000133085	ENST00000258411.3:c.493G>A	2.37:g.219754822G>A	ENSP00000258411:p.Gly165Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_025216	Q53S44|Q96TA7|Q9H7S8	Missense_Mutation	SNP	ENST00000258411.3	37	CCDS2426.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	16.51	3.143104	0.57044	0.00227	0.010698	ENSG00000135925	ENST00000258411	T	0.76060	-0.99	4.46	4.46	0.54185	.	0.457875	0.21825	N	0.068570	T	0.69296	0.3095	M	0.66297	2.02	0.80722	D	1	B	0.24576	0.106	B	0.31751	0.135	T	0.74444	-0.3663	10	0.59425	D	0.04	.	16.2054	0.82126	0.0:0.0:1.0:0.0	.	165	Q9GZT5	WN10A_HUMAN	R	165	ENSP00000258411:G165R	ENSP00000258411:G165R	G	+	1	0	WNT10A	219463066	1.000000	0.71417	0.989000	0.46669	0.487000	0.33371	7.398000	0.79919	2.478000	0.83669	0.655000	0.94253	GGG	G|0.993;A|0.007	0.007	strong		0.642	WNT10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256730.2	NM_025216	
MON1B	22879	hgsc.bcm.edu	37	16	77228866	77228866	+	Silent	SNP	T	T	C	rs2232504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:77228866T>C	ENST00000248248.3	+	4	1460	c.1110T>C	c.(1108-1110)gtT>gtC	p.V370V	MON1B_ENST00000545553.1_Silent_p.V224V|MON1B_ENST00000320859.6_Intron|MON1B_ENST00000439557.2_Silent_p.V261V	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	370										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						GGCGCCTGGTTGAAGATGGGA	0.637													C|||	3900	0.778754	0.9107	0.755	5008	,	,		17923	0.8651		0.5835	False		,,,				2504	0.729				p.V370V		Atlas-SNP	.											MON1B,NS,carcinoma,+2,1	MON1B	55	1	0			c.T1110C						PASS	.	C		3803,593	258.9+/-262.7	1645,513,40	60.0	57.0	58.0		1110	-9.6	0.1	16	dbSNP_98	58	5138,3462	505.9+/-376.5	1524,2090,686	no	coding-synonymous	MON1B	NM_014940.2		3169,2603,726	CC,CT,TT		40.2558,13.4895,31.2019		370/548	77228866	8941,4055	2198	4300	6498	SO:0001819	synonymous_variant	22879	exon4			CCTGGTTGAAGAT	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"""MON1 homolog B (yeast)"""			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.1110T>C	16.37:g.77228866T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_014940	B4DDZ0|O94949	Silent	SNP	ENST00000248248.3	37	CCDS10925.1																																																																																			T|0.276;C|0.724	0.724	strong		0.637	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940	
FBN3	84467	hgsc.bcm.edu	37	19	8191184	8191184	+	Missense_Mutation	SNP	C	C	T	rs35025963	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8191184C>T	ENST00000600128.1	-	21	3016	c.2602G>A	c.(2602-2604)Gat>Aat	p.D868N	FBN3_ENST00000601739.1_Missense_Mutation_p.D868N|FBN3_ENST00000270509.2_Missense_Mutation_p.D868N			Q75N90	FBN3_HUMAN	fibrillin 3	868			D -> N (in dbSNP:rs35025963).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CAGTTACCATCGCAGGTGACA	0.647													C|||	1500	0.299521	0.0938	0.3228	5008	,	,		15630	0.379		0.2823	False		,,,				2504	0.4969				p.D868N		Atlas-SNP	.											.	FBN3	300	.	0			c.G2602A						PASS	.	C	ASN/ASP	563,3837		50,463,1687	41.0	40.0	41.0		2602	0.8	0.0	19	dbSNP_126	41	2368,6198		334,1700,2249	yes	missense	FBN3	NM_032447.3	23	384,2163,3936	TT,TC,CC		27.6442,12.7955,22.6053	benign	868/2810	8191184	2931,10035	2200	4283	6483	SO:0001583	missense	84467	exon20			TACCATCGCAGGT		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.2602G>A	19.37:g.8191184C>T	ENSP00000470498:p.Asp868Asn	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	137	64	0.467153	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	615	0.2815934065934066	60	0.12195121951219512	118	0.3259668508287293	214	0.3741258741258741	223	0.2941952506596306	c	8.987	0.976745	0.18812	0.127955	0.276442	ENSG00000142449	ENST00000270509	D	0.90844	-2.74	3.05	0.768	0.18487	Matrix fibril-associated (2);	0.187814	0.45126	U	0.000389	T	0.00012	0.0000	N	0.20401	0.57	0.42668	P	0.006492999999999971	B	0.25048	0.117	B	0.17098	0.017	T	0.08680	-1.0710	9	0.31617	T	0.26	.	5.0229	0.14370	0.1654:0.6381:0.0:0.1965	rs35025963;rs62123265	868	Q75N90	FBN3_HUMAN	N	868	ENSP00000270509:D868N	ENSP00000270509:D868N	D	-	1	0	FBN3	8097184	1.000000	0.71417	0.028000	0.17463	0.010000	0.07245	2.090000	0.41682	0.130000	0.18549	0.555000	0.69702	GAT	C|0.760;T|0.240	0.240	strong		0.647	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
MUC5B	727897	hgsc.bcm.edu	37	11	1258387	1258387	+	Missense_Mutation	SNP	G	G	A	rs202160055		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1258387G>A	ENST00000529681.1	+	25	3348	c.3290G>A	c.(3289-3291)cGc>cAc	p.R1097H	MUC5B_ENST00000447027.1_Missense_Mutation_p.R1100H	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1097	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCCGCCTGCCGCTCCCAGGTG	0.682																																					p.R1097H		Atlas-SNP	.											MUC5B,NS,carcinoma,+1,4	MUC5B	473	4	0			c.G3290A						scavenged	.						10.0	16.0	14.0					11																	1258387		1900	4086	5986	SO:0001583	missense	727897	exon25			CCTGCCGCTCCCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.3290G>A	11.37:g.1258387G>A	ENSP00000436812:p.Arg1097His	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	24	3	0.125	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	6.941	0.543406	0.13250	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.72505	-0.66;-0.66	4.38	-0.728	0.11162	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.30198	0.0757	N	0.00135	-2.02	0.26154	N	0.980103	B;B;B	0.24132	0.004;0.098;0.098	B;B;B	0.12837	0.001;0.008;0.008	T	0.37934	-0.9684	9	0.87932	D	0	.	8.5449	0.33415	0.6733:0.0:0.3267:0.0	rs35573593	1097;1790;1100	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	H	1097;1100;1098;1167	ENSP00000436812:R1097H;ENSP00000415793:R1100H	ENSP00000343037:R1098H	R	+	2	0	MUC5B	1214963	0.002000	0.14202	0.101000	0.21167	0.007000	0.05969	0.139000	0.16036	-0.476000	0.06842	-0.379000	0.06801	CGC	.	.	weak		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SYNE1	23345	hgsc.bcm.edu	37	6	152730807	152730807	+	Missense_Mutation	SNP	C	C	G	rs374482089		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152730807C>G	ENST00000367255.5	-	43	6869	c.6268G>C	c.(6268-6270)Gaa>Caa	p.E2090Q	SYNE1_ENST00000265368.4_Missense_Mutation_p.E2090Q|SYNE1_ENST00000341594.5_Missense_Mutation_p.E2127Q|SYNE1_ENST00000448038.1_Missense_Mutation_p.E2097Q|SYNE1_ENST00000423061.1_Missense_Mutation_p.E2097Q|RNA5SP223_ENST00000365174.1_RNA	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2090					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTCTGATATTCTCTCATTAAG	0.368										HNSCC(10;0.0054)																											p.E2097Q		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G6289C						PASS	.	C	GLN/GLU,GLN/GLU	0,4406		0,0,2203	98.0	96.0	96.0		6268,6289	5.9	1.0	6		96	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SYNE1	NM_182961.3,NM_033071.3	29,29	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	benign,benign	2090/8798,2097/8750	152730807	1,13005	2203	4300	6503	SO:0001583	missense	23345	exon43			GATATTCTCTCAT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.6268G>C	6.37:g.152730807C>G	ENSP00000356224:p.Glu2090Gln	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658164	0.47467	0.0	1.16E-4	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	5.92	5.92	0.95590	.	0.192526	0.36134	N	0.002765	T	0.18841	0.0452	L	0.59436	1.845	0.80722	D	1	P;B;B;B	0.38250	0.624;0.011;0.023;0.019	B;B;B;B	0.39706	0.307;0.005;0.008;0.011	T	0.02244	-1.1189	10	0.12430	T	0.62	.	14.4744	0.67537	0.0:0.9305:0.0:0.0695	.	2073;2090;2090;2097	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	Q	2090;2097;2090;2097;2127	ENSP00000356224:E2090Q;ENSP00000396024:E2097Q;ENSP00000265368:E2090Q;ENSP00000390975:E2097Q;ENSP00000341887:E2127Q	ENSP00000265368:E2090Q	E	-	1	0	SYNE1	152772500	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.922000	0.63404	2.822000	0.97130	0.650000	0.86243	GAA	.	.	weak		0.368	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
STX1A	6804	hgsc.bcm.edu	37	7	73122977	73122977	+	Silent	SNP	G	G	A	rs2229854	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73122977G>A	ENST00000222812.3	-	3	176	c.150C>T	c.(148-150)aaC>aaT	p.N50N	STX1A_ENST00000395156.3_Silent_p.N50N|STX1A_ENST00000395154.3_Silent_p.N50N|MIR4284_ENST00000578924.1_RNA|STX1A_ENST00000395155.3_Silent_p.N50N	NM_004603.3	NP_004594.1	Q16623	STX1A_HUMAN	syntaxin 1A (brain)	50					calcium ion-dependent exocytosis (GO:0017156)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of insulin secretion (GO:0050796)|response to gravity (GO:0009629)|secretion by cell (GO:0032940)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)	actomyosin (GO:0042641)|cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synaptic vesicle membrane (GO:0030672)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)	calcium channel inhibitor activity (GO:0019855)			large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(55;0.0908)|all_lung(88;0.198)				CCTCCTCCACGTTCTCTGCGA	0.612													G|||	335	0.066893	0.1006	0.0821	5008	,	,		18121	0.0		0.0944	False		,,,				2504	0.0511				p.N50N		Atlas-SNP	.											.	STX1A	16	.	0			c.C150T						PASS	.	G	,	404,4002	199.1+/-222.7	18,368,1817	125.0	90.0	102.0		150,150	-3.6	0.9	7	dbSNP_98	102	789,7811	185.3+/-233.1	39,711,3550	no	coding-synonymous,coding-synonymous	STX1A	NM_001165903.1,NM_004603.3	,	57,1079,5367	AA,AG,GG		9.1744,9.1693,9.1727	,	50/252,50/289	73122977	1193,11813	2203	4300	6503	SO:0001819	synonymous_variant	6804	exon3			CTCCACGTTCTCT		CCDS34655.1, CCDS55120.1	7q11.2	2008-07-18			ENSG00000106089	ENSG00000106089			11433	protein-coding gene	gene with protein product		186590		STX1		1321498	Standard	NM_001165903		Approved	HPC-1, p35-1	uc003tyx.3	Q16623	OTTHUMG00000137422	ENST00000222812.3:c.150C>T	7.37:g.73122977G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	129	48	0.372093	NM_004603	O15447|O15448|Q12936|Q75MD9|Q7Z5K3|Q9BPZ6	Silent	SNP	ENST00000222812.3	37	CCDS34655.1																																																																																			G|0.908;A|0.092	0.092	strong		0.612	STX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268422.1	NM_004603	
FST	10468	hgsc.bcm.edu	37	5	52781029	52781029	+	Silent	SNP	G	G	A	rs11746136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:52781029G>A	ENST00000256759.3	+	5	1307	c.924G>A	c.(922-924)ctG>ctA	p.L308L	FST_ENST00000396947.3_Silent_p.L308L	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	308	Kazal-like 3. {ECO:0000255|PROSITE- ProRule:PRU00798}.				BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				GTGTGCTACTGGAAGTAAAGC	0.502													G|||	45	0.00898562	0.0144	0.013	5008	,	,		17704	0.0		0.0169	False		,,,				2504	0.0				p.L308L		Atlas-SNP	.											.	FST	42	.	0			c.G924A						PASS	.	G	,	81,4325	70.9+/-108.8	1,79,2123	120.0	105.0	110.0		924,924	3.5	1.0	5	dbSNP_120	110	140,8460	69.4+/-131.9	2,136,4162	no	coding-synonymous,coding-synonymous	FST	NM_006350.3,NM_013409.2	,	3,215,6285	AA,AG,GG		1.6279,1.8384,1.6992	,	308/318,308/345	52781029	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	10468	exon5			GCTACTGGAAGTA	M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.924G>A	5.37:g.52781029G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_013409	B5BU94|Q9BTH0	Silent	SNP	ENST00000256759.3	37	CCDS3959.1	31	0.014194139194139194	11	0.022357723577235773	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	3.057	-0.193992	0.06259	0.018384	0.016279	ENSG00000134363	ENST00000497789	.	.	.	5.35	3.52	0.40303	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.3382	7.2089	0.25923	0.1577:0.0:0.6997:0.1425	rs11746136	.	.	.	X	93	.	.	W	+	2	0	FST	52816786	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.792000	0.47837	0.705000	0.31890	0.655000	0.94253	TGG	G|0.983;A|0.017	0.017	strong		0.502	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409	
PLXNB3	5365	hgsc.bcm.edu	37	X	153035798	153035798	+	Missense_Mutation	SNP	G	G	A	rs2266879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153035798G>A	ENST00000361971.5	+	9	1906	c.1792G>A	c.(1792-1794)Gtc>Atc	p.V598I	PLXNB3_ENST00000538966.1_Missense_Mutation_p.V621I|PLXNB3_ENST00000538776.1_Missense_Mutation_p.V251I|PLXNB3_ENST00000538282.1_Missense_Mutation_p.V208I|PLXNB3_ENST00000538543.1_Missense_Mutation_p.V148I	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	598			V -> I (in dbSNP:rs2266879). {ECO:0000269|PubMed:14702039}.		axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCAGACCACGTCACTGTGCC	0.642													G|||	1137	0.301192	0.177	0.2378	3775	,	,		13509	0.0804		0.4791	False		,,,				2504	0.1789				p.V621I		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G1861A						PASS	.		ILE/VAL,ILE/VAL	1017,2810		131,607,148,892,419	76.0	50.0	59.0		1861,1792	-2.9	0.0	X	dbSNP_100	59	4336,2389		1034,1079,1189,315,680	yes	missense,missense	PLXNB3	NM_001163257.1,NM_005393.2	29,29	1165,1686,1337,1207,1099	AA,AG,A,GG,G		35.5242,26.5743,49.2703	benign,benign	621/1933,598/1910	153035798	5353,5199	2197	4297	6494	SO:0001583	missense	5365	exon10			GACCACGTCACTG	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1792G>A	X.37:g.153035798G>A	ENSP00000355378:p.Val598Ile	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	610	0.3676913803496082	78	0.18055555555555555	66	0.2185430463576159	31	0.05719557195571956	253	0.4755639097744361	g	5.719	0.317087	0.10845	0.265743	0.644758	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538543;ENST00000538282	T;T;T;T;T	0.70164	5.1;5.06;4.51;1.75;-0.46	4.78	-2.94	0.05581	.	1.088280	0.07055	N	0.832721	T	0.00012	0.0000	N	0.25245	0.725	0.52501	P	4.999999999999449E-5	B;P;B;B	0.44776	0.018;0.843;0.055;0.018	B;B;B;B	0.33295	0.007;0.161;0.026;0.012	T	0.36480	-0.9746	9	0.30078	T	0.28	.	11.2095	0.48790	0.5531:0.0:0.4469:0.0	rs2266879	251;148;621;598	B7Z3H9;F5GZZ4;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	I	621;598;251;148;208	ENSP00000442736:V621I;ENSP00000355378:V598I;ENSP00000445569:V251I;ENSP00000444086:V148I;ENSP00000441919:V208I	ENSP00000355378:V598I	V	+	1	0	PLXNB3	152688992	0.000000	0.05858	0.037000	0.18230	0.021000	0.10359	-0.430000	0.06973	-1.033000	0.03299	-0.303000	0.09236	GTC	G|0.542;A|0.458	0.458	strong		0.642	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
TRAF6	7189	hgsc.bcm.edu	37	11	36518764	36518764	+	Missense_Mutation	SNP	C	C	T	rs577802750		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:36518764C>T	ENST00000526995.1	-	4	746	c.500G>A	c.(499-501)cGt>cAt	p.R167H	TRAF6_ENST00000348124.5_Missense_Mutation_p.R167H|TRAF6_ENST00000529150.1_5'Flank	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	167	Interaction with TAX1BP1.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				TTGGAAGGGACGCTGGCATTG	0.378																																					p.R167H		Atlas-SNP	.											.	TRAF6	56	.	0			c.G500A						PASS	.						72.0	75.0	74.0					11																	36518764		2202	4298	6500	SO:0001583	missense	7189	exon4			AAGGGACGCTGGC		CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"""RING-type (C3HC4) zinc fingers"""	12036	protein-coding gene	gene with protein product		602355	"""TNF receptor-associated factor 6"""			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.500G>A	11.37:g.36518764C>T	ENSP00000433623:p.Arg167His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_004620	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Missense_Mutation	SNP	ENST00000526995.1	37	CCDS7901.1	.	.	.	.	.	.	.	.	.	.	C	6.898	0.535263	0.13188	.	.	ENSG00000175104	ENST00000526995;ENST00000348124	T;T	0.25579	1.79;1.79	5.49	-1.99	0.07457	Zinc finger, TRAF-type (1);	0.684611	0.15781	N	0.244901	T	0.13586	0.0329	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16928	-1.0386	10	0.42905	T	0.14	-4.1496	7.0542	0.25089	0.1248:0.5163:0.0:0.3588	.	167	Q9Y4K3	TRAF6_HUMAN	H	167	ENSP00000433623:R167H;ENSP00000337853:R167H	ENSP00000337853:R167H	R	-	2	0	TRAF6	36475340	0.055000	0.20627	0.000000	0.03702	0.226000	0.24999	1.129000	0.31381	-0.206000	0.10203	0.650000	0.86243	CGT	.	.	none		0.378	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803	
LOXHD1	125336	hgsc.bcm.edu	37	18	44149474	44149474	+	Silent	SNP	G	G	A	rs2086005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44149474G>A	ENST00000398722.4	-	9	1340	c.1341C>T	c.(1339-1341)aaC>aaT	p.N447N	LOXHD1_ENST00000441551.2_Silent_p.N725N|LOXHD1_ENST00000536736.1_Silent_p.N725N			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	447	PLAT 4. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						CTTTGAGGTTGTTGTCAGAGA	0.488													G|||	309	0.0617013	0.0045	0.1052	5008	,	,		21822	0.0496		0.1372	False		,,,				2504	0.0429				p.N725N		Atlas-SNP	.											.	LOXHD1	367	.	0			c.C2175T						PASS	.	G		33,1351		1,31,660	133.0	116.0	121.0		2175	0.2	1.0	18	dbSNP_96	121	506,2676		41,424,1126	no	coding-synonymous	LOXHD1	NM_144612.6		42,455,1786	AA,AG,GG		15.9019,2.3844,11.8046		725/2212	44149474	539,4027	692	1591	2283	SO:0001819	synonymous_variant	125336	exon16			GAGGTTGTTGTCA	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1341C>T	18.37:g.44149474G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	113	65	0.575221	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000398722.4	37		173	0.07921245421245421	3	0.006097560975609756	44	0.12154696132596685	29	0.050699300699300696	97	0.1279683377308707	G	9.503	1.103818	0.20632	0.023844	0.159019	ENSG00000167210	ENST00000441551	.	.	.	5.66	0.187	0.15109	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6151	0.51086	0.4543:0.0:0.5456:0.0	rs2086005;rs2086005	.	.	.	X	706	.	.	Q	-	1	0	LOXHD1	42403472	0.995000	0.38212	0.997000	0.53966	0.988000	0.76386	0.430000	0.21428	0.082000	0.17018	0.655000	0.94253	CAA	G|0.917;A|0.083	0.083	strong		0.488	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
TAP2	6891	hgsc.bcm.edu	37	6	32800412	32800412	+	Missense_Mutation	SNP	C	C	T	rs1800454	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32800412C>T	ENST00000452392.2	-	6	1308	c.1135G>A	c.(1135-1137)Gta>Ata	p.V379I	TAP2_ENST00000374899.4_Missense_Mutation_p.V379I|TAP2_ENST00000374897.2_Missense_Mutation_p.V379I|TAP2_ENST00000485701.1_5'UTR			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	ACCCTCCTTACGAGCAGGTAC	0.552													C|||	731	0.145966	0.152	0.1369	5008	,	,		18457	0.1905		0.1531	False		,,,				2504	0.091				p.V379I		Atlas-SNP	.											TAP2_ENST00000458336,NS,carcinoma,0,4	TAP2	98	4	0			c.G1135A	GRCh37	CM920658	TAP2	M	rs1800454	PASS	.	C	ILE/VAL,ILE/VAL	450,2570		32,386,1092	89.0	78.0	82.0		1135,1135	-9.9	0.0	6	dbSNP_89	82	742,4676		58,626,2025	yes	missense,missense	TAP2	NM_000544.3,NM_018833.2	29,29	90,1012,3117	TT,TC,CC		13.6951,14.9007,14.1266	benign,benign	379/704,379/654	32800412	1192,7246	1510	2709	4219	SO:0001583	missense	6891	exon6			TCCTTACGAGCAG	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1135G>A	6.37:g.32800412C>T	ENSP00000391806:p.Val379Ile	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	189	186	0.984127	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000452392.2	37		335	0.1533882783882784	67	0.13617886178861788	49	0.13535911602209943	97	0.16958041958041958	122	0.16094986807387862	C	0.866	-0.733797	0.03111	0.149007	0.136951	ENSG00000204267;ENSG00000204267;ENSG00000204267;ENSG00000250264	ENST00000556934;ENST00000374899;ENST00000374897;ENST00000452392	D;D;D	0.88509	-2.39;-2.39;-2.39	4.96	-9.93	0.00452	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	2.160830	0.02792	N	0.122180	T	0.29223	0.0727	N	0.00985	-1.075	0.09310	P	0.999993	B;B;B;B	0.20780	0.048;0.029;0.029;0.029	B;B;B;B	0.20955	0.032;0.012;0.012;0.012	T	0.48525	-0.9028	9	0.02654	T	1	-57.7115	1.346	0.02163	0.1525:0.1691:0.2177:0.4608	rs1800454;rs2228392;rs4148873;rs59850737;rs1800454	379;380;379;379	E7ENX8;Q59H06;Q03519;Q9UP03	.;.;TAP2_HUMAN;.	I	379	ENSP00000364034:V379I;ENSP00000364032:V379I;ENSP00000391806:V379I	ENSP00000364032:V379I	V	-	1	0	XXbac-BPG246D15.9;TAP2	32908390	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-1.955000	0.01523	-2.988000	0.00280	-2.275000	0.00273	GTA	C|0.860;T|0.140	0.140	strong		0.552	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
MUC4	4585	hgsc.bcm.edu	37	3	195506746	195506746	+	Missense_Mutation	SNP	G	G	A	rs192522651		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506746G>A	ENST00000463781.3	-	2	12164	c.11705C>T	c.(11704-11706)gCc>gTc	p.A3902V	MUC4_ENST00000475231.1_Missense_Mutation_p.A3902V|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3902V(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGAGGGGTGGCGTGACGTGT	0.597																																					p.A3902V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,4	MUC4	1505	4	2	Substitution - Missense(2)	kidney(2)	c.C11705T						PASS	.						10.0	9.0	9.0					3																	195506746		528	1056	1584	SO:0001583	missense	4585	exon2			GGGGTGGCGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11705C>T	3.37:g.195506746G>A	ENSP00000417498:p.Ala3902Val	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	108	0.04945054945054945	8	0.016260162601626018	19	0.052486187845303865	56	0.0979020979020979	25	0.032981530343007916	g	7.407	0.633932	0.14322	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.45;1.42	.	.	.	.	.	.	.	.	T	0.00384	0.0012	N	0.19112	0.55	0.09310	N	1	B	0.22909	0.077	B	0.09377	0.004	T	0.24048	-1.0171	7	.	.	.	.	2.8356	0.05513	3.0E-4:2.0E-4:0.5012:0.4983	.	3774	E7ESK3	.	V	3902	ENSP00000417498:A3902V;ENSP00000420243:A3902V	.	A	-	2	0	MUC4	196991525	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	0.241000	0.18065	0.064000	0.16427	0.064000	0.15345	GCC	G|0.951;A|0.049	0.049	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CNDP1	84735	hgsc.bcm.edu	37	18	72238472	72238472	+	Missense_Mutation	SNP	C	C	A	rs73973908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72238472C>A	ENST00000358821.3	+	7	1036	c.808C>A	c.(808-810)Cat>Aat	p.H270N	CNDP1_ENST00000582365.1_Missense_Mutation_p.H227N	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	270						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.H270N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		TGGCATCCTTCATGAACCAAT	0.413													C|||	809	0.161542	0.2262	0.1297	5008	,	,		22319	0.1419		0.1282	False		,,,				2504	0.1513				p.H270N	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											CNDP1,NS,carcinoma,0,1	CNDP1	98	1	1	Substitution - Missense(1)	stomach(1)	c.C808A						PASS	.	C	ASN/HIS	860,3546	340.7+/-306.4	84,692,1427	240.0	206.0	218.0		808	-11.6	0.0	18	dbSNP_130	218	1166,7434	238.3+/-269.8	87,992,3221	yes	missense	CNDP1	NM_032649.5	68	171,1684,4648	AA,AC,CC		13.5581,19.5188,15.5774	benign	270/508	72238472	2026,10980	2203	4300	6503	SO:0001583	missense	84735	exon7			ATCCTTCATGAAC		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.808C>A	18.37:g.72238472C>A	ENSP00000351682:p.His270Asn	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	292	104	0.356164	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	332	0.152014652014652	99	0.20121951219512196	44	0.12154696132596685	84	0.14685314685314685	105	0.13852242744063326	C	12.02	1.812873	0.32053	0.195188	0.135581	ENSG00000150656	ENST00000358821	T	0.56776	0.44	5.82	-11.6	0.00059	Peptidase M20, dimerisation (1);	0.576924	0.19497	N	0.112834	T	0.00039	0.0001	L	0.28649	0.875	0.58432	P	5.000000000032756E-6	B	0.14805	0.011	B	0.17722	0.019	T	0.48525	-0.9028	9	0.49607	T	0.09	-4.675	32.931	0.99999	0.0939:0.9061:0.0:0.0	.	270	Q96KN2	CNDP1_HUMAN	N	270	ENSP00000351682:H270N	ENSP00000351682:H270N	H	+	1	0	CNDP1	70389452	0.000000	0.05858	0.000000	0.03702	0.891000	0.51852	-0.509000	0.06336	-2.037000	0.00920	-0.467000	0.05162	CAT	C|0.848;A|0.152	0.152	strong		0.413	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
HERC2	8924	hgsc.bcm.edu	37	15	28386626	28386626	+	Silent	SNP	C	C	T	rs11636232	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28386626C>T	ENST00000261609.7	-	78	12075	c.11967G>A	c.(11965-11967)caG>caA	p.Q3989Q		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTCCGATTAACTGCACGGGTC	0.537													c|||	429	0.0856629	0.0151	0.0908	5008	,	,		16725	0.0		0.3221	False		,,,				2504	0.0225				p.Q3989Q		Atlas-SNP	.											.	HERC2	501	.	0			c.G11967A						PASS	.	C		343,4063	176.6+/-205.7	11,321,1871	85.0	78.0	81.0		11967	1.9	0.6	15	dbSNP_120	81	3289,5311	493.0+/-373.5	636,2017,1647	no	coding-synonymous	HERC2	NM_004667.4		647,2338,3518	TT,TC,CC		38.2442,7.7848,27.9256		3989/4835	28386626	3632,9374	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon78			GATTAACTGCACG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.11967G>A	15.37:g.28386626C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	191	90	0.471204	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|0.783;T|0.217	0.217	strong		0.537	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
CSPG4	1464	hgsc.bcm.edu	37	15	75982428	75982428	+	Silent	SNP	C	C	T	rs7182906	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75982428C>T	ENST00000308508.5	-	3	1070	c.978G>A	c.(976-978)ggG>ggA	p.G326G		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	326	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTGCATCCAGCCCCCCGAGAA	0.632													C|||	1423	0.284145	0.2277	0.4006	5008	,	,		20377	0.1865		0.3817	False		,,,				2504	0.2781				p.G326G		Atlas-SNP	.											CSPG4,NS,carcinoma,0,1	CSPG4	175	1	0			c.G978A						PASS	.						20.0	18.0	18.0					15																	75982428		2192	4291	6483	SO:0001819	synonymous_variant	1464	exon3			ATCCAGCCCCCCG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.978G>A	15.37:g.75982428C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	180	80	0.444444	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			C|0.702;T|0.298	0.298	strong		0.632	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
TTN	7273	hgsc.bcm.edu	37	2	179650701	179650701	+	Silent	SNP	C	C	T	rs6715406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179650701C>T	ENST00000591111.1	-	14	2468	c.2244G>A	c.(2242-2244)gaG>gaA	p.E748E	TTN_ENST00000342175.6_Silent_p.E702E|TTN_ENST00000360870.5_Silent_p.E748E|TTN_ENST00000460472.2_Silent_p.E702E|TTN_ENST00000342992.6_Silent_p.E748E|TTN_ENST00000359218.5_Silent_p.E702E|TTN_ENST00000589042.1_Silent_p.E748E			Q8WZ42	TITIN_HUMAN	titin	33589					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTGGGGAGGCTCAGCTACCT	0.517													C|||	1025	0.204673	0.1445	0.1916	5008	,	,		20748	0.0685		0.4135	False		,,,				2504	0.2209				p.E748E		Atlas-SNP	.											.	TTN	18412	.	0			c.G2244A						PASS	.	C	,,,,	881,3525	342.5+/-307.2	91,699,1413	97.0	88.0	91.0		2106,2244,2244,2106,2106	5.9	1.0	2	dbSNP_116	91	3489,5111	510.8+/-377.6	733,2023,1544	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	824,2722,2957	TT,TC,CC		40.5698,19.9955,33.5999	,,,,	702/26927,748/33424,748/5605,702/27052,702/27119	179650701	4370,8636	2203	4300	6503	SO:0001819	synonymous_variant	7273	exon14			GGGAGGCTCAGCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2244G>A	2.37:g.179650701C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.722;T|0.278	0.278	strong		0.517	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
VNN1	8876	hgsc.bcm.edu	37	6	133015271	133015271	+	Missense_Mutation	SNP	T	T	C	rs2272996	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:133015271T>C	ENST00000367928.4	-	3	405	c.392A>G	c.(391-393)aAc>aGc	p.N131S		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	131	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		N -> S (in dbSNP:rs2272996). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		ATAGATAGAGTTGTTCTTGGC	0.433													T|||	1332	0.265974	0.1725	0.1916	5008	,	,		17060	0.3621		0.2972	False		,,,				2504	0.3139				p.N131S		Atlas-SNP	.											.	VNN1	69	.	0			c.A392G						PASS	.	T	SER/ASN	840,3566	331.8+/-302.1	84,672,1447	141.0	128.0	132.0		392	6.1	0.4	6	dbSNP_100	132	2320,6280	388.5+/-342.6	309,1702,2289	yes	missense	VNN1	NM_004666.2	46	393,2374,3736	CC,CT,TT		26.9767,19.0649,24.2965	probably-damaging	131/514	133015271	3160,9846	2203	4300	6503	SO:0001583	missense	8876	exon3			ATAGAGTTGTTCT	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.392A>G	6.37:g.133015271T>C	ENSP00000356905:p.Asn131Ser	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	192	117	0.609375	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	597	0.2733516483516483	91	0.18495934959349594	62	0.1712707182320442	216	0.3776223776223776	228	0.3007915567282322	T	19.74	3.883832	0.72410	0.190649	0.269767	ENSG00000112299	ENST00000367928	D	0.85861	-2.04	6.07	6.07	0.98685	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.064498	0.64402	D	0.000007	D	0.89646	0.6775	M	0.68728	2.09	0.26675	P	0.9716475	D	0.67145	0.996	D	0.72075	0.976	D	0.89228	0.3575	9	0.44086	T	0.13	-24.5999	16.6277	0.84984	0.0:0.0:0.0:1.0	rs2272996;rs60821439;rs2272996	131	O95497	VNN1_HUMAN	S	131	ENSP00000356905:N131S	ENSP00000356905:N131S	N	-	2	0	VNN1	133056964	1.000000	0.71417	0.443000	0.26883	0.833000	0.47200	3.909000	0.56363	2.330000	0.79161	0.528000	0.53228	AAC	T|0.736;C|0.264	0.264	strong		0.433	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
TMC5	79838	hgsc.bcm.edu	37	16	19475099	19475099	+	Splice_Site	SNP	C	C	A	rs61737709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19475099C>A	ENST00000396229.2	+	8	1987	c.1238C>A	c.(1237-1239)gCt>gAt	p.A413D	TMC5_ENST00000381414.4_Splice_Site_p.A413D|TMC5_ENST00000541464.1_Splice_Site_p.A413D|TMC5_ENST00000542583.2_Splice_Site_p.A413D|TMC5_ENST00000219821.5_Splice_Site_p.A167D|TMC5_ENST00000561503.1_Splice_Site_p.A54D|TMC5_ENST00000564959.1_Splice_Site_p.A96D	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	413					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TGATTCCAGGCTTATCGGAGA	0.483													C|||	354	0.0706869	0.0159	0.0461	5008	,	,		19577	0.1429		0.0408	False		,,,				2504	0.1186				p.A413D		Atlas-SNP	.											.	TMC5	169	.	0			c.C1238A						PASS	.	C	ASP/ALA,ASP/ALA,ASP/ALA	81,4313	69.8+/-107.6	0,81,2116	104.0	91.0	95.0		1238,1238,500	-2.6	0.0	16	dbSNP_129	95	351,8249	119.4+/-178.7	5,341,3954	yes	missense-near-splice,missense-near-splice,missense-near-splice	TMC5	NM_001105248.1,NM_001105249.1,NM_024780.4	126,126,126	5,422,6070	AA,AC,CC		4.0814,1.8434,3.3246	possibly-damaging,possibly-damaging,possibly-damaging	413/1007,413/949,167/761	19475099	432,12562	2197	4300	6497	SO:0001630	splice_region_variant	79838	exon8			TCCAGGCTTATCG	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1237-1C>A	16.37:g.19475099C>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	140	0.0641025641025641	11	0.022357723577235773	16	0.04419889502762431	82	0.14335664335664336	31	0.040897097625329816	C	9.406	1.079208	0.20227	0.018434	0.040814	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	5.68	-2.62	0.06152	.	1.334810	0.04658	N	0.408430	T	0.00412	0.0013	L	0.52011	1.625	0.80722	P	0.0	B;B;B;B;B;B	0.17465	0.004;0.022;0.004;0.002;0.002;0.004	B;B;B;B;B;B	0.18263	0.01;0.021;0.01;0.004;0.004;0.01	T	0.08126	-1.0737	9	0.37606	T	0.19	0.0251	3.2936	0.06958	0.2035:0.3748:0.2941:0.1276	rs61737709	413;96;167;167;413;413	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	D	413;413;413;413;167;96	ENSP00000441227:A413D;ENSP00000370822:A413D;ENSP00000379531:A413D;ENSP00000446274:A413D;ENSP00000219821:A167D	ENSP00000219821:A167D	A	+	2	0	TMC5	19382600	0.000000	0.05858	0.034000	0.17996	0.243000	0.25628	-1.065000	0.03458	-0.194000	0.10399	0.650000	0.86243	GCT	C|0.956;A|0.044	0.044	strong		0.483	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	Missense_Mutation
TLDC1	57707	hgsc.bcm.edu	37	16	84522897	84522897	+	Missense_Mutation	SNP	G	G	C	rs436278	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84522897G>C	ENST00000343629.6	-	4	698	c.516C>G	c.(514-516)gaC>gaG	p.D172E	TLDC1_ENST00000561807.1_5'Flank|TLDC1_ENST00000535580.1_Missense_Mutation_p.D145E	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	172			D -> E (in dbSNP:rs436278). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:15489334}.			lysosomal membrane (GO:0005765)		p.D172E(1)									GCAGCTTCATGTCAGAGAGCA	0.582													C|||	3109	0.620807	0.3933	0.6542	5008	,	,		17059	0.8998		0.4612	False		,,,				2504	0.7812				p.D172E		Atlas-SNP	.											KIAA1609,NS,carcinoma,0,1	KIAA1609	39	1	1	Substitution - Missense(1)	prostate(1)	c.C516G						PASS	.	C	GLU/ASP	1857,2543	633.0+/-395.9	393,1071,736	50.0	47.0	48.0		516	3.1	1.0	16	dbSNP_80	48	3856,4744	608.4+/-395.4	869,2118,1313	yes	missense	KIAA1609	NM_020947.3	45	1262,3189,2049	CC,CG,GG		44.8372,42.2045,43.9462	benign	172/457	84522897	5713,7287	2200	4300	6500	SO:0001583	missense	57707	exon4			CTTCATGTCAGAG	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.516C>G	16.37:g.84522897G>C	ENSP00000343635:p.Asp172Glu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	113	51	0.451327	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	37	CCDS32498.1	1277	0.5847069597069597	186	0.3780487804878049	212	0.585635359116022	517	0.9038461538461539	362	0.47757255936675463	C	3.839	-0.034215	0.07543	0.422045	0.448372	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.06933	3.44;3.24	5.04	3.06	0.35304	.	0.616396	0.15973	N	0.235695	T	0.00012	0.0000	N	0.00074	-2.255	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24870	-1.0148	9	0.02654	T	1	-23.748	4.4693	0.11704	0.0:0.5967:0.2082:0.195	rs436278;rs691510;rs17856687;rs436278	145;172	F5GWS3;Q6P9B6	.;K1609_HUMAN	E	172;145	ENSP00000343635:D172E;ENSP00000441997:D145E	ENSP00000343635:D172E	D	-	3	2	KIAA1609	83080398	0.734000	0.28142	0.994000	0.49952	0.785000	0.44390	0.946000	0.29069	1.127000	0.42034	-0.187000	0.12897	GAC	G|0.511;C|0.489	0.489	strong		0.582	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
LAMA5	3911	hgsc.bcm.edu	37	20	60897104	60897104	+	Missense_Mutation	SNP	C	C	T	rs141208202	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60897104C>T	ENST00000252999.3	-	48	6533	c.6467G>A	c.(6466-6468)gGg>gAg	p.G2156E		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2156	Laminin EGF-like 22. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCCCACAGGCCCGCCTGGAAC	0.657													.|||	82	0.0163738	0.003	0.0418	5008	,	,		11915	0.0		0.0437	False		,,,				2504	0.0051				p.G2156E		Atlas-SNP	.											.	LAMA5	268	.	0			c.G6467A						PASS	.	C	GLU/GLY	33,4359		0,33,2163	45.0	41.0	43.0		6467	1.1	0.0	20	dbSNP_134	43	369,8199		7,355,3922	yes	missense	LAMA5	NM_005560.3	98	7,388,6085	TT,TC,CC		4.3067,0.7514,3.1019	possibly-damaging	2156/3696	60897104	402,12558	2196	4284	6480	SO:0001583	missense	3911	exon48			ACAGGCCCGCCTG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.6467G>A	20.37:g.60897104C>T	ENSP00000252999:p.Gly2156Glu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	28	17	0.607143	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	49	0.022435897435897436	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	31	0.040897097625329816	c	6.876	0.530970	0.13127	0.007514	0.043067	ENSG00000130702	ENST00000252999	T	0.18657	2.2	4.19	1.11	0.20524	EGF-like, laminin (2);	0.764022	0.12436	U	0.469157	T	0.02083	0.0065	N	0.08118	0	0.09310	N	0.999993	B	0.26935	0.164	B	0.25405	0.06	T	0.29701	-1.0003	10	0.39692	T	0.17	.	8.5676	0.33550	0.0:0.7346:0.0:0.2654	.	2156	O15230	LAMA5_HUMAN	E	2156	ENSP00000252999:G2156E	ENSP00000252999:G2156E	G	-	2	0	LAMA5	60330499	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.871000	0.28023	0.081000	0.16988	-0.350000	0.07774	GGG	C|0.973;T|0.027	0.027	strong		0.657	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
FAM173B	134145	hgsc.bcm.edu	37	5	10236693	10236693	+	Missense_Mutation	SNP	A	A	G	rs17360625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:10236693A>G	ENST00000511437.1	-	3	353	c.341T>C	c.(340-342)gTt>gCt	p.V114A	FAM173B_ENST00000280330.8_5'UTR|FAM173B_ENST00000510047.1_Missense_Mutation_p.V114A|FAM173B_ENST00000510052.1_5'UTR	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	114			V -> A (in dbSNP:rs17360625).			integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						TTCATAACCAACTGCTGTGAA	0.408													A|||	73	0.0145767	0.0008	0.0346	5008	,	,		17403	0.0		0.0408	False		,,,				2504	0.0072				p.V114A		Atlas-SNP	.											.	FAM173B	24	.	0			c.T341C						PASS	.	A	ALA/VAL	23,3697		0,23,1837	92.0	90.0	91.0		341	2.8	0.0	5	dbSNP_123	91	246,7972		4,238,3867	yes	missense	FAM173B	NM_199133.2	64	4,261,5704	GG,GA,AA		2.9934,0.6183,2.2533	possibly-damaging	114/234	10236693	269,11669	1860	4109	5969	SO:0001583	missense	134145	exon3			TAACCAACTGCTG		CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.341T>C	5.37:g.10236693A>G	ENSP00000422338:p.Val114Ala	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	114	42	0.368421	NM_199133	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	37	CCDS43301.1	43	0.019688644688644688	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	28	0.036939313984168866	A	10.55	1.381302	0.24944	0.006183	0.029934	ENSG00000150756	ENST00000511437;ENST00000510047	T;T	0.27720	1.65;1.65	5.23	2.85	0.33270	.	0.264128	0.37348	N	0.002140	T	0.07863	0.0197	M	0.69358	2.11	0.18873	N	0.999989	B;B	0.24368	0.102;0.045	B;B	0.26614	0.054;0.071	T	0.10753	-1.0616	10	0.26408	T	0.33	-22.3375	9.0209	0.36200	0.8527:0.0:0.1473:0.0	rs17360625;rs52792909;rs17360625	114;114	E9PBZ4;Q6P4H8	.;F173B_HUMAN	A	114	ENSP00000422338:V114A;ENSP00000420876:V114A	ENSP00000420876:V114A	V	-	2	0	FAM173B	10289693	0.993000	0.37304	0.001000	0.08648	0.984000	0.73092	4.120000	0.57897	0.453000	0.26858	0.533000	0.62120	GTT	A|0.979;G|0.021	0.021	strong		0.408	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133	
MARCH7	64844	hgsc.bcm.edu	37	2	160604781	160604781	+	Missense_Mutation	SNP	G	G	A	rs142330597		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160604781G>A	ENST00000259050.4	+	5	1102	c.980G>A	c.(979-981)cGt>cAt	p.R327H	MARCH7_ENST00000539065.1_Missense_Mutation_p.R271H|MARCH7_ENST00000409175.1_Missense_Mutation_p.R327H|MARCH7_ENST00000409591.1_Missense_Mutation_p.R289H	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	327	Ser-rich.				protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						TCACAGTCCCGTAGTAATGTA	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		19489	0.0		0.001	False		,,,				2504	0.0				p.R327H		Atlas-SNP	.											MARCH7,NS,carcinoma,+1,1	MARCH7	48	1	0			c.G980A						PASS	.	G	HIS/ARG	0,4404		0,0,2202	52.0	56.0	54.0		980	5.7	1.0	2	dbSNP_134	54	11,8589	8.4+/-32.0	0,11,4289	yes	missense	MARCH7	NM_022826.2	29	0,11,6491	AA,AG,GG		0.1279,0.0,0.0846	possibly-damaging	327/705	160604781	11,12993	2202	4300	6502	SO:0001583	missense	64844	exon5			AGTCCCGTAGTAA	AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	17393	protein-coding gene	gene with protein product		613334	"""axotrophin"", ""membrane-associated ring finger (C3HC4) 7"""	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.980G>A	2.37:g.160604781G>A	ENSP00000259050:p.Arg327His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.780091	0.70222	0.0	0.001279	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000409591	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.72	5.72	0.89469	.	0.363453	0.33382	N	0.004966	T	0.45637	0.1352	L	0.29908	0.895	0.30173	N	0.801097	D;D;D	0.69078	0.997;0.99;0.99	P;P;B	0.57548	0.823;0.469;0.374	T	0.36432	-0.9748	10	0.41790	T	0.15	-7.7841	19.8788	0.96888	0.0:0.0:1.0:0.0	.	271;289;327	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	H	327;271;327;289	ENSP00000386830:R327H;ENSP00000442992:R271H;ENSP00000259050:R327H;ENSP00000387238:R289H	ENSP00000259050:R327H	R	+	2	0	MARCH7	160313027	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	6.983000	0.76180	2.683000	0.91414	0.655000	0.94253	CGT	G|0.999;A|0.001	0.001	strong		0.398	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
POTEM	641455	hgsc.bcm.edu	37	14	20010235	20010235	+	Missense_Mutation	SNP	A	A	G	rs113380635		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20010235A>G	ENST00000551509.1	-	5	974	c.923T>C	c.(922-924)gTt>gCt	p.V308A	RP11-244H18.1_ENST00000547584.1_lincRNA|RNU6-1268P_ENST00000391214.1_RNA	NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	308										endometrium(4)|kidney(1)|lung(4)	9						AAGTATGAGAACAGTTCTAAA	0.368																																					p.V308A		Atlas-SNP	.											POTEM_ENST00000551509,NS,carcinoma,0,4	POTEM	51	4	0			c.T923C						scavenged	.						42.0	37.0	39.0					14																	20010235		365	763	1128	SO:0001583	missense	641455	exon5			ATGAGAACAGTTC		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37096	protein-coding gene	gene with protein product	"""prostate-specific P704P"""					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.923T>C	14.37:g.20010235A>G	ENSP00000452296:p.Val308Ala	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	4	3	0.75	NM_001145442		Missense_Mutation	SNP	ENST00000551509.1	37	CCDS45076.1	.	.	.	.	.	.	.	.	.	.	g	5.617	0.298596	0.10622	.	.	ENSG00000187537	ENST00000551509;ENST00000439503;ENST00000344684	T	0.60040	0.22	0.906	0.906	0.19314	Ankyrin repeat-containing domain (4);	0.000000	0.32655	N	0.005811	T	0.10723	0.0262	N	0.00039	-2.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25187	-1.0139	8	.	.	.	.	3.4158	0.07375	0.2955:0.0:0.7045:0.0	.	308	A6NI47	POTEM_HUMAN	A	308;393;308	ENSP00000452296:V308A	.	V	-	2	0	POTEM	19080235	0.621000	0.27077	0.813000	0.32504	0.042000	0.13812	0.922000	0.28734	-0.020000	0.14032	-1.160000	0.01791	GTT	A|0.250;G|0.750	0.750	weak		0.368	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442	
PLA2G4E	123745	hgsc.bcm.edu	37	15	42287578	42287578	+	Silent	SNP	G	G	A	rs1668586	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42287578G>A	ENST00000399518.3	-	12	1713	c.1227C>T	c.(1225-1227)acC>acT	p.T409T	CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Silent_p.T380T	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	397	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		CTGATAGACCGGTGATGTAGC	0.602													A|||	3297	0.658347	0.5083	0.6816	5008	,	,		18768	0.5704		0.8479	False		,,,				2504	0.7403				p.T409T		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.C1227T						PASS	.	A		2384,1682		718,948,367	59.0	60.0	60.0		1227	-9.8	0.8	15	dbSNP_89	60	7344,1066		3214,916,75	no	coding-synonymous	PLA2G4E	NM_001206670.1		3932,1864,442	AA,AG,GG		12.6754,41.3674,22.0263		409/869	42287578	9728,2748	2033	4205	6238	SO:0001819	synonymous_variant	123745	exon12			TAGACCGGTGATG		CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1227C>T	15.37:g.42287578G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	116	114	0.982759	NM_001206670	Q6ZSC0	Silent	SNP	ENST00000399518.3	37	CCDS55962.1																																																																																			G|0.328;A|0.672	0.672	strong		0.602	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	
ZNF853	54753	hgsc.bcm.edu	37	7	6661256	6661256	+	Missense_Mutation	SNP	C	C	G	rs11971880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6661256C>G	ENST00000457543.3	+	3	1192	c.634C>G	c.(634-636)Cag>Gag	p.Q212E		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	212	Gln-rich.		Q -> E (in dbSNP:rs11971880).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						ggaacagttacagcagcagca	0.512													C|||	493	0.0984425	0.1558	0.0994	5008	,	,		25510	0.0546		0.0855	False		,,,				2504	0.0787				p.Q212E		Atlas-SNP	.											.	ZNF853	32	.	0			c.C634G						PASS	.	C	GLU/GLN	212,1172		17,178,497	85.0	95.0	92.0		634	3.0	0.0	7	dbSNP_120	92	322,2860		12,298,1281	yes	missense	ZNF853	NM_017560.1	29	29,476,1778	GG,GC,CC		10.1194,15.3179,11.6951	probably-damaging	212/660	6661256	534,4032	692	1591	2283	SO:0001583	missense	54753	exon3			CAGTTACAGCAGC	AL133055	CCDS59048.1	7p22.1	2013-01-08				ENSG00000236609		"""Zinc fingers, C2H2-type"""	21767	protein-coding gene	gene with protein product							Standard	NM_017560		Approved	DKFZp434J1015	uc011jwz.2	P0CG23		ENST00000457543.3:c.634C>G	7.37:g.6661256C>G	ENSP00000455585:p.Gln212Glu	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	330	162	0.490909	NM_017560		Missense_Mutation	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			C|0.905;G|0.095	0.095	strong		0.512	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
POLN	353497	hgsc.bcm.edu	37	4	2194953	2194953	+	Silent	SNP	G	G	A	rs10002583	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2194953G>A	ENST00000511885.2	-	7	1352	c.999C>T	c.(997-999)ggC>ggT	p.G333G	POLN_ENST00000382865.1_Silent_p.G333G|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	333					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			TGCCATCATTGCCAAAAAACT	0.353								DNA polymerases (catalytic subunits)					A|||	1656	0.330671	0.6029	0.2464	5008	,	,		17739	0.372		0.1243	False		,,,				2504	0.1922				p.G333G		Atlas-SNP	.											.	POLN	82	.	0			c.C999T						PASS	.	A		2359,2045	566.1+/-381.8	663,1033,506	85.0	92.0	89.0		999	3.1	0.6	4	dbSNP_119	89	993,7607	773.5+/-407.7	60,873,3367	no	coding-synonymous	POLN	NM_181808.2		723,1906,3873	AA,AG,GG		11.5465,46.4351,25.7767		333/901	2194953	3352,9652	2202	4300	6502	SO:0001819	synonymous_variant	353497	exon5			ATCATTGCCAAAA	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.999C>T	4.37:g.2194953G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	178	76	0.426966	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Silent	SNP	ENST00000511885.2	37	CCDS3360.1																																																																																			G|0.735;A|0.265	0.265	strong		0.353	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
TCTN3	26123	hgsc.bcm.edu	37	10	97447373	97447373	+	Silent	SNP	A	A	T	rs10786229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:97447373A>T	ENST00000371217.5	-	4	626	c.603T>A	c.(601-603)acT>acA	p.T201T	TCTN3_ENST00000430368.2_Intron|TCTN3_ENST00000265993.9_Silent_p.T219T|TCTN3_ENST00000371209.5_Silent_p.T201T			Q6NUS6	TECT3_HUMAN	tectonic family member 3	201					apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		GTGGTGATTGAGTTTGGAATG	0.448													A|||	2127	0.42472	0.4236	0.255	5008	,	,		17807	0.7133		0.3469	False		,,,				2504	0.3292				p.T201T		Atlas-SNP	.											.	TCTN3	66	.	0			c.T603A						PASS	.	A	,	1829,2577	534.8+/-374.1	384,1061,758	100.0	96.0	97.0		,603	-2.4	0.0	10	dbSNP_120	97	2746,5854	438.1+/-358.8	449,1848,2003	no	intron,coding-synonymous	TCTN3	NM_001143973.1,NM_015631.5	,	833,2909,2761	TT,TA,AA		31.9302,41.5116,35.1761	,	,201/608	97447373	4575,8431	2203	4300	6503	SO:0001819	synonymous_variant	26123	exon4			TGATTGAGTTTGG	AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"""Tectonic proteins"""	24519	protein-coding gene	gene with protein product		613847	"""chromosome 10 open reading frame 61"""	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.603T>A	10.37:g.97447373A>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_015631	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Silent	SNP	ENST00000371217.5	37	CCDS31258.2																																																																																			A|0.624;T|0.376	0.376	strong		0.448	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631	
EDEM1	9695	hgsc.bcm.edu	37	3	5229643	5229643	+	Silent	SNP	C	C	T	rs144177905	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:5229643C>T	ENST00000256497.4	+	1	286	c.153C>T	c.(151-153)ggC>ggT	p.G51G	EDEM1_ENST00000445686.1_5'Flank|AC026202.1_ENST00000600805.1_Missense_Mutation_p.A114T|AC026202.3_ENST00000439325.1_RNA	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	51					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		GCCCCGACGGCCCCGCGTCGC	0.736													c|||	84	0.0167732	0.0008	0.013	5008	,	,		8316	0.001		0.0408	False		,,,				2504	0.0327				p.G51G		Atlas-SNP	.											.	EDEM1	45	.	0			c.C153T						PASS	.			18,3802		0,18,1892	4.0	5.0	5.0		153	3.5	0.3	3	dbSNP_134	5	227,7631		2,223,3704	no	coding-synonymous	EDEM1	NM_014674.2		2,241,5596	TT,TC,CC		2.8888,0.4712,2.098		51/658	5229643	245,11433	1910	3929	5839	SO:0001819	synonymous_variant	9695	exon1			CGACGGCCCCGCG	D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.153C>T	3.37:g.5229643C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	21	15	0.714286	NM_014674	A8K9C8|B4DXP3	Silent	SNP	ENST00000256497.4	37	CCDS33686.1																																																																																			C|0.985;T|0.015	0.015	strong		0.736	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674	
CRABP1	1381	hgsc.bcm.edu	37	15	78632830	78632830	+	Silent	SNP	C	C	G	rs1127472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78632830C>G	ENST00000299529.6	+	1	165	c.60C>G	c.(58-60)ctC>ctG	p.L20L		NM_004378.2	NP_004369.1	P29762	RABP1_HUMAN	cellular retinoic acid binding protein 1	20					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoic acid binding (GO:0001972)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			breast(1)|lung(4)|skin(1)	6					Alitretinoin(DB00523)|Tretinoin(DB00755)	ACGAGCTGCTCAAGGCACTGG	0.711													C|||	2668	0.532748	0.3434	0.7104	5008	,	,		13100	0.498		0.6322	False		,,,				2504	0.5961				p.L20L	Ovarian(146;578 3231 38536)	Atlas-SNP	.											CRABP1,NS,carcinoma,0,1	CRABP1	21	1	0			c.C60G						PASS	.	C		1674,2712		328,1018,847	23.0	21.0	22.0		60	3.4	1.0	15	dbSNP_86	22	5858,2724		2012,1834,445	no	coding-synonymous	CRABP1	NM_004378.2		2340,2852,1292	GG,GC,CC		31.7409,38.1669,41.9186		20/138	78632830	7532,5436	2193	4291	6484	SO:0001819	synonymous_variant	1381	exon1			GCTGCTCAAGGCA		CCDS10301.1	15q24	2013-03-01	2001-11-28		ENSG00000166426	ENSG00000166426		"""Fatty acid binding protein family"""	2338	protein-coding gene	gene with protein product		180230	"""cellular retinoic acid-binding protein 1"""	RBP5		9154115	Standard	NM_004378		Approved	CRABP, CRABP-I, CRABPI	uc002bdp.2	P29762	OTTHUMG00000143862	ENST00000299529.6:c.60C>G	15.37:g.78632830C>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	127	124	0.976378	NM_004378	Q6IAY7|Q8WTV5	Silent	SNP	ENST00000299529.6	37	CCDS10301.1																																																																																			C|0.453;G|0.547	0.547	strong		0.711	CRABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290110.2	NM_004378	
ZNF214	7761	hgsc.bcm.edu	37	11	7022717	7022717	+	Missense_Mutation	SNP	T	T	C	rs1156526	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7022717T>C	ENST00000278314.4	-	3	512	c.197A>G	c.(196-198)tAc>tGc	p.Y66C	ZNF214_ENST00000531083.1_5'UTR|ZNF214_ENST00000536068.1_Missense_Mutation_p.Y66C	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		Y -> C (in dbSNP:rs1156526).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		GCCTTGCCAGTAGGAAAAATT	0.393													C|||	2968	0.592652	0.416	0.6354	5008	,	,		17954	0.7073		0.6223	False		,,,				2504	0.6524				p.Y66C	Ovarian(22;251 657 736 21522 46864)	Atlas-SNP	.											.	ZNF214	65	.	0			c.A197G						PASS	.	C	CYS/TYR	1818,2584	629.4+/-395.3	368,1082,751	121.0	127.0	125.0		197	-0.0	0.1	11	dbSNP_87	125	5328,3262	475.1+/-369.0	1670,1988,637	yes	missense	ZNF214	NM_013249.2	194	2038,3070,1388	CC,CT,TT		37.9744,41.2994,44.9969	benign	66/607	7022717	7146,5846	2201	4295	6496	SO:0001583	missense	7761	exon3			TGCCAGTAGGAAA	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"""Zinc fingers, C2H2-type"", ""-"""	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.197A>G	11.37:g.7022717T>C	ENSP00000278314:p.Tyr66Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_013249	B2R8Q1	Missense_Mutation	SNP	ENST00000278314.4	37	CCDS31418.1	1286	0.5888278388278388	204	0.4146341463414634	222	0.6132596685082873	388	0.6783216783216783	472	0.6226912928759895	C	0.003	-2.540209	0.00143	0.412994	0.620256	ENSG00000149050	ENST00000278314;ENST00000536068	T;T	0.05139	3.49;3.49	4.14	-0.00722	0.14010	Krueppel-associated box (1);	0.520211	0.16344	N	0.218548	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13098	-1.0522	9	0.23891	T	0.37	.	0.8929	0.01257	0.152:0.2747:0.2967:0.2767	rs1156526;rs17193385;rs52834751;rs60011445;rs1156526	66	Q9UL59	ZN214_HUMAN	C	66	ENSP00000278314:Y66C;ENSP00000445373:Y66C	ENSP00000278314:Y66C	Y	-	2	0	ZNF214	6979293	0.000000	0.05858	0.082000	0.20525	0.161000	0.22273	-0.816000	0.04477	-0.081000	0.12662	-0.119000	0.15052	TAC	C|0.558;N|0.000	0.558	strong		0.393	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
RIPK4	54101	hgsc.bcm.edu	37	21	43161877	43161877	+	Silent	SNP	C	C	T	rs3746893	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43161877C>T	ENST00000352483.2	-	9	1684	c.1620G>A	c.(1618-1620)gcG>gcA	p.A540A	RIPK4_ENST00000542057.1_Silent_p.A429A|RIPK4_ENST00000544709.1_Silent_p.A429A|RIPK4_ENST00000332512.3_Silent_p.A492A|AP001615.9_ENST00000423276.1_RNA			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	540					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TGATCTTCCGCGCCAGCAGGA	0.622													C|||	2204	0.440096	0.2806	0.4654	5008	,	,		20718	0.5704		0.4811	False		,,,				2504	0.4611				p.A492A		Atlas-SNP	.											.	RIPK4	151	.	0			c.G1476A						PASS	.	C		1415,2991	463.0+/-353.4	210,995,998	109.0	92.0	98.0		1476	0.8	0.7	21	dbSNP_107	98	3772,4828	535.7+/-382.9	848,2076,1376	yes	coding-synonymous	RIPK4	NM_020639.2		1058,3071,2374	TT,TC,CC		43.8605,32.1153,39.8816		492/785	43161877	5187,7819	2203	4300	6503	SO:0001819	synonymous_variant	54101	exon8			CTTCCGCGCCAGC	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1620G>A	21.37:g.43161877C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	58	56	0.965517	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				C|0.576;T|0.424	0.424	strong		0.622	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
MUTYH	4595	hgsc.bcm.edu	37	1	45797505	45797505	+	Missense_Mutation	SNP	C	C	G	rs587780083|rs3219489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45797505C>G	ENST00000372098.3	-	12	1138	c.1005G>C	c.(1003-1005)caG>caC	p.Q335H	MUTYH_ENST00000448481.1_Missense_Mutation_p.Q321H|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000354383.6_Missense_Mutation_p.Q311H|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000450313.1_Missense_Mutation_p.Q338H|MUTYH_ENST00000372100.5_Missense_Mutation_p.Q321H|MUTYH_ENST00000372104.1_Missense_Mutation_p.Q310H|MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000372110.3_Missense_Mutation_p.Q325H|MUTYH_ENST00000528013.2_Missense_Mutation_p.Q324H|MUTYH_ENST00000456914.2_Missense_Mutation_p.Q310H|MUTYH_ENST00000372115.3_Missense_Mutation_p.Q324H|MUTYH_ENST00000355498.2_Missense_Mutation_p.Q310H			Q9UIF7	MUTYH_HUMAN	mutY homolog	335			Q -> H (in dbSNP:rs3219489). {ECO:0000269|PubMed:12606733, ECO:0000269|Ref.4}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					ACAGGTGGCACTGTCCAGTGT	0.642			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis				C|||	1570	0.313498	0.2579	0.4841	5008	,	,		17085	0.3909		0.2445	False		,,,				2504	0.2587				p.Q338H		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.G1014C	GRCh37	CM083726	MUTYH	M	rs3219489	PASS	.	C	HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN	1161,3241		169,823,1209	15.0	18.0	17.0		972,933,930,930,1014,1005	1.3	1.0	1	dbSNP_106	17	2143,6457		256,1631,2413	yes	missense,missense,missense,missense,missense,missense	MUTYH	NM_001048171.1,NM_001048172.1,NM_001048173.1,NM_001048174.1,NM_001128425.1,NM_012222.2	24,24,24,24,24,24	425,2454,3622	GG,GC,CC		24.9186,26.3744,25.4115	benign,benign,benign,benign,benign,benign	324/536,311/523,310/522,310/522,338/550,335/547	45797505	3304,9698	2201	4300	6501	SO:0001583	missense	4595	exon12	Familial Cancer Database	MAP, MYH-associated polyposis	GTGGCACTGTCCA	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.1005G>C	1.37:g.45797505C>G	ENSP00000361170:p.Gln335His	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	37	CCDS520.1	696	0.31868131868131866	124	0.25203252032520324	149	0.4116022099447514	240	0.4195804195804196	183	0.24142480211081793	C	2.170	-0.390088	0.04932	0.263744	0.249186	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000525481;ENST00000412971	T;T;T;T;T;T;T;T;T;T;T	0.22945	3.23;3.23;3.23;3.23;3.23;3.22;3.22;3.22;3.22;3.23;1.93	5.66	1.26	0.21427	.	0.475733	0.24445	N	0.038471	T	0.00012	0.0000	M	0.69823	2.125	0.38421	P	0.05381199999999997	B;P;B;P;B;B;B	0.38745	0.343;0.645;0.326;0.645;0.219;0.324;0.219	B;B;B;B;B;B;B	0.34346	0.086;0.124;0.18;0.124;0.087;0.124;0.06	T	0.44360	-0.9333	9	0.42905	T	0.14	-13.6442	2.4732	0.04569	0.1089:0.4092:0.1175:0.3645	rs3219489;rs3811430;rs3219489	338;335;325;335;324;218;311	E5KP25;E5KP26;Q9UIF7-2;Q9UIF7;E5KP27;D3DPZ6;E5KP28	.;.;.;MUTYH_HUMAN;.;.;.	H	310;321;310;311;310;335;325;324;338;321;182;182	ENSP00000361176:Q310H;ENSP00000409718:Q321H;ENSP00000407590:Q310H;ENSP00000346354:Q311H;ENSP00000347685:Q310H;ENSP00000361170:Q335H;ENSP00000361182:Q325H;ENSP00000361187:Q324H;ENSP00000408176:Q338H;ENSP00000361172:Q321H;ENSP00000410263:Q182H	ENSP00000346354:Q311H	Q	-	3	2	MUTYH	45570092	0.034000	0.19679	1.000000	0.80357	0.077000	0.17291	0.051000	0.14141	0.240000	0.21263	-0.140000	0.14226	CAG	C|0.710;G|0.290	0.290	strong		0.642	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222	
CLCA2	9635	hgsc.bcm.edu	37	1	86909582	86909582	+	Missense_Mutation	SNP	G	G	A	rs1413426	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86909582G>A	ENST00000370565.4	+	10	1763	c.1601G>A	c.(1600-1602)gGt>gAt	p.G534D		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	534			G -> D (in dbSNP:rs1413426).		cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CAGGCCAGTGGTCCTCCTGAG	0.393													G|||	513	0.102436	0.1362	0.1052	5008	,	,		16996	0.0585		0.0934	False		,,,				2504	0.1094				p.G534D	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.G1601A						PASS	.	G	ASP/GLY	588,3818	258.0+/-262.2	36,516,1651	146.0	134.0	138.0		1601	3.2	0.0	1	dbSNP_88	138	706,7894	174.2+/-224.5	30,646,3624	yes	missense	CLCA2	NM_006536.5	94	66,1162,5275	AA,AG,GG		8.2093,13.3454,9.9493	benign	534/944	86909582	1294,11712	2203	4300	6503	SO:0001583	missense	9635	exon10			CCAGTGGTCCTCC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1601G>A	1.37:g.86909582G>A	ENSP00000359596:p.Gly534Asp	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	98	33	0.336735	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	192	0.08791208791208792	57	0.11585365853658537	41	0.1132596685082873	27	0.0472027972027972	67	0.08839050131926121	G	0.037	-1.303422	0.01353	0.133454	0.082093	ENSG00000137975	ENST00000370565	T	0.34667	1.35	5.13	3.25	0.37280	Domain of unknown function DUF1973 (1);	0.835260	0.10867	N	0.625379	T	0.09642	0.0237	L	0.45137	1.4	0.80722	P	0.0	B	0.06786	0.001	B	0.12156	0.007	T	0.27773	-1.0064	9	0.13853	T	0.58	-4.0188	3.444	0.07474	0.206:0.0:0.4484:0.3456	rs1413426;rs2390058;rs17099757;rs52811376;rs1413426	534	Q9UQC9	CLCA2_HUMAN	D	534	ENSP00000359596:G534D	ENSP00000359596:G534D	G	+	2	0	CLCA2	86682170	0.000000	0.05858	0.016000	0.15963	0.077000	0.17291	0.705000	0.25675	0.746000	0.32786	0.650000	0.86243	GGT	G|0.904;A|0.096	0.096	strong		0.393	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
PAK7	57144	hgsc.bcm.edu	37	20	9547018	9547018	+	Missense_Mutation	SNP	C	C	G	rs11700112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:9547018C>G	ENST00000378429.3	-	6	1550	c.1004G>C	c.(1003-1005)cGa>cCa	p.R335P	PAK7_ENST00000353224.5_Missense_Mutation_p.R335P|PAK7_ENST00000378423.1_Missense_Mutation_p.R335P	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	335	Linker.		R -> P (in dbSNP:rs11700112). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			CATCTGTGCTCGATCGTAATC	0.537													C|||	583	0.116414	0.0499	0.1787	5008	,	,		20027	0.2381		0.0954	False		,,,				2504	0.0583				p.R335P		Atlas-SNP	.											.	PAK7	194	.	0			c.G1004C	GRCh37	CM065365	PAK7	M	rs11700112	PASS	.	C	PRO/ARG,PRO/ARG	235,4171	138.4+/-174.2	9,217,1977	104.0	106.0	105.0		1004,1004	5.0	1.0	20	dbSNP_120	105	814,7786	189.4+/-236.2	40,734,3526	yes	missense,missense	PAK7	NM_020341.3,NM_177990.2	103,103	49,951,5503	GG,GC,CC		9.4651,5.3336,8.0655	benign,benign	335/720,335/720	9547018	1049,11957	2203	4300	6503	SO:0001583	missense	57144	exon5			TGTGCTCGATCGT	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"""p21(CDKN1A)-activated kinase 7"""			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1004G>C	20.37:g.9547018C>G	ENSP00000367686:p.Arg335Pro	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	305	0.13965201465201466	19	0.03861788617886179	71	0.19613259668508287	146	0.25524475524475526	69	0.09102902374670185	C	13.14	2.148585	0.37923	0.053336	0.094651	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.73575	-0.76;-0.76;-0.76	5.94	5.0	0.66597	.	0.129994	0.53938	D	0.000045	T	0.00039	0.0001	L	0.40543	1.245	0.09310	P	0.9999999490538	P;B	0.43477	0.808;0.0	P;B	0.46718	0.525;0.0	T	0.00783	-1.1568	8	.	.	.	.	15.1715	0.72878	0.0:0.9326:0.0:0.0674	rs11700112;rs11700112	335;335	B0AZM9;Q9P286	.;PAK7_HUMAN	P	335;335;335;283	ENSP00000367686:R335P;ENSP00000322957:R335P;ENSP00000367679:R335P	.	R	-	2	0	PAK7	9495018	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	5.261000	0.65496	1.519000	0.48950	0.591000	0.81541	CGA	C|0.888;G|0.112;T|0.000	0.112	strong		0.537	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
MEX3B	84206	hgsc.bcm.edu	37	15	82336551	82336551	+	Silent	SNP	C	C	T	rs61752329	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:82336551C>T	ENST00000329713.4	-	2	1095	c.660G>A	c.(658-660)gaG>gaA	p.E220E	MEX3B_ENST00000558133.1_3'UTR|AC026956.1_ENST00000410589.1_RNA	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	220	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						GCGCCTCAATCTCCTCTCGAG	0.607													C|||	292	0.0583067	0.0053	0.0893	5008	,	,		14393	0.0387		0.0636	False		,,,				2504	0.1227				p.E220E		Atlas-SNP	.											.	MEX3B	50	.	0			c.G660A						PASS	.	C		67,4339	62.3+/-99.4	1,65,2137	155.0	141.0	146.0		660	2.1	1.0	15	dbSNP_129	146	801,7799	187.9+/-235.0	39,723,3538	yes	coding-synonymous	MEX3B	NM_032246.3		40,788,5675	TT,TC,CC		9.314,1.5207,6.6738		220/570	82336551	868,12138	2203	4300	6503	SO:0001819	synonymous_variant	84206	exon2			CTCAATCTCCTCT	AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	25297	protein-coding gene	gene with protein product		611008	"""ring finger and KH domain containing 3"", ""mex-3 homolog B (C. elegans)"""	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.660G>A	15.37:g.82336551C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	115	62	0.53913	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Silent	SNP	ENST00000329713.4	37	CCDS10319.1																																																																																			C|0.940;T|0.060	0.060	strong		0.607	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645	
SYT10	341359	hgsc.bcm.edu	37	12	33535289	33535289	+	Silent	SNP	G	G	A	rs10844571	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:33535289G>A	ENST00000228567.3	-	5	1661	c.1365C>T	c.(1363-1365)taC>taT	p.Y455Y	SYT10_ENST00000535526.1_Silent_p.Y274Y	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	455	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					CATACCTATCGTAATCCATGA	0.458													G|||	996	0.198882	0.1619	0.2839	5008	,	,		16125	0.0655		0.2296	False		,,,				2504	0.2945				p.Y455Y		Atlas-SNP	.											.	SYT10	109	.	0			c.C1365T						PASS	.	G		759,3647	309.7+/-291.2	73,613,1517	189.0	164.0	173.0		1365	-7.7	0.1	12	dbSNP_120	173	1975,6625	346.0+/-326.0	231,1513,2556	no	coding-synonymous	SYT10	NM_198992.3		304,2126,4073	AA,AG,GG		22.9651,17.2265,21.0211		455/524	33535289	2734,10272	2203	4300	6503	SO:0001819	synonymous_variant	341359	exon5			CCTATCGTAATCC	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"""Synaptotagmins"""	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.1365C>T	12.37:g.33535289G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	100	61	0.61	NM_198992	Q495U2	Silent	SNP	ENST00000228567.3	37	CCDS8732.1																																																																																			G|0.800;A|0.200	0.200	strong		0.458	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992	
HRC	3270	hgsc.bcm.edu	37	19	49658367	49658367	+	Missense_Mutation	SNP	C	C	T	rs3745298	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49658367C>T	ENST00000252825.4	-	1	314	c.128G>A	c.(127-129)aGc>aAc	p.S43N	TRPM4_ENST00000355712.5_5'Flank|TRPM4_ENST00000252826.5_5'Flank|HRC_ENST00000595625.1_Missense_Mutation_p.S43N|TRPM4_ENST00000427978.2_5'Flank	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	43			S -> N (in dbSNP:rs3745298).		cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		GACTCCAGTGCTGTTGTTCCG	0.622													T|||	2362	0.471645	0.6029	0.5072	5008	,	,		17079	0.3105		0.4274	False		,,,				2504	0.4806				p.S43N	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G128A						PASS	.	T	ASN/SER	2502,1904	544.6+/-376.6	722,1058,423	109.0	105.0	106.0		128	1.0	0.0	19	dbSNP_107	106	3883,4717	608.0+/-395.3	885,2113,1302	yes	missense	HRC	NM_002152.2	46	1607,3171,1725	TT,TC,CC		45.1512,43.2138,49.0927	benign	43/700	49658367	6385,6621	2203	4300	6503	SO:0001583	missense	3270	exon1			CCAGTGCTGTTGT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.128G>A	19.37:g.49658367C>T	ENSP00000252825:p.Ser43Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	33	0.366667	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	969	0.44368131868131866	277	0.5630081300813008	199	0.5497237569060773	178	0.3111888111888112	315	0.4155672823218997	T	0.004	-2.383829	0.00202	0.567862	0.451512	ENSG00000130528	ENST00000252825	T	0.07216	3.21	3.26	0.99	0.19807	.	.	.	.	.	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39143	-0.9628	8	0.02654	T	1	-0.65	2.5446	0.04734	0.2012:0.241:0.0:0.5578	rs3745298;rs17272777;rs59685011;rs3745298	43	P23327	SRCH_HUMAN	N	43	ENSP00000252825:S43N	ENSP00000252825:S43N	S	-	2	0	HRC	54350179	0.633000	0.27181	0.006000	0.13384	0.023000	0.10783	0.529000	0.23019	-0.153000	0.11137	-0.361000	0.07541	AGC	C|0.523;T|0.477	0.477	strong		0.622	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
C12orf60	144608	hgsc.bcm.edu	37	12	14976178	14976178	+	Missense_Mutation	SNP	T	T	A	rs7307438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:14976178T>A	ENST00000330828.2	+	2	513	c.309T>A	c.(307-309)aaT>aaA	p.N103K	C12orf60_ENST00000527783.1_Intron	NM_175874.3	NP_787070.2	Q5U649	CL060_HUMAN	chromosome 12 open reading frame 60	103			N -> K (in dbSNP:rs7307438).							breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	9						AGAGTACCAATGTAGAGGAGT	0.438													T|||	953	0.190296	0.3238	0.0893	5008	,	,		20369	0.0823		0.1431	False		,,,				2504	0.2413				p.N103K		Atlas-SNP	.											.	C12orf60	31	.	0			c.T309A						PASS	.	T	LYS/ASN	1147,3259	407.5+/-334.3	148,851,1204	144.0	141.0	142.0		309	-1.9	0.0	12	dbSNP_116	142	1312,7288	259.4+/-282.6	107,1098,3095	yes	missense	C12orf60	NM_175874.3	94	255,1949,4299	AA,AT,TT		15.2558,26.0327,18.9067	benign	103/246	14976178	2459,10547	2203	4300	6503	SO:0001583	missense	144608	exon2			TACCAATGTAGAG	BC038836	CCDS8667.1	12p12.3	2012-08-16			ENSG00000182993	ENSG00000182993			28726	protein-coding gene	gene with protein product						12477932	Standard	NM_175874		Approved	MGC47869	uc001rcj.4	Q5U649	OTTHUMG00000167473	ENST00000330828.2:c.309T>A	12.37:g.14976178T>A	ENSP00000331691:p.Asn103Lys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	156	90	0.576923	NM_175874	A8K1M7|Q5XKK8|Q8IXY2	Missense_Mutation	SNP	ENST00000330828.2	37	CCDS8667.1	356	0.163003663003663	154	0.3130081300813008	44	0.12154696132596685	56	0.0979020979020979	102	0.1345646437994723	T	11.77	1.737679	0.30774	0.260327	0.152558	ENSG00000182993	ENST00000330828	T	0.13420	2.59	4.95	-1.91	0.07641	.	0.589703	0.15289	N	0.270244	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.27656	0.184	B	0.27500	0.08	T	0.42599	-0.9442	9	0.07030	T	0.85	-23.9843	4.3307	0.11062	0.1526:0.3523:0.0:0.4951	rs7307438;rs12820474;rs52817077;rs7307438	103	Q5U649	CL060_HUMAN	K	103	ENSP00000331691:N103K	ENSP00000331691:N103K	N	+	3	2	C12orf60	14867445	0.000000	0.05858	0.000000	0.03702	0.215000	0.24574	0.559000	0.23485	-0.144000	0.11314	0.459000	0.35465	AAT	T|0.822;A|0.178	0.178	strong		0.438	C12orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394735.1	NM_175874	
CCDC174	51244	hgsc.bcm.edu	37	3	14712433	14712433	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14712433A>G	ENST00000383794.3	+	11	1209	c.1136A>G	c.(1135-1137)cAg>cGg	p.Q379R	CCDC174_ENST00000476763.1_3'UTR|CCDC174_ENST00000303688.7_Missense_Mutation_p.Q303R	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	379						cytoplasm (GO:0005737)|nucleus (GO:0005634)											TCGAAGAGGCAGTCAGATCTC	0.423																																					p.Q379R		Atlas-SNP	.											.	.	.	.	0			c.A1136G						PASS	.						44.0	42.0	42.0					3																	14712433		2203	4300	6503	SO:0001583	missense	51244	exon11			AGAGGCAGTCAGA	AF151046	CCDS2620.2	3p25.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000154781	ENSG00000154781			28033	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 19"""	C3orf19		11042152	Standard	NM_016474		Approved	FLJ33839	uc003byw.3	Q6PII3	OTTHUMG00000129837	ENST00000383794.3:c.1136A>G	3.37:g.14712433A>G	ENSP00000373304:p.Gln379Arg	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	206	91	0.441748	NM_016474	Q96CS5	Missense_Mutation	SNP	ENST00000383794.3	37	CCDS2620.2	.	.	.	.	.	.	.	.	.	.	A	10.78	1.447406	0.25987	.	.	ENSG00000154781	ENST00000383794;ENST00000303688;ENST00000285042	T;T	0.41065	1.01;1.07	5.38	5.38	0.77491	.	0.056905	0.64402	D	0.000002	T	0.28499	0.0705	L	0.43923	1.385	0.24589	N	0.993836	B	0.06786	0.001	B	0.06405	0.002	T	0.22173	-1.0224	10	0.11794	T	0.64	-35.5946	4.9429	0.13975	0.751:0.0:0.0857:0.1633	.	379	Q6PII3	CC019_HUMAN	R	379;303;206	ENSP00000373304:Q379R;ENSP00000302344:Q303R	ENSP00000285042:Q206R	Q	+	2	0	C3orf19	14687437	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.611000	0.54132	2.042000	0.60477	0.482000	0.46254	CAG	.	.	none		0.423	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474	
TRIP4	9325	hgsc.bcm.edu	37	15	64710827	64710827	+	Silent	SNP	T	T	C	rs4776494	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:64710827T>C	ENST00000261884.3	+	9	1318	c.1258T>C	c.(1258-1260)Ttg>Ctg	p.L420L	RN7SL707P_ENST00000582206.1_RNA	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	420					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						TCAGCACCAGTTGCGAATCCA	0.483													T|||	569	0.113618	0.0121	0.4222	5008	,	,		16815	0.0327		0.1441	False		,,,				2504	0.0838				p.L420L		Atlas-SNP	.											.	TRIP4	43	.	0			c.T1258C						PASS	.	T		149,4257	102.1+/-140.7	1,147,2055	102.0	87.0	92.0		1258	-3.8	0.1	15	dbSNP_111	92	1372,7228	266.0+/-286.5	103,1166,3031	no	coding-synonymous	TRIP4	NM_016213.4		104,1313,5086	CC,CT,TT		15.9535,3.3818,11.6946		420/582	64710827	1521,11485	2203	4300	6503	SO:0001819	synonymous_variant	9325	exon9			CACCAGTTGCGAA	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"""-"""	12310	protein-coding gene	gene with protein product	"""zinc finger, C2HC5-type"""	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.1258T>C	15.37:g.64710827T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Silent	SNP	ENST00000261884.3	37	CCDS10194.1																																																																																			T|0.892;C|0.108	0.108	strong		0.483	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213	
ZNF805	390980	hgsc.bcm.edu	37	19	57760057	57760057	+	Missense_Mutation	SNP	G	G	A	rs3746231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57760057G>A	ENST00000414468.2	+	3	242	c.242G>A	c.(241-243)gGc>gAc	p.G81D	ZNF805_ENST00000354309.4_5'UTR|ZNF805_ENST00000535550.1_5'UTR	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	81	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(3)|lung(1)|stomach(1)	9						CTCTCCCAAGGCACCTGTCCA	0.577													.|||	1836	0.366613	0.2489	0.4496	5008	,	,		19467	0.1687		0.5746	False		,,,				2504	0.4571				p.G81D		Atlas-SNP	.											.	ZNF805	30	.	0			c.G242A						PASS	.	G	ASP/GLY,	383,1001		52,279,361	59.0	54.0	56.0		242,	2.5	0.0	19	dbSNP_107	56	1646,1536		429,788,374	no	missense,utr-5	ZNF805	NM_001023563.3,NM_001145078.1	94,	481,1067,735	AA,AG,GG		48.2715,27.6734,44.4371	benign,	81/628,	57760057	2029,2537	692	1591	2283	SO:0001583	missense	390980	exon3			CCCAAGGCACCTG	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.242G>A	19.37:g.57760057G>A	ENSP00000412999:p.Gly81Asp	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_001023563	B4DNM5	Missense_Mutation	SNP	ENST00000414468.2	37	CCDS46207.1	792	0.3626373626373626	114	0.23170731707317074	166	0.4585635359116022	100	0.17482517482517482	412	0.5435356200527705	G	2.919	-0.223725	0.06061	0.276734	0.517285	ENSG00000204524	ENST00000414468	T	0.21191	2.02	4.67	2.54	0.30619	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	L	0.31420	0.93	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.42799	-0.9430	8	0.23891	T	0.37	.	8.8209	0.35025	0.2708:0.0:0.7292:0.0	rs3746231;rs60834144;rs3746231	81	Q5CZA5	ZN805_HUMAN	D	81	ENSP00000412999:G81D	ENSP00000412999:G81D	G	+	2	0	ZNF805	62451869	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	0.190000	0.17057	0.214000	0.20742	-0.797000	0.03246	GGC	G|0.643;A|0.357	0.357	strong		0.577	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563	
GPER1	2852	hgsc.bcm.edu	37	7	1131411	1131411	+	Missense_Mutation	SNP	C	C	T	rs11544331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:1131411C>T	ENST00000297469.3	+	2	738	c.47C>T	c.(46-48)cCa>cTa	p.P16L	GPER1_ENST00000401670.1_Missense_Mutation_p.P16L|C7orf50_ENST00000397098.3_Intron|GPER1_ENST00000397088.3_Missense_Mutation_p.P16L|GPER1_ENST00000397092.1_Missense_Mutation_p.P16L|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	16			P -> L (in dbSNP:rs11544331). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19054851}.		apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										GAGATGTACCCAGGCACCGCG	0.652													C|||	696	0.138978	0.1021	0.2104	5008	,	,		16292	0.0248		0.2048	False		,,,				2504	0.1881				p.P16L		Atlas-SNP	.											.	GPER	25	.	0			c.C47T						PASS	.		LEU/PRO,LEU/PRO,,,LEU/PRO,	507,3897	232.0+/-245.7	34,439,1729	53.0	57.0	55.0		47,47,,,47,	-0.1	0.0	7	dbSNP_120	55	2106,6494	358.5+/-331.2	276,1554,2470	yes	missense,missense,intron,intron,missense,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	98,98,,,98,	310,1993,4199	TT,TC,CC		24.4884,11.5123,20.0938	benign,benign,,,benign,	16/376,16/376,,,16/376,	1131411	2613,10391	2202	4300	6502	SO:0001583	missense	2852	exon2			TGTACCCAGGCAC	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"""G protein-coupled receptor 30"""	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.47C>T	7.37:g.1131411C>T	ENSP00000297469:p.Pro16Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Missense_Mutation	SNP	ENST00000297469.3	37	CCDS5322.1	319	0.14606227106227107	70	0.14227642276422764	66	0.18232044198895028	19	0.033216783216783216	164	0.21635883905013192	C	10.93	1.490502	0.26686	0.115123	0.244884	ENSG00000164850	ENST00000401670;ENST00000413368;ENST00000397092;ENST00000297469;ENST00000397088;ENST00000508834	T;T;T;T;T	0.67171	-0.25;1.03;-0.25;-0.25;-0.25	5.02	-0.101	0.13618	.	0.664049	0.13173	N	0.408117	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09640	-1.0665	9	0.31617	T	0.26	.	8.8766	0.35350	0.0:0.5996:0.0:0.4004	rs11544331;rs17850769	16	Q99527	GPER_HUMAN	L	16	ENSP00000385151:P16L;ENSP00000410487:P16L;ENSP00000380281:P16L;ENSP00000297469:P16L;ENSP00000380277:P16L	ENSP00000297469:P16L	P	+	2	0	GPER	1097937	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.053000	0.14184	-0.347000	0.08299	0.655000	0.94253	CCA	C|0.808;T|0.192	0.192	strong		0.652	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
ACE	1636	hgsc.bcm.edu	37	17	61573761	61573761	+	Silent	SNP	T	T	C	rs4362	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:61573761T>C	ENST00000290866.4	+	23	3411	c.3387T>C	c.(3385-3387)ttT>ttC	p.F1129F	ACE_ENST00000577647.1_Silent_p.F555F|ACE_ENST00000421982.2_Intron|ACE_ENST00000490216.2_Silent_p.F555F|ACE_ENST00000413513.3_Intron|ACE_ENST00000428043.1_Silent_p.F1129F|ACE_ENST00000290863.6_Silent_p.F555F	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1129	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	CCAGGTACTTTGTCAGCTTCA	0.617													C|||	2942	0.58746	0.6225	0.5893	5008	,	,		17808	0.6081		0.4433	False		,,,				2504	0.6656				p.F1129F		Atlas-SNP	.											.	ACE	187	.	0			c.T3387C						PASS	.	C	,,	2552,1854	538.7+/-375.1	739,1074,390	101.0	97.0	98.0		3387,,1665	-2.7	0.0	17	dbSNP_36	98	4020,4580	597.5+/-393.8	924,2172,1204	no	coding-synonymous,intron,coding-synonymous	ACE	NM_000789.3,NM_001178057.1,NM_152830.2	,,	1663,3246,1594	CC,CT,TT		46.7442,42.079,49.4695	,,	1129/1307,,555/733	61573761	6572,6434	2203	4300	6503	SO:0001819	synonymous_variant	1636	exon23			GTACTTTGTCAGC	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.3387T>C	17.37:g.61573761T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	207	207	1	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	37	CCDS11637.1																																																																																			T|0.478;C|0.522	0.522	strong		0.617	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
KLF12	11278	hgsc.bcm.edu	37	13	74339104	74339104	+	Silent	SNP	G	G	T	rs3764134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:74339104G>T	ENST00000377669.2	-	5	866	c.840C>A	c.(838-840)ggC>ggA	p.G280G	KLF12_ENST00000377666.4_Silent_p.G280G	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	280					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		tcattcgattgccccggaccc	0.358													T|||	2042	0.407748	0.388	0.389	5008	,	,		16354	0.1815		0.5209	False		,,,				2504	0.5644				p.G280G		Atlas-SNP	.											.	KLF12	42	.	0			c.C840A						PASS	.	T		1780,2626	643.4+/-397.8	346,1088,769	95.0	90.0	91.0		840	2.9	1.0	13	dbSNP_107	91	4897,3703	529.4+/-381.6	1404,2089,807	no	coding-synonymous	KLF12	NM_007249.4		1750,3177,1576	TT,TG,GG		43.0581,40.3995,48.6622		280/403	74339104	6677,6329	2203	4300	6503	SO:0001819	synonymous_variant	11278	exon6			TCGATTGCCCCGG	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6346	protein-coding gene	gene with protein product	"""KLF12 zinc finger transcriptional repressor"", ""AP-2rep transcription factor"", ""AP-2 repressor"""	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.840C>A	13.37:g.74339104G>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Silent	SNP	ENST00000377669.2	37	CCDS9449.1																																																																																			G|0.544;T|0.456	0.456	strong		0.358	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249	
C1orf141	400757	hgsc.bcm.edu	37	1	67558756	67558756	+	Missense_Mutation	SNP	C	C	T	rs41313272|rs112014958	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:67558756C>T	ENST00000371007.2	-	8	1244	c.1135G>A	c.(1135-1137)Gaa>Aaa	p.E379K	C1orf141_ENST00000544837.1_Missense_Mutation_p.E379K|C1orf141_ENST00000371006.1_Missense_Mutation_p.E379K	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	379										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						TTATTTAGTTCATATATATAT	0.299													T|||	582	0.116214	0.2617	0.085	5008	,	,		15815	0.0645		0.0507	False		,,,				2504	0.0624				p.E379K		Atlas-SNP	.											.	C1orf141	58	.	0			c.G1135A						PASS	.	T	LYS/GLU	767,3637		101,565,1536	52.0	57.0	55.0		1135	2.2	0.0	1	dbSNP_127	55	289,8301		10,269,4016	yes	missense	C1orf141	NM_001013674.1	56	111,834,5552	TT,TC,CC		3.3644,17.416,8.1268	benign	379/401	67558756	1056,11938	2202	4295	6497	SO:0001583	missense	400757	exon8			TTAGTTCATATAT	BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.1135G>A	1.37:g.67558756C>T	ENSP00000360046:p.Glu379Lys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	82	29	0.353659	NM_001276351	Q0P5P5|Q5JVX5	Missense_Mutation	SNP	ENST00000371007.2	37	CCDS30745.1	223	0.1021062271062271	128	0.2601626016260163	19	0.052486187845303865	32	0.055944055944055944	44	0.05804749340369393	T	0.333	-0.954711	0.02285	0.17416	0.033644	ENSG00000203963	ENST00000371007;ENST00000371006;ENST00000544837	T;T;T	0.28895	1.59;1.59;1.59	4.77	2.24	0.28232	.	0.523615	0.16296	N	0.220692	T	0.01661	0.0053	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43032	-0.9416	9	0.02654	T	1	-5.481	3.3393	0.07113	0.1683:0.2115:0.0:0.6202	rs41313272;rs58853081	379	Q5JVX7	CA141_HUMAN	K	379	ENSP00000360046:E379K;ENSP00000360045:E379K;ENSP00000444018:E379K	ENSP00000360045:E379K	E	-	1	0	C1orf141	67331344	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.301000	0.19174	0.014000	0.14944	-1.256000	0.01477	GAA	C|0.903;T|0.097	0.097	strong		0.299	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674	
CCL15	6359	hgsc.bcm.edu	37	17	34328461	34328461	+	Missense_Mutation	SNP	A	A	G	rs854625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34328461A>G	ENST00000354059.4	-	1	623	c.71T>C	c.(70-72)aTa>aCa	p.I24T	RP11-104J23.1_ENST00000590192.1_RNA|CCL14_ENST00000536149.1_5'UTR|CCL15-CCL14_ENST00000481427.2_Missense_Mutation_p.I24T	NM_032965.4	NP_116741.1	Q16663	CCL15_HUMAN	chemokine (C-C motif) ligand 15	24			I -> T (in dbSNP:rs854625). {ECO:0000269|PubMed:10213461, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9548457, ECO:0000269|PubMed:9600961, ECO:0000269|Ref.5}.		cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|immune response (GO:0006955)|positive chemotaxis (GO:0050918)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)|receptor binding (GO:0005102)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTCACCATTTATGAACTGGGC	0.582													G|||	3751	0.749002	0.5613	0.9078	5008	,	,		16742	0.6339		0.9642	False		,,,				2504	0.7873				p.I24T		Atlas-SNP	.											.	CCL15	15	.	0			c.T71C						PASS	.	G	THR/ILE	2500,1906	542.2+/-376.0	725,1050,428	90.0	68.0	76.0		71	-4.8	0.0	17	dbSNP_86	76	8258,342	117.4+/-177.0	3962,334,4	yes	missense	CCL15	NM_032965.4	89	4687,1384,432	GG,GA,AA		3.9767,43.2592,17.2843	benign	24/114	34328461	10758,2248	2203	4300	6503	SO:0001583	missense	6359	exon1			CCATTTATGAACT	AF031587	CCDS11304.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000267596	ENSG00000275718		"""Chemokine ligands"", ""Endogenous ligands"""	10613	protein-coding gene	gene with protein product	"""leukotactin 1"", ""CC chemokine 3"", ""macrophage inflammatory protein 5"", ""chemokine CC-2"", ""MIP-1 delta"""	601393	"""small inducible cytokine subfamily A (Cys-Cys), member 15"""	SCYA15		8661057	Standard	NM_032965		Approved	HCC-2, NCC-3, SCYL3, MIP-5, Lkn-1, MIP-1d, HMRP-2B	uc010wcu.2	Q16663	OTTHUMG00000188406	ENST00000354059.4:c.71T>C	17.37:g.34328461A>G	ENSP00000293276:p.Ile24Thr	Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	226	225	0.995575	NM_032965	B2RU34|E1P651|Q9UM74	Missense_Mutation	SNP	ENST00000354059.4	37	CCDS11304.1	1704	0.7802197802197802	272	0.5528455284552846	328	0.9060773480662984	376	0.6573426573426573	728	0.9604221635883905	G	0.006	-2.106246	0.00356	0.567408	0.960233	ENSG00000161574	ENST00000354059	T	0.04917	3.53	3.32	-4.81	0.03180	.	3.741260	0.01012	N	0.003857	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31447	-0.9943	9	0.13108	T	0.6	.	12.3274	0.55020	0.4188:0.0:0.5812:0.0	rs854625;rs1128444;rs1719173;rs3177316;rs3185422;rs11553773;rs16971829;rs17410383;rs52834916;rs59761819;rs854625	24	Q16663	CCL15_HUMAN	T	24	ENSP00000293276:I24T	ENSP00000293276:I24T	I	-	2	0	CCL15	31352574	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.300000	0.00521	-1.807000	0.01236	-1.838000	0.00587	ATA	A|0.198;G|0.802	0.802	strong		0.582	CCL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256584.2	NM_004167	
MEFV	4210	hgsc.bcm.edu	37	16	3304762	3304762	+	Silent	SNP	A	A	G	rs224225	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3304762A>G	ENST00000219596.1	-	2	345	c.306T>C	c.(304-306)gaT>gaC	p.D102D	MEFV_ENST00000339854.4_Intron|MEFV_ENST00000541159.1_Intron|MEFV_ENST00000536379.1_Intron	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	102					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CTGCGGAATCATCTGTGCCGT	0.577													G|||	1950	0.389377	0.5265	0.5937	5008	,	,		15005	0.1577		0.4732	False		,,,				2504	0.2117				p.D102D		Atlas-SNP	.											MEFV,NS,carcinoma,0,1	MEFV	170	1	0			c.T306C						PASS	.	G	,	2168,2164		591,986,589	49.0	54.0	52.0		306,	1.0	0.0	16	dbSNP_79	52	3945,4557		975,1995,1281	no	coding-synonymous,intron	MEFV	NM_000243.2,NM_001198536.1	,	1566,2981,1870	GG,GA,AA		46.4008,49.9538,47.6313	,	102/782,	3304762	6113,6721	2166	4251	6417	SO:0001819	synonymous_variant	4210	exon2			GGAATCATCTGTG	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.306T>C	16.37:g.3304762A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			A|0.557;G|0.443	0.443	strong		0.577	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
TBC1D19	55296	hgsc.bcm.edu	37	4	26585881	26585881	+	Silent	SNP	C	C	T	rs4692549	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:26585881C>T	ENST00000264866.4	+	1	344	c.66C>T	c.(64-66)tcC>tcT	p.S22S	TBC1D19_ENST00000511789.1_Silent_p.S22S	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	22							Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				TCAAGGGCTCCAATTTGTACT	0.607													C|||	1568	0.313099	0.1672	0.2795	5008	,	,		15170	0.3601		0.3946	False		,,,				2504	0.4018				p.S22S		Atlas-SNP	.											.	TBC1D19	53	.	0			c.C66T						PASS	.	C		951,3455	349.5+/-310.4	118,715,1370	50.0	49.0	49.0		66	2.2	0.9	4	dbSNP_111	49	3513,5087	501.4+/-375.5	720,2073,1507	no	coding-synonymous	TBC1D19	NM_018317.2		838,2788,2877	TT,TC,CC		40.8488,21.5842,34.3226		22/527	26585881	4464,8542	2203	4300	6503	SO:0001819	synonymous_variant	55296	exon1			GGGCTCCAATTTG	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.66C>T	4.37:g.26585881C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_018317	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	37	CCDS3439.1																																																																																			C|0.679;T|0.321	0.321	strong		0.607	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317	
GNB3	2784	hgsc.bcm.edu	37	12	6954864	6954864	+	Missense_Mutation	SNP	G	G	A	rs5442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6954864G>A	ENST00000229264.3	+	10	1219	c.814G>A	c.(814-816)Ggc>Agc	p.G272S	GNB3_ENST00000435982.2_Missense_Mutation_p.G271S|CDCA3_ENST00000422785.3_3'UTR|CDCA3_ENST00000604599.1_5'UTR	NM_002075.2	NP_002066.1	P16520	GBB3_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 3	272			G -> S (in dbSNP:rs5442). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|stomach(1)	20						CATCATCTGCGGCATCACGTC	0.592													G|||	98	0.0195687	0.0008	0.0317	5008	,	,		-128	0.0		0.0666	False		,,,				2504	0.0082				p.G272S		Atlas-SNP	.											.	GNB3	36	.	0			c.G814A						PASS	.	G	SER/GLY	60,4346	58.1+/-94.6	0,60,2143	173.0	160.0	164.0		814	4.6	1.0	12	dbSNP_52	164	586,8014	155.8+/-209.8	24,538,3738	yes	missense	GNB3	NM_002075.2	56	24,598,5881	AA,AG,GG		6.814,1.3618,4.9669	possibly-damaging	272/341	6954864	646,12360	2203	4300	6503	SO:0001583	missense	2784	exon10			ATCTGCGGCATCA		CCDS8564.1, CCDS73427.1	12p13	2013-01-10			ENSG00000111664	ENSG00000111664		"""WD repeat domain containing"""	4400	protein-coding gene	gene with protein product		139130				11770079, 16600389	Standard	XM_005253680		Approved		uc001qrd.3	P16520	OTTHUMG00000168517	ENST00000229264.3:c.814G>A	12.37:g.6954864G>A	ENSP00000229264:p.Gly272Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	157	78	0.496815	NM_002075	Q96B71|Q9BQC0	Missense_Mutation	SNP	ENST00000229264.3	37	CCDS8564.1	69	0.03159340659340659	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	58	0.07651715039577836	G	27.7	4.855061	0.91355	0.013618	0.06814	ENSG00000111664	ENST00000229264;ENST00000435982;ENST00000537035	T;T;T	0.59364	0.27;0.27;0.27	4.63	4.63	0.57726	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.14399	0.0348	M	0.67397	2.05	0.80722	D	1	D;D	0.69078	0.997;0.967	D;D	0.70227	0.968;0.921	T	0.51301	-0.8723	10	0.41790	T	0.15	-9.5829	17.6726	0.88222	0.0:0.0:1.0:0.0	rs5442;rs2230333;rs16932941;rs17844824;rs17857535;rs17857681;rs59150134;rs5442	271;272	E9PCP0;P16520	.;GBB3_HUMAN	S	272;271;231	ENSP00000229264:G272S;ENSP00000414734:G271S;ENSP00000445967:G231S	ENSP00000229264:G272S	G	+	1	0	GNB3	6825125	1.000000	0.71417	0.959000	0.39883	0.632000	0.37999	9.657000	0.98554	2.383000	0.81215	0.655000	0.94253	GGC	G|0.955;A|0.045	0.045	strong		0.592	GNB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400006.1	NM_002075	
PREX1	57580	hgsc.bcm.edu	37	20	47269233	47269233	+	Missense_Mutation	SNP	C	C	G	rs41283558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:47269233C>G	ENST00000371941.3	-	21	2380	c.2358G>C	c.(2356-2358)caG>caC	p.Q786H	PREX1_ENST00000396220.1_Missense_Mutation_p.Q786H	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	786			Q -> H (in dbSNP:rs41283558). {ECO:0000269|PubMed:17974005}.		actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GGTAGATCCACTGGTACAGGC	0.652													C|||	749	0.149561	0.0197	0.2118	5008	,	,		15382	0.1468		0.1849	False		,,,				2504	0.2474				p.Q786H		Atlas-SNP	.											PREX1_ENST00000396220,colon,carcinoma,0,2	PREX1	441	2	0			c.G2358C						PASS	.	C	HIS/GLN	250,4156	144.2+/-179.2	10,230,1963	58.0	47.0	51.0		2358	3.6	1.0	20	dbSNP_127	51	1623,6977	299.4+/-304.4	148,1327,2825	yes	missense	PREX1	NM_020820.3	24	158,1557,4788	GG,GC,CC		18.8721,5.6741,14.401	benign	786/1660	47269233	1873,11133	2203	4300	6503	SO:0001583	missense	57580	exon21			GATCCACTGGTAC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2358G>C	20.37:g.47269233C>G	ENSP00000361009:p.Gln786His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	68	41	0.602941	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	310	0.14194139194139194	13	0.026422764227642278	81	0.22375690607734808	81	0.14160839160839161	135	0.17810026385224276	C	13.41	2.228164	0.39399	0.056741	0.188721	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.41758	0.99;0.99	4.5	3.56	0.40772	PDZ/DHR/GLGF (1);	0.117523	0.37219	N	0.002182	T	0.00039	0.0001	L	0.50333	1.59	0.21675	P	0.999593756	B;B	0.16603	0.009;0.018	B;B	0.21546	0.019;0.035	T	0.09122	-1.0689	9	0.36615	T	0.2	.	13.9532	0.64131	0.1531:0.8469:0.0:0.0	rs41283558	786;83	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	H	786	ENSP00000361009:Q786H;ENSP00000379522:Q786H	ENSP00000361009:Q786H	Q	-	3	2	PREX1	46702640	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	3.347000	0.52200	0.893000	0.36288	-0.224000	0.12420	CAG	C|0.852;G|0.148	0.148	strong		0.652	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
BRMS1	25855	hgsc.bcm.edu	37	11	66105194	66105194	+	3'UTR	SNP	G	G	A	rs1052566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66105194G>A	ENST00000359957.3	-	0	1060				BRMS1_ENST00000425825.2_Missense_Mutation_p.A273V|RIN1_ENST00000530056.1_5'Flank|RIN1_ENST00000424433.2_5'Flank|RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000311320.4_5'Flank	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1						apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						AGGAGTCCAGGCCAGTGCCAG	0.682													G|||	1336	0.266773	0.034	0.2161	5008	,	,		17840	0.3284		0.2714	False		,,,				2504	0.5491				p.A273V	GBM(7;55 307 2662 20856 28942)	Atlas-SNP	.											.	BRMS1	42	.	0			c.C818T						PASS	.	G	,VAL/ALA	356,4040		20,316,1862	22.0	28.0	26.0		,818	-4.2	0.0	11	dbSNP_86	26	2563,6027		379,1805,2111	yes	utr-3,missense	BRMS1	NM_015399.3,NM_001024957.1	,64	399,2121,3973	AA,AG,GG		29.837,8.0983,22.4781	,benign	,273/291	66105194	2919,10067	2198	4295	6493	SO:0001624	3_prime_UTR_variant	25855	exon10			GTCCAGGCCAGTG	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.*159C>T	11.37:g.66105194G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_001024957	Q6IAI2	Missense_Mutation	SNP	ENST00000359957.3	37	CCDS8135.1	508	0.2326007326007326	20	0.04065040650406504	88	0.2430939226519337	188	0.32867132867132864	212	0.2796833773087071	G	1.743	-0.491122	0.04322	0.080983	0.29837	ENSG00000174744	ENST00000425825	.	.	.	2.79	-4.24	0.03777	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44802	-0.9304	7	0.29301	T	0.29	.	4.6989	0.12818	0.4247:0.1659:0.4094:0.0	rs1052566;rs3178148;rs3192977	273	G5E9I4	.	V	273	.	ENSP00000396052:A273V	A	-	2	0	BRMS1	65861770	0.001000	0.12720	0.000000	0.03702	0.317000	0.28152	-0.952000	0.03881	-0.973000	0.03555	0.400000	0.26472	GCC	G|0.765;A|0.235	0.235	strong		0.682	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399	
PHTF2	57157	hgsc.bcm.edu	37	7	77552127	77552127	+	Intron	SNP	G	G	A	rs848486	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:77552127G>A	ENST00000248550.7	+	10	1195				PHTF2_ENST00000454592.1_Intron|PHTF2_ENST00000275575.7_Intron|PHTF2_ENST00000416283.2_Intron|PHTF2_ENST00000450574.1_Missense_Mutation_p.R350H|PHTF2_ENST00000307305.8_Intron|PHTF2_ENST00000415251.2_Missense_Mutation_p.R346H|PHTF2_ENST00000422959.2_Intron|PHTF2_ENST00000424760.1_Intron			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						GTATACATACGTATCTATTTT	0.259													A|||	3019	0.602835	0.4349	0.6859	5008	,	,		17641	0.7808		0.5527	False		,,,				2504	0.6391				p.R350H		Atlas-SNP	.											.	PHTF2	104	.	0			c.G1049A						PASS	.	A	,,HIS/ARG,HIS/ARG,	1661,1923		405,851,536	27.0	24.0	25.0		,,1049,1037,	-0.8	0.0	7	dbSNP_86	25	4735,3379		1433,1869,755	yes	intron,intron,missense,missense,intron	PHTF2	NM_001127357.1,NM_001127358.1,NM_001127359.1,NM_001127360.1,NM_020432.4	,,29,29,	1838,2720,1291	AA,AG,GG		41.6441,46.3449,45.324	,,,,	,,350/357,346/353,	77552127	6396,5302	1792	4057	5849	SO:0001627	intron_variant	57157	exon9			ACATACGTATCTA	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1119+32G>A	7.37:g.77552127G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_001127359	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	37		1335	0.6112637362637363	212	0.43089430894308944	252	0.6961325966850829	447	0.7814685314685315	424	0.5593667546174143	A	12.87	2.068590	0.36470	0.463449	0.583559	ENSG00000006576	ENST00000415251;ENST00000450574	.	.	.	4.87	-0.832	0.10785	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32322	-0.9911	5	.	.	.	.	6.3219	0.21223	0.391:0.2279:0.3811:0.0	rs848486;rs57120629	350;346	G5E9H7;E9PEE3	.;.	H	346;350	.	.	R	+	2	0	PHTF2	77390063	0.000000	0.05858	0.000000	0.03702	0.213000	0.24496	-2.200000	0.01237	-0.252000	0.09528	-0.254000	0.11334	CGT	G|0.399;A|0.601	0.601	strong		0.259	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432	
ADAM29	11086	hgsc.bcm.edu	37	4	175898983	175898983	+	Missense_Mutation	SNP	A	A	T	rs139492823	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175898983A>T	ENST00000359240.3	+	5	2977	c.2307A>T	c.(2305-2307)caA>caT	p.Q769H	ADAM29_ENST00000445694.1_Missense_Mutation_p.Q769H|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.Q769H|ADAM29_ENST00000404450.4_Missense_Mutation_p.Q769H	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	769	9 X 9 AA approximate repeats.			QPRVM -> HPQLT (in Ref. 1; AAF03777). {ECO:0000305}.	spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCCAGAGTCAACCTCGGGTGA	0.572																																					p.Q769H	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.A2307T						PASS	.						174.0	153.0	160.0					4																	175898983		2203	4300	6503	SO:0001583	missense	11086	exon4			GAGTCAACCTCGG	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2307A>T	4.37:g.175898983A>T	ENSP00000352177:p.Gln769His	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	210	26	0.12381	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	A	8.298	0.819246	0.16607	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01963	4.53;4.53;4.53;4.53	0.945	-0.731	0.11151	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.48927	-0.8991	8	.	.	.	.	2.1103	0.03701	0.4116:0.338:0.2504:0.0	.	769	Q9UKF5	ADA29_HUMAN	H	769	ENSP00000352177:Q769H;ENSP00000414544:Q769H;ENSP00000384229:Q769H;ENSP00000423517:Q769H	.	Q	+	3	2	ADAM29	176135558	0.000000	0.05858	0.012000	0.15200	0.123000	0.20343	0.110000	0.15437	-0.185000	0.10550	0.372000	0.22366	CAA	A|0.996;T|0.005	0.005	strong		0.572	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
OBSCN	84033	hgsc.bcm.edu	37	1	228494790	228494790	+	Missense_Mutation	SNP	G	G	A	rs435776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228494790G>A	ENST00000422127.1	+	45	12159	c.12115G>A	c.(12115-12117)Gga>Aga	p.G4039R	OBSCN_ENST00000284548.11_Missense_Mutation_p.G4039R|OBSCN_ENST00000570156.2_Missense_Mutation_p.G4996R|OBSCN_ENST00000366709.4_Missense_Mutation_p.G1158R|OBSCN_ENST00000366707.4_Missense_Mutation_p.G1673R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4039	Ig-like 41.		G -> R (in dbSNP:rs435776).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTGGTACGCGGAGTGGAGCA	0.642													G|||	1345	0.26857	0.0605	0.3775	5008	,	,		18993	0.249		0.4841	False		,,,				2504	0.271				p.G4996R		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,2	OBSCN	2142	2	0			c.G14986A						PASS	.	G	ARG/GLY,ARG/GLY	513,3873		42,429,1722	66.0	79.0	74.0		12115,12115	0.3	0.0	1	dbSNP_80	74	4232,4336		1070,2092,1122	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	125,125	1112,2521,2844	AA,AG,GG		49.3931,11.6963,36.6296	probably-damaging,probably-damaging	4039/7969,4039/6621	228494790	4745,8209	2193	4284	6477	SO:0001583	missense	84033	exon56			GTACGCGGAGTGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12115G>A	1.37:g.228494790G>A	ENSP00000409493:p.Gly4039Arg	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	339	167	0.492625	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	663	0.30357142857142855	35	0.07113821138211382	136	0.3756906077348066	134	0.23426573426573427	358	0.47229551451187335	G	10.99	1.506355	0.26949	0.116963	0.493931	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.04654	3.58;3.58;3.58;3.58	5.81	0.336	0.15958	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.527305	0.18679	N	0.134218	T	0.00012	0.0000	L	0.37630	1.12	0.80722	P	0.0	P;B	0.43578	0.811;0.058	B;B	0.34652	0.187;0.012	T	0.34403	-0.9830	9	0.15066	T	0.55	.	7.3643	0.26764	0.325:0.1044:0.5706:0.0	rs435776;rs61021469;rs435776	4039;4039	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	R	4039;4039;1673;1158	ENSP00000284548:G4039R;ENSP00000409493:G4039R;ENSP00000355668:G1673R;ENSP00000355670:G1158R	ENSP00000284548:G4039R	G	+	1	0	OBSCN	226561413	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.390000	0.07332	-0.169000	0.10834	0.462000	0.41574	GGA	G|0.711;A|0.289	0.289	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CDAN1	146059	hgsc.bcm.edu	37	15	43022868	43022868	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43022868G>A	ENST00000356231.3	-	14	2125	c.2102C>T	c.(2101-2103)tCc>tTc	p.S701F		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	701					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GTCAGCAAAGGAGAGAAACTC	0.622																																					p.S701F		Atlas-SNP	.											.	CDAN1	70	.	0			c.C2102T						PASS	.						38.0	41.0	40.0					15																	43022868		2203	4299	6502	SO:0001583	missense	146059	exon14			GCAAAGGAGAGAA	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2102C>T	15.37:g.43022868G>A	ENSP00000348564:p.Ser701Phe	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	186	10	0.0537634	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	G	31	5.097079	0.94197	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86432	-2.12	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.93887	0.8044	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93948	0.7229	10	0.87932	D	0	-20.6001	19.9915	0.97366	0.0:0.0:1.0:0.0	.	701	Q8IWY9	CDAN1_HUMAN	F	701;699	ENSP00000348564:S701F	ENSP00000267892:S699F	S	-	2	0	CDAN1	40810160	1.000000	0.71417	0.705000	0.30386	0.941000	0.58515	9.420000	0.97426	2.723000	0.93209	0.655000	0.94253	TCC	.	.	none		0.622	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
PGPEP1L	145814	hgsc.bcm.edu	37	15	99514335	99514335	+	Missense_Mutation	SNP	A	A	G	rs116915938	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:99514335A>G	ENST00000378919.6	-	3	279	c.74T>C	c.(73-75)cTg>cCg	p.L25P	PGPEP1L_ENST00000535714.1_5'UTR|RP11-654A16.3_ENST00000559468.1_RNA	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	25							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						AGGCAGCTCCAGAGTCCGCAG	0.607													A|||	21	0.00419329	0.0008	0.0086	5008	,	,		14940	0.0		0.0139	False		,,,				2504	0.0				p.L25P		Atlas-SNP	.											.	PGPEP1L	26	.	0			c.T74C						PASS	.	A	PRO/LEU,	5,3981		0,5,1988	49.0	49.0	49.0		74,	4.3	0.4	15	dbSNP_132	49	131,8215		0,131,4042	yes	missense,utr-5	PGPEP1L	NM_001102612.2,NM_001167902.1	98,	0,136,6030	GG,GA,AA		1.5696,0.1254,1.1028	probably-damaging,	25/197,	99514335	136,12196	1993	4173	6166	SO:0001583	missense	145814	exon3			AGCTCCAGAGTCC		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.74T>C	15.37:g.99514335A>G	ENSP00000368199:p.Leu25Pro	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	A	11.94	1.788245	0.31593	0.001254	0.015696	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.45276	0.9	4.34	4.34	0.51931	.	.	.	.	.	T	0.44932	0.1317	M	0.73598	2.24	0.33697	D	0.614006	D	0.71674	0.998	D	0.66196	0.942	T	0.66795	-0.5833	9	0.36615	T	0.2	-8.2929	13.6897	0.62537	1.0:0.0:0.0:0.0	.	25	A6NFU8	PGPIL_HUMAN	P	25;18	ENSP00000368199:L25P	ENSP00000368199:L25P	L	-	2	0	PGPEP1L	97331858	0.987000	0.35691	0.366000	0.25914	0.056000	0.15407	3.974000	0.56852	1.963000	0.57068	0.528000	0.53228	CTG	A|0.991;G|0.009	0.009	strong		0.607	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48602951	48602951	+	Missense_Mutation	SNP	C	C	A	rs11564534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48602951C>A	ENST00000599921.1	-	5	781	c.424G>T	c.(424-426)Gtt>Ttt	p.V142F	PLA2G4C_ENST00000413144.2_Missense_Mutation_p.V142F|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.V142F|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.V152F			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	142	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		V -> F (in dbSNP:rs11564534). {ECO:0000269|Ref.3}.		arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		TTAGAGATAACCATGTAGGCC	0.527													C|||	27	0.00539137	0.0015	0.0115	5008	,	,		17923	0.0		0.008	False		,,,				2504	0.0092				p.V152F		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.G454T						PASS	.	C	PHE/VAL,PHE/VAL,PHE/VAL	11,4395	17.9+/-39.9	0,11,2192	131.0	121.0	124.0		454,424,424	-0.7	0.0	19	dbSNP_120	124	118,8482	62.4+/-124.4	0,118,4182	yes	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	50,50,50	0,129,6374	AA,AC,CC		1.3721,0.2497,0.9918	probably-damaging,probably-damaging,probably-damaging	152/552,142/528,142/542	48602951	129,12877	2203	4300	6503	SO:0001583	missense	8605	exon5			AGATAACCATGTA	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.424G>T	19.37:g.48602951C>A	ENSP00000469473:p.Val142Phe	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	17.72	3.458337	0.63401	0.002497	0.013721	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.12774	2.65;2.65	3.17	-0.681	0.11342	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.666538	0.13092	U	0.414448	T	0.13329	0.0323	L	0.52759	1.655	0.09310	N	1	P;P;P	0.50369	0.93;0.869;0.934	P;P;P	0.53102	0.718;0.577;0.654	T	0.09840	-1.0656	10	0.59425	D	0.04	-10.5211	6.6121	0.22757	0.0:0.606:0.0:0.394	rs11564534;rs52825630;rs11564534	152;142;142	B4DI40;Q8WWC5;Q9UP65	.;.;PA24C_HUMAN	F	142	ENSP00000346228:V142F;ENSP00000400036:V142F	ENSP00000346228:V142F	V	-	1	0	PLA2G4C	53294763	0.003000	0.15002	0.011000	0.14972	0.828000	0.46876	0.003000	0.13083	0.006000	0.14734	0.411000	0.27672	GTT	C|0.991;A|0.009	0.009	strong		0.527	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
EPPK1	83481	hgsc.bcm.edu	37	8	144940290	144940290	+	Missense_Mutation	SNP	C	C	G	rs201976887		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144940290C>G	ENST00000525985.1	-	2	7203	c.7132G>C	c.(7132-7134)Gac>Cac	p.D2378H				P58107	EPIPL_HUMAN	epiplakin 1	2378						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCGCTGGGGTCGGCCAGGACG	0.682																																					p.D2378H		Atlas-SNP	.											EPPK1,NS,carcinoma,0,5	EPPK1	199	5	0			c.G7132C						PASS	.	C	HIS/ASP	51,4341	20.2+/-43.8	0,51,2145	315.0	292.0	300.0		7132	3.6	0.8	8		300	22,8530	7.1+/-27.0	0,22,4254	no	missense	EPPK1	NM_031308.1	81	0,73,6399	GG,GC,CC		0.2572,1.1612,0.564	probably-damaging	2378/2420	144940290	73,12871	2196	4276	6472	SO:0001583	missense	83481	exon1			TGGGGTCGGCCAG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.7132G>C	8.37:g.144940290C>G	ENSP00000436337:p.Asp2378His	Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	215	16	0.0744186	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	22.4	4.279155	0.80692	0.011612	0.002572	ENSG00000227184	ENST00000525985	T	0.74737	-0.87	4.43	3.56	0.40772	.	.	.	.	.	D	0.83133	0.5188	M	0.89785	3.06	0.42176	D	0.991666	D	0.89917	1.0	D	0.91635	0.999	D	0.86316	0.1689	9	0.62326	D	0.03	.	10.4012	0.44231	0.0:0.9038:0.0:0.0962	.	2378	E9PPU0	.	H	2378	ENSP00000436337:D2378H	ENSP00000436337:D2378H	D	-	1	0	EPPK1	145012278	1.000000	0.71417	0.773000	0.31616	0.942000	0.58702	7.555000	0.82223	1.223000	0.43536	0.591000	0.81541	GAC	.	.	weak		0.682	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
TCF20	6942	hgsc.bcm.edu	37	22	42606257	42606257	+	Silent	SNP	C	C	T	rs2070116	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:42606257C>T	ENST00000359486.3	-	1	5191	c.5055G>A	c.(5053-5055)tcG>tcA	p.S1685S	TCF20_ENST00000335626.4_Silent_p.S1685S|TCF20_ENST00000404876.1_5'Flank	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1685					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GCATAAAGGACGAGGCCGGGA	0.567													C|||	1138	0.227236	0.115	0.3228	5008	,	,		17784	0.3006		0.2286	False		,,,				2504	0.2342				p.S1685S		Atlas-SNP	.											.	TCF20	164	.	0			c.G5055A						PASS	.	C	,	589,3817	258.9+/-262.7	31,527,1645	71.0	71.0	71.0		5055,5055	-11.9	0.1	22	dbSNP_96	71	1906,6694	337.8+/-322.5	201,1504,2595	no	coding-synonymous,coding-synonymous	TCF20	NM_005650.1,NM_181492.1	,	232,2031,4240	TT,TC,CC		22.1628,13.3681,19.1835	,	1685/1961,1685/1939	42606257	2495,10511	2203	4300	6503	SO:0001819	synonymous_variant	6942	exon1			AAAGGACGAGGCC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.5055G>A	22.37:g.42606257C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	183	112	0.612022	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	37	CCDS14033.1																																																																																			C|0.788;T|0.212	0.212	strong		0.567	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3483205	3483205	+	Silent	SNP	C	C	T	rs6767	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:3483205C>T	ENST00000324266.5	+	12	2376	c.2181C>T	c.(2179-2181)ttC>ttT	p.F727F	TRAPPC12_ENST00000382110.2_Silent_p.F727F|TRAPPC12-AS1_ENST00000453806.1_RNA	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	727					vesicle-mediated transport (GO:0016192)												GGGACAGCTTCAACACACAGT	0.542													T|||	2431	0.485423	0.6006	0.353	5008	,	,		20322	0.4653		0.4185	False		,,,				2504	0.5133				p.F727F		Atlas-SNP	.											.	.	.	.	0			c.C2181T						PASS	.	T		2465,1941	551.2+/-378.2	709,1047,447	65.0	66.0	65.0		2181	-1.1	1.0	2	dbSNP_52	65	3327,5273	643.8+/-400.0	650,2027,1623	no	coding-synonymous	TTC15	NM_016030.5		1359,3074,2070	TT,TC,CC		38.686,44.0536,44.5333		727/736	3483205	5792,7214	2203	4300	6503	SO:0001819	synonymous_variant	51112	exon12			CAGCTTCAACACA	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.2181C>T	2.37:g.3483205C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	181	79	0.436464	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1	1015	0.46474358974358976	286	0.5813008130081301	133	0.3674033149171271	281	0.49125874125874125	315	0.4155672823218997	T	9.482	1.098402	0.20552	0.559464	0.38686	ENSG00000171853	ENST00000416918	.	.	.	5.09	-1.12	0.09808	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8795	0.46929	0.0:0.3874:0.0:0.6126	rs6767;rs17680;rs1127120;rs3171903;rs56947181;rs6767	.	.	.	X	114	.	.	Q	+	1	0	TTC15	3462212	0.999000	0.42202	0.968000	0.41197	0.918000	0.54935	0.604000	0.24164	-0.489000	0.06716	-1.213000	0.01624	CAA	C|0.531;T|0.469	0.469	strong		0.542	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
ZNF440	126070	hgsc.bcm.edu	37	19	11942771	11942771	+	Silent	SNP	G	G	A	rs436411	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11942771G>A	ENST00000304060.5	+	4	944	c.780G>A	c.(778-780)gaG>gaA	p.E260E		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						AATATCAGGAGTGTGGGAAAG	0.383													a|||	1679	0.335264	0.5272	0.3285	5008	,	,		21077	0.1597		0.3638	False		,,,				2504	0.2321				p.E260E		Atlas-SNP	.											.	ZNF440	56	.	0			c.G780A						PASS	.	A		2221,2177	548.5+/-377.6	565,1091,543	73.0	75.0	75.0		780	0.0	0.0	19	dbSNP_80	75	3337,5251	629.6+/-398.3	615,2107,1572	no	coding-synonymous	ZNF440	NM_152357.2		1180,3198,2115	AA,AG,GG		38.8565,49.4998,42.7999		260/596	11942771	5558,7428	2199	4294	6493	SO:0001819	synonymous_variant	126070	exon4			TCAGGAGTGTGGG	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"""Zinc fingers, C2H2-type"", ""-"""	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.780G>A	19.37:g.11942771G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_152357	Q8N1R9	Silent	SNP	ENST00000304060.5	37	CCDS42503.1																																																																																			G|0.655;A|0.345	0.345	strong		0.383	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357	
KY	339855	hgsc.bcm.edu	37	3	134369716	134369716	+	Silent	SNP	C	C	A	rs13060869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:134369716C>A	ENST00000423778.2	-	1	148	c.87G>T	c.(85-87)acG>acT	p.T29T	KY_ENST00000508956.1_Silent_p.T29T|KY_ENST00000503669.1_Silent_p.T29T	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	29					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGTCTGAGAGCGTACCCTGTG	0.662													C|||	711	0.141973	0.1097	0.1758	5008	,	,		13584	0.0208		0.2863	False		,,,				2504	0.138				p.T29T		Atlas-SNP	.											.	KY	92	.	0			c.G87T						PASS	.	C		507,3631		29,449,1591	39.0	44.0	43.0		87	2.8	0.6	3	dbSNP_121	43	2394,6006		339,1716,2145	no	coding-synonymous	KY	NM_178554.4		368,2165,3736	AA,AC,CC		28.5,12.2523,23.1377		29/662	134369716	2901,9637	2069	4200	6269	SO:0001819	synonymous_variant	339855	exon1			TGAGAGCGTACCC	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.87G>T	3.37:g.134369716C>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			C|0.832;A|0.168	0.168	strong		0.662	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
OR2G2	81470	hgsc.bcm.edu	37	1	247752161	247752161	+	Missense_Mutation	SNP	T	T	C	rs10925085	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247752161T>C	ENST00000320065.1	+	1	500	c.500T>C	c.(499-501)cTg>cCg	p.L167P	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	167			L -> P (in dbSNP:rs10925085).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ACCCTCACCCTGCAGCTGCCC	0.542													T|||	1540	0.307508	0.0582	0.3501	5008	,	,		21547	0.5228		0.4125	False		,,,				2504	0.2843				p.L167P		Atlas-SNP	.											.	OR2G2	88	.	0			c.T500C						PASS	.	T	PRO/LEU	465,3941	220.4+/-237.8	28,409,1766	187.0	170.0	176.0		500	4.3	1.0	1	dbSNP_120	176	3464,5136	508.7+/-377.1	676,2112,1512	yes	missense	OR2G2	NM_001001915.1	98	704,2521,3278	CC,CT,TT		40.2791,10.5538,30.2091	probably-damaging	167/318	247752161	3929,9077	2203	4300	6503	SO:0001583	missense	81470	exon1			TCACCCTGCAGCT	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.500T>C	1.37:g.247752161T>C	ENSP00000326349:p.Leu167Pro	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	226	92	0.40708	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	772	0.3534798534798535	31	0.06300813008130081	127	0.35082872928176795	303	0.5297202797202797	311	0.4102902374670185	T	14.84	2.655025	0.47467	0.105538	0.402791	ENSG00000177489	ENST00000320065	T	0.00235	8.48	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30890	U	0.008678	T	0.00012	0.0000	M	0.87180	2.865	0.34693	P	0.274065	D	0.76494	0.999	D	0.77557	0.99	T	0.04165	-1.0972	9	0.87932	D	0	.	11.4683	0.50252	0.0:0.0:0.0:1.0	rs10925085;rs52797659;rs61693533;rs10925085	167	Q8NGZ5	OR2G2_HUMAN	P	167	ENSP00000326349:L167P	ENSP00000326349:L167P	L	+	2	0	OR2G2	245818784	0.000000	0.05858	0.995000	0.50966	0.624000	0.37722	0.342000	0.19926	1.789000	0.52484	0.481000	0.45027	CTG	T|0.676;C|0.324	0.324	strong		0.542	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
KRT78	196374	hgsc.bcm.edu	37	12	53242440	53242440	+	Missense_Mutation	SNP	A	A	G	rs2013335	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53242440A>G	ENST00000304620.4	-	1	338	c.275T>C	c.(274-276)cTg>cCg	p.L92P	KRT78_ENST00000359499.4_5'Flank	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	92	Head.		L -> P (in dbSNP:rs2013335). {ECO:0000269|PubMed:14702039}.			extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						TGGGGTCAGCAGATTCTGGTT	0.607													A|||	2581	0.515375	0.2965	0.5519	5008	,	,		15103	0.5188		0.5785	False		,,,				2504	0.7168				p.L92P		Atlas-SNP	.											.	KRT78	41	.	0			c.T275C						PASS	.	A	PRO/LEU	1503,2903	478.5+/-358.2	280,943,980	89.0	68.0	75.0		275	5.2	0.9	12	dbSNP_92	75	4766,3834	610.9+/-395.7	1347,2072,881	yes	missense	KRT78	NM_173352.2	98	1627,3015,1861	GG,GA,AA		44.5814,34.1126,48.2008	probably-damaging	92/521	53242440	6269,6737	2203	4300	6503	SO:0001583	missense	196374	exon1			GTCAGCAGATTCT	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.275T>C	12.37:g.53242440A>G	ENSP00000306261:p.Leu92Pro	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	206	206	1	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	37	CCDS8840.1	1085	0.4967948717948718	164	0.3333333333333333	190	0.5248618784530387	302	0.527972027972028	429	0.5659630606860159	A	20.2	3.942107	0.73557	0.341126	0.554186	ENSG00000170423	ENST00000304620	T	0.78707	-1.2	5.18	5.18	0.71444	.	.	.	.	.	T	0.00012	0.0000	M	0.93720	3.45	0.09310	P	0.999999117095	D	0.89917	1.0	D	0.87578	0.998	T	0.37079	-0.9721	8	0.87932	D	0	.	14.1531	0.65401	1.0:0.0:0.0:0.0	rs2013335;rs58948697;rs2013335	92	Q8N1N4	K2C78_HUMAN	P	92	ENSP00000306261:L92P	ENSP00000306261:L92P	L	-	2	0	KRT78	51528707	1.000000	0.71417	0.944000	0.38274	0.939000	0.58152	7.510000	0.81708	2.081000	0.62600	0.402000	0.26972	CTG	A|0.507;G|0.493	0.493	strong		0.607	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352	
DMRT3	58524	hgsc.bcm.edu	37	9	990653	990653	+	Missense_Mutation	SNP	G	G	T	rs16927037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:990653G>T	ENST00000190165.2	+	2	1105	c.1067G>T	c.(1066-1068)gGg>gTg	p.G356V		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	356			G -> V (in dbSNP:rs16927037).		adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		CCCTTGGCTGGGCCTCTGCAG	0.577													T|||	272	0.0543131	0.0182	0.0879	5008	,	,		17560	0.0754		0.0646	False		,,,				2504	0.047				p.G356V		Atlas-SNP	.											DMRT3,NS,carcinoma,+1,1	DMRT3	83	1	0			c.G1067T						PASS	.	T	VAL/GLY	117,4289	815.9+/-416.2	2,113,2088	72.0	69.0	70.0		1067	3.8	0.0	9	dbSNP_123	70	569,8031	794.0+/-407.5	22,525,3753	yes	missense	DMRT3	NM_021240.2	109	24,638,5841	TT,TG,GG		6.6163,2.6555,5.2745	benign	356/473	990653	686,12320	2203	4300	6503	SO:0001583	missense	58524	exon2			TGGCTGGGCCTCT	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1067G>T	9.37:g.990653G>T	ENSP00000190165:p.Gly356Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	37	CCDS6443.1	134	0.06135531135531135	11	0.022357723577235773	31	0.0856353591160221	44	0.07692307692307693	48	0.0633245382585752	T	0.008	-1.868069	0.00547	0.026555	0.066163	ENSG00000064218	ENST00000190165	T	0.18016	2.24	4.95	3.79	0.43588	.	0.552933	0.17182	N	0.183841	T	0.00241	0.0007	N	0.01352	-0.895	0.22389	N	0.999144	B	0.02656	0.0	B	0.01281	0.0	T	0.40079	-0.9582	10	0.16896	T	0.51	-8.5349	11.9564	0.52984	0.0:0.0:0.2747:0.7253	rs16927037;rs16927037	356	Q9NQL9	DMRT3_HUMAN	V	356	ENSP00000190165:G356V	ENSP00000190165:G356V	G	+	2	0	DMRT3	980653	1.000000	0.71417	0.032000	0.17829	0.468000	0.32798	4.676000	0.61627	0.232000	0.21100	-0.363000	0.07495	GGG	G|0.946;T|0.054	0.054	strong		0.577	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240	
CUBN	8029	hgsc.bcm.edu	37	10	17113479	17113479	+	Silent	SNP	G	G	A	rs17432826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:17113479G>A	ENST00000377833.4	-	19	2636	c.2571C>T	c.(2569-2571)aaC>aaT	p.N857N		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	857	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGACAGTGAAGTTGAGGAGAA	0.413													G|||	66	0.0131789	0.0015	0.0115	5008	,	,		15013	0.001		0.0239	False		,,,				2504	0.0317				p.N857N		Atlas-SNP	.											.	CUBN	515	.	0			c.C2571T						PASS	.	G		20,4386	27.2+/-55.0	0,20,2183	88.0	87.0	87.0		2571	1.3	1.0	10	dbSNP_123	87	214,8386	90.9+/-153.0	2,210,4088	no	coding-synonymous	CUBN	NM_001081.3		2,230,6271	AA,AG,GG		2.4884,0.4539,1.7992		857/3624	17113479	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon19			AGTGAAGTTGAGG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2571C>T	10.37:g.17113479G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			G|0.986;A|0.014	0.014	strong		0.413	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
MTUS1	57509	hgsc.bcm.edu	37	8	17541999	17541999	+	Silent	SNP	T	T	C	rs2979792	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17541999T>C	ENST00000262102.6	-	7	2900	c.2676A>G	c.(2674-2676)acA>acG	p.T892T	MTUS1_ENST00000519263.1_Silent_p.T838T|MTUS1_ENST00000381869.3_Silent_p.T838T|MTUS1_ENST00000297488.6_Silent_p.T58T|MTUS1_ENST00000381861.3_Silent_p.T139T|MTUS1_ENST00000544260.1_Silent_p.T37T|MTUS1_ENST00000518713.1_5'UTR|MIR548V_ENST00000584165.1_RNA	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	892					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		CATCGGGAGCTGTCTGTGGCT	0.413													C|||	1267	0.252995	0.0711	0.2752	5008	,	,		20314	0.374		0.4135	False		,,,				2504	0.1933				p.T892T		Atlas-SNP	.											.	MTUS1	144	.	0			c.A2676G						PASS	.	C	,,,,	488,3352		32,424,1464	232.0	228.0	229.0		2676,2514,417,111,174	-5.9	0.5	8	dbSNP_101	229	3103,5153		578,1947,1603	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2,NM_001001931.2,NM_001166393.1,NM_020749.4	,,,,	610,2371,3067	CC,CT,TT		37.5848,12.7083,29.6875	,,,,	892/1271,838/1217,139/518,37/416,58/437	17541999	3591,8505	1920	4128	6048	SO:0001819	synonymous_variant	57509	exon7			GGGAGCTGTCTGT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2676A>G	8.37:g.17541999T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			T|0.699;C|0.301	0.301	strong		0.413	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
BTBD16	118663	hgsc.bcm.edu	37	10	124096035	124096035	+	Silent	SNP	T	T	C	rs3817281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124096035T>C	ENST00000260723.4	+	15	1541	c.1290T>C	c.(1288-1290)tcT>tcC	p.S430S	BTBD16_ENST00000368994.2_Silent_p.S431S|BTBD16_ENST00000495370.2_3'UTR	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	430										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				ACCTGGAATCTCCCTCTGCGG	0.572													C|||	2300	0.459265	0.3956	0.4856	5008	,	,		17882	0.6935		0.326	False		,,,				2504	0.4223				p.S430S		Atlas-SNP	.											.	BTBD16	44	.	0			c.T1290C						PASS	.	C		1571,2835	654.3+/-399.7	293,985,925	67.0	57.0	60.0		1290	-6.6	0.0	10	dbSNP_107	60	2746,5854	670.0+/-402.7	445,1856,1999	no	coding-synonymous	BTBD16	NM_144587.2		738,2841,2924	CC,CT,TT		31.9302,35.6559,33.1924		430/507	124096035	4317,8689	2203	4300	6503	SO:0001819	synonymous_variant	118663	exon15			GGAATCTCCCTCT	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1290T>C	10.37:g.124096035T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_144587	A6NM63|Q4VXL1|Q96LN0	Silent	SNP	ENST00000260723.4	37	CCDS31301.1																																																																																			T|0.613;C|0.387	0.387	strong		0.572	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
SLC26A9	115019	hgsc.bcm.edu	37	1	205889329	205889329	+	Silent	SNP	C	C	T	rs16856470	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205889329C>T	ENST00000367135.3	-	18	2198	c.2085G>A	c.(2083-2085)gtG>gtA	p.V695V	SLC26A9_ENST00000340781.4_Silent_p.V695V|SLC26A9_ENST00000367134.2_Silent_p.V695V	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	695	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			AGAAGACCTTCACGCCGATCT	0.493													C|||	238	0.047524	0.0696	0.0605	5008	,	,		21337	0.001		0.0785	False		,,,				2504	0.0245				p.V695V		Atlas-SNP	.											.	SLC26A9	176	.	0			c.G2085A						PASS	.	C	,	334,4072	175.9+/-205.1	12,310,1881	184.0	164.0	171.0		2085,2085	2.5	1.0	1	dbSNP_123	171	695,7905	172.9+/-223.5	31,633,3636	no	coding-synonymous,coding-synonymous	SLC26A9	NM_052934.3,NM_134325.2	,	43,943,5517	TT,TC,CC		8.0814,7.5806,7.9117	,	695/792,695/888	205889329	1029,11977	2203	4300	6503	SO:0001819	synonymous_variant	115019	exon18			GACCTTCACGCCG	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"""Solute carriers"""	14469	protein-coding gene	gene with protein product	"""anion transporter/exchanger-9"""	608481	"""solute carrier family 26, member 9"""			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.2085G>A	1.37:g.205889329C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	245	110	0.44898	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Silent	SNP	ENST00000367135.3	37	CCDS30990.1																																																																																			C|0.930;T|0.070	0.070	strong		0.493	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
COL5A3	50509	hgsc.bcm.edu	37	19	10114252	10114252	+	Missense_Mutation	SNP	C	C	G	rs61742765	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10114252C>G	ENST00000264828.3	-	6	923	c.838G>C	c.(838-840)Gca>Cca	p.A280P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	280	Nonhelical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TGGTTCTCTGCGGAGTCAGGA	0.537											OREG0025228	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	493	0.0984425	0.0182	0.1297	5008	,	,		21102	0.0169		0.1839	False		,,,				2504	0.181				p.A280P		Atlas-SNP	.											.	COL5A3	243	.	0			c.G838C						PASS	.	G	PRO/ALA	225,4181	805.4+/-415.8	9,207,1987	215.0	167.0	183.0		838	2.8	0.3	19	dbSNP_129	183	1712,6888	737.2+/-407.0	165,1382,2753	yes	missense	COL5A3	NM_015719.3	27	174,1589,4740	GG,GC,CC		19.907,5.1067,14.8931	benign	280/1746	10114252	1937,11069	2203	4300	6503	SO:0001583	missense	50509	exon6			TCTCTGCGGAGTC	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.838G>C	19.37:g.10114252C>G	ENSP00000264828:p.Ala280Pro	Somatic	218	0	0	662	WXS	Illumina HiSeq	Phase_I	195	98	0.502564	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	209	0.09569597069597069	13	0.026422764227642278	52	0.143646408839779	7	0.012237762237762238	137	0.18073878627968337	G	10.09	1.255883	0.22965	0.051067	0.19907	ENSG00000080573	ENST00000264828	D	0.89810	-2.57	3.86	2.82	0.32997	.	3.571210	0.01478	N	0.016576	T	0.00271	0.0008	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33214	-0.9877	9	0.25106	T	0.35	.	5.3174	0.15862	0.1145:0.2095:0.676:0.0	rs61742765	280	P25940	CO5A3_HUMAN	P	280	ENSP00000264828:A280P	ENSP00000264828:A280P	A	-	1	0	COL5A3	9975252	0.523000	0.26274	0.340000	0.25575	0.237000	0.25408	1.159000	0.31749	0.428000	0.26173	-0.368000	0.07277	GCA	C|0.852;G|0.148	0.148	strong		0.537	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
CCRL2	9034	hgsc.bcm.edu	37	3	46450070	46450070	+	Missense_Mutation	SNP	T	T	A	rs3204849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46450070T>A	ENST00000399036.3	+	2	852	c.500T>A	c.(499-501)tTc>tAc	p.F167Y	CCRL2_ENST00000357392.4_Missense_Mutation_p.F179Y|RP11-24F11.2_ENST00000451485.1_RNA|CCRL2_ENST00000400880.3_Missense_Mutation_p.F167Y|CCRL2_ENST00000400882.2_Missense_Mutation_p.F167Y	NM_003965.4	NP_003956.2	O00421	CCRL2_HUMAN	chemokine (C-C motif) receptor-like 2	167			F -> Y (in dbSNP:rs3204849). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16641997, ECO:0000269|PubMed:9473515, ECO:0000269|Ref.2, ECO:0000269|Ref.6}.		chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CCR chemokine receptor binding (GO:0048020)|chemokine receptor activity (GO:0004950)|chemokine receptor binding (GO:0042379)			lung(3)|ovary(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)		TTGCCTGAATTCGTGGTTTAT	0.478													T|||	1747	0.348842	0.0885	0.379	5008	,	,		20164	0.5615		0.3996	False		,,,				2504	0.408				p.F179Y		Atlas-SNP	.											.	CCRL2	23	.	0			c.T536A						PASS	.	T	TYR/PHE,TYR/PHE	486,3330		23,440,1445	86.0	81.0	83.0		536,500	-7.8	0.0	3	dbSNP_105	83	3245,5035		657,1931,1552	yes	missense,missense	CCRL2	NM_001130910.1,NM_003965.4	22,22	680,2371,2997	AA,AT,TT		39.1908,12.7358,30.8449	benign,benign	179/357,167/345	46450070	3731,8365	1908	4140	6048	SO:0001583	missense	9034	exon2			CTGAATTCGTGGT	AF014958	CCDS43079.1, CCDS46814.1	3p21	2013-07-18	2013-07-18	2013-07-18	ENSG00000121797	ENSG00000121797		"""GPCR / Class A : Chemokine receptors : Atypical"""	1612	protein-coding gene	gene with protein product	"""atypical chemokine receptor 5"""	608379				9473515	Standard	NM_001130910		Approved	HCR, CRAM-B, CKRX, CRAM-A, ACKR5	uc003cpp.4	O00421	OTTHUMG00000156318	ENST00000399036.3:c.500T>A	3.37:g.46450070T>A	ENSP00000381994:p.Phe167Tyr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	93	62	0.666667	NM_001130910	B4DKQ8|O75307|Q4VBB0|Q6IPX0|Q7KYQ9|Q96KP5|Q9UPG0	Missense_Mutation	SNP	ENST00000399036.3	37	CCDS43079.1	808	0.36996336996337	52	0.10569105691056911	146	0.40331491712707185	305	0.5332167832167832	305	0.4023746701846966	T	15.21	2.766215	0.49574	0.127358	0.391908	ENSG00000121797	ENST00000399036;ENST00000357392;ENST00000400880;ENST00000433848;ENST00000400882	T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16	5.4	-7.81	0.01210	GPCR, rhodopsin-like superfamily (1);	1.873720	0.02792	N	0.122158	T	0.00012	0.0000	M	0.67397	2.05	0.80722	P	0.0	P;P	0.40197	0.706;0.642	B;B	0.38954	0.142;0.286	T	0.26710	-1.0095	9	0.87932	D	0	.	3.5343	0.07788	0.1011:0.4167:0.2213:0.2609	rs3204849;rs34060313	179;167	O00421-2;O00421	.;CCRL2_HUMAN	Y	167;179;167;167;167	ENSP00000381994:F167Y;ENSP00000349967:F179Y;ENSP00000383677:F167Y;ENSP00000414957:F167Y;ENSP00000383678:F167Y	ENSP00000349967:F179Y	F	+	2	0	CCRL2	46425074	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.295000	0.19065	-1.990000	0.00978	-0.619000	0.04042	TTC	T|0.631;A|0.369	0.369	strong		0.478	CCRL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343909.2		
NMT1	4836	hgsc.bcm.edu	37	17	43176804	43176804	+	Silent	SNP	C	C	T	rs2239923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:43176804C>T	ENST00000592782.1	+	9	1047	c.916C>T	c.(916-918)Ctg>Ttg	p.L306L	NMT1_ENST00000258960.2_Silent_p.L306L			P30419	NMT1_HUMAN	N-myristoyltransferase 1	306					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				CCCACGGAAGCTGATTGAAGT	0.557											OREG0024470	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1122	0.224042	0.059	0.2017	5008	,	,		19639	0.2748		0.2992	False		,,,				2504	0.3333				p.L306L		Atlas-SNP	.											.	NMT1	31	.	0			c.C916T						PASS	.	C		406,4000	199.8+/-223.2	13,380,1810	130.0	109.0	116.0		916	3.3	1.0	17	dbSNP_98	116	2487,6113	409.7+/-349.9	343,1801,2156	no	coding-synonymous	NMT1	NM_021079.3		356,2181,3966	TT,TC,CC		28.9186,9.2147,22.2436		306/497	43176804	2893,10113	2203	4300	6503	SO:0001819	synonymous_variant	4836	exon8			CGGAAGCTGATTG		CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"""alternative, short form NMT-S"", ""myristoyl-CoA:protein N-myristoyltransferase"", ""long form, NMT-L"""	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.916C>T	17.37:g.43176804C>T		Somatic	276	0	0	914	WXS	Illumina HiSeq	Phase_I	216	215	0.99537	NM_021079	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1																																																																																			C|0.780;T|0.220	0.220	strong		0.557	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
BAZ2B	29994	hgsc.bcm.edu	37	2	160289480	160289480	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160289480C>T	ENST00000392783.2	-	9	2183	c.1688G>A	c.(1687-1689)gGg>gAg	p.G563E	BAZ2B_ENST00000343439.5_Missense_Mutation_p.G561E|BAZ2B_ENST00000355831.2_Missense_Mutation_p.G563E|BAZ2B_ENST00000392782.1_Missense_Mutation_p.G561E	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G563V(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						TTTTTCCTTCCCTTGACTATG	0.443																																					p.G563E		Atlas-SNP	.											BAZ2B,rectum,carcinoma,-1,5	BAZ2B	196	5	1	Substitution - Missense(1)	lung(1)	c.G1688A						scavenged	.						199.0	184.0	189.0					2																	160289480		1908	4125	6033	SO:0001583	missense	29994	exon9			TCCTTCCCTTGAC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.1688G>A	2.37:g.160289480C>T	ENSP00000376534:p.Gly563Glu	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	197	3	0.0152284	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	16.26	3.073616	0.55646	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.92	5.92	0.95590	.	0.000000	0.37669	U	0.001981	T	0.71400	0.3335	L	0.51422	1.61	0.46981	D	0.999278	D;P;P;P;P	0.89917	1.0;0.928;0.634;0.634;0.501	D;P;B;B;B	0.83275	0.996;0.494;0.219;0.219;0.109	T	0.69041	-0.5250	10	0.45353	T	0.12	-8.9802	16.5572	0.84488	0.0:0.8697:0.1303:0.0	.	563;367;561;561;563	Q9UIF8-3;Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;.;BAZ2B_HUMAN	E	561;563;563;561;500	ENSP00000376533:G561E;ENSP00000376534:G563E;ENSP00000348087:G563E;ENSP00000339670:G561E	ENSP00000339670:G561E	G	-	2	0	BAZ2B	159997726	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.270000	0.65547	2.818000	0.97014	0.655000	0.94253	GGG	.	.	none		0.443	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
CNTN6	27255	hgsc.bcm.edu	37	3	1424745	1424745	+	Silent	SNP	C	C	T	rs4684146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:1424745C>T	ENST00000446702.2	+	18	2913	c.2286C>T	c.(2284-2286)gtC>gtT	p.V762V	CNTN6_ENST00000350110.2_Silent_p.V762V|CNTN6_ENST00000539053.1_Silent_p.V690V			Q9UQ52	CNTN6_HUMAN	contactin 6	762	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		CAAGGTTTGTCTACAGAAATG	0.453													T|||	767	0.153155	0.2284	0.1744	5008	,	,		18026	0.0645		0.1571	False		,,,				2504	0.1237				p.V762V		Atlas-SNP	.											.	CNTN6	245	.	0			c.C2286T						PASS	.	T		1017,3389	728.8+/-410.0	124,769,1310	163.0	150.0	154.0		2286	-9.5	0.0	3	dbSNP_111	154	1606,6994	743.2+/-407.2	171,1264,2865	no	coding-synonymous	CNTN6	NM_014461.2		295,2033,4175	TT,TC,CC		18.6744,23.0822,20.1676		762/1029	1424745	2623,10383	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon18			GTTTGTCTACAGA	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2286C>T	3.37:g.1424745C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	236	116	0.491525	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			C|0.816;T|0.184	0.184	strong		0.453	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
UGGT2	55757	hgsc.bcm.edu	37	13	96540204	96540204	+	Missense_Mutation	SNP	T	T	G	rs12876018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:96540204T>G	ENST00000376747.3	-	26	3050	c.2980A>C	c.(2980-2982)Atg>Ctg	p.M994L		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	994			M -> L (in dbSNP:rs12876018). {ECO:0000269|PubMed:10694380, ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						TTTATCTTCATGTTGATAATC	0.299													T|||	1679	0.335264	0.2874	0.2795	5008	,	,		15405	0.3135		0.4423	False		,,,				2504	0.3517				p.M994L		Atlas-SNP	.											.	UGGT2	127	.	0			c.A2980C						PASS	.	T	LEU/MET	1298,3108	433.7+/-343.7	198,902,1103	50.0	56.0	54.0		2980	2.9	1.0	13	dbSNP_121	54	3537,5061	511.1+/-377.6	741,2055,1503	yes	missense	UGGT2	NM_020121.3	15	939,2957,2606	GG,GT,TT		41.1375,29.4598,37.1809	benign	994/1517	96540204	4835,8169	2203	4299	6502	SO:0001583	missense	55757	exon26			TCTTCATGTTGAT	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.2980A>C	13.37:g.96540204T>G	ENSP00000365938:p.Met994Leu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	167	94	0.562874	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	780	0.35714285714285715	148	0.3008130081300813	134	0.3701657458563536	171	0.29895104895104896	327	0.4313984168865435	T	12.42	1.933612	0.34096	0.294598	0.411375	ENSG00000102595	ENST00000376747	T	0.27402	1.67	5.37	2.86	0.33363	.	0.313121	0.37906	N	0.001885	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.9999999999330268	B	0.25667	0.131	B	0.26614	0.071	T	0.40739	-0.9547	9	0.51188	T	0.08	-7.9969	6.1583	0.20350	0.0:0.1502:0.1363:0.7135	rs12876018;rs17189888;rs52805137;rs57422721;rs12876018	994	Q9NYU1	UGGG2_HUMAN	L	994	ENSP00000365938:M994L	ENSP00000365938:M994L	M	-	1	0	UGGT2	95338205	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	0.980000	0.29513	0.314000	0.23086	0.533000	0.62120	ATG	G|0.356;N|0.001	0.356	strong		0.299	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
ABCG2	9429	hgsc.bcm.edu	37	4	89052323	89052323	+	Missense_Mutation	SNP	G	G	T	rs2231142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:89052323G>T	ENST00000237612.3	-	5	966	c.421C>A	c.(421-423)Cag>Aag	p.Q141K	ABCG2_ENST00000515655.1_Missense_Mutation_p.Q141K	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	141	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		Q -> K (polymorphism associated with high serum levels of uric acid and increased risk of gout; results in lower urate transport rates compared to wild-type; dbSNP:rs2231142). {ECO:0000269|PubMed:12111378, ECO:0000269|PubMed:12544509, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16702730, ECO:0000269|Ref.11, ECO:0000269|Ref.8}.		cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.Q141K(1)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	GCTGAGAACTGTAAGTTTTCT	0.398													G|||	598	0.119409	0.0129	0.1412	5008	,	,		22358	0.2907		0.0944	False		,,,				2504	0.0971				p.Q141K		Atlas-SNP	.											ABCG2,NS,carcinoma,0,1	ABCG2	151	1	1	Substitution - Missense(1)	stomach(1)	c.C421A	GRCh37	CM057428	ABCG2	M	rs2231142	PASS	.	G	LYS/GLN	142,4264	100.3+/-138.9	3,136,2064	211.0	190.0	197.0	http://omim.org/entry/612670|http://www.ncbi.nlm.nih.gov/pubmed?term	421	5.4	1.0	4	dbSNP_98	197	957,7643	209.3+/-250.5	47,863,3390	yes	missense	ABCG2	NM_004827.2	53	50,999,5454	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	11.1279,3.2229,8.4499	benign	141/656	89052323	1099,11907	2203	4300	6503	SO:0001583	missense	9429	exon5			AGAACTGTAAGTT	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"""CD molecules"", ""ATP binding cassette transporters / subfamily G"""	74	protein-coding gene	gene with protein product		603756	"""ATP-binding cassette, sub-family G (WHITE), member 2"""			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.421C>A	4.37:g.89052323G>T	ENSP00000237612:p.Gln141Lys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	304	0.1391941391941392	8	0.016260162601626018	55	0.15193370165745856	167	0.291958041958042	74	0.09762532981530343	G	13.84	2.358265	0.41801	0.032229	0.111279	ENSG00000118777	ENST00000515655;ENST00000237612	T;T	0.38401	1.14;1.14	5.37	5.37	0.77165	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.166420	0.53938	D	0.000050	T	0.00012	0.0000	N	0.11724	0.165	0.26721	P	0.9707709	B;B;B	0.34214	0.442;0.372;0.257	B;B;B	0.36186	0.219;0.216;0.216	T	0.42949	-0.9421	9	0.26408	T	0.33	-0.0036	19.0867	0.93206	0.0:0.0:1.0:0.0	rs2231142;rs3736117;rs12721641;rs28365035;rs52809243;rs58973676;rs2231142	141;141;141	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	K	141	ENSP00000426917:Q141K;ENSP00000237612:Q141K	ENSP00000237612:Q141K	Q	-	1	0	ABCG2	89271347	0.985000	0.35326	0.996000	0.52242	0.985000	0.73830	1.742000	0.38248	2.677000	0.91161	0.655000	0.94253	CAG	G|0.883;T|0.117	0.117	strong		0.398	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827	
CHSY3	337876	hgsc.bcm.edu	37	5	129521126	129521126	+	Missense_Mutation	SNP	A	A	G	rs2015018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:129521126A>G	ENST00000305031.4	+	3	2649	c.2291A>G	c.(2290-2292)gAt>gGt	p.D764G		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	764			D -> G (in dbSNP:rs2015018).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		CCCACTGATGATTACTTCATA	0.403													A|||	2832	0.565495	0.2269	0.6744	5008	,	,		22288	0.6647		0.7565	False		,,,				2504	0.6472				p.D764G		Atlas-SNP	.											.	CHSY3	92	.	0			c.A2291G						PASS	.	A	GLY/ASP	1486,2920	474.8+/-357.1	256,974,973	100.0	97.0	98.0		2291	1.7	0.0	5	dbSNP_92	98	6441,2159	714.0+/-406.0	2417,1607,276	yes	missense	CHSY3	NM_175856.4	94	2673,2581,1249	GG,GA,AA		25.1047,33.7267,39.0512	benign	764/883	129521126	7927,5079	2203	4300	6503	SO:0001583	missense	337876	exon3			CTGATGATTACTT	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.2291A>G	5.37:g.129521126A>G	ENSP00000302629:p.Asp764Gly	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_175856	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	37	CCDS34223.1	1285	0.5883699633699634	99	0.20121951219512196	249	0.6878453038674033	376	0.6573426573426573	561	0.7401055408970977	A	0.181	-1.061795	0.01950	0.337267	0.748953	ENSG00000198108	ENST00000305031	T	0.15718	2.4	4.09	1.72	0.24424	.	0.651897	0.14129	N	0.339481	T	0.00012	0.0000	L	0.46157	1.445	0.35410	P	0.207619	B	0.06786	0.001	B	0.04013	0.001	T	0.14615	-1.0466	8	.	.	.	.	6.8301	0.23905	0.6319:0.0:0.3681:0.0	rs2015018;rs17769790;rs52794865;rs57870430;rs2015018	764	Q70JA7	CHSS3_HUMAN	G	764	ENSP00000302629:D764G	.	D	+	2	0	CHSY3	129549025	1.000000	0.71417	0.044000	0.18714	0.029000	0.11900	2.692000	0.47018	0.388000	0.25054	-0.297000	0.09499	GAT	A|0.403;G|0.597	0.597	strong		0.403	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856	
PEAK1	79834	hgsc.bcm.edu	37	15	77407114	77407114	+	Missense_Mutation	SNP	C	C	G	rs1867780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:77407114C>G	ENST00000560626.2	-	7	5100	c.4625G>C	c.(4624-4626)aGc>aCc	p.S1542T	PEAK1_ENST00000312493.4_Missense_Mutation_p.S1542T			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1542	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> T (in dbSNP:rs1867780). {ECO:0000269|PubMed:17344846}.		cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TGAGGTGGGGCTGGGCTCTGC	0.582													C|||	989	0.197484	0.0696	0.2536	5008	,	,		18231	0.2153		0.2873	False		,,,				2504	0.2198				p.S1542T		Atlas-SNP	.											.	.	.	.	0			c.G4625C						PASS	.	C	THR/SER	416,3388		29,358,1515	54.0	55.0	55.0		4625	3.5	0.7	15	dbSNP_92	55	2356,5898		355,1646,2126	no	missense	PEAK1	NM_024776.3	58	384,2004,3641	GG,GC,CC		28.5437,10.9359,22.9889	benign	1542/1747	77407114	2772,9286	1902	4127	6029	SO:0001583	missense	0	exon8			GTGGGGCTGGGCT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.4625G>C	15.37:g.77407114C>G	ENSP00000452796:p.Ser1542Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	480	0.21978021978021978	41	0.08333333333333333	90	0.24861878453038674	130	0.22727272727272727	219	0.28891820580474936	C	9.359	1.067504	0.20067	0.109359	0.285437	ENSG00000173517	ENST00000312493	T	0.68479	-0.33	5.47	3.49	0.39957	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.647154	0.14457	U	0.318453	T	0.00012	0.0000	N	0.08118	0	0.50632	P	1.1700000000003374E-4	B	0.10296	0.003	B	0.10450	0.005	T	0.18335	-1.0340	9	0.21540	T	0.41	-1.0031	7.1818	0.25776	0.0:0.6645:0.1217:0.2138	rs1867780;rs3743480;rs52820530;rs59760970;rs1867780	1542	Q9H792	PEAK1_HUMAN	T	1542	ENSP00000309230:S1542T	ENSP00000309230:S1542T	S	-	2	0	AC087465.1	75194169	1.000000	0.71417	0.689000	0.30133	0.860000	0.49131	1.665000	0.37449	0.596000	0.29794	0.561000	0.74099	AGC	C|0.750;G|0.250	0.250	strong		0.582	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
TMEM194B	100131211	hgsc.bcm.edu	37	2	191379268	191379268	+	Silent	SNP	G	G	A	rs4586658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:191379268G>A	ENST00000409150.3	-	7	930	c.864C>T	c.(862-864)gcC>gcT	p.A288A		NM_001142645.1	NP_001136117.1	A6NFY4	T194B_HUMAN	transmembrane protein 194B	288						integral component of membrane (GO:0016021)											ACTGAGGCACGGCCACACCAG	0.522													G|||	2667	0.532548	0.3321	0.696	5008	,	,		16189	0.5833		0.5765	False		,,,				2504	0.59				p.A288A		Atlas-SNP	.											.	TMEM194B	18	.	0			c.C864T						PASS	.	G		473,911		86,301,305	73.0	73.0	73.0		864	-0.5	0.0	2	dbSNP_111	73	1822,1360		520,782,289	no	coding-synonymous	TMEM194B	NM_001142645.1		606,1083,594	AA,AG,GG		42.7404,34.1763,49.7372		288/418	191379268	2295,2271	692	1591	2283	SO:0001819	synonymous_variant	100131211	exon7			AGGCACGGCCACA		CCDS46476.1	2q32.2	2008-06-10			ENSG00000189362	ENSG00000189362			33700	protein-coding gene	gene with protein product							Standard	NM_001142645		Approved		uc010zgf.2	A6NFY4	OTTHUMG00000154454	ENST00000409150.3:c.864C>T	2.37:g.191379268G>A		Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	372	371	0.997312	NM_001142645	B4DYG6	Silent	SNP	ENST00000409150.3	37	CCDS46476.1																																																																																			G|0.492;A|0.508	0.508	strong		0.522	TMEM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335299.1	XM_001723498	
SALL3	27164	hgsc.bcm.edu	37	18	76757145	76757145	+	Silent	SNP	C	C	T	rs148335210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:76757145C>T	ENST00000537592.2	+	3	3726	c.3726C>T	c.(3724-3726)ccC>ccT	p.P1242P	SALL3_ENST00000575389.2_Silent_p.P1170P|SALL3_ENST00000536229.3_Silent_p.P1037P	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1242					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P1242P(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CCCAGCTCCCCGTGAGTCTTG	0.612													C|||	6	0.00119808	0.0	0.0029	5008	,	,		17088	0.0		0.003	False		,,,				2504	0.001				p.P1242P		Atlas-SNP	.											SALL3,NS,malignant_melanoma,+2,1	SALL3	162	1	1	Substitution - coding silent(1)	lung(1)	c.C3726T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	94.0	90.0	92.0		3726	-10.8	0.0	18	dbSNP_134	92	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	SALL3	NM_171999.2		0,14,6489	TT,TC,CC		0.1163,0.0908,0.1076		1242/1301	76757145	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	27164	exon3			GCTCCCCGTGAGT	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.3726C>T	18.37:g.76757145C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	4	0.0465116	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	37	CCDS12013.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
POLR2M	81488	hgsc.bcm.edu	37	15	58000981	58000981	+	Silent	SNP	C	C	T	rs1062707	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:58000981C>T	ENST00000299638.3	+	2	397	c.183C>T	c.(181-183)gcC>gcT	p.A61A	GCOM1_ENST00000380568.3_Intron|GCOM1_ENST00000484300.1_Intron|POLR2M_ENST00000464308.1_3'UTR|POLR2M_ENST00000380563.2_Silent_p.A61A|GCOM1_ENST00000380569.2_Intron|POLR2M_ENST00000380557.4_Intron|GCOM1_ENST00000587652.1_Silent_p.A458A	NM_015532.3	NP_056347.1	P0CAP2	GRL1A_HUMAN	polymerase (RNA) II (DNA directed) polypeptide M	61					maintenance of ER location (GO:0051685)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)	DNA-directed RNA polymerase activity (GO:0003899)										TGAAAGCTGCCATTGCAGAAT	0.348													C|||	2486	0.496406	0.2443	0.6873	5008	,	,		20815	0.4048		0.7674	False		,,,				2504	0.5174				p.A61A		Atlas-SNP	.											.	POLR2M	2	.	0			c.C183T						PASS	.	C	,,,	1471,2913	462.6+/-353.3	260,951,981	58.0	59.0	59.0		,,,183	4.2	1.0	15	dbSNP_86	59	6612,1972	717.2+/-406.1	2553,1506,233	no	intron,intron,intron,coding-synonymous	GRINL1A,GCOM1	NM_001018090.3,NM_001018091.3,NM_001018102.1,NM_015532.3	,,,	2813,2457,1214	TT,TC,CC		22.973,33.5538,37.6696	,,,	,,,61/369	58000981	8083,4885	2192	4292	6484	SO:0001819	synonymous_variant	81488	exon2			AGCTGCCATTGCA	AF326773	CCDS32252.1, CCDS42045.1	15q21.3	2013-01-21	2011-11-07	2011-11-07		ENSG00000255529		"""RNA polymerase subunits"""	14862	protein-coding gene	gene with protein product		606485	"""glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A"""	GRINL1A		16769904, 22850672	Standard	NM_015532		Approved	Gdown, Gdown1, GCOM1	uc002aev.1	P0CAP2	OTTHUMG00000166486	ENST00000299638.3:c.183C>T	15.37:g.58000981C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	198	83	0.419192	NM_015532	Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5|Q9Y3V6	Silent	SNP	ENST00000299638.3	37	CCDS32252.1																																																																																			C|0.426;T|0.574	0.574	strong		0.348	POLR2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255719.2		
TMEM131	23505	hgsc.bcm.edu	37	2	98409046	98409046	+	Missense_Mutation	SNP	G	G	A	rs12995673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:98409046G>A	ENST00000186436.5	-	31	4175	c.3947C>T	c.(3946-3948)cCg>cTg	p.P1316L		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1316	Pro-rich.					integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						TTCAGGCTGCGGCTCCTGGGG	0.682													G|||	737	0.147165	0.0522	0.2046	5008	,	,		15915	0.0119		0.3917	False		,,,				2504	0.1227				p.P1316L		Atlas-SNP	.											.	TMEM131	258	.	0			c.C3947T						PASS	.	G	LEU/PRO	409,3805		21,367,1719	20.0	24.0	23.0		3947	3.9	0.9	2	dbSNP_121	23	3100,5366		567,1966,1700	yes	missense	TMEM131	NM_015348.1	98	588,2333,3419	AA,AG,GG		36.6171,9.7057,27.6735	benign	1316/1884	98409046	3509,9171	2107	4233	6340	SO:0001583	missense	23505	exon31			GGCTGCGGCTCCT	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.3947C>T	2.37:g.98409046G>A	ENSP00000186436:p.Pro1316Leu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_015348		Missense_Mutation	SNP	ENST00000186436.5	37	CCDS46368.1	416	0.19047619047619047	24	0.04878048780487805	75	0.20718232044198895	6	0.01048951048951049	311	0.4102902374670185	G	11.78	1.741897	0.30865	0.097057	0.366171	ENSG00000075568	ENST00000186436	T	0.19105	2.17	5.91	3.94	0.45596	.	0.779755	0.12489	N	0.464371	T	0.00012	0.0000	N	0.22421	0.69	0.31392	P	0.677675	B	0.11235	0.004	B	0.04013	0.001	T	0.45877	-0.9231	9	0.30078	T	0.28	-4.2451	8.8937	0.35451	0.0823:0.0:0.6775:0.2402	rs12995673	1316	Q92545	TM131_HUMAN	L	1316	ENSP00000186436:P1316L	ENSP00000186436:P1316L	P	-	2	0	TMEM131	97775478	0.977000	0.34250	0.930000	0.37139	0.781000	0.44180	1.805000	0.38883	1.505000	0.48720	0.655000	0.94253	CCG	G|0.781;A|0.219	0.219	strong		0.682	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
SCNN1A	6337	hgsc.bcm.edu	37	12	6472753	6472753	+	Silent	SNP	C	C	A	rs55859427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6472753C>A	ENST00000228916.2	-	3	638	c.540G>T	c.(538-540)ctG>ctT	p.L180L	SCNN1A_ENST00000358945.3_Silent_p.L180L|SCNN1A_ENST00000396966.2_Silent_p.L180L|SCNN1A_ENST00000538979.1_Intron|SCNN1A_ENST00000543768.1_Silent_p.L203L|SCNN1A_ENST00000360168.3_Silent_p.L239L|SCNN1A_ENST00000540037.1_5'UTR	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	180					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	GAGTCCCCCGCAGGTCGCGAC	0.682													C|||	36	0.0071885	0.0	0.0072	5008	,	,		10426	0.0		0.0209	False		,,,				2504	0.0102				p.L239L		Atlas-SNP	.											.	SCNN1A	54	.	0			c.G717T						PASS	.	C	,,	17,4383		0,17,2183	13.0	15.0	14.0		540,609,717	-0.9	0.0	12	dbSNP_129	14	150,8444		5,140,4152	no	coding-synonymous,coding-synonymous,coding-synonymous	SCNN1A	NM_001038.5,NM_001159575.1,NM_001159576.1	,,	5,157,6335	AA,AC,CC		1.7454,0.3864,1.2852	,,	180/670,203/693,239/729	6472753	167,12827	2200	4297	6497	SO:0001819	synonymous_variant	6337	exon2			CCCCCGCAGGTCG	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.540G>T	12.37:g.6472753C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	17	11	0.647059	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Silent	SNP	ENST00000228916.2	37	CCDS8543.1																																																																																			C|0.985;A|0.015	0.015	strong		0.682	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1		
ADAMTS2	9509	hgsc.bcm.edu	37	5	178564906	178564906	+	Silent	SNP	G	G	A	rs369654932		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178564906G>A	ENST00000251582.7	-	12	1916	c.1815C>T	c.(1813-1815)taC>taT	p.Y605Y		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	605	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GCTGGAAGTCGTAGGCAAGGC	0.682																																					p.Y605Y		Atlas-SNP	.											ADAMTS2,colon,carcinoma,0,1	ADAMTS2	190	1	0			c.C1815T						PASS	.	G		0,4264		0,0,2132	14.0	14.0	14.0		1815	-0.5	1.0	5		14	2,8428		0,2,4213	no	coding-synonymous	ADAMTS2	NM_014244.4		0,2,6345	AA,AG,GG		0.0237,0.0,0.0158		605/1212	178564906	2,12692	2132	4215	6347	SO:0001819	synonymous_variant	9509	exon12			GAAGTCGTAGGCA	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.1815C>T	5.37:g.178564906G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	77	24	0.311688	NM_014244		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			.	.	weak		0.682	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
TAB2	23118	hgsc.bcm.edu	37	6	149700491	149700491	+	Silent	SNP	G	G	A	rs3734296	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:149700491G>A	ENST00000367456.1	+	4	2017	c.1440G>A	c.(1438-1440)gtG>gtA	p.V480V	TAB2_ENST00000286332.5_Silent_p.V480V|TAB2_ENST00000538427.1_Silent_p.V480V|TAB2_ENST00000536230.1_Silent_p.V448V|TAB2_ENST00000392282.1_Silent_p.V480V			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	480					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						CACCAGGGGTGGTGTCCCCTA	0.453													G|||	1092	0.218051	0.0552	0.2507	5008	,	,		18785	0.5496		0.0944	False		,,,				2504	0.2004				p.V480V		Atlas-SNP	.											.	TAB2	55	.	0			c.G1440A						PASS	.	G		277,4129	156.3+/-189.4	8,261,1934	91.0	87.0	89.0		1440	-4.4	0.2	6	dbSNP_107	89	909,7691	202.7+/-245.9	53,803,3444	no	coding-synonymous	TAB2	NM_015093.4		61,1064,5378	AA,AG,GG		10.5698,6.2869,9.1189		480/694	149700491	1186,11820	2203	4300	6503	SO:0001819	synonymous_variant	23118	exon5			AGGGGTGGTGTCC	AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 2"""	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.1440G>A	6.37:g.149700491G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	37	CCDS5214.1																																																																																			G|0.856;A|0.144	0.144	strong		0.453	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3		
PER3	8863	hgsc.bcm.edu	37	1	7887248	7887248	+	Silent	SNP	G	G	A	rs2859387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7887248G>A	ENST00000361923.2	+	17	2410	c.2235G>A	c.(2233-2235)ccG>ccA	p.P745P	PER3_ENST00000377532.3_Silent_p.P753P|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	745	CSNK1E binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAGCTGCCGGAGCCGCCAG	0.632													G|||	2588	0.516773	0.5333	0.4597	5008	,	,		14514	0.8026		0.3718	False		,,,				2504	0.3896				p.P745P		Atlas-SNP	.											PER3,NS,carcinoma,+1,1	PER3	95	1	0			c.G2235A						PASS	.	G		2207,2153		589,1029,562	21.0	26.0	24.0		2235	-8.8	0.0	1	dbSNP_100	24	3035,5501		587,1861,1820	no	coding-synonymous	PER3	NM_016831.1		1176,2890,2382	AA,AG,GG		35.5553,49.3807,40.6483		745/1202	7887248	5242,7654	2180	4268	6448	SO:0001819	synonymous_variant	8863	exon17			GCTGCCGGAGCCG	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2235G>A	1.37:g.7887248G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			G|0.567;A|0.433	0.433	strong		0.632	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
KIAA1211	57482	hgsc.bcm.edu	37	4	57182647	57182647	+	Silent	SNP	G	G	A	rs3822003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57182647G>A	ENST00000504228.1	+	6	3084	c.2979G>A	c.(2977-2979)gcG>gcA	p.A993A	KIAA1211_ENST00000264229.6_Silent_p.A993A|KIAA1211_ENST00000541073.1_Silent_p.A986A			Q6ZU35	K1211_HUMAN	KIAA1211	993	Pro-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CTCGCCGAGCGGGGAGGCCGG	0.667													G|||	949	0.189497	0.0174	0.2061	5008	,	,		13721	0.253		0.339	False		,,,				2504	0.1912				p.A993A		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G2979A						PASS	.	G		297,3731		13,271,1730	34.0	43.0	40.0		2979	-10.1	0.0	4	dbSNP_107	40	2817,5535		481,1855,1840	no	coding-synonymous	KIAA1211	NM_020722.1		494,2126,3570	AA,AG,GG		33.7284,7.3734,25.1535		993/1234	57182647	3114,9266	2014	4176	6190	SO:0001819	synonymous_variant	57482	exon8			CCGAGCGGGGAGG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.2979G>A	4.37:g.57182647G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			G|0.773;A|0.227	0.227	strong		0.667	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
ADSSL1	122622	hgsc.bcm.edu	37	14	105207040	105207040	+	Silent	SNP	C	C	T	rs12894569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105207040C>T	ENST00000330877.2	+	6	664	c.579C>T	c.(577-579)tcC>tcT	p.S193S	ADSSL1_ENST00000332972.5_Silent_p.S236S	NM_152328.3	NP_689541.1			adenylosuccinate synthase like 1											central_nervous_system(1)|cervix(1)|kidney(1)|lung(5)|ovary(2)|prostate(1)	11		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)		ATGAGTTTTCCTCCAGGTACC	0.602													C|||	380	0.0758786	0.0794	0.1182	5008	,	,		20166	0.0149		0.1064	False		,,,				2504	0.0726				p.S236S		Atlas-SNP	.											.	ADSSL1	37	.	0			c.C708T						PASS	.	C	,	437,3969	210.5+/-231.0	18,401,1784	91.0	95.0	94.0		579,708	-0.3	0.1	14	dbSNP_121	94	976,7624	211.7+/-252.2	58,860,3382	no	coding-synonymous,coding-synonymous	ADSSL1	NM_152328.3,NM_199165.1	,	76,1261,5166	TT,TC,CC		11.3488,9.9183,10.8642	,	193/458,236/501	105207040	1413,11593	2203	4300	6503	SO:0001819	synonymous_variant	122622	exon6			GTTTTCCTCCAGG	AK095921	CCDS9990.1, CCDS9991.1	14q32.33	2010-08-05			ENSG00000185100	ENSG00000185100			20093	protein-coding gene	gene with protein product		612498					Standard	NM_199165		Approved	FLJ38602	uc001ype.3	Q8N142		ENST00000330877.2:c.579C>T	14.37:g.105207040C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_199165		Silent	SNP	ENST00000330877.2	37	CCDS9990.1																																																																																			C|0.902;T|0.098	0.098	strong		0.602	ADSSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410529.1		
JAKMIP3	282973	hgsc.bcm.edu	37	10	133955427	133955427	+	Missense_Mutation	SNP	A	A	G	rs11592585	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:133955427A>G	ENST00000298622.4	+	10	1615	c.1477A>G	c.(1477-1479)Atg>Gtg	p.M493V		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	493			M -> V (in dbSNP:rs11592585).			Golgi apparatus (GO:0005794)		p.M493V(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TCTCCAGGGCATGGCCAAGGA	0.642													A|||	935	0.186701	0.0408	0.232	5008	,	,		16582	0.2371		0.3419	False		,,,				2504	0.1401				p.M493V		Atlas-SNP	.											JAKMIP3,NS,carcinoma,0,1	JAKMIP3	69	1	1	Substitution - Missense(1)	prostate(1)	c.A1477G						PASS	.	A	VAL/MET	417,3981		20,377,1802	75.0	54.0	61.0		1477	-1.7	1.0	10	dbSNP_120	61	3041,5545		522,1997,1774	yes	missense	JAKMIP3	NM_001105521.2	21	542,2374,3576	GG,GA,AA		35.4181,9.4816,26.6328	benign	493/845	133955427	3458,9526	2199	4293	6492	SO:0001583	missense	282973	exon10			CAGGGCATGGCCA	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1477A>G	10.37:g.133955427A>G	ENSP00000298622:p.Met493Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	500	0.22893772893772893	18	0.036585365853658534	91	0.2513812154696133	131	0.229020979020979	260	0.34300791556728233	A	10.98	1.503688	0.26949	0.094816	0.354181	ENSG00000188385	ENST00000298622	T	0.20598	2.06	3.87	-1.72	0.08107	.	0.570968	0.17020	N	0.190165	T	0.00012	0.0000	L	0.47716	1.5	0.20074	P	0.999933551	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	9	0.27785	T	0.31	-14.708	4.6571	0.12622	0.4005:0.3058:0.2937:0.0	rs11592585;rs57375718;rs11592585	493	Q5VZ66	JKIP3_HUMAN	V	493	ENSP00000298622:M493V	ENSP00000298622:M493V	M	+	1	0	JAKMIP3	133805417	0.001000	0.12720	0.986000	0.45419	0.976000	0.68499	-0.349000	0.07731	-0.382000	0.07870	0.459000	0.35465	ATG	A|0.782;G|0.218	0.218	strong		0.642	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28338423	28338423	+	Silent	SNP	C	C	G	rs55933916	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:28338423C>G	ENST00000284987.5	-	1	409	c.288G>C	c.(286-288)cgG>cgC	p.R96R		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	96					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						AGAGGAACCTCCGGCCGCCCG	0.697													C|||	497	0.0992412	0.1036	0.0951	5008	,	,		14001	0.0069		0.2048	False		,,,				2504	0.0828				p.R96R	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											ADAMTS5,NS,carcinoma,0,1	ADAMTS5	184	1	0			c.G288C						PASS	.	C		490,3904		24,442,1731	55.0	52.0	53.0		288	0.3	1.0	21	dbSNP_129	53	1678,6908		166,1346,2781	no	coding-synonymous	ADAMTS5	NM_007038.3		190,1788,4512	GG,GC,CC		19.5434,11.1516,16.7026		96/931	28338423	2168,10812	2197	4293	6490	SO:0001819	synonymous_variant	11096	exon1			GAACCTCCGGCCG	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.288G>C	21.37:g.28338423C>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	152	56	0.368421	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	37	CCDS13579.1																																																																																			C|0.849;G|0.151	0.151	strong		0.697	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
CHN2	1124	hgsc.bcm.edu	37	7	29539639	29539639	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:29539639G>A	ENST00000222792.6	+	9	1426	c.896G>A	c.(895-897)cGg>cAg	p.R299Q	CHN2_ENST00000421775.2_Intron|CHN2_ENST00000439711.2_Missense_Mutation_p.R163Q|CHN2_ENST00000435288.2_Intron|CHN2_ENST00000495789.2_Missense_Mutation_p.R312Q|CHN2_ENST00000424025.2_Missense_Mutation_p.R118Q|CHN2_ENST00000539389.1_Missense_Mutation_p.R155Q|CHN2_ENST00000410098.1_3'UTR|CHN2_ENST00000546235.1_Missense_Mutation_p.R284Q|CHN2_ENST00000539406.1_Missense_Mutation_p.R374Q|CHN2_ENST00000409041.4_Missense_Mutation_p.R163Q	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	299	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						ATATGCATTCGGGAAATTGAA	0.378																																					p.R299Q	Ovarian(1;44 48 13232 18918 31480)	Atlas-SNP	.											.	CHN2	98	.	0			c.G896A						PASS	.						69.0	63.0	65.0					7																	29539639		2203	4300	6503	SO:0001583	missense	1124	exon9			GCATTCGGGAAAT	L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"""Rho GTPase activating proteins"", ""SH2 domain containing"""	1944	protein-coding gene	gene with protein product	"""beta chimerin"", ""chimaerin 2"""	602857	"""chimerin (chimaerin) 2"""			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.896G>A	7.37:g.29539639G>A	ENSP00000222792:p.Arg299Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	67	9	0.134328	NM_004067	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Missense_Mutation	SNP	ENST00000222792.6	37	CCDS5420.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177801	0.38413	.	.	ENSG00000106069	ENST00000539406;ENST00000222792;ENST00000495789;ENST00000539389;ENST00000546235;ENST00000446446;ENST00000409041;ENST00000424025;ENST00000439711	T;T;T;T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23;2.23;2.23;2.23	5.6	5.6	0.85130	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.109458	0.64402	D	0.000006	T	0.07458	0.0188	N	0.10945	0.07	0.80722	D	1	B;B;B;B;B;B;P;B;B;B;B;B;B;B	0.39665	0.031;0.006;0.046;0.206;0.051;0.104;0.682;0.051;0.224;0.055;0.014;0.083;0.224;0.014	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.24006	0.002;0.004;0.002;0.015;0.01;0.037;0.05;0.015;0.016;0.006;0.002;0.016;0.01;0.002	T	0.36915	-0.9728	10	0.28530	T	0.3	.	12.8884	0.58057	0.0753:0.0:0.9247:0.0	.	92;284;312;374;118;118;163;163;163;155;299;69;163;299	B7Z215;B7Z1W9;B7Z1V0;F5H003;B3VCF1;B3VCF2;B3VCF5;B3VCF7;B3VCF6;B3VCG1;A4D1A2;B3VCF8;E9PGE0;P52757	.;.;.;.;.;.;.;.;.;.;.;.;.;CHIO_HUMAN	Q	374;299;312;155;284;124;163;118;163	ENSP00000444063:R374Q;ENSP00000222792:R299Q;ENSP00000438587:R312Q;ENSP00000440526:R155Q;ENSP00000442812:R284Q;ENSP00000396867:R124Q;ENSP00000386849:R163Q;ENSP00000406337:R118Q;ENSP00000387425:R163Q	ENSP00000222792:R299Q	R	+	2	0	CHN2	29506164	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.894000	0.63206	2.800000	0.96347	0.455000	0.32223	CGG	.	.	none		0.378	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067	
MYH3	4621	hgsc.bcm.edu	37	17	10542471	10542471	+	Silent	SNP	T	T	G	rs2285475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10542471T>G	ENST00000583535.1	-	25	3225	c.3138A>C	c.(3136-3138)cgA>cgC	p.R1046R	MYH3_ENST00000226209.7_Silent_p.R1046R	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1046					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CCAGGTCTACTCGGAGCTTCT	0.453													G|||	2336	0.466454	0.2398	0.5346	5008	,	,		19613	0.3839		0.7584	False		,,,				2504	0.5092				p.R1046R		Atlas-SNP	.											MYH3,caecum,carcinoma,-1,1	MYH3	227	1	0			c.A3138C						PASS	.	G		1302,3104	698.1+/-406.3	198,906,1099	135.0	121.0	126.0		3138	-11.3	0.4	17	dbSNP_100	126	6263,2337	390.5+/-343.3	2261,1741,298	no	coding-synonymous	MYH3	NM_002470.3		2459,2647,1397	GG,GT,TT		27.1744,29.5506,41.8345		1046/1941	10542471	7565,5441	2203	4300	6503	SO:0001819	synonymous_variant	4621	exon25			GTCTACTCGGAGC		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.3138A>C	17.37:g.10542471T>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	37	CCDS11157.1																																																																																			T|0.464;G|0.536	0.536	strong		0.453	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
MAP4	4134	hgsc.bcm.edu	37	3	48040283	48040283	+	Missense_Mutation	SNP	C	C	T	rs11711953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:48040283C>T	ENST00000360240.6	-	2	586	c.68G>A	c.(67-69)cGg>cAg	p.R23Q	MAP4_ENST00000434267.1_Missense_Mutation_p.R23Q|MAP4_ENST00000439356.1_Missense_Mutation_p.R23Q|MAP4_ENST00000426837.2_Missense_Mutation_p.R23Q|MAP4_ENST00000383737.4_Missense_Mutation_p.R23Q|MAP4_ENST00000395734.3_Missense_Mutation_p.R23Q	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	23			R -> Q (in dbSNP:rs11711953).		cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	AATGAAGTCCCGCTTTATCTC	0.468													C|||	146	0.0291534	0.0008	0.0346	5008	,	,		19003	0.0		0.0726	False		,,,				2504	0.0491				p.R23Q		Atlas-SNP	.											.	MAP4	176	.	0			c.G68A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	74,4332	65.8+/-103.3	0,74,2129	187.0	168.0	175.0		68,68,68	4.6	1.0	3	dbSNP_120	175	672,7928	168.7+/-220.2	21,630,3649	yes	missense,missense,missense	MAP4	NM_001134364.1,NM_002375.4,NM_030885.3	43,43,43	21,704,5778	TT,TC,CC		7.814,1.6795,5.7358	probably-damaging,probably-damaging,probably-damaging	23/1136,23/1153,23/100	48040283	746,12260	2203	4300	6503	SO:0001583	missense	4134	exon2			AAGTCCCGCTTTA		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.68G>A	3.37:g.48040283C>T	ENSP00000353375:p.Arg23Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	177	86	0.485876	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	75|75	0.034340659340659344|0.034340659340659344	1|1	0.0020325203252032522|0.0020325203252032522	14|14	0.03867403314917127|0.03867403314917127	0|0	0.0|0.0	60|60	0.079155672823219|0.079155672823219	C|C	18.82|18.82	3.704374|3.704374	0.68615|0.68615	0.016795|0.016795	0.07814|0.07814	ENSG00000047849|ENSG00000047849	ENST00000423088|ENST00000383737;ENST00000395734;ENST00000426837;ENST00000360240;ENST00000434267;ENST00000439356	.|T;T;T;T;T;T	.|0.52295	.|0.67;0.67;0.67;0.67;0.67;0.67	4.56|4.56	4.56|4.56	0.56223|0.56223	.|.	.|.	.|.	.|.	.|.	T|T	0.08537|0.08537	0.0212|0.0212	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.999;1.0;1.0	.|D;D;D;D	.|0.85130	.|0.994;0.99;0.997;0.996	T|T	0.11372|0.11372	-1.0590|-1.0590	5|9	.|0.39692	.|T	.|0.17	-7.7369|-7.7369	13.0269|13.0269	0.58821|0.58821	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs11711953;rs52793755;rs61530442;rs11711953|rs11711953;rs52793755;rs61530442;rs11711953	.|23;23;23;23	.|C9JFC3;Q86V26;P27816-6;P27816	.|.;.;.;MAP4_HUMAN	R|Q	30|23	.|ENSP00000373243:R23Q;ENSP00000379083:R23Q;ENSP00000407602:R23Q;ENSP00000353375:R23Q;ENSP00000402767:R23Q;ENSP00000397414:R23Q	.|ENSP00000353375:R23Q	G|R	-|-	1|2	0|0	MAP4|MAP4	48015287|48015287	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.939000|0.939000	0.58152|0.58152	2.639000|2.639000	0.46570|0.46570	2.535000|2.535000	0.85469|0.85469	0.467000|0.467000	0.42956|0.42956	GGG|CGG	C|0.948;T|0.052	0.052	strong		0.468	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375	
SEMA4B	10509	hgsc.bcm.edu	37	15	90768320	90768320	+	Silent	SNP	C	C	T	rs11073918	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90768320C>T	ENST00000411539.2	+	10	1575	c.1315C>T	c.(1315-1317)Ctg>Ttg	p.L439L	SEMA4B_ENST00000379122.3_Silent_p.L434L|SEMA4B_ENST00000332496.6_Silent_p.L439L	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	434	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)			NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			CCGCATGCTGCTGCTGCAGCC	0.617													C|||	1308	0.261182	0.0802	0.317	5008	,	,		20606	0.37		0.2584	False		,,,				2504	0.3569				p.L439L		Atlas-SNP	.											.	SEMA4B	51	.	0			c.C1315T						PASS	.	C	,	503,3789		38,427,1681	52.0	61.0	58.0		1315,1315	4.2	0.9	15	dbSNP_120	58	1954,6536		227,1500,2518	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	265,1927,4199	TT,TC,CC		23.0153,11.7195,19.2223	,	439/838,439/838	90768320	2457,10325	2146	4245	6391	SO:0001819	synonymous_variant	10509	exon11			ATGCTGCTGCTGC	AB051532	CCDS45347.1	15q25	2008-07-18						"""Semaphorins"""	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.1315C>T	15.37:g.90768320C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	104	61	0.586538	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Silent	SNP	ENST00000411539.2	37	CCDS45347.1																																																																																			C|0.755;T|0.245	0.245	strong		0.617	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
MUC4	4585	hgsc.bcm.edu	37	3	195515449	195515449	+	Missense_Mutation	SNP	A	A	T	rs200672669	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515449A>T	ENST00000463781.3	-	2	3461	c.3002T>A	c.(3001-3003)gTa>gAa	p.V1001E	MUC4_ENST00000475231.1_Missense_Mutation_p.V1001E|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	425	Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V1001A(1)|p.V1001E(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATACTGAGGAAGC	0.587																																					p.V1001E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,12	MUC4	1505	12	2	Substitution - Missense(2)	prostate(1)|endometrium(1)	c.T3002A						scavenged	.						45.0	36.0	39.0					3																	195515449		2193	4257	6450	SO:0001583	missense	4585	exon2			GTGGATACTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3002T>A	3.37:g.195515449A>T	ENSP00000417498:p.Val1001Glu	Somatic	593	14	0.0236088		WXS	Illumina HiSeq	Phase_I	208	22	0.105769	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	7.806	0.714656	0.15306	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37752	1.19;1.18	1.24	-2.48	0.06423	.	.	.	.	.	T	0.13543	0.0328	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.01281	0.0	T	0.24261	-1.0165	8	.	.	.	.	2.7997	0.05411	0.2821:0.0:0.4902:0.2277	.	1001	E7ESK3	.	E	1001	ENSP00000417498:V1001E;ENSP00000420243:V1001E	.	V	-	2	0	MUC4	196999844	.	.	0.000000	0.03702	0.127000	0.20565	.	.	-0.712000	0.04988	0.055000	0.15244	GTA	A|0.956;G|0.036;T|0.008	0.008	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR10G2	26534	hgsc.bcm.edu	37	14	22102745	22102745	+	Missense_Mutation	SNP	C	C	A	rs41314525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:22102745C>A	ENST00000542433.1	-	1	351	c.254G>T	c.(253-255)cGg>cTg	p.R85L		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	85			R -> L (in dbSNP:rs41314525).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		CAAAATAAGCCGAGGAACGGT	0.527													.|||	1173	0.234225	0.2746	0.1859	5008	,	,		21829	0.2808		0.1948	False		,,,				2504	0.2065				p.R85L		Atlas-SNP	.											.	OR10G2	35	.	0			c.G254T						PASS	.	C	LEU/ARG	1087,3319	394.0+/-329.1	139,809,1255	61.0	56.0	58.0		254	1.6	0.5	14	dbSNP_127	58	1549,7051	291.1+/-300.1	144,1261,2895	yes	missense	OR10G2	NM_001005466.1	102	283,2070,4150	AA,AC,CC		18.0116,24.6709,20.2676	benign	85/311	22102745	2636,10370	2203	4300	6503	SO:0001583	missense	26534	exon1			ATAAGCCGAGGAA		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.254G>T	14.37:g.22102745C>A	ENSP00000445383:p.Arg85Leu	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	270	132	0.488889	NM_001005466	B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	37	CCDS32047.1	525	0.2403846153846154	131	0.266260162601626	67	0.1850828729281768	169	0.29545454545454547	158	0.20844327176781002	C	3.673	-0.067195	0.07273	0.246709	0.180116	ENSG00000255582	ENST00000542433	T	0.03212	4.01	3.79	1.65	0.23941	GPCR, rhodopsin-like superfamily (1);	0.197894	0.24848	N	0.035104	T	0.00012	0.0000	L	0.45051	1.395	0.80722	P	0.0	B	0.12630	0.006	B	0.13407	0.009	T	0.48536	-0.9027	9	0.87932	D	0	-3.183	3.1156	0.06373	0.2243:0.5309:0.0:0.2448	rs41314525;rs61755908;rs41314525	85	Q8NGC3	O10G2_HUMAN	L	85	ENSP00000445383:R85L	ENSP00000445383:R85L	R	-	2	0	OR10G2	21172585	0.000000	0.05858	0.457000	0.27056	0.045000	0.14185	0.179000	0.16840	0.760000	0.33108	0.563000	0.77884	CGG	C|0.782;A|0.218	0.218	strong		0.527	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
PIP4K2A	5305	hgsc.bcm.edu	37	10	22839628	22839628	+	Missense_Mutation	SNP	T	T	C	rs2230469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:22839628T>C	ENST00000376573.4	-	7	980	c.752A>G	c.(751-753)aAc>aGc	p.N251S	PIP4K2A_ENST00000323883.7_Missense_Mutation_p.N111S|PIP4K2A_ENST00000545335.1_Missense_Mutation_p.N192S	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	251	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.		N -> S (in dbSNP:rs10828317). {ECO:0000269|PubMed:7639683}.		megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						GACCTTCTTGTTGTTGTCATC	0.363											OREG0020068	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1063	0.21226	0.0696	0.134	5008	,	,		18073	0.3839		0.3131	False		,,,				2504	0.18				p.N251S		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.A752G	GRCh37	CM068312	PIP4K2A	M	rs10828317	PASS	.	T	SER/ASN	456,3948	217.4+/-235.8	29,398,1775	180.0	175.0	177.0		752	6.1	1.0	10	dbSNP_120	177	2740,5860	437.2+/-358.5	451,1838,2011	yes	missense	PIP4K2A	NM_005028.4	46	480,2236,3786	CC,CT,TT		31.8605,10.3542,24.5771	benign	251/407	22839628	3196,9808	2202	4300	6502	SO:0001583	missense	5305	exon7			TTCTTGTTGTTGT	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"""phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"""	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.752A>G	10.37:g.22839628T>C	ENSP00000365757:p.Asn251Ser	Somatic	163	0	0	759	WXS	Illumina HiSeq	Phase_I	179	87	0.486034	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Missense_Mutation	SNP	ENST00000376573.4	37	CCDS7141.1	564	0.25824175824175827	38	0.07723577235772358	44	0.12154696132596685	232	0.40559440559440557	250	0.32981530343007914	T	9.613	1.131741	0.21041	0.103542	0.318605	ENSG00000150867	ENST00000376573;ENST00000323883;ENST00000545335	T;T;T	0.34275	1.37;1.37;1.37	6.07	6.07	0.98685	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.042713	0.85682	D	0.000000	T	0.00012	0.0000	N	0.11673	0.155	0.09310	P	0.999999748043	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.004	T	0.45760	-0.9239	9	0.15066	T	0.55	-58.1863	16.6277	0.84984	0.0:0.0:0.0:1.0	rs10828317;rs52795826;rs59726485;rs10828317	111;251	B4DH09;P48426	.;PI42A_HUMAN	S	251;111;192	ENSP00000365757:N251S;ENSP00000326294:N111S;ENSP00000442098:N192S	ENSP00000326294:N111S	N	-	2	0	PIP4K2A	22879634	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.912000	0.69948	2.330000	0.79161	0.528000	0.53228	AAC	T|0.753;C|0.247	0.247	strong		0.363	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	
MAGEB16	139604	hgsc.bcm.edu	37	X	35821127	35821127	+	Nonsense_Mutation	SNP	C	C	T	rs4829392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:35821127C>T	ENST00000399989.1	+	2	1093	c.814C>T	c.(814-816)Cga>Tga	p.R272*	MAGEB16_ENST00000399985.1_Nonsense_Mutation_p.R272*|MAGEB16_ENST00000399987.1_Nonsense_Mutation_p.R272*|MAGEB16_ENST00000399992.1_Nonsense_Mutation_p.R304*|MAGEB16_ENST00000399988.1_Nonsense_Mutation_p.R272*	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	272	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						TGATCCTGCACGATATGAATT	0.483													C|||	2342	0.620397	0.4478	0.4121	3775	,	,		15380	0.5694		0.4195	False		,,,				2504	0.4785				p.R272X		Atlas-SNP	.											.	MAGEB16	64	.	0			c.C814T						PASS	.	C	stop/ARG	2170,1655		540,782,308,305,263	38.0	38.0	38.0		814	-1.3	0.0	X	dbSNP_111	38	3581,3147		694,1206,987,528,885	yes	stop-gained	MAGEB16	NM_001099921.1		1234,1988,1295,833,1148	TT,TC,T,CC,C		46.7747,43.268,45.5036		272/325	35821127	5751,4802	2198	4300	6498	SO:0001587	stop_gained	139604	exon2			CCTGCACGATATG		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.814C>T	X.37:g.35821127C>T	ENSP00000382871:p.Arg272*	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	167	167	1	NM_001099921	A8MU30	Nonsense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	1014	0.6112115732368897	151	0.4415204678362573	102	0.4146341463414634	212	0.5792349726775956	230	0.3885135135135135	C	16.21	3.060037	0.55325	0.56732	0.532253	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	.	.	.	3.13	-1.27	0.09347	.	0.391845	0.25596	N	0.029598	.	.	.	.	.	.	0.09310	P	0.99999629397	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9248	0.19104	0.5383:0.2869:0.1748:0.0	rs4829392;rs52830693;rs4829392	.	.	.	X	272;304;272;272;272	.	ENSP00000382867:R272X	R	+	1	2	MAGEB16	35731048	0.000000	0.05858	0.000000	0.03702	0.404000	0.30871	0.056000	0.14256	-0.423000	0.07394	-0.340000	0.08031	CGA	C|0.356;0|0.042	.	strong		0.483	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
PDS5B	23047	hgsc.bcm.edu	37	13	33232435	33232435	+	Silent	SNP	A	A	G	rs2301393	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:33232435A>G	ENST00000315596.10	+	4	558	c.372A>G	c.(370-372)caA>caG	p.Q124Q		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	124					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		AGAGCCCACAATTCAATAGGT	0.269													A|||	1359	0.271366	0.2337	0.3559	5008	,	,		14898	0.1389		0.4702	False		,,,				2504	0.1943				p.Q124Q		Atlas-SNP	.											.	PDS5B	141	.	0			c.A372G						PASS	.	A		973,2617		134,705,956	54.0	51.0	52.0		372	-1.5	1.0	13	dbSNP_100	52	3475,4649		756,1963,1343	no	coding-synonymous	PDS5B	NM_015032.3		890,2668,2299	GG,GA,AA		42.7745,27.1031,37.9717		124/1448	33232435	4448,7266	1795	4062	5857	SO:0001819	synonymous_variant	23047	exon4			CCCACAATTCAAT	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.372A>G	13.37:g.33232435A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	154	151	0.980519	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Silent	SNP	ENST00000315596.10	37	CCDS41878.1																																																																																			A|0.686;G|0.314	0.314	strong		0.269	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
ADSS	159	hgsc.bcm.edu	37	1	244583585	244583585	+	Missense_Mutation	SNP	T	T	C	rs55648210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:244583585T>C	ENST00000366535.3	-	8	993	c.677A>G	c.(676-678)aAg>aGg	p.K226R	ADSS_ENST00000462358.1_5'UTR	NM_001126.3	NP_001117.2			adenylosuccinate synthase											endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)	all_cancers(173;0.0896)|all_epithelial(177;0.172)	all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014)			TGGTTTAATCTTTTCCATATA	0.333													T|||	72	0.014377	0.0	0.0058	5008	,	,		18137	0.0		0.0189	False		,,,				2504	0.0501				p.K226R		Atlas-SNP	.											.	ADSS	49	.	0			c.A677G						PASS	.	T	ARG/LYS	39,4363	40.0+/-72.8	0,39,2162	90.0	82.0	84.0		677	4.7	1.0	1	dbSNP_129	84	215,8383	80.9+/-143.5	1,213,4085	yes	missense	ADSS	NM_001126.3	26	1,252,6247	CC,CT,TT		2.5006,0.886,1.9538	benign	226/457	244583585	254,12746	2201	4299	6500	SO:0001583	missense	159	exon8			TTAATCTTTTCCA	BC012356	CCDS1624.1	1q44	2008-02-05			ENSG00000035687	ENSG00000035687	6.3.4.4		292	protein-coding gene	gene with protein product		103060				2004783, 1592113	Standard	NM_001126		Approved		uc001iaj.3	P30520	OTTHUMG00000040102	ENST00000366535.3:c.677A>G	1.37:g.244583585T>C	ENSP00000355493:p.Lys226Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_001126		Missense_Mutation	SNP	ENST00000366535.3	37	CCDS1624.1	21	0.009615384615384616	0	0.0	5	0.013812154696132596	0	0.0	16	0.021108179419525065	T	5.214	0.225034	0.09916	0.00886	0.025006	ENSG00000035687	ENST00000366535;ENST00000449326	T	0.41065	1.01	5.64	4.73	0.59995	.	0.127094	0.64402	N	0.000002	T	0.05090	0.0136	N	0.01705	-0.755	0.36651	D	0.877374	B	0.02656	0.0	B	0.01281	0.0	T	0.15009	-1.0452	10	0.02654	T	1	-6.873	11.9388	0.52888	0.0:0.8481:0.0:0.1519	rs55648210;rs61750994	226	P30520	PURA2_HUMAN	R	226;205	ENSP00000355493:K226R	ENSP00000355493:K226R	K	-	2	0	ADSS	242650208	0.990000	0.36364	1.000000	0.80357	0.994000	0.84299	2.658000	0.46733	1.512000	0.48834	-0.220000	0.12472	AAG	T|0.980;C|0.020	0.020	strong		0.333	ADSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096697.1	NM_001126	
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69094507	69094507	+	Missense_Mutation	SNP	T	T	A	rs2319797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69094507T>A	ENST00000332644.5	-	9	1203	c.1042A>T	c.(1042-1044)Aca>Tca	p.T348S		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	348	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		T -> S (in dbSNP:rs2319797). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						CATAACATTGTATCAGTCACA	0.358													T|||	3598	0.71845	0.4297	0.6023	5008	,	,		19683	0.9901		0.7306	False		,,,				2504	0.8988				p.T348S		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.A1042T						PASS	.	T	SER/THR	2304,2102	601.4+/-389.7	614,1076,513	138.0	124.0	129.0		1042	0.5	0.0	4	dbSNP_100	129	6700,1900	727.9+/-406.7	2590,1520,190	yes	missense	TMPRSS11B	NM_182502.3	58	3204,2596,703	AA,AT,TT		22.093,47.7077,30.7704	benign	348/417	69094507	9004,4002	2203	4300	6503	SO:0001583	missense	132724	exon9			ACATTGTATCAGT	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.1042A>T	4.37:g.69094507T>A	ENSP00000330475:p.Thr348Ser	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	276	276	1	NM_182502	A8K4D9	Missense_Mutation	SNP	ENST00000332644.5	37	CCDS3521.1	1568	0.717948717948718	209	0.4247967479674797	237	0.6546961325966851	567	0.9912587412587412	555	0.7321899736147758	T	2.807	-0.247950	0.05867	0.522923	0.77907	ENSG00000185873	ENST00000332644	D	0.92446	-3.04	4.62	0.489	0.16854	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.584031	0.14283	N	0.329382	T	0.00012	0.0000	N	0.04724	-0.175	0.80722	P	0.0	B	0.31256	0.316	B	0.27076	0.076	T	0.31194	-0.9952	9	0.40728	T	0.16	.	2.6718	0.05069	0.2774:0.2249:0.0:0.4977	rs2319797;rs52796926;rs2319797	348	Q86T26	TM11B_HUMAN	S	348	ENSP00000330475:T348S	ENSP00000330475:T348S	T	-	1	0	TMPRSS11B	68777102	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.054000	0.11826	0.362000	0.24319	-0.408000	0.06270	ACA	T|0.292;A|0.708	0.708	strong		0.358	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
SPATA32	124783	hgsc.bcm.edu	37	17	43333125	43333125	+	Missense_Mutation	SNP	C	C	T	rs11651968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:43333125C>T	ENST00000331780.4	-	4	519	c.424G>A	c.(424-426)Gtg>Atg	p.V142M	SPATA32_ENST00000543122.1_Missense_Mutation_p.V121M|MAP3K14-AS1_ENST00000590100.1_RNA|MAP3K14-AS1_ENST00000591263.1_RNA|MAP3K14-AS1_ENST00000588698.1_RNA|MAP3K14-AS1_ENST00000588160.1_RNA|MAP3K14-AS1_ENST00000588504.1_RNA|MAP3K14-AS1_ENST00000585346.1_RNA|MAP3K14-AS1_ENST00000592422.1_RNA	NM_152343.2	NP_689556.2	Q96LK8	SPT32_HUMAN	spermatogenesis associated 32	142			V -> M (in dbSNP:rs11651968). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		spermatogenesis (GO:0007283)	perinuclear region of cytoplasm (GO:0048471)											CAGGCAGACACGTGGTTCTCC	0.587													C|||	1558	0.311102	0.1104	0.4294	5008	,	,		17541	0.3046		0.4245	False		,,,				2504	0.3885				p.V142M		Atlas-SNP	.											.	.	.	.	0			c.G424A						PASS	.	C	MET/VAL	671,3735	285.5+/-278.2	47,577,1579	101.0	93.0	96.0		424	-3.8	0.0	17	dbSNP_120	96	3960,4640	550.7+/-385.8	917,2126,1257	yes	missense	C17orf46	NM_152343.2	21	964,2703,2836	TT,TC,CC		46.0465,15.2292,35.6066	possibly-damaging	142/385	43333125	4631,8375	2203	4300	6503	SO:0001583	missense	124783	exon4			CAGACACGTGGTT	AK058143	CCDS32669.1	17q21.31	2013-10-11	2012-10-08	2012-10-08	ENSG00000184361	ENSG00000184361			26349	protein-coding gene	gene with protein product	"""acrosome expressed 2"""		"""chromosome 17 open reading frame 46"", ""testis expressed 34"""	C17orf46, TEX34		18621766	Standard	NM_152343		Approved	FLJ25414, AEP2, VAD1.2	uc002iis.1	Q96LK8	OTTHUMG00000180363	ENST00000331780.4:c.424G>A	17.37:g.43333125C>T	ENSP00000331532:p.Val142Met	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	37	0.37	NM_152343	Q7Z4U1|Q8N6V6	Missense_Mutation	SNP	ENST00000331780.4	37	CCDS32669.1	723	0.33104395604395603	67	0.13617886178861788	148	0.4088397790055249	188	0.32867132867132864	320	0.42216358839050133	C	12.47	1.946359	0.34377	0.152292	0.460465	ENSG00000184361	ENST00000331780;ENST00000543122	T;T	0.53857	0.6;0.6	3.9	-3.82	0.04281	.	1.610090	0.03935	N	0.285979	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.47350	0.894	B	0.37346	0.247	T	0.20840	-1.0263	9	0.35671	T	0.21	1.1262	5.3052	0.15799	0.0:0.275:0.1646:0.5604	rs11651968;rs17845838;rs17858807;rs58610600;rs11651968	142	Q96LK8	CQ046_HUMAN	M	142;121	ENSP00000331532:V142M;ENSP00000442724:V121M	ENSP00000331532:V142M	V	-	1	0	C17orf46	40688908	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.742000	0.00798	-0.575000	0.05982	0.555000	0.69702	GTG	C|0.650;G|0.000;T|0.350	0.350	strong		0.587	SPATA32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450946.1	NM_152343	
SEPT4	5414	hgsc.bcm.edu	37	17	56598991	56598991	+	Missense_Mutation	SNP	T	T	A	rs17741424	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56598991T>A	ENST00000317268.3	-	8	1108	c.932A>T	c.(931-933)gAg>gTg	p.E311V	SEPT4_ENST00000457347.2_Missense_Mutation_p.E326V|SEPT4_ENST00000426861.1_3'UTR|SEPT4_ENST00000317256.6_Missense_Mutation_p.E292V|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000412945.3_Missense_Mutation_p.E303V|SEPT4_ENST00000393086.1_Missense_Mutation_p.E292V|SEPT4_ENST00000580809.1_3'UTR|SEPT4_ENST00000583114.1_Missense_Mutation_p.E164V|SEPT4_ENST00000579371.1_Missense_Mutation_p.E212V|SEPT4_ENST00000580844.1_Missense_Mutation_p.E212V	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	311	Septin-type G.		E -> V (in dbSNP:rs17741424).		apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCAAAATGCTCAATCTCCTC	0.522													T|||	218	0.0435304	0.0045	0.0533	5008	,	,		19419	0.0		0.1243	False		,,,				2504	0.0511				p.E326V		Atlas-SNP	.											SEPT4,lymph_node,lymphoid_neoplasm,0,1	SEPT4	48	1	0			c.A977T						PASS	.	T	VAL/GLU,VAL/GLU,,VAL/GLU	101,4305	80.4+/-118.8	1,99,2103	123.0	118.0	120.0		908,932,,875	5.6	1.0	17	dbSNP_123	120	1037,7563	220.1+/-257.9	69,899,3332	yes	missense,missense,utr-3,missense	SEPT4	NM_001198713.1,NM_004574.3,NM_080415.2,NM_080416.2	121,121,,121	70,998,5435	AA,AT,TT		12.0581,2.2923,8.7498	possibly-damaging,possibly-damaging,,possibly-damaging	303/471,311/479,,292/460	56598991	1138,11868	2203	4300	6503	SO:0001583	missense	5414	exon9			AAATGCTCAATCT	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"""Septins"""	9165	protein-coding gene	gene with protein product	"""bradeoin"", ""septin-M"""	603696	"""peanut-like 2 (Drosophila)"""	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.932A>T	17.37:g.56598991T>A	ENSP00000321674:p.Glu311Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	173	76	0.439306	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Missense_Mutation	SNP	ENST00000317268.3	37	CCDS11610.1	112	0.05128205128205128	2	0.0040650406504065045	24	0.06629834254143646	0	0.0	86	0.11345646437994723	T	8.736	0.917894	0.17982	0.022923	0.120581	ENSG00000108387	ENST00000412945;ENST00000457347;ENST00000317256;ENST00000317268;ENST00000393086	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.59	5.59	0.84812	.	0.112753	0.64402	D	0.000011	T	0.00724	0.0024	L	0.41079	1.255	0.09310	P	0.999999833909	P;P;B;P;P	0.48089	0.726;0.905;0.422;0.833;0.768	P;P;P;P;P	0.54140	0.499;0.605;0.499;0.68;0.743	T	0.05616	-1.0874	9	0.62326	D	0.03	.	13.7051	0.62633	0.0:0.0:0.0:1.0	rs17741424;rs52801197;rs17741424	303;326;292;164;311	O43236-3;O43236-4;O43236-2;O43236-5;O43236	.;.;.;.;SEPT4_HUMAN	V	303;325;292;311;292	ENSP00000414779:E303V;ENSP00000321071:E292V;ENSP00000321674:E311V;ENSP00000376801:E292V	ENSP00000321071:E292V	E	-	2	0	SEPT4	53953990	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	5.151000	0.64875	2.116000	0.64780	0.455000	0.32223	GAG	T|0.923;A|0.077	0.077	strong		0.522	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	
PLOD3	8985	hgsc.bcm.edu	37	7	100855180	100855180	+	Silent	SNP	G	G	A	rs11546152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100855180G>A	ENST00000223127.3	-	11	1577	c.1179C>T	c.(1177-1179)gcC>gcT	p.A393A		NM_001084.4	NP_001075.1	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	393					basement membrane assembly (GO:0070831)|cellular protein modification process (GO:0006464)|cellular response to hormone stimulus (GO:0032870)|collagen fibril organization (GO:0030199)|endothelial cell morphogenesis (GO:0001886)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|lung morphogenesis (GO:0060425)|neural tube development (GO:0021915)|protein localization (GO:0008104)|vasodilation (GO:0042311)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen galactosyltransferase activity (GO:0050211)|procollagen glucosyltransferase activity (GO:0033823)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	31	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	GGACAGCGTCGGCGTCCAGGC	0.662													g|||	18	0.00359425	0.0008	0.0101	5008	,	,		15879	0.001		0.007	False		,,,				2504	0.002				p.A393A		Atlas-SNP	.											.	PLOD3	79	.	0			c.C1179T						PASS	.	G		10,4396	11.4+/-27.6	0,10,2193	48.0	40.0	42.0		1179	-8.5	0.0	7	dbSNP_120	42	103,8497	52.3+/-112.8	1,101,4198	no	coding-synonymous	PLOD3	NM_001084.4		1,111,6391	AA,AG,GG		1.1977,0.227,0.8688		393/739	100855180	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	8985	exon11			AGCGTCGGCGTCC	AF046889	CCDS5715.1	7q22.1	2011-08-24			ENSG00000106397	ENSG00000106397	1.14.11.4		9083	protein-coding gene	gene with protein product	"""lysyl hydroxlase 3"""	603066				9724729, 9582318	Standard	NM_001084		Approved	LH3	uc003uyd.3	O60568	OTTHUMG00000157111	ENST00000223127.3:c.1179C>T	7.37:g.100855180G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_001084	B2R6W6|Q540C3	Silent	SNP	ENST00000223127.3	37	CCDS5715.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	1	0.0017482517482517483	8	0.010554089709762533	g	2.305	-0.359232	0.05138	0.00227	0.011977	ENSG00000106397	ENST00000421736	.	.	.	4.26	-8.53	0.00916	.	.	.	.	.	T	0.42675	0.1213	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59423	-0.7457	4	.	.	.	-43.7393	11.1018	0.48179	0.1494:0.0:0.6433:0.2073	rs11546152	.	.	.	L	184	.	.	P	-	2	0	PLOD3	100641900	0.000000	0.05858	0.017000	0.16124	0.283000	0.27025	-7.212000	0.00041	-2.278000	0.00677	-0.619000	0.04042	CCG	G|0.993;A|0.007	0.007	strong		0.662	PLOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347470.1		
HSD17B7	51478	hgsc.bcm.edu	37	1	162775267	162775267	+	Silent	SNP	C	C	T	rs12563263	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:162775267C>T	ENST00000254521.3	+	8	943	c.888C>T	c.(886-888)taC>taT	p.Y296Y	HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367917.3_Silent_p.Y261Y	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	296					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					GAAGAAATTACATTATGACCC	0.458													C|||	916	0.182907	0.1467	0.2536	5008	,	,		21225	0.1369		0.3211	False		,,,				2504	0.0869				p.Y296Y		Atlas-SNP	.											.	HSD17B7	25	.	0			c.C888T						PASS	.	C		758,3648	303.8+/-288.1	69,620,1514	55.0	50.0	52.0		888	-9.4	0.0	1	dbSNP_120	52	2812,5782	438.1+/-358.8	470,1872,1955	no	coding-synonymous	HSD17B7	NM_016371.2		539,2492,3469	TT,TC,CC		32.7205,17.2038,27.4615		296/342	162775267	3570,9430	2203	4297	6500	SO:0001819	synonymous_variant	51478	exon8			AAATTACATTATG	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5215	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 37C, member 1"""	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.888C>T	1.37:g.162775267C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	297	124	0.417508	NM_016371	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Silent	SNP	ENST00000254521.3	37	CCDS1242.1																																																																																			T|1.000;|0.000	1.000	weak		0.458	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371	
CES1	1066	hgsc.bcm.edu	37	16	55862762	55862762	+	Silent	SNP	C	C	G	rs3826194	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55862762C>G	ENST00000361503.4	-	2	304	c.174G>C	c.(172-174)ccG>ccC	p.P58P	CES1_ENST00000422046.2_Silent_p.P58P|CES1_ENST00000566555.1_5'Flank|CES1_ENST00000360526.3_Silent_p.P59P			P23141	EST1_HUMAN	carboxylesterase 1	58					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	GTCCAAGAGGCGGCTTGGCAA	0.552																																					p.P59P	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,caecum,carcinoma,0,2	CES1	78	2	0			c.G177C						PASS	.						100.0	93.0	95.0					16																	55862762		2198	4300	6498	SO:0001819	synonymous_variant	1066	exon2			AAGAGGCGGCTTG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.174G>C	16.37:g.55862762C>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	116	22	0.189655	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																			C|0.766;G|0.234	0.234	strong		0.552	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
ROCK1	6093	hgsc.bcm.edu	37	18	18534948	18534948	+	Missense_Mutation	SNP	G	G	C	rs201390233		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:18534948G>C	ENST00000399799.2	-	31	4589	c.3649C>G	c.(3649-3651)Caa>Gaa	p.Q1217E		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	1217	Auto-inhibitory.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		Q -> E (in dbSNP:rs2847092). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Q1217E(1)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TTTTCAGCTTGTTGTACTGGT	0.363																																					p.Q1217E		Atlas-SNP	.											ROCK1_ENST00000399799,NS,carcinoma,0,1	ROCK1	162	1	1	Substitution - Missense(1)	prostate(1)	c.C3649G						scavenged	.						121.0	99.0	107.0					18																	18534948		2203	4300	6503	SO:0001583	missense	6093	exon31			CAGCTTGTTGTAC		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.3649C>G	18.37:g.18534948G>C	ENSP00000382697:p.Gln1217Glu	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	213	13	0.0610329	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	G	6.245	0.413238	0.11812	.	.	ENSG00000067900	ENST00000399799	T	0.63255	-0.03	5.43	5.43	0.79202	Pleckstrin homology domain (3);	0.060893	0.64402	D	0.000002	T	0.47248	0.1435	N	0.16903	0.455	0.47659	D	0.999489	B	0.27264	0.173	B	0.32022	0.139	T	0.44711	-0.9310	10	0.02654	T	1	.	19.2276	0.93824	0.0:0.0:1.0:0.0	.	1217	Q13464	ROCK1_HUMAN	E	1217	ENSP00000382697:Q1217E	ENSP00000382697:Q1217E	Q	-	1	0	ROCK1	16788946	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.303000	0.65738	2.530000	0.85305	0.543000	0.68304	CAA	G|0.985;C|0.015	0.015	strong		0.363	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406	
DYNC1I2	1781	hgsc.bcm.edu	37	2	172585298	172585298	+	Silent	SNP	T	T	C	rs62184168		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:172585298T>C	ENST00000397119.3	+	14	1496	c.1329T>C	c.(1327-1329)gaT>gaC	p.D443D	DYNC1I2_ENST00000409197.1_Silent_p.D417D|DYNC1I2_ENST00000508530.1_Silent_p.D417D|DYNC1I2_ENST00000409773.1_Silent_p.D443D|DYNC1I2_ENST00000263811.4_Silent_p.D437D|DYNC1I2_ENST00000409453.1_Silent_p.D443D|DYNC1I2_ENST00000409317.1_Silent_p.D437D|DYNC1I2_ENST00000340296.4_Silent_p.D417D|DYNC1I2_ENST00000358002.6_Silent_p.D435D|DYNC1I2_ENST00000410079.3_Silent_p.D435D|DYNC1I2_ENST00000534253.2_Silent_p.D443D	NM_001378.1	NP_001369.1	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2	443					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|G2/M transition of mitotic cell cycle (GO:0000086)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|microtubule (GO:0005874)|vesicle (GO:0031982)	microtubule motor activity (GO:0003777)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.198)			CTGTTGGAGATGTCAACAACT	0.398																																					p.D443D		Atlas-SNP	.											DYNC1I2,NS,carcinoma,0,1	DYNC1I2	43	1	0			c.T1329C						scavenged	.						67.0	65.0	65.0					2																	172585298		1866	4092	5958	SO:0001819	synonymous_variant	1781	exon14			TGGAGATGTCAAC	AK055491	CCDS46450.1, CCDS63054.1, CCDS63056.1, CCDS63057.1	2q31.1	2013-01-10	2005-11-24	2005-11-24	ENSG00000077380	ENSG00000077380		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2964	protein-coding gene	gene with protein product		603331	"""dynein, cytoplasmic, intermediate polypeptide 2"""	DNCI2		10049579, 16260502	Standard	NM_001378		Approved		uc002uha.2	Q13409	OTTHUMG00000154061	ENST00000397119.3:c.1329T>C	2.37:g.172585298T>C		Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	338	14	0.0414201	NM_001378	B7ZA04|D3DPD4|D3DPD5|D3DPD6|Q32LY9|Q53S84|Q5BJF8|Q7Z4X1|Q96NG7|Q96S87|Q9BXZ5|Q9NT58	Silent	SNP	ENST00000397119.3	37	CCDS46450.1																																																																																			T|0.333;C|0.667	0.667	strong		0.398	DYNC1I2-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333683.2	NM_001378	
ZFYVE28	57732	hgsc.bcm.edu	37	4	2341194	2341194	+	Silent	SNP	T	T	C	rs2071680	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2341194T>C	ENST00000290974.2	-	4	846	c.507A>G	c.(505-507)gcA>gcG	p.A169A	ZFYVE28_ENST00000515312.1_Silent_p.A99A|ZFYVE28_ENST00000515169.1_Silent_p.A99A|ZFYVE28_ENST00000509171.1_Silent_p.A122A|ZFYVE28_ENST00000503000.1_Silent_p.A169A|ZFYVE28_ENST00000511071.1_Silent_p.A169A	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	169					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						GCTCAAACTCTGCGAACAGGA	0.622													c|||	3216	0.642173	0.6944	0.7075	5008	,	,		18243	0.6994		0.5815	False		,,,				2504	0.5286				p.A169A		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.A507G						PASS	.	C	,,,,,	2989,1417	461.5+/-352.9	1012,965,226	87.0	68.0	74.0		507,507,366,297,297,507	-9.0	0.0	4	dbSNP_96	74	4916,3684	524.1+/-380.5	1407,2102,791	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFYVE28	NM_001172656.1,NM_001172657.1,NM_001172658.1,NM_001172659.1,NM_001172660.1,NM_020972.2	,,,,,	2419,3067,1017	CC,CT,TT		42.8372,32.1607,39.2204	,,,,,	169/858,169/288,122/173,99/818,99/164,169/888	2341194	7905,5101	2203	4300	6503	SO:0001819	synonymous_variant	57732	exon4			AAACTCTGCGAAC	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"""Zinc fingers, FYVE domain containing"""	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.507A>G	4.37:g.2341194T>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	182	182	1	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Silent	SNP	ENST00000290974.2	37	CCDS33942.1																																																																																			T|0.375;C|0.625	0.625	strong		0.622	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
NT5C	30833	hgsc.bcm.edu	37	17	73127348	73127348	+	Missense_Mutation	SNP	G	G	A	rs11541956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73127348G>A	ENST00000245552.2	-	2	290	c.203C>T	c.(202-204)cCg>cTg	p.P68L	NT5C_ENST00000579082.1_5'UTR|NT5C_ENST00000578337.1_5'UTR|NT5C_ENST00000582170.1_Missense_Mutation_p.P68L|NT5C_ENST00000582160.1_5'UTR	NM_014595.2	NP_055410.1	Q8TCD5	NT5C_HUMAN	5', 3'-nucleotidase, cytosolic	68			P -> L (in dbSNP:rs11541956). {ECO:0000269|PubMed:15489334}.		dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine deoxyribonucleotide catabolic process (GO:0009223)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotidase activity (GO:0008252)|pyrimidine nucleotide binding (GO:0019103)					all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Lamivudine(DB00709)	GAAAAAGCCCGGGGCTTCGTA	0.652													G|||	40	0.00798722	0.0008	0.0159	5008	,	,		12233	0.0		0.0249	False		,,,				2504	0.0031				p.P68L		Atlas-SNP	.											.	NT5C	3	.	0			c.C203T						PASS	.	G	LEU/PRO	23,4383	25.3+/-52.1	0,23,2180	36.0	43.0	41.0		203	3.4	0.2	17	dbSNP_120	41	242,8358	94.7+/-156.6	4,234,4062	yes	missense	NT5C	NM_014595.1	98	4,257,6242	AA,AG,GG		2.814,0.522,2.0375	probably-damaging	68/202	73127348	265,12741	2203	4300	6503	SO:0001583	missense	30833	exon2			AAGCCCGGGGCTT	AF154829	CCDS11715.1	17q25	2011-03-29	2002-05-23		ENSG00000125458	ENSG00000125458	3.1.3.5		17144	protein-coding gene	gene with protein product		191720	"""5' nucleotidase, deoxy (pyrimidine), cytosolic type C"", ""uridine 5-prime monophosphate hydrolase 2"""	UMPH2		10899995	Standard	NM_014595		Approved	DNT1, DNT-1, PN-I, cdN, dNT-1	uc002jmx.3	Q8TCD5		ENST00000245552.2:c.203C>T	17.37:g.73127348G>A	ENSP00000245552:p.Pro68Leu	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	231	113	0.489177	NM_001252377	Q96HS6|Q9NP82	Missense_Mutation	SNP	ENST00000245552.2	37	CCDS11715.1	27	0.012362637362637362	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	21	0.027704485488126648	G	12.25	1.882990	0.33255	0.00522	0.02814	ENSG00000125458	ENST00000245552	T	0.48836	0.8	4.35	3.36	0.38483	HAD-like domain (2);	0.372569	0.27581	N	0.018735	T	0.34774	0.0909	M	0.68317	2.08	0.80722	D	1	D	0.71674	0.998	P	0.61070	0.883	T	0.51293	-0.8724	10	0.56958	D	0.05	-1.2806	9.557	0.39346	0.0:0.0:0.6178:0.3822	rs11541956;rs17851989	68	Q8TCD5	NT5C_HUMAN	L	68	ENSP00000245552:P68L	ENSP00000245552:P68L	P	-	2	0	NT5C	70638943	0.998000	0.40836	0.217000	0.23759	0.737000	0.42083	3.393000	0.52544	1.154000	0.42482	0.555000	0.69702	CCG	G|0.983;A|0.017	0.017	strong		0.652	NT5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445853.1		
OR13D1	286365	hgsc.bcm.edu	37	9	107457725	107457725	+	Silent	SNP	G	G	A	rs12338899	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107457725G>A	ENST00000318763.5	+	1	1066	c.1023G>A	c.(1021-1023)ctG>ctA	p.L341L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	341						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						GCAGACATCTGCATTTATTGA	0.408													G|||	1353	0.270168	0.1657	0.183	5008	,	,		19813	0.4821		0.1909	False		,,,				2504	0.3364				p.L341L		Atlas-SNP	.											.	OR13D1	42	.	0			c.G1023A						PASS	.	G		789,3617	314.4+/-293.6	75,639,1489	58.0	59.0	59.0		1023	-6.9	0.0	9	dbSNP_120	59	1824,6776	323.0+/-315.8	224,1376,2700	yes	coding-synonymous	OR13D1	NM_001004484.1		299,2015,4189	AA,AG,GG		21.2093,17.9074,20.0907		341/347	107457725	2613,10393	2203	4300	6503	SO:0001819	synonymous_variant	286365	exon1			ACATCTGCATTTA		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"""GPCR / Class A : Olfactory receptors"""	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.1023G>A	9.37:g.107457725G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_001004484	B9EIS1|Q6IFL1	Silent	SNP	ENST00000318763.5	37	CCDS35094.1																																																																																			G|0.786;A|0.214	0.214	strong		0.408	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
DHCR7	1717	hgsc.bcm.edu	37	11	71146691	71146691	+	Silent	SNP	A	A	G	rs760241	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71146691A>G	ENST00000355527.3	-	9	1434	c.1158T>C	c.(1156-1158)gaT>gaC	p.D386D	DHCR7_ENST00000407721.2_Silent_p.D386D	NM_001163817.1|NM_001360.2	NP_001157289.1|NP_001351.2	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	386					blood vessel development (GO:0001568)|cell differentiation (GO:0030154)|cholesterol biosynthetic process (GO:0006695)|lung development (GO:0030324)|multicellular organism growth (GO:0035264)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|regulation of cholesterol biosynthetic process (GO:0045540)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear outer membrane (GO:0005640)	7-dehydrocholesterol reductase activity (GO:0047598)			endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(1)|skin(1)	19						GCCTCTGCCCATCGGCGGATG	0.657									Smith-Lemli-Opitz syndrome				A|||	3788	0.75639	0.6861	0.7666	5008	,	,		15743	0.7688		0.9553	False		,,,				2504	0.6268				p.D386D		Atlas-SNP	.											DHCR7_ENST00000355527,NS,carcinoma,0,4	DHCR7	98	4	0			c.T1158C						PASS	.	A	,	3191,1209	670.6+/-402.3	1164,863,173	30.0	30.0	30.0		1158,1158	-10.2	0.0	11	dbSNP_86	30	8124,464	767.6+/-407.6	3848,428,18	no	coding-synonymous,coding-synonymous	DHCR7	NM_001163817.1,NM_001360.2	,	5012,1291,191	GG,GA,AA		5.4029,27.4773,12.8811	,	386/476,386/476	71146691	11315,1673	2200	4294	6494	SO:0001819	synonymous_variant	1717	exon9	Familial Cancer Database	SLOS type I & II	CTGCCCATCGGCG	AF034544	CCDS8200.1	11q13.4	2014-09-17	2004-02-13				1.3.1.21		2860	protein-coding gene	gene with protein product		602858	"""Smith-Lemli-Opitz syndrome"""	SLOS		9465114, 9634533	Standard	NM_001360		Approved		uc001oql.3	Q9UBM7		ENST00000355527.3:c.1158T>C	11.37:g.71146691A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_001163817	B2R6Z2|O60492|O60717	Silent	SNP	ENST00000355527.3	37	CCDS8200.1	1792	0.8205128205128205	321	0.6524390243902439	281	0.7762430939226519	467	0.8164335664335665	723	0.9538258575197889	A	0.336	-0.953340	0.02285	0.725227	0.945971	ENSG00000172893	ENST00000525137	D	0.99259	-5.64	5.12	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999691532	.	.	.	.	.	.	T	0.50524	-0.8818	5	0.56958	D	0.05	-29.8158	11.9429	0.52911	0.592:0.0:0.3279:0.0801	rs760241;rs3794056;rs17161502;rs17849255;rs56469998;rs760241	.	.	.	T	220	ENSP00000435956:M220T	ENSP00000435956:M220T	M	-	2	0	DHCR7	70824339	0.047000	0.20315	0.001000	0.08648	0.009000	0.06853	-0.798000	0.04565	-2.600000	0.00451	-1.981000	0.00455	ATG	T|0.000;G|0.822;C|0.009;A|0.168	0.822	strong		0.657	DHCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394243.1	NM_001360	
PADI2	11240	hgsc.bcm.edu	37	1	17396703	17396703	+	Silent	SNP	T	T	C	rs2076595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17396703T>C	ENST00000375486.4	-	15	1707	c.1644A>G	c.(1642-1644)ctA>ctG	p.L548L	PADI2_ENST00000466151.1_5'UTR|PADI2_ENST00000444885.2_Silent_p.L432L	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	548					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GGTTCCAGTCTAGGCAGCGCT	0.602													C|||	2227	0.444688	0.3094	0.536	5008	,	,		19975	0.3929		0.5905	False		,,,				2504	0.4663				p.L548L		Atlas-SNP	.											.	PADI2	72	.	0			c.A1644G						PASS	.	C		1728,2678	649.3+/-398.9	334,1060,809	145.0	136.0	139.0		1644	1.7	1.0	1	dbSNP_96	139	5151,3449	506.6+/-376.6	1514,2123,663	no	coding-synonymous	PADI2	NM_007365.2		1848,3183,1472	CC,CT,TT		40.1047,39.2192,47.109		548/666	17396703	6879,6127	2203	4300	6503	SO:0001819	synonymous_variant	11240	exon15			CCAGTCTAGGCAG	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1644A>G	1.37:g.17396703T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	CCDS177.1																																																																																			T|0.505;C|0.495	0.495	strong		0.602	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
MUC2	4583	hgsc.bcm.edu	37	11	1093195	1093195	+	Missense_Mutation	SNP	T	T	A	rs56096036		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1093195T>A	ENST00000441003.2	+	30	5041	c.5014T>A	c.(5014-5016)Tcc>Acc	p.S1672T	MUC2_ENST00000359061.5_Missense_Mutation_p.S1639T|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cggcacacagtccccaacccc	0.632																																					p.S1672T		Atlas-SNP	.											MUC2_ENST00000441003,colon,carcinoma,0,2	MUC2	614	2	0			c.T5014A						scavenged	.						148.0	214.0	191.0					11																	1093195		1798	3273	5071	SO:0001583	missense	4583	exon30			ACACAGTCCCCAA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5014T>A	11.37:g.1093195T>A	ENSP00000415183:p.Ser1672Thr	Somatic	57	12	0.210526		WXS	Illumina HiSeq	Phase_I	56	10	0.178571	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	3.450	-0.112202	0.06881	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.06933	3.24;3.47	1.75	-2.07	0.07276	.	1.323100	0.06959	U	0.815957	T	0.04227	0.0117	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44513	-0.9323	9	0.19590	T	0.45	.	2.168	0.03842	0.3614:0.0:0.1733:0.4653	rs56096036	1672	E7EUV1	.	T	1672;1639	ENSP00000415183:S1672T;ENSP00000351956:S1639T	ENSP00000351956:S1639T	S	+	1	0	MUC2	1083195	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.353000	0.20130	-1.459000	0.01914	-1.489000	0.00976	TCC	.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZNF845	91664	hgsc.bcm.edu	37	19	53856701	53856701	+	Missense_Mutation	SNP	C	C	T	rs572189568		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53856701C>T	ENST00000595091.1	+	5	2992	c.2773C>T	c.(2773-2775)Cgt>Tgt	p.R925C	ZNF845_ENST00000458035.1_Missense_Mutation_p.R925C			Q96IR2	ZN845_HUMAN	zinc finger protein 845	925					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						CAAAACCTTCCGTCACAATTC	0.363													.|||	1	0.000199681	0.0	0.0	5008	,	,		21839	0.001		0.0	False		,,,				2504	0.0				p.R925C		Atlas-SNP	.											ZNF845,NS,carcinoma,-1,6	ZNF845	101	6	0			c.C2773T						scavenged	.						34.0	31.0	32.0					19																	53856701		692	1591	2283	SO:0001583	missense	91664	exon4			ACCTTCCGTCACA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2773C>T	19.37:g.53856701C>T	ENSP00000470005:p.Arg925Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	139	5	0.0359712	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	C	5.640	0.302783	0.10678	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.36699	1.24	2.0	-2.89	0.05665	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41166	0.1147	L	0.52759	1.655	0.09310	N	1	D	0.62365	0.991	P	0.59595	0.86	T	0.30119	-0.9989	9	0.49607	T	0.09	.	4.835	0.13460	0.4533:0.3727:0.0:0.174	.	925	Q96IR2	ZN845_HUMAN	C	925;841	ENSP00000388311:R925C	ENSP00000412086:R841C	R	+	1	0	ZNF845	58548513	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.369000	0.01076	-1.061000	0.03185	-1.959000	0.00480	CGT	.	.	none		0.363	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
URB1	9875	hgsc.bcm.edu	37	21	33757947	33757947	+	Missense_Mutation	SNP	A	A	T	rs58978310	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:33757947A>T	ENST00000382751.3	-	2	304	c.189T>A	c.(187-189)gaT>gaA	p.D63E		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	63						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						CATCATACACATCTTCTCGTG	0.388													A|||	603	0.120407	0.2443	0.0821	5008	,	,		18902	0.0417		0.1133	False		,,,				2504	0.0685				p.D63E		Atlas-SNP	.											.	URB1	176	.	0			c.T189A						PASS	.	A	GLU/ASP	317,1067		32,253,407	184.0	140.0	154.0		189	-7.4	0.0	21	dbSNP_129	154	369,2813		27,315,1249	yes	missense	URB1	NM_014825.2	45	59,568,1656	TT,TA,AA		11.5965,22.9046,15.0241	benign	63/2272	33757947	686,3880	692	1591	2283	SO:0001583	missense	9875	exon2			ATACACATCTTCT	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.189T>A	21.37:g.33757947A>T	ENSP00000372199:p.Asp63Glu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	127	50	0.393701	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	250	0.11446886446886446	114	0.23170731707317074	31	0.0856353591160221	22	0.038461538461538464	83	0.10949868073878628	A	8.880	0.951322	0.18431	0.229046	0.115965	ENSG00000142207	ENST00000382751	T	0.31510	1.49	5.29	-7.38	0.01407	.	0.198259	0.41823	D	0.000815	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	5.000000000032756E-6	B	0.21071	0.051	B	0.12156	0.007	T	0.25012	-1.0144	9	0.19590	T	0.45	-17.1729	3.9847	0.09511	0.4121:0.2161:0.2974:0.0745	rs58978310	63	O60287	NPA1P_HUMAN	E	63	ENSP00000372199:D63E	ENSP00000372199:D63E	D	-	3	2	URB1	32679818	0.000000	0.05858	0.001000	0.08648	0.523000	0.34469	-1.471000	0.02344	-1.062000	0.03181	-0.464000	0.05259	GAT	A|0.887;T|0.113	0.113	strong		0.388	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
TPR	7175	hgsc.bcm.edu	37	1	186291512	186291512	+	Silent	SNP	T	T	C	rs10911846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:186291512T>C	ENST00000367478.4	-	45	6695	c.6399A>G	c.(6397-6399)acA>acG	p.T2133T		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	2133					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TACTTGGAACTGTTCTGTCTT	0.338			T	NTRK1	papillary thyroid								T|||	151	0.0301518	0.0446	0.013	5008	,	,		20682	0.001		0.0388	False		,,,				2504	0.044				p.T2133T		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A6399G						PASS	.	T		166,3574		1,164,1705	109.0	104.0	105.0		6399	-5.4	0.9	1	dbSNP_120	105	367,7849		11,345,3752	no	coding-synonymous	TPR	NM_003292.2		12,509,5457	CC,CT,TT		4.4669,4.4385,4.458		2133/2364	186291512	533,11423	1870	4108	5978	SO:0001819	synonymous_variant	7175	exon45			TGGAACTGTTCTG	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.6399A>G	1.37:g.186291512T>C		Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	485	192	0.395876	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																			T|0.965;C|0.035	0.035	strong		0.338	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
CERK	64781	hgsc.bcm.edu	37	22	47108189	47108189	+	Splice_Site	SNP	C	C	T	rs9616101	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:47108189C>T	ENST00000216264.8	-	4	493	c.381G>A	c.(379-381)acG>acA	p.T127T	CERK_ENST00000541677.1_5'UTR	NM_022766.5	NP_073603.2	Q8TCT0	CERK1_HUMAN	ceramide kinase	127					ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lipid phosphorylation (GO:0046834)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)			cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	20		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TTGGTCTGGACGCTGTAAGAC	0.383													C|||	98	0.0195687	0.0166	0.0245	5008	,	,		20225	0.001		0.0348	False		,,,				2504	0.0235				p.T127T		Atlas-SNP	.											.	CERK	40	.	0			c.G381A						PASS	.	C		108,4298	85.3+/-124.0	1,106,2096	163.0	124.0	137.0		381	-10.4	0.0	22	dbSNP_119	137	263,8337	101.4+/-162.7	2,259,4039	yes	coding-synonymous-near-splice	CERK	NM_022766.5		3,365,6135	TT,TC,CC		3.0581,2.4512,2.8525		127/538	47108189	371,12635	2203	4300	6503	SO:0001630	splice_region_variant	64781	exon4			TCTGGACGCTGTA	AB079066	CCDS14077.1	22q13.31	2008-06-10			ENSG00000100422	ENSG00000100422			19256	protein-coding gene	gene with protein product		610307				11956206, 11258795	Standard	NM_022766		Approved	hCERK, FLJ23239, dA59H18.3, DKFZp434E0211, FLJ21430, KIAA1646, LK4, dA59H18.2	uc003bia.3	Q8TCT0	OTTHUMG00000150395	ENST00000216264.8:c.380-1G>A	22.37:g.47108189C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	119	78	0.655462	NM_022766	A0JNT4|A8K611|Q6NX59|Q9BYB3|Q9UGE5	Silent	SNP	ENST00000216264.8	37	CCDS14077.1																																																																																			C|0.976;T|0.024	0.024	strong		0.383	CERK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317924.2	NM_022766	Silent
HMP19	51617	hgsc.bcm.edu	37	5	173491300	173491300	+	Silent	SNP	G	G	A	rs17076802|rs34300847	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:173491300G>A	ENST00000303177.3	+	3	457	c.195G>A	c.(193-195)ccG>ccA	p.P65P	NSG2_ENST00000521959.1_3'UTR|NSG2_ENST00000521585.1_Silent_p.P65P	NM_015980.4	NP_057064.1	Q9Y328	NSG2_HUMAN		65					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											TCCGGGTGCCGAAAATCGCTG	0.483													G|||	394	0.0786741	0.0038	0.0447	5008	,	,		16822	0.0873		0.1083	False		,,,				2504	0.1646				p.P65P		Atlas-SNP	.											.	HMP19	21	.	0			c.G195A						PASS	.	G		86,4320	73.1+/-111.1	1,84,2118	80.0	76.0	77.0		195	1.8	1.0	5	dbSNP_123	77	817,7783	189.0+/-235.8	48,721,3531	no	coding-synonymous	HMP19	NM_015980.3		49,805,5649	AA,AG,GG		9.5,1.9519,6.9429		65/172	173491300	903,12103	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			GGTGCCGAAAATC																												ENST00000303177.3:c.195G>A	5.37:g.173491300G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	55	0.670732	NM_015980	B2R5Y0|D3DQN0|Q9UHX8	Silent	SNP	ENST00000303177.3	37	CCDS4391.1																																																																																			G|0.924;A|0.075	0.075	strong		0.483	NSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252966.2		
CCDC168	643677	hgsc.bcm.edu	37	13	103385064	103385064	+	Missense_Mutation	SNP	T	T	C	rs200932361	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103385064T>C	ENST00000322527.2	-	1	4095	c.4096A>G	c.(4096-4098)Aag>Gag	p.K1366E		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1366																	CCTCTCTCCTTCTCCAGATTG	0.433													T|||	10	0.00199681	0.0	0.0	5008	,	,		18776	0.0		0.005	False		,,,				2504	0.0051				p.K5995E		Atlas-SNP	.											.	.	.	.	0			c.A17983G						PASS	.	T	GLU/LYS	1,1383		0,1,691	250.0	192.0	210.0		17983	-1.8	0.0	13		210	14,3168		0,14,1577	yes	missense	CCDC168	NM_001146197.1	56	0,15,2268	CC,CT,TT		0.44,0.0723,0.3285	benign	5995/7082	103385064	15,4551	692	1591	2283	SO:0001583	missense	643677	exon4			TCTCCTTCTCCAG		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.4096A>G	13.37:g.103385064T>C	ENSP00000320232:p.Lys1366Glu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	182	77	0.423077	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		.	.	.	.	.	.	.	.	.	.	T	0.010	-1.755496	0.00663	7.23E-4	0.0044	ENSG00000175820	ENST00000322527	T	0.05319	3.46	2.42	-1.75	0.08031	.	.	.	.	.	T	0.02494	0.0076	N	0.08118	0	0.09310	N	1	B	0.22211	0.066	B	0.26614	0.071	T	0.47911	-0.9080	9	0.10111	T	0.7	.	2.8777	0.05636	0.0:0.3174:0.2529:0.4297	.	1366	Q8NDH2	CC168_HUMAN	E	1366	ENSP00000320232:K1366E	ENSP00000320232:K1366E	K	-	1	0	CCDC168	102183065	0.007000	0.16637	0.001000	0.08648	0.014000	0.08584	-0.379000	0.07437	-0.376000	0.07943	0.377000	0.23210	AAG	.	.	weak		0.433	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
HINFP	25988	hgsc.bcm.edu	37	11	119005132	119005132	+	Missense_Mutation	SNP	C	C	T	rs100803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:119005132C>T	ENST00000350777.2	+	10	1541	c.1478C>T	c.(1477-1479)gCc>gTc	p.A493V		NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	493	Interaction with NPAT.		A -> V (in dbSNP:rs100803). {ECO:0000269|PubMed:15489334}.		DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CCTCCCCCAGCCCCTGAGCCA	0.562											OREG0021397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2012	0.401757	0.1687	0.2839	5008	,	,		19450	0.7183		0.4433	False		,,,				2504	0.4315				p.A493V		Atlas-SNP	.											.	HINFP	50	.	0			c.C1478T						PASS	.	C	VAL/ALA,VAL/ALA	843,3557	330.4+/-301.5	75,693,1432	43.0	48.0	46.0		1478,1478	-0.7	0.0	11	dbSNP_83	46	3610,4980	518.7+/-379.3	790,2030,1475	yes	missense,missense	HINFP	NM_015517.4,NM_198971.2	64,64	865,2723,2907	TT,TC,CC		42.0256,19.1591,34.2802	benign,benign	493/518,493/518	119005132	4453,8537	2200	4295	6495	SO:0001583	missense	25988	exon11			CCCCAGCCCCTGA	AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"""Zinc fingers, C2H2-type"""	17850	protein-coding gene	gene with protein product	"""histone nuclear factor P"""	607099	"""MBD2-interacting zinc finger 1"", ""MBD2-interacting zinc finger"""	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.1478C>T	11.37:g.119005132C>T	ENSP00000318085:p.Ala493Val	Somatic	78	0	0	1492	WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_015517	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	37	CCDS8414.1	966	0.4423076923076923	90	0.18292682926829268	120	0.3314917127071823	422	0.7377622377622378	334	0.44063324538258575	C	5.618	0.298738	0.10622	0.191591	0.420256	ENSG00000172273	ENST00000350777	T	0.10099	2.91	4.9	-0.697	0.11284	.	1.282940	0.05442	N	0.547761	T	0.00012	0.0000	N	0.12182	0.205	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.23833	-1.0177	9	0.36615	T	0.2	-0.0432	2.4679	0.04557	0.1403:0.4289:0.2726:0.1583	rs100803;rs753835;rs3741335;rs3889924;rs17844880;rs17856531;rs17857597;rs17857666;rs17858206;rs61095432	493	Q9BQA5	HINFP_HUMAN	V	493	ENSP00000318085:A493V	ENSP00000318085:A493V	A	+	2	0	HINFP	118510342	0.002000	0.14202	0.000000	0.03702	0.091000	0.18340	-0.098000	0.11024	-0.001000	0.14495	-0.136000	0.14681	GCC	C|0.611;T|0.389	0.389	strong		0.562	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	NM_015517	
LRRC48	83450	hgsc.bcm.edu	37	17	17896090	17896090	+	Silent	SNP	C	C	T	rs4368210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17896090C>T	ENST00000399187.1	+	6	674	c.456C>T	c.(454-456)ctC>ctT	p.L152L	LRRC48_ENST00000399182.1_Silent_p.L152L|LRRC48_ENST00000584166.1_Silent_p.L152L|LRRC48_ENST00000313838.8_Silent_p.L152L|LRRC48_ENST00000411504.2_Silent_p.L152L	NM_031294.3	NP_112584.3	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48	152						cytoplasm (GO:0005737)				breast(1)|large_intestine(2)|lung(2)|pancreas(1)|urinary_tract(1)	7	all_neural(463;0.228)					TCATCTACCTCCGGCGGTTCA	0.522													C|||	2914	0.581869	0.4145	0.5187	5008	,	,		21689	0.8641		0.3748	False		,,,				2504	0.7751				p.L152L		Atlas-SNP	.											.	LRRC48	49	.	0			c.C456T						PASS	.	C	,,,	1609,2367		338,933,717	49.0	49.0	49.0		456,456,456,456	3.0	1.0	17	dbSNP_111	49	2746,5586		449,1848,1869	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRRC48	NM_001130090.1,NM_001130091.1,NM_001130092.1,NM_031294.3	,,,	787,2781,2586	TT,TC,CC		32.9573,40.4678,35.3835	,,,	152/524,152/458,152/458,152/524	17896090	4355,7953	1988	4166	6154	SO:0001819	synonymous_variant	83450	exon6			CTACCTCCGGCGG	AK093317	CCDS45622.1, CCDS45623.1	17p11.2	2014-07-18			ENSG00000171962	ENSG00000171962			25384	protein-coding gene	gene with protein product						11997338, 23354437	Standard	NM_001130090		Approved	DKFZP586M1120	uc021trk.1	Q9H069	OTTHUMG00000059355	ENST00000399187.1:c.456C>T	17.37:g.17896090C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_031294	A8KAE6|Q86SF9|Q86W73|Q8IWG0	Silent	SNP	ENST00000399187.1	37	CCDS45622.1																																																																																			C|0.475;T|0.525	0.525	strong		0.522	LRRC48-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131945.3	NM_031294	
TENM4	26011	hgsc.bcm.edu	37	11	78380199	78380199	+	Silent	SNP	C	C	T	rs61745709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:78380199C>T	ENST00000278550.7	-	32	7653	c.7191G>A	c.(7189-7191)caG>caA	p.Q2397Q		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2397					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CTATGATGATCTGAAAGTTGG	0.517													C|||	136	0.0271565	0.0189	0.0418	5008	,	,		18377	0.0		0.0696	False		,,,				2504	0.0123				p.Q2397Q		Atlas-SNP	.											.	.	.	.	0			c.G7191A						PASS	.	C		76,3822		1,74,1874	57.0	57.0	57.0		7191	5.7	1.0	11	dbSNP_129	57	482,7810		15,452,3679	no	coding-synonymous	ODZ4	NM_001098816.2		16,526,5553	TT,TC,CC		5.8128,1.9497,4.5775		2397/2770	78380199	558,11632	1949	4146	6095	SO:0001819	synonymous_variant	26011	exon32			GATGATCTGAAAG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.7191G>A	11.37:g.78380199C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	194	88	0.453608	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			C|0.950;T|0.050	0.050	strong		0.517	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
UNC13C	440279	hgsc.bcm.edu	37	15	54841874	54841874	+	Silent	SNP	A	A	G	rs9302181	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:54841874A>G	ENST00000260323.11	+	27	5862	c.5862A>G	c.(5860-5862)caA>caG	p.Q1954Q	UNC13C_ENST00000537900.1_Silent_p.Q1952Q|UNC13C_ENST00000545554.1_Silent_p.Q1954Q	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1954	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ATCTTGGACAATTATCCAAAC	0.343													A|||	1822	0.363818	0.1346	0.2853	5008	,	,		17350	0.5258		0.3887	False		,,,				2504	0.5368				p.Q1954Q		Atlas-SNP	.											.	UNC13C	674	.	0			c.A5862G						PASS	.	A		639,2961		52,535,1213	135.0	126.0	129.0		5862	-3.7	1.0	15	dbSNP_119	129	3092,5036		595,1902,1567	no	coding-synonymous	UNC13C	NM_001080534.1		647,2437,2780	GG,GA,AA		38.0413,17.75,31.8128		1954/2215	54841874	3731,7997	1800	4064	5864	SO:0001819	synonymous_variant	440279	exon26			TGGACAATTATCC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5862A>G	15.37:g.54841874A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																			A|0.596;G|0.404	0.404	strong		0.343	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
PELI1	57162	hgsc.bcm.edu	37	2	64327544	64327544	+	Silent	SNP	G	G	T	rs329498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:64327544G>T	ENST00000358912.4	-	4	733	c.291C>A	c.(289-291)acC>acA	p.T97T	PELI1_ENST00000466177.2_5'UTR	NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	97					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						GAAACATATCGGTGTTGCTGT	0.348													G|||	1781	0.355631	0.0885	0.3127	5008	,	,		15856	0.752		0.2992	False		,,,				2504	0.3967				p.T97T		Atlas-SNP	.											.	PELI1	34	.	0			c.C291A						PASS	.	G		607,3799	263.4+/-265.5	41,525,1637	155.0	137.0	143.0		291	0.2	1.0	2	dbSNP_79	143	2613,5987	423.3+/-354.3	403,1807,2090	no	coding-synonymous	PELI1	NM_020651.3		444,2332,3727	TT,TG,GG		30.3837,13.7767,24.7578		97/419	64327544	3220,9786	2203	4300	6503	SO:0001819	synonymous_variant	57162	exon4			CATATCGGTGTTG		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"""Pellino homologs"""	8827	protein-coding gene	gene with protein product		614797	"""pellino (Drosophila) homolog 1"", ""pellino homolog 1 (Drosophila)"""			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.291C>A	2.37:g.64327544G>T		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_020651	Q96SM0|Q9GZY5|Q9HCX0	Silent	SNP	ENST00000358912.4	37	CCDS1876.1																																																																																			T|0.297;G|0.703;C|0.000	0.297	strong		0.348	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651	
ZNF180	7733	hgsc.bcm.edu	37	19	45001346	45001346	+	Missense_Mutation	SNP	G	G	A	rs2571108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45001346G>A	ENST00000221327.4	-	2	403	c.122C>T	c.(121-123)gCc>gTc	p.A41V	ZNF180_ENST00000391956.4_Missense_Mutation_p.A41V|ZNF180_ENST00000592529.1_Missense_Mutation_p.A14V|ZNF180_ENST00000586637.1_Missense_Mutation_p.P10S|ZNF180_ENST00000587047.1_Missense_Mutation_p.P43S|ZNF180_ENST00000585514.1_5'UTR	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	41			A -> V (in dbSNP:rs2571108). {ECO:0000269|PubMed:12743021}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CTGTGCACAGGCCTTCGGGGG	0.622													G|||	1307	0.260982	0.1498	0.1844	5008	,	,		15070	0.3562		0.3857	False		,,,				2504	0.2393				p.A41V	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											ZNF180,colon,carcinoma,0,1	ZNF180	103	1	0			c.C122T						PASS	.	G	VAL/ALA	884,3522	336.5+/-304.4	97,690,1416	39.0	38.0	38.0		122	0.4	0.0	19	dbSNP_100	38	3057,5543	465.4+/-366.5	553,1951,1796	yes	missense	ZNF180	NM_013256.3	64	650,2641,3212	AA,AG,GG		35.5465,20.0635,30.3014	benign	41/693	45001346	3941,9065	2203	4300	6503	SO:0001583	missense	7733	exon2			GCACAGGCCTTCG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.122C>T	19.37:g.45001346G>A	ENSP00000221327:p.Ala41Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	663	0.30357142857142855	67	0.13617886178861788	71	0.19613259668508287	222	0.3881118881118881	303	0.3997361477572559	G	9.934	1.215647	0.22373	0.200635	0.355465	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.08720	3.21;3.06	3.85	0.423	0.16463	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.10450	0.005;0.002;0.002	T	0.46233	-0.9206	8	0.02654	T	1	0.0079	4.3819	0.11299	0.2115:0.1858:0.6027:0.0	rs2571108;rs2571108	41;40;41	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	V	41	ENSP00000221327:A41V;ENSP00000375818:A41V	ENSP00000221327:A41V	A	-	2	0	ZNF180	49693186	0.053000	0.20554	0.005000	0.12908	0.043000	0.13939	0.391000	0.20784	0.219000	0.20840	-0.165000	0.13383	GCC	G|0.703;A|0.297	0.297	strong		0.622	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
MOV10L1	54456	hgsc.bcm.edu	37	22	50572473	50572473	+	Missense_Mutation	SNP	G	G	A	rs2340601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50572473G>A	ENST00000262794.5	+	14	2031	c.1948G>A	c.(1948-1950)Gtc>Atc	p.V650I	MOV10L1_ENST00000395858.3_Missense_Mutation_p.V650I|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Missense_Mutation_p.V650I|MOV10L1_ENST00000540615.1_Missense_Mutation_p.V630I	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	650			V -> I (in dbSNP:rs2340601).		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.V650I(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		ACTTGAACACGTCATCCACTT	0.338													G|||	1242	0.248003	0.1218	0.3847	5008	,	,		16603	0.254		0.2356	False		,,,				2504	0.3282				p.V650I		Atlas-SNP	.											MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	1	Substitution - Missense(1)	stomach(1)	c.G1948A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	667,3739	284.0+/-277.4	55,557,1591	118.0	106.0	110.0		1948,1888,1948	5.8	0.0	22	dbSNP_100	110	2049,6551	358.1+/-331.0	246,1557,2497	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	29,29,29	301,2114,4088	AA,AG,GG		23.8256,15.1384,20.8827	possibly-damaging,possibly-damaging,possibly-damaging	650/1166,630/1166,650/1212	50572473	2716,10290	2203	4300	6503	SO:0001583	missense	54456	exon14			GAACACGTCATCC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1948G>A	22.37:g.50572473G>A	ENSP00000262794:p.Val650Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	105	78	0.742857	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	530	0.24267399267399267	54	0.10975609756097561	123	0.3397790055248619	181	0.31643356643356646	172	0.22691292875989447	G	14.38	2.518497	0.44763	0.151384	0.238256	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;T;D	0.85411	-1.79;-1.79;-1.38;-1.98	5.78	5.78	0.91487	.	0.317187	0.38326	N	0.001735	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.999999999875443	P;P;P	0.47962	0.903;0.743;0.619	B;B;B	0.36766	0.232;0.117;0.117	T	0.04178	-1.0971	9	0.30854	T	0.27	-27.556	19.6307	0.95700	0.0:0.0:1.0:0.0	rs2340601;rs3736687;rs17248063;rs52826881;rs61128514;rs2340601	630;650;650	F5H403;A8MXC6;Q9BXT6	.;.;M10L1_HUMAN	I	650;650;650;630	ENSP00000438978:V650I;ENSP00000262794:V650I;ENSP00000379199:V650I;ENSP00000438542:V630I	ENSP00000262794:V650I	V	+	1	0	MOV10L1	48914600	0.645000	0.27286	0.011000	0.14972	0.979000	0.70002	4.303000	0.59098	2.730000	0.93505	0.655000	0.94253	GTC	G|0.776;A|0.224	0.224	strong		0.338	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
SLC35G6	643664	hgsc.bcm.edu	37	17	7385454	7385454	+	Missense_Mutation	SNP	G	G	A	rs3760422	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7385454G>A	ENST00000412468.2	+	2	266	c.151G>A	c.(151-153)Gct>Act	p.A51T	ZBTB4_ENST00000380599.4_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	51	EamA 1.		A -> T (in dbSNP:rs3760422).			integral component of membrane (GO:0016021)											GGGCCTGCCTGCTGGCTTCGT	0.662													G|||	928	0.185304	0.1165	0.2392	5008	,	,		17801	0.1935		0.161	False		,,,				2504	0.2566				p.A51T		Atlas-SNP	.											.	.	.	.	0			c.G151A						PASS	.	G	THR/ALA,	587,3819	256.7+/-261.4	44,499,1660	55.0	62.0	60.0		151,	4.0	1.0	17	dbSNP_107	60	1268,7330	251.1+/-277.7	99,1070,3130	no	missense,intron	ZBTB4,SLC35G6	NM_001102614.1,NM_020899.3	58,	143,1569,4790	AA,AG,GG		14.7476,13.3227,14.2648	probably-damaging,	51/339,	7385454	1855,11149	2203	4299	6502	SO:0001583	missense	643664	exon2			CTGCCTGCTGGCT		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.151G>A	17.37:g.7385454G>A	ENSP00000396523:p.Ala51Thr	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	387	0.1771978021978022	54	0.10975609756097561	91	0.2513812154696133	120	0.2097902097902098	122	0.16094986807387862	G	11.57	1.678465	0.29783	0.133227	0.147476	ENSG00000181222	ENST00000412468	T	0.27890	1.64	4.04	4.04	0.47022	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.30395	P	0.780636	D	0.76494	0.999	D	0.85130	0.997	T	0.17899	-1.0354	8	0.23891	T	0.37	-4.4801	11.4032	0.49883	0.0:0.1843:0.8157:0.0	rs3760422;rs12945890;rs61072970;rs3760422	51	P0C7Q6	S35G6_HUMAN	T	51	ENSP00000396523:A51T	ENSP00000396523:A51T	A	+	1	0	SLC35G6	7326178	0.643000	0.27269	0.989000	0.46669	0.086000	0.17979	2.163000	0.42377	1.959000	0.56917	0.462000	0.41574	GCT	G|0.841;A|0.159	0.159	strong		0.662	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
SPTBN4	57731	hgsc.bcm.edu	37	19	40978640	40978640	+	Missense_Mutation	SNP	G	G	A	rs73931308	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40978640G>A	ENST00000352632.3	+	2	198	c.112G>A	c.(112-114)Gct>Act	p.A38T	SPTBN4_ENST00000595535.1_Missense_Mutation_p.A38T|SPTBN4_ENST00000338932.3_Missense_Mutation_p.A38T|SPTBN4_ENST00000598249.1_Missense_Mutation_p.A38T|SPTBN4_ENST00000344104.3_Missense_Mutation_p.A38T			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	38	Actin-binding.				actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.A38T(1)		breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGAGCAGCCGGCTGCGTCCAC	0.672													G|||	898	0.179313	0.3086	0.1297	5008	,	,		11188	0.0099		0.1581	False		,,,				2504	0.2362				p.A38T		Atlas-SNP	.											SPTBN4,colon,carcinoma,-2,3	SPTBN4	213	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.G112A						PASS	.	G	THR/ALA	1313,3089		199,915,1087	26.0	21.0	23.0		112	6.0	0.1	19	dbSNP_130	23	1340,7256		117,1106,3075	yes	missense	SPTBN4	NM_020971.2	58	316,2021,4162	AA,AG,GG		15.5886,29.8274,20.4108	possibly-damaging	38/2565	40978640	2653,10345	2201	4298	6499	SO:0001583	missense	57731	exon2			CAGCCGGCTGCGT	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.112G>A	19.37:g.40978640G>A	ENSP00000263373:p.Ala38Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	37	CCDS12559.1	344	0.1575091575091575	160	0.3252032520325203	58	0.16022099447513813	4	0.006993006993006993	122	0.16094986807387862	G	11.35	1.611694	0.28712	0.298274	0.155886	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000344104	T;T;T	0.77489	-1.0;-1.0;-1.1	6.03	6.03	0.97812	.	0.246358	0.21027	U	0.081415	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999999988	B;P	0.38395	0.084;0.629	B;B	0.34873	0.063;0.191	T	0.09930	-1.0652	9	0.48119	T	0.1	.	16.0667	0.80887	0.0:0.0:1.0:0.0	.	38;38	Q9H254;Q71S06	SPTN4_HUMAN;.	T	38	ENSP00000263373:A38T;ENSP00000340345:A38T;ENSP00000340741:A38T	ENSP00000340345:A38T	A	+	1	0	SPTBN4	45670480	0.017000	0.18338	0.078000	0.20375	0.060000	0.15804	2.134000	0.42102	2.854000	0.98071	0.655000	0.94253	GCT	G|0.811;A|0.189	0.189	strong		0.672	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
HDAC9	9734	hgsc.bcm.edu	37	7	18993870	18993870	+	Silent	SNP	C	C	T	rs2389998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:18993870C>T	ENST00000432645.2	+	23	3030	c.3030C>T	c.(3028-3030)ttC>ttT	p.F1010F	HDAC9_ENST00000441542.2_Intron|HDAC9_ENST00000401921.1_Intron|HDAC9_ENST00000406451.4_Intron	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	1010					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	CTTTAAAGTTCTCTTAAAAAT	0.294													T|||	3874	0.773562	0.7927	0.8184	5008	,	,		15936	0.7302		0.7714	False		,,,				2504	0.7628				p.F1010F		Atlas-SNP	.											.	HDAC9	560	.	0			c.C3030T						PASS	.	T	,,	2867,685		1159,549,68	17.0	16.0	17.0		3030,,	1.5	0.0	7	dbSNP_100	17	6052,1998		2286,1480,259	no	coding-synonymous,intron,intron	HDAC9	NM_058176.2,NM_178423.1,NM_178425.2	,,	3445,2029,327	TT,TC,CC		24.8199,19.2849,23.1253	,,	1010/1012,,	18993870	8919,2683	1776	4025	5801	SO:0001819	synonymous_variant	9734	exon23			AAAGTTCTCTTAA	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.3030C>T	7.37:g.18993870C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_058176	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			C|0.237;T|0.763	0.763	strong		0.294	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
GBP7	388646	hgsc.bcm.edu	37	1	89599070	89599070	+	Silent	SNP	T	T	C	rs151091316		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89599070T>C	ENST00000294671.2	-	10	1671	c.1533A>G	c.(1531-1533)gaA>gaG	p.E511E		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	511						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TTTGCTGCTGTTCCTTCTGTT	0.438																																					p.E511E		Atlas-SNP	.											.	GBP7	57	.	0			c.A1533G						PASS	.																																			SO:0001819	synonymous_variant	388646	exon10			CTGCTGTTCCTTC	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1533A>G	1.37:g.89599070T>C		Somatic	508	0	0		WXS	Illumina HiSeq	Phase_I	568	87	0.153169	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			.	.	weak		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
CATSPER1	117144	hgsc.bcm.edu	37	11	65793454	65793454	+	Missense_Mutation	SNP	C	C	T	rs1203998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65793454C>T	ENST00000312106.5	-	1	534	c.397G>A	c.(397-399)Ggt>Agt	p.G133S		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	133	His-rich.		G -> S (in dbSNP:rs1203998).		calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TGGAACCCACCGTATTGGGAC	0.557													T|||	1685	0.336462	0.4546	0.4625	5008	,	,		23104	0.3859		0.2763	False		,,,				2504	0.0982				p.G133S		Atlas-SNP	.											.	CATSPER1	101	.	0			c.G397A						PASS	.	T	SER/GLY	1941,2461	622.4+/-393.9	429,1083,689	76.0	65.0	69.0		397	-3.4	0.0	11	dbSNP_87	69	2390,6202	700.4+/-405.1	323,1744,2229	yes	missense	CATSPER1	NM_053054.3	56	752,2827,2918	TT,TC,CC		27.8166,44.0936,33.3308	benign	133/781	65793454	4331,8663	2201	4296	6497	SO:0001583	missense	117144	exon1			ACCCACCGTATTG	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.397G>A	11.37:g.65793454C>T	ENSP00000309052:p.Gly133Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	809	0.37042124542124544	236	0.4796747967479675	143	0.39502762430939226	220	0.38461538461538464	210	0.2770448548812665	T	3.768	-0.048212	0.07407	0.440936	0.278166	ENSG00000175294	ENST00000312106	D	0.96587	-4.06	3.61	-3.4	0.04853	.	1.234910	0.06153	N	0.674630	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.15694	-1.0428	9	0.02654	T	1	.	6.871	0.24121	0.0:0.3272:0.1272:0.5455	rs1203998;rs52832806;rs60332406;rs1203998	133	Q8NEC5	CTSR1_HUMAN	S	133	ENSP00000309052:G133S	ENSP00000309052:G133S	G	-	1	0	CATSPER1	65550030	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-2.144000	0.01296	-1.063000	0.03177	-0.817000	0.03123	GGT	C|0.656;T|0.344	0.344	strong		0.557	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
P2RY2	5029	hgsc.bcm.edu	37	11	72946204	72946204	+	Missense_Mutation	SNP	C	C	T	rs1626154	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:72946204C>T	ENST00000311131.2	+	3	1467	c.1000C>T	c.(1000-1002)Cgc>Tgc	p.R334C	P2RY2_ENST00000393596.2_Missense_Mutation_p.R334C|P2RY2_ENST00000393597.2_Missense_Mutation_p.R334C	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	334			R -> C (in dbSNP:rs1626154). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.6}.		cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CCCGGCTCGCCGCAGGCTGGG	0.652													C|||	457	0.091254	0.0212	0.1571	5008	,	,		14819	0.0506		0.2087	False		,,,				2504	0.0603				p.R334C		Atlas-SNP	.											.	P2RY2	54	.	0			c.C1000T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	178,4220		6,166,2027	29.0	34.0	32.0		1000,1000,1000	3.4	0.9	11	dbSNP_89	32	1595,6989		152,1291,2849	yes	missense,missense,missense	P2RY2	NM_002564.2,NM_176071.1,NM_176072.1	180,180,180	158,1457,4876	TT,TC,CC		18.5811,4.0473,13.6574	probably-damaging,probably-damaging,probably-damaging	334/378,334/378,334/378	72946204	1773,11209	2199	4292	6491	SO:0001583	missense	5029	exon3			GCTCGCCGCAGGC	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.1000C>T	11.37:g.72946204C>T	ENSP00000310305:p.Arg334Cys	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	52	47	0.903846	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	263	0.12042124542124542	16	0.032520325203252036	62	0.1712707182320442	34	0.05944055944055944	151	0.19920844327176782	C	10.24	1.296099	0.23650	0.040473	0.185811	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.26660	1.72;1.72;1.72	4.44	3.44	0.39384	.	1.660570	0.03269	N	0.184484	T	0.00012	0.0000	N	0.08118	0	0.27732	P	0.9447875	D	0.61697	0.99	B	0.43809	0.432	T	0.19031	-1.0318	9	0.59425	D	0.04	.	9.8209	0.40883	0.0:0.7905:0.2095:0.0	rs1626154;rs1626154	334	P41231	P2RY2_HUMAN	C	334	ENSP00000377222:R334C;ENSP00000310305:R334C;ENSP00000377221:R334C	ENSP00000310305:R334C	R	+	1	0	P2RY2	72623852	0.012000	0.17670	0.929000	0.37066	0.293000	0.27360	1.895000	0.39778	2.196000	0.70406	0.561000	0.74099	CGC	C|0.873;T|0.127	0.127	strong		0.652	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
SERPINA11	256394	hgsc.bcm.edu	37	14	94912799	94912799	+	Silent	SNP	G	G	A	rs12888805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94912799G>A	ENST00000334708.3	-	3	850	c.786C>T	c.(784-786)acC>acT	p.T262T	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	262					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		TCTGGAGGACGGTGCAAGCCA	0.532													G|||	1301	0.259784	0.0605	0.2695	5008	,	,		20967	0.1815		0.4513	False		,,,				2504	0.4059				p.T262T		Atlas-SNP	.											SERPINA11,right_lower_lobe,carcinoma,-1,1	SERPINA11	53	1	0			c.C786T						PASS	.	G		587,3819	258.6+/-262.5	46,495,1662	138.0	122.0	127.0		786	-10.8	0.1	14	dbSNP_121	127	3525,5075	515.2+/-378.5	701,2123,1476	no	coding-synonymous	SERPINA11	NM_001080451.1		747,2618,3138	AA,AG,GG		40.9884,13.3227,31.6162		262/423	94912799	4112,8894	2203	4300	6503	SO:0001819	synonymous_variant	256394	exon3			GAGGACGGTGCAA	BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"""Serine (or cysteine) peptidase inhibitors"""	19193	protein-coding gene	gene with protein product			"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"""			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.786C>T	14.37:g.94912799G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	209	111	0.5311	NM_001080451	B2RV07	Silent	SNP	ENST00000334708.3	37	CCDS32149.1																																																																																			G|0.707;A|0.293	0.293	strong		0.532	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451	
WDFY4	57705	hgsc.bcm.edu	37	10	50025446	50025446	+	Missense_Mutation	SNP	G	G	T	rs12268007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50025446G>T	ENST00000325239.5	+	31	5524	c.5497G>T	c.(5497-5499)Gcc>Tcc	p.A1833S	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1833						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CCCCCTGGGAGCCCAAAAGGT	0.622													G|||	833	0.166334	0.2905	0.1542	5008	,	,		18222	0.1071		0.1223	False		,,,				2504	0.1135				p.A1833S		Atlas-SNP	.											.	WDFY4	205	.	0			c.G5497T						PASS	.	G	SER/ALA	397,987		60,277,355	24.0	31.0	29.0		5497	-1.6	0.0	10	dbSNP_120	29	338,2844		18,302,1271	yes	missense	WDFY4	NM_020945.1	99	78,579,1626	TT,TG,GG		10.6223,28.685,16.0972	benign	1833/3185	50025446	735,3831	692	1591	2283	SO:0001583	missense	57705	exon32			CTGGGAGCCCAAA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5497G>T	10.37:g.50025446G>T	ENSP00000320563:p.Ala1833Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	339|339	0.15521978021978022|0.15521978021978022	124|124	0.25203252032520324|0.25203252032520324	52|52	0.143646408839779|0.143646408839779	71|71	0.12412587412587413|0.12412587412587413	92|92	0.12137203166226913|0.12137203166226913	G|G	1.092|1.092	-0.663764|-0.663764	0.03428|0.03428	0.28685|0.28685	0.106223|0.106223	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000312002;ENST00000374161	T|.	0.55760|.	0.5|.	5.24|5.24	-1.59|-1.59	0.08453|0.08453	.|.	0.981883|.	0.08311|.	N|.	0.965312|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02011|0.02011	-0.69|-0.69	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.12630|.	0.006;0.0|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.42548|0.42548	-0.9445|-0.9445	8|4	.|.	.|.	.|.	.|.	5.3947|5.3947	0.16263|0.16263	0.3875:0.2776:0.335:0.0|0.3875:0.2776:0.335:0.0	rs12268007;rs12268007|rs12268007;rs12268007	361;1833|.	F2Z372;Q6ZS81|.	.;WDFY4_HUMAN|.	S|I	1833|923;379	ENSP00000320563:A1833S|.	.|.	A|S	+|+	1|2	0|0	WDFY4|WDFY4	49695452|49695452	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.080000|0.080000	0.17528|0.17528	-1.238000|-1.238000	0.02919|0.02919	-0.578000|-0.578000	0.05959|0.05959	-0.302000|-0.302000	0.09304|0.09304	GCC|AGC	G|0.836;T|0.164	0.164	strong		0.622	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
OR5D14	219436	hgsc.bcm.edu	37	11	55563900	55563900	+	Missense_Mutation	SNP	T	T	C	rs297055	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55563900T>C	ENST00000335605.1	+	1	869	c.869T>C	c.(868-870)cTg>cCg	p.L290P		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	290			L -> P (in dbSNP:rs297055).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L290P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				CTGAACCCTCTGATCTACAGC	0.408													t|||	1086	0.216853	0.326	0.1844	5008	,	,		17041	0.1458		0.2525	False		,,,				2504	0.1288				p.L290P		Atlas-SNP	.											OR5D14,NS,carcinoma,-1,3	OR5D14	116	3	1	Substitution - Missense(1)	stomach(1)	c.T869C						PASS	.	T	PRO/LEU	1414,2986	451.6+/-349.7	252,910,1038	55.0	54.0	55.0		869	5.1	1.0	11	dbSNP_79	55	2204,6388	368.9+/-335.3	305,1594,2397	yes	missense	OR5D14	NM_001004735.1	98	557,2504,3435	CC,CT,TT		25.6518,32.1364,27.8479	probably-damaging	290/315	55563900	3618,9374	2200	4296	6496	SO:0001583	missense	219436	exon1			ACCCTCTGATCTA	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"""GPCR / Class A : Olfactory receptors"""	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.869T>C	11.37:g.55563900T>C	ENSP00000334456:p.Leu290Pro	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	524	0.23992673992673993	171	0.3475609756097561	66	0.18232044198895028	87	0.1520979020979021	200	0.2638522427440633	t	14.05	2.420915	0.42918	0.321364	0.256518	ENSG00000186113	ENST00000335605	T	0.46451	0.87	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35179	N	0.003382	T	0.00012	0.0000	M	0.90369	3.11	0.44966	P	0.0020139999999999603	P	0.49559	0.925	P	0.45712	0.491	T	0.22208	-1.0223	9	0.87932	D	0	-13.9526	13.7086	0.62654	0.0:0.0:0.0:1.0	rs297055;rs52801945;rs60885889;rs297055	290	Q8NGL3	OR5DE_HUMAN	P	290	ENSP00000334456:L290P	ENSP00000334456:L290P	L	+	2	0	OR5D14	55320476	0.122000	0.22280	1.000000	0.80357	0.991000	0.79684	3.008000	0.49544	1.916000	0.55485	0.523000	0.50628	CTG	T|0.746;C|0.254	0.254	strong		0.408	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
LCT	3938	hgsc.bcm.edu	37	2	136594158	136594158	+	Silent	SNP	G	G	A	rs2236783	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:136594158G>A	ENST00000264162.2	-	1	592	c.582C>T	c.(580-582)acC>acT	p.T194T		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	194	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CATCACTGAGGGTCTGGAGTT	0.517													g|||	1745	0.348442	0.1233	0.402	5008	,	,		19559	0.372		0.5964	False		,,,				2504	0.3354				p.T194T		Atlas-SNP	.											.	LCT	309	.	0			c.C582T						PASS	.			1049,3357		122,805,1276	147.0	110.0	123.0		582	-0.4	0.0	2	dbSNP_98	123	6004,2596		2182,1640,478	no	coding-synonymous	LCT	NM_002299.2		2304,2445,1754	AA,AG,GG		30.186,23.8084,45.7712		194/1928	136594158	7053,5953	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon1			ACTGAGGGTCTGG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.582C>T	2.37:g.136594158G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	219	219	1	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.584;A|0.416	0.416	strong		0.517	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
DXO	1797	hgsc.bcm.edu	37	6	31939319	31939319	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31939319C>T	ENST00000375349.3	-	2	545	c.134G>A	c.(133-135)cGc>cAc	p.R45H	STK19_ENST00000375333.2_5'Flank|DXO_ENST00000375356.3_Missense_Mutation_p.R45H|DXO_ENST00000478221.1_Intron|DXO_ENST00000337523.5_Missense_Mutation_p.R45H|STK19_ENST00000375331.2_5'Flank			O77932	DXO_HUMAN	decapping exoribonuclease	45					metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										TTCCGAAGGGCGCCGGTAGAA	0.602																																					p.R45H		Atlas-SNP	.											.	DOM3Z	20	.	0			c.G134A						PASS	.						88.0	95.0	93.0					6																	31939319		2203	4300	6503	SO:0001583	missense	1797	exon2			GAAGGGCGCCGGT	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"""DOM-3 (C. elegans) homolog Z"", ""dom-3 homolog Z (C. elegans)"""	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.134G>A	6.37:g.31939319C>T	ENSP00000364498:p.Arg45His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	118	35	0.29661	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Missense_Mutation	SNP	ENST00000375349.3	37	CCDS4732.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.356161	0.82243	.	.	ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356	T;T;T	0.21031	2.03;2.03;2.03	4.92	4.03	0.46877	.	0.198410	0.46442	D	0.000300	T	0.23806	0.0576	M	0.75884	2.315	0.80722	D	1	D;D	0.67145	0.996;0.994	P;P	0.52554	0.702;0.512	T	0.05484	-1.0882	10	0.66056	D	0.02	0.0351	11.4467	0.50127	0.3265:0.6735:0.0:0.0	.	45;45	F8WC68;O77932	.;DOM3Z_HUMAN	H	45	ENSP00000337759:R45H;ENSP00000364498:R45H;ENSP00000364505:R45H	ENSP00000337759:R45H	R	-	2	0	DOM3Z	32047298	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	2.796000	0.47869	1.234000	0.43709	0.561000	0.74099	CGC	.	.	none		0.602	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3		
CALCR	799	hgsc.bcm.edu	37	7	93055753	93055753	+	Missense_Mutation	SNP	A	A	G	rs1801197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:93055753A>G	ENST00000394441.1	-	13	1655	c.1340T>C	c.(1339-1341)cTg>cCg	p.L447P	CALCR_ENST00000360249.4_Missense_Mutation_p.L463P|CALCR_ENST00000421592.1_Missense_Mutation_p.L463P|CALCR_ENST00000426151.1_Missense_Mutation_p.L447P|CALCR_ENST00000359558.2_Missense_Mutation_p.L481P	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	481					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	TTCATTCCTCAGCTCCTGATG	0.557													G|||	2722	0.54353	0.5408	0.4308	5008	,	,		18060	0.8611		0.3052	False		,,,				2504	0.545				p.L481P		Atlas-SNP	.											CALCR_ENST00000359558,NS,adenoma,0,2	CALCR	200	2	0			c.T1442C	GRCh37	CM980299	CALCR	M	rs1801197	PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU	2073,2333	606.2+/-390.7	470,1133,600	170.0	158.0	162.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1442,1340,1340	1.3	0.0	7	dbSNP_89	162	2187,6413	712.5+/-405.9	296,1595,2409	yes	missense,missense,missense	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	98,98,98	766,2728,3009	GG,GA,AA		25.4302,47.0495,32.7541	benign,benign,benign	481/509,447/475,447/475	93055753	4260,8746	2203	4300	6503	SO:0001583	missense	799	exon16			TTCCTCAGCTCCT	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1340T>C	7.37:g.93055753A>G	ENSP00000377959:p.Leu447Pro	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	189	189	1	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	1154	0.5283882783882784	274	0.556910569105691	157	0.43370165745856354	497	0.8688811188811189	226	0.29815303430079154	G	0.389	-0.924704	0.02377	0.470495	0.254302	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.50001	0.76;0.78;0.78;0.91;0.91	5.11	1.3	0.21679	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53005	P	3.2000000000032E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15521	-1.0434	7	0.28530	T	0.3	.	4.6969	0.12808	0.3355:0.1492:0.5153:0.0	rs1801197;rs3181601;rs10368963;rs11769260;rs17165394;rs58887934;rs1801197	481;447	F5H605;A4D1G6	.;.	P	481;463;463;447;447	ENSP00000352561:L481P;ENSP00000353385:L463P;ENSP00000399552:L463P;ENSP00000377959:L447P;ENSP00000389295:L447P	ENSP00000352561:L481P	L	-	2	0	CALCR	92893689	0.940000	0.31905	0.014000	0.15608	0.178000	0.23041	1.787000	0.38704	-0.050000	0.13356	-0.790000	0.03334	CTG	A|0.561;G|0.439	0.439	strong		0.557	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
LILRA6	79168	hgsc.bcm.edu	37	19	54744794	54744794	+	Missense_Mutation	SNP	G	G	A	rs434127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54744794G>A	ENST00000396365.2	-	5	907	c.868C>T	c.(868-870)Cac>Tac	p.H290Y	LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000245621.5_Missense_Mutation_p.H290Y|LILRA6_ENST00000419410.2_Missense_Mutation_p.H290Y|LILRA6_ENST00000440558.2_Missense_Mutation_p.H290Y	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	290	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGCCCCCGTGGGAGGGGCTC	0.667																																					p.H290Y		Atlas-SNP	.											.	LILRA6	75	.	0			c.C868T						PASS	.						53.0	65.0	61.0					19																	54744794		2203	4300	6503	SO:0001583	missense	79168	exon5			CCCCGTGGGAGGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.868C>T	19.37:g.54744794G>A	ENSP00000379651:p.His290Tyr	Somatic	477	0	0		WXS	Illumina HiSeq	Phase_I	646	152	0.235294	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	G	4.311	0.057030	0.08339	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.00824	5.65;5.65;5.65;5.65	1.91	0.716	0.18191	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.760220	0.11527	N	0.555114	T	0.02193	0.0068	M	0.67397	2.05	0.09310	N	0.999999	B;P;B;B	0.52170	0.052;0.951;0.02;0.214	B;P;B;B	0.53954	0.292;0.738;0.049;0.139	T	0.47623	-0.9103	10	0.26408	T	0.33	.	5.2469	0.15502	0.0:0.0:0.6602:0.3398	.	290;290;290;290	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	Y	290	ENSP00000390120:H290Y;ENSP00000411227:H290Y;ENSP00000379651:H290Y;ENSP00000245621:H290Y	ENSP00000245621:H290Y	H	-	1	0	LILRA6	59436606	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	0.093000	0.15086	0.320000	0.23234	0.162000	0.16502	CAC	G|0.857;A|0.143	0.143	strong		0.667	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257443	114257443	+	Missense_Mutation	SNP	A	A	C	rs377465547	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:114257443A>C	ENST00000306507.5	+	1	783	c.610A>C	c.(610-612)Aag>Cag	p.K204Q		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	204					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K204Q(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GAAGCGTTTCAAGCGCCACCA	0.682													.|||	1167	0.233027	0.1029	0.3184	5008	,	,		11316	0.501		0.1302	False		,,,				2504	0.1779				p.K204Q		Atlas-SNP	.											FOXD4L1,NS,carcinoma,0,1	FOXD4L1	48	1	1	Substitution - Missense(1)	breast(1)	c.A610C						scavenged	.	A	GLN/LYS	1,2995		0,1,1497	16.0	22.0	20.0		610	2.6	1.0	2		20	1,6035		0,1,3017	no	missense	FOXD4L1	NM_012184.4	53	0,2,4514	CC,CA,AA		0.0166,0.0334,0.0221	benign	204/409	114257443	2,9030	1498	3018	4516	SO:0001583	missense	200350	exon1			CGTTTCAAGCGCC	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.610A>C	2.37:g.114257443A>C	ENSP00000302756:p.Lys204Gln	Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	56	14	0.25	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	.	.	.	.	.	.	.	.	.	.	.	13.43	2.234654	0.39498	3.34E-4	1.66E-4	ENSG00000184492	ENST00000306507	D	0.96168	-3.93	2.57	2.57	0.30868	.	0.000000	0.35378	U	0.003255	D	0.89546	0.6746	N	0.20986	0.625	0.49798	D	0.999826	B	0.25563	0.129	B	0.25614	0.062	D	0.85812	0.1380	10	0.48119	T	0.1	.	8.6531	0.34046	1.0:0.0:0.0:0.0	.	204	Q9NU39	FX4L1_HUMAN	Q	204	ENSP00000302756:K204Q	ENSP00000302756:K204Q	K	+	1	0	FOXD4L1	113973913	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	8.525000	0.90583	1.190000	0.43042	0.155000	0.16302	AAG	.	.	weak		0.682	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
ETS2	2114	hgsc.bcm.edu	37	21	40191638	40191638	+	Silent	SNP	A	A	G	rs461155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:40191638A>G	ENST00000360214.3	+	9	1483	c.1023A>G	c.(1021-1023)ccA>ccG	p.P341P	ETS2_ENST00000360938.3_Silent_p.P341P	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	341					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				GGAGTGACCCAGTGGAGCAAG	0.552													G|||	2908	0.580671	0.5613	0.5778	5008	,	,		18494	0.4563		0.838	False		,,,				2504	0.4724				p.P481P		Atlas-SNP	.											.	ETS2	87	.	0			c.A1443G						PASS	.	G		2730,1676	509.8+/-367.3	870,990,343	63.0	50.0	54.0		1023	-5.8	0.0	21	dbSNP_80	54	7292,1308	257.3+/-281.4	3085,1122,93	no	coding-synonymous	ETS2	NM_005239.4		3955,2112,436	GG,GA,AA		15.2093,38.039,22.9433		341/470	40191638	10022,2984	2203	4300	6503	SO:0001819	synonymous_variant	2114	exon9			TGACCCAGTGGAG		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.1023A>G	21.37:g.40191638A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001256295	A6NM68|D3DSH6|Q53Y89	Silent	SNP	ENST00000360214.3	37	CCDS13659.1																																																																																			A|0.297;G|0.703	0.703	strong		0.552	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
BTN3A1	11119	hgsc.bcm.edu	37	6	26409890	26409890	+	Missense_Mutation	SNP	G	G	C	rs41266839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26409890G>C	ENST00000289361.6	+	5	1213	c.845G>C	c.(844-846)aGa>aCa	p.R282T	BTN3A1_ENST00000476549.2_Missense_Mutation_p.R282T|BTN3A1_ENST00000414912.2_Missense_Mutation_p.R230T|BTN3A1_ENST00000425234.2_Missense_Mutation_p.R282T	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	282			R -> T (in dbSNP:rs41266839). {ECO:0000269|PubMed:14702039}.		activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						ACTCAGTTCAGAAAGAAAAAG	0.512													G|||	91	0.0181709	0.003	0.0288	5008	,	,		18500	0.0		0.0666	False		,,,				2504	0.0				p.R282T		Atlas-SNP	.											.	BTN3A1	80	.	0			c.G845C						PASS	.	G	THR/ARG,THR/ARG,THR/ARG,THR/ARG	79,4327		1,77,2125	106.0	118.0	114.0		689,845,845,845	-1.3	0.0	6	dbSNP_127	114	701,7899		29,643,3628	yes	missense,missense,missense,missense	BTN3A1	NM_001145008.1,NM_001145009.1,NM_007048.5,NM_194441.2	71,71,71,71	30,720,5753	CC,CG,GG		8.1512,1.793,5.9972	benign,benign,benign,benign	230/462,282/379,282/514,282/353	26409890	780,12226	2203	4300	6503	SO:0001583	missense	11119	exon5			AGTTCAGAAAGAA	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.845G>C	6.37:g.26409890G>C	ENSP00000289361:p.Arg282Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	48	0.631579	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	37	CCDS4608.1	69	0.03159340659340659	4	0.008130081300813009	9	0.024861878453038673	0	0.0	56	0.07387862796833773	.	2.133	-0.398534	0.04865	0.01793	0.081512	ENSG00000026950	ENST00000476549;ENST00000289361;ENST00000425234;ENST00000414912	T;T;T;T	0.46819	3.92;1.2;3.93;0.86	1.06	-1.33	0.09172	.	.	.	.	.	T	0.12944	0.0314	L	0.53249	1.67	0.09310	N	1	P;B;B;B	0.35328	0.495;0.008;0.0;0.0	B;B;B;B	0.25987	0.065;0.007;0.002;0.001	T	0.13415	-1.0510	9	0.27082	T	0.32	.	2.4299	0.04469	0.2529:0.3251:0.422:0.0	rs41266839	230;282;282;282	E9PGB4;O00481-3;O00481-2;O00481	.;.;.;BT3A1_HUMAN	T	282;282;282;230	ENSP00000420010:R282T;ENSP00000289361:R282T;ENSP00000396684:R282T;ENSP00000406667:R230T	ENSP00000289361:R282T	R	+	2	0	BTN3A1	26517869	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.252000	0.00266	-0.510000	0.06523	-0.199000	0.12753	AGA	G|0.951;C|0.049	0.049	strong		0.512	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3		
TIRAP	114609	hgsc.bcm.edu	37	11	126162468	126162468	+	Missense_Mutation	SNP	G	G	A	rs3802813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:126162468G>A	ENST00000392680.2	+	5	569	c.164G>A	c.(163-165)aGc>aAc	p.S55N	RP11-712L6.5_ENST00000528876.1_5'Flank|RP11-712L6.7_ENST00000533378.1_RNA|TIRAP_ENST00000392679.1_Missense_Mutation_p.S55N|TIRAP_ENST00000392678.3_Missense_Mutation_p.S55N	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	55			S -> N (does not affect NF-kappa-B activation and TNF-alpha production; dbSNP:rs3802813). {ECO:0000269|PubMed:11544529, ECO:0000269|PubMed:14702039}.		3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)			breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		TCACAGGACAGCCCACTACCC	0.587													G|||	479	0.095647	0.0613	0.1383	5008	,	,		17785	0.1756		0.0417	False		,,,				2504	0.0849				p.S55N		Atlas-SNP	.											.	TIRAP	37	.	0			c.G164A						PASS	.	G	ASN/SER,ASN/SER	272,4130	152.5+/-186.2	7,258,1936	116.0	99.0	105.0		164,164	-2.2	0.0	11	dbSNP_107	105	318,8278	112.3+/-172.5	7,304,3987	yes	missense,missense	TIRAP	NM_001039661.1,NM_148910.2	46,46	14,562,5923	AA,AG,GG		3.6994,6.179,4.5392	benign,benign	55/222,55/236	126162468	590,12408	2201	4298	6499	SO:0001583	missense	114609	exon5			AGGACAGCCCACT	AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.164G>A	11.37:g.126162468G>A	ENSP00000376447:p.Ser55Asn	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Missense_Mutation	SNP	ENST00000392680.2	37	CCDS8472.1	206	0.09432234432234432	32	0.06504065040650407	50	0.13812154696132597	90	0.15734265734265734	34	0.044854881266490766	G	9.309	1.055139	0.19907	0.06179	0.036994	ENSG00000150455	ENST00000392679;ENST00000279992;ENST00000392678;ENST00000392680	T;T;T	0.10960	2.87;2.82;2.87	5.21	-2.15	0.07102	.	1.250100	0.05220	N	0.508327	T	0.00039	0.0001	L	0.35723	1.085	0.80722	P	0.0	B;B	0.12013	0.003;0.005	B;B	0.08055	0.002;0.003	T	0.43015	-0.9417	9	0.38643	T	0.18	-11.2992	4.6123	0.12408	0.2174:0.0:0.4219:0.3607	rs3802813;rs60787873;rs3802813	55;55	P58753;Q56UH9	TIRAP_HUMAN;.	N	55	ENSP00000376446:S55N;ENSP00000376445:S55N;ENSP00000376447:S55N	ENSP00000279992:S55N	S	+	2	0	TIRAP	125667678	.	.	0.000000	0.03702	0.009000	0.06853	.	.	-0.249000	0.09569	0.655000	0.94253	AGC	G|0.936;A|0.064	0.064	strong		0.587	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910	
C1orf111	284680	hgsc.bcm.edu	37	1	162344069	162344069	+	Silent	SNP	G	G	A	rs13823	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:162344069G>A	ENST00000367935.5	-	3	634	c.555C>T	c.(553-555)tgC>tgT	p.C185C	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	185										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			AGCAGGCCACGCACTTGTAGC	0.582													G|||	379	0.0756789	0.003	0.1124	5008	,	,		18001	0.0804		0.0596	False		,,,				2504	0.1595				p.C185C		Atlas-SNP	.											.	C1orf111	26	.	0			c.C555T						PASS	.	G		42,4364	45.3+/-79.5	0,42,2161	153.0	148.0	150.0		555	-3.1	0.1	1	dbSNP_52	150	457,8143	137.5+/-194.4	9,439,3852	no	coding-synonymous	C1orf111	NM_182581.3		9,481,6013	AA,AG,GG		5.314,0.9532,3.8367		185/262	162344069	499,12507	2203	4300	6503	SO:0001819	synonymous_variant	284680	exon3			GGCCACGCACTTG	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.555C>T	1.37:g.162344069G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	165	59	0.357576	NM_182581	Q6X961|Q8NEC3	Silent	SNP	ENST00000367935.5	37	CCDS1238.1																																																																																			G|0.952;A|0.048	0.048	strong		0.582	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581	
LRRC55	219527	hgsc.bcm.edu	37	11	56954846	56954846	+	Silent	SNP	C	C	T	rs716745	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56954846C>T	ENST00000497933.1	+	2	1065	c.918C>T	c.(916-918)ttC>ttT	p.F306F		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	276					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						TCATTGCGTTCGTGGGCTTCG	0.587													C|||	1211	0.241813	0.1422	0.255	5008	,	,		20458	0.1925		0.3817	False		,,,				2504	0.274				p.F306F		Atlas-SNP	.											.	LRRC55	52	.	0			c.C918T						PASS	.	C		790,3612	319.3+/-296.1	69,652,1480	172.0	116.0	135.0		918	-7.3	0.2	11	dbSNP_86	135	3263,5329	490.4+/-372.8	658,1947,1691	no	coding-synonymous	LRRC55	NM_001005210.2		727,2599,3171	TT,TC,CC		37.9772,17.9464,31.1913		306/342	56954846	4053,8941	2201	4296	6497	SO:0001819	synonymous_variant	219527	exon2			TGCGTTCGTGGGC		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.918C>T	11.37:g.56954846C>T		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	212	209	0.985849	NM_001005210	A7E2U7|B2RN81	Silent	SNP	ENST00000497933.1	37	CCDS31539.1																																																																																			C|0.718;T|0.282	0.282	strong		0.587	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
L1TD1	54596	hgsc.bcm.edu	37	1	62675619	62675619	+	Silent	SNP	C	C	T	rs4625314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:62675619C>T	ENST00000498273.1	+	4	1468	c.1173C>T	c.(1171-1173)gcC>gcT	p.A391A	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	391	Glu-rich.							p.A391A(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						ATGAAGAGGCCTCAGGGATGG	0.493													C|||	1495	0.298522	0.2769	0.3473	5008	,	,		16813	0.1091		0.492	False		,,,				2504	0.2894				p.A391A		Atlas-SNP	.											L1TD1,NS,carcinoma,0,1	L1TD1	114	1	1	Substitution - coding silent(1)	stomach(1)	c.C1173T						PASS	.	C	,	1485,2921	448.1+/-348.6	247,991,965	60.0	67.0	64.0		1173,1173	-2.5	0.0	1	dbSNP_111	64	4405,4193	563.7+/-388.2	1145,2115,1039	no	coding-synonymous,coding-synonymous	L1TD1	NM_001164835.1,NM_019079.4	,	1392,3106,2004	TT,TC,CC		48.7672,33.704,45.2938	,	391/866,391/866	62675619	5890,7114	2203	4299	6502	SO:0001819	synonymous_variant	54596	exon5			AGAGGCCTCAGGG	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1173C>T	1.37:g.62675619C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Silent	SNP	ENST00000498273.1	37	CCDS619.1																																																																																			C|0.605;T|0.395	0.395	strong		0.493	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
MICA	100507436	hgsc.bcm.edu	37	6	31378956	31378956	+	Missense_Mutation	SNP	C	C	G	rs1051790	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31378956C>G	ENST00000449934.2	+	3	487	c.433C>G	c.(433-435)Ctg>Gtg	p.L145V	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CTCCCAAAACCTGGAGACTGA	0.522													c|||	1093	0.218251	0.2723	0.2118	5008	,	,		20699	0.122		0.1948	False		,,,				2504	0.273				p.L145V		Atlas-SNP	.											.	MICA	21	.	0			c.C433G						PASS	.	C	VAL/LEU	338,1046		43,252,397	68.0	60.0	63.0		433	1.9	0.0	6	dbSNP_86	63	489,2693		39,411,1141	yes	missense	MICA	NM_001177519.1	32	82,663,1538	GG,GC,CC		15.3677,24.422,18.1121	probably-damaging	145/333	31378956	827,3739	692	1591	2283	SO:0001583	missense	100507436	exon3			CAAAACCTGGAGA	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.433C>G	6.37:g.31378956C>G	ENSP00000413079:p.Leu145Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	213	107	0.502347	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	414	0.18956043956043955	138	0.2804878048780488	66	0.18232044198895028	93	0.16258741258741258	117	0.15435356200527706	N	7.509	0.654194	0.14580	0.24422	0.153677	ENSG00000204520	ENST00000364810;ENST00000449934	T	0.00700	5.82	1.94	1.94	0.25998	.	0.504913	0.14706	N	0.303268	T	0.01695	0.0054	M	0.85859	2.78	0.80722	P	0.0	D	0.76494	0.999	D	0.85130	0.997	T	0.40059	-0.9583	9	0.59425	D	0.04	.	5.7228	0.17996	0.3182:0.6818:0.0:0.0	rs1051790;rs3819271;rs17883141;rs1051790	145	Q96QC4	.	V	145	ENSP00000413079:L145V	ENSP00000365394:L145V	L	+	1	2	MICA	31486935	0.000000	0.05858	0.004000	0.12327	0.030000	0.12068	-0.198000	0.09505	1.130000	0.42092	0.306000	0.20318	CTG	C|0.812;G|0.188	0.188	strong		0.522	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
VAV1	7409	hgsc.bcm.edu	37	19	6850767	6850767	+	Splice_Site	SNP	C	C	T	rs36097961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6850767C>T	ENST00000602142.1	+	24	2298	c.2216C>T	c.(2215-2217)aCg>aTg	p.T739M	VAV1_ENST00000596764.1_Splice_Site_p.T707M|VAV1_ENST00000539284.1_Splice_Site_p.T642M|VAV1_ENST00000304076.2_Splice_Site_p.T717M|VAV1_ENST00000599806.1_Splice_Site_p.T684M	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	739	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		T -> M (in dbSNP:rs36097961).		apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						CGGGGGCTTACGGTAAGGGTC	0.532													C|||	94	0.01877	0.0015	0.0173	5008	,	,		17189	0.004		0.0586	False		,,,				2504	0.0174				p.T739M		Atlas-SNP	.											VAV1,NS,carcinoma,+1,1	VAV1	140	1	0			c.C2216T						PASS	.	C	MET/THR	59,4347	56.2+/-92.4	0,59,2144	92.0	87.0	88.0		2216	-5.1	0.0	19	dbSNP_126	88	580,8020	156.3+/-210.2	27,526,3747	yes	missense-near-splice	VAV1	NM_005428.2	81	27,585,5891	TT,TC,CC		6.7442,1.3391,4.9131	benign	739/846	6850767	639,12367	2203	4300	6503	SO:0001630	splice_region_variant	7409	exon24			GGCTTACGGTAAG		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12657	protein-coding gene	gene with protein product		164875	"""vav 1 oncogene"""	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.2217+1C>T	19.37:g.6850767C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	CCDS12174.1	56	0.02564102564102564	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	47	0.06200527704485488	C	11.49	1.653804	0.29425	0.013391	0.067442	ENSG00000141968	ENST00000304076;ENST00000539284	D	0.88818	-2.43	3.92	-5.12	0.02893	SH2 motif (5);	1.927670	0.02284	N	0.069679	T	0.31009	0.0783	N	0.17764	0.52	0.09310	N	0.999992	B;P;B;B	0.38863	0.025;0.65;0.005;0.006	B;B;B;B	0.40782	0.044;0.34;0.03;0.018	T	0.63506	-0.6622	10	0.27785	T	0.31	.	10.4042	0.44248	0.0:0.3177:0.0:0.6823	rs36097961;rs61750004	642;739;684;739	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	M	739;642	ENSP00000443242:T642M	ENSP00000302269:T739M	T	+	2	0	VAV1	6801767	0.000000	0.05858	0.020000	0.16555	0.938000	0.57974	-1.136000	0.03222	-0.785000	0.04522	0.561000	0.74099	ACG	C|0.956;T|0.044	0.044	strong		0.532	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1		Missense_Mutation
TRIM26	7726	hgsc.bcm.edu	37	6	30164497	30164497	+	Silent	SNP	G	G	A	rs61748990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30164497G>A	ENST00000454678.2	-	6	997	c.561C>T	c.(559-561)taC>taT	p.Y187Y	TRIM26_ENST00000487829.1_5'Flank|TRIM26_ENST00000437089.1_Silent_p.Y187Y|TRIM26_ENST00000453195.1_Silent_p.Y187Y	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	187					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						CAGCCACAATGTACTGCCTCT	0.617													G|||	234	0.0467252	0.0764	0.0231	5008	,	,		19249	0.0575		0.0149	False		,,,				2504	0.045				p.Y187Y		Atlas-SNP	.											.	TRIM26	74	.	0			c.C561T						PASS	.	G	,	302,4104	153.3+/-186.9	9,284,1910	54.0	44.0	48.0		561,561	1.4	0.0	6	dbSNP_129	48	153,8447	69.4+/-131.9	2,149,4149	no	coding-synonymous,coding-synonymous	TRIM26	NM_001242783.1,NM_003449.4	,	11,433,6059	AA,AG,GG		1.7791,6.8543,3.4984	,	187/540,187/540	30164497	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	7726	exon5			CACAATGTACTGC	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.561C>T	6.37:g.30164497G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_001242783	A6NG96|Q5SRL2	Silent	SNP	ENST00000454678.2	37	CCDS4678.1																																																																																			G|0.967;A|0.033	0.033	strong		0.617	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	
EME1	146956	hgsc.bcm.edu	37	17	48456193	48456193	+	Missense_Mutation	SNP	T	T	C	rs12450550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48456193T>C	ENST00000338165.4	+	5	1131	c.1049T>C	c.(1048-1050)aTc>aCc	p.I350T	EME1_ENST00000393271.2_Missense_Mutation_p.I350T|EME1_ENST00000511648.2_Missense_Mutation_p.I350T	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	350			I -> T (in dbSNP:rs12450550).		DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.I350T(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			GTAACTGACATCACAGCAAAG	0.473								Direct reversal of damage;Homologous recombination					T|||	714	0.142572	0.0416	0.2911	5008	,	,		21774	0.0804		0.2445	False		,,,				2504	0.1329				p.I350T		Atlas-SNP	.											EME1,NS,carcinoma,0,1	EME1	39	1	1	Substitution - Missense(1)	stomach(1)	c.T1049C						scavenged	.	T	THR/ILE,THR/ILE	357,4049	183.6+/-211.2	21,315,1867	87.0	89.0	88.0		1049,1049	2.1	0.0	17	dbSNP_120	88	2244,6356	380.3+/-339.6	297,1650,2353	yes	missense,missense	EME1	NM_001166131.1,NM_152463.2	89,89	318,1965,4220	CC,CT,TT		26.093,8.1026,19.9985	benign,benign	350/584,350/571	48456193	2601,10405	2203	4300	6503	SO:0001583	missense	146956	exon5			CTGACATCACAGC	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"""	610885	"""essential meiotic endonuclease 1 homolog 1 (S. pombe)"""			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.1049T>C	17.37:g.48456193T>C	ENSP00000339897:p.Ile350Thr	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	177	90	0.508475	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	37	CCDS11565.1	340	0.15567765567765568	19	0.03861788617886179	94	0.2596685082872928	44	0.07692307692307693	183	0.24142480211081793	T	13.58	2.279564	0.40294	0.081026	0.26093	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511648	T;T;T	0.23754	1.89;1.89;1.89	5.58	2.1	0.27182	ERCC4 domain (2);	1.100420	0.06824	N	0.792688	T	0.00012	0.0000	M	0.65498	2.005	0.53005	P	3.2000000000032E-5	P;P	0.43352	0.804;0.695	B;B	0.40066	0.292;0.318	T	0.22347	-1.0219	9	0.59425	D	0.04	-21.7026	8.9778	0.35946	0.0:0.2212:0.0:0.7788	rs12450550;rs17714916;rs52794199;rs56987872;rs12450550	350;350	Q96AY2-2;Q96AY2	.;EME1_HUMAN	T	350	ENSP00000339897:I350T;ENSP00000376952:I350T;ENSP00000421700:I350T	ENSP00000339897:I350T	I	+	2	0	EME1	45811192	0.076000	0.21285	0.023000	0.16930	0.240000	0.25518	1.796000	0.38794	0.468000	0.27243	-0.451000	0.05528	ATC	C|0.175;N|0.000	0.175	strong		0.473	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
UNC13A	23025	hgsc.bcm.edu	37	19	17737486	17737486	+	Silent	SNP	G	G	A	rs113693450	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17737486G>A	ENST00000519716.2	-	34	4028	c.4029C>T	c.(4027-4029)gaC>gaT	p.D1343D	UNC13A_ENST00000252773.7_Silent_p.D1343D|UNC13A_ENST00000550896.1_Silent_p.D1341D|UNC13A_ENST00000551649.1_Silent_p.D1343D|UNC13A_ENST00000552293.1_Silent_p.D1343D|UNC13A_ENST00000428389.2_Silent_p.D1431D	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1343					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CATTGTCCGCGTCCTGGGCCA	0.622													g|||	85	0.0169728	0.0068	0.0274	5008	,	,		20526	0.001		0.0517	False		,,,				2504	0.0041				p.D1343D		Atlas-SNP	.											UNC13A_ENST00000519716,NS,carcinoma,0,2	UNC13A	299	2	0			c.C4029T						PASS	.			42,4274		0,42,2116	28.0	29.0	29.0		4029	-4.9	0.9	19	dbSNP_132	29	509,7995		16,477,3759	no	coding-synonymous	UNC13A	NM_001080421.2		16,519,5875	AA,AG,GG		5.9854,0.9731,4.298		1343/1704	17737486	551,12269	2158	4252	6410	SO:0001819	synonymous_variant	23025	exon33			GTCCGCGTCCTGG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.4029C>T	19.37:g.17737486G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			G|0.971;A|0.029	0.029	strong		0.622	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
ADARB2	105	hgsc.bcm.edu	37	10	1230850	1230850	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:1230850C>T	ENST00000381312.1	-	9	2319	c.1994G>A	c.(1993-1995)cGg>cAg	p.R665Q	ADARB2_ENST00000381305.1_Missense_Mutation_p.R67Q|ADARB2_ENST00000381310.3_Missense_Mutation_p.R174Q	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	665	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CTTGCAGAGCCGGGATGGGCC	0.662																																					p.R665Q		Atlas-SNP	.											ADARB2,NS,carcinoma,+1,1	ADARB2	95	1	0			c.G1994A						scavenged	.						42.0	39.0	40.0					10																	1230850		2203	4300	6503	SO:0001583	missense	105	exon9			CAGAGCCGGGATG	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1994G>A	10.37:g.1230850C>T	ENSP00000370713:p.Arg665Gln	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	186	2	0.0107527	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	37	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.492511	0.84962	.	.	ENSG00000185736	ENST00000381312;ENST00000381310;ENST00000381305	D;D;D	0.94417	-3.42;-3.42;-3.42	5.14	5.14	0.70334	Adenosine deaminase/editase (3);	0.046945	0.85682	N	0.000000	D	0.97377	0.9142	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.948;0.962;1.0	D	0.97495	1.0056	10	0.51188	T	0.08	-29.8787	18.5827	0.91177	0.0:1.0:0.0:0.0	.	665;67;174	Q9NS39;Q5VW43;Q5VW42	RED2_HUMAN;.;.	Q	665;174;67	ENSP00000370713:R665Q;ENSP00000370711:R174Q;ENSP00000370706:R67Q	ENSP00000370706:R67Q	R	-	2	0	ADARB2	1220850	0.981000	0.34729	0.911000	0.35937	0.215000	0.24574	7.706000	0.84615	2.395000	0.81488	0.561000	0.74099	CGG	.	.	none		0.662	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
TMEM161B	153396	hgsc.bcm.edu	37	5	87498849	87498849	+	Silent	SNP	G	G	A	rs3097146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:87498849G>A	ENST00000296595.6	-	9	968	c.844C>T	c.(844-846)Ctg>Ttg	p.L282L	TMEM161B_ENST00000509387.1_Silent_p.L155L|TMEM161B_ENST00000511218.1_Silent_p.L100L|TMEM161B_ENST00000514135.1_Silent_p.L282L|TMEM161B_ENST00000512429.1_Silent_p.L271L|TMEM161B_ENST00000506536.1_Silent_p.L100L	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	282						integral component of membrane (GO:0016021)				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		ACCCAGAGCAGAACCATAAAT	0.358													G|||	2409	0.48103	0.1036	0.6095	5008	,	,		17516	0.7897		0.5875	False		,,,				2504	0.4724				p.L282L		Atlas-SNP	.											.	TMEM161B	46	.	0			c.C844T						PASS	.	G		845,3561	331.0+/-301.8	92,661,1450	153.0	142.0	146.0		844	4.9	1.0	5	dbSNP_103	146	5208,3392	639.6+/-399.5	1576,2056,668	no	coding-synonymous	TMEM161B	NM_153354.3		1668,2717,2118	AA,AG,GG		39.4419,19.1784,46.5401		282/488	87498849	6053,6953	2203	4300	6503	SO:0001819	synonymous_variant	153396	exon9			AGAGCAGAACCAT	BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.844C>T	5.37:g.87498849G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	206	205	0.995146	NM_153354	Q5CZH7|Q6UWQ6	Silent	SNP	ENST00000296595.6	37	CCDS4065.1																																																																																			G|0.530;A|0.470	0.470	strong		0.358	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254094.1	NM_153354	
ZNF696	79943	hgsc.bcm.edu	37	8	144378184	144378184	+	Silent	SNP	C	C	G	rs2235115	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144378184C>G	ENST00000330143.3	+	3	748	c.339C>G	c.(337-339)ggC>ggG	p.G113G		NM_030895.2	NP_112157.2	Q9H7X3	ZN696_HUMAN	zinc finger protein 696	113					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CAGGCCCCGGCGCAGAGGGCG	0.692													G|||	2537	0.506589	0.2239	0.6499	5008	,	,		14162	0.6726		0.4682	False		,,,				2504	0.6554				p.G113G		Atlas-SNP	.											.	ZNF696	18	.	0			c.C339G						PASS	.	G		989,3259		160,669,1295	6.0	7.0	6.0		339	-5.3	0.0	8	dbSNP_98	6	3578,4716		868,1842,1437	no	coding-synonymous	ZNF696	NM_030895.2		1028,2511,2732	GG,GC,CC		43.1396,23.2815,36.4137		113/375	144378184	4567,7975	2124	4147	6271	SO:0001819	synonymous_variant	79943	exon3			CCCCGGCGCAGAG	AK024191	CCDS6399.1	8q24.3	2013-01-08				ENSG00000185730		"""Zinc fingers, C2H2-type"""	25872	protein-coding gene	gene with protein product							Standard	NM_030895		Approved	FLJ14129	uc003yxy.4	Q9H7X3		ENST00000330143.3:c.339C>G	8.37:g.144378184C>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	29	22	0.758621	NM_030895	A0AVE2	Silent	SNP	ENST00000330143.3	37	CCDS6399.1																																																																																			C|0.518;G|0.482	0.482	strong		0.692	ZNF696-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381164.2	NM_030895	
SLC22A18	5002	hgsc.bcm.edu	37	11	2943671	2943671	+	Missense_Mutation	SNP	G	G	C	rs1129782	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:2943671G>C	ENST00000380574.1	+	10	1403	c.972G>C	c.(970-972)tgG>tgC	p.W324C	SLC22A18_ENST00000312221.5_Missense_Mutation_p.W324C|SLC22A18_ENST00000441077.1_3'UTR|SLC22A18_ENST00000449793.2_Missense_Mutation_p.W226C|SLC22A18_ENST00000347936.2_Missense_Mutation_p.W324C			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	324			W -> C (in dbSNP:rs1129782).		drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		CCCAGGCCTGGATGTCCAGCG	0.657													G|||	647	0.129193	0.0076	0.134	5008	,	,		11711	0.123		0.2018	False		,,,				2504	0.2219				p.W324C		Atlas-SNP	.											.	SLC22A18	20	.	0			c.G972C						PASS	.	G	CYS/TRP,CYS/TRP	166,4234	103.8+/-142.4	5,156,2039	65.0	45.0	52.0		972,972	2.5	0.7	11	dbSNP_86	52	1778,6820	297.4+/-303.4	173,1432,2694	yes	missense,missense	SLC22A18	NM_002555.5,NM_183233.2	215,215	178,1588,4733	CC,CG,GG		20.6792,3.7727,14.9561	benign,benign	324/425,324/425	2943671	1944,11054	2200	4299	6499	SO:0001583	missense	5002	exon10			GGCCTGGATGTCC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"""Solute carriers"""	10964	protein-coding gene	gene with protein product		602631	"""solute carrier family 22 (organic cation transporter), member 1-like"""	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.972G>C	11.37:g.2943671G>C	ENSP00000369948:p.Trp324Cys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	159	69	0.433962	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	274	0.12545787545787546	7	0.014227642276422764	43	0.11878453038674033	71	0.12412587412587413	153	0.20184696569920843	G	4.917	0.170328	0.09339	0.037727	0.206792	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574	T;T;T;T	0.80994	0.28;0.28;-1.44;0.28	4.56	2.49	0.30216	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.874893	0.09614	N	0.778444	T	0.00073	0.0002	N	0.03608	-0.345	0.29262	P	0.871274	B;B	0.13145	0.007;0.002	B;B	0.09377	0.004;0.0	T	0.04855	-1.0922	9	0.62326	D	0.03	-8.7963	11.9756	0.53089	0.0:0.3348:0.6652:0.0	rs1129782;rs3177634;rs3188051;rs11559226;rs1129782	226;324	E9PRM7;Q96BI1	.;S22AI_HUMAN	C	324;324;226;324	ENSP00000307859:W324C;ENSP00000311139:W324C;ENSP00000392072:W226C;ENSP00000369948:W324C	ENSP00000311139:W324C	W	+	3	0	SLC22A18	2900247	0.533000	0.26354	0.749000	0.31150	0.286000	0.27126	0.687000	0.25407	0.867000	0.35654	0.549000	0.68633	TGG	G|0.866;C|0.134	0.134	strong		0.657	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
DTX4	23220	hgsc.bcm.edu	37	11	58940278	58940278	+	Splice_Site	SNP	G	G	T	rs12796683	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:58940278G>T	ENST00000227451.3	+	1	314	c.210G>T	c.(208-210)acG>acT	p.T70T	DTX4_ENST00000532982.1_Intron	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	70	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				GCCAAGACACGGGTGAGCCAG	0.697													G|||	1262	0.251997	0.152	0.3646	5008	,	,		9870	0.2679		0.2147	False		,,,				2504	0.3292				p.T70T		Atlas-SNP	.											.	DTX4	84	.	0			c.G210T						PASS	.	G		683,3671		61,561,1555	12.0	15.0	14.0		210	-2.2	1.0	11	dbSNP_121	14	1861,6707		199,1463,2622	yes	coding-synonymous-near-splice	DTX4	NM_015177.1		260,2024,4177	TT,TG,GG		21.7204,15.6867,19.6874		70/620	58940278	2544,10378	2177	4284	6461	SO:0001630	splice_region_variant	23220	exon1			AGACACGGGTGAG	AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"""RING-type (C3HC4) zinc fingers"""	29151	protein-coding gene	gene with protein product			"""deltex 4 homolog (Drosophila)"", ""deltex homolog 4 (Drosophila)"""			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.211+1G>T	11.37:g.58940278G>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	118	51	0.432203	NM_015177	Q0VF38	Silent	SNP	ENST00000227451.3	37	CCDS44612.1																																																																																			G|0.762;T|0.238	0.238	strong		0.697	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213	Silent
OPRL1	4987	hgsc.bcm.edu	37	20	62729431	62729431	+	Silent	SNP	C	C	T	rs2229205	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62729431C>T	ENST00000349451.3	+	5	922	c.510C>T	c.(508-510)gtC>gtT	p.V170V	OPRL1_ENST00000355631.4_Silent_p.V170V|OPRL1_ENST00000336866.2_Silent_p.V170V	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	170					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					CCCAGGCTGTCAATGTGGCCA	0.617													C|||	583	0.116414	0.1127	0.0951	5008	,	,		18792	0.1508		0.1541	False		,,,				2504	0.0624				p.V170V		Atlas-SNP	.											.	OPRL1	47	.	0			c.C510T						PASS	.	C	,,	464,3942	218.1+/-236.3	21,422,1760	109.0	95.0	100.0		510,510,510	3.0	0.9	20	dbSNP_98	100	1347,7249	262.8+/-284.6	104,1139,3055	no	coding-synonymous,coding-synonymous,coding-synonymous	OPRL1	NM_000913.4,NM_001200019.1,NM_182647.2	,,	125,1561,4815	TT,TC,CC		15.6701,10.5311,13.9286	,,	170/371,170/371,170/371	62729431	1811,11191	2203	4298	6501	SO:0001819	synonymous_variant	4987	exon3			GGCTGTCAATGTG		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"""GPCR / Class A : Opioid receptors"""	8155	protein-coding gene	gene with protein product	"""LC132 receptor-like"", ""orphanin FQ receptor"", ""kappa3-related opioid receptor"""	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.510C>T	20.37:g.62729431C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	154	82	0.532468	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Silent	SNP	ENST00000349451.3	37	CCDS13556.1																																																																																			C|0.861;T|0.139	0.139	strong		0.617	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647	
SREBF1	6720	hgsc.bcm.edu	37	17	17723595	17723595	+	Missense_Mutation	SNP	G	G	A	rs115855236	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17723595G>A	ENST00000261646.5	-	2	516	c.332C>T	c.(331-333)cCg>cTg	p.P111L	SREBF1_ENST00000355815.4_Missense_Mutation_p.P141L|SREBF1_ENST00000338854.5_Missense_Mutation_p.P111L|SREBF1_ENST00000395757.1_5'Flank|SREBF1_ENST00000583732.1_Intron|SREBF1_ENST00000435530.2_Missense_Mutation_p.P111L	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	111	Pro/Ser-rich.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						GGGCATGGACGGGTACATCTT	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		17350	0.0		0.003	False		,,,				2504	0.0				p.P141L		Atlas-SNP	.											.	SREBF1	47	.	0			c.C422T						PASS	.	G	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	65.0	72.0	69.0		422,332	2.2	0.9	17	dbSNP_132	69	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	SREBF1	NM_001005291.2,NM_004176.4	98,98	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	probably-damaging,probably-damaging	141/1178,111/1148	17723595	9,12997	2203	4300	6503	SO:0001583	missense	6720	exon3			ATGGACGGGTACA	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"""Basic helix-loop-helix proteins"""	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.332C>T	17.37:g.17723595G>A	ENSP00000261646:p.Pro111Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	37	CCDS11189.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	6.553	0.470364	0.12461	2.27E-4	9.3E-4	ENSG00000072310	ENST00000338854;ENST00000355815;ENST00000261646;ENST00000418712;ENST00000423161;ENST00000435530	T;T;T;T;T	0.79454	0.49;0.53;0.54;-0.11;-1.27	4.52	2.2	0.27929	.	0.352176	0.24580	N	0.037309	T	0.67449	0.2894	L	0.54323	1.7	0.09310	N	1	P;P;P;P	0.47545	0.897;0.897;0.725;0.82	B;B;B;B	0.41135	0.256;0.186;0.134;0.348	T	0.59037	-0.7529	10	0.31617	T	0.26	-8.4746	6.4826	0.22071	0.1164:0.1911:0.6925:0.0	.	111;87;111;141	B0I4X3;B0I4X4;P36956;P36956-4	.;.;SRBP1_HUMAN;.	L	111;141;111;87;37;111	ENSP00000345822:P111L;ENSP00000348069:P141L;ENSP00000261646:P111L;ENSP00000411516:P37L;ENSP00000413389:P111L	ENSP00000261646:P111L	P	-	2	0	SREBF1	17664320	0.781000	0.28676	0.877000	0.34402	0.264000	0.26372	2.529000	0.45632	2.081000	0.62600	0.555000	0.69702	CCG	G|0.999;A|0.001	0.001	strong		0.647	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176	
RNF5	6048	hgsc.bcm.edu	37	6	32147696	32147696	+	Silent	SNP	G	G	A	rs3130349	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32147696G>A	ENST00000375094.3	+	4	473	c.315G>A	c.(313-315)ccG>ccA	p.P105P	AGPAT1_ENST00000395499.1_5'Flank|AGPAT1_ENST00000336984.6_5'Flank|AGPAT1_ENST00000490711.1_5'Flank|AGPAT1_ENST00000395497.1_5'Flank|RNF5_ENST00000427134.2_Silent_p.P105P|AGPAT1_ENST00000375104.2_5'Flank	NM_006913.3	NP_008844.1	Q99942	RNF5_HUMAN	ring finger protein 5, E3 ubiquitin protein ligase	105					cellular protein catabolic process (GO:0044257)|ER-associated misfolded protein catabolic process (GO:0071712)|negative regulation of autophagy (GO:0010507)|protein destabilization (GO:0031648)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of autophagic vacuole assembly (GO:2000785)|response to bacterium (GO:0009617)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(7)|urinary_tract(2)	10						GACCAGCTCCGGAGAGCAGAG	0.542													A|||	667	0.133187	0.1241	0.0865	5008	,	,		18422	0.0933		0.159	False		,,,				2504	0.1933				p.P105P		Atlas-SNP	.											.	RNF5	16	.	0			c.G315A						PASS	.	A		500,3906	773.7+/-414.0	29,442,1732	92.0	107.0	102.0		315	-10.3	0.3	6	dbSNP_103	102	1568,7032	742.8+/-407.2	140,1288,2872	yes	coding-synonymous	RNF5	NM_006913.3		169,1730,4604	AA,AG,GG		18.2326,11.3482,15.9004		105/181	32147696	2068,10938	2203	4300	6503	SO:0001819	synonymous_variant	6048	exon4			AGCTCCGGAGAGC	U89336	CCDS4745.1	6p21.31	2013-01-09	2012-02-23			ENSG00000204308		"""RING-type (C3HC4) zinc fingers"""	10068	protein-coding gene	gene with protein product		602677	"""ring finger protein 5"""			9533025	Standard	NM_006913		Approved	NG2, G16, RING5, RMA1	uc031snv.1	Q99942	OTTHUMG00000031093	ENST00000375094.3:c.315G>A	6.37:g.32147696G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	304	131	0.430921	NM_006913	A2BFI6|B2R4K3|Q0VDB7|Q9UMQ2	Silent	SNP	ENST00000375094.3	37	CCDS4745.1																																																																																			G|0.863;A|0.137	0.137	strong		0.542	RNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076133.2	NM_006913	
DUOX2	50506	hgsc.bcm.edu	37	15	45397993	45397993	+	Missense_Mutation	SNP	C	C	T	rs138353181	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45397993C>T	ENST00000603300.1	-	18	2384	c.2182G>A	c.(2182-2184)Gcc>Acc	p.A728T	DUOX2_ENST00000389039.6_Missense_Mutation_p.A728T	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	728					adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		TGCACAAAGGCGCCCCGTTCC	0.592													C|||	39	0.00778754	0.0	0.0202	5008	,	,		18848	0.0		0.0239	False		,,,				2504	0.001				p.A728T		Atlas-SNP	.											.	DUOX2	137	.	0			c.G2182A						PASS	.	C	THR/ALA	8,4388	14.3+/-33.2	0,8,2190	74.0	71.0	72.0		2182	-3.5	0.0	15	dbSNP_134	72	68,8528	41.7+/-99.0	0,68,4230	yes	missense	DUOX2	NM_014080.4	58	0,76,6420	TT,TC,CC		0.7911,0.182,0.585	benign	728/1549	45397993	76,12916	2198	4298	6496	SO:0001583	missense	50506	exon18			CAAAGGCGCCCCG	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.2182G>A	15.37:g.45397993C>T	ENSP00000475084:p.Ala728Thr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	22	0.010073260073260074	0	0.0	10	0.027624309392265192	0	0.0	12	0.0158311345646438	C	5.210	0.224214	0.09863	0.00182	0.007911	ENSG00000140279	ENST00000389039	.	.	.	5.48	-3.46	0.04767	.	1.074620	0.07011	N	0.825073	T	0.07908	0.0198	N	0.12961	0.28	0.09310	N	1	B;B	0.19935	0.007;0.04	B;B	0.11329	0.002;0.006	T	0.21518	-1.0243	9	0.15952	T	0.53	-1.9998	9.522	0.39140	0.0:0.5971:0.1325:0.2704	.	728;290	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	T	728	.	ENSP00000373691:A728T	A	-	1	0	DUOX2	43185285	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	0.052000	0.14163	-0.642000	0.05480	-0.345000	0.07892	GCC	C|0.993;T|0.007	0.007	strong		0.592	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
RAD51B	5890	hgsc.bcm.edu	37	14	68353893	68353893	+	Missense_Mutation	SNP	A	A	G	rs34594234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:68353893A>G	ENST00000487270.1	+	7	776	c.728A>G	c.(727-729)aAg>aGg	p.K243R	RAD51B_ENST00000488612.1_Missense_Mutation_p.K243R|RAD51B_ENST00000471583.1_Missense_Mutation_p.K243R|RAD51B_ENST00000390683.3_Missense_Mutation_p.K243R|RAD51B_ENST00000487861.1_Missense_Mutation_p.K243R|RAD51B_ENST00000469165.2_3'UTR	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	243			K -> R (in dbSNP:rs34594234). {ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						TCCTCCTTGAAGTATTTGGCT	0.358								Direct reversal of damage					A|||	15	0.00299521	0.0	0.0043	5008	,	,		14243	0.0		0.0089	False		,,,				2504	0.0031				p.K243R		Atlas-SNP	.											.	RAD51B	80	.	0			c.A728G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	17,4389	22.3+/-47.3	0,17,2186	74.0	76.0	76.0		728,728,728	5.9	1.0	14	dbSNP_126	76	97,8503	51.1+/-111.2	2,93,4205	yes	missense,missense,missense	RAD51B	NM_002877.5,NM_133509.3,NM_133510.3	26,26,26	2,110,6391	GG,GA,AA		1.1279,0.3858,0.8765	probably-damaging,probably-damaging,probably-damaging	243/351,243/385,243/351	68353893	114,12892	2203	4300	6503	SO:0001583	missense	5890	exon7			CCTTGAAGTATTT	U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185			9822	protein-coding gene	gene with protein product		602948	"""RAD51 (S. cerevisiae)-like 1"", ""RAD51-like 1 (S. cerevisiae)"", ""RAD51 homolog B (S. cerevisiae)"""	RAD51L1		6261043, 9207106	Standard	NM_002877		Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000487270.1:c.728A>G	14.37:g.68353893A>G	ENSP00000419471:p.Lys243Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	152	67	0.440789	NM_133509	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Missense_Mutation	SNP	ENST00000487270.1	37	CCDS9789.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	A	25.4	4.630716	0.87660	0.003858	0.011279	ENSG00000182185	ENST00000487861;ENST00000471583;ENST00000487270;ENST00000488612;ENST00000390683;ENST00000402498;ENST00000342389	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.9	5.9	0.94986	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66819	0.2828	L	0.33293	1	0.44485	D	0.997423	D;D;D;D;D;P	0.89917	1.0;1.0;1.0;1.0;1.0;0.746	D;D;D;D;D;P	0.97110	1.0;1.0;1.0;1.0;1.0;0.8	T	0.69595	-0.5103	10	0.34782	T	0.22	-21.1874	14.8985	0.70661	1.0:0.0:0.0:0.0	rs34594234	243;243;243;243;243;243	C9JYJ0;C9JSP9;O15315-4;O15315;O15315-1;O15315-2	.;.;.;RA51B_HUMAN;.;.	R	243	ENSP00000419881:K243R;ENSP00000418859:K243R;ENSP00000419471:K243R;ENSP00000420061:K243R;ENSP00000375101:K243R	ENSP00000343531:K243R	K	+	2	0	RAD51B	67423646	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.799000	0.75160	2.266000	0.75297	0.528000	0.53228	AAG	A|0.992;G|0.008	0.008	strong		0.358	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1		
BANK1	55024	hgsc.bcm.edu	37	4	102839287	102839287	+	Missense_Mutation	SNP	G	G	A	rs3733197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:102839287G>A	ENST00000322953.4	+	7	1421	c.1147G>A	c.(1147-1149)Gca>Aca	p.A383T	BANK1_ENST00000504592.1_Missense_Mutation_p.A368T|BANK1_ENST00000444316.2_Missense_Mutation_p.A353T|BANK1_ENST00000428908.1_Missense_Mutation_p.A250T|BANK1_ENST00000508653.1_Missense_Mutation_p.A250T	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	383			A -> T (influences susceptibility to SLE; dbSNP:rs3733197). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18204447}.		B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		TTCAGACCCCGCACATATTGC	0.363													G|||	1136	0.226837	0.1498	0.219	5008	,	,		15219	0.254		0.3489	False		,,,				2504	0.183				p.A383T		Atlas-SNP	.											.	BANK1	95	.	0			c.G1147A	GRCh37	CM080096	BANK1	M	rs3733197	PASS	.	G	THR/ALA,THR/ALA,THR/ALA	812,3592	310.0+/-291.3	85,642,1475	63.0	66.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1057,748,1147	1.9	0.1	4	dbSNP_107	65	3053,5547	465.6+/-366.6	542,1969,1789	yes	missense,missense,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	58,58,58	627,2611,3264	AA,AG,GG		35.5,18.4378,29.7216	benign,benign,benign	353/756,250/653,383/786	102839287	3865,9139	2202	4300	6502	SO:0001583	missense	55024	exon7			GACCCCGCACATA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1147G>A	4.37:g.102839287G>A	ENSP00000320509:p.Ala383Thr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	547	0.25045787545787546	70	0.14227642276422764	83	0.2292817679558011	125	0.21853146853146854	269	0.3548812664907652	G	4.252	0.045840	0.08196	0.184378	0.355	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	4.55	1.85	0.25348	Ankyrin repeat-containing domain (1);	0.537909	0.15287	N	0.270369	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	D;D;D	0.76494	0.999;0.983;0.983	P;P;P	0.59357	0.856;0.608;0.608	T	0.29671	-1.0004	9	0.08381	T	0.77	.	4.0106	0.09621	0.2958:0.1862:0.518:0.0	rs3733197;rs52823400;rs3733197	250;383;368	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	T	368;383;250;250;353	ENSP00000421443:A368T;ENSP00000320509:A383T;ENSP00000412748:A250T;ENSP00000422314:A250T;ENSP00000388817:A353T	ENSP00000320509:A383T	A	+	1	0	BANK1	103058310	0.059000	0.20769	0.056000	0.19401	0.127000	0.20565	0.723000	0.25939	0.163000	0.19507	-0.126000	0.14955	GCA	G|0.725;A|0.275	0.275	strong		0.363	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
SAGE1	55511	hgsc.bcm.edu	37	X	134978425	134978425	+	Silent	SNP	G	G	A	rs5930805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:134978425G>A	ENST00000370709.3	+	1	24	c.24G>A	c.(22-24)acG>acA	p.T8T	SAGE1_ENST00000535938.1_Silent_p.T8T|SAGE1_ENST00000324447.3_Silent_p.T8T|SAGE1_ENST00000537770.1_Silent_p.T8T			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	8						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CACTTCAAACGAGTCAACCAA	0.403													g|||	611	0.161854	0.0673	0.1614	3775	,	,		11604	0.1012		0.2058	False		,,,				2504	0.1033				p.T8T		Atlas-SNP	.											.	SAGE1	160	.	0			c.G24A						PASS	.	G		545,3290		29,416,71,1187,500	108.0	88.0	95.0		24	0.8	0.0	X	dbSNP_114	95	1753,4975		188,923,454,1317,1418	no	coding-synonymous	SAGE1	NM_018666.2		217,1339,525,2504,1918	AA,AG,A,GG,G		26.0553,14.2112,21.7552		8/905	134978425	2298,8265	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon2			TCAAACGAGTCAA	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.24G>A	X.37:g.134978425G>A		Somatic	458	0	0		WXS	Illumina HiSeq	Phase_I	247	247	1	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			G|0.792;A|0.208	0.208	strong		0.403	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
MUC16	94025	hgsc.bcm.edu	37	19	9074950	9074950	+	Missense_Mutation	SNP	G	G	T	rs2591591	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9074950G>T	ENST00000397910.4	-	3	12699	c.12496C>A	c.(12496-12498)Cat>Aat	p.H4166N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4168	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTTGTAGCATGGATAGGTACC	0.502													G|||	1195	0.238618	0.1649	0.2104	5008	,	,		21932	0.249		0.3121	False		,,,				2504	0.272				p.H4166N		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12496A						PASS	.	G	ASN/HIS	718,3230		67,584,1323	157.0	146.0	149.0		12496	-2.4	0.0	19	dbSNP_100	149	2408,5922		347,1714,2104	yes	missense	MUC16	NM_024690.2	68	414,2298,3427	TT,TG,GG		28.9076,18.1864,25.4602	possibly-damaging	4166/14508	9074950	3126,9152	1974	4165	6139	SO:0001583	missense	94025	exon3			TAGCATGGATAGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12496C>A	19.37:g.9074950G>T	ENSP00000381008:p.His4166Asn	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	235	104	0.442553	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	534	0.2445054945054945	92	0.18699186991869918	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	g	5.100	0.204049	0.09704	0.181864	0.289076	ENSG00000181143	ENST00000397910	T	0.21031	2.03	1.49	-2.4	0.06583	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	.	.	.	P	0.34977	0.478	B	0.23716	0.048	T	0.43114	-0.9411	8	0.87932	D	0	.	5.1886	0.15197	0.5643:0.0:0.4357:0.0	rs2591591;rs59166931;rs2591591	4166	B5ME49	.	N	4166	ENSP00000381008:H4166N	ENSP00000381008:H4166N	H	-	1	0	MUC16	8935950	0.000000	0.05858	0.000000	0.03702	0.408000	0.30992	-0.296000	0.08287	-0.632000	0.05553	0.313000	0.20887	CAT	G|0.758;T|0.242	0.242	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OR1L8	138881	hgsc.bcm.edu	37	9	125330125	125330125	+	Missense_Mutation	SNP	C	C	G	rs10739614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:125330125C>G	ENST00000304865.2	-	1	713	c.632G>C	c.(631-633)cGt>cCt	p.R211P		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	211			R -> P (in dbSNP:rs10739614). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GCAGAGAAAACGAGTCACCAA	0.428													G|||	3618	0.722444	0.7186	0.6513	5008	,	,		24563	0.9841		0.6143	False		,,,				2504	0.6196				p.R211P		Atlas-SNP	.											.	OR1L8	90	.	0			c.G632C						PASS	.	G	PRO/ARG	3079,1327	444.7+/-347.4	1070,939,194	81.0	71.0	75.0		632	3.6	0.0	9	dbSNP_120	75	5194,3406	502.9+/-375.8	1538,2118,644	yes	missense	OR1L8	NM_001004454.1	103	2608,3057,838	GG,GC,CC		39.6047,30.118,36.3909	benign	211/310	125330125	8273,4733	2203	4300	6503	SO:0001583	missense	138881	exon1			AGAAAACGAGTCA		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"""GPCR / Class A : Olfactory receptors"""	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.632G>C	9.37:g.125330125C>G	ENSP00000306607:p.Arg211Pro	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_001004454	A3KFM3|B9EIR6|Q6IF15|Q96R79	Missense_Mutation	SNP	ENST00000304865.2	37	CCDS35124.1	1610	0.7371794871794872	352	0.7154471544715447	236	0.6519337016574586	568	0.993006993006993	454	0.5989445910290238	G	0.003	-2.493135	0.00159	0.69882	0.603953	ENSG00000171496	ENST00000304865	T	0.20881	2.04	4.49	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45606	N	0.000360	T	0.00012	0.0000	N	0.00000	-3.915	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39354	-0.9618	9	0.02654	T	1	-25.2211	10.7988	0.46476	0.0:0.1424:0.7095:0.1481	rs10739614;rs17278594;rs10739614	211	Q8NGR8	OR1L8_HUMAN	P	211	ENSP00000306607:R211P	ENSP00000306607:R211P	R	-	2	0	OR1L8	124369946	0.000000	0.05858	0.008000	0.14137	0.110000	0.19582	0.231000	0.17872	0.678000	0.31325	-2.755000	0.00123	CGT	C|0.330;G|0.670	0.670	strong		0.428	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26193982	26193982	+	Silent	SNP	C	C	G	rs738642	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26193982C>G	ENST00000407587.2	+	12	2608	c.2439C>G	c.(2437-2439)ctC>ctG	p.L813L	MYO18B_ENST00000335473.7_Silent_p.L813L|MYO18B_ENST00000536101.1_Silent_p.L813L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	813	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TGGAGATGCTCGGCATCTCAG	0.627													G|||	3427	0.684305	0.3888	0.7363	5008	,	,		17733	0.879		0.7217	False		,,,				2504	0.8078				p.L813L		Atlas-SNP	.											.	MYO18B	322	.	0			c.C2439G						PASS	.	G		1814,2106		426,962,572	53.0	55.0	55.0		2439	4.4	1.0	22	dbSNP_86	55	6105,2191		2248,1609,291	no	coding-synonymous	MYO18B	NM_032608.5		2674,2571,863	GG,GC,CC		26.4103,46.2755,35.1752		813/2568	26193982	7919,4297	1960	4148	6108	SO:0001819	synonymous_variant	84700	exon12			GATGCTCGGCATC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2439C>G	22.37:g.26193982C>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				C|0.318;G|0.682	0.682	strong		0.627	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
CIC	23152	hgsc.bcm.edu	37	19	42799049	42799049	+	Silent	SNP	C	C	T	rs1052023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:42799049C>T	ENST00000575354.2	+	20	4573	c.4533C>T	c.(4531-4533)atC>atT	p.I1511I	CIC_ENST00000572681.2_Silent_p.I2417I|CIC_ENST00000160740.3_Silent_p.I1509I	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				AGTTGAAGATCCGTGAGGTGC	0.627			"""Mis, F, S"""		oligodendroglioma								C|||	600	0.119808	0.0106	0.1945	5008	,	,		14163	0.0		0.3907	False		,,,				2504	0.0593				p.I1511I		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.C4533T						PASS	.	C		339,4067	173.0+/-202.9	15,309,1879	53.0	53.0	53.0		4533	3.4	1.0	19	dbSNP_86	53	3246,5354	475.6+/-369.2	620,2006,1674	no	coding-synonymous	CIC	NM_015125.3		635,2315,3553	TT,TC,CC		37.7442,7.6941,27.5642		1511/1609	42799049	3585,9421	2203	4300	6503	SO:0001819	synonymous_variant	23152	exon20			GAAGATCCGTGAG	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4533C>T	19.37:g.42799049C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Silent	SNP	ENST00000575354.2	37	CCDS12601.1																																																																																			C|0.756;T|0.244	0.244	strong		0.627	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
TMEM194B	100131211	hgsc.bcm.edu	37	2	191379211	191379211	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:191379211G>A	ENST00000409150.3	-	7	987	c.921C>T	c.(919-921)caC>caT	p.H307H		NM_001142645.1	NP_001136117.1	A6NFY4	T194B_HUMAN	transmembrane protein 194B	307						integral component of membrane (GO:0016021)											TCAGTGGGTAGTGCAGACTCC	0.478																																					p.H307H		Atlas-SNP	.											TMEM194B_ENST00000409150,NS,carcinoma,-2,2	TMEM194B	18	2	0			c.C921T						scavenged	.						39.0	38.0	39.0					2																	191379211		692	1591	2283	SO:0001819	synonymous_variant	100131211	exon7			TGGGTAGTGCAGA		CCDS46476.1	2q32.2	2008-06-10			ENSG00000189362	ENSG00000189362			33700	protein-coding gene	gene with protein product							Standard	NM_001142645		Approved		uc010zgf.2	A6NFY4	OTTHUMG00000154454	ENST00000409150.3:c.921C>T	2.37:g.191379211G>A		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	360	4	0.0111111	NM_001142645	B4DYG6	Silent	SNP	ENST00000409150.3	37	CCDS46476.1																																																																																			.	.	none		0.478	TMEM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335299.1	XM_001723498	
MPPED2	744	hgsc.bcm.edu	37	11	30433028	30433028	+	Missense_Mutation	SNP	G	G	A	rs146268212		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:30433028G>A	ENST00000358117.5	-	6	994	c.872C>T	c.(871-873)cCa>cTa	p.P291L	MPPED2_ENST00000524667.1_5'UTR|MPPED2_ENST00000448418.2_Intron	NM_001584.2	NP_001575.1	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	291					nervous system development (GO:0007399)		hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(15)|skin(2)|upper_aerodigestive_tract(2)	33						GGAACCCTGTGGGTTTGGAAG	0.418																																					p.P291L		Atlas-SNP	.											.	MPPED2	106	.	0			c.C872T						PASS	.	G	,LEU/PRO	0,4404		0,0,2202	112.0	97.0	102.0		,872	5.6	1.0	11	dbSNP_134	102	1,8597	1.2+/-3.3	0,1,4298	no	intron,missense	MPPED2	NM_001145399.1,NM_001584.2	,98	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	,probably-damaging	,291/295	30433028	1,13001	2202	4299	6501	SO:0001583	missense	744	exon6			CCCTGTGGGTTTG	U57911	CCDS7870.1, CCDS44560.1	11p13	2008-07-18	2005-10-10	2005-10-10	ENSG00000066382	ENSG00000066382			1180	protein-coding gene	gene with protein product		600911	"""chromosome 11 open reading frame 8"""	C11orf8		8666403, 9266672	Standard	NM_001584		Approved	239FB, D11S302E, Hs.46638, FAM1B, dJ873F21.1, dJ1024C24.1	uc001msr.3	Q15777	OTTHUMG00000166159	ENST00000358117.5:c.872C>T	11.37:g.30433028G>A	ENSP00000350833:p.Pro291Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_001584	D3DQZ5|E9PB10|Q59GE6	Missense_Mutation	SNP	ENST00000358117.5	37	CCDS7870.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376204	0.82682	0.0	1.16E-4	ENSG00000066382	ENST00000358117	T	0.51325	0.71	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74352	-0.3693	10	0.52906	T	0.07	-7.0431	19.8808	0.96899	0.0:0.0:1.0:0.0	.	291	Q15777	MPPD2_HUMAN	L	291	ENSP00000350833:P291L	ENSP00000350833:P291L	P	-	2	0	MPPED2	30389604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.771000	0.95319	0.561000	0.74099	CCA	G|1.000;A|0.000	0.000	weak		0.418	MPPED2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388155.2	NM_001584	
UCK1	83549	hgsc.bcm.edu	37	9	134406071	134406071	+	Intron	SNP	C	C	G	rs7867616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:134406071C>G	ENST00000372215.4	-	2	202				UCK1_ENST00000459858.1_Intron|UCK1_ENST00000372208.3_Intron|UCK1_ENST00000372210.3_Intron|UCK1_ENST00000372211.3_Missense_Mutation_p.E29Q	NM_001261450.1|NM_001261451.1|NM_031432.2	NP_001248379.1|NP_001248380.1|NP_113620.1	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1						CTP salvage (GO:0044211)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		TGGAACCGCTCGTCCTGTGAC	0.642													C|||	4318	0.86222	0.6785	0.8905	5008	,	,		13852	0.999		0.838	False		,,,				2504	0.9744				p.E29Q	Melanoma(42;523 1129 28385 43975 48113)	Atlas-SNP	.											.	UCK1	29	.	0			c.G85C						PASS	.		,	3136,1270	701.7+/-406.8	1119,898,186	66.0	62.0	64.0		,	2.6	0.0	9	dbSNP_116	64	7419,1181	764.5+/-407.6	3196,1027,77	no	intron,intron	UCK1	NM_001135954.1,NM_031432.2	,	4315,1925,263	GG,GC,CC		13.7326,28.8243,18.8451	,	,	134406071	10555,2451	2203	4300	6503	SO:0001627	intron_variant	83549	exon2			ACCGCTCGTCCTG	AF237290	CCDS6944.1, CCDS48046.1, CCDS59151.1, CCDS59152.1	9q34.1	2008-02-05			ENSG00000130717	ENSG00000130717	2.7.1.48		14859	protein-coding gene	gene with protein product		609328				11306702	Standard	NM_031432		Approved	URK1, FLJ12255	uc031tfj.1	Q9HA47	OTTHUMG00000020823	ENST00000372215.4:c.109-39G>C	9.37:g.134406071C>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001261451	Q5JT09|Q5JT10|Q5JT12|Q5JT13|Q6IA74|Q96BJ0	Missense_Mutation	SNP	ENST00000372215.4	37	CCDS6944.1	1865	0.8539377289377289	340	0.6910569105691057	315	0.8701657458563536	571	0.9982517482517482	639	0.8430079155672823	c	9.202	1.028618	0.19512	0.711757	0.862674	ENSG00000130717	ENST00000372211	.	.	.	3.49	2.57	0.30868	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.399999999995849E-5	.	.	.	.	.	.	T	0.27434	-1.0074	3	.	.	.	-5.1104	8.773	0.34745	0.0:0.7667:0.2333:0.0	rs7867616;rs59415928	.	.	.	Q	29	.	.	E	-	1	0	UCK1	133395892	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.335000	0.19806	0.432000	0.26286	-0.455000	0.05494	GAG	C|0.139;G|0.861	0.861	strong		0.642	UCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054726.1	NM_031432	
OR51I1	390063	hgsc.bcm.edu	37	11	5461991	5461991	+	Missense_Mutation	SNP	C	C	A	rs1498486	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5461991C>A	ENST00000380211.1	-	1	753	c.754G>T	c.(754-756)Gcc>Tcc	p.A252S	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	252			A -> S (in dbSNP:rs1498486).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACATAAAAGGCCAGCACTGCA	0.488													C|||	1519	0.303315	0.1437	0.464	5008	,	,		22186	0.1319		0.5368	False		,,,				2504	0.3415				p.A252S		Atlas-SNP	.											OR51I1,colon,carcinoma,+1,1	OR51I1	66	1	0			c.G754T						PASS	.	C	SER/ALA	890,3512	343.3+/-307.6	103,684,1414	125.0	107.0	113.0		754	1.5	0.3	11	dbSNP_88	113	4696,3898	607.0+/-395.2	1286,2124,887	yes	missense	OR51I1	NM_001005288.2	99	1389,2808,2301	AA,AC,CC		45.3572,20.2181,42.9825	possibly-damaging	252/315	5461991	5586,7410	2201	4297	6498	SO:0001583	missense	390063	exon1			AAAAGGCCAGCAC	BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"""GPCR / Class A : Olfactory receptors"""	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.754G>T	11.37:g.5461991C>A	ENSP00000369559:p.Ala252Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	775	0.35485347985347987	102	0.2073170731707317	157	0.43370165745856354	80	0.13986013986013987	436	0.575197889182058	C	16.14	3.039566	0.55003	0.202181	0.546428	ENSG00000167359	ENST00000321307;ENST00000380211	T	0.00158	8.65	5.47	1.46	0.22682	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000035	T	0.00012	0.0000	L	0.53617	1.68	0.80722	P	0.0	P	0.48016	0.904	P	0.45998	0.5	T	0.00000	-1.2890	9	0.66056	D	0.02	.	7.2519	0.26154	0.0:0.5395:0.0:0.4605	rs1498486;rs17294756;rs52805577;rs61686769;rs1498486	252	Q9H343	O51I1_HUMAN	S	249;252	ENSP00000369559:A252S	ENSP00000439622:A249S	A	-	1	0	OR51I1	5418567	0.000000	0.05858	0.258000	0.24420	0.973000	0.67179	-0.682000	0.05185	0.682000	0.31407	0.551000	0.68910	GCC	C|0.614;A|0.386	0.386	strong		0.488	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288	
GPR157	80045	hgsc.bcm.edu	37	1	9165669	9165669	+	Missense_Mutation	SNP	G	G	A	rs12075362	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:9165669G>A	ENST00000377411.4	-	3	810	c.668C>T	c.(667-669)gCg>gTg	p.A223V	GPR157_ENST00000414642.2_Intron	NM_024980.4	NP_079256.4	Q5UAW9	GP157_HUMAN	G protein-coupled receptor 157	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(4)|prostate(1)	5	all_lung(157;0.185)	all_epithelial(116;5.02e-20)|all_lung(118;3.6e-06)|Lung NSC(185;7.93e-06)|Renal(390;0.000147)|Breast(348;0.000688)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.16e-07)|COAD - Colon adenocarcinoma(227;7.73e-05)|Kidney(185;0.000252)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.00178)|BRCA - Breast invasive adenocarcinoma(304;0.00186)|READ - Rectum adenocarcinoma(331;0.0642)		CTTCTTGTCCGCCATGGAGGA	0.657													G|||	214	0.0427316	0.0923	0.0231	5008	,	,		20009	0.001		0.0278	False		,,,				2504	0.0481				p.A223V		Atlas-SNP	.											.	GPR157	14	.	0			c.C668T						PASS	.	G	VAL/ALA	387,4019	191.2+/-216.9	16,355,1832	66.0	61.0	63.0		668	3.9	0.3	1	dbSNP_120	63	379,8221	123.1+/-182.0	3,373,3924	no	missense	GPR157	NM_024980.4	64	19,728,5756	AA,AG,GG		4.407,8.7835,5.8896	probably-damaging	223/336	9165669	766,12240	2203	4300	6503	SO:0001583	missense	80045	exon3			TTGTCCGCCATGG	AK022194	CCDS100.2	1p36.22	2012-08-21			ENSG00000180758	ENSG00000180758		"""GPCR / Class B : Orphans"""	23687	protein-coding gene	gene with protein product						10574461	Standard	XM_005263496		Approved	FLJ12132	uc001apq.1	Q5UAW9	OTTHUMG00000001758	ENST00000377411.4:c.668C>T	1.37:g.9165669G>A	ENSP00000366628:p.Ala223Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	208	118	0.567308	NM_024980	A2A334|Q8WWB8|Q9HA73	Missense_Mutation	SNP	ENST00000377411.4	37	CCDS100.2	67	0.030677655677655676	36	0.07317073170731707	9	0.024861878453038673	2	0.0034965034965034965	20	0.026385224274406333	G	17.41	3.382146	0.61845	0.087835	0.04407	ENSG00000180758	ENST00000377411	T	0.37752	1.18	4.82	3.91	0.45181	GPCR, family 2-like (1);	0.099178	0.64402	D	0.000002	T	0.02119	0.0066	L	0.48986	1.54	0.80722	D	1	D	0.63046	0.992	P	0.53313	0.723	T	0.00270	-1.1860	10	0.66056	D	0.02	-9.6716	12.4347	0.55593	0.082:0.0:0.918:0.0	rs12075362	223	Q5UAW9	GP157_HUMAN	V	223	ENSP00000366628:A223V	ENSP00000366628:A223V	A	-	2	0	GPR157	9088256	1.000000	0.71417	0.310000	0.25168	0.138000	0.21146	6.935000	0.75886	1.180000	0.42898	0.549000	0.68633	GCG	G|0.949;A|0.051	0.051	strong		0.657	GPR157-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127658.2	NM_024980	
SPTBN5	51332	hgsc.bcm.edu	37	15	42160635	42160635	+	Silent	SNP	C	C	G	rs2290556	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42160635C>G	ENST00000320955.6	-	33	6245	c.6018G>C	c.(6016-6018)ggG>ggC	p.G2006G	MIR4310_ENST00000582950.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2006					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GTGCCTGCTGCCCCAGCTGGG	0.687													G|||	293	0.0585064	0.0416	0.0576	5008	,	,		15754	0.0159		0.0547	False		,,,				2504	0.1299				p.G1971G		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G5913C						PASS	.	G		131,3825		3,125,1850	15.0	19.0	18.0		5913	-1.3	1.0	15	dbSNP_100	18	410,7880		13,384,3748	no	coding-synonymous	SPTBN5	NM_016642.2		16,509,5598	GG,GC,CC		4.9457,3.3114,4.4178		1971/3640	42160635	541,11705	1978	4145	6123	SO:0001819	synonymous_variant	51332	exon33			CTGCTGCCCCAGC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.6018G>C	15.37:g.42160635C>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	153	67	0.437909	NM_016642		Silent	SNP	ENST00000320955.6	37																																																																																				C|0.939;G|0.061	0.061	strong		0.687	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
ABCF2	10061	hgsc.bcm.edu	37	7	150916228	150916228	+	Silent	SNP	G	G	A	rs6949587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150916228G>A	ENST00000287844.2	-	8	1048	c.939C>T	c.(937-939)taC>taT	p.Y313Y	ABCF2_ENST00000473874.1_5'UTR|ABCF2_ENST00000222388.2_Silent_p.Y313Y	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	313	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCGTCTTCACGTACTGATCAT	0.498													G|||	2100	0.419329	0.2095	0.4107	5008	,	,		19404	0.7202		0.4563	False		,,,				2504	0.3609				p.Y313Y		Atlas-SNP	.											.	ABCF2	54	.	0			c.C939T						PASS	.	G	,	992,3414	368.8+/-318.8	111,770,1322	173.0	151.0	158.0		939,939	0.3	1.0	7	dbSNP_116	158	3537,5063	514.7+/-378.4	717,2103,1480	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	828,2873,2802	AA,AG,GG		41.1279,22.5148,34.8224	,	313/635,313/624	150916228	4529,8477	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon8			CTTCACGTACTGA	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"""ATP binding cassette transporters / subfamily F"""	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.939C>T	7.37:g.150916228G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			G|0.611;A|0.389	0.389	strong		0.498	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
MUC4	4585	hgsc.bcm.edu	37	3	195505851	195505851	+	Silent	SNP	T	T	C	rs200522168		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195505851T>C	ENST00000463781.3	-	2	13059	c.12600A>G	c.(12598-12600)tcA>tcG	p.S4200S	MUC4_ENST00000475231.1_Silent_p.S4200S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGTGGATGCTGAGGAAGTGT	0.592																																					p.S4200S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.A12600G						scavenged	.						18.0	14.0	15.0					3																	195505851		689	1574	2263	SO:0001819	synonymous_variant	4585	exon2			GGATGCTGAGGAA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12600A>G	3.37:g.195505851T>C		Somatic	247	4	0.0161943		WXS	Illumina HiSeq	Phase_I	233	38	0.16309	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR52L1	338751	hgsc.bcm.edu	37	11	6007613	6007613	+	Missense_Mutation	SNP	T	T	G	rs4354673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6007613T>G	ENST00000332249.4	-	1	602	c.548A>C	c.(547-549)aAa>aCa	p.K183T		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	183			K -> T (in dbSNP:rs4354673). {ECO:0000269|PubMed:14983052, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAAGATAAGTTTTCCCAACAA	0.483													.|||	3567	0.71226	0.4206	0.8228	5008	,	,		24224	0.8671		0.8171	False		,,,				2504	0.7607				p.K183T	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.A548C						PASS	.	T	THR/LYS	2069,1943		545,979,482	104.0	98.0	100.0		548	-0.2	0.0	11	dbSNP_111	100	6594,1732		2616,1362,185	yes	missense	OR52L1	NM_001005173.2	78	3161,2341,667	GG,GT,TT		20.8023,48.4297,29.786	benign	183/330	6007613	8663,3675	2006	4163	6169	SO:0001583	missense	338751	exon1			ATAAGTTTTCCCA	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.548A>C	11.37:g.6007613T>G	ENSP00000330338:p.Lys183Thr	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	256	255	0.996094	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	1638	0.75	217	0.4410569105691057	293	0.8093922651933702	511	0.8933566433566433	617	0.8139841688654353	T	4.518	0.096072	0.08681	0.515703	0.791977	ENSG00000183313	ENST00000332249	T	0.00123	8.7	3.73	-0.167	0.13347	GPCR, rhodopsin-like superfamily (1);	1.557440	0.03930	N	0.285183	T	0.00012	0.0000	N	0.25485	0.75	0.80722	P	0.0	P	0.36354	0.549	B	0.31946	0.138	T	0.27905	-1.0060	9	0.66056	D	0.02	.	7.7071	0.28657	0.0:0.4907:0.0:0.5093	rs4354673;rs61105290;rs4354673	183	Q8NGH7	O52L1_HUMAN	T	183	ENSP00000330338:K183T	ENSP00000330338:K183T	K	-	2	0	OR52L1	5964189	0.000000	0.05858	0.001000	0.08648	0.206000	0.24218	-0.099000	0.11007	0.004000	0.14682	0.260000	0.18958	AAA	T|0.269;G|0.731	0.731	strong		0.483	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
ZUFSP	221302	hgsc.bcm.edu	37	6	116973182	116973182	+	Missense_Mutation	SNP	T	T	C	rs4946188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116973182T>C	ENST00000368576.3	-	6	1378	c.1135A>G	c.(1135-1137)Aac>Gac	p.N379D	ZUFSP_ENST00000368573.1_3'UTR|ZUFSP_ENST00000471919.1_5'UTR	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	379			N -> D (in dbSNP:rs4946188). {ECO:0000269|PubMed:14702039}.				metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		AAGCAATCGTTGTAAGCATCA	0.323													C|||	2030	0.405351	0.5076	0.4928	5008	,	,		19570	0.3056		0.2932	False		,,,				2504	0.4233				p.N379D		Atlas-SNP	.											ZUFSP,NS,carcinoma,0,1	ZUFSP	46	1	0			c.A1135G						PASS	.	C	ASP/ASN	2088,2318	603.5+/-390.1	475,1138,590	117.0	121.0	120.0		1135	1.5	0.4	6	dbSNP_111	120	2404,6196	699.1+/-405.1	321,1762,2217	yes	missense	ZUFSP	NM_145062.2	23	796,2900,2807	CC,CT,TT		27.9535,47.3899,34.5379	benign	379/579	116973182	4492,8514	2203	4300	6503	SO:0001583	missense	221302	exon6			AATCGTTGTAAGC	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"""Zinc fingers, C2H2-type"""	21224	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 113"""	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.1135A>G	6.37:g.116973182T>C	ENSP00000357565:p.Asn379Asp	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation	SNP	ENST00000368576.3	37	CCDS5110.1	807	0.3695054945054945	242	0.491869918699187	164	0.4530386740331492	172	0.3006993006993007	229	0.3021108179419525	C	3.231	-0.157533	0.06544	0.473899	0.279535	ENSG00000153975	ENST00000368576	T	0.41400	1.0	5.83	1.52	0.23074	.	0.579616	0.20593	N	0.089307	T	0.07098	0.0180	N	0.19112	0.55	0.43304	P	0.004693999999999976	B	0.02656	0.0	B	0.06405	0.002	T	0.32798	-0.9893	9	0.08837	T	0.75	6.0687	5.3231	0.15891	0.0:0.2902:0.1594:0.5504	rs4946188;rs52824326;rs57266096;rs4946188	379	Q96AP4	ZUFSP_HUMAN	D	379	ENSP00000357565:N379D	ENSP00000357565:N379D	N	-	1	0	ZUFSP	117079875	0.957000	0.32711	0.356000	0.25785	0.915000	0.54546	0.628000	0.24522	0.108000	0.17862	-0.757000	0.03467	AAC	T|0.640;C|0.360	0.360	strong		0.323	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062	
OCEL1	79629	hgsc.bcm.edu	37	19	17337928	17337928	+	Silent	SNP	C	C	T	rs1045201	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17337928C>T	ENST00000215061.4	+	3	416	c.372C>T	c.(370-372)gcC>gcT	p.A124A	OCEL1_ENST00000597836.1_Silent_p.A68A|OCEL1_ENST00000601576.1_3'UTR|OCEL1_ENST00000601529.1_Silent_p.A124A	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	124										central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						TCTCCCAGGCCCTCCTGGGCG	0.612													C|||	397	0.0792732	0.1203	0.0879	5008	,	,		14459	0.001		0.0775	False		,,,				2504	0.1002				p.A124A		Atlas-SNP	.											OCEL1,colon,carcinoma,0,1	OCEL1	20	1	0			c.C372T						scavenged	.	C		484,3922	224.6+/-240.7	27,430,1746	68.0	79.0	75.0		372	-5.0	0.0	19	dbSNP_86	75	674,7926	168.3+/-219.8	22,630,3648	no	coding-synonymous	OCEL1	NM_024578.1		49,1060,5394	TT,TC,CC		7.8372,10.985,8.9036		124/265	17337928	1158,11848	2203	4300	6503	SO:0001819	synonymous_variant	79629	exon3			CCAGGCCCTCCTG	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.372C>T	19.37:g.17337928C>T		Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_024578		Silent	SNP	ENST00000215061.4	37	CCDS12351.1																																																																																			C|0.914;T|0.086	0.086	strong		0.612	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578	
NPBWR2	2832	hgsc.bcm.edu	37	20	62737537	62737537	+	Silent	SNP	C	C	A	rs4809400	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62737537C>A	ENST00000369768.1	-	1	987	c.648G>T	c.(646-648)acG>acT	p.T216T		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	216					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					CCAGGACCAACGTGTAGACAC	0.652													C|||	425	0.0848642	0.0189	0.0893	5008	,	,		20635	0.0823		0.1362	False		,,,				2504	0.1207				p.T216T		Atlas-SNP	.											.	NPBWR2	36	.	0			c.G648T						PASS	.	C		148,4256	100.3+/-138.9	2,144,2056	58.0	50.0	52.0		648	-7.8	0.0	20	dbSNP_111	52	1022,7558	214.3+/-254.0	60,902,3328	no	coding-synonymous	NPBWR2	NM_005286.2		62,1046,5384	AA,AC,CC		11.9114,3.3606,9.0111		216/334	62737537	1170,11814	2202	4290	6492	SO:0001819	synonymous_variant	2832	exon1			GACCAACGTGTAG	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4530	protein-coding gene	gene with protein product		600731	"""G protein-coupled receptor 8"""	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.648G>T	20.37:g.62737537C>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_005286	Q6NWQ6|Q9H4K3	Silent	SNP	ENST00000369768.1	37	CCDS13557.1																																																																																			C|0.908;A|0.092	0.092	strong		0.652	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286	
MEOX1	4222	hgsc.bcm.edu	37	17	41738823	41738823	+	Missense_Mutation	SNP	G	G	A	rs9898682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41738823G>A	ENST00000318579.4	-	1	499	c.80C>T	c.(79-81)tCg>tTg	p.S27L	MEOX1_ENST00000393661.2_Intron|MEOX1_ENST00000549132.1_5'UTR|MEOX1_ENST00000329168.3_Missense_Mutation_p.S27L	NM_001040002.1|NM_004527.3	NP_001035091.1|NP_004518.1	P50221	MEOX1_HUMAN	mesenchyme homeobox 1	27			S -> L (in dbSNP:rs9898682).		multicellular organismal development (GO:0007275)|somite specification (GO:0001757)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		ATTGCCTTCCGAGTGGGGGTT	0.672													G|||	670	0.133786	0.3578	0.0749	5008	,	,		9828	0.001		0.0855	False		,,,				2504	0.0593				p.S27L		Atlas-SNP	.											MEOX1,NS,carcinoma,0,1	MEOX1	29	1	0			c.C80T						scavenged	.	G	,LEU/SER,LEU/SER	1313,3039		177,959,1040	15.0	20.0	18.0		,80,80	4.7	0.9	17	dbSNP_119	18	857,7663		47,763,3450	yes	intron,missense,missense	MEOX1	NM_001040002.1,NM_004527.3,NM_013999.3	,145,145	224,1722,4490	AA,AG,GG		10.0587,30.17,16.8583	,benign,benign	,27/255,27/185	41738823	2170,10702	2176	4260	6436	SO:0001583	missense	4222	exon1			CCTTCCGAGTGGG		CCDS11466.1, CCDS11467.1, CCDS42343.1	17q21.31	2014-07-15	2005-12-22					"""Homeoboxes / ANTP class : HOXL subclass"""	7013	protein-coding gene	gene with protein product		600147	"""mesenchyme homeo box 1"""			7987315	Standard	NM_013999		Approved	MOX1	uc002idz.3	P50221	OTTHUMG00000170513	ENST00000318579.4:c.80C>T	17.37:g.41738823G>A	ENSP00000321684:p.Ser27Leu	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_004527	A8K524|A8MWF9|Q15069	Missense_Mutation	SNP	ENST00000318579.4	37	CCDS11466.1	240	0.10989010989010989	145	0.29471544715447157	29	0.08011049723756906	1	0.0017482517482517483	65	0.08575197889182058	G	16.82	3.229159	0.58777	0.3017	0.100587	ENSG00000005102	ENST00000318579;ENST00000329168	D;T	0.91686	-2.89;0.4	4.68	4.68	0.58851	.	0.077195	0.52532	D	0.000069	T	0.00039	0.0001	L	0.50333	1.59	0.21802	P	0.999531407	P;P	0.50066	0.931;0.713	P;B	0.44597	0.454;0.116	T	0.00000	-1.3094	9	0.72032	D	0.01	-16.3974	15.5634	0.76269	0.0:0.0:1.0:0.0	rs9898682;rs58352701;rs9898682	27;27	Q15069;P50221	.;MEOX1_HUMAN	L	27	ENSP00000321684:S27L;ENSP00000328678:S27L	ENSP00000321684:S27L	S	-	2	0	MEOX1	39094349	0.687000	0.27671	0.924000	0.36721	0.802000	0.45316	3.961000	0.56759	2.430000	0.82344	0.563000	0.77884	TCG	G|0.889;A|0.111	0.111	strong		0.672	MEOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409452.1		
GRAMD3	65983	hgsc.bcm.edu	37	5	125802027	125802027	+	Intron	SNP	G	G	A	rs62394179	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:125802027G>A	ENST00000285689.3	+	2	664				GRAMD3_ENST00000544396.1_Intron|GRAMD3_ENST00000543198.1_Splice_Site_p.R82K|RP11-517I3.1_ENST00000512779.1_RNA|GRAMD3_ENST00000514932.1_Intron|GRAMD3_ENST00000542322.1_Splice_Site_p.E76K|GRAMD3_ENST00000515200.1_Splice_Site_p.R82K|GRAMD3_ENST00000502348.1_Intron|GRAMD3_ENST00000511134.1_Intron|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000513040.1_Intron	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3							cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		TCAGGACCAAGAGTAAGTCTT	0.408													G|||	932	0.186102	0.2436	0.1772	5008	,	,		19851	0.1399		0.2664	False		,,,				2504	0.0798				p.E76K		Atlas-SNP	.											.	GRAMD3	30	.	0			c.G226A						PASS	.	G	,,LYS/GLU,,	334,1050		37,260,395	222.0	168.0	185.0		,,226,,	2.5	0.0	5	dbSNP_129	185	819,2363		93,633,865	yes	intron,intron,missense-near-splice,intron,intron	GRAMD3	NM_001146319.1,NM_001146320.1,NM_001146321.1,NM_001146322.1,NM_023927.2	,,56,,	130,893,1260	AA,AG,GG		25.7385,24.1329,25.2519	,,,,	,,76/441,,	125802027	1153,3413	692	1591	2283	SO:0001627	intron_variant	65983	exon3			GACCAAGAGTAAG	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.203+790G>A	5.37:g.125802027G>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	213	109	0.511737	NM_001146321	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	37	CCDS4136.1	462|462	0.21153846153846154|0.21153846153846154	107|107	0.21747967479674796|0.21747967479674796	81|81	0.22375690607734808|0.22375690607734808	83|83	0.1451048951048951|0.1451048951048951	191|191	0.2519788918205805|0.2519788918205805	G|G	3.980|3.980	-0.006697|-0.006697	0.07773|0.07773	0.241329|0.241329	0.257385|0.257385	ENSG00000155324|ENSG00000155324	ENST00000542322|ENST00000515200;ENST00000543198	T|T;T	0.32272|0.28454	1.46|1.61;1.61	3.42|3.42	2.54|2.54	0.30619|0.30619	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	1.999999999946489E-6|1.999999999946489E-6	B|.	0.16166|.	0.016|.	B|.	0.10450|.	0.005|.	T|T	0.36456|0.36456	-0.9747|-0.9747	6|5	.|0.07482	.|T	.|0.82	.|.	6.5573|6.5573	0.22468|0.22468	0.1315:0.0:0.8685:0.0|0.1315:0.0:0.8685:0.0	rs62394179|rs62394179	76|.	B7Z3R1|.	.|.	K|K	76|82	ENSP00000441876:E76K|ENSP00000426143:R82K;ENSP00000442902:R82K	.|ENSP00000421494:R82K	E|R	+|+	1|2	0|0	GRAMD3|GRAMD3	125829926|125829926	0.224000|0.224000	0.23674|0.23674	0.006000|0.006000	0.13384|0.13384	0.588000|0.588000	0.36517|0.36517	0.739000|0.739000	0.26173|0.26173	1.027000|1.027000	0.39758|0.39758	0.609000|0.609000	0.83330|0.83330	GAG|AGA	G|0.787;A|0.213	0.213	strong		0.408	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927	
SLC13A5	284111	hgsc.bcm.edu	37	17	6599095	6599095	+	Silent	SNP	G	G	A	rs56224509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6599095G>A	ENST00000433363.2	-	7	1238	c.1005C>T	c.(1003-1005)ccC>ccT	p.P335P	SLC13A5_ENST00000381074.4_Silent_p.P292P|SLC13A5_ENST00000293800.6_Silent_p.P318P|SLC13A5_ENST00000573648.1_Silent_p.P335P	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5	335					transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						GCATGAAGCCGGGGTCTCGGG	0.587													G|||	184	0.0367412	0.0212	0.0432	5008	,	,		19160	0.001		0.0835	False		,,,				2504	0.0419				p.P335P		Atlas-SNP	.											.	SLC13A5	57	.	0			c.C1005T						PASS	.	G	,	161,4245	110.4+/-148.6	1,159,2043	106.0	111.0	109.0		1005,1005	-10.6	0.1	17	dbSNP_129	109	777,7823	183.2+/-231.5	40,697,3563	no	coding-synonymous,coding-synonymous	SLC13A5	NM_001143838.1,NM_177550.3	,	41,856,5606	AA,AG,GG		9.0349,3.6541,7.2121	,	335/523,335/569	6599095	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	284111	exon7			GAAGCCGGGGTCT	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"""Solute carriers"""	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.1005C>T	17.37:g.6599095G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	167	88	0.526946	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Silent	SNP	ENST00000433363.2	37	CCDS11079.1																																																																																			G|0.937;A|0.063	0.063	strong		0.587	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550	
ITPR3	3710	hgsc.bcm.edu	37	6	33659472	33659472	+	Missense_Mutation	SNP	C	C	G	rs2229642	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33659472C>G	ENST00000374316.5	+	54	8366	c.7306C>G	c.(7306-7308)Ctc>Gtc	p.L2436V	ITPR3_ENST00000605930.1_Missense_Mutation_p.L2436V			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2436			L -> V (in dbSNP:rs2229642). {ECO:0000269|PubMed:8081734}.		activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TGTCTCAGGGCTCTCGGTGCC	0.627													G|||	2903	0.579673	0.2156	0.6138	5008	,	,		20079	0.8998		0.4851	False		,,,				2504	0.8149				p.L2436V		Atlas-SNP	.											.	ITPR3	409	.	0			c.C7306G						PASS	.	G	VAL/LEU	1356,3050	691.6+/-405.4	202,952,1049	149.0	109.0	123.0		7306	2.0	0.0	6	dbSNP_98	123	3956,4644	602.3+/-394.5	960,2036,1304	yes	missense	ITPR3	NM_002224.3	32	1162,2988,2353	GG,GC,CC		46.0,30.7762,40.8427	benign	2436/2672	33659472	5312,7694	2203	4300	6503	SO:0001583	missense	3710	exon53			TCAGGGCTCTCGG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.7306C>G	6.37:g.33659472C>G	ENSP00000363435:p.Leu2436Val	Somatic	347	0	0		WXS	Illumina HiSeq	Phase_I	384	383	0.997396	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	1217	0.5572344322344323	116	0.23577235772357724	224	0.6187845303867403	506	0.8846153846153846	371	0.4894459102902375	G	0.015	-1.540438	0.00934	0.307762	0.46	ENSG00000096433	ENST00000374316	D	0.91407	-2.84	5.24	2.02	0.26589	Ion transport (1);	0.995168	0.08159	N	0.988773	T	0.63721	0.2535	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.40869	-0.9540	9	0.25106	T	0.35	-40.2093	3.5621	0.07887	0.3436:0.1909:0.4655:0.0	rs2229642;rs3818522;rs11553151;rs17586191;rs52808083;rs57893350;rs2229642	2436;2106	Q14573;Q59ES2	ITPR3_HUMAN;.	V	2436	ENSP00000363435:L2436V	ENSP00000363435:L2436V	L	+	1	0	ITPR3	33767450	0.290000	0.24343	0.004000	0.12327	0.048000	0.14542	0.566000	0.23593	0.331000	0.23511	-0.216000	0.12614	CTC	C|0.521;G|0.478	0.478	strong		0.627	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
PRIMPOL	201973	hgsc.bcm.edu	37	4	185615764	185615764	+	Missense_Mutation	SNP	C	C	A	rs14969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:185615764C>A	ENST00000314970.6	+	14	1947	c.1514C>A	c.(1513-1515)aCa>aAa	p.T505K	PRIMPOL_ENST00000515774.1_Missense_Mutation_p.T376K|PRIMPOL_ENST00000503752.1_Missense_Mutation_p.T505K|PRIMPOL_ENST00000510864.1_3'UTR|PRIMPOL_ENST00000512834.1_Missense_Mutation_p.T504K	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	505	Interaction with RPA1.		T -> K (in dbSNP:rs14969).		mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										AGGCTGTCAACAGGTGCATCT	0.413													C|||	733	0.146366	0.3011	0.1369	5008	,	,		20112	0.001		0.1481	False		,,,				2504	0.092				p.T505K		Atlas-SNP	.											.	CCDC111	43	.	0			c.C1514A						PASS	.	C	,LYS/THR	1220,3186	421.3+/-339.3	165,890,1148	97.0	100.0	99.0		,1514	0.0	0.0	4	dbSNP_52	99	1407,7193	271.1+/-289.3	117,1173,3010	yes	utr-3,missense	MLF1IP,CCDC111	NM_024629.3,NM_152683.2	,78	282,2063,4158	AA,AC,CC		16.3605,27.6895,20.1984	,benign	,505/561	185615764	2627,10379	2203	4300	6503	SO:0001583	missense	201973	exon14			TGTCAACAGGTGC	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.1514C>A	4.37:g.185615764C>A	ENSP00000313816:p.Thr505Lys	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	218	105	0.481651	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Missense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	313	0.1433150183150183	151	0.30691056910569103	57	0.1574585635359116	0	0.0	105	0.13852242744063326	C	0.026	-1.374732	0.01214	0.276895	0.163605	ENSG00000164306	ENST00000314970;ENST00000515774;ENST00000503752;ENST00000512834	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	4.37	-0.00219	0.14031	.	2.209650	0.01988	N	0.045328	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35943	-0.9768	9	0.12430	T	0.62	-9.0119	4.1821	0.10380	0.1577:0.4244:0.3259:0.092	rs14969;rs3184981;rs58650800;rs14969	376;505;504	D3DP56;Q96LW4;D6RDM1	.;CC111_HUMAN;.	K	505;376;505;504	ENSP00000313816:T505K;ENSP00000421913:T376K;ENSP00000420860:T505K;ENSP00000425316:T504K	ENSP00000313816:T505K	T	+	2	0	CCDC111	185852758	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	-0.366000	0.07563	0.055000	0.16094	-0.226000	0.12346	ACA	C|0.824;A|0.176	0.176	strong		0.413	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
STKLD1	169436	hgsc.bcm.edu	37	9	136268912	136268912	+	Silent	SNP	A	A	G	rs28510482	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136268912A>G	ENST00000371957.3	+	15	1670	c.1563A>G	c.(1561-1563)gcA>gcG	p.A521A	C9orf96_ENST00000371955.1_Silent_p.A54A	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		521							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GGGAAATGGCAGAAGCCAGCT	0.652													G|||	823	0.164337	0.2073	0.1715	5008	,	,		16710	0.0516		0.165	False		,,,				2504	0.2168				p.A521A		Atlas-SNP	.											.	C9orf96	77	.	0			c.A1563G						PASS	.	G		864,3542	741.0+/-411.2	92,680,1431	41.0	41.0	41.0		1563	-9.2	0.0	9	dbSNP_125	41	1517,7083	744.8+/-407.2	146,1225,2929	no	coding-synonymous	C9orf96	NM_153710.3		238,1905,4360	GG,GA,AA		17.6395,19.6096,18.3069		521/681	136268912	2381,10625	2203	4300	6503	SO:0001819	synonymous_variant	169436	exon15			AATGGCAGAAGCC																												ENST00000371957.3:c.1563A>G	9.37:g.136268912A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	37	CCDS35169.1																																																																																			A|0.830;G|0.170	0.170	strong		0.652	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
ACOX2	8309	hgsc.bcm.edu	37	3	58517520	58517520	+	Silent	SNP	A	A	G	rs57216393	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58517520A>G	ENST00000302819.5	-	6	894	c.603T>C	c.(601-603)caT>caC	p.H201H	ACOX2_ENST00000459701.2_Silent_p.H201H	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	201					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		GGACCAGGGCATGGGTGGCTG	0.627													G|||	355	0.0708866	0.2262	0.0375	5008	,	,		18088	0.0		0.0189	False		,,,				2504	0.0112				p.H201H		Atlas-SNP	.											.	ACOX2	53	.	0			c.T603C						PASS	.	G		884,3522	741.6+/-411.3	92,700,1411	59.0	53.0	55.0		603	-9.4	0.1	3	dbSNP_129	55	184,8416	810.9+/-407.1	3,178,4119	no	coding-synonymous	ACOX2	NM_003500.3		95,878,5530	GG,GA,AA		2.1395,20.0635,8.2116		201/682	58517520	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon6			CAGGGCATGGGTG	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.603T>C	3.37:g.58517520A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			A|0.923;G|0.077	0.077	strong		0.627	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
FAM177B	400823	hgsc.bcm.edu	37	1	222919895	222919895	+	Missense_Mutation	SNP	T	T	G	rs2378607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:222919895T>G	ENST00000445590.2	+	3	274	c.8T>G	c.(7-9)aTt>aGt	p.I3S	FAM177B_ENST00000360827.2_Missense_Mutation_p.I3S	NM_207468.2	NP_997351.2	A6PVY3	F177B_HUMAN	family with sequence similarity 177, member B	3			I -> S (in dbSNP:rs2378607).							breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	8						ATTATGGAGATTGACGGTTTC	0.378													T|||	2951	0.589257	0.2375	0.7378	5008	,	,		19808	0.7708		0.6998	False		,,,				2504	0.6585				p.I3S		Atlas-SNP	.											.	FAM177B	19	.	0			c.T8G						PASS	.	T	SER/ILE	1306,3100	439.4+/-345.7	216,874,1113	78.0	68.0	71.0		8	2.3	1.0	1	dbSNP_100	71	5820,2780	676.7+/-403.3	1987,1846,467	yes	missense	FAM177B	NM_207468.2	142	2203,2720,1580	GG,GT,TT		32.3256,29.6414,45.2099	benign	3/159	222919895	7126,5880	2203	4300	6503	SO:0001583	missense	400823	exon3			TGGAGATTGACGG	AK125494	CCDS1535.2	1q41	2008-08-08			ENSG00000197520	ENSG00000197520			34395	protein-coding gene	gene with protein product							Standard	NM_207468		Approved	RP11-452F19.2, FLJ43505	uc001hnt.3	A6PVY3	OTTHUMG00000037766	ENST00000445590.2:c.8T>G	1.37:g.222919895T>G	ENSP00000414451:p.Ile3Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_207468	Q6ZUN8	Missense_Mutation	SNP	ENST00000445590.2	37	CCDS1535.2	1384	0.6336996336996337	134	0.27235772357723576	258	0.712707182320442	462	0.8076923076923077	530	0.6992084432717678	t	6.577	0.474751	0.12521	0.296414	0.676744	ENSG00000197520	ENST00000434700;ENST00000445590;ENST00000360827;ENST00000456298	T;T;T;T	0.46063	0.89;1.44;1.44;0.88	4.67	2.3	0.28687	.	0.282386	0.24774	N	0.035708	T	0.00012	0.0000	N	0.22421	0.69	0.47778	P	4.870000000000152E-4	B	0.12630	0.006	B	0.12156	0.007	T	0.27640	-1.0068	9	0.15952	T	0.53	-8.5047	3.7419	0.08533	0.6941:0.0:0.1067:0.1992	rs2378607;rs17533190;rs2378607	3	A6PVY3	F177B_HUMAN	S	3	ENSP00000391615:I3S;ENSP00000414451:I3S;ENSP00000354070:I3S;ENSP00000400233:I3S	ENSP00000354070:I3S	I	+	2	0	FAM177B	220986518	1.000000	0.71417	0.985000	0.45067	0.786000	0.44442	1.053000	0.30442	0.167000	0.19631	-0.700000	0.03674	ATT	T|0.421;G|0.579	0.579	strong		0.378	FAM177B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092151.2	NM_207468	
RHOT2	89941	hgsc.bcm.edu	37	16	720986	720986	+	Missense_Mutation	SNP	G	G	A	rs1139897	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:720986G>A	ENST00000315082.4	+	10	848	c.734G>A	c.(733-735)cGg>cAg	p.R245Q		NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	245			R -> Q (in dbSNP:rs1139897). {ECO:0000269|PubMed:12482879}.		cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				CGGGAGGACCGGCTGACCCTG	0.692													G|||	1635	0.326478	0.0393	0.3646	5008	,	,		9342	0.6845		0.2575	False		,,,				2504	0.3896				p.R245Q		Atlas-SNP	.											.	RHOT2	35	.	0			c.G734A						PASS	.	G	GLN/ARG	294,4074		8,278,1898	28.0	29.0	28.0		734	2.1	0.1	16	dbSNP_86	28	1920,6668		209,1502,2583	no	missense	RHOT2	NM_138769.1	43	217,1780,4481	AA,AG,GG		22.3568,6.7308,17.0886	benign	245/619	720986	2214,10742	2184	4294	6478	SO:0001583	missense	89941	exon10			AGGACCGGCTGAC	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.734G>A	16.37:g.720986G>A	ENSP00000321971:p.Arg245Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Missense_Mutation	SNP	ENST00000315082.4	37	CCDS10417.1	752	0.3443223443223443	23	0.046747967479674794	130	0.35911602209944754	390	0.6818181818181818	209	0.2757255936675462	G	12.31	1.899957	0.33535	0.067308	0.223568	ENSG00000140983	ENST00000315082	T	0.10477	2.87	5.11	2.08	0.27032	EF hand associated, type-2 (1);EF-hand-like domain (1);	0.209202	0.49305	N	0.000152	T	0.00012	0.0000	N	0.12182	0.205	0.38701	P	0.04701299999999997	B;B	0.34329	0.449;0.027	B;B	0.26864	0.074;0.025	T	0.04165	-1.0972	9	0.66056	D	0.02	-14.1341	9.3233	0.37977	0.2389:0.0:0.7611:0.0	rs1139897;rs3743913;rs11557861;rs61475528;rs1139897	118;245	Q8IXI1-2;Q8IXI1	.;MIRO2_HUMAN	Q	245	ENSP00000321971:R245Q	ENSP00000321971:R245Q	R	+	2	0	RHOT2	660987	0.987000	0.35691	0.114000	0.21550	0.230000	0.25150	3.188000	0.50958	0.189000	0.20188	0.561000	0.74099	CGG	G|0.755;A|0.245	0.245	strong		0.692	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
SUN1	23353	hgsc.bcm.edu	37	7	897492	897492	+	Silent	SNP	A	A	G	rs10950789	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:897492A>G	ENST00000405266.1	+	14	1557	c.1533A>G	c.(1531-1533)acA>acG	p.T511T	SUN1_ENST00000452783.2_Silent_p.T371T|SUN1_ENST00000425407.2_Silent_p.T391T|SUN1_ENST00000413514.2_Silent_p.T272T|SUN1_ENST00000389574.3_Silent_p.T391T|SUN1_ENST00000401592.1_Silent_p.T474T|SUN1_ENST00000456758.2_Silent_p.T663T			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	501					cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TCCTGCCCACAGTCGAGCACC	0.567													G|||	2188	0.436901	0.5144	0.4669	5008	,	,		15932	0.4821		0.3479	False		,,,				2504	0.3558				p.T474T		Atlas-SNP	.											.	SUN1	157	.	0			c.A1422G						PASS	.	G	,,	2013,2181		509,995,593	168.0	182.0	178.0		1422,1113,1173	-6.4	0.0	7	dbSNP_120	178	2755,5677		454,1847,1915	no	coding-synonymous,coding-synonymous,coding-synonymous	SUN1	NM_001130965.2,NM_001171944.1,NM_025154.5	,,	963,2842,2508	GG,GA,AA		32.6731,47.9971,37.7633	,,	474/786,371/683,391/703	897492	4768,7858	2097	4216	6313	SO:0001819	synonymous_variant	23353	exon13			GCCCACAGTCGAG	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.1533A>G	7.37:g.897492A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_001130965	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	37		968	0.4432234432234432	235	0.47764227642276424	175	0.48342541436464087	290	0.506993006993007	268	0.35356200527704484	G	5.560	0.288222	0.10513	0.479971	0.326731	ENSG00000164828	ENST00000433212	.	.	.	5.08	-6.38	0.01957	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47983	-0.9074	3	.	.	.	0.04	0.2186	0.00165	0.314:0.1549:0.2327:0.2983	rs10950789;rs11555975;rs60471374	.	.	.	G	323	.	.	S	+	1	0	SUN1	864018	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.960000	0.03849	-1.729000	0.01364	-2.212000	0.00299	AGT	A|0.604;G|0.396	0.396	strong		0.567	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
ANO2	57101	hgsc.bcm.edu	37	12	5744495	5744495	+	Missense_Mutation	SNP	T	T	C	rs200078432	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:5744495T>C	ENST00000356134.5	-	18	1713	c.1642A>G	c.(1642-1644)Atc>Gtc	p.I548V	ANO2_ENST00000538154.1_5'UTR|ANO2_ENST00000327087.8_Missense_Mutation_p.I547V|ANO2_ENST00000546188.1_Missense_Mutation_p.I548V	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	552					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CCAAAGACGATTGAGAATGTC	0.483													T|||	10	0.00199681	0.0	0.0	5008	,	,		17725	0.0		0.0099	False		,,,				2504	0.0				p.I547V		Atlas-SNP	.											.	ANO2	309	.	0			c.A1639G						PASS	.	T	VAL/ILE	10,3918		0,10,1954	77.0	74.0	75.0		1639	5.0	0.4	12	dbSNP_132	75	60,8264		0,60,4102	yes	missense	ANO2	NM_020373.2	29	0,70,6056	CC,CT,TT		0.7208,0.2546,0.5713	benign	547/999	5744495	70,12182	1964	4162	6126	SO:0001583	missense	57101	exon17			AGACGATTGAGAA	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1642A>G	12.37:g.5744495T>C	ENSP00000348453:p.Ile548Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_020373	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	T	1.251	-0.618595	0.03663	0.002546	0.007208	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277;ENST00000545860	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.02	5.02	0.67125	.	0.106110	0.64402	D	0.000007	T	0.34832	0.0911	N	0.20685	0.6	0.09310	N	1	B	0.29378	0.243	B	0.31946	0.138	T	0.19386	-1.0307	10	0.31617	T	0.26	.	5.6934	0.17843	0.0:0.1827:0.0:0.8173	.	547	Q9NQ90-3	.	V	547;548;548;552;107	ENSP00000314048:I547V;ENSP00000348453:I548V;ENSP00000440981:I548V;ENSP00000443813:I107V	ENSP00000314048:I547V	I	-	1	0	ANO2	5614756	0.004000	0.15560	0.410000	0.26471	0.936000	0.57629	1.013000	0.29937	2.132000	0.65825	0.445000	0.29226	ATC	T|0.997;C|0.003	0.003	strong		0.483	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
DCUN1D3	123879	hgsc.bcm.edu	37	16	20873767	20873767	+	Silent	SNP	T	T	G	rs7187522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20873767T>G	ENST00000324344.4	-	2	379	c.94A>C	c.(94-96)Agg>Cgg	p.R32R	ERI2_ENST00000564349.1_Intron|DCUN1D3_ENST00000563934.1_Silent_p.R32R	NM_173475.2	NP_775746.1	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 3	32					negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)	perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)	14				GBM - Glioblastoma multiforme(48;0.249)		CCTGCACCCCTCCTGCTATGT	0.597													G|||	2803	0.559704	0.4818	0.6182	5008	,	,		20275	0.379		0.7068	False		,,,				2504	0.6585				p.R32R		Atlas-SNP	.											.	DCUN1D3	29	.	0			c.A94C						PASS	.	G		2234,2168	583.9+/-385.9	572,1090,539	221.0	200.0	207.0		94	5.1	1.0	16	dbSNP_116	207	6179,2421	399.8+/-346.6	2212,1755,333	no	coding-synonymous	DCUN1D3	NM_173475.2		2784,2845,872	GG,GT,TT		28.1512,49.2503,35.2946		32/305	20873767	8413,4589	2201	4300	6501	SO:0001819	synonymous_variant	123879	exon2			CACCCCTCCTGCT	BC040442	CCDS10592.1	16p12.3	2013-06-10	2013-06-10		ENSG00000188215	ENSG00000188215			28734	protein-coding gene	gene with protein product			"""DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)"""			15988528	Standard	NM_173475		Approved	MGC48972, FLJ41725, DKFZp686O0290	uc002dhz.3	Q8IWE4	OTTHUMG00000131553	ENST00000324344.4:c.94A>C	16.37:g.20873767T>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_173475	B3KVY4	Silent	SNP	ENST00000324344.4	37	CCDS10592.1																																																																																			T|0.408;G|0.592	0.592	strong		0.597	DCUN1D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254415.2	NM_173475	
MAGEA6	4105	hgsc.bcm.edu	37	X	151869745	151869745	+	Silent	SNP	C	C	T	rs7057497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:151869745C>T	ENST00000329342.5	+	3	660	c.435C>T	c.(433-435)taC>taT	p.Y145Y		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	145	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					ATTGGCAGTACTTCTTTCCTG	0.522													t|||	468	0.123974	0.171	0.0576	3775	,	,		15359	0.0278		0.1252	False		,,,				2504	0.0491				p.Y145Y		Atlas-SNP	.											.	MAGEA6	53	.	0			c.C435T						PASS	.	C	,	852,2982		80,560,132,992,438	165.0	146.0	152.0		435,435	-0.6	0.0	X	dbSNP_116	152	1061,5667		60,636,305,1732,1567	no	coding-synonymous,coding-synonymous	MAGEA6	NM_005363.2,NM_175868.1	,	140,1196,437,2724,2005	TT,TC,T,CC,C		15.7699,22.2222,18.1121	,	145/315,145/315	151869745	1913,8649	2202	4300	6502	SO:0001819	synonymous_variant	4105	exon3			GCAGTACTTCTTT		CCDS76050.1	Xq28	2009-03-13			ENSG00000197172	ENSG00000197172			6804	protein-coding gene	gene with protein product	"""MAGE-6 antigen"", ""melanoma-associated antigen 6"", ""melanoma antigen family A 6"", ""cancer/testis antigen family 1, member 6"""	300176		MAGE6		8575766	Standard	NM_005363		Approved	CT1.6	uc004ffq.1	P43360	OTTHUMG00000022642	ENST00000329342.5:c.435C>T	X.37:g.151869745C>T		Somatic	736	0	0		WXS	Illumina HiSeq	Phase_I	271	270	0.99631	NM_005363	A8IF93|Q6NW44	Silent	SNP	ENST00000329342.5	37	CCDS14708.1																																																																																			C|0.838;T|0.162	0.162	strong		0.522	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363	
KIAA1456	57604	hgsc.bcm.edu	37	8	12878830	12878830	+	Silent	SNP	C	C	T	rs3739309	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:12878830C>T	ENST00000524591.2	+	5	1131	c.642C>T	c.(640-642)agC>agT	p.S214S	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	214							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						GGTCCCACAGCGTGGGCTATG	0.448													C|||	1479	0.295327	0.1876	0.2738	5008	,	,		22185	0.127		0.4811	False		,,,				2504	0.4387				p.S214S		Atlas-SNP	.											.	KIAA1456	20	.	0			c.C642T						PASS	.	C	,	782,2982		86,610,1186	125.0	113.0	117.0		264,642	0.7	0.2	8	dbSNP_107	117	3808,4430		893,2022,1204	no	coding-synonymous,coding-synonymous	KIAA1456	NM_001099677.1,NM_020844.2	,	979,2632,2390	TT,TC,CC		46.2248,20.7758,38.2436	,	88/329,214/455	12878830	4590,7412	1882	4119	6001	SO:0001819	synonymous_variant	57604	exon5			CCACAGCGTGGGC	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"""chromosome 8 open reading frame 79"""	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.642C>T	8.37:g.12878830C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	148	75	0.506757	NM_020844	Q96AW6	Silent	SNP	ENST00000524591.2	37	CCDS47808.1																																																																																			C|0.651;T|0.349	0.349	strong		0.448	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677	
RHBDL2	54933	hgsc.bcm.edu	37	1	39352271	39352271	+	Missense_Mutation	SNP	G	G	T	rs2147914	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39352271G>T	ENST00000289248.2	-	8	1825	c.817C>A	c.(817-819)Ctg>Atg	p.L273M	RHBDL2_ENST00000538156.1_Missense_Mutation_p.L340M|RHBDL2_ENST00000372985.3_Missense_Mutation_p.L353M|RHBDL2_ENST00000372990.1_Missense_Mutation_p.L273M|RP5-864K19.4_ENST00000433671.2_RNA			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	273			L -> M (in dbSNP:rs2147914).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			GGATCTTTCAGCAGTGCTTTA	0.428													G|||	1555	0.310503	0.1452	0.4798	5008	,	,		19848	0.2718		0.4513	False		,,,				2504	0.3088				p.L273M		Atlas-SNP	.											RHBDL2,bladder,carcinoma,+2,1	RHBDL2	28	1	0			c.C817A						PASS	.	G	MET/LEU	827,3579	328.0+/-300.3	81,665,1457	126.0	118.0	121.0		817	6.0	1.0	1	dbSNP_96	121	3915,4685	546.8+/-385.0	881,2153,1266	yes	missense	RHBDL2	NM_017821.3	15	962,2818,2723	TT,TG,GG		45.5233,18.7699,36.4601	probably-damaging	273/304	39352271	4742,8264	2203	4300	6503	SO:0001583	missense	54933	exon8			CTTTCAGCAGTGC	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"""rhomboid (veinlet, Drosophila)-like 2"""				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.817C>A	1.37:g.39352271G>T	ENSP00000289248:p.Leu273Met	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Missense_Mutation	SNP	ENST00000289248.2	37	CCDS30680.1	754	0.34523809523809523	74	0.15040650406504066	170	0.4696132596685083	168	0.2937062937062937	342	0.45118733509234826	G	19.75	3.885071	0.72410	0.187699	0.455233	ENSG00000158315	ENST00000372990;ENST00000289248;ENST00000538156;ENST00000372985	T;T;T;T	0.34667	1.41;1.41;1.36;1.35	6.03	6.03	0.97812	.	0.071091	0.64402	D	0.000020	T	0.00012	0.0000	L	0.47716	1.5	0.23361	P	0.99783142	D;D	0.64830	0.994;0.988	P;P	0.59221	0.854;0.74	T	0.53201	-0.8472	9	0.33141	T	0.24	-13.991	10.462	0.44585	0.0:0.1432:0.7085:0.1483	rs2147914;rs3790440;rs17559036;rs61115096;rs2147914	353;273	B7Z1Y9;Q9NX52	.;RHBL2_HUMAN	M	273;273;340;353	ENSP00000362081:L273M;ENSP00000289248:L273M;ENSP00000439227:L340M;ENSP00000362076:L353M	ENSP00000289248:L273M	L	-	1	2	RHBDL2	39124858	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.757000	0.47557	2.861000	0.98227	0.655000	0.94253	CTG	G|0.652;T|0.348	0.348	strong		0.428	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821	
CD80	941	hgsc.bcm.edu	37	3	119263680	119263680	+	Silent	SNP	C	C	T	rs2228017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:119263680C>T	ENST00000264246.3	-	3	497	c.135G>A	c.(133-135)gtG>gtA	p.V45V	CD80_ENST00000383669.3_Silent_p.V45V|CD80_ENST00000478182.1_Silent_p.V45V|CD80_ENST00000383668.3_Silent_p.V45V	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	45	Ig-like V-type.				cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	ACAGCGTTGCCACTTCTTTCA	0.428													C|||	1107	0.221046	0.1679	0.2147	5008	,	,		20312	0.2669		0.2624	False		,,,				2504	0.2076				p.V45V	Melanoma(132;135 1764 1806 5833 14593)	Atlas-SNP	.											.	CD80	35	.	0			c.G135A						PASS	.	C		816,3590	325.9+/-299.3	64,688,1451	118.0	103.0	108.0		135	-0.8	0.0	3	dbSNP_98	108	2141,6459	367.8+/-334.9	256,1629,2415	no	coding-synonymous	CD80	NM_005191.3		320,2317,3866	TT,TC,CC		24.8953,18.5202,22.7357		45/289	119263680	2957,10049	2203	4300	6503	SO:0001819	synonymous_variant	941	exon3			CGTTGCCACTTCT		CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1700	protein-coding gene	gene with protein product	"""B-lymphocyte activation antigen B7"""	112203	"""CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)"", ""CD80 molecule """	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.135G>A	3.37:g.119263680C>T		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	248	125	0.504032	NM_005191	Q5DTA9|Q5DTB0	Silent	SNP	ENST00000264246.3	37	CCDS2989.1																																																																																			C|0.766;T|0.234	0.234	strong		0.428	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191	
PUSL1	126789	hgsc.bcm.edu	37	1	1246303	1246303	+	Silent	SNP	G	G	A	rs41285824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1246303G>A	ENST00000379031.5	+	7	791	c.714G>A	c.(712-714)acG>acA	p.T238T	PUSL1_ENST00000470520.1_3'UTR|ACAP3_ENST00000354700.5_5'Flank|CPSF3L_ENST00000462432.1_5'Flank	NM_153339.1	NP_699170.1	Q8N0Z8	PUSL1_HUMAN	pseudouridylate synthase-like 1	238					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			lung(3)|skin(1)|urinary_tract(1)	5	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.95e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGAGGATGACGGCTGTGCTGG	0.652													G|||	71	0.0141773	0.0061	0.0274	5008	,	,		14617	0.0		0.0417	False		,,,				2504	0.002				p.T238T		Atlas-SNP	.											.	PUSL1	12	.	0			c.G714A						PASS	.	G		20,4386	29.9+/-59.1	0,20,2183	76.0	87.0	83.0		714	-6.6	0.8	1	dbSNP_127	83	249,8339	98.4+/-159.9	8,233,4053	no	coding-synonymous	PUSL1	NM_153339.1		8,253,6236	AA,AG,GG		2.8994,0.4539,2.0702		238/304	1246303	269,12725	2203	4294	6497	SO:0001819	synonymous_variant	126789	exon7			GATGACGGCTGTG	AK027721	CCDS20.1	1p36.33	2008-02-05			ENSG00000169972	ENSG00000169972			26914	protein-coding gene	gene with protein product						12477932	Standard	NM_153339		Approved	FLJ90811	uc001aed.3	Q8N0Z8	OTTHUMG00000003361	ENST00000379031.5:c.714G>A	1.37:g.1246303G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	199	69	0.346734	NM_153339	B4DP76|Q5TA41	Silent	SNP	ENST00000379031.5	37	CCDS20.1																																																																																			G|0.979;A|0.021	0.021	strong		0.652	PUSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009438.1	NM_153339	
DERA	51071	hgsc.bcm.edu	37	12	16189279	16189279	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:16189279A>G	ENST00000428559.2	+	8	1076	c.864A>G	c.(862-864)atA>atG	p.I288M	DERA_ENST00000532964.1_Missense_Mutation_p.I245M|DERA_ENST00000526530.1_Missense_Mutation_p.I200M	NM_015954.2	NP_057038.2	Q9Y315	DEOC_HUMAN	deoxyribose-phosphate aldolase (putative)	288					deoxyribonucleoside catabolic process (GO:0046121)|deoxyribonucleotide catabolic process (GO:0009264)|deoxyribose phosphate catabolic process (GO:0046386)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	deoxyribose-phosphate aldolase activity (GO:0004139)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		Hepatocellular(102;0.121)				TCTTTCGAATAGGTGCCAGTA	0.458																																					p.I288M		Atlas-SNP	.											.	DERA	20	.	0			c.A864G						PASS	.						101.0	99.0	99.0					12																	16189279		1867	4110	5977	SO:0001583	missense	51071	exon8			TCGAATAGGTGCC	AF132960	CCDS44838.1, CCDS73451.1	12p12.3	2010-06-24	2010-06-24		ENSG00000023697	ENSG00000023697	4.1.2.4		24269	protein-coding gene	gene with protein product			"""2-deoxyribose-5-phosphate aldolase homolog (C. elegans)"""			12546782	Standard	XM_006719083		Approved	CGI-26, DEOC	uc001rde.3	Q9Y315	OTTHUMG00000165537	ENST00000428559.2:c.864A>G	12.37:g.16189279A>G	ENSP00000416583:p.Ile288Met	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_015954	Q53HN9|Q6PHW2	Missense_Mutation	SNP	ENST00000428559.2	37	CCDS44838.1	.	.	.	.	.	.	.	.	.	.	A	16.36	3.102495	0.56183	.	.	ENSG00000023697	ENST00000428559;ENST00000532964;ENST00000526530	.	.	.	5.57	-0.0832	0.13695	Aldolase-type TIM barrel (1);	0.155772	0.56097	D	0.000032	T	0.67040	0.2851	M	0.91249	3.19	0.47407	D	0.99941	P	0.52577	0.954	P	0.52957	0.714	T	0.64685	-0.6349	9	0.72032	D	0.01	-25.8467	3.2921	0.06953	0.2024:0.4745:0.0912:0.2318	.	288	Q9Y315	DEOC_HUMAN	M	288;245;200	.	ENSP00000416583:I288M	I	+	3	3	DERA	16080546	0.982000	0.34865	0.979000	0.43373	0.913000	0.54294	0.125000	0.15749	0.039000	0.15632	-0.327000	0.08410	ATA	.	.	none		0.458	DERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384731.1	NM_015954	
RNF175	285533	hgsc.bcm.edu	37	4	154644537	154644537	+	Missense_Mutation	SNP	T	T	C	rs10517577	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:154644537T>C	ENST00000347063.4	-	5	847	c.475A>G	c.(475-477)Atg>Gtg	p.M159V	RNF175_ENST00000274068.4_Missense_Mutation_p.M31V|RP11-153M7.5_ENST00000505051.1_RNA|RNF175_ENST00000506505.1_5'UTR	NM_173662.2	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	159			M -> V (in dbSNP:rs10517577).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	13	all_hematologic(180;0.093)	Renal(120;0.118)				ATTGTAAACATGATCGCCAAG	0.388													T|||	467	0.0932508	0.0053	0.1628	5008	,	,		16695	0.004		0.2247	False		,,,				2504	0.1196				p.M159V		Atlas-SNP	.											.	RNF175	40	.	0			c.A475G						PASS	.	T	VAL/MET	160,3704		4,152,1776	100.0	86.0	90.0		475	0.7	1.0	4	dbSNP_119	90	1923,6345		194,1535,2405	yes	missense	RNF175	NM_173662.2	21	198,1687,4181	CC,CT,TT		23.2583,4.1408,17.1695	benign	159/329	154644537	2083,10049	1932	4134	6066	SO:0001583	missense	285533	exon5			TAAACATGATCGC	BC034385	CCDS47149.1	4q31.3	2008-02-05			ENSG00000145428	ENSG00000145428		"""RING-type (C3HC4) zinc fingers"""	27735	protein-coding gene	gene with protein product							Standard	NM_173662		Approved	FLJ34190	uc003int.3	Q8N4F7	OTTHUMG00000161557	ENST00000347063.4:c.475A>G	4.37:g.154644537T>C	ENSP00000340979:p.Met159Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_173662	C9JL66|Q8NB61	Missense_Mutation	SNP	ENST00000347063.4	37	CCDS47149.1	245	0.11217948717948718	2	0.0040650406504065045	61	0.1685082872928177	1	0.0017482517482517483	181	0.23878627968337732	T	13.82	2.350213	0.41599	0.041408	0.232583	ENSG00000145428	ENST00000347063;ENST00000274068;ENST00000508248	T;T;T	0.77229	-1.08;-1.08;-1.08	4.34	0.707	0.18139	.	0.198777	0.49916	N	0.000139	T	0.00039	0.0001	L	0.55481	1.735	0.25431	P	0.9881882	P;B	0.36683	0.565;0.002	B;B	0.36335	0.222;0.008	T	0.01894	-1.1252	9	0.30854	T	0.27	-5.8208	7.4098	0.27011	0.0:0.2644:0.0:0.7356	rs10517577;rs17370896;rs52808550;rs57008646;rs10517577	31;159	Q8NB61;Q8N4F7	.;RN175_HUMAN	V	159;31;99	ENSP00000340979:M159V;ENSP00000274068:M31V;ENSP00000427472:M99V	ENSP00000274068:M31V	M	-	1	0	RNF175	154863987	1.000000	0.71417	0.996000	0.52242	0.935000	0.57460	3.291000	0.51764	0.136000	0.18733	0.455000	0.32223	ATG	T|0.917;C|0.083	0.083	strong		0.388	RNF175-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365286.1	NM_173662	
ZNF133	7692	hgsc.bcm.edu	37	20	18296076	18296076	+	Missense_Mutation	SNP	G	G	A	rs2228273	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:18296076G>A	ENST00000316358.4	+	4	678	c.581G>A	c.(580-582)gGg>gAg	p.G194E	ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000538547.1_Missense_Mutation_p.G99E|ZNF133_ENST00000396026.3_Missense_Mutation_p.G197E|ZNF133_ENST00000535822.1_Missense_Mutation_p.G99E|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000402618.2_Missense_Mutation_p.G131E|ZNF133_ENST00000401790.1_Missense_Mutation_p.G194E|ZNF133_ENST00000377671.3_Missense_Mutation_p.G193E	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	194			G -> E (in dbSNP:rs2228273).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						GCTCAGTCAGGGAACCCTGAG	0.542													G|||	604	0.120607	0.1528	0.1037	5008	,	,		20164	0.1379		0.0825	False		,,,				2504	0.1104				p.G193E		Atlas-SNP	.											.	ZNF133	63	.	0			c.G578A						PASS	.	G	GLU/GLY,GLU/GLY	653,3753	259.5+/-263.1	52,549,1602	72.0	80.0	77.0		578,578	1.1	0.0	20	dbSNP_98	77	679,7921	163.8+/-216.2	29,621,3650	yes	missense,missense	ZNF133	NM_001083330.1,NM_003434.4	98,98	81,1170,5252	AA,AG,GG		7.8953,14.8207,10.2414	possibly-damaging,possibly-damaging	193/654,193/654	18296076	1332,11674	2203	4300	6503	SO:0001583	missense	7692	exon4			AGTCAGGGAACCC	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.581G>A	20.37:g.18296076G>A	ENSP00000346090:p.Gly194Glu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Missense_Mutation	SNP	ENST00000316358.4	37		274	0.12545787545787546	93	0.18902439024390244	32	0.08839779005524862	86	0.15034965034965034	63	0.08311345646437995	G	0	-2.621583	0.00118	0.148207	0.078953	ENSG00000125846	ENST00000377671;ENST00000396026;ENST00000402618;ENST00000401790;ENST00000538547;ENST00000535822;ENST00000316358	T;T;T;T;T;T;T	0.06608	3.46;3.43;3.28;3.43;3.34;3.34;3.43	4.15	1.08	0.20341	.	0.266580	0.27168	N	0.020608	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;P;P	0.42375	0.105;0.126;0.67;0.778	B;B;B;B	0.41466	0.021;0.008;0.196;0.358	T	0.48258	-0.9051	9	0.72032	D	0.01	-7.1046	6.6448	0.22929	0.3:0.0:0.7:0.0	rs2228273;rs52800593;rs2228273	131;197;194;193	B4DIB8;B4DHU7;P52736;P52736-2	.;.;ZN133_HUMAN;.	E	193;197;131;194;99;99;194	ENSP00000366899:G193E;ENSP00000400897:G197E;ENSP00000385279:G131E;ENSP00000383945:G194E;ENSP00000442978:G99E;ENSP00000439427:G99E;ENSP00000346090:G194E	ENSP00000346090:G194E	G	+	2	0	ZNF133	18244076	0.000000	0.05858	0.007000	0.13788	0.186000	0.23388	0.082000	0.14847	0.287000	0.22375	0.561000	0.74099	GGG	A|0.112;C|0.006	0.112	strong		0.542	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
THAP9	79725	hgsc.bcm.edu	37	4	83838262	83838262	+	Missense_Mutation	SNP	G	G	T	rs897945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:83838262G>T	ENST00000302236.5	+	5	948	c.897G>T	c.(895-897)ttG>ttT	p.L299F	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	299			L -> F (in dbSNP:rs897945). {ECO:0000269|PubMed:14702039}.		DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				GTCACAGTTTGCAGGGGTTTA	0.413													G|||	1629	0.32528	0.0651	0.6484	5008	,	,		20952	0.2004		0.5507	False		,,,				2504	0.3446				p.L299F		Atlas-SNP	.											THAP9,colon,carcinoma,+2,1	THAP9	65	1	0			c.G897T						PASS	.	G	PHE/LEU	666,3740	282.2+/-276.4	68,530,1605	136.0	127.0	130.0		897	2.8	1.0	4	dbSNP_86	130	4799,3801	613.2+/-396.1	1359,2081,860	yes	missense	THAP9	NM_024672.4	22	1427,2611,2465	TT,TG,GG		44.1977,15.1158,42.0191	probably-damaging	299/904	83838262	5465,7541	2203	4300	6503	SO:0001583	missense	79725	exon5			CAGTTTGCAGGGG	AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"""THAP (C2CH-type zinc finger) domain containing"""	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.897G>T	4.37:g.83838262G>T	ENSP00000305533:p.Leu299Phe	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_024672	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	801	0.36675824175824173	32	0.06504065040650407	220	0.6077348066298343	124	0.21678321678321677	425	0.5606860158311345	G	7.015	0.557611	0.13436	0.151158	0.558023	ENSG00000168152	ENST00000302236;ENST00000536314	T	0.46063	0.88	3.7	2.85	0.33270	.	1.365610	0.05330	N	0.528170	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.999999999612521	P	0.48162	0.906	B	0.38378	0.272	T	0.41251	-0.9519	9	0.20519	T	0.43	-2.6801	9.1917	0.37204	0.104:0.0:0.896:0.0	rs897945;rs17354399;rs52815233;rs59971666;rs897945	299	Q9H5L6	THAP9_HUMAN	F	299	ENSP00000305533:L299F	ENSP00000305533:L299F	L	+	3	2	THAP9	84057286	0.829000	0.29322	0.999000	0.59377	0.224000	0.24922	0.295000	0.19065	1.141000	0.42275	0.650000	0.86243	TTG	G|0.624;T|0.375	0.375	strong		0.413	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118228763	118228763	+	Missense_Mutation	SNP	T	T	C	rs7077408	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:118228763T>C	ENST00000369230.3	+	9	1140	c.994T>C	c.(994-996)Ttc>Ctc	p.F332L		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	332			F -> L (in dbSNP:rs7077408).		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		TAGATTTCACTTCAAAAATAT	0.348													C|||	900	0.179712	0.3283	0.1441	5008	,	,		15776	0.2341		0.0557	False		,,,				2504	0.0757				p.F332L		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.T994C						PASS	.	C	LEU/PHE	1386,3020	686.3+/-404.7	217,952,1034	78.0	79.0	79.0		994	1.6	0.2	10	dbSNP_116	79	461,8135	796.8+/-407.5	18,425,3855	yes	missense	PNLIPRP3	NM_001011709.2	22	235,1377,4889	CC,CT,TT		5.363,31.4571,14.2055	benign	332/468	118228763	1847,11155	2203	4298	6501	SO:0001583	missense	119548	exon9			TTTCACTTCAAAA	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.994T>C	10.37:g.118228763T>C	ENSP00000358232:p.Phe332Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_001011709		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	392	0.1794871794871795	158	0.32113821138211385	57	0.1574585635359116	136	0.23776223776223776	41	0.05408970976253298	C	0.229	-1.022676	0.02061	0.314571	0.05363	ENSG00000203837	ENST00000369230	D	0.90444	-2.67	4.68	1.57	0.23409	Lipase, N-terminal (1);	0.382269	0.17745	N	0.163424	T	0.00012	0.0000	N	0.00313	-1.665	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17471	-1.0368	9	0.10111	T	0.7	.	3.5849	0.07967	0.126:0.4897:0.2444:0.1398	rs7077408;rs57481738;rs7077408	332	Q17RR3	LIPR3_HUMAN	L	332	ENSP00000358232:F332L	ENSP00000358232:F332L	F	+	1	0	PNLIPRP3	118218753	0.000000	0.05858	0.192000	0.23308	0.877000	0.50540	-0.055000	0.11807	0.205000	0.20568	-0.186000	0.12905	TTC	T|0.839;C|0.161	0.161	strong		0.348	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
AVIL	10677	hgsc.bcm.edu	37	12	58204145	58204145	+	Missense_Mutation	SNP	T	T	C	rs112269561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:58204145T>C	ENST00000257861.3	-	6	1178	c.748A>G	c.(748-750)Atc>Gtc	p.I250V	AVIL_ENST00000537081.1_Missense_Mutation_p.I243V	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	250	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					TACAACATGATAGTTGATTTC	0.517													T|||	4	0.000798722	0.0	0.0029	5008	,	,		20424	0.0		0.002	False		,,,				2504	0.0				p.I250V		Atlas-SNP	.											.	AVIL	60	.	0			c.A748G						PASS	.	T	VAL/ILE	3,4403	6.2+/-15.9	0,3,2200	101.0	94.0	96.0		748	3.8	0.4	12	dbSNP_132	96	23,8577	16.6+/-54.9	0,23,4277	yes	missense	AVIL	NM_006576.3	29	0,26,6477	CC,CT,TT		0.2674,0.0681,0.1999	benign	250/820	58204145	26,12980	2203	4300	6503	SO:0001583	missense	10677	exon6			ACATGATAGTTGA	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.748A>G	12.37:g.58204145T>C	ENSP00000257861:p.Ile250Val	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	200	77	0.385	NM_006576	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	37	CCDS8959.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	0.019	-1.460982	0.01062	6.81E-4	0.002674	ENSG00000135407	ENST00000537081;ENST00000257861	T;T	0.28666	1.6;1.6	4.91	3.76	0.43208	.	0.289986	0.37669	N	0.001998	T	0.16428	0.0395	N	0.12853	0.265	0.35038	D	0.759429	B;B	0.25441	0.013;0.126	B;B	0.34346	0.013;0.18	T	0.18493	-1.0335	10	0.05833	T	0.94	-8.5477	9.7898	0.40699	0.0:0.0833:0.0:0.9167	.	243;250	O75366-2;O75366	.;AVIL_HUMAN	V	243;250	ENSP00000443207:I243V;ENSP00000257861:I250V	ENSP00000257861:I250V	I	-	1	0	AVIL	56490412	0.319000	0.24607	0.433000	0.26760	0.524000	0.34500	0.494000	0.22467	0.892000	0.36259	-0.297000	0.09499	ATC	T|0.999;C|0.001	0.001	strong		0.517	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576	
CFAP57	149465	hgsc.bcm.edu	37	1	43664218	43664218	+	Silent	SNP	C	C	T	rs603123	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43664218C>T	ENST00000372492.4	+	8	1653	c.1329C>T	c.(1327-1329)caC>caT	p.H443H	WDR65_ENST00000528956.1_Silent_p.H443H|RNA5SP46_ENST00000362370.1_RNA	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		443										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CATCTGGACACTTCATTGTAG	0.398													C|||	1012	0.202077	0.2829	0.2089	5008	,	,		21125	0.002		0.3181	False		,,,				2504	0.1748				p.H443H		Atlas-SNP	.											.	WDR65	76	.	0			c.C1329T						PASS	.	C	,,	1102,3304	396.3+/-330.0	128,846,1229	101.0	93.0	96.0		1329,1329,1329	2.9	0.8	1	dbSNP_83	96	2456,6144	405.4+/-348.5	362,1732,2206	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	490,2578,3435	TT,TC,CC		28.5581,25.0113,27.3566	,,	443/699,443/699,443/699	43664218	3558,9448	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon8			TGGACACTTCATT																												ENST00000372492.4:c.1329C>T	1.37:g.43664218C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				C|0.742;T|0.258	0.258	strong		0.398	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152059	151152059	+	Silent	SNP	G	G	A	rs2073065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:151152059G>A	ENST00000358517.2	+	15	2023	c.1812G>A	c.(1810-1812)agG>agA	p.R604R	PLEKHG1_ENST00000367328.1_Silent_p.R604R			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	604							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CTGGTCACAGGATTGTCAGGC	0.532													G|||	690	0.13778	0.0711	0.2046	5008	,	,		20267	0.128		0.1252	False		,,,				2504	0.2035				p.R604R		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.G1812A						PASS	.	G		333,4073	174.4+/-204.0	12,309,1882	68.0	66.0	67.0		1812	4.7	0.9	6	dbSNP_96	67	1265,7335	251.4+/-277.9	115,1035,3150	no	coding-synonymous	PLEKHG1	NM_001029884.1		127,1344,5032	AA,AG,GG		14.7093,7.5579,12.2866		604/1386	151152059	1598,11408	2203	4300	6503	SO:0001819	synonymous_variant	57480	exon16			TCACAGGATTGTC	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.1812G>A	6.37:g.151152059G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																			G|0.882;A|0.118	0.118	strong		0.532	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
TYRO3	7301	hgsc.bcm.edu	37	15	41860490	41860490	+	Missense_Mutation	SNP	T	T	A	rs12148316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41860490T>A	ENST00000263798.3	+	8	1261	c.1037T>A	c.(1036-1038)aTc>aAc	p.I346N	TYRO3_ENST00000559066.1_Missense_Mutation_p.I301N	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	346	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> N (in dbSNP:rs12148316).		apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GAAGAAGTGATCCCCGAGGCC	0.577													T|||	775	0.154752	0.0946	0.1671	5008	,	,		17669	0.0109		0.2922	False		,,,				2504	0.2342				p.I346N		Atlas-SNP	.											TYRO3_ENST00000263798,colon,carcinoma,0,2	TYRO3	169	2	0			c.T1037A						PASS	.	T	ASN/ILE	542,3864	245.9+/-254.7	32,478,1693	60.0	58.0	59.0		1037	4.0	1.0	15	dbSNP_120	59	2512,6088	408.4+/-349.5	324,1864,2112	no	missense	TYRO3	NM_006293.3	149	356,2342,3805	AA,AT,TT		29.2093,12.3014,23.4815	benign	346/891	41860490	3054,9952	2203	4300	6503	SO:0001583	missense	7301	exon8			AAGTGATCCCCGA	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1037T>A	15.37:g.41860490T>A	ENSP00000263798:p.Ile346Asn	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	212	76	0.358491	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	341	0.15613553113553114	45	0.09146341463414634	65	0.17955801104972377	5	0.008741258741258742	226	0.29815303430079154	T	11.51	1.659473	0.29515	0.123014	0.292093	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.72615	-0.67	5.09	3.95	0.45737	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.194192	0.25839	N	0.027971	T	0.00012	0.0000	L	0.44542	1.39	0.29829	P	0.8302080000000001	B	0.33318	0.408	B	0.31614	0.133	T	0.13229	-1.0517	9	0.20519	T	0.43	-5.0066	8.7958	0.34878	0.3005:0.0:0.0:0.6995	rs12148316	346	Q06418	TYRO3_HUMAN	N	278;346	ENSP00000263798:I346N	ENSP00000263798:I346N	I	+	2	0	TYRO3	39647782	0.370000	0.25047	0.999000	0.59377	0.998000	0.95712	0.484000	0.22308	0.938000	0.37419	0.533000	0.62120	ATC	T|0.803;A|0.197	0.197	strong		0.577	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		
TRPV3	162514	hgsc.bcm.edu	37	17	3447914	3447914	+	Silent	SNP	C	C	T	rs1039519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3447914C>T	ENST00000576742.1	-	4	591	c.270G>A	c.(268-270)caG>caA	p.Q90Q	TRPV3_ENST00000301365.4_Silent_p.Q90Q|TRPV3_ENST00000572519.1_Silent_p.Q90Q	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	90					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	TCACATCATCCTGAGGAGACT	0.582													c|||	3318	0.66254	0.5461	0.7781	5008	,	,		16033	0.7937		0.5885	False		,,,				2504	0.6789				p.Q90Q		Atlas-SNP	.											.	TRPV3	85	.	0			c.G270A						PASS	.			2464,1942	620.9+/-393.6	680,1104,419	40.0	39.0	39.0		270	3.2	1.0	17	dbSNP_86	39	5160,3440	634.3+/-398.8	1527,2106,667	no	coding-synonymous	TRPV3	NM_145068.2		2207,3210,1086	TT,TC,CC		40.0,44.0763,41.3809		90/791	3447914	7624,5382	2203	4300	6503	SO:0001819	synonymous_variant	162514	exon4			ATCATCCTGAGGA	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.270G>A	17.37:g.3447914C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Silent	SNP	ENST00000576742.1	37	CCDS11029.1																																																																																			C|0.383;T|0.617	0.617	strong		0.582	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068	
AK9	221264	hgsc.bcm.edu	37	6	109894773	109894773	+	Missense_Mutation	SNP	T	T	A	rs12175588	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:109894773T>A	ENST00000424296.2	-	21	2292	c.2216A>T	c.(2215-2217)gAt>gTt	p.D739V	AK9_ENST00000341338.6_5'UTR	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	739					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										CTCCTCTTCATCCTCATTATC	0.388													T|||	1223	0.244209	0.1089	0.2839	5008	,	,		18633	0.3433		0.2197	False		,,,				2504	0.3221				p.D739V		Atlas-SNP	.											.	AKD1	223	.	0			c.A2216T						PASS	.	T	VAL/ASP	167,1217		13,141,538	143.0	117.0	125.0		2216	-2.1	0.0	6	dbSNP_120	125	751,2431		87,577,927	yes	missense	AKD1	NM_001145128.2	152	100,718,1465	AA,AT,TT		23.6015,12.0665,20.1051	benign	739/1912	109894773	918,3648	692	1591	2283	SO:0001583	missense	221264	exon21			TCTTCATCCTCAT	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.2216A>T	6.37:g.109894773T>A	ENSP00000410186:p.Asp739Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	100	36	0.36	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	CCDS55048.1	476	0.21794871794871795	51	0.10365853658536585	94	0.2596685082872928	163	0.28496503496503495	168	0.22163588390501318	T	18.06	3.539938	0.65085	0.120665	0.236015	ENSG00000155085	ENST00000424296	T	0.64991	-0.13	4.26	-2.13	0.07144	.	.	.	.	.	T	0.14313	0.0346	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10042	-1.0647	7	.	.	.	-1.5517	2.0014	0.03468	0.1298:0.1374:0.225:0.5078	rs12175588;rs52832625;rs12175588	739	Q5TCS8	AKD1_HUMAN	V	739	ENSP00000410186:D739V	.	D	-	2	0	AKD1	110001466	0.000000	0.05858	0.000000	0.03702	0.683000	0.39861	0.167000	0.16602	-0.415000	0.07484	-0.445000	0.05633	GAT	T|0.780;A|0.220	0.220	strong		0.388	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100803982	100803982	+	Silent	SNP	C	C	T	rs79213484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100803982C>T	ENST00000298815.8	+	7	696	c.693C>T	c.(691-693)aaC>aaT	p.N231N	snoU13_ENST00000459511.1_RNA|ARHGAP42_ENST00000524892.2_Silent_p.N197N	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	231	BAR.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TGCAGTTCAACTTGCAGAATG	0.388													C|||	41	0.0081869	0.0015	0.0115	5008	,	,		15042	0.0		0.0268	False		,,,				2504	0.0041				p.N231N		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.C693T						PASS	.	C		6,1378		0,6,686	132.0	102.0	111.0		693	4.6	1.0	11	dbSNP_132	111	99,3083		1,97,1493	no	coding-synonymous	ARHGAP42	NM_152432.2		1,103,2179	TT,TC,CC		3.1113,0.4335,2.2996		231/875	100803982	105,4461	692	1591	2283	SO:0001819	synonymous_variant	143872	exon7			GTTCAACTTGCAG			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.693C>T	11.37:g.100803982C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	132	75	0.568182	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				C|0.983;T|0.017	0.017	strong		0.388	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
UGGT2	55757	hgsc.bcm.edu	37	13	96506664	96506664	+	Silent	SNP	A	A	G	rs11070154	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:96506664A>G	ENST00000376747.3	-	35	4144	c.4074T>C	c.(4072-4074)acT>acC	p.T1358T		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1358	Glucosyltransferase.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)	p.T1358T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						CACAAAATGGAGTATACCCAT	0.383													A|||	1648	0.329073	0.2526	0.2622	5008	,	,		17269	0.3155		0.4394	False		,,,				2504	0.3804				p.T1358T		Atlas-SNP	.											UGGT2,NS,carcinoma,0,1	UGGT2	127	1	1	Substitution - coding silent(1)	prostate(1)	c.T4074C						PASS	.	A		1187,3219	414.6+/-336.9	168,851,1184	91.0	87.0	88.0		4074	-4.8	0.9	13	dbSNP_120	88	3582,5018	517.2+/-379.0	764,2054,1482	no	coding-synonymous	UGGT2	NM_020121.3		932,2905,2666	GG,GA,AA		41.6512,26.9405,36.6677		1358/1517	96506664	4769,8237	2203	4300	6503	SO:0001819	synonymous_variant	55757	exon35			AAATGGAGTATAC	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.4074T>C	13.37:g.96506664A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	181	90	0.497238	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Silent	SNP	ENST00000376747.3	37	CCDS9480.1																																																																																			A|0.648;G|0.352	0.352	strong		0.383	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
FRA10AC1	118924	hgsc.bcm.edu	37	10	95458141	95458141	+	Silent	SNP	A	A	G	rs11187597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:95458141A>G	ENST00000359204.4	-	3	287	c.90T>C	c.(88-90)gaT>gaC	p.D30D	FRA10AC1_ENST00000371430.2_Silent_p.D30D|FRA10AC1_ENST00000536233.1_Silent_p.D30D|FRA10AC1_ENST00000394100.2_Silent_p.D30D	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1	30						nucleus (GO:0005634)				NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						GCAGTAAGTCATCTTCAACTG	0.313													G|||	1806	0.360623	0.0696	0.4539	5008	,	,		14806	0.3978		0.5447	False		,,,				2504	0.4601				p.D30D		Atlas-SNP	.											.	FRA10AC1	68	.	0			c.T90C						PASS	.	G		630,3776	765.8+/-413.4	61,508,1634	117.0	109.0	112.0		90	-1.8	1.0	10	dbSNP_120	112	4440,4160	565.5+/-388.5	1125,2190,985	no	coding-synonymous	FRA10AC1	NM_145246.4		1186,2698,2619	GG,GA,AA		48.3721,14.2987,38.982		30/316	95458141	5070,7936	2203	4300	6503	SO:0001819	synonymous_variant	118924	exon3			TAAGTCATCTTCA	AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"""chromosome 10 open reading frame 4"""	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.90T>C	10.37:g.95458141A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_145246	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Silent	SNP	ENST00000359204.4	37	CCDS7430.1																																																																																			A|0.613;G|0.387	0.387	strong		0.313	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246	
HLA-C	3107	hgsc.bcm.edu	37	6	31239049	31239049	+	Silent	SNP	G	G	T	rs1065406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31239049G>T	ENST00000376228.5	-	3	434	c.420C>A	c.(418-420)tcC>tcA	p.S140S	HLA-C_ENST00000383329.3_Silent_p.S140S	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	140	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CGTCGTAGGCGGACTGGTCAT	0.706													g|||	270	0.0539137	0.0439	0.049	5008	,	,		13032	0.0377		0.0398	False		,,,				2504	0.1022				p.S140S		Atlas-SNP	.											.	HLA-C	92	.	0			c.C420A						PASS	.						34.0	26.0	29.0					6																	31239049		2177	4252	6429	SO:0001819	synonymous_variant	3107	exon3			GTAGGCGGACTGG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.420C>A	6.37:g.31239049G>T		Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	214	51	0.238318	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	150	0.06868131868131869	32	0.06504065040650407	18	0.049723756906077346	57	0.09965034965034965	43	0.05672823218997362	.	5.915	0.352896	0.11182	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.59	-3.28	0.05033	.	.	.	.	.	T	0.07188	0.0182	.	.	.	0.24072	N	0.995975	.	.	.	.	.	.	T	0.34800	-0.9814	4	.	.	.	.	3.1816	0.06587	0.3131:0.0:0.2669:0.42	rs1065406;rs2308578;rs3176001;rs3180085;rs16868251;rs17840081	.	.	.	S	140	.	.	R	-	1	0	HLA-C	31347028	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.910000	0.00699	-0.884000	0.03976	-1.236000	0.01555	CGC	T|0.055;G|0.945	0.055	strong		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PLXNA4	91584	hgsc.bcm.edu	37	7	132070054	132070054	+	Intron	SNP	T	T	C	rs741664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:132070054T>C	ENST00000359827.3	-	4	2334				PLXNA4_ENST00000423507.2_Splice_Site_p.M458V|PLXNA4_ENST00000321063.4_Intron			Q9HCM2	PLXA4_HUMAN	plexin A4						anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GTACCAGGCATCTGGAAAAGA	0.498													T|||	1277	0.254992	0.0333	0.3112	5008	,	,		18793	0.129		0.5865	False		,,,				2504	0.3037				p.M458V		Atlas-SNP	.											.	PLXNA4	873	.	0			c.A1372G						PASS	.	T	VAL/MET,	427,3411		25,377,1517	61.0	60.0	60.0		1372,	-4.6	0.0	7	dbSNP_86	60	4805,3475		1405,1995,740	yes	missense-near-splice,intron	PLXNA4	NM_001105543.1,NM_020911.1	21,	1430,2372,2257	CC,CT,TT		41.9686,11.1256,43.1754	,	458/493,	132070054	5232,6886	1919	4140	6059	SO:0001627	intron_variant	91584	exon4			CAGGCATCTGGAA	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1372-87073A>G	7.37:g.132070054T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	66	39	0.590909	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	661	0.30265567765567764	20	0.04065040650406504	120	0.3314917127071823	82	0.14335664335664336	439	0.579155672823219	T	0.022	-1.413205	0.01145	0.111256	0.580314	ENSG00000221866	ENST00000423507	T	0.02631	4.22	4.38	-4.6	0.03390	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44452	-0.9327	7	0.02654	T	1	.	0.4898	0.00562	0.3174:0.1444:0.3025:0.2357	rs741664;rs17820148;rs60373167;rs741664	458	Q9HCM2-2	.	V	458	ENSP00000392772:M458V	ENSP00000392772:M458V	M	-	1	0	PLXNA4	131720594	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.474000	0.06607	-0.485000	0.06754	0.383000	0.25322	ATG	C|0.318;N|0.000	0.318	strong		0.498	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
NLRP14	338323	hgsc.bcm.edu	37	11	7079038	7079038	+	Missense_Mutation	SNP	G	G	A	rs10839708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7079038G>A	ENST00000299481.4	+	7	2768	c.2422G>A	c.(2422-2424)Gag>Aag	p.E808K		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	808			E -> K (in dbSNP:rs10839708). {ECO:0000269|PubMed:16931801}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GCTTTTGTGTGAGGCCTTAAG	0.383													G|||	2834	0.565895	0.3502	0.6124	5008	,	,		21400	0.7063		0.6024	False		,,,				2504	0.6421				p.E808K		Atlas-SNP	.											.	NLRP14	187	.	0			c.G2422A						PASS	.	G	LYS/GLU	1588,2814	492.5+/-362.4	294,1000,907	239.0	213.0	222.0		2422	4.0	1.0	11	dbSNP_120	222	5055,3537	630.7+/-398.4	1502,2051,743	yes	missense	NLRP14	NM_176822.3	56	1796,3051,1650	AA,AG,GG		41.1662,36.0745,48.8764	benign	808/1094	7079038	6643,6351	2201	4296	6497	SO:0001583	missense	338323	exon7			TTGTGTGAGGCCT	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.2422G>A	11.37:g.7079038G>A	ENSP00000299481:p.Glu808Lys	Somatic	478	0	0		WXS	Illumina HiSeq	Phase_I	458	217	0.473799	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	1230	0.5631868131868132	173	0.3516260162601626	214	0.5911602209944752	386	0.6748251748251748	457	0.6029023746701847	G	22.4	4.278511	0.80692	0.360745	0.588338	ENSG00000158077	ENST00000299481	T	0.41400	1.0	4.89	3.98	0.46160	.	0.000000	0.44483	D	0.000452	T	0.00012	0.0000	L	0.49699	1.58	0.30466	P	0.773848	P	0.52692	0.955	P	0.53224	0.721	T	0.38520	-0.9657	9	0.28530	T	0.3	.	9.4719	0.38847	0.0996:0.0:0.9004:0.0	rs10839708;rs17280430;rs52825881;rs59059579;rs10839708	808	Q86W24	NAL14_HUMAN	K	808	ENSP00000299481:E808K	ENSP00000299481:E808K	E	+	1	0	NLRP14	7035614	1.000000	0.71417	0.977000	0.42913	0.959000	0.62525	3.157000	0.50716	1.205000	0.43262	0.585000	0.79938	GAG	G|0.472;A|0.528	0.528	strong		0.383	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
MAP1A	4130	hgsc.bcm.edu	37	15	43818959	43818959	+	Missense_Mutation	SNP	C	C	G	rs375898111		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43818959C>G	ENST00000300231.5	+	4	5738	c.5288C>G	c.(5287-5289)cCa>cGa	p.P1763R	MAP1A_ENST00000382031.1_Missense_Mutation_p.P2001R|MAP1A_ENST00000399453.1_Missense_Mutation_p.P1763R			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1763					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GAATCCTCACCACAGAAGGGG	0.572																																					p.P1763R		Atlas-SNP	.											.	MAP1A	189	.	0			c.C5288G						PASS	.	C	ARG/PRO	0,3894		0,0,1947	74.0	76.0	76.0		5288	4.5	0.5	15		76	1,8265		0,1,4132	no	missense	MAP1A	NM_002373.5	103	0,1,6079	GG,GC,CC		0.0121,0.0,0.0082	benign	1763/2804	43818959	1,12159	1947	4133	6080	SO:0001583	missense	4130	exon4			CCTCACCACAGAA	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.5288C>G	15.37:g.43818959C>G	ENSP00000300231:p.Pro1763Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	C	2.185	-0.386740	0.04966	0.0	1.21E-4	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01854	4.6;4.61;4.61	4.46	4.46	0.54185	.	0.268702	0.20049	N	0.100342	T	0.03390	0.0098	L	0.32530	0.975	0.20563	N	0.999883	B	0.32467	0.372	B	0.36989	0.238	T	0.38672	-0.9650	10	0.66056	D	0.02	0.9333	15.0779	0.72090	0.0:1.0:0.0:0.0	.	1763	P78559	MAP1A_HUMAN	R	2001;1763;1763	ENSP00000371462:P2001R;ENSP00000382380:P1763R;ENSP00000300231:P1763R	ENSP00000300231:P1763R	P	+	2	0	MAP1A	41606251	0.953000	0.32496	0.451000	0.26982	0.145000	0.21501	2.451000	0.44952	2.321000	0.78463	0.455000	0.32223	CCA	.	.	weak		0.572	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
SDCBP2	27111	hgsc.bcm.edu	37	20	1293247	1293247	+	Missense_Mutation	SNP	C	C	T	rs2273959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1293247C>T	ENST00000360779.3	-	6	717	c.544G>A	c.(544-546)Gtg>Atg	p.V182M	SDCBP2_ENST00000339987.3_Missense_Mutation_p.V182M|SDCBP2_ENST00000467129.1_5'Flank|SDCBP2_ENST00000381808.3_Missense_Mutation_p.V97M|SDCBP2_ENST00000381812.1_Missense_Mutation_p.V182M	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	182	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.		V -> M (in dbSNP:rs2273959). {ECO:0000269|PubMed:11152476, ECO:0000269|Ref.3}.		intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.V97M(1)		endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						CGAACCACCACGACAATCTTA	0.627													T|||	1626	0.324681	0.4047	0.3847	5008	,	,		17791	0.0913		0.4592	False		,,,				2504	0.2761				p.V182M		Atlas-SNP	.											SDCBP2,NS,carcinoma,0,1	SDCBP2	78	1	1	Substitution - Missense(1)	stomach(1)	c.G544A						PASS	.	T	MET/VAL,MET/VAL,MET/VAL	1791,2615	640.5+/-397.3	365,1061,777	105.0	89.0	94.0		544,289,544	4.5	1.0	20	dbSNP_100	94	4225,4375	582.9+/-391.5	1052,2121,1127	yes	missense,missense,missense	SDCBP2	NM_001199784.1,NM_015685.5,NM_080489.4	21,21,21	1417,3182,1904	TT,TC,CC		49.1279,40.6491,46.2556	benign,benign,benign	182/293,97/208,182/293	1293247	6016,6990	2203	4300	6503	SO:0001583	missense	27111	exon6			CCACCACGACAAT	AF131809	CCDS13013.1, CCDS42848.1	20p13	2008-07-02			ENSG00000125775	ENSG00000125775			15756	protein-coding gene	gene with protein product						11152476	Standard	NM_080489		Approved	ST-2, SITAC18	uc021vzn.1	Q9H190	OTTHUMG00000031661	ENST00000360779.3:c.544G>A	20.37:g.1293247C>T	ENSP00000354013:p.Val182Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	37	CCDS42848.1	727	0.33287545787545786	190	0.3861788617886179	147	0.40607734806629836	57	0.09965034965034965	333	0.4393139841688654	t	0.020	-1.445829	0.01089	0.406491	0.491279	ENSG00000125775	ENST00000381812;ENST00000381808;ENST00000360779;ENST00000339987	T;T;T;T	0.27720	1.65;1.65;1.65;1.65	4.51	4.51	0.55191	PDZ/DHR/GLGF (4);	0.184810	0.48767	N	0.000168	T	0.00012	0.0000	N	0.02213	-0.635	0.58432	P	8.000000000008E-6	B	0.06786	0.001	B	0.12837	0.008	T	0.45160	-0.9280	9	0.02654	T	1	-12.8919	10.1249	0.42643	0.0:0.0804:0.0:0.9196	rs2273959;rs52828596;rs57052980;rs2273959	182	Q9H190	SDCB2_HUMAN	M	182;97;182;182	ENSP00000371233:V182M;ENSP00000371229:V97M;ENSP00000354013:V182M;ENSP00000342935:V182M	ENSP00000342935:V182M	V	-	1	0	SDCBP2	1241247	1.000000	0.71417	0.995000	0.50966	0.357000	0.29423	1.973000	0.40550	0.859000	0.35456	-0.361000	0.07541	GTG	C|0.592;T|0.408	0.408	strong		0.627	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489	
MCF2	4168	hgsc.bcm.edu	37	X	138679712	138679712	+	Silent	SNP	T	T	A	rs1051619	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:138679712T>A	ENST00000370576.4	-	18	2171	c.1962A>T	c.(1960-1962)ggA>ggT	p.G654G	MCF2_ENST00000370578.4_Silent_p.G799G|MCF2_ENST00000536274.1_Silent_p.G615G|MCF2_ENST00000520602.1_Silent_p.G714G|AL033403.1_ENST00000401295.2_RNA|MCF2_ENST00000414978.1_Silent_p.G714G|MCF2_ENST00000519895.1_Silent_p.G730G|MCF2_ENST00000338585.6_Silent_p.G670G|MCF2_ENST00000370573.4_Silent_p.G654G	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	654	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					ACAGAGCAGATCCTTCACAGT	0.328													T|||	726	0.192318	0.0204	0.2075	3775	,	,		14365	0.0466		0.3728	False		,,,				2504	0.136				p.G730G		Atlas-SNP	.											.	MCF2	432	.	0			c.A2190T						PASS	.	T	,,,,,	362,3473		17,274,54,1341,517	103.0	87.0	93.0		2142,2190,1845,1962,2010,1962	1.5	0.0	X	dbSNP_86	93	3458,3266		620,1261,957,546,913	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MCF2	NM_001099855.1,NM_001171876.1,NM_001171877.1,NM_001171878.1,NM_001171879.1,NM_005369.4	,,,,,	637,1535,1011,1887,1430	AA,AT,A,TT,T		48.5723,9.4394,36.1777	,,,,,	714/986,730/1002,615/822,654/861,670/942,654/926	138679712	3820,6739	2203	4297	6500	SO:0001819	synonymous_variant	4168	exon22			AGCAGATCCTTCA		CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"""Rho guanine nucleotide exchange factors"""	6940	protein-coding gene	gene with protein product	"""Oncogene MCF2 (oncogene DBL)"""	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.1962A>T	X.37:g.138679712T>A		Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	186	185	0.994624	NM_001171876	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Silent	SNP	ENST00000370576.4	37	CCDS14667.1	405	0.244122965641953	12	0.02459016393442623	60	0.19480519480519481	22	0.039711191335740074	191	0.32154882154882153	T	1.295	-0.606460	0.03717	0.094394	0.514277	ENSG00000101977	ENST00000437564	.	.	.	5.69	1.45	0.22620	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19300	P	0.999970659	.	.	.	.	.	.	T	0.48375	-0.9041	3	.	.	.	.	5.805	0.18434	0.1285:0.2461:0.0:0.6255	rs1051619;rs3192018;rs17284775;rs17879934;rs1051619	.	.	.	F	158	.	.	I	-	1	0	MCF2	138507378	0.002000	0.14202	0.021000	0.16686	0.333000	0.28666	-0.162000	0.10012	0.279000	0.22186	0.486000	0.48141	ATC	T|0.720;0|0.003	.	strong		0.328	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369	
SLC40A1	30061	hgsc.bcm.edu	37	2	190430177	190430177	+	Silent	SNP	A	A	G	rs2304704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:190430177A>G	ENST00000261024.2	-	6	1089	c.663T>C	c.(661-663)gtT>gtC	p.V221V		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	221					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			TCCAGAGCAGAACGTACTCCA	0.473													A|||	2755	0.55012	0.1558	0.6772	5008	,	,		19900	0.8075		0.6054	False		,,,				2504	0.6708				p.V221V		Atlas-SNP	.											.	SLC40A1	51	.	0			c.T663C						PASS	.	A		1018,3388	376.6+/-322.1	108,802,1293	87.0	84.0	85.0		663	3.5	1.0	2	dbSNP_100	85	5505,3095	659.2+/-401.6	1756,1993,551	no	coding-synonymous	SLC40A1	NM_014585.5		1864,2795,1844	GG,GA,AA		35.9884,23.1049,49.8462		221/572	190430177	6523,6483	2203	4300	6503	SO:0001819	synonymous_variant	30061	exon6			GAGCAGAACGTAC	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"""Solute carriers"""	10909	protein-coding gene	gene with protein product	"""ferroportin 1"""	604653	"""solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"""	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.663T>C	2.37:g.190430177A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Silent	SNP	ENST00000261024.2	37	CCDS2299.1																																																																																			A|0.460;G|0.540	0.540	strong		0.473	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2		
GRIN3A	116443	hgsc.bcm.edu	37	9	104433034	104433034	+	Silent	SNP	A	A	G	rs10512285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:104433034A>G	ENST00000361820.3	-	3	2260	c.1660T>C	c.(1660-1662)Ttg>Ctg	p.L554L		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	554					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	AGGCTGTCCAATGTGGAAGAG	0.448													A|||	1340	0.267572	0.1241	0.3617	5008	,	,		21313	0.2173		0.4056	False		,,,				2504	0.3047				p.L554L		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T1660C						PASS	.	A		789,3617	316.1+/-294.4	73,643,1487	114.0	105.0	108.0		1660	-2.4	0.0	9	dbSNP_119	108	3551,5049	515.9+/-378.7	726,2099,1475	no	coding-synonymous	GRIN3A	NM_133445.2		799,2742,2962	GG,GA,AA		41.2907,17.9074,33.3692		554/1116	104433034	4340,8666	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			TGTCCAATGTGGA		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.1660T>C	9.37:g.104433034A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	190	109	0.573684	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|0.698;G|0.302	0.302	strong		0.448	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
PLEC	5339	hgsc.bcm.edu	37	8	145011204	145011204	+	Silent	SNP	A	A	G	rs6993938	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145011204A>G	ENST00000322810.4	-	5	958	c.789T>C	c.(787-789)gcT>gcC	p.A263A	PLEC_ENST00000354589.3_Silent_p.A126A|PLEC_ENST00000357649.2_Silent_p.A130A|PLEC_ENST00000356346.3_Silent_p.A112A|PLEC_ENST00000398774.2_Silent_p.A94A|PLEC_ENST00000345136.3_Silent_p.A126A|PLEC_ENST00000527096.1_Silent_p.A153A|PLEC_ENST00000436759.2_Silent_p.A153A|PLEC_ENST00000354958.2_Silent_p.A104A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	263	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.|Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.A153A(1)|p.A263A(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GGTTGCCGTCAGCGATGTCAT	0.622													G|||	1164	0.232428	0.0613	0.2882	5008	,	,		17817	0.1458		0.4066	False		,,,				2504	0.3344				p.A263A		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,-2,8	PLEC	1144	8	2	Substitution - coding silent(2)	stomach(2)	c.T789C						PASS	.	G	,,,,,,,	453,3867		28,397,1735	96.0	103.0	101.0		459,336,312,789,282,378,390,378	-11.4	0.0	8	dbSNP_116	101	3317,5259		646,2025,1617	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	674,2422,3352	GG,GA,AA		38.6777,10.4861,29.2339	,,,,,,,	153/4575,112/4534,104/4526,263/4685,94/4516,126/4548,130/4552,126/4548	145011204	3770,9126	2160	4288	6448	SO:0001819	synonymous_variant	5339	exon5			GCCGTCAGCGATG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.789T>C	8.37:g.145011204A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	154	65	0.422078	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.729;C|0.001;G|0.270	0.270	strong		0.622	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
RREB1	6239	hgsc.bcm.edu	37	6	7211818	7211818	+	Missense_Mutation	SNP	G	G	A	rs1334576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:7211818G>A	ENST00000349384.6	+	8	897	c.583G>A	c.(583-585)Ggg>Agg	p.G195R	RREB1_ENST00000334984.6_Missense_Mutation_p.G195R|RREB1_ENST00000379933.3_Missense_Mutation_p.G195R|RREB1_ENST00000379938.2_Missense_Mutation_p.G195R	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	195			G -> R (in dbSNP:rs1334576). {ECO:0000269|PubMed:15067362, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21703425}.		multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GGTAGAAGACGGGCAGTCAGG	0.458													G|||	2292	0.457668	0.32	0.4308	5008	,	,		16453	0.5327		0.4076	False		,,,				2504	0.637				p.G195R		Atlas-SNP	.											.	RREB1	242	.	0			c.G583A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	1475,2931	475.9+/-357.4	243,989,971	121.0	113.0	116.0		583,583,583,583	2.9	0.0	6	dbSNP_88	116	3451,5149	506.6+/-376.6	687,2077,1536	yes	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	125,125,125,125	930,3066,2507	AA,AG,GG		40.1279,33.4771,37.8748	probably-damaging,probably-damaging,probably-damaging,probably-damaging	195/1688,195/1743,195/1477,195/1688	7211818	4926,8080	2203	4300	6503	SO:0001583	missense	6239	exon8			GAAGACGGGCAGT	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.583G>A	6.37:g.7211818G>A	ENSP00000305560:p.Gly195Arg	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	189	95	0.502645	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	927	0.42445054945054944	172	0.34959349593495936	154	0.425414364640884	292	0.5104895104895105	309	0.4076517150395778	G	12.02	1.811580	0.32053	0.334771	0.401279	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T	0.11385	2.9;2.85;2.9;2.78;2.89	6.06	2.93	0.34026	.	0.599517	0.15531	N	0.257488	T	0.07369	0.0186	L	0.51422	1.61	0.80722	P	0.0	D;D;B	0.71674	0.997;0.998;0.139	P;P;B	0.59546	0.859;0.823;0.027	T	0.23904	-1.0175	9	0.23302	T	0.38	-50.4784	1.897	0.03260	0.1631:0.1215:0.4717:0.2437	rs1334576;rs17672663;rs17846344;rs17859378;rs52793584;rs60410842;rs1334576	195;195;195	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	R	195	ENSP00000369265:G195R;ENSP00000369270:G195R;ENSP00000305560:G195R;ENSP00000335574:G195R;ENSP00000419511:G195R	ENSP00000335574:G195R	G	+	1	0	RREB1	7156817	0.133000	0.22466	0.039000	0.18376	0.029000	0.11900	0.911000	0.28584	1.580000	0.49851	0.655000	0.94253	GGG	G|0.596;N|0.000	.	strong		0.458	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
ATP2C2	9914	hgsc.bcm.edu	37	16	84432176	84432176	+	Silent	SNP	G	G	A	rs4782948	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84432176G>A	ENST00000262429.4	+	2	260	c.171G>A	c.(169-171)gcG>gcA	p.A57A	ATP2C2_ENST00000416219.2_Silent_p.A57A	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	57					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						CCAAGGAAGCGTGCAAATGCC	0.438													g|||	66	0.0131789	0.0008	0.0231	5008	,	,		14131	0.001		0.0378	False		,,,				2504	0.0102				p.A57A		Atlas-SNP	.											.	ATP2C2	75	.	0			c.G171A						PASS	.	A		20,3800		0,20,1890	55.0	57.0	57.0		171	-10.4	0.0	16	dbSNP_111	57	314,7946		6,302,3822	no	coding-synonymous	ATP2C2	NM_014861.2		6,322,5712	AA,AG,GG		3.8015,0.5236,2.7649		57/947	84432176	334,11746	1910	4130	6040	SO:0001819	synonymous_variant	9914	exon2			GGAAGCGTGCAAA	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.171G>A	16.37:g.84432176G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	67	25	0.373134	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Silent	SNP	ENST00000262429.4	37	CCDS42207.1																																																																																			G|0.974;A|0.026	0.026	strong		0.438	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
PCDHB16	57717	hgsc.bcm.edu	37	5	140564088	140564088	+	Missense_Mutation	SNP	C	C	T	rs13176519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140564088C>T	ENST00000361016.2	+	1	3109	c.1954C>T	c.(1954-1956)Cgc>Tgc	p.R652C		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	652	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.			R -> C (in Ref. 3; BAB13447). {ECO:0000305}.	calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGAGCCTCCGCGCTCGGCCAC	0.716													C|||	1355	0.270567	0.0484	0.3055	5008	,	,		12564	0.5298		0.2306	False		,,,				2504	0.32				p.R652C		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C1954T						PASS	.						17.0	20.0	19.0					5																	140564088		2102	4146	6248	SO:0001583	missense	57717	exon1			CCTCCGCGCTCGG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1954C>T	5.37:g.140564088C>T	ENSP00000354293:p.Arg652Cys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	14	13	0.928571	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	571	0.26144688644688646	15	0.03048780487804878	86	0.23756906077348067	302	0.527972027972028	168	0.22163588390501318	c	14.06	2.422182	0.43020	.	.	ENSG00000196963	ENST00000361016	T	0.55234	0.53	3.75	1.8	0.24995	Cadherin (4);Cadherin-like (1);	1.580290	0.04823	N	0.437375	T	0.00012	0.0000	M	0.71581	2.175	0.26867	P	0.9678304	B	0.22683	0.073	B	0.27715	0.082	T	0.45498	-0.9257	9	0.62326	D	0.03	.	7.6146	0.28150	0.1683:0.7384:0.0:0.0934	rs13176519;rs17844665	652	Q9NRJ7	PCDBG_HUMAN	C	652	ENSP00000354293:R652C	ENSP00000354293:R652C	R	+	1	0	PCDHB16	140544272	0.002000	0.14202	0.884000	0.34674	0.827000	0.46813	1.911000	0.39937	0.511000	0.28236	0.298000	0.19748	CGC	.	.	weak		0.716	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
NOL6	65083	hgsc.bcm.edu	37	9	33467397	33467397	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:33467397G>A	ENST00000379471.2	-	13	1807	c.1720C>T	c.(1720-1722)Cct>Tct	p.P574S	NOL6_ENST00000455041.2_Missense_Mutation_p.P522S|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	574					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		CCCACCTCAGGCTGGTCTGCC	0.617											OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P574S		Atlas-SNP	.											.	NOL6	85	.	0			c.C1720T						PASS	.						56.0	54.0	54.0					9																	33467397		2203	4300	6503	SO:0001583	missense	65083	exon13			CCTCAGGCTGGTC	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.1720C>T	9.37:g.33467397G>A	ENSP00000368784:p.Pro574Ser	Somatic	153	0	0	840	WXS	Illumina HiSeq	Phase_I	165	30	0.181818	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	37		.	.	.	.	.	.	.	.	.	.	G	16.58	3.162530	0.57368	.	.	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.06	4.12	0.48240	.	0.154190	0.64402	D	0.000013	T	0.37156	0.0993	L	0.45422	1.42	0.58432	D	0.999999	P;P;P;P;P	0.40398	0.716;0.499;0.499;0.708;0.555	B;B;B;B;B	0.42245	0.381;0.161;0.161;0.331;0.248	T	0.06006	-1.0851	10	0.19147	T	0.46	.	14.0961	0.65023	0.0:0.1492:0.8508:0.0	.	522;571;574;574;574	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4-3;Q9H6R4	.;.;.;.;NOL6_HUMAN	S	574;574;574;130;574;522	ENSP00000313978:P574S;ENSP00000297990:P574S;ENSP00000368784:P574S;ENSP00000395915:P522S	ENSP00000297990:P574S	P	-	1	0	NOL6	33457397	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.752000	0.55172	2.638000	0.89438	0.655000	0.94253	CCT	.	.	none		0.617	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
FAM186A	121006	hgsc.bcm.edu	37	12	50745821	50745821	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745821T>A	ENST00000327337.5	-	4	4793	c.4794A>T	c.(4792-4794)gaA>gaT	p.E1598D	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Missense_Mutation_p.E1598D	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1598								p.E1598D(1)									GGATCCCCAGTTCCTGCGCCT	0.682																																					p.E1598D	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,-1,6	FAM186A	181	6	1	Substitution - Missense(1)	skin(1)	c.A4794T						PASS	.						6.0	6.0	6.0					12																	50745821		685	1557	2242	SO:0001583	missense	121006	exon4			CCCCAGTTCCTGC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4794A>T	12.37:g.50745821T>A	ENSP00000329995:p.Glu1598Asp	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	254	24	0.0944882	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	t	0.464	-0.887781	0.02511	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.04317	3.65;3.65	4.05	-8.09	0.01090	.	.	.	.	.	T	0.02012	0.0063	N	0.08118	0	0.09310	N	1	B;B	0.19706	0.038;0.0	B;B	0.14578	0.011;0.0	T	0.33497	-0.9866	9	0.11794	T	0.64	.	8.6931	0.34278	0.5013:0.0:0.3403:0.1584	.	1598;1598	F5GYN0;A6NE01	.;F186A_HUMAN	D	1598	ENSP00000441337:E1598D;ENSP00000329995:E1598D	ENSP00000329995:E1598D	E	-	3	2	FAM186A	49032088	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.664000	0.00399	-5.832000	0.00009	-5.863000	0.00000	GAA	.	.	none		0.682	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
GRN	2896	hgsc.bcm.edu	37	17	42427630	42427630	+	Silent	SNP	T	T	C	rs63750768|rs25646|rs63749801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42427630T>C	ENST00000053867.3	+	5	446	c.384T>C	c.(382-384)gaT>gaC	p.D128D	GRN_ENST00000589265.1_Silent_p.D128D	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	128					blastocyst hatching (GO:0001835)|cell death (GO:0008219)|embryo implantation (GO:0007566)|positive regulation of epithelial cell proliferation (GO:0050679)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	growth factor activity (GO:0008083)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		AGTGCCCTGATAGTCAGTTCG	0.582													T|||	428	0.0854633	0.0015	0.0605	5008	,	,		15756	0.2718		0.0298	False		,,,				2504	0.0818				p.D128D		Atlas-SNP	.											.	GRN	51	.	0			c.T384C	GRCh37	CD075437	GRN	D	rs25646	PASS	.	T		37,4369	41.6+/-74.8	0,37,2166	226.0	191.0	203.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	384	-8.4	0.0	17	dbSNP_72	203	242,8358	97.2+/-158.9	4,234,4062	no	coding-synonymous	GRN	NM_002087.2		4,271,6228	CC,CT,TT		2.814,0.8398,2.1452		128/594	42427630	279,12727	2203	4300	6503	SO:0001819	synonymous_variant	2896	exon5			CCCTGATAGTCAG	M75161	CCDS11483.1	17q21.32	2014-09-17				ENSG00000030582			4601	protein-coding gene	gene with protein product	"""progranulin"""	138945				1417868, 9826678	Standard	XM_005257253		Approved	PCDGF, PGRN, CLN11	uc002igp.1	P28799		ENST00000053867.3:c.384T>C	17.37:g.42427630T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	161	72	0.447205	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	Silent	SNP	ENST00000053867.3	37	CCDS11483.1	174	0.07967032967032966	0	0.0	11	0.03038674033149171	140	0.24475524475524477	23	0.030343007915567283	T	0.244	-1.011225	0.02095	0.008398	0.02814	ENSG00000030582	ENST00000393566	.	.	.	4.22	-8.45	0.00946	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.11991	-1.0565	4	0.33141	T	0.24	-0.8191	8.5901	0.33682	0.0:0.4219:0.3313:0.2468	rs25646;rs3815057;rs17250980;rs25646	.	.	.	T	35	.	ENSP00000377196:I35T	I	+	2	0	GRN	39783156	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.310000	0.00517	-2.030000	0.00929	-0.648000	0.03929	ATA	T|0.946;C|0.054	0.054	strong		0.582	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087	
SPAG5	10615	hgsc.bcm.edu	37	17	26919344	26919344	+	Silent	SNP	T	T	C	rs113667723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:26919344T>C	ENST00000321765.5	-	3	1250	c.918A>G	c.(916-918)acA>acG	p.T306T		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	306					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					GTGTCAGGCATGTGGACAGAA	0.453													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		22177	0.0		0.0099	False		,,,				2504	0.0				p.T306T		Atlas-SNP	.											.	SPAG5	92	.	0			c.A918G						PASS	.	T		11,4395	15.5+/-35.6	0,11,2192	135.0	121.0	126.0		918	-1.2	0.0	17	dbSNP_132	126	111,8489	59.8+/-121.6	1,109,4190	no	coding-synonymous	SPAG5	NM_006461.3		1,120,6382	CC,CT,TT		1.2907,0.2497,0.938		306/1194	26919344	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	10615	exon3			CAGGCATGTGGAC	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.918A>G	17.37:g.26919344T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Silent	SNP	ENST00000321765.5	37	CCDS32594.1																																																																																			T|0.992;C|0.008	0.008	strong		0.453	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
CALCOCO2	10241	hgsc.bcm.edu	37	17	46926615	46926615	+	Splice_Site	SNP	G	G	A	rs550510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46926615G>A	ENST00000258947.3	+	5	520	c.419G>A	c.(418-420)gGa>gAa	p.G140E	CALCOCO2_ENST00000508679.1_Splice_Site_p.G68E|CALCOCO2_ENST00000509507.1_Splice_Site_p.G161E|CALCOCO2_ENST00000416445.2_Intron|CALCOCO2_ENST00000448105.2_Splice_Site_p.G164E	NM_001261390.1|NM_001261391.1|NM_001261393.1|NM_001261395.1|NM_005831.4	NP_001248319.1|NP_001248320.1|NP_001248322.1|NP_001248324.1|NP_005822.1	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2	140			G -> E (in dbSNP:rs550510). {ECO:0000269|PubMed:14702039}.		response to interferon-gamma (GO:0034341)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)	p.G140E(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	15						CTTTTGTAGGGAGAGGTGGAA	0.463													G|||	1218	0.243211	0.025	0.219	5008	,	,		18654	0.6538		0.173	False		,,,				2504	0.2045				p.G164E		Atlas-SNP	.											CALCOCO2,NS,carcinoma,0,1	CALCOCO2	29	1	1	Substitution - Missense(1)	stomach(1)	c.G491A						PASS	.	G	GLU/GLY	157,4249	106.0+/-144.5	0,157,2046	109.0	109.0	109.0		419	2.8	1.0	17	dbSNP_83	109	1213,7387	243.9+/-273.3	84,1045,3171	yes	missense-near-splice	CALCOCO2	NM_005831.3	98	84,1202,5217	AA,AG,GG		14.1047,3.5633,10.5336	benign	140/447	46926615	1370,11636	2203	4300	6503	SO:0001630	splice_region_variant	10241	exon6			TGTAGGGAGAGGT	BC004130	CCDS11538.1, CCDS58558.1, CCDS58559.1, CCDS58560.1, CCDS58561.1	17q21.32	2006-02-09				ENSG00000136436			29912	protein-coding gene	gene with protein product		604587				7540613	Standard	NM_001261390		Approved	MGC17318, NDP52	uc010wlr.3	Q13137		ENST00000258947.3:c.418-1G>A	17.37:g.46926615G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	148	69	0.466216	NM_001261390	B2RBT0|B4DDC4|B4DDT4|B4DP36|B4E0C0|E7ENK0|E7ETP5|E9PBE5|Q53FQ5|Q53HB5|Q6IBN9|Q9BTF7	Missense_Mutation	SNP	ENST00000258947.3	37	CCDS11538.1	595	0.2724358974358974	15	0.03048780487804878	61	0.1685082872928177	379	0.6625874125874126	140	0.18469656992084432	G	12.46	1.944420	0.34283	0.035633	0.141047	ENSG00000136436	ENST00000258947;ENST00000509507;ENST00000448105;ENST00000509415;ENST00000513119;ENST00000508679;ENST00000505071;ENST00000502761	T;T;T;T;T;T;T;T	0.49139	2.67;2.75;2.67;1.63;2.32;2.57;0.79;3.04	5.94	2.83	0.33086	.	0.204155	0.34555	N	0.003867	T	0.00012	0.0000	L	0.35854	1.095	0.35022	P	0.24208700000000005	B;B;B	0.25743	0.133;0.029;0.03	B;B;B	0.34824	0.19;0.071;0.071	T	0.44590	-0.9318	9	0.02654	T	1	-7.7311	6.3909	0.21585	0.1536:0.0:0.6992:0.1472	rs550510;rs3760450;rs11539411;rs52810328;rs58937427;rs550510	164;161;140	B4DP36;E9PBE5;Q13137	.;.;CACO2_HUMAN	E	140;161;164;112;68;68;149;140	ENSP00000258947:G140E;ENSP00000424352:G161E;ENSP00000398523:G164E;ENSP00000425692:G112E;ENSP00000425090:G68E;ENSP00000423437:G68E;ENSP00000422697:G149E;ENSP00000424889:G140E	ENSP00000258947:G140E	G	+	2	0	CALCOCO2	44281614	1.000000	0.71417	0.980000	0.43619	0.915000	0.54546	0.728000	0.26013	0.383000	0.24910	0.561000	0.74099	GGA	G|0.815;A|0.185	0.185	strong		0.463	CALCOCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360866.1	NM_005831	Missense_Mutation
EEPD1	80820	hgsc.bcm.edu	37	7	36327317	36327317	+	Missense_Mutation	SNP	C	C	T	rs196594	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:36327317C>T	ENST00000242108.4	+	6	1964	c.1246C>T	c.(1246-1248)Ccc>Tcc	p.P416S	EEPD1_ENST00000534978.1_Missense_Mutation_p.P416S	NM_030636.2	NP_085139.2	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family domain containing 1	416			P -> S (in dbSNP:rs196594).		DNA repair (GO:0006281)		DNA binding (GO:0003677)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|skin(1)	18						GAGCGAGAATCCCAGCAAGAA	0.557													C|||	221	0.0441294	0.0076	0.0692	5008	,	,		20744	0.0188		0.1024	False		,,,				2504	0.0419				p.P416S		Atlas-SNP	.											.	EEPD1	47	.	0			c.C1246T						PASS	.	C	SER/PRO	92,4314	74.7+/-112.8	1,90,2112	134.0	112.0	119.0		1246	2.2	0.1	7	dbSNP_79	119	934,7666	205.8+/-248.1	39,856,3405	yes	missense	EEPD1	NM_030636.2	74	40,946,5517	TT,TC,CC		10.8605,2.0881,7.8887	benign	416/570	36327317	1026,11980	2203	4300	6503	SO:0001583	missense	80820	exon6			GAGAATCCCAGCA	AK027386	CCDS34619.1	7p14.2	2007-12-07	2007-12-07		ENSG00000122547	ENSG00000122547			22223	protein-coding gene	gene with protein product							Standard	NM_030636		Approved	KIAA1706	uc003tfa.3	Q7L9B9	OTTHUMG00000154904	ENST00000242108.4:c.1246C>T	7.37:g.36327317C>T	ENSP00000242108:p.Pro416Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	128	68	0.53125	NM_030636	Q96K64|Q9C0F7	Missense_Mutation	SNP	ENST00000242108.4	37	CCDS34619.1	127	0.05815018315018315	3	0.006097560975609756	36	0.09944751381215469	12	0.02097902097902098	76	0.10026385224274406	C	1.388	-0.581648	0.03854	0.020881	0.108605	ENSG00000122547	ENST00000242108;ENST00000534978	T;T	0.20738	2.05;2.05	4.72	2.23	0.28157	Endonuclease/exonuclease/phosphatase (2);	0.727053	0.13604	N	0.375640	T	0.00241	0.0007	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28427	-1.0044	9	0.13108	T	0.6	-4.9046	1.2941	0.02066	0.2712:0.3523:0.2373:0.1392	rs196594;rs1643331;rs17274985;rs52798189;rs60571123;rs196594	416	Q7L9B9	EEPD1_HUMAN	S	416	ENSP00000242108:P416S;ENSP00000442692:P416S	ENSP00000242108:P416S	P	+	1	0	EEPD1	36293842	0.000000	0.05858	0.106000	0.21319	0.086000	0.17979	0.058000	0.14301	0.799000	0.34018	0.407000	0.27541	CCC	C|0.925;T|0.075	0.075	strong		0.557	EEPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337602.1	NM_030636	
OR7D2	162998	hgsc.bcm.edu	37	19	9296991	9296991	+	Silent	SNP	C	C	T	rs267605820		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9296991C>T	ENST00000344248.2	+	1	713	c.534C>T	c.(532-534)ttC>ttT	p.F178F		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	178					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						CACATTTTTTCTGCGAACTGA	0.448																																					p.F178F		Atlas-SNP	.											OR7D2,NS,carcinoma,0,1	OR7D2	55	1	0			c.C534T						scavenged	.						186.0	177.0	180.0					19																	9296991		2203	4300	6503	SO:0001819	synonymous_variant	162998	exon1			TTTTTTCTGCGAA	AK095468	CCDS32900.1	19p13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.534C>T	19.37:g.9296991C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	151	3	0.0198676	NM_175883	Q6IFJ7|Q8N133	Silent	SNP	ENST00000344248.2	37	CCDS32900.1																																																																																			.	.	none		0.448	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1		
MAGEA4	4103	hgsc.bcm.edu	37	X	151092653	151092653	+	Missense_Mutation	SNP	G	G	A	rs1047251	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:151092653G>A	ENST00000360243.2	+	3	784	c.517G>A	c.(517-519)Gcc>Acc	p.A173T	MAGEA4_ENST00000393920.1_Missense_Mutation_p.A173T|MAGEA4_ENST00000370337.4_Missense_Mutation_p.A173T|MAGEA4_ENST00000276344.2_Missense_Mutation_p.A173T|MAGEA4_ENST00000393921.1_Missense_Mutation_p.A173T|MAGEA4_ENST00000370340.3_Missense_Mutation_p.A173T|MAGEA4_ENST00000370335.1_Missense_Mutation_p.A173T	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	173	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		A -> T (in dbSNP:rs1047251). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7642112, ECO:0000269|PubMed:7927540, ECO:0000269|PubMed:8037761}.							breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					AGTGGACCCCGCCAGCAACAC	0.502													A|||	2019	0.534834	0.4773	0.2925	3775	,	,		14730	0.4504		0.3976	False		,,,				2504	0.3384				p.A173T		Atlas-SNP	.											.	MAGEA4	68	.	0			c.G517A						PASS	.	A	THR/ALA,THR/ALA,THR/ALA,THR/ALA	2351,1484		612,781,346,239,225	107.0	106.0	107.0		517,517,517,517	-0.4	0.0	X	dbSNP_86	107	3653,3075		713,1184,1043,531,829	yes	missense,missense,missense,missense	MAGEA4	NM_001011548.1,NM_001011549.1,NM_001011550.1,NM_002362.4	58,58,58,58	1325,1965,1389,770,1054	AA,AG,A,GG,G		45.7045,38.6962,43.1601	benign,benign,benign,benign	173/318,173/318,173/318,173/318	151092653	6004,4559	2203	4300	6503	SO:0001583	missense	4103	exon3			GACCCCGCCAGCA		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.517G>A	X.37:g.151092653G>A	ENSP00000353379:p.Ala173Thr	Somatic	385	1	0.0025974		WXS	Illumina HiSeq	Phase_I	230	229	0.995652	NM_001011548	Q14798	Missense_Mutation	SNP	ENST00000360243.2	37	CCDS14702.1	877	0.5286317058468957	148	0.43529411764705883	79	0.2668918918918919	159	0.3878048780487805	221	0.3797250859106529	A	0.018	-1.467449	0.01053	0.613038	0.542955	ENSG00000147381	ENST00000276344;ENST00000448295;ENST00000393921;ENST00000430273;ENST00000370337;ENST00000441865;ENST00000393920;ENST00000370340;ENST00000416020;ENST00000425182;ENST00000457310;ENST00000370335;ENST00000360243;ENST00000431971	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.04502	3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61	2.37	-0.42	0.12336	.	1.277240	0.05684	N	0.591025	T	0.00012	0.0000	N	0.01219	-0.95	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.33752	-0.9856	8	.	.	.	.	0.041	0.00008	0.3237:0.1809:0.1837:0.3117	rs1047251;rs3187282;rs17220978;rs17845555;rs17858453;rs52807844;rs57643014	173	P43358	MAGA4_HUMAN	T	173	ENSP00000276344:A173T;ENSP00000391904:A173T;ENSP00000377498:A173T;ENSP00000394149:A173T;ENSP00000359362:A173T;ENSP00000402624:A173T;ENSP00000377497:A173T;ENSP00000359365:A173T;ENSP00000394073:A173T;ENSP00000400900:A173T;ENSP00000402186:A173T;ENSP00000359360:A173T;ENSP00000353379:A173T;ENSP00000390096:A173T	.	A	+	1	0	MAGEA4	150843309	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.022000	0.03611	-0.660000	0.05352	-0.885000	0.02943	GCC	0|0.004;A|0.556	0.556	strong		0.502	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362	
HIVEP1	3096	hgsc.bcm.edu	37	6	12120588	12120588	+	Missense_Mutation	SNP	C	C	T	rs2228209	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:12120588C>T	ENST00000379388.2	+	4	892	c.560C>T	c.(559-561)aCg>aTg	p.T187M		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	187			T -> M (in dbSNP:rs2228209).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TGTGGCACTACGTCCCCCTCC	0.453													C|||	1039	0.207468	0.0204	0.245	5008	,	,		21426	0.2232		0.339	False		,,,				2504	0.2822				p.T187M		Atlas-SNP	.											.	HIVEP1	242	.	0			c.C560T						PASS	.	C	MET/THR	273,3831		9,255,1788	115.0	107.0	110.0		560	3.7	0.0	6	dbSNP_98	110	2934,5488		512,1910,1789	yes	missense	HIVEP1	NM_002114.2	81	521,2165,3577	TT,TC,CC		34.8373,6.652,25.6027	probably-damaging	187/2719	12120588	3207,9319	2052	4211	6263	SO:0001583	missense	3096	exon4			GCACTACGTCCCC	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.560C>T	6.37:g.12120588C>T	ENSP00000368698:p.Thr187Met	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	489	0.2239010989010989	15	0.03048780487804878	88	0.2430939226519337	134	0.23426573426573427	252	0.3324538258575198	C	13.07	2.128471	0.37533	0.06652	0.348373	ENSG00000095951	ENST00000379388	T	0.10382	2.88	5.5	3.68	0.42216	.	0.678176	0.12199	N	0.490468	T	0.06188	0.0160	L	0.56769	1.78	0.80722	P	0.0	D	0.58268	0.982	P	0.47528	0.549	T	0.30504	-0.9976	8	.	.	.	-1.54	4.9232	0.13880	0.263:0.5365:0.1291:0.0714	rs2228209;rs3800500;rs17609127;rs52832234;rs60943307;rs2228209	187	P15822	ZEP1_HUMAN	M	187	ENSP00000368698:T187M	.	T	+	2	0	HIVEP1	12228574	0.000000	0.05858	0.000000	0.03702	0.656000	0.38851	0.644000	0.24766	0.651000	0.30788	0.591000	0.81541	ACG	C|0.744;N|0.001	.	strong		0.453	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
KIAA0556	23247	hgsc.bcm.edu	37	16	27781309	27781309	+	Missense_Mutation	SNP	G	G	A	rs11644502	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:27781309G>A	ENST00000261588.4	+	21	4122	c.4103G>A	c.(4102-4104)cGg>cAg	p.R1368Q		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1368			R -> Q (in dbSNP:rs11644502).			extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						GACTACCTACGGGCTCAGCTG	0.632													G|||	146	0.0291534	0.003	0.0159	5008	,	,		16200	0.0		0.0656	False		,,,				2504	0.0665				p.R1368Q		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G4103A						PASS	.	G	GLN/ARG	48,4346	47.5+/-82.1	1,46,2150	71.0	82.0	79.0		4103	3.9	0.1	16	dbSNP_120	79	575,8025	155.7+/-209.7	18,539,3743	yes	missense	KIAA0556	NM_015202.2	43	19,585,5893	AA,AG,GG		6.686,1.0924,4.7945	benign	1368/1619	27781309	623,12371	2197	4300	6497	SO:0001583	missense	23247	exon21			ACCTACGGGCTCA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.4103G>A	16.37:g.27781309G>A	ENSP00000261588:p.Arg1368Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	89	36	0.404494	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	57	0.0260989010989011	3	0.006097560975609756	6	0.016574585635359115	1	0.0017482517482517483	47	0.06200527704485488	G	1.898	-0.453900	0.04540	0.010924	0.06686	ENSG00000047578	ENST00000261588	T	0.13538	2.58	5.03	3.88	0.44766	.	0.183165	0.48767	N	0.000176	T	0.00210	0.0006	N	0.00112	-2.095	0.20307	N	0.999914	B	0.02656	0.0	B	0.04013	0.001	T	0.41752	-0.9491	10	0.02654	T	1	-18.958	7.3677	0.26783	0.8236:0.0:0.1764:0.0	rs11644502;rs57880151;rs11644502	1368	O60303	K0556_HUMAN	Q	1368	ENSP00000261588:R1368Q	ENSP00000261588:R1368Q	R	+	2	0	KIAA0556	27688810	1.000000	0.71417	0.066000	0.19879	0.044000	0.14063	3.795000	0.55499	0.766000	0.33244	-0.290000	0.09829	CGG	G|0.956;A|0.044	0.044	strong		0.632	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
DYRK2	8445	hgsc.bcm.edu	37	12	68043643	68043643	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:68043643G>A	ENST00000344096.3	+	2	529	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	DYRK2_ENST00000537632.1_3'UTR|DYRK2_ENST00000393555.3_Intron	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	39					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		GGGGCCACCCGGAGCGGAGTG	0.741																																					p.R39Q		Atlas-SNP	.											.	DYRK2	63	.	0			c.G116A						PASS	.						12.0	14.0	13.0					12																	68043643		2187	4283	6470	SO:0001583	missense	8445	exon2			CCACCCGGAGCGG	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.116G>A	12.37:g.68043643G>A	ENSP00000342105:p.Arg39Gln	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	52	34	0.653846	NM_006482	B2R9V9|Q9BRB5	Missense_Mutation	SNP	ENST00000344096.3	37	CCDS8978.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.475230	0.26511	.	.	ENSG00000127334	ENST00000344096	T	0.66638	-0.22	3.91	3.01	0.34805	.	0.416053	0.21001	N	0.081872	T	0.47322	0.1439	N	0.19112	0.55	0.80722	D	1	B	0.11235	0.004	B	0.01281	0.0	T	0.28839	-1.0031	9	.	.	.	.	10.5729	0.45211	0.0975:0.0:0.9025:0.0	.	39	Q92630	DYRK2_HUMAN	Q	39	ENSP00000342105:R39Q	.	R	+	2	0	DYRK2	66329910	1.000000	0.71417	0.998000	0.56505	0.278000	0.26855	4.423000	0.59861	0.997000	0.38969	-0.258000	0.10820	CGG	.	.	none		0.741	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
SLC6A15	55117	hgsc.bcm.edu	37	12	85277608	85277608	+	Intron	SNP	C	C	T	rs17183612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:85277608C>T	ENST00000266682.5	-	5	1298				SLC6A15_ENST00000450363.3_Silent_p.L262L|SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Intron	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15						amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						TGGTGATTAGCAGAATGAGGA	0.408													C|||	552	0.110224	0.0076	0.2219	5008	,	,		17451	0.002		0.3042	False		,,,				2504	0.0818				p.L262L		Atlas-SNP	.											.	SLC6A15	159	.	0			c.G786A						PASS	.	C	,,	274,4132	154.8+/-188.1	13,248,1942	83.0	75.0	78.0		,786,	-1.3	0.0	12	dbSNP_123	78	2570,6030	418.1+/-352.7	411,1748,2141	no	intron,coding-synonymous,intron	SLC6A15	NM_001146335.1,NM_018057.5,NM_182767.4	,,	424,1996,4083	TT,TC,CC		29.8837,6.2188,21.8668	,,	,262/290,	85277608	2844,10162	2203	4300	6503	SO:0001627	intron_variant	55117	exon5			GATTAGCAGAATG	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.756+29G>A	12.37:g.85277608C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Silent	SNP	ENST00000266682.5	37	CCDS9026.1																																																																																			C|0.801;T|0.199	0.199	strong		0.408	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
LINC00283	100874057	hgsc.bcm.edu	37	13	103396716	103396716	+	RNA	SNP	C	C	G	rs6491708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103396716C>G	ENST00000430111.1	+	0	1089									long intergenic non-protein coding RNA 283																		GCAGTTTTCTCAGAAATAGAA	0.373													C|||	3479	0.694688	0.5424	0.7493	5008	,	,		19636	0.5913		0.827	False		,,,				2504	0.8323				p.E2111Q		Atlas-SNP	.											.	.	.	.	0			c.G6331C						PASS	.	C	GLN/GLU	773,611		217,339,136	69.0	55.0	59.0		6331	0.4	0.0	13	dbSNP_116	59	2544,636		1024,496,70	yes	missense	CCDC168	NM_001146197.1	29	1241,835,206	GG,GC,CC		20.0,44.1474,27.3225		2111/7082	103396716	3317,1247	692	1590	2282			643677	exon4			TTTTCTCAGAAAT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103396716C>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.327;G|0.673	0.673	strong		0.373	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
F13B	2165	hgsc.bcm.edu	37	1	197009798	197009798	+	Silent	SNP	A	A	G	rs5998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197009798A>G	ENST00000367412.1	-	11	1849	c.1806T>C	c.(1804-1806)aaT>aaC	p.N602N	F13B_ENST00000490002.1_5'UTR	NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	602	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						TGTGTGGTCTATTGTCAAAAT	0.294													A|||	2629	0.52496	0.1921	0.6455	5008	,	,		16714	0.8194		0.501	False		,,,				2504	0.6104				p.N602N		Atlas-SNP	.											.	F13B	137	.	0			c.T1806C						PASS	.	A		1010,3390	369.3+/-319.0	137,736,1327	59.0	56.0	57.0		1806	-4.4	0.9	1	dbSNP_52	57	4038,4552	551.5+/-385.9	967,2104,1224	no	coding-synonymous	F13B	NM_001994.2		1104,2840,2551	GG,GA,AA		47.0081,22.9545,38.8607		602/662	197009798	5048,7942	2200	4295	6495	SO:0001819	synonymous_variant	2165	exon11			TGGTCTATTGTCA	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.1806T>C	1.37:g.197009798A>G		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	305	149	0.488525	NM_001994	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	37	CCDS1388.1																																																																																			A|0.547;G|0.453	0.453	strong		0.294	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994	
SHQ1	55164	hgsc.bcm.edu	37	3	72891547	72891547	+	Missense_Mutation	SNP	A	A	C	rs78491606	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:72891547A>C	ENST00000325599.8	-	3	354	c.215T>G	c.(214-216)tTt>tGt	p.F72C	SHQ1_ENST00000463369.1_Missense_Mutation_p.F44C	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	72	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.				negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		GCGAATGGTAAAAATTCCTTA	0.403													A|||	21	0.00419329	0.0008	0.0058	5008	,	,		13803	0.0		0.0149	False		,,,				2504	0.001				p.F72C		Atlas-SNP	.											.	SHQ1	60	.	0			c.T215G						PASS	.	A	CYS/PHE	19,4387	26.2+/-53.5	0,19,2184	63.0	63.0	63.0		215	6.0	1.0	3	dbSNP_131	63	157,8443	71.6+/-134.2	1,155,4144	no	missense	SHQ1	NM_018130.2	205	1,174,6328	CC,CA,AA		1.8256,0.4312,1.3532	probably-damaging	72/578	72891547	176,12830	2203	4300	6503	SO:0001583	missense	55164	exon3			ATGGTAAAAATTC	BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"""SHQ1 homolog (S. cerevisiae)"""			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.215T>G	3.37:g.72891547A>C	ENSP00000315182:p.Phe72Cys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_018130	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	37	CCDS33788.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	0	0.0	11	0.014511873350923483	A	22.7	4.330244	0.81690	0.004312	0.018256	ENSG00000144736	ENST00000325599;ENST00000463369	T;T	0.37915	1.55;1.17	5.96	5.96	0.96718	CS-like domain (1);HSP20-like chaperone (1);	0.051164	0.85682	D	0.000000	T	0.43411	0.1246	M	0.70275	2.135	0.58432	D	0.999992	D	0.89917	1.0	D	0.70935	0.971	T	0.57382	-0.7821	10	0.87932	D	0	0.0048	15.4115	0.74929	1.0:0.0:0.0:0.0	.	72	Q6PI26	SHQ1_HUMAN	C	72;44	ENSP00000315182:F72C;ENSP00000417452:F44C	ENSP00000315182:F72C	F	-	2	0	SHQ1	72974237	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.278000	0.89899	2.285000	0.76669	0.482000	0.46254	TTT	A|0.989;C|0.011	0.011	strong		0.403	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130	
GEMIN4	50628	hgsc.bcm.edu	37	17	650510	650510	+	Missense_Mutation	SNP	T	T	C	rs61753060	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:650510T>C	ENST00000319004.5	-	2	891	c.773A>G	c.(772-774)cAg>cGg	p.Q258R	GEMIN4_ENST00000437269.1_Missense_Mutation_p.R171G|GEMIN4_ENST00000576778.1_Missense_Mutation_p.Q247R	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	258					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		AGACACCTCCTGGGGGTCGTC	0.612													T|||	111	0.0221645	0.0234	0.0058	5008	,	,		19984	0.0446		0.0089	False		,,,				2504	0.0225				p.Q258R		Atlas-SNP	.											.	GEMIN4	116	.	0			c.A773G						PASS	.	T	ARG/GLN	63,4279		0,63,2108	97.0	107.0	104.0		773	4.4	1.0	17	dbSNP_129	104	88,8434		1,86,4174	yes	missense	GEMIN4	NM_015721.2	43	1,149,6282	CC,CT,TT		1.0326,1.4509,1.1738	benign	258/1059	650510	151,12713	2171	4261	6432	SO:0001583	missense	50628	exon2			ACCTCCTGGGGGT	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.773A>G	17.37:g.650510T>C	ENSP00000321706:p.Gln258Arg	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	164	68	0.414634	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	44|44	0.020146520146520148|0.020146520146520148	12|12	0.024390243902439025|0.024390243902439025	1|1	0.0027624309392265192|0.0027624309392265192	25|25	0.043706293706293704|0.043706293706293704	6|6	0.0079155672823219|0.0079155672823219	T|T	10.17|10.17	1.276986|1.276986	0.23307|0.23307	0.014509|0.014509	0.010326|0.010326	ENSG00000179409|ENSG00000179409	ENST00000319004|ENST00000437269	T|.	0.15139|.	2.45|.	5.5|5.5	4.43|4.43	0.53597|0.53597	.|.	0.561060|.	0.18662|.	N|.	0.134683|.	T|T	0.09774|0.09774	0.0240|0.0240	L|L	0.46157|0.46157	1.445|1.445	0.20489|0.20489	N|N	0.999894|0.999894	B|B	0.15473|0.09022	0.013|0.002	B|B	0.15052|0.08055	0.012|0.003	T|T	0.06445|0.06445	-1.0826|-1.0826	10|8	0.15952|0.52906	T|T	0.53|0.07	-18.1695|-18.1695	5.8258|5.8258	0.18552|0.18552	0.1594:0.082:0.0:0.7586|0.1594:0.082:0.0:0.7586	rs61753060|rs61753060	258|171	P57678|E7EN12	GEMI4_HUMAN|.	R|G	258|171	ENSP00000321706:Q258R|.	ENSP00000321706:Q258R|ENSP00000392460:R171G	Q|R	-|-	2|1	0|2	GEMIN4|GEMIN4	597260|597260	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.757000|0.757000	0.42996|0.42996	2.088000|2.088000	0.41663|0.41663	2.094000|2.094000	0.63399|0.63399	0.528000|0.528000	0.53228|0.53228	CAG|AGG	T|0.981;C|0.019	0.019	strong		0.612	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
TMCO3	55002	hgsc.bcm.edu	37	13	114150107	114150107	+	Silent	SNP	C	C	T	rs11164135	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:114150107C>T	ENST00000434316.2	+	2	570	c.211C>T	c.(211-213)Ctg>Ttg	p.L71L	TMCO3_ENST00000375391.1_Silent_p.L71L|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	71						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			TCTGAACAAACTGAAAACTGC	0.542													C|||	630	0.125799	0.0772	0.281	5008	,	,		18842	0.1151		0.0696	False		,,,				2504	0.1503				p.L71L		Atlas-SNP	.											.	TMCO3	77	.	0			c.C211T						PASS	.	C		378,4028	189.5+/-215.6	17,344,1842	50.0	50.0	50.0		211	4.6	0.6	13	dbSNP_120	50	613,7987	161.1+/-214.1	28,557,3715	no	coding-synonymous	TMCO3	NM_017905.4		45,901,5557	TT,TC,CC		7.1279,8.5792,7.6196		71/678	114150107	991,12015	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon2			AACAAACTGAAAA	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.211C>T	13.37:g.114150107C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			C|0.913;T|0.087	0.087	strong		0.542	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
SPATC1L	84221	hgsc.bcm.edu	37	21	47581869	47581869	+	Silent	SNP	G	G	A	rs139199473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47581869G>A	ENST00000291672.5	-	4	1718	c.657C>T	c.(655-657)taC>taT	p.Y219Y	SPATC1L_ENST00000330205.6_Silent_p.Y65Y	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	219																	CCGTGAAGCCGTAGAGCCGCG	0.731																																					p.Y219Y		Atlas-SNP	.											.	.	.	.	0			c.C657T						PASS	.	G	,	2,4390		0,2,2194	32.0	28.0	29.0		657,195	-8.4	0.7	21	dbSNP_134	29	10,8576		0,10,4283	no	coding-synonymous,coding-synonymous	C21orf56	NM_001142854.1,NM_032261.4	,	0,12,6477	AA,AG,GG		0.1165,0.0455,0.0925	,	219/341,65/187	47581869	12,12966	2196	4293	6489	SO:0001819	synonymous_variant	84221	exon4			GAAGCCGTAGAGC	BC009497	CCDS13732.1, CCDS46653.1	21q22.3	2013-01-21	2012-11-12	2012-11-12	ENSG00000160284	ENSG00000160284			1298	protein-coding gene	gene with protein product	"""speriolin-like protein"""	612412	"""chromosome 21 open reading frame 56"""	C21orf56			Standard	NM_032261		Approved		uc011afu.2	Q9H0A9	OTTHUMG00000090487	ENST00000291672.5:c.657C>T	21.37:g.47581869G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Silent	SNP	ENST00000291672.5	37	CCDS46653.1																																																																																			G|1.000;A|0.000	0.000	strong		0.731	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
SLC25A26	115286	hgsc.bcm.edu	37	3	66419942	66419942	+	Silent	SNP	A	A	G	rs1129179	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:66419942A>G	ENST00000413054.1	+	6	419	c.345A>G	c.(343-345)gcA>gcG	p.A115A	SLC25A26_ENST00000336733.6_Silent_p.A115A|SLC25A26_ENST00000354883.6_Silent_p.A203A|SLC25A26_ENST00000484768.1_3'UTR|SLC25A26_ENST00000536651.1_3'UTR			Q70HW3	SAMC_HUMAN	solute carrier family 25 (S-adenosylmethionine carrier), member 26	203					S-adenosyl-L-methionine transmembrane transport (GO:1901962)|S-adenosyl-L-methionine transport (GO:0015805)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	S-adenosyl-L-methionine transmembrane transporter activity (GO:0000095)			endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)|stomach(2)|urinary_tract(1)	8		Lung NSC(201;0.00774)		BRCA - Breast invasive adenocarcinoma(55;0.00046)|KIRC - Kidney renal clear cell carcinoma(15;0.0515)|Kidney(15;0.0648)		TAGACGTGGCAAAGACAAGAA	0.408													A|||	495	0.0988419	0.0363	0.1138	5008	,	,		22024	0.0873		0.1839	False		,,,				2504	0.0971				p.A203A		Atlas-SNP	.											.	SLC25A26	12	.	0			c.A609G						PASS	.	A	,	291,4115	154.4+/-187.8	5,281,1917	92.0	83.0	86.0		345,609	-0.8	1.0	3	dbSNP_86	86	1641,6959	280.5+/-294.5	167,1307,2826	no	coding-synonymous,coding-synonymous	SLC25A26	NM_001164796.1,NM_173471.3	,	172,1588,4743	GG,GA,AA		19.0814,6.6046,14.8547	,	115/187,203/275	66419942	1932,11074	2203	4300	6503	SO:0001819	synonymous_variant	115286	exon9			CGTGGCAAAGACA	AJ580932	CCDS54604.1, CCDS2905.2	3p14.2	2013-05-22	2012-03-29		ENSG00000144741	ENSG00000144741		"""Solute carriers"""	20661	protein-coding gene	gene with protein product		611037	"""solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 26"""			14674884	Standard	NM_173471		Approved		uc011bfq.2	Q70HW3	OTTHUMG00000149917	ENST00000413054.1:c.345A>G	3.37:g.66419942A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_173471	A8K758|B3KRZ7|Q7Z786|Q96E68	Silent	SNP	ENST00000413054.1	37		251	0.11492673992673992	16	0.032520325203252036	46	0.1270718232044199	45	0.07867132867132867	144	0.18997361477572558	A	7.990	0.753079	0.15778	0.066046	0.190814	ENSG00000144741	ENST00000413054	.	.	.	5.38	-0.784	0.10954	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999999998	.	.	.	.	.	.	T	0.23726	-1.0180	3	.	.	.	-14.2864	3.9139	0.09214	0.3837:0.3951:0.1241:0.0971	rs1129179;rs3186774;rs17415499;rs1129179	.	.	.	R	140	.	.	Q	+	2	0	SLC25A26	66502632	0.833000	0.29383	0.999000	0.59377	0.567000	0.35839	-0.003000	0.12901	0.005000	0.14708	-0.313000	0.08912	CAA	A|0.869;G|0.131;T|0.000	0.131	strong		0.408	SLC25A26-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000313895.2	NM_173471	
OVCH2	341277	hgsc.bcm.edu	37	11	7712561	7712561	+	RNA	SNP	T	T	A	rs4519083	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7712561T>A	ENST00000533663.1	-	0	296				OVCH2_ENST00000534193.2_RNA|OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		TTTCATCTGATTGGAAGCTGA	0.522													T|||	861	0.171925	0.2776	0.1383	5008	,	,		17664	0.1627		0.1382	False		,,,				2504	0.0971				p.Q526H		Atlas-SNP	.											.	OVCH2	47	.	0			c.A1578T						PASS	.	T	HIS/GLN	958,2910		123,712,1099	62.0	62.0	62.0		1578	-1.6	0.4	11	dbSNP_111	62	1212,7064		79,1054,3005	yes	missense	OVCH2	NM_198185.2	24	202,1766,4104	AA,AT,TT		14.6448,24.7673,17.8689	benign	526/565	7712561	2170,9974	1934	4138	6072			341277	exon15			ATCTGATTGGAAG	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"""ovochymase 2"""			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		11.37:g.7712561T>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_198185		Missense_Mutation	SNP	ENST00000533663.1	37		374	0.17124542124542125	136	0.2764227642276423	55	0.15193370165745856	86	0.15034965034965034	97	0.1279683377308707	T	5.155	0.214109	0.09810	0.247673	0.146448	ENSG00000183378	ENST00000454689	T	0.27256	1.68	5.62	-1.65	0.08291	.	0.171732	0.27744	N	0.018040	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.43491	-0.9388	6	0.12103	T	0.63	-0.789	6.3134	0.21176	0.0:0.46:0.2284:0.3116	rs4519083;rs4519083	.	.	.	H	526	ENSP00000407158:Q526H	ENSP00000407158:Q526H	Q	-	3	2	OVCH2	7669137	0.777000	0.28628	0.412000	0.26496	0.015000	0.08874	-0.316000	0.08071	-0.655000	0.05387	-0.385000	0.06624	CAA	T|0.823;A|0.177	0.177	strong		0.522	OVCH2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000383928.1	NM_198185	
DHTKD1	55526	hgsc.bcm.edu	37	10	12162789	12162789	+	Missense_Mutation	SNP	C	C	A	rs143212640	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:12162789C>A	ENST00000263035.4	+	17	2724	c.2662C>A	c.(2662-2664)Cgt>Agt	p.R888S		NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	888					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			CTTATAGCTCCGTCTGGTGGG	0.478													C|||	5	0.000998403	0.003	0.0014	5008	,	,		17266	0.0		0.0	False		,,,				2504	0.0				p.R888S		Atlas-SNP	.											.	DHTKD1	104	.	0			c.C2662A						PASS	.	C	SER/ARG	1,4405	2.1+/-5.4	0,1,2202	78.0	71.0	74.0		2662	5.8	1.0	10	dbSNP_134	74	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DHTKD1	NM_018706.5	110	0,3,6500	AA,AC,CC		0.0233,0.0227,0.0231	benign	888/920	12162789	3,13003	2203	4300	6503	SO:0001583	missense	55526	exon17			TAGCTCCGTCTGG	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2662C>A	10.37:g.12162789C>A	ENSP00000263035:p.Arg888Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	37	CCDS7087.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	14.01	2.408119	0.42715	2.27E-4	2.33E-4	ENSG00000181192	ENST00000263035	T	0.05025	3.51	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.07593	0.0191	L	0.56340	1.77	0.80722	D	1	B	0.33826	0.427	B	0.33960	0.173	T	0.02371	-1.1169	10	0.59425	D	0.04	-10.3571	19.6057	0.95580	0.0:1.0:0.0:0.0	.	888	Q96HY7	DHTK1_HUMAN	S	888	ENSP00000263035:R888S	ENSP00000263035:R888S	R	+	1	0	DHTKD1	12202795	1.000000	0.71417	0.995000	0.50966	0.087000	0.18053	3.169000	0.50809	2.722000	0.93159	0.655000	0.94253	CGT	C|0.998;A|0.002	0.002	strong		0.478	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706	
CCDC33	80125	hgsc.bcm.edu	37	15	74560776	74560776	+	Missense_Mutation	SNP	G	G	T	rs56107695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:74560776G>T	ENST00000398814.3	+	5	954	c.523G>T	c.(523-525)Ggc>Tgc	p.G175C	CCDC33_ENST00000321288.5_Missense_Mutation_p.G378C	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	378										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CCGCTACATCGGCTGCAACCA	0.622													G|||	411	0.0820687	0.0113	0.1297	5008	,	,		14486	0.0774		0.0845	False		,,,				2504	0.1462				p.G175C		Atlas-SNP	.											.	CCDC33	160	.	0			c.G523T						PASS	.	G	CYS/GLY	82,3794		0,82,1856	46.0	52.0	50.0		523	3.8	0.0	15	dbSNP_129	50	825,7475		45,735,3370	yes	missense	CCDC33	NM_025055.3	159	45,817,5226	TT,TG,GG		9.9398,2.1156,7.4491	probably-damaging	175/756	74560776	907,11269	1938	4150	6088	SO:0001583	missense	80125	exon5			TACATCGGCTGCA	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.523G>T	15.37:g.74560776G>T	ENSP00000381795:p.Gly175Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	160	0.07326007326007326	10	0.02032520325203252	49	0.13535911602209943	40	0.06993006993006994	61	0.08047493403693931	G	9.905	1.207964	0.22205	0.021156	0.099398	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.26373	1.74;2.1	4.69	3.78	0.43462	.	0.295637	0.28327	N	0.015742	T	0.00356	0.0011	M	0.67953	2.075	0.80722	P	0.0	D	0.54601	0.967	P	0.60541	0.876	T	0.07009	-1.0795	9	0.72032	D	0.01	.	9.1664	0.37054	0.1027:0.0:0.8973:0.0	rs56107695	175	Q8N5R6-6	.	C	378;175	ENSP00000325012:G378C;ENSP00000381795:G175C	ENSP00000325012:G378C	G	+	1	0	CCDC33	72347829	0.834000	0.29399	0.003000	0.11579	0.024000	0.10985	2.465000	0.45075	0.978000	0.38470	-0.299000	0.09455	GGC	G|0.908;T|0.092	0.092	strong		0.622	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
EXOC2	55770	hgsc.bcm.edu	37	6	564145	564145	+	Silent	SNP	A	A	G	rs2277095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:564145A>G	ENST00000230449.4	-	16	1812	c.1677T>C	c.(1675-1677)caT>caC	p.H559H	EXOC2_ENST00000448181.3_Silent_p.H154H	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	559					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		TCAACGATTCATGAGTAAGTC	0.463													A|||	680	0.135783	0.1203	0.0576	5008	,	,		22822	0.4266		0.0268	False		,,,				2504	0.0245				p.H559H		Atlas-SNP	.											.	EXOC2	81	.	0			c.T1677C						PASS	.	A		461,3945	218.4+/-236.5	17,427,1759	103.0	94.0	97.0		1677	-3.4	0.5	6	dbSNP_100	97	218,8382	92.6+/-154.6	4,210,4086	no	coding-synonymous	EXOC2	NM_018303.4		21,637,5845	GG,GA,AA		2.5349,10.463,5.2207		559/925	564145	679,12327	2203	4300	6503	SO:0001819	synonymous_variant	55770	exon16			CGATTCATGAGTA	AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"""SEC5-like 1 (S. cerevisiae)"""	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1677T>C	6.37:g.564145A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Silent	SNP	ENST00000230449.4	37	CCDS34327.1																																																																																			A|0.907;G|0.093	0.093	strong		0.463	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
LAMC3	10319	hgsc.bcm.edu	37	9	133911706	133911706	+	Silent	SNP	C	C	T	rs2275131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133911706C>T	ENST00000361069.4	+	4	1096	c.963C>T	c.(961-963)gcC>gcT	p.A321A	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	321	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CCGAGGCTGCCCACGAGTGTC	0.677													C|||	1995	0.398363	0.1641	0.4885	5008	,	,		14573	0.6647		0.4791	False		,,,				2504	0.2935				p.A321A		Atlas-SNP	.											LAMC3,NS,carcinoma,0,1	LAMC3	167	1	0			c.C963T						PASS	.	C		951,3433		125,701,1366	18.0	21.0	20.0		963	4.1	0.8	9	dbSNP_100	20	4190,4386		1066,2058,1164	no	coding-synonymous	LAMC3	NM_006059.3		1191,2759,2530	TT,TC,CC		48.8573,21.6925,39.6682		321/1576	133911706	5141,7819	2192	4288	6480	SO:0001819	synonymous_variant	10319	exon4			GGCTGCCCACGAG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.963C>T	9.37:g.133911706C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			C|0.579;T|0.421	0.421	strong		0.677	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
KCNK10	54207	hgsc.bcm.edu	37	14	88652389	88652389	+	Silent	SNP	C	C	T	rs3742692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:88652389C>T	ENST00000340700.5	-	7	1558	c.1107G>A	c.(1105-1107)gcG>gcA	p.A369A	KCNK10_ENST00000312350.5_Silent_p.A374A|KCNK10_ENST00000319231.5_Silent_p.A374A	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	369					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						GGATGGTGGCCGCCCGCTGCA	0.667													C|||	1091	0.217851	0.028	0.1614	5008	,	,		15139	0.3681		0.2744	False		,,,				2504	0.3016				p.A374A		Atlas-SNP	.											KCNK10_ENST00000319231,NS,carcinoma,0,3	KCNK10	273	3	0			c.G1122A						PASS	.	C	,,	294,4094		19,256,1919	26.0	25.0	26.0		1107,1122,1122	-7.6	0.3	14	dbSNP_107	26	2384,6188		363,1658,2265	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNK10	NM_021161.4,NM_138317.2,NM_138318.2	,,	382,1914,4184	TT,TC,CC		27.8115,6.7001,20.6636	,,	369/539,374/544,374/544	88652389	2678,10282	2194	4286	6480	SO:0001819	synonymous_variant	54207	exon7			GGTGGCCGCCCGC	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6273	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 97"""	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.1107G>A	14.37:g.88652389C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Silent	SNP	ENST00000340700.5	37	CCDS9880.1																																																																																			C|0.786;T|0.214	0.214	strong		0.667	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	
TRMT13	54482	hgsc.bcm.edu	37	1	100598866	100598866	+	Missense_Mutation	SNP	G	G	A	rs35216047|rs472498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:100598866G>A	ENST00000370141.2	+	1	148	c.142G>A	c.(142-144)Gcg>Acg	p.A48T	SASS6_ENST00000462159.1_5'Flank|SASS6_ENST00000287482.5_5'Flank|TRMT13_ENST00000370143.1_Missense_Mutation_p.A48T|TRMT13_ENST00000370139.1_Missense_Mutation_p.A17T|SASS6_ENST00000535161.1_5'Flank	NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	48			A -> V (in dbSNP:rs687513).	A -> M (in Ref. 1; BAA92074 and 3; AAH75811). {ECO:0000305}.	tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										CGCTGGAGCCGCGGAGGTGTG	0.547													G|||	3788	0.75639	0.3752	0.8905	5008	,	,		17012	0.9286		0.8519	False		,,,				2504	0.9008				p.A48T		Atlas-SNP	.											.	.	.	.	0			c.G142A						PASS	.	G	THR/ALA	2012,2394	541.7+/-375.8	478,1056,669	61.0	59.0	60.0		142	4.1	1.0	1	dbSNP_83	60	7271,1329	746.5+/-407.3	3080,1111,109	yes	missense	CCDC76	NM_019083.2	58	3558,2167,778	AA,AG,GG		15.4535,45.665,28.6252	benign	48/482	100598866	9283,3723	2203	4300	6503	SO:0001583	missense	54482	exon1			GGAGCCGCGGAGG	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"""coiled-coil domain containing 76"""	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.142G>A	1.37:g.100598866G>A	ENSP00000359160:p.Ala48Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_019083	Q5VVL0|Q9NW65	Missense_Mutation	SNP	ENST00000370141.2	37	CCDS765.1	1369	0.6268315018315018	144	0.2926829268292683	271	0.7486187845303868	457	0.798951048951049	497	0.6556728232189973	G	17.08	3.297064	0.60086	0.45665	0.845465	ENSG00000122435	ENST00000370143;ENST00000370141;ENST00000370139	T;T;T	0.47528	0.87;0.87;0.84	4.99	4.07	0.47477	.	0.240042	0.40908	D	0.000994	T	0.15522	0.0374	L	0.32530	0.975	0.37821	P	0.071608	B;B	0.27971	0.196;0.196	B;B	0.22601	0.04;0.04	T	0.06954	-1.0798	9	0.15952	T	0.53	-6.197	10.3764	0.44085	0.0:0.1889:0.677:0.1341	rs472498;rs472498	48;48	B4DQS9;Q9NUP7	.;TRM13_HUMAN	T	48;48;17	ENSP00000359162:A48T;ENSP00000359160:A48T;ENSP00000359158:A17T	ENSP00000359158:A17T	A	+	1	0	CCDC76	100371454	0.755000	0.28372	0.984000	0.44739	0.972000	0.66771	2.196000	0.42686	1.308000	0.44962	0.650000	0.86243	GCG	G|0.313;A|0.687	0.687	strong		0.547	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083	
BRCA1	672	hgsc.bcm.edu	37	17	41234470	41234470	+	Silent	SNP	A	A	G	rs397509161|rs1060915	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41234470A>G	ENST00000357654.3	-	12	4426	c.4308T>C	c.(4306-4308)tcT>tcC	p.S1436S	BRCA1_ENST00000354071.3_Silent_p.S1436S|BRCA1_ENST00000351666.3_Silent_p.S253S|BRCA1_ENST00000309486.4_Silent_p.S1140S|BRCA1_ENST00000352993.3_Silent_p.S294S|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000493795.1_Silent_p.S1389S|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Silent_p.S333S|BRCA1_ENST00000346315.3_Silent_p.S1436S|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Silent_p.S1436S|BRCA1_ENST00000468300.1_Silent_p.S333S	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1436					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CAAGGGCAGAAGAGTCACTTA	0.448			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			A|||	1684	0.336262	0.1596	0.3646	5008	,	,		20402	0.371		0.3579	False		,,,				2504	0.4969				p.S1436S		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.T4308C	GRCh37	CD086610	BRCA1	D	rs1060915	PASS	.	A	,,,,	832,3574	328.8+/-300.7	77,678,1448	232.0	201.0	212.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4308,4167,999,999,4308	0.3	0.0	17	dbSNP_86	212	2804,5796	444.4+/-360.7	446,1912,1942	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	,,,,	523,2590,3390	GG,GA,AA		32.6047,18.8833,27.9563	,,,,	1436/1864,1389/1817,333/760,333/700,1436/1885	41234470	3636,9370	2203	4300	6503	SO:0001819	synonymous_variant	672	exon12	Familial Cancer Database		GGCAGAAGAGTCA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.4308T>C	17.37:g.41234470A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	164	94	0.573171	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1	663	0.30357142857142855	63	0.12804878048780488	139	0.3839779005524862	189	0.3304195804195804	272	0.35883905013192613	A	7.064	0.566994	0.13560	0.188833	0.326047	ENSG00000012048	ENST00000461574	.	.	.	5.26	0.257	0.15574	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44636	-0.9315	3	.	.	.	.	2.9468	0.05848	0.3693:0.0:0.2857:0.345	rs1060915;rs2229039;rs3201861;rs3737558;rs4986843;rs8176184;rs17434734;rs17739641;rs58905919;rs1060915	.	.	.	P	201	.	.	L	-	2	0	BRCA1	38487996	0.000000	0.05858	0.000000	0.03702	0.190000	0.23558	-0.119000	0.10676	0.129000	0.18514	0.533000	0.62120	CTT	A|0.713;G|0.287	0.287	strong		0.448	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
COL6A3	1293	hgsc.bcm.edu	37	2	238247734	238247734	+	Missense_Mutation	SNP	C	C	G	rs36104025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238247734C>G	ENST00000295550.4	-	39	8943	c.8491G>C	c.(8491-8493)Gat>Cat	p.D2831H	COL6A3_ENST00000472056.1_Missense_Mutation_p.D2224H|COL6A3_ENST00000409809.1_Missense_Mutation_p.D2625H|COL6A3_ENST00000346358.4_Missense_Mutation_p.D2631H|COL6A3_ENST00000347401.3_Missense_Mutation_p.D2630H|COL6A3_ENST00000353578.4_Missense_Mutation_p.D2625H	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2831	Nonhelical region.		D -> H (in dbSNP:rs36104025). {ECO:0000269|PubMed:15689448, ECO:0000269|PubMed:17886299, ECO:0000269|PubMed:9536084}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTCCTGATATCTGGGGACAAG	0.333													C|||	163	0.0325479	0.0083	0.0447	5008	,	,		19123	0.0		0.0716	False		,,,				2504	0.0501				p.D2831H		Atlas-SNP	.											.	COL6A3	608	.	0			c.G8491C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP	83,4323	69.8+/-107.6	4,75,2124	71.0	70.0	70.0		8491,6670,7873	5.1	1.0	2	dbSNP_126	70	853,7747	194.7+/-240.0	48,757,3495	yes	missense,missense,missense	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	81,81,81	52,832,5619	GG,GC,CC		9.9186,1.8838,7.1967	probably-damaging,probably-damaging,probably-damaging	2831/3178,2224/2571,2625/2972	238247734	936,12070	2203	4300	6503	SO:0001583	missense	1293	exon39			TGATATCTGGGGA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8491G>C	2.37:g.238247734C>G	ENSP00000295550:p.Asp2831His	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	90	0.04120879120879121	6	0.012195121951219513	16	0.04419889502762431	0	0.0	68	0.08970976253298153	C	14.74	2.624546	0.46840	0.018838	0.099186	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.89939	-2.59;-2.57;-2.55;-2.56;-2.55;-2.55	5.09	5.09	0.68999	.	0.118877	0.36893	N	0.002355	T	0.40839	0.1133	M	0.64997	1.995	0.53688	D	0.999971	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.921;0.964;0.997	T	0.72906	-0.4150	10	0.72032	D	0.01	.	18.52	0.90948	0.0:1.0:0.0:0.0	rs36104025	2224;2625;2831	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	H	2831;2630;2625;2224;2625;2631	ENSP00000295550:D2831H;ENSP00000315609:D2630H;ENSP00000315873:D2625H;ENSP00000418285:D2224H;ENSP00000386844:D2625H;ENSP00000295546:D2631H	ENSP00000295550:D2831H	D	-	1	0	COL6A3	237912473	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.416000	0.66417	2.378000	0.81104	0.655000	0.94253	GAT	C|0.942;G|0.058	0.058	strong		0.333	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
TENM2	57451	hgsc.bcm.edu	37	5	167553880	167553880	+	Silent	SNP	C	C	T	rs10055910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:167553880C>T	ENST00000518659.1	+	12	2370	c.2331C>T	c.(2329-2331)caC>caT	p.H777H	TENM2_ENST00000403607.2_Silent_p.H610H|TENM2_ENST00000520394.1_Silent_p.H545H|CTB-178M22.1_ENST00000517408.1_RNA|TENM2_ENST00000519204.1_Silent_p.H656H|TENM2_ENST00000545108.1_Silent_p.H777H	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	777	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										GCATTGAGCACGGGACCTGTA	0.607													C|||	778	0.155351	0.2572	0.1758	5008	,	,		16535	0.003		0.2336	False		,,,				2504	0.0798				p.H777H		Atlas-SNP	.											.	.	.	.	0			c.C2331T						PASS	.	C		897,3189		97,703,1243	44.0	51.0	49.0		2331	4.8	1.0	5	dbSNP_119	49	1952,6406		229,1494,2456	no	coding-synonymous	ODZ2	NM_001122679.1		326,2197,3699	TT,TC,CC		23.3549,21.953,22.8946		777/2766	167553880	2849,9595	2043	4179	6222	SO:0001819	synonymous_variant	57451	exon12			TGAGCACGGGACC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.2331C>T	5.37:g.167553880C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	191	128	0.670157	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				C|0.828;T|0.172	0.172	strong		0.607	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
BRCA1	672	hgsc.bcm.edu	37	17	41246481	41246481	+	Missense_Mutation	SNP	T	T	C	rs80357796|rs1799950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41246481T>C	ENST00000357654.3	-	10	1185	c.1067A>G	c.(1066-1068)cAg>cGg	p.Q356R	BRCA1_ENST00000354071.3_Missense_Mutation_p.Q356R|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.Q60R|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.Q309R|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.Q356R|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.Q356R|BRCA1_ENST00000468300.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	356			Q -> R (common polymorphism; dbSNP:rs1799950). {ECO:0000269|PubMed:7894493, ECO:0000269|Ref.5, ECO:0000269|Ref.6}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TGGCAGTTTCTGCTTATTCCA	0.408			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			T|||	109	0.0217652	0.003	0.0461	5008	,	,		22610	0.0		0.0596	False		,,,				2504	0.0133				p.Q356R		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.A1067G	GRCh37	CM014322	BRCA1	M	rs1799950	PASS	.	T	ARG/GLN,ARG/GLN,,,ARG/GLN	45,4361	47.5+/-82.1	0,45,2158	238.0	222.0	227.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1067,926,,,1067	3.7	0.0	17	dbSNP_89	227	552,8048	151.6+/-206.3	18,516,3766	yes	missense,missense,intron,intron,missense	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	43,43,,,43	18,561,5924	CC,CT,TT		6.4186,1.0213,4.5902	possibly-damaging,possibly-damaging,,,possibly-damaging	356/1864,309/1817,,,356/1885	41246481	597,12409	2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		AGTTTCTGCTTAT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.1067A>G	17.37:g.41246481T>C	ENSP00000350283:p.Gln356Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	61|61	0.027930402930402932|0.027930402930402932	2|2	0.0040650406504065045|0.0040650406504065045	18|18	0.049723756906077346|0.049723756906077346	0|0	0.0|0.0	41|41	0.05408970976253298|0.05408970976253298	T|T	9.735|9.735	1.163374|1.163374	0.21538|0.21538	0.010213|0.010213	0.064186|0.064186	ENSG00000012048|ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795;ENST00000470026;ENST00000477152;ENST00000497488;ENST00000494123|ENST00000473961	D;D;D;D;D;D;D;D;D;D|.	0.91843|.	-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92|.	4.81|4.81	3.71|3.71	0.42584|0.42584	.|.	0.255608|.	0.28247|.	N|.	0.016049|.	T|T	0.29556|0.29556	0.0737|0.0737	H|H	0.95187|0.95187	3.635|3.635	0.09310|0.09310	N|N	1|1	D;D;D;D;D;D|.	0.76494|.	0.997;0.997;0.987;0.999;0.998;0.995|.	D;D;D;D;D;D|.	0.76575|.	0.933;0.933;0.944;0.988;0.988;0.969|.	T|T	0.53344|0.53344	-0.8452|-0.8452	10|5	0.66056|.	D|.	0.02|.	.|.	10.444|10.444	0.44483|0.44483	0.0:0.0:0.1705:0.8295|0.0:0.0:0.1705:0.8295	rs1799950;rs4986851;rs17846597;rs17859679;rs52822238;rs1799950|rs1799950;rs4986851;rs17846597;rs17859679;rs52822238;rs1799950	356;315;356;356;356;356|.	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2|.	.;.;.;.;BRCA1_HUMAN;.|.	R|G	356;356;356;356;60;356;309;356;330;60;356|222	ENSP00000350283:Q356R;ENSP00000326002:Q356R;ENSP00000246907:Q356R;ENSP00000310938:Q60R;ENSP00000418960:Q356R;ENSP00000418775:Q309R;ENSP00000419274:Q356R;ENSP00000419988:Q330R;ENSP00000418986:Q60R;ENSP00000419103:Q356R|.	ENSP00000310938:Q60R|.	Q|R	-|-	2|1	0|2	BRCA1|BRCA1	38500007|38500007	0.996000|0.996000	0.38824|0.38824	0.045000|0.045000	0.18777|0.18777	0.005000|0.005000	0.04900|0.04900	2.364000|2.364000	0.44187|0.44187	0.939000|0.939000	0.37446|0.37446	0.533000|0.533000	0.62120|0.62120	CAG|AGA	T|0.960;C|0.040	0.040	strong		0.408	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
ANKRD12	23253	hgsc.bcm.edu	37	18	9254785	9254785	+	Missense_Mutation	SNP	C	C	T	rs17498752	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:9254785C>T	ENST00000262126.4	+	9	1760	c.1520C>T	c.(1519-1521)aCt>aTt	p.T507I	ANKRD12_ENST00000400020.3_Missense_Mutation_p.T484I|ANKRD12_ENST00000383440.2_Missense_Mutation_p.T484I	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	507			T -> I (in dbSNP:rs17498752).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						ACAGTAAATACTGGACTAGAT	0.308													C|||	231	0.0461262	0.0408	0.0447	5008	,	,		19707	0.0446		0.0706	False		,,,				2504	0.0307				p.T507I		Atlas-SNP	.											.	ANKRD12	167	.	0			c.C1520T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	202,4200	115.4+/-153.4	10,182,2009	51.0	53.0	52.0		1451,1451,1520	5.9	0.4	18	dbSNP_123	52	644,7952	158.2+/-211.7	25,594,3679	yes	missense,missense,missense	ANKRD12	NM_001083625.2,NM_001204056.1,NM_015208.4	89,89,89	35,776,5688	TT,TC,CC		7.4919,4.5888,6.5087	benign,benign,benign	484/2040,484/2040,507/2063	9254785	846,12152	2201	4298	6499	SO:0001583	missense	23253	exon9			TAAATACTGGACT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1520C>T	18.37:g.9254785C>T	ENSP00000262126:p.Thr507Ile	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	125	75	0.6	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	123	0.05631868131868132	19	0.03861788617886179	17	0.04696132596685083	29	0.050699300699300696	58	0.07651715039577836	C	13.65	2.300313	0.40694	0.045888	0.074919	ENSG00000101745	ENST00000383440;ENST00000262126;ENST00000359158	D;D	0.92545	-3.06;-3.06	5.86	5.86	0.93980	.	0.275088	0.41823	D	0.000803	T	0.48519	0.1504	L	0.43152	1.355	0.27502	P	0.9519687	P;P;B	0.42203	0.773;0.573;0.437	P;B;B	0.45829	0.494;0.232;0.117	T	0.74266	-0.3721	9	0.36615	T	0.2	-21.2968	20.1951	0.98241	0.0:1.0:0.0:0.0	rs17498752;rs52833875;rs59978019;rs17498752	134;484;507	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	I	484;507;214	ENSP00000372932:T484I;ENSP00000262126:T507I	ENSP00000262126:T507I	T	+	2	0	ANKRD12	9244785	1.000000	0.71417	0.437000	0.26809	0.800000	0.45204	7.294000	0.78760	2.780000	0.95670	0.585000	0.79938	ACT	C|0.938;T|0.062	0.062	strong		0.308	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
CARM1	10498	hgsc.bcm.edu	37	19	11031118	11031118	+	Silent	SNP	C	C	T	rs370080653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11031118C>T	ENST00000327064.4	+	11	1393	c.1203C>T	c.(1201-1203)acC>acT	p.T401T	CARM1_ENST00000344150.4_Silent_p.T401T	NM_199141.1	NP_954592.1	Q86X55	CARM1_HUMAN	coactivator-associated arginine methyltransferase 1	401	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cellular lipid metabolic process (GO:0044255)|endochondral bone morphogenesis (GO:0060350)|histone H3-R17 methylation (GO:0034971)|histone H3-R2 methylation (GO:0034970)|histone methylation (GO:0016571)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of protein binding (GO:0032091)|pathogenesis (GO:0009405)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-R17 specific) (GO:0035642)|histone-arginine N-methyltransferase activity (GO:0008469)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|lysine-acetylated histone binding (GO:0070577)|protein methyltransferase activity (GO:0008276)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	13						ACAGAATGACCGTGTGGCTGT	0.637													c|||	2	0.000399361	0.0	0.0	5008	,	,		18314	0.002		0.0	False		,,,				2504	0.0				p.T401T		Atlas-SNP	.											CARM1,NS,carcinoma,0,1	CARM1	47	1	0			c.C1203T						scavenged	.						56.0	48.0	51.0					19																	11031118		2203	4299	6502	SO:0001819	synonymous_variant	10498	exon11			AATGACCGTGTGG	AF055027	CCDS12250.1	19p13.2	2010-10-11			ENSG00000142453	ENSG00000142453		"""Protein arginine methyltransferases"""	23393	protein-coding gene	gene with protein product		603934				10381882, 11724789	Standard	NM_199141		Approved	PRMT4	uc002mpz.3	Q86X55		ENST00000327064.4:c.1203C>T	19.37:g.11031118C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	3	0.0288462	NM_199141	A6NN38	Silent	SNP	ENST00000327064.4	37	CCDS12250.1																																																																																			.	.	weak		0.637	CARM1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452625.1	XM_032719	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68705674	68705674	+	Missense_Mutation	SNP	C	C	A	rs17612126	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:68705674C>A	ENST00000255078.3	+	14	2747	c.2636C>A	c.(2635-2637)aCg>aAg	p.T879K		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	879			T -> K (in HMN6; dbSNP:rs17612126). {ECO:0000269|PubMed:15797190}.		ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GATCTGCCCACGGAGGAGGAC	0.562													C|||	987	0.197085	0.0166	0.438	5008	,	,		17099	0.2212		0.2654	False		,,,				2504	0.1748				p.T879K		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.C2636A	GRCh37	CM055288	IGHMBP2	M	rs17612126	PASS	.	C	LYS/THR	342,4058	176.6+/-205.7	17,308,1875	68.0	72.0	71.0		2636	-3.6	0.0	11	dbSNP_123	71	2387,6201	396.4+/-345.4	341,1705,2248	yes	missense	IGHMBP2	NM_002180.2	78	358,2013,4123	AA,AC,CC		27.7946,7.7727,21.0117	benign	879/994	68705674	2729,10259	2200	4294	6494	SO:0001583	missense	3508	exon14			TGCCCACGGAGGA	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.2636C>A	11.37:g.68705674C>A	ENSP00000255078:p.Thr879Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	493	0.22573260073260074	9	0.018292682926829267	139	0.3839779005524862	144	0.2517482517482518	201	0.26517150395778366	C	0.585	-0.835530	0.02713	0.077727	0.277946	ENSG00000132740	ENST00000255078	D	0.89415	-2.51	3.9	-3.62	0.04543	Zinc finger, AN1-type (1);	7.534400	0.00166	N	0.000004	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	1.0000000000287557E-6	B	0.28552	0.215	B	0.20577	0.03	T	0.44651	-0.9314	9	0.05959	T	0.93	-10.2922	0.3694	0.00377	0.2403:0.26:0.2553:0.2443	rs17612126;rs52812152;rs61068197;rs17612126	879	P38935	SMBP2_HUMAN	K	879	ENSP00000255078:T879K	ENSP00000255078:T879K	T	+	2	0	IGHMBP2	68462250	0.523000	0.26274	0.000000	0.03702	0.020000	0.10135	0.878000	0.28126	-0.893000	0.03930	0.462000	0.41574	ACG	C|0.791;A|0.209	0.209	strong		0.562	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
GFM2	84340	hgsc.bcm.edu	37	5	74046464	74046464	+	Silent	SNP	C	C	T	rs17852781	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:74046464C>T	ENST00000296805.3	-	7	916	c.459G>A	c.(457-459)gaG>gaA	p.E153E	GFM2_ENST00000509430.1_Silent_p.E153E|GFM2_ENST00000427854.2_Silent_p.E153E|GFM2_ENST00000345239.2_Silent_p.E153E	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TTAGGCACCGCTCAACCTCCA	0.403													C|||	909	0.18151	0.2466	0.2003	5008	,	,		18814	0.1855		0.1024	False		,,,				2504	0.1575				p.E153E		Atlas-SNP	.											.	GFM2	38	.	0			c.G459A						PASS	.	C	,,	944,3462	358.6+/-314.5	102,740,1361	91.0	78.0	82.0		459,459,459	-0.6	1.0	5	dbSNP_123	82	839,7761	192.5+/-238.5	42,755,3503	no	coding-synonymous,coding-synonymous,coding-synonymous	GFM2	NM_032380.3,NM_170681.1,NM_170691.1	,,	144,1495,4864	TT,TC,CC		9.7558,21.4253,13.7091	,,	153/780,153/514,153/733	74046464	1783,11223	2203	4300	6503	SO:0001819	synonymous_variant	84340	exon7			GCACCGCTCAACC	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.459G>A	5.37:g.74046464C>T		Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	350	156	0.445714	NM_032380		Silent	SNP	ENST00000296805.3	37	CCDS4023.1																																																																																			C|0.854;T|0.146	0.146	strong		0.403	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
GNPAT	8443	hgsc.bcm.edu	37	1	231376806	231376806	+	5'Flank	SNP	G	G	C	rs2274067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:231376806G>C	ENST00000366647.4	+	0	0				C1orf131_ENST00000366649.2_Missense_Mutation_p.L28V|C1orf131_ENST00000366651.3_Missense_Mutation_p.L28V|C1orf131_ENST00000471936.1_5'UTR|GNPAT_ENST00000366646.3_5'Flank|C1orf131_ENST00000318906.2_Missense_Mutation_p.L28V	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				GCGTCAAGAAGTGTCGGAGAA	0.607													G|||	441	0.0880591	0.0356	0.2003	5008	,	,		15558	0.0863		0.0616	False		,,,				2504	0.1084				p.L28V		Atlas-SNP	.											.	C1orf131	30	.	0			c.C82G						PASS	.	G	VAL/LEU	210,4196	129.4+/-166.1	4,202,1997	112.0	113.0	113.0		82	3.1	0.0	1	dbSNP_100	113	888,7712	199.7+/-243.7	52,784,3464	yes	missense	C1orf131	NM_152379.2	32	56,986,5461	CC,CG,GG		10.3256,4.7662,8.4423	probably-damaging	28/294	231376806	1098,11908	2203	4300	6503	SO:0001631	upstream_gene_variant	128061	exon1			CAAGAAGTGTCGG	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024		1.37:g.231376806G>C	Exception_encountered	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_152379	B4DNM9|Q5TBH7|Q9BWC2	Missense_Mutation	SNP	ENST00000366647.4	37	CCDS1592.1	175	0.08012820512820513	31	0.06300813008130081	47	0.1298342541436464	50	0.08741258741258741	47	0.06200527704485488	G	16.78	3.218801	0.58560	0.047662	0.103256	ENSG00000143633	ENST00000366649;ENST00000318906;ENST00000366651;ENST00000366648;ENST00000451322	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.06	3.14	0.36123	.	0.295055	0.27266	N	0.020149	T	0.00328	0.0010	M	0.68952	2.095	0.80722	P	0.0	D;D;D;D;D	0.71674	0.998;0.997;0.998;0.998;0.998	D;D;D;D;D	0.83275	0.996;0.932;0.996;0.996;0.996	T	0.02668	-1.1126	9	0.62326	D	0.03	-13.3122	7.914	0.29808	0.0877:0.1623:0.75:0.0	rs2274067;rs17800413;rs17846596;rs17859678;rs56447138;rs2274067	28;28;28;28;28	B4E0F7;Q8NDD1-4;Q8NDD1;Q8NDD1-3;Q8NDD1-2	.;.;CA131_HUMAN;.;.	V	28;28;28;18;11	ENSP00000355609:L28V;ENSP00000321341:L28V;ENSP00000355611:L28V;ENSP00000401677:L11V	ENSP00000321341:L28V	L	-	1	0	C1orf131	229443429	0.517000	0.26226	0.003000	0.11579	0.012000	0.07955	3.041000	0.49807	0.689000	0.31550	0.650000	0.86243	CTT	G|0.919;C|0.081	0.081	strong		0.607	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1		
ZNF45	7596	hgsc.bcm.edu	37	19	44418343	44418343	+	Silent	SNP	C	C	T	rs406968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44418343C>T	ENST00000269973.5	-	10	2335	c.1245G>A	c.(1243-1245)ccG>ccA	p.P415P	ZNF45_ENST00000589703.1_Silent_p.P415P|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	415					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						CACACTGATACGGTTTCTCTC	0.463													C|||	2629	0.52496	0.3343	0.647	5008	,	,		22173	0.7996		0.5169	False		,,,				2504	0.4213				p.P415P		Atlas-SNP	.											ZNF45,caecum,carcinoma,0,1	ZNF45	51	1	0			c.G1245A						PASS	.	C		1581,2825	494.1+/-362.9	294,993,916	90.0	85.0	87.0		1245	-7.4	0.4	19	dbSNP_80	87	4352,4248	581.0+/-391.2	1118,2116,1066	no	coding-synonymous	ZNF45	NM_003425.3		1412,3109,1982	TT,TC,CC		49.3953,35.8829,45.6174		415/683	44418343	5933,7073	2203	4300	6503	SO:0001819	synonymous_variant	7596	exon10			CTGATACGGTTTC	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"""Zinc fingers, C2H2-type"", ""-"""	13111	protein-coding gene	gene with protein product		194554	"""zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)"", ""zinc finger protein 13"""	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.1245G>A	19.37:g.44418343C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	215	106	0.493023	NM_003425	P17016|P78472|Q9P1U9	Silent	SNP	ENST00000269973.5	37	CCDS12632.1																																																																																			C|0.504;T|0.496	0.496	strong		0.463	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
EP300	2033	hgsc.bcm.edu	37	22	41551039	41551039	+	Silent	SNP	T	T	A	rs20552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:41551039T>A	ENST00000263253.7	+	17	4402	c.3183T>A	c.(3181-3183)acT>acA	p.T1061T		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1061					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TGATGCCAACTTTGGAGGCAC	0.388			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				A|||	3375	0.673922	0.5091	0.7695	5008	,	,		17967	0.8175		0.6352	False		,,,				2504	0.7209				p.T1061T		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.T3183A						PASS	.	A		2246,2160	582.1+/-385.5	583,1080,540	214.0	200.0	205.0		3183	-2.4	0.2	22	dbSNP_67	205	5338,3262	490.3+/-372.8	1690,1958,652	no	coding-synonymous	EP300	NM_001429.3		2273,3038,1192	AA,AT,TT		37.9302,49.0241,41.6885		1061/2415	41551039	7584,5422	2203	4300	6503	SO:0001819	synonymous_variant	2033	exon17	Familial Cancer Database	Broad Thumb-Hallux syndrome	GCCAACTTTGGAG	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3183T>A	22.37:g.41551039T>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	37	CCDS14010.1																																																																																			T|0.375;A|0.625	0.625	strong		0.388	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
ZCCHC7	84186	hgsc.bcm.edu	37	9	37304232	37304232	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37304232C>T	ENST00000336755.5	+	4	808	c.702C>T	c.(700-702)taC>taT	p.Y234Y	ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_5'UTR	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	234						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		CCCAGCGGTACTATTCAGCCA	0.363																																					p.Y234Y		Atlas-SNP	.											.	ZCCHC7	56	.	0			c.C702T						PASS	.						99.0	95.0	96.0					9																	37304232		2203	4300	6503	SO:0001819	synonymous_variant	84186	exon4			GCGGTACTATTCA	AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"""Zinc fingers, CCHC domain containing"""	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.702C>T	9.37:g.37304232C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	107	25	0.233645	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Silent	SNP	ENST00000336755.5	37	CCDS6608.2																																																																																			.	.	none		0.363	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226	
ZNF880	400713	hgsc.bcm.edu	37	19	52888049	52888049	+	Missense_Mutation	SNP	C	C	A	rs75346003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52888049C>A	ENST00000422689.2	+	4	1231	c.1216C>A	c.(1216-1218)Caa>Aaa	p.Q406K		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	406					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CACGGGAGAGCAACCTTACAA	0.398																																					p.Q406K		Atlas-SNP	.											ZNF880,colon,carcinoma,-1,2	ZNF880	45	2	0			c.C1216A						PASS	.						69.0	63.0	65.0					19																	52888049		1568	3582	5150	SO:0001583	missense	400713	exon4			GGAGAGCAACCTT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1216C>A	19.37:g.52888049C>A	ENSP00000406318:p.Gln406Lys	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	14	0.325581	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.634723	0.00114	.	.	ENSG00000221923	ENST00000422689	T	0.10860	2.83	1.84	0.731	0.18277	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01835	0.0058	N	0.00128	-2.045	0.20638	N	0.999879	B	0.17667	0.023	B	0.14023	0.01	T	0.46105	-0.9215	8	.	.	.	.	6.7224	0.23338	0.7399:0.2601:0.0:0.0	.	406	Q6PDB4	ZN880_HUMAN	K	406	ENSP00000406318:Q406K	.	Q	+	1	0	ZNF880	57579861	0.006000	0.16342	0.407000	0.26434	0.151000	0.21798	0.708000	0.25719	0.007000	0.14760	-0.493000	0.04662	CAA	C|0.872;A|0.128	0.128	strong		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ANP32D	23519	hgsc.bcm.edu	37	12	48866792	48866792	+	Silent	SNP	C	C	T	rs7966826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48866792C>T	ENST00000266594.1	+	1	345	c.345C>T	c.(343-345)ctC>ctT	p.L115L		NM_012404.2	NP_036536.2	O95626	AN32D_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member D	115						nuclear matrix (GO:0016363)		p.L115L(1)		central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	9						TAGAAAACCTCGAGAGCTTAG	0.413													c|||	1454	0.290335	0.1604	0.3357	5008	,	,		20687	0.6548		0.0815	False		,,,				2504	0.273				p.L115L		Atlas-SNP	.											ANP32D,NS,carcinoma,0,1	ANP32D	15	1	1	Substitution - coding silent(1)	stomach(1)	c.C345T						PASS	.	C		683,3723	286.0+/-278.5	51,581,1571	85.0	85.0	85.0		345	-1.5	0.0	12	dbSNP_116	85	555,8045	151.2+/-206.0	18,519,3763	no	coding-synonymous	ANP32D	NM_012404.2		69,1100,5334	TT,TC,CC		6.4535,15.5016,9.5187		115/132	48866792	1238,11768	2203	4300	6503	SO:0001819	synonymous_variant	23519	exon1			AAACCTCGAGAGC	U71084	CCDS31788.1	12q13.12	2008-08-04			ENSG00000139223	ENSG00000139223		"""ANP32 acidic nuclear phosphoproteins"""	16676	protein-coding gene	gene with protein product	"""pp32 related 2"""	606878				10086381, 10400610	Standard	NM_012404		Approved	PP32R2	uc010slt.2	O95626	OTTHUMG00000162681	ENST00000266594.1:c.345C>T	12.37:g.48866792C>T		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	253	113	0.44664	NM_012404	Q6NTC4	Silent	SNP	ENST00000266594.1	37	CCDS31788.1																																																																																			C|0.833;T|0.167	0.167	strong		0.413	ANP32D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370058.1	NM_012404	
NACA2	342538	hgsc.bcm.edu	37	17	59668021	59668021	+	Missense_Mutation	SNP	G	G	C	rs61739273	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59668021G>C	ENST00000521764.1	-	1	542	c.521C>G	c.(520-522)aCa>aGa	p.T174R		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	174					myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					TTCTACACCTGTTTCATCGAC	0.423													G|||	747	0.149161	0.0575	0.1037	5008	,	,		21948	0.1667		0.1471	False		,,,				2504	0.2894				p.T174R		Atlas-SNP	.											NACA2,NS,carcinoma,0,2	NACA2	33	2	0			c.C521G						PASS	.	G	ARG/THR	329,4077	171.9+/-202.1	15,299,1889	304.0	274.0	284.0		521	0.8	0.8	17	dbSNP_129	284	1249,7351	248.6+/-276.2	97,1055,3148	yes	missense	NACA2	NM_199290.3	71	112,1354,5037	CC,CG,GG		14.5233,7.4671,12.1329	possibly-damaging	174/216	59668021	1578,11428	2203	4300	6503	SO:0001583	missense	342538	exon1			ACACCTGTTTCAT	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.521C>G	17.37:g.59668021G>C	ENSP00000427802:p.Thr174Arg	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	263	119	0.452471	NM_199290	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	254	0.1163003663003663	26	0.052845528455284556	40	0.11049723756906077	73	0.12762237762237763	115	0.1517150395778364	G	12.97	2.098780	0.37048	0.074671	0.145233	ENSG00000253506	ENST00000521764	T	0.48836	0.8	0.753	0.753	0.18404	.	0.154695	0.40728	U	0.001024	T	0.00384	0.0012	M	0.92367	3.3	0.20403	P	0.9999081527	B	0.29909	0.261	B	0.29440	0.102	T	0.10847	-1.0612	8	.	.	.	.	7.3227	0.26536	0.0:0.0:1.0:0.0	rs61739273	174	Q9H009	NACA2_HUMAN	R	174	ENSP00000427802:T174R	.	T	-	2	0	NACA2	57022803	1.000000	0.71417	0.822000	0.32727	0.313000	0.28021	3.630000	0.54273	0.702000	0.31825	0.411000	0.27672	ACA	G|0.868;C|0.132	0.132	strong		0.423	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
MCEE	84693	hgsc.bcm.edu	37	2	71351487	71351487	+	Missense_Mutation	SNP	G	G	A	rs11541017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71351487G>A	ENST00000244217.5	-	2	244	c.227C>T	c.(226-228)gCg>gTg	p.A76V	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	76			A -> V (in dbSNP:rs11541017).		cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						AAGAGGGACCGCTTCACTTAC	0.473													g|||	914	0.182508	0.0318	0.2695	5008	,	,		15349	0.0446		0.3956	False		,,,				2504	0.2474				p.A76V		Atlas-SNP	.											MCEE,colon,carcinoma,0,2	MCEE	19	2	0			c.C227T						scavenged	.	A	VAL/ALA	357,4049	183.3+/-210.9	17,323,1863	104.0	106.0	105.0		227	-4.1	0.0	2	dbSNP_120	105	3202,5398	484.1+/-371.3	627,1948,1725	yes	missense	MCEE	NM_032601.3	64	644,2271,3588	AA,AG,GG		37.2326,8.1026,27.3643	benign	76/177	71351487	3559,9447	2203	4300	6503	SO:0001583	missense	84693	exon2			GGGACCGCTTCAC	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"""glyoxalase domain containing 2"""	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.227C>T	2.37:g.71351487G>A	ENSP00000244217:p.Ala76Val	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_032601	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	450	0.20604395604395603	15	0.03048780487804878	109	0.3011049723756906	26	0.045454545454545456	300	0.39577836411609496	g	9.982	1.228432	0.22542	0.081026	0.372326	ENSG00000124370	ENST00000244217	T	0.62639	0.01	5.39	-4.05	0.03998	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.856358	0.10314	N	0.689564	T	0.00012	0.0000	N	0.13299	0.325	0.80722	P	0.0	B	0.15930	0.015	B	0.08055	0.003	T	0.37150	-0.9718	9	0.18710	T	0.47	-16.0397	7.0962	0.25311	0.4702:0.0:0.4227:0.107	rs11541017;rs59298445;rs11541017	76	Q96PE7	MCEE_HUMAN	V	76	ENSP00000244217:A76V	ENSP00000244217:A76V	A	-	2	0	MCEE	71204995	0.000000	0.05858	0.000000	0.03702	0.597000	0.36814	-0.150000	0.10189	-1.116000	0.02969	-0.127000	0.14921	GCG	G|0.753;A|0.247	0.247	strong		0.473	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601	
PIAS4	51588	hgsc.bcm.edu	37	19	4028783	4028783	+	Silent	SNP	C	C	T	rs2289863	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4028783C>T	ENST00000262971.2	+	6	853	c.738C>T	c.(736-738)acC>acT	p.T246T	PIAS4_ENST00000596144.1_3'UTR	NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	246	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(3)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		TCAACCTCACCCACCTCATGT	0.662													C|||	2958	0.590655	0.1188	0.7622	5008	,	,		12251	0.9147		0.7167	False		,,,				2504	0.6431				p.T246T		Atlas-SNP	.											PIAS4,colon,carcinoma,0,1	PIAS4	40	1	0			c.C738T						PASS	.	C		985,3421	362.1+/-316.0	104,777,1322	98.0	84.0	89.0		738	1.0	1.0	19	dbSNP_100	89	6404,2196	708.2+/-405.6	2411,1582,307	no	coding-synonymous	PIAS4	NM_015897.2		2515,2359,1629	TT,TC,CC		25.5349,22.3559,43.1878		246/511	4028783	7389,5617	2203	4300	6503	SO:0001819	synonymous_variant	51588	exon6			CCTCACCCACCTC	AF077952	CCDS12118.1	19p13.3	2011-10-11						"""Zinc fingers, MIZ-type"""	17002	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 6"""	605989				9724754	Standard	NM_015897		Approved	Piasg, PIASY, FLJ12419, ZMIZ6	uc002lzg.3	Q8N2W9		ENST00000262971.2:c.738C>T	19.37:g.4028783C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	122	47	0.385246	NM_015897	O75926|Q96G19|Q9UN16	Silent	SNP	ENST00000262971.2	37	CCDS12118.1																																																																																			C|0.412;T|0.588	0.588	strong		0.662	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897	
C6orf195	154386	hgsc.bcm.edu	37	6	2623930	2623930	+	Missense_Mutation	SNP	G	G	A	rs9503233	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:2623930G>A	ENST00000296847.3	-	3	650	c.127C>T	c.(127-129)Ccc>Tcc	p.P43S		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	43			P -> S (in dbSNP:rs9503233). {ECO:0000269|PubMed:15489334}.							cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				CTTAGAGCGGGCCTGGCTCCT	0.622													G|||	542	0.108227	0.0832	0.1009	5008	,	,		18472	0.0337		0.2107	False		,,,				2504	0.1186				p.P43S		Atlas-SNP	.											.	C6orf195	10	.	0			c.C127T						PASS	.	G	SER/PRO	406,3626		22,362,1632	45.0	53.0	50.0		127	-2.5	0.0	6	dbSNP_119	50	1691,6643		167,1357,2643	yes	missense	C6orf195	NM_152554.2	74	189,1719,4275	AA,AG,GG		20.2904,10.0694,16.9578	benign	43/128	2623930	2097,10269	2016	4167	6183	SO:0001583	missense	154386	exon3			GAGCGGGCCTGGC	AK056496	CCDS43416.1	6p25.2	2008-10-21			ENSG00000164385	ENSG00000164385			21600	protein-coding gene	gene with protein product							Standard	NM_152554		Approved	FLJ31934, bA145H9.2	uc003mtw.2	Q96MT4	OTTHUMG00000014122	ENST00000296847.3:c.127C>T	6.37:g.2623930G>A	ENSP00000296847:p.Pro43Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_152554	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Missense_Mutation	SNP	ENST00000296847.3	37	CCDS43416.1	255	0.11675824175824176	46	0.09349593495934959	34	0.09392265193370165	19	0.033216783216783216	156	0.20580474934036938	G	5.756	0.323829	0.10900	0.100694	0.202904	ENSG00000164385	ENST00000296847	T	0.39787	1.06	3.16	-2.52	0.06346	.	.	.	.	.	T	0.07279	0.0184	N	0.08118	0	0.80722	P	0.0	B	0.24823	0.112	B	0.17979	0.02	T	0.24512	-1.0158	8	0.87932	D	0	.	6.064	0.19854	0.1051:0.0:0.2675:0.6274	rs9503233;rs52796843;rs60879034;rs9503233	43	Q96MT4	CF195_HUMAN	S	43	ENSP00000296847:P43S	ENSP00000296847:P43S	P	-	1	0	C6orf195	2568929	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.080000	0.11339	-0.617000	0.05664	-0.229000	0.12294	CCC	G|0.875;A|0.125	0.125	strong		0.622	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554	
C12orf4	57102	hgsc.bcm.edu	37	12	4627414	4627414	+	Silent	SNP	C	C	T	rs35924298	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:4627414C>T	ENST00000261250.3	-	8	930	c.843G>A	c.(841-843)caG>caA	p.Q281Q	C12orf4_ENST00000545746.1_Silent_p.Q281Q	NM_020374.2	NP_065107.1	Q9NQ89	CL004_HUMAN	chromosome 12 open reading frame 4	281										NS(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		TGGTCTTCAACTGGGCTCCTG	0.428													C|||	238	0.047524	0.0023	0.0735	5008	,	,		16358	0.003		0.1282	False		,,,				2504	0.0532				p.Q281Q		Atlas-SNP	.											.	C12orf4	58	.	0			c.G843A						PASS	.	C		87,4319	73.6+/-111.7	0,87,2116	105.0	108.0	107.0		843	4.3	1.0	12	dbSNP_126	107	1016,7584	217.4+/-256.1	63,890,3347	no	coding-synonymous	C12orf4	NM_020374.2		63,977,5463	TT,TC,CC		11.814,1.9746,8.4807		281/553	4627414	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	57102	exon8			CTTCAACTGGGCT	AJ272205	CCDS8528.1	12p13.3	2012-08-10			ENSG00000047621	ENSG00000047621			1184	protein-coding gene	gene with protein product							Standard	NM_020374		Approved		uc001qms.3	Q9NQ89	OTTHUMG00000168258	ENST00000261250.3:c.843G>A	12.37:g.4627414C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_020374	D3DUQ8|Q6MZH5	Silent	SNP	ENST00000261250.3	37	CCDS8528.1																																																																																			C|0.922;T|0.078	0.078	strong		0.428	C12orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398992.1	NM_020374	
KCTD3	51133	hgsc.bcm.edu	37	1	215793834	215793834	+	Silent	SNP	G	G	A	rs14137	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:215793834G>A	ENST00000259154.4	+	18	2616	c.2322G>A	c.(2320-2322)gcG>gcA	p.A774A	KCTD3_ENST00000495537.1_3'UTR	NM_016121.3	NP_057205.2	Q9Y597	KCTD3_HUMAN	potassium channel tetramerization domain containing 3	774					protein homooligomerization (GO:0051260)					breast(4)|endometrium(2)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)	33				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)		CCTATCTGGCGTCATCACCAA	0.433													G|||	2075	0.414337	0.2867	0.6124	5008	,	,		16915	0.3492		0.6372	False		,,,				2504	0.2843				p.A774A		Atlas-SNP	.											.	KCTD3	101	.	0			c.G2322A						PASS	.	G		1399,3007	452.0+/-349.9	252,895,1056	114.0	113.0	114.0		2322	-11.5	0.0	1	dbSNP_52	114	5634,2966	663.1+/-402.0	1858,1918,524	no	coding-synonymous	KCTD3	NM_016121.3		2110,2813,1580	AA,AG,GG		34.4884,31.7522,45.925		774/816	215793834	7033,5973	2203	4300	6503	SO:0001819	synonymous_variant	51133	exon18			TCTGGCGTCATCA	AK024547	CCDS1515.1	1q41	2013-06-20	2013-06-20		ENSG00000136636	ENSG00000136636			21305	protein-coding gene	gene with protein product		613272	"""potassium channel tetramerisation domain containing 3"""			10508479	Standard	NM_016121		Approved	NY-REN-45	uc001hks.3	Q9Y597	OTTHUMG00000037019	ENST00000259154.4:c.2322G>A	1.37:g.215793834G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_016121	A0AV15|D3DTA6|Q49AG7|Q504Q9|Q6PJN6|Q8ND58|Q8NDJ0|Q8WX16	Silent	SNP	ENST00000259154.4	37	CCDS1515.1																																																																																			G|0.503;A|0.497	0.497	strong		0.433	KCTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089871.2	NM_016121	
RARS	5917	hgsc.bcm.edu	37	5	167933158	167933158	+	Missense_Mutation	SNP	T	T	A	rs2305734	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:167933158T>A	ENST00000231572.3	+	10	1244	c.1190T>A	c.(1189-1191)tTt>tAt	p.F397Y	RARS_ENST00000538719.1_Missense_Mutation_p.F191Y	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	397			F -> Y (in dbSNP:rs2305734).		arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		CAAAGACTATTTGAGGAAAAA	0.353													T|||	220	0.0439297	0.0038	0.0418	5008	,	,		19735	0.0635		0.0785	False		,,,				2504	0.044				p.F397Y		Atlas-SNP	.											.	RARS	58	.	0			c.T1190A						PASS	.	T	TYR/PHE	157,4249		2,153,2048	149.0	145.0	146.0		1190	3.1	0.1	5	dbSNP_100	146	1483,7117		162,1159,2979	yes	missense	RARS	NM_002887.3	22	164,1312,5027	AA,AT,TT		17.2442,3.5633,12.6096	benign	397/661	167933158	1640,11366	2203	4300	6503	SO:0001583	missense	5917	exon10			GACTATTTGAGGA	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1190T>A	5.37:g.167933158T>A	ENSP00000231572:p.Phe397Tyr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Missense_Mutation	SNP	ENST00000231572.3	37	CCDS4367.1	228	0.1043956043956044	10	0.02032520325203252	41	0.1132596685082873	43	0.07517482517482517	134	0.17678100263852242	T	0.270	-0.993336	0.02145	0.035633	0.172442	ENSG00000113643	ENST00000231572;ENST00000538719	T;T	0.63913	-0.07;-0.07	5.58	3.13	0.36017	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.478529	0.26995	N	0.021457	T	0.00144	0.0004	L	0.41824	1.3	0.80722	P	0.0	B	0.06786	0.001	B	0.19148	0.024	T	0.05699	-1.0869	9	0.59425	D	0.04	-1.9146	4.3967	0.11367	0.206:0.0619:0.1064:0.6257	rs2305734;rs17633764;rs2305734	397	P54136	SYRC_HUMAN	Y	397;191	ENSP00000231572:F397Y;ENSP00000439108:F191Y	ENSP00000231572:F397Y	F	+	2	0	RARS	167865736	0.996000	0.38824	0.121000	0.21740	0.944000	0.59088	2.391000	0.44424	0.120000	0.18254	-2.514000	0.00186	TTT	T|0.869;A|0.131	0.131	strong		0.353	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
GSDMC	56169	hgsc.bcm.edu	37	8	130760774	130760774	+	Silent	SNP	C	C	T	rs4733559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:130760774C>T	ENST00000276708.4	-	14	2381	c.1500G>A	c.(1498-1500)tcG>tcA	p.S500S		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	500						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						GCTGCAGCAACGAGAGAGTCC	0.582													C|||	516	0.103035	0.0121	0.2147	5008	,	,		14276	0.0218		0.2157	False		,,,				2504	0.1145				p.S500S		Atlas-SNP	.											.	GSDMC	71	.	0			c.G1500A						PASS	.	C		202,4204	126.6+/-163.6	8,186,2009	129.0	123.0	125.0		1500	-9.5	0.0	8	dbSNP_111	125	1878,6722	334.5+/-321.0	212,1454,2634	no	coding-synonymous	GSDMC	NM_031415.2		220,1640,4643	TT,TC,CC		21.8372,4.5847,15.9926		500/509	130760774	2080,10926	2203	4300	6503	SO:0001819	synonymous_variant	56169	exon14			CAGCAACGAGAGA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.1500G>A	8.37:g.130760774C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_031415	Q5XKF3|Q6P494	Silent	SNP	ENST00000276708.4	37	CCDS6360.1																																																																																			C|0.868;T|0.132	0.132	strong		0.582	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
ANKRD12	23253	hgsc.bcm.edu	37	18	9258531	9258531	+	Silent	SNP	C	C	T	rs3744823	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:9258531C>T	ENST00000262126.4	+	9	5506	c.5266C>T	c.(5266-5268)Cta>Tta	p.L1756L	ANKRD12_ENST00000400020.3_Silent_p.L1733L|ANKRD12_ENST00000383440.2_Silent_p.L1733L|RP11-888D10.4_ENST00000609701.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1756						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						TAGCTGTACACTATTATCAGA	0.363													C|||	311	0.0621006	0.0991	0.049	5008	,	,		22341	0.0446		0.0706	False		,,,				2504	0.0307				p.L1756L		Atlas-SNP	.											.	ANKRD12	167	.	0			c.C5266T						PASS	.	C	,,	440,3966	211.8+/-231.9	22,396,1785	90.0	84.0	86.0		5197,5197,5266	2.4	0.1	18	dbSNP_107	86	654,7946	164.3+/-216.7	27,600,3673	no	coding-synonymous,coding-synonymous,coding-synonymous	ANKRD12	NM_001083625.2,NM_001204056.1,NM_015208.4	,,	49,996,5458	TT,TC,CC		7.6047,9.9864,8.4115	,,	1733/2040,1733/2040,1756/2063	9258531	1094,11912	2203	4300	6503	SO:0001819	synonymous_variant	23253	exon9			TGTACACTATTAT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5266C>T	18.37:g.9258531C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	37	CCDS11843.1																																																																																			C|0.924;T|0.076	0.076	strong		0.363	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
HOXA1	3198	hgsc.bcm.edu	37	7	27135314	27135314	+	Missense_Mutation	SNP	C	C	T	rs368428758|rs10951154|rs544314279	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:27135314C>T	ENST00000343060.4	-	1	279	c.218G>A	c.(217-219)cGc>cAc	p.R73H	HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000495032.1_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOXA1_ENST00000355633.5_Missense_Mutation_p.R73H|HOTAIRM1_ENST00000429611.3_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	73	Poly-His.		H -> R (frequent polymorphism in individuals of European or African origin; dbSNP:rs10951154). {ECO:0000269|PubMed:11091361, ECO:0000269|PubMed:14702039}.		abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						Ctgggggtggcgatggtggtg	0.647											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	T|||	3910	0.780751	0.407	0.8444	5008	,	,		11467	0.994		0.8479	False		,,,				2504	0.9519				p.R73H		Atlas-SNP	.											.	HOXA1	64	.	0			c.G218A						PASS	.	T	HIS/ARG,HIS/ARG	2136,2270	585.8+/-386.3	516,1104,583	39.0	41.0	40.0		218,218	2.5	1.0	7	dbSNP_120	40	7364,1236	241.0+/-271.5	3164,1036,100	yes	missense,missense	HOXA1	NM_005522.4,NM_153620.2	29,29	3680,2140,683	TT,TC,CC		14.3721,48.4793,26.9568	possibly-damaging,possibly-damaging	73/336,73/138	27135314	9500,3506	2203	4300	6503	SO:0001583	missense	3198	exon1			GGGTGGCGATGGT		CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"""Homeoboxes / ANTP class : HOXL subclass"""	5099	protein-coding gene	gene with protein product		142955	"""homeo box A1"""	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.218G>A	7.37:g.27135314C>T	ENSP00000343246:p.Arg73His	Somatic	54	0	0	792	WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_153620	A4D184|B2R8U7|O43363	Missense_Mutation	SNP	ENST00000343060.4	37	CCDS5401.1	1750	0.8012820512820513	231	0.4695121951219512	310	0.856353591160221	567	0.9912587412587412	642	0.8469656992084432	T	0.030	-1.343645	0.01277	0.484793	0.856279	ENSG00000105991	ENST00000343060;ENST00000355633	T;T	0.29655	1.56;1.56	3.68	2.53	0.30540	.	1.098180	0.07000	N	0.823224	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28170	-1.0052	8	0.14252	T	0.57	.	4.9074	0.13806	0.0:0.2694:0.0:0.7306	rs10951154;rs17500501;rs17846000;rs17858984;rs10951154	73	E7ERT8	.	H	73	ENSP00000343246:R73H;ENSP00000347851:R73H	ENSP00000343246:R73H	R	-	2	0	HOXA1	27101839	0.995000	0.38212	0.997000	0.53966	0.695000	0.40330	1.330000	0.33781	0.320000	0.23234	-0.891000	0.02926	CGC	C|0.261;T|0.739	0.739	strong		0.647	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1		
ALPK2	115701	hgsc.bcm.edu	37	18	56202418	56202418	+	Silent	SNP	T	T	C	rs10469212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56202418T>C	ENST00000361673.3	-	5	5214	c.5001A>G	c.(4999-5001)aaA>aaG	p.K1667K	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1667						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCTGCAGTAATTTAGGGGCTT	0.517													C|||	4660	0.930511	0.764	0.9611	5008	,	,		18792	1.0		0.996	False		,,,				2504	0.9949				p.K1667K		Atlas-SNP	.											.	ALPK2	487	.	0			c.A5001G						PASS	.	C		3542,864	337.3+/-304.8	1433,676,94	79.0	84.0	82.0		5001	-3.4	0.0	18	dbSNP_119	82	8570,30	21.0+/-64.5	4270,30,0	no	coding-synonymous	ALPK2	NM_052947.3		5703,706,94	CC,CT,TT		0.3488,19.6096,6.8738		1667/2171	56202418	12112,894	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			CAGTAATTTAGGG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.5001A>G	18.37:g.56202418T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			T|0.071;C|0.929	0.929	strong		0.517	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
DES	1674	hgsc.bcm.edu	37	2	220285309	220285309	+	Silent	SNP	C	C	T	rs1058261	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220285309C>T	ENST00000373960.3	+	4	914	c.828C>T	c.(826-828)gaC>gaT	p.D276D		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	276	Coil 2A.|Rod.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CCCTCAGGGACATCCGGGCTC	0.587													C|||	1690	0.33746	0.475	0.3429	5008	,	,		21149	0.1835		0.3648	False		,,,				2504	0.2781				p.D276D		Atlas-SNP	.											.	DES	53	.	0			c.C828T						PASS	.	C		1944,2462	551.4+/-378.3	437,1070,696	70.0	64.0	66.0		828	4.7	1.0	2	dbSNP_86	66	3057,5543	469.8+/-367.7	567,1923,1810	no	coding-synonymous	DES	NM_001927.3		1004,2993,2506	TT,TC,CC		35.5465,44.1217,38.4515		276/471	220285309	5001,8005	2203	4300	6503	SO:0001819	synonymous_variant	1674	exon4			CAGGGACATCCGG	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.828C>T	2.37:g.220285309C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Silent	SNP	ENST00000373960.3	37	CCDS33383.1																																																																																			C|0.634;T|0.366	0.366	strong		0.587	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
FAM71B	153745	hgsc.bcm.edu	37	5	156589585	156589585	+	Missense_Mutation	SNP	A	A	G	rs31208	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:156589585A>G	ENST00000302938.4	-	2	1786	c.1691T>C	c.(1690-1692)aTg>aCg	p.M564T		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	564			M -> T (in dbSNP:rs31208). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTCTCCACCATCTTAGCCAC	0.502													A|||	574	0.114617	0.2436	0.0922	5008	,	,		19806	0.0139		0.1243	False		,,,				2504	0.0501				p.M564T		Atlas-SNP	.											.	FAM71B	145	.	0			c.T1691C						PASS	.	A	THR/MET	1034,3372	382.5+/-324.5	125,784,1294	281.0	274.0	276.0		1691	0.9	0.0	5	dbSNP_76	276	1165,7435	238.2+/-269.8	76,1013,3211	yes	missense	FAM71B	NM_130899.2	81	201,1797,4505	GG,GA,AA		13.5465,23.468,16.9076	benign	564/606	156589585	2199,10807	2203	4300	6503	SO:0001583	missense	153745	exon2			TCCACCATCTTAG		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1691T>C	5.37:g.156589585A>G	ENSP00000305596:p.Met564Thr	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	296	97	0.327703	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	254	0.1163003663003663	123	0.25	30	0.08287292817679558	10	0.017482517482517484	91	0.12005277044854881	A	0.005	-2.137566	0.00335	0.23468	0.135465	ENSG00000170613	ENST00000302938	T	0.17691	2.26	3.87	0.954	0.19595	.	1.609550	0.03833	N	0.269439	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35773	-0.9775	9	0.02654	T	1	-0.7755	2.6679	0.05058	0.2627:0.0:0.5112:0.2261	rs31208;rs17851963;rs17852269;rs52832622;rs59767396;rs31208	564	Q8TC56	FA71B_HUMAN	T	564	ENSP00000305596:M564T	ENSP00000305596:M564T	M	-	2	0	FAM71B	156522163	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.172000	0.16704	0.170000	0.19704	-0.242000	0.12053	ATG	A|0.858;G|0.142	0.142	strong		0.502	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
DNAH2	146754	hgsc.bcm.edu	37	17	7735934	7735934	+	Missense_Mutation	SNP	G	G	A	rs61745181	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7735934G>A	ENST00000572933.1	+	83	14224	c.12764G>A	c.(12763-12765)cGg>cAg	p.R4255Q	DNAH2_ENST00000389173.2_Missense_Mutation_p.R4255Q			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	4255					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GCCTGGACCCGGGACTTGGCC	0.547													G|||	575	0.114816	0.0038	0.2478	5008	,	,		16887	0.1409		0.0616	False		,,,				2504	0.1984				p.R4255Q		Atlas-SNP	.											.	DNAH2	498	.	0			c.G12764A						PASS	.	G	GLN/ARG	99,4307	78.3+/-116.7	3,93,2107	93.0	100.0	98.0		12764	5.4	1.0	17	dbSNP_129	98	653,7947	166.7+/-218.6	18,617,3665	yes	missense	DNAH2	NM_020877.2	43	21,710,5772	AA,AG,GG		7.593,2.2469,5.7819	possibly-damaging	4255/4428	7735934	752,12254	2203	4300	6503	SO:0001583	missense	146754	exon82			GGACCCGGGACTT	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.12764G>A	17.37:g.7735934G>A	ENSP00000458355:p.Arg4255Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	112	41	0.366071	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	194	0.08882783882783883	4	0.008130081300813009	68	0.1878453038674033	80	0.13986013986013987	42	0.055408970976253295	G	25.5	4.642337	0.87859	0.022469	0.07593	ENSG00000183914	ENST00000389173	T	0.08008	3.14	5.41	5.41	0.78517	Dynein heavy chain (1);	0.065840	0.64402	D	0.000020	T	0.00039	0.0001	L	0.52364	1.645	0.09310	P	1.0	P	0.52692	0.955	P	0.51079	0.658	T	0.50800	-0.8785	9	0.13470	T	0.59	.	17.9726	0.89118	0.0:0.0:1.0:0.0	rs61745181	4255	Q9P225	DYH2_HUMAN	Q	4255	ENSP00000373825:R4255Q	ENSP00000373825:R4255Q	R	+	2	0	DNAH2	7676659	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.481000	0.73608	2.546000	0.85860	0.591000	0.81541	CGG	G|0.935;A|0.065	0.065	strong		0.547	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
OR5B12	390191	hgsc.bcm.edu	37	11	58207494	58207494	+	Missense_Mutation	SNP	A	A	G	rs140525146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:58207494A>G	ENST00000302572.2	-	1	152	c.131T>C	c.(130-132)aTt>aCt	p.I44T		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AATCAATTCAATCATCCCCAG	0.488													A|||	11	0.00219649	0.0076	0.0014	5008	,	,		18591	0.0		0.0	False		,,,				2504	0.0				p.I44T		Atlas-SNP	.											.	OR5B12	80	.	0			c.T131C						PASS	.	A	THR/ILE	53,4349	52.9+/-88.7	2,49,2150	76.0	85.0	82.0		131	1.1	0.0	11	dbSNP_134	82	4,8586	3.7+/-12.6	0,4,4291	yes	missense	OR5B12	NM_001004733.2	89	2,53,6441	GG,GA,AA		0.0466,1.204,0.4387	benign	44/315	58207494	57,12935	2201	4295	6496	SO:0001583	missense	390191	exon1			AATTCAATCATCC	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.131T>C	11.37:g.58207494A>G	ENSP00000306657:p.Ile44Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	5.557	0.287633	0.10513	0.01204	4.66E-4	ENSG00000172362	ENST00000302572	T	0.00640	6.03	4.74	1.11	0.20524	GPCR, rhodopsin-like superfamily (1);	1.336050	0.05196	N	0.503944	T	0.00815	0.0027	M	0.85777	2.775	0.09310	N	1	B	0.18741	0.03	B	0.24394	0.053	T	0.47328	-0.9126	10	0.62326	D	0.03	-6.3258	7.7035	0.28636	0.7459:0.0:0.254:0.0	.	44	Q96R08	OR5BC_HUMAN	T	44	ENSP00000306657:I44T	ENSP00000306657:I44T	I	-	2	0	OR5B12	57964070	0.014000	0.17966	0.049000	0.19019	0.222000	0.24845	2.799000	0.47892	0.087000	0.17167	0.459000	0.35465	ATT	A|0.995;G|0.005	0.005	strong		0.488	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
OR4D6	219983	hgsc.bcm.edu	37	11	59224608	59224608	+	Missense_Mutation	SNP	A	A	G	rs1453544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59224608A>G	ENST00000300127.2	+	1	198	c.175A>G	c.(175-177)Atg>Gtg	p.M59V		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	59			M -> V (in dbSNP:rs1453544).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						ACACACTCCTATGTACTTTCT	0.448													A|||	627	0.1252	0.0197	0.1326	5008	,	,		20337	0.1141		0.2525	False		,,,				2504	0.1431				p.M59V		Atlas-SNP	.											OR4D6,NS,adenoma,0,1	OR4D6	65	1	0			c.A175G						PASS	.	A	VAL/MET	244,4158	143.8+/-178.8	10,224,1967	145.0	122.0	130.0		175	4.9	0.9	11	dbSNP_88	130	2264,6326	383.5+/-340.8	283,1698,2314	yes	missense	OR4D6	NM_001004708.1	21	293,1922,4281	GG,GA,AA		26.3562,5.5429,19.3042	probably-damaging	59/315	59224608	2508,10484	2201	4295	6496	SO:0001583	missense	219983	exon1			ACTCCTATGTACT	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.175A>G	11.37:g.59224608A>G	ENSP00000300127:p.Met59Val	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	270	139	0.514815	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	349	0.15979853479853479	18	0.036585365853658534	59	0.16298342541436464	71	0.12412587412587413	201	0.26517150395778366	A	13.29	2.192610	0.38707	0.055429	0.263562	ENSG00000166884	ENST00000300127	T	0.09350	2.99	6.01	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	M	0.91406	3.205	0.32048	P	0.5973200000000001	P	0.50819	0.939	P	0.54759	0.76	T	0.10989	-1.0606	9	0.87932	D	0	-29.9948	11.1494	0.48449	0.9274:0.0:0.0726:0.0	rs1453544;rs52794667;rs57726108;rs1453544	59	Q8NGJ1	OR4D6_HUMAN	V	59	ENSP00000300127:M59V	ENSP00000300127:M59V	M	+	1	0	OR4D6	58981184	1.000000	0.71417	0.862000	0.33874	0.497000	0.33675	7.516000	0.81772	1.088000	0.41272	0.533000	0.62120	ATG	A|0.815;G|0.185	0.185	strong		0.448	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240805	39240805	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39240805G>T	ENST00000391417.4	+	1	347	c.347G>T	c.(346-348)cGc>cTc	p.R116L		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	141	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						agctgctgccgcccctgctgc	0.672																																					p.R116L		Atlas-SNP	.											KRTAP4-7,caecum,carcinoma,+1,1	KRTAP4-7	49	1	0			c.G347T						scavenged	.						18.0	18.0	18.0					17																	39240805		692	1587	2279	SO:0001583	missense	100132476	exon1			GCTGCCGCCCCTG	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.347G>T	17.37:g.39240805G>T	ENSP00000375236:p.Arg116Leu	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	109	9	0.0825688	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	6.805	0.517638	0.13005	.	.	ENSG00000240871	ENST00000391417	T	0.00606	6.26	3.15	2.13	0.27403	.	0.163808	0.19966	U	0.102091	T	0.00496	0.0016	.	.	.	0.09310	N	1	B	0.18461	0.028	B	0.15052	0.012	T	0.45804	-0.9236	9	0.28530	T	0.3	.	9.2621	0.37619	0.0:0.0:0.7821:0.2179	.	171	Q9BYR0	KRA47_HUMAN	L	116	ENSP00000375236:R116L	ENSP00000375236:R116L	R	+	2	0	KRTAP4-7	36494331	0.000000	0.05858	0.028000	0.17463	0.502000	0.33828	-0.081000	0.11321	0.603000	0.29913	0.289000	0.19496	CGC	.	.	none		0.672	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
FTHL17	53940	hgsc.bcm.edu	37	X	31089930	31089930	+	Silent	SNP	C	C	T	rs438870	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:31089930C>T	ENST00000359202.3	-	1	240	c.141G>A	c.(139-141)gtG>gtA	p.V47V		NM_031894.2	NP_114100.1	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	47	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)		ferric iron binding (GO:0008199)			endometrium(2)|large_intestine(2)|liver(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	23						TCTCCAGGGCCACGTCGTCCC	0.587													C|||	1016	0.269139	0.3669	0.1066	3775	,	,		10846	0.2004		0.1272	False		,,,				2504	0.1299				p.V47V		Atlas-SNP	.											.	FTHL17	99	.	0			c.G141A						PASS	.	C		1659,2174		306,801,246,524,325	91.0	79.0	83.0		141	0.6	0.0	X	dbSNP_80	83	974,5754		51,597,275,1780,1597	no	coding-synonymous	FTHL17	NM_031894.2		357,1398,521,2304,1922	TT,TC,T,CC,C		14.4768,43.282,24.9314		47/184	31089930	2633,7928	2202	4300	6502	SO:0001819	synonymous_variant	53940	exon1			CAGGGCCACGTCG	AF285592	CCDS14227.1	Xp21.2	2010-07-06			ENSG00000132446	ENSG00000132446			3987	protein-coding gene	gene with protein product	"""cancer/testis antigen 38"""	300308				11279525	Standard	NM_031894		Approved	CT38	uc004dcl.1	Q9BXU8	OTTHUMG00000021332	ENST00000359202.3:c.141G>A	X.37:g.31089930C>T		Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	NM_031894	Q6NT24|Q6NTE2	Silent	SNP	ENST00000359202.3	37	CCDS14227.1																																																																																			C|0.735;0|0.004	.	strong		0.587	FTHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056178.1	NM_031894	
ATP2B2	491	hgsc.bcm.edu	37	3	10443827	10443827	+	Silent	SNP	G	G	C	rs13084776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:10443827G>C	ENST00000352432.4	-	3	672	c.603C>G	c.(601-603)gtC>gtG	p.V201V	ATP2B2_ENST00000397077.1_Silent_p.V201V|ATP2B2_ENST00000343816.4_Silent_p.V201V|ATP2B2_ENST00000383800.4_Silent_p.V201V|ATP2B2_ENST00000360273.2_Silent_p.V201V			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	201					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						CAGGGATCTGGACCACCTGGC	0.572													G|||	848	0.169329	0.1233	0.3256	5008	,	,		19126	0.0099		0.2097	False		,,,				2504	0.2434				p.V201V	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.C603G						PASS	.	G	,	582,3824	257.4+/-261.8	31,520,1652	132.0	144.0	140.0		603,603	1.4	1.0	3	dbSNP_121	140	1848,6752	329.6+/-318.8	203,1442,2655	no	coding-synonymous,coding-synonymous	ATP2B2	NM_001001331.2,NM_001683.3	,	234,1962,4307	CC,CG,GG		21.4884,13.2093,18.6837	,	201/1244,201/1199	10443827	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	491	exon4			GATCTGGACCACC	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.603C>G	3.37:g.10443827G>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_001683	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																			G|0.823;C|0.177	0.177	strong		0.572	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
SRRM4	84530	hgsc.bcm.edu	37	12	119588962	119588962	+	Missense_Mutation	SNP	G	G	A	rs2723880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:119588962G>A	ENST00000267260.4	+	10	1605	c.1217G>A	c.(1216-1218)cGa>cAa	p.R406Q		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	406	Ser-rich.		R -> Q (in dbSNP:rs2723880).		cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CACTCGTCCCGATCCCCAAAT	0.567													G|||	1228	0.245208	0.1641	0.3804	5008	,	,		18490	0.1468		0.3966	False		,,,				2504	0.2045				p.R406Q		Atlas-SNP	.											.	SRRM4	131	.	0			c.G1217A						PASS	.	G	GLN/ARG	689,3221		60,569,1326	78.0	82.0	81.0		1217	2.6	1.0	12	dbSNP_100	81	3203,5087		615,1973,1557	yes	missense	SRRM4	NM_194286.3	43	675,2542,2883	AA,AG,GG		38.6369,17.6215,31.9016	possibly-damaging	406/612	119588962	3892,8308	1955	4145	6100	SO:0001583	missense	84530	exon10			CGTCCCGATCCCC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.1217G>A	12.37:g.119588962G>A	ENSP00000267260:p.Arg406Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	602	0.27564102564102566	74	0.15040650406504066	139	0.3839779005524862	80	0.13986013986013987	309	0.4076517150395778	G	22.3	4.265032	0.80358	0.176215	0.386369	ENSG00000139767	ENST00000267260	T	0.25250	1.81	5.58	2.63	0.31362	.	0.488214	0.18593	N	0.136681	T	0.00012	0.0000	L	0.40543	1.245	0.49798	P	1.7500000000003624E-4	B	0.24132	0.098	B	0.12837	0.008	T	0.47169	-0.9138	8	.	.	.	-0.6904	3.8042	0.08770	0.1511:0.1305:0.5842:0.1342	rs2723880;rs52812470;rs59964857;rs2723880	406	A7MD48	SRRM4_HUMAN	Q	406	ENSP00000267260:R406Q	.	R	+	2	0	SRRM4	118073345	0.270000	0.24152	0.970000	0.41538	0.964000	0.63967	0.685000	0.25378	1.489000	0.48450	0.655000	0.94253	CGA	G|0.714;A|0.286	0.286	strong		0.567	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
LIPC	3990	hgsc.bcm.edu	37	15	58834741	58834741	+	Silent	SNP	G	G	T	rs690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:58834741G>T	ENST00000356113.6	+	6	1080	c.465G>T	c.(463-465)gtG>gtT	p.V155V	LIPC_ENST00000299022.5_Silent_p.V155V|LIPC_ENST00000414170.3_Silent_p.V155V|LIPC_ENST00000433326.2_Silent_p.V94V			P11150	LIPC_HUMAN	lipase, hepatic	155					cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		AGGAATCTGTGCAACTCTCTC	0.562													T|||	2394	0.478035	0.5484	0.4308	5008	,	,		21003	0.2401		0.5606	False		,,,				2504	0.5767				p.V155V		Atlas-SNP	.											.	LIPC	56	.	0			c.G465T						PASS	.	T		2460,1924	548.5+/-377.6	691,1078,423	177.0	156.0	163.0		465	-7.9	0.0	15	dbSNP_36	163	5047,3537	515.3+/-378.6	1493,2061,738	no	coding-synonymous	LIPC	NM_000236.2		2184,3139,1161	TT,TG,GG		41.2046,43.8869,42.1114		155/500	58834741	7507,5461	2192	4292	6484	SO:0001819	synonymous_variant	3990	exon4			ATCTGTGCAACTC		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.465G>T	15.37:g.58834741G>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Silent	SNP	ENST00000356113.6	37	CCDS10166.1																																																																																			G|0.489;T|0.511	0.511	strong		0.562	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1		
TNK1	8711	hgsc.bcm.edu	37	17	7286266	7286266	+	Silent	SNP	C	C	T	rs1554947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7286266C>T	ENST00000576812.1	+	2	390	c.21C>T	c.(19-21)tcC>tcT	p.S7S	TNK1_ENST00000311668.2_Silent_p.S7S|TNK1_ENST00000570896.1_Silent_p.S7S	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				AGGCTGGCTCCCTGTGGCTAC	0.557													.|||	1372	0.273962	0.0356	0.3934	5008	,	,		20569	0.4593		0.4056	False		,,,				2504	0.1851				p.S7S		Atlas-SNP	.											.	TNK1	31	.	0			c.C21T						PASS	.	C		409,3943		19,371,1786	53.0	57.0	56.0		21	2.6	0.9	17	dbSNP_88	56	3381,5181		662,2057,1562	no	coding-synonymous	TNK1	NM_003985.3		681,2428,3348	TT,TC,CC		39.4884,9.398,29.348		7/662	7286266	3790,9124	2176	4281	6457	SO:0001819	synonymous_variant	8711	exon2			TGGCTCCCTGTGG	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.21C>T	17.37:g.7286266C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_003985		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			C|0.631;T|0.369	0.369	strong		0.557	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	
JMJD4	65094	hgsc.bcm.edu	37	1	227920186	227920186	+	Silent	SNP	G	G	A	rs35575794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:227920186G>A	ENST00000366758.3	-	6	1298	c.1299C>T	c.(1297-1299)gaC>gaT	p.D433D	JMJD4_ENST00000438896.2_Silent_p.D417D|JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000480897.1_3'UTR|SNAP47_ENST00000315781.5_5'Flank|SNAP47_ENST00000366759.4_5'Flank|SNAP47_ENST00000366760.1_Intron	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	433										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				CTCTCTGGAAGTCGGGGTGCG	0.617													G|||	98	0.0195687	0.0023	0.0202	5008	,	,		19261	0.0		0.0656	False		,,,				2504	0.0153				p.D433D		Atlas-SNP	.											.	JMJD4	28	.	0			c.C1299T						PASS	.	G	,	64,4342	59.9+/-96.7	1,62,2140	77.0	67.0	70.0		1251,1299	3.9	1.0	1	dbSNP_126	70	571,8029	152.8+/-207.3	21,529,3750	no	coding-synonymous,coding-synonymous	JMJD4	NM_001161465.1,NM_023007.2	,	22,591,5890	AA,AG,GG		6.6395,1.4526,4.8824	,	417/448,433/464	227920186	635,12371	2203	4300	6503	SO:0001819	synonymous_variant	65094	exon6			CTGGAAGTCGGGG	AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.1299C>T	1.37:g.227920186G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	198	102	0.515152	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Silent	SNP	ENST00000366758.3	37	CCDS1561.1	57	0.0260989010989011	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	47	0.06200527704485488	G	1.043	-0.678172	0.03378	0.014526	0.066395	ENSG00000081692	ENST00000438896	.	.	.	4.9	3.91	0.45181	.	.	.	.	.	T	0.10551	0.0258	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.08743	-1.0707	4	.	.	.	-40.3933	10.0022	0.41935	0.107:0.0:0.893:0.0	rs35575794;rs61750987	.	.	.	I	410	.	.	T	-	2	0	JMJD4	225986809	1.000000	0.71417	0.996000	0.52242	0.091000	0.18340	2.793000	0.47845	2.544000	0.85801	0.462000	0.41574	ACT	G|0.956;A|0.044	0.044	strong		0.617	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98164184	98164184	+	RNA	SNP	C	C	G	rs13001728	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:98164184C>G	ENST00000443455.1	-	0	1598							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		CTGGTGGTTGCTCAAAAGACA	0.308													.|||	1438	0.287141	0.1036	0.4164	5008	,	,		19015	0.1796		0.6402	False		,,,				2504	0.1912				p.E496D		Atlas-SNP	.											.	.	.	.	0			c.G1488C						PASS	.	C	ASP/GLU	679,2981		67,545,1218	40.0	33.0	35.0		1488	-1.4	0.0	2	dbSNP_121	35	5099,3023		1632,1835,594	no	missense	ANKRD36B	NM_025190.3	45	1699,2380,1812	GG,GC,CC		37.2199,18.5519,49.0409	probably-damaging	496/1354	98164184	5778,6004	1830	4061	5891			57730	exon21			TGGTTGCTCAAAA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98164184C>G		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	264	264	1	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				C|0.590;G|0.410	0.410	strong		0.308	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
PLXND1	23129	hgsc.bcm.edu	37	3	129297255	129297255	+	Missense_Mutation	SNP	T	T	C	rs112755880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:129297255T>C	ENST00000324093.4	-	9	2441	c.2263A>G	c.(2263-2265)Acc>Gcc	p.T755A	PLXND1_ENST00000393239.1_Missense_Mutation_p.T755A	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	755					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GAGAGCAGGGTCCGGGGGCAG	0.617																																					p.T755A	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.A2263G						PASS	.	T	ALA/THR	5,4399		0,5,2197	32.0	36.0	35.0		2263	4.6	1.0	3	dbSNP_132	35	30,8566		0,30,4268	yes	missense	PLXND1	NM_015103.2	58	0,35,6465	CC,CT,TT		0.349,0.1135,0.2692	benign	755/1926	129297255	35,12965	2202	4298	6500	SO:0001583	missense	23129	exon9			GCAGGGTCCGGGG	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.2263A>G	3.37:g.129297255T>C	ENSP00000317128:p.Thr755Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.505945	0.26949	0.001135	0.00349	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.33654	1.45;1.4	4.62	4.62	0.57501	.	0.643158	0.13899	N	0.355056	T	0.23572	0.0570	N	0.14661	0.345	0.23581	N	0.997361	B	0.12630	0.006	B	0.06405	0.002	T	0.16600	-1.0397	10	0.87932	D	0	.	10.4209	0.44350	0.0:0.0:0.0:1.0	.	755	Q9Y4D7	PLXD1_HUMAN	A	755	ENSP00000317128:T755A;ENSP00000376931:T755A	ENSP00000317128:T755A	T	-	1	0	PLXND1	130779945	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	2.729000	0.47327	1.708000	0.51301	0.459000	0.35465	ACC	T|0.997;C|0.003	0.003	strong		0.617	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
C6orf89	221477	hgsc.bcm.edu	37	6	36882353	36882353	+	Silent	SNP	A	A	G	rs2272275	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:36882353A>G	ENST00000480824.2	+	6	873	c.579A>G	c.(577-579)gaA>gaG	p.E193E	C6orf89_ENST00000355190.3_Silent_p.E200E|C6orf89_ENST00000510325.2_Silent_p.E87E|C6orf89_ENST00000373685.1_Silent_p.E193E|C6orf89_ENST00000359359.2_Silent_p.E87E			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	193					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						TGTTGGAGGAAGAGATTCAGC	0.493													G|||	1393	0.278155	0.3116	0.2493	5008	,	,		21496	0.3234		0.2326	False		,,,				2504	0.2536				p.E200E		Atlas-SNP	.											.	C6orf89	39	.	0			c.A600G						PASS	.	G		1427,2979	683.8+/-404.3	244,939,1020	170.0	178.0	175.0		600	2.2	0.7	6	dbSNP_100	175	2013,6587	721.8+/-406.4	252,1509,2539	no	coding-synonymous	C6orf89	NM_152734.3		496,2448,3559	GG,GA,AA		23.407,32.3877,26.4493		200/355	36882353	3440,9566	2203	4300	6503	SO:0001819	synonymous_variant	221477	exon5			GGAGGAAGAGATT	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"""bombesin receptor activated protein"""					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.579A>G	6.37:g.36882353A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	165	94	0.569697	NM_152734	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Silent	SNP	ENST00000480824.2	37																																																																																				A|0.727;G|0.273	0.273	strong		0.493	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734	
TAS1R2	80834	hgsc.bcm.edu	37	1	19175846	19175846	+	Missense_Mutation	SNP	T	T	C	rs28374389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19175846T>C	ENST00000375371.3	-	4	1477	c.1456A>G	c.(1456-1458)Atc>Gtc	p.I486V	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	486			I -> V (in dbSNP:rs28374389). {ECO:0000269|PubMed:11917125}.		detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GTGTTGTTGATGGTGTGCCAG	0.637													T|||	631	0.125998	0.1369	0.245	5008	,	,		14893	0.002		0.2087	False		,,,				2504	0.0695				p.I486V		Atlas-SNP	.											.	TAS1R2	134	.	0			c.A1456G						PASS	.	T	VAL/ILE	654,3752	277.8+/-273.9	50,554,1599	80.0	70.0	73.0		1456	-1.9	0.1	1	dbSNP_125	73	1769,6831	319.0+/-313.9	210,1349,2741	yes	missense	TAS1R2	NM_152232.2	29	260,1903,4340	CC,CT,TT		20.5698,14.8434,18.6299	benign	486/840	19175846	2423,10583	2203	4300	6503	SO:0001583	missense	80834	exon4			TGTTGATGGTGTG		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.1456A>G	1.37:g.19175846T>C	ENSP00000364520:p.Ile486Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	64	18	0.28125	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	318	0.14560439560439561	71	0.1443089430894309	94	0.2596685082872928	1	0.0017482517482517483	152	0.20052770448548812	T	2.501	-0.315238	0.05422	0.148434	0.205698	ENSG00000179002	ENST00000375371	D	0.88124	-2.34	4.4	-1.92	0.07618	.	0.473418	0.17601	N	0.168433	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03287	-1.1052	9	0.16896	T	0.51	.	9.8404	0.40996	0.0:0.5455:0.3022:0.1523	rs28374389	486	Q8TE23	TS1R2_HUMAN	V	486	ENSP00000364520:I486V	ENSP00000364520:I486V	I	-	1	0	TAS1R2	19048433	0.000000	0.05858	0.093000	0.20910	0.133000	0.20885	-0.359000	0.07632	-0.169000	0.10834	-0.396000	0.06452	ATC	T|0.832;C|0.168	0.168	strong		0.637	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
STK40	83931	hgsc.bcm.edu	37	1	36807481	36807481	+	Missense_Mutation	SNP	C	C	T	rs3795498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36807481C>T	ENST00000373129.3	-	12	1589	c.1183G>A	c.(1183-1185)Gcc>Acc	p.A395T	STK40_ENST00000373130.3_Missense_Mutation_p.A400T|STK40_ENST00000359297.2_3'UTR|STK40_ENST00000373132.3_Missense_Mutation_p.A395T	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	395			A -> T (in dbSNP:rs3795498). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A395T(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CAGCTCCGGGCGTCATGGATG	0.637													C|||	897	0.179113	0.1672	0.1369	5008	,	,		18658	0.1429		0.2336	False		,,,				2504	0.2065				p.A395T		Atlas-SNP	.											SgK495,NS,lymphoid_neoplasm,0,2	STK40	53	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G1183A						PASS	.	C	THR/ALA	858,3548	336.0+/-304.2	89,680,1434	52.0	51.0	51.0		1183	5.1	1.0	1	dbSNP_107	51	2177,6423	371.6+/-336.3	290,1597,2413	yes	missense	STK40	NM_032017.1	58	379,2277,3847	TT,TC,CC		25.314,19.4734,23.3354	benign	395/436	36807481	3035,9971	2203	4300	6503	SO:0001583	missense	83931	exon12			TCCGGGCGTCATG	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.1183G>A	1.37:g.36807481C>T	ENSP00000362221:p.Ala395Thr	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	141	54	0.382979	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	37	CCDS407.1	376	0.17216117216117216	77	0.1565040650406504	55	0.15193370165745856	71	0.12412587412587413	173	0.22823218997361477	C	18.13	3.554608	0.65425	0.194734	0.25314	ENSG00000196182	ENST00000373129;ENST00000373130;ENST00000373132	T;T;T	0.63096	-0.02;-0.02;-0.02	5.11	5.11	0.69529	.	0.104349	0.64402	D	0.000003	T	0.00012	0.0000	N	0.14661	0.345	0.21147	P	0.999770197	B;B	0.19935	0.04;0.024	B;B	0.10450	0.005;0.002	T	0.03202	-1.1061	9	0.32370	T	0.25	-13.8877	17.5055	0.87743	0.0:1.0:0.0:0.0	rs3795498;rs17856244;rs57485791;rs3795498	400;395	Q8N2I9-4;Q8N2I9	.;STK40_HUMAN	T	395;400;395	ENSP00000362221:A395T;ENSP00000362222:A400T;ENSP00000362224:A395T	ENSP00000362221:A395T	A	-	1	0	STK40	36580068	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	5.664000	0.68045	2.370000	0.80446	0.514000	0.50259	GCC	C|0.795;T|0.205	0.205	strong		0.637	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017	
SLFNL1	200172	hgsc.bcm.edu	37	1	41485902	41485902	+	Missense_Mutation	SNP	C	C	G	rs3738368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:41485902C>G	ENST00000359345.1	-	1	3007	c.431G>C	c.(430-432)aGa>aCa	p.R144T	SLFNL1_ENST00000302946.8_Missense_Mutation_p.R144T|SLFNL1_ENST00000372613.2_Missense_Mutation_p.R144T|SLFNL1_ENST00000439569.2_Missense_Mutation_p.R144T|SLFNL1_ENST00000372611.1_Missense_Mutation_p.R144T|SLFNL1_ENST00000397197.2_Missense_Mutation_p.R144T	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	144			R -> T (in dbSNP:rs3738368).				ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				ACTTACCTCTCTGTGGCTGAA	0.617													C|||	912	0.182109	0.0166	0.2896	5008	,	,		16809	0.1687		0.3042	False		,,,				2504	0.2178				p.R144T		Atlas-SNP	.											.	SLFNL1	37	.	0			c.G431C						PASS	.	C	THR/ARG,THR/ARG	329,4077	171.2+/-201.5	12,305,1886	62.0	64.0	63.0		431,431	3.8	0.2	1	dbSNP_107	63	2645,5955	425.6+/-355.0	428,1789,2083	yes	missense,missense	SLFNL1	NM_001168247.1,NM_144990.3	71,71	440,2094,3969	GG,GC,CC		30.7558,7.4671,22.8664	probably-damaging,probably-damaging	144/408,144/408	41485902	2974,10032	2203	4300	6503	SO:0001583	missense	200172	exon3			ACCTCTCTGTGGC	BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.431G>C	1.37:g.41485902C>G	ENSP00000352299:p.Arg144Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_001168247	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	442	0.20238095238095238	12	0.024390243902439025	108	0.2983425414364641	101	0.17657342657342656	221	0.29155672823219	C	9.864	1.197201	0.22037	0.074671	0.307558	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	5.63	3.77	0.43336	.	0.397216	0.23740	N	0.045022	T	0.00012	0.0000	L	0.59436	1.845	0.37239	P	0.09398899999999999	P;P;D	0.55605	0.946;0.86;0.972	P;P;B	0.48840	0.592;0.453;0.335	T	0.10683	-1.0619	9	0.72032	D	0.01	-0.14	8.5891	0.33677	0.0:0.8238:0.0:0.1762	rs3738368;rs17357926;rs58566626;rs3738368	144;144;144	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	T	144	ENSP00000304401:R144T;ENSP00000361696:R144T;ENSP00000361694:R144T;ENSP00000352299:R144T;ENSP00000398938:R144T;ENSP00000380381:R144T	ENSP00000304401:R144T	R	-	2	0	SLFNL1	41258489	0.301000	0.24444	0.233000	0.24025	0.015000	0.08874	0.322000	0.19576	0.746000	0.32786	-0.291000	0.09656	AGA	C|0.777;G|0.222	0.222	strong		0.617	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990	
PDZD2	23037	hgsc.bcm.edu	37	5	32090294	32090294	+	Missense_Mutation	SNP	G	G	A	rs10066063	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:32090294G>A	ENST00000438447.1	+	20	7128	c.6740G>A	c.(6739-6741)cGg>cAg	p.R2247Q	PDZD2_ENST00000282493.3_Missense_Mutation_p.R2247Q			O15018	PDZD2_HUMAN	PDZ domain containing 2	2247			R -> Q (in dbSNP:rs10066063).		cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GGTCGCTCTCGGGACAGCCAG	0.597													G|||	581	0.116014	0.0431	0.1412	5008	,	,		17880	0.2351		0.0746	False		,,,				2504	0.1166				p.R2247Q		Atlas-SNP	.											.	PDZD2	306	.	0			c.G6740A						PASS	.	G	GLN/ARG	241,4165	141.9+/-177.2	4,233,1966	130.0	140.0	137.0		6740	0.4	0.0	5	dbSNP_119	137	767,7833	183.2+/-231.5	34,699,3567	yes	missense	PDZD2	NM_178140.2	43	38,932,5533	AA,AG,GG		8.9186,5.4698,7.7503	benign	2247/2840	32090294	1008,11998	2203	4300	6503	SO:0001583	missense	23037	exon19			GCTCTCGGGACAG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.6740G>A	5.37:g.32090294G>A	ENSP00000402033:p.Arg2247Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	167	77	0.461078	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	257	0.11767399267399267	18	0.036585365853658534	40	0.11049723756906077	148	0.25874125874125875	51	0.06728232189973615	G	1.375	-0.584903	0.03827	0.054698	0.089186	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.05649	3.41;3.41	4.66	0.432	0.16529	.	0.920619	0.09030	N	0.858893	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.18166	0.026	B	0.10450	0.005	T	0.48281	-0.9049	9	0.11485	T	0.65	.	3.7093	0.08413	0.3991:0.0:0.4169:0.184	rs10066063;rs52821994;rs61543309;rs10066063	2247	O15018	PDZD2_HUMAN	Q	2247;2048;2247	ENSP00000402033:R2247Q;ENSP00000282493:R2247Q	ENSP00000282493:R2247Q	R	+	2	0	PDZD2	32126051	0.000000	0.05858	0.005000	0.12908	0.090000	0.18270	0.560000	0.23500	0.145000	0.18977	0.561000	0.74099	CGG	G|0.898;A|0.102	0.102	strong		0.597	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
SLC37A3	84255	hgsc.bcm.edu	37	7	140051091	140051091	+	Silent	SNP	G	G	A	rs12703775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:140051091G>A	ENST00000326232.9	-	9	1067	c.864C>T	c.(862-864)tgC>tgT	p.C288C	SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000340308.3_Silent_p.C288C|SLC37A3_ENST00000447932.2_Silent_p.C288C	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	288					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.C288C(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					CTCCAGGAAGGCAACATGCCT	0.473													G|||	1914	0.382188	0.3026	0.3703	5008	,	,		20177	0.4137		0.4553	False		,,,				2504	0.3906				p.C288C	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											SLC37A3,NS,carcinoma,0,1	SLC37A3	80	1	1	Substitution - coding silent(1)	stomach(1)	c.C864T						PASS	.	G	,	1451,2955	469.2+/-355.4	229,993,981	135.0	111.0	119.0		864,864	1.4	0.9	7	dbSNP_121	119	3934,4666	548.6+/-385.4	891,2152,1257	no	coding-synonymous,coding-synonymous	SLC37A3	NM_032295.2,NM_207113.1	,	1120,3145,2238	AA,AG,GG		45.7442,32.9324,41.404	,	288/444,288/495	140051091	5385,7621	2203	4300	6503	SO:0001819	synonymous_variant	84255	exon9			AGGAAGGCAACAT	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.864C>T	7.37:g.140051091G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	150	61	0.406667	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Silent	SNP	ENST00000326232.9	37	CCDS5859.1	875|875	0.40064102564102566|0.40064102564102566	152|152	0.3089430894308943|0.3089430894308943	143|143	0.39502762430939226|0.39502762430939226	230|230	0.4020979020979021|0.4020979020979021	350|350	0.46174142480211083|0.46174142480211083	G|G	9.531|9.531	1.110842|1.110842	0.20714|0.20714	0.329324|0.329324	0.457442|0.457442	ENSG00000157800|ENSG00000157800	ENST00000485734|ENST00000492027	.|.	.|.	.|.	5.33|5.33	1.4|1.4	0.22301|0.22301	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999975845|0.9999999999975845	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.47222|0.47222	-0.9134|-0.9134	3|3	.|.	.|.	.|.	-28.2614|-28.2614	9.3106|9.3106	0.37903|0.37903	0.3043:0.0:0.6957:0.0|0.3043:0.0:0.6957:0.0	rs12703775;rs57065524|rs12703775;rs57065524	.|.	.|.	.|.	V|S	67|23	.|.	.|.	A|P	-|-	2|1	0|0	SLC37A3|SLC37A3	139697560|139697560	1.000000|1.000000	0.71417|0.71417	0.904000|0.904000	0.35570|0.35570	0.871000|0.871000	0.50021|0.50021	0.753000|0.753000	0.26376|0.26376	0.035000|0.035000	0.15519|0.15519	0.655000|0.655000	0.94253|0.94253	GCC|CCT	G|0.579;A|0.421	0.421	strong		0.473	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	
EPHX1	2052	hgsc.bcm.edu	37	1	226019633	226019633	+	Missense_Mutation	SNP	T	T	C	rs1051740	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:226019633T>C	ENST00000366837.4	+	3	533	c.337T>C	c.(337-339)Tac>Cac	p.Y113H	EPHX1_ENST00000467015.1_3'UTR|EPHX1_ENST00000272167.5_Missense_Mutation_p.Y113H	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	113			Y -> H (in allele EPHX1*3; 55% of wild type enzyme activity; dbSNP:rs1051740). {ECO:0000269|PubMed:11058921, ECO:0000269|PubMed:12173035, ECO:0000269|PubMed:7516776, ECO:0000269|Ref.8}.		aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TCTCAACAGATACCCTCACTT	0.448													T|||	1569	0.313299	0.1407	0.3199	5008	,	,		22077	0.4821		0.3042	False		,,,				2504	0.3773				p.Y113H		Atlas-SNP	.											.	EPHX1	57	.	0			c.T337C	GRCh37	CM940369	EPHX1	M	rs1051740	PASS	.	T	HIS/TYR,HIS/TYR	776,3630	314.9+/-293.9	59,658,1486	109.0	98.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	337,337	5.6	0.9	1	dbSNP_86	101	2577,6023	419.2+/-353.0	395,1787,2118	yes	missense,missense	EPHX1	NM_000120.3,NM_001136018.2	83,83	454,2445,3604	CC,CT,TT		29.9651,17.6123,25.7804	probably-damaging,probably-damaging	113/456,113/456	226019633	3353,9653	2203	4300	6503	SO:0001583	missense	2052	exon3			AACAGATACCCTC	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.337T>C	1.37:g.226019633T>C	ENSP00000355802:p.Tyr113His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	37	CCDS1547.1	690	0.3159340659340659	78	0.15853658536585366	121	0.3342541436464088	260	0.45454545454545453	231	0.30474934036939316	T	29.3	4.990224	0.93106	0.176123	0.299651	ENSG00000143819	ENST00000445856;ENST00000272167;ENST00000448202;ENST00000366837	T;T;T;T	0.04119	3.7;3.7;3.7;3.7	5.58	5.58	0.84498	Epoxide hydrolase, N-terminal (1);	0.064587	0.64402	D	0.000005	T	0.00012	0.0000	M	0.71920	2.185	0.09310	P	0.999999030378	D	0.71674	0.998	D	0.75484	0.986	T	0.50197	-0.8856	9	0.87932	D	0	5.918	15.7585	0.78058	0.0:0.0:0.0:1.0	rs1051740;rs1800444;rs2259405;rs3192120;rs16845366;rs52794507;rs59266540;rs1051740	113	P07099	HYEP_HUMAN	H	113	ENSP00000398491:Y113H;ENSP00000272167:Y113H;ENSP00000408469:Y113H;ENSP00000355802:Y113H	ENSP00000272167:Y113H	Y	+	1	0	EPHX1	224086256	1.000000	0.71417	0.932000	0.37286	0.991000	0.79684	7.809000	0.86057	2.136000	0.66102	0.454000	0.30748	TAC	C|0.290;N|0.000	0.290	strong		0.448	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
HEATR1	55127	hgsc.bcm.edu	37	1	236749649	236749649	+	Missense_Mutation	SNP	T	T	C	rs2794763	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:236749649T>C	ENST00000366582.3	-	15	1933	c.1819A>G	c.(1819-1821)Atg>Gtg	p.M607V	HEATR1_ENST00000366581.2_Missense_Mutation_p.M607V	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	607			M -> V (in dbSNP:rs2794763). {ECO:0000269|Ref.1}.		rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TTGATAACCATAAATGGCAGC	0.368													T|||	1848	0.36901	0.0348	0.464	5008	,	,		17902	0.4712		0.6223	False		,,,				2504	0.3875				p.M607V		Atlas-SNP	.											.	HEATR1	197	.	0			c.A1819G						PASS	.	T	VAL/MET	561,3845	246.8+/-255.3	45,471,1687	105.0	107.0	106.0		1819	5.4	1.0	1	dbSNP_100	106	5371,3227	649.3+/-400.6	1688,1995,616	yes	missense	HEATR1	NM_018072.5	21	1733,2466,2303	CC,CT,TT		37.532,12.7326,45.6167	possibly-damaging	607/2145	236749649	5932,7072	2203	4299	6502	SO:0001583	missense	55127	exon15			TAACCATAAATGG	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"""UTP10, small subunit (SSU) processome component, homolog (yeast)"""					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1819A>G	1.37:g.236749649T>C	ENSP00000355541:p.Met607Val	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	335	334	0.997015	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	962	0.44047619047619047	29	0.05894308943089431	181	0.5	281	0.49125874125874125	471	0.6213720316622692	T	10.99	1.507829	0.27036	0.127326	0.62468	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.53206	0.63;0.63	5.42	5.42	0.78866	Armadillo-like helical (1);Armadillo-type fold (1);	0.044132	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	1.0	P	0.37141	0.584	B	0.24701	0.055	T	0.43245	-0.9403	9	0.59425	D	0.04	.	15.7547	0.78015	0.0:0.0:0.0:1.0	rs2794763;rs3738542;rs52832651;rs58596551;rs2794763	607	Q9H583	HEAT1_HUMAN	V	607	ENSP00000355541:M607V;ENSP00000355540:M607V	ENSP00000355540:M607V	M	-	1	0	HEATR1	234816272	1.000000	0.71417	0.966000	0.40874	0.121000	0.20230	4.261000	0.58841	2.180000	0.69256	0.460000	0.39030	ATG	T|0.565;C|0.435	0.435	strong		0.368	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
NEK10	152110	hgsc.bcm.edu	37	3	27326097	27326097	+	Silent	SNP	G	G	T	rs11129280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:27326097G>T	ENST00000429845.2	-	23	2372	c.2010C>A	c.(2008-2010)acC>acA	p.T670T	NEK10_ENST00000341435.5_Silent_p.T670T|NEK10_ENST00000357467.2_Silent_p.T67T			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	670	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						ACTTACTAACGGTTACTTTGT	0.378													T|||	1061	0.211861	0.1218	0.3516	5008	,	,		15934	0.1002		0.2734	False		,,,				2504	0.2863				p.T670T		Atlas-SNP	.											.	NEK10	271	.	0			c.C2010A						PASS	.	T		716,3690	757.8+/-412.8	69,578,1556	123.0	115.0	117.0		2010	-5.8	0.6	3	dbSNP_120	117	2329,6271	703.8+/-405.4	349,1631,2320	yes	coding-synonymous	NEK10	NM_199347.2		418,2209,3876	TT,TG,GG		27.0814,16.2506,23.4123		670/713	27326097	3045,9961	2203	4300	6503	SO:0001819	synonymous_variant	152110	exon23			ACTAACGGTTACT	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.2010C>A	3.37:g.27326097G>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	37		464|464	0.21245421245421245|0.21245421245421245	64|64	0.13008130081300814|0.13008130081300814	132|132	0.36464088397790057|0.36464088397790057	58|58	0.10139860139860139|0.10139860139860139	210|210	0.2770448548812665|0.2770448548812665	T|T	9.473|9.473	1.096174|1.096174	0.20552|0.20552	0.162506|0.162506	0.270814|0.270814	ENSG00000163491|ENSG00000163491	ENST00000424275|ENST00000435584	.|.	.|.	.|.	6.02|6.02	-5.81|-5.81	0.02340|0.02340	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999993107|0.9999999999993107	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24190|0.24190	-1.0167|-1.0167	3|3	.|.	.|.	.|.	.|.	17.0958|17.0958	0.86634|0.86634	0.0781:0.0:0.624:0.2978|0.0781:0.0:0.624:0.2978	rs11129280;rs17681183;rs11129280|rs11129280;rs17681183;rs11129280	.|.	.|.	.|.	Q|S	157|127	.|.	.|.	P|R	-|-	2|1	0|0	NEK10|NEK10	27301101|27301101	0.190000|0.190000	0.23276|0.23276	0.621000|0.621000	0.29145|0.29145	0.956000|0.956000	0.61745|0.61745	-0.757000|-0.757000	0.04772|0.04772	-0.744000|-0.744000	0.04778|0.04778	-0.264000|-0.264000	0.10439|0.10439	CCG|CGT	G|0.774;T|0.226	0.226	strong		0.378	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	
ENTPD4	9583	hgsc.bcm.edu	37	8	23290451	23290451	+	Silent	SNP	C	C	T	rs17089244	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:23290451C>T	ENST00000358689.4	-	13	2074	c.1839G>A	c.(1837-1839)ccG>ccA	p.P613P	ENTPD4_ENST00000521321.1_Intron|ENTPD4_ENST00000417069.2_Silent_p.P605P|ENTPD4_ENST00000356206.6_Intron	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	613					UDP catabolic process (GO:0006256)	cytoplasmic vesicle (GO:0031410)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)	uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	25		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		ACAAGGTCCCCGGGGCATTCT	0.587													C|||	676	0.134984	0.1702	0.0706	5008	,	,		14977	0.123		0.0954	False		,,,				2504	0.1861				p.P613P		Atlas-SNP	.											.	ENTPD4	56	.	0			c.G1839A						PASS	.	C	,	668,3710		57,554,1578	21.0	24.0	23.0		1815,1839	-11.4	0.0	8	dbSNP_123	23	714,7858		30,654,3602	no	coding-synonymous,coding-synonymous	ENTPD4	NM_001128930.2,NM_004901.4	,	87,1208,5180	TT,TC,CC		8.3294,15.2581,10.6718	,	605/609,613/617	23290451	1382,11568	2189	4286	6475	SO:0001819	synonymous_variant	9583	exon13			GGTCCCCGGGGCA	AJ131358	CCDS6041.1, CCDS47827.1	8p21.3	2014-05-16	2004-09-22	2004-09-22	ENSG00000197217	ENSG00000197217			14573	protein-coding gene	gene with protein product		607577	"""lysosomal apyrase-like 1"""	LYSAL1		10393803, 9205841	Standard	NM_001128930		Approved	LALP70, LAP70, KIAA0392, NTPDase-4, UDPase	uc003xdl.3	Q9Y227	OTTHUMG00000097852	ENST00000358689.4:c.1839G>A	8.37:g.23290451C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_004901	D3DSS3|O15092	Silent	SNP	ENST00000358689.4	37	CCDS6041.1																																																																																			C|0.877;T|0.123	0.123	strong		0.587	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901	
HLA-B	3106	hgsc.bcm.edu	37	6	31323116	31323116	+	Silent	SNP	C	C	T	rs1131446	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31323116C>T	ENST00000412585.2	-	4	901	c.873G>A	c.(871-873)ccG>ccA	p.P291P		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	291	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TGAGGGGCTTCGGCAGCCCCT	0.577									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	485	0.096845	0.0749	0.0922	5008	,	,		21693	0.0754		0.1074	False		,,,				2504	0.1411				p.P291P		Atlas-SNP	.											HLA-B,rectum,carcinoma,0,1	HLA-B	54	1	0			c.G873A						PASS	.						60.0	57.0	58.0					6																	31323116		2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	GGGCTTCGGCAGC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.873G>A	6.37:g.31323116C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	266	31	0.116541	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			C|0.943;T|0.057	0.057	strong		0.577	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SERPING1	710	hgsc.bcm.edu	37	11	57373646	57373646	+	Silent	SNP	C	C	T	rs143760635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57373646C>T	ENST00000278407.4	+	5	1076	c.849C>T	c.(847-849)tcC>tcT	p.S283S	SERPING1_ENST00000403558.1_Silent_p.S317S|SERPING1_ENST00000340687.6_Silent_p.S283S|SERPING1_ENST00000378324.2_Silent_p.S231S|SERPING1_ENST00000378323.4_Silent_p.S288S	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	283					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S283S(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						GTCTGCCCTCCGATACCCGCC	0.542													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20271	0.0		0.001	False		,,,				2504	0.0				p.S283S		Atlas-SNP	.											SERPING1,NS,carcinoma,0,1	SERPING1	57	1	1	Substitution - coding silent(1)	lung(1)	c.C849T						PASS	.	C	,	1,4401	2.1+/-5.4	0,1,2200	190.0	178.0	183.0		849,849	-10.3	0.0	11	dbSNP_134	183	22,8570	16.0+/-53.3	0,22,4274	no	coding-synonymous,coding-synonymous	SERPING1	NM_000062.2,NM_001032295.1	,	0,23,6474	TT,TC,CC		0.2561,0.0227,0.177	,	283/501,283/501	57373646	23,12971	2201	4296	6497	SO:0001819	synonymous_variant	710	exon4			GCCCTCCGATACC	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"""Serine (or cysteine) peptidase inhibitors"""	1228	protein-coding gene	gene with protein product	"""plasma protease C1 inhibitor"", ""angioedema, hereditary"""	606860	"""serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"""	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.849C>T	11.37:g.57373646C>T		Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	239	124	0.518828	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Silent	SNP	ENST00000278407.4	37	CCDS7962.1																																																																																			C|0.999;T|0.001	0.001	strong		0.542	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062	
LHFPL5	222662	hgsc.bcm.edu	37	6	35773659	35773659	+	Missense_Mutation	SNP	A	A	G	rs148435294		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:35773659A>G	ENST00000373853.1	+	1	590	c.212A>G	c.(211-213)aAc>aGc	p.N71S	LHFPL5_ENST00000360215.1_Missense_Mutation_p.N71S			Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5	71					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transport (GO:0006811)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)				endometrium(4)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|urinary_tract(1)	20						TGCGTGGGTAACGTGCTGTCC	0.592																																					p.N71S		Atlas-SNP	.											LHFPL5,NS,carcinoma,-1,1	LHFPL5	44	1	0			c.A212G						scavenged	.		SER/ASN	0,4406		0,0,2203	235.0	215.0	222.0		212	5.5	1.0	6	dbSNP_134	222	1,8599	1.2+/-3.3	0,1,4299	no	missense	LHFPL5	NM_182548.3	46	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	71/220	35773659	1,13005	2203	4300	6503	SO:0001583	missense	222662	exon1			TGGGTAACGTGCT	BC028630	CCDS4812.1	6p21.31	2014-01-28				ENSG00000197753			21253	protein-coding gene	gene with protein product		609427	"""deafness, autosomal recessive 67"""	DFNB67		16459341	Standard	NM_182548		Approved	MGC33835, dJ510O8.8, Tmhs	uc003olg.1	Q8TAF8		ENST00000373853.1:c.212A>G	6.37:g.35773659A>G	ENSP00000362960:p.Asn71Ser	Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	399	6	0.0150376	NM_182548	B3KX66	Missense_Mutation	SNP	ENST00000373853.1	37	CCDS4812.1	.	.	.	.	.	.	.	.	.	.	a	13.64	2.297911	0.40694	0.0	1.16E-4	ENSG00000197753	ENST00000373853;ENST00000360215	T;T	0.71222	-0.55;-0.55	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.62853	0.2462	L	0.31752	0.955	0.48975	D	0.999733	D	0.76494	0.999	D	0.79108	0.992	T	0.63247	-0.6680	10	0.06625	T	0.88	-27.1157	15.6075	0.76685	1.0:0.0:0.0:0.0	.	71	Q8TAF8	TMHS_HUMAN	S	71	ENSP00000362960:N71S;ENSP00000353346:N71S	ENSP00000353346:N71S	N	+	2	0	LHFPL5	35881637	1.000000	0.71417	1.000000	0.80357	0.362000	0.29581	6.221000	0.72243	2.096000	0.63516	0.381000	0.24937	AAC	A|1.000;G|0.000	0.000	weak		0.592	LHFPL5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040323.1	NM_182548	
PPFIA4	8497	hgsc.bcm.edu	37	1	203025583	203025583	+	Silent	SNP	G	G	A	rs61748818	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:203025583G>A	ENST00000447715.2	+	23	2562	c.2121G>A	c.(2119-2121)acG>acA	p.T707T	PPFIA4_ENST00000272198.6_Silent_p.T223T|PPFIA4_ENST00000295706.4_Silent_p.T223T|PPFIA4_ENST00000367240.2_Silent_p.T708T|PPFIA4_ENST00000414050.2_Silent_p.T436T|PPFIA4_ENST00000599966.1_Silent_p.T223T			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	707					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CACCCAGGACGCTGCGGCTAG	0.572													g|||	285	0.0569089	0.0091	0.0331	5008	,	,		19076	0.0962		0.0547	False		,,,				2504	0.1002				p.T223T		Atlas-SNP	.											.	PPFIA4	139	.	0			c.G669A						PASS	.			48,4028		0,48,1990	39.0	45.0	43.0		669	2.8	1.0	1	dbSNP_129	43	422,7924		8,406,3759	no	coding-synonymous	PPFIA4	NM_015053.1		8,454,5749	AA,AG,GG		5.0563,1.1776,3.7836		223/702	203025583	470,11952	2038	4173	6211	SO:0001819	synonymous_variant	8497	exon5			CAGGACGCTGCGG	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2121G>A	1.37:g.203025583G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	130	52	0.4	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	37																																																																																				G|0.944;A|0.056	0.056	strong		0.572	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
DSPP	1834	hgsc.bcm.edu	37	4	88536460	88536460	+	Silent	SNP	C	C	T	rs199691318		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536460C>T	ENST00000282478.7	+	4	2679	c.2646C>T	c.(2644-2646)agC>agT	p.S882S	DSPP_ENST00000399271.1_Silent_p.S882S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	882	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgatagcagtgacagca	0.498																																					p.S882S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2646T						PASS	.						73.0	87.0	82.0					4																	88536460		1617	2929	4546	SO:0001819	synonymous_variant	1834	exon5			TGATAGCAGTGAC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2646C>T	4.37:g.88536460C>T		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	305	43	0.140984	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
BBS1	582	hgsc.bcm.edu	37	11	66297363	66297363	+	Silent	SNP	C	C	T	rs3816492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66297363C>T	ENST00000318312.7	+	14	1464	c.1413C>T	c.(1411-1413)ctC>ctT	p.L471L	BBS1_ENST00000455748.2_Silent_p.L374L|BBS1_ENST00000393994.2_Silent_p.L342L|CTD-3074O7.11_ENST00000419755.3_Silent_p.L508L|ZDHHC24_ENST00000526986.1_Intron	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	471					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						TGCAGGCCCTCGAGTCCAGCC	0.672									Bardet-Biedl syndrome				C|||	718	0.143371	0.0136	0.1441	5008	,	,		16469	0.1548		0.2396	False		,,,				2504	0.2076				p.L471L	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											.	BBS1	58	.	0			c.C1413T						PASS	.	C		211,4189	128.2+/-165.1	3,205,1992	64.0	44.0	51.0		1413	-8.9	0.7	11	dbSNP_107	51	1978,6612	342.7+/-324.6	221,1536,2538	yes	coding-synonymous	BBS1	NM_024649.4		224,1741,4530	TT,TC,CC		23.0268,4.7955,16.8514		471/594	66297363	2189,10801	2200	4295	6495	SO:0001819	synonymous_variant	582	exon14	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGCCCTCGAGTCC	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.1413C>T	11.37:g.66297363C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_024649	Q32MM9|Q32MN0|Q96SN4	Silent	SNP	ENST00000318312.7	37	CCDS8142.1																																																																																			C|0.843;T|0.157	0.157	strong		0.672	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2		
SLC1A4	6509	hgsc.bcm.edu	37	2	65245365	65245365	+	Missense_Mutation	SNP	G	G	A	rs759458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:65245365G>A	ENST00000234256.3	+	6	1438	c.1195G>A	c.(1195-1197)Gta>Ata	p.V399I	SLC1A4_ENST00000531327.1_Missense_Mutation_p.V101I	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	399			V -> I (in dbSNP:rs759458).		amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	ACTCAACAACGTAGAGCTCAA	0.493													G|||	961	0.191893	0.1354	0.1945	5008	,	,		21801	0.1091		0.2435	False		,,,				2504	0.2986				p.V399I		Atlas-SNP	.											SLC1A4,NS,carcinoma,-2,1	SLC1A4	33	1	0			c.G1195A						PASS	.	G	ILE/VAL,ILE/VAL	772,3634	313.0+/-292.9	68,636,1499	142.0	131.0	135.0		301,1195	0.2	0.0	2	dbSNP_86	135	2257,6343	382.3+/-340.3	297,1663,2340	yes	missense,missense	SLC1A4	NM_001193493.1,NM_003038.4	29,29	365,2299,3839	AA,AG,GG		26.2442,17.5216,23.2893	benign,benign	101/235,399/533	65245365	3029,9977	2203	4300	6503	SO:0001583	missense	6509	exon6			AACAACGTAGAGC		CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"""Solute carriers"""	10942	protein-coding gene	gene with protein product	"""alanine/serine/cysteine/threonine transporter"""	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.1195G>A	2.37:g.65245365G>A	ENSP00000234256:p.Val399Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_003038	B7Z3C0|D6W5F0	Missense_Mutation	SNP	ENST00000234256.3	37	CCDS1879.1	393	0.17994505494505494	59	0.11991869918699187	88	0.2430939226519337	62	0.10839160839160839	184	0.24274406332453827	G	5.480	0.273673	0.10403	0.175216	0.262442	ENSG00000115902	ENST00000531327;ENST00000448784;ENST00000234256	T;T	0.58940	0.3;0.3	6.17	0.22	0.15279	.	0.444350	0.25711	N	0.028808	T	0.00012	0.0000	N	0.10809	0.05	0.80722	P	0.0	B;B;B	0.18166	0.002;0.026;0.002	B;B;B	0.13407	0.002;0.009;0.004	T	0.24799	-1.0150	8	.	.	.	-27.4704	5.6816	0.17780	0.2405:0.0:0.565:0.1945	rs759458;rs1064513;rs59381701;rs759458	399;101;399	P43007;B7Z3C0;B2R7N6	SATT_HUMAN;.;.	I	101;319;399	ENSP00000431942:V101I;ENSP00000234256:V399I	.	V	+	1	0	SLC1A4	65098869	0.004000	0.15560	0.003000	0.11579	0.253000	0.25986	0.495000	0.22483	-0.237000	0.09739	0.655000	0.94253	GTA	G|0.791;N|0.001	.	strong		0.493	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038	
PFKP	5214	hgsc.bcm.edu	37	10	3172121	3172121	+	Silent	SNP	C	C	T	rs1052333	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:3172121C>T	ENST00000381125.4	+	17	1870	c.1794C>T	c.(1792-1794)gcC>gcT	p.A598A	PFKP_ENST00000381072.1_Silent_p.A16A|PFKP_ENST00000381075.2_Silent_p.A590A	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	598	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		GGCTCGCGGCCGGAGCTGATG	0.632													c|||	2065	0.41234	0.469	0.3761	5008	,	,		15467	0.37		0.3936	False		,,,				2504	0.4243				p.A598A		Atlas-SNP	.											PFKP_ENST00000381075,NS,carcinoma,0,2	PFKP	182	2	0			c.C1794T						PASS	.	G	,	1979,2427		448,1083,672	45.0	44.0	45.0		1770,1794	-9.0	0.0	10	dbSNP_86	45	3119,5481		571,1977,1752	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	1019,3060,2424	TT,TC,CC		36.2674,44.916,39.1973	,	590/777,598/785	3172121	5098,7908	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon17			CGCGGCCGGAGCT	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1794C>T	10.37:g.3172121C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	885	0.4052197802197802	221	0.4491869918699187	149	0.4116022099447514	210	0.36713286713286714	305	0.4023746701846966	N	0.036	-1.304876	0.01353	0.44916	0.362674	ENSG00000067057	ENST00000413079	.	.	.	4.49	-8.98	0.00754	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999936	.	.	.	.	.	.	T	0.31806	-0.9930	3	.	.	.	.	0.6695	0.00856	0.2114:0.1981:0.2652:0.3253	rs1052333;rs17845873;rs17858848;rs61479798;rs1052333	.	.	.	W	162	.	.	R	+	1	2	PFKP	3162121	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-4.635000	0.00205	-3.442000	0.00162	-1.465000	0.01017	CGG	C|0.611;T|0.389	0.389	strong		0.632	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
MFF	56947	hgsc.bcm.edu	37	2	228194480	228194480	+	Missense_Mutation	SNP	A	A	T	rs3211097|rs386655869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228194480A>T	ENST00000353339.3	+	3	460	c.19A>T	c.(19-21)Agt>Tgt	p.S7C	MFF_ENST00000409565.1_Intron|MFF_ENST00000392059.1_Missense_Mutation_p.S7C|MFF_ENST00000349901.7_Intron|MFF_ENST00000337110.7_Intron|MFF_ENST00000524634.1_Intron|MFF_ENST00000476924.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000409616.1_5'UTR	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	7			S -> C (in dbSNP:rs3211097).|S -> I (in dbSNP:rs3211098).		mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						AGGAACAAGCAGTGACACATC	0.368													A|||	1349	0.269369	0.0961	0.245	5008	,	,		17571	0.2431		0.3678	False		,,,				2504	0.4468				p.S7C		Atlas-SNP	.											.	MFF	48	.	0			c.A19T						PASS	.	A	CYS/SER	521,3885		30,461,1712	125.0	117.0	120.0		19	4.8	1.0	2	dbSNP_105	120	3003,5597		552,1899,1849	yes	missense	MFF	NM_020194.4	112	582,2360,3561	TT,TA,AA		34.9186,11.8248,27.0952	probably-damaging	7/343	228194480	3524,9482	2203	4300	6503	SO:0001583	missense	56947	exon3			ACAAGCAGTGACA	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.19A>T	2.37:g.228194480A>T	ENSP00000302037:p.Ser7Cys	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	149	64	0.42953	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	SNP	ENST00000353339.3	37	CCDS2465.1	429	0.19642857142857142	32	0.06504065040650407	88	0.2430939226519337	107	0.18706293706293706	202	0.26649076517150394	A	14.82	2.649436	0.47362	0.118248	0.349186	ENSG00000168958	ENST00000353339;ENST00000436237;ENST00000443428;ENST00000392059	T;T;T;T	0.61859	1.33;0.07;1.32;1.33	5.97	4.8	0.61643	.	0.300115	0.29253	N	0.012695	T	0.00012	0.0000	N	0.22421	0.69	0.36388	P	0.13765799999999995	B	0.02656	0.0	B	0.04013	0.001	T	0.32824	-0.9892	8	.	.	.	-1.6615	10.3927	0.44181	0.8539:0.0:0.0:0.1461	rs3211097;rs10166885;rs17414924;rs3211097	7	Q9GZY8	MFF_HUMAN	C	7	ENSP00000302037:S7C;ENSP00000411386:S7C;ENSP00000391829:S7C;ENSP00000375912:S7C	.	S	+	1	0	MFF	227902724	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.440000	0.52886	1.049000	0.40321	0.528000	0.53228	AGT	A|0.744;T|0.256	0.256	strong		0.368	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194	
CARD10	29775	hgsc.bcm.edu	37	22	37900771	37900771	+	Silent	SNP	A	A	G	rs3817806	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:37900771A>G	ENST00000403299.1	-	9	1605	c.1389T>C	c.(1387-1389)tgT>tgC	p.C463C	CARD10_ENST00000406271.3_Silent_p.C177C|CARD10_ENST00000251973.5_Silent_p.C463C			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	463					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GGGAGGAGGCACAGGCCTGGA	0.622													A|||	551	0.110024	0.053	0.0461	5008	,	,		17960	0.125		0.0755	False		,,,				2504	0.2526				p.C463C		Atlas-SNP	.											.	CARD10	55	.	0			c.T1389C						PASS	.	A		226,4180	132.9+/-169.3	4,218,1981	52.0	39.0	43.0		1389	-3.5	0.9	22	dbSNP_107	43	519,8081	144.8+/-200.6	13,493,3794	no	coding-synonymous	CARD10	NM_014550.3		17,711,5775	GG,GA,AA		6.0349,5.1294,5.7281		463/1033	37900771	745,12261	2203	4300	6503	SO:0001819	synonymous_variant	29775	exon8			GGAGGCACAGGCC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1389T>C	22.37:g.37900771A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	28	0.363636	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			A|0.934;G|0.066	0.066	strong		0.622	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
RPS6KL1	83694	hgsc.bcm.edu	37	14	75386576	75386576	+	Missense_Mutation	SNP	G	G	A	rs2286913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:75386576G>A	ENST00000555647.1	-	4	649	c.362C>T	c.(361-363)cCg>cTg	p.P121L	RPS6KL1_ENST00000358328.4_Missense_Mutation_p.P121L|RPS6KL1_ENST00000557413.1_Missense_Mutation_p.P121L|RPS6KL1_ENST00000354625.2_Missense_Mutation_p.P121L|RPS6KL1_ENST00000554900.1_5'UTR			Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	121			P -> L (in dbSNP:rs2286913). {ECO:0000269|PubMed:17344846}.			ribosome (GO:0005840)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(234;0.00658)		ACTGCTCAGCGGCCGCTGCAG	0.647													G|||	1492	0.297923	0.0174	0.3876	5008	,	,		14334	0.5853		0.3738	False		,,,				2504	0.2393				p.P121L		Atlas-SNP	.											RPS6KL1,colon,carcinoma,0,1	RPS6KL1	35	1	0			c.C362T						PASS	.	G	LEU/PRO	368,4038	178.7+/-207.4	22,324,1857	26.0	27.0	27.0		362	4.1	0.3	14	dbSNP_100	27	3149,5449	456.4+/-364.1	574,2001,1724	yes	missense	RPS6KL1	NM_031464.4	98	596,2325,3581	AA,AG,GG		36.6248,8.3522,27.0455	benign	121/550	75386576	3517,9487	2203	4299	6502	SO:0001583	missense	83694	exon3			CTCAGCGGCCGCT	BC004540	CCDS9834.1, CCDS9834.2	14q24.2	2011-04-05				ENSG00000198208			20222	protein-coding gene	gene with protein product							Standard	NM_031464		Approved	MGC11287	uc010tux.2	Q9Y6S9		ENST00000555647.1:c.362C>T	14.37:g.75386576G>A	ENSP00000452027:p.Pro121Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_031464	A6NGM9|Q69YT9|Q6ZMQ6|Q96NR9|Q9BSU9	Missense_Mutation	SNP	ENST00000555647.1	37	CCDS9834.2	754	0.34523809523809523	12	0.024390243902439025	136	0.3756906077348066	318	0.5559440559440559	288	0.37994722955145116	G	7.553	0.663135	0.14710	0.083522	0.366248	ENSG00000198208	ENST00000555647;ENST00000354625;ENST00000557413;ENST00000358328	T;T;T;T	0.22539	1.95;3.3;1.95;1.95	4.99	4.07	0.47477	MIT (1);	0.411157	0.26812	N	0.022368	T	0.00012	0.0000	L	0.29908	0.895	0.32626	P	0.522599	B;P;B	0.36027	0.106;0.533;0.186	B;B;B	0.28553	0.03;0.091;0.024	T	0.36529	-0.9744	9	0.35671	T	0.21	-4.1088	13.2998	0.60317	0.0:0.1589:0.8411:0.0	rs2286913;rs2286913	121;121;121	Q9Y6S9;Q9Y6S9-4;Q9Y6S9-2	RPKL1_HUMAN;.;.	L	121	ENSP00000452027:P121L;ENSP00000346644:P121L;ENSP00000450567:P121L;ENSP00000351086:P121L	ENSP00000346644:P121L	P	-	2	0	RPS6KL1	74456329	0.998000	0.40836	0.306000	0.25113	0.017000	0.09413	3.053000	0.49901	1.297000	0.44761	0.655000	0.94253	CCG	G|0.708;A|0.292	0.292	strong		0.647	RPS6KL1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413732.1		
CD93	22918	hgsc.bcm.edu	37	20	23065879	23065879	+	Silent	SNP	G	G	A	rs34170527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23065879G>A	ENST00000246006.4	-	1	1098	c.951C>T	c.(949-951)tgC>tgT	p.C317C		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	317	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GTCCCAGGACGCACGTGGCCC	0.637													G|||	121	0.0241613	0.0023	0.0216	5008	,	,		16645	0.0		0.0626	False		,,,				2504	0.0409				p.C317C		Atlas-SNP	.											.	CD93	84	.	0			c.C951T						PASS	.	G		58,4348	54.9+/-90.9	0,58,2145	40.0	44.0	43.0		951	-6.6	0.0	20	dbSNP_126	43	572,8028	150.7+/-205.6	17,538,3745	no	coding-synonymous	CD93	NM_012072.3		17,596,5890	AA,AG,GG		6.6512,1.3164,4.8439		317/653	23065879	630,12376	2203	4300	6503	SO:0001819	synonymous_variant	22918	exon1			CAGGACGCACGTG	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"""CD molecules"""	15855	protein-coding gene	gene with protein product		120577	"""matrix-remodelling associated 4"", ""complement component 1, q subcomponent, receptor 1"", ""CD93 antigen"""	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.951C>T	20.37:g.23065879G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	198	101	0.510101	NM_012072	O00274	Silent	SNP	ENST00000246006.4	37	CCDS13149.1																																																																																			G|0.958;A|0.042	0.042	strong		0.637	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072	
SVIL	6840	hgsc.bcm.edu	37	10	29821523	29821523	+	Silent	SNP	T	T	C	rs1328323	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29821523T>C	ENST00000355867.4	-	8	2525	c.1773A>G	c.(1771-1773)aaA>aaG	p.K591K	SVIL_ENST00000375398.2_Silent_p.K591K|SVIL_ENST00000375400.3_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	591					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CGACAGAGACTTTTGTGTCCA	0.577													C|||	1489	0.297324	0.3351	0.3818	5008	,	,		20218	0.0764		0.4245	False		,,,				2504	0.2832				p.K591K		Atlas-SNP	.											.	SVIL	226	.	0			c.A1773G						PASS	.	C	,	1556,2850	669.8+/-402.2	283,990,930	71.0	65.0	67.0		,1773	4.5	1.0	10	dbSNP_88	67	3807,4793	611.6+/-395.8	843,2121,1336	no	intron,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	1126,3111,2266	CC,CT,TT		44.2674,35.3155,41.2348	,	,591/2215	29821523	5363,7643	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			AGAGACTTTTGTG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1773A>G	10.37:g.29821523T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	185	101	0.545946	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			C|0.381;G|0.000;T|0.619	0.381	strong		0.577	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
EIF5B	9669	hgsc.bcm.edu	37	2	99978048	99978048	+	Silent	SNP	G	G	A	rs12233086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:99978048G>A	ENST00000289371.6	+	4	886	c.684G>A	c.(682-684)gtG>gtA	p.V228V		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	228					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TTAAGACAGTGGCCCAAAAGA	0.398													G|||	848	0.169329	0.1051	0.2839	5008	,	,		17320	0.25		0.1481	False		,,,				2504	0.1135				p.V228V	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											.	EIF5B	95	.	0			c.G684A						PASS	.	G		460,3224		38,384,1420	53.0	53.0	53.0		684	4.0	1.0	2	dbSNP_120	53	1104,7056		81,942,3057	no	coding-synonymous	EIF5B	NM_015904.3		119,1326,4477	AA,AG,GG		13.5294,12.4864,13.205		228/1221	99978048	1564,10280	1842	4080	5922	SO:0001819	synonymous_variant	9669	exon4			GACAGTGGCCCAA	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"""translation initiation factor IF2"""	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.684G>A	2.37:g.99978048G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	279	121	0.433692	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																			G|0.842;A|0.158	0.158	strong		0.398	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904	
AIFM3	150209	hgsc.bcm.edu	37	22	21330787	21330787	+	Silent	SNP	C	C	T	rs7285694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21330787C>T	ENST00000399167.2	+	11	1230	c.990C>T	c.(988-990)gcC>gcT	p.A330A	AIFM3_ENST00000405089.1_Silent_p.A336A|AIFM3_ENST00000335375.5_Silent_p.A318A|AIFM3_ENST00000465606.1_3'UTR|AIFM3_ENST00000440238.2_Silent_p.A330A|AIFM3_ENST00000399163.2_Silent_p.A330A|AIFM3_ENST00000333607.6_Silent_p.A330A	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	330					cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			TGAGGCTGGCCCGAGGCCGCA	0.612													C|||	958	0.191294	0.1959	0.1888	5008	,	,		19537	0.1062		0.2992	False		,,,				2504	0.1636				p.A336A		Atlas-SNP	.											.	AIFM3	49	.	0			c.C1008T						PASS	.	C	,,	877,3529	336.0+/-304.2	92,693,1418	74.0	52.0	59.0		990,1008,990	3.7	1.0	22	dbSNP_116	59	2657,5943	421.7+/-353.8	450,1757,2093	no	coding-synonymous,coding-synonymous,coding-synonymous	AIFM3	NM_001018060.2,NM_001146288.1,NM_144704.2	,,	542,2450,3511	TT,TC,CC		30.8953,19.9047,27.1721	,,	330/599,336/605,330/606	21330787	3534,9472	2203	4300	6503	SO:0001819	synonymous_variant	150209	exon11			GCTGGCCCGAGGC	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.990C>T	22.37:g.21330787C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Silent	SNP	ENST00000399167.2	37	CCDS13786.1																																																																																			C|0.743;T|0.257	0.257	strong		0.612	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704	
ZBED4	9889	hgsc.bcm.edu	37	22	50278568	50278568	+	Missense_Mutation	SNP	A	A	G	rs910799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50278568A>G	ENST00000216268.5	+	2	1735	c.1258A>G	c.(1258-1260)Ata>Gta	p.I420V		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	420			I -> V (in dbSNP:rs910799). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		TTCCGATGACATAGGGGAGGC	0.557													G|||	3094	0.617812	0.1831	0.8242	5008	,	,		18698	0.8264		0.8022	False		,,,				2504	0.6544				p.I420V		Atlas-SNP	.											.	ZBED4	102	.	0			c.A1258G						PASS	.	G	VAL/ILE	1292,3114	696.1+/-406.0	192,908,1103	56.0	60.0	59.0		1258	0.5	0.0	22	dbSNP_86	59	6858,1742	313.9+/-311.6	2734,1390,176	yes	missense	ZBED4	NM_014838.2	29	2926,2298,1279	GG,GA,AA		20.2558,29.3236,37.3366	benign	420/1172	50278568	8150,4856	2203	4300	6503	SO:0001583	missense	9889	exon2			GATGACATAGGGG	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.1258A>G	22.37:g.50278568A>G	ENSP00000216268:p.Ile420Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	1450	0.6639194139194139	91	0.18495934959349594	293	0.8093922651933702	465	0.8129370629370629	601	0.7928759894459103	G	0.013	-1.643533	0.00792	0.293236	0.797442	ENSG00000100426	ENST00000216268	T	0.42131	0.98	5.08	0.478	0.16789	.	0.901488	0.09405	N	0.806631	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44483	-0.9325	9	0.05351	T	0.99	-2.6086	2.0173	0.03500	0.3433:0.1188:0.4101:0.1278	rs910799;rs5769769;rs60411744;rs910799	420	O75132	ZBED4_HUMAN	V	420	ENSP00000216268:I420V	ENSP00000216268:I420V	I	+	1	0	ZBED4	48664572	0.011000	0.17503	0.000000	0.03702	0.001000	0.01503	1.047000	0.30367	0.044000	0.15775	-0.733000	0.03571	ATA	A|0.371;G|0.629	0.629	strong		0.557	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
PARP4	143	hgsc.bcm.edu	37	13	25021154	25021154	+	Splice_Site	SNP	C	C	T	rs61947037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25021154C>T	ENST00000381989.3	-	26	3390	c.3285G>A	c.(3283-3285)caG>caA	p.Q1095Q		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1095					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GTCTTCTTACCTGTGTGCAGT	0.468													c|||	2480	0.495208	0.1967	0.5951	5008	,	,		15400	0.6062		0.5278	False		,,,				2504	0.68				p.Q1095Q		Atlas-SNP	.											.	PARP4	142	.	0			c.G3285A						PASS	.	C		694,3710		139,416,1647	81.0	65.0	71.0		3285	3.8	1.0	13	dbSNP_129	71	4242,4352		1312,1618,1367	no	coding-synonymous-near-splice	PARP4	NM_006437.3		1451,2034,3014	TT,TC,CC		49.36,15.7584,37.9751		1095/1725	25021154	4936,8062	2202	4297	6499	SO:0001630	splice_region_variant	143	exon26			TCTTACCTGTGTG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3285+1G>A	13.37:g.25021154C>T		Somatic	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	105	99	0.942857	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.555;T|0.445	0.445	strong		0.468	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	Silent
GPR111	222611	hgsc.bcm.edu	37	6	47649573	47649573	+	Silent	SNP	C	C	T	rs10807371|rs71538333	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:47649573C>T	ENST00000296862.1	+	6	1278	c.1278C>T	c.(1276-1278)agC>agT	p.S426S	GPR111_ENST00000507065.1_Silent_p.S358S|GPR111_ENST00000398742.2_Silent_p.S358S			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	426	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GTAGGCCAAGCAAATTGTTTA	0.438													C|||	2551	0.509385	0.4448	0.4323	5008	,	,		22594	0.3085		0.6272	False		,,,				2504	0.7372				p.S358S		Atlas-SNP	.											.	GPR111	123	.	0			c.C1074T						PASS	.	C		1753,2103		395,963,570	138.0	131.0	133.0		1074	3.7	0.6	6	dbSNP_120	133	5324,2930		1737,1850,540	yes	coding-synonymous	GPR111	NM_153839.6		2132,2813,1110	TT,TC,CC		35.4979,45.4616,41.5607		358/643	47649573	7077,5033	1928	4127	6055	SO:0001819	synonymous_variant	222611	exon7			GCCAAGCAAATTG	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.1278C>T	6.37:g.47649573C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Silent	SNP	ENST00000296862.1	37																																																																																				CA|0.500;TG|0.500	.	alt		0.438	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
TAOK2	9344	hgsc.bcm.edu	37	16	29998200	29998200	+	Silent	SNP	A	A	G	rs4077410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:29998200A>G	ENST00000308893.4	+	16	3650	c.2607A>G	c.(2605-2607)acA>acG	p.T869T	TAOK2_ENST00000279394.3_Intron|TAOK2_ENST00000416441.2_Silent_p.T696T|TAOK2_ENST00000543033.1_Silent_p.T756T	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	869	Glu-rich.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						AGGCTGGGACATGGAGCTTGT	0.597													G|||	2427	0.484625	0.5408	0.4107	5008	,	,		17434	0.379		0.5249	False		,,,				2504	0.5286				p.T869T		Atlas-SNP	.											TAOK2_ENST00000308893,NS,carcinoma,0,1	TAOK2	142	1	0			c.A2607G						scavenged	.	G	,	2388,2006	562.2+/-380.9	639,1110,448	97.0	95.0	96.0		,2607	-5.4	0.0	16	dbSNP_108	96	4491,4109	561.9+/-387.9	1188,2115,997	yes	intron,coding-synonymous	TAOK2	NM_004783.2,NM_016151.2	,	1827,3225,1445	GG,GA,AA		47.7791,45.6532,47.0602	,	,869/1236	29998200	6879,6115	2197	4300	6497	SO:0001819	synonymous_variant	9344	exon16			TGGGACATGGAGC	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.2607A>G	16.37:g.29998200A>G		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	151	79	0.523179	NM_016151	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Silent	SNP	ENST00000308893.4	37	CCDS10663.1																																																																																			A|0.495;G|0.505	0.505	strong		0.597	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151	
TDP2	51567	hgsc.bcm.edu	37	6	24653283	24653283	+	Silent	SNP	T	T	C	rs11559067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:24653283T>C	ENST00000378198.4	-	6	905	c.735A>G	c.(733-735)ttA>ttG	p.L245L	TDP2_ENST00000478285.1_5'Flank|TDP2_ENST00000545995.1_Silent_p.L275L|TDP2_ENST00000341060.3_Silent_p.L187L			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	245					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						GCATTTTCTTTAAAACCATTT	0.428								Direct reversal of damage					T|||	60	0.0119808	0.003	0.0202	5008	,	,		17943	0.001		0.0318	False		,,,				2504	0.0092				p.L245L		Atlas-SNP	.											.	TDP2	29	.	0			c.A735G						PASS	.	T		39,4367	43.1+/-76.7	0,39,2164	212.0	222.0	219.0		735	-1.5	0.0	6	dbSNP_120	219	322,8278	113.5+/-173.5	7,308,3985	no	coding-synonymous	TDP2	NM_016614.2		7,347,6149	CC,CT,TT		3.7442,0.8852,2.7756		245/363	24653283	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	51567	exon6			TTTCTTTAAAACC	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"""TRAF and TNF receptor associated protein"""	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.735A>G	6.37:g.24653283T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Silent	SNP	ENST00000378198.4	37	CCDS4557.1																																																																																			T|0.977;C|0.023	0.023	strong		0.428	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1		
PODXL	5420	hgsc.bcm.edu	37	7	131195959	131195959	+	Missense_Mutation	SNP	C	C	T	rs3735035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:131195959C>T	ENST00000378555.3	-	2	581	c.334G>A	c.(334-336)Ggc>Agc	p.G112S	PODXL_ENST00000541194.1_Missense_Mutation_p.G114S|PODXL_ENST00000322985.9_Missense_Mutation_p.G112S|PODXL_ENST00000465001.1_5'UTR|PODXL_ENST00000537928.1_Missense_Mutation_p.G112S			O00592	PODXL_HUMAN	podocalyxin-like	112	Thr-rich.		G -> S (in dbSNP:rs3735035).		cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					TTGCCTGAGCCGCCTCCTCTA	0.567													C|||	1822	0.363818	0.0363	0.3948	5008	,	,		19092	0.6518		0.4354	False		,,,				2504	0.4141				p.G112S		Atlas-SNP	.											.	PODXL	53	.	0			c.G334A						PASS	.	C	SER/GLY,SER/GLY	470,3936	219.7+/-237.4	26,418,1759	161.0	163.0	163.0		334,334	-5.6	0.0	7	dbSNP_107	163	4070,4530	559.7+/-387.5	966,2138,1196	yes	missense,missense	PODXL	NM_001018111.2,NM_005397.3	56,56	992,2556,2955	TT,TC,CC		47.3256,10.6673,34.907	benign,benign	112/559,112/527	131195959	4540,8466	2203	4300	6503	SO:0001583	missense	5420	exon2			CTGAGCCGCCTCC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.334G>A	7.37:g.131195959C>T	ENSP00000367817:p.Gly112Ser	Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	286	127	0.444056	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	856	0.39194139194139194	30	0.06097560975609756	130	0.35911602209944754	351	0.6136363636363636	345	0.4551451187335092	C	3.668	-0.068070	0.07228	0.106673	0.473256	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.10573	3.06;2.86;3.06;3.02	2.82	-5.63	0.02474	.	16.508200	0.00166	N	0.000000	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.18610	0.029;0.017	B;B	0.06405	0.002;0.001	T	0.41305	-0.9516	9	0.09084	T	0.74	1.8737	1.2318	0.01945	0.3764:0.2453:0.2502:0.1281	rs3735035;rs17744768;rs52837657;rs60330344;rs3735035	112;112	O00592-2;O00592	.;PODXL_HUMAN	S	114;112;102;112;112	ENSP00000440518:G114S;ENSP00000442655:G112S;ENSP00000367817:G112S;ENSP00000319782:G112S	ENSP00000319782:G112S	G	-	1	0	PODXL	130846499	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.188000	0.03064	-2.759000	0.00371	-1.890000	0.00535	GGC	C|0.627;T|0.373	0.373	strong		0.567	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
NOTCH4	4855	hgsc.bcm.edu	37	6	32168771	32168771	+	Silent	SNP	G	G	T	rs3134942	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32168771G>T	ENST00000375023.3	-	23	4290	c.4152C>A	c.(4150-4152)gtC>gtA	p.V1384V		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1384					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CCACACCCATGACCACCACAA	0.602													T|||	389	0.0776757	0.0991	0.0476	5008	,	,		17672	0.0278		0.1034	False		,,,				2504	0.0951				p.V1384V		Atlas-SNP	.											NOTCH4,colon,carcinoma,0,1	NOTCH4	201	1	0			c.C4152A						PASS	.	T		276,2746		11,254,1246	75.0	50.0	59.0		4152	0.8	1.0	6	dbSNP_103	59	699,4719		45,609,2055	no	coding-synonymous	NOTCH4	NM_004557.3		56,863,3301	TT,TG,GG		12.9014,9.133,11.5521		1384/2004	32168771	975,7465	1511	2709	4220	SO:0001819	synonymous_variant	4855	exon23			ACCCATGACCACC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4152C>A	6.37:g.32168771G>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	172	72	0.418605	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			G|0.909;T|0.091	0.091	strong		0.602	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
SV2C	22987	hgsc.bcm.edu	37	5	75427935	75427935	+	Silent	SNP	G	G	A	rs10070440	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:75427935G>A	ENST00000502798.2	+	2	802	c.360G>A	c.(358-360)cgG>cgA	p.R120R	SV2C_ENST00000322285.7_Silent_p.R120R	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	120					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		ACAAGGACCGGCGGGAGCTGG	0.552													G|||	2367	0.472644	0.2625	0.4467	5008	,	,		19566	0.3224		0.7396	False		,,,				2504	0.6554				p.R120R		Atlas-SNP	.											SV2C,NS,carcinoma,+2,2	SV2C	97	2	0			c.G360A						PASS	.	G		1445,2665		271,903,881	98.0	114.0	109.0		360	-11.4	0.0	5	dbSNP_119	109	6388,2022		2426,1536,243	no	coding-synonymous	SV2C	NM_014979.1		2697,2439,1124	AA,AG,GG		24.0428,35.1582,37.4361		120/728	75427935	7833,4687	2055	4205	6260	SO:0001819	synonymous_variant	22987	exon2			GGACCGGCGGGAG	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.360G>A	5.37:g.75427935G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_014979	Q496K1|Q9UPU8	Silent	SNP	ENST00000502798.2	37	CCDS43331.1																																																																																			G|0.480;A|0.520	0.520	strong		0.552	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4		
RNF215	200312	hgsc.bcm.edu	37	22	30782089	30782089	+	Silent	SNP	A	A	G	rs5997629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30782089A>G	ENST00000382363.3	-	3	545	c.471T>C	c.(469-471)ctT>ctC	p.L157L		NM_001017981.1	NP_001017981.1	Q9Y6U7	RN215_HUMAN	ring finger protein 215	157						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)	6						TCAGGATGAGAAGAAGCAGGG	0.607													G|||	1763	0.352037	0.3222	0.353	5008	,	,		17396	0.3929		0.3111	False		,,,				2504	0.3916				p.L157L		Atlas-SNP	.											.	RNF215	19	.	0			c.T471C						PASS	.	G		1435,2969	658.4+/-400.4	254,927,1021	43.0	40.0	41.0		471	-0.1	1.0	22	dbSNP_114	41	2543,6057	662.9+/-402.0	361,1821,2118	no	coding-synonymous	RNF215	NM_001017981.1		615,2748,3139	GG,GA,AA		29.5698,32.584,30.5906		157/378	30782089	3978,9026	2202	4300	6502	SO:0001819	synonymous_variant	200312	exon3			GATGAGAAGAAGC		CCDS33633.1	22q12.2	2013-01-09			ENSG00000099999	ENSG00000099999		"""RING-type (C3HC4) zinc fingers"""	33434	protein-coding gene	gene with protein product							Standard	NM_001017981		Approved		uc003ahp.3	Q9Y6U7	OTTHUMG00000151016	ENST00000382363.3:c.471T>C	22.37:g.30782089A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_001017981	A6NEL1	Silent	SNP	ENST00000382363.3	37	CCDS33633.1	752	0.3443223443223443	176	0.35772357723577236	114	0.3149171270718232	223	0.38986013986013984	239	0.3153034300791557	G	10.87	1.473926	0.26423	0.32584	0.295698	ENSG00000099999	ENST00000215798	.	.	.	4.61	-0.0468	0.13846	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45396	-0.9264	3	.	.	.	-17.5385	5.1726	0.15118	0.3224:0.1381:0.5396:0.0	rs5997629;rs7288193;rs56627483;rs5997629	.	.	.	P	95	.	.	S	-	1	0	RNF215	29112089	1.000000	0.71417	0.956000	0.39512	0.996000	0.88848	0.733000	0.26087	-0.472000	0.06881	-0.124000	0.14976	TCT	A|0.674;G|0.326	0.326	strong		0.607	RNF215-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320960.1	NM_001017981	
LMOD1	25802	hgsc.bcm.edu	37	1	201869257	201869257	+	Missense_Mutation	SNP	G	G	A	rs2820312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201869257G>A	ENST00000367288.4	-	2	1130	c.884C>T	c.(883-885)aCg>aTg	p.T295M	RP11-307B6.3_ENST00000458139.1_RNA|RP11-307B6.3_ENST00000414927.1_RNA	NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	295			T -> M (in dbSNP:rs2820312).		muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GCCACTGGGCGTCTGTTTCTC	0.507													g|||	1091	0.217851	0.205	0.2219	5008	,	,		20434	0.1012		0.3032	False		,,,				2504	0.2648				p.T295M		Atlas-SNP	.											.	LMOD1	59	.	0			c.C884T						PASS	.	A	MET/THR	830,3194		66,698,1248	72.0	74.0	73.0		884	0.6	0.0	1	dbSNP_100	73	2618,5716		402,1814,1951	yes	missense	LMOD1	NM_012134.2	81	468,2512,3199	AA,AG,GG		31.4135,20.6262,27.901	possibly-damaging	295/601	201869257	3448,8910	2012	4167	6179	SO:0001583	missense	25802	exon2			CTGGGCGTCTGTT	X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.884C>T	1.37:g.201869257G>A	ENSP00000356257:p.Thr295Met	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	404	402	0.995049	NM_012134	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	37	CCDS53457.1	527	0.2413003663003663	132	0.2682926829268293	89	0.24585635359116023	64	0.11188811188811189	242	0.31926121372031663	g	10.27	1.305016	0.23736	0.206262	0.314135	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	D	0.92397	-3.03	5.32	0.581	0.17407	.	1.726880	0.03514	N	0.219988	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;P	0.51653	0.004;0.947	B;B	0.31547	0.002;0.132	T	0.14896	-1.0456	9	0.30078	T	0.28	-2.9137	8.7241	0.34458	0.1205:0.2326:0.6469:0.0	rs2820312;rs3820435;rs52806101;rs58496028;rs2820312	244;295	B4E3S9;P29536	.;LMOD1_HUMAN	M	295;295;244	ENSP00000356257:T295M	ENSP00000356257:T295M	T	-	2	0	LMOD1	200135880	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.111000	0.15458	-0.089000	0.12484	-2.465000	0.00204	ACG	G|0.763;A|0.237	0.237	strong		0.507	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2		
NOP56	10528	hgsc.bcm.edu	37	20	2636059	2636059	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2636059C>T	ENST00000329276.5	+	6	1174	c.658C>T	c.(658-660)Cga>Tga	p.R220*	SNORD57_ENST00000448188.1_RNA|IDH3B_ENST00000488299.1_5'Flank|SNORD86_ENST00000391196.1_RNA|SNORA51_ENST00000606420.1_RNA|SNORD110_ENST00000408189.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORD56_ENST00000413522.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	220					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TATTGGAAACCGAAGGGAACT	0.537																																					p.R220X		Atlas-SNP	.											NOP56,NS,carcinoma,-2,1	NOP56	73	1	0			c.C658T						PASS	.						127.0	122.0	124.0					20																	2636059		2203	4300	6503	SO:0001587	stop_gained	10528	exon6			GGAAACCGAAGGG	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.658C>T	20.37:g.2636059C>T	ENSP00000370589:p.Arg220*	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	131	19	0.145038	NM_006392	Q2M3T6|Q9NQ05	Nonsense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.905811	0.92107	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.0976	12.2785	0.54751	0.1695:0.8305:0.0:0.0	.	.	.	.	X	220;249	.	ENSP00000370589:R220X	R	+	1	2	NOP56	2584059	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	2.769000	0.47654	2.672000	0.90937	0.561000	0.74099	CGA	.	.	none		0.537	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
KLHL2	11275	hgsc.bcm.edu	37	4	166239083	166239083	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:166239083T>G	ENST00000226725.6	+	14	1974	c.1715T>G	c.(1714-1716)gTt>gGt	p.V572G	KLHL2_ENST00000538127.1_Missense_Mutation_p.V484G|KLHL2_ENST00000514860.1_Missense_Mutation_p.V576G|KLHL2_ENST00000421009.2_Missense_Mutation_p.V475G|KLHL2_ENST00000509028.1_3'UTR|KLHL2_ENST00000506761.1_Missense_Mutation_p.V406G	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	572					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		AAATGGACAGTTGTGTCATCG	0.388																																					p.V576G		Atlas-SNP	.											.	KLHL2	42	.	0			c.T1727G						PASS	.						159.0	154.0	156.0					4																	166239083		2203	4300	6503	SO:0001583	missense	11275	exon14			GGACAGTTGTGTC	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"""Kelch-like"", ""BTB/POZ domain containing"""	6353	protein-coding gene	gene with protein product	"""mayven"""	605774	"""kelch (Drosophila)-like 2 (Mayven)"", ""kelch-like 2, Mayven (Drosophila)"""			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.1715T>G	4.37:g.166239083T>G	ENSP00000226725:p.Val572Gly	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	154	19	0.123377	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	37	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.897708	0.72639	.	.	ENSG00000109466	ENST00000226725;ENST00000514860;ENST00000538127;ENST00000421009;ENST00000506761	T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15	6.17	6.17	0.99709	Galactose oxidase, beta-propeller (1);	0.125811	0.56097	D	0.000040	T	0.73651	0.3614	L	0.28192	0.835	0.80722	D	1	P;B;P	0.37015	0.578;0.361;0.578	B;B;B	0.42625	0.393;0.298;0.393	T	0.76503	-0.2935	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	576;572;572	B4DFH7;B2RD18;O95198	.;.;KLHL2_HUMAN	G	572;576;484;475;406	ENSP00000226725:V572G;ENSP00000424198:V576G;ENSP00000437526:V484G;ENSP00000408974:V475G;ENSP00000424108:V406G	ENSP00000226725:V572G	V	+	2	0	KLHL2	166458533	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.655000	0.83696	2.371000	0.80710	0.533000	0.62120	GTT	.	.	none		0.388	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1		
ISL2	64843	hgsc.bcm.edu	37	15	76630303	76630303	+	Silent	SNP	T	T	C	rs4636879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:76630303T>C	ENST00000290759.4	+	2	403	c.243T>C	c.(241-243)taT>taC	p.Y81Y	RP11-685G9.2_ENST00000559539.1_RNA	NM_145805.1	NP_665804.1	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	81	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|peripheral nervous system neuron development (GO:0048935)|regulation of transcription, DNA-templated (GO:0006355)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord motor neuron cell fate specification (GO:0021520)|visceral motor neuron differentiation (GO:0021524)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6						AGCGGGACTATGTCAGGTGAG	0.731													T|||	3451	0.689097	0.2118	0.879	5008	,	,		13104	0.8879		0.7982	False		,,,				2504	0.8824				p.Y81Y	GBM(97;953 1391 16164 31496 36951)	Atlas-SNP	.											.	ISL2	20	.	0			c.T243C						PASS	.	T		1344,3050	429.5+/-342.2	215,914,1068	45.0	34.0	38.0		243	1.1	1.0	15	dbSNP_111	38	6935,1653	706.0+/-405.5	2800,1335,159	no	coding-synonymous	ISL2	NM_145805.1		3015,2249,1227	CC,CT,TT		19.2478,30.5872,36.2271		81/360	76630303	8279,4703	2197	4294	6491	SO:0001819	synonymous_variant	64843	exon2			GGACTATGTCAGG	AK001022	CCDS10290.1	15q24.3	2012-03-09	2007-07-13		ENSG00000159556	ENSG00000159556		"""Homeoboxes / LIM class"""	18524	protein-coding gene	gene with protein product		609481	"""ISL2 transcription factor, LIM/homeodomain, (islet-2)"""				Standard	NM_145805		Approved	FLJ10160	uc002bbw.1	Q96A47	OTTHUMG00000143723	ENST00000290759.4:c.243T>C	15.37:g.76630303T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	44	27	0.613636	NM_145805	B3KM37	Silent	SNP	ENST00000290759.4	37	CCDS10290.1																																																																																			T|0.354;C|0.646	0.646	strong		0.731	ISL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289779.1		
DRD2	1813	hgsc.bcm.edu	37	11	113283459	113283459	+	Silent	SNP	G	G	A	rs6277	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:113283459G>A	ENST00000362072.3	-	7	1301	c.957C>T	c.(955-957)ccC>ccT	p.P319P	DRD2_ENST00000535984.1_5'Flank|DRD2_ENST00000355319.2_Silent_p.P321P|DRD2_ENST00000538967.1_Silent_p.P321P|RP11-159N11.3_ENST00000546284.1_RNA|DRD2_ENST00000346454.3_Silent_p.P290P|DRD2_ENST00000542968.1_Silent_p.P319P|DRD2_ENST00000544518.1_Silent_p.P318P	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	319	Interaction with PPP1R9B. {ECO:0000250}.				activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CGGGGCTGTCGGGAGTGCTGT	0.617													G|||	1222	0.24401	0.0552	0.3256	5008	,	,		14821	0.0625		0.5437	False		,,,				2504	0.32				p.P319P		Atlas-SNP	.											.	DRD2	98	.	0			c.C957T	GRCh37	CM030215	DRD2	M	rs6277	PASS	.	G	,	628,3774	272.8+/-271.0	49,530,1622	116.0	98.0	104.0		957,870	-9.2	0.0	11	dbSNP_52	104	4685,3907	604.2+/-394.8	1292,2101,903	no	coding-synonymous,coding-synonymous	DRD2	NM_000795.3,NM_016574.3	,	1341,2631,2525	AA,AG,GG		45.4725,14.2662,40.8881	,	319/444,290/415	113283459	5313,7681	2201	4296	6497	SO:0001819	synonymous_variant	1813	exon7			GCTGTCGGGAGTG	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"""GPCR / Class A : Dopamine receptors"""	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.957C>T	11.37:g.113283459G>A		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	386	183	0.474093	NM_000795	Q9NZR3|Q9UPA9	Silent	SNP	ENST00000362072.3	37	CCDS8361.1																																																																																			G|0.641;A|0.359	0.359	strong		0.617	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795	
RPS6KA2	6196	hgsc.bcm.edu	37	6	166862233	166862233	+	Silent	SNP	T	T	C	rs2230730	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:166862233T>C	ENST00000265678.4	-	14	1534	c.1311A>G	c.(1309-1311)acA>acG	p.T437T	RPS6KA2_ENST00000503859.1_Silent_p.T445T|RPS6KA2_ENST00000481261.2_Silent_p.T348T|RPS6KA2_ENST00000510118.1_Silent_p.T462T|RPS6KA2_ENST00000405189.3_Silent_p.T348T	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	437	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		ACTCGGTGTCTGTGGCTTTAT	0.582													C|||	996	0.198882	0.1876	0.2723	5008	,	,		24814	0.0764		0.3082	False		,,,				2504	0.1759				p.T445T		Atlas-SNP	.											RPS6KA2_ENST00000503859,NS,carcinoma,-1,2	RPS6KA2	212	2	0			c.A1335G						PASS	.	C	,	931,3475	736.1+/-410.7	99,733,1371	238.0	158.0	185.0		1335,1311	-8.8	0.6	6	dbSNP_120	185	2587,6013	688.1+/-404.3	387,1813,2100	no	coding-synonymous,coding-synonymous	RPS6KA2	NM_001006932.1,NM_021135.4	,	486,2546,3471	CC,CT,TT		30.0814,21.1303,27.0491	,	445/742,437/734	166862233	3518,9488	2203	4300	6503	SO:0001819	synonymous_variant	6196	exon15			GGTGTCTGTGGCT	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"""ribosomal protein S6 kinase, 90kD, polypeptide 2"""			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.1311A>G	6.37:g.166862233T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	92	0.541176	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Silent	SNP	ENST00000265678.4	37	CCDS5294.1																																																																																			T|0.764;C|0.236;A|0.000	0.236	strong		0.582	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
RNF169	254225	hgsc.bcm.edu	37	11	74546905	74546905	+	Silent	SNP	G	G	A	rs1125609	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:74546905G>A	ENST00000299563.4	+	6	1270	c.1257G>A	c.(1255-1257)caG>caA	p.Q419Q		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	419					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						GAAGCCTGCAGAAGCAGACTT	0.488													G|||	1251	0.2498	0.171	0.1931	5008	,	,		19862	0.2609		0.2087	False		,,,				2504	0.4274				p.Q419Q		Atlas-SNP	.											RNF169,colon,carcinoma,0,1	RNF169	36	1	0			c.G1257A						PASS	.	G		652,3124		59,534,1295	96.0	97.0	97.0		1257	6.0	1.0	11	dbSNP_86	97	1577,6683		120,1337,2673	no	coding-synonymous	RNF169	NM_001098638.1		179,1871,3968	AA,AG,GG		19.092,17.2669,18.5194		419/709	74546905	2229,9807	1888	4130	6018	SO:0001819	synonymous_variant	254225	exon6			CCTGCAGAAGCAG	AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"""RING-type (C3HC4) zinc fingers"""	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.1257G>A	11.37:g.74546905G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_001098638	Q6N015	Silent	SNP	ENST00000299563.4	37	CCDS41691.1																																																																																			G|0.788;A|0.212	0.212	strong		0.488	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886	
LRRC15	131578	hgsc.bcm.edu	37	3	194081692	194081692	+	Silent	SNP	G	G	A	rs13090956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:194081692G>A	ENST00000347624.3	-	2	166	c.81C>T	c.(79-81)agC>agT	p.S27S	LRRC15_ENST00000428839.1_Silent_p.S33S|LRRC15_ENST00000439944.2_Silent_p.S33S	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	27	LRRNT.				negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		AGGTACACTCGCTAGGGCAGC	0.632													G|||	279	0.0557109	0.0348	0.049	5008	,	,		20719	0.0258		0.0924	False		,,,				2504	0.0818				p.S33S		Atlas-SNP	.											.	LRRC15	137	.	0			c.C99T						PASS	.	G	,	189,4217	118.0+/-155.7	3,183,2017	35.0	31.0	33.0		99,81	-9.9	0.0	3	dbSNP_121	33	871,7729	194.5+/-239.9	34,803,3463	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	37,986,5480	AA,AG,GG		10.1279,4.2896,8.1501	,	33/588,27/582	194081692	1060,11946	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			ACACTCGCTAGGG	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.81C>T	3.37:g.194081692G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	40	38	0.95	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			G|0.921;A|0.079	0.079	strong		0.632	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
PRMT8	56341	hgsc.bcm.edu	37	12	3701464	3701464	+	Silent	SNP	G	G	A	rs34000611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:3701464G>A	ENST00000382622.3	+	9	1437	c.1047G>A	c.(1045-1047)cgG>cgA	p.R349R	PRMT8_ENST00000261252.4_3'UTR|PRMT8_ENST00000452611.2_Silent_p.R340R	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	349	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			TCACTGTCCGGAGGGGGGAGG	0.547													G|||	516	0.103035	0.1218	0.0836	5008	,	,		19044	0.1052		0.1332	False		,,,				2504	0.0583				p.R349R		Atlas-SNP	.											PRMT8_ENST00000452611,NS,carcinoma,+1,2	PRMT8	97	2	0			c.G1047A						PASS	.	G		580,3826	258.9+/-262.7	37,506,1660	120.0	122.0	121.0		1047	1.1	1.0	12	dbSNP_126	121	1145,7455	236.2+/-268.5	81,983,3236	no	coding-synonymous	PRMT8	NM_019854.3		118,1489,4896	AA,AG,GG		13.314,13.1639,13.2631		349/395	3701464	1725,11281	2203	4300	6503	SO:0001819	synonymous_variant	56341	exon9			TGTCCGGAGGGGG	AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"""Protein arginine methyltransferases"""	5188	protein-coding gene	gene with protein product		610086	"""HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"", ""HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"""	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.1047G>A	12.37:g.3701464G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_019854	B2RDP0|Q8TBJ8	Silent	SNP	ENST00000382622.3	37	CCDS8521.2																																																																																			G|0.881;A|0.119	0.119	strong		0.547	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854	
ZNF286B	729288	hgsc.bcm.edu	37	17	18565350	18565350	+	Missense_Mutation	SNP	G	G	C	rs9912644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18565350G>C	ENST00000545289.1	-	5	1719	c.1469C>G	c.(1468-1470)aCc>aGc	p.T490S	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	490					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T490S(2)		endometrium(1)|lung(1)	2						TTTCTCTCCGGTATGAGTTCT	0.393													.|||	1496	0.298722	0.2095	0.4092	5008	,	,		22635	0.3611		0.3827	False		,,,				2504	0.1902				p.T490S		Atlas-SNP	.											ZNF286B,NS,carcinoma,0,1	ZNF286B	75	1	2	Substitution - Missense(2)	endometrium(2)	c.C1469G						PASS	.						103.0	101.0	102.0					17																	18565350		692	1591	2283	SO:0001583	missense	729288	exon5			TCTCCGGTATGAG		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1469C>G	17.37:g.18565350G>C	ENSP00000461413:p.Thr490Ser	Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	359	160	0.445682	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.648;C|0.352	0.352	strong		0.393	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
MROH6	642475	hgsc.bcm.edu	37	8	144657801	144657801	+	5'Flank	SNP	G	G	A	rs9771743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144657801G>A	ENST00000398882.3	-	0	0				NAPRT1_ENST00000426292.3_Silent_p.G393G|RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000276844.7_Silent_p.G393G|NAPRT1_ENST00000460623.1_5'UTR|NAPRT1_ENST00000435154.3_Silent_p.G393G|NAPRT1_ENST00000449291.2_Silent_p.G393G	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6																		CCTTATAGACGCCACCCAGGG	0.647													G|||	924	0.184505	0.1853	0.2579	5008	,	,		11518	0.0923		0.171	False		,,,				2504	0.2403				p.G393G		Atlas-SNP	.											.	NAPRT1	47	.	0			c.C1179T						PASS	.	G		814,3572		79,656,1458	23.0	22.0	22.0		1179	-3.8	1.0	8	dbSNP_119	22	1404,7192		109,1186,3003	yes	coding-synonymous	NAPRT1	NM_145201.4		188,1842,4461	AA,AG,GG		16.3332,18.5591,17.0852		393/539	144657801	2218,10764	2193	4298	6491	SO:0001631	upstream_gene_variant	93100	exon9			ATAGACGCCACCC	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164		8.37:g.144657801G>A	Exception_encountered	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	236	127	0.538136	NM_145201	A8MWB1	Silent	SNP	ENST00000398882.3	37	CCDS47928.1																																																																																			G|0.836;A|0.164	0.164	strong		0.647	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878	
SOX30	11063	hgsc.bcm.edu	37	5	157078632	157078632	+	Missense_Mutation	SNP	G	G	A	rs13181859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:157078632G>A	ENST00000265007.6	-	1	796	c.455C>T	c.(454-456)cCt>cTt	p.P152L	SOX30_ENST00000519442.1_Intron|SOX30_ENST00000311371.5_Missense_Mutation_p.P152L	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	152					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGCCCCTCGAGGCCCCACTGA	0.682													.|||	16	0.00319489	0.0	0.0072	5008	,	,		14330	0.0		0.002	False		,,,				2504	0.0092				p.P152L	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.C455T						PASS	.	G	LEU/PRO,LEU/PRO	1,4355		0,1,2177	15.0	18.0	17.0		455,455	2.2	0.0	5	dbSNP_121	17	28,8462		0,28,4217	yes	missense,missense	SOX30	NM_007017.2,NM_178424.1	98,98	0,29,6394	AA,AG,GG		0.3298,0.023,0.2258	benign,benign	152/502,152/754	157078632	29,12817	2178	4245	6423	SO:0001583	missense	11063	exon1			CCTCGAGGCCCCA	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.455C>T	5.37:g.157078632G>A	ENSP00000265007:p.Pro152Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	128	89	0.695312	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	G	3.133	-0.178037	0.06380	2.3E-4	0.003298	ENSG00000039600	ENST00000311371;ENST00000265007	D;D	0.97665	-4.48;-4.13	4.09	2.25	0.28309	.	1.098170	0.07137	N	0.846598	D	0.89220	0.6653	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.32829	0.386;0.0	B;B	0.28232	0.087;0.0	D	0.84664	0.0708	10	0.72032	D	0.01	.	2.6853	0.05106	0.094:0.1461:0.3488:0.4112	rs13181859	152;152	O94993-2;O94993	.;SOX30_HUMAN	L	152	ENSP00000309343:P152L;ENSP00000265007:P152L	ENSP00000265007:P152L	P	-	2	0	SOX30	157011210	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.788000	0.26872	0.351000	0.24027	0.305000	0.20034	CCT	G|0.998;A|0.002	0.002	strong		0.682	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
MLC1	23209	hgsc.bcm.edu	37	22	50515273	50515273	+	Silent	SNP	G	G	A	rs267607236|rs6010165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50515273G>A	ENST00000311597.5	-	7	1200	c.594C>T	c.(592-594)taC>taT	p.Y198Y	MLC1_ENST00000450140.2_Silent_p.Y146Y|MLC1_ENST00000395876.2_Silent_p.Y198Y|MLC1_ENST00000538737.1_Silent_p.Y164Y|MLC1_ENST00000535444.1_Silent_p.Y119Y|MLC1_ENST00000431262.2_Silent_p.Y168Y	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	198					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		TTCTTACTGAGTAAGATTTCA	0.502													A|||	654	0.130591	0.0847	0.1585	5008	,	,		18136	0.0913		0.1153	False		,,,				2504	0.229				p.Y198Y		Atlas-SNP	.											.	MLC1	48	.	0			c.C594T						PASS	.	A	,	448,3958	785.3+/-414.7	25,398,1780	104.0	109.0	108.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	594,594	-3.4	0.3	22	dbSNP_114	108	1021,7579	771.9+/-407.7	57,907,3336	no	coding-synonymous,coding-synonymous	MLC1	NM_015166.3,NM_139202.2	,	82,1305,5116	AA,AG,GG		11.8721,10.168,11.2948	,	198/378,198/378	50515273	1469,11537	2203	4300	6503	SO:0001819	synonymous_variant	23209	exon7			TACTGAGTAAGAT	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.594C>T	22.37:g.50515273G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	67	44	0.656716	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			G|0.884;A|0.116	0.116	strong		0.502	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
LCT	3938	hgsc.bcm.edu	37	2	136561557	136561557	+	Silent	SNP	G	G	A	rs2304371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:136561557G>A	ENST00000264162.2	-	11	4616	c.4606C>T	c.(4606-4608)Ctg>Ttg	p.L1536L		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1536	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GGCTCATTCAGCGTGATCCAA	0.522													G|||	3306	0.660144	0.4047	0.7507	5008	,	,		20923	0.7758		0.7485	False		,,,				2504	0.7311				p.L1536L		Atlas-SNP	.											.	LCT	309	.	0			c.C4606T						PASS	.	G		2172,2234	585.3+/-386.2	536,1100,567	142.0	108.0	120.0		4606	2.8	0.7	2	dbSNP_100	120	6875,1725	737.2+/-407.0	2785,1305,210	no	coding-synonymous	LCT	NM_002299.2		3321,2405,777	AA,AG,GG		20.0581,49.2964,30.4398		1536/1928	136561557	9047,3959	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon11			CATTCAGCGTGAT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4606C>T	2.37:g.136561557G>A		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.327;A|0.673	0.673	strong		0.522	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
NAV2	89797	hgsc.bcm.edu	37	11	19901632	19901632	+	Silent	SNP	G	G	A	rs11025310	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:19901632G>A	ENST00000396087.3	+	5	828	c.729G>A	c.(727-729)gcG>gcA	p.A243A	NAV2_ENST00000360655.4_Silent_p.A179A|NAV2_ENST00000540292.1_Silent_p.A174A|NAV2_ENST00000534229.1_3'UTR|NAV2_ENST00000349880.4_Silent_p.A243A|NAV2_ENST00000396085.1_Silent_p.A243A|NAV2_ENST00000527559.2_Silent_p.A172A	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	243	Gln-rich.				glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						ACCAGCCAGCGCCACATCAGC	0.632													G|||	1562	0.311901	0.1702	0.3199	5008	,	,		16911	0.3274		0.4871	False		,,,				2504	0.3016				p.A243A		Atlas-SNP	.											NAV2,caecum,carcinoma,+1,1	NAV2	255	1	0			c.G729A						PASS	.	G	,,	777,3619	303.2+/-287.8	77,623,1498	35.0	32.0	33.0		537,729,729	-2.3	0.9	11	dbSNP_120	33	3817,4769	525.6+/-380.8	857,2103,1333	no	coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	934,2726,2831	AA,AG,GG		44.4561,17.6752,35.3875	,,	179/2366,243/2430,243/2433	19901632	4594,8388	2198	4293	6491	SO:0001819	synonymous_variant	89797	exon5			GCCAGCGCCACAT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.729G>A	11.37:g.19901632G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			G|0.645;A|0.355	0.355	strong		0.632	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
COL15A1	1306	hgsc.bcm.edu	37	9	101831995	101831995	+	Missense_Mutation	SNP	G	G	A	rs10519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:101831995G>A	ENST00000375001.3	+	42	4417	c.3994G>A	c.(3994-3996)Gtc>Atc	p.V1332I		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1332	Nonhelical region 10 (NC10).		V -> I (in dbSNP:rs10519).		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CCCCCATGGCGTCCGCCTTGT	0.502													g|||	914	0.182508	0.2602	0.1153	5008	,	,		17520	0.2758		0.0596	False		,,,				2504	0.1554				p.V1332I		Atlas-SNP	.											COL15A1,colon,carcinoma,0,1	COL15A1	211	1	0			c.G3994A						PASS	.	A	ILE/VAL	1056,3350	387.0+/-326.3	123,810,1270	110.0	115.0	113.0		3994	2.9	0.4	9	dbSNP_52	113	537,8063	149.4+/-204.5	13,511,3776	yes	missense	COL15A1	NM_001855.3	29	136,1321,5046	AA,AG,GG		6.2442,23.9673,12.2482	benign	1332/1389	101831995	1593,11413	2203	4300	6503	SO:0001583	missense	1306	exon42			CATGGCGTCCGCC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.3994G>A	9.37:g.101831995G>A	ENSP00000364140:p.Val1332Ile	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	359	0.16437728937728938	124	0.25203252032520324	41	0.1132596685082873	144	0.2517482517482518	50	0.06596306068601583	g	8.198	0.797528	0.16327	0.239673	0.062442	ENSG00000204291	ENST00000375001	T	0.42513	0.97	6.17	2.94	0.34122	Collagenase NC10/endostatin (1);C-type lectin fold (1);C-type lectin-like (1);	0.214980	0.47455	N	0.000235	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.32268	-0.9913	9	0.07644	T	0.81	-12.17	4.5283	0.11992	0.4105:0.1596:0.4299:0.0	rs10519;rs1051089;rs3191468;rs11541244;rs57446173	1332	P39059	COFA1_HUMAN	I	1332	ENSP00000364140:V1332I	ENSP00000364140:V1332I	V	+	1	0	COL15A1	100871816	0.011000	0.17503	0.390000	0.26220	0.054000	0.15201	0.279000	0.18771	0.449000	0.26747	-0.713000	0.03633	GTC	G|0.860;A|0.140	0.140	strong		0.502	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
LARS	51520	hgsc.bcm.edu	37	5	145519821	145519821	+	Silent	SNP	G	G	A	rs17493851	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145519821G>A	ENST00000394434.2	-	21	2260	c.2094C>T	c.(2092-2094)gaC>gaT	p.D698D	LARS_ENST00000545646.1_Silent_p.D652D|LARS_ENST00000510191.1_Silent_p.D644D|LARS_ENST00000274562.9_Silent_p.D671D	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	698					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.D698D(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	TAGGCCATTTGTCACTTCACA	0.343													G|||	910	0.181709	0.0076	0.3775	5008	,	,		16403	0.1984		0.2525	False		,,,				2504	0.1881				p.D698D		Atlas-SNP	.											LARS,colon,carcinoma,0,2	LARS	100	2	1	Substitution - coding silent(1)	stomach(1)	c.C2094T						PASS	.	G		265,4141	148.0+/-182.4	12,241,1950	69.0	68.0	68.0		2094	2.7	1.0	5	dbSNP_123	68	2398,6202	398.1+/-346.0	352,1694,2254	yes	coding-synonymous	LARS	NM_020117.9		364,1935,4204	AA,AG,GG		27.8837,6.0145,20.4752		698/1177	145519821	2663,10343	2203	4300	6503	SO:0001819	synonymous_variant	51520	exon21			CCATTTGTCACTT	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2094C>T	5.37:g.145519821G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	204	59	0.289216	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			G|0.799;A|0.201	0.201	strong		0.343	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
PLCB3	5331	hgsc.bcm.edu	37	11	64026144	64026144	+	Silent	SNP	G	G	A	rs2244625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64026144G>A	ENST00000540288.1	+	11	1315	c.1212G>A	c.(1210-1212)tcG>tcA	p.S404S	PLCB3_ENST00000279230.6_Silent_p.S404S|PLCB3_ENST00000325234.5_Silent_p.S337S	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	404	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						TCAAGACCTCGCCCTACCCCG	0.602													G|||	2048	0.408946	0.1611	0.5202	5008	,	,		18076	0.2688		0.667	False		,,,				2504	0.544				p.S404S		Atlas-SNP	.											PLCB3,colon,carcinoma,+1,1	PLCB3	103	1	0			c.G1212A						PASS	.	G	,	1057,3345	385.8+/-325.9	138,781,1282	113.0	95.0	101.0		1212,1011	-1.2	1.0	11	dbSNP_100	101	5852,2742	680.3+/-403.6	1993,1866,438	no	coding-synonymous,coding-synonymous	PLCB3	NM_000932.2,NM_001184883.1	,	2131,2647,1720	AA,AG,GG		31.906,24.0118,46.8375	,	404/1235,337/1168	64026144	6909,6087	2201	4297	6498	SO:0001819	synonymous_variant	5331	exon11			GACCTCGCCCTAC	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.1212G>A	11.37:g.64026144G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																			G|0.521;A|0.479	0.479	strong		0.602	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
TMIGD2	126259	hgsc.bcm.edu	37	19	4294623	4294623	+	Missense_Mutation	SNP	C	C	A	rs58237134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4294623C>A	ENST00000301272.2	-	4	548	c.503G>T	c.(502-504)tGg>tTg	p.W168L	TMIGD2_ENST00000595645.1_Missense_Mutation_p.W168L|TMIGD2_ENST00000600114.1_Missense_Mutation_p.W48L|TMIGD2_ENST00000600349.1_Intron	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	168			W -> L (in dbSNP:rs58237134).		positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGGCACCCCACACGATCGC	0.637													A|||	894	0.178514	0.1543	0.1931	5008	,	,		13901	0.0873		0.2068	False		,,,				2504	0.2658				p.W168L		Atlas-SNP	.											.	TMIGD2	38	.	0			c.G503T						PASS	.	A	LEU/TRP,LEU/TRP	776,3630	751.6+/-412.2	69,638,1496	119.0	142.0	134.0		503,503	1.9	0.0	19	dbSNP_129	134	1785,6815	732.2+/-406.8	192,1401,2707	yes	missense,missense	TMIGD2	NM_001169126.1,NM_144615.2	61,61	261,2039,4203	AA,AC,CC		20.7558,17.6123,19.6909	benign,benign	168/279,168/283	4294623	2561,10445	2203	4300	6503	SO:0001583	missense	126259	exon4			GCACCCCACACGA	BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.503G>T	19.37:g.4294623C>A	ENSP00000301272:p.Trp168Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	NM_144615	Q6UW59	Missense_Mutation	SNP	ENST00000301272.2	37	CCDS12126.1	374	0.17124542124542125	92	0.18699186991869918	71	0.19613259668508287	68	0.11888111888111888	143	0.18865435356200527	A	0.011	-1.720885	0.00700	0.176123	0.207558	ENSG00000167664	ENST00000301272	T	0.28454	1.61	2.94	1.86	0.25419	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39057	-0.9632	8	0.02654	T	1	.	7.1594	0.25654	0.536:0.464:0.0:0.0	rs58237134;rs61753894	168;168	Q96BF3-2;Q96BF3	.;TMIG2_HUMAN	L	168	ENSP00000301272:W168L	ENSP00000301272:W168L	W	-	2	0	TMIGD2	4245623	0.024000	0.19004	0.032000	0.17829	0.002000	0.02628	0.579000	0.23788	-0.036000	0.13669	-0.384000	0.06662	TGG	C|0.806;A|0.194	0.194	strong		0.637	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615	
PHIP	55023	hgsc.bcm.edu	37	6	79656570	79656570	+	Silent	SNP	G	G	A	rs2275290	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:79656570G>A	ENST00000275034.4	-	37	4395	c.4228C>T	c.(4228-4230)Ctg>Ttg	p.L1410L	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1410					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AAAGCAGACAGGCGCAAACTC	0.328													G|||	1393	0.278155	0.3359	0.317	5008	,	,		15389	0.1855		0.3688	False		,,,				2504	0.1748				p.L1410L		Atlas-SNP	.											.	PHIP	177	.	0			c.C4228T						PASS	.	G		1502,2904	450.8+/-349.5	255,992,956	61.0	62.0	62.0		4228	2.9	0.6	6	dbSNP_100	62	2994,5606	455.9+/-363.9	524,1946,1830	no	coding-synonymous	PHIP	NM_017934.5		779,2938,2786	AA,AG,GG		34.814,34.0899,34.5687		1410/1822	79656570	4496,8510	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon37			CAGACAGGCGCAA	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4228C>T	6.37:g.79656570G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			G|0.674;A|0.326	0.326	strong		0.328	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
OR51A2	401667	hgsc.bcm.edu	37	11	4976671	4976671	+	Silent	SNP	G	G	A	rs2595984	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4976671G>A	ENST00000380371.1	-	1	272	c.273C>T	c.(271-273)gcC>gcT	p.A91A	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A91A(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGTTTCAGGGGCATTGAACA	0.438													A|||	746	0.148962	0.1036	0.2061	5008	,	,		14045	0.2183		0.1918	False		,,,				2504	0.0542				p.A91A		Atlas-SNP	.											OR51A2,rectum,carcinoma,0,1	OR51A2	40	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C273T						scavenged	.						132.0	99.0	111.0					11																	4976671		1918	3466	5384	SO:0001819	synonymous_variant	401667	exon1			TTCAGGGGCATTG	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.273C>T	11.37:g.4976671G>A		Somatic	651	0	0		WXS	Illumina HiSeq	Phase_I	347	7	0.0201729	NM_001004748		Silent	SNP	ENST00000380371.1	37	CCDS31368.1																																																																																			G|0.880;A|0.120	0.120	strong		0.438	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
ZNF280A	129025	hgsc.bcm.edu	37	22	22869545	22869545	+	Missense_Mutation	SNP	T	T	G	rs361580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22869545T>G	ENST00000302097.3	-	2	662	c.410A>C	c.(409-411)tAc>tCc	p.Y137S	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	137			Y -> S (in dbSNP:rs361580). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9074928}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		CGAATCTGAGTAATTGGGAGA	0.478													G|||	2373	0.473842	0.239	0.7334	5008	,	,		17218	0.4147		0.7038	False		,,,				2504	0.4315				p.Y137S		Atlas-SNP	.											.	ZNF280A	67	.	0			c.A410C						PASS	.	G	SER/TYR	1344,3062	684.2+/-404.4	220,904,1079	66.0	64.0	65.0		410	-2.5	0.0	22	dbSNP_79	65	5835,2765	428.1+/-355.8	2006,1823,471	yes	missense	ZNF280A	NM_080740.3	144	2226,2727,1550	GG,GT,TT		32.1512,30.5039,44.8024	benign	137/543	22869545	7179,5827	2203	4300	6503	SO:0001583	missense	129025	exon2			TCTGAGTAATTGG	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.410A>C	22.37:g.22869545T>G	ENSP00000302855:p.Tyr137Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	1155	0.5288461538461539	126	0.25609756097560976	254	0.7016574585635359	244	0.42657342657342656	531	0.7005277044854882	G	0.024	-1.384710	0.01194	0.305039	0.678488	ENSG00000169548	ENST00000302097	T	0.14893	2.47	3.7	-2.5	0.06384	.	.	.	.	.	T	0.00012	0.0000	N	0.00182	-1.905	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42137	-0.9469	8	0.02654	T	1	0.5428	0.6421	0.00812	0.1921:0.2836:0.2359:0.2884	rs361580;rs695675;rs17846522;rs17859595	137	P59817	Z280A_HUMAN	S	137	ENSP00000302855:Y137S	ENSP00000302855:Y137S	Y	-	2	0	ZNF280A	21199545	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.053000	0.14184	-0.684000	0.05183	-0.127000	0.14921	TAC	T|0.451;G|0.549	0.549	strong		0.478	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
MUC16	94025	hgsc.bcm.edu	37	19	9069792	9069792	+	Missense_Mutation	SNP	G	G	A	rs1862458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9069792G>A	ENST00000397910.4	-	3	17857	c.17654C>T	c.(17653-17655)tCc>tTc	p.S5885F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5887	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCCTTCCCAGGAAGCTGTGCT	0.502													G|||	1006	0.200879	0.0938	0.2824	5008	,	,		21349	0.3254		0.167	False		,,,				2504	0.1943				p.S5885F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C17654T						PASS	.	G	PHE/SER	403,3541		18,367,1587	175.0	160.0	165.0		17654	1.9	0.0	19	dbSNP_92	165	1510,6798		137,1236,2781	yes	missense	MUC16	NM_024690.2	155	155,1603,4368	AA,AG,GG		18.1753,10.2181,15.6138	probably-damaging	5885/14508	9069792	1913,10339	1972	4154	6126	SO:0001583	missense	94025	exon3			TCCCAGGAAGCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.17654C>T	19.37:g.9069792G>A	ENSP00000381008:p.Ser5885Phe	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	165	83	0.50303	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	479	0.21932234432234432	56	0.11382113821138211	92	0.2541436464088398	205	0.3583916083916084	126	0.1662269129287599	g	4.115	0.019520	0.08006	0.102181	0.181753	ENSG00000181143	ENST00000397910	T	0.24908	1.83	1.87	1.87	0.25490	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	.	.	.	D	0.65815	0.995	D	0.69824	0.966	T	0.38090	-0.9677	8	0.87932	D	0	.	7.2365	0.26072	0.0:0.0:1.0:0.0	rs1862458;rs52791883;rs56970751;rs1862458	5885	B5ME49	.	F	5885	ENSP00000381008:S5885F	ENSP00000381008:S5885F	S	-	2	0	MUC16	8930792	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.065000	0.11617	1.369000	0.46134	0.305000	0.20034	TCC	G|0.798;A|0.202	0.202	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FAM47A	158724	hgsc.bcm.edu	37	X	34148877	34148877	+	Missense_Mutation	SNP	C	C	G	rs5973088		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:34148877C>G	ENST00000346193.3	-	1	1570	c.1519G>C	c.(1519-1521)Gag>Cag	p.E507Q		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	507			Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.					p.E507Q(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TTGGGAGGCTCCGAGCGGAGA	0.647																																					p.E507Q		Atlas-SNP	.											.	FAM47A	249	.	1	Substitution - Missense(1)	kidney(1)	c.G1519C						PASS	.						29.0	29.0	29.0					X																	34148877		2181	4247	6428	SO:0001583	missense	158724	exon1			GAGGCTCCGAGCG	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1519G>C	X.37:g.34148877C>G	ENSP00000345029:p.Glu507Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	63	13	0.206349	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	6	0.003616636528028933	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	2	0.002638522427440633	c	9.299	1.052687	0.19907	.	.	ENSG00000185448	ENST00000346193	T	0.14391	2.51	0.226	0.226	0.15353	.	.	.	.	.	T	0.05227	0.0139	L	0.27053	0.805	0.09310	N	1	B	0.24483	0.104	B	0.16722	0.016	T	0.41466	-0.9507	8	0.17832	T	0.49	.	.	.	.	rs5973088	507	Q5JRC9	FA47A_HUMAN	Q	507	ENSP00000345029:E507Q	ENSP00000345029:E507Q	E	-	1	0	FAM47A	34058798	0.053000	0.20554	0.000000	0.03702	0.001000	0.01503	1.713000	0.37951	0.283000	0.22279	0.287000	0.19450	GAG	C|0.996;G|0.004	0.004	strong		0.647	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408	
HLA-A	3105	hgsc.bcm.edu	37	6	29910731	29910731	+	Missense_Mutation	SNP	G	G	A	rs79361534|rs281864737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29910731G>A	ENST00000396634.1	+	4	612	c.271G>A	c.(271-273)Gtg>Atg	p.V91M	HLA-A_ENST00000376806.5_Missense_Mutation_p.V91M|HLA-A_ENST00000376809.5_Missense_Mutation_p.V91M|HLA-A_ENST00000376802.2_Missense_Mutation_p.V91M			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	91	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GACACGGAATGTGAAGGCCCA	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	454	0.090655	0.0847	0.0476	5008	,	,		12317	0.0188		0.1262	False		,,,				2504	0.1667				p.V91M		Atlas-SNP	.											.	HLA-A	89	.	0			c.G271A						PASS	.	G	MET/VAL	353,4047		18,317,1865	80.0	84.0	82.0		271	-6.4	0.0	6	dbSNP_127	82	1485,7097		170,1145,2976	no	missense	HLA-A	NM_002116.7	21	188,1462,4841	AA,AG,GG		17.3037,8.0227,14.1581	benign	91/366	29910731	1838,11144	2200	4291	6491	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGGAATGTGAAGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.271G>A	6.37:g.29910731G>A	ENSP00000379873:p.Val91Met	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	265	100	0.377358	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	198	0.09065934065934066	45	0.09146341463414634	19	0.052486187845303865	12	0.02097902097902098	122	0.16094986807387862	.	5.403	0.259593	0.10239	0.080227	0.173037	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00010	9.4;9.4;9.4;9.4	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	754.410000	0.00447	U	0.000088	T	0.00039	0.0001	L	0.28054	0.825	0.80722	P	0.0	B;B;B;B;B	0.17667	0.002;0.023;0.002;0.011;0.002	B;B;B;B;B	0.23419	0.005;0.046;0.005;0.012;0.005	T	0.09207	-1.0685	9	0.41790	T	0.15	.	4.2384	0.10637	0.2942:0.0:0.1814:0.5244	rs41564215	91;91;91;91;91	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	M	91	ENSP00000379873:V91M;ENSP00000366002:V91M;ENSP00000366005:V91M;ENSP00000365998:V91M	ENSP00000348012:V91M	V	+	1	0	HLA-A	30018710	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.711000	0.00195	-1.498000	0.01824	-1.251000	0.01509	GTG	A|0.124;G|0.876	0.124	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
GSDMA	284110	hgsc.bcm.edu	37	17	38131187	38131187	+	Missense_Mutation	SNP	C	C	A	rs56030650	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38131187C>A	ENST00000301659.4	+	10	1059	c.941C>A	c.(940-942)aCc>aAc	p.T314N		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	314			T -> N (in dbSNP:rs56030650). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CATGAAGTGACCCTGGAGGCA	0.547													C|||	1917	0.382788	0.3132	0.3847	5008	,	,		15256	0.4742		0.4573	False		,,,				2504	0.3047				p.T314N		Atlas-SNP	.											.	GSDMA	26	.	0			c.C941A						PASS	.	C	ASN/THR	1260,2530		201,858,836	41.0	41.0	41.0		941	4.0	1.0	17	dbSNP_129	41	3880,4342		922,2036,1153	yes	missense	GSDMA	NM_178171.4	65	1123,2894,1989	AA,AC,CC		47.1905,33.2454,42.7905	probably-damaging	314/446	38131187	5140,6872	1895	4111	6006	SO:0001583	missense	284110	exon10			AAGTGACCCTGGA	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.941C>A	17.37:g.38131187C>A	ENSP00000301659:p.Thr314Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	914	0.4184981684981685	143	0.29065040650406504	149	0.4116022099447514	275	0.4807692307692308	347	0.4577836411609499	C	12.65	2.002462	0.35320	0.332454	0.471905	ENSG00000167914	ENST00000301659	T	0.23348	1.91	6.03	3.96	0.45880	.	0.424311	0.22282	N	0.062101	T	0.00012	0.0000	L	0.57536	1.79	0.33723	P	0.38275899999999996	D	0.54772	0.968	P	0.50314	0.637	T	0.49570	-0.8926	9	0.25751	T	0.34	-10.8739	13.3157	0.60405	0.0:0.6007:0.3993:0.0	rs56030650;rs56793200;rs61759528	314	Q96QA5	GSDMA_HUMAN	N	314	ENSP00000301659:T314N	ENSP00000301659:T314N	T	+	2	0	GSDMA	35384713	0.996000	0.38824	0.987000	0.45799	0.177000	0.22998	1.437000	0.34991	0.779000	0.33543	0.655000	0.94253	ACC	C|0.572;A|0.428	0.428	strong		0.547	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
IQCA1	79781	hgsc.bcm.edu	37	2	237374309	237374309	+	Silent	SNP	C	C	T	rs35432941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:237374309C>T	ENST00000409907.3	-	6	1039	c.765G>A	c.(763-765)caG>caA	p.Q255Q	IQCA1_ENST00000309507.5_Silent_p.Q251Q|IQCA1_ENST00000431676.2_Silent_p.Q255Q	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	255							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						CCTTTTCAGCCTGGATTACTG	0.428													C|||	372	0.0742812	0.0076	0.0764	5008	,	,		19184	0.001		0.1849	False		,,,				2504	0.1247				p.Q262Q		Atlas-SNP	.											.	IQCA1	170	.	0			c.G786A						PASS	.	C		140,3670		5,130,1770	105.0	93.0	97.0		765	-0.5	0.1	2	dbSNP_126	97	1735,6525		174,1387,2569	no	coding-synonymous	IQCA1	NM_024726.3		179,1517,4339	TT,TC,CC		21.0048,3.6745,15.5344		255/823	237374309	1875,10195	1905	4130	6035	SO:0001819	synonymous_variant	79781	exon6			TTCAGCCTGGATT	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.765G>A	2.37:g.237374309C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	174	81	0.465517	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Silent	SNP	ENST00000409907.3	37	CCDS46549.1	177	0.08104395604395605	6	0.012195121951219513	26	0.0718232044198895	0	0.0	145	0.19129287598944592	C	0.806	-0.753650	0.03041	0.036745	0.210048	ENSG00000132321	ENST00000418802	.	.	.	5.37	-0.467	0.12150	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.50313	P	1.32000000000021E-4	.	.	.	.	.	.	T	0.29181	-1.0020	3	.	.	.	.	0.1116	0.00057	0.2791:0.2582:0.2037:0.259	rs35432941;rs62189792	.	.	.	S	274	.	.	G	-	1	0	IQCA1	237039048	0.928000	0.31464	0.108000	0.21378	0.302000	0.27658	0.225000	0.17757	-0.011000	0.14247	0.563000	0.77884	GGC	C|0.896;T|0.104	0.104	strong		0.428	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
HOXC9	3225	hgsc.bcm.edu	37	12	54394497	54394497	+	Silent	SNP	C	C	T	rs2241820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:54394497C>T	ENST00000303450.4	+	1	595	c.525C>T	c.(523-525)gcC>gcT	p.A175A	HOXC-AS1_ENST00000512427.1_RNA|HOXC9_ENST00000504557.1_Intron|HOXC9_ENST00000508190.1_Silent_p.A175A|HOXC-AS1_ENST00000505700.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron	NM_006897.1	NP_008828.1	P31274	HXC9_HUMAN	homeobox C9	175					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(3)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14						AGGAGAAGGCCGACCTGGACC	0.692													C|||	2895	0.578075	0.4667	0.5346	5008	,	,		12030	0.7609		0.6014	False		,,,				2504	0.547				p.A175A		Atlas-SNP	.											.	HOXC9	25	.	0			c.C525T						PASS	.	C		1809,1381		539,731,325	6.0	7.0	7.0		525	1.1	1.0	12	dbSNP_98	7	4221,2551		1360,1501,525	no	coding-synonymous	HOXC9	NM_006897.1		1899,2232,850	TT,TC,CC		37.6698,43.2915,39.47		175/261	54394497	6030,3932	1595	3386	4981	SO:0001819	synonymous_variant	3225	exon1			GAAGGCCGACCTG		CCDS8869.1	12q13.13	2011-06-20	2005-12-22			ENSG00000180806		"""Homeoboxes / ANTP class : HOXL subclass"""	5130	protein-coding gene	gene with protein product		142971	"""homeo box C9"""	HOX3, HOX3B		1973146	Standard	NM_006897		Approved		uc001seq.3	P31274		ENST00000303450.4:c.525C>T	12.37:g.54394497C>T		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	14	6	0.428571	NM_006897	B2RCN7|Q9H1I0	Silent	SNP	ENST00000303450.4	37	CCDS8869.1																																																																																			C|0.388;T|0.612	0.612	strong		0.692	HOXC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358958.1		
PCSK1	5122	hgsc.bcm.edu	37	5	95728974	95728974	+	Missense_Mutation	SNP	G	G	C	rs6234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:95728974G>C	ENST00000311106.3	-	14	2230	c.1993C>G	c.(1993-1995)Cag>Gag	p.Q665E	PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.Q618E	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	665			Q -> E (in dbSNP:rs6234). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:17595246, ECO:0000269|PubMed:8666140}.		cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AGCATGGCCTGGGAAGGGGCT	0.552													C|||	1298	0.259185	0.1808	0.2349	5008	,	,		17556	0.3591		0.2604	False		,,,				2504	0.2781				p.Q665E		Atlas-SNP	.											.	PCSK1	93	.	0			c.C1993G						PASS	.	C	GLU/GLN,GLU/GLN,GLU/GLN	849,3557	745.1+/-411.6	76,697,1430	90.0	93.0	92.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1993,1852,1063	-0.3	0.0	5	dbSNP_52	92	2397,6203	700.2+/-405.1	304,1789,2207	yes	missense,missense,missense	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	29,29,29	380,2486,3637	CC,CG,GG		27.8721,19.2692,24.9577	benign,benign,benign	665/754,618/707,355/444	95728974	3246,9760	2203	4300	6503	SO:0001583	missense	5122	exon14			TGGCCTGGGAAGG		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1993C>G	5.37:g.95728974G>C	ENSP00000308024:p.Gln665Glu	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	307	156	0.508143	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	564	0.25824175824175827	74	0.15040650406504066	85	0.23480662983425415	196	0.34265734265734266	209	0.2757255936675462	C	0.226	-1.024627	0.02061	0.192692	0.278721	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.64618	0.05;-0.11	5.62	-0.272	0.12919	.	0.788543	0.12504	N	0.463051	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29274	-1.0017	9	0.02654	T	1	-11.0777	11.1807	0.48627	0.0:0.3751:0.4891:0.1358	rs6234;rs17847297;rs52799711;rs6234	618;665	E9PHA1;P29120	.;NEC1_HUMAN	E	665;618	ENSP00000308024:Q665E;ENSP00000421600:Q618E	ENSP00000308024:Q665E	Q	-	1	0	PCSK1	95754730	0.013000	0.17824	0.045000	0.18777	0.016000	0.09150	0.132000	0.15891	-0.210000	0.10140	-0.815000	0.03128	CAG	G|0.744;C|0.254	0.254	strong		0.552	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
IL10RA	3587	hgsc.bcm.edu	37	11	117864063	117864063	+	Missense_Mutation	SNP	A	A	G	rs3135932	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:117864063A>G	ENST00000227752.3	+	4	595	c.475A>G	c.(475-477)Agc>Ggc	p.S159G	IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000545409.1_Missense_Mutation_p.S10G|IL10RA_ENST00000541785.1_Missense_Mutation_p.S139G	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	159			S -> G (in dbSNP:rs3135932). {ECO:0000269|Ref.2}.		cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		CACATATGAAAGCATCTTCAG	0.542													A|||	409	0.0816693	0.0068	0.0865	5008	,	,		19665	0.0069		0.167	False		,,,				2504	0.1687				p.S159G		Atlas-SNP	.											.	IL10RA	46	.	0			c.A475G	GRCh37	CM067993	IL10RA	M	rs3135932	PASS	.	A	GLY/SER	137,4263	98.0+/-136.7	4,129,2067	98.0	87.0	91.0		475	2.0	0.1	11	dbSNP_103	91	1415,7177	273.3+/-290.6	116,1183,2997	yes	missense	IL10RA	NM_001558.3	56	120,1312,5064	GG,GA,AA		16.4688,3.1136,11.9458	benign	159/579	117864063	1552,11440	2200	4296	6496	SO:0001583	missense	3587	exon4			TATGAAAGCATCT	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.475A>G	11.37:g.117864063A>G	ENSP00000227752:p.Ser159Gly	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	180	0.08241758241758242	6	0.012195121951219513	39	0.10773480662983426	6	0.01048951048951049	129	0.17018469656992086	A	13.45	2.241546	0.39598	0.031136	0.164688	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.44482	0.92;0.92;0.92	5.73	2.05	0.26809	Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.089620	0.06794	N	0.787561	T	0.00109	0.0003	L	0.56769	1.78	0.58432	P	5.000000000032756E-6	P;P	0.44690	0.841;0.754	B;B	0.32211	0.142;0.067	T	0.06445	-1.0826	9	0.37606	T	0.19	-0.2013	6.5959	0.22672	0.4886:0.3718:0.0:0.1396	rs3135932;rs4252272;rs17513192;rs3135932	139;159	F5GYV8;Q13651	.;I10R1_HUMAN	G	159;139;10;139	ENSP00000227752:S159G;ENSP00000441397:S139G;ENSP00000443019:S10G	ENSP00000227752:S159G	S	+	1	0	IL10RA	117369273	0.206000	0.23470	0.098000	0.21074	0.803000	0.45373	0.409000	0.21082	0.088000	0.17205	0.533000	0.62120	AGC	A|0.893;G|0.107	0.107	strong		0.542	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
SLC4A1AP	22950	hgsc.bcm.edu	37	2	27887034	27887034	+	Missense_Mutation	SNP	C	C	A	rs9678851	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:27887034C>A	ENST00000326019.6	+	1	697	c.415C>A	c.(415-417)Ccg>Acg	p.P139T	SUPT7L_ENST00000404798.2_5'Flank|SUPT7L_ENST00000405491.1_5'Flank|SUPT7L_ENST00000337768.5_5'Flank|SUPT7L_ENST00000406540.1_5'Flank|SUPT7L_ENST00000464789.2_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	139			P -> T (in dbSNP:rs9678851). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19690332}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					GTCGCGCCCCCCGACAGCGGT	0.652													C|||	1698	0.339058	0.2534	0.3501	5008	,	,		15682	0.0794		0.5388	False		,,,				2504	0.5092				p.P139T		Atlas-SNP	.											.	SLC4A1AP	63	.	0			c.C415A						PASS	.	C	THR/PRO	1376,3028	437.8+/-345.1	201,974,1027	44.0	51.0	49.0		415	-1.9	0.0	2	dbSNP_119	49	4827,3773	594.4+/-393.3	1360,2107,833	yes	missense	SLC4A1AP	NM_018158.2	38	1561,3081,1860	AA,AC,CC		43.8721,31.2443,47.7007	benign	139/797	27887034	6203,6801	2202	4300	6502	SO:0001583	missense	22950	exon1			CGCCCCCCGACAG		CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"""lung cancer oncogene 3"""	602655	"""solute carrier family 4 (anion exchanger), member 1, adapter protein"""			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.415C>A	2.37:g.27887034C>A	ENSP00000323837:p.Pro139Thr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	141	75	0.531915	NM_018158	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Missense_Mutation	SNP	ENST00000326019.6	37	CCDS33166.1	744	0.34065934065934067	130	0.26422764227642276	153	0.42265193370165743	45	0.07867132867132867	416	0.5488126649076517	C	11.78	1.740201	0.30865	0.312443	0.561279	ENSG00000163798	ENST00000326019	T	0.35973	1.28	4.7	-1.94	0.07571	.	1.031550	0.07703	N	0.940809	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.18166	0.026	B	0.15870	0.014	T	0.48163	-0.9059	9	0.10902	T	0.67	-0.0166	7.7146	0.28698	0.0:0.3641:0.4132:0.2226	rs9678851;rs17757122;rs9678851	139	Q9BWU0	NADAP_HUMAN	T	139	ENSP00000323837:P139T	ENSP00000323837:P139T	P	+	1	0	SLC4A1AP	27740538	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.550000	0.06034	-0.042000	0.13535	-0.266000	0.10368	CCG	C|0.590;A|0.410	0.410	strong		0.652	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158	
IFNGR1	3459	hgsc.bcm.edu	37	6	137519588	137519588	+	Silent	SNP	A	A	C	rs11914	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:137519588A>C	ENST00000367739.4	-	7	1171	c.1050T>G	c.(1048-1050)tcT>tcG	p.S350S	IFNGR1_ENST00000543628.1_Silent_p.S322S	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	350					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	CTGTTATACTAGAAAGTTCTT	0.453													A|||	471	0.0940495	0.0492	0.111	5008	,	,		17682	0.1062		0.1471	False		,,,				2504	0.0757				p.S350S		Atlas-SNP	.											.	IFNGR1	46	.	0			c.T1050G						PASS	.	A		267,4139	152.9+/-186.6	9,249,1945	120.0	118.0	119.0		1050	-11.4	0.0	6	dbSNP_52	119	1406,7194	273.1+/-290.5	109,1188,3003	no	coding-synonymous	IFNGR1	NM_000416.2		118,1437,4948	CC,CA,AA		16.3488,6.0599,12.8633		350/490	137519588	1673,11333	2203	4300	6503	SO:0001819	synonymous_variant	3459	exon7			TATACTAGAAAGT		CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"""Interferons"", ""CD molecules"""	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.1050T>G	6.37:g.137519588A>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_000416	B4DFT7|E1P587|Q53Y96	Silent	SNP	ENST00000367739.4	37	CCDS5185.1																																																																																			A|0.874;C|0.126	0.126	strong		0.453	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1		
NUP107	57122	hgsc.bcm.edu	37	12	69082805	69082805	+	Silent	SNP	G	G	A	rs2259588	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:69082805G>A	ENST00000229179.4	+	2	404	c.72G>A	c.(70-72)cgG>cgA	p.R24R	RP11-637A17.2_ENST00000500695.2_lincRNA|NUP107_ENST00000539906.1_5'UTR|NUP107_ENST00000378905.2_5'UTR	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	24					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			GGACTGCACGGAAACAGAGTG	0.383													G|||	1105	0.220647	0.0582	0.2983	5008	,	,		18358	0.3065		0.2903	False		,,,				2504	0.2249				p.R24R		Atlas-SNP	.											NUP107,NS,carcinoma,+2,1	NUP107	88	1	0			c.G72A						PASS	.	G		404,4002	200.4+/-223.7	20,364,1819	140.0	132.0	135.0		72	-1.5	0.9	12	dbSNP_100	135	2322,6278	390.4+/-343.3	314,1694,2292	no	coding-synonymous	NUP107	NM_020401.2		334,2058,4111	AA,AG,GG		27.0,9.1693,20.9596		24/926	69082805	2726,10280	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon2			TGCACGGAAACAG	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.72G>A	12.37:g.69082805G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	137	73	0.532847	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			G|0.777;A|0.223	0.223	strong		0.383	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
MUC4	4585	hgsc.bcm.edu	37	3	195506775	195506775	+	Silent	SNP	G	G	A	rs79609066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506775G>A	ENST00000463781.3	-	2	12135	c.11676C>T	c.(11674-11676)acC>acT	p.T3892T	MUC4_ENST00000475231.1_Silent_p.T3892T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3892T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAA	0.592													.|||	23	0.00459265	0.0	0.0014	5008	,	,		8217	0.0		0.0	False		,,,				2504	0.0225				p.T3892T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - coding silent(1)	kidney(1)	c.C11676T						PASS	.						11.0	9.0	10.0					3																	195506775		565	1303	1868	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11676C>T	3.37:g.195506775G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	71	52	0.732394	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.767;A|0.233	0.233	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CYP4F3	4051	hgsc.bcm.edu	37	19	15760053	15760053	+	Silent	SNP	G	G	A	rs1053037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15760053G>A	ENST00000221307.8	+	6	656	c.609G>A	c.(607-609)ctG>ctA	p.L203L	CYP4F3_ENST00000586182.2_Silent_p.L203L|CYP4F3_ENST00000585846.1_Silent_p.L203L|CYP4F3_ENST00000591058.1_Silent_p.L203L	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	203					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						TGGACAGTCTGCAGAAATGTG	0.572													.|||	432	0.086262	0.0234	0.1225	5008	,	,		19031	0.0397		0.2028	False		,,,				2504	0.0736				p.L203L		Atlas-SNP	.											.	CYP4F3	69	.	0			c.G609A						PASS	.	G	,,	184,4222		4,176,2023	119.0	104.0	109.0		609,609,609	2.3	1.0	19	dbSNP_86	109	1588,7012		160,1268,2872	yes	coding-synonymous,coding-synonymous,coding-synonymous	CYP4F3	NM_000896.2,NM_001199208.1,NM_001199209.1	,,	164,1444,4895	AA,AG,GG		18.4651,4.1761,13.6245	,,	203/521,203/521,203/521	15760053	1772,11234	2203	4300	6503	SO:0001819	synonymous_variant	4051	exon6			CAGTCTGCAGAAA	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"""Cytochrome P450s"""	2646	protein-coding gene	gene with protein product		601270	"""cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"""	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.609G>A	19.37:g.15760053G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	208	105	0.504808	NM_001199209	B7Z8Z3|O60634|Q5U740	Silent	SNP	ENST00000221307.8	37	CCDS12332.1																																																																																			G|0.880;A|0.120	0.120	strong		0.572	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896	
CYP4A22	284541	hgsc.bcm.edu	37	1	47610065	47610065	+	Missense_Mutation	SNP	A	A	C	rs149718343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:47610065A>C	ENST00000371891.3	+	7	858	c.827A>C	c.(826-828)aAg>aCg	p.K276T	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000294337.3_Missense_Mutation_p.K276T|CYP4A22_ENST00000371890.3_Missense_Mutation_p.E224D|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	276			K -> T (in allele CYP4A22*8, allele CYP4A22*11, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs149718343). {ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CAACTACAGAAGGAGGGGGAG	0.532													A|||	710	0.141773	0.0121	0.1009	5008	,	,		21439	0.3075		0.0775	False		,,,				2504	0.2413				p.K276T	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.A827C						PASS	.	A	THR/LYS	113,4293	87.3+/-125.9	0,113,2090	95.0	94.0	94.0		827	1.5	0.0	1	dbSNP_134	94	754,7846	180.6+/-229.5	38,678,3584	no	missense	CYP4A22	NM_001010969.2	78	38,791,5674	CC,CA,AA		8.7674,2.5647,6.6662	benign	276/520	47610065	867,12139	2203	4300	6503	SO:0001583	missense	284541	exon7			TACAGAAGGAGGG		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.827A>C	1.37:g.47610065A>C	ENSP00000360958:p.Lys276Thr	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	216	75	0.347222	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	259|259	0.11858974358974358|0.11858974358974358	6|6	0.012195121951219513|0.012195121951219513	38|38	0.10497237569060773|0.10497237569060773	164|164	0.2867132867132867|0.2867132867132867	51|51	0.06728232189973615|0.06728232189973615	a|a	10.40|10.40	1.339406|1.339406	0.24339|0.24339	0.025647|0.025647	0.087674|0.087674	ENSG00000162365|ENSG00000162365	ENST00000371890|ENST00000371891;ENST00000294337	T|T;T	0.72942|0.68624	-0.7|-0.34;-0.34	1.51|1.51	1.51|1.51	0.23008|0.23008	.|.	.|1.346730	.|0.04228	.|N	.|0.334792	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.28458|0.28458	0.855|0.855	0.51482|0.51482	P|P	7.699999999999374E-5|7.699999999999374E-5	B|P	0.09022|0.34699	0.002|0.464	B|P	0.04013|0.45913	0.001|0.497	T|T	0.16928|0.16928	-1.0386|-1.0386	8|9	0.49607|0.41790	T|T	0.09|0.15	.|.	8.9843|8.9843	0.35983|0.35983	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	224|276	Q5TCH5|Q5TCH4	.|CP4AM_HUMAN	D|T	224|276	ENSP00000360957:E224D|ENSP00000360958:K276T;ENSP00000294337:K276T	ENSP00000360957:E224D|ENSP00000294337:K276T	E|K	+|+	3|2	2|0	CYP4A22|CYP4A22	47382652|47382652	0.208000|0.208000	0.23494|0.23494	0.034000|0.034000	0.17996|0.17996	0.690000|0.690000	0.40134|0.40134	3.462000|3.462000	0.53042|0.53042	0.702000|0.702000	0.31825|0.31825	0.163000|0.163000	0.16589|0.16589	GAA|AAG	A|1.000;|0.000	.	weak		0.532	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
ITPR3	3710	hgsc.bcm.edu	37	6	33638180	33638180	+	Silent	SNP	C	C	T	rs2229634	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33638180C>T	ENST00000374316.5	+	20	3328	c.2268C>T	c.(2266-2268)ggC>ggT	p.G756G	ITPR3_ENST00000605930.1_Silent_p.G756G			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	756					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	AGCAGCTGGGCGTGGACCTGA	0.612													C|||	1680	0.335463	0.1619	0.281	5008	,	,		17637	0.4722		0.2833	False		,,,				2504	0.5215				p.G756G		Atlas-SNP	.											.	ITPR3	409	.	0			c.C2268T						PASS	.	C		803,3603	321.3+/-297.0	80,643,1480	135.0	122.0	127.0		2268	-6.1	0.8	6	dbSNP_98	127	2574,6026	419.1+/-353.0	368,1838,2094	yes	coding-synonymous	ITPR3	NM_002224.3		448,2481,3574	TT,TC,CC		29.9302,18.2251,25.9649		756/2672	33638180	3377,9629	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon19			GCTGGGCGTGGAC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.2268C>T	6.37:g.33638180C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	162	91	0.561728	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.719;T|0.281	0.281	strong		0.612	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
HS6ST1	9394	hgsc.bcm.edu	37	2	129026358	129026358	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:129026358T>C	ENST00000259241.6	-	2	627	c.614A>G	c.(613-615)aAg>aGg	p.K205R		NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	205					angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		CAACGACGTCTTCCACGTGGC	0.637																																					p.K205R		Atlas-SNP	.											.	HS6ST1	31	.	0			c.A614G						PASS	.						37.0	41.0	40.0					2																	129026358		2136	4244	6380	SO:0001583	missense	9394	exon2			GACGTCTTCCACG	AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720		"""Sulfotransferases, membrane-bound"""	5201	protein-coding gene	gene with protein product		604846		HS6ST		9535912	Standard	NM_004807		Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000259241.6:c.614A>G	2.37:g.129026358T>C	ENSP00000259241:p.Lys205Arg	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	265	30	0.113208	NM_004807	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Missense_Mutation	SNP	ENST00000259241.6	37	CCDS42748.1	.	.	.	.	.	.	.	.	.	.	T	19.05	3.752695	0.69533	.	.	ENSG00000136720	ENST00000259241	T	0.75050	-0.9	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.84410	0.5466	M	0.72576	2.205	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.85075	0.0942	9	.	.	.	.	14.4384	0.67298	0.0:0.0:0.0:1.0	.	205	O60243	H6ST1_HUMAN	R	205	ENSP00000259241:K205R	.	K	-	2	0	HS6ST1	128742828	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	5.971000	0.70440	1.813000	0.52934	0.379000	0.24179	AAG	.	.	none		0.637	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331572.1	NM_004807	
ADAM15	8751	hgsc.bcm.edu	37	1	155023917	155023917	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:155023917C>T	ENST00000356955.2	+	1	156	c.55C>T	c.(55-57)Cct>Tct	p.P19S	ADAM15_ENST00000531455.1_Missense_Mutation_p.P19S|ADAM15_ENST00000355956.2_Missense_Mutation_p.P19S|ADAM15_ENST00000271836.6_Missense_Mutation_p.P19S|ADAM15_ENST00000368412.3_Missense_Mutation_p.P19S|ADAM15_ENST00000449910.2_Missense_Mutation_p.P19S|ADAM15_ENST00000359280.4_Missense_Mutation_p.P19S|ADAM15_ENST00000368410.2_Missense_Mutation_p.P19S|ADAM15_ENST00000447332.3_Missense_Mutation_p.P19S|ADAM15_ENST00000368413.1_Missense_Mutation_p.P19S|ADAM15_ENST00000360674.4_Missense_Mutation_p.P19S|ADAM15_ENST00000472434.1_3'UTR	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	19					angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CAGCCCTCTGCCTTCCTGGCC	0.701																																					p.P19S		Atlas-SNP	.											.	ADAM15	92	.	0			c.C55T						PASS	.																																			SO:0001583	missense	8751	exon1			CCTCTGCCTTCCT	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"""ADAM metallopeptidase domain containing"""	193	protein-coding gene	gene with protein product	"""metargidin"""	605548	"""a disintegrin and metalloproteinase domain 15 (metargidin)"""			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.55C>T	1.37:g.155023917C>T	ENSP00000349436:p.Pro19Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_003815	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	37	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.747467	0.49257	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000368410;ENST00000271836;ENST00000368413;ENST00000531455	T;T;T;T;T;T;T;T;T;T	0.03889	5.77;5.76;5.77;5.67;5.56;5.77;3.77;5.75;3.78;5.73	4.56	1.58	0.23477	.	0.195638	0.25189	N	0.032473	T	0.00998	0.0033	L	0.27053	0.805	0.21020	N	0.999802	B;B;B;B;B;B;B;B;B;B	0.27765	0.118;0.118;0.118;0.188;0.188;0.188;0.188;0.188;0.188;0.118	B;B;B;B;B;B;B;B;B;B	0.25759	0.029;0.029;0.029;0.063;0.063;0.063;0.063;0.063;0.063;0.029	T	0.47661	-0.9100	10	0.41790	T	0.15	.	3.3412	0.07119	0.2058:0.5753:0.0:0.2189	.	19;19;19;19;19;19;19;19;19;19	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444	.;.;.;.;.;.;.;.;.;ADA15_HUMAN	S	19	ENSP00000349436:P19S;ENSP00000403843:P19S;ENSP00000352226:P19S;ENSP00000353892:P19S;ENSP00000357397:P19S;ENSP00000348227:P19S;ENSP00000357395:P19S;ENSP00000271836:P19S;ENSP00000357398:P19S;ENSP00000432927:P19S	ENSP00000271836:P19S	P	+	1	0	ADAM15	153290541	0.990000	0.36364	0.995000	0.50966	0.543000	0.35085	0.603000	0.24149	0.354000	0.24105	0.313000	0.20887	CCT	.	.	none		0.701	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	
RASGRP3	25780	hgsc.bcm.edu	37	2	33759395	33759395	+	Silent	SNP	C	C	T	rs35933402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33759395C>T	ENST00000403687.3	+	11	1829	c.1089C>T	c.(1087-1089)tcC>tcT	p.S363S	RASGRP3_ENST00000402538.3_Silent_p.S363S|RASGRP3_ENST00000407811.1_Silent_p.S363S	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	363	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					TGTAGCTTTCCCTGGACCTCT	0.328													C|||	442	0.0882588	0.0484	0.1931	5008	,	,		17421	0.006		0.1501	False		,,,				2504	0.089				p.S363S		Atlas-SNP	.											.	RASGRP3	87	.	0			c.C1089T						PASS	.	C	,,	200,3414		7,186,1614	103.0	88.0	93.0		1089,1089,1089	1.7	1.0	2	dbSNP_126	93	1225,6923		81,1063,2930	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRP3	NM_001139488.1,NM_015376.2,NM_170672.2	,,	88,1249,4544	TT,TC,CC		15.0344,5.534,12.1153	,,	363/691,363/690,363/691	33759395	1425,10337	1807	4074	5881	SO:0001819	synonymous_variant	25780	exon12			GCTTTCCCTGGAC	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"""EF-hand domain containing"""	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1089C>T	2.37:g.33759395C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_170672	D6W583|O94931|Q53SD7	Silent	SNP	ENST00000403687.3	37	CCDS46256.1																																																																																			C|0.890;T|0.110	0.110	strong		0.328	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376	
KIAA0391	9692	hgsc.bcm.edu	37	14	35592538	35592538	+	Silent	SNP	C	C	G	rs941653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:35592538C>G	ENST00000557565.1	+	2	468	c.87C>G	c.(85-87)gtC>gtG	p.V29V	KIAA0391_ENST00000534898.4_Silent_p.V29V|KIAA0391_ENST00000250377.7_5'UTR|PPP2R3C_ENST00000261475.5_5'Flank|KIAA0391_ENST00000604948.1_Intron|KIAA0391_ENST00000603544.1_Silent_p.V29V|KIAA0391_ENST00000321130.10_Silent_p.V29V|PPP2R3C_ENST00000555644.1_5'Flank|KIAA0391_ENST00000603588.1_Intron|KIAA0391_ENST00000605870.1_Intron	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	29					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		ACTCTTATGTCTCGCTGTTTC	0.463													C|||	1211	0.241813	0.2474	0.2118	5008	,	,		18602	0.3542		0.165	False		,,,				2504	0.2188				p.V29V		Atlas-SNP	.											.	KIAA0391	35	.	0			c.C87G						PASS	.	C		939,3467	358.9+/-314.6	97,745,1361	61.0	55.0	57.0		87	-1.5	0.0	14	dbSNP_86	57	1460,7140	277.9+/-293.1	128,1204,2968	no	coding-synonymous	KIAA0391	NM_014672.2		225,1949,4329	GG,GC,CC		16.9767,21.3118,18.4453		29/584	35592538	2399,10607	2203	4300	6503	SO:0001819	synonymous_variant	9692	exon2			TTATGTCTCGCTG	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"""mitochondrial RNase P subunit 3"", ""proteinaceous RNase P"""	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.87C>G	14.37:g.35592538C>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Silent	SNP	ENST00000557565.1	37	CCDS32063.1																																																																																			C|0.792;G|0.208	0.208	strong		0.463	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672	
ABCC6	368	hgsc.bcm.edu	37	16	16278863	16278863	+	Missense_Mutation	SNP	G	G	T	rs8058694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:16278863G>T	ENST00000205557.7	-	15	1925	c.1896C>A	c.(1894-1896)caC>caA	p.H632Q	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	632	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		H -> Q (in dbSNP:rs8058694). {ECO:0000269|PubMed:10954200, ECO:0000269|PubMed:11536079, ECO:0000269|PubMed:11776382, ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:19339160}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	AGGTGGCACTGTGTATGGTGA	0.597													G|||	1666	0.332668	0.3245	0.4769	5008	,	,		17607	0.1627		0.4861	False		,,,				2504	0.2587				p.H632Q		Atlas-SNP	.											.	ABCC6	110	.	0			c.C1896A						PASS	.	G	GLN/HIS	1574,2820	492.2+/-362.3	287,1000,910	169.0	129.0	142.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1896	-9.0	0.0	16	dbSNP_116	142	4313,4287	578.7+/-390.8	1084,2145,1071	yes	missense	ABCC6	NM_001171.5	24	1371,3145,1981	TT,TG,GG		49.8488,35.8216,45.3055	benign	632/1504	16278863	5887,7107	2197	4300	6497	SO:0001583	missense	368	exon15			GGCACTGTGTATG	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1896C>A	16.37:g.16278863G>T	ENSP00000205557:p.His632Gln	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	214	113	0.528037	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	782	0.35805860805860806	156	0.3170731707317073	162	0.44751381215469616	95	0.1660839160839161	369	0.4868073878627968	G	9.447	1.089665	0.20390	0.358216	0.501512	ENSG00000091262	ENST00000205557;ENST00000456970;ENST00000546056	D;D	0.90004	-2.6;-2.6	5.13	-8.99	0.00751	ABC transporter-like (1);	0.857990	0.09944	N	0.735553	T	0.00012	0.0000	N	0.01446	-0.86	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.28681	-1.0036	9	0.26408	T	0.33	.	4.3691	0.11239	0.0798:0.3838:0.1417:0.3947	rs8058694;rs52827050;rs56728784;rs8058694	644;632	F5GWQ0;O95255	.;MRP6_HUMAN	Q	632;632;644	ENSP00000205557:H632Q;ENSP00000405002:H632Q	ENSP00000205557:H632Q	H	-	3	2	ABCC6	16186364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.090000	0.03372	-1.176000	0.02747	-0.182000	0.12963	CAC	G|0.607;T|0.393	0.393	strong		0.597	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
TUBAL3	79861	hgsc.bcm.edu	37	10	5436073	5436073	+	Missense_Mutation	SNP	G	G	A	rs34080891	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:5436073G>A	ENST00000380419.3	-	4	785	c.748C>T	c.(748-750)Cgg>Tgg	p.R250W	TUBAL3_ENST00000479328.1_Missense_Mutation_p.R210W	NM_024803.2	NP_079079.1	A6NHL2	TBAL3_HUMAN	tubulin, alpha-like 3	250			R -> W (in dbSNP:rs34080891).		microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(7)|prostate(2)|skin(3)	25						CCTTCAAACCGGAGGGAGGCA	0.488													G|||	223	0.0445288	0.0696	0.0259	5008	,	,		23181	0.0		0.0348	False		,,,				2504	0.0798				p.R250W		Atlas-SNP	.											.	TUBAL3	54	.	0			c.C748T						PASS	.	G	TRP/ARG,TRP/ARG	238,4168	138.8+/-174.5	3,232,1968	130.0	127.0	128.0		628,748	1.2	0.6	10	dbSNP_126	128	272,8328	104.2+/-165.2	4,264,4032	yes	missense,missense	TUBAL3	NM_001171864.1,NM_024803.2	101,101	7,496,6000	AA,AG,GG		3.1628,5.4017,3.9213	probably-damaging,probably-damaging	210/407,250/447	5436073	510,12496	2203	4300	6503	SO:0001583	missense	79861	exon4			CAAACCGGAGGGA	AK025318	CCDS7066.2, CCDS53491.1	10p15.1	2007-03-15			ENSG00000178462	ENSG00000178462		"""Tubulins"""	23534	protein-coding gene	gene with protein product							Standard	NM_024803		Approved	FLJ21665	uc001ihy.3	A6NHL2	OTTHUMG00000017595	ENST00000380419.3:c.748C>T	10.37:g.5436073G>A	ENSP00000369784:p.Arg250Trp	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_024803	B4DKL2|Q4QQJ5|Q9H6Z0	Missense_Mutation	SNP	ENST00000380419.3	37	CCDS7066.2	73	0.033424908424908424	35	0.07113821138211382	14	0.03867403314917127	0	0.0	24	0.0316622691292876	G	13.63	2.293691	0.40594	0.054017	0.031628	ENSG00000178462	ENST00000380419;ENST00000479328	T;T	0.74632	-0.86;-0.86	4.2	1.21	0.21127	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.47093	D	0.000245	T	0.54143	0.1840	H	0.99806	4.795	0.32439	N	0.546999	D;P	0.89917	1.0;0.858	D;B	0.97110	1.0;0.117	T	0.78147	-0.2317	10	0.87932	D	0	.	7.2129	0.25943	0.0852:0.0:0.3855:0.5293	rs34080891	210;250	A6NHL2-2;A6NHL2	.;TBAL3_HUMAN	W	250;210	ENSP00000369784:R250W;ENSP00000418799:R210W	ENSP00000369784:R250W	R	-	1	2	TUBAL3	5426073	0.023000	0.18921	0.601000	0.28877	0.573000	0.36030	0.284000	0.18864	0.133000	0.18654	0.650000	0.86243	CGG	G|0.962;A|0.038	0.038	strong		0.488	TUBAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046548.2	NM_024803	
MAMDC2	256691	hgsc.bcm.edu	37	9	72741298	72741298	+	Silent	SNP	G	G	A	rs2296773	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:72741298G>A	ENST00000377182.4	+	6	1484	c.867G>A	c.(865-867)gcG>gcA	p.A289A	MAMDC2-AS1_ENST00000591368.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	289	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						GGAACCTTGCGGAGGTCGAGT	0.547													G|||	506	0.101038	0.0061	0.0331	5008	,	,		20556	0.2044		0.0825	False		,,,				2504	0.1902				p.A289A		Atlas-SNP	.											MAMDC2,colon,carcinoma,+1,1	MAMDC2	55	1	0			c.G867A						PASS	.	G		75,4331	67.0+/-104.6	1,73,2129	79.0	58.0	65.0		867	-12.1	0.0	9	dbSNP_100	65	668,7932	168.8+/-220.3	26,616,3658	no	coding-synonymous	MAMDC2	NM_153267.4		27,689,5787	AA,AG,GG		7.7674,1.7022,5.7127		289/687	72741298	743,12263	2203	4300	6503	SO:0001819	synonymous_variant	256691	exon6			CCTTGCGGAGGTC	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.867G>A	9.37:g.72741298G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	26	0.325	NM_153267	Q5VW47|Q8WX43|Q96BM4	Silent	SNP	ENST00000377182.4	37	CCDS6631.1																																																																																			G|0.928;A|0.072	0.072	strong		0.547	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267	
FAM181A	90050	hgsc.bcm.edu	37	14	94394715	94394715	+	Silent	SNP	C	C	T	rs11554726	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94394715C>T	ENST00000267594.5	+	3	577	c.270C>T	c.(268-270)tcC>tcT	p.S90S	FAM181A_ENST00000557719.1_Silent_p.S28S|FAM181A_ENST00000557000.2_Silent_p.S28S|FAM181A-AS1_ENST00000554742.1_RNA|FAM181A_ENST00000556222.1_Silent_p.S28S	NM_001207073.1|NM_001207074.1|NM_138344.4	NP_001194002.1|NP_001194003.1|NP_612353.3	Q8N9Y4	F181A_HUMAN	family with sequence similarity 181, member A	90										cervix(1)|endometrium(2)|large_intestine(8)|lung(4)|prostate(1)|skin(2)	18						TGGATAAGTCCGCACCCTGCC	0.622													C|||	416	0.0830671	0.1309	0.0461	5008	,	,		16710	0.001		0.1173	False		,,,				2504	0.0941				p.S90S		Atlas-SNP	.											.	FAM181A	42	.	0			c.C270T						PASS	.	C	,,,,	514,3892	234.2+/-247.1	28,458,1717	60.0	53.0	55.0		84,84,84,84,270	-9.3	0.0	14	dbSNP_120	55	1124,7476	232.5+/-266.1	77,970,3253	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FAM181A	NM_001207071.1,NM_001207072.1,NM_001207073.1,NM_001207074.1,NM_138344.4	,,,,	105,1428,4970	TT,TC,CC		13.0698,11.6659,12.5942	,,,,	28/293,28/293,28/293,28/293,90/355	94394715	1638,11368	2203	4300	6503	SO:0001819	synonymous_variant	90050	exon3			TAAGTCCGCACCC	BC009073	CCDS9914.1, CCDS55939.1	14q32.12	2011-11-30	2008-07-22	2008-07-22	ENSG00000140067	ENSG00000140067			20491	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 152"""	C14orf152			Standard	NM_138344		Approved		uc021saz.1	Q8N9Y4	OTTHUMG00000171297	ENST00000267594.5:c.270C>T	14.37:g.94394715C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_138344	B2RD39|Q96GY1	Silent	SNP	ENST00000267594.5	37	CCDS9914.1																																																																																			C|0.889;T|0.111	0.111	strong		0.622	FAM181A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412840.1	NM_138344	
CHGB	1114	hgsc.bcm.edu	37	20	5903848	5903848	+	Missense_Mutation	SNP	C	C	G	rs236152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:5903848C>G	ENST00000378961.4	+	4	1262	c.1058C>G	c.(1057-1059)gCc>gGc	p.A353G		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	353			A -> G (in dbSNP:rs236152). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GGCGTCCAGGCCCCTGAGGAC	0.527													C|||	2581	0.515375	0.6573	0.5231	5008	,	,		20028	0.5288		0.3499	False		,,,				2504	0.4744				p.A353G		Atlas-SNP	.											.	CHGB	112	.	0			c.C1058G	GRCh37	CM043990	CHGB	M	rs236152	PASS	.	C	GLY/ALA	2735,1671	645.1+/-398.1	870,995,338	76.0	80.0	79.0		1058	-1.1	0.0	20	dbSNP_79	79	3091,5509	456.5+/-364.1	553,1985,1762	yes	missense	CHGB	NM_001819.2	60	1423,2980,2100	GG,GC,CC		35.9419,37.9256,44.7947	benign	353/678	5903848	5826,7180	2203	4300	6503	SO:0001583	missense	1114	exon4			TCCAGGCCCCTGA		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1058C>G	20.37:g.5903848C>G	ENSP00000368244:p.Ala353Gly	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	1025	0.4693223443223443	308	0.6260162601626016	163	0.45027624309392267	293	0.5122377622377622	261	0.34432717678100266	C	0.515	-0.864782	0.02590	0.620744	0.359419	ENSG00000089199	ENST00000378961	T	0.05580	3.42	5.27	-1.14	0.09741	.	0.712485	0.12872	N	0.432199	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.30679	-0.9970	9	0.10377	T	0.69	-0.0614	4.5883	0.12294	0.188:0.3751:0.3568:0.0801	rs236152;rs236152	353	P05060	SCG1_HUMAN	G	353	ENSP00000368244:A353G	ENSP00000368244:A353G	A	+	2	0	CHGB	5851848	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.447000	0.06828	-0.043000	0.13513	-0.261000	0.10672	GCC	C|0.545;G|0.455	0.455	strong		0.527	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
KCNF1	3754	hgsc.bcm.edu	37	2	11053740	11053740	+	Silent	SNP	C	C	T	rs3732105	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:11053740C>T	ENST00000295082.1	+	1	1678	c.1188C>T	c.(1186-1188)atC>atT	p.I396I		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	396					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		GTGGTGTCATCGCCATCGCCC	0.602													C|||	2419	0.483027	0.3389	0.4928	5008	,	,		22218	0.5099		0.6322	False		,,,				2504	0.4898				p.I396I		Atlas-SNP	.											.	KCNF1	70	.	0			c.C1188T						PASS	.	C		1657,2749	506.1+/-366.3	300,1057,846	152.0	112.0	125.0		1188	-6.7	0.9	2	dbSNP_107	125	5502,3098	658.8+/-401.6	1754,1994,552	no	coding-synonymous	KCNF1	NM_002236.4		2054,3051,1398	TT,TC,CC		36.0233,37.6078,44.9562		396/495	11053740	7159,5847	2203	4300	6503	SO:0001819	synonymous_variant	3754	exon1			TGTCATCGCCATC	AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.1188C>T	2.37:g.11053740C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_002236	O43527|Q585L3	Silent	SNP	ENST00000295082.1	37	CCDS1676.1																																																																																			C|0.471;T|0.529	0.529	strong		0.602	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236	
ZNF524	147807	hgsc.bcm.edu	37	19	56114237	56114237	+	Silent	SNP	G	G	A	rs310459	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56114237G>A	ENST00000591046.1	+	1	993	c.759G>A	c.(757-759)gaG>gaA	p.E253E	ZNF865_ENST00000568956.1_5'Flank|ZNF524_ENST00000301073.3_Silent_p.E253E			Q96C55	ZN524_HUMAN	zinc finger protein 524	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(2)|lung(6)|prostate(1)	10			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		GGGCCGAGGAGGAGGAGGAGA	0.692													g|||	4197	0.838059	0.705	0.8314	5008	,	,		14216	0.8413		0.9304	False		,,,				2504	0.9243				p.E253E		Atlas-SNP	.											.	ZNF524	18	.	0			c.G759A						PASS	.	A		3000,980		1108,784,98	10.0	9.0	9.0		759	-3.5	0.0	19	dbSNP_79	9	7276,520		3403,470,25	no	coding-synonymous	ZNF524	NM_153219.2		4511,1254,123	AA,AG,GG		6.6701,24.6231,12.7378		253/265	56114237	10276,1500	1990	3898	5888	SO:0001819	synonymous_variant	147807	exon2			CGAGGAGGAGGAG	BC014666	CCDS12929.1	19q13.43	2013-01-08				ENSG00000171443		"""Zinc fingers, C2H2-type"""	28322	protein-coding gene	gene with protein product						12477932	Standard	NM_153219		Approved	MGC23143	uc002qlk.1	Q96C55		ENST00000591046.1:c.759G>A	19.37:g.56114237G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_153219	Q6NW31|Q96IL7	Silent	SNP	ENST00000591046.1	37	CCDS12929.1																																																																																			G|0.147;A|0.853	0.853	strong		0.692	ZNF524-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457938.1	NM_153219	
C10orf54	64115	hgsc.bcm.edu	37	10	73521371	73521371	+	Silent	SNP	C	C	T	rs3747867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:73521371C>T	ENST00000394957.3	-	2	553	c.495G>A	c.(493-495)gaG>gaA	p.E165E	CDH23_ENST00000224721.6_Intron|C10orf54_ENST00000481568.2_5'UTR	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	165					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GCACCTGCAGCTCCATGGCAC	0.622													C|||	934	0.186502	0.1551	0.1729	5008	,	,		23685	0.1935		0.2744	False		,,,				2504	0.1411				p.E165E		Atlas-SNP	.											.	C10orf54	29	.	0			c.G495A						PASS	.	C	,	800,3606	303.8+/-288.1	67,666,1470	37.0	29.0	32.0		,495	3.8	1.0	10	dbSNP_107	32	2175,6425	356.1+/-330.2	267,1641,2392	no	intron,coding-synonymous	CDH23,C10orf54	NM_022124.5,NM_022153.1	,	334,2307,3862	TT,TC,CC		25.2907,18.1571,22.8741	,	,165/312	73521371	2975,10031	2203	4300	6503	SO:0001819	synonymous_variant	64115	exon2			CTGCAGCTCCATG	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"""Immunoglobulin superfamily / V-set domain containing"""	30085	protein-coding gene	gene with protein product	"""stress induced secreted protein 1"""	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.495G>A	10.37:g.73521371C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Silent	SNP	ENST00000394957.3	37	CCDS31218.1																																																																																			C|0.779;T|0.221	0.221	strong		0.622	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153	
KREMEN1	83999	hgsc.bcm.edu	37	22	29533572	29533572	+	Missense_Mutation	SNP	C	C	G	rs34920087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29533572C>G	ENST00000407188.1	+	6	868	c.868C>G	c.(868-870)Ctg>Gtg	p.L290V	KREMEN1_ENST00000400338.2_Missense_Mutation_p.L292V|KREMEN1_ENST00000327813.5_Missense_Mutation_p.L292V|KREMEN1_ENST00000400335.4_Missense_Mutation_p.L292V			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	290	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						CCGCCCACCTCTGTCCTTCAA	0.542													C|||	543	0.108427	0.0726	0.111	5008	,	,		18222	0.0427		0.1958	False		,,,				2504	0.1329				p.L292V		Atlas-SNP	.											.	KREMEN1	46	.	0			c.C874G						PASS	.	C	VAL/LEU,VAL/LEU	314,3586		11,292,1647	68.0	69.0	69.0		874,874	-8.7	0.0	22	dbSNP_126	69	1438,6846		130,1178,2834	yes	missense,missense	KREMEN1	NM_001039570.2,NM_032045.4	32,32	141,1470,4481	GG,GC,CC		17.3588,8.0513,14.3795	benign,benign	292/459,292/493	29533572	1752,10432	1950	4142	6092	SO:0001583	missense	83999	exon6			CCACCTCTGTCCT	AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762			17550	protein-coding gene	gene with protein product		609898	"""kringle containing transmembrane protein"""	KREMEN		11267660	Standard	NM_001039570		Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.868C>G	22.37:g.29533572C>G	ENSP00000385431:p.Leu290Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	51	0.62963	NM_001039570	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Missense_Mutation	SNP	ENST00000407188.1	37	CCDS43000.2	250	0.11446886446886446	44	0.08943089430894309	41	0.1132596685082873	12	0.02097902097902098	153	0.20184696569920843	C	12.47	1.946617	0.34377	0.080513	0.173588	ENSG00000183762	ENST00000400335;ENST00000400338;ENST00000327813;ENST00000407188	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.99	-8.68	0.00859	CUB (5);	0.511667	0.15093	N	0.280963	T	0.00012	0.0000	L	0.45137	1.4	0.80722	P	0.0	B;B;B	0.27625	0.183;0.152;0.065	B;B;B	0.30943	0.122;0.08;0.035	T	0.01500	-1.1339	9	0.25106	T	0.35	.	20.4747	0.99174	0.0:0.9009:0.0:0.0991	rs34920087;rs58049194;rs61741867	290;292;292	Q96MU8;Q96MU8-2;Q96MU8-3	KREM1_HUMAN;.;.	V	292;292;292;290	ENSP00000383189:L292V;ENSP00000383192:L292V;ENSP00000331242:L292V;ENSP00000385431:L290V	ENSP00000331242:L292V	L	+	1	2	KREMEN1	27863572	0.000000	0.05858	0.010000	0.14722	0.982000	0.71751	-0.438000	0.06905	-1.629000	0.01546	0.467000	0.42956	CTG	C|0.862;G|0.138	0.138	strong		0.542	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507836	195507836	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507836C>G	ENST00000463781.3	-	2	11074	c.10615G>C	c.(10615-10617)Gtc>Ctc	p.V3539L	MUC4_ENST00000475231.1_Missense_Mutation_p.V3539L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3539L(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGCTGGTGACAGGAAGAGGC	0.617																																					p.V3539L		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	skin(2)	c.G10615C						PASS	.						27.0	27.0	27.0					3																	195507836		681	1578	2259	SO:0001583	missense	4585	exon2			TGGTGACAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10615G>C	3.37:g.195507836C>G	ENSP00000417498:p.Val3539Leu	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	692	37	0.0534682	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	3.354	-0.131924	0.06753	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.4;1.39	0.743	-1.49	0.08718	.	0.000000	0.23275	U	0.049970	T	0.17831	0.0428	N	0.19112	0.55	0.09310	N	1	B	0.33494	0.414	B	0.35899	0.213	T	0.15665	-1.0429	9	.	.	.	.	4.8397	0.13483	0.3414:0.6586:0.0:1.0E-4	.	3411	E7ESK3	.	L	3539	ENSP00000417498:V3539L;ENSP00000420243:V3539L	.	V	-	1	0	MUC4	196992615	0.000000	0.05858	0.015000	0.15790	0.015000	0.08874	-0.219000	0.09228	0.088000	0.17205	0.089000	0.15464	GTC	.	.	none		0.617	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SNAPC3	6619	hgsc.bcm.edu	37	9	15459821	15459821	+	Missense_Mutation	SNP	A	A	C	rs3087653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:15459821A>C	ENST00000380821.3	+	9	1369	c.1193A>C	c.(1192-1194)gAa>gCa	p.E398A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	398			E -> A (in dbSNP:rs3087653).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		AAACTGGGGGAATTCCTTGCT	0.413													A|||	193	0.0385383	0.0416	0.0231	5008	,	,		16799	0.0		0.0596	False		,,,				2504	0.0634				p.E398A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.A1193C						PASS	.	A	ALA/GLU	145,4261	101.2+/-139.8	0,145,2058	134.0	122.0	126.0		1193	5.9	1.0	9	dbSNP_102	126	425,8175	131.8+/-189.6	13,399,3888	yes	missense	SNAPC3	NM_001039697.1	107	13,544,5946	CC,CA,AA		4.9419,3.291,4.3826	probably-damaging	398/412	15459821	570,12436	2203	4300	6503	SO:0001583	missense	6619	exon9			TGGGGGAATTCCT	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.1193A>C	9.37:g.15459821A>C	ENSP00000370200:p.Glu398Ala	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	138	44	0.318841	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	78	0.03571428571428571	26	0.052845528455284556	11	0.03038674033149171	0	0.0	41	0.05408970976253298	A	31	5.081553	0.94050	0.03291	0.049419	ENSG00000164975	ENST00000380821	T	0.44083	0.93	5.86	5.86	0.93980	.	0.138414	0.64402	D	0.000005	T	0.17450	0.0419	M	0.65498	2.005	0.80722	D	1	D	0.57571	0.98	P	0.53224	0.721	T	0.31447	-0.9943	10	0.56958	D	0.05	-42.6534	16.5602	0.84551	1.0:0.0:0.0:0.0	rs3087653;rs3198208;rs52828246;rs3087653	398	Q92966	SNPC3_HUMAN	A	398	ENSP00000370200:E398A	ENSP00000370200:E398A	E	+	2	0	SNAPC3	15449821	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.283000	0.78640	2.367000	0.80283	0.528000	0.53228	GAA	A|0.956;C|0.044	0.044	strong		0.413	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
BEND7	222389	hgsc.bcm.edu	37	10	13494594	13494594	+	Silent	SNP	T	T	C	rs2277222	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:13494594T>C	ENST00000396900.2	-	7	1127	c.1128A>G	c.(1126-1128)gtA>gtG	p.V376V	BEND7_ENST00000486542.1_5'UTR|BEND7_ENST00000341083.3_Silent_p.V324V|BEND7_ENST00000378605.3_Silent_p.V337V|BEND7_ENST00000396898.2_Silent_p.V389V			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	376	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.					extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						GTAGAATCTGTACCCAATCTC	0.363													T|||	1785	0.35643	0.1218	0.3458	5008	,	,		18852	0.6696		0.3429	False		,,,				2504	0.3722				p.V337V		Atlas-SNP	.											.	BEND7	85	.	0			c.A1011G						PASS	.	T	,	697,3709	291.8+/-281.7	60,577,1566	142.0	143.0	143.0		1011,972	-5.5	0.9	10	dbSNP_100	143	2829,5771	446.0+/-361.1	458,1913,1929	no	coding-synonymous,coding-synonymous	BEND7	NM_001100912.1,NM_152751.2	,	518,2490,3495	CC,CT,TT		32.8953,15.8193,27.1106	,	337/375,324/469	13494594	3526,9480	2203	4300	6503	SO:0001819	synonymous_variant	222389	exon6			AATCTGTACCCAA	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.1128A>G	10.37:g.13494594T>C		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	301	138	0.458472	NM_001100912	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				T|0.677;C|0.323	0.323	strong		0.363	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
MUC16	94025	hgsc.bcm.edu	37	19	9075584	9075584	+	Silent	SNP	T	T	A	rs2547069	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9075584T>A	ENST00000397910.4	-	3	12065	c.11862A>T	c.(11860-11862)acA>acT	p.T3954T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3956	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.T3954T(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGACCCAGCCTGTGGTCTCTA	0.512													T|||	1054	0.210463	0.0628	0.2046	5008	,	,		20855	0.249		0.3101	False		,,,				2504	0.272				p.T3954T		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - coding silent(2)	stomach(2)	c.A11862T						PASS	.	T		409,3615		23,363,1626	70.0	67.0	68.0		11862	-4.2	0.0	19	dbSNP_100	68	2400,5928		340,1720,2104	no	coding-synonymous	MUC16	NM_024690.2		363,2083,3730	AA,AT,TT		28.8184,10.164,22.7413		3954/14508	9075584	2809,9543	2012	4164	6176	SO:0001819	synonymous_variant	94025	exon3			CCAGCCTGTGGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11862A>T	19.37:g.9075584T>A		Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	416	195	0.46875	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.771;A|0.229	0.229	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MST1L	11223	hgsc.bcm.edu	37	1	17087343	17087343	+	RNA	SNP	G	G	C	rs186420363		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17087343G>C	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TGGCAACCATGGCTGCTCACA	0.617																																					p.H81D		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	0			c.C241G						PASS	.																																					11223	exon3			AACCATGGCTGCT	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17087343G>C		Somatic	517	0	0		WXS	Illumina HiSeq	Phase_I	560	92	0.164286	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	10.03	1.239714	0.22711	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552;ENST00000545160	.	.	.	.	.	.	.	0.336100	0.21565	N	0.072502	T	0.27663	0.0680	.	.	.	.	.	.	P	0.40398	0.716	B	0.36567	0.228	T	0.27571	-1.0070	6	0.56958	D	0.05	.	5.8178	0.18506	0.001:0.0:0.999:0.0	.	81	Q2TV78-2	.	D	51;81;81;13	.	ENSP00000439273:H81D	H	-	1	0	MST1P9	16959930	0.925000	0.31364	0.000000	0.03702	0.000000	0.00434	1.257000	0.32932	-0.000000	0.14550	0.000000	0.15137	CAT	.	.	weak		0.617	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
LATS1	9113	hgsc.bcm.edu	37	6	149983216	149983216	+	Silent	SNP	G	G	A	rs3924871	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:149983216G>A	ENST00000543571.1	-	8	3589	c.3042C>T	c.(3040-3042)gaC>gaT	p.D1014D	LATS1_ENST00000253339.5_Silent_p.D1014D	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		CACTGGAGAAGTCAATTGTTT	0.373													A|||	2758	0.550719	0.5749	0.6326	5008	,	,		17648	0.8214		0.3588	False		,,,				2504	0.3783				p.D1014D		Atlas-SNP	.											.	LATS1	241	.	0			c.C3042T						PASS	.	A		2364,2042	567.4+/-382.1	638,1088,477	117.0	120.0	119.0		3042	3.1	1.0	6	dbSNP_108	119	3133,5467	657.0+/-401.4	552,2029,1719	no	coding-synonymous	LATS1	NM_004690.2		1190,3117,2196	AA,AG,GG		36.4302,46.3459,42.2651		1014/1131	149983216	5497,7509	2203	4300	6503	SO:0001819	synonymous_variant	9113	exon8			GGAGAAGTCAATT	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.3042C>T	6.37:g.149983216G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_004690		Silent	SNP	ENST00000543571.1	37	CCDS34551.1																																																																																			G|0.512;A|0.488	0.488	strong		0.373	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690	
GPR98	84059	hgsc.bcm.edu	37	5	89989779	89989779	+	Silent	SNP	G	G	A	rs16876822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:89989779G>A	ENST00000405460.2	+	33	7302	c.7206G>A	c.(7204-7206)gaG>gaA	p.E2402E		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2402					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGGCAATGGAGGAAGGTCAAG	0.488													G|||	1613	0.322085	0.2073	0.5029	5008	,	,		17789	0.375		0.3191	False		,,,				2504	0.2975				p.E2402E		Atlas-SNP	.											.	GPR98	605	.	0			c.G7206A						PASS	.	G		797,3013		92,613,1200	73.0	69.0	70.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7206	4.2	1.0	5	dbSNP_123	70	2704,5546		448,1808,1869	no	coding-synonymous	GPR98	NM_032119.3		540,2421,3069	AA,AG,GG		32.7758,20.9186,29.0299		2402/6307	89989779	3501,8559	1905	4125	6030	SO:0001819	synonymous_variant	84059	exon33			AATGGAGGAAGGT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.7206G>A	5.37:g.89989779G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																			G|0.672;A|0.328	0.328	strong		0.488	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
MNT	4335	hgsc.bcm.edu	37	17	2290345	2290345	+	Silent	SNP	G	G	A	rs61742229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:2290345G>A	ENST00000174618.4	-	6	2004	c.1599C>T	c.(1597-1599)gcC>gcT	p.A533A	RP1-59D14.1_ENST00000571775.1_RNA|MNT_ENST00000575374.1_5'Flank	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	533					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		GCCCCAGGCCGGCCGTGCCGT	0.697													G|||	113	0.0225639	0.0045	0.0447	5008	,	,		12225	0.0		0.0686	False		,,,				2504	0.0072				p.A533A		Atlas-SNP	.											.	MNT	35	.	0			c.C1599T						PASS	.	G		66,4254		2,62,2096	25.0	30.0	28.0		1599	-9.8	0.3	17	dbSNP_129	28	685,7781		24,637,3572	no	coding-synonymous	MNT	NM_020310.2		26,699,5668	AA,AG,GG		8.0912,1.5278,5.8736		533/583	2290345	751,12035	2160	4233	6393	SO:0001819	synonymous_variant	4335	exon6			CAGGCCGGCCGTG	Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	7188	protein-coding gene	gene with protein product	"""myc antagonist"", ""Max-interacting protein"""	603039	"""MAX binding protein"", ""MNT, MAX dimerization protein"""			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.1599C>T	17.37:g.2290345G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_020310	A8K6D1|D3DTI7|Q1ED38	Silent	SNP	ENST00000174618.4	37	CCDS11018.1																																																																																			G|0.958;A|0.042	0.042	strong		0.697	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310	
ANK2	287	hgsc.bcm.edu	37	4	114275942	114275942	+	Silent	SNP	C	C	G	rs3796928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:114275942C>G	ENST00000357077.4	+	38	6221	c.6168C>G	c.(6166-6168)ctC>ctG	p.L2056L	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Silent_p.L2023L|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2056					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GCCAGAGACTCCCGGTAACGG	0.468													C|||	595	0.11881	0.3563	0.0533	5008	,	,		19930	0.0466		0.0249	False		,,,				2504	0.0153				p.L2056L		Atlas-SNP	.											.	ANK2	576	.	0			c.C6168G						PASS	.	C	,,	1300,3106	431.2+/-342.8	186,928,1089	76.0	87.0	83.0		,6168,	1.0	0.0	4	dbSNP_107	83	210,8390	89.4+/-151.6	5,200,4095	no	intron,coding-synonymous,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,,	191,1128,5184	GG,GC,CC		2.4419,29.5052,11.61	,,	,2056/3958,	114275942	1510,11496	2203	4300	6503	SO:0001819	synonymous_variant	287	exon38			GAGACTCCCGGTA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6168C>G	4.37:g.114275942C>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	155	74	0.477419	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																			C|0.884;G|0.116	0.116	strong		0.468	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
KIF1B	23095	hgsc.bcm.edu	37	1	10364057	10364057	+	Intron	SNP	A	A	G	rs41274462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:10364057A>G	ENST00000377086.1	+	22	2317				KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377081.1_Intron|KIF1B_ENST00000377093.4_Silent_p.T938T|KIF1B_ENST00000377083.1_Silent_p.T938T|RN7SL731P_ENST00000584329.1_RNA			O60333	KIF1B_HUMAN	kinesin family member 1B						anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		AGGAGATAACAAAGCAGCTTC	0.502													G|||	33	0.00658946	0.0	0.0101	5008	,	,		20253	0.0		0.0229	False		,,,				2504	0.0031				p.T938T		Atlas-SNP	.											.	KIF1B	242	.	0			c.A2814G						PASS	.	G	,	22,4384	819.6+/-416.4	0,22,2181	75.0	78.0	77.0		,2814	-10.1	0.4	1	dbSNP_127	77	221,8379	807.1+/-407.2	3,215,4082	no	intron,coding-synonymous	KIF1B	NM_015074.3,NM_183416.3	,	3,237,6263	GG,GA,AA		2.5698,0.4993,1.8684	,	,938/1154	10364057	243,12763	2203	4300	6503	SO:0001627	intron_variant	23095	exon21			GATAACAAAGCAG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.2115+6753A>G	1.37:g.10364057A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																				A|0.984;G|0.016	0.016	strong		0.502	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
MSH5	4439	hgsc.bcm.edu	37	6	31727897	31727897	+	Silent	SNP	C	C	T	rs3115672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31727897C>T	ENST00000375755.3	+	19	2002	c.1716C>T	c.(1714-1716)acC>acT	p.T572T	MSH5_ENST00000431848.2_Silent_p.T271T|MSH5_ENST00000534153.4_Silent_p.T589T|MSH5_ENST00000395853.1_Silent_p.T246T|SAPCD1_ENST00000425424.1_5'Flank|MSH5_ENST00000375742.3_Silent_p.T589T|MSH5_ENST00000375740.3_Silent_p.T589T|MSH5-SAPCD1_ENST00000493662.2_Silent_p.T589T|SAPCD1_ENST00000415669.2_5'Flank|MSH5_ENST00000375750.3_Silent_p.T572T|MSH5_ENST00000375703.3_Silent_p.T572T	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	572					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						GTGCCCGAACCTTTGTGCCCA	0.532								Direct reversal of damage;Mismatch excision repair (MMR)					C|||	169	0.033746	0.0567	0.0274	5008	,	,		21313	0.0		0.0746	False		,,,				2504	0.0				p.T589T		Atlas-SNP	.											MSH5_ENST00000375742,bladder,carcinoma,+1,2	MSH5	108	2	0			c.C1767T						PASS	.	C	,,,	299,4107	162.5+/-194.5	8,283,1912	109.0	110.0	109.0		1716,1767,1716,1716	0.1	1.0	6	dbSNP_103	109	932,7668	205.5+/-247.9	55,822,3423	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MSH5	NM_002441.4,NM_025259.5,NM_172165.3,NM_172166.3	,,,	63,1105,5335	TT,TC,CC		10.8372,6.7862,9.4649	,,,	572/835,589/823,572/836,572/835	31727897	1231,11775	2203	4300	6503	SO:0001819	synonymous_variant	4439	exon19			CCGAACCTTTGTG	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.1716C>T	6.37:g.31727897C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	139	57	0.410072	NM_025259	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Silent	SNP	ENST00000375755.3	37	CCDS4720.1																																																																																			C|0.923;T|0.077	0.077	strong		0.532	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549583	32549583	+	Missense_Mutation	SNP	T	T	C	rs17433947		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549583T>C	ENST00000360004.5	-	3	508	c.403A>G	c.(403-405)Acc>Gcc	p.T135A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	135	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AGGGGCTGGGTCTTTGAAGGA	0.507										Multiple Myeloma(14;0.17)																											p.T135A		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A403G						PASS	.						66.0	82.0	76.0					6																	32549583		1510	2709	4219	SO:0001583	missense	3123	exon3			GCTGGGTCTTTGA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.403A>G	6.37:g.32549583T>C	ENSP00000353099:p.Thr135Ala	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	372	37	0.0994624	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	10.80	1.451590	0.26074	.	.	ENSG00000196126	ENST00000360004	T	0.02787	4.16	3.87	1.14	0.20703	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.480425	0.24686	N	0.036424	T	0.03959	0.0111	M	0.62088	1.915	0.25150	N	0.990439	D	0.54964	0.969	D	0.73708	0.981	T	0.28170	-1.0052	10	0.72032	D	0.01	.	5.5797	0.17243	0.0:0.1048:0.1704:0.7249	.	135	P01911	2B1F_HUMAN	A	135	ENSP00000353099:T135A	ENSP00000353099:T135A	T	-	1	0	HLA-DRB1	32657561	0.000000	0.05858	0.754000	0.31244	0.116000	0.19942	-1.406000	0.02490	0.483000	0.27608	-0.639000	0.03973	ACC	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PODXL	5420	hgsc.bcm.edu	37	7	131195712	131195712	+	Missense_Mutation	SNP	G	G	A	rs12670788	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:131195712G>A	ENST00000378555.3	-	2	828	c.581C>T	c.(580-582)tCg>tTg	p.S194L	PODXL_ENST00000541194.1_Missense_Mutation_p.S196L|PODXL_ENST00000322985.9_Missense_Mutation_p.S194L|PODXL_ENST00000465001.1_5'Flank|PODXL_ENST00000537928.1_Missense_Mutation_p.S194L			O00592	PODXL_HUMAN	podocalyxin-like	194	Thr-rich.		S -> L (in dbSNP:rs12670788). {ECO:0000269|PubMed:9188463}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					AGGATGCGTCGAAGTGGGTTG	0.527													G|||	1820	0.363419	0.0363	0.3948	5008	,	,		19195	0.6518		0.4324	False		,,,				2504	0.4151				p.S194L		Atlas-SNP	.											.	PODXL	53	.	0			c.C581T						PASS	.	G	LEU/SER,LEU/SER	472,3934	220.4+/-237.8	27,418,1758	207.0	180.0	189.0		581,581	-2.0	0.0	7	dbSNP_120	189	4077,4523	560.3+/-387.6	972,2133,1195	yes	missense,missense	PODXL	NM_001018111.2,NM_005397.3	145,145	999,2551,2953	AA,AG,GG		47.407,10.7127,34.9762	benign,benign	194/559,194/527	131195712	4549,8457	2203	4300	6503	SO:0001583	missense	5420	exon2			TGCGTCGAAGTGG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.581C>T	7.37:g.131195712G>A	ENSP00000367817:p.Ser194Leu	Somatic	439	1	0.0022779		WXS	Illumina HiSeq	Phase_I	463	211	0.455724	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	856	0.39194139194139194	30	0.06097560975609756	130	0.35911602209944754	351	0.6136363636363636	345	0.4551451187335092	g	4.782	0.145408	0.09134	0.107127	0.47407	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.14391	2.51;2.6;2.51;2.81	3.08	-2.05	0.07321	.	28.627400	0.00166	N	0.000001	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.33022	0.394;0.273	B;B	0.22880	0.042;0.019	T	0.44019	-0.9355	9	0.21014	T	0.42	.	1.1922	0.01867	0.2085:0.3236:0.3025:0.1654	rs12670788;rs17823063;rs60946866;rs12670788	194;194	O00592-2;O00592	.;PODXL_HUMAN	L	196;194;184;194;194	ENSP00000440518:S196L;ENSP00000442655:S194L;ENSP00000367817:S194L;ENSP00000319782:S194L	ENSP00000319782:S194L	S	-	2	0	PODXL	130846252	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.157000	0.10085	-0.524000	0.06400	-4.755000	0.00003	TCG	G|0.634;A|0.366	0.366	strong		0.527	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859906	144859906	+	Missense_Mutation	SNP	G	G	T	rs182136884		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859906G>T	ENST00000369354.3	-	38	6367	c.6178C>A	c.(6178-6180)Cag>Aag	p.Q2060K	PDE4DIP_ENST00000313382.9_Missense_Mutation_p.Q1954K|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.Q2060K|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.Q2145K|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.Q2196K|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2060					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGAATGCTCTGCTCCAGCTGC	0.577			T	PDGFRB	MPD																																p.Q2060K		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6178A						PASS	.						82.0	77.0	79.0					1																	144859906		2203	4298	6501	SO:0001583	missense	9659	exon38			TGCTCTGCTCCAG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6178C>A	1.37:g.144859906G>T	ENSP00000358360:p.Gln2060Lys	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	306	17	0.0555556	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	1.396	-0.579398	0.03854	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01505	4.82;4.91;4.91;4.92;4.91	5.1	0.961	0.19638	.	.	.	.	.	T	0.00608	0.0020	L	0.43152	1.355	0.80722	D	1	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.0	T	0.45731	-0.9241	9	0.34782	T	0.22	.	2.6421	0.04974	0.1614:0.2665:0.4356:0.1366	.	1954;2060	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	K	1954;2060;2060;2145;2196	ENSP00000327209:Q1954K;ENSP00000358360:Q2060K;ENSP00000358363:Q2060K;ENSP00000435654:Q2145K;ENSP00000358366:Q2196K	ENSP00000327209:Q1954K	Q	-	1	0	PDE4DIP	143571263	0.990000	0.36364	0.996000	0.52242	0.001000	0.01503	0.798000	0.27014	0.255000	0.21593	-0.894000	0.02916	CAG	G|1.000;T|0.000	0.000	strong		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
OR2M3	127062	hgsc.bcm.edu	37	1	248366702	248366702	+	Silent	SNP	G	G	A	rs4916112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248366702G>A	ENST00000456743.1	+	1	371	c.333G>A	c.(331-333)gaG>gaA	p.E111E		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TTGGCTCTGAGTGCTTTCTTT	0.448													A|||	2419	0.483027	0.3306	0.5072	5008	,	,		19244	0.4325		0.6083	False		,,,				2504	0.5951				p.E111E		Atlas-SNP	.											.	OR2M3	116	.	0			c.G333A						PASS	.	A		1684,2722	654.9+/-399.8	294,1096,813	247.0	253.0	251.0		333	-0.2	0.0	1	dbSNP_111	251	5311,3289	491.9+/-373.2	1639,2033,628	no	coding-synonymous	OR2M3	NM_001004689.1		1933,3129,1441	AA,AG,GG		38.2442,38.2206,46.2171		111/313	248366702	6995,6011	2203	4300	6503	SO:0001819	synonymous_variant	127062	exon1			CTCTGAGTGCTTT		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"""GPCR / Class A : Olfactory receptors"""	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.333G>A	1.37:g.248366702G>A		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	347	346	0.997118	NM_001004689	B9EH06|Q6IEY0	Silent	SNP	ENST00000456743.1	37	CCDS31107.1																																																																																			G|0.470;A|0.530	0.530	strong		0.448	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689	
PRIMPOL	201973	hgsc.bcm.edu	37	4	185599489	185599489	+	Silent	SNP	G	G	A	rs34985821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:185599489G>A	ENST00000314970.6	+	8	1381	c.948G>A	c.(946-948)caG>caA	p.Q316Q	PRIMPOL_ENST00000512834.1_Silent_p.Q316Q|PRIMPOL_ENST00000515774.1_Silent_p.Q187Q|PRIMPOL_ENST00000503752.1_Silent_p.Q316Q	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	316					mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										TTCCTATACAGTCAAAAGATG	0.318													G|||	307	0.0613019	0.0272	0.1066	5008	,	,		13541	0.001		0.1243	False		,,,				2504	0.0726				p.Q316Q		Atlas-SNP	.											.	CCDC111	43	.	0			c.G948A						PASS	.	G		175,4227	111.6+/-149.8	4,167,2030	50.0	52.0	52.0		948	-1.9	0.0	4	dbSNP_126	52	1186,7404	238.3+/-269.8	93,1000,3202	no	coding-synonymous	CCDC111	NM_152683.2		97,1167,5232	AA,AG,GG		13.8068,3.9755,10.4757		316/561	185599489	1361,11631	2201	4295	6496	SO:0001819	synonymous_variant	201973	exon8			TATACAGTCAAAA	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.948G>A	4.37:g.185599489G>A		Somatic	337	1	0.00296736		WXS	Illumina HiSeq	Phase_I	410	201	0.490244	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Silent	SNP	ENST00000314970.6	37	CCDS3837.1	144	0.06593406593406594	15	0.03048780487804878	41	0.1132596685082873	0	0.0	88	0.11609498680738786	G	7.626	0.677847	0.14841	0.039755	0.138068	ENSG00000164306	ENST00000508001	.	.	.	5.95	-1.91	0.07641	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.28267	-1.0049	4	0.14656	T	0.56	-6.382	6.4791	0.22053	0.5647:0.0:0.178:0.2573	rs34985821	.	.	.	N	20	.	ENSP00000424639:S20N	S	+	2	0	CCDC111	185836483	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.522000	0.06237	-0.186000	0.10533	0.655000	0.94253	AGT	G|0.904;A|0.096	0.096	strong		0.318	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
NELFB	25920	hgsc.bcm.edu	37	9	140147273	140147273	+	5'Flank	SNP	C	C	T	rs61759822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140147273C>T	ENST00000343053.4	+	0	0				C9orf173_ENST00000388931.3_Missense_Mutation_p.L218F|C9orf173_ENST00000412566.1_Missense_Mutation_p.L218F	NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B						gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CCAGTCCCTGCTTCAGGCCTC	0.667													C|||	715	0.142772	0.0204	0.1066	5008	,	,		12190	0.3075		0.1243	False		,,,				2504	0.183				p.L218F		Atlas-SNP	.											.	C9orf173	19	.	0			c.C652T						PASS	.	C	PHE/LEU	174,3596		4,166,1715	12.0	14.0	13.0		652	1.6	0.0	9	dbSNP_129	13	866,7272		57,752,3260	yes	missense	C9orf173	NM_001004353.2	22	61,918,4975	TT,TC,CC		10.6414,4.6154,8.7336	benign	218/309	140147273	1040,10868	1885	4069	5954	SO:0001631	upstream_gene_variant	441476	exon5			TCCCTGCTTCAGG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778		9.37:g.140147273C>T	Exception_encountered	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_001004353	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Missense_Mutation	SNP	ENST00000343053.4	37	CCDS7040.1	331	0.15155677655677655	13	0.026422764227642278	37	0.10220994475138122	184	0.32167832167832167	97	0.1279683377308707	C	9.287	1.049649	0.19827	0.046154	0.106414	ENSG00000197768	ENST00000388931;ENST00000412566	T;T	0.59502	0.26;0.44	3.65	1.63	0.23807	.	1.740450	0.03652	N	0.241159	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	D;D	0.58268	0.982;0.982	P;P	0.54210	0.745;0.745	T	0.04153	-1.0973	9	0.32370	T	0.25	.	8.2084	0.31469	0.4328:0.5672:0.0:0.0	rs61759822	218;218	Q8N7X2-2;Q8N7X2-4	.;.	F	218	ENSP00000373583:L218F;ENSP00000391218:L218F	ENSP00000373583:L218F	L	+	1	0	C9orf173	139267094	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	-1.225000	0.02956	0.274000	0.22072	-0.310000	0.09108	CTT	C|0.847;T|0.153	0.153	strong		0.667	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	
MIA3	375056	hgsc.bcm.edu	37	1	222802376	222802376	+	Missense_Mutation	SNP	A	A	G	rs2936052	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:222802376A>G	ENST00000344922.5	+	4	1839	c.1814A>G	c.(1813-1815)aAa>aGa	p.K605R	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Missense_Mutation_p.K605R|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	605			K -> R (in dbSNP:rs2936052).		chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.K605R(2)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		AATGGGGCCAAACTGCACACG	0.473													A|||	1472	0.29393	0.3222	0.3977	5008	,	,		20855	0.3085		0.168	False		,,,				2504	0.2965				p.K605R		Atlas-SNP	.											MIA3,NS,carcinoma,0,2	MIA3	167	2	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.A1814G						PASS	.	A	ARG/LYS	1151,2895		158,835,1030	89.0	93.0	92.0		1814	-1.2	0.0	1	dbSNP_101	92	1464,6890		135,1194,2848	yes	missense	MIA3	NM_198551.2	26	293,2029,3878	GG,GA,AA		17.5245,28.4478,21.0887	benign	605/1908	222802376	2615,9785	2023	4177	6200	SO:0001583	missense	375056	exon4			GGGCCAAACTGCA		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.1814A>G	1.37:g.222802376A>G	ENSP00000340900:p.Lys605Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	593	0.2715201465201465	166	0.33739837398373984	121	0.3342541436464088	178	0.3111888111888112	128	0.16886543535620052	A	8.754	0.922005	0.17982	0.284478	0.175245	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831	T;T	0.04603	3.59;3.59	4.32	-1.21	0.09524	.	.	.	.	.	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	B;B	0.12630	0.002;0.006	B;B	0.08055	0.003;0.003	T	0.42882	-0.9425	8	0.42905	T	0.14	.	4.7772	0.13185	0.4785:0.2848:0.2367:0.0	rs2936052;rs9441838;rs17163324	605;605	Q5JRA6-2;Q5JRA6	.;MIA3_HUMAN	R	605	ENSP00000340900:K605R;ENSP00000340587:K605R	ENSP00000325973:K605R	K	+	2	0	MIA3	220868999	0.009000	0.17119	0.000000	0.03702	0.017000	0.09413	2.198000	0.42705	-0.458000	0.07023	0.254000	0.18369	AAA	A|0.758;G|0.242	0.242	strong		0.473	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
RFPL2	10739	hgsc.bcm.edu	37	22	32589090	32589090	+	Missense_Mutation	SNP	C	C	T	rs8135276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:32589090C>T	ENST00000400237.1	-	4	1290	c.355G>A	c.(355-357)Gcc>Acc	p.A119T	RFPL2_ENST00000400236.3_Missense_Mutation_p.A29T|RFPL2_ENST00000489846.1_5'UTR|RFPL2_ENST00000248983.4_Missense_Mutation_p.A29T|RFPL2_ENST00000248980.4_Missense_Mutation_p.A58T			O75678	RFPL2_HUMAN	ret finger protein-like 2	119			A -> T (in dbSNP:rs8135276).				zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						AGGCAGACGGCGCATCCACAC	0.527													.|||	565	0.112819	0.1543	0.0793	5008	,	,		18441	0.0625		0.1481	False		,,,				2504	0.0961				p.A119T		Atlas-SNP	.											.	RFPL2	81	.	0			c.G355A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	585,3821	258.9+/-262.7	34,517,1652	100.0	97.0	98.0		355,85,85,172	-1.3	0.0	22	dbSNP_116	98	1265,7335	251.4+/-277.9	77,1111,3112	no	missense,missense,missense,missense	RFPL2	NM_001098527.2,NM_001159545.1,NM_001159546.1,NM_006605.3	58,58,58,58	111,1628,4764	TT,TC,CC		14.7093,13.2773,14.2242	benign,benign,benign,benign	119/379,29/289,29/289,58/318	32589090	1850,11156	2203	4300	6503	SO:0001583	missense	10739	exon4			AGACGGCGCATCC	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"""RING-type (C3HC4) zinc fingers"""	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.355G>A	22.37:g.32589090C>T	ENSP00000383096:p.Ala119Thr	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	285	155	0.54386	NM_001098527		Missense_Mutation	SNP	ENST00000400237.1	37	CCDS43009.2	247	0.1130952380952381	74	0.15040650406504066	31	0.0856353591160221	33	0.057692307692307696	109	0.1437994722955145	C	0.641	-0.813279	0.02798	0.132773	0.147093	ENSG00000128253	ENST00000248980;ENST00000248983;ENST00000400236;ENST00000400237	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	0.636	-1.27	0.09347	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	.	.	.	.	T	0.00039	0.0001	N	0.01824	-0.7	0.80722	P	0.0	B;B	0.23249	0.082;0.001	B;B	0.15052	0.012;0.001	T	0.29518	-1.0009	7	0.02654	T	1	.	.	.	.	rs8135276	119;58	O75678;O75678-3	RFPL2_HUMAN;.	T	58;29;29;119	ENSP00000248980:A58T;ENSP00000248983:A29T;ENSP00000383095:A29T;ENSP00000383096:A119T	ENSP00000248980:A58T	A	-	1	0	RFPL2	30919090	1.000000	0.71417	0.000000	0.03702	0.002000	0.02628	0.757000	0.26433	-1.220000	0.02594	-1.628000	0.00784	GCC	C|0.875;T|0.125	0.125	strong		0.527	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605	
ARSD	414	hgsc.bcm.edu	37	X	2835989	2835989	+	Missense_Mutation	SNP	A	A	C	rs143238998		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2835989A>C	ENST00000381154.1	-	5	794	c.719T>G	c.(718-720)tTt>tGt	p.F240C	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	240					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGAGATGAAAAACAGGCAGCC	0.587													a|||	14	0.00370861	0.0061	0.0	3775	,	,		14194	0.0		0.001	False		,,,				2504	0.0051				p.F240C		Atlas-SNP	.											.	ARSD	47	.	0			c.T719G						PASS	.						32.0	35.0	34.0					X																	2835989		2203	4300	6503	SO:0001583	missense	414	exon5			ATGAAAAACAGGC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.719T>G	X.37:g.2835989A>C	ENSP00000370546:p.Phe240Cys	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	125	47	0.376	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	a	10.61	1.399704	0.25291	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.93763	-3.28	3.36	2.17	0.27698	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.480244	0.20299	U	0.095070	D	0.92041	0.7478	M	0.77103	2.36	0.21697	N	0.999581	B;B	0.20459	0.045;0.045	B;B	0.30105	0.111;0.078	D	0.84817	0.0794	10	0.49607	T	0.09	.	7.7176	0.28712	0.8916:0.0:0.1084:0.0	.	240;240	E9PAW5;P51689	.;ARSD_HUMAN	C	240	ENSP00000370546:F240C	ENSP00000217890:F240C	F	-	2	0	ARSD	2845989	0.512000	0.26186	0.000000	0.03702	0.078000	0.17371	1.565000	0.36386	0.176000	0.19873	0.233000	0.17823	TTT	.	.	weak		0.587	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
BUB1B	701	hgsc.bcm.edu	37	15	40488851	40488851	+	Silent	SNP	G	G	A	rs1047130	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40488851G>A	ENST00000287598.6	+	9	1359	c.1164G>A	c.(1162-1164)gcG>gcA	p.A388A	BUB1B_ENST00000412359.3_Silent_p.A402A	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	388					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		ATCAGCAAGCGTCTGAGGAGA	0.428			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				G|||	955	0.190695	0.0182	0.3242	5008	,	,		18833	0.1627		0.327	False		,,,				2504	0.2178				p.A388A		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.G1164A						PASS	.	G		315,4091	168.0+/-198.9	12,291,1900	103.0	104.0	103.0		1164	-2.8	0.4	15	dbSNP_86	103	2630,5970	424.6+/-354.7	409,1812,2079	no	coding-synonymous	BUB1B	NM_001211.5		421,2103,3979	AA,AG,GG		30.5814,7.1493,22.6434		388/1051	40488851	2945,10061	2203	4300	6503	SO:0001819	synonymous_variant	701	exon9	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GCAAGCGTCTGAG	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.1164G>A	15.37:g.40488851G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			G|0.793;A|0.207	0.207	strong		0.428	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
COL4A5	1287	hgsc.bcm.edu	37	X	107867476	107867476	+	Silent	SNP	A	A	T	rs104886373		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:107867476A>T	ENST00000361603.2	+	34	3172	c.2928A>T	c.(2926-2928)ggA>ggT	p.G976G	COL4A5_ENST00000328300.6_Silent_p.G976G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	976	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GTATACCTGGAGTTTCAGGGC	0.448									Alport syndrome with Diffuse Leiomyomatosis																												p.G976G		Atlas-SNP	.											.	COL4A5	262	.	0			c.A2928T						PASS	.						103.0	82.0	89.0					X																	107867476		2203	4300	6503	SO:0001819	synonymous_variant	1287	exon34	Familial Cancer Database		ACCTGGAGTTTCA	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.2928A>T	X.37:g.107867476A>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	44	16	0.363636	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	A	3.794	-0.043138	0.07452	.	.	ENSG00000188153	ENST00000505728	.	.	.	5.5	2.99	0.34606	.	.	.	.	.	T	0.45716	0.1356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34354	-0.9832	4	.	.	.	.	2.442	0.04497	0.5622:0.1178:0.0786:0.2414	.	.	.	.	V	54	.	.	E	+	2	0	COL4A5	107754132	0.702000	0.27816	0.732000	0.30844	0.498000	0.33706	1.305000	0.33493	0.715000	0.32103	0.441000	0.28932	GAG	.	.	none		0.448	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		
NLRC5	84166	hgsc.bcm.edu	37	16	57080528	57080528	+	Missense_Mutation	SNP	C	C	A	rs289723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:57080528C>A	ENST00000262510.6	+	22	3538	c.3313C>A	c.(3313-3315)Cag>Aag	p.Q1105K	NLRC5_ENST00000539144.1_Missense_Mutation_p.Q1105K|NLRC5_ENST00000436936.1_Missense_Mutation_p.Q1105K|NLRC5_ENST00000308149.7_Missense_Mutation_p.Q1105K	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1105			Q -> K (in dbSNP:rs289723). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AGGGTTCCGTCAGCGCTGCAT	0.557													C|||	843	0.168331	0.034	0.2911	5008	,	,		15508	0.1081		0.2455	False		,,,				2504	0.2454				p.Q1105K		Atlas-SNP	.											.	NLRC5	186	.	0			c.C3313A						PASS	.	C	LYS/GLN	355,4041	182.2+/-210.1	8,339,1851	93.0	83.0	86.0		3313	1.5	0.0	16	dbSNP_79	86	2499,6101	411.7+/-350.6	368,1763,2169	yes	missense	NLRC5	NM_032206.3	53	376,2102,4020	AA,AC,CC		29.0581,8.0755,21.9606	benign	1105/1867	57080528	2854,10142	2198	4300	6498	SO:0001583	missense	84166	exon21			TTCCGTCAGCGCT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.3313C>A	16.37:g.57080528C>A	ENSP00000262510:p.Gln1105Lys	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	195	106	0.54359	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	389|389	0.17811355311355312|0.17811355311355312	20|20	0.04065040650406504|0.04065040650406504	104|104	0.287292817679558|0.287292817679558	74|74	0.12937062937062938|0.12937062937062938	191|191	0.2519788918205805|0.2519788918205805	C|C	5.154|5.154	0.213957|0.213957	0.09810|0.09810	0.080755|0.080755	0.290581|0.290581	ENSG00000140853|ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144|ENST00000538805	T;T;T;T|.	0.72942|.	-0.51;-0.53;-0.7;-0.53|.	3.55|3.55	1.52|1.52	0.23074|0.23074	.|.	1.238210|.	0.06245|.	N|.	0.691069|.	T|.	0.00012|.	0.0000|.	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.18013|.	0.017;0.017;0.025|.	B;B;B|.	0.15484|.	0.004;0.009;0.013|.	T|.	0.15607|.	-1.0431|.	9|.	0.02654|.	T|.	1|.	.|.	5.0579|5.0579	0.14542|0.14542	0.0:0.6681:0.2131:0.1188|0.0:0.6681:0.2131:0.1188	rs289723;rs59401549;rs289723|rs289723;rs59401549;rs289723	790;1105;1105|.	Q9H6Y0;Q86WI3-6;Q86WI3|.	.;.;NLRC5_HUMAN|.	K|X	1105|857	ENSP00000262510:Q1105K;ENSP00000308886:Q1105K;ENSP00000389739:Q1105K;ENSP00000441727:Q1105K|.	ENSP00000262510:Q1105K|.	Q|S	+|+	1|2	0|0	NLRC5|NLRC5	55638029|55638029	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	0.665000|0.665000	0.25083|0.25083	0.475000|0.475000	0.27415|0.27415	-0.254000|-0.254000	0.11334|0.11334	CAG|TCA	T|0.002;G|0.001	.	strong		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
ADAMTS10	81794	hgsc.bcm.edu	37	19	8651562	8651562	+	Silent	SNP	A	A	G	rs4476282	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8651562A>G	ENST00000597188.1	-	20	2553	c.2283T>C	c.(2281-2283)ccT>ccC	p.P761P	ADAMTS10_ENST00000270328.4_Silent_p.P761P|ADAMTS10_ENST00000595838.1_Silent_p.P248P	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	761	Spacer.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						GGGGGGTCCCAGGCAGCCCCT	0.642											OREG0025221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	925	0.184704	0.2322	0.2061	5008	,	,		14798	0.125		0.2097	False		,,,				2504	0.1411				p.P761P		Atlas-SNP	.											ADAMTS10,NS,carcinoma,0,2	ADAMTS10	132	2	0			c.T2283C						PASS	.	G		962,3444	699.5+/-406.5	101,760,1342	45.0	53.0	51.0		2283	-9.9	0.5	19	dbSNP_111	51	1864,6736	706.5+/-405.5	201,1462,2637	no	coding-synonymous	ADAMTS10	NM_030957.2		302,2222,3979	GG,GA,AA		21.6744,21.8339,21.7284		761/1104	8651562	2826,10180	2203	4300	6503	SO:0001819	synonymous_variant	81794	exon20			GGTCCCAGGCAGC	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13201	protein-coding gene	gene with protein product		608990	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"""				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.2283T>C	19.37:g.8651562A>G		Somatic	109	0	0	81	WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_030957	M0QZE4	Silent	SNP	ENST00000597188.1	37	CCDS12206.1																																																																																			A|0.790;G|0.210	0.210	strong		0.642	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957	
CYP26B1	56603	hgsc.bcm.edu	37	2	72361960	72361960	+	Missense_Mutation	SNP	A	A	G	rs2241057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:72361960A>G	ENST00000001146.2	-	4	994	c.791T>C	c.(790-792)tTg>tCg	p.L264S	CYP26B1_ENST00000412253.1_Missense_Mutation_p.L73S|CYP26B1_ENST00000546307.1_Missense_Mutation_p.L189S	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	264			L -> S (in dbSNP:rs2241057). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						CAGGGCGTCCAAGTAGTCCTT	0.632													G|||	864	0.172524	0.2897	0.2104	5008	,	,		19841	0.0754		0.165	False		,,,				2504	0.0951				p.L264S		Atlas-SNP	.											.	CYP26B1	73	.	0			c.T791C						PASS	.	G	SER/LEU	1242,3164	704.3+/-407.1	194,854,1155	168.0	133.0	145.0		791	3.3	0.2	2	dbSNP_98	145	1321,7279	757.4+/-407.5	98,1125,3077	yes	missense	CYP26B1	NM_019885.2	145	292,1979,4232	GG,GA,AA		15.3605,28.1888,19.7063	benign	264/513	72361960	2563,10443	2203	4300	6503	SO:0001583	missense	56603	exon4			GCGTCCAAGTAGT		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"""Cytochrome P450s"""	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.791T>C	2.37:g.72361960A>G	ENSP00000001146:p.Leu264Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	171	77	0.450292	NM_019885	B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Missense_Mutation	SNP	ENST00000001146.2	37	CCDS1919.1	378	0.17307692307692307	144	0.2926829268292683	68	0.1878453038674033	44	0.07692307692307693	122	0.16094986807387862	G	6.725	0.502526	0.12822	0.281888	0.153605	ENSG00000003137	ENST00000001146;ENST00000412253;ENST00000546307	T;T;T	0.68903	-0.36;-0.36;-0.36	5.11	3.32	0.38043	.	0.349370	0.30686	N	0.009087	T	0.00012	0.0000	N	0.03608	-0.345	0.54753	P	1.2000000000012001E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.14309	-1.0477	9	0.10902	T	0.67	-6.5183	9.699	0.40175	0.2294:0.0:0.7706:0.0	rs2241057;rs58208933;rs2241057	189;247;264	B7Z2K6;B7Z2P4;Q9NR63	.;.;CP26B_HUMAN	S	264;73;189	ENSP00000001146:L264S;ENSP00000401465:L73S;ENSP00000443304:L189S	ENSP00000001146:L264S	L	-	2	0	CYP26B1	72215468	0.059000	0.20769	0.221000	0.23827	0.957000	0.61999	2.483000	0.45233	0.295000	0.22570	-0.119000	0.15052	TTG	A|0.814;G|0.186	0.186	strong		0.632	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885	
RNF25	64320	hgsc.bcm.edu	37	2	219529881	219529881	+	Silent	SNP	G	G	A	rs2303564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219529881G>A	ENST00000295704.2	-	8	1103	c.663C>T	c.(661-663)ccC>ccT	p.P221P		NM_022453.2	NP_071898.2	Q96BH1	RNF25_HUMAN	ring finger protein 25	221					positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|NF-kappaB binding (GO:0051059)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCTTACCATGGGCTGTTGGG	0.468													G|||	371	0.0740815	0.1233	0.0216	5008	,	,		20459	0.1171		0.0219	False		,,,				2504	0.0542				p.P221P		Atlas-SNP	.											.	RNF25	40	.	0			c.C663T						PASS	.	G		441,3965	213.8+/-233.3	25,391,1787	88.0	81.0	84.0		663	1.2	1.0	2	dbSNP_100	84	282,8318	106.0+/-166.9	5,272,4023	no	coding-synonymous	RNF25	NM_022453.2		30,663,5810	AA,AG,GG		3.2791,10.0091,5.559		221/460	219529881	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	64320	exon8			TACCATGGGCTGT		CCDS2420.1	2q35	2008-02-05			ENSG00000163481	ENSG00000163481		"""RING-type (C3HC4) zinc fingers"""	14662	protein-coding gene	gene with protein product						12748188	Standard	NM_022453		Approved	AO7, FLJ13906	uc002vit.3	Q96BH1	OTTHUMG00000133077	ENST00000295704.2:c.663C>T	2.37:g.219529881G>A		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	284	147	0.517606	NM_022453	A8K0D6|Q53HQ5|Q9H874	Silent	SNP	ENST00000295704.2	37	CCDS2420.1																																																																																			G|0.936;A|0.064	0.064	strong		0.468	RNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256721.1	NM_022453	
FYCO1	79443	hgsc.bcm.edu	37	3	46010007	46010007	+	Silent	SNP	T	T	C	rs13071283	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46010007T>C	ENST00000296137.2	-	8	1024	c.819A>G	c.(817-819)caA>caG	p.Q273Q	FYCO1_ENST00000535325.1_Silent_p.Q273Q	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	273					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CTGTCTGCAGTTGCTCCCCTT	0.627													T|||	551	0.110024	0.0197	0.0634	5008	,	,		19918	0.004		0.1243	False		,,,				2504	0.3599				p.Q273Q		Atlas-SNP	.											.	FYCO1	115	.	0			c.A819G						PASS	.	T		138,4268	98.5+/-137.1	1,136,2066	94.0	82.0	86.0		819	0.5	1.0	3	dbSNP_121	86	963,7637	210.5+/-251.4	51,861,3388	no	coding-synonymous	FYCO1	NM_024513.2		52,997,5454	CC,CT,TT		11.1977,3.1321,8.4653		273/1479	46010007	1101,11905	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			CTGCAGTTGCTCC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.819A>G	3.37:g.46010007T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			T|0.917;C|0.083	0.083	strong		0.627	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
PSG11	5680	hgsc.bcm.edu	37	19	43523026	43523026	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:43523026A>G	ENST00000401740.1	-	3	708	c.605T>C	c.(604-606)cTc>cCc	p.L202P	PSG11_ENST00000320078.7_Missense_Mutation_p.L202P|PSG11_ENST00000403486.1_Missense_Mutation_p.L80P|PSG11_ENST00000306322.7_Missense_Mutation_p.L80P|PSG11_ENST00000595312.1_5'UTR			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	202	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				AAATAGAAAGAGGGTCCTGTT	0.502																																					p.L202P		Atlas-SNP	.											PSG11,NS,carcinoma,+1,1	PSG11	57	1	0			c.T605C						scavenged	.						253.0	263.0	260.0					19																	43523026		2200	4298	6498	SO:0001583	missense	5680	exon3			AGAAAGAGGGTCC	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.605T>C	19.37:g.43523026A>G	ENSP00000384995:p.Leu202Pro	Somatic	295	2	0.00677966		WXS	Illumina HiSeq	Phase_I	269	5	0.0185874	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	a	10.38	1.335180	0.24253	.	.	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.01379	4.96;4.96;4.96;4.96	1.13	1.13	0.20643	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10637	0.0260	H	0.96301	3.8	0.20403	N	0.999904	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.08371	-1.0725	9	0.87932	D	0	.	4.3746	0.11263	1.0:0.0:0.0:0.0	.	80;202	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	P	202;80;80;202	ENSP00000319140:L202P;ENSP00000385427:L80P;ENSP00000304913:L80P;ENSP00000384995:L202P	ENSP00000304913:L80P	L	-	2	0	PSG11	48214866	0.977000	0.34250	0.046000	0.18839	0.014000	0.08584	2.091000	0.41691	0.477000	0.27464	0.155000	0.16302	CTC	.	.	none		0.502	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859817	144859817	+	Silent	SNP	G	G	A	rs587702923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859817G>A	ENST00000369354.3	-	38	6456	c.6267C>T	c.(6265-6267)tcC>tcT	p.S2089S	PDE4DIP_ENST00000313382.9_Silent_p.S1983S|PDE4DIP_ENST00000369356.4_Silent_p.S2089S|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Silent_p.S2174S|PDE4DIP_ENST00000369359.4_Silent_p.S2225S|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2089					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCTGGTTAATGGAGGAGGGGC	0.582			T	PDGFRB	MPD																																p.S2089S		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6267T						PASS	.						65.0	62.0	63.0					1																	144859817		2203	4300	6503	SO:0001819	synonymous_variant	9659	exon38			GTTAATGGAGGAG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6267C>T	1.37:g.144859817G>A		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	402	26	0.0646766	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			.	.	none		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SPAG16	79582	hgsc.bcm.edu	37	2	214727221	214727221	+	Missense_Mutation	SNP	A	A	C	rs2042791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:214727221A>C	ENST00000331683.5	+	11	1178	c.1083A>C	c.(1081-1083)caA>caC	p.Q361H	SPAG16_ENST00000374309.3_Missense_Mutation_p.Q267H	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	361			Q -> H (in dbSNP:rs2042791). {ECO:0000269|PubMed:11867345}.		cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.Q361H(1)		endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TCTCCATGCAACCCCACAAAG	0.463													C|||	1924	0.384185	0.205	0.4006	5008	,	,		21486	0.501		0.3688	False		,,,				2504	0.5102				p.Q361H		Atlas-SNP	.											SPAG16,NS,carcinoma,0,1	SPAG16	134	1	1	Substitution - Missense(1)	stomach(1)	c.A1083C						scavenged	.	C	HIS/GLN	1008,3398	729.1+/-410.0	117,774,1312	125.0	112.0	116.0		1083	-1.4	0.9	2	dbSNP_94	116	3250,5350	648.1+/-400.5	623,2004,1673	yes	missense	SPAG16	NM_024532.3	24	740,2778,2985	CC,CA,AA		37.7907,22.8779,32.7387	benign	361/632	214727221	4258,8748	2203	4300	6503	SO:0001583	missense	79582	exon11			CATGCAACCCCAC	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1083A>C	2.37:g.214727221A>C	ENSP00000332592:p.Gln361His	Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	165	84	0.509091	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	824	0.3772893772893773	109	0.22154471544715448	133	0.3674033149171271	294	0.513986013986014	288	0.37994722955145116	C	0.007	-1.962849	0.00461	0.228779	0.377907	ENSG00000144451	ENST00000331683;ENST00000374309;ENST00000451561	T;T;T	0.57907	0.37;0.37;0.37	5.74	-1.4	0.08968	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.227351	0.31233	N	0.008011	T	0.00012	0.0000	N	0.00170	-1.935	0.58432	P	2.9999999999752447E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.47995	-0.9073	9	0.23302	T	0.38	.	7.967	0.30104	0.1068:0.3532:0.0:0.5401	rs2042791;rs52830989;rs60027582;rs2042791	267;212;361	B4DYB5;Q8N0X2-2;Q8N0X2	.;.;SPG16_HUMAN	H	361;267;47	ENSP00000332592:Q361H;ENSP00000363428:Q267H;ENSP00000416600:Q47H	ENSP00000332592:Q361H	Q	+	3	2	SPAG16	214435466	0.352000	0.24895	0.906000	0.35671	0.004000	0.04260	-0.692000	0.05127	-0.330000	0.08514	-0.756000	0.03474	CAA	A|0.653;C|0.347	0.347	strong		0.463	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
ACTR3C	653857	hgsc.bcm.edu	37	7	149981856	149981856	+	Missense_Mutation	SNP	G	G	A	rs117425825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149981856G>A	ENST00000539352.1	-	6	801	c.550C>T	c.(550-552)Cgt>Tgt	p.R184C	ACTR3C_ENST00000252071.4_Missense_Mutation_p.R184C	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	184						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)										TACAGCGGACGCCGCACATCG	0.403													G|||	105	0.0209665	0.003	0.0187	5008	,	,		13887	0.0		0.0457	False		,,,				2504	0.0429				p.R184C		Atlas-SNP	.											.	.	.	.	0			c.C550T						PASS	.	G	CYS/ARG,CYS/ARG	13,1371		0,13,679	85.0	73.0	77.0		550,550	2.2	0.9	7	dbSNP_132	77	125,3057		1,123,1467	yes	missense,missense	ACTR3C	NM_001164458.1,NM_001164459.1	180,180	1,136,2146	AA,AG,GG		3.9283,0.9393,3.0223	probably-damaging,probably-damaging	184/211,184/211	149981856	138,4428	692	1591	2283	SO:0001583	missense	653857	exon6			GCGGACGCCGCAC		CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.550C>T	7.37:g.149981856G>A	ENSP00000440990:p.Arg184Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_001164459	Q5CZI4	Missense_Mutation	SNP	ENST00000539352.1	37	CCDS47744.1	43	0.019688644688644688	0	0.0	10	0.027624309392265192	1	0.0017482517482517483	32	0.04221635883905013	G	13.83	2.352944	0.41700	0.009393	0.039283	ENSG00000106526	ENST00000478393;ENST00000252071;ENST00000539352	T;T;T	0.09350	2.99;2.99;2.99	2.16	2.16	0.27623	.	0.221425	0.28151	N	0.016416	T	0.14141	0.0342	H	0.97587	4.035	0.39214	D	0.963377	D	0.89917	1.0	D	0.68943	0.961	T	0.52961	-0.8505	9	.	.	.	.	10.4552	0.44546	0.0:0.0:1.0:0.0	.	184	Q9C0K3	ARP3C_HUMAN	C	182;184;184	ENSP00000417426:R182C;ENSP00000252071:R184C;ENSP00000440990:R184C	.	R	-	1	0	ACTR3C	149612789	1.000000	0.71417	0.896000	0.35187	0.654000	0.38779	4.696000	0.61774	1.511000	0.48818	0.398000	0.26397	CGT	G|0.976;A|0.024	0.024	strong		0.403	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2		
MUC2	4583	hgsc.bcm.edu	37	11	1092971	1092971	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1092971C>T	ENST00000441003.2	+	30	4817	c.4790C>T	c.(4789-4791)aCa>aTa	p.T1597I	MUC2_ENST00000359061.5_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaaccccaacacccaccggc	0.632																																					p.T1597I		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.C4790T						scavenged	.						47.0	82.0	70.0					11																	1092971		1782	3233	5015	SO:0001583	missense	4583	exon30			CCCCAACACCCAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4790C>T	11.37:g.1092971C>T	ENSP00000415183:p.Thr1597Ile	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	121	6	0.0495868	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.395	-0.338980	0.05243	.	.	ENSG00000198788	ENST00000441003	T	0.14640	2.49	1.75	0.762	0.18454	.	.	.	.	.	T	0.07143	0.0181	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.41520	-0.9504	8	0.22109	T	0.4	.	4.3366	0.11089	0.0:0.6142:0.0:0.3858	.	1597	E7EUV1	.	I	1597	ENSP00000415183:T1597I	ENSP00000415183:T1597I	T	+	2	0	MUC2	1082971	0.029000	0.19370	0.001000	0.08648	0.134000	0.20937	1.107000	0.31110	0.104000	0.17725	0.121000	0.15741	ACA	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SPP2	6694	hgsc.bcm.edu	37	2	234959642	234959642	+	Missense_Mutation	SNP	C	C	T	rs34347825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234959642C>T	ENST00000168148.3	+	2	201	c.113C>T	c.(112-114)tCc>tTc	p.S38F	SPP2_ENST00000373368.1_Missense_Mutation_p.S38F|SPP2_ENST00000492481.1_3'UTR	NM_006944.2	NP_008875.1	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa	38			S -> F (in dbSNP:rs34347825). {ECO:0000269|PubMed:15062857}.		bone remodeling (GO:0046849)|negative regulation of endopeptidase activity (GO:0010951)|protein complex assembly (GO:0006461)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	endopeptidase inhibitor activity (GO:0004866)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)		TACGATCCATCCTCCTTAAGG	0.512													C|||	17	0.00339457	0.0	0.0144	5008	,	,		19633	0.0		0.007	False		,,,				2504	0.0				p.S38F		Atlas-SNP	.											.	SPP2	35	.	0			c.C113T						PASS	.	C	PHE/SER	7,4399	12.9+/-30.5	0,7,2196	141.0	118.0	126.0		113	4.4	0.1	2	dbSNP_126	126	64,8536	38.8+/-94.9	0,64,4236	yes	missense	SPP2	NM_006944.2	155	0,71,6432	TT,TC,CC		0.7442,0.1589,0.5459	possibly-damaging	38/212	234959642	71,12935	2203	4300	6503	SO:0001583	missense	6694	exon2			ATCCATCCTCCTT		CCDS2511.1	2q37.1	2012-08-14	2002-08-29		ENSG00000072080	ENSG00000072080			11256	protein-coding gene	gene with protein product		602637	"""secreted phosphoprotein 2, 24kD"""			9533032	Standard	XM_005246102		Approved	SPP24	uc002vvk.1	Q13103	OTTHUMG00000059208	ENST00000168148.3:c.113C>T	2.37:g.234959642C>T	ENSP00000168148:p.Ser38Phe	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	184	91	0.494565	NM_006944	A4QMV3|Q3B892|Q546M5	Missense_Mutation	SNP	ENST00000168148.3	37	CCDS2511.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	12.60	1.987057	0.35036	0.001589	0.007442	ENSG00000072080	ENST00000373368;ENST00000168148	T;T	0.50001	0.76;0.76	5.38	4.45	0.53987	.	1.384140	0.04525	N	0.385354	T	0.51568	0.1682	L	0.51422	1.61	0.09310	N	1	D	0.62365	0.991	P	0.55161	0.77	T	0.48163	-0.9059	10	0.66056	D	0.02	-4.2781	11.2458	0.48996	0.0:0.8155:0.1844:0.0	rs34347825;rs34347825	38	Q13103	SPP24_HUMAN	F	38	ENSP00000362466:S38F;ENSP00000168148:S38F	ENSP00000168148:S38F	S	+	2	0	SPP2	234624381	0.002000	0.14202	0.140000	0.22221	0.020000	0.10135	1.445000	0.35079	2.528000	0.85240	0.650000	0.86243	TCC	C|0.995;T|0.005	0.005	strong		0.512	SPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131313.3	NM_006944	
CORO7	79585	hgsc.bcm.edu	37	16	4445327	4445327	+	Missense_Mutation	SNP	C	C	T	rs3747579	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4445327C>T	ENST00000251166.4	-	7	723	c.578G>A	c.(577-579)cGg>cAg	p.R193Q	CORO7_ENST00000574025.1_Missense_Mutation_p.R108Q|CORO7_ENST00000423908.2_Missense_Mutation_p.R25Q|CORO7-PAM16_ENST00000572467.1_Missense_Mutation_p.R193Q|CORO7_ENST00000537233.2_Missense_Mutation_p.R175Q|CORO7_ENST00000539968.1_5'UTR	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	193			R -> Q (in dbSNP:rs3747579). {ECO:0000269|PubMed:14702039}.		actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						GTCAAAGATCCGCAGCTGCTT	0.607													C|||	2541	0.507388	0.1172	0.5836	5008	,	,		18193	0.7817		0.7097	False		,,,				2504	0.4898				p.R193Q		Atlas-SNP	.											CORO7,NS,carcinoma,0,1	CORO7	73	1	0			c.G578A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	961,3433	363.1+/-316.4	113,735,1349	72.0	73.0	73.0		524,323,578,578	4.2	1.0	16	dbSNP_107	73	6154,2446	697.8+/-405.0	2222,1710,368	yes	missense,missense,missense,missense	CORO7,CORO7-PAM16	NM_001201472.1,NM_001201473.1,NM_001201479.1,NM_024535.4	43,43,43,43	2335,2445,1717	TT,TC,CC		28.4419,21.8707,45.244	probably-damaging,probably-damaging,probably-damaging,probably-damaging	175/908,108/841,193/1049,193/926	4445327	7115,5879	2197	4300	6497	SO:0001583	missense	79585	exon7			AAGATCCGCAGCT	AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"""Coronins"", ""WD repeat domain containing"""	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.578G>A	16.37:g.4445327C>T	ENSP00000251166:p.Arg193Gln	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_024535	B4DFD6|B4DL18|I3L416|Q17RK4	Missense_Mutation	SNP	ENST00000251166.4	37	CCDS10513.1	1296	0.5934065934065934	59	0.11991869918699187	216	0.5966850828729282	471	0.8234265734265734	550	0.7255936675461742	C	17.84	3.487498	0.63962	0.218707	0.715581	ENSG00000103426	ENST00000251166;ENST00000537233;ENST00000423908	T;T	0.67865	-0.29;4.88	4.17	4.17	0.49024	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.422202	0.23997	N	0.042517	T	0.00012	0.0000	M	0.85373	2.75	0.27201	P	0.9601589	P;D	0.71674	0.855;0.998	B;D	0.76575	0.11;0.988	T	0.38178	-0.9673	9	0.59425	D	0.04	-26.2535	11.8635	0.52480	0.0:1.0:0.0:0.0	rs3747579;rs52808084;rs56564879;rs57253852;rs3747579	108;193	P57737-2;P57737	.;CORO7_HUMAN	Q	193;108;25	ENSP00000251166:R193Q;ENSP00000391530:R25Q	ENSP00000251166:R193Q	R	-	2	0	CORO7	4385328	0.120000	0.22244	0.993000	0.49108	0.986000	0.74619	1.096000	0.30976	2.135000	0.66039	0.563000	0.77884	CGG	C|0.451;T|0.549	0.549	strong		0.607	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535	
BRCA1	672	hgsc.bcm.edu	37	17	41244000	41244000	+	Missense_Mutation	SNP	T	T	C	rs80357956|rs16942	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41244000T>C	ENST00000357654.3	-	10	3666	c.3548A>G	c.(3547-3549)aAa>aGa	p.K1183R	BRCA1_ENST00000354071.3_Missense_Mutation_p.K1183R|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.K887R|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.K1136R|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.K1183R|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.K1183R|BRCA1_ENST00000468300.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1183			K -> R (common polymorphism; dbSNP:rs16942). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:14722926, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7894493, ECO:0000269|Ref.6}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K1183fs*4(1)|p.K1183R(1)		NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		AAGCTCTCCTTTCTGGACGCT	0.428			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			C|||	1766	0.352636	0.2179	0.3746	5008	,	,		20679	0.371		0.3549	False		,,,				2504	0.498				p.K1183R		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,NS,carcinoma,0,1	BRCA1	304	1	2	Substitution - Missense(1)|Deletion - Frameshift(1)	stomach(1)|endometrium(1)	c.A3548G						PASS	.	C	ARG/LYS,ARG/LYS,,,ARG/LYS	1050,3356	721.5+/-409.2	114,822,1267	80.0	74.0	76.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3548,3407,,,3548	-2.3	0.0	17	dbSNP_60	76	2790,5810	673.5+/-403.0	441,1908,1951	yes	missense,missense,intron,intron,missense	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	26,26,,,26	555,2730,3218	CC,CT,TT		32.4419,23.8311,29.5248	benign,benign,,,benign	1183/1864,1136/1817,,,1183/1885	41244000	3840,9166	2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		TCTCCTTTCTGGA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.3548A>G	17.37:g.41244000T>C	ENSP00000350283:p.Lys1183Arg	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	708	0.3241758241758242	106	0.21544715447154472	143	0.39502762430939226	189	0.3304195804195804	270	0.3562005277044855	C	0.004	-2.282426	0.00251	0.238311	0.324419	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35;-0.35	5.31	-2.35	0.06684	.	0.543999	0.18098	N	0.151790	T	0.00012	0.0000	N	0.00972	-1.085	0.80722	P	0.0	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.0;0.0;0.001;0.002;0.001;0.002	T	0.21586	-1.0241	9	0.02654	T	1	.	7.8272	0.29322	0.1183:0.2486:0.0:0.6331	rs16942;rs17672119;rs52827882;rs59688547;rs16942	1183;1142;1183;1183;1183;1183	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	R	1183;1183;1183;1183;887;1183;1136	ENSP00000350283:K1183R;ENSP00000326002:K1183R;ENSP00000246907:K1183R;ENSP00000310938:K887R;ENSP00000418960:K1183R;ENSP00000418775:K1136R	ENSP00000310938:K887R	K	-	2	0	BRCA1	38497526	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.365000	0.07573	-0.437000	0.07243	-0.726000	0.03593	AAA	T|0.695;C|0.305	0.305	strong		0.428	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
ZBBX	79740	hgsc.bcm.edu	37	3	167023573	167023573	+	Missense_Mutation	SNP	C	C	T	rs140166106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167023573C>T	ENST00000392766.2	-	17	1923	c.1583G>A	c.(1582-1584)aGc>aAc	p.S528N	ZBBX_ENST00000307529.5_Missense_Mutation_p.S528N|ZBBX_ENST00000392764.1_Missense_Mutation_p.S499N|ZBBX_ENST00000455345.2_Missense_Mutation_p.S528N|ZBBX_ENST00000392767.2_Missense_Mutation_p.S528N	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	528						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						AGTGTCCTTGCTTTCAAGTGA	0.338													C|||	36	0.0071885	0.0015	0.0029	5008	,	,		14470	0.001		0.0189	False		,,,				2504	0.0123				p.S528N		Atlas-SNP	.											.	ZBBX	299	.	0			c.G1583A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	9,3615		0,9,1803	74.0	64.0	67.0		1583,1496,1583	-0.1	0.0	3	dbSNP_134	67	160,7990		0,160,3915	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	46,46,46	0,169,5718	TT,TC,CC		1.9632,0.2483,1.4354	benign,benign,benign	528/840,499/772,528/801	167023573	169,11605	1812	4075	5887	SO:0001583	missense	79740	exon17			TCCTTGCTTTCAA	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1583G>A	3.37:g.167023573C>T	ENSP00000376519:p.Ser528Asn	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	299	158	0.528428	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	16	0.007326007326007326	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	0.841	-0.741910	0.03088	0.002483	0.019632	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.11169	2.97;2.97;2.97;2.97;2.8	5.0	-0.114	0.13564	.	0.723811	0.14467	N	0.317853	T	0.04003	0.0112	L	0.53249	1.67	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.11329	0.006;0.0	T	0.36601	-0.9741	10	0.23302	T	0.38	0.5835	4.5456	0.12079	0.1438:0.5214:0.0:0.3348	.	528;528	A8MT70-2;A8MT70	.;ZBBX_HUMAN	N	528;528;528;528;499	ENSP00000376519:S528N;ENSP00000376520:S528N;ENSP00000390232:S528N;ENSP00000305065:S528N;ENSP00000376517:S499N	ENSP00000305065:S528N	S	-	2	0	ZBBX	168506267	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.791000	0.04599	-0.141000	0.11374	-0.766000	0.03442	AGC	C|0.989;T|0.011	0.011	strong		0.338	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
C12orf54	121273	hgsc.bcm.edu	37	12	48888594	48888594	+	Missense_Mutation	SNP	C	C	T	rs11458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48888594C>T	ENST00000548364.1	+	7	313	c.256C>T	c.(256-258)Cca>Tca	p.P86S	RP11-722P11.4_ENST00000551847.1_RNA|C12orf54_ENST00000314014.2_Missense_Mutation_p.P86S			Q6X4T0	CL054_HUMAN	chromosome 12 open reading frame 54	86			P -> S (in dbSNP:rs11458). {ECO:0000269|Ref.1}.							endometrium(1)|large_intestine(4)	5						CATAAGGCCTCCAGATTCCTT	0.493													C|||	1137	0.227037	0.0371	0.2594	5008	,	,		20088	0.1478		0.4394	False		,,,				2504	0.3241				p.P86S		Atlas-SNP	.											.	C12orf54	11	.	0			c.C256T						PASS	.		SER/PRO	454,3952	216.1+/-234.9	27,400,1776	115.0	117.0	116.0		256	1.7	0.1	12	dbSNP_52	116	3966,4634	552.2+/-386.1	902,2162,1236	yes	missense	C12orf54	NM_152319.3	74	929,2562,3012	TT,TC,CC		46.1163,10.3041,33.9843	benign	86/128	48888594	4420,8586	2203	4300	6503	SO:0001583	missense	121273	exon8			AGGCCTCCAGATT	BC031670	CCDS8764.1	12q13.11	2011-01-31			ENSG00000177627	ENSG00000177627			28553	protein-coding gene	gene with protein product						12477932	Standard	NM_152319		Approved	MGC35033	uc001rrr.3	Q6X4T0	OTTHUMG00000170019	ENST00000548364.1:c.256C>T	12.37:g.48888594C>T	ENSP00000447109:p.Pro86Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_152319	Q6X4S9|Q8N5S2	Missense_Mutation	SNP	ENST00000548364.1	37	CCDS8764.1	594	0.27197802197802196	32	0.06504065040650407	106	0.292817679558011	103	0.18006993006993008	353	0.4656992084432718	C	10.88	1.475188	0.26511	0.103041	0.461163	ENSG00000177627	ENST00000314014;ENST00000548364	T;T	0.61627	0.09;0.09	4.74	1.73	0.24493	.	0.537306	0.15751	N	0.246416	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.21753	0.06	B	0.20184	0.028	T	0.47222	-0.9134	9	0.14252	T	0.57	-2.5036	6.3094	0.21156	0.0:0.6587:0.0:0.3413	rs11458;rs1132190;rs3192741;rs7131975;rs17342728;rs17350393;rs17827594;rs52790501;rs58721339;rs11458	86	Q6X4T0	CL054_HUMAN	S	86	ENSP00000316898:P86S;ENSP00000447109:P86S	ENSP00000316898:P86S	P	+	1	0	C12orf54	47174861	0.725000	0.28048	0.122000	0.21767	0.020000	0.10135	0.025000	0.13577	0.236000	0.21180	0.651000	0.88453	CCA	C|0.697;T|0.303	0.303	strong		0.493	C12orf54-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406875.1	NM_152319	
CPA4	51200	hgsc.bcm.edu	37	7	129950740	129950740	+	Missense_Mutation	SNP	G	G	T	rs2171492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:129950740G>T	ENST00000222482.4	+	9	935	c.907G>T	c.(907-909)Ggc>Tgc	p.G303C	CPA4_ENST00000493259.1_Missense_Mutation_p.G199C|CPA4_ENST00000445470.2_Missense_Mutation_p.G270C	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	303			G -> C (in dbSNP:rs2171492).		histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					GAATTTCAAGGGCTTCATCGA	0.512													T|||	1586	0.316693	0.2065	0.3156	5008	,	,		20193	0.374		0.3638	False		,,,				2504	0.3589				p.G303C		Atlas-SNP	.											.	CPA4	47	.	0			c.G907T						PASS	.	T	CYS/GLY,CYS/GLY	1003,3403	730.5+/-410.2	123,757,1323	148.0	142.0	144.0		808,907	0.5	1.0	7	dbSNP_96	144	3310,5290	645.2+/-400.1	644,2022,1634	yes	missense,missense	CPA4	NM_001163446.1,NM_016352.3	159,159	767,2779,2957	TT,TG,GG		38.4884,22.7644,33.1616	benign,benign	270/389,303/422	129950740	4313,8693	2203	4300	6503	SO:0001583	missense	51200	exon9			TTCAAGGGCTTCA	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.907G>T	7.37:g.129950740G>T	ENSP00000222482:p.Gly303Cys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	37	CCDS5818.1	719	0.3292124542124542	108	0.21951219512195122	122	0.3370165745856354	227	0.3968531468531469	262	0.34564643799472294	T	12.75	2.032247	0.35893	0.227644	0.384884	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.11063	2.81;2.81;2.81	6.17	0.479	0.16796	Peptidase M14, carboxypeptidase A (2);	0.437819	0.26746	N	0.022720	T	0.00012	0.0000	N	0.16130	0.375	0.52099	P	5.100000000002325E-5	B;B	0.15141	0.012;0.004	B;B	0.28849	0.095;0.021	T	0.49031	-0.8981	9	0.51188	T	0.08	.	11.7939	0.52088	0.1397:0.0:0.6312:0.2291	rs2171492;rs17327657;rs52837974;rs58222478;rs2171492	270;303	B7Z576;Q9UI42	.;CBPA4_HUMAN	C	270;303;108;199	ENSP00000412947:G270C;ENSP00000222482:G303C;ENSP00000419660:G199C	ENSP00000222482:G303C	G	+	1	0	CPA4	129737976	0.998000	0.40836	0.992000	0.48379	0.691000	0.40173	0.552000	0.23376	-0.068000	0.12953	-1.131000	0.01979	GGC	G|0.677;T|0.323	0.323	strong		0.512	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
UGT2B17	7367	hgsc.bcm.edu	37	4	69416556	69416556	+	Silent	SNP	T	T	C	rs13102139		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69416556T>C	ENST00000317746.2	-	5	1194	c.1152A>G	c.(1150-1152)gcA>gcG	p.A384A		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	384					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	CATGGTAGATTGCCTCATAGA	0.428																																					p.A384A	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.A1152G						PASS	.						143.0	105.0	118.0					4																	69416556		2108	3990	6098	SO:0001819	synonymous_variant	7367	exon5			GTAGATTGCCTCA	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.1152A>G	4.37:g.69416556T>C		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	339	110	0.324484	NM_001077		Silent	SNP	ENST00000317746.2	37	CCDS3523.1																																																																																			T|0.250;C|0.750	0.750	weak		0.428	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	
NLRP10	338322	hgsc.bcm.edu	37	11	7981521	7981521	+	Silent	SNP	C	C	T	rs11608118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7981521C>T	ENST00000328600.2	-	2	1799	c.1638G>A	c.(1636-1638)aaG>aaA	p.K546K		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	546					defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CTTTAAAATGCTTCAGATCCT	0.398													C|||	320	0.0638978	0.0363	0.0432	5008	,	,		19762	0.0863		0.1024	False		,,,				2504	0.0532				p.K546K		Atlas-SNP	.											.	NLRP10	146	.	0			c.G1638A						PASS	.	C		181,4221	115.9+/-153.8	6,169,2026	61.0	62.0	62.0		1638	3.4	0.6	11	dbSNP_120	62	781,7811	184.3+/-232.3	38,705,3553	no	coding-synonymous	NLRP10	NM_176821.3		44,874,5579	TT,TC,CC		9.0899,4.1118,7.4034		546/656	7981521	962,12032	2201	4296	6497	SO:0001819	synonymous_variant	338322	exon2			AAAATGCTTCAGA	AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"""Nucleotide-binding domain and leucine rich repeat containing"""	21464	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"""	609662	"""NACHT, leucine rich repeat and PYD containing 10"""	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1638G>A	11.37:g.7981521C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	127	53	0.417323	NM_176821	Q2M3C4|Q6JGT0	Silent	SNP	ENST00000328600.2	37	CCDS7784.1																																																																																			C|0.930;T|0.070	0.070	strong		0.398	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821	
GP6	51206	hgsc.bcm.edu	37	19	55526359	55526359	+	Missense_Mutation	SNP	A	A	T	rs1654413	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55526359A>T	ENST00000417454.1	-	8	977	c.950T>A	c.(949-951)cTg>cAg	p.L317Q	GP6_ENST00000310373.3_Silent_p.A318A|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Missense_Mutation_p.L299Q|CTC-550B14.7_ENST00000586845.1_RNA	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	317			L -> Q (in dbSNP:rs1654413). {ECO:0000269|PubMed:11027634, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		TTTCCGGGTCAGCGGGAGGGG	0.667													T|||	3630	0.72484	0.5265	0.8256	5008	,	,		14476	0.8135		0.8429	False		,,,				2504	0.7086				p.L317Q		Atlas-SNP	.											GP6,colon,carcinoma,0,1	GP6	55	1	0			c.T950A						PASS	.	T	,GLN/LEU	2142,1690		614,914,388	18.0	22.0	21.0		954,950	-0.9	0.0	19	dbSNP_89	21	6849,1389		2857,1135,127	yes	coding-synonymous,missense	GP6	NM_001083899.1,NM_016363.4	,113	3471,2049,515	TT,TA,AA		16.8609,44.1023,25.5095	,	318/621,317/340	55526359	8991,3079	1916	4119	6035	SO:0001583	missense	51206	exon8			CGGGTCAGCGGGA	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.950T>A	19.37:g.55526359A>T	ENSP00000394922:p.Leu317Gln	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_016363	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	37	CCDS46184.1	1681	0.7696886446886447	271	0.5508130081300813	306	0.8453038674033149	471	0.8234265734265734	633	0.8350923482849604	T	1.529	-0.544785	0.04024	0.558977	0.831391	ENSG00000088053	ENST00000417454;ENST00000333884	T;T	0.00488	7.09;7.04	2.65	-0.947	0.10382	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21245	-1.0251	7	0.22109	T	0.4	.	0.9097	0.01291	0.297:0.1077:0.1543:0.441	rs1654413;rs5030706;rs61141073	299;317	Q9HCN6-2;Q9HCN6	.;GPVI_HUMAN	Q	317;299	ENSP00000394922:L317Q;ENSP00000334552:L299Q	ENSP00000334552:L299Q	L	-	2	0	GP6	60218171	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.867000	0.04241	-1.326000	0.02266	-3.579000	0.00029	CTG	A|0.225;T|0.775	0.775	strong		0.667	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
SLC26A9	115019	hgsc.bcm.edu	37	1	205896647	205896647	+	Silent	SNP	A	A	G	rs34803033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205896647A>G	ENST00000367135.3	-	10	1301	c.1188T>C	c.(1186-1188)gcT>gcC	p.A396A	SLC26A9_ENST00000340781.4_Silent_p.A396A|SLC26A9_ENST00000367134.2_Silent_p.A396A	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	396					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			CTCCATCCACAGCCAGAGTGA	0.532													A|||	380	0.0758786	0.1823	0.0605	5008	,	,		19974	0.0		0.0755	False		,,,				2504	0.0215				p.A396A		Atlas-SNP	.											.	SLC26A9	176	.	0			c.T1188C						PASS	.	A	,	750,3656	306.3+/-289.4	59,632,1512	63.0	67.0	65.0		1188,1188	-2.1	1.0	1	dbSNP_126	65	664,7936	168.3+/-219.8	27,610,3663	no	coding-synonymous,coding-synonymous	SLC26A9	NM_052934.3,NM_134325.2	,	86,1242,5175	GG,GA,AA		7.7209,17.0222,10.8719	,	396/792,396/888	205896647	1414,11592	2203	4300	6503	SO:0001819	synonymous_variant	115019	exon10			ATCCACAGCCAGA	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"""Solute carriers"""	14469	protein-coding gene	gene with protein product	"""anion transporter/exchanger-9"""	608481	"""solute carrier family 26, member 9"""			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.1188T>C	1.37:g.205896647A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Silent	SNP	ENST00000367135.3	37	CCDS30990.1																																																																																			A|0.897;G|0.103	0.103	strong		0.532	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
NELFB	25920	hgsc.bcm.edu	37	9	140147152	140147152	+	5'Flank	SNP	C	C	G	rs28376526	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140147152C>G	ENST00000343053.4	+	0	0				C9orf173_ENST00000388931.3_Silent_p.P177P|C9orf173_ENST00000412566.1_Silent_p.P177P	NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B						gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TCAGCCGGCCCGCCTTCCCCG	0.706													C|||	3054	0.609824	0.4924	0.7608	5008	,	,		10116	0.4772		0.7237	False		,,,				2504	0.681				p.P177P		Atlas-SNP	.											.	C9orf173	19	.	0			c.C531G						PASS	.	C		2055,1687		610,835,426	5.0	6.0	6.0		531	-3.2	0.0	9	dbSNP_125	6	6011,1957		2391,1229,364	no	coding-synonymous	C9orf173	NM_001004353.2		3001,2064,790	GG,GC,CC		24.5607,45.0828,31.1187		177/309	140147152	8066,3644	1871	3984	5855	SO:0001631	upstream_gene_variant	441476	exon5			CCGGCCCGCCTTC	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778		9.37:g.140147152C>G	Exception_encountered	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	65	38	0.584615	NM_001004353	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	37	CCDS7040.1																																																																																			C|0.388;G|0.612	0.612	strong		0.706	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	
OR56A4	120793	hgsc.bcm.edu	37	11	6023640	6023640	+	Missense_Mutation	SNP	T	T	C	rs11040249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6023640T>C	ENST00000330728.4	-	1	784	c.739A>G	c.(739-741)Atc>Gtc	p.I247V		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGAAAGTGATGTCATCACAA	0.423													.|||	824	0.164537	0.0582	0.1945	5008	,	,		24555	0.0794		0.2684	False		,,,				2504	0.2679				p.I247V		Atlas-SNP	.											.	OR56A4	66	.	0			c.A739G						PASS	.	T	VAL/ILE	477,3925	223.3+/-239.8	30,417,1754	50.0	50.0	50.0		739	3.7	0.0	11	dbSNP_120	50	2562,6030	417.3+/-352.4	397,1768,2131	yes	missense	OR56A4	NM_001005179.2	29	427,2185,3885	CC,CT,TT		29.8184,10.836,23.3877	benign	247/366	6023640	3039,9955	2201	4296	6497	SO:0001583	missense	120793	exon1			AAGTGATGTCATC	BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"""GPCR / Class A : Olfactory receptors"""	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.739A>G	11.37:g.6023640T>C	ENSP00000328215:p.Ile247Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_001005179	B9EH17	Missense_Mutation	SNP	ENST00000330728.4	37	CCDS31404.1	358	0.16391941391941392	36	0.07317073170731707	67	0.1850828729281768	46	0.08041958041958042	209	0.2757255936675462	T	8.238	0.806233	0.16467	0.10836	0.298184	ENSG00000183389	ENST00000330728	T	0.00107	8.72	3.72	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36740	U	0.002434	T	0.00012	0.0000	L	0.51914	1.62	0.80722	P	0.0	B	0.06786	0.001	B	0.17722	0.019	T	0.21999	-1.0229	9	0.45353	T	0.12	.	11.6678	0.51383	0.0:0.0:0.0:1.0	rs11040249;rs59527403;rs11040249	195	Q8NGH8	O56A4_HUMAN	V	247	ENSP00000328215:I247V	ENSP00000328215:I247V	I	-	1	0	OR56A4	5980216	0.000000	0.05858	0.040000	0.18447	0.988000	0.76386	0.189000	0.17037	1.669000	0.50854	0.533000	0.62120	ATC	T|0.797;C|0.203	0.203	strong		0.423	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
PER1	5187	hgsc.bcm.edu	37	17	8046772	8046772	+	Missense_Mutation	SNP	C	C	G	rs2585405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8046772C>G	ENST00000317276.4	-	19	3121	c.2884G>C	c.(2884-2886)Gcc>Ccc	p.A962P	PER1_ENST00000581082.1_Missense_Mutation_p.A939P|PER1_ENST00000578089.1_5'UTR	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	962	Pro-rich.		A -> P (in dbSNP:rs2585405). {ECO:0000269|PubMed:10857746, ECO:0000269|PubMed:10940553, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9323128, ECO:0000269|PubMed:9333243, ECO:0000269|PubMed:9455484, ECO:0000269|Ref.9}.		circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGACTCGGGGCGAGGGCGGGC	0.647			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					G|||	3865	0.771765	0.7549	0.8357	5008	,	,		10857	0.5337		0.8917	False		,,,				2504	0.8712				p.A962P		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.G2884C						PASS	.	G	PRO/ALA	3460,944		1412,636,154	29.0	24.0	26.0		2884	3.2	0.4	17	dbSNP_100	26	7713,887		3522,669,109	yes	missense	PER1	NM_002616.2	27	4934,1305,263	GG,GC,CC		10.314,21.4351,14.0803	possibly-damaging	962/1291	8046772	11173,1831	2202	4300	6502	SO:0001583	missense	5187	exon19			TCGGGGCGAGGGC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2884G>C	17.37:g.8046772C>G	ENSP00000314420:p.Ala962Pro	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	199	199	1	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	1683	0.7706043956043956	365	0.741869918699187	303	0.8370165745856354	328	0.5734265734265734	687	0.9063324538258575	G	0.015	-1.546402	0.00926	0.785649	0.89686	ENSG00000179094	ENST00000317276	T	0.13420	2.59	5.35	3.22	0.36961	.	0.468716	0.20988	N	0.082081	T	0.00012	0.0000	N	0.04508	-0.205	0.49483	P	2.0699999999995722E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.16070	-1.0415	9	0.16420	T	0.52	-7.1852	12.9354	0.58311	0.0:0.4846:0.5154:0.0	rs2585405	962	O15534	PER1_HUMAN	P	962	ENSP00000314420:A962P	ENSP00000314420:A962P	A	-	1	0	PER1	7987497	0.866000	0.29940	0.392000	0.26245	0.003000	0.03518	1.592000	0.36676	0.658000	0.30925	-0.352000	0.07741	GCC	C|0.170;G|0.830	0.830	strong		0.647	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
CFL1	1072	hgsc.bcm.edu	37	11	65623519	65623519	+	Silent	SNP	G	G	A	rs4621	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65623519G>A	ENST00000525451.2	-	3	913	c.198C>T	c.(196-198)gaC>gaT	p.D66D	CFL1_ENST00000531413.1_Silent_p.D49D|CFL1_ENST00000308162.5_Silent_p.D66D|CFL1_ENST00000527344.1_Silent_p.D49D|CFL1_ENST00000531407.1_Silent_p.D49D|CFL1_ENST00000534769.1_Silent_p.D104D|CFL1_ENST00000524553.1_Silent_p.D49D			P23528	COF1_HUMAN	cofilin 1 (non-muscle)	66	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin cytoskeleton organization (GO:0030036)|actin filament depolymerization (GO:0030042)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytoskeleton organization (GO:0007010)|establishment of cell polarity (GO:0030010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|mitotic cytokinesis (GO:0000281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell size (GO:0045792)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of actin filament depolymerization (GO:0030836)|protein import into nucleus (GO:0006606)|protein phosphorylation (GO:0006468)|regulation of cell morphogenesis (GO:0022604)|response to amino acid (GO:0043200)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				breast(1)|kidney(1)|large_intestine(2)|lung(2)	6				READ - Rectum adenocarcinoma(159;0.169)		TGGCGTAGGGGTCGTCGACAG	0.557													G|||	2143	0.427915	0.2012	0.4063	5008	,	,		20187	0.3313		0.668	False		,,,				2504	0.6022				p.D66D	Esophageal Squamous(90;820 1366 3932 32351 42291)	Atlas-SNP	.											.	CFL1	15	.	0			c.C198T						PASS	.	G		1152,3250	408.6+/-334.7	153,846,1202	155.0	139.0	144.0		198	0.8	1.0	11	dbSNP_52	144	5738,2856	673.1+/-403.0	1893,1952,452	no	coding-synonymous	CFL1	NM_005507.2		2046,2798,1654	AA,AG,GG		33.2325,26.1699,46.9837		66/167	65623519	6890,6106	2201	4297	6498	SO:0001819	synonymous_variant	1072	exon2			GTAGGGGTCGTCG	X95404	CCDS8114.1	11q13.1	2010-12-03			ENSG00000172757	ENSG00000172757			1874	protein-coding gene	gene with protein product		601442		CFL		8800436	Standard	NM_005507		Approved		uc001ofs.3	P23528		ENST00000525451.2:c.198C>T	11.37:g.65623519G>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	237	234	0.987342	NM_005507	B3KUQ1|Q53Y87|Q9UCA2	Silent	SNP	ENST00000525451.2	37	CCDS8114.1																																																																																			G|0.491;A|0.509	0.509	strong		0.557	CFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390701.3	NM_005507	
MDM1	56890	hgsc.bcm.edu	37	12	68708869	68708869	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:68708869A>G	ENST00000303145.7	-	9	1444	c.1358T>C	c.(1357-1359)gTa>gCa	p.V453A	MDM1_ENST00000411698.2_Missense_Mutation_p.V418A|MDM1_ENST00000540418.1_Missense_Mutation_p.V173A	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	453					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		CTGTTTCTGTACGTCTTCACT	0.527																																					p.V453A		Atlas-SNP	.											MDM1,NS,carcinoma,-1,1	MDM1	74	1	0			c.T1358C						scavenged	.						203.0	194.0	197.0					12																	68708869		2203	4300	6503	SO:0001583	missense	56890	exon9			TTCTGTACGTCTT	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"""Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"""			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.1358T>C	12.37:g.68708869A>G	ENSP00000302537:p.Val453Ala	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	315	4	0.0126984	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	.	.	.	.	.	.	.	.	.	.	A	2.062	-0.415131	0.04766	.	.	ENSG00000111554	ENST00000540418;ENST00000303145;ENST00000411698	T;T;T	0.20463	2.07;2.07;2.07	4.59	-9.16	0.00694	.	2.501490	0.01212	N	0.007875	T	0.09069	0.0224	N	0.14661	0.345	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.08055	0.002;0.003	T	0.15896	-1.0421	9	.	.	.	16.5168	3.6817	0.08313	0.1447:0.1972:0.4447:0.2134	.	418;453	E7EPQ3;Q8TC05	.;MDM1_HUMAN	A	173;453;418	ENSP00000443815:V173A;ENSP00000302537:V453A;ENSP00000391006:V418A	.	V	-	2	0	MDM1	66995136	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.614000	0.02057	-1.868000	0.01142	-0.429000	0.05907	GTA	.	.	none		0.527	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128	
ACAT2	39	hgsc.bcm.edu	37	6	160198359	160198359	+	Silent	SNP	C	C	T	rs3464	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:160198359C>T	ENST00000367048.4	+	7	2543	c.783C>T	c.(781-783)gtC>gtT	p.V261V	ACAT2_ENST00000541436.1_Silent_p.V290V|ACAT2_ENST00000472052.1_3'UTR|SNORA20_ENST00000384662.1_RNA	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	261					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CTGCAGCTGTCGTTCTTATGA	0.423													C|||	1308	0.261182	0.1755	0.2161	5008	,	,		20467	0.4266		0.2127	False		,,,				2504	0.2883				p.V261V		Atlas-SNP	.											.	ACAT2	32	.	0			c.C783T						PASS	.	C		840,3566	333.3+/-302.9	89,662,1452	155.0	147.0	150.0		783	3.3	1.0	6	dbSNP_36	150	1500,7100	284.7+/-296.8	140,1220,2940	no	coding-synonymous	ACAT2	NM_005891.2		229,1882,4392	TT,TC,CC		17.4419,19.0649,17.9917		261/398	160198359	2340,10666	2203	4300	6503	SO:0001819	synonymous_variant	39	exon7			AGCTGTCGTTCTT	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	100678	"""acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)"", ""acetyl-Coenzyme A acetyltransferase 2"""			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.783C>T	6.37:g.160198359C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	178	83	0.466292	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Silent	SNP	ENST00000367048.4	37	CCDS5268.1																																																																																			C|0.797;T|0.203	0.203	strong		0.423	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891	
C1orf186	440712	hgsc.bcm.edu	37	1	206239415	206239415	+	Silent	SNP	C	C	T	rs28639473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206239415C>T	ENST00000331555.5	-	6	1121	c.483G>A	c.(481-483)ctG>ctA	p.L161L		NM_001007544.1	NP_001007545.1	Q6ZWK4	CA186_HUMAN	chromosome 1 open reading frame 186	161						integral component of membrane (GO:0016021)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.0754)			CTGGCTCAGACAGAGCAGGGT	0.403													C|||	391	0.0780751	0.0106	0.0634	5008	,	,		20370	0.0744		0.0626	False		,,,				2504	0.1994				p.L161L		Atlas-SNP	.											.	C1orf186	26	.	0			c.G483A						PASS	.	C		83,4323	69.2+/-107.0	2,79,2122	112.0	100.0	104.0		483	2.9	0.0	1	dbSNP_125	104	735,7865	178.5+/-227.8	43,649,3608	no	coding-synonymous	C1orf186	NM_001007544.1		45,728,5730	TT,TC,CC		8.5465,1.8838,6.2894		161/173	206239415	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	440712	exon6			CTCAGACAGAGCA	AK122631	CCDS73014.1	1q32.1	2014-05-06			ENSG00000196533	ENSG00000263961			25341	protein-coding gene	gene with protein product							Standard	XM_005272738		Approved	FLJ16052	uc001hdt.2	Q6ZWK4	OTTHUMG00000184376	ENST00000331555.5:c.483G>A	1.37:g.206239415C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	NM_001007544		Silent	SNP	ENST00000331555.5	37	CCDS30995.1																																																																																			C|0.936;T|0.064	0.064	strong		0.403	C1orf186-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088002.1	NM_001007544	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643255	1643255	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1643255G>A	ENST00000399682.1	-	1	113	c.69C>T	c.(67-69)ggC>ggT	p.G23G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)		p.G23G(1)		NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		cagagccacagcccccacagc	0.687																																					p.G23G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	1	Substitution - coding silent(1)	kidney(1)	c.C69T						scavenged	.						4.0	8.0	7.0					11																	1643255		646	1526	2172	SO:0001819	synonymous_variant	387267	exon1			GCCACAGCCCCCA	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.69C>T	11.37:g.1643255G>A		Somatic	337	13	0.0385757		WXS	Illumina HiSeq	Phase_I	231	14	0.0606061	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
UGT2B28	54490	hgsc.bcm.edu	37	4	70160309	70160309	+	Missense_Mutation	SNP	C	C	G	rs6828191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70160309C>G	ENST00000335568.5	+	6	1374	c.1372C>G	c.(1372-1374)Cat>Gat	p.H458D	UGT2B28_ENST00000511240.1_3'UTR	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	458			H -> D (in dbSNP:rs6828191). {ECO:0000269|PubMed:19054851}.		metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						AAAGCCCCTGCATCGAGCAGT	0.403													N|||	1888	0.376997	0.2678	0.4524	5008	,	,		13110	0.3819		0.4771	False		,,,				2504	0.363				p.H458D		Atlas-SNP	.											.	UGT2B28	101	.	0			c.C1372G						PASS	.	G	,ASP/HIS	1420,2626		454,512,1057	55.0	63.0	60.0		,1372	1.9	0.9	4	dbSNP_116	60	4311,4147		1351,1609,1269	no	utr-3,missense	UGT2B28	NM_001207004.1,NM_053039.1	,81	1805,2121,2326	GG,GC,CC		49.0305,35.0964,45.8333	,benign	,458/530	70160309	5731,6773	2023	4229	6252	SO:0001583	missense	54490	exon6			CCCCTGCATCGAG	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1372C>G	4.37:g.70160309C>G	ENSP00000334276:p.His458Asp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	101	99	0.980198	NM_053039	B5BUM0|Q9BY62|Q9BY63	Missense_Mutation	SNP	ENST00000335568.5	37	CCDS3528.1	865	0.39606227106227104	114	0.23170731707317074	158	0.43646408839779005	212	0.3706293706293706	381	0.5026385224274407	-	0.004	-2.368089	0.00209	0.350964	0.509695	ENSG00000135226	ENST00000335568	T	0.35421	1.31	1.85	1.85	0.25348	.	0.000000	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00001	-3.85	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48536	-0.9027	9	0.02654	T	1	.	7.9462	0.29987	0.0:0.2584:0.7416:0.0	rs6828191	458	Q9BY64	UDB28_HUMAN	D	458	ENSP00000334276:H458D	ENSP00000334276:H458D	H	+	1	0	UGT2B28	70194898	1.000000	0.71417	0.868000	0.34077	0.021000	0.10359	4.502000	0.60400	0.124000	0.18369	-1.122000	0.02009	CAT	C|0.601;G|0.399	0.399	strong		0.403	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
PSMG2	56984	hgsc.bcm.edu	37	18	12718593	12718593	+	Silent	SNP	A	A	G	rs2302768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:12718593A>G	ENST00000317615.6	+	4	1048	c.366A>G	c.(364-366)tcA>tcG	p.S122S	PSMG2_ENST00000590217.1_Silent_p.S122S|PSMG2_ENST00000585331.2_Silent_p.S91S	NM_020232.4	NP_064617.2			proteasome (prosome, macropain) assembly chaperone 2											lung(1)|prostate(2)|skin(1)	4						TTGTTCTTTCAAGCAGTCATT	0.383													G|||	1469	0.293331	0.2466	0.281	5008	,	,		16839	0.3046		0.4324	False		,,,				2504	0.2106				p.S122S		Atlas-SNP	.											.	PSMG2	17	.	0			c.A366G						PASS	.	G	,	1337,3069	693.3+/-405.7	193,951,1059	146.0	135.0	139.0		366,273	-10.9	0.0	18	dbSNP_100	139	3853,4747	609.1+/-395.5	874,2105,1321	yes	coding-synonymous,coding-synonymous	PSMG2	NM_020232.4,NM_147163.1	,	1067,3056,2380	GG,GA,AA		44.8023,30.345,39.9047	,	122/265,91/234	12718593	5190,7816	2203	4300	6503	SO:0001819	synonymous_variant	56984	exon4			TCTTTCAAGCAGT	AF276707	CCDS11862.1, CCDS67440.1	18p11.21	2012-01-25	2007-10-23	2007-10-23	ENSG00000128789	ENSG00000128789			24929	protein-coding gene	gene with protein product	"""hepatocellular carcinoma susceptibility protein"", ""CD40 ligand-activated specific transcript 3"""	609702	"""tumor necrosis factor superfamily, member 5-induced protein 1"""	TNFSF5IP1		11854909, 12147697, 17189198	Standard	NM_147163		Approved	HCCA3, MDS003, MGC15092, CLAST3, HsT1707, PAC2	uc002krk.3	Q969U7	OTTHUMG00000131703	ENST00000317615.6:c.366A>G	18.37:g.12718593A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_020232		Silent	SNP	ENST00000317615.6	37	CCDS11862.1																																																																																			A|0.636;G|0.364	0.364	strong		0.383	PSMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254615.1	NM_020232	
ZNF207	7756	hgsc.bcm.edu	37	17	30689985	30689985	+	Missense_Mutation	SNP	A	A	G	rs140641814		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:30689985A>G	ENST00000321233.6	+	6	758	c.604A>G	c.(604-606)Atg>Gtg	p.M202V	ZNF207_ENST00000577908.1_Missense_Mutation_p.M218V|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000394673.2_Missense_Mutation_p.M218V|ZNF207_ENST00000394670.4_Missense_Mutation_p.M218V|ZNF207_ENST00000341711.6_Missense_Mutation_p.M119V|ZNF207_ENST00000342555.6_Missense_Mutation_p.M221V	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	202					attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			ACCACCTCTGATGCCTGGAAT	0.363																																					p.M218V		Atlas-SNP	.											.	ZNF207	32	.	0			c.A652G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	0,4406		0,0,2203	111.0	108.0	109.0		652,652,604	5.7	1.0	17	dbSNP_134	109	1,8599		0,1,4299	no	missense,missense,missense	ZNF207	NM_001032293.2,NM_001098507.1,NM_003457.3	21,21,21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign,benign	218/464,218/495,202/479	30689985	1,13005	2203	4300	6503	SO:0001583	missense	7756	exon7			CCTCTGATGCCTG	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.604A>G	17.37:g.30689985A>G	ENSP00000322777:p.Met202Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_001098507	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	37	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	A	3.923	-0.017677	0.07681	0.0	1.16E-4	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000341711;ENST00000342555	T;T;T	0.54279	0.95;0.88;0.58	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.46464	0.1394	L	0.50333	1.59	0.80722	D	1	B;B;B;B;B	0.24576	0.106;0.106;0.106;0.039;0.106	B;B;B;B;B	0.15484	0.013;0.013;0.013;0.013;0.013	T	0.38286	-0.9668	10	0.17369	T	0.5	.	16.0101	0.80396	1.0:0.0:0.0:0.0	.	202;221;218;218;202	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	V	218;202;221;218;119;202	ENSP00000378165:M218V;ENSP00000378168:M202V;ENSP00000344913:M119V	ENSP00000322777:M218V	M	+	1	0	ZNF207	27714098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.267000	0.78462	2.171000	0.68590	0.533000	0.62120	ATG	A|1.000;G|0.000	0.000	weak		0.363	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2		
CA9	768	hgsc.bcm.edu	37	9	35679251	35679251	+	Missense_Mutation	SNP	A	A	G	rs3829078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35679251A>G	ENST00000378357.4	+	7	1081	c.977A>G	c.(976-978)cAa>cGa	p.Q326R	CA9_ENST00000493245.1_3'UTR	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	326	Catalytic.		Q -> R (in dbSNP:rs3829078).		bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	CGCTACTTCCAATATGAGGGG	0.557													a|||	246	0.0491214	0.0189	0.0605	5008	,	,		18803	0.0288		0.1044	False		,,,				2504	0.046				p.Q326R		Atlas-SNP	.											.	CA9	48	.	0			c.A977G						PASS	.	A	ARG/GLN	132,4274	94.4+/-133.1	1,130,2072	214.0	204.0	207.0		977	2.5	1.0	9	dbSNP_107	207	969,7631	211.3+/-251.9	59,851,3390	yes	missense	CA9	NM_001216.2	43	60,981,5462	GG,GA,AA		11.2674,2.9959,8.4653	benign	326/460	35679251	1101,11905	2203	4300	6503	SO:0001583	missense	768	exon7			ACTTCCAATATGA	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.977A>G	9.37:g.35679251A>G	ENSP00000367608:p.Gln326Arg	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	239	113	0.472803	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	37	CCDS6585.1	123	0.05631868131868132	5	0.01016260162601626	23	0.06353591160220995	16	0.027972027972027972	79	0.10422163588390501	A	0.517	-0.864069	0.02590	0.029959	0.112674	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.46819	0.86	5.37	2.55	0.30701	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.315107	0.23865	N	0.043801	T	0.00178	0.0005	N	0.00072	-2.265	0.21627	N	0.999619	B;B	0.10296	0.003;0.002	B;B	0.06405	0.001;0.002	T	0.31971	-0.9924	10	0.02654	T	1	.	7.9303	0.29899	0.2604:0.0:0.7396:0.0	rs3829078;rs52790275;rs56739441;rs3829078	326;326	F5H404;Q16790	.;CAH9_HUMAN	R	326	ENSP00000367608:Q326R	ENSP00000367608:Q326R	Q	+	2	0	CA9	35669251	0.998000	0.40836	0.983000	0.44433	0.574000	0.36063	1.505000	0.35736	0.342000	0.23796	-0.407000	0.06327	CAA	A|0.932;G|0.068	0.068	strong		0.557	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
AKR1C4	1109	hgsc.bcm.edu	37	10	5242164	5242164	+	Silent	SNP	A	A	G	rs17306779	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:5242164A>G	ENST00000380448.1	+	4	358	c.105A>G	c.(103-105)gtA>gtG	p.V35V	AKR1C4_ENST00000263126.1_Silent_p.V35V|AKR1CL1_ENST00000445191.1_Intron			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	35					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)	p.V35V(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						ACAGAGCTGTAGAGGTCACCA	0.448													G|||	827	0.165136	0.0961	0.2464	5008	,	,		22801	0.129		0.2207	False		,,,				2504	0.181				p.V35V		Atlas-SNP	.											AKR1C4,NS,carcinoma,0,1	AKR1C4	57	1	1	Substitution - coding silent(1)	stomach(1)	c.A105G						scavenged	.	G		487,3919	781.8+/-414.5	26,435,1742	108.0	96.0	100.0		105	-6.9	0.0	10	dbSNP_123	100	1965,6635	723.9+/-406.5	221,1523,2556	no	coding-synonymous	AKR1C4	NM_001818.3		247,1958,4298	GG,GA,AA		22.8488,11.0531,18.8528		35/324	5242164	2452,10554	2203	4300	6503	SO:0001819	synonymous_variant	1109	exon2			AGCTGTAGAGGTC	M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"""Aldo-keto reductases"""	387	protein-coding gene	gene with protein product	"""chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"""	600451	"""aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"""	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.105A>G	10.37:g.5242164A>G		Somatic	203	2	0.00985222		WXS	Illumina HiSeq	Phase_I	220	114	0.518182	NM_001818	Q5T6A3|Q8WW84|Q9NS54	Silent	SNP	ENST00000380448.1	37	CCDS7064.1																																																																																			A|0.824;G|0.176	0.176	strong		0.448	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	
TSPAN17	26262	hgsc.bcm.edu	37	5	176081907	176081907	+	Silent	SNP	C	C	T	rs11267007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176081907C>T	ENST00000503045.1	+	5	454	c.399C>T	c.(397-399)tgC>tgT	p.C133C	TSPAN17_ENST00000310032.8_Silent_p.C156C|TSPAN17_ENST00000405525.2_Silent_p.C156C|TSPAN17_ENST00000508164.1_Silent_p.C156C|TSPAN17_ENST00000298564.10_Intron|TSPAN17_ENST00000515708.1_Silent_p.C156C			Q96FV3	TSN17_HUMAN	tetraspanin 17	156					establishment of protein localization to organelle (GO:0072594)|protein ubiquitination (GO:0016567)	integral component of membrane (GO:0016021)|ubiquitin ligase complex (GO:0000151)	enzyme binding (GO:0019899)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	13	all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGTCTTGCTGCGGAGCCCGAG	0.632													c|||	1155	0.230631	0.0227	0.1484	5008	,	,		17541	0.4504		0.2604	False		,,,				2504	0.3129				p.C156C		Atlas-SNP	.											TSPAN17,NS,carcinoma,0,1	TSPAN17	33	1	0			c.C468T						PASS	.	T	,,	225,4181	133.3+/-169.7	7,211,1985	33.0	35.0	34.0		468,468,468	-3.4	1.0	5	dbSNP_120	34	2194,6406	365.8+/-334.1	269,1656,2375	no	coding-synonymous,coding-synonymous,coding-synonymous	TSPAN17	NM_001006616.2,NM_012171.2,NM_130465.4	,,	276,1867,4360	TT,TC,CC		25.5116,5.1067,18.5991	,,	156/264,156/333,156/330	176081907	2419,10587	2203	4300	6503	SO:0001819	synonymous_variant	26262	exon5			TTGCTGCGGAGCC	AF174603	CCDS34298.1, CCDS47346.1, CCDS47346.2, CCDS54952.1	5q35.3	2013-02-14	2005-03-21	2005-03-21	ENSG00000048140	ENSG00000048140		"""Tetraspanins"""	13594	protein-coding gene	gene with protein product			"""F-box only protein 23, transmembrane 4 superfamily member 17"""	FBXO23, TM4SF17		10531035, 10531037	Standard	NM_012171		Approved	FBX23	uc003met.3	Q96FV3	OTTHUMG00000163230	ENST00000503045.1:c.399C>T	5.37:g.176081907C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	205	55	0.268293	NM_001006616	Q6NXF7|Q96S98|Q9UKB9	Silent	SNP	ENST00000503045.1	37		525	0.2403846153846154	13	0.026422764227642278	57	0.1574585635359116	272	0.4755244755244755	183	0.24142480211081793	c	9.190	1.025885	0.19512	0.051067	0.255116	ENSG00000048140	ENST00000507471	.	.	.	5.23	-3.44	0.04796	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39702	-0.9601	3	.	.	.	-8.0088	13.4813	0.61336	0.0:0.1708:0.0:0.8292	rs11267007;rs13183488;rs61477696;rs13183488	.	.	.	V	89	.	.	A	+	2	0	TSPAN17	176014513	0.112000	0.22096	0.976000	0.42696	0.904000	0.53231	-0.590000	0.05760	-0.590000	0.05866	-1.402000	0.01139	GCG	C|0.791;G|0.000;N|0.001;T|0.208	0.208	strong		0.632	TSPAN17-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372215.1		
GFAP	2670	hgsc.bcm.edu	37	17	42987523	42987523	+	Intron	SNP	G	G	A	rs9908084|rs386797323	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42987523G>A	ENST00000253408.5	-	7	1237				GFAP_ENST00000588735.1_Intron|GFAP_ENST00000435360.2_Missense_Mutation_p.T426M	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein						astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				AGCCGGCGGCGTTCCATTTAC	0.537													G|||	529	0.105631	0.1021	0.1081	5008	,	,		18163	0.005		0.167	False		,,,				2504	0.1493				p.T426M		Atlas-SNP	.											.	GFAP	88	.	0			c.C1277T						PASS	.	G	MET/THR,,	299,2837		12,275,1281	215.0	191.0	198.0		1277,,	3.8	0.9	17	dbSNP_119	198	1196,5968		93,1010,2479	no	missense,utr-3,intron	GFAP	NM_001131019.2,NM_001242376.1,NM_002055.4	81,,	105,1285,3760	AA,AG,GG		16.6946,9.5344,14.5146	,,	426/432,,	42987523	1495,8805	1568	3582	5150	SO:0001627	intron_variant	2670	exon8			GGCGGCGTTCCAT	S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"""Intermediate filaments type III"""	4235	protein-coding gene	gene with protein product	"""intermediate filament protein"""	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.1171+459C>T	17.37:g.42987523G>A		Somatic	319	1	0.0031348		WXS	Illumina HiSeq	Phase_I	295	160	0.542373	NM_001131019	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Missense_Mutation	SNP	ENST00000253408.5	37	CCDS11491.1	179	0.08195970695970696	36	0.07317073170731707	46	0.1270718232044199	2	0.0034965034965034965	95	0.12532981530343007	G	13.54	2.267411	0.40095	0.095344	0.166946	ENSG00000131095	ENST00000435360	D	0.84730	-1.89	4.79	3.8	0.43715	.	.	.	.	.	T	0.00440	0.0014	N	0.08118	0	0.09310	P	0.999999999608325	B	0.13145	0.007	B	0.04013	0.001	T	0.32877	-0.9890	8	0.72032	D	0.01	.	9.5131	0.39089	0.0951:0.0:0.9049:0.0	rs9908084;rs9908084	426	E9PAX3	.	M	426	ENSP00000403962:T426M	ENSP00000403962:T426M	T	-	2	0	GFAP	40343049	1.000000	0.71417	0.910000	0.35882	0.158000	0.22134	1.941000	0.40233	1.599000	0.50093	0.655000	0.94253	ACG	G|0.911;A|0.089	0.089	strong		0.537	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055	
CUL3	8452	hgsc.bcm.edu	37	2	225346646	225346646	+	Silent	SNP	T	T	C	rs2070127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:225346646T>C	ENST00000264414.4	-	14	2330	c.1992A>G	c.(1990-1992)caA>caG	p.Q664Q	CUL3_ENST00000344951.4_Silent_p.Q598Q|CUL3_ENST00000409096.1_Silent_p.Q640Q|CUL3_ENST00000409777.1_Silent_p.Q640Q	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	664					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TGGATGTGAATTGATCATTAA	0.318													T|||	1165	0.232628	0.2534	0.2262	5008	,	,		15330	0.2401		0.1312	False		,,,				2504	0.3057				p.Q670Q		Atlas-SNP	.											.	CUL3	96	.	0			c.A2010G						PASS	.	T		1119,3287	398.5+/-330.9	163,793,1247	124.0	122.0	123.0		1992	2.1	1.0	2	dbSNP_96	123	1149,7451	236.0+/-268.3	86,977,3237	no	coding-synonymous	CUL3	NM_003590.3		249,1770,4484	CC,CT,TT		13.3605,25.3972,17.4381		664/769	225346646	2268,10738	2203	4300	6503	SO:0001819	synonymous_variant	8452	exon14			TGTGAATTGATCA	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1992A>G	2.37:g.225346646T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Silent	SNP	ENST00000264414.4	37	CCDS2462.1																																																																																			T|0.816;C|0.184	0.184	strong		0.318	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2		
C16orf71	146562	hgsc.bcm.edu	37	16	4790446	4790446	+	Missense_Mutation	SNP	C	C	T	rs35599524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4790446C>T	ENST00000299320.5	+	4	1047	c.569C>T	c.(568-570)tCa>tTa	p.S190L	C16orf71_ENST00000590191.1_Missense_Mutation_p.S204L|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	190			S -> L (in dbSNP:rs35599524).							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						AGCACTGCCTCACAAGAATCT	0.612													C|||	73	0.0145767	0.0061	0.0245	5008	,	,		17919	0.0069		0.0239	False		,,,				2504	0.0174				p.S190L		Atlas-SNP	.											.	C16orf71	46	.	0			c.C569T						PASS	.	C	LEU/SER	53,4341	53.6+/-89.4	1,51,2145	41.0	44.0	43.0		569	-0.2	0.0	16	dbSNP_126	43	218,8382	89.7+/-151.9	2,214,4084	yes	missense	C16orf71	NM_139170.2	145	3,265,6229	TT,TC,CC		2.5349,1.2062,2.0856	benign	190/521	4790446	271,12723	2197	4300	6497	SO:0001583	missense	146562	exon4			CTGCCTCACAAGA	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.569C>T	16.37:g.4790446C>T	ENSP00000299320:p.Ser190Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	32	0.014652014652014652	2	0.0040650406504065045	3	0.008287292817679558	6	0.01048951048951049	21	0.027704485488126648	C	10.63	1.404118	0.25291	0.012062	0.025349	ENSG00000166246	ENST00000299320	T	0.12147	2.71	4.18	-0.182	0.13287	.	1.917540	0.03379	N	0.200152	T	0.03390	0.0098	L	0.50333	1.59	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28554	-1.0040	10	0.02654	T	1	0.8564	4.4743	0.11727	0.0:0.4558:0.2178:0.3264	rs35599524	190	Q8IYS4	CP071_HUMAN	L	190	ENSP00000299320:S190L	ENSP00000299320:S190L	S	+	2	0	C16orf71	4730447	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.499000	0.06413	-0.065000	0.13021	-0.232000	0.12228	TCA	C|0.981;T|0.019	0.019	strong		0.612	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
PLA2R1	22925	hgsc.bcm.edu	37	2	160885418	160885418	+	Missense_Mutation	SNP	G	G	C	rs35771982	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160885418G>C	ENST00000283243.7	-	5	1104	c.898C>G	c.(898-900)Cac>Gac	p.H300D	PLA2R1_ENST00000392771.1_Missense_Mutation_p.H300D	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	300	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.		H -> D (in dbSNP:rs35771982). {ECO:0000269|PubMed:7721806}.		cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CAGCCAGCGTGTTCATCCAGC	0.478													G|||	1257	0.250998	0.0371	0.268	5008	,	,		19325	0.3532		0.4702	False		,,,				2504	0.1973				p.H300D		Atlas-SNP	.											.	PLA2R1	153	.	0			c.C898G						PASS	.	G	ASP/HIS,ASP/HIS,ASP/HIS	442,3964	213.1+/-232.8	23,396,1784	123.0	96.0	105.0		898,898,898	-0.9	0.0	2	dbSNP_126	105	4200,4400	569.8+/-389.2	1057,2086,1157	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	81,81,81	1080,2482,2941	CC,CG,GG		48.8372,10.0318,35.6912	benign,benign,benign	300/1325,300/1462,300/1464	160885418	4642,8364	2203	4300	6503	SO:0001583	missense	22925	exon5			CAGCGTGTTCATC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.898C>G	2.37:g.160885418G>C	ENSP00000283243:p.His300Asp	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	286	285	0.996503	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	697	0.3191391941391941	23	0.046747967479674794	109	0.3011049723756906	201	0.3513986013986014	364	0.48021108179419525	G	0.014	-1.576005	0.00887	0.100318	0.488372	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15017	2.46;2.46	5.83	-0.954	0.10359	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.824431	0.11259	N	0.582814	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44605	-0.9317	9	0.11794	T	0.64	.	5.4776	0.16704	0.0:0.3217:0.2728:0.4055	rs35771982;rs60910735;rs62175486	300;300;300	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	D	300	ENSP00000283243:H300D;ENSP00000376524:H300D	ENSP00000283243:H300D	H	-	1	0	PLA2R1	160593664	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.203000	0.09438	-0.102000	0.12197	-1.036000	0.02392	CAC	G|0.655;C|0.345	0.345	strong		0.478	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
ANKRD12	23253	hgsc.bcm.edu	37	18	9255784	9255784	+	Missense_Mutation	SNP	C	C	A	rs72939232	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:9255784C>A	ENST00000262126.4	+	9	2759	c.2519C>A	c.(2518-2520)aCc>aAc	p.T840N	ANKRD12_ENST00000400020.3_Missense_Mutation_p.T817N|ANKRD12_ENST00000383440.2_Missense_Mutation_p.T817N	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	840						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						GAAAGAAAAACCTTTGAAAAA	0.289													A|||	298	0.0595048	0.09	0.0476	5008	,	,		18075	0.0446		0.0706	False		,,,				2504	0.0307				p.T840N		Atlas-SNP	.											.	ANKRD12	167	.	0			c.C2519A						PASS	.	A	ASN/THR,ASN/THR,ASN/THR	358,4020		15,328,1846	26.0	28.0	27.0		2450,2450,2519	0.1	0.9	18	dbSNP_130	27	624,7934		23,578,3678	yes	missense,missense,missense	ANKRD12	NM_001083625.2,NM_001204056.1,NM_015208.4	65,65,65	38,906,5524	AA,AC,CC		7.2914,8.1772,7.5912	benign,benign,benign	817/2040,817/2040,840/2063	9255784	982,11954	2189	4279	6468	SO:0001583	missense	23253	exon9			GAAAAACCTTTGA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2519C>A	18.37:g.9255784C>A	ENSP00000262126:p.Thr840Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	123	75	0.609756	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	146	0.06684981684981685	40	0.08130081300813008	19	0.052486187845303865	29	0.050699300699300696	58	0.07651715039577836	A	0.001	-3.135384	0.00030	0.081772	0.072914	ENSG00000101745	ENST00000383440;ENST00000262126;ENST00000400020	T;T	0.38722	1.12;1.12	5.55	0.138	0.14793	.	0.319242	0.37623	N	0.002009	T	0.00384	0.0012	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12553	-1.0543	9	0.02654	T	1	-1.4276	0.1437	0.00086	0.3253:0.2337:0.2028:0.2381	.	817;840	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	N	817;840;111	ENSP00000372932:T817N;ENSP00000262126:T840N	ENSP00000262126:T840N	T	+	2	0	ANKRD12	9245784	0.975000	0.34042	0.879000	0.34478	0.065000	0.16274	1.935000	0.40173	-0.507000	0.06549	-1.236000	0.01555	ACC	C|0.930;A|0.070	0.070	strong		0.289	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
ZFR	51663	hgsc.bcm.edu	37	5	32400266	32400266	+	Missense_Mutation	SNP	A	A	G	rs1051489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:32400266A>G	ENST00000265069.8	-	9	1661	c.1559T>C	c.(1558-1560)aTa>aCa	p.I520T		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	520			I -> T (in dbSNP:rs1051489). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		GGTTCCTTTTATGTCTTCTGC	0.348													A|||	1166	0.232827	0.0779	0.2522	5008	,	,		16483	0.2698		0.337	False		,,,				2504	0.2832				p.I520T		Atlas-SNP	.											.	ZFR	98	.	0			c.T1559C						PASS	.	A	THR/ILE	507,3899	232.0+/-245.7	25,457,1721	137.0	122.0	127.0		1559	6.2	1.0	5	dbSNP_86	127	2943,5657	457.8+/-364.4	503,1937,1860	yes	missense	ZFR	NM_016107.3	89	528,2394,3581	GG,GA,AA		34.2209,11.507,26.5262	benign	520/1075	32400266	3450,9556	2203	4300	6503	SO:0001583	missense	51663	exon9			CCTTTTATGTCTT	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1559T>C	5.37:g.32400266A>G	ENSP00000265069:p.Ile520Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	131	63	0.480916	NM_016107	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	37	CCDS34139.1	570	0.260989010989011	48	0.0975609756097561	112	0.30939226519337015	166	0.2902097902097902	244	0.32189973614775724	A	10.44	1.351153	0.24512	0.11507	0.342209	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.04654	3.58	6.16	6.16	0.99307	.	0.448419	0.23554	N	0.046933	T	0.00012	0.0000	N	0.03608	-0.345	0.48040	P	4.3000000000004146E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.52917	-0.8511	9	0.14252	T	0.57	.	12.6258	0.56628	0.8622:0.1378:0.0:0.0	rs1051489;rs3191875;rs17846613;rs17859700;rs61138909;rs1051489	520	Q96KR1	ZFR_HUMAN	T	520;498	ENSP00000265069:I520T	ENSP00000265069:I520T	I	-	2	0	ZFR	32436023	0.986000	0.35501	0.999000	0.59377	0.980000	0.70556	3.036000	0.49767	2.367000	0.80283	0.528000	0.53228	ATA	A|0.734;G|0.266	0.266	strong		0.348	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1251803	1251803	+	Silent	SNP	C	C	T	rs9922076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1251803C>T	ENST00000348261.5	+	9	1601	c.1353C>T	c.(1351-1353)tcC>tcT	p.S451S	CACNA1H_ENST00000358590.4_Silent_p.S451S|CACNA1H_ENST00000565831.1_Silent_p.S451S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	451					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCAGCTTCTCCGAGCCTGGCA	0.647													C|||	415	0.0828674	0.0174	0.0807	5008	,	,		17242	0.0625		0.1223	False		,,,				2504	0.1534				p.S451S		Atlas-SNP	.											CACNA1H_ENST00000358590,NS,carcinoma,0,2	CACNA1H	317	2	0			c.C1353T						PASS	.	C	,	144,4166		2,140,2013	19.0	23.0	22.0		1353,1353	-7.7	0.6	16	dbSNP_119	22	1101,7403		80,941,3231	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	82,1081,5244	TT,TC,CC		12.9468,3.3411,9.7159	,	451/2348,451/2354	1251803	1245,11569	2155	4252	6407	SO:0001819	synonymous_variant	8912	exon9			CTTCTCCGAGCCT	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1353C>T	16.37:g.1251803C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	175	94	0.537143	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.925;T|0.075	0.075	strong		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
PDXDC1	23042	hgsc.bcm.edu	37	16	15111218	15111218	+	Missense_Mutation	SNP	C	C	T	rs4985162	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15111218C>T	ENST00000396410.4	+	11	999	c.902C>T	c.(901-903)cCg>cTg	p.P301L	PDXDC1_ENST00000447912.2_Missense_Mutation_p.P210L|PDXDC1_ENST00000569715.1_Missense_Mutation_p.P274L|PDXDC1_ENST00000455313.2_Missense_Mutation_p.P278L|PDXDC1_ENST00000535621.2_Missense_Mutation_p.P301L|PDXDC1_ENST00000450288.2_Missense_Mutation_p.P273L|PDXDC1_ENST00000563679.1_Missense_Mutation_p.P319L|PDXDC1_ENST00000325823.7_Missense_Mutation_p.P286L|RP11-680G24.5_ENST00000565178.1_RNA	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	301			P -> L (in dbSNP:rs4985162). {ECO:0000269|PubMed:14702039}.		carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACTCCTGGCCCGTGGCTGGGT	0.502																																					p.P301L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C902T						PASS	.	C	LEU/PRO	639,3755		23,593,1581	86.0	91.0	89.0		902	4.5	0.5	16	dbSNP_111	89	1574,7020		29,1516,2752	no	missense	PDXDC1	NM_015027.2	98	52,2109,4333	TT,TC,CC		18.3151,14.5426,17.0388	benign	301/789	15111218	2213,10775	2197	4297	6494	SO:0001583	missense	23042	exon11			CTGGCCCGTGGCT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.902C>T	16.37:g.15111218C>T	ENSP00000379691:p.Pro301Leu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	159	40	0.251572	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	583	0.26694139194139194	58	0.11788617886178862	127	0.35082872928176795	246	0.43006993006993005	152	0.20052770448548812	C	13.70	2.316841	0.40996	0.145426	0.183151	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000537781;ENST00000455313	T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19	5.45	4.49	0.54785	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.261616	0.44285	N	0.000468	T	0.00012	0.0000	N	0.19112	0.55	0.22479	P	0.999063953	B;B;B;B;B	0.15930	0.006;0.015;0.006;0.006;0.0	B;B;B;B;B	0.16722	0.006;0.016;0.01;0.01;0.001	T	0.46317	-0.9200	9	0.25106	T	0.35	-12.0274	12.4403	0.55621	0.0:0.9177:0.0:0.0823	rs4985162	273;210;301;301;278	E7EPL4;E7EMH5;Q86XE2;Q6P996;Q6P996-2	.;.;.;PDXD1_HUMAN;.	L	286;210;301;301;273;7;278	ENSP00000322807:P286L;ENSP00000400310:P210L;ENSP00000437835:P301L;ENSP00000379691:P301L;ENSP00000391147:P273L;ENSP00000406703:P278L	ENSP00000322807:P286L	P	+	2	0	PDXDC1	15018719	0.931000	0.31567	0.484000	0.27391	0.957000	0.61999	3.082000	0.50128	1.260000	0.44134	0.542000	0.68232	CCG	.	.	weak		0.502	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
UNC5C	8633	hgsc.bcm.edu	37	4	96256616	96256616	+	Silent	SNP	A	A	G	rs4699423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:96256616A>G	ENST00000453304.1	-	2	639	c.291T>C	c.(289-291)agT>agC	p.S97S	UNC5C_ENST00000506749.1_Silent_p.S97S|UNC5C_ENST00000504962.1_Silent_p.S97S	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	97	Ig-like.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		GAACCCATTCACTATTACACT	0.408													A|||	2397	0.478634	0.1324	0.5418	5008	,	,		18797	0.8343		0.4573	False		,,,				2504	0.5573				p.S97S		Atlas-SNP	.											.	UNC5C	141	.	0			c.T291C						PASS	.	A		809,3597	322.6+/-297.7	86,637,1480	132.0	126.0	128.0		291	-0.2	1.0	4	dbSNP_111	128	3933,4665	547.2+/-385.1	896,2141,1262	no	coding-synonymous	UNC5C	NM_003728.3		982,2778,2742	GG,GA,AA		45.7432,18.3613,36.4657		97/932	96256616	4742,8262	2203	4299	6502	SO:0001819	synonymous_variant	8633	exon2			CCATTCACTATTA	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.291T>C	4.37:g.96256616A>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	266	116	0.43609	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			A|0.582;G|0.418	0.418	strong		0.408	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
ABCC1	4363	hgsc.bcm.edu	37	16	16228242	16228242	+	Silent	SNP	G	G	A	rs2230671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:16228242G>A	ENST00000399410.3	+	28	4177	c.4002G>A	c.(4000-4002)tcG>tcA	p.S1334S	ABCC1_ENST00000345148.5_Silent_p.S1334S|ABCC1_ENST00000349029.5_Silent_p.S1219S|ABCC1_ENST00000346370.5_Silent_p.S1278S|ABCC1_ENST00000351154.5_Silent_p.S1275S|ABCC1_ENST00000399408.2_Silent_p.S1344S	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1334	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CTGGGAAGTCGTCCCTGACCC	0.612													G|||	877	0.17512	0.0666	0.2867	5008	,	,		17174	0.121		0.2922	False		,,,				2504	0.1779				p.S1334S		Atlas-SNP	.											.	ABCC1	156	.	0			c.G4002A						PASS	.	G	,,,,	413,3825		20,373,1726	80.0	87.0	85.0		4002,3825,3834,3657,4002	-11.8	0.2	16	dbSNP_98	85	2343,6111		318,1707,2202	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	338,2080,3928	AA,AG,GG		27.7147,9.7452,21.7145	,,,,	1334/1532,1275/1473,1278/1476,1219/1417,1334/1467	16228242	2756,9936	2119	4227	6346	SO:0001819	synonymous_variant	4363	exon28			GAAGTCGTCCCTG	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.4002G>A	16.37:g.16228242G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	62	23	0.370968	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			A|0.144;C|0.214;G|0.608;T|0.034	0.144	strong		0.612	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
TBC1D32	221322	hgsc.bcm.edu	37	6	121401996	121401996	+	Missense_Mutation	SNP	T	T	G	rs56300302	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:121401996T>G	ENST00000398212.2	-	32	3744	c.3695A>C	c.(3694-3696)gAa>gCa	p.E1232A	TBC1D32_ENST00000275159.6_Missense_Mutation_p.E1273A|TBC1D32_ENST00000398197.2_5'UTR	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	1232	Rab-GAP TBC.				cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TTCCATGTATTCAAAATAATC	0.383													T|||	73	0.0145767	0.0189	0.0202	5008	,	,		15540	0.002		0.0139	False		,,,				2504	0.0184				p.E1232A		Atlas-SNP	.											C6orf170,NS,carcinoma,-1,1	C6orf170	146	1	0			c.A3695C						scavenged	.	T	ALA/GLU	44,3710		1,42,1834	100.0	93.0	95.0		3695	5.6	1.0	6	dbSNP_129	95	129,8115		3,123,3996	yes	missense	C6orf170	NM_152730.4	107	4,165,5830	GG,GT,TT		1.5648,1.1721,1.4419	possibly-damaging	1232/1258	121401996	173,11825	1877	4122	5999	SO:0001583	missense	221322	exon32			ATGTATTCAAAAT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.3695A>C	6.37:g.121401996T>G	ENSP00000381270:p.Glu1232Ala	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	160	59	0.36875	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	28	0.01282051282051282	11	0.022357723577235773	6	0.016574585635359115	0	0.0	11	0.014511873350923483	T	18.36	3.606885	0.66558	0.011721	0.015648	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.25579	1.79;1.79	5.55	5.55	0.83447	Rab-GAP/TBC domain (1);	0.229097	0.42294	D	0.000726	T	0.16896	0.0406	L	0.56769	1.78	0.54753	D	0.999989	B	0.23990	0.095	B	0.20384	0.029	T	0.03086	-1.1074	10	0.66056	D	0.02	.	15.1725	0.72884	0.0:0.0:0.0:1.0	rs56300302	1232	Q96NH3	BROMI_HUMAN	A	1273;1232	ENSP00000275159:E1273A;ENSP00000381270:E1232A	ENSP00000275159:E1273A	E	-	2	0	C6orf170	121443695	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.177000	0.58276	2.228000	0.72767	0.528000	0.53228	GAA	T|0.984;G|0.016	0.016	strong		0.383	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
COG2	22796	hgsc.bcm.edu	37	1	230829139	230829139	+	Silent	SNP	A	A	G	rs1051038	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:230829139A>G	ENST00000366669.4	+	18	2332	c.2217A>G	c.(2215-2217)taA>taG	p.*739*	COG2_ENST00000366668.3_Silent_p.*738*|COG2_ENST00000534989.1_Silent_p.*680*|COG2_ENST00000535166.1_Silent_p.*623*|COG2_ENST00000546013.1_Silent_p.*428*	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	0					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AGCAGCCTTAAGCATCTTGGA	0.483													A|||	1726	0.344649	0.2345	0.4352	5008	,	,		17468	0.5913		0.2087	False		,,,				2504	0.3149				p.X739X		Atlas-SNP	.											.	COG2	61	.	0			c.A2217G						PASS	.	A	,	887,3519	340.2+/-306.1	89,709,1405	52.0	54.0	53.0		2214,2217	-0.2	0.0	1	dbSNP_86	53	1891,6709	329.3+/-318.7	217,1457,2626	no	coding-synonymous,coding-synonymous	COG2	NM_001145036.1,NM_007357.2	,	306,2166,4031	GG,GA,AA		21.9884,20.1316,21.3594	,	738/738,739/739	230829139	2778,10228	2203	4300	6503	SO:0001819	synonymous_variant	22796	exon18			GCCTTAAGCATCT	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.2217A>G	1.37:g.230829139A>G		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	199	94	0.472362	NM_007357	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																			A|0.735;G|0.265	0.265	strong		0.483	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
TTC28	23331	hgsc.bcm.edu	37	22	28504183	28504183	+	Silent	SNP	G	G	A	rs9625408	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:28504183G>A	ENST00000397906.2	-	7	1791	c.1650C>T	c.(1648-1650)cgC>cgT	p.R550R		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	550					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						CCTGTGAGGCGCGGTCATTCA	0.582													G|||	276	0.0551118	0.0439	0.0677	5008	,	,		16746	0.003		0.0746	False		,,,				2504	0.0951				p.R550R		Atlas-SNP	.											.	TTC28	84	.	0			c.C1650T						PASS	.	G		73,1311		0,73,619	84.0	80.0	81.0		1650	-11.8	0.4	22	dbSNP_119	81	264,2918		15,234,1342	no	coding-synonymous	TTC28	NM_001145418.1		15,307,1961	AA,AG,GG		8.2967,5.2746,7.3806		550/2482	28504183	337,4229	692	1591	2283	SO:0001819	synonymous_variant	23331	exon7			TGAGGCGCGGTCA	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.1650C>T	22.37:g.28504183G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			G|0.949;A|0.051	0.051	strong		0.582	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
RAB39A	54734	hgsc.bcm.edu	37	11	107833065	107833065	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:107833065A>C	ENST00000320578.2	+	2	687	c.621A>C	c.(619-621)gaA>gaC	p.E207D		NM_017516.1	NP_059986.1	Q14964	RB39A_HUMAN	RAB39A, member RAS oncogene family	207					phagosome acidification (GO:0090383)|phagosome-lysosome fusion (GO:0090385)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)										CTTCTGAGGAAGCAGTAAAGC	0.383																																					p.E207D		Atlas-SNP	.											.	.	.	.	0			c.A621C						PASS	.						49.0	55.0	53.0					11																	107833065		2200	4298	6498	SO:0001583	missense	54734	exon2			TGAGGAAGCAGTA	X99962	CCDS8338.1	11q22.3	2011-11-22	2011-11-22	2011-11-22	ENSG00000179331	ENSG00000179331		"""RAB, member RAS oncogene"""	16521	protein-coding gene	gene with protein product	"""rab-related GTP-binding protein"""		"""RAB39, member RAS oncogene family"""	RAB39		9119394	Standard	NM_017516		Approved		uc001pjt.3	Q14964	OTTHUMG00000166367	ENST00000320578.2:c.621A>C	11.37:g.107833065A>C	ENSP00000322594:p.Glu207Asp	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_017516	A8KAA4|Q8N6W2	Missense_Mutation	SNP	ENST00000320578.2	37	CCDS8338.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.323277	0.24080	.	.	ENSG00000179331	ENST00000320578	T	0.66995	-0.24	5.55	3.27	0.37495	.	0.000000	0.64402	D	0.000010	T	0.45034	0.1322	N	0.19112	0.55	0.32971	D	0.52234	B	0.16166	0.016	B	0.12156	0.007	T	0.43766	-0.9371	10	0.13108	T	0.6	.	8.0299	0.30459	0.7816:0.0:0.2184:0.0	.	207	Q14964	RB39A_HUMAN	D	207	ENSP00000322594:E207D	ENSP00000322594:E207D	E	+	3	2	RAB39	107338275	0.984000	0.35163	1.000000	0.80357	0.984000	0.73092	0.350000	0.20079	0.553000	0.29044	0.482000	0.46254	GAA	.	.	none		0.383	RAB39A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389423.1	NM_017516	
KIAA1109	84162	hgsc.bcm.edu	37	4	123171659	123171659	+	Missense_Mutation	SNP	T	T	A	rs56363411	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:123171659T>A	ENST00000264501.4	+	37	6226	c.5853T>A	c.(5851-5853)gaT>gaA	p.D1951E	KIAA1109_ENST00000388738.3_Missense_Mutation_p.D1951E|KIAA1109_ENST00000455637.1_Missense_Mutation_p.D1951E			Q2LD37	K1109_HUMAN	KIAA1109	1951			D -> E (in dbSNP:rs56363411).		regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATGTCTCTGATGATAATCTTC	0.403													T|||	56	0.0111821	0.0023	0.0231	5008	,	,		14231	0.0		0.0288	False		,,,				2504	0.0082				p.D1951E		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T5853A						PASS	.	T	GLU/ASP	25,3757		1,23,1867	123.0	117.0	119.0		5853	0.0	1.0	4	dbSNP_129	119	268,7930		6,256,3837	yes	missense	KIAA1109	NM_015312.3	45	7,279,5704	AA,AT,TT		3.2691,0.661,2.4457	benign	1951/5006	123171659	293,11687	1891	4099	5990	SO:0001583	missense	84162	exon35			CTCTGATGATAAT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.5853T>A	4.37:g.123171659T>A	ENSP00000264501:p.Asp1951Glu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	31|31	0.014194139194139194|0.014194139194139194	2|2	0.0040650406504065045|0.0040650406504065045	11|11	0.03038674033149171|0.03038674033149171	0|0	0.0|0.0	18|18	0.023746701846965697|0.023746701846965697	T|T	11.44|11.44	1.639401|1.639401	0.29157|0.29157	0.00661|0.00661	0.032691|0.032691	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	T;T;T|.	0.26660|.	2.31;2.31;1.72|.	5.63|5.63	0.0142|0.0142	0.14099|0.14099	.|.	0.112528|.	0.33591|.	U|.	0.004741|.	T|T	0.13329|0.13329	0.0323|0.0323	L|L	0.47716|0.47716	1.5|1.5	0.30755|0.30755	N|N	0.744712|0.744712	B;B|.	0.12013|.	0.005;0.0|.	B;B|.	0.12156|.	0.007;0.002|.	T|T	0.30090|0.30090	-0.9990|-0.9990	10|5	0.06891|.	T|.	0.86|.	.|.	1.477|1.477	0.02428|0.02428	0.1685:0.2167:0.1044:0.5104|0.1685:0.2167:0.1044:0.5104	rs56363411|rs56363411	1950;1951|.	Q2LD37-2;Q2LD37|.	.;K1109_HUMAN|.	E|K	1951|524	ENSP00000264501:D1951E;ENSP00000373390:D1951E;ENSP00000389925:D1951E|.	ENSP00000264501:D1951E|.	D|M	+|+	3|2	2|0	KIAA1109|KIAA1109	123391109|123391109	0.968000|0.968000	0.33430|0.33430	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	0.029000|0.029000	0.13666|0.13666	0.078000|0.078000	0.16900|0.16900	0.528000|0.528000	0.53228|0.53228	GAT|ATG	T|0.982;A|0.018	0.018	strong		0.403	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
KCNQ1	3784	hgsc.bcm.edu	37	11	2869188	2869188	+	Silent	SNP	C	C	T	rs11601907	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:2869188C>T	ENST00000155840.5	+	16	2094	c.1986C>T	c.(1984-1986)taC>taT	p.Y662Y	KCNQ1_ENST00000335475.5_Silent_p.Y535Y|KCNQ1_ENST00000526095.1_3'UTR|KCNQ1-AS1_ENST00000440887.2_RNA	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	662					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	TGCCCACCTACGAGCAGCTGA	0.716													C|||	417	0.0832668	0.0242	0.1081	5008	,	,		13923	0.0		0.2386	False		,,,				2504	0.0716				p.Y662Y		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1986T						PASS	.	C	,	241,4067		10,221,1923	10.0	10.0	10.0		1986,1605	-2.3	1.0	11	dbSNP_120	10	1984,6538		231,1522,2508	no	coding-synonymous,coding-synonymous	KCNQ1	NM_000218.2,NM_181798.1	,	241,1743,4431	TT,TC,CC		23.2809,5.5942,17.3422	,	662/677,535/550	2869188	2225,10605	2154	4261	6415	SO:0001819	synonymous_variant	3784	exon16			CACCTACGAGCAG	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6294	protein-coding gene	gene with protein product	"""Jervell and Lange-Nielsen syndrome 1"""	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1986C>T	11.37:g.2869188C>T		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			C|0.892;T|0.108	0.108	strong		0.716	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
THSD7A	221981	hgsc.bcm.edu	37	7	11676107	11676107	+	Silent	SNP	G	G	A	rs61996270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:11676107G>A	ENST00000423059.4	-	2	923	c.672C>T	c.(670-672)ccC>ccT	p.P224P	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	224	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CGAACTGCGGGGGCGCCACCA	0.622										HNSCC(18;0.044)			G|||	84	0.0167732	0.0098	0.0245	5008	,	,		15704	0.0		0.0487	False		,,,				2504	0.0051				p.P224P		Atlas-SNP	.											.	THSD7A	219	.	0			c.C672T						PASS	.	G		72,3984		3,66,1959	26.0	27.0	27.0		672	-3.5	0.2	7	dbSNP_129	27	494,7894		19,456,3719	no	coding-synonymous	THSD7A	NM_015204.2		22,522,5678	AA,AG,GG		5.8894,1.7751,4.5484		224/1658	11676107	566,11878	2028	4194	6222	SO:0001819	synonymous_variant	221981	exon2			CTGCGGGGGCGCC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.672C>T	7.37:g.11676107G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	25	0.373134	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			G|0.972;A|0.028	0.028	strong		0.622	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
PIWIL4	143689	hgsc.bcm.edu	37	11	94322353	94322353	+	Silent	SNP	G	G	A	rs11020846|rs386756343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:94322353G>A	ENST00000299001.6	+	8	1192	c.981G>A	c.(979-981)caG>caA	p.Q327Q	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	327	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.		Q -> L (in dbSNP:rs11020845). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ACACCTTTCAGAAGCGGGATG	0.398													G|||	942	0.188099	0.0598	0.1873	5008	,	,		18396	0.2817		0.2813	False		,,,				2504	0.1697				p.Q327Q		Atlas-SNP	.											.	PIWIL4	70	.	0			c.G981A						PASS	.	G		21,4381		7,7,2187	178.0	161.0	167.0		981	4.0	0.8	11	dbSNP_120	167	308,8288		118,72,4108	no	coding-synonymous	PIWIL4	NM_152431.2		125,79,6295	AA,AG,GG		3.5831,0.4771,2.5312		327/853	94322353	329,12669	2201	4298	6499	SO:0001819	synonymous_variant	143689	exon8			CTTTCAGAAGCGG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.981G>A	11.37:g.94322353G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	192	99	0.515625	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			G|0.793;A|0.207	0.207	strong		0.398	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
TNP2	7142	hgsc.bcm.edu	37	16	11362729	11362729	+	Missense_Mutation	SNP	G	G	A	rs11640138	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11362729G>A	ENST00000312693.3	-	1	460	c.391C>T	c.(391-393)Cgg>Tgg	p.R131W	RMI2_ENST00000572173.1_Intron	NM_005425.4	NP_005416.1	Q05952	STP2_HUMAN	transition protein 2 (during histone to protamine replacement)	131			R -> W (in dbSNP:rs11640138).		acrosome reaction (GO:0007340)|binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.0?(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						CCTGAGCTCCGCGTCTTGGTT	0.557													G|||	1669	0.333267	0.264	0.3487	5008	,	,		20710	0.2401		0.5358	False		,,,				2504	0.3037				p.R131W		Atlas-SNP	.											TNP2,NS,carcinoma,+2,1	TNP2	15	1	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C391T						PASS	.	G	TRP/ARG	1080,2884		138,804,1040	44.0	45.0	45.0		391	1.7	0.3	16	dbSNP_120	45	4437,3875		1214,2009,933	yes	missense	TNP2	NM_005425.4	101	1352,2813,1973	AA,AG,GG		46.6193,27.2452,44.9413	probably-damaging	131/139	11362729	5517,6759	1982	4156	6138	SO:0001583	missense	7142	exon1			AGCTCCGCGTCTT		CCDS45410.1	16p13.13	2008-08-01				ENSG00000178279			11952	protein-coding gene	gene with protein product		190232				1395729, 2250010	Standard	NM_005425		Approved	TP2	uc002das.3	Q05952		ENST00000312693.3:c.391C>T	16.37:g.11362729G>A	ENSP00000325738:p.Arg131Trp	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_005425	Q9NZB0	Missense_Mutation	SNP	ENST00000312693.3	37	CCDS45410.1	824	0.3772893772893773	125	0.2540650406504065	143	0.39502762430939226	143	0.25	413	0.5448548812664907	G	9.951	1.220264	0.22457	0.272452	0.533807	ENSG00000178279	ENST00000312693	T	0.54479	0.57	3.69	1.74	0.24563	.	0.265469	0.20223	N	0.096660	T	0.00012	0.0000	L	0.35854	1.095	0.49687	P	1.8200000000001548E-4	P	0.46912	0.886	B	0.37015	0.239	T	0.48570	-0.9024	9	0.52906	T	0.07	-5.3047	5.9656	0.19322	0.2364:0.0:0.7636:0.0	rs11640138;rs17807085;rs52838377;rs59366167;rs11640138	131	Q05952	STP2_HUMAN	W	131	ENSP00000325738:R131W	ENSP00000325738:R131W	R	-	1	2	TNP2	11270230	0.995000	0.38212	0.270000	0.24601	0.008000	0.06430	2.741000	0.47426	0.546000	0.28920	0.650000	0.86243	CGG	G|0.637;A|0.363	0.363	strong		0.557	TNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417806.1	NM_005425	
CCDC180	100499483	hgsc.bcm.edu	37	9	100071728	100071728	+	Silent	SNP	G	G	A	rs3747507	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100071728G>A	ENST00000357054.1	+	17	1586	c.651G>A	c.(649-651)agG>agA	p.R217R	CCDC180_ENST00000529487.1_Silent_p.R78R|CCDC180_ENST00000411667.2_Silent_p.R78R|CCDC180_ENST00000395220.1_Silent_p.R217R|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_Silent_p.R78R			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	217						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CGGCCACCAGGAAGCGGGCTG	0.607													G|||	1365	0.272564	0.2958	0.3501	5008	,	,		18304	0.2887		0.1839	False		,,,				2504	0.2607				p.R78R		Atlas-SNP	.											.	.	.	.	0			c.G234A						PASS	.	G		1183,3223	413.7+/-336.6	156,871,1176	56.0	55.0	56.0		234	2.4	1.0	9	dbSNP_107	56	1567,7033	295.0+/-302.2	137,1293,2870	no	coding-synonymous	C9orf174	NM_020893.2		293,2164,4046	AA,AG,GG		18.2209,26.8498,21.1441		78/1702	100071728	2750,10256	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			CACCAGGAAGCGG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.651G>A	9.37:g.100071728G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	130	52	0.4	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				G|0.774;A|0.226	0.226	strong		0.607	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
GAS6	2621	hgsc.bcm.edu	37	13	114531565	114531565	+	Silent	SNP	C	C	G	rs8191975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:114531565C>G	ENST00000327773.6	-	11	1409	c.1263G>C	c.(1261-1263)ctG>ctC	p.L421L	GAS6_ENST00000355761.4_Silent_p.L367L|GAS6_ENST00000418959.3_Silent_p.L122L|GAS6_ENST00000357389.3_Silent_p.L464L|GAS6_ENST00000450766.1_Silent_p.L148L|GAS6-AS1_ENST00000458001.1_RNA	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	464	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				activation of protein kinase B activity (GO:0032148)|apoptotic cell clearance (GO:0043277)|B cell chemotaxis (GO:0035754)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interferon-alpha (GO:0035457)|cellular response to starvation (GO:0009267)|cellular response to vitamin K (GO:0071307)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|extracellular matrix assembly (GO:0085029)|fusion of virus membrane with host plasma membrane (GO:0019064)|hematopoietic stem cell migration to bone marrow (GO:0097241)|leukocyte migration (GO:0050900)|macrophage cytokine production (GO:0010934)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of oligodendrocyte apoptotic process (GO:1900142)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of renal albumin absorption (GO:2000533)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|peptidyl-serine phosphorylation (GO:0018105)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phagocytosis (GO:0050766)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of TOR signaling (GO:0032008)|post-translational protein modification (GO:0043687)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein targeting to plasma membrane (GO:0072661)|proteolysis (GO:0006508)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|viral entry into host cell (GO:0046718)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|platelet alpha granule lumen (GO:0031093)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|phosphatidylserine binding (GO:0001786)|protein tyrosine kinase activator activity (GO:0030296)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(4)|ovary(1)	5	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				CTCCCACGGTCAGGTTCAGAT	0.577													a|||	898	0.179313	0.1702	0.1412	5008	,	,		17287	0.2014		0.0676	False		,,,				2504	0.3108				p.L421L		Atlas-SNP	.											GAS6_ENST00000357389,NS,carcinoma,-2,3	GAS6	75	3	0			c.G1263C						PASS	.		,,	769,3637		80,609,1514	147.0	127.0	134.0		1263,444,366	-8.2	0.4	13	dbSNP_117	134	620,7980		19,582,3699	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS6	NM_000820.2,NM_001143945.1,NM_001143946.1	,,	99,1191,5213	GG,GC,CC		7.2093,17.4535,10.6797	,,	421/679,148/406,122/380	114531565	1389,11617	2203	4300	6503	SO:0001819	synonymous_variant	2621	exon11			CACGGTCAGGTTC		CCDS45072.1	13q34	2008-07-18			ENSG00000183087	ENSG00000183087			4168	protein-coding gene	gene with protein product	"""AXL stimulatory factor"""	600441		AXLLG		8336730	Standard	NM_000820		Approved	AXSF, FLJ34709, DKFZp666G247	uc001vud.3	Q14393	OTTHUMG00000017395	ENST00000327773.6:c.1263G>C	13.37:g.114531565C>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	141	62	0.439716	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Silent	SNP	ENST00000327773.6	37	CCDS45072.1																																																																																			C|0.892;G|0.108	0.108	strong		0.577	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820	
TMA16	55319	hgsc.bcm.edu	37	4	164440581	164440581	+	Missense_Mutation	SNP	T	T	C	rs1561736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:164440581T>C	ENST00000358572.5	+	7	868	c.527T>C	c.(526-528)aTt>aCt	p.I176T	TMA16_ENST00000513272.1_3'UTR|TMA16_ENST00000513134.1_Intron	NM_018352.2	NP_060822.2	Q96EY4	TMA16_HUMAN	translation machinery associated 16 homolog (S. cerevisiae)	176			I -> T (in dbSNP:rs1561736). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)		p.I176T(1)									AGGAAAACTATTATAACTGTA	0.373													T|||	1916	0.382588	0.2526	0.6052	5008	,	,		18042	0.3423		0.4742	False		,,,				2504	0.3476				p.I176T		Atlas-SNP	.											C4orf43,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T527C						PASS	.	T	THR/ILE	1026,2688		147,732,978	53.0	53.0	53.0		527	-0.5	0.0	4	dbSNP_88	53	3916,4252		965,1986,1133	no	missense	C4orf43	NM_018352.2	89	1112,2718,2111	CC,CT,TT		47.9432,27.6252,41.5923	benign	176/204	164440581	4942,6940	1857	4084	5941	SO:0001583	missense	55319	exon7			AAACTATTATAAC		CCDS43278.1	4q32.3	2012-03-02	2012-03-02	2012-03-02	ENSG00000198498	ENSG00000198498			25638	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 43"""	C4orf43		12477932	Standard	NM_018352		Approved	FLJ11184	uc003iqq.4	Q96EY4	OTTHUMG00000161528	ENST00000358572.5:c.527T>C	4.37:g.164440581T>C	ENSP00000351380:p.Ile176Thr	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	239	119	0.497908	NM_018352	Q0P6E4|Q0P6J1|Q9NUR7	Missense_Mutation	SNP	ENST00000358572.5	37	CCDS43278.1	901	0.4125457875457875	124	0.25203252032520324	216	0.5966850828729282	197	0.34440559440559443	364	0.48021108179419525	T	2.009	-0.427555	0.04701	0.276252	0.479432	ENSG00000198498	ENST00000358572	T	0.21734	1.99	5.05	-0.516	0.11950	.	1.344700	0.04600	N	0.398357	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45041	-0.9288	9	0.07990	T	0.79	3.0277	3.462	0.07536	0.3859:0.1705:0.0:0.4436	rs1561736;rs3207217;rs17043749;rs17845311;rs17858149;rs1561736	176	Q96EY4	CD043_HUMAN	T	176	ENSP00000351380:I176T	ENSP00000351380:I176T	I	+	2	0	C4orf43	164660031	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.439000	0.06897	-0.127000	0.11661	0.533000	0.62120	ATT	T|0.582;C|0.418	0.418	strong		0.373	TMA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365208.1	NM_018352	
MLH1	4292	hgsc.bcm.edu	37	3	37089131	37089131	+	Missense_Mutation	SNP	A	A	C	rs587778949|rs63749986|rs35502531|rs63750449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37089131A>C	ENST00000231790.2	+	16	2069	c.1853A>C	c.(1852-1854)aAg>aCg	p.K618T	MLH1_ENST00000536378.1_Missense_Mutation_p.K377T|MLH1_ENST00000458205.2_Missense_Mutation_p.K377T|MLH1_ENST00000455445.2_Missense_Mutation_p.K377T|MLH1_ENST00000539477.1_Missense_Mutation_p.K377T|MLH1_ENST00000435176.1_Missense_Mutation_p.K520T	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	618	Interaction with EXO1.		K -> A (common polymorphism; requires 2 nucleotide substitutions; dbSNP:rs35502531). {ECO:0000269|PubMed:10598809, ECO:0000269|PubMed:10713887, ECO:0000269|PubMed:11726306, ECO:0000269|PubMed:11870161, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12373605, ECO:0000269|PubMed:16083711, ECO:0000269|PubMed:18033691, ECO:0000269|PubMed:9311737}.|K -> R (in colorectal cancer; dbSNP:rs63750449). {ECO:0000269|PubMed:14504054}.|K -> T (in HNPCC2; type II). {ECO:0000269|PubMed:10573010, ECO:0000269|PubMed:11839723, ECO:0000269|PubMed:12095971, ECO:0000269|PubMed:7757073, ECO:0000269|PubMed:8872463}.|Missing (in HNPCC2). {ECO:0000269|PubMed:16451135}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.K618del(1)|p.0?(1)|p.K618T(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						CTGAAGAAGAAGGCTGAGATG	0.428		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	16	0.00319489	0.0008	0.0072	5008	,	,		20491	0.0		0.0099	False		,,,				2504	0.0				p.K618T		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,colon,carcinoma,0,5	MLH1	226	5	3	Substitution - Missense(1)|Whole gene deletion(1)|Deletion - In frame(1)	large_intestine(2)|ovary(1)	c.A1853C	GRCh37	CM950808	MLH1	M	rs63750449	PASS	.	A	THR/LYS,THR/LYS,THR/LYS,THR/LYS	9,4397	15.5+/-35.6	0,9,2194	158.0	161.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1853,1559,1130,1130	5.3	1.0	3	dbSNP_130	160	40,8560	22.2+/-67.0	0,40,4260	yes	missense,missense,missense,missense	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	78,78,78,78	0,49,6454	CC,CA,AA		0.4651,0.2043,0.3767	probably-damaging,probably-damaging,probably-damaging,probably-damaging	618/757,520/659,377/516,377/516	37089131	49,12957	2203	4300	6503	SO:0001583	missense	4292	exon16	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AGAAGAAGGCTGA	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.1853A>C	3.37:g.37089131A>C	ENSP00000231790:p.Lys618Thr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	134	80	0.597015	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	9	0.004120879120879121	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	23.0	4.366099	0.82463	0.002043	0.004651	ENSG00000076242	ENST00000231790;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	D;D;D;D;D;D	0.94650	-3.48;-3.48;-3.48;-3.48;-3.48;-3.48	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.96430	0.8835	M	0.87097	2.86	0.80722	D	1	D;D;D;D	0.76494	0.999;0.997;0.999;0.997	D;D;D;D	0.73708	0.981;0.968;0.981;0.975	D	0.95622	0.8682	10	0.66056	D	0.02	-23.9591	15.372	0.74573	1.0:0.0:0.0:0.0	rs63750449	520;618;618;618	E9PCU2;B2R6K0;Q53GX1;P40692	.;.;.;MLH1_HUMAN	T	618;482;377;377;377;520;377	ENSP00000231790:K618T;ENSP00000402667:K377T;ENSP00000443665:K377T;ENSP00000398272:K377T;ENSP00000402564:K520T;ENSP00000444286:K377T	ENSP00000231790:K618T	K	+	2	0	MLH1	37064135	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.339000	0.79282	2.044000	0.60594	0.477000	0.44152	AAG	A|0.995;C|0.005	0.005	strong		0.428	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
RPGR	6103	hgsc.bcm.edu	37	X	38147269	38147269	+	Missense_Mutation	SNP	G	G	A	rs41312104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:38147269G>A	ENST00000339363.3	-	14	1765	c.1598C>T	c.(1597-1599)aCg>aTg	p.T533M	RPGR_ENST00000309513.3_Missense_Mutation_p.T471M|RPGR_ENST00000378505.2_Missense_Mutation_p.T533M|RPGR_ENST00000342811.3_Missense_Mutation_p.T533M|RPGR_ENST00000318842.7_Missense_Mutation_p.T533M|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000338898.3_3'UTR			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	533	Glu-rich.		T -> M (in dbSNP:rs41312104). {ECO:0000269|PubMed:10980543}.		cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						TGTATCCTGCGTCAGTTCCCC	0.328													G|||	34	0.00900662	0.0008	0.0086	3775	,	,		15606	0.0		0.0268	False		,,,				2504	0.0				p.T533M		Atlas-SNP	.											.	RPGR	175	.	0			c.C1598T						PASS	.	A	MET/THR,MET/THR	13,3820		0,12,1,1619,570	177.0	146.0	156.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1598,1598	-3.7	0.0	X	dbSNP_127	156	197,6531		1,138,57,2289,1815	yes	missense,missense	RPGR	NM_000328.2,NM_001034853.1	81,81	1,150,58,3908,2385	AA,AG,A,GG,G		2.9281,0.3392,1.9884	benign,benign	533/816,533/1153	38147269	210,10351	2202	4300	6502	SO:0001583	missense	6103	exon14			TCCTGCGTCAGTT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.1598C>T	X.37:g.38147269G>A	ENSP00000343671:p.Thr533Met	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	91	89	0.978022	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		27	0.0162748643761302	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	15	0.020161290322580645	g	0.242	-1.013083	0.02095	0.003392	0.029281	ENSG00000156313	ENST00000339363;ENST00000309513;ENST00000318842;ENST00000342811;ENST00000378505	T;T;T;T;T	0.36340	2.26;3.7;3.7;1.32;1.26	4.16	-3.74	0.04385	.	0.991846	0.08189	N	0.984272	T	0.02848	0.0085	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.31077	0.307;0.274	B;B	0.19148	0.009;0.024	T	0.10109	-1.0644	9	0.38643	T	0.18	.	0.7649	0.01013	0.2809:0.1039:0.2504:0.3649	rs41312104;rs62635012	533;533	E9PE28;Q92834-2	.;.	M	533;471;533;533;533	ENSP00000343671:T533M;ENSP00000308783:T471M;ENSP00000322219:T533M;ENSP00000339531:T533M;ENSP00000367766:T533M	ENSP00000308783:T471M	T	-	2	0	RPGR	38032213	0.001000	0.12720	0.000000	0.03702	0.008000	0.06430	0.075000	0.14686	-1.482000	0.01860	-3.286000	0.00047	ACG	G|0.983;A|0.017	0.017	strong		0.328	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
ALPK2	115701	hgsc.bcm.edu	37	18	56247600	56247600	+	Missense_Mutation	SNP	C	C	A	rs9944810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56247600C>A	ENST00000361673.3	-	4	621	c.408G>T	c.(406-408)agG>agT	p.R136S	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	136			R -> S (in dbSNP:rs9944810).			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TCTGATTTGCCCTTTCTTCTT	0.493													A|||	2418	0.482827	0.3306	0.4755	5008	,	,		21643	0.6022		0.5	False		,,,				2504	0.5532				p.R136S		Atlas-SNP	.											.	ALPK2	487	.	0			c.G408T						PASS	.	A	SER/ARG	1480,2752		300,880,936	284.0	272.0	276.0		408	-6.2	0.0	18	dbSNP_119	276	4213,4229		1090,2033,1098	yes	missense	ALPK2	NM_052947.3	110	1390,2913,2034	AA,AC,CC		49.9052,34.9716,44.9187	benign	136/2171	56247600	5693,6981	2116	4221	6337	SO:0001583	missense	115701	exon4			ATTTGCCCTTTCT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.408G>T	18.37:g.56247600C>A	ENSP00000354991:p.Arg136Ser	Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	260	258	0.992308	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	1042	0.47710622710622713	139	0.28252032520325204	177	0.4889502762430939	354	0.6188811188811189	372	0.49076517150395776	A	0.956	-0.704751	0.03255	0.349716	0.499052	ENSG00000198796	ENST00000361673	T	0.39056	1.1	5.65	-6.19	0.02078	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	8	0.17369	T	0.5	6.1102	3.3774	0.07242	0.4685:0.2586:0.186:0.087	rs9944810;rs9944810	136	Q86TB3	ALPK2_HUMAN	S	136	ENSP00000354991:R136S	ENSP00000354991:R136S	R	-	3	2	ALPK2	54398580	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.613000	0.05610	-1.702000	0.01411	-0.520000	0.04383	AGG	A|0.485;C|0.515;G|0.000;T|0.000	0.485	strong		0.493	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
EIF4G1	1981	hgsc.bcm.edu	37	3	184046470	184046470	+	Silent	SNP	C	C	T	rs2230571	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:184046470C>T	ENST00000346169.2	+	27	4276	c.4005C>T	c.(4003-4005)caC>caT	p.H1335H	EIF4G1_ENST00000319274.6_Silent_p.H1335H|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000424196.1_Silent_p.H1342H|EIF4G1_ENST00000435046.2_Silent_p.H1139H|EIF4G1_ENST00000414031.1_Silent_p.H1295H|EIF4G1_ENST00000441154.1_Silent_p.H1172H|EIF4G1_ENST00000342981.4_Silent_p.H1336H|EIF4G1_ENST00000427845.1_Silent_p.H1249H|EIF4G1_ENST00000411531.1_Silent_p.H1296H|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000382330.3_Silent_p.H1342H|EIF4G1_ENST00000392537.2_Silent_p.H1248H|EIF4G1_ENST00000352767.3_Silent_p.H1342H|EIF4G1_ENST00000350481.5_Silent_p.H1171H|EIF4G1_ENST00000434061.2_Silent_p.H1140H	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1335	MI. {ECO:0000255|PROSITE- ProRule:PRU00698}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACATCCCCCACGTGTGGCTCT	0.532													C|||	672	0.134185	0.0219	0.1354	5008	,	,		19260	0.0506		0.2346	False		,,,				2504	0.2679				p.H1342H		Atlas-SNP	.											EIF4G1,NS,adenoma,0,1	EIF4G1	151	1	0			c.C4026T						PASS	.	C	,,,,,,	252,4154	146.1+/-180.8	11,230,1962	149.0	149.0	149.0		4026,4026,3420,4008,4005,3513,3744	-4.2	1.0	3	dbSNP_98	149	2115,6485	365.1+/-333.8	282,1551,2467	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	,,,,,,	293,1781,4429	TT,TC,CC		24.593,5.7195,18.1993	,,,,,,	1342/1607,1342/1607,1140/1405,1336/1601,1335/1600,1171/1436,1248/1513	184046470	2367,10639	2203	4300	6503	SO:0001819	synonymous_variant	1981	exon28			CCCCCACGTGTGG	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4005C>T	3.37:g.184046470C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	151	56	0.370861	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			C|0.850;T|0.150	0.150	strong		0.532	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
PPP1R17	10842	hgsc.bcm.edu	37	7	31732084	31732084	+	Missense_Mutation	SNP	T	T	G	rs36047130	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:31732084T>G	ENST00000342032.3	+	2	657	c.29T>G	c.(28-30)cTg>cGg	p.L10R	PPP1R17_ENST00000409146.3_Missense_Mutation_p.L10R	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	10			L -> R (in dbSNP:rs36047130).		central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)										ATGCAGCCACTGGAACTCTCA	0.443													T|||	136	0.0271565	0.0378	0.0187	5008	,	,		19810	0.0099		0.0129	False		,,,				2504	0.0511				p.L10R		Atlas-SNP	.											.	.	.	.	0			c.T29G						PASS	.	T	ARG/LEU,ARG/LEU	115,4291	87.3+/-125.9	1,113,2089	118.0	103.0	108.0		29,29	2.4	0.7	7	dbSNP_126	108	117,8483	62.1+/-124.0	4,109,4187	yes	missense,missense	C7orf16	NM_001145123.2,NM_006658.4	102,102	5,222,6276	GG,GT,TT		1.3605,2.6101,1.7838	probably-damaging,probably-damaging	10/105,10/156	31732084	232,12774	2203	4300	6503	SO:0001583	missense	10842	exon2			AGCCACTGGAACT	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16973	protein-coding gene	gene with protein product	"""G-substrate"""	604088	"""chromosome 7 open reading frame 16"""	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.29T>G	7.37:g.31732084T>G	ENSP00000340125:p.Leu10Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_006658	B4DE58|Q9UDQ0	Missense_Mutation	SNP	ENST00000342032.3	37	CCDS5436.1	47	0.02152014652014652	24	0.04878048780487805	10	0.027624309392265192	6	0.01048951048951049	7	0.009234828496042216	T	11.13	1.548557	0.27652	0.026101	0.013605	ENSG00000106341	ENST00000342032;ENST00000409146	T;T	0.32272	1.46;1.49	6.16	2.42	0.29668	.	0.098144	0.42821	D	0.000660	T	0.03477	0.0100	L	0.48362	1.52	0.09310	N	0.999999	B;B	0.20671	0.047;0.01	B;B	0.18263	0.021;0.009	T	0.07520	-1.0768	10	0.40728	T	0.16	-4.3833	4.5569	0.12141	0.1061:0.0684:0.2386:0.5869	rs36047130	10;10	B4DE58;O96001	.;PPR17_HUMAN	R	10	ENSP00000340125:L10R;ENSP00000386459:L10R	ENSP00000340125:L10R	L	+	2	0	C7orf16	31698609	0.966000	0.33281	0.657000	0.29651	0.763000	0.43281	1.109000	0.31135	1.115000	0.41800	0.528000	0.53228	CTG	T|0.979;G|0.021	0.021	strong		0.443	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658	
NUP107	57122	hgsc.bcm.edu	37	12	69115698	69115698	+	Silent	SNP	G	G	A	rs17851475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:69115698G>A	ENST00000229179.4	+	16	1721	c.1389G>A	c.(1387-1389)caG>caA	p.Q463Q	NUP107_ENST00000539906.1_Silent_p.Q434Q|NUP107_ENST00000378905.2_Silent_p.Q312Q	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	463					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TGGTAGAACAGGAGATCCAGA	0.468													G|||	1101	0.219848	0.059	0.2968	5008	,	,		16799	0.2996		0.2922	False		,,,				2504	0.226				p.Q463Q		Atlas-SNP	.											.	NUP107	88	.	0			c.G1389A						PASS	.	G		404,4002	200.8+/-224.0	20,364,1819	115.0	114.0	115.0		1389	2.1	1.0	12	dbSNP_123	115	2348,6252	393.9+/-344.5	319,1710,2271	no	coding-synonymous	NUP107	NM_020401.2		339,2074,4090	AA,AG,GG		27.3023,9.1693,21.1595		463/926	69115698	2752,10254	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon16			AGAACAGGAGATC	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.1389G>A	12.37:g.69115698G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			G|0.782;A|0.218	0.218	strong		0.468	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
TMEM2	23670	hgsc.bcm.edu	37	9	74345158	74345158	+	Silent	SNP	G	G	A	rs25694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:74345158G>A	ENST00000377044.4	-	9	2324	c.1785C>T	c.(1783-1785)acC>acT	p.T595T	TMEM2_ENST00000377066.5_Silent_p.T532T	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	595					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		CAAACCCAATGGTGTCTTTTA	0.383													G|||	407	0.08127	0.0393	0.0476	5008	,	,		18302	0.0198		0.0815	False		,,,				2504	0.2249				p.T595T		Atlas-SNP	.											.	TMEM2	112	.	0			c.C1785T						PASS	.	G	,	174,4232	113.8+/-151.8	6,162,2035	74.0	71.0	72.0		1596,1785	2.3	1.0	9	dbSNP_72	72	717,7883	175.0+/-225.2	30,657,3613	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	36,819,5648	AA,AG,GG		8.3372,3.9492,6.8507	,	532/1321,595/1384	74345158	891,12115	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon9			CCCAATGGTGTCT		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1785C>T	9.37:g.74345158G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			G|0.935;A|0.065	0.065	strong		0.383	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
TNFSF13	8741	hgsc.bcm.edu	37	17	7462581	7462581	+	Silent	SNP	G	G	C	rs12942687	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7462581G>C	ENST00000338784.4	+	1	668	c.225G>C	c.(223-225)ggG>ggC	p.G75G	SENP3_ENST00000321337.7_5'Flank|TNFSF13_ENST00000380535.4_Silent_p.G75G|TNFSF12-TNFSF13_ENST00000293826.4_Intron|TNFSF12_ENST00000557233.1_Intron|SENP3_ENST00000429205.2_5'Flank|TNFSF13_ENST00000396545.4_Silent_p.G75G|TNFSF13_ENST00000483039.1_Intron|TNFSF13_ENST00000349228.4_Silent_p.G75G|TNFSF13_ENST00000396542.1_Silent_p.G58G	NM_003808.3	NP_003799.1	O75888	TNF13_HUMAN	tumor necrosis factor (ligand) superfamily, member 13	75					gene expression (GO:0010467)|immunoglobulin production in mucosal tissue (GO:0002426)|mRNA metabolic process (GO:0016071)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	receptor binding (GO:0005102)			large_intestine(2)|lung(2)|skin(1)	5		Prostate(122;0.157)				CCCAGAATGGGGAAGGGTATC	0.637													G|||	59	0.0117812	0.0015	0.0548	5008	,	,		15883	0.0		0.0149	False		,,,				2504	0.0041				p.G75G		Atlas-SNP	.											.	TNFSF13	12	.	0			c.G225C						PASS	.	G	,,,,,,	9,4255		0,9,2123	11.0	11.0	11.0		225,225,174,225,225,225,	-2.6	0.0	17	dbSNP_121	11	102,8236		0,102,4067	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	TNFSF13,TNFSF12-TNFSF13	NM_001198622.1,NM_001198623.1,NM_001198624.1,NM_003808.3,NM_172087.2,NM_172088.2,NM_172089.3	,,,,,,	0,111,6190	CC,CG,GG		1.2233,0.2111,0.8808	,,,,,,	75/224,75/223,58/206,75/251,75/235,75/248,	7462581	111,12491	2132	4169	6301	SO:0001819	synonymous_variant	8741	exon1			GAATGGGGAAGGG	AF046888	CCDS11111.1, CCDS11112.1, CCDS42256.1, CCDS56019.1, CCDS73957.1	17p13.1	2007-07-23			ENSG00000161955	ENSG00000161955		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11928	protein-coding gene	gene with protein product		604472				9743536	Standard	NM_172088		Approved	APRIL, CD256		O75888	OTTHUMG00000108145	ENST00000338784.4:c.225G>C	17.37:g.7462581G>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	228	123	0.539474	NM_001198623	A8MYD5|B4DVT2|Q541E1|Q5U0G8|Q96HV6|Q9P1M8|Q9P1M9	Silent	SNP	ENST00000338784.4	37	CCDS11111.1																																																																																			G|0.989;C|0.011	0.011	strong		0.637	TNFSF13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226948.2	NM_003808	
ECHDC3	79746	hgsc.bcm.edu	37	10	11805339	11805339	+	Silent	SNP	C	C	T	rs17850531	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:11805339C>T	ENST00000379215.4	+	5	919	c.708C>T	c.(706-708)atC>atT	p.I236I	ECHDC3_ENST00000496136.1_3'UTR	NM_024693.4	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl CoA hydratase domain containing 3	236						mitochondrion (GO:0005739)	catalytic activity (GO:0003824)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)	4						CCATGCGGATCGCTAGGAAGA	0.622													C|||	987	0.197085	0.0197	0.2435	5008	,	,		19195	0.3075		0.2107	False		,,,				2504	0.2761				p.I236I		Atlas-SNP	.											.	ECHDC3	12	.	0			c.C708T						PASS	.	C		239,4167	140.0+/-175.5	9,221,1973	90.0	74.0	79.0		708	-11.5	0.0	10	dbSNP_123	79	1777,6823	318.6+/-313.7	173,1431,2696	no	coding-synonymous	ECHDC3	NM_024693.4		182,1652,4669	TT,TC,CC		20.6628,5.4244,15.5005		236/304	11805339	2016,10990	2203	4300	6503	SO:0001819	synonymous_variant	79746	exon5			GCGGATCGCTAGG	AF275677	CCDS7084.1	10p14	2010-04-30	2010-04-30		ENSG00000134463	ENSG00000134463			23489	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 3"""			12477932	Standard	NM_024693		Approved	FLJ20909	uc001ikw.4	Q96DC8	OTTHUMG00000017675	ENST00000379215.4:c.708C>T	10.37:g.11805339C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_024693	Q53HR9|Q5W0J7|Q8WYY8|Q9BVL8|Q9H7G4	Silent	SNP	ENST00000379215.4	37	CCDS7084.1																																																																																			C|0.831;T|0.169	0.169	strong		0.622	ECHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046771.1	NM_024693	
ITLN1	55600	hgsc.bcm.edu	37	1	160851894	160851894	+	Silent	SNP	G	G	A	rs2274908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:160851894G>A	ENST00000326245.3	-	4	373	c.258C>T	c.(256-258)caC>caT	p.H86H	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	86	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			TGTCATTCTCGTGCACGCTGG	0.597													G|||	2894	0.577875	0.3147	0.6945	5008	,	,		18194	0.6944		0.6779	False		,,,				2504	0.6278				p.H86H		Atlas-SNP	.											.	ITLN1	45	.	0			c.C258T						PASS	.	G		1625,2781	500.3+/-364.7	297,1031,875	102.0	88.0	93.0		258	-7.7	0.2	1	dbSNP_100	93	5857,2743	680.0+/-403.6	2020,1817,463	no	coding-synonymous	ITLN1	NM_017625.2		2317,2848,1338	AA,AG,GG		31.8953,36.8815,42.4727		86/314	160851894	7482,5524	2203	4300	6503	SO:0001819	synonymous_variant	55600	exon4			ATTCTCGTGCACG	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.258C>T	1.37:g.160851894G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	233	135	0.579399	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	CCDS1211.1																																																																																			.	.	weak		0.597	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
SARS2	54938	hgsc.bcm.edu	37	19	39416887	39416887	+	Silent	SNP	C	C	T	rs11544093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39416887C>T	ENST00000221431.6	-	2	480	c.321G>A	c.(319-321)gaG>gaA	p.E107E	SARS2_ENST00000430193.3_Silent_p.E107E|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.G177R|SARS2_ENST00000448145.2_Silent_p.E107E|SARS2_ENST00000594171.1_5'UTR|SARS2_ENST00000600042.1_Silent_p.E107E	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	107					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CCTTCTCTTCCTCCAGGCTCC	0.597													C|||	951	0.189896	0.087	0.1556	5008	,	,		19123	0.3313		0.1879	False		,,,				2504	0.2096				p.E107E		Atlas-SNP	.											.	SARS2	33	.	0			c.G321A						PASS	.	C	,	419,3987	204.1+/-226.4	26,367,1810	73.0	56.0	61.0		321,321	-0.2	1.0	19	dbSNP_120	61	1368,7232	265.3+/-286.1	108,1152,3040	no	coding-synonymous,coding-synonymous	SARS2	NM_001145901.1,NM_017827.3	,	134,1519,4850	TT,TC,CC		15.907,9.5098,13.7398	,	107/521,107/519	39416887	1787,11219	2203	4300	6503	SO:0001819	synonymous_variant	54938	exon2			CTCTTCCTCCAGG	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"""Aminoacyl tRNA synthetases / Class II"""	17697	protein-coding gene	gene with protein product	"""serine tRNA ligase 2, mitochondrial"""	612804	"""serine-tRNA ligase, mitochondrial"", ""seryl-tRNA synthetase 2"""	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.321G>A	19.37:g.39416887C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	37	CCDS33017.1																																																																																			C|0.842;T|0.158	0.158	strong		0.597	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827	
DNAH12	201625	hgsc.bcm.edu	37	3	57494138	57494138	+	Missense_Mutation	SNP	A	A	C	rs6445902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:57494138A>C	ENST00000351747.2	-	7	852	c.672T>G	c.(670-672)gaT>gaG	p.D224E	DNAH12_ENST00000389536.4_Missense_Mutation_p.D224E|DNAH12_ENST00000311202.6_Missense_Mutation_p.D224E	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	224	Stem. {ECO:0000250}.		D -> E (in dbSNP:rs6445902).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						ACAAAACTGTATCAGCAAATG	0.313													A|||	1180	0.235623	0.4947	0.1556	5008	,	,		16893	0.0813		0.164	False		,,,				2504	0.1748				p.D224E		Atlas-SNP	.											.	DNAH12	182	.	0			c.T672G						PASS	.	A	GLU/ASP,GLU/ASP	2073,2333	562.5+/-381.0	497,1079,627	56.0	60.0	59.0		672,672	-0.6	1.0	3	dbSNP_116	59	1636,6960	299.8+/-304.6	163,1310,2825	yes	missense,missense	DNAH12	NM_178504.4,NM_198564.3	45,45	660,2389,3452	CC,CA,AA		19.0321,47.0495,28.5264	benign,benign	224/3093,224/458	57494138	3709,9293	2203	4298	6501	SO:0001583	missense	201625	exon7			AACTGTATCAGCA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.672T>G	3.37:g.57494138A>C	ENSP00000295937:p.Asp224Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_198564	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		468	0.21428571428571427	253	0.5142276422764228	52	0.143646408839779	41	0.07167832167832168	122	0.16094986807387862	A	9.093	1.002223	0.19121	0.470495	0.190321	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536;ENST00000311202	T;T;T;T	0.21191	2.18;2.02;3.6;3.03	5.18	-0.563	0.11778	.	0.479527	0.20493	N	0.091254	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.34399	0.452;0.009	B;B	0.27076	0.076;0.01	T	0.45234	-0.9275	9	0.21540	T	0.41	.	2.3089	0.04181	0.4462:0.122:0.3122:0.1196	rs6445902;rs52833741;rs57120596;rs6445902	224;224	Q6ZR08-4;Q6ZR08	.;DYH12_HUMAN	E	224	ENSP00000295937:D224E;ENSP00000418137:D224E;ENSP00000374187:D224E;ENSP00000312554:D224E	ENSP00000312554:D224E	D	-	3	2	DNAH12	57469178	0.008000	0.16893	0.965000	0.40720	0.948000	0.59901	0.339000	0.19875	-0.003000	0.14444	0.377000	0.23210	GAT	A|0.746;C|0.254	0.254	strong		0.313	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
TMEM63B	55362	hgsc.bcm.edu	37	6	44115169	44115169	+	Missense_Mutation	SNP	G	G	A	rs4714759	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44115169G>A	ENST00000259746.9	+	12	1102	c.919G>A	c.(919-921)Gtg>Atg	p.V307M	TMEM63B_ENST00000323267.6_Missense_Mutation_p.V307M			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	307			V -> M (in dbSNP:rs4714759). {ECO:0000269|PubMed:17974005}.		ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.V307M(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			CAAGGAGAACGTGCCTACCAT	0.607													G|||	521	0.104034	0.0068	0.0965	5008	,	,		20519	0.2252		0.0974	False		,,,				2504	0.1227				p.V307M		Atlas-SNP	.											TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	1	Substitution - Missense(1)	stomach(1)	c.G919A						PASS	.	G	MET/VAL	110,4296	86.8+/-125.4	2,106,2095	147.0	110.0	122.0		919	2.7	0.9	6	dbSNP_111	122	920,7680	204.5+/-247.2	53,814,3433	yes	missense	TMEM63B	NM_018426.1	21	55,920,5528	AA,AG,GG		10.6977,2.4966,7.9194	benign	307/833	44115169	1030,11976	2203	4300	6503	SO:0001583	missense	55362	exon12			GAGAACGTGCCTA	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.919G>A	6.37:g.44115169G>A	ENSP00000259746:p.Val307Met	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	259	113	0.436293	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Missense_Mutation	SNP	ENST00000259746.9	37	CCDS34461.1	255	0.11675824175824176	3	0.006097560975609756	38	0.10497237569060773	143	0.25	71	0.09366754617414248	G	12.24	1.879303	0.33162	0.024966	0.106977	ENSG00000137216	ENST00000259746;ENST00000323267	T;T	0.44083	0.93;0.93	4.53	2.74	0.32292	.	0.674800	0.15009	N	0.285696	T	0.10423	0.0255	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.23058	0.007;0.079	B;B	0.15870	0.006;0.014	T	0.07908	-1.0748	9	0.48119	T	0.1	.	3.4756	0.07583	0.266:0.2077:0.5263:0.0	rs4714759;rs52838417;rs58281604;rs4714759	307;307	Q5T3F8;Q5T3F8-2	TM63B_HUMAN;.	M	307	ENSP00000259746:V307M;ENSP00000327154:V307M	ENSP00000259746:V307M	V	+	1	0	TMEM63B	44223147	0.521000	0.26258	0.941000	0.38009	0.977000	0.68977	2.132000	0.42083	1.254000	0.44035	0.650000	0.86243	GTG	G|0.903;A|0.097	0.097	strong		0.607	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
TFF3	7033	hgsc.bcm.edu	37	21	43733628	43733628	+	Missense_Mutation	SNP	C	C	T	rs118095917	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43733628C>T	ENST00000518498.1	-	2	472	c.238G>A	c.(238-240)Gtg>Atg	p.V80M	TFF3_ENST00000291525.10_Missense_Mutation_p.V116M|TFF3_ENST00000489676.1_5'UTR			Q07654	TFF3_HUMAN	trefoil factor 3 (intestinal)	66					defense response (GO:0006952)|digestion (GO:0007586)|response to peptide hormone (GO:0043434)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				cervix(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	6						CACCAAGGCACTCCAGGGATC	0.647													C|||	13	0.00259585	0.0008	0.0029	5008	,	,		17802	0.0		0.0089	False		,,,				2504	0.001				p.V80M		Atlas-SNP	.											.	TFF3	9	.	0			c.G238A						PASS	.	C	MET/VAL	4,4402	8.1+/-20.4	0,4,2199	66.0	60.0	62.0		238	4.4	0.9	21	dbSNP_132	62	52,8548	34.3+/-88.2	0,52,4248	yes	missense	TFF3	NM_003226.3	21	0,56,6447	TT,TC,CC		0.6047,0.0908,0.4306	probably-damaging	80/95	43733628	56,12950	2203	4300	6503	SO:0001583	missense	7033	exon2			AAGGCACTCCAGG	AF432265	CCDS33565.1, CCDS33565.2	21q22.3	2006-05-16			ENSG00000160180	ENSG00000160180			11757	protein-coding gene	gene with protein product		600633				7718582, 9043862	Standard	NM_003226		Approved	HITF, ITF	uc002zav.3	Q07654	OTTHUMG00000086798	ENST00000518498.1:c.238G>A	21.37:g.43733628C>T	ENSP00000430690:p.Val80Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_003226	E9PBB5|Q96NX0|Q9UDA5	Missense_Mutation	SNP	ENST00000518498.1	37	CCDS33565.2	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	14.53	2.562451	0.45694	9.08E-4	0.006047	ENSG00000160180	ENST00000518498;ENST00000291525;ENST00000398431	T;T	0.60040	0.22;0.22	4.43	4.43	0.53597	P-type trefoil (5);	0.000000	0.51477	D	0.000082	T	0.69088	0.3072	.	.	.	0.38165	D	0.939147	D	0.76494	0.999	D	0.77004	0.989	T	0.77965	-0.2389	8	.	.	.	-28.7951	17.0517	0.86520	0.0:1.0:0.0:0.0	.	66	Q07654	TFF3_HUMAN	M	80;116;68	ENSP00000430690:V80M;ENSP00000291525:V116M	.	V	-	1	0	TFF3	42606697	0.990000	0.36364	0.892000	0.35008	0.033000	0.12548	3.147000	0.50639	1.997000	0.58415	0.561000	0.74099	GTG	C|0.996;T|0.004	0.004	strong		0.647	TFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195358.2	NM_003226	
PMS2	5395	hgsc.bcm.edu	37	7	6026988	6026988	+	Missense_Mutation	SNP	G	G	A	rs1805321	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6026988G>A	ENST00000265849.7	-	11	1513	c.1408C>T	c.(1408-1410)Cct>Tct	p.P470S	PMS2_ENST00000406569.3_Missense_Mutation_p.P470S|PMS2_ENST00000441476.2_Missense_Mutation_p.P364S|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	470			P -> S (in dbSNP:rs1805321). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TCTTTCTGAGGTCTCAGGACG	0.567			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				G|||	1794	0.358227	0.2723	0.428	5008	,	,		16764	0.3601		0.4374	False		,,,				2504	0.3415				p.P470S		Atlas-SNP	.	yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.C1408T						PASS	.	G	SER/PRO	1242,3164	428.7+/-342.0	177,888,1138	106.0	102.0	103.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1408	0.6	0.0	7	dbSNP_98	103	3620,4980	523.7+/-380.4	743,2134,1423	no	missense	PMS2	NM_000535.5	74	920,3022,2561	AA,AG,GG		42.093,28.1888,37.3827	benign	470/863	6026988	4862,8144	2203	4300	6503	SO:0001583	missense	5395	exon11	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTGAGGTCTCAG		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1408C>T	7.37:g.6026988G>A	ENSP00000265849:p.Pro470Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	861	0.3942307692307692	148	0.3008130081300813	153	0.42265193370165743	223	0.38986013986013984	337	0.4445910290237467	g	1.779	-0.482327	0.04383	0.281888	0.42093	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.84944	1.14;1.14;-1.92	5.84	0.572	0.17357	.	2.392390	0.01199	N	0.007524	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B;B;B	0.16603	0.018;0.002;0.006	B;B;B	0.10450	0.005;0.001;0.005	T	0.29212	-1.0019	9	0.09084	T	0.74	-5.0156	2.3347	0.04244	0.2519:0.1234:0.4861:0.1386	rs1805321;rs57467937;rs1805321	470;470;364	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	S	470;423;364;470	ENSP00000265849:P470S;ENSP00000392843:P364S;ENSP00000384308:P470S	ENSP00000265849:P470S	P	-	1	0	PMS2	5993514	0.001000	0.12720	0.006000	0.13384	0.004000	0.04260	0.265000	0.18515	0.386000	0.24997	-0.145000	0.13849	CCT	G|0.639;A|0.361	0.361	strong		0.567	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
ESPNL	339768	hgsc.bcm.edu	37	2	239039075	239039075	+	Missense_Mutation	SNP	G	G	T	rs13006204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:239039075G>T	ENST00000343063.3	+	9	1983	c.1720G>T	c.(1720-1722)Gca>Tca	p.A574S	ESPNL_ENST00000409506.1_Missense_Mutation_p.A206S|ESPNL_ENST00000409169.1_Missense_Mutation_p.A530S|ESPNL_ENST00000477241.1_3'UTR	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	574			A -> S (in dbSNP:rs13006204). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGCTGAGCCCGCAGGGTCTGC	0.706													G|||	1954	0.390176	0.3411	0.3876	5008	,	,		13997	0.4415		0.3827	False		,,,				2504	0.4131				p.A574S		Atlas-SNP	.											.	ESPNL	63	.	0			c.G1720T						PASS	.	G	SER/ALA	1547,2753		314,919,917	7.0	10.0	9.0		1720	-5.0	0.0	2	dbSNP_121	9	3307,5193		687,1933,1630	no	missense	ESPNL	NM_194312.2	99	1001,2852,2547	TT,TG,GG		38.9059,35.9767,37.9219	benign	574/1006	239039075	4854,7946	2150	4250	6400	SO:0001583	missense	339768	exon9			GAGCCCGCAGGGT	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1720G>T	2.37:g.239039075G>T	ENSP00000339115:p.Ala574Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	846	0.3873626373626374	177	0.3597560975609756	150	0.4143646408839779	236	0.4125874125874126	283	0.3733509234828496	G	0.019	-1.458749	0.01062	0.359767	0.389059	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.62105	0.05;1.15;0.74	2.52	-5.03	0.02973	.	8.367350	0.00721	N	0.000888	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.16603	0.001;0.018	B;B	0.06405	0.001;0.002	T	0.16867	-1.0388	9	0.13853	T	0.58	-0.9182	1.4149	0.02299	0.3048:0.148:0.3979:0.1493	rs13006204	530;574	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	S	574;530;206	ENSP00000339115:A574S;ENSP00000386577:A530S;ENSP00000386579:A206S	ENSP00000339115:A574S	A	+	1	0	ESPNL	238703814	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-3.396000	0.00485	-1.405000	0.02048	-1.763000	0.00667	GCA	G|0.611;T|0.389	0.389	strong		0.706	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
DNAH5	1767	hgsc.bcm.edu	37	5	13701536	13701536	+	Missense_Mutation	SNP	T	T	C	rs3734110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13701536T>C	ENST00000265104.4	-	77	13452	c.13348A>G	c.(13348-13350)Att>Gtt	p.I4450V		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4450			I -> V (in dbSNP:rs3734110). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039}.		cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTACTAGAAATCCAAGAAGCC	0.363									Kartagener syndrome				C|||	2522	0.503594	0.5295	0.5187	5008	,	,		16237	0.4474		0.5457	False		,,,				2504	0.4724				p.I4450V		Atlas-SNP	.											DNAH5,NS,carcinoma,+2,1	DNAH5	868	1	0			c.A13348G						PASS	.	C	VAL/ILE	2223,2183	555.7+/-379.3	587,1049,567	63.0	70.0	68.0		13348	4.9	1.0	5	dbSNP_107	68	4726,3874	530.4+/-381.8	1275,2176,849	yes	missense	DNAH5	NM_001369.2	29	1862,3225,1416	CC,CT,TT		45.0465,49.5461,46.5708	benign	4450/4625	13701536	6949,6057	2203	4300	6503	SO:0001583	missense	1767	exon77	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TAGAAATCCAAGA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13348A>G	5.37:g.13701536T>C	ENSP00000265104:p.Ile4450Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	68	0.653846	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	1113	0.5096153846153846	267	0.5426829268292683	195	0.5386740331491713	234	0.4090909090909091	417	0.5501319261213721	C	9.791	1.178017	0.21787	0.504539	0.549535	ENSG00000039139	ENST00000265104	T	0.08282	3.11	5.78	4.91	0.64330	Dynein heavy chain (1);	0.377697	0.27478	N	0.019187	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.34650	-0.9820	9	0.28530	T	0.3	.	7.6741	0.28476	0.0:0.6802:0.1197:0.2002	rs3734110;rs13162128;rs61544221;rs3734110	4450	Q8TE73	DYH5_HUMAN	V	4450	ENSP00000265104:I4450V	ENSP00000265104:I4450V	I	-	1	0	DNAH5	13754536	0.999000	0.42202	1.000000	0.80357	0.812000	0.45895	1.084000	0.30828	0.804000	0.34136	-0.186000	0.12905	ATT	T|0.482;C|0.518	0.518	strong		0.363	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
FBXO44	93611	hgsc.bcm.edu	37	1	11718859	11718859	+	Silent	SNP	C	C	T	rs150816569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11718859C>T	ENST00000251547.5	+	5	637	c.555C>T	c.(553-555)caC>caT	p.H185H	FBXO44_ENST00000376770.1_Silent_p.H185H|FBXO44_ENST00000376768.1_Missense_Mutation_p.R176C|FBXO44_ENST00000376762.4_Missense_Mutation_p.R144C|FBXO44_ENST00000376760.1_Missense_Mutation_p.R144C|FBXO44_ENST00000251546.4_Missense_Mutation_p.R144C	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	185	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CGTCCGCGCACGCGCCTCTGG	0.692													C|||	24	0.00479233	0.0008	0.0159	5008	,	,		14300	0.0		0.0119	False		,,,				2504	0.0				p.R144C		Atlas-SNP	.											.	FBXO44	20	.	0			c.C430T						PASS	.	C	,,CYS/ARG,CYS/ARG	16,4390	23.3+/-48.9	0,16,2187	61.0	61.0	61.0		555,555,430,430	-3.8	0.1	1	dbSNP_134	61	83,8517	48.9+/-108.6	2,79,4219	yes	coding-synonymous,coding-synonymous,missense,missense	FBXO44	NM_001014765.1,NM_033182.5,NM_183412.2,NM_183413.2	,,180,180	2,95,6406	TT,TC,CC		0.9651,0.3631,0.7612	,,,	185/256,185/256,144/225,144/225	11718859	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	93611	exon4			CGCGCACGCGCCT	AY040878	CCDS131.1, CCDS132.1	1p36.21	2008-03-26			ENSG00000132879	ENSG00000132879		"""F-boxes /  ""other"""""	24847	protein-coding gene	gene with protein product		609111				12383498	Standard	XM_005263535		Approved	FBX30, FBG3, MGC14140, Fbxo6a, Fbx44	uc001asm.3	Q9H4M3	OTTHUMG00000002071	ENST00000251547.5:c.555C>T	1.37:g.11718859C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	54	0.701299	NM_183412	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	37	CCDS132.1	17	0.007783882783882784	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	8	0.010554089709762533	C	5.363	0.252260	0.10185	0.003631	0.009651	ENSG00000132879	ENST00000251546;ENST00000425796;ENST00000376768;ENST00000376762;ENST00000376760	T;T;T;T;T	0.40225	1.3;1.12;1.04;1.3;1.3	5.01	-3.78	0.04333	.	0.423822	0.29737	N	0.011321	T	0.14700	0.0355	.	.	.	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10965	-1.0607	9	0.41790	T	0.15	-28.3452	13.2172	0.59867	0.0:0.7229:0.0:0.2771	.	176;144	B7Z1P2;Q9H4M3-2	.;.	C	144;144;176;144;144	ENSP00000251546:R144C;ENSP00000389820:R144C;ENSP00000365959:R176C;ENSP00000365953:R144C;ENSP00000365951:R144C	ENSP00000251546:R144C	R	+	1	0	FBXO44	11641446	0.000000	0.05858	0.059000	0.19551	0.034000	0.12701	-1.363000	0.02592	-0.722000	0.04922	-0.409000	0.06214	CGC	C|0.992;T|0.008	0.008	strong		0.692	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412	
LARP1B	55132	hgsc.bcm.edu	37	4	129043286	129043286	+	Silent	SNP	C	C	T	rs3733320	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:129043286C>T	ENST00000326639.6	+	11	1678	c.1467C>T	c.(1465-1467)taC>taT	p.Y489Y	LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000441387.1_Silent_p.Y489Y|LARP1B_ENST00000264584.5_Silent_p.Y442Y|LARP1B_ENST00000512292.1_Silent_p.Y489Y|LARP1B_ENST00000427266.1_Silent_p.Y489Y	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	489						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						ATGGCTTATACTATTATGAAC	0.383													T|||	2959	0.590855	0.3964	0.696	5008	,	,		17754	0.5288		0.6759	False		,,,				2504	0.7556				p.Y489Y		Atlas-SNP	.											.	LARP1B	120	.	0			c.C1467T						PASS	.	T	,	2009,2397	613.0+/-392.1	450,1109,644	103.0	97.0	99.0		1467,1467	4.9	1.0	4	dbSNP_107	99	5718,2882	453.2+/-363.2	1917,1884,499	no	coding-synonymous,coding-synonymous	LARP1B	NM_018078.2,NM_178043.1	,	2367,2993,1143	TT,TC,CC		33.5116,45.5969,40.589	,	489/915,489/523	129043286	7727,5279	2203	4300	6503	SO:0001819	synonymous_variant	55132	exon11			CTTATACTATTAT		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"""La ribonucleoprotein domain containing"""	24704	protein-coding gene	gene with protein product			"""La ribonucleoprotein domain family, member 2"""	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.1467C>T	4.37:g.129043286C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_178043	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Silent	SNP	ENST00000326639.6	37	CCDS3738.1																																																																																			C|0.423;T|0.577	0.577	strong		0.383	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078	
STOX2	56977	hgsc.bcm.edu	37	4	184931818	184931818	+	Silent	SNP	G	G	A	rs4861597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:184931818G>A	ENST00000308497.4	+	3	3262	c.1827G>A	c.(1825-1827)acG>acA	p.T609T	STOX2_ENST00000438269.1_Silent_p.T609T	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	609					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		CTAGTGAGACGGTGCTCACGG	0.502													G|||	2144	0.428115	0.4123	0.3156	5008	,	,		20530	0.6022		0.2972	False		,,,				2504	0.4847				p.T609T		Atlas-SNP	.											.	STOX2	142	.	0			c.G1827A						PASS	.	G		1533,2383		301,931,726	54.0	55.0	55.0		1827	-7.6	0.1	4	dbSNP_111	55	2232,6076		318,1596,2240	no	coding-synonymous	STOX2	NM_020225.1		619,2527,2966	AA,AG,GG		26.8657,39.1471,30.8001		609/927	184931818	3765,8459	1958	4154	6112	SO:0001819	synonymous_variant	56977	exon3			TGAGACGGTGCTC	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.1827G>A	4.37:g.184931818G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	226	114	0.504425	NM_020225	A6H8U4|Q9NPS8	Silent	SNP	ENST00000308497.4	37	CCDS47167.1																																																																																			G|0.583;A|0.417	0.417	strong		0.502	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
A2ML1	144568	hgsc.bcm.edu	37	12	9016456	9016456	+	Missense_Mutation	SNP	C	C	T	rs73040625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:9016456C>T	ENST00000299698.7	+	29	3749	c.3569C>T	c.(3568-3570)gCg>gTg	p.A1190V	A2ML1_ENST00000539547.1_Missense_Mutation_p.A699V	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						TCTGAGCCTGCGGCTGTAGAT	0.493													C|||	113	0.0225639	0.0015	0.0375	5008	,	,		-128	0.0		0.0736	False		,,,				2504	0.0112				p.A1190V		Atlas-SNP	.											.	A2ML1	199	.	0			c.C3569T						PASS	.	C	VAL/ALA	58,3810		1,56,1877	76.0	75.0	75.0		3569	-1.4	0.0	12	dbSNP_130	75	684,7620		30,624,3498	yes	missense	A2ML1	NM_144670.3	64	31,680,5375	TT,TC,CC		8.237,1.4995,6.096	benign	1190/1455	9016456	742,11430	1934	4152	6086	SO:0001583	missense	144568	exon29			AGCCTGCGGCTGT	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.3569C>T	12.37:g.9016456C>T	ENSP00000299698:p.Ala1190Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	158	86	0.544304	NM_144670		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	76	0.0347985347985348	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	57	0.07519788918205805	C	10.21	1.286592	0.23478	0.014995	0.08237	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	T;T;T	0.37411	1.2;1.2;1.2	4.39	-1.35	0.09114	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	2.157560	0.02058	N	0.050561	T	0.01222	0.0040	N	0.13272	0.32	0.09310	N	1	B	0.26363	0.147	B	0.26094	0.066	T	0.17018	-1.0383	10	0.44086	T	0.13	.	8.9867	0.35999	0.2037:0.5711:0.0:0.2252	.	1190	A8K2U0	A2ML1_HUMAN	V	1190;1190;740;699	ENSP00000299698:A1190V;ENSP00000443174:A740V;ENSP00000438292:A699V	ENSP00000299698:A1190V	A	+	2	0	A2ML1	8907723	0.000000	0.05858	0.001000	0.08648	0.457000	0.32468	-0.559000	0.05971	-0.242000	0.09667	-2.756000	0.00123	GCG	C|0.949;T|0.051	0.051	strong		0.493	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
CCDC125	202243	hgsc.bcm.edu	37	5	68616331	68616331	+	Missense_Mutation	SNP	C	C	T	rs10471774	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:68616331C>T	ENST00000396496.2	-	2	144	c.37G>A	c.(37-39)Gtg>Atg	p.V13M	CCDC125_ENST00000383374.2_Missense_Mutation_p.V13M|CCDC125_ENST00000511257.1_De_novo_Start_OutOfFrame|CCDC125_ENST00000396499.1_Missense_Mutation_p.V13M|CCDC125_ENST00000460090.1_5'UTR			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	13			V -> M (in dbSNP:rs10471774). {ECO:0000269|PubMed:19787194}.			cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		CAGAGCTGCACGTCTGACTCA	0.423													c|||	1305	0.260583	0.062	0.2968	5008	,	,		21831	0.2837		0.4543	False		,,,				2504	0.2802				p.V13M		Atlas-SNP	.											.	CCDC125	41	.	0			c.G37A						PASS	.	C	MET/VAL	578,3828	257.4+/-261.8	41,496,1666	113.0	107.0	109.0		37	4.0	0.0	5	dbSNP_119	109	3811,4789	538.9+/-383.5	864,2083,1353	yes	missense	CCDC125	NM_176816.3	21	905,2579,3019	TT,TC,CC		44.314,13.1185,33.746	possibly-damaging	13/512	68616331	4389,8617	2203	4300	6503	SO:0001583	missense	202243	exon1			GCTGCACGTCTGA	AB024691	CCDS4000.1, CCDS75255.1	5q13.2	2008-02-05			ENSG00000183323	ENSG00000183323			28924	protein-coding gene	gene with protein product		613781					Standard	XM_005248461		Approved	KENAE	uc003jvv.1	Q86Z20	OTTHUMG00000131259	ENST00000396496.2:c.37G>A	5.37:g.68616331C>T	ENSP00000379754:p.Val13Met	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_176816	Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	37	CCDS4000.1	673	0.30815018315018317	28	0.056910569105691054	135	0.3729281767955801	157	0.2744755244755245	353	0.4656992084432718	c	15.98	2.992915	0.54041	0.131185	0.44314	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000383374	T;T;T	0.46819	0.91;0.91;0.86	4.92	4.02	0.46733	.	0.793398	0.10812	N	0.631478	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	D;D	0.64830	0.994;0.994	P;P	0.50754	0.649;0.482	T	0.47169	-0.9138	9	0.46703	T	0.11	-20.8152	11.3743	0.49719	0.0:0.8163:0.1837:0.0	rs10471774;rs52811895;rs56777974;rs10471774	13;13	F8W912;Q86Z20	.;CC125_HUMAN	M	13	ENSP00000379754:V13M;ENSP00000379756:V13M;ENSP00000372865:V13M	ENSP00000372865:V13M	V	-	1	0	CCDC125	68652087	0.051000	0.20477	0.003000	0.11579	0.201000	0.24016	2.597000	0.46214	1.170000	0.42753	0.457000	0.33378	GTG	C|0.689;T|0.311	0.311	strong		0.423	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816	
CAST	831	hgsc.bcm.edu	37	5	96086334	96086334	+	Missense_Mutation	SNP	G	G	C	rs754615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:96086334G>C	ENST00000341926.3	+	18	1385	c.1223G>C	c.(1222-1224)tGt>tCt	p.C408S	CAST_ENST00000508579.1_Missense_Mutation_p.C123S|CAST_ENST00000515663.1_Missense_Mutation_p.C131S|CAST_ENST00000359176.4_Missense_Mutation_p.C472S|CAST_ENST00000509903.1_Missense_Mutation_p.C373S|CAST_ENST00000508608.1_Missense_Mutation_p.C454S|CAST_ENST00000395813.1_Missense_Mutation_p.C491S|CAST_ENST00000504465.1_Missense_Mutation_p.C336S|CAST_ENST00000325674.7_Missense_Mutation_p.C456S|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000395812.2_Missense_Mutation_p.C450S|CAST_ENST00000511782.1_Missense_Mutation_p.C394S|CAST_ENST00000309190.5_Missense_Mutation_p.C386S|CAST_ENST00000338252.3_Missense_Mutation_p.C395S|CAST_ENST00000511049.1_Missense_Mutation_p.C394S|CAST_ENST00000510756.1_Missense_Mutation_p.C469S|CAST_ENST00000508830.1_Missense_Mutation_p.C491S			P20810	ICAL_HUMAN	calpastatin	408			C -> S (in dbSNP:rs754615). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:2577276, ECO:0000269|Ref.12, ECO:0000269|Ref.15}.		negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		GAGGCTGTGTGTCGGACCTCC	0.493													C|||	1471	0.29373	0.3064	0.2911	5008	,	,		15918	0.1161		0.4105	False		,,,				2504	0.3415				p.C450S		Atlas-SNP	.											.	CAST	58	.	0			c.G1349C						PASS	.	C	SER/CYS,SER/CYS,SER/CYS	1420,2986	684.4+/-404.4	241,938,1024	84.0	77.0	80.0		1349,1184,1157	4.5	0.0	5	dbSNP_86	80	3278,5322	647.5+/-400.4	619,2040,1641	yes	missense,missense,missense	CAST	NM_001042440.2,NM_001190442.1,NM_173060.3	112,112,112	860,2978,2665	CC,CG,GG		38.1163,32.2288,36.1218	benign,benign,benign	450/751,395/696,386/687	96086334	4698,8308	2203	4300	6503	SO:0001583	missense	831	exon18			CTGTGTGTCGGAC	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.1223G>C	5.37:g.96086334G>C	ENSP00000339914:p.Cys408Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	37		653|653	0.298992673992674|0.298992673992674	147|147	0.29878048780487804|0.29878048780487804	119|119	0.3287292817679558|0.3287292817679558	84|84	0.14685314685314685|0.14685314685314685	303|303	0.3997361477572559|0.3997361477572559	C|C	5.535|5.535	0.283691|0.283691	0.10458|0.10458	0.322288|0.322288	0.381163|0.381163	ENSG00000153113|ENSG00000153113	ENST00000338252;ENST00000508830;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782;ENST00000508579;ENST00000515663|ENST00000437034	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.14516|.	2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5|.	5.35|5.35	4.46|4.46	0.54185|0.54185	.|.	1.019010|.	0.07783|.	N|.	0.953654|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00065|0.00065	-2.305|-2.305	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B|.	0.04013|.	0.0;0.001;0.001;0.001;0.001;0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	T|T	0.40887|0.40887	-0.9539|-0.9539	9|4	0.05525|.	T|.	0.97|.	2.7089|2.7089	12.6063|12.6063	0.56525|0.56525	0.0:0.6805:0.3195:0.0|0.0:0.6805:0.3195:0.0	rs754615;rs1057450;rs3198040;rs17419910;rs17479995;rs61279874;rs754615|rs754615;rs1057450;rs3198040;rs17419910;rs17479995;rs61279874;rs754615	336;256;454;131;159;131;394;373;386;367;408;456;450;472;469;491;395|.	E9PDE4;B7Z8S8;B7Z468;E7EQA0;Q86YM9;E7EPY6;E7EVY3;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2|.	.;.;.;.;.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.|.	S|L	395;491;491;472;456;450;469;454;408;394;386;408;336;373;394;123;131|160	ENSP00000343421:C395S;ENSP00000425721:C491S;ENSP00000379158:C491S;ENSP00000352098:C472S;ENSP00000320319:C456S;ENSP00000379157:C450S;ENSP00000422176:C469S;ENSP00000422677:C454S;ENSP00000339914:C408S;ENSP00000421130:C394S;ENSP00000312523:C386S;ENSP00000422325:C408S;ENSP00000425670:C336S;ENSP00000426946:C373S;ENSP00000423638:C394S;ENSP00000425787:C123S;ENSP00000422929:C131S|.	ENSP00000312523:C386S|.	C|V	+|+	2|1	0|0	CAST|CAST	96112090|96112090	0.002000|0.002000	0.14202|0.14202	0.007000|0.007000	0.13788|0.13788	0.082000|0.082000	0.17680|0.17680	0.989000|0.989000	0.29629|0.29629	0.719000|0.719000	0.32188|0.32188	-0.127000|-0.127000	0.14921|0.14921	TGT|GTC	G|0.670;C|0.330	0.330	strong		0.493	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	
ALPK3	57538	hgsc.bcm.edu	37	15	85383640	85383640	+	Missense_Mutation	SNP	G	G	A	rs3803405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85383640G>A	ENST00000258888.5	+	5	1903	c.1736G>A	c.(1735-1737)gGg>gAg	p.G579E		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	579			G -> E (in dbSNP:rs3803405). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GCTGCACGGGGGCCTGGGTCC	0.672													G|||	691	0.137979	0.0159	0.1643	5008	,	,		14771	0.1329		0.2575	False		,,,				2504	0.1667				p.G579E		Atlas-SNP	.											.	ALPK3	289	.	0			c.G1736A						PASS	.	G	GLU/GLY	243,4159		11,221,1969	21.0	24.0	23.0		1736	2.7	0.1	15	dbSNP_107	23	2322,6274		315,1692,2291	yes	missense	ALPK3	NM_020778.4	98	326,1913,4260	AA,AG,GG		27.0126,5.5202,19.7338	probably-damaging	579/1908	85383640	2565,10433	2201	4298	6499	SO:0001583	missense	57538	exon5			CACGGGGGCCTGG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.1736G>A	15.37:g.85383640G>A	ENSP00000258888:p.Gly579Glu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	72	27	0.375	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	359	0.16437728937728938	7	0.014227642276422764	72	0.19889502762430938	81	0.14160839160839161	199	0.262532981530343	G	15.43	2.831448	0.50845	0.055202	0.270126	ENSG00000136383	ENST00000258888	T	0.58797	0.31	4.63	2.68	0.31781	.	0.701763	0.13520	N	0.381774	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.27997	0.197	B	0.28638	0.092	T	0.12915	-1.0529	9	0.42905	T	0.14	-25.0097	6.5307	0.22326	0.1001:0.1836:0.7163:0.0	rs3803405;rs60841515;rs3803405	579	Q96L96	ALPK3_HUMAN	E	579	ENSP00000258888:G579E	ENSP00000258888:G579E	G	+	2	0	ALPK3	83184644	0.004000	0.15560	0.136000	0.22124	0.102000	0.19082	0.123000	0.15708	1.163000	0.42636	-0.300000	0.09419	GGG	G|0.815;A|0.185	0.185	strong		0.672	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
EGF	1950	hgsc.bcm.edu	37	4	110884396	110884396	+	Silent	SNP	A	A	G	rs11568953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110884396A>G	ENST00000265171.5	+	9	1825	c.1380A>G	c.(1378-1380)gaA>gaG	p.E460E	EGF_ENST00000509793.1_Silent_p.E418E|EGF_ENST00000503392.1_Silent_p.E460E	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	460	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	TATCCTGGGAATGTGATTGCT	0.453													A|||	22	0.00439297	0.0015	0.0043	5008	,	,		15769	0.0		0.0169	False		,,,				2504	0.0				p.E460E		Atlas-SNP	.											.	EGF	113	.	0			c.A1380G						PASS	.	A	,,	9,4397	15.5+/-35.6	0,9,2194	223.0	208.0	213.0		1380,1254,1380	0.7	1.0	4	dbSNP_120	213	123,8477	64.2+/-126.4	2,119,4179	no	coding-synonymous,coding-synonymous,coding-synonymous	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	,,	2,128,6373	GG,GA,AA		1.4302,0.2043,1.0149	,,	460/1167,418/1166,460/1208	110884396	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	1950	exon9			CTGGGAATGTGAT	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.1380A>G	4.37:g.110884396A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Silent	SNP	ENST00000265171.5	37	CCDS3689.1																																																																																			A|0.990;G|0.010	0.010	strong		0.453	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		
CAMSAP3	57662	hgsc.bcm.edu	37	19	7675369	7675369	+	Silent	SNP	C	C	T	rs62113420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7675369C>T	ENST00000160298.4	+	6	869	c.768C>T	c.(766-768)tgC>tgT	p.C256C	CAMSAP3_ENST00000446248.2_Silent_p.C283C	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	256	CH.				epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)			cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						CAGAGGTGTGCTTGAAGGACC	0.632													C|||	371	0.0740815	0.0862	0.0994	5008	,	,		14322	0.002		0.161	False		,,,				2504	0.0245				p.C283C		Atlas-SNP	.											.	CAMSAP3	131	.	0			c.C849T						PASS	.	C	,	310,3818		16,278,1770	87.0	96.0	93.0		849,768	4.3	1.0	19	dbSNP_129	93	1141,7251		65,1011,3120	no	coding-synonymous,coding-synonymous	CAMSAP3	NM_001080429.2,NM_020902.1	,	81,1289,4890	TT,TC,CC		13.5963,7.5097,11.5895	,	283/1277,256/1250	7675369	1451,11069	2064	4196	6260	SO:0001819	synonymous_variant	57662	exon8			GGTGTGCTTGAAG	AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 80"""	612685	"""KIAA1543"""	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.768C>T	19.37:g.7675369C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_001080429	Q8NDF1	Silent	SNP	ENST00000160298.4	37	CCDS42489.1																																																																																			C|0.897;T|0.103	0.103	strong		0.632	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362	
PDLIM5	10611	hgsc.bcm.edu	37	4	95506842	95506842	+	Silent	SNP	G	G	A	rs11097431	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:95506842G>A	ENST00000317968.4	+	6	973	c.837G>A	c.(835-837)caG>caA	p.Q279Q	PDLIM5_ENST00000380176.3_3'UTR|PDLIM5_ENST00000437932.1_Silent_p.Q170Q|PDLIM5_ENST00000538141.1_Silent_p.Q156Q|PDLIM5_ENST00000542407.1_Silent_p.Q157Q|PDLIM5_ENST00000508216.1_Silent_p.Q176Q|PDLIM5_ENST00000380180.3_Silent_p.Q176Q|PDLIM5_ENST00000450793.1_Silent_p.Q176Q|PDLIM5_ENST00000514743.1_Silent_p.Q176Q|PDLIM5_ENST00000318007.5_Silent_p.Q156Q	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	279					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)	p.Q176Q(1)|p.Q279Q(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		GAACAACTCAGTCTCGCTCTT	0.453													G|||	864	0.172524	0.2504	0.1643	5008	,	,		13926	0.1141		0.2038	False		,,,				2504	0.1012				p.Q279Q		Atlas-SNP	.											PDLIM5_ENST00000380180,NS,carcinoma,0,2	PDLIM5	76	2	2	Substitution - coding silent(2)	prostate(2)	c.G837A						PASS	.	G	,,,	1159,3247	410.0+/-335.2	153,853,1197	112.0	96.0	101.0		510,528,468,837	3.6	1.0	4	dbSNP_120	101	1832,6768	328.4+/-318.3	202,1428,2670	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDLIM5	NM_001011513.2,NM_001011515.1,NM_001011516.1,NM_006457.3	,,,	355,2281,3867	AA,AG,GG		21.3023,26.305,22.9971	,,,	170/488,176/235,156/215,279/597	95506842	2991,10015	2203	4300	6503	SO:0001819	synonymous_variant	10611	exon6			AACTCAGTCTCGC	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.837G>A	4.37:g.95506842G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Silent	SNP	ENST00000317968.4	37	CCDS3641.1	430	0.19688644688644688	146	0.2967479674796748	63	0.17403314917127072	57	0.09965034965034965	164	0.21635883905013192	G	9.808	1.182442	0.21870	0.26305	0.213023	ENSG00000163110	ENST00000513341	.	.	.	5.31	3.58	0.41010	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.08166	-1.0735	3	.	.	.	.	12.3552	0.55171	0.1184:0.0:0.8816:0.0	rs11097431;rs11097431	.	.	.	N	138	.	.	S	+	2	0	PDLIM5	95725865	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.098000	0.50259	0.719000	0.32188	0.650000	0.86243	AGT	G|0.784;A|0.216	0.216	strong		0.453	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
C9orf129	445577	hgsc.bcm.edu	37	9	96097662	96097662	+	Missense_Mutation	SNP	G	G	A	rs4744219	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:96097662G>A	ENST00000375419.1	-	3	722	c.359C>T	c.(358-360)gCg>gTg	p.A120V		NM_001098808.1	NP_001092278.1	Q5T035	CI129_HUMAN	chromosome 9 open reading frame 129	120										endometrium(2)|large_intestine(1)|lung(1)|ovary(2)	6						TCACTTTGTCGCCCCTCCGCT	0.632													G|||	315	0.0628994	0.0219	0.0749	5008	,	,		18181	0.0337		0.1481	False		,,,				2504	0.0521				p.A120V		Atlas-SNP	.											.	C9orf129	18	.	0			c.C359T						PASS	.						14.0	16.0	15.0					9																	96097662		2197	4286	6483	SO:0001583	missense	445577	exon3			TTTGTCGCCCCTC		CCDS43850.1	9q22.31	2012-04-02			ENSG00000204352	ENSG00000204352			31116	protein-coding gene	gene with protein product							Standard	NM_001098808		Approved	bA165J3.3	uc010mre.3	Q5T035	OTTHUMG00000020248	ENST00000375419.1:c.359C>T	9.37:g.96097662G>A	ENSP00000364568:p.Ala120Val	Somatic	449	0	0		WXS	Illumina HiSeq	Phase_I	532	211	0.396617	NM_001098808		Missense_Mutation	SNP	ENST00000375419.1	37	CCDS43850.1	182	0.08333333333333333	14	0.028455284552845527	30	0.08287292817679558	22	0.038461538461538464	116	0.15303430079155672	G	13.09	2.132457	0.37630	.	.	ENSG00000204352	ENST00000375419	T	0.51325	0.71	2.56	2.56	0.30785	.	.	.	.	.	T	0.00178	0.0005	N	0.24115	0.695	0.35885	P	0.17073799999999995	P	0.39920	0.695	B	0.27500	0.08	T	0.12915	-1.0529	8	0.72032	D	0.01	.	13.5524	0.61740	0.0:0.0:1.0:0.0	rs4744219	120	Q5T035	CI129_HUMAN	V	120	ENSP00000364568:A120V	ENSP00000364568:A120V	A	-	2	0	C9orf129	95137483	1.000000	0.71417	0.993000	0.49108	0.423000	0.31445	7.245000	0.78237	1.438000	0.47492	0.298000	0.19748	GCG	.	.	weak		0.632	C9orf129-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053147.1	NM_001098808	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807953	18807953	+	Missense_Mutation	SNP	C	C	A	rs11261022	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:18807953C>A	ENST00000400664.1	+	1	530	c.478C>A	c.(478-480)Cgc>Agc	p.R160S		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	160			R -> S (in dbSNP:rs11261022).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCATTTCCCCCGCTTGGGCAG	0.642													C|||	1400	0.279553	0.2534	0.3401	5008	,	,		17782	0.2321		0.3628	False		,,,				2504	0.2352				p.R160S		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C478A						PASS	.	C	SER/ARG	1039,3127		137,765,1181	32.0	37.0	35.0		478	-4.0	0.0	1	dbSNP_120	35	2972,5484		509,1954,1765	yes	missense	KLHDC7A	NM_152375.2	110	646,2719,2946	AA,AC,CC		35.1466,24.94,31.7778	benign	160/778	18807953	4011,8611	2083	4228	6311	SO:0001583	missense	127707	exon1			TTCCCCCGCTTGG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.478C>A	1.37:g.18807953C>A	ENSP00000383505:p.Arg160Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	58	41	0.706897	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	670	0.3067765567765568	140	0.2845528455284553	105	0.2900552486187845	139	0.243006993006993	286	0.37730870712401055	C	11.86	1.764864	0.31228	0.2494	0.351466	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.72051	-0.62	4.65	-3.99	0.04069	.	3.517270	0.05457	U	0.550465	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18166	0.026	B	0.12837	0.008	T	0.13926	-1.0491	9	0.12430	T	0.62	.	2.446	0.04506	0.1147:0.3232:0.3378:0.2243	rs11261022	160	Q5VTJ3	KLD7A_HUMAN	S	160;97	ENSP00000383505:R160S	ENSP00000383505:R160S	R	+	1	0	KLHDC7A	18680540	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-4.138000	0.00287	-0.507000	0.06549	-0.216000	0.12614	CGC	C|0.671;A|0.329	0.329	strong		0.642	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
UBR5	51366	hgsc.bcm.edu	37	8	103306033	103306033	+	Silent	SNP	T	T	C	rs16869352	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:103306033T>C	ENST00000520539.1	-	34	4995	c.4389A>G	c.(4387-4389)gtA>gtG	p.V1463V	UBR5_ENST00000220959.4_Silent_p.V1463V|UBR5_ENST00000521922.1_Silent_p.V1457V|UBR5_ENST00000519528.1_5'Flank	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	1463					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			ATGCTTGGAATACACGCTTGC	0.398													T|||	122	0.024361	0.0045	0.0216	5008	,	,		22490	0.0198		0.0626	False		,,,				2504	0.0184				p.V1463V	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.A4389G						PASS	.	T		55,4351	54.2+/-90.2	0,55,2148	90.0	74.0	79.0		4389	-2.4	1.0	8	dbSNP_123	79	573,8027	154.2+/-208.4	19,535,3746	no	coding-synonymous	UBR5	NM_015902.5		19,590,5894	CC,CT,TT		6.6628,1.2483,4.8285		1463/2800	103306033	628,12378	2203	4300	6503	SO:0001819	synonymous_variant	51366	exon34			TTGGAATACACGC	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.4389A>G	8.37:g.103306033T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	144	81	0.5625	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																			T|0.957;C|0.043	0.043	strong		0.398	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
SNAPC4	6621	hgsc.bcm.edu	37	9	139272045	139272045	+	Missense_Mutation	SNP	C	C	A	rs79283598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139272045C>A	ENST00000298532.2	-	21	4602	c.4234G>T	c.(4234-4236)Gca>Tca	p.A1412S		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		TCCCTGTCTGCAAGTTCCAGC	0.677													C|||	68	0.0135783	0.0023	0.0187	5008	,	,		15784	0.001		0.0477	False		,,,				2504	0.0031				p.A1412S		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G4234T						PASS	.		SER/ALA	26,4380	29.0+/-57.7	0,26,2177	38.0	37.0	37.0		4234	-7.5	0.0	9	dbSNP_131	37	273,8317	100.3+/-161.8	4,265,4026	yes	missense	SNAPC4	NM_003086.2	99	4,291,6203	AA,AC,CC		3.1781,0.5901,2.3007	benign	1412/1470	139272045	299,12697	2203	4295	6498	SO:0001583	missense	6621	exon21			TGTCTGCAAGTTC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.4234G>T	9.37:g.139272045C>A	ENSP00000298532:p.Ala1412Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	45	0.020604395604395604	2	0.0040650406504065045	6	0.016574585635359115	1	0.0017482517482517483	36	0.047493403693931395	c	0.796	-0.757231	0.03019	0.005901	0.031781	ENSG00000165684	ENST00000298532	T	0.21191	2.02	3.74	-7.47	0.01365	.	7.836560	0.00531	N	0.000204	T	0.01320	0.0043	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13255	-1.0516	10	0.40728	T	0.16	1.8076	1.6888	0.02847	0.3671:0.1135:0.0831:0.4363	.	1412	Q5SXM2	SNPC4_HUMAN	S	1412	ENSP00000298532:A1412S	ENSP00000298532:A1412S	A	-	1	0	SNAPC4	138391866	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.362000	0.01082	-3.382000	0.00175	-0.387000	0.06579	GCA	C|0.976;A|0.024	0.024	strong		0.677	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
CSMD1	64478	hgsc.bcm.edu	37	8	2965244	2965244	+	Silent	SNP	T	T	C	rs3824271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:2965244T>C	ENST00000520002.1	-	46	7389	c.6834A>G	c.(6832-6834)gaA>gaG	p.E2278E	CSMD1_ENST00000400186.3_Silent_p.E2278E|CSMD1_ENST00000542608.1_Silent_p.E2277E|CSMD1_ENST00000537824.1_Silent_p.E2277E|CSMD1_ENST00000602723.1_Silent_p.E2278E|CSMD1_ENST00000602557.1_Silent_p.E2278E			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2278	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TATTACCTATTTCGAAATCAT	0.358													T|||	4205	0.839657	0.7352	0.8545	5008	,	,		17247	0.9464		0.7952	False		,,,				2504	0.9059				p.E2277E		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A6831G						PASS	.	T		2790,930		1050,690,120	142.0	133.0	136.0		6831	-1.3	1.0	8	dbSNP_107	136	6590,1590		2669,1252,169	no	coding-synonymous	CSMD1	NM_033225.5		3719,1942,289	CC,CT,TT		19.4377,25.0,21.1765		2277/3565	2965244	9380,2520	1860	4090	5950	SO:0001819	synonymous_variant	64478	exon45			ACCTATTTCGAAA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6834A>G	8.37:g.2965244T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		1802	0.825091575091575	357	0.725609756097561	310	0.856353591160221	550	0.9615384615384616	585	0.7717678100263852	T	2.733	-0.263931	0.05754	0.75	0.805623	ENSG00000183117	ENST00000335551	.	.	.	5.24	-1.26	0.09376	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.26538	-1.0100	3	.	.	.	.	9.8063	0.40795	0.0:0.3523:0.0:0.6477	rs3824271;rs52789861;rs56571466;rs58615460;rs3824271	.	.	.	D	1758	.	.	N	-	1	0	CSMD1	2952651	0.995000	0.38212	0.996000	0.52242	0.247000	0.25773	0.183000	0.16919	-0.216000	0.10048	0.450000	0.29827	AAT	T|0.176;C|0.824	0.824	strong		0.358	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SULT1A2	6799	hgsc.bcm.edu	37	16	28603721	28603721	+	Missense_Mutation	SNP	C	C	T	rs141581853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28603721C>T	ENST00000395630.1	-	7	988	c.638G>A	c.(637-639)cGc>cAc	p.R213H	SULT1A2_ENST00000533150.1_Missense_Mutation_p.R180H|SULT1A2_ENST00000335715.4_Missense_Mutation_p.R213H	NM_177528.2	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	213					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine biosynthetic process (GO:0009309)|catecholamine metabolic process (GO:0006584)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|sulfotransferase activity (GO:0008146)	p.R213H(4)		NS(2)|breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|skin(2)	14						TGGCAGGGAGCGCCCCACAAA	0.532													.|||	134	0.0267572	0.0363	0.0677	5008	,	,		20273	0.005		0.0268	False		,,,				2504	0.0072				p.R213H		Atlas-SNP	.											SULT1A2,colon,carcinoma,0,4	SULT1A2	27	4	4	Substitution - Missense(4)	skin(2)|large_intestine(1)|NS(1)	c.G638A						PASS	.						132.0	119.0	123.0					16																	28603721		2197	4300	6497	SO:0001583	missense	6799	exon7			AGGGAGCGCCCCA	U34804	CCDS10636.1	16p12.1	2008-02-05			ENSG00000197165	ENSG00000197165	2.8.2.1	"""Sulfotransferases, cytosolic"""	11454	protein-coding gene	gene with protein product		601292		STP2		8661000, 8912648	Standard	NM_001054		Approved	HAST4	uc002dqh.2	P50226	OTTHUMG00000048082	ENST00000395630.1:c.638G>A	16.37:g.28603721C>T	ENSP00000378992:p.Arg213His	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	340	23	0.0676471	NM_001054	A9QY25|P78393|Q14CJ7	Missense_Mutation	SNP	ENST00000395630.1	37	CCDS10636.1	.	.	.	.	.	.	.	.	.	.	c	15.21	2.765812	0.49574	.	.	ENSG00000197165	ENST00000533150;ENST00000335715;ENST00000395630	D;D;D	0.82526	-1.62;-1.62;-1.62	4.98	3.0	0.34707	Sulfotransferase domain (1);	0.265029	0.30329	N	0.009878	T	0.81307	0.4795	M	0.85462	2.755	0.22081	N	0.999373	B	0.12013	0.005	B	0.06405	0.002	T	0.73867	-0.3847	10	0.62326	D	0.03	.	6.5172	0.22254	0.0:0.7359:0.0:0.2641	.	213	P50226	ST1A2_HUMAN	H	180;213;213	ENSP00000435271:R180H;ENSP00000338742:R213H;ENSP00000378992:R213H	ENSP00000338742:R213H	R	-	2	0	SULT1A2	28511222	0.000000	0.05858	1.000000	0.80357	0.908000	0.53690	-0.149000	0.10204	2.300000	0.77407	0.456000	0.33151	CGC	C|0.683;T|0.317	0.317	strong		0.532	SULT1A2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109415.2	NM_001054	
STAMBP	10617	hgsc.bcm.edu	37	2	74077556	74077556	+	Silent	SNP	G	G	T	rs77000353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74077556G>T	ENST00000394070.2	+	7	1424	c.921G>T	c.(919-921)ggG>ggT	p.G307G	STAMBP_ENST00000486458.1_3'UTR|STAMBP_ENST00000394073.1_Silent_p.G307G|STAMBP_ENST00000409707.1_Silent_p.G307G|STAMBP_ENST00000339566.3_Silent_p.G307G	NM_213622.2	NP_998787.1	O95630	STABP_HUMAN	STAM binding protein	307	MPN.				JAK-STAT cascade (GO:0007259)|mitotic cytokinesis (GO:0000281)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of cell proliferation (GO:0008284)|protein deubiquitination (GO:0016579)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	18						AAAGTGCTGGGTCTGATTACT	0.468													G|||	56	0.0111821	0.0015	0.0086	5008	,	,		19685	0.006		0.0169	False		,,,				2504	0.0256				p.G307G		Atlas-SNP	.											.	STAMBP	37	.	0			c.G921T						PASS	.	G	,,	18,4388	23.3+/-48.9	0,18,2185	149.0	131.0	137.0		921,921,921	-4.0	0.9	2	dbSNP_133	137	132,8468	66.3+/-128.7	0,132,4168	yes	coding-synonymous,coding-synonymous,coding-synonymous	STAMBP	NM_006463.4,NM_201647.2,NM_213622.2	,,	0,150,6353	TT,TG,GG		1.5349,0.4085,1.1533	,,	307/425,307/425,307/425	74077556	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	10617	exon8			TGCTGGGTCTGAT	BC007682	CCDS1929.1	2p24.3-p24.1	2008-02-05			ENSG00000124356	ENSG00000124356			16950	protein-coding gene	gene with protein product		606247				10383417	Standard	NM_006463		Approved	AMSH	uc002sjs.3	O95630	OTTHUMG00000129817	ENST00000394070.2:c.921G>T	2.37:g.74077556G>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	187	185	0.989305	NM_006463	B5M0B6|D6W5H7|Q3MJE7	Silent	SNP	ENST00000394070.2	37	CCDS1929.1																																																																																			G|0.988;T|0.012	0.012	strong		0.468	STAMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252048.2	NM_006463	
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959773	45959773	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45959773C>T	ENST00000400375.1	-	1	305	c.261G>A	c.(259-261)ccG>ccA	p.P87P	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	87	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.P87P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						tgcagcaagccggctggcagc	0.672																																					p.P87P		Atlas-SNP	.											KRTAP10-1,NS,carcinoma,0,1	KRTAP10-1	34	1	1	Substitution - coding silent(1)	prostate(1)	c.G261A						scavenged	.						38.0	44.0	42.0					21																	45959773		2183	4271	6454	SO:0001819	synonymous_variant	386677	exon1			GCAAGCCGGCTGG	AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"""Keratin associated proteins"""	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.261G>A	21.37:g.45959773C>T		Somatic	184	4	0.0217391		WXS	Illumina HiSeq	Phase_I	154	10	0.0649351	NM_198691	Q0VAR0|Q0VAR1	Silent	SNP	ENST00000400375.1	37	CCDS42954.1																																																																																			.	.	weak		0.672	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1		
CD3E	916	hgsc.bcm.edu	37	11	118178007	118178007	+	Silent	SNP	C	C	T	rs1126924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118178007C>T	ENST00000361763.4	+	3	345	c.54C>T	c.(52-54)ggC>ggT	p.G18G	CD3E_ENST00000528600.1_Silent_p.G18G	NM_000733.3	NP_000724.1	P07766	CD3E_HUMAN	CD3e molecule, epsilon (CD3-TCR complex)	18					apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of smoothened signaling pathway (GO:0045879)|negative thymic T cell selection (GO:0045060)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell anergy (GO:0002669)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)|regulation of immune response (GO:0050776)|response to nutrient (GO:0007584)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)|SH3 domain binding (GO:0017124)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)	p.G18G(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|ovary(2)|stomach(1)	8	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)	TTCTAGTTGGCGTTTGGGGGC	0.373													C|||	1129	0.225439	0.0386	0.4625	5008	,	,		20142	0.1865		0.3052	False		,,,				2504	0.2679				p.G18G		Atlas-SNP	.											CD3E,NS,carcinoma,0,1	CD3E	23	1	1	Substitution - coding silent(1)	stomach(1)	c.C54T						PASS	.	C		382,4018	194.7+/-219.5	20,342,1838	132.0	116.0	121.0		54	-6.5	0.1	11	dbSNP_111	121	2744,5848	437.2+/-358.5	450,1844,2002	no	coding-synonymous	CD3E	NM_000733.3		470,2186,3840	TT,TC,CC		31.9367,8.6818,24.061		18/208	118178007	3126,9866	2200	4296	6496	SO:0001819	synonymous_variant	916	exon3			AGTTGGCGTTTGG	X03884	CCDS31685.1	11q23	2014-09-17	2006-03-28		ENSG00000198851	ENSG00000198851		"""CD molecules"""	1674	protein-coding gene	gene with protein product		186830	"""CD3e antigen, epsilon polypeptide (TiT3 complex)"""				Standard	NM_000733		Approved		uc001psq.4	P07766	OTTHUMG00000166968	ENST00000361763.4:c.54C>T	11.37:g.118178007C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_000733	A8K997	Silent	SNP	ENST00000361763.4	37	CCDS31685.1																																																																																			C|0.768;T|0.232	0.232	strong		0.373	CD3E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392120.1	NM_000733	
NPEPL1	79716	hgsc.bcm.edu	37	20	57268867	57268867	+	Silent	SNP	C	C	A	rs3746396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57268867C>A	ENST00000356091.6	+	2	513	c.225C>A	c.(223-225)acC>acA	p.T75T	NPEPL1_ENST00000525967.1_Silent_p.T47T|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525817.1_Silent_p.T27T	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	75						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			ACTACGCCACCGTGGCTGCCC	0.672													C|||	1502	0.29992	0.1982	0.2983	5008	,	,		17151	0.376		0.3429	False		,,,				2504	0.316				p.T75T		Atlas-SNP	.											.	NPEPL1	36	.	0			c.C225A						PASS	.	C	,,	920,3252		125,670,1291	42.0	50.0	47.0		141,81,225	-9.7	0.3	20	dbSNP_107	47	3298,5108		693,1912,1598	no	coding-synonymous,coding-synonymous,coding-synonymous	NPEPL1	NM_001204872.1,NM_001204873.1,NM_024663.3	,,	818,2582,2889	AA,AC,CC		39.2339,22.0518,33.5347	,,	47/496,27/476,75/524	57268867	4218,8360	2086	4203	6289	SO:0001819	synonymous_variant	79716	exon2			CGCCACCGTGGCT	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.225C>A	20.37:g.57268867C>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	204	100	0.490196	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																			C|0.647;A|0.353	0.353	strong		0.672	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
SHB	6461	hgsc.bcm.edu	37	9	37948724	37948724	+	Silent	SNP	T	T	C	rs3827519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37948724T>C	ENST00000377707.3	-	5	1819	c.1254A>G	c.(1252-1254)ggA>ggG	p.G418G	RP11-613M10.9_ENST00000540557.1_3'UTR	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	418	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.G418G(1)		central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		TCTCGGCGTCTCCTCTGCTGA	0.602													T|||	705	0.140775	0.1778	0.1052	5008	,	,		18186	0.1369		0.1103	False		,,,				2504	0.1513				p.G418G		Atlas-SNP	.											SHB,NS,carcinoma,0,2	SHB	31	2	1	Substitution - coding silent(1)	stomach(1)	c.A1254G						PASS	.	T		688,3682		55,578,1552	60.0	68.0	66.0		1254	-8.2	0.4	9	dbSNP_107	66	904,7664		45,814,3425	no	coding-synonymous	SHB	NM_003028.2		100,1392,4977	CC,CT,TT		10.5509,15.7437,12.3048		418/510	37948724	1592,11346	2185	4284	6469	SO:0001819	synonymous_variant	6461	exon5			GGCGTCTCCTCTG		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"""SH2 domain containing"""	10838	protein-coding gene	gene with protein product		600314	"""SHB adaptor protein (a Src homology 2 protein)"", ""SHB (Src homology 2 domain containing) adaptor protein B"""			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.1254A>G	9.37:g.37948724T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_003028	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	Silent	SNP	ENST00000377707.3	37	CCDS43806.1																																																																																			T|0.883;C|0.117	0.117	strong		0.602	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1		
ASAP1	50807	hgsc.bcm.edu	37	8	131072829	131072829	+	Missense_Mutation	SNP	T	T	C	rs117019764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:131072829T>C	ENST00000518721.1	-	28	3415	c.3188A>G	c.(3187-3189)aAt>aGt	p.N1063S	ASAP1_ENST00000357668.1_Missense_Mutation_p.N1063S	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	1063					cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						ACCCACCGTATTGATTTTTCT	0.532													T|||	8	0.00159744	0.0	0.0	5008	,	,		18855	0.0		0.007	False		,,,				2504	0.001				p.N1063S		Atlas-SNP	.											.	ASAP1	133	.	0			c.A3188G						PASS	.	T	SER/ASN	1,4405	2.1+/-5.4	0,1,2202	188.0	198.0	195.0		3188	5.7	1.0	8	dbSNP_132	195	32,8568	22.2+/-67.0	0,32,4268	yes	missense	ASAP1	NM_018482.2	46	0,33,6470	CC,CT,TT		0.3721,0.0227,0.2537	probably-damaging	1063/1130	131072829	33,12973	2203	4300	6503	SO:0001583	missense	50807	exon28			ACCGTATTGATTT	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2720	protein-coding gene	gene with protein product	"""centaurin, beta 4"""	605953	"""development and differentiation enhancing factor 1"""	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.3188A>G	8.37:g.131072829T>C	ENSP00000429900:p.Asn1063Ser	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	251	128	0.50996	NM_018482	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	37	CCDS6362.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	T	14.18	2.458698	0.43634	2.27E-4	0.003721	ENSG00000153317	ENST00000343135;ENST00000357668;ENST00000518721	T;T	0.27402	1.67;1.67	5.66	5.66	0.87406	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.25005	0.0607	L	0.53249	1.67	0.80722	D	1	B;B;P	0.40431	0.451;0.451;0.717	B;B;B	0.41271	0.112;0.112;0.352	T	0.03354	-1.1045	10	0.21540	T	0.41	.	15.0838	0.72135	0.0:0.0:0.0:1.0	.	1063;1063;1066	B2RNV3;Q9ULH1;Q9ULH1-2	.;ASAP1_HUMAN;.	S	1066;1063;1063	ENSP00000350297:N1063S;ENSP00000429900:N1063S	ENSP00000344591:N1066S	N	-	2	0	ASAP1	131142011	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.762000	0.68809	2.146000	0.66826	0.533000	0.62120	AAT	T|0.998;C|0.002	0.002	strong		0.532	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482	
CDH5	1003	hgsc.bcm.edu	37	16	66432381	66432381	+	Missense_Mutation	SNP	T	T	C	rs16956504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:66432381T>C	ENST00000341529.3	+	10	1656	c.1508T>C	c.(1507-1509)aTa>aCa	p.I503T	CDH5_ENST00000539168.1_5'UTR	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	503	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> T (in dbSNP:rs16956504).		adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	ATCTCCGCAATAGACAAGGAC	0.483													T|||	218	0.0435304	0.003	0.0447	5008	,	,		20964	0.0		0.1113	False		,,,				2504	0.0726				p.I503T		Atlas-SNP	.											.	CDH5	111	.	0			c.T1508C						PASS	.	T	THR/ILE	71,4331	65.8+/-103.3	1,69,2131	150.0	126.0	134.0		1508	-4.5	0.8	16	dbSNP_123	134	930,7670	204.7+/-247.3	58,814,3428	yes	missense	CDH5	NM_001795.3	89	59,883,5559	CC,CT,TT		10.814,1.6129,7.6988	benign	503/785	66432381	1001,12001	2201	4300	6501	SO:0001583	missense	1003	exon10			CCGCAATAGACAA	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"""CD molecules"", ""Cadherins / Major cadherins"""	1764	protein-coding gene	gene with protein product	"""VE-cadherin"""	601120	"""cadherin 5, type 2, VE-cadherin (vascular epithelium)"""			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.1508T>C	16.37:g.66432381T>C	ENSP00000344115:p.Ile503Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_001795	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	37	CCDS10804.1	112	0.05128205128205128	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	93	0.12269129287598944	T	9.148	1.015519	0.19355	0.016129	0.10814	ENSG00000179776	ENST00000341529;ENST00000379531;ENST00000539262	T	0.44482	0.92	4.95	-4.5	0.03493	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00210	0.0006	N	0.01289	-0.905	0.35243	P	0.22196000000000005	B	0.02656	0.0	B	0.10450	0.005	T	0.23404	-1.0189	8	0.28530	T	0.3	.	13.6298	0.62189	0.0:0.6081:0.0:0.3919	rs16956504;rs16956504	503	P33151	CADH5_HUMAN	T	503;388;244	ENSP00000344115:I503T	ENSP00000344115:I503T	I	+	2	0	CDH5	64989882	0.101000	0.21875	0.776000	0.31678	0.989000	0.77384	-0.467000	0.06664	-0.795000	0.04462	0.459000	0.35465	ATA	T|0.940;C|0.060	0.060	strong		0.483	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795	
LCA5	167691	hgsc.bcm.edu	37	6	80228535	80228535	+	Missense_Mutation	SNP	T	T	G	rs34068461	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:80228535T>G	ENST00000392959.1	-	3	688	c.77A>C	c.(76-78)gAt>gCt	p.D26A	LCA5_ENST00000369846.4_Missense_Mutation_p.D26A|LCA5_ENST00000467898.3_Missense_Mutation_p.D26A	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	26			D -> A (in dbSNP:rs34068461).		intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		CGTTTCAAAATCAGATAAGTA	0.418													T|||	867	0.173123	0.0741	0.2334	5008	,	,		17933	0.2192		0.173	False		,,,				2504	0.2168				p.D26A		Atlas-SNP	.											.	LCA5	71	.	0			c.A77C						PASS	.	T	ALA/ASP,ALA/ASP	338,4068	178.0+/-206.8	12,314,1877	301.0	284.0	290.0		77,77	4.1	0.9	6	dbSNP_126	290	1559,7041	294.2+/-301.7	129,1301,2870	yes	missense,missense	LCA5	NM_001122769.2,NM_181714.3	126,126	141,1615,4747	GG,GT,TT		18.1279,7.6714,14.5856	probably-damaging,probably-damaging	26/698,26/698	80228535	1897,11109	2203	4300	6503	SO:0001583	missense	167691	exon2			TCAAAATCAGATA		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"""lebercilin"""	611408	"""chromosome 6 open reading frame 152"""	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.77A>C	6.37:g.80228535T>G	ENSP00000376686:p.Asp26Ala	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	214	88	0.411215	NM_001122769	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	CCDS4990.1	376	0.17216117216117216	43	0.08739837398373984	84	0.23204419889502761	129	0.22552447552447552	120	0.158311345646438	T	17.17	3.320429	0.60634	0.076714	0.181279	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.62788	-0.0;-0.0	5.28	4.09	0.47781	.	0.662303	0.14761	N	0.299945	T	0.42494	0.1205	L	0.59436	1.845	0.29152	P	0.87834	B;B	0.20671	0.004;0.047	B;B	0.23419	0.01;0.046	T	0.43410	-0.9393	9	0.62326	D	0.03	-2.4209	10.295	0.43618	0.0:0.0:0.1657:0.8343	rs34068461	26;26	B4DRL2;Q86VQ0	.;LCA5_HUMAN	A	26	ENSP00000358861:D26A;ENSP00000376686:D26A	ENSP00000358861:D26A	D	-	2	0	LCA5	80285254	0.997000	0.39634	0.864000	0.33941	0.599000	0.36880	2.917000	0.48821	0.986000	0.38683	0.533000	0.62120	GAT	T|0.843;G|0.157	0.157	strong		0.418	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714	
TRIOBP	11078	hgsc.bcm.edu	37	22	38120343	38120343	+	Missense_Mutation	SNP	A	A	G	rs71317067		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38120343A>G	ENST00000406386.3	+	7	2035	c.1780A>G	c.(1780-1782)Aca>Gca	p.T594A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	594					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T594A(5)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAATAGAGCTACACGAGACAA	0.572																																					p.T594A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,5	TRIOBP	262	5	5	Substitution - Missense(5)	skin(2)|large_intestine(1)|NS(1)|prostate(1)	c.A1780G						scavenged	.						112.0	164.0	147.0					22																	38120343		1955	4165	6120	SO:0001583	missense	11078	exon7			AGAGCTACACGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1780A>G	22.37:g.38120343A>G	ENSP00000384312:p.Thr594Ala	Somatic	558	12	0.0215054		WXS	Illumina HiSeq	Phase_I	658	18	0.0273556	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	-	7.079	0.569772	0.13560	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20738	2.05	2.6	0.164	0.14990	.	.	.	.	.	T	0.11879	0.0289	L	0.28115	0.83	0.09310	N	0.999998	B	0.21381	0.055	B	0.12837	0.008	T	0.32745	-0.9895	9	0.26408	T	0.33	.	5.3198	0.15876	0.5376:0.0:0.0:0.4624	.	594	Q9H2D6	TARA_HUMAN	A	594	ENSP00000384312:T594A	ENSP00000384312:T594A	T	+	1	0	TRIOBP	36450289	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.521000	0.06245	-0.162000	0.10964	-1.765000	0.00666	ACA	A|0.500;G|0.500	0.500	weak		0.572	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
IQCE	23288	hgsc.bcm.edu	37	7	2613062	2613062	+	Silent	SNP	T	T	C	rs61739566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2613062T>C	ENST00000402050.2	+	6	589	c.405T>C	c.(403-405)ccT>ccC	p.P135P	IQCE_ENST00000438376.2_Silent_p.P119P|IQCE_ENST00000325979.7_Silent_p.P70P|IQCE_ENST00000404984.1_Silent_p.P84P	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	135						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		GTCATGTCCCTGGGACTCCTG	0.348													T|||	483	0.0964457	0.1263	0.0994	5008	,	,		21532	0.001		0.1421	False		,,,				2504	0.1053				p.P135P		Atlas-SNP	.											.	IQCE	66	.	0			c.T405C						PASS	.	T	,	485,3185		35,415,1385	154.0	138.0	143.0		357,405	-10.9	0.0	7	dbSNP_129	143	1321,6845		107,1107,2869	no	coding-synonymous,coding-synonymous	IQCE	NM_001100390.1,NM_152558.3	,	142,1522,4254	CC,CT,TT		16.1768,13.2153,15.2585	,	119/680,135/696	2613062	1806,10030	1835	4083	5918	SO:0001819	synonymous_variant	23288	exon6			TGTCCCTGGGACT	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.405T>C	7.37:g.2613062T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	37	CCDS43542.1																																																																																			T|0.884;C|0.116	0.116	strong		0.348	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
RCC1	1104	hgsc.bcm.edu	37	1	28861636	28861636	+	Silent	SNP	G	G	A	rs2066726	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:28861636G>A	ENST00000373833.6	+	8	801	c.516G>A	c.(514-516)gtG>gtA	p.V172V	RCC1_ENST00000398958.2_Silent_p.V172V|RCC1_ENST00000373832.1_Silent_p.V172V|RCC1_ENST00000373831.3_Silent_p.V203V|RCC1_ENST00000429051.1_3'UTR			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	172					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		AGCTGGATGTGCCTGTGGTAA	0.577													G|||	1121	0.223842	0.3101	0.2478	5008	,	,		21255	0.0724		0.3072	False		,,,				2504	0.1605				p.V203V		Atlas-SNP	.											.	RCC1	61	.	0			c.G609A						PASS	.	G	,,,	1306,3100	441.4+/-346.4	200,906,1097	160.0	143.0	149.0		609,567,516,516	-0.6	0.0	1	dbSNP_94	149	2342,6258	392.3+/-344.0	298,1746,2256	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RCC1	NM_001048194.2,NM_001048195.2,NM_001048199.2,NM_001269.4	,,,	498,2652,3353	AA,AG,GG		27.2326,29.6414,28.0486	,,,	203/453,189/439,172/422,172/422	28861636	3648,9358	2203	4300	6503	SO:0001819	synonymous_variant	1104	exon6			GGATGTGCCTGTG	X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"""chromosome condensation 1"""	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.516G>A	1.37:g.28861636G>A		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	209	126	0.602871	NM_001048194	Q16269|Q6NT97	Silent	SNP	ENST00000373833.6	37	CCDS323.1																																																																																			G|0.728;A|0.272	0.272	strong		0.577	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269	
OR2T12	127064	hgsc.bcm.edu	37	1	248457993	248457993	+	Missense_Mutation	SNP	C	C	G	rs11204625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248457993C>G	ENST00000317996.1	-	1	887	c.888G>C	c.(886-888)aaG>aaC	p.K296N		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	296			K -> N (in dbSNP:rs11204625).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			TCAGGGCTTCCTTGACCTCAC	0.473													N|||	1067	0.213059	0.0091	0.2464	5008	,	,		18443	0.3591		0.174	False		,,,				2504	0.3548				p.K296N		Atlas-SNP	.											.	OR2T12	113	.	0			c.G888C						PASS	.	C	ASN/LYS	194,4212		4,186,2013	165.0	160.0	161.0		888	-3.4	0.0	1	dbSNP_120	161	1474,7126		128,1218,2954	no	missense	OR2T12	NM_001004692.1	94	132,1404,4967	GG,GC,CC		17.1395,4.4031,12.8249	probably-damaging	296/321	248457993	1668,11338	2203	4300	6503	SO:0001583	missense	127064	exon1			GGCTTCCTTGACC	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.888G>C	1.37:g.248457993C>G	ENSP00000324583:p.Lys296Asn	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	340	156	0.458824	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	424	0.19413919413919414	8	0.016260162601626018	74	0.20441988950276244	198	0.34615384615384615	144	0.18997361477572558	-	11.27	1.588879	0.28357	0.044031	0.171395	ENSG00000177201	ENST00000317996	T	0.40756	1.02	1.71	-3.42	0.04825	.	0.258640	0.19945	U	0.102541	T	0.00012	0.0000	M	0.69248	2.105	0.80722	P	0.0	P	0.52316	0.952	P	0.52598	0.703	T	0.11108	-1.0601	9	0.34782	T	0.22	.	4.0137	0.09634	0.1652:0.4839:0.0:0.351	rs11204625;rs11204625	296	Q8NG77	O2T12_HUMAN	N	296	ENSP00000324583:K296N	ENSP00000324583:K296N	K	-	3	2	OR2T12	246524616	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-0.317000	0.08060	-0.825000	0.04290	0.418000	0.28097	AAG	.	.	weak		0.473	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
LTBP1	4052	hgsc.bcm.edu	37	2	33447202	33447202	+	Silent	SNP	C	C	T	rs2290448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33447202C>T	ENST00000404816.2	+	9	2213	c.1860C>T	c.(1858-1860)aaC>aaT	p.N620N	LTBP1_ENST00000407925.1_Silent_p.N294N|LTBP1_ENST00000418533.2_Silent_p.N294N|LTBP1_ENST00000390003.4_Silent_p.N294N|LTBP1_ENST00000402934.1_Silent_p.N294N|LTBP1_ENST00000354476.3_Silent_p.N620N|LTBP1_ENST00000404525.1_Silent_p.N294N			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	620					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AGCGGGTTAACAACACCTTTT	0.383													C|||	1666	0.332668	0.1936	0.4337	5008	,	,		19452	0.3323		0.4861	False		,,,				2504	0.2914				p.N620N		Atlas-SNP	.											.	LTBP1	317	.	0			c.C1860T						PASS	.	C	,,,,	1019,3387	375.6+/-321.7	109,801,1293	117.0	101.0	106.0		882,882,882,882,1860	2.2	1.0	2	dbSNP_100	106	4214,4386	570.6+/-389.4	1021,2172,1107	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	1130,2973,2400	TT,TC,CC		49.0,23.1276,40.2353	,,,,	294/1396,294/1354,294/1343,294/1301,620/1722	33447202	5233,7773	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon9			GGTTAACAACACC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1860C>T	2.37:g.33447202C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			C|0.608;T|0.392	0.392	strong		0.383	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
ALMS1	7840	hgsc.bcm.edu	37	2	73828538	73828538	+	Missense_Mutation	SNP	G	G	A	rs1052161	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:73828538G>A	ENST00000264448.6	+	19	12197	c.12086G>A	c.(12085-12087)aGg>aAg	p.R4029K	ALMS1_ENST00000409009.1_Missense_Mutation_p.R3987K|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4029				R -> K (in Ref. 1; CAD10391 and 3; BAA20786). {ECO:0000305}.	endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GACCTACTGAGGCCATTTGTG	0.592													A|||	2916	0.582268	0.2466	0.7061	5008	,	,		18466	0.7599		0.6561	False		,,,				2504	0.6892				p.R4029K		Atlas-SNP	.											.	ALMS1	384	.	0			c.G12086A						PASS	.	A	LYS/ARG	1498,2904	618.6+/-393.2	281,936,984	29.0	34.0	32.0		12086	-6.3	0.0	2	dbSNP_86	32	5479,3121	457.4+/-364.3	1739,2001,560	yes	missense	ALMS1	NM_015120.4	26	2020,2937,1544	AA,AG,GG		36.2907,34.03,46.339	benign	4029/4168	73828538	6977,6025	2201	4300	6501	SO:0001583	missense	7840	exon19			TACTGAGGCCATT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.12086G>A	2.37:g.73828538G>A	ENSP00000264448:p.Arg4029Lys	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	286	125	0.437063	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	1272	0.5824175824175825	124	0.25203252032520324	252	0.6961325966850829	410	0.7167832167832168	486	0.6411609498680739	A	2.887	-0.230570	0.05983	0.3403	0.637093	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.05319	3.46;3.46	5.17	-6.29	0.02013	.	1.180180	0.06066	N	0.659294	T	0.00012	0.0000	N	0.01874	-0.695	0.48452	P	3.429999999999822E-4	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.38265	-0.9669	9	0.02654	T	1	.	12.9421	0.58350	0.2574:0.0992:0.6434:0.0	rs1052161;rs1320373;rs3192572;rs17266496;rs17848874;rs52825392;rs56597987;rs60369267;rs1052161	3987;4029	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	K	3987;4029	ENSP00000386627:R3987K;ENSP00000264448:R4029K	ENSP00000264448:R4029K	R	+	2	0	ALMS1	73682046	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-1.799000	0.01746	-2.132000	0.00814	-0.361000	0.07541	AGG	G|0.424;N|0.000	.	strong		0.592	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
TMEM52	339456	hgsc.bcm.edu	37	1	1849529	1849529	+	Missense_Mutation	SNP	A	A	G	rs28640257	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1849529A>G	ENST00000310991.3	-	5	429	c.422T>C	c.(421-423)aTg>aCg	p.M141T	TMEM52_ENST00000378602.3_Missense_Mutation_p.M126T	NM_178545.3	NP_848640.1	Q8NDY8	TMM52_HUMAN	transmembrane protein 52	141			M -> T (in dbSNP:rs28640257). {ECO:0000269|PubMed:12975309}.|M -> V (in dbSNP:rs4459050).			integral component of membrane (GO:0016021)		p.M141T(1)		NS(1)|prostate(1)|stomach(1)	3	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGGAGGAGCCATGGAGTCCAG	0.627													A|||	1763	0.352037	0.053	0.5072	5008	,	,		19495	0.4623		0.4901	False		,,,				2504	0.3906				p.M141T		Atlas-SNP	.											TMEM52,NS,carcinoma,0,2	TMEM52	21	2	1	Substitution - Missense(1)	stomach(1)	c.T422C						PASS	.	A	THR/MET	532,3874		39,454,1710	90.0	88.0	89.0		422	0.2	0.0	1	dbSNP_125	89	4288,4312		1092,2104,1104	no	missense	TMEM52	NM_178545.3	81	1131,2558,2814	GG,GA,AA		49.8605,12.0744,37.0598	benign	141/210	1849529	4820,8186	2203	4300	6503	SO:0001583	missense	339456	exon5			GGAGCCATGGAGT	AJ278736	CCDS35.1	1p36.33	2008-02-05			ENSG00000178821	ENSG00000178821			27916	protein-coding gene	gene with protein product							Standard	NM_178545		Approved		uc001aij.2	Q8NDY8	OTTHUMG00000000944	ENST00000310991.3:c.422T>C	1.37:g.1849529A>G	ENSP00000311122:p.Met141Thr	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	182	64	0.351648	NM_178545	Q4VXS6|Q6UX25	Missense_Mutation	SNP	ENST00000310991.3	37	CCDS35.1	846	0.3873626373626374	32	0.06504065040650407	183	0.505524861878453	258	0.45104895104895104	373	0.4920844327176781	.	3.602	-0.081358	0.07141	0.120744	0.498605	ENSG00000178821	ENST00000378602;ENST00000310991	T;T	0.31510	1.49;1.49	3.84	0.201	0.15186	.	0.206931	0.29515	N	0.011934	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.14438	0.002;0.01	B;B	0.12837	0.002;0.008	T	0.47209	-0.9135	9	0.16420	T	0.52	-5.174	3.3609	0.07186	0.6178:0.0:0.2079:0.1743	rs28640257	141;126	Q8NDY8;Q8NDY8-2	TMM52_HUMAN;.	T	126;141	ENSP00000367865:M126T;ENSP00000311122:M141T	ENSP00000311122:M141T	M	-	2	0	TMEM52	1839389	0.000000	0.05858	0.018000	0.16275	0.849000	0.48306	0.105000	0.15333	0.143000	0.18926	0.459000	0.35465	ATG	A|0.613;G|0.387;T|0.000	0.387	strong		0.627	TMEM52-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002781.1	NM_178545	
ZNF268	10795	hgsc.bcm.edu	37	12	133768553	133768553	+	Missense_Mutation	SNP	A	A	T	rs61960670	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133768553A>T	ENST00000536435.2	+	5	751	c.421A>T	c.(421-423)Atg>Ttg	p.M141L	ZNF268_ENST00000228289.5_Missense_Mutation_p.M141L|ZNF268_ENST00000541009.2_Missense_Mutation_p.M141L|ZNF268_ENST00000416488.1_Missense_Mutation_p.M306L|ZNF268_ENST00000537565.1_Intron|ZNF268_ENST00000536899.2_Intron|ZNF268_ENST00000539248.2_Intron|CTD-2140B24.4_ENST00000540096.2_Missense_Mutation_p.M306L|ZNF268_ENST00000542986.2_Missense_Mutation_p.M126L|ZNF268_ENST00000542711.2_Silent_p.V31V|ZNF268_ENST00000541211.2_Silent_p.V98V|ZNF268_ENST00000592241.1_Missense_Mutation_p.M74L	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	141	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		AGAGCTGTGTATGGTGCAGGC	0.398													A|||	722	0.144169	0.0083	0.1571	5008	,	,		18153	0.1121		0.2396	False		,,,				2504	0.2536				p.M141L		Atlas-SNP	.											.	ZNF268	71	.	0			c.A421T						PASS	.	A	LEU/MET,LEU/MET,,,,,LEU/MET,LEU/MET,LEU/MET	194,3686		6,182,1752	150.0	145.0	146.0		421,172,,,294,93,220,421,421	-2.5	0.1	12	dbSNP_129	146	2209,6109		302,1605,2252	yes	missense,missense,intron,intron,coding-synonymous,coding-synonymous,missense,missense,missense	ZNF268	NM_001165881.2,NM_001165882.2,NM_001165883.1,NM_001165884.2,NM_001165885.1,NM_001165886.1,NM_001165887.1,NM_003415.2,NM_152943.2	15,15,,,,,15,15,15	308,1787,4004	TT,TA,AA		26.5569,5.0,19.7	benign,benign,,,,,benign,benign,benign	141/948,58/865,,,98/168,31/101,74/127,141/948,141/194	133768553	2403,9795	1940	4159	6099	SO:0001583	missense	10795	exon5			CTGTGTATGGTGC	X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"""Zinc fingers, C2H2-type"", ""-"""	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.421A>T	12.37:g.133768553A>T	ENSP00000444412:p.Met141Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_152943	Q8TDG8|Q96RH4|Q9BZJ9	Missense_Mutation	SNP	ENST00000536435.2	37	CCDS45012.1	309	0.14148351648351648	6	0.012195121951219513	61	0.1685082872928177	61	0.10664335664335664	181	0.23878627968337732	A	0.076	-1.193631	0.01594	0.05	0.265569	ENSG00000090612	ENST00000416488;ENST00000541009;ENST00000542986;ENST00000228289;ENST00000534953	T;T;T	0.07327	5.93;5.44;3.2	3.38	-2.54	0.06307	Krueppel-associated box (2);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48854	-0.8998	6	.	.	.	.	5.1496	0.15002	0.5528:0.1507:0.2964:0.0	rs61960670	141	Q14587	ZN268_HUMAN	L	306;141;74;141;65	ENSP00000409295:M306L;ENSP00000439539:M141L;ENSP00000228289:M141L	.	M	+	1	0	ZNF268	132278626	0.008000	0.16893	0.097000	0.21041	0.064000	0.16182	-0.439000	0.06897	-0.679000	0.05217	-1.964000	0.00472	ATG	A|0.835;T|0.165	0.165	strong		0.398	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
PIWIL4	143689	hgsc.bcm.edu	37	11	94322352	94322352	+	Missense_Mutation	SNP	A	A	T	rs11020845|rs386756343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:94322352A>T	ENST00000299001.6	+	8	1191	c.980A>T	c.(979-981)cAg>cTg	p.Q327L	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	327	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.		Q -> L (in dbSNP:rs11020845). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CACACCTTTCAGAAGCGGGAT	0.398													A|||	942	0.188099	0.0598	0.1873	5008	,	,		18440	0.2817		0.2813	False		,,,				2504	0.1697				p.Q327L		Atlas-SNP	.											.	PIWIL4	70	.	0			c.A980T						PASS	.	A	LEU/GLN	24,4378		9,6,2186	177.0	161.0	166.0		980	-3.5	0.7	11	dbSNP_120	166	314,8282		126,62,4110	yes	missense	PIWIL4	NM_152431.2	113	135,68,6296	TT,TA,AA		3.6529,0.5452,2.6004	benign	327/853	94322352	338,12660	2201	4298	6499	SO:0001583	missense	143689	exon8			CCTTTCAGAAGCG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.980A>T	11.37:g.94322352A>T	ENSP00000299001:p.Gln327Leu	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	193	101	0.523316	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	370	0.16941391941391942	21	0.042682926829268296	69	0.19060773480662985	116	0.20279720279720279	164	0.21635883905013192	A	14.47	2.546340	0.45383	0.005452	0.036529	ENSG00000134627	ENST00000299001	T	0.14144	2.53	4.96	-3.53	0.04667	Argonaute/Dicer protein, PAZ (4);	0.810725	0.11154	N	0.593796	T	0.00012	0.0000	L	0.58969	1.84	0.09310	P	0.999999830308	B	0.26708	0.157	B	0.33121	0.158	T	0.41448	-0.9508	9	0.44086	T	0.13	-1.6396	2.9704	0.05920	0.3688:0.1246:0.3849:0.1216	rs11020845;rs11020845	327	Q7Z3Z4	PIWL4_HUMAN	L	327	ENSP00000299001:Q327L	ENSP00000299001:Q327L	Q	+	2	0	PIWIL4	93962000	0.291000	0.24352	0.714000	0.30535	0.988000	0.76386	-0.490000	0.06482	-0.492000	0.06687	-0.388000	0.06559	CAG	A|0.793;T|0.207	0.207	strong		0.398	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
SLC25A32	81034	hgsc.bcm.edu	37	8	104427359	104427359	+	5'Flank	SNP	A	A	C	rs3134295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:104427359A>C	ENST00000297578.4	-	0	0				DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000297579.5_Missense_Mutation_p.R47S|DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|SLC25A32_ENST00000543107.1_5'Flank	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	CGGGGCACAGACACTACGTCA	0.667													c|||	2145	0.428315	0.4985	0.4294	5008	,	,		16891	0.3462		0.4722	False		,,,				2504	0.3722				p.R47S		Atlas-SNP	.											DCAF13,NS,carcinoma,0,1	DCAF13	66	1	0			c.A141C						scavenged	.	-	SER/ARG,	2186,2220		537,1112,554	46.0	45.0	45.0		141,	1.0	0.0	8	dbSNP_103	45	3825,4775		878,2069,1353	yes	missense,utr-5	DCAF13,SLC25A32	NM_015420.6,NM_030780.3	110,	1415,3181,1907	CC,CA,AA		44.4767,49.6142,46.2171	benign,	47/598,	104427359	6011,6995	2203	4300	6503	SO:0001631	upstream_gene_variant	25879	exon1			GCACAGACACTAC	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		8.37:g.104427359A>C	Exception_encountered	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	111	46	0.414414	NM_015420	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	CCDS6300.1	983	0.4500915750915751	244	0.4959349593495935	170	0.4696132596685083	203	0.3548951048951049	366	0.48284960422163586	C	2.986	-0.209151	0.06140	0.496142	0.444767	ENSG00000164934	ENST00000297579	T	0.76968	-1.06	4.05	0.973	0.19710	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53688	P	2.599999999997049E-5	.	.	.	.	.	.	T	0.34725	-0.9817	5	0.02654	T	1	1.0596	2.054	0.03577	0.357:0.3658:0.174:0.1032	rs3134295;rs52825097;rs57877210;rs3134295	.	.	.	S	47	ENSP00000297579:R47S	ENSP00000297579:R47S	R	+	3	2	DCAF13	104496535	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.250000	0.00540	0.137000	0.18759	-0.127000	0.14921	AGA	A|0.537;C|0.463	0.463	strong		0.667	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
XYLT1	64131	hgsc.bcm.edu	37	16	17202801	17202801	+	Silent	SNP	G	G	A	rs34511974	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:17202801G>A	ENST00000261381.6	-	12	2715	c.2631C>T	c.(2629-2631)ccC>ccT	p.P877P		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	877					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGCTGAGGACGGGGTTTAGGC	0.617													G|||	514	0.102636	0.0045	0.2478	5008	,	,		18519	0.002		0.1491	False		,,,				2504	0.1881				p.P877P		Atlas-SNP	.											XYLT1,colon,carcinoma,0,1	XYLT1	147	1	0			c.C2631T						PASS	.	G		154,4240	105.6+/-144.1	3,148,2046	100.0	100.0	100.0		2631	-11.6	0.1	16	dbSNP_126	100	1342,7258	261.9+/-284.1	96,1150,3054	no	coding-synonymous	XYLT1	NM_022166.3		99,1298,5100	AA,AG,GG		15.6047,3.5048,11.513		877/960	17202801	1496,11498	2197	4300	6497	SO:0001819	synonymous_variant	64131	exon12			GAGGACGGGGTTT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2631C>T	16.37:g.17202801G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	37	CCDS10569.1																																																																																			G|0.888;A|0.112	0.112	strong		0.617	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
ZBTB46	140685	hgsc.bcm.edu	37	20	62378349	62378349	+	Silent	SNP	C	C	T	rs5019252	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62378349C>T	ENST00000245663.4	-	5	1854	c.1704G>A	c.(1702-1704)gaG>gaA	p.E568E	ZBTB46_ENST00000302995.2_Silent_p.E568E|ZBTB46_ENST00000395104.1_Silent_p.E568E|RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	568					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GCGAGTCTTCCTCATCCTTGT	0.726													c|||	1350	0.269569	0.1498	0.379	5008	,	,		10337	0.3472		0.336	False		,,,				2504	0.2055				p.E568E		Atlas-SNP	.											ZBTB46,rectum,carcinoma,0,1	ZBTB46	72	1	0			c.G1704A						PASS	.	T		770,3626		79,612,1507	25.0	24.0	25.0		1704	-7.5	0.0	20	dbSNP_113	25	2820,5768		445,1930,1919	no	coding-synonymous	ZBTB46	NM_025224.3		524,2542,3426	TT,TC,CC		32.8365,17.5159,27.6494		568/590	62378349	3590,9394	2198	4294	6492	SO:0001819	synonymous_variant	140685	exon5			GTCTTCCTCATCC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1704G>A	20.37:g.62378349C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	22	16	0.727273	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.724;T|0.276	0.276	strong		0.726	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
OAF	220323	hgsc.bcm.edu	37	11	120099658	120099658	+	Missense_Mutation	SNP	A	A	G	rs2508489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:120099658A>G	ENST00000328965.4	+	4	1142	c.629A>G	c.(628-630)cAc>cGc	p.H210R	OAF_ENST00000531220.1_Missense_Mutation_p.H94R	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	210			H -> R (in dbSNP:rs2508489).			extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		GTGGGGGACCACGGGAAGCCC	0.667													a|||	2792	0.557508	0.5121	0.7622	5008	,	,		13808	0.1478		0.8907	False		,,,				2504	0.5532				p.H210R		Atlas-SNP	.											.	OAF	12	.	0			c.A629G						PASS	.	A	ARG/HIS	2518,1876		719,1080,398	33.0	30.0	31.0		629	0.7	0.0	11	dbSNP_100	31	7560,1020		3317,926,47	yes	missense	OAF	NM_178507.2	29	4036,2006,445	GG,GA,AA		11.8881,42.6946,22.3216	benign	210/274	120099658	10078,2896	2197	4290	6487	SO:0001583	missense	220323	exon4			GGGACCACGGGAA	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.629A>G	11.37:g.120099658A>G	ENSP00000332613:p.His210Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_178507		Missense_Mutation	SNP	ENST00000328965.4	37	CCDS8430.1	1294	0.5924908424908425	260	0.5284552845528455	280	0.7734806629834254	78	0.13636363636363635	676	0.8918205804749341	a	0.496	-0.873110	0.02570	0.573054	0.881119	ENSG00000184232	ENST00000328965;ENST00000531220	T;T	0.27557	1.66;1.66	4.72	0.675	0.17952	.	0.764860	0.12925	N	0.427865	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14062	-1.0486	9	0.22109	T	0.4	-0.3173	4.6872	0.12764	0.2474:0.0:0.6029:0.1497	rs2508489;rs3740737;rs57023106	210	Q86UD1	OAF_HUMAN	R	210;94	ENSP00000332613:H210R;ENSP00000431865:H94R	ENSP00000332613:H210R	H	+	2	0	OAF	119604868	0.019000	0.18553	0.000000	0.03702	0.000000	0.00434	1.205000	0.32308	-0.152000	0.11156	-0.147000	0.13772	CAC	A|0.283;G|0.717	0.717	strong		0.667	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507	
AKAP2	11217	hgsc.bcm.edu	37	9	112900466	112900466	+	Missense_Mutation	SNP	C	C	T	rs61735424	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:112900466C>T	ENST00000259318.7	+	2	2156	c.1949C>T	c.(1948-1950)gCg>gTg	p.A650V	AKAP2_ENST00000555236.1_Missense_Mutation_p.A881V|AKAP2_ENST00000510514.5_Missense_Mutation_p.A881V|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.A881V|AKAP2_ENST00000374525.1_Missense_Mutation_p.A739V|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.A881V|AKAP2_ENST00000482335.1_3'UTR|AKAP2_ENST00000434623.2_Missense_Mutation_p.A739V	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	650										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						GAAGACAGGGCGCTCAGGGAA	0.552													C|||	80	0.0159744	0.0023	0.0202	5008	,	,		16777	0.0		0.0358	False		,,,				2504	0.0276				p.A881V		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.C2642T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	46,4360	43.1+/-76.7	1,44,2158	24.0	29.0	27.0		2216,1949,2216,2642,2642	-4.0	0.0	9	dbSNP_129	27	412,8188	127.5+/-185.8	15,382,3903	yes	missense,missense,missense,missense,missense	AKAP2,PALM2-AKAP2	NM_001004065.4,NM_001136562.2,NM_001198656.1,NM_007203.4,NM_147150.2	64,64,64,64,64	16,426,6061	TT,TC,CC		4.7907,1.044,3.5215	benign,benign,benign,benign,benign	739/949,650/860,739/962,881/1104,881/1091	112900466	458,12548	2203	4300	6503	SO:0001583	missense	445815	exon8			ACAGGGCGCTCAG	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.1949C>T	9.37:g.112900466C>T	ENSP00000259318:p.Ala650Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	37	CCDS48003.1	46	0.021062271062271064	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	34	0.044854881266490766	C	7.473	0.647030	0.14516	0.01044	0.047907	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.46819	1.59;1.59;1.59;1.59;1.59;1.59;0.86;1.59	5.88	-3.95	0.04118	.	0.846275	0.10511	N	0.666141	T	0.03959	0.0111	N	0.20685	0.6	0.09310	N	0.999991	B;B;B;B;B;B;B;B	0.19583	0.002;0.002;0.017;0.037;0.022;0.007;0.007;0.004	B;B;B;B;B;B;B;B	0.11329	0.002;0.002;0.002;0.006;0.003;0.006;0.006;0.002	T	0.09037	-1.0693	10	0.39692	T	0.17	-2.4798	3.2787	0.06907	0.1348:0.2282:0.1082:0.5288	rs61735424	650;739;733;739;740;881;881;699	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	V	881;881;881;881;739;739;699;650	ENSP00000363654:A881V;ENSP00000305861:A881V;ENSP00000451476:A881V;ENSP00000421522:A881V;ENSP00000404782:A739V;ENSP00000363649:A739V;ENSP00000419268:A699V;ENSP00000259318:A650V	ENSP00000259318:A650V	A	+	2	0	PALM2-AKAP2;AKAP2	111940287	0.006000	0.16342	0.007000	0.13788	0.919000	0.55068	-0.009000	0.12765	-0.573000	0.05998	-0.880000	0.02959	GCG	C|0.969;T|0.031	0.031	strong		0.552	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
CCDC88B	283234	hgsc.bcm.edu	37	11	64124515	64124515	+	Silent	SNP	T	T	C	rs612448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64124515T>C	ENST00000356786.5	+	27	4424	c.4380T>C	c.(4378-4380)ccT>ccC	p.P1460P	CCDC88B_ENST00000301897.4_Silent_p.P123P|RPS6KA4_ENST00000334205.4_5'Flank|CCDC88B_ENST00000359902.2_Missense_Mutation_p.L565P|RPS6KA4_ENST00000294261.4_5'Flank|CCDC88B_ENST00000463837.1_3'UTR|RPS6KA4_ENST00000528057.1_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1460						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTCTAGGCCCTGAGGTACAGG	0.632													C|||	1303	0.260184	0.0303	0.4107	5008	,	,		17803	0.1845		0.4334	False		,,,				2504	0.364				p.P1460P		Atlas-SNP	.											CCDC88B_ENST00000359902,NS,carcinoma,-1,1	CCDC88B	89	1	0			c.T4380C						PASS	.	C		426,3976		23,380,1798	133.0	102.0	112.0		4380	0.6	0.0	11	dbSNP_83	112	3738,4856		794,2150,1353	no	coding-synonymous	CCDC88B	NM_032251.5		817,2530,3151	CC,CT,TT		43.4955,9.6774,32.0406		1460/1477	64124515	4164,8832	2201	4297	6498	SO:0001819	synonymous_variant	283234	exon27			AGGCCCTGAGGTA	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.4380T>C	11.37:g.64124515T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	179	96	0.536313	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2	605	0.27701465201465203	21	0.042682926829268296	141	0.38950276243093923	104	0.18181818181818182	339	0.4472295514511873	N	11.12	1.545644	0.27652	0.096774	0.434955	ENSG00000168071	ENST00000359902	T	0.57907	0.37	3.89	0.573	0.17363	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46652	-0.9176	6	.	.	.	.	3.3622	0.07190	0.0:0.4118:0.2053:0.3829	rs612448;rs58613170;rs612448	549	A6NC98-5	.	P	565	ENSP00000352974:L565P	.	L	+	2	0	CCDC88B	63881091	0.000000	0.05858	0.010000	0.14722	0.161000	0.22273	-0.393000	0.07305	0.007000	0.14760	-0.511000	0.04467	CTG	T|0.706;C|0.294	0.294	strong		0.632	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
SNAP29	9342	hgsc.bcm.edu	37	22	21213416	21213416	+	Silent	SNP	A	A	G	rs1061064	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21213416A>G	ENST00000215730.7	+	1	146	c.18A>G	c.(16-18)aaA>aaG	p.K6K	PI4KA_ENST00000255882.6_5'Flank|PI4KA_ENST00000572273.1_5'Flank	NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	6					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			CTTACCCTAAAAGCTACAATC	0.731													A|||	2021	0.403554	0.1604	0.4323	5008	,	,		12279	0.372		0.5249	False		,,,				2504	0.6196				p.K6K		Atlas-SNP	.											SNAP29,NS,carcinoma,0,1	SNAP29	22	1	0			c.A18G						PASS	.	A		909,3459		120,669,1395	10.0	12.0	12.0		18	-2.2	0.2	22	dbSNP_86	12	4457,4057		1243,1971,1043	no	coding-synonymous	SNAP29	NM_004782.3		1363,2640,2438	GG,GA,AA		47.6509,20.8104,41.655		6/259	21213416	5366,7516	2184	4257	6441	SO:0001819	synonymous_variant	9342	exon1			CCCTAAAAGCTAC	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"""soluble 29 kDa NSF attachment protein"""	604202	"""synaptosomal-associated protein, 29kD"""			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.18A>G	22.37:g.21213416A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	32	0.372093	NM_004782		Silent	SNP	ENST00000215730.7	37	CCDS13784.1																																																																																			A|0.600;G|0.400	0.400	strong		0.731	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782	
MYO1G	64005	hgsc.bcm.edu	37	7	45016621	45016621	+	Missense_Mutation	SNP	C	C	T	rs61739531	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45016621C>T	ENST00000258787.7	-	2	281	c.145G>A	c.(145-147)Gtg>Atg	p.V49M		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	49	Myosin motor.		V -> M (in allele HA-2M; the HA-2V allele constitute the HA-2 epitope while HA-2M is not recognized by HA-2 cytotoxic T lymphocytes; dbSNP:rs61739531). {ECO:0000269|PubMed:11544309}.			extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						TAGGGGTTCACGGACACCAGC	0.627													C|||	686	0.136981	0.1293	0.1859	5008	,	,		19617	0.0952		0.2296	False		,,,				2504	0.0603				p.V49M		Atlas-SNP	.											MYO1G,bladder,carcinoma,+2,1	MYO1G	86	1	0			c.G145A						PASS	.	C	MET/VAL	652,3754	276.9+/-273.4	50,552,1601	76.0	71.0	72.0		145	3.9	1.0	7	dbSNP_129	72	1829,6771	329.2+/-318.6	194,1441,2665	yes	missense	MYO1G	NM_033054.2	21	244,1993,4266	TT,TC,CC		21.2674,14.798,19.0758	benign	49/1019	45016621	2481,10525	2203	4300	6503	SO:0001583	missense	64005	exon2			GGTTCACGGACAC	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.145G>A	7.37:g.45016621C>T	ENSP00000258787:p.Val49Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	37	CCDS34629.1	359	0.16437728937728938	59	0.11991869918699187	70	0.19337016574585636	51	0.08916083916083917	179	0.23614775725593667	C	15.91	2.971733	0.53614	0.14798	0.212674	ENSG00000136286	ENST00000258787	D	0.90955	-2.76	3.93	3.93	0.45458	Myosin head, motor domain (3);	0.000000	0.33834	N	0.004504	T	0.00210	0.0006	L	0.51853	1.615	0.19775	P	0.9999526654	D	0.60160	0.987	P	0.53593	0.73	T	0.00359	-1.1791	9	0.37606	T	0.19	.	9.7576	0.40513	0.0:0.8973:0.0:0.1027	rs61739531	49	B0I1T2	MYO1G_HUMAN	M	49	ENSP00000258787:V49M	ENSP00000258787:V49M	V	-	1	0	MYO1G	44983146	0.998000	0.40836	0.988000	0.46212	0.863000	0.49368	3.760000	0.55235	2.199000	0.70637	0.655000	0.94253	GTG	C|0.817;T|0.183	0.183	strong		0.627	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
ANKRD53	79998	hgsc.bcm.edu	37	2	71211815	71211815	+	Silent	SNP	G	G	A	rs3796098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71211815G>A	ENST00000360589.3	+	6	1012	c.978G>A	c.(976-978)ctG>ctA	p.L326L	AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000457410.1_Silent_p.L292L|ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000272421.6_3'UTR	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	326										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						GCCACTCTCTGGTCTCCAATA	0.577											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	675	0.134784	0.0825	0.1254	5008	,	,		18367	0.1617		0.2276	False		,,,				2504	0.089				p.L326L		Atlas-SNP	.											ANKRD53_ENST00000360589,NS,carcinoma,0,1	ANKRD53	55	1	0			c.G978A						PASS	.	G	,	146,1238		7,132,553	53.0	59.0	58.0		978,	0.8	0.0	2	dbSNP_107	58	690,2492		78,534,979	yes	coding-synonymous,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	,	85,666,1532	AA,AG,GG		21.6845,10.5491,18.3092	,	326/531,	71211815	836,3730	692	1591	2283	SO:0001819	synonymous_variant	79998	exon6			CTCTCTGGTCTCC	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.978G>A	2.37:g.71211815G>A		Somatic	138	0	0	1128	WXS	Illumina HiSeq	Phase_I	154	76	0.493506	NM_001115116	Q8IYP8	Silent	SNP	ENST00000360589.3	37	CCDS46321.1																																																																																			G|0.837;A|0.163	0.163	strong		0.577	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
UBE3B	89910	hgsc.bcm.edu	37	12	109972462	109972462	+	Missense_Mutation	SNP	G	G	A	rs374046452		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109972462G>A	ENST00000342494.3	+	28	3677	c.3082G>A	c.(3082-3084)Ggc>Agc	p.G1028S	UBE3B_ENST00000434735.2_Missense_Mutation_p.G1028S	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	1028	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						GGAGCCAGGCGGCCGCCTGCC	0.632																																					p.G1028S		Atlas-SNP	.											.	UBE3B	116	.	0			c.G3082A						PASS	.	G	SER/GLY,SER/GLY	1,4405	2.1+/-5.4	0,1,2202	64.0	59.0	60.0		3082,3082	5.3	1.0	12		60	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	UBE3B	NM_130466.2,NM_183415.1	56,56	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,benign	1028/1069,1028/1069	109972462	2,13004	2203	4300	6503	SO:0001583	missense	89910	exon28			CCAGGCGGCCGCC	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.3082G>A	12.37:g.109972462G>A	ENSP00000340596:p.Gly1028Ser	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	174	37	0.212644	NM_130466	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.924638	0.52653	2.27E-4	1.16E-4	ENSG00000151148	ENST00000434735;ENST00000342494	T;T	0.41065	1.01;1.01	5.3	5.3	0.74995	HECT (4);	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	N	0.02539	-0.55	0.80722	D	1	B	0.25105	0.118	B	0.22386	0.039	T	0.10086	-1.0645	10	0.25106	T	0.35	-23.3915	17.9631	0.89092	0.0:0.0:1.0:0.0	.	1028	Q7Z3V4	UBE3B_HUMAN	S	1028	ENSP00000391529:G1028S;ENSP00000340596:G1028S	ENSP00000340596:G1028S	G	+	1	0	UBE3B	108456845	1.000000	0.71417	0.956000	0.39512	0.961000	0.63080	9.385000	0.97223	2.474000	0.83562	0.563000	0.77884	GGC	.	.	weak		0.632	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047710	46047710	+	Silent	SNP	T	T	C	rs8131142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46047710T>C	ENST00000397911.3	+	1	671	c.622T>C	c.(622-624)Ttg>Ctg	p.L208L	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	208	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GGCTTCCTCTTTGTGCTGCCA	0.632													C|||	3246	0.648163	0.5711	0.6787	5008	,	,		20040	0.6637		0.7107	False		,,,				2504	0.6503				p.L208L		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.T622C						PASS	.	C	,	2517,1889	542.5+/-376.0	725,1067,411	192.0	214.0	206.0		,622	-1.4	0.0	21	dbSNP_116	206	5789,2811	442.8+/-360.2	1943,1903,454	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	2668,2970,865	CC,CT,TT		32.686,42.8734,36.1372	,	,208/293	46047710	8306,4700	2203	4300	6503	SO:0001819	synonymous_variant	386676	exon1			TCCTCTTTGTGCT	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.622T>C	21.37:g.46047710T>C		Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	218	101	0.463303	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			T|0.339;C|0.661	0.661	strong		0.632	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
CDH8	1006	hgsc.bcm.edu	37	16	61687701	61687701	+	Silent	SNP	C	C	T	rs16963768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:61687701C>T	ENST00000577390.1	-	12	3165	c.2211G>A	c.(2209-2211)acG>acA	p.T737T	CDH8_ENST00000577730.1_Intron|CDH8_ENST00000299345.6_Intron	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	737					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATGGCGGGGCCGTGGGATCAT	0.507													T|||	537	0.107228	0.2095	0.1009	5008	,	,		14956	0.0198		0.1262	False		,,,				2504	0.044				p.T737T		Atlas-SNP	.											CDH8,rectum,carcinoma,-1,1	CDH8	273	1	0			c.G2211A						scavenged	.	T		882,3524	742.8+/-411.4	89,704,1410	64.0	70.0	68.0		2211	-5.6	0.7	16	dbSNP_123	68	1081,7519	769.3+/-407.6	71,939,3290	no	coding-synonymous	CDH8	NM_001796.4		160,1643,4700	TT,TC,CC		12.5698,20.0182,15.093		737/800	61687701	1963,11043	2203	4300	6503	SO:0001819	synonymous_variant	1006	exon12			CGGGGCCGTGGGA	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.2211G>A	16.37:g.61687701C>T		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																			C|0.868;N|0.000	.	strong		0.507	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
PCLO	27445	hgsc.bcm.edu	37	7	82581859	82581859	+	Missense_Mutation	SNP	C	C	T	rs976714	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82581859C>T	ENST00000333891.9	-	5	8747	c.8410G>A	c.(8410-8412)Gca>Aca	p.A2804T	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.A2804T	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTGTAACTTGCACTAGCTGTG	0.458													C|||	1603	0.320088	0.1029	0.389	5008	,	,		21680	0.4405		0.3608	False		,,,				2504	0.3988				p.A2804T		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,+1,2	PCLO	1506	2	0			c.G8410A						PASS	.	C	THR/ALA,THR/ALA	565,3531		41,483,1524	200.0	176.0	184.0		8410,8410	-5.0	0.1	7	dbSNP_86	184	3018,5356		549,1920,1718	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	58,58	590,2403,3242	TT,TC,CC		36.0401,13.7939,28.733	benign,benign	2804/5143,2804/4936	82581859	3583,8887	2048	4187	6235	SO:0001583	missense	27445	exon5			AACTTGCACTAGC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8410G>A	7.37:g.82581859C>T	ENSP00000334319:p.Ala2804Thr	Somatic	471	0	0		WXS	Illumina HiSeq	Phase_I	463	221	0.477322	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	711	0.32554945054945056	46	0.09349593495934959	135	0.3729281767955801	253	0.4423076923076923	277	0.3654353562005277	C	6.515	0.463151	0.12402	0.137939	0.360401	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16743	2.32;2.32	5.69	-5.02	0.02982	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48293	-0.9048	8	0.87932	D	0	.	1.6918	0.02853	0.2103:0.2657:0.0973:0.4267	rs976714;rs10350430;rs61026231;rs976714	2804;2804	Q9Y6V0-5;Q9Y6V0-6	.;.	T	2735;2804;2804	ENSP00000334319:A2804T;ENSP00000388393:A2804T	ENSP00000334319:A2804T	A	-	1	0	PCLO	82419795	0.000000	0.05858	0.067000	0.19924	0.627000	0.37826	-1.275000	0.02817	-0.998000	0.03446	-0.793000	0.03317	GCA	C|0.673;T|0.327	0.327	strong		0.458	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
RALGAPB	57148	hgsc.bcm.edu	37	20	37199443	37199443	+	Silent	SNP	G	G	A	rs139543103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:37199443G>A	ENST00000262879.6	+	28	4379	c.4095G>A	c.(4093-4095)gaG>gaA	p.E1365E	RALGAPB_ENST00000397040.1_Silent_p.E1365E|RALGAPB_ENST00000397038.1_Silent_p.E1144E|RALGAPB_ENST00000397042.3_Silent_p.E1362E			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1365	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TGATGACAGAGATCAGTACTG	0.358													G|||	14	0.00279553	0.0	0.0043	5008	,	,		17277	0.0		0.0109	False		,,,				2504	0.0				p.E1365E		Atlas-SNP	.											.	RALGAPB	134	.	0			c.G4095A						PASS	.	G		18,4388	24.3+/-50.5	0,18,2185	82.0	83.0	83.0		4095	1.1	1.0	20	dbSNP_134	83	118,8482	62.4+/-124.4	1,116,4183	no	coding-synonymous	RALGAPB	NM_020336.2		1,134,6368	AA,AG,GG		1.3721,0.4085,1.0457		1365/1495	37199443	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	57148	exon28			GACAGAGATCAGT	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.4095G>A	20.37:g.37199443G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	37	CCDS13305.1																																																																																			G|0.991;A|0.009	0.009	strong		0.358	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
SMG1	23049	hgsc.bcm.edu	37	16	18853744	18853744	+	Silent	SNP	T	T	C	rs12926959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:18853744T>C	ENST00000446231.2	-	40	6664	c.6252A>G	c.(6250-6252)aaA>aaG	p.K2084K	SMG1_ENST00000389467.3_Silent_p.K2084K			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2084					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						AACTTGCACGTTTCTGTGCTC	0.388													T|||	253	0.0505192	0.0507	0.0692	5008	,	,		22357	0.001		0.0686	False		,,,				2504	0.0695				p.K2084K		Atlas-SNP	.											.	SMG1	401	.	0			c.A6252G						PASS	.	T		198,3630		8,182,1724	88.0	78.0	81.0		6252	3.3	1.0	16	dbSNP_121	81	723,7561		32,659,3451	no	coding-synonymous	SMG1	NM_015092.4		40,841,5175	CC,CT,TT		8.7277,5.1724,7.604		2084/3662	18853744	921,11191	1914	4142	6056	SO:0001819	synonymous_variant	23049	exon40			TGCACGTTTCTGT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.6252A>G	16.37:g.18853744T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	36	0.36	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			T|0.942;C|0.058	0.058	strong		0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
UGT1A6	54578	hgsc.bcm.edu	37	2	234601669	234601669	+	Missense_Mutation	SNP	T	T	G	rs6759892	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234601669T>G	ENST00000305139.6	+	1	158	c.19T>G	c.(19-21)Tca>Gca	p.S7A	UGT1A6_ENST00000406651.1_5'Flank|UGT1A6_ENST00000480628.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|AC114812.8_ENST00000439336.1_RNA|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	7			S -> A (in allele UGT1A6*2, allele UGT1A6*3 and allele UGT1A6*4; dbSNP:rs6759892). {ECO:0000269|PubMed:15284531}.		cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	CCTCCTTCGCTCATTTCAGAG	0.478													G|||	1814	0.36222	0.3767	0.3444	5008	,	,		17751	0.2242		0.3827	False		,,,				2504	0.4765				p.S7A		Atlas-SNP	.											.	UGT1A6	63	.	0			c.T19G	GRCh37	CM057769	UGT1A6	M	rs6759892	PASS	.	G	ALA/SER,,,,,	1700,2706		341,1018,844	45.0	49.0	48.0		19,,,,,	-0.7	0.0	2	dbSNP_116	48	3557,5043		749,2059,1492	yes	missense,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2,NM_205862.1	99,,,,,	1090,3077,2336	GG,GT,TT		41.3605,38.5837,40.4198	,,,,,	7/533,,,,,	234601669	5257,7749	2203	4300	6503	SO:0001583	missense	54578	exon1			CTTCGCTCATTTC	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.19T>G	2.37:g.234601669T>G	ENSP00000303174:p.Ser7Ala	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	253	134	0.529644	NM_001072	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1	751	0.34386446886446886	189	0.38414634146341464	135	0.3729281767955801	136	0.23776223776223776	291	0.3839050131926121	G	0.023	-1.395150	0.01175	0.385837	0.413605	ENSG00000167165	ENST00000441351;ENST00000305139	T;T	0.58506	1.61;0.33	4.58	-0.718	0.11205	.	.	.	.	.	T	0.00012	0.0000	N	0.01473	-0.845	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32903	-0.9889	8	0.02654	T	1	.	0.7682	0.01019	0.2218:0.1509:0.3261:0.3012	rs6759892;rs17670302;rs60624335;rs6759892	7;7	B8K289;P19224	.;UD16_HUMAN	A	7	ENSP00000389637:S7A;ENSP00000303174:S7A	ENSP00000303174:S7A	S	+	1	0	UGT1A6	234266408	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.178000	0.09782	-0.187000	0.10516	-0.729000	0.03580	TCA	G|0.364;N|0.000	0.364	strong		0.478	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
GBP3	2635	hgsc.bcm.edu	37	1	89479063	89479063	+	Missense_Mutation	SNP	G	G	A	rs4656077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89479063G>A	ENST00000370481.4	-	6	893	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	GBP3_ENST00000475853.2_5'Flank	NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	258	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		AAGAACTTCCGGATACAGAGT	0.403													.|||	1671	0.333666	0.1793	0.2925	5008	,	,		18338	0.3075		0.4404	False		,,,				2504	0.4888				p.R225W		Atlas-SNP	.											.	GBP3	53	.	0			c.C673T						PASS	.	G	TRP/ARG	1150,3256	388.4+/-326.9	142,866,1195	100.0	107.0	104.0		673	2.9	0.9	1	dbSNP_111	104	3902,4698	534.8+/-382.7	871,2160,1269	yes	missense	GBP3	NM_018284.2	101	1013,3026,2464	AA,AG,GG		45.3721,26.1008,38.8436	probably-damaging	225/596	89479063	5052,7954	2203	4300	6503	SO:0001583	missense	2635	exon6			ACTTCCGGATACA	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.673C>T	1.37:g.89479063G>A	ENSP00000359512:p.Arg225Trp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	705	0.3228021978021978	81	0.16463414634146342	124	0.3425414364640884	161	0.28146853146853146	339	0.4472295514511873	G	17.09	3.299634	0.60195	0.261008	0.453721	ENSG00000117226	ENST00000370481;ENST00000235878	T	0.77877	-1.13	3.85	2.92	0.33932	Guanylate-binding protein, N-terminal (1);	0.250311	0.32503	N	0.006009	D	0.87954	0.6308	H	0.95151	3.63	0.53005	P	3.100000000000325E-5	P;D	0.89917	0.928;1.0	B;D	0.77557	0.288;0.99	D	0.90092	0.4178	8	.	.	.	.	10.8342	0.46677	0.0:0.0:0.8105:0.1895	rs4656077;rs4656077	91;225	F6X827;Q9H0R5	.;GBP3_HUMAN	W	225	ENSP00000359512:R225W	.	R	-	1	2	GBP3	89251651	0.989000	0.36119	0.878000	0.34440	0.753000	0.42808	2.438000	0.44837	0.940000	0.37473	0.514000	0.50259	CGG	G|0.661;A|0.339	0.339	strong		0.403	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
NPC1	4864	hgsc.bcm.edu	37	18	21140432	21140432	+	Missense_Mutation	SNP	T	T	C	rs1805081	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21140432T>C	ENST00000269228.5	-	6	1198	c.644A>G	c.(643-645)cAt>cGt	p.H215R	NPC1_ENST00000412552.2_5'Flank|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	215			H -> R (common polymorphism in Japanese; dbSNP:rs1805081). {ECO:0000269|PubMed:10480349, ECO:0000269|PubMed:11479732, ECO:0000269|PubMed:11754101, ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:12955717, ECO:0000269|PubMed:15774455, ECO:0000269|PubMed:16098014}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CTCCATCCCATGGACTGGAAA	0.423													T|||	1095	0.21865	0.0197	0.2637	5008	,	,		18777	0.256		0.3837	False		,,,				2504	0.2474				p.H215R		Atlas-SNP	.											.	NPC1	114	.	0			c.A644G						PASS	.	T	ARG/HIS	387,4019	193.3+/-218.5	18,351,1834	59.0	54.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	644	-1.1	0.0	18	dbSNP_89	55	3462,5138	507.9+/-376.9	694,2074,1532	yes	missense	NPC1	NM_000271.4	29	712,2425,3366	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	40.2558,8.7835,29.594	benign	215/1279	21140432	3849,9157	2203	4300	6503	SO:0001583	missense	4864	exon6			ATCCCATGGACTG	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.644A>G	18.37:g.21140432T>C	ENSP00000269228:p.His215Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	535	0.24496336996336995	16	0.032520325203252036	89	0.24585635359116023	130	0.22727272727272727	300	0.39577836411609496	T	9.736	1.163509	0.21538	0.087835	0.402558	ENSG00000141458	ENST00000269228;ENST00000540608	D	0.90069	-2.61	5.73	-1.13	0.09775	.	0.802760	0.12270	N	0.483913	T	0.00012	0.0000	N	0.21448	0.665	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16928	-1.0386	9	0.18276	T	0.48	-0.456	0.3945	0.00416	0.2773:0.1416:0.2309:0.3501	rs1805081;rs3745025;rs17878967;rs57242554;rs1805081	215	O15118	NPC1_HUMAN	R	215;60	ENSP00000269228:H215R	ENSP00000269228:H215R	H	-	2	0	NPC1	19394430	0.005000	0.15991	0.000000	0.03702	0.858000	0.48976	0.589000	0.23939	-0.172000	0.10779	0.533000	0.62120	CAT	T|0.733;C|0.267	0.267	strong		0.423	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
TIRAP	114609	hgsc.bcm.edu	37	11	126162607	126162607	+	Silent	SNP	G	G	A	rs3802814	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:126162607G>A	ENST00000392680.2	+	5	708	c.303G>A	c.(301-303)caG>caA	p.Q101Q	RP11-712L6.5_ENST00000528876.1_5'Flank|RP11-712L6.7_ENST00000533378.1_RNA|TIRAP_ENST00000392679.1_Silent_p.Q101Q|TIRAP_ENST00000392678.3_Silent_p.Q101Q	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	101	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)			breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		TGGCCGCCCAGGACCTGGTCT	0.627													G|||	411	0.0820687	0.0091	0.0793	5008	,	,		18710	0.0139		0.172	False		,,,				2504	0.1605				p.Q101Q		Atlas-SNP	.											.	TIRAP	37	.	0			c.G303A						PASS	.	G	,	125,4277	91.1+/-129.8	1,123,2077	43.0	38.0	40.0		303,303	4.4	1.0	11	dbSNP_107	40	1282,7314	246.0+/-274.6	110,1062,3126	no	coding-synonymous,coding-synonymous	TIRAP	NM_001039661.1,NM_148910.2	,	111,1185,5203	AA,AG,GG		14.9139,2.8396,10.8247	,	101/222,101/236	126162607	1407,11591	2201	4298	6499	SO:0001819	synonymous_variant	114609	exon5			CGCCCAGGACCTG	AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.303G>A	11.37:g.126162607G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Silent	SNP	ENST00000392680.2	37	CCDS8472.1																																																																																			G|0.907;A|0.093	0.093	strong		0.627	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910	
FAM209A	200232	hgsc.bcm.edu	37	20	55100005	55100005	+	Silent	SNP	T	T	C	rs2426632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55100005T>C	ENST00000371328.3	+	1	464	c.141T>C	c.(139-141)aaT>aaC	p.N47N	FAM209A_ENST00000481560.1_3'UTR|GCNT7_ENST00000243913.4_Intron	NM_001012971.3	NP_001012989.2	Q5JX71	F209A_HUMAN	family with sequence similarity 209, member A	47						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TTCGGCAGAATCTACCAGAGC	0.498																																					p.N47N		Atlas-SNP	.											.	.	.	.	0			c.T141C						PASS	.						154.0	139.0	144.0					20																	55100005		2203	4300	6503	SO:0001819	synonymous_variant	200232	exon1			GCAGAATCTACCA	AL109806	CCDS33493.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000124103	ENSG00000124103			16100	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 106"""	C20orf106			Standard	NM_001012971		Approved	dJ1153D9.3		Q5JX71	OTTHUMG00000032799	ENST00000371328.3:c.141T>C	20.37:g.55100005T>C		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	393	89	0.226463	NM_001012971	Q05C43	Silent	SNP	ENST00000371328.3	37	CCDS33493.1																																																																																			T|0.974;C|0.026	0.026	strong		0.498	FAM209A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079815.2		
MYH15	22989	hgsc.bcm.edu	37	3	108147728	108147728	+	Splice_Site	SNP	T	T	C	rs3900940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108147728T>C	ENST00000273353.3	-	28	3429	c.3373A>G	c.(3373-3375)Act>Gct	p.T1125A		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1125			T -> A (in dbSNP:rs3900940).			cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTTATTTGAGTCTGTAGCAAG	0.388													T|||	846	0.16893	0.1241	0.2032	5008	,	,		18526	0.0119		0.3131	False		,,,				2504	0.2188				p.T1125A		Atlas-SNP	.											.	MYH15	223	.	0			c.A3373G	GRCh37	CM074941	MYH15	M	rs3900940	PASS	.	T	ALA/THR	524,3160		31,462,1349	76.0	71.0	73.0		3373	-1.7	0.0	3	dbSNP_108	73	2352,5806		337,1678,2064	yes	missense-near-splice	MYH15	NM_014981.1	58	368,2140,3413	CC,CT,TT		28.8306,14.2237,24.2864	benign	1125/1947	108147728	2876,8966	1842	4079	5921	SO:0001630	splice_region_variant	22989	exon28			TTTGAGTCTGTAG	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3373-1A>G	3.37:g.108147728T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	402	0.18406593406593408	62	0.12601626016260162	93	0.2569060773480663	0	0.0	247	0.3258575197889182	T	0.022	-1.409432	0.01155	0.142237	0.288306	ENSG00000144821	ENST00000273353	T	0.74947	-0.89	5.63	-1.67	0.08238	Myosin tail (1);	.	.	.	.	T	0.00012	0.0000	N	0.00890	-1.11	0.31558	P	0.657914	B	0.06786	0.001	B	0.13407	0.009	T	0.12319	-1.0552	8	0.02654	T	1	.	5.5574	0.17123	0.1708:0.5263:0.0:0.3029	rs3900940;rs17610187;rs52830059;rs57572156;rs3900940	1125	Q9Y2K3	MYH15_HUMAN	A	1125	ENSP00000273353:T1125A	ENSP00000273353:T1125A	T	-	1	0	MYH15	109630418	1.000000	0.71417	0.010000	0.14722	0.083000	0.17756	1.227000	0.32576	-0.097000	0.12307	0.528000	0.53228	ACT	T|0.802;C|0.198	0.198	strong		0.388	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	Missense_Mutation
CLDN5	7122	hgsc.bcm.edu	37	22	19511925	19511925	+	Nonsense_Mutation	SNP	G	G	A	rs885985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:19511925G>A	ENST00000406028.1	-	2	1169	c.109C>T	c.(109-111)Cag>Tag	p.Q37*	CLDN5_ENST00000403084.1_Nonsense_Mutation_p.Q37*|CLDN5_ENST00000413119.2_Nonsense_Mutation_p.Q37*			O00501	CLD5_HUMAN	claudin 5	0					calcium-independent cell-cell adhesion (GO:0016338)|myelination (GO:0042552)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			liver(1)|lung(2)|prostate(1)	4	Colorectal(54;0.0993)					CGCACCTCCTGGGTCTGCCAG	0.751													A|||	2488	0.496805	0.2073	0.5879	5008	,	,		11791	0.5298		0.5567	False		,,,				2504	0.728				p.Q37X		Atlas-SNP	.											.	CLDN5	22	.	0			c.C109T						PASS	.						3.0	4.0	4.0					22																	19511925		571	1393	1964	SO:0001587	stop_gained	7122	exon1			CCTCCTGGGTCTG	AF000959	CCDS13763.2	22q11.21	2008-08-01	2008-08-01		ENSG00000184113	ENSG00000184113		"""Claudins"""	2047	protein-coding gene	gene with protein product		602101	"""transmembrane protein deleted in velocardiofacial syndrome"""	AWAL, TMVCF		9441748, 9192844	Standard	NM_003277		Approved	CPETRL1, BEC1	uc002zpu.2	O00501	OTTHUMG00000150441	ENST00000406028.1:c.109C>T	22.37:g.19511925G>A	ENSP00000385477:p.Gln37*	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_001130861	B3KS11|Q53XW2|Q8WUW3	Nonsense_Mutation	SNP	ENST00000406028.1	37	CCDS13763.2	1017	0.46565934065934067	109	0.22154471544715448	199	0.5497237569060773	287	0.5017482517482518	422	0.5567282321899736	A	23.9	4.466684	0.84425	.	.	ENSG00000184113	ENST00000406028;ENST00000403084;ENST00000413119	.	.	.	5.24	-6.49	0.01890	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	3.0235	0.06083	0.3175:0.1814:0.409:0.0921	rs885985;rs17209295;rs885985	.	.	.	X	37	.	ENSP00000384554:Q37X	Q	-	1	0	CLDN5	17891925	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.689000	0.05144	-1.461000	0.01909	-2.530000	0.00182	CAG	G|0.554;A|0.446	0.446	strong		0.751	CLDN5-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318122.3	NM_003277	
ARHGEF37	389337	hgsc.bcm.edu	37	5	148989122	148989122	+	Silent	SNP	C	C	T	rs2400891	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:148989122C>T	ENST00000333677.6	+	4	485	c.322C>T	c.(322-324)Ctg>Ttg	p.L108L	RNU6-588P_ENST00000410281.1_RNA	NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	108	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L108L(1)		large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						TAACATATTTCTGGAATTCCA	0.532													C|||	1889	0.377196	0.2799	0.3343	5008	,	,		21872	0.3641		0.5507	False		,,,				2504	0.3742				p.L108L		Atlas-SNP	.											ARHGEF37,NS,carcinoma,0,1	ARHGEF37	45	1	1	Substitution - coding silent(1)	stomach(1)	c.C322T						PASS	.	C		1255,2861		217,821,1020	105.0	106.0	106.0		322	2.9	1.0	5	dbSNP_100	106	4547,3855		1223,2101,877	no	coding-synonymous	ARHGEF37	NM_001001669.2		1440,2922,1897	TT,TC,CC		45.8819,30.4908,46.3493		108/676	148989122	5802,6716	2058	4201	6259	SO:0001819	synonymous_variant	389337	exon4			ATATTTCTGGAAT	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.322C>T	5.37:g.148989122C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	125	43	0.344	NM_001001669	Q6ZW51	Silent	SNP	ENST00000333677.6	37	CCDS43385.1																																																																																			C|0.573;N|0.000	.	strong		0.532	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
TRAPPC11	60684	hgsc.bcm.edu	37	4	184614874	184614874	+	Silent	SNP	C	C	T	rs4862234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:184614874C>T	ENST00000334690.6	+	21	2572	c.2370C>T	c.(2368-2370)acC>acT	p.T790T	TRAPPC11_ENST00000512476.1_Silent_p.T396T|TRAPPC11_ENST00000357207.4_Silent_p.T790T	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	790					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											TGAAGCTCACCGCTGGCTTAA	0.388													C|||	1117	0.223043	0.3268	0.1974	5008	,	,		17881	0.1776		0.2177	False		,,,				2504	0.1534				p.T790T		Atlas-SNP	.											.	.	.	.	0			c.C2370T						PASS	.	C	,	1417,2989	462.3+/-353.2	223,971,1009	112.0	112.0	112.0		2370,2370	-0.9	1.0	4	dbSNP_111	112	1932,6668	341.4+/-324.0	221,1490,2589	no	coding-synonymous,coding-synonymous	C4orf41	NM_021942.4,NM_199053.1	,	444,2461,3598	TT,TC,CC		22.4651,32.1607,25.7497	,	790/1134,790/1087	184614874	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	60684	exon21			GCTCACCGCTGGC		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"""Trafficking protein particle complex"""	25751	protein-coding gene	gene with protein product	"""gryzun homolog (Drosophila)"", ""foie gras homolog (zebrafish)"""	614138	"""chromosome 4 open reading frame 41"""	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.2370C>T	4.37:g.184614874C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	83	50	0.60241	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Silent	SNP	ENST00000334690.6	37	CCDS34112.1																																																																																			C|0.756;T|0.244	0.244	strong		0.388	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
MATN2	4147	hgsc.bcm.edu	37	8	98991221	98991221	+	Missense_Mutation	SNP	A	A	G	rs1869609	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:98991221A>G	ENST00000520016.1	+	5	1190	c.1066A>G	c.(1066-1068)Aaa>Gaa	p.K356E	MATN2_ENST00000254898.5_Missense_Mutation_p.K356E|MATN2_ENST00000522025.2_Missense_Mutation_p.K72E|MATN2_ENST00000524308.1_Missense_Mutation_p.K356E|MATN2_ENST00000521689.1_Missense_Mutation_p.K356E			O00339	MATN2_HUMAN	matrilin 2	356	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.		K -> E (in dbSNP:rs1869609). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TAACCCAGATAAAAAAACGTG	0.438													A|||	2072	0.413738	0.3729	0.4409	5008	,	,		20803	0.2937		0.662	False		,,,				2504	0.318				p.K356E		Atlas-SNP	.											.	MATN2	165	.	0			c.A1066G						PASS	.	A	GLU/LYS,GLU/LYS	1851,2263		439,973,645	110.0	105.0	106.0		1066,1066	-2.3	0.1	8	dbSNP_92	106	5546,2880		1808,1930,475	yes	missense,missense	MATN2	NM_002380.3,NM_030583.2	56,56	2247,2903,1120	GG,GA,AA		34.1799,44.9927,41.0128	benign,benign	356/957,356/938	98991221	7397,5143	2057	4213	6270	SO:0001583	missense	4147	exon6			CCAGATAAAAAAA	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1066A>G	8.37:g.98991221A>G	ENSP00000430487:p.Lys356Glu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	1009	0.461996336996337	189	0.38414634146341464	170	0.4696132596685083	150	0.26223776223776224	500	0.6596306068601583	A	11.06	1.528751	0.27387	0.449927	0.658201	ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016;ENST00000519585;ENST00000522270	D;D;D;D;D;D;D	0.96491	-4.03;-4.03;-4.03;-4.03;-4.03;-4.03;-4.03	5.49	-2.27	0.06846	Epidermal growth factor-like (1);EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.398494	0.23838	N	0.044079	T	0.00012	0.0000	L	0.43598	1.365	0.34608	P	0.28268899999999997	B;B;B;B	0.12013	0.002;0.002;0.005;0.002	B;B;B;B	0.20384	0.019;0.007;0.029;0.007	T	0.41215	-0.9521	9	0.42905	T	0.14	-2.6418	5.1626	0.15070	0.4673:0.2627:0.2701:0.0	rs1869609;rs17840656;rs17850658;rs59922734;rs1869609	356;356;356;356	E9PF03;O00339-2;O00339;Q8N2G3	.;.;MATN2_HUMAN;.	E	356;356;356;356;72;356;72;53	ENSP00000429977:K356E;ENSP00000254898:K356E;ENSP00000430221:K356E;ENSP00000429010:K72E;ENSP00000430487:K356E;ENSP00000429042:K72E;ENSP00000429825:K53E	ENSP00000254898:K356E	K	+	1	0	MATN2	99060397	0.015000	0.18098	0.113000	0.21522	0.563000	0.35712	0.083000	0.14871	-0.258000	0.09446	-0.408000	0.06270	AAA	T|0.009;G|0.459	0.459	strong		0.438	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
MKI67	4288	hgsc.bcm.edu	37	10	129906427	129906427	+	Missense_Mutation	SNP	C	C	A	rs41306015	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:129906427C>A	ENST00000368654.3	-	13	4052	c.3677G>T	c.(3676-3678)gGc>gTc	p.G1226V	MKI67_ENST00000368653.3_Missense_Mutation_p.G866V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1226	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTCTTTAAAGCCAGCCAGGTC	0.517													C|||	199	0.0397364	0.0008	0.0648	5008	,	,		19806	0.0		0.0944	False		,,,				2504	0.0593				p.G1226V		Atlas-SNP	.											.	MKI67	363	.	0			c.G3677T						PASS	.	C	VAL/GLY,VAL/GLY	84,4322	73.1+/-111.1	1,82,2120	116.0	114.0	115.0		2597,3677	3.3	0.4	10	dbSNP_127	115	847,7753	193.9+/-239.5	46,755,3499	no	missense,missense	MKI67	NM_001145966.1,NM_002417.4	109,109	47,837,5619	AA,AC,CC		9.8488,1.9065,7.1582	probably-damaging,probably-damaging	866/2897,1226/3257	129906427	931,12075	2203	4300	6503	SO:0001583	missense	4288	exon13			TTAAAGCCAGCCA	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3677G>T	10.37:g.129906427C>A	ENSP00000357643:p.Gly1226Val	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	255	123	0.482353	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	96	0.04395604395604396	2	0.0040650406504065045	22	0.06077348066298342	1	0.0017482517482517483	71	0.09366754617414248	C	14.32	2.499339	0.44455	0.019065	0.098488	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03242	4.0;4.0	3.33	3.33	0.38152	.	0.581914	0.14252	N	0.331374	T	0.00412	0.0013	M	0.71206	2.165	0.47778	P	4.889999999999617E-4	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;1.0	T	0.13764	-1.0497	9	0.35671	T	0.21	.	13.3531	0.60613	0.0:1.0:0.0:0.0	rs41306015;rs61729208	1225;866;1226	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	1226;866;1225	ENSP00000357643:G1226V;ENSP00000357642:G866V	ENSP00000357642:G866V	G	-	2	0	MKI67	129796417	0.001000	0.12720	0.354000	0.25760	0.019000	0.09904	1.029000	0.30140	1.875000	0.54330	0.462000	0.41574	GGC	C|0.937;A|0.063	0.063	strong		0.517	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
MFSD6	54842	hgsc.bcm.edu	37	2	191301368	191301368	+	Missense_Mutation	SNP	A	A	G	rs9646748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:191301368A>G	ENST00000392328.1	+	3	937	c.613A>G	c.(613-615)Agg>Ggg	p.R205G	MFSD6_ENST00000281416.7_Missense_Mutation_p.R205G	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	205			R -> G (in dbSNP:rs9646748). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:20123006, ECO:0000269|Ref.4}.		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						TTTGGAAACAAGGCTCAATGT	0.433													G|||	2466	0.492412	0.4266	0.6427	5008	,	,		22706	0.6181		0.4483	False		,,,				2504	0.3906				p.R205G		Atlas-SNP	.											.	MFSD6	58	.	0			c.A613G						PASS	.	G	GLY/ARG	1940,2466	617.9+/-393.1	445,1050,708	76.0	81.0	79.0		613	5.2	0.0	2	dbSNP_119	79	3755,4845	612.9+/-396.0	829,2097,1374	yes	missense	MFSD6	NM_017694.3	125	1274,3147,2082	GG,GA,AA		43.6628,44.0309,43.7875	benign	205/792	191301368	5695,7311	2203	4300	6503	SO:0001583	missense	54842	exon3			GAAACAAGGCTCA		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.613A>G	2.37:g.191301368A>G	ENSP00000376141:p.Arg205Gly	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	1108	0.5073260073260073	199	0.40447154471544716	217	0.5994475138121547	352	0.6153846153846154	340	0.44854881266490765	G	0.303	-0.972835	0.02215	0.440309	0.436628	ENSG00000151690	ENST00000392328;ENST00000281416	T;T	0.29917	1.55;1.55	5.25	5.25	0.73442	Major facilitator superfamily domain, general substrate transporter (1);	0.859177	0.10675	N	0.647079	T	0.00012	0.0000	N	0.01352	-0.895	0.36623	P	0.12414199999999997	B	0.02656	0.0	B	0.01281	0.0	T	0.41052	-0.9530	9	0.13853	T	0.58	0.2618	13.3583	0.60642	0.0754:0.0:0.9246:0.0	rs9646748;rs59869310;rs9646748	205	Q6ZSS7	MFSD6_HUMAN	G	205	ENSP00000376141:R205G;ENSP00000281416:R205G	ENSP00000281416:R205G	R	+	1	2	MFSD6	191009613	0.002000	0.14202	0.002000	0.10522	0.010000	0.07245	1.232000	0.32636	1.468000	0.48064	-0.176000	0.13171	AGG	A|0.532;G|0.468	0.468	strong		0.433	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
SAMD9	54809	hgsc.bcm.edu	37	7	92734983	92734983	+	Missense_Mutation	SNP	A	A	G	rs6969691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:92734983A>G	ENST00000379958.2	-	3	697	c.428T>C	c.(427-429)aTa>aCa	p.I143T		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	143			I -> T (in dbSNP:rs6969691).			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTATCTTCTATGAGCTCAAC	0.358													A|||	764	0.152556	0.2905	0.1268	5008	,	,		20645	0.1359		0.1292	False		,,,				2504	0.0256				p.I143T		Atlas-SNP	.											.	SAMD9	239	.	0			c.T428C						PASS	.	A	THR/ILE,THR/ILE	1183,3223	414.6+/-336.9	164,855,1184	123.0	134.0	130.0		428,428	-4.0	0.0	7	dbSNP_116	130	1116,7484	230.1+/-264.6	84,948,3268	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	89,89	248,1803,4452	GG,GA,AA		12.9767,26.8498,17.6765	benign,benign	143/1590,143/1590	92734983	2299,10707	2203	4300	6503	SO:0001583	missense	54809	exon2			TCTTCTATGAGCT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.428T>C	7.37:g.92734983A>G	ENSP00000369292:p.Ile143Thr	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	228	107	0.469298	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	382	0.1749084249084249	146	0.2967479674796748	51	0.1408839779005525	94	0.16433566433566432	91	0.12005277044854881	A	4.275	0.050167	0.08243	0.268498	0.129767	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.13089	2.62;2.62	4.32	-4.02	0.04034	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47560	-0.9108	8	0.11182	T	0.66	.	5.2975	0.15760	0.367:0.0:0.397:0.2361	rs6969691;rs10363606;rs60909665;rs6969691	143	Q5K651	SAMD9_HUMAN	T	143	ENSP00000369292:I143T;ENSP00000414529:I143T	ENSP00000369292:I143T	I	-	2	0	SAMD9	92572919	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.406000	0.07187	-0.592000	0.05851	-0.322000	0.08575	ATA	A|0.818;G|0.182	0.182	strong		0.358	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
BSG	682	hgsc.bcm.edu	37	19	579627	579627	+	Silent	SNP	C	C	T	rs1803202	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:579627C>T	ENST00000333511.3	+	3	613	c.543C>T	c.(541-543)gaC>gaT	p.D181D	BSG_ENST00000574970.1_3'UTR|BSG_ENST00000545507.2_5'UTR|BSG_ENST00000353555.4_Silent_p.D65D|BSG_ENST00000346916.4_Intron	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	181	Ig-like C2-type.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGAAGGAGGACGCGCTGCCCG	0.642													C|||	945	0.188698	0.2095	0.0908	5008	,	,		15615	0.2282		0.1103	False		,,,				2504	0.2699				p.D181D		Atlas-SNP	.											.	BSG	48	.	0			c.C543T						PASS	.	C	,,	744,3656	299.6+/-285.9	60,624,1516	61.0	52.0	55.0		543,195,	0.2	0.4	19	dbSNP_89	55	865,7733	195.4+/-240.6	53,759,3487	no	coding-synonymous,coding-synonymous,intron	BSG	NM_001728.2,NM_198589.1,NM_198591.1	,,	113,1383,5003	TT,TC,CC		10.0605,16.9091,12.3788	,,	181/386,65/270,	579627	1609,11389	2200	4299	6499	SO:0001819	synonymous_variant	682	exon3			GGAGGACGCGCTG	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1116	protein-coding gene	gene with protein product	"""Ok blood group"""	109480	"""basigin"""	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.543C>T	19.37:g.579627C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Silent	SNP	ENST00000333511.3	37	CCDS12033.1																																																																																			C|0.866;T|0.134	0.134	strong		0.642	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728	
CCDC67	159989	hgsc.bcm.edu	37	11	93129483	93129483	+	Missense_Mutation	SNP	G	G	C	rs386756254|rs12288277	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:93129483G>C	ENST00000298050.3	+	11	1418	c.1318G>C	c.(1318-1320)Gaa>Caa	p.E440Q	CCDC67_ENST00000525646.1_Missense_Mutation_p.E182Q	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	440			E -> G (in dbSNP:rs12282288).|E -> Q (in dbSNP:rs12288277).	E -> R (in Ref. 3; BAB71673). {ECO:0000305}.	cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				AGACCCCGGAGAATACATGGT	0.358													C|||	1335	0.266573	0.1929	0.1888	5008	,	,		18794	0.3363		0.2833	False		,,,				2504	0.3323				p.E440Q		Atlas-SNP	.											.	CCDC67	57	.	0			c.G1318C						PASS	.	C	GLN/GLU	6,3662		0,6,1828	51.0	47.0	48.0		1318	4.3	0.5	11	dbSNP_120	48	25,8145		3,19,4063	yes	missense	CCDC67	NM_181645.3	29	3,25,5891	CC,CG,GG		0.306,0.1636,0.2619	benign	440/605	93129483	31,11807	1834	4085	5919	SO:0001583	missense	159989	exon11			CCCGGAGAATACA	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.1318G>C	11.37:g.93129483G>C	ENSP00000298050:p.Glu440Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	130	68	0.523077	NM_181645	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	CCDS44707.1	457	0.20924908424908426	63	0.12804878048780488	66	0.18232044198895028	161	0.28146853146853146	167	0.22031662269129287	C	2.060	-0.415727	0.04766	0.001636	0.00306	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000525646	T;T;T	0.23147	1.92;1.92;1.92	5.26	4.29	0.51040	.	1.241300	0.05530	N	0.563720	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39251	-0.9623	9	0.15066	T	0.55	.	7.8248	0.29309	0.2425:0.6166:0.1409:0.0	rs12288277;rs58616132;rs12288277	440;440	Q05D60;E9PJR5	CCD67_HUMAN;.	Q	440;440;182	ENSP00000432111:E440Q;ENSP00000298050:E440Q;ENSP00000435079:E182Q	ENSP00000298050:E440Q	E	+	1	0	CCDC67	92769131	0.087000	0.21565	0.495000	0.27527	0.058000	0.15608	1.216000	0.32443	1.473000	0.48159	-0.127000	0.14921	GAA	C|0.236;G|0.764	0.236	strong		0.358	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645	
ANKRD27	84079	hgsc.bcm.edu	37	19	33106621	33106621	+	Silent	SNP	C	C	T	rs405858|rs200055396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33106621C>T	ENST00000306065.4	-	22	2276	c.2118G>A	c.(2116-2118)gcG>gcA	p.A706A		NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	706					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					ATTCGGGGTCCGCTGCACTGA	0.557													c|||	2408	0.480831	0.4365	0.4755	5008	,	,		18541	0.3175		0.662	False		,,,				2504	0.5266				p.A706A		Atlas-SNP	.											ANKRD27,NS,carcinoma,-1,1	ANKRD27	86	1	0			c.G2118A						PASS	.	T		2072,2334	569.1+/-382.5	494,1084,625	142.0	103.0	116.0		2118	-10.4	0.0	19	dbSNP_80	116	5865,2735	681.9+/-403.8	1974,1917,409	no	coding-synonymous	ANKRD27	NM_032139.2		2468,3001,1034	TT,TC,CC		31.8023,47.0268,38.9743		706/1051	33106621	7937,5069	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon22			GGGGTCCGCTGCA	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2118G>A	19.37:g.33106621C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			C|0.445;T|0.555	0.555	strong		0.557	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
COL6A6	131873	hgsc.bcm.edu	37	3	130300650	130300650	+	Silent	SNP	T	T	C	rs6439249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130300650T>C	ENST00000358511.6	+	8	3824	c.3793T>C	c.(3793-3795)Ttg>Ctg	p.L1265L	COL6A6_ENST00000453409.2_Silent_p.L1265L	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1265	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						ACTGAATAGCTTGAAGGATAT	0.408													T|||	2896	0.578275	0.2943	0.7824	5008	,	,		17974	0.4444		0.8638	False		,,,				2504	0.6616				p.L1265L		Atlas-SNP	.											.	COL6A6	497	.	0			c.T3793C						PASS	.	T		1606,2204		334,938,633	155.0	150.0	152.0		3793	0.6	0.9	3	dbSNP_116	152	7227,983		3187,853,65	no	coding-synonymous	COL6A6	NM_001102608.1		3521,1791,698	CC,CT,TT		11.9732,42.1522,26.5141		1265/2264	130300650	8833,3187	1905	4105	6010	SO:0001819	synonymous_variant	131873	exon8			AATAGCTTGAAGG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3793T>C	3.37:g.130300650T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			T|0.383;C|0.617	0.617	strong		0.408	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
ABCB11	8647	hgsc.bcm.edu	37	2	169789016	169789016	+	Silent	SNP	T	T	C	rs497692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:169789016T>C	ENST00000263817.6	-	24	3208	c.3084A>G	c.(3082-3084)gcA>gcG	p.A1028A		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	1028	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.A1028A(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CAAGAGCTGTTGCACTCAGTA	0.493													C|||	2488	0.496805	0.2254	0.5086	5008	,	,		19594	0.6409		0.5318	False		,,,				2504	0.6708				p.A1028A		Atlas-SNP	.											ABCB11,colon,carcinoma,-1,2	ABCB11	136	2	1	Substitution - coding silent(1)	stomach(1)	c.A3084G						PASS	.	C		1076,2938		160,756,1091	84.0	81.0	82.0		3084	-10.8	0.0	2	dbSNP_83	82	4552,3814		1240,2072,871	yes	coding-synonymous	ABCB11	NM_003742.2		1400,2828,1962	CC,CT,TT		45.5893,26.8062,45.4604		1028/1322	169789016	5628,6752	2007	4183	6190	SO:0001819	synonymous_variant	8647	exon24			AGCTGTTGCACTC	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.3084A>G	2.37:g.169789016T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			T|0.519;C|0.481	0.481	strong		0.493	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
TMEM184A	202915	hgsc.bcm.edu	37	7	1587440	1587440	+	Missense_Mutation	SNP	G	G	A	rs61747419	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:1587440G>A	ENST00000297477.5	-	8	1266	c.950C>T	c.(949-951)tCc>tTc	p.S317F	TMEM184A_ENST00000449955.1_5'Flank	NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	317					germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		CAGGGCCACGGAGGCGAACAG	0.642													G|||	17	0.00339457	0.0	0.0086	5008	,	,		17254	0.0		0.0109	False		,,,				2504	0.0				p.S317F		Atlas-SNP	.											.	TMEM184A	35	.	0			c.C950T						PASS	.		PHE/SER	6,4332		0,6,2163	45.0	54.0	51.0		950	5.8	0.0	7	dbSNP_129	51	87,8491		1,85,4203	yes	missense	TMEM184A	NM_001097620.1	155	1,91,6366	AA,AG,GG		1.0142,0.1383,0.72	probably-damaging	317/414	1587440	93,12823	2169	4289	6458	SO:0001583	missense	202915	exon8			GCCACGGAGGCGA		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.950C>T	7.37:g.1587440G>A	ENSP00000297477:p.Ser317Phe	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_001097620	Q8TBQ6	Missense_Mutation	SNP	ENST00000297477.5	37	CCDS43537.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	17.25	3.340697	0.60963	0.001383	0.010142	ENSG00000164855	ENST00000297477	T	0.50277	0.75	5.82	5.82	0.92795	.	0.205916	0.41823	U	0.000801	T	0.67748	0.2926	M	0.85041	2.73	0.43745	D	0.996242	D	0.71674	0.998	D	0.76071	0.987	T	0.75184	-0.3407	10	0.87932	D	0	-6.871	20.0773	0.97749	0.0:0.0:1.0:0.0	rs61747419	317	Q6ZMB5	T184A_HUMAN	F	317	ENSP00000297477:S317F	ENSP00000297477:S317F	S	-	2	0	TMEM184A	1553966	1.000000	0.71417	0.026000	0.17262	0.093000	0.18481	9.557000	0.98129	2.750000	0.94351	0.561000	0.74099	TCC	G|0.992;A|0.008	0.008	strong		0.642	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689	
PTCH2	8643	hgsc.bcm.edu	37	1	45293752	45293752	+	Silent	SNP	T	T	C	rs2295997	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45293752T>C	ENST00000372192.3	-	14	1951	c.1821A>G	c.(1819-1821)gaA>gaG	p.E607E	PTCH2_ENST00000447098.2_Silent_p.E607E	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	607					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GGCTGCTGGCTTCACAGTGGG	0.622									Basal Cell Nevus syndrome				T|||	1065	0.21266	0.2156	0.2522	5008	,	,		19432	0.2897		0.1412	False		,,,				2504	0.1748				p.E607E		Atlas-SNP	.											.	PTCH2	96	.	0			c.A1821G						PASS	.	T	,	887,3519	340.5+/-306.2	82,723,1398	83.0	90.0	88.0		1821,1821	2.4	1.0	1	dbSNP_100	88	1447,7153	276.5+/-292.4	131,1185,2984	no	coding-synonymous,coding-synonymous	PTCH2	NM_001166292.1,NM_003738.4	,	213,1908,4382	CC,CT,TT		16.8256,20.1316,17.9456	,	607/1147,607/1204	45293752	2334,10672	2203	4300	6503	SO:0001819	synonymous_variant	8643	exon14	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	GCTGGCTTCACAG	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.1821A>G	1.37:g.45293752T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	34	0.755556	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Silent	SNP	ENST00000372192.3	37	CCDS516.1																																																																																			T|0.813;C|0.187	0.187	strong		0.622	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
C17orf59	54785	hgsc.bcm.edu	37	17	8092694	8092694	+	Silent	SNP	T	T	G	rs8531	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8092694T>G	ENST00000389017.4	-	1	870	c.765A>C	c.(763-765)ccA>ccC	p.P255P	MIR3676_ENST00000579470.1_RNA	NM_017622.2	NP_060092.2	Q96GS4	CQ059_HUMAN	chromosome 17 open reading frame 59	255	Pro-rich.									large_intestine(2)|lung(3)|urinary_tract(1)	6						CGGGGTCGATTGGGGGAATGG	0.716													G|||	3008	0.600639	0.6029	0.4971	5008	,	,		14381	0.2887		0.827	False		,,,				2504	0.7597				p.P255P		Atlas-SNP	.											.	C17orf59	19	.	0			c.A765C						PASS	.	G		2924,1468		981,962,253	12.0	13.0	13.0		765	2.3	1.0	17	dbSNP_52	13	7050,1534		2940,1170,182	no	coding-synonymous	C17orf59	NM_017622.2		3921,2132,435	GG,GT,TT		17.8705,33.4244,23.135		255/358	8092694	9974,3002	2196	4292	6488	SO:0001819	synonymous_variant	54785	exon1			GTCGATTGGGGGA	BC018880	CCDS11133.2	17p13.1	2005-12-16			ENSG00000196544	ENSG00000196544			25939	protein-coding gene	gene with protein product						12477932	Standard	NM_017622		Approved	FLJ20014	uc010vut.2	Q96GS4	OTTHUMG00000153930	ENST00000389017.4:c.765A>C	17.37:g.8092694T>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_017622	Q53HS4|Q9NXW8	Silent	SNP	ENST00000389017.4	37	CCDS11133.2																																																																																			T|0.355;G|0.645	0.645	strong		0.716	C17orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333072.1	NM_017622	
SLC4A1	6521	hgsc.bcm.edu	37	17	42327847	42327847	+	Missense_Mutation	SNP	G	G	C	rs377326869		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42327847G>C	ENST00000262418.6	-	20	2870	c.2715C>G	c.(2713-2715)gaC>gaG	p.D905E	AC003102.1_ENST00000399246.2_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	905	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		TGGCCACTTCGTCGTATTCAT	0.592																																					p.D905E		Atlas-SNP	.											.	SLC4A1	104	.	0			c.C2715G						PASS	.						109.0	75.0	86.0					17																	42327847		2203	4300	6503	SO:0001583	missense	6521	exon20			CACTTCGTCGTAT		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.2715C>G	17.37:g.42327847G>C	ENSP00000262418:p.Asp905Glu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	G	1.789	-0.479900	0.04383	.	.	ENSG00000004939	ENST00000262418	T	0.73363	-0.74	4.91	-5.15	0.02866	.	0.251137	0.30649	N	0.009173	T	0.58352	0.2116	L	0.40543	1.245	0.30038	N	0.81285	B	0.10296	0.003	B	0.08055	0.003	T	0.46076	-0.9217	10	0.20046	T	0.44	.	13.9273	0.63970	0.7677:0.0:0.2323:0.0	.	905	P02730	B3AT_HUMAN	E	905	ENSP00000262418:D905E	ENSP00000262418:D905E	D	-	3	2	SLC4A1	39683373	0.000000	0.05858	0.009000	0.14445	0.005000	0.04900	-1.941000	0.01542	-0.728000	0.04882	-0.224000	0.12420	GAC	.	.	alt		0.592	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
CSPG4	1464	hgsc.bcm.edu	37	15	75977920	75977920	+	Silent	SNP	A	A	G	rs62027240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75977920A>G	ENST00000308508.5	-	4	4004	c.3912T>C	c.(3910-3912)ccT>ccC	p.P1304P		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1304	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						AGCTCTGCACAGGGTCCAGGC	0.637													G|||	1975	0.394369	0.2723	0.5303	5008	,	,		18636	0.2728		0.5209	False		,,,				2504	0.4581				p.P1304P		Atlas-SNP	.											CSPG4,NS,carcinoma,0,1	CSPG4	175	1	0			c.T3912C						PASS	.	G		1178,3192		201,776,1208	13.0	13.0	13.0		3912	-5.7	0.7	15	dbSNP_129	13	4360,4132		1226,1908,1112	no	coding-synonymous	CSPG4	NM_001897.4		1427,2684,2320	GG,GA,AA		48.6576,26.9565,43.0571		1304/2323	75977920	5538,7324	2185	4246	6431	SO:0001819	synonymous_variant	1464	exon4			CTGCACAGGGTCC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.3912T>C	15.37:g.75977920A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			A|0.620;G|0.380	0.380	strong		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
EIF5B	9669	hgsc.bcm.edu	37	2	99995517	99995517	+	Silent	SNP	C	C	T	rs11896520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:99995517C>T	ENST00000289371.6	+	11	2080	c.1878C>T	c.(1876-1878)acC>acT	p.T626T		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	626					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATGTAAACACCGAAAAGCTAA	0.299													C|||	758	0.151358	0.09	0.3012	5008	,	,		14631	0.0149		0.2753	False		,,,				2504	0.1411				p.T626T	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											EIF5B,caecum,carcinoma,0,1	EIF5B	95	1	0			c.C1878T						PASS	.	C		362,3280		12,338,1471	75.0	66.0	69.0		1878	-3.9	1.0	2	dbSNP_120	69	2231,5933		284,1663,2135	no	coding-synonymous	EIF5B	NM_015904.3		296,2001,3606	TT,TC,CC		27.3273,9.9396,21.9634		626/1221	99995517	2593,9213	1821	4082	5903	SO:0001819	synonymous_variant	9669	exon11			AAACACCGAAAAG	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"""translation initiation factor IF2"""	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.1878C>T	2.37:g.99995517C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																			C|0.813;T|0.187	0.187	strong		0.299	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904	
DEFB127	140850	hgsc.bcm.edu	37	20	139576	139576	+	Missense_Mutation	SNP	C	C	A	rs16995685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:139576C>A	ENST00000382388.3	+	2	286	c.211C>A	c.(211-213)Cgt>Agt	p.R71S		NM_139074.3	NP_620713.1	Q9H1M4	DB127_HUMAN	defensin, beta 127	71			R -> S (in dbSNP:rs16995685). {ECO:0000269|PubMed:11854508}.		defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			AAAGCCACCTCGTCCAAAGCC	0.388													C|||	1623	0.324081	0.0431	0.3487	5008	,	,		20057	0.5407		0.3419	False		,,,				2504	0.4448				p.R71S		Atlas-SNP	.											.	DEFB127	15	.	0			c.C211A						PASS	.	C	SER/ARG	399,4007	199.4+/-223.0	18,363,1822	109.0	93.0	98.0		211	1.2	0.0	20	dbSNP_123	98	3030,5570	466.8+/-366.9	519,1992,1789	yes	missense	DEFB127	NM_139074.2	110	537,2355,3611	AA,AC,CC		35.2326,9.0558,26.3648	benign	71/100	139576	3429,9577	2203	4300	6503	SO:0001583	missense	140850	exon2			CCACCTCGTCCAA	AY358796	CCDS12991.1	20p13	2008-02-01	2002-05-09	2002-05-10	ENSG00000088782	ENSG00000088782		"""Defensins, beta"""	16206	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 73"""	C20orf73		11854508	Standard	NM_139074		Approved	bA530N10.2, DEF-27	uc002wcy.2	Q9H1M4	OTTHUMG00000031617	ENST00000382388.3:c.211C>A	20.37:g.139576C>A	ENSP00000371825:p.Arg71Ser	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	220	110	0.5	NM_139074	Q14DW7	Missense_Mutation	SNP	ENST00000382388.3	37	CCDS12991.1	702	0.32142857142857145	19	0.03861788617886179	135	0.3729281767955801	287	0.5017482517482518	261	0.34432717678100266	C	0.491	-0.875449	0.02550	0.090558	0.352326	ENSG00000088782	ENST00000382388	T	0.15256	2.44	3.26	1.24	0.21308	.	0.768263	0.10589	N	0.656961	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.21520	0.057	B	0.20184	0.028	T	0.45512	-0.9256	8	0.26408	T	0.33	-0.2158	4.0324	0.09714	0.2294:0.6438:0.0:0.1268	rs16995685;rs16995685	71	Q9H1M4	DB127_HUMAN	S	71	ENSP00000371825:R71S	ENSP00000371825:R71S	R	+	1	0	DEFB127	87576	0.004000	0.15560	0.003000	0.11579	0.001000	0.01503	0.595000	0.24029	0.367000	0.24454	-0.657000	0.03884	CGT	C|0.718;A|0.282	0.282	strong		0.388	DEFB127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077429.1	NM_139074	
TDRD7	23424	hgsc.bcm.edu	37	9	100190780	100190780	+	Silent	SNP	A	A	G	rs1381532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100190780A>G	ENST00000355295.4	+	2	328	c.33A>G	c.(31-33)ctA>ctG	p.L11L	TDRD7_ENST00000422139.2_Intron	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	11	HTH OST-type 1. {ECO:0000255|PROSITE- ProRule:PRU00975}.				germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				CAAAGATGCTACGAGCTGTTC	0.433													G|||	2729	0.544928	0.6127	0.598	5008	,	,		20612	0.5804		0.5119	False		,,,				2504	0.4131				p.L11L		Atlas-SNP	.											.	TDRD7	78	.	0			c.A33G						PASS	.	G		2664,1742	518.6+/-369.8	797,1070,336	100.0	96.0	97.0		33	-4.7	0.9	9	dbSNP_88	97	4090,4510	592.4+/-393.0	978,2134,1188	no	coding-synonymous	TDRD7	NM_014290.2		1775,3204,1524	GG,GA,AA		47.5581,39.537,48.0701		11/1099	100190780	6754,6252	2203	4300	6503	SO:0001819	synonymous_variant	23424	exon2			GATGCTACGAGCT	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"""Tudor domain containing"""	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.33A>G	9.37:g.100190780A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	NM_014290	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Silent	SNP	ENST00000355295.4	37	CCDS6725.1																																																																																			A|0.469;G|0.531	0.531	strong		0.433	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290	
AP3D1	8943	hgsc.bcm.edu	37	19	2114175	2114175	+	Silent	SNP	T	T	C	rs55698722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:2114175T>C	ENST00000345016.5	-	22	2781	c.2550A>G	c.(2548-2550)aaA>aaG	p.K850K	AP3D1_ENST00000350812.6_Silent_p.K681K|AP3D1_ENST00000355272.6_Silent_p.K850K|AP3D1_ENST00000356926.4_Silent_p.K759K	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	850	Lys-rich.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		tctctttGTGTTTTTTCTCTT	0.483													C|||	388	0.077476	0.0756	0.0677	5008	,	,		19994	0.0		0.1153	False		,,,				2504	0.1278				p.K850K		Atlas-SNP	.											.	AP3D1	81	.	0			c.A2550G						PASS	.	C	,	328,3566		11,306,1630	90.0	89.0	89.0		2277,2550	1.2	1.0	19	dbSNP_129	89	1278,6998		104,1070,2964	no	coding-synonymous,coding-synonymous	AP3D1	NM_001077523.1,NM_003938.5	,	115,1376,4594	CC,CT,TT		15.4422,8.4232,13.1964	,	759/1113,850/1154	2114175	1606,10564	1947	4138	6085	SO:0001819	synonymous_variant	8943	exon22			TTTGTGTTTTTTC	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.2550A>G	19.37:g.2114175T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	166	93	0.560241	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																			A|0.000;C|0.073;G|0.000;T|0.926	0.073	strong		0.483	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
SLCO1B7	338821	hgsc.bcm.edu	37	12	21201663	21201663	+	Missense_Mutation	SNP	G	G	A	rs11045689	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:21201663G>A	ENST00000421593.2	+	8	1012	c.1012G>A	c.(1012-1014)Gct>Act	p.A338T	SLCO1B3_ENST00000553473.1_Intron|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.A385T|LST3_ENST00000381541.3_Missense_Mutation_p.A385T|LST3_ENST00000540229.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	338				A -> T (in Ref. 1; AAQ03085). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						CGCCCTACCTGCTGTTGCAAT	0.373													G|||	2373	0.473842	0.0885	0.634	5008	,	,		8003	0.3829		0.6402	False		,,,				2504	0.8037				p.A338T		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.G1012A						PASS	.	G	THR/ALA	810,3110		98,614,1248	34.0	33.0	33.0		1012	-4.0	0.0	12	dbSNP_120	33	5522,2860		1829,1864,498	yes	missense	SLCO1B7	NM_001009562.4	58	1927,2478,1746	AA,AG,GG		34.1207,20.6633,48.5287		338/641	21201663	6332,5970	1960	4191	6151	SO:0001583	missense	338821	exon8			CTACCTGCTGTTG	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.1012G>A	12.37:g.21201663G>A	ENSP00000394168:p.Ala338Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	1020	0.46703296703296704	58	0.11788617886178862	230	0.6353591160220995	234	0.4090909090909091	498	0.6569920844327177	.	2.948	-0.217340	0.06101	0.206633	0.658793	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;D	0.81739	-1.49;-1.49;-1.53	3.45	-4.01	0.04045	.	0.409800	0.25817	N	0.028113	T	0.00012	0.0000	N	0.04132	-0.27	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.15052	0.012;0.008	T	0.42103	-0.9471	9	0.21540	T	0.41	.	3.7602	0.08601	0.2411:0.0:0.4128:0.3461	rs11045689;rs52835474;rs60529983;rs11045689	338;385	G3V0H7;F5H094	.;.	T	385;385;338	ENSP00000370952:A385T;ENSP00000452013:A385T;ENSP00000394168:A338T	ENSP00000370952:A385T	A	+	1	0	SLCO1B7;RP11-545J16.1	21092930	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.874000	0.04210	-0.643000	0.05473	-0.507000	0.04495	GCT	G|0.507;A|0.493	0.493	strong		0.373	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
TRIM21	6737	hgsc.bcm.edu	37	11	4411471	4411471	+	Missense_Mutation	SNP	G	G	A	rs200488796		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4411471G>A	ENST00000254436.7	-	2	281	c.169C>T	c.(169-171)Cgc>Tgc	p.R57C	TRIM21_ENST00000543625.1_Missense_Mutation_p.R57C	NM_003141.3	NP_003132.2	P19474	RO52_HUMAN	tripartite motif containing 21	57					cell cycle (GO:0007049)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein deubiquitination (GO:0090086)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral entry into host cell (GO:0046598)|protein autoubiquitination (GO:0051865)|protein destabilization (GO:0031648)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)	16		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		AGCAGAAAGCGCTGCCGGCAC	0.582													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.R57C		Atlas-SNP	.											.	TRIM21	45	.	0			c.C169T						PASS	.	G	CYS/ARG	0,4246		0,0,2123	90.0	94.0	93.0		169	-1.4	0.0	11		93	17,8461		0,17,4222	yes	missense	TRIM21	NM_003141.3	180	0,17,6345	AA,AG,GG		0.2005,0.0,0.1336	possibly-damaging	57/476	4411471	17,12707	2123	4239	6362	SO:0001583	missense	6737	exon2			GAAAGCGCTGCCG	AF391283	CCDS44525.1	11p15.5-p15.3	2014-02-14	2011-01-25	2004-11-26		ENSG00000132109		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	11312	protein-coding gene	gene with protein product		109092	"""Sjogren syndrome antigen A1 (52kDa, ribonucleoprotein autoantigen SS-A/Ro)"", ""tripartite motif-containing 21"""	SSA1		8094596	Standard	NM_003141		Approved	RNF81, RO52, Ro/SSA	uc001lyy.1	P19474		ENST00000254436.7:c.169C>T	11.37:g.4411471G>A	ENSP00000254436:p.Arg57Cys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	123	69	0.560976	NM_003141	Q5XPV5|Q96RF8	Missense_Mutation	SNP	ENST00000254436.7	37	CCDS44525.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	5.894	0.349073	0.11182	0.0	0.002005	ENSG00000132109	ENST00000254436;ENST00000543625	D;D	0.84223	-1.82;-1.82	4.46	-1.39	0.08997	Zinc finger, RING/FYVE/PHD-type (1);	4.312490	0.00166	N	0.000018	T	0.72228	0.3434	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.62224	-0.6899	10	0.62326	D	0.03	.	7.6016	0.28079	0.1865:0.0:0.6493:0.1642	.	57	P19474	RO52_HUMAN	C	57	ENSP00000254436:R57C;ENSP00000444045:R57C	ENSP00000254436:R57C	R	-	1	0	TRIM21	4368047	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.155000	0.03163	-0.237000	0.09739	0.655000	0.94253	CGC	G|1.000;A|0.000	0.000	strong		0.582	TRIM21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385842.1	NM_003141	
SETMAR	6419	hgsc.bcm.edu	37	3	4354697	4354697	+	Missense_Mutation	SNP	G	G	A	rs6801634	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:4354697G>A	ENST00000358065.4	+	2	339	c.272G>A	c.(271-273)cGc>cAc	p.R91H	SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000462115.1_3'UTR|SETMAR_ENST00000430981.1_Missense_Mutation_p.R91H|SETMAR_ENST00000425863.1_Missense_Mutation_p.R91H	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	91	Histone-lysine N-methyltransferase.|Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.			R -> H (in Ref. 1; BAG63636). {ECO:0000305}.	DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		TCCTGTCTCCGCCATGGAGAG	0.483								Chromatin Structure					G|||	609	0.121605	0.1014	0.1167	5008	,	,		18899	0.0982		0.16	False		,,,				2504	0.137				p.R91H		Atlas-SNP	.											.	SETMAR	30	.	0			c.G272A						PASS	.	G	HIS/ARG	458,3948	220.4+/-237.8	24,410,1769	84.0	76.0	79.0		272	1.0	0.8	3	dbSNP_116	79	1215,7385	245.6+/-274.3	70,1075,3155	yes	missense	SETMAR	NM_006515.3	29	94,1485,4924	AA,AG,GG		14.1279,10.3949,12.8633	possibly-damaging	91/685	4354697	1673,11333	2203	4300	6503	SO:0001583	missense	6419	exon2			GTCTCCGCCATGG	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.272G>A	3.37:g.4354697G>A	ENSP00000373354:p.Arg91His	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	175	80	0.457143	NM_001243723	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	37	CCDS2563.2	273	0.125	54	0.10975609756097561	43	0.11878453038674033	54	0.0944055944055944	122	0.16094986807387862	G	9.041	0.989745	0.18966	0.103949	0.141279	ENSG00000170364	ENST00000358065;ENST00000430981;ENST00000425863	D;D;T	0.89552	-2.53;-2.53;-1.09	5.13	1.01	0.19927	Pre-SET zinc-binding sub-group (1);Pre-SET domain (2);	.	.	.	.	T	0.01124	0.0037	M	0.64567	1.98	0.58432	P	1.0000000000287557E-6	P;P;B	0.43750	0.816;0.699;0.031	B;B;B	0.29716	0.106;0.058;0.006	T	0.41680	-0.9495	8	0.56958	D	0.05	.	3.9103	0.09201	0.1543:0.1976:0.5295:0.1185	rs6801634;rs52791578;rs58831512;rs6801634	91;78;91	E7EN68;Q53H47;C9JHK2	.;SETMR_HUMAN;.	H	91	ENSP00000373354:R91H;ENSP00000403000:R91H;ENSP00000403145:R91H	ENSP00000373354:R91H	R	+	2	0	SETMAR	4329697	0.003000	0.15002	0.809000	0.32408	0.376000	0.30014	0.089000	0.15002	0.571000	0.29365	-0.262000	0.10625	CGC	G|0.871;A|0.129	0.129	strong		0.483	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515	
ADAT1	23536	hgsc.bcm.edu	37	16	75642801	75642801	+	Missense_Mutation	SNP	G	G	A	rs77029992	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:75642801G>A	ENST00000307921.3	-	8	1274	c.1129C>T	c.(1129-1131)Cgc>Tgc	p.R377C	RP11-77K12.8_ENST00000564489.1_RNA	NM_012091.3	NP_036223.2	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	377	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|RNA binding (GO:0003723)|tRNA-specific adenosine deaminase activity (GO:0008251)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)	19						ACCGCACTGCGGCTCTGTTCA	0.473													G|||	27	0.00539137	0.0008	0.0086	5008	,	,		21246	0.0		0.0189	False		,,,				2504	0.001				p.R377C		Atlas-SNP	.											.	ADAT1	45	.	0			c.C1129T						PASS	.	G	CYS/ARG	20,4376	27.2+/-55.0	0,20,2178	80.0	74.0	76.0		1129	5.1	1.0	16	dbSNP_131	76	240,8360	97.2+/-158.9	3,234,4063	yes	missense	ADAT1	NM_012091.3	180	3,254,6241	AA,AG,GG		2.7907,0.455,2.0006	probably-damaging	377/503	75642801	260,12736	2198	4300	6498	SO:0001583	missense	23536	exon8			CACTGCGGCTCTG	AF125188	CCDS10922.1	16q23	2008-02-05			ENSG00000065457	ENSG00000065457			228	protein-coding gene	gene with protein product		604230				10430867	Standard	NM_012091		Approved		uc002feo.2	Q9BUB4	OTTHUMG00000137611	ENST00000307921.3:c.1129C>T	16.37:g.75642801G>A	ENSP00000310015:p.Arg377Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_012091	Q9NVB7|Q9UNG3	Missense_Mutation	SNP	ENST00000307921.3	37	CCDS10922.1	22	0.010073260073260074	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	16	0.021108179419525065	G	14.21	2.467031	0.43839	0.00455	0.027907	ENSG00000065457	ENST00000307921;ENST00000542252	D	0.94184	-3.37	6.03	5.09	0.68999	Adenosine deaminase/editase (3);	0.476723	0.23298	N	0.049703	D	0.85124	0.5625	M	0.90542	3.125	0.58432	D	0.999999	B	0.27140	0.169	B	0.20767	0.031	D	0.87066	0.2156	10	0.56958	D	0.05	1.6221	8.8692	0.35305	0.0749:0.0:0.7765:0.1486	.	377	Q9BUB4	ADAT1_HUMAN	C	377;348	ENSP00000310015:R377C	ENSP00000310015:R377C	R	-	1	0	ADAT1	74200302	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	3.454000	0.52986	1.568000	0.49683	0.557000	0.71058	CGC	G|0.983;A|0.017	0.017	strong		0.473	ADAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269027.1	NM_012091	
GRIN3A	116443	hgsc.bcm.edu	37	9	104449294	104449294	+	Silent	SNP	G	G	A	rs33945236	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:104449294G>A	ENST00000361820.3	-	2	1488	c.888C>T	c.(886-888)aaC>aaT	p.N296N		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	296					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	TAGCGGTGATGTTGATGATAG	0.483													G|||	614	0.122604	0.0068	0.1902	5008	,	,		19332	0.1716		0.167	False		,,,				2504	0.135				p.N296N		Atlas-SNP	.											GRIN3A,colon,carcinoma,0,1	GRIN3A	186	1	0			c.C888T						PASS	.	G		155,4251	104.3+/-142.8	6,143,2054	144.0	128.0	133.0		888	2.7	1.0	9	dbSNP_126	133	1457,7143	277.6+/-293.0	125,1207,2968	no	coding-synonymous	GRIN3A	NM_133445.2		131,1350,5022	AA,AG,GG		16.9419,3.5179,12.3943		296/1116	104449294	1612,11394	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon2			GGTGATGTTGATG		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.888C>T	9.37:g.104449294G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	203	96	0.472906	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			G|0.865;A|0.135	0.135	strong		0.483	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
CYP4F2	8529	hgsc.bcm.edu	37	19	15996820	15996820	+	Missense_Mutation	SNP	G	G	A	rs2074900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15996820G>A	ENST00000011989.7	-	7	863	c.515C>T	c.(514-516)aCc>aTc	p.T172I	CYP4F2_ENST00000221700.6_Silent_p.H343H					cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GCTTTGCAAGGTGGTACAGGA	0.597													.|||	1167	0.233027	0.1725	0.2421	5008	,	,		17400	0.2222		0.2972	False		,,,				2504	0.2536				p.H343H		Atlas-SNP	.											.	CYP4F2	97	.	0			c.C1029T						PASS	.	G		836,3570	331.2+/-301.9	75,686,1442	89.0	79.0	82.0		1029	1.5	1.0	19	dbSNP_96	82	2708,5892	433.6+/-357.5	435,1838,2027	no	coding-synonymous	CYP4F2	NM_001082.3		510,2524,3469	AA,AG,GG		31.4884,18.9741,27.249		343/521	15996820	3544,9462	2203	4300	6503	SO:0001583	missense	8529	exon9			TGCAAGGTGGTAC	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000011989.7:c.515C>T	19.37:g.15996820G>A	ENSP00000011989:p.Thr172Ile	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	89	0.494444	NM_001082		Silent	SNP	ENST00000011989.7	37		556	0.25457875457875456	107	0.21747967479674796	79	0.21823204419889503	135	0.23601398601398602	235	0.3100263852242744	g	9.429	1.085048	0.20390	0.189741	0.314884	ENSG00000186115	ENST00000011989	T	0.25414	1.8	2.63	1.49	0.22878	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46678	P	8.430000000000382E-4	B	0.11235	0.004	B	0.13407	0.009	T	0.35748	-0.9776	7	0.87932	D	0	.	5.1868	0.15187	0.3008:0.0:0.6992:0.0	rs2074900;rs2230747;rs61124408	172	B4DV75	.	I	172	ENSP00000011989:T172I	ENSP00000011989:T172I	T	-	2	0	CYP4F2	15857820	1.000000	0.71417	0.969000	0.41365	0.423000	0.31445	2.531000	0.45650	0.379000	0.24794	0.313000	0.20887	ACC	G|0.734;A|0.266	0.266	strong		0.597	CYP4F2-201	KNOWN	basic	protein_coding	protein_coding		NM_001082	
RHBG	57127	hgsc.bcm.edu	37	1	156347131	156347131	+	Missense_Mutation	SNP	G	G	A	rs2245623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156347131G>A	ENST00000368249.1	+	2	265	c.227G>A	c.(226-228)gGc>gAc	p.G76D	RHBG_ENST00000255013.3_Missense_Mutation_p.G7D|RHBG_ENST00000537040.1_Intron|RHBG_ENST00000451864.2_Missense_Mutation_p.G7D|RHBG_ENST00000400992.2_Missense_Mutation_p.G7D|RHBG_ENST00000368246.2_Missense_Mutation_p.G76D	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	76			G -> D (in dbSNP:rs2245623). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GTGGGCTTTGGCTTCCTCATG	0.637													G|||	1355	0.270567	0.1936	0.2781	5008	,	,		21225	0.1012		0.4563	False		,,,				2504	0.3528				p.G76D		Atlas-SNP	.											.	RHBG	133	.	0			c.G227A						PASS	.	G	ASP/GLY	993,3413	365.9+/-317.6	106,781,1316	142.0	144.0	143.0		227	4.9	1.0	1	dbSNP_100	143	3847,4753	537.9+/-383.3	886,2075,1339	yes	missense	RHBG	NM_020407.3	94	992,2856,2655	AA,AG,GG		44.7326,22.5374,37.2136	probably-damaging	76/459	156347131	4840,8166	2203	4300	6503	SO:0001583	missense	57127	exon2			GCTTTGGCTTCCT	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.227G>A	1.37:g.156347131G>A	ENSP00000357232:p.Gly76Asp	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	370	142	0.383784	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		608	0.2783882783882784	95	0.19308943089430894	109	0.3011049723756906	58	0.10139860139860139	346	0.45646437994722955	G	34	5.389342	0.95988	0.225374	0.447326	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000400992;ENST00000255013;ENST00000451864	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	4.86	4.86	0.63082	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	D	0.91744	0.7389	H	0.94582	3.555	0.09310	P	0.9999999999972279	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93736	0.7046	9	0.87932	D	0	-6.6399	16.7188	0.85405	0.0:0.0:1.0:0.0	rs2245623;rs17387461;rs2245623	76;7;113	Q9H310;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.	D	76;76;7;7;7	ENSP00000357232:G76D;ENSP00000357229:G76D;ENSP00000383777:G7D;ENSP00000255013:G7D;ENSP00000389836:G7D	ENSP00000255013:G7D	G	+	2	0	RHBG	154613755	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.395000	0.97266	2.512000	0.84698	0.561000	0.74099	GGC	G|0.713;A|0.287	0.287	strong		0.637	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
DCAF6	55827	hgsc.bcm.edu	37	1	168014204	168014204	+	Missense_Mutation	SNP	T	T	A	rs41271647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:168014204T>A	ENST00000312263.6	+	14	1970	c.1766T>A	c.(1765-1767)cTt>cAt	p.L589H	DCAF6_ENST00000367843.3_Missense_Mutation_p.L609H|DCAF6_ENST00000432587.2_Missense_Mutation_p.L635H|DCAF6_ENST00000367840.3_Missense_Mutation_p.L666H	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	589					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						GACCTCAATCTTGATCGCTCT	0.423													T|||	200	0.0399361	0.003	0.0605	5008	,	,		20427	0.0		0.0915	False		,,,				2504	0.0634				p.L666H		Atlas-SNP	.											.	DCAF6	99	.	0			c.T1997A						PASS	.	T	HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU	74,4332	66.4+/-103.9	0,74,2129	118.0	127.0	124.0		1766,1997,1904,1826	-1.9	0.6	1	dbSNP_127	124	837,7763	192.8+/-238.7	39,759,3502	yes	missense,missense,missense,missense	DCAF6	NM_001017977.2,NM_001198956.1,NM_001198957.1,NM_018442.3	99,99,99,99	39,833,5631	AA,AT,TT		9.7326,1.6795,7.0045	benign,benign,benign,benign	589/861,666/952,635/921,609/881	168014204	911,12095	2203	4300	6503	SO:0001583	missense	55827	exon16			TCAATCTTGATCG	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30002	protein-coding gene	gene with protein product		610494	"""IQ motif and WD repeats 1"""	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.1766T>A	1.37:g.168014204T>A	ENSP00000311949:p.Leu589His	Somatic	399	0	0		WXS	Illumina HiSeq	Phase_I	502	199	0.396414	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	103	0.04716117216117216	1	0.0020325203252032522	30	0.08287292817679558	0	0.0	72	0.09498680738786279	T	3.954	-0.011668	0.07727	0.016795	0.097326	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.16	-1.9	0.07665	WD40 repeat-like-containing domain (1);	0.834564	0.10756	N	0.637779	T	0.02767	0.0083	N	0.03608	-0.345	0.19300	N	0.999975	B;B;B;B	0.11235	0.001;0.004;0.0;0.002	B;B;B;B	0.14023	0.002;0.01;0.002;0.004	T	0.43940	-0.9360	9	0.14656	T	0.56	.	3.6996	0.08378	0.3525:0.2041:0.0:0.4433	rs41271647;rs61746944	635;666;589;609	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	H	609;635;589;666	ENSP00000356817:L609H;ENSP00000396238:L635H;ENSP00000311949:L589H;ENSP00000356814:L666H	ENSP00000311949:L589H	L	+	2	0	DCAF6	166280828	0.796000	0.28864	0.553000	0.28255	0.506000	0.33950	-0.069000	0.11542	-0.024000	0.13941	0.383000	0.25322	CTT	T|0.933;A|0.067	0.067	strong		0.423	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179858444	179858444	+	Intron	SNP	G	G	A	rs2245425	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:179858444G>A	ENST00000606911.2	+	3	744				TOR1AIP1_ENST00000435319.4_Intron|TOR1AIP1_ENST00000474875.1_Intron|TOR1AIP1_ENST00000271583.3_Splice_Site|TOR1AIP1_ENST00000528443.2_Splice_Site			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1						positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						TCCTATATTAGCAGTGAGTGA	0.323													G|||	3182	0.635383	0.4644	0.6916	5008	,	,		16866	0.7778		0.6064	False		,,,				2504	0.7096				.		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.554-1G>A						PASS	.	G		2219,2187	590.7+/-387.4	553,1113,537	102.0	102.0	102.0			5.3	0.1	1	dbSNP_100	102	5362,3234	649.3+/-400.6	1674,2014,610	no	intron	TOR1AIP1	NM_015602.2		2227,3127,1147	AA,AG,GG		37.6221,49.6369,41.6936			179858444	7581,5421	2203	4298	6501	SO:0001627	intron_variant	26092	exon3			ATATTAGCAGTGA		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.554-4G>A	1.37:g.179858444G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Splice_Site	SNP	ENST00000606911.2	37	CCDS1335.1	1369	0.6268315018315018	218	0.44308943089430897	241	0.6657458563535912	451	0.7884615384615384	459	0.6055408970976254	G	11.86	1.764619	0.31228	0.503631	0.623779	ENSG00000143337	ENST00000528443;ENST00000271583	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7301	0.69374	0.0:0.0:1.0:0.0	rs2245425;rs16854913;rs59592554;rs2245425	.	.	.	.	-1	.	.	.	+	.	.	TOR1AIP1	178125067	0.993000	0.37304	0.123000	0.21794	0.006000	0.05464	4.200000	0.58433	2.598000	0.87819	0.557000	0.71058	.	G|0.377;A|0.623	0.623	strong		0.323	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602	
SOX12	6666	hgsc.bcm.edu	37	20	306733	306733	+	Silent	SNP	G	G	A	rs73071018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:306733G>A	ENST00000342665.2	+	1	495	c.165G>A	c.(163-165)cgG>cgA	p.R55R	RP5-1103G7.4_ENST00000414676.1_RNA|RP5-1103G7.4_ENST00000442637.1_RNA|SOX12_ENST00000544632.1_Silent_p.R55R	NM_006943.2	NP_008874.2	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	55					cell fate commitment (GO:0045165)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord development (GO:0021510)	nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R55R(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		all_cancers(10;0.000331)|Lung NSC(37;0.0496)|all_lung(30;0.0831)|all_epithelial(17;0.0868)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			AGCACGAACGGCGGAAGATCA	0.672													G|||	29	0.00579073	0.0015	0.0115	5008	,	,		7149	0.0		0.0179	False		,,,				2504	0.001				p.R55R		Atlas-SNP	.											SOX12,NS,lymphoid_neoplasm,0,1	SOX12	8	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G165A						PASS	.	G		15,4391		0,15,2188	35.0	29.0	31.0		165	3.6	1.0	20	dbSNP_130	31	188,8408		1,186,4111	no	coding-synonymous	SOX12	NM_006943.2		1,201,6299	AA,AG,GG		2.1871,0.3404,1.5613		55/316	306733	203,12799	2203	4298	6501	SO:0001819	synonymous_variant	6666	exon1			CGAACGGCGGAAG	U35612	CCDS12995.1	20p13	2008-07-28	2002-07-22	2002-07-26	ENSG00000177732	ENSG00000177732		"""SRY (sex determining region Y)-boxes"""	11198	protein-coding gene	gene with protein product		601947	"""SRY (sex determining region Y)-box 22"""	SOX22		9215677	Standard	NM_006943		Approved		uc002wdh.4	O15370	OTTHUMG00000031623	ENST00000342665.2:c.165G>A	20.37:g.306733G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	157	89	0.566879	NM_006943	Q5D038|Q9NUD4	Silent	SNP	ENST00000342665.2	37	CCDS12995.1																																																																																			G|0.985;A|0.015	0.015	strong		0.672	SOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077435.2	NM_006943	
FLT4	2324	hgsc.bcm.edu	37	5	180030313	180030313	+	Missense_Mutation	SNP	C	C	A	rs307821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:180030313C>A	ENST00000261937.6	-	30	4049	c.3971G>T	c.(3970-3972)cGg>cTg	p.R1324L		NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1324					blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCGGGCCCCCCGCTCAGGCCG	0.652																																					p.R1324L	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.G3971T						PASS	.	C	LEU/ARG	230,4174		3,224,1975	22.0	22.0	22.0		3971	-8.8	0.0	5	dbSNP_79	22	934,7666		36,862,3402	yes	missense	FLT4	NM_182925.4	102	39,1086,5377	AA,AC,CC		10.8605,5.2225,8.9511	benign	1324/1364	180030313	1164,11840	2202	4300	6502	SO:0001583	missense	2324	exon30			GCCCCCCGCTCAG	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3971G>T	5.37:g.180030313C>A	ENSP00000261937:p.Arg1324Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	120	49	0.408333	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	124	0.056776556776556776	24	0.04878048780487805	26	0.0718232044198895	0	0.0	74	0.09762532981530343	C	6.173	0.400048	0.11696	0.052225	0.108605	ENSG00000037280	ENST00000261937	T	0.74632	-0.86	4.41	-8.82	0.00810	.	.	.	.	.	T	0.01124	0.0037	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.07520	-1.0768	8	0.41790	T	0.15	.	2.0121	0.03490	0.161:0.3731:0.1746:0.2913	rs307821;rs1309976	1324	P35916	VGFR3_HUMAN	L	1324	ENSP00000261937:R1324L	ENSP00000261937:R1324L	R	-	2	0	FLT4	179962919	0.000000	0.05858	0.000000	0.03702	0.260000	0.26232	-2.138000	0.01303	-2.673000	0.00413	-0.724000	0.03597	CGG	C|0.922;A|0.078	0.078	strong		0.652	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
OSBPL10	114884	hgsc.bcm.edu	37	3	31712393	31712393	+	Silent	SNP	C	C	T	rs3749405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:31712393C>T	ENST00000396556.2	-	9	1931	c.1809G>A	c.(1807-1809)ccG>ccA	p.P603P	OSBPL10_ENST00000438237.2_Silent_p.P539P	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	603					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		GCTCCACCCACGGGATGGTGA	0.567													T|||	2832	0.565495	0.854	0.4107	5008	,	,		20776	0.6756		0.3728	False		,,,				2504	0.3701				p.P603P		Atlas-SNP	.											OSBPL10_ENST00000396556,extremity,malignant_melanoma,-1,6	OSBPL10	160	6	0			c.G1809A						PASS	.	T	,	3339,1067	389.1+/-327.2	1266,807,130	134.0	118.0	123.0		1617,1809	-10.9	0.0	3	dbSNP_107	123	3086,5514	659.5+/-401.7	533,2020,1747	no	coding-synonymous,coding-synonymous	OSBPL10	NM_001174060.1,NM_017784.4	,	1799,2827,1877	TT,TC,CC		35.8837,24.217,49.4003	,	539/701,603/765	31712393	6425,6581	2203	4300	6503	SO:0001819	synonymous_variant	114884	exon9			CACCCACGGGATG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1809G>A	3.37:g.31712393C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	NM_017784	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1	1223	0.559981684981685	412	0.8373983739837398	150	0.4143646408839779	379	0.6625874125874126	282	0.3720316622691293	T	0.057	-1.232567	0.01505	0.75783	0.358837	ENSG00000144645	ENST00000429492	.	.	.	5.47	-10.9	0.00192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999976	.	.	.	.	.	.	T	0.24440	-1.0160	3	.	.	.	-18.8515	1.9525	0.03370	0.1631:0.2346:0.2062:0.396	rs3749405;rs17383168;rs17849743;rs3749405	.	.	.	H	372	.	.	R	-	2	0	OSBPL10	31687397	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-6.416000	0.00067	-6.038000	0.00007	-2.931000	0.00088	CGT	C|0.470;T|0.530	0.530	strong		0.567	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
OSBPL10	114884	hgsc.bcm.edu	37	3	31789582	31789582	+	Missense_Mutation	SNP	T	T	C	rs2290532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:31789582T>C	ENST00000396556.2	-	5	882	c.760A>G	c.(760-762)Aac>Gac	p.N254D	OSBPL10_ENST00000438237.2_Missense_Mutation_p.N190D|OSBPL10_ENST00000467647.1_5'UTR	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	254			N -> D (in dbSNP:rs2290532).		lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		TGCACAAGGTTCTTCTGCTGC	0.587													T|||	2141	0.427516	0.0461	0.5576	5008	,	,		17939	0.7401		0.4404	False		,,,				2504	0.5153				p.N254D		Atlas-SNP	.											.	OSBPL10	160	.	0			c.A760G						PASS	.	T	ASP/ASN,ASP/ASN	511,3895	235.5+/-248.0	30,451,1722	66.0	52.0	57.0		568,760	4.5	1.0	3	dbSNP_100	57	3774,4826	531.3+/-382.0	825,2124,1351	yes	missense,missense	OSBPL10	NM_001174060.1,NM_017784.4	23,23	855,2575,3073	CC,CT,TT		43.8837,11.5978,32.9463	benign,benign	190/701,254/765	31789582	4285,8721	2203	4300	6503	SO:0001583	missense	114884	exon5			CAAGGTTCTTCTG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.760A>G	3.37:g.31789582T>C	ENSP00000379804:p.Asn254Asp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	1001	0.4583333333333333	27	0.054878048780487805	190	0.5248618784530387	445	0.777972027972028	339	0.4472295514511873	T	13.65	2.299228	0.40694	0.115978	0.438837	ENSG00000144645	ENST00000396556;ENST00000438237;ENST00000428241	T;T;T	0.40756	1.02;1.02;1.02	5.63	4.48	0.54585	.	0.186293	0.56097	D	0.000023	T	0.00012	0.0000	L	0.33668	1.02	0.32366	P	0.556513	D;B;B	0.63046	0.992;0.011;0.011	P;B;B	0.53360	0.724;0.006;0.009	T	0.11842	-1.0571	9	0.07325	T	0.83	-24.1001	11.4451	0.50118	0.0:0.0702:0.0:0.9298	rs2290532;rs17451508;rs52825393;rs59854988;rs2290532	190;254;22	B4E212;Q9BXB5;Q59ED9	.;OSB10_HUMAN;.	D	254;190;62	ENSP00000379804:N254D;ENSP00000406124:N190D;ENSP00000399200:N62D	ENSP00000379804:N254D	N	-	1	0	OSBPL10	31764586	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	5.965000	0.70387	0.966000	0.38159	0.459000	0.35465	AAC	C|0.372;N|0.000	0.372	strong		0.587	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
TRAIP	10293	hgsc.bcm.edu	37	3	49866584	49866584	+	Silent	SNP	T	T	G	rs35129566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49866584T>G	ENST00000331456.2	-	15	1475	c.1362A>C	c.(1360-1362)acA>acC	p.T454T		NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	454	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GAGAAGGCACTGTCTTCACCC	0.537													T|||	677	0.135184	0.2746	0.1412	5008	,	,		22461	0.0129		0.166	False		,,,				2504	0.0368				p.T454T		Atlas-SNP	.											.	TRAIP	47	.	0			c.A1362C						PASS	.	T		1155,3251	408.9+/-334.8	145,865,1193	266.0	195.0	219.0		1362	1.3	0.0	3	dbSNP_126	219	1579,7021	295.0+/-302.2	141,1297,2862	no	coding-synonymous	TRAIP	NM_005879.2		286,2162,4055	GG,GT,TT		18.3605,26.2143,21.0211		454/470	49866584	2734,10272	2203	4300	6503	SO:0001819	synonymous_variant	10293	exon15			AGGCACTGTCTTC	BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"""RING-type (C3HC4) zinc fingers"""	30764	protein-coding gene	gene with protein product	"""ring finger protein 206"""	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.1362A>C	3.37:g.49866584T>G		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	207	111	0.536232	NM_005879	B5BU84|B5BUL3|O00467	Silent	SNP	ENST00000331456.2	37	CCDS2806.1																																																																																			T|0.809;G|0.191	0.191	strong		0.537	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879	
LRRK2	120892	hgsc.bcm.edu	37	12	40742254	40742254	+	Silent	SNP	G	G	A	rs10878405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:40742254G>A	ENST00000298910.7	+	43	6382	c.6324G>A	c.(6322-6324)gaG>gaA	p.E2108E		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2108	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CTATGGTTGAGAAATTAATTA	0.308													G|||	1371	0.273762	0.1241	0.2349	5008	,	,		14989	0.3383		0.3231	False		,,,				2504	0.3865				p.E2108E		Atlas-SNP	.											.	LRRK2	763	.	0			c.G6324A						PASS	.	G		646,3760	272.8+/-271.0	46,554,1603	87.0	86.0	86.0		6324	3.2	1.0	12	dbSNP_120	86	2684,5914	427.6+/-355.6	408,1868,2023	no	coding-synonymous	LRRK2	NM_198578.3		454,2422,3626	AA,AG,GG		31.2166,14.6618,25.6075		2108/2528	40742254	3330,9674	2203	4299	6502	SO:0001819	synonymous_variant	120892	exon43			GGTTGAGAAATTA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6324G>A	12.37:g.40742254G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																			G|0.735;A|0.265	0.265	strong		0.308	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
SLC19A1	6573	hgsc.bcm.edu	37	21	46957794	46957794	+	Missense_Mutation	SNP	T	T	C	rs1051266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46957794T>C	ENST00000311124.4	-	2	232	c.80A>G	c.(79-81)cAc>cGc	p.H27R	SLC19A1_ENST00000567670.1_Missense_Mutation_p.H27R|SLC19A1_ENST00000380010.4_Missense_Mutation_p.H27R	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	27			H -> R (in dbSNP:rs1051266). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7615551, ECO:0000269|PubMed:7641195, ECO:0000269|PubMed:7826387, ECO:0000269|Ref.6}.		folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	GCACACGAGGTGCCGCCAGGA	0.657													C|||	2447	0.488618	0.3268	0.5821	5008	,	,		11906	0.4742		0.5487	False		,,,				2504	0.5941				p.H27R		Atlas-SNP	.											.	SLC19A1	53	.	0			c.A80G	GRCh37	CM004369	SLC19A1	M	rs1051266	PASS	.	C	ARG/HIS,ARG/HIS	1717,2669		358,1001,834	47.0	36.0	40.0		80,80	2.8	0.2	21	dbSNP_86	40	4894,3700		1416,2062,819	yes	missense,missense	SLC19A1	NM_001205206.1,NM_194255.2	29,29	1774,3063,1653	CC,CT,TT		43.0533,39.1473,49.0678	benign,benign	27/490,27/592	46957794	6611,6369	2193	4297	6490	SO:0001583	missense	6573	exon2			ACGAGGTGCCGCC	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"""Solute carriers"""	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.80A>G	21.37:g.46957794T>C	ENSP00000308895:p.His27Arg	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_001205206	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	37	CCDS13725.1	1073	0.4913003663003663	171	0.3475609756097561	205	0.5662983425414365	269	0.47027972027972026	428	0.5646437994722955	C	4.113	0.019156	0.08006	0.391473	0.569467	ENSG00000173638	ENST00000311124;ENST00000380010;ENST00000427839;ENST00000443742;ENST00000528477	T;T;T;T;D	0.85171	-1.39;-1.39;0.36;0.36;-1.95	3.85	2.77	0.32553	Major facilitator superfamily domain, general substrate transporter (1);	1.430790	0.04629	N	0.403225	T	0.00012	0.0000	N	0.00841	-1.15	0.24554	P	0.99400732	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34079	-0.9843	9	0.23891	T	0.37	-11.6327	4.7202	0.12915	0.4069:0.4723:0.0:0.1207	rs1051266;rs3171496;rs17844977;rs17857726;rs61510559;rs1051266	49;27;27	D3DSM6;E9PFY4;P41440	.;.;S19A1_HUMAN	R	27	ENSP00000308895:H27R;ENSP00000369347:H27R;ENSP00000401850:H27R;ENSP00000411345:H27R;ENSP00000435780:H27R	ENSP00000308895:H27R	H	-	2	0	SLC19A1	45782222	0.827000	0.29292	0.164000	0.22755	0.036000	0.12997	1.608000	0.36847	0.766000	0.33244	-0.197000	0.12766	CAC	T|0.518;C|0.482	0.482	strong		0.657	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155241735	155241735	+	Missense_Mutation	SNP	C	C	T	rs79535970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155241735C>T	ENST00000357232.4	-	14	3450	c.3451G>A	c.(3451-3453)Gca>Aca	p.A1151T		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1151	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ACTATTTGTGCTGTCAGTGAT	0.473													C|||	98	0.0195687	0.0023	0.0288	5008	,	,		21213	0.0		0.0706	False		,,,				2504	0.0041				p.A1151T		Atlas-SNP	.											.	DCHS2	594	.	0			c.G3451A						PASS	.	C	THR/ALA	52,4354	52.3+/-87.9	1,50,2152	190.0	184.0	186.0		3451	5.6	0.0	4	dbSNP_131	186	557,8043	151.9+/-206.6	16,525,3759	yes	missense	DCHS2	NM_017639.3	58	17,575,5911	TT,TC,CC		6.4767,1.1802,4.6825	probably-damaging	1151/2917	155241735	609,12397	2203	4300	6503	SO:0001583	missense	54798	exon14			TTTGTGCTGTCAG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.3451G>A	4.37:g.155241735C>T	ENSP00000349768:p.Ala1151Thr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	71	0.03250915750915751	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	57	0.07519788918205805	C	25.7	4.666544	0.88251	0.011802	0.064767	ENSG00000197410	ENST00000357232	T	0.61158	0.13	5.59	5.59	0.84812	Cadherin (3);Cadherin-like (1);	0.175226	0.38778	N	0.001569	T	0.21550	0.0519	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.63242	-0.6681	10	0.51188	T	0.08	.	19.5985	0.95549	0.0:1.0:0.0:0.0	.	1151	Q6V1P9	PCD23_HUMAN	T	1151	ENSP00000349768:A1151T	ENSP00000349768:A1151T	A	-	1	0	DCHS2	155461185	0.998000	0.40836	0.047000	0.18901	0.893000	0.52053	7.487000	0.81328	2.636000	0.89361	0.563000	0.77884	GCA	C|0.959;T|0.041	0.041	strong		0.473	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
UMODL1	89766	hgsc.bcm.edu	37	21	43557698	43557698	+	Missense_Mutation	SNP	A	A	C	rs3819142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43557698A>C	ENST00000408910.2	+	22	3925	c.3925A>C	c.(3925-3927)Aac>Cac	p.N1309H	UMODL1_ENST00000400424.2_Missense_Mutation_p.N1237H|UMODL1_ENST00000408989.2_Missense_Mutation_p.N1437H|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400427.1_Missense_Mutation_p.N1365H	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1309			N -> H (in dbSNP:rs3819142). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15194491, ECO:0000269|PubMed:16026467}.		adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						AATCCAGTCCAACAACTTCAG	0.552													A|||	1105	0.220647	0.1452	0.245	5008	,	,		15859	0.256		0.1769	False		,,,				2504	0.3139				p.N1437H	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.A4309C						PASS	.	A	HIS/ASN,HIS/ASN,HIS/ASN,HIS/ASN	640,3448		53,534,1457	106.0	108.0	107.0		3925,4093,3709,4309	1.2	0.0	21	dbSNP_107	107	1507,6873		133,1241,2816	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	68,68,68,68	186,1775,4273	CC,CA,AA		17.9833,15.6556,17.2201	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1309/1319,1365/1375,1237/1247,1437/1447	43557698	2147,10321	2044	4190	6234	SO:0001583	missense	89766	exon21			CAGTCCAACAACT		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.3925A>C	21.37:g.43557698A>C	ENSP00000386147:p.Asn1309His	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	402	0.18406593406593408	61	0.12398373983739837	75	0.20718232044198895	134	0.23426573426573427	132	0.1741424802110818	A	9.441	1.088116	0.20390	0.156556	0.179833	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.72505	-0.66;-0.64;-0.66;-0.65	3.03	1.19	0.21007	.	0.518994	0.15619	N	0.253004	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P	0.43287	0.681;0.802	B;B	0.31245	0.126;0.116	T	0.07046	-1.0793	8	.	.	.	-15.1051	7.5416	0.27742	0.2168:0.0:0.7832:0.0	rs3819142;rs52825619;rs57468422;rs3819142	1437;1309	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	H	1365;1237;1437;1309	ENSP00000383279:N1365H;ENSP00000383276:N1237H;ENSP00000386126:N1437H;ENSP00000386147:N1309H	.	N	+	1	0	UMODL1	42430767	0.215000	0.23574	0.011000	0.14972	0.004000	0.04260	2.218000	0.42889	0.336000	0.23639	-1.098000	0.02139	AAC	A|0.810;C|0.190	0.190	strong		0.552	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
TROAP	10024	hgsc.bcm.edu	37	12	49723963	49723963	+	Silent	SNP	A	A	G	rs4243545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49723963A>G	ENST00000257909.3	+	13	1411	c.1335A>G	c.(1333-1335)gaA>gaG	p.E445E	TROAP_ENST00000547923.1_Silent_p.E153E|TROAP_ENST00000551245.1_Silent_p.E445E	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	445					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)		p.E445E(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						TGAGACAGGAAGTAGAGGGGC	0.532													G|||	972	0.194089	0.4123	0.1138	5008	,	,		19065	0.0407		0.1531	False		,,,				2504	0.1564				p.E445E		Atlas-SNP	.											TROAP,NS,carcinoma,0,1	TROAP	80	1	1	Substitution - coding silent(1)	stomach(1)	c.A1335G						PASS	.	G		1686,2720	629.2+/-395.2	314,1058,831	105.0	110.0	108.0		1335	1.6	0.8	12	dbSNP_111	108	1408,7188	725.2+/-406.5	122,1164,3012	no	coding-synonymous	TROAP	NM_005480.3		436,2222,3843	GG,GA,AA		16.3797,38.266,23.7963		445/779	49723963	3094,9908	2203	4298	6501	SO:0001819	synonymous_variant	10024	exon13			ACAGGAAGTAGAG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.1335A>G	12.37:g.49723963A>G		Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	264	134	0.507576	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Silent	SNP	ENST00000257909.3	37	CCDS8784.1																																																																																			A|0.789;G|0.211	0.211	strong		0.532	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
CEP104	9731	hgsc.bcm.edu	37	1	3753136	3753136	+	Missense_Mutation	SNP	A	A	T	rs2275824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:3753136A>T	ENST00000378230.3	-	10	1564	c.1240T>A	c.(1240-1242)Tta>Ata	p.L414I	CEP104_ENST00000460038.1_Intron	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	414			L -> I (in dbSNP:rs2275824).			centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						GGCTCCCCTAACATGCCTCCC	0.498													A|||	1516	0.302716	0.0605	0.487	5008	,	,		15252	0.3383		0.4284	False		,,,				2504	0.3333				p.L414I		Atlas-SNP	.											.	CEP104	79	.	0			c.T1240A						PASS	.	A	ILE/LEU	547,3859	248.1+/-256.1	35,477,1691	117.0	100.0	106.0		1240	-3.2	0.0	1	dbSNP_100	106	3732,4868	532.3+/-382.2	811,2110,1379	yes	missense	CEP104	NM_014704.3	5	846,2587,3070	TT,TA,AA		43.3953,12.4149,32.9002	benign	414/926	3753136	4279,8727	2203	4300	6503	SO:0001583	missense	9731	exon10			CCCCTAACATGCC	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"""glycine, glutamate, thienylcyclohexylpiperidine binding protein"""		"""KIAA0562"""	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.1240T>A	1.37:g.3753136A>T	ENSP00000367476:p.Leu414Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	732	0.33516483516483514	43	0.08739837398373984	164	0.4530386740331492	201	0.3513986013986014	324	0.42744063324538256	A	13.24	2.178767	0.38511	0.124149	0.433953	ENSG00000116198	ENST00000378230;ENST00000443466	T;T	0.16324	2.35;2.35	5.68	-3.25	0.05079	.	1.068090	0.07236	N	0.863386	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B	0.17465	0.021;0.022	B;B	0.17433	0.018;0.008	T	0.49031	-0.8981	9	0.28530	T	0.3	.	2.5751	0.04804	0.3497:0.3628:0.0785:0.209	rs2275824;rs52833684;rs2275824	414;414	O60308-3;O60308	.;CE104_HUMAN	I	414;108	ENSP00000367476:L414I;ENSP00000411927:L108I	ENSP00000367476:L414I	L	-	1	2	CEP104	3742996	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.281000	0.08456	-0.328000	0.08539	0.528000	0.53228	TTA	A|0.664;T|0.336	0.336	strong		0.498	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704	
NUCB2	4925	hgsc.bcm.edu	37	11	17351683	17351683	+	Missense_Mutation	SNP	C	C	G	rs757081	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:17351683C>G	ENST00000529010.1	+	12	1231	c.1012C>G	c.(1012-1014)Cag>Gag	p.Q338E	NUCB2_ENST00000458064.2_Missense_Mutation_p.Q308E|NUCB2_ENST00000323688.6_Missense_Mutation_p.Q338E	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	338	Binds to necdin. {ECO:0000250}.		Q -> E (in dbSNP:rs757081).			cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						GACATTAGATCAGCAACAGTT	0.284													C|||	1191	0.237819	0.0182	0.2795	5008	,	,		16337	0.3552		0.3111	False		,,,				2504	0.3088				p.Q338E		Atlas-SNP	.											.	NUCB2	31	.	0			c.C1012G						PASS	.	C	GLU/GLN	210,3390		5,200,1595	20.0	18.0	18.0		1012	5.7	1.0	11	dbSNP_86	18	2604,5522		412,1780,1871	yes	missense	NUCB2	NM_005013.2	29	417,1980,3466	GG,GC,CC		32.0453,5.8333,23.998	benign	338/421	17351683	2814,8912	1800	4063	5863	SO:0001583	missense	4925	exon12			TTAGATCAGCAAC	AF052642	CCDS41623.1	11p15.1	2013-01-10						"""EF-hand domain containing"""	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.1012C>G	11.37:g.17351683C>G	ENSP00000436455:p.Gln338Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_005013	A8K642|D3DQX5|Q8NFT5	Missense_Mutation	SNP	ENST00000529010.1	37	CCDS41623.1	560|560	0.2564102564102564|0.2564102564102564	14|14	0.028455284552845527|0.028455284552845527	101|101	0.27900552486187846|0.27900552486187846	220|220	0.38461538461538464|0.38461538461538464	225|225	0.29683377308707126|0.29683377308707126	C|C	11.12|11.12	1.546059|1.546059	0.27652|0.27652	0.058333|0.058333	0.320453|0.320453	ENSG00000070081|ENSG00000070081	ENST00000323688;ENST00000529010;ENST00000458064|ENST00000527580	T;T;T|.	0.17370|.	2.38;2.38;2.28|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.209202|.	0.51477|.	D|.	0.000092|.	T|.	0.00012|.	0.0000|.	L|L	0.39566|0.39566	1.225|1.225	0.19300|0.19300	P|P	0.9999784196|0.9999784196	B;B|.	0.21309|.	0.004;0.054|.	B;B|.	0.24006|.	0.007;0.05|.	T|.	0.35871|.	-0.9771|.	9|.	0.11794|.	T|.	0.64|.	-4.6078|-4.6078	15.3316|15.3316	0.74215|0.74215	0.0:0.8608:0.1392:0.0|0.0:0.8608:0.1392:0.0	rs757081;rs52826791;rs757081|rs757081;rs52826791;rs757081	308;338|.	E7EV42;P80303|.	.;NUCB2_HUMAN|.	E|X	338;338;308|115	ENSP00000320168:Q338E;ENSP00000436455:Q338E;ENSP00000408702:Q308E|.	ENSP00000320168:Q338E|.	Q|S	+|+	1|2	0|0	NUCB2|NUCB2	17308259|17308259	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	3.992000|3.992000	0.56980|0.56980	2.692000|2.692000	0.91855|0.91855	0.655000|0.655000	0.94253|0.94253	CAG|TCA	C|0.738;G|0.262	0.262	strong		0.284	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013	
AZGP1	563	hgsc.bcm.edu	37	7	99569394	99569394	+	Silent	SNP	G	G	A	rs17295356	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99569394G>A	ENST00000292401.4	-	2	448	c.312C>T	c.(310-312)atC>atT	p.I104I	AZGP1_ENST00000411734.1_Silent_p.I101I	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	104					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					AATACTCCACGATGTCTTTCA	0.532													G|||	1875	0.374401	0.0734	0.4885	5008	,	,		18963	0.6409		0.4105	False		,,,				2504	0.3885				p.I104I		Atlas-SNP	.											.	AZGP1	41	.	0			c.C312T						PASS	.	G		587,3819	258.9+/-262.7	40,507,1656	164.0	134.0	144.0		312	1.5	0.6	7	dbSNP_123	144	3376,5224	500.0+/-375.1	682,2012,1606	no	coding-synonymous	AZGP1	NM_001185.3		722,2519,3262	AA,AG,GG		39.2558,13.3227,30.4706		104/299	99569394	3963,9043	2203	4300	6503	SO:0001819	synonymous_variant	563	exon2			CTCCACGATGTCT	BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"""Immunoglobulin superfamily / C1-set domain containing"""	910	protein-coding gene	gene with protein product		194460	"""alpha-2-glycoprotein 1, zinc"""			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.312C>T	7.37:g.99569394G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	141	69	0.489362	NM_001185	D6W5T8|O60386|Q5XKQ4|Q8N4N0	Silent	SNP	ENST00000292401.4	37	CCDS5680.1																																																																																			G|0.657;A|0.343	0.343	strong		0.532	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4	NM_001185	
EIF2S3	1968	hgsc.bcm.edu	37	X	24075862	24075862	+	Missense_Mutation	SNP	A	A	G	rs16997659	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:24075862A>G	ENST00000253039.4	+	4	627	c.374A>G	c.(373-375)aAa>aGa	p.K125R		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	125	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.		K -> R (in dbSNP:rs16997659).		cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						GGGAACTTCAAATTAGTCAGG	0.423													A|||	386	0.102252	0.0219	0.1023	3775	,	,		11437	0.006		0.1123	False		,,,				2504	0.1708				p.K125R		Atlas-SNP	.											.	EIF2S3	31	.	0			c.A374G						PASS	.	A	ARG/LYS	146,3689		3,125,15,1504,556	62.0	59.0	60.0		374	3.8	1.0	X	dbSNP_123	60	1077,5651		59,671,288,1698,1584	yes	missense	EIF2S3	NM_001415.3	26	62,796,303,3202,2140	GG,GA,G,AA,A		16.0077,3.807,11.5782	benign	125/473	24075862	1223,9340	2203	4300	6503	SO:0001583	missense	1968	exon4			ACTTCAAATTAGT	L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"""eukaryotic translation initiation factor 2G"""	300161	"""eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"""	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.374A>G	X.37:g.24075862A>G	ENSP00000253039:p.Lys125Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001415	B5BTZ4	Missense_Mutation	SNP	ENST00000253039.4	37	CCDS14210.1	142	0.08559373116335142	7	0.014644351464435146	27	0.07758620689655173	2	0.0035087719298245615	61	0.08739255014326648	A	10.25	1.297530	0.23650	0.03807	0.160077	ENSG00000130741	ENST00000253039	T	0.70986	-0.53	5.02	3.85	0.44370	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	T	0.00300	0.0009	.	.	.	0.21950	P	0.999451154	B	0.02656	0.0	B	0.10450	0.005	T	0.06570	-1.0819	8	0.18276	T	0.48	.	10.0729	0.42343	0.9192:0.0:0.0808:0.0	rs16997659;rs16997659	125	P41091	IF2G_HUMAN	R	125	ENSP00000253039:K125R	ENSP00000253039:K125R	K	+	2	0	EIF2S3	23985783	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	6.988000	0.76212	0.675000	0.31264	0.412000	0.27726	AAA	A|0.888;0|0.013	.	strong		0.423	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415	
ITGA3	3675	hgsc.bcm.edu	37	17	48158685	48158685	+	Silent	SNP	C	C	T	rs55893410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48158685C>T	ENST00000320031.8	+	23	3162	c.2832C>T	c.(2830-2832)gaC>gaT	p.D944D	ITGA3_ENST00000007722.7_Silent_p.D944D	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	944					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						ATTACAGAGACTTTGACCGAG	0.562													C|||	401	0.0800719	0.1868	0.0994	5008	,	,		18324	0.0179		0.0229	False		,,,				2504	0.045				p.D944D		Atlas-SNP	.											.	ITGA3	128	.	0			c.C2832T						PASS	.	C	,	746,3658		64,618,1520	75.0	57.0	63.0		2832,2832	3.3	1.0	17	dbSNP_129	63	243,8355		4,235,4060	no	coding-synonymous,coding-synonymous	ITGA3	NM_002204.2,NM_005501.2	,	68,853,5580	TT,TC,CC		2.8262,16.9391,7.6065	,	944/1052,944/1067	48158685	989,12013	2202	4299	6501	SO:0001819	synonymous_variant	3675	exon23			CAGAGACTTTGAC	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.2832C>T	17.37:g.48158685C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	37	CCDS11558.1																																																																																			C|0.929;T|0.071	0.071	strong		0.562	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
PARP14	54625	hgsc.bcm.edu	37	3	122419210	122419210	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122419210T>C	ENST00000474629.2	+	6	2075	c.1809T>C	c.(1807-1809)gtT>gtC	p.V603V		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	603					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GCATTGAAGTTGAGAACAAAG	0.393																																					p.V603V		Atlas-SNP	.											.	PARP14	242	.	0			c.T1809C						PASS	.						37.0	35.0	36.0					3																	122419210		1870	4093	5963	SO:0001819	synonymous_variant	54625	exon6			TGAAGTTGAGAAC	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1809T>C	3.37:g.122419210T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	72	16	0.222222	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																			.	.	none		0.393	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
ZBBX	79740	hgsc.bcm.edu	37	3	167035332	167035332	+	Missense_Mutation	SNP	T	T	C	rs34465133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167035332T>C	ENST00000392766.2	-	13	1377	c.1037A>G	c.(1036-1038)cAt>cGt	p.H346R	ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000307529.5_Missense_Mutation_p.H346R|ZBBX_ENST00000392764.1_Missense_Mutation_p.H317R|ZBBX_ENST00000455345.2_Missense_Mutation_p.H346R|ZBBX_ENST00000392767.2_Missense_Mutation_p.H346R	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	346			H -> R (in dbSNP:rs34465133).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						AGTGGTTTCATGTGGATGTGG	0.333													C|||	28	0.00559105	0.0008	0.0058	5008	,	,		17626	0.0		0.0229	False		,,,				2504	0.0				p.H346R		Atlas-SNP	.											.	ZBBX	299	.	0			c.A1037G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS	8,3698		0,8,1845	191.0	174.0	179.0		1037,950,1037	0.3	0.0	3	dbSNP_126	179	179,8009		1,177,3916	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	29,29,29	1,185,5761	CC,CT,TT		2.1861,0.2159,1.5722	benign,benign,benign	346/840,317/772,346/801	167035332	187,11707	1853	4094	5947	SO:0001583	missense	79740	exon13			GTTTCATGTGGAT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1037A>G	3.37:g.167035332T>C	ENSP00000376519:p.His346Arg	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	219	78	0.356164	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	26	0.011904761904761904	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	22	0.029023746701846966	C	7.094	0.572764	0.13623	0.002159	0.021861	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.08896	3.21;3.21;3.21;3.21;3.04	5.34	0.327	0.15913	.	0.965568	0.08617	N	0.919032	T	0.01287	0.0042	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47636	-0.9102	10	0.11182	T	0.66	3.6647	5.0072	0.14293	0.0:0.4377:0.1458:0.4165	rs34465133	346;346	A8MT70-2;A8MT70	.;ZBBX_HUMAN	R	346;346;346;346;317	ENSP00000376519:H346R;ENSP00000376520:H346R;ENSP00000390232:H346R;ENSP00000305065:H346R;ENSP00000376517:H317R	ENSP00000305065:H346R	H	-	2	0	ZBBX	168518026	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.546000	0.02188	-0.059000	0.13154	-0.128000	0.14901	CAT	T|0.987;C|0.013	0.013	strong		0.333	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971109	45971109	+	Missense_Mutation	SNP	G	G	A	rs200984587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45971109G>A	ENST00000391621.1	-	1	279	c.233C>T	c.(232-234)tCg>tTg	p.S78L	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	78	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CTGGCAGCACGAGGGCGTGCA	0.687																																					p.S78L		Atlas-SNP	.											KRTAP10-2,caecum,carcinoma,0,1	KRTAP10-2	21	1	0			c.C233T						scavenged	.																																			SO:0001583	missense	386679	exon1			CAGCACGAGGGCG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.233C>T	21.37:g.45971109G>A	ENSP00000375479:p.Ser78Leu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	117	27	0.230769	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	g	5.987	0.366047	0.11352	.	.	ENSG00000205445	ENST00000391621	T	0.01572	4.76	3.44	1.48	0.22813	.	.	.	.	.	T	0.03305	0.0096	M	0.87682	2.9	0.09310	N	1	B	0.22683	0.073	B	0.16289	0.015	T	0.40384	-0.9566	9	0.51188	T	0.08	.	2.1189	0.03721	0.1176:0.1948:0.4883:0.1993	.	78	P60368	KR102_HUMAN	L	78	ENSP00000375479:S78L	ENSP00000375479:S78L	S	-	2	0	KRTAP10-2	44795537	0.060000	0.20803	0.001000	0.08648	0.073000	0.16967	1.997000	0.40786	0.133000	0.18654	0.456000	0.33151	TCG	.	.	weak		0.687	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
ATXN1L	342371	hgsc.bcm.edu	37	16	71884430	71884430	+	Missense_Mutation	SNP	C	C	G	rs199599582		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:71884430C>G	ENST00000427980.2	+	3	1080	c.787C>G	c.(787-789)Ctg>Gtg	p.L263V	ATXN1L_ENST00000569119.1_Intron	NM_001137675.3	NP_001131147.1	P0C7T5	ATX1L_HUMAN	ataxin 1-like	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)	4						CCAGTCTGCTCTGGAAGCAGC	0.532																																					p.L263V		Atlas-SNP	.											.	ATXN1L	18	.	0			c.C787G						PASS	.	C	VAL/LEU	0,1384		0,0,692	35.0	36.0	36.0		787	5.2	1.0	16		36	2,3180		0,2,1589	yes	missense	ATXN1L	NM_001137675.2	32	0,2,2281	GG,GC,CC		0.0629,0.0,0.0438	benign	263/690	71884430	2,4564	692	1591	2283	SO:0001583	missense	342371	exon3			TCTGCTCTGGAAG		CCDS45523.1	16q22.2	2014-09-04			ENSG00000224470	ENSG00000224470			33279	protein-coding gene	gene with protein product	"""brother of ataxin 1"""	614301				16121196, 17322884, 21475249	Standard	NM_001137675		Approved	BOAT1	uc002fbd.3	P0C7T5	OTTHUMG00000176872	ENST00000427980.2:c.787C>G	16.37:g.71884430C>G	ENSP00000415822:p.Leu263Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_001137675		Missense_Mutation	SNP	ENST00000427980.2	37	CCDS45523.1	.	.	.	.	.	.	.	.	.	.	C	7.589	0.670309	0.14776	0.0	6.29E-4	ENSG00000224470	ENST00000427980	T	0.32023	1.47	5.25	5.25	0.73442	.	.	.	.	.	T	0.17109	0.0411	N	0.14661	0.345	0.28195	N	0.927604	B	0.30914	0.3	B	0.19666	0.026	T	0.06698	-1.0812	9	0.27082	T	0.32	.	11.2832	0.49208	0.0:0.9077:0.0:0.0923	.	263	P0C7T5	ATX1L_HUMAN	V	263	ENSP00000415822:L263V	ENSP00000415822:L263V	L	+	1	2	ATXN1L	70441931	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	0.900000	0.28431	2.631000	0.89168	0.555000	0.69702	CTG	.	.	weak		0.532	ATXN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434171.1	NM_001137675.2	
C12orf43	64897	hgsc.bcm.edu	37	12	121442214	121442214	+	Silent	SNP	G	G	A	rs3751150	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121442214G>A	ENST00000288757.3	-	6	553	c.531C>T	c.(529-531)atC>atT	p.I177I	C12orf43_ENST00000539736.1_Silent_p.I167I|C12orf43_ENST00000537817.1_Silent_p.I178I|C12orf43_ENST00000445832.3_Silent_p.I147I|C12orf43_ENST00000536407.2_Intron|C12orf43_ENST00000366211.2_Silent_p.I136I	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	177										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CAGGGCTGTGGATGGCTGACT	0.592													.|||	545	0.108826	0.0038	0.0663	5008	,	,		18827	0.251		0.1233	False		,,,				2504	0.1196				p.I177I		Atlas-SNP	.											.	C12orf43	30	.	0			c.C531T						PASS	.	G		130,4276	94.4+/-133.1	3,124,2076	117.0	132.0	127.0		531	1.4	1.0	12	dbSNP_107	127	1053,7547	221.7+/-259.0	65,923,3312	no	coding-synonymous	C12orf43	NM_022895.1		68,1047,5388	AA,AG,GG		12.2442,2.9505,9.0958		177/263	121442214	1183,11823	2203	4300	6503	SO:0001819	synonymous_variant	64897	exon6			GCTGTGGATGGCT	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.531C>T	12.37:g.121442214G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	149	70	0.469799	NM_022895	Q53HF0|Q9H9Z7	Silent	SNP	ENST00000288757.3	37	CCDS9210.1	255	0.11675824175824176	2	0.0040650406504065045	22	0.06077348066298342	134	0.23426573426573427	97	0.1279683377308707	G	1.261	-0.615723	0.03663	0.029505	0.122442	ENSG00000157895	ENST00000546272	.	.	.	5.73	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999324428	.	.	.	.	.	.	T	0.24657	-1.0154	3	.	.	.	-9.6331	3.5732	0.07925	0.1563:0.2909:0.4391:0.1138	rs3751150;rs17845432;rs17858304;rs3751150	.	.	.	F	131	.	.	S	-	2	0	C12orf43	119926597	0.993000	0.37304	0.994000	0.49952	0.030000	0.12068	0.373000	0.20484	0.322000	0.23283	-0.165000	0.13383	TCC	G|0.899;A|0.101	0.101	strong		0.592	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
LILRB3	11025	hgsc.bcm.edu	37	19	54726299	54726299	+	Missense_Mutation	SNP	A	A	C	rs80077296		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54726299A>C	ENST00000391750.1	-	4	342	c.206T>G	c.(205-207)tTg>tGg	p.L69W	LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000346401.6_Missense_Mutation_p.L69W|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000424807.1_Missense_Mutation_p.L69W|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.L69W|LILRA6_ENST00000440558.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	69	Ig-like C2-type 1.		L -> W (in dbSNP:rs620207).		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ATTTCTGTCCAAGGGCTCTGG	0.577																																					p.L69W		Atlas-SNP	.											.	LILRB3	67	.	0			c.T206G						PASS	.						43.0	61.0	55.0					19																	54726299		1940	3951	5891	SO:0001583	missense	11025	exon3			CTGTCCAAGGGCT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.206T>G	19.37:g.54726299A>C	ENSP00000375630:p.Leu69Trp	Somatic	514	0	0		WXS	Illumina HiSeq	Phase_I	531	159	0.299435	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.875472	0.00537	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000445347	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	3.08	0.16	0.14972	Immunoglobulin-like fold (1);	1.026710	0.07786	N	0.954165	T	0.02083	0.0065	N	0.00742	-1.23	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.08055	0.002;0.003	T	0.42899	-0.9424	9	0.02654	T	1	.	0.7419	0.00975	0.2133:0.3829:0.2094:0.1944	.	69;69	O75022;O75022-3	LIRB3_HUMAN;.	W	69	ENSP00000375630:L69W;ENSP00000412771:L69W;ENSP00000345184:L69W;ENSP00000245620:L69W;ENSP00000388199:L69W	ENSP00000245620:L69W	L	-	2	0	LILRB3	59418111	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.983000	0.01488	-0.123000	0.11745	-0.209000	0.12711	TTG	C|1.000;|0.000	1.000	weak		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
ASB1	51665	hgsc.bcm.edu	37	2	239353001	239353001	+	Silent	SNP	C	C	T	rs2290075	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:239353001C>T	ENST00000264607.4	+	4	760	c.513C>T	c.(511-513)gaC>gaT	p.D171D	ASB1_ENST00000409297.1_Silent_p.D70D	NM_001040445.1	NP_001035535.1	Q9Y576	ASB1_HUMAN	ankyrin repeat and SOCS box containing 1	171					intracellular signal transduction (GO:0035556)|male genitalia development (GO:0030539)|negative regulation of cytokine biosynthetic process (GO:0042036)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				breast(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		all_epithelial(40;2.65e-14)|Breast(86;7.61e-05)|Renal(207;0.00183)|all_lung(227;0.0283)|Ovarian(221;0.0365)|Lung NSC(271;0.0941)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)		CTGATGTTGACGTCAACCACC	0.582													C|||	425	0.0848642	0.1505	0.0173	5008	,	,		18357	0.0794		0.0417	False		,,,				2504	0.0941				p.D171D		Atlas-SNP	.											.	ASB1	25	.	0			c.C513T						PASS	.	C		599,3807	246.2+/-254.9	33,533,1637	61.0	49.0	53.0		513	-5.1	0.7	2	dbSNP_100	53	214,8386	84.5+/-147.0	1,212,4087	no	coding-synonymous	ASB1	NM_001040445.1		34,745,5724	TT,TC,CC		2.4884,13.5951,6.251		171/336	239353001	813,12193	2203	4300	6503	SO:0001819	synonymous_variant	51665	exon4			TGTTGACGTCAAC	AF156777	CCDS33416.1	2q37	2013-01-10	2011-01-25		ENSG00000065802	ENSG00000065802		"""Ankyrin repeat domain containing"""	16011	protein-coding gene	gene with protein product		605758	"""ankyrin repeat and SOCS box-containing 1"""				Standard	XR_241235		Approved	ASB-1	uc002vyg.3	Q9Y576	OTTHUMG00000152866	ENST00000264607.4:c.513C>T	2.37:g.239353001C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_001040445	A6NL50|Q4ZG29|Q9ULS4	Silent	SNP	ENST00000264607.4	37	CCDS33416.1																																																																																			C|0.937;T|0.063	0.063	strong		0.582	ASB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328294.1	NM_001040445	
KLF3	51274	hgsc.bcm.edu	37	4	38696385	38696385	+	Silent	SNP	C	C	T	rs142916199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38696385C>T	ENST00000261438.5	+	5	1019	c.714C>T	c.(712-714)atC>atT	p.I238I		NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	238	Pro-rich.				cellular response to peptide (GO:1901653)|multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18						CTTCGGTCATCGTGCAGCCTG	0.458													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19533	0.0		0.001	False		,,,				2504	0.0				p.I238I		Atlas-SNP	.											.	KLF3	40	.	0			c.C714T						PASS	.	C		0,4406		0,0,2203	137.0	135.0	136.0		714	-12.3	0.3	4	dbSNP_134	136	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	KLF3	NM_016531.5		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		238/346	38696385	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	51274	exon5			GGTCATCGTGCAG	AF285837	CCDS3444.1	4p16.1-p15.2	2013-01-08			ENSG00000109787	ENSG00000109787		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	16516	protein-coding gene	gene with protein product	"""basic Kruppel-like factor"""	609392				18391014	Standard	NM_016531		Approved	BKLF	uc003gth.4	P57682	OTTHUMG00000097821	ENST00000261438.5:c.714C>T	4.37:g.38696385C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Silent	SNP	ENST00000261438.5	37	CCDS3444.1																																																																																			C|0.999;T|0.001	0.001	strong		0.458	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2		
TSKS	60385	hgsc.bcm.edu	37	19	50251422	50251422	+	Missense_Mutation	SNP	C	C	T	rs34701020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50251422C>T	ENST00000246801.3	-	4	581	c.499G>A	c.(499-501)Gag>Aag	p.E167K	TSKS_ENST00000358830.3_5'Flank	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	167			E -> K (in dbSNP:rs34701020).		negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		ACAGAACACTCGCTCTGGAGC	0.557													C|||	164	0.0327476	0.0545	0.0144	5008	,	,		20009	0.001		0.0239	False		,,,				2504	0.0583				p.E167K		Atlas-SNP	.											.	TSKS	97	.	0			c.G499A						PASS	.	C	LYS/GLU	183,4223	116.3+/-154.2	4,175,2024	129.0	108.0	115.0		499	4.6	1.0	19	dbSNP_126	115	235,8365	95.4+/-157.2	3,229,4068	yes	missense	TSKS	NM_021733.1	56	7,404,6092	TT,TC,CC		2.7326,4.1534,3.2139	benign	167/593	50251422	418,12588	2203	4300	6503	SO:0001583	missense	60385	exon4			AACACTCGCTCTG	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.499G>A	19.37:g.50251422C>T	ENSP00000246801:p.Glu167Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	50	0.022893772893772892	30	0.06097560975609756	6	0.016574585635359115	1	0.0017482517482517483	13	0.017150395778364115	C	12.09	1.833424	0.32421	0.041534	0.027326	ENSG00000126467	ENST00000246801	T	0.72505	-0.66	5.6	4.57	0.56435	.	0.259880	0.27846	N	0.017613	T	0.11024	0.0269	N	0.17082	0.46	0.80722	D	1	B	0.18013	0.025	B	0.11329	0.006	T	0.13442	-1.0509	10	0.39692	T	0.17	-28.8819	10.6997	0.45920	0.0:0.9115:0.0:0.0885	rs34701020;rs57691185	167	Q9UJT2	TSKS_HUMAN	K	167	ENSP00000246801:E167K	ENSP00000246801:E167K	E	-	1	0	TSKS	54943234	0.978000	0.34361	0.969000	0.41365	0.284000	0.27059	2.556000	0.45862	1.376000	0.46267	-0.448000	0.05591	GAG	C|0.971;T|0.029	0.029	strong		0.557	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
MED13	9969	hgsc.bcm.edu	37	17	60038404	60038404	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:60038404T>C	ENST00000397786.2	-	23	5380	c.5304A>G	c.(5302-5304)ccA>ccG	p.P1768P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1768					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGTCCTTCACTGGAGCCAGAA	0.338																																					p.P1768P		Atlas-SNP	.											MED13,NS,carcinoma,-1,1	MED13	181	1	0			c.A5304G						PASS	.						112.0	97.0	102.0					17																	60038404		1828	4074	5902	SO:0001819	synonymous_variant	9969	exon23			CTTCACTGGAGCC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.5304A>G	17.37:g.60038404T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	37	CCDS42366.1																																																																																			.	.	none		0.338	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
CENPN	55839	hgsc.bcm.edu	37	16	81056441	81056441	+	Intron	SNP	T	T	G	rs3743503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81056441T>G	ENST00000305850.5	+	7	1423				RP11-303E16.3_ENST00000561808.1_RNA|CENPN_ENST00000439957.3_Intron|RP11-303E16.3_ENST00000566390.1_RNA|CENPN_ENST00000428963.2_Intron|RP11-303E16.3_ENST00000562315.1_RNA|CMC2_ENST00000565914.1_5'Flank|CENPN_ENST00000299572.5_Nonstop_Mutation_p.*205E|CENPN_ENST00000393335.3_Intron	NM_001100624.2|NM_001270474.1	NP_001094094.2|NP_001257403.1	Q96H22	CENPN_HUMAN	centromere protein N						CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|large_intestine(5)|lung(4)	10						AGCTTGCAATTAGTGAACATG	0.338													t|||	664	0.132588	0.0658	0.1369	5008	,	,		17491	0.2063		0.1262	False		,,,				2504	0.1503				p.X205E		Atlas-SNP	.											.	CENPN	84	.	0			c.T613G						PASS	.	T	,,GLU/stop	295,4109	149.9+/-184.0	8,279,1915	54.0	58.0	56.0		,,613	-8.3	0.0	16	dbSNP_107	56	1003,7597	211.8+/-252.3	66,871,3363	yes	intron,intron,stop-lost	CENPN	NM_001100624.1,NM_001100625.1,NM_018455.4	,,	74,1150,5278	GG,GT,TT		11.6628,6.6985,9.9815	,,	,,205/205	81056441	1298,11706	2202	4300	6502	SO:0001627	intron_variant	55839	exon7			TGCAATTAGTGAA	AK026313	CCDS10931.1, CCDS42199.1, CCDS42200.1, CCDS58482.1, CCDS58483.1	16q23.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000166451	ENSG00000166451			30873	protein-coding gene	gene with protein product		611509	"""chromosome 16 open reading frame 60"""	C16orf60		16622419	Standard	NM_001100625		Approved	FLJ13607, FLJ22660, BM039	uc002ffy.4	Q96H22	OTTHUMG00000137628	ENST00000305850.5:c.633+138T>G	16.37:g.81056441T>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_018455	A8MZE6|B3KN53|B4DJD1|B4DPY7|C9JJM5|D3DUK8|E7ES30|E7ETS3|Q9NZ83	Missense_Mutation	SNP	ENST00000305850.5	37	CCDS42200.1	312	0.14285714285714285	36	0.07317073170731707	54	0.14917127071823205	121	0.21153846153846154	101	0.13324538258575197	T	0.869	-0.732616	0.03135	0.066985	0.116628	ENSG00000166451	ENST00000299572	.	.	.	4.16	-8.33	0.00992	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.2879	0.04131	0.4934:0.2626:0.0955:0.1485	rs3743503;rs52826364;rs61114085;rs3743503	.	.	.	E	205	.	.	X	+	1	0	CENPN	79613942	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.047000	0.14056	-1.710000	0.01397	-1.133000	0.01973	TAG	T|0.878;G|0.122	0.122	strong		0.338	CENPN-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269051.1	NM_018455	
TNRC18	84629	hgsc.bcm.edu	37	7	5399044	5399044	+	Silent	SNP	C	C	G	rs12531309	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5399044C>G	ENST00000430969.1	-	15	5166	c.4818G>C	c.(4816-4818)tcG>tcC	p.S1606S	TNRC18_ENST00000399537.4_Silent_p.S1606S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1606							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TGATGAAGTCCGACGAGGCCT	0.547													G|||	1278	0.255192	0.2489	0.2536	5008	,	,		21101	0.2808		0.2594	False		,,,				2504	0.2342				p.S1606S		Atlas-SNP	.											.	TNRC18	311	.	0			c.G4818C						PASS	.	G		984,2968		134,716,1126	213.0	214.0	214.0		4818	-11.1	0.0	7	dbSNP_120	214	2414,5914		339,1736,2089	no	coding-synonymous	TNRC18	NM_001080495.2		473,2452,3215	GG,GC,CC		28.9866,24.8988,27.671		1606/2969	5399044	3398,8882	1976	4164	6140	SO:0001819	synonymous_variant	84629	exon15			GAAGTCCGACGAG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4818G>C	7.37:g.5399044C>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	177	83	0.468927	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			C|0.729;G|0.271	0.271	strong		0.547	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
FOXM1	2305	hgsc.bcm.edu	37	12	2973615	2973615	+	Silent	SNP	T	T	C	rs2072360	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:2973615T>C	ENST00000359843.3	-	8	1205	c.1137A>G	c.(1135-1137)gtA>gtG	p.V379V	FOXM1_ENST00000342628.2_Silent_p.V379V|FOXM1_ENST00000361953.3_Silent_p.V364V|FOXM1_ENST00000537018.1_5'Flank	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	379					cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			ACTGGATAGGTACCAGGTATG	0.602													C|||	1314	0.26238	0.3464	0.2248	5008	,	,		18498	0.2192		0.1928	False		,,,				2504	0.2914				p.V379V		Atlas-SNP	.											.	FOXM1	62	.	0			c.A1137G						PASS	.	C	,,	1480,2926	678.9+/-403.6	254,972,977	80.0	79.0	79.0		1137,1137,1092	-2.7	1.0	12	dbSNP_96	79	1626,6974	741.3+/-407.1	164,1298,2838	no	coding-synonymous,coding-synonymous,coding-synonymous	FOXM1	NM_021953.3,NM_202002.2,NM_202003.2	,,	418,2270,3815	CC,CT,TT		18.907,33.5906,23.8813	,,	379/764,379/802,364/749	2973615	3106,9900	2203	4300	6503	SO:0001819	synonymous_variant	2305	exon8			GATAGGTACCAGG	Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"""Forkhead boxes"""	3818	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 2"""	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.1137A>G	12.37:g.2973615T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_021953	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Silent	SNP	ENST00000359843.3	37	CCDS8515.1	504	0.23076923076923078	161	0.32723577235772355	80	0.22099447513812154	114	0.1993006993006993	149	0.19656992084432717	C	9.818	1.184914	0.21870	0.335906	0.18907	ENSG00000111206	ENST00000535350	.	.	.	4.82	-2.68	0.06041	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999993	.	.	.	.	.	.	T	0.43718	-0.9374	3	.	.	.	.	1.0477	0.01573	0.1869:0.1731:0.2038:0.4362	rs2072360;rs58518661;rs2072360	.	.	.	A	105	.	.	T	-	1	0	FOXM1	2843876	0.288000	0.24324	0.990000	0.47175	0.800000	0.45204	-0.301000	0.08232	-0.428000	0.07339	-0.974000	0.02594	ACC	T|0.759;C|0.241	0.241	strong		0.602	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953	
MVK	4598	hgsc.bcm.edu	37	12	110013879	110013879	+	Missense_Mutation	SNP	G	G	A	rs104895327|rs7957619	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:110013879G>A	ENST00000228510.3	+	3	231	c.155G>A	c.(154-156)aGc>aAc	p.S52N	MMAB_ENST00000266839.5_5'Flank|MMAB_ENST00000545712.2_5'Flank|MVK_ENST00000535044.1_3'UTR|MMAB_ENST00000540016.1_5'Flank|MVK_ENST00000541384.1_5'UTR|MVK_ENST00000392727.3_Missense_Mutation_p.S52N|MVK_ENST00000539696.1_Intron|MVK_ENST00000539575.1_Missense_Mutation_p.S52N	NM_000431.2|NM_001114185.1	NP_000422.1|NP_001107657.1	Q03426	KIME_HUMAN	mevalonate kinase	52			S -> N (in dbSNP:rs7957619). {ECO:0000269|PubMed:11313769, ECO:0000269|PubMed:15536479}.		cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|negative regulation of inflammatory response (GO:0050728)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|mevalonate kinase activity (GO:0004496)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8						GTGGACCTCAGCTTACCCAAC	0.502													G|||	380	0.0758786	0.1029	0.098	5008	,	,		19049	0.0		0.1471	False		,,,				2504	0.0286				p.S52N		Atlas-SNP	.											.	MVK	42	.	0			c.G155A						PASS	.	G	ASN/SER,ASN/SER	392,4014	194.0+/-219.0	18,356,1829	86.0	76.0	79.0		155,155	-4.1	0.0	12	dbSNP_116	79	1119,7481	231.4+/-265.4	69,981,3250	yes	missense,missense	MVK	NM_000431.2,NM_001114185.1	46,46	87,1337,5079	AA,AG,GG		13.0116,8.897,11.6177	benign,benign	52/397,52/397	110013879	1511,11495	2203	4300	6503	SO:0001583	missense	4598	exon3			ACCTCAGCTTACC	M88468	CCDS9132.1, CCDS73522.1	12q24	2014-09-17	2008-01-30		ENSG00000110921	ENSG00000110921	2.7.1.36		7530	protein-coding gene	gene with protein product	"""LH receptor mRNA-binding protein"", ""mevalonic aciduria"""	251170	"""mevalonate kinase (mevalonic aciduria)"""			1377680	Standard	XM_005253883		Approved	LRBP, MK	uc001toy.4	Q03426	OTTHUMG00000169256	ENST00000228510.3:c.155G>A	12.37:g.110013879G>A	ENSP00000228510:p.Ser52Asn	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_000431		Missense_Mutation	SNP	ENST00000228510.3	37	CCDS9132.1	204	0.09340659340659341	51	0.10365853658536585	43	0.11878453038674033	0	0.0	110	0.14511873350923482	G	0.024	-1.393647	0.01175	0.08897	0.130116	ENSG00000110921	ENST00000539335;ENST00000546277;ENST00000228510;ENST00000392727;ENST00000539575	D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88	5.25	-4.11	0.03928	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.464242	0.25596	N	0.029591	T	0.00754	0.0025	N	0.00991	-1.07	0.20307	P	0.99991635	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.0	T	0.46541	-0.9184	9	0.12103	T	0.63	-3.8097	7.7576	0.28933	0.3512:0.0:0.5294:0.1194	rs7957619;rs52800176;rs58148787;rs7957619	52;52	F5H8H2;Q03426	.;KIME_HUMAN	N	52	ENSP00000440379:S52N;ENSP00000438153:S52N;ENSP00000228510:S52N;ENSP00000376487:S52N;ENSP00000443551:S52N	ENSP00000228510:S52N	S	+	2	0	MVK	108498262	0.103000	0.21917	0.020000	0.16555	0.177000	0.22998	0.118000	0.15605	-0.505000	0.06568	-0.471000	0.05019	AGC	G|0.892;A|0.108	0.108	strong		0.502	MVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403143.1	NM_000431	
MADD	8567	hgsc.bcm.edu	37	11	47298360	47298360	+	Silent	SNP	G	G	A	rs326214	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:47298360G>A	ENST00000311027.5	+	5	1206	c.1041G>A	c.(1039-1041)gaG>gaA	p.E347E	MADD_ENST00000342922.4_Silent_p.E347E|MADD_ENST00000395344.3_Silent_p.E347E|MADD_ENST00000402799.1_Silent_p.E347E|MADD_ENST00000406482.1_Silent_p.E347E|MADD_ENST00000402192.2_Silent_p.E347E|MADD_ENST00000407859.3_Silent_p.E347E|MADD_ENST00000395336.3_Silent_p.E347E|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000349238.3_Silent_p.E347E	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		ACCCACTGGAGTATATGTTTC	0.527													G|||	2354	0.470048	0.3109	0.6369	5008	,	,		22714	0.2738		0.6899	False		,,,				2504	0.5429				p.E347E		Atlas-SNP	.											MADD,colon,carcinoma,+1,1	MADD	172	1	0			c.G1041A						PASS	.	G	,,,,,,,,,	1588,2814	494.5+/-363.0	270,1048,883	255.0	192.0	214.0		1041,1041,1041,1041,1041,1041,1041,1041,1041,1041	4.0	1.0	11	dbSNP_79	214	5952,2644	686.8+/-404.2	2049,1854,395	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MADD	NM_001135943.1,NM_001135944.1,NM_003682.3,NM_130470.2,NM_130471.2,NM_130472.2,NM_130473.2,NM_130474.2,NM_130475.2,NM_130476.2	,,,,,,,,,	2319,2902,1278	AA,AG,GG		30.7585,36.0745,41.9911	,,,,,,,,,	347/1545,347/1542,347/1648,347/1589,347/1566,347/1546,347/1609,347/1480,347/1582,347/1588	47298360	7540,5458	2201	4298	6499	SO:0001819	synonymous_variant	8567	exon5			ACTGGAGTATATG	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1041G>A	11.37:g.47298360G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_130474		Silent	SNP	ENST00000311027.5	37	CCDS7930.1																																																																																			G|0.446;A|0.554	0.554	strong		0.527	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
Unknown	0	hgsc.bcm.edu	37	11	124095525	124095525	+	IGR	SNP	T	T	C	rs11219508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124095525T>C								OR10D3 (38573 upstream) : OR8G1 (24897 downstream)																							CTCTTCCTCCTGTTCTTAGGA	0.507													t|||	2157	0.430711	0.5431	0.3372	5008	,	,		17975	0.3155		0.337	False		,,,				2504	0.5603				p.L43P		Atlas-SNP	.											.	.	.	.	0			c.T128C						PASS	.	T	PRO/LEU	1980,2256		485,1010,623	119.0	121.0	121.0		128	1.8	0.0	11	dbSNP_120	121	2756,5800		460,1836,1982	no	missense	OR8G2	NM_001007249.1	98	945,2846,2605	CC,CT,TT		32.2113,46.7422,37.0231	probably-damaging	43/305	124095525	4736,8056	2118	4278	6396	SO:0001628	intergenic_variant	26492	exon1			TCCTCCTGTTCTT																													11.37:g.124095525T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	200	96	0.48	NM_001007249		Missense_Mutation	SNP		37																																																																																				.	.	weak	0	0.507								
FNDC7	163479	hgsc.bcm.edu	37	1	109268441	109268441	+	Missense_Mutation	SNP	G	G	A	rs11582005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109268441G>A	ENST00000370017.3	+	6	1203	c.926G>A	c.(925-927)aGt>aAt	p.S309N	FNDC7_ENST00000271311.2_Missense_Mutation_p.S310N	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	309	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> N (in dbSNP:rs11582005).			extracellular region (GO:0005576)		p.S76N(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		GCTTGGTCCAGTGTAGATCTG	0.468													g|||	849	0.169529	0.3215	0.0865	5008	,	,		13449	0.0992		0.1412	False		,,,				2504	0.1247				p.S309N		Atlas-SNP	.											FNDC7,NS,carcinoma,0,1	FNDC7	113	1	1	Substitution - Missense(1)	stomach(1)	c.G926A						PASS	.	A	ASN/SER	1308,3098	442.5+/-346.7	205,898,1100	153.0	134.0	140.0		926	-8.0	0.0	1	dbSNP_120	140	1301,7299	258.3+/-282.0	100,1101,3099	yes	missense	FNDC7	NM_001144937.1	46	305,1999,4199	AA,AG,GG		15.1279,29.6868,20.06	benign	309/734	109268441	2609,10397	2203	4300	6503	SO:0001583	missense	163479	exon6			GGTCCAGTGTAGA		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.926G>A	1.37:g.109268441G>A	ENSP00000359034:p.Ser309Asn	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	37	CCDS44185.1	365	0.1671245421245421	162	0.32926829268292684	32	0.08839779005524862	60	0.1048951048951049	111	0.14643799472295516	g	1.406	-0.576763	0.03854	0.296868	0.151279	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.23147	1.92;1.92	5.9	-8.02	0.01118	Fibronectin, type III (3);	0.712224	0.14967	N	0.288052	T	0.04452	0.0122	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.22765	-1.0207	9	0.28530	T	0.3	-2.9951	14.2542	0.66040	0.3755:0.0844:0.5401:0.0	rs11582005;rs52796157;rs59157354;rs11582005	310;309	Q5VTL7;E9PAZ5	FNDC7_HUMAN;.	N	309;310	ENSP00000359034:S309N;ENSP00000271311:S310N	ENSP00000271311:S310N	S	+	2	0	FNDC7	109069964	0.000000	0.05858	0.001000	0.08648	0.816000	0.46133	-1.892000	0.01610	-2.225000	0.00724	-2.021000	0.00431	AGT	G|0.816;A|0.184	0.184	strong		0.468	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
CAPN1	823	hgsc.bcm.edu	37	11	64981587	64981587	+	IGR	SNP	G	G	A	rs11605632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64981587G>A	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		TGGGGCCCCTGAGCCCTGCCG	0.711													G|||	1875	0.374401	0.3797	0.5101	5008	,	,		14217	0.2629		0.4165	False		,,,				2504	0.3425				p.E82K		Atlas-SNP	.											SLC22A20,NS,carcinoma,0,2	SLC22A20	36	2	0			c.G244A						PASS	.	G	LYS/GLU	1324,2354		251,822,766	6.0	8.0	8.0		244	4.5	0.0	11	dbSNP_120	8	3156,4890		677,1802,1544	yes	missense	SLC22A20	NM_001004326.4	56	928,2624,2310	AA,AG,GG		39.2245,35.9978,38.2122	benign	82/350	64981587	4480,7244	1839	4023	5862	SO:0001628	intergenic_variant	440044	exon1			GCCCCTGAGCCCT	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		11.37:g.64981587G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			G|0.621;A|0.379	0.379	strong		0.711	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
SGSM1	129049	hgsc.bcm.edu	37	22	25251027	25251027	+	Silent	SNP	T	T	C	rs201064977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:25251027T>C	ENST00000400359.4	+	6	527	c.520T>C	c.(520-522)Ttg>Ctg	p.L174L	SGSM1_ENST00000400358.4_Silent_p.L174L	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	174	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TGCATCTTTGTTGGGTAAGTT	0.532													T|||	4	0.000798722	0.0	0.0029	5008	,	,		19277	0.0		0.002	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	SGSM1	150	.	0			c.T520C						PASS	.	T	,,,	1,3963		0,1,1981	95.0	95.0	95.0		520,520,520,520	-0.5	0.9	22		95	41,8295		0,41,4127	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	0,42,6108	CC,CT,TT		0.4918,0.0252,0.3415	,,,	174/1149,174/1094,174/1033,174/1088	25251027	42,12258	1982	4168	6150	SO:0001819	synonymous_variant	129049	exon6			TCTTTGTTGGGTA	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.520T>C	22.37:g.25251027T>C		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	271	115	0.424354	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																			T|0.998;C|0.002	0.002	strong		0.532	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
SERPINA9	327657	hgsc.bcm.edu	37	14	94933709	94933709	+	Silent	SNP	C	C	T	rs6575433	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94933709C>T	ENST00000380365.3	-	3	717	c.639G>A	c.(637-639)gaG>gaA	p.E213E	SERPINA9_ENST00000424550.2_Silent_p.E82E|SERPINA9_ENST00000546329.1_Silent_p.E195E|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000298845.7_Silent_p.E131E|SERPINA9_ENST00000337425.5_Silent_p.E231E|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000448305.2_Silent_p.E133E			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	213					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		GAAAGGGCTTCTCCCACTTGG	0.458													C|||	1736	0.346645	0.2126	0.3588	5008	,	,		21008	0.1825		0.5427	False		,,,				2504	0.4867				p.E231E		Atlas-SNP	.											.	SERPINA9	105	.	0			c.G693A						PASS	.	C	,	994,2806		120,754,1026	64.0	60.0	61.0		393,693	0.5	0.9	14	dbSNP_116	61	4326,3936		1123,2080,928	no	coding-synonymous,coding-synonymous	SERPINA9	NM_001042518.1,NM_175739.3	,	1243,2834,1954	TT,TC,CC		47.6398,26.1579,44.1055	,	131/336,231/436	94933709	5320,6742	1900	4131	6031	SO:0001819	synonymous_variant	327657	exon3			GGGCTTCTCCCAC	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.639G>A	14.37:g.94933709C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	23	0.370968	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Silent	SNP	ENST00000380365.3	37																																																																																				C|0.636;T|0.364	0.364	strong		0.458	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69095197	69095197	+	Missense_Mutation	SNP	T	T	C	rs12331141	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69095197T>C	ENST00000332644.5	-	8	885	c.724A>G	c.(724-726)Att>Gtt	p.I242V		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	242	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		I -> V (in dbSNP:rs12331141). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						TTTACTACAATTCCAAAGTTG	0.353													T|||	3596	0.718051	0.4297	0.6023	5008	,	,		18668	0.9901		0.7306	False		,,,				2504	0.8967				p.I242V		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.A724G						PASS	.	T	VAL/ILE	2303,2103	598.3+/-389.1	613,1077,513	55.0	54.0	54.0		724	0.6	0.0	4	dbSNP_120	54	6697,1903	724.3+/-406.5	2589,1519,192	yes	missense	TMPRSS11B	NM_182502.3	29	3202,2596,705	CC,CT,TT		22.1279,47.7304,30.8012	benign	242/417	69095197	9000,4006	2203	4300	6503	SO:0001583	missense	132724	exon8			CTACAATTCCAAA	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.724A>G	4.37:g.69095197T>C	ENSP00000330475:p.Ile242Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_182502	A8K4D9	Missense_Mutation	SNP	ENST00000332644.5	37	CCDS3521.1	1566	0.717032967032967	209	0.4247967479674797	237	0.6546961325966851	567	0.9912587412587412	553	0.7295514511873351	T	0.012	-1.661019	0.00772	0.522696	0.778721	ENSG00000185873	ENST00000332644	D	0.88896	-2.44	4.62	0.639	0.17747	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.702199	0.12296	N	0.481557	T	0.00012	0.0000	N	0.16130	0.375	0.80722	P	0.0	B	0.10296	0.003	B	0.12837	0.008	T	0.29941	-0.9995	9	0.16420	T	0.52	.	4.989	0.14205	0.0:0.1742:0.1561:0.6698	rs12331141;rs60758802;rs12331141	242	Q86T26	TM11B_HUMAN	V	242	ENSP00000330475:I242V	ENSP00000330475:I242V	I	-	1	0	TMPRSS11B	68777792	0.961000	0.32948	0.042000	0.18584	0.061000	0.15899	1.437000	0.34991	0.042000	0.15717	0.459000	0.35465	ATT	T|0.292;C|0.708	0.708	strong		0.353	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
INTU	27152	hgsc.bcm.edu	37	4	128584580	128584580	+	Silent	SNP	G	G	A	rs4833380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:128584580G>A	ENST00000335251.6	+	4	916	c.813G>A	c.(811-813)acG>acA	p.T271T	INTU_ENST00000296461.5_Silent_p.T271T	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	271					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						AAAGGGAGACGTCCCATCCAA	0.403													A|||	3255	0.64996	0.7474	0.6023	5008	,	,		18606	0.5526		0.5646	False		,,,				2504	0.7403				p.T271T		Atlas-SNP	.											.	INTU	92	.	0			c.G813A						PASS	.	A		3175,1231	424.7+/-340.5	1130,915,158	117.0	114.0	115.0		813	-7.8	0.0	4	dbSNP_111	115	4769,3831	540.3+/-383.8	1329,2111,860	no	coding-synonymous	INTU	NM_015693.3		2459,3026,1018	AA,AG,GG		44.5465,27.9392,38.9205		271/943	128584580	7944,5062	2203	4300	6503	SO:0001819	synonymous_variant	27152	exon4			GGAGACGTCCCAT	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"""PDZ domain containing 6"", ""inturned planar cell polarity effector homolog (Drosophila)"""	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.813G>A	4.37:g.128584580G>A		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Silent	SNP	ENST00000335251.6	37	CCDS34061.1																																																																																			G|0.390;A|0.610	0.610	strong		0.403	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707	
ENG	2022	hgsc.bcm.edu	37	9	130605385	130605385	+	Silent	SNP	C	C	T	rs45605432|rs11545664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:130605385C>T	ENST00000373203.4	-	2	607	c.207G>A	c.(205-207)ctG>ctA	p.L69L	ENG_ENST00000344849.3_Silent_p.L69L|RNA5SP296_ENST00000410523.1_RNA	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	69	Required for interaction with EGL.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						TTGGGAACTCCAGGAAGAGGA	0.627									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia				C|||	552	0.110224	0.236	0.085	5008	,	,		18695	0.0466		0.1044	False		,,,				2504	0.0297				p.L69L		Atlas-SNP	.											.	ENG	44	.	0			c.G207A						PASS	.	C	,	1109,3297	398.3+/-330.8	139,831,1233	155.0	158.0	157.0		207,207	4.2	1.0	9	dbSNP_123	157	892,7708	199.9+/-243.8	42,808,3450	no	coding-synonymous,coding-synonymous	ENG	NM_000118.2,NM_001114753.1	,	181,1639,4683	TT,TC,CC		10.3721,25.1702,15.3852	,	69/626,69/659	130605385	2001,11005	2203	4300	6503	SO:0001819	synonymous_variant	2022	exon2	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	GAACTCCAGGAAG	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"""CD molecules"""	3349	protein-coding gene	gene with protein product		131195	"""Osler-Rendu-Weber syndrome 1"""	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.207G>A	9.37:g.130605385C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_001114753	Q14248|Q14926|Q5T9C0	Silent	SNP	ENST00000373203.4	37	CCDS48029.1																																																																																			C|0.852;T|0.148	0.148	strong		0.627	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458515	4458515	+	Missense_Mutation	SNP	G	G	T	rs117128211	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4458515G>T	ENST00000254718.4	-	1	411	c.105C>A	c.(103-105)ttC>ttA	p.F35L	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.F35L			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	35	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						AGAAGTCCAAGAACTCGCGAC	0.637													G|||	74	0.0147764	0.0008	0.0086	5008	,	,		16072	0.0		0.0348	False		,,,				2504	0.0327				p.F35L		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C105A						PASS	.	G	LEU/PHE,LEU/PHE	19,4383	20.2+/-43.8	0,19,2182	27.0	27.0	27.0		105,105	2.9	1.0	17	dbSNP_132	27	241,8351	93.1+/-155.1	5,231,4060	yes	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	22,22	5,250,6242	TT,TG,GG		2.8049,0.4316,2.0009	probably-damaging,probably-damaging	35/1333,35/1329	4458515	260,12734	2201	4296	6497	SO:0001583	missense	10514	exon1			GTCCAAGAACTCG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.105C>A	17.37:g.4458515G>T	ENSP00000254718:p.Phe35Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	29	0.013278388278388278	0	0.0	3	0.008287292817679558	0	0.0	26	0.03430079155672823	G	19.15	3.772199	0.69992	0.004316	0.028049	ENSG00000132382	ENST00000381556;ENST00000254718;ENST00000426435	T;T	0.56103	0.48;0.48	4.94	2.93	0.34026	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	L	0.34521	1.04	0.35719	D	0.817008	D;D	0.71674	0.997;0.998	D;D	0.72982	0.954;0.979	T	0.49457	-0.8938	10	0.11794	T	0.64	-29.3099	7.6026	0.28085	0.2721:0.0:0.7279:0.0	.	35;35	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	L	35	ENSP00000370968:F35L;ENSP00000254718:F35L	ENSP00000254718:F35L	F	-	3	2	MYBBP1A	4405264	1.000000	0.71417	0.998000	0.56505	0.252000	0.25951	1.905000	0.39878	0.662000	0.31006	-0.191000	0.12829	TTC	G|0.983;T|0.017	0.017	strong		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
USP6	9098	hgsc.bcm.edu	37	17	5058808	5058808	+	Missense_Mutation	SNP	G	G	A	rs9899177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5058808G>A	ENST00000574788.1	+	31	4965	c.2735G>A	c.(2734-2736)cGg>cAg	p.R912Q	USP6_ENST00000304328.5_Missense_Mutation_p.R595Q|USP6_ENST00000250066.6_Missense_Mutation_p.R912Q|USP6_ENST00000332776.4_3'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	912	USP.		R -> Q (in dbSNP:rs9899177). {ECO:0000269|PubMed:1565468}.		cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GTGCATACCCGGAAGAAAGAC	0.478			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								G|||	1688	0.337061	0.1936	0.6052	5008	,	,		15543	0.1706		0.6034	False		,,,				2504	0.2382				p.R912Q		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6_ENST00000250066,NS,carcinoma,-1,1	USP6	213	1	0			c.G2735A						PASS	.	G	GLN/ARG	1292,3114	438.4+/-345.3	189,914,1100	178.0	155.0	163.0		2735	2.9	1.0	17	dbSNP_119	163	5474,3126	657.7+/-401.5	1744,1986,570	yes	missense	USP6	NM_004505.2	43	1933,2900,1670	AA,AG,GG		36.3488,29.3236,47.9779	probably-damaging	912/1407	5058808	6766,6240	2203	4300	6503	SO:0001583	missense	9098	exon23			ATACCCGGAAGAA	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.2735G>A	17.37:g.5058808G>A	ENSP00000460380:p.Arg912Gln	Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	259	258	0.996139	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	867	0.39697802197802196	106	0.21544715447154472	220	0.6077348066298343	92	0.16083916083916083	449	0.5923482849604221	G	17.49	3.402406	0.62288	0.293236	0.636512	ENSG00000129204	ENST00000250066;ENST00000304328	T;T	0.13420	2.99;2.59	2.91	2.91	0.33838	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.099183	0.64402	D	0.000002	T	0.00012	0.0000	L	0.55990	1.75	0.31282	P	0.69051	D;D	0.76494	0.996;0.999	P;P	0.60541	0.755;0.876	T	0.02966	-1.1088	9	0.07990	T	0.79	.	11.6235	0.51132	0.0:0.0:1.0:0.0	rs9899177;rs58814329;rs9899177	595;912	P35125-2;P35125	.;UBP6_HUMAN	Q	912;595	ENSP00000250066:R912Q;ENSP00000305473:R595Q	ENSP00000250066:R912Q	R	+	2	0	USP6	4999532	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.359000	0.73060	1.614000	0.50241	0.398000	0.26397	CGG	G|0.541;A|0.459	0.459	strong		0.478	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
ZNF469	84627	hgsc.bcm.edu	37	16	88496008	88496008	+	Silent	SNP	T	T	C	rs12918876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88496008T>C	ENST00000437464.1	+	1	2130	c.2130T>C	c.(2128-2130)ccT>ccC	p.P710P	ZNF469_ENST00000565624.1_Silent_p.P710P	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	710	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GTGCGCCGCCTCCGTACCCCA	0.697													C|||	3027	0.604433	0.3079	0.7161	5008	,	,		10377	0.6052		0.7495	False		,,,				2504	0.7761				p.P710P		Atlas-SNP	.											.	ZNF469	121	.	0			c.T2130C						PASS	.						4.0	4.0	4.0					16																	88496008		656	1508	2164	SO:0001819	synonymous_variant	84627	exon1			GCCGCCTCCGTAC	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.2130T>C	16.37:g.88496008T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	70	19	0.271429	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			T|0.388;C|0.612	0.612	strong		0.697	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610008	32610008	+	Silent	SNP	C	C	T	rs2308890	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32610008C>T	ENST00000343139.5	+	3	693	c.591C>T	c.(589-591)gaC>gaT	p.D197D	HLA-DQA1_ENST00000374949.2_Silent_p.D197D|HLA-DQA1_ENST00000395363.1_Silent_p.D197D	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	196	Alpha-2.|Ig-like C1-type.		K -> E (in allele DQA1*02:01, allele DQA1*03:01, allele DQA1*03:02, allele DQA1*03:03, allele DQA1*04:01, allele DQA1*04:02, allele DQA1*04:04, allele DQA1*06:01 and allele DQA1*06:02).|K -> Q (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05 and allele DQA1*01:07).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GGGGCCTGGACCAGCCTCTTC	0.448													.|||	1472	0.29393	0.1959	0.3833	5008	,	,		13880	0.3333		0.3201	False		,,,				2504	0.2955				p.D197D		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C591T						PASS	.	T		623,2391		125,373,1009	100.0	105.0	103.0		591	-8.2	0.0	6	dbSNP_123	103	1761,3651		417,927,1362	no	coding-synonymous	HLA-DQA1	NM_002122.3		542,1300,2371	TT,TC,CC		32.5388,20.6702,28.2934		197/256	32610008	2384,6042	1507	2706	4213	SO:0001819	synonymous_variant	3117	exon3			CCTGGACCAGCCT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.591C>T	6.37:g.32610008C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	206	147	0.713592	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1	598	0.27380952380952384	67	0.13617886178861788	109	0.3011049723756906	193	0.3374125874125874	229	0.3021108179419525	.	0.690	-0.794762	0.02862	0.206702	0.325388	ENSG00000196735	ENST00000486548	.	.	.	4.08	-8.17	0.01057	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.20703	P	0.999863693	.	.	.	.	.	.	T	0.19614	-1.0300	3	.	.	.	.	2.8614	0.05588	0.1097:0.1325:0.3147:0.4432	rs2308890;rs9272752	.	.	.	I	170	.	.	T	+	2	0	HLA-DQA1	32717986	0.000000	0.05858	0.000000	0.03702	0.463000	0.32649	-6.856000	0.00051	-1.995000	0.00971	-0.753000	0.03488	ACC	C|0.717;T|0.283	0.283	strong		0.448	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
ZNF280A	129025	hgsc.bcm.edu	37	22	22868497	22868497	+	Missense_Mutation	SNP	G	G	C	rs361762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22868497G>C	ENST00000302097.3	-	2	1710	c.1458C>G	c.(1456-1458)ttC>ttG	p.F486L		NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	486			F -> L (in dbSNP:rs361762). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9074928}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TTTCACGAGGGAACCCTTGCA	0.443													C|||	2372	0.473642	0.2383	0.732	5008	,	,		16526	0.4127		0.7048	False		,,,				2504	0.4335				p.F486L		Atlas-SNP	.											.	ZNF280A	67	.	0			c.C1458G						PASS	.	C	LEU/PHE	1357,3049	687.8+/-404.9	220,917,1066	127.0	111.0	116.0		1458	0.5	0.1	22	dbSNP_79	116	5854,2746	435.1+/-357.9	2007,1840,453	yes	missense	ZNF280A	NM_080740.3	22	2227,2757,1519	CC,CG,GG		31.9302,30.7989,44.5564	benign	486/543	22868497	7211,5795	2203	4300	6503	SO:0001583	missense	129025	exon2			ACGAGGGAACCCT	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.1458C>G	22.37:g.22868497G>C	ENSP00000302855:p.Phe486Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	1153	0.5279304029304029	126	0.25609756097560976	254	0.7016574585635359	243	0.42482517482517484	530	0.6992084432717678	C	0.003	-2.455226	0.00173	0.307989	0.680698	ENSG00000169548	ENST00000302097	T	0.00824	5.65	3.76	0.473	0.16763	.	.	.	.	.	T	0.00012	0.0000	N	0.00082	-2.215	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	8	0.02654	T	1	0.1076	0.7824	0.01043	0.3215:0.3317:0.1569:0.1899	rs361762;rs695261;rs3747097;rs17857435	486	P59817	Z280A_HUMAN	L	486	ENSP00000302855:F486L	ENSP00000302855:F486L	F	-	3	2	ZNF280A	21198497	0.830000	0.29337	0.055000	0.19348	0.029000	0.11900	-0.219000	0.09228	-0.038000	0.13624	-0.736000	0.03550	TTC	G|0.455;C|0.545	0.545	strong		0.443	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
ZNF559	84527	hgsc.bcm.edu	37	19	9449888	9449888	+	Missense_Mutation	SNP	A	A	G	rs77267061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9449888A>G	ENST00000393883.2	+	4	701	c.53A>G	c.(52-54)gAt>gGt	p.D18G	ZNF559_ENST00000586255.1_Missense_Mutation_p.D46G|ZNF559_ENST00000585352.1_Missense_Mutation_p.D18G|ZNF177_ENST00000605471.1_Intron|ZNF559_ENST00000587557.1_Missense_Mutation_p.D82G|ZNF559_ENST00000538743.1_Intron|ZNF559_ENST00000317221.7_Missense_Mutation_p.D18G|ZNF177_ENST00000446085.4_Intron|ZNF559_ENST00000603380.1_Missense_Mutation_p.D18G|ZNF559_ENST00000592504.1_Missense_Mutation_p.D18G|ZNF177_ENST00000602856.1_Intron|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000592896.1_Missense_Mutation_p.D46G|ZNF177_ENST00000602738.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	18	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						ACCTTTGAGGATGTGGCTGTG	0.473													A|||	335	0.066893	0.0378	0.0807	5008	,	,		23090	0.0972		0.0368	False		,,,				2504	0.0961				p.D82G		Atlas-SNP	.											.	ZNF559	77	.	0			c.A245G						PASS	.	A	,GLY/ASP,,GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP,,GLY/ASP	166,4240	109.9+/-148.2	6,154,2043	228.0	192.0	204.0		,245,,245,137,53,53,53,,53	2.3	0.1	19	dbSNP_131	204	403,8197	127.5+/-185.8	14,375,3911	yes	intron,missense,utr-5,missense,missense,missense,missense,missense,intron,missense	ZNF559,ZNF559-ZNF177	NM_001172650.2,NM_001202406.1,NM_001202407.1,NM_001202408.1,NM_001202409.1,NM_001202410.1,NM_001202411.1,NM_001202412.1,NM_001202425.1,NM_032497.2	,94,,94,94,94,94,94,,94	20,529,5954	GG,GA,AA		4.686,3.7676,4.3749	,probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging	,82/603,,82/149,46/113,18/85,18/85,18/85,,18/539	9449888	569,12437	2203	4300	6503	SO:0001583	missense	84527	exon4			TTGAGGATGTGGC	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"""Zinc fingers, C2H2-type"", ""-"""	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.53A>G	19.37:g.9449888A>G	ENSP00000377461:p.Asp18Gly	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	208	98	0.471154	NM_001202408	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	130	0.05952380952380952	17	0.034552845528455285	31	0.0856353591160221	54	0.0944055944055944	28	0.036939313984168866	A	14.95	2.688920	0.48097	0.037676	0.04686	ENSG00000188321	ENST00000317221;ENST00000393883	T;T	0.11930	2.73;2.73	2.32	2.32	0.28847	Krueppel-associated box (4);	.	.	.	.	T	0.02267	0.0070	H	0.95917	3.74	0.51767	D	0.999936	D	0.76494	0.999	D	0.77557	0.99	T	0.03524	-1.1028	9	0.87932	D	0	.	8.5163	0.33248	1.0:0.0:0.0:0.0	.	18	Q9BR84	ZN559_HUMAN	G	18	ENSP00000325393:D18G;ENSP00000377461:D18G	ENSP00000325393:D18G	D	+	2	0	ZNF559	9310888	0.993000	0.37304	0.121000	0.21740	0.933000	0.57130	2.783000	0.47766	1.314000	0.45095	0.260000	0.18958	GAT	A|0.948;G|0.052	0.052	strong		0.473	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497	
ZNF202	7753	hgsc.bcm.edu	37	11	123598941	123598941	+	Silent	SNP	T	T	C	rs2282644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123598941T>C	ENST00000529691.1	-	5	951	c.732A>G	c.(730-732)gtA>gtG	p.V244V	ZNF202_ENST00000336139.4_Silent_p.V244V|ZNF202_ENST00000530393.1_Silent_p.V244V			O95125	ZN202_HUMAN	zinc finger protein 202	244	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		GGGAAAAGCATACGGCCACAT	0.458													T|||	1148	0.229233	0.0159	0.2968	5008	,	,		20310	0.3552		0.2694	False		,,,				2504	0.2986				p.V244V		Atlas-SNP	.											.	ZNF202	72	.	0			c.A732G						PASS	.	T		264,4140	149.2+/-183.4	13,238,1951	124.0	115.0	118.0		732	-8.9	0.1	11	dbSNP_100	118	2411,6187	402.3+/-347.4	342,1727,2230	no	coding-synonymous	ZNF202	NM_003455.2		355,1965,4181	CC,CT,TT		28.0414,5.9946,20.5738		244/649	123598941	2675,10327	2202	4299	6501	SO:0001819	synonymous_variant	7753	exon7			AAAGCATACGGCC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.732A>G	11.37:g.123598941T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	136	56	0.411765	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Silent	SNP	ENST00000529691.1	37	CCDS8443.1																																																																																			T|0.784;C|0.216	0.216	strong		0.458	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
CCM2	83605	hgsc.bcm.edu	37	7	45104131	45104131	+	Missense_Mutation	SNP	G	G	A	rs11552377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45104131G>A	ENST00000258781.6	+	4	507	c.358G>A	c.(358-360)Gtc>Atc	p.V120I	CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000381112.3_Missense_Mutation_p.V141I|CCM2_ENST00000474617.1_Missense_Mutation_p.V114I|CCM2_ENST00000544363.1_Missense_Mutation_p.V120I|CCM2_ENST00000475551.1_Missense_Mutation_p.V114I|CCM2_ENST00000541586.1_Missense_Mutation_p.V62I	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	120	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.		V -> I (in dbSNP:rs11552377). {ECO:0000269|PubMed:14740320}.		blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TGCGTACAACGTCAAGCTGGC	0.587													G|||	541	0.108027	0.0166	0.1671	5008	,	,		19600	0.1091		0.174	False		,,,				2504	0.1207				p.V141I		Atlas-SNP	.											.	CCM2	42	.	0			c.G421A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	176,4230	114.6+/-152.6	1,174,2028	79.0	53.0	62.0		421,184,358,358	3.2	1.0	7	dbSNP_120	62	1582,7018	295.9+/-302.6	140,1302,2858	yes	missense,missense,missense,missense	CCM2	NM_001029835.2,NM_001167934.1,NM_001167935.1,NM_031443.3	29,29,29,29	141,1476,4886	AA,AG,GG		18.3953,3.9946,13.5168	benign,benign,benign,benign	141/466,62/387,120/354,120/445	45104131	1758,11248	2203	4300	6503	SO:0001583	missense	83605	exon4			TACAACGTCAAGC	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.358G>A	7.37:g.45104131G>A	ENSP00000258781:p.Val120Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	37	CCDS5500.1	254	0.1163003663003663	8	0.016260162601626018	65	0.17955801104972377	50	0.08741258741258741	131	0.17282321899736147	G	10.82	1.458249	0.26161	0.039946	0.183953	ENSG00000136280	ENST00000258781;ENST00000541586;ENST00000544363;ENST00000475551;ENST00000381112;ENST00000474617	T;T;T;T;T;T	0.54071	0.59;0.59;0.93;0.59;0.59;0.93	5.32	3.15	0.36227	Phosphotyrosine interaction domain (1);	0.255439	0.39544	N	0.001340	T	0.00073	0.0002	L	0.28115	0.83	0.29732	P	0.8377749999999999	P;P;B;B;B;B	0.40032	0.586;0.699;0.027;0.015;0.027;0.015	B;B;B;B;B;B	0.29176	0.099;0.083;0.009;0.006;0.017;0.006	T	0.12319	-1.0552	9	0.18710	T	0.47	-40.2272	9.6734	0.40026	0.2402:0.0:0.7598:0.0	rs11552377;rs17451775;rs11552377	113;83;141;120;62;120	B7Z5A6;B7Z8D5;E9PDJ3;F5H0E1;F5H551;Q9BSQ5	.;.;.;.;.;CCM2_HUMAN	I	120;62;120;114;141;114	ENSP00000258781:V120I;ENSP00000444725:V62I;ENSP00000438035:V120I;ENSP00000417180:V114I;ENSP00000370503:V141I;ENSP00000419474:V114I	ENSP00000258781:V120I	V	+	1	0	CCM2	45070656	0.995000	0.38212	0.998000	0.56505	0.962000	0.63368	2.274000	0.43390	1.244000	0.43870	0.655000	0.94253	GTC	G|0.879;A|0.121	0.121	strong		0.587	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	
PCDHGA2	56113	hgsc.bcm.edu	37	5	140720516	140720516	+	Missense_Mutation	SNP	C	C	G	rs35592458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140720516C>G	ENST00000394576.2	+	1	1978	c.1978C>G	c.(1978-1980)Ctc>Gtc	p.L660V	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	660	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACTGTCACGCTCACCGTGGC	0.687													c|||	1933	0.385982	0.0204	0.4222	5008	,	,		15471	0.5903		0.4722	False		,,,				2504	0.5552				p.L660V		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.C1978G						PASS	.	C	,VAL/LEU,VAL/LEU	425,3965		22,381,1792	31.0	38.0	36.0		,1978,1978	2.0	0.9	5	dbSNP_126	36	4148,4416		1031,2086,1165	no	intron,missense,missense	PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_032009.1	,32,32	1053,2467,2957	GG,GC,CC		48.4353,9.6811,35.3018	,,	,660/933,660/824	140720516	4573,8381	2195	4282	6477	SO:0001583	missense	56113	exon1			GTCACGCTCACCG	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.1978C>G	5.37:g.140720516C>G	ENSP00000378077:p.Leu660Val	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	130	86	0.661538	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	37	CCDS47289.1	850	0.3891941391941392	19	0.03861788617886179	147	0.40607734806629836	339	0.5926573426573427	345	0.4551451187335092	.	3.374	-0.127759	0.06753	0.096811	0.484353	ENSG00000081853	ENST00000394576	T	0.54866	0.55	5.14	2.01	0.26516	Cadherin (4);Cadherin-like (1);	0.226298	0.21714	U	0.070227	T	0.00012	0.0000	N	0.04724	-0.175	0.58432	P	6.999999999979245E-6	B;B	0.23854	0.092;0.031	B;B	0.34418	0.182;0.173	T	0.44081	-0.9351	9	0.23891	T	0.37	.	3.4939	0.07648	0.1135:0.5182:0.2035:0.1648	rs35592458;rs59122610	660;660	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	V	660	ENSP00000378077:L660V	ENSP00000378077:L660V	L	+	1	0	PCDHGA2	140700700	0.000000	0.05858	0.862000	0.33874	0.007000	0.05969	-1.561000	0.02158	0.676000	0.31285	-0.330000	0.08379	CTC	C|0.686;G|0.314	0.314	strong		0.687	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
SIGIRR	59307	hgsc.bcm.edu	37	11	407954	407954	+	Missense_Mutation	SNP	G	G	C	rs111819059	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:407954G>C	ENST00000431843.2	-	5	650	c.344C>G	c.(343-345)cCt>cGt	p.P115R	SIGIRR_ENST00000529486.1_5'UTR|SIGIRR_ENST00000382520.2_Missense_Mutation_p.P115R|SIGIRR_ENST00000397632.3_Missense_Mutation_p.P115R|SIGIRR_ENST00000332725.3_Missense_Mutation_p.P115R|SIGIRR_ENST00000531205.1_Missense_Mutation_p.P115R	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	115					acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTGGCTTGTAGGGCCTGCGGA	0.667													g|||	34	0.00678914	0.0	0.0014	5008	,	,		13907	0.0228		0.004	False		,,,				2504	0.0061				p.P115R		Atlas-SNP	.											.	SIGIRR	22	.	0			c.C344G						PASS	.	G	ARG/PRO,ARG/PRO,ARG/PRO	6,4396	12.9+/-30.5	0,6,2195	43.0	49.0	47.0		344,344,344	0.6	0.0	11	dbSNP_132	47	51,8541	31.2+/-83.2	0,51,4245	no	missense,missense,missense	SIGIRR	NM_001135053.1,NM_001135054.1,NM_021805.2	103,103,103	0,57,6440	CC,CG,GG		0.5936,0.1363,0.4387	benign,benign,benign	115/411,115/411,115/411	407954	57,12937	2201	4296	6497	SO:0001583	missense	59307	exon5			CTTGTAGGGCCTG		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30575	protein-coding gene	gene with protein product	"""single immunoglobulin domain IL1R1 related"""	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.344C>G	11.37:g.407954G>C	ENSP00000403104:p.Pro115Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_001135053	Q3KQY2|Q6UXI3|Q9H733	Missense_Mutation	SNP	ENST00000431843.2	37	CCDS31325.1	19|19	0.0086996336996337|0.0086996336996337	0|0	0.0|0.0	0|0	0.0|0.0	16|16	0.027972027972027972|0.027972027972027972	3|3	0.00395778364116095|0.00395778364116095	g|g	2.516|2.516	-0.311794|-0.311794	0.05422|0.05422	0.001363|0.001363	0.005936|0.005936	ENSG00000185187|ENSG00000185187	ENST00000528209|ENST00000431843;ENST00000397632;ENST00000332725;ENST00000531205;ENST00000382520	T|T;T;T;T;T	0.22336|0.03607	1.96|3.89;3.89;3.89;3.87;3.87	3.68|3.68	0.645|0.645	0.17782|0.17782	.|.	.|1.471020	.|0.03785	.|N	.|0.262028	T|T	0.01156|0.01156	0.0038|0.0038	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	.|B;B	.|0.32324	.|0.364;0.068	.|B;B	.|0.22753	.|0.041;0.015	T|T	0.44421|0.44421	-0.9329|-0.9329	7|10	0.39692|0.33141	T|T	0.17|0.24	.|.	7.2108|7.2108	0.25933|0.25933	0.4235:0.0:0.5765:0.0|0.4235:0.0:0.5765:0.0	.|.	.|115;115	.|C9JFX4;Q6IA17	.|.;SIGIR_HUMAN	V|R	23|115	ENSP00000435135:L23V|ENSP00000403104:P115R;ENSP00000380756:P115R;ENSP00000333656:P115R;ENSP00000433022:P115R;ENSP00000371960:P115R	ENSP00000435135:L23V|ENSP00000333656:P115R	L|P	-|-	1|2	2|0	SIGIRR|SIGIRR	397954|397954	0.037000|0.037000	0.19845|0.19845	0.021000|0.021000	0.16686|0.16686	0.052000|0.052000	0.14988|0.14988	2.008000|2.008000	0.40893|0.40893	0.035000|0.035000	0.15519|0.15519	-0.680000|-0.680000	0.03767|0.03767	CTA|CCT	G|0.995;C|0.005	0.005	strong		0.667	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805	
DNAJB13	374407	hgsc.bcm.edu	37	11	73681090	73681090	+	Silent	SNP	C	C	T	rs2306819	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:73681090C>T	ENST00000339764.1	+	8	1633	c.882C>T	c.(880-882)ttC>ttT	p.F294F	RP11-167N4.2_ENST00000537019.1_RNA|DNAJB13_ENST00000537753.1_Silent_p.F119F|DNAJB13_ENST00000543947.1_Silent_p.F119F	NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	294					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					TCATCTTCTTCGACATCCAGT	0.562													c|||	1263	0.252196	0.2095	0.3847	5008	,	,		18781	0.1637		0.3161	False		,,,				2504	0.2413				p.F294F		Atlas-SNP	.											.	DNAJB13	28	.	0			c.C882T						PASS	.	C		959,3441	362.9+/-316.3	97,765,1338	151.0	132.0	138.0		882	-6.4	0.9	11	dbSNP_100	138	2677,5909	429.8+/-356.3	392,1893,2008	no	coding-synonymous	DNAJB13	NM_153614.2		489,2658,3346	TT,TC,CC		31.1787,21.7955,27.9994		294/317	73681090	3636,9350	2200	4293	6493	SO:0001819	synonymous_variant	374407	exon8			CTTCTTCGACATC	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"""Heat shock proteins / DNAJ (HSP40)"""	30718	protein-coding gene	gene with protein product	"""radial spoke 16 homolog A (Chlamydomonas)"""	610263	"""DnaJ (Hsp40) related, subfamily B, member 13"""				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.882C>T	11.37:g.73681090C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_153614	B3LEP4|Q8IZW5	Silent	SNP	ENST00000339764.1	37	CCDS8227.1	579	0.2651098901098901	107	0.21747967479674796	130	0.35911602209944754	94	0.16433566433566432	248	0.32717678100263853	C	12.58	1.979869	0.34942	0.217955	0.311787	ENSG00000187726	ENST00000542350	.	.	.	5.54	-6.43	0.01926	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999713483	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2747	0.43504	0.0:0.2988:0.094:0.6072	rs2306819;rs57057868;rs2306819	.	.	.	X	195	.	.	R	+	1	2	DNAJB13	73358738	0.032000	0.19561	0.862000	0.33874	0.988000	0.76386	-0.949000	0.03893	-1.213000	0.02617	-0.365000	0.07479	CGA	C|0.731;T|0.269	0.269	strong		0.562	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614	
DYTN	391475	hgsc.bcm.edu	37	2	207572133	207572133	+	Silent	SNP	A	A	C	rs67248530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:207572133A>C	ENST00000452335.2	-	3	305	c.189T>G	c.(187-189)tcT>tcG	p.S63S	DYTN_ENST00000477734.1_5'Flank	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	63						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GGAGTGCCTGAGAAAGTTGCT	0.532													A|||	287	0.0573083	0.0499	0.1873	5008	,	,		17270	0.0		0.0676	False		,,,				2504	0.0235				p.S63S		Atlas-SNP	.											.	DYTN	168	.	0			c.T189G						PASS	.	A		180,3632		8,164,1734	62.0	60.0	61.0		189	-8.9	0.0	2	dbSNP_130	61	573,7689		22,529,3580	no	coding-synonymous	DYTN	NM_001093730.1		30,693,5314	CC,CA,AA		6.9354,4.7219,6.2365		63/579	207572133	753,11321	1906	4131	6037	SO:0001819	synonymous_variant	391475	exon3			TGCCTGAGAAAGT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.189T>G	2.37:g.207572133A>C		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	202	97	0.480198	NM_001093730		Silent	SNP	ENST00000452335.2	37	CCDS46502.1																																																																																			A|0.951;C|0.049	0.049	strong		0.532	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
OR10H5	284433	hgsc.bcm.edu	37	19	15905251	15905251	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15905251T>C	ENST00000308940.8	+	1	491	c.393T>C	c.(391-393)cgT>cgC	p.R131R		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						ACCCCCTGCGTTACAACGTGC	0.622																																					p.R131R		Atlas-SNP	.											OR10H5,colon,carcinoma,+1,1	OR10H5	49	1	0			c.T393C						scavenged	.						121.0	101.0	108.0					19																	15905251		2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			CCTGCGTTACAAC	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.393T>C	19.37:g.15905251T>C		Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	282	9	0.0319149	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			.	.	none		0.622	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
SCARA5	286133	hgsc.bcm.edu	37	8	27767231	27767231	+	Missense_Mutation	SNP	C	C	G	rs17058207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27767231C>G	ENST00000354914.3	-	5	1431	c.946G>C	c.(946-948)Gat>Cat	p.D316H	SCARA5_ENST00000301906.4_Missense_Mutation_p.D273H|SCARA5_ENST00000524352.1_Missense_Mutation_p.D316H|SCARA5_ENST00000380385.2_Missense_Mutation_p.D91H|SCARA5_ENST00000518030.1_Missense_Mutation_p.D273H|RP11-597M17.1_ENST00000517735.1_RNA	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	316	Collagen-like.		D -> H (in dbSNP:rs17058207). {ECO:0000269|Ref.3}.		cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		TTTCCTTCATCCCCCTGATCA	0.577													c|||	918	0.183307	0.1634	0.0706	5008	,	,		18293	0.376		0.0924	False		,,,				2504	0.1851				p.D316H		Atlas-SNP	.											.	SCARA5	53	.	0			c.G946C						PASS	.		HIS/ASP	589,3639		41,507,1566	94.0	62.0	73.0		946	-1.9	0.2	8	dbSNP_123	73	637,7529		27,583,3473	yes	missense	SCARA5	NM_173833.5	81	68,1090,5039	GG,GC,CC		7.8006,13.9309,9.8919	benign	316/496	27767231	1226,11168	2114	4083	6197	SO:0001583	missense	286133	exon5			CTTCATCCCCCTG	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"""scavenger receptor class A, member 5 (putative)"""			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.946G>C	8.37:g.27767231C>G	ENSP00000346990:p.Asp316His	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	125	50	0.4	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	37	CCDS6064.1	387	0.1771978021978022	100	0.2032520325203252	22	0.06077348066298342	191	0.3339160839160839	74	0.09762532981530343	C	7.087	0.571454	0.13623	0.139309	0.078006	ENSG00000168079	ENST00000354914;ENST00000380385;ENST00000517320;ENST00000524352;ENST00000518030;ENST00000301906	D;D;D;D;D	0.93189	-3.18;-3.18;-3.18;-3.18;-3.18	4.99	-1.85	0.07784	.	0.751599	0.13024	N	0.419834	T	0.00012	0.0000	L	0.28014	0.82	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.003;0.002	T	0.04885	-1.0920	9	0.12766	T	0.61	.	5.1821	0.15165	0.0:0.2863:0.166:0.5477	rs17058207;rs52827400;rs57572280;rs17058207	91;316;273;316	Q6ZMJ2-4;Q6ZMJ2-2;Q6ZMJ2-3;Q6ZMJ2	.;.;.;SCAR5_HUMAN	H	316;91;116;316;273;273	ENSP00000346990:D316H;ENSP00000369746:D91H;ENSP00000428663:D316H;ENSP00000430713:D273H;ENSP00000301906:D273H	ENSP00000301906:D273H	D	-	1	0	SCARA5	27823150	0.039000	0.19947	0.178000	0.23040	0.949000	0.60115	-0.072000	0.11486	-0.045000	0.13468	-0.291000	0.09656	GAT	C|0.835;G|0.165	0.165	strong		0.577	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
HCFC1	3054	hgsc.bcm.edu	37	X	153215839	153215839	+	Silent	SNP	G	G	A	rs3027875		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153215839G>A	ENST00000310441.7	-	24	6825	c.5859C>T	c.(5857-5859)tgC>tgT	p.C1953C	HCFC1_ENST00000354233.3_Silent_p.C1884C|HCFC1_ENST00000369984.4_Silent_p.C1998C	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1953	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGCTGGGCCCGCAGTACACCC	0.652													G|||	722	0.191258	0.0197	0.1816	3775	,	,		11049	0.002		0.4821	False		,,,				2504	0.0849				p.C1953C		Atlas-SNP	.											.	HCFC1	284	.	0			c.C5859T						PASS	.	G		298,3211		22,216,38,1232,531	41.0	47.0	45.0		5859	-5.3	0.9	X	dbSNP_102	45	4106,2410		924,1122,1136,313,662	no	coding-synonymous	HCFC1	NM_005334.2		946,1338,1174,1545,1193	AA,AG,A,GG,G		36.9859,8.4924,43.9302		1953/2036	153215839	4404,5621	2039	4157	6196	SO:0001819	synonymous_variant	3054	exon24			GGGCCCGCAGTAC		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.5859C>T	X.37:g.153215839G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1	475	0.2863170584689572	17	0.035269709543568464	46	0.15333333333333332	2	0.0034965034965034965	261	0.4943181818181818	G	10.91	1.485602	0.26686	0.084924	0.630141	ENSG00000172534	ENST00000444191	.	.	.	5.42	-5.26	0.02772	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11108	-1.0601	3	.	.	.	.	15.8112	0.78565	0.7732:0.0:0.2268:0.0	rs3027875	.	.	.	W	529	.	.	R	-	1	2	HCFC1	152869033	0.009000	0.17119	0.935000	0.37517	0.942000	0.58702	-0.600000	0.05693	-1.195000	0.02680	-0.411000	0.06167	CGG	G|0.712;A|0.288	0.288	strong		0.652	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
URGCP	55665	hgsc.bcm.edu	37	7	43916491	43916491	+	Silent	SNP	G	G	A	rs2232109	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43916491G>A	ENST00000453200.1	-	6	3064	c.2571C>T	c.(2569-2571)gaC>gaT	p.D857D	URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_Silent_p.D814D|URGCP_ENST00000223341.7_Silent_p.D814D|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000402306.3_Silent_p.D848D|URGCP_ENST00000443736.1_Silent_p.D814D|URGCP_ENST00000336086.6_Silent_p.D814D			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	857	VLIG-type G.				cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCCGGAAGCCGTCGCCCTGTT	0.642													G|||	366	0.0730831	0.028	0.0908	5008	,	,		18388	0.0149		0.1292	False		,,,				2504	0.1237				p.D857D		Atlas-SNP	.											.	URGCP	170	.	0			c.C2571T						PASS	.	G	,,,	193,3793		3,187,1803	29.0	30.0	30.0		2571,2442,,2544	-6.8	0.0	7	dbSNP_98	30	1068,7278		57,954,3162	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	,,,	60,1141,4965	AA,AG,GG		12.7965,4.8419,10.2254	,,,	857/932,814/889,,848/923	43916491	1261,11071	1993	4173	6166	SO:0001819	synonymous_variant	55665	exon6			GAAGCCGTCGCCC		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2571C>T	7.37:g.43916491G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Silent	SNP	ENST00000453200.1	37	CCDS47578.1																																																																																			G|0.918;A|0.082	0.082	strong		0.642	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
TCEB3B	51224	hgsc.bcm.edu	37	18	44560123	44560123	+	Missense_Mutation	SNP	C	C	T	rs72921305	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44560123C>T	ENST00000332567.4	-	1	1865	c.1513G>A	c.(1513-1515)Gga>Aga	p.G505R	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	505	Activation domain. {ECO:0000250}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						ACTCTGCGTCCAGGGAAAGCA	0.602													C|||	38	0.00758786	0.0008	0.0101	5008	,	,		18259	0.006		0.0209	False		,,,				2504	0.0031				p.G505R		Atlas-SNP	.											.	TCEB3B	141	.	0			c.G1513A						PASS	.	C	ARG/GLY,	17,4389	23.3+/-48.9	0,17,2186	71.0	81.0	78.0		1513,	2.1	0.0	18	dbSNP_130	78	125,8475	61.3+/-123.2	0,125,4175	yes	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	125,	0,142,6361	TT,TC,CC		1.4535,0.3858,1.0918	possibly-damaging,	505/754,	44560123	142,12864	2203	4300	6503	SO:0001583	missense	51224	exon1			TGCGTCCAGGGAA	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1513G>A	18.37:g.44560123C>T	ENSP00000331302:p.Gly505Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	143	59	0.412587	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	25	0.011446886446886446	1	0.0020325203252032522	4	0.011049723756906077	5	0.008741258741258742	15	0.01978891820580475	C	14.04	2.416024	0.42817	0.003858	0.014535	ENSG00000206181	ENST00000332567	T	0.16196	2.36	2.1	2.1	0.27182	.	0.126699	0.35262	N	0.003338	T	0.10508	0.0257	M	0.69358	2.11	0.19575	N	0.999967	P	0.42556	0.783	B	0.44044	0.439	T	0.04885	-1.0920	10	0.72032	D	0.01	-27.8142	7.7614	0.28955	0.0:1.0:0.0:0.0	.	505	Q8IYF1	ELOA2_HUMAN	R	505	ENSP00000331302:G505R	ENSP00000331302:G505R	G	-	1	0	TCEB3B	42814121	0.050000	0.20438	0.002000	0.10522	0.001000	0.01503	2.357000	0.44125	1.505000	0.48720	0.609000	0.83330	GGA	C|0.988;T|0.012	0.012	strong		0.602	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
FAM86A	196483	hgsc.bcm.edu	37	16	5139186	5139186	+	Missense_Mutation	SNP	G	G	C	rs12928528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:5139186G>C	ENST00000427587.4	-	7	882	c.814C>G	c.(814-816)Cac>Gac	p.H272D	FAM86A_ENST00000458008.4_Missense_Mutation_p.H238D|FAM86A_ENST00000587133.1_Missense_Mutation_p.H211D	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	272			H -> D (in dbSNP:rs12928528). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						GCCCGCTGGTGCTCCCGGCAG	0.622													g|||	2176	0.434505	0.0703	0.464	5008	,	,		15603	0.5833		0.5895	False		,,,				2504	0.593				p.H272D		Atlas-SNP	.											FAM86A,NS,carcinoma,0,1	FAM86A	32	1	0			c.C814G						scavenged	.	G	ASP/HIS,ASP/HIS	472,2534		45,382,1076	55.0	65.0	62.0		814,712	-2.0	0.0	16	dbSNP_121	62	3085,2327		864,1357,485	no	missense,missense	FAM86A	NM_201400.2,NM_201598.2	81,81	909,1739,1561	CC,CG,GG		42.997,15.7019,42.2547	benign,benign	272/331,238/297	5139186	3557,4861	1503	2706	4209	SO:0001583	missense	196483	exon7			GCTGGTGCTCCCG	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.814C>G	16.37:g.5139186G>C	ENSP00000398502:p.His272Asp	Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_201400	D3DUF0|Q96S85	Missense_Mutation	SNP	ENST00000427587.4	37	CCDS10529.1	1029	0.47115384615384615	57	0.11585365853658537	184	0.5082872928176796	343	0.5996503496503497	445	0.5870712401055409	g	0.001	-2.915346	0.00055	0.157019	0.57003	ENSG00000118894	ENST00000458008;ENST00000427587	T;T	0.15952	2.38;2.38	4.05	-2.01	0.07410	.	1.611030	0.03850	N	0.272086	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.42699	-0.9436	9	0.09843	T	0.71	.	2.7619	0.05308	0.1355:0.2586:0.4323:0.1736	rs12928528;rs17855416	238;272	Q96G04-2;Q96G04	.;FA86A_HUMAN	D	238;272	ENSP00000389710:H238D;ENSP00000398502:H272D	ENSP00000398502:H272D	H	-	1	0	FAM86A	5079187	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.600000	0.05693	-0.443000	0.07180	-1.653000	0.00756	CAC	G|0.559;C|0.441	0.441	strong		0.622	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400	
IL17RB	55540	hgsc.bcm.edu	37	3	53883722	53883722	+	Silent	SNP	C	C	G	rs1025689	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:53883722C>G	ENST00000288167.3	+	3	135	c.126C>G	c.(124-126)ccC>ccG	p.P42P		NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B	42					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|regulation of cell growth (GO:0001558)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		ATCTAATCCCCGGAGACTTGA	0.498													C|||	2154	0.430112	0.0802	0.4597	5008	,	,		17510	0.4722		0.6332	False		,,,				2504	0.6299				p.P42P		Atlas-SNP	.											.	IL17RB	27	.	0			c.C126G						PASS	.	C		775,3631	313.6+/-293.2	71,633,1499	148.0	146.0	147.0		126	-7.7	0.8	3	dbSNP_86	147	5421,3179	654.1+/-401.1	1691,2039,570	no	coding-synonymous	IL17RB	NM_018725.3		1762,2672,2069	GG,GC,CC		36.9651,17.5897,47.6396		42/503	53883722	6196,6810	2203	4300	6503	SO:0001819	synonymous_variant	55540	exon3			AATCCCCGGAGAC	AF212365	CCDS2874.1	3p21.1	2008-02-05		2003-07-09	ENSG00000056736	ENSG00000056736		"""Interleukins and interleukin receptors"""	18015	protein-coding gene	gene with protein product		605458	"""interleukin 17B receptor"""	IL17BR		10749887, 10815801	Standard	NM_018725		Approved	IL17RH1, EVI27, CRL4	uc003dha.3	Q9NRM6	OTTHUMG00000158280	ENST00000288167.3:c.126C>G	3.37:g.53883722C>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_018725	Q9BPZ0|Q9NRL4|Q9NRM5	Silent	SNP	ENST00000288167.3	37	CCDS2874.1																																																																																			C|0.534;G|0.466	0.466	strong		0.498	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234	
CRTAC1	55118	hgsc.bcm.edu	37	10	99696003	99696003	+	Silent	SNP	G	G	A	rs35027739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:99696003G>A	ENST00000370597.3	-	3	700	c.345C>T	c.(343-345)atC>atT	p.I115I	CRTAC1_ENST00000298819.4_Silent_p.I115I|CRTAC1_ENST00000370591.2_Silent_p.I115I	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	115						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		CTGTGACCCCGATGGCGTTCC	0.632													G|||	538	0.107428	0.0613	0.0893	5008	,	,		17709	0.0208		0.166	False		,,,				2504	0.2117				p.I115I		Atlas-SNP	.											.	CRTAC1	86	.	0			c.C345T						PASS	.	G	,	342,4064	177.3+/-206.3	19,304,1880	73.0	57.0	63.0		345,345	-3.0	1.0	10	dbSNP_126	63	1713,6887	314.7+/-311.9	179,1355,2766	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	198,1659,4646	AA,AG,GG		19.9186,7.7621,15.8004	,	115/646,115/662	99696003	2055,10951	2203	4300	6503	SO:0001819	synonymous_variant	55118	exon3			GACCCCGATGGCG	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.345C>T	10.37:g.99696003G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																			G|0.861;A|0.139	0.139	strong		0.632	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
MUC16	94025	hgsc.bcm.edu	37	19	9058624	9058624	+	Missense_Mutation	SNP	G	G	A	rs11878666	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9058624G>A	ENST00000397910.4	-	3	29025	c.28822C>T	c.(28822-28824)Ccc>Tcc	p.P9608S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9610	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCACCAGAGGGCATCTTGTAA	0.527													G|||	964	0.192492	0.0908	0.2824	5008	,	,		21210	0.3313		0.167	False		,,,				2504	0.1493				p.P9608S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C28822T						PASS	.	G	SER/PRO	409,3633		18,373,1630	106.0	98.0	100.0		28822	-5.0	0.0	19	dbSNP_120	100	1518,6844		136,1246,2799	yes	missense	MUC16	NM_024690.2	74	154,1619,4429	AA,AG,GG		18.1536,10.1188,15.5353	benign	9608/14508	9058624	1927,10477	2021	4181	6202	SO:0001583	missense	94025	exon3			CAGAGGGCATCTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28822C>T	19.37:g.9058624G>A	ENSP00000381008:p.Pro9608Ser	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	286	133	0.465035	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	481	0.22023809523809523	54	0.10975609756097561	93	0.2569060773480663	208	0.36363636363636365	126	0.1662269129287599	g	8.218	0.801892	0.16397	0.101188	0.181536	ENSG00000181143	ENST00000397910	T	0.01505	4.82	2.5	-5.0	0.03001	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B	0.19817	0.039	B	0.18263	0.021	T	0.46596	-0.9180	7	0.87932	D	0	.	2.0697	0.03610	0.5346:0.1429:0.1786:0.144	rs11878666;rs52808802;rs11878666	9608	B5ME49	.	S	9608	ENSP00000381008:P9608S	ENSP00000381008:P9608S	P	-	1	0	MUC16	8919624	0.000000	0.05858	0.000000	0.03702	0.542000	0.35054	-0.925000	0.03992	-1.950000	0.01030	0.305000	0.20034	CCC	G|0.785;A|0.215	0.215	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TPO	7173	hgsc.bcm.edu	37	2	1499927	1499927	+	Missense_Mutation	SNP	A	A	C	rs732609	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:1499927A>C	ENST00000345913.4	+	12	2264	c.2173A>C	c.(2173-2175)Act>Cct	p.T725P	TPO_ENST00000337415.3_Missense_Mutation_p.T725P|TPO_ENST00000382198.1_Missense_Mutation_p.T552P|TPO_ENST00000349624.3_Missense_Mutation_p.T552P|TPO_ENST00000346956.3_Missense_Mutation_p.T725P|TPO_ENST00000329066.4_Missense_Mutation_p.T725P|TPO_ENST00000382201.3_Missense_Mutation_p.T668P|TPO_ENST00000497517.2_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	725			T -> P (in dbSNP:rs732609). {ECO:0000269|PubMed:12454013, ECO:0000269|PubMed:3453124, ECO:0000269|PubMed:3475693, ECO:0000269|PubMed:7550241, ECO:0000269|Ref.6}.		cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGACAGCATCACTGGCATGAA	0.537													C|||	2496	0.498403	0.6498	0.438	5008	,	,		14798	0.4087		0.4026	False		,,,				2504	0.5276				p.T725P		Atlas-SNP	.											.	TPO	224	.	0			c.A2173C						PASS	.	C	PRO/THR,PRO/THR,PRO/THR,PRO/THR,PRO/THR,PRO/THR	2676,1730	516.0+/-369.1	831,1014,358	57.0	58.0	58.0		2173,2173,2002,2002,2173,1654	4.4	0.1	2	dbSNP_86	58	3441,5159	636.0+/-399.1	678,2085,1537	yes	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	38,38,38,38,38,38	1509,3099,1895	CC,CA,AA		40.0116,39.2646,47.0321	benign,benign,benign,benign,benign,benign	725/934,725/934,668/877,668/877,725/890,552/761	1499927	6117,6889	2203	4300	6503	SO:0001583	missense	7173	exon12			AGCATCACTGGCA		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2173A>C	2.37:g.1499927A>C	ENSP00000318820:p.Thr725Pro	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	1029	0.47115384615384615	329	0.6686991869918699	157	0.43370165745856354	248	0.43356643356643354	295	0.3891820580474934	C	0.014	-1.590934	0.00864	0.607354	0.400116	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607	T;T;T;T;T;T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5	4.39	4.39	0.52855	.	0.154798	0.64402	N	0.000016	T	0.00012	0.0000	N	0.00021	-2.755	0.09310	P	1.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47249	-0.9132	9	0.02654	T	1	-17.571	11.1959	0.48713	0.1431:0.719:0.1379:0.0	rs732609;rs1042585;rs3182054;rs17788434;rs59072806;rs732609	725;552;668;725	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	P	725;725;725;552;725;668;552;654;199	ENSP00000337263:T725P;ENSP00000318820:T725P;ENSP00000263886:T725P;ENSP00000332044:T552P;ENSP00000329869:T725P;ENSP00000371636:T668P;ENSP00000371633:T552P;ENSP00000405788:T654P;ENSP00000419461:T199P	ENSP00000329869:T725P	T	+	1	0	TPO	1478934	0.985000	0.35326	0.103000	0.21229	0.004000	0.04260	3.471000	0.53107	0.993000	0.38866	-0.217000	0.12591	ACT	A|0.520;C|0.480	0.480	strong		0.537	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
CD6	923	hgsc.bcm.edu	37	11	60785463	60785463	+	Silent	SNP	C	C	T	rs12417503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60785463C>T	ENST00000313421.7	+	11	2001	c.1815C>T	c.(1813-1815)gcC>gcT	p.A605A	CD6_ENST00000452451.2_Silent_p.A564A|CD6_ENST00000344028.5_Silent_p.A573A|CD6_ENST00000352009.5_Silent_p.A573A|CD6_ENST00000346437.4_Silent_p.A532A	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	605					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						TGGAGCTGGCCGGCACCCAGC	0.587													C|||	446	0.0890575	0.0832	0.1239	5008	,	,		16155	0.001		0.1958	False		,,,				2504	0.0532				p.A605A	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											CD6_ENST00000313421,NS,carcinoma,+2,2	CD6	122	2	0			c.C1815T						PASS	.	C		425,3973		19,387,1793	41.0	46.0	44.0		1815	-4.3	0.5	11	dbSNP_120	44	1430,7150		125,1180,2985	no	coding-synonymous	CD6	NM_006725.3		144,1567,4778	TT,TC,CC		16.6667,9.6635,14.2934		605/669	60785463	1855,11123	2199	4290	6489	SO:0001819	synonymous_variant	923	exon11			GCTGGCCGGCACC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1815C>T	11.37:g.60785463C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	37	CCDS7999.1																																																																																			C|0.875;T|0.125	0.125	strong		0.587	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
ARID3C	138715	hgsc.bcm.edu	37	9	34627764	34627764	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:34627764G>A	ENST00000378909.2	-	1	340	c.248C>T	c.(247-249)cCc>cTc	p.P83L		NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	83					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		AGGCGAGCTGGGGCCCTGGGC	0.627																																					p.P83L		Atlas-SNP	.											ARID3C,right_upper_lobe,carcinoma,+1,2	ARID3C	33	2	0			c.C248T						scavenged	.						51.0	48.0	49.0					9																	34627764		2203	4300	6503	SO:0001583	missense	138715	exon1			GAGCTGGGGCCCT		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"""-"""	21209	protein-coding gene	gene with protein product			"""AT rich interactive domain 3C (BRIGHT- like)"""				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.248C>T	9.37:g.34627764G>A	ENSP00000368189:p.Pro83Leu	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	190	2	0.0105263	NM_001017363		Missense_Mutation	SNP	ENST00000378909.2	37	CCDS35006.1	.	.	.	.	.	.	.	.	.	.	g	9.595	1.127048	0.20959	.	.	ENSG00000205143	ENST00000378909	T	0.47177	0.85	5.15	4.25	0.50352	.	1.687060	0.03031	N	0.152002	T	0.43456	0.1248	L	0.27053	0.805	0.21675	N	0.999599	B	0.24186	0.099	B	0.25405	0.06	T	0.41413	-0.9510	10	0.52906	T	0.07	-6.5411	12.8592	0.57903	0.0:0.164:0.836:0.0	.	83	A6NKF2	ARI3C_HUMAN	L	83	ENSP00000368189:P83L	ENSP00000368189:P83L	P	-	2	0	ARID3C	34617764	0.547000	0.26465	0.871000	0.34182	0.265000	0.26407	3.506000	0.53364	1.385000	0.46445	0.486000	0.48141	CCC	.	.	none		0.627	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061	
LMF2	91289	hgsc.bcm.edu	37	22	50945256	50945256	+	Silent	SNP	A	A	G	rs131824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50945256A>G	ENST00000474879.2	-	2	318	c.303T>C	c.(301-303)ccT>ccC	p.P101P	NCAPH2_ENST00000395698.3_5'Flank|NCAPH2_ENST00000395701.3_5'Flank|LMF2_ENST00000216080.5_Silent_p.P76P|NCAPH2_ENST00000299821.11_5'Flank|LMF2_ENST00000380796.3_Silent_p.P101P|NCAPH2_ENST00000420993.2_5'Flank|LMF2_ENST00000505981.1_5'UTR	NM_033200.2	NP_149977.2	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	101						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		AGTAGATGACAGGGTGGCGCA	0.662													.|||	1606	0.320687	0.5182	0.3069	5008	,	,		15694	0.0377		0.4185	False		,,,				2504	0.2546				p.P101P		Atlas-SNP	.											.	LMF2	40	.	0			c.T303C						PASS	.			2111,2271		500,1111,580	33.0	30.0	31.0		303	-2.6	0.0	22	dbSNP_78	31	3649,4941		767,2115,1413	no	coding-synonymous	LMF2	NM_033200.2		1267,3226,1993	GG,GA,AA		42.4796,48.1743,44.4033		101/708	50945256	5760,7212	2191	4295	6486	SO:0001819	synonymous_variant	91289	exon2			GATGACAGGGTGG	BC002942	CCDS14093.1, CCDS14093.2	22q13.33	2008-02-04	2007-11-29	2007-11-29	ENSG00000100258	ENSG00000100258			25096	protein-coding gene	gene with protein product			"""transmembrane protein 153"", ""transmembrane protein 112B"""	TMEM153, TMEM112B		12477932	Standard	NM_033200		Approved		uc003blp.2	Q9BU23	OTTHUMG00000150206	ENST00000474879.2:c.303T>C	22.37:g.50945256A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	111	68	0.612613	NM_033200	A6NEZ0|Q13392|Q6ZNR2|Q8WU74|Q96C62	Silent	SNP	ENST00000474879.2	37	CCDS14093.2	727	0.33287545787545786	261	0.5304878048780488	129	0.356353591160221	17	0.02972027972027972	320	0.42216358839050133	g	2.587	-0.296187	0.05532	0.481743	0.424796	ENSG00000100258	ENST00000487499	.	.	.	4.37	-2.61	0.06171	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47058	-0.9146	3	.	.	.	1.2215	1.9743	0.03412	0.2491:0.3852:0.2349:0.1308	rs131824	.	.	.	P	107	.	.	L	-	2	0	LMF2	49292122	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.755000	0.04782	-0.490000	0.06707	-1.769000	0.00663	CTG	A|0.593;G|0.407	0.407	strong		0.662	LMF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316833.2	NM_033200	
OR6T1	219874	hgsc.bcm.edu	37	11	123814489	123814489	+	Silent	SNP	A	A	G	rs4936859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123814489A>G	ENST00000321252.2	-	1	91	c.57T>C	c.(55-57)agT>agC	p.S19S		NM_001005187.1	NP_001005187.1	Q8NGN1	OR6T1_HUMAN	olfactory receptor, family 6, subfamily T, member 1	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		TGAGGTGGCTACTGGGGAAAC	0.483													A|||	1317	0.262979	0.056	0.3228	5008	,	,		19052	0.3839		0.3181	False		,,,				2504	0.319				p.S19S		Atlas-SNP	.											.	OR6T1	85	.	0			c.T57C						PASS	.	A		476,3928	224.6+/-240.7	30,416,1756	106.0	101.0	102.0		57	-7.5	0.0	11	dbSNP_111	102	2871,5727	452.0+/-362.8	460,1951,1888	no	coding-synonymous	OR6T1	NM_001005187.1		490,2367,3644	GG,GA,AA		33.3915,10.8084,25.7422		19/324	123814489	3347,9655	2202	4299	6501	SO:0001819	synonymous_variant	219874	exon1			GTGGCTACTGGGG	AB065759	CCDS31700.1	11q24.1	2012-08-09			ENSG00000181499	ENSG00000181499		"""GPCR / Class A : Olfactory receptors"""	14848	protein-coding gene	gene with protein product							Standard	NM_001005187		Approved		uc010sab.2	Q8NGN1	OTTHUMG00000165962	ENST00000321252.2:c.57T>C	11.37:g.123814489A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001005187	Q6IFE7	Silent	SNP	ENST00000321252.2	37	CCDS31700.1																																																																																			A|0.746;G|0.254	0.254	strong		0.483	OR6T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387264.1	NM_001005187	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134815	32134815	+	Missense_Mutation	SNP	G	G	A	rs16919122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32134815G>A	ENST00000312561.4	+	4	1340	c.926G>A	c.(925-927)cGa>cAa	p.R309Q	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	309			R -> Q (in dbSNP:rs16919122). {ECO:0000269|PubMed:10997877}.														CCTCAGAGTCGAGAAATGCTG	0.408													G|||	561	0.112021	0.1362	0.183	5008	,	,		21052	0.0655		0.1203	False		,,,				2504	0.0685				p.R309Q		Atlas-SNP	.											.	.	.	.	0			c.G926A						PASS	.	G	GLN/ARG	637,3769	275.2+/-272.4	44,549,1610	93.0	89.0	90.0		926	0.3	0.0	12	dbSNP_123	90	975,7625	211.1+/-251.8	57,861,3382	yes	missense	C12orf35	NM_018169.3	43	101,1410,4992	AA,AG,GG		11.3372,14.4576,12.3943	benign	309/1748	32134815	1612,11394	2203	4300	6503	SO:0001583	missense	55196	exon4			AGAGTCGAGAAAT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.926G>A	12.37:g.32134815G>A	ENSP00000310338:p.Arg309Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	50	0.390625	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	271	0.12408424908424909	73	0.1483739837398374	67	0.1850828729281768	40	0.06993006993006994	91	0.12005277044854881	G	1.870	-0.460463	0.04508	0.144576	0.113372	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.04502	4.24;3.61	5.34	0.344	0.16006	.	0.896444	0.09336	N	0.816138	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.48151	-0.9060	8	.	.	.	.	5.1251	0.14880	0.4273:0.382:0.1907:0.0	rs16919122;rs16919122	309	Q9HCM1	CL035_HUMAN	Q	309	ENSP00000310338:R309Q;ENSP00000370442:R309Q	.	R	+	2	0	C12orf35	32026082	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.222000	0.17699	0.089000	0.17243	-0.378000	0.06908	CGA	G|0.878;A|0.122	0.122	strong		0.408	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
MTMR3	8897	hgsc.bcm.edu	37	22	30403996	30403996	+	Silent	SNP	C	C	T	rs2074204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30403996C>T	ENST00000401950.2	+	11	1326	c.984C>T	c.(982-984)gcC>gcT	p.A328A	MTMR3_ENST00000351488.3_Silent_p.A328A|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000333027.3_Silent_p.A328A|MTMR3_ENST00000406629.1_Silent_p.A328A|MTMR3_ENST00000323630.5_Silent_p.A192A	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	328	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.|Substrate binding. {ECO:0000250}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			CAAACCGAGCCAAAGGAGGAG	0.522													C|||	1670	0.333466	0.5356	0.2392	5008	,	,		20059	0.2629		0.2256	False		,,,				2504	0.3108				p.A328A		Atlas-SNP	.											.	MTMR3	106	.	0			c.C984T						PASS	.	C	,,	2114,2292	576.2+/-384.2	494,1126,583	102.0	90.0	94.0		984,984,984	4.7	1.0	22	dbSNP_96	94	2133,6467	366.8+/-334.5	249,1635,2416	no	coding-synonymous,coding-synonymous,coding-synonymous	MTMR3	NM_021090.3,NM_153050.2,NM_153051.2	,,	743,2761,2999	TT,TC,CC		24.8023,47.98,32.6542	,,	328/1199,328/1171,328/1162	30403996	4247,8759	2203	4300	6503	SO:0001819	synonymous_variant	8897	exon11			CCGAGCCAAAGGA	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.984C>T	22.37:g.30403996C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	217	104	0.479263	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	37	CCDS13870.1																																																																																			C|0.678;T|0.322	0.322	strong		0.522	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	
TFEC	22797	hgsc.bcm.edu	37	7	115624478	115624478	+	Missense_Mutation	SNP	C	C	G	rs35695387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:115624478C>G	ENST00000265440.7	-	2	198	c.18G>C	c.(16-18)caG>caC	p.Q6H	TFEC_ENST00000393485.1_Missense_Mutation_p.Q6H|TFEC_ENST00000484212.1_Missense_Mutation_p.Q96H|TFEC_ENST00000320239.7_Missense_Mutation_p.Q6H	NM_012252.3	NP_036384.1	O14948	TFEC_HUMAN	transcription factor EC	6	Necessary for transcriptional transactivation.		Q -> H (in dbSNP:rs35695387).		cellular response to heat (GO:0034605)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|kidney(1)|large_intestine(5)|lung(13)|prostate(2)|skin(1)|urinary_tract(2)	25			STAD - Stomach adenocarcinoma(10;0.00878)			GATTGATGATCTGATGATCAA	0.493													C|||	67	0.0133786	0.0015	0.0101	5008	,	,		16222	0.001		0.0169	False		,,,				2504	0.0409				p.Q6H		Atlas-SNP	.											TFEC,colon,carcinoma,0,1	TFEC	51	1	0			c.G18C						PASS	.	C	HIS/GLN,HIS/GLN	36,4370	40.8+/-73.8	0,36,2167	179.0	157.0	164.0		18,18	2.0	0.1	7	dbSNP_126	164	263,8337	101.6+/-162.9	5,253,4042	yes	missense,missense	TFEC	NM_001018058.2,NM_012252.3	24,24	5,289,6209	GG,GC,CC		3.0581,0.8171,2.2989	possibly-damaging,possibly-damaging	6/319,6/348	115624478	299,12707	2203	4300	6503	SO:0001583	missense	22797	exon2			GATGATCTGATGA	D43945	CCDS5762.1, CCDS34738.1, CCDS59076.1	7q31.2	2013-05-21			ENSG00000105967	ENSG00000105967		"""Basic helix-loop-helix proteins"""	11754	protein-coding gene	gene with protein product		604732				9256061	Standard	NM_012252		Approved	TCFEC, TFECL, bHLHe34	uc003vhj.2	O14948	OTTHUMG00000023518	ENST00000265440.7:c.18G>C	7.37:g.115624478C>G	ENSP00000265440:p.Gln6His	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	249	117	0.46988	NM_001018058	B2R8X5|Q5H9U8|Q709A4|Q8N6J9	Missense_Mutation	SNP	ENST00000265440.7	37	CCDS5762.1	15	0.006868131868131868	0	0.0	3	0.008287292817679558	0	0.0	12	0.0158311345646438	C	11.80	1.747878	0.30955	0.008171	0.030581	ENSG00000105967	ENST00000265440;ENST00000320239;ENST00000393485;ENST00000484212	T;T;T;T	0.19250	2.21;2.16;2.41;2.46	4.89	2.05	0.26809	.	0.197880	0.44097	D	0.000484	T	0.06188	0.0160	N	0.14661	0.345	0.28799	N	0.898863	D;P;P;P	0.63880	0.993;0.911;0.911;0.883	P;P;P;B	0.56042	0.79;0.562;0.465;0.438	T	0.04128	-1.0975	10	0.87932	D	0	-1.5896	5.2814	0.15678	0.1618:0.6636:0.0:0.1746	rs35695387	96;6;6;6	B7Z757;O14948-3;O14948-2;O14948	.;.;.;TFEC_HUMAN	H	6;6;6;96	ENSP00000265440:Q6H;ENSP00000318676:Q6H;ENSP00000377125:Q6H;ENSP00000417432:Q96H	ENSP00000265440:Q6H	Q	-	3	2	TFEC	115411714	0.735000	0.28153	0.099000	0.21106	0.321000	0.28281	0.385000	0.20685	0.191000	0.20236	0.655000	0.94253	CAG	C|0.982;G|0.018	0.018	strong		0.493	TFEC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059839.4	NM_012252	
PIEZO1	9780	hgsc.bcm.edu	37	16	88793155	88793155	+	Missense_Mutation	SNP	C	C	T	rs185326407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88793155C>T	ENST00000301015.9	-	25	3913	c.3667G>A	c.(3667-3669)Gtc>Atc	p.V1223I		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1223					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						ATGACGGTGACGTTGTACAGA	0.687													C|||	6	0.00119808	0.0	0.0014	5008	,	,		13508	0.0		0.005	False		,,,				2504	0.0				p.V1223I		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G3667A						PASS	.	C	ILE/VAL	1,1383		0,1,691	46.0	43.0	44.0		3667	4.5	1.0	16		44	10,3168		0,10,1579	yes	missense	PIEZO1	NM_001142864.2	29	0,11,2270	TT,TC,CC		0.3147,0.0723,0.2411	possibly-damaging	1223/2522	88793155	11,4551	692	1589	2281	SO:0001583	missense	9780	exon25			CGGTGACGTTGTA	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.3667G>A	16.37:g.88793155C>T	ENSP00000301015:p.Val1223Ile	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	7|7	0.003205128205128205|0.003205128205128205	1|1	0.0020325203252032522|0.0020325203252032522	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	C|C	16.91|16.91	3.252370|3.252370	0.59212|0.59212	7.23E-4|7.23E-4	0.003147|0.003147	ENSG00000103335|ENSG00000103335	ENST00000451779|ENST00000301015	.|T	.|0.15952	.|2.38	4.51|4.51	4.51|4.51	0.55191|0.55191	.|.	.|0.283471	.|0.34291	.|N	.|0.004099	T|T	0.07999|0.07999	0.0200|0.0200	L|L	0.46947|0.46947	1.48|1.48	0.80722|0.80722	D|D	1|1	.|P	.|0.41748	.|0.761	.|B	.|0.29176	.|0.099	T|T	0.09818|0.09818	-1.0657|-1.0657	5|10	.|0.25106	.|T	.|0.35	-59.6841|-59.6841	9.855|9.855	0.41079|0.41079	0.0:0.9038:0.0:0.0962|0.0:0.9038:0.0:0.0962	.|.	.|1223	.|Q92508	.|PIEZ1_HUMAN	H|I	1168|1223	.|ENSP00000301015:V1223I	.|ENSP00000301015:V1223I	R|V	-|-	2|1	0|0	FAM38A|FAM38A	87320656|87320656	0.969000|0.969000	0.33509|0.33509	0.991000|0.991000	0.47740|0.47740	0.962000|0.962000	0.63368|0.63368	2.164000|2.164000	0.42387|0.42387	2.354000|2.354000	0.79902|0.79902	0.491000|0.491000	0.48974|0.48974	CGT|GTC	C|0.997;T|0.003	0.003	strong		0.687	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
C1orf87	127795	hgsc.bcm.edu	37	1	60506762	60506762	+	Silent	SNP	G	G	A	rs74843231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:60506762G>A	ENST00000371201.3	-	4	491	c.384C>T	c.(382-384)acC>acT	p.T128T	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	128							calcium ion binding (GO:0005509)	p.T128T(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						ACTGGTCTCCGGTTGGTACAG	0.507													G|||	267	0.0533147	0.0234	0.072	5008	,	,		20972	0.0645		0.0755	False		,,,				2504	0.046				p.T128T	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											C1orf87,NS,carcinoma,0,1	C1orf87	55	1	1	Substitution - coding silent(1)	stomach(1)	c.C384T						PASS	.	G		133,4273	95.3+/-134.0	1,131,2071	115.0	97.0	103.0		384	-1.9	0.9	1	dbSNP_131	103	643,7957	164.1+/-216.5	26,591,3683	no	coding-synonymous	C1orf87	NM_152377.2		27,722,5754	AA,AG,GG		7.4767,3.0186,5.9665		128/547	60506762	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	127795	exon4			GTCTCCGGTTGGT	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"""carcinoma-related EF-hand protein"""					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.384C>T	1.37:g.60506762G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	222	100	0.45045	NM_152377	Q6ZU07|Q8IVS0	Silent	SNP	ENST00000371201.3	37	CCDS614.1																																																																																			G|0.938;A|0.062	0.062	strong		0.507	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	
PRB2	653247	hgsc.bcm.edu	37	12	11546439	11546439	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:11546439G>A	ENST00000389362.4	-	3	608	c.573C>T	c.(571-573)ccC>ccT	p.P191P	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	191	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGGGACCTTGGGGCTGGTTGC	0.602																																					p.P191P		Atlas-SNP	.											PRB2_ENST00000389362,rectum,carcinoma,-1,2	PRB2	168	2	0			c.C573T						scavenged	.						132.0	133.0	133.0					12																	11546439		2160	4260	6420	SO:0001819	synonymous_variant	653247	exon3			ACCTTGGGGCTGG	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.573C>T	12.37:g.11546439G>A		Somatic	419	7	0.0167064		WXS	Illumina HiSeq	Phase_I	484	9	0.018595	NM_006248	O00599|P02811|P04281	Silent	SNP	ENST00000389362.4	37	CCDS41757.2																																																																																			.	.	none		0.602	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
TRAK2	66008	hgsc.bcm.edu	37	2	202252478	202252478	+	Silent	SNP	A	A	G	rs35620793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:202252478A>G	ENST00000332624.3	-	13	2072	c.1644T>C	c.(1642-1644)agT>agC	p.S548S		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	548					protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						CTCGAAGGCAACTGGCACTGC	0.493													A|||	103	0.0205671	0.0038	0.0519	5008	,	,		19358	0.0		0.0586	False		,,,				2504	0.0031				p.S548S		Atlas-SNP	.											.	TRAK2	62	.	0			c.T1644C						PASS	.	A		41,4365	45.3+/-79.5	0,41,2162	99.0	103.0	102.0		1644	0.8	1.0	2	dbSNP_126	102	536,8064	147.7+/-203.1	16,504,3780	no	coding-synonymous	TRAK2	NM_015049.2		16,545,5942	GG,GA,AA		6.2326,0.9305,4.4364		548/915	202252478	577,12429	2203	4300	6503	SO:0001819	synonymous_variant	66008	exon13			AAGGCAACTGGCA	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.1644T>C	2.37:g.202252478A>G		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	213	96	0.450704	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Silent	SNP	ENST00000332624.3	37	CCDS2347.1																																																																																			A|0.959;G|0.041	0.041	strong		0.493	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
BTBD16	118663	hgsc.bcm.edu	37	10	124096041	124096041	+	Silent	SNP	T	T	C	rs1129973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124096041T>C	ENST00000260723.4	+	15	1547	c.1296T>C	c.(1294-1296)tcT>tcC	p.S432S	BTBD16_ENST00000368994.2_Silent_p.S433S|BTBD16_ENST00000495370.2_3'UTR	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	432								p.S432S(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				AATCTCCCTCTGCGGTCTACG	0.557													C|||	2302	0.459665	0.3956	0.487	5008	,	,		17801	0.6935		0.327	False		,,,				2504	0.4223				p.S432S		Atlas-SNP	.											BTBD16,NS,lymphoid_neoplasm,0,1	BTBD16	44	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1296C						PASS	.	C		1588,2818	663.4+/-401.2	292,1004,907	69.0	59.0	63.0		1296	-2.8	0.0	10	dbSNP_86	63	2771,5829	677.6+/-403.4	446,1879,1975	no	coding-synonymous	BTBD16	NM_144587.2		738,2883,2882	CC,CT,TT		32.2209,36.0418,33.5153		432/507	124096041	4359,8647	2203	4300	6503	SO:0001819	synonymous_variant	118663	exon15			TCCCTCTGCGGTC	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1296T>C	10.37:g.124096041T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_144587	A6NM63|Q4VXL1|Q96LN0	Silent	SNP	ENST00000260723.4	37	CCDS31301.1																																																																																			T|0.621;C|0.379	0.379	strong		0.557	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
MYO7B	4648	hgsc.bcm.edu	37	2	128388862	128388862	+	Missense_Mutation	SNP	G	G	C	rs13025959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:128388862G>C	ENST00000409816.2	+	35	4973	c.4941G>C	c.(4939-4941)gaG>gaC	p.E1647D	MYO7B_ENST00000409090.1_Missense_Mutation_p.E500D|MYO7B_ENST00000428314.1_Missense_Mutation_p.E1647D|MYO7B_ENST00000389524.4_Missense_Mutation_p.E1647D			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1647	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.|SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.		E -> D (in dbSNP:rs13025959).			extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		ATTCCTGCGAGCCGCTGCGAC	0.647													G|||	842	0.168131	0.0499	0.1239	5008	,	,		15507	0.1349		0.2018	False		,,,				2504	0.3589				p.E1647D		Atlas-SNP	.											.	MYO7B	359	.	0			c.G4941C						PASS	.	G	ASP/GLU	318,3896		11,296,1800	24.0	31.0	29.0		4941	4.9	1.0	2	dbSNP_121	29	1605,6889		137,1331,2779	yes	missense	MYO7B	NM_001080527.1	45	148,1627,4579	CC,CG,GG		18.8957,7.5463,15.1322	possibly-damaging	1647/2117	128388862	1923,10785	2107	4247	6354	SO:0001583	missense	4648	exon36			CTGCGAGCCGCTG		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.4941G>C	2.37:g.128388862G>C	ENSP00000386461:p.Glu1647Asp	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	316	0.1446886446886447	26	0.052845528455284556	48	0.13259668508287292	88	0.15384615384615385	154	0.20316622691292877	g	12.16	1.855954	0.32791	0.075463	0.188957	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000409090	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.77	4.89	0.63831	MyTH4 domain (2);	0.057264	0.64402	D	0.000001	T	0.00073	0.0002	L	0.46819	1.47	0.24833	P	0.99251638	P	0.45044	0.849	B	0.38562	0.276	T	0.12578	-1.0542	9	0.25106	T	0.35	.	6.7962	0.23727	0.1477:0.0:0.7088:0.1435	rs13025959;rs17261992;rs13025959	1647	Q6PIF6	MYO7B_HUMAN	D	1647;1647;742;1647;500	ENSP00000374175:E1647D;ENSP00000415090:E1647D;ENSP00000386461:E1647D;ENSP00000386850:E500D	ENSP00000272666:E742D	E	+	3	2	MYO7B	128105332	1.000000	0.71417	0.999000	0.59377	0.084000	0.17831	2.170000	0.42443	1.447000	0.47661	0.655000	0.94253	GAG	G|0.845;C|0.155	0.155	strong		0.647	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
BGN	633	hgsc.bcm.edu	37	X	152771509	152771509	+	Silent	SNP	C	C	T	rs1126499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:152771509C>T	ENST00000331595.4	+	4	726	c.540C>T	c.(538-540)agC>agT	p.S180S	BGN_ENST00000480756.1_3'UTR	NM_001711.4	NP_001702.1	P21810	PGS1_HUMAN	biglycan	180					blood vessel remodeling (GO:0001974)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|glycosaminoglycan binding (GO:0005539)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GAGTGTTCAGCGGGCTCCGGA	0.607													C|||	1266	0.335364	0.0726	0.2853	3775	,	,		11034	0.3016		0.3767	False		,,,				2504	0.2955				p.S180S		Atlas-SNP	.											.	BGN	44	.	0			c.C540T						PASS	.	C		628,3207		40,453,95,1139,476	50.0	46.0	47.0		540	-9.4	0.5	X	dbSNP_86	47	3135,3593		508,1207,912,713,960	no	coding-synonymous	BGN	NM_001711.4		548,1660,1007,1852,1436	TT,TC,T,CC,C		46.5963,16.3755,35.6243		180/369	152771509	3763,6800	2203	4300	6503	SO:0001819	synonymous_variant	633	exon4			GTTCAGCGGGCTC	AK092954	CCDS14721.1	Xq28	2008-02-05			ENSG00000182492	ENSG00000182492		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1044	protein-coding gene	gene with protein product	"""biglycan proteoglycan"""	301870				1612609	Standard	NM_001711		Approved	DSPG1, SLRR1A	uc004fhr.2	P21810	OTTHUMG00000024205	ENST00000331595.4:c.540C>T	X.37:g.152771509C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_001711	D3DWU3|P13247	Silent	SNP	ENST00000331595.4	37	CCDS14721.1																																																																																			C|0.658;T|0.342	0.342	strong		0.607	BGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060981.1	NM_001711	
OR10G9	219870	hgsc.bcm.edu	37	11	123893728	123893728	+	Missense_Mutation	SNP	G	G	C	rs200621698	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123893728G>C	ENST00000375024.1	+	1	9	c.9G>C	c.(7-9)aaG>aaC	p.K3N		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	3						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		AAATGTCCAAGACCAGCCTCG	0.517																																					p.K3N		Atlas-SNP	.											OR10G9,NS,carcinoma,+2,1	OR10G9	80	1	0			c.G9C						scavenged	.						140.0	131.0	134.0					11																	123893728		2201	4299	6500	SO:0001583	missense	219870	exon1			GTCCAAGACCAGC	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.9G>C	11.37:g.123893728G>C	ENSP00000364164:p.Lys3Asn	Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	417	43	0.103118	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.759443	0.00657	.	.	ENSG00000236981	ENST00000375024	T	0.04454	3.62	3.61	-3.89	0.04193	.	0.116776	0.37809	N	0.001939	T	0.00496	0.0016	N	0.00005	-3.295	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37798	-0.9690	10	0.02654	T	1	.	7.6102	0.28126	0.0:0.1837:0.1405:0.6758	.	3	Q8NGN4	O10G9_HUMAN	N	3	ENSP00000364164:K3N	ENSP00000364164:K3N	K	+	3	2	OR10G9	123398938	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.027000	0.01433	-1.263000	0.02455	-1.622000	0.00790	AAG	G|0.960;C|0.039	0.039	strong		0.517	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
ITGA10	8515	hgsc.bcm.edu	37	1	145536082	145536082	+	Missense_Mutation	SNP	G	G	A	rs2274616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145536082G>A	ENST00000369304.3	+	17	2349	c.2174G>A	c.(2173-2175)cGg>cAg	p.R725Q	ITGA10_ENST00000538811.1_Missense_Mutation_p.R594Q|ITGA10_ENST00000539363.1_Missense_Mutation_p.R582Q	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	725			R -> Q (in dbSNP:rs2274616).		axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TTGTCCCCTCGGAGGCTCCGG	0.557													G|||	582	0.116214	0.0961	0.1383	5008	,	,		19331	0.0704		0.1441	False		,,,				2504	0.1462				p.R725Q		Atlas-SNP	.											ITGA10,NS,carcinoma,-1,1	ITGA10	131	1	0			c.G2174A						PASS	.	G	GLN/ARG	483,3923	226.9+/-242.2	22,439,1742	102.0	95.0	97.0		2174	2.4	0.6	1	dbSNP_100	97	1383,7217	267.8+/-287.5	107,1169,3024	yes	missense	ITGA10	NM_003637.3	43	129,1608,4766	AA,AG,GG		16.0814,10.9623,14.3472	benign	725/1168	145536082	1866,11140	2203	4300	6503	SO:0001583	missense	8515	exon17			CCCCTCGGAGGCT	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.2174G>A	1.37:g.145536082G>A	ENSP00000358310:p.Arg725Gln	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	258	146	0.565891	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	278	0.12728937728937728	61	0.12398373983739837	54	0.14917127071823205	45	0.07867132867132867	118	0.15567282321899736	G	12.04	1.817184	0.32145	0.109623	0.160814	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.44083	0.93;0.93;0.93	5.28	2.38	0.29361	Integrin alpha-2 (1);	0.391778	0.24136	N	0.041206	T	0.10809	0.0264	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B	0.21381	0.05;0.05;0.049;0.055	B;B;B;B	0.18871	0.022;0.022;0.008;0.023	T	0.10086	-1.0645	9	0.40728	T	0.16	.	3.9803	0.09492	0.2552:0.0:0.5795:0.1653	rs2274616;rs52834043;rs57401273;rs2274616	691;594;582;725	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	Q	725;691;582;594	ENSP00000358310:R725Q;ENSP00000439894:R582Q;ENSP00000440011:R594Q	ENSP00000358310:R725Q	R	+	2	0	ITGA10	144247439	0.316000	0.24580	0.586000	0.28679	0.821000	0.46438	0.539000	0.23175	0.361000	0.24292	-0.448000	0.05591	CGG	G|0.869;A|0.131	0.131	strong		0.557	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	
MLC1	23209	hgsc.bcm.edu	37	22	50515270	50515270	+	Splice_Site	SNP	T	T	C	rs267607236|rs6010164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50515270T>C	ENST00000311597.5	-	7	1203	c.597A>G	c.(595-597)tcA>tcG	p.S199S	MLC1_ENST00000450140.2_Splice_Site_p.S147S|MLC1_ENST00000395876.2_Splice_Site_p.S199S|MLC1_ENST00000538737.1_Splice_Site_p.S165S|MLC1_ENST00000535444.1_Splice_Site_p.S120S|MLC1_ENST00000431262.2_Splice_Site_p.S169S	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	199					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		GTTTTCTTACTGAGTAAGATT	0.498													T|||	654	0.130591	0.0847	0.1585	5008	,	,		18136	0.0913		0.1153	False		,,,				2504	0.229				p.S199S		Atlas-SNP	.											.	MLC1	48	.	0			c.A597G	GRCh37	CD012018	MLC1	D	rs6010164	PASS	.	T	,	449,3957	213.8+/-233.3	25,399,1779	103.0	108.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	597,597	-6.9	0.3	22	dbSNP_114	106	1021,7579	218.5+/-256.9	57,907,3336	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	MLC1	NM_015166.3,NM_139202.2	,	82,1306,5115	CC,CT,TT		11.8721,10.1906,11.3025	,	199/378,199/378	50515270	1470,11536	2203	4300	6503	SO:0001630	splice_region_variant	23209	exon7			TCTTACTGAGTAA	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.597+1A>G	22.37:g.50515270T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	64	41	0.640625	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			T|0.887;C|0.113	0.113	strong		0.498	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	Silent
TTN	7273	hgsc.bcm.edu	37	2	179638238	179638238	+	Silent	SNP	G	G	A	rs2291306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179638238G>A	ENST00000591111.1	-	32	7769	c.7545C>T	c.(7543-7545)taC>taT	p.Y2515Y	TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Silent_p.Y2469Y|TTN_ENST00000360870.5_Silent_p.Y2515Y|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000460472.2_Silent_p.Y2469Y|TTN_ENST00000342992.6_Silent_p.Y2515Y|TTN_ENST00000359218.5_Silent_p.Y2469Y|TTN_ENST00000589042.1_Silent_p.Y2515Y			Q8WZ42	TITIN_HUMAN	titin	12836	Ig-like 14.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTATCAGCTTGTAAGGTCCTT	0.393													G|||	378	0.0754792	0.0809	0.0706	5008	,	,		20564	0.0218		0.0954	False		,,,				2504	0.1063				p.Y2515Y		Atlas-SNP	.											.	TTN	18412	.	0			c.C7545T						PASS	.	G	,,,,	338,4068	177.3+/-206.3	18,302,1883	138.0	131.0	133.0		7407,7545,7545,7407,7407	4.0	1.0	2	dbSNP_100	133	986,7614	213.5+/-253.4	69,848,3383	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	87,1150,5266	AA,AG,GG		11.4651,7.6714,10.1799	,,,,	2469/26927,2515/33424,2515/5605,2469/27052,2469/27119	179638238	1324,11682	2203	4300	6503	SO:0001819	synonymous_variant	7273	exon32			CAGCTTGTAAGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.7545C>T	2.37:g.179638238G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.916;A|0.084	0.084	strong		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MUC16	94025	hgsc.bcm.edu	37	19	9046876	9046876	+	Missense_Mutation	SNP	G	G	T	rs4804378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9046876G>T	ENST00000397910.4	-	5	34958	c.34755C>A	c.(34753-34755)agC>agA	p.S11585R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11587	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAACCGTTGTGCTGGTTTCTG	0.522													G|||	927	0.185104	0.062	0.2752	5008	,	,		23096	0.3363		0.167	False		,,,				2504	0.1503				p.S11585R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C34755A						PASS	.		ARG/SER	303,3659		15,273,1693	137.0	134.0	135.0		34755	-0.2	0.0	19	dbSNP_111	135	1507,6803		139,1229,2787	yes	missense	MUC16	NM_024690.2	110	154,1502,4480	TT,TG,GG		18.1348,7.6477,14.749	benign	11585/14508	9046876	1810,10462	1981	4155	6136	SO:0001583	missense	94025	exon5			CGTTGTGCTGGTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34755C>A	19.37:g.9046876G>T	ENSP00000381008:p.Ser11585Arg	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	464	0.21245421245421245	34	0.06910569105691057	91	0.2513812154696133	213	0.3723776223776224	126	0.1662269129287599	g	4.341	0.062787	0.08388	0.076477	0.181348	ENSG00000181143	ENST00000397910	T	0.03181	4.02	2.29	-0.244	0.13031	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	.	.	.	B	0.30889	0.299	B	0.24394	0.053	T	0.45659	-0.9246	8	0.87932	D	0	.	4.6081	0.12387	0.0:0.1924:0.3015:0.506	rs4804378;rs52826356;rs57949188;rs4804378	11585	B5ME49	.	R	11585	ENSP00000381008:S11585R	ENSP00000381008:S11585R	S	-	3	2	MUC16	8907876	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.329000	0.02677	-0.010000	0.14271	0.197000	0.17608	AGC	G|0.807;T|0.193	0.193	strong		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TOR3A	64222	hgsc.bcm.edu	37	1	179055020	179055020	+	Silent	SNP	C	C	T	rs2296376	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:179055020C>T	ENST00000367627.3	+	3	1383	c.631C>T	c.(631-633)Ctg>Ttg	p.L211L	TOR3A_ENST00000352445.6_Silent_p.L211L|TOR3A_ENST00000495145.1_3'UTR	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	211					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						ATATGTGGACCTGTACAAGGT	0.582													C|||	663	0.132388	0.1112	0.0663	5008	,	,		21673	0.255		0.1402	False		,,,				2504	0.0736				p.L211L		Atlas-SNP	.											.	TOR3A	28	.	0			c.C631T						PASS	.	C		466,3940	217.8+/-236.0	21,424,1758	59.0	53.0	55.0		631	-0.4	0.6	1	dbSNP_100	55	1061,7539	220.1+/-257.9	61,939,3300	no	coding-synonymous	TOR3A	NM_022371.3		82,1363,5058	TT,TC,CC		12.3372,10.5765,11.7407		211/398	179055020	1527,11479	2203	4300	6503	SO:0001819	synonymous_variant	64222	exon3			GTGGACCTGTACA	BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"""ATP-dependant interferon responsive"""	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.631C>T	1.37:g.179055020C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	110	62	0.563636	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Silent	SNP	ENST00000367627.3	37	CCDS1329.1																																																																																			C|0.872;T|0.128	0.128	strong		0.582	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371	
CARD8	22900	hgsc.bcm.edu	37	19	48722180	48722180	+	Silent	SNP	C	C	T	rs10500299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48722180C>T	ENST00000359009.4	-	8	1245	c.933G>A	c.(931-933)gaG>gaA	p.E311E	CARD8_ENST00000521613.1_Silent_p.E367E|CARD8_ENST00000391898.3_Silent_p.E417E|CARD8_ENST00000357778.5_Silent_p.E142E|CARD8_ENST00000447740.2_Silent_p.E367E|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000520015.1_Intron|CARD8_ENST00000520153.1_Silent_p.E367E|CARD8_ENST00000520753.1_Intron|CARD8_ENST00000519940.1_Silent_p.E417E			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	311					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		TTTCAGTAATCTCAAGTTGAA	0.463													T|||	1300	0.259585	0.2042	0.3487	5008	,	,		17821	0.1766		0.2465	False		,,,				2504	0.3701				p.E417E		Atlas-SNP	.											.	CARD8	53	.	0			c.G1251A						PASS	.	T	,,,,	920,3486	739.1+/-411.0	92,736,1375	157.0	149.0	151.0		1251,1101,,,1101	1.2	0.0	19	dbSNP_119	151	2429,6171	699.2+/-405.1	379,1671,2250	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	,,,,	471,2407,3625	TT,TC,CC		28.2442,20.8806,25.7497	,,,,	417/538,367/488,,,367/488	48722180	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	22900	exon9			AGTAATCTCAAGT	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.933G>A	19.37:g.48722180C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	178	86	0.483146	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Silent	SNP	ENST00000359009.4	37																																																																																				C|0.758;T|0.242	0.242	strong		0.463	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733050	52733050	+	Missense_Mutation	SNP	T	T	A	rs12335014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:52733050T>A	ENST00000360540.5	-	7	1341	c.935A>T	c.(934-936)aAc>aTc	p.N312I	PCMTD1_ENST00000544451.1_Missense_Mutation_p.N236I|PCMTD1_ENST00000522514.1_Missense_Mutation_p.N312I|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	312			N -> I (in dbSNP:rs12335014). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				ctcttctttgttatcctcttc	0.398													T|||	2231	0.445487	0.0514	0.6254	5008	,	,		15882	0.4792		0.6292	False		,,,				2504	0.6268				p.N312I		Atlas-SNP	.											.	PCMTD1	73	.	0			c.A935T						PASS	.	T	ILE/ASN	717,3689	293.8+/-282.8	72,573,1558	101.0	84.0	90.0		935	0.4	0.9	8	dbSNP_120	90	5648,2952	633.8+/-398.8	1797,2054,449	no	missense	PCMTD1	NM_052937.2	149	1869,2627,2007	AA,AT,TT		34.3256,16.2733,48.939	benign	312/358	52733050	6365,6641	2203	4300	6503	SO:0001583	missense	115294	exon6			TCTTTGTTATCCT		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.935A>T	8.37:g.52733050T>A	ENSP00000353739:p.Asn312Ile	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	292	252	0.863014	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	954	0.4368131868131868	29	0.05894308943089431	216	0.5966850828729282	253	0.4423076923076923	456	0.6015831134564644	T	13.01	2.110648	0.37242	0.162733	0.656744	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.49139	0.79;0.79;0.79	5.97	0.36	0.16097	.	0.799495	0.12261	N	0.484695	T	0.00012	0.0000	N	0.22421	0.69	0.27279	P	0.9581572	P;B	0.34757	0.467;0.004	B;B	0.31614	0.133;0.008	T	0.39522	-0.9610	9	0.44086	T	0.13	-11.6135	5.5868	0.17279	0.0:0.3404:0.1421:0.5175	rs12335014;rs17853079;rs52825998;rs12335014	236;312	F5H1M8;Q96MG8	.;PCMD1_HUMAN	I	312;236;312	ENSP00000353739:N312I;ENSP00000444026:N236I;ENSP00000428099:N312I	ENSP00000353739:N312I	N	-	2	0	PCMTD1	52895603	0.969000	0.33509	0.925000	0.36789	0.993000	0.82548	0.918000	0.28678	0.044000	0.15775	0.533000	0.62120	AAC	T|0.570;A|0.430	0.430	strong		0.398	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
PER1	5187	hgsc.bcm.edu	37	17	8048169	8048169	+	Silent	SNP	T	T	C	rs2253820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8048169T>C	ENST00000317276.4	-	18	2598	c.2361A>G	c.(2359-2361)acA>acG	p.T787T	PER1_ENST00000581082.1_Silent_p.T767T|PER1_ENST00000354903.5_Silent_p.T771T|PER1_ENST00000578089.1_Intron	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	787	Required for phosphorylation by CSNK1E. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CTTCCTTCTGTGTGTGCAGGG	0.677			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					T|||	2856	0.570288	0.5061	0.5029	5008	,	,		14226	0.2847		0.8241	False		,,,				2504	0.7382				p.T787T		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.A2361G						PASS	.	T		2440,1966		674,1092,437	40.0	29.0	33.0		2361	0.6	1.0	17	dbSNP_100	33	7190,1410		3038,1114,148	no	coding-synonymous	PER1	NM_002616.2		3712,2206,585	CC,CT,TT		16.3953,44.621,25.9573		787/1291	8048169	9630,3376	2203	4300	6503	SO:0001819	synonymous_variant	5187	exon18			CTTCTGTGTGTGC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2361A>G	17.37:g.8048169T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_002616	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	37	CCDS11131.1																																																																																			T|0.361;C|0.639	0.639	strong		0.677	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
WNT16	51384	hgsc.bcm.edu	37	7	120972016	120972016	+	Missense_Mutation	SNP	C	C	A	rs74389152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:120972016C>A	ENST00000222462.2	+	3	921	c.631C>A	c.(631-633)Cag>Aag	p.Q211K	WNT16_ENST00000361301.2_Missense_Mutation_p.Q201K	NM_057168.1	NP_476509.1	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family, member 16	211					bone remodeling (GO:0046849)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|optic cup formation involved in camera-type eye development (GO:0003408)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|replicative senescence (GO:0090399)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)	18	all_neural(327;0.117)					AGCTGGAAGGCAGGTATGTAT	0.378													C|||	4	0.000798722	0.0	0.0	5008	,	,		19182	0.0		0.003	False		,,,				2504	0.001				p.Q211K		Atlas-SNP	.											.	WNT16	97	.	0			c.C631A						PASS	.	C	LYS/GLN,LYS/GLN	3,4403	6.2+/-15.9	0,3,2200	51.0	52.0	51.0		601,631	6.0	1.0	7	dbSNP_131	51	20,8580	14.6+/-50.1	0,20,4280	yes	missense,missense	WNT16	NM_016087.2,NM_057168.1	53,53	0,23,6480	AA,AC,CC		0.2326,0.0681,0.1768	benign,benign	201/356,211/366	120972016	23,12983	2203	4300	6503	SO:0001583	missense	51384	exon3			GGAAGGCAGGTAT	AF152584	CCDS5780.1, CCDS5781.1	7q31	2008-07-18			ENSG00000002745	ENSG00000002745		"""Wingless-type MMTV integration sites"""	16267	protein-coding gene	gene with protein product		606267				10500199	Standard	NM_016087		Approved		uc003vjw.3	Q9UBV4	OTTHUMG00000156963	ENST00000222462.2:c.631C>A	7.37:g.120972016C>A	ENSP00000222462:p.Gln211Lys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_057168	Q2M3G1|Q9Y5C0	Missense_Mutation	SNP	ENST00000222462.2	37	CCDS5781.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	7.287	0.610367	0.14066	6.81E-4	0.002326	ENSG00000002745	ENST00000361301;ENST00000222462	T;T	0.74632	-0.86;-0.86	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.60856	0.2301	N	0.13098	0.295	0.58432	D	0.999997	B;B	0.21688	0.059;0.059	B;B	0.29353	0.101;0.101	T	0.57723	-0.7762	10	0.05436	T	0.98	.	20.547	0.99278	0.0:1.0:0.0:0.0	.	211;201	Q9UBV4;E9PH60	WNT16_HUMAN;.	K	201;211	ENSP00000355065:Q201K;ENSP00000222462:Q211K	ENSP00000222462:Q211K	Q	+	1	0	WNT16	120759252	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.875000	0.56108	2.850000	0.98022	0.650000	0.86243	CAG	C|0.998;A|0.002	0.002	strong		0.378	WNT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346843.1	NM_057168	
OR2T3	343173	hgsc.bcm.edu	37	1	248637417	248637417	+	Missense_Mutation	SNP	C	C	T	rs74711605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248637417C>T	ENST00000359594.2	+	1	791	c.766C>T	c.(766-768)Ctc>Ttc	p.L256F		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGTGCTGCTGCTCTTCGGTGC	0.542													.|||	1453	0.290136	0.2572	0.2853	5008	,	,		31032	0.3661		0.2097	False		,,,				2504	0.3425				p.L256F		Atlas-SNP	.											.	OR2T3	79	.	0			c.C766T						PASS	.																																			SO:0001583	missense	343173	exon1			CTGCTGCTCTTCG		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.766C>T	1.37:g.248637417C>T	ENSP00000352604:p.Leu256Phe	Somatic	946	0	0		WXS	Illumina HiSeq	Phase_I	933	256	0.274384	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	t	0.011	-1.693742	0.00731	.	.	ENSG00000196539	ENST00000359594	T	0.00014	9.19	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	N	0.00047	-2.435	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39099	-0.9630	9	0.02654	T	1	.	5.7877	0.18343	0.0:0.1506:0.0:0.8494	.	256	Q8NH03	OR2T3_HUMAN	F	256	ENSP00000352604:L256F	ENSP00000352604:L256F	L	+	1	0	OR2T3	246704040	0.941000	0.31946	0.001000	0.08648	0.007000	0.05969	2.358000	0.44134	0.006000	0.14734	-1.455000	0.01032	CTC	C|0.889;T|0.111	0.111	strong		0.542	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
MUC5B	727897	hgsc.bcm.edu	37	11	1264965	1264965	+	Silent	SNP	G	G	A	rs4963051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1264965G>A	ENST00000529681.1	+	31	6913	c.6855G>A	c.(6853-6855)acG>acA	p.T2285T	MUC5B_ENST00000447027.1_Silent_p.T2288T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2285	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCACAGCCACGGCCACACCCA	0.677													g|||	559	0.111621	0.1467	0.0821	5008	,	,		15513	0.005		0.1918	False		,,,				2504	0.1125				p.T2285T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G6855A						PASS	.	G		578,3668		40,498,1585	79.0	114.0	102.0		6855	-2.8	0.0	11	dbSNP_111	102	1422,7008		145,1132,2938	no	coding-synonymous	MUC5B	NM_002458.2		185,1630,4523	AA,AG,GG		16.8683,13.6128,15.7778		2285/5763	1264965	2000,10676	2123	4215	6338	SO:0001819	synonymous_variant	727897	exon31			AGCCACGGCCACA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.6855G>A	11.37:g.1264965G>A		Somatic	551	1	0.00181488		WXS	Illumina HiSeq	Phase_I	422	236	0.559242	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.873;A|0.127	0.127	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
UGT2B28	54490	hgsc.bcm.edu	37	4	70152481	70152481	+	Silent	SNP	A	A	G	rs141618560	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70152481A>G	ENST00000335568.5	+	3	884	c.882A>G	c.(880-882)gaA>gaG	p.E294E	UGT2B28_ENST00000511240.1_Silent_p.E294E	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	294					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.E294E(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						AAATGGAGGAATTTGTACAGA	0.393													a|||	49	0.00978435	0.0159	0.0043	5008	,	,		10804	0.004		0.005	False		,,,				2504	0.0164				p.E294E		Atlas-SNP	.											UGT2B28,NS,carcinoma,0,4	UGT2B28	101	4	1	Substitution - coding silent(1)	kidney(1)	c.A882G						scavenged	.	G	,	12,4124		0,12,2056	125.0	143.0	138.0		882,882	-1.6	0.9	4	dbSNP_134	138	9,8499		0,9,4245	no	coding-synonymous,coding-synonymous	UGT2B28	NM_001207004.1,NM_053039.1	,	0,21,6301	GG,GA,AA		0.1058,0.2901,0.1661	,	294/336,294/530	70152481	21,12623	2068	4254	6322	SO:0001819	synonymous_variant	54490	exon3			GGAGGAATTTGTA	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.882A>G	4.37:g.70152481A>G		Somatic	202	2	0.00990099		WXS	Illumina HiSeq	Phase_I	111	5	0.045045	NM_053039	B5BUM0|Q9BY62|Q9BY63	Silent	SNP	ENST00000335568.5	37	CCDS3528.1																																																																																			A|1.000;G|0.000	0.000	weak		0.393	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
FRAS1	80144	hgsc.bcm.edu	37	4	79284694	79284694	+	Missense_Mutation	SNP	C	C	T	rs6835769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:79284694C>T	ENST00000325942.6	+	21	2890	c.2450C>T	c.(2449-2451)gCa>gTa	p.A817V	FRAS1_ENST00000264895.6_Missense_Mutation_p.A817V	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	817			A -> V (in dbSNP:rs6835769).		cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CAGCACTGTGCAGCTGATCTC	0.587													C|||	1680	0.335463	0.1278	0.5562	5008	,	,		20238	0.2004		0.5557	False		,,,				2504	0.3722				p.A817V		Atlas-SNP	.											.	FRAS1	779	.	0			c.C2450T						PASS	.	C	VAL/ALA,VAL/ALA	800,3450		95,610,1420	42.0	41.0	42.0		2450,2450	0.6	0.0	4	dbSNP_116	42	4650,3834		1278,2094,870	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	64,64	1373,2704,2290	TT,TC,CC		45.1909,18.8235,42.7988	benign,benign	817/1977,817/4013	79284694	5450,7284	2125	4242	6367	SO:0001583	missense	80144	exon21			ACTGTGCAGCTGA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.2450C>T	4.37:g.79284694C>T	ENSP00000326330:p.Ala817Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	790	0.3617216117216117	45	0.09146341463414634	198	0.5469613259668509	121	0.21153846153846154	426	0.5620052770448549	C	0.172	-1.070942	0.01918	0.188235	0.548091	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.28666	1.6;1.62	5.12	0.556	0.17253	.	1.234460	0.05524	N	0.562672	T	0.00012	0.0000	N	0.02830	-0.485	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.43228	-0.9404	9	0.02654	T	1	.	8.5026	0.33168	0.0:0.3754:0.0:0.6246	rs6835769;rs17459391;rs52828154;rs58632925;rs6835769	817;817	E9PHH6;A2RRR8	.;.	V	817	ENSP00000326330:A817V;ENSP00000264895:A817V	ENSP00000264895:A817V	A	+	2	0	FRAS1	79503718	0.000000	0.05858	0.001000	0.08648	0.432000	0.31715	-0.088000	0.11198	0.138000	0.18790	0.585000	0.79938	GCA	C|0.660;T|0.340	0.340	strong		0.587	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
IQCK	124152	hgsc.bcm.edu	37	16	19775403	19775403	+	Missense_Mutation	SNP	A	A	C	rs149444739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19775403A>C	ENST00000320394.6	+	7	1273	c.574A>C	c.(574-576)Att>Ctt	p.I192L	CTD-2380F24.1_ENST00000568843.1_RNA|IQCK_ENST00000433597.2_Missense_Mutation_p.I104L|IQCK_ENST00000562762.1_3'UTR|CTD-2380F24.1_ENST00000565817.1_RNA|IQCK_ENST00000541926.1_Missense_Mutation_p.I192L|CTD-2380F24.1_ENST00000564490.1_RNA|IQCK_ENST00000564186.1_Missense_Mutation_p.I192L	NM_153208.1	NP_694940.1	Q8N0W5	IQCK_HUMAN	IQ motif containing K	192										kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						ATTTTTCTCCATTCCATTTGT	0.368																																					p.I192L		Atlas-SNP	.											.	IQCK	35	.	0			c.A574C						PASS	.	A	LEU/ILE	5,4389	8.1+/-20.4	0,5,2192	79.0	76.0	77.0		574	5.1	1.0	16	dbSNP_134	77	40,8560	26.8+/-75.7	0,40,4260	yes	missense	IQCK	NM_153208.1	5	0,45,6452	CC,CA,AA		0.4651,0.1138,0.3463	probably-damaging	192/288	19775403	45,12949	2197	4300	6497	SO:0001583	missense	124152	exon7			TTCTCCATTCCAT	AF520569	CCDS10580.1	16p12.3	2008-02-05			ENSG00000174628	ENSG00000174628			28556	protein-coding gene	gene with protein product						10493829	Standard	NM_153208		Approved	MGC35048, FLJ36575	uc002dgr.3	Q8N0W5	OTTHUMG00000131453	ENST00000320394.6:c.574A>C	16.37:g.19775403A>C	ENSP00000324901:p.Ile192Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_153208	B2RDU0|O43327|Q8NFF4	Missense_Mutation	SNP	ENST00000320394.6	37	CCDS10580.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314559	0.81358	0.001138	0.004651	ENSG00000174628	ENST00000320394;ENST00000541926;ENST00000433597	T;T;T	0.23348	1.91;1.91;1.91	5.11	5.11	0.69529	.	0.000000	0.51477	D	0.000092	T	0.49932	0.1586	M	0.74881	2.28	0.38431	D	0.94645	D;D	0.67145	0.996;0.996	D;D	0.80764	0.994;0.994	T	0.55186	-0.8180	9	.	.	.	-15.7553	13.6471	0.62288	1.0:0.0:0.0:0.0	.	192;192	B4DXE1;Q8N0W5	.;IQCK_HUMAN	L	192;192;104	ENSP00000324901:I192L;ENSP00000439344:I192L;ENSP00000406013:I104L	.	I	+	1	0	IQCK	19682904	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.500000	0.66943	2.152000	0.67230	0.528000	0.53228	ATT	A|0.996;C|0.004	0.004	strong		0.368	IQCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254273.2	NM_153208	
NUP153	9972	hgsc.bcm.edu	37	6	17637404	17637404	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:17637404G>A	ENST00000262077.2	-	16	2443	c.2444C>T	c.(2443-2445)tCc>tTc	p.S815F	NUP153_ENST00000537253.1_Missense_Mutation_p.S846F	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	815					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			AGACATACAGGACACACACTT	0.348																																					p.S815F		Atlas-SNP	.											NUP153,NS,carcinoma,0,1	NUP153	116	1	0			c.C2444T						scavenged	.						91.0	86.0	88.0					6																	17637404		2203	4300	6503	SO:0001583	missense	9972	exon16			ATACAGGACACAC	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"""nucleoporin 153kD"""			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.2444C>T	6.37:g.17637404G>A	ENSP00000262077:p.Ser815Phe	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	211	3	0.014218	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	37	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.807768	0.90623	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.56611	0.45;0.45	5.73	5.73	0.89815	Zinc finger, RanBP2-type (4);	0.128581	0.34932	N	0.003566	T	0.59622	0.2207	L	0.57536	1.79	0.51233	D	0.999917	P;P;P	0.47604	0.898;0.84;0.86	P;P;P	0.54026	0.713;0.637;0.74	T	0.61173	-0.7116	10	0.87932	D	0	-3.5649	20.2602	0.98440	0.0:0.0:1.0:0.0	.	846;795;815	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	F	815;795;846	ENSP00000262077:S815F;ENSP00000444029:S846F	ENSP00000262077:S815F	S	-	2	0	NUP153	17745383	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.465000	0.80898	2.861000	0.98227	0.655000	0.94253	TCC	.	.	none		0.348	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		
DNAH8	1769	hgsc.bcm.edu	37	6	38746176	38746176	+	Missense_Mutation	SNP	G	G	A	rs61748601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38746176G>A	ENST00000359357.3	+	12	1578	c.1324G>A	c.(1324-1326)Gca>Aca	p.A442T	DNAH8_ENST00000441566.1_Missense_Mutation_p.A442T|DNAH8_ENST00000449981.2_Missense_Mutation_p.A659T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	442					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ACAAATACAGGCATTTATGAA	0.308													G|||	427	0.0852636	0.053	0.2334	5008	,	,		15929	0.0198		0.1362	False		,,,				2504	0.0389				p.A659T		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G1975A						PASS	.	G	THR/ALA	287,4119	151.8+/-185.6	8,271,1924	57.0	62.0	60.0		1975	3.5	1.0	6	dbSNP_129	60	1305,7291	252.5+/-278.5	94,1117,3087	yes	missense	DNAH8	NM_001206927.1	58	102,1388,5011	AA,AG,GG		15.1815,6.5138,12.2443	benign	659/4708	38746176	1592,11410	2203	4298	6501	SO:0001583	missense	1769	exon14			ATACAGGCATTTA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.1324G>A	6.37:g.38746176G>A	ENSP00000352312:p.Ala442Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	125	38	0.304	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		231	0.10576923076923077	31	0.06300813008130081	78	0.2154696132596685	14	0.024475524475524476	108	0.1424802110817942	G	5.727	0.318627	0.10845	0.065138	0.151815	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.55760	0.5;0.5;0.5	5.38	3.55	0.40652	Dynein heavy chain, domain-1 (1);	0.218905	0.36234	N	0.002710	T	0.06735	0.0172	N	0.01656	-0.775	0.27748	P	0.944242	B	0.02656	0.0	B	0.10450	0.005	T	0.27706	-1.0066	9	0.11182	T	0.66	.	4.7673	0.13139	0.1818:0.0:0.6235:0.1947	rs61748601	442	Q96JB1	DYH8_HUMAN	T	647;647;442;442	ENSP00000333363:A647T;ENSP00000352312:A442T;ENSP00000402294:A442T	ENSP00000333363:A647T	A	+	1	0	DNAH8	38854154	0.503000	0.26115	0.999000	0.59377	0.891000	0.51852	0.659000	0.24994	1.222000	0.43521	-0.274000	0.10170	GCA	G|0.880;A|0.120	0.120	strong		0.308	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
HYDIN	54768	hgsc.bcm.edu	37	16	71054116	71054116	+	Missense_Mutation	SNP	T	T	C	rs183427172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:71054116T>C	ENST00000393567.2	-	22	3441	c.3291A>G	c.(3289-3291)atA>atG	p.I1097M	HYDIN_ENST00000448089.2_Missense_Mutation_p.I1049M	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1097					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CAGTCTCACATATAAAGAAGG	0.502													T|||	8	0.00159744	0.0	0.0014	5008	,	,		16126	0.0		0.005	False		,,,				2504	0.002				p.I1097M		Atlas-SNP	.											.	HYDIN	788	.	0			c.A3291G						PASS	.	T	MET/ILE	2,3636		0,2,1817	35.0	37.0	37.0		3291	-9.2	0.0	16		37	23,8143		0,23,4060	yes	missense	HYDIN	NM_032821.2	10	0,25,5877	CC,CT,TT		0.2817,0.055,0.2118	possibly-damaging	1097/5121	71054116	25,11779	1819	4083	5902	SO:0001583	missense	54768	exon22			CTCACATATAAAG	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.3291A>G	16.37:g.71054116T>C	ENSP00000377197:p.Ile1097Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	14.02	2.410733	0.42817	5.5E-4	0.002817	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089	T;T	0.11063	2.81;2.81	4.61	-9.21	0.00678	.	0.254648	0.19540	U	0.111835	T	0.04363	0.0120	L	0.43923	1.385	0.51482	D	0.999923	P	0.40107	0.703	B	0.34385	0.181	T	0.38200	-0.9672	10	0.28530	T	0.3	.	1.6982	0.02866	0.2194:0.232:0.3592:0.1895	.	1097	F8WD23	.	M	1097;1097;1049	ENSP00000377197:I1097M;ENSP00000398544:I1049M	ENSP00000313052:I1097M	I	-	3	3	HYDIN	69611617	0.357000	0.24938	0.045000	0.18777	0.300000	0.27592	-0.549000	0.06041	-1.172000	0.02762	-0.394000	0.06481	ATA	T|0.998;C|0.002	0.002	strong		0.502	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
MICB	4277	hgsc.bcm.edu	37	6	31473561	31473561	+	Missense_Mutation	SNP	A	A	G	rs1065075	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31473561A>G	ENST00000252229.6	+	2	317	c.238A>G	c.(238-240)Aag>Gag	p.K80E	MICB_ENST00000538442.1_Missense_Mutation_p.K48E|MICB_ENST00000399150.3_Missense_Mutation_p.K80E	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						CCTGGGAGCTAAGACCTGGGA	0.572													a|||	1417	0.282947	0.3835	0.1902	5008	,	,		20308	0.2748		0.2634	False		,,,				2504	0.2413				p.K80E		Atlas-SNP	.											.	MICB	26	.	0			c.A238G						PASS	.	G	GLU/LYS	926,1650		172,582,534	39.0	43.0	41.0		238	-5.3	0.0	6	dbSNP_86	41	1565,3539		242,1081,1229	yes	missense	MICB	NM_005931.3	56	414,1663,1763	GG,GA,AA		30.6622,35.9472,32.4349	benign	80/384	31473561	2491,5189	1288	2552	3840	SO:0001583	missense	4277	exon2			GGAGCTAAGACCT		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"""Immunoglobulin superfamily / C1-set domain containing"""	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.238A>G	6.37:g.31473561A>G	ENSP00000252229:p.Lys80Glu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	155	65	0.419355	NM_005931		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	614	0.28113553113553114	198	0.4024390243902439	77	0.212707182320442	130	0.22727272727272727	209	0.2757255936675462	N	0.009	-1.797801	0.00617	0.359472	0.306622	ENSG00000204516	ENST00000538442;ENST00000399150;ENST00000252229	T;T;T	0.01335	5.0;5.0;5.0	2.64	-5.29	0.02747	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.673345	0.12089	N	0.500570	T	0.00109	0.0003	N	0.01152	-0.98	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.13407	0.004;0.009;0.001	T	0.32771	-0.9894	9	0.02654	T	1	.	3.1138	0.06367	0.1191:0.3073:0.4311:0.1425	rs1065075;rs3175107;rs16897483;rs59872907	48;80;80	F5H7Q8;A2AC57;Q29980	.;.;MICB_HUMAN	E	48;80;80	ENSP00000442345:K48E;ENSP00000382103:K80E;ENSP00000252229:K80E	ENSP00000252229:K80E	K	+	1	0	MICB	31581540	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.679000	0.05203	-1.442000	0.01955	-2.116000	0.00351	AAG	A|0.712;G|0.288	0.288	strong		0.572	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931	
GSTP1	2950	hgsc.bcm.edu	37	11	67352689	67352689	+	Missense_Mutation	SNP	A	A	G	rs1695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67352689A>G	ENST00000398606.3	+	5	562	c.313A>G	c.(313-315)Atc>Gtc	p.I105V	GSTP1_ENST00000498765.1_3'UTR|GSTP1_ENST00000398603.1_Missense_Mutation_p.I105V	NM_000852.3	NP_000843.1	P09211	GSTP1_HUMAN	glutathione S-transferase pi 1	105	GST C-terminal.		I -> V (in allele GSTP1*B and allele GSTP1*C; dbSNP:rs1695). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9092542, ECO:0000269|Ref.9}.		cellular response to lipopolysaccharide (GO:0071222)|central nervous system development (GO:0007417)|common myeloid progenitor cell proliferation (GO:0035726)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biosynthetic process (GO:0009890)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of leukocyte proliferation (GO:0070664)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|nitric oxide storage (GO:0035732)|positive regulation of superoxide anion generation (GO:0032930)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of stress-activated MAPK cascade (GO:0032872)|response to reactive oxygen species (GO:0000302)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|TRAF2-GSTP1 complex (GO:0097057)|vesicle (GO:0031982)	dinitrosyl-iron complex binding (GO:0035731)|glutathione transferase activity (GO:0004364)|JUN kinase binding (GO:0008432)|kinase regulator activity (GO:0019207)|nitric oxide binding (GO:0070026)|S-nitrosoglutathione binding (GO:0035730)			central_nervous_system(1)|cervix(1)|endometrium(4)|lung(2)|ovary(1)	9					Busulfan(DB01008)|Carboplatin(DB00958)|Chlorambucil(DB00291)|Cisplatin(DB00515)|Clomipramine(DB01242)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	CTGCAAATACATCTCCCTCAT	0.597													G|||	1766	0.352636	0.4803	0.4755	5008	,	,		16168	0.1786		0.331	False		,,,				2504	0.2945				p.I105V		Atlas-SNP	.											.	GSTP1	21	.	0			c.A313G	GRCh37	CM990713	GSTP1	M	rs1695	PASS	.	G	VAL/ILE	1749,2419		372,1005,707	90.0	98.0	96.0		313	-1.2	0.0	11	dbSNP_36	96	2786,5614		485,1816,1899	yes	missense	GSTP1	NM_000852.3	29	857,2821,2606	GG,GA,AA		33.1667,41.9626,36.0837	benign	105/211	67352689	4535,8033	2084	4200	6284	SO:0001583	missense	2950	exon5			AAATACATCTCCC	U12472	CCDS41679.1	11q13.2	2014-09-17	2008-07-18		ENSG00000084207	ENSG00000084207	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4638	protein-coding gene	gene with protein product		134660		FAEES3, GST3		1885604, 7587384, 19915149	Standard	NM_000852		Approved	GSTP	uc001omf.3	P09211	OTTHUMG00000137430	ENST00000398606.3:c.313A>G	11.37:g.67352689A>G	ENSP00000381607:p.Ile105Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_000852	O00460|Q15690|Q5TZY3	Missense_Mutation	SNP	ENST00000398606.3	37	CCDS41679.1	709	0.32463369963369965	218	0.44308943089430897	154	0.425414364640884	95	0.1660839160839161	242	0.31926121372031663	G	0.004	-2.264068	0.00262	0.419626	0.331667	ENSG00000084207	ENST00000398606;ENST00000398603	T;T	0.03358	3.96;3.96	5.31	-1.16	0.09678	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	1.719730	0.04143	N	0.319940	T	0.00012	0.0000	N	0.02129	-0.67	0.22001	P	0.999424	B	0.02656	0.0	B	0.01281	0.0	T	0.43556	-0.9384	9	0.02654	T	1	-0.9274	6.9834	0.24715	0.3594:0.12:0.5206:0.0	rs1695;rs4609;rs947894;rs1138257;rs2230827;rs11553891;rs17353321;rs17856342;rs56971933;rs1695	105	P09211	GSTP1_HUMAN	V	105	ENSP00000381607:I105V;ENSP00000381604:I105V	ENSP00000381604:I105V	I	+	1	0	GSTP1	67109265	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.510000	0.02262	-0.473000	0.06871	-2.931000	0.00088	ATC	A|0.689;G|0.311	0.311	strong		0.597	GSTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268504.1	NM_000852	
CARD9	64170	hgsc.bcm.edu	37	9	139270901	139270901	+	5'Flank	SNP	G	G	A	rs61745672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139270901G>A	ENST00000371732.5	-	0	0				CARD9_ENST00000371734.3_5'Flank|CARD9_ENST00000315908.7_5'Flank|SNAPC4_ENST00000298532.2_Silent_p.S1439S	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9						defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		CCAGGCAGGAGGAAGCAGAGC	0.607													G|||	171	0.0341454	0.0091	0.0461	5008	,	,		20815	0.002		0.1064	False		,,,				2504	0.0184				p.S1439S		Atlas-SNP	.											.	SNAPC4	82	.	0			c.C4317T						PASS	.	G		117,4289	87.3+/-125.9	3,111,2089	140.0	136.0	137.0		4317	0.3	0.0	9	dbSNP_129	137	823,7777	190.1+/-236.7	36,751,3513	no	coding-synonymous	SNAPC4	NM_003086.2		39,862,5602	AA,AG,GG		9.5698,2.6555,7.2274		1439/1470	139270901	940,12066	2203	4300	6503	SO:0001631	upstream_gene_variant	6621	exon22			GCAGGAGGAAGCA	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925		9.37:g.139270901G>A	Exception_encountered	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_003086	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			G|0.934;A|0.066	0.066	strong		0.607	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
KIFAP3	22920	hgsc.bcm.edu	37	1	169951997	169951997	+	Silent	SNP	C	C	T	rs33943686	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169951997C>T	ENST00000361580.2	-	14	1745	c.1518G>A	c.(1516-1518)ggG>ggA	p.G506G	KIFAP3_ENST00000538366.1_Silent_p.G428G|KIFAP3_ENST00000367765.1_Silent_p.G466G|KIFAP3_ENST00000540905.1_Silent_p.G208G|KIFAP3_ENST00000367767.1_Silent_p.G462G	NM_014970.3	NP_055785.2	Q92845	KIFA3_HUMAN	kinesin-associated protein 3	506					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|membrane organization (GO:0061024)|microtubule-based movement (GO:0007018)|microtubule-based process (GO:0007017)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of calcium-dependent cell-cell adhesion (GO:0046587)|protein complex assembly (GO:0006461)|protein localization (GO:0008104)|signal transduction (GO:0007165)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule cytoskeleton (GO:0015630)	kinesin binding (GO:0019894)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|prostate(2)|skin(3)|urinary_tract(2)	35	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CTGCAAGGTCCCCAACATAAT	0.313													C|||	1372	0.273962	0.087	0.2867	5008	,	,		13409	0.503		0.326	False		,,,				2504	0.228				p.G506G		Atlas-SNP	.											.	KIFAP3	102	.	0			c.G1518A						PASS	.	C	,,,	484,3922	208.8+/-229.8	34,416,1753	52.0	50.0	51.0		1284,1386,1398,1518	1.3	1.0	1	dbSNP_126	51	2759,5837	424.4+/-354.6	484,1791,2023	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIFAP3	NM_001204514.1,NM_001204516.1,NM_001204517.1,NM_014970.3	,,,	518,2207,3776	TT,TC,CC		32.0963,10.985,24.9423	,,,	428/715,462/749,466/753,506/793	169951997	3243,9759	2203	4298	6501	SO:0001819	synonymous_variant	22920	exon14			AAGGTCCCCAACA	U59919	CCDS1288.1, CCDS55659.1, CCDS55660.1, CCDS55661.1	1q24.2	2012-09-20			ENSG00000075945	ENSG00000075945			17060	protein-coding gene	gene with protein product	"""Smg GDS"""	601836				8900189	Standard	NM_014970		Approved	SMAP, KAP3, FLA3, KAP-1	uc001ggv.3	Q92845	OTTHUMG00000035947	ENST00000361580.2:c.1518G>A	1.37:g.169951997C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	37	0.362745	NM_014970	B1AKU4|B1AKU5|B2RDL1|B7Z8A3|F5H591|Q8NHU7|Q9H416	Silent	SNP	ENST00000361580.2	37	CCDS1288.1																																																																																			C|0.728;T|0.272	0.272	strong		0.313	KIFAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087568.1	NM_014970	
KIF13A	63971	hgsc.bcm.edu	37	6	17834198	17834198	+	Silent	SNP	T	T	G	rs4716189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:17834198T>G	ENST00000259711.6	-	12	1365	c.1260A>C	c.(1258-1260)atA>atC	p.I420I	KIF13A_ENST00000378843.2_Silent_p.I420I|KIF13A_ENST00000378826.2_Silent_p.I420I|KIF13A_ENST00000378814.5_Silent_p.I420I|KIF13A_ENST00000378816.5_Silent_p.I420I	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	420					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			CTACCTGTGCTATCTCTTCTG	0.378													G|||	2187	0.436701	0.2988	0.5144	5008	,	,		17599	0.4018		0.496	False		,,,				2504	0.5429				p.I420I		Atlas-SNP	.											.	KIF13A	276	.	0			c.A1260C						PASS	.	G	,,,	1238,2446		214,810,818	144.0	133.0	137.0		1260,1260,1260,1260	-2.6	0.9	6	dbSNP_111	137	3953,4239		950,2053,1093	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	1164,2863,1911	GG,GT,TT		48.2544,33.6048,43.71	,,,	420/1771,420/1758,420/1750,420/1806	17834198	5191,6685	1842	4096	5938	SO:0001819	synonymous_variant	63971	exon12			CTGTGCTATCTCT	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1260A>C	6.37:g.17834198T>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			T|0.583;G|0.417	0.417	strong		0.378	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
PABPC4L	132430	hgsc.bcm.edu	37	4	135121601	135121601	+	Missense_Mutation	SNP	C	C	T	rs10009368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:135121601C>T	ENST00000421491.3	-	2	830	c.574G>A	c.(574-576)Gtt>Att	p.V192I	PABPC4L_ENST00000529122.2_Missense_Mutation_p.V250I			P0CB38	PAB4L_HUMAN	poly(A) binding protein, cytoplasmic 4-like	192	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.		V -> I (in dbSNP:rs10009368).				nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)	3						TTTATGTAAACATTGGTGAAT	0.403													T|||	3189	0.636781	0.7179	0.5403	5008	,	,		20019	0.9841		0.329	False		,,,				2504	0.5542				p.V250I		Atlas-SNP	.											.	PABPC4L	60	.	0			c.G748A						PASS	.	T	ILE/VAL	925,459		310,305,77	133.0	114.0	120.0		748	-1.0	0.0	4	dbSNP_119	120	981,2201		143,695,753	yes	missense	PABPC4L	NM_001114734.1	29	453,1000,830	TT,TC,CC		30.8297,33.1647,41.7433	benign	250/429	135121601	1906,2660	692	1591	2283	SO:0001583	missense	132430	exon2			TGTAAACATTGGT	AY672099		4q28.3	2013-02-12				ENSG00000254535		"""RNA binding motif (RRM) containing"""	31955	protein-coding gene	gene with protein product							Standard	NM_001114734		Approved		uc010ioe.3	P0CB38		ENST00000421491.3:c.574G>A	4.37:g.135121601C>T	ENSP00000463233:p.Val192Ile	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	216	214	0.990741	NM_001114734		Missense_Mutation	SNP	ENST00000421491.3	37																																																																																				C|0.348;T|0.652	0.652	strong		0.403	PABPC4L-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364399.2	NM_001114734	
SPTBN5	51332	hgsc.bcm.edu	37	15	42145936	42145936	+	Missense_Mutation	SNP	G	G	C	rs1197660	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42145936G>C	ENST00000320955.6	-	58	10051	c.9824C>G	c.(9823-9825)gCc>gGc	p.A3275G	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3275			A -> G (in dbSNP:rs1197660).		actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CAGTCGGCAGGCCTCCGTCTG	0.672													G|||	1474	0.294329	0.4523	0.2349	5008	,	,		16740	0.0337		0.3489	False		,,,				2504	0.3354				p.A3240G		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C9719G						PASS	.	G	GLY/ALA	1691,2325		388,915,705	24.0	29.0	27.0		9719	2.9	0.1	15	dbSNP_87	27	2801,5507		502,1797,1855	yes	missense	SPTBN5	NM_016642.2	60	890,2712,2560	CC,CG,GG		33.7145,42.1066,36.4492	possibly-damaging	3240/3640	42145936	4492,7832	2008	4154	6162	SO:0001583	missense	51332	exon58			CGGCAGGCCTCCG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.9824C>G	15.37:g.42145936G>C	ENSP00000317790:p.Ala3275Gly	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		575	0.2632783882783883	217	0.4410569105691057	89	0.24585635359116023	14	0.024475524475524476	255	0.33641160949868076	.	14.97	2.695561	0.48202	0.421066	0.337145	ENSG00000137877	ENST00000320955	T	0.34472	1.36	4.74	2.86	0.33363	.	0.298852	0.27117	N	0.020856	T	0.00012	0.0000	M	0.76002	2.32	0.49687	P	1.8300000000004424E-4	P	0.37061	0.58	B	0.38683	0.279	T	0.46162	-0.9211	9	0.22109	T	0.4	.	9.1685	0.37065	0.1688:0.0:0.8312:0.0	rs1197660;rs1197660	3275	Q9NRC6	SPTN5_HUMAN	G	3275	ENSP00000317790:A3275G	ENSP00000317790:A3275G	A	-	2	0	SPTBN5	39933228	0.909000	0.30893	0.146000	0.22360	0.058000	0.15608	2.647000	0.46639	0.542000	0.28846	0.313000	0.20887	GCC	G|0.736;C|0.264	0.264	strong		0.672	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
EVC2	132884	hgsc.bcm.edu	37	4	5642274	5642274	+	Silent	SNP	T	T	C	rs13131655	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:5642274T>C	ENST00000344408.5	-	10	1490	c.1437A>G	c.(1435-1437)gaA>gaG	p.E479E	EVC2_ENST00000344938.1_Silent_p.E479E|EVC2_ENST00000310917.2_Silent_p.E399E	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	479					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						ACTCTTCTGCTTCCTCCATTG	0.463													T|||	1152	0.230032	0.5318	0.1542	5008	,	,		22239	0.001		0.2237	False		,,,				2504	0.1186				p.E479E		Atlas-SNP	.											.	EVC2	202	.	0			c.A1437G						PASS	.	T	,	2027,2379	564.7+/-381.5	477,1073,653	411.0	346.0	368.0		1197,1437	0.0	0.9	4	dbSNP_121	368	1809,6791	325.9+/-317.1	185,1439,2676	no	coding-synonymous,coding-synonymous	EVC2	NM_001166136.1,NM_147127.4	,	662,2512,3329	CC,CT,TT		21.0349,46.0054,29.4941	,	399/1229,479/1309	5642274	3836,9170	2203	4300	6503	SO:0001819	synonymous_variant	132884	exon10			TTCTGCTTCCTCC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1437A>G	4.37:g.5642274T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	214	102	0.476636	NM_147127	Q86YT3|Q86YT4|Q8NG49	Silent	SNP	ENST00000344408.5	37	CCDS3382.2																																																																																			T|0.716;C|0.284	0.284	strong		0.463	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
TEP1	7011	hgsc.bcm.edu	37	14	20847202	20847202	+	Silent	SNP	A	A	G	rs938887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20847202A>G	ENST00000262715.5	-	36	5230	c.5190T>C	c.(5188-5190)gaT>gaC	p.D1730D	TEP1_ENST00000545983.1_Silent_p.D68D|TEP1_ENST00000556935.1_Silent_p.D1622D	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1730					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GAAAGAGTGTATCATCGGAGA	0.567													A|||	1528	0.305112	0.4531	0.3559	5008	,	,		20391	0.2718		0.2058	False		,,,				2504	0.2055				p.D1730D		Atlas-SNP	.											.	TEP1	224	.	0			c.T5190C						PASS	.	A		1861,2545	539.6+/-375.3	389,1083,731	108.0	101.0	103.0		5190	-11.9	0.0	14	dbSNP_86	103	1688,6912	310.0+/-309.6	162,1364,2774	no	coding-synonymous	TEP1	NM_007110.4		551,2447,3505	GG,GA,AA		19.6279,42.2379,27.2874		1730/2628	20847202	3549,9457	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon36			GAGTGTATCATCG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5190T>C	14.37:g.20847202A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			A|0.719;C|0.001	.	strong		0.567	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
ADAM21	8747	hgsc.bcm.edu	37	14	70924542	70924542	+	Missense_Mutation	SNP	G	G	C	rs79958245	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70924542G>C	ENST00000603540.1	+	2	584	c.326G>C	c.(325-327)tGt>tCt	p.C109S	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.C109S	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	109					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		CCAGATGACTGTTACTATCAT	0.488																																					p.C109S		Atlas-SNP	.											.	ADAM21	181	.	0			c.G326C						PASS	.	G	SER/CYS	112,4294	83.4+/-121.9	0,112,2091	104.0	132.0	122.0		326	3.8	1.0	14	dbSNP_131	122	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADAM21	NM_003813.3	112	0,113,6390	CC,CG,GG		0.0116,2.542,0.8688	probably-damaging	109/723	70924542	113,12893	2203	4300	6503	SO:0001583	missense	8747	exon2			ATGACTGTTACTA	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.326G>C	14.37:g.70924542G>C	ENSP00000474385:p.Cys109Ser	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	254	71	0.279528	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	16.44	3.125317	0.56721	0.02542	1.16E-4	ENSG00000139985	ENST00000267499	T	0.11930	2.73	3.76	3.76	0.43208	Peptidase M12B, propeptide (1);	0.000000	0.47093	U	0.000245	T	0.27765	0.0683	H	0.96970	3.915	0.38555	D	0.94956	D	0.89917	1.0	D	0.97110	1.0	T	0.68580	-0.5371	10	0.87932	D	0	.	16.0998	0.81163	0.0:0.0:1.0:0.0	.	109	Q9UKJ8	ADA21_HUMAN	S	109	ENSP00000267499:C109S	ENSP00000267499:C109S	C	+	2	0	ADAM21	69994295	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.048000	0.57390	2.090000	0.63153	0.557000	0.71058	TGT	G|0.992;C|0.008	0.008	strong		0.488	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
COL24A1	255631	hgsc.bcm.edu	37	1	86557967	86557967	+	Missense_Mutation	SNP	G	G	A	rs11161732	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86557967G>A	ENST00000370571.2	-	6	2002	c.1636C>T	c.(1636-1638)Cct>Tct	p.P546S	COL24A1_ENST00000436319.1_Missense_Mutation_p.P546S	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	546			P -> S (in dbSNP:rs11161732). {ECO:0000269|PubMed:12874293}.		extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		CCAGGAACAGGTTGACCTGGG	0.299													g|||	1854	0.370208	0.3563	0.4467	5008	,	,		14797	0.3849		0.3767	False		,,,				2504	0.3129				p.P546S		Atlas-SNP	.											.	COL24A1	202	.	0			c.C1636T						PASS	.	G	SER/PRO	1273,2313		229,815,749	51.0	49.0	50.0		1636	3.9	1.0	1	dbSNP_120	50	3097,5009		589,1919,1545	yes	missense	COL24A1	NM_152890.5	74	818,2734,2294	AA,AG,GG		38.2063,35.4992,37.376	benign	546/1715	86557967	4370,7322	1793	4053	5846	SO:0001583	missense	255631	exon6			GAACAGGTTGACC	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.1636C>T	1.37:g.86557967G>A	ENSP00000359603:p.Pro546Ser	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	159	75	0.471698	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	832	0.38095238095238093	186	0.3780487804878049	155	0.4281767955801105	218	0.3811188811188811	273	0.36015831134564646	g	7.702	0.693226	0.15039	0.354992	0.382063	ENSG00000171502	ENST00000370571;ENST00000436319	D;T	0.93366	-3.21;2.35	4.81	3.91	0.45181	.	0.211715	0.23793	N	0.044515	T	0.73768	0.3629	N	0.03608	-0.345	0.52099	P	5.2000000000052005E-5	B;B	0.12013	0.0;0.005	B;B	0.14023	0.0;0.01	T	0.67417	-0.5676	9	0.46703	T	0.11	.	11.1546	0.48480	0.0:0.8136:0.1864:0.0	rs11161732;rs57096855;rs11161732	546;546	F8WDM8;Q17RW2	.;COOA1_HUMAN	S	546	ENSP00000359603:P546S;ENSP00000392531:P546S	ENSP00000359603:P546S	P	-	1	0	COL24A1	86330555	1.000000	0.71417	0.996000	0.52242	0.880000	0.50808	2.830000	0.48136	1.275000	0.44379	-0.220000	0.12472	CCT	G|0.616;A|0.384	0.384	strong		0.299	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
ADAM21	8747	hgsc.bcm.edu	37	14	70924432	70924432	+	Silent	SNP	C	C	T	rs553149454		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70924432C>T	ENST00000603540.1	+	2	474	c.216C>T	c.(214-216)caC>caT	p.H72H	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.H72H	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	72					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.H72H(2)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GCCAGAAACACGTTGTTCATA	0.537													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20886	0.0		0.0	False		,,,				2504	0.0				p.H72H		Atlas-SNP	.											ADAM21_ENST00000267499,colon,carcinoma,0,2	ADAM21	181	2	2	Substitution - coding silent(2)	large_intestine(2)	c.C216T						scavenged	.						122.0	128.0	126.0					14																	70924432		2203	4300	6503	SO:0001819	synonymous_variant	8747	exon2			GAAACACGTTGTT	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.216C>T	14.37:g.70924432C>T		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	265	14	0.0528302	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			.	.	none		0.537	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
ABI3BP	25890	hgsc.bcm.edu	37	3	100617680	100617680	+	Silent	SNP	C	C	T	rs2245370	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:100617680C>T	ENST00000284322.5	-	4	517	c.408G>A	c.(406-408)tcG>tcA	p.S136S	ABI3BP_ENST00000532144.1_Intron|ABI3BP_ENST00000495063.1_Silent_p.S136S|ABI3BP_ENST00000471714.1_Silent_p.S136S	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	136	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						ACAGGAAGACCGAGCTCGGTG	0.473													C|||	3646	0.728035	0.7519	0.6715	5008	,	,		19837	0.9335		0.5239	False		,,,				2504	0.7342				p.S136S		Atlas-SNP	.											.	ABI3BP	305	.	0			c.G408A						PASS	.	C		2988,1252		1079,830,211	96.0	106.0	103.0		408	-10.9	0.4	3	dbSNP_100	103	4166,4334		1012,2142,1096	no	coding-synonymous	ABI3BP	NM_015429.3		2091,2972,1307	TT,TC,CC		49.0118,29.5283,43.8462		136/1076	100617680	7154,5586	2120	4250	6370	SO:0001819	synonymous_variant	25890	exon4			GAAGACCGAGCTC	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.408G>A	3.37:g.100617680C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Silent	SNP	ENST00000284322.5	37	CCDS46880.1																																																																																			C|0.280;T|0.720	0.720	strong		0.473	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		
GPR111	222611	hgsc.bcm.edu	37	6	47649574	47649574	+	Missense_Mutation	SNP	A	A	G	rs10807372|rs71538333	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:47649574A>G	ENST00000296862.1	+	6	1279	c.1279A>G	c.(1279-1281)Aaa>Gaa	p.K427E	GPR111_ENST00000507065.1_Missense_Mutation_p.K359E|GPR111_ENST00000398742.2_Missense_Mutation_p.K359E			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	427	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.			K -> E (in Ref. 3; ABC41928). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TAGGCCAAGCAAATTGTTTAC	0.443													A|||	2551	0.509385	0.4448	0.4323	5008	,	,		22627	0.3085		0.6272	False		,,,				2504	0.7372				p.K359E		Atlas-SNP	.											.	GPR111	123	.	0			c.A1075G						PASS	.	A	GLU/LYS	1754,2104		397,960,572	139.0	131.0	134.0		1075	1.6	0.5	6	dbSNP_120	134	5326,2926		1739,1848,539	yes	missense	GPR111	NM_153839.6	56	2136,2808,1111	GG,GA,AA		35.4581,45.464,41.5359	benign	359/643	47649574	7080,5030	1929	4126	6055	SO:0001583	missense	222611	exon7			CCAAGCAAATTGT	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.1279A>G	6.37:g.47649574A>G	ENSP00000296862:p.Lys427Glu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		839	0.3841575091575092	161	0.32723577235772355	158	0.43646408839779005	148	0.25874125874125875	372	0.49076517150395776	A	8.406	0.843036	0.16963	0.45464	0.645419	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.35789	2.06;2.04;1.29	5.53	1.64	0.23874	GPS domain (2);	0.720175	0.13186	N	0.407111	T	0.06872	0.0175	N	0.19112	0.55	0.80722	P	0.0	B;B	0.14012	0.002;0.009	B;B	0.16289	0.006;0.015	T	0.24261	-1.0165	9	0.39692	T	0.17	.	1.3446	0.02161	0.4879:0.2189:0.1677:0.1255	rs10807372;rs52833782;rs60948975;rs10807372	359;427	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	E	359;427;359	ENSP00000422934:K359E;ENSP00000296862:K427E;ENSP00000381727:K359E	ENSP00000296862:K427E	K	+	1	0	GPR111	47757533	0.000000	0.05858	0.493000	0.27502	0.973000	0.67179	0.485000	0.22324	0.401000	0.25424	0.482000	0.46254	AAA	A|0.519;G|0.481	0.481	strong		0.443	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
ALPK2	115701	hgsc.bcm.edu	37	18	56204747	56204747	+	Missense_Mutation	SNP	G	G	A	rs3826593	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204747G>A	ENST00000361673.3	-	5	2885	c.2672C>T	c.(2671-2673)aCc>aTc	p.T891I	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	891			T -> I (in dbSNP:rs3826593). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GAAAGTACTGGTAAAAAGAGG	0.473													g|||	3999	0.798522	0.6369	0.7767	5008	,	,		21843	0.8363		0.9215	False		,,,				2504	0.8671				p.T891I		Atlas-SNP	.											.	ALPK2	487	.	0			c.C2672T						PASS	.	G	ILE/THR	3008,1398	687.5+/-404.9	1041,926,236	73.0	70.0	71.0		2672	-4.0	0.0	18	dbSNP_107	71	7966,634	790.8+/-407.6	3701,564,35	yes	missense	ALPK2	NM_052947.3	89	4742,1490,271	AA,AG,GG		7.3721,31.7295,15.6236	benign	891/2171	56204747	10974,2032	2203	4300	6503	SO:0001583	missense	115701	exon5			GTACTGGTAAAAA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2672C>T	18.37:g.56204747G>A	ENSP00000354991:p.Thr891Ile	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	1768	0.8095238095238095	288	0.5853658536585366	295	0.8149171270718232	494	0.8636363636363636	691	0.9116094986807388	g	1.626	-0.520336	0.04171	0.682705	0.926279	ENSG00000198796	ENST00000361673	T	0.42513	0.97	5.57	-4.01	0.04045	.	1.683430	0.03064	N	0.156341	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36163	-0.9759	9	0.31617	T	0.26	0.3772	1.8997	0.03265	0.2792:0.4048:0.1758:0.1402	rs3826593;rs52821205;rs61323060;rs3826593	891;891	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	I	891	ENSP00000354991:T891I	ENSP00000354991:T891I	T	-	2	0	ALPK2	54355727	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.595000	0.05727	-0.550000	0.06183	-0.374000	0.07098	ACC	G|0.175;A|0.825	0.825	strong		0.473	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ZAR1	326340	hgsc.bcm.edu	37	4	48493237	48493237	+	Missense_Mutation	SNP	G	G	A	rs79858408	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:48493237G>A	ENST00000327939.4	+	1	969	c.929G>A	c.(928-930)aGc>aAc	p.S310N		NM_175619.1	NP_783318.1	Q86SH2	ZAR1_HUMAN	zygote arrest 1	310					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(4)	5						TCGCCACGGAGCCCGGAGCTG	0.761													G|||	1949	0.389177	0.1702	0.5749	5008	,	,		9687	0.4484		0.5109	False		,,,				2504	0.3671				p.S310N		Atlas-SNP	.											.	ZAR1	15	.	0			c.G929A						PASS	.	G	ASN/SER	395,2045		61,273,886	2.0	2.0	2.0		929	2.6	0.0	4	dbSNP_131	2	1688,2870		387,914,978	yes	missense	ZAR1	NM_175619.1	46	448,1187,1864	AA,AG,GG		37.0338,16.1885,29.7656	possibly-damaging	310/425	48493237	2083,4915	1220	2279	3499	SO:0001583	missense	326340	exon1			CACGGAGCCCGGA	AY193890	CCDS3483.1	4p11	2014-02-20			ENSG00000182223	ENSG00000182223			20436	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 6"""	607520				12539046	Standard	NM_175619		Approved	Z3CXXC6	uc003gyd.3	Q86SH2	OTTHUMG00000102093	ENST00000327939.4:c.929G>A	4.37:g.48493237G>A	ENSP00000329803:p.Ser310Asn	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_175619		Missense_Mutation	SNP	ENST00000327939.4	37	CCDS3483.1	999	0.4574175824175824	102	0.2073170731707317	212	0.585635359116022	293	0.5122377622377622	392	0.5171503957783641	G	12.26	1.884874	0.33255	0.161885	0.370338	ENSG00000182223	ENST00000327939	.	.	.	3.45	2.57	0.30868	.	0.618990	0.15975	U	0.235593	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	B	0.23058	0.079	B	0.28916	0.096	T	0.42120	-0.9470	8	0.33141	T	0.24	-3.6173	2.2144	0.03955	0.1154:0.1965:0.4865:0.2016	.	310	Q86SH2	ZAR1_HUMAN	N	310	.	ENSP00000329803:S310N	S	+	2	0	ZAR1	48187994	0.953000	0.32496	0.002000	0.10522	0.011000	0.07611	2.705000	0.47127	0.378000	0.24764	0.561000	0.74099	AGC	G|0.542;A|0.458	0.458	strong		0.761	ZAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219927.3		
POR	5447	hgsc.bcm.edu	37	7	75609677	75609677	+	Silent	SNP	A	A	G	rs1135612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:75609677A>G	ENST00000461988.1	+	5	492	c.387A>G	c.(385-387)ccA>ccG	p.P129P	POR_ENST00000475509.1_3'UTR|POR_ENST00000439269.1_5'Flank|POR_ENST00000545601.1_5'UTR|POR_ENST00000394893.1_Silent_p.P129P|POR_ENST00000419840.1_5'UTR|POR_ENST00000450476.1_5'Flank	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	126	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GCAGCCTGCCAGAGATCGACA	0.627													A|||	1249	0.249401	0.0552	0.4035	5008	,	,		18095	0.4504		0.2445	False		,,,				2504	0.2004				p.P129P		Atlas-SNP	.											POR,NS,carcinoma,0,1	POR	46	1	0			c.A387G						PASS	.	A		313,3791		20,273,1759	53.0	59.0	57.0		387	-9.6	0.0	7	dbSNP_86	57	2101,6263		264,1573,2345	yes	coding-synonymous	POR	NM_000941.2		284,1846,4104	GG,GA,AA		25.1196,7.6267,19.3616		129/681	75609677	2414,10054	2052	4182	6234	SO:0001819	synonymous_variant	5447	exon5			CCTGCCAGAGATC	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.387A>G	7.37:g.75609677A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	37	CCDS5579.1	623	0.28525641025641024	26	0.052845528455284556	143	0.39502762430939226	255	0.4458041958041958	199	0.262532981530343	A	0.957	-0.704665	0.03255	0.076267	0.251196	ENSG00000127948	ENST00000447222	.	.	.	4.81	-9.62	0.00547	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999194	.	.	.	.	.	.	T	0.28038	-1.0056	3	.	.	.	-13.7498	0.1049	0.00051	0.2682:0.2151:0.1846:0.3322	rs1135612;rs2228102;rs2286818;rs3178962;rs3198391;rs11540671;rs12669302;rs61690444	.	.	.	G	102	.	.	R	+	1	2	POR	75447613	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-5.483000	0.00119	-3.832000	0.00101	-1.215000	0.01618	AGA	A|0.715;G|0.284;T|0.000	0.284	strong		0.627	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
CCND1	595	hgsc.bcm.edu	37	11	69462910	69462910	+	Splice_Site	SNP	G	G	A	rs9344	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:69462910G>A	ENST00000227507.2	+	4	950	c.723G>A	c.(721-723)ccG>ccA	p.P241P	CCND1_ENST00000536559.1_3'UTR	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	241					canonical Wnt signaling pathway (GO:0060070)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|lactation (GO:0007595)|Leydig cell differentiation (GO:0033327)|liver development (GO:0001889)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ regeneration (GO:0031100)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|positive regulation of protein phosphorylation (GO:0001934)|re-entry into mitotic cell cycle (GO:0000320)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to organonitrogen compound (GO:0010243)|response to UV-A (GO:0070141)|response to vitamin E (GO:0033197)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)|transcriptional repressor complex (GO:0017053)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|proline-rich region binding (GO:0070064)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			NS(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|ovary(1)|urinary_tract(1)	23	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)	AGTGTGACCCGGTAAGTGAGG	0.617			T	"""IGH@, FSTL3"""	"""CLL, B-ALL, breast"""					Multiple Myeloma(6;0.086)			G|||	2071	0.413538	0.1876	0.3487	5008	,	,		18173	0.5714		0.497	False		,,,				2504	0.5164				p.P241P	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"""L, E"""	CCND1_ENST00000227507,NS,adenoma,0,1	CCND1	107	1	0			c.G723A	GRCh37	CS004528	CCND1	S	rs9344	PASS	.	G		1021,3379	373.7+/-320.9	127,767,1306	96.0	79.0	85.0		723	2.0	1.0	11	dbSNP_52	85	4002,4586	553.5+/-386.3	934,2134,1226	yes	coding-synonymous-near-splice	CCND1	NM_053056.2		1061,2901,2532	AA,AG,GG		46.5999,23.2045,38.6742		241/296	69462910	5023,7965	2200	4294	6494	SO:0001630	splice_region_variant	595	exon4			TGACCCGGTAAGT	Z23022	CCDS8191.1	11q13	2008-07-18	2005-09-12		ENSG00000110092	ENSG00000110092			1582	protein-coding gene	gene with protein product	"""parathyroid adenomatosis 1"", ""B-cell CLL/lymphoma 1"", ""G1/S-specific cyclin D1"""	168461	"""cyclin D1 (PRAD1: parathyroid adenomatosis 1)"""	BCL1, D11S287E, PRAD1		1826542, 1833066	Standard	XM_006718653		Approved	U21B31	uc001opa.3	P24385	OTTHUMG00000167877	ENST00000227507.2:c.723+1G>A	11.37:g.69462910G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_053056	Q6LEF0	Silent	SNP	ENST00000227507.2	37	CCDS8191.1																																																																																			G|0.602;A|0.398	0.398	strong		0.617	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056	Silent
LASP1	3927	hgsc.bcm.edu	37	17	37074932	37074932	+	Silent	SNP	C	C	T	rs3744075	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:37074932C>T	ENST00000318008.6	+	7	1018	c.687C>T	c.(685-687)atC>atT	p.I229I	LASP1_ENST00000433206.2_Silent_p.I173I|RP1-56K13.3_ENST00000580121.1_RNA|LASP1_ENST00000435347.3_Silent_p.I229I	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	229	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						GGGACACCATCGTCAACGTGC	0.647			T	MLL	AML								C|||	295	0.0589058	0.0091	0.0793	5008	,	,		16660	0.0883		0.0686	False		,,,				2504	0.0716				p.I229I		Atlas-SNP	.		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	.	LASP1	24	.	0			c.C687T						PASS	.	C		75,4331	66.4+/-103.9	1,73,2129	122.0	107.0	112.0		687	-2.6	1.0	17	dbSNP_107	112	602,7998	158.9+/-212.3	21,560,3719	yes	coding-synonymous	LASP1	NM_006148.2		22,633,5848	TT,TC,CC		7.0,1.7022,5.2053		229/262	37074932	677,12329	2203	4300	6503	SO:0001819	synonymous_variant	3927	exon7			CACCATCGTCAAC		CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.687C>T	17.37:g.37074932C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	102	38	0.372549	NM_006148	B4DGQ0|Q96ED2|Q96IG0	Silent	SNP	ENST00000318008.6	37	CCDS11331.1																																																																																			C|0.944;T|0.056	0.056	strong		0.647	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148	
LOXHD1	125336	hgsc.bcm.edu	37	18	44126909	44126909	+	Missense_Mutation	SNP	T	T	C	rs1893566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44126909T>C	ENST00000398722.4	-	15	2628	c.2629A>G	c.(2629-2631)Agg>Ggg	p.R877G	LOXHD1_ENST00000300591.6_Missense_Mutation_p.R44G|LOXHD1_ENST00000441893.2_Missense_Mutation_p.R88G|LOXHD1_ENST00000582408.1_Missense_Mutation_p.R44G|LOXHD1_ENST00000441551.2_Missense_Mutation_p.R949G|LOXHD1_ENST00000579038.1_5'UTR|LOXHD1_ENST00000536736.1_Missense_Mutation_p.R1155G			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	877				R -> G (in Ref. 4; AAH41860). {ECO:0000305}.	calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						CCGCCTCCCCTACCCTCCTCG	0.577													C|||	3479	0.694688	0.5877	0.7003	5008	,	,		19275	0.6677		0.829	False		,,,				2504	0.7249				p.R1155G		Atlas-SNP	.											.	LOXHD1	367	.	0			c.A3463G						PASS	.	C	GLY/ARG,GLY/ARG	866,518		272,322,98	83.0	89.0	87.0		3463,130	4.9	0.1	18	dbSNP_92	87	2657,525		1107,443,41	yes	missense,missense	LOXHD1	NM_144612.6,NM_001145472.2	125,125	1379,765,139	CC,CT,TT		16.4991,37.4277,22.8428	benign,benign	1155/2212,44/1115	44126909	3523,1043	692	1591	2283	SO:0001583	missense	125336	exon22			CTCCCCTACCCTC	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.2629A>G	18.37:g.44126909T>C	ENSP00000381707:p.Arg877Gly	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		1518|1518	0.695054945054945|0.695054945054945	278|278	0.5650406504065041|0.5650406504065041	253|253	0.6988950276243094|0.6988950276243094	374|374	0.6538461538461539|0.6538461538461539	613|613	0.8087071240105541|0.8087071240105541	C|C	6.089|6.089	0.384649|0.384649	0.11524|0.11524	0.625723|0.625723	0.835009|0.835009	ENSG00000167210|ENSG00000167210	ENST00000300591;ENST00000398722;ENST00000536736;ENST00000441893;ENST00000335730;ENST00000536111;ENST00000420097|ENST00000441551	T;T;T;T;T|.	0.25414|.	1.92;3.37;3.37;3.39;1.8|.	4.9|4.9	4.9|4.9	0.64082|0.64082	.|.	0.261826|.	0.38326|.	N|.	0.001730|.	T|.	0.00012|.	0.0000|.	N|N	0.00926|0.00926	-1.1|-1.1	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.12630|.	0.006;0.0;0.006|.	B;B;B|.	0.12156|.	0.007;0.0;0.007|.	T|.	0.22417|.	-1.0217|.	9|.	0.31617|.	T|.	0.26|.	.|.	9.4732|9.4732	0.38856|0.38856	0.0:0.9017:0.0:0.0983|0.0:0.9017:0.0:0.0983	rs1893566;rs12955945;rs17857259;rs52802285;rs56935520;rs1893566|rs1893566;rs12955945;rs17857259;rs52802285;rs56935520;rs1893566	1155;88;877|.	F5GZB4;F8WA52;Q8IVV2-2|.	.;.;.|.	G|W	44;877;1155;88;877;57;57|1135	ENSP00000300591:R44G;ENSP00000381707:R877G;ENSP00000444586:R1155G;ENSP00000409062:R88G;ENSP00000440060:R57G|.	ENSP00000300591:R44G|.	R|X	-|-	1|2	2|0	LOXHD1|LOXHD1	42380907|42380907	0.127000|0.127000	0.22367|0.22367	0.083000|0.083000	0.20561|0.20561	0.008000|0.008000	0.06430|0.06430	1.438000|1.438000	0.35002|0.35002	1.072000|1.072000	0.40860|0.40860	-0.226000|-0.226000	0.12346|0.12346	AGG|TAG	T|0.306;C|0.694	0.694	strong		0.577	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
USP19	10869	hgsc.bcm.edu	37	3	49156473	49156473	+	Missense_Mutation	SNP	C	C	G	rs11552724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49156473C>G	ENST00000398888.2	-	2	424	c.106G>C	c.(106-108)Gat>Cat	p.D36H	USP19_ENST00000453664.1_Missense_Mutation_p.D36H|USP19_ENST00000398898.2_Missense_Mutation_p.D36H|USP19_ENST00000398896.1_5'Flank|USP19_ENST00000417901.1_Missense_Mutation_p.D36H|USP19_ENST00000398892.3_Missense_Mutation_p.D36H|USP19_ENST00000434032.2_Missense_Mutation_p.D36H|USP19_ENST00000488993.1_5'UTR	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	36			D -> H (in dbSNP:rs11552724).		ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGATCTCCATCCTTGCTCTCC	0.552													C|||	266	0.053115	0.0083	0.0648	5008	,	,		18934	0.0496		0.1153	False		,,,				2504	0.045				p.D36H		Atlas-SNP	.											.	USP19	158	.	0			c.G106C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	86,3914		0,86,1914	206.0	224.0	218.0		106,106,106,106	3.0	1.0	3	dbSNP_120	218	886,7452		49,788,3332	yes	missense,missense,missense,missense	USP19	NM_001199160.1,NM_001199161.1,NM_001199162.1,NM_006677.2	81,81,81,81	49,874,5246	GG,GC,CC		10.626,2.15,7.8781	benign,benign,benign,benign	36/1420,36/1385,36/1373,36/1319	49156473	972,11366	2000	4169	6169	SO:0001583	missense	10869	exon2			CTCCATCCTTGCT	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.106G>C	3.37:g.49156473C>G	ENSP00000381863:p.Asp36His	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	169	67	0.39645	NM_001199160	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	159	0.07280219780219781	4	0.008130081300813009	28	0.07734806629834254	40	0.06993006993006994	87	0.11477572559366754	C	18.29	3.590425	0.66219	0.0215	0.10626	ENSG00000172046	ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032;ENST00000306026;ENST00000425298	T;T;T;T;T;T;T	0.34072	1.91;2.07;2.07;1.91;2.06;2.07;1.38	5.73	3.02	0.34903	.	0.702916	0.14102	N	0.341312	T	0.00845	0.0028	N	0.19112	0.55	0.31634	P	0.648713	P;P;P;B;P	0.49090	0.684;0.498;0.498;0.437;0.919	P;B;B;B;P	0.59171	0.453;0.369;0.369;0.278;0.853	T	0.15665	-1.0429	9	0.72032	D	0.01	-6.184	10.8902	0.46992	0.0:0.8012:0.0:0.1988	rs11552724;rs13094868;rs52801489;rs11552724	99;36;36;36;36	A5PKX8;E9PEG8;E7EN22;O94966;O94966-2	.;.;.;UBP19_HUMAN;.	H	36	ENSP00000381872:D36H;ENSP00000395260:D36H;ENSP00000400090:D36H;ENSP00000381867:D36H;ENSP00000381863:D36H;ENSP00000401197:D36H;ENSP00000303503:D36H	ENSP00000303503:D36H	D	-	1	0	USP19	49131477	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.247000	0.58750	0.367000	0.24454	0.655000	0.94253	GAT	C|0.905;G|0.095	0.095	strong		0.552	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
GUCY2F	2986	hgsc.bcm.edu	37	X	108708552	108708552	+	Missense_Mutation	SNP	A	A	G	rs12008095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:108708552A>G	ENST00000218006.2	-	3	1142	c.851T>C	c.(850-852)cTg>cCg	p.L284P		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	284			L -> P (in dbSNP:rs12008095). {ECO:0000269|PubMed:17344846}.		intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						ACTGTAGAGCAGGGCATCATA	0.478													A|||	611	0.161854	0.0113	0.1412	3775	,	,		15658	0.0377		0.2913	False		,,,				2504	0.1708				p.L284P		Atlas-SNP	.											.	GUCY2F	178	.	0			c.T851C						PASS	.	A	PRO/LEU	273,3562		7,222,37,1403,534	176.0	137.0	151.0		851	3.9	1.0	X	dbSNP_120	151	2470,4258		318,1142,692,968,1180	yes	missense	GUCY2F	NM_001522.2	98	325,1364,729,2371,1714	GG,GA,G,AA,A		36.7122,7.1186,25.968	probably-damaging	284/1109	108708552	2743,7820	2203	4300	6503	SO:0001583	missense	2986	exon3			TAGAGCAGGGCAT	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.851T>C	X.37:g.108708552A>G	ENSP00000218006:p.Leu284Pro	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	109	107	0.981651	NM_001522	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	37	CCDS14545.1	319	0.19228450874020495	5	0.0102880658436214	43	0.1303030303030303	9	0.016129032258064516	162	0.26557377049180325	A	18.24	3.579314	0.65878	0.071186	0.367122	ENSG00000101890	ENST00000218006	D	0.83837	-1.77	3.94	3.94	0.45596	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000002	T	0.00012	0.0000	M	0.79475	2.455	0.09310	P	0.999999999739281	P	0.51240	0.943	P	0.58577	0.841	T	0.00542	-1.1680	9	0.35671	T	0.21	.	10.183	0.42980	1.0:0.0:0.0:0.0	rs12008095;rs52818490;rs57978660;rs12008095	284	P51841	GUC2F_HUMAN	P	284	ENSP00000218006:L284P	ENSP00000218006:L284P	L	-	2	0	GUCY2F	108595208	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.579000	0.90781	1.764000	0.52075	0.486000	0.48141	CTG	A|0.790;0|0.012	.	strong		0.478	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522	
CCDC168	643677	hgsc.bcm.edu	37	13	103391634	103391634	+	5'Flank	SNP	C	C	T	rs7322112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103391634C>T	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		AGGCCCATTACATCTTTCACA	0.313													T|||	3504	0.699681	0.562	0.7478	5008	,	,		21243	0.5913		0.826	False		,,,				2504	0.8333				p.V3805I		Atlas-SNP	.											.	.	.	.	0			c.G11413A						PASS	.	T	ILE/VAL	787,597		225,337,130	72.0	53.0	59.0		11413	2.5	0.0	13	dbSNP_116	59	2540,636		1022,496,70	yes	missense	CCDC168	NM_001146197.1	29	1247,833,200	TT,TC,CC		20.0252,43.1358,27.0395		3805/7082	103391634	3327,1233	692	1588	2280	SO:0001631	upstream_gene_variant	643677	exon4			CCATTACATCTTT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287		13.37:g.103391634C>T	Exception_encountered	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	125	52	0.416	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37																																																																																				C|0.324;T|0.676	0.676	strong		0.313	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
TMC5	79838	hgsc.bcm.edu	37	16	19481020	19481020	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19481020G>A	ENST00000396229.2	+	10	2404	c.1655G>A	c.(1654-1656)cGg>cAg	p.R552Q	TMC5_ENST00000381414.4_Missense_Mutation_p.R552Q|TMC5_ENST00000541464.1_Missense_Mutation_p.R552Q|TMC5_ENST00000542583.2_Missense_Mutation_p.R552Q|TMC5_ENST00000219821.5_Missense_Mutation_p.R306Q|TMC5_ENST00000561503.1_Missense_Mutation_p.R193Q|TMC5_ENST00000564959.1_Missense_Mutation_p.R235Q	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	552					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						AAGTATTTCCGGAACAACTTC	0.473																																					p.R552Q		Atlas-SNP	.											TMC5_ENST00000396229,NS,malignant_melanoma,0,2	TMC5	169	2	0			c.G1655A						PASS	.						117.0	107.0	111.0					16																	19481020		2197	4300	6497	SO:0001583	missense	79838	exon10			ATTTCCGGAACAA	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1655G>A	16.37:g.19481020G>A	ENSP00000379531:p.Arg552Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	145	28	0.193103	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990463	0.35131	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49	5.65	5.65	0.86999	.	0.249267	0.41605	D	0.000859	T	0.47154	0.1430	M	0.64260	1.97	0.29006	N	0.887155	P;P;P;P;P;P	0.45902	0.868;0.81;0.74;0.622;0.676;0.782	B;B;B;B;B;B	0.42386	0.386;0.372;0.218;0.109;0.216;0.386	T	0.52238	-0.8602	10	0.27082	T	0.32	-25.7205	6.6578	0.22996	0.0715:0.1292:0.6653:0.134	.	552;235;306;306;552;552	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	Q	552;552;552;552;306;235	ENSP00000441227:R552Q;ENSP00000370822:R552Q;ENSP00000379531:R552Q;ENSP00000446274:R552Q;ENSP00000219821:R306Q	ENSP00000219821:R306Q	R	+	2	0	TMC5	19388521	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.204000	0.42761	2.663000	0.90544	0.655000	0.94253	CGG	.	.	none		0.473	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	
GSTZ1	2954	hgsc.bcm.edu	37	14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	rs7972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:77793237G>A	ENST00000556627.1	+	3	255	c.124G>A	c.(124-126)Ggg>Agg	p.G42R	GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000557639.1_5'UTR|GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R|GSTZ1_ENST00000557053.1_5'UTR|GSTZ1_ENST00000554279.1_Missense_Mutation_p.G42R|GSTZ1_ENST00000393734.1_5'UTR|GSTZ1_ENST00000361389.4_5'UTR			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	42	GST N-terminal.		R -> G (in allele GSTZ1*B and allele GSTZ1*C; dbSNP:rs7972). {ECO:0000269|PubMed:10373324, ECO:0000269|PubMed:10739172, ECO:0000269|PubMed:12508121, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9417084, ECO:0000269|PubMed:9925947, ECO:0000269|Ref.6, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)			lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	CATAAAGGATGGGGGCCAACA	0.567													G|||	153	0.0305511	0.0038	0.0274	5008	,	,		21279	0.0		0.1113	False		,,,				2504	0.0174				p.G42R		Atlas-SNP	.											.	GSTZ1	35	.	0			c.G124A						PASS	.	G	,ARG/GLY,ARG/GLY	78,4326	62.9+/-100.1	0,78,2124	43.0	35.0	37.0		,124,124	5.6	1.0	14	dbSNP_52	37	707,7893	164.3+/-216.7	41,625,3634	yes	utr-5,missense,missense	GSTZ1	NM_001513.3,NM_145870.2,NM_145871.2	,125,125	41,703,5758	AA,AG,GG		8.2209,1.7711,6.0366	,benign,benign	,42/217,42/175	77793237	785,12219	2202	4300	6502	SO:0001583	missense	2954	exon3			AAGGATGGGGGCC	U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"""Glutathione S-transferases / Soluble"""	4643	protein-coding gene	gene with protein product	"""maleylacetoacetate isomerase"""	603758	"""glutathione transferase zeta 1"""			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.124G>A	14.37:g.77793237G>A	ENSP00000450487:p.Gly42Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_145871	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		109	0.04990842490842491	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	96	0.1266490765171504	G	28.3	4.909294	0.92107	0.017711	0.082209	ENSG00000100577	ENST00000216465;ENST00000554279;ENST00000349555;ENST00000556627;ENST00000553586	T;T;T;T;T	0.18810	4.45;3.14;2.19;2.36;4.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.00637	0.0021	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.83275	0.996	T	0.00335	-1.1808	8	0.72032	D	0.01	-6.8373	16.4581	0.84029	0.0:0.0:1.0:0.0	rs7972;rs1128968;rs2266617;rs3177429;rs3186383;rs11551317;rs17353483;rs17750846;rs52835763;rs58270987;rs7972	42	A6NED0	.	R	42;42;42;42;43	ENSP00000216465:G42R;ENSP00000452498:G42R;ENSP00000314404:G42R;ENSP00000450487:G42R;ENSP00000451976:G43R	ENSP00000216465:G42R	G	+	1	0	GSTZ1	76862990	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.705000	0.68355	2.614000	0.88457	0.655000	0.94253	GGG	G|0.949;A|0.051	0.051	strong		0.567	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870	
CYP2C18	1562	hgsc.bcm.edu	37	10	96493058	96493058	+	Missense_Mutation	SNP	C	C	T	rs1126545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96493058C>T	ENST00000285979.6	+	8	1353	c.1154C>T	c.(1153-1155)aCg>aTg	p.T385M	CYP2C19_ENST00000464755.1_3'UTR|CYP2C18_ENST00000339022.5_Missense_Mutation_p.T326M	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	385			T -> M (in dbSNP:rs2281891). {ECO:0000269|PubMed:2009263, ECO:0000269|PubMed:8333835}.		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	TTTCAGGGCACGACCATAATA	0.413													C|||	1096	0.21885	0.1611	0.1023	5008	,	,		21210	0.3135		0.1451	False		,,,				2504	0.3579				p.T385M		Atlas-SNP	.											.	CYP2C18	79	.	0			c.C1154T						PASS	.	C	MET/THR,MET/THR	721,3685	298.4+/-285.3	58,605,1540	166.0	151.0	156.0		1154,977	0.1	0.0	10	dbSNP_100	156	1275,7325	253.6+/-279.2	95,1085,3120	yes	missense,missense	CYP2C18	NM_000772.2,NM_001128925.1	81,81	153,1690,4660	TT,TC,CC		14.8256,16.364,15.3468	,	385/491,326/432	96493058	1996,11010	2203	4300	6503	SO:0001583	missense	1562	exon8			AGGGCACGACCAT	M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"""Cytochrome P450s"""	2620	protein-coding gene	gene with protein product		601131	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"""	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.1154C>T	10.37:g.96493058C>T	ENSP00000285979:p.Thr385Met	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	199	84	0.422111	NM_000772	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Missense_Mutation	SNP	ENST00000285979.6	37	CCDS7435.1	429	0.19642857142857142	79	0.16056910569105692	47	0.1298342541436464	191	0.3339160839160839	112	0.14775725593667546	c	12.24	1.877472	0.33162	0.16364	0.148256	ENSG00000108242	ENST00000339022;ENST00000285979	T;T	0.74002	-0.8;-0.8	4.05	0.102	0.14522	.	0.064493	0.64402	N	0.000009	T	0.00012	0.0000	M	0.91612	3.225	0.09310	P	0.9999951645	P;D	0.89917	0.872;1.0	B;D	0.71870	0.218;0.975	T	0.06338	-1.0832	9	0.66056	D	0.02	.	7.9161	0.29818	0.0:0.6345:0.0:0.3655	rs2281891;rs52807492;rs57536820;rs2281891	326;385	Q4VAT5;P33260	.;CP2CI_HUMAN	M	326;385	ENSP00000341293:T326M;ENSP00000285979:T385M	ENSP00000285979:T385M	T	+	2	0	CYP2C18	96483048	0.998000	0.40836	0.027000	0.17364	0.001000	0.01503	3.922000	0.56462	-0.177000	0.10690	-1.679000	0.00737	ACG	C|0.827;T|0.173	0.173	strong		0.413	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772	
MUC4	4585	hgsc.bcm.edu	37	3	195511780	195511780	+	Missense_Mutation	SNP	G	G	A	rs391928|rs71291863	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195511780G>A	ENST00000463781.3	-	2	7130	c.6671C>T	c.(6670-6672)cCt>cTt	p.P2224L	MUC4_ENST00000475231.1_Missense_Mutation_p.P2224L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P2224L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GACAAGAAGAGGGATGGCGTG	0.592																																					p.P2224L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	1	Substitution - Missense(1)	prostate(1)	c.C6671T						scavenged	.						34.0	32.0	33.0					3																	195511780		654	1584	2238	SO:0001583	missense	4585	exon2			AGAAGAGGGATGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6671C>T	3.37:g.195511780G>A	ENSP00000417498:p.Pro2224Leu	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	387	117	0.302326	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	4.046	0.006276	0.07866	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36699	1.24;1.25	.	.	.	.	.	.	.	.	T	0.19927	0.0479	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.24548	-1.0157	6	.	.	.	.	.	.	.	.	2224	E7ESK3	.	L	2224	ENSP00000417498:P2224L;ENSP00000420243:P2224L	.	P	-	2	0	MUC4	196996175	0.116000	0.22171	0.001000	0.08648	0.003000	0.03518	0.211000	0.17474	0.488000	0.27723	0.064000	0.15345	CCT	G|0.789;A|0.211	0.211	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
IVL	3713	hgsc.bcm.edu	37	1	152882952	152882952	+	Missense_Mutation	SNP	G	G	C	rs11807064	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152882952G>C	ENST00000368764.3	+	2	743	c.679G>C	c.(679-681)Gag>Cag	p.E227Q	IVL_ENST00000392667.2_Missense_Mutation_p.E81Q			P07476	INVO_HUMAN	involucrin	227	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		E -> Q (in dbSNP:rs11807064). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2873896}.		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ggagctcccagagcagcagga	0.687																																					p.E227Q		Atlas-SNP	.											IVL,caecum,carcinoma,0,3	IVL	100	3	0			c.G679C						PASS	.						1.0	2.0	2.0					1																	152882952		1226	2796	4022	SO:0001583	missense	3713	exon2			CTCCCAGAGCAGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.679G>C	1.37:g.152882952G>C	ENSP00000357753:p.Glu227Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	168	17	0.10119	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	9	0.004120879120879121	8	0.016260162601626018	0	0.0	0	0.0	1	0.0013192612137203166	G	10.99	1.507992	0.27036	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10288	3.09;2.89	3.65	-6.24	0.02046	.	.	.	.	.	T	0.01976	0.0062	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.47114	-0.9142	9	0.24483	T	0.36	.	7.2256	0.26014	0.4858:0.2031:0.3111:0.0	rs62652338	227	P07476	INVO_HUMAN	Q	227;81	ENSP00000357753:E227Q;ENSP00000376435:E81Q	ENSP00000357753:E227Q	E	+	1	0	IVL	151149576	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.094000	0.15107	-0.793000	0.04475	0.414000	0.27820	GAG	G|0.995;C|0.005	0.005	strong		0.687	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
ANKRD36	375248	hgsc.bcm.edu	37	2	97883094	97883094	+	Missense_Mutation	SNP	T	T	G	rs62156176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97883094T>G	ENST00000461153.2	+	64	4082	c.3838T>G	c.(3838-3840)Tgg>Ggg	p.W1280G	ANKRD36_ENST00000420699.2_Missense_Mutation_p.W1280G			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1280								p.W1084G(2)|p.W1280G(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						AACAGGCGGTTGGAAATCTGG	0.338																																					p.W1280G		Atlas-SNP	.											ANKRD36_ENST00000420699,NS,carcinoma,0,4	ANKRD36	170	4	4	Substitution - Missense(4)	prostate(2)|endometrium(2)	c.T3838G						PASS	.						151.0	119.0	129.0					2																	97883094		692	1591	2283	SO:0001583	missense	375248	exon64			GGCGGTTGGAAAT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.3838T>G	2.37:g.97883094T>G	ENSP00000419530:p.Trp1280Gly	Somatic	813	1	0.00123001		WXS	Illumina HiSeq	Phase_I	948	318	0.335443	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	0.018	-1.470424	0.01044	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000461694	T;T	0.28255	1.62;1.62	0.569	-0.453	0.12201	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22208	-1.0223	8	0.41790	T	0.15	.	.	.	.	rs62156176	1280;105	A6QL64;A6QL64-3	AN36A_HUMAN;.	G	1280;1280;547	ENSP00000419530:W1280G;ENSP00000391950:W1280G	ENSP00000391950:W1280G	W	+	1	0	ANKRD36	97246821	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.272000	0.08560	-0.248000	0.09583	-1.372000	0.01188	TGG	T|0.905;G|0.095	0.095	strong		0.338	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
TMEM261	90871	hgsc.bcm.edu	37	9	7799606	7799606	+	Silent	SNP	C	C	A	rs14059	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:7799606C>A	ENST00000358227.4	-	1	461	c.129G>T	c.(127-129)ctG>ctT	p.L43L	TMEM261_ENST00000484082.1_Intron	NM_033428.1	NP_219500.1	Q96GE9	TM261_HUMAN	transmembrane protein 261	43						integral component of membrane (GO:0016021)											AGGTCTTCAACAGGCGGTGTT	0.667													c|||	1889	0.377196	0.267	0.5389	5008	,	,		10006	0.38		0.3897	False		,,,				2504	0.3957				p.L43L		Atlas-SNP	.											.	C9orf123	7	.	0			c.G129T						PASS	.	C		1229,3177	409.7+/-335.1	176,877,1150	36.0	39.0	38.0		129	-7.3	0.0	9	dbSNP_52	38	3407,5193	485.0+/-371.5	668,2071,1561	no	coding-synonymous	C9orf123	NM_033428.1		844,2948,2711	AA,AC,CC		39.6163,27.8938,35.6451		43/113	7799606	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	90871	exon1			CTTCAACAGGCGG	BC009510	CCDS34989.1	9p24.1	2014-02-21	2013-09-11	2013-09-11	ENSG00000137038	ENSG00000137038			30536	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 123"""	C9orf123		21666724	Standard	NM_033428		Approved	MGC4730	uc003zkj.3	Q96GE9	OTTHUMG00000019539	ENST00000358227.4:c.129G>T	9.37:g.7799606C>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_033428	A8K9B7|Q5T6Y9|Q9NT74	Silent	SNP	ENST00000358227.4	37	CCDS34989.1																																																																																			C|0.639;A|0.361	0.361	strong		0.667	TMEM261-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051705.1	NM_033428	
PDIA3	2923	hgsc.bcm.edu	37	15	44061802	44061802	+	Silent	SNP	C	C	T	rs1053492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:44061802C>T	ENST00000300289.5	+	10	1372	c.1224C>T	c.(1222-1224)caC>caT	p.H408H	PDIA3_ENST00000538521.1_Silent_p.H388H	NM_005313.4	NP_005304.3	P30101	PDIA3_HUMAN	protein disulfide isomerase family A, member 3	408	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.	Contributes to redox potential value. {ECO:0000250}.			antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein N-linked glycosylation via asparagine (GO:0018279)|protein retention in ER lumen (GO:0006621)|proteolysis (GO:0006508)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|phospholipase C activity (GO:0004629)|poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(2)|skin(1)	17		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)		GGTGTGGTCACTGTAAGAACC	0.393													C|||	2527	0.504593	0.0703	0.6931	5008	,	,		19459	0.63		0.7117	False		,,,				2504	0.6155				p.H408H		Atlas-SNP	.											PDIA3,bladder,carcinoma,+1,1	PDIA3	40	1	0			c.C1224T						PASS	.	C		874,3522	341.2+/-306.6	98,678,1422	114.0	112.0	113.0		1224	4.9	1.0	15	dbSNP_86	113	6166,2426	697.3+/-404.9	2197,1772,327	no	coding-synonymous	PDIA3	NM_005313.4		2295,2450,1749	TT,TC,CC		28.2356,19.8817,45.7961		408/506	44061802	7040,5948	2198	4296	6494	SO:0001819	synonymous_variant	2923	exon10			TGGTCACTGTAAG		CCDS10101.1	15q15	2009-11-20	2005-06-29	2005-03-03	ENSG00000167004	ENSG00000167004	5.3.4.1	"""Protein disulfide isomerases"""	4606	protein-coding gene	gene with protein product		602046	"""glucose regulated protein, 58kDa"", ""protein disulfide isomerase-associated 3"""	GRP58		8974399	Standard	NM_005313		Approved	P58, ERp61, ERp57, ERp60, GRP57, PI-PLC, HsT17083	uc001zsu.3	P30101	OTTHUMG00000044444	ENST00000300289.5:c.1224C>T	15.37:g.44061802C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	169	161	0.952663	NM_005313	Q13453|Q14255|Q8IYF8|Q9UMU7	Silent	SNP	ENST00000300289.5	37	CCDS10101.1																																																																																			C|0.466;T|0.534	0.534	strong		0.393	PDIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103532.3	NM_005313	
FSIP2	401024	hgsc.bcm.edu	37	2	186678633	186678633	+	Missense_Mutation	SNP	C	C	T	rs17826666	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:186678633C>T	ENST00000424728.1	+	18	20189	c.20189C>T	c.(20188-20190)aCt>aTt	p.T6730I	FSIP2_ENST00000343098.5_Missense_Mutation_p.T6819I			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6730				T -> I (in Ref. 2; BX648733). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						ATTGAAAGTACTGAAGCAATC	0.403													C|||	265	0.0529153	0.0038	0.0634	5008	,	,		19953	0.0079		0.1004	False		,,,				2504	0.1094				p.T6819I		Atlas-SNP	.											.	FSIP2	251	.	0			c.C20456T						PASS	.	C	ILE/THR	72,3748		0,72,1838	89.0	85.0	86.0		20456	-5.7	0.0	2	dbSNP_123	86	776,7482		27,722,3380	yes	missense	FSIP2	NM_173651.2	89	27,794,5218	TT,TC,CC		9.3969,1.8848,7.021	benign	6819/6997	186678633	848,11230	1910	4129	6039	SO:0001583	missense	401024	exon18			AAAGTACTGAAGC	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.20189C>T	2.37:g.186678633C>T	ENSP00000401306:p.Thr6730Ile	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	224	120	0.535714	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		120	0.054945054945054944	4	0.008130081300813009	27	0.07458563535911603	4	0.006993006993006993	85	0.11213720316622691	C	3.880	-0.026082	0.07589	0.018848	0.093969	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.39229	1.09;1.09	5.29	-5.67	0.02444	.	1.038600	0.07609	N	0.925119	T	0.00468	0.0015	N	0.12182	0.205	0.80722	P	0.0	.	.	.	.	.	.	T	0.19128	-1.0315	7	0.21014	T	0.42	.	13.0578	0.58990	0.0:0.6171:0.0:0.3829	rs17826666;rs17826666	.	.	.	I	6819;6730	ENSP00000344403:T6819I;ENSP00000401306:T6730I	ENSP00000344403:T6819I	T	+	2	0	FSIP2	186386878	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.829000	0.01701	-1.109000	0.02996	-1.036000	0.02392	ACT	C|0.944;T|0.056	0.056	strong		0.403	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
GPR111	222611	hgsc.bcm.edu	37	6	47649222	47649222	+	Silent	SNP	T	T	G	rs8180544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:47649222T>G	ENST00000296862.1	+	6	927	c.927T>G	c.(925-927)tcT>tcG	p.S309S	GPR111_ENST00000507065.1_Silent_p.S241S|GPR111_ENST00000398742.2_Silent_p.S241S			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	309					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TCACTTTTTCTATGAGAATTA	0.393																																					p.S241S		Atlas-SNP	.											GPR111_ENST00000296862,upper_leg,malignant_melanoma,+1,2	GPR111	123	2	0			c.T723G						PASS	.	G		1788,1962		422,944,509	126.0	119.0	121.0		723	-10.4	0.4	6	dbSNP_117	121	5323,2901		1732,1859,521	no	coding-synonymous	GPR111	NM_153839.6		2154,2803,1030	GG,GT,TT		35.2748,47.68,40.613		241/643	47649222	7111,4863	1875	4112	5987	SO:0001819	synonymous_variant	222611	exon7			TTTTTCTATGAGA	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.927T>G	6.37:g.47649222T>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	122	73	0.598361	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Silent	SNP	ENST00000296862.1	37																																																																																				T|0.468;G|0.532	0.532	strong		0.393	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
ST6GALNAC1	55808	hgsc.bcm.edu	37	17	74625715	74625715	+	Silent	SNP	T	T	C	rs8081258	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74625715T>C	ENST00000156626.7	-	2	409	c.210A>G	c.(208-210)gcA>gcG	p.A70A	ST6GALNAC1_ENST00000590878.1_5'UTR	NM_018414.3	NP_060884.1	Q9NSC7	SIA7A_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	70					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	22						TTGTCCTCCTTGCCCTTGTGG	0.537													T|||	383	0.0764776	0.1271	0.0634	5008	,	,		19270	0.001		0.0924	False		,,,				2504	0.0787				p.A70A		Atlas-SNP	.											.	ST6GALNAC1	42	.	0			c.A210G						PASS	.	T		498,3908	232.6+/-246.1	27,444,1732	168.0	150.0	156.0		210	-2.6	0.0	17	dbSNP_116	156	864,7736	195.6+/-240.8	41,782,3477	no	coding-synonymous	ST6GALNAC1	NM_018414.3		68,1226,5209	CC,CT,TT		10.0465,11.3028,10.4721		70/601	74625715	1362,11644	2203	4300	6503	SO:0001819	synonymous_variant	55808	exon2			CCTCCTTGCCCTT	Y11339	CCDS11748.1	17q25.3	2013-03-01	2005-02-07	2005-02-07	ENSG00000070526	ENSG00000070526		"""Sialyltransferases"""	23614	protein-coding gene	gene with protein product		610138	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) A"""	SIAT7A			Standard	NM_001289107		Approved	ST6GalNAcI	uc002jsh.3	Q9NSC7	OTTHUMG00000180369	ENST00000156626.7:c.210A>G	17.37:g.74625715T>C		Somatic	471	0	0		WXS	Illumina HiSeq	Phase_I	435	433	0.995402	NM_018414	Q6UW90|Q9NSC6	Silent	SNP	ENST00000156626.7	37	CCDS11748.1																																																																																			T|0.901;C|0.099	0.099	strong		0.537	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450974.1	NM_018414	
TRIM7	81786	hgsc.bcm.edu	37	5	180622615	180622615	+	Missense_Mutation	SNP	C	C	T	rs254460	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:180622615C>T	ENST00000274773.7	-	7	1148	c.1087G>A	c.(1087-1089)Ggc>Agc	p.G363S	TRIM7_ENST00000422067.2_Missense_Mutation_p.G155S|TRIM7_ENST00000393315.1_Missense_Mutation_p.G155S|TRIM7_ENST00000504241.1_5'UTR|CTC-338M12.6_ENST00000509080.1_RNA|CTC-338M12.6_ENST00000512508.1_RNA|TRIM7_ENST00000361809.3_Missense_Mutation_p.G155S|CTC-338M12.5_ENST00000514487.1_RNA|CTC-338M12.5_ENST00000508877.1_RNA|CTC-338M12.6_ENST00000502812.2_RNA|TRIM7_ENST00000393319.3_Missense_Mutation_p.G181S	NM_203293.1	NP_976038.1	Q9C029	TRIM7_HUMAN	tripartite motif containing 7	363	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		G -> S (in dbSNP:rs254460).			cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|stomach(1)	17	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)		AGGCGCACGCCCTTAAGATCC	0.677													t|||	936	0.186901	0.1604	0.1167	5008	,	,		13507	0.2014		0.1769	False		,,,				2504	0.2679				p.G363S	Esophageal Squamous(128;2258 2308 35507 48647)	Atlas-SNP	.											.	TRIM7	56	.	0			c.G1087A						PASS	.	T	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	666,3704		44,578,1563	43.0	49.0	47.0		1087,463,463,463,541	4.6	1.0	5	dbSNP_79	47	1412,7082		128,1156,2963	yes	missense,missense,missense,missense,missense	TRIM7	NM_203293.1,NM_203294.1,NM_203295.1,NM_203296.1,NM_203297.1	56,56,56,56,56	172,1734,4526	TT,TC,CC		16.6235,15.2403,16.1536	benign,benign,benign,benign,benign	363/512,155/304,155/304,155/304,181/330	180622615	2078,10786	2185	4247	6432	SO:0001583	missense	81786	exon7			GCACGCCCTTAAG	AF220032	CCDS4462.1, CCDS4463.1, CCDS4464.1, CCDS43414.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146054	ENSG00000146054		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16278	protein-coding gene	gene with protein product	"""glycogenin-interacting protein"", ""tripartite motif protein TRIM7"""	609315	"""tripartite motif-containing 7"""			11331580	Standard	NM_203294		Approved	RNF90, GNIP	uc003mmz.1	Q9C029	OTTHUMG00000130963	ENST00000274773.7:c.1087G>A	5.37:g.180622615C>T	ENSP00000274773:p.Gly363Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	61	38	0.622951	NM_203293	A2RUE4|D3DWR7|Q969F5|Q96F67|Q96J89|Q96J90	Missense_Mutation	SNP	ENST00000274773.7	37	CCDS4462.1	353	0.16163003663003664	77	0.1565040650406504	45	0.12430939226519337	95	0.1660839160839161	136	0.17941952506596306	T	7.205	0.594267	0.13875	0.152403	0.166235	ENSG00000146054	ENST00000274773;ENST00000393315;ENST00000361809;ENST00000393319;ENST00000422067	T;T;T;T;T	0.08720	3.06;3.06;3.06;3.06;3.06	4.57	4.57	0.56435	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.000000	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00124	-2.055	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36065	-0.9763	9	0.05959	T	0.93	.	8.4199	0.32694	0.0:0.0951:0.0:0.9049	rs254460;rs58595081;rs254460	363;181	Q9C029;Q9C029-4	TRIM7_HUMAN;.	S	363;155;155;181;155	ENSP00000274773:G363S;ENSP00000376991:G155S;ENSP00000355059:G155S;ENSP00000376994:G181S;ENSP00000391458:G155S	ENSP00000274773:G363S	G	-	1	0	TRIM7	180555221	1.000000	0.71417	0.990000	0.47175	0.065000	0.16274	2.480000	0.45206	0.613000	0.30089	-0.380000	0.06706	GGC	C|0.831;T|0.169	0.169	strong		0.677	TRIM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253569.3	NM_203296	
CA6	765	hgsc.bcm.edu	37	1	9009406	9009406	+	Missense_Mutation	SNP	C	C	T	rs2274327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:9009406C>T	ENST00000377443.2	+	2	168	c.164C>T	c.(163-165)aCg>aTg	p.T55M	CA6_ENST00000377436.3_Missense_Mutation_p.T55M|CA6_ENST00000480186.3_Missense_Mutation_p.T55M|CA6_ENST00000476083.1_Intron|CA6_ENST00000377442.2_Intron	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	55			T -> M (in dbSNP:rs2274327).		bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	CTACAGAGGACGAAGGTGCGG	0.582													C|||	1353	0.270168	0.0809	0.3775	5008	,	,		19246	0.2431		0.4155	False		,,,				2504	0.3282				p.T55M		Atlas-SNP	.											.	CA6	47	.	0			c.C164T						PASS	.	C	MET/THR	635,3771	274.0+/-271.7	53,529,1621	56.0	49.0	51.0		164	-7.7	0.0	1	dbSNP_100	51	3559,5041	516.5+/-378.8	732,2095,1473	yes	missense	CA6	NM_001215.2	81	785,2624,3094	TT,TC,CC		41.3837,14.4122,32.2467	probably-damaging	55/309	9009406	4194,8812	2203	4300	6503	SO:0001583	missense	765	exon2			AGAGGACGAAGGT	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.164C>T	1.37:g.9009406C>T	ENSP00000366662:p.Thr55Met	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Missense_Mutation	SNP	ENST00000377443.2	37	CCDS30578.1	639	0.2925824175824176	48	0.0975609756097561	145	0.4005524861878453	147	0.256993006993007	299	0.3944591029023747	C	16.20	3.056074	0.55325	0.144122	0.413837	ENSG00000131686	ENST00000319474;ENST00000549778;ENST00000377443;ENST00000377436	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	5.55	-7.73	0.01245	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.896444	0.09959	N	0.733659	T	0.00012	0.0000	L	0.31420	0.93	0.80722	P	0.0	D	0.60160	0.987	P	0.53006	0.715	T	0.20140	-1.0284	9	0.56958	D	0.05	.	12.5466	0.56203	0.2599:0.1215:0.6186:0.0	rs2274327;rs17389244;rs60942560;rs2274327	55	P23280	CAH6_HUMAN	M	55	ENSP00000325786:T55M;ENSP00000447108:T55M;ENSP00000366662:T55M;ENSP00000366654:T55M	ENSP00000325786:T55M	T	+	2	0	CA6	8931993	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.262000	0.08682	-1.540000	0.01730	-1.053000	0.02334	ACG	C|0.706;N|0.000	.	strong		0.582	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
PTCHD3	374308	hgsc.bcm.edu	37	10	27688109	27688109	+	Missense_Mutation	SNP	T	T	C	rs2429485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:27688109T>C	ENST00000438700.3	-	4	1535	c.1418A>G	c.(1417-1419)gAt>gGt	p.D473G		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	473	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.		D -> G (in dbSNP:rs2429485). {ECO:0000269|PubMed:14702039}.		spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TCGTATGTCATCTGCAAGGTT	0.393													T|||	2755	0.55012	0.5257	0.5202	5008	,	,		13743	0.37		0.6829	False		,,,				2504	0.6534				p.D473G		Atlas-SNP	.											.	PTCHD3	140	.	0			c.A1418G						PASS	.	T	GLY/ASP	2355,2051	604.7+/-390.4	623,1109,471	78.0	68.0	72.0		1418	-0.1	0.0	10	dbSNP_100	72	5856,2744	674.8+/-403.1	2005,1846,449	yes	missense	PTCHD3	NM_001034842.3	94	2628,2955,920	CC,CT,TT		31.907,46.5502,36.8676	benign	473/768	27688109	8211,4795	2203	4300	6503	SO:0001583	missense	374308	exon4			ATGTCATCTGCAA	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1418A>G	10.37:g.27688109T>C	ENSP00000417658:p.Asp473Gly	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	1160	0.5311355311355311	264	0.5365853658536586	203	0.5607734806629834	178	0.3111888111888112	515	0.679419525065963	T	0.006	-2.107772	0.00356	0.534498	0.68093	ENSG00000182077	ENST00000438700	D	0.85629	-2.01	3.84	-0.118	0.13547	Sterol-sensing domain (1);	0.827780	0.11084	N	0.601465	T	0.00012	0.0000	N	0.17278	0.47	0.80722	P	0.0	B	0.06786	0.001	B	0.12837	0.008	T	0.43637	-0.9379	9	0.22109	T	0.4	-3.6306	1.1839	0.01851	0.1333:0.1764:0.2582:0.4321	rs2429485;rs17387998;rs52802595;rs57298801;rs2429485	473	Q3KNS1	PTHD3_HUMAN	G	473	ENSP00000417658:D473G	ENSP00000417658:D473G	D	-	2	0	PTCHD3	27728115	0.079000	0.21365	0.000000	0.03702	0.005000	0.04900	2.124000	0.42006	-0.224000	0.09928	-0.604000	0.04097	GAT	T|0.414;C|0.586	0.586	strong		0.393	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
ALX4	60529	hgsc.bcm.edu	37	11	44286566	44286566	+	Silent	SNP	G	G	A	rs3802805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:44286566G>A	ENST00000329255.3	-	4	1177	c.1074C>T	c.(1072-1074)caC>caT	p.H358H		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	358					anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						TCTGGCCCACGTGACTGCCAG	0.677													G|||	1795	0.358427	0.1248	0.5202	5008	,	,		16259	0.5258		0.334	False		,,,				2504	0.4121				p.H358H		Atlas-SNP	.											ALX4,NS,adenoma,0,1	ALX4	58	1	0			c.C1074T						PASS	.	G		733,3673	291.0+/-281.2	66,601,1536	47.0	43.0	45.0		1074	3.0	1.0	11	dbSNP_107	45	2838,5760	430.8+/-356.6	470,1898,1931	no	coding-synonymous	ALX4	NM_021926.3		536,2499,3467	AA,AG,GG		33.0077,16.6364,27.4608		358/412	44286566	3571,9433	2203	4299	6502	SO:0001819	synonymous_variant	60529	exon4			GCCCACGTGACTG	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.1074C>T	11.37:g.44286566G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_021926	Q96JN7|Q9H198|Q9HAY9	Silent	SNP	ENST00000329255.3	37	CCDS31468.1																																																																																			G|0.699;A|0.301	0.301	strong		0.677	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
PPTC7	160760	hgsc.bcm.edu	37	12	110974890	110974890	+	Silent	SNP	T	T	C	rs10849900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:110974890T>C	ENST00000354300.3	-	6	1155	c.867A>G	c.(865-867)ccA>ccG	p.P289P		NM_139283.1	NP_644812.1	Q8NI37	PPTC7_HUMAN	PTC7 protein phosphatase homolog (S. cerevisiae)	289	PP2C-like.					mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.P289P(1)		endometrium(1)|large_intestine(2)|lung(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	9						TGATGTCATCTGGCTTTCCAC	0.383													T|||	1625	0.324481	0.1309	0.2781	5008	,	,		20337	0.3889		0.3161	False		,,,				2504	0.5613				p.P289P		Atlas-SNP	.											PPTC7,NS,carcinoma,0,1	PPTC7	30	1	1	Substitution - coding silent(1)	stomach(1)	c.A867G						PASS	.	T		637,3769	273.4+/-271.3	55,527,1621	199.0	169.0	179.0		867	0.4	1.0	12	dbSNP_120	179	2738,5862	436.3+/-358.3	446,1846,2008	no	coding-synonymous	PPTC7	NM_139283.1		501,2373,3629	CC,CT,TT		31.8372,14.4576,25.9496		289/305	110974890	3375,9631	2203	4300	6503	SO:0001819	synonymous_variant	160760	exon6			GTCATCTGGCTTT	AF385435	CCDS9149.1	12q24.11	2009-11-05				ENSG00000196850			30695	protein-coding gene	gene with protein product	"""T cell activation protein phosphatase 2C"""	609668				15177553	Standard	NM_139283		Approved	TA-PP2C	uc001trh.1	Q8NI37	OTTHUMG00000169529	ENST00000354300.3:c.867A>G	12.37:g.110974890T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	50	0.595238	NM_139283	B3KWC5|Q68DZ7|Q6UY82	Silent	SNP	ENST00000354300.3	37	CCDS9149.1																																																																																			T|0.725;C|0.275	0.275	strong		0.383	PPTC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404635.1	NM_139283	
PLEKHG3	26030	hgsc.bcm.edu	37	14	65197767	65197767	+	Silent	SNP	G	G	A	rs229624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:65197767G>A	ENST00000394691.1	+	7	876	c.729G>A	c.(727-729)aaG>aaA	p.K243K	PLEKHG3_ENST00000247226.7_Silent_p.K187K			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	243	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		AAATTGCCAAGCATTTTGATG	0.572													G|||	619	0.123602	0.1067	0.0965	5008	,	,		20433	0.0308		0.1849	False		,,,				2504	0.1984				p.K187K		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.G561A						PASS	.	G		510,3896	235.2+/-247.8	36,438,1729	181.0	161.0	168.0		561	-3.7	1.0	14	dbSNP_79	168	1692,6908	310.5+/-309.9	154,1384,2762	no	coding-synonymous	PLEKHG3	NM_015549.1		190,1822,4491	AA,AG,GG		19.6744,11.5751,16.9306		187/1164	65197767	2202,10804	2203	4300	6503	SO:0001819	synonymous_variant	26030	exon5			TGCCAAGCATTTT	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20364	protein-coding gene	gene with protein product			"""KIAA0599"""	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.729G>A	14.37:g.65197767G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Silent	SNP	ENST00000394691.1	37																																																																																				G|0.853;A|0.147	0.147	strong		0.572	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549	
OVCH1	341350	hgsc.bcm.edu	37	12	29596365	29596365	+	Missense_Mutation	SNP	T	T	C	rs78265994	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:29596365T>C	ENST00000318184.5	-	25	3085	c.3086A>G	c.(3085-3087)aAg>aGg	p.K1029R	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	1029						extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AGTTGTTGGCTTCATCGGGAA	0.363													T|||	207	0.0413339	0.0151	0.0591	5008	,	,		16493	0.001		0.0915	False		,,,				2504	0.0542				p.K1029R		Atlas-SNP	.											.	OVCH1	195	.	0			c.A3086G						PASS	.	T	ARG/LYS	90,3574		1,88,1743	131.0	131.0	131.0		3086	1.2	0.1	12	dbSNP_131	131	660,7528		30,600,3464	yes	missense	OVCH1	NM_183378.2	26	31,688,5207	CC,CT,TT		8.0606,2.4563,6.328	possibly-damaging	1029/1135	29596365	750,11102	1832	4094	5926	SO:0001583	missense	341350	exon25			GTTGGCTTCATCG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.3086A>G	12.37:g.29596365T>C	ENSP00000326708:p.Lys1029Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		95	0.043498168498168496	8	0.016260162601626018	15	0.04143646408839779	0	0.0	72	0.09498680738786279	T	2.410	-0.335546	0.05278	0.024563	0.080606	ENSG00000187950	ENST00000318184;ENST00000537054	T;T	0.34072	1.38;2.12	2.43	1.22	0.21188	CUB (2);	.	.	.	.	T	0.00440	0.0014	N	0.08118	0	0.80722	P	0.0	P	0.39480	0.675	B	0.22386	0.039	T	0.12811	-1.0533	8	0.34782	T	0.22	.	5.3715	0.16142	0.0:0.0:0.2973:0.7027	.	1029	Q7RTY7	OVCH1_HUMAN	R	1029;54	ENSP00000326708:K1029R;ENSP00000445480:K54R	ENSP00000326708:K1029R	K	-	2	0	OVCH1	29487632	0.202000	0.23423	0.070000	0.20053	0.083000	0.17756	1.476000	0.35420	0.348000	0.23949	0.533000	0.62120	AAG	T|0.952;C|0.048	0.048	strong		0.363	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
APPL1	26060	hgsc.bcm.edu	37	3	57293908	57293908	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:57293908C>A	ENST00000288266.3	+	17	1666	c.1519C>A	c.(1519-1521)Ctt>Att	p.L507I		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	507	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		TGTCCGATTCCTTGGTTCAAT	0.318																																					p.L507I		Atlas-SNP	.											.	APPL1	59	.	0			c.C1519A						PASS	.						76.0	75.0	76.0					3																	57293908		2203	4300	6503	SO:0001583	missense	26060	exon17			CGATTCCTTGGTT	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"""Pleckstrin homology (PH) domain containing"""	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.1519C>A	3.37:g.57293908C>A	ENSP00000288266:p.Leu507Ile	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	137	23	0.167883	NM_012096	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	C	32	5.114466	0.94339	.	.	ENSG00000157500	ENST00000288266	T	0.33216	1.42	5.43	5.43	0.79202	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.60077	0.2241	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.63287	-0.6671	10	0.87932	D	0	.	19.6173	0.95639	0.0:1.0:0.0:0.0	.	490;507	B4DQX8;Q9UKG1	.;DP13A_HUMAN	I	507	ENSP00000288266:L507I	ENSP00000288266:L507I	L	+	1	0	APPL1	57268948	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.729000	0.84864	2.712000	0.92718	0.557000	0.71058	CTT	.	.	none		0.318	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	
PARD3B	117583	hgsc.bcm.edu	37	2	205829991	205829991	+	Silent	SNP	C	C	T	rs236843	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:205829991C>T	ENST00000406610.2	+	3	546	c.339C>T	c.(337-339)gcC>gcT	p.A113A	PARD3B_ENST00000462231.1_Silent_p.A113A|PARD3B_ENST00000358768.2_Silent_p.A113A|PARD3B_ENST00000351153.1_Silent_p.A113A|PARD3B_ENST00000349953.3_Silent_p.A113A	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	113					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		CCCAACTGGCCGCATTTAAGC	0.473													T|||	4025	0.803714	0.9629	0.7536	5008	,	,		15327	0.7718		0.6153	False		,,,				2504	0.8507				p.A113A		Atlas-SNP	.											PARD3B_ENST00000358768,colon,carcinoma,0,3	PARD3B	314	3	0			c.C339T						PASS	.	T	,,	3248,446		1426,396,25	76.0	79.0	78.0		339,339,339	4.6	0.9	2	dbSNP_79	78	4646,3548		1335,1976,786	no	coding-synonymous,coding-synonymous,coding-synonymous	PARD3B	NM_057177.6,NM_152526.5,NM_205863.3	,,	2761,2372,811	TT,TC,CC		43.3,12.0736,33.5969	,,	113/1137,113/1144,113/1105	205829991	7894,3994	1847	4097	5944	SO:0001819	synonymous_variant	117583	exon3			ACTGGCCGCATTT	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.339C>T	2.37:g.205829991C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	174	80	0.45977	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				C|0.267;T|0.732	0.732	strong		0.473	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
CYP2C9	1559	hgsc.bcm.edu	37	10	96702047	96702047	+	Missense_Mutation	SNP	C	C	T	rs1799853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96702047C>T	ENST00000260682.6	+	3	442	c.430C>T	c.(430-432)Cgt>Tgt	p.R144C	CYP2C9_ENST00000461906.1_3'UTR	NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	144			R -> C (in allele CYP2C9*2; dbSNP:rs1799853). {ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2827463, ECO:0000269|PubMed:3697070, ECO:0000269|PubMed:8946475, ECO:0000269|PubMed:9110362, ECO:0000269|Ref.3}.		arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	CATTGAGGACCGTGTTCAAGA	0.498													C|||	240	0.0479233	0.0083	0.0994	5008	,	,		20423	0.001		0.1243	False		,,,				2504	0.0348				p.R144C	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											.	CYP2C9	82	.	0			c.C430T	GRCh37	CM994193	CYP2C9	M	rs1799853	PASS	.	C	CYS/ARG	118,4288		4,110,2089	154.0	146.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	430	1.4	0.1	10	dbSNP_89	149	1124,7470		75,974,3248	yes	missense	CYP2C9	NM_000771.3	180	79,1084,5337	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	13.0789,2.6782,9.5538	probably-damaging	144/491	96702047	1242,11758	2203	4297	6500	SO:0001583	missense	1559	exon3			GAGGACCGTGTTC	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"""Cytochrome P450s"""	2623	protein-coding gene	gene with protein product		601130	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"""	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.430C>T	10.37:g.96702047C>T	ENSP00000260682:p.Arg144Cys	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	245	125	0.510204	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	149	0.06822344322344322	9	0.018292682926829267	45	0.12430939226519337	2	0.0034965034965034965	93	0.12269129287598944	.	16.06	3.014845	0.54468	0.026782	0.130789	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.69926	-0.44	3.54	1.42	0.22433	.	0.089345	0.47093	U	0.000246	T	0.02418	0.0074	M	0.74647	2.275	0.23144	P	0.99822706	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.989;0.989;0.995	T	0.51810	-0.8658	9	0.72032	D	0.01	.	5.9087	0.19016	0.4066:0.4141:0.1794:0.0	rs1799853;rs17110268;rs60690363;rs1799853	144;144;144	Q5VX92;P11712;Q8WW80	.;CP2C9_HUMAN;.	C	144	ENSP00000260682:R144C	ENSP00000260682:R144C	R	+	1	0	CYP2C9	96692037	0.000000	0.05858	0.125000	0.21846	0.884000	0.51177	-0.307000	0.08167	0.194000	0.20326	0.484000	0.47621	CGT	C|1.000;|0.000	.	weak		0.498	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771	
MTMR2	8898	hgsc.bcm.edu	37	11	95580926	95580926	+	Silent	SNP	G	G	A	rs566204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:95580926G>A	ENST00000346299.5	-	10	1471	c.1131C>T	c.(1129-1131)acC>acT	p.T377T	MTMR2_ENST00000393223.3_Silent_p.T305T|MTMR2_ENST00000352297.7_Silent_p.T305T|MTMR2_ENST00000484818.1_5'Flank|MTMR2_ENST00000409459.1_Silent_p.T305T	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	377	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACAACCAGTGGGTTTCCTCAA	0.378													A|||	1048	0.209265	0.0923	0.2378	5008	,	,		19645	0.253		0.3708	False		,,,				2504	0.136				p.T377T		Atlas-SNP	.											.	MTMR2	79	.	0			c.C1131T						PASS	.	A	,,	585,3817	771.7+/-413.8	43,499,1659	140.0	139.0	139.0		1131,915,915	-9.1	0.6	11	dbSNP_83	139	3289,5307	646.7+/-400.3	598,2093,1607	no	coding-synonymous,coding-synonymous,coding-synonymous	MTMR2	NM_016156.5,NM_201278.2,NM_201281.2	,,	641,2592,3266	AA,AG,GG		38.262,13.2894,29.8046	,,	377/644,305/572,305/572	95580926	3874,9124	2201	4298	6499	SO:0001819	synonymous_variant	8898	exon10			CCAGTGGGTTTCC	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1131C>T	11.37:g.95580926G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	271	271	1	NM_016156	A6NN98|Q9UPS9	Silent	SNP	ENST00000346299.5	37	CCDS8305.1																																																																																			G|0.715;A|0.285	0.285	strong		0.378	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156	
DBF4	10926	hgsc.bcm.edu	37	7	87537188	87537188	+	Missense_Mutation	SNP	A	A	G	rs61747462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:87537188A>G	ENST00000265728.1	+	12	2239	c.1735A>G	c.(1735-1737)Aaa>Gaa	p.K579E		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	579					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				TCGAAAAGTGAAAATAATATT	0.333													A|||	29	0.00579073	0.0008	0.013	5008	,	,		19546	0.0		0.0169	False		,,,				2504	0.002				p.K579E		Atlas-SNP	.											.	DBF4	67	.	0			c.A1735G						PASS	.	A	GLU/LYS	16,4388		0,16,2186	46.0	53.0	51.0		1735	4.0	1.0	7	dbSNP_129	51	99,8435		1,97,4169	no	missense	DBF4	NM_006716.3	56	1,113,6355	GG,GA,AA		1.1601,0.3633,0.8889	possibly-damaging	579/675	87537188	115,12823	2202	4267	6469	SO:0001583	missense	10926	exon12			AAAGTGAAAATAA	AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"""Zinc fingers, DBF-type"""	17364	protein-coding gene	gene with protein product	"""activator of S phase kinase"", ""chiffon homolog (Drosophila)"", ""zinc finger, DBF-type containing 1"", ""DBF4 zinc finger A"""	604281	"""DBF4 homolog (S. cerevisiae)"""			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1735A>G	7.37:g.87537188A>G	ENSP00000265728:p.Lys579Glu	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	269	130	0.483271	NM_006716	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	14	0.00641025641025641	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	10	0.013192612137203167	A	13.61	2.289011	0.40494	0.003633	0.011601	ENSG00000006634	ENST00000265728	T	0.37235	1.21	5.13	3.98	0.46160	.	0.088141	0.47852	D	0.000204	T	0.25005	0.0607	L	0.56769	1.78	0.30535	N	0.767027	B;B	0.26195	0.144;0.068	B;B	0.21708	0.036;0.036	T	0.35674	-0.9779	10	0.66056	D	0.02	-9.6101	8.964	0.35865	0.9161:0.0:0.0839:0.0	rs61747462	355;579	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	E	579	ENSP00000265728:K579E	ENSP00000265728:K579E	K	+	1	0	DBF4	87375124	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.387000	0.59626	1.934000	0.56057	0.528000	0.53228	AAA	A|0.992;G|0.008	0.008	strong		0.333	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716	
EFCAB7	84455	hgsc.bcm.edu	37	1	63999826	63999826	+	Missense_Mutation	SNP	C	C	T	rs6693255	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:63999826C>T	ENST00000371088.4	+	6	989	c.743C>T	c.(742-744)aCa>aTa	p.T248I	RNU7-123P_ENST00000515911.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	248			T -> I (in dbSNP:rs6693255). {ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						GTTTCCTTCACAGTTACCATG	0.353													C|||	726	0.144968	0.0855	0.1614	5008	,	,		15556	0.1855		0.1441	False		,,,				2504	0.1728				p.T248I		Atlas-SNP	.											EFCAB7,NS,carcinoma,+1,1	EFCAB7	45	1	0			c.C743T						PASS	.	C	ILE/THR	393,4013	195.0+/-219.7	13,367,1823	100.0	98.0	98.0		743	1.5	1.0	1	dbSNP_116	98	1325,7275	260.5+/-283.3	92,1141,3067	yes	missense	EFCAB7	NM_032437.2	89	105,1508,4890	TT,TC,CC		15.407,8.9197,13.2093	benign	248/630	63999826	1718,11288	2203	4300	6503	SO:0001583	missense	84455	exon6			CCTTCACAGTTAC	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.743C>T	1.37:g.63999826C>T	ENSP00000360129:p.Thr248Ile	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	138	50	0.362319	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	325	0.1488095238095238	51	0.10365853658536585	61	0.1685082872928177	105	0.18356643356643357	108	0.1424802110817942	C	3.616	-0.078505	0.07184	0.089197	0.15407	ENSG00000203965	ENST00000371088	T	0.58652	0.32	5.65	1.49	0.22878	.	0.529823	0.23072	N	0.052243	T	0.25269	0.0614	L	0.47716	1.5	0.21719	P	0.999579407	B	0.30763	0.294	B	0.26517	0.07	T	0.06356	-1.0831	9	0.72032	D	0.01	-5.8298	4.209	0.10502	0.1277:0.5984:0.1245:0.1495	rs6693255;rs17856494;rs52831553;rs56659953;rs6693255	248	A8K855	EFCB7_HUMAN	I	248	ENSP00000360129:T248I	ENSP00000360129:T248I	T	+	2	0	EFCAB7	63772414	0.160000	0.22878	0.976000	0.42696	0.393000	0.30537	0.578000	0.23773	0.744000	0.32741	-0.136000	0.14681	ACA	C|0.857;T|0.143	0.143	strong		0.353	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
POLDIP3	84271	hgsc.bcm.edu	37	22	43010817	43010817	+	Missense_Mutation	SNP	G	G	A	rs28627172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43010817G>A	ENST00000252115.5	-	1	151	c.47C>T	c.(46-48)gCg>gTg	p.A16V	RNU12_ENST00000362512.1_lincRNA|POLDIP3_ENST00000348657.2_Missense_Mutation_p.A16V|POLDIP3_ENST00000339677.6_Missense_Mutation_p.A16V	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	16					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						TCCTTTCGCCGCCGCCCCGCG	0.672													G|||	617	0.123203	0.2799	0.0922	5008	,	,		12786	0.0		0.1083	False		,,,				2504	0.0757				p.A16V	Ovarian(52;967 1128 5875 19997 42537)	Atlas-SNP	.											POLDIP3_ENST00000339677,NS,carcinoma,0,2	POLDIP3	58	2	0			c.C47T						PASS	.	G	VAL/ALA,VAL/ALA	1030,3376	374.4+/-321.2	139,752,1312	46.0	50.0	48.0		47,47	3.4	0.1	22	dbSNP_125	48	1192,7408	239.6+/-270.6	94,1004,3202	yes	missense,missense	POLDIP3	NM_032311.3,NM_178136.1	64,64	233,1756,4514	AA,AG,GG		13.8605,23.3772,17.0844	benign,benign	16/422,16/393	43010817	2222,10784	2203	4300	6503	SO:0001583	missense	84271	exon1			TTCGCCGCCGCCC		CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"""RNA binding motif (RRM) containing"""	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.47C>T	22.37:g.43010817G>A	ENSP00000252115:p.Ala16Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_178136	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	252	0.11538461538461539	141	0.2865853658536585	30	0.08287292817679558	0	0.0	81	0.10686015831134564	G	10.27	1.303509	0.23736	0.233772	0.138605	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000415122;ENST00000339677;ENST00000452567	.	.	.	4.4	3.37	0.38596	.	0.265748	0.37393	N	0.002116	T	0.00012	0.0000	L	0.44542	1.39	0.42617	P	0.006661999999999946	B;P;B;B	0.47106	0.001;0.89;0.165;0.002	B;B;B;B	0.36719	0.0;0.231;0.038;0.0	T	0.36504	-0.9745	8	0.26408	T	0.33	-18.6813	7.0789	0.25219	0.0753:0.1231:0.6754:0.1261	rs28627172	16;16;16;16	B4E0L0;Q6R954;Q9BY77-2;Q9BY77	.;.;.;PDIP3_HUMAN	V	16	.	ENSP00000252115:A16V	A	-	2	0	POLDIP3	41340761	0.025000	0.19082	0.050000	0.19076	0.597000	0.36814	0.872000	0.28037	0.604000	0.29930	-1.151000	0.01829	GCG	G|0.845;A|0.155	0.155	strong		0.672	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311	
OR6N1	128372	hgsc.bcm.edu	37	1	158736217	158736217	+	Missense_Mutation	SNP	G	G	A	rs857828	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158736217G>A	ENST00000335094.2	-	1	275	c.256C>T	c.(256-258)Ctc>Ttc	p.L86F		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	86				L -> F (in Ref. 3; AAK95093). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					TTCTCACTGAGCAAGTTTGCC	0.498													G|||	18	0.00359425	0.0	0.0	5008	,	,		20366	0.0		0.0099	False		,,,				2504	0.0082				p.L86F		Atlas-SNP	.											.	OR6N1	96	.	0			c.C256T						PASS	.	G	PHE/LEU	10,4396	17.9+/-39.9	0,10,2193	82.0	76.0	78.0		256	5.1	1.0	1	dbSNP_86	78	79,8521	46.7+/-105.8	1,77,4222	yes	missense	OR6N1	NM_001005185.1	22	1,87,6415	AA,AG,GG		0.9186,0.227,0.6843	probably-damaging	86/313	158736217	89,12917	2203	4300	6503	SO:0001583	missense	128372	exon1			CACTGAGCAAGTT	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.256C>T	1.37:g.158736217G>A	ENSP00000335535:p.Leu86Phe	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	118	76	0.644068	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	15.99	2.995570	0.54147	0.00227	0.009186	ENSG00000197403	ENST00000335094	T	0.10668	2.85	5.1	5.1	0.69264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	D	0.000856	T	0.11707	0.0285	L	0.46157	1.445	0.30949	N	0.725006	D	0.61080	0.989	P	0.60949	0.881	T	0.06162	-1.0842	10	0.23302	T	0.38	-21.3514	13.7262	0.62759	0.0:0.1556:0.8444:0.0	rs857828;rs1633200	86	Q8NGY5	OR6N1_HUMAN	F	86	ENSP00000335535:L86F	ENSP00000335535:L86F	L	-	1	0	OR6N1	157002841	0.011000	0.17503	1.000000	0.80357	0.995000	0.86356	0.349000	0.20055	2.623000	0.88846	0.655000	0.94253	CTC	G|0.994;A|0.006	0.006	strong		0.498	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383012	39383012	+	Missense_Mutation	SNP	C	C	T	rs9903833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39383012C>T	ENST00000377721.3	+	1	113	c.106C>T	c.(106-108)Ccc>Tcc	p.P36S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.P36S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	36	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].		P -> S (in dbSNP:rs9903833). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CAGCAGCACACCCTGCTGCCA	0.642																																					p.P36S		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.C106T						PASS	.						51.0	47.0	48.0					17																	39383012		2202	4298	6500	SO:0001583	missense	83899	exon1			AGCACACCCTGCT	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.106C>T	17.37:g.39383012C>T	ENSP00000366950:p.Pro36Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	120	93	0.775	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	1204	0.5512820512820513	262	0.532520325203252	227	0.6270718232044199	298	0.5209790209790209	417	0.5501319261213721	.	7.176	0.588686	0.13812	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01159	5.57;5.25	2.85	0.535	0.17133	.	.	.	.	.	T	0.00012	0.0000	N	0.01751	-0.74	0.44221	P	0.002942	B	0.22604	0.072	B	0.19666	0.026	T	0.11966	-1.0566	8	0.02654	T	1	.	7.7358	0.28812	0.5744:0.4256:0.0:0.0	rs9903833;rs60053887	36	Q9BYQ4	KRA92_HUMAN	S	36	ENSP00000366950:P36S;ENSP00000398325:P36S	ENSP00000366950:P36S	P	+	1	0	KRTAP9-2	36636538	0.000000	0.05858	0.320000	0.25306	0.991000	0.79684	-2.240000	0.01197	0.134000	0.18681	0.552000	0.68991	CCC	C|0.448;T|0.552	0.552	strong		0.642	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
FAM101A	144347	hgsc.bcm.edu	37	12	124798801	124798801	+	Silent	SNP	C	C	T	rs12318072	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124798801C>T	ENST00000389727.3	+	3	381	c.381C>T	c.(379-381)ccC>ccT	p.P127P	FAM101A_ENST00000546355.1_Silent_p.P46P|FAM101A_ENST00000324038.3_Silent_p.P46P|FAM101A_ENST00000338359.4_Silent_p.P46P			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	127										endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		TCTATGCGCCCGTACCCACCG	0.632													C|||	1749	0.349241	0.4592	0.3444	5008	,	,		18625	0.4117		0.159	False		,,,				2504	0.3354				p.P46P		Atlas-SNP	.											FAM101A,NS,carcinoma,0,2	FAM101A	10	2	0			c.C138T						PASS	.	C	,	1861,2545	537.1+/-374.7	402,1057,744	86.0	75.0	79.0		138,138	-9.4	0.0	12	dbSNP_120	79	1478,7122	280.1+/-294.3	134,1210,2956	no	coding-synonymous,coding-synonymous	FAM101A,ZNF664-FAM101A	NM_001204299.1,NM_181709.4	,	536,2267,3700	TT,TC,CC		17.186,42.2379,25.6728	,	46/136,46/136	124798801	3339,9667	2203	4300	6503	SO:0001819	synonymous_variant	144347	exon3			TGCGCCCGTACCC		CCDS9258.1	12q24.31	2012-11-30			ENSG00000178882	ENSG00000178882			27051	protein-coding gene	gene with protein product		615927				12477932	Standard	NM_181709		Approved	FLJ44614	uc001ugd.2	Q6ZTI6	OTTHUMG00000168609	ENST00000389727.3:c.381C>T	12.37:g.124798801C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_181709	A5D8T5	Silent	SNP	ENST00000389727.3	37																																																																																				C|0.714;T|0.286	0.286	strong		0.632	FAM101A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_181709	
FREM2	341640	hgsc.bcm.edu	37	13	39263023	39263023	+	Silent	SNP	C	C	T	rs12874397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:39263023C>T	ENST00000280481.7	+	1	1758	c.1542C>T	c.(1540-1542)gcC>gcT	p.A514A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	514					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGCTGGCAGCCGGCCAGGTGG	0.602													C|||	422	0.0842652	0.0061	0.1239	5008	,	,		14684	0.004		0.2634	False		,,,				2504	0.0603				p.A514A		Atlas-SNP	.											.	FREM2	385	.	0			c.C1542T						PASS	.	C		190,4216	115.9+/-153.8	4,182,2017	25.0	25.0	25.0		1542	-9.4	0.2	13	dbSNP_121	25	2241,6357	355.9+/-330.1	314,1613,2372	no	coding-synonymous	FREM2	NM_207361.4		318,1795,4389	TT,TC,CC		26.0642,4.3123,18.6942		514/3170	39263023	2431,10573	2203	4299	6502	SO:0001819	synonymous_variant	341640	exon1			GGCAGCCGGCCAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1542C>T	13.37:g.39263023C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|0.841;T|0.159	0.159	strong		0.602	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
ALPK1	80216	hgsc.bcm.edu	37	4	113345147	113345147	+	Missense_Mutation	SNP	A	A	G	rs6533616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:113345147A>G	ENST00000458497.1	+	6	802	c.523A>G	c.(523-525)Aat>Gat	p.N175D	ALPK1_ENST00000504176.2_Missense_Mutation_p.N97D|ALPK1_ENST00000177648.9_Missense_Mutation_p.N175D	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	175			N -> D (in dbSNP:rs6533616). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		AATAAGCAACAATGGAGCAAC	0.373													A|||	254	0.0507188	0.053	0.0677	5008	,	,		20200	0.002		0.1163	False		,,,				2504	0.0184				p.N175D		Atlas-SNP	.											.	ALPK1	125	.	0			c.A523G						PASS	.	A	ASP/ASN,ASP/ASN	326,4080	173.4+/-203.2	12,302,1889	124.0	115.0	118.0		523,523	3.2	0.6	4	dbSNP_116	118	960,7640	210.1+/-251.1	43,874,3383	yes	missense,missense	ALPK1	NM_001102406.1,NM_025144.3	23,23	55,1176,5272	GG,GA,AA		11.1628,7.399,9.8877	benign,benign	175/1245,175/1245	113345147	1286,11720	2203	4300	6503	SO:0001583	missense	80216	exon6			AGCAACAATGGAG	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.523A>G	4.37:g.113345147A>G	ENSP00000398048:p.Asn175Asp	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	150	0.06868131868131869	31	0.06300813008130081	28	0.07734806629834254	2	0.0034965034965034965	89	0.11741424802110818	A	12.05	1.821169	0.32237	0.07399	0.111628	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.29917	1.55;1.55;1.55	5.62	3.16	0.36331	.	0.367258	0.30611	N	0.009252	T	0.00271	0.0008	L	0.32530	0.975	0.40707	P	0.017461999999999978	B;B	0.13145	0.007;0.005	B;B	0.13407	0.009;0.003	T	0.08638	-1.0712	9	0.39692	T	0.17	-4.6853	5.5579	0.17127	0.7087:0.1465:0.1448:0.0	rs6533616;rs17528925;rs56753375;rs6533616	97;175	F5H138;Q96QP1	.;ALPK1_HUMAN	D	175;175;97	ENSP00000398048:N175D;ENSP00000177648:N175D;ENSP00000426044:N97D	ENSP00000177648:N175D	N	+	1	0	ALPK1	113564596	0.478000	0.25917	0.613000	0.29037	0.980000	0.70556	1.242000	0.32755	0.414000	0.25790	0.524000	0.50904	AAT	A|0.920;G|0.080	0.080	strong		0.373	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
CD44	960	hgsc.bcm.edu	37	11	35211471	35211471	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:35211471G>A	ENST00000428726.2	+	5	649	c.526G>A	c.(526-528)Gat>Aat	p.D176N	CD44_ENST00000415148.2_Missense_Mutation_p.D176N|CD44_ENST00000526669.2_Intron|CD44_ENST00000360158.4_Missense_Mutation_p.D176N|CD44_ENST00000278386.6_Intron|CD44_ENST00000437706.2_Missense_Mutation_p.D176N|CD44_ENST00000434472.2_Missense_Mutation_p.D176N|CD44_ENST00000433354.2_Missense_Mutation_p.D176N|CD44_ENST00000263398.6_Missense_Mutation_p.D176N|CD44_ENST00000449691.2_Missense_Mutation_p.D176N|CD44_ENST00000352818.4_Missense_Mutation_p.D176N|CD44_ENST00000433892.2_Missense_Mutation_p.D176N	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	176					blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	CCCTACTGATGATGACGTGAG	0.502																																					p.D176N		Atlas-SNP	.											.	CD44	48	.	0			c.G526A						PASS	.						123.0	98.0	106.0					11																	35211471		2202	4298	6500	SO:0001583	missense	960	exon5			ACTGATGATGACG	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.526G>A	11.37:g.35211471G>A	ENSP00000398632:p.Asp176Asn	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	239	120	0.502092	NM_001001391	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	37	CCDS7897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.4|21.4	4.140023|4.140023	0.77775|0.77775	.|.	.|.	ENSG00000026508|ENSG00000026508	ENST00000263398;ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000360158;ENST00000428726;ENST00000433892;ENST00000434472;ENST00000352818;ENST00000525211;ENST00000526000;ENST00000279452;ENST00000531110;ENST00000525688;ENST00000278385;ENST00000533222|ENST00000527889;ENST00000531873;ENST00000525685	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.36699|.	1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.411612|.	0.26136|.	N|.	0.026133|.	T|T	0.59702|0.59702	0.2213|0.2213	M|M	0.65975|0.65975	2.015|2.015	0.26051|0.26051	N|N	0.981485|0.981485	P;P;P;D;P;D|.	0.71674|.	0.453;0.614;0.798;0.998;0.867;0.993|.	B;P;P;D;P;D|.	0.76575|.	0.42;0.49;0.815;0.988;0.803;0.946|.	T|T	0.55366|0.55366	-0.8152|-0.8152	10|5	0.35671|.	T|.	0.21|.	-24.8201|-24.8201	15.6093|15.6093	0.76704|0.76704	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	176;176;176;176;176;176|.	B6EAT9;P16070-11;P16070-12;P16070-10;P16070-4;P16070|.	.;.;.;.;.;CD44_HUMAN|.	N|I	176;176;176;176;176;176;176;176;176;176;155;154;136;50;15;12;9|131;96;43	ENSP00000263398:D176N;ENSP00000389830:D176N;ENSP00000414567:D176N;ENSP00000391008:D176N;ENSP00000403990:D176N;ENSP00000353280:D176N;ENSP00000398632:D176N;ENSP00000392331:D176N;ENSP00000404447:D176N;ENSP00000309732:D176N;ENSP00000432405:D155N;ENSP00000434465:D154N;ENSP00000279452:D136N;ENSP00000436549:D50N;ENSP00000436980:D15N;ENSP00000278385:D12N;ENSP00000435321:D9N|.	ENSP00000263398:D176N|.	D|M	+|+	1|3	0|0	CD44|CD44	35168047|35168047	0.417000|0.417000	0.25432|0.25432	0.083000|0.083000	0.20561|0.20561	0.003000|0.003000	0.03518|0.03518	2.101000|2.101000	0.41787|0.41787	2.745000|2.745000	0.94114|0.94114	0.655000|0.655000	0.94253|0.94253	GAT|ATG	.	.	none		0.502	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
DYX1C1	161582	hgsc.bcm.edu	37	15	55759193	55759193	+	Missense_Mutation	SNP	T	T	C	rs600753	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:55759193T>C	ENST00000321149.3	-	5	939	c.572A>G	c.(571-573)gAa>gGa	p.E191G	DYX1C1_ENST00000348518.3_Missense_Mutation_p.E191G|DYX1C1_ENST00000457155.2_Missense_Mutation_p.E191G|DYX1C1_ENST00000380679.1_Missense_Mutation_p.E191G|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000448430.2_Missense_Mutation_p.E191G	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	191			E -> G (in dbSNP:rs600753). {ECO:0000269|PubMed:12954984, ECO:0000269|PubMed:15489334}.		cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		tttttttctttcttctttaat	0.299													T|||	2646	0.528355	0.2806	0.6715	5008	,	,		13485	0.746		0.501	False		,,,				2504	0.5654				p.E191G		Atlas-SNP	.											.	DYX1C1	54	.	0			c.A572G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU	1360,2968		219,922,1023	29.0	28.0	29.0		572,572,572	2.5	0.8	15	dbSNP_83	29	4448,4088		1200,2048,1020	yes	missense,missense,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	98,98,98	1419,2970,2043	CC,CT,TT		47.8913,31.4233,45.1493	possibly-damaging,possibly-damaging,possibly-damaging	191/377,191/382,191/421	55759193	5808,7056	2164	4268	6432	SO:0001583	missense	161582	exon5			TTTCTTTCTTCTT		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.572A>G	15.37:g.55759193T>C	ENSP00000323275:p.Glu191Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	1161	0.5315934065934066	144	0.2926829268292683	233	0.643646408839779	406	0.7097902097902098	378	0.49868073878627966	T	11.06	1.527805	0.27299	0.314233	0.521087	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.49432	2.58;2.58;0.78;3.25;0.78	2.47	2.47	0.30058	.	0.942418	0.08791	N	0.893192	T	0.00012	0.0000	N	0.14661	0.345	0.35594	P	0.19267500000000004	B;B;B	0.21821	0.061;0.041;0.021	B;B;B	0.26094	0.066;0.02;0.016	T	0.42207	-0.9465	9	0.45353	T	0.12	.	6.8751	0.24143	0.0:0.0:0.0:1.0	rs600753;rs17855757;rs52829955;rs59372631;rs600753	191;191;191	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	G	191	ENSP00000403412:E191G;ENSP00000370054:E191G;ENSP00000402640:E191G;ENSP00000323275:E191G;ENSP00000299561:E191G	ENSP00000323275:E191G	E	-	2	0	DYX1C1	53546485	0.896000	0.30565	0.817000	0.32601	0.787000	0.44495	2.440000	0.44855	1.368000	0.46115	0.460000	0.39030	GAA	T|0.503;C|0.497	0.497	strong		0.299	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
MOB3C	148932	hgsc.bcm.edu	37	1	47080665	47080665	+	Intron	SNP	C	C	T	rs11211328	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:47080665C>T	ENST00000319928.3	-	2	181				MKNK1_ENST00000545730.1_Intron|MOB3C_ENST00000371940.1_5'UTR|MOB3C_ENST00000477318.1_Intron|MOB3C_ENST00000271139.8_Missense_Mutation_p.M28I	NM_201403.2	NP_958805.1	Q70IA8	MOB3C_HUMAN	MOB kinase activator 3C								metal ion binding (GO:0046872)										TCATCTCATCCATCCCGACTC	0.463													C|||	1275	0.254593	0.2413	0.3271	5008	,	,		15620	0.246		0.2654	False		,,,				2504	0.2188				p.M28I		Atlas-SNP	.											.	MOB3C	1	.	0			c.G84A						PASS	.	C	ILE/MET,	1074,3332	391.0+/-327.9	143,788,1272	80.0	79.0	79.0		84,	-0.1	0.0	1	dbSNP_120	79	2166,6434	370.3+/-335.8	254,1658,2388	yes	missense,intron	MOB3C	NM_145279.4,NM_201403.2	10,	397,2446,3660	TT,TC,CC		25.186,24.3759,24.9116	,	28/269,	47080665	3240,9766	2203	4300	6503	SO:0001627	intron_variant	148932	exon1			CTCATCCATCCCG	AK091808	CCDS539.1, CCDS540.1	1p34.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000142961	ENSG00000142961		"""MOB kinase activators"""	29800	protein-coding gene	gene with protein product			"""MOB1, Mps One Binder kinase activator-like 2C (yeast)"""	MOBKL2C		12477932	Standard	NM_145279		Approved	MOB1E	uc001cqe.4	Q70IA8	OTTHUMG00000007989	ENST00000319928.3:c.50-1622G>A	1.37:g.47080665C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_145279	D3DQ22|Q0VA98|Q5TC10|Q5TC11|Q8NAZ2|Q8NF28	Missense_Mutation	SNP	ENST00000319928.3	37	CCDS540.1	585	0.26785714285714285	128	0.2601626016260163	122	0.3370165745856354	146	0.25524475524475526	189	0.24934036939313983	C	10.54	1.377711	0.24944	0.243759	0.25186	ENSG00000142961	ENST00000271139	.	.	.	3.5	-0.136	0.13473	.	3.731830	0.01478	U	0.016542	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.30621	-0.9972	5	0.11794	T	0.64	-1.6724	5.769	0.18243	0.0:0.527:0.0:0.473	rs11211328;rs52833882;rs58382771;rs11211328	.	.	.	I	28	.	ENSP00000271139:M28I	M	-	3	0	MOBKL2C	46853252	0.002000	0.14202	0.000000	0.03702	0.020000	0.10135	0.609000	0.24238	-0.020000	0.14032	-0.136000	0.14681	ATG	C|0.743;T|0.257	0.257	strong		0.463	MOB3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145279	
SF3B1	23451	hgsc.bcm.edu	37	2	198270017	198270017	+	Silent	SNP	T	T	C	rs35493573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:198270017T>C	ENST00000335508.6	-	10	1510	c.1419A>G	c.(1417-1419)caA>caG	p.Q473Q	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	473	Interaction with PPP1R8.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TATCAAAGTATTGAATATCAT	0.303			Mis		myelodysplastic syndrome								T|||	68	0.0135783	0.0091	0.0014	5008	,	,		16834	0.0		0.002	False		,,,				2504	0.0542				p.Q473Q		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	SF3B1,NS,carcinoma,-2,1	SF3B1	1038	1	0			c.A1419G						PASS	.	T		9,4397	15.5+/-35.6	0,9,2194	43.0	46.0	45.0		1419	0.5	1.0	2	dbSNP_126	45	23,8573	16.6+/-54.9	0,23,4275	no	coding-synonymous	SF3B1	NM_012433.2		0,32,6469	CC,CT,TT		0.2676,0.2043,0.2461		473/1305	198270017	32,12970	2203	4298	6501	SO:0001819	synonymous_variant	23451	exon10			AAAGTATTGAATA	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1419A>G	2.37:g.198270017T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	77	0.578947	NM_012433	E9PCH3	Silent	SNP	ENST00000335508.6	37	CCDS33356.1																																																																																			T|0.994;C|0.006	0.006	strong		0.303	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
ADAM23	8745	hgsc.bcm.edu	37	2	207459467	207459467	+	Silent	SNP	C	C	T	rs3732079	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:207459467C>T	ENST00000264377.3	+	23	2413	c.2085C>T	c.(2083-2085)gcC>gcT	p.A695A	ADAM23_ENST00000374415.3_Silent_p.A695A|ADAM23_ENST00000374416.1_Silent_p.A695A	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	695					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A695A(1)		NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		TTAGTGGTGCCCATGTAGTTT	0.428													T|||	896	0.178914	0.2595	0.2205	5008	,	,		21136	0.1736		0.1193	False		,,,				2504	0.1074				p.A695A	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											ADAM23,NS,carcinoma,0,1	ADAM23	239	1	1	Substitution - coding silent(1)	stomach(1)	c.C2085T						PASS	.	T		980,3426	732.4+/-410.4	108,764,1331	171.0	174.0	173.0		2085	0.8	1.0	2	dbSNP_107	173	855,7745	780.2+/-407.7	52,751,3497	no	coding-synonymous	ADAM23	NM_003812.2		160,1515,4828	TT,TC,CC		9.9419,22.2424,14.1089		695/833	207459467	1835,11171	2203	4300	6503	SO:0001819	synonymous_variant	8745	exon23			TGGTGCCCATGTA	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"""ADAM metallopeptidase domain containing"""	202	protein-coding gene	gene with protein product		603710	"""a disintegrin and metalloproteinase domain 23"""			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.2085C>T	2.37:g.207459467C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	239	115	0.481172	NM_003812	A2RU59	Silent	SNP	ENST00000264377.3	37	CCDS2369.1																																																																																			C|0.856;G|0.000;T|0.144	0.144	strong		0.428	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	
GUCY2D	3000	hgsc.bcm.edu	37	17	7906519	7906519	+	Missense_Mutation	SNP	G	G	T	rs61749665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7906519G>T	ENST00000254854.4	+	2	304	c.154G>T	c.(154-156)Gcc>Tcc	p.A52S		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	52			A -> S (in LCA1; unknown pathological significance; dbSNP:rs61749665). {ECO:0000269|PubMed:21602930, ECO:0000269|PubMed:8944027}.		intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				cgccctctccgccgTGTTCAC	0.776													G|||	2083	0.415935	0.1369	0.4107	5008	,	,		7307	0.6935		0.327	False		,,,				2504	0.6022				p.A52S		Atlas-SNP	.											.	GUCY2D	82	.	0			c.G154T						PASS	.	G	SER/ALA	396,2736		31,334,1201	2.0	2.0	2.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	154	0.2	0.0	17	dbSNP_129	2	1601,4981		200,1201,1890	no	missense	GUCY2D	NM_000180.3	99	231,1535,3091	TT,TG,GG		24.3239,12.6437,20.558	benign	52/1104	7906519	1997,7717	1566	3291	4857	SO:0001583	missense	3000	exon2			CTCTCCGCCGTGT	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.154G>T	17.37:g.7906519G>T	ENSP00000254854:p.Ala52Ser	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	18	17	0.944444	NM_000180	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	823	0.3768315018315018	61	0.12398373983739837	132	0.36464088397790057	383	0.6695804195804196	247	0.3258575197889182	G	10.96	1.499163	0.26861	0.126437	0.243239	ENSG00000132518	ENST00000254854	D	0.83075	-1.68	4.65	0.187	0.15109	.	0.608923	0.13562	N	0.378720	T	0.00012	0.0000	M	0.65498	2.005	0.80722	P	0.0	B	0.27117	0.168	B	0.21546	0.035	T	0.48681	-0.9014	9	0.09590	T	0.72	.	3.8844	0.09091	0.2473:0.0:0.4661:0.2866	rs61749665	52	Q02846	GUC2D_HUMAN	S	52	ENSP00000254854:A52S	ENSP00000254854:A52S	A	+	1	0	GUCY2D	7847244	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.039000	0.12124	-0.193000	0.10415	-0.188000	0.12872	GCC	G|0.623;T|0.377	0.377	strong		0.776	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
KRT77	374454	hgsc.bcm.edu	37	12	53088484	53088484	+	Missense_Mutation	SNP	C	C	T	rs10783528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53088484C>T	ENST00000341809.3	-	5	1034	c.1006G>A	c.(1006-1008)Gat>Aat	p.D336N	KRT77_ENST00000537195.1_Missense_Mutation_p.D103N|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	336	Coil 2.|Rod.			D -> N (in Ref. 1; CAD91892). {ECO:0000305}.		cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CGCACTGCATCGATGATGCTG	0.587													C|||	1594	0.318291	0.1377	0.281	5008	,	,		19567	0.5813		0.3559	False		,,,				2504	0.2791				p.D336N		Atlas-SNP	.											.	KRT77	58	.	0			c.G1006A						PASS	.	C	ASN/ASP	875,3531	342.8+/-307.3	90,695,1418	139.0	97.0	111.0		1006	0.5	0.0	12	dbSNP_120	111	2918,5682	456.7+/-364.1	504,1910,1886	yes	missense	KRT77	NM_175078.2	23	594,2605,3304	TT,TC,CC		33.9302,19.8593,29.1635	benign	336/579	53088484	3793,9213	2203	4300	6503	SO:0001583	missense	374454	exon5			CTGCATCGATGAT	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1006G>A	12.37:g.53088484C>T	ENSP00000342710:p.Asp336Asn	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_175078	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	37	CCDS8837.1	801	0.36675824175824173	65	0.13211382113821138	114	0.3149171270718232	345	0.6031468531468531	277	0.3654353562005277	C	10.17	1.275491	0.23307	0.198593	0.339302	ENSG00000189182	ENST00000341809;ENST00000537195	T;T	0.78816	-1.21;-1.07	4.94	0.542	0.17174	Filament (1);	.	.	.	.	T	0.00012	0.0000	N	0.16903	0.455	0.80722	P	0.0	B	0.32731	0.382	B	0.22386	0.039	T	0.46638	-0.9177	8	0.66056	D	0.02	.	8.2491	0.31706	0.0:0.515:0.3418:0.1432	rs10783528;rs52810493;rs58359758;rs10783528	336	Q7Z794	K2C1B_HUMAN	N	336;103	ENSP00000342710:D336N;ENSP00000440803:D103N	ENSP00000342710:D336N	D	-	1	0	KRT77	51374751	0.000000	0.05858	0.004000	0.12327	0.187000	0.23431	-0.031000	0.12287	0.188000	0.20168	0.555000	0.69702	GAT	C|0.676;T|0.324	0.324	strong		0.587	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
KIAA1324	57535	hgsc.bcm.edu	37	1	109737063	109737063	+	Silent	SNP	C	C	T	rs2359246	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109737063C>T	ENST00000369939.3	+	15	2151	c.1968C>T	c.(1966-1968)aaC>aaT	p.N656N	KIAA1324_ENST00000529753.1_Silent_p.N569N|KIAA1324_ENST00000369938.1_3'UTR	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	656					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		TGTGCTACAACGATTGCACCT	0.562													C|||	3574	0.713658	0.3033	0.7968	5008	,	,		17619	0.9702		0.7634	False		,,,				2504	0.8937				p.N656N		Atlas-SNP	.											.	KIAA1324	77	.	0			c.C1968T						PASS	.	C		1623,2783	500.3+/-364.7	298,1027,878	122.0	97.0	106.0		1968	-4.2	0.8	1	dbSNP_100	106	6527,2073	718.3+/-406.2	2473,1581,246	no	coding-synonymous	KIAA1324	NM_020775.3		2771,2608,1124	TT,TC,CC		24.1047,36.8361,37.3366		656/1014	109737063	8150,4856	2203	4300	6503	SO:0001819	synonymous_variant	57535	exon15			CTACAACGATTGC	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.1968C>T	1.37:g.109737063C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																			C|0.337;T|0.663	0.663	strong		0.562	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
KLRG1	10219	hgsc.bcm.edu	37	12	9161648	9161648	+	Silent	SNP	T	T	C	rs3026251	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:9161648T>C	ENST00000266551.4	+	4	450	c.435T>C	c.(433-435)gaT>gaC	p.D145D	KLRG1_ENST00000538029.1_3'UTR|KLRG1_ENST00000356986.3_Silent_p.D145D	NM_005810.3	NP_005801.3	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G, member 1	145	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8						GGTGGGAAGATGGATCACCTC	0.443													C|||	1269	0.253395	0.0545	0.2997	5008	,	,		-128	0.379		0.2634	False		,,,				2504	0.3497				p.D145D		Atlas-SNP	.											.	KLRG1	16	.	0			c.T435C						PASS	.	C		337,4069	795.6+/-415.3	13,311,1879	89.0	86.0	87.0		435	-0.4	1.0	12	dbSNP_102	87	2572,6028	689.7+/-404.4	382,1808,2110	no	coding-synonymous	KLRG1	NM_005810.3		395,2119,3989	CC,CT,TT		29.907,7.6487,22.3666		145/190	9161648	2909,10097	2203	4300	6503	SO:0001819	synonymous_variant	10219	exon4			GGAAGATGGATCA	AF097358	CCDS8599.1	12p13.31	2011-08-30			ENSG00000139187	ENSG00000139187		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	6380	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member A"""	604874				9862378, 9842918, 16461340, 16140789	Standard	NM_005810		Approved	MAFA, 2F1, MAFA-L, CLEC15A	uc001qvg.3	Q96E93		ENST00000266551.4:c.435T>C	12.37:g.9161648T>C		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	206	104	0.504854	NM_005810	B7ZAM2|O43198|O75613	Silent	SNP	ENST00000266551.4	37																																																																																				T|0.754;C|0.246	0.246	strong		0.443	KLRG1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399145.1	NM_005810	
SV2B	9899	hgsc.bcm.edu	37	15	91827271	91827271	+	Missense_Mutation	SNP	A	A	G	rs117361551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:91827271A>G	ENST00000394232.1	+	11	1998	c.1528A>G	c.(1528-1530)Atc>Gtc	p.I510V	SV2B_ENST00000330276.4_Missense_Mutation_p.I510V|SV2B_ENST00000545111.2_Missense_Mutation_p.I359V	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	510					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GCACAAGTTCATCAACTGTCG	0.507													A|||	56	0.0111821	0.0008	0.013	5008	,	,		19869	0.0		0.0169	False		,,,				2504	0.0297				p.I510V		Atlas-SNP	.											.	SV2B	98	.	0			c.A1528G						PASS	.	A	VAL/ILE,VAL/ILE	12,4384	19.1+/-41.9	0,12,2186	192.0	184.0	187.0		1075,1528	5.6	1.0	15	dbSNP_132	187	127,8469	64.9+/-127.2	2,123,4173	yes	missense,missense	SV2B	NM_001167580.1,NM_014848.4	29,29	2,135,6359	GG,GA,AA		1.4774,0.273,1.0699	benign,benign	359/533,510/684	91827271	139,12853	2198	4298	6496	SO:0001583	missense	9899	exon12			AAGTTCATCAACT	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1528A>G	15.37:g.91827271A>G	ENSP00000377779:p.Ile510Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	10.16	1.274723	0.23307	0.00273	0.014774	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.41400	1.0;1.0;1.0	5.61	5.61	0.85477	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.099589	0.64402	D	0.000004	T	0.21145	0.0509	L	0.39245	1.2	0.47584	D	0.999462	B	0.23937	0.094	B	0.31016	0.123	T	0.08911	-1.0699	10	0.12766	T	0.61	-31.4023	14.6867	0.69055	1.0:0.0:0.0:0.0	.	510	Q7L1I2	SV2B_HUMAN	V	359;510;510	ENSP00000443243:I359V;ENSP00000377779:I510V;ENSP00000332818:I510V	ENSP00000332818:I510V	I	+	1	0	SV2B	89628275	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.317000	0.43770	2.152000	0.67230	0.477000	0.44152	ATC	A|0.990;G|0.010	0.010	strong		0.507	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
ANGPT2	285	hgsc.bcm.edu	37	8	6371291	6371291	+	Silent	SNP	A	A	G	rs2916747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:6371291A>G	ENST00000325203.5	-	7	1581	c.1107T>C	c.(1105-1107)taT>taC	p.Y369Y	ANGPT2_ENST00000523120.1_Silent_p.Y368Y|ANGPT2_ENST00000338312.6_Silent_p.Y317Y|MCPH1_ENST00000344683.5_Intron|ANGPT2_ENST00000415216.1_Silent_p.Y368Y			O15123	ANGP2_HUMAN	angiopoietin 2	369	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		TTTTAAGCACATAGCGTTGCT	0.373													A|||	878	0.175319	0.354	0.0793	5008	,	,		17950	0.1637		0.0417	False		,,,				2504	0.1513				p.Y369Y		Atlas-SNP	.											.	ANGPT2	126	.	0			c.T1107C						PASS	.	A	,,,	1401,3005	459.4+/-352.3	219,963,1021	104.0	104.0	104.0		1104,951,1107,	-7.4	0.0	8	dbSNP_101	104	347,8253	117.0+/-176.6	8,331,3961	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ANGPT2,MCPH1	NM_001118887.1,NM_001118888.1,NM_001147.2,NM_024596.3	,,,	227,1294,4982	GG,GA,AA		4.0349,31.7975,13.44	,,,	368/496,317/445,369/497,	6371291	1748,11258	2203	4300	6503	SO:0001819	synonymous_variant	285	exon7			AAGCACATAGCGT	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"""Fibrinogen C domain containing"""	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.1107T>C	8.37:g.6371291A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	138	70	0.507246	NM_001147	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Silent	SNP	ENST00000325203.5	37	CCDS5958.1																																																																																			A|0.859;G|0.141	0.141	strong		0.373	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147	
TXNDC11	51061	hgsc.bcm.edu	37	16	11773662	11773662	+	Missense_Mutation	SNP	C	C	G	rs3190321	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11773662C>G	ENST00000356957.3	-	13	2454	c.2347G>C	c.(2347-2349)Gtc>Ctc	p.V783L	TXNDC11_ENST00000283033.5_Missense_Mutation_p.V756L|TXNDC11_ENST00000570917.1_5'UTR			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	783	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.		V -> L (in dbSNP:rs3190321). {ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GTGATGGGGACGTCTTCGGGG	0.502													G|||	2263	0.451877	0.4342	0.3285	5008	,	,		19542	0.4345		0.5557	False		,,,				2504	0.4744				p.V756L		Atlas-SNP	.											.	TXNDC11	75	.	0			c.G2266C						PASS	.	G	LEU/VAL	1914,2480	621.4+/-393.7	423,1068,706	62.0	50.0	54.0		2266	3.6	1.0	16	dbSNP_105	54	4661,3939	539.3+/-383.6	1234,2193,873	yes	missense	TXNDC11	NM_015914.5	32	1657,3261,1579	GG,GC,CC		45.8023,43.5594,49.3997	benign	756/959	11773662	6575,6419	2197	4300	6497	SO:0001583	missense	51061	exon12			TGGGGACGTCTTC	BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"""EF-hand binding protein 1"""					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.2347G>C	16.37:g.11773662C>G	ENSP00000349439:p.Val783Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Missense_Mutation	SNP	ENST00000356957.3	37		1008	0.46153846153846156	201	0.40853658536585363	124	0.3425414364640884	256	0.44755244755244755	427	0.5633245382585752	G	1.789	-0.480073	0.04383	0.435594	0.541977	ENSG00000153066	ENST00000356957;ENST00000283033	T;T	0.11930	2.95;2.73	5.91	3.63	0.41609	Thioredoxin-like fold (2);	0.302325	0.32952	N	0.005449	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39820	-0.9595	9	0.06891	T	0.86	-27.7888	9.1018	0.36673	0.0991:0.2825:0.6184:0.0	rs3190321;rs17416702;rs60110283;rs3190321	783;756	Q6PKC3;Q6PKC3-2	TXD11_HUMAN;.	L	783;756	ENSP00000349439:V783L;ENSP00000283033:V756L	ENSP00000283033:V756L	V	-	1	0	TXNDC11	11681163	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	1.521000	0.35910	0.850000	0.35239	-0.764000	0.03450	GTC	C|0.513;G|0.487	0.487	strong		0.502	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914	
LAMB3	3914	hgsc.bcm.edu	37	1	209823354	209823354	+	Silent	SNP	G	G	A	rs2228339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:209823354G>A	ENST00000356082.4	-	3	272	c.138C>T	c.(136-138)acC>acT	p.T46T	LAMB3_ENST00000391911.1_Silent_p.T46T|LAMB3_ENST00000367030.3_Silent_p.T46T	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	46	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.T46T(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TCAGTCCACAGGTAGATGAAG	0.617													G|||	1492	0.297923	0.2088	0.4078	5008	,	,		17612	0.3393		0.2674	False		,,,				2504	0.3292				p.T46T		Atlas-SNP	.											LAMB3,NS,carcinoma,0,1	LAMB3	136	1	1	Substitution - coding silent(1)	stomach(1)	c.C138T						PASS	.	G	,,	1002,3404	373.7+/-320.9	106,790,1307	90.0	77.0	82.0		138,138,138	5.4	1.0	1	dbSNP_107	82	2150,6450	370.0+/-335.7	277,1596,2427	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	383,2386,3734	AA,AG,GG		25.0,22.7417,24.235	,,	46/1173,46/1173,46/1173	209823354	3152,9854	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon3			TCCACAGGTAGAT	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.138C>T	1.37:g.209823354G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			G|0.739;A|0.261	0.261	strong		0.617	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
EHD1	10938	hgsc.bcm.edu	37	11	64645871	64645871	+	Silent	SNP	A	A	G	rs1211284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64645871A>G	ENST00000320631.3	-	1	320	c.66T>C	c.(64-66)gcT>gcC	p.A22A	EHD1_ENST00000359393.2_Silent_p.A22A	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	22					blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						GCAGCCCCTCAGCCACCGTCT	0.667													A|||	3254	0.64976	0.3396	0.817	5008	,	,		14189	0.5615		0.8777	False		,,,				2504	0.8067				p.A22A		Atlas-SNP	.											.	EHD1	31	.	0			c.T66C						PASS	.	A		1986,2416	534.5+/-374.0	476,1034,691	42.0	41.0	41.0		66	-2.6	1.0	11	dbSNP_87	41	7554,1040	744.2+/-407.2	3329,896,72	no	coding-synonymous	EHD1	NM_006795.2		3805,1930,763	GG,GA,AA		12.1015,45.1159,26.5928		22/535	64645871	9540,3456	2201	4297	6498	SO:0001819	synonymous_variant	10938	exon1			CCCCTCAGCCACC	AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047		"""EF-hand domain containing"""	3242	protein-coding gene	gene with protein product	"""testilin"""	605888		PAST1		10395801, 10673336	Standard	NM_001282444		Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.66T>C	11.37:g.64645871A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_006795	O14611|Q2M3Q4|Q9UNR3	Silent	SNP	ENST00000320631.3	37	CCDS8084.1																																																																																			A|0.301;G|0.699	0.699	strong		0.667	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143229.2	NM_006795	
URB1	9875	hgsc.bcm.edu	37	21	33717877	33717877	+	Silent	SNP	G	G	A	rs2833779	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:33717877G>A	ENST00000382751.3	-	23	3991	c.3876C>T	c.(3874-3876)tcC>tcT	p.S1292S	RN7SL109P_ENST00000493105.2_RNA	NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1292						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						GAATGACAGCGGAAGACACTA	0.537													G|||	866	0.172923	0.2958	0.0908	5008	,	,		20039	0.1379		0.1213	False		,,,				2504	0.1544				p.S1292S		Atlas-SNP	.											.	URB1	176	.	0			c.C3876T						PASS	.	G		386,998		59,268,365	26.0	26.0	26.0		3876	-6.5	0.6	21	dbSNP_100	26	404,2778		29,346,1216	no	coding-synonymous	URB1	NM_014825.2		88,614,1581	AA,AG,GG		12.6964,27.8902,17.3018		1292/2272	33717877	790,3776	692	1591	2283	SO:0001819	synonymous_variant	9875	exon23			GACAGCGGAAGAC	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.3876C>T	21.37:g.33717877G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			G|0.822;A|0.178	0.178	strong		0.537	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
C21orf2	755	hgsc.bcm.edu	37	21	45750145	45750145	+	Missense_Mutation	SNP	T	T	C	rs11552066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45750145T>C	ENST00000339818.4	-	7	914	c.707A>G	c.(706-708)cAg>cGg	p.Q236R	AP001062.8_ENST00000422357.1_RNA|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000397956.3_Missense_Mutation_p.Q355R|C21orf2_ENST00000325223.7_Missense_Mutation_p.Q235R	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	236					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		CACAGTCTGCTGCACGGCCTC	0.701													T|||	432	0.086262	0.0348	0.1657	5008	,	,		15202	0.0298		0.1213	False		,,,				2504	0.1217				p.Q355R		Atlas-SNP	.											.	C21orf2	10	.	0			c.A1064G						PASS	.	T	ARG/GLN	192,4168		2,188,1990	13.0	13.0	13.0		707	2.8	0.1	21	dbSNP_120	13	939,7611		53,833,3389	no	missense	C21orf2	NM_004928.2	43	55,1021,5379	CC,CT,TT		10.9825,4.4037,8.7607	possibly-damaging	236/257	45750145	1131,11779	2180	4275	6455	SO:0001583	missense	755	exon7			GTCTGCTGCACGG	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.707A>G	21.37:g.45750145T>C	ENSP00000344566:p.Gln236Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_001271441	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	167	0.07646520146520147	25	0.0508130081300813	41	0.1132596685082873	10	0.017482517482517484	91	0.12005277044854881	T	9.745	1.165795	0.21538	0.044037	0.109825	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.40756	1.56;1.02;1.57	5.13	2.77	0.32553	.	0.575196	0.19755	N	0.106812	T	0.00412	0.0013	L	0.50333	1.59	0.44000	P	0.003299000000000052	B;B;B;B	0.16166	0.004;0.016;0.003;0.01	B;B;B;B	0.11329	0.004;0.005;0.002;0.006	T	0.20273	-1.0280	9	0.02654	T	1	-17.6614	7.3568	0.26723	0.0:0.1776:0.0:0.8224	rs11552066	235;355;236;195	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	R	236;355;235	ENSP00000344566:Q236R;ENSP00000381047:Q355R;ENSP00000317302:Q235R	ENSP00000317302:Q235R	Q	-	2	0	C21orf2	44574573	0.999000	0.42202	0.107000	0.21349	0.065000	0.16274	2.749000	0.47492	0.299000	0.22661	-0.256000	0.11100	CAG	T|0.913;C|0.087	0.087	strong		0.701	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
FAM161A	84140	hgsc.bcm.edu	37	2	62066986	62066986	+	Missense_Mutation	SNP	G	G	C	rs139266382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:62066986G>C	ENST00000405894.3	-	3	1254	c.1153C>G	c.(1153-1155)Cag>Gag	p.Q385E	FAM161A_ENST00000404929.1_Missense_Mutation_p.Q385E	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	385					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCTCTCAGCTGTGTCCTAAGG	0.453													G|||	4	0.000798722	0.0015	0.0	5008	,	,		19117	0.0		0.002	False		,,,				2504	0.0				p.Q385E		Atlas-SNP	.											.	FAM161A	200	.	0			c.C1153G						PASS	.	G	GLU/GLN,GLU/GLN	4,3922		0,4,1959	100.0	101.0	101.0		1153,1153	3.8	0.0	2	dbSNP_134	101	39,8259		0,39,4110	yes	missense,missense	FAM161A	NM_001201543.1,NM_032180.2	29,29	0,43,6069	CC,CG,GG		0.47,0.1019,0.3518	possibly-damaging,possibly-damaging	385/717,385/661	62066986	43,12181	1963	4149	6112	SO:0001583	missense	84140	exon3			TCAGCTGTGTCCT		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1153C>G	2.37:g.62066986G>C	ENSP00000385893:p.Gln385Glu	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	257	114	0.44358	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.89	2.967701	0.53507	0.001019	0.0047	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.21191	2.02;2.02	5.67	3.83	0.44106	.	0.603842	0.18460	N	0.140544	T	0.34716	0.0907	M	0.72894	2.215	0.09310	N	1	D;D	0.58620	0.982;0.983	P;P	0.56434	0.764;0.798	T	0.12630	-1.0540	10	0.27785	T	0.31	-12.0385	9.065	0.36458	0.0702:0.0:0.6683:0.2615	.	385;385	Q3B820;Q3B820-3	F161A_HUMAN;.	E	385	ENSP00000385158:Q385E;ENSP00000385893:Q385E	ENSP00000385158:Q385E	Q	-	1	0	FAM161A	61920490	0.918000	0.31147	0.000000	0.03702	0.014000	0.08584	3.936000	0.56568	0.700000	0.31782	-0.140000	0.14226	CAG	G|0.998;C|0.002	0.002	strong		0.453	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156910020	156910020	+	Missense_Mutation	SNP	C	C	T	rs144803270		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156910020C>T	ENST00000361409.2	-	35	4334	c.3592G>A	c.(3592-3594)Gct>Act	p.A1198T	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.A1238T|ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.A614T	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1198					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCGGAGTCAGCGAGCCCTTCC	0.627																																					p.A1238T		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G3712A						PASS	.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	77.0	69.0	72.0		3592,3712	4.2	0.8	1	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1198/1523,1238/1563	156910020	1,13005	2203	4300	6503	SO:0001583	missense	9826	exon36			AGTCAGCGAGCCC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"""Rho guanine nucleotide exchange factors"""	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.3592G>A	1.37:g.156910020C>T	ENSP00000354644:p.Ala1198Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	168	85	0.505952	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569825	0.86439	0.0	1.16E-4	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.76709	-1.0;-0.99;-1.04	4.16	4.16	0.48862	.	0.000000	0.48286	D	0.000200	T	0.77738	0.4175	L	0.34521	1.04	0.40759	D	0.982985	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.993;0.997	T	0.79708	-0.1690	10	0.48119	T	0.1	-10.0453	15.3955	0.74790	0.0:1.0:0.0:0.0	.	614;1198;1238	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	T	1238;1198;614	ENSP00000357177:A1238T;ENSP00000354644:A1198T;ENSP00000313470:A614T	ENSP00000313470:A614T	A	-	1	0	ARHGEF11	155176644	0.999000	0.42202	0.770000	0.31555	0.925000	0.55904	5.158000	0.64917	2.135000	0.66039	0.561000	0.74099	GCT	C|1.000;T|0.000	0.000	weak		0.627	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
LVRN	206338	hgsc.bcm.edu	37	5	115298518	115298518	+	Silent	SNP	A	A	G	rs12522632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:115298518A>G	ENST00000357872.4	+	1	328	c.204A>G	c.(202-204)ccA>ccG	p.P68P	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		68						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AGCCGACGCCAACCCCGAAAC	0.701																																					p.P68P		Atlas-SNP	.											FLJ90650,NS,carcinoma,0,1	.	.	1	0			c.A204G						PASS	.	G		3640,694		1527,586,54	24.0	27.0	26.0		204	-2.9	0.0	5	dbSNP_120	26	6927,1585		2813,1301,142	no	coding-synonymous	AQPEP	NM_173800.4		4340,1887,196	GG,GA,AA		18.6208,16.0129,17.7409		68/991	115298518	10567,2279	2167	4256	6423	SO:0001819	synonymous_variant	0	exon1			GACGCCAACCCCG																												ENST00000357872.4:c.204A>G	5.37:g.115298518A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			A|0.190;G|0.810	0.810	strong		0.701	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
FRG1	2483	hgsc.bcm.edu	37	4	190878589	190878589	+	Missense_Mutation	SNP	A	A	G	rs561930100	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:190878589A>G	ENST00000226798.4	+	6	691	c.469A>G	c.(469-471)Att>Gtt	p.I157V	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	157					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TAGCTGCTTTATTAGATGCAA	0.363													.|||	11	0.00219649	0.0015	0.0058	5008	,	,		28209	0.001		0.004	False		,,,				2504	0.0				p.I157V		Atlas-SNP	.											FRG1,NS,carcinoma,0,1	FRG1	76	1	0			c.A469G						scavenged	.						15.0	18.0	17.0					4																	190878589		2157	4266	6423	SO:0001583	missense	2483	exon6			TGCTTTATTAGAT	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.469A>G	4.37:g.190878589A>G	ENSP00000226798:p.Ile157Val	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	482	21	0.0435685	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	10.14	1.269261	0.23221	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.42900	2.02;0.96	4.19	4.19	0.49359	Actin cross-linking (1);	0.049103	0.85682	D	0.000000	T	0.25938	0.0632	L	0.28014	0.82	0.48696	D	0.999699	B	0.09022	0.002	B	0.18871	0.023	T	0.08086	-1.0739	10	0.20519	T	0.43	-23.3336	6.6273	0.22837	0.8897:0.0:0.1103:0.0	.	157	Q14331	FRG1_HUMAN	V	157;29;94	ENSP00000226798:I157V;ENSP00000435943:I94V	ENSP00000226798:I157V	I	+	1	0	FRG1	191115583	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	5.196000	0.65136	1.677000	0.50941	0.373000	0.22412	ATT	.	.	none		0.363	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
CCDC81	60494	hgsc.bcm.edu	37	11	86123467	86123467	+	Silent	SNP	G	G	A	rs3741006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:86123467G>A	ENST00000445632.2	+	11	1529	c.1257G>A	c.(1255-1257)gcG>gcA	p.A419A	CCDC81_ENST00000528728.1_Silent_p.A154A|CCDC81_ENST00000354755.1_Silent_p.A329A|CCDC81_ENST00000278487.3_Silent_p.A154A	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	419										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				TCAGTCCTGCGCTTAATGCTC	0.373													G|||	1613	0.322085	0.2216	0.3991	5008	,	,		20396	0.2718		0.3897	False		,,,				2504	0.3855				p.A419A		Atlas-SNP	.											.	CCDC81	89	.	0			c.G1257A						PASS	.	G	,	1081,3323	393.5+/-328.9	130,821,1251	117.0	116.0	116.0		1257,987	0.2	0.9	11	dbSNP_107	116	3378,5220	500.3+/-375.2	657,2064,1578	no	coding-synonymous,coding-synonymous	CCDC81	NM_001156474.1,NM_021827.4	,	787,2885,2829	AA,AG,GG		39.2882,24.5459,34.2947	,	419/653,329/563	86123467	4459,8543	2202	4299	6501	SO:0001819	synonymous_variant	60494	exon11			TCCTGCGCTTAAT	AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.1257G>A	11.37:g.86123467G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Silent	SNP	ENST00000445632.2	37	CCDS53691.1																																																																																			G|0.678;A|0.322	0.322	strong		0.373	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827	
UBXN10	127733	hgsc.bcm.edu	37	1	20517187	20517187	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20517187C>T	ENST00000375099.3	+	2	217	c.133C>T	c.(133-135)Cgg>Tgg	p.R45W		NM_152376.3	NP_689589.1	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	45								p.R45W(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|skin(2)	14						CGCCAAGGGACGGACAAGACC	0.537																																					p.R45W		Atlas-SNP	.											UBXN10,NS,carcinoma,0,3	UBXN10	29	3	1	Substitution - Missense(1)	kidney(1)	c.C133T						scavenged	.						98.0	85.0	89.0					1																	20517187		2203	4300	6503	SO:0001583	missense	127733	exon2			AAGGGACGGACAA	AK058158	CCDS205.1	1p36.13	2008-07-25	2008-07-25	2008-07-25	ENSG00000162543	ENSG00000162543		"""UBX domain containing"""	26354	protein-coding gene	gene with protein product			"""UBX domain containing 3"""	UBXD3		12477932	Standard	NM_152376		Approved	FLJ25429	uc001bdb.3	Q96LJ8	OTTHUMG00000002708	ENST00000375099.3:c.133C>T	1.37:g.20517187C>T	ENSP00000364240:p.Arg45Trp	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	123	3	0.0243902	NM_152376	Q5R386	Missense_Mutation	SNP	ENST00000375099.3	37	CCDS205.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.913432	0.72983	.	.	ENSG00000162543	ENST00000375099	.	.	.	5.23	5.23	0.72850	.	0.000000	0.64402	D	0.000015	T	0.78910	0.4358	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81335	-0.0979	9	0.87932	D	0	-18.0001	17.361	0.87350	0.0:1.0:0.0:0.0	.	45	Q96LJ8	UBX10_HUMAN	W	45	.	ENSP00000364240:R45W	R	+	1	2	UBXN10	20389774	1.000000	0.71417	0.879000	0.34478	0.443000	0.32047	5.162000	0.64942	2.444000	0.82710	0.655000	0.94253	CGG	.	.	none		0.537	UBXN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007693.1	NM_152376	
RHOU	58480	hgsc.bcm.edu	37	1	228871693	228871693	+	Silent	SNP	C	C	T	rs3738073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228871693C>T	ENST00000366691.3	+	1	870	c.204C>T	c.(202-204)agC>agT	p.S68S		NM_021205.5	NP_067028.1			ras homolog family member U											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	13	Breast(184;0.162)	Prostate(94;0.183)				TGGTGGTGAGCTACACCACCA	0.751													c|||	646	0.128994	0.0893	0.0951	5008	,	,		7479	0.0427		0.172	False		,,,				2504	0.2515				p.S68S		Atlas-SNP	.											.	RHOU	20	.	0			c.C204T						PASS	.			451,3945		35,381,1782	20.0	25.0	23.0		204	3.7	1.0	1	dbSNP_107	23	1682,6908		177,1328,2790	no	coding-synonymous	RHOU	NM_021205.5		212,1709,4572	TT,TC,CC		19.5809,10.2593,16.4254		68/259	228871693	2133,10853	2198	4295	6493	SO:0001819	synonymous_variant	58480	exon1			GGTGAGCTACACC		CCDS1575.1	1q42.11-q42.3	2012-02-27	2012-02-27	2004-03-24	ENSG00000116574	ENSG00000116574			17794	protein-coding gene	gene with protein product	"""Ryu GTPase"", ""Wnt-1 responsive Cdc42 homolog"", ""2310026M05Rik"", ""GTP-binding protein like 1"", ""CDC42-like GTPase"", ""GTP-binding protein SB128"", ""ras-like gene family member U"""	606366	"""ras homolog gene family, member U"""	ARHU		11459829	Standard	NM_021205		Approved	WRCH-1, DJ646B12.2, FLJ10616, WRCH1, CDC42L1, hG28K, fJ646B12.2	uc001htf.3	Q7L0Q8	OTTHUMG00000037919	ENST00000366691.3:c.204C>T	1.37:g.228871693C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_021205		Silent	SNP	ENST00000366691.3	37	CCDS1575.1																																																																																			T|0.149;G|0.000;C|0.851	0.149	strong		0.751	RHOU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092555.1	NM_021205	
ABL1	25	hgsc.bcm.edu	37	9	133760380	133760380	+	Silent	SNP	C	C	G	rs56017837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760380C>G	ENST00000318560.5	+	11	3084	c.2703C>G	c.(2701-2703)ccC>ccG	p.P901P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	901	DNA-binding. {ECO:0000250}.|Poly-Pro.|Pro-rich.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCCCGCCGCCCCCACCAGCAG	0.672			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	4	0.000798722	0.0	0.0014	5008	,	,		15690	0.0		0.002	False		,,,				2504	0.001				p.P920P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2760G						PASS	.	C	,	0,4338		0,0,2169	8.0	11.0	10.0		2703,2760	-2.0	0.8	9	dbSNP_129	10	14,8502		0,14,4244	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	0,14,6413	GG,GC,CC		0.1644,0.0,0.1089	,	901/1131,920/1150	133760380	14,12840	2169	4258	6427	SO:0001819	synonymous_variant	25	exon11			GCCGCCCCCACCA	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2703C>G	9.37:g.133760380C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			.	.	weak		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
ZNF709	163051	hgsc.bcm.edu	37	19	12576049	12576049	+	Silent	SNP	G	G	A	rs7259240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12576049G>A	ENST00000397732.3	-	4	858	c.687C>T	c.(685-687)tgC>tgT	p.C229C	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Silent_p.C229C	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	229					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						ACGTTTTCCCGCATTCTTTAC	0.403													G|||	1432	0.285942	0.233	0.428	5008	,	,		20248	0.1171		0.496	False		,,,				2504	0.2147				p.C229C	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.C687T						PASS	.	G		1186,3208	374.2+/-321.1	167,852,1178	103.0	107.0	105.0		687	0.1	0.2	19	dbSNP_116	105	4326,4274	564.3+/-388.3	1097,2132,1071	no	coding-synonymous	ZNF709	NM_152601.3		1264,2984,2249	AA,AG,GG		49.6977,26.9914,42.4196		229/642	12576049	5512,7482	2197	4300	6497	SO:0001819	synonymous_variant	163051	exon4			TTTCCCGCATTCT	AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"""Zinc fingers, C2H2-type"", ""-"""	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.687C>T	19.37:g.12576049G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	184	74	0.402174	NM_152601	A8K4E6	Silent	SNP	ENST00000397732.3	37	CCDS42504.1																																																																																			G|0.611;A|0.389	0.389	strong		0.403	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601	
ADRBK1	156	hgsc.bcm.edu	37	11	67034266	67034266	+	Silent	SNP	C	C	A	rs2228418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67034266C>A	ENST00000308595.5	+	1	386	c.96C>A	c.(94-96)atC>atA	p.I32I	ADRBK1_ENST00000526285.1_Silent_p.I32I	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	32	N-terminal.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	GCAAGAAGATCCTGCTGCCCG	0.746													C|||	3249	0.648762	0.1747	0.5994	5008	,	,		5377	0.746		0.9195	False		,,,				2504	0.9458				p.I32I		Atlas-SNP	.											.	ADRBK1	51	.	0			c.C96A						PASS	.	C		1582,2660		315,952,854	8.0	9.0	8.0		96	3.2	1.0	11	dbSNP_120	8	7762,580		3623,516,32	no	coding-synonymous	ADRBK1	NM_001619.3		3938,1468,886	AA,AC,CC		6.9528,37.2937,25.747		32/690	67034266	9344,3240	2121	4171	6292	SO:0001819	synonymous_variant	156	exon1			GAAGATCCTGCTG	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"""Pleckstrin homology (PH) domain containing"""	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.96C>A	11.37:g.67034266C>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_001619	B0ZBE1|Q13837|Q6GTT3	Silent	SNP	ENST00000308595.5	37	CCDS8156.1																																																																																			C|0.360;A|0.640	0.640	strong		0.746	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619	
RIC1	57589	hgsc.bcm.edu	37	9	5774225	5774225	+	Silent	SNP	T	T	G	rs3739648	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:5774225T>G	ENST00000414202.2	+	26	4442	c.4251T>G	c.(4249-4251)acT>acG	p.T1417T	KIAA1432_ENST00000418622.3_Silent_p.T1338T|KIAA1432_ENST00000449720.2_Silent_p.T1301T	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		AGGATGGGACTTACGACTGTT	0.498													T|||	1662	0.331869	0.1233	0.2968	5008	,	,		19529	0.5853		0.2853	False		,,,				2504	0.4254				p.T1417T		Atlas-SNP	.											KIAA1432,NS,carcinoma,+2,1	KIAA1432	97	1	0			c.T4251G						PASS	.	T	,	610,3796	266.5+/-267.3	47,516,1640	79.0	66.0	71.0		4140,4251	0.3	1.0	9	dbSNP_107	71	2639,5961	424.5+/-354.7	408,1823,2069	no	coding-synonymous,coding-synonymous	KIAA1432	NM_001206557.1,NM_020829.3	,	455,2339,3709	GG,GT,TT		30.686,13.8448,24.9808	,	1380/1387,1417/1424	5774225	3249,9757	2203	4300	6503	SO:0001819	synonymous_variant	57589	exon26			TGGGACTTACGAC																												ENST00000414202.2:c.4251T>G	9.37:g.5774225T>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_020829		Silent	SNP	ENST00000414202.2	37	CCDS34982.2	741	0.3392857142857143	48	0.0975609756097561	114	0.3149171270718232	350	0.6118881118881119	229	0.3021108179419525	T	6.032	0.374309	0.11409	0.138448	0.30686	ENSG00000107036	ENST00000545641	.	.	.	5.7	0.353	0.16058	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999835	.	.	.	.	.	.	T	0.47812	-0.9088	3	.	.	.	-11.366	10.5079	0.44845	0.0:0.439:0.0:0.561	rs3739648;rs58954556;rs3739648	.	.	.	V	1309	.	.	L	+	1	2	KIAA1432	5764225	0.988000	0.35896	0.997000	0.53966	0.989000	0.77384	0.146000	0.16180	0.127000	0.18452	0.379000	0.24179	TTA	T|0.717;G|0.283	0.283	strong		0.498	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3		
DENND6B	414918	hgsc.bcm.edu	37	22	50753263	50753263	+	Silent	SNP	G	G	A	rs113856947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50753263G>A	ENST00000413817.3	-	10	917	c.846C>T	c.(844-846)ccC>ccT	p.P282P	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	282					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										AGGACACGTCGGGCGAGGGTG	0.682													G|||	23	0.00459265	0.0008	0.0072	5008	,	,		17171	0.0		0.0089	False		,,,				2504	0.0082				p.P282P		Atlas-SNP	.											.	.	.	.	0			c.C846T						PASS	.	G		11,4179		0,11,2084	26.0	35.0	32.0		846	-7.3	0.3	22	dbSNP_132	32	70,8310		0,70,4120	no	coding-synonymous	FAM116B	NM_001001794.3		0,81,6204	AA,AG,GG		0.8353,0.2625,0.6444		282/586	50753263	81,12489	2095	4190	6285	SO:0001819	synonymous_variant	414918	exon10			CACGTCGGGCGAG	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.846C>T	22.37:g.50753263G>A		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	186	76	0.408602	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	G	11.25	1.583626	0.28268	0.002625	0.008353	ENSG00000205593	ENST00000433760	.	.	.	5.01	-7.27	0.01461	.	0.000000	0.85682	D	0.000000	T	0.34106	0.0886	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49214	-0.8963	6	0.87932	D	0	-21.3129	0.6044	0.00750	0.3433:0.203:0.2759:0.1779	.	.	.	.	L	303	.	ENSP00000414072:P303L	P	-	2	0	FAM116B	49095835	0.000000	0.05858	0.317000	0.25265	0.735000	0.41995	-3.056000	0.00625	-0.646000	0.05452	0.305000	0.20034	CCG	G|0.994;A|0.006	0.006	strong		0.682	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
GALNT4	8693	hgsc.bcm.edu	37	12	89916811	89916811	+	Missense_Mutation	SNP	C	C	T	rs2230283	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:89916811C>T	ENST00000529983.2	-	1	1772	c.1516G>A	c.(1516-1518)Gta>Ata	p.V506I	POC1B_ENST00000393179.4_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000541909.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000549035.1_Intron|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.V503I|GALNT4_ENST00000413530.1_Missense_Mutation_p.V334I	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	506	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		V -> I (in dbSNP:rs2230283). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9804815}.		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.V506I(1)		endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TGCTCAGGTACCTCTGCACAT	0.363													C|||	1028	0.205272	0.1536	0.2435	5008	,	,		19332	0.1369		0.3529	False		,,,				2504	0.1667				p.V506I		Atlas-SNP	.											GALNT4,NS,carcinoma,0,1	GALNT4	38	1	1	Substitution - Missense(1)	prostate(1)	c.G1516A						PASS	.	C	,ILE/VAL,ILE/VAL,ILE/VAL,	657,3021		60,537,1242	61.0	57.0	59.0		,1507,1000,1516,	5.9	0.2	12	dbSNP_98	59	2808,5382		474,1860,1761	yes	intron,missense,missense,missense,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,29,29,29,	534,2397,3003	TT,TC,CC		34.2857,17.863,29.1962	,benign,benign,benign,	,503/576,334/407,506/579,	89916811	3465,8403	1839	4095	5934	SO:0001583	missense	8693	exon1			CAGGTACCTCTGC	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1516G>A	12.37:g.89916811C>T	ENSP00000436604:p.Val506Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	530	0.24267399267399267	88	0.17886178861788618	84	0.23204419889502761	83	0.1451048951048951	275	0.3627968337730871	C	23.6	4.430637	0.83776	0.17863	0.342857	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.33438	1.41;1.41;1.41	5.93	5.93	0.95920	Ricin B-related lectin (1);Ricin B lectin (3);	.	.	.	.	T	0.00012	0.0000	L	0.61036	1.89	0.21256	P	0.999749278	P;P	0.46578	0.855;0.88	P;P	0.56216	0.753;0.794	T	0.09773	-1.0659	8	0.54805	T	0.06	.	19.3377	0.94326	0.0:1.0:0.0:0.0	rs2230283;rs17464272;rs52822348;rs57746596;rs2230283	503;506	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	I	503;334;506	ENSP00000447852:V503I;ENSP00000389686:V334I;ENSP00000436604:V506I	ENSP00000436604:V506I	V	-	1	0	GALNT4;RP11-1109F11.4	88440942	1.000000	0.71417	0.220000	0.23810	0.991000	0.79684	7.429000	0.80309	2.814000	0.96858	0.591000	0.81541	GTA	C|0.758;T|0.242	0.242	strong		0.363	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
CSPG4	1464	hgsc.bcm.edu	37	15	75982185	75982185	+	Silent	SNP	T	T	C	rs77341302	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75982185T>C	ENST00000308508.5	-	3	1313	c.1221A>G	c.(1219-1221)ccA>ccG	p.P407P		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	407	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GCTCCATGGCTGGCCAAGCCT	0.612													t|||	429	0.0856629	0.289	0.0231	5008	,	,		22046	0.005		0.0169	False		,,,				2504	0.0092				p.P407P		Atlas-SNP	.											CSPG4,NS,carcinoma,-2,1	CSPG4	175	1	0			c.A1221G						scavenged	.						24.0	25.0	24.0					15																	75982185		2192	4276	6468	SO:0001819	synonymous_variant	1464	exon3			CATGGCTGGCCAA	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1221A>G	15.37:g.75982185T>C		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	133	45	0.338346	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			T|0.983;C|0.018	0.018	strong		0.612	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552072	32552072	+	Missense_Mutation	SNP	T	T	G	rs17879995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32552072T>G	ENST00000360004.5	-	2	289	c.184A>C	c.(184-186)Aac>Cac	p.N62H		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	62	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TCCTCCTGGTTATAGAAGTAT	0.607										Multiple Myeloma(14;0.17)			T|||	511	0.102037	0.0333	0.1888	5008	,	,		9156	0.1111		0.1441	False		,,,				2504	0.0808				p.N62H		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A184C						PASS	.						34.0	32.0	33.0					6																	32552072		2192	4275	6467	SO:0001583	missense	3123	exon2			CCTGGTTATAGAA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.184A>C	6.37:g.32552072T>G	ENSP00000353099:p.Asn62His	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	106	43	0.40566	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	276	0.12637362637362637	12	0.024390243902439025	70	0.19337016574585636	75	0.13111888111888112	119	0.15699208443271767	.	11.90	1.775623	0.31411	.	.	ENSG00000196126	ENST00000360004	T	0.00441	7.41	3.52	3.52	0.40303	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	0.149573	0.56097	D	0.000021	T	0.01029	0.0034	H	0.97659	4.05	0.58432	P	1.0000000000287557E-6	D	0.89917	1.0	D	0.97110	1.0	T	0.04723	-1.0931	9	0.62326	D	0.03	.	10.2994	0.43644	0.0:0.0:0.0:1.0	rs17879995	62	P01911	2B1F_HUMAN	H	62	ENSP00000353099:N62H	ENSP00000353099:N62H	N	-	1	0	HLA-DRB1	32660050	0.887000	0.30362	0.019000	0.16419	0.015000	0.08874	2.002000	0.40835	1.609000	0.50190	0.372000	0.22366	AAC	T|0.871;G|0.129	0.129	strong		0.607	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PNPLA5	150379	hgsc.bcm.edu	37	22	44282276	44282276	+	Missense_Mutation	SNP	A	A	G	rs739231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:44282276A>G	ENST00000597664.1	-	6	985	c.856T>C	c.(856-858)Tgg>Cgg	p.W286R	PNPLA5_ENST00000593866.1_Missense_Mutation_p.W172R|PNPLA5_ENST00000381198.2_Missense_Mutation_p.W172R|PNPLA5_ENST00000216177.4_Missense_Mutation_p.W286R			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	286			W -> R (in dbSNP:rs739231). {ECO:0000269|PubMed:14702039}.		lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CCCCCCTTCCAGCGTTGGTCA	0.587													G|||	2516	0.502396	0.2436	0.4597	5008	,	,		18495	0.9048		0.3748	False		,,,				2504	0.5992				p.W286R		Atlas-SNP	.											.	PNPLA5	46	.	0			c.T856C						PASS	.	G	ARG/TRP,ARG/TRP	1175,3231	711.3+/-408.0	165,845,1193	96.0	82.0	87.0		514,856	-2.7	0.0	22	dbSNP_86	87	3209,5391	652.7+/-401.0	585,2039,1676	yes	missense,missense	PNPLA5	NM_001177675.1,NM_138814.3	101,101	750,2884,2869	GG,GA,AA		37.314,26.6682,33.7075	benign,benign	172/316,286/430	44282276	4384,8622	2203	4300	6503	SO:0001583	missense	150379	exon6			CCTTCCAGCGTTG	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.856T>C	22.37:g.44282276A>G	ENSP00000471069:p.Trp286Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	37		1066	0.4880952380952381	113	0.22967479674796748	157	0.43370165745856354	508	0.8881118881118881	288	0.37994722955145116	G	2.853	-0.237927	0.05944	0.266682	0.37314	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.39406	1.56;1.08;1.8	4.2	-2.74	0.05932	.	1.460160	0.04604	N	0.399060	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.25537	-1.0129	9	0.15499	T	0.54	-1.3098	1.9577	0.03379	0.183:0.4234:0.2208:0.1728	rs739231;rs5764378;rs17493115;rs52834315;rs60718837;rs739231	194;172;286	E9PGS4;Q7Z6Z6-2;Q7Z6Z6	.;.;PLPL5_HUMAN	R	286;172;194	ENSP00000216177:W286R;ENSP00000370595:W172R;ENSP00000405732:W194R	ENSP00000216177:W286R	W	-	1	0	PNPLA5	42613609	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.878000	0.04192	-0.705000	0.05035	-1.288000	0.01363	TGG	A|0.572;G|0.428	0.428	strong		0.587	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
SLC15A1	6564	hgsc.bcm.edu	37	13	99376181	99376181	+	Missense_Mutation	SNP	C	C	T	rs2297322	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:99376181C>T	ENST00000376503.5	-	5	405	c.350G>A	c.(349-351)aGc>aAc	p.S117N		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	117			S -> N (in dbSNP:rs2297322). {ECO:0000269|PubMed:12436193, ECO:0000269|PubMed:16258023}.|S -> R (in dbSNP:rs8187821). {ECO:0000269|PubMed:16258023}.		digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CACAGGAAGGCTGTCGGGGGT	0.512													C|||	1545	0.308506	0.3548	0.2363	5008	,	,		21342	0.4385		0.1292	False		,,,				2504	0.3476				p.S117N		Atlas-SNP	.											.	SLC15A1	92	.	0			c.G350A						PASS	.	C	ASN/SER	1315,3091	443.1+/-346.9	190,935,1078	250.0	184.0	206.0		350	-11.3	0.0	13	dbSNP_100	206	947,7653	206.9+/-248.8	53,841,3406	yes	missense	SLC15A1	NM_005073.3	46	243,1776,4484	TT,TC,CC		11.0116,29.8457,17.392	benign	117/709	99376181	2262,10744	2203	4300	6503	SO:0001583	missense	6564	exon5			GGAAGGCTGTCGG	U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"""Solute carriers"""	10920	protein-coding gene	gene with protein product	"""peptide transporter HPEPT1"", ""bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)"", ""solute carrier family 15 oligopeptide transporter member 1"""	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.350G>A	13.37:g.99376181C>T	ENSP00000365686:p.Ser117Asn	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	157	80	0.509554	NM_005073	Q5VW82	Missense_Mutation	SNP	ENST00000376503.5	37	CCDS9489.1	602	0.27564102564102566	161	0.32723577235772355	95	0.26243093922651933	241	0.42132867132867136	105	0.13852242744063326	C	11.28	1.591231	0.28357	0.298457	0.110116	ENSG00000088386	ENST00000376503;ENST00000376494;ENST00000313260	T	0.04603	3.59	5.65	-11.3	0.00108	Major facilitator superfamily domain, general substrate transporter (1);	0.486708	0.24735	N	0.036040	T	0.00012	0.0000	N	0.04880	-0.145	0.58432	P	8.000000000008E-6	B;B	0.16603	0.018;0.0	B;B	0.20577	0.03;0.006	T	0.41556	-0.9502	9	0.10377	T	0.69	-18.7336	13.485	0.61359	0.0618:0.084:0.1096:0.7445	rs2297322;rs10285589;rs2297322	85;117	Q9BZ22;P46059	.;S15A1_HUMAN	N	117;85;127	ENSP00000365686:S117N	ENSP00000318937:S127N	S	-	2	0	SLC15A1	98174182	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.084000	0.03393	-2.807000	0.00349	-0.136000	0.14681	AGC	C|0.768;T|0.232	0.232	strong		0.512	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073	
TSC2	7249	hgsc.bcm.edu	37	16	2136842	2136842	+	Silent	SNP	C	C	T	rs45517384|rs137854272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2136842C>T	ENST00000219476.3	+	38	5589	c.4959C>T	c.(4957-4959)tcC>tcT	p.S1653S	TSC2_ENST00000568454.1_Silent_p.S1597S|TSC2_ENST00000401874.2_Silent_p.S1586S|TSC2_ENST00000439673.2_Silent_p.S1550S|TSC2_ENST00000382538.6_Silent_p.S1538S|TSC2_ENST00000353929.4_Silent_p.S1610S|TSC2_ENST00000350773.4_Silent_p.S1630S	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1653	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.		S -> F (in TSC2). {ECO:0000269|PubMed:15024740}.		acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				ACAATGACTCCGGTGAGGACT	0.612			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				c|||	17	0.00339457	0.0023	0.0086	5008	,	,		20855	0.0		0.008	False		,,,				2504	0.0				p.S1653S		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.C4959T						PASS	.	T	,,	11,4377	16.8+/-37.8	0,11,2183	71.0	52.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4959,4758,4890	-9.4	0.2	16	dbSNP_127	59	127,8453	60.6+/-122.4	0,127,4163	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	0,138,6346	TT,TC,CC		1.4802,0.2507,1.0642	,,	1653/1808,1586/1741,1630/1785	2136842	138,12830	2194	4290	6484	SO:0001819	synonymous_variant	7249	exon38	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TGACTCCGGTGAG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.4959C>T	16.37:g.2136842C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			C|0.992;T|0.008	0.008	strong		0.612	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
OBP2A	29991	hgsc.bcm.edu	37	9	138439809	138439809	+	Missense_Mutation	SNP	T	T	C	rs72766544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:138439809T>C	ENST00000539850.1	+	4	396	c.370T>C	c.(370-372)Tac>Cac	p.Y124H	OBP2A_ENST00000342114.4_Missense_Mutation_p.L79P|OBP2A_ENST00000371776.1_Missense_Mutation_p.Y124H|OBP2A_ENST00000340780.3_Missense_Mutation_p.Y124H			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	124					response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		GGGCCTGCGCTACATGGGAAA	0.617													.|||	773	0.154353	0.0582	0.134	5008	,	,		16945	0.1567		0.2525	False		,,,				2504	0.1953				p.Y124H		Atlas-SNP	.											.	OBP2A	21	.	0			c.T370C						PASS	.	C	HIS/TYR	410,3996	785.5+/-414.8	34,342,1827	41.0	38.0	39.0		370	-0.1	0.0	9	dbSNP_130	39	2253,6347	706.1+/-405.5	302,1649,2349	yes	missense	OBP2A	NM_014582.2	83	336,1991,4176	CC,CT,TT		26.1977,9.3055,20.4752	benign	124/171	138439809	2663,10343	2203	4300	6503	SO:0001583	missense	29991	exon4			CTGCGCTACATGG	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.370T>C	9.37:g.138439809T>C	ENSP00000441028:p.Tyr124His	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	369|369	0.16895604395604397|0.16895604395604397	34|34	0.06910569105691057|0.06910569105691057	60|60	0.16574585635359115|0.16574585635359115	82|82	0.14335664335664336|0.14335664335664336	193|193	0.2546174142480211|0.2546174142480211	c|c	0.004|0.004	-2.310517|-2.310517	0.00237|0.00237	0.093055|0.093055	0.261977|0.261977	ENSG00000122136|ENSG00000122136	ENST00000342114|ENST00000340780;ENST00000371776;ENST00000539850	T|T;T;T	0.09073|0.10960	3.02|2.82;3.01;3.01	2.25|2.25	-0.0665|-0.0665	0.13764|0.13764	.|Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.|0.858893	.|0.09691	.|N	.|0.768386	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01048|0.01048	-1.04|-1.04	0.80722|0.80722	P|P	0.0|0.0	B|B;B	0.02656|0.02656	0.0|0.0;0.0	B|B;B	0.01281|0.04013	0.0|0.001;0.001	T|T	0.45205|0.45205	-0.9277|-0.9277	8|9	0.35671|0.10902	T|T	0.21|0.67	-0.9531|-0.9531	1.1399|1.1399	0.01763|0.01763	0.1961:0.3382:0.3111:0.1546|0.1961:0.3382:0.3111:0.1546	.|.	79|124;124	Q5T8A4|Q5T8A5;Q9NY56	.|.;OBP2A_HUMAN	P|H	79|124	ENSP00000340950:L79P|ENSP00000342097:Y124H;ENSP00000360841:Y124H;ENSP00000441028:Y124H	ENSP00000340950:L79P|ENSP00000342097:Y124H	L|Y	+|+	2|1	0|0	OBP2A|OBP2A	137579630|137579630	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.078000|-2.078000	0.01370|0.01370	-0.350000|-0.350000	0.08262|0.08262	-1.623000|-1.623000	0.00790|0.00790	CTA|TAC	T|0.804;C|0.196	0.196	strong		0.617	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	
FAM209B	388799	hgsc.bcm.edu	37	20	55108510	55108510	+	Missense_Mutation	SNP	G	G	A	rs386815438|rs201542308	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55108510G>A	ENST00000371325.1	+	1	209	c.113G>A	c.(112-114)tGt>tAt	p.C38Y		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	38				PC -> QY (in Ref. 2; AAI05793). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)											AAGGTGCCGTGTGGAGAGCAC	0.537													G|||	60	0.0119808	0.0023	0.0101	5008	,	,		20350	0.003		0.0109	False		,,,				2504	0.0368				p.C38Y		Atlas-SNP	.											.	.	.	.	0			c.G113A						PASS	.						171.0	143.0	153.0					20																	55108510		2203	4291	6494	SO:0001583	missense	388799	exon1			TGCCGTGTGGAGA	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.113G>A	20.37:g.55108510G>A	ENSP00000360376:p.Cys38Tyr	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	188	29	0.154255	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	G	1.503	-0.551408	0.03996	.	.	ENSG00000213714	ENST00000371325	T	0.08634	3.07	2.8	2.8	0.32819	.	0.000000	0.53938	D	0.000044	T	0.12050	0.0293	N	0.16833	0.445	0.29281	N	0.870017	D	0.69078	0.997	D	0.83275	0.996	T	0.05419	-1.0886	10	0.30854	T	0.27	-14.443	9.141	0.36903	0.0:0.0:1.0:0.0	.	38	Q5JX69	CT107_HUMAN	Y	38	ENSP00000360376:C38Y	ENSP00000360376:C38Y	C	+	2	0	C20orf107	54541917	0.914000	0.31030	0.949000	0.38748	0.015000	0.08874	2.274000	0.43390	1.556000	0.49512	0.393000	0.25936	TGT	.	.	weak		0.537	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
CDC27	996	hgsc.bcm.edu	37	17	45234327	45234327	+	Missense_Mutation	SNP	C	C	T	rs7350889		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45234327C>T	ENST00000066544.3	-	7	887	c.794G>A	c.(793-795)gGt>gAt	p.G265D	CDC27_ENST00000527547.1_Missense_Mutation_p.G265D|CDC27_ENST00000446365.2_Missense_Mutation_p.G204D|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Missense_Mutation_p.G265D	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	265					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.G265D(2)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAACTTCGACCAGTTTTTGG	0.368																																					p.G265D		Atlas-SNP	.											CDC27_ENST00000531206,NS,adenoma,0,4	CDC27	337	4	2	Substitution - Missense(2)	skin(2)	c.G794A						scavenged	.						60.0	65.0	63.0					17																	45234327		2201	4295	6496	SO:0001583	missense	996	exon7			CTTCGACCAGTTT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.794G>A	17.37:g.45234327C>T	ENSP00000066544:p.Gly265Asp	Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	61	4	0.0655738	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.725453	0.48833	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.3;-0.11;-0.31;0.86	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.52853	0.1760	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.32350	0.251;0.366;0.247;0.251	B;B;B;B	0.27076	0.045;0.056;0.076;0.055	T	0.51694	-0.8673	10	0.33141	T	0.24	1.6987	17.2083	0.86924	0.0:1.0:0.0:0.0	rs7350889;rs7350889	204;265;265;265	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	D	265;265;204;265;265	ENSP00000066544:G265D;ENSP00000434614:G265D;ENSP00000392802:G204D;ENSP00000437339:G265D;ENSP00000432105:G265D	ENSP00000066544:G265D	G	-	2	0	CDC27	42589326	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.618000	0.67722	2.665000	0.90641	0.460000	0.39030	GGT	C|1.000;|0.000	.	weak		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
CHRNA7	1139	hgsc.bcm.edu	37	15	32450704	32450704	+	Silent	SNP	G	G	A	rs201822909		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:32450704G>A	ENST00000306901.3	+	7	787	c.690G>A	c.(688-690)acG>acA	p.T230T	CHRNA7_ENST00000454250.3_Silent_p.T259T|CHRNA7_ENST00000455693.2_Silent_p.T49T	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	230					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)	p.T230T(1)|p.T140T(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GCCGCAGGACGCTCTACTATG	0.582																																					p.T259T	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-SNP	.											CHRNA7_ENST00000437966,caecum,carcinoma,0,11	CHRNA7	57	11	2	Substitution - coding silent(2)	ovary(2)	c.G777A						scavenged	.						119.0	100.0	107.0					15																	32450704		2200	4297	6497	SO:0001819	synonymous_variant	1139	exon7			CAGGACGCTCTAC	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1960	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 7 (neuronal)"""	118511	"""cholinergic receptor, nicotinic, alpha polypeptide 7"""			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.690G>A	15.37:g.32450704G>A		Somatic	1058	33	0.0311909		WXS	Illumina HiSeq	Phase_I	1143	397	0.347332	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Silent	SNP	ENST00000306901.3	37	CCDS10027.1																																																																																			G|0.705;A|0.295	0.295	strong		0.582	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2		
MUC16	94025	hgsc.bcm.edu	37	19	9049910	9049910	+	Missense_Mutation	SNP	C	C	T	rs56307190	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9049910C>T	ENST00000397910.4	-	5	31924	c.31721G>A	c.(31720-31722)cGt>cAt	p.R10574H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10576	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCCCCAGAACGAGAGACCAG	0.498													C|||	928	0.185304	0.0628	0.2752	5008	,	,		20093	0.3363		0.167	False		,,,				2504	0.1503				p.R10574H		Atlas-SNP	.											.	MUC16	4315	.	0			c.G31721A						PASS	.		HIS/ARG	303,3471		14,275,1598	134.0	124.0	127.0		31721	-0.1	0.0	19	dbSNP_129	127	1499,6711		137,1225,2743	yes	missense	MUC16	NM_024690.2	29	151,1500,4341	TT,TC,CC		18.2582,8.0286,15.0367	benign	10574/14508	9049910	1802,10182	1887	4105	5992	SO:0001583	missense	94025	exon5			CCAGAACGAGAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31721G>A	19.37:g.9049910C>T	ENSP00000381008:p.Arg10574His	Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	290	154	0.531034	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	462	0.21153846153846154	32	0.06504065040650407	91	0.2513812154696133	213	0.3723776223776224	126	0.1662269129287599	c	6.957	0.546438	0.13312	0.080286	0.182582	ENSG00000181143	ENST00000397910	T	0.02916	4.11	3.2	-0.111	0.13576	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	.	.	.	B	0.14012	0.009	B	0.09377	0.004	T	0.42849	-0.9427	8	0.87932	D	0	.	5.6847	0.17797	0.0:0.6388:0.0:0.3612	rs56307190;rs61748894	10574	B5ME49	.	H	10574	ENSP00000381008:R10574H	ENSP00000381008:R10574H	R	-	2	0	MUC16	8910910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.183000	0.16919	0.055000	0.16094	-0.711000	0.03637	CGT	C|0.794;T|0.206	0.206	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
STOML2	30968	hgsc.bcm.edu	37	9	35101522	35101522	+	Silent	SNP	G	G	A	rs35119429	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35101522G>A	ENST00000356493.5	-	6	542	c.480C>T	c.(478-480)gcC>gcT	p.A160A	STOML2_ENST00000452248.2_Intron|STOML2_ENST00000487490.1_5'Flank	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	160					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CTTGGTTGATGGCATCCACAA	0.547													G|||	139	0.0277556	0.0741	0.013	5008	,	,		18469	0.0		0.0179	False		,,,				2504	0.0143				p.A160A		Atlas-SNP	.											.	STOML2	27	.	0			c.C480T						PASS	.	G		310,4096	166.9+/-198.0	10,290,1903	132.0	132.0	132.0		480	2.4	1.0	9	dbSNP_126	132	118,8482	61.7+/-123.6	1,116,4183	no	coding-synonymous	STOML2	NM_013442.1		11,406,6086	AA,AG,GG		1.3721,7.0359,3.2908		160/357	35101522	428,12578	2203	4300	6503	SO:0001819	synonymous_variant	30968	exon6			GTTGATGGCATCC	AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.480C>T	9.37:g.35101522G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_013442	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Silent	SNP	ENST00000356493.5	37	CCDS6577.1																																																																																			G|0.972;A|0.028	0.028	strong		0.547	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052273.1	NM_013442	
EPHB2	2048	hgsc.bcm.edu	37	1	23208925	23208925	+	Silent	SNP	G	G	A	rs2229872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:23208925G>A	ENST00000400191.3	+	6	1395	c.1377G>A	c.(1375-1377)ccG>ccA	p.P459P	EPHB2_ENST00000374632.3_Silent_p.P459P|EPHB2_ENST00000374630.3_Silent_p.P459P|EPHB2_ENST00000465676.1_3'UTR|EPHB2_ENST00000544305.1_Silent_p.P459P|EPHB2_ENST00000374627.1_Silent_p.P453P	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	459	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		GGTCCCAGCCGGACCAGCCCA	0.602													G|||	1074	0.214457	0.1989	0.1585	5008	,	,		22352	0.4901		0.0755	False		,,,				2504	0.1339				p.P459P		Atlas-SNP	.											EPHB2_ENST00000374632,NS,adenoma,0,1	EPHB2	257	1	0			c.G1377A						PASS	.	G	,	728,3678	299.8+/-286.0	63,602,1538	150.0	136.0	141.0		1377,1377	-8.2	0.8	1	dbSNP_126	141	807,7793	188.6+/-235.5	41,725,3534	no	coding-synonymous,coding-synonymous	EPHB2	NM_004442.6,NM_017449.3	,	104,1327,5072	AA,AG,GG		9.3837,16.5229,11.8022	,	459/988,459/987	23208925	1535,11471	2203	4300	6503	SO:0001819	synonymous_variant	2048	exon6			CCAGCCGGACCAG	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1377G>A	1.37:g.23208925G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	37																																																																																				G|0.854;A|0.146	0.146	strong		0.602	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
SLC16A4	9122	hgsc.bcm.edu	37	1	110925550	110925550	+	Silent	SNP	T	T	G	rs35653868	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110925550T>G	ENST00000369779.4	-	3	375	c.126A>C	c.(124-126)gcA>gcC	p.A42A	SLC16A4_ENST00000541986.1_Intron|SLC16A4_ENST00000472422.2_Silent_p.A42A|LAMTOR5-AS1_ENST00000590413.1_RNA|SLC16A4_ENST00000369781.4_Silent_p.A42A|SLC16A4_ENST00000497687.1_Intron|SLC16A4_ENST00000437429.2_Intron	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	42					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CAAAGAAAATTGCAAAAGTCT	0.418													T|||	118	0.0235623	0.0015	0.0346	5008	,	,		21003	0.0		0.0845	False		,,,				2504	0.0072				p.A42A		Atlas-SNP	.											.	SLC16A4	47	.	0			c.A126C						PASS	.	T	,,,,	67,4339	62.3+/-99.4	0,67,2136	111.0	108.0	109.0		126,,,126,126	-4.2	1.0	1	dbSNP_126	109	638,7962	164.2+/-216.6	29,580,3691	no	coding-synonymous,intron,intron,coding-synonymous,coding-synonymous	SLC16A4	NM_001201546.1,NM_001201547.1,NM_001201548.1,NM_001201549.1,NM_004696.2	,,,,	29,647,5827	GG,GT,TT		7.4186,1.5207,5.4206	,,,,	42/440,,,42/320,42/488	110925550	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	9122	exon3			GAAAATTGCAAAA	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.126A>C	1.37:g.110925550T>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	36	0.321429	NM_001201546	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Silent	SNP	ENST00000369779.4	37	CCDS823.1																																																																																			T|0.946;G|0.054	0.054	strong		0.418	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696	
EDEM3	80267	hgsc.bcm.edu	37	1	184663581	184663581	+	Silent	SNP	T	T	C	rs9425634	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:184663581T>C	ENST00000318130.8	-	20	2681	c.2415A>G	c.(2413-2415)caA>caG	p.Q805Q	EDEM3_ENST00000367512.3_Silent_p.Q778Q|EDEM3_ENST00000466392.1_5'Flank	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	805					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CAGAGGATGGTTGTTCTTCAT	0.353													T|||	2114	0.422125	0.1906	0.3963	5008	,	,		19518	0.5873		0.4324	False		,,,				2504	0.5726				p.Q805Q		Atlas-SNP	.											.	EDEM3	63	.	0			c.A2415G						PASS	.	T		1058,3342	365.1+/-317.3	144,770,1286	31.0	27.0	29.0		2415	-2.4	0.7	1	dbSNP_119	29	3817,4777	500.2+/-375.2	886,2045,1366	no	coding-synonymous	EDEM3	NM_025191.3		1030,2815,2652	CC,CT,TT		44.4147,24.0455,37.5173		805/933	184663581	4875,8119	2200	4297	6497	SO:0001819	synonymous_variant	80267	exon20			GGATGGTTGTTCT	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"""chromosome 1 open reading frame 22"""	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.2415A>G	1.37:g.184663581T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Silent	SNP	ENST00000318130.8	37	CCDS1363.2																																																																																			T|0.612;C|0.388	0.388	strong		0.353	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191	
ZAP70	7535	hgsc.bcm.edu	37	2	98354511	98354511	+	Silent	SNP	G	G	A	rs3192177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:98354511G>A	ENST00000264972.5	+	13	1892	c.1677G>A	c.(1675-1677)gaG>gaA	p.E559E	ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000451498.2_Silent_p.E252E|ZAP70_ENST00000442208.1_Silent_p.E433E	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	559	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						AGCGGATGGAGTGCCCACCAG	0.612													G|||	743	0.148363	0.087	0.2075	5008	,	,		17953	0.0109		0.3618	False		,,,				2504	0.1115				p.E559E		Atlas-SNP	.											.	ZAP70	77	.	0			c.G1677A						PASS	.	G	,	555,3851	245.0+/-254.1	39,477,1687	91.0	87.0	89.0		1677,756	1.6	1.0	2	dbSNP_105	89	2939,5661	444.1+/-360.6	510,1919,1871	no	coding-synonymous,coding-synonymous	ZAP70	NM_001079.3,NM_207519.1	,	549,2396,3558	AA,AG,GG		34.1744,12.5965,26.8645	,	559/620,252/313	98354511	3494,9512	2203	4300	6503	SO:0001819	synonymous_variant	7535	exon13			GATGGAGTGCCCA	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"""SH2 domain containing"""	12858	protein-coding gene	gene with protein product		176947	"""zeta-chain (TCR) associated protein kinase (70 kD)"""	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.1677G>A	2.37:g.98354511G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	174	80	0.45977	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Silent	SNP	ENST00000264972.5	37	CCDS33254.1																																																																																			G|0.786;A|0.214	0.214	strong		0.612	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1		
DDX58	23586	hgsc.bcm.edu	37	9	32459450	32459450	+	Silent	SNP	T	T	G	rs3205166	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:32459450T>G	ENST00000379883.2	-	17	2557	c.2400A>C	c.(2398-2400)gtA>gtC	p.V800V	DDX58_ENST00000379868.1_Silent_p.V597V|DDX58_ENST00000379882.1_Silent_p.V755V|DDX58_ENST00000542096.1_Silent_p.V729V	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	800	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CCTTATCAGGTACAGGTTTTG	0.363													T|||	1574	0.314297	0.202	0.3602	5008	,	,		17599	0.4524		0.3529	False		,,,				2504	0.2515				p.V800V		Atlas-SNP	.											.	DDX58	82	.	0			c.A2400C						PASS	.	T		1056,3350	386.3+/-326.1	120,816,1267	186.0	165.0	172.0		2400	-6.8	0.0	9	dbSNP_105	172	3120,5480	474.8+/-368.9	555,2010,1735	no	coding-synonymous	DDX58	NM_014314.3		675,2826,3002	GG,GT,TT		36.2791,23.9673,32.1083		800/926	32459450	4176,8830	2203	4300	6503	SO:0001819	synonymous_variant	23586	exon17			ATCAGGTACAGGT	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2400A>C	9.37:g.32459450T>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Silent	SNP	ENST00000379883.2	37	CCDS6526.1																																																																																			T|0.672;G|0.328	0.328	strong		0.363	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
PPP6R1	22870	hgsc.bcm.edu	37	19	55756980	55756980	+	Silent	SNP	A	A	G	rs3745920	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55756980A>G	ENST00000412770.2	-	3	860	c.294T>C	c.(292-294)gcT>gcC	p.A98A	PPP6R1_ENST00000587283.1_Silent_p.A98A	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	98	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						GGGACTCATCAGCACCCAGGG	0.622													A|||	1022	0.204073	0.0635	0.2738	5008	,	,		13837	0.1111		0.336	False		,,,				2504	0.3047				p.A98A		Atlas-SNP	.											PPP6R1_ENST00000412770,NS,carcinoma,0,2	PPP6R1	63	2	0			c.T294C						PASS	.	A		414,3694		24,366,1664	44.0	47.0	46.0		294	-10.3	0.0	19	dbSNP_107	46	2881,5509		503,1875,1817	no	coding-synonymous	PPP6R1	NM_014931.3		527,2241,3481	GG,GA,AA		34.3385,10.0779,26.3642		98/882	55756980	3295,9203	2054	4195	6249	SO:0001819	synonymous_variant	22870	exon3			CTCATCAGCACCC	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.294T>C	19.37:g.55756980A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	53	17	0.320755	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Silent	SNP	ENST00000412770.2	37	CCDS46186.1																																																																																			A|0.789;G|0.211	0.211	strong		0.622	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
PTPN21	11099	hgsc.bcm.edu	37	14	88938652	88938652	+	Missense_Mutation	SNP	A	A	G	rs2274736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:88938652A>G	ENST00000556564.1	-	15	3091	c.2807T>C	c.(2806-2808)gTg>gCg	p.V936A	PTPN21_ENST00000328736.3_Missense_Mutation_p.V936A	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	936	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		V -> A (in dbSNP:rs2274736). {ECO:0000269|PubMed:7519780}.		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTCCACTCTCACATCATCATA	0.428													G|||	1982	0.395767	0.5227	0.2781	5008	,	,		17688	0.38		0.2962	False		,,,				2504	0.4264				p.V936A		Atlas-SNP	.											.	PTPN21	113	.	0			c.T2807C						PASS	.	G	ALA/VAL	2230,2176	585.1+/-386.2	555,1120,528	208.0	181.0	190.0		2807	5.9	0.1	14	dbSNP_100	190	2933,5667	668.9+/-402.6	490,1953,1857	yes	missense	PTPN21	NM_007039.3	64	1045,3073,2385	GG,GA,AA		34.1047,49.3872,39.6971	benign	936/1175	88938652	5163,7843	2203	4300	6503	SO:0001583	missense	11099	exon15			ACTCTCACATCAT	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.2807T>C	14.37:g.88938652A>G	ENSP00000452414:p.Val936Ala	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	205	98	0.478049	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	799	0.3658424908424908	258	0.524390243902439	103	0.2845303867403315	205	0.3583916083916084	233	0.3073878627968338	G	10.25	1.298031	0.23650	0.506128	0.341047	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.12774	2.65;2.65	5.86	5.86	0.93980	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.169720	0.52532	N	0.000078	T	0.00012	0.0000	N	0.01048	-1.04	0.52099	P	5.100000000002325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43245	-0.9403	9	0.28530	T	0.3	.	15.2622	0.73634	0.067:0.0:0.933:0.0	rs2274736;rs60443733;rs2274736	936	Q16825	PTN21_HUMAN	A	936	ENSP00000330276:V936A;ENSP00000452414:V936A	ENSP00000330276:V936A	V	-	2	0	PTPN21	88008405	1.000000	0.71417	0.050000	0.19076	0.315000	0.28087	3.948000	0.56660	1.502000	0.48669	-0.119000	0.15052	GTG	G|0.389;N|0.000	0.389	strong		0.428	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
CD207	50489	hgsc.bcm.edu	37	2	71058226	71058226	+	Silent	SNP	C	C	T	rs2080390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71058226C>T	ENST00000410009.3	-	6	987	c.942G>A	c.(940-942)acG>acA	p.T314T		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	314	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TGAAAAGAAACGTTTTGTCAC	0.488													C|||	689	0.13758	0.0386	0.2406	5008	,	,		18402	0.0794		0.2197	False		,,,				2504	0.1738				p.T314T		Atlas-SNP	.											.	CD207	47	.	0			c.G942A						PASS	.	C		251,3645		6,239,1703	120.0	113.0	115.0		942	-4.1	0.0	2	dbSNP_96	115	2068,6206		255,1558,2324	no	coding-synonymous	CD207	NM_015717.3		261,1797,4027	TT,TC,CC		24.994,6.4425,19.0551		314/329	71058226	2319,9851	1948	4137	6085	SO:0001819	synonymous_variant	50489	exon6			AAGAAACGTTTTG	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"""C-type lectin domain containing"", ""CD molecules"""	17935	protein-coding gene	gene with protein product		604862	"""CD207 antigen, langerin"""			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.942G>A	2.37:g.71058226C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	171	76	0.444444	NM_015717		Silent	SNP	ENST00000410009.3	37																																																																																				C|0.863;T|0.137	0.137	strong		0.488	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
TGM4	7047	hgsc.bcm.edu	37	3	44943104	44943104	+	Missense_Mutation	SNP	G	G	C	rs937838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:44943104G>C	ENST00000296125.4	+	7	814	c.746G>C	c.(745-747)aGt>aCt	p.S249T	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	249			S -> T (in dbSNP:rs937838).		mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.S249T(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	TGGACAGGCAGTGCCCCGATC	0.567													G|||	352	0.0702875	0.0552	0.1225	5008	,	,		20649	0.0268		0.0855	False		,,,				2504	0.0828				p.S249T		Atlas-SNP	.											TGM4,NS,carcinoma,0,1	TGM4	82	1	1	Substitution - Missense(1)	stomach(1)	c.G746C						PASS	.	G	THR/SER	263,4143	149.2+/-183.4	10,243,1950	119.0	108.0	112.0		746	2.8	0.0	3	dbSNP_86	112	781,7819	183.5+/-231.7	33,715,3552	yes	missense	TGM4	NM_003241.3	58	43,958,5502	CC,CG,GG		9.0814,5.9691,8.0271	probably-damaging	249/685	44943104	1044,11962	2203	4300	6503	SO:0001583	missense	7047	exon7			CAGGCAGTGCCCC	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"""Transglutaminases"""	11780	protein-coding gene	gene with protein product		600585	"""transglutaminase 4 (prostate)"""			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.746G>C	3.37:g.44943104G>C	ENSP00000296125:p.Ser249Thr	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	191	131	0.685864	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	149	0.06822344322344322	26	0.052845528455284556	43	0.11878453038674033	14	0.024475524475524476	66	0.0870712401055409	G	19.07	3.755813	0.69648	0.059691	0.090814	ENSG00000163810	ENST00000296125	T	0.57907	0.37	2.84	2.84	0.33178	.	0.000000	0.52532	U	0.000062	T	0.03651	0.0104	M	0.89904	3.07	0.20307	P	0.9999149955	D	0.76494	0.999	D	0.91635	0.999	T	0.61212	-0.7108	9	0.87932	D	0	.	14.4392	0.67303	0.0:0.0:1.0:0.0	rs937838;rs52797165;rs937838	249	P49221	TGM4_HUMAN	T	249	ENSP00000296125:S249T	ENSP00000296125:S249T	S	+	2	0	TGM4	44918108	1.000000	0.71417	0.002000	0.10522	0.015000	0.08874	8.226000	0.89785	1.523000	0.49018	0.563000	0.77884	AGT	G|0.924;C|0.076	0.076	strong		0.567	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
GRK6	2870	hgsc.bcm.edu	37	5	176867943	176867943	+	Silent	SNP	A	A	G	rs335435	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176867943A>G	ENST00000355472.5	+	15	1734	c.1566A>G	c.(1564-1566)caA>caG	p.Q522Q	GRK6_ENST00000355958.5_Silent_p.Q522Q|PRR7-AS1_ENST00000425316.3_RNA|PRR7-AS1_ENST00000514846.1_RNA|PRR7-AS1_ENST00000511565.1_RNA|GRK6_ENST00000528793.1_Silent_p.Q522Q|GRK6_ENST00000393576.3_Silent_p.Q488Q	NM_001004106.2|NM_002082.3	NP_001004106.1|NP_002073.2	P43250	GRK6_HUMAN	G protein-coupled receptor kinase 6	522					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)			breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(5)|stomach(1)	25	all_cancers(89;1.15e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGTGCTTCCAAGAGCTGAATG	0.632													G|||	1758	0.351038	0.3215	0.3617	5008	,	,		18340	0.2619		0.5249	False		,,,				2504	0.2965				p.Q522Q		Atlas-SNP	.											.	GRK6	48	.	0			c.A1566G						PASS	.	G	,,	1504,2902	673.8+/-402.8	260,984,959	48.0	48.0	48.0		1566,1566,1566	5.1	1.0	5	dbSNP_79	48	4782,3818	536.5+/-383.0	1316,2150,834	no	coding-synonymous,coding-synonymous,coding-synonymous	GRK6	NM_001004105.2,NM_001004106.2,NM_002082.3	,,	1576,3134,1793	GG,GA,AA		44.3953,34.1353,48.3315	,,	522/561,522/577,522/590	176867943	6286,6720	2203	4300	6503	SO:0001819	synonymous_variant	2870	exon15			CTTCCAAGAGCTG		CCDS34303.1, CCDS43406.1, CCDS47348.1	5q35	2011-01-14	2004-02-04	2004-02-06	ENSG00000198055	ENSG00000198055			4545	protein-coding gene	gene with protein product		600869		GPRK6		8415712	Standard	NM_002082		Approved		uc021yiu.1	P43250	OTTHUMG00000163401	ENST00000355472.5:c.1566A>G	5.37:g.176867943A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_002082	O60541|Q13652	Silent	SNP	ENST00000355472.5	37	CCDS34303.1																																																																																			A|0.553;G|0.447	0.447	strong		0.632	GRK6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373204.1	NM_002082	
PASK	23178	hgsc.bcm.edu	37	2	242082262	242082262	+	Silent	SNP	T	T	C	rs6709462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242082262T>C	ENST00000405260.1	-	2	884	c.186A>G	c.(184-186)acA>acG	p.T62T	PASK_ENST00000358649.4_Silent_p.T62T|PASK_ENST00000403638.3_Silent_p.T62T|PASK_ENST00000234040.4_Silent_p.T62T|PASK_ENST00000544142.1_Missense_Mutation_p.Q11R|PASK_ENST00000539818.1_Intron	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	62					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CAGAGAGCGCTGTCCTGCTCT	0.557													C|||	2993	0.597644	0.4508	0.6167	5008	,	,		20296	0.9097		0.4622	False		,,,				2504	0.6002				p.T62T		Atlas-SNP	.											PASK_ENST00000234040,colon,carcinoma,-1,2	PASK	230	2	0			c.A186G						PASS	.	C		1995,2411	615.0+/-392.5	447,1101,655	82.0	70.0	74.0		186	-6.0	0.0	2	dbSNP_116	74	3947,4653	601.5+/-394.4	870,2207,1223	no	coding-synonymous	PASK	NM_015148.2		1317,3308,1878	CC,CT,TT		45.8953,45.2792,45.6866		62/1324	242082262	5942,7064	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon2			GAGCGCTGTCCTG	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.186A>G	2.37:g.242082262T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_001252122	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1	1303	0.5966117216117216	225	0.4573170731707317	212	0.585635359116022	523	0.9143356643356644	343	0.4525065963060686	C	0.294	-0.978391	0.02197	0.452792	0.458953	ENSG00000115687	ENST00000544142	T	0.66280	-0.2	4.39	-5.98	0.02220	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35525	-0.9785	7	0.87932	D	0	.	1.5711	0.02615	0.2099:0.2624:0.1035:0.4241	rs6709462;rs17384140;rs58425904;rs6709462	11	F5GYW7	.	R	11	ENSP00000441374:Q11R	ENSP00000441374:Q11R	Q	-	2	0	PASK	241730935	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.216000	0.09266	-2.056000	0.00898	-0.930000	0.02707	CAG	T|0.480;C|0.520	0.520	strong		0.557	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205306590	205306590	+	Silent	SNP	G	G	A	rs3210952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205306590G>A	ENST00000367156.3	-	9	1806	c.990C>T	c.(988-990)gcC>gcT	p.A330A	KLHDC8A_ENST00000537168.1_Silent_p.A217A|KLHDC8A_ENST00000367155.3_Silent_p.A330A|KLHDC8A_ENST00000539253.1_Silent_p.A330A|KLHDC8A_ENST00000460687.1_Silent_p.A196A	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	330										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CACCTCCCACGGCGAGGAGGC	0.587													g|||	894	0.178514	0.0219	0.17	5008	,	,		19856	0.3383		0.2127	False		,,,				2504	0.1963				p.A330A		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.C990T						PASS	.	A		203,4203	126.6+/-163.6	1,201,2001	198.0	177.0	184.0		990	-10.9	0.2	1	dbSNP_105	184	1604,6996	299.3+/-304.4	151,1302,2847	no	coding-synonymous	KLHDC8A	NM_018203.1		152,1503,4848	AA,AG,GG		18.6512,4.6074,13.8936		330/351	205306590	1807,11199	2203	4300	6503	SO:0001819	synonymous_variant	55220	exon6			TCCCACGGCGAGG		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.990C>T	1.37:g.205306590G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_018203	B3KU70|Q9NVG5	Silent	SNP	ENST00000367156.3	37	CCDS30985.1																																																																																			G|0.841;A|0.159	0.159	strong		0.587	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
OR4L1	122742	hgsc.bcm.edu	37	14	20529043	20529043	+	Silent	SNP	C	C	G	rs1959628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20529043C>G	ENST00000315683.1	+	1	840	c.840C>G	c.(838-840)ccC>ccG	p.P280P		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TTATCACACCCTTACTGAATC	0.353													C|||	2146	0.428514	0.3623	0.3934	5008	,	,		18716	0.5357		0.3221	False		,,,				2504	0.5419				p.P280P		Atlas-SNP	.											.	OR4L1	98	.	0			c.C840G						PASS	.	C		1587,2819		285,1017,901	78.0	80.0	79.0		840	-2.2	1.0	14	dbSNP_92	79	2776,5824		486,1804,2010	no	coding-synonymous	OR4L1	NM_001004717.1		771,2821,2911	GG,GC,CC		32.2791,36.0191,33.5461		280/313	20529043	4363,8643	2203	4300	6503	SO:0001819	synonymous_variant	122742	exon1			CACACCCTTACTG		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.840C>G	14.37:g.20529043C>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_001004717	Q6IEZ5	Silent	SNP	ENST00000315683.1	37	CCDS32029.1																																																																																			C|0.638;G|0.362	0.362	strong		0.353	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
DEAF1	10522	hgsc.bcm.edu	37	11	654043	654043	+	Silent	SNP	G	G	A	rs10902188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:654043G>A	ENST00000382409.3	-	11	1996	c.1512C>T	c.(1510-1512)tgC>tgT	p.C504C	DEAF1_ENST00000338675.6_Silent_p.C429C|DEAF1_ENST00000525904.1_5'UTR	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	504					anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		CGCAGTTAACGCAGGACTGCT	0.627													G|||	518	0.103435	0.0552	0.1729	5008	,	,		14599	0.1528		0.0815	False		,,,				2504	0.091				p.C504C		Atlas-SNP	.											.	DEAF1	47	.	0			c.C1512T						PASS	.	G		249,4157	143.8+/-178.8	14,221,1968	115.0	87.0	96.0		1512	-2.0	1.0	11	dbSNP_120	96	712,7888	174.0+/-224.4	29,654,3617	no	coding-synonymous	DEAF1	NM_021008.2		43,875,5585	AA,AG,GG		8.2791,5.6514,7.3889		504/566	654043	961,12045	2203	4300	6503	SO:0001819	synonymous_variant	10522	exon11			GTTAACGCAGGAC	AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"""Zinc fingers, MYND-type"""	14677	protein-coding gene	gene with protein product		602635	"""deformed epidermal autoregulatory factor 1 (Drosophila)"""			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.1512C>T	11.37:g.654043G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_021008	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Silent	SNP	ENST00000382409.3	37	CCDS31327.1																																																																																			G|0.911;A|0.089	0.089	strong		0.627	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008	
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628948	1628948	+	Missense_Mutation	SNP	G	G	A	rs117085626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1628948G>A	ENST00000399685.1	-	1	745	c.668C>T	c.(667-669)tCc>tTc	p.S223F		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	223	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		GGACTGGGAGGAGCAGGGCTT	0.602													g|||	312	0.0623003	0.0061	0.1138	5008	,	,		19294	0.002		0.1352	False		,,,				2504	0.089				p.S223F		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.C668T						PASS	.	G	PHE/SER	122,4282	89.7+/-128.4	4,114,2084	157.0	162.0	160.0		668	2.1	0.6	11	dbSNP_132	160	1066,7532	224.5+/-260.9	64,938,3297	no	missense	KRTAP5-3	NM_001012708.2	155	68,1052,5381	AA,AG,GG		12.3982,2.7702,9.1371	possibly-damaging	223/239	1628948	1188,11814	2202	4299	6501	SO:0001583	missense	387266	exon1			TGGGAGGAGCAGG	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"""Keratin associated proteins"""	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.668C>T	11.37:g.1628948G>A	ENSP00000382592:p.Ser223Phe	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	194	103	0.530928	NM_001012708	Q6PL44|Q701N3	Missense_Mutation	SNP	ENST00000399685.1	37	CCDS41591.1	147	0.0673076923076923	3	0.006097560975609756	51	0.1408839779005525	0	0.0	93	0.12269129287598944	G	4.922	0.171317	0.09391	0.027702	0.123982	ENSG00000196224	ENST00000399685	T	0.00995	5.46	3.02	2.1	0.27182	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.41921	P	0.00948300000000002	P	0.36249	0.545	B	0.35607	0.206	T	0.54629	-0.8265	8	0.56958	D	0.05	.	10.0527	0.42225	0.0:0.7914:0.2086:0.0	.	223	Q6L8H2	KRA53_HUMAN	F	223	ENSP00000382592:S223F	ENSP00000382592:S223F	S	-	2	0	KRTAP5-3	1585524	0.997000	0.39634	0.623000	0.29173	0.119000	0.20118	0.255000	0.18333	0.608000	0.30000	-0.748000	0.03510	TCC	G|0.917;A|0.083	0.083	strong		0.602	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1		
SEMA5B	54437	hgsc.bcm.edu	37	3	122630346	122630346	+	Missense_Mutation	SNP	T	T	C	rs2303983	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122630346T>C	ENST00000357599.3	-	21	3469	c.3083A>G	c.(3082-3084)gAc>gGc	p.D1028G	SEMA5B_ENST00000195173.4_Missense_Mutation_p.D1026G|SEMA5B_ENST00000451055.2_Missense_Mutation_p.D1082G	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	1028			D -> G (in dbSNP:rs2303983). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		ACCTGCACAGTCGGTGGCCTC	0.632													C|||	3044	0.607827	0.5575	0.6254	5008	,	,		19505	0.3571		0.8091	False		,,,				2504	0.7147				p.D1082G		Atlas-SNP	.											.	SEMA5B	303	.	0			c.A3245G						PASS	.	C	GLY/ASP	2552,1854	519.0+/-369.9	743,1066,394	56.0	50.0	52.0		3083	3.2	0.2	3	dbSNP_100	52	7153,1447	266.4+/-286.7	2973,1207,120	yes	missense	SEMA5B	NM_001031702.2	94	3716,2273,514	CC,CT,TT		16.8256,42.079,25.3806	benign	1028/1152	122630346	9705,3301	2203	4300	6503	SO:0001583	missense	54437	exon21			GCACAGTCGGTGG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.3083A>G	3.37:g.122630346T>C	ENSP00000350215:p.Asp1028Gly	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	1305|1305	0.5975274725274725|0.5975274725274725	263|263	0.5345528455284553|0.5345528455284553	244|244	0.6740331491712708|0.6740331491712708	196|196	0.34265734265734266|0.34265734265734266	602|602	0.7941952506596306|0.7941952506596306	C|C	0.943|0.943	-0.708967|-0.708967	0.03230|0.03230	0.57921|0.57921	0.831744|0.831744	ENSG00000082684|ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583|ENST00000451541	T;T;T;T|.	0.34667|.	1.35;1.38;1.41;1.47|.	5.02|5.02	3.19|3.19	0.36642|0.36642	.|.	1.133010|.	0.06112|.	N|.	0.667284|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	P|P	6.999999999979245E-6|6.999999999979245E-6	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.0|.	T|T	0.16424|0.16424	-1.0403|-1.0403	9|4	0.27785|.	T|.	0.31|.	.|.	5.9395|5.9395	0.19186|0.19186	0.0:0.559:0.1346:0.3064|0.0:0.559:0.1346:0.3064	rs2303983;rs58478743;rs2303983|rs2303983;rs58478743;rs2303983	934;1028|.	D3YTI7;Q9P283|.	.;SEM5B_HUMAN|.	G|A	1028;1026;934;1082;1028|74	ENSP00000350215:D1028G;ENSP00000195173:D1026G;ENSP00000389588:D1082G;ENSP00000377208:D1028G|.	ENSP00000195173:D1026G|.	D|T	-|-	2|1	0|0	SEMA5B|SEMA5B	124113036|124113036	0.962000|0.962000	0.33011|0.33011	0.176000|0.176000	0.23000|0.23000	0.053000|0.053000	0.15095|0.15095	1.895000|1.895000	0.39778|0.39778	0.054000|0.054000	0.16065|0.16065	-1.736000|-1.736000	0.00690|0.00690	GAC|ACT	T|0.335;C|0.665	0.665	strong		0.632	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
MYH3	4621	hgsc.bcm.edu	37	17	10542765	10542765	+	Silent	SNP	A	A	G	rs2285474	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10542765A>G	ENST00000583535.1	-	24	3039	c.2952T>C	c.(2950-2952)tcT>tcC	p.S984S	MYH3_ENST00000226209.7_Silent_p.S984S	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	984					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CATCTAACCCAGAGAGTTCCT	0.423													a|||	2336	0.466454	0.2398	0.5346	5008	,	,		20746	0.3839		0.7584	False		,,,				2504	0.5092				p.S984S		Atlas-SNP	.											.	MYH3	227	.	0			c.T2952C						PASS	.	A		1302,3104	432.8+/-343.4	199,904,1100	59.0	57.0	58.0		2952	-11.1	0.0	17	dbSNP_100	58	6267,2333	699.8+/-405.1	2260,1747,293	no	coding-synonymous	MYH3	NM_002470.3		2459,2651,1393	GG,GA,AA		27.1279,29.5506,41.8038		984/1941	10542765	7569,5437	2203	4300	6503	SO:0001819	synonymous_variant	4621	exon24			TAACCCAGAGAGT		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2952T>C	17.37:g.10542765A>G		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	220	219	0.995455	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	37	CCDS11157.1																																																																																			G|0.531;N|0.001	0.531	strong		0.423	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
ZNF286A	57335	hgsc.bcm.edu	37	17	15604485	15604485	+	Silent	SNP	T	T	C	rs78494624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:15604485T>C	ENST00000464847.2	+	2	610	c.57T>C	c.(55-57)tcT>tcC	p.S19S	ZNF286A_ENST00000583566.1_Silent_p.S19S|ZNF286A_ENST00000593105.1_Silent_p.S9S|ZNF286A_ENST00000585194.1_Silent_p.S19S|ZNF286A_ENST00000421016.1_Silent_p.S19S|ZNF286A_ENST00000413242.2_Silent_p.S19S|ZNF286A_ENST00000395894.2_Silent_p.S19S|ZNF286A_ENST00000395893.2_Silent_p.S19S|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000581529.1_Silent_p.S9S|ZNF286A_ENST00000580259.1_Silent_p.S19S|ZNF286A_ENST00000472486.1_Silent_p.S9S			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	19					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S19S(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		CCCAGGATTCTCCCCATTTCC	0.473																																					p.S19S		Atlas-SNP	.											ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	1	Substitution - coding silent(1)	pancreas(1)	c.T57C						PASS	.						275.0	242.0	253.0					17																	15604485		2203	4300	6503	SO:0001819	synonymous_variant	57335	exon3			GGATTCTCCCCAT	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.57T>C	17.37:g.15604485T>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	300	56	0.186667	NM_020652	B4DKF9|Q96JF3	Silent	SNP	ENST00000464847.2	37	CCDS11172.1																																																																																			T|0.895;C|0.105	0.105	strong		0.473	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
RRBP1	6238	hgsc.bcm.edu	37	20	17600357	17600357	+	Missense_Mutation	SNP	G	G	A	rs11960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:17600357G>A	ENST00000377813.1	-	19	3899	c.3596C>T	c.(3595-3597)tCg>tTg	p.S1199L	RRBP1_ENST00000246043.4_Missense_Mutation_p.S1199L|RRBP1_ENST00000377807.2_Missense_Mutation_p.S766L|RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000360807.4_Missense_Mutation_p.S766L|RRBP1_ENST00000455029.2_Missense_Mutation_p.S540L			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1199				S -> L (in Ref. 2, 5 and 6; AAH00099). {ECO:0000305}.	osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						CTCCAAATGCGACGTGTGCTC	0.647													G|||	1993	0.397963	0.0424	0.5893	5008	,	,		20345	0.255		0.7465	False		,,,				2504	0.5317				p.S766L		Atlas-SNP	.											.	RRBP1	157	.	0			c.C2297T						PASS	.	G	LEU/SER,LEU/SER	684,3722	284.3+/-277.5	65,554,1584	60.0	42.0	48.0		2297,2297	2.8	0.2	20	dbSNP_52	48	6235,2365	700.6+/-405.2	2240,1755,305	yes	missense,missense	RRBP1	NM_001042576.1,NM_004587.2	145,145	2305,2309,1889	AA,AG,GG		27.5,15.5243,46.8015	benign,benign	766/978,766/978	17600357	6919,6087	2203	4300	6503	SO:0001583	missense	6238	exon19			AAATGCGACGTGT	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"""ribosome binding protein 1 (dog 180kD homolog)"", ""ribosome binding protein 1 homolog 180kDa (dog)"""			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.3596C>T	20.37:g.17600357G>A	ENSP00000367044:p.Ser1199Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	37		986	0.45146520146520147	39	0.07926829268292683	224	0.6187845303867403	150	0.26223776223776224	573	0.7559366754617414	G	5.983	0.365254	0.11352	0.155243	0.725	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	T;T;T;T;T	0.34275	1.37;2.14;1.37;2.14;1.37	5.84	2.85	0.33270	.	0.267054	0.20136	N	0.098483	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B	0.23490	0.062;0.086	B;B	0.15870	0.014;0.005	T	0.19063	-1.0317	9	0.33940	T	0.23	-0.8384	8.0622	0.30640	0.1445:0.1319:0.7236:0.0	rs11960;rs1052976;rs1132039;rs2229890;rs3193460;rs11551702;rs57375895;rs11960	766;1199	Q9P2E9-3;Q9P2E9	.;RRBP1_HUMAN	L	766;1199;766;1199;540	ENSP00000354045:S766L;ENSP00000367044:S1199L;ENSP00000367038:S766L;ENSP00000246043:S1199L;ENSP00000401206:S540L	ENSP00000246043:S1199L	S	-	2	0	RRBP1	17548357	0.583000	0.26757	0.213000	0.23690	0.039000	0.13416	2.602000	0.46257	0.389000	0.25086	0.563000	0.77884	TCG	G|0.509;A|0.491	0.491	strong		0.647	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576	
MAGEB16	139604	hgsc.bcm.edu	37	X	35821055	35821055	+	Missense_Mutation	SNP	A	A	G	rs4829390|rs370444095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:35821055A>G	ENST00000399989.1	+	2	1021	c.742A>G	c.(742-744)Atg>Gtg	p.M248V	MAGEB16_ENST00000399985.1_Missense_Mutation_p.M248V|MAGEB16_ENST00000399987.1_Missense_Mutation_p.M248V|MAGEB16_ENST00000399992.1_Missense_Mutation_p.M280V|MAGEB16_ENST00000399988.1_Missense_Mutation_p.M248V	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	248	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		M -> K (in dbSNP:rs4829391).|M -> V (in dbSNP:rs4829390).							breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						AGAGCCCAGAATGCTCATCAC	0.502													G|||	2342	0.620397	0.4478	0.4121	3775	,	,		15852	0.5694		0.4195	False		,,,				2504	0.4785				p.M248V		Atlas-SNP	.											.	MAGEB16	64	.	0			c.A742G						PASS	.	G	VAL/MET	423,3332		76,144,127,1372,444	45.0	44.0	44.0		742	-6.1	0.0	X	dbSNP_111	44	767,5940		105,231,326,2086,1537	yes	missense	MAGEB16	NM_001099921.1	21	181,375,453,3458,1981	GG,GA,G,AA,A		11.4358,11.265,11.3745	benign	248/325	35821055	1190,9272	2163	4285	6448	SO:0001583	missense	139604	exon2			CCCAGAATGCTCA		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.742A>G	X.37:g.35821055A>G	ENSP00000382871:p.Met248Val	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	906	0.546112115732369	144	0.391304347826087	94	0.3700787401574803	192	0.49740932642487046	201	0.3338870431893688	G	4.024	0.001860	0.07819	0.11265	0.114358	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04502	3.61;3.61;3.61;3.61;3.61	3.06	-6.12	0.02124	.	0.726440	0.13630	N	0.373788	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.11235	0.004	B	0.10450	0.005	T	0.48969	-0.8987	9	0.87932	D	0	.	7.4099	0.27011	0.4068:0.38:0.2132:0.0	rs4829390	248	A2A368	MAGBG_HUMAN	V	248;280;248;248;248	ENSP00000382870:M248V;ENSP00000382874:M280V;ENSP00000382869:M248V;ENSP00000382871:M248V;ENSP00000382867:M248V	ENSP00000382867:M248V	M	+	1	0	MAGEB16	35730976	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.986000	0.01484	-4.139000	0.00070	-0.346000	0.07831	ATG	A|0.455;G|0.545	0.545	strong		0.502	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
ENPP5	59084	hgsc.bcm.edu	37	6	46129345	46129345	+	Silent	SNP	G	G	A	rs2235881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46129345G>A	ENST00000371383.2	-	5	1412	c.1152C>T	c.(1150-1152)acC>acT	p.T384T	ENPP5_ENST00000230565.3_Silent_p.T384T					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						GTGGCATGGCGGTGATATTGA	0.458													G|||	2236	0.446486	0.1899	0.4467	5008	,	,		19626	0.4494		0.5348	False		,,,				2504	0.6994				p.T384T		Atlas-SNP	.											.	ENPP5	44	.	0			c.C1152T						PASS	.	G		1049,3357	383.7+/-325.0	126,797,1280	238.0	235.0	236.0		1152	-8.1	0.0	6	dbSNP_98	236	4592,4008	598.8+/-394.0	1220,2152,928	no	coding-synonymous	ENPP5	NM_021572.4		1346,2949,2208	AA,AG,GG		46.6047,23.8084,43.3723		384/478	46129345	5641,7365	2203	4300	6503	SO:0001819	synonymous_variant	59084	exon4			CATGGCGGTGATA	AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.1152C>T	6.37:g.46129345G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	178	66	0.370787	NM_021572		Silent	SNP	ENST00000371383.2	37	CCDS4915.1																																																																																			G|0.569;T|0.002	.	strong		0.458	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
DOC2A	8448	hgsc.bcm.edu	37	16	30018500	30018500	+	Silent	SNP	C	C	T	rs3935873	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:30018500C>T	ENST00000350119.4	-	6	838	c.648G>A	c.(646-648)caG>caA	p.Q216Q	DOC2A_ENST00000564979.1_Silent_p.Q216Q|DOC2A_ENST00000564944.1_Silent_p.Q216Q	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	216	Interaction with UNC13D.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						AGACCGGGACCTGGCGCTCGA	0.642													C|||	1749	0.349241	0.1573	0.3141	5008	,	,		15186	0.378		0.4414	False		,,,				2504	0.5092				p.Q216Q		Atlas-SNP	.											.	DOC2A	40	.	0			c.G648A						PASS	.	C		774,3620	304.4+/-288.4	78,618,1501	31.0	34.0	33.0		648	4.2	1.0	16	dbSNP_108	33	3823,4777	525.6+/-380.8	864,2095,1341	no	coding-synonymous	DOC2A	NM_003586.2		942,2713,2842	TT,TC,CC		44.4535,17.6149,35.3779		216/401	30018500	4597,8397	2197	4300	6497	SO:0001819	synonymous_variant	8448	exon6			CGGGACCTGGCGC	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.648G>A	16.37:g.30018500C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Silent	SNP	ENST00000350119.4	37	CCDS10666.1																																																																																			C|0.660;T|0.340	0.340	strong		0.642	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
CCDC124	115098	hgsc.bcm.edu	37	19	18047283	18047283	+	Silent	SNP	T	T	G	rs4808722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18047283T>G	ENST00000597436.1	+	2	161	c.54T>G	c.(52-54)cgT>cgG	p.R18R	CCDC124_ENST00000445755.2_Silent_p.R18R	NM_138442.3	NP_612451.1	Q96CT7	CC124_HUMAN	coiled-coil domain containing 124	18					cell cycle (GO:0007049)|cell division (GO:0051301)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(2)	3						CCCGGGCACGTAGGGCAGAGG	0.637													G|||	1841	0.367612	0.6248	0.2522	5008	,	,		15506	0.1161		0.3857	False		,,,				2504	0.3425				p.R18R		Atlas-SNP	.											.	CCDC124	8	.	0			c.T54G						PASS	.	G	,	2554,1852		755,1044,404	40.0	38.0	39.0		54,54	2.3	1.0	19	dbSNP_111	39	3190,5408		600,1990,1709	no	coding-synonymous,coding-synonymous	CCDC124	NM_001136203.1,NM_138442.3	,	1355,3034,2113	GG,GT,TT		37.1017,42.0336,44.171	,	18/224,18/224	18047283	5744,7260	2203	4299	6502	SO:0001819	synonymous_variant	115098	exon2			GGCACGTAGGGCA	BC013949	CCDS12369.1	19p13.11	2014-02-20				ENSG00000007080			25171	protein-coding gene	gene with protein product						23894443	Standard	NM_138442		Approved		uc002nhs.3	Q96CT7		ENST00000597436.1:c.54T>G	19.37:g.18047283T>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_138442		Silent	SNP	ENST00000597436.1	37	CCDS12369.1																																																																																			T|0.594;G|0.406	0.406	strong		0.637	CCDC124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466484.1	NM_138442	
MAP3K11	4296	hgsc.bcm.edu	37	11	65367223	65367223	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65367223A>G	ENST00000530153.1	-	9	1598	c.1077T>C	c.(1075-1077)ccT>ccC	p.P359P	MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000309100.3_Silent_p.P616P|MAP3K11_ENST00000532507.1_Silent_p.P32P					mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						GCTCCAGGCTAGGCCGCGGGG	0.697																																					p.P616P		Atlas-SNP	.											.	MAP3K11	67	.	0			c.T1848C						PASS	.						7.0	8.0	8.0					11																	65367223		2068	4080	6148	SO:0001819	synonymous_variant	4296	exon9			CAGGCTAGGCCGC		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.1077T>C	11.37:g.65367223A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	30	4	0.133333	NM_002419		Silent	SNP	ENST00000530153.1	37																																																																																				.	.	none		0.697	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		
FUT5	2527	hgsc.bcm.edu	37	19	5867177	5867177	+	Missense_Mutation	SNP	G	G	A	rs778970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:5867177G>A	ENST00000588525.1	-	2	647	c.560C>T	c.(559-561)cCg>cTg	p.P187L	FUT5_ENST00000252675.5_Missense_Mutation_p.P187L	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	187			P -> L (in dbSNP:rs778970).		carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						GCCGGACCACGGCTCCAGCCA	0.662													G|||	2238	0.446885	0.2905	0.5706	5008	,	,		12307	0.5863		0.4563	False		,,,				2504	0.4172				p.P187L		Atlas-SNP	.											.	FUT5	29	.	0			c.C560T						PASS	.						17.0	16.0	17.0					19																	5867177		2162	4222	6384	SO:0001583	missense	2527	exon2			GACCACGGCTCCA		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.560C>T	19.37:g.5867177G>A	ENSP00000466880:p.Pro187Leu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_002034	A8K4X2	Missense_Mutation	SNP	ENST00000588525.1	37	CCDS12154.1	1034	0.4734432234432234	139	0.28252032520325204	202	0.5580110497237569	357	0.6241258741258742	336	0.44327176781002636	G	9.702	1.154871	0.21371	.	.	ENSG00000130383	ENST00000252675	T	0.24908	1.83	2.34	1.25	0.21368	.	0.240689	0.29335	U	0.012460	T	0.00012	0.0000	M	0.77486	2.375	0.48762	P	2.950000000000452E-4	P	0.46621	0.881	P	0.45794	0.493	T	0.43081	-0.9413	9	0.22706	T	0.39	.	2.534	0.04710	0.1847:0.0:0.5298:0.2854	rs778970;rs3745634;rs3854697;rs57372090	187	Q11128	FUT5_HUMAN	L	187	ENSP00000252675:P187L	ENSP00000252675:P187L	P	-	2	0	FUT5	5818177	0.056000	0.20664	0.579000	0.28588	0.136000	0.21042	0.493000	0.22451	0.275000	0.22094	0.407000	0.27541	CCG	A|1.000;|0.000	1.000	weak		0.662	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
DCLRE1A	9937	hgsc.bcm.edu	37	10	115609915	115609915	+	Missense_Mutation	SNP	C	C	G	rs3750898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115609915C>G	ENST00000361384.2	-	2	1866	c.949G>C	c.(949-951)Gat>Cat	p.D317H	DCLRE1A_ENST00000369305.1_Missense_Mutation_p.D317H	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	317			D -> H (in dbSNP:rs3750898). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		TGTGAATCATCCGGTTTTTCA	0.388								Other identified genes with known or suspected DNA repair function					C|||	3294	0.657748	0.3086	0.817	5008	,	,		20913	0.8185		0.7942	False		,,,				2504	0.7106				p.D317H		Atlas-SNP	.											.	DCLRE1A	80	.	0			c.G949C						PASS	.	C	HIS/ASP	1693,2713	512.9+/-368.2	325,1043,835	136.0	128.0	131.0		949	4.1	1.0	10	dbSNP_107	131	6603,1997	722.4+/-406.4	2535,1533,232	yes	missense	DCLRE1A	NM_014881.3	81	2860,2576,1067	GG,GC,CC		23.2209,38.4249,36.2141	possibly-damaging	317/1041	115609915	8296,4710	2203	4300	6503	SO:0001583	missense	9937	exon2			AATCATCCGGTTT		CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"""PSO2 homolog (S. cerevisiae)"""	609682	"""DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"""			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.949G>C	10.37:g.115609915C>G	ENSP00000355185:p.Asp317His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_014881	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Missense_Mutation	SNP	ENST00000361384.2	37	CCDS7584.1	1527	0.6991758241758241	170	0.34552845528455284	294	0.8121546961325967	472	0.8251748251748252	591	0.7796833773087071	C	18.82	3.704827	0.68615	0.384249	0.767791	ENSG00000198924	ENST00000361384;ENST00000369305	T;T	0.67865	-0.29;-0.29	6.02	4.13	0.48395	.	0.857054	0.10601	N	0.655643	T	0.00012	0.0000	L	0.57536	1.79	0.38063	P	0.06387799999999999	D	0.63880	0.993	P	0.53185	0.72	T	0.28839	-1.0031	9	0.52906	T	0.07	-4.0187	10.1303	0.42674	0.1343:0.7966:0.0:0.0691	rs3750898;rs17235101;rs17855758;rs52822954;rs60893685;rs3750898	317	Q6PJP8	DCR1A_HUMAN	H	317	ENSP00000355185:D317H;ENSP00000358311:D317H	ENSP00000355185:D317H	D	-	1	0	DCLRE1A	115599905	0.100000	0.21855	0.996000	0.52242	0.710000	0.40934	0.905000	0.28504	1.517000	0.48917	0.650000	0.86243	GAT	C|0.339;G|0.661	0.661	strong		0.388	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881	
NIPSNAP1	8508	hgsc.bcm.edu	37	22	29957570	29957570	+	Silent	SNP	G	G	A	rs1058642	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29957570G>A	ENST00000216121.7	-	6	758	c.504C>T	c.(502-504)ctC>ctT	p.L168L		NM_001202502.1|NM_003634.3	NP_001189431.1|NP_003625.2	Q9BPW8	NIPS1_HUMAN	nipsnap homolog 1 (C. elegans)	168					sensory perception of pain (GO:0019233)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|synaptic membrane (GO:0097060)	neurotransmitter binding (GO:0042165)	p.?(1)		large_intestine(2)|lung(2)|skin(1)	5						AGCTGAACTCGAGGAGCAGCT	0.577													G|||	911	0.181909	0.2133	0.1571	5008	,	,		20245	0.1468		0.2744	False		,,,				2504	0.0982				p.L168L		Atlas-SNP	.											.	NIPSNAP1	17	.	1	Unknown(1)	lung(1)	c.C504T						PASS	.	G	,	955,3451	362.9+/-316.3	106,743,1354	101.0	96.0	98.0		444,504	-9.7	0.0	22	dbSNP_86	98	2351,6249	393.1+/-344.2	300,1751,2249	yes	coding-synonymous,coding-synonymous	NIPSNAP1	NM_001202502.1,NM_003634.3	,	406,2494,3603	AA,AG,GG		27.3372,21.675,25.419	,	148/265,168/285	29957570	3306,9700	2203	4300	6503	SO:0001819	synonymous_variant	8508	exon6			GAACTCGAGGAGC	AJ001258	CCDS13860.1	22q12	2013-09-12	2001-11-28		ENSG00000184117	ENSG00000184117			7827	protein-coding gene	gene with protein product	"""4-nitrophenylphosphatase domain and non-neuronal SNAP25-like 1"""	603249	"""NIPSNAP, C. elegans, homolog 1"""			9661659	Standard	NM_003634		Approved		uc003afx.4	Q9BPW8	OTTHUMG00000151294	ENST00000216121.7:c.504C>T	22.37:g.29957570G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_003634	B2RAY3|O43800	Silent	SNP	ENST00000216121.7	37	CCDS13860.1	480	0.21978021978021978	117	0.23780487804878048	73	0.20165745856353592	89	0.1555944055944056	201	0.26517150395778366	G	7.620	0.676691	0.14841	0.21675	0.273372	ENSG00000184117	ENST00000415100	.	.	.	4.83	-9.67	0.00531	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.6728	9.0159	0.36170	0.3038:0.5436:0.0921:0.0606	rs1058642;rs3199284;rs17420578	.	.	.	X	185	.	.	R	-	1	2	NIPSNAP1	28287570	0.061000	0.20836	0.028000	0.17463	0.818000	0.46254	-0.643000	0.05421	-2.274000	0.00680	-1.244000	0.01528	CGA	G|0.757;A|0.243	0.243	strong		0.577	NIPSNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322117.1		
KIAA1377	57562	hgsc.bcm.edu	37	11	101832590	101832590	+	Missense_Mutation	SNP	C	C	A	rs11225089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:101832590C>A	ENST00000263468.8	+	6	1094	c.824C>A	c.(823-825)tCc>tAc	p.S275Y	KIAA1377_ENST00000537689.1_Missense_Mutation_p.S76Y	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	275			S -> Y (in dbSNP:rs11225089).							breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		CATTCCACATCCATCCAGCGG	0.373													C|||	598	0.119409	0.025	0.1037	5008	,	,		17605	0.2748		0.0517	False		,,,				2504	0.1677				p.S275Y		Atlas-SNP	.											KIAA1377,NS,carcinoma,+1,1	KIAA1377	111	1	0			c.C824A						PASS	.	C	TYR/SER	112,4294	85.8+/-124.5	2,108,2093	71.0	69.0	70.0		824	3.9	0.0	11	dbSNP_120	70	334,8264	116.5+/-176.2	5,324,3970	yes	missense	KIAA1377	NM_020802.2	144	7,432,6063	AA,AC,CC		3.8846,2.542,3.4297	probably-damaging	275/1118	101832590	446,12558	2203	4299	6502	SO:0001583	missense	57562	exon6			CCACATCCATCCA	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.824C>A	11.37:g.101832590C>A	ENSP00000263468:p.Ser275Tyr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	247	0.1130952380952381	19	0.03861788617886179	37	0.10220994475138122	154	0.2692307692307692	37	0.048812664907651716	C	11.11	1.541129	0.27563	0.02542	0.038846	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.09350	2.99;2.99	5.79	3.92	0.45320	.	0.872596	0.09897	N	0.741566	T	0.00012	0.0000	L	0.61036	1.89	0.80722	P	0.0	D	0.59767	0.986	P	0.57152	0.814	T	0.32079	-0.9920	9	0.66056	D	0.02	-0.4923	10.1059	0.42533	0.0:0.7945:0.0:0.2055	rs11225089;rs52803305;rs61175740;rs11225089	275	Q9P2H0	K1377_HUMAN	Y	275;76	ENSP00000263468:S275Y;ENSP00000443184:S76Y	ENSP00000263468:S275Y	S	+	2	0	KIAA1377	101337800	0.056000	0.20664	0.012000	0.15200	0.167000	0.22549	1.806000	0.38892	1.457000	0.47850	0.655000	0.94253	TCC	C|0.932;A|0.068	0.068	strong		0.373	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
CAPN15	6650	hgsc.bcm.edu	37	16	601632	601632	+	Silent	SNP	T	T	C	rs3213574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:601632T>C	ENST00000219611.2	+	9	2676	c.2313T>C	c.(2311-2313)ggT>ggC	p.G771G	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	771	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GCAGTGAGGGTGTCTTCTGGA	0.677													c|||	3592	0.717252	0.8268	0.6758	5008	,	,		14094	0.7788		0.5199	False		,,,				2504	0.7382				p.G771G		Atlas-SNP	.											SOLH,NS,carcinoma,+1,1	SOLH	47	1	0			c.T2313C						PASS	.			3446,952	351.3+/-311.2	1355,736,108	43.0	50.0	48.0		2313	-3.6	1.0	16	dbSNP_106	48	4476,4118	558.0+/-387.2	1149,2178,970	no	coding-synonymous	SOLH	NM_005632.2		2504,2914,1078	CC,CT,TT		47.9172,21.6462,39.024		771/1087	601632	7922,5070	2199	4297	6496	SO:0001819	synonymous_variant	6650	exon9			TGAGGGTGTCTTC	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2313T>C	16.37:g.601632T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent	SNP	ENST00000219611.2	37	CCDS10410.1																																																																																			T|0.359;C|0.641	0.641	strong		0.677	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	
CHRNB3	1142	hgsc.bcm.edu	37	8	42587659	42587659	+	Silent	SNP	G	G	C	rs4953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:42587659G>C	ENST00000289957.2	+	5	1337	c.1209G>C	c.(1207-1209)tcG>tcC	p.S403S		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	403					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	GATACATTTCGAGACATGTGA	0.368													A|||	184	0.0367412	0.0575	0.0216	5008	,	,		19624	0.002		0.0358	False		,,,				2504	0.0562				p.S403S		Atlas-SNP	.											CHRNB3,NS,carcinoma,0,1	CHRNB3	74	1	0			c.G1209C						PASS	.	A		214,4192		5,204,1994	30.0	32.0	32.0		1209	-11.7	0.0	8	dbSNP_52	32	333,8259		8,317,3971	no	coding-synonymous	CHRNB3	NM_000749.3		13,521,5965	CC,CG,GG		3.8757,4.857,4.2083		403/459	42587659	547,12451	2203	4296	6499	SO:0001819	synonymous_variant	1142	exon5			CATTTCGAGACAT	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1963	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 3 (neuronal)"""	118508	"""cholinergic receptor, nicotinic, beta polypeptide 3"""			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.1209G>C	8.37:g.42587659G>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_000749	Q15827	Silent	SNP	ENST00000289957.2	37	CCDS6134.1																																																																																			G|0.959;C|0.041	0.041	strong		0.368	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1		
CERK	64781	hgsc.bcm.edu	37	22	47095235	47095235	+	Missense_Mutation	SNP	C	C	A	rs13057352	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:47095235C>A	ENST00000216264.8	-	8	1030	c.918G>T	c.(916-918)ttG>ttT	p.L306F	CERK_ENST00000541677.1_Missense_Mutation_p.L108F	NM_022766.5	NP_073603.2	Q8TCT0	CERK1_HUMAN	ceramide kinase	306			L -> F (in dbSNP:rs13057352).		ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lipid phosphorylation (GO:0046834)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)			cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	20		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TGGCAAGACCCAACCACCGTT	0.542													C|||	80	0.0159744	0.0015	0.0403	5008	,	,		18562	0.0		0.0368	False		,,,				2504	0.0133				p.L306F		Atlas-SNP	.											.	CERK	40	.	0			c.G918T						PASS	.	C	PHE/LEU	38,4368	43.8+/-77.6	0,38,2165	232.0	168.0	189.0		918	5.1	1.0	22	dbSNP_121	189	364,8236	121.3+/-180.4	8,348,3944	yes	missense	CERK	NM_022766.5	22	8,386,6109	AA,AC,CC		4.2326,0.8625,3.0909	benign	306/538	47095235	402,12604	2203	4300	6503	SO:0001583	missense	64781	exon8			AAGACCCAACCAC	AB079066	CCDS14077.1	22q13.31	2008-06-10			ENSG00000100422	ENSG00000100422			19256	protein-coding gene	gene with protein product		610307				11956206, 11258795	Standard	NM_022766		Approved	hCERK, FLJ23239, dA59H18.3, DKFZp434E0211, FLJ21430, KIAA1646, LK4, dA59H18.2	uc003bia.3	Q8TCT0	OTTHUMG00000150395	ENST00000216264.8:c.918G>T	22.37:g.47095235C>A	ENSP00000216264:p.Leu306Phe	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	176	50	0.284091	NM_022766	A0JNT4|A8K611|Q6NX59|Q9BYB3|Q9UGE5	Missense_Mutation	SNP	ENST00000216264.8	37	CCDS14077.1	43	0.019688644688644688	0	0.0	19	0.052486187845303865	0	0.0	24	0.0316622691292876	c	12.61	1.988628	0.35131	0.008625	0.042326	ENSG00000100422	ENST00000216264;ENST00000541677	T;T	0.50813	0.73;0.73	5.09	5.09	0.68999	.	0.150443	0.56097	D	0.000022	T	0.11367	0.0277	M	0.67397	2.05	0.44862	D	0.997877	B	0.22800	0.075	B	0.23275	0.045	T	0.15292	-1.0442	10	0.49607	T	0.09	-0.037	10.6911	0.45870	0.0:0.9117:0.0:0.0883	rs13057352;rs52834701;rs13057352	306	Q8TCT0	CERK1_HUMAN	F	306;108	ENSP00000216264:L306F;ENSP00000438659:L108F	ENSP00000216264:L306F	L	-	3	2	CERK	45473899	1.000000	0.71417	1.000000	0.80357	0.148000	0.21650	3.330000	0.52068	2.370000	0.80446	0.655000	0.94253	TTG	C|0.973;A|0.027	0.027	strong		0.542	CERK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317924.2	NM_022766	
ARRB2	409	hgsc.bcm.edu	37	17	4622638	4622638	+	Silent	SNP	C	C	T	rs1045280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4622638C>T	ENST00000269260.2	+	11	1073	c.840C>T	c.(838-840)agC>agT	p.S280S	ARRB2_ENST00000571206.1_Silent_p.S88S|ARRB2_ENST00000572457.1_Silent_p.S88S|ARRB2_ENST00000412477.3_Silent_p.S301S|ARRB2_ENST00000346341.2_Silent_p.S265S|ARRB2_ENST00000574954.1_Silent_p.S88S|ARRB2_ENST00000381488.6_Silent_p.S265S|ARRB2_ENST00000575877.1_Intron	NM_001257328.1|NM_001257330.1|NM_004313.3	NP_001244257.1|NP_001244259.1|NP_004304.1	P32121	ARRB2_HUMAN	arrestin, beta 2	280	Interaction with TRAF6.				adult walking behavior (GO:0007628)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell chemotaxis (GO:0060326)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|Notch signaling pathway (GO:0007219)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|receptor internalization (GO:0031623)|regulation of androgen receptor signaling pathway (GO:0060765)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	angiotensin receptor binding (GO:0031701)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|ubiquitin protein ligase binding (GO:0031625)			large_intestine(1)|liver(2)|lung(3)|prostate(1)	7						CACTGCTCAGCGACAACCGGG	0.602													C|||	3353	0.669529	0.4047	0.7205	5008	,	,		15652	0.8254		0.6879	False		,,,				2504	0.8119				p.S301S		Atlas-SNP	.											.	ARRB2	30	.	0			c.C903T						PASS	.	C	,	1982,2424	557.6+/-379.8	433,1116,654	95.0	87.0	90.0		840,795	-4.6	0.5	17	dbSNP_86	90	5815,2785	678.1+/-403.4	1973,1869,458	no	coding-synonymous,coding-synonymous	ARRB2	NM_004313.3,NM_199004.1	,	2406,2985,1112	TT,TC,CC		32.3837,44.9841,40.0507	,	280/410,265/395	4622638	7797,5209	2203	4300	6503	SO:0001819	synonymous_variant	409	exon11			GCTCAGCGACAAC		CCDS11050.1, CCDS11051.1, CCDS58504.1, CCDS58505.1, CCDS59276.1	17p13	2008-12-11			ENSG00000141480	ENSG00000141480			712	protein-coding gene	gene with protein product	"""arrestin 3"""	107941		ARR2		7695743	Standard	NM_001257329		Approved	BARR2, DKFZp686L0365	uc002fyl.3	P32121	OTTHUMG00000090759	ENST00000269260.2:c.840C>T	17.37:g.4622638C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_001257328	B4DLW0|B5B0C0|B7WPL3|D3DTK2|H0Y688|Q0Z8D3|Q2PP19|Q6ICT3|Q8N7Y2|Q9UEQ6	Silent	SNP	ENST00000269260.2	37	CCDS11050.1																																																																																			C|0.376;T|0.624	0.624	strong		0.602	ARRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439552.1	NM_004313	
HJURP	55355	hgsc.bcm.edu	37	2	234761225	234761225	+	Missense_Mutation	SNP	C	C	T	rs2286430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234761225C>T	ENST00000411486.2	-	3	291	c.226G>A	c.(226-228)Gaa>Aaa	p.E76K	HJURP_ENST00000432087.1_Missense_Mutation_p.E76K|HJURP_ENST00000441687.1_Missense_Mutation_p.E76K	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	76			E -> K (in dbSNP:rs2286430). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17823411, ECO:0000269|Ref.2}.		cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		ATCTCTCCTTCGTTTCTTTCC	0.383													C|||	1733	0.346046	0.1029	0.5086	5008	,	,		19534	0.3938		0.5159	False		,,,				2504	0.3354				p.E76K		Atlas-SNP	.											.	HJURP	72	.	0			c.G226A						PASS	.	C	LYS/GLU	717,3689	295.3+/-283.6	64,589,1550	158.0	128.0	138.0		226	-5.3	0.0	2	dbSNP_100	138	4395,4205	580.7+/-391.1	1123,2149,1028	yes	missense	HJURP	NM_018410.3	56	1187,2738,2578	TT,TC,CC		48.8953,16.2733,39.3049	benign	76/749	234761225	5112,7894	2203	4300	6503	SO:0001583	missense	55355	exon3			CTCCTTCGTTTCT		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.226G>A	2.37:g.234761225C>T	ENSP00000414109:p.Glu76Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	871|871	0.39880952380952384|0.39880952380952384	52|52	0.10569105691056911|0.10569105691056911	177|177	0.4889502762430939|0.4889502762430939	235|235	0.41083916083916083|0.41083916083916083	407|407	0.5369393139841688|0.5369393139841688	C|C	1.323|1.323	-0.598848|-0.598848	0.03744|0.03744	0.162733|0.162733	0.511047|0.511047	ENSG00000123485|ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924|ENST00000454020	T;T;T;T|T	0.48201|0.36157	0.82;0.82;0.82;0.82|1.27	3.55|3.55	-5.31|-5.31	0.02730|0.02730	Centromere protein Scm3, N-terminal (1);|.	1.405580|.	0.04824|.	N|.	0.437524|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.17268|.	0.017;0.006;0.021|.	B;B;B|.	0.12156|.	0.003;0.002;0.007|.	T|T	0.45629|0.45629	-0.9248|-0.9248	9|6	0.05620|0.87932	T|D	0.96|0	-0.0036|-0.0036	5.8643|5.8643	0.18767|0.18767	0.0:0.4239:0.3121:0.264|0.0:0.4239:0.3121:0.264	rs2286430;rs11546250;rs61495737;rs2286430|rs2286430;rs11546250;rs61495737;rs2286430	76;76;76|.	Q8NCD3-3;Q8NCD3-2;Q8NCD3|.	.;.;HJURP_HUMAN|.	K|Q	76|67	ENSP00000414109:E76K;ENSP00000407208:E76K;ENSP00000401944:E76K;ENSP00000393253:E76K|ENSP00000414051:R67Q	ENSP00000414109:E76K|ENSP00000414051:R67Q	E|R	-|-	1|2	0|0	HJURP|HJURP	234425964|234425964	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.461000|0.461000	0.32589|0.32589	-3.158000|-3.158000	0.00579|0.00579	-1.191000|-1.191000	0.02695|0.02695	-0.302000|-0.302000	0.09304|0.09304	GAA|CGA	C|0.621;T|0.379	0.379	strong		0.383	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
FAM81A	145773	hgsc.bcm.edu	37	15	59806496	59806496	+	Missense_Mutation	SNP	G	G	T	rs111778770	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:59806496G>T	ENST00000288228.5	+	7	846	c.659G>T	c.(658-660)gGt>gTt	p.G220V		NM_152450.2	NP_689663.2	Q8TBF8	FA81A_HUMAN	family with sequence similarity 81, member A	220										endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10						AGATTTAAAGGTACAGTTGAG	0.308													G|||	25	0.00499201	0.0	0.0029	5008	,	,		16381	0.0		0.0089	False		,,,				2504	0.0143				p.G220V		Atlas-SNP	.											.	FAM81A	31	.	0			c.G659T						PASS	.	G	VAL/GLY	9,3561		0,9,1776	49.0	48.0	48.0		659	5.8	1.0	15	dbSNP_132	48	84,8024		0,84,3970	yes	missense	FAM81A	NM_152450.2	109	0,93,5746	TT,TG,GG		1.036,0.2521,0.7964	probably-damaging	220/369	59806496	93,11585	1785	4054	5839	SO:0001583	missense	145773	exon7			TTAAAGGTACAGT		CCDS45269.1	15q22.2	2012-10-02			ENSG00000157470	ENSG00000157470			28379	protein-coding gene	gene with protein product							Standard	NM_152450		Approved	MGC26690	uc002agc.2	Q8TBF8	OTTHUMG00000171915	ENST00000288228.5:c.659G>T	15.37:g.59806496G>T	ENSP00000288228:p.Gly220Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_152450		Missense_Mutation	SNP	ENST00000288228.5	37	CCDS45269.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	18.54	3.647080	0.67358	0.002521	0.01036	ENSG00000157470	ENST00000288228	T	0.74209	-0.82	5.77	5.77	0.91146	.	0.160805	0.44483	D	0.000455	T	0.72993	0.3530	L	0.43152	1.355	0.52501	D	0.999955	D	0.69078	0.997	D	0.63793	0.918	T	0.77112	-0.2708	10	0.66056	D	0.02	-16.165	10.6169	0.45456	0.0912:0.0:0.9088:0.0	.	220	Q8TBF8	FA81A_HUMAN	V	220	ENSP00000288228:G220V	ENSP00000288228:G220V	G	+	2	0	FAM81A	57593788	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.009000	0.49552	2.885000	0.99019	0.655000	0.94253	GGT	G|0.995;T|0.005	0.005	strong		0.308	FAM81A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415876.1	NM_152450	
LOXHD1	125336	hgsc.bcm.edu	37	18	44063598	44063598	+	Missense_Mutation	SNP	G	G	A	rs1377016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44063598G>A	ENST00000398722.4	-	33	5458	c.5459C>T	c.(5458-5460)gCc>gTc	p.A1820V	LOXHD1_ENST00000398705.2_Missense_Mutation_p.A337V|LOXHD1_ENST00000398686.4_Missense_Mutation_p.A337V|LOXHD1_ENST00000300591.6_Missense_Mutation_p.A987V|LOXHD1_ENST00000441893.2_Missense_Mutation_p.A969V|LOXHD1_ENST00000582408.1_Missense_Mutation_p.A925V|LOXHD1_ENST00000441551.2_Missense_Mutation_p.A1892V|LOXHD1_ENST00000579038.1_Missense_Mutation_p.A891V|LOXHD1_ENST00000536736.1_Missense_Mutation_p.A2036V			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1820	PLAT 13. {ECO:0000255|PROSITE- ProRule:PRU00152}.			A -> V (in Ref. 4; AAH47720). {ECO:0000305}.	calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						GACATGCCAGGCAAGTTCTCT	0.552													A|||	1898	0.378994	0.2005	0.3905	5008	,	,		22330	0.7292		0.3121	False		,,,				2504	0.32				p.A2036V		Atlas-SNP	.											.	LOXHD1	367	.	0			c.C6107T						PASS	.						143.0	116.0	124.0					18																	44063598		692	1591	2283	SO:0001583	missense	125336	exon39			TGCCAGGCAAGTT	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.5459C>T	18.37:g.44063598G>A	ENSP00000381707:p.Ala1820Val	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		894	0.40934065934065933	82	0.16666666666666666	146	0.40331491712707185	434	0.7587412587412588	232	0.30606860158311344	A	9.892	1.204488	0.22205	.	.	ENSG00000167210	ENST00000300591;ENST00000398722;ENST00000398705;ENST00000536736;ENST00000441893;ENST00000398686	T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.78	3.21	0.36854	Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40701	-0.9549	8	0.16896	T	0.51	.	4.2209	0.10558	0.5165:0.0:0.249:0.2345	rs1377016;rs17846413;rs17859457;rs57156492;rs1377016	2036;969;1820	F5GZB4;F8WA52;Q8IVV2	.;.;LOXH1_HUMAN	V	987;1820;337;2036;969;337	ENSP00000300591:A987V;ENSP00000381707:A1820V;ENSP00000381692:A337V;ENSP00000444586:A2036V;ENSP00000409062:A969V;ENSP00000381676:A337V	ENSP00000300591:A987V	A	-	2	0	LOXHD1	42317596	0.993000	0.37304	0.978000	0.43139	0.744000	0.42396	0.675000	0.25232	0.066000	0.16515	-0.360000	0.07572	GCC	G|0.598;A|0.402	0.402	strong		0.552	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
TUBGCP5	114791	hgsc.bcm.edu	37	15	22846932	22846932	+	Silent	SNP	G	G	A	rs118137061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:22846932G>A	ENST00000283645.4	+	8	937	c.807G>A	c.(805-807)caG>caA	p.Q269Q	TUBGCP5_ENST00000453949.2_Silent_p.Q269Q	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	269					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CTGAGACTCAGGTTATTCGGG	0.348													G|||	45	0.00898562	0.0008	0.0101	5008	,	,		17602	0.0		0.0129	False		,,,				2504	0.0245				p.Q269Q		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.G807A						PASS	.	G	,	13,4393		0,13,2190	131.0	113.0	119.0		807,807	-1.6	0.7	15	dbSNP_132	119	178,8422		1,176,4123	no	coding-synonymous,coding-synonymous	TUBGCP5	NM_001102610.1,NM_052903.4	,	1,189,6313	AA,AG,GG		2.0698,0.2951,1.4686	,	269/1025,269/1025	22846932	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	114791	exon8			GACTCAGGTTATT	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"""gamma-tubulin complex component GCP5"""	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.807G>A	15.37:g.22846932G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_052903	E9PB12|Q6IQ52|Q96PY8	Silent	SNP	ENST00000283645.4	37	CCDS10008.1																																																																																			G|0.988;A|0.012	0.012	strong		0.348	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903	
MCF2L	23263	hgsc.bcm.edu	37	13	113728781	113728781	+	Silent	SNP	G	G	A	rs3814264	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:113728781G>A	ENST00000375608.3	+	11	1168	c.1110G>A	c.(1108-1110)gcG>gcA	p.A370A	MCF2L_ENST00000423482.2_Silent_p.A338A|MCF2L_ENST00000535094.2_Silent_p.A340A|MCF2L_ENST00000375601.3_Silent_p.A344A|MCF2L_ENST00000375604.2_Silent_p.A397A|MCF2L_ENST00000375597.4_Silent_p.A338A|MCF2L_ENST00000397030.1_Silent_p.A373A|MCF2L_ENST00000421756.1_Silent_p.A344A|MCF2L_ENST00000434480.2_Silent_p.A346A|MCF2L_ENST00000442652.2_Silent_p.A370A			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	370					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				TGGACGCAGCGTCCCAGAAGA	0.582													G|||	1103	0.220248	0.0356	0.3314	5008	,	,		16659	0.4593		0.2237	False		,,,				2504	0.1411				p.A340A		Atlas-SNP	.											.	MCF2L	182	.	0			c.G1020A						PASS	.	G	,	314,4092	167.6+/-198.6	13,288,1902	81.0	76.0	78.0		1020,1014	2.8	0.9	13	dbSNP_107	78	1839,6761	330.1+/-319.0	182,1475,2643	yes	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	195,1763,4545	AA,AG,GG		21.3837,7.1266,16.5539	,	340/1126,338/1124	113728781	2153,10853	2203	4300	6503	SO:0001819	synonymous_variant	23263	exon10			CGCAGCGTCCCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.1110G>A	13.37:g.113728781G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	207	206	0.995169	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		569	0.26053113553113555	26	0.052845528455284556	107	0.2955801104972376	264	0.46153846153846156	172	0.22691292875989447	G	2.214	-0.379936	0.05000	0.071266	0.213837	ENSG00000126217	ENST00000397017	.	.	.	4.87	2.81	0.32909	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999963344	.	.	.	.	.	.	T	0.50162	-0.8860	3	.	.	.	.	9.4825	0.38908	0.0868:0.0:0.7666:0.1465	rs3814264;rs3814264	.	.	.	I	1	.	.	V	+	1	0	MCF2L	112776782	1.000000	0.71417	0.908000	0.35775	0.007000	0.05969	2.757000	0.47557	2.234000	0.73211	0.655000	0.94253	GTC	G|0.809;A|0.191	0.191	strong		0.582	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
MGAM	8972	hgsc.bcm.edu	37	7	141796131	141796131	+	Splice_Site	SNP	G	G	A	rs6975672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:141796131G>A	ENST00000549489.2	+	42	5015	c.4920G>A	c.(4918-4920)gaG>gaA	p.E1640E	MGAM_ENST00000475668.2_Splice_Site_p.E2536E	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1640	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CCCTTTCCAGGTTTGTGTCAG	0.557													g|||	3395	0.677915	0.4614	0.7262	5008	,	,		18511	0.8423		0.8131	False		,,,				2504	0.6278				p.E1640E		Atlas-SNP	.											.	MGAM	767	.	0			c.G4920A						PASS	.						47.0	39.0	41.0					7																	141796131		1820	4042	5862	SO:0001630	splice_region_variant	8972	exon42			TTCCAGGTTTGTG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4920-1G>A	7.37:g.141796131G>A		Somatic	503	1	0.00198807		WXS	Illumina HiSeq	Phase_I	528	428	0.810606	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			.	.	weak		0.557	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		Silent
SRGAP1	57522	hgsc.bcm.edu	37	12	64485153	64485153	+	Missense_Mutation	SNP	G	G	A	rs74691643	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:64485153G>A	ENST00000355086.3	+	12	2058	c.1534G>A	c.(1534-1536)Gtc>Atc	p.V512I	SRGAP1_ENST00000543397.1_Intron|SRGAP1_ENST00000357825.3_Intron|RP11-196H14.2_ENST00000535594.1_RNA	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	512	F-BAR domain.|Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		GGAAACATTCGTCAAGGTACT	0.478													G|||	123	0.0245607	0.0015	0.013	5008	,	,		15968	0.0159		0.0189	False		,,,				2504	0.0787				p.V512I		Atlas-SNP	.											.	SRGAP1	146	.	0			c.G1534A						PASS	.	G	ILE/VAL	16,4390	23.3+/-48.9	0,16,2187	78.0	80.0	79.0		1534	2.9	1.0	12	dbSNP_131	79	157,8443	75.4+/-138.0	2,153,4145	yes	missense	SRGAP1	NM_020762.2	29	2,169,6332	AA,AG,GG		1.8256,0.3631,1.3302	benign	512/1086	64485153	173,12833	2203	4300	6503	SO:0001583	missense	57522	exon12			ACATTCGTCAAGG	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1534G>A	12.37:g.64485153G>A	ENSP00000347198:p.Val512Ile	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	37	0.587302	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	36	0.016483516483516484	1	0.0020325203252032522	7	0.019337016574585635	13	0.022727272727272728	15	0.01978891820580475	G	3.369	-0.128761	0.06753	0.003631	0.018256	ENSG00000196935	ENST00000355086	T	0.44482	0.92	5.75	2.86	0.33363	Rho GTPase-activating protein domain (2);Rho GTPase activation protein (1);	0.522213	0.13917	N	0.353860	T	0.11067	0.0270	N	0.11756	0.17	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04796	-1.0926	9	.	.	.	.	7.2827	0.26320	0.4257:0.0:0.5743:0.0	.	512	Q7Z6B7	SRGP1_HUMAN	I	512	ENSP00000347198:V512I	.	V	+	1	0	SRGAP1	62771420	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.528000	0.45624	0.868000	0.35678	0.655000	0.94253	GTC	G|0.983;A|0.017	0.017	strong		0.478	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
RHOBTB3	22836	hgsc.bcm.edu	37	5	95091201	95091201	+	Missense_Mutation	SNP	A	A	G	rs34899	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:95091201A>G	ENST00000379982.3	+	6	1292	c.784A>G	c.(784-786)Aat>Gat	p.N262D	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	262	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.		N -> D (in dbSNP:rs34899). {ECO:0000269|PubMed:10048485, ECO:0000269|PubMed:12426103}.		ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		TTACAACCCCAATTTAAAGAA	0.423													G|||	2379	0.47504	0.357	0.3415	5008	,	,		16213	0.6895		0.4324	False		,,,				2504	0.5521				p.N262D		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.A784G						PASS	.	G	ASP/ASN	1711,2695	651.9+/-399.3	318,1075,810	170.0	163.0	165.0		784	5.2	0.0	5	dbSNP_76	165	3579,5021	628.2+/-398.1	732,2115,1453	yes	missense	RHOBTB3	NM_014899.3	23	1050,3190,2263	GG,GA,AA		41.6163,38.8334,40.6735	benign	262/612	95091201	5290,7716	2203	4300	6503	SO:0001583	missense	22836	exon6			AACCCCAATTTAA	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"""BTB/POZ domain containing"""	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.784A>G	5.37:g.95091201A>G	ENSP00000369318:p.Asn262Asp	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	277	134	0.483755	NM_014899	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	37	CCDS4077.1	1046	0.47893772893772896	176	0.35772357723577236	136	0.3756906077348066	414	0.7237762237762237	320	0.42216358839050133	G	0.007	-1.962568	0.00461	0.388334	0.416163	ENSG00000164292	ENST00000379982	T	0.69175	-0.38	6.08	5.21	0.72293	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (1);	0.356359	0.35646	N	0.003075	T	0.00012	0.0000	N	0.01874	-0.695	0.44018	P	0.003263000000000016	B	0.02656	0.0	B	0.01281	0.0	T	0.45920	-0.9228	9	0.02654	T	1	-9.0521	12.9585	0.58444	0.1877:0.0:0.8123:0.0	rs34899;rs1221525;rs3201267;rs17857251;rs52811008;rs57550478;rs34899	262	O94955	RHBT3_HUMAN	D	262	ENSP00000369318:N262D	ENSP00000369318:N262D	N	+	1	0	RHOBTB3	95116957	1.000000	0.71417	0.013000	0.15412	0.000000	0.00434	2.538000	0.45710	0.484000	0.27630	-2.314000	0.00255	AAT	A|0.561;G|0.439	0.439	strong		0.423	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
ANGEL1	23357	hgsc.bcm.edu	37	14	77275630	77275630	+	Missense_Mutation	SNP	C	C	A	rs34270005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:77275630C>A	ENST00000251089.2	-	2	533	c.421G>T	c.(421-423)Ggg>Tgg	p.G141W	ANGEL1_ENST00000554941.1_5'UTR	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	141			G -> W (in dbSNP:rs34270005).							breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		CCCTCCACCCCCTCCACCTCC	0.637													C|||	234	0.0467252	0.0809	0.0403	5008	,	,		18327	0.0		0.0577	False		,,,				2504	0.0419				p.G141W		Atlas-SNP	.											ANGEL1,NS,carcinoma,0,1	ANGEL1	63	1	0			c.G421T						PASS	.	C	TRP/GLY	335,4071	170.1+/-200.6	14,307,1882	32.0	35.0	34.0		421	4.7	0.1	14	dbSNP_126	34	431,8169	131.8+/-189.6	15,401,3884	yes	missense	ANGEL1	NM_015305.3	184	29,708,5766	AA,AC,CC		5.0116,7.6033,5.8896	probably-damaging	141/671	77275630	766,12240	2203	4300	6503	SO:0001583	missense	23357	exon2			CCACCCCCTCCAC	AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523			19961	protein-coding gene	gene with protein product				KIAA0759		11943475	Standard	NM_015305		Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.421G>T	14.37:g.77275630C>A	ENSP00000251089:p.Gly141Trp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_015305	B4DWL7|O94859|Q8NCS9	Missense_Mutation	SNP	ENST00000251089.2	37	CCDS9852.1	95	0.043498168498168496	36	0.07317073170731707	13	0.03591160220994475	0	0.0	46	0.06068601583113457	C	6.819	0.520194	0.13005	0.076033	0.050116	ENSG00000013523	ENST00000251089	T	0.24538	1.85	5.6	4.7	0.59300	.	.	.	.	.	T	0.01387	0.0045	N	0.08118	0	0.20307	N	0.999912	D;D	0.76494	0.999;0.998	D;D	0.74674	0.984;0.965	T	0.04153	-1.0973	9	0.72032	D	0.01	.	6.3431	0.21335	0.0:0.6977:0.1842:0.118	rs34270005	141;141	B4DVG4;Q9UNK9	.;ANGE1_HUMAN	W	141	ENSP00000251089:G141W	ENSP00000251089:G141W	G	-	1	0	ANGEL1	76345383	0.903000	0.30736	0.066000	0.19879	0.088000	0.18126	3.226000	0.51254	1.353000	0.45828	-0.176000	0.13171	GGG	C|0.945;A|0.055	0.055	strong		0.637	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305	
SAGE1	55511	hgsc.bcm.edu	37	X	134991078	134991078	+	Silent	SNP	A	A	G	rs5974570	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:134991078A>G	ENST00000370709.3	+	12	1497	c.1497A>G	c.(1495-1497)caA>caG	p.Q499Q	SAGE1_ENST00000535938.1_Silent_p.Q499Q|SAGE1_ENST00000324447.3_Silent_p.Q499Q|SAGE1_ENST00000537770.1_Intron			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	499						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GCAAACCCCAAACTGATAAGG	0.443													a|||	611	0.161854	0.0673	0.1614	3775	,	,		15680	0.1012		0.2058	False		,,,				2504	0.1033				p.Q499Q		Atlas-SNP	.											.	SAGE1	160	.	0			c.A1497G						PASS	.	A		560,3275		31,427,71,1174,500	217.0	154.0	175.0		1497	-2.8	0.0	X	dbSNP_114	175	1754,4974		188,923,455,1317,1417	no	coding-synonymous	SAGE1	NM_018666.2		219,1350,526,2491,1917	GG,GA,G,AA,A		26.0702,14.6023,21.9067		499/905	134991078	2314,8249	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon13			ACCCCAAACTGAT	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.1497A>G	X.37:g.134991078A>G		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			A|0.806;G|0.194	0.194	strong		0.443	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
MTHFR	4524	hgsc.bcm.edu	37	1	11854896	11854896	+	Silent	SNP	G	G	A	rs2066462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11854896G>A	ENST00000376592.1	-	6	1184	c.1056C>T	c.(1054-1056)agC>agT	p.S352S	MTHFR_ENST00000376585.1_Silent_p.S393S|MTHFR_ENST00000376583.3_Silent_p.S393S|MTHFR_ENST00000376590.3_Silent_p.S352S			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	352					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	TGGGGTGGGCGCTGAGAGCCC	0.607													G|||	518	0.103435	0.0772	0.0576	5008	,	,		20032	0.1181		0.1024	False		,,,				2504	0.1575				p.S352S		Atlas-SNP	.											.	MTHFR	65	.	0			c.C1056T						PASS	.	G		387,4019	189.9+/-215.9	20,347,1836	47.0	49.0	48.0		1056	-5.1	0.9	1	dbSNP_94	48	835,7765	189.8+/-236.5	41,753,3506	no	coding-synonymous	MTHFR	NM_005957.4		61,1100,5342	AA,AG,GG		9.7093,8.7835,9.3957		352/657	11854896	1222,11784	2203	4300	6503	SO:0001819	synonymous_variant	4524	exon7			GTGGGCGCTGAGA	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.1056C>T	1.37:g.11854896G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Silent	SNP	ENST00000376592.1	37	CCDS137.1																																																																																			G|0.910;A|0.090	0.090	strong		0.607	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
WBP1L	54838	hgsc.bcm.edu	37	10	104572963	104572963	+	Missense_Mutation	SNP	T	T	C	rs284860	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:104572963T>C	ENST00000369889.4	+	4	1046	c.904T>C	c.(904-906)Tcc>Ccc	p.S302P	WBP1L_ENST00000448841.1_Missense_Mutation_p.S323P	NM_017787.4	NP_060257.4	Q9NX94	WBP1L_HUMAN	WW domain binding protein 1-like	302			S -> P (in dbSNP:rs284860). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)											CCTCTGTCAGTCCTCTGAGGA	0.632													c|||	2721	0.543331	0.5212	0.5764	5008	,	,		14099	0.3988		0.5954	False		,,,				2504	0.6452				p.S323P		Atlas-SNP	.											.	.	.	.	0			c.T967C						PASS	.	C	PRO/SER,PRO/SER	2379,2027	541.9+/-375.9	655,1069,479	43.0	49.0	47.0		967,904	5.0	1.0	10	dbSNP_79	47	5071,3529	499.4+/-375.0	1491,2089,720	yes	missense,missense	C10orf26	NM_001083913.1,NM_017787.4	74,74	2146,3158,1199	CC,CT,TT		41.0349,46.0054,42.7187	benign,benign	323/364,302/343	104572963	7450,5556	2203	4300	6503	SO:0001583	missense	54838	exon4			TGTCAGTCCTCTG	AK056285	CCDS7540.1, CCDS44473.1	10q24.33	2012-05-02	2012-05-02	2012-05-02	ENSG00000166272	ENSG00000166272			23510	protein-coding gene	gene with protein product	"""outcome predictor in acute leukemia 1"""	611129	"""chromosome 10 open reading frame 26"""	C10orf26			Standard	NM_017787		Approved	FLJ20154, OPAL1	uc001kwf.4	Q9NX94	OTTHUMG00000018968	ENST00000369889.4:c.904T>C	10.37:g.104572963T>C	ENSP00000358905:p.Ser302Pro	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_001083913	B3KPF4|B7Z6S7|D3DR90|Q1EG70|Q2HIY7|Q5F2G6	Missense_Mutation	SNP	ENST00000369889.4	37	CCDS7540.1	1196	0.5476190476190477	277	0.5630081300813008	221	0.6104972375690608	247	0.4318181818181818	451	0.5949868073878628	c	3.293	-0.144511	0.06627	0.539946	0.589651	ENSG00000166272	ENST00000448841;ENST00000369889	T;T	0.31247	1.5;1.5	5.93	5.02	0.67125	.	0.517262	0.23228	N	0.050492	T	0.00012	0.0000	N	0.02539	-0.55	0.43574	P	0.004090999999999956	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39542	-0.9609	9	0.21540	T	0.41	-5.9084	8.4169	0.32676	0.0:0.6876:0.1623:0.1501	rs284860;rs3740404;rs284860	323;302	Q9NX94-2;Q9NX94	.;OPA1L_HUMAN	P	323;302	ENSP00000414721:S323P;ENSP00000358905:S302P	ENSP00000358905:S302P	S	+	1	0	C10orf26	104562953	0.068000	0.21057	1.000000	0.80357	0.908000	0.53690	0.607000	0.24209	0.848000	0.35191	-0.224000	0.12420	TCC	T|0.431;G|0.002	.	strong		0.632	WBP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050100.1	NM_017787	
SUPT3H	8464	hgsc.bcm.edu	37	6	44982593	44982593	+	Silent	SNP	G	G	A	rs12528232	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44982593G>A	ENST00000371459.1	-	5	474	c.309C>T	c.(307-309)atC>atT	p.I103I	SUPT3H_ENST00000306867.5_Silent_p.I103I|SUPT3H_ENST00000371460.1_Silent_p.I114I|SUPT3H_ENST00000371461.2_Silent_p.I114I	NM_001261823.1|NM_003599.3	NP_001248752.1|NP_003590.1	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog (S. cerevisiae)	185					chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	transcription coactivator activity (GO:0003713)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	12						TGTAGTCTCGGATAAACATGT	0.284													G|||	714	0.142572	0.0242	0.255	5008	,	,		15397	0.252		0.1282	False		,,,				2504	0.1247				p.I114I		Atlas-SNP	.											.	SUPT3H	75	.	0			c.C342T						PASS	.	G	,	198,4206	119.2+/-156.9	7,184,2011	131.0	109.0	117.0		309,342	3.1	1.0	6	dbSNP_120	117	1130,7468	227.2+/-262.7	74,982,3243	no	coding-synonymous,coding-synonymous	SUPT3H	NM_003599.2,NM_181356.1	,	81,1166,5254	AA,AG,GG		13.1426,4.4959,10.2138	,	103/318,114/329	44982593	1328,11674	2202	4299	6501	SO:0001819	synonymous_variant	8464	exon7			GTCTCGGATAAAC	AF069734	CCDS34465.1, CCDS34466.1, CCDS75464.1	6p21.1-p12.3	2008-05-15	2001-11-28		ENSG00000196284	ENSG00000196284			11466	protein-coding gene	gene with protein product		602947	"""suppressor of Ty (S.cerevisiae) 3 homolog"""			9674425, 9726987	Standard	NM_003599		Approved	SPT3, SPT3L	uc003oxp.4	O75486	OTTHUMG00000014773	ENST00000371459.1:c.309C>T	6.37:g.44982593G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	181	106	0.585635	NM_181356	A6NKG9|B2R9Q5|O76066|Q5TAV9|Q86VN7	Silent	SNP	ENST00000371459.1	37	CCDS34465.1																																																																																			G|0.873;A|0.127	0.127	strong		0.284	SUPT3H-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106911.2	NM_181356	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240729	39240729	+	Missense_Mutation	SNP	A	A	G	rs200532954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39240729A>G	ENST00000391417.4	+	1	271	c.271A>G	c.(271-273)Atg>Gtg	p.M91V		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	116	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						cagctgctgtatgtccagctg	0.677													g|||	366	0.0730831	0.0272	0.0663	5008	,	,		17277	0.1012		0.1431	False		,,,				2504	0.0389				p.M91V		Atlas-SNP	.											KRTAP4-9_ENST00000377734,bladder,carcinoma,0,4	KRTAP4-7	49	4	0			c.A271G						scavenged	.						11.0	17.0	15.0					17																	39240729		684	1582	2266	SO:0001583	missense	100132476	exon1			TGCTGTATGTCCA	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.271A>G	17.37:g.39240729A>G	ENSP00000375236:p.Met91Val	Somatic	112	5	0.0446429		WXS	Illumina HiSeq	Phase_I	115	33	0.286957	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.030	-1.342089	0.01277	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00567	6.54	3.74	-2.07	0.07276	.	5.393590	0.01146	N	0.006314	T	0.00300	0.0009	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46679	-0.9174	9	0.05959	T	0.93	.	9.7653	0.40557	0.3807:0.0:0.6193:0.0	.	91	Q9BYR0	KRA47_HUMAN	V	91;82	ENSP00000375236:M91V	ENSP00000375236:M91V	M	+	1	0	KRTAP4-9;KRTAP4-7	36494255	0.000000	0.05858	0.006000	0.13384	0.872000	0.50106	-4.081000	0.00299	-0.949000	0.03663	-0.374000	0.07098	ATG	.	.	weak		0.677	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
ZNF878	729747	hgsc.bcm.edu	37	19	12154799	12154799	+	Missense_Mutation	SNP	G	G	C	rs570415622|rs67102109	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12154799G>C	ENST00000547628.1	-	4	1554	c.1417C>G	c.(1417-1419)Cac>Gac	p.H473D	CTD-2006C1.2_ENST00000591838.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA|ZNF878_ENST00000602107.1_Missense_Mutation_p.H520D|CTD-2006C1.2_ENST00000591898.1_RNA|CTD-2006C1.10_ENST00000547473.1_Intron	NM_001080404.2	NP_001073873.2	C9JN71	ZN878_HUMAN	zinc finger protein 878	473					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						TCTCCAGTGTGAGTCCTTTTA	0.393													G|||	350	0.0698882	0.0688	0.0677	5008	,	,		22077	0.0595		0.0765	False		,,,				2504	0.0767				p.H473D		Atlas-SNP	.											.	ZNF878	172	.	0			c.C1417G						PASS	.	G	ASP/HIS	284,4094	140.8+/-176.2	8,268,1913	53.0	60.0	58.0		1417	1.3	0.0	19	dbSNP_130	58	624,7964	158.2+/-211.7	22,580,3692	yes	missense	ZNF878	NM_001080404.2	81	30,848,5605	CC,CG,GG		7.266,6.487,7.0029	probably-damaging	473/532	12154799	908,12058	2189	4294	6483	SO:0001583	missense	729747	exon4			CAGTGTGAGTCCT		CCDS45984.1, CCDS45984.2	19p13.2	2013-01-08				ENSG00000257446		"""Zinc fingers, C2H2-type"", ""-"""	37246	protein-coding gene	gene with protein product							Standard	NM_001080404		Approved		uc021upl.1	C9JN71		ENST00000547628.1:c.1417C>G	19.37:g.12154799G>C	ENSP00000447931:p.His473Asp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_001080404		Missense_Mutation	SNP	ENST00000547628.1	37	CCDS45984.2	153	0.07005494505494506	30	0.06097560975609756	26	0.0718232044198895	37	0.06468531468531469	60	0.079155672823219	G	19.58	3.854331	0.71719	0.06487	0.07266	ENSG00000257446;ENSG00000232371	ENST00000547628;ENST00000440730	T	0.67698	-0.28	1.3	1.3	0.21679	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30039	0.0752	H	0.96777	3.88	0.26597	P	0.9730968	D	0.69078	0.997	D	0.68483	0.958	T	0.74783	-0.3548	8	0.87932	D	0	.	9.503	0.39028	0.0:0.0:1.0:0.0	.	473	C9JN71	ZN878_HUMAN	D	473;520	ENSP00000447931:H473D	ENSP00000447931:H473D	H	-	1	0	AC022415.4;ZNF878	12015799	1.000000	0.71417	0.016000	0.15963	0.904000	0.53231	4.594000	0.61041	0.675000	0.31264	0.313000	0.20887	CAC	G|0.927;C|0.073	0.073	strong		0.393	ZNF878-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403723.1	NM_001080404	
STAG3	10734	hgsc.bcm.edu	37	7	99778285	99778285	+	Missense_Mutation	SNP	A	A	C	rs2272343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99778285A>C	ENST00000426455.1	+	2	513	c.106A>C	c.(106-108)Acc>Ccc	p.T36P	STAG3_ENST00000394018.2_Missense_Mutation_p.T36P|STAG3_ENST00000317296.5_Missense_Mutation_p.T36P	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	36					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)		p.T36P(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTCAAACCATACCTCAGAGGG	0.517													A|||	530	0.105831	0.0295	0.1081	5008	,	,		20339	0.0595		0.2296	False		,,,				2504	0.1278				p.T36P		Atlas-SNP	.											STAG3,NS,carcinoma,0,1	STAG3	121	1	1	Substitution - Missense(1)	stomach(1)	c.A106C						PASS	.	A	PRO/THR	309,4097	164.7+/-196.3	11,287,1905	139.0	123.0	128.0		106	-4.8	0.0	7	dbSNP_100	128	2016,6584	350.0+/-327.7	235,1546,2519	yes	missense	STAG3	NM_012447.2	38	246,1833,4424	CC,CA,AA		23.4419,7.0132,17.8764	benign	36/1226	99778285	2325,10681	2203	4300	6503	SO:0001583	missense	10734	exon2			AACCATACCTCAG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.106A>C	7.37:g.99778285A>C	ENSP00000400359:p.Thr36Pro	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	264	0.12087912087912088	19	0.03861788617886179	34	0.09392265193370165	32	0.055944055944055944	179	0.23614775725593667	A	13.78	2.339174	0.41398	0.070132	0.234419	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000416412;ENST00000339784;ENST00000317296;ENST00000422690;ENST00000439782	T;T;T	0.26660	1.9;1.72;1.9	4.56	-4.79	0.03200	.	2.141280	0.02215	N	0.063490	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	P;B	0.37864	0.61;0.0	B;B	0.26517	0.07;0.0	T	0.19844	-1.0293	9	0.30854	T	0.27	0.7833	12.7389	0.57239	0.3537:0.0:0.6463:0.0	rs2272343;rs11536559	36;36	B4DZ10;Q9UJ98	.;STAG3_HUMAN	P	36	ENSP00000400359:T36P;ENSP00000377586:T36P;ENSP00000319318:T36P	ENSP00000319318:T36P	T	+	1	0	STAG3	99616221	0.000000	0.05858	0.000000	0.03702	0.309000	0.27889	-1.170000	0.03118	-0.790000	0.04492	0.260000	0.18958	ACC	A|0.837;C|0.163	0.163	strong		0.517	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
PECR	55825	hgsc.bcm.edu	37	2	216908679	216908679	+	Silent	SNP	C	C	T	rs2303842	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:216908679C>T	ENST00000265322.7	-	7	848	c.774G>A	c.(772-774)tcG>tcA	p.S258S		NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	258					fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)	p.S258S(1)		endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	CCACATCCACCGACTGTCCAG	0.502													C|||	703	0.140375	0.0431	0.1455	5008	,	,		18933	0.12		0.2346	False		,,,				2504	0.1922				p.S258S		Atlas-SNP	.											PECR,NS,carcinoma,0,1	PECR	22	1	1	Substitution - coding silent(1)	stomach(1)	c.G774A						PASS	.	C		347,4059	180.5+/-208.7	13,321,1869	71.0	65.0	67.0		774	2.7	0.9	2	dbSNP_100	67	2150,6450	367.0+/-334.5	292,1566,2442	no	coding-synonymous	PECR	NM_018441.5		305,1887,4311	TT,TC,CC		25.0,7.8756,19.1988		258/304	216908679	2497,10509	2203	4300	6503	SO:0001819	synonymous_variant	55825	exon7			ATCCACCGACTGT	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18281	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 29C, member 1"""	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.774G>A	2.37:g.216908679C>T		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	222	112	0.504505	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Silent	SNP	ENST00000265322.7	37	CCDS33375.1																																																																																			C|0.838;T|0.161	0.161	strong		0.502	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441	
OR4A16	81327	hgsc.bcm.edu	37	11	55111238	55111238	+	Missense_Mutation	SNP	C	C	A	rs11229158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55111238C>A	ENST00000314721.2	+	1	612	c.562C>A	c.(562-564)Ctt>Att	p.L188I		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	188			L -> I (in dbSNP:rs11229158).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						ACTGTTGTGCCTTGACACCTA	0.423													.|||	2076	0.414537	0.1853	0.5548	5008	,	,		21969	0.5387		0.494	False		,,,				2504	0.4151				p.L188I		Atlas-SNP	.											.	OR4A16	120	.	0			c.C562A						PASS	.	C	ILE/LEU	1018,3384	727.8+/-409.9	129,760,1312	275.0	238.0	251.0		562	-0.1	0.9	11	dbSNP_120	251	4181,4411	584.7+/-391.8	1030,2121,1145	yes	missense	OR4A16	NM_001005274.1	5	1159,2881,2457	AA,AC,CC		48.6615,23.1259,40.0108	benign	188/329	55111238	5199,7795	2201	4296	6497	SO:0001583	missense	81327	exon1			TTGTGCCTTGACA	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"""GPCR / Class A : Olfactory receptors"""	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.562C>A	11.37:g.55111238C>A	ENSP00000325128:p.Leu188Ile	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	238	113	0.47479	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	967	0.44276556776556775	69	0.1402439024390244	207	0.5718232044198895	307	0.5367132867132867	384	0.5065963060686016	a	2.096	-0.407234	0.04832	0.231259	0.486615	ENSG00000181961	ENST00000314721	T	0.00123	8.7	2.54	-0.125	0.13519	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.02213	-0.635	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31336	-0.9947	8	0.51188	T	0.08	.	3.4202	0.07391	0.3926:0.2067:0.0:0.4006	rs11229158;rs11229158	188	Q8NH70	O4A16_HUMAN	I	188	ENSP00000325128:L188I	ENSP00000325128:L188I	L	+	1	0	OR4A16	54867814	0.000000	0.05858	0.895000	0.35142	0.006000	0.05464	-1.795000	0.01752	-0.174000	0.10743	-1.224000	0.01588	CTT	C|0.584;A|0.416	0.416	strong		0.423	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274	
TRIO	7204	hgsc.bcm.edu	37	5	14368975	14368975	+	Silent	SNP	C	C	T	rs13189406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:14368975C>T	ENST00000344204.4	+	17	3057	c.3033C>T	c.(3031-3033)aaC>aaT	p.N1011N	TRIO_ENST00000509967.2_Silent_p.N962N|TRIO_ENST00000537187.1_Silent_p.N1011N	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1011					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					AGCTCGTCAACGCCTCTGTCG	0.507													C|||	884	0.176518	0.0794	0.2334	5008	,	,		21946	0.0615		0.2763	False		,,,				2504	0.2832				p.N1011N		Atlas-SNP	.											.	TRIO	305	.	0			c.C3033T						PASS	.	C		481,3925	227.5+/-242.7	26,429,1748	151.0	133.0	139.0		3033	-10.2	0.1	5	dbSNP_121	139	2533,6067	414.1+/-351.3	391,1751,2158	no	coding-synonymous	TRIO	NM_007118.2		417,2180,3906	TT,TC,CC		29.4535,10.9169,23.1739		1011/3098	14368975	3014,9992	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon17			CGTCAACGCCTCT	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.3033C>T	5.37:g.14368975C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	210	73	0.347619	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			C|0.797;T|0.203	0.203	strong		0.507	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
SYNE1	23345	hgsc.bcm.edu	37	6	152510429	152510429	+	Silent	SNP	G	G	A	rs139590550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152510429G>A	ENST00000367255.5	-	128	23860	c.23259C>T	c.(23257-23259)cgC>cgT	p.R7753R	SYNE1_ENST00000265368.4_Silent_p.R7753R|SYNE1_ENST00000341594.5_Silent_p.R7365R|SYNE1_ENST00000448038.1_Silent_p.R7682R|SYNE1_ENST00000423061.1_Silent_p.R7682R|SYNE1_ENST00000356820.4_Silent_p.R2277R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7753					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAAGCTCTACGCGTTCATTAA	0.438										HNSCC(10;0.0054)			G|||	6	0.00119808	0.0008	0.0043	5008	,	,		13873	0.0		0.002	False		,,,				2504	0.0				p.R7753R		Atlas-SNP	.											SYNE1_ENST00000423061,caecum,carcinoma,0,7	SYNE1	3227	7	0			c.C23259T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	147.0	138.0	141.0		23046,23259	4.2	0.8	6	dbSNP_134	141	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	0,21,6482	AA,AG,GG		0.2326,0.0227,0.1615	,	7682/8750,7753/8798	152510429	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon128			CTCTACGCGTTCA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.23259C>T	6.37:g.152510429G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			G|0.998;A|0.002	0.002	strong		0.438	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
ALS2CL	259173	hgsc.bcm.edu	37	3	46729757	46729757	+	Missense_Mutation	SNP	C	C	G	rs7642448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46729757C>G	ENST00000318962.4	-	3	216	c.133G>C	c.(133-135)Gag>Cag	p.E45Q	ALS2CL_ENST00000415953.1_Missense_Mutation_p.E45Q	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	45			E -> Q (in dbSNP:rs7642448). {ECO:0000269|PubMed:17974005}.		endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CGCAGGCACTCTCTGCCCCAG	0.617													C|||	2246	0.448482	0.736	0.3991	5008	,	,		20682	0.3046		0.3161	False		,,,				2504	0.3793				p.E45Q		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G133C						PASS	.	C	GLN/GLU,GLN/GLU	2839,1567	657.0+/-400.2	921,997,285	36.0	37.0	37.0		133,133	4.4	0.6	3	dbSNP_116	37	2641,5959	418.8+/-352.9	400,1841,2059	yes	missense,missense	ALS2CL	NM_001190707.1,NM_147129.3	29,29	1321,2838,2344	GG,GC,CC		30.7093,35.5651,42.1344	possibly-damaging,possibly-damaging	45/954,45/954	46729757	5480,7526	2203	4300	6503	SO:0001583	missense	259173	exon3			GGCACTCTCTGCC	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.133G>C	3.37:g.46729757C>G	ENSP00000313670:p.Glu45Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	875	0.40064102564102566	337	0.6849593495934959	146	0.40331491712707185	159	0.27797202797202797	233	0.3073878627968338	C	11.66	1.703594	0.30232	0.644349	0.307093	ENSG00000178038	ENST00000318962;ENST00000415953	T;T	0.56275	0.47;0.47	4.36	4.36	0.52297	.	0.111814	0.39407	N	0.001379	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.9999999999980187	D	0.60575	0.988	P	0.52109	0.69	T	0.40739	-0.9547	9	0.39692	T	0.17	.	12.5671	0.56316	0.0:1.0:0.0:0.0	rs7642448;rs59127538;rs7642448	45	Q60I27	AL2CL_HUMAN	Q	45	ENSP00000313670:E45Q;ENSP00000413223:E45Q	ENSP00000313670:E45Q	E	-	1	0	ALS2CL	46704761	0.845000	0.29573	0.643000	0.29450	0.182000	0.23217	3.504000	0.53347	2.413000	0.81919	0.591000	0.81541	GAG	C|0.587;G|0.413	0.413	strong		0.617	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
CPZ	8532	hgsc.bcm.edu	37	4	8594616	8594616	+	Missense_Mutation	SNP	G	G	C	rs79736750	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:8594616G>C	ENST00000360986.4	+	1	230	c.56G>C	c.(55-57)cGg>cCg	p.R19P	CPZ_ENST00000315782.6_Missense_Mutation_p.R19P|CPZ_ENST00000382480.2_5'UTR|CPZ_ENST00000506287.1_3'UTR	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	19					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GCCGCTGCCCGGCCGGGGTGC	0.716													G|||	487	0.0972444	0.0227	0.0807	5008	,	,		9050	0.0476		0.162	False		,,,				2504	0.1943				p.R19P		Atlas-SNP	.											.	CPZ	95	.	0			c.G56C						PASS	.	G	PRO/ARG,,PRO/ARG	147,3233		8,131,1551	2.0	3.0	3.0		56,,56	0.8	0.0	4	dbSNP_131	3	1040,6070		84,872,2599	no	missense,utr-5,missense	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	103,,103	92,1003,4150	CC,CG,GG		14.6273,4.3491,11.3155	possibly-damaging,,possibly-damaging	19/653,,19/642	8594616	1187,9303	1690	3555	5245	SO:0001583	missense	8532	exon1			CTGCCCGGCCGGG	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"""metallocarboxypeptidase Z"""	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.56G>C	4.37:g.8594616G>C	ENSP00000354255:p.Arg19Pro	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_003652	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	196	0.08974358974358974	20	0.04065040650406504	32	0.08839779005524862	21	0.03671328671328671	123	0.16226912928759896	G	9.624	1.134623	0.21123	0.043491	0.146273	ENSG00000109625	ENST00000360986;ENST00000315782	T;T	0.58210	0.68;0.35	1.74	0.828	0.18841	.	14.553000	0.00559	N	0.000270	T	0.00300	0.0009	N	0.19112	0.55	0.58432	P	2.9999999999752447E-6	D;P	0.64830	0.994;0.931	D;B	0.65233	0.933;0.084	T	0.08827	-1.0703	9	0.34782	T	0.22	.	4.5504	0.12108	0.2087:0.0:0.7913:0.0	.	19;19	Q66K79-2;Q66K79	.;CBPZ_HUMAN	P	19	ENSP00000354255:R19P;ENSP00000315074:R19P	ENSP00000315074:R19P	R	+	2	0	CPZ	8645516	0.015000	0.18098	0.001000	0.08648	0.102000	0.19082	0.349000	0.20055	0.272000	0.22027	0.298000	0.19748	CGG	G|0.910;C|0.090	0.090	strong		0.716	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
KRT74	121391	hgsc.bcm.edu	37	12	52966368	52966368	+	Silent	SNP	C	C	T	rs78832381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52966368C>T	ENST00000305620.2	-	2	602	c.555G>A	c.(553-555)aaG>aaA	p.K185K	KRT74_ENST00000549343.1_Silent_p.K185K	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	185	Linker 1.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)			kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		GCTCCAGGTTCTTCTTGCAGT	0.562													C|||	79	0.0157748	0.003	0.0389	5008	,	,		20869	0.0		0.0398	False		,,,				2504	0.0082				p.K185K		Atlas-SNP	.											.	KRT74	67	.	0			c.G555A						PASS	.	C		42,4364	46.0+/-80.4	1,40,2162	151.0	139.0	143.0		555	-3.5	0.8	12	dbSNP_132	143	310,8290	111.4+/-171.7	7,296,3997	no	coding-synonymous	KRT74	NM_175053.3		8,336,6159	TT,TC,CC		3.6047,0.9532,2.7064		185/530	52966368	352,12654	2203	4300	6503	SO:0001819	synonymous_variant	121391	exon2			CAGGTTCTTCTTG	BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.555G>A	12.37:g.52966368C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	270	116	0.42963	NM_175053	B5MD61|Q86Y45	Silent	SNP	ENST00000305620.2	37	CCDS8832.1																																																																																			C|0.974;T|0.026	0.026	strong		0.562	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053	
ATAD5	79915	hgsc.bcm.edu	37	17	29214387	29214387	+	Missense_Mutation	SNP	T	T	C	rs11657270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29214387T>C	ENST00000321990.4	+	19	4633	c.4255T>C	c.(4255-4257)Tat>Cat	p.Y1419H		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1419			Y -> H (in dbSNP:rs11657270).		cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				ATTAACCCTTTATCGTAAGTT	0.368													T|||	723	0.144369	0.0719	0.1859	5008	,	,		18356	0.1359		0.1074	False		,,,				2504	0.2597				p.Y1419H		Atlas-SNP	.											.	ATAD5	150	.	0			c.T4255C						PASS	.	T	HIS/TYR	323,4083	166.2+/-197.5	14,295,1894	77.0	82.0	80.0		4255	2.0	0.8	17	dbSNP_120	80	898,7702	196.8+/-241.6	37,824,3439	yes	missense	ATAD5	NM_024857.3	83	51,1119,5333	CC,CT,TT		10.4419,7.3309,9.388	benign	1419/1845	29214387	1221,11785	2203	4300	6503	SO:0001583	missense	79915	exon19			ACCCTTTATCGTA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4255T>C	17.37:g.29214387T>C	ENSP00000313171:p.Tyr1419His	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	274	0.12545787545787546	45	0.09146341463414634	65	0.17955801104972377	92	0.16083916083916083	72	0.09498680738786279	T	2.914	-0.224752	0.06022	0.073309	0.104419	ENSG00000176208	ENST00000321990	T	0.16597	2.33	5.77	1.95	0.26073	.	0.817337	0.12029	N	0.506113	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44298	-0.9337	9	0.14656	T	0.56	.	8.7899	0.34843	0.0:0.323:0.0:0.677	rs11657270;rs11657270	1419	Q96QE3	ATAD5_HUMAN	H	1419	ENSP00000313171:Y1419H	ENSP00000313171:Y1419H	Y	+	1	0	ATAD5	26238513	0.108000	0.22018	0.774000	0.31636	0.600000	0.36913	0.445000	0.21677	0.425000	0.26087	-1.111000	0.02071	TAT	T|0.887;C|0.113	0.113	strong		0.368	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
ANGPTL2	23452	hgsc.bcm.edu	37	9	129854199	129854199	+	Silent	SNP	G	G	A	rs2297866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:129854199G>A	ENST00000373425.3	-	4	1649	c.1032C>T	c.(1030-1032)gaC>gaT	p.D344D	RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000424082.2_Intron|RALGPS1_ENST00000259351.5_Intron|RALGPS1_ENST00000394022.3_Intron|ANGPTL2_ENST00000373417.1_Silent_p.D42D	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	344	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						AGTATTCGCCGTCAATGTTCC	0.567													G|||	1455	0.290535	0.1127	0.3429	5008	,	,		19768	0.2966		0.4761	False		,,,				2504	0.2965				p.D344D		Atlas-SNP	.											.	ANGPTL2	46	.	0			c.C1032T						PASS	.	G	,,,,	738,3668	304.1+/-288.3	61,616,1526	201.0	193.0	196.0		,,,1032,	-10.2	0.2	9	dbSNP_100	196	3969,4631	551.7+/-386.0	929,2111,1260	no	intron,intron,intron,coding-synonymous,intron	RALGPS1,ANGPTL2	NM_001190728.1,NM_001190729.1,NM_001190730.1,NM_012098.2,NM_014636.2	,,,,	990,2727,2786	AA,AG,GG		46.1512,16.7499,36.191	,,,,	,,,344/494,	129854199	4707,8299	2203	4300	6503	SO:0001819	synonymous_variant	23452	exon4			TTCGCCGTCAATG	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"""Fibrinogen C domain containing"""	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.1032C>T	9.37:g.129854199G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	217	110	0.506912	NM_012098	Q5JT58|Q8NCH7	Silent	SNP	ENST00000373425.3	37	CCDS6868.1																																																																																			G|0.672;A|0.328	0.328	strong		0.567	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098	
SEC16B	89866	hgsc.bcm.edu	37	1	177902753	177902753	+	Missense_Mutation	SNP	G	G	C	rs591120	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177902753G>C	ENST00000308284.6	-	21	2679	c.2590C>G	c.(2590-2592)Cca>Gca	p.P864A	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	864			P -> A (in dbSNP:rs591120). {ECO:0000269|PubMed:17974005}.		COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						ATACTTCGTGGTCTAGCAGCC	0.468													C|||	2048	0.408946	0.4644	0.4409	5008	,	,		20099	0.2808		0.4463	False		,,,				2504	0.4049				p.P864A		Atlas-SNP	.											.	SEC16B	92	.	0			c.C2590G						PASS	.	C	ALA/PRO	1777,2067		402,973,547	56.0	57.0	57.0		2590	2.7	0.0	1	dbSNP_83	57	3541,4735		771,1999,1368	yes	missense	SEC16B	NM_033127.2	27	1173,2972,1915	CC,CG,GG		42.7864,46.2279,43.8779	benign	864/1061	177902753	5318,6802	1922	4138	6060	SO:0001583	missense	89866	exon21			TTCGTGGTCTAGC	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2590C>G	1.37:g.177902753G>C	ENSP00000308339:p.Pro864Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	899	0.4116300366300366	215	0.4369918699186992	144	0.39779005524861877	199	0.3479020979020979	341	0.449868073878628	C	7.408	0.634161	0.14322	0.462279	0.427864	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.12039	2.72	5.65	2.73	0.32206	.	0.628825	0.15398	N	0.264476	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43196	-0.9406	9	0.06236	T	0.91	0.5442	4.338	0.11095	0.1591:0.4825:0.2788:0.0796	rs591120;rs3813650;rs17360447;rs52790094;rs591120	419;865;864	B1AM07;B1AM08;Q96JE7	.;.;SC16B_HUMAN	A	864;548;579	ENSP00000308339:P864A	ENSP00000239472:P579A	P	-	1	0	AL359075.1	176169376	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.320000	0.08028	0.052000	0.16007	-0.120000	0.15030	CCA	G|0.588;C|0.412	0.412	strong		0.468	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
MUC4	4585	hgsc.bcm.edu	37	3	195511556	195511556	+	Missense_Mutation	SNP	T	T	A	rs79961534		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195511556T>A	ENST00000463781.3	-	2	7354	c.6895A>T	c.(6895-6897)Aca>Tca	p.T2299S	MUC4_ENST00000475231.1_Missense_Mutation_p.T2299S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T2299S(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCGTGACCTGTGGATGCTGAG	0.587																																					p.T2299S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	stomach(2)	c.A6895T						scavenged	.						7.0	7.0	7.0					3																	195511556		545	1393	1938	SO:0001583	missense	4585	exon2			GACCTGTGGATGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6895A>T	3.37:g.195511556T>A	ENSP00000417498:p.Thr2299Ser	Somatic	146	2	0.0136986		WXS	Illumina HiSeq	Phase_I	203	67	0.330049	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	T	4.627	0.116607	0.08881	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.42900	0.96;1.12	.	.	.	.	0.395708	0.11245	U	0.584203	T	0.12433	0.0302	N	0.02539	-0.55	0.09310	N	1	B	0.33494	0.414	B	0.22386	0.039	T	0.13818	-1.0495	8	.	.	.	.	2.7352	0.05238	0.0:0.3911:0.0:0.6089	.	2299	E7ESK3	.	S	2299	ENSP00000417498:T2299S;ENSP00000420243:T2299S	.	T	-	1	0	MUC4	196995951	0.000000	0.05858	0.007000	0.13788	0.015000	0.08874	-0.430000	0.06973	0.408000	0.25621	0.055000	0.15244	ACA	T|0.996;A|0.004	0.004	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BTBD11	121551	hgsc.bcm.edu	37	12	108035903	108035903	+	Silent	SNP	T	T	C	rs9919712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:108035903T>C	ENST00000280758.5	+	14	3405	c.2877T>C	c.(2875-2877)gaT>gaC	p.D959D	BTBD11_ENST00000490090.2_Silent_p.D959D|BTBD11_ENST00000420571.2_Silent_p.D840D|BTBD11_ENST00000357167.4_Silent_p.D496D|BTBD11_ENST00000494235.2_Silent_p.D38D	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	959	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CGACAAATGATGGCACCTGCA	0.478													t|||	980	0.195687	0.3835	0.1383	5008	,	,		19176	0.003		0.1948	False		,,,				2504	0.182				p.D959D		Atlas-SNP	.											.	BTBD11	122	.	0			c.T2877C						PASS	.	T	,	1441,2965	468.1+/-355.0	215,1011,977	159.0	148.0	152.0		1488,2877	2.0	1.0	12	dbSNP_119	152	1624,6976	302.0+/-305.7	146,1332,2822	no	coding-synonymous,coding-synonymous	BTBD11	NM_001017523.1,NM_001018072.1	,	361,2343,3799	CC,CT,TT		18.8837,32.7054,23.566	,	496/642,959/1105	108035903	3065,9941	2203	4300	6503	SO:0001819	synonymous_variant	121551	exon14			AAATGATGGCACC	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2877T>C	12.37:g.108035903T>C		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	218	102	0.46789	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			T|0.779;C|0.221	0.221	strong		0.478	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557504	32557504	+	Missense_Mutation	SNP	G	G	A	rs17879020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32557504G>A	ENST00000360004.5	-	1	121	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	6					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CCTCCAGGGAGCTTCAGACAC	0.582										Multiple Myeloma(14;0.17)																											p.L6F		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C16T						PASS	.						77.0	91.0	86.0					6																	32557504		1511	2709	4220	SO:0001583	missense	3123	exon1			CAGGGAGCTTCAG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.16C>T	6.37:g.32557504G>A	ENSP00000353099:p.Leu6Phe	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	390	79	0.202564	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	4.787	0.146342	0.09134	.	.	ENSG00000196126	ENST00000360004	T	0.00281	8.32	4.51	-6.2	0.02072	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.35542	1.07	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.34453	-0.9828	9	0.07030	T	0.85	.	0.7046	0.00913	0.3901:0.1208:0.2505:0.2385	rs17879020;rs34518239	6	P01911	2B1F_HUMAN	F	6	ENSP00000353099:L6F	ENSP00000353099:L6F	L	-	1	0	HLA-DRB1	32665482	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.135000	0.10420	-0.923000	0.03785	-1.250000	0.01514	CTC	G|0.978;A|0.022	0.022	strong		0.582	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
HTRA1	5654	hgsc.bcm.edu	37	10	124268261	124268261	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124268261G>A	ENST00000368984.3	+	6	1223	c.1095G>A	c.(1093-1095)acG>acA	p.T365T		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	365	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|kidney(1)|large_intestine(8)|lung(7)	17		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				AGTTCCTCACGGAGTCCCATG	0.517																																					p.T365T		Atlas-SNP	.											HTRA1,colon,carcinoma,+2,2	HTRA1	40	2	0			c.G1095A						PASS	.						98.0	102.0	100.0					10																	124268261		2203	4300	6503	SO:0001819	synonymous_variant	5654	exon6			CCTCACGGAGTCC	AF097709	CCDS7630.1	10q26.3	2014-01-28	2005-08-18	2005-08-18	ENSG00000166033	ENSG00000166033		"""Serine peptidases / Serine peptidases"""	9476	protein-coding gene	gene with protein product		602194	"""protease, serine, 11 (IGF binding)"""	PRSS11		8977104	Standard	NM_002775		Approved	HtrA, IGFBP5-protease, ARMD7	uc001lgj.2	Q92743	OTTHUMG00000019186	ENST00000368984.3:c.1095G>A	10.37:g.124268261G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	11	0.171875	NM_002775	D3DRE4|Q9UNS5	Silent	SNP	ENST00000368984.3	37	CCDS7630.1																																																																																			.	.	none		0.517	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775	
OR12D3	81797	hgsc.bcm.edu	37	6	29342775	29342775	+	Missense_Mutation	SNP	G	G	A	rs3749971	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29342775G>A	ENST00000396806.3	-	1	293	c.290C>T	c.(289-291)aCc>aTc	p.T97I	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	97			T -> I (in dbSNP:rs3749971). {ECO:0000269|PubMed:14574404}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						GTGTAGCTGGGTGATACAGCC	0.468													G|||	155	0.0309505	0.0106	0.0288	5008	,	,		20049	0.0327		0.0746	False		,,,				2504	0.0133				p.T97I		Atlas-SNP	.											OR12D3,NS,carcinoma,0,3	OR12D3	55	3	0			c.C290T						PASS	.	G	ILE/THR	71,2949		1,69,1440	57.0	60.0	59.0		290	2.3	0.8	6	dbSNP_107	59	515,4901		28,459,2221	yes	missense	OR12D3	NM_030959.2	89	29,528,3661	AA,AG,GG		9.5089,2.351,6.9464	benign	97/317	29342775	586,7850	1510	2708	4218	SO:0001583	missense	81797	exon1			AGCTGGGTGATAC		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"""GPCR / Class A : Olfactory receptors"""	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.290C>T	6.37:g.29342775G>A	ENSP00000380023:p.Thr97Ile	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	131	68	0.519084	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	96	0.04395604395604396	8	0.016260162601626018	9	0.024861878453038673	18	0.03146853146853147	61	0.08047493403693931	G	2.381	-0.342065	0.05243	0.02351	0.095089	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.01240	5.12	4.18	2.32	0.28847	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00608	0.0020	L	0.35723	1.085	0.80722	P	0.0	B	0.17465	0.022	B	0.18561	0.022	T	0.41752	-0.9491	8	0.38643	T	0.18	-4.3866	9.8495	0.41048	0.1766:0.0:0.8234:0.0	rs3749971;rs17346008;rs58992854;rs3749971	97	Q9UGF7	O12D3_HUMAN	I	97	ENSP00000380023:T97I	ENSP00000366348:T97I	T	-	2	0	OR12D3	29450754	0.000000	0.05858	0.829000	0.32907	0.092000	0.18411	0.870000	0.28010	0.946000	0.37632	0.195000	0.17529	ACC	G|0.942;A|0.058	0.058	strong		0.468	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
NMS	129521	hgsc.bcm.edu	37	2	101086966	101086966	+	Missense_Mutation	SNP	C	C	T	rs13411940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:101086966C>T	ENST00000376865.1	+	1	23	c.16C>T	c.(16-18)Ccc>Tcc	p.P6S		NM_001011717.1	NP_001011717.1	Q5H8A3	NMS_HUMAN	neuromedin S	6			P -> S (in dbSNP:rs13411940).		neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)		p.P6S(1)		breast(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)	14						ACATCTTCGTCCCCAGTTCCC	0.542													C|||	1356	0.270767	0.2776	0.1931	5008	,	,		18141	0.3502		0.2048	False		,,,				2504	0.3027				p.P6S		Atlas-SNP	.											NMS,NS,carcinoma,0,1	NMS	26	1	1	Substitution - Missense(1)	stomach(1)	c.C16T						PASS	.	C	SER/PRO	1196,3210	417.6+/-338.0	164,868,1171	394.0	340.0	358.0		16	2.5	0.0	2	dbSNP_121	358	1896,6704	336.8+/-322.0	217,1462,2621	yes	missense	NMS	NM_001011717.1	74	381,2330,3792	TT,TC,CC		22.0465,27.1448,23.7736	benign	6/154	101086966	3092,9914	2203	4300	6503	SO:0001583	missense	129521	exon1			CTTCGTCCCCAGT	AB164464	CCDS33259.1	2q11.2	2013-02-26			ENSG00000204640	ENSG00000204640		"""Endogenous ligands"""	32203	protein-coding gene	gene with protein product	"""prepro-NMS"""					15635449	Standard	NM_001011717		Approved		uc002tan.1	Q5H8A3	OTTHUMG00000153142	ENST00000376865.1:c.16C>T	2.37:g.101086966C>T	ENSP00000366061:p.Pro6Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_001011717		Missense_Mutation	SNP	ENST00000376865.1	37	CCDS33259.1	578	0.26465201465201466	138	0.2804878048780488	79	0.21823204419889503	193	0.3374125874125874	168	0.22163588390501318	C	11.18	1.563248	0.27915	0.271448	0.220465	ENSG00000204640	ENST00000376865	T	0.50813	0.73	4.33	2.53	0.30540	.	0.194078	0.32287	N	0.006318	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B	0.32302	0.363	B	0.28916	0.096	T	0.28459	-1.0043	9	0.54805	T	0.06	-6.7097	5.9059	0.19001	0.0:0.6767:0.2141:0.1092	rs13411940;rs56567182;rs58703521;rs13411940	6	Q5H8A3	NMS_HUMAN	S	6	ENSP00000366061:P6S	ENSP00000366061:P6S	P	+	1	0	NMS	100453398	0.001000	0.12720	0.003000	0.11579	0.004000	0.04260	0.009000	0.13219	0.579000	0.29504	0.655000	0.94253	CCC	C|0.746;T|0.254	0.254	strong		0.542	NMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329737.1	NM_001011717	
MYO5A	4644	hgsc.bcm.edu	37	15	52689631	52689631	+	Missense_Mutation	SNP	T	T	G	rs1724577	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:52689631T>G	ENST00000399231.3	-	10	1329	c.1086A>C	c.(1084-1086)gaA>gaC	p.E362D	MYO5A_ENST00000358212.6_Missense_Mutation_p.E362D|MYO5A_ENST00000356338.6_Missense_Mutation_p.E362D|MYO5A_ENST00000553916.1_Missense_Mutation_p.E362D|MYO5A_ENST00000399233.2_Missense_Mutation_p.E362D	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	362	Myosin motor.			E -> D (in Ref. 1; CAA69035/CAA69036 and 2; AAD00702). {ECO:0000305}.	actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		CACCCATGAGTTCACAGAAGA	0.458													G|||	4441	0.886781	0.6657	0.9769	5008	,	,		19761	0.9802		0.996	False		,,,				2504	0.9131				p.E362D		Atlas-SNP	.											.	MYO5A	145	.	0			c.A1086C						PASS	.	G	ASP/GLU,ASP/GLU	2881,1071		1048,785,143	106.0	93.0	97.0		1086,1086	-4.7	0.8	15	dbSNP_89	97	8301,35		4133,35,0	yes	missense,missense	MYO5A	NM_000259.3,NM_001142495.1	45,45	5181,820,143	GG,GT,TT		0.4199,27.1002,9.0007	benign,benign	362/1856,362/1829	52689631	11182,1106	1976	4168	6144	SO:0001583	missense	4644	exon10			CATGAGTTCACAG		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.1086A>C	15.37:g.52689631T>G	ENSP00000382177:p.Glu362Asp	Somatic	201	2	0.00995025		WXS	Illumina HiSeq	Phase_I	189	189	1	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	1999	0.9152930402930403	336	0.6829268292682927	351	0.9696132596685083	557	0.9737762237762237	755	0.996042216358839	G	5.319	0.244194	0.10077	0.728998	0.995801	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000553916	D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32	5.4	-4.65	0.03339	Myosin head, motor domain (2);	0.181155	0.64402	N	0.000020	T	0.00012	0.0000	N	0.21282	0.65	0.47949	P	4.4200000000005346E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.44452	-0.9327	9	0.07644	T	0.81	.	1.9649	0.03393	0.3368:0.0899:0.3891:0.1842	rs1724577;rs16964968;rs52815767;rs1724577	362;362	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	D	362	ENSP00000382177:E362D;ENSP00000382179:E362D;ENSP00000348693:E362D;ENSP00000350945:E362D;ENSP00000451109:E362D	ENSP00000348693:E362D	E	-	3	2	MYO5A	50476923	0.675000	0.27558	0.838000	0.33150	0.414000	0.31173	-0.114000	0.10757	-1.087000	0.03081	-0.754000	0.03487	GAA	T|0.066;G|0.934	0.934	strong		0.458	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
VWA5B1	127731	hgsc.bcm.edu	37	1	20656824	20656824	+	Missense_Mutation	SNP	A	A	G	rs2072752	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20656824A>G	ENST00000375079.2	+	10	1602	c.1406A>G	c.(1405-1407)aAc>aGc	p.N469S	VWA5B1_ENST00000289825.4_Missense_Mutation_p.N186S|VWA5B1_ENST00000375083.4_Missense_Mutation_p.N469S|VWA5B1_ENST00000289815.8_Missense_Mutation_p.N469S	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	469	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		N -> S (in dbSNP:rs2072752).			extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GGCGCTGTCAACAACACAGGG	0.632													A|||	901	0.179912	0.0113	0.1859	5008	,	,		18624	0.3601		0.167	False		,,,				2504	0.2311				p.N469S		Atlas-SNP	.											VWA5B1,NS,carcinoma,0,1	VWA5B1	44	1	0			c.A1406G						PASS	.	A	SER/ASN	53,1331		0,53,639	66.0	66.0	66.0		1406	-8.4	0.1	1	dbSNP_96	66	564,2618		51,462,1078	yes	missense	VWA5B1	NM_001039500.2	46	51,515,1717	GG,GA,AA		17.7247,3.8295,13.5129	benign	469/1216	20656824	617,3949	692	1591	2283	SO:0001583	missense	127731	exon10			CTGTCAACAACAC	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.1406A>G	1.37:g.20656824A>G	ENSP00000364220:p.Asn469Ser	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	119	45	0.378151	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	37		451	0.2065018315018315	11	0.022357723577235773	72	0.19889502762430938	238	0.4160839160839161	130	0.17150395778364116	A	0.374	-0.932215	0.02359	0.038295	0.177247	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000289825;ENST00000375079	T;T;T;T	0.14893	2.47;2.47;2.47;2.47	5.08	-8.42	0.00957	von Willebrand factor, type A (3);	0.256100	0.44902	N	0.000413	T	0.00012	0.0000	N	0.00890	-1.11	0.36558	P	0.12775199999999998	B;B;B	0.10296	0.002;0.003;0.0	B;B;B	0.14023	0.01;0.003;0.004	T	0.29971	-0.9994	9	0.02654	T	1	-9.687	17.855	0.88760	0.1813:0.0:0.8187:0.0	rs2072752;rs60044721;rs2072752	469;469;186	Q5TIE3;Q5TIE3-2;Q5TIE3-3	VW5B1_HUMAN;.;.	S	469;469;469;186;469	ENSP00000289815:N469S;ENSP00000364224:N469S;ENSP00000289825:N186S;ENSP00000364220:N469S	ENSP00000289815:N469S	N	+	2	0	VWA5B1	20529411	1.000000	0.71417	0.058000	0.19502	0.249000	0.25844	1.507000	0.35758	-1.430000	0.01985	-1.098000	0.02139	AAC	A|0.806;G|0.194	0.194	strong		0.632	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
GAK	2580	hgsc.bcm.edu	37	4	843508	843508	+	Missense_Mutation	SNP	C	C	T	rs1134921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:843508C>T	ENST00000314167.4	-	28	3999	c.3889G>A	c.(3889-3891)Gac>Aac	p.D1297N	GAK_ENST00000511163.1_Missense_Mutation_p.D1218N|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1297	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.		D -> N (in dbSNP:rs1134921). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GACCAGGCGTCATTCAGCTCC	0.632													C|||	422	0.0842652	0.0053	0.1715	5008	,	,		14500	0.1319		0.1223	False		,,,				2504	0.0409				p.D1297N		Atlas-SNP	.											.	GAK	104	.	0			c.G3889A						PASS	.	C	ASN/ASP	111,4295	85.3+/-124.0	3,105,2095	59.0	56.0	57.0		3889	4.8	0.5	4	dbSNP_86	57	1112,7488	225.8+/-261.7	74,964,3262	yes	missense	GAK	NM_005255.2	23	77,1069,5357	TT,TC,CC		12.9302,2.5193,9.4034	probably-damaging	1297/1312	843508	1223,11783	2203	4300	6503	SO:0001583	missense	2580	exon28			AGGCGTCATTCAG	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3889G>A	4.37:g.843508C>T	ENSP00000314499:p.Asp1297Asn	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	180	77	0.427778	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	250|250	0.11446886446886446|0.11446886446886446	6|6	0.012195121951219513|0.012195121951219513	64|64	0.17679558011049723|0.17679558011049723	90|90	0.15734265734265734|0.15734265734265734	90|90	0.11873350923482849|0.11873350923482849	C|C	18.45|18.45	3.627461|3.627461	0.66901|0.66901	0.025193|0.025193	0.129302|0.129302	ENSG00000178950|ENSG00000178950	ENST00000398567;ENST00000314167;ENST00000511163|ENST00000511980	T;T|.	0.29655|.	1.56;1.56|.	4.76|4.76	4.76|4.76	0.60689|0.60689	Heat shock protein DnaJ, N-terminal (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00178|0.00178	0.0005|0.0005	L|L	0.38953|0.38953	1.18|1.18	0.09310|0.09310	P|P	0.99999999819712|0.99999999819712	D;D;D;D|.	0.89917|.	0.999;1.0;0.999;0.999|.	D;D;D;D|.	0.97110|.	1.0;0.999;1.0;1.0|.	T|T	0.03221|0.03221	-1.1059|-1.1059	9|4	0.42905|.	T|.	0.14|.	-36.0573|-36.0573	15.2715|15.2715	0.73705|0.73705	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs1134921;rs3087764;rs3197299;rs56708161;rs1134921|rs1134921;rs3087764;rs3197299;rs56708161;rs1134921	1199;1218;1297;1182|.	B4DS37;E9PGR2;O14976;Q59HA5|.	.;.;GAK_HUMAN;.|.	N|I	573;1297;1218|452	ENSP00000314499:D1297N;ENSP00000421361:D1218N|.	ENSP00000314499:D1297N|.	D|M	-|-	1|3	0|0	GAK|GAK	833508|833508	1.000000|1.000000	0.71417|0.71417	0.492000|0.492000	0.27490|0.27490	0.390000|0.390000	0.30446|0.30446	7.295000|7.295000	0.78780|0.78780	2.167000|2.167000	0.68274|0.68274	0.643000|0.643000	0.83706|0.83706	GAC|ATG	C|0.900;T|0.100	0.100	strong		0.632	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
ACTN2	88	hgsc.bcm.edu	37	1	236925844	236925844	+	Silent	SNP	G	G	A	rs12063382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:236925844G>A	ENST00000366578.4	+	21	2776	c.2610G>A	c.(2608-2610)tcG>tcA	p.S870S	ACTN2_ENST00000542672.1_Silent_p.S870S|ACTN2_ENST00000546208.1_Silent_p.S364S	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	870					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			CCGCCTACTCGGGCCCAGGCA	0.587													G|||	982	0.196086	0.2057	0.1729	5008	,	,		16949	0.2183		0.171	False		,,,				2504	0.2025				p.S870S		Atlas-SNP	.											.	ACTN2	191	.	0			c.G2610A						PASS	.	G		828,3578	327.7+/-300.2	87,654,1462	55.0	51.0	52.0		2610	-10.9	0.1	1	dbSNP_120	52	1197,7403	242.9+/-272.7	72,1053,3175	yes	coding-synonymous	ACTN2	NM_001103.2		159,1707,4637	AA,AG,GG		13.9186,18.7926,15.5697		870/895	236925844	2025,10981	2203	4300	6503	SO:0001819	synonymous_variant	88	exon21			CTACTCGGGCCCA	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"""EF-hand domain containing"""	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.2610G>A	1.37:g.236925844G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	185	74	0.4	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Silent	SNP	ENST00000366578.4	37	CCDS1613.1																																																																																			G|0.832;A|0.168	0.168	strong		0.587	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103	
CEP120	153241	hgsc.bcm.edu	37	5	122718736	122718736	+	Missense_Mutation	SNP	G	G	C	rs6595440	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:122718736G>C	ENST00000306467.5	-	12	2108	c.1804C>G	c.(1804-1806)Cta>Gta	p.L602V	CEP120_ENST00000328236.5_Missense_Mutation_p.L602V|CEP120_ENST00000306481.6_Missense_Mutation_p.L576V			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	602			L -> V (in dbSNP:rs6595440). {ECO:0000269|PubMed:14702039}.		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						TAATCTTCTAGAGTCACTGTG	0.254													G|||	2065	0.41234	0.2935	0.4078	5008	,	,		17690	0.506		0.4453	False		,,,				2504	0.4458				p.L602V		Atlas-SNP	.											.	CEP120	72	.	0			c.C1804G						PASS	.	G	VAL/LEU,VAL/LEU	1415,2985	427.0+/-341.4	238,939,1023	43.0	44.0	44.0		1726,1804	1.9	0.7	5	dbSNP_116	44	3666,4926	507.5+/-376.8	780,2106,1410	yes	missense,missense	CEP120	NM_001166226.1,NM_153223.3	32,32	1018,3045,2433	CC,CG,GG		42.6676,32.1591,39.1087	probably-damaging,probably-damaging	576/961,602/987	122718736	5081,7911	2200	4296	6496	SO:0001583	missense	153241	exon13			CTTCTAGAGTCAC	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.1804C>G	5.37:g.122718736G>C	ENSP00000303058:p.Leu602Val	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	189	189	1	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	37	CCDS4134.2	955	0.43727106227106227	149	0.30284552845528456	146	0.40331491712707185	295	0.5157342657342657	365	0.4815303430079156	G	16.01	3.001820	0.54254	0.321591	0.426676	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481;ENST00000508442	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.92	1.93	0.25924	.	0.080760	0.51477	N	0.000094	T	0.00012	0.0000	M	0.73962	2.25	0.09310	P	0.9999999999999104	D	0.89917	1.0	D	0.91635	0.999	T	0.47661	-0.9100	9	0.72032	D	0.01	-12.0814	6.9203	0.24385	0.2901:0.1153:0.5945:0.0	rs6595440;rs17474014;rs52804850;rs57437586;rs6595440	602	Q8N960	CE120_HUMAN	V	602;602;576;576	ENSP00000303058:L602V;ENSP00000327504:L602V;ENSP00000307419:L576V;ENSP00000421620:L576V	ENSP00000303058:L602V	L	-	1	2	CEP120	122746635	1.000000	0.71417	0.710000	0.30468	0.945000	0.59286	2.765000	0.47621	0.058000	0.16222	-0.142000	0.14014	CTA	G|0.598;C|0.402	0.402	strong		0.254	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149001551	149001551	+	Missense_Mutation	SNP	A	A	C	rs4629585	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:149001551A>C	ENST00000333677.6	+	9	1424	c.1261A>C	c.(1261-1263)Atg>Ctg	p.M421L		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	421	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.		M -> L (in dbSNP:rs4629585).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GGGCCAGATCATGTGCACATT	0.597													C|||	2188	0.436901	0.3797	0.4769	5008	,	,		20370	0.5		0.34	False		,,,				2504	0.5204				p.M421L		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.A1261C						PASS	.	C	LEU/MET	1617,2629		330,957,836	38.0	47.0	44.0		1261	4.1	1.0	5	dbSNP_111	44	3010,5458		529,1952,1753	yes	missense	ARHGEF37	NM_001001669.2	15	859,2909,2589	CC,CA,AA		35.5456,38.0829,36.393	benign	421/676	149001551	4627,8087	2123	4234	6357	SO:0001583	missense	389337	exon9			CAGATCATGTGCA	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1261A>C	5.37:g.149001551A>C	ENSP00000328083:p.Met421Leu	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	249	154	0.618474	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	891	0.40796703296703296	176	0.35772357723577236	151	0.4171270718232044	305	0.5332167832167832	259	0.341688654353562	C	0.062	-1.222824	0.01530	0.380829	0.355456	ENSG00000183111	ENST00000333677	T	0.47177	0.85	6.17	4.1	0.47936	BAR (2);	0.071421	0.56097	N	0.000024	T	0.00012	0.0000	N	0.00088	-2.19	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46775	-0.9167	9	0.02654	T	1	-1.3808	8.8224	0.35034	0.1207:0.6947:0.0:0.1846	rs4629585;rs52811837;rs57716052;rs4629585	421	A1IGU5	ARH37_HUMAN	L	421	ENSP00000328083:M421L	ENSP00000328083:M421L	M	+	1	0	ARHGEF37	148981744	0.017000	0.18338	1.000000	0.80357	0.242000	0.25591	0.122000	0.15687	0.956000	0.37904	-0.121000	0.15023	ATG	A|0.596;C|0.404	0.404	strong		0.597	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
CYYR1	116159	hgsc.bcm.edu	37	21	27852724	27852724	+	Silent	SNP	A	A	G	rs966410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:27852724A>G	ENST00000299340.4	-	3	544	c.201T>C	c.(199-201)gtT>gtC	p.V67V	AP001597.1_ENST00000357401.3_RNA|CYYR1_ENST00000435845.2_3'UTR|CYYR1_ENST00000400043.3_Silent_p.V67V|AP001597.1_ENST00000414486.1_RNA	NM_052954.2	NP_443186.1	Q96J86	CYYR1_HUMAN	cysteine/tyrosine-rich 1	67						integral component of membrane (GO:0016021)				large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	15						CTATTCCAAAAACAATGCCCG	0.443													A|||	2287	0.456669	0.6021	0.3444	5008	,	,		17962	0.3353		0.4483	False		,,,				2504	0.4734				p.V67V		Atlas-SNP	.											.	CYYR1	38	.	0			c.T201C						PASS	.	A		2463,1943	622.6+/-394.0	684,1095,424	121.0	110.0	114.0		201	0.2	1.0	21	dbSNP_86	114	3925,4675	548.1+/-385.3	882,2161,1257	no	coding-synonymous	CYYR1	NM_052954.2		1566,3256,1681	GG,GA,AA		45.6395,44.099,49.1158		67/155	27852724	6388,6618	2203	4300	6503	SO:0001819	synonymous_variant	116159	exon3			TCCAAAAACAATG	AY061853	CCDS13578.1	21q21.2	2014-07-04	2005-07-24		ENSG00000166265	ENSG00000166265			16274	protein-coding gene	gene with protein product			"""cysteine and tyrosine-rich 1"""	C21orf95		12036297, 12062809, 24981926	Standard	NM_052954		Approved		uc002ymd.3	Q96J86	OTTHUMG00000078689	ENST00000299340.4:c.201T>C	21.37:g.27852724A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_052954	A0A059TD09|A8MTU9|B2R845|Q53ER3|Q5JPD0|Q96NV7|R9QAJ4|W8CQB3	Silent	SNP	ENST00000299340.4	37	CCDS13578.1																																																																																			A|0.549;G|0.451	0.451	strong		0.443	CYYR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171654.2	NM_052954	
SLC22A25	387601	hgsc.bcm.edu	37	11	62951221	62951221	+	Missense_Mutation	SNP	C	C	G	rs11231397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62951221C>G	ENST00000306494.6	-	5	898	c.899G>C	c.(898-900)aGa>aCa	p.R300T	SLC22A25_ENST00000403374.2_Missense_Mutation_p.R134T|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						TGCAGCTTTTCTAAGTTCCTT	0.483													C|||	2105	0.420327	0.2617	0.4438	5008	,	,		21198	0.5317		0.3946	False		,,,				2504	0.5297				p.R300T		Atlas-SNP	.											.	SLC22A25	87	.	0			c.G899C						PASS	.	C	THR/ARG	1306,3096	439.8+/-345.8	175,956,1070	290.0	263.0	272.0		899	-3.9	0.4	11	dbSNP_120	272	3239,5355	487.8+/-372.2	637,1965,1695	yes	missense	SLC22A25	NM_199352.3	71	812,2921,2765	GG,GC,CC		37.6891,29.6683,34.9723	probably-damaging	300/548	62951221	4545,8451	2201	4297	6498	SO:0001583	missense	387601	exon5			GCTTTTCTAAGTT	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.899G>C	11.37:g.62951221C>G	ENSP00000307443:p.Arg300Thr	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	260	257	0.988462	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	875	0.40064102564102566	120	0.24390243902439024	135	0.3729281767955801	333	0.5821678321678322	287	0.3786279683377309	C	1.583	-0.531111	0.04112	0.296683	0.376891	ENSG00000196600	ENST00000306494;ENST00000403374	T;T	0.74526	0.27;-0.85	2.56	-3.87	0.04218	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.468291	0.22454	N	0.059854	T	0.00012	0.0000	M	0.88450	2.955	0.24720	P	0.99315045	D;D	0.67145	0.984;0.996	D;D	0.66497	0.925;0.944	T	0.44726	-0.9309	9	0.62326	D	0.03	.	3.2969	0.06969	0.1915:0.3105:0.0:0.498	rs11231397;rs52813421;rs11231397	298;300	A4IF29;Q6T423	.;S22AP_HUMAN	T	300;134	ENSP00000307443:R300T;ENSP00000384208:R134T	ENSP00000307443:R300T	R	-	2	0	SLC22A25	62707797	0.000000	0.05858	0.366000	0.25914	0.539000	0.34962	-0.657000	0.05335	-1.156000	0.02818	0.121000	0.15741	AGA	C|0.621;G|0.379	0.379	strong		0.483	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
HSDL2	84263	hgsc.bcm.edu	37	9	115167994	115167994	+	Missense_Mutation	SNP	A	A	T	rs41280175	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:115167994A>T	ENST00000398805.3	+	3	499	c.272A>T	c.(271-273)aAa>aTa	p.K91I	HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000398803.1_Missense_Mutation_p.K91I|HSDL2_ENST00000262542.7_5'UTR|HSDL2_ENST00000539114.1_5'UTR	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	91						membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						GCCATCAAGAAATTTGGAGGT	0.318													A|||	10	0.00199681	0.0008	0.0058	5008	,	,		16111	0.0		0.005	False		,,,				2504	0.0				p.K91I		Atlas-SNP	.											.	HSDL2	24	.	0			c.A272T						PASS	.	A	ILE/LYS,ILE/LYS	7,3743		0,7,1868	128.0	126.0	126.0		272,272	3.2	1.0	9	dbSNP_127	126	107,8109		1,105,4002	yes	missense,missense	HSDL2	NM_001195822.1,NM_032303.4	102,102	1,112,5870	TT,TA,AA		1.3023,0.1867,0.9527	benign,benign	91/346,91/419	115167994	114,11852	1875	4108	5983	SO:0001583	missense	84263	exon3			TCAAGAAATTTGG	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18572	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 13C, member 1"""		"""chromosome 9 open reading frame 99"""	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.272A>T	9.37:g.115167994A>T	ENSP00000381785:p.Lys91Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	46	32	0.695652	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	37	CCDS43864.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	A	12.14	1.848888	0.32699	0.001867	0.013023	ENSG00000119471	ENST00000398805;ENST00000398803	D;D	0.88431	-2.38;-2.38	5.57	3.15	0.36227	NAD(P)-binding domain (1);	0.456598	0.25677	N	0.029030	D	0.82296	0.5006	M	0.69823	2.125	0.80722	D	1	P;B	0.45902	0.868;0.064	B;B	0.42138	0.377;0.159	T	0.79027	-0.1971	10	0.39692	T	0.17	.	6.4508	0.21902	0.6281:0.2284:0.1434:0.0	rs41280175	91;91	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	I	91	ENSP00000381785:K91I;ENSP00000381783:K91I	ENSP00000381783:K91I	K	+	2	0	HSDL2	114207815	0.922000	0.31269	0.991000	0.47740	0.021000	0.10359	0.964000	0.29306	0.369000	0.24510	0.260000	0.18958	AAA	A|0.995;T|0.005	0.005	strong		0.318	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303	
TMEM259	91304	hgsc.bcm.edu	37	19	1014377	1014377	+	Silent	SNP	A	A	G	rs1058506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1014377A>G	ENST00000356663.3	-	2	442	c.321T>C	c.(319-321)cgT>cgC	p.R107R	TMEM259_ENST00000333175.5_Silent_p.R107R	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	107						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GGATGCCCTCACGCGGCCACT	0.652													a|||	955	0.190695	0.2315	0.121	5008	,	,		17000	0.1141		0.2028	False		,,,				2504	0.2515				p.R107R		Atlas-SNP	.											C19orf6,NS,carcinoma,-1,2	.	.	2	0			c.T321C						PASS	.	A	,	836,3568	316.9+/-294.8	72,692,1438	37.0	36.0	36.0		321,321	-8.4	0.1	19	dbSNP_86	36	1523,7075	281.3+/-295.0	146,1231,2922	no	coding-synonymous,coding-synonymous	C19orf6	NM_001033026.1,NM_033420.3	,	218,1923,4360	GG,GA,AA		17.7134,18.9827,18.1434	,	107/621,107/409	1014377	2359,10643	2202	4299	6501	SO:0001819	synonymous_variant	91304	exon2			GCCCTCACGCGGC	BC008957	CCDS12052.1, CCDS32862.1	19p13.3	2013-02-06	2013-02-06	2013-02-06	ENSG00000182087	ENSG00000182087			17039	protein-coding gene	gene with protein product	"""membralin"", ""aspecific BCL2 ARE-binding protein 1"""	611011	"""chromosome 19 open reading frame 6"""	C19orf6		12638133, 16084606	Standard	XM_005259675		Approved	MGC4022, ASBABP1, MBRL	uc002lqr.1	Q4ZIN3		ENST00000356663.3:c.321T>C	19.37:g.1014377A>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	187	63	0.336898	NM_033420	O60392|Q8NF79|Q96H30	Silent	SNP	ENST00000356663.3	37	CCDS32862.1																																																																																			A|0.821;G|0.179	0.179	strong		0.652	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20905250	20905250	+	Silent	SNP	C	C	T	rs6487138	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:20905250C>T	ENST00000266509.2	+	15	2295	c.1927C>T	c.(1927-1929)Ctg>Ttg	p.L643L	SLCO1C1_ENST00000545102.1_Missense_Mutation_p.S559F|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.S677F|SLCO1C1_ENST00000540354.1_Silent_p.L594L|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.S677F	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	643					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	ACATATATATCTGGGACTAAC	0.299													C|||	2351	0.469449	0.2012	0.5677	5008	,	,		17354	0.5923		0.495	False		,,,				2504	0.6094				p.S677F		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C2030T						PASS	.	C	PHE/SER,,PHE/SER,	1092,3312	370.3+/-319.5	138,816,1248	41.0	41.0	41.0		1676,1780,2030,1927	5.4	1.0	12	dbSNP_116	41	4649,3947	591.6+/-392.9	1248,2153,897	yes	missense,coding-synonymous,missense,coding-synonymous	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	155,,155,	1386,2969,2145	TT,TC,CC		45.9167,24.7956,44.1615	,,,	559/613,594/664,677/731,643/713	20905250	5741,7259	2202	4298	6500	SO:0001819	synonymous_variant	53919	exon16			ATATATCTGGGAC	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1927C>T	12.37:g.20905250C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	164	76	0.463415	NM_001145946	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	1046	0.47893772893772896	110	0.22357723577235772	192	0.5303867403314917	358	0.6258741258741258	386	0.5092348284960422	C	16.43	3.120305	0.56613	0.247956	0.540833	ENSG00000139155	ENST00000545604;ENST00000381552;ENST00000545102	T;T;T	0.39997	1.05;1.05;1.11	5.37	5.37	0.77165	.	2.483440	0.01020	N	0.003979	T	0.00012	0.0000	.	.	.	0.31879	P	0.618765	P;P	0.51537	0.946;0.91	P;P	0.55999	0.789;0.498	T	0.46275	-0.9203	8	0.59425	D	0.04	.	16.1483	0.81586	0.0:1.0:0.0:0.0	rs6487138	559;677	F5GZD6;Q5JPA4	.;.	F	677;677;559	ENSP00000444149:S677F;ENSP00000370964:S677F;ENSP00000444527:S559F	ENSP00000370964:S677F	S	+	2	0	SLCO1C1	20796517	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.654000	0.46699	2.797000	0.96272	0.655000	0.94253	TCT	C|0.547;T|0.453	0.453	strong		0.299	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
PRKAR1A	5573	hgsc.bcm.edu	37	17	66511627	66511627	+	Silent	SNP	G	G	A	rs281864787|rs3730349	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:66511627G>A	ENST00000589228.1	+	2	215	c.87G>A	c.(85-87)gcG>gcA	p.A29A	PRKAR1A_ENST00000358598.2_Silent_p.A29A|PRKAR1A_ENST00000536854.2_Silent_p.A29A|PRKAR1A_ENST00000588188.2_Silent_p.A29A|PRKAR1A_ENST00000392711.1_Silent_p.A29A|PRKAR1A_ENST00000586397.1_Silent_p.A29A	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	29	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					ACATTCAAGCGCTGCTCAAAG	0.507			"""T, Mis, N, F, S"""	RET	papillary thyroid	"""myxoma, endocrine, papillary thyroid"""			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of				A|||	39	0.00778754	0.0008	0.0058	5008	,	,		16720	0.0		0.0308	False		,,,				2504	0.0031				p.A29A	Ovarian(167;637 1670 33025 39608 46699 51856)	Atlas-SNP	.	yes	"""Dom, Rec"""	yes	Carney complex	17	17q23-q24	5573	"""protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"""		"""E, M"""	.	PRKAR1A	48	.	0			c.G87A						PASS	.	A	,,	22,4384	824.1+/-416.5	0,22,2181	88.0	71.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	87,87,87	-10.2	0.4	17	dbSNP_107	77	198,8402	810.4+/-407.1	4,190,4106	no	coding-synonymous,coding-synonymous,coding-synonymous	PRKAR1A	NM_002734.3,NM_212471.1,NM_212472.1	,,	4,212,6287	AA,AG,GG		2.3023,0.4993,1.6915	,,	29/382,29/382,29/382	66511627	220,12786	2203	4300	6503	SO:0001819	synonymous_variant	5573	exon1	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;	TCAAGCGCTGCTC		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"""Carney complex type 1"""	188830	"""tissue specific extinguisher 1"""	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.87G>A	17.37:g.66511627G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_001276290	K7ER48|Q567S7	Silent	SNP	ENST00000589228.1	37	CCDS11678.1																																																																																			G|0.986;A|0.014	0.014	strong		0.507	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1		
FOXD4L1	200350	hgsc.bcm.edu	37	2	114256840	114256840	+	Silent	SNP	C	C	T	rs147906017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:114256840C>T	ENST00000306507.5	+	1	180	c.7C>T	c.(7-9)Ctg>Ttg	p.L3L		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	3					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						CGCCATGAACCTGCCAAGAGC	0.632																																					p.L3L		Atlas-SNP	.											FOXD4L1,colon,carcinoma,-2,1	FOXD4L1	48	1	0			c.C7T						PASS	.						28.0	38.0	34.0					2																	114256840		2154	4219	6373	SO:0001819	synonymous_variant	200350	exon1			ATGAACCTGCCAA	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.7C>T	2.37:g.114256840C>T		Somatic	304	1	0.00328947		WXS	Illumina HiSeq	Phase_I	242	91	0.376033	NM_012184	B3KWN1|B9EGF3	Silent	SNP	ENST00000306507.5	37	CCDS2117.1																																																																																			.	.	weak		0.632	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
SURF2	6835	hgsc.bcm.edu	37	9	136228006	136228006	+	Silent	SNP	G	G	A	rs34939258	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136228006G>A	ENST00000371964.4	+	6	803	c.762G>A	c.(760-762)caG>caA	p.Q254Q	SURF4_ENST00000467910.1_5'Flank	NM_017503.3	NP_059973.4	Q15527	SURF2_HUMAN	surfeit 2	254						nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(145;4.87e-07)|Epithelial(140;4.02e-06)|all cancers(34;3.71e-05)		CCTGTAAACAGCCAGGTTAAT	0.458													G|||	157	0.0313498	0.0038	0.0389	5008	,	,		20944	0.0198		0.0815	False		,,,				2504	0.0235				p.Q254Q		Atlas-SNP	.											.	SURF2	9	.	0			c.G762A						PASS	.	G		75,4331	67.0+/-104.6	1,73,2129	135.0	136.0	136.0		762	1.2	0.0	9	dbSNP_126	136	725,7875	176.6+/-226.4	35,655,3610	no	coding-synonymous	SURF2	NM_017503.3		36,728,5739	AA,AG,GG		8.4302,1.7022,6.151		254/257	136228006	800,12206	2203	4300	6503	SO:0001819	synonymous_variant	6835	exon6			TAAACAGCCAGGT		CCDS6967.1	9q33-q34	2008-07-21			ENSG00000148291	ENSG00000148291			11475	protein-coding gene	gene with protein product	"""surfeit locus protein 2"""	185630					Standard	NM_017503		Approved		uc004cdi.2	Q15527	OTTHUMG00000020867	ENST00000371964.4:c.762G>A	9.37:g.136228006G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_017503	Q6IBP9|Q96CD1	Silent	SNP	ENST00000371964.4	37	CCDS6967.1																																																																																			G|0.940;A|0.060	0.060	strong		0.458	SURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054883.1	NM_017503	
PTX4	390667	hgsc.bcm.edu	37	16	1537839	1537839	+	Missense_Mutation	SNP	G	G	A	rs2745101	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1537839G>A	ENST00000447419.2	-	2	299	c.274C>T	c.(274-276)Cgg>Tgg	p.R92W	PTX4_ENST00000293922.1_Missense_Mutation_p.R87W|PTX4_ENST00000440447.2_Missense_Mutation_p.R92W			Q96A99	PTX4_HUMAN	pentraxin 4, long	92			R -> W (in dbSNP:rs2745101).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GCCTGTGACCGGTTGACTGCC	0.652													G|||	1333	0.266174	0.1679	0.1945	5008	,	,		16731	0.5079		0.2316	False		,,,				2504	0.2362				p.R87W		Atlas-SNP	.											.	PTX4	46	.	0			c.C259T						PASS	.	G	TRP/ARG	697,3701		57,583,1559	76.0	79.0	78.0		259	-0.6	0.0	16	dbSNP_100	78	2102,6492		238,1626,2433	yes	missense	PTX4	NM_001013658.1	101	295,2209,3992	AA,AG,GG		24.4589,15.8481,21.544	probably-damaging	87/474	1537839	2799,10193	2199	4297	6496	SO:0001583	missense	390667	exon2			GTGACCGGTTGAC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.274C>T	16.37:g.1537839G>A	ENSP00000445277:p.Arg92Trp	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		645	0.29532967032967034	74	0.15040650406504066	67	0.1850828729281768	315	0.5506993006993007	189	0.24934036939313983	G	10.43	1.346709	0.24426	0.158481	0.244589	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.05382	3.6;3.45	5.78	-0.593	0.11667	.	2.089320	0.01936	N	0.041576	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.13145	0.007	B	0.08055	0.003	T	0.47497	-0.9113	9	0.72032	D	0.01	.	2.2422	0.04023	0.179:0.1478:0.523:0.1502	rs2745101;rs2745101	87	Q96A99-2	.	W	92;87	ENSP00000445277:R92W;ENSP00000293922:R87W	ENSP00000293922:R87W	R	-	1	2	PTX4	1477840	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	0.282000	0.18829	-0.015000	0.14150	-0.251000	0.11542	CGG	G|0.753;A|0.247	0.247	strong		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
PITRM1	10531	hgsc.bcm.edu	37	10	3181126	3181126	+	Missense_Mutation	SNP	C	C	T	rs17849904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:3181126C>T	ENST00000224949.4	-	25	2921	c.2887G>A	c.(2887-2889)Gta>Ata	p.V963I	PITRM1_ENST00000380994.1_Missense_Mutation_p.V521I|PITRM1_ENST00000380989.2_Missense_Mutation_p.V964I|PITRM1_ENST00000451104.2_Missense_Mutation_p.V865I|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000464395.1_5'UTR|PITRM1-AS1_ENST00000441377.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	963			V -> I (in dbSNP:rs17849904). {ECO:0000269|PubMed:15489334}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						GGAGCATCTACGGTTGAGAAG	0.473													C|||	176	0.0351438	0.0038	0.0576	5008	,	,		21710	0.0		0.0944	False		,,,				2504	0.0368				p.V964I		Atlas-SNP	.											.	PITRM1	109	.	0			c.G2890A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	44,3950		0,44,1953	188.0	188.0	188.0		2890,2593,2887	5.5	0.5	10	dbSNP_123	188	687,7663		19,649,3507	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	29,29,29	19,693,5460	TT,TC,CC		8.2275,1.1017,5.9219	benign,benign,benign	964/1039,865/940,963/1038	3181126	731,11613	1997	4175	6172	SO:0001583	missense	10531	exon25			CATCTACGGTTGA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.2887G>A	10.37:g.3181126C>T	ENSP00000224949:p.Val963Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	160	87	0.54375	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	100	0.045787545787545784	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	73	0.09630606860158311	c	10.97	1.502821	0.26949	0.011017	0.082275	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104;ENST00000455371	T;T;T;T;T	0.08984	3.03;3.03;3.03;3.03;3.03	5.54	5.54	0.83059	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.054483	0.64402	D	0.000001	T	0.00241	0.0007	L	0.39085	1.19	0.53688	D	0.999977	B;B;B;B;B;B	0.29270	0.061;0.24;0.073;0.073;0.185;0.073	B;B;B;B;B;B	0.21708	0.008;0.036;0.017;0.026;0.026;0.017	T	0.50154	-0.8861	10	0.15952	T	0.53	-27.7539	19.4783	0.94998	0.0:1.0:0.0:0.0	rs17849904;rs17849904	956;865;964;963;898;956	E9PDX6;E7ES23;C9JSL2;Q5JRX3;E9PDX7;B4DH07	.;.;.;PREP_HUMAN;.;.	I	963;956;964;521;865;144	ENSP00000224949:V963I;ENSP00000370377:V964I;ENSP00000370382:V521I;ENSP00000401201:V865I;ENSP00000399307:V144I	ENSP00000224949:V963I	V	-	1	0	PITRM1	3171126	1.000000	0.71417	0.497000	0.27552	0.022000	0.10575	5.252000	0.65445	2.598000	0.87819	0.462000	0.41574	GTA	C|0.954;T|0.046	0.046	strong		0.473	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
FGF21	26291	hgsc.bcm.edu	37	19	49261218	49261218	+	Missense_Mutation	SNP	G	G	A	rs142980324		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49261218G>A	ENST00000593756.1	+	4	943	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	FUT1_ENST00000310160.3_5'Flank|FGF21_ENST00000222157.3_Missense_Mutation_p.R124Q			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	124					cell-cell signaling (GO:0007267)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TGCAGCTTCCGGGAGCTGCTT	0.582																																					p.R124Q		Atlas-SNP	.											.	FGF21	21	.	0			c.G371A						PASS	.	G	GLN/ARG	0,4402		0,0,2201	158.0	173.0	168.0		371	3.4	1.0	19	dbSNP_134	168	4,8592	3.7+/-12.6	0,4,4294	yes	missense	FGF21	NM_019113.2	43	0,4,6495	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	124/210	49261218	4,12994	2201	4298	6499	SO:0001583	missense	26291	exon3			GCTTCCGGGAGCT	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.371G>A	19.37:g.49261218G>A	ENSP00000471477:p.Arg124Gln	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	132	57	0.431818	NM_019113	Q8N683	Missense_Mutation	SNP	ENST00000593756.1	37	CCDS12734.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814192	0.70912	0.0	4.65E-4	ENSG00000105550	ENST00000222157	D	0.81579	-1.51	4.44	3.4	0.38934	.	0.076506	0.49916	D	0.000128	T	0.80969	0.4726	M	0.74258	2.255	0.37112	D	0.900381	D	0.53745	0.962	P	0.48270	0.572	T	0.82814	-0.0271	10	0.46703	T	0.11	-15.5157	8.3528	0.32312	0.1087:0.0:0.8913:0.0	.	124	Q9NSA1	FGF21_HUMAN	Q	124	ENSP00000222157:R124Q	ENSP00000222157:R124Q	R	+	2	0	FGF21	53953030	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.173000	0.31920	1.220000	0.43490	0.511000	0.50034	CGG	G|1.000;A|0.000	0.000	weak		0.582	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1		
HRG	3273	hgsc.bcm.edu	37	3	186389559	186389559	+	Missense_Mutation	SNP	T	T	C	rs386669201|rs10770	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186389559T>C	ENST00000232003.4	+	4	619	c.539T>C	c.(538-540)aTc>aCc	p.I180T		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	180	Cystatin 2.		I -> T (in dbSNP:rs10770).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GTGGACCGAATCGAGAGAGTT	0.498													T|||	677	0.135184	0.2012	0.111	5008	,	,		18142	0.0913		0.1163	False		,,,				2504	0.1278				p.I180T		Atlas-SNP	.											.	HRG	81	.	0			c.T539C						PASS	.	T	THR/ILE	929,3477	355.4+/-313.0	99,731,1373	81.0	84.0	83.0		539	2.8	0.0	3	dbSNP_52	83	1060,7540	223.8+/-260.4	68,924,3308	yes	missense	HRG	NM_000412.2	89	167,1655,4681	CC,CT,TT		12.3256,21.0849,15.2929	possibly-damaging	180/526	186389559	1989,11017	2203	4300	6503	SO:0001583	missense	3273	exon4			ACCGAATCGAGAG		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.539T>C	3.37:g.186389559T>C	ENSP00000232003:p.Ile180Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	164	69	0.420732	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	278	0.12728937728937728	108	0.21951219512195122	35	0.09668508287292818	50	0.08741258741258741	85	0.11213720316622691	T	4.264	0.048071	0.08243	0.210849	0.123256	ENSG00000113905	ENST00000232003	T	0.15017	2.46	5.22	2.81	0.32909	Proteinase inhibitor I25, cystatin (1);	0.723695	0.11798	N	0.528462	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.27625	0.183	B	0.15870	0.014	T	0.37549	-0.9701	9	0.66056	D	0.02	-2.7599	5.0395	0.14452	0.0:0.0978:0.1852:0.7171	rs10770;rs3181915;rs3733011;rs11547939;rs52821842;rs61347487;rs10770	180	P04196	HRG_HUMAN	T	180	ENSP00000232003:I180T	ENSP00000232003:I180T	I	+	2	0	HRG	187872253	0.031000	0.19500	0.013000	0.15412	0.040000	0.13550	2.411000	0.44600	0.386000	0.24997	0.459000	0.35465	ATC	C|0.145;N|0.000	0.145	strong		0.498	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
SERPINB7	8710	hgsc.bcm.edu	37	18	61471662	61471662	+	Silent	SNP	G	G	T	rs34505921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:61471662G>T	ENST00000398019.2	+	8	1261	c.936G>T	c.(934-936)tcG>tcT	p.S312S	SERPINB7_ENST00000546027.1_Silent_p.S312S|SERPINB7_ENST00000336429.2_Silent_p.S312S|SERPINB7_ENST00000540675.1_Silent_p.S295S	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	312					negative regulation of endopeptidase activity (GO:0010951)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	27		Esophageal squamous(42;0.129)				GGATTGCTTCGGGGGGTCGTC	0.428													A|||	254	0.0507188	0.084	0.0432	5008	,	,		18164	0.0238		0.0179	False		,,,				2504	0.0726				p.S312S		Atlas-SNP	.											SERPINB7,NS,malignant_melanoma,+1,1	SERPINB7	66	1	0			c.G936T						PASS	.	A	,	312,4092		11,290,1901	44.0	46.0	46.0		936,936	-12.2	0.0	18	dbSNP_126	46	199,8401		1,197,4102	no	coding-synonymous,coding-synonymous	SERPINB7	NM_001040147.1,NM_003784.2	,	12,487,6003	TT,TG,GG		2.314,7.0845,3.9296	,	312/381,312/381	61471662	511,12493	2202	4300	6502	SO:0001819	synonymous_variant	8710	exon8			TGCTTCGGGGGGT	AF027866	CCDS11988.1, CCDS58633.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166396	ENSG00000166396		"""Serine (or cysteine) peptidase inhibitors"""	13902	protein-coding gene	gene with protein product		603357	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7"""			24172014	Standard	NM_003784		Approved	MEGSIN	uc002ljl.4	O75635	OTTHUMG00000060591	ENST00000398019.2:c.936G>T	18.37:g.61471662G>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	68	42	0.617647	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Silent	SNP	ENST00000398019.2	37	CCDS11988.1																																																																																			G|0.962;T|0.038	0.038	strong		0.428	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784	
LRBA	987	hgsc.bcm.edu	37	4	151719263	151719263	+	Silent	SNP	A	A	G	rs1129998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:151719263A>G	ENST00000357115.3	-	34	5793	c.5550T>C	c.(5548-5550)gtT>gtC	p.V1850V	LRBA_ENST00000507224.1_Silent_p.V1850V|LRBA_ENST00000510413.1_Silent_p.V1850V|LRBA_ENST00000535741.1_Silent_p.V1850V	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1850						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					CCAATTCCACAACTGAACTAC	0.313													A|||	605	0.120807	0.0091	0.1081	5008	,	,		16351	0.1518		0.2624	False		,,,				2504	0.1033				p.V1850V		Atlas-SNP	.											.	LRBA	253	.	0			c.T5550C						PASS	.	A	,	230,4176	135.3+/-171.4	5,220,1978	87.0	84.0	85.0		5550,5550	3.5	1.0	4	dbSNP_86	85	2046,6548	352.1+/-328.5	248,1550,2499	yes	coding-synonymous,coding-synonymous	LRBA	NM_001199282.2,NM_006726.4	,	253,1770,4477	GG,GA,AA		23.8073,5.2202,17.5077	,	1850/2864,1850/2864	151719263	2276,10724	2203	4297	6500	SO:0001819	synonymous_variant	987	exon34			TTCCACAACTGAA	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.5550T>C	4.37:g.151719263A>G		Somatic	414	0	0		WXS	Illumina HiSeq	Phase_I	457	219	0.479212	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	37	CCDS3773.1	350	0.16025641025641027	4	0.008130081300813009	49	0.13535911602209943	102	0.17832167832167833	195	0.25725593667546176	A	9.830	1.188139	0.21954	0.052202	0.238073	ENSG00000198589	ENST00000509835	.	.	.	5.83	3.46	0.39613	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23368	-1.0190	3	.	.	.	.	4.9513	0.14015	0.7203:0.0:0.1436:0.1361	rs1129998;rs3188419;rs7674188;rs17589531;rs1129998	.	.	.	S	503	.	.	L	-	2	0	LRBA	151938713	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.750000	0.38329	1.038000	0.40049	0.528000	0.53228	TTG	A|0.839;G|0.161	0.161	strong		0.313	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
CRLS1	54675	hgsc.bcm.edu	37	20	6011934	6011934	+	Missense_Mutation	SNP	C	C	T	rs41282950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:6011934C>T	ENST00000378863.4	+	4	735	c.578C>T	c.(577-579)cCa>cTa	p.P193L	CRLS1_ENST00000452938.1_Intron|CRLS1_ENST00000378868.4_Missense_Mutation_p.P94L|CRLS1_ENST00000464921.1_3'UTR	NM_019095.4	NP_061968.1	Q9UJA2	CRLS1_HUMAN	cardiolipin synthase 1	193					cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			lung(3)|ovary(1)	4						TTTTCAGTTCCACTTACTTAC	0.328													C|||	259	0.0517173	0.0038	0.0908	5008	,	,		18607	0.0099		0.1292	False		,,,				2504	0.0521				p.P193L		Atlas-SNP	.											.	CRLS1	14	.	0			c.C578T						PASS	.	C	LEU/PRO,LEU/PRO	101,4305	79.3+/-117.8	1,99,2103	135.0	119.0	124.0		281,578	5.7	1.0	20	dbSNP_127	124	1082,7516	226.6+/-262.3	72,938,3289	yes	missense,missense	CRLS1	NM_001127458.1,NM_019095.4	98,98	73,1037,5392	TT,TC,CC		12.5843,2.2923,9.0972	possibly-damaging,possibly-damaging	94/203,193/302	6011934	1183,11821	2203	4299	6502	SO:0001583	missense	54675	exon4			CAGTTCCACTTAC	AF241784	CCDS13096.1, CCDS46578.1	20p13-p12.3	2006-04-04	2006-04-04	2006-04-04	ENSG00000088766	ENSG00000088766			16148	protein-coding gene	gene with protein product	"""GCD10 homolog (S. cerevisiae)"""	608188	"""chromosome 20 open reading frame 155"""	C20orf155		16547353	Standard	NM_019095		Approved	dJ967N21.6, CLS1, GCD10	uc002wmn.4	Q9UJA2	OTTHUMG00000031823	ENST00000378863.4:c.578C>T	20.37:g.6011934C>T	ENSP00000368140:p.Pro193Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_019095	D3DW09|E9PAT4|Q27RP0|Q69YQ5	Missense_Mutation	SNP	ENST00000378863.4	37	CCDS13096.1	143	0.06547619047619048	1	0.0020325203252032522	38	0.10497237569060773	3	0.005244755244755245	101	0.13324538258575197	C	19.27	3.795241	0.70452	0.022923	0.125843	ENSG00000088766	ENST00000378863;ENST00000378868	.	.	.	5.74	5.74	0.90152	.	0.212969	0.48286	D	0.000187	T	0.00906	0.0030	L	0.35414	1.06	0.09310	P	0.999999637676	P;P	0.52316	0.817;0.952	P;P	0.53401	0.474;0.725	T	0.01834	-1.1264	8	0.11485	T	0.65	-25.3787	17.4153	0.87498	0.0:1.0:0.0:0.0	rs41282950;rs62642499	94;193	Q9UJA2-2;Q9UJA2	.;CRLS1_HUMAN	L	193;94	.	ENSP00000368140:P193L	P	+	2	0	CRLS1	5959934	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.175000	0.71949	2.716000	0.92895	0.563000	0.77884	CCA	C|0.908;T|0.092	0.092	strong		0.328	CRLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077902.2	NM_019095	
COQ10B	80219	hgsc.bcm.edu	37	2	198334871	198334871	+	Silent	SNP	A	A	C	rs140640160		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:198334871A>C	ENST00000263960.2	+	4	663	c.525A>C	c.(523-525)ccA>ccC	p.P175P	COQ10B_ENST00000409010.1_Silent_p.P147P|COQ10B_ENST00000409398.1_Silent_p.P125P|COQ10B_ENST00000545340.1_Silent_p.P132P	NM_025147.3	NP_079423.1	Q9H8M1	CQ10B_HUMAN	coenzyme Q10 homolog B (S. cerevisiae)	175						mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(2)|lung(3)	6			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)			CTGGCTACCCAAGAACTTGTA	0.353													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16923	0.0		0.0	False		,,,				2504	0.0				p.P175P		Atlas-SNP	.											.	COQ10B	18	.	0			c.A525C						PASS	.	A		3,4403	4.2+/-10.8	0,3,2200	126.0	111.0	116.0		525	-0.2	1.0	2	dbSNP_134	116	14,8586	8.4+/-32.0	0,14,4286	no	coding-synonymous	COQ10B	NM_025147.3		0,17,6486	CC,CA,AA		0.1628,0.0681,0.1307		175/239	198334871	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	80219	exon4			CTACCCAAGAACT	AK023510	CCDS2319.1	2q33.1	2008-02-05	2006-04-04		ENSG00000115520	ENSG00000115520			25819	protein-coding gene	gene with protein product			"""coenzyme Q10 homolog B (yeast)"""				Standard	NM_025147		Approved	FLJ13448	uc002uuh.1	Q9H8M1	OTTHUMG00000132745	ENST00000263960.2:c.525A>C	2.37:g.198334871A>C		Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	329	165	0.50152	NM_025147	B7Z1Y4	Silent	SNP	ENST00000263960.2	37	CCDS2319.1																																																																																			A|0.998;C|0.002	0.002	strong		0.353	COQ10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256105.2	NM_025147	
ZNF668	79759	hgsc.bcm.edu	37	16	31075175	31075175	+	Silent	SNP	G	G	A	rs2303223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31075175G>A	ENST00000538906.1	-	2	1390	c.606C>T	c.(604-606)ggC>ggT	p.G202G	AC135050.5_ENST00000568708.1_RNA|ZNF668_ENST00000535577.1_Silent_p.G202G|ZNF668_ENST00000426488.2_Silent_p.G225G|ZNF668_ENST00000300849.4_Silent_p.G202G|ZNF668_ENST00000539836.3_Silent_p.G225G|ZNF668_ENST00000394983.2_Silent_p.G202G|ZNF668_ENST00000564456.1_5'Flank	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	202					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CATAGGCTTTGCCGCAACGCT	0.672													G|||	1732	0.345847	0.0174	0.4092	5008	,	,		18553	0.8859		0.3877	False		,,,				2504	0.1452				p.G225G	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											ZNF668,NS,carcinoma,-2,1	ZNF668	121	1	0			c.C675T						scavenged	.	G	,,,	390,3998		24,342,1828	16.0	16.0	16.0		606,675,606,606	0.6	1.0	16	dbSNP_100	16	3446,5152		692,2062,1545	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	716,2404,3373	AA,AG,GG		40.0791,8.8879,29.5395	,,,	202/620,225/643,202/620,202/620	31075175	3836,9150	2194	4299	6493	SO:0001819	synonymous_variant	79759	exon3			GGCTTTGCCGCAA		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.606C>T	16.37:g.31075175G>A		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																			G|0.657;A|0.343	0.343	strong		0.672	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
CACNB3	784	hgsc.bcm.edu	37	12	49221622	49221622	+	Silent	SNP	G	G	A	rs1045340	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49221622G>A	ENST00000301050.2	+	13	1594	c.1395G>A	c.(1393-1395)gaG>gaA	p.E465E	CACNB3_ENST00000547392.1_Silent_p.E438E|CACNB3_ENST00000547230.1_Silent_p.E424E|CACNB3_ENST00000540990.1_Silent_p.E452E|CACNB3_ENST00000536187.2_Silent_p.E464E	NM_000725.3	NP_000716.2	P54284	CACB3_HUMAN	calcium channel, voltage-dependent, beta 3 subunit	465					axon guidance (GO:0007411)|calcium ion transport (GO:0006816)|membrane depolarization (GO:0051899)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|membrane (GO:0016020)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(1)|large_intestine(5)|lung(4)|prostate(1)	12					Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGGACTCAGAGCACAACCACA	0.642													G|||	2164	0.432109	0.3124	0.4121	5008	,	,		18085	0.6151		0.4662	False		,,,				2504	0.3845				p.E465E		Atlas-SNP	.											.	CACNB3	51	.	0			c.G1395A						PASS	.	G	,,,	1450,2956	469.2+/-355.4	251,948,1004	75.0	72.0	73.0		1395,1272,1392,1356	3.7	1.0	12	dbSNP_86	73	3975,4625	548.7+/-385.4	917,2141,1242	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNB3	NM_000725.3,NM_001206915.1,NM_001206916.1,NM_001206917.1	,,,	1168,3089,2246	AA,AG,GG		46.2209,32.9097,41.7115	,,,	465/485,424/444,464/484,452/472	49221622	5425,7581	2203	4300	6503	SO:0001819	synonymous_variant	784	exon13			CTCAGAGCACAAC		CCDS8769.1, CCDS55821.1, CCDS55822.1, CCDS55823.1	12q13	2008-05-02				ENSG00000167535		"""Calcium channel subunits"""	1403	protein-coding gene	gene with protein product		601958		CACNLB3		8119293	Standard	NM_000725		Approved		uc010sly.2	P54284		ENST00000301050.2:c.1395G>A	12.37:g.49221622G>A		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	294	136	0.462585	NM_000725	A8K0Z4|B7Z4Q1|B7Z973|B7ZAK8|F5GZW7|F5H2P6|F8VSG3|Q13913	Silent	SNP	ENST00000301050.2	37	CCDS8769.1																																																																																			G|0.568;A|0.432	0.432	strong		0.642	CACNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408886.1		
GRWD1	83743	hgsc.bcm.edu	37	19	48949286	48949286	+	Silent	SNP	G	G	T	rs1643487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48949286G>T	ENST00000253237.5	+	1	257	c.24G>T	c.(22-24)cgG>cgT	p.R8R		NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	8						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		AGGGTCGGCGGCGCACGTGTG	0.682											OREG0025607	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3607	0.720248	0.5711	0.817	5008	,	,		15301	0.6131		0.8847	False		,,,				2504	0.7945				p.R8R		Atlas-SNP	.											.	GRWD1	41	.	0			c.G24T						PASS	.	G		2733,1637		859,1015,311	14.0	20.0	18.0		24	-3.0	0.1	19	dbSNP_89	18	7834,742		3585,664,39	no	coding-synonymous	GRWD1	NM_031485.3		4444,1679,350	TT,TG,GG		8.6521,37.46,18.3763		8/447	48949286	10567,2379	2185	4288	6473	SO:0001819	synonymous_variant	83743	exon1			TCGGCGGCGCACG	AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"""WD repeat domain containing"""	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.24G>T	19.37:g.48949286G>T		Somatic	118	0	0	958	WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_031485	Q8TF59	Silent	SNP	ENST00000253237.5	37	CCDS12720.1																																																																																			G|0.256;T|0.744	0.744	strong		0.682	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466122.1	NM_031485	
EPHA8	2046	hgsc.bcm.edu	37	1	22919904	22919904	+	Silent	SNP	C	C	T	rs209696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22919904C>T	ENST00000166244.3	+	6	1473	c.1401C>T	c.(1399-1401)aaC>aaT	p.N467N		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	467	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGCAGCCGAACGGCATCATCC	0.672													C|||	1684	0.336262	0.3918	0.353	5008	,	,		15063	0.1726		0.2664	False		,,,				2504	0.4898				p.N467N		Atlas-SNP	.											.	EPHA8	221	.	0			c.C1401T						PASS	.	C		1655,2741		329,997,872	22.0	21.0	21.0		1401	-3.7	1.0	1	dbSNP_79	21	2104,6486		271,1562,2462	no	coding-synonymous	EPHA8	NM_020526.3		600,2559,3334	TT,TC,CC		24.4936,37.6479,28.9466		467/1006	22919904	3759,9227	2198	4295	6493	SO:0001819	synonymous_variant	2046	exon6			GCCGAACGGCATC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1401C>T	1.37:g.22919904C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																			C|0.706;T|0.294	0.294	strong		0.672	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
ADCY8	114	hgsc.bcm.edu	37	8	131922027	131922027	+	Silent	SNP	T	T	G	rs12545028	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:131922027T>G	ENST00000286355.5	-	6	3659	c.1567A>C	c.(1567-1569)Agg>Cgg	p.R523R	ADCY8_ENST00000377928.3_Silent_p.R523R	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	523					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TGCCACTTCCTTAGTCCCAAA	0.473										HNSCC(32;0.087)			T|||	525	0.104832	0.0666	0.1311	5008	,	,		20298	0.0605		0.16	False		,,,				2504	0.1268				p.R523R		Atlas-SNP	.											.	ADCY8	291	.	0			c.A1567C						PASS	.	T		431,3975	207.5+/-228.8	17,397,1789	261.0	211.0	228.0		1567	4.0	0.8	8	dbSNP_120	228	1571,7029	294.2+/-301.7	139,1293,2868	no	coding-synonymous	ADCY8	NM_001115.2		156,1690,4657	GG,GT,TT		18.2674,9.7821,15.3929		523/1252	131922027	2002,11004	2203	4300	6503	SO:0001819	synonymous_variant	114	exon6			ACTTCCTTAGTCC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1567A>C	8.37:g.131922027T>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	194	194	1	NM_001115		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																			T|0.866;G|0.134	0.134	strong		0.473	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
LINS	55180	hgsc.bcm.edu	37	15	101110096	101110096	+	Missense_Mutation	SNP	T	T	C	rs12915007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:101110096T>C	ENST00000314742.8	-	7	1843	c.1621A>G	c.(1621-1623)Att>Gtt	p.I541V	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	541			I -> V (in dbSNP:rs12915007).							central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						TTATTGCAAATGGTGAAAAAA	0.333													T|||	365	0.0728834	0.0477	0.0937	5008	,	,		19131	0.1954		0.0169	False		,,,				2504	0.0235				p.I541V		Atlas-SNP	.											.	LINS	62	.	0			c.A1621G						PASS	.	T	VAL/ILE	155,4251	103.8+/-142.4	1,153,2049	62.0	61.0	61.0		1621	0.4	0.2	15	dbSNP_121	61	121,8479	63.9+/-126.0	1,119,4180	yes	missense	LINS	NM_001040616.2	29	2,272,6229	CC,CT,TT		1.407,3.5179,2.1221	benign	541/758	101110096	276,12730	2203	4300	6503	SO:0001583	missense	55180	exon7			TGCAAATGGTGAA	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"""lines homolog 1 (Drosophila)"""	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1621A>G	15.37:g.101110096T>C	ENSP00000318423:p.Ile541Val	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_001040616	Q96FW2|Q9NVQ3	Missense_Mutation	SNP	ENST00000314742.8	37	CCDS10385.1	176	0.08058608058608059	23	0.046747967479674794	32	0.08839779005524862	107	0.18706293706293706	14	0.018469656992084433	T	9.256	1.042091	0.19748	0.035179	0.01407	ENSG00000140471	ENST00000314742	T	0.16743	2.32	5.77	0.409	0.16382	.	0.656803	0.15430	N	0.262790	T	0.00012	0.0000	L	0.28115	0.83	0.53005	P	3.500000000000725E-5	B	0.30563	0.285	B	0.35470	0.203	T	0.43893	-0.9363	9	0.19147	T	0.46	-2.8628	6.8575	0.24048	0.0:0.2716:0.1235:0.6049	rs12915007;rs52808538;rs58496105;rs12915007	541	Q8NG48	LINES_HUMAN	V	541	ENSP00000318423:I541V	ENSP00000318423:I541V	I	-	1	0	LINS	98927619	0.030000	0.19436	0.168000	0.22838	0.939000	0.58152	0.094000	0.15107	0.126000	0.18424	0.533000	0.62120	ATT	T|0.953;C|0.047	0.047	strong		0.333	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
SVIL	6840	hgsc.bcm.edu	37	10	29747417	29747417	+	Silent	SNP	C	C	T	rs1887465	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29747417C>T	ENST00000355867.4	-	37	7256	c.6504G>A	c.(6502-6504)ccG>ccA	p.P2168P	SVIL_ENST00000375398.2_Silent_p.P2168P|SVIL_ENST00000375400.3_Silent_p.P1742P|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000535393.1_Silent_p.P1082P|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000438202.1_RNA|PTCHD3P1_ENST00000430295.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2168	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.				cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CGACCCCCTCCGGGAGTGGCC	0.552													C|||	1800	0.359425	0.2852	0.3746	5008	,	,		15050	0.5565		0.2465	False		,,,				2504	0.362				p.P2168P		Atlas-SNP	.											.	SVIL	226	.	0			c.G6504A						PASS	.	C	,	1301,3105	436.1+/-344.5	193,915,1095	42.0	46.0	44.0		5226,6504	-8.8	0.1	10	dbSNP_92	44	1844,6756	329.8+/-318.9	197,1450,2653	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	390,2365,3748	TT,TC,CC		21.4419,29.5279,24.1811	,	1742/1789,2168/2215	29747417	3145,9861	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon37			CCCCTCCGGGAGT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.6504G>A	10.37:g.29747417C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	111	71	0.63964	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			C|0.733;T|0.267	0.267	strong		0.552	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
KIAA0922	23240	hgsc.bcm.edu	37	4	154513722	154513722	+	Silent	SNP	C	C	T	rs7669741	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:154513722C>T	ENST00000409663.3	+	18	1957	c.1905C>T	c.(1903-1905)caC>caT	p.H635H	KIAA0922_ENST00000440693.1_Intron|KIAA0922_ENST00000409959.3_Silent_p.H636H	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	635						integral component of membrane (GO:0016021)		p.H488H(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				CCCTAGTGCACCTGCTCCACA	0.483													C|||	1130	0.225639	0.1483	0.2147	5008	,	,		20958	0.2361		0.3072	False		,,,				2504	0.2434				p.H636H		Atlas-SNP	.											KIAA0922,NS,carcinoma,0,1	KIAA0922	214	1	1	Substitution - coding silent(1)	stomach(1)	c.C1908T						PASS	.	C	,	794,3612	320.4+/-296.6	66,662,1475	133.0	119.0	124.0		1908,1905	0.2	0.7	4	dbSNP_116	124	2670,5930	430.5+/-356.5	426,1818,2056	no	coding-synonymous,coding-synonymous	KIAA0922	NM_001131007.1,NM_015196.3	,	492,2480,3531	TT,TC,CC		31.0465,18.0209,26.6339	,	636/1611,635/1610	154513722	3464,9542	2203	4300	6503	SO:0001819	synonymous_variant	23240	exon18			AGTGCACCTGCTC	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.1905C>T	4.37:g.154513722C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																			C|0.745;T|0.255	0.255	strong		0.483	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
ATP13A2	23400	hgsc.bcm.edu	37	1	17312743	17312743	+	Silent	SNP	C	C	T	rs3170740	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17312743C>T	ENST00000326735.8	-	29	3549	c.3516G>A	c.(3514-3516)ccG>ccA	p.P1172P	ATP13A2_ENST00000452699.1_Silent_p.P1167P|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Missense_Mutation_p.A1072T			Q9NQ11	AT132_HUMAN	ATPase type 13A2	1172					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CGGGCAGCGGCGGCCAGGGCT	0.711													C|||	1659	0.33127	0.1445	0.4553	5008	,	,		12200	0.246		0.5099	False		,,,				2504	0.3998				p.A1072T		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G3214A						PASS	.	C	,THR/ALA,	944,3410		135,674,1368	16.0	24.0	22.0		3501,3214,3516	-7.1	0.0	1	dbSNP_105	22	4491,4055		1201,2089,983	yes	coding-synonymous,missense,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,58,	1336,2763,2351	TT,TC,CC		47.4491,21.6812,42.1318	,,	1167/1176,1072/1159,1172/1181	17312743	5435,7465	2177	4273	6450	SO:0001819	synonymous_variant	23400	exon27			CAGCGGCGGCCAG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.3516G>A	1.37:g.17312743C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	50	33	0.66	NM_001141974	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	37	CCDS175.1	773	0.35393772893772896	65	0.13211382113821138	158	0.43646408839779005	161	0.28146853146853146	389	0.5131926121372031	C	0.008	-1.900646	0.00517	0.216812	0.525509	ENSG00000159363	ENST00000341676;ENST00000502418	D;D	0.96967	-3.3;-4.19	3.56	-7.11	0.01542	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.26789	P	0.9694444	B	0.06786	0.001	B	0.04013	0.001	T	0.18681	-1.0329	7	0.02654	T	1	-23.2806	7.7309	0.28786	0.0:0.2877:0.2133:0.499	rs3170740	1072	Q5JXY1	.	T	1072;312	ENSP00000341115:A1072T;ENSP00000423065:A312T	ENSP00000341115:A1072T	A	-	1	0	ATP13A2	17185330	0.001000	0.12720	0.015000	0.15790	0.046000	0.14306	-2.548000	0.00930	-1.707000	0.01402	-0.914000	0.02751	GCC	C|0.645;T|0.355	0.355	strong		0.711	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
CLCA2	9635	hgsc.bcm.edu	37	1	86909493	86909493	+	Silent	SNP	C	C	T	rs2390059	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86909493C>T	ENST00000370565.4	+	10	1674	c.1512C>T	c.(1510-1512)gtC>gtT	p.V504V		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	504					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		GTGAAAATGTCAAACCTCACC	0.383													T|||	561	0.112021	0.171	0.1081	5008	,	,		17482	0.0585		0.0934	False		,,,				2504	0.1094				p.V504V	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C1512T						PASS	.	T		765,3641	754.9+/-412.5	69,627,1507	110.0	99.0	102.0		1512	-7.1	0.0	1	dbSNP_100	102	709,7891	787.1+/-407.6	30,649,3621	no	coding-synonymous	CLCA2	NM_006536.5		99,1276,5128	TT,TC,CC		8.2442,17.3627,11.3332		504/944	86909493	1474,11532	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon10			AAATGTCAAACCT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1512C>T	1.37:g.86909493C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			T|0.113;G|0.000;C|0.887	0.113	strong		0.383	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
KLHL25	64410	hgsc.bcm.edu	37	15	86311593	86311593	+	Silent	SNP	C	C	A	rs8041288	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:86311593C>A	ENST00000337975.5	-	2	1723	c.1449G>T	c.(1447-1449)cgG>cgT	p.R483R	KLHL25_ENST00000536947.1_Silent_p.R483R|MIR1276_ENST00000408707.1_RNA|KLHL25_ENST00000559131.1_Intron	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	483					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of translational initiation (GO:0006446)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						CGGCTGTGTACCGCCAAGGCT	0.617													C|||	311	0.0621006	0.0772	0.0663	5008	,	,		18137	0.001		0.0825	False		,,,				2504	0.0808				p.R483R		Atlas-SNP	.											.	KLHL25	58	.	0			c.G1449T						PASS	.	C		404,4000	198.1+/-222.0	15,374,1813	79.0	74.0	76.0		1449	-1.7	1.0	15	dbSNP_116	76	973,7625	209.3+/-250.5	57,859,3383	no	coding-synonymous	KLHL25	NM_022480.3		72,1233,5196	AA,AC,CC		11.3166,9.1735,10.5907		483/590	86311593	1377,11625	2202	4299	6501	SO:0001819	synonymous_variant	64410	exon2			TGTGTACCGCCAA		CCDS10339.1	15q25.3	2013-02-22	2013-02-22		ENSG00000183655	ENSG00000183655		"""Kelch-like"", ""BTB/POZ domain containing"""	25732	protein-coding gene	gene with protein product	"""ectodermal-neural cortex 2"""		"""kelch-like 25 (Drosophila)"""				Standard	XM_006720635		Approved	FLJ12587, ENC2, ENC-2	uc002bly.3	Q9H0H3	OTTHUMG00000148672	ENST00000337975.5:c.1449G>T	15.37:g.86311593C>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_022480	B2RDH2|B3KRT7	Silent	SNP	ENST00000337975.5	37	CCDS10339.1																																																																																			C|0.909;A|0.091	0.091	strong		0.617	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480	
BPIFC	254240	hgsc.bcm.edu	37	22	32808078	32808078	+	IGR	SNP	G	G	A	rs11545749	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:32808078G>A	ENST00000397452.1	-	0	2091				RTCB_ENST00000216038.5_Silent_p.I22I|RTCB_ENST00000451746.2_Silent_p.I22I			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C							extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										AGCCCTTCTTGATCCTCCAGC	0.577													G|||	290	0.0579073	0.1188	0.0303	5008	,	,		16916	0.0139		0.0527	False		,,,				2504	0.046				p.I22I		Atlas-SNP	.											.	C22orf28	43	.	0			c.C66T						PASS	.	G		478,3928	224.3+/-240.5	33,412,1758	106.0	106.0	106.0		66	5.0	1.0	22	dbSNP_120	106	372,8228	122.2+/-181.2	15,342,3943	no	coding-synonymous	C22orf28	NM_014306.4		48,754,5701	AA,AG,GG		4.3256,10.8488,6.5354		22/506	32808078	850,12156	2203	4300	6503	SO:0001628	intergenic_variant	51493	exon1			CTTCTTGATCCTC	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273		22.37:g.32808078G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_014306	A2RRF1	Silent	SNP	ENST00000397452.1	37	CCDS13906.1																																																																																			G|0.934;A|0.066	0.066	strong		0.577	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
CEP170	9859	hgsc.bcm.edu	37	1	243329075	243329075	+	Silent	SNP	T	T	C	rs61833876		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:243329075T>C	ENST00000366542.1	-	13	2238	c.2187A>G	c.(2185-2187)aaA>aaG	p.K729K	CEP170_ENST00000490813.1_5'Flank|CEP170_ENST00000366543.1_Silent_p.K631K|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Silent_p.K631K|RP11-261C10.4_ENST00000422938.1_RNA	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	729						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			CACTTTTCTCTTTTCCAGGAG	0.413																																					p.K729K		Atlas-SNP	.											.	CEP170	153	.	0			c.A2187G						PASS	.						195.0	180.0	185.0					1																	243329075		1853	4091	5944	SO:0001819	synonymous_variant	9859	exon13			TTTCTCTTTTCCA	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2187A>G	1.37:g.243329075T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	308	64	0.207792	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	C	0.733	-0.779384	0.02929	.	.	ENSG00000143702	ENST00000336415	T	0.47869	0.83	5.25	2.17	0.27698	.	0.262387	0.32952	N	0.005443	T	0.35158	0.0922	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.05007	-1.0912	7	0.16420	T	0.52	-4.5936	6.1109	0.20100	0.0:0.4336:0.0:0.5664	rs61833876	.	.	.	R	693	ENSP00000338161:K693R	ENSP00000338161:K693R	K	-	2	0	CEP170	241395698	1.000000	0.71417	0.962000	0.40283	0.478000	0.33099	0.760000	0.26475	0.238000	0.21222	-0.338000	0.08134	AAG	T|0.500;C|0.500	0.500	weak		0.413	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
CATSPER1	117144	hgsc.bcm.edu	37	11	65793797	65793797	+	Silent	SNP	G	G	A	rs1893316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65793797G>A	ENST00000312106.5	-	1	191	c.54C>T	c.(52-54)aaC>aaT	p.N18N		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	18					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						ACCTATCTGCGTTATTGGTGT	0.557													G|||	831	0.165935	0.0106	0.389	5008	,	,		21811	0.2292		0.2435	False		,,,				2504	0.0726				p.N18N		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C54T						PASS	.	G		237,4165	139.6+/-175.2	6,225,1970	181.0	139.0	153.0		54	0.7	0.0	11	dbSNP_92	153	2079,6513	359.0+/-331.4	241,1597,2458	no	coding-synonymous	CATSPER1	NM_053054.3		247,1822,4428	AA,AG,GG		24.1969,5.3839,17.8236		18/781	65793797	2316,10678	2201	4296	6497	SO:0001819	synonymous_variant	117144	exon1			ATCTGCGTTATTG	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.54C>T	11.37:g.65793797G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_053054	Q96P76	Silent	SNP	ENST00000312106.5	37	CCDS8127.1																																																																																			G|0.825;A|0.175	0.175	strong		0.557	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
OR6F1	343169	hgsc.bcm.edu	37	1	247875313	247875313	+	Missense_Mutation	SNP	G	G	A	rs61730474	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247875313G>A	ENST00000302084.2	-	1	792	c.745C>T	c.(745-747)Ctc>Ttc	p.L249F	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	249						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			TACCAAATGAGCACCACGGTG	0.537													G|||	25	0.00499201	0.0008	0.0086	5008	,	,		21543	0.0		0.0159	False		,,,				2504	0.002				p.L249F		Atlas-SNP	.											OR6F1,NS,carcinoma,+1,1	OR6F1	88	1	0			c.C745T						scavenged	.	G	PHE/LEU	12,4394	19.1+/-41.9	0,12,2191	109.0	100.0	103.0		745	-1.1	0.1	1	dbSNP_129	103	125,8475	65.3+/-127.6	0,125,4175	yes	missense	OR6F1	NM_001005286.1	22	0,137,6366	AA,AG,GG		1.4535,0.2724,1.0534	possibly-damaging	249/309	247875313	137,12869	2203	4300	6503	SO:0001583	missense	343169	exon1			AAATGAGCACCAC	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"""GPCR / Class A : Olfactory receptors"""	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.745C>T	1.37:g.247875313G>A	ENSP00000305640:p.Leu249Phe	Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_001005286	B2RNV6|Q6IF02|Q96R39	Missense_Mutation	SNP	ENST00000302084.2	37	CCDS31095.1	19	0.0086996336996337	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	14	0.018469656992084433	G	3.147	-0.174994	0.06421	0.002724	0.014535	ENSG00000169214	ENST00000302084	T	0.39406	1.08	3.72	-1.09	0.09904	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39341	N	0.001398	T	0.11580	0.0282	N	0.25286	0.73	0.09310	N	1	B	0.29301	0.241	B	0.28916	0.096	T	0.08330	-1.0727	10	0.49607	T	0.09	-41.0015	5.2298	0.15416	0.1516:0.0:0.2167:0.6317	.	249	Q8NGZ6	OR6F1_HUMAN	F	249	ENSP00000305640:L249F	ENSP00000305640:L249F	L	-	1	0	OR6F1	245941936	0.000000	0.05858	0.051000	0.19133	0.006000	0.05464	-0.187000	0.09656	0.004000	0.14682	-0.293000	0.09583	CTC	G|0.991;A|0.009	0.009	strong		0.537	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286	
SACS	26278	hgsc.bcm.edu	37	13	23908034	23908034	+	Silent	SNP	A	A	G	rs2737700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:23908034A>G	ENST00000382292.3	-	9	10254	c.9981T>C	c.(9979-9981)gcT>gcC	p.A3327A	SACS_ENST00000402364.1_Silent_p.A2577A|SACS_ENST00000382298.3_Silent_p.A3327A			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3327					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GAATACAGCCAGCTTTCATTA	0.418													A|||	1696	0.338658	0.1233	0.3991	5008	,	,		20613	0.4127		0.4394	False		,,,				2504	0.407				p.A3327A		Atlas-SNP	.											.	SACS	871	.	0			c.T9981C						PASS	.	A		766,3640	302.7+/-287.5	83,600,1520	70.0	68.0	69.0		9981	-0.6	1.0	13	dbSNP_100	69	3787,4809	532.3+/-382.2	828,2131,1339	no	coding-synonymous	SACS	NM_014363.4		911,2731,2859	GG,GA,AA		44.0554,17.3854,35.0177		3327/4580	23908034	4553,8449	2203	4298	6501	SO:0001819	synonymous_variant	26278	exon10			ACAGCCAGCTTTC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9981T>C	13.37:g.23908034A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	96	29	0.302083	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			A|0.664;G|0.336	0.336	strong		0.418	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
DSG1	1828	hgsc.bcm.edu	37	18	28913599	28913599	+	Silent	SNP	C	C	T	rs12967407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:28913599C>T	ENST00000257192.4	+	7	944	c.732C>T	c.(730-732)ggC>ggT	p.G244G		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	244	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			ACCGAGATGGCGGGGCAGATG	0.423													C|||	1641	0.327676	0.292	0.2882	5008	,	,		18910	0.0665		0.501	False		,,,				2504	0.4949				p.G244G		Atlas-SNP	.											DSG1,colon,carcinoma,+2,1	DSG1	176	1	0			c.C732T	GRCh37	CM014354	DSG1	M	rs12967407	scavenged	.	C		1396,3010	460.0+/-352.4	216,964,1023	141.0	127.0	132.0		732	-11.6	0.2	18	dbSNP_121	132	4281,4319	575.4+/-390.2	1043,2195,1062	no	coding-synonymous	DSG1	NM_001942.2		1259,3159,2085	TT,TC,CC		49.7791,31.6841,43.6491		244/1050	28913599	5677,7329	2203	4300	6503	SO:0001819	synonymous_variant	1828	exon7			AGATGGCGGGGCA	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.732C>T	18.37:g.28913599C>T		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	143	40	0.27972	NM_001942	B7Z845	Silent	SNP	ENST00000257192.4	37	CCDS11896.1																																																																																			C|0.616;T|0.384	0.384	strong		0.423	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
COL6A5	256076	hgsc.bcm.edu	37	3	130187817	130187817	+	Silent	SNP	T	T	C	rs322113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130187817T>C	ENST00000432398.2	+	38	7463	c.6969T>C	c.(6967-6969)atT>atC	p.I2323I	COL6A5_ENST00000265379.6_Silent_p.I2323I	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2323	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ACTTTCACATTGCCCCCACTC	0.468													C|||	4458	0.890176	0.8253	0.9092	5008	,	,		20383	0.8899		0.9115	False		,,,				2504	0.9427				p.I2323I		Atlas-SNP	.											.	COL6A5	205	.	0			c.T6969C						PASS	.	C		3457,629		1454,549,40	80.0	79.0	79.0		6969	-8.9	0.0	3	dbSNP_79	79	7602,766		3459,684,41	no	coding-synonymous	COL6A5	NM_153264.5		4913,1233,81	CC,CT,TT		9.1539,15.394,11.2012		2323/2527	130187817	11059,1395	2043	4184	6227	SO:0001819	synonymous_variant	256076	exon38			TCACATTGCCCCC	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.6969T>C	3.37:g.130187817T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37		1937	0.8869047619047619	415	0.8434959349593496	319	0.8812154696132597	511	0.8933566433566433	692	0.9129287598944591	C	0.015	-1.570165	0.00895	0.84606	0.908461	ENSG00000172752	ENST00000512836	.	.	.	5.34	-8.9	0.00782	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.50813	P	1.0699999999996823E-4	.	.	.	.	.	.	T	0.06698	-1.0812	3	.	.	.	.	5.4268	0.16429	0.0902:0.4436:0.099:0.3671	rs322113	.	.	.	R	575	.	.	C	+	1	0	COL6A5	131670507	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-0.538000	0.06120	-2.736000	0.00381	-2.998000	0.00077	TGC	T|0.105;C|0.895	0.895	strong		0.468	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
CLEC4M	10332	hgsc.bcm.edu	37	19	7831628	7831628	+	Missense_Mutation	SNP	G	G	A	rs2277998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7831628G>A	ENST00000327325.5	+	5	989	c.871G>A	c.(871-873)Gac>Aac	p.D291N	CLEC4M_ENST00000597522.1_Missense_Mutation_p.D199N|CLEC4M_ENST00000359059.5_Missense_Mutation_p.D224N|CLEC4M_ENST00000394122.2_Missense_Mutation_p.D279N|CLEC4M_ENST00000596363.1_Missense_Mutation_p.D263N|CLEC4M_ENST00000596707.1_Missense_Mutation_p.D224N|CLEC4M_ENST00000248228.4_Missense_Mutation_p.D269N|CLEC4M_ENST00000595496.1_Missense_Mutation_p.D155N|CLEC4M_ENST00000357361.2_Missense_Mutation_p.D291N|CLEC4M_ENST00000334806.5_Missense_Mutation_p.D240N	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	291	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		D -> N (in dbSNP:rs2277998). {ECO:0000269|Ref.5}.		antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						GAACTGGCACGACTCCGTCAC	0.602													g|||	887	0.177117	0.0113	0.3573	5008	,	,		15081	0.1389		0.2962	False		,,,				2504	0.1902				p.D291N		Atlas-SNP	.											CLEC4M,right_lower_lobe,carcinoma,-2,2	CLEC4M	58	2	0			c.G871A						PASS	.	A	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	302,4104	162.9+/-194.8	11,280,1912	99.0	90.0	93.0		718,799,463,670,595,733,802,787,871	-5.1	0.0	19	dbSNP_100	93	2704,5896	433.6+/-357.5	430,1844,2026	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	CLEC4M	NM_001144904.1,NM_001144905.1,NM_001144906.1,NM_001144907.1,NM_001144908.1,NM_001144909.1,NM_001144910.1,NM_001144911.1,NM_014257.4	23,23,23,23,23,23,23,23,23	441,2124,3938	AA,AG,GG		31.4419,6.8543,23.1124	benign,benign,benign,benign,benign,benign,benign,benign,benign	240/349,267/376,155/264,224/333,199/233,245/354,268/377,263/297,291/400	7831628	3006,10000	2203	4300	6503	SO:0001583	missense	10332	exon5			TGGCACGACTCCG	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.871G>A	19.37:g.7831628G>A	ENSP00000316228:p.Asp291Asn	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	157	65	0.414013	NM_014257	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	SNP	ENST00000327325.5	37	CCDS12187.1	438	0.20054945054945056	10	0.02032520325203252	110	0.30386740331491713	88	0.15384615384615385	230	0.3034300791556728	g	3.314	-0.140125	0.06669	0.068543	0.314419	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000334806;ENST00000359059;ENST00000357361;ENST00000358690	T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1	2.57	-5.14	0.02875	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.00012	0.0000	M	0.67700	2.07	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.24258	0.056;0.029;0.1;0.009;0.003;0.006;0.075;0.01	B;B;B;B;B;B;B;B	0.19946	0.014;0.004;0.012;0.027;0.002;0.008;0.017;0.013	T	0.25433	-1.0132	8	0.40728	T	0.16	.	1.8763	0.03219	0.2781:0.1053:0.4222:0.1944	rs2277998;rs17303108;rs52822524;rs2277998	240;224;291;279;268;263;155;199	B4E2Z5;Q9H2X3-5;Q9H2X3;E7ENS9;Q9H2X3-8;Q9H2X3-9;Q9H2X3-7;Q9H2X3-4	.;.;CLC4M_HUMAN;.;.;.;.;.	N	291;279;269;240;224;291;235	ENSP00000316228:D291N;ENSP00000377680:D279N;ENSP00000248228:D269N;ENSP00000335228:D240N;ENSP00000351954:D224N;ENSP00000349924:D291N	ENSP00000248228:D269N	D	+	1	0	CLEC4M	7737628	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.143000	0.01297	-3.295000	0.00194	-3.689000	0.00024	GAC	G|0.787;A|0.213	0.213	strong		0.602	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	
ADPRH	141	hgsc.bcm.edu	37	3	119301139	119301139	+	Silent	SNP	C	C	T	rs20568	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:119301139C>T	ENST00000478399.1	+	2	1528	c.123C>T	c.(121-123)ggC>ggT	p.G41G	ADPRH_ENST00000357003.3_Silent_p.G41G|RP11-190C22.9_ENST00000609385.1_RNA|ADPRH_ENST00000478927.1_Silent_p.G41G|ADPRH_ENST00000465513.1_Silent_p.G41G|ADPRH_ENST00000471850.1_Intron			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	41					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		CCCAGCTGGGCGGCTTGGATG	0.582													C|||	733	0.146366	0.1271	0.0476	5008	,	,		18431	0.2579		0.0577	False		,,,				2504	0.2188				p.G41G	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											.	ADPRH	33	.	0			c.C123T						PASS	.	C		411,3995	203.5+/-225.9	15,381,1807	81.0	79.0	80.0		123	-11.8	0.0	3	dbSNP_67	80	538,8062	149.4+/-204.5	13,512,3775	no	coding-synonymous	ADPRH	NM_001125.2		28,893,5582	TT,TC,CC		6.2558,9.3282,7.2966		41/358	119301139	949,12057	2203	4300	6503	SO:0001819	synonymous_variant	141	exon3			GCTGGGCGGCTTG	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.123C>T	3.37:g.119301139C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	205	94	0.458537	NM_001125	B2R8H1|D3DN83	Silent	SNP	ENST00000478399.1	37	CCDS2990.1																																																																																			C|0.915;T|0.085	0.085	strong		0.582	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557497	32557497	+	Missense_Mutation	SNP	C	C	T	rs111934004		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32557497C>T	ENST00000360004.5	-	1	128	c.23G>A	c.(22-24)gGa>gAa	p.G8E		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	8					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCAGGAGCCTCCAGGGAGCTT	0.592										Multiple Myeloma(14;0.17)																											p.G8E		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G23A						PASS	.						81.0	96.0	90.0					6																	32557497		1511	2709	4220	SO:0001583	missense	3123	exon1			GAGCCTCCAGGGA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.23G>A	6.37:g.32557497C>T	ENSP00000353099:p.Gly8Glu	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	405	50	0.123457	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	15.35	2.808305	0.50421	.	.	ENSG00000196126	ENST00000360004	T	0.00265	8.39	4.68	0.718	0.18202	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00178	0.0005	M	0.69823	2.125	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.42832	-0.9428	9	0.87932	D	0	.	4.7199	0.12913	0.0:0.4558:0.3496:0.1945	.	8	P01911	2B1F_HUMAN	E	8	ENSP00000353099:G8E	ENSP00000353099:G8E	G	-	2	0	HLA-DRB1	32665475	0.000000	0.05858	0.003000	0.11579	0.026000	0.11368	0.820000	0.27323	0.595000	0.29777	0.462000	0.41574	GGA	C|0.500;T|0.500	0.500	weak		0.592	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SCYL1	57410	hgsc.bcm.edu	37	11	65293819	65293819	+	Silent	SNP	G	G	A	rs75169347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000279270.6_Silent_p.K200K|SCYL1_ENST00000527009.1_Silent_p.K57K|SCYL1_ENST00000420247.2_Silent_p.K200K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000524944.1_Silent_p.K200K	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						TCAGAGAGAAGTGGTGGGTGA	0.657													G|||	91	0.0181709	0.0015	0.0303	5008	,	,		16563	0.0		0.0616	False		,,,				2504	0.0061				p.K200K		Atlas-SNP	.											.	SCYL1	76	.	0			c.G600A						PASS	.	G	,	34,4166		0,34,2066	16.0	19.0	18.0		600,600	-1.8	0.8	11	dbSNP_131	18	504,7942		14,476,3733	no	coding-synonymous,coding-synonymous	SCYL1	NM_001048218.1,NM_020680.3	,	14,510,5799	AA,AG,GG		5.9673,0.8095,4.2543	,	200/792,200/809	65293819	538,12108	2100	4223	6323	SO:0001819	synonymous_variant	57410	exon4			AGAGAAGTGGTGG	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.600G>A	11.37:g.65293819G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	110	44	0.4	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Silent	SNP	ENST00000270176.5	37	CCDS41672.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680	
ALDH4A1	8659	hgsc.bcm.edu	37	1	19201928	19201928	+	Missense_Mutation	SNP	C	C	T	rs2230709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19201928C>T	ENST00000375341.3	-	13	1665	c.1408G>A	c.(1408-1410)Gtt>Att	p.V470I	ALDH4A1_ENST00000538839.1_Missense_Mutation_p.V419I|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.V470I|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.V410I	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	470			V -> I (in dbSNP:rs2230709). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTGCTGTCAACCAGCTGCAGC	0.622											OREG0013164	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	240	0.0479233	0.0212	0.0677	5008	,	,		19146	0.001		0.1392	False		,,,				2504	0.0245				p.V470I		Atlas-SNP	.											.	ALDH4A1	72	.	0			c.G1408A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	181,4225	116.7+/-154.6	6,169,2028	128.0	118.0	122.0		1228,1408,1408	5.1	1.0	1	dbSNP_98	122	1276,7324	254.1+/-279.5	106,1064,3130	yes	missense,missense,missense	ALDH4A1	NM_001161504.1,NM_003748.3,NM_170726.2	29,29,29	112,1233,5158	TT,TC,CC		14.8372,4.108,11.2025	benign,benign,benign	410/504,470/564,470/564	19201928	1457,11549	2203	4300	6503	SO:0001583	missense	8659	exon13			TGTCAACCAGCTG	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"""Aldehyde dehydrogenases"""	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.1408G>A	1.37:g.19201928C>T	ENSP00000364490:p.Val470Ile	Somatic	145	0	0	731	WXS	Illumina HiSeq	Phase_I	148	66	0.445946	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	37	CCDS188.1	141	0.06456043956043957	7	0.014227642276422764	33	0.09116022099447514	1	0.0017482517482517483	100	0.13192612137203166	C	12.27	1.886798	0.33348	0.04108	0.148372	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309	T;T;T;T	0.76968	-1.06;-1.06;1.65;-1.06	5.08	5.08	0.68730	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.051384	0.64402	D	0.000001	T	0.00468	0.0015	N	0.04805	-0.155	0.23113	P	0.99827054	B	0.18863	0.031	B	0.29785	0.107	T	0.13737	-1.0498	9	0.27785	T	0.31	-40.571	7.9431	0.29969	0.0:0.8246:0.0:0.1754	rs2230709;rs17479168;rs17850218;rs60503155;rs2230709	470	P30038	AL4A1_HUMAN	I	470;470;419;410	ENSP00000290597:V470I;ENSP00000364490:V470I;ENSP00000446071:V419I;ENSP00000442988:V410I	ENSP00000290597:V470I	V	-	1	0	ALDH4A1	19074515	0.983000	0.35010	0.992000	0.48379	0.768000	0.43524	2.133000	0.42093	2.367000	0.80283	0.313000	0.20887	GTT	C|0.915;T|0.085	0.085	strong		0.622	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1		
GCNT1	2650	hgsc.bcm.edu	37	9	79117751	79117751	+	Missense_Mutation	SNP	A	A	G	rs2282683	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79117751A>G	ENST00000376730.4	+	4	937	c.454A>G	c.(454-456)Att>Gtt	p.I152V	GCNT1_ENST00000536223.1_Missense_Mutation_p.I152V|GCNT1_ENST00000442371.1_Missense_Mutation_p.I152V|GCNT1_ENST00000444201.2_Missense_Mutation_p.I152V	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	152	Catalytic. {ECO:0000250}.		I -> V (in dbSNP:rs2282683). {ECO:0000269|PubMed:1329093, ECO:0000269|PubMed:7579796}.		cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						TTTCTATTGCATTCATGTGGA	0.443													A|||	1180	0.235623	0.239	0.2478	5008	,	,		19763	0.1974		0.2276	False		,,,				2504	0.2699				p.I152V		Atlas-SNP	.											.	GCNT1	52	.	0			c.A454G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	970,3436	361.6+/-315.8	126,718,1359	70.0	71.0	71.0		454,454,454,454,454	4.9	1.0	9	dbSNP_100	71	1852,6748	328.0+/-318.1	193,1466,2641	yes	missense,missense,missense,missense,missense	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	29,29,29,29,29	319,2184,4000	GG,GA,AA		21.5349,22.0154,21.6977	benign,benign,benign,benign,benign	152/429,152/429,152/429,152/429,152/429	79117751	2822,10184	2203	4300	6503	SO:0001583	missense	2650	exon4			TATTGCATTCATG	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.454A>G	9.37:g.79117751A>G	ENSP00000365920:p.Ile152Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	121	55	0.454545	NM_001490	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	505	0.23122710622710624	113	0.22967479674796748	91	0.2513812154696133	125	0.21853146853146854	176	0.23218997361477572	a	8.141	0.785332	0.16189	0.220154	0.215349	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.11063	2.81;2.81;2.81;2.81	6.07	4.94	0.65067	.	0.163576	0.53938	N	0.000049	T	0.00012	0.0000	L	0.31294	0.92	0.28431	P	0.9172873	B	0.22480	0.07	B	0.39185	0.293	T	0.50651	-0.8803	8	.	.	.	.	11.9491	0.52944	0.9329:0.0:0.0671:0.0	rs2282683;rs52805917;rs61476015;rs2282683	152	Q02742	GCNT1_HUMAN	V	152	ENSP00000440883:I152V;ENSP00000415454:I152V;ENSP00000390703:I152V;ENSP00000365920:I152V	.	I	+	1	0	GCNT1	78307571	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	2.458000	0.45014	1.128000	0.42052	0.533000	0.62120	ATT	A|0.773;G|0.227	0.227	strong		0.443	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
ATP13A2	23400	hgsc.bcm.edu	37	1	17313654	17313654	+	Silent	SNP	C	C	T	rs761421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17313654C>T	ENST00000326735.8	-	26	3003	c.2970G>A	c.(2968-2970)gtG>gtA	p.V990V	ATP13A2_ENST00000452699.1_Silent_p.V985V|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.V946V			Q9NQ11	AT132_HUMAN	ATPase type 13A2	990					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CCGGTGGCCGCACCCGTCCCA	0.687													C|||	1734	0.346246	0.171	0.4582	5008	,	,		13199	0.252		0.508	False		,,,				2504	0.4346				p.V990V		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G2970A						PASS	.	C	,,	1046,3360	380.6+/-323.8	133,780,1290	46.0	43.0	44.0		2955,2838,2970	-5.5	0.9	1	dbSNP_86	44	4488,4110	583.2+/-391.5	1155,2178,966	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	1288,2958,2256	TT,TC,CC		47.8018,23.7404,42.5561	,,	985/1176,946/1159,990/1181	17313654	5534,7470	2203	4299	6502	SO:0001819	synonymous_variant	23400	exon26			TGGCCGCACCCGT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2970G>A	1.37:g.17313654C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	41	30	0.731707	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			C|0.600;T|0.400	0.400	strong		0.687	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
CYB5R3	1727	hgsc.bcm.edu	37	22	43032811	43032811	+	Missense_Mutation	SNP	A	A	T	rs370253340		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43032811A>T	ENST00000352397.5	-	2	315	c.63T>A	c.(61-63)agT>agA	p.S21R	CYB5R3_ENST00000407623.3_5'UTR|CYB5R3_ENST00000361740.4_Missense_Mutation_p.S54R|CYB5R3_ENST00000396303.3_5'UTR|CYB5R3_ENST00000402438.1_5'UTR|CYB5R3_ENST00000407332.1_5'UTR	NM_000398.6	NP_000389.1	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3	21					blood circulation (GO:0008015)|cholesterol biosynthetic process (GO:0006695)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|hemoglobin complex (GO:0005833)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|FAD binding (GO:0071949)|flavin adenine dinucleotide binding (GO:0050660)|NAD binding (GO:0051287)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6					Flavin adenine dinucleotide(DB03147)	TCATGAGCAGACTGTACAGGA	0.622																																					p.S54R		Atlas-SNP	.											.	CYB5R3	31	.	0			c.T162A						PASS	.	A	,,,ARG/SER,ARG/SER	0,4406		0,0,2203	78.0	67.0	71.0		,,,162,63	0.2	0.9	22		71	1,8599	1.2+/-3.3	0,1,4299	no	utr-5,utr-5,utr-5,missense,missense	CYB5R3	NM_001129819.2,NM_001171661.1,NM_007326.4,NM_001171660.1,NM_000398.6	,,,110,110	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	,,,benign,benign	,,,54/335,21/302	43032811	1,13005	2203	4300	6503	SO:0001583	missense	1727	exon2			GAGCAGACTGTAC	M16461	CCDS14040.1, CCDS33658.1, CCDS54535.1	22q13.2	2012-10-02		2005-07-13	ENSG00000100243	ENSG00000100243	1.6.2.2		2873	protein-coding gene	gene with protein product		613213	"""diaphorase (NADH) (cytochrome b-5 reductase)"""	DIA1		2479590, 3268037	Standard	NM_001129819		Approved		uc011aps.2	P00387	OTTHUMG00000150745	ENST00000352397.5:c.63T>A	22.37:g.43032811A>T	ENSP00000338461:p.Ser21Arg	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	14	0.285714	NM_001171660	B1AHF2|B7Z7L3|O75675|Q8TDL8|Q8WTS8|Q9UEN4|Q9UEN5|Q9UL55|Q9UL56	Missense_Mutation	SNP	ENST00000352397.5	37	CCDS33658.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.881744	0.33255	0.0	1.16E-4	ENSG00000100243	ENST00000361740;ENST00000352397	D;D	0.87256	-2.23;-2.2	4.82	0.217	0.15264	.	0.474289	0.25037	N	0.033621	T	0.75982	0.3924	L	0.44542	1.39	0.80722	D	1	P;B	0.37864	0.61;0.007	B;B	0.29942	0.109;0.025	T	0.65191	-0.6228	10	0.25751	T	0.34	-14.0956	8.2667	0.31819	0.3607:0.0:0.6393:0.0	.	54;21	B7Z7L3;P00387	.;NB5R3_HUMAN	R	54;21	ENSP00000354468:S54R;ENSP00000338461:S21R	ENSP00000338461:S21R	S	-	3	2	CYB5R3	41362755	0.801000	0.28930	0.938000	0.37757	0.799000	0.45148	0.491000	0.22419	-0.057000	0.13199	0.260000	0.18958	AGT	.	.	weak		0.622	CYB5R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320439.1		
FBXL18	80028	hgsc.bcm.edu	37	7	5530954	5530954	+	Silent	SNP	G	G	A	rs11975313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5530954G>A	ENST00000382368.3	-	4	2031	c.1908C>T	c.(1906-1908)ttC>ttT	p.F636F	FBXL18_ENST00000453700.3_Silent_p.F636F	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	636									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		AGCGAGCCATGAAGGCCAGCA	0.667													G|||	900	0.179712	0.2685	0.2061	5008	,	,		17403	0.0377		0.1392	False		,,,				2504	0.229				p.F636F		Atlas-SNP	.											.	FBXL18	99	.	0			c.C1908T						PASS	.	G		1048,3184		131,786,1199	17.0	22.0	20.0		1908	4.0	1.0	7	dbSNP_120	20	1100,7380		72,956,3212	no	coding-synonymous	FBXL18	NM_024963.4		203,1742,4411	AA,AG,GG		12.9717,24.7637,16.8974		636/719	5530954	2148,10564	2116	4240	6356	SO:0001819	synonymous_variant	80028	exon4			AGCCATGAAGGCC	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"""F-boxes / Leucine-rich repeats"""	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.1908C>T	7.37:g.5530954G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Silent	SNP	ENST00000382368.3	37	CCDS43546.1	320|320	0.14652014652014653|0.14652014652014653	123|123	0.25|0.25	66|66	0.18232044198895028|0.18232044198895028	22|22	0.038461538461538464|0.038461538461538464	109|109	0.1437994722955145|0.1437994722955145	G|G	2.467|2.467	-0.322730|-0.322730	0.05350|0.05350	0.247637|0.247637	0.129717|0.129717	ENSG00000155034|ENSG00000155034	ENST00000297035|ENST00000458142	.|.	.|.	.|.	4.91|4.91	4.01|4.01	0.46588|0.46588	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.13710|0.13710	-1.0499|-1.0499	4|3	0.87932|.	D|.	0|.	.|.	8.0964|8.0964	0.30831|0.30831	0.1852:0.0:0.8148:0.0|0.1852:0.0:0.8148:0.0	rs11975313;rs11975313|rs11975313;rs11975313	.|.	.|.	.|.	Y|L	196|520	.|.	ENSP00000297035:H196Y|.	H|S	-|-	1|2	0|0	FBXL18|FBXL18	5497480|5497480	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.096000|0.096000	0.18686|0.18686	3.304000|3.304000	0.51866|0.51866	1.041000|1.041000	0.40125|0.40125	0.561000|0.561000	0.74099|0.74099	CAT|TCA	G|0.849;A|0.151	0.151	strong		0.667	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963	
UBE2H	7328	hgsc.bcm.edu	37	7	129479138	129479138	+	Silent	SNP	T	T	C	rs12539800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:129479138T>C	ENST00000355621.3	-	6	729	c.336A>G	c.(334-336)ttA>ttG	p.L112L	UBE2H_ENST00000473814.2_Silent_p.L81L	NM_001202498.1|NM_003344.3	NP_001189427.1|NP_003335.1	P62256	UBE2H_HUMAN	ubiquitin-conjugating enzyme E2H	112					protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|skin(1)	10	Melanoma(18;0.0435)					GATAGGCCAATAACTGAGGCA	0.418													C|||	215	0.0429313	0.0106	0.0519	5008	,	,		19825	0.0397		0.1044	False		,,,				2504	0.0204				p.L112L		Atlas-SNP	.											.	UBE2H	17	.	0			c.A336G						PASS	.	C	,,	105,4301	817.1+/-416.3	1,103,2099	135.0	122.0	126.0		126,336,243	4.5	1.0	7	dbSNP_120	126	794,7806	783.2+/-407.6	40,714,3546	no	coding-synonymous,coding-synonymous,coding-synonymous	UBE2H	NM_001202498.1,NM_003344.3,NM_182697.2	,,	41,817,5645	CC,CT,TT		9.2326,2.3831,6.9122	,,	42/114,112/184,81/153	129479138	899,12107	2203	4300	6503	SO:0001819	synonymous_variant	7328	exon6			GGCCAATAACTGA	BC006277	CCDS5814.1, CCDS47710.1	7q32	2012-07-20	2011-05-19		ENSG00000186591	ENSG00000186591	6.3.2.19	"""Ubiquitin-conjugating enzymes E2"""	12484	protein-coding gene	gene with protein product	"""GID complex subunit 3, UBC8 homolog (S. cerevisiae)"""	601082	"""ubiquitin-conjugating enzyme E2H (homologous to yeast UBC8)"", ""ubiquitin-conjugating enzyme E2H (UBC8 homolog, yeast)"""			8132613	Standard	NM_003344		Approved	UBCH, UBC8, GID3	uc003vpf.2	P62256	OTTHUMG00000157650	ENST00000355621.3:c.336A>G	7.37:g.129479138T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	NM_003344	A4D1L6|C9JY93|P37286|Q7Z6F4	Silent	SNP	ENST00000355621.3	37	CCDS5814.1																																																																																			T|0.939;C|0.061	0.061	strong		0.418	UBE2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349327.2	NM_003344	
CHRNA9	55584	hgsc.bcm.edu	37	4	40337523	40337523	+	Silent	SNP	C	C	T	rs56241474	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:40337523C>T	ENST00000310169.2	+	1	178	c.39C>T	c.(37-39)atC>atT	p.I13I		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	13					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|inner ear morphogenesis (GO:0042472)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine-activated cation-selective channel activity (GO:0004889)|calcium channel activity (GO:0005262)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(4)|stomach(1)	33					Galantamine(DB00674)|Nicotine(DB00184)	TTTGCTGGATCTACTTTGCTG	0.512													T|||	1087	0.217053	0.2995	0.2464	5008	,	,		21546	0.0496		0.2734	False		,,,				2504	0.1994				p.I13I	Esophageal Squamous(115;1297 1602 22235 25158 43327)	Atlas-SNP	.											CHRNA9,NS,adenoma,0,1	CHRNA9	53	1	0			c.C39T						PASS	.	T		1266,3140	702.9+/-406.9	190,886,1127	157.0	134.0	142.0		39	4.2	1.0	4	dbSNP_129	142	2622,5978	687.5+/-404.2	421,1780,2099	no	coding-synonymous	CHRNA9	NM_017581.2		611,2666,3226	TT,TC,CC		30.4884,28.7335,29.8939		13/480	40337523	3888,9118	2203	4300	6503	SO:0001819	synonymous_variant	55584	exon1			CTGGATCTACTTT	AF227732	CCDS3459.1	4p14	2012-02-11	2012-02-07		ENSG00000174343	ENSG00000174343		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	14079	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 9 (neuronal)"""	605116	"""cholinergic receptor, nicotinic, alpha polypeptide 9"""				Standard	NM_017581		Approved	NACHRA9	uc003gva.2	Q9UGM1	OTTHUMG00000099375	ENST00000310169.2:c.39C>T	4.37:g.40337523C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	269	143	0.531599	NM_017581	Q14CY7|Q4W5A2|Q9NYV2	Silent	SNP	ENST00000310169.2	37	CCDS3459.1																																																																																			C|0.721;T|0.279	0.279	strong		0.512	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1		
PLBD1	79887	hgsc.bcm.edu	37	12	14664595	14664595	+	Silent	SNP	A	A	G	rs10846013	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:14664595A>G	ENST00000240617.5	-	7	1547	c.895T>C	c.(895-897)Ttg>Ctg	p.L299L		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	299					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						GTCTGCAGCAATATCAATCCA	0.413													A|||	1420	0.283546	0.1876	0.3919	5008	,	,		20168	0.1925		0.2555	False		,,,				2504	0.4591				p.L299L		Atlas-SNP	.											.	PLBD1	36	.	0			c.T895C						PASS	.	A		859,3547	335.2+/-303.8	68,723,1412	70.0	69.0	69.0		895	-11.6	0.0	12	dbSNP_120	69	2619,5981	424.4+/-354.6	397,1825,2078	no	coding-synonymous	PLBD1	NM_024829.5		465,2548,3490	GG,GA,AA		30.4535,19.4961,26.7415		299/554	14664595	3478,9528	2203	4300	6503	SO:0001819	synonymous_variant	79887	exon7			GCAGCAATATCAA	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"""PLB homolog 1 (Dictyostelium)"""					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.895T>C	12.37:g.14664595A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_024829	A8K4E9|Q9BVV3|Q9H625	Silent	SNP	ENST00000240617.5	37	CCDS31751.1																																																																																			A|0.734;G|0.266	0.266	strong		0.413	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923180	43923180	+	Missense_Mutation	SNP	G	G	A	rs242944	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:43923180G>A	ENST00000329196.5	+	1	925	c.908G>A	c.(907-909)cGc>cAc	p.R303H	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	303			R -> H (in dbSNP:rs242944). {ECO:0000269|PubMed:12139484, ECO:0000269|PubMed:15489334}.			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CTGGTGTGCCGCCTGTCCCTG	0.607													G|||	3051	0.609225	0.3669	0.6412	5008	,	,		19394	0.7986		0.5557	False		,,,				2504	0.774				p.R303H		Atlas-SNP	.											.	.	.	.	0			c.G908A						PASS	.	G	HIS/ARG	1723,2683	516.2+/-369.1	329,1065,809	71.0	76.0	74.0		908	-8.5	0.0	17	dbSNP_79	74	4803,3797	609.5+/-395.5	1364,2075,861	no	missense	IMP5	NM_175882.2	29	1693,3140,1670	AA,AG,GG		44.1512,39.1058,49.8232	benign	303/685	43923180	6526,6480	2203	4300	6503	SO:0001583	missense	162540	exon1			TGTGCCGCCTGTC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.908G>A	17.37:g.43923180G>A	ENSP00000332488:p.Arg303His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	1287	0.5892857142857143	176	0.35772357723577236	207	0.5718232044198895	470	0.8216783216783217	434	0.5725593667546174	G	3.544	-0.093134	0.07053	0.391058	0.558488	ENSG00000185294	ENST00000329196	T	0.17854	2.25	5.38	-8.51	0.00923	.	.	.	.	.	T	0.00012	0.0000	N	0.16201	0.385	0.53688	P	2.599999999997049E-5	B	0.18166	0.026	B	0.18263	0.021	T	0.24368	-1.0162	8	0.38643	T	0.18	-13.3789	5.449	0.16552	0.3049:0.1053:0.4859:0.1038	rs242944;rs17690422;rs57248845;rs242944	303	Q8IUH8	IMP5_HUMAN	H	303	ENSP00000332488:R303H	ENSP00000332488:R303H	R	+	2	0	AC217771.1	41278960	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.364000	0.07583	-1.677000	0.01455	-1.788000	0.00630	CGC	G|0.466;A|0.534	0.534	strong		0.607	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
ZNF33B	7582	hgsc.bcm.edu	37	10	43089156	43089156	+	Silent	SNP	C	C	T	rs7904627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43089156C>T	ENST00000359467.3	-	5	1356	c.1242G>A	c.(1240-1242)caG>caA	p.Q414Q	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						ATGCATTACACTGATAGGGTT	0.423													T|||	727	0.145168	0.3056	0.1859	5008	,	,		20866	0.0675		0.1024	False		,,,				2504	0.0235				p.Q414Q	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.G1242A						PASS	.	T		1315,3091	695.6+/-406.0	205,905,1093	102.0	108.0	106.0		1242	-4.8	0.8	10	dbSNP_116	106	674,7926	787.8+/-407.6	31,612,3657	no	coding-synonymous	ZNF33B	NM_006955.1		236,1517,4750	TT,TC,CC		7.8372,29.8457,15.2929		414/779	43089156	1989,11017	2203	4300	6503	SO:0001819	synonymous_variant	7582	exon5			ATTACACTGATAG	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"""Zinc fingers, C2H2-type"", ""-"""	13097	protein-coding gene	gene with protein product		194522	"""zinc finger protein 33b (KOX 31)"", ""zinc finger protein 11B"""	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1242G>A	10.37:g.43089156C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	169	79	0.467456	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Silent	SNP	ENST00000359467.3	37	CCDS7198.1																																																																																			C|0.852;T|0.148	0.148	strong		0.423	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
TRPC1	7220	hgsc.bcm.edu	37	3	142524858	142524858	+	Silent	SNP	G	G	A	rs1132030	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:142524858G>A	ENST00000476941.1	+	13	2649	c.2163G>A	c.(2161-2163)agG>agA	p.R721R	TRPC1_ENST00000273482.6_Silent_p.R687R	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	721					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						AGGAATGGAGGAATTTGAAAC	0.348													A|||	1832	0.365815	0.736	0.1772	5008	,	,		17698	0.3552		0.2058	False		,,,				2504	0.1748				p.R721R		Atlas-SNP	.											.	TRPC1	82	.	0			c.G2163A						PASS	.	A		2808,1598	492.0+/-362.3	898,1012,293	91.0	102.0	98.0		2061	3.0	1.0	3	dbSNP_86	98	1606,6994	741.3+/-407.1	168,1270,2862	no	coding-synonymous	TRPC1	NM_003304.4		1066,2282,3155	AA,AG,GG		18.6744,36.2687,33.9382		687/760	142524858	4414,8592	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon13			ATGGAGGAATTTG	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2163G>A	3.37:g.142524858G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	155	60	0.387097	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			A|0.353;G|0.647;T|0.000	0.353	strong		0.348	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
SPEG	10290	hgsc.bcm.edu	37	2	220342004	220342004	+	Silent	SNP	G	G	A	rs45519033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220342004G>A	ENST00000312358.7	+	20	4698	c.4566G>A	c.(4564-4566)gaG>gaA	p.E1522E	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1522	Ig-like 8.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TGCAGGACGAGGTGCTGCTGA	0.627													G|||	204	0.0407348	0.0091	0.0937	5008	,	,		15120	0.0268		0.0567	False		,,,				2504	0.044				p.E1522E		Atlas-SNP	.											.	SPEG	272	.	0			c.G4566A						PASS	.	G		89,4221		0,89,2066	44.0	49.0	48.0		4566	4.2	1.0	2	dbSNP_127	48	583,7885		17,549,3668	no	coding-synonymous	SPEG	NM_005876.4		17,638,5734	AA,AG,GG		6.8847,2.065,5.259		1522/3268	220342004	672,12106	2155	4234	6389	SO:0001819	synonymous_variant	10290	exon20			GGACGAGGTGCTG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4566G>A	2.37:g.220342004G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			G|0.945;A|0.055	0.055	strong		0.627	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
FDFT1	2222	hgsc.bcm.edu	37	8	11683622	11683622	+	Silent	SNP	T	T	C	rs2229247	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11683622T>C	ENST00000220584.4	+	5	822	c.600T>C	c.(598-600)gaT>gaC	p.D200D	FDFT1_ENST00000528812.1_Silent_p.D136D|FDFT1_ENST00000525777.1_Silent_p.D115D|FDFT1_ENST00000528643.1_Silent_p.D115D|FDFT1_ENST00000538689.1_Silent_p.D89D|FDFT1_ENST00000443614.2_Silent_p.D157D|FDFT1_ENST00000525900.1_Silent_p.D193D|FDFT1_ENST00000530664.1_Silent_p.D136D|FDFT1_ENST00000446331.2_3'UTR	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	200					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		TTGGTGAAGATACAGAACGTG	0.488													T|||	203	0.0405351	0.0923	0.0331	5008	,	,		18817	0.0		0.0378	False		,,,				2504	0.0204				p.D200D		Atlas-SNP	.											.	FDFT1	25	.	0			c.T600C						PASS	.	T		371,4035	189.5+/-215.6	21,329,1853	124.0	119.0	121.0		600	-1.1	0.0	8	dbSNP_98	121	240,8360	96.1+/-157.9	4,232,4064	no	coding-synonymous	FDFT1	NM_004462.3		25,561,5917	CC,CT,TT		2.7907,8.4203,4.6978		200/418	11683622	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	2222	exon5			TGAAGATACAGAA	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.600T>C	8.37:g.11683622T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	176	83	0.471591	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Silent	SNP	ENST00000220584.4	37	CCDS5985.1																																																																																			T|0.957;C|0.043	0.043	strong		0.488	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
C10orf113	387638	hgsc.bcm.edu	37	10	21415006	21415006	+	Missense_Mutation	SNP	T	T	C	rs11591355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:21415006T>C	ENST00000534331.1	-	2	264	c.214A>G	c.(214-216)Agg>Ggg	p.R72G	C10orf113_ENST00000529198.1_3'UTR|NEBL_ENST00000417816.2_Intron|C10orf113_ENST00000377118.4_Missense_Mutation_p.R62G	NM_001010896.2	NP_001010896.2	Q5VZT2	CJ113_HUMAN	chromosome 10 open reading frame 113	72			R -> G (in dbSNP:rs11591355).							endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|pancreas(1)	7						ACCAGCTTCCTGGGAGGCCTC	0.597													T|||	750	0.14976	0.0061	0.1095	5008	,	,		16903	0.3115		0.1342	False		,,,				2504	0.2219				p.R72G		Atlas-SNP	.											.	C10orf113	32	.	0			c.A214G						PASS	.	T	,,,GLY/ARG	110,4296	76.8+/-115.0	2,106,2095	55.0	58.0	57.0		,,,214	-1.2	0.0	10	dbSNP_120	57	1215,7383	235.7+/-268.2	87,1041,3171	yes	intron,utr-3,intron,missense	NEBL,C10orf113	NM_001173484.1,NM_001177483.1,NM_213569.2,NM_001010896.2	,,,125	89,1147,5266	CC,CT,TT		14.1312,2.4966,10.1892	,,,benign	,,,72/156	21415006	1325,11679	2203	4299	6502	SO:0001583	missense	387638	exon2			GCTTCCTGGGAGG		CCDS31162.1, CCDS31162.2, CCDS53496.1	10p12.31	2012-06-12			ENSG00000204683	ENSG00000204683			31447	protein-coding gene	gene with protein product							Standard	NM_001010896		Approved	bA165O3.1	uc001iqm.3	Q5VZT2	OTTHUMG00000017786	ENST00000534331.1:c.214A>G	10.37:g.21415006T>C	ENSP00000433646:p.Arg72Gly	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_001010896	B9EIM9|E9PRX7	Missense_Mutation	SNP	ENST00000534331.1	37	CCDS31162.2	302	0.1382783882783883	4	0.008130081300813009	36	0.09944751381215469	161	0.28146853146853146	101	0.13324538258575197	T	12.49	1.952931	0.34471	0.024966	0.141312	ENSG00000204683	ENST00000534331;ENST00000377118	T;T	0.39592	1.07;1.07	4.33	-1.21	0.09524	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.34900	-0.9810	8	0.87932	D	0	1.017	2.3618	0.04309	0.3688:0.2239:0.0:0.4073	rs11591355	72	Q5VZT2	CJ113_HUMAN	G	72;62	ENSP00000433646:R72G;ENSP00000366322:R62G	ENSP00000366322:R62G	R	-	1	2	C10orf113	21455012	0.625000	0.27111	0.004000	0.12327	0.398000	0.30690	0.502000	0.22594	-0.000000	0.14550	-0.467000	0.05162	AGG	T|0.882;C|0.118	0.118	strong		0.597	C10orf113-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047108.3	NM_001010896	
SKAP2	8935	hgsc.bcm.edu	37	7	26765596	26765596	+	Missense_Mutation	SNP	C	C	A	rs1129771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:26765596C>A	ENST00000345317.2	-	8	917	c.604G>T	c.(604-606)Gct>Tct	p.A202S	SKAP2_ENST00000489977.1_5'UTR|SKAP2_ENST00000539623.1_Missense_Mutation_p.A30S	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	202	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		A -> S (in dbSNP:rs1129771). {ECO:0000269|PubMed:9755858, ECO:0000269|PubMed:9837776, ECO:0000269|Ref.5}.		B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						TTGGGAGAAGCTGCTGTAAAC	0.318													C|||	600	0.119808	0.298	0.1196	5008	,	,		19143	0.005		0.0815	False		,,,				2504	0.0368				p.A202S		Atlas-SNP	.											.	SKAP2	40	.	0			c.G604T						PASS	.	C	SER/ALA	1046,3360	382.1+/-324.3	132,782,1289	73.0	71.0	71.0		604	3.3	1.0	7	dbSNP_86	71	749,7849	179.2+/-228.4	34,681,3584	yes	missense	SKAP2	NM_003930.3	99	166,1463,4873	AA,AC,CC		8.7113,23.7404,13.8034	benign	202/360	26765596	1795,11209	2203	4299	6502	SO:0001583	missense	8935	exon8			GAGAAGCTGCTGT		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"""Pleckstrin homology (PH) domain containing"""	15687	protein-coding gene	gene with protein product		605215	"""src family associated phosphoprotein 2"""	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.604G>T	7.37:g.26765596C>A	ENSP00000005587:p.Ala202Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	28	19	0.678571	NM_003930	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	37	CCDS5400.1	234	0.10714285714285714	141	0.2865853658536585	36	0.09944751381215469	4	0.006993006993006993	53	0.06992084432717678	C	0.489	-0.876184	0.02550	0.237404	0.087113	ENSG00000005020	ENST00000345317;ENST00000539623;ENST00000535331	T;T	0.10573	2.86;2.86	6.03	3.28	0.37604	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.222163	0.46758	D	0.000271	T	0.00012	0.0000	N	0.02213	-0.635	0.21499	P	0.999665634	B;B	0.11235	0.004;0.0	B;B	0.18871	0.023;0.003	T	0.46624	-0.9178	9	0.02654	T	1	-15.9968	6.6118	0.22755	0.1245:0.6788:0.0:0.1967	rs1129771;rs3188028;rs11972717;rs17415882;rs1129771	187;202	B7Z5N4;O75563	.;SKAP2_HUMAN	S	202;30;187	ENSP00000005587:A202S;ENSP00000443593:A30S	ENSP00000005587:A202S	A	-	1	0	SKAP2	26732121	0.919000	0.31177	1.000000	0.80357	0.944000	0.59088	0.492000	0.22435	0.890000	0.36211	-0.137000	0.14449	GCT	C|0.873;A|0.127	0.127	strong		0.318	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1		
SEMA3A	10371	hgsc.bcm.edu	37	7	83590852	83590852	+	Silent	SNP	T	T	C	rs797821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:83590852T>C	ENST00000265362.4	-	17	2465	c.2151A>G	c.(2149-2151)acA>acG	p.T717T	SEMA3A_ENST00000436949.1_Silent_p.T717T	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	717					apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						ACTCATCCATTGTGTTGAGAT	0.468													C|||	3065	0.612021	0.475	0.6902	5008	,	,		19046	0.6915		0.6412	False		,,,				2504	0.6299				p.T717T		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A2151G						PASS	.	C		2179,2227	591.6+/-387.6	531,1117,555	195.0	170.0	178.0		2151	-11.6	0.2	7	dbSNP_86	178	5411,3189	482.4+/-370.9	1682,2047,571	no	coding-synonymous	SEMA3A	NM_006080.2		2213,3164,1126	CC,CT,TT		37.0814,49.4553,41.6423		717/772	83590852	7590,5416	2203	4300	6503	SO:0001819	synonymous_variant	10371	exon17			ATCCATTGTGTTG	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.2151A>G	7.37:g.83590852T>C		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	317	152	0.479495	NM_006080		Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																			T|0.401;G|0.006	.	strong		0.468	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080	
OR6Q1	219952	hgsc.bcm.edu	37	11	57799183	57799183	+	Silent	SNP	C	C	T	rs7123727	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57799183C>T	ENST00000302622.3	+	1	782	c.759C>T	c.(757-759)agC>agT	p.S253S	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				CTGTGGTGAGCCTCTTCTATG	0.517													C|||	754	0.150559	0.0938	0.1614	5008	,	,		22234	0.1022		0.2823	False		,,,				2504	0.1339				p.S253S		Atlas-SNP	.											.	OR6Q1	58	.	0			c.C759T						PASS	.	C		497,3905	230.4+/-244.6	30,437,1734	183.0	157.0	166.0		759	3.3	0.9	11	dbSNP_116	166	2503,6089	410.7+/-350.2	351,1801,2144	no	coding-synonymous	OR6Q1	NM_001005186.2		381,2238,3878	TT,TC,CC		29.1318,11.2903,23.0876		253/318	57799183	3000,9994	2201	4296	6497	SO:0001819	synonymous_variant	219952	exon1			GGTGAGCCTCTTC	AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"""GPCR / Class A : Olfactory receptors"""	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.759C>T	11.37:g.57799183C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	186	185	0.994624	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Silent	SNP	ENST00000302622.3	37	CCDS31541.1																																																																																			C|0.778;T|0.222	0.222	strong		0.517	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971152	45971152	+	Missense_Mutation	SNP	G	G	A	rs199607801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45971152G>A	ENST00000391621.1	-	1	236	c.190C>T	c.(190-192)Ccc>Tcc	p.P64S	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	64	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CAGGCGCTGGGCTCACAGGCC	0.706																																					p.P64S		Atlas-SNP	.											KRTAP10-2,colon,carcinoma,0,1	KRTAP10-2	21	1	0			c.C190T						scavenged	.						33.0	39.0	37.0					21																	45971152		2198	4287	6485	SO:0001583	missense	386679	exon1			CGCTGGGCTCACA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.190C>T	21.37:g.45971152G>A	ENSP00000375479:p.Pro64Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	114	44	0.385965	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	g	0.927	-0.713936	0.03206	.	.	ENSG00000205445	ENST00000391621	T	0.00672	5.89	2.06	-0.231	0.13086	.	.	.	.	.	T	0.00552	0.0018	N	0.13140	0.3	0.09310	N	1	B	0.20164	0.042	B	0.10450	0.005	T	0.44982	-0.9292	9	0.33940	T	0.23	.	5.0625	0.14564	0.3226:0.0:0.6774:0.0	.	64	P60368	KR102_HUMAN	S	64	ENSP00000375479:P64S	ENSP00000375479:P64S	P	-	1	0	KRTAP10-2	44795580	0.000000	0.05858	0.165000	0.22776	0.031000	0.12232	-0.338000	0.07842	-0.390000	0.07774	0.306000	0.20318	CCC	G|0.978;A|0.022	0.022	strong		0.706	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71277083	71277083	+	Silent	SNP	C	C	T	rs146926834	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71277083C>T	ENST00000398531.1	+	1	475	c.450C>T	c.(448-450)tgC>tgT	p.C150C	KRTAP5-10_ENST00000376536.4_Silent_p.C102C	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	150	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						Cctgctgctgctcctcaggct	0.632													c|||	231	0.0461262	0.0023	0.0187	5008	,	,		12160	0.1052		0.0348	False		,,,				2504	0.0757				p.C150C		Atlas-SNP	.											.	KRTAP5-10	37	.	0			c.C450T						PASS	.	C		44,4356		0,44,2156	86.0	105.0	99.0		450	-1.7	0.0	11	dbSNP_134	99	282,8304		3,276,4014	no	coding-synonymous	KRTAP5-10	NM_001012710.1		3,320,6170	TT,TC,CC		3.2844,1.0,2.5104		150/203	71277083	326,12660	2200	4293	6493	SO:0001819	synonymous_variant	387273	exon1			CTGCTGCTCCTCA	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.450C>T	11.37:g.71277083C>T		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	285	147	0.515789	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			C|0.959;T|0.041	0.041	strong		0.632	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
CYP11B1	1584	hgsc.bcm.edu	37	8	143956706	143956706	+	Silent	SNP	G	G	A	rs5293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143956706G>A	ENST00000292427.4	-	7	1176	c.1144C>T	c.(1144-1146)Ctg>Ttg	p.L382L	CYP11B1_ENST00000517471.1_Silent_p.L382L|CYP11B1_ENST00000377675.3_Silent_p.L453L	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	382					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)	p.L382L(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	ACTCGCTCCAGAAACAGACCC	0.607									Familial Hyperaldosteronism type I				.|||	14	0.00279553	0.0008	0.0043	5008	,	,		15997	0.0		0.006	False		,,,				2504	0.0041				p.L382L		Atlas-SNP	.											CYP11B1,NS,carcinoma,0,1	CYP11B1	128	1	1	Substitution - coding silent(1)	lung(1)	c.C1144T						scavenged	.						61.0	61.0	61.0					8																	143956706		2203	4300	6503	SO:0001819	synonymous_variant	1584	exon7	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GCTCCAGAAACAG	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.1144C>T	8.37:g.143956706G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	109	16	0.146789	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			G|0.903;A|0.097	0.097	strong		0.607	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
IGSF5	150084	hgsc.bcm.edu	37	21	41142940	41142940	+	Silent	SNP	G	G	A	rs2837200	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:41142940G>A	ENST00000380588.4	+	4	619	c.516G>A	c.(514-516)ccG>ccA	p.P172P	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	172	Ig-like V-type 2.				single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				CCCGGCTCCCGGATATTTCCT	0.502													G|||	509	0.101637	0.0121	0.1412	5008	,	,		15276	0.0		0.2873	False		,,,				2504	0.1084				p.P172P		Atlas-SNP	.											.	IGSF5	62	.	0			c.G516A						PASS	.	G		260,4146	148.4+/-182.8	10,240,1953	65.0	64.0	64.0		516	-1.9	0.0	21	dbSNP_100	64	2716,5884	431.4+/-356.8	450,1816,2034	no	coding-synonymous	IGSF5	NM_001080444.1		460,2056,3987	AA,AG,GG		31.5814,5.901,22.8817		172/408	41142940	2976,10030	2203	4300	6503	SO:0001819	synonymous_variant	150084	exon4			GCTCCCGGATATT		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.516G>A	21.37:g.41142940G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001080444		Silent	SNP	ENST00000380588.4	37	CCDS33562.1																																																																																			G|0.803;A|0.197	0.197	strong		0.502	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
FANCI	55215	hgsc.bcm.edu	37	15	89838318	89838318	+	Missense_Mutation	SNP	A	A	T	rs35875311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89838318A>T	ENST00000310775.7	+	24	2715	c.2629A>T	c.(2629-2631)Ata>Tta	p.I877L	FANCI_ENST00000300027.8_Intron	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	877				I -> L (in Ref. 6; BAB47423). {ECO:0000305}.	cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CCTCTGTGACATAACTCGGTA	0.478								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				A|||	298	0.0595048	0.0038	0.072	5008	,	,		19029	0.0595		0.0924	False		,,,				2504	0.092				p.I877L		Atlas-SNP	.											.	FANCI	129	.	0			c.A2629T						PASS	.	A	LEU/ILE,	29,1349		1,27,661	117.0	105.0	108.0		2629,	6.0	1.0	15	dbSNP_126	108	349,2831		17,315,1258	yes	missense,intron	FANCI	NM_001113378.1,NM_018193.2	5,	18,342,1919	TT,TA,AA		10.9748,2.1045,8.2931	benign,	877/1329,	89838318	378,4180	689	1590	2279	SO:0001583	missense	55215	exon24	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGTGACATAACTC	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.2629A>T	15.37:g.89838318A>T	ENSP00000310842:p.Ile877Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	140	0.0641025641025641	2	0.0040650406504065045	25	0.06906077348066299	37	0.06468531468531469	76	0.10026385224274406	A	19.13	3.766935	0.69878	0.021045	0.109748	ENSG00000140525	ENST00000310775	T	0.73897	-0.79	5.98	5.98	0.97165	.	0.101413	0.36409	U	0.002613	T	0.03348	0.0097	L	0.48362	1.52	0.80722	D	1	B	0.22604	0.072	B	0.25140	0.058	T	0.36578	-0.9742	10	0.13108	T	0.6	-2.4301	16.4696	0.84102	1.0:0.0:0.0:0.0	rs35875311	877	Q9NVI1	FANCI_HUMAN	L	877	ENSP00000310842:I877L	ENSP00000310842:I877L	I	+	1	0	FANCI	87639322	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.129000	0.57957	2.289000	0.77006	0.482000	0.46254	ATA	A|0.931;T|0.069	0.069	strong		0.478	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592524	167592524	+	Missense_Mutation	SNP	T	T	C	rs2989545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167592524T>C	ENST00000366832.2	+	6	814	c.683T>C	c.(682-684)cTg>cCg	p.L228P		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	228										endometrium(1)|kidney(2)|lung(3)	6						TCCCGAAGTCTGCAAAACTCC	0.602																																					p.L228P		Atlas-SNP	.											.	TCP10L2	41	.	0			c.T683C						PASS	.						22.0	25.0	24.0					6																	167592524		692	1586	2278	SO:0001583	missense	401285	exon6			GAAGTCTGCAAAA		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.683T>C	6.37:g.167592524T>C	ENSP00000355797:p.Leu228Pro	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	109	48	0.440367	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	.	.	.	.	.	.	.	.	.	.	N	3.564	-0.089011	0.07097	.	.	ENSG00000166984	ENST00000366832	T	0.19669	2.13	1.87	0.683	0.17998	.	.	.	.	.	T	0.03095	0.0091	N	0.11201	0.11	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40496	-0.9560	8	0.48119	T	0.1	.	5.4648	0.16637	0.0:0.1826:0.0:0.8174	rs2989545;rs59337236	228	B9ZVM9	TCP2L_HUMAN	P	228	ENSP00000355797:L228P	ENSP00000283507:L228P	L	+	2	0	TCP10L2	167512514	0.002000	0.14202	0.006000	0.13384	0.011000	0.07611	0.093000	0.15086	-0.165000	0.10908	-1.687000	0.00730	CTG	.	.	weak		0.602	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
TTC21A	199223	hgsc.bcm.edu	37	3	39161456	39161456	+	Missense_Mutation	SNP	G	G	A	rs1274972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:39161456G>A	ENST00000431162.2	+	8	1003	c.869G>A	c.(868-870)aGg>aAg	p.R290K	TTC21A_ENST00000440121.1_Missense_Mutation_p.R241K|TTC21A_ENST00000301819.6_Missense_Mutation_p.R290K			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	290			R -> K (in dbSNP:rs1274972).							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CTAGAGACAAGGGAACCCGAA	0.458													G|||	2282	0.455671	0.8495	0.3429	5008	,	,		18365	0.2738		0.334	False		,,,				2504	0.316				p.R290K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G869A						PASS	.	G	LYS/ARG,LYS/ARG	2803,953		1044,715,119	114.0	123.0	120.0		722,869	1.8	0.4	3	dbSNP_87	120	2777,5435		486,1805,1815	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	26,26	1530,2520,1934	AA,AG,GG		33.8164,25.3727,46.6243	benign,benign	241/1273,290/1321	39161456	5580,6388	1878	4106	5984	SO:0001583	missense	199223	exon8			AGACAAGGGAACC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.869G>A	3.37:g.39161456G>A	ENSP00000398211:p.Arg290Lys	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	162	86	0.530864	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	959	0.4391025641025641	410	0.8333333333333334	133	0.3674033149171271	166	0.2902097902097902	250	0.32981530343007914	G	3.931	-0.016256	0.07681	0.746273	0.338164	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.34472	1.36;1.36;2.31	5.67	1.76	0.24704	.	0.359920	0.28989	N	0.013481	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.002	B;B;B	0.14578	0.006;0.011;0.005	T	0.13872	-1.0493	9	0.27785	T	0.31	-0.8765	6.5884	0.22634	0.2034:0.2446:0.552:0.0	rs1274972;rs61530584;rs1274972	241;290;290	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	290;282;290;241	ENSP00000301819:R290K;ENSP00000398211:R290K;ENSP00000410882:R241K	ENSP00000301819:R290K	R	+	2	0	TTC21A	39136460	0.007000	0.16637	0.354000	0.25760	0.288000	0.27193	0.778000	0.26732	0.315000	0.23110	-0.175000	0.13238	AGG	G|0.555;A|0.445	0.445	strong		0.458	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
CDH6	1004	hgsc.bcm.edu	37	5	31294254	31294254	+	Silent	SNP	C	C	T	rs147617483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:31294254C>T	ENST00000265071.2	+	3	679	c.414C>T	c.(412-414)ccC>ccT	p.P138P	CDH6_ENST00000514738.1_Silent_p.P83P	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	138	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P138P(1)		NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CAGGGAGACCCGTGGAGCCCG	0.473													C|||	6	0.00119808	0.0	0.0043	5008	,	,		18421	0.0		0.003	False		,,,				2504	0.0				p.P138P		Atlas-SNP	.											.	CDH6	175	.	1	Substitution - coding silent(1)	lung(1)	c.C414T						PASS	.	C		8,4398	12.9+/-30.5	0,8,2195	134.0	135.0	134.0		414	-11.5	0.2	5	dbSNP_134	134	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous	CDH6	NM_004932.3		0,63,6440	TT,TC,CC		0.6395,0.1816,0.4844		138/791	31294254	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	1004	exon3			GAGACCCGTGGAG	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.414C>T	5.37:g.31294254C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			C|0.995;T|0.005	0.005	strong		0.473	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
NPAP1	23742	hgsc.bcm.edu	37	15	24921771	24921771	+	Missense_Mutation	SNP	G	G	C	rs1563102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:24921771G>C	ENST00000329468.2	+	1	1231	c.757G>C	c.(757-759)Gga>Cga	p.G253R		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	253			G -> R (in dbSNP:rs1563102). {ECO:0000269|PubMed:10783265}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCGGCATCTTGGAAAGCCTGA	0.637													G|||	1370	0.273562	0.0129	0.3516	5008	,	,		15590	0.4673		0.325	False		,,,				2504	0.318				p.G253R		Atlas-SNP	.											C15orf2,NS,carcinoma,0,2	.	.	2	0			c.G757C						PASS	.	G	ARG/GLY	276,4128		13,250,1939	33.0	36.0	35.0		757	-4.1	0.0	15	dbSNP_88	35	2643,5955		405,1833,2061	yes	missense	C15orf2	NM_018958.2	125	418,2083,4000	CC,CG,GG		30.7397,6.267,22.4504	possibly-damaging	253/1157	24921771	2919,10083	2202	4299	6501	SO:0001583	missense	23742	exon1			CATCTTGGAAAGC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.757G>C	15.37:g.24921771G>C	ENSP00000333735:p.Gly253Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	638	0.29212454212454214	10	0.02032520325203252	125	0.3453038674033149	276	0.4825174825174825	227	0.2994722955145119	.	11.44	1.639244	0.29157	0.06267	0.307397	ENSG00000185823	ENST00000329468	T	0.10477	2.87	2.07	-4.13	0.03904	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.45594	0.862	P	0.51101	0.659	T	0.23655	-1.0182	8	0.10111	T	0.7	.	5.3948	0.16263	0.0:0.4581:0.2796:0.2623	rs1563102;rs3784245;rs1563102	253	Q9NZP6	CO002_HUMAN	R	253	ENSP00000333735:G253R	ENSP00000333735:G253R	G	+	1	0	C15orf2	22472864	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.085000	0.03390	-1.084000	0.03092	0.436000	0.28706	GGA	G|0.744;C|0.256	0.256	strong		0.637	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
USP49	25862	hgsc.bcm.edu	37	6	41773576	41773576	+	Silent	SNP	G	G	C	rs2185798	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41773576G>C	ENST00000394253.3	-	3	1475	c.1146C>G	c.(1144-1146)ctC>ctG	p.L382L	USP49_ENST00000373006.1_Silent_p.L382L|USP49_ENST00000373010.1_Silent_p.L382L|USP49_ENST00000297229.2_Silent_p.L382L|USP49_ENST00000373009.3_Silent_p.L382L			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	382	USP.				histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			ACACTGAGTGGAGCATGGCGA	0.602													G|||	2750	0.549121	0.5174	0.6801	5008	,	,		19980	0.5407		0.4911	False		,,,				2504	0.5675				p.L382L		Atlas-SNP	.											.	USP49	58	.	0			c.C1146G						PASS	.	G		2332,2074	607.0+/-390.9	625,1082,496	64.0	59.0	60.0		1146	-5.7	1.0	6	dbSNP_96	60	4141,4459	564.6+/-388.3	979,2183,1138	no	coding-synonymous	USP49	NM_018561.3		1604,3265,1634	CC,CG,GG		48.1512,47.0722,49.7693		382/641	41773576	6473,6533	2203	4300	6503	SO:0001819	synonymous_variant	25862	exon4			TGAGTGGAGCATG	AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663		"""Ubiquitin-specific peptidases"""	20078	protein-coding gene	gene with protein product			"""ubiquitin specific protease 49"""			14715245	Standard	NM_018561		Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.1146C>G	6.37:g.41773576G>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Silent	SNP	ENST00000394253.3	37																																																																																				G|0.480;C|0.520	0.520	strong		0.602	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561	
WDR73	84942	hgsc.bcm.edu	37	15	85189464	85189464	+	Silent	SNP	T	T	G	rs2271431	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85189464T>G	ENST00000434634.2	-	6	528	c.468A>C	c.(466-468)cgA>cgC	p.R156R	WDR73_ENST00000398528.3_5'UTR	NM_032856.2	NP_116245.2	Q6P4I2	WDR73_HUMAN	WD repeat domain 73	156										cervix(1)|large_intestine(1)|lung(1)	3						CCTGCAGACTTCGGAGCCTCG	0.602													G|||	737	0.147165	0.0287	0.1902	5008	,	,		17725	0.1379		0.2734	False		,,,				2504	0.1564				p.R156R		Atlas-SNP	.											.	WDR73	15	.	0			c.A468C						PASS	.	G		247,3761		7,233,1764	47.0	51.0	50.0		468	-2.1	0.0	15	dbSNP_100	50	2280,6066		290,1700,2183	no	coding-synonymous	WDR73	NM_032856.2		297,1933,3947	GG,GT,TT		27.3185,6.1627,20.4549		156/379	85189464	2527,9827	2004	4173	6177	SO:0001819	synonymous_variant	84942	exon6			CAGACTTCGGAGC	AK027200	CCDS45339.1	15q25.2	2013-01-09				ENSG00000177082		"""WD repeat domain containing"""	25928	protein-coding gene	gene with protein product						12477932	Standard	NM_032856		Approved	FLJ14888, HSPC264	uc002bkw.2	Q6P4I2		ENST00000434634.2:c.468A>C	15.37:g.85189464T>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_032856	Q96JZ1|Q9P0B7	Silent	SNP	ENST00000434634.2	37	CCDS45339.1																																																																																			T|0.830;G|0.170	0.170	strong		0.602	WDR73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418195.1	NM_032856	
OR1I1	126370	hgsc.bcm.edu	37	19	15198441	15198441	+	Missense_Mutation	SNP	G	G	T	rs73008811	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198441G>T	ENST00000209540.2	+	1	651	c.565G>T	c.(565-567)Ggc>Tgc	p.G189C		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	189						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						GAAGCTCTCCGGCTCAGACAC	0.547													T|||	912	0.182109	0.0242	0.219	5008	,	,		22257	0.2371		0.17	False		,,,				2504	0.3252				p.G189C		Atlas-SNP	.											.	OR1I1	58	.	0			c.G565T						PASS	.	T	CYS/GLY	203,4203	808.0+/-415.9	3,197,2003	118.0	104.0	108.0		565	3.8	1.0	19	dbSNP_130	108	1453,7147	751.0+/-407.4	108,1237,2955	yes	missense	OR1I1	NM_001004713.1	159	111,1434,4958	TT,TG,GG		16.8953,4.6074,12.7326	benign	189/356	15198441	1656,11350	2203	4300	6503	SO:0001583	missense	126370	exon1			CTCTCCGGCTCAG	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.565G>T	19.37:g.15198441G>T	ENSP00000209540:p.Gly189Cys	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	157	88	0.56051	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	351	0.16071428571428573	17	0.034552845528455285	76	0.20994475138121546	119	0.20804195804195805	139	0.18337730870712401	T	0.666	-0.803773	0.02819	0.046074	0.168953	ENSG00000094661	ENST00000209540	T	0.00000	10.21	4.79	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34777	N	0.003689	T	0.00012	0.0000	N	0.00001	-3.675	0.40422	P	0.020145999999999997	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.02654	T	1	.	6.7456	0.23460	0.1509:0.0:0.1578:0.6913	.	189	O60431	OR1I1_HUMAN	C	189	ENSP00000209540:G189C	ENSP00000209540:G189C	G	+	1	0	OR1I1	15059441	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	2.503000	0.45407	0.325000	0.23359	-0.375000	0.07067	GGC	G|0.866;T|0.134	0.134	strong		0.547	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
PLSCR4	57088	hgsc.bcm.edu	37	3	145938619	145938619	+	Missense_Mutation	SNP	T	T	C	rs3762685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:145938619T>C	ENST00000354952.2	-	3	341	c.101A>G	c.(100-102)aAt>aGt	p.N34S	PLSCR4_ENST00000383083.2_Missense_Mutation_p.N34S|PLSCR4_ENST00000493382.1_Missense_Mutation_p.N34S|PLSCR4_ENST00000446574.2_Missense_Mutation_p.N34S|PLSCR4_ENST00000433593.2_Missense_Mutation_p.N19S	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	34	Proline-rich domain (PRD). {ECO:0000250}.		N -> S (in dbSNP:rs3762685). {ECO:0000269|PubMed:10930526, ECO:0000269|Ref.2}.		cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)			kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						AAAATGAGAATTGTATTCAGG	0.383													T|||	1547	0.308906	0.3457	0.415	5008	,	,		15089	0.1915		0.341	False		,,,				2504	0.272				p.N34S		Atlas-SNP	.											.	PLSCR4	44	.	0			c.A101G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	1544,2862	484.9+/-360.2	282,980,941	103.0	96.0	98.0		101,56,101	-8.5	0.1	3	dbSNP_107	98	3021,5579	464.5+/-366.3	547,1927,1826	yes	missense,missense,missense	PLSCR4	NM_001128306.1,NM_001177304.1,NM_020353.2	46,46,46	829,2907,2767	CC,CT,TT		35.1279,35.0431,35.0992	benign,benign,benign	34/240,19/225,34/330	145938619	4565,8441	2203	4300	6503	SO:0001583	missense	57088	exon3			TGAGAATTGTATT	AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.101A>G	3.37:g.145938619T>C	ENSP00000347038:p.Asn34Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	160	74	0.4625	NM_020353	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Missense_Mutation	SNP	ENST00000354952.2	37	CCDS3133.1	683	0.31272893772893773	164	0.3333333333333333	134	0.3701657458563536	117	0.20454545454545456	268	0.35356200527704484	T	4.895	0.166350	0.09339	0.350431	0.351279	ENSG00000114698	ENST00000354952;ENST00000383083;ENST00000433593;ENST00000446574;ENST00000493382;ENST00000460350;ENST00000460885;ENST00000476202;ENST00000481701;ENST00000498625	T;T;T;T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04	4.73	-8.49	0.00931	.	0.999489	0.08099	N	0.998132	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.40590	-0.9555	9	0.08837	T	0.75	.	0.8042	0.01081	0.2348:0.308:0.2393:0.2179	rs3762685;rs52810966;rs58731158;rs3762685	34;34	E9PHR9;Q9NRQ2	.;PLS4_HUMAN	S	34;34;19;34;34;34;34;34;34;34	ENSP00000347038:N34S;ENSP00000372561:N34S;ENSP00000415605:N19S;ENSP00000399315:N34S;ENSP00000419040:N34S;ENSP00000417896:N34S;ENSP00000420385:N34S;ENSP00000418173:N34S;ENSP00000418419:N34S;ENSP00000417248:N34S	ENSP00000347038:N34S	N	-	2	0	PLSCR4	147421309	0.008000	0.16893	0.075000	0.20258	0.432000	0.31715	-2.202000	0.01235	-1.326000	0.02266	-0.295000	0.09555	AAT	T|0.671;C|0.329	0.329	strong		0.383	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353	
NUP54	53371	hgsc.bcm.edu	37	4	77055474	77055474	+	Silent	SNP	A	A	G	rs11097244	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:77055474A>G	ENST00000264883.3	-	5	704	c.564T>C	c.(562-564)gaT>gaC	p.D188D	NUP54_ENST00000342467.6_Silent_p.D8D|NUP54_ENST00000458189.2_Silent_p.D8D|NUP54_ENST00000515460.1_5'UTR|NUP54_ENST00000514987.1_Silent_p.D140D	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	188	9 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						CCACTAGCCCATCTTCATCTT	0.343													A|||	777	0.155152	0.0567	0.1297	5008	,	,		16365	0.3512		0.1312	False		,,,				2504	0.1288				p.D188D		Atlas-SNP	.											NUP54,colon,carcinoma,-2,1	NUP54	48	1	0			c.T564C						PASS	.	A		308,4098	165.8+/-197.2	15,278,1910	69.0	60.0	63.0		564	4.7	1.0	4	dbSNP_120	63	1300,7300	256.2+/-280.8	101,1098,3101	no	coding-synonymous	NUP54	NM_017426.2		116,1376,5011	GG,GA,AA		15.1163,6.9905,12.3635		188/508	77055474	1608,11398	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon5			TAGCCCATCTTCA	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.564T>C	4.37:g.77055474A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			A|0.865;G|0.135	0.135	strong		0.343	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
ZNF382	84911	hgsc.bcm.edu	37	19	37118439	37118439	+	Missense_Mutation	SNP	C	C	T	rs61732180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:37118439C>T	ENST00000292928.2	+	5	1753	c.1640C>T	c.(1639-1641)aCg>aTg	p.T547M	ZNF382_ENST00000423582.1_Missense_Mutation_p.T498M|CTD-3234P18.2_ENST00000585467.1_lincRNA|ZNF382_ENST00000435416.1_Missense_Mutation_p.T546M|ZNF382_ENST00000439428.1_Missense_Mutation_p.T546M	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	547	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding. {ECO:0000250}.			T -> M (in Ref. 6; AAI32676). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			GTAGAAACCACGGGAATTCAG	0.373													c|||	654	0.130591	0.0106	0.1196	5008	,	,		19009	0.1438		0.2346	False		,,,				2504	0.18				p.T547M		Atlas-SNP	.											.	ZNF382	87	.	0			c.C1640T						PASS	.	C	MET/THR	171,4235	109.9+/-148.2	3,165,2035	57.0	55.0	55.0		1640	2.0	0.0	19	dbSNP_129	55	1872,6728	327.9+/-318.0	209,1454,2637	yes	missense	ZNF382	NM_032825.3	81	212,1619,4672	TT,TC,CC		21.7674,3.8811,15.7081	benign	547/551	37118439	2043,10963	2203	4300	6503	SO:0001583	missense	84911	exon5			AAACCACGGGAAT	AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"""Zinc fingers, C2H2-type"", ""-"""	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.1640C>T	19.37:g.37118439C>T	ENSP00000292928:p.Thr547Met	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_032825	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Missense_Mutation	SNP	ENST00000292928.2	37	CCDS33004.1	321	0.14697802197802198	9	0.018292682926829267	47	0.1298342541436464	85	0.1486013986013986	180	0.23746701846965698	C	3.121	-0.180615	0.06380	0.038811	0.217674	ENSG00000161298	ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416	T;T;T;T	0.06068	3.35;3.44;3.45;3.46	4.21	1.99	0.26369	Zinc finger, C2H2 (1);	1.397220	0.04676	N	0.411459	T	0.00012	0.0000	L	0.35487	1.065	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45308	-0.9270	9	0.56958	D	0.05	.	5.4956	0.16802	0.0:0.0968:0.1736:0.7296	rs61732180	546;546;547	Q96SR6-2;Q96SR6-3;Q96SR6	.;.;ZN382_HUMAN	M	498;547;546;546	ENSP00000389722:T498M;ENSP00000292928:T547M;ENSP00000407593:T546M;ENSP00000410113:T546M	ENSP00000292928:T547M	T	+	2	0	ZNF382	41810279	0.001000	0.12720	0.009000	0.14445	0.652000	0.38707	0.770000	0.26618	0.218000	0.20820	-0.383000	0.06682	ACG	C|0.845;T|0.155	0.155	strong		0.373	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825	
UGT2B4	7363	hgsc.bcm.edu	37	4	70361334	70361334	+	Silent	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70361334A>C	ENST00000305107.6	-	1	292	c.246T>G	c.(244-246)acT>acG	p.T82T	UGT2B4_ENST00000381096.3_Intron|UGT2B4_ENST00000506580.1_5'UTR|UGT2B4_ENST00000512583.1_Silent_p.T82T	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	82					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	ACTCAGTTTTAGTTAAAGATA	0.373																																					p.T82T		Atlas-SNP	.											.	UGT2B4	105	.	0			c.T246G						PASS	.						53.0	54.0	54.0					4																	70361334		2133	4279	6412	SO:0001819	synonymous_variant	7363	exon1			AGTTTTAGTTAAA	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"""UDP glucuronosyltransferases"""	12553	protein-coding gene	gene with protein product		600067	"""UDP glycosyltransferase 2 family, polypeptide B4"""			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.246T>G	4.37:g.70361334A>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	143	24	0.167832	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	CCDS43234.1																																																																																			.	.	none		0.373	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
C18orf8	29919	hgsc.bcm.edu	37	18	21100240	21100240	+	Silent	SNP	C	C	T	rs1367083	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21100240C>T	ENST00000269221.3	+	10	1034	c.924C>T	c.(922-924)ccC>ccT	p.P308P	C18orf8_ENST00000590868.1_Silent_p.P260P	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	308						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CCGTGCTTCCCGCTCGATCGA	0.532													C|||	3102	0.619409	0.5522	0.6513	5008	,	,		18050	0.8849		0.4742	False		,,,				2504	0.5634				p.P308P		Atlas-SNP	.											.	C18orf8	58	.	0			c.C924T						PASS	.	C		2372,2034	610.4+/-391.6	636,1100,467	139.0	112.0	121.0		924	-11.0	0.0	18	dbSNP_88	121	4103,4497	562.1+/-387.9	968,2167,1165	no	coding-synonymous	C18orf8	NM_013326.3		1604,3267,1632	TT,TC,CC		47.7093,46.1643,49.7847		308/658	21100240	6475,6531	2203	4300	6503	SO:0001819	synonymous_variant	29919	exon10			GCTTCCCGCTCGA	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"""colon cancer associated protein Mic1"", ""macrophage inhibitory cytokine 1"""					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.924C>T	18.37:g.21100240C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	132	48	0.363636	NM_013326	Q9BU17|Q9Y5M0	Silent	SNP	ENST00000269221.3	37	CCDS32803.1																																																																																			T|0.538;G|0.000;C|0.462;A|0.000	0.538	strong		0.532	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326	
MEGF6	1953	hgsc.bcm.edu	37	1	3425183	3425183	+	Silent	SNP	G	G	A	rs61735125	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:3425183G>A	ENST00000356575.4	-	13	1825	c.1599C>T	c.(1597-1599)tgC>tgT	p.C533C	MEGF6_ENST00000294599.4_Silent_p.C428C	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	533	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GGCCCAGGAGGCAGGTCCCTC	0.642													G|||	325	0.0648962	0.028	0.0519	5008	,	,		17150	0.1032		0.0507	False		,,,				2504	0.0992				p.C533C	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C1599T						PASS	.	G		145,4025		4,137,1944	47.0	54.0	52.0		1599	3.5	0.9	1	dbSNP_129	52	502,7904		12,478,3713	no	coding-synonymous	MEGF6	NM_001409.3		16,615,5657	AA,AG,GG		5.9719,3.4772,5.1447		533/1542	3425183	647,11929	2085	4203	6288	SO:0001819	synonymous_variant	1953	exon13			CAGGAGGCAGGTC	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.1599C>T	1.37:g.3425183G>A		Somatic	340	1	0.00294118		WXS	Illumina HiSeq	Phase_I	322	175	0.543478	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1																																																																																			G|0.940;A|0.060	0.060	strong		0.642	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
APBB3	10307	hgsc.bcm.edu	37	5	139940233	139940233	+	Silent	SNP	G	G	A	rs250431	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139940233G>A	ENST00000357560.4	-	11	1466	c.1023C>T	c.(1021-1023)caC>caT	p.H341H	SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000358580.5_Intron|APBB3_ENST00000507279.1_5'Flank|APBB3_ENST00000356738.2_Silent_p.H346H|APBB3_ENST00000354402.5_Silent_p.H348H|APBB3_ENST00000508496.2_Silent_p.H118H|APBB3_ENST00000412920.3_Silent_p.H339H|APBB3_ENST00000511201.2_Intron|SRA1_ENST00000336283.6_5'Flank	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	341	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGAATGGGGTGTGCAGTCA	0.582													G|||	3162	0.63139	0.292	0.7248	5008	,	,		19374	0.8254		0.7137	False		,,,				2504	0.7393				p.H348H		Atlas-SNP	.											APBB3,NS,carcinoma,-1,1	APBB3	34	1	0			c.C1044T						PASS	.	G	,,,	1633,2773	501.7+/-365.1	297,1039,867	62.0	53.0	56.0		1044,1038,1023,1017	-0.3	1.0	5	dbSNP_79	56	6011,2589	689.2+/-404.3	2102,1807,391	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	APBB3	NM_006051.3,NM_133172.2,NM_133173.2,NM_133174.2	,,,	2399,2846,1258	AA,AG,GG		30.1047,37.0631,41.2271	,,,	348/494,346/492,341/487,339/485	139940233	7644,5362	2203	4300	6503	SO:0001819	synonymous_variant	10307	exon10			AATGGGGTGTGCA	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1023C>T	5.37:g.139940233G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	127	53	0.417323	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Silent	SNP	ENST00000357560.4	37	CCDS4229.1																																																																																			G|0.389;A|0.611	0.611	strong		0.582	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
MUC16	94025	hgsc.bcm.edu	37	19	9058907	9058907	+	Missense_Mutation	SNP	G	G	C	rs1833777	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9058907G>C	ENST00000397910.4	-	3	28742	c.28539C>G	c.(28537-28539)caC>caG	p.H9513Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9515	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTTCAAAAACGTGAATTGCCT	0.478													C|||	2098	0.41893	0.3593	0.3934	5008	,	,		21029	0.503		0.3946	False		,,,				2504	0.456				p.H9513Q		Atlas-SNP	.											MUC16_ENST00000397910,caecum,carcinoma,-2,2	MUC16	4315	2	0			c.C28539G						PASS	.	C	GLN/HIS	1482,2484		305,872,806	150.0	146.0	147.0		28539	-4.4	0.0	19	dbSNP_92	147	3047,5285		551,1945,1670	yes	missense	MUC16	NM_024690.2	24	856,2817,2476	CC,CG,GG		36.5699,37.3676,36.8271	benign	9513/14508	9058907	4529,7769	1983	4166	6149	SO:0001583	missense	94025	exon3			AAAAACGTGAATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28539C>G	19.37:g.9058907G>C	ENSP00000381008:p.His9513Gln	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	157	72	0.458599	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	908	0.4157509157509158	176	0.35772357723577236	146	0.40331491712707185	284	0.4965034965034965	302	0.39841688654353563	c	1.009	-0.688602	0.03328	0.373676	0.365699	ENSG00000181143	ENST00000397910	T	0.25912	1.77	2.22	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.44034	-0.9354	8	0.87932	D	0	.	0.8809	0.01234	0.1622:0.2737:0.2988:0.2654	rs1833777;rs1833777	9513	B5ME49	.	Q	9513	ENSP00000381008:H9513Q	ENSP00000381008:H9513Q	H	-	3	2	MUC16	8919907	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.662000	0.00400	-3.470000	0.00157	-2.130000	0.00343	CAC	G|0.589;C|0.411	0.411	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF880	400713	hgsc.bcm.edu	37	19	52888245	52888245	+	Missense_Mutation	SNP	A	A	G	rs55748277	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52888245A>G	ENST00000422689.2	+	4	1427	c.1412A>G	c.(1411-1413)aAg>aGg	p.K471R		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	471					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GAATGTGGCAAGGACTTCACT	0.388													A|||	2061	0.411542	0.3555	0.3919	5008	,	,		22737	0.3492		0.4205	False		,,,				2504	0.5562				p.K471R		Atlas-SNP	.											.	ZNF880	45	.	0			c.A1412G						PASS	.	A	ARG/LYS	529,855		102,325,265	83.0	75.0	77.0		1412	-0.5	0.0	19	dbSNP_129	77	1216,1966		222,772,597	no	missense	ZNF880	NM_001145434.1	26	324,1097,862	GG,GA,AA		38.215,38.2225,38.2173	possibly-damaging	471/578	52888245	1745,2821	692	1591	2283	SO:0001583	missense	400713	exon4			GTGGCAAGGACTT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1412A>G	19.37:g.52888245A>G	ENSP00000406318:p.Lys471Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	802	0.36721611721611724	164	0.3333333333333333	148	0.4088397790055249	179	0.3129370629370629	311	0.4102902374670185	A	13.64	2.296527	0.40594	0.382225	0.38215	ENSG00000221923	ENST00000422689	T	0.26223	1.75	2.03	-0.46	0.12175	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.35854	1.095	0.58432	P	9.99999999995449E-6	D	0.62365	0.991	D	0.63703	0.917	T	0.43750	-0.9372	7	.	.	.	.	6.4253	0.21766	0.7772:0.0:0.2228:0.0	rs55748277;rs62108357	471	Q6PDB4	ZN880_HUMAN	R	471	ENSP00000406318:K471R	.	K	+	2	0	ZNF880	57580057	0.060000	0.20803	0.007000	0.13788	0.010000	0.07245	1.664000	0.37439	-0.387000	0.07809	0.450000	0.29827	AAG	A|0.631;G|0.369	0.369	strong		0.388	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
PGS1	9489	hgsc.bcm.edu	37	17	76423151	76423151	+	IGR	SNP	C	C	T	rs3209030	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76423151C>T	ENST00000262764.6	+	0	2201				DNAH17_ENST00000389840.5_Silent_p.P4232P|DNAH17_ENST00000585328.1_Silent_p.P4204P|DNAH17_ENST00000586052.1_5'UTR	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TGAAAGTCTCCGGAATCTTCT	0.562													C|||	416	0.0830671	0.1127	0.0605	5008	,	,		18579	0.0317		0.0895	False		,,,				2504	0.1053				p.P4209P	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.G12627A						PASS	.	C		352,4054		15,322,1866	44.0	35.0	38.0		12627	-9.9	0.3	17	dbSNP_105	38	787,7809		45,697,3556	no	coding-synonymous	DNAH17	NM_173628.3		60,1019,5422	TT,TC,CC		9.1554,7.9891,8.7602		4209/4463	76423151	1139,11863	2203	4298	6501	SO:0001628	intergenic_variant	8632	exon78			AGTCTCCGGAATC		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76423151C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	113	43	0.380531	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	37	CCDS42391.1																																																																																			C|0.914;T|0.086	0.086	strong		0.562	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
MED12	9968	hgsc.bcm.edu	37	X	70354254	70354254	+	Silent	SNP	G	G	A	rs375001801		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:70354254G>A	ENST00000374080.3	+	34	4697	c.4665G>A	c.(4663-4665)acG>acA	p.T1555T	MED12_ENST00000333646.6_Silent_p.T1555T|MED12_ENST00000374102.1_Silent_p.T1555T			Q93074	MED12_HUMAN	mediator complex subunit 12	1555					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.T1555T(2)		breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					AGCAGACCACGGAGTGGGCCA	0.592			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.T1555T		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	2	Substitution - coding silent(2)	endometrium(2)	c.G4665A						PASS	.			0,3706		0,0,1571,564	40.0	38.0	39.0		4665	-8.9	0.5	X		39	1,6607		0,1,2401,1804	no	coding-synonymous	MED12	NM_005120.2		0,1,3972,2368	AA,AG,GG,G		0.0151,0.0,0.0097		1555/2178	70354254	1,10313	2135	4206	6341	SO:0001819	synonymous_variant	9968	exon34			GACCACGGAGTGG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.4665G>A	X.37:g.70354254G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1																																																																																			.	.	weak		0.592	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
ATP13A2	23400	hgsc.bcm.edu	37	1	17313343	17313343	+	Silent	SNP	G	G	A	rs9435659	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17313343G>A	ENST00000326735.8	-	27	3225	c.3192C>T	c.(3190-3192)gcC>gcT	p.A1064A	ATP13A2_ENST00000452699.1_Silent_p.A1059A|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.A1020A			Q9NQ11	AT132_HUMAN	ATPase type 13A2	1064					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CCTTGGACACGGCTGCAGCCA	0.662													G|||	1695	0.338458	0.1369	0.4568	5008	,	,		13447	0.2599		0.5089	False		,,,				2504	0.4325				p.A1064A		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C3192T						PASS	.	G	,,	915,3491	346.2+/-308.9	101,713,1389	64.0	54.0	57.0		3177,3060,3192	-4.5	0.0	1	dbSNP_119	57	4501,4099	586.8+/-392.1	1158,2185,957	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	1259,2898,2346	AA,AG,GG		47.6628,20.7671,41.6423	,,	1059/1176,1020/1159,1064/1181	17313343	5416,7590	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon27			GGACACGGCTGCA	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.3192C>T	1.37:g.17313343G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	72	50	0.694444	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			G|0.606;A|0.394	0.394	strong		0.662	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
TFAP2C	7022	hgsc.bcm.edu	37	20	55209257	55209257	+	Silent	SNP	T	T	C	rs35023929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55209257T>C	ENST00000201031.2	+	5	1098	c.855T>C	c.(853-855)atT>atC	p.I285I	TFAP2C_ENST00000544508.1_Silent_p.I116I	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	285					cell-cell signaling (GO:0007267)|cerebral cortex development (GO:0021987)|dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis (GO:0060598)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|forebrain neuron fate commitment (GO:0021877)|germ-line stem cell maintenance (GO:0030718)|hair follicle development (GO:0001942)|keratinocyte development (GO:0003334)|male gonad development (GO:0008584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sebaceous gland development (GO:0048733)|somatic stem cell maintenance (GO:0035019)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			TGGACAAGATTGGGTTGAATC	0.463													T|||	312	0.0623003	0.0068	0.072	5008	,	,		16001	0.001		0.17	False		,,,				2504	0.0828				p.I285I		Atlas-SNP	.											.	TFAP2C	51	.	0			c.T855C						PASS	.	T		134,4272	96.7+/-135.4	1,132,2070	77.0	79.0	78.0		855	-3.4	0.4	20	dbSNP_126	78	1474,7126	281.3+/-295.0	123,1228,2949	no	coding-synonymous	TFAP2C	NM_003222.3		124,1360,5019	CC,CT,TT		17.1395,3.0413,12.3635		285/451	55209257	1608,11398	2203	4300	6503	SO:0001819	synonymous_variant	7022	exon5			CAAGATTGGGTTG		CCDS13454.1	20q13.2	2008-07-17	2001-11-28		ENSG00000087510	ENSG00000087510			11744	protein-coding gene	gene with protein product	"""estrogen receptor factor 1"""	601602	"""transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma)"""			8661133	Standard	NM_003222		Approved	AP2-GAMMA, ERF1, TFAP2G, hAP-2g	uc002xya.3	Q92754	OTTHUMG00000032805	ENST00000201031.2:c.855T>C	20.37:g.55209257T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_003222	B4DWK3|O00685|O00730|Q86V30|Q8IVB6|Q9P1X2	Silent	SNP	ENST00000201031.2	37	CCDS13454.1																																																																																			T|0.892;C|0.108	0.108	strong		0.463	TFAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079823.2	NM_003222	
KIRREL3	84623	hgsc.bcm.edu	37	11	126391297	126391297	+	Silent	SNP	T	T	G	rs12269776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:126391297T>G	ENST00000525144.2	-	4	595	c.346A>C	c.(346-348)Agg>Cgg	p.R116R	KIRREL3_ENST00000529097.2_Silent_p.R116R|KIRREL3_ENST00000525704.2_Silent_p.R116R	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	116	Ig-like C2-type 1.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AGCTCTGCCCTCAGGATCTTC	0.632													G|||	1126	0.22484	0.5015	0.2075	5008	,	,		15796	0.0446		0.2008	False		,,,				2504	0.0736				p.R116R		Atlas-SNP	.											.	KIRREL3	183	.	0			c.A346C						PASS	.	G	,	1786,2446		387,1012,717	42.0	54.0	50.0		346,346	2.5	1.0	11	dbSNP_120	50	1771,6703		184,1403,2650	no	coding-synonymous,coding-synonymous	KIRREL3	NM_001161707.1,NM_032531.3	,	571,2415,3367	GG,GT,TT		20.8992,42.2023,27.9946	,	116/601,116/779	126391297	3557,9149	2116	4237	6353	SO:0001819	synonymous_variant	84623	exon4			CTGCCCTCAGGAT	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.346A>C	11.37:g.126391297T>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	156	85	0.544872	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	37	CCDS53723.1																																																																																			T|0.764;G|0.236	0.236	strong		0.632	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
ABCA7	10347	hgsc.bcm.edu	37	19	1062285	1062285	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1062285C>T	ENST00000263094.6	+	42	5916	c.5685C>T	c.(5683-5685)cgC>cgT	p.R1895R	ABCA7_ENST00000435683.2_Silent_p.R1757R|ABCA7_ENST00000433129.1_Silent_p.R1895R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1895	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCGCCTGCGCGGTGTCCCGG	0.677																																					p.R1895R		Atlas-SNP	.											.	ABCA7	174	.	0			c.C5685T						PASS	.						84.0	91.0	89.0					19																	1062285		2203	4296	6499	SO:0001819	synonymous_variant	10347	exon42			CCTGCGCGGTGTC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5685C>T	19.37:g.1062285C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	10	0.192308	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			.	.	none		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
TAF1L	138474	hgsc.bcm.edu	37	9	32630472	32630472	+	Silent	SNP	T	T	C	rs10758145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:32630472T>C	ENST00000242310.4	-	1	5195	c.5106A>G	c.(5104-5106)aaA>aaG	p.K1702K	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1702					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GGCACATCTGTTTTTCTGGAG	0.483													C|||	1733	0.346046	0.5106	0.245	5008	,	,		24091	0.3681		0.2435	False		,,,				2504	0.2781				p.K1702K		Atlas-SNP	.											.	TAF1L	382	.	0			c.A5106G						PASS	.	C		2107,2299	601.6+/-389.7	488,1131,584	167.0	154.0	158.0		5106	0.5	0.5	9	dbSNP_120	158	1986,6614	722.6+/-406.4	230,1526,2544	no	coding-synonymous	TAF1L	NM_153809.2		718,2657,3128	CC,CT,TT		23.093,47.8212,31.4701		1702/1827	32630472	4093,8913	2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			CATCTGTTTTTCT	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5106A>G	9.37:g.32630472T>C		Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	306	170	0.555556	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			T|0.672;C|0.328	0.328	strong		0.483	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
HMHA1	23526	hgsc.bcm.edu	37	19	1068738	1068738	+	Missense_Mutation	SNP	G	G	A	rs1801284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1068738G>A	ENST00000313093.2	+	2	647	c.416G>A	c.(415-417)cGt>cAt	p.R139H	HMHA1_ENST00000539243.2_Missense_Mutation_p.R155H|HMHA1_ENST00000543365.1_5'Flank|HMHA1_ENST00000592335.1_5'Flank|HMHA1_ENST00000590214.1_Missense_Mutation_p.R166H|HMHA1_ENST00000536472.1_Intron|HMHA1_ENST00000586866.1_Missense_Mutation_p.R143H	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	139			R -> H (in allele HA-1H; induction of CTL recognition for epitope HA-1; dbSNP:rs1801284). {ECO:0000269|PubMed:10958358, ECO:0000269|PubMed:16202172, ECO:0000269|PubMed:16399573, ECO:0000269|PubMed:9461441, ECO:0000269|PubMed:9820595, ECO:0000269|Ref.5}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGTGTGTTGCGTGACGGTGAG	0.652													g|||	2027	0.404752	0.5265	0.3862	5008	,	,		16379	0.3611		0.3449	False		,,,				2504	0.3599				p.R155H		Atlas-SNP	.											HMHA1,colon,carcinoma,+1,1	HMHA1	78	1	0			c.G464A	GRCh37	CM982053	HMHA1	M	rs1801284	PASS	.	A	HIS/ARG	2239,2155		577,1085,535	37.0	37.0	37.0		416	-8.4	0.0	19	dbSNP_89	37	3014,5580		558,1898,1841	yes	missense	HMHA1	NM_012292.2	29	1135,2983,2376	AA,AG,GG		35.071,49.0442,40.445	benign	139/1137	1068738	5253,7735	2197	4297	6494	SO:0001583	missense	23526	exon2			TGTTGCGTGACGG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.416G>A	19.37:g.1068738G>A	ENSP00000316772:p.Arg139His	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	201	71	0.353234	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	37	CCDS32863.1	877	0.4015567765567766	234	0.47560975609756095	139	0.3839779005524862	231	0.40384615384615385	273	0.36015831134564646	g	3.168	-0.170620	0.06421	0.509558	0.35071	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000412039	T;T	0.21543	2.0;2.01	4.22	-8.44	0.00950	.	1.071480	0.07178	N	0.853538	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	B;B	0.13594	0.008;0.003	B;B	0.06405	0.002;0.001	T	0.42258	-0.9462	9	0.41790	T	0.15	-0.0868	16.3572	0.83239	0.254:0.0:0.6707:0.0753	rs1801284;rs3764654;rs17846690;rs17859790;rs59638554;rs1801284	155;139	F6QP70;Q92619	.;HMHA1_HUMAN	H	155;139;139;133	ENSP00000439601:R155H;ENSP00000316772:R139H	ENSP00000316772:R139H	R	+	2	0	HMHA1	1019738	0.000000	0.05858	0.000000	0.03702	0.170000	0.22686	-1.052000	0.03503	-4.781000	0.00032	-3.258000	0.00049	CGT	G|0.602;A|0.398	0.398	strong		0.652	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
MLIP	90523	hgsc.bcm.edu	37	6	53989526	53989526	+	Missense_Mutation	SNP	G	G	A	rs4712056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:53989526G>A	ENST00000274897.5	+	3	588	c.475G>A	c.(475-477)Gtc>Atc	p.V159I	MLIP_ENST00000370877.2_Missense_Mutation_p.V107I|MLIP_ENST00000509997.1_Missense_Mutation_p.V107I|MLIP_ENST00000502396.1_Missense_Mutation_p.V170I|MLIP_ENST00000511744.1_3'UTR|MLIP_ENST00000358276.5_Missense_Mutation_p.V153I|MLIP_ENST00000514921.1_Missense_Mutation_p.V159I|MLIP_ENST00000370876.2_Missense_Mutation_p.V97I	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	159			V -> I (in dbSNP:rs4712056). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						CACCGCAGCTGTCCGGCCCAA	0.527													G|||	3083	0.615615	0.4667	0.5115	5008	,	,		16140	0.7331		0.6491	False		,,,				2504	0.7352				p.V159I		Atlas-SNP	.											.	MLIP	84	.	0			c.G475A						PASS	.	G	ILE/VAL	2211,2195	589.9+/-387.2	539,1133,531	80.0	78.0	78.0		475	-8.0	0.0	6	dbSNP_111	78	5505,3095	658.9+/-401.6	1750,2005,545	yes	missense	MLIP	NM_138569.2	29	2289,3138,1076	AA,AG,GG		35.9884,49.8184,40.6735	benign	159/459	53989526	7716,5290	2203	4300	6503	SO:0001583	missense	90523	exon3			GCAGCTGTCCGGC	AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"""muscle-enriched A-type lamin interacting protein"""	614106	"""chromosome 6 open reading frame 142"""	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.475G>A	6.37:g.53989526G>A	ENSP00000274897:p.Val159Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	NM_138569	B7Z2N0|D6RE05|Q96H08|Q96NF7	Missense_Mutation	SNP	ENST00000274897.5	37	CCDS4954.1	1322	0.6053113553113553	223	0.4532520325203252	187	0.5165745856353591	417	0.7290209790209791	495	0.6530343007915568	G	7.384	0.629414	0.14257	0.501816	0.640116	ENSG00000146147	ENST00000274897;ENST00000514921;ENST00000370877;ENST00000509997;ENST00000370876;ENST00000447836;ENST00000511678;ENST00000503951;ENST00000502396;ENST00000358276;ENST00000370878;ENST00000514433	T;T;T;T;T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4	5.68	-7.97	0.01139	.	1.329660	0.04588	N	0.396175	T	0.05135	0.0137	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.27732	0.058;0.019;0.022;0.187	B;B;B;B	0.21917	0.025;0.007;0.014;0.037	T	0.12941	-1.0528	8	.	.	.	3.065	1.1271	0.01737	0.4382:0.1984:0.1633:0.2001	rs4712056;rs61349178;rs4712056	170;97;159;159	Q5VWP3-3;Q5VWP3-2;Q5VWP3;D6RE05	.;.;MLIP_HUMAN;.	I	159;159;107;107;97;41;41;118;170;153;41;160	ENSP00000274897:V159I;ENSP00000425142:V159I;ENSP00000359914:V107I;ENSP00000427584:V107I;ENSP00000359913:V97I;ENSP00000411917:V41I;ENSP00000427057:V41I;ENSP00000426830:V118I;ENSP00000426290:V170I;ENSP00000351019:V153I;ENSP00000421444:V160I	.	V	+	1	0	MLIP	54097485	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.711000	0.05019	-1.268000	0.02439	-0.142000	0.14014	GTC	G|0.398;A|0.602	0.602	strong		0.527	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569	
SIM1	6492	hgsc.bcm.edu	37	6	100868779	100868779	+	Missense_Mutation	SNP	G	G	T	rs3734354	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:100868779G>T	ENST00000369208.3	-	10	1836	c.1054C>A	c.(1054-1056)Cca>Aca	p.P352T	SIM1_ENST00000262901.4_Missense_Mutation_p.P352T			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	352	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.		P -> T (in dbSNP:rs3734354).		cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.P352T(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GAGAAGGCTGGTTTGGAGGCT	0.537													G|||	892	0.178115	0.0038	0.2089	5008	,	,		14363	0.4067		0.1471	False		,,,				2504	0.1881				p.P352T		Atlas-SNP	.											SIM1,NS,carcinoma,+2,2	SIM1	173	2	1	Substitution - Missense(1)	stomach(1)	c.C1054A						PASS	.	G	THR/PRO	138,4268	95.7+/-134.4	2,134,2067	109.0	98.0	102.0		1054	5.8	1.0	6	dbSNP_107	102	1171,7429	237.9+/-269.6	62,1047,3191	yes	missense	SIM1	NM_005068.2	38	64,1181,5258	TT,TG,GG		13.6163,3.1321,10.0646	possibly-damaging	352/767	100868779	1309,11697	2203	4300	6503	SO:0001583	missense	6492	exon9			AGGCTGGTTTGGA	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1054C>A	6.37:g.100868779G>T	ENSP00000358210:p.Pro352Thr	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	159	93	0.584906	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	430	0.19688644688644688	5	0.01016260162601626	76	0.20994475138121546	236	0.4125874125874126	113	0.14907651715039577	G	17.17	3.320485	0.60634	0.031321	0.136163	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.03772	3.81;3.81	5.8	5.8	0.92144	Single-minded, C-terminal (1);	0.208574	0.48767	D	0.000176	T	0.03827	0.0108	L	0.50333	1.59	0.09310	P	0.99999845931	B	0.21147	0.052	B	0.17098	0.017	T	0.35525	-0.9785	9	0.42905	T	0.14	.	20.0567	0.97653	0.0:0.0:1.0:0.0	rs3734354;rs52789631;rs56928625;rs3734354	352	P81133	SIM1_HUMAN	T	352	ENSP00000358210:P352T;ENSP00000262901:P352T	ENSP00000262901:P352T	P	-	1	0	SIM1	100975500	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.059000	0.71133	2.752000	0.94435	0.650000	0.86243	CCA	T|0.145;G|0.854;A|0.000	0.145	strong		0.537	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
KLF17	128209	hgsc.bcm.edu	37	1	44595047	44595047	+	Missense_Mutation	SNP	T	T	A	rs11210969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:44595047T>A	ENST00000372299.3	+	2	162	c.104T>A	c.(103-105)aTc>aAc	p.I35N	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	35			I -> N (in dbSNP:rs11210969). {ECO:0000269|PubMed:14702039}.		gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.I35N(1)		NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					TCAGCGCCCATCTTGAACATG	0.498													T|||	1089	0.217452	0.121	0.255	5008	,	,		18875	0.2044		0.2962	False		,,,				2504	0.2536				p.I35N		Atlas-SNP	.											KLF17,NS,carcinoma,0,1	KLF17	92	1	1	Substitution - Missense(1)	stomach(1)	c.T104A						PASS	.	T	ASN/ILE	645,3761	276.0+/-272.9	56,533,1614	126.0	118.0	120.0		104	1.2	0.0	1	dbSNP_120	120	2509,6091	411.2+/-350.4	361,1787,2152	yes	missense	KLF17	NM_173484.3	149	417,2320,3766	AA,AT,TT		29.1744,14.6391,24.2503	benign	35/390	44595047	3154,9852	2203	4300	6503	SO:0001583	missense	128209	exon2			CGCCCATCTTGAA	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.104T>A	1.37:g.44595047T>A	ENSP00000361373:p.Ile35Asn	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	110	44	0.4	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	502	0.22985347985347984	60	0.12195121951219512	91	0.2513812154696133	125	0.21853146853146854	226	0.29815303430079154	T	8.842	0.942534	0.18281	0.146391	0.291744	ENSG00000171872	ENST00000372299	T	0.13420	2.59	4.78	1.18	0.20946	.	1.018550	0.07854	N	0.965188	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.45902	0.868	B	0.42851	0.4	T	0.45600	-0.9250	9	0.54805	T	0.06	.	3.9088	0.09194	0.0:0.1891:0.1838:0.6271	rs11210969;rs17381026;rs52807679;rs56504303;rs11210969	35	Q5JT82	KLF17_HUMAN	N	35	ENSP00000361373:I35N	ENSP00000361373:I35N	I	+	2	0	KLF17	44367634	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.624000	0.24462	0.189000	0.20188	-0.263000	0.10527	ATC	T|0.767;A|0.233	0.233	strong		0.498	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
NIN	51199	hgsc.bcm.edu	37	14	51224417	51224417	+	Missense_Mutation	SNP	G	G	C	rs2236316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:51224417G>C	ENST00000382041.3	-	18	3521	c.3331C>G	c.(3331-3333)Cca>Gca	p.P1111A	NIN_ENST00000382043.4_Intron|NIN_ENST00000245441.5_Missense_Mutation_p.P1111A|NIN_ENST00000453196.1_Missense_Mutation_p.P1111A|NIN_ENST00000530997.2_Missense_Mutation_p.P1111A|NIN_ENST00000324330.9_Missense_Mutation_p.P1111A|NIN_ENST00000389868.3_Intron	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1111			P -> A (in dbSNP:rs2236316).		centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TCAGTAGCTGGCTCATCCAAA	0.423			T	PDGFRB	MPD								G|||	933	0.186302	0.0628	0.2565	5008	,	,		20641	0.1617		0.2734	False		,,,				2504	0.2393				p.P1111A		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C3331G						PASS	.	G	,ALA/PRO,ALA/PRO,ALA/PRO	456,3950	217.8+/-236.0	21,414,1768	133.0	136.0	135.0		,3331,3331,3331	-4.1	0.0	14	dbSNP_98	135	2157,6443	369.9+/-335.7	277,1603,2420	yes	intron,missense,missense,missense	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,27,27,27	298,2017,4188	CC,CG,GG		25.0814,10.3495,20.0907	,benign,benign,benign	,1111/2134,1111/2047,1111/2091	51224417	2613,10393	2203	4300	6503	SO:0001583	missense	51199	exon18			TAGCTGGCTCATC	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.3331C>G	14.37:g.51224417G>C	ENSP00000371472:p.Pro1111Ala	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	181	84	0.464088	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	403|403	0.18452380952380953|0.18452380952380953	45|45	0.09146341463414634|0.09146341463414634	84|84	0.23204419889502761|0.23204419889502761	86|86	0.15034965034965034|0.15034965034965034	188|188	0.24802110817941952|0.24802110817941952	G|G	0.007|0.007	-2.003729|-2.003729	0.00431|0.00431	0.103495|0.103495	0.250814|0.250814	ENSG00000100503|ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853|ENST00000245441;ENST00000311149;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196	.|T;T;T;T	.|0.06449	.|3.57;3.31;3.3;3.31	5.93|5.93	-4.1|-4.1	0.03940|0.03940	.|.	.|1.425020	.|0.04346	.|N	.|0.354818	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.09022	.|0.001;0.001;0.001;0.002	.|B;B;B;B	.|0.09377	.|0.002;0.001;0.001;0.004	T|T	0.47045|0.47045	-0.9147|-0.9147	4|9	.|0.07030	.|T	.|0.85	1.3606|1.3606	8.4876|8.4876	0.33080|0.33080	0.2578:0.3897:0.3525:0.0|0.2578:0.3897:0.3525:0.0	rs2236316;rs17719470;rs52791150;rs56485217;rs2236316|rs2236316;rs17719470;rs52791150;rs56485217;rs2236316	.|1117;1111;1111;1111	.|Q8N4C6-5;C9J066;Q8N4C6;Q8N4C6-7	.|.;.;NIN_HUMAN;.	G|A	601|1111;1094;1117;1111;1111;1111	.|ENSP00000245441:P1111A;ENSP00000371472:P1111A;ENSP00000324210:P1111A;ENSP00000412391:P1111A	.|ENSP00000245441:P1111A	A|P	-|-	2|1	0|0	NIN|NIN	50294167|50294167	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.044000|0.044000	0.14063|0.14063	-0.337000|-0.337000	0.07852|0.07852	-0.361000|-0.361000	0.08125|0.08125	0.563000|0.563000	0.77884|0.77884	GCC|CCA	G|0.805;C|0.195	0.195	strong		0.423	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
ADAR	103	hgsc.bcm.edu	37	1	154560614	154560614	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154560614G>A	ENST00000368474.4	-	11	3205	c.3006C>T	c.(3004-3006)acC>acT	p.T1002T	ADAR_ENST00000292205.5_Silent_p.T1045T|ADAR_ENST00000368471.3_Silent_p.T707T	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	1002	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TCTCCACCTTGGTGCGGAGCT	0.552																																					p.T1002T		Atlas-SNP	.											.	ADAR	113	.	0			c.C3006T						PASS	.						256.0	231.0	239.0					1																	154560614		2203	4300	6503	SO:0001819	synonymous_variant	103	exon11			CACCTTGGTGCGG	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.3006C>T	1.37:g.154560614G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Silent	SNP	ENST00000368474.4	37	CCDS1071.1																																																																																			.	.	none		0.552	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
IZUMO1	284359	hgsc.bcm.edu	37	19	49244260	49244260	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49244260C>T	ENST00000332955.2	-	10	1505	c.958G>A	c.(958-960)Gat>Aat	p.D320N	RASIP1_ENST00000594232.1_5'Flank|RASIP1_ENST00000222145.4_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	320					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TTGATGAAATCGATCACCTTC	0.517																																					p.D320N		Atlas-SNP	.											.	IZUMO1	30	.	0			c.G958A						PASS	.						118.0	104.0	109.0					19																	49244260		2203	4300	6503	SO:0001583	missense	284359	exon10			TGAAATCGATCAC	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"""-"""	28539	protein-coding gene	gene with protein product	"""oocyte binding/fusion factor"""	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.958G>A	19.37:g.49244260C>T	ENSP00000327786:p.Asp320Asn	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	C	9.996	1.232155	0.22626	.	.	ENSG00000182264	ENST00000332955	T	0.26660	1.72	3.11	-1.93	0.07594	.	3.286190	0.01067	N	0.004759	T	0.12860	0.0312	N	0.19112	0.55	0.09310	N	1	B	0.28470	0.213	B	0.15870	0.014	T	0.08351	-1.0726	10	0.12430	T	0.62	0.0495	3.5485	0.07837	0.0:0.4402:0.1948:0.365	.	320	Q8IYV9	IZUM1_HUMAN	N	320	ENSP00000327786:D320N	ENSP00000327786:D320N	D	-	1	0	IZUMO1	53936072	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.629000	0.05508	-0.218000	0.10018	-0.150000	0.13652	GAT	.	.	none		0.517	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575	
DNAH5	1767	hgsc.bcm.edu	37	5	13829799	13829799	+	Silent	SNP	G	G	A	rs1348689	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13829799G>A	ENST00000265104.4	-	38	6368	c.6264C>T	c.(6262-6264)gcC>gcT	p.A2088A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2088	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCTGCCGTCCGGCATAGCCAG	0.423									Kartagener syndrome				G|||	2220	0.443291	0.4705	0.4207	5008	,	,		21016	0.626		0.3698	False		,,,				2504	0.3098				p.A2088A		Atlas-SNP	.											.	DNAH5	868	.	0			c.C6264T						PASS	.	G		2011,2395	561.5+/-380.7	451,1109,643	69.0	66.0	67.0		6264	-9.1	0.7	5	dbSNP_88	67	3135,5465	478.5+/-369.9	576,1983,1741	no	coding-synonymous	DNAH5	NM_001369.2		1027,3092,2384	AA,AG,GG		36.4535,45.6423,39.5664		2088/4625	13829799	5146,7860	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon38	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCGTCCGGCATAG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6264C>T	5.37:g.13829799G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.574;A|0.426	0.426	strong		0.423	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
SPINK5	11005	hgsc.bcm.edu	37	5	147481430	147481430	+	Silent	SNP	A	A	G	rs6896303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147481430A>G	ENST00000256084.7	+	15	1431	c.1389A>G	c.(1387-1389)ggA>ggG	p.G463G	SPINK5_ENST00000398454.1_Silent_p.G463G|SPINK5_ENST00000359874.3_Silent_p.G463G	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	463	Kazal-like 7. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G463G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCCAGATGGAAAAATGCATG	0.502													G|||	2168	0.432907	0.1989	0.6167	5008	,	,		16733	0.4851		0.4861	False		,,,				2504	0.5102				p.G463G		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - coding silent(1)	stomach(1)	c.A1389G						PASS	.	G	,,	956,2828		123,710,1059	108.0	105.0	106.0		1389,1389,1389	0.3	0.7	5	dbSNP_116	106	4220,4016		1070,2080,968	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	1193,2790,2027	GG,GA,AA		48.7615,25.2643,43.0616	,,	463/1095,463/917,463/1065	147481430	5176,6844	1892	4118	6010	SO:0001819	synonymous_variant	11005	exon15			AGATGGAAAAATG	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1389A>G	5.37:g.147481430A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	128	124	0.96875	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			A|0.545;G|0.455	0.455	strong		0.502	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
SLAMF9	89886	hgsc.bcm.edu	37	1	159923904	159923904	+	Silent	SNP	A	A	C	rs145274502	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:159923904A>C	ENST00000368093.3	-	1	140	c.24T>G	c.(22-24)ctT>ctG	p.L8L	SLAMF9_ENST00000466773.1_5'Flank|SLAMF9_ENST00000368092.3_Silent_p.L8L	NM_033438.3	NP_254273.2	Q96A28	SLAF9_HUMAN	SLAM family member 9	8						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCAGGAGAAGAAGCAGCCAAG	0.597													a|||	61	0.0121805	0.0023	0.0187	5008	,	,		18670	0.0		0.0368	False		,,,				2504	0.0082				p.L8L		Atlas-SNP	.											.	SLAMF9	41	.	0			c.T24G						PASS	.	A	,,	20,4386		1,18,2184	95.0	91.0	92.0		24,24,24	1.3	0.0	1	dbSNP_134	92	304,8296		10,284,4006	no	coding-synonymous,coding-synonymous,coding-synonymous	SLAMF9	NM_001146172.1,NM_001146173.1,NM_033438.3	,,	11,302,6190	CC,CA,AA		3.5349,0.4539,2.4912	,,	8/199,8/112,8/290	159923904	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	89886	exon1			GAGAAGAAGCAGC	AY034613	CCDS1191.1, CCDS53392.1	1q23.1	2013-01-11			ENSG00000162723	ENSG00000162723		"""Immunoglobulin superfamily / V-set domain containing"""	18430	protein-coding gene	gene with protein product		608589				11685473	Standard	NM_033438		Approved	CD2F-10, CD84-H1, SF2001	uc001fus.3	Q96A28	OTTHUMG00000024074	ENST00000368093.3:c.24T>G	1.37:g.159923904A>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_033438	Q5JRQ9|Q5JRR0|Q6UWG1	Silent	SNP	ENST00000368093.3	37	CCDS1191.1																																																																																			A|0.977;C|0.023	0.023	strong		0.597	SLAMF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060630.1	NM_033438	
NOP9	161424	hgsc.bcm.edu	37	14	24771285	24771285	+	Missense_Mutation	SNP	G	G	A	rs4280164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24771285G>A	ENST00000267425.3	+	4	1016	c.923G>A	c.(922-924)aGt>aAt	p.S308N	DHRS1_ENST00000288111.7_5'Flank|NOP9_ENST00000396802.3_Missense_Mutation_p.S308N|DHRS1_ENST00000396813.1_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	308			S -> N (in dbSNP:rs4280164). {ECO:0000269|PubMed:15489334}.				poly(A) RNA binding (GO:0044822)										GGCTACCTGAGTACTCGCGGT	0.507													G|||	753	0.150359	0.1581	0.3473	5008	,	,		21235	0.004		0.1849	False		,,,				2504	0.1155				p.S308N		Atlas-SNP	.											.	.	.	.	0			c.G923A						PASS	.	G	ASN/SER	736,3670	303.2+/-287.8	63,610,1530	122.0	117.0	118.0		923	5.2	1.0	14	dbSNP_111	118	1783,6817	322.1+/-315.4	189,1405,2706	yes	missense	C14orf21	NM_174913.1	46	252,2015,4236	AA,AG,GG		20.7326,16.7045,19.368	possibly-damaging	308/637	24771285	2519,10487	2203	4300	6503	SO:0001583	missense	161424	exon4			ACCTGAGTACTCG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.923G>A	14.37:g.24771285G>A	ENSP00000267425:p.Ser308Asn	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	159	91	0.572327	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	336	0.15384615384615385	72	0.14634146341463414	108	0.2983425414364641	4	0.006993006993006993	152	0.20052770448548812	G	18.02	3.531149	0.64972	0.167045	0.207326	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.14022	2.54;2.54	5.21	5.21	0.72293	Armadillo-type fold (1);	0.219735	0.45606	D	0.000347	T	0.00012	0.0000	L	0.54323	1.7	0.29261	P	0.871328	P	0.50819	0.939	P	0.50378	0.639	T	0.51458	-0.8703	9	0.17369	T	0.5	-6.0418	13.4219	0.61003	0.0:0.1579:0.8421:0.0	rs4280164;rs17852257;rs52803285;rs56947421;rs4280164	308	Q86U38	CN021_HUMAN	N	308	ENSP00000267425:S308N;ENSP00000380020:S308N	ENSP00000267425:S308N	S	+	2	0	C14orf21	23841125	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	3.940000	0.56599	2.717000	0.92951	0.655000	0.94253	AGT	G|0.835;A|0.165	0.165	strong		0.507	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
MASP1	5648	hgsc.bcm.edu	37	3	186953808	186953808	+	Intron	SNP	C	C	T	rs850312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186953808C>T	ENST00000337774.5	-	10	1693				MASP1_ENST00000495249.1_5'UTR|MASP1_ENST00000296280.6_Silent_p.L617L|MASP1_ENST00000392472.2_Silent_p.L504L	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)						complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.L617L(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TGACATACTGCAGGACATCTG	0.562													C|||	1061	0.211861	0.0265	0.3473	5008	,	,		21420	0.2034		0.3479	False		,,,				2504	0.2352				p.L617L		Atlas-SNP	.											MASP1_ENST00000296280,NS,carcinoma,0,1	MASP1	240	1	1	Substitution - coding silent(1)	stomach(1)	c.G1851A						PASS	.	C	,	299,4107	164.0+/-195.7	15,269,1919	109.0	94.0	99.0		,1851	-6.7	0.3	3	dbSNP_86	99	2918,5682	456.7+/-364.1	497,1924,1879	no	intron,coding-synonymous	MASP1	NM_001879.5,NM_139125.3	,	512,2193,3798	TT,TC,CC		33.9302,6.7862,24.7347	,	,617/729	186953808	3217,9789	2203	4300	6503	SO:0001627	intron_variant	5648	exon11			ATACTGCAGGACA	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"""Serine peptidases / Serine peptidases"""	6901	protein-coding gene	gene with protein product		600521	"""mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"""	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1303+5460G>A	3.37:g.186953808C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Silent	SNP	ENST00000337774.5	37	CCDS33907.1																																																																																			T|0.232;G|0.004	0.232	strong		0.562	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879	
F13A1	2162	hgsc.bcm.edu	37	6	6152137	6152137	+	Missense_Mutation	SNP	C	C	G	rs5988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:6152137C>G	ENST00000264870.3	-	14	2219	c.1954G>C	c.(1954-1956)Gag>Cag	p.E652Q		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	652			Q -> E (in allele F13A*1A and allele F13A*1B; dbSNP:rs5988). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TTGGTAAACTCAACTGTCACA	0.448													C|||	971	0.19389	0.2292	0.2046	5008	,	,		20265	0.0923		0.2406	False		,,,				2504	0.1953				p.E652Q		Atlas-SNP	.											.	F13A1	135	.	0			c.G1954C						PASS	.	C	GLN/GLU	881,3525	343.6+/-307.7	100,681,1422	89.0	80.0	83.0		1954	4.5	1.0	6	dbSNP_52	83	2003,6597	349.8+/-327.6	237,1529,2534	yes	missense	F13A1	NM_000129.3	29	337,2210,3956	GG,GC,CC		23.2907,19.9955,22.1744	benign	652/733	6152137	2884,10122	2203	4300	6503	SO:0001583	missense	2162	exon14			TAAACTCAACTGT	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1954G>C	6.37:g.6152137C>G	ENSP00000264870:p.Glu652Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	146	84	0.575342	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	412	0.18864468864468864	93	0.18902439024390244	91	0.2513812154696133	60	0.1048951048951049	168	0.22163588390501318	C	15.85	2.954677	0.53293	0.199955	0.232907	ENSG00000124491	ENST00000264870	T	0.68765	-0.35	5.37	4.5	0.54988	.	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	.	.	.	0.20873	P	0.999837872	.	.	.	.	.	.	T	0.49643	-0.8918	6	0.17832	T	0.49	.	13.3365	0.60520	0.1587:0.8413:0.0:0.0	rs5988;rs3191130;rs52826565;rs5988	.	.	.	Q	652	ENSP00000264870:E652Q	ENSP00000264870:E652Q	E	-	1	0	F13A1	6097136	0.999000	0.42202	0.994000	0.49952	0.406000	0.30931	4.372000	0.59530	1.484000	0.48361	0.650000	0.86243	GAG	C|0.786;G|0.214	0.214	strong		0.448	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
SALL4	57167	hgsc.bcm.edu	37	20	50405502	50405502	+	Silent	SNP	C	C	G	rs17802735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:50405502C>G	ENST00000217086.4	-	3	2751	c.2640G>C	c.(2638-2640)tcG>tcC	p.S880S	SALL4_ENST00000371539.3_Silent_p.S103S|SALL4_ENST00000395997.3_Silent_p.S443S	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	880					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CGCTAGCAGACGAGAAGTTCT	0.552													C|||	249	0.0497204	0.003	0.0735	5008	,	,		18738	0.001		0.1272	False		,,,				2504	0.0665				p.S880S		Atlas-SNP	.											.	SALL4	168	.	0			c.G2640C						PASS	.	C		124,4282	90.6+/-129.3	7,110,2086	79.0	67.0	71.0		2640	-11.5	0.0	20	dbSNP_123	71	1146,7454	234.7+/-267.5	76,994,3230	no	coding-synonymous	SALL4	NM_020436.3		83,1104,5316	GG,GC,CC		13.3256,2.8143,9.7647		880/1054	50405502	1270,11736	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon3			AGCAGACGAGAAG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2640G>C	20.37:g.50405502C>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			C|0.916;G|0.084	0.084	strong		0.552	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
FAM209B	388799	hgsc.bcm.edu	37	20	55108508	55108508	+	Silent	SNP	G	G	A	rs150517677|rs386815438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55108508G>A	ENST00000371325.1	+	1	207	c.111G>A	c.(109-111)ccG>ccA	p.P37P		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	37				PC -> QY (in Ref. 2; AAI05793). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)											GGAAGGTGCCGTGTGGAGAGC	0.537													G|||	51	0.0101837	0.003	0.0086	5008	,	,		20351	0.003		0.0099	False		,,,				2504	0.0286				p.P37P		Atlas-SNP	.											.	.	.	.	0			c.G111A						PASS	.						169.0	142.0	151.0					20																	55108508		2203	4286	6489	SO:0001819	synonymous_variant	388799	exon1			GGTGCCGTGTGGA	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.111G>A	20.37:g.55108508G>A		Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	181	26	0.143646	NM_001013646	Q3KRB5	Silent	SNP	ENST00000371325.1	37	CCDS33494.1																																																																																			G|0.985;A|0.015	0.015	strong		0.537	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
SLC35E1	79939	hgsc.bcm.edu	37	19	16666101	16666101	+	Silent	SNP	G	G	C	rs2287869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:16666101G>C	ENST00000595753.1	-	5	881	c.864C>G	c.(862-864)ccC>ccG	p.P288P	SLC35E1_ENST00000593812.1_5'Flank|CTD-3222D19.11_ENST00000597357.1_RNA|CTD-3222D19.2_ENST00000409035.1_Intron	NM_024881.4	NP_079157.3	Q96K37	S35E1_HUMAN	solute carrier family 35, member E1	288					transport (GO:0006810)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(2)|ovary(1)	15						AGTAGCTCAGGGGGCTAACGA	0.572													G|||	2016	0.402556	0.0356	0.5058	5008	,	,		21284	0.5149		0.5368	False		,,,				2504	0.5716				p.P288P		Atlas-SNP	.											.	SLC35E1	48	.	0			c.C864G						PASS	.	G		520,3886	237.1+/-249.0	30,460,1713	150.0	111.0	124.0		864	-6.4	1.0	19	dbSNP_100	124	4939,3661	622.0+/-397.3	1436,2067,797	no	coding-synonymous	SLC35E1	NM_024881.4		1466,2527,2510	CC,CG,GG		42.5698,11.8021,41.9729		288/411	16666101	5459,7547	2203	4300	6503	SO:0001819	synonymous_variant	79939	exon5			GCTCAGGGGGCTA	AK024313	CCDS12346.2	19p13.11	2013-05-22			ENSG00000127526	ENSG00000127526		"""Solute carriers"""	20803	protein-coding gene	gene with protein product							Standard	NM_024881		Approved	FLJ14251	uc010xph.2	Q96K37	OTTHUMG00000152575	ENST00000595753.1:c.864C>G	19.37:g.16666101G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	98	35	0.357143	NM_024881	Q8NBQ2|Q96JV7	Silent	SNP	ENST00000595753.1	37	CCDS12346.2																																																																																			G|0.568;C|0.432	0.432	strong		0.572	SLC35E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326809.2	NM_024881	
RNF141	50862	hgsc.bcm.edu	37	11	10555589	10555589	+	Silent	SNP	A	A	G	rs1065052	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:10555589A>G	ENST00000265981.2	-	2	259	c.117T>C	c.(115-117)ctT>ctC	p.L39L	RNF141_ENST00000528665.1_Silent_p.L39L	NM_016422.3	NP_057506.2	Q8WVD5	RN141_HUMAN	ring finger protein 141	39					protein autoubiquitination (GO:0051865)|regulation of transcription, DNA-templated (GO:0006355)		DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|urinary_tract(1)	9				all cancers(16;4.63e-08)|Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.064)		CTACTCTCCCAAGAAATTCTT	0.398													A|||	1786	0.356629	0.0295	0.4006	5008	,	,		18038	0.6954		0.4135	False		,,,				2504	0.3599				p.L39L	Ovarian(8;377 410 25844 26058 41491)	Atlas-SNP	.											.	RNF141	16	.	0			c.T117C						PASS	.	A		390,4012	192.6+/-218.0	23,344,1834	153.0	135.0	141.0		117	3.7	1.0	11	dbSNP_86	141	3610,4978	522.3+/-380.1	759,2092,1443	no	coding-synonymous	RNF141	NM_016422.3		782,2436,3277	GG,GA,AA		42.0354,8.8596,30.7929		39/231	10555589	4000,8990	2201	4294	6495	SO:0001819	synonymous_variant	50862	exon2			TCTCCCAAGAAAT	AF214680	CCDS7803.1	11p15.3	2013-01-09			ENSG00000110315	ENSG00000110315		"""RING-type (C3HC4) zinc fingers"""	21159	protein-coding gene	gene with protein product						11672448	Standard	NM_016422		Approved	ZFP26, ZNF230	uc001mis.1	Q8WVD5		ENST00000265981.2:c.117T>C	11.37:g.10555589A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_016422	A8K149|Q9NZB4	Silent	SNP	ENST00000265981.2	37	CCDS7803.1																																																																																			A|0.658;G|0.342	0.342	strong		0.398	RNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385888.1	NM_016422	
HNRNPLL	92906	hgsc.bcm.edu	37	2	38829737	38829737	+	Missense_Mutation	SNP	G	G	A	rs34376380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:38829737G>A	ENST00000449105.3	-	1	371	c.32C>T	c.(31-33)aCg>aTg	p.T11M	HNRNPLL_ENST00000498516.1_5'UTR|HNRNPLL_ENST00000378915.3_Missense_Mutation_p.T11M|HNRNPLL_ENST00000409636.1_Missense_Mutation_p.T6M|HNRNPLL_ENST00000409328.1_Missense_Mutation_p.T11M|HNRNPLL_ENST00000608859.1_Missense_Mutation_p.T11M|AC011247.3_ENST00000457097.1_RNA|HNRNPLL_ENST00000358367.4_Missense_Mutation_p.T11M|HNRNPLL_ENST00000410076.1_Missense_Mutation_p.T6M			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	11					mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										CTCCTCGTACGTCTCCCTGGG	0.716													G|||	54	0.0107827	0.0008	0.013	5008	,	,		10283	0.001		0.0417	False		,,,				2504	0.001				p.T11M		Atlas-SNP	.											.	HNRPLL	19	.	0			c.C32T						PASS	.	G	MET/THR,MET/THR	28,4322		0,28,2147	22.0	17.0	19.0		17,32	5.1	1.0	2	dbSNP_126	19	204,8290		0,204,4043	yes	missense,missense	HNRPLL	NM_001142650.1,NM_138394.3	81,81	0,232,6190	AA,AG,GG		2.4017,0.6437,1.8063	possibly-damaging,possibly-damaging	6/538,11/543	38829737	232,12612	2175	4247	6422	SO:0001583	missense	92906	exon1			TCGTACGTCTCCC	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"""RNA binding motif (RRM) containing"""	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.32C>T	2.37:g.38829737G>A	ENSP00000390625:p.Thr11Met	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	15	8	0.533333	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Missense_Mutation	SNP	ENST00000449105.3	37		33	0.01510989010989011	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	29	0.03825857519788918	G	17.06	3.293077	0.60086	0.006437	0.024017	ENSG00000143889	ENST00000449105;ENST00000409636;ENST00000378915;ENST00000409328;ENST00000358367;ENST00000410076	.	.	.	5.06	5.06	0.68205	.	0.292444	0.24755	N	0.035877	T	0.04318	0.0119	N	0.08118	0	0.27677	N	0.946585	B;B	0.31859	0.343;0.343	B;B	0.25614	0.062;0.062	T	0.06899	-1.0801	9	0.72032	D	0.01	.	11.138	0.48386	0.0:0.0:0.816:0.184	rs34376380	6;11	C9J9G0;D6W592	.;.	M	11;6;11;11;11;6	.	ENSP00000351136:T11M	T	-	2	0	HNRPLL	38683241	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.615000	0.46368	2.366000	0.80165	0.561000	0.74099	ACG	G|0.983;A|0.017	0.017	strong		0.716	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394	
A4GALT	53947	hgsc.bcm.edu	37	22	43089849	43089849	+	Missense_Mutation	SNP	T	T	C	rs11541159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43089849T>C	ENST00000401850.1	-	2	598	c.109A>G	c.(109-111)Atg>Gtg	p.M37V	A4GALT_ENST00000249005.2_Missense_Mutation_p.M37V|A4GALT_ENST00000381278.3_Missense_Mutation_p.M37V|A4GALT_ENST00000465765.2_5'Flank			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	37			M -> V (in dbSNP:rs11541159). {ECO:0000269|PubMed:10747952, ECO:0000269|PubMed:10993874, ECO:0000269|Ref.4}.		globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						CAGTAGATCATGATGGAGACG	0.627													T|||	1756	0.350639	0.5083	0.3415	5008	,	,		12771	0.1319		0.3827	False		,,,				2504	0.3364				p.M37V		Atlas-SNP	.											.	A4GALT	35	.	0			c.A109G						PASS	.	T	VAL/MET	2075,2329		499,1077,626	29.0	20.0	23.0		109	-4.6	0.0	22	dbSNP_120	23	3183,5415		599,1985,1715	yes	missense	A4GALT	NM_017436.4	21	1098,3062,2341	CC,CT,TT		37.0202,47.1163,40.4399	benign	37/354	43089849	5258,7744	2202	4299	6501	SO:0001583	missense	53947	exon3			AGATCATGATGGA		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"""Gb3 synthase"", ""CD77 synthase"", ""globotriaosylceramide synthase"", ""lactosylceramide 4-alpha-galactosyltransferase"""	607922	"""alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"""			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.109A>G	22.37:g.43089849T>C	ENSP00000384794:p.Met37Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_017436	B2R7C4|Q9P1X5	Missense_Mutation	SNP	ENST00000401850.1	37	CCDS14041.1	736	0.336996336996337	236	0.4796747967479675	146	0.40331491712707185	75	0.13111888111888112	279	0.36807387862796836	T	9.896	1.205490	0.22205	0.471163	0.370202	ENSG00000128274	ENST00000401850;ENST00000249005;ENST00000381278;ENST00000535654	T;T;T	0.80033	-1.33;-1.33;-1.33	5.34	-4.6	0.03390	.	0.593745	0.14525	U	0.314222	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14200	-1.0481	9	0.05833	T	0.94	-19.2207	3.7109	0.08420	0.1021:0.3574:0.3264:0.2141	rs11541159;rs17846531;rs17859605;rs59149669;rs11541159	37	Q9NPC4	A4GAT_HUMAN	V	37	ENSP00000384794:M37V;ENSP00000249005:M37V;ENSP00000370678:M37V	ENSP00000249005:M37V	M	-	1	0	A4GALT	41419793	0.000000	0.05858	0.016000	0.15963	0.941000	0.58515	-1.483000	0.02318	-1.433000	0.01977	0.459000	0.35465	ATG	T|0.620;C|0.380	0.380	strong		0.627	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
LILRB1	10859	hgsc.bcm.edu	37	19	55143083	55143083	+	Missense_Mutation	SNP	T	T	C	rs1061679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55143083T>C	ENST00000396331.1	+	5	560	c.203T>C	c.(202-204)cTc>cCc	p.L68P	LILRB1_ENST00000418536.2_Missense_Mutation_p.L68P|LILRB1_ENST00000396315.1_Missense_Mutation_p.L68P|LILRB1_ENST00000427581.2_Missense_Mutation_p.L104P|LILRB1_ENST00000396332.4_Missense_Mutation_p.L68P|LILRB1_ENST00000434867.2_Missense_Mutation_p.L68P|LILRB1_ENST00000396321.2_Missense_Mutation_p.L68P|LILRB1_ENST00000324602.7_Missense_Mutation_p.L68P|LILRB1_ENST00000396317.1_Missense_Mutation_p.L68P|LILRB1_ENST00000448689.1_Missense_Mutation_p.L68P|LILRB1_ENST00000396327.3_Missense_Mutation_p.L68P|AC009892.1_ENST00000578908.1_RNA	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	68	Ig-like C2-type 1.		L -> P (in dbSNP:rs1061679). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20600445, ECO:0000269|PubMed:9285411}.		cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		AAAACAGCACTCTGGATTACA	0.557										HNSCC(37;0.09)			N|||	2345	0.468251	0.618	0.4899	5008	,	,		16994	0.5982		0.3032	False		,,,				2504	0.2863				p.L68P		Atlas-SNP	.											.	LILRB1	140	.	0			c.T203C						PASS	.	C	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	2561,1845	635.3+/-396.4	750,1061,392	156.0	151.0	153.0		203,203,203,203	-3.2	0.0	19	dbSNP_86	153	2761,5839	439.2+/-359.1	430,1901,1969	yes	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	98,98,98,98	1180,2962,2361	CC,CT,TT		32.1047,41.8747,40.9196	benign,benign,benign,benign	68/653,68/652,68/652,68/651	55143083	5322,7684	2203	4300	6503	SO:0001583	missense	10859	exon4			CAGCACTCTGGAT	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.203T>C	19.37:g.55143083T>C	ENSP00000379622:p.Leu68Pro	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	319	155	0.485893	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	998	0.45695970695970695	287	0.5833333333333334	161	0.4447513812154696	330	0.5769230769230769	220	0.29023746701846964	T	0.001	-3.114359	0.00032	0.581253	0.321047	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.00691	5.84;5.84;5.84;5.84;5.84;5.84;5.84;5.84;5.84;5.84;5.84	1.58	-3.16	0.05217	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.065730	0.01064	N	0.004683	T	0.00012	0.0000	N	0.01505	-0.83	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.001	T	0.36648	-0.9739	9	0.06891	T	0.86	.	0.3542	0.00354	0.1961:0.3113:0.1939:0.2987	rs1061679;rs3202769;rs61439746	68;68;68;68;68	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	P	68;68;68;68;68;68;68;68;104;68;68	ENSP00000379614:L68P;ENSP00000391514:L68P;ENSP00000409968:L68P;ENSP00000379622:L68P;ENSP00000379618:L68P;ENSP00000315997:L68P;ENSP00000405243:L68P;ENSP00000379623:L68P;ENSP00000395004:L104P;ENSP00000379610:L68P;ENSP00000379608:L68P	ENSP00000315997:L68P	L	+	2	0	LILRB1	59834895	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.288000	0.00525	-1.373000	0.02134	-3.790000	0.00020	CTC	T|0.545;C|0.455	0.455	strong		0.557	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
HTR3D	200909	hgsc.bcm.edu	37	3	183756742	183756742	+	Silent	SNP	C	C	T	rs55674402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183756742C>T	ENST00000382489.3	+	8	1344	c.1344C>T	c.(1342-1344)gtC>gtT	p.V448V	HTR3D_ENST00000334128.2_Silent_p.V273V|HTR3D_ENST00000428798.2_Silent_p.V398V|HTR3D_ENST00000453435.1_Silent_p.V227V	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	448					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.V273V(1)		large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	TCATCACCGTCATATGCCTCT	0.567													C|||	1558	0.311102	0.1906	0.3487	5008	,	,		19416	0.3194		0.4066	False		,,,				2504	0.3405				p.V448V		Atlas-SNP	.											HTR3D,NS,carcinoma,0,1	HTR3D	65	1	1	Substitution - coding silent(1)	stomach(1)	c.C1344T						PASS	.	C	,,	941,3465		102,737,1364	154.0	140.0	145.0		1194,1344,819	3.2	0.0	3	dbSNP_129	145	3469,5131		720,2029,1551	no	coding-synonymous,coding-synonymous,coding-synonymous	HTR3D	NM_001145143.1,NM_001163646.1,NM_182537.2	,,	822,2766,2915	TT,TC,CC		40.3372,21.3572,33.9074	,,	398/405,448/455,273/280	183756742	4410,8596	2203	4300	6503	SO:0001819	synonymous_variant	200909	exon8			CACCGTCATATGC	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24004	protein-coding gene	gene with protein product		610122	"""5-hydroxytryptamine (serotonin) receptor 3 family member D"""			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.1344C>T	3.37:g.183756742C>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	306	111	0.362745	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Silent	SNP	ENST00000382489.3	37	CCDS54685.1																																																																																			C|0.658;T|0.342	0.342	strong		0.567	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	
FEZ1	9638	hgsc.bcm.edu	37	11	125351472	125351472	+	Missense_Mutation	SNP	A	A	T	rs597570	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:125351472A>T	ENST00000278919.3	-	3	603	c.369T>A	c.(367-369)gaT>gaA	p.D123E	FEZ1_ENST00000527350.1_5'UTR	NM_005103.4	NP_005094.1	Q99689	FEZ1_HUMAN	fasciculation and elongation protein zeta 1 (zygin I)	123			D -> E (in dbSNP:rs597570).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|establishment of mitochondrion localization (GO:0051654)|nervous system development (GO:0007399)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|transport (GO:0006810)	axon (GO:0030424)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	24	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0934)		CGATGTTTGGATCCCTCCAGT	0.493													A|||	706	0.140974	0.2262	0.1153	5008	,	,		18714	0.0635		0.1918	False		,,,				2504	0.0716				p.D123E	Melanoma(180;509 2033 10762 15939 24711)	Atlas-SNP	.											.	FEZ1	47	.	0			c.T369A						PASS	.	A	GLU/ASP	951,3451	361.6+/-315.8	104,743,1354	173.0	173.0	173.0		369	3.0	1.0	11	dbSNP_83	173	1601,6997	297.5+/-303.5	161,1279,2859	yes	missense	FEZ1	NM_005103.4	45	265,2022,4213	TT,TA,AA		18.6206,21.6038,19.6308	benign	123/393	125351472	2552,10448	2201	4299	6500	SO:0001583	missense	9638	exon3			GTTTGGATCCCTC	U60060	CCDS31716.1, CCDS44758.1	11q24.2	2005-09-29			ENSG00000149557	ENSG00000149557			3659	protein-coding gene	gene with protein product		604825				9096408, 15843383	Standard	NM_005103		Approved		uc001qbx.3	Q99689	OTTHUMG00000165886	ENST00000278919.3:c.369T>A	11.37:g.125351472A>T	ENSP00000278919:p.Asp123Glu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	172	99	0.575581	NM_005103	O00679|O00728|Q6IBI7	Missense_Mutation	SNP	ENST00000278919.3	37	CCDS31716.1	340	0.15567765567765568	115	0.23373983739837398	43	0.11878453038674033	40	0.06993006993006994	142	0.18733509234828497	A	12.29	1.892948	0.33442	0.216038	0.186206	ENSG00000149557	ENST00000278919	T	0.29655	1.56	5.89	3.0	0.34707	.	0.508737	0.24220	N	0.040449	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.9999999999999257	B;B	0.33777	0.425;0.134	B;B	0.34931	0.192;0.067	T	0.27739	-1.0065	9	0.15499	T	0.54	-22.4086	9.1883	0.37184	0.2986:0.0:0.7014:0.0	rs597570;rs3740900;rs52823327;rs597570	123;123	B4DKG5;Q99689	.;FEZ1_HUMAN	E	123	ENSP00000278919:D123E	ENSP00000278919:D123E	D	-	3	2	FEZ1	124856682	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.214000	0.42853	0.801000	0.34066	-0.242000	0.12053	GAT	A|0.805;T|0.195	0.195	strong		0.493	FEZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386875.1	NM_005103	
ATRNL1	26033	hgsc.bcm.edu	37	10	117486763	117486763	+	Silent	SNP	G	G	T	rs2254619	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:117486763G>T	ENST00000355044.3	+	27	3927	c.3801G>T	c.(3799-3801)ctG>ctT	p.L1267L	ATRNL1_ENST00000423111.2_Silent_p.L318L|ATRNL1_ENST00000303745.7_Silent_p.L60L	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1267					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TCCAGCAACTGCTTCGAGAAC	0.428													G|||	1007	0.201078	0.0983	0.2565	5008	,	,		17727	0.0387		0.4195	False		,,,				2504	0.2434				p.L1267L		Atlas-SNP	.											.	ATRNL1	219	.	0			c.G3801T						PASS	.	G		610,3796	268.9+/-268.7	38,534,1631	46.0	44.0	45.0		3801	2.9	1.0	10	dbSNP_100	45	3538,5062	514.7+/-378.5	709,2120,1471	no	coding-synonymous	ATRNL1	NM_207303.2		747,2654,3102	TT,TG,GG		41.1395,13.8448,31.893		1267/1380	117486763	4148,8858	2203	4300	6503	SO:0001819	synonymous_variant	26033	exon27			GCAACTGCTTCGA	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3801G>T	10.37:g.117486763G>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1																																																																																			G|0.735;T|0.265	0.265	strong		0.428	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
PLSCR4	57088	hgsc.bcm.edu	37	3	145917761	145917761	+	Missense_Mutation	SNP	T	T	C	rs1061409	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:145917761T>C	ENST00000354952.2	-	6	703	c.463A>G	c.(463-465)Att>Gtt	p.I155V	PLSCR4_ENST00000383083.2_Intron|PLSCR4_ENST00000493382.1_Missense_Mutation_p.I155V|PLSCR4_ENST00000446574.2_Missense_Mutation_p.I155V|PLSCR4_ENST00000433593.2_Intron	NM_020353.2	NP_065086.2	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4	155			I -> V (in dbSNP:rs1061409). {ECO:0000269|PubMed:10930526, ECO:0000269|Ref.2}.		cellular response to lipopolysaccharide (GO:0071222)|phospholipid scrambling (GO:0017121)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|enzyme binding (GO:0019899)|phospholipid scramblase activity (GO:0017128)			kidney(1)|large_intestine(6)|lung(9)|urinary_tract(1)	17						TCGGTTACAATGTAAACCATC	0.373													T|||	1203	0.240216	0.0991	0.3847	5008	,	,		18175	0.1925		0.3429	False		,,,				2504	0.272				p.I155V		Atlas-SNP	.											.	PLSCR4	44	.	0			c.A463G						PASS	.	T	,,VAL/ILE	676,3730	284.6+/-277.7	51,574,1578	89.0	87.0	88.0		,,463	-4.7	0.1	3	dbSNP_86	88	2997,5603	463.8+/-366.1	535,1927,1838	yes	intron,intron,missense	PLSCR4	NM_001128306.1,NM_001177304.1,NM_020353.2	,,29	586,2501,3416	CC,CT,TT		34.8488,15.3427,28.2408	,,benign	,,155/330	145917761	3673,9333	2203	4300	6503	SO:0001583	missense	57088	exon6			TTACAATGTAAAC	AF199023	CCDS3133.1, CCDS54651.1	3q24	2008-07-18			ENSG00000114698	ENSG00000114698			16497	protein-coding gene	gene with protein product		607612				10930526	Standard	NM_020353		Approved		uc003evt.4	Q9NRQ2	OTTHUMG00000159415	ENST00000354952.2:c.463A>G	3.37:g.145917761T>C	ENSP00000347038:p.Ile155Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	156	74	0.474359	NM_020353	A8K2E9|Q2TTR3|Q658L3|Q6ZR73|Q7Z505	Missense_Mutation	SNP	ENST00000354952.2	37	CCDS3133.1	562	0.2573260073260073	55	0.11178861788617886	122	0.3370165745856354	117	0.20454545454545456	268	0.35356200527704484	T	9.200	1.028131	0.19512	0.153427	0.348488	ENSG00000114698	ENST00000354952;ENST00000446574;ENST00000493382;ENST00000460350;ENST00000476202	T;T;T;T;T	0.29397	1.57;1.57;1.57;2.04;2.04	4.87	-4.72	0.03269	.	0.919954	0.09282	N	0.823544	T	0.00012	0.0000	N	0.11927	0.2	0.25293	P	0.9893425	B	0.02656	0.0	B	0.04013	0.001	T	0.45454	-0.9260	9	0.42905	T	0.14	.	2.8737	0.05625	0.5697:0.1473:0.1:0.183	rs1061409;rs3202511;rs3762689;rs17348947;rs58938364;rs1061409	155	Q9NRQ2	PLS4_HUMAN	V	155	ENSP00000347038:I155V;ENSP00000399315:I155V;ENSP00000419040:I155V;ENSP00000417896:I155V;ENSP00000418173:I155V	ENSP00000347038:I155V	I	-	1	0	PLSCR4	147400451	0.004000	0.15560	0.095000	0.20976	0.564000	0.35744	-1.353000	0.02617	-0.906000	0.03866	0.533000	0.62120	ATT	T|0.734;C|0.266	0.266	strong		0.373	PLSCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355172.1	NM_020353	
DTNBP1	84062	hgsc.bcm.edu	37	6	15524698	15524698	+	Intron	SNP	T	T	C	rs16876573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:15524698T>C	ENST00000344537.5	-	9	984				DTNBP1_ENST00000355917.3_Intron|DTNBP1_ENST00000338950.5_Silent_p.P290P|DTNBP1_ENST00000462989.2_Intron	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1						actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			GTCTCACCTTTGGAGGGGAGT	0.562									Hermansky-Pudlak syndrome				T|||	162	0.0323482	0.0091	0.0231	5008	,	,		22488	0.001		0.0507	False		,,,				2504	0.0838				p.P290P		Atlas-SNP	.											.	DTNBP1	56	.	0			c.A870G						PASS	.	T	,	83,4323	70.9+/-108.8	1,81,2121	303.0	253.0	270.0		,870	-1.3	0.0	6	dbSNP_123	270	373,8227	122.7+/-181.7	9,355,3936	no	intron,coding-synonymous	DTNBP1	NM_032122.4,NM_183040.2	,	10,436,6057	CC,CT,TT		4.3372,1.8838,3.5061	,	,290/304	15524698	456,12550	2203	4300	6503	SO:0001627	intron_variant	84062	exon9	Familial Cancer Database	HPS, HPS1-8	CACCTTTGGAGGG	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.811+58A>G	6.37:g.15524698T>C		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	257	256	0.996109	NM_183040	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Silent	SNP	ENST00000344537.5	37	CCDS4534.1																																																																																			T|0.966;C|0.034	0.034	strong		0.562	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	
TATDN1	83940	hgsc.bcm.edu	37	8	125499363	125499363	+	IGR	SNP	G	G	A	rs72713066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:125499363G>A	ENST00000276692.6	-	0	1018				RP11-158K1.3_ENST00000518639.1_RNA|RNF139_ENST00000303545.3_Silent_p.S491S	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TGTTTGAGTCGGGAAGTAAAA	0.363													G|||	768	0.153355	0.1203	0.0504	5008	,	,		21535	0.1915		0.0338	False		,,,				2504	0.3548				p.S491S		Atlas-SNP	.											.	RNF139	57	.	0			c.G1473A						PASS	.	G		466,3940	205.2+/-227.1	23,420,1760	97.0	103.0	101.0		1473	0.1	1.0	8	dbSNP_130	101	417,8183	127.7+/-186.0	10,397,3893	no	coding-synonymous	RNF139	NM_007218.3		33,817,5653	AA,AG,GG		4.8488,10.5765,6.7892		491/665	125499363	883,12123	2203	4300	6503	SO:0001628	intergenic_variant	11236	exon2			TGAGTCGGGAAGT	AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068		8.37:g.125499363G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	58	0.585859	NM_007218	B2R5J0|Q8TD02|Q9BY40	Silent	SNP	ENST00000276692.6	37	CCDS6351.1																																																																																			G|0.919;A|0.081	0.081	strong		0.363	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026	
SNX19	399979	hgsc.bcm.edu	37	11	130780015	130780015	+	Silent	SNP	C	C	T	rs1781	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130780015C>T	ENST00000265909.4	-	4	2501	c.1932G>A	c.(1930-1932)ccG>ccA	p.P644P	SNX19_ENST00000545537.1_5'UTR|SNX19_ENST00000530356.1_Silent_p.P24P|SNX19_ENST00000539184.1_Silent_p.P87P|SNX19_ENST00000534726.1_5'Flank|SNX19_ENST00000533318.1_5'UTR|SNX19_ENST00000533214.1_Silent_p.P644P|SNX19_ENST00000528555.1_Silent_p.P24P	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	644	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TAGCGATCTCCGGAATGGCAC	0.453													C|||	2889	0.576877	0.2436	0.6686	5008	,	,		19605	0.6448		0.6342	False		,,,				2504	0.8333				p.P644P		Atlas-SNP	.											.	SNX19	84	.	0			c.G1932A						PASS	.	C		1427,2975	464.0+/-353.7	240,947,1014	96.0	92.0	93.0		1932	-0.2	1.0	11	dbSNP_36	93	5681,2913	670.2+/-402.7	1877,1927,493	no	coding-synonymous	SNX19	NM_014758.2		2117,2874,1507	TT,TC,CC		33.8957,32.4171,45.3062		644/993	130780015	7108,5888	2201	4297	6498	SO:0001819	synonymous_variant	399979	exon4			GATCTCCGGAATG	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1932G>A	11.37:g.130780015C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	37	CCDS31721.1																																																																																			C|0.454;T|0.546	0.546	strong		0.453	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
DHX34	9704	hgsc.bcm.edu	37	19	47883086	47883086	+	Silent	SNP	T	T	G	rs28522883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47883086T>G	ENST00000328771.4	+	14	3175	c.2826T>G	c.(2824-2826)gcT>gcG	p.A942A		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	942					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		TCCTGGCGGCTTCCCTGCGGC	0.662													T|||	438	0.0874601	0.0734	0.1009	5008	,	,		17228	0.0069		0.1441	False		,,,				2504	0.1217				p.A942A		Atlas-SNP	.											.	DHX34	98	.	0			c.T2826G						PASS	.	T		380,4026	191.2+/-216.9	17,346,1840	46.0	48.0	47.0		2826	-7.4	0.0	19	dbSNP_125	47	1323,7277	257.3+/-281.4	80,1163,3057	no	coding-synonymous	DHX34	NM_014681.5		97,1509,4897	GG,GT,TT		15.3837,8.6246,13.094		942/1144	47883086	1703,11303	2203	4300	6503	SO:0001819	synonymous_variant	9704	exon14			GGCGGCTTCCCTG	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.2826T>G	19.37:g.47883086T>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	37	CCDS12700.1																																																																																			T|0.878;G|0.122	0.122	strong		0.662	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
ATP9B	374868	hgsc.bcm.edu	37	18	76873288	76873288	+	Silent	SNP	A	A	G	rs34331564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:76873288A>G	ENST00000426216.2	+	4	509	c.492A>G	c.(490-492)gtA>gtG	p.V164V	ATP9B_ENST00000307671.7_Silent_p.V164V|ATP9B_ENST00000458297.2_Silent_p.V112V|ATP9B_ENST00000586722.1_Silent_p.V164V|ATP9B_ENST00000591464.1_Intron	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	164					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V164V(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		ATTTTCTAGTAATATCCTGCT	0.289													A|||	338	0.067492	0.0015	0.0533	5008	,	,		14455	0.1746		0.0676	False		,,,				2504	0.0562				p.V164V		Atlas-SNP	.											ATP9B,NS,carcinoma,0,1	ATP9B	96	1	1	Substitution - coding silent(1)	stomach(1)	c.A492G						PASS	.	A		82,4324	69.2+/-107.0	1,80,2122	48.0	48.0	48.0		492	2.1	1.0	18	dbSNP_126	48	839,7751	189.8+/-236.5	42,755,3498	no	coding-synonymous	ATP9B	NM_198531.3		43,835,5620	GG,GA,AA		9.7672,1.8611,7.0868		164/1148	76873288	921,12075	2203	4295	6498	SO:0001819	synonymous_variant	374868	exon4			TCTAGTAATATCC	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.492A>G	18.37:g.76873288A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	40	0.338983	NM_198531	O60872|Q08AD8|Q08AD9	Silent	SNP	ENST00000426216.2	37	CCDS12014.1																																																																																			A|0.930;G|0.070	0.070	strong		0.289	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
TMEM8A	58986	hgsc.bcm.edu	37	16	426432	426432	+	Missense_Mutation	SNP	T	T	C	rs2071915	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:426432T>C	ENST00000431232.2	-	6	1088	c.928A>G	c.(928-930)Atc>Gtc	p.I310V	TMEM8A_ENST00000476735.1_5'Flank|TMEM8A_ENST00000250930.3_Missense_Mutation_p.I117V	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	310			I -> V (in dbSNP:rs2071915). {ECO:0000269|PubMed:11006113, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						AGGGGCTGGATGGTCACGCTC	0.647													C|||	2667	0.532548	0.6188	0.4712	5008	,	,		16721	0.3036		0.5378	False		,,,				2504	0.6902				p.I310V		Atlas-SNP	.											.	TMEM8A	49	.	0			c.A928G						PASS	.	C	VAL/ILE	2746,1652		848,1050,301	25.0	27.0	27.0		928	-9.1	0.0	16	dbSNP_96	27	4870,3724		1411,2048,838	yes	missense	TMEM8A	NM_021259.2	29	2259,3098,1139	CC,CT,TT		43.3326,37.5625,41.3793	benign	310/772	426432	7616,5376	2199	4297	6496	SO:0001583	missense	58986	exon6			GCTGGATGGTCAC	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.928A>G	16.37:g.426432T>C	ENSP00000401338:p.Ile310Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	1086	0.49725274725274726	335	0.6808943089430894	179	0.494475138121547	163	0.28496503496503495	409	0.5395778364116095	C	0.012	-1.684225	0.00745	0.624375	0.566674	ENSG00000129925	ENST00000431232;ENST00000250930	T;T	0.28666	2.01;1.6	4.57	-9.13	0.00704	.	3.050000	0.00628	N	0.000477	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26985	-1.0087	9	0.22109	T	0.4	-13.6961	4.298	0.10911	0.0755:0.2978:0.203:0.4237	rs2071915;rs17797276;rs17845651;rs17858585;rs56985763;rs2071915	310	Q9HCN3	TMM8A_HUMAN	V	310;117	ENSP00000401338:I310V;ENSP00000250930:I117V	ENSP00000250930:I117V	I	-	1	0	TMEM8A	366433	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.095000	0.01350	-5.232000	0.00018	-4.127000	0.00010	ATC	C|0.542;N|0.001	0.542	strong		0.647	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
MCAT	27349	hgsc.bcm.edu	37	22	43529314	43529314	+	Missense_Mutation	SNP	G	G	C	rs13815	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43529314G>C	ENST00000290429.6	-	4	953	c.908C>G	c.(907-909)gCg>gGg	p.A303G	MCAT_ENST00000327555.5_3'UTR	NM_173467.4	NP_775738.3	Q8IVS2	FABD_HUMAN	malonyl CoA:ACP acyltransferase (mitochondrial)	303			A -> G (in dbSNP:rs13815). {ECO:0000269|PubMed:15489334}.		fatty acid biosynthetic process (GO:0006633)|metabolic process (GO:0008152)	mitochondrion (GO:0005739)	[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	11		Ovarian(80;0.0694)				GTATCTATGCGCGTGGACGTT	0.577													C|||	2452	0.489617	0.2216	0.5432	5008	,	,		18221	0.6369		0.663	False		,,,				2504	0.4836				p.A303G		Atlas-SNP	.											MCAT,NS,carcinoma,-1,1	MCAT	26	1	0			c.C908G						PASS	.	C	,GLY/ALA	1280,3126	701.0+/-406.7	196,888,1119	97.0	92.0	94.0		,908	5.5	0.1	22	dbSNP_52	94	5845,2755	437.5+/-358.6	1998,1849,453	yes	utr-3,missense	MCAT	NM_014507.3,NM_173467.4	,60	2194,2737,1572	CC,CG,GG		32.0349,29.0513,45.2176	,benign	,303/391	43529314	7125,5881	2203	4300	6503	SO:0001583	missense	27349	exon4			CTATGCGCGTGGA	AL359401	CCDS14045.1, CCDS33660.1	22q13.2	2010-04-27			ENSG00000100294	ENSG00000100294	2.3.1.39		29622	protein-coding gene	gene with protein product		614479				12882974	Standard	NM_173467		Approved	MT, MCT, fabD, FASN2C, NET62	uc003bdl.1	Q8IVS2	OTTHUMG00000150704	ENST00000290429.6:c.908C>G	22.37:g.43529314G>C	ENSP00000290429:p.Ala303Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_173467	B0QY72|O95510|O95511	Missense_Mutation	SNP	ENST00000290429.6	37	CCDS33660.1	1191	0.5453296703296703	120	0.24390243902439024	211	0.5828729281767956	345	0.6031468531468531	515	0.679419525065963	C	1.352	-0.591281	0.03799	0.290513	0.679651	ENSG00000100294	ENST00000290429	T	0.39056	1.1	5.46	5.46	0.80206	Acyl transferase/acyl hydrolase/lysophospholipase (1);Acyl transferase (1);Acyl transferase domain (1);	0.052506	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01686	-0.76	0.41100	P	0.014334999999999987	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.05351	T	0.99	-24.9297	16.4628	0.84069	0.0:0.8686:0.1313:0.0	rs13815;rs713813;rs3884877;rs17846328;rs17859359;rs13815	303	Q8IVS2	FABD_HUMAN	G	303	ENSP00000290429:A303G	ENSP00000290429:A303G	A	-	2	0	MCAT	41859258	0.766000	0.28496	0.126000	0.21872	0.004000	0.04260	2.987000	0.49378	1.322000	0.45245	-0.120000	0.15030	GCG	G|0.474;C|0.526	0.526	strong		0.577	MCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319677.2	NM_173467	
SYN1	6853	hgsc.bcm.edu	37	X	47466361	47466361	+	Silent	SNP	A	A	G	rs1142636	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:47466361A>G	ENST00000295987.7	-	3	634	c.510T>C	c.(508-510)aaT>aaC	p.N170N	SYN1_ENST00000340666.4_Silent_p.N170N	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	170	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						CCTTCACCCCATTCCGAAGAA	0.498													G|||	1392	0.368742	0.3616	0.2911	3775	,	,		10146	0.1954		0.2684	False		,,,				2504	0.2505				p.N170N		Atlas-SNP	.											.	SYN1	84	.	0			c.T510C						PASS	.	G	,	1660,2175		312,793,243,527,328	128.0	104.0	112.0		510,510	2.2	1.0	X	dbSNP_86	112	2547,4181		350,1166,681,912,1191	no	coding-synonymous,coding-synonymous	SYN1	NM_006950.3,NM_133499.2	,	662,1959,924,1439,1519	GG,GA,G,AA,A		37.8567,43.2855,39.8277	,	170/706,170/670	47466361	4207,6356	2203	4300	6503	SO:0001819	synonymous_variant	6853	exon3			CACCCCATTCCGA		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.510T>C	X.37:g.47466361A>G		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_006950	B1AJQ1|O75825|Q5H9A9	Silent	SNP	ENST00000295987.7	37	CCDS14280.1																																																																																			T|0.141;G|0.294;C|0.097;A|0.468	0.294	strong		0.498	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950	
CASS4	57091	hgsc.bcm.edu	37	20	55033635	55033635	+	Silent	SNP	C	C	T	rs3746624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55033635C>T	ENST00000360314.3	+	7	2418	c.2193C>T	c.(2191-2193)aaC>aaT	p.N731N	AL121914.1_ENST00000390795.2_RNA|CASS4_ENST00000371336.3_Silent_p.N731N|CASS4_ENST00000434344.1_Silent_p.N294N	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	731					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						ACGTGCGCAACGAGATCCTCC	0.627													C|||	1846	0.36861	0.0711	0.4784	5008	,	,		19357	0.6786		0.335	False		,,,				2504	0.408				p.N731N		Atlas-SNP	.											.	CASS4	121	.	0			c.C2193T						PASS	.	C	,,,	494,3912	230.4+/-244.6	36,422,1745	74.0	59.0	64.0		2031,882,2193,2193	-8.1	0.1	20	dbSNP_107	64	2890,5710	451.8+/-362.8	463,1964,1873	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	,,,	499,2386,3618	TT,TC,CC		33.6047,11.212,26.0188	,,,	677/733,294/350,731/787,731/787	55033635	3384,9622	2203	4300	6503	SO:0001819	synonymous_variant	57091	exon6			GCGCAACGAGATC	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.2193C>T	20.37:g.55033635C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Silent	SNP	ENST00000360314.3	37	CCDS33492.1																																																																																			C|0.699;T|0.301	0.301	strong		0.627	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
TRIOBP	11078	hgsc.bcm.edu	37	22	38121152	38121152	+	Missense_Mutation	SNP	C	C	A	rs9610841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38121152C>A	ENST00000406386.3	+	7	2844	c.2589C>A	c.(2587-2589)aaC>aaA	p.N863K		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	863			N -> K (in dbSNP:rs9610841).		actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AACGAGACAACCCTGGAACCT	0.493													C|||	1684	0.336262	0.1536	0.2853	5008	,	,		19774	0.5863		0.3877	False		,,,				2504	0.3088				p.N863K		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,+1,1	TRIOBP	262	1	0			c.C2589A						PASS	.	C	LYS/ASN	713,3343		76,561,1391	136.0	146.0	142.0		2589	1.5	0.0	22	dbSNP_119	142	3588,4772		770,2048,1362	yes	missense	TRIOBP	NM_001039141.2	94	846,2609,2753	AA,AC,CC		42.9187,17.5789,34.6408	probably-damaging	863/2366	38121152	4301,8115	2028	4180	6208	SO:0001583	missense	11078	exon7			AGACAACCCTGGA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.2589C>A	22.37:g.38121152C>A	ENSP00000384312:p.Asn863Lys	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	189	187	0.989418	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	820	0.37545787545787546	84	0.17073170731707318	113	0.31215469613259667	330	0.5769230769230769	293	0.3865435356200528	C	16.23	3.063622	0.55432	0.175789	0.429187	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20738	2.05	5.0	1.51	0.23008	.	.	.	.	.	T	0.00012	0.0000	M	0.64404	1.975	0.58432	P	1.0000000000287557E-6	B	0.33694	0.421	B	0.25140	0.058	T	0.41360	-0.9513	8	0.59425	D	0.04	.	4.9617	0.14070	0.1683:0.64:0.0:0.1918	rs9610841;rs57925914;rs9610841	863	Q9H2D6	TARA_HUMAN	K	863	ENSP00000384312:N863K	ENSP00000384312:N863K	N	+	3	2	TRIOBP	36451098	0.000000	0.05858	0.037000	0.18230	0.473000	0.32948	-0.011000	0.12721	0.622000	0.30249	0.460000	0.39030	AAC	C|0.623;A|0.377	0.377	strong		0.493	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
GPR98	84059	hgsc.bcm.edu	37	5	90151589	90151589	+	Missense_Mutation	SNP	G	G	A	rs2247870	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:90151589G>A	ENST00000405460.2	+	82	17722	c.17626G>A	c.(17626-17628)Gtt>Att	p.V5876I	GPR98_ENST00000425867.2_Missense_Mutation_p.V1537I	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5876	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.			V -> I (in Ref. 1; AAD55586, 2; AAL30811 and 6; BAA31661). {ECO:0000305}.	detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.V5876I(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTGCAAAGTGGTTGAGGAAAC	0.413													G|||	2299	0.459065	0.1309	0.6931	5008	,	,		20690	0.5665		0.5606	False		,,,				2504	0.5215				p.V5876I		Atlas-SNP	.											GPR98,NS,carcinoma,0,1	GPR98	605	1	1	Substitution - Missense(1)	stomach(1)	c.G17626A						PASS	.	G	ILE/VAL	759,3129		70,619,1255	297.0	274.0	281.0		17626	4.6	1.0	5	dbSNP_100	281	4531,3749		1235,2061,844	yes	missense	GPR98	NM_032119.3	29	1305,2680,2099	AA,AG,GG		45.2778,19.5216,43.4747	benign	5876/6307	90151589	5290,6878	1944	4140	6084	SO:0001583	missense	84059	exon82			AAAGTGGTTGAGG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.17626G>A	5.37:g.90151589G>A	ENSP00000384582:p.Val5876Ile	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	285	132	0.463158	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	1082	0.49542124542124544	72	0.14634146341463414	244	0.6740331491712708	334	0.583916083916084	432	0.5699208443271768	G	12.62	1.991585	0.35131	0.195216	0.547222	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.70164	-0.46;-0.46	5.5	4.64	0.57946	GPS domain (3);	0.111041	0.64402	D	0.000012	T	0.00012	0.0000	L	0.41710	1.295	0.20403	P	0.9999025175	B;P;B	0.36974	0.012;0.576;0.01	B;B;B	0.34242	0.016;0.178;0.009	T	0.46857	-0.9161	8	.	.	.	.	11.3472	0.49567	0.1921:0.0:0.8079:0.0	rs2247870;rs56587026;rs60466685;rs2247870	1537;5876;1537	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	I	5876;5876;1537	ENSP00000384582:V5876I;ENSP00000392618:V1537I	.	V	+	1	0	GPR98	90187345	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.899000	0.48679	1.465000	0.48006	-0.216000	0.12614	GTT	G|0.534;A|0.466	0.466	strong		0.413	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
TTC37	9652	hgsc.bcm.edu	37	5	94882781	94882781	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94882781G>A	ENST00000358746.2	-	4	372	c.74C>T	c.(73-75)gCt>gTt	p.A25V		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	25						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						GTGTTTCAAAGCTTCTTTGTA	0.338																																					p.A25V		Atlas-SNP	.											.	TTC37	128	.	0			c.C74T						PASS	.						178.0	180.0	179.0					5																	94882781		2203	4300	6503	SO:0001583	missense	9652	exon4			TTCAAAGCTTCTT	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.74C>T	5.37:g.94882781G>A	ENSP00000351596:p.Ala25Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.165839	0.57476	.	.	ENSG00000198677	ENST00000358746;ENST00000514952;ENST00000513823	D;T;D	0.83591	-1.74;-0.69;-1.74	5.38	4.5	0.54988	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.064313	0.64402	N	0.000008	T	0.81983	0.4938	M	0.67953	2.075	0.51767	D	0.999938	B;B	0.20887	0.032;0.049	B;B	0.31390	0.016;0.129	T	0.78758	-0.2079	10	0.49607	T	0.09	.	10.6469	0.45626	0.1497:0.0:0.8503:0.0	.	25;25	D6RCE2;Q6PGP7	.;TTC37_HUMAN	V	25	ENSP00000351596:A25V;ENSP00000423742:A25V;ENSP00000425403:A25V	ENSP00000351596:A25V	A	-	2	0	TTC37	94908537	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.086000	0.64474	1.235000	0.43724	0.591000	0.81541	GCT	.	.	none		0.338	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
OR2AK2	391191	hgsc.bcm.edu	37	1	248129304	248129304	+	Missense_Mutation	SNP	T	T	C	rs143777155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248129304T>C	ENST00000366480.3	+	1	770	c.671T>C	c.(670-672)cTa>cCa	p.L224P	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			ATCTTGCTACTACCATTCCTA	0.453													.|||	8	0.00159744	0.0	0.0029	5008	,	,		20749	0.0		0.003	False		,,,				2504	0.0031				p.L224P	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.T671C						PASS	.	T	PRO/LEU,	2,4404		0,2,2201	92.0	80.0	84.0		671,	1.3	0.0	1	dbSNP_134	84	11,8589		0,11,4289	yes	missense,intron	OR2L13,OR2AK2	NM_001004491.1,NM_175911.2	98,	0,13,6490	CC,CT,TT		0.1279,0.0454,0.1	probably-damaging,	224/336,	248129304	13,12993	2203	4300	6503	SO:0001583	missense	391191	exon1			TGCTACTACCATT	BK004457	CCDS31102.1	1q44	2012-08-09			ENSG00000187080	ENSG00000187080		"""GPCR / Class A : Olfactory receptors"""	19569	protein-coding gene	gene with protein product				OR2AK1P			Standard	NM_001004491		Approved		uc010pzd.2	Q8NG84	OTTHUMG00000040201	ENST00000366480.3:c.671T>C	1.37:g.248129304T>C	ENSP00000355436:p.Leu224Pro	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	150	77	0.513333	NM_001004491	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	37	CCDS31102.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	.	10.89	1.477945	0.26511	4.54E-4	0.001279	ENSG00000187080	ENST00000366480	T	0.45668	0.89	2.48	1.33	0.21861	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.52041	0.1710	L	0.50847	1.595	0.09310	N	0.999995	D	0.89917	1.0	D	0.79108	0.992	T	0.31724	-0.9933	9	0.56958	D	0.05	.	5.7206	0.17985	0.0:0.1483:0.0:0.8517	.	224	Q8NG84	O2AK2_HUMAN	P	224	ENSP00000355436:L224P	ENSP00000355436:L224P	L	+	2	0	OR2AK2	246195927	0.000000	0.05858	0.005000	0.12908	0.130000	0.20726	-0.642000	0.05427	0.372000	0.24591	0.379000	0.24179	CTA	T|0.998;C|0.002	0.002	strong		0.453	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491	
APBB2	323	hgsc.bcm.edu	37	4	41015899	41015899	+	Missense_Mutation	SNP	C	C	T	rs4861358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:41015899C>T	ENST00000295974.8	-	6	1165	c.536G>A	c.(535-537)cGa>cAa	p.R179Q	APBB2_ENST00000513140.1_Missense_Mutation_p.R179Q|APBB2_ENST00000506352.1_Missense_Mutation_p.R179Q|APBB2_ENST00000508593.1_Missense_Mutation_p.R179Q	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	179			R -> Q (in dbSNP:rs4861358). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						GTGATTGCCTCGGTTCTGCTC	0.522													C|||	3376	0.674121	0.3222	0.7262	5008	,	,		17551	0.8978		0.7505	False		,,,				2504	0.8037				p.R179Q	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.G536A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	1543,2311		316,911,700	166.0	151.0	156.0		536,536,536	-2.0	0.0	4	dbSNP_111	156	6336,1926		2427,1482,222	yes	missense,missense,missense	APBB2	NM_001166050.1,NM_004307.1,NM_173075.4	43,43,43	2743,2393,922	TT,TC,CC		23.3115,40.0363,34.9703	benign,benign,benign	179/759,179/760,179/737	41015899	7879,4237	1927	4131	6058	SO:0001583	missense	323	exon6			TTGCCTCGGTTCT	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.536G>A	4.37:g.41015899C>T	ENSP00000295974:p.Arg179Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_173075	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	37	CCDS54761.1	1513	0.6927655677655677	155	0.3150406504065041	262	0.7237569060773481	520	0.9090909090909091	576	0.7598944591029023	C	0.232	-1.020406	0.02061	0.400363	0.766885	ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000513140;ENST00000508593;ENST00000506352	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.6	-2.0	0.07433	.	1.468110	0.04553	N	0.390303	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B	0.12630	0.002;0.004;0.006;0.004	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.21965	-1.0230	9	0.11485	T	0.65	0.1451	2.8538	0.05565	0.3621:0.1219:0.0676:0.4483	rs4861358;rs52810922;rs61624316;rs4861358	162;179;179;179	B4DJ88;E9PG87;Q92870-2;Q92870	.;.;.;APBB2_HUMAN	Q	179;178;179;179;179	ENSP00000295974:R179Q;ENSP00000426018:R179Q;ENSP00000427211:R179Q;ENSP00000421539:R179Q	ENSP00000295974:R179Q	R	-	2	0	APBB2	40710656	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.384000	0.20668	-0.155000	0.11098	-2.720000	0.00132	CGA	C|0.308;T|0.692	0.692	strong		0.522	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
FAM169B	283777	hgsc.bcm.edu	37	15	99023968	99023968	+	Silent	SNP	T	T	G	rs4528551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:99023968T>G	ENST00000558256.1	-	4	294	c.45A>C	c.(43-45)ctA>ctC	p.L15L	FAM169B_ENST00000332908.4_Silent_p.L15L	NM_182562.2	NP_872368.2	Q8N8A8	F169B_HUMAN	family with sequence similarity 169, member B	15										large_intestine(3)|lung(3)|urinary_tract(1)	7						TAATGGCGTTTAGAATGAAAA	0.373													T|||	1687	0.336861	0.2027	0.4957	5008	,	,		22923	0.3413		0.3519	False		,,,				2504	0.3855				p.L15L		Atlas-SNP	.											.	FAM169B	23	.	0			c.A45C						PASS	.	T		930,2798		117,696,1051	83.0	79.0	80.0		45	-10.5	0.0	15	dbSNP_111	80	2928,5264		514,1900,1682	no	coding-synonymous	FAM169B	NM_182562.2		631,2596,2733	GG,GT,TT		35.7422,24.9464,32.3658		15/193	99023968	3858,8062	1864	4096	5960	SO:0001819	synonymous_variant	283777	exon4			GGCGTTTAGAATG		CCDS45360.1	15q26.3	2008-08-08			ENSG00000185087	ENSG00000185087			26835	protein-coding gene	gene with protein product							Standard	NM_182562		Approved	FLJ39743, KIAA0888L	uc002buk.1	Q8N8A8		ENST00000558256.1:c.45A>C	15.37:g.99023968T>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_182562	B5MDL8	Silent	SNP	ENST00000558256.1	37	CCDS45360.1																																																																																			T|0.666;G|0.334	0.334	strong		0.373	FAM169B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415488.1	NM_182562	
ABCA1	19	hgsc.bcm.edu	37	9	107562804	107562804	+	Missense_Mutation	SNP	T	T	C	rs2230808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107562804T>C	ENST00000374736.3	-	35	5154	c.4760A>G	c.(4759-4761)aAa>aGa	p.K1587R		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1587			K -> R (associated with HDL cholesterol; dbSNP:rs2230808). {ECO:0000269|PubMed:10092505, ECO:0000269|PubMed:10431238, ECO:0000269|PubMed:10884428, ECO:0000269|PubMed:10938021, ECO:0000269|PubMed:11238261, ECO:0000269|PubMed:11352567, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:15520867, ECO:0000269|Ref.2}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GACATTATTTTTGGTGTCCAG	0.398													T|||	2696	0.538339	0.1324	0.7478	5008	,	,		20994	0.5883		0.7922	False		,,,				2504	0.6258				p.K1587R		Atlas-SNP	.											.	ABCA1	244	.	0			c.A4760G	GRCh37	CM042912	ABCA1	M	rs2230808	PASS	.	T	ARG/LYS	1069,3337	388.6+/-327.0	141,787,1275	186.0	157.0	167.0		4760	5.9	1.0	9	dbSNP_98	167	6540,2060	719.3+/-406.3	2486,1568,246	yes	missense	ABCA1	NM_005502.3	26	2627,2355,1521	CC,CT,TT		23.9535,24.2624,41.4962	benign	1587/2262	107562804	7609,5397	2203	4300	6503	SO:0001583	missense	19	exon35			TTATTTTTGGTGT	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.4760A>G	9.37:g.107562804T>C	ENSP00000363868:p.Lys1587Arg	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	190	190	1	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	1288	0.5897435897435898	85	0.17276422764227642	256	0.7071823204419889	349	0.6101398601398601	598	0.7889182058047494	T	10.84	1.465085	0.26335	0.242624	0.760465	ENSG00000165029	ENST00000374736	D	0.87256	-2.23	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.11870	0.19	0.09310	P	1.0	B	0.16603	0.018	B	0.21360	0.034	T	0.35699	-0.9778	9	0.02654	T	1	.	16.3798	0.83452	0.0:0.0:0.0:1.0	rs2230808;rs2234886;rs57688810;rs2230808	1587	O95477	ABCA1_HUMAN	R	1587	ENSP00000363868:K1587R	ENSP00000363868:K1587R	K	-	2	0	ABCA1	106602625	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.978000	0.70501	2.271000	0.75665	0.533000	0.62120	AAA	T|0.422;C|0.578	0.578	strong		0.398	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
OR9G4	283189	hgsc.bcm.edu	37	11	56510623	56510623	+	Missense_Mutation	SNP	A	A	G	rs513873	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56510623A>G	ENST00000302957.3	-	1	664	c.665T>C	c.(664-666)gTa>gCa	p.V222A		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	222			V -> A (in dbSNP:rs513873).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						GCTGGAGAGTACTGTGAAGCC	0.468													A|||	945	0.188698	0.2163	0.1599	5008	,	,		21139	0.0853		0.2992	False		,,,				2504	0.1646				p.V222A		Atlas-SNP	.											.	OR9G4	73	.	0			c.T665C						PASS	.	A	ALA/VAL	1052,3350	384.7+/-325.4	118,816,1267	101.0	92.0	95.0		665	5.1	1.0	11	dbSNP_83	95	2745,5847	436.3+/-358.3	444,1857,1995	yes	missense	OR9G4	NM_001005284.1	64	562,2673,3262	GG,GA,AA		31.9483,23.8982,29.2212	possibly-damaging	222/328	56510623	3797,9197	2201	4296	6497	SO:0001583	missense	283189	exon1			GAGAGTACTGTGA	BK004400	CCDS31537.1	11q11	2012-08-09			ENSG00000172457	ENSG00000172457		"""GPCR / Class A : Olfactory receptors"""	15322	protein-coding gene	gene with protein product							Standard	NM_001005284		Approved		uc010rjo.2	Q8NGQ1	OTTHUMG00000166932	ENST00000302957.3:c.665T>C	11.37:g.56510623A>G	ENSP00000307515:p.Val222Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_001005284	Q6IF62|Q96RA9	Missense_Mutation	SNP	ENST00000302957.3	37	CCDS31537.1	445	0.20375457875457875	112	0.22764227642276422	54	0.14917127071823205	46	0.08041958041958042	233	0.3073878627968338	A	14.16	2.452759	0.43531	0.238982	0.319483	ENSG00000172457	ENST00000302957	T	0.38077	1.16	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35772	N	0.002985	T	0.00012	0.0000	L	0.35542	1.07	0.33213	P	0.44635800000000003	D	0.76494	0.999	D	0.80764	0.994	T	0.32188	-0.9916	9	0.19590	T	0.45	-48.116	13.8217	0.63325	1.0:0.0:0.0:0.0	rs513873;rs52807984;rs60956810;rs513873	222	Q8NGQ1	OR9G4_HUMAN	A	222	ENSP00000307515:V222A	ENSP00000307515:V222A	V	-	2	0	OR9G4	56267199	0.047000	0.20315	0.991000	0.47740	0.912000	0.54170	3.072000	0.50049	2.131000	0.65755	0.523000	0.50628	GTA	A|0.748;G|0.252	0.252	strong		0.468	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284	
SDK1	221935	hgsc.bcm.edu	37	7	4153824	4153824	+	Silent	SNP	A	A	G	rs2141076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4153824A>G	ENST00000404826.2	+	25	3880	c.3741A>G	c.(3739-3741)gaA>gaG	p.E1247E	SDK1_ENST00000389531.3_Silent_p.E1247E	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1247	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AGTGGATGGAATACGAGCTGC	0.642													A|||	655	0.130791	0.2504	0.0836	5008	,	,		15561	0.001		0.1223	False		,,,				2504	0.1452				p.E1247E		Atlas-SNP	.											.	SDK1	361	.	0			c.A3741G						PASS	.	A		995,3411	369.1+/-318.9	121,753,1329	49.0	47.0	48.0		3741	-2.6	0.9	7	dbSNP_96	48	1163,7437	237.4+/-269.2	72,1019,3209	no	coding-synonymous	SDK1	NM_152744.3		193,1772,4538	GG,GA,AA		13.5233,22.5828,16.5923		1247/2214	4153824	2158,10848	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon25			GATGGAATACGAG	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3741A>G	7.37:g.4153824A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	126	71	0.563492	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			A|0.851;G|0.149	0.149	strong		0.642	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
PTPRH	5794	hgsc.bcm.edu	37	19	55715309	55715309	+	Missense_Mutation	SNP	C	C	T	rs45535035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55715309C>T	ENST00000376350.3	-	5	749	c.727G>A	c.(727-729)Gtt>Att	p.V243I	PTPRH_ENST00000263434.5_Intron|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	243	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs45535035).		apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GTGCACTGAACGCAGTAGGTC	0.577													C|||	623	0.124401	0.1558	0.0994	5008	,	,		15751	0.0327		0.1978	False		,,,				2504	0.1186				p.V243I		Atlas-SNP	.											.	PTPRH	139	.	0			c.G727A						PASS	.	C	,ILE/VAL	718,3688	300.4+/-286.3	70,578,1555	184.0	150.0	162.0		,727	2.5	0.5	19	dbSNP_127	162	1526,7074	288.9+/-299.0	145,1236,2919	yes	intron,missense	PTPRH	NM_001161440.1,NM_002842.3	,29	215,1814,4474	TT,TC,CC		17.7442,16.296,17.2536	,benign	,243/1116	55715309	2244,10762	2203	4300	6503	SO:0001583	missense	5794	exon5			ACTGAACGCAGTA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.727G>A	19.37:g.55715309C>T	ENSP00000365528:p.Val243Ile	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	208	103	0.495192	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	277	0.12683150183150182	66	0.13414634146341464	42	0.11602209944751381	12	0.02097902097902098	157	0.20712401055408972	C	0.029	-1.344619	0.01277	0.16296	0.177442	ENSG00000080031	ENST00000376350	T	0.60672	0.17	3.75	2.49	0.30216	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.964989	0.08388	N	0.953456	T	0.00039	0.0001	N	0.11313	0.125	0.23204	P	0.99812677	P;B	0.41159	0.74;0.369	B;B	0.28305	0.088;0.042	T	0.04191	-1.0970	9	0.02654	T	1	.	6.8978	0.24265	0.0:0.8304:0.0:0.1696	rs45535035;rs61734209	65;243	Q9HD43-2;Q9HD43	.;PTPRH_HUMAN	I	243	ENSP00000365528:V243I	ENSP00000365528:V243I	V	-	1	0	PTPRH	60407121	0.006000	0.16342	0.473000	0.27253	0.136000	0.21042	-0.050000	0.11904	0.582000	0.29556	0.511000	0.50034	GTT	C|0.840;T|0.160	0.160	strong		0.577	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
NBPF10	100132406	hgsc.bcm.edu	37	1	145293469	145293469	+	Missense_Mutation	SNP	G	G	C	rs6671324		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145293469G>C	ENST00000369339.3	+	3	317	c.64G>C	c.(64-66)Gag>Cag	p.E22Q	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000342960.5_Missense_Mutation_p.E22Q|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	293						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AGAAATCAACGAGACATTGCG	0.517																																					p.E22Q		Atlas-SNP	.											.	NBPF10	221	.	0			c.G64C						PASS	.																																			SO:0001583	missense	100132406	exon1			ATCAACGAGACAT	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.64G>C	1.37:g.145293469G>C	ENSP00000358345:p.Glu22Gln	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	199	13	0.0653266	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	0.003	-2.490659	0.00161	.	.	ENSG00000163386	ENST00000369339;ENST00000342960	T	0.03181	4.02	1.21	-1.37	0.09056	.	.	.	.	.	T	0.00845	0.0028	N	0.26042	0.785	0.09310	N	1	P	0.46621	0.881	B	0.43990	0.438	T	0.36261	-0.9755	9	0.09084	T	0.74	.	6.6617	0.23018	0.0:0.4052:0.5948:0.0	rs6671324	22	A8MQ30	.	Q	22	ENSP00000345684:E22Q	ENSP00000345684:E22Q	E	+	1	0	NBPF10	144004826	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-1.862000	0.01653	-0.414000	0.07495	-1.406000	0.01132	GAG	.	.	weak		0.517	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
SEC16B	89866	hgsc.bcm.edu	37	1	177901658	177901658	+	Silent	SNP	C	C	T	rs7554597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177901658C>T	ENST00000308284.6	-	24	3068	c.2979G>A	c.(2977-2979)gcG>gcA	p.A993A	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	993					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CCCCAGCGCCCGCAGCTGCTC	0.652													C|||	1141	0.227835	0.2655	0.2622	5008	,	,		16820	0.1052		0.2604	False		,,,				2504	0.2454				p.A993A		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2979A						PASS	.	C		1084,3004		158,768,1118	11.0	15.0	13.0		2979	-1.3	0.0	1	dbSNP_116	13	1743,6483		202,1339,2572	no	coding-synonymous	SEC16B	NM_033127.2		360,2107,3690	TT,TC,CC		21.1889,26.5166,22.9576		993/1061	177901658	2827,9487	2044	4113	6157	SO:0001819	synonymous_variant	89866	exon24			AGCGCCCGCAGCT	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2979G>A	1.37:g.177901658C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	162	92	0.567901	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			C|0.785;T|0.215	0.215	strong		0.652	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
ZNF765	91661	hgsc.bcm.edu	37	19	53911510	53911510	+	Silent	SNP	G	G	A	rs8182488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53911510G>A	ENST00000396408.3	+	4	819	c.702G>A	c.(700-702)caG>caA	p.Q234Q	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		GGAAACATCAGTTAATCCATT	0.383													.|||	1140	0.227636	0.0522	0.3775	5008	,	,		22745	0.1042		0.3201	False		,,,				2504	0.3906				p.Q234Q		Atlas-SNP	.											.	ZNF765	61	.	0			c.G702A						PASS	.	G		420,3980	195.0+/-219.7	24,372,1804	76.0	76.0	76.0		702	0.4	0.0	19	dbSNP_117	76	2840,5756	440.4+/-359.5	474,1892,1932	no	coding-synonymous	ZNF765	NM_001040185.1		498,2264,3736	AA,AG,GG		33.0386,9.5455,25.0846		234/524	53911510	3260,9736	2200	4298	6498	SO:0001819	synonymous_variant	91661	exon4			ACATCAGTTAATC	BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"""Zinc fingers, C2H2-type"", ""-"""	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.702G>A	19.37:g.53911510G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	206	88	0.427184	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Silent	SNP	ENST00000396408.3	37	CCDS46171.1																																																																																			G|0.796;A|0.204	0.204	strong		0.383	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372	
SHCBP1	79801	hgsc.bcm.edu	37	16	46652188	46652188	+	Missense_Mutation	SNP	A	A	G	rs146004470	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:46652188A>G	ENST00000303383.3	-	2	466	c.200T>C	c.(199-201)tTc>tCc	p.F67S	SHCBP1_ENST00000564272.1_5'Flank	NM_024745.4	NP_079021	Q8NEM2	SHCBP_HUMAN	SHC SH2-domain binding protein 1	67					fibroblast growth factor receptor signaling pathway (GO:0008543)|regulation of neural precursor cell proliferation (GO:2000177)					breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)				AATTTCTGGGAAAAAGGTTTT	0.338																																					p.F67S		Atlas-SNP	.											.	SHCBP1	54	.	0			c.T200C						PASS	.	A	SER/PHE	2,4402		0,2,2200	58.0	63.0	62.0		200	3.6	0.8	16	dbSNP_134	62	7,8593		0,7,4293	yes	missense	SHCBP1	NM_024745.4	155	0,9,6493	GG,GA,AA		0.0814,0.0454,0.0692	probably-damaging	67/673	46652188	9,12995	2202	4300	6502	SO:0001583	missense	79801	exon2			TCTGGGAAAAAGG	AK055931	CCDS10720.1	16q11	2008-02-05			ENSG00000171241	ENSG00000171241			29547	protein-coding gene	gene with protein product		611027				10086341	Standard	NM_024745		Approved	FLJ22009	uc002eec.4	Q8NEM2	OTTHUMG00000132540	ENST00000303383.3:c.200T>C	16.37:g.46652188A>G	ENSP00000306473:p.Phe67Ser	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	180	92	0.511111	NM_024745	Q96N60|Q9BVS0|Q9H6P6	Missense_Mutation	SNP	ENST00000303383.3	37	CCDS10720.1	.	.	.	.	.	.	.	.	.	.	.	14.33	2.503524	0.44558	4.54E-4	8.14E-4	ENSG00000171241	ENST00000303383	T	0.29397	1.57	3.59	3.59	0.41128	.	0.060699	0.64402	D	0.000002	T	0.32675	0.0837	L	0.60455	1.87	0.43982	D	0.996674	P	0.43169	0.8	B	0.41860	0.368	T	0.29640	-1.0005	10	0.87932	D	0	-4.4485	12.3184	0.54971	1.0:0.0:0.0:0.0	.	67	Q8NEM2	SHCBP_HUMAN	S	67	ENSP00000306473:F67S	ENSP00000306473:F67S	F	-	2	0	SHCBP1	45209689	0.997000	0.39634	0.831000	0.32960	0.510000	0.34073	7.683000	0.84093	1.502000	0.48669	0.482000	0.46254	TTC	A|0.999;G|0.001	0.001	strong		0.338	SHCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255740.1	NM_024745	
HLA-C	3107	hgsc.bcm.edu	37	6	31239108	31239108	+	Missense_Mutation	SNP	T	T	A	rs1131118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31239108T>A	ENST00000376228.5	-	3	375	c.361A>T	c.(361-363)Agg>Tgg	p.R121W	HLA-C_ENST00000383329.3_Missense_Mutation_p.R121W	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	121	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CCAGACATCCTCTGGAGGGTG	0.701													N|||	1342	0.267971	0.2179	0.2839	5008	,	,		10532	0.3026		0.2664	False		,,,				2504	0.2904				p.R121W		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	0			c.A361T						PASS	.	A	TRP/ARG	967,3349		93,781,1284	20.0	19.0	19.0		361	-5.6	0.0	6	dbSNP_86	19	1933,6525		189,1555,2485	no	missense	HLA-C	NM_002117.5	101	282,2336,3769	AA,AT,TT		22.8541,22.405,22.7024	benign	121/367	31239108	2900,9874	2158	4229	6387	SO:0001583	missense	3107	exon3			ACATCCTCTGGAG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.361A>T	6.37:g.31239108T>A	ENSP00000365402:p.Arg121Trp	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	3.319|3.319	-0.139116|-0.139116	0.06669|0.06669	0.22405|0.22405	0.228541|0.228541	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00010	.|9.41;9.41	2.81|2.81	-5.62|-5.62	0.02481|0.02481	.|MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|1.047180	.|0.07713	.|N	.|0.942312	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11255|0.11255	0.115|0.115	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.24368	.|0.102;0.062;0.03;0.03;0.03	.|B;B;B;B;B	.|0.36335	.|0.222;0.027;0.027;0.014;0.027	T|T	0.16808|0.16808	-1.0390|-1.0390	5|9	0.62326|0.42905	D|T	0.03|0.14	.|.	4.3487|4.3487	0.11144|0.11144	0.3799:0.2718:0.0:0.3483|0.3799:0.2718:0.0:0.3483	rs1131118;rs2308566;rs3177883;rs3190686;rs11547358;rs17366166;rs17413520;rs28367579|rs1131118;rs2308566;rs3177883;rs3190686;rs11547358;rs17366166;rs17413520;rs28367579	.|121;96;121;121;121	.|A2AEA4;Q92671;A6H578;A2AEA2;P10321	.|.;.;.;.;1C07_HUMAN	V|W	120|121;121;121;158	.|ENSP00000365402:R121W;ENSP00000372819:R121W	ENSP00000365412:E115V|ENSP00000365402:R121W	E|R	-|-	2|1	0|2	HLA-C|HLA-C	31347087|31347087	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-6.442000|-6.442000	0.00066|0.00066	-2.961000|-2.961000	0.00290|0.00290	-2.002000|-2.002000	0.00443|0.00443	GAG|AGG	T|0.768;A|0.232	0.232	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
C3orf30	152405	hgsc.bcm.edu	37	3	118865609	118865609	+	Silent	SNP	C	C	T	rs10934483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:118865609C>T	ENST00000295622.1	+	1	613	c.573C>T	c.(571-573)tcC>tcT	p.S191S	RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	191										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		GAAGAGCTTCCGAGCAGATGG	0.517													c|||	717	0.143171	0.1331	0.0663	5008	,	,		22755	0.2361		0.1531	False		,,,				2504	0.1053				p.S191S		Atlas-SNP	.											C3orf30,rectum,carcinoma,0,1	C3orf30	64	1	0			c.C573T						PASS	.	T		519,3887	239.3+/-250.5	28,463,1712	91.0	94.0	93.0		573	-8.2	0.0	3	dbSNP_120	93	1187,7413	242.1+/-272.2	73,1041,3186	no	coding-synonymous	C3orf30	NM_152539.2		101,1504,4898	TT,TC,CC		13.8023,11.7794,13.117		191/537	118865609	1706,11300	2203	4300	6503	SO:0001819	synonymous_variant	152405	exon1			AGCTTCCGAGCAG	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.573C>T	3.37:g.118865609C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_152539	A1L4B7	Silent	SNP	ENST00000295622.1	37	CCDS2984.1	359	0.16437728937728938	79	0.16056910569105692	22	0.06077348066298342	131	0.229020979020979	127	0.16754617414248021	c	4.219	0.039534	0.08148	0.117794	0.138023	ENSG00000163424	ENST00000460150	.	.	.	4.09	-8.17	0.01057	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.7772	9.1284	0.36830	0.0:0.4138:0.1026:0.4836	rs10934483;rs10934483	.	.	.	X	155	.	.	R	+	1	2	C3orf30	120348299	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.657000	0.01979	-1.809000	0.01232	-1.402000	0.01139	CGA	C|0.855;T|0.145	0.145	strong		0.517	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
MOV10L1	54456	hgsc.bcm.edu	37	22	50589196	50589196	+	Silent	SNP	C	C	A	rs2294396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50589196C>A	ENST00000262794.5	+	21	2843	c.2760C>A	c.(2758-2760)ggC>ggA	p.G920G	MOV10L1_ENST00000395852.1_Silent_p.G47G|MOV10L1_ENST00000395858.3_Silent_p.G920G|MOV10L1_ENST00000354853.2_Intron|MOV10L1_ENST00000395843.1_Intron|MOV10L1_ENST00000545383.1_Silent_p.G920G|MOV10L1_ENST00000540615.1_Silent_p.G900G	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	920					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGCAGCTCGGCCCAGTCATTA	0.607													C|||	723	0.144369	0.0219	0.1081	5008	,	,		18749	0.2431		0.172	False		,,,				2504	0.2055				p.G920G		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C2760A						PASS	.	C	,,,	170,4236		2,166,2035	139.0	100.0	113.0		2760,2700,141,2760	-6.0	0.3	22	dbSNP_100	113	1290,7310		96,1098,3106	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_001164106.1,NM_018995.2	,,,	98,1264,5141	AA,AC,CC		15.0,3.8584,11.2256	,,,	920/1166,900/1166,47/339,920/1212	50589196	1460,11546	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon21			GCTCGGCCCAGTC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2760C>A	22.37:g.50589196C>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	42	0.33871	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			C|0.878;A|0.122	0.122	strong		0.607	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
IGSF22	283284	hgsc.bcm.edu	37	11	18743180	18743180	+	Missense_Mutation	SNP	C	C	G	rs10832975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18743180C>G	ENST00000513874.1	-	4	419	c.280G>C	c.(280-282)Gcc>Ccc	p.A94P	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	94	Ig-like 1.		A -> P (in dbSNP:rs10832975).							NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TGGGGTTTGGCGTTCCCCTGC	0.587											OREG0020822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1803	0.360024	0.171	0.5187	5008	,	,		17972	0.3224		0.3897	False		,,,				2504	0.5112				p.A94P		Atlas-SNP	.											IGSF22_ENST00000513874,NS,carcinoma,0,2	IGSF22	211	2	0			c.G280C						PASS	.	G	PRO/ALA	865,3119		102,661,1229	103.0	104.0	104.0		280	4.4	1.0	11	dbSNP_120	104	3270,5036		665,1940,1548	yes	missense	IGSF22	NM_173588.3	27	767,2601,2777	GG,GC,CC		39.3691,21.7118,33.6452	benign	94/1327	18743180	4135,8155	1992	4153	6145	SO:0001583	missense	283284	exon4			GTTTGGCGTTCCC	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.280G>C	11.37:g.18743180C>G	ENSP00000421191:p.Ala94Pro	Somatic	136	0	0	90	WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	767	0.35119047619047616	92	0.18699186991869918	186	0.5138121546961326	179	0.3129370629370629	310	0.40897097625329815	G	7.324	0.617487	0.14129	0.217118	0.393691	ENSG00000179057	ENST00000513874	T	0.57907	0.37	5.33	4.39	0.52855	.	0.256726	0.20434	N	0.092411	T	0.00012	0.0000	N	0.00025	-2.68	0.52501	P	4.700000000001925E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.49303	-0.8954	9	0.02654	T	1	.	13.1751	0.59621	0.0:0.3071:0.6929:0.0	rs10832975;rs52802422;rs56874939;rs10832975	94	D6RGV7	.	P	94	ENSP00000421191:A94P	ENSP00000322422:A94P	A	-	1	0	IGSF22	18699756	1.000000	0.71417	0.995000	0.50966	0.868000	0.49771	5.417000	0.66423	0.606000	0.29965	-0.120000	0.15030	GCC	C|0.636;G|0.364	0.364	strong		0.587	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
TFB2M	64216	hgsc.bcm.edu	37	1	246707858	246707858	+	Silent	SNP	A	A	G	rs3129568	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:246707858A>G	ENST00000366514.4	-	7	1169	c.984T>C	c.(982-984)ttT>ttC	p.F328F		NM_022366.2	NP_071761.1	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	328					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(1)|kidney(12)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			TGCGCCTCCCAAAACAGTGCT	0.338													G|||	767	0.153155	0.1732	0.219	5008	,	,		17523	0.003		0.2803	False		,,,				2504	0.1033				p.F328F		Atlas-SNP	.											.	TFB2M	46	.	0			c.T984C						PASS	.	G		824,3582	743.6+/-411.5	88,648,1467	85.0	91.0	89.0		984	4.0	1.0	1	dbSNP_103	89	2307,6293	705.2+/-405.5	337,1633,2330	no	coding-synonymous	TFB2M	NM_022366.2		425,2281,3797	GG,GA,AA		26.8256,18.7018,24.0735		328/397	246707858	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	64216	exon7			CCTCCCAAAACAG	AK026835	CCDS1627.1	1q44	2008-02-05			ENSG00000162851	ENSG00000162851			18559	protein-coding gene	gene with protein product		607055					Standard	NM_022366		Approved	FLJ23182, FLJ22661, Hkp1	uc001ibn.3	Q9H5Q4	OTTHUMG00000040091	ENST00000366514.4:c.984T>C	1.37:g.246707858A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	NM_022366	Q9H626	Silent	SNP	ENST00000366514.4	37	CCDS1627.1																																																																																			A|0.783;G|0.217	0.217	strong		0.338	TFB2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096673.1	NM_022366	
POM121L12	285877	hgsc.bcm.edu	37	7	53103571	53103571	+	Silent	SNP	G	G	A	rs11238248	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:53103571G>A	ENST00000408890.4	+	1	223	c.207G>A	c.(205-207)ggG>ggA	p.G69G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	69										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						TCCAGTGGGGGCGCCCGGTGC	0.706													g|||	1646	0.328674	0.1725	0.4308	5008	,	,		11528	0.3026		0.4861	False		,,,				2504	0.3323				p.G69G		Atlas-SNP	.											.	POM121L12	146	.	0			c.G207A						PASS	.	A		812,3026		96,620,1203	23.0	28.0	26.0		207	-1.0	0.0	7	dbSNP_120	26	4179,4089		1058,2063,1013	no	coding-synonymous	POM121L12	NM_182595.3		1154,2683,2216	AA,AG,GG		49.4557,21.1569,41.2275		69/297	53103571	4991,7115	1919	4134	6053	SO:0001819	synonymous_variant	285877	exon1			GTGGGGGCGCCCG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.207G>A	7.37:g.53103571G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.585;A|0.415	0.415	strong		0.706	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
ALDH1A2	8854	hgsc.bcm.edu	37	15	58256127	58256127	+	Missense_Mutation	SNP	C	C	T	rs4646626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:58256127C>T	ENST00000249750.4	-	9	1809	c.1042G>A	c.(1042-1044)Gta>Ata	p.V348I	ALDH1A2_ENST00000537372.1_Missense_Mutation_p.V327I|ALDH1A2_ENST00000558231.1_Missense_Mutation_p.V319I|ALDH1A2_ENST00000559517.1_Missense_Mutation_p.V252I|ALDH1A2_ENST00000347587.3_Missense_Mutation_p.V310I	NM_003888.3	NP_003879.2	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1 family, member A2	348			V -> I (in dbSNP:rs4646626). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9819382, ECO:0000269|Ref.3}.		9-cis-retinoic acid biosynthetic process (GO:0042904)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|cardiac muscle tissue development (GO:0048738)|cellular response to retinoic acid (GO:0071300)|determination of bilateral symmetry (GO:0009855)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract development (GO:0048566)|embryonic forelimb morphogenesis (GO:0035115)|face development (GO:0060324)|heart morphogenesis (GO:0003007)|hindbrain development (GO:0030902)|kidney development (GO:0001822)|liver development (GO:0001889)|lung development (GO:0030324)|midgut development (GO:0007494)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|neural crest cell development (GO:0014032)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|proximal/distal pattern formation (GO:0009954)|regulation of endothelial cell proliferation (GO:0001936)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to vitamin A (GO:0033189)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)|retinoic acid receptor signaling pathway (GO:0048384)|retinol metabolic process (GO:0042572)|ureter maturation (GO:0035799)|vitamin A metabolic process (GO:0006776)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|retinal binding (GO:0016918)|retinal dehydrogenase activity (GO:0001758)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	Tretinoin(DB00755)|Vitamin A(DB00162)	CTCCCCACTACGCGCCTCTTG	0.527													T|||	1867	0.372804	0.3676	0.3991	5008	,	,		17990	0.3065		0.5358	False		,,,				2504	0.2618				p.V348I		Atlas-SNP	.											.	ALDH1A2	69	.	0			c.G1042A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1656,2728	654.8+/-399.8	318,1020,854	81.0	83.0	82.0		979,1042,928,754	4.5	1.0	15	dbSNP_111	82	4464,4120	563.5+/-388.1	1160,2144,988	yes	missense,missense,missense,missense	ALDH1A2	NM_001206897.1,NM_003888.3,NM_170696.2,NM_170697.2	29,29,29,29	1478,3164,1842	TT,TC,CC		47.9963,37.7737,47.1931	benign,benign,benign,benign	327/498,348/519,310/481,252/423	58256127	6120,6848	2192	4292	6484	SO:0001583	missense	8854	exon9			CCACTACGCGCCT	AB015228	CCDS10163.1, CCDS10164.1, CCDS45266.1, CCDS55968.1	15q21.2	2011-02-18			ENSG00000128918	ENSG00000128918		"""Aldehyde dehydrogenases"""	15472	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 2"""	603687				9819382	Standard	NM_003888		Approved	RALDH2	uc002aex.3	O94788	OTTHUMG00000132624	ENST00000249750.4:c.1042G>A	15.37:g.58256127C>T	ENSP00000249750:p.Val348Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_003888	B3KY52|B4DZR2|F5H2Y9|H0YM00|Q2PJS6|Q8NHQ4|Q9UBR8|Q9UFY0	Missense_Mutation	SNP	ENST00000249750.4	37	CCDS10163.1	893	0.4088827838827839	184	0.37398373983739835	140	0.3867403314917127	177	0.3094405594405594	392	0.5171503957783641	T	12.44	1.939770	0.34189	0.377737	0.520037	ENSG00000128918	ENST00000249750;ENST00000430119;ENST00000543386;ENST00000347587;ENST00000537372	T;T;T	0.76316	-1.01;-1.01;-1.01	5.6	4.49	0.54785	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.159895	0.64402	N	0.000003	T	0.00012	0.0000	L	0.38953	1.18	0.80722	P	0.0	B;B;B	0.14805	0.0;0.011;0.0	B;B;B	0.10450	0.0;0.005;0.001	T	0.45381	-0.9265	9	0.15066	T	0.55	.	8.2061	0.31456	0.0:0.2776:0.0:0.7224	rs4646626;rs58168294;rs4646626	327;310;348	F5H2Y9;O94788-2;O94788	.;.;AL1A2_HUMAN	I	348;252;319;310;327	ENSP00000249750:V348I;ENSP00000309623:V310I;ENSP00000438296:V327I	ENSP00000249750:V348I	V	-	1	0	ALDH1A2	56043419	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	1.981000	0.40628	0.495000	0.27882	-0.269000	0.10298	GTA	C|0.566;T|0.434	0.434	strong		0.527	ALDH1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255869.1		
WDYHV1	55093	hgsc.bcm.edu	37	8	124440260	124440260	+	Silent	SNP	G	G	A	rs10505435	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:124440260G>A	ENST00000287387.2	+	2	305	c.180G>A	c.(178-180)aaG>aaA	p.K60K	WDYHV1_ENST00000518125.1_5'Flank|WDYHV1_ENST00000523356.1_Silent_p.K60K|WDYHV1_ENST00000517609.1_3'UTR|WDYHV1_ENST00000523984.1_De_novo_Start_InFrame	NM_018024.1	NP_060494.1	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	60					cellular protein modification process (GO:0006464)	cytosol (GO:0005829)|nucleus (GO:0005634)	protein-N-terminal glutamine amidohydrolase activity (GO:0070773)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(3)	17						ATGAGAGGAAGATGGTAAGTT	0.328													G|||	25	0.00499201	0.0015	0.0058	5008	,	,		18005	0.0		0.0179	False		,,,				2504	0.001				p.K60K		Atlas-SNP	.											.	WDYHV1	30	.	0			c.G180A						PASS	.	G		14,4392	20.2+/-43.8	0,14,2189	113.0	126.0	122.0		180	2.1	1.0	8	dbSNP_119	122	182,8416	80.4+/-143.0	2,178,4119	no	coding-synonymous	WDYHV1	NM_018024.1		2,192,6308	AA,AG,GG		2.1168,0.3177,1.5072		60/206	124440260	196,12808	2203	4299	6502	SO:0001819	synonymous_variant	55093	exon2			GAGGAAGATGGTA	AK001066	CCDS6344.1, CCDS64965.1	8q24.13	2008-10-01	2008-10-01	2008-10-01		ENSG00000156795			25490	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 32"""	C8orf32		12477932	Standard	NM_018024		Approved	FLJ10204	uc003yqn.1	Q96HA8		ENST00000287387.2:c.180G>A	8.37:g.124440260G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_018024	B4DE68|Q9NW95	Silent	SNP	ENST00000287387.2	37	CCDS6344.1																																																																																			G|0.989;A|0.011	0.011	strong		0.328	WDYHV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381772.1	NM_018024	
BICD1	636	hgsc.bcm.edu	37	12	32458756	32458756	+	Silent	SNP	C	C	T	rs11051922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32458756C>T	ENST00000281474.5	+	4	808	c.705C>T	c.(703-705)ctC>ctT	p.L235L	BICD1_ENST00000548411.1_Silent_p.L235L	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	235					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AAGAAGCCCTCGAGACTTTAA	0.458													C|||	28	0.00559105	0.0008	0.0058	5008	,	,		16322	0.0		0.0189	False		,,,				2504	0.0041				p.L235L		Atlas-SNP	.											.	BICD1	89	.	0			c.C705T						PASS	.	C	,	19,4387	26.2+/-53.5	0,19,2184	63.0	60.0	61.0		705,705	-8.6	0.0	12	dbSNP_120	61	204,8396	87.9+/-150.2	5,194,4101	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	5,213,6285	TT,TC,CC		2.3721,0.4312,1.7146	,	235/836,235/976	32458756	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	636	exon4			AGCCCTCGAGACT	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.705C>T	12.37:g.32458756C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			C|0.988;T|0.012	0.012	strong		0.458	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
GPR152	390212	hgsc.bcm.edu	37	11	67218787	67218787	+	Missense_Mutation	SNP	G	G	A	rs137906019		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67218787G>A	ENST00000312457.2	-	1	1413	c.1409C>T	c.(1408-1410)aCg>aTg	p.T470M	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	470						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			GGACCCTCACGTGGGGCCTGC	0.687													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13832	0.0		0.0	False		,,,				2504	0.0				p.T470M	Pancreas(102;800 1581 2723 7382 33622)	Atlas-SNP	.											.	GPR152	41	.	0			c.C1409T						PASS	.	G	MET/THR	0,4364		0,0,2182	28.0	38.0	35.0		1409	2.4	0.5	11	dbSNP_134	35	18,8506		0,18,4244	yes	missense	GPR152	NM_206997.1	81	0,18,6426	AA,AG,GG		0.2112,0.0,0.1397	benign	470/471	67218787	18,12870	2182	4262	6444	SO:0001583	missense	390212	exon1			CCTCACGTGGGGC	AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"""GPCR / Class A : Orphans"""	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.1409C>T	11.37:g.67218787G>A	ENSP00000310255:p.Thr470Met	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_206997	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	37	CCDS8165.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.15	1.853057	0.32699	0.0	0.002112	ENSG00000175514	ENST00000312457	T	0.19938	2.11	4.28	2.37	0.29283	.	0.439888	0.16902	N	0.194879	T	0.13756	0.0333	L	0.29908	0.895	0.20489	N	0.999897	B	0.17038	0.02	B	0.12156	0.007	T	0.21827	-1.0234	10	0.87932	D	0	.	5.1949	0.15232	0.1064:0.0:0.6923:0.2012	.	470	Q8TDT2	GP152_HUMAN	M	470	ENSP00000310255:T470M	ENSP00000310255:T470M	T	-	2	0	GPR152	66975363	0.706000	0.27856	0.469000	0.27204	0.026000	0.11368	0.692000	0.25482	0.423000	0.26033	-0.226000	0.12346	ACG	G|0.998;A|0.002	0.002	strong		0.687	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1		
DOK7	285489	hgsc.bcm.edu	37	4	3494898	3494898	+	Silent	SNP	C	C	T	rs6850908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:3494898C>T	ENST00000340083.5	+	7	1250	c.1185C>T	c.(1183-1185)taC>taT	p.Y395Y	DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR|DOK7_ENST00000389653.2_Silent_p.Y395Y	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	395					neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CAGTCGAGTACCAGGTGCCCA	0.692													.|||	1100	0.219649	0.0386	0.1441	5008	,	,		14813	0.502		0.2237	False		,,,				2504	0.2229				p.Y395Y		Atlas-SNP	.											DOK7,NS,carcinoma,0,1	DOK7	44	1	0			c.C1185T						PASS	.	C	,	291,4089		15,261,1914	15.0	15.0	15.0		,1185	2.8	1.0	4	dbSNP_116	15	1780,6802		194,1392,2705	yes	utr-3,coding-synonymous	DOK7	NM_001164673.1,NM_173660.4	,	209,1653,4619	TT,TC,CC		20.7411,6.6438,15.9775	,	,395/505	3494898	2071,10891	2190	4291	6481	SO:0001819	synonymous_variant	285489	exon7			CGAGTACCAGGTG	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.1185C>T	4.37:g.3494898C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Silent	SNP	ENST00000340083.5	37	CCDS3370.2																																																																																			C|0.794;T|0.206	0.206	strong		0.692	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
PFKFB2	5208	hgsc.bcm.edu	37	1	207238419	207238419	+	Silent	SNP	C	C	T	rs72741390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207238419C>T	ENST00000367080.3	+	8	670	c.546C>T	c.(544-546)aaC>aaT	p.N182N	PFKFB2_ENST00000367079.2_Silent_p.N182N|PFKFB2_ENST00000411990.2_Silent_p.N84N|PFKFB2_ENST00000545806.1_Silent_p.N149N|PFKFB2_ENST00000541914.1_5'UTR	NM_006212.2	NP_006203.2	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	182	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose catabolic process (GO:0006007)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|lactate metabolic process (GO:0006089)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	20	Prostate(682;0.19)					CTGAAAGGAACAGAGAGAACG	0.458													C|||	555	0.110823	0.0257	0.1542	5008	,	,		16547	0.0079		0.2753	False		,,,				2504	0.1319				p.N182N		Atlas-SNP	.											.	PFKFB2	70	.	0			c.C546T						PASS	.	C	,	257,4149	149.9+/-184.0	7,243,1953	118.0	105.0	109.0		546,546	4.0	1.0	1	dbSNP_130	109	2240,6360	380.1+/-339.5	312,1616,2372	no	coding-synonymous,coding-synonymous	PFKFB2	NM_001018053.1,NM_006212.2	,	319,1859,4325	TT,TC,CC		26.0465,5.833,19.1988	,	182/472,182/506	207238419	2497,10509	2203	4300	6503	SO:0001819	synonymous_variant	5208	exon8			AAGGAACAGAGAG		CCDS31003.1, CCDS31004.1	1q31-q32.2	2012-07-13			ENSG00000123836	ENSG00000123836	2.7.1.105, 3.1.3.46		8873	protein-coding gene	gene with protein product		171835					Standard	XM_005273162		Approved		uc001hfg.3	O60825	OTTHUMG00000036033	ENST00000367080.3:c.546C>T	1.37:g.207238419C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	150	89	0.593333	NM_001018053	O60824|Q5VVQ3|Q5VVQ4|Q9H3P1	Silent	SNP	ENST00000367080.3	37	CCDS31004.1																																																																																			C|0.815;T|0.185	0.185	strong		0.458	PFKFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087838.1		
CAPN9	10753	hgsc.bcm.edu	37	1	230923313	230923313	+	Missense_Mutation	SNP	C	C	T	rs12731961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:230923313C>T	ENST00000271971.2	+	13	1677	c.1564C>T	c.(1564-1566)Cgg>Tgg	p.R522W	CAPN9_ENST00000366666.2_Missense_Mutation_p.R459W|CAPN9_ENST00000354537.1_Missense_Mutation_p.R496W|RP11-99J16__A.2_ENST00000452640.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000412344.1_RNA	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	522	Domain IV.|EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.		R -> W (in dbSNP:rs12731961). {ECO:0000269|Ref.3}.		digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GGAGGAGCAGCGGTTTCGGGC	0.522													C|||	982	0.196086	0.3207	0.1542	5008	,	,		19755	0.0813		0.1819	False		,,,				2504	0.1902				p.R522W		Atlas-SNP	.											.	CAPN9	116	.	0			c.C1564T						PASS	.	C	TRP/ARG,TRP/ARG	1255,3151	430.1+/-342.5	191,873,1139	118.0	99.0	105.0		1564,1486	3.2	0.4	1	dbSNP_121	105	1661,6939	306.2+/-307.8	158,1345,2797	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	101,101	349,2218,3936	TT,TC,CC		19.314,28.4839,22.4204	possibly-damaging,possibly-damaging	522/691,496/665	230923313	2916,10090	2203	4300	6503	SO:0001583	missense	10753	exon13			GAGCAGCGGTTTC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1564C>T	1.37:g.230923313C>T	ENSP00000271971:p.Arg522Trp	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	137	62	0.452555	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	381	0.17445054945054944	150	0.3048780487804878	56	0.15469613259668508	35	0.06118881118881119	140	0.18469656992084432	C	8.961	0.970662	0.18659	0.284839	0.19314	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	D;D;D	0.95103	-3.61;-3.61;-3.61	5.17	3.18	0.36537	EF-hand-like domain (1);	0.641175	0.17553	N	0.170097	T	0.00039	0.0001	L	0.34521	1.04	0.80722	P	0.0	P;P;P	0.52061	0.917;0.95;0.917	B;P;B	0.45138	0.28;0.471;0.28	T	0.00000	-1.3148	9	0.72032	D	0.01	.	12.7937	0.57549	0.0:0.6867:0.3133:0.0	rs12731961;rs52797755;rs56556331;rs58840974;rs12731961	459;496;522	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	W	522;496;459	ENSP00000271971:R522W;ENSP00000346538:R496W;ENSP00000355626:R459W	ENSP00000271971:R522W	R	+	1	2	CAPN9	228989936	0.185000	0.23213	0.373000	0.26003	0.052000	0.14988	0.780000	0.26760	1.128000	0.42052	0.655000	0.94253	CGG	C|0.793;T|0.207	0.207	strong		0.522	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
ICAM1	3383	hgsc.bcm.edu	37	19	10394792	10394792	+	Missense_Mutation	SNP	G	G	A	rs1799969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10394792G>A	ENST00000264832.3	+	4	1046	c.721G>A	c.(721-723)Ggg>Agg	p.G241R	ICAM1_ENST00000423829.2_Intron|ICAM4_ENST00000393717.2_5'Flank|CTD-2369P2.8_ENST00000589379.1_RNA|CTD-2369P2.5_ENST00000592893.1_RNA|ICAM4_ENST00000380770.3_5'Flank|ICAM4_ENST00000340992.4_5'Flank	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	241	Ig-like C2-type 3.		G -> R (in dbSNP:rs1799969). {ECO:0000269|PubMed:7525451, ECO:0000269|PubMed:8557254, ECO:0000269|Ref.6}.		adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	TTCCCTGGACGGGCTGTTCCC	0.637													G|||	284	0.0567093	0.0061	0.1988	5008	,	,		15642	0.001		0.1213	False		,,,				2504	0.0153				p.G241R		Atlas-SNP	.											.	ICAM1	32	.	0			c.G721A	GRCh37	CM032586	ICAM1	M	rs1799969	PASS	.	G	ARG/GLY	91,4315	75.2+/-113.4	0,91,2112	70.0	63.0	66.0	http://www.ncbi.nlm.nih.gov/pubmed?term	721	2.2	0.1	19	dbSNP_89	66	925,7675	205.1+/-247.6	60,805,3435	yes	missense	ICAM1	NM_000201.2	125	60,896,5547	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	10.7558,2.0654,7.8118	probably-damaging	241/533	10394792	1016,11990	2203	4300	6503	SO:0001583	missense	3383	exon4			CTGGACGGGCTGT		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	5344	protein-coding gene	gene with protein product	"""human rhinovirus receptor"""	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.721G>A	19.37:g.10394792G>A	ENSP00000264832:p.Gly241Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_000201	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	37	CCDS12231.1	155	0.07097069597069597	1	0.0020325203252032522	55	0.15193370165745856	0	0.0	99	0.13060686015831136	G	15.85	2.955403	0.53293	0.020654	0.107558	ENSG00000090339	ENST00000264832	T	0.04015	3.73	4.32	2.16	0.27623	Immunoglobulin-like fold (1);	0.764374	0.11145	N	0.594819	T	0.00073	0.0002	L	0.48218	1.51	0.58432	P	8.000000000008E-6	D	0.89917	1.0	D	0.91635	0.999	T	0.32666	-0.9898	9	0.56958	D	0.05	-22.3007	5.3555	0.16059	0.1115:0.2097:0.6788:0.0	rs1799969;rs17722938;rs58330169;rs1799969	241	P05362	ICAM1_HUMAN	R	241	ENSP00000264832:G241R	ENSP00000264832:G241R	G	+	1	0	ICAM1	10255792	0.380000	0.25131	0.104000	0.21259	0.077000	0.17291	2.206000	0.42779	1.151000	0.42436	-0.693000	0.03709	GGG	G|0.927;A|0.073	0.073	strong		0.637	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1		
MEST	4232	hgsc.bcm.edu	37	7	130140729	130140729	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:130140729C>T	ENST00000223215.4	+	9	968	c.747C>T	c.(745-747)gaC>gaT	p.D249D	MEST_ENST00000437945.1_Silent_p.D249D|hsa-mir-335_ENST00000604666.1_RNA|MEST_ENST00000341441.5_Silent_p.D240D|MEST_ENST00000378576.4_Intron|MEST_ENST00000416162.2_Intron|MEST_ENST00000393187.1_Silent_p.D240D|MEST_ENST00000462132.1_3'UTR	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript	249					mesoderm development (GO:0007498)|regulation of lipid storage (GO:0010883)|response to retinoic acid (GO:0032526)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(2)	12	Melanoma(18;0.0435)					TAGTCATTGACAGGTAAGAAG	0.512																																					p.D249D	Colon(126;2182 2305 6517 35181)	Atlas-SNP	.											.	MEST	28	.	0			c.C747T						PASS	.						98.0	78.0	85.0					7																	130140729		2203	4300	6503	SO:0001819	synonymous_variant	4232	exon9			CATTGACAGGTAA		CCDS5822.1, CCDS5823.1, CCDS59081.1	7q32	2014-08-22	2012-12-07		ENSG00000106484	ENSG00000106484			7028	protein-coding gene	gene with protein product	"""Paternally-expressed gene 1"""	601029	"""mesoderm specific transcript (mouse) homolog"", ""mesoderm specific transcript homolog (mouse)"""			8884280	Standard	NM_002402		Approved	PEG1	uc003vqg.3	Q5EB52	OTTHUMG00000156661	ENST00000223215.4:c.747C>T	7.37:g.130140729C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_002402	B2R6S1|O14973|O15007|Q6AI49|Q92571	Silent	SNP	ENST00000223215.4	37	CCDS5822.1																																																																																			.	.	none		0.512	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345183.2	NM_002402	
TPO	7173	hgsc.bcm.edu	37	2	1418210	1418210	+	Silent	SNP	G	G	A	rs28909989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:1418210G>A	ENST00000345913.4	+	2	121	c.30G>A	c.(28-30)acG>acA	p.T10T	TPO_ENST00000382198.1_Silent_p.T10T|TPO_ENST00000382269.3_Silent_p.T10T|TPO_ENST00000337415.3_Silent_p.T10T|TPO_ENST00000539820.1_Silent_p.T10T|TPO_ENST00000382201.3_Silent_p.T10T|TPO_ENST00000349624.3_Silent_p.T10T|TPO_ENST00000497517.2_Intron|TPO_ENST00000329066.4_Silent_p.T10T|TPO_ENST00000346956.3_Silent_p.T10T	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	10					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGTCTGTCACGCTGGTTATGG	0.498													G|||	9	0.00179712	0.0008	0.0	5008	,	,		17467	0.0		0.007	False		,,,				2504	0.001				p.T10T		Atlas-SNP	.											TPO,NS,carcinoma,+1,1	TPO	224	1	0			c.G30A						scavenged	.	G	,,,,,	6,4400	11.4+/-27.6	0,6,2197	87.0	81.0	83.0		30,30,30,30,30,30	-9.9	0.0	2	dbSNP_125	83	50,8550	32.3+/-84.9	0,50,4250	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	0,56,6447	AA,AG,GG		0.5814,0.1362,0.4306	,,,,,	10/934,10/934,10/877,10/877,10/890,10/761	1418210	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	7173	exon2			TGTCACGCTGGTT		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.30G>A	2.37:g.1418210G>A		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	141	53	0.375887	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1																																																																																			G|0.996;A|0.004	0.004	strong		0.498	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
SLC52A1	55065	hgsc.bcm.edu	37	17	4936972	4936972	+	Missense_Mutation	SNP	G	G	A	rs346821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4936972G>A	ENST00000424747.1	-	3	1524	c.812C>T	c.(811-813)gCc>gTc	p.A271V	SLC52A1_ENST00000254853.5_Missense_Mutation_p.A271V|SLC52A1_ENST00000512825.2_Missense_Mutation_p.A271V	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	271			A -> V (in dbSNP:rs346821). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21089064}.		riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										CAGCTGATGGGCCTCAGGGTC	0.617													G|||	2650	0.529153	0.73	0.6369	5008	,	,		21492	0.2331		0.6402	False		,,,				2504	0.3722				p.A271V		Atlas-SNP	.											.	.	.	.	0			c.C812T						PASS	.	G	VAL/ALA,VAL/ALA	3241,1165	703.8+/-407.0	1185,871,147	67.0	50.0	56.0		812,812	0.8	0.0	17	dbSNP_79	56	5710,2890	663.1+/-402.0	1887,1936,477	no	missense,missense	GPR172B	NM_001104577.1,NM_017986.3	64,64	3072,2807,624	AA,AG,GG		33.6047,26.4412,31.1779	benign,benign	271/449,271/449	4936972	8951,4055	2203	4300	6503	SO:0001583	missense	55065	exon3			TGATGGGCCTCAG	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"""Solute carriers"""	30225	protein-coding gene	gene with protein product	"""riboflavin transporter 1"""	607883	"""G protein-coupled receptor 172B"""	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.812C>T	17.37:g.4936972G>A	ENSP00000399979:p.Ala271Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Missense_Mutation	SNP	ENST00000424747.1	37	CCDS11066.1	1212	0.554945054945055	358	0.7276422764227642	238	0.6574585635359116	131	0.229020979020979	485	0.6398416886543535	G	10.58	1.389727	0.25118	0.735588	0.663953	ENSG00000132517	ENST00000254853;ENST00000512825;ENST00000424747	T;T;T	0.75050	-0.9;-0.73;-0.9	0.784	0.784	0.18578	.	0.914259	0.09338	N	0.815895	T	0.00012	0.0000	N	0.19112	0.55	0.29785	P	0.833669	B;B	0.20550	0.046;0.012	B;B	0.25291	0.059;0.008	T	0.45323	-0.9269	9	0.25106	T	0.35	.	7.3913	0.26911	0.0:0.0:1.0:0.0	rs346821;rs3744703;rs17855720;rs57849699;rs346821	271;271	F5H5Y1;Q9NWF4	.;RFT_HUMAN	V	271	ENSP00000254853:A271V;ENSP00000443026:A271V;ENSP00000399979:A271V	ENSP00000254853:A271V	A	-	2	0	GPR172B	4877696	.	.	0.026000	0.17262	0.095000	0.18619	.	.	0.699000	0.31761	0.563000	0.77884	GCC	G|0.356;A|0.644	0.644	strong		0.617	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
CENPU	79682	hgsc.bcm.edu	37	4	185637699	185637699	+	Missense_Mutation	SNP	A	A	G	rs6552804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:185637699A>G	ENST00000281453.5	-	6	540	c.470T>C	c.(469-471)aTa>aCa	p.I157T	MLF1IP_ENST00000541971.1_Missense_Mutation_p.I157T|MLF1IP_ENST00000506535.1_5'Flank	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		TTGTGTACTTATTTTCTCTGC	0.418													A|||	724	0.144569	0.295	0.1354	5008	,	,		16847	0.001		0.1481	False		,,,				2504	0.092				p.I157T		Atlas-SNP	.											.	MLF1IP	33	.	0			c.T470C						PASS	.	A	THR/ILE	1188,3218	416.1+/-337.4	159,870,1174	146.0	130.0	136.0		470	-7.8	0.0	4	dbSNP_116	136	1407,7193	271.1+/-289.3	117,1173,3010	yes	missense	MLF1IP	NM_024629.3	89	276,2043,4184	GG,GA,AA		16.3605,26.9632,19.9523	benign	157/419	185637699	2595,10411	2203	4300	6503	SO:0001583	missense	79682	exon6			GTACTTATTTTCT																												ENST00000281453.5:c.470T>C	4.37:g.185637699A>G	ENSP00000281453:p.Ile157Thr	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	363	154	0.424242	NM_024629		Missense_Mutation	SNP	ENST00000281453.5	37	CCDS3838.1	307	0.14056776556776557	145	0.29471544715447157	56	0.15469613259668508	0	0.0	106	0.13984168865435356	A	1.405	-0.577006	0.03854	0.269632	0.163605	ENSG00000151725	ENST00000281453;ENST00000541665;ENST00000541971;ENST00000514781	T;T;T	0.22743	1.94;1.94;1.94	3.9	-7.79	0.01218	.	1.516070	0.04345	N	0.354643	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B;B	0.14012	0.0;0.009	B;B	0.15052	0.001;0.012	T	0.37056	-0.9722	9	0.13470	T	0.59	-31.0236	1.544	0.02561	0.3069:0.1148:0.3517:0.2266	rs6552804;rs52802357;rs59579517;rs6552804	157;157	Q09GN1;Q71F23	.;CENPU_HUMAN	T	157;157;157;128	ENSP00000281453:I157T;ENSP00000445862:I157T;ENSP00000423167:I128T	ENSP00000281453:I157T	I	-	2	0	MLF1IP	185874693	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.801000	0.04550	-2.532000	0.00491	-1.773000	0.00660	ATA	A|0.825;G|0.175	0.175	strong		0.418	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		
FAM222A	84915	hgsc.bcm.edu	37	12	110206760	110206760	+	Silent	SNP	C	C	A	rs79456911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:110206760C>A	ENST00000538780.1	+	3	1742	c.1026C>A	c.(1024-1026)ggC>ggA	p.G342G	FAM222A-AS1_ENST00000541460.1_RNA|FAM222A-AS1_ENST00000541723.1_RNA|FAM222A_ENST00000358906.3_Silent_p.G342G	NM_032829.2	NP_116218.2	Q5U5X8	F222A_HUMAN	family with sequence similarity 222, member A	342																	TCACCGTAGGCCAGTACTTTG	0.701													C|||	29	0.00579073	0.0015	0.0043	5008	,	,		14090	0.0		0.0149	False		,,,				2504	0.0092				p.G342G		Atlas-SNP	.											.	.	.	.	0			c.C1026A						PASS	.	C		12,4352		0,12,2170	14.0	13.0	13.0		1026	0.1	1.0	12	dbSNP_131	13	56,8518		0,56,4231	no	coding-synonymous	C12orf34	NM_032829.2		0,68,6401	AA,AC,CC		0.6531,0.275,0.5256		342/453	110206760	68,12870	2182	4287	6469	SO:0001819	synonymous_variant	84915	exon3			CGTAGGCCAGTAC	AK027627	CCDS9133.1	12q24.11	2012-04-27	2012-04-27	2012-04-27	ENSG00000139438	ENSG00000139438			25915	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 34"""	C12orf34		12477932	Standard	NM_032829		Approved	FLJ14721	uc001tpd.2	Q5U5X8	OTTHUMG00000169260	ENST00000538780.1:c.1026C>A	12.37:g.110206760C>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_032829	Q8NCD5|Q96SP6	Silent	SNP	ENST00000538780.1	37	CCDS9133.1																																																																																			C|0.994;A|0.006	0.006	strong		0.701	FAM222A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403175.1	NM_032829	
ZNF502	91392	hgsc.bcm.edu	37	3	44762830	44762830	+	Missense_Mutation	SNP	A	A	G	rs56084453	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:44762830A>G	ENST00000296091.4	+	4	777	c.521A>G	c.(520-522)cAg>cGg	p.Q174R	ZNF502_ENST00000436624.2_Missense_Mutation_p.Q174R|ZNF502_ENST00000449836.1_Missense_Mutation_p.Q174R	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	174			Q -> R (in dbSNP:rs56084453).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		ACCCAACATCAGAGAACTCAT	0.408													A|||	531	0.10603	0.0129	0.1571	5008	,	,		21464	0.0446		0.2247	False		,,,				2504	0.137				p.Q174R		Atlas-SNP	.											ZNF502,NS,carcinoma,-1,1	ZNF502	58	1	0			c.A521G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	190,4216	119.6+/-157.3	5,180,2018	126.0	137.0	133.0		521,521,521,521	4.7	1.0	3	dbSNP_129	133	1862,6738	329.3+/-318.7	195,1472,2633	yes	missense,missense,missense,missense	ZNF502	NM_001134440.1,NM_001134441.1,NM_001134442.1,NM_033210.4	43,43,43,43	200,1652,4651	GG,GA,AA		21.6512,4.3123,15.7773	benign,benign,benign,benign	174/545,174/545,174/545,174/545	44762830	2052,10954	2203	4300	6503	SO:0001583	missense	91392	exon4			AACATCAGAGAAC	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"""Zinc fingers, C2H2-type"""	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.521A>G	3.37:g.44762830A>G	ENSP00000296091:p.Gln174Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	37	CCDS2719.1	282	0.12912087912087913	10	0.02032520325203252	73	0.20165745856353592	29	0.050699300699300696	170	0.22427440633245382	A	15.35	2.807929	0.50421	0.043123	0.216512	ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624;ENST00000427783	T;T;T	0.07327	3.2;3.2;3.2	4.7	4.7	0.59300	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.16098	0.37	0.37027	P	0.103526	P	0.52463	0.953	P	0.47864	0.559	T	0.52305	-0.8593	8	0.54805	T	0.06	-5.6043	13.5531	0.61745	1.0:0.0:0.0:0.0	rs56084453;rs61740962	174	Q8TBZ5	ZN502_HUMAN	R	174	ENSP00000397390:Q174R;ENSP00000296091:Q174R;ENSP00000406469:Q174R	ENSP00000296091:Q174R	Q	+	2	0	ZNF502	44737834	0.049000	0.20398	0.972000	0.41901	0.997000	0.91878	0.860000	0.27871	2.109000	0.64355	0.533000	0.62120	CAG	A|0.848;G|0.152	0.152	strong		0.408	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210	
TMEM2	23670	hgsc.bcm.edu	37	9	74344821	74344821	+	Silent	SNP	T	T	C	rs25693	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:74344821T>C	ENST00000377044.4	-	10	2528	c.1989A>G	c.(1987-1989)tcA>tcG	p.S663S	TMEM2_ENST00000377066.5_Silent_p.S600S	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	663					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TCCAGAAAGTTGAAACAGCCC	0.383													C|||	407	0.08127	0.0393	0.0476	5008	,	,		16682	0.0198		0.0815	False		,,,				2504	0.2249				p.S663S		Atlas-SNP	.											.	TMEM2	112	.	0			c.A1989G						PASS	.	C	,	174,4232	808.3+/-415.9	6,162,2035	83.0	90.0	87.0		1800,1989	0.4	1.0	9	dbSNP_72	87	717,7883	786.6+/-407.6	31,655,3614	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	37,817,5649	CC,CT,TT		8.3372,3.9492,6.8507	,	600/1321,663/1384	74344821	891,12115	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon10			GAAAGTTGAAACA		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1989A>G	9.37:g.74344821T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			T|0.937;C|0.063	0.063	strong		0.383	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
LPIN1	23175	hgsc.bcm.edu	37	2	11911761	11911761	+	Silent	SNP	C	C	T	rs11538448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:11911761C>T	ENST00000256720.2	+	4	645	c.552C>T	c.(550-552)atC>atT	p.I184I	LPIN1_ENST00000396098.1_Silent_p.I190I|LPIN1_ENST00000449576.2_Silent_p.I233I|LPIN1_ENST00000425416.2_Silent_p.I190I|LPIN1_ENST00000396099.1_Silent_p.I190I	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	184					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TGTTCCCCATCGAGATGAGCT	0.493													C|||	254	0.0507188	0.0061	0.0692	5008	,	,		18791	0.001		0.1382	False		,,,				2504	0.0593				p.I233I		Atlas-SNP	.											.	LPIN1	99	.	0			c.C699T						PASS	.	C		123,4283	84.8+/-123.5	0,123,2080	57.0	41.0	46.0		552	-9.1	1.0	2	dbSNP_120	46	1208,7392	234.4+/-267.4	83,1042,3175	no	coding-synonymous	LPIN1	NM_145693.1		83,1165,5255	TT,TC,CC		14.0465,2.7916,10.2337		184/891	11911761	1331,11675	2203	4300	6503	SO:0001819	synonymous_variant	23175	exon5			CCCCATCGAGATG	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.552C>T	2.37:g.11911761C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																			C|0.912;T|0.088	0.088	strong		0.493	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
FMN1	342184	hgsc.bcm.edu	37	15	33260973	33260973	+	Missense_Mutation	SNP	C	C	T	rs150962800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:33260973C>T	ENST00000559047.1	-	5	2928	c.2929G>A	c.(2929-2931)Gag>Aag	p.E977K	SNORD77_ENST00000391113.1_RNA|FMN1_ENST00000334528.9_Missense_Mutation_p.E754K|FMN1_ENST00000561249.1_Missense_Mutation_p.E879K			Q68DA7	FMN1_HUMAN	formin 1	977	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.|Pro-rich.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CAACTGGGCTCGATGGCTGGT	0.507													C|||	39	0.00778754	0.0008	0.0173	5008	,	,		10701	0.001		0.0189	False		,,,				2504	0.0061				p.E754K		Atlas-SNP	.											.	FMN1	174	.	0			c.G2260A						PASS	.	C	LYS/GLU	14,3668		0,14,1827	125.0	121.0	122.0		2260	4.4	0.9	15	dbSNP_134	122	184,7998		3,178,3910	yes	missense	FMN1	NM_001103184.2	56	3,192,5737	TT,TC,CC		2.2488,0.3802,1.6689	probably-damaging	754/1197	33260973	198,11666	1841	4091	5932	SO:0001583	missense	342184	exon4			TGGGCTCGATGGC	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2929G>A	15.37:g.33260973C>T	ENSP00000454047:p.Glu977Lys	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	324	164	0.506173	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		27	0.012362637362637362	1	0.0020325203252032522	9	0.024861878453038673	1	0.0017482517482517483	16	0.021108179419525065	C	13.16	2.153144	0.38021	0.003802	0.022488	ENSG00000248905	ENST00000334528	T	0.15718	2.4	4.42	4.42	0.53409	.	0.052449	0.85682	D	0.000000	T	0.19725	0.0474	L	0.47190	1.495	.	.	.	D	0.69078	0.997	D	0.69142	0.962	T	0.08659	-1.0711	9	0.45353	T	0.12	.	17.2139	0.86937	0.0:1.0:0.0:0.0	.	754	Q68DA7-5	.	K	754	ENSP00000333950:E754K	ENSP00000333950:E754K	E	-	1	0	FMN1	31048265	1.000000	0.71417	0.943000	0.38184	0.517000	0.34286	5.800000	0.69108	2.279000	0.76181	0.650000	0.86243	GAG	C|0.987;T|0.013	0.013	strong		0.507	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499179	59499179	+	Missense_Mutation	SNP	G	G	A	rs3809530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:59499179G>A	ENST00000307144.4	+	1	138	c.40G>A	c.(40-42)Gtg>Atg	p.V14M	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	14			V -> M (in dbSNP:rs3809530). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						CAGCCAGAGAGTGAGCTCGGT	0.587													G|||	2017	0.402756	0.2814	0.3905	5008	,	,		20610	0.5496		0.2714	False		,,,				2504	0.5593				p.V14M		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.G40A						PASS	.	G	,MET/VAL	1272,3110	430.6+/-342.6	197,878,1116	41.0	39.0	39.0		,40	1.5	0.0	15	dbSNP_107	39	2368,6212	392.2+/-343.9	323,1722,2245	yes	intron,missense	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,21	520,2600,3361	AA,AG,GG		27.5991,29.0278,28.0821	,benign	,14/382	59499179	3640,9322	2191	4290	6481	SO:0001583	missense	92483	exon1			CAGAGAGTGAGCT	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.40G>A	15.37:g.59499179G>A	ENSP00000302393:p.Val14Met	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	160	77	0.48125	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	37	CCDS10171.1	793	0.3630952380952381	137	0.2784552845528455	122	0.3370165745856354	330	0.5769230769230769	204	0.2691292875989446	G	7.458	0.644080	0.14451	0.290278	0.275991	ENSG00000171989	ENST00000307144	T	0.72051	-0.62	1.49	1.49	0.22878	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.19200	0.034	B	0.14023	0.01	T	0.46721	-0.9171	8	0.37606	T	0.19	.	6.8004	0.23748	0.0:0.0:1.0:0.0	rs3809530;rs17856653;rs52798006;rs3809530	14	Q9BYZ2	LDH6B_HUMAN	M	14	ENSP00000302393:V14M	ENSP00000302393:V14M	V	+	1	0	LDHAL6B	57286471	0.088000	0.21588	0.003000	0.11579	0.113000	0.19764	0.474000	0.22148	0.710000	0.31997	0.305000	0.20034	GTG	G|0.690;A|0.310	0.310	strong		0.587	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
NKAIN4	128414	hgsc.bcm.edu	37	20	61880169	61880169	+	Missense_Mutation	SNP	T	T	G	rs1129659	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61880169T>G	ENST00000370316.3	-	3	360	c.271A>C	c.(271-273)Aag>Cag	p.K91Q	NKAIN4_ENST00000370313.1_Missense_Mutation_p.K29Q|NKAIN4_ENST00000370307.2_Missense_Mutation_p.K29Q|NKAIN4_ENST00000466885.1_5'Flank	NM_152864.3	NP_690603.3	Q8IVV8	NKAI4_HUMAN	Na+/K+ transporting ATPase interacting 4	91			K -> Q (in dbSNP:rs1129659).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|lung(1)|ovary(1)	4	all_cancers(38;2.72e-09)					GCACTCACCTTTAAGAGGCCA	0.602													G|||	2109	0.421126	0.4349	0.4352	5008	,	,		16379	0.5069		0.3579	False		,,,				2504	0.3691				p.K91Q		Atlas-SNP	.											NKAIN4,NS,carcinoma,0,1	NKAIN4	23	1	0			c.A271C						PASS	.	G	GLN/LYS	1847,2559	626.3+/-394.7	395,1057,751	56.0	44.0	48.0		271	2.2	1.0	20	dbSNP_86	48	3230,5366	645.0+/-400.1	631,1968,1699	yes	missense	NKAIN4	NM_152864.3	53	1026,3025,2450	GG,GT,TT		37.5756,41.9201,39.0478	benign	91/209	61880169	5077,7925	2203	4298	6501	SO:0001583	missense	128414	exon3			TCACCTTTAAGAG	BC041812	CCDS13514.1	20q13.33	2007-10-04	2007-10-04	2007-10-04	ENSG00000101198	ENSG00000101198		"""Na+/K+ transporting ATPase interacting"""	16191	protein-coding gene	gene with protein product		612873	"""chromosome 20 open reading frame 58"""	C20orf58		17606467	Standard	NM_152864		Approved	bA261N11.2, FAM77A	uc002yek.3	Q8IVV8	OTTHUMG00000032959	ENST00000370316.3:c.271A>C	20.37:g.61880169T>G	ENSP00000359340:p.Lys91Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_152864	Q4VXQ6|Q9BQU8|Q9BQU9	Missense_Mutation	SNP	ENST00000370316.3	37	CCDS13514.1	956	0.43772893772893773	218	0.44308943089430897	149	0.4116022099447514	307	0.5367132867132867	282	0.3720316622691293	G	3.253	-0.152941	0.06585	0.419201	0.375756	ENSG00000101198	ENST00000370313;ENST00000370316;ENST00000370307;ENST00000370317	T;T;T;T	0.15952	2.38;2.38;2.38;2.38	3.38	2.24	0.28232	.	0.063724	0.64402	N	0.000009	T	0.00012	0.0000	L	0.44542	1.39	0.52501	P	4.099999999995774E-5	B;B	0.14012	0.003;0.009	B;B	0.21151	0.021;0.033	T	0.43410	-0.9393	9	0.27785	T	0.31	-0.1702	10.2258	0.43225	0.0:0.0:0.3151:0.6849	rs1129659;rs2273496;rs3177595;rs3187816;rs52799800;rs60056869;rs1129659	29;91	A6NNM2;Q8IVV8	.;NKAI4_HUMAN	Q	29;91;29;21	ENSP00000359336:K29Q;ENSP00000359340:K91Q;ENSP00000359330:K29Q;ENSP00000359341:K21Q	ENSP00000359330:K29Q	K	-	1	0	NKAIN4	61350614	0.940000	0.31905	0.952000	0.39060	0.011000	0.07611	1.467000	0.35321	-0.136000	0.11475	-0.982000	0.02568	AAG	T|0.594;G|0.406	0.406	strong		0.602	NKAIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080117.3	NM_152864	
PER3	8863	hgsc.bcm.edu	37	1	7889941	7889941	+	Silent	SNP	C	C	T	rs2640908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7889941C>T	ENST00000361923.2	+	18	3082	c.2907C>T	c.(2905-2907)acC>acT	p.T969T	PER3_ENST00000377532.3_Silent_p.T978T|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	969	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CTGCTACTACCGGTGCACTGT	0.507													C|||	1524	0.304313	0.3154	0.1599	5008	,	,		20352	0.4851		0.1978	False		,,,				2504	0.3149				p.T969T		Atlas-SNP	.											.	PER3	95	.	0			c.C2907T						PASS	.	C		1333,3073	447.3+/-348.3	201,931,1071	132.0	120.0	124.0		2907	-0.8	0.0	1	dbSNP_100	124	1618,6982	299.8+/-304.6	160,1298,2842	no	coding-synonymous	PER3	NM_016831.1		361,2229,3913	TT,TC,CC		18.814,30.2542,22.6895		969/1202	7889941	2951,10055	2203	4300	6503	SO:0001819	synonymous_variant	8863	exon18			TACTACCGGTGCA	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2907C>T	1.37:g.7889941C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	162	64	0.395062	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			C|0.736;T|0.264	0.264	strong		0.507	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
TNKS2	80351	hgsc.bcm.edu	37	10	93608142	93608142	+	Silent	SNP	G	G	A	rs3758499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:93608142G>A	ENST00000371627.4	+	19	2740	c.2361G>A	c.(2359-2361)gcG>gcA	p.A787A		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	787					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				TACCCTAGGCGGATGATGTCA	0.443													G|||	2015	0.402356	0.2375	0.4078	5008	,	,		17019	0.5456		0.3002	False		,,,				2504	0.5787				p.A787A		Atlas-SNP	.											.	TNKS2	103	.	0			c.G2361A						PASS	.	G		1047,3359	382.5+/-324.5	113,821,1269	65.0	61.0	62.0		2361	-6.9	1.0	10	dbSNP_107	62	2660,5940	429.1+/-356.1	387,1886,2027	no	coding-synonymous	TNKS2	NM_025235.3		500,2707,3296	AA,AG,GG		30.9302,23.7631,28.5022		787/1167	93608142	3707,9299	2203	4300	6503	SO:0001819	synonymous_variant	80351	exon19			CTAGGCGGATGAT	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.2361G>A	10.37:g.93608142G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	103	40	0.38835	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Silent	SNP	ENST00000371627.4	37	CCDS7417.1																																																																																			G|0.687;A|0.313	0.313	strong		0.443	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235	
SERPINF2	5345	hgsc.bcm.edu	37	17	1649022	1649022	+	Silent	SNP	C	C	T	rs35259159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1649022C>T	ENST00000324015.3	+	5	263	c.186C>T	c.(184-186)gcC>gcT	p.A62A	SERPINF2_ENST00000450523.2_Intron|SERPINF2_ENST00000382061.4_Silent_p.A62A	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	62					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	GCCAGACTGCCCTGAAGAGTC	0.642													C|||	92	0.0183706	0.0015	0.0389	5008	,	,		14485	0.0		0.0596	False		,,,				2504	0.0031				p.A62A		Atlas-SNP	.											.	SERPINF2	33	.	0			c.C186T						PASS	.	C	,,	70,4336	63.5+/-100.7	0,70,2133	41.0	43.0	43.0		186,186,	4.1	0.0	17	dbSNP_126	43	510,8090	143.4+/-199.5	20,470,3810	no	coding-synonymous,coding-synonymous,intron	SERPINF2	NM_000934.3,NM_001165920.1,NM_001165921.1	,,	20,540,5943	TT,TC,CC		5.9302,1.5887,4.4595	,,	62/492,62/492,	1649022	580,12426	2203	4300	6503	SO:0001819	synonymous_variant	5345	exon5			GACTGCCCTGAAG	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"""Serine (or cysteine) peptidase inhibitors"""	9075	protein-coding gene	gene with protein product	"""alpha-2-plasmin inhibitor"", ""alpha-2-antiplasmin"""	613168	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"""	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.186C>T	17.37:g.1649022C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Silent	SNP	ENST00000324015.3	37	CCDS11011.1																																																																																			C|0.960;T|0.040	0.040	strong		0.642	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934	
ATP12A	479	hgsc.bcm.edu	37	13	25267017	25267017	+	Missense_Mutation	SNP	A	A	C	rs56291145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25267017A>C	ENST00000381946.3	+	10	1527	c.1360A>C	c.(1360-1362)Aat>Cat	p.N454H	ATP12A_ENST00000218548.6_Missense_Mutation_p.N460H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	454					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		AGGACAGGAAAATGTCCCCAT	0.453													A|||	74	0.0147764	0.0023	0.0187	5008	,	,		21024	0.001		0.0388	False		,,,				2504	0.0184				p.N460H	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A1378C						PASS	.	A	HIS/ASN,HIS/ASN	25,4381	33.5+/-64.1	0,25,2178	157.0	145.0	149.0		1378,1360	5.7	0.1	13	dbSNP_129	149	332,8268	116.6+/-176.3	5,322,3973	yes	missense,missense	ATP12A	NM_001185085.1,NM_001676.5	68,68	5,347,6151	CC,CA,AA		3.8605,0.5674,2.7449	benign,benign	460/1046,454/1040	25267017	357,12649	2203	4300	6503	SO:0001583	missense	479	exon10			CAGGAAAATGTCC	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1360A>C	13.37:g.25267017A>C	ENSP00000371372:p.Asn454His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	42	0.019230769230769232	3	0.006097560975609756	6	0.016574585635359115	1	0.0017482517482517483	32	0.04221635883905013	A	10.05	1.245297	0.22796	0.005674	0.038605	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.80123	-1.34;-1.34	5.65	5.65	0.86999	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.486738	0.23874	N	0.043705	T	0.36963	0.0986	N	0.13198	0.31	0.09310	N	1	B;B	0.30889	0.242;0.299	B;B	0.38156	0.197;0.266	T	0.52472	-0.8571	10	0.40728	T	0.16	.	8.3857	0.32499	0.9132:0.0:0.0868:0.0	rs56291145;rs61729900	460;454	P54707-2;P54707	.;AT12A_HUMAN	H	460;454	ENSP00000218548:N460H;ENSP00000371372:N454H	ENSP00000218548:N460H	N	+	1	0	ATP12A	24165017	0.002000	0.14202	0.133000	0.22050	0.757000	0.42996	1.843000	0.39259	2.154000	0.67381	0.533000	0.62120	AAT	A|0.975;C|0.025	0.025	strong		0.453	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
OR51I2	390064	hgsc.bcm.edu	37	11	5475597	5475597	+	Silent	SNP	C	C	T	rs11037503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5475597C>T	ENST00000341449.2	+	1	960	c.879C>T	c.(877-879)agC>agT	p.S293S	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	293					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATTTATAGCGCCAAGACAA	0.448													C|||	861	0.171925	0.0454	0.3012	5008	,	,		18397	0.0417		0.3718	False		,,,				2504	0.18				p.S293S		Atlas-SNP	.											.	OR51I2	76	.	0			c.C879T						PASS	.	C		448,3954	213.1+/-232.8	35,378,1788	144.0	140.0	141.0		879	-4.6	0.8	11	dbSNP_120	141	3236,5358	488.4+/-372.4	609,2018,1670	no	coding-synonymous	OR51I2	NM_001004754.2		644,2396,3458	TT,TC,CC		37.6542,10.1772,28.3472		293/313	5475597	3684,9312	2201	4297	6498	SO:0001819	synonymous_variant	390064	exon1			TTATAGCGCCAAG	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"""GPCR / Class A : Olfactory receptors"""	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.879C>T	11.37:g.5475597C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	78	0.962963	NM_001004754	Q6IF81	Silent	SNP	ENST00000341449.2	37	CCDS31383.1																																																																																			C|0.757;T|0.243	0.243	strong		0.448	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
SLC26A9	115019	hgsc.bcm.edu	37	1	205884138	205884138	+	3'UTR	SNP	C	C	T	rs140760240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205884138C>T	ENST00000367135.3	-	0	2836				SLC26A9_ENST00000340781.4_Missense_Mutation_p.R849Q|SLC26A9_ENST00000367134.2_Missense_Mutation_p.R849Q	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9						anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)	p.R849L(1)		NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			TTGGCTCACTCGTAAAAGCTG	0.567													C|||	38	0.00758786	0.0008	0.0043	5008	,	,		20842	0.0179		0.006	False		,,,				2504	0.0102				p.R849Q		Atlas-SNP	.											.	SLC26A9	176	.	1	Substitution - Missense(1)	lung(1)	c.G2546A						PASS	.	C	GLN/ARG,	5,4401	9.9+/-24.2	0,5,2198	140.0	127.0	132.0		2546,	2.8	0.0	1	dbSNP_134	132	46,8554	30.1+/-81.4	0,46,4254	yes	missense,utr-3	SLC26A9	NM_134325.2,NM_052934.3	43,	0,51,6452	TT,TC,CC		0.5349,0.1135,0.3921	possibly-damaging,	849/888,	205884138	51,12955	2203	4300	6503	SO:0001624	3_prime_UTR_variant	115019	exon22			CTCACTCGTAAAA	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"""Solute carriers"""	14469	protein-coding gene	gene with protein product	"""anion transporter/exchanger-9"""	608481	"""solute carrier family 26, member 9"""			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.*347G>A	1.37:g.205884138C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	189	104	0.550265	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	16	0.007326007326007326	0	0.0	1	0.0027624309392265192	10	0.017482517482517484	5	0.006596306068601583	C	11.06	1.528814	0.27387	0.001135	0.005349	ENSG00000174502	ENST00000340781;ENST00000367134	D;D	0.93604	-3.25;-3.25	5.59	2.76	0.32466	.	14.346700	0.00166	N	0.000003	T	0.76709	0.4025	N	0.08118	0	0.09310	N	1	P;B	0.51653	0.947;0.262	B;B	0.35278	0.199;0.102	T	0.75717	-0.3220	10	0.33141	T	0.24	.	12.6077	0.56532	0.0:0.9104:0.0:0.0896	.	849;96	B1AVM8;Q8NAY2	.;.	Q	849	ENSP00000341682:R849Q;ENSP00000356102:R849Q	ENSP00000341682:R849Q	R	-	2	0	SLC26A9	204150761	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.025000	0.12413	0.334000	0.23590	-2.715000	0.00133	CGA	C|0.993;T|0.007	0.007	strong		0.567	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
CKB	1152	hgsc.bcm.edu	37	14	103986255	103986255	+	Silent	SNP	C	C	T	rs1803283	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:103986255C>T	ENST00000348956.2	-	8	1449	c.1092G>A	c.(1090-1092)gaG>gaA	p.E364E		NM_001823.4	NP_001814.2	P12277	KCRB_HUMAN	creatine kinase, brain	364	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular chloride ion homeostasis (GO:0030644)|cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			lung(2)|prostate(1)	3		Melanoma(154;0.155)	Epithelial(46;0.14)		Creatine(DB00148)	CCAGCCGCTGCTCCATCTCGA	0.627													C|||	3200	0.638978	0.4312	0.7334	5008	,	,		17408	0.8224		0.6421	False		,,,				2504	0.6605				p.E364E	Esophageal Squamous(186;2492 2823 49929 50127)	Atlas-SNP	.											.	CKB	9	.	0			c.G1092A						PASS	.	C		2174,2230	576.4+/-384.2	552,1070,580	45.0	42.0	43.0		1092	4.1	1.0	14	dbSNP_89	43	5418,3180	647.8+/-400.4	1720,1978,601	no	coding-synonymous	CKB	NM_001823.3		2272,3048,1181	TT,TC,CC		36.9853,49.3642,41.609		364/382	103986255	7592,5410	2202	4299	6501	SO:0001819	synonymous_variant	1152	exon8			CCGCTGCTCCATC		CCDS9981.1	14q32.32	2012-10-02			ENSG00000166165	ENSG00000166165	2.7.3.2		1991	protein-coding gene	gene with protein product		123280		CKBB			Standard	NM_001823		Approved		uc001ynf.2	P12277	OTTHUMG00000171786	ENST00000348956.2:c.1092G>A	14.37:g.103986255C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001823	A8K236|B2R5R4|Q2LE07|Q6FG40|Q9UC66	Silent	SNP	ENST00000348956.2	37	CCDS9981.1																																																																																			C|0.398;T|0.602	0.602	strong		0.627	CKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415111.1		
SPATA2L	124044	hgsc.bcm.edu	37	16	89764237	89764237	+	Silent	SNP	C	C	T	rs11866038	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:89764237C>T	ENST00000289805.5	-	3	848	c.780G>A	c.(778-780)agG>agA	p.R260R	SPATA2L_ENST00000335360.7_Intron	NM_152339.3	NP_689552.2	Q8IUW3	SPA2L_HUMAN	spermatogenesis associated 2-like	260										breast(1)|cervix(1)|endometrium(1)|lung(2)|skin(1)	6		Lung NSC(15;0.00043)|all_lung(18;0.000665)|all_hematologic(23;0.0355)		BRCA - Breast invasive adenocarcinoma(80;0.0272)		AGAGTGGTGGCCTGTAGGCCA	0.692													C|||	589	0.117612	0.2216	0.0591	5008	,	,		15425	0.0427		0.0547	False		,,,				2504	0.1605				p.R260R		Atlas-SNP	.											.	SPATA2L	16	.	0			c.G780A						PASS	.	C		865,3511		80,705,1403	10.0	11.0	11.0		780	0.6	0.0	16	dbSNP_120	11	416,8154		9,398,3878	no	coding-synonymous	SPATA2L	NM_152339.3		89,1103,5281	TT,TC,CC		4.8541,19.7669,9.8949		260/425	89764237	1281,11665	2188	4285	6473	SO:0001819	synonymous_variant	124044	exon3			TGGTGGCCTGTAG	AF070574	CCDS10985.1	16q24.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000158792	ENSG00000158792			28393	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 76"""	C16orf76		8619474	Standard	NM_152339		Approved	MGC26885, tamo	uc002foj.3	Q8IUW3	OTTHUMG00000138047	ENST00000289805.5:c.780G>A	16.37:g.89764237C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_152339	D3DX85|Q8NHV3	Silent	SNP	ENST00000289805.5	37	CCDS10985.1																																																																																			C|0.920;T|0.080	0.080	strong		0.692	SPATA2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269923.1	NM_152339	
FCGR2A	2212	hgsc.bcm.edu	37	1	161487914	161487914	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161487914C>T	ENST00000271450.6	+	7	968	c.930C>T	c.(928-930)aaC>aaT	p.N310N	FCGR2A_ENST00000486608.1_3'UTR|RP11-25K21.6_ENST00000537821.2_RNA|FCGR2A_ENST00000367972.4_Silent_p.N309N	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	310					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TTCCTCCCAACGACCATGTCA	0.448																																					p.N310N		Atlas-SNP	.											FCGR2A,colon,carcinoma,0,1	FCGR2A	38	1	0			c.C930T						scavenged	.						77.0	77.0	77.0					1																	161487914		2203	4297	6500	SO:0001819	synonymous_variant	2212	exon7			TCCCAACGACCAT	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3616	protein-coding gene	gene with protein product	"""Immunoglobulin G Fc receptor II"""	146790	"""Fc fragment of IgG, low affinity IIa, receptor for (CD32)"""	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.930C>T	1.37:g.161487914C>T		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	416	35	0.0841346	NM_001136219	Q8WUN1|Q8WW64	Silent	SNP	ENST00000271450.6	37	CCDS44264.1																																																																																			C|0.250;T|0.750	0.750	weak		0.448	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642	
KIF26B	55083	hgsc.bcm.edu	37	1	245772651	245772651	+	Missense_Mutation	SNP	C	C	G	rs61754955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:245772651C>G	ENST00000407071.2	+	8	2175	c.1735C>G	c.(1735-1737)Ctc>Gtc	p.L579V	KIF26B_ENST00000366518.4_Missense_Mutation_p.L198V	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	579	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCTCTTCAAGCTCATAAACGA	0.552													C|||	107	0.0213658	0.0053	0.0648	5008	,	,		17935	0.0278		0.0149	False		,,,				2504	0.0123				p.L579V		Atlas-SNP	.											.	KIF26B	343	.	0			c.C1735G						PASS	.	C	VAL/LEU	28,3818		0,28,1895	38.0	38.0	38.0		1735	5.2	1.0	1	dbSNP_129	38	154,8102		2,150,3976	yes	missense	KIF26B	NM_018012.3	32	2,178,5871	GG,GC,CC		1.8653,0.728,1.5039	probably-damaging	579/2109	245772651	182,11920	1923	4128	6051	SO:0001583	missense	55083	exon8			TTCAAGCTCATAA	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1735C>G	1.37:g.245772651C>G	ENSP00000385545:p.Leu579Val	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	225	105	0.466667	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	37	CCDS44342.1	54	0.024725274725274724	5	0.01016260162601626	20	0.055248618784530384	14	0.024475524475524476	15	0.01978891820580475	C	16.22	3.060277	0.55432	0.00728	0.018653	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.74947	-0.89;-0.89	5.22	5.22	0.72569	Kinesin, motor domain (4);	.	.	.	.	T	0.37073	0.0990	L	0.52759	1.655	0.58432	D	0.999999	P;P	0.47191	0.891;0.877	P;P	0.59948	0.866;0.809	T	0.65751	-0.6092	9	0.56958	D	0.05	.	12.9655	0.58481	0.0:0.915:0.0:0.085	rs61754955	198;579	B7WPD9;Q2KJY2	.;KI26B_HUMAN	V	579;198;195	ENSP00000385545:L579V;ENSP00000355475:L198V	ENSP00000355475:L198V	L	+	1	0	KIF26B	243839274	1.000000	0.71417	0.991000	0.47740	0.947000	0.59692	2.028000	0.41088	2.590000	0.87494	0.650000	0.86243	CTC	C|0.976;G|0.024	0.024	strong		0.552	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
MUC4	4585	hgsc.bcm.edu	37	3	195513806	195513806	+	Missense_Mutation	SNP	C	C	G	rs199976859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513806C>G	ENST00000463781.3	-	2	5104	c.4645G>C	c.(4645-4647)Gac>Cac	p.D1549H	MUC4_ENST00000475231.1_Missense_Mutation_p.D1549H|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.M1535_T1550delMPLPVTSPSSASTGDT(4)|p.D1549H(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGTGTCACCTGTGGAT	0.582																																					p.D1549H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	5	Deletion - In frame(4)|Substitution - Missense(1)	stomach(4)|kidney(1)	c.G4645C						scavenged	.						6.0	5.0	5.0					3																	195513806		644	1466	2110	SO:0001583	missense	4585	exon2			TGGTGTCACCTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4645G>C	3.37:g.195513806C>G	ENSP00000417498:p.Asp1549His	Somatic	201	5	0.0248756		WXS	Illumina HiSeq	Phase_I	188	47	0.25	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	4.687	0.127710	0.08981	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33654	1.41;1.4	0.844	0.844	0.18943	.	.	.	.	.	T	0.23649	0.0572	N	0.19112	0.55	0.09310	N	1	D	0.54964	0.969	P	0.47162	0.54	T	0.09100	-1.0690	8	.	.	.	.	3.7845	0.08694	0.0:0.6622:0.0:0.3378	.	1549	E7ESK3	.	H	1549	ENSP00000417498:D1549H;ENSP00000420243:D1549H	.	D	-	1	0	MUC4	196998201	0.000000	0.05858	0.071000	0.20095	0.071000	0.16799	-2.804000	0.00759	0.088000	0.17205	0.089000	0.15464	GAC	C|0.932;G|0.068	0.068	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SMCR8	140775	hgsc.bcm.edu	37	17	18221134	18221134	+	Silent	SNP	C	C	T	rs1563631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18221134C>T	ENST00000406438.3	+	1	2511	c.2031C>T	c.(2029-2031)taC>taT	p.Y677Y	TOP3A_ENST00000542570.1_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	677						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CCACCAGCTACGTGAGCAGTG	0.577													C|||	895	0.178714	0.1611	0.2421	5008	,	,		20625	0.0605		0.3062	False		,,,				2504	0.1483				p.Y677Y		Atlas-SNP	.											SMCR8,colon,carcinoma,0,1	SMCR8	62	1	0			c.C2031T						PASS	.	C		922,3484	355.1+/-312.9	87,748,1368	77.0	75.0	76.0		2031	-9.4	0.0	17	dbSNP_88	76	2597,6003	423.1+/-354.3	382,1833,2085	yes	coding-synonymous	SMCR8	NM_144775.2		469,2581,3453	TT,TC,CC		30.1977,20.926,27.0567		677/938	18221134	3519,9487	2203	4300	6503	SO:0001819	synonymous_variant	140775	exon1			CAGCTACGTGAGC	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2031C>T	17.37:g.18221134C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			C|0.770;T|0.230	0.230	strong		0.577	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
RIMBP2	23504	hgsc.bcm.edu	37	12	130941150	130941150	+	Silent	SNP	G	G	C	rs2277361	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:130941150G>C	ENST00000261655.4	-	4	361	c.198C>G	c.(196-198)ggC>ggG	p.G66G	RIMBP2_ENST00000536002.1_5'UTR|RIMBP2_ENST00000535703.1_5'UTR	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	66					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		GGTCAATCTTGCCAGCGTGCT	0.612													C|||	1853	0.370008	0.3714	0.2622	5008	,	,		18755	0.377		0.4374	False		,,,				2504	0.3681				p.G66G		Atlas-SNP	.											.	RIMBP2	220	.	0			c.C198G						PASS	.	C		1747,2659	644.0+/-397.9	313,1121,769	47.0	38.0	41.0		198	-1.9	0.0	12	dbSNP_100	41	3913,4687	603.2+/-394.6	879,2155,1266	no	coding-synonymous	RIMBP2	NM_015347.4		1192,3276,2035	CC,CG,GG		45.5,39.6505,43.5184		66/1053	130941150	5660,7346	2203	4300	6503	SO:0001819	synonymous_variant	23504	exon4			AATCTTGCCAGCG	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.198C>G	12.37:g.130941150G>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_015347	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																			G|0.590;C|0.410	0.410	strong		0.612	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
ATAD5	79915	hgsc.bcm.edu	37	17	29162173	29162173	+	Silent	SNP	T	T	C	rs11655623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29162173T>C	ENST00000321990.4	+	2	1452	c.1074T>C	c.(1072-1074)ccT>ccC	p.P358P	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	358					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TATCTGATCCTGAGAATGAAC	0.373													t|||	902	0.180112	0.2027	0.1931	5008	,	,		19186	0.1359		0.1083	False		,,,				2504	0.2597				p.P358P		Atlas-SNP	.											.	ATAD5	150	.	0			c.T1074C						PASS	.	C		781,3613		69,643,1485	46.0	49.0	48.0		1074	1.1	1.0	17	dbSNP_120	48	899,7701		39,821,3440	no	coding-synonymous	ATAD5	NM_024857.3		108,1464,4925	CC,CT,TT		10.4535,17.7742,12.929		358/1845	29162173	1680,11314	2197	4300	6497	SO:0001819	synonymous_variant	79915	exon2			TGATCCTGAGAAT		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.1074T>C	17.37:g.29162173T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																			T|0.859;C|0.141	0.141	strong		0.373	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
BRIP1	83990	hgsc.bcm.edu	37	17	59761336	59761336	+	Missense_Mutation	SNP	C	C	A	rs587781744		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59761336C>A	ENST00000259008.2	-	20	3338	c.3071G>T	c.(3070-3072)gGg>gTg	p.G1024V		NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	1024	Interaction with BRCA1.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						CTCTGATGACCCGAGCTCAGG	0.403			"""F, N, Mis"""			"""AML, leukemia, breast"""		Involved in tolerance or repair of DNA crosslinks																													p.G1024V		Atlas-SNP	.	yes	Rec		"""Fanconi anaemia J, breast cancer susceptiblity"""	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"""L, E"""	BRIP1_ENST00000259008,NS,carcinoma,-1,4	BRIP1	237	4	0			c.G3071T						scavenged	.						114.0	109.0	110.0					17																	59761336		2203	4300	6503	SO:0001583	missense	83990	exon20			GATGACCCGAGCT	AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"""Fanconi anemia, complementation groups"""	20473	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-associated helicase 1"""	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.3071G>T	17.37:g.59761336C>A	ENSP00000259008:p.Gly1024Val	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_032043	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	37	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	C	2.733	-0.263935	0.05754	.	.	ENSG00000136492	ENST00000259008	T	0.73681	-0.77	5.33	2.23	0.28157	.	1.080930	0.06971	N	0.818190	T	0.56673	0.2001	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.17722	0.019	T	0.40720	-0.9548	9	.	.	.	-0.8307	7.1819	0.25778	0.0:0.7123:0.0:0.2877	.	1024	Q9BX63	FANCJ_HUMAN	V	1024	ENSP00000259008:G1024V	.	G	-	2	0	BRIP1	57116118	0.000000	0.05858	0.016000	0.15963	0.065000	0.16274	-0.987000	0.03743	0.316000	0.23135	-0.145000	0.13849	GGG	.	.	none		0.403	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043	
DTHD1	401124	hgsc.bcm.edu	37	4	36345377	36345377	+	Silent	SNP	G	G	A	rs2270880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:36345377G>A	ENST00000456874.2	+	9	2335	c.2277G>A	c.(2275-2277)gaG>gaA	p.E759E	DTHD1_ENST00000507598.1_Silent_p.E799E|RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000503528.1_3'UTR|DTHD1_ENST00000357504.3_Silent_p.E594E	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	759	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						TTGCAGAAGAGCTCAAATTCA	0.458													G|||	541	0.108027	0.0106	0.062	5008	,	,		19226	0.121		0.165	False		,,,				2504	0.2004				p.E759E		Atlas-SNP	.											.	DTHD1	63	.	0			c.G2277A						PASS	.	G	,	62,1322		3,56,633	19.0	17.0	18.0		1782,2277	4.3	1.0	4	dbSNP_100	18	526,2656		43,440,1108	no	coding-synonymous,coding-synonymous	DTHD1	NM_001136536.3,NM_001170700.1	,	46,496,1741	AA,AG,GG		16.5305,4.4798,12.8778	,	594/617,759/782	36345377	588,3978	692	1591	2283	SO:0001819	synonymous_variant	401124	exon9			AGAAGAGCTCAAA	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.2277G>A	4.37:g.36345377G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			G|0.895;A|0.105	0.105	strong		0.458	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
NELFB	25920	hgsc.bcm.edu	37	9	140167022	140167022	+	Silent	SNP	G	G	A	rs3204123	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140167022G>A	ENST00000343053.4	+	12	1888	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	517					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GGGTGGCCCCGTCTAAGCTGG	0.687													g|||	3081	0.615216	0.5129	0.7608	5008	,	,		16657	0.4782		0.7276	False		,,,				2504	0.6759				p.P517P		Atlas-SNP	.											COBRA1,NS,carcinoma,0,2	.	.	2	0			c.G1551A						PASS	.			2391,2011		661,1069,471	21.0	20.0	21.0		1551	-9.5	0.0	9	dbSNP_105	21	6529,2065		2500,1529,268	no	coding-synonymous	COBRA1	NM_015456.3		3161,2598,739	AA,AG,GG		24.0284,45.6838,31.3635		517/581	140167022	8920,4076	2201	4297	6498	SO:0001819	synonymous_variant	25920	exon12			GGCCCCGTCTAAG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.1551G>A	9.37:g.140167022G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	37	CCDS7040.1																																																																																			A|0.666;C|0.000;G|0.333;T|0.000	0.666	strong		0.687	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	
MAP3K1	4214	hgsc.bcm.edu	37	5	56155672	56155672	+	Missense_Mutation	SNP	A	A	G	rs56069227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:56155672A>G	ENST00000399503.3	+	3	764	c.764A>G	c.(763-765)aAc>aGc	p.N255S	AC008937.2_ENST00000415589.1_RNA|snoU13_ENST00000459264.1_RNA	NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	255					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TCTCCTGGCAACTCCCCATCA	0.488													A|||	83	0.0165735	0.025	0.0216	5008	,	,		15055	0.0		0.0338	False		,,,				2504	0.001				p.N255S		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A764G						PASS	.	A	SER/ASN	79,3755		1,77,1839	42.0	42.0	42.0		764	3.9	0.9	5	dbSNP_129	42	229,8029		5,219,3905	yes	missense	MAP3K1	NM_005921.1	46	6,296,5744	GG,GA,AA		2.7731,2.0605,2.5471	benign	255/1513	56155672	308,11784	1917	4129	6046	SO:0001583	missense	4214	exon3			CTGGCAACTCCCC	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.764A>G	5.37:g.56155672A>G	ENSP00000382423:p.Asn255Ser	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	229	116	0.50655	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	40	0.018315018315018316	6	0.012195121951219513	9	0.024861878453038673	0	0.0	25	0.032981530343007916	A	13.57	2.277282	0.40294	0.020605	0.027731	ENSG00000095015	ENST00000399503	T	0.63255	-0.03	5.72	3.93	0.45458	.	0.316826	0.39544	N	0.001335	T	0.10465	0.0256	N	0.01352	-0.895	0.26121	N	0.98055	B	0.02656	0.0	B	0.01281	0.0	T	0.14448	-1.0472	10	0.02654	T	1	.	11.7667	0.51935	0.1441:0.0:0.8559:0.0	rs56069227;rs61736548	255	Q13233	M3K1_HUMAN	S	255	ENSP00000382423:N255S	ENSP00000382423:N255S	N	+	2	0	MAP3K1	56191429	1.000000	0.71417	0.938000	0.37757	0.734000	0.41952	3.001000	0.49488	0.871000	0.35750	-0.242000	0.12053	AAC	A|0.976;G|0.024	0.024	strong		0.488	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
OR1A2	26189	hgsc.bcm.edu	37	17	3101578	3101578	+	Missense_Mutation	SNP	G	G	T	rs2241091	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3101578G>T	ENST00000381951.1	+	1	766	c.766G>T	c.(766-768)Ggc>Tgc	p.G256C		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	256			G -> C (in dbSNP:rs2241091). {ECO:0000269|PubMed:15489334}.		positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						TACAACGATGGGCATGTATTT	0.448													G|||	1410	0.28155	0.0318	0.2853	5008	,	,		18285	0.5595		0.3509	False		,,,				2504	0.2587				p.G256C		Atlas-SNP	.											.	OR1A2	52	.	0			c.G766T						PASS	.	G	CYS/GLY	417,3989	203.8+/-226.2	26,365,1812	114.0	109.0	110.0		766	3.0	1.0	17	dbSNP_98	110	3178,5422	480.8+/-370.5	592,1994,1714	yes	missense	OR1A2	NM_012352.1	159	618,2359,3526	TT,TG,GG		36.9535,9.4644,27.6411	probably-damaging	256/310	3101578	3595,9411	2203	4300	6503	SO:0001583	missense	26189	exon1			ACGATGGGCATGT	AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"""GPCR / Class A : Olfactory receptors"""	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.766G>T	17.37:g.3101578G>T	ENSP00000371377:p.Gly256Cys	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	217	114	0.525346	NM_012352	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Missense_Mutation	SNP	ENST00000381951.1	37	CCDS11021.1	711	0.32554945054945056	15	0.03048780487804878	119	0.3287292817679558	313	0.5472027972027972	264	0.3482849604221636	G	13.62	2.292025	0.40594	0.094644	0.369535	ENSG00000172150	ENST00000381951	T	0.00115	8.71	4.0	3.02	0.34903	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000111	T	0.00012	0.0000	L	0.50847	1.595	0.40982	P	0.015216000000000007	D	0.89917	1.0	D	0.91635	0.999	T	0.01966	-1.1238	9	0.87932	D	0	.	3.7968	0.08743	0.2056:0.0:0.6014:0.1931	rs2241091;rs17222222;rs52817904;rs59482978;rs2241091	256	Q9Y585	OR1A2_HUMAN	C	256	ENSP00000371377:G256C	ENSP00000371377:G256C	G	+	1	0	OR1A2	3048328	0.000000	0.05858	0.999000	0.59377	0.648000	0.38561	0.125000	0.15749	1.030000	0.39839	0.543000	0.68304	GGC	G|0.704;T|0.295	0.295	strong		0.448	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352	
TAS2R46	259292	hgsc.bcm.edu	37	12	11214360	11214360	+	Silent	SNP	C	C	T	rs73260771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:11214360C>T	ENST00000533467.1	-	1	533	c.534G>A	c.(532-534)acG>acA	p.T178T	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	178					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		GGATGGTTACCGTTGTATTTG	0.373													.|||	621	0.124002	0.1029	0.2248	5008	,	,		21835	0.0		0.2773	False		,,,				2504	0.0511				p.T178T		Atlas-SNP	.											.	TAS2R46	43	.	0			c.G534A						PASS	.	C		593,3809	239.9+/-250.9	50,493,1658	174.0	177.0	176.0		534	-5.1	0.0	12	dbSNP_130	176	2238,6358	370.8+/-336.0	307,1624,2367	no	coding-synonymous	TAS2R46	NM_176887.2		357,2117,4025	TT,TC,CC		26.0354,13.4711,21.7803		178/310	11214360	2831,10167	2201	4298	6499	SO:0001819	synonymous_variant	259292	exon1			GGTTACCGTTGTA	AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.534G>A	12.37:g.11214360C>T		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	223	107	0.479821	NM_176887	P59548|Q645X6	Silent	SNP	ENST00000533467.1	37	CCDS53748.1																																																																																			C|0.833;T|0.167	0.167	strong		0.373	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887	
CNGB1	1258	hgsc.bcm.edu	37	16	57996932	57996932	+	Silent	SNP	G	G	A	rs17821448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:57996932G>A	ENST00000251102.8	-	5	387	c.327C>T	c.(325-327)ggC>ggT	p.G109G	CNGB1_ENST00000564448.1_Silent_p.G109G|CNGB1_ENST00000311183.4_Silent_p.G109G	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	109					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						CCTTCTCTACGCCCTTCATGA	0.647													g|||	1573	0.314097	0.0552	0.304	5008	,	,		19314	0.3403		0.497	False		,,,				2504	0.456				p.G109G	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.C327T						PASS	.		,	491,3681		26,439,1621	90.0	85.0	87.0		327,327	-2.8	0.0	16	dbSNP_123	87	4124,4304		999,2126,1089	no	coding-synonymous,coding-synonymous	CNGB1	NM_001135639.1,NM_001297.4	,	1025,2565,2710	AA,AG,GG		48.9321,11.7689,36.627	,	109/300,109/1252	57996932	4615,7985	2086	4214	6300	SO:0001819	synonymous_variant	1258	exon5			CTCTACGCCCTTC	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.327C>T	16.37:g.57996932G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	85	82	0.964706	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																			G|0.665;A|0.334	0.334	strong		0.647	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
OXNAD1	92106	hgsc.bcm.edu	37	3	16327855	16327855	+	Missense_Mutation	SNP	T	T	G	rs842274	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:16327855T>G	ENST00000285083.5	+	5	655	c.190T>G	c.(190-192)Tca>Gca	p.S64A	OXNAD1_ENST00000606098.1_Missense_Mutation_p.S64A|OXNAD1_ENST00000544043.1_Missense_Mutation_p.S82A|OXNAD1_ENST00000435829.2_Missense_Mutation_p.S82A|OXNAD1_ENST00000605932.1_Missense_Mutation_p.S64A	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	64	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		S -> A (in dbSNP:rs842274). {ECO:0000269|Ref.1}.			mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						TTAGATTGTGTCAGCAGCTAA	0.478													T|||	2169	0.433107	0.3056	0.4712	5008	,	,		17571	0.4762		0.4334	False		,,,				2504	0.5337				p.S64A		Atlas-SNP	.											.	OXNAD1	31	.	0			c.T190G						PASS	.	T	ALA/SER	1547,2859	484.4+/-360.0	274,999,930	179.0	154.0	162.0		190	2.9	0.6	3	dbSNP_86	162	3655,4945	524.7+/-380.6	788,2079,1433	yes	missense	OXNAD1	NM_138381.3	99	1062,3078,2363	GG,GT,TT		42.5,35.1112,39.9969	benign	64/313	16327855	5202,7804	2203	4300	6503	SO:0001583	missense	92106	exon5			ATTGTGTCAGCAG	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.190T>G	3.37:g.16327855T>G	ENSP00000285083:p.Ser64Ala	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	230	102	0.443478	NM_138381	Q2HYC7|Q59FA4	Missense_Mutation	SNP	ENST00000285083.5	37	CCDS2630.1	908	0.4157509157509158	136	0.2764227642276423	170	0.4696132596685083	284	0.4965034965034965	318	0.41952506596306066	T	13.47	2.248105	0.39697	0.351112	0.425	ENSG00000154814	ENST00000285083;ENST00000435829;ENST00000544043	T;T;T	0.22336	2.29;1.96;2.28	5.26	2.89	0.33648	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);	0.235250	0.44902	N	0.000405	T	0.00012	0.0000	L	0.29908	0.895	0.33960	P	0.354468	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.001	T	0.47471	-0.9115	9	0.20519	T	0.43	-5.9895	6.6934	0.23185	0.235:0.0:0.1618:0.6031	rs842274;rs3821707;rs17330471;rs52798805;rs58580702;rs842274	82;64	F5H620;Q96HP4	.;OXND1_HUMAN	A	64;64;82	ENSP00000285083:S64A;ENSP00000389872:S64A;ENSP00000437967:S82A	ENSP00000285083:S64A	S	+	1	0	OXNAD1	16302859	1.000000	0.71417	0.602000	0.28890	0.827000	0.46813	1.867000	0.39499	0.317000	0.23160	0.533000	0.62120	TCA	T|0.589;G|0.405	0.405	strong		0.478	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
HLTF	6596	hgsc.bcm.edu	37	3	148766666	148766666	+	Silent	SNP	T	T	C	rs34474865	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:148766666T>C	ENST00000310053.5	-	16	1933	c.1740A>G	c.(1738-1740)agA>agG	p.R580R	HLTF_ENST00000392912.2_Silent_p.R580R|HLTF_ENST00000465259.1_Silent_p.R579R|HLTF_ENST00000494055.1_Silent_p.R580R	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	580	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AAACCCATCTTCTTTCTGATT	0.333													T|||	136	0.0271565	0.0015	0.0605	5008	,	,		15402	0.0		0.0795	False		,,,				2504	0.0123				p.R580R		Atlas-SNP	.											.	HLTF	87	.	0			c.A1740G						PASS	.	T	,	59,4347	57.4+/-93.9	0,59,2144	167.0	154.0	159.0		1740,1740	0.7	1.0	3	dbSNP_126	159	615,7983	160.3+/-213.4	18,579,3702	no	coding-synonymous,coding-synonymous	HLTF	NM_003071.3,NM_139048.2	,	18,638,5846	CC,CT,TT		7.1528,1.3391,5.183	,	580/1010,580/1010	148766666	674,12330	2203	4299	6502	SO:0001819	synonymous_variant	6596	exon16			CCATCTTCTTTCT	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.1740A>G	3.37:g.148766666T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	132	77	0.583333	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Silent	SNP	ENST00000310053.5	37	CCDS33875.1																																																																																			T|0.950;C|0.050	0.050	strong		0.333	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
ZNF862	643641	hgsc.bcm.edu	37	7	149561323	149561323	+	Missense_Mutation	SNP	G	G	A	rs62621237	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149561323G>A	ENST00000223210.4	+	8	3705	c.3460G>A	c.(3460-3462)Gag>Aag	p.E1154K	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	1154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						GGAGCCTCCCGAGAGACTCCT	0.637													G|||	54	0.0107827	0.0015	0.0187	5008	,	,		16795	0.0		0.0298	False		,,,				2504	0.0092				p.E1154K		Atlas-SNP	.											.	ZNF862	97	.	0			c.G3460A						PASS	.	G	LYS/GLU	20,3740		0,20,1860	27.0	30.0	29.0		3460	-3.1	0.0	7	dbSNP_129	29	305,7921		1,303,3809	yes	missense	ZNF862	NM_001099220.1	56	1,323,5669	AA,AG,GG		3.7078,0.5319,2.7115	benign	1154/1170	149561323	325,11661	1880	4113	5993	SO:0001583	missense	643641	exon8			CCTCCCGAGAGAC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.3460G>A	7.37:g.149561323G>A	ENSP00000223210:p.Glu1154Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_001099220	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	37	CCDS47741.1	33	0.01510989010989011	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	24	0.0316622691292876	G	13.40	2.227265	0.39399	0.005319	0.037078	ENSG00000106479	ENST00000223210	T	0.01068	5.38	4.38	-3.07	0.05363	.	1.768670	0.03274	N	0.185154	T	0.00271	0.0008	N	0.14661	0.345	0.09310	N	1	B	0.24368	0.102	B	0.08055	0.003	T	0.47222	-0.9134	10	0.52906	T	0.07	-1.6029	5.9819	0.19411	0.4175:0.139:0.4434:0.0	rs62621237	1154	O60290	ZN862_HUMAN	K	1154	ENSP00000223210:E1154K	ENSP00000223210:E1154K	E	+	1	0	ZNF862	149192256	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.013000	0.03645	-0.633000	0.05545	0.655000	0.94253	GAG	A|0.021;G|0.979	0.021	strong		0.637	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
Unknown	0	hgsc.bcm.edu	37	X	71379853	71379853	+	IGR	SNP	C	C	T	rs7880917		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:71379853C>T								BX119917.1 (7589 upstream) : PIN4 (21672 downstream)																							GAAATGCCTCCGCTGAAGGCC	0.498													C|||	1372	0.363444	0.2156	0.389	3775	,	,		15788	0.0317		0.5517	False		,,,				2504	0.2352				p.S58S		Atlas-SNP	.											.	FLJ44635	13	.	0			c.C174T						PASS	.	C		1215,2620		162,711,180,759,391	96.0	84.0	88.0		174	0.5	0.2	X	dbSNP_116	88	4972,1756		1355,902,1360,171,512	no	coding-synonymous	FLJ44635	NM_207422.2		1517,1613,1540,930,903	TT,TC,T,CC,C		26.0999,31.6819,41.4276		58/141	71379853	6187,4376	2203	4300	6503	SO:0001628	intergenic_variant	0	exon2			TGCCTCCGCTGAA																													X.37:g.71379853C>T		Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_207422		Silent	SNP		37																																																																																				C|0.581;T|0.419	0.419	strong	0	0.498								
RTTN	25914	hgsc.bcm.edu	37	18	67687860	67687860	+	Silent	SNP	T	T	C	rs2304378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:67687860T>C	ENST00000255674.6	-	45	6430	c.6144A>G	c.(6142-6144)gtA>gtG	p.V2048V	RTTN_ENST00000454359.1_3'UTR|RTTN_ENST00000579986.1_5'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	2048					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CCTTCTGAATTACTCCTTTAC	0.393													T|||	763	0.152356	0.0605	0.1311	5008	,	,		19560	0.1806		0.2286	False		,,,				2504	0.184				p.V2048V		Atlas-SNP	.											.	RTTN	184	.	0			c.A6144G						PASS	.	T		329,3529		12,305,1612	152.0	145.0	147.0		6144	-4.0	1.0	18	dbSNP_100	147	1719,6509		172,1375,2567	no	coding-synonymous	RTTN	NM_173630.3		184,1680,4179	CC,CT,TT		20.8921,8.5277,16.9452		2048/2227	67687860	2048,10038	1929	4114	6043	SO:0001819	synonymous_variant	25914	exon45			CTGAATTACTCCT	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.6144A>G	18.37:g.67687860T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	116	41	0.353448	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	37	CCDS42443.1																																																																																			T|0.826;C|0.174	0.174	strong		0.393	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
IL36A	27179	hgsc.bcm.edu	37	2	113763575	113763575	+	Missense_Mutation	SNP	A	A	G	rs895497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113763575A>G	ENST00000259211.6	+	2	446	c.35A>G	c.(34-36)cAg>cGg	p.Q12R		NM_014440.1	NP_055255.1	Q9UHA7	IL36A_HUMAN	interleukin 36, alpha	12			Q -> R (in dbSNP:rs895497). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)			large_intestine(1)|lung(3)|ovary(2)|skin(1)|stomach(2)	9						ACACCTCAGCAGGGGAGCATT	0.463													G|||	4210	0.840655	0.764	0.8156	5008	,	,		21196	0.9901		0.7247	False		,,,				2504	0.9274				p.Q12R		Atlas-SNP	.											IL36A,NS,carcinoma,0,2	IL36A	17	2	0			c.A35G						PASS	.	G	ARG/GLN	2945,875		1148,649,113	104.0	106.0	105.0		35	-7.6	0.0	2	dbSNP_86	105	5799,2441		2040,1719,361	yes	missense	IL36A	NM_014440.1	43	3188,2368,474	GG,GA,AA		29.6238,22.9058,27.4959	benign	12/159	113763575	8744,3316	1910	4120	6030	SO:0001583	missense	27179	exon2			CTCAGCAGGGGAG	AF201831	CCDS42734.1	2q12-q14.1	2011-07-14	2011-06-06	2011-06-06	ENSG00000136694	ENSG00000136694		"""Interleukins and interleukin receptors"""	15562	protein-coding gene	gene with protein product		605509	"""interleukin 1 family, member 6 (epsilon)"""	IL1F6		10625660	Standard	XM_005263639		Approved	FIL1, FIL1E, IL-1F6, IL1(EPSILON), MGC129553, MGC129552	uc010yxr.2	Q9UHA7	OTTHUMG00000153320	ENST00000259211.6:c.35A>G	2.37:g.113763575A>G	ENSP00000259211:p.Gln12Arg	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	185	90	0.486486	NM_014440	B2RAD9|Q53SR7|Q5BLR4|Q7RTZ8	Missense_Mutation	SNP	ENST00000259211.6	37	CCDS42734.1	1794	0.8214285714285714	382	0.7764227642276422	287	0.7928176795580111	570	0.9965034965034965	555	0.7321899736147758	G	6.833	0.522839	0.13066	0.770942	0.703762	ENSG00000136694	ENST00000259211	T	0.17213	2.29	4.9	-7.62	0.01294	.	4.855280	0.00751	N	0.001070	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31779	-0.9931	9	0.15952	T	0.53	-29.7709	0.7536	0.00994	0.417:0.1454:0.2213:0.2163	rs895497;rs52799607;rs56872263;rs895497	12	Q9UHA7	IL36A_HUMAN	R	12	ENSP00000259211:Q12R	ENSP00000259211:Q12R	Q	+	2	0	IL36A	113480046	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.459000	0.01000	-2.239000	0.00711	-4.544000	0.00004	CAG	A|0.212;G|0.788	0.788	strong		0.463	IL36A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330711.1	NM_014440	
PPP1R36	145376	hgsc.bcm.edu	37	14	65053999	65053999	+	Missense_Mutation	SNP	T	T	C	rs45482504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:65053999T>C	ENST00000298705.1	+	10	895	c.799T>C	c.(799-801)Ttt>Ctt	p.F267L	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	267			F -> L (in dbSNP:rs45482504).		negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										AGGGAGACTCTTTCGTACCAA	0.418													T|||	392	0.0782748	0.0431	0.0504	5008	,	,		17225	0.0347		0.0944	False		,,,				2504	0.1738				p.F267L		Atlas-SNP	.											.	.	.	.	0			c.T799C						PASS	.	T	LEU/PHE	263,4143	149.9+/-184.0	12,239,1952	151.0	144.0	146.0		799	4.4	1.0	14	dbSNP_127	146	840,7760	193.7+/-239.3	33,774,3493	yes	missense	C14orf50	NM_172365.1	22	45,1013,5445	CC,CT,TT		9.7674,5.9691,8.4807	benign	267/423	65053999	1103,11903	2203	4300	6503	SO:0001583	missense	145376	exon10			AGACTCTTTCGTA		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20097	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 50"""	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.799T>C	14.37:g.65053999T>C	ENSP00000298705:p.Phe267Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	157	69	0.43949	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	126	0.057692307692307696	18	0.036585365853658534	19	0.052486187845303865	21	0.03671328671328671	68	0.08970976253298153	T	14.94	2.686750	0.48097	0.059691	0.097674	ENSG00000165807	ENST00000298705	T	0.35421	1.31	5.55	4.42	0.53409	.	0.117824	0.42420	D	0.000714	T	0.00666	0.0022	L	0.55017	1.72	0.29862	P	0.827531	B	0.22414	0.069	B	0.20955	0.032	T	0.10543	-1.0625	9	0.05959	T	0.93	-23.0466	7.4184	0.27057	0.0:0.0945:0.0:0.9055	rs45482504	267	Q96LQ0	PPR36_HUMAN	L	267	ENSP00000298705:F267L	ENSP00000298705:F267L	F	+	1	0	C14orf50	64123752	0.998000	0.40836	1.000000	0.80357	0.982000	0.71751	2.327000	0.43858	2.099000	0.63709	0.533000	0.62120	TTT	T|0.924;C|0.076	0.076	strong		0.418	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
ZNF90	7643	hgsc.bcm.edu	37	19	20228941	20228941	+	Missense_Mutation	SNP	A	A	G	rs61998186	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20228941A>G	ENST00000418063.2	+	4	690	c.578A>G	c.(577-579)aAa>aGa	p.K193R	ZNF90_ENST00000474284.1_Intron	NM_007138.1	NP_009069.1	Q03938	ZNF90_HUMAN	zinc finger protein 90	193					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|lung(2)|ovary(1)|skin(1)	5						ACACATAAGAAAATTCATACT	0.383													a|||	614	0.122604	0.0076	0.1873	5008	,	,		20447	0.3393		0.0885	False		,,,				2504	0.044				p.K193R		Atlas-SNP	.											ZNF90_ENST00000418063,NS,carcinoma,-1,2	ZNF90	93	2	0			c.A578G						PASS	.	A	ARG/LYS	24,1360		0,24,668	27.0	25.0	26.0		578	1.2	0.1	19	dbSNP_129	26	300,2882		14,272,1305	no	missense	ZNF90	NM_007138.1	26	14,296,1973	GG,GA,AA		9.428,1.7341,7.0959	benign	193/602	20228941	324,4242	692	1591	2283	SO:0001583	missense	7643	exon4			ATAAGAAAATTCA	M61870	CCDS46028.1	19p12	2013-01-08	2006-02-01		ENSG00000213988	ENSG00000213988		"""Zinc fingers, C2H2-type"", ""-"""	13165	protein-coding gene	gene with protein product		603973	"""zinc finger protein 90 (HTF9)"""			8467795	Standard	NM_007138		Approved	HTF9	uc002nor.2	Q03938	OTTHUMG00000158057	ENST00000418063.2:c.578A>G	19.37:g.20228941A>G	ENSP00000410466:p.Lys193Arg	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_007138	B9EH87	Missense_Mutation	SNP	ENST00000418063.2	37	CCDS46028.1	314	0.14377289377289376	7	0.014227642276422764	56	0.15469613259668508	184	0.32167832167832167	67	0.08839050131926121	A	0.017	-1.495373	0.01009	0.017341	0.09428	ENSG00000213988	ENST00000418063	T	0.12984	2.63	1.18	1.18	0.20946	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.02697	-0.525	0.58432	P	4.000000000004E-6	B	0.26512	0.151	B	0.30716	0.119	T	0.48293	-0.9048	7	.	.	.	.	2.9598	0.05889	0.701:0.0:0.299:0.0	rs61998186	193	Q03938	ZNF90_HUMAN	R	193	ENSP00000410466:K193R	.	K	+	2	0	ZNF90	20089941	0.000000	0.05858	0.075000	0.20258	0.075000	0.17131	-0.704000	0.05058	0.251000	0.21505	0.248000	0.18094	AAA	A|0.869;G|0.131	0.131	strong		0.383	ZNF90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350101.1	NM_007138	
HERC1	8925	hgsc.bcm.edu	37	15	63970456	63970456	+	Missense_Mutation	SNP	T	T	C	rs2228510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63970456T>C	ENST00000443617.2	-	37	6745	c.6658A>G	c.(6658-6660)Atc>Gtc	p.I2220V	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2220			I -> V (in dbSNP:rs2228510). {ECO:0000269|PubMed:8861955}.		cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.I2220V(1)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						AGGATACGGATGAGCTGAATA	0.448													T|||	1833	0.366014	0.4599	0.4395	5008	,	,		19832	0.0704		0.5368	False		,,,				2504	0.316				p.I2220V		Atlas-SNP	.											HERC1_ENST00000443617,NS,carcinoma,0,1	HERC1	624	1	1	Substitution - Missense(1)	stomach(1)	c.A6658G						PASS	.	T	VAL/ILE	1817,2043		439,939,552	45.0	42.0	43.0		6658	4.6	1.0	15	dbSNP_98	43	4546,3748		1236,2074,837	yes	missense	HERC1	NM_003922.3	29	1675,3013,1389	CC,CT,TT		45.1893,47.0725,47.6469	benign	2220/4862	63970456	6363,5791	1930	4147	6077	SO:0001583	missense	8925	exon37			TACGGATGAGCTG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.6658A>G	15.37:g.63970456T>C	ENSP00000390158:p.Ile2220Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	783	0.3585164835164835	206	0.4186991869918699	156	0.430939226519337	41	0.07167832167832168	380	0.5013192612137203	T	13.44	2.237397	0.39498	0.470725	0.548107	ENSG00000103657	ENST00000443617	T	0.28666	1.6	5.7	4.56	0.56223	.	0.150685	0.43579	D	0.000542	T	0.00012	0.0000	L	0.36672	1.1	0.25098	P	0.99080285	B	0.06786	0.001	B	0.04013	0.001	T	0.42344	-0.9457	9	0.72032	D	0.01	.	11.8289	0.52283	0.0:0.0:0.2784:0.7216	rs2228510;rs3751525;rs60880144;rs2228510	2220	Q15751	HERC1_HUMAN	V	2220	ENSP00000390158:I2220V	ENSP00000390158:I2220V	I	-	1	0	HERC1	61757509	0.999000	0.42202	0.997000	0.53966	0.957000	0.61999	2.202000	0.42743	0.977000	0.38444	-0.313000	0.08912	ATC	T|0.632;C|0.368	0.368	strong		0.448	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
HDGFL1	154150	hgsc.bcm.edu	37	6	22570245	22570245	+	Silent	SNP	G	G	A	rs6900627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:22570245G>A	ENST00000230012.3	+	1	568	c.441G>A	c.(439-441)agG>agA	p.R147R	HDGFL1_ENST00000510882.2_Silent_p.R147R	NM_138574.2	NP_612641.2	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	147	Glu-rich.									kidney(1)|large_intestine(3)|lung(7)	11	Ovarian(93;0.163)					CGCTGAAGAGGAGCGCGGGGG	0.716													G|||	862	0.172125	0.2352	0.2075	5008	,	,		10556	0.001		0.2684	False		,,,				2504	0.1391				p.R147R		Atlas-SNP	.											.	HDGFL1	33	.	0			c.G441A						PASS	.	G		780,3036		80,620,1208	6.0	5.0	6.0		441	3.2	0.0	6	dbSNP_116	6	1799,5881		231,1337,2272	no	coding-synonymous	HDGFL1	NM_138574.2		311,1957,3480	AA,AG,GG		23.4245,20.4403,22.4339		147/252	22570245	2579,8917	1908	3840	5748	SO:0001819	synonymous_variant	154150	exon1			GAAGAGGAGCGCG	AK056824	CCDS34347.1	6p22.2	2008-02-05	2005-04-07	2005-04-07	ENSG00000112273	ENSG00000112273			21095	protein-coding gene	gene with protein product			"""PWWP domain containing 1"""	PWWP1			Standard	NM_138574		Approved	dJ309H15.1	uc003nds.3	Q5TGJ6	OTTHUMG00000016206	ENST00000230012.3:c.441G>A	6.37:g.22570245G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_138574	Q96MJ6	Silent	SNP	ENST00000230012.3	37	CCDS34347.1																																																																																			G|0.820;A|0.180	0.180	strong		0.716	HDGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043500.1	NM_138574	
GPR183	1880	hgsc.bcm.edu	37	13	99948178	99948178	+	Silent	SNP	C	C	A	rs2230342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:99948178C>A	ENST00000376414.4	-	2	305	c.222G>T	c.(220-222)gtG>gtT	p.V74V	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	74					G-protein coupled receptor signaling pathway (GO:0007186)|humoral immune response (GO:0006959)|immune response (GO:0006955)|mature B cell differentiation involved in immune response (GO:0002313)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|oxysterol binding (GO:0008142)			cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						TATCAGAAATCACCAAATTTG	0.418													C|||	1286	0.256789	0.2103	0.2421	5008	,	,		20245	0.1875		0.3748	False		,,,				2504	0.2802				p.V74V		Atlas-SNP	.											.	GPR183	38	.	0			c.G222T						PASS	.	C	,,	1080,3326	391.4+/-328.1	133,814,1256	121.0	113.0	116.0		,222,	1.2	1.0	13	dbSNP_98	116	3211,5389	485.2+/-371.6	604,2003,1693	no	intron,coding-synonymous,intron	GPR183,UBAC2	NM_001144072.1,NM_004951.4,NM_177967.3	,,	737,2817,2949	AA,AC,CC		37.3372,24.512,32.9925	,,	,74/362,	99948178	4291,8715	2203	4300	6503	SO:0001819	synonymous_variant	1880	exon2			AGAAATCACCAAA	L08177	CCDS9492.1	13q32.3	2012-08-21	2008-07-21	2008-07-21	ENSG00000169508	ENSG00000169508		"""GPCR / Class A : Orphans"""	3128	protein-coding gene	gene with protein product	"""EBV-induced G-protein coupled receptor 2"""	605741	"""Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor)"""	EBI2		8383238	Standard	NM_004951		Approved		uc001vog.3	P32249	OTTHUMG00000017263	ENST00000376414.4:c.222G>T	13.37:g.99948178C>A		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	227	227	1	NM_004951	B2R8N5|Q53F99|Q5JUH7	Silent	SNP	ENST00000376414.4	37	CCDS9492.1																																																																																			C|0.698;A|0.302	0.302	strong		0.418	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951	
MYO3A	53904	hgsc.bcm.edu	37	10	26462790	26462790	+	Silent	SNP	G	G	A	rs3740232	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:26462790G>A	ENST00000265944.5	+	30	3763	c.3597G>A	c.(3595-3597)gaG>gaA	p.E1199E	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1199					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1199E(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ATGAGGAAGAGGTTAAGCAAG	0.418													G|||	1648	0.329073	0.2262	0.317	5008	,	,		19882	0.3532		0.3429	False		,,,				2504	0.4376				p.E1199E		Atlas-SNP	.											MYO3A,colon,carcinoma,0,2	MYO3A	371	2	1	Substitution - coding silent(1)	stomach(1)	c.G3597A						PASS	.	G		1105,3301	396.7+/-330.2	139,827,1237	87.0	86.0	86.0		3597	0.0	0.0	10	dbSNP_107	86	2884,5716	452.0+/-362.8	486,1912,1902	no	coding-synonymous	MYO3A	NM_017433.4		625,2739,3139	AA,AG,GG		33.5349,25.0794,30.6705		1199/1617	26462790	3989,9017	2203	4300	6503	SO:0001819	synonymous_variant	53904	exon30			GGAAGAGGTTAAG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3597G>A	10.37:g.26462790G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																			G|0.681;A|0.319	0.319	strong		0.418	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
C1QB	713	hgsc.bcm.edu	37	1	22987744	22987744	+	Silent	SNP	C	C	T	rs149718049	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22987744C>T	ENST00000314933.6	+	3	759	c.627C>T	c.(625-627)acC>acT	p.T209T	C1QB_ENST00000509305.1_Silent_p.T207T	NM_000491.3	NP_000482.3	P02746	C1QB_HUMAN	complement component 1, q subcomponent, B chain	209	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|inner ear development (GO:0048839)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(1)|lung(9)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.06e-27)|Colorectal(126;1.58e-07)|GBM - Glioblastoma multiforme(114;6.72e-06)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000551)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AGGTCACCACCGGTGGCATGG	0.587																																					p.T209T		Atlas-SNP	.											.	C1QB	40	.	0			c.C627T						PASS	.	C		0,4406		0,0,2203	60.0	55.0	57.0		627	-6.8	0.0	1	dbSNP_134	57	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	C1QB	NM_000491.3		0,8,6495	TT,TC,CC		0.093,0.0,0.0615		209/254	22987744	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	713	exon3			CACCACCGGTGGC	X03084	CCDS228.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173369	ENSG00000173369		"""Complement system"""	1242	protein-coding gene	gene with protein product		120570	"""complement component 1, q subcomponent, beta polypeptide"""			1537612	Standard	XM_005245982		Approved		uc001bgd.3	P02746	OTTHUMG00000002896	ENST00000314933.6:c.627C>T	1.37:g.22987744C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	91	54	0.593407	NM_000491	Q5T959|Q96H17	Silent	SNP	ENST00000314933.6	37	CCDS228.1																																																																																			C|0.999;T|0.001	0.001	strong		0.587	C1QB-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000491	
PAXIP1	22976	hgsc.bcm.edu	37	7	154738409	154738409	+	Missense_Mutation	SNP	T	T	C	rs3501	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:154738409T>C	ENST00000404141.1	-	18	3191	c.3037A>G	c.(3037-3039)Atg>Gtg	p.M1013V	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Missense_Mutation_p.M1013V			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	1013	BRCT 6. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.		M -> V (in dbSNP:rs3501). {ECO:0000269|PubMed:17974005}.		adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)		p.M979V(1)		NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		TTGTGCTCCATGAGCTTCCGG	0.512													T|||	1179	0.235423	0.0726	0.3818	5008	,	,		15607	0.2083		0.3012	False		,,,				2504	0.3119				p.M1013V		Atlas-SNP	.											PAXIP1_ENST00000397192,caecum,carcinoma,0,3	PAXIP1	150	3	1	Substitution - Missense(1)	stomach(1)	c.A3037G						PASS	.	T	VAL/MET	391,3623		19,353,1635	76.0	74.0	75.0		3037	0.2	1.0	7	dbSNP_36	75	2251,6097		310,1631,2233	yes	missense	PAXIP1	NM_007349.3	21	329,1984,3868	CC,CT,TT		26.9645,9.7409,21.3719	benign	1013/1070	154738409	2642,9720	2007	4174	6181	SO:0001583	missense	22976	exon18			GCTCCATGAGCTT	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.3037A>G	7.37:g.154738409T>C	ENSP00000384048:p.Met1013Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	505	0.23122710622710624	40	0.08130081300813008	130	0.35911602209944754	118	0.2062937062937063	217	0.2862796833773087	T	12.30	1.897499	0.33535	0.097409	0.269645	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.41758	0.99;0.99	5.34	0.184	0.15086	BRCT (1);	0.162750	0.40640	N	0.001047	T	0.00012	0.0000	L	0.36672	1.1	0.26425	P	0.9760338	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45011	-0.9290	9	0.13853	T	0.58	-19.4618	5.5358	0.17011	0.0:0.2232:0.1342:0.6426	rs3501;rs52823645;rs3501	979;1013	Q6ZW49-1;Q6ZW49	.;PAXI1_HUMAN	V	1013;1013;837;966	ENSP00000384048:M1013V;ENSP00000380376:M1013V	ENSP00000319149:M966V	M	-	1	0	PAXIP1	154369342	1.000000	0.71417	0.964000	0.40570	0.940000	0.58332	1.156000	0.31712	-0.203000	0.10251	0.454000	0.30748	ATG	T|0.770;C|0.230	0.230	strong		0.512	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
GJA9	81025	hgsc.bcm.edu	37	1	39340862	39340862	+	Silent	SNP	A	A	G	rs874243	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39340862A>G	ENST00000360786.3	-	1	1161	c.909T>C	c.(907-909)tcT>tcC	p.S303S	MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000454994.2_Silent_p.S303S|RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA|GJA9_ENST00000357771.3_Silent_p.S303S|MYCBP_ENST00000397572.2_5'Flank			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	303					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			GGAATACAGAAGATGAATTTA	0.383													A|||	519	0.103634	0.0061	0.1167	5008	,	,		19276	0.1319		0.2177	False		,,,				2504	0.0798				p.S303S		Atlas-SNP	.											.	GJA9	55	.	0			c.T909C						PASS	.	A		189,4217	119.6+/-157.3	8,173,2022	97.0	95.0	96.0		909	3.8	0.1	1	dbSNP_86	96	1824,6776	326.6+/-317.4	199,1426,2675	no	coding-synonymous	GJA9	NM_030772.4		207,1599,4697	GG,GA,AA		21.2093,4.2896,15.4775		303/516	39340862	2013,10993	2203	4300	6503	SO:0001819	synonymous_variant	81025	exon2			TACAGAAGATGAA	AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"""Ion channels / Gap junction proteins (connexins)"""	19155	protein-coding gene	gene with protein product	"""connexin 59"""	611923	"""gap junction protein, alpha 10, 59kDa"""	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.909T>C	1.37:g.39340862A>G		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	221	138	0.624434	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000360786.3	37	CCDS432.1																																																																																			G|0.140;N|0.000	0.140	strong		0.383	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20134739	20134739	+	3'UTR	SNP	C	C	T	rs9605070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20134739C>T	ENST00000334554.7	+	0	4255				ZDHHC8_ENST00000405930.3_Silent_p.S774S	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8						locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					TTTTCCCCAGCCTCTCGGGGC	0.721													C|||	674	0.134585	0.0129	0.1138	5008	,	,		13169	0.0873		0.2207	False		,,,				2504	0.274				p.S774S		Atlas-SNP	.											ZDHHC8_ENST00000405930,rectum,carcinoma,0,1	ZDHHC8	77	1	0			c.C2322T						PASS	.																																			SO:0001624	3_prime_UTR_variant	29801	exon11			CCCCAGCCTCTCG	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.*1816C>T	22.37:g.20134739C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																			C|0.880;T|0.120	0.120	strong		0.721	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373	
AKNAD1	254268	hgsc.bcm.edu	37	1	109366286	109366286	+	Missense_Mutation	SNP	C	C	T	rs7522157	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109366286C>T	ENST00000370001.3	-	12	2229	c.1961G>A	c.(1960-1962)tGt>tAt	p.C654Y	AKNAD1_ENST00000369995.3_Missense_Mutation_p.C654Y|AKNAD1_ENST00000357393.4_Missense_Mutation_p.C361Y|AKNAD1_ENST00000369994.1_Missense_Mutation_p.C624Y	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	654			C -> Y (in dbSNP:rs7522157). {ECO:0000269|Ref.6}.			cytoplasm (GO:0005737)		p.C654Y(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						AGAATCAGAACAGAAGCTGTG	0.438													C|||	830	0.165735	0.0598	0.1787	5008	,	,		19769	0.1121		0.2873	False		,,,				2504	0.2301				p.C654Y		Atlas-SNP	.											AKNAD1,NS,adenoma,0,2	AKNAD1	83	2	1	Substitution - Missense(1)	stomach(1)	c.G1961A						PASS	.	C	TYR/CYS	474,3932	222.6+/-239.4	24,426,1753	122.0	110.0	114.0		1961	-3.2	0.0	1	dbSNP_116	114	2706,5894	434.1+/-357.6	434,1838,2028	yes	missense	AKNAD1	NM_152763.3	194	458,2264,3781	TT,TC,CC		31.4651,10.7581,24.4503	possibly-damaging	654/837	109366286	3180,9826	2203	4300	6503	SO:0001583	missense	254268	exon12			TCAGAACAGAAGC	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.1961G>A	1.37:g.109366286C>T	ENSP00000359018:p.Cys654Tyr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	166	66	0.39759	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	376	0.17216117216117216	29	0.05894308943089431	63	0.17403314917127072	72	0.1258741258741259	212	0.2796833773087071	C	3.789	-0.044103	0.07452	0.107581	0.314651	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.83	-3.24	0.05094	.	0.899723	0.09329	N	0.817134	T	0.02012	0.0063	N	0.12746	0.255	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.002	T	0.48127	-0.9062	9	0.16420	T	0.52	0.472	6.5162	0.22248	0.1528:0.5632:0.0:0.2839	rs7522157;rs9440617;rs17562500;rs52807178;rs59423546;rs7522157	361;654	B4DET8;Q5T1N1	.;AKND1_HUMAN	Y	654;361;624;654	ENSP00000359018:C654Y;ENSP00000349968:C361Y;ENSP00000359011:C624Y;ENSP00000359012:C654Y	ENSP00000349968:C361Y	C	-	2	0	AKNAD1	109167809	0.000000	0.05858	0.000000	0.03702	0.868000	0.49771	-2.023000	0.01438	-0.360000	0.08138	0.561000	0.74099	TGT	C|0.793;G|0.000;N|0.000;T|0.206	0.206	strong		0.438	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
FAT2	2196	hgsc.bcm.edu	37	5	150946132	150946132	+	Silent	SNP	G	G	A	rs3734059	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150946132G>A	ENST00000261800.5	-	1	2373	c.2361C>T	c.(2359-2361)atC>atT	p.I787I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	787	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTACATTGAGGATGTAGAAAT	0.502													G|||	2101	0.419529	0.441	0.4539	5008	,	,		21698	0.3562		0.4901	False		,,,				2504	0.3589				p.I787I		Atlas-SNP	.											.	FAT2	465	.	0			c.C2361T						PASS	.	G		1960,2446	554.6+/-379.1	423,1114,666	74.0	71.0	72.0		2361	3.0	1.0	5	dbSNP_107	72	4497,4103	592.2+/-392.9	1182,2133,985	no	coding-synonymous	FAT2	NM_001447.2		1605,3247,1651	AA,AG,GG		47.7093,44.4848,49.6463		787/4350	150946132	6457,6549	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			ATTGAGGATGTAG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2361C>T	5.37:g.150946132G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	100	37	0.37	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.527;A|0.473	0.473	strong		0.502	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
SLC22A2	6582	hgsc.bcm.edu	37	6	160645832	160645832	+	Silent	SNP	C	C	T	rs316003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:160645832C>T	ENST00000366953.3	-	10	1764	c.1506G>A	c.(1504-1506)gtG>gtA	p.V502V	SLC22A2_ENST00000491092.1_5'UTR	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	502					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	CCAAGCCAAGCACGCCTGAAA	0.403													C|||	3471	0.693091	0.4244	0.8386	5008	,	,		16767	0.7966		0.7654	False		,,,				2504	0.772				p.V502V		Atlas-SNP	.											.	SLC22A2	78	.	0			c.G1506A						PASS	.	C		2119,2287	577.4+/-384.4	529,1061,613	81.0	79.0	80.0		1506	2.7	0.1	6	dbSNP_79	80	6604,1996	723.1+/-406.4	2517,1570,213	no	coding-synonymous	SLC22A2	NM_003058.3		3046,2631,826	TT,TC,CC		23.2093,48.0935,32.931		502/556	160645832	8723,4283	2203	4300	6503	SO:0001819	synonymous_variant	6582	exon10			GCCAAGCACGCCT	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"""Solute carriers"""	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.1506G>A	6.37:g.160645832C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Silent	SNP	ENST00000366953.3	37	CCDS5276.1																																																																																			C|0.301;T|0.699	0.699	strong		0.403	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058	
OLR1	4973	hgsc.bcm.edu	37	12	10313448	10313448	+	Missense_Mutation	SNP	C	C	G	rs11053646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10313448C>G	ENST00000309539.3	-	4	561	c.501G>C	c.(499-501)aaG>aaC	p.K167N	OLR1_ENST00000543993.1_Intron|OLR1_ENST00000544577.1_Intron|OLR1_ENST00000545927.1_Missense_Mutation_p.K167N|OLR1_ENST00000432556.2_Intron	NM_002543.3	NP_002534.1	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like) receptor 1	167	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		K -> N (common polymorphism; myocardial infarction susceptibility; dbSNP:rs11053646). {ECO:0000269|PubMed:12646194, ECO:0000269|PubMed:14702039}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell death (GO:0008219)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|lipoprotein metabolic process (GO:0042157)|proteolysis (GO:0006508)|response to hydrogen peroxide (GO:0042542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|low-density lipoprotein receptor activity (GO:0005041)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						TCTCTTGGCTCTTTTCCCAGT	0.443													C|||	817	0.163139	0.2209	0.0476	5008	,	,		19453	0.1746		0.0835	False		,,,				2504	0.2372				p.K167N		Atlas-SNP	.											.	OLR1	29	.	0			c.G501C	GRCh37	CM033655	OLR1	M	rs11053646	PASS	.	C	,ASN/LYS,ASN/LYS	919,3487	355.1+/-312.9	95,729,1379	187.0	180.0	182.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,501,501	-0.2	0.6	12	dbSNP_120	182	781,7819	185.3+/-233.1	34,713,3553	yes	intron,missense,missense	OLR1	NM_001172632.1,NM_001172633.1,NM_002543.3	,94,94	129,1442,4932	GG,GC,CC		9.0814,20.8579,13.0709	,possibly-damaging,possibly-damaging	,167/190,167/274	10313448	1700,11306	2203	4300	6503	SO:0001583	missense	4973	exon4			TTGGCTCTTTTCC	D89050	CCDS8618.1, CCDS53745.1, CCDS53746.1	12p13.1-p12.3	2011-08-30	2006-12-07		ENSG00000173391	ENSG00000173391		"""C-type lectin domain containing"""	8133	protein-coding gene	gene with protein product		602601	"""oxidised low density lipoprotein (lectin-like) receptor 1"""			9763655	Standard	NM_002543		Approved	LOX-1, SCARE1, CLEC8A	uc001qxo.1	P78380	OTTHUMG00000168527	ENST00000309539.3:c.501G>C	12.37:g.10313448C>G	ENSP00000309124:p.Lys167Asn	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_001172633	A8K7V9|B4DI48|G3V1I4|Q2PP00|Q7Z484	Missense_Mutation	SNP	ENST00000309539.3	37	CCDS8618.1	288	0.13186813186813187	96	0.1951219512195122	17	0.04696132596685083	109	0.19055944055944055	66	0.0870712401055409	C	0.545	-0.851895	0.02651	0.208579	0.090814	ENSG00000173391	ENST00000309539;ENST00000545927;ENST00000539518;ENST00000538745;ENST00000339968	T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32	4.98	-0.211	0.13172	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.390912	0.24445	N	0.038462	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.999999695872	P	0.38473	0.633	B	0.33339	0.162	T	0.43147	-0.9409	9	0.20519	T	0.43	.	3.5856	0.07970	0.1778:0.2948:0.0:0.5274	rs11053646;rs35996025;rs60209320;rs11053646	167	P78380	OLR1_HUMAN	N	167;167;114;63;63	ENSP00000309124:K167N;ENSP00000439251:K167N;ENSP00000442389:K114N;ENSP00000438925:K63N;ENSP00000340572:K63N	ENSP00000309124:K167N	K	-	3	2	OLR1	10204715	0.952000	0.32445	0.591000	0.28745	0.139000	0.21198	-0.010000	0.12743	-0.143000	0.11334	-0.140000	0.14226	AAG	C|0.862;G|0.138	0.138	strong		0.443	OLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400091.1	NM_002543	
OTOA	146183	hgsc.bcm.edu	37	16	21742179	21742179	+	Silent	SNP	C	C	T	rs139312489		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:21742179C>T	ENST00000286149.4	+	20	2272	c.2271C>T	c.(2269-2271)gcC>gcT	p.A757A	OTOA_ENST00000388956.4_Silent_p.A664A|OTOA_ENST00000388958.3_Silent_p.A743A|OTOA_ENST00000388957.3_Silent_p.A419A			Q7RTW8	OTOAN_HUMAN	otoancorin	757					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		ACTGGACAGCCGAGACCACGA	0.448																																					p.A743A		Atlas-SNP	.											OTOA_ENST00000388957,NS,carcinoma,0,2	OTOA	144	2	0			c.C2229T						scavenged	.						103.0	82.0	89.0					16																	21742179		2195	4268	6463	SO:0001819	synonymous_variant	146183	exon20			GACAGCCGAGACC	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.2271C>T	16.37:g.21742179C>T		Somatic	1368	5	0.00365497		WXS	Illumina HiSeq	Phase_I	651	100	0.15361	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Silent	SNP	ENST00000286149.4	37																																																																																				C|0.500;T|0.500	0.500	weak		0.448	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
EYS	346007	hgsc.bcm.edu	37	6	64488001	64488001	+	Missense_Mutation	SNP	T	T	C	rs74636274	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:64488001T>C	ENST00000370621.3	-	40	8322	c.7796A>G	c.(7795-7797)cAc>cGc	p.H2599R	PHF3_ENST00000420043.1_3'UTR|EYS_ENST00000370616.2_Missense_Mutation_p.H2599R|EYS_ENST00000503581.1_Missense_Mutation_p.H2599R			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2599	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		H -> R (in dbSNP:rs74636274). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGCATTTGGGTGGCCCTCAGG	0.473													T|||	23	0.00459265	0.0	0.0043	5008	,	,		17905	0.0		0.0109	False		,,,				2504	0.0092				p.H2599R		Atlas-SNP	.											.	EYS	527	.	0			c.A7796G						PASS	.	T	ARG/HIS	1,1383		0,1,691	100.0	82.0	88.0		7796	1.5	0.5	6	dbSNP_131	88	35,3147		0,35,1556	yes	missense	EYS	NM_001142800.1	29	0,36,2247	CC,CT,TT		1.0999,0.0723,0.7884	benign	2599/3145	64488001	36,4530	692	1591	2283	SO:0001583	missense	346007	exon40			TTTGGGTGGCCCT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.7796A>G	6.37:g.64488001T>C	ENSP00000359655:p.His2599Arg	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	250	114	0.456	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		9|9|9	0.004120879120879121|0.004120879120879121|0.004120879120879121	0|0|0	0.0|0.0|0.0	2|2|2	0.0055248618784530384|0.0055248618784530384|0.0055248618784530384	0|0|0	0.0|0.0|0.0	7|7|7	0.009234828496042216|0.009234828496042216|0.009234828496042216	T|T|T	9.321|9.321|9.321	1.057987|1.057987|1.057987	0.19987|0.19987|0.19987	7.23E-4|7.23E-4|7.23E-4	0.010999|0.010999|0.010999	ENSG00000188107|ENSG00000188107|ENSG00000118482	ENST00000503581;ENST00000370621;ENST00000370616|ENST00000398580|ENST00000505138	D;T;T|.|.	0.81659|.|.	-1.52;-1.49;-1.49|.|.	4.02|4.02|4.02	1.47|1.47|1.47	0.22746|0.22746|0.22746	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);|.|.	0.285145|.|.	0.21597|.|.	N|.|.	0.072010|.|.	T|T|T	0.14874|0.14874|0.14874	0.0359|0.0359|0.0359	N|N|N	0.11201|0.11201|0.11201	0.11|0.11|0.11	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;B|.|.	0.23540|.|.	0.087;0.053|.|.	B;B|.|.	0.20384|.|.	0.029;0.013|.|.	T|T|T	0.05937|0.05937|0.05937	-1.0855|-1.0855|-1.0855	10|5|5	0.25106|.|.	T|.|.	0.35|.|.	.|.|.	7.1543|7.1543|7.1543	0.25628|0.25628|0.25628	0.0:0.1867:0.0:0.8133|0.0:0.1867:0.0:0.8133|0.0:0.1867:0.0:0.8133	.|.|.	2599;2599|.|.	Q5T1H1-1;Q5T1H1|.|.	.;EYS_HUMAN|.|.	R|A|R	2599|371|136	ENSP00000424243:H2599R;ENSP00000359655:H2599R;ENSP00000359650:H2599R|.|.	ENSP00000359650:H2599R|.|.	H|T|W	-|-|+	2|1|1	0|0|0	EYS|EYS|PHF3	64545960|64545960|64545960	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.475000|0.475000|0.475000	0.27278|0.27278|0.27278	0.032000|0.032000|0.032000	0.12392|0.12392|0.12392	1.000000|1.000000|1.000000	0.29770|0.29770|0.29770	0.020000|0.020000|0.020000	0.15106|0.15106|0.15106	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	CAC|ACC|TGG	T|0.996;C|0.004	0.004	strong		0.473	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
TDRD7	23424	hgsc.bcm.edu	37	9	100194406	100194406	+	Missense_Mutation	SNP	T	T	C	rs2045732	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100194406T>C	ENST00000355295.4	+	4	744	c.449T>C	c.(448-450)gTt>gCt	p.V150A	TDRD7_ENST00000422139.2_Missense_Mutation_p.V76A	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	150			V -> A (in dbSNP:rs2045732). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)	p.V150A(1)		endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				GGAAACTCTGTTGGAGTTAAG	0.413													C|||	2728	0.544728	0.6127	0.598	5008	,	,		21263	0.5784		0.5129	False		,,,				2504	0.4131				p.V150A		Atlas-SNP	.											TDRD7,NS,carcinoma,0,1	TDRD7	78	1	1	Substitution - Missense(1)	stomach(1)	c.T449C						PASS	.	C	ALA/VAL	2664,1742	519.0+/-369.9	797,1070,336	157.0	158.0	158.0		449	1.0	0.0	9	dbSNP_94	158	4088,4512	592.6+/-393.0	978,2132,1190	yes	missense	TDRD7	NM_014290.2	64	1775,3202,1526	CC,CT,TT		47.5349,39.537,48.0855	benign	150/1099	100194406	6752,6254	2203	4300	6503	SO:0001583	missense	23424	exon4			ACTCTGTTGGAGT	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"""Tudor domain containing"""	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.449T>C	9.37:g.100194406T>C	ENSP00000347444:p.Val150Ala	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	NM_014290	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Missense_Mutation	SNP	ENST00000355295.4	37	CCDS6725.1	1239	0.5673076923076923	308	0.6260162601626016	214	0.5911602209944752	327	0.5716783216783217	390	0.5145118733509235	C	0.056	-1.236835	0.01493	0.60463	0.475349	ENSG00000196116	ENST00000355295;ENST00000422139	T;T	0.12255	2.7;2.7	4.98	0.998	0.19857	.	1.655750	0.02869	N	0.131355	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.14438	0.01	B	0.06405	0.002	T	0.40776	-0.9545	9	0.13470	T	0.59	-0.3418	5.7697	0.18247	0.2585:0.0841:0.0:0.6574	rs2045732;rs17332669;rs52796736;rs57645526;rs2045732	150	Q8NHU6	TDRD7_HUMAN	A	150;76	ENSP00000347444:V150A;ENSP00000413608:V76A	ENSP00000347444:V150A	V	+	2	0	TDRD7	99234227	0.031000	0.19500	0.012000	0.15200	0.004000	0.04260	-0.001000	0.12947	0.092000	0.17331	-1.333000	0.01266	GTT	T|0.469;C|0.531	0.531	strong		0.413	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290	
POLR1A	25885	hgsc.bcm.edu	37	2	86315741	86315741	+	Silent	SNP	C	C	T	rs2288120	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:86315741C>T	ENST00000263857.6	-	6	1056	c.678G>A	c.(676-678)acG>acA	p.T226T	POLR1A_ENST00000409681.1_Silent_p.T226T			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	226					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						TGGCTGGAAACGTGATAGTCA	0.552													C|||	3295	0.657947	0.3139	0.8228	5008	,	,		19197	0.6567		0.84	False		,,,				2504	0.82				p.T226T		Atlas-SNP	.											.	POLR1A	137	.	0			c.G678A						PASS	.	C		1716,2356		334,1048,654	137.0	127.0	130.0		678	-4.4	0.7	2	dbSNP_100	130	7089,1275		2998,1093,91	no	coding-synonymous	POLR1A	NM_015425.3		3332,2141,745	TT,TC,CC		15.2439,42.1415,29.1975		226/1721	86315741	8805,3631	2036	4182	6218	SO:0001819	synonymous_variant	25885	exon6			TGGAAACGTGATA	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.678G>A	2.37:g.86315741C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	160	160	1	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Silent	SNP	ENST00000263857.6	37	CCDS42706.1																																																																																			C|0.307;T|0.693	0.693	strong		0.552	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
RPL9	6133	hgsc.bcm.edu	37	4	39458051	39458051	+	Silent	SNP	A	A	G	rs2125313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:39458051A>G	ENST00000449470.2	-	4	814	c.366T>C	c.(364-366)taT>taC	p.Y122Y	RPL9_ENST00000295955.9_Silent_p.Y122Y|LIAS_ENST00000381846.1_5'Flank|LIAS_ENST00000340169.2_5'Flank|LIAS_ENST00000261434.3_5'Flank|LIAS_ENST00000513731.1_5'Flank	NM_001024921.2	NP_001020092.1	P32969	RL9_HUMAN	ribosomal protein L9	122					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|skin(1)	8						CCCTGCGGATATATTTTTCAC	0.413													G|||	3470	0.692891	0.5272	0.8069	5008	,	,		16663	0.7212		0.6799	False		,,,				2504	0.82				p.Y122Y		Atlas-SNP	.											.	RPL9	16	.	0			c.T366C						PASS	.	G	,	2426,1980	541.7+/-375.8	691,1044,468	46.0	48.0	47.0		366,366	1.5	1.0	4	dbSNP_96	47	6023,2577	416.3+/-352.1	2093,1837,370	no	coding-synonymous,coding-synonymous	RPL9	NM_000661.4,NM_001024921.2	,	2784,2881,838	GG,GA,AA		29.9651,44.9387,35.0377	,	122/193,122/193	39458051	8449,4557	2203	4300	6503	SO:0001819	synonymous_variant	6133	exon5			GCGGATATATTTT	D14531	CCDS3452.1	4p13	2011-04-06			ENSG00000163682	ENSG00000163682		"""L ribosomal proteins"""	10369	protein-coding gene	gene with protein product		603686				8597601, 8415001	Standard	XM_005262661		Approved	L9	uc021sso.1	P32969	OTTHUMG00000099367	ENST00000449470.2:c.366T>C	4.37:g.39458051A>G		Somatic	401	0	0		WXS	Illumina HiSeq	Phase_I	384	212	0.552083	NM_000661		Silent	SNP	ENST00000449470.2	37	CCDS3452.1	1487	0.6808608058608059	261	0.5304878048780488	285	0.787292817679558	428	0.7482517482517482	513	0.6767810026385225	G	1.549	-0.539856	0.04053	0.550613	0.700349	ENSG00000163682	ENST00000508595	.	.	.	5.66	1.53	0.23141	.	0.000000	0.64402	U	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25187	-1.0139	5	0.30078	T	0.28	.	10.5401	0.45029	0.4386:0.0:0.5614:0.0	rs2125313;rs61653338	.	.	.	H	119	.	ENSP00000425250:Y119H	Y	-	1	0	RPL9	39134446	1.000000	0.71417	0.996000	0.52242	0.185000	0.23345	1.174000	0.31932	0.088000	0.17205	-0.974000	0.02594	TAT	A|0.341;G|0.659	0.659	strong		0.413	RPL9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361018.1		
C15orf52	388115	hgsc.bcm.edu	37	15	40627845	40627845	+	Silent	SNP	G	G	A	rs55641696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40627845G>A	ENST00000559313.1	-	11	1134	c.1119C>T	c.(1117-1119)agC>agT	p.S373S	C15orf52_ENST00000397536.2_Silent_p.S163S	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	373							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		GCTCCATCCCGCTCTGCTTCT	0.647													G|||	733	0.146366	0.0855	0.1686	5008	,	,		17103	0.0278		0.2803	False		,,,				2504	0.1973				p.S373S		Atlas-SNP	.											.	C15orf52	47	.	0			c.C1119T						PASS	.	G		443,3913		25,393,1760	43.0	44.0	44.0		1119	0.1	0.0	15	dbSNP_129	44	2221,6283		313,1595,2344	no	coding-synonymous	C15orf52	NM_207380.2		338,1988,4104	AA,AG,GG		26.1171,10.1699,20.7154		373/535	40627845	2664,10196	2178	4252	6430	SO:0001819	synonymous_variant	388115	exon11			CATCCCGCTCTGC	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.1119C>T	15.37:g.40627845G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Silent	SNP	ENST00000559313.1	37	CCDS10055.2																																																																																			G|0.836;A|0.164	0.164	strong		0.647	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
ABCA13	154664	hgsc.bcm.edu	37	7	48285485	48285485	+	Missense_Mutation	SNP	C	C	T	rs1880738	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:48285485C>T	ENST00000435803.1	+	13	1541	c.1517C>T	c.(1516-1518)cCg>cTg	p.P506L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	506			P -> L (in dbSNP:rs1880738).		transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GCTGTCTGCCCGAATGGTCGT	0.468													C|||	2036	0.40655	0.1596	0.4366	5008	,	,		17442	0.6181		0.4115	False		,,,				2504	0.4959				p.P506L		Atlas-SNP	.											ABCA13_ENST00000435803,NS,carcinoma,0,2	ABCA13	1192	2	0			c.C1517T						PASS	.	C	LEU/PRO	672,3066		67,538,1264	89.0	81.0	83.0		1517	-2.7	0.0	7	dbSNP_92	83	3535,4691		752,2031,1330	yes	missense	ABCA13	NM_152701.3	98	819,2569,2594	TT,TC,CC		42.9735,17.9775,35.1638	benign	506/5059	48285485	4207,7757	1869	4113	5982	SO:0001583	missense	154664	exon13			TCTGCCCGAATGG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.1517C>T	7.37:g.48285485C>T	ENSP00000411096:p.Pro506Leu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	866	0.3965201465201465	63	0.12804878048780488	156	0.430939226519337	340	0.5944055944055944	307	0.4050131926121372	C	10.17	1.276424	0.23307	0.179775	0.429735	ENSG00000179869	ENST00000435803	T	0.81330	-1.48	5.06	-2.68	0.06041	.	1.036610	0.07718	N	0.943236	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41378	-0.9512	9	0.10377	T	0.69	.	0.6855	0.00882	0.1924:0.2748:0.1379:0.3948	rs1880738;rs17712198;rs52816810;rs59929558;rs1880738	506	Q86UQ4	ABCAD_HUMAN	L	506	ENSP00000411096:P506L	ENSP00000411096:P506L	P	+	2	0	ABCA13	48256031	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.065000	0.14466	-0.277000	0.09193	-0.136000	0.14681	CCG	C|0.624;T|0.376	0.376	strong		0.468	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
TMEM55A	55529	hgsc.bcm.edu	37	8	92033502	92033502	+	Silent	SNP	T	T	C	rs34503257	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:92033502T>C	ENST00000285419.3	-	2	551	c.237A>G	c.(235-237)acA>acG	p.T79T	GS1-251I9.3_ENST00000517920.1_RNA	NM_018710.2	NP_061180.1	Q8N4L2	TM55A_HUMAN	transmembrane protein 55A	79						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	13			BRCA - Breast invasive adenocarcinoma(11;0.033)			CATTGCAAACTGTGCACTTAA	0.378													T|||	466	0.0930511	0.1868	0.0418	5008	,	,		17831	0.0516		0.0726	False		,,,				2504	0.0665				p.T79T		Atlas-SNP	.											.	TMEM55A	34	.	0			c.A237G						PASS	.	T		694,3712	289.5+/-280.5	53,588,1562	110.0	100.0	103.0		237	-10.7	0.1	8	dbSNP_126	103	797,7803	187.9+/-235.0	34,729,3537	no	coding-synonymous	TMEM55A	NM_018710.2		87,1317,5099	CC,CT,TT		9.2674,15.7512,11.4639		79/258	92033502	1491,11515	2203	4300	6503	SO:0001819	synonymous_variant	55529	exon2			GCAAACTGTGCAC	BC033892	CCDS6252.1	8q21.3	2005-08-09			ENSG00000155099	ENSG00000155099			25452	protein-coding gene	gene with protein product		609864				12477932	Standard	NM_018710		Approved	DKFZp762O076	uc003yes.3	Q8N4L2	OTTHUMG00000164019	ENST00000285419.3:c.237A>G	8.37:g.92033502T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_018710	B2R9H4|Q68CU2	Silent	SNP	ENST00000285419.3	37	CCDS6252.1																																																																																			T|0.896;C|0.104	0.104	strong		0.378	TMEM55A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376778.1	NM_018710	
MUC4	4585	hgsc.bcm.edu	37	3	195513515	195513515	+	Missense_Mutation	SNP	C	C	T	rs201194776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513515C>T	ENST00000463781.3	-	2	5395	c.4936G>A	c.(4936-4938)Gcc>Acc	p.A1646T	MUC4_ENST00000475231.1_Missense_Mutation_p.A1646T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.N1637_T1652delNASSLSTGHATPLHVT(2)|p.A1646T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.587													.|||	3	0.000599042	0.0008	0.0014	5008	,	,		15070	0.0		0.001	False		,,,				2504	0.0				p.A1646T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	3	Deletion - In frame(2)|Substitution - Missense(1)	stomach(2)|endometrium(1)	c.G4936A						scavenged	.						29.0	35.0	33.0					3																	195513515		689	1579	2268	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4936G>A	3.37:g.195513515C>T	ENSP00000417498:p.Ala1646Thr	Somatic	639	2	0.00312989		WXS	Illumina HiSeq	Phase_I	929	162	0.174381	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.077	0.382480	0.11524	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.46;1.47	0.605	-1.21	0.09524	.	.	.	.	.	T	0.14399	0.0348	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.01281	0.0	T	0.21655	-1.0239	8	.	.	.	.	2.184	0.03881	0.2468:0.2138:0.0:0.5394	.	1646	E7ESK3	.	T	1646	ENSP00000417498:A1646T;ENSP00000420243:A1646T	.	A	-	1	0	MUC4	196997910	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.394000	0.07296	-2.601000	0.00451	-2.041000	0.00417	GCC	C|0.965;T|0.036	0.036	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAM185A	222234	hgsc.bcm.edu	37	7	102427889	102427889	+	Missense_Mutation	SNP	C	C	T	rs116082009	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:102427889C>T	ENST00000413034.2	+	7	1039	c.1039C>T	c.(1039-1041)Cgt>Tgt	p.R347C	FAM185A_ENST00000409231.3_Missense_Mutation_p.R230C	NM_001145268.1	NP_001138740	Q8N0U4	F185A_HUMAN	family with sequence similarity 185, member A	347										kidney(1)	1						GGCTGAAGTTCGTAAAGATGA	0.403													C|||	590	0.117812	0.1407	0.1542	5008	,	,		19248	0.0119		0.1948	False		,,,				2504	0.091				p.R347C		Atlas-SNP	.											.	FAM185A	10	.	0			c.C1039T						PASS	.						191.0	152.0	164.0					7																	102427889		692	1591	2283	SO:0001583	missense	222234	exon7			GAAGTTCGTAAAG	BC029175	CCDS47676.1, CCDS47677.1	7q22.1	2009-07-09			ENSG00000222011	ENSG00000222011			22412	protein-coding gene	gene with protein product							Standard	NM_001145268		Approved	MGC35361	uc011klf.2	Q8N0U4	OTTHUMG00000154140	ENST00000413034.2:c.1039C>T	7.37:g.102427889C>T	ENSP00000395340:p.Arg347Cys	Somatic	652	1	0.00153374		WXS	Illumina HiSeq	Phase_I	663	324	0.488688	NM_001145268	A8MUR7|B4DQD3|C9IZ91	Missense_Mutation	SNP	ENST00000413034.2	37	CCDS47676.1	292	0.1336996336996337	64	0.13008130081300814	66	0.18232044198895028	5	0.008741258741258742	157	0.20712401055408972	C	12.82	2.052152	0.36181	.	.	ENSG00000222011	ENST00000432852;ENST00000409231;ENST00000413034	T;T	0.45668	0.89;0.93	4.09	2.16	0.27623	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.13710	-1.0499	8	0.52906	T	0.07	0.6665	6.9447	0.24512	0.0:0.771:0.0:0.229	rs17842496;rs17842496	247;230;347	B4DMG7;Q8N0U4-3;Q8N0U4	.;.;F185A_HUMAN	C	247;230;347	ENSP00000387066:R230C;ENSP00000395340:R347C	ENSP00000387066:R230C	R	+	1	0	FAM185A	102215125	0.000000	0.05858	0.001000	0.08648	0.863000	0.49368	0.422000	0.21296	0.883000	0.36040	0.536000	0.68110	CGT	C|0.859;T|0.141	0.141	strong		0.403	FAM185A-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349482.1	NM_001145268	
BAGE2	85319	hgsc.bcm.edu	37	21	11049592	11049592	+	RNA	SNP	C	C	T	rs3906134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:11049592C>T	ENST00000470054.1	-	0	516							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CCCGGGCTGTCGCACACTGCA	0.388																																					p.A103A		Atlas-SNP	.											.	.	.	.	0			c.G309A						PASS	.						72.0	57.0	62.0					21																	11049592		692	1591	2283			85318	exon4			GGCTGTCGCACAC	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11049592C>T		Somatic	441	0	0		WXS	Illumina HiSeq	Phase_I	563	51	0.0905861	NM_182481	A8K925|Q08ER0	Silent	SNP	ENST00000470054.1	37																																																																																				C|0.750;T|0.250	0.250	strong		0.388	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
BCS1L	617	hgsc.bcm.edu	37	2	219527712	219527712	+	Silent	SNP	C	C	T	rs33946522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219527712C>T	ENST00000431802.1	+	7	1695	c.996C>T	c.(994-996)aaC>aaT	p.N332N	BCS1L_ENST00000465706.1_3'UTR|BCS1L_ENST00000392109.1_Silent_p.N332N|BCS1L_ENST00000392111.2_Silent_p.N332N|BCS1L_ENST00000392110.2_Silent_p.N332N|BCS1L_ENST00000359273.3_Silent_p.N332N|BCS1L_ENST00000412366.1_Silent_p.N332N|BCS1L_ENST00000439945.1_Silent_p.N332N			Q9Y276	BCS1_HUMAN	BC1 (ubiquinol-cytochrome c reductase) synthesis-like	332					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex III assembly (GO:0034551)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|mitochondrion organization (GO:0007005)	mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	8		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGACCACCAACCACGTTGACA	0.587													C|||	384	0.0766773	0.1248	0.0231	5008	,	,		18351	0.123		0.0258	False		,,,				2504	0.0542				p.N332N		Atlas-SNP	.											.	BCS1L	22	.	0			c.C996T						PASS	.	C	,	441,3965	214.1+/-233.5	25,391,1787	108.0	94.0	99.0		996,996	3.0	1.0	2	dbSNP_126	99	282,8318	105.8+/-166.7	5,272,4023	no	coding-synonymous,coding-synonymous	BCS1L	NM_001079866.1,NM_004328.4	,	30,663,5810	TT,TC,CC		3.2791,10.0091,5.559	,	332/420,332/420	219527712	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	617	exon8			CACCAACCACGTT	AF026849	CCDS2419.1	2q35	2014-09-17	2012-10-12		ENSG00000074582	ENSG00000074582		"""ATPases / AAA-type"", ""Mitochondrial respiratory chain complex assembly factors"""	1020	protein-coding gene	gene with protein product	"""GRACILE syndrome"", ""Bjornstad syndrome"""	603647	"""BCS1 (yeast homolog)-like"", ""BCS1-like (yeast)"", ""BCS1-like (S. cerevisiae)"""			9878253, 17314340	Standard	NM_001079866		Approved	Hs.6719, BCS, h-BCS, BJS	uc002viq.3	Q9Y276	OTTHUMG00000133114	ENST00000431802.1:c.996C>T	2.37:g.219527712C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_001257343	B3KTW9|Q7Z2V7	Silent	SNP	ENST00000431802.1	37	CCDS2419.1	165|165	0.07554945054945054|0.07554945054945054	54|54	0.10975609756097561|0.10975609756097561	12|12	0.03314917127071823|0.03314917127071823	82|82	0.14335664335664336|0.14335664335664336	17|17	0.022427440633245383|0.022427440633245383	C|C	4.146|4.146	0.025554|0.025554	0.08054|0.08054	0.100091|0.100091	0.032791|0.032791	ENSG00000074582|ENSG00000074582	ENST00000426649|ENST00000436603	.|.	.|.	.|.	4.94|4.94	2.99|2.99	0.34606|0.34606	.|.	.|.	.|.	.|.	.|.	T|T	0.00384|0.00384	0.0012|0.0012	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.09818|0.09818	-1.0657|-1.0657	3|3	.|.	.|.	.|.	1.6405|1.6405	7.6929|7.6929	0.28577|0.28577	0.0:0.6794:0.0:0.3206|0.0:0.6794:0.0:0.3206	rs33946522;rs56589807;rs57086470;rs33946522|rs33946522;rs56589807;rs57086470;rs33946522	.|.	.|.	.|.	S|I	114|114	.|.	.|.	P|T	+|+	1|2	0|0	BCS1L|BCS1L	219235956|219235956	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.603000|0.603000	0.37013|0.37013	1.118000|1.118000	0.31246|0.31246	1.307000|1.307000	0.44944|0.44944	-0.258000|-0.258000	0.10820|0.10820	CCA|ACC	C|0.932;G|0.000;T|0.068	0.068	strong		0.587	BCS1L-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336756.1	NM_004328	
UAP1L1	91373	hgsc.bcm.edu	37	9	139975195	139975195	+	Silent	SNP	C	C	T	rs41302685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139975195C>T	ENST00000409858.3	+	7	1265	c.1233C>T	c.(1231-1233)aaC>aaT	p.N411N	UAP1L1_ENST00000360271.3_Silent_p.N288N	NM_207309.2	NP_997192.2	Q3KQV9	UAP1L_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1 like 1	411							uridylyltransferase activity (GO:0070569)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CACTGAAGAACGCAGAGCCAG	0.662													C|||	399	0.0796725	0.0431	0.0519	5008	,	,		17273	0.0853		0.0755	False		,,,				2504	0.1472				p.N411N		Atlas-SNP	.											UAP1L1_ENST00000409858,NS,carcinoma,0,2	UAP1L1	46	2	0			c.C1233T						PASS	.	C		225,4181	128.2+/-165.1	2,221,1980	71.0	74.0	73.0		1233	-8.2	0.0	9	dbSNP_127	73	748,7852	173.2+/-223.7	29,690,3581	no	coding-synonymous	UAP1L1	NM_207309.2		31,911,5561	TT,TC,CC		8.6977,5.1067,7.4812		411/508	139975195	973,12033	2203	4300	6503	SO:0001819	synonymous_variant	91373	exon7			GAAGAACGCAGAG	AK022632	CCDS7028.2	9q34.3	2014-07-31	2014-07-31		ENSG00000197355	ENSG00000197355			28082	protein-coding gene	gene with protein product							Standard	NM_207309		Approved		uc010ncb.3	Q3KQV9	OTTHUMG00000020962	ENST00000409858.3:c.1233C>T	9.37:g.139975195C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_207309	A2AMJ8|Q5SPZ2|Q69YQ3|Q6ZR38	Silent	SNP	ENST00000409858.3	37	CCDS7028.2																																																																																			C|0.927;T|0.073	0.073	strong		0.662	UAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055216.2	XM_038063	
SHF	90525	hgsc.bcm.edu	37	15	45491136	45491136	+	Missense_Mutation	SNP	C	C	G	rs62026667	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45491136C>G	ENST00000290894.8	-	2	631	c.137G>C	c.(136-138)tGg>tCg	p.W46S	CTD-2651B20.7_ENST00000568314.1_RNA|CTD-2651B20.6_ENST00000563103.1_RNA|SHF_ENST00000318390.6_Missense_Mutation_p.W103S|RP11-519G16.2_ENST00000560034.1_RNA	NM_138356.2	NP_612365			Src homology 2 domain containing F											endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		CGTGAGCATCCAGGAATGGGG	0.607											OREG0023105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	198	0.0395367	0.003	0.062	5008	,	,		17412	0.001		0.1143	False		,,,				2504	0.0358				p.W46S		Atlas-SNP	.											.	SHF	27	.	0			c.G137C						PASS	.	C	SER/TRP	82,3874		2,78,1898	52.0	56.0	55.0		137	0.3	0.0	15	dbSNP_129	55	851,7485		44,763,3361	yes	missense	SHF	NM_138356.2	177	46,841,5259	GG,GC,CC		10.2087,2.0728,7.5903	benign	46/424	45491136	933,11359	1978	4168	6146	SO:0001583	missense	90525	exon2			AGCATCCAGGAAT	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"""SH2 domain containing"""	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.137G>C	15.37:g.45491136C>G	ENSP00000290894:p.Trp46Ser	Somatic	104	0	0	932	WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_138356		Missense_Mutation	SNP	ENST00000290894.8	37	CCDS10120.2	107	0.04899267399267399	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	83	0.10949868073878628	C	14.15	2.450179	0.43531	0.020728	0.102087	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390	T;T	0.43294	1.47;0.95	3.44	0.306	0.15806	.	29.593600	0.00166	N	0.000000	T	0.00496	0.0016	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.04593	-1.0940	9	0.20046	T	0.44	0.1759	2.0018	0.03469	0.2051:0.4781:0.1996:0.1172	rs62026667	46	Q7M4L6	SHF_HUMAN	S	46;46;103	ENSP00000290894:W46S;ENSP00000315978:W103S	ENSP00000290894:W46S	W	-	2	0	SHF	43278428	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.056000	0.11787	0.084000	0.17077	0.655000	0.94253	TGG	C|0.938;G|0.062	0.062	strong		0.607	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254141.2	NM_138356	
MAST3	23031	hgsc.bcm.edu	37	19	18257750	18257750	+	Silent	SNP	C	C	T	rs2072490	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18257750C>T	ENST00000262811.6	+	25	3135	c.3135C>T	c.(3133-3135)ggC>ggT	p.G1045G	AC007192.6_ENST00000600364.2_RNA	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	1045							ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						TCAAGGTGGGCCCCGCCCGGA	0.667													C|||	2697	0.538538	0.348	0.5245	5008	,	,		12768	0.6796		0.502	False		,,,				2504	0.6984				p.G1045G		Atlas-SNP	.											.	MAST3	83	.	0			c.C3135T						PASS	.			1371,2527		286,799,864	22.0	25.0	24.0		3135	-2.7	0.9	19	dbSNP_96	24	4127,4041		1117,1893,1074	yes	coding-synonymous	MAST3	NM_015016.1		1403,2692,1938	TT,TC,CC		49.4736,35.1719,45.5661		1045/1310	18257750	5498,6568	1949	4084	6033	SO:0001819	synonymous_variant	23031	exon25			GGTGGGCCCCGCC	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.3135C>T	19.37:g.18257750C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	178	100	0.561798	NM_015016	Q7LDZ8|Q9UPI0	Silent	SNP	ENST00000262811.6	37	CCDS46014.1																																																																																			C|0.495;T|0.505	0.505	strong		0.667	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150	
OGDHL	55753	hgsc.bcm.edu	37	10	50960209	50960209	+	Silent	SNP	G	G	A	rs1258184	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50960209G>A	ENST00000374103.4	-	5	649	c.564C>T	c.(562-564)ctC>ctT	p.L188L	OGDHL_ENST00000419399.1_Silent_p.L131L|OGDHL_ENST00000432695.1_5'UTR	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	188					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CCCGCAGAGAGAGGGTGTTTT	0.592													G|||	2325	0.464257	0.1407	0.4798	5008	,	,		18974	0.9107		0.4642	False		,,,				2504	0.4305				p.L188L		Atlas-SNP	.											.	OGDHL	149	.	0			c.C564T						PASS	.	G	,,	875,3531	338.4+/-305.3	95,685,1423	55.0	55.0	55.0		393,,564	-9.7	0.7	10	dbSNP_87	55	4170,4430	565.4+/-388.5	1014,2142,1144	no	coding-synonymous,utr-5,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	1109,2827,2567	AA,AG,GG		48.4884,19.8593,38.7898	,,	131/954,,188/1011	50960209	5045,7961	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon5			CAGAGAGAGGGTG	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.564C>T	10.37:g.50960209G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			G|0.567;A|0.433	0.433	strong		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
CYP2D6	1565	hgsc.bcm.edu	37	22	42526763	42526763	+	Missense_Mutation	SNP	C	C	T	rs769258	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:42526763C>T	ENST00000360608.5	-	1	145	c.31G>A	c.(31-33)Gtg>Atg	p.V11M	CYP2D6_ENST00000359033.4_Missense_Mutation_p.V11M|CYP2D6_ENST00000389970.3_Missense_Mutation_p.V11M|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000608288.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	11			V -> M (in allele CYP2D6*35; dbSNP:rs769258). {ECO:0000269|PubMed:15469410}.		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GCCACTATCACGGCCAGGGGC	0.672													C|||	84	0.0167732	0.0023	0.0274	5008	,	,		19497	0.003		0.0527	False		,,,				2504	0.0061				p.V11M		Atlas-SNP	.											.	CYP2D6	104	.	0			c.G31A	GRCh37	CM033368	CYP2D6	M	rs769258	PASS	.	C	MET/VAL,MET/VAL	36,4352		1,34,2159	41.0	40.0	40.0		31,31	-3.0	0.0	22	dbSNP_86	40	499,8091		23,453,3819	no	missense,missense	CYP2D6	NM_000106.4,NM_001025161.1	21,21	24,487,5978	TT,TC,CC		5.8091,0.8204,4.1224	possibly-damaging,possibly-damaging	11/498,11/447	42526763	535,12443	2194	4295	6489	SO:0001583	missense	1565	exon1			CTATCACGGCCAG	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.31G>A	22.37:g.42526763C>T	ENSP00000353820:p.Val11Met	Somatic	308	1	0.00324675		WXS	Illumina HiSeq	Phase_I	337	201	0.596439	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	60	0.027472527472527472	6	0.012195121951219513	15	0.04143646408839779	3	0.005244755244755245	36	0.047493403693931395	c	3.418	-0.118739	0.06838	0.008204	0.058091	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000359033	T;T;T	0.12361	2.69;2.69;2.69	3.46	-3.03	0.05429	.	1.246930	0.05772	N	0.606947	T	0.00468	0.0015	N	0.08118	0	0.09310	N	1	P;P	0.38711	0.643;0.643	B;B	0.19148	0.024;0.024	T	0.26815	-1.0092	10	0.49607	T	0.09	.	0.9967	0.01469	0.1609:0.262:0.1584:0.4187	rs769258;rs769258	11;11	Q6NXU8;Q6NWU0	.;.	M	11	ENSP00000353820:V11M;ENSP00000374620:V11M;ENSP00000351927:V11M	ENSP00000351927:V11M	V	-	1	0	CYP2D6	40856707	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-2.219000	0.01218	-0.478000	0.06823	-0.516000	0.04426	GTG	C|0.971;T|0.029	0.029	strong		0.672	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
PXDNL	137902	hgsc.bcm.edu	37	8	52323908	52323908	+	Missense_Mutation	SNP	A	A	G	rs117864200	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:52323908A>G	ENST00000356297.4	-	16	2064	c.1964T>C	c.(1963-1965)aTt>aCt	p.I655T	PXDNL_ENST00000543296.1_Missense_Mutation_p.I655T	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	655					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CATTTCCACAATCAGTGGGTC	0.493													A|||	48	0.00958466	0.0008	0.013	5008	,	,		17432	0.0		0.0278	False		,,,				2504	0.0102				p.I655T		Atlas-SNP	.											.	PXDNL	414	.	0			c.T1964C						PASS	.	A	THR/ILE	19,3901		0,19,1941	57.0	58.0	58.0		1964	2.4	0.0	8	dbSNP_132	58	209,8091		3,203,3944	yes	missense	PXDNL	NM_144651.4	89	3,222,5885	GG,GA,AA		2.5181,0.4847,1.8658	benign	655/1464	52323908	228,11992	1960	4150	6110	SO:0001583	missense	137902	exon16			TCCACAATCAGTG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1964T>C	8.37:g.52323908A>G	ENSP00000348645:p.Ile655Thr	Somatic	289	2	0.00692042		WXS	Illumina HiSeq	Phase_I	252	252	1	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	26	0.011904761904761904	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	19	0.025065963060686015	A	0.022	-1.416402	0.01136	0.004847	0.025181	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.62941	0.04;-0.01	4.46	2.41	0.29592	.	.	.	.	.	T	0.09291	0.0229	N	0.00926	-1.1	0.25894	N	0.983434	B	0.02656	0.0	B	0.04013	0.001	T	0.18713	-1.0328	9	0.02654	T	1	.	7.7251	0.28755	0.2431:0.0:0.7569:0.0	.	655	A1KZ92	PXDNL_HUMAN	T	655	ENSP00000348645:I655T;ENSP00000444865:I655T	ENSP00000348645:I655T	I	-	2	0	PXDNL	52486461	1.000000	0.71417	0.001000	0.08648	0.004000	0.04260	5.607000	0.67648	0.196000	0.20367	-0.408000	0.06270	ATT	A|0.986;G|0.014	0.014	strong		0.493	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
FICD	11153	hgsc.bcm.edu	37	12	108910962	108910962	+	Silent	SNP	C	C	T	rs2303634	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:108910962C>T	ENST00000552695.1	+	2	448	c.213C>T	c.(211-213)gcC>gcT	p.A71A	FICD_ENST00000361549.2_Silent_p.A71A|FICD_ENST00000552758.1_Silent_p.A71A	NM_007076.2	NP_009007.2	Q9BVA6	FICD_HUMAN	FIC domain containing	71					negative regulation of Rho GTPase activity (GO:0034259)|protein adenylylation (GO:0018117)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein adenylyltransferase activity (GO:0070733)			NS(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|upper_aerodigestive_tract(2)	15						CGCAGCATGCCGCCACCAAGT	0.657													C|||	199	0.0397364	0.031	0.0245	5008	,	,		18155	0.0179		0.0378	False		,,,				2504	0.0869				p.A71A		Atlas-SNP	.											FICD,NS,carcinoma,+1,1	FICD	35	1	0			c.C213T						PASS	.	C		165,4241	107.3+/-145.7	3,159,2041	37.0	34.0	35.0		213	-7.2	0.0	12	dbSNP_100	35	323,8275	110.8+/-171.2	5,313,3981	no	coding-synonymous	FICD	NM_007076.2		8,472,6022	TT,TC,CC		3.7567,3.7449,3.7527		71/459	108910962	488,12516	2203	4299	6502	SO:0001819	synonymous_variant	11153	exon2			GCATGCCGCCACC	AF049611	CCDS9116.1	12q24.1	2007-12-05				ENSG00000198855			18416	protein-coding gene	gene with protein product	"""huntingtin interacting protein 13"", ""fic S-phase protein cell division homolog (E. coli)"""					9700202	Standard	NM_007076		Approved	HYPE, HIP13	uc001tmx.1	Q9BVA6		ENST00000552695.1:c.213C>T	12.37:g.108910962C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_007076	O75406	Silent	SNP	ENST00000552695.1	37	CCDS9116.1	67	0.030677655677655676	13	0.026422764227642278	9	0.024861878453038673	15	0.026223776223776224	30	0.0395778364116095	C	0.511	-0.866325	0.02590	0.037449	0.037567	ENSG00000198855	ENST00000549641	.	.	.	5.42	-7.17	0.01511	.	.	.	.	.	T	0.03520	0.0101	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.22208	-1.0223	4	.	.	.	-16.1544	2.1527	0.03804	0.1247:0.2771:0.2894:0.3087	rs2303634	.	.	.	L	22	.	.	P	+	2	0	FICD	107435092	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-3.164000	0.00576	-0.978000	0.03533	-0.258000	0.10820	CCG	C|0.969;T|0.031	0.031	strong		0.657	FICD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404842.1	NM_007076	
MPRIP	23164	hgsc.bcm.edu	37	17	17046024	17046024	+	Missense_Mutation	SNP	C	C	A	rs3744137	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17046024C>A	ENST00000341712.4	+	8	980	c.980C>A	c.(979-981)cCa>cAa	p.P327Q	MPRIP_ENST00000395804.3_Missense_Mutation_p.P327Q|MPRIP_ENST00000395811.5_Missense_Mutation_p.P327Q|MPRIP_ENST00000444976.1_Missense_Mutation_p.P327Q			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	327	Interaction with F-actin. {ECO:0000250}.		P -> Q (in dbSNP:rs3744137). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.			actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						GGGCCCTCACCATCCAGCGAC	0.632													C|||	2227	0.444688	0.0749	0.4986	5008	,	,		17634	0.7113		0.5229	False		,,,				2504	0.5511				p.P327Q		Atlas-SNP	.											.	MPRIP	87	.	0			c.C980A						PASS	.	C	GLN/PRO,GLN/PRO	636,3770	273.4+/-271.3	54,528,1621	89.0	80.0	83.0		980,980	1.6	0.0	17	dbSNP_107	83	4518,4082	592.6+/-393.0	1191,2136,973	no	missense,missense	MPRIP	NM_015134.3,NM_201274.3	76,76	1245,2664,2594	AA,AC,CC		47.4651,14.4349,39.6279	,	327/1039,327/1026	17046024	5154,7852	2203	4300	6503	SO:0001583	missense	23164	exon8			CCTCACCATCCAG	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.980C>A	17.37:g.17046024C>A	ENSP00000342379:p.Pro327Gln	Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	275	137	0.498182	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	37	CCDS32578.1	1027	0.47023809523809523	42	0.08536585365853659	172	0.47513812154696133	396	0.6923076923076923	417	0.5501319261213721	C	3.672	-0.067284	0.07273	0.144349	0.525349	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	T;T;T;T	0.22945	1.93;2.18;2.18;2.18	5.04	1.63	0.23807	.	.	.	.	.	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B;B	0.16603	0.018;0.0	B;B	0.14578	0.011;0.001	T	0.32824	-0.9892	8	0.32370	T	0.25	.	5.4532	0.16576	0.15:0.61:0.0:0.2399	rs3744137;rs11551187;rs17794556;rs61101436;rs3744137	327;327	Q6WCQ1-2;Q6WCQ1	.;MPRIP_HUMAN	Q	327	ENSP00000400189:P327Q;ENSP00000379156:P327Q;ENSP00000379149:P327Q;ENSP00000342379:P327Q	ENSP00000342379:P327Q	P	+	2	0	MPRIP	16986749	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	0.648000	0.24828	1.113000	0.41760	0.561000	0.74099	CCA	C|0.592;A|0.408	0.408	strong		0.632	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047633	46047633	+	Missense_Mutation	SNP	A	A	G	rs8127342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46047633A>G	ENST00000397911.3	+	1	594	c.545A>G	c.(544-546)tAc>tGc	p.Y182C	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	182	25 X 5 AA repeats of C-C-X(3).		Y -> C (in dbSNP:rs8127342). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CAGCAGTCCTACTGTGTGCCT	0.592													G|||	3191	0.637181	0.5219	0.6772	5008	,	,		22988	0.6667		0.7167	False		,,,				2504	0.6524				p.Y182C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.A545G						PASS	.	G	,CYS/TYR	2344,2062	568.0+/-382.3	633,1078,492	248.0	264.0	259.0		,545	1.3	0.0	21	dbSNP_116	259	5810,2790	442.8+/-360.2	1958,1894,448	no	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,194	2591,2972,940	GG,GA,AA		32.4419,46.7998,37.3059	,benign	,182/293	46047633	8154,4852	2203	4300	6503	SO:0001583	missense	386676	exon1			AGTCCTACTGTGT	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.545A>G	21.37:g.46047633A>G	ENSP00000381009:p.Tyr182Cys	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	274	131	0.478102	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	1408	0.6446886446886447	259	0.5264227642276422	245	0.6767955801104972	364	0.6363636363636364	540	0.712401055408971	g	0	-2.837910	0.00069	0.532002	0.675581	ENSG00000221837	ENST00000397911	T	0.00768	5.72	3.45	1.28	0.21552	.	.	.	.	.	T	0.00012	0.0000	N	0.00000	-4.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35425	-0.9789	7	.	.	.	.	6.7087	0.23264	0.1159:0.5079:0.3762:0.0	rs8127342	182	P60411	KR109_HUMAN	C	182	ENSP00000381009:Y182C	.	Y	+	2	0	KRTAP10-9	44872061	0.001000	0.12720	0.004000	0.12327	0.010000	0.07245	0.351000	0.20096	0.092000	0.17331	-0.176000	0.13171	TAC	A|0.343;G|0.657	0.657	strong		0.592	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
SYTL2	54843	hgsc.bcm.edu	37	11	85448679	85448679	+	Missense_Mutation	SNP	G	G	A	rs17744245	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:85448679G>A	ENST00000528231.1	-	4	687	c.410C>T	c.(409-411)gCt>gTt	p.A137V	SYTL2_ENST00000316356.4_Missense_Mutation_p.A137V|SYTL2_ENST00000527523.1_Missense_Mutation_p.A89V|SYTL2_ENST00000389960.4_Missense_Mutation_p.A137V|SYTL2_ENST00000524452.1_Missense_Mutation_p.A137V	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	137					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CACACTGGAAGCTGGATTTAC	0.378													G|||	103	0.0205671	0.0023	0.0749	5008	,	,		20740	0.0109		0.0268	False		,,,				2504	0.0102				p.A137V		Atlas-SNP	.											.	SYTL2	231	.	0			c.C410T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	25,4381	31.7+/-61.6	0,25,2178	122.0	108.0	113.0		410,410,410	2.0	1.0	11	dbSNP_123	113	231,8367	95.2+/-157.0	2,227,4070	yes	missense,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3	64,64,64	2,252,6248	AA,AG,GG		2.6867,0.5674,1.9686	,,	137/935,137/936,137/911	85448679	256,12748	2203	4299	6502	SO:0001583	missense	54843	exon5			CTGGAAGCTGGAT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.410C>T	11.37:g.85448679G>A	ENSP00000431701:p.Ala137Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_032943	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	47	0.02152014652014652	1	0.0020325203252032522	22	0.06077348066298342	8	0.013986013986013986	16	0.021108179419525065	G	9.425	1.084066	0.20309	0.005674	0.026867	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.25414	1.86;1.87;1.88;1.8;1.86	5.06	2.0	0.26442	.	.	.	.	.	T	0.02047	0.0064	L	0.54323	1.7	0.80722	D	1	B;B;B;B	0.09022	0.002;0.002;0.001;0.002	B;B;B;B	0.13407	0.006;0.009;0.002;0.004	T	0.07139	-1.0788	8	.	.	.	.	5.1131	0.14819	0.1865:0.0:0.6437:0.1698	rs17744245;rs52819374;rs17744245	89;137;137;137	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13	.;.;SYTL2_HUMAN;.	V	137;137;137;89;137	ENSP00000374610:A137V;ENSP00000318803:A137V;ENSP00000431701:A137V;ENSP00000434010:A89V;ENSP00000435238:A137V	.	A	-	2	0	SYTL2	85126327	0.988000	0.35896	0.997000	0.53966	0.350000	0.29205	1.285000	0.33261	1.262000	0.44165	0.561000	0.74099	GCT	G|0.979;A|0.021	0.021	strong		0.378	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
BTNL2	56244	hgsc.bcm.edu	37	6	32363844	32363844	+	Silent	SNP	C	C	T	rs9268480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32363844C>T	ENST00000374993.1	-	5	1049	c.1050G>A	c.(1048-1050)caG>caA	p.Q350Q	BTNL2_ENST00000414363.1_Silent_p.Q140Q|BTNL2_ENST00000540315.1_Silent_p.Q140Q|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000454136.3_Silent_p.Q350Q|BTNL2_ENST00000544175.1_Silent_p.Q73Q|BTNL2_ENST00000374995.3_Silent_p.Q256Q|BTNL2_ENST00000429232.2_Silent_p.Q257Q	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	350	Ig-like V-type 3.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						AACTGGCCTCCTGGTAGACAT	0.468													c|||	1040	0.207668	0.1672	0.3127	5008	,	,		20109	0.1141		0.2734	False		,,,				2504	0.2168				p.Q350Q		Atlas-SNP	.											.	BTNL2	50	.	0			c.G1050A						PASS	.			520,2500		44,432,1034	79.0	84.0	82.0	http://omim.org/entry/604519|http://www.ncbi.nlm.nih.gov/pubmed?term	1050	1.4	1.0	6	dbSNP_118	82	1526,3890		200,1126,1382	no	coding-synonymous	BTNL2	NM_019602.1		244,1558,2416	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	28.1758,17.2185,24.2532		350/456	32363844	2046,6390	1510	2708	4218	SO:0001819	synonymous_variant	56244	exon5			GGCCTCCTGGTAG	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.1050G>A	6.37:g.32363844C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	119	44	0.369748	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				C|0.785;N|0.000	.	strong		0.468	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
GP6	51206	hgsc.bcm.edu	37	19	55526345	55526345	+	Missense_Mutation	SNP	T	T	G	rs1671152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55526345T>G	ENST00000417454.1	-	8	991	c.964A>C	c.(964-966)Aac>Cac	p.N322H	GP6_ENST00000310373.3_Missense_Mutation_p.K323T|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Missense_Mutation_p.N304H|CTC-550B14.7_ENST00000586845.1_RNA	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	322			N -> H (in dbSNP:rs1671152). {ECO:0000269|PubMed:11027634, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		TGACCCCCGTTTGATTTCCGG	0.662													G|||	4122	0.823083	0.6672	0.9164	5008	,	,		14866	0.9673		0.8588	False		,,,				2504	0.7822				p.K323T		Atlas-SNP	.											GP6,rectum,carcinoma,0,2	GP6	55	2	0			c.A968C						PASS	.	G	HIS/ASN,THR/LYS	2707,1215		943,821,197	23.0	26.0	25.0	http://www.ncbi.nlm.nih.gov/pubmed?term	964,968	2.7	0.0	19	dbSNP_89	25	7026,1254		2988,1050,102	yes	missense,missense	GP6	NM_016363.4,NM_001083899.1	68,78	3931,1871,299	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	15.1449,30.9791,20.2344	benign,benign	322/340,323/621	55526345	9733,2469	1961	4140	6101	SO:0001583	missense	51206	exon8			CCCCGTTTGATTT	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.964A>C	19.37:g.55526345T>G	ENSP00000394922:p.Asn322His	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_001083899	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	37	CCDS46184.1	1874|1874	0.858058608058608|0.858058608058608	338|338	0.6869918699186992|0.6869918699186992	328|328	0.9060773480662984|0.9060773480662984	562|562	0.9825174825174825|0.9825174825174825	646|646	0.8522427440633246|0.8522427440633246	G|G	0.026|0.026	-1.370532|-1.370532	0.01225|0.01225	0.690209|0.690209	0.848551|0.848551	ENSG00000088053|ENSG00000088053	ENST00000310373|ENST00000417454;ENST00000333884	T|T;T	0.00557|0.00492	6.62|7.05;7.01	2.65|2.65	2.65|2.65	0.31530|0.31530	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B|B;B	0.02656|0.02656	0.0|0.0;0.0	B|B;B	0.01281|0.01281	0.0|0.0;0.0	T|T	0.46816|0.46816	-0.9164|-0.9164	7|7	0.02654|0.31617	T|T	1|0.26	.|.	6.9339|6.9339	0.24457|0.24457	0.0:0.0:0.7258:0.2742|0.0:0.0:0.7258:0.2742	rs1671152;rs16986173;rs59836180;rs1671152|rs1671152;rs16986173;rs59836180;rs1671152	323|304;322	Q9HCN6-3|Q9HCN6-2;Q9HCN6	.|.;GPVI_HUMAN	T|H	323|322;304	ENSP00000308782:K323T|ENSP00000394922:N322H;ENSP00000334552:N304H	ENSP00000308782:K323T|ENSP00000334552:N304H	K|N	-|-	2|1	0|0	GP6|GP6	60218157|60218157	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	0.067000|0.067000	0.14510|0.14510	0.680000|0.680000	0.31366|0.31366	-0.217000|-0.217000	0.12591|0.12591	AAA|AAC	T|0.165;G|0.835	0.835	strong		0.662	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
MRPS30	10884	hgsc.bcm.edu	37	5	44809162	44809162	+	Missense_Mutation	SNP	G	G	C	rs3747479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:44809162G>C	ENST00000507110.1	+	1	136	c.98G>C	c.(97-99)tGc>tCc	p.C33S	RP11-53O19.1_ENST00000505401.1_RNA|RP11-53O19.1_ENST00000514597.1_RNA|RP11-53O19.1_ENST00000508945.1_RNA|RP11-53O19.1_ENST00000505637.1_RNA|RP11-53O19.1_ENST00000508123.1_RNA|RP11-53O19.1_ENST00000505302.1_RNA|RP11-53O19.1_ENST00000503452.1_RNA|RP11-53O19.1_ENST00000503179.1_RNA	NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	33			C -> S (in dbSNP:rs3747479). {ECO:0000269|PubMed:10640817, ECO:0000269|PubMed:11230166, ECO:0000269|Ref.2}.		apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					GAAACGACCTGCCAAGACGTC	0.672													G|||	1996	0.398562	0.2466	0.4553	5008	,	,		12993	0.5357		0.3738	False		,,,				2504	0.4479				p.C33S		Atlas-SNP	.											MRPS30_ENST00000507110,NS,carcinoma,0,4	MRPS30	90	4	0			c.G98C						PASS	.	G	SER/CYS	1150,3158		202,746,1206	10.0	12.0	11.0		98	-0.5	0.0	5	dbSNP_107	11	3110,5358		629,1852,1753	yes	missense	MRPS30	NM_016640.3	112	831,2598,2959	CC,CG,GG		36.7265,26.6945,33.3438	benign	33/440	44809162	4260,8516	2154	4234	6388	SO:0001583	missense	10884	exon1			CGACCTGCCAAGA	AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"""Mitochondrial ribosomal proteins / small subunits"""	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.98G>C	5.37:g.44809162G>C	ENSP00000424328:p.Cys33Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_016640	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	Missense_Mutation	SNP	ENST00000507110.1	37	CCDS3951.1	887	0.40613553113553114	139	0.28252032520325204	157	0.43370165745856354	306	0.534965034965035	285	0.3759894459102902	G	5.819	0.335379	0.11013	0.266945	0.367265	ENSG00000112996	ENST00000507110	T	0.16324	2.35	5.14	-0.478	0.12093	.	2.286390	0.01507	N	0.017754	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.45891	-0.9230	9	0.13853	T	0.58	2.2095	4.9665	0.14093	0.0754:0.3817:0.3416:0.2013	rs3747479	33	Q9NP92	RT30_HUMAN	S	33	ENSP00000424328:C33S	ENSP00000424328:C33S	C	+	2	0	MRPS30	44844919	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.300000	0.19156	0.066000	0.16515	0.655000	0.94253	TGC	A|0.000;C|0.396;G|0.604	0.396	strong		0.672	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640	
PABPC4L	132430	hgsc.bcm.edu	37	4	135121066	135121066	+	Missense_Mutation	SNP	T	T	G	rs11099273	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:135121066T>G	ENST00000421491.3	-	2	1365	c.1109A>C	c.(1108-1110)cAc>cCc	p.H370P	PABPC4L_ENST00000529122.2_Missense_Mutation_p.H428P			P0CB38	PAB4L_HUMAN	poly(A) binding protein, cytoplasmic 4-like	370			H -> P (in dbSNP:rs11099273).				nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)	3						TCTTTCCTAGTGTCTCTGGGC	0.463													T|||	3155	0.629992	0.6936	0.536	5008	,	,		15139	0.9841		0.329	False		,,,				2504	0.5552				p.H428P		Atlas-SNP	.											.	PABPC4L	60	.	0			c.A1283C						PASS	.						32.0	27.0	29.0					4																	135121066		692	1591	2283	SO:0001583	missense	132430	exon2			TCCTAGTGTCTCT	AY672099		4q28.3	2013-02-12				ENSG00000254535		"""RNA binding motif (RRM) containing"""	31955	protein-coding gene	gene with protein product							Standard	NM_001114734		Approved		uc010ioe.3	P0CB38		ENST00000421491.3:c.1109A>C	4.37:g.135121066T>G	ENSP00000463233:p.His370Pro	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001114734		Missense_Mutation	SNP	ENST00000421491.3	37																																																																																				T|0.365;G|0.635	0.635	strong		0.463	PABPC4L-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364399.2	NM_001114734	
HECW1	23072	hgsc.bcm.edu	37	7	43506113	43506113	+	Silent	SNP	A	A	C	rs138489968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43506113A>C	ENST00000395891.2	+	15	3464	c.2859A>C	c.(2857-2859)ccA>ccC	p.P953P	HECW1_ENST00000453890.1_Silent_p.P919P	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	953					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TGCAGTCCCCAGCGGTCAAGT	0.498													A|||	29	0.00579073	0.0023	0.0058	5008	,	,		15535	0.001		0.0169	False		,,,				2504	0.0041				p.P953P		Atlas-SNP	.											.	HECW1	540	.	0			c.A2859C						PASS	.	A		12,3884		0,12,1936	113.0	107.0	109.0		2859	-4.4	0.8	7	dbSNP_134	109	186,8096		2,182,3957	no	coding-synonymous	HECW1	NM_015052.3		2,194,5893	CC,CA,AA		2.2458,0.308,1.6259		953/1607	43506113	198,11980	1948	4141	6089	SO:0001819	synonymous_variant	23072	exon15			GTCCCCAGCGGTC	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.2859A>C	7.37:g.43506113A>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			A|0.990;C|0.010	0.010	strong		0.498	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
TCF19	6941	hgsc.bcm.edu	37	6	31129310	31129310	+	Missense_Mutation	SNP	C	C	T	rs7750641	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31129310C>T	ENST00000376257.3	+	3	1079	c.325C>T	c.(325-327)Ccc>Tcc	p.P109S	TCF19_ENST00000376255.4_Missense_Mutation_p.P109S|TCF19_ENST00000496421.1_3'UTR	NM_007109.2	NP_009040.2	Q9Y242	TCF19_HUMAN	transcription factor 19	109			P -> S (in dbSNP:rs7750641). {ECO:0000269|PubMed:14574404}.		cell proliferation (GO:0008283)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						CCCTGAAGGGCCCCCAGGAAC	0.542													C|||	119	0.023762	0.0091	0.0303	5008	,	,		16616	0.0		0.0855	False		,,,				2504	0.0				p.P109S		Atlas-SNP	.											TCF19,colon,carcinoma,0,1	TCF19	16	1	0			c.C325T						PASS	.	C	SER/PRO,SER/PRO	67,2239		1,65,1087	87.0	93.0	91.0		325,325	-1.2	0.4	6	dbSNP_116	91	592,4420		37,518,1951	yes	missense,missense	TCF19	NM_001077511.1,NM_007109.2	74,74	38,583,3038	TT,TC,CC		11.8117,2.9055,9.0052	benign,benign	109/346,109/346	31129310	659,6659	1153	2506	3659	SO:0001583	missense	6941	exon3			GAAGGGCCCCCAG	U25826	CCDS43446.1	6p21.3	2013-01-28	2009-02-05		ENSG00000137310	ENSG00000137310		"""Zinc fingers, PHD-type"""	11629	protein-coding gene	gene with protein product		600912				1868030, 8595903	Standard	NM_001077511		Approved	SC1	uc003nss.3	Q9Y242	OTTHUMG00000031274	ENST00000376257.3:c.325C>T	6.37:g.31129310C>T	ENSP00000365433:p.Pro109Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	150	68	0.453333	NM_001077511	A6NCT8|B0UY11|Q0EFA8|Q13176|Q15967|Q5SQ89|Q5STD6|Q5STF5|Q9BUM2|Q9UBH7	Missense_Mutation	SNP	ENST00000376257.3	37	CCDS43446.1	84	0.038461538461538464	7	0.014227642276422764	10	0.027624309392265192	0	0.0	67	0.08839050131926121	C	11.15	1.554187	0.27739	0.029055	0.118117	ENSG00000137310	ENST00000376257;ENST00000376255;ENST00000542218	T;T;T	0.22134	2.05;2.05;1.97	5.71	-1.19	0.09585	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.729507	0.13820	N	0.360476	T	0.05914	0.0154	L	0.56769	1.78	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35475	-0.9787	10	0.33940	T	0.23	-23.8533	4.3142	0.10984	0.21:0.3167:0.3941:0.0793	rs7750641;rs9263793;rs57999952;rs7750641	109	Q9Y242	TCF19_HUMAN	S	109;109;29	ENSP00000365433:P109S;ENSP00000365431:P109S;ENSP00000439397:P29S	ENSP00000365431:P109S	P	+	1	0	TCF19	31237289	0.018000	0.18449	0.445000	0.26908	0.921000	0.55340	-0.156000	0.10100	-0.211000	0.10124	0.549000	0.68633	CCC	C|0.947;T|0.053	0.053	strong		0.542	TCF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076595.2	NM_007109	
FAM179A	165186	hgsc.bcm.edu	37	2	29240673	29240673	+	Missense_Mutation	SNP	G	G	A	rs35166194	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29240673G>A	ENST00000379558.4	+	10	1562	c.1211G>A	c.(1210-1212)cGg>cAg	p.R404Q	FAM179A_ENST00000465300.1_Intron|FAM179A_ENST00000403861.2_Intron	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	404										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CTTCCCCTCCGGGGCAGCGGG	0.612													G|||	1030	0.205671	0.2413	0.1859	5008	,	,		20368	0.1567		0.2485	False		,,,				2504	0.1779				p.R404Q		Atlas-SNP	.											.	FAM179A	106	.	0			c.G1211A						PASS	.	G	GLN/ARG	858,3198		92,674,1262	27.0	31.0	30.0		1211	3.3	1.0	2	dbSNP_126	30	1952,6390		240,1472,2459	yes	missense	FAM179A	NM_199280.2	43	332,2146,3721	AA,AG,GG		23.3997,21.1538,22.6649	probably-damaging	404/1020	29240673	2810,9588	2028	4171	6199	SO:0001583	missense	165186	exon10			CCCTCCGGGGCAG	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.1211G>A	2.37:g.29240673G>A	ENSP00000368876:p.Arg404Gln	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	219	105	0.479452	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	454	0.2078754578754579	114	0.23170731707317074	70	0.19337016574585636	80	0.13986013986013987	190	0.25065963060686014	G	9.972	1.225871	0.22542	0.211538	0.233997	ENSG00000189350	ENST00000379558	T	0.09538	2.97	4.18	3.29	0.37713	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.53688	P	2.8999999999945736E-5	P	0.47253	0.892	B	0.35182	0.197	T	0.48163	-0.9059	8	0.39692	T	0.17	.	3.4568	0.07518	0.1891:0.2611:0.5498:0.0	rs35166194	404	Q6ZUX3	F179A_HUMAN	Q	404	ENSP00000368876:R404Q	ENSP00000368876:R404Q	R	+	2	0	FAM179A	29094177	0.258000	0.24033	0.956000	0.39512	0.038000	0.13279	1.692000	0.37731	2.312000	0.78011	0.563000	0.77884	CGG	G|0.779;A|0.221	0.221	strong		0.612	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
XPOT	11260	hgsc.bcm.edu	37	12	64812733	64812733	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:64812733G>A	ENST00000332707.5	+	6	877	c.348G>A	c.(346-348)gaG>gaA	p.E116E		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	116	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)	p.E116E(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		TTGTTACAGAGTATCTCACTA	0.438																																					p.E116E		Atlas-SNP	.											XPOT,bladder,carcinoma,0,5	XPOT	105	5	1	Substitution - coding silent(1)	kidney(1)	c.G348A						scavenged	.						113.0	107.0	109.0					12																	64812733		2203	4300	6503	SO:0001819	synonymous_variant	11260	exon6			TACAGAGTATCTC	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"""Exportins"""	12826	protein-coding gene	gene with protein product		603180	"""exportin, tRNA (nuclear export receptor for tRNAs)"""			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.348G>A	12.37:g.64812733G>A		Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	242	5	0.0206612	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	37	CCDS31852.1																																																																																			.	.	none		0.438	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235	
NEUROD1	4760	hgsc.bcm.edu	37	2	182542998	182542998	+	Missense_Mutation	SNP	G	G	T	rs8192556	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:182542998G>T	ENST00000295108.3	-	2	1047	c.590C>A	c.(589-591)cCt>cAt	p.P197H	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	197			P -> H (in dbSNP:rs8192556).		amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			GTTCTGCTCAGGCAGAAAAGT	0.622													G|||	48	0.00958466	0.0015	0.0043	5008	,	,		18263	0.0		0.0249	False		,,,				2504	0.0184				p.P197H		Atlas-SNP	.											.	NEUROD1	67	.	0			c.C590A						PASS	.	G	HIS/PRO	19,4387	29.0+/-57.7	0,19,2184	53.0	58.0	56.0		590	6.0	1.0	2	dbSNP_117	56	232,8368	94.0+/-155.9	6,220,4074	yes	missense	NEUROD1	NM_002500.3	77	6,239,6258	TT,TG,GG		2.6977,0.4312,1.9299	probably-damaging	197/357	182542998	251,12755	2203	4300	6503	SO:0001583	missense	4760	exon2			TGCTCAGGCAGAA	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"""Basic helix-loop-helix proteins"""	7762	protein-coding gene	gene with protein product	"""beta-cell E-box transactivator 2"", ""neurogenic helix-loop-helix protein NEUROD"""	601724	"""neurogenic differentiation 1"""	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.590C>A	2.37:g.182542998G>T	ENSP00000295108:p.Pro197His	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	15	0.319149	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	37	CCDS2283.1	22	0.010073260073260074	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	20	0.026385224274406333	G	13.20	2.165709	0.38217	0.004312	0.026977	ENSG00000162992	ENST00000295108	T	0.65549	-0.16	6.02	6.02	0.97574	Neurogenic differentiation factor, domain of unknown function (1);	0.000000	0.85682	D	0.000000	T	0.43831	0.1265	M	0.71581	2.175	0.80722	D	1	P	0.34757	0.467	B	0.37304	0.246	T	0.61700	-0.7009	10	0.62326	D	0.03	-29.3937	19.1109	0.93315	0.0:0.0:1.0:0.0	rs8192556;rs8192556	197	Q13562	NDF1_HUMAN	H	197	ENSP00000295108:P197H	ENSP00000295108:P197H	P	-	2	0	NEUROD1	182251243	1.000000	0.71417	0.976000	0.42696	0.958000	0.62258	6.775000	0.75018	2.850000	0.98022	0.650000	0.86243	CCT	G|0.981;T|0.019	0.019	strong		0.622	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500	
NLRP8	126205	hgsc.bcm.edu	37	19	56466227	56466227	+	Missense_Mutation	SNP	A	A	G	rs7259764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56466227A>G	ENST00000291971.3	+	3	874	c.803A>G	c.(802-804)cAg>cGg	p.Q268R	NLRP8_ENST00000590542.1_Missense_Mutation_p.Q268R	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	268	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		Q -> R (in dbSNP:rs7259764).		neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CCTGGATCTCAGGACCTCGTG	0.517													A|||	359	0.0716853	0.1241	0.062	5008	,	,		21128	0.005		0.0716	False		,,,				2504	0.0767				p.Q268R		Atlas-SNP	.											NLRP8_ENST00000291971,NS,carcinoma,+1,2	NLRP8	225	2	0			c.A803G						PASS	.	A	ARG/GLN	559,3847	252.1+/-258.6	41,477,1685	181.0	179.0	179.0		803	-2.8	0.0	19	dbSNP_116	179	511,8089	145.3+/-201.0	18,475,3807	yes	missense	NLRP8	NM_176811.2	43	59,952,5492	GG,GA,AA		5.9419,12.6872,8.227	benign	268/1049	56466227	1070,11936	2203	4300	6503	SO:0001583	missense	126205	exon3			GATCTCAGGACCT	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.803A>G	19.37:g.56466227A>G	ENSP00000291971:p.Gln268Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	153	80	0.522876	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	138	0.06318681318681318	59	0.11991869918699187	26	0.0718232044198895	1	0.0017482517482517483	52	0.06860158311345646	A	12.91	2.079765	0.36662	0.126872	0.059419	ENSG00000179709	ENST00000291971	T	0.18960	2.18	2.04	-2.85	0.05734	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.00300	0.0009	L	0.45470	1.425	0.80722	P	0.0	D;P	0.76494	0.999;0.885	D;P	0.65010	0.931;0.566	T	0.04885	-1.0920	8	0.44086	T	0.13	.	4.1677	0.10315	0.3214:0.2213:0.4573:0.0	rs7259764;rs52837562;rs58007135;rs7259764	268;268	Q86W28-2;Q86W28	.;NALP8_HUMAN	R	268	ENSP00000291971:Q268R	ENSP00000291971:Q268R	Q	+	2	0	NLRP8	61158039	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.332000	0.01109	-0.984000	0.03507	0.421000	0.28195	CAG	A|0.922;G|0.078	0.078	strong		0.517	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
ALPK2	115701	hgsc.bcm.edu	37	18	56203898	56203898	+	Missense_Mutation	SNP	T	T	G	rs3809977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56203898T>G	ENST00000361673.3	-	5	3734	c.3521A>C	c.(3520-3522)cAc>cCc	p.H1174P	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1174			H -> P (in dbSNP:rs3809977). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TGCGGGTGAGTGGGCCGTGGG	0.577													T|||	3364	0.671725	0.4675	0.6772	5008	,	,		18930	0.7966		0.7674	False		,,,				2504	0.7168				p.H1174P		Atlas-SNP	.											.	ALPK2	487	.	0			c.A3521C						PASS	.	T	PRO/HIS	2276,2130	595.4+/-388.4	597,1082,524	90.0	79.0	83.0		3521	-1.6	0.0	18	dbSNP_107	83	6601,1999	720.3+/-406.3	2550,1501,249	yes	missense	ALPK2	NM_052947.3	77	3147,2583,773	GG,GT,TT		23.2442,48.3432,31.7469	possibly-damaging	1174/2171	56203898	8877,4129	2203	4300	6503	SO:0001583	missense	115701	exon5			GGTGAGTGGGCCG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3521A>C	18.37:g.56203898T>G	ENSP00000354991:p.His1174Pro	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	1521	0.6964285714285714	212	0.43089430894308944	255	0.7044198895027625	466	0.8146853146853147	588	0.7757255936675461	T	16.11	3.030988	0.54790	0.516568	0.767558	ENSG00000198796	ENST00000361673	T	0.46063	0.88	5.51	-1.63	0.08345	.	1.463380	0.03761	N	0.258088	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	D;P	0.64830	0.994;0.937	P;B	0.62740	0.906;0.4	T	0.49716	-0.8910	9	0.42905	T	0.14	0.5345	1.0429	0.01563	0.1474:0.1691:0.3048:0.3787	rs3809977;rs59846580;rs3809977	1169;1174	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	P	1174	ENSP00000354991:H1174P	ENSP00000354991:H1174P	H	-	2	0	ALPK2	54354878	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.327000	0.07955	-0.171000	0.10797	0.496000	0.49642	CAC	T|0.316;G|0.684	0.684	strong		0.577	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
STKLD1	169436	hgsc.bcm.edu	37	9	136268897	136268897	+	Silent	SNP	G	G	A	rs36079470	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136268897G>A	ENST00000371957.3	+	15	1655	c.1548G>A	c.(1546-1548)gcG>gcA	p.A516A	C9orf96_ENST00000371955.1_Silent_p.A49A	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		516							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CCTACCCTGCGGATGGGGAAA	0.652													G|||	123	0.0245607	0.0038	0.036	5008	,	,		17206	0.001		0.0686	False		,,,				2504	0.0235				p.A516A		Atlas-SNP	.											.	C9orf96	77	.	0			c.G1548A						PASS	.	G		58,4348	56.8+/-93.2	2,54,2147	43.0	42.0	43.0		1548	-2.4	0.0	9	dbSNP_126	43	669,7931	166.5+/-218.5	35,599,3666	no	coding-synonymous	C9orf96	NM_153710.3		37,653,5813	AA,AG,GG		7.7791,1.3164,5.5897		516/681	136268897	727,12279	2203	4300	6503	SO:0001819	synonymous_variant	169436	exon15			CCCTGCGGATGGG																												ENST00000371957.3:c.1548G>A	9.37:g.136268897G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	37	CCDS35169.1																																																																																			G|0.952;A|0.048	0.048	strong		0.652	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
CLCC1	23155	hgsc.bcm.edu	37	1	109479959	109479959	+	Missense_Mutation	SNP	G	G	A	rs56223817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109479959G>A	ENST00000369971.2	-	10	1252	c.1123C>T	c.(1123-1125)Cgg>Tgg	p.R375W	CLCC1_ENST00000415331.1_Missense_Mutation_p.R325W|CLCC1_ENST00000369969.2_Missense_Mutation_p.R254W|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000302500.4_Missense_Mutation_p.R254W|CLCC1_ENST00000356970.2_Missense_Mutation_p.R375W|CLCC1_ENST00000369968.2_Missense_Mutation_p.R190W|CLCC1_ENST00000369976.1_Intron|CLCC1_ENST00000369970.3_Missense_Mutation_p.R325W|CLCC1_ENST00000348264.2_Missense_Mutation_p.R190W	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	375						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		TCCCGTGGCCGAAGTGCCTGG	0.502													G|||	28	0.00559105	0.0008	0.0101	5008	,	,		15234	0.0		0.0189	False		,,,				2504	0.001				p.R375W		Atlas-SNP	.											.	CLCC1	55	.	0			c.C1123T						PASS	.	G	TRP/ARG,TRP/ARG	20,4386	26.2+/-53.5	0,20,2183	65.0	68.0	67.0		1123,973	-3.2	0.0	1	dbSNP_129	67	211,8389	89.9+/-152.1	1,209,4090	yes	missense,missense	CLCC1	NM_001048210.1,NM_015127.3	101,101	1,229,6273	AA,AG,GG		2.4535,0.4539,1.7761	probably-damaging,probably-damaging	375/552,325/502	109479959	231,12775	2203	4300	6503	SO:0001583	missense	23155	exon10			GTGGCCGAAGTGC	AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"""Mid1-related chloride channel (yeast)"""					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.1123C>T	1.37:g.109479959G>A	ENSP00000358988:p.Arg375Trp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	88	35	0.397727	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Missense_Mutation	SNP	ENST00000369971.2	37	CCDS41362.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	G	11.51	1.659254	0.29515	0.004539	0.024535	ENSG00000121940	ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369969;ENST00000369968;ENST00000369970;ENST00000348264;ENST00000302500	T;T;T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75	5.57	-3.24	0.05094	.	1.525790	0.03219	N	0.177288	T	0.29423	0.0733	N	0.08118	0	0.09310	N	1	B;D;P;D	0.63880	0.008;0.993;0.948;0.958	B;P;P;P	0.59288	0.006;0.855;0.491;0.625	T	0.48445	-0.9035	10	0.62326	D	0.03	0.9604	16.0968	0.81132	0.062:0.6602:0.2778:0.0	rs56223817	190;254;325;375	Q96S66-4;Q96S66-3;Q96S66-2;Q96S66	.;.;.;CLCC1_HUMAN	W	375;375;325;254;190;325;190;254	ENSP00000349456:R375W;ENSP00000358988:R375W;ENSP00000411591:R325W;ENSP00000358986:R254W;ENSP00000358985:R190W;ENSP00000358987:R325W;ENSP00000337243:R190W;ENSP00000306552:R254W	ENSP00000306552:R254W	R	-	1	2	CLCC1	109281482	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.093000	0.15086	-0.797000	0.04450	-0.809000	0.03173	CGG	G|0.986;A|0.014	0.014	strong		0.502	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127	
PIGZ	80235	hgsc.bcm.edu	37	3	196674259	196674259	+	Silent	SNP	G	G	A	rs61179255	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:196674259G>A	ENST00000412723.1	-	3	1655	c.1509C>T	c.(1507-1509)acC>acT	p.T503T		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	503					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		CTGGTTGTCTGGTGAAGCTTT	0.647													G|||	528	0.105431	0.0151	0.0879	5008	,	,		16353	0.0694		0.1491	False		,,,				2504	0.2321				p.T503T		Atlas-SNP	.											.	PIGZ	34	.	0			c.C1509T						PASS	.	G		183,4223	117.1+/-155.0	1,181,2021	57.0	55.0	55.0		1509	4.2	0.9	3	dbSNP_129	55	1337,7263	259.2+/-282.6	108,1121,3071	yes	coding-synonymous	PIGZ	NM_025163.2		109,1302,5092	AA,AG,GG		15.5465,4.1534,11.6869		503/580	196674259	1520,11486	2203	4300	6503	SO:0001819	synonymous_variant	80235	exon3			TTGTCTGGTGAAG	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.1509C>T	3.37:g.196674259G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	39	25	0.641026	NM_025163	Q9H9G6	Silent	SNP	ENST00000412723.1	37	CCDS3324.1																																																																																			G|0.889;A|0.111	0.111	strong		0.647	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
MUC16	94025	hgsc.bcm.edu	37	19	9063935	9063935	+	Silent	SNP	G	G	A	rs2252675	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9063935G>A	ENST00000397910.4	-	3	23714	c.23511C>T	c.(23509-23511)agC>agT	p.S7837S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7839	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S7837S(2)|p.S3470S(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTTCAGAGCCGCTGGACTCCC	0.542													G|||	1053	0.210264	0.0628	0.2003	5008	,	,		20983	0.249		0.3101	False		,,,				2504	0.274				p.S7837S		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,3	MUC16	4315	3	3	Substitution - coding silent(3)	stomach(3)	c.C23511T						PASS	.			418,3682		24,370,1656	75.0	74.0	74.0		23511	-3.4	0.0	19	dbSNP_100	74	2390,6004		338,1714,2145	no	coding-synonymous	MUC16	NM_024690.2		362,2084,3801	AA,AG,GG		28.4727,10.1951,22.4748		7837/14508	9063935	2808,9686	2050	4197	6247	SO:0001819	synonymous_variant	94025	exon3			AGAGCCGCTGGAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.23511C>T	19.37:g.9063935G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	229	120	0.524017	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.772;A|0.228	0.228	strong		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF443	10224	hgsc.bcm.edu	37	19	12541543	12541543	+	Silent	SNP	A	A	G	rs74181783|rs79866505|rs386806904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12541543A>G	ENST00000301547.5	-	4	1640	c.1443T>C	c.(1441-1443)ctT>ctC	p.L481L	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	481					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						AGGCTTTCCCAAGTTTGCATT	0.403													.|||	228	0.0455272	0.0431	0.0331	5008	,	,		20895	0.0		0.0497	False		,,,				2504	0.1002				p.L481L		Atlas-SNP	.											.	ZNF443	63	.	0			c.T1443C						PASS	.						64.0	69.0	67.0					19																	12541543		2201	4300	6501	SO:0001819	synonymous_variant	10224	exon4			TTTCCCAAGTTTG	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1443T>C	19.37:g.12541543A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	114	44	0.385965	NM_005815		Silent	SNP	ENST00000301547.5	37	CCDS32918.1																																																																																			A|0.948;G|0.052	0.052	strong		0.403	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
REPIN1	29803	hgsc.bcm.edu	37	7	150068605	150068605	+	Missense_Mutation	SNP	G	G	A	rs17173702	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150068605G>A	ENST00000425389.2	+	1	353	c.275G>A	c.(274-276)cGt>cAt	p.R92H	REPIN1_ENST00000518462.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000444957.1_Missense_Mutation_p.R92H|REPIN1_ENST00000489432.2_Missense_Mutation_p.R149H|REPIN1_ENST00000540729.1_Missense_Mutation_p.R92H|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000518514.1_3'UTR|REPIN1_ENST00000397281.2_Missense_Mutation_p.R92H|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000482680.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	92			R -> H (in dbSNP:rs17173702).		DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			GAGTGTGGCCGTCGCTTTCGC	0.672													G|||	1164	0.232428	0.0227	0.1527	5008	,	,		14905	0.3988		0.2793	False		,,,				2504	0.3528				p.R149H		Atlas-SNP	.											.	REPIN1	74	.	0			c.G446A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	217,4035		8,201,1917	20.0	23.0	22.0		446,275,275,275	3.6	0.0	7	dbSNP_123	22	2270,6180		287,1696,2242	yes	missense,missense,missense,missense	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	29,29,29,29	295,1897,4159	AA,AG,GG		26.8639,5.1035,19.5796	probably-damaging,probably-damaging,probably-damaging,probably-damaging	149/625,92/568,92/568,92/568	150068605	2487,10215	2126	4225	6351	SO:0001583	missense	29803	exon3			GTGGCCGTCGCTT	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.275G>A	7.37:g.150068605G>A	ENSP00000388287:p.Arg92His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Missense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	546	0.25	15	0.03048780487804878	63	0.17403314917127072	243	0.42482517482517484	225	0.29683377308707126	G	10.69	1.420773	0.25639	0.051035	0.268639	ENSG00000214022	ENST00000519397;ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000461637;ENST00000425389	T;T;T;T;T;T;T;T	0.55588	0.51;2.37;2.37;2.37;2.37;2.37;2.37;2.37	5.54	3.6	0.41247	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	.	.	.	.	T	0.00012	0.0000	L	0.49778	1.585	0.47511	P	5.600000000000049E-4	B;B	0.17268	0.021;0.021	B;B	0.15052	0.012;0.012	T	0.34725	-0.9817	8	0.87932	D	0	-6.7004	4.7515	0.13063	0.1912:0.1804:0.6283:0.0	rs17173702	149;92	C9J3L7;Q9BWE0	.;REPI1_HUMAN	H	92;92;92;92;149;151;152;149;92	ENSP00000428562:R92H;ENSP00000445016:R92H;ENSP00000380451:R92H;ENSP00000407714:R92H;ENSP00000417291:R149H;ENSP00000419789:R151H;ENSP00000419872:R152H;ENSP00000388287:R92H	ENSP00000380451:R92H	R	+	2	0	REPIN1	149699538	0.000000	0.05858	0.014000	0.15608	0.772000	0.43724	0.281000	0.18810	1.305000	0.44909	0.462000	0.41574	CGT	G|0.761;C|0.000;A|0.238	0.238	strong		0.672	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
NOX3	50508	hgsc.bcm.edu	37	6	155775980	155775980	+	Silent	SNP	G	G	T	rs12195525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:155775980G>T	ENST00000159060.2	-	3	322	c.220C>A	c.(220-222)Cga>Aga	p.R74R		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	74	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		ATAAGGTTTCGACTGACAGGT	0.368													G|||	644	0.128594	0.1067	0.2291	5008	,	,		17917	0.1171		0.1044	False		,,,				2504	0.1237				p.R74R		Atlas-SNP	.											NOX3,rectum,carcinoma,+1,1	NOX3	93	1	0			c.C220A						PASS	.	G		472,3934	216.1+/-234.9	30,412,1761	65.0	65.0	65.0		220	5.9	1.0	6	dbSNP_120	65	965,7635	208.9+/-250.2	57,851,3392	no	coding-synonymous	NOX3	NM_015718.2		87,1263,5153	TT,TG,GG		11.2209,10.7127,11.0487		74/569	155775980	1437,11569	2203	4300	6503	SO:0001819	synonymous_variant	50508	exon3			GGTTTCGACTGAC	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.220C>A	6.37:g.155775980G>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	37	CCDS5250.1																																																																																			G|0.886;T|0.114	0.114	strong		0.368	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
AGBL1	123624	hgsc.bcm.edu	37	15	86807542	86807542	+	Silent	SNP	C	C	T	rs10520617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:86807542C>T	ENST00000441037.2	+	10	1097	c.1002C>T	c.(1000-1002)gcC>gcT	p.A334A	AGBL1_ENST00000421325.2_Silent_p.A334A|AGBL1_ENST00000389298.3_Silent_p.A65A	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	334					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						CTCAGTATGCCAATCACCACC	0.453													C|||	641	0.127995	0.084	0.1974	5008	,	,		19447	0.0278		0.1789	False		,,,				2504	0.1892				p.A334A		Atlas-SNP	.											.	AGBL1	151	.	0			c.C1002T						PASS	.	C		435,3967		23,389,1789	45.0	48.0	47.0		1002	3.5	0.7	15	dbSNP_119	47	1648,6948		157,1334,2807	no	coding-synonymous	AGBL1	NM_152336.2		180,1723,4596	TT,TC,CC		19.1717,9.8819,16.0255		334/1067	86807542	2083,10915	2201	4298	6499	SO:0001819	synonymous_variant	123624	exon10			GTATGCCAATCAC	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.1002C>T	15.37:g.86807542C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			C|0.875;T|0.125	0.125	strong		0.453	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
TTC21A	199223	hgsc.bcm.edu	37	3	39152345	39152345	+	Missense_Mutation	SNP	G	G	A	rs1112438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:39152345G>A	ENST00000431162.2	+	4	406	c.272G>A	c.(271-273)cGa>cAa	p.R91Q	GORASP1_ENST00000319283.3_5'Flank|TTC21A_ENST00000440121.1_Missense_Mutation_p.R91Q|TTC21A_ENST00000301819.6_Missense_Mutation_p.R91Q			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	91			R -> Q (in dbSNP:rs1112438).							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TTTACAGACCGAGAAGCAATT	0.542													G|||	1741	0.347644	0.5681	0.2911	5008	,	,		22574	0.252		0.2714	False		,,,				2504	0.2669				p.R91Q		Atlas-SNP	.											TTC21A,caecum,carcinoma,0,1	TTC21A	96	1	0			c.G272A						PASS	.	G	GLN/ARG,GLN/ARG	1928,1994		483,962,516	59.0	61.0	60.0		272,272	0.6	0.8	3	dbSNP_86	60	2377,5959		360,1657,2151	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	43,43	843,2619,2667	AA,AG,GG		28.5149,49.1586,35.1199	benign,benign	91/1273,91/1321	39152345	4305,7953	1961	4168	6129	SO:0001583	missense	199223	exon4			CAGACCGAGAAGC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.272G>A	3.37:g.39152345G>A	ENSP00000398211:p.Arg91Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_001105513	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	733	0.3356227106227106	264	0.5365853658536586	111	0.30662983425414364	154	0.2692307692307692	204	0.2691292875989446	G	15.81	2.943055	0.53079	0.491586	0.285149	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.63096	0.34;0.34;-0.02	5.74	0.555	0.17247	Tetratricopeptide-like helical (1);	1.254700	0.05507	N	0.559506	T	0.00012	0.0000	L	0.45137	1.4	0.80722	P	0.0	B;B;B;B;B	0.27416	0.178;0.068;0.116;0.07;0.068	B;B;B;B;B	0.17433	0.018;0.008;0.008;0.003;0.008	T	0.42050	-0.9474	9	0.25106	T	0.35	3.0433	2.0891	0.03652	0.2241:0.2337:0.4224:0.1198	rs1112438;rs4557093;rs17855762;rs52803003;rs59061178;rs1112438	91;91;91;91;91	Q8NDW8-6;Q8NDW8-5;Q8NDW8-7;Q8NDW8;F5H6V8	.;.;.;TT21A_HUMAN;.	Q	91	ENSP00000301819:R91Q;ENSP00000398211:R91Q;ENSP00000410882:R91Q	ENSP00000301819:R91Q	R	+	2	0	TTC21A	39127349	0.349000	0.24870	0.838000	0.33150	0.989000	0.77384	0.487000	0.22356	-0.189000	0.10482	0.655000	0.94253	CGA	G|0.662;A|0.338	0.338	strong		0.542	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
C19orf57	79173	hgsc.bcm.edu	37	19	14001206	14001206	+	Missense_Mutation	SNP	G	G	A	rs144502446	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14001206G>A	ENST00000586783.1	-	5	462	c.463C>T	c.(463-465)Ctc>Ttc	p.L155F	C19orf57_ENST00000454313.1_Missense_Mutation_p.L155F|C19orf57_ENST00000346736.2_Missense_Mutation_p.L155F|C19orf57_ENST00000591586.1_Intron			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	155					multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			GCCTCCTGGAGGGGGACCCCC	0.677													G|||	14	0.00279553	0.0023	0.0014	5008	,	,		13636	0.0		0.0089	False		,,,				2504	0.001				p.L155F		Atlas-SNP	.											.	C19orf57	34	.	0			c.C463T						PASS	.	G	PHE/LEU	5,4397		0,5,2196	28.0	34.0	32.0		463	-5.3	0.0	19	dbSNP_134	32	55,8527		0,55,4236	yes	missense	C19orf57	NM_024323.3	22	0,60,6432	AA,AG,GG		0.6409,0.1136,0.4621	benign	155/638	14001206	60,12924	2201	4291	6492	SO:0001583	missense	79173	exon6			CCTGGAGGGGGAC	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.463C>T	19.37:g.14001206G>A	ENSP00000465822:p.Leu155Phe	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	38	28	0.736842	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		10	0.004578754578754579	2	0.0040650406504065045	0	0.0	0	0.0	8	0.010554089709762533	G	0.447	-0.895879	0.02472	0.001136	0.006409	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.27402	1.67;1.67	2.65	-5.29	0.02747	.	.	.	.	.	T	0.07818	0.0196	N	0.11560	0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.09796	-1.0658	9	0.32370	T	0.25	5.6759	0.5749	0.00702	0.256:0.2127:0.323:0.2083	.	155;155	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	F	155	ENSP00000404382:L155F;ENSP00000254336:L155F	ENSP00000254336:L155F	L	-	1	0	C19orf57	13862206	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.466000	0.00229	-3.561000	0.00141	-1.672000	0.00744	CTC	G|0.994;A|0.006	0.006	strong		0.677	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
MAMSTR	284358	hgsc.bcm.edu	37	19	49218602	49218602	+	Silent	SNP	C	C	T	rs12979278	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49218602C>T	ENST00000318083.6	-	5	405	c.342G>A	c.(340-342)gcG>gcA	p.A114A	MAMSTR_ENST00000377367.3_Silent_p.A11A|MAMSTR_ENST00000594582.1_Silent_p.A11A|MAMSTR_ENST00000356751.4_Silent_p.A11A|MAMSTR_ENST00000419611.1_Silent_p.A11A			Q6ZN01	MASTR_HUMAN	MEF2 activating motif and SAP domain containing transcriptional regulator	114	Pro-rich.				positive regulation of myotube differentiation (GO:0010831)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)			endometrium(1)|ovary(1)	2						CTTGGGGGTCCGCCCTGGATC	0.622													T|||	1192	0.238019	0.1823	0.3141	5008	,	,		11288	0.0208		0.4911	False		,,,				2504	0.2229				p.A114A		Atlas-SNP	.											.	MAMSTR	36	.	0			c.G342A						PASS	.	T	,	1156,3144		217,722,1211	19.0	25.0	23.0		342,33	-7.2	0.0	19	dbSNP_121	23	4554,3938		1280,1994,972	no	coding-synonymous,coding-synonymous	MAMSTR	NM_001130915.1,NM_182574.2	,	1497,2716,2183	TT,TC,CC		46.3731,26.8837,44.6373	,	114/416,11/313	49218602	5710,7082	2150	4246	6396	SO:0001819	synonymous_variant	284358	exon5			GGGGTCCGCCCTG	AK093389	CCDS12730.1, CCDS46137.1, CCDS74415.1	19q13.33	2009-07-09			ENSG00000176909	ENSG00000176909			26689	protein-coding gene	gene with protein product	"""MEF2-activating SAP transcriptional regulator"""	610349				16818234	Standard	NM_182574		Approved	MASTR, FLJ36070	uc002pkg.2	Q6ZN01		ENST00000318083.6:c.342G>A	19.37:g.49218602C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_001130915	B7ZKX4|Q3KQU9|Q8N9Y3	Silent	SNP	ENST00000318083.6	37	CCDS46137.1																																																																																			C|0.660;T|0.340	0.340	strong		0.622	MAMSTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466179.1	NM_182574	
ATP10D	57205	hgsc.bcm.edu	37	4	47560002	47560002	+	Missense_Mutation	SNP	C	C	A	rs34208443	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:47560002C>A	ENST00000273859.3	+	12	2415	c.2146C>A	c.(2146-2148)Cca>Aca	p.P716T	AC092597.3_ENST00000508081.1_RNA	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	716			P -> T (in dbSNP:rs34208443).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						CCCTGGACAGCCATTGGCCTG	0.582													C|||	387	0.0772764	0.0272	0.0879	5008	,	,		19067	0.0079		0.1909	False		,,,				2504	0.092				p.P716T		Atlas-SNP	.											ATP10D,NS,carcinoma,-1,1	ATP10D	168	1	0			c.C2146A						PASS	.	C	THR/PRO	225,4181	134.5+/-170.7	4,217,1982	62.0	57.0	59.0		2146	0.4	0.0	4	dbSNP_126	59	1626,6974	301.2+/-305.3	163,1300,2837	yes	missense	ATP10D	NM_020453.3	38	167,1517,4819	AA,AC,CC		18.907,5.1067,14.2319	benign	716/1427	47560002	1851,11155	2203	4300	6503	SO:0001583	missense	57205	exon12			GGACAGCCATTGG	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.2146C>A	4.37:g.47560002C>A	ENSP00000273859:p.Pro716Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	211	0.09661172161172162	14	0.028455284552845527	42	0.11602209944751381	5	0.008741258741258742	150	0.19788918205804748	C	7.444	0.641307	0.14451	0.051067	0.18907	ENSG00000145246	ENST00000273859	T	0.38077	1.16	5.24	0.389	0.16269	HAD-like domain (1);	0.647822	0.16543	N	0.209830	T	0.00012	0.0000	N	0.25647	0.755	0.54753	P	1.6000000000016E-5	B	0.16802	0.019	B	0.16722	0.016	T	0.23583	-1.0184	9	0.10636	T	0.68	-8.4018	0.865	0.01202	0.1493:0.2624:0.2909:0.2974	rs34208443	716	Q9P241	AT10D_HUMAN	T	716	ENSP00000273859:P716T	ENSP00000273859:P716T	P	+	1	0	ATP10D	47254759	0.000000	0.05858	0.020000	0.16555	0.001000	0.01503	-0.414000	0.07114	0.374000	0.24650	-0.305000	0.09177	CCA	C|0.865;A|0.135	0.135	strong		0.582	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
MUC16	94025	hgsc.bcm.edu	37	19	9075635	9075635	+	Silent	SNP	G	G	A	rs2547070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9075635G>A	ENST00000397910.4	-	3	12014	c.11811C>T	c.(11809-11811)tcC>tcT	p.S3937S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3938	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTCTGTGGTGGACTCAGAAG	0.493													G|||	1054	0.210463	0.0628	0.2046	5008	,	,		20997	0.249		0.3101	False		,,,				2504	0.272				p.S3937S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C11811T						PASS	.	G		403,3505		23,357,1574	69.0	65.0	66.0		11811	-0.2	0.0	19	dbSNP_100	66	2385,5881		341,1703,2089	no	coding-synonymous	MUC16	NM_024690.2		364,2060,3663	AA,AG,GG		28.8531,10.3122,22.9013		3937/14508	9075635	2788,9386	1954	4133	6087	SO:0001819	synonymous_variant	94025	exon3			TGTGGTGGACTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11811C>T	19.37:g.9075635G>A		Somatic	295	1	0.00338983		WXS	Illumina HiSeq	Phase_I	314	143	0.455414	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.788;A|0.212	0.212	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KIAA1683	80726	hgsc.bcm.edu	37	19	18375882	18375882	+	Missense_Mutation	SNP	G	G	C	rs12608777	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18375882G>C	ENST00000600328.3	-	3	2661	c.2468C>G	c.(2467-2469)cCg>cGg	p.P823R	KIAA1683_ENST00000600359.3_Missense_Mutation_p.P777R|KIAA1683_ENST00000392413.4_Missense_Mutation_p.P823R			Q9H0B3	K1683_HUMAN	KIAA1683	823			P -> R (in dbSNP:rs12608777). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						ACAGGCTGCCGGGCATGGTCC	0.677													G|||	761	0.151957	0.0257	0.1196	5008	,	,		16464	0.3036		0.1292	False		,,,				2504	0.2127				p.P823R		Atlas-SNP	.											KIAA1683,NS,carcinoma,-1,1	KIAA1683	190	1	0			c.C2468G						scavenged	.	G	ARG/PRO,ARG/PRO,ARG/PRO	178,4228	112.1+/-150.2	1,176,2026	60.0	59.0	59.0		2468,2330,2468	-1.3	0.0	19	dbSNP_120	59	1177,7417	225.8+/-261.7	82,1013,3202	no	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	103,103,103	83,1189,5228	CC,CG,GG		13.6956,4.0399,10.4231	possibly-damaging,possibly-damaging,possibly-damaging	823/1368,777/1135,823/1181	18375882	1355,11645	2203	4297	6500	SO:0001583	missense	80726	exon3			GCTGCCGGGCATG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2468C>G	19.37:g.18375882G>C	ENSP00000470780:p.Pro823Arg	Somatic	41	1	0.0243902		WXS	Illumina HiSeq	Phase_I	32	20	0.625	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	311	0.1423992673992674	15	0.03048780487804878	35	0.09668508287292818	167	0.291958041958042	94	0.12401055408970976	G	9.122	1.009200	0.19277	0.040399	0.136956	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000411671	T;T;T	0.03580	3.96;3.96;3.88	3.87	-1.29	0.09288	.	1.359350	0.05345	N	0.530918	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P;D	0.64830	0.924;0.994	B;P	0.60886	0.269;0.88	T	0.45818	-0.9235	9	0.29301	T	0.29	-3.4881	3.2366	0.06766	0.2478:0.0:0.3126:0.4396	rs12608777;rs17797810;rs12608777	823;823	E9PDE0;Q9H0B3	.;K1683_HUMAN	R	823;823;777;437	ENSP00000376213:P823R;ENSP00000352774:P823R;ENSP00000404501:P777R	ENSP00000352774:P823R	P	-	2	0	KIAA1683	18236882	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.023000	0.12456	0.016000	0.14998	-0.373000	0.07131	CCG	G|0.879;C|0.121	0.121	strong		0.677	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
ESPNL	339768	hgsc.bcm.edu	37	2	239039057	239039057	+	Missense_Mutation	SNP	A	A	G	rs13033248	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:239039057A>G	ENST00000343063.3	+	9	1965	c.1702A>G	c.(1702-1704)Atc>Gtc	p.I568V	ESPNL_ENST00000409506.1_Missense_Mutation_p.I200V|ESPNL_ENST00000409169.1_Missense_Mutation_p.I524V|ESPNL_ENST00000477241.1_3'UTR	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	568			I -> V (in dbSNP:rs13033248). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGAGGCCTCAATCCCAGCGGC	0.711													A|||	1976	0.394569	0.3411	0.3876	5008	,	,		14221	0.4444		0.3847	False		,,,				2504	0.4305				p.I568V		Atlas-SNP	.											.	ESPNL	63	.	0			c.A1702G						PASS	.	A	VAL/ILE	1561,2787		305,951,918	9.0	12.0	11.0		1702	-2.8	0.0	2	dbSNP_121	11	3366,5156		703,1960,1598	no	missense	ESPNL	NM_194312.2	29	1008,2911,2516	GG,GA,AA		39.4978,35.9016,38.2828	benign	568/1006	239039057	4927,7943	2174	4261	6435	SO:0001583	missense	339768	exon9			GCCTCAATCCCAG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1702A>G	2.37:g.239039057A>G	ENSP00000339115:p.Ile568Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	33	32	0.969697	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	856	0.39194139194139194	179	0.3638211382113821	150	0.4143646408839779	240	0.4195804195804196	287	0.3786279683377309	A	0	-2.766231	0.00082	0.359016	0.394978	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.61274	0.12;1.23;0.81	3.37	-2.79	0.05841	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36286	-0.9754	8	0.02654	T	1	0.231	0.1428	0.00085	0.2568:0.1676:0.237:0.3387	rs13033248	524;568	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	V	568;524;200	ENSP00000339115:I568V;ENSP00000386577:I524V;ENSP00000386579:I200V	ENSP00000339115:I568V	I	+	1	0	ESPNL	238703796	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.058000	0.11750	-0.164000	0.10927	-0.548000	0.04221	ATC	A|0.615;G|0.385	0.385	strong		0.711	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103153765	103153765	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:103153765T>G	ENST00000375735.2	+	73	10985	c.10841T>G	c.(10840-10842)cTt>cGt	p.L3614R	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L3621R	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3614					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CGTGATCAGCTTCCGTCTTGG	0.328																																					p.L3621R		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10862G						PASS	.						69.0	68.0	68.0					11																	103153765		1829	4067	5896	SO:0001583	missense	79659	exon74			ATCAGCTTCCGTC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10841T>G	11.37:g.103153765T>G	ENSP00000364887:p.Leu3614Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	136	29	0.213235	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.978729	0.53720	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.08634	3.07;3.07	5.44	5.44	0.79542	Dynein heavy chain (1);	2.073920	0.01925	N	0.040832	T	0.18173	0.0436	M	0.66297	2.02	0.37386	D	0.912237	B;B	0.24043	0.096;0.078	B;B	0.31442	0.13;0.116	T	0.44205	-0.9343	10	0.20046	T	0.44	.	14.4816	0.67587	0.0:0.0:0.0:1.0	.	3614;3621	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	R	3614;3621	ENSP00000364887:L3614R;ENSP00000381167:L3621R	ENSP00000364887:L3614R	L	+	2	0	DYNC2H1	102658975	1.000000	0.71417	0.989000	0.46669	0.970000	0.65996	3.813000	0.55636	2.062000	0.61559	0.377000	0.23210	CTT	.	.	none		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
SLC6A17	388662	hgsc.bcm.edu	37	1	110709719	110709719	+	Silent	SNP	T	T	C	rs35600013|rs7527375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110709719T>C	ENST00000331565.4	+	2	653	c.168T>C	c.(166-168)gaT>gaC	p.D56D	RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000443008.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	56					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		AGGAGCTGGATGCAGAGGACC	0.607													C|||	1968	0.392971	0.4652	0.353	5008	,	,		14134	0.2143		0.5249	False		,,,				2504	0.3722				p.D56D		Atlas-SNP	.											.	SLC6A17	86	.	0			c.T168C						PASS	.	C	,VAL/ILE	2258,2148		577,1104,522	72.0	58.0	63.0		168,292	-7.0	0.0	1	dbSNP_116	63	4519,4081		1273,1973,1054	no	coding-synonymous,missense	SLC6A17,LOC100130800	NM_001010898.2,XM_001719118.1	,29	1850,3077,1576	CC,CT,TT		47.4535,48.7517,47.8933	,	56/728,98/154	110709719	6777,6229	2203	4300	6503	SO:0001819	synonymous_variant	388662	exon2			GCTGGATGCAGAG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.168T>C	1.37:g.110709719T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	105	42	0.4	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	CCDS30799.1																																																																																			T|0.518;C|0.482	0.482	strong		0.607	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
HLA-A	3105	hgsc.bcm.edu	37	6	29910663	29910663	+	Missense_Mutation	SNP	G	G	A	rs707910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29910663G>A	ENST00000396634.1	+	4	544	c.203G>A	c.(202-204)aGg>aAg	p.R68K	HLA-A_ENST00000376806.5_Missense_Mutation_p.R68K|HLA-A_ENST00000376809.5_Missense_Mutation_p.R68K|HLA-A_ENST00000376802.2_Missense_Mutation_p.R68K			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	68	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCGAGCCAGAGGATGGAGCCG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	454	0.090655	0.0847	0.0476	5008	,	,		14754	0.0188		0.1262	False		,,,				2504	0.1667				p.R68K		Atlas-SNP	.											.	HLA-A	89	.	0			c.G203A						PASS	.	G	LYS/ARG	347,4057		17,313,1872	48.0	46.0	47.0		203	2.8	0.4	6	dbSNP_86	47	1395,7203		130,1135,3034	no	missense	HLA-A	NM_002116.7	26	147,1448,4906	AA,AG,GG		16.2247,7.8792,13.3979	benign	68/366	29910663	1742,11260	2202	4299	6501	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCCAGAGGATGGA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.203G>A	6.37:g.29910663G>A	ENSP00000379873:p.Arg68Lys	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	289	108	0.373702	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	168	0.07692307692307693	39	0.07926829268292683	17	0.04696132596685083	10	0.017482517482517484	102	0.1345646437994723	.	13.11	2.139534	0.37728	0.078792	0.162247	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00816	5.66;5.66;5.66;5.66	3.72	2.85	0.33270	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.236115	0.21148	U	0.079368	T	0.02047	0.0064	M	0.80508	2.5	0.58432	P	5.000000000032756E-6	P;B;B;B;B	0.51147	0.942;0.0;0.0;0.0;0.0	D;B;B;B;B	0.74348	0.983;0.001;0.002;0.001;0.004	T	0.23547	-1.0185	9	0.87932	D	0	.	7.302	0.26426	0.1248:0.0:0.8752:0.0	rs707910;rs2230979;rs3200124;rs9260131;rs16896268;rs41541315	68;68;68;68;68	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	K	68	ENSP00000379873:R68K;ENSP00000366002:R68K;ENSP00000366005:R68K;ENSP00000365998:R68K	ENSP00000348012:R68K	R	+	2	0	HLA-A	30018642	0.002000	0.14202	0.442000	0.26870	0.608000	0.37181	0.867000	0.27968	0.936000	0.37367	0.478000	0.44815	AGG	A|0.112;G|0.888	0.112	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
FMN2	56776	hgsc.bcm.edu	37	1	240256822	240256822	+	Silent	SNP	C	C	A	rs10926124	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:240256822C>A	ENST00000319653.9	+	1	1643	c.1413C>A	c.(1411-1413)gcC>gcA	p.A471A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	471					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AGCACCGGGCCGACGGCGGCC	0.741													C|||	1652	0.329872	0.09	0.3357	5008	,	,		11042	0.3006		0.5249	False		,,,				2504	0.4796				p.A471A		Atlas-SNP	.											FMN2,NS,carcinoma,+1,1	FMN2	451	1	0			c.C1413A						scavenged	.	C		701,3587		91,519,1534	10.0	14.0	13.0		1413	-7.9	0.0	1	dbSNP_120	13	4311,4019		1186,1939,1040	no	coding-synonymous	FMN2	NM_020066.4		1277,2458,2574	AA,AC,CC		48.2473,16.3479,39.721		471/1723	240256822	5012,7606	2144	4165	6309	SO:0001819	synonymous_variant	56776	exon1			CCGGGCCGACGGC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1413C>A	1.37:g.240256822C>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			C|0.617;A|0.383	0.383	strong		0.741	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
GPATCH1	55094	hgsc.bcm.edu	37	19	33608733	33608733	+	Silent	SNP	C	C	A	rs2287681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33608733C>A	ENST00000170564.2	+	16	2513	c.2199C>A	c.(2197-2199)acC>acA	p.T733T		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	733					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					CAATACAGACCGTCAACAAAG	0.463													A|||	1810	0.361422	0.2746	0.4899	5008	,	,		18763	0.4831		0.2396	False		,,,				2504	0.3875				p.T733T	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C2199A						PASS	.	A		1141,3265	716.3+/-408.6	148,845,1210	81.0	80.0	80.0		2199	-4.8	0.0	19	dbSNP_100	80	2117,6483	716.2+/-406.1	258,1601,2441	yes	coding-synonymous	GPATCH1	NM_018025.2		406,2446,3651	AA,AC,CC		24.6163,25.8965,25.05		733/932	33608733	3258,9748	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon16			ACAGACCGTCAAC	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.2199C>A	19.37:g.33608733C>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.699;A|0.301	0.301	strong		0.463	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
MYH13	8735	hgsc.bcm.edu	37	17	10236465	10236465	+	Silent	SNP	G	G	A	rs2240579	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10236465G>A	ENST00000418404.3	-	18	2263	c.2100C>T	c.(2098-2100)aaC>aaT	p.N700N	RP11-401O9.3_ENST00000577743.1_RNA|MYH13_ENST00000252172.4_Silent_p.N700N			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	700	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CGAGGACCCCGTTACAGCGCA	0.572													G|||	2146	0.428514	0.2292	0.5836	5008	,	,		19498	0.3968		0.6362	False		,,,				2504	0.407				p.N700N		Atlas-SNP	.											MYH13_ENST00000252172,NS,carcinoma,0,2	MYH13	533	2	0			c.C2100T						PASS	.	G		1315,2543		249,817,863	28.0	34.0	32.0		2100	-1.6	1.0	17	dbSNP_98	32	5181,2643		1796,1589,527	no	coding-synonymous	MYH13	NM_003802.2		2045,2406,1390	AA,AG,GG		33.7807,34.085,44.3931		700/1939	10236465	6496,5186	1929	3912	5841	SO:0001819	synonymous_variant	8735	exon19			GACCCCGTTACAG	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.2100C>T	17.37:g.10236465G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	29	9	0.310345	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			G|0.544;A|0.455	0.455	strong		0.572	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
ATF5	22809	hgsc.bcm.edu	37	19	50435998	50435998	+	Silent	SNP	C	C	T	rs34877198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50435998C>T	ENST00000423777.2	+	3	875	c.498C>T	c.(496-498)tgC>tgT	p.C166C	NUP62_ENST00000422090.2_5'Flank|MIR4751_ENST00000578027.1_RNA|ATF5_ENST00000595125.1_Silent_p.C166C|CTC-326K19.6_ENST00000451973.1_Intron	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	166	Interaction with PTP4A1. {ECO:0000250}.				multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|transcription corepressor activity (GO:0003714)			NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	CCATCTACTGCCGCAACGAGG	0.677													C|||	415	0.0828674	0.0688	0.0591	5008	,	,		7755	0.0942		0.0666	False		,,,				2504	0.1237				p.C166C	GBM(48;768 989 9196 9511 26329)	Atlas-SNP	.											.	ATF5	27	.	0			c.C498T						PASS	.	C	,	328,4076		12,304,1886	22.0	19.0	20.0		498,498	1.9	0.2	19	dbSNP_126	20	685,7909		24,637,3636	no	coding-synonymous,coding-synonymous	ATF5	NM_001193646.1,NM_012068.5	,	36,941,5522	TT,TC,CC		7.9707,7.4478,7.7935	,	166/283,166/283	50435998	1013,11985	2202	4297	6499	SO:0001819	synonymous_variant	22809	exon4			CTACTGCCGCAAC	AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"""basic leucine zipper proteins"""	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.498C>T	19.37:g.50435998C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Silent	SNP	ENST00000423777.2	37	CCDS12789.1																																																																																			C|0.924;T|0.076	0.076	strong		0.677	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2		
AATF	26574	hgsc.bcm.edu	37	17	35346641	35346641	+	Silent	SNP	T	T	C	rs1045056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:35346641T>C	ENST00000225402.5	+	7	1496	c.1245T>C	c.(1243-1245)tcT>tcC	p.S415S		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	415	RB1 and SP1 binding.				apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				CCAAGCGCTCTGTCTATCGAG	0.493													T|||	785	0.156749	0.0628	0.1542	5008	,	,		18574	0.0357		0.3419	False		,,,				2504	0.2198				p.S415S	NSCLC(49;901 1159 19183 41572 46244)	Atlas-SNP	.											.	AATF	36	.	0			c.T1245C						PASS	.	T		424,3982	204.8+/-226.9	25,374,1804	190.0	189.0	190.0		1245	3.9	1.0	17	dbSNP_86	190	2733,5867	435.9+/-358.1	440,1853,2007	no	coding-synonymous	AATF	NM_012138.3		465,2227,3811	CC,CT,TT		31.7791,9.6232,24.2734		415/561	35346641	3157,9849	2203	4300	6503	SO:0001819	synonymous_variant	26574	exon7			GCGCTCTGTCTAT	AF083208	CCDS32632.1	17q12	2014-05-06			ENSG00000108270	ENSG00000275700			19235	protein-coding gene	gene with protein product		608463				11027528, 10783144	Standard	NM_012138		Approved	DED, CHE-1, CHE1, BFR2	uc002hni.3	Q9NY61	OTTHUMG00000188458	ENST00000225402.5:c.1245T>C	17.37:g.35346641T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	109	68	0.623853	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Silent	SNP	ENST00000225402.5	37	CCDS32632.1																																																																																			T|0.782;C|0.218	0.218	strong		0.493	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138	
IGFN1	91156	hgsc.bcm.edu	37	1	201183363	201183363	+	Silent	SNP	C	C	T	rs2282415	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201183363C>T	ENST00000335211.4	+	13	8917	c.8787C>T	c.(8785-8787)gcC>gcT	p.A2929A	IGFN1_ENST00000451870.2_Silent_p.A472A|IGFN1_ENST00000295591.8_Silent_p.A89A	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	472						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CGGGGGAGGCCGCCACACTCT	0.637													T|||	1628	0.32508	0.2542	0.3184	5008	,	,		15865	0.3095		0.3479	False		,,,				2504	0.4182				p.A2929A		Atlas-SNP	.											.	IGFN1	220	.	0			c.C8787T						PASS	.	T		1188,3218	690.3+/-405.2	151,886,1166	50.0	39.0	43.0		8787	-5.4	0.0	1	dbSNP_100	43	2867,5731	652.2+/-400.9	492,1883,1924	no	coding-synonymous	IGFN1	NM_001164586.1		643,2769,3090	TT,TC,CC		33.345,26.9632,31.1827		2929/3709	201183363	4055,8949	2203	4299	6502	SO:0001819	synonymous_variant	91156	exon13			GGAGGCCGCCACA	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.8787C>T	1.37:g.201183363C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	701	0.320970695970696	132	0.2682926829268293	114	0.3149171270718232	191	0.3339160839160839	264	0.3482849604221636	T	7.400	0.632592	0.14322	0.269632	0.33345	ENSG00000163395	ENST00000412892	.	.	.	3.39	-5.38	0.02673	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.37842	-0.9688	3	.	.	.	.	6.0299	0.19675	0.1971:0.5084:0.0:0.2945	rs2282415;rs17424119;rs58385923;rs2282415	.	.	.	C	347	.	.	R	+	1	0	IGFN1	199449986	0.000000	0.05858	0.009000	0.14445	0.156000	0.22039	-3.675000	0.00396	-1.165000	0.02786	-0.817000	0.03123	CGC	C|0.687;T|0.313	0.313	strong		0.637	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905132	1905132	+	Silent	SNP	G	G	A	rs3735876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:1905132G>A	ENST00000398564.1	+	29	3813	c.3813G>A	c.(3811-3813)tcG>tcA	p.S1271S	ARHGEF10_ENST00000521927.1_3'UTR|ARHGEF10_ENST00000262112.6_Silent_p.S1242S|ARHGEF10_ENST00000518288.1_Silent_p.S1270S|ARHGEF10_ENST00000520359.1_Silent_p.S1208S|ARHGEF10_ENST00000349830.3_Silent_p.S1246S			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1271	Ser-rich.				centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		TGGGAGATTCGCTGGGATCGA	0.577													G|||	1843	0.368011	0.2133	0.2349	5008	,	,		18564	0.5714		0.4016	False		,,,				2504	0.4274				p.S1246S		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.G3738A						PASS	.	G		1172,3234	413.7+/-336.6	160,852,1191	134.0	127.0	129.0		3738	-11.2	0.0	8	dbSNP_107	129	3323,5277	495.2+/-374.0	630,2063,1607	no	coding-synonymous	ARHGEF10	NM_014629.2		790,2915,2798	AA,AG,GG		38.6395,26.6001,34.561		1246/1345	1905132	4495,8511	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon29			AGATTCGCTGGGA	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3813G>A	8.37:g.1905132G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				G|0.648;A|0.352	0.352	strong		0.577	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
MCOLN3	55283	hgsc.bcm.edu	37	1	85488030	85488030	+	Silent	SNP	G	G	A	rs2028304	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:85488030G>A	ENST00000370589.2	-	10	1201	c.1149C>T	c.(1147-1149)ctC>ctT	p.L383L	WDR63_ENST00000370596.1_Intron|MCOLN3_ENST00000341115.4_Silent_p.L327L|MCOLN3_ENST00000474447.1_5'UTR	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	383					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		CAAGCCACACGAGCATGGTAG	0.393													A|||	3987	0.796126	0.8298	0.7522	5008	,	,		21851	0.7331		0.84	False		,,,				2504	0.8016				p.L383L		Atlas-SNP	.											.	MCOLN3	74	.	0			c.C1149T						PASS	.	A		3677,729	301.3+/-286.8	1533,611,59	85.0	80.0	81.0		1149	-11.5	0.2	1	dbSNP_94	81	7384,1216	244.3+/-273.6	3157,1070,73	no	coding-synonymous	MCOLN3	NM_018298.9		4690,1681,132	AA,AG,GG		14.1395,16.5456,14.9546		383/554	85488030	11061,1945	2203	4300	6503	SO:0001819	synonymous_variant	55283	exon10			CCACACGAGCATG	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1149C>T	1.37:g.85488030G>A		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	183	183	1	NM_018298	Q5T4H5|Q5T4H6|Q9NV09	Silent	SNP	ENST00000370589.2	37	CCDS701.1																																																																																			G|0.174;A|0.826	0.826	strong		0.393	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298	
ACSL1	2180	hgsc.bcm.edu	37	4	185701549	185701549	+	Silent	SNP	G	G	T	rs1803898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:185701549G>T	ENST00000515030.1	-	5	739	c.414C>A	c.(412-414)atC>atA	p.I138I	ACSL1_ENST00000504900.1_Silent_p.I138I|ACSL1_ENST00000281455.2_Silent_p.I138I|ACSL1_ENST00000513317.1_Silent_p.I138I|ACSL1_ENST00000437665.3_5'UTR|ACSL1_ENST00000454703.2_5'UTR|ACSL1_ENST00000504342.1_Silent_p.I138I|ACSL1_ENST00000507295.1_Intron			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	138					adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	AGCCCTTCTGGATCAGTGCTG	0.463													G|||	805	0.160743	0.0303	0.1729	5008	,	,		18206	0.0645		0.3489	False		,,,				2504	0.2342				p.I138I		Atlas-SNP	.											.	ACSL1	77	.	0			c.C414A						PASS	.	G		323,4083	170.9+/-201.2	9,305,1889	134.0	136.0	135.0		414	4.0	1.0	4	dbSNP_89	135	2890,5710	452.5+/-363.0	474,1942,1884	no	coding-synonymous	ACSL1	NM_001995.2		483,2247,3773	TT,TG,GG		33.6047,7.3309,24.704		138/699	185701549	3213,9793	2203	4300	6503	SO:0001819	synonymous_variant	2180	exon5			CTTCTGGATCAGT	BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	6.2.1.3	"""Acyl-CoA synthetase family"""	3569	protein-coding gene	gene with protein product	"""lignoceroyl-CoA synthase"", ""long-chain fatty-acid-coenzyme A ligase 1"""	152425	"""fatty-acid-Coenzyme A ligase, long-chain 2"""	FACL2		2341402, 1531127	Standard	XM_005262828		Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.414C>A	4.37:g.185701549G>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Silent	SNP	ENST00000515030.1	37	CCDS3839.1																																																																																			G|0.787;T|0.213	0.213	strong		0.463	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	
C18orf8	29919	hgsc.bcm.edu	37	18	21109250	21109250	+	Silent	SNP	T	T	C	rs1788825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21109250T>C	ENST00000269221.3	+	15	1514	c.1404T>C	c.(1402-1404)ttT>ttC	p.F468F	C18orf8_ENST00000590868.1_Silent_p.F420F	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	468						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGTCAGCCTTTGTGGAAAAGA	0.552													C|||	4159	0.830471	0.9599	0.7781	5008	,	,		18838	0.9236		0.6531	False		,,,				2504	0.7791				p.F468F		Atlas-SNP	.											.	C18orf8	58	.	0			c.T1404C						PASS	.	C		4011,395	199.4+/-223.0	1823,365,15	64.0	59.0	61.0		1404	0.9	0.0	18	dbSNP_89	61	5565,3035	466.3+/-366.7	1812,1941,547	no	coding-synonymous	C18orf8	NM_013326.3		3635,2306,562	CC,CT,TT		35.2907,8.965,26.3724		468/658	21109250	9576,3430	2203	4300	6503	SO:0001819	synonymous_variant	29919	exon15			AGCCTTTGTGGAA	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"""colon cancer associated protein Mic1"", ""macrophage inhibitory cytokine 1"""					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.1404T>C	18.37:g.21109250T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_013326	Q9BU17|Q9Y5M0	Silent	SNP	ENST00000269221.3	37	CCDS32803.1																																																																																			T|0.236;G|0.000;C|0.764	0.764	strong		0.552	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134240	32134240	+	Silent	SNP	C	C	T	rs2388982	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32134240C>T	ENST00000312561.4	+	4	765	c.351C>T	c.(349-351)aaC>aaT	p.N117N	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	117																	TTACCCAAAACGTATGGTTGA	0.413													T|||	3635	0.725839	0.7118	0.7608	5008	,	,		23740	0.7827		0.6928	False		,,,				2504	0.6953				p.N117N		Atlas-SNP	.											.	.	.	.	0			c.C351T						PASS	.	T		3109,1297	440.2+/-345.9	1097,915,191	77.0	72.0	73.0		351	2.1	0.0	12	dbSNP_100	73	5964,2636	426.0+/-355.2	2066,1832,402	no	coding-synonymous	C12orf35	NM_018169.3		3163,2747,593	TT,TC,CC		30.6512,29.4371,30.2399		117/1748	32134240	9073,3933	2203	4300	6503	SO:0001819	synonymous_variant	55196	exon4			CCAAAACGTATGG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.351C>T	12.37:g.32134240C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	165	78	0.472727	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	CCDS8725.2																																																																																			C|0.283;T|0.717	0.717	strong		0.413	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
SPATA21	374955	hgsc.bcm.edu	37	1	16730308	16730308	+	Missense_Mutation	SNP	G	G	T	rs41269193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16730308G>T	ENST00000335496.1	-	10	1397	c.915C>A	c.(913-915)caC>caA	p.H305Q	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Missense_Mutation_p.H282Q	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	305							calcium ion binding (GO:0005509)	p.H305Q(1)		breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		TGTGGGGGTTGTGGGGAGCCA	0.572													G|||	256	0.0511182	0.0061	0.0677	5008	,	,		17205	0.0685		0.0736	False		,,,				2504	0.0593				p.H305Q		Atlas-SNP	.											SPATA21,NS,carcinoma,0,1	SPATA21	47	1	1	Substitution - Missense(1)	stomach(1)	c.C915A						scavenged	.	G	GLN/HIS	66,4340	62.3+/-99.4	2,62,2139	88.0	90.0	89.0		915	-4.0	0.4	1	dbSNP_127	89	583,8017	155.7+/-209.7	29,525,3746	yes	missense	SPATA21	NM_198546.1	24	31,587,5885	TT,TG,GG		6.7791,1.498,4.99	benign	305/470	16730308	649,12357	2203	4300	6503	SO:0001583	missense	374955	exon10			GGGGTTGTGGGGA		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.915C>A	1.37:g.16730308G>T	ENSP00000335612:p.His305Gln	Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	163	64	0.392638	NM_198546	B9EK40|F5GXP5	Missense_Mutation	SNP	ENST00000335496.1	37	CCDS172.1	124	0.056776556776556776	4	0.008130081300813009	29	0.08011049723756906	39	0.06818181818181818	52	0.06860158311345646	G	9.308	1.054863	0.19907	0.01498	0.067791	ENSG00000187144	ENST00000491418;ENST00000335496;ENST00000540400	T;T;T	0.62788	1.03;0.0;-0.0	4.84	-4.0	0.04057	.	1.010520	0.07943	N	0.979693	T	0.02767	0.0083	N	0.22421	0.69	0.09310	N	1	B;B	0.29805	0.257;0.167	B;B	0.26864	0.074;0.034	T	0.03773	-1.1005	10	0.30078	T	0.28	-1.0246	8.3285	0.32171	0.0:0.1622:0.5541:0.2837	rs41269193	282;305	F5GXP5;Q7Z572	.;SPT21_HUMAN	Q	13;305;282	ENSP00000420753:H13Q;ENSP00000335612:H305Q;ENSP00000440046:H282Q	ENSP00000335612:H305Q	H	-	3	2	SPATA21	16602895	0.084000	0.21492	0.360000	0.25837	0.924000	0.55760	-0.795000	0.04580	-0.546000	0.06216	-0.410000	0.06199	CAC	G|0.944;T|0.056	0.056	strong		0.572	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
FCGBP	8857	hgsc.bcm.edu	37	19	40368391	40368391	+	Silent	SNP	G	G	A	rs76288738	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40368391G>A	ENST00000221347.6	-	28	12964	c.12957C>T	c.(12955-12957)gaC>gaT	p.D4319D		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4319						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGCAAAGAATGTCACGGTCCC	0.622													G|||	594	0.11861	0.264	0.0447	5008	,	,		26515	0.0516		0.0557	False		,,,				2504	0.1084				p.D4319D		Atlas-SNP	.											.	FCGBP	416	.	0			c.C12957T						PASS	.						176.0	178.0	177.0					19																	40368391		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon28			AAGAATGTCACGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12957C>T	19.37:g.40368391G>A		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	488	79	0.161885	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.967;A|0.033	0.033	strong		0.622	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
MUC20	200958	hgsc.bcm.edu	37	3	195452799	195452799	+	Missense_Mutation	SNP	C	C	T	rs2550232		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195452799C>T	ENST00000447234.2	+	2	1451	c.1325C>T	c.(1324-1326)aCa>aTa	p.T442I	MUC20_ENST00000436408.1_Missense_Mutation_p.T442I|MUC20_ENST00000320736.6_Missense_Mutation_p.T271I|MUC20_ENST00000445522.2_Missense_Mutation_p.T407I	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	442			T -> I (in dbSNP:rs2550232). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14565953, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.T442I(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GCCTCAGACACAGATCTCATC	0.532																																					p.T271I		Atlas-SNP	.											MUC20,NS,carcinoma,0,1	MUC20	84	1	1	Substitution - Missense(1)	stomach(1)	c.C812T						PASS	.						32.0	28.0	29.0					3																	195452799		2010	4148	6158	SO:0001583	missense	200958	exon3			CAGACACAGATCT	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1325C>T	3.37:g.195452799C>T	ENSP00000414350:p.Thr442Ile	Somatic	565	1	0.00176991		WXS	Illumina HiSeq	Phase_I	549	285	0.519126	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	C	5.403	0.259635	0.10239	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.13657	2.99;2.99;3.16;2.57	4.27	-2.63	0.06133	.	1.775520	0.02976	N	0.144951	T	0.06690	0.0171	N	0.11201	0.11	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.31280	-0.9949	9	0.12430	T	0.62	5.5294	5.5723	0.17204	0.0:0.4472:0.1347:0.4182	rs2550232;rs3906442	271	E9PH32	.	I	442;271;442;407	ENSP00000414350:T442I;ENSP00000325431:T271I;ENSP00000396774:T442I;ENSP00000405629:T407I	ENSP00000325431:T271I	T	+	2	0	MUC20	196938470	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.576000	0.05854	-0.731000	0.04862	-0.291000	0.09656	ACA	C|0.500;T|0.500	0.500	weak		0.532	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
FAN1	22909	hgsc.bcm.edu	37	15	31229420	31229420	+	Silent	SNP	T	T	C	rs2955795	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:31229420T>C	ENST00000362065.4	+	14	3306	c.3015T>C	c.(3013-3015)caT>caC	p.H1005H		NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	1005	VRR-NUC.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						AAGTCTGCCATGTGGTTGCAG	0.438								Direct reversal of damage					T|||	2289	0.457069	0.1089	0.4654	5008	,	,		17523	0.8294		0.4473	False		,,,				2504	0.5481				p.H1005H		Atlas-SNP	.											.	FAN1	77	.	0			c.T3015C						PASS	.	T		741,3663	303.5+/-288.0	71,599,1532	110.0	109.0	109.0		3015	-10.6	0.1	15	dbSNP_101	109	3787,4813	536.4+/-383.0	814,2159,1327	no	coding-synonymous	FAN1	NM_014967.4		885,2758,2859	CC,CT,TT		44.0349,16.8256,34.8201		1005/1018	31229420	4528,8476	2202	4300	6502	SO:0001819	synonymous_variant	22909	exon14			CTGCCATGTGGTT		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.3015T>C	15.37:g.31229420T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	95	31	0.326316	NM_014967	A8K4M2|Q86WU8	Silent	SNP	ENST00000362065.4	37	CCDS32186.1																																																																																			T|0.603;C|0.397	0.397	strong		0.438	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967	
ZNF280A	129025	hgsc.bcm.edu	37	22	22869209	22869209	+	Missense_Mutation	SNP	C	C	G	rs362124	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22869209C>G	ENST00000302097.3	-	2	998	c.746G>C	c.(745-747)gGc>gCc	p.G249A	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	249			G -> A (in dbSNP:rs362124). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9074928}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		CATTGCCAGGCCAGACTCATT	0.403													C|||	2371	0.473442	0.2383	0.732	5008	,	,		18879	0.4147		0.7038	False		,,,				2504	0.4315				p.G249A		Atlas-SNP	.											.	ZNF280A	67	.	0			c.G746C						PASS	.	C	ALA/GLY	1357,3049	445.5+/-347.7	220,917,1066	126.0	115.0	119.0		746	-2.8	0.0	22	dbSNP_79	119	5855,2745	677.8+/-403.4	2009,1837,454	yes	missense	ZNF280A	NM_080740.3	60	2229,2754,1520	GG,GC,CC		31.9186,30.7989,44.5487	possibly-damaging	249/543	22869209	7212,5794	2203	4300	6503	SO:0001583	missense	129025	exon2			GCCAGGCCAGACT	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.746G>C	22.37:g.22869209C>G	ENSP00000302855:p.Gly249Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	1156	0.5293040293040293	127	0.258130081300813	254	0.7016574585635359	244	0.42657342657342656	531	0.7005277044854882	C	9.455	1.091525	0.20471	0.307989	0.680814	ENSG00000169548	ENST00000302097	T	0.01185	5.21	3.66	-2.85	0.05734	.	.	.	.	.	T	0.00012	0.0000	M	0.61703	1.905	0.80722	P	0.0	P	0.37141	0.584	B	0.35114	0.196	T	0.07347	-1.0777	8	0.49607	T	0.09	0.0112	2.5252	0.04689	0.4699:0.2772:0.1536:0.0994	rs362124;rs695335;rs16989246;rs17846524;rs17859597	249	P59817	Z280A_HUMAN	A	249	ENSP00000302855:G249A	ENSP00000302855:G249A	G	-	2	0	ZNF280A	21199209	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.278000	0.02809	-0.404000	0.07610	-0.165000	0.13383	GGC	C|0.454;G|0.546	0.546	strong		0.403	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
OR52H1	390067	hgsc.bcm.edu	37	11	5566489	5566489	+	Missense_Mutation	SNP	C	C	T	rs10769054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5566489C>T	ENST00000322653.4	-	1	290	c.265G>A	c.(265-267)Gca>Aca	p.A89T	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	89			A -> T (in dbSNP:rs10769054).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATACTGAGTGCTTTAGGCACA	0.473													T|||	1940	0.38738	0.4713	0.5144	5008	,	,		23870	0.0853		0.5775	False		,,,				2504	0.2996				p.A89T		Atlas-SNP	.											.	OR52H1	46	.	0			c.G265A						PASS	.	T	THR/ALA	2043,2359	610.5+/-391.6	493,1057,651	86.0	80.0	82.0		265	2.0	1.0	11	dbSNP_120	82	5204,3390	501.7+/-375.5	1569,2066,662	yes	missense	OR52H1	NM_001005289.1	58	2062,3123,1313	TT,TC,CC		39.4461,46.4107,44.2367	benign	89/321	5566489	7247,5749	2201	4297	6498	SO:0001583	missense	390067	exon1			TGAGTGCTTTAGG	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.265G>A	11.37:g.5566489C>T	ENSP00000326259:p.Ala89Thr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	121	69	0.570248	NM_001005289	B9EH26|Q6IF79	Missense_Mutation	SNP	ENST00000322653.4	37	CCDS31386.1	904	0.4139194139194139	219	0.4451219512195122	186	0.5138121546961326	58	0.10139860139860139	441	0.5817941952506597	T	9.564	1.119258	0.20877	0.464107	0.605539	ENSG00000181616	ENST00000322653	T	0.03004	4.08	5.56	2.04	0.26737	GPCR, rhodopsin-like superfamily (1);	1.365940	0.04472	N	0.376211	T	0.00012	0.0000	N	0.02960	-0.455	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35475	-0.9787	9	0.37606	T	0.19	.	5.3019	0.15783	0.0:0.3117:0.1448:0.5434	rs10769054;rs52834035;rs57868016;rs10769054	89	Q8NGJ2	O52H1_HUMAN	T	89	ENSP00000326259:A89T	ENSP00000326259:A89T	A	-	1	0	OR52H1	5523065	0.000000	0.05858	0.985000	0.45067	0.854000	0.48673	-0.302000	0.08221	0.088000	0.17205	-0.269000	0.10298	GCA	C|0.520;T|0.480	0.480	strong		0.473	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
CTTN	2017	hgsc.bcm.edu	37	11	70253475	70253475	+	Silent	SNP	C	C	T	rs2298397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:70253475C>T	ENST00000301843.8	+	3	278	c.72C>T	c.(70-72)acC>acT	p.T24T	CTTN_ENST00000346329.3_Silent_p.T24T|CTTN_ENST00000376561.3_Silent_p.T24T|CTTN_ENST00000527622.1_3'UTR	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	24					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		ACTGGGAGACCGACCCTGATT	0.572													C|||	706	0.140974	0.0325	0.2651	5008	,	,		16440	0.1062		0.2376	False		,,,				2504	0.136				p.T24T		Atlas-SNP	.											.	CTTN	162	.	0			c.C72T						PASS	.	C	,,	356,4002		15,326,1838	21.0	23.0	22.0		72,72,72	-11.0	0.1	11	dbSNP_100	22	1849,6689		197,1455,2617	no	coding-synonymous,coding-synonymous,coding-synonymous	CTTN	NM_001184740.1,NM_005231.3,NM_138565.2	,,	212,1781,4455	TT,TC,CC		21.6561,8.1689,17.0983	,,	24/635,24/551,24/514	70253475	2205,10691	2179	4269	6448	SO:0001819	synonymous_variant	2017	exon3			GGAGACCGACCCT	AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"""ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"""	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.72C>T	11.37:g.70253475C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_001184740	Q8N707|Q96H99	Silent	SNP	ENST00000301843.8	37	CCDS41680.1	356	0.163003663003663	20	0.04065040650406504	89	0.24585635359116023	67	0.11713286713286714	180	0.23746701846965698	C	4.787	0.146369	0.09134	0.081689	0.216561	ENSG00000085733	ENST00000415461	.	.	.	5.48	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999998	.	.	.	.	.	.	T	0.11767	-1.0574	3	.	.	.	-39.5588	1.2588	0.01997	0.271:0.1249:0.1798:0.4243	rs2298397;rs3209200;rs11546011;rs17334986;rs17410320;rs2298397	.	.	.	L	6	.	.	P	+	2	0	CTTN	69931123	0.000000	0.05858	0.084000	0.20598	0.566000	0.35808	-4.692000	0.00198	-3.381000	0.00175	-0.749000	0.03505	CCG	C|0.847;T|0.153	0.153	strong		0.572	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565	
FAM184B	27146	hgsc.bcm.edu	37	4	17690072	17690072	+	Missense_Mutation	SNP	T	T	C	rs61741063	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:17690072T>C	ENST00000265018.3	-	7	1783	c.1571A>G	c.(1570-1572)cAg>cGg	p.Q524R		NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	524										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						GCTGCAGTGCTGGCGGCCTAA	0.453													T|||	81	0.0161741	0.0023	0.0173	5008	,	,		14996	0.0		0.0209	False		,,,				2504	0.046				p.Q524R		Atlas-SNP	.											FAM184B,colon,carcinoma,+1,1	FAM184B	38	1	0			c.A1571G						PASS	.	T	ARG/GLN	5,1379		0,5,687	145.0	137.0	140.0		1571	1.3	0.0	4	dbSNP_129	140	91,3091		2,87,1502	yes	missense	FAM184B	NM_015688.1	43	2,92,2189	CC,CT,TT		2.8598,0.3613,2.1025	possibly-damaging	524/1061	17690072	96,4470	692	1591	2283	SO:0001583	missense	27146	exon7			CAGTGCTGGCGGC		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.1571A>G	4.37:g.17690072T>C	ENSP00000265018:p.Gln524Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	134	64	0.477612	NM_015688		Missense_Mutation	SNP	ENST00000265018.3	37	CCDS47033.1	24	0.01098901098901099	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	16	0.021108179419525065	T	6.018	0.371697	0.11409	0.003613	0.028598	ENSG00000047662	ENST00000265018	T	0.31769	1.48	5.36	1.3	0.21679	.	2.532610	0.01336	N	0.011418	T	0.09686	0.0238	N	0.08118	0	0.09310	N	1	D	0.53885	0.963	P	0.50896	0.653	T	0.35450	-0.9788	10	0.17832	T	0.49	1.3019	10.7448	0.46175	0.0:0.0:0.4863:0.5137	.	524	Q9ULE4	F184B_HUMAN	R	524	ENSP00000265018:Q524R	ENSP00000265018:Q524R	Q	-	2	0	FAM184B	17299170	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.864000	0.04254	0.004000	0.14682	-0.316000	0.08728	CAG	T|0.986;C|0.014	0.014	strong		0.453	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
ZNF594	84622	hgsc.bcm.edu	37	17	5087040	5087040	+	Missense_Mutation	SNP	A	A	G	rs9908414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5087040A>G	ENST00000399604.4	-	1	652	c.512T>C	c.(511-513)aTt>aCt	p.I171T	ZNF594_ENST00000575779.1_Missense_Mutation_p.I171T			Q96JF6	ZN594_HUMAN	zinc finger protein 594	171			I -> T (in dbSNP:rs9908414).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CTGATGTATAATAAGATTTGA	0.338													a|||	1134	0.226438	0.1233	0.4265	5008	,	,		20145	0.0972		0.4354	False		,,,				2504	0.1421				p.I171T		Atlas-SNP	.											ZNF594,caecum,carcinoma,0,1	ZNF594	89	1	0			c.T512C						PASS	.						80.0	83.0	82.0					17																	5087040		1993	4200	6193	SO:0001583	missense	84622	exon2			TGTATAATAAGAT	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.512T>C	17.37:g.5087040A>G	ENSP00000382513:p.Ile171Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	604	0.2765567765567766	69	0.1402439024390244	157	0.43370165745856354	51	0.08916083916083917	327	0.4313984168865435	a	0.001	-4.054948	0.00002	.	.	ENSG00000180626	ENST00000399604	T	0.37584	1.19	2.29	-2.72	0.05968	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46871	-0.9160	8	0.08837	T	0.75	.	6.3503	0.21373	0.5162:0.0:0.4838:0.0	rs9908414;rs17178125;rs52818653;rs58970192;rs9908414	171	Q96JF6	ZN594_HUMAN	T	171	ENSP00000382513:I171T	ENSP00000382513:I171T	I	-	2	0	ZNF594	5027764	0.000000	0.05858	0.203000	0.23512	0.000000	0.00434	-1.675000	0.01947	-0.853000	0.04136	-1.319000	0.01295	ATT	A|0.710;G|0.290	0.290	strong		0.338	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
WDR76	79968	hgsc.bcm.edu	37	15	44120559	44120559	+	Missense_Mutation	SNP	T	T	G	rs678084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:44120559T>G	ENST00000263795.6	+	2	527	c.457T>G	c.(457-459)Tcc>Gcc	p.S153A	WDR76_ENST00000381246.2_Missense_Mutation_p.S89A	NM_001167941.1|NM_024908.3	NP_001161413.1|NP_079184.2	Q9H967	WDR76_HUMAN	WD repeat domain 76	153			S -> A (in dbSNP:rs678084). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17041588}.							breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)	20		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)		TACCACACCATCCCTGGTAAG	0.398													G|||	4160	0.830671	0.7073	0.8963	5008	,	,		17943	1.0		0.8131	False		,,,				2504	0.7945				p.S153A		Atlas-SNP	.											.	WDR76	34	.	0			c.T457G						PASS	.	G	ALA/SER,ALA/SER	3254,1142	401.9+/-332.2	1197,860,141	66.0	57.0	60.0		265,457	2.5	0.5	15	dbSNP_83	60	7028,1568	287.7+/-298.4	2854,1320,124	yes	missense,missense	WDR76	NM_001167941.1,NM_024908.3	99,99	4051,2180,265	GG,GT,TT		18.241,25.9782,20.859	benign,benign	89/563,153/627	44120559	10282,2710	2198	4298	6496	SO:0001583	missense	79968	exon2			ACACCATCCCTGG	AK023035	CCDS10106.1, CCDS53938.1	15q15.3	2013-01-09			ENSG00000092470	ENSG00000092470		"""WD repeat domain containing"""	25773	protein-coding gene	gene with protein product						12860291	Standard	NM_024908		Approved	FLJ12973	uc001zti.2	Q9H967	OTTHUMG00000060143	ENST00000263795.6:c.457T>G	15.37:g.44120559T>G	ENSP00000263795:p.Ser153Ala	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_024908	A0MNP5|Q05CI4	Missense_Mutation	SNP	ENST00000263795.6	37	CCDS10106.1	1850	0.8470695970695971	348	0.7073170731707317	320	0.8839779005524862	572	1.0	610	0.8047493403693932	G	11.19	1.564843	0.27915	0.740218	0.81759	ENSG00000092470	ENST00000263795;ENST00000381246;ENST00000452115	D;D;T	0.82344	-1.58;-1.6;0.97	4.5	2.54	0.30619	.	0.420675	0.22264	N	0.062379	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26258	-1.0108	9	0.27082	T	0.32	-14.7988	3.2832	0.06922	0.0959:0.1722:0.5539:0.1781	rs678084;rs17846489;rs17859552;rs52824676;rs61046551;rs678084	153	Q9H967	WDR76_HUMAN	A	153;89;89	ENSP00000263795:S153A;ENSP00000370645:S89A;ENSP00000404665:S89A	ENSP00000263795:S153A	S	+	1	0	WDR76	41907851	0.980000	0.34600	0.524000	0.27887	0.632000	0.37999	1.393000	0.34497	0.235000	0.21160	-0.215000	0.12644	TCC	T|0.202;G|0.798	0.798	strong		0.398	WDR76-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133482.2	NM_024908	
ART4	420	hgsc.bcm.edu	37	12	14993439	14993439	+	Missense_Mutation	SNP	C	C	T	rs11276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:14993439C>T	ENST00000228936.4	-	2	1174	c.793G>A	c.(793-795)Gac>Aac	p.D265N	RP11-233G1.4_ENST00000444324.2_RNA|C12orf60_ENST00000527783.1_Intron	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	265			N -> D (in Do(b), Hy1 and Hy2; dbSNP:rs11276). {ECO:0000269|Ref.3}.		arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)	p.D265N(1)		large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						TGCAACCAGTCTCCTCTTGGG	0.453													T|||	1466	0.292732	0.2685	0.3746	5008	,	,		19820	0.0982		0.3728	False		,,,				2504	0.3855				p.D265N		Atlas-SNP	.											ART4,colon,carcinoma,0,2	ART4	27	2	1	Substitution - Missense(1)	stomach(1)	c.G793A	GRCh37	CM003671	ART4	M	rs11276	scavenged	.	T	ASN/ASP	1230,3176	705.8+/-407.3	175,880,1148	78.0	77.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	793	1.1	1.0	12	dbSNP_52	77	3400,5200	640.5+/-399.6	701,1998,1601	yes	missense	ART4	NM_021071.2	23	876,2878,2749	TT,TC,CC		39.5349,27.9165,35.599	benign	265/315	14993439	4630,8376	2203	4300	6503	SO:0001583	missense	420	exon2			ACCAGTCTCCTCT	X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"""CD molecules"", ""Blood group antigens"""	726	protein-coding gene	gene with protein product		110600	"""Dombrock blood group"", ""ADP-ribosyltransferase 4 (DO blood group)"", ""ADP-ribosyltransferase 4"""	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.793G>A	12.37:g.14993439C>T	ENSP00000228936:p.Asp265Asn	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	193	98	0.507772	NM_021071	Q9BZ50|Q9BZ51|Q9HB06	Missense_Mutation	SNP	ENST00000228936.4	37	CCDS8668.1	611	0.27976190476190477	138	0.2804878048780488	147	0.40607734806629836	54	0.0944055944055944	272	0.35883905013192613	T	0.009	-1.812577	0.00600	0.279165	0.395349	ENSG00000111339	ENST00000228936;ENST00000420600	T;T	0.07114	3.22;3.22	4.31	1.07	0.20283	.	0.341865	0.30060	N	0.010520	T	0.00012	0.0000	.	.	.	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.44205	-0.9343	8	0.02654	T	1	-12.09	0.5532	0.00666	0.1885:0.2815:0.1651:0.3649	rs11276;rs1044829;rs3168584;rs17377780;rs52837548;rs57198415;rs11276	265	A8K6J7	.	N	265;248	ENSP00000228936:D265N;ENSP00000405689:D248N	ENSP00000228936:D265N	D	-	1	0	ART4	14884706	0.575000	0.26692	0.956000	0.39512	0.157000	0.22087	0.311000	0.19380	-0.052000	0.13311	-0.254000	0.11334	GAC	C|0.688;T|0.312	0.312	strong		0.453	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071	
TMTC1	83857	hgsc.bcm.edu	37	12	29689157	29689157	+	Silent	SNP	C	C	T	rs36070392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:29689157C>T	ENST00000539277.1	-	11	1828	c.1770G>A	c.(1768-1770)tcG>tcA	p.S590S	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000256062.5_Silent_p.S482S|TMTC1_ENST00000552618.1_Silent_p.S614S|TMTC1_ENST00000381224.2_Silent_p.S544S|TMTC1_ENST00000551659.1_Silent_p.S652S	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	590						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					CAGCCAATAACGAAGCTAAGC	0.338													C|||	85	0.0169728	0.0	0.0591	5008	,	,		19647	0.0089		0.003	False		,,,				2504	0.0327				p.S590S		Atlas-SNP	.											.	TMTC1	147	.	0			c.G1770A						PASS	.	C	,	11,4395	19.1+/-41.9	1,9,2193	161.0	149.0	153.0		1770,1446	-11.3	0.0	12	dbSNP_126	153	65,8535	38.8+/-94.9	1,63,4236	no	coding-synonymous,coding-synonymous	TMTC1	NM_001193451.1,NM_175861.3	,	2,72,6429	TT,TC,CC		0.7558,0.2497,0.5843	,	590/883,482/775	29689157	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	83857	exon11			CAATAACGAAGCT		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.1770G>A	12.37:g.29689157C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Silent	SNP	ENST00000539277.1	37	CCDS53772.1																																																																																			C|0.993;T|0.007	0.007	strong		0.338	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	
SYT8	90019	hgsc.bcm.edu	37	11	1857751	1857751	+	Missense_Mutation	SNP	C	C	G	rs3741231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1857751C>G	ENST00000381968.3	+	6	783	c.655C>G	c.(655-657)Cca>Gca	p.P219A	SYT8_ENST00000341958.3_Missense_Mutation_p.P205A|TNNI2_ENST00000381911.1_5'Flank|SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381906.1_5'Flank	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	219					acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GCTCCGTCTGCCACTGGGCAC	0.662													C|||	1692	0.337859	0.2398	0.3732	5008	,	,		14859	0.3026		0.3926	False		,,,				2504	0.4254				p.P219A		Atlas-SNP	.											.	SYT8	29	.	0			c.C655G						PASS	.	C	ALA/PRO	1150,3254		163,824,1215	23.0	27.0	26.0		655	2.3	0.0	11	dbSNP_107	26	3269,5323		656,1957,1683	yes	missense	SYT8	NM_138567.3	27	819,2781,2898	GG,GC,CC		38.047,26.1126,34.0028	probably-damaging	219/402	1857751	4419,8577	2202	4296	6498	SO:0001583	missense	90019	exon6			CGTCTGCCACTGG	AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"""Synaptotagmins"""	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.655C>G	11.37:g.1857751C>G	ENSP00000371394:p.Pro219Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	738|738	0.33791208791208793|0.33791208791208793	115|115	0.23373983739837398|0.23373983739837398	141|141	0.38950276243093923|0.38950276243093923	177|177	0.3094405594405594|0.3094405594405594	305|305	0.4023746701846966|0.4023746701846966	c|c	14.91|14.91	2.675253|2.675253	0.47781|0.47781	0.261126|0.261126	0.38047|0.38047	ENSG00000149043|ENSG00000149043	ENST00000381978|ENST00000381968;ENST00000341958	.|T;T	.|0.09350	.|2.99;2.99	3.28|3.28	2.33|2.33	0.28932|0.28932	.|C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.62266|0.62266	1.93|1.93	0.29145|0.29145	P|P	0.878737|0.878737	.|P;P	.|0.39282	.|0.666;0.666	.|B;B	.|0.33339	.|0.162;0.162	T|T	0.46992|0.46992	-0.9151|-0.9151	4|8	.|0.59425	.|D	.|0.04	.|.	8.09|8.09	0.30795|0.30795	0.0:0.745:0.1598:0.0952|0.0:0.745:0.1598:0.0952	rs3741231;rs57303263|rs3741231;rs57303263	.|219;205	.|Q8NBV8;A6NCR4	.|SYT8_HUMAN;.	G|A	217|219;205	.|ENSP00000371394:P219A;ENSP00000343691:P205A	.|ENSP00000343691:P205A	A|P	+|+	2|1	0|0	SYT8|SYT8	1814327|1814327	0.099000|0.099000	0.21834|0.21834	0.015000|0.015000	0.15790|0.15790	0.505000|0.505000	0.33919|0.33919	1.232000|1.232000	0.32636|0.32636	0.459000|0.459000	0.27016|0.27016	0.313000|0.313000	0.20887|0.20887	GCC|CCA	C|0.667;G|0.333	0.333	strong		0.662	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
CHGB	1114	hgsc.bcm.edu	37	20	5903067	5903067	+	Missense_Mutation	SNP	T	T	A	rs6085324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:5903067T>A	ENST00000378961.4	+	4	481	c.277T>A	c.(277-279)Tcg>Acg	p.S93T		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	93			S -> T (in dbSNP:rs6085324). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)	p.S93T(1)		breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						AGCTGATGCCTCGGAAGCCCA	0.493													T|||	1165	0.232628	0.0749	0.2392	5008	,	,		18246	0.379		0.2594	False		,,,				2504	0.2628				p.S93T		Atlas-SNP	.											CHGB,colon,carcinoma,0,2	CHGB	112	2	1	Substitution - Missense(1)	stomach(1)	c.T277A						PASS	.	T	THR/SER	530,3876	240.6+/-251.3	39,452,1712	52.0	53.0	53.0		277	0.7	0.0	20	dbSNP_114	53	2285,6315	378.2+/-338.8	307,1671,2322	yes	missense	CHGB	NM_001819.2	58	346,2123,4034	AA,AT,TT		26.5698,12.0291,21.6439	possibly-damaging	93/678	5903067	2815,10191	2203	4300	6503	SO:0001583	missense	1114	exon4			GATGCCTCGGAAG		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.277T>A	20.37:g.5903067T>A	ENSP00000368244:p.Ser93Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	119	72	0.605042	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	529	0.24221611721611722	48	0.0975609756097561	78	0.2154696132596685	206	0.36013986013986016	197	0.2598944591029024	T	9.771	1.172828	0.21704	0.120291	0.265698	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.02067	4.47;4.47	4.26	0.681	0.17986	.	0.988393	0.08223	N	0.978839	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B	0.17268	0.021	B	0.19666	0.026	T	0.41179	-0.9523	9	0.25106	T	0.35	-4.0E-4	3.7604	0.08602	0.1617:0.1884:0.0:0.6498	rs6085324	93	P05060	SCG1_HUMAN	T	93;73	ENSP00000368244:S93T;ENSP00000416643:S73T	ENSP00000368244:S93T	S	+	1	0	CHGB	5851067	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.677000	0.25262	0.081000	0.16988	0.460000	0.39030	TCG	T|0.776;A|0.224	0.224	strong		0.493	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
HIST1H2BF	8343	hgsc.bcm.edu	37	6	26199903	26199903	+	Silent	SNP	C	C	T	rs34961555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26199903C>T	ENST00000359985.1	+	1	156	c.117C>T	c.(115-117)tcC>tcT	p.S39S	HIST1H2AD_ENST00000341023.1_5'Flank|HIST1H3D_ENST00000356476.2_5'Flank|HIST1H3D_ENST00000377831.5_5'Flank	NM_003522.3	NP_003513.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bf	39					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(7)|upper_aerodigestive_tract(3)	17		all_hematologic(11;0.196)				AGAGCTATTCCGTGTACGTGT	0.547													C|||	88	0.0175719	0.0038	0.0259	5008	,	,		20850	0.0		0.0646	False		,,,				2504	0.0				p.S39S		Atlas-SNP	.											.	HIST1H2BF	25	.	0			c.C117T						PASS	.	C		83,4323		1,81,2121	219.0	201.0	207.0		117	-7.8	0.1	6	dbSNP_126	207	653,7947		26,601,3673	no	coding-synonymous	HIST1H2BF	NM_003522.3		27,682,5794	TT,TC,CC		7.593,1.8838,5.6589		39/127	26199903	736,12270	2203	4300	6503	SO:0001819	synonymous_variant	8343	exon1			CTATTCCGTGTAC	Z80779	CCDS4592.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197846	ENSG00000277224		"""Histones / Replication-dependent"""	4752	protein-coding gene	gene with protein product		602804	"""H2B histone family, member G"", ""histone 1, H2bf"""	H2BFG		9119399, 12408966	Standard	NM_003522		Approved	H2B/g	uc003ngx.3	P62807	OTTHUMG00000014445	ENST00000359985.1:c.117C>T	6.37:g.26199903C>T		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	308	150	0.487013	NM_003522	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000359985.1	37	CCDS4592.1																																																																																			C|0.953;T|0.047	0.047	strong		0.547	HIST1H2BF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040108.1	NM_003522	
CHGB	1114	hgsc.bcm.edu	37	20	5903894	5903894	+	Silent	SNP	A	A	G	rs236153	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:5903894A>G	ENST00000378961.4	+	4	1308	c.1104A>G	c.(1102-1104)gaA>gaG	p.E368E		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	368						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GAGGAAGTGAAGAATACAGGG	0.512													G|||	2580	0.515176	0.6573	0.5231	5008	,	,		20454	0.5288		0.3499	False		,,,				2504	0.4734				p.E368E		Atlas-SNP	.											.	CHGB	112	.	0			c.A1104G						PASS	.	G		2743,1663	505.2+/-366.1	871,1001,331	103.0	103.0	103.0		1104	-4.0	0.1	20	dbSNP_79	103	3092,5508	657.7+/-401.5	551,1990,1759	no	coding-synonymous	CHGB	NM_001819.2		1422,2991,2090	GG,GA,AA		35.9535,37.744,44.8639		368/678	5903894	5835,7171	2203	4300	6503	SO:0001819	synonymous_variant	1114	exon4			AAGTGAAGAATAC		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1104A>G	20.37:g.5903894A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Silent	SNP	ENST00000378961.4	37	CCDS13092.1																																																																																			A|0.533;G|0.467	0.467	strong		0.512	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
DKKL1	27120	hgsc.bcm.edu	37	19	49867913	49867913	+	Missense_Mutation	SNP	G	G	A	rs919364	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49867913G>A	ENST00000221498.2	+	2	490	c.85G>A	c.(85-87)Gct>Act	p.A29T	DKKL1_ENST00000594268.1_Intron|TEAD2_ENST00000601519.1_5'Flank|TEAD2_ENST00000593945.1_5'Flank|TEAD2_ENST00000311227.2_5'Flank|TEAD2_ENST00000539846.1_5'Flank	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	29			A -> T (in dbSNP:rs919364).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GATCCCCTCCGCTGCAGCTCC	0.627													A|||	1300	0.259585	0.3457	0.2104	5008	,	,		15578	0.1766		0.3111	False		,,,				2504	0.2106				p.A29T		Atlas-SNP	.											.	DKKL1	23	.	0			c.G85A						PASS	.	A	THR/ALA,,THR/ALA	1429,2977	683.3+/-404.2	252,925,1026	58.0	51.0	54.0		85,,85	-0.6	0.1	19	dbSNP_86	54	2728,5872	680.6+/-403.7	423,1882,1995	yes	missense,utr-5,missense	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	58,,58	675,2807,3021	AA,AG,GG		31.7209,32.433,31.9622	benign,,benign	29/212,,29/243	49867913	4157,8849	2203	4300	6503	SO:0001583	missense	27120	exon2			CCCTCCGCTGCAG	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.85G>A	19.37:g.49867913G>A	ENSP00000221498:p.Ala29Thr	Somatic	241	2	0.00829876		WXS	Illumina HiSeq	Phase_I	180	180	1	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	587	0.26877289377289376	172	0.34959349593495936	85	0.23480662983425415	108	0.1888111888111888	222	0.2928759894459103	A	6.302	0.423838	0.11928	0.32433	0.317209	ENSG00000104901	ENST00000221498	T	0.12879	2.64	3.36	-0.557	0.11800	.	1.217580	0.06218	N	0.686307	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43572	-0.9383	9	0.02654	T	1	1.3103	0.2643	0.00223	0.2897:0.1597:0.283:0.2677	rs919364;rs60520264;rs919364	29	Q9UK85	DKKL1_HUMAN	T	29	ENSP00000221498:A29T	ENSP00000221498:A29T	A	+	1	0	DKKL1	54559725	0.000000	0.05858	0.107000	0.21349	0.832000	0.47134	-1.722000	0.01868	-0.298000	0.08921	-0.361000	0.07541	GCT	G|0.704;A|0.296	0.296	strong		0.627	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	
PTPRF	5792	hgsc.bcm.edu	37	1	44072066	44072066	+	Silent	SNP	C	C	T	rs10890266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:44072066C>T	ENST00000359947.4	+	20	3979	c.3639C>T	c.(3637-3639)ccC>ccT	p.P1213P	PTPRF_ENST00000372413.3_Silent_p.P1204P|PTPRF_ENST00000372414.3_Silent_p.P1213P|PTPRF_ENST00000422171.2_Silent_p.P561P|PTPRF_ENST00000438120.1_Silent_p.P1204P|PTPRF_ENST00000496447.1_3'UTR	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1213					cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ACAACCGGCCCCTGTCTCCGG	0.572													C|||	1408	0.28115	0.0303	0.2752	5008	,	,		15878	0.4702		0.3648	False		,,,				2504	0.3436				p.P1213P		Atlas-SNP	.											.	PTPRF	172	.	0			c.C3639T						PASS	.	C	,	413,3993	202.8+/-225.5	21,371,1811	137.0	148.0	144.0		3639,3612	-0.5	1.0	1	dbSNP_120	144	3111,5489	475.5+/-369.1	574,1963,1763	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	595,2334,3574	TT,TC,CC		36.1744,9.3736,27.0952	,	1213/1908,1204/1899	44072066	3524,9482	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon20			CCGGCCCCTGTCT	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3639C>T	1.37:g.44072066C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	51	0.579545	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	636|636	0.29120879120879123|0.29120879120879123	19|19	0.03861788617886179|0.03861788617886179	113|113	0.31215469613259667|0.31215469613259667	229|229	0.40034965034965037|0.40034965034965037	275|275	0.3627968337730871|0.3627968337730871	C|C	9.612|9.612	1.131657|1.131657	0.21041|0.21041	0.093736|0.093736	0.361744|0.361744	ENSG00000142949|ENSG00000142949	ENST00000429895|ENST00000412568;ENST00000414879	T|T;T	0.25414|0.38077	1.8|1.17;1.16	5.2|5.2	-0.529|-0.529	0.11901|0.11901	.|.	0.000000|0.000000	0.34002|0.34002	N|N	0.004350|0.004350	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999843067|0.999999843067	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39121|0.39121	-0.9629|-0.9629	6|6	0.51188|0.56958	T|D	0.08|0.05	.|.	1.5715|1.5715	0.02616|0.02616	0.1907:0.2989:0.3086:0.2018|0.1907:0.2989:0.3086:0.2018	rs10890266;rs59351132;rs10890266|rs10890266;rs59351132;rs10890266	.|.	.|.	.|.	L|S	859|586;627	ENSP00000408952:P859L|ENSP00000391764:P586S;ENSP00000416343:P627S	ENSP00000408952:P859L|ENSP00000361484:P536S	P|P	+|+	2|1	0|0	PTPRF|PTPRF	43844653|43844653	0.007000|0.007000	0.16637|0.16637	0.998000|0.998000	0.56505|0.56505	0.993000|0.993000	0.82548|0.82548	-1.265000|-1.265000	0.02844|0.02844	0.019000|0.019000	0.15079|0.15079	0.561000|0.561000	0.74099|0.74099	CCC|CCT	C|0.727;N|0.000	.	strong		0.572	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
CHRNA3	1136	hgsc.bcm.edu	37	15	78894420	78894420	+	Silent	SNP	A	A	G	rs8192480|rs74315118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78894420A>G	ENST00000326828.5	-	5	948	c.564T>C	c.(562-564)gaT>gaC	p.D188D	CHRNA3_ENST00000348639.3_Silent_p.D188D	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	188					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	TCAGGACCAGATCGATTTTCG	0.488													A|||	14	0.00279553	0.0008	0.0	5008	,	,		18118	0.0		0.0099	False		,,,				2504	0.0031				p.D188D		Atlas-SNP	.											.	CHRNA3	56	.	0			c.T564C						PASS	.	A	,	3,4389	6.2+/-15.9	0,3,2193	180.0	160.0	167.0		564,564	0.9	1.0	15	dbSNP_117	167	39,8547	26.3+/-74.7	1,37,4255	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	1,40,6448	GG,GA,AA		0.4542,0.0683,0.3236	,	188/506,188/490	78894420	42,12936	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			GACCAGATCGATT		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.564T>C	15.37:g.78894420A>G		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	189	93	0.492063	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			A|0.995;G|0.005	0.005	strong		0.488	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
TTC28	23331	hgsc.bcm.edu	37	22	28389453	28389453	+	Silent	SNP	T	T	C	rs470101	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:28389453T>C	ENST00000397906.2	-	18	5439	c.5298A>G	c.(5296-5298)acA>acG	p.T1766T	TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000433317.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000424161.1_RNA|TTC28-AS1_ENST00000430525.1_RNA|TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000428584.1_RNA|TTC28-AS1_ENST00000435348.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	1766					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						TCTGCTGGGATGTGTACATGG	0.637													C|||	395	0.0788738	0.0991	0.0937	5008	,	,		19292	0.0069		0.1034	False		,,,				2504	0.09				p.T1766T		Atlas-SNP	.											.	TTC28	84	.	0			c.A5298G						PASS	.	C		144,1240		7,130,555	69.0	66.0	67.0		5298	-8.9	0.5	22	dbSNP_80	67	381,2801		26,329,1236	no	coding-synonymous	TTC28	NM_001145418.1		33,459,1791	CC,CT,TT		11.9736,10.4046,11.498		1766/2482	28389453	525,4041	692	1591	2283	SO:0001819	synonymous_variant	23331	exon18			CTGGGATGTGTAC	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.5298A>G	22.37:g.28389453T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			T|0.926;C|0.074	0.074	strong		0.637	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42434254	42434254	+	Silent	SNP	G	G	A	rs655427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42434254G>A	ENST00000382396.4	-	20	2564	c.2478C>T	c.(2476-2478)aaC>aaT	p.N826N	PLA2G4F_ENST00000397272.3_Silent_p.N828N			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	826	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		AGGTCTCCACGTTGTTCAGGA	0.602													A|||	2000	0.399361	0.3964	0.415	5008	,	,		16500	0.3452		0.5487	False		,,,				2504	0.2945				p.N826N		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.C2478T						PASS	.	A		1819,2587	638.6+/-397.0	370,1079,754	81.0	76.0	77.0		2478	-10.4	0.0	15	dbSNP_83	77	4536,4062	560.1+/-387.5	1203,2130,966	no	coding-synonymous	PLA2G4F	NM_213600.3		1573,3209,1720	AA,AG,GG		47.2435,41.2846,48.8696		826/850	42434254	6355,6649	2203	4299	6502	SO:0001819	synonymous_variant	255189	exon20			CTCCACGTTGTTC		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.2478C>T	15.37:g.42434254G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																			G|0.540;N|0.000	.	strong		0.602	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
LILRB2	10288	hgsc.bcm.edu	37	19	54782919	54782919	+	Missense_Mutation	SNP	C	C	T	rs386056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54782919C>T	ENST00000391749.4	-	6	974	c.703G>A	c.(703-705)Gtg>Atg	p.V235M	LILRB2_ENST00000391746.1_Missense_Mutation_p.V235M|LILRB2_ENST00000434421.1_Missense_Mutation_p.V119M|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391748.1_Missense_Mutation_p.V235M|LILRB2_ENST00000314446.5_Missense_Mutation_p.V235M	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	235	Ig-like C2-type 3.		V -> M (in dbSNP:rs386056).		cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCAGGGGCCACGACAGGACCC	0.577													.|||	1261	0.251797	0.1256	0.2392	5008	,	,		16650	0.6052		0.173	False		,,,				2504	0.1483				p.V235M		Atlas-SNP	.											.	LILRB2	94	.	0			c.G703A						PASS	.	C	MET/VAL,MET/VAL	676,3730	285.2+/-278.0	42,592,1569	93.0	94.0	94.0		703,703	-3.9	0.0	19	dbSNP_80	94	1563,7037	293.8+/-301.5	155,1253,2892	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	21,21	197,1845,4461	TT,TC,CC		18.1744,15.3427,17.2151	benign,benign	235/598,235/599	54782919	2239,10767	2203	4300	6503	SO:0001583	missense	10288	exon6			GGGCCACGACAGG	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.703G>A	19.37:g.54782919C>T	ENSP00000375629:p.Val235Met	Somatic	443	0	0		WXS	Illumina HiSeq	Phase_I	517	241	0.466151	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	729	0.33379120879120877	71	0.1443089430894309	93	0.2569060773480663	426	0.7447552447552448	139	0.18337730870712401	C	11.86	1.765440	0.31228	0.153427	0.181744	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33	2.44	-3.93	0.04143	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.090410	0.02456	N	0.086115	T	0.00012	0.0000	M	0.92169	3.28	0.80722	P	0.0	P;B;B	0.43352	0.804;0.443;0.42	B;B;B	0.43809	0.432;0.432;0.199	T	0.52298	-0.8594	9	0.54805	T	0.06	.	10.3378	0.43860	0.0:0.2758:0.7242:0.0	rs386056	235;252;235	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	M	235;235;235;235;119	ENSP00000375628:V235M;ENSP00000319960:V235M;ENSP00000375629:V235M;ENSP00000375626:V235M;ENSP00000410117:V119M	ENSP00000319960:V235M	V	-	1	0	LILRB2	59474731	0.003000	0.15002	0.001000	0.08648	0.009000	0.06853	-0.385000	0.07379	-0.189000	0.10482	-0.535000	0.04281	GTG	C|0.787;T|0.213	0.213	strong		0.577	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
OTOF	9381	hgsc.bcm.edu	37	2	26699855	26699855	+	Silent	SNP	G	G	C	rs2272069	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:26699855G>C	ENST00000272371.2	-	22	2706	c.2580C>G	c.(2578-2580)gtC>gtG	p.V860V	OTOF_ENST00000338581.6_Silent_p.V113V|OTOF_ENST00000339598.3_Silent_p.V113V|OTOF_ENST00000402415.3_Silent_p.V170V|OTOF_ENST00000403946.3_Silent_p.V860V	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	860					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGCATAGGCGACACGCTTGT	0.602													G|||	2512	0.501597	0.2617	0.5418	5008	,	,		7767	0.8542		0.4225	False		,,,				2504	0.5153				p.V860V	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C2580G						PASS	.	G	,,,	1188,3192	408.9+/-334.8	169,850,1171	69.0	54.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	339,2580,510,339	1.6	1.0	2	dbSNP_100	60	3269,5315	486.2+/-371.8	600,2069,1623	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	769,2919,2794	CC,CG,GG		38.0825,27.1233,34.3798	,,,	113/1231,860/1998,170/1308,113/1231	26699855	4457,8507	2190	4292	6482	SO:0001819	synonymous_variant	9381	exon22			ATAGGCGACACGC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2580C>G	2.37:g.26699855G>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			G|0.597;C|0.403	0.403	strong		0.602	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
ALOX12	239	hgsc.bcm.edu	37	17	6904934	6904934	+	Missense_Mutation	SNP	A	A	G	rs434473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6904934A>G	ENST00000251535.6	+	8	1018	c.965A>G	c.(964-966)aAc>aGc	p.N322S	RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000574377.1_Intron|AC027763.2_ENST00000575727.1_Intron|AC027763.2_ENST00000399540.2_3'UTR	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	322	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		N -> S (in dbSNP:rs434473). {ECO:0000269|PubMed:2244907, ECO:0000269|PubMed:2377602, ECO:0000269|Ref.4}.		aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						CAGCCTCCCAACCCCAGCTCT	0.493													A|||	1709	0.341254	0.1528	0.268	5008	,	,		18924	0.4712		0.4016	False		,,,				2504	0.4519				p.N322S		Atlas-SNP	.											.	ALOX12	49	.	0			c.A965G						PASS	.	A	SER/ASN	862,3544	340.2+/-306.1	80,702,1421	158.0	158.0	158.0		965	-4.4	0.8	17	dbSNP_80	158	3626,4974	523.0+/-380.2	767,2092,1441	yes	missense	ALOX12	NM_000697.2	46	847,2794,2862	GG,GA,AA		42.1628,19.5642,34.5072	benign	322/664	6904934	4488,8518	2203	4300	6503	SO:0001583	missense	239	exon8			CTCCCAACCCCAG	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.965A>G	17.37:g.6904934A>G	ENSP00000251535:p.Asn322Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_000697	O95569|Q6ISF8|Q9UQM4	Missense_Mutation	SNP	ENST00000251535.6	37	CCDS11084.1	749	0.34294871794871795	78	0.15853658536585366	107	0.2955801104972376	262	0.458041958041958	302	0.39841688654353563	A	0.780	-0.762597	0.02996	0.195642	0.421628	ENSG00000108839	ENST00000251535	T	0.76186	-1.0	4.78	-4.4	0.03600	Lipoxygenase, C-terminal (3);	0.561606	0.20079	N	0.099691	T	0.00012	0.0000	N	0.05383	-0.06	0.46586	P	8.820000000000494E-4	B	0.02656	0.0	B	0.09377	0.004	T	0.23440	-1.0188	9	0.07813	T	0.8	-10.9398	8.2298	0.31590	0.3783:0.1187:0.503:0.0	rs434473;rs1126668;rs57549908;rs434473	322	P18054	LOX12_HUMAN	S	322	ENSP00000251535:N322S	ENSP00000251535:N322S	N	+	2	0	ALOX12	6845658	0.000000	0.05858	0.829000	0.32907	0.091000	0.18340	-0.487000	0.06505	-0.672000	0.05266	-0.380000	0.06706	AAC	A|0.648;G|0.352	0.352	strong		0.493	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
C10orf71	118461	hgsc.bcm.edu	37	10	50531137	50531137	+	Missense_Mutation	SNP	A	A	T	rs41281949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50531137A>T	ENST00000374144.3	+	3	835	c.547A>T	c.(547-549)Agt>Tgt	p.S183C	C10orf71_ENST00000323868.4_Missense_Mutation_p.S183C			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	183										endometrium(1)	1						TCCAGAAAACAGTGTCAACTT	0.542													A|||	38	0.00758786	0.0008	0.0144	5008	,	,		19466	0.0		0.0179	False		,,,				2504	0.0092				p.S183C		Atlas-SNP	.											.	C10orf71	179	.	0			c.A547T						PASS	.	A	CYS/SER,CYS/SER	8,3982		0,8,1987	32.0	34.0	33.0		547,547	3.2	0.1	10	dbSNP_127	33	106,8232		0,106,4063	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	112,112	0,114,6050	TT,TA,AA		1.2713,0.2005,0.9247	possibly-damaging,possibly-damaging	183/1436,183/720	50531137	114,12214	1995	4169	6164	SO:0001583	missense	118461	exon3			GAAAACAGTGTCA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.547A>T	10.37:g.50531137A>T	ENSP00000363259:p.Ser183Cys	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	18	0.008241758241758242	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	12	0.0158311345646438	A	15.17	2.752975	0.49362	0.002005	0.012713	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.15487	2.42;3.55	5.19	3.24	0.37175	.	0.125201	0.36002	N	0.002841	T	0.05593	0.0147	N	0.08118	0	0.09310	N	0.999999	D	0.63046	0.992	P	0.49502	0.613	T	0.07673	-1.0760	10	0.72032	D	0.01	.	8.4581	0.32912	0.2657:0.0:0.7343:0.0	rs41281949	183	Q711Q0-3	.	C	183	ENSP00000318713:S183C;ENSP00000363259:S183C	ENSP00000318713:S183C	S	+	1	0	C10orf71	50201143	0.982000	0.34865	0.064000	0.19789	0.714000	0.41099	1.979000	0.40608	0.493000	0.27837	0.459000	0.35465	AGT	A|0.992;T|0.008	0.008	strong		0.542	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
ZNF30	90075	hgsc.bcm.edu	37	19	35435589	35435589	+	Silent	SNP	C	C	T	rs3761066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35435589C>T	ENST00000601142.1	+	5	1956	c.1719C>T	c.(1717-1719)tgC>tgT	p.C573C	ZNF30_ENST00000426813.2_Silent_p.C492C|ZNF30_ENST00000303586.7_Silent_p.C574C|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000439785.1_Silent_p.C574C			P17039	ZNF30_HUMAN	zinc finger protein 30	573					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		GTAAGGAATGCGGGAAGGCCT	0.393													C|||	1214	0.242412	0.2284	0.1945	5008	,	,		22802	0.3869		0.1849	False		,,,				2504	0.2055				p.C574C		Atlas-SNP	.											.	ZNF30	44	.	0			c.C1722T						PASS	.	C	,,	957,3419	324.0+/-298.4	107,743,1338	51.0	58.0	56.0		1722,1722,1719	1.0	0.2	19	dbSNP_107	56	1505,7089	277.5+/-292.9	123,1259,2915	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	,,	230,2002,4253	TT,TC,CC		17.5122,21.8693,18.9823	,,	574/625,574/625,573/624	35435589	2462,10508	2188	4297	6485	SO:0001819	synonymous_variant	90075	exon5			GGAATGCGGGAAG	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1719C>T	19.37:g.35435589C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Silent	SNP	ENST00000601142.1	37	CCDS46045.1																																																																																			C|0.747;T|0.253	0.253	strong		0.393	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
SEC31A	22872	hgsc.bcm.edu	37	4	83795806	83795806	+	Silent	SNP	T	T	C	rs10025654	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:83795806T>C	ENST00000395310.2	-	6	779	c.597A>G	c.(595-597)agA>agG	p.R199R	SEC31A_ENST00000443462.2_Silent_p.R194R|SEC31A_ENST00000505472.1_Silent_p.R199R|SEC31A_ENST00000509142.1_Silent_p.R199R|SEC31A_ENST00000505984.1_Silent_p.R199R|SEC31A_ENST00000355196.2_Silent_p.R199R|SEC31A_ENST00000348405.4_Silent_p.R199R|SEC31A_ENST00000326950.5_Silent_p.R199R|SEC31A_ENST00000508479.1_Silent_p.R199R|SEC31A_ENST00000436790.2_5'UTR|SEC31A_ENST00000500777.2_Silent_p.R199R|SEC31A_ENST00000508502.1_Silent_p.R199R|SEC31A_ENST00000448323.1_Silent_p.R199R|SEC31A_ENST00000264405.5_5'Flank|SEC31A_ENST00000432794.1_Silent_p.R199R|SEC31A_ENST00000513858.1_Silent_p.R199R|SEC31A_ENST00000311785.7_Silent_p.R199R	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	199	Interaction with SEC13.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				GCTCATTTTTTCTAAGATCCC	0.428													T|||	1766	0.352636	0.1029	0.6758	5008	,	,		18100	0.2629		0.5616	False		,,,				2504	0.3384				p.R199R		Atlas-SNP	.											.	SEC31A	227	.	0			c.A597G						PASS	.	T	,,,,,	837,3569	332.0+/-302.3	94,649,1460	130.0	128.0	129.0		597,597,597,582,597,597	-3.6	1.0	4	dbSNP_119	129	4943,3657	623.2+/-397.4	1423,2097,780	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEC31A	NM_001077206.2,NM_001077207.2,NM_001077208.2,NM_001191049.1,NM_014933.3,NM_016211.3	,,,,,	1517,2746,2240	CC,CT,TT		42.5233,18.9968,44.441	,,,,,	199/1107,199/1221,199/1206,194/1201,199/1221,199/1182	83795806	5780,7226	2203	4300	6503	SO:0001819	synonymous_variant	22872	exon6			ATTTTTTCTAAGA	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.597A>G	4.37:g.83795806T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_001077206	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	37	CCDS3596.1																																																																																			T|0.602;C|0.398	0.398	strong		0.428	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211	
SNPH	9751	hgsc.bcm.edu	37	20	1286057	1286057	+	Missense_Mutation	SNP	G	G	T	rs150050410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1286057G>T	ENST00000381873.3	+	6	1080	c.844G>T	c.(844-846)Ggc>Tgc	p.G282C	SNPH_ENST00000381867.1_Missense_Mutation_p.G326C	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	282					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)			endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CAGCTCCTTCGGCCTGGGCCC	0.662													G|||	55	0.0109824	0.0008	0.0187	5008	,	,		18623	0.0		0.0209	False		,,,				2504	0.0204				p.G282C		Atlas-SNP	.											.	SNPH	89	.	0			c.G844T						PASS	.	G	CYS/GLY	12,4394	16.8+/-37.8	0,12,2191	38.0	37.0	37.0		844	2.5	1.0	20	dbSNP_134	37	114,8486	57.9+/-119.4	1,112,4187	no	missense	SNPH	NM_014723.2	159	1,124,6378	TT,TG,GG		1.3256,0.2724,0.9688	benign	282/495	1286057	126,12880	2203	4300	6503	SO:0001583	missense	9751	exon6			TCCTTCGGCCTGG		CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.844G>T	20.37:g.1286057G>T	ENSP00000371297:p.Gly282Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_014723	Q8IYI3	Missense_Mutation	SNP	ENST00000381873.3	37	CCDS13012.1	30	0.013736263736263736	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	19	0.025065963060686015	G	3.016	-0.202738	0.06219	0.002724	0.013256	ENSG00000101298	ENST00000381873;ENST00000381867	.	.	.	4.75	2.46	0.29980	.	0.484707	0.20167	N	0.097815	T	0.05044	0.0135	N	0.02011	-0.69	0.24187	N	0.99557	P;P	0.43857	0.819;0.819	P;P	0.48368	0.575;0.575	T	0.04216	-1.0968	9	0.51188	T	0.08	-11.5473	6.1469	0.20291	0.7668:0.0:0.2332:0.0	.	326;282	O15079-2;O15079	.;SNPH_HUMAN	C	282;326	.	ENSP00000371291:G326C	G	+	1	0	SNPH	1234057	0.000000	0.05858	0.987000	0.45799	0.141000	0.21300	-0.148000	0.10219	0.327000	0.23409	0.561000	0.74099	GGC	G|0.990;T|0.010	0.010	strong		0.662	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723	
DLEC1	9940	hgsc.bcm.edu	37	3	38081031	38081031	+	Silent	SNP	A	A	T	rs7616776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38081031A>T	ENST00000308059.6	+	1	336	c.315A>T	c.(313-315)tcA>tcT	p.S105S	DLEC1_ENST00000346219.3_Silent_p.S105S|DLEC1_ENST00000452631.2_Silent_p.S105S					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		ACTTGTACTCAGCCGAGGTCA	0.632													g|||	1715	0.342452	0.2927	0.3429	5008	,	,		19111	0.5546		0.3032	False		,,,				2504	0.2311				p.S105S		Atlas-SNP	.											DLEC1_ENST00000346219,NS,carcinoma,0,2	DLEC1	278	2	0			c.A315T						PASS	.	G	,	1240,2908		182,876,1016	55.0	59.0	58.0		315,315	-6.2	0.0	3	dbSNP_116	58	2475,5941		387,1701,2120	no	coding-synonymous,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	569,2577,3136	TT,TA,AA		29.4083,29.8939,29.5686	,	105/1756,105/1779	38081031	3715,8849	2074	4208	6282	SO:0001819	synonymous_variant	9940	exon1			GTACTCAGCCGAG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.315A>T	3.37:g.38081031A>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_007337		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			A|0.652;T|0.348	0.348	strong		0.632	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
KIAA0754	643314	hgsc.bcm.edu	37	1	39876573	39876573	+	Missense_Mutation	SNP	A	A	C	rs74607331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39876573A>C	ENST00000530275.1	+	1	423	c.228A>C	c.(226-228)ttA>ttC	p.L76F	MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000567887.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	76	13 X 13 AA approximate tandem repeat of P-T-S-P-A-A-A-V-P-T-P-E-E.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TTAAAAACTTAAGTGGAGACT	0.448											OREG0013393	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	22	0.00439297	0.0	0.0086	5008	,	,		21714	0.0		0.0159	False		,,,				2504	0.0				p.L212F		Atlas-SNP	.											KIAA0754_ENST00000530275,NS,carcinoma,+2,2	KIAA0754	93	2	0			c.A636C						PASS	.	A	,,PHE/LEU	11,3737		0,11,1863	72.0	73.0	72.0		,,636	-0.7	0.6	1	dbSNP_132	72	110,8098		2,106,3996	yes	intron,intron,missense	MACF1,KIAA0754	NM_012090.4,NM_033044.3,NM_015038.1	,,22	2,117,5859	CC,CA,AA		1.3402,0.2935,1.012	,,benign	,,212/1428	39876573	121,11835	1874	4104	5978	SO:0001583	missense	643314	exon1			AAACTTAAGTGGA			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.228A>C	1.37:g.39876573A>C	ENSP00000431179:p.Leu76Phe	Somatic	206	0	0	889	WXS	Illumina HiSeq	Phase_I	176	51	0.289773	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	11.25	1.583420	0.28268	0.002935	0.013402	ENSG00000255103	ENST00000530275	T	0.31247	1.5	4.78	-0.745	0.11098	.	.	.	.	.	T	0.08714	0.0216	L	0.27053	0.805	0.09310	N	1	B	0.27932	0.194	B	0.26094	0.066	T	0.24977	-1.0145	9	0.87932	D	0	.	2.8467	0.05546	0.1825:0.4305:0.2676:0.1194	.	76	O94854	K0754_HUMAN	F	76	ENSP00000431179:L76F	ENSP00000431179:L76F	L	+	3	2	RP4-562N20.1	39649160	0.000000	0.05858	0.643000	0.29450	0.853000	0.48598	0.209000	0.17435	0.196000	0.20367	0.454000	0.30748	TTA	A|0.988;C|0.012	0.012	strong		0.448	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
TJP1	7082	hgsc.bcm.edu	37	15	30008889	30008889	+	Silent	SNP	G	G	A	rs2229518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:30008889G>A	ENST00000346128.6	-	23	4602	c.4128C>T	c.(4126-4128)gcC>gcT	p.A1376A	TJP1_ENST00000356107.6_Silent_p.A1376A|TJP1_ENST00000545208.2_Silent_p.A1296A|TJP1_ENST00000400011.2_Silent_p.A1300A	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1376					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		GATGGCTGGCGGCAATGTGTG	0.403													G|||	3940	0.786741	0.6437	0.8242	5008	,	,		16060	0.8641		0.8241	False		,,,				2504	0.8354				p.A1376A	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.C4128T						PASS	.	G	,	2624,1138		915,794,172	81.0	84.0	83.0		4128,3888	-0.7	0.4	15	dbSNP_98	83	6894,1354		2887,1120,117	no	coding-synonymous,coding-synonymous	TJP1	NM_003257.3,NM_175610.2	,	3802,1914,289	AA,AG,GG		16.4161,30.2499,20.7494	,	1376/1749,1296/1669	30008889	9518,2492	1881	4124	6005	SO:0001819	synonymous_variant	7082	exon23			GCTGGCGGCAATG		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"""zona occludens 1"", ""tight junction protein ZO-1"""	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.4128C>T	15.37:g.30008889G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	37	CCDS42007.1																																																																																			G|0.213;A|0.787	0.787	strong		0.403	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257	
DNAJB8	165721	hgsc.bcm.edu	37	3	128181777	128181777	+	Silent	SNP	A	A	G	rs2659690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:128181777A>G	ENST00000469083.1	-	2	2869	c.312T>C	c.(310-312)ttT>ttC	p.F104F	DNAJB8_ENST00000319153.3_Silent_p.F104F|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	104					chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CCAGGCCACCAAAAAACTCCC	0.637													G|||	2374	0.474042	0.388	0.5389	5008	,	,		17408	0.4058		0.6352	False		,,,				2504	0.4489				p.F104F		Atlas-SNP	.											.	DNAJB8	34	.	0			c.T312C						PASS	.	G		1820,2586	637.5+/-396.8	383,1054,766	71.0	72.0	72.0		312	-5.8	0.0	3	dbSNP_100	72	5341,3259	490.0+/-372.7	1644,2053,603	no	coding-synonymous	DNAJB8	NM_153330.2		2027,3107,1369	GG,GA,AA		37.8953,41.3073,44.9408		104/233	128181777	7161,5845	2203	4300	6503	SO:0001819	synonymous_variant	165721	exon3			GCCACCAAAAAAC		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"""Heat shock proteins / DNAJ (HSP40)"""	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.312T>C	3.37:g.128181777A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_153330	B3KWV7	Silent	SNP	ENST00000469083.1	37	CCDS3048.1																																																																																			G|0.508;N|0.000	0.508	strong		0.637	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
CAMK2D	817	hgsc.bcm.edu	37	4	114429407	114429407	+	Intron	SNP	C	C	T	rs11098193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:114429407C>T	ENST00000342666.5	-	13	984				CAMK2D_ENST00000394524.3_Intron|CAMK2D_ENST00000454265.2_Silent_p.S334S|CAMK2D_ENST00000429180.1_Intron|CAMK2D_ENST00000511664.1_Intron|CAMK2D_ENST00000418639.2_Intron|CAMK2D_ENST00000379773.2_Intron|CAMK2D_ENST00000508738.1_Silent_p.S334S|CAMK2D_ENST00000296402.5_Intron|CAMK2D_ENST00000514328.1_Intron|CAMK2D_ENST00000394522.3_Intron|CAMK2D_ENST00000394526.2_Silent_p.S334S|CAMK2D_ENST00000505990.1_Intron|CAMK2D_ENST00000515496.1_Silent_p.S334S			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta						calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		TCTGAACACTCGAACTGGACT	0.353													C|||	646	0.128994	0.0348	0.1556	5008	,	,		17779	0.0883		0.2714	False		,,,				2504	0.1329				p.S334S		Atlas-SNP	.											.	CAMK2D	55	.	0			c.G1002A						PASS	.	C	,,,,,	214,2888		10,194,1347	52.0	44.0	46.0		,,,,,1002	5.6	1.0	4	dbSNP_120	46	1597,5443		188,1221,2111	no	intron,intron,intron,intron,intron,coding-synonymous	CAMK2D	NM_001221.3,NM_172114.1,NM_172115.2,NM_172127.2,NM_172128.2,NM_172129.1	,,,,,	198,1415,3458	TT,TC,CC		22.6847,6.8988,17.8564	,,,,,	,,,,,334/490	114429407	1811,8331	1551	3520	5071	SO:0001627	intron_variant	817	exon14			AACACTCGAACTG	U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"""	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.984+1386G>A	4.37:g.114429407C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	176	76	0.431818	NM_172129	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Silent	SNP	ENST00000342666.5	37	CCDS3703.1																																																																																			C|0.853;T|0.147	0.147	strong		0.353	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2		
AURKB	9212	hgsc.bcm.edu	37	17	8108339	8108339	+	Silent	SNP	G	G	A	rs2241909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8108339G>A	ENST00000585124.1	-	9	978	c.885C>T	c.(883-885)tcC>tcT	p.S295S	AURKB_ENST00000534871.1_Silent_p.S254S|AURKB_ENST00000316199.6_Silent_p.S296S|AURKB_ENST00000578549.1_Silent_p.S263S|AURKB_ENST00000535053.1_3'UTR	NM_004217.3	NP_004208.2	Q96GD4	AURKB_HUMAN	aurora kinase B	295	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				abscission (GO:0009838)|aging (GO:0007568)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|attachment of spindle microtubules to kinetochore (GO:0008608)|cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|cleavage furrow formation (GO:0036089)|cytokinesis checkpoint (GO:0031565)|histone H3-S28 phosphorylation (GO:0043988)|histone modification (GO:0016570)|mitotic cell cycle (GO:0000278)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytokinesis (GO:0032467)|protein autophosphorylation (GO:0046777)|protein localization to kinetochore (GO:0034501)|protein phosphorylation (GO:0006468)|regulation of chromosome segregation (GO:0051983)|spindle checkpoint (GO:0031577)|spindle midzone assembly involved in mitosis (GO:0051256)|spindle stabilization (GO:0043146)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|central_nervous_system(1)|lung(2)	4						CCATGGGCACGGAAGCGGGGA	0.592													A|||	3109	0.620807	0.5545	0.696	5008	,	,		15417	0.5179		0.66	False		,,,				2504	0.7229				p.S295S	NSCLC(134;1161 2470 43664 51568)	Atlas-SNP	.											.	AURKB	47	.	0			c.C885T						PASS	.	A		2491,1915	547.2+/-377.2	701,1089,413	64.0	60.0	61.0		885	-5.9	0.0	17	dbSNP_98	61	5551,3049	468.2+/-367.2	1804,1943,553	no	coding-synonymous	AURKB	NM_004217.2		2505,3032,966	AA,AG,GG		35.4535,43.4635,38.167		295/345	8108339	8042,4964	2203	4300	6503	SO:0001819	synonymous_variant	9212	exon9			GGGCACGGAAGCG	AF004022	CCDS11134.1, CCDS58514.1, CCDS67162.1	17p13.1	2013-01-17	2003-07-21	2003-07-23	ENSG00000178999	ENSG00000178999		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	11390	protein-coding gene	gene with protein product	"""aurora-B"", ""aurora-1"", ""protein phosphatase 1, regulatory subunit 48"""	604970	"""serine/threonine kinase 12"""	STK12		9858806	Standard	NM_001256834		Approved	Aik2, IPL1, AurB, AIM-1, ARK2, STK5, PPP1R48	uc002gkm.4	Q96GD4	OTTHUMG00000108189	ENST00000585124.1:c.885C>T	17.37:g.8108339G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_004217	B4DNM4|C7G533|C7G534|C7G535|D3DTR4|J9JID1|O14630|O60446|O95083|Q96DV5|Q9UQ46	Silent	SNP	ENST00000585124.1	37	CCDS11134.1																																																																																			G|0.385;A|0.615	0.615	strong		0.592	AURKB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000226995.2	NM_004217	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921137	12921137	+	Missense_Mutation	SNP	T	T	A	rs17039283	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12921137T>A	ENST00000240189.2	+	4	1015	c.928T>A	c.(928-930)Ttg>Atg	p.L310M		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	310			L -> M (in dbSNP:rs17039283).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAGAGGACTTGAAGTGTCT	0.493																																					p.L310M		Atlas-SNP	.											PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	0			c.T928A						scavenged	.						132.0	134.0	133.0					1																	12921137		2202	4297	6499	SO:0001583	missense	65122	exon4			GAGGACTTGAAGT		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.928T>A	1.37:g.12921137T>A	ENSP00000240189:p.Leu310Met	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	210	4	0.0190476	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	.	.	.	.	.	.	.	.	.	.	G	2.970	-0.212708	0.06140	.	.	ENSG00000120952	ENST00000240189	T	0.01076	5.37	0.824	-1.65	0.08291	.	0.471727	0.17963	N	0.156117	T	0.00936	0.0031	N	0.25825	0.765	0.09310	N	1	B	0.06786	0.001	B	0.21360	0.034	T	0.44742	-0.9308	10	0.38643	T	0.18	.	5.2047	0.15285	0.0:0.0:0.2907:0.7093	rs17039283	310	O60811	PRAM2_HUMAN	M	310	ENSP00000240189:L310M	ENSP00000240189:L310M	L	+	1	2	PRAMEF2	12843724	0.011000	0.17503	0.001000	0.08648	0.011000	0.07611	-0.072000	0.11486	-1.430000	0.01985	-1.205000	0.01647	TTG	T|1.000;|0.000	.	weak		0.493	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
FABP2	2169	hgsc.bcm.edu	37	4	120240238	120240238	+	Silent	SNP	T	T	C	rs1511025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:120240238T>C	ENST00000274024.3	-	4	644	c.357A>G	c.(355-357)gtA>gtG	p.V119V		NM_000134.3	NP_000125.2	P12104	FABPI_HUMAN	fatty acid binding protein 2, intestinal	119					digestion (GO:0007586)	cytoplasm (GO:0005737)	fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			breast(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	8					Estradiol(DB00783)|Ibuprofen(DB01050)|Sulfinpyrazone(DB01138)	CTCCTTCATATACATAAGTCT	0.299													T|||	1668	0.333067	0.4017	0.33	5008	,	,		11767	0.3948		0.3121	False		,,,				2504	0.2004				p.V119V		Atlas-SNP	.											FABP2,NS,carcinoma,-1,1	FABP2	21	1	0			c.A357G						PASS	.	T		1656,2750	503.4+/-365.5	308,1040,855	107.0	108.0	108.0		357	-10.1	0.0	4	dbSNP_88	108	2817,5775	443.7+/-360.5	465,1887,1944	no	coding-synonymous	FABP2	NM_000134.3		773,2927,2799	CC,CT,TT		32.7863,37.5851,34.413		119/133	120240238	4473,8525	2203	4296	6499	SO:0001819	synonymous_variant	2169	exon4			TTCATATACATAA	J03465	CCDS3712.1	4q28-q31	2013-03-01			ENSG00000145384	ENSG00000145384		"""Fatty acid binding protein family"""	3556	protein-coding gene	gene with protein product		134640					Standard	NM_000134		Approved	I-FABP	uc003icw.3	P12104	OTTHUMG00000132972	ENST00000274024.3:c.357A>G	4.37:g.120240238T>C		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	202	202	1	NM_000134	Q2NKJ1	Silent	SNP	ENST00000274024.3	37	CCDS3712.1																																																																																			T|0.654;C|0.346	0.346	strong		0.299	FABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256531.1	NM_000134	
FKBP2	2286	hgsc.bcm.edu	37	11	64009879	64009879	+	Missense_Mutation	SNP	G	G	A	rs4672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64009879G>A	ENST00000394540.3	+	2	490	c.20G>A	c.(19-21)cGg>cAg	p.R7Q	FKBP2_ENST00000449942.2_Missense_Mutation_p.R7Q|FKBP2_ENST00000309366.4_Missense_Mutation_p.R7Q	NM_057092.2	NP_476433.1	P26885	FKBP2_HUMAN	FK506 binding protein 2, 13kDa	7			R -> Q (in dbSNP:rs4672). {ECO:0000269|PubMed:15489334}.		chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(2)|lung(3)	5						AGCTGGTTCCGGGTCCTGACA	0.642													G|||	125	0.0249601	0.0038	0.0533	5008	,	,		14699	0.0		0.0736	False		,,,				2504	0.0092				p.R7Q		Atlas-SNP	.											.	FKBP2	8	.	0			c.G20A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	73,4329	66.4+/-103.9	1,71,2129	87.0	73.0	78.0		20,20,20	2.3	1.0	11	dbSNP_52	78	683,7911	171.2+/-222.1	31,621,3645	yes	missense,missense,missense	FKBP2	NM_001135208.1,NM_004470.3,NM_057092.2	43,43,43	32,692,5774	AA,AG,GG		7.9474,1.6583,5.8172	benign,benign,benign	7/143,7/143,7/143	64009879	756,12240	2201	4297	6498	SO:0001583	missense	2286	exon2			GGTTCCGGGTCCT	M75099	CCDS8063.1	11q13.1-q13.3	2008-07-18	2002-08-29			ENSG00000173486			3718	protein-coding gene	gene with protein product	"""FK506 binding protein 2 (13kD)"", ""peptidyl-prolyl cis-trans isomerase"", ""rapamycin-binding protein"", ""proline isomerase"""	186946	"""FK506-binding protein 2 (13kD)"""			1713687	Standard	NM_004470		Approved	FKBP-13, PPIase	uc001nyy.3	P26885		ENST00000394540.3:c.20G>A	11.37:g.64009879G>A	ENSP00000378046:p.Arg7Gln	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_004470	Q5BJH9|Q9BTS7	Missense_Mutation	SNP	ENST00000394540.3	37	CCDS8063.1	70	0.03205128205128205	0	0.0	21	0.058011049723756904	0	0.0	49	0.06464379947229551	G	12.40	1.925613	0.34002	0.016583	0.079474	ENSG00000173486	ENST00000309366;ENST00000449942;ENST00000535135;ENST00000394540	T;T;T;T	0.36340	1.27;1.27;1.26;1.27	3.21	2.3	0.28687	.	0.681821	0.12736	N	0.443436	T	0.00815	0.0027	N	0.08118	0	0.21386	N	0.999703	B	0.02656	0.0	B	0.01281	0.0	T	0.14448	-1.0472	10	0.28530	T	0.3	.	5.7934	0.18373	0.1084:0.0:0.7014:0.1902	rs4672;rs1142655;rs3206195;rs11545831;rs17353686;rs4672	7	P26885	FKBP2_HUMAN	Q	7	ENSP00000310935:R7Q;ENSP00000398147:R7Q;ENSP00000438749:R7Q;ENSP00000378046:R7Q	ENSP00000310935:R7Q	R	+	2	0	FKBP2	63766455	0.913000	0.31002	0.999000	0.59377	0.921000	0.55340	-1.217000	0.02979	0.931000	0.37242	-0.448000	0.05591	CGG	G|0.952;A|0.048	0.048	strong		0.642	FKBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396401.2	NM_004470	
BOC	91653	hgsc.bcm.edu	37	3	112991959	112991959	+	Silent	SNP	C	C	T	rs11710894	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:112991959C>T	ENST00000495514.1	+	8	1709	c.1005C>T	c.(1003-1005)ccC>ccT	p.P335P	BOC_ENST00000355385.3_Silent_p.P335P|BOC_ENST00000273395.4_Silent_p.P335P			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	335	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGGTCATCCCCTGGGGCCAGA	0.637													C|||	1496	0.298722	0.2231	0.3948	5008	,	,		18599	0.4107		0.1998	False		,,,				2504	0.319				p.P335P		Atlas-SNP	.											.	BOC	139	.	0			c.C1005T						PASS	.	C		976,3430	367.1+/-318.1	110,756,1337	73.0	72.0	73.0		1005	-8.1	0.5	3	dbSNP_120	73	1488,7112	281.8+/-295.3	138,1212,2950	no	coding-synonymous	BOC	NM_033254.2		248,1968,4287	TT,TC,CC		17.3023,22.1516,18.9451		335/1115	112991959	2464,10542	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon8			CATCCCCTGGGGC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1005C>T	3.37:g.112991959C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	183	98	0.535519	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.773;T|0.227	0.227	strong		0.637	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
C9orf131	138724	hgsc.bcm.edu	37	9	35044398	35044398	+	Missense_Mutation	SNP	T	T	C	rs34368082	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35044398T>C	ENST00000312292.5	+	2	1819	c.1772T>C	c.(1771-1773)aTa>aCa	p.I591T	FLJ00273_ENST00000595331.1_5'Flank|C9orf131_ENST00000354479.5_Missense_Mutation_p.I518T|C9orf131_ENST00000421362.2_Missense_Mutation_p.I543T	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	591										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			TGTGGGGACATACAAAAGACA	0.547													T|||	44	0.00878594	0.0038	0.0115	5008	,	,		16870	0.0		0.0169	False		,,,				2504	0.0143				p.I591T		Atlas-SNP	.											.	C9orf131	71	.	0			c.T1772C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	24,4382	30.8+/-60.4	0,24,2179	109.0	112.0	111.0		1667,1553,1628,1772	-4.5	0.0	9	dbSNP_126	111	128,8472	64.9+/-127.2	1,126,4173	yes	missense,missense,missense,missense	C9orf131	NM_001040410.1,NM_001040411.1,NM_001040412.1,NM_203299.2	89,89,89,89	1,150,6352	CC,CT,TT		1.4884,0.5447,1.1687	probably-damaging,probably-damaging,probably-damaging,probably-damaging	556/1045,518/1007,543/1032,591/1080	35044398	152,12854	2203	4300	6503	SO:0001583	missense	138724	exon2			GGGACATACAAAA	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.1772T>C	9.37:g.35044398T>C	ENSP00000308279:p.Ile591Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_203299	A6NLE6|E9PB26|Q86XC6|Q9UF74	Missense_Mutation	SNP	ENST00000312292.5	37	CCDS6572.2	17	0.007783882783882784	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	11	0.014511873350923483	T	7.636	0.679844	0.14907	0.005447	0.014884	ENSG00000174038	ENST00000421362;ENST00000354479;ENST00000312292;ENST00000435140	T;T;T	0.19806	2.13;2.12;2.13	4.46	-4.47	0.03525	.	1.190300	0.06038	N	0.654342	T	0.11153	0.0272	L	0.46741	1.465	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.42749	-0.9433	10	0.07325	T	0.83	0.7665	10.9476	0.47310	0.0:0.531:0.0:0.469	rs34368082	66;591;518;543	B4DXT9;Q5VYM1;A6NLE6;E9PB26	.;CI131_HUMAN;.;.	T	543;518;591;66	ENSP00000393683:I543T;ENSP00000346472:I518T;ENSP00000308279:I591T	ENSP00000308279:I591T	I	+	2	0	C9orf131	35034398	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.495000	0.02294	-0.989000	0.03485	-0.254000	0.11334	ATA	T|0.991;C|0.009	0.009	strong		0.547	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299	
SEMA3C	10512	hgsc.bcm.edu	37	7	80378319	80378319	+	Silent	SNP	G	G	C	rs2272351	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:80378319G>C	ENST00000265361.3	-	17	2298	c.1737C>G	c.(1735-1737)gtC>gtG	p.V579V	SEMA3C_ENST00000544525.1_Silent_p.V597V|SEMA3C_ENST00000419255.2_Silent_p.V579V	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	579	Ig-like C2-type.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CTCCATACTGGACAATTTCAG	0.418													G|||	4268	0.852236	0.7209	0.9049	5008	,	,		18430	0.7679		0.9901	False		,,,				2504	0.9376				p.V579V		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C1737G						PASS	.	G		3383,1023	728.6+/-410.0	1299,785,119	99.0	91.0	94.0		1737	2.8	1.0	7	dbSNP_100	94	8525,73	815.8+/-406.9	4226,73,0	no	coding-synonymous	SEMA3C	NM_006379.3		5525,858,119	CC,CG,GG		0.849,23.2183,8.4282		579/752	80378319	11908,1096	2203	4299	6502	SO:0001819	synonymous_variant	10512	exon17			ATACTGGACAATT	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1737C>G	7.37:g.80378319G>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			G|0.093;C|0.907	0.907	strong		0.418	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
EXOC3L4	91828	hgsc.bcm.edu	37	14	103566904	103566904	+	Silent	SNP	G	G	A	rs1057640	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:103566904G>A	ENST00000380069.3	+	1	424	c.348G>A	c.(346-348)caG>caA	p.Q116Q	RP11-736N17.8_ENST00000559843.1_RNA	NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	116					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						GTGTCAGCCAGCAGGCATCCA	0.612													G|||	1017	0.203075	0.0787	0.3055	5008	,	,		17369	0.3433		0.1531	False		,,,				2504	0.2055				p.Q116Q		Atlas-SNP	.											.	EXOC3L4	35	.	0			c.G348A						PASS	.	G		364,4042	176.6+/-205.7	18,328,1857	23.0	23.0	23.0		348	3.1	0.0	14	dbSNP_86	23	1304,7296	237.5+/-269.3	122,1060,3118	no	coding-synonymous	EXOC3L4	NM_001077594.1		140,1388,4975	AA,AG,GG		15.1628,8.2615,12.8249		116/723	103566904	1668,11338	2203	4300	6503	SO:0001819	synonymous_variant	91828	exon1			CAGCCAGCAGGCA	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 73"""	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.348G>A	14.37:g.103566904G>A		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	192	106	0.552083	NM_001077594	Q14CR2	Silent	SNP	ENST00000380069.3	37	CCDS32163.1																																																																																			G|0.830;A|0.170	0.170	strong		0.612	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093	
PDPR	55066	hgsc.bcm.edu	37	16	70182390	70182390	+	Missense_Mutation	SNP	T	T	G	rs62050978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70182390T>G	ENST00000288050.4	+	17	2943	c.1986T>G	c.(1984-1986)aaT>aaG	p.N662K	PDPR_ENST00000542659.1_Missense_Mutation_p.N7K|PDPR_ENST00000398122.3_Missense_Mutation_p.N562K|PDPR_ENST00000567046.1_Missense_Mutation_p.N20K|PDPR_ENST00000568530.1_Missense_Mutation_p.N662K|PDPR_ENST00000562100.1_3'UTR	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	662				N -> K (in Ref. 3; CAH10555). {ECO:0000305}.	cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GCTATGCAAATGGGATCCGGG	0.562																																					p.N662K		Atlas-SNP	.											.	PDPR	66	.	0			c.T1986G						PASS	.						76.0	74.0	75.0					16																	70182390		2119	4229	6348	SO:0001583	missense	55066	exon17			TGCAAATGGGATC		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1986T>G	16.37:g.70182390T>G	ENSP00000288050:p.Asn662Lys	Somatic	377	0	0		WXS	Illumina HiSeq	Phase_I	524	130	0.248092	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	T	14.38	2.518492	0.44763	.	.	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055;ENST00000542659	T;T;D	0.91407	-0.38;-0.31;-2.84	5.15	-1.15	0.09709	Glycine cleavage T-protein, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84795	0.5551	L	0.50333	1.59	0.53688	D	0.999977	B	0.19583	0.037	B	0.18263	0.021	T	0.70073	-0.4972	10	0.25751	T	0.34	.	11.2784	0.49180	0.0:0.427:0.0:0.573	rs62050978	662	Q8NCN5	PDPR_HUMAN	K	662;562;390;7	ENSP00000288050:N662K;ENSP00000381190:N562K;ENSP00000441690:N7K	ENSP00000205055:N390K	N	+	3	2	PDPR	68739891	0.005000	0.15991	0.763000	0.31416	0.987000	0.75469	-1.180000	0.03088	-0.552000	0.06167	-0.451000	0.05528	AAT	T|0.500;G|0.500	0.500	strong		0.562	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
AVEN	57099	hgsc.bcm.edu	37	15	34159969	34159969	+	Missense_Mutation	SNP	C	C	A	rs61729120	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:34159969C>A	ENST00000306730.3	-	5	829	c.700G>T	c.(700-702)Ggg>Tgg	p.G234W	RP11-3D4.2_ENST00000560268.1_RNA|AVEN_ENST00000558136.1_5'Flank	NM_020371.2	NP_065104.1	Q9NQS1	AVEN_HUMAN	apoptosis, caspase activation inhibitor	234					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	intracellular (GO:0005622)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|stomach(1)	7		all_lung(180;1.78e-08)		all cancers(64;1.66e-15)|GBM - Glioblastoma multiforme(113;1.42e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0359)		CCTCCAGGCCCCAAGGGCCCC	0.542													C|||	35	0.00698882	0.0008	0.0058	5008	,	,		17300	0.0		0.0258	False		,,,				2504	0.0041				p.G234W		Atlas-SNP	.											.	AVEN	30	.	0			c.G700T						PASS	.	C	TRP/GLY	14,4388	21.2+/-45.6	0,14,2187	57.0	57.0	57.0		700	4.7	0.4	15	dbSNP_129	57	115,8481	62.4+/-124.4	1,113,4184	yes	missense	AVEN	NM_020371.2	184	1,127,6371	AA,AC,CC		1.3378,0.318,0.9925	probably-damaging	234/363	34159969	129,12869	2201	4298	6499	SO:0001583	missense	57099	exon5			CAGGCCCCAAGGG	AF283508	CCDS10030.1	15q13.1	2011-10-19		2008-07-07	ENSG00000169857	ENSG00000169857			13509	protein-coding gene	gene with protein product	"""cell death regulator aven"", ""programmed cell death 12"""	605265				10949025	Standard	XM_005254563		Approved	PDCD12	uc001zhj.3	Q9NQS1	OTTHUMG00000129371	ENST00000306730.3:c.700G>T	15.37:g.34159969C>A	ENSP00000306822:p.Gly234Trp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_020371		Missense_Mutation	SNP	ENST00000306730.3	37	CCDS10030.1	24	0.01098901098901099	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	22	0.029023746701846966	C	16.16	3.043481	0.55003	0.00318	0.013378	ENSG00000169857	ENST00000306730	T	0.48522	0.81	4.72	4.72	0.59763	.	0.660669	0.13941	N	0.352195	T	0.35740	0.0942	L	0.46157	1.445	0.23320	N	0.997916	D	0.71674	0.998	D	0.68039	0.955	T	0.35500	-0.9786	10	0.56958	D	0.05	-5.0646	12.7976	0.57567	0.1626:0.8374:0.0:0.0	rs61729120	234	Q9NQS1	AVEN_HUMAN	W	234	ENSP00000306822:G234W	ENSP00000306822:G234W	G	-	1	0	AVEN	31947261	0.184000	0.23200	0.381000	0.26106	0.741000	0.42261	2.040000	0.41203	2.440000	0.82611	0.591000	0.81541	GGG	C|0.989;A|0.011	0.011	strong		0.542	AVEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251523.2	NM_020371	
RHCG	51458	hgsc.bcm.edu	37	15	90023558	90023558	+	Missense_Mutation	SNP	G	G	A	rs17807723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90023558G>A	ENST00000268122.4	-	4	672	c.604C>T	c.(604-606)Cgc>Tgc	p.R202C	RHCG_ENST00000544600.1_Missense_Mutation_p.R202C	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	202			R -> C (in dbSNP:rs17807723).		amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					TCTAGGTTGCGTCGGTAGAGG	0.567													G|||	398	0.0794728	0.0318	0.1023	5008	,	,		21861	0.0437		0.162	False		,,,				2504	0.0798				p.R202C		Atlas-SNP	.											.	RHCG	49	.	0			c.C604T						PASS	.	G	CYS/ARG	173,4227	114.6+/-152.6	5,163,2032	225.0	203.0	210.0		604	3.4	0.1	15	dbSNP_123	210	1165,7433	238.1+/-269.7	92,981,3226	yes	missense	RHCG	NM_016321.1	180	97,1144,5258	AA,AG,GG		13.5497,3.9318,10.2939	possibly-damaging	202/480	90023558	1338,11660	2200	4299	6499	SO:0001583	missense	51458	exon4			GGTTGCGTCGGTA	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"""Solute carriers"""	18140	protein-coding gene	gene with protein product		605381	"""chromosome 15 open reading frame 6"", ""Rhesus blood group, C glycoprotein"""	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.604C>T	15.37:g.90023558G>A	ENSP00000268122:p.Arg202Cys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_016321	A8K4D4|Q6X3Y4	Missense_Mutation	SNP	ENST00000268122.4	37	CCDS10351.1	196	0.08974358974358974	21	0.042682926829268296	35	0.09668508287292818	19	0.033216783216783216	121	0.15963060686015831	G	17.65	3.441389	0.63067	0.039318	0.135497	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	T;T	0.44482	0.92;0.92	5.34	3.39	0.38822	Ammonium transporter AmtB-like (3);	0.416227	0.29093	N	0.013167	T	0.00241	0.0007	L	0.34521	1.04	0.36478	P	0.13232100000000002	D;D	0.76494	0.999;0.999	P;P	0.58970	0.849;0.849	T	0.02698	-1.1122	8	.	.	.	-5.9769	14.093	0.65002	0.0:0.0:0.7168:0.2832	rs17807723;rs52804243;rs17807723	202;202	A8K4D4;Q9UBD6	.;RHCG_HUMAN	C	202;202;193	ENSP00000438123:R202C;ENSP00000268122:R202C	.	R	-	1	0	RHCG	87824562	1.000000	0.71417	0.099000	0.21106	0.604000	0.37047	6.523000	0.73787	0.593000	0.29745	-0.318000	0.08688	CGC	G|0.905;A|0.095	0.095	strong		0.567	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321	
BCL9	607	hgsc.bcm.edu	37	1	147091972	147091972	+	Missense_Mutation	SNP	C	C	T	rs3820129	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:147091972C>T	ENST00000234739.3	+	8	2751	c.2011C>T	c.(2011-2013)Cct>Tct	p.P671S		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	671	Pro-rich.		P -> S (in dbSNP:rs3820129).		canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					CCACATGGAGCCTGGGAATAA	0.572			T	"""IGH@, IGL@"""	B-ALL								C|||	911	0.181909	0.0227	0.2061	5008	,	,		18011	0.0982		0.4125	False		,,,				2504	0.229				p.P671S		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.C2011T						PASS	.	C	SER/PRO	394,4012	196.4+/-220.7	21,352,1830	47.0	53.0	51.0		2011	3.9	1.0	1	dbSNP_107	51	3457,5143	502.5+/-375.7	716,2025,1559	yes	missense	BCL9	NM_004326.2	74	737,2377,3389	TT,TC,CC		40.1977,8.9424,29.6094	probably-damaging	671/1427	147091972	3851,9155	2203	4300	6503	SO:0001583	missense	607	exon8			ATGGAGCCTGGGA	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.2011C>T	1.37:g.147091972C>T	ENSP00000234739:p.Pro671Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	156	67	0.429487	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	475	0.2174908424908425	12	0.024390243902439025	92	0.2541436464088398	48	0.08391608391608392	323	0.4261213720316623	C	16.27	3.077060	0.55753	0.089424	0.401977	ENSG00000116128	ENST00000234739	T	0.55234	0.53	4.83	3.92	0.45320	.	0.055303	0.85682	N	0.000000	T	0.26521	0.0648	L	0.32530	0.975	0.09310	P	0.999999516491	B;B	0.23058	0.079;0.079	B;B	0.21917	0.037;0.037	T	0.19289	-1.0310	9	0.59425	D	0.04	-3.7125	13.1561	0.59518	0.0:0.923:0.0:0.077	rs3820129;rs17361777;rs56446267;rs61641056;rs3820129	671;671	Q1JQ81;O00512	.;BCL9_HUMAN	S	671	ENSP00000234739:P671S	ENSP00000234739:P671S	P	+	1	0	BCL9	145558596	1.000000	0.71417	0.962000	0.40283	0.940000	0.58332	5.929000	0.70096	1.263000	0.44181	0.591000	0.81541	CCT	C|0.747;T|0.253	0.253	strong		0.572	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	
HIVEP2	3097	hgsc.bcm.edu	37	6	143074700	143074700	+	Silent	SNP	T	T	C	rs169098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:143074700T>C	ENST00000367604.1	-	9	7524	c.6885A>G	c.(6883-6885)ccA>ccG	p.P2295P	HIVEP2_ENST00000367603.2_Silent_p.P2295P|RP1-67K17.3_ENST00000437067.1_RNA|HIVEP2_ENST00000012134.2_Silent_p.P2295P			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	2295					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GAGTGCTAGGTGGACCAGATG	0.527													C|||	3856	0.769968	0.8669	0.7176	5008	,	,		20477	0.8313		0.6074	False		,,,				2504	0.7802				p.P2295P	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.A6885G						PASS	.	C		3372,678		1397,578,50	90.0	92.0	91.0		6885	-2.9	0.9	6	dbSNP_79	91	5351,3027		1706,1939,544	no	coding-synonymous	HIVEP2	NM_006734.3		3103,2517,594	CC,CT,TT		36.1303,16.7407,29.8117		2295/2447	143074700	8723,3705	2025	4189	6214	SO:0001819	synonymous_variant	3097	exon10			GCTAGGTGGACCA	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.6885A>G	6.37:g.143074700T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	119	44	0.369748	NM_006734	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																			T|0.258;C|0.742	0.742	strong		0.527	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256470	24256470	+	Silent	SNP	C	C	T	rs2291577	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:24256470C>T	ENST00000256412.4	+	9	1066	c.846C>T	c.(844-846)agC>agT	p.S282S	ADAMDEC1_ENST00000522298.1_Silent_p.S203S|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Silent_p.S203S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	282	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TGGTGCCCAGCGCAAGCACCA	0.483													C|||	1467	0.292931	0.0968	0.4539	5008	,	,		19362	0.2034		0.4235	False		,,,				2504	0.4018				p.S282S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.C846T						PASS	.	C	,,	674,3732	286.3+/-278.7	52,570,1581	118.0	110.0	113.0		609,609,846	-0.4	0.0	8	dbSNP_100	113	3783,4817	536.6+/-383.0	826,2131,1343	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	878,2701,2924	TT,TC,CC		43.9884,15.2973,34.2688	,,	203/392,203/392,282/471	24256470	4457,8549	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon9			GCCCAGCGCAAGC	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.846C>T	8.37:g.24256470C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			C|0.670;T|0.330	0.330	strong		0.483	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
COL18A1	80781	hgsc.bcm.edu	37	21	46927489	46927489	+	Silent	SNP	A	A	G	rs12483761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46927489A>G	ENST00000359759.4	+	37	4497	c.4476A>G	c.(4474-4476)acA>acG	p.T1492T	COL18A1_ENST00000355480.5_Silent_p.T1257T|SLC19A1_ENST00000567670.1_Intron|COL18A1_ENST00000400337.2_Silent_p.T1077T			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1492	Nonhelical region 11 (NC11).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		AGGCCCGGACACCACTCCCAC	0.632													A|||	593	0.118411	0.1551	0.2176	5008	,	,		14650	0.0278		0.1332	False		,,,				2504	0.0767				p.T1254T		Atlas-SNP	.											.	COL18A1	129	.	0			c.A3762G						PASS	.	A	,	565,3459		40,485,1487	57.0	65.0	63.0		3771,3231	-6.9	0.0	21	dbSNP_120	63	1099,7233		75,949,3142	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	115,1434,4629	GG,GA,AA		13.1901,14.0408,13.4671	,	1257/1520,1077/1340	46927489	1664,10692	2012	4166	6178	SO:0001819	synonymous_variant	80781	exon38			CCGGACACCACTC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.4476A>G	21.37:g.46927489A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	190	93	0.489474	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				A|0.882;G|0.118	0.118	strong		0.632	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
PAICS	10606	hgsc.bcm.edu	37	4	57314612	57314612	+	Missense_Mutation	SNP	C	C	G	rs138933625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57314612C>G	ENST00000512576.1	+	4	583	c.422C>G	c.(421-423)tCt>tGt	p.S141C	PAICS_ENST00000514888.1_Missense_Mutation_p.S49C|PAICS_ENST00000264221.2_Missense_Mutation_p.S141C|PAICS_ENST00000399688.3_Missense_Mutation_p.S148C	NM_001079524.1	NP_001072992.1	P22234	PUR6_HUMAN	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase	141	SAICAR synthetase.				'de novo' IMP biosynthetic process (GO:0006189)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|phosphoribosylaminoimidazole carboxylase activity (GO:0004638)|phosphoribosylaminoimidazolesuccinocarboxamide synthase activity (GO:0004639)			endometrium(1)|kidney(2)|large_intestine(1)|urinary_tract(1)	5	Glioma(25;0.08)|all_neural(26;0.101)				L-Aspartic Acid(DB00128)	CCACAGTGGTCTGAGGAACAG	0.363													C|||	117	0.0233626	0.0023	0.0504	5008	,	,		18441	0.0		0.0696	False		,,,				2504	0.0092				p.S148C	GBM(53;429 1144 8755 40726)	Atlas-SNP	.											PAICS,NS,haematopoietic_neoplasm,0,1	PAICS	21	1	0			c.C443G						PASS	.	C	CYS/SER,CYS/SER,CYS/SER	51,3635		0,51,1792	39.0	36.0	37.0		422,443,422	5.5	1.0	4	dbSNP_134	37	464,7738		15,434,3652	yes	missense,missense,missense	PAICS	NM_001079524.1,NM_001079525.1,NM_006452.3	112,112,112	15,485,5444	GG,GC,CC		5.6572,1.3836,4.3321	possibly-damaging,possibly-damaging,possibly-damaging	141/426,148/433,141/426	57314612	515,11373	1843	4101	5944	SO:0001583	missense	10606	exon5			AGTGGTCTGAGGA	X53793	CCDS47060.1, CCDS47061.1	4q12	2012-07-13			ENSG00000128050	ENSG00000128050	4.1.1.21, 6.3.2.6		8587	protein-coding gene	gene with protein product		172439		PAIS		2253271, 8106516	Standard	NM_006452		Approved	ADE2H1, AIRC	uc003hbt.1	P22234	OTTHUMG00000160957	ENST00000512576.1:c.422C>G	4.37:g.57314612C>G	ENSP00000421096:p.Ser141Cys	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	242	126	0.520661	NM_001079525	E9PDH9|Q68CQ5	Missense_Mutation	SNP	ENST00000512576.1	37	CCDS47061.1	65	0.02976190476190476	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	45	0.059366754617414245	C	20.4	3.983941	0.74474	0.013836	0.056572	ENSG00000128050	ENST00000514888;ENST00000264221;ENST00000505164;ENST00000399688;ENST00000512576	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	5.53	5.53	0.82687	ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.09468	0.0233	L	0.40543	1.245	0.80722	D	1	P;P;P	0.37955	0.612;0.558;0.612	B;B;B	0.43225	0.412;0.289;0.412	T	0.05767	-1.0865	10	0.51188	T	0.08	-24.3153	19.8372	0.96661	0.0:1.0:0.0:0.0	rs11549969	141;148;141	E9PBS1;P22234-2;P22234	.;.;PUR6_HUMAN	C	49;141;141;148;141	ENSP00000424907:S49C;ENSP00000264221:S141C;ENSP00000424053:S141C;ENSP00000382595:S148C;ENSP00000421096:S141C	ENSP00000264221:S141C	S	+	2	0	PAICS	57009369	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	7.689000	0.84165	2.770000	0.95276	0.655000	0.94253	TCT	C|0.962;G|0.038	0.038	strong		0.363	PAICS-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363136.2	NM_006452	
NLRP14	338323	hgsc.bcm.edu	37	11	7059981	7059981	+	Missense_Mutation	SNP	G	G	A	rs61063081	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7059981G>A	ENST00000299481.4	+	2	510	c.164G>A	c.(163-165)cGg>cAg	p.R55Q		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	55	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		R -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:16931801}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		AAGGCCAGGCGGGAGGACCTG	0.443													G|||	482	0.096246	0.0666	0.1297	5008	,	,		18849	0.0179		0.2147	False		,,,				2504	0.0716				p.R55Q		Atlas-SNP	.											.	NLRP14	187	.	0			c.G164A						PASS	.	G	GLN/ARG	370,4032	182.9+/-210.6	13,344,1844	58.0	63.0	61.0		164	2.2	0.0	11	dbSNP_129	61	1840,6752	325.0+/-316.7	200,1440,2656	yes	missense	NLRP14	NM_176822.3	43	213,1784,4500	AA,AG,GG		21.4153,8.4053,17.0078	probably-damaging	55/1094	7059981	2210,10784	2201	4296	6497	SO:0001583	missense	338323	exon2			CCAGGCGGGAGGA	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.164G>A	11.37:g.7059981G>A	ENSP00000299481:p.Arg55Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	247	0.1130952380952381	24	0.04878048780487805	48	0.13259668508287292	13	0.022727272727272728	162	0.21372031662269128	G	14.50	2.554234	0.45487	0.084053	0.214153	ENSG00000158077	ENST00000299481	T	0.53857	0.6	4.22	2.23	0.28157	Pyrin (2);DEATH-like (2);	0.529188	0.15927	N	0.237859	T	0.00109	0.0003	M	0.78456	2.415	0.80722	P	0.0	D	0.76494	0.999	P	0.62089	0.898	T	0.17289	-1.0374	9	0.19147	T	0.46	.	10.4223	0.44356	0.0:0.3865:0.6135:0.0	rs61063081;rs61879042	55	Q86W24	NAL14_HUMAN	Q	55	ENSP00000299481:R55Q	ENSP00000299481:R55Q	R	+	2	0	NLRP14	7016557	0.001000	0.12720	0.000000	0.03702	0.948000	0.59901	0.751000	0.26348	0.659000	0.30945	0.655000	0.94253	CGG	G|0.835;A|0.165	0.165	strong		0.443	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
ADAM21	8747	hgsc.bcm.edu	37	14	70925665	70925665	+	Silent	SNP	G	G	A	rs10148733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70925665G>A	ENST00000603540.1	+	2	1707	c.1449G>A	c.(1447-1449)caG>caA	p.Q483Q	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.Q483Q	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	483	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		CATCTCATCAGTGTCCAGAAG	0.463													G|||	452	0.0902556	0.1808	0.0389	5008	,	,		23319	0.0754		0.0368	False		,,,				2504	0.0746				p.Q483Q		Atlas-SNP	.											.	ADAM21	181	.	0			c.G1449A						PASS	.	G		647,3759	276.9+/-273.4	51,545,1607	80.0	74.0	76.0		1449	-1.1	1.0	14	dbSNP_119	76	324,8276	113.7+/-173.7	5,314,3981	no	coding-synonymous	ADAM21	NM_003813.3		56,859,5588	AA,AG,GG		3.7674,14.6845,7.4658		483/723	70925665	971,12035	2203	4300	6503	SO:0001819	synonymous_variant	8747	exon2			TCATCAGTGTCCA	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.1449G>A	14.37:g.70925665G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	167	68	0.407186	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			G|0.914;A|0.086	0.086	strong		0.463	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
SPTAN1	6709	hgsc.bcm.edu	37	9	131371241	131371241	+	Missense_Mutation	SNP	A	A	G	rs145038571		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131371241A>G	ENST00000372731.4	+	35	4690	c.4580A>G	c.(4579-4581)aAt>aGt	p.N1527S	SPTAN1_ENST00000372739.3_Missense_Mutation_p.N1527S|SPTAN1_ENST00000358161.5_Missense_Mutation_p.N1527S	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1527					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						AGCCGGCGCAATGAGGTCTTG	0.572													A|||	1	0.000199681	0.0	0.0014	5008	,	,		20265	0.0		0.0	False		,,,				2504	0.0				p.N1527S	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A4580G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	118.0	121.0	120.0		4580,4520,4580	5.8	1.0	9	dbSNP_134	120	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense,missense	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	46,46,46	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	benign,benign,benign	1527/2478,1507/2453,1527/2473	131371241	14,12992	2203	4300	6503	SO:0001583	missense	6709	exon35			GGCGCAATGAGGT	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4580A>G	9.37:g.131371241A>G	ENSP00000361816:p.Asn1527Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	13.35	2.209863	0.39003	0.0	0.001628	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.46063	0.88;1.39;0.88	5.77	5.77	0.91146	.	0.141471	0.64402	D	0.000005	T	0.27900	0.0687	N	0.16266	0.395	0.54753	D	0.999983	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.11227	-1.0596	10	0.11485	T	0.65	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	1507;1527;1527	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	S	1527;1527;1527;1507	ENSP00000350882:N1527S;ENSP00000361816:N1527S;ENSP00000361824:N1527S	ENSP00000350882:N1527S	N	+	2	0	SPTAN1	130411062	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.013000	0.57138	2.326000	0.78906	0.533000	0.62120	AAT	A|0.999;G|0.001	0.001	strong		0.572	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
NMI	9111	hgsc.bcm.edu	37	2	152139416	152139416	+	Missense_Mutation	SNP	G	G	A	rs1048135	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:152139416G>A	ENST00000243346.5	-	2	517	c.47C>T	c.(46-48)tCg>tTg	p.S16L		NM_004688.2	NP_004679.2	Q13287	NMI_HUMAN	N-myc (and STAT) interactor	16			S -> L (in dbSNP:rs1048135).		inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription cofactor activity (GO:0003712)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.0571)		TTCATCTGGCGAATGCTCCTT	0.259													G|||	1566	0.3127	0.0545	0.4885	5008	,	,		13379	0.3839		0.4374	False		,,,				2504	0.3354				p.S16L		Atlas-SNP	.											NMI,colon,carcinoma,+1,1	NMI	21	1	0			c.C47T						PASS	.	G	LEU/SER	473,3925	203.8+/-226.2	21,431,1747	54.0	53.0	53.0		47	-4.6	0.0	2	dbSNP_86	53	3835,4727	530.2+/-381.7	845,2145,1291	yes	missense	NMI	NM_004688.2	145	866,2576,3038	AA,AG,GG		44.7909,10.7549,33.2407	benign	16/308	152139416	4308,8652	2199	4281	6480	SO:0001583	missense	9111	exon2			TCTGGCGAATGCT	U32849	CCDS2192.1	2q23	2008-05-23			ENSG00000123609	ENSG00000123609			7854	protein-coding gene	gene with protein product		603525				8668343, 9989503	Standard	NM_004688		Approved		uc002txi.2	Q13287	OTTHUMG00000131867	ENST00000243346.5:c.47C>T	2.37:g.152139416G>A	ENSP00000243346:p.Ser16Leu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	150	59	0.393333	NM_004688	B5BU69|Q53TI8|Q9BVE5	Missense_Mutation	SNP	ENST00000243346.5	37	CCDS2192.1	754	0.34523809523809523	30	0.06097560975609756	177	0.4889502762430939	211	0.3688811188811189	336	0.44327176781002636	G	5.125	0.208667	0.09757	0.107549	0.447909	ENSG00000123609	ENST00000243346;ENST00000414946	T;T	0.67865	1.6;-0.29	3.93	-4.59	0.03400	.	8.640450	0.00166	N	0.000000	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.31392	-0.9945	9	0.23891	T	0.37	13.0622	0.4636	0.00520	0.2341:0.1642:0.3082:0.2935	rs1048135;rs3188113;rs17412355;rs17804427;rs52833796;rs57852846;rs1048135	16;16;16	B4DQD4;C9JW17;Q13287	.;.;NMI_HUMAN	L	16	ENSP00000243346:S16L;ENSP00000387373:S16L	ENSP00000243346:S16L	S	-	2	0	NMI	151847662	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.958000	0.00674	-1.082000	0.03101	-0.242000	0.12053	TCG	G|0.672;N|0.000	.	strong		0.259	NMI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254817.2	NM_004688	
PNPLA8	50640	hgsc.bcm.edu	37	7	108155377	108155377	+	Missense_Mutation	SNP	G	G	A	rs139626312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:108155377G>A	ENST00000422087.1	-	4	965	c.559C>T	c.(559-561)Cgc>Tgc	p.R187C	PNPLA8_ENST00000388728.5_Missense_Mutation_p.R187C|PNPLA8_ENST00000483879.1_Intron|PNPLA8_ENST00000453144.1_Missense_Mutation_p.R87C|PNPLA8_ENST00000436062.1_Missense_Mutation_p.R187C|PNPLA8_ENST00000257694.8_Missense_Mutation_p.R187C|PNPLA8_ENST00000426128.2_Missense_Mutation_p.R187C	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	187					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						AAAAGACTGCGTTTACCTATA	0.294													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18615	0.0		0.004	False		,,,				2504	0.002				p.R187C		Atlas-SNP	.											PNPLA8,caecum,carcinoma,+1,2	PNPLA8	82	2	0			c.C559T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	52.0	55.0	54.0		559	3.8	0.1	7	dbSNP_134	54	43,8557	27.9+/-77.7	0,43,4257	yes	missense	PNPLA8	NM_015723.2	180	0,49,6454	AA,AG,GG		0.5,0.1362,0.3767	possibly-damaging	187/783	108155377	49,12957	2203	4300	6503	SO:0001583	missense	50640	exon2			GACTGCGTTTACC	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"""Patatin-like phospholipase domain containing"""	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.559C>T	7.37:g.108155377G>A	ENSP00000410804:p.Arg187Cys	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	37	CCDS34733.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	10.38	1.334998	0.24253	0.001362	0.005	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000453144;ENST00000436062;ENST00000453085;ENST00000427008	D;D;D;D;D;D;D	0.97959	-3.43;-4.63;-3.43;-4.63;-4.62;-4.63;-4.62	5.78	3.83	0.44106	.	0.974744	0.08470	N	0.941087	D	0.90445	0.7008	N	0.08118	0	0.09310	N	1	P	0.47762	0.9	B	0.40009	0.316	D	0.86221	0.1631	10	0.66056	D	0.02	.	8.1982	0.31409	0.0:0.2353:0.4795:0.2852	.	187	Q9NP80	PLPL8_HUMAN	C	187;187;187;187;87;187;87;187	ENSP00000394988:R187C;ENSP00000257694:R187C;ENSP00000373380:R187C;ENSP00000410804:R187C;ENSP00000387789:R87C;ENSP00000406779:R187C;ENSP00000402274:R87C	ENSP00000257694:R187C	R	-	1	0	PNPLA8	107942613	0.537000	0.26386	0.086000	0.20670	0.523000	0.34469	0.688000	0.25422	1.406000	0.46857	0.591000	0.81541	CGC	G|0.997;A|0.003	0.003	strong		0.294	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723	
HRNR	388697	hgsc.bcm.edu	37	1	152192825	152192825	+	Missense_Mutation	SNP	C	C	T	rs6666097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152192825C>T	ENST00000368801.2	-	3	1355	c.1280G>A	c.(1279-1281)gGc>gAc	p.G427D	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	427			G -> D (in dbSNP:rs6666097).		establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCACGCTGGCCGTGGCCTGG	0.617													C|||	1730	0.345447	0.2073	0.2795	5008	,	,		21348	0.2917		0.5855	False		,,,				2504	0.3875				p.G427D		Atlas-SNP	.											HRNR,NS,carcinoma,+1,1	HRNR	403	1	0			c.G1280A						PASS	.	C	ASP/GLY	1145,3261	406.0+/-333.7	150,845,1208	74.0	77.0	76.0		1280	0.3	0.0	1	dbSNP_116	76	5083,3517	632.4+/-398.6	1502,2079,719	no	missense	HRNR	NM_001009931.1	94	1652,2924,1927	TT,TC,CC		40.8953,25.9873,47.8856	possibly-damaging	427/2851	152192825	6228,6778	2203	4300	6503	SO:0001583	missense	388697	exon3			CGCTGGCCGTGGC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1280G>A	1.37:g.152192825C>T	ENSP00000357791:p.Gly427Asp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	868	0.3974358974358974	109	0.22154471544715448	131	0.36187845303867405	182	0.3181818181818182	446	0.5883905013192612	C	7.616	0.675748	0.14841	0.259873	0.591047	ENSG00000197915	ENST00000368801	T	0.04156	3.69	3.61	0.311	0.15831	.	.	.	.	.	T	0.01124	0.0037	L	0.27053	0.805	0.80722	P	0.0	P	0.47409	0.895	B	0.41412	0.356	T	0.50180	-0.8858	8	0.35671	T	0.21	.	3.5232	0.07750	0.196:0.5671:0.0:0.2369	rs6666097	427	Q86YZ3	HORN_HUMAN	D	427	ENSP00000357791:G427D	ENSP00000357791:G427D	G	-	2	0	HRNR	150459449	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.075000	0.11431	0.181000	0.19994	0.644000	0.83932	GGC	C|0.545;T|0.455	0.455	strong		0.617	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
ZNF440	126070	hgsc.bcm.edu	37	19	11941221	11941221	+	Missense_Mutation	SNP	T	T	A	rs424132	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11941221T>A	ENST00000304060.5	+	2	291	c.127T>A	c.(127-129)Tta>Ata	p.L43I		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	43	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		L -> I (in dbSNP:rs424132).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CCTGACCTCTTTAGGTAAGGA	0.443													g|||	1609	0.321286	0.4758	0.3271	5008	,	,		19585	0.1597		0.3628	False		,,,				2504	0.2321				p.L43I		Atlas-SNP	.											.	ZNF440	56	.	0			c.T127A						PASS	.						103.0	112.0	109.0					19																	11941221		2203	4297	6500	SO:0001583	missense	126070	exon2			ACCTCTTTAGGTA	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"""Zinc fingers, C2H2-type"", ""-"""	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.127T>A	19.37:g.11941221T>A	ENSP00000305373:p.Leu43Ile	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	231	111	0.480519	NM_152357	Q8N1R9	Missense_Mutation	SNP	ENST00000304060.5	37	CCDS42503.1	589	0.2696886446886447	168	0.34146341463414637	102	0.281767955801105	79	0.1381118881118881	240	0.316622691292876	a	0.001	-4.623390	0.00000	.	.	ENSG00000171295	ENST00000304060;ENST00000427505;ENST00000414255	T;T;T	0.02446	4.29;4.29;4.29	1.74	-3.49	0.04724	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	N	0.16166	0.38	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45804	-0.9236	8	0.02654	T	1	.	1.758	0.02986	0.3493:0.1726:0.3585:0.1196	rs424132	43	Q8IYI8	ZN440_HUMAN	I	43;46;45	ENSP00000305373:L43I;ENSP00000393489:L46I;ENSP00000411974:L45I	ENSP00000305373:L43I	L	+	1	2	ZNF440	11802221	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-2.264000	0.01173	-4.525000	0.00044	-5.145000	0.00001	TTA	T|0.703;A|0.297	0.297	strong		0.443	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357	
USH1C	10083	hgsc.bcm.edu	37	11	17519742	17519742	+	Missense_Mutation	SNP	C	C	G	rs1064074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:17519742C>G	ENST00000318024.4	-	19	1665	c.1557G>C	c.(1555-1557)gaG>gaC	p.E519D	USH1C_ENST00000529563.1_5'UTR|USH1C_ENST00000005226.7_Missense_Mutation_p.E819D|USH1C_ENST00000527720.1_Missense_Mutation_p.E488D|USH1C_ENST00000527020.1_Missense_Mutation_p.E500D	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	519	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.		E -> D (in dbSNP:rs1064074). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9610721}.		auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						GCAGGGCAGCCTCAGCCTCAG	0.592													C|||	2108	0.420927	0.4168	0.3718	5008	,	,		20632	0.3026		0.5636	False		,,,				2504	0.4366				p.E819D		Atlas-SNP	.											USH1C,NS,carcinoma,-2,1	USH1C	157	1	0			c.G2457C						PASS	.	C	ASP/GLU,ASP/GLU	1886,2514	541.7+/-375.8	417,1052,731	217.0	174.0	189.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1557,2457	3.4	1.0	11	dbSNP_86	189	4803,3783	613.7+/-396.1	1354,2095,844	yes	missense,missense	USH1C	NM_005709.3,NM_153676.3	45,45	1771,3147,1575	GG,GC,CC		44.0601,42.8636,48.4907	benign,benign	519/553,819/900	17519742	6689,6297	2200	4293	6493	SO:0001583	missense	10083	exon24			GGCAGCCTCAGCC	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"""harmonin"""	605242	"""deafness, autosomal recessive 18"""	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1557G>C	11.37:g.17519742C>G	ENSP00000317018:p.Glu519Asp	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	160	158	0.9875	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	37	CCDS31438.1	949	0.43452380952380953	218	0.44308943089430897	143	0.39502762430939226	161	0.28146853146853146	427	0.5633245382585752	C	15.44	2.834873	0.50951	0.428636	0.559399	ENSG00000006611	ENST00000318024;ENST00000527720;ENST00000527020;ENST00000005226	T;T;T;T	0.27104	1.69;1.69;1.69;1.69	5.27	3.37	0.38596	PDZ/DHR/GLGF (4);	0.066566	0.64402	D	0.000011	T	0.00012	0.0000	N	0.08118	0	0.36615	P	0.12457799999999997	B;B;B	0.20550	0.006;0.013;0.046	B;B;B	0.25506	0.016;0.03;0.061	T	0.39881	-0.9592	9	0.30078	T	0.28	.	11.099	0.48163	0.0:0.8429:0.0:0.1571	rs1064074;rs3179923;rs17851377;rs61092531;rs1064074	500;519;819	Q9Y6N9-4;Q9Y6N9;Q7RTU8	.;USH1C_HUMAN;.	D	519;488;500;819	ENSP00000317018:E519D;ENSP00000432944:E488D;ENSP00000436934:E500D;ENSP00000005226:E819D	ENSP00000005226:E819D	E	-	3	2	USH1C	17476318	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	0.600000	0.24104	1.218000	0.43458	0.561000	0.74099	GAG	C|0.515;G|0.483	0.483	strong		0.592	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
KRT75	9119	hgsc.bcm.edu	37	12	52827786	52827786	+	Silent	SNP	C	C	T	rs2232385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52827786C>T	ENST00000252245.5	-	1	523	c.303G>A	c.(301-303)ggG>ggA	p.G101G		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	101	Gly-rich.|Head.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		CAACTCCACCCCCATAGCCAA	0.597													C|||	765	0.152756	0.2247	0.2104	5008	,	,		15648	0.0754		0.1213	False		,,,				2504	0.1268				p.G101G		Atlas-SNP	.											KRT75,colon,carcinoma,-2,1	KRT75	75	1	0			c.G303A						PASS	.	C		916,3490	350.5+/-310.9	97,722,1384	115.0	121.0	119.0		303	-2.6	0.1	12	dbSNP_98	119	947,7653	208.0+/-249.6	55,837,3408	no	coding-synonymous	KRT75	NM_004693.2		152,1559,4792	TT,TC,CC		11.0116,20.7898,14.3242		101/552	52827786	1863,11143	2203	4300	6503	SO:0001819	synonymous_variant	9119	exon1			TCCACCCCCATAG	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.303G>A	12.37:g.52827786C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	173	76	0.439306	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																			C|0.856;T|0.144	0.144	strong		0.597	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
HERC1	8925	hgsc.bcm.edu	37	15	63937209	63937209	+	Missense_Mutation	SNP	C	C	G	rs2229749	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63937209C>G	ENST00000443617.2	-	57	11253	c.11166G>C	c.(11164-11166)gaG>gaC	p.E3722D		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3722			E -> D (in dbSNP:rs2229749). {ECO:0000269|PubMed:8861955}.		cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.E3722D(1)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TTGATTCCTGCTCCCACCATC	0.408													G|||	3187	0.636382	0.8744	0.647	5008	,	,		17258	0.1022		0.8956	False		,,,				2504	0.591				p.E3722D		Atlas-SNP	.											HERC1_ENST00000443617,NS,carcinoma,0,1	HERC1	624	1	1	Substitution - Missense(1)	stomach(1)	c.G11166C						PASS	.	G	ASP/GLU	3337,557		1433,471,43	174.0	164.0	167.0		11166	-3.3	1.0	15	dbSNP_98	167	7302,994		3205,892,51	yes	missense	HERC1	NM_003922.3	45	4638,1363,94	GG,GC,CC		11.9817,14.3041,12.7235	benign	3722/4862	63937209	10639,1551	1947	4148	6095	SO:0001583	missense	8925	exon57			TTCCTGCTCCCAC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.11166G>C	15.37:g.63937209C>G	ENSP00000390158:p.Glu3722Asp	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	1417	0.6488095238095238	435	0.8841463414634146	251	0.6933701657458563	58	0.10139860139860139	673	0.8878627968337731	G	0.625	-0.819633	0.02776	0.856959	0.880183	ENSG00000103657	ENST00000443617	T	0.22336	1.96	5.96	-3.28	0.05033	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.204766	0.40064	N	0.001190	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.43212	-0.9405	9	0.02654	T	1	.	2.83	0.05497	0.1622:0.3595:0.2524:0.2258	rs2229749;rs7162473;rs52812237;rs56862839	3722	Q15751	HERC1_HUMAN	D	3722	ENSP00000390158:E3722D	ENSP00000390158:E3722D	E	-	3	2	HERC1	61724262	0.621000	0.27077	0.983000	0.44433	0.581000	0.36288	-0.224000	0.09164	-0.303000	0.08856	-1.556000	0.00890	GAG	C|0.338;G|0.662	0.662	strong		0.408	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
SH2D4A	63898	hgsc.bcm.edu	37	8	19221700	19221700	+	Missense_Mutation	SNP	G	G	A	rs34608771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:19221700G>A	ENST00000265807.3	+	7	1235	c.824G>A	c.(823-825)aGc>aAc	p.S275N	SH2D4A_ENST00000518040.1_Missense_Mutation_p.S230N|SH2D4A_ENST00000519207.1_Missense_Mutation_p.S275N	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	275			S -> N (in dbSNP:rs34608771). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AGGCTGCAAAGCCCCTTGCGT	0.527													G|||	891	0.177915	0.0946	0.2378	5008	,	,		14052	0.0595		0.3072	False		,,,				2504	0.2372				p.S275N		Atlas-SNP	.											.	SH2D4A	49	.	0			c.G824A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	556,3850	249.0+/-256.6	36,484,1683	81.0	82.0	81.0		824,689,824	3.9	0.0	8	dbSNP_126	81	2669,5931	427.8+/-355.7	416,1837,2047	yes	missense,missense,missense	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	46,46,46	452,2321,3730	AA,AG,GG		31.0349,12.6192,24.7962	benign,benign,benign	275/455,230/410,275/455	19221700	3225,9781	2203	4300	6503	SO:0001583	missense	63898	exon7			TGCAAAGCCCCTT	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.824G>A	8.37:g.19221700G>A	ENSP00000265807:p.Ser275Asn	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	401	0.18360805860805862	40	0.08130081300813008	95	0.26243093922651933	32	0.055944055944055944	234	0.3087071240105541	G	11.29	1.596322	0.28445	0.126192	0.310349	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207	T;D;T	0.94537	2.62;-3.45;2.62	5.75	3.94	0.45596	.	0.730267	0.13855	N	0.358071	T	0.00012	0.0000	L	0.28344	0.845	0.80722	P	0.0	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.07481	-1.0770	9	0.13853	T	0.58	.	7.9302	0.29897	0.1895:0.0:0.8105:0.0	rs34608771	230;275	B4DDR1;Q9H788	.;SH24A_HUMAN	N	275;230;275	ENSP00000265807:S275N;ENSP00000429482:S230N;ENSP00000428684:S275N	ENSP00000265807:S275N	S	+	2	0	SH2D4A	19265980	0.001000	0.12720	0.006000	0.13384	0.008000	0.06430	0.087000	0.14958	0.754000	0.32968	0.563000	0.77884	AGC	G|0.764;A|0.236	0.236	strong		0.527	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
USP22	23326	hgsc.bcm.edu	37	17	20911204	20911204	+	Silent	SNP	G	G	T	rs11541311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:20911204G>T	ENST00000261497.4	-	9	1412	c.1209C>A	c.(1207-1209)atC>atA	p.I403I	USP22_ENST00000455117.2_Intron|USP22_ENST00000537526.2_Silent_p.I391I	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	403	USP.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						AACAGGCTACGATGGGCAGTT	0.488													G|||	780	0.155751	0.0159	0.1326	5008	,	,		17819	0.1667		0.2465	False		,,,				2504	0.2566				p.I403I		Atlas-SNP	.											.	USP22	45	.	0			c.C1209A						PASS	.	G		176,3664		9,158,1753	136.0	124.0	128.0		1209	-7.8	0.3	17	dbSNP_120	128	1813,6489		201,1411,2539	no	coding-synonymous	USP22	NM_015276.1		210,1569,4292	TT,TG,GG		21.8381,4.5833,16.3812		403/526	20911204	1989,10153	1920	4151	6071	SO:0001819	synonymous_variant	23326	exon9			GGCTACGATGGGC	AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"""Ubiquitin-specific peptidases"""	12621	protein-coding gene	gene with protein product		612116	"""ubiquitin specific protease 22"", ""ubiquitin specific peptidase 3-like"""	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.1209C>A	17.37:g.20911204G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Silent	SNP	ENST00000261497.4	37	CCDS42285.1																																																																																			G|0.838;T|0.162	0.162	strong		0.488	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1		
PSMB5	5693	hgsc.bcm.edu	37	14	23504021	23504021	+	Missense_Mutation	SNP	G	G	A	rs11543947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:23504021G>A	ENST00000361611.6	-	1	333	c.70C>T	c.(70-72)Cgt>Tgt	p.R24C	PSMB5_ENST00000425762.2_Intron|AL132780.1_ENST00000385031.1_RNA|PSMB5_ENST00000493471.2_Missense_Mutation_p.R24C|PSMB5_ENST00000460922.2_Missense_Mutation_p.R24C	NM_002797.3	NP_002788.1	P28074	PSB5_HUMAN	proteasome (prosome, macropain) subunit, beta type, 5	24			R -> C (in dbSNP:rs11543947).		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to oxidative stress (GO:0006979)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)|Carfilzomib(DB08889)	AGATCTGCACGACCCCCAAGT	0.582													G|||	180	0.0359425	0.0234	0.0288	5008	,	,		16780	0.001		0.0626	False		,,,				2504	0.0665				p.R24C		Atlas-SNP	.											.	PSMB5	31	.	0			c.C70T						PASS	.	G	,CYS/ARG,CYS/ARG	169,4237	110.8+/-149.0	5,159,2039	55.0	53.0	54.0		,70,70	3.4	1.0	14	dbSNP_120	54	711,7889	174.5+/-224.7	22,667,3611	yes	intron,missense,missense	PSMB5	NM_001130725.1,NM_001144932.1,NM_002797.3	,180,180	27,826,5650	AA,AG,GG		8.2674,3.8357,6.7661	,probably-damaging,probably-damaging	,24/204,24/264	23504021	880,12126	2203	4300	6503	SO:0001583	missense	5693	exon1			CTGCACGACCCCC	D29011	CCDS9584.1, CCDS45083.1, CCDS45084.1	14q11.2	2008-08-29			ENSG00000100804	ENSG00000100804		"""Proteasome (prosome, macropain) subunits"""	9542	protein-coding gene	gene with protein product		600306				8066462, 8811196	Standard	NM_001130725		Approved	X, MB1	uc001wii.3	P28074	OTTHUMG00000028713	ENST00000361611.6:c.70C>T	14.37:g.23504021G>A	ENSP00000355325:p.Arg24Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_001144932	B2R4N9|B4DUM9|D3DS43|E9PAV2|Q16242|Q6PEW2|Q7Z3B5|Q86T01|Q9TNN9	Missense_Mutation	SNP	ENST00000361611.6	37	CCDS9584.1	67	0.030677655677655676	10	0.02032520325203252	11	0.03038674033149171	1	0.0017482517482517483	45	0.059366754617414245	G	15.41	2.824549	0.50739	0.038357	0.082674	ENSG00000100804	ENST00000361611;ENST00000493471;ENST00000460922	T;T;T	0.51071	0.72;0.72;0.72	5.22	3.37	0.38596	.	0.462115	0.23461	N	0.047933	T	0.01489	0.0048	N	0.19112	0.55	0.80722	D	1	B;B	0.13145	0.007;0.0	B;B	0.08055	0.003;0.0	T	0.04090	-1.0978	10	0.59425	D	0.04	-0.5438	4.4264	0.11505	0.0814:0.2848:0.4874:0.1464	rs11543947;rs52796051;rs56952751;rs11543947	24;24	P28074-2;P28074	.;PSB5_HUMAN	C	24	ENSP00000355325:R24C;ENSP00000452424:R24C;ENSP00000451286:R24C	ENSP00000334973:R24C	R	-	1	0	PSMB5	22573861	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	1.316000	0.33620	0.570000	0.29347	0.555000	0.69702	CGT	G|0.946;A|0.054	0.054	strong		0.582	PSMB5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071695.4	NM_002797	
EML5	161436	hgsc.bcm.edu	37	14	89151392	89151392	+	Silent	SNP	C	C	A	rs17204164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:89151392C>A	ENST00000380664.5	-	20	2948	c.2949G>T	c.(2947-2949)gtG>gtT	p.V983V	EML5_ENST00000352093.5_Silent_p.V945V|EML5_ENST00000554922.1_Silent_p.V983V			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	983						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CACTTTTATCCACTTCTAGTA	0.318													C|||	134	0.0267572	0.003	0.0259	5008	,	,		15603	0.0		0.0755	False		,,,				2504	0.0368				p.V983V		Atlas-SNP	.											.	EML5	141	.	0			c.G2949T						PASS	.	C		62,3594		3,56,1769	164.0	149.0	154.0		2949	3.1	1.0	14	dbSNP_123	154	659,7495		31,597,3449	no	coding-synonymous	EML5	NM_183387.2		34,653,5218	AA,AC,CC		8.0819,1.6958,6.105		983/1978	89151392	721,11089	1828	4077	5905	SO:0001819	synonymous_variant	161436	exon20			TTTATCCACTTCT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.2949G>T	14.37:g.89151392C>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Silent	SNP	ENST00000380664.5	37	CCDS45148.1																																																																																			C|0.962;A|0.038	0.038	strong		0.318	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
DOCK5	80005	hgsc.bcm.edu	37	8	25222165	25222165	+	Missense_Mutation	SNP	A	A	G	rs2271111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:25222165A>G	ENST00000276440.7	+	30	3112	c.3068A>G	c.(3067-3069)cAg>cGg	p.Q1023R		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1023			Q -> R (in dbSNP:rs2271111).		positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.Q1023R(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GCTATAAATCAGTTTGCTGAA	0.418													A|||	1230	0.245607	0.0711	0.304	5008	,	,		18344	0.3562		0.3698	False		,,,				2504	0.1984				p.Q1023R	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											DOCK5,NS,carcinoma,0,1	DOCK5	167	1	1	Substitution - Missense(1)	stomach(1)	c.A3068G						PASS	.	A	ARG/GLN	487,3919	213.8+/-233.3	26,435,1742	137.0	117.0	124.0		3068	4.3	1.0	8	dbSNP_100	124	2886,5714	414.1+/-351.3	498,1890,1912	yes	missense	DOCK5	NM_024940.6	43	524,2325,3654	GG,GA,AA		33.5581,11.0531,25.9342	benign	1023/1871	25222165	3373,9633	2203	4300	6503	SO:0001583	missense	80005	exon30			TAAATCAGTTTGC		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3068A>G	8.37:g.25222165A>G	ENSP00000276440:p.Gln1023Arg	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	182	86	0.472527	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	634	0.2902930402930403	37	0.07520325203252033	120	0.3314917127071823	189	0.3304195804195804	288	0.37994722955145116	A	10.21	1.287145	0.23478	0.110531	0.335581	ENSG00000147459	ENST00000276440	T	0.23950	1.88	5.62	4.34	0.51931	.	0.058883	0.64402	D	0.000001	T	0.00012	0.0000	L	0.41710	1.295	0.23920	P	0.99646016	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.41858	-0.9485	9	0.08837	T	0.75	.	7.572	0.27913	0.7907:0.0:0.073:0.1362	rs2271111;rs52835832;rs58353884;rs2271111	1013;1023	D3DSS6;Q9H7D0	.;DOCK5_HUMAN	R	1023	ENSP00000276440:Q1023R	ENSP00000276440:Q1023R	Q	+	2	0	DOCK5	25278082	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.300000	0.59079	2.142000	0.66516	0.528000	0.53228	CAG	A|0.749;G|0.251	0.251	strong		0.418	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
DYSF	8291	hgsc.bcm.edu	37	2	71738987	71738987	+	Silent	SNP	C	C	T	rs34603128	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71738987C>T	ENST00000258104.3	+	5	670	c.393C>T	c.(391-393)ccC>ccT	p.P131P	DYSF_ENST00000410041.1_Silent_p.P132P|DYSF_ENST00000429174.2_Silent_p.P131P|DYSF_ENST00000409762.1_Silent_p.P131P|DYSF_ENST00000409366.1_Silent_p.P132P|DYSF_ENST00000394120.2_Silent_p.P132P|DYSF_ENST00000410020.3_Silent_p.P132P|DYSF_ENST00000409651.1_Silent_p.P132P|DYSF_ENST00000409582.3_Silent_p.P131P|DYSF_ENST00000409744.1_Silent_p.P132P|DYSF_ENST00000413539.2_Silent_p.P131P	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	131					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GAGCTGTGCCCCTGTTCCCGC	0.672													C|||	562	0.11222	0.2065	0.1196	5008	,	,		16645	0.0119		0.1481	False		,,,				2504	0.046				p.P132P		Atlas-SNP	.											.	DYSF	536	.	0			c.C396T						PASS	.	C	,,,,,,,,,,,,,	663,3289		59,545,1372	59.0	44.0	49.0		396,393,393,393,393,393,393,396,396,396,396,396,396,393	2.6	0.8	2	dbSNP_126	49	822,6746		45,732,3007	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	104,1277,4379	TT,TC,CC		10.8615,16.7763,12.8906	,,,,,,,,,,,,,	132/2082,131/2067,131/2088,131/2102,131/2112,131/2098,131/2119,132/2113,132/2103,132/2089,132/2099,132/2068,132/2120,131/2081	71738987	1485,10035	1976	3784	5760	SO:0001819	synonymous_variant	8291	exon5			TGTGCCCCTGTTC	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.393C>T	2.37:g.71738987C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_001130984	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			C|0.861;T|0.139	0.139	strong		0.672	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
IQCE	23288	hgsc.bcm.edu	37	7	2611878	2611878	+	Silent	SNP	T	T	C	rs2917751	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2611878T>C	ENST00000402050.2	+	5	496	c.312T>C	c.(310-312)acT>acC	p.T104T	IQCE_ENST00000438376.2_Silent_p.T88T|IQCE_ENST00000325979.7_Silent_p.T39T|IQCE_ENST00000404984.1_Silent_p.T53T	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	104						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		ATGCGTGGACTGGCGTCCCCG	0.572													C|||	3312	0.661342	0.6301	0.6931	5008	,	,		19703	0.5159		0.7604	False		,,,				2504	0.729				p.T104T		Atlas-SNP	.											.	IQCE	66	.	0			c.T312C						PASS	.	C	,	2651,1407		875,901,253	69.0	74.0	72.0		264,312	3.8	0.1	7	dbSNP_101	72	6324,2034		2381,1562,236	no	coding-synonymous,coding-synonymous	IQCE	NM_001100390.1,NM_152558.3	,	3256,2463,489	CC,CT,TT		24.336,34.6723,27.7142	,	88/680,104/696	2611878	8975,3441	2029	4179	6208	SO:0001819	synonymous_variant	23288	exon5			GTGGACTGGCGTC	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.312T>C	7.37:g.2611878T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	37	CCDS43542.1																																																																																			T|0.301;C|0.699	0.699	strong		0.572	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
SLC9A4	389015	hgsc.bcm.edu	37	2	103095404	103095404	+	Silent	SNP	G	G	A	rs11692304	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:103095404G>A	ENST00000295269.4	+	2	820	c.363G>A	c.(361-363)tcG>tcA	p.S121S		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	121					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						ACCACAAATCGCCTCCGGTCA	0.607													G|||	1698	0.339058	0.2776	0.3314	5008	,	,		17601	0.2321		0.5219	False		,,,				2504	0.3497				p.S121S		Atlas-SNP	.											SLC9A4,NS,carcinoma,+1,1	SLC9A4	115	1	0			c.G363A						PASS	.	G		1337,3069	446.7+/-348.1	202,933,1068	69.0	64.0	66.0		363	-11.4	0.0	2	dbSNP_120	66	4126,4474	563.3+/-388.1	1020,2086,1194	no	coding-synonymous	SLC9A4	NM_001011552.3		1222,3019,2262	AA,AG,GG		47.9767,30.345,42.0037		121/799	103095404	5463,7543	2203	4300	6503	SO:0001819	synonymous_variant	389015	exon2			CAAATCGCCTCCG		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.363G>A	2.37:g.103095404G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_001011552	Q69YK0	Silent	SNP	ENST00000295269.4	37	CCDS33264.1																																																																																			G|0.609;A|0.391	0.391	strong		0.607	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
BCL2A1	597	hgsc.bcm.edu	37	15	80263217	80263217	+	Missense_Mutation	SNP	C	C	T	rs3826007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:80263217C>T	ENST00000267953.3	-	1	571	c.245G>A	c.(244-246)gGc>gAc	p.G82D	BCL2A1_ENST00000335661.6_Missense_Mutation_p.G82D	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	82			G -> D (in dbSNP:rs3826007). {ECO:0000269|Ref.6}.		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						GTTAATGATGCCGTCTTCAAA	0.403													C|||	1019	0.203474	0.0703	0.1599	5008	,	,		21004	0.2063		0.2545	False		,,,				2504	0.3589				p.G82D		Atlas-SNP	.											.	BCL2A1	28	.	0			c.G245A	GRCh37	CM064994	BCL2A1	M	rs3826007	PASS	.	C	ASP/GLY,ASP/GLY	406,4000	200.8+/-224.0	20,366,1817	207.0	193.0	197.0		245,245	5.6	0.8	15	dbSNP_107	197	2186,6414	373.7+/-337.1	259,1668,2373	yes	missense,missense	BCL2A1	NM_001114735.1,NM_004049.3	94,94	279,2034,4190	TT,TC,CC		25.4186,9.2147,19.9293	probably-damaging,probably-damaging	82/164,82/176	80263217	2592,10414	2203	4300	6503	SO:0001583	missense	597	exon1			ATGATGCCGTCTT		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.245G>A	15.37:g.80263217C>T	ENSP00000267953:p.Gly82Asp	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	238	128	0.537815	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	421	0.19276556776556777	31	0.06300813008130081	69	0.19060773480662985	128	0.22377622377622378	193	0.2546174142480211	C	16.22	3.062546	0.55432	0.092147	0.254186	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.54279	0.58;0.58	5.63	5.63	0.86233	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);Apoptosis regulator, Bcl-2, BH1 motif, conserved site (1);	1.583130	0.03463	N	0.212436	T	0.00073	0.0002	M	0.87328	2.875	0.18873	P	0.9999886628	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.39313	-0.9620	9	0.72032	D	0.01	-20.7853	17.8901	0.88869	0.0:1.0:0.0:0.0	rs3826007;rs60753792;rs3826007	82;82	Q86W13;Q16548	.;B2LA1_HUMAN	D	82	ENSP00000267953:G82D;ENSP00000335250:G82D	ENSP00000267953:G82D	G	-	2	0	BCL2A1	78050272	1.000000	0.71417	0.824000	0.32777	0.019000	0.09904	4.115000	0.57865	2.652000	0.90054	0.655000	0.94253	GGC	C|0.805;T|0.195	0.195	strong		0.403	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
ETFB	2109	hgsc.bcm.edu	37	19	51850290	51850290	+	Missense_Mutation	SNP	G	G	A	rs1130426	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51850290G>A	ENST00000309244.4	-	5	552	c.461C>T	c.(460-462)aCg>aTg	p.T154M	CTD-2616J11.16_ENST00000594311.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.T245M|CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.16_ENST00000601148.1_RNA	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	154			T -> M (in dbSNP:rs1130426). {ECO:0000269|PubMed:10356313, ECO:0000269|PubMed:15498874}.		cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		CCCCTCCAGCGTCACCTGGGA	0.617													G|||	2102	0.419728	0.472	0.451	5008	,	,		19007	0.2887		0.5686	False		,,,				2504	0.3088				p.T245M		Atlas-SNP	.											.	ETFB	46	.	0			c.C734T						PASS	.	G	MET/THR,MET/THR	2242,2164	588.3+/-386.9	549,1144,510	58.0	39.0	45.0		734,461	5.2	1.0	19	dbSNP_86	45	4805,3795	611.8+/-395.9	1350,2105,845	yes	missense,missense	ETFB	NM_001014763.1,NM_001985.2	81,81	1899,3249,1355	AA,AG,GG		44.1279,49.1148,45.8173	probably-damaging,probably-damaging	245/347,154/256	51850290	7047,5959	2203	4300	6503	SO:0001583	missense	2109	exon4			TCCAGCGTCACCT	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.461C>T	19.37:g.51850290G>A	ENSP00000311930:p.Thr154Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	1013	0.46382783882783885	241	0.4898373983739837	178	0.49171270718232046	168	0.2937062937062937	426	0.5620052770448549	G	22.0	4.229291	0.79688	0.508852	0.558721	ENSG00000105379	ENST00000309244;ENST00000354232	D;D	0.83075	-1.68;-1.68	5.2	5.2	0.72013	Electron transfer flavoprotein, alpha/beta-subunit, N-terminal (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.278610	0.35739	N	0.003016	T	0.00012	0.0000	L	0.55834	1.745	0.26377	P	0.9767906	D;D	0.76494	0.98;0.999	P;P	0.58210	0.696;0.835	T	0.49698	-0.8912	9	0.62326	D	0.03	.	11.6543	0.51309	0.0:0.0:0.8226:0.1773	rs1130426;rs1801446;rs2230253;rs3177751;rs3189246;rs17416267;rs52818865;rs60424048;rs3177751	154;245	P38117;P38117-2	ETFB_HUMAN;.	M	154;245	ENSP00000311930:T154M;ENSP00000346173:T245M	ENSP00000311930:T154M	T	-	2	0	ETFB	56542102	0.996000	0.38824	0.952000	0.39060	0.948000	0.59901	3.682000	0.54656	2.573000	0.86826	0.561000	0.74099	ACG	T|0.000;G|0.497;C|0.000;A|0.503	0.503	strong		0.617	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71366957	71366957	+	Missense_Mutation	SNP	C	C	A	rs3732240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71366957C>A	ENST00000244230.2	+	6	1625	c.1273C>A	c.(1273-1275)Ctg>Atg	p.L425M		NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	425			L -> M (in dbSNP:rs3732240).		negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)	p.L425M(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						CACCCTTCAACTGGAAGATAT	0.343													C|||	584	0.116613	0.0015	0.0735	5008	,	,		22147	0.4345		0.0159	False		,,,				2504	0.0787				p.L425M		Atlas-SNP	.											MPHOSPH10,NS,carcinoma,0,1	MPHOSPH10	81	1	1	Substitution - Missense(1)	stomach(1)	c.C1273A						PASS	.	C	MET/LEU	28,4378	34.3+/-65.2	0,28,2175	138.0	141.0	140.0		1273	5.3	0.7	2	dbSNP_107	140	122,8478	63.1+/-125.2	0,122,4178	yes	missense	MPHOSPH10	NM_005791.2	15	0,150,6353	AA,AC,CC		1.4186,0.6355,1.1533	probably-damaging	425/682	71366957	150,12856	2203	4300	6503	SO:0001583	missense	10199	exon6			CTTCAACTGGAAG	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1273C>A	2.37:g.71366957C>A	ENSP00000244230:p.Leu425Met	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	287	0.13141025641025642	1	0.0020325203252032522	22	0.06077348066298342	251	0.4388111888111888	13	0.017150395778364115	C	23.8	4.464524	0.84425	0.006355	0.014186	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.22134	1.97;1.97	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.82517	2.595	0.09310	P	0.999999709811	D	0.89917	1.0	D	0.87578	0.998	T	0.42413	-0.9453	9	0.66056	D	0.02	.	16.8902	0.86085	0.0:1.0:0.0:0.0	rs3732240;rs17006677;rs3732240	425	O00566	MPP10_HUMAN	M	425;285	ENSP00000244230:L425M;ENSP00000393034:L285M	ENSP00000244230:L425M	L	+	1	2	MPHOSPH10	71220465	1.000000	0.71417	0.736000	0.30914	0.989000	0.77384	5.452000	0.66638	2.669000	0.90835	0.585000	0.79938	CTG	C|0.956;A|0.044	0.044	strong		0.343	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
PLXNB2	23654	hgsc.bcm.edu	37	22	50720622	50720622	+	Silent	SNP	C	C	T	rs11547728	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50720622C>T	ENST00000449103.1	-	19	3248	c.3108G>A	c.(3106-3108)caG>caA	p.Q1036Q	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Silent_p.Q1036Q			O15031	PLXB2_HUMAN	plexin B2	1036	IPT/TIG 3.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCGTCATGGGCTGCAGGGATT	0.692													C|||	1911	0.381589	0.3192	0.3112	5008	,	,		14210	0.2688		0.4791	False		,,,				2504	0.5317				p.Q1036Q		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G3108A						PASS	.	C		1385,2663		246,893,885	23.0	27.0	25.0		3108	2.3	0.2	22	dbSNP_120	25	3874,4438		926,2022,1208	no	coding-synonymous	PLXNB2	NM_012401.3		1172,2915,2093	TT,TC,CC		46.6073,34.2144,42.5485		1036/1839	50720622	5259,7101	2024	4156	6180	SO:0001819	synonymous_variant	23654	exon19			CATGGGCTGCAGG		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3108G>A	22.37:g.50720622C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																			C|0.609;T|0.391	0.391	strong		0.692	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
NACA2	342538	hgsc.bcm.edu	37	17	59667953	59667953	+	Nonsense_Mutation	SNP	G	G	A	rs17610181	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59667953G>A	ENST00000521764.1	-	1	610	c.589C>T	c.(589-591)Cga>Tga	p.R197*		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	197	UBA.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					TTCAGAGCTCGGACTGCCTTT	0.403													G|||	741	0.147963	0.0575	0.1037	5008	,	,		22626	0.1667		0.1471	False		,,,				2504	0.2832				p.R197X		Atlas-SNP	.											.	NACA2	33	.	0			c.C589T						PASS	.	G	stop/ARG	329,4077	171.9+/-202.1	15,299,1889	257.0	228.0	238.0		589	-0.3	0.9	17	dbSNP_123	238	1249,7351	248.5+/-276.1	97,1055,3148	no	stop-gained	NACA2	NM_199290.3		112,1354,5037	AA,AG,GG		14.5233,7.4671,12.1329		197/216	59667953	1578,11428	2203	4300	6503	SO:0001587	stop_gained	342538	exon1			GAGCTCGGACTGC	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.589C>T	17.37:g.59667953G>A	ENSP00000427802:p.Arg197*	Somatic	290	1	0.00344828		WXS	Illumina HiSeq	Phase_I	325	136	0.418462	NM_199290	Q2VIR9	Nonsense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	254	0.1163003663003663	26	0.052845528455284556	40	0.11049723756906077	73	0.12762237762237763	115	0.1517150395778364	G	18.41	3.617954	0.66787	0.074671	0.145233	ENSG00000253506	ENST00000521764	.	.	.	0.753	-0.349	0.12609	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.09310	P	0.9999998989	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9511	0.14015	0.2556:0.0:0.7444:0.0	rs17610181;rs52809144;rs17610181	.	.	.	X	197	.	.	R	-	1	2	NACA2	57022735	1.000000	0.71417	0.903000	0.35520	0.781000	0.44180	4.753000	0.62183	-0.112000	0.11979	0.411000	0.27672	CGA	G|0.879;A|0.121	0.121	strong		0.403	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
FAM120B	84498	hgsc.bcm.edu	37	6	170627651	170627651	+	Silent	SNP	G	G	A	rs9460113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:170627651G>A	ENST00000476287.1	+	2	1281	c.1173G>A	c.(1171-1173)acG>acA	p.T391T	FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000537664.1_Silent_p.T414T|FAM120B_ENST00000540480.1_Silent_p.T403T	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	391					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		AAGTTCCCACGTGTACAGGCC	0.542													G|||	2500	0.499201	0.5749	0.5951	5008	,	,		20319	0.124		0.671	False		,,,				2504	0.5389				p.T391T		Atlas-SNP	.											.	FAM120B	108	.	0			c.G1173A						PASS	.	G		2524,1882	629.5+/-395.3	716,1092,395	177.0	185.0	182.0		1173	-0.5	0.0	6	dbSNP_119	182	5736,2864	672.2+/-402.9	1940,1856,504	no	coding-synonymous	FAM120B	NM_032448.1		2656,2948,899	AA,AG,GG		33.3023,42.7145,36.4909		391/911	170627651	8260,4746	2203	4300	6503	SO:0001819	synonymous_variant	84498	exon2			TCCCACGTGTACA	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1173G>A	6.37:g.170627651G>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	195	195	1	NM_032448	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	37	CCDS5314.1																																																																																			G|0.427;A|0.573	0.573	strong		0.542	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
KDM4C	23081	hgsc.bcm.edu	37	9	7174673	7174673	+	Missense_Mutation	SNP	G	G	A	rs913588	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:7174673G>A	ENST00000381309.3	+	22	3680	c.3115G>A	c.(3115-3117)Gta>Ata	p.V1039I	KDM4C_ENST00000442236.2_Missense_Mutation_p.V784I|KDM4C_ENST00000428870.2_Missense_Mutation_p.V726I	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	1039			V -> I (in dbSNP:rs913588). {ECO:0000269|PubMed:15489334}.		histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						GGCCGACCCTGTATACCGCAC	0.468													G|||	1594	0.318291	0.3215	0.3919	5008	,	,		19345	0.1151		0.4751	False		,,,				2504	0.3098				p.V1039I		Atlas-SNP	.											.	KDM4C	186	.	0			c.G3115A						PASS	.	G	ILE/VAL	1546,2860	488.0+/-361.1	271,1004,928	165.0	170.0	168.0		3115	4.7	1.0	9	dbSNP_86	168	4279,4321	576.0+/-390.3	1074,2131,1095	yes	missense	KDM4C	NM_015061.3	29	1345,3135,2023	AA,AG,GG		49.7558,35.0885,44.787	benign	1039/1057	7174673	5825,7181	2203	4300	6503	SO:0001583	missense	23081	exon22			GACCCTGTATACC	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.3115G>A	9.37:g.7174673G>A	ENSP00000370710:p.Val1039Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_015061	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	753	0.3447802197802198	165	0.3353658536585366	133	0.3674033149171271	75	0.13111888111888112	380	0.5013192612137203	G	11.78	1.740653	0.30865	0.350885	0.497558	ENSG00000107077	ENST00000381309;ENST00000442236;ENST00000428870	T;T;T	0.34275	1.37;1.37;1.37	5.69	4.74	0.60224	.	0.240620	0.33005	N	0.005393	T	0.00012	0.0000	N	0.01874	-0.695	0.47153	P	6.610000000000227E-4	B;B	0.30406	0.278;0.011	B;B	0.24974	0.057;0.006	T	0.33420	-0.9869	9	0.32370	T	0.25	-13.4956	11.1935	0.48698	0.0:0.1374:0.7201:0.1425	rs913588;rs17597498;rs56477554;rs59891141;rs913588	784;1039	E7EV17;Q9H3R0	.;KDM4C_HUMAN	I	1039;784;726	ENSP00000370710:V1039I;ENSP00000409353:V784I;ENSP00000405739:V726I	ENSP00000370710:V1039I	V	+	1	0	KDM4C	7164673	0.447000	0.25673	0.994000	0.49952	0.875000	0.50365	2.329000	0.43876	2.671000	0.90904	0.591000	0.81541	GTA	G|0.609;A|0.391	0.391	strong		0.468	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
SRSF6	6431	hgsc.bcm.edu	37	20	42087079	42087079	+	Silent	SNP	C	C	G	rs147967864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:42087079C>G	ENST00000244020.3	+	2	292	c.186C>G	c.(184-186)ggC>ggG	p.G62G		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	62	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						AGCTCTGCGGCGAGCGCGTGA	0.721													C|||	96	0.0191693	0.0015	0.0303	5008	,	,		7632	0.0		0.0606	False		,,,				2504	0.0123				p.G62G		Atlas-SNP	.											.	SRSF6	37	.	0			c.C186G						PASS	.	C		40,4106		0,40,2033	6.0	6.0	6.0		186	-2.8	1.0	20	dbSNP_134	6	413,7863		7,399,3732	no	coding-synonymous	SRSF6	NM_006275.5		7,439,5765	GG,GC,CC		4.9903,0.9648,3.6468		62/345	42087079	453,11969	2073	4138	6211	SO:0001819	synonymous_variant	6431	exon2			CTGCGGCGAGCGC	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10788	protein-coding gene	gene with protein product	"""pre-mRNA splicing factor SRP55"", ""SR splicing factor 6"""	601944	"""splicing factor, arginine/serine-rich 6"""	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.186C>G	20.37:g.42087079C>G		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	22	15	0.681818	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Silent	SNP	ENST00000244020.3	37	CCDS13318.1																																																																																			C|0.972;G|0.028	0.028	strong		0.721	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275	
FAAH	2166	hgsc.bcm.edu	37	1	46871746	46871746	+	Silent	SNP	G	G	A	rs41305628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46871746G>A	ENST00000243167.8	+	6	906	c.822G>A	c.(820-822)gaG>gaA	p.E274E	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	274					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	ATGGACAGGAGGCAGGTGAGG	0.632											OREG0013458	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	71	0.0141773	0.0008	0.0231	5008	,	,		16684	0.0		0.0427	False		,,,				2504	0.0112				p.E274E		Atlas-SNP	.											.	FAAH	36	.	0			c.G822A						PASS	.	G		44,4362	47.5+/-82.1	0,44,2159	77.0	77.0	77.0		822	-1.5	0.2	1	dbSNP_127	77	390,8210	125.0+/-183.6	10,370,3920	no	coding-synonymous	FAAH	NM_001441.2		10,414,6079	AA,AG,GG		4.5349,0.9986,3.3369		274/580	46871746	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	2166	exon6			ACAGGAGGCAGGT	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.822G>A	1.37:g.46871746G>A		Somatic	87	0	0	942	WXS	Illumina HiSeq	Phase_I	104	66	0.634615	NM_001441	D3DQ19|Q52M86|Q5TDF8	Silent	SNP	ENST00000243167.8	37	CCDS535.1																																																																																			G|0.970;A|0.030	0.030	strong		0.632	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
GNAT3	346562	hgsc.bcm.edu	37	7	80088041	80088041	+	Silent	SNP	G	G	A	rs2074674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:80088041G>A	ENST00000398291.3	-	8	1104	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	337					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						CTGTAACTGCGTCAAACACAA	0.338													A|||	2341	0.467452	0.4168	0.4481	5008	,	,		16205	0.7421		0.3201	False		,,,				2504	0.4182				p.D337D		Atlas-SNP	.											GNAT3_ENST00000398291,NS,carcinoma,0,2	GNAT3	65	2	0			c.C1011T						PASS	.	A		1537,2159		327,883,638	80.0	80.0	80.0		1011	3.2	1.0	7	dbSNP_96	80	2628,5574		444,1740,1917	no	coding-synonymous	GNAT3	NM_001102386.1		771,2623,2555	AA,AG,GG		32.041,41.5855,35.0059		337/355	80088041	4165,7733	1848	4101	5949	SO:0001819	synonymous_variant	346562	exon8			AACTGCGTCAAAC		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.1011C>T	7.37:g.80088041G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Silent	SNP	ENST00000398291.3	37	CCDS47625.1																																																																																			G|0.553;A|0.447	0.447	strong		0.338	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370	
SKA3	221150	hgsc.bcm.edu	37	13	21729267	21729267	+	3'UTR	SNP	G	G	A	rs11147977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:21729267G>A	ENST00000314759.5	-	0	1385				SKA3_ENST00000400018.3_Missense_Mutation_p.T381I	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CAGTTTCTGTGTTGGATAGAT	0.363																																					p.T381I		Atlas-SNP	.											.	SKA3	76	.	0			c.C1142T						PASS	.						141.0	146.0	144.0					13																	21729267		2202	4300	6502	SO:0001624	3_prime_UTR_variant	221150	exon8			TTCTGTGTTGGAT	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.*22C>T	13.37:g.21729267G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	149	28	0.187919	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	234	0.10714285714285714	10	0.02032520325203252	48	0.13259668508287292	96	0.16783216783216784	80	0.10554089709762533	A	1.991	-0.431860	0.04669	.	.	ENSG00000165480	ENST00000400018	T	0.22945	1.93	4.07	-0.905	0.10527	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30357	-0.9981	8	0.41790	T	0.15	.	4.7384	0.13001	0.4657:0.1694:0.365:0.0	rs11147977;rs52815571;rs61114986;rs11147977	381	Q8IX90-3	.	I	381	ENSP00000382896:T381I	ENSP00000382896:T381I	T	-	2	0	SKA3	20627267	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.200000	0.17257	-0.416000	0.07473	-0.893000	0.02921	ACA	G|0.905;A|0.095	0.095	strong		0.363	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
DHCR7	1717	hgsc.bcm.edu	37	11	71155129	71155129	+	Silent	SNP	G	G	A	rs4316537	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71155129G>A	ENST00000355527.3	-	4	507	c.231C>T	c.(229-231)acC>acT	p.T77T	DHCR7_ENST00000407721.2_Silent_p.T77T	NM_001163817.1|NM_001360.2	NP_001157289.1|NP_001351.2	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	77					blood vessel development (GO:0001568)|cell differentiation (GO:0030154)|cholesterol biosynthetic process (GO:0006695)|lung development (GO:0030324)|multicellular organism growth (GO:0035264)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|regulation of cholesterol biosynthetic process (GO:0045540)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear outer membrane (GO:0005640)	7-dehydrocholesterol reductase activity (GO:0047598)			endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(1)|skin(1)	19						GAGCATGTCCGGTGACGATGT	0.577									Smith-Lemli-Opitz syndrome				G|||	527	0.105232	0.1657	0.0447	5008	,	,		18849	0.0933		0.0646	False		,,,				2504	0.1207				p.T77T		Atlas-SNP	.											.	DHCR7	98	.	0			c.C231T						PASS	.	G	,	561,3839	247.8+/-255.9	41,479,1680	68.0	51.0	57.0		231,231	-9.0	0.0	11	dbSNP_111	57	530,8058	146.6+/-202.2	14,502,3778	no	coding-synonymous,coding-synonymous	DHCR7	NM_001163817.1,NM_001360.2	,	55,981,5458	AA,AG,GG		6.1714,12.75,8.4001	,	77/476,77/476	71155129	1091,11897	2200	4294	6494	SO:0001819	synonymous_variant	1717	exon4	Familial Cancer Database	SLOS type I & II	ATGTCCGGTGACG	AF034544	CCDS8200.1	11q13.4	2014-09-17	2004-02-13				1.3.1.21		2860	protein-coding gene	gene with protein product		602858	"""Smith-Lemli-Opitz syndrome"""	SLOS		9465114, 9634533	Standard	NM_001360		Approved		uc001oql.3	Q9UBM7		ENST00000355527.3:c.231C>T	11.37:g.71155129G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	114	48	0.421053	NM_001163817	B2R6Z2|O60492|O60717	Silent	SNP	ENST00000355527.3	37	CCDS8200.1																																																																																			G|0.911;A|0.089	0.089	strong		0.577	DHCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394243.1	NM_001360	
MYLK	4638	hgsc.bcm.edu	37	3	123332995	123332995	+	Missense_Mutation	SNP	G	G	A	rs200490629		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:123332995G>A	ENST00000475616.1	-	31	5701	c.5702C>T	c.(5701-5703)aCg>aTg	p.T1901M	MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000360304.3_Missense_Mutation_p.T1901M|MYLK_ENST00000578202.1_Missense_Mutation_p.T140M|MYLK-AS1_ENST00000463408.1_RNA|MYLK_ENST00000346322.5_Missense_Mutation_p.T1832M|MYLK_ENST00000359169.1_Missense_Mutation_p.T1850M|MYLK-AS1_ENST00000470449.1_RNA|MYLK_ENST00000583087.1_Missense_Mutation_p.T141M|MYLK_ENST00000354792.5_Missense_Mutation_p.T701M|MYLK_ENST00000418370.2_Missense_Mutation_p.T141M|MYLK_ENST00000360772.3_Missense_Mutation_p.T1850M			Q15746	MYLK_HUMAN	myosin light chain kinase	1901					actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TTCCTCCATCGTTTCCACAAT	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		19431	0.0		0.001	False		,,,				2504	0.0				p.T1901M		Atlas-SNP	.											.	MYLK	224	.	0			c.C5702T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	171.0	177.0	175.0		5702,5495,5549,5342,419,422	5.3	1.0	3		175	1,8599		0,1,4299	yes	missense,missense,missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3,NM_053031.2,NM_053032.2	81,81,81,81,81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1901/1915,1832/1846,1850/1864,1781/1795,140/154,141/155	123332995	1,13005	2203	4300	6503	SO:0001583	missense	4638	exon34			TCCATCGTTTCCA	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.5702C>T	3.37:g.123332995G>A	ENSP00000418335:p.Thr1901Met	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	142	78	0.549296	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.77	3.471882	0.63737	0.0	1.16E-4	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000418370;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.27	5.27	0.74061	.	.	.	.	.	T	0.42698	0.1214	N	0.08118	0	0.36368	D	0.86111	D;D;D;D;D;P	0.89917	1.0;0.999;1.0;1.0;1.0;0.889	D;D;D;D;D;B	0.74674	0.984;0.928;0.96;0.97;0.964;0.03	T	0.54227	-0.8325	9	0.52906	T	0.07	.	12.4119	0.55471	0.0761:0.0:0.9239:0.0	.	1900;1781;1850;1832;1901;213	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746;Q05D81	.;.;.;.;MYLK_HUMAN;.	M	1850;1901;1850;141;1832;701;1901	ENSP00000354004:T1850M;ENSP00000353452:T1901M;ENSP00000352088:T1850M;ENSP00000428967:T141M;ENSP00000320622:T1832M;ENSP00000346846:T701M;ENSP00000418335:T1901M	ENSP00000320622:T1832M	T	-	2	0	MYLK	124815685	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.648000	0.67930	2.732000	0.93576	0.650000	0.86243	ACG	G|1.000;A|0.000	0.000	strong		0.448	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
TMEM126B	55863	hgsc.bcm.edu	37	11	85347173	85347173	+	Missense_Mutation	SNP	C	C	T	rs17850847	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:85347173C>T	ENST00000358867.6	+	5	616	c.593C>T	c.(592-594)gCg>gTg	p.A198V	TMEM126B_ENST00000534341.1_3'UTR|TMEM126B_ENST00000393375.1_Missense_Mutation_p.A168V	NM_018480.4	NP_060950.3	Q8IUX1	T126B_HUMAN	transmembrane protein 126B	198			A -> V (in dbSNP:rs17850847). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(3)|prostate(1)	7		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				AAATTAATGGCGATTCCTCTA	0.343													C|||	43	0.00858626	0.0023	0.0115	5008	,	,		18215	0.0		0.0268	False		,,,				2504	0.0051				p.A198V		Atlas-SNP	.											.	TMEM126B	13	.	0			c.C593T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	17,4389	24.3+/-50.5	0,17,2186	97.0	86.0	90.0		533,503,593	-5.9	0.0	11	dbSNP_123	90	221,8377	92.8+/-154.8	3,215,4081	yes	missense,missense,missense	TMEM126B	NM_001193537.1,NM_001193538.1,NM_018480.3	64,64,64	3,232,6267	TT,TC,CC		2.5704,0.3858,1.8302	benign,benign,benign	178/211,168/201,198/231	85347173	238,12766	2203	4299	6502	SO:0001583	missense	55863	exon5			TAATGGCGATTCC		CCDS8267.1, CCDS8267.2, CCDS53686.1	11q14.1	2013-05-24				ENSG00000171204		"""Mitochondrial respiratory chain complex assembly factors"""	30883	protein-coding gene	gene with protein product		615533				22982022	Standard	NM_018480		Approved	HT007	uc001pap.4	Q8IUX1		ENST00000358867.6:c.593C>T	11.37:g.85347173C>T	ENSP00000351737:p.Ala198Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_018480	A8K535|A8MSS0|Q32Q09|Q8WVU3|Q96EP3|Q9NZ29	Missense_Mutation	SNP	ENST00000358867.6	37	CCDS8267.2	21|21	0.009615384615384616|0.009615384615384616	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	17|17	0.022427440633245383|0.022427440633245383	C|C	1.128|1.128	-0.653300|-0.653300	0.03480|0.03480	0.003858|0.003858	0.025704|0.025704	ENSG00000171204|ENSG00000171204	ENST00000358867;ENST00000393375|ENST00000531274	T;T|.	0.32988|.	1.43;1.43|.	5.38|5.38	-5.93|-5.93	0.02254|0.02254	.|.	2.176540|.	0.01497|.	N|.	0.017325|.	T|.	0.08935|.	0.0221|.	N|N	0.11560|0.11560	0.145|0.145	0.09310|0.09310	N|N	1|1	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|.	0.15321|.	-1.0441|.	9|.	.|.	.|.	.|.	.|.	16.1701|16.1701	0.81808|0.81808	0.0:0.7222:0.0:0.2778|0.0:0.7222:0.0:0.2778	rs17850847|rs17850847	198|.	Q8IUX1|.	T126B_HUMAN|.	V|X	198;168|116	ENSP00000351737:A198V;ENSP00000377039:A168V|.	.|.	A|R	+|+	2|1	0|2	TMEM126B|TMEM126B	85024821|85024821	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.606000|-0.606000	0.05654|0.05654	-1.429000|-1.429000	0.01987|0.01987	-2.244000|-2.244000	0.00286|0.00286	GCG|CGA	C|0.983;T|0.017	0.017	strong		0.343	TMEM126B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392164.1	NM_018480	
MUC16	94025	hgsc.bcm.edu	37	19	9076083	9076083	+	Missense_Mutation	SNP	G	G	A	rs2547072	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9076083G>A	ENST00000397910.4	-	3	11566	c.11363C>T	c.(11362-11364)aCa>aTa	p.T3788I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3789	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCAGCTGGTGTGACTGCACT	0.522													G|||	1243	0.248203	0.2005	0.2118	5008	,	,		21894	0.249		0.3121	False		,,,				2504	0.272				p.T3788I		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	2	0			c.C11363T						PASS	.	G	ILE/THR	843,3259		99,645,1307	170.0	165.0	167.0		11363	-3.8	0.0	19	dbSNP_100	167	2422,5998		346,1730,2134	yes	missense	MUC16	NM_024690.2	89	445,2375,3441	AA,AG,GG		28.7648,20.551,26.0741	benign	3788/14508	9076083	3265,9257	2051	4210	6261	SO:0001583	missense	94025	exon3			GCTGGTGTGACTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11363C>T	19.37:g.9076083G>A	ENSP00000381008:p.Thr3788Ile	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	180	81	0.45	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	g	2.614	-0.290069	0.05568	0.20551	0.287648	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.93	-3.8	0.04307	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.23540	0.087	B	0.26416	0.069	T	0.48364	-0.9042	8	0.87932	D	0	.	2.3025	0.04165	0.302:0.0:0.2829:0.4151	rs2547072;rs17418366;rs60517166;rs2547072	3788	B5ME49	.	I	3788	ENSP00000381008:T3788I	ENSP00000381008:T3788I	T	-	2	0	MUC16	8937083	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	-0.039000	0.12124	-0.874000	0.04027	0.313000	0.20887	ACA	G|0.750;A|0.250	0.250	strong		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
RBBP6	5930	hgsc.bcm.edu	37	16	24583406	24583406	+	Silent	SNP	A	A	G	rs7593	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:24583406A>G	ENST00000319715.4	+	18	5451	c.5019A>G	c.(5017-5019)gcA>gcG	p.A1673A	RBBP6_ENST00000348022.2_Silent_p.A1639A|RBBP6_ENST00000381039.3_Silent_p.A833A	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1673					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TGGAGAAAGCAAAAGAGAGCC	0.458													G|||	1559	0.311302	0.3464	0.3343	5008	,	,		18720	0.0893		0.4095	False		,,,				2504	0.3753				p.A1673A		Atlas-SNP	.											.	RBBP6	158	.	0			c.A5019G						PASS	.	G	,	1613,2781	658.3+/-400.4	291,1031,875	59.0	67.0	64.0		5019,4917	-4.5	0.9	16	dbSNP_52	64	3431,5169	632.8+/-398.7	689,2053,1558	no	coding-synonymous,coding-synonymous	RBBP6	NM_006910.4,NM_018703.3	,	980,3084,2433	GG,GA,AA		39.8953,36.7091,38.8179	,	1673/1793,1639/1759	24583406	5044,7950	2197	4300	6497	SO:0001819	synonymous_variant	5930	exon18			GAAAGCAAAAGAG		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.5019A>G	16.37:g.24583406A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	155	77	0.496774	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	ENST00000319715.4	37	CCDS10621.1																																																																																			A|0.650;G|0.350	0.350	strong		0.458	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
MUC2	4583	hgsc.bcm.edu	37	11	1092928	1092928	+	Missense_Mutation	SNP	T	T	A	rs12791677		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1092928T>A	ENST00000441003.2	+	30	4774	c.4747T>A	c.(4747-4749)Tcg>Acg	p.S1583T	MUC2_ENST00000359061.5_Missense_Mutation_p.S1584T|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gaccccaacatcgacacccat	0.632																																					p.S1583T		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,0,4	MUC2	614	4	0			c.T4747A						scavenged	.																																			SO:0001583	missense	4583	exon30			CCAACATCGACAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4747T>A	11.37:g.1092928T>A	ENSP00000415183:p.Ser1583Thr	Somatic	133	14	0.105263		WXS	Illumina HiSeq	Phase_I	143	17	0.118881	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	T	0.629	-0.817927	0.02776	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12255	2.7;3.41	1.75	-3.51	0.04696	.	3.022220	0.02729	N	0.114829	T	0.06005	0.0156	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.29119	-1.0022	9	0.12766	T	0.61	.	0.5592	0.00676	0.2873:0.3401:0.1565:0.2162	.	1583	E7EUV1	.	T	1583;1584	ENSP00000415183:S1583T;ENSP00000351956:S1584T	ENSP00000351956:S1584T	S	+	1	0	MUC2	1082928	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-3.679000	0.00395	-2.640000	0.00429	-1.550000	0.00899	TCG	.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128839156	128839156	+	Silent	SNP	T	T	C	rs3740829	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:128839156T>C	ENST00000310343.9	-	22	5909	c.5910A>G	c.(5908-5910)gaA>gaG	p.E1970E	ARHGAP32_ENST00000392657.3_Silent_p.E1621E|ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000527272.1_Silent_p.E1621E	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1970	Interaction with FYN.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TGAGGTGTTCTTCCTCCTTGT	0.542													T|||	378	0.0754792	0.1104	0.0605	5008	,	,		20504	0.0506		0.1133	False		,,,				2504	0.0256				p.E1970E		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.A5910G						PASS	.	T	,	378,4024	191.2+/-216.9	17,344,1840	126.0	120.0	122.0		5910,4863	-11.3	0.0	11	dbSNP_107	122	643,7951	162.7+/-215.4	29,585,3683	no	coding-synonymous,coding-synonymous	ARHGAP32	NM_001142685.1,NM_014715.3	,	46,929,5523	CC,CT,TT		7.482,8.587,7.8563	,	1970/2088,1621/1739	128839156	1021,11975	2201	4297	6498	SO:0001819	synonymous_variant	9743	exon22			GTGTTCTTCCTCC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.5910A>G	11.37:g.128839156T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	183	87	0.47541	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			T|0.918;C|0.082	0.082	strong		0.542	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
ERCC2	2068	hgsc.bcm.edu	37	19	45854919	45854919	+	Missense_Mutation	SNP	T	T	G	rs13181	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45854919T>G	ENST00000391945.4	-	23	2328	c.2251A>C	c.(2251-2253)Aag>Cag	p.K751Q	ERCC2_ENST00000391944.3_Missense_Mutation_p.K673Q	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	751			K -> Q (may be linked to a reduced activity; dbSNP:rs13181). {ECO:0000269|PubMed:11245433, ECO:0000269|PubMed:11470747, ECO:0000269|PubMed:11709541, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TCTATCCTCTTCAGCGTCTCC	0.607			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	1185	0.236621	0.1921	0.2147	5008	,	,		16775	0.0764		0.3638	False		,,,				2504	0.3466				p.K751Q		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	.	ERCC2	78	.	0			c.A2251C	GRCh37	CM004814	ERCC2	M	rs13181	PASS	.	G	GLN/LYS	1037,3369	724.9+/-409.6	119,799,1285	125.0	129.0	128.0		2251	4.3	0.9	19	dbSNP_52	128	3203,5397	651.5+/-400.8	642,1919,1739	yes	missense	ERCC2	NM_000400.3	53	761,2718,3024	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	37.2442,23.5361,32.6003	benign	751/761	45854919	4240,8766	2203	4300	6503	SO:0001583	missense	2068	exon23	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TCCTCTTCAGCGT		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.2251A>C	19.37:g.45854919T>G	ENSP00000375809:p.Lys751Gln	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	113	44	0.389381	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	37	CCDS33049.1	517	0.2367216117216117	102	0.2073170731707317	77	0.212707182320442	51	0.08916083916083917	287	0.3786279683377309	G	1.232	-0.623727	0.03636	0.235361	0.372442	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	T;D	0.82711	-1.42;-1.64	4.29	4.29	0.51040	.	0.612831	0.16775	N	0.200058	T	0.00012	0.0000	N	0.20881	0.62	0.09310	P	0.9999999999999628	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.05733	-1.0867	9	0.06494	T	0.89	-14.1137	11.3922	0.49822	0.0:0.0:0.8176:0.1824	rs13181;rs1052559;rs3170171;rs3859422;rs17285142;rs17355147;rs17359310;rs60606175;rs13181	673;751	E7EVE9;P18074	.;ERCC2_HUMAN	Q	701;727;751;673	ENSP00000375809:K751Q;ENSP00000375808:K673Q	ENSP00000375805:K701Q	K	-	1	0	ERCC2	50546759	0.991000	0.36638	0.917000	0.36280	0.036000	0.12997	1.198000	0.32223	1.046000	0.40249	-0.217000	0.12591	AAG	A|0.006;C|0.001	.	strong		0.607	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
BBS12	166379	hgsc.bcm.edu	37	4	123664247	123664247	+	Silent	SNP	G	G	A	rs309371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:123664247G>A	ENST00000314218.3	+	2	1393	c.1200G>A	c.(1198-1200)gtG>gtA	p.V400V	BBS12_ENST00000542236.1_Silent_p.V400V	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	400			V -> M (in BBS12). {ECO:0000269|PubMed:21344540}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						CAAATCACGTGTTACAGGTGT	0.408									Bardet-Biedl syndrome				g|||	464	0.0926518	0.3109	0.0403	5008	,	,		22873	0.0		0.0249	False		,,,				2504	0.0				p.V400V		Atlas-SNP	.											.	BBS12	63	.	0			c.G1200A						PASS	.	A	,	1192,3214	414.8+/-337.0	161,870,1172	67.0	72.0	71.0		1200,1200	-11.2	0.0	4	dbSNP_79	71	188,8412	82.9+/-145.4	2,184,4114	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	163,1054,5286	AA,AG,GG		2.186,27.054,10.6105	,	400/711,400/711	123664247	1380,11626	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TCACGTGTTACAG	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1200G>A	4.37:g.123664247G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	57	0.398601	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			G|0.895;A|0.105	0.105	strong		0.408	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
APRT	353	hgsc.bcm.edu	37	16	88873824	88873824	+	IGR	SNP	C	C	G	rs141663679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88873824C>G	ENST00000378364.3	-	0	947				CDT1_ENST00000301019.4_Missense_Mutation_p.P471A	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase						adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	CGAACGCAAGCCTGCGCTCAG	0.667													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17483	0.0		0.002	False		,,,				2504	0.002				p.P471A		Atlas-SNP	.											.	CDT1	30	.	0			c.C1411G						PASS	.	C	ALA/PRO	3,4391	6.2+/-15.9	0,3,2194	60.0	49.0	53.0		1411	3.5	0.8	16	dbSNP_134	53	44,8556	29.0+/-79.6	0,44,4256	yes	missense	CDT1	NM_030928.3	27	0,47,6450	GG,GC,CC		0.5116,0.0683,0.3617	benign	471/547	88873824	47,12947	2197	4300	6497	SO:0001628	intergenic_variant	81620	exon9			CGCAAGCCTGCGC		CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741			16.37:g.88873824C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	147	87	0.591837	NM_030928	G5E9J2|Q3KP55|Q68DF9	Missense_Mutation	SNP	ENST00000378364.3	37	CCDS32511.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	9.456	1.091956	0.20471	6.83E-4	0.005116	ENSG00000167513	ENST00000301019	T	0.77098	-1.07	5.43	3.49	0.39957	.	0.056769	0.64402	D	0.000001	T	0.63838	0.2545	M	0.61703	1.905	0.53688	D	0.999975	B	0.26744	0.158	B	0.23419	0.046	T	0.60722	-0.7207	10	0.27785	T	0.31	-16.1815	8.6516	0.34038	0.0:0.7221:0.1338:0.144	.	471	Q9H211	CDT1_HUMAN	A	471	ENSP00000301019:P471A	ENSP00000301019:P471A	P	+	1	0	CDT1	87401325	1.000000	0.71417	0.843000	0.33291	0.003000	0.03518	2.711000	0.47177	0.667000	0.31107	-0.251000	0.11542	CCT	C|0.998;G|0.002	0.002	strong		0.667	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485	
PCDHA2	56146	hgsc.bcm.edu	37	5	140174622	140174622	+	Missense_Mutation	SNP	G	G	A	rs9686540	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140174622G>A	ENST00000526136.1	+	1	73	c.73G>A	c.(73-75)Gag>Aag	p.E25K	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.E25K|PCDHA2_ENST00000520672.2_Missense_Mutation_p.E25K|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	25			E -> K (in dbSNP:rs9686540).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCAGCCTGGGAGGTGGGGAG	0.632													.|||	2635	0.526158	0.4811	0.5908	5008	,	,		14195	0.5317		0.5378	False		,,,				2504	0.5235				p.E25K		Atlas-SNP	.											.	PCDHA2	404	.	0			c.G73A						PASS	.	G	,LYS/GLU,,LYS/GLU	2173,2231		534,1105,563	31.0	37.0	35.0		,73,,73	-0.1	0.0	5	dbSNP_119	35	4524,4076		1194,2136,970	no	intron,missense,intron,missense	PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_031411.1,NM_031495.1	,56,,56	1728,3241,1533	AA,AG,GG		47.3953,49.3415,48.5005	,,,	,25/949,,25/825	140174622	6697,6307	2202	4300	6502	SO:0001583	missense	56146	exon1			GCCTGGGAGGTGG	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"""Cadherins / Protocadherins : Clustered"""	8668	other	complex locus constituent	"""KIAA0345-like 12"""	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.73G>A	5.37:g.140174622G>A	ENSP00000431748:p.Glu25Lys	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	172	61	0.354651	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	1162	0.532051282051282	251	0.5101626016260162	195	0.5386740331491713	310	0.541958041958042	406	0.5356200527704486	g	5.895	0.349276	0.11182	0.493415	0.526047	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.51325	0.78;0.71;0.71	4.01	-0.127	0.13510	Cadherin (1);	0.733453	0.11097	U	0.600150	T	0.00012	0.0000	L	0.31664	0.95	0.80722	P	0.0	B;B;B	0.16802	0.019;0.011;0.019	B;B;B	0.20577	0.03;0.02;0.03	T	0.44862	-0.9300	9	0.40728	T	0.16	.	2.3657	0.04318	0.1678:0.2979:0.3986:0.1357	rs9686540;rs17844243	25;25;25	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	K	25	ENSP00000430584:E25K;ENSP00000367372:E25K;ENSP00000431748:E25K	ENSP00000367372:E25K	E	+	1	0	PCDHA2	140154806	0.096000	0.21769	0.011000	0.14972	0.033000	0.12548	0.314000	0.19432	-0.144000	0.11314	0.549000	0.68633	GAG	G|0.493;A|0.507	0.507	strong		0.632	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905	
CLCN2	1181	hgsc.bcm.edu	37	3	184075047	184075047	+	Silent	SNP	A	A	G	rs2228291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:184075047A>G	ENST00000265593.4	-	9	1077	c.906T>C	c.(904-906)atT>atC	p.I302I	EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000434054.2_Silent_p.I258I|CLCN2_ENST00000344937.7_Silent_p.I302I|CLCN2_ENST00000423355.2_5'UTR|CLCN2_ENST00000457512.1_Silent_p.I302I|CLCN2_ENST00000475279.1_5'Flank	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	302					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	AGAGGGCTGTAATAGTCTCTA	0.627													A|||	1778	0.355032	0.4735	0.4352	5008	,	,		16498	0.373		0.2356	False		,,,				2504	0.2423				p.I302I		Atlas-SNP	.											.	CLCN2	74	.	0			c.T906C						PASS	.	A	,,,	1931,2475	545.8+/-376.9	426,1079,698	51.0	56.0	54.0		906,774,906,906	-8.3	0.1	3	dbSNP_98	54	2045,6555	352.5+/-328.7	239,1567,2494	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLCN2	NM_001171087.1,NM_001171088.1,NM_001171089.1,NM_004366.4	,,,	665,2646,3192	GG,GA,AA		23.7791,43.8266,30.5705	,,,	302/882,258/855,302/870,302/899	184075047	3976,9030	2203	4300	6503	SO:0001819	synonymous_variant	1181	exon9			GGCTGTAATAGTC	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"""Ion channels / Chloride channels : Voltage-sensitive"""	2020	protein-coding gene	gene with protein product		600570	"""chloride channel 2"""			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.906T>C	3.37:g.184075047A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_001171087	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Silent	SNP	ENST00000265593.4	37	CCDS3263.1																																																																																			A|0.659;G|0.341	0.341	strong		0.627	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1		
MYPOP	339344	hgsc.bcm.edu	37	19	46404579	46404579	+	Silent	SNP	A	A	G	rs10423899	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46404579A>G	ENST00000322217.5	-	2	539	c.453T>C	c.(451-453)ccT>ccC	p.P151P		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	151	Pro-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						CGTAGCGCTGAGGGCAGGCGC	0.692													G|||	4235	0.845647	0.7746	0.8559	5008	,	,		13236	1.0		0.7823	False		,,,				2504	0.8405				p.P151P		Atlas-SNP	.											.	MYPOP	23	.	0			c.T453C						PASS	.	G		2959,717		1196,567,75	10.0	10.0	10.0		453	0.5	0.1	19	dbSNP_119	10	6018,1336		2490,1038,149	yes	coding-synonymous	MYPOP	NM_001012643.2		3686,1605,224	GG,GA,AA		18.167,19.5049,18.6129		151/400	46404579	8977,2053	1838	3677	5515	SO:0001819	synonymous_variant	339344	exon2			GCGCTGAGGGCAG	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"""p42 Myb-related transcription factor, partner of profilin"""					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.453T>C	19.37:g.46404579A>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_001012643		Silent	SNP	ENST00000322217.5	37	CCDS33055.1																																																																																			A|0.160;G|0.840	0.840	strong		0.692	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643	
PROP1	5626	hgsc.bcm.edu	37	5	177419967	177419967	+	Missense_Mutation	SNP	C	C	T	rs1800197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:177419967C>T	ENST00000308304.2	-	3	732	c.424G>A	c.(424-426)Gcc>Acc	p.A142T		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	142			A -> T (in dbSNP:rs1800197).		blood vessel development (GO:0001568)|canonical Wnt signaling pathway (GO:0060070)|cell migration (GO:0016477)|central nervous system development (GO:0007417)|dorsal/ventral pattern formation (GO:0009953)|hypophysis morphogenesis (GO:0048850)|hypothalamus cell differentiation (GO:0021979)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatotropin secreting cell differentiation (GO:0060126)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)	p.A142T(1)		endometrium(1)|large_intestine(2)|lung(9)|stomach(1)	13	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTGGAAAAGGCGGCAGGAGAC	0.587													C|||	1025	0.204673	0.1218	0.3012	5008	,	,		16521	0.0972		0.2664	False		,,,				2504	0.2955				p.A142T		Atlas-SNP	.											PROP1,NS,carcinoma,0,1	PROP1	28	1	1	Substitution - Missense(1)	stomach(1)	c.G424A						PASS	.	C	THR/ALA	574,3832		38,498,1667	154.0	141.0	145.0		424	-7.5	0.4	5	dbSNP_89	145	2523,6077		382,1759,2159	yes	missense	PROP1	NM_006261.4	58	420,2257,3826	TT,TC,CC		29.3372,13.0277,23.8121	benign	142/227	177419967	3097,9909	2203	4300	6503	SO:0001583	missense	5626	exon3			AAAAGGCGGCAGG	AF076215	CCDS4430.1	5q35.3	2011-06-20	2007-07-12		ENSG00000175325	ENSG00000175325		"""Homeoboxes / PRD class"""	9455	protein-coding gene	gene with protein product		601538	"""prophet of Pit1, paired-like homeodomain transcription factor"""			9462743	Standard	NM_006261		Approved		uc003mif.1	O75360	OTTHUMG00000130887	ENST00000308304.2:c.424G>A	5.37:g.177419967C>T	ENSP00000311290:p.Ala142Thr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	156	154	0.987179	NM_006261		Missense_Mutation	SNP	ENST00000308304.2	37	CCDS4430.1	439	0.20100732600732601	79	0.16056910569105692	110	0.30386740331491713	45	0.07867132867132867	205	0.2704485488126649	.	0.010	-1.783005	0.00634	0.130277	0.293372	ENSG00000175325	ENST00000308304	D	0.90504	-2.68	3.75	-7.49	0.01355	.	0.374024	0.19648	N	0.109300	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32241	-0.9914	9	0.18276	T	0.48	-6.671	4.5819	0.12262	0.0986:0.4276:0.0992:0.3745	rs1800197;rs2233786;rs17240663;rs52809470;rs57963305;rs1800197	142	O75360	PROP1_HUMAN	T	142	ENSP00000311290:A142T	ENSP00000311290:A142T	A	-	1	0	PROP1	177352573	0.000000	0.05858	0.424000	0.26647	0.026000	0.11368	-0.814000	0.04486	-2.936000	0.00299	-1.446000	0.01064	GCC	C|0.785;T|0.214	0.214	strong		0.587	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261	
LCNL1	401562	hgsc.bcm.edu	37	9	139879196	139879196	+	Silent	SNP	C	C	T	rs201494183		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139879196C>T	ENST00000408973.2	+	3	822	c.228C>T	c.(226-228)ttC>ttT	p.F76F	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	76																	GAGTGGCCTTCTCCGACTACC	0.687													c|||	1	0.000199681	0.0	0.0	5008	,	,		13386	0.0		0.001	False		,,,				2504	0.0				p.F76F		Atlas-SNP	.											.	LCNL1	4	.	0			c.C228T						PASS	.			3,4273		0,3,2135	30.0	33.0	32.0		228	2.0	0.0	9		32	38,8454		0,38,4208	no	coding-synonymous	LCNL1	NM_207510.3		0,41,6343	TT,TC,CC		0.4475,0.0702,0.3211		76/165	139879196	41,12727	2138	4246	6384	SO:0001819	synonymous_variant	401562	exon3			GGCCTTCTCCGAC		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"""Lipocalins"""	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	ENST00000408973.2:c.228C>T	9.37:g.139879196C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_207510		Silent	SNP	ENST00000408973.2	37	CCDS43908.1																																																																																			C|0.996;T|0.004	0.004	strong		0.687	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1817367	1817367	+	Silent	SNP	G	G	A	rs7003969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:1817367G>A	ENST00000398564.1	+	7	705	c.705G>A	c.(703-705)gaG>gaA	p.E235E	ARHGEF10_ENST00000398560.1_Silent_p.E235E|ARHGEF10_ENST00000262112.6_Silent_p.E235E|ARHGEF10_ENST00000518288.1_Silent_p.E235E|ARHGEF10_ENST00000520359.1_Silent_p.E211E|ARHGEF10_ENST00000349830.3_Silent_p.E210E			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	235					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CAGATCCAGAGGAAGCAATTT	0.428													A|||	1181	0.235823	0.0983	0.2061	5008	,	,		18247	0.5179		0.2157	False		,,,				2504	0.1728				p.E210E		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.G630A						PASS	.	A		509,3897	778.8+/-414.3	28,453,1722	117.0	114.0	115.0		630	2.0	1.0	8	dbSNP_116	115	2033,6567	720.2+/-406.3	255,1523,2522	no	coding-synonymous	ARHGEF10	NM_014629.2		283,1976,4244	AA,AG,GG		23.6395,11.5524,19.5448		210/1345	1817367	2542,10464	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon7			TCCAGAGGAAGCA	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.705G>A	8.37:g.1817367G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	238	105	0.441176	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				G|0.777;A|0.223	0.223	strong		0.428	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
GRIA1	2890	hgsc.bcm.edu	37	5	153029960	153029960	+	Silent	SNP	T	T	C	rs707176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:153029960T>C	ENST00000285900.5	+	4	874	c.531T>C	c.(529-531)atT>atC	p.I177I	GRIA1_ENST00000518783.1_Silent_p.I187I|GRIA1_ENST00000518142.1_Silent_p.I97I|GRIA1_ENST00000518862.1_3'UTR|GRIA1_ENST00000521843.2_Silent_p.I108I|GRIA1_ENST00000340592.5_Silent_p.I177I|GRIA1_ENST00000448073.4_Silent_p.I187I	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	177					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	CAGTCAACATTTTGACAACCA	0.493													T|||	777	0.155152	0.0976	0.2839	5008	,	,		18146	0.0198		0.3221	False		,,,				2504	0.1094				p.I187I		Atlas-SNP	.											.	GRIA1	321	.	0			c.T561C						PASS	.	T	,	651,3755	279.0+/-274.6	44,563,1596	118.0	113.0	115.0		531,531	4.0	1.0	5	dbSNP_86	115	2896,5704	454.9+/-363.6	499,1898,1903	no	coding-synonymous,coding-synonymous	GRIA1	NM_000827.3,NM_001114183.1	,	543,2461,3499	CC,CT,TT		33.6744,14.7753,27.272	,	177/907,177/907	153029960	3547,9459	2203	4300	6503	SO:0001819	synonymous_variant	2890	exon4			CAACATTTTGACA		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.531T>C	5.37:g.153029960T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	182	121	0.664835	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Silent	SNP	ENST00000285900.5	37	CCDS4322.1																																																																																			T|0.766;C|0.234	0.234	strong		0.493	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3		
BAIAP3	8938	hgsc.bcm.edu	37	16	1388618	1388618	+	Missense_Mutation	SNP	G	G	A	rs11642118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1388618G>A	ENST00000324385.5	+	2	331	c.173G>A	c.(172-174)cGc>cAc	p.R58H	BAIAP3_ENST00000397488.2_Missense_Mutation_p.R23H|BAIAP3_ENST00000426824.3_Missense_Mutation_p.R23H|BAIAP3_ENST00000568887.1_Missense_Mutation_p.R23H|BAIAP3_ENST00000397489.1_Missense_Mutation_p.R23H|BAIAP3_ENST00000562208.1_Missense_Mutation_p.R23H|BAIAP3_ENST00000421665.2_Missense_Mutation_p.R23H	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	58					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				TCCTTCCGCCGCAGGACTGAG	0.701													G|||	29	0.00579073	0.0008	0.0058	5008	,	,		11840	0.0		0.0159	False		,,,				2504	0.0082				p.R58H		Atlas-SNP	.											.	BAIAP3	88	.	0			c.G173A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	14,4368		0,14,2177	38.0	30.0	33.0		68,68,68,68,173	3.7	1.0	16	dbSNP_120	33	173,8421		0,173,4124	yes	missense,missense,missense,missense,missense	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	29,29,29,29,29	0,187,6301	AA,AG,GG		2.013,0.3195,1.4411	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	23/1117,23/1153,23/1130,23/1125,58/1188	1388618	187,12789	2191	4297	6488	SO:0001583	missense	8938	exon2			TCCGCCGCAGGAC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.173G>A	16.37:g.1388618G>A	ENSP00000324510:p.Arg58His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	37	CCDS10434.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	G	23.3	4.403503	0.83230	0.003195	0.02013	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.73258	-0.66;-0.68;-0.69;-0.68;-0.73	4.71	3.67	0.42095	.	0.128592	0.47852	D	0.000202	T	0.62539	0.2436	L	0.56769	1.78	0.22666	N	0.998872	D;D;D;D;D	0.76494	0.998;0.999;0.998;0.996;0.996	P;P;P;P;P	0.59487	0.791;0.858;0.791;0.732;0.732	T	0.61505	-0.7049	10	0.72032	D	0.01	-30.7447	9.6106	0.39661	0.0:0.0:0.7913:0.2087	rs11642118	23;58;23;58;23	E7EUB9;B4DGA2;B4DIK3;O94812;A2A2B2	.;.;.;BAIP3_HUMAN;.	H	23;23;58;23;23	ENSP00000407242:R23H;ENSP00000380625:R23H;ENSP00000324510:R58H;ENSP00000380626:R23H;ENSP00000409533:R23H	ENSP00000324510:R58H	R	+	2	0	BAIAP3	1328619	0.887000	0.30362	0.966000	0.40874	0.961000	0.63080	2.875000	0.48491	2.327000	0.79052	0.491000	0.48974	CGC	G|0.989;A|0.011	0.011	strong		0.701	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
DFFB	1677	hgsc.bcm.edu	37	1	3800242	3800242	+	Silent	SNP	A	A	G	rs3205087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:3800242A>G	ENST00000378209.3	+	7	1277	c.954A>G	c.(952-954)ccA>ccG	p.P318P	AL691523.1_ENST00000579705.1_RNA	NM_004402.2	NP_004393.1	O76075	DFFB_HUMAN	DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase)	318					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			endometrium(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		ACTGTGACCCAAGCAGAATCT	0.488													A|||	1782	0.355831	0.3124	0.3256	5008	,	,		16180	0.3482		0.4105	False		,,,				2504	0.3875				p.P318P		Atlas-SNP	.											.	DFFB	30	.	0			c.A954G						PASS	.	A		1491,2915	477.4+/-357.9	251,989,963	136.0	130.0	132.0		954	-10.9	0.0	1	dbSNP_105	132	3879,4721	544.4+/-384.6	868,2143,1289	no	coding-synonymous	DFFB	NM_004402.2		1119,3132,2252	GG,GA,AA		45.1047,33.8402,41.2886		318/339	3800242	5370,7636	2203	4300	6503	SO:0001819	synonymous_variant	1677	exon7			TGACCCAAGCAGA		CCDS52.1, CCDS72693.1	1p36.3	2014-03-06	2002-08-29		ENSG00000169598	ENSG00000169598			2773	protein-coding gene	gene with protein product		601883				9108473, 9560346	Standard	NM_004402		Approved	CAD, CPAN, DFF-40, DFF40	uc001alc.3	O76075	OTTHUMG00000003525	ENST00000378209.3:c.954A>G	1.37:g.3800242A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	107	63	0.588785	NM_004402	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000378209.3	37	CCDS52.1																																																																																			A|0.607;G|0.393	0.393	strong		0.488	DFFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009821.2	NM_001282669	
LEPREL1	55214	hgsc.bcm.edu	37	3	189713205	189713205	+	Silent	SNP	T	T	C	rs9821880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:189713205T>C	ENST00000319332.5	-	2	704	c.507A>G	c.(505-507)gaA>gaG	p.E169E	LEPREL1_ENST00000427335.2_5'UTR	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	169					collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TGTGAGCTGCTTCCACTGCTT	0.408													T|||	1607	0.320887	0.2035	0.3069	5008	,	,		15965	0.4881		0.3002	False		,,,				2504	0.3384				p.E169E		Atlas-SNP	.											.	LEPREL1	95	.	0			c.A507G						PASS	.	T	,	942,3464	342.5+/-307.2	94,754,1355	105.0	91.0	96.0		,507	4.1	1.0	3	dbSNP_119	96	2669,5931	416.4+/-352.1	435,1799,2066	no	utr-5,coding-synonymous	LEPREL1	NM_001134418.1,NM_018192.3	,	529,2553,3421	CC,CT,TT		31.0349,21.3799,27.7641	,	,169/709	189713205	3611,9395	2203	4300	6503	SO:0001819	synonymous_variant	55214	exon2			AGCTGCTTCCACT		CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 2"""	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.507A>G	3.37:g.189713205T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_018192	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Silent	SNP	ENST00000319332.5	37	CCDS3294.1																																																																																			C|0.302;N|0.001	0.302	strong		0.408	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192	
OR2F1	26211	hgsc.bcm.edu	37	7	143657427	143657427	+	Missense_Mutation	SNP	C	C	T	rs2072164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:143657427C>T	ENST00000392899.1	+	1	401	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	122			R -> C (in dbSNP:rs2072164).		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					GGCCTATGACCGCTATGTGGC	0.547													C|||	573	0.114417	0.0908	0.1744	5008	,	,		20383	0.1617		0.0706	False		,,,				2504	0.1002				p.R122C		Atlas-SNP	.											.	OR2F1	71	.	0			c.C364T						PASS	.	C	CYS/ARG	371,4035	189.9+/-215.9	16,339,1848	197.0	165.0	176.0		364	4.5	1.0	7	dbSNP_96	176	540,8060	149.7+/-204.7	15,510,3775	yes	missense	OR2F1	NM_012369.2	180	31,849,5623	TT,TC,CC		6.2791,8.4203,7.0045	possibly-damaging	122/318	143657427	911,12095	2203	4300	6503	SO:0001583	missense	26211	exon1			TATGACCGCTATG	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"""GPCR / Class A : Olfactory receptors"""	8246	protein-coding gene	gene with protein product		608497	"""olfactory receptor, family 2, subfamily F, member 1"""	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.364C>T	7.37:g.143657427C>T	ENSP00000376633:p.Arg122Cys	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	206	105	0.509709	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	37	CCDS5887.1	263	0.12042124542124542	44	0.08943089430894309	58	0.16022099447513813	102	0.17832167832167833	59	0.07783641160949868	C	14.46	2.542464	0.45280	0.084203	0.062791	ENSG00000213215	ENST00000392899	T	0.77358	-1.09	5.41	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000045	T	0.00552	0.0018	M	0.89163	3.01	0.20307	P	0.9999113421	B	0.15719	0.014	B	0.14023	0.01	T	0.51787	-0.8661	9	0.87932	D	0	-13.4453	12.1368	0.53977	0.0:0.9174:0.0:0.0826	rs2072164;rs52837212;rs61344302;rs2072164	122	Q13607	OR2F1_HUMAN	C	122	ENSP00000376633:R122C	ENSP00000376633:R122C	R	+	1	0	OR2F1	143288360	0.996000	0.38824	1.000000	0.80357	0.990000	0.78478	2.186000	0.42593	1.513000	0.48852	0.655000	0.94253	CGC	C|0.910;T|0.090	0.090	strong		0.547	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1		
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259841	71259841	+	Silent	SNP	C	C	T	rs189729045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71259841C>T	ENST00000528743.2	+	1	376	c.138C>T	c.(136-138)tgC>tgT	p.C46C		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	46	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						AGCCCGTGTGCTGCTGTGTTC	0.652													c|||	16	0.00319489	0.0	0.0086	5008	,	,		18955	0.0		0.007	False		,,,				2504	0.0031				p.C46C		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.C138T						PASS	.	C		7,4393		0,7,2193	95.0	107.0	103.0		138	1.6	1.0	11		103	85,8503		0,85,4209	no	coding-synonymous	KRTAP5-9	NM_005553.3		0,92,6402	TT,TC,CC		0.9898,0.1591,0.7083		46/170	71259841	92,12896	2200	4294	6494	SO:0001819	synonymous_variant	3846	exon1			CGTGTGCTGCTGT	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"""Keratin associated proteins"""	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.138C>T	11.37:g.71259841C>T		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	355	159	0.447887	NM_005553	Q14564|Q3MIP8	Silent	SNP	ENST00000528743.2	37	CCDS53677.1																																																																																			C|0.996;T|0.004	0.004	strong		0.652	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
MYH11	4629	hgsc.bcm.edu	37	16	15839034	15839034	+	Silent	SNP	G	G	A	rs587781048|rs1050113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15839034G>A	ENST00000300036.5	-	20	2581	c.2472C>T	c.(2470-2472)gcC>gcT	p.A824A	MYH11_ENST00000396324.3_Silent_p.A831A|MYH11_ENST00000576790.2_Silent_p.A824A|MYH11_ENST00000452625.2_Silent_p.A831A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	824					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGAGGTAGGCGGCGCAGTTCC	0.627			T	CBFB	AML								G|||	1270	0.253594	0.1112	0.2695	5008	,	,		18020	0.3542		0.339	False		,,,				2504	0.2434				p.A831A		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	MYH11_ENST00000396324,NS,carcinoma,-2,4	MYH11	520	4	0			c.C2493T						PASS	.	G	,,,	651,3743	279.9+/-275.1	53,545,1599	82.0	80.0	81.0		2493,2493,2472,2472	-9.6	0.3	16	dbSNP_86	81	2769,5831	440.5+/-359.5	471,1827,2002	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	524,2372,3601	AA,AG,GG		32.1977,14.8157,26.3198	,,,	831/1946,831/1980,824/1973,824/1939	15839034	3420,9574	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon21			GTAGGCGGCGCAG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.2472C>T	16.37:g.15839034G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			T|0.000;G|0.726;C|0.000;A|0.274	0.274	strong		0.627	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
OR5D16	390144	hgsc.bcm.edu	37	11	55606302	55606302	+	Silent	SNP	G	G	T	rs6591699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55606302G>T	ENST00000378396.1	+	1	75	c.75G>T	c.(73-75)ctG>ctT	p.L25L		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				ACCTGGAACTGCAAATTCCCC	0.418													N|||	3371	0.673123	0.6112	0.683	5008	,	,		17728	0.7718		0.6163	False		,,,				2504	0.7065				p.L25L		Atlas-SNP	.											OR5D16,NS,carcinoma,+1,1	OR5D16	94	1	0			c.G75T						PASS	.	G		2788,1614		906,976,319	111.0	102.0	105.0		75	-3.2	0.0	11	dbSNP_116	105	5389,3203		1699,1991,606	no	coding-synonymous	OR5D16	NM_001005496.1		2605,2967,925	TT,TG,GG		37.2789,36.6652,37.071		25/329	55606302	8177,4817	2201	4296	6497	SO:0001819	synonymous_variant	390144	exon1			GGAACTGCAAATT	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.75G>T	11.37:g.55606302G>T		Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	357	151	0.422969	NM_001005496	Q6IF65|Q96RB4	Silent	SNP	ENST00000378396.1	37	CCDS31512.1																																																																																			G|0.350;T|0.650	0.650	strong		0.418	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
VPS13D	55187	hgsc.bcm.edu	37	1	12429611	12429611	+	Silent	SNP	C	C	T	rs2295338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12429611C>T	ENST00000358136.3	+	54	10792	c.10662C>T	c.(10660-10662)gaC>gaT	p.D3554D	VPS13D_ENST00000356315.4_Silent_p.D3529D|VPS13D_ENST00000496628.1_3'UTR	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ATGCCTGGGACGAACCCACCT	0.502													C|||	324	0.0646965	0.1142	0.0634	5008	,	,		17469	0.0179		0.0427	False		,,,				2504	0.0695				p.D3554D		Atlas-SNP	.											.	VPS13D	316	.	0			c.C10662T						PASS	.	C	,	457,3949	216.1+/-234.9	24,409,1770	143.0	144.0	144.0		10662,10587	-6.5	0.7	1	dbSNP_100	144	313,8287	111.8+/-172.0	8,297,3995	no	coding-synonymous,coding-synonymous	VPS13D	NM_015378.2,NM_018156.2	,	32,706,5765	TT,TC,CC		3.6395,10.3722,5.9203	,	3554/4389,3529/4364	12429611	770,12236	2203	4300	6503	SO:0001819	synonymous_variant	55187	exon54			CTGGGACGAACCC	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.10662C>T	1.37:g.12429611C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	157	69	0.43949	NM_015378		Silent	SNP	ENST00000358136.3	37	CCDS30588.1	139	0.06364468864468864	56	0.11382113821138211	33	0.09116022099447514	14	0.024475524475524476	36	0.047493403693931395	C	9.101	1.004065	0.19199	0.103722	0.036395	ENSG00000048707	ENST00000011700	.	.	.	5.93	-6.53	0.01866	.	.	.	.	.	T	0.02083	0.0065	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.51371	-0.8714	3	.	.	.	.	18.7169	0.91679	0.0:0.1617:0.0:0.8383	rs2295338;rs56588517;rs2295338	.	.	.	M	2376	.	.	T	+	2	0	VPS13D	12352198	0.771000	0.28555	0.748000	0.31131	0.959000	0.62525	-0.140000	0.10342	-1.561000	0.01684	-0.806000	0.03193	ACG	C|0.940;T|0.060	0.060	strong		0.502	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
CRLF3	51379	hgsc.bcm.edu	37	17	29113016	29113016	+	Silent	SNP	A	A	G	rs34756112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29113016A>G	ENST00000324238.6	-	7	1117	c.993T>C	c.(991-993)gaT>gaC	p.D331D	CRLF3_ENST00000577725.1_Intron|CRLF3_ENST00000544695.1_Silent_p.D215D	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	331					G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				CTCCTATGCTATCTCTTCTGT	0.378													a|||	810	0.161741	0.1354	0.1902	5008	,	,		15663	0.1359		0.1074	False		,,,				2504	0.2597				p.D331D	Pancreas(30;346 881 29244 33464 41299)	Atlas-SNP	.											.	CRLF3	36	.	0			c.T993C						PASS	.	G		614,3792	266.8+/-267.5	36,542,1625	194.0	173.0	180.0		993	1.9	1.0	17	dbSNP_126	180	994,7606	214.5+/-254.1	62,870,3368	no	coding-synonymous	CRLF3	NM_015986.3		98,1412,4993	GG,GA,AA		11.5581,13.9355,12.3635		331/443	29113016	1608,11398	2203	4300	6503	SO:0001819	synonymous_variant	51379	exon7			TATGCTATCTCTT	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.993T>C	17.37:g.29113016A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_015986	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Silent	SNP	ENST00000324238.6	37	CCDS32607.1																																																																																			A|0.868;G|0.132	0.132	strong		0.378	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1		
MUC4	4585	hgsc.bcm.edu	37	3	195511668	195511668	+	Silent	SNP	G	G	A	rs71291861|rs3107748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195511668G>A	ENST00000463781.3	-	2	7242	c.6783C>T	c.(6781-6783)gaC>gaT	p.D2261D	MUC4_ENST00000475231.1_Silent_p.D2261D|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGCGTCGGTGACAG	0.582													.|||	2203	0.439896	0.236	0.4352	5008	,	,		10401	0.7054		0.4602	False		,,,				2504	0.4243				p.D2261D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	0			c.C6783T						scavenged	.						34.0	33.0	33.0					3																	195511668		679	1584	2263	SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6783C>T	3.37:g.195511668G>A		Somatic	254	3	0.011811		WXS	Illumina HiSeq	Phase_I	451	116	0.257206	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.762;A|0.238	0.238	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388324	1388324	+	Missense_Mutation	SNP	A	A	C	rs74377230		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388324A>C	ENST00000324803.4	+	1	2985	c.25A>C	c.(25-27)Aat>Cat	p.N9H		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	9					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCTTTGTGCCAATGTGGAGTG	0.537																																					p.N9H		Atlas-SNP	.											CRIPAK,caecum,carcinoma,0,1	CRIPAK	185	1	0			c.A25C						scavenged	.						124.0	130.0	128.0					4																	1388324		2203	4300	6503	SO:0001583	missense	285464	exon1			TGTGCCAATGTGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.25A>C	4.37:g.1388324A>C	ENSP00000323978:p.Asn9His	Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	230	33	0.143478	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	G	0.580	-0.837604	0.02692	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.23348	1.91	.	.	.	.	.	.	.	.	T	0.09598	0.0236	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	7	0.49607	T	0.09	.	.	.	.	.	9	Q8N1N5	CRPAK_HUMAN	H	9;2	ENSP00000323978:N9H	ENSP00000323978:N9H	N	+	1	0	CRIPAK	1378324	0.752000	0.28338	0.019000	0.16419	0.027000	0.11550	-1.046000	0.03525	-1.644000	0.01517	-1.639000	0.00775	AAT	A|0.833;C|0.167	0.167	weak		0.537	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
OR1I1	126370	hgsc.bcm.edu	37	19	15198507	15198507	+	Missense_Mutation	SNP	T	T	C	rs8108721	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198507T>C	ENST00000209540.2	+	1	717	c.631T>C	c.(631-633)Ttc>Ctc	p.F211L		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	211			F -> L (in dbSNP:rs8108721).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						CACCAGCCCATTCTCCTGCAT	0.537													C|||	3370	0.672923	0.3812	0.7723	5008	,	,		22056	0.622		0.829	False		,,,				2504	0.8885				p.F211L		Atlas-SNP	.											.	OR1I1	58	.	0			c.T631C						PASS	.	C	LEU/PHE	1941,2465	623.4+/-394.1	416,1109,678	161.0	123.0	136.0		631	2.4	0.0	19	dbSNP_116	136	7254,1346	262.7+/-284.6	3055,1144,101	yes	missense	OR1I1	NM_001004713.1	22	3471,2253,779	CC,CT,TT		15.6512,44.0536,29.3019	benign	211/356	15198507	9195,3811	2203	4300	6503	SO:0001583	missense	126370	exon1			AGCCCATTCTCCT	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.631T>C	19.37:g.15198507T>C	ENSP00000209540:p.Phe211Leu	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	192	191	0.994792	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	1453	0.6652930402930403	192	0.3902439024390244	282	0.7790055248618785	349	0.6101398601398601	630	0.8311345646437994	C	0.036	-1.306501	0.01353	0.440536	0.843488	ENSG00000094661	ENST00000209540	T	0.32988	1.43	4.64	2.39	0.29439	GPCR, rhodopsin-like superfamily (1);	0.000000	0.27976	N	0.017087	T	0.00012	0.0000	N	0.25060	0.705	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.44907	-0.9297	9	0.02654	T	1	.	3.758	0.08593	0.1697:0.5545:0.0:0.2758	rs8108721;rs58043021;rs8108721	211	O60431	OR1I1_HUMAN	L	211	ENSP00000209540:F211L	ENSP00000209540:F211L	F	+	1	0	OR1I1	15059507	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-0.383000	0.07398	0.173000	0.19788	-0.227000	0.12334	TTC	T|0.313;C|0.687	0.687	strong		0.537	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
ARNT2	9915	hgsc.bcm.edu	37	15	80884025	80884025	+	Missense_Mutation	SNP	G	G	A	rs4072568	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:80884025G>A	ENST00000303329.4	+	18	2200	c.2035G>A	c.(2035-2037)Ggt>Agt	p.G679S	ARNT2_ENST00000527771.1_Missense_Mutation_p.G668S|ARNT2_ENST00000533983.1_Missense_Mutation_p.G668S	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	679			G -> S (in dbSNP:rs4072568). {ECO:0000269|PubMed:9205841}.		central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			CCAGCAGCCCGGTCAGACTGA	0.637													G|||	561	0.112021	0.1377	0.1066	5008	,	,		18357	0.003		0.166	False		,,,				2504	0.138				p.G679S		Atlas-SNP	.											ARNT2,NS,carcinoma,-1,1	ARNT2	88	1	0			c.G2035A						PASS	.	G	SER/GLY	602,3804	263.8+/-265.7	33,536,1634	111.0	107.0	108.0		2035	1.7	1.0	15	dbSNP_108	108	1684,6916	309.4+/-309.4	182,1320,2798	yes	missense	ARNT2	NM_014862.3	56	215,1856,4432	AA,AG,GG		19.5814,13.6632,17.5765	benign	679/718	80884025	2286,10720	2203	4300	6503	SO:0001583	missense	9915	exon18			CAGCCCGGTCAGA	AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"""Basic helix-loop-helix proteins"""	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.2035G>A	15.37:g.80884025G>A	ENSP00000307479:p.Gly679Ser	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	189	94	0.497355	NM_014862	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	239	0.10943223443223443	72	0.14634146341463414	45	0.12430939226519337	0	0.0	122	0.16094986807387862	G	10.84	1.462974	0.26248	0.136632	0.195814	ENSG00000172379	ENST00000360062;ENST00000303329	T	0.03920	3.76	5.07	1.74	0.24563	.	0.276124	0.39274	N	0.001420	T	0.00012	0.0000	N	0.02011	-0.69	0.35400	P	0.20852800000000005	B	0.06786	0.001	B	0.06405	0.002	T	0.46992	-0.9151	9	0.11794	T	0.64	.	6.8547	0.24034	0.4281:0.0:0.5719:0.0	rs4072568;rs17608916;rs52827902;rs56876472;rs4072568	679	Q9HBZ2	ARNT2_HUMAN	S	668;679	ENSP00000307479:G679S	ENSP00000307479:G679S	G	+	1	0	ARNT2	78671080	1.000000	0.71417	0.976000	0.42696	0.991000	0.79684	2.649000	0.46656	0.533000	0.28675	0.313000	0.20887	GGT	G|0.856;A|0.144	0.144	strong		0.637	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2		
ANKRD30B	374860	hgsc.bcm.edu	37	18	14848820	14848820	+	Missense_Mutation	SNP	C	C	T	rs4090319	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:14848820C>T	ENST00000358984.4	+	34	3110	c.2930C>T	c.(2929-2931)aCg>aTg	p.T977M		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	977				T -> M (in Ref. 3; AAK27326 and 4; BAG57852). {ECO:0000305}.				p.T977M(1)		breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						ATGGAACAAACGAAAAATAAG	0.348													C|||	2007	0.400759	0.0257	0.5173	5008	,	,		15920	0.5685		0.4801	False		,,,				2504	0.5706				p.T977M		Atlas-SNP	.											ANKRD30B_ENST00000358984,NS,carcinoma,0,1	ANKRD30B	237	1	1	Substitution - Missense(1)	kidney(1)	c.C2930T						PASS	.						76.0	56.0	62.0					18																	14848820		692	1587	2279	SO:0001583	missense	374860	exon34			AACAAACGAAAAA	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.2930C>T	18.37:g.14848820C>T	ENSP00000351875:p.Thr977Met	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	228	93	0.407895	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	37	CCDS54182.1	777	0.3557692307692308	21	0.042682926829268296	165	0.4558011049723757	281	0.49125874125874125	310	0.40897097625329815	C	0.001	-3.829587	0.00004	.	.	ENSG00000180777	ENST00000358984;ENST00000320584;ENST00000277669	T	0.15952	2.38	1.48	0.0525	0.14302	.	.	.	.	.	T	0.00012	0.0000	N	0.01048	-1.04	0.09310	P	0.999999854054	B;B	0.12630	0.0;0.006	B;B	0.04013	0.0;0.001	T	0.45469	-0.9259	8	0.02654	T	1	.	4.8651	0.13604	0.0:0.1894:0.0:0.8106	rs4090319	1062;977	Q9BXX2;F8WAG3	AN30B_HUMAN;.	M	977;371;397	ENSP00000351875:T977M	ENSP00000277669:T397M	T	+	2	0	ANKRD30B	14838820	0.992000	0.36948	0.027000	0.17364	0.012000	0.07955	2.178000	0.42519	0.068000	0.16574	-1.169000	0.01745	ACG	.	.	weak		0.348	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084048	31084048	+	Intron	SNP	A	A	G	rs3094216	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31084048A>G	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Silent_p.C448C	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						ACTTGCTGCCACAAGGCTGAA	0.617													A|||	940	0.1877	0.2065	0.1527	5008	,	,		18491	0.1637		0.1879	False		,,,				2504	0.2117				p.C448C		Atlas-SNP	.											.	CDSN	48	.	0			c.T1344C						PASS	.	A	,	996,3410	370.3+/-319.5	95,806,1302	40.0	41.0	40.0		1344,	-3.1	1.0	6	dbSNP_103	40	1931,6669	339.9+/-323.4	227,1477,2596	yes	coding-synonymous,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	,	322,2283,3898	GG,GA,AA		22.4535,22.6055,22.505	,	448/530,	31084048	2927,10079	2203	4300	6503	SO:0001627	intron_variant	1041	exon2			GCTGCCACAAGGC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1380A>G	6.37:g.31084048A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	163	77	0.472393	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																			A|0.790;G|0.210	0.210	strong		0.617	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
OR10G2	26534	hgsc.bcm.edu	37	14	22102439	22102439	+	Missense_Mutation	SNP	C	C	G	rs35963889	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:22102439C>G	ENST00000542433.1	-	1	657	c.560G>C	c.(559-561)cGc>cCc	p.R187P		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	187			R -> P (in dbSNP:rs35963889).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R187P(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		CAATACTGCGCGGATGTCACA	0.547													.|||	1907	0.380791	0.4682	0.2637	5008	,	,		18353	0.494		0.2694	False		,,,				2504	0.3436				p.R187P		Atlas-SNP	.											OR10G2,NS,carcinoma,0,2	OR10G2	35	2	1	Substitution - Missense(1)	stomach(1)	c.G560C						PASS	.	G	PRO/ARG	1331,3073		375,581,1246	92.0	100.0	97.0		560	3.6	1.0	14	dbSNP_126	97	1182,7392		249,684,3354	no	missense	OR10G2	NM_001005466.1	103	624,1265,4600	GG,GC,CC		13.7859,30.2225,19.3635	benign	187/311	22102439	2513,10465	2202	4287	6489	SO:0001583	missense	26534	exon1			ACTGCGCGGATGT		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.560G>C	14.37:g.22102439C>G	ENSP00000445383:p.Arg187Pro	Somatic	471	0	0		WXS	Illumina HiSeq	Phase_I	348	94	0.270115	NM_001005466	B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	37	CCDS32047.1	688	0.315018315018315	180	0.36585365853658536	83	0.2292817679558011	247	0.4318181818181818	178	0.23482849604221637	G	0.007	-1.995151	0.00435	0.302225	0.137859	ENSG00000255582	ENST00000542433	T	0.00026	8.94	3.64	3.64	0.41730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	N	0.000276	T	0.00012	0.0000	N	0.00028	-2.63	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.04128	-1.0975	9	0.30854	T	0.27	-4.3413	10.8294	0.46652	0.0:0.194:0.8059:0.0	rs35963889;rs61748305;rs35963889	187	Q8NGC3	O10G2_HUMAN	P	187	ENSP00000445383:R187P	ENSP00000445383:R187P	R	-	2	0	OR10G2	21172279	0.000000	0.05858	0.959000	0.39883	0.694000	0.40290	0.593000	0.23999	0.753000	0.32945	-0.371000	0.07208	CGC	C|0.586;G|0.414	0.414	strong		0.547	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
SHROOM3	57619	hgsc.bcm.edu	37	4	77631425	77631425	+	Missense_Mutation	SNP	T	T	A	rs3821979	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:77631425T>A	ENST00000296043.6	+	3	1393	c.440T>A	c.(439-441)cTt>cAt	p.L147H	SHROOM3_ENST00000473602.1_3'UTR	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	147			L -> H (in dbSNP:rs3821979).		actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			GGGGTTAAACTTCGGCTGAAG	0.577													T|||	1097	0.21905	0.1611	0.2032	5008	,	,		18546	0.3363		0.1093	False		,,,				2504	0.3006				p.L147H		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T440A	GRCh37	CM063143	SHROOM3	M	rs3821979	PASS	.	T	HIS/LEU	760,3646	310.0+/-291.3	62,636,1505	85.0	73.0	77.0		440	3.8	1.0	4	dbSNP_107	77	1131,7469	233.3+/-266.6	83,965,3252	yes	missense	SHROOM3	NM_020859.3	99	145,1601,4757	AA,AT,TT		13.1512,17.2492,14.5394	probably-damaging	147/1997	77631425	1891,11115	2203	4300	6503	SO:0001583	missense	57619	exon3			TTAAACTTCGGCT	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.440T>A	4.37:g.77631425T>A	ENSP00000296043:p.Leu147His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	404	0.184981684981685	80	0.16260162601626016	70	0.19337016574585636	173	0.30244755244755245	81	0.10686015831134564	T	15.60	2.882384	0.51908	0.172492	0.131512	ENSG00000138771	ENST00000296043	T	0.34472	1.36	4.96	3.78	0.43462	.	0.000000	0.36101	N	0.002789	T	0.00012	0.0000	M	0.62723	1.935	0.31241	P	0.695171	D	0.71674	0.998	P	0.60789	0.879	T	0.15896	-1.0421	9	0.87932	D	0	-2.793	7.8964	0.29708	0.0:0.0961:0.0:0.9039	rs3821979;rs52831344;rs3821979	147	Q8TF72	SHRM3_HUMAN	H	147	ENSP00000296043:L147H	ENSP00000296043:L147H	L	+	2	0	SHROOM3	77850449	0.921000	0.31238	1.000000	0.80357	0.879000	0.50718	0.142000	0.16096	1.002000	0.39104	0.482000	0.46254	CTT	T|0.843;A|0.157	0.157	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
CSPG4	1464	hgsc.bcm.edu	37	15	75982186	75982186	+	Missense_Mutation	SNP	G	G	A	rs199819221	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75982186G>A	ENST00000308508.5	-	3	1312	c.1220C>T	c.(1219-1221)cCa>cTa	p.P407L		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	407	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTCCATGGCTGGCCAAGCCTC	0.612													G|||	105	0.0209665	0.0439	0.0144	5008	,	,		21714	0.001		0.0288	False		,,,				2504	0.0072				p.P407L		Atlas-SNP	.											CSPG4,NS,carcinoma,-1,1	CSPG4	175	1	0			c.C1220T						scavenged	.						24.0	25.0	24.0					15																	75982186		2194	4279	6473	SO:0001583	missense	1464	exon3			ATGGCTGGCCAAG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1220C>T	15.37:g.75982186G>A	ENSP00000312506:p.Pro407Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	137	47	0.343066	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	0.054	-1.242041	0.01481	.	.	ENSG00000173546	ENST00000308508	T	0.37915	1.17	4.74	2.79	0.32731	.	0.523000	0.18155	N	0.149957	T	0.19446	0.0467	N	0.24115	0.695	0.09310	N	0.999997	B	0.09022	0.002	B	0.04013	0.001	T	0.26224	-1.0109	10	0.11182	T	0.66	.	6.6966	0.23203	0.0854:0.0:0.6068:0.3079	.	407	Q6UVK1	CSPG4_HUMAN	L	407	ENSP00000312506:P407L	ENSP00000312506:P407L	P	-	2	0	CSPG4	73769241	0.120000	0.22244	0.232000	0.24009	0.360000	0.29518	0.292000	0.19011	0.557000	0.29117	0.555000	0.69702	CCA	.	.	weak		0.612	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
HSPA4L	22824	hgsc.bcm.edu	37	4	128741710	128741710	+	Missense_Mutation	SNP	T	T	C	rs35518193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:128741710T>C	ENST00000296464.4	+	14	2213	c.1802T>C	c.(1801-1803)aTt>aCt	p.I601T	HSPA4L_ENST00000505726.1_Missense_Mutation_p.I575T|HSPA4L_ENST00000508776.1_Missense_Mutation_p.I601T|HSPA4L_ENST00000439123.2_Missense_Mutation_p.I632T	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	601			I -> T (in dbSNP:rs35518193).		protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						AACAGCTACATTGAAAATGAG	0.343													T|||	100	0.0199681	0.003	0.0447	5008	,	,		16572	0.001		0.0537	False		,,,				2504	0.0102				p.I601T		Atlas-SNP	.											HSPA4L,NS,carcinoma,-1,2	HSPA4L	82	2	0			c.T1802C						PASS	.	T	THR/ILE	53,4353	52.3+/-87.9	0,53,2150	92.0	85.0	87.0		1802	4.7	1.0	4	dbSNP_126	87	451,8149	134.9+/-192.2	14,423,3863	yes	missense	HSPA4L	NM_014278.2	89	14,476,6013	CC,CT,TT		5.2442,1.2029,3.8751	benign	601/840	128741710	504,12502	2203	4300	6503	SO:0001583	missense	22824	exon14			GCTACATTGAAAA	AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"""Heat shock proteins / HSP70"""	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.1802T>C	4.37:g.128741710T>C	ENSP00000296464:p.Ile601Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	123	49	0.398374	NM_014278	A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	37	CCDS3734.1	58	0.026556776556776556	2	0.0040650406504065045	18	0.049723756906077346	1	0.0017482517482517483	37	0.048812664907651716	T	13.09	2.133545	0.37630	0.012029	0.052442	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000505726	T;T;T;T	0.01076	5.37;5.37;5.37;5.37	4.72	4.72	0.59763	.	0.064564	0.64402	D	0.000008	T	0.00241	0.0007	N	0.20574	0.59	0.47737	D	0.9995	B;P;P	0.43826	0.117;0.818;0.818	B;B;B	0.42163	0.223;0.378;0.378	T	0.82174	-0.0588	10	0.19147	T	0.46	.	14.3819	0.66916	0.0:0.0:0.0:1.0	rs35518193;rs61752611;rs35518193	575;601;601	E9PDE8;A2ICT2;O95757	.;.;HS74L_HUMAN	T	601;632;601;575	ENSP00000422482:I601T;ENSP00000393926:I632T;ENSP00000296464:I601T;ENSP00000425645:I575T	ENSP00000296464:I601T	I	+	2	0	HSPA4L	128961160	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.923000	0.75817	1.984000	0.57885	0.528000	0.53228	ATT	T|0.967;C|0.033	0.033	strong		0.343	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278	
NOTCH4	4855	hgsc.bcm.edu	37	6	32190390	32190390	+	Missense_Mutation	SNP	T	T	G	rs915894	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32190390T>G	ENST00000375023.3	-	3	487	c.349A>C	c.(349-351)Aag>Cag	p.K117Q		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	117			K -> Q (in dbSNP:rs915894). {ECO:0000269|PubMed:14574404, ECO:0000269|Ref.4}.		cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TCTTCAAGCTTGGCCTGGCAT	0.627													G|||	1997	0.398762	0.3714	0.3285	5008	,	,		18522	0.5109		0.3519	False		,,,				2504	0.4182				p.K117Q		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A349C						PASS	.	G	GLN/LYS	1664,2742	646.3+/-398.3	324,1016,863	66.0	70.0	69.0		349	2.4	0.0	6	dbSNP_86	69	3177,5423	645.4+/-400.2	590,1997,1713	yes	missense	NOTCH4	NM_004557.3	53	914,3013,2576	GG,GT,TT		36.9419,37.7667,37.2213	benign	117/2004	32190390	4841,8165	2203	4300	6503	SO:0001583	missense	4855	exon3			CAAGCTTGGCCTG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.349A>C	6.37:g.32190390T>G	ENSP00000364163:p.Lys117Gln	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	256	105	0.410156	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	836	0.38278388278388276	159	0.3231707317073171	120	0.3314917127071823	286	0.5	271	0.3575197889182058	G	3.312	-0.140568	0.06669	0.377667	0.369419	ENSG00000204301	ENST00000375023	D	0.91843	-2.92	3.28	2.36	0.29203	.	2.488560	0.01877	N	0.037616	T	0.74291	0.3697	N	0.12853	0.265	0.09310	P	0.99999858293	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.58752	-0.7581	9	0.38643	T	0.18	.	9.6611	0.39956	0.0:0.0:0.6258:0.3742	rs915894;rs17604639;rs915894	117;117	Q6P3V5;Q99466	.;NOTC4_HUMAN	Q	117	ENSP00000364163:K117Q	ENSP00000364163:K117Q	K	-	1	0	NOTCH4	32298368	0.008000	0.16893	0.025000	0.17156	0.073000	0.16967	1.331000	0.33793	0.361000	0.24292	-0.217000	0.12591	AAG	T|0.623;G|0.377	0.377	strong		0.627	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
AKR1E2	83592	hgsc.bcm.edu	37	10	4889403	4889403	+	Nonsense_Mutation	SNP	C	C	T	rs12240276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:4889403C>T	ENST00000298375.7	+	9	972	c.901C>T	c.(901-903)Cga>Tga	p.R301*	AKR1E2_ENST00000532248.1_Nonsense_Mutation_p.R244*|AKR1E2_ENST00000345253.5_Nonsense_Mutation_p.R203*|AKR1E2_ENST00000334019.4_Nonsense_Mutation_p.R244*	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	301						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	1,5-anhydro-D-fructose reductase activity (GO:0050571)			NS(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)	15						CAGGAATCTCCGACTGGCCAT	0.363													C|||	393	0.0784744	0.1006	0.0879	5008	,	,		18282	0.0		0.1342	False		,,,				2504	0.0654				p.R301X	NSCLC(43;343 1097 20371 28813 45509)	Atlas-SNP	.											.	AKR1E2	30	.	0			c.C901T						PASS	.	C	stop/ARG	436,3970	209.2+/-230.0	16,404,1783	139.0	131.0	134.0		901	4.5	0.1	10	dbSNP_120	134	990,7610	214.8+/-254.3	62,866,3372	yes	stop-gained	AKR1E2	NM_001040177.1		78,1270,5155	TT,TC,CC		11.5116,9.8956,10.9642		301/321	4889403	1426,11580	2203	4300	6503	SO:0001587	stop_gained	83592	exon9			AATCTCCGACTGG	AB040820	CCDS31134.1, CCDS59210.1, CCDS59209.1	10p15.2	2009-09-09	2009-09-09	2009-09-09	ENSG00000165568	ENSG00000165568		"""Aldo-keto reductases"""	23437	protein-coding gene	gene with protein product			"""aldo-keto reductase family 1, member C-like 2"""	AKRDC1, AKR1CL2			Standard	NM_001271021		Approved	MGC10612	uc001ihi.4	Q96JD6	OTTHUMG00000017577	ENST00000298375.7:c.901C>T	10.37:g.4889403C>T	ENSP00000298375:p.Arg301*	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	199	103	0.517588	NM_001040177	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Nonsense_Mutation	SNP	ENST00000298375.7	37	CCDS31134.1	169	0.07738095238095238	46	0.09349593495934959	31	0.0856353591160221	0	0.0	92	0.12137203166226913	C	10.97	1.502954	0.26949	0.098956	0.115116	ENSG00000165568	ENST00000298375;ENST00000532248;ENST00000334019;ENST00000345253	.	.	.	4.47	4.47	0.54385	.	0.061588	0.64402	D	0.000005	.	.	.	.	.	.	0.20975	P	0.99981642	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0518	0.71877	0.0:1.0:0.0:0.0	rs12240276;rs52824371;rs56813881;rs12240276	.	.	.	X	301;244;244;203	.	ENSP00000298375:R301X	R	+	1	2	AKR1E2	4879403	0.269000	0.24143	0.089000	0.20774	0.041000	0.13682	3.131000	0.50515	2.490000	0.84030	0.561000	0.74099	CGA	C|0.901;T|0.099	0.099	strong		0.363	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436	
NACAD	23148	hgsc.bcm.edu	37	7	45124465	45124465	+	Missense_Mutation	SNP	A	A	T	rs3735495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45124465A>T	ENST00000490531.2	-	2	1333	c.1314T>A	c.(1312-1314)gaT>gaA	p.D438E		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	438			D -> E (in dbSNP:rs3735495).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						ACACAGTCCCATCCTGAGCCT	0.612													T|||	1391	0.277756	0.1573	0.402	5008	,	,		20664	0.2857		0.334	False		,,,				2504	0.2863				p.D438E		Atlas-SNP	.											.	NACAD	44	.	0			c.T1314A						PASS	.	T	GLU/ASP	290,1094		23,244,425	18.0	20.0	20.0		1314	-5.2	0.0	7	dbSNP_107	20	1116,2066		188,740,663	yes	missense	NACAD	NM_001146334.1	45	211,984,1088	TT,TA,AA		35.0723,20.9538,30.7928	benign	438/1563	45124465	1406,3160	692	1591	2283	SO:0001583	missense	23148	exon2			AGTCCCATCCTGA	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1314T>A	7.37:g.45124465A>T	ENSP00000420477:p.Asp438Glu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	639	0.2925824175824176	94	0.1910569105691057	141	0.38950276243093923	150	0.26223776223776224	254	0.33509234828496043	T	0.037	-1.301109	0.01364	0.209538	0.350723	ENSG00000136274	ENST00000490531	T	0.10382	2.88	2.6	-5.2	0.02823	.	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42882	-0.9425	8	0.02654	T	1	.	0.0621	0.00016	0.3137:0.1922:0.2349:0.2592	rs3735495;rs9639906;rs3735495	438	O15069	NACAD_HUMAN	E	438	ENSP00000420477:D438E	ENSP00000420477:D438E	D	-	3	2	NACAD	45090990	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.322000	0.02695	-2.714000	0.00392	-1.400000	0.01143	GAT	A|0.707;T|0.293	0.293	strong		0.612	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
WDR62	284403	hgsc.bcm.edu	37	19	36594676	36594676	+	Missense_Mutation	SNP	C	C	G	rs35811023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36594676C>G	ENST00000270301.7	+	30	3931	c.3931C>G	c.(3931-3933)Cag>Gag	p.Q1311E	WDR62_ENST00000401500.2_Missense_Mutation_p.Q1316E			O43379	WDR62_HUMAN	WD repeat domain 62	1311			Q -> E (in dbSNP:rs35811023).		cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CGTGGATACCCAGCCTGGCGT	0.677													C|||	7	0.00139776	0.0008	0.0	5008	,	,		19234	0.0		0.006	False		,,,				2504	0.0				p.Q1316E		Atlas-SNP	.											.	WDR62	102	.	0			c.C3946G						PASS	.	C	GLU/GLN,GLU/GLN	9,4397	15.5+/-35.6	0,9,2194	71.0	62.0	65.0		3946,3931	1.5	0.0	19	dbSNP_126	65	54,8546	34.8+/-89.0	0,54,4246	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	29,29	0,63,6440	GG,GC,CC		0.6279,0.2043,0.4844	benign,benign	1316/1524,1311/1519	36594676	63,12943	2203	4300	6503	SO:0001583	missense	284403	exon30			GATACCCAGCCTG	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.3931C>G	19.37:g.36594676C>G	ENSP00000270301:p.Gln1311Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	C	6.239	0.412249	0.11812	0.002043	0.006279	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.46451	0.96;0.87	5.06	1.47	0.22746	.	0.568333	0.16576	N	0.208382	T	0.13970	0.0338	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.25882	-1.0119	10	0.02654	T	1	-5.5063	7.7082	0.28663	0.3295:0.5109:0.1597:0.0	rs35811023;rs62636634	1316;1311	O43379-4;O43379	.;WDR62_HUMAN	E	1316;1311	ENSP00000384792:Q1316E;ENSP00000270301:Q1311E	ENSP00000270301:Q1311E	Q	+	1	0	WDR62	41286516	0.003000	0.15002	0.007000	0.13788	0.008000	0.06430	0.484000	0.22308	0.689000	0.31550	0.555000	0.69702	CAG	C|0.995;G|0.005	0.005	strong		0.677	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
NR1I3	9970	hgsc.bcm.edu	37	1	161202605	161202605	+	Silent	SNP	G	G	A	rs2307424	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161202605G>A	ENST00000367982.4	-	5	695	c.540C>T	c.(538-540)ccC>ccT	p.P180P	NR1I3_ENST00000367983.4_Silent_p.P180P|NR1I3_ENST00000428574.2_Silent_p.P180P|NR1I3_ENST00000442691.2_Silent_p.P180P|NR1I3_ENST00000479324.1_5'Flank|NR1I3_ENST00000367980.2_Silent_p.P180P|NR1I3_ENST00000508387.1_Intron|NR1I3_ENST00000505005.1_Silent_p.P180P|NR1I3_ENST00000515621.1_Silent_p.P105P|NR1I3_ENST00000506209.1_Silent_p.P151P|NR1I3_ENST00000412844.2_Silent_p.P151P|NR1I3_ENST00000504010.1_Silent_p.P151P|NR1I3_ENST00000367984.4_Silent_p.P180P|NR1I3_ENST00000511944.1_Intron|NR1I3_ENST00000511676.1_Silent_p.P151P|NR1I3_ENST00000512372.1_Silent_p.P151P|NR1I3_ENST00000367979.2_Silent_p.P180P|NR1I3_ENST00000437437.2_Silent_p.P151P|NR1I3_ENST00000511748.1_Intron|NR1I3_ENST00000508740.1_Silent_p.P151P|NR1I3_ENST00000367981.3_Silent_p.P151P|NR1I3_ENST00000515452.1_Silent_p.P180P|NR1I3_ENST00000367985.3_Silent_p.P180P|NR1I3_ENST00000502985.1_Intron			Q14994	NR1I3_HUMAN	nuclear receptor subfamily 1, group I, member 3	180					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	15	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			ACCGGAAGACGGGCAGGTCCT	0.498													G|||	1684	0.336262	0.1067	0.3256	5008	,	,		20654	0.5188		0.3489	False		,,,				2504	0.453				p.P180P		Atlas-SNP	.											.	NR1I3	74	.	0			c.C540T						PASS	.	G	,,,,,,,,,,,,,,	632,3774	270.1+/-269.4	43,546,1614	112.0	112.0	112.0		540,453,540,453,453,540,453,453,453,540,453,540,540,540,540	-1.4	0.8	1	dbSNP_100	112	2878,5722	450.4+/-362.4	480,1918,1902	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NR1I3	NM_001077469.2,NM_001077470.2,NM_001077471.2,NM_001077472.2,NM_001077473.2,NM_001077474.2,NM_001077475.2,NM_001077476.2,NM_001077477.2,NM_001077478.2,NM_001077479.2,NM_001077480.2,NM_001077481.2,NM_001077482.2,NM_005122.4	,,,,,,,,,,,,,,	523,2464,3516	AA,AG,GG		33.4651,14.3441,26.9875	,,,,,,,,,,,,,,	180/341,151/281,180/310,151/325,151/316,180/297,151/268,151/312,151/307,180/340,151/320,180/353,180/315,180/358,180/349	161202605	3510,9496	2203	4300	6503	SO:0001819	synonymous_variant	9970	exon5			GAAGACGGGCAGG	Z30425	CCDS1228.1, CCDS41427.1, CCDS41428.1, CCDS41429.1, CCDS41430.1, CCDS44260.1, CCDS44261.1, CCDS44262.1, CCDS53405.1, CCDS53406.1, CCDS53407.1, CCDS53408.1, CCDS53409.1, CCDS53410.1, CCDS53411.1	1q23.3	2013-01-16			ENSG00000143257	ENSG00000143257		"""Nuclear hormone receptors"""	7969	protein-coding gene	gene with protein product	"""constitutive androstane receptor"""	603881				8114692	Standard	NM_001077480		Approved	MB67, CAR1, CAR	uc001fzp.3	Q14994	OTTHUMG00000034347	ENST00000367982.4:c.540C>T	1.37:g.161202605G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	79	25	0.316456	NM_005122	E9PB75|E9PC13|E9PDU3|E9PGH6|E9PH10|E9PHC8|E9PHN4|F1D8Q0|F1D8Q1|Q0VAC9|Q4U0F0|Q5VTW5|Q5VTW6|Q6GZ68|Q6GZ76|Q6GZ77|Q6GZ78|Q6GZ79|Q6GZ82|Q6GZ83|Q6GZ84|Q6GZ85|Q6GZ87|Q6GZ89	Silent	SNP	ENST00000367982.4	37	CCDS41430.1																																																																																			G|0.688;A|0.312	0.312	strong		0.498	NR1I3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083048.2		
ENTPD7	57089	hgsc.bcm.edu	37	10	101451194	101451194	+	Silent	SNP	A	A	C	rs72832512	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:101451194A>C	ENST00000370489.4	+	8	940	c.762A>C	c.(760-762)gtA>gtC	p.V254V		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	254						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		GAAGGACAGTAGGGATACTGG	0.428													A|||	80	0.0159744	0.0023	0.013	5008	,	,		16832	0.001		0.0338	False		,,,				2504	0.0337				p.V254V		Atlas-SNP	.											.	ENTPD7	44	.	0			c.A762C						PASS	.	A		25,4381	31.7+/-61.6	0,25,2178	111.0	102.0	105.0		762	-0.1	1.0	10	dbSNP_130	105	314,8286	111.8+/-172.0	6,302,3992	no	coding-synonymous	ENTPD7	NM_020354.3		6,327,6170	CC,CA,AA		3.6512,0.5674,2.6065		254/605	101451194	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	57089	exon8			GACAGTAGGGATA	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.762A>C	10.37:g.101451194A>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_020354	B2RB83|B3KP21|D3DR64	Silent	SNP	ENST00000370489.4	37	CCDS7480.1																																																																																			A|0.978;C|0.022	0.022	strong		0.428	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
PPP1R1A	5502	hgsc.bcm.edu	37	12	54974803	54974803	+	Silent	SNP	C	C	T	rs8407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:54974803C>T	ENST00000257905.8	-	6	605	c.435G>A	c.(433-435)gaG>gaA	p.E145E	PPP1R1A_ENST00000547431.1_Missense_Mutation_p.R72K	NM_006741.3	NP_006732	Q13522	PPR1A_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1A	145	Interaction with PPP1R15A.				glycogen metabolic process (GO:0005977)|negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein serine/threonine phosphatase inhibitor activity (GO:0004865)			lung(2)	2						TACTGCCTCTCTCGTGAGTTT	0.542													C|||	829	0.165535	0.0348	0.2666	5008	,	,		17061	0.0595		0.3012	False		,,,				2504	0.2403				p.E145E		Atlas-SNP	.											PPP1R1A_ENST00000257905,NS,carcinoma,-2,2	PPP1R1A	18	2	0			c.G435A						PASS	.	C		284,3490		5,274,1608	203.0	190.0	194.0		435	4.9	1.0	12	dbSNP_52	194	2522,5724		381,1760,1982	no	coding-synonymous	PPP1R1A	NM_006741.3		386,2034,3590	TT,TC,CC		30.5845,7.5252,23.3444		145/172	54974803	2806,9214	1887	4123	6010	SO:0001819	synonymous_variant	5502	exon6			GCCTCTCTCGTGA	U48707	CCDS44912.1	12q13.2	2012-04-17			ENSG00000135447	ENSG00000135447	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9286	protein-coding gene	gene with protein product		613246				8611507	Standard	NM_006741		Approved		uc001sgg.2	Q13522	OTTHUMG00000169934	ENST00000257905.8:c.435G>A	12.37:g.54974803C>T		Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	380	165	0.434211	NM_006741	Q6IB01|Q8TBJ2|Q8WWV2	Silent	SNP	ENST00000257905.8	37	CCDS44912.1	381	0.17445054945054944	20	0.04065040650406504	94	0.2596685082872928	39	0.06818181818181818	228	0.3007915567282322	C	5.450	0.268099	0.10349	0.075252	0.305845	ENSG00000135447	ENST00000379690;ENST00000553113	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.04053	-1.0981	4	0.02654	T	1	.	14.0661	0.64831	0.0:1.0:0.0:0.0	rs8407;rs867623;rs1050103;rs3190383;rs17795135;rs17845698;rs17858640;rs8407	.	.	.	K	72;64	.	ENSP00000369012:R72K	R	-	2	0	PPP1R1A	53261070	0.985000	0.35326	0.963000	0.40424	0.460000	0.32559	3.445000	0.52921	2.458000	0.83093	0.655000	0.94253	AGA	C|0.825;T|0.175	0.175	strong		0.542	PPP1R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406604.1	NM_006741	
CHFR	55743	hgsc.bcm.edu	37	12	133435716	133435716	+	Silent	SNP	T	T	G	rs35011845	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133435716T>G	ENST00000432561.2	-	8	958	c.885A>C	c.(883-885)ccA>ccC	p.P295P	CHFR_ENST00000443047.2_Silent_p.P203P|CHFR_ENST00000266880.7_Silent_p.P295P|CHFR_ENST00000315585.7_Silent_p.P254P|CHFR_ENST00000537522.1_5'Flank|CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000450056.2_Silent_p.P283P			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	295					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		CCATCTTGTCTGGCTTCCCAG	0.592													T|||	712	0.142173	0.0106	0.1585	5008	,	,		18006	0.1726		0.2793	False		,,,				2504	0.136				p.P295P		Atlas-SNP	.											.	CHFR	83	.	0			c.A885C						PASS	.	T	,,,,	223,4183	137.3+/-173.1	9,205,1989	216.0	124.0	155.0		885,885,849,609,762	-11.0	0.1	12	dbSNP_126	155	2569,6031	417.4+/-352.4	384,1801,2115	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CHFR	NM_001161344.1,NM_001161345.1,NM_001161346.1,NM_001161347.1,NM_018223.2	,,,,	393,2006,4104	GG,GT,TT		29.8721,5.0613,21.467	,,,,	295/665,295/664,283/653,203/573,254/624	133435716	2792,10214	2203	4300	6503	SO:0001819	synonymous_variant	55743	exon8			CTTGTCTGGCTTC	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.885A>C	12.37:g.133435716T>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Silent	SNP	ENST00000432561.2	37	CCDS53849.1																																																																																			T|0.796;G|0.204	0.204	strong		0.592	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
SYPL2	284612	hgsc.bcm.edu	37	1	110019439	110019439	+	Missense_Mutation	SNP	A	A	G	rs62623713	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110019439A>G	ENST00000369872.3	+	4	512	c.296A>G	c.(295-297)gAg>gGg	p.E99G	SYPL2_ENST00000475497.1_3'UTR|SYPL2_ENST00000401021.3_Missense_Mutation_p.E99G	NM_001040709.1	NP_001035799.1	Q5VXT5	SYPL2_HUMAN	synaptophysin-like 2	99	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.			E -> G (in Ref. 2; BAD18604). {ECO:0000305}.	cellular calcium ion homeostasis (GO:0006874)|substantia nigra development (GO:0021762)	integral component of synaptic vesicle membrane (GO:0030285)	transporter activity (GO:0005215)			breast(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)		TGCGATGAAGAGTCCAGCTCC	0.582													A|||	151	0.0301518	0.0144	0.0159	5008	,	,		17314	0.002		0.0547	False		,,,				2504	0.0654				p.E99G		Atlas-SNP	.											SYPL2,NS,carcinoma,-1,1	SYPL2	41	1	0			c.A296G						PASS	.	A	GLY/GLU	109,3975		2,105,1935	84.0	87.0	86.0		296	3.3	0.0	1	dbSNP_129	86	475,7899		12,451,3724	yes	missense	SYPL2	NM_001040709.1	98	14,556,5659	GG,GA,AA		5.6723,2.669,4.6878	possibly-damaging	99/273	110019439	584,11874	2042	4187	6229	SO:0001583	missense	284612	exon4			ATGAAGAGTCCAG	AK131459	CCDS41365.1	1p13.3	2008-02-05			ENSG00000143028	ENSG00000143028			27638	protein-coding gene	gene with protein product	"""mitsugumin-29"""					12975309	Standard	NM_001040709		Approved	Mg29	uc001dxp.3	Q5VXT5	OTTHUMG00000010969	ENST00000369872.3:c.296A>G	1.37:g.110019439A>G	ENSP00000358888:p.Glu99Gly	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	NM_001040709	A8K0E8|A8KAL7|I0IT67|Q6ZMX1	Missense_Mutation	SNP	ENST00000369872.3	37	CCDS41365.1	64	0.029304029304029304	9	0.018292682926829267	8	0.022099447513812154	1	0.0017482517482517483	46	0.06068601583113457	A	6.996	0.553889	0.13374	0.02669	0.056723	ENSG00000143028	ENST00000401021;ENST00000369872	T	0.32515	1.45	5.64	3.32	0.38043	Marvel (1);MARVEL-like domain (1);	1.132410	0.06169	N	0.677290	T	0.04003	0.0112	N	0.03917	-0.325	0.09310	N	1	B;B;B;B	0.12013	0.005;0.0;0.0;0.001	B;B;B;B	0.14578	0.011;0.001;0.001;0.004	T	0.41034	-0.9531	10	0.13853	T	0.58	.	7.1401	0.25552	0.744:0.0:0.256:0.0	rs62623713	99;7;99;99	B4DYR7;Q14DL7;Q5VXT5;Q5VXT5-2	.;.;SYPL2_HUMAN;.	G	99	ENSP00000358888:E99G	ENSP00000358888:E99G	E	+	2	0	SYPL2	109820962	0.021000	0.18746	0.005000	0.12908	0.506000	0.33950	1.418000	0.34782	0.421000	0.25980	0.374000	0.22700	GAG	A|0.962;G|0.038	0.038	strong		0.582	SYPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030191.1	NM_001006603	
IRX2	153572	hgsc.bcm.edu	37	5	2749539	2749539	+	Silent	SNP	G	G	C	rs61748183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:2749539G>C	ENST00000382611.6	-	2	860	c.612C>G	c.(610-612)ccC>ccG	p.P204P	C5orf38_ENST00000397835.4_5'Flank|C5orf38_ENST00000505778.1_5'Flank|C5orf38_ENST00000515640.1_5'Flank|IRX2_ENST00000302057.5_Silent_p.P204P|C5orf38_ENST00000457752.2_5'Flank|C5orf38_ENST00000334000.3_5'Flank|IRX2_ENST00000502957.1_5'UTR	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	204					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26				GBM - Glioblastoma multiforme(108;0.204)		GCGCCTTGTCGGGACTCTCGT	0.652													G|||	5	0.000998403	0.0	0.0	5008	,	,		14303	0.0		0.004	False		,,,				2504	0.001				p.P204P		Atlas-SNP	.											.	IRX2	60	.	0			c.C612G						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	94.0	86.0	89.0		612,612	-6.5	0.0	5	dbSNP_129	89	47,8553	30.1+/-81.4	0,47,4253	no	coding-synonymous,coding-synonymous	IRX2	NM_001134222.1,NM_033267.4	,	0,50,6453	CC,CG,GG		0.5465,0.0681,0.3844	,	204/472,204/472	2749539	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	153572	exon2			CTTGTCGGGACTC	AF319967	CCDS3868.1	5p15.33	2011-06-20	2007-07-13		ENSG00000170561	ENSG00000170561		"""Homeoboxes / TALE class"""	14359	protein-coding gene	gene with protein product		606198				11435706	Standard	NM_033267		Approved		uc003jdb.3	Q9BZI1	OTTHUMG00000090377	ENST00000382611.6:c.612C>G	5.37:g.2749539G>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	266	155	0.582707	NM_001134222	Q68A19|Q7Z2I7	Silent	SNP	ENST00000382611.6	37	CCDS3868.1																																																																																			G|0.997;C|0.003	0.003	strong		0.652	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2		
ITIH4	3700	hgsc.bcm.edu	37	3	52860816	52860816	+	Silent	SNP	C	C	T	rs2276816	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:52860816C>T	ENST00000266041.4	-	4	606	c.510G>A	c.(508-510)aaG>aaA	p.K170K	ITIH4_ENST00000434759.3_Silent_p.K82K|ITIH4_ENST00000485816.1_Silent_p.K170K|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000346281.5_Silent_p.K170K|ITIH4-AS1_ENST00000478366.1_RNA|ITIH4_ENST00000406595.1_Silent_p.K170K	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	170					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CCTGCAGGTGCTTGACCAGCT	0.617													C|||	354	0.0706869	0.0023	0.1037	5008	,	,		19514	0.0575		0.1252	False		,,,				2504	0.0971				p.K170K		Atlas-SNP	.											.	ITIH4	74	.	0			c.G510A						PASS	.	C	,	104,4302	81.9+/-120.4	2,100,2101	42.0	42.0	42.0		510,510	2.4	1.0	3	dbSNP_100	42	975,7625	210.7+/-251.5	68,839,3393	no	coding-synonymous,coding-synonymous	ITIH4	NM_001166449.1,NM_002218.4	,	70,939,5494	TT,TC,CC		11.3372,2.3604,8.2962	,	170/901,170/931	52860816	1079,11927	2203	4300	6503	SO:0001819	synonymous_variant	3700	exon4			CAGGTGCTTGACC	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"""plasma Kallikrein-sensitive glycoprotein"""	600564	"""inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"""	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.510G>A	3.37:g.52860816C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	CCDS2865.1	156	0.07142857142857142	0	0.0	26	0.0718232044198895	38	0.06643356643356643	92	0.12137203166226913	C	9.720	1.159442	0.21454	0.023604	0.113372	ENSG00000055955	ENST00000441637	.	.	.	5.53	2.36	0.29203	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00844	-1.1543	4	.	.	.	-29.6721	4.3415	0.11112	0.1551:0.4784:0.0:0.3665	rs2276816;rs17419961;rs2276816	.	.	.	T	40	.	.	A	-	1	0	ITIH4	52835856	0.224000	0.23674	1.000000	0.80357	0.977000	0.68977	0.055000	0.14229	0.709000	0.31976	0.655000	0.94253	GCA	C|0.919;T|0.081	0.081	strong		0.617	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
ZNF449	203523	hgsc.bcm.edu	37	X	134494878	134494878	+	Silent	SNP	C	C	T	rs141878135	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:134494878C>T	ENST00000339249.4	+	5	1574	c.1434C>T	c.(1432-1434)ctC>ctT	p.L478L		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	478					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GACCAAGCCTCGTTATTCATT	0.423																																					p.L478L		Atlas-SNP	.											.	ZNF449	68	.	0			c.C1434T						PASS	.	C		2,3833		0,2,0,1630,571	121.0	120.0	121.0		1434	0.2	1.0	X	dbSNP_134	121	10,6716		0,7,3,2420,1869	no	coding-synonymous	ZNF449	NM_152695.5		0,9,3,4050,2440	TT,TC,T,CC,C		0.1487,0.0522,0.1136		478/519	134494878	12,10549	2203	4299	6502	SO:0001819	synonymous_variant	203523	exon5			AAGCCTCGTTATT	AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"""-"", ""Zinc fingers, C2H2-type"""	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.1434C>T	X.37:g.134494878C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_152695	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Silent	SNP	ENST00000339249.4	37	CCDS14649.1																																																																																			C|0.999;T|0.001	0.001	strong		0.423	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695	
ZNF782	158431	hgsc.bcm.edu	37	9	99581568	99581568	+	Missense_Mutation	SNP	T	T	C	rs34763627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:99581568T>C	ENST00000481138.1	-	6	1398	c.737A>G	c.(736-738)aAt>aGt	p.N246S	ZNF782_ENST00000535338.1_Missense_Mutation_p.N114S|ZNF782_ENST00000466833.1_5'Flank	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	246			N -> S (in dbSNP:rs34763627).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				CCCAAATTTATTGAAATTGTA	0.313													T|||	159	0.0317492	0.0023	0.0519	5008	,	,		19228	0.002		0.1064	False		,,,				2504	0.0112				p.N246S		Atlas-SNP	.											.	ZNF782	64	.	0			c.A737G						PASS	.	T	SER/ASN	88,4318	68.7+/-106.4	2,84,2117	70.0	76.0	74.0		737	-3.5	0.0	9	dbSNP_126	74	934,7664	203.4+/-246.4	57,820,3422	yes	missense	ZNF782	NM_001001662.1	46	59,904,5539	CC,CT,TT		10.863,1.9973,7.8591	benign	246/700	99581568	1022,11982	2203	4299	6502	SO:0001583	missense	158431	exon6			AATTTATTGAAAT	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.737A>G	9.37:g.99581568T>C	ENSP00000419397:p.Asn246Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	100	0.045787545787545784	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	76	0.10026385224274406	T	8.866	0.948211	0.18356	0.019973	0.10863	ENSG00000196597	ENST00000481138;ENST00000535338	T;T	0.06528	3.51;3.29	3.33	-3.52	0.04682	.	0.697460	0.11782	N	0.530109	T	0.00073	0.0002	N	0.17764	0.52	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.44205	-0.9343	10	0.28530	T	0.3	.	3.8127	0.08804	0.3002:0.3826:0.0:0.3171	rs34763627	246	Q6ZMW2	ZN782_HUMAN	S	246;114	ENSP00000419397:N246S;ENSP00000440624:N114S	ENSP00000419397:N246S	N	-	2	0	ZNF782	98621389	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-1.910000	0.01584	-0.766000	0.04639	-0.296000	0.09543	AAT	T|0.930;C|0.070	0.070	strong		0.313	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
LAMA5	3911	hgsc.bcm.edu	37	20	60897487	60897487	+	Missense_Mutation	SNP	C	C	T	rs2274934	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60897487C>T	ENST00000252999.3	-	47	6250	c.6184G>A	c.(6184-6186)Gat>Aat	p.D2062N		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2062	Laminin EGF-like 20. {ECO:0000255|PROSITE-ProRule:PRU00460}.		D -> N (in dbSNP:rs2274934). {ECO:0000269|PubMed:11821406, ECO:0000269|PubMed:9628581}.		angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CCGCAGCCATCGAAACCAAAA	0.672													.|||	2393	0.477835	0.0976	0.5159	5008	,	,		11156	0.747		0.5547	False		,,,				2504	0.6084				p.D2062N		Atlas-SNP	.											.	LAMA5	268	.	0			c.G6184A						PASS	.	C	ASN/ASP	647,3647		65,517,1565	9.0	12.0	11.0		6184	2.8	0.1	20	dbSNP_100	11	4883,3619		1464,1955,832	no	missense	LAMA5	NM_005560.3	23	1529,2472,2397	TT,TC,CC		42.5665,15.0675,43.2166	possibly-damaging	2062/3696	60897487	5530,7266	2147	4251	6398	SO:0001583	missense	3911	exon47			AGCCATCGAAACC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.6184G>A	20.37:g.60897487C>T	ENSP00000252999:p.Asp2062Asn	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	1118	0.5119047619047619	64	0.13008130081300814	184	0.5082872928176796	441	0.7709790209790209	429	0.5659630606860159	c	10.33	1.319163	0.23994	0.150675	0.574335	ENSG00000130702	ENST00000252999	T	0.32023	1.47	3.82	2.83	0.33086	EGF-like, laminin (4);	0.605183	0.16797	U	0.199131	T	0.00012	0.0000	N	0.25094	0.71	0.09310	P	1.0	B	0.25563	0.129	B	0.18871	0.023	T	0.17806	-1.0357	9	0.22706	T	0.39	.	7.0499	0.25067	0.0:0.7291:0.1768:0.0942	rs2274934;rs2274934	2062	O15230	LAMA5_HUMAN	N	2062	ENSP00000252999:D2062N	ENSP00000252999:D2062N	D	-	1	0	LAMA5	60330882	0.025000	0.19082	0.068000	0.19968	0.008000	0.06430	0.835000	0.27531	0.768000	0.33290	0.485000	0.47835	GAT	C|0.463;T|0.537	0.537	strong		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SLC7A2	6542	hgsc.bcm.edu	37	8	17396415	17396415	+	Intron	SNP	G	G	C	rs13259978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17396415G>C	ENST00000494857.1	+	3	196				SLC7A2_ENST00000004531.10_Missense_Mutation_p.D28H|SLC7A2_ENST00000470360.1_Missense_Mutation_p.D28H|SLC7A2_ENST00000398090.3_Missense_Mutation_p.D28H|SLC7A2_ENST00000522656.1_Intron	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2						amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	ACCGGTTTGCGACAGCAAGTT	0.413													G|||	967	0.193091	0.295	0.1744	5008	,	,		17605	0.1141		0.2038	False		,,,				2504	0.1391				p.D28H		Atlas-SNP	.											.	SLC7A2	157	.	0			c.G82C						PASS	.	G	,HIS/ASP,HIS/ASP	1012,2652		143,726,963	99.0	89.0	92.0		,82,82	-1.8	0.0	8	dbSNP_121	92	1725,6447		238,1249,2599	yes	intron,missense,missense	SLC7A2	NM_001008539.3,NM_001164771.1,NM_003046.5	,81,81	381,1975,3562	CC,CG,GG		21.1087,27.6201,23.1244	,benign,benign	,28/699,28/698	17396415	2737,9099	1832	4086	5918	SO:0001627	intron_variant	6542	exon1			GTTTGCGACAGCA	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.-22-4412G>C	8.37:g.17396415G>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	93	63	0.677419	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	37	CCDS34852.1	395	0.18086080586080586	124	0.25203252032520324	66	0.18232044198895028	58	0.10139860139860139	147	0.19393139841688653	G	7.037	0.561770	0.13498	0.276201	0.211087	ENSG00000003989	ENST00000470360;ENST00000004531;ENST00000398090	D;D;D	0.89343	-2.5;-2.36;-2.5	3.54	-1.78	0.07957	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09487	-1.0672	7	0.49607	T	0.09	.	0.5525	0.00665	0.1741:0.3011:0.1787:0.3461	rs13259978	28;28	P52569-3;P52569-2	.;.	H	28	ENSP00000419873:D28H;ENSP00000004531:D28H;ENSP00000381164:D28H	ENSP00000004531:D28H	D	+	1	0	SLC7A2	17440794	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.069000	0.11542	-0.398000	0.07679	-0.256000	0.11100	GAC	A|0.011;C|0.200;G|0.789	0.200	strong		0.413	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
CDCA2	157313	hgsc.bcm.edu	37	8	25364331	25364331	+	Missense_Mutation	SNP	G	G	A	rs4872318	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:25364331G>A	ENST00000330560.3	+	15	2626	c.2149G>A	c.(2149-2151)Gta>Ata	p.V717I	CDCA2_ENST00000380665.3_Missense_Mutation_p.V702I|CDCA2_ENST00000521098.2_3'UTR	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	717			V -> I (in dbSNP:rs4872318). {ECO:0000269|PubMed:12188893, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:21406692}.		mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		TTGTGCTTCTGTAACTGAAGA	0.393													G|||	1134	0.226438	0.031	0.3602	5008	,	,		18117	0.0982		0.3549	False		,,,				2504	0.3957				p.V717I		Atlas-SNP	.											.	CDCA2	78	.	0			c.G2149A						PASS	.	G	ILE/VAL	372,4034	176.2+/-205.4	19,334,1850	38.0	39.0	38.0		2149	0.8	0.0	8	dbSNP_111	38	2977,5623	452.4+/-362.9	502,1973,1825	yes	missense	CDCA2	NM_152562.2	29	521,2307,3675	AA,AG,GG		34.6163,8.443,25.7497	probably-damaging	717/1024	25364331	3349,9657	2203	4300	6503	SO:0001583	missense	157313	exon15			GCTTCTGTAACTG	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 81"""					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.2149G>A	8.37:g.25364331G>A	ENSP00000328228:p.Val717Ile	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	37	CCDS6049.1	469	0.21474358974358973	14	0.028455284552845527	118	0.3259668508287293	62	0.10839160839160839	275	0.3627968337730871	G	14.92	2.678756	0.47886	0.08443	0.346163	ENSG00000184661	ENST00000330560;ENST00000380665;ENST00000434814	T;T	0.47869	0.83;0.83	5.07	0.754	0.18410	.	0.967502	0.08533	N	0.931768	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	P;P	0.42908	0.793;0.793	B;B	0.40940	0.344;0.344	T	0.27706	-1.0066	9	0.36615	T	0.2	-0.7116	2.265	0.04077	0.0998:0.1708:0.3786:0.3508	rs4872318;rs17792792;rs4872318	702;717	E9PEI0;Q69YH5	.;CDCA2_HUMAN	I	717;702;116	ENSP00000328228:V717I;ENSP00000370040:V702I	ENSP00000328228:V717I	V	+	1	0	CDCA2	25420248	0.001000	0.12720	0.003000	0.11579	0.011000	0.07611	0.451000	0.21779	0.261000	0.21753	-0.188000	0.12872	GTA	G|0.761;A|0.239	0.239	strong		0.393	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562	
CENPU	79682	hgsc.bcm.edu	37	4	185634144	185634144	+	Missense_Mutation	SNP	T	T	C	rs4616798	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:185634144T>C	ENST00000281453.5	-	7	712	c.642A>G	c.(640-642)atA>atG	p.I214M	MLF1IP_ENST00000541971.1_Missense_Mutation_p.I214M|MLF1IP_ENST00000506535.1_5'UTR	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		TGTCATGAGATATCTTCCCTT	0.299													C|||	724	0.144569	0.295	0.1354	5008	,	,		16274	0.001		0.1481	False		,,,				2504	0.092				p.I214M		Atlas-SNP	.											.	MLF1IP	33	.	0			c.A642G						PASS	.	C	MET/ILE	1189,3215	708.9+/-407.7	161,867,1174	113.0	109.0	111.0		642	0.4	0.0	4	dbSNP_111	111	1406,7190	750.3+/-407.4	119,1168,3011	yes	missense	MLF1IP	NM_024629.3	10	280,2035,4185	CC,CT,TT		16.3564,26.9982,19.9615	benign	214/419	185634144	2595,10405	2202	4298	6500	SO:0001583	missense	79682	exon7			ATGAGATATCTTC																												ENST00000281453.5:c.642A>G	4.37:g.185634144T>C	ENSP00000281453:p.Ile214Met	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_024629		Missense_Mutation	SNP	ENST00000281453.5	37	CCDS3838.1	306	0.1401098901098901	145	0.29471544715447157	56	0.15469613259668508	0	0.0	105	0.13852242744063326	C	0.001	-2.945452	0.00052	0.269982	0.163564	ENSG00000151725	ENST00000281453;ENST00000541665;ENST00000541971	T;T	0.22134	1.97;1.97	4.03	0.371	0.16168	.	1.079220	0.07109	N	0.841860	T	0.00012	0.0000	N	0.01267	-0.92	0.80722	P	0.0	B;B	0.09022	0.0;0.002	B;B	0.09377	0.002;0.004	T	0.43621	-0.9380	9	0.44086	T	0.13	-20.3821	8.2661	0.31815	0.0:0.6043:0.0:0.3957	rs4616798;rs58095997;rs4616798	214;214	Q09GN1;Q71F23	.;CENPU_HUMAN	M	214	ENSP00000281453:I214M;ENSP00000445862:I214M	ENSP00000281453:I214M	I	-	3	3	MLF1IP	185871138	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-3.075000	0.00616	-0.189000	0.10482	-0.722000	0.03604	ATA	T|0.826;C|0.174	0.174	strong		0.299	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		
PARP9	83666	hgsc.bcm.edu	37	3	122259606	122259606	+	Missense_Mutation	SNP	T	T	C	rs9851180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122259606T>C	ENST00000360356.2	-	8	1810	c.1583A>G	c.(1582-1584)tAt>tGt	p.Y528C	PARP9_ENST00000477522.2_Missense_Mutation_p.Y493C|PARP9_ENST00000471785.1_Missense_Mutation_p.Y493C|PARP9_ENST00000462315.1_Missense_Mutation_p.Y493C|PARP9_ENST00000492382.1_Missense_Mutation_p.Y73C	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	528			Y -> C (in dbSNP:rs9851180). {ECO:0000269|PubMed:11110709, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		GTGGGCCTCATACATCTCTTC	0.448													T|||	2537	0.506589	0.4191	0.4092	5008	,	,		18134	0.6548		0.5567	False		,,,				2504	0.4898				p.Y528C		Atlas-SNP	.											PARP9,NS,carcinoma,-1,1	PARP9	72	1	0			c.A1583G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	2068,2338	569.2+/-382.6	477,1114,612	139.0	139.0	139.0		1583,1478,1478,1478,1478,1583	-8.7	0.0	3	dbSNP_119	139	4879,3721	619.4+/-396.9	1398,2083,819	yes	missense,missense,missense,missense,missense,missense	PARP9	NM_001146102.1,NM_001146103.1,NM_001146104.1,NM_001146105.1,NM_001146106.1,NM_031458.2	194,194,194,194,194,194	1875,3197,1431	CC,CT,TT		43.2674,46.936,46.5862	benign,benign,benign,benign,benign,benign	528/855,493/820,493/820,493/820,493/711,528/855	122259606	6947,6059	2203	4300	6503	SO:0001583	missense	83666	exon8			GCCTCATACATCT	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"""Poly (ADP-ribose) polymerases"""	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.1583A>G	3.37:g.122259606T>C	ENSP00000353512:p.Tyr528Cys	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	242	114	0.471074	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	37	CCDS3014.1	1171	0.5361721611721612	218	0.44308943089430897	158	0.43646408839779005	378	0.6608391608391608	417	0.5501319261213721	T	8.048	0.765420	0.15914	0.46936	0.567326	ENSG00000138496	ENST00000360356;ENST00000492382;ENST00000477522;ENST00000471785;ENST00000452457;ENST00000462315	T;T;T;T;T	0.16743	3.32;3.0;3.17;3.17;2.32	4.83	-8.73	0.00841	.	2.264100	0.01312	N	0.010677	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47182	-0.9137	9	0.54805	T	0.06	.	7.7858	0.29091	0.0:0.2362:0.2134:0.5505	rs9851180;rs56494261;rs57842345;rs9851180	493;528;73;493	E9PFM7;Q8IXQ6;G5E9U8;Q8IXQ6-2	.;PARP9_HUMAN;.;.	C	528;73;493;493;451;493	ENSP00000353512:Y528C;ENSP00000417664:Y73C;ENSP00000419506:Y493C;ENSP00000419001:Y493C;ENSP00000418894:Y493C	ENSP00000353512:Y528C	Y	-	2	0	PARP9	123742296	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.579000	0.02123	-1.542000	0.01725	-0.774000	0.03386	TAT	T|0.466;C|0.534	0.534	strong		0.448	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458	
RPAP1	26015	hgsc.bcm.edu	37	15	41829230	41829230	+	Silent	SNP	A	A	G	rs721772	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41829230A>G	ENST00000304330.4	-	2	210	c.94T>C	c.(94-96)Ttg>Ctg	p.L32L	RPAP1_ENST00000561603.1_Silent_p.L32L	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	32						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TTCTTCACCAACTGCACTGCT	0.592													A|||	1960	0.391374	0.1528	0.3862	5008	,	,		18053	0.4464		0.5199	False		,,,				2504	0.5286				p.L32L		Atlas-SNP	.											.	RPAP1	111	.	0			c.T94C						PASS	.	A		1020,3386	377.8+/-322.6	111,798,1294	121.0	104.0	110.0		94	-9.6	0.0	15	dbSNP_86	110	4485,4115	592.2+/-392.9	1161,2163,976	no	coding-synonymous	RPAP1	NM_015540.2		1272,2961,2270	GG,GA,AA		47.8488,23.1502,42.3266		32/1394	41829230	5505,7501	2203	4300	6503	SO:0001819	synonymous_variant	26015	exon2			TCACCAACTGCAC	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.94T>C	15.37:g.41829230A>G		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	37	CCDS10079.1																																																																																			A|0.592;G|0.408	0.408	strong		0.592	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
SETD8	387893	hgsc.bcm.edu	37	12	123892235	123892235	+	Silent	SNP	G	G	A	rs61955128	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123892235G>A	ENST00000402868.3	+	8	1470	c.1044G>A	c.(1042-1044)ccG>ccA	p.P348P	SETD8_ENST00000330479.4_Silent_p.P348P			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	389	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AAGCCCACCCGTGGCTGAAGC	0.562													G|||	26	0.00519169	0.0083	0.0014	5008	,	,		14479	0.003		0.003	False		,,,				2504	0.0082				p.P348P		Atlas-SNP	.											SETD8,NS,neuroblastoma,0,1	SETD8	35	1	0			c.G1044A						scavenged	.						15.0	15.0	15.0					12																	123892235		2194	4279	6473	SO:0001819	synonymous_variant	387893	exon8			CCACCCGTGGCTG	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"""Chromatin-modifying enzymes / K-methyltransferases"""	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.1044G>A	12.37:g.123892235G>A		Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	75	3	0.04	NM_020382	A8K9D0|Q86W83|Q8TD09	Silent	SNP	ENST00000402868.3	37	CCDS9247.1																																																																																			G|0.999;A|0.001	0.001	strong		0.562	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	
OR52K1	390036	hgsc.bcm.edu	37	11	4510587	4510587	+	Missense_Mutation	SNP	C	C	T	rs331510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4510587C>T	ENST00000307632.3	+	1	479	c.457C>T	c.(457-459)Cgg>Tgg	p.R153W		NM_001005171.2	NP_001005171.2	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K, member 1	153			R -> W (in dbSNP:rs331510). {ECO:0000269|PubMed:14983052, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(18)|skin(2)|stomach(1)	32		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)		TGCTGTGGCCCGGGCTGTGAC	0.572													C|||	1105	0.220647	0.115	0.1441	5008	,	,		19921	0.2282		0.2416	False		,,,				2504	0.3885				p.R153W		Atlas-SNP	.											OR52K1,NS,carcinoma,-1,1	OR52K1	70	1	0			c.C457T						PASS	.	C	TRP/ARG	575,3827	255.5+/-260.7	32,511,1658	98.0	84.0	89.0		457	2.2	0.1	11	dbSNP_79	89	1976,6620	346.3+/-326.1	234,1508,2556	no	missense	OR52K1	NM_001005171.2	101	266,2019,4214	TT,TC,CC		22.9874,13.0622,19.6261	benign	153/315	4510587	2551,10447	2201	4298	6499	SO:0001583	missense	390036	exon1			GTGGCCCGGGCTG	AB065790	CCDS31352.1	11p15.4	2012-08-09			ENSG00000196778	ENSG00000196778		"""GPCR / Class A : Olfactory receptors"""	15222	protein-coding gene	gene with protein product							Standard	NM_001005171		Approved		uc001lza.2	Q8NGK4	OTTHUMG00000165705	ENST00000307632.3:c.457C>T	11.37:g.4510587C>T	ENSP00000302422:p.Arg153Trp	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	276	129	0.467391	NM_001005171	B9EH54|Q6IFK5	Missense_Mutation	SNP	ENST00000307632.3	37	CCDS31352.1	434	0.1987179487179487	55	0.11178861788617886	69	0.19060773480662985	144	0.2517482517482518	166	0.21899736147757257	C	5.539	0.284441	0.10513	0.130622	0.229874	ENSG00000196778	ENST00000307632	T	0.00030	8.9	4.07	2.18	0.27775	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000957	T	0.00012	0.0000	M	0.82056	2.57	0.80722	P	0.0	B	0.22276	0.067	B	0.21360	0.034	T	0.32561	-0.9902	9	0.72032	D	0.01	.	7.9006	0.29731	0.1611:0.7509:0.0:0.0881	rs331510;rs12420202;rs331510	153	Q8NGK4	O52K1_HUMAN	W	153	ENSP00000302422:R153W	ENSP00000302422:R153W	R	+	1	2	OR52K1	4467163	0.000000	0.05858	0.052000	0.19188	0.132000	0.20833	-2.560000	0.00921	0.661000	0.30985	-0.426000	0.05927	CGG	C|0.809;T|0.191	0.191	strong		0.572	OR52K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385846.1	NM_001005171	
RNF133	168433	hgsc.bcm.edu	37	7	122338071	122338071	+	Missense_Mutation	SNP	A	A	G	rs113127267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:122338071A>G	ENST00000340112.2	-	1	1139	c.902T>C	c.(901-903)cTt>cCt	p.L301P	CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000334010.7_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	301					protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						CAAAACTTTAAGAATATCACA	0.383													A|||	9	0.00179712	0.0	0.0014	5008	,	,		20051	0.0		0.006	False		,,,				2504	0.002				p.L301P	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.T902C						PASS	.	A	,,,PRO/LEU	4,4402	8.1+/-20.4	0,4,2199	80.0	81.0	80.0		,,,902	5.5	1.0	7	dbSNP_132	80	55,8543	33.8+/-87.4	0,55,4244	yes	intron,intron,intron,missense	CADPS2,RNF133	NM_001009571.3,NM_001167940.1,NM_017954.10,NM_139175.1	,,,98	0,59,6443	GG,GA,AA		0.6397,0.0908,0.4537	,,,probably-damaging	,,,301/377	122338071	59,12945	2203	4299	6502	SO:0001583	missense	168433	exon1			ACTTTAAGAATAT	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"""RING-type (C3HC4) zinc fingers"""	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.902T>C	7.37:g.122338071A>G	ENSP00000344489:p.Leu301Pro	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	134	69	0.514925	NM_139175	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	14.28	2.489317	0.44249	9.08E-4	0.006397	ENSG00000188050	ENST00000340112	T	0.68479	-0.33	5.53	5.53	0.82687	.	0.000000	0.56097	U	0.000021	T	0.65709	0.2717	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.72377	-0.4312	10	0.66056	D	0.02	.	10.0982	0.42488	0.8506:0.0:0.0:0.1494	.	301	Q8WVZ7	RN133_HUMAN	P	301	ENSP00000344489:L301P	ENSP00000344489:L301P	L	-	2	0	RNF133	122125307	1.000000	0.71417	0.995000	0.50966	0.527000	0.34593	4.633000	0.61318	2.099000	0.63709	0.402000	0.26972	CTT	A|0.997;G|0.003	0.003	strong		0.383	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175	
DENND1B	163486	hgsc.bcm.edu	37	1	197480986	197480986	+	IGR	SNP	C	C	T	rs10494755	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197480986C>T								CRB1 (33401 upstream) : DENND1B (40398 downstream)																							TCCATTTCACCTGAGTAAGGA	0.418													C|||	205	0.0409345	0.0386	0.0605	5008	,	,		15599	0.0		0.0944	False		,,,				2504	0.0174				p.G563S		Atlas-SNP	.											.	DENND1B	108	.	0			c.G1687A						PASS	.	C	SER/GLY	193,4213	120.8+/-158.4	10,173,2020	118.0	116.0	117.0		1687	5.7	0.9	1	dbSNP_119	117	835,7765	191.1+/-237.4	46,743,3511	yes	missense	DENND1B	NM_001195215.1	56	56,916,5531	TT,TC,CC		9.7093,4.3804,7.904	benign	563/776	197480986	1028,11978	2203	4300	6503	SO:0001628	intergenic_variant	163486	exon22			TTTCACCTGAGTA																													1.37:g.197480986C>T		Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	291	131	0.450172	NM_001195215		Missense_Mutation	SNP		37		105	0.04807692307692308	14	0.028455284552845527	21	0.058011049723756904	0	0.0	70	0.09234828496042216	C	32	5.141844	0.94560	0.043804	0.097093	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419	T	0.35605	1.3	5.7	5.7	0.88788	.	0.266469	0.29233	U	0.012756	T	0.01558	0.0050	M	0.76328	2.33	0.09310	P	1.0	P	0.40794	0.729	B	0.40009	0.316	T	0.01977	-1.1236	9	0.40728	T	0.16	.	19.844	0.96702	0.0:1.0:0.0:0.0	rs10494755;rs17563123;rs52813298;rs58844482;rs10494755	563	Q6P3S1-5	.	S	203;563;543	ENSP00000375839:G203S	ENSP00000375839:G203S	G	-	1	0	DENND1B	195747609	0.998000	0.40836	0.925000	0.36789	0.942000	0.58702	5.282000	0.65615	2.690000	0.91761	0.650000	0.86243	GGT	C|0.936;T|0.064	0.064	strong	0	0.418								
ENPP3	5169	hgsc.bcm.edu	37	6	131995313	131995313	+	Silent	SNP	A	A	G	rs9493048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:131995313A>G	ENST00000414305.1	+	9	982	c.654A>G	c.(652-654)ccA>ccG	p.P218P	ENPP3_ENST00000427148.2_Silent_p.P184P|ENPP3_ENST00000543135.1_Silent_p.P184P|ENPP3_ENST00000358229.5_Silent_p.P218P|ENPP3_ENST00000470930.1_3'UTR|ENPP3_ENST00000357639.3_Silent_p.P218P			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	218	Phosphodiesterase.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		GCTTGTATCCAGAGTCACATG	0.289													G|||	1539	0.307308	0.5401	0.2349	5008	,	,		19518	0.3254		0.1024	False		,,,				2504	0.2362				p.P218P		Atlas-SNP	.											.	ENPP3	117	.	0			c.A654G						PASS	.	G		2009,2397	612.6+/-392.0	454,1101,648	50.0	47.0	48.0		654	-3.8	0.9	6	dbSNP_119	48	941,7659	772.8+/-407.7	59,823,3418	no	coding-synonymous	ENPP3	NM_005021.3		513,1924,4066	GG,GA,AA		10.9419,45.5969,22.6818		218/876	131995313	2950,10056	2203	4300	6503	SO:0001819	synonymous_variant	5169	exon8			GTATCCAGAGTCA	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.654A>G	6.37:g.131995313A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_005021	Q5JTL3	Silent	SNP	ENST00000414305.1	37	CCDS5148.1																																																																																			A|0.740;G|0.260	0.260	strong		0.289	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		
KIF2C	11004	hgsc.bcm.edu	37	1	45226084	45226084	+	Silent	SNP	G	G	A	rs1140279	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45226084G>A	ENST00000372224.4	+	15	1613	c.1500G>A	c.(1498-1500)gcG>gcA	p.A500A	RP11-269F19.2_ENST00000440985.1_RNA|KIF2C_ENST00000372217.1_Silent_p.A446A|KIF2C_ENST00000372222.3_Silent_p.A387A|RP11-269F19.2_ENST00000428791.1_RNA|KIF2C_ENST00000372218.4_Silent_p.A459A	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	500	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					AGCGAGGCGCGGACACTTCCA	0.567													G|||	955	0.190695	0.1362	0.2464	5008	,	,		20856	0.2857		0.1382	False		,,,				2504	0.181				p.A500A		Atlas-SNP	.											KIF2C,NS,carcinoma,+2,1	KIF2C	68	1	0			c.G1500A						PASS	.	G		637,3769	273.4+/-271.3	49,539,1615	47.0	46.0	46.0		1500	-10.8	0.4	1	dbSNP_86	46	1450,7150	276.8+/-292.5	129,1192,2979	no	coding-synonymous	KIF2C	NM_006845.3		178,1731,4594	AA,AG,GG		16.8605,14.4576,16.0464		500/726	45226084	2087,10919	2203	4300	6503	SO:0001819	synonymous_variant	11004	exon15			AGGCGCGGACACT	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"""Kinesins"""	6393	protein-coding gene	gene with protein product		604538	"""kinesin-like 6 (mitotic centromere-associated kinesin)"""	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.1500G>A	1.37:g.45226084G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	94	62	0.659574	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Silent	SNP	ENST00000372224.4	37	CCDS512.1																																																																																			G|0.834;A|0.166	0.166	strong		0.567	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626566	140626566	+	Missense_Mutation	SNP	A	A	C	rs618506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140626566A>C	ENST00000231173.3	+	1	1420	c.1420A>C	c.(1420-1422)Agc>Cgc	p.S474R		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	474	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> R (in dbSNP:rs618506). {ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGCAGTGTCAGCGCCACAGA	0.652													A|||	1264	0.252396	0.0113	0.2911	5008	,	,		14763	0.5258		0.2316	False		,,,				2504	0.2904				p.S474R		Atlas-SNP	.											.	PCDHB15	138	.	0			c.A1420C						PASS	.	A	ARG/SER	185,4221	115.4+/-153.4	4,177,2022	70.0	78.0	76.0		1420	-1.6	0.5	5	dbSNP_83	76	1897,6683	329.7+/-318.9	213,1471,2606	no	missense	PCDHB15	NM_018935.2	110	217,1648,4628	CC,CA,AA		22.1096,4.1988,16.0327	benign	474/788	140626566	2082,10904	2203	4290	6493	SO:0001583	missense	56121	exon1			AGTGTCAGCGCCA	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1420A>C	5.37:g.140626566A>C	ENSP00000231173:p.Ser474Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	164	112	0.682927	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	558	0.2554945054945055	7	0.014227642276422764	85	0.23480662983425415	297	0.5192307692307693	169	0.22295514511873352	A	13.75	2.330539	0.41297	0.041988	0.221096	ENSG00000113248	ENST00000231173	T	0.01838	4.61	4.52	-1.64	0.08318	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.48260	1.515	0.80722	P	0.0	B	0.20550	0.046	B	0.28991	0.097	T	0.27571	-1.0070	8	0.46703	T	0.11	.	9.9134	0.41419	0.4169:0.5062:0.0769:0.0	rs618506;rs3776094;rs17844622;rs17857170;rs618506	474	Q9Y5E8	PCDBF_HUMAN	R	474	ENSP00000231173:S474R	ENSP00000231173:S474R	S	+	1	0	PCDHB15	140606750	0.000000	0.05858	0.524000	0.27887	0.883000	0.51084	-0.446000	0.06837	-0.070000	0.12908	0.397000	0.26171	AGC	A|0.815;C|0.185	0.185	strong		0.652	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
ERO1LB	56605	hgsc.bcm.edu	37	1	236413230	236413230	+	Missense_Mutation	SNP	T	T	A	rs2477599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:236413230T>A	ENST00000354619.5	-	5	587	c.386A>T	c.(385-387)gAt>gTt	p.D129V	ERO1LB_ENST00000327333.8_Missense_Mutation_p.D129V	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	129			D -> V (in dbSNP:rs2477599). {ECO:0000269|PubMed:15489334}.		4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	TTGCTCACAATCTTCTAATTC	0.279													T|||	1680	0.335463	0.1354	0.3646	5008	,	,		15154	0.1329		0.6014	False		,,,				2504	0.5204				p.D129V		Atlas-SNP	.											.	ERO1LB	48	.	0			c.A386T						PASS	.	T	VAL/ASP	858,3546	337.6+/-304.9	86,686,1430	146.0	130.0	136.0		386	4.7	0.8	1	dbSNP_100	136	5117,3469	632.1+/-398.6	1514,2089,690	yes	missense	ERO1LB	NM_019891.3	152	1600,2775,2120	AA,AT,TT		40.403,19.4823,45.9969	benign	129/468	236413230	5975,7015	2202	4293	6495	SO:0001583	missense	56605	exon5			TCACAATCTTCTA	AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.386A>T	1.37:g.236413230T>A	ENSP00000346635:p.Asp129Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	754	0.34523809523809523	75	0.1524390243902439	131	0.36187845303867405	75	0.13111888111888112	473	0.6240105540897097	T	16.85	3.236060	0.58886	0.194823	0.59597	ENSG00000086619	ENST00000354619;ENST00000327333;ENST00000366589	D;T;D	0.82255	-1.59;0.88;-1.59	5.85	4.72	0.59763	.	0.217492	0.49916	D	0.000135	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.99999810693	P;B	0.49185	0.92;0.1	P;B	0.45712	0.491;0.042	T	0.49844	-0.8896	9	0.56958	D	0.05	-17.6697	11.2036	0.48756	0.0:0.0:0.2933:0.7067	rs2477599;rs17853094;rs17854313;rs2477599	129;129	B4DF57;Q86YB8	.;ERO1B_HUMAN	V	129;129;10	ENSP00000346635:D129V;ENSP00000377574:D129V;ENSP00000355548:D10V	ENSP00000377574:D129V	D	-	2	0	ERO1LB	234479853	1.000000	0.71417	0.809000	0.32408	0.980000	0.70556	4.282000	0.58971	1.025000	0.39708	-0.475000	0.04921	GAT	T|0.570;A|0.430	0.430	strong		0.279	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891	
NRXN2	9379	hgsc.bcm.edu	37	11	64457892	64457892	+	Missense_Mutation	SNP	G	G	A	rs141807338		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64457892G>A	ENST00000377551.1	-	4	1046	c.835C>T	c.(835-837)Cac>Tac	p.H279Y	NRXN2_ENST00000377559.3_Intron|NRXN2_ENST00000265459.6_Missense_Mutation_p.H279Y|NRXN2_ENST00000409571.1_Missense_Mutation_p.H279Y			Q9P2S2	NRX2A_HUMAN	neurexin 2	279					adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GTTGGCTGGTGCACATCGCCG	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		15787	0.0		0.001	False		,,,				2504	0.0				p.H279Y		Atlas-SNP	.											.	NRXN2	247	.	0			c.C835T						PASS	.	G	TYR/HIS,	0,4402		0,0,2201	58.0	53.0	54.0		835,	4.5	1.0	11	dbSNP_134	54	2,8592	2.2+/-6.3	0,2,4295	no	missense,intron	NRXN2	NM_015080.3,NM_138732.2	83,	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	benign,	279/1713,	64457892	2,12994	2201	4297	6498	SO:0001583	missense	9379	exon5			GCTGGTGCACATC		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.835C>T	11.37:g.64457892G>A	ENSP00000366774:p.His279Tyr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	37	CCDS8077.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	3.483|3.483	-0.105541|-0.105541	0.06967|0.06967	0.0|0.0	2.33E-4|2.33E-4	ENSG00000110076|ENSG00000110076	ENST00000437746|ENST00000377551;ENST00000265459;ENST00000409571;ENST00000442300	.|T;T;T;T	.|0.59772	.|0.24;0.24;0.32;1.31	4.47|4.47	4.47|4.47	0.54385|0.54385	.|.	.|.	.|.	.|.	.|.	T|T	0.31040|0.31040	0.0784|0.0784	N|N	0.08118|0.08118	0|0	0.35143|0.35143	D|D	0.769073|0.769073	.|P	.|0.43909	.|0.821	.|B	.|0.38225	.|0.268	T|T	0.43343|0.43343	-0.9397|-0.9397	5|9	.|0.02654	.|T	.|1	.|.	12.9884|12.9884	0.58604|0.58604	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|279	.|Q9P2S2	.|NRX2A_HUMAN	V|Y	68|279;279;279;50	.|ENSP00000366774:H279Y;ENSP00000265459:H279Y;ENSP00000386416:H279Y;ENSP00000388971:H50Y	.|ENSP00000265459:H279Y	A|H	-|-	2|1	0|0	NRXN2|NRXN2	64214468|64214468	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	3.226000|3.226000	0.51254|0.51254	2.216000|2.216000	0.71823|0.71823	0.442000|0.442000	0.29010|0.29010	GCA|CAC	G|1.000;A|0.000	0.000	strong		0.627	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
PERP	64065	hgsc.bcm.edu	37	6	138413269	138413269	+	Silent	SNP	A	A	G	rs648396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138413269A>G	ENST00000421351.3	-	3	662	c.492T>C	c.(490-492)atT>atC	p.I164I		NM_022121.4	NP_071404.2	Q96FX8	PERP_HUMAN	PERP, TP53 apoptosis effector	164					activation of cysteine-type endopeptidase activity (GO:0097202)|amelogenesis (GO:0097186)|desmosome organization (GO:0002934)|heterotypic cell-cell adhesion (GO:0034113)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of proteolysis (GO:0045862)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(1)|lung(1)|prostate(1)	5	Breast(32;0.0799)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000878)|OV - Ovarian serous cystadenocarcinoma(155;0.000997)		AGGCACAGCCAATCAGGATAA	0.522													G|||	3166	0.632188	0.5545	0.5288	5008	,	,		18524	0.7232		0.5775	False		,,,				2504	0.773				p.I164I		Atlas-SNP	.											.	PERP	15	.	0			c.T492C						PASS	.	G		2342,2064	569.5+/-382.6	628,1086,489	83.0	78.0	80.0		492	-10.2	0.1	6	dbSNP_83	80	4752,3848	541.9+/-384.1	1313,2126,861	no	coding-synonymous	PERP	NM_022121.4		1941,3212,1350	GG,GA,AA		44.7442,46.8452,45.4559		164/194	138413269	7094,5912	2203	4300	6503	SO:0001819	synonymous_variant	64065	exon3			ACAGCCAATCAGG	AF317550	CCDS5188.1	6q24	2014-04-29			ENSG00000112378	ENSG00000112378			17637	protein-coding gene	gene with protein product	"""keratinocyte associated protein 1"""	609301				11062687	Standard	NM_022121		Approved	PIGPC1, dJ496H19.1, KCP1, THW, KRTCAP1	uc003qht.2	Q96FX8	OTTHUMG00000015668	ENST00000421351.3:c.492T>C	6.37:g.138413269A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	87	58	0.666667	NM_022121	B2RB73|E1P590|Q8IWS3|Q8N1J6|Q8NC16|Q9H1C5|Q9H230	Silent	SNP	ENST00000421351.3	37	CCDS5188.1																																																																																			A|0.435;G|0.565	0.565	strong		0.522	PERP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042423.2	NM_022121	
SPINK5	11005	hgsc.bcm.edu	37	5	147480955	147480955	+	Missense_Mutation	SNP	A	A	G	rs2303067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147480955A>G	ENST00000256084.7	+	14	1300	c.1258A>G	c.(1258-1260)Aaa>Gaa	p.K420E	SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000398454.1_Missense_Mutation_p.K420E|SPINK5_ENST00000359874.3_Missense_Mutation_p.K420E	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	420	Kazal-like 6. {ECO:0000255|PROSITE- ProRule:PRU00798}.		K -> E (in dbSNP:rs2303067). {ECO:0000269|PubMed:10419450, ECO:0000269|PubMed:11544479, ECO:0000269|PubMed:16374478}.		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGGAAGGTAAATCAAGAAA	0.383													G|||	2169	0.433107	0.1989	0.6167	5008	,	,		17991	0.4851		0.4871	False		,,,				2504	0.5102				p.K420E		Atlas-SNP	.											.	SPINK5	245	.	0			c.A1258G	GRCh37	CM013815	SPINK5	M	rs2303067	PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS	946,2756		121,704,1026	124.0	110.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1258,1258,1258	2.8	0.5	5	dbSNP_100	114	4204,3986		1071,2062,962	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	56,56,56	1192,2766,1988	GG,GA,AA		48.6691,25.5538,43.3064	benign,benign,benign	420/1095,420/917,420/1065	147480955	5150,6742	1851	4095	5946	SO:0001583	missense	11005	exon14			GAAGGTAAATCAA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1258A>G	5.37:g.147480955A>G	ENSP00000256084:p.Lys420Glu	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	270	269	0.996296	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	936	0.42857142857142855	111	0.22560975609756098	213	0.5883977900552486	263	0.4597902097902098	349	0.4604221635883905	G	0.156	-1.086008	0.01873	0.255538	0.513309	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.03801	3.8;3.8;3.8;3.8	3.72	2.84	0.33178	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	1.088120	0.07087	N	0.838072	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	5.000000000032756E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.002	T	0.41161	-0.9524	9	0.02654	T	1	-6.8235	4.7186	0.12906	0.1116:0.0:0.6761:0.2123	rs2303067;rs17775367;rs17860505;rs52832839;rs56830970;rs2303067	420;420;420	Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;ISK5_HUMAN;.	E	420;420;401;420	ENSP00000381472:K420E;ENSP00000352936:K420E;ENSP00000421519:K401E;ENSP00000256084:K420E	ENSP00000256084:K420E	K	+	1	0	SPINK5	147461148	0.127000	0.22367	0.464000	0.27143	0.640000	0.38277	0.153000	0.16323	0.538000	0.28769	-0.128000	0.14901	AAA	A|0.569;G|0.431	0.431	strong		0.383	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
ZNF554	115196	hgsc.bcm.edu	37	19	2833802	2833802	+	Missense_Mutation	SNP	A	A	G	rs867168	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:2833802A>G	ENST00000317243.5	+	5	767	c.569A>G	c.(568-570)gAg>gGg	p.E190G	ZNF554_ENST00000591265.1_3'UTR	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	190			E -> G (in dbSNP:rs867168).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGCAGTTAGAGGACAGCCAT	0.502													A|||	1150	0.229633	0.0204	0.4164	5008	,	,		18096	0.4425		0.2127	False		,,,				2504	0.1779				p.E190G		Atlas-SNP	.											.	ZNF554	47	.	0			c.A569G						PASS	.	A	GLY/GLU	171,3611		0,171,1720	85.0	88.0	87.0		569	1.4	0.0	19	dbSNP_86	87	1451,6789		119,1213,2788	yes	missense	ZNF554	NM_001102651.1	98	119,1384,4508	GG,GA,AA		17.6092,4.5214,13.4919	possibly-damaging	190/539	2833802	1622,10400	1891	4120	6011	SO:0001583	missense	115196	exon5			AGTTAGAGGACAG	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.569A>G	19.37:g.2833802A>G	ENSP00000321132:p.Glu190Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	126	74	0.587302	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	572	0.2619047619047619	12	0.024390243902439025	141	0.38950276243093923	249	0.4353146853146853	170	0.22427440633245382	A	8.935	0.964366	0.18583	0.045214	0.176092	ENSG00000172006	ENST00000317243	T	0.08807	3.05	2.57	1.39	0.22231	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.48293	-0.9048	8	0.23302	T	0.38	.	1.8775	0.03221	0.5646:0.0:0.1624:0.273	rs867168;rs17763848;rs52831157;rs58761543;rs867168	190	Q86TJ5	ZN554_HUMAN	G	190	ENSP00000321132:E190G	ENSP00000321132:E190G	E	+	2	0	ZNF554	2784802	.	.	0.025000	0.17156	0.028000	0.11728	.	.	1.200000	0.43188	0.448000	0.29417	GAG	A|0.773;G|0.227	0.227	strong		0.502	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
ADCY4	196883	hgsc.bcm.edu	37	14	24803710	24803710	+	Missense_Mutation	SNP	G	G	A	rs77202343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24803710G>A	ENST00000310677.4	-	2	262	c.149C>T	c.(148-150)gCc>gTc	p.A50V	ADCY4_ENST00000558563.1_5'UTR|ADCY4_ENST00000396747.3_5'UTR|ADCY4_ENST00000418030.2_Missense_Mutation_p.A50V|RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000554068.2_Missense_Mutation_p.A50V	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	50					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		CCTGCCGCTGGCCCAGGCCAC	0.637													G|||	42	0.00838658	0.0023	0.0101	5008	,	,		11094	0.0		0.0229	False		,,,				2504	0.0092				p.A50V		Atlas-SNP	.											.	ADCY4	86	.	0			c.C149T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	21,4081		0,21,2030	5.0	5.0	5.0		149,149,149	5.4	1.0	14	dbSNP_131	5	159,7961		2,155,3903	no	missense,missense,missense	ADCY4	NM_001198568.1,NM_001198592.1,NM_139247.3	64,64,64	2,176,5933	AA,AG,GG		1.9581,0.5119,1.4728	benign,benign,benign	50/1078,50/1078,50/1078	24803710	180,12042	2051	4060	6111	SO:0001583	missense	196883	exon2			CCGCTGGCCCAGG	AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"""Adenylate cyclases"""	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.149C>T	14.37:g.24803710G>A	ENSP00000312126:p.Ala50Val	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	37	CCDS9627.1	26	0.011904761904761904	3	0.006097560975609756	3	0.008287292817679558	0	0.0	20	0.026385224274406333	G	35	5.421899	0.96111	0.005119	0.019581	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030	T;T;T	0.76316	-1.01;-1.01;-1.01	5.45	5.45	0.79879	.	0.000000	0.46145	D	0.000314	T	0.66066	0.2752	L	0.50333	1.59	0.80722	D	1	D;D	0.63046	0.992;0.985	D;P	0.66602	0.945;0.771	T	0.71174	-0.4670	10	0.15499	T	0.54	.	16.8265	0.85933	0.0:0.0:1.0:0.0	.	50;50	G3V258;Q8NFM4	.;ADCY4_HUMAN	V	50	ENSP00000312126:A50V;ENSP00000452250:A50V;ENSP00000393177:A50V	ENSP00000312126:A50V	A	-	2	0	ADCY4	23873550	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.145000	0.71769	2.838000	0.97847	0.655000	0.94253	GCC	G|0.987;A|0.013	0.013	strong		0.637	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4		
MFSD12	126321	hgsc.bcm.edu	37	19	3548231	3548231	+	Missense_Mutation	SNP	A	A	G	rs2240751	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:3548231A>G	ENST00000355415.2	-	3	713	c.544T>C	c.(544-546)Tac>Cac	p.Y182H	MFSD12_ENST00000389395.3_Missense_Mutation_p.Y182H|MFSD12_ENST00000591878.1_Intron|AC005786.7_ENST00000589360.1_RNA|MFSD12_ENST00000398558.4_Missense_Mutation_p.Y182H	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	182			Y -> H (in dbSNP:rs2240751).		transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						GCGGCGCCGTAGACGGTGATG	0.682													A|||	406	0.0810703	0.0015	0.1671	5008	,	,		14841	0.2688		0.0099	False		,,,				2504	0.0072				p.Y182H		Atlas-SNP	.											MFSD12,NS,carcinoma,0,2	MFSD12	22	2	0			c.T544C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR	13,4011		0,13,1999	10.0	16.0	14.0		544,544,544	4.4	0.5	19	dbSNP_98	14	51,8171		0,51,4060	yes	missense,missense,missense	C19orf28	NM_001042680.1,NM_021731.2,NM_174983.3	83,83,83	0,64,6059	GG,GA,AA		0.6203,0.3231,0.5226	probably-damaging,probably-damaging,probably-damaging	182/474,182/539,182/481	3548231	64,12182	2012	4111	6123	SO:0001583	missense	126321	exon3			CGCCGTAGACGGT	AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 28"""	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.544T>C	19.37:g.3548231A>G	ENSP00000347583:p.Tyr182His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_001042680	A8MXP7|D6W615|E9PAJ8|Q8N459	Missense_Mutation	SNP	ENST00000355415.2	37	CCDS42465.1	227	0.10393772893772894	1	0.0020325203252032522	33	0.09116022099447514	186	0.32517482517482516	7	0.009234828496042216	A	19.90	3.912662	0.72983	0.003231	0.006203	ENSG00000161091	ENST00000389395;ENST00000398558;ENST00000355415	T;T;T	0.81163	-1.46;-1.46;-1.46	4.45	4.45	0.53987	Major facilitator superfamily domain, general substrate transporter (1);	0.061993	0.64402	D	0.000003	T	0.00012	0.0000	M	0.85197	2.74	0.09310	P	0.99999878827	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.997	T	0.00008	-1.2484	9	0.72032	D	0.01	-16.0667	11.4692	0.50257	1.0:0.0:0.0:0.0	rs2240751;rs2240751	182;173;182	Q6NUT3;Q6NUT3-2;A8MXP7	CS028_HUMAN;.;.	H	182	ENSP00000374046:Y182H;ENSP00000381566:Y182H;ENSP00000347583:Y182H	ENSP00000347583:Y182H	Y	-	1	0	C19orf28	3499231	1.000000	0.71417	0.513000	0.27749	0.554000	0.35429	8.153000	0.89640	1.647000	0.50633	0.454000	0.30748	TAC	A|0.872;G|0.128	0.128	strong		0.682	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983	
DNAH6	1768	hgsc.bcm.edu	37	2	84848596	84848596	+	Missense_Mutation	SNP	G	G	A	rs61733547	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:84848596G>A	ENST00000237449.6	+	25	4000	c.3992G>A	c.(3991-3993)cGt>cAt	p.R1331H	DNAH6_ENST00000389394.3_Missense_Mutation_p.R1331H|DNAH6_ENST00000398278.2_Missense_Mutation_p.R1331H			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1331	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ATGTGGTGCCGTGATTTGACT	0.343													G|||	90	0.0179712	0.0008	0.0288	5008	,	,		20917	0.0		0.0557	False		,,,				2504	0.0133				p.R1331H		Atlas-SNP	.											.	DNAH6	194	.	0			c.G3992A						PASS	.	G	HIS/ARG	15,1369		0,15,677	109.0	94.0	98.0		3992	4.1	1.0	2	dbSNP_129	98	181,3001		4,173,1414	yes	missense	DNAH6	NM_001370.1	29	4,188,2091	AA,AG,GG		5.6882,1.0838,4.2926	possibly-damaging	1331/4159	84848596	196,4370	692	1591	2283	SO:0001583	missense	1768	exon26			GGTGCCGTGATTT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3992G>A	2.37:g.84848596G>A	ENSP00000237449:p.Arg1331His	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	170	80	0.470588	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	58	0.026556776556776556	0	0.0	14	0.03867403314917127	0	0.0	44	0.05804749340369393	G	18.27	3.588064	0.66105	0.010838	0.056882	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.58797	0.31;0.31;0.31	5.02	4.13	0.48395	.	.	.	.	.	T	0.08802	0.0218	L	0.58354	1.805	0.29575	N	0.84958	P	0.41546	0.754	B	0.30179	0.112	T	0.27606	-1.0069	9	0.45353	T	0.12	.	11.769	0.51947	0.0878:0.0:0.9122:0.0	rs61733547	1331	Q9C0G6	DYH6_HUMAN	H	1331	ENSP00000374045:R1331H;ENSP00000381326:R1331H;ENSP00000237449:R1331H	ENSP00000237449:R1331H	R	+	2	0	DNAH6	84702107	1.000000	0.71417	0.956000	0.39512	0.867000	0.49689	4.676000	0.61627	2.326000	0.78906	0.563000	0.77884	CGT	G|0.971;A|0.029	0.029	strong		0.343	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
DOCK6	57572	hgsc.bcm.edu	37	19	11327626	11327626	+	Silent	SNP	A	A	G	rs4804152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11327626A>G	ENST00000294618.7	-	30	3869	c.3858T>C	c.(3856-3858)gaT>gaC	p.D1286D	CTC-510F12.2_ENST00000588634.1_RNA|DOCK6_ENST00000319867.7_Silent_p.D625D	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1286					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GGTACAGCAAATCCAACAGAC	0.607													G|||	2902	0.579473	0.5401	0.5634	5008	,	,		18186	0.5784		0.6779	False		,,,				2504	0.544				p.D1286D		Atlas-SNP	.											.	DOCK6	104	.	0			c.T3858C						PASS	.	G		2496,1728		761,974,377	63.0	64.0	63.0		3858	5.1	1.0	19	dbSNP_111	63	5910,2540		2061,1788,376	no	coding-synonymous	DOCK6	NM_020812.2		2822,2762,753	GG,GA,AA		30.0592,40.9091,33.6752		1286/2048	11327626	8406,4268	2112	4225	6337	SO:0001819	synonymous_variant	57572	exon30			CAGCAAATCCAAC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.3858T>C	19.37:g.11327626A>G		Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	252	251	0.996032	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			A|0.394;G|0.606	0.606	strong		0.607	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
TUBGCP5	114791	hgsc.bcm.edu	37	15	22840279	22840279	+	Silent	SNP	G	G	T	rs61744212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:22840279G>T	ENST00000283645.4	+	4	475	c.345G>T	c.(343-345)ctG>ctT	p.L115L	TUBGCP5_ENST00000453949.2_Silent_p.L115L	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	115					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CACTTCTTCTGTGTCTGTCAG	0.358													G|||	679	0.135583	0.0363	0.0389	5008	,	,		17876	0.4504		0.0885	False		,,,				2504	0.0624				p.L115L		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.G345T						PASS	.	G	,	208,4198		4,200,1999	125.0	119.0	121.0		345,345	0.6	1.0	15	dbSNP_129	121	846,7754		47,752,3501	no	coding-synonymous,coding-synonymous	TUBGCP5	NM_001102610.1,NM_052903.4	,	51,952,5500	TT,TG,GG		9.8372,4.7208,8.104	,	115/1025,115/1025	22840279	1054,11952	2203	4300	6503	SO:0001819	synonymous_variant	114791	exon4			TCTTCTGTGTCTG	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"""gamma-tubulin complex component GCP5"""	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.345G>T	15.37:g.22840279G>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	172	89	0.517442	NM_052903	E9PB12|Q6IQ52|Q96PY8	Silent	SNP	ENST00000283645.4	37	CCDS10008.1																																																																																			A|0.001;G|0.893;T|0.106	0.106	strong		0.358	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903	
ULK3	25989	hgsc.bcm.edu	37	15	75130093	75130093	+	Splice_Site	SNP	T	T	C	rs12898397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75130093T>C	ENST00000440863.2	-	14	1425	c.1334A>G	c.(1333-1335)aAg>aGg	p.K445R	ULK3_ENST00000569437.1_Intron|ULK3_ENST00000568667.1_Splice_Site_p.K456R	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	445			K -> R (in dbSNP:rs12898397).		autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)	2						TGTGCCCACCTTGACCTGCTC	0.612													T|||	1940	0.38738	0.0915	0.5432	5008	,	,		16963	0.3403		0.5795	False		,,,				2504	0.5276				p.K445R		Atlas-SNP	.											.	ULK3	30	.	0			c.A1334G						PASS	.	T	ARG/LYS	709,3487		77,555,1466	41.0	50.0	47.0		1334	5.2	1.0	15	dbSNP_121	47	4977,3427		1499,1979,724	yes	missense-near-splice	ULK3	NM_001099436.1	26	1576,2534,2190	CC,CT,TT		40.7782,16.897,45.127	possibly-damaging	445/473	75130093	5686,6914	2098	4202	6300	SO:0001630	splice_region_variant	25989	exon14			CCCACCTTGACCT	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"""unc-51-like kinase 3 (C. elegans)"""				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.1335+1A>G	15.37:g.75130093T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Missense_Mutation	SNP	ENST00000440863.2	37	CCDS45305.1	880	0.40293040293040294	47	0.09552845528455285	197	0.5441988950276243	199	0.3479020979020979	437	0.5765171503957783	T	15.80	2.939286	0.52972	0.16897	0.592218	ENSG00000140474	ENST00000440863;ENST00000418051	T	0.30981	1.51	5.23	5.23	0.72850	MIT (1);	.	.	.	.	T	0.00012	0.0000	L	0.57536	1.79	0.22693	P	0.99884618	D;B	0.69078	0.997;0.294	D;B	0.75020	0.985;0.057	T	0.49457	-0.8938	8	0.27785	T	0.31	-16.8689	12.5013	0.55957	0.0:0.0:0.0:1.0	rs12898397	456;445	B4DFT0;Q6PHR2	.;ULK3_HUMAN	R	445;456	ENSP00000400312:K445R	ENSP00000393658:K456R	K	-	2	0	ULK3	72917146	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	5.637000	0.67854	1.978000	0.57642	0.459000	0.35465	AAG	T|0.596;C|0.404	0.404	strong		0.612	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518	Missense_Mutation
NLRP1	22861	hgsc.bcm.edu	37	17	5442790	5442790	+	Missense_Mutation	SNP	C	C	T	rs61754791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5442790C>T	ENST00000572272.1	-	7	2814	c.2815G>A	c.(2815-2817)Gtg>Atg	p.V939M	NLRP1_ENST00000577119.1_Missense_Mutation_p.V939M|NLRP1_ENST00000354411.3_Missense_Mutation_p.V939M|NLRP1_ENST00000345221.3_Missense_Mutation_p.V939M|NLRP1_ENST00000269280.4_Missense_Mutation_p.V939M|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000262467.5_Missense_Mutation_p.V939M			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	939					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				AGCAGTCGCACGCCAACGTCA	0.622													C|||	58	0.0115815	0.0318	0.0058	5008	,	,		18777	0.0		0.0109	False		,,,				2504	0.001				p.V939M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G2815A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	105,4301	82.9+/-121.4	3,99,2101	79.0	62.0	67.0		2815,2815,2815,2815,2815	0.5	0.0	17	dbSNP_129	67	134,8466	67.7+/-130.1	2,130,4168	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	5,229,6269	TT,TC,CC		1.5581,2.3831,1.8376	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	939/1376,939/1430,939/1474,939/1444,939/1400	5442790	239,12767	2203	4300	6503	SO:0001583	missense	22861	exon7			GTCGCACGCCAAC	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.2815G>A	17.37:g.5442790C>T	ENSP00000460475:p.Val939Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	26	0.011904761904761904	14	0.028455284552845527	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.12	2.440438	0.43326	0.023831	0.015581	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	3.7	0.477	0.16784	.	0.224064	0.22878	N	0.054551	T	0.10680	0.0261	M	0.74546	2.27	0.09310	N	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.997;1.0	D;D;D;D;P;D	0.91635	0.912;0.999;0.997;0.982;0.896;0.982	T	0.03641	-1.1017	10	0.87932	D	0	.	2.8517	0.05560	0.2212:0.5366:0.0:0.2423	rs61754791	205;939;939;939;939;939	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	939;939;939;939;939;205	ENSP00000442029:V939M;ENSP00000262467:V939M;ENSP00000269280:V939M;ENSP00000346390:V939M;ENSP00000324366:V939M	ENSP00000262467:V939M	V	-	1	0	NLRP1	5383514	0.000000	0.05858	0.004000	0.12327	0.009000	0.06853	0.004000	0.13106	0.155000	0.19261	0.650000	0.86243	GTG	A|0.000;C|0.986;T|0.014	0.014	strong		0.622	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
BMP8B	656	hgsc.bcm.edu	37	1	40229393	40229393	+	Silent	SNP	G	G	A	rs77290565	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:40229393G>A	ENST00000372827.3	-	5	1314	c.939C>T	c.(937-939)ctC>ctT	p.L313L	PPIE_ENST00000372830.1_3'UTR|PPIE_ENST00000356511.2_Silent_p.P290P|BMP8B_ENST00000397360.2_Silent_p.L338L	NM_001720.3	NP_001711.2	P34820	BMP8B_HUMAN	bone morphogenetic protein 8b	313					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|growth (GO:0040007)|ossification (GO:0001503)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)				endometrium(1)|liver(1)|ovary(1)|urinary_tract(1)	4	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CCAGCCAGCCGAGGTCCTGGA	0.547																																					p.L313L		Atlas-SNP	.											PPIE_ENST00000356511,brain,glioma,+1,1	BMP8B	20	1	0			c.C939T						scavenged	.						66.0	63.0	64.0					1																	40229393		2202	4299	6501	SO:0001819	synonymous_variant	656	exon5			CCAGCCGAGGTCC	BC023526	CCDS444.1	1p35-p32	2014-01-30	2008-05-22	2003-10-22	ENSG00000116985	ENSG00000116985		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1075	protein-coding gene	gene with protein product	"""osteogenic protein 2"""	602284	"""bone morphogenetic protein 8 (osteogenic protein 2)"""	BMP8		1460021, 9070944	Standard	NM_001720		Approved	OP-2	uc001cdz.1	P34820	OTTHUMG00000009247	ENST00000372827.3:c.939C>T	1.37:g.40229393G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	195	23	0.117949	NM_001720	E7EMY8|Q32NE5|Q53ZM7|Q9NUF0	Silent	SNP	ENST00000372827.3	37	CCDS444.1																																																																																			G|0.968;A|0.032	0.032	strong		0.547	BMP8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025641.1	NM_001720	
NAV2	89797	hgsc.bcm.edu	37	11	20117232	20117232	+	Silent	SNP	T	T	C	rs2289566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:20117232T>C	ENST00000396087.3	+	33	6207	c.6108T>C	c.(6106-6108)caT>caC	p.H2036H	NAV2_ENST00000533917.1_Silent_p.H1041H|NAV2_ENST00000360655.4_Silent_p.H1913H|NAV2_ENST00000540292.1_Silent_p.H1967H|NAV2_ENST00000349880.4_Silent_p.H1977H|NAV2_ENST00000396085.1_Silent_p.H1980H|NAV2_ENST00000527559.2_Silent_p.H1965H|NAV2_ENST00000311043.8_Silent_p.H1041H	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2036					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CCAGACCACATCTCTTTCTTA	0.458													C|||	2271	0.453474	0.2239	0.438	5008	,	,		20775	0.8899		0.3012	False		,,,				2504	0.4816				p.H2036H		Atlas-SNP	.											.	NAV2	255	.	0			c.T6108C						PASS	.	C	,,,	973,3433	732.5+/-410.4	107,759,1337	243.0	219.0	227.0		5739,3123,5931,5940	2.7	0.9	11	dbSNP_100	227	2371,6229	701.9+/-405.2	335,1701,2264	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	442,2460,3601	CC,CT,TT		27.5698,22.0835,25.7112	,,,	1913/2366,1041/1494,1977/2430,1980/2433	20117232	3344,9662	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon32			ACCACATCTCTTT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.6108T>C	11.37:g.20117232T>C		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	278	124	0.446043	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			T|0.656;C|0.344	0.344	strong		0.458	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
MGAT5B	146664	hgsc.bcm.edu	37	17	74942478	74942478	+	Silent	SNP	C	C	T	rs8067984	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74942478C>T	ENST00000569840.2	+	16	2443	c.1869C>T	c.(1867-1869)taC>taT	p.Y623Y	MGAT5B_ENST00000301618.4_Silent_p.Y621Y|MGAT5B_ENST00000428789.2_Silent_p.Y632Y	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	623					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ACCTACCCTACGAGTACACCT	0.657													C|||	1784	0.35623	0.2451	0.2651	5008	,	,		16241	0.5357		0.4026	False		,,,				2504	0.3384				p.Y632Y		Atlas-SNP	.											.	MGAT5B	98	.	0			c.C1896T						PASS	.	C	,,	1210,3196	419.6+/-338.7	176,858,1169	88.0	62.0	70.0		1869,1863,1896	-3.6	1.0	17	dbSNP_116	70	3312,5288	493.4+/-373.6	641,2030,1629	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	817,2888,2798	TT,TC,CC		38.5116,27.4626,34.7686	,,	623/793,621/791,632/802	74942478	4522,8484	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon14			ACCCTACGAGTAC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1869C>T	17.37:g.74942478C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			C|0.639;T|0.361	0.361	strong		0.657	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
APOB	338	hgsc.bcm.edu	37	2	21232195	21232195	+	Silent	SNP	G	G	A	rs693	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:21232195G>A	ENST00000233242.1	-	26	7672	c.7545C>T	c.(7543-7545)acC>acT	p.T2515T		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2515					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATCTTCTAGGGTCTCTCGGA	0.438													G|||	1257	0.250998	0.2095	0.3775	5008	,	,		21485	0.0615		0.4423	False		,,,				2504	0.2157				p.T2515T		Atlas-SNP	.											.	APOB	761	.	0			c.C7545T						PASS	.	G		1082,3324	391.4+/-328.1	140,802,1261	128.0	107.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7545	3.2	0.9	2	dbSNP_36	114	4301,4299	577.5+/-390.6	1092,2117,1091	no	coding-synonymous	APOB	NM_000384.2		1232,2919,2352	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	49.9884,24.5574,41.3886		2515/4564	21232195	5383,7623	2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			TTCTAGGGTCTCT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.7545C>T	2.37:g.21232195G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			G|0.665;N|0.000	.	strong		0.438	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
SENP6	26054	hgsc.bcm.edu	37	6	76344431	76344431	+	Missense_Mutation	SNP	C	C	T	rs17414086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:76344431C>T	ENST00000447266.2	+	5	840	c.362C>T	c.(361-363)aCg>aTg	p.T121M	SENP6_ENST00000370014.3_Missense_Mutation_p.T121M|SENP6_ENST00000327284.8_Missense_Mutation_p.T121M|SENP6_ENST00000370010.2_Missense_Mutation_p.T121M	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	121			T -> M (in dbSNP:rs17414086). {ECO:0000269|PubMed:10799485, ECO:0000269|PubMed:9872452}.		protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				AGTGAAAATACGCAAAATACG	0.318													C|||	779	0.155551	0.0121	0.1931	5008	,	,		17545	0.0595		0.327	False		,,,				2504	0.2454				p.T121M		Atlas-SNP	.											.	SENP6	189	.	0			c.C362T						PASS	.	C	MET/THR,MET/THR	224,3478		13,198,1640	96.0	85.0	89.0		362,362	3.7	1.0	6	dbSNP_123	89	2915,5255		523,1869,1693	yes	missense,missense	SENP6	NM_001100409.1,NM_015571.2	81,81	536,2067,3333	TT,TC,CC		35.6793,6.0508,26.4404	possibly-damaging,possibly-damaging	121/1106,121/1113	76344431	3139,8733	1851	4085	5936	SO:0001583	missense	26054	exon5			AAAATACGCAAAA		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.362C>T	6.37:g.76344431C>T	ENSP00000402527:p.Thr121Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_001100409	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	37	CCDS47454.1	362	0.16575091575091574	5	0.01016260162601626	80	0.22099447513812154	29	0.050699300699300696	248	0.32717678100263853	C	9.316	1.056883	0.19907	0.060508	0.356793	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000538088;ENST00000327284;ENST00000447266;ENST00000483859;ENST00000424947	T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83	5.5	3.73	0.42828	.	0.529195	0.21759	N	0.069557	T	0.28101	0.0693	L	0.36672	1.1	0.09310	P	0.99999999882185	D;P;D	0.52996	0.957;0.927;0.957	B;B;P	0.47981	0.439;0.255;0.563	T	0.10613	-1.0622	9	0.52906	T	0.07	-7.6876	10.3397	0.43870	0.0:0.7846:0.0:0.2154	rs17414086;rs52797714;rs17414086	121;121;121	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	M	121;121;121;121;121;12;11	ENSP00000359027:T121M;ENSP00000359031:T121M;ENSP00000321820:T121M;ENSP00000402527:T121M;ENSP00000426480:T12M;ENSP00000391426:T11M	ENSP00000321820:T121M	T	+	2	0	SENP6	76401151	0.864000	0.29904	0.993000	0.49108	0.048000	0.14542	0.928000	0.28831	0.710000	0.31997	-0.203000	0.12734	ACG	C|0.803;N|0.000	.	strong		0.318	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
SPHKAP	80309	hgsc.bcm.edu	37	2	228883029	228883029	+	Missense_Mutation	SNP	A	A	C	rs3811515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228883029A>C	ENST00000392056.3	-	7	2587	c.2541T>G	c.(2539-2541)caT>caG	p.H847Q	SPHKAP_ENST00000344657.5_Missense_Mutation_p.H847Q	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	847			H -> Q (in dbSNP:rs3811515). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.H847Q(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCTCACTGTGATGAGGGCTTT	0.493													A|||	1115	0.222644	0.0318	0.2464	5008	,	,		21416	0.2242		0.2406	False		,,,				2504	0.4438				p.H847Q		Atlas-SNP	.											SPHKAP,NS,carcinoma,0,1	SPHKAP	750	1	1	Substitution - Missense(1)	stomach(1)	c.T2541G						PASS	.	A	GLN/HIS,GLN/HIS	282,4124	156.3+/-189.4	13,256,1934	745.0	703.0	717.0		2541,2541	1.0	0.0	2	dbSNP_107	717	2167,6433	371.6+/-336.3	287,1593,2420	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	24,24	300,1849,4354	CC,CA,AA		25.1977,6.4004,18.8298	possibly-damaging,possibly-damaging	847/1701,847/1672	228883029	2449,10557	2203	4300	6503	SO:0001583	missense	80309	exon7			ACTGTGATGAGGG		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2541T>G	2.37:g.228883029A>C	ENSP00000375909:p.His847Gln	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	372	167	0.448925	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	469	0.21474358974358973	26	0.052845528455284556	96	0.26519337016574585	156	0.2727272727272727	191	0.2519788918205805	A	5.226	0.227206	0.09916	0.064004	0.251977	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11169	2.8;2.8	5.97	0.984	0.19773	.	1.321610	0.04419	N	0.367345	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;B	0.16802	0.011;0.019	B;B	0.15052	0.003;0.012	T	0.39742	-0.9599	9	0.59425	D	0.04	.	6.0637	0.19852	0.5854:0.2766:0.138:0.0	rs3811515;rs17266858;rs52816852;rs56487013;rs57755256;rs3811515	847;847	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	Q	847	ENSP00000375909:H847Q;ENSP00000339886:H847Q	ENSP00000339886:H847Q	H	-	3	2	SPHKAP	228591273	0.031000	0.19500	0.000000	0.03702	0.414000	0.31173	0.219000	0.17641	0.148000	0.19059	0.533000	0.62120	CAT	A|0.784;C|0.216	0.216	strong		0.493	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
FAM186A	121006	hgsc.bcm.edu	37	12	50745677	50745677	+	Silent	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745677T>A	ENST00000327337.5	-	4	4937	c.4938A>T	c.(4936-4938)gcA>gcT	p.A1646A	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Silent_p.A1646A	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1646																	GGACTCCCAGTGCCTGGGCCT	0.607																																					p.A1646A	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,rectum,carcinoma,0,4	FAM186A	181	4	0			c.A4938T						PASS	.						30.0	30.0	30.0					12																	50745677		692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			TCCCAGTGCCTGG		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4938A>T	12.37:g.50745677T>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	169	11	0.0650888	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			.	.	none		0.607	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
OCA2	4948	hgsc.bcm.edu	37	15	28230318	28230318	+	Missense_Mutation	SNP	C	C	T	rs1800407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28230318C>T	ENST00000354638.3	-	13	1411	c.1256G>A	c.(1255-1257)cGg>cAg	p.R419Q	OCA2_ENST00000353809.5_Missense_Mutation_p.R395Q|OCA2_ENST00000382996.2_Missense_Mutation_p.R419Q	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	419			R -> Q (polymorphism associated with green/hazel eye color; dbSNP:rs1800407). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:12163334, ECO:0000269|PubMed:15889046, ECO:0000269|PubMed:18252222, ECO:0000269|PubMed:7601462}.|R -> W (in OCA2; dbSNP:rs143218168).		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CACCCGTCCCCGGGAGAGCCG	0.567									Oculocutaneous Albinism				C|||	127	0.0253594	0.0015	0.0317	5008	,	,		19816	0.001		0.0755	False		,,,				2504	0.0266				p.R419Q		Atlas-SNP	.											.	OCA2	173	.	0			c.G1256A	GRCh37	CM025432	OCA2	M	rs1800407	PASS	.	C	GLN/ARG	54,4352	52.9+/-88.7	0,54,2149	95.0	73.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1256	4.4	0.2	15	dbSNP_89	80	669,7931	166.2+/-218.2	27,615,3658	yes	missense	OCA2	NM_000275.2	43	27,669,5807	TT,TC,CC		7.7791,1.2256,5.559	probably-damaging	419/839	28230318	723,12283	2203	4300	6503	SO:0001583	missense	4948	exon13	Familial Cancer Database		CGTCCCCGGGAGA		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1256G>A	15.37:g.28230318C>T	ENSP00000346659:p.Arg419Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	76	0.0347985347985348	0	0.0	15	0.04143646408839779	1	0.0017482517482517483	60	0.079155672823219	C	21.8	4.202313	0.79127	0.012256	0.077791	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.85955	-2.05;-2.05;-2.05	5.35	4.44	0.53790	Divalent ion symporter (1);	0.000000	0.85682	D	0.000000	T	0.39358	0.1075	L	0.45470	1.425	0.29970	P	0.818602	D;D	0.89917	0.994;1.0	P;D	0.75484	0.879;0.986	T	0.72953	-0.4135	9	0.36615	T	0.2	-17.4895	13.4028	0.60893	0.0:0.9242:0.0:0.0758	rs1800407;rs52791072;rs1800407	395;419	Q04671-2;Q04671	.;P_HUMAN	Q	419;395;419	ENSP00000346659:R419Q;ENSP00000261276:R395Q;ENSP00000372457:R419Q	ENSP00000261276:R395Q	R	-	2	0	OCA2	25903913	1.000000	0.71417	0.152000	0.22495	0.788000	0.44548	7.083000	0.76859	1.384000	0.46424	-0.136000	0.14681	CGG	C|0.952;T|0.048	0.048	strong		0.567	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
CEACAM20	125931	hgsc.bcm.edu	37	19	45017249	45017249	+	RNA	SNP	T	T	C	rs1465723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45017249T>C	ENST00000454753.1	-	0	1687							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				ATTTCTGATGTAGAGAAAATA	0.602											OREG0025538	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	584	0.116613	0.0613	0.1383	5008	,	,		14648	0.0645		0.2376	False		,,,				2504	0.1053				p.Y470C		Atlas-SNP	.											.	CEACAM20	31	.	0			c.A1409G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	322,3624		11,300,1662	72.0	70.0	70.0		1409,1130,1130,1409	1.6	0.0	19	dbSNP_88	70	1766,6564		206,1354,2605	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	194,194,194,194	217,1654,4267	CC,CT,TT		21.2005,8.1602,17.0088	benign,benign,benign,benign	470/597,377/492,377/504,470/585	45017249	2088,10188	1973	4165	6138			125931	exon7			CTGATGTAGAGAA	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45017249T>C		Somatic	81	0	0	928	WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				T|0.864;C|0.136	0.136	strong		0.602	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
NAT14	57106	hgsc.bcm.edu	37	19	55998317	55998317	+	Missense_Mutation	SNP	C	C	A	rs118182626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55998317C>A	ENST00000205194.4	+	3	918	c.615C>A	c.(613-615)gaC>gaA	p.D205E	SSC5D_ENST00000587166.1_5'Flank|NAT14_ENST00000592719.1_Intron|SSC5D_ENST00000389623.6_5'Flank|NAT14_ENST00000587400.1_Intron	NM_020378.3	NP_065111.1	Q8WUY8	NAT14_HUMAN	N-acetyltransferase 14 (GCN5-related, putative)	205	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of transcription, DNA-templated (GO:0045893)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|N-acetyltransferase activity (GO:0008080)			central_nervous_system(1)|large_intestine(1)|ovary(1)|pancreas(1)	4	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0527)		TCAGCAAAGACCTGTGAAGCT	0.652													c|||	78	0.0155751	0.0008	0.036	5008	,	,		12211	0.0		0.0328	False		,,,				2504	0.0194				p.D205E		Atlas-SNP	.											.	NAT14	11	.	0			c.C615A						PASS	.	C	GLU/ASP	22,4034		0,22,2006	9.0	10.0	9.0		615	0.6	1.0	19	dbSNP_132	9	279,7729		2,275,3727	yes	missense	NAT14	NM_020378.3	45	2,297,5733	AA,AC,CC		3.484,0.5424,2.495	benign	205/207	55998317	301,11763	2028	4004	6032	SO:0001583	missense	57106	exon3			CAAAGACCTGTGA	AB055059	CCDS12926.1	19q13.42	2011-11-25	2008-09-24		ENSG00000090971	ENSG00000090971			28918	protein-coding gene	gene with protein product	"""K562 cells-derived leucine zipper-like protein 1"""		"""N-acetyltransferase 14"""			10873651	Standard	NM_020378		Approved	KLP1	uc002qle.2	Q8WUY8		ENST00000205194.4:c.615C>A	19.37:g.55998317C>A	ENSP00000205194:p.Asp205Glu	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	7	0.875	NM_020378	Q8TDY7|Q9NS72	Missense_Mutation	SNP	ENST00000205194.4	37	CCDS12926.1	46	0.021062271062271064	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	29	0.03825857519788918	.	16.91	3.253386	0.59212	0.005424	0.03484	ENSG00000090971	ENST00000205194	.	.	.	4.44	0.636	0.17729	GCN5-related N-acetyltransferase (GNAT) domain (1);	0.238192	0.30809	N	0.008836	T	0.14527	0.0351	L	0.34521	1.04	0.35928	D	0.8323	B	0.14012	0.009	B	0.12837	0.008	T	0.36016	-0.9765	9	0.48119	T	0.1	-29.4319	11.7987	0.52114	0.455:0.5449:0.0:0.0	.	205	Q8WUY8	NAT14_HUMAN	E	205	.	ENSP00000205194:D205E	D	+	3	2	NAT14	60690129	0.982000	0.34865	1.000000	0.80357	0.839000	0.47603	0.051000	0.14141	0.394000	0.25230	0.455000	0.32223	GAC	C|0.978;A|0.022	0.022	strong		0.652	NAT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453339.1	NM_020378	
RPN2	6185	hgsc.bcm.edu	37	20	35852309	35852309	+	Missense_Mutation	SNP	G	G	A	rs117475222	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:35852309G>A	ENST00000237530.6	+	10	1432	c.1121G>A	c.(1120-1122)gGc>gAc	p.G374D	RPN2_ENST00000373622.5_Missense_Mutation_p.G342D	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	374					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				ACTGAAGTTGGCATCACAAAT	0.468													G|||	72	0.014377	0.0008	0.0072	5008	,	,		20811	0.001		0.0169	False		,,,				2504	0.0491				p.G374D		Atlas-SNP	.											.	RPN2	45	.	0			c.G1121A						PASS	.	G	ASP/GLY,ASP/GLY	21,4385	28.1+/-56.4	0,21,2182	111.0	92.0	99.0		1025,1121	5.2	1.0	20	dbSNP_132	99	156,8444	74.8+/-137.4	3,150,4147	yes	missense,missense	RPN2	NM_001135771.1,NM_002951.3	94,94	3,171,6329	AA,AG,GG		1.814,0.4766,1.3609	possibly-damaging,possibly-damaging	342/616,374/632	35852309	177,12829	2203	4300	6503	SO:0001583	missense	6185	exon10			AAGTTGGCATCAC	Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"""oligosaccharyltransferase complex subunit (non-catalytic)"""	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1121G>A	20.37:g.35852309G>A	ENSP00000237530:p.Gly374Asp	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_002951	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Missense_Mutation	SNP	ENST00000237530.6	37	CCDS13291.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	17.15	3.315403	0.60524	0.004766	0.01814	ENSG00000118705	ENST00000237530;ENST00000373622	T;T	0.42900	0.96;0.96	5.25	5.25	0.73442	.	0.103999	0.64402	D	0.000004	T	0.24198	0.0586	L	0.44542	1.39	0.50313	D	0.999866	P;P;P;P	0.44344	0.833;0.833;0.737;0.605	B;B;B;B	0.43508	0.422;0.422;0.324;0.324	T	0.02484	-1.1152	10	0.23302	T	0.38	-9.8661	16.4036	0.83650	0.0:0.0:1.0:0.0	.	249;342;374;374	A6NKT1;Q5JYR6;P04844;B2RE46	.;.;RPN2_HUMAN;.	D	374;342	ENSP00000237530:G374D;ENSP00000362724:G342D	ENSP00000237530:G374D	G	+	2	0	RPN2	35285723	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.310000	0.72830	2.729000	0.93468	0.650000	0.86243	GGC	G|0.988;A|0.012	0.012	strong		0.468	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951	
OR8D4	338662	hgsc.bcm.edu	37	11	123777302	123777302	+	Missense_Mutation	SNP	T	T	G	rs17127947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123777302T>G	ENST00000321355.2	+	1	194	c.164T>G	c.(163-165)cTt>cGt	p.L55R		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	55			L -> R (in dbSNP:rs17127947).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L55R(1)		large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		AATCGTCAACTTCATACCCCC	0.408													T|||	934	0.186502	0.2844	0.1455	5008	,	,		20366	0.0933		0.1829	False		,,,				2504	0.183				p.L55R		Atlas-SNP	.											OR8D4,NS,carcinoma,0,1	OR8D4	62	1	1	Substitution - Missense(1)	stomach(1)	c.T164G						PASS	.	T	ARG/LEU	1081,3323	392.4+/-328.5	140,801,1261	243.0	230.0	235.0		164	5.7	0.8	11	dbSNP_123	235	1636,6962	303.2+/-306.3	164,1308,2827	yes	missense	OR8D4	NM_001005197.1	102	304,2109,4088	GG,GT,TT		19.0277,24.5459,20.8968	probably-damaging	55/315	123777302	2717,10285	2202	4299	6501	SO:0001583	missense	338662	exon1			GTCAACTTCATAC	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.164T>G	11.37:g.123777302T>G	ENSP00000325381:p.Leu55Arg	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	236	97	0.411017	NM_001005197	Q6IFE9	Missense_Mutation	SNP	ENST00000321355.2	37	CCDS31698.1	406	0.1858974358974359	133	0.2703252032520325	57	0.1574585635359116	75	0.13111888111888112	141	0.18601583113456466	T	15.75	2.926498	0.52759	0.245459	0.190277	ENSG00000181518	ENST00000321355	T	0.14766	2.48	5.67	5.67	0.87782	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	D	0.000647	T	0.00012	0.0000	H	0.98802	4.335	0.20873	P	0.999832108	D	0.89917	1.0	D	0.79108	0.992	T	0.23511	-1.0186	9	0.87932	D	0	.	14.8892	0.70594	0.0:0.0:0.0:1.0	rs17127947;rs17127947	55	Q8NGM9	OR8D4_HUMAN	R	55	ENSP00000325381:L55R	ENSP00000325381:L55R	L	+	2	0	OR8D4	123282512	1.000000	0.71417	0.780000	0.31762	0.121000	0.20230	7.872000	0.87187	2.143000	0.66587	0.533000	0.62120	CTT	G|0.199;N|0.000	0.199	strong		0.408	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
HIVEP1	3096	hgsc.bcm.edu	37	6	12120445	12120445	+	Silent	SNP	A	A	G	rs2228215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:12120445A>G	ENST00000379388.2	+	4	749	c.417A>G	c.(415-417)caA>caG	p.Q139Q		NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	139					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTCTGCAGCAACCATCTGAAC	0.443													T|||	1101	0.219848	0.0628	0.2478	5008	,	,		19938	0.2242		0.34	False		,,,				2504	0.2843				p.Q139Q		Atlas-SNP	.											.	HIVEP1	242	.	0			c.A417G						PASS	.	T		369,3537		21,327,1605	95.0	90.0	92.0		417	-7.9	0.0	6	dbSNP_98	92	2909,5385		510,1889,1748	no	coding-synonymous	HIVEP1	NM_002114.2		531,2216,3353	GG,GA,AA		35.0735,9.447,26.8689		139/2719	12120445	3278,8922	1953	4147	6100	SO:0001819	synonymous_variant	3096	exon4			GCAGCAACCATCT	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.417A>G	6.37:g.12120445A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	ENST00000379388.2	37	CCDS43426.1																																																																																			A|0.745;C|0.002	.	strong		0.443	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
CSF2RB	1439	hgsc.bcm.edu	37	22	37333794	37333794	+	Silent	SNP	A	A	G	rs131840	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:37333794A>G	ENST00000403662.3	+	14	2166	c.1944A>G	c.(1942-1944)ccA>ccG	p.P648P	CSF2RB_ENST00000406230.1_Silent_p.P654P|CSF2RB_ENST00000262825.5_Silent_p.P654P|CSF2RB_ENST00000536485.1_Silent_p.P595P			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	648					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	CGATGGGACCAGGACAGGCCG	0.692													G|||	4018	0.802316	0.6157	0.8761	5008	,	,		13977	0.9385		0.7932	False		,,,				2504	0.8712				p.P648P		Atlas-SNP	.											.	CSF2RB	104	.	0			c.A1944G						PASS	.	G		2877,1489		969,939,275	9.0	11.0	10.0		1944	-4.8	0.0	22	dbSNP_78	10	6929,1581		2845,1239,171	no	coding-synonymous	CSF2RB	NM_000395.2		3814,2178,446	GG,GA,AA		18.5781,34.1044,23.8428		648/898	37333794	9806,3070	2183	4255	6438	SO:0001819	synonymous_variant	1439	exon14			GGGACCAGGACAG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1944A>G	22.37:g.37333794A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_000395	Q5JZI1|Q6ICE0	Silent	SNP	ENST00000403662.3	37	CCDS13936.1																																																																																			A|0.198;G|0.802	0.802	strong		0.692	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
STAT1	6772	hgsc.bcm.edu	37	2	191874667	191874667	+	Silent	SNP	A	A	G	rs2066802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:191874667A>G	ENST00000361099.3	-	3	450	c.63T>C	c.(61-63)ctT>ctC	p.L21L	STAT1_ENST00000392323.2_Silent_p.L23L|STAT1_ENST00000540176.1_Silent_p.L21L|STAT1_ENST00000409465.1_Silent_p.L21L|STAT1_ENST00000392322.3_Silent_p.L21L	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	21					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			TGTCATCATAAAGCTGGTGAA	0.393													A|||	574	0.114617	0.0734	0.0504	5008	,	,		19108	0.2272		0.0696	False		,,,				2504	0.1462				p.L21L		Atlas-SNP	.											.	STAT1	93	.	0			c.T63C						PASS	.	A	,	320,4086	171.6+/-201.8	10,300,1893	157.0	149.0	152.0		63,63	-2.9	1.0	2	dbSNP_94	152	532,8068	147.7+/-203.1	17,498,3785	no	coding-synonymous,coding-synonymous	STAT1	NM_007315.3,NM_139266.2	,	27,798,5678	GG,GA,AA		6.186,7.2628,6.5508	,	21/751,21/713	191874667	852,12154	2203	4300	6503	SO:0001819	synonymous_variant	6772	exon3			ATCATAAAGCTGG		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.63T>C	2.37:g.191874667A>G		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	203	92	0.453202	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Silent	SNP	ENST00000361099.3	37	CCDS2309.1																																																																																			A|0.909;G|0.091	0.091	strong		0.393	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315	
NDST3	9348	hgsc.bcm.edu	37	4	119161795	119161795	+	Silent	SNP	G	G	A	rs617430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:119161795G>A	ENST00000296499.5	+	11	2638	c.2235G>A	c.(2233-2235)ccG>ccA	p.P745P		NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	745	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)	p.P745P(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						GTTTGGTCCCGGGGTGGTATG	0.488													G|||	1244	0.248403	0.0454	0.3588	5008	,	,		15669	0.2083		0.3688	False		,,,				2504	0.362				p.P745P		Atlas-SNP	.											NDST3,NS,carcinoma,0,1	NDST3	107	1	1	Substitution - coding silent(1)	prostate(1)	c.G2235A						PASS	.	G		420,3986	205.8+/-227.6	30,360,1813	85.0	80.0	82.0		2235	-11.0	0.4	4	dbSNP_83	82	3443,5157	506.3+/-376.6	683,2077,1540	no	coding-synonymous	NDST3	NM_004784.2		713,2437,3353	AA,AG,GG		40.0349,9.5325,29.7017		745/874	119161795	3863,9143	2203	4300	6503	SO:0001819	synonymous_variant	9348	exon11			GGTCCCGGGGTGG	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"""Sulfotransferases, membrane-bound"""	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.2235G>A	4.37:g.119161795G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	166	82	0.493976	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Silent	SNP	ENST00000296499.5	37	CCDS3708.1																																																																																			G|0.732;A|0.268	0.268	strong		0.488	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	
UGT1A6	54578	hgsc.bcm.edu	37	2	234602202	234602202	+	Missense_Mutation	SNP	A	A	C	rs1105879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234602202A>C	ENST00000305139.6	+	1	691	c.552A>C	c.(550-552)agA>agC	p.R184S	UGT1A6_ENST00000406651.1_5'Flank|UGT1A6_ENST00000480628.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|AC114812.8_ENST00000439336.1_RNA|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	184			R -> S (in allele UGT1A6*2 and allele UGT1A6*4; dbSNP:rs1105879). {ECO:0000269|PubMed:15284531, ECO:0000269|PubMed:19204906, ECO:0000269|PubMed:9429234, ECO:0000269|Ref.4}.		cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	CATTCAGCAGAAGCCCAGACC	0.502													A|||	1626	0.324681	0.3018	0.3012	5008	,	,		19814	0.2242		0.333	False		,,,				2504	0.4673				p.R184S		Atlas-SNP	.											.	UGT1A6	63	.	0			c.A552C	GRCh37	CM057768	UGT1A6	M	rs1105879	PASS	.	A	SER/ARG,,,,,	1345,3061	450.0+/-349.2	223,899,1081	157.0	148.0	151.0		552,,,,,	-3.3	0.0	2	dbSNP_86	151	3076,5524	471.0+/-368.0	563,1950,1787	yes	missense,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2,NM_205862.1	110,,,,,	786,2849,2868	CC,CA,AA		35.7674,30.5266,33.992	,,,,,	184/533,,,,,	234602202	4421,8585	2203	4300	6503	SO:0001583	missense	54578	exon1			CAGCAGAAGCCCA	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.552A>C	2.37:g.234602202A>C	ENSP00000303174:p.Arg184Ser	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	167	89	0.532934	NM_001072	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1	662	0.3031135531135531	157	0.31910569105691056	116	0.32044198895027626	136	0.23776223776223776	253	0.3337730870712401	A	11.30	1.597632	0.28445	0.305266	0.357674	ENSG00000167165	ENST00000441351;ENST00000305139	T;T	0.59502	0.26;3.34	5.31	-3.31	0.04988	.	.	.	.	.	T	0.00012	0.0000	L	0.45137	1.4	0.45899	P	0.0012510000000000021	B	0.19706	0.038	B	0.29524	0.103	T	0.40590	-0.9555	8	0.46703	T	0.11	.	9.9644	0.41715	0.1906:0.1494:0.66:0.0	rs1105879;rs4365457;rs17684024;rs61226878;rs1105879	184	P19224	UD16_HUMAN	S	184	ENSP00000389637:R184S;ENSP00000303174:R184S	ENSP00000303174:R184S	R	+	3	2	UGT1A6	234266941	0.000000	0.05858	0.000000	0.03702	0.434000	0.31775	-0.753000	0.04792	-0.435000	0.07264	0.533000	0.62120	AGA	A|0.682;C|0.318	0.318	strong		0.502	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
CCNB3	85417	hgsc.bcm.edu	37	X	50085217	50085217	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:50085217C>T	ENST00000376042.1	+	9	3831	c.3533C>T	c.(3532-3534)aCc>aTc	p.T1178I	CCNB3_ENST00000376038.1_Missense_Mutation_p.T74I|CCNB3_ENST00000276014.7_Missense_Mutation_p.T1178I|CCNB3_ENST00000348603.2_Missense_Mutation_p.T74I			Q8WWL7	CCNB3_HUMAN	cyclin B3	1178					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TTTGAGATGACCCATGAGACC	0.493																																					p.T1178I		Atlas-SNP	.											.	CCNB3	367	.	0			c.C3533T						PASS	.						221.0	179.0	194.0					X																	50085217		2203	4300	6503	SO:0001583	missense	85417	exon8			AGATGACCCATGA	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.3533C>T	X.37:g.50085217C>T	ENSP00000365210:p.Thr1178Ile	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	87	26	0.298851	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	C	4.077	0.012091	0.07912	.	.	ENSG00000147082	ENST00000376042;ENST00000376038;ENST00000348603;ENST00000276014	T;T;T;T	0.12465	2.68;2.75;2.75;2.68	5.11	-1.37	0.09056	Cyclin, N-terminal (1);Cyclin-like (3);	0.889284	0.09724	N	0.764028	T	0.14614	0.0353	L	0.41710	1.295	0.23820	N	0.996759	P;B;P	0.37688	0.605;0.411;0.605	P;B;B	0.45946	0.498;0.176;0.37	T	0.37502	-0.9703	9	.	.	.	.	7.004	0.24826	0.328:0.4757:0.1963:0.0	.	1178;74;1178	A8K8T9;Q8WWL7-2;Q8WWL7	.;.;CCNB3_HUMAN	I	1178;74;74;1178	ENSP00000365210:T1178I;ENSP00000365206:T74I;ENSP00000338682:T74I;ENSP00000276014:T1178I	.	T	+	2	0	CCNB3	50101957	0.933000	0.31639	0.312000	0.25196	0.443000	0.32047	-0.013000	0.12678	-0.093000	0.12396	-0.568000	0.04159	ACC	.	.	none		0.493	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1		
PRUNE2	158471	hgsc.bcm.edu	37	9	79321871	79321871	+	Silent	SNP	C	C	T	rs577993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79321871C>T	ENST00000376718.3	-	8	5442	c.5319G>A	c.(5317-5319)acG>acA	p.T1773T	PRUNE2_ENST00000428286.1_Silent_p.T1414T	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1773					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TTTCAGTCTCCGTTAATGGTG	0.458													C|||	2586	0.516374	0.3722	0.6571	5008	,	,		22996	0.4464		0.6153	False		,,,				2504	0.5818				p.T1773T		Atlas-SNP	.											PRUNE2_ENST00000376718,colon,carcinoma,-1,1	PRUNE2	331	1	0			c.G5319A						PASS	.	C		1351,1785		289,773,506	139.0	108.0	117.0		5319	-3.5	0.0	9	dbSNP_83	117	4581,2583		1478,1625,479	yes	coding-synonymous	PRUNE2	NM_015225.2		1767,2398,985	TT,TC,CC		36.0553,43.0804,42.4078		1773/3089	79321871	5932,4368	1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			AGTCTCCGTTAAT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.5319G>A	9.37:g.79321871C>T		Somatic	387	0	0		WXS	Illumina HiSeq	Phase_I	373	194	0.520107	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	1157	0.5297619047619048	198	0.4024390243902439	239	0.6602209944751382	259	0.4527972027972028	461	0.6081794195250659	C	0.012	-1.652482	0.00785	0.430804	0.639447	ENSG00000106772	ENST00000426088	.	.	.	5.73	-3.5	0.04710	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.43540	-0.9385	3	.	.	.	-0.1167	1.431	0.02333	0.1858:0.2539:0.1136:0.4467	rs577993;rs756355;rs17180774;rs56418952;rs61542287;rs577993	.	.	.	R	1095	.	.	G	-	1	0	PRUNE2	78511691	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.645000	0.05409	-0.334000	0.08463	0.655000	0.94253	GGA	C|0.473;T|0.527	0.527	strong		0.458	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
SLC44A5	204962	hgsc.bcm.edu	37	1	75702674	75702674	+	Silent	SNP	G	G	A	rs17096508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:75702674G>A	ENST00000370855.5	-	11	851	c.738C>T	c.(736-738)ctC>ctT	p.L246L	SLC44A5_ENST00000535611.1_Silent_p.L116L|SLC44A5_ENST00000370859.3_Silent_p.L246L	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	246					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						TCACTTACATGAGAATCCAAT	0.318													G|||	582	0.116214	0.1172	0.0821	5008	,	,		18032	0.0397		0.2008	False		,,,				2504	0.1309				p.L246L		Atlas-SNP	.											.	SLC44A5	231	.	0			c.C738T						PASS	.	G	,	531,3875	238.7+/-250.0	36,459,1708	64.0	58.0	60.0		738,738	3.5	1.0	1	dbSNP_123	60	1819,6781	322.9+/-315.8	194,1431,2675	no	coding-synonymous,coding-synonymous	SLC44A5	NM_001130058.1,NM_152697.4	,	230,1890,4383	AA,AG,GG		21.1512,12.0517,18.0686	,	246/718,246/720	75702674	2350,10656	2203	4300	6503	SO:0001819	synonymous_variant	204962	exon11			TTACATGAGAATC	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.738C>T	1.37:g.75702674G>A		Somatic	413	1	0.00242131		WXS	Illumina HiSeq	Phase_I	310	185	0.596774	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	37	CCDS667.1																																																																																			G|0.845;A|0.155	0.155	strong		0.318	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697	
RFXAP	5994	hgsc.bcm.edu	37	13	37393904	37393904	+	Missense_Mutation	SNP	T	T	C	rs193240312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:37393904T>C	ENST00000255476.2	+	1	544	c.410T>C	c.(409-411)aTg>aCg	p.M137T		NM_000538.3	NP_000529.1	O00287	RFXAP_HUMAN	regulatory factor X-associated protein	137					positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;3.5e-07)|Epithelial(112;1.27e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.0069)|BRCA - Breast invasive adenocarcinoma(63;0.0116)|GBM - Glioblastoma multiforme(144;0.0405)		GGGGGCAGCATGAGCAAGACC	0.652													T|||	39	0.00778754	0.0015	0.0043	5008	,	,		10751	0.0		0.0199	False		,,,				2504	0.0143				p.M137T		Atlas-SNP	.											RFXAP,NS,carcinoma,0,1	RFXAP	14	1	0			c.T410C						PASS	.	T	THR/MET	8,4368		0,8,2180	23.0	20.0	21.0		410	-2.5	0.0	13		21	150,8392		1,148,4122	yes	missense	RFXAP	NM_000538.3	81	1,156,6302	CC,CT,TT		1.756,0.1828,1.2231	benign	137/273	37393904	158,12760	2188	4271	6459	SO:0001583	missense	5994	exon1			GCAGCATGAGCAA	Y12812	CCDS9359.1	13q14	2014-09-17			ENSG00000133111	ENSG00000133111			9988	protein-coding gene	gene with protein product		601861				9118943	Standard	NM_000538		Approved		uc001uvu.1	O00287	OTTHUMG00000016738	ENST00000255476.2:c.410T>C	13.37:g.37393904T>C	ENSP00000255476:p.Met137Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	NM_000538	B2R9T8|Q5VZM6|Q8TC40	Missense_Mutation	SNP	ENST00000255476.2	37	CCDS9359.1	15	0.006868131868131868	2	0.0040650406504065045	0	0.0	0	0.0	13	0.017150395778364115	t	1.104	-0.660357	0.03454	0.001828	0.01756	ENSG00000133111	ENST00000255476	.	.	.	4.02	-2.46	0.06461	.	1.358100	0.04628	N	0.403151	T	0.10551	0.0258	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18023	-1.0350	9	0.10377	T	0.69	0.3107	9.0699	0.36486	0.0:0.5126:0.0:0.4874	.	137	O00287	RFXAP_HUMAN	T	137	.	ENSP00000255476:M137T	M	+	2	0	RFXAP	36291904	0.222000	0.23652	0.031000	0.17742	0.079000	0.17450	0.101000	0.15251	-0.452000	0.07087	-0.262000	0.10625	ATG	T|0.993;C|0.007	0.007	strong		0.652	RFXAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044521.1	NM_000538	
ALPK2	115701	hgsc.bcm.edu	37	18	56204932	56204932	+	Missense_Mutation	SNP	T	T	G	rs3809973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204932T>G	ENST00000361673.3	-	5	2700	c.2487A>C	c.(2485-2487)aaA>aaC	p.K829N	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	829			K -> N (in dbSNP:rs3809973).	K -> S (in Ref. 1; CAD89922). {ECO:0000305}.		nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GAGGCGAATATTTATCAACTG	0.418													T|||	2025	0.404353	0.4319	0.4294	5008	,	,		23287	0.2361		0.5726	False		,,,				2504	0.3497				p.K829N		Atlas-SNP	.											.	ALPK2	487	.	0			c.A2487C						PASS	.	T	ASN/LYS	1984,2422	555.8+/-379.4	446,1092,665	87.0	85.0	86.0		2487	4.4	0.4	18	dbSNP_107	86	4588,4012	597.0+/-393.7	1237,2114,949	yes	missense	ALPK2	NM_052947.3	94	1683,3206,1614	GG,GT,TT		46.6512,45.0295,49.4695	probably-damaging	829/2171	56204932	6572,6434	2203	4300	6503	SO:0001583	missense	115701	exon5			CGAATATTTATCA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2487A>C	18.37:g.56204932T>G	ENSP00000354991:p.Lys829Asn	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	153	64	0.418301	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	955	0.43727106227106227	189	0.38414634146341464	184	0.5082872928176796	137	0.2395104895104895	445	0.5870712401055409	T	13.19	2.163361	0.38217	0.450295	0.533488	ENSG00000198796	ENST00000361673	T	0.50813	0.73	5.57	4.36	0.52297	.	1.150850	0.06324	N	0.705000	T	0.00012	0.0000	L	0.54323	1.7	0.53688	P	2.199999999996649E-5	D;D	0.65815	0.995;0.976	P;P	0.61592	0.891;0.524	T	0.43343	-0.9397	9	0.54805	T	0.06	-8.4207	10.1922	0.43032	0.0:0.0:0.1787:0.8213	rs3809973;rs56693680;rs3809973	829;829	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	N	829	ENSP00000354991:K829N	ENSP00000354991:K829N	K	-	3	2	ALPK2	54355912	0.831000	0.29352	0.362000	0.25862	0.039000	0.13416	1.866000	0.39489	2.126000	0.65437	0.482000	0.46254	AAA	T|0.534;G|0.466	0.466	strong		0.418	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ZNF146	7705	hgsc.bcm.edu	37	19	36727365	36727365	+	Missense_Mutation	SNP	G	G	A	rs2070132	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36727365G>A	ENST00000443387.2	+	4	1015	c.23G>A	c.(22-24)aGa>aAa	p.R8K	ZNF565_ENST00000355114.5_Intron|ZNF146_ENST00000456324.1_Missense_Mutation_p.R8K	NM_007145.2	NP_009076.2	Q15072	OZF_HUMAN	zinc finger protein 146	8			R -> K (in dbSNP:rs2070132). {ECO:0000269|PubMed:11306801, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8107129}.		regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11	Esophageal squamous(110;0.162)					AGCCAGCAGAGAATTTACAGT	0.433													G|||	1938	0.386981	0.3041	0.33	5008	,	,		18898	0.4683		0.3807	False		,,,				2504	0.4622				p.R8K		Atlas-SNP	.											.	ZNF146	32	.	0			c.G23A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	1500,2906	472.2+/-356.3	272,956,975	44.0	46.0	46.0		23,23,23	-1.9	0.3	19	dbSNP_96	46	3401,5199	499.6+/-375.0	697,2007,1596	yes	missense,missense,missense	ZNF146	NM_001099638.1,NM_001099639.1,NM_007145.2	26,26,26	969,2963,2571	AA,AG,GG		39.5465,34.0445,37.6826	benign,benign,benign	8/293,8/293,8/293	36727365	4901,8105	2203	4300	6503	SO:0001583	missense	7705	exon3			AGCAGAGAATTTA	X70394	CCDS12492.1	19q13.1	2013-01-08				ENSG00000167635		"""Zinc fingers, C2H2-type"""	12931	protein-coding gene	gene with protein product		601505				10449921, 8641144	Standard	NM_001099639		Approved	OZF	uc010eeu.3	Q15072		ENST00000443387.2:c.23G>A	19.37:g.36727365G>A	ENSP00000392095:p.Arg8Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_001099638	Q2TB94	Missense_Mutation	SNP	ENST00000443387.2	37	CCDS12492.1	815	0.3731684981684982	154	0.3130081300813008	134	0.3701657458563536	243	0.42482517482517484	284	0.37467018469656993	G	11.56	1.675475	0.29783	0.340445	0.395465	ENSG00000167635	ENST00000443387;ENST00000456324	T;T	0.17054	2.3;2.3	4.46	-1.92	0.07618	.	0.499069	0.17087	N	0.187536	T	0.00012	0.0000	L	0.31578	0.945	0.39327	P	0.03465399999999996	B	0.06786	0.001	B	0.08055	0.003	T	0.48559	-0.9025	9	0.52906	T	0.07	-9.1357	9.9012	0.41348	0.5376:0.0:0.4624:0.0	rs2070132;rs17639642;rs52831725;rs59509631;rs2070132	8	Q15072	OZF_HUMAN	K	8	ENSP00000392095:R8K;ENSP00000400391:R8K	ENSP00000392095:R8K	R	+	2	0	ZNF146	41419205	0.000000	0.05858	0.294000	0.24946	0.816000	0.46133	-0.758000	0.04766	-0.180000	0.10637	-0.806000	0.03193	AGA	G|0.622;A|0.378	0.378	strong		0.433	ZNF146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451706.1	NM_007145	
CWC27	10283	hgsc.bcm.edu	37	5	64273018	64273018	+	Silent	SNP	G	G	A	rs1309581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:64273018G>A	ENST00000381070.3	+	13	1426	c.1209G>A	c.(1207-1209)acG>acA	p.T403T	CWC27_ENST00000545000.1_3'UTR	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	403					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						TTGCTGAAACGCCTGAAAATG	0.358													G|||	1761	0.351637	0.2519	0.3876	5008	,	,		18195	0.3026		0.4125	False		,,,				2504	0.4489				p.T403T		Atlas-SNP	.											.	CWC27	47	.	0			c.G1209A						PASS	.	G		1287,3119	432.8+/-343.4	203,881,1119	80.0	74.0	76.0		1209	0.7	1.0	5	dbSNP_87	76	3875,4725	543.3+/-384.4	906,2063,1331	no	coding-synonymous	CWC27	NM_005869.2		1109,2944,2450	AA,AG,GG		45.0581,29.2102,39.6894		403/473	64273018	5162,7844	2203	4300	6503	SO:0001819	synonymous_variant	10283	exon13			TGAAACGCCTGAA	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"""serologically defined colon cancer antigen 10"""	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.1209G>A	5.37:g.64273018G>A		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	242	240	0.991736	NM_005869	O60529|O60530|Q96EM3	Silent	SNP	ENST00000381070.3	37	CCDS3982.2																																																																																			G|0.631;A|0.369	0.369	strong		0.358	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
ARMC3	219681	hgsc.bcm.edu	37	10	23290952	23290952	+	Silent	SNP	C	C	T	rs12259839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:23290952C>T	ENST00000298032.5	+	12	1614	c.1530C>T	c.(1528-1530)gaC>gaT	p.D510D	ARMC3_ENST00000409049.3_Silent_p.D510D|ARMC3_ENST00000409983.3_Silent_p.D510D|ARMC3_ENST00000376528.4_Silent_p.D247D	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	510						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GTGCTGGTGACGAGCTGACGG	0.532													C|||	348	0.0694888	0.1649	0.0346	5008	,	,		15926	0.001		0.0616	False		,,,				2504	0.044				p.D510D		Atlas-SNP	.											.	ARMC3	102	.	0			c.C1530T						PASS	.	C		600,3806	264.4+/-266.0	48,504,1651	121.0	102.0	108.0		1530	-11.8	0.0	10	dbSNP_120	108	475,8125	139.5+/-196.2	14,447,3839	no	coding-synonymous	ARMC3	NM_173081.3		62,951,5490	TT,TC,CC		5.5233,13.6178,8.2654		510/873	23290952	1075,11931	2203	4300	6503	SO:0001819	synonymous_variant	219681	exon12			TGGTGACGAGCTG	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1530C>T	10.37:g.23290952C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	200	94	0.47	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Silent	SNP	ENST00000298032.5	37	CCDS7142.1																																																																																			C|0.920;T|0.080	0.080	strong		0.532	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081	
IPO7	10527	hgsc.bcm.edu	37	11	9450115	9450115	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:9450115A>G	ENST00000379719.3	+	13	1506	c.1364A>G	c.(1363-1365)tAc>tGc	p.Y455C	SNORA23_ENST00000365128.1_RNA|CTD-2371O3.2_ENST00000531111.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	455					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		CAGATGGAATACATGTTGCAG	0.308																																					p.Y455C		Atlas-SNP	.											IPO7,NS,carcinoma,-1,1	IPO7	72	1	0			c.A1364G						scavenged	.						49.0	49.0	49.0					11																	9450115		2201	4292	6493	SO:0001583	missense	10527	exon13			TGGAATACATGTT	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"""Importins"""	9852	protein-coding gene	gene with protein product		605586	"""RAN binding protein 7"""	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.1364A>G	11.37:g.9450115A>G	ENSP00000369042:p.Tyr455Cys	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	246	3	0.0121951	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	37	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217880	0.39201	.	.	ENSG00000205339	ENST00000379719	T	0.23552	1.9	5.36	5.36	0.76844	Armadillo-like helical (1);Armadillo-type fold (1);	0.111469	0.64402	D	0.000009	T	0.24275	0.0588	L	0.36672	1.1	0.42513	D	0.992972	B	0.28933	0.228	B	0.35899	0.213	T	0.08046	-1.0741	10	0.54805	T	0.06	.	10.5712	0.45202	0.8561:0.0:0.0:0.1439	.	455	O95373	IPO7_HUMAN	C	455	ENSP00000369042:Y455C	ENSP00000369042:Y455C	Y	+	2	0	IPO7	9406691	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	5.710000	0.68392	2.007000	0.58848	0.482000	0.46254	TAC	.	.	none		0.308	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391	
ATP6V0A2	23545	hgsc.bcm.edu	37	12	124210782	124210782	+	Silent	SNP	T	T	C	rs1399961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124210782T>C	ENST00000330342.3	+	5	719	c.471T>C	c.(469-471)agT>agC	p.S157S		NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	157					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		CCTTAGAGAGTGATTCTTTGT	0.418													C|||	3755	0.7498	0.7027	0.7709	5008	,	,		20389	0.9474		0.6233	False		,,,				2504	0.7249				p.S157S		Atlas-SNP	.											.	ATP6V0A2	68	.	0			c.T471C						PASS	.	C		2984,1422	464.5+/-353.9	1027,930,246	106.0	106.0	106.0		471	-11.8	0.0	12	dbSNP_88	106	5338,3262	490.3+/-372.8	1674,1990,636	no	coding-synonymous	ATP6V0A2	NM_012463.3		2701,2920,882	CC,CT,TT		37.9302,32.2742,36.0141		157/857	124210782	8322,4684	2203	4300	6503	SO:0001819	synonymous_variant	23545	exon5			AGAGAGTGATTCT	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"""ATPases / V-type"""	18481	protein-coding gene	gene with protein product	"""infantile malignant osteopetrosis"""	611716	"""infantile malignant osteopetrosis"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 2"", ""ATPase, H+ transporting, lysosomal V0 subunit A2"""			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.471T>C	12.37:g.124210782T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_012463	A8K026|Q6NUM0	Silent	SNP	ENST00000330342.3	37	CCDS9254.1																																																																																			T|0.317;C|0.683	0.683	strong		0.418	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463	
MATN3	4148	hgsc.bcm.edu	37	2	20202929	20202929	+	Silent	SNP	C	C	T	rs28452699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:20202929C>T	ENST00000407540.3	-	3	971	c.909G>A	c.(907-909)acG>acA	p.T303T	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Intron	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	303	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> M (in dbSNP:rs28939676). {ECO:0000269|PubMed:12736871, ECO:0000269|PubMed:14729835, ECO:0000269|PubMed:15459972}.		extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACCTGAACACGTTTTCTTGT	0.527													C|||	731	0.145966	0.1407	0.1974	5008	,	,		18880	0.0367		0.1978	False		,,,				2504	0.1759				p.T303T		Atlas-SNP	.											.	MATN3	28	.	0			c.G909A						PASS	.	C		574,3468		38,498,1485	125.0	117.0	120.0		909	-11.0	0.0	2	dbSNP_125	120	1796,6544		189,1418,2563	no	coding-synonymous	MATN3	NM_002381.4		227,1916,4048	TT,TC,CC		21.5348,14.2009,19.1407		303/487	20202929	2370,10012	2021	4170	6191	SO:0001819	synonymous_variant	4148	exon3			TGAACACGTTTTC	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.909G>A	2.37:g.20202929C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_002381	B2CPU0|Q4ZG02	Silent	SNP	ENST00000407540.3	37	CCDS46226.1																																																																																			C|0.827;T|0.173	0.173	strong		0.527	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
CCP110	9738	hgsc.bcm.edu	37	16	19548461	19548461	+	Silent	SNP	C	C	T	rs62000395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19548461C>T	ENST00000381396.5	+	4	1717	c.1470C>T	c.(1468-1470)ggC>ggT	p.G490G	CCP110_ENST00000396212.2_Silent_p.G490G|CCP110_ENST00000396208.2_Silent_p.G490G	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	490	Interaction with CEP76.				cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						ATGAGAGAGGCGCACACATAA	0.418													C|||	365	0.0728834	0.0023	0.0432	5008	,	,		21319	0.1746		0.0427	False		,,,				2504	0.1155				p.G490G		Atlas-SNP	.											.	CCP110	57	.	0			c.C1470T						PASS	.	C	,	43,4351	45.3+/-79.5	0,43,2154	83.0	76.0	78.0		1470,1470	-8.1	0.0	16	dbSNP_129	78	269,8331	103.8+/-164.8	3,263,4034	no	coding-synonymous,coding-synonymous	CCP110	NM_001199022.1,NM_014711.4	,	3,306,6188	TT,TC,CC		3.1279,0.9786,2.4011	,	490/1013,490/992	19548461	312,12682	2197	4300	6497	SO:0001819	synonymous_variant	9738	exon4			GAGAGGCGCACAC	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.1470C>T	16.37:g.19548461C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	ENST00000381396.5	37	CCDS55992.1																																																																																			C|0.961;T|0.039	0.039	strong		0.418	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
CDHR3	222256	hgsc.bcm.edu	37	7	105665004	105665004	+	Missense_Mutation	SNP	C	C	A	rs117406926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:105665004C>A	ENST00000317716.9	+	15	2334	c.2254C>A	c.(2254-2256)Cct>Act	p.P752T	CDHR3_ENST00000343407.5_Missense_Mutation_p.T254N|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000542731.1_Missense_Mutation_p.P752T|CDHR3_ENST00000478080.1_Missense_Mutation_p.P664T	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	752					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						GAACAAGGAACCTCTGTAAGT	0.527													C|||	10	0.00199681	0.0	0.0043	5008	,	,		21315	0.0		0.007	False		,,,				2504	0.0				p.P752T		Atlas-SNP	.											.	CDHR3	153	.	0			c.C2254A						PASS	.	C	THR/PRO	15,3955		0,15,1970	98.0	94.0	95.0		2254	0.1	0.1	7	dbSNP_132	95	128,8196		0,128,4034	yes	missense	CDHR3	NM_152750.4	38	0,143,6004	AA,AC,CC		1.5377,0.3778,1.1632	benign	752/886	105665004	143,12151	1985	4162	6147	SO:0001583	missense	222256	exon15			AAGGAACCTCTGT	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.2254C>A	7.37:g.105665004C>A	ENSP00000325954:p.Pro752Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	C|C	1.122|1.122	-0.655135|-0.655135	0.03480|0.03480	0.003778|0.003778	0.015377|0.015377	ENSG00000128536|ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080|ENST00000343407;ENST00000466045	T;T;T|T;T	0.56776|0.76448	0.46;0.48;0.44|-1.02;-0.39	5.83|5.83	0.0731|0.0731	0.14389|0.14389	.|.	0.377636|.	0.25698|.	N|.	0.028897|.	T|T	0.45856|0.45856	0.1363|0.1363	L|L	0.31664|0.31664	0.95|0.95	0.09310|0.09310	N|N	1|1	B;B|B	0.06786|0.13145	0.001;0.001|0.007	B;B|B	0.08055|0.11329	0.003;0.003|0.006	T|T	0.47446|0.47446	-0.9117|-0.9117	10|9	0.16420|0.56958	T|D	0.52|0.05	-0.3969|-0.3969	3.7476|3.7476	0.08554|0.08554	0.2276:0.5208:0.1112:0.1405|0.2276:0.5208:0.1112:0.1405	.|.	739;752|252	B3KYA0;Q6ZTQ4|Q6ZTQ4-2	.;CDHR3_HUMAN|.	T|N	752;752;664|254;293	ENSP00000439766:P752T;ENSP00000325954:P752T;ENSP00000417771:P664T|ENSP00000341510:T254N;ENSP00000419017:T293N	ENSP00000325954:P752T|ENSP00000341510:T254N	P|T	+|+	1|2	0|0	CDHR3|CDHR3	105452240|105452240	0.000000|0.000000	0.05858|0.05858	0.071000|0.071000	0.20095|0.20095	0.109000|0.109000	0.19521|0.19521	-0.488000|-0.488000	0.06497|0.06497	0.066000|0.066000	0.16515|0.16515	-0.150000|-0.150000	0.13652|0.13652	CCT|ACC	C|0.995;A|0.005	0.005	strong		0.527	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
TCTE1	202500	hgsc.bcm.edu	37	6	44255459	44255459	+	Missense_Mutation	SNP	G	G	A	rs324146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44255459G>A	ENST00000371505.4	-	2	226	c.104C>T	c.(103-105)cCa>cTa	p.P35L	TMEM151B_ENST00000438774.2_Intron|TCTE1_ENST00000371504.1_5'Flank|TCTE1_ENST00000371503.3_5'UTR|RP11-444E17.6_ENST00000505802.1_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	35			P -> L (in dbSNP:rs324146). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGAGAGCTGTGGGCTTGTGCT	0.552													G|||	3228	0.644569	0.4773	0.8098	5008	,	,		22579	0.6002		0.7843	False		,,,				2504	0.6554				p.P35L		Atlas-SNP	.											.	TCTE1	77	.	0			c.C104T						PASS	.	G	LEU/PRO	2418,1988	617.3+/-392.9	661,1096,446	210.0	145.0	167.0		104	0.6	0.0	6	dbSNP_79	167	6950,1650	740.5+/-407.1	2824,1302,174	yes	missense	TCTE1	NM_182539.3	98	3485,2398,620	AA,AG,GG		19.186,45.1203,27.9717	benign	35/502	44255459	9368,3638	2203	4300	6503	SO:0001583	missense	202500	exon2			AGCTGTGGGCTTG	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.104C>T	6.37:g.44255459G>A	ENSP00000360560:p.Pro35Leu	Somatic	633	1	0.00157978		WXS	Illumina HiSeq	Phase_I	694	377	0.543228	NM_182539	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	37	CCDS4910.1	1474	0.674908424908425	236	0.4796747967479675	295	0.8149171270718232	349	0.6101398601398601	594	0.783641160949868	G	13.55	2.269869	0.40095	0.548797	0.80814	ENSG00000146221	ENST00000371505	T	0.19938	2.11	4.44	0.555	0.17247	.	1.091740	0.07107	N	0.841424	T	0.07908	0.0198	M	0.63428	1.95	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.37407	-0.9707	9	0.59425	D	0.04	-0.7612	3.5257	0.07759	0.1932:0.0:0.4582:0.3486	rs324146;rs577627;rs17857043;rs52811778;rs60042531;rs324146	35	Q5JU00	TCTE1_HUMAN	L	35	ENSP00000360560:P35L	ENSP00000360560:P35L	P	-	2	0	TCTE1	44363437	0.000000	0.05858	0.000000	0.03702	0.474000	0.32979	-0.155000	0.10115	-0.014000	0.14175	0.411000	0.27672	CCA	G|0.304;A|0.696	0.696	strong		0.552	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
SPEF2	79925	hgsc.bcm.edu	37	5	35705844	35705844	+	Missense_Mutation	SNP	A	A	C	rs72738833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:35705844A>C	ENST00000356031.3	+	18	2753	c.2599A>C	c.(2599-2601)Aag>Cag	p.K867Q	SPEF2_ENST00000509059.1_Missense_Mutation_p.K862Q|SPEF2_ENST00000440995.2_Missense_Mutation_p.K862Q|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	867					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGAAATAGATAAGGAATCTTT	0.289													A|||	64	0.0127796	0.0015	0.0331	5008	,	,		14949	0.0		0.0338	False		,,,				2504	0.0051				p.K867Q		Atlas-SNP	.											SPEF2_ENST00000356031,colon,carcinoma,-2,1	SPEF2	324	1	0			c.A2599C						PASS	.	A	GLN/LYS	25,3541		1,23,1759	40.0	35.0	36.0		2599	0.5	0.1	5	dbSNP_130	36	283,7815		5,273,3771	yes	missense	SPEF2	NM_024867.3	53	6,296,5530	CC,CA,AA		3.4947,0.7011,2.6406	benign	867/1823	35705844	308,11356	1783	4049	5832	SO:0001583	missense	79925	exon18			ATAGATAAGGAAT	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"""cancer/testis antigen 122"""	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.2599A>C	5.37:g.35705844A>C	ENSP00000348314:p.Lys867Gln	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	222	132	0.594595	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	40	0.018315018315018316	1	0.0020325203252032522	11	0.03038674033149171	2	0.0034965034965034965	26	0.03430079155672823	A	4.337	0.062014	0.08339	0.007011	0.034947	ENSG00000152582	ENST00000356031;ENST00000509059;ENST00000440995;ENST00000504054	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.77	0.545	0.17190	.	0.361408	0.31697	N	0.007214	T	0.05914	0.0154	L	0.47716	1.5	0.09310	N	0.999999	P;P;B	0.38078	0.483;0.617;0.335	B;B;B	0.31101	0.116;0.124;0.08	T	0.12889	-1.0530	10	0.22706	T	0.39	.	4.5847	0.12277	0.4511:0.3025:0.2464:0.0	.	862;862;867	D6REZ4;Q9C093-2;Q9C093	.;.;SPEF2_HUMAN	Q	867;862;862;373	ENSP00000348314:K867Q;ENSP00000421593:K862Q;ENSP00000412125:K862Q;ENSP00000421744:K373Q	ENSP00000348314:K867Q	K	+	1	0	SPEF2	35741601	0.046000	0.20272	0.066000	0.19879	0.391000	0.30476	0.017000	0.13399	-0.122000	0.11766	0.528000	0.53228	AAG	A|0.974;C|0.026	0.026	strong		0.289	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
USP53	54532	hgsc.bcm.edu	37	4	120214030	120214030	+	Missense_Mutation	SNP	T	T	G	rs3749591	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:120214030T>G	ENST00000274030.6	+	19	4065	c.2886T>G	c.(2884-2886)agT>agG	p.S962R	USP53_ENST00000450251.1_Missense_Mutation_p.S962R	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53									p.S961R(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						CGAAGCACAGTTTAAGTACAG	0.388													T|||	1226	0.244808	0.1195	0.2824	5008	,	,		21325	0.3859		0.3032	False		,,,				2504	0.182				p.S962R		Atlas-SNP	.											USP53,NS,carcinoma,0,1	USP53	69	1	1	Substitution - Missense(1)	stomach(1)	c.T2886G						PASS	.	T	ARG/SER	527,3265		37,453,1406	81.0	73.0	76.0		2886	-1.7	0.0	4	dbSNP_107	76	2598,5662		400,1798,1932	yes	missense	USP53	NM_019050.2	110	437,2251,3338	GG,GT,TT		31.4528,13.8977,25.9293	benign	962/1074	120214030	3125,8927	1896	4130	6026	SO:0001583	missense	54532	exon18			GCACAGTTTAAGT	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"""Ubiquitin-specific peptidases"""	29255	protein-coding gene	gene with protein product			"""ubiquitin specific protease 53"""			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.2886T>G	4.37:g.120214030T>G	ENSP00000274030:p.Ser962Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	37	CCDS43265.1	601	0.2751831501831502	52	0.10569105691056911	87	0.24033149171270718	231	0.40384615384615385	231	0.30474934036939316	T	12.58	1.979529	0.34942	0.138977	0.314528	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.47869	0.83;0.83	5.02	-1.66	0.08265	.	0.901431	0.09698	N	0.767375	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P	0.35433	0.501	B	0.27500	0.08	T	0.34850	-0.9812	9	0.54805	T	0.06	-6.1731	6.3273	0.21251	0.1345:0.43:0.0:0.4356	rs3749591;rs17595370;rs52832840;rs59311247;rs3749591	962	Q70EK8	UBP53_HUMAN	R	962	ENSP00000274030:S962R;ENSP00000409906:S962R	ENSP00000274030:S962R	S	+	3	2	USP53	120433478	0.000000	0.05858	0.000000	0.03702	0.977000	0.68977	-0.174000	0.09839	-0.151000	0.11176	-0.361000	0.07541	AGT	T|0.725;G|0.275	0.275	strong		0.388	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
KCTD9	54793	hgsc.bcm.edu	37	8	25287397	25287397	+	Silent	SNP	T	T	C	rs1812594	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:25287397T>C	ENST00000221200.4	-	12	1366	c.1146A>G	c.(1144-1146)ctA>ctG	p.L382L		NM_017634.3	NP_060104.2	Q7L273	KCTD9_HUMAN	potassium channel tetramerization domain containing 9	382					protein homooligomerization (GO:0051260)					breast(1)|endometrium(2)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	12		all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Epithelial(17;2.39e-12)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0438)		GTGACATGTGTAGTGGTGTCA	0.428													T|||	809	0.161542	0.062	0.1988	5008	,	,		17653	0.2421		0.2167	False		,,,				2504	0.1299				p.L382L		Atlas-SNP	.											.	KCTD9	33	.	0			c.A1146G						PASS	.	T		396,4010	196.4+/-220.7	24,348,1831	136.0	122.0	127.0		1146	-4.8	1.0	8	dbSNP_92	127	1794,6806	322.6+/-315.6	192,1410,2698	no	coding-synonymous	KCTD9	NM_017634.3		216,1758,4529	CC,CT,TT		20.8605,8.9877,16.8384		382/390	25287397	2190,10816	2203	4300	6503	SO:0001819	synonymous_variant	54793	exon12			CATGTGTAGTGGT	BC021216	CCDS6048.1	8p21.1	2013-06-20	2013-06-20		ENSG00000104756	ENSG00000104756		"""BTB/POZ domain containing"""	22401	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 9"""			11483580	Standard	NM_017634		Approved	FLJ20038, BTBD27	uc003xeo.3	Q7L273	OTTHUMG00000099428	ENST00000221200.4:c.1146A>G	8.37:g.25287397T>C		Somatic	591	0	0		WXS	Illumina HiSeq	Phase_I	546	267	0.489011	NM_017634	Q6NUM8|Q9NXV4	Silent	SNP	ENST00000221200.4	37	CCDS6048.1																																																																																			T|0.828;C|0.172	0.172	strong		0.428	KCTD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216890.1	NM_017634	
PSG5	5673	hgsc.bcm.edu	37	19	43680269	43680269	+	Missense_Mutation	SNP	G	G	C	rs1058259	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:43680269G>C	ENST00000366175.3	-	3	592	c.462C>G	c.(460-462)aaC>aaG	p.N154K	PSG5_ENST00000407568.1_Intron|PSG5_ENST00000342951.6_Missense_Mutation_p.N154K|PSG5_ENST00000599812.1_Missense_Mutation_p.N247K|PSG5_ENST00000404580.1_Missense_Mutation_p.N154K|PSG5_ENST00000407356.1_Missense_Mutation_p.N154K			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	154	Ig-like C2-type 1.		N -> K (in dbSNP:rs1058259). {ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2735907}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				GTTTTGAGTTGTTGATGGTGA	0.478													G|||	622	0.124201	0.1702	0.1369	5008	,	,		21803	0.0		0.2614	False		,,,				2504	0.0399				p.N154K		Atlas-SNP	.											.	PSG5	58	.	0			c.C462G						PASS	.	G	LYS/ASN,LYS/ASN	850,3554	333.9+/-303.2	100,650,1452	242.0	225.0	231.0		462,462	1.2	0.0	19	dbSNP_86	231	2225,6365	378.1+/-338.8	338,1549,2408	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	94,94	438,2199,3860	CC,CG,GG		25.9022,19.3006,23.6648	probably-damaging,probably-damaging	154/336,154/336	43680269	3075,9919	2202	4295	6497	SO:0001583	missense	5673	exon3			TGAGTTGTTGATG		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.462C>G	19.37:g.43680269G>C	ENSP00000382334:p.Asn154Lys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	31	0.326316	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	332	0.152014652014652	78	0.15853658536585366	51	0.1408839779005525	0	0.0	203	0.2678100263852243	g	8.010	0.757313	0.15846	0.193006	0.259022	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951;ENST00000404580	T;T;T;T	0.12147	2.71;2.71;2.71;2.71	1.23	1.23	0.21249	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.91920	3.255	0.58432	P	5.999999999950489E-6	B;B	0.27765	0.002;0.188	B;B	0.44108	0.064;0.441	T	0.12041	-1.0563	8	0.66056	D	0.02	.	5.7748	0.18273	0.0:0.0:1.0:0.0	rs1058259;rs1962165;rs3174797;rs4387696;rs11549988;rs1058259	247;154	Q15228;Q15238	.;PSG5_HUMAN	K	154	ENSP00000382334:N154K;ENSP00000386008:N154K;ENSP00000344413:N154K;ENSP00000385250:N154K	ENSP00000344413:N154K	N	-	3	2	PSG5	48372109	0.164000	0.22935	0.030000	0.17652	0.014000	0.08584	1.323000	0.33701	0.630000	0.30394	0.184000	0.17185	AAC	.	.	weak		0.478	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
WSCD2	9671	hgsc.bcm.edu	37	12	108618630	108618630	+	Missense_Mutation	SNP	C	C	T	rs3764002	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:108618630C>T	ENST00000332082.4	+	6	1615	c.797C>T	c.(796-798)aCt>aTt	p.T266I	WSCD2_ENST00000261400.3_Missense_Mutation_p.T266I|WSCD2_ENST00000549903.1_Missense_Mutation_p.T266I|WSCD2_ENST00000547525.1_Missense_Mutation_p.T266I			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	266	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.		T -> I (in dbSNP:rs3764002). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						GACTTCTGCACTGAGAAGGTG	0.592													C|||	1287	0.256989	0.0144	0.1657	5008	,	,		22314	0.5476		0.2594	False		,,,				2504	0.3476				p.T266I		Atlas-SNP	.											.	WSCD2	125	.	0			c.C797T						PASS	.	C	ILE/THR	193,3799		3,187,1806	62.0	61.0	61.0		797	5.4	1.0	12	dbSNP_107	61	2151,6217		310,1531,2343	yes	missense	WSCD2	NM_014653.2	89	313,1718,4149	TT,TC,CC		25.7051,4.8347,18.9644	probably-damaging	266/566	108618630	2344,10016	1996	4184	6180	SO:0001583	missense	9671	exon5			TCTGCACTGAGAA		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.797C>T	12.37:g.108618630C>T	ENSP00000331933:p.Thr266Ile	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	568	0.2600732600732601	8	0.016260162601626018	62	0.1712707182320442	287	0.5017482517482518	211	0.2783641160949868	C	23.7	4.443960	0.83993	0.048347	0.257051	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000551638;ENST00000332082;ENST00000549903	T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51	5.39	5.39	0.77823	Carbohydrate-binding WSC (2);Carbohydrate-binding WSC, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	0.99999999374288	D;D	0.76494	0.997;0.999	D;D	0.85130	0.91;0.997	T	0.48937	-0.8990	9	0.35671	T	0.21	-20.9307	17.8977	0.88893	0.0:1.0:0.0:0.0	rs3764002;rs52812734;rs57199422;rs3764002	266;266	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	I	266;266;113;266;266	ENSP00000448047:T266I;ENSP00000261400:T266I;ENSP00000446744:T113I;ENSP00000331933:T266I;ENSP00000447272:T266I	ENSP00000261400:T266I	T	+	2	0	WSCD2	107142760	1.000000	0.71417	0.967000	0.41034	0.953000	0.61014	7.560000	0.82277	2.804000	0.96469	0.655000	0.94253	ACT	C|0.745;T|0.255	0.255	strong		0.592	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653	
QSOX1	5768	hgsc.bcm.edu	37	1	180148012	180148012	+	Missense_Mutation	SNP	G	G	C	rs17855475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180148012G>C	ENST00000367602.3	+	5	673	c.599G>C	c.(598-600)gGt>gCt	p.G200A	QSOX1_ENST00000367600.5_Missense_Mutation_p.G200A			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	200			G -> A (in dbSNP:rs17855475). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16806532, ECO:0000269|Ref.4}.		cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						TCCTACCTGGGTAGAGAGGTG	0.507											OREG0014018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	497	0.0992412	0.0968	0.1081	5008	,	,		18248	0.003		0.1421	False		,,,				2504	0.1513				p.G200A		Atlas-SNP	.											.	QSOX1	79	.	0			c.G599C						PASS	.	G	ALA/GLY,ALA/GLY	557,3849	249.3+/-256.8	41,475,1687	99.0	104.0	102.0		599,599	5.9	1.0	1	dbSNP_123	102	1365,7235	264.6+/-285.7	119,1127,3054	yes	missense,missense	QSOX1	NM_001004128.2,NM_002826.4	60,60	160,1602,4741	CC,CG,GG		15.8721,12.6419,14.7778	probably-damaging,probably-damaging	200/605,200/748	180148012	1922,11084	2203	4300	6503	SO:0001583	missense	5768	exon5			ACCTGGGTAGAGA	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.599G>C	1.37:g.180148012G>C	ENSP00000356574:p.Gly200Ala	Somatic	100	0	0	1959	WXS	Illumina HiSeq	Phase_I	114	70	0.614035	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Missense_Mutation	SNP	ENST00000367602.3	37	CCDS1337.1	209	0.09569597069597069	48	0.0975609756097561	44	0.12154696132596685	1	0.0017482517482517483	116	0.15303430079155672	G	26.9	4.780744	0.90195	0.126419	0.158721	ENSG00000116260	ENST00000367602;ENST00000367600	T;T	0.07800	3.19;3.16	5.91	5.91	0.95273	.	0.144731	0.64402	D	0.000007	T	0.00144	0.0004	M	0.79805	2.47	0.09310	P	0.99999999989847	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.954	T	0.00044	-1.2222	9	0.38643	T	0.18	-15.3101	17.2153	0.86941	0.0:0.0:1.0:0.0	rs17855475;rs17855475	200;200	O00391;O00391-2	QSOX1_HUMAN;.	A	200	ENSP00000356574:G200A;ENSP00000356572:G200A	ENSP00000356572:G200A	G	+	2	0	QSOX1	178414635	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.654000	0.83653	2.793000	0.96121	0.655000	0.94253	GGT	G|0.866;C|0.134	0.134	strong		0.507	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
CDH15	1013	hgsc.bcm.edu	37	16	89259993	89259993	+	Silent	SNP	A	A	G	rs3815615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:89259993A>G	ENST00000289746.2	+	12	2036	c.1971A>G	c.(1969-1971)caA>caG	p.Q657Q		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	657					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		ACGATGAGCAAGGAGGCGGGG	0.662													G|||	2503	0.4998	0.3389	0.3775	5008	,	,		8160	0.8333		0.4473	False		,,,				2504	0.5143				p.Q657Q		Atlas-SNP	.											.	CDH15	54	.	0			c.A1971G						PASS	.	G		1475,2877		257,961,958	21.0	20.0	21.0		1971	2.5	1.0	16	dbSNP_107	21	3643,4929		816,2011,1459	no	coding-synonymous	CDH15	NM_004933.2		1073,2972,2417	GG,GA,AA		42.4988,33.8925,39.6007		657/815	89259993	5118,7806	2176	4286	6462	SO:0001819	synonymous_variant	1013	exon12			TGAGCAAGGAGGC	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.1971A>G	16.37:g.89259993A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_004933		Silent	SNP	ENST00000289746.2	37	CCDS10976.1																																																																																			A|0.565;G|0.435	0.435	strong		0.662	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
C4B	721	hgsc.bcm.edu	37	6	31996966	31996966	+	Missense_Mutation	SNP	G	G	A	rs2746414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31996966G>A	ENST00000435363.2	+	28	3611	c.3527G>A	c.(3526-3528)aGc>aAc	p.S1176N	C4B_ENST00000425700.2_Missense_Mutation_p.S1176N	NM_001002029.3	NP_001002029.3	P0C0L5	CO4B_HUMAN	complement component 4B (Chido blood group)	1176			S -> N (in allotype C4B1a; dbSNP:rs2746414). {ECO:0000269|PubMed:14989716}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|detection of molecule of bacterial origin (GO:0032490)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|complement binding (GO:0001848)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	TCAAAGGCAAGCTCATTTTTG	0.617																																					p.S1176N		Atlas-SNP	.											.	C4A	15	.	0			c.G3527A						PASS	.						107.0	90.0	95.0					6																	31996966		1559	3552	5111	SO:0001583	missense	720	exon28			AGGCAAGCTCATT	AF019413	CCDS47405.1	6p21.3	2014-09-17	2009-01-06		ENSG00000224389	ENSG00000224389		"""Blood group antigens"", ""Complement system"""	1324	protein-coding gene	gene with protein product		120820	"""complement component 4B"""				Standard	NM_001002029		Approved	CPAMD3, C4F, CO4, C4B1, C4B3, CH	uc011jpm.2	P0C0L5	OTTHUMG00000031187	ENST00000435363.2:c.3527G>A	6.37:g.31996966G>A	ENSP00000415941:p.Ser1176Asn	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	243	75	0.308642	NM_007293	A2BHY4|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q6U2E9|Q6U2G1|Q6U2I5|Q6U2L1|Q6U2L7|Q6U2L9|Q6U2M5|Q6VCV8|Q96SA7|Q9NPK5|Q9UIP5	Missense_Mutation	SNP	ENST00000435363.2	37	CCDS47405.1	183	0.08379120879120878	58	0.11788617886178862	21	0.058011049723756904	37	0.06468531468531469	67	0.08839050131926121	A	0.004	-2.280506	0.00254	.	.	ENSG00000224389	ENST00000435363;ENST00000425700	T;T	0.13657	2.57;2.57	4.66	0.91	0.19337	.	.	.	.	.	T	0.01765	0.0056	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.48822	-0.9001	7	0.16420	T	0.52	.	3.9585	0.09401	0.5167:0.1842:0.2991:0.0	rs17874654;rs60964411	1176;1176	F5GXS0;Q6U2E9	.;.	N	1176	ENSP00000415941:S1176N;ENSP00000391933:S1176N	ENSP00000391933:S1176N	S	+	2	0	C4B	32104944	0.000000	0.05858	0.052000	0.19188	0.150000	0.21749	0.251000	0.18257	-0.086000	0.12550	-1.236000	0.01555	AGC	G|0.716;A|0.284	0.284	strong		0.617	C4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076368.5	NM_001002029	
SLC27A6	28965	hgsc.bcm.edu	37	5	128301971	128301971	+	Silent	SNP	T	T	C	rs2577541	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:128301971T>C	ENST00000262462.4	+	1	1151	c.141T>C	c.(139-141)taT>taC	p.Y47Y	SLC27A6_ENST00000395266.1_Silent_p.Y47Y|SLC27A6_ENST00000506176.1_Silent_p.Y47Y			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	47					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		TGAAGAAGTATGAAAAGAGAG	0.448													C|||	1019	0.203474	0.171	0.255	5008	,	,		20526	0.0585		0.3678	False		,,,				2504	0.1912				p.Y47Y		Atlas-SNP	.											.	SLC27A6	112	.	0			c.T141C						PASS	.	C	,	952,3454	735.5+/-410.7	88,776,1339	123.0	123.0	123.0		141,141	3.5	0.0	5	dbSNP_100	123	3252,5348	649.1+/-400.6	619,2014,1667	no	coding-synonymous,coding-synonymous	SLC27A6	NM_001017372.1,NM_014031.3	,	707,2790,3006	CC,CT,TT		37.814,21.6069,32.3235	,	47/620,47/620	128301971	4204,8802	2203	4300	6503	SO:0001819	synonymous_variant	28965	exon1			GAAGTATGAAAAG	AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"""Acyl-CoA synthetase family"", ""Solute carriers"""	11000	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 2"""	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.141T>C	5.37:g.128301971T>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	199	97	0.487437	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Silent	SNP	ENST00000262462.4	37	CCDS4145.1																																																																																			T|0.719;C|0.281	0.281	strong		0.448	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031	
PCDHA4	56144	hgsc.bcm.edu	37	5	140187102	140187102	+	Silent	SNP	A	A	G	rs3822347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140187102A>G	ENST00000530339.1	+	1	330	c.330A>G	c.(328-330)gtA>gtG	p.V110V	PCDHA4_ENST00000512229.2_Silent_p.V110V|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.V110V|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	110	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTGATCGTAGACAGGCCGC	0.562																																					p.V110V		Atlas-SNP	.											.	PCDHA4	419	.	0			c.A330G						PASS	.						71.0	78.0	75.0					5																	140187102		2203	4298	6501	SO:0001819	synonymous_variant	56144	exon1			GATCGTAGACAGG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.330A>G	5.37:g.140187102A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	162	52	0.320988	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	weak		0.562	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
FOXD4	2298	hgsc.bcm.edu	37	9	116800	116800	+	Nonstop_Mutation	SNP	C	C	G	rs79220013	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:116800C>G	ENST00000382500.2	-	1	1617	c.1320G>C	c.(1318-1320)taG>taC	p.*440Y		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	0					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.*440Y(1)		endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CCACCTGGCTCTAGGAGGGCC	0.642																																					p.X440Y		Atlas-SNP	.											FOXD4_ENST00000382500,NS,carcinoma,0,1	FOXD4	75	1	1	Nonstop extension(1)	large_intestine(1)	c.G1320C						scavenged	.	C	TYR/stop	490,3462		34,422,1520	16.0	20.0	19.0		1320	1.5	0.7	9	dbSNP_131	19	1918,5986		195,1528,2229	no	stop-lost	FOXD4	NM_207305.3		229,1950,3749	GG,GC,CC		24.2662,12.3988,20.3104		440/440	116800	2408,9448	1976	3952	5928	SO:0001578	stop_lost	2298	exon1			CTGGCTCTAGGAG	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.1320G>C	9.37:g.116800C>G		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	227	131	0.577093	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	502	0.22985347985347984	49	0.09959349593495935	69	0.19060773480662985	166	0.2902097902097902	218	0.287598944591029	.	4.305	0.055848	0.08291	0.123988	0.242662	ENSG00000170122	ENST00000382500	.	.	.	2.41	1.47	0.22746	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7839	0.23662	0.0:0.8374:0.0:0.1626	.	.	.	.	Y	440	.	.	X	-	3	2	FOXD4	106800	0.004000	0.15560	0.657000	0.29651	0.049000	0.14656	1.312000	0.33574	1.347000	0.45714	0.473000	0.43528	TAG	C|0.766;G|0.234	0.234	strong		0.642	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
HLA-A	3105	hgsc.bcm.edu	37	6	29913037	29913037	+	Missense_Mutation	SNP	G	G	A	rs1137631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29913037G>A	ENST00000396634.1	+	9	1413	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	HLA-A_ENST00000376806.5_Missense_Mutation_p.V364M|HLA-A_ENST00000376809.5_Missense_Mutation_p.V358M|HLA-A_ENST00000376802.2_Intron			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	358					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GGGCTCTGATGTGTCCCTCAC	0.527									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.V358M		Atlas-SNP	.											HLA-A,caecum,carcinoma,0,1	HLA-A	89	1	0			c.G1072A						PASS	.	G	MET/VAL	921,3485		63,795,1345	112.0	107.0	109.0		1072	0.0	0.0	6	dbSNP_86	109	1247,7353		75,1097,3128	no	missense	HLA-A	NM_002116.7	21	138,1892,4473	AA,AG,GG		14.5,20.9033,16.6692	probably-damaging	358/366	29913037	2168,10838	2203	4300	6503	SO:0001583	missense	3105	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TCTGATGTGTCCC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.1072G>A	6.37:g.29913037G>A	ENSP00000379873:p.Val358Met	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	308	71	0.230519	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	412	0.18864468864468864	131	0.266260162601626	66	0.18232044198895028	101	0.17657342657342656	114	0.1503957783641161	.	4.763	0.141947	0.09083	0.209033	0.145	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809	T;T;T	0.02890	4.12;4.12;4.12	3.32	0.00338	0.14054	MHC class I, alpha chain, C-terminal (2);	1.163110	0.07081	U	0.836996	T	0.07548	0.0190	M	0.89214	3.015	0.80722	P	0.0	B;D;B	0.76494	0.024;0.999;0.024	B;D;B	0.87578	0.114;0.998;0.114	T	0.05517	-1.0880	9	0.87932	D	0	.	5.5556	0.17115	0.0:0.1827:0.3799:0.4374	rs1137631;rs2231120;rs2735100;rs3179375;rs3201428;rs3823341;rs17434512;rs41559513	358;364;358	P13746;Q5SRN5;P04439	1A11_HUMAN;.;1A03_HUMAN	M	358;364;107;358	ENSP00000379873:V358M;ENSP00000366002:V364M;ENSP00000366005:V358M	ENSP00000366002:V364M	V	+	1	0	HLA-A	30021016	0.001000	0.12720	0.000000	0.03702	0.022000	0.10575	-0.040000	0.12104	-0.132000	0.11557	0.485000	0.47835	GTG	G|0.829;A|0.171	0.171	strong		0.527	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CCDC88C	440193	hgsc.bcm.edu	37	14	91883129	91883129	+	Silent	SNP	G	G	A	rs45437097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:91883129G>A	ENST00000389857.6	-	2	200	c.114C>T	c.(112-114)taC>taT	p.Y38Y	CCDC88C_ENST00000554165.1_5'UTR|RP11-895M11.3_ENST00000557524.1_lincRNA|CCDC88C_ENST00000389856.5_Silent_p.Y30Y|CCDC88C_ENST00000553403.1_Silent_p.Y38Y	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	38					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				CTAAATCCATGTACATAGTCA	0.488													G|||	540	0.107827	0.056	0.1297	5008	,	,		19364	0.0228		0.2177	False		,,,				2504	0.137				p.Y38Y		Atlas-SNP	.											.	CCDC88C	192	.	0			c.C114T						PASS	.	G		329,3583		13,303,1640	52.0	51.0	51.0		114	-0.0	1.0	14	dbSNP_127	51	1930,6364		240,1450,2457	no	coding-synonymous	CCDC88C	NM_001080414.3		253,1753,4097	AA,AG,GG		23.2698,8.41,18.5073		38/2029	91883129	2259,9947	1956	4147	6103	SO:0001819	synonymous_variant	440193	exon2			ATCCATGTACATA		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.114C>T	14.37:g.91883129G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	132	57	0.431818	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			G|0.855;A|0.145	0.145	strong		0.488	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
FAT2	2196	hgsc.bcm.edu	37	5	150945483	150945483	+	Missense_Mutation	SNP	C	C	T	rs3734055	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150945483C>T	ENST00000261800.5	-	1	3022	c.3010G>A	c.(3010-3012)Ggt>Agt	p.G1004S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1004	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.		G -> S (in dbSNP:rs3734055).		epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGCCTCCCACCATCACTGGCC	0.597													T|||	2016	0.402556	0.3767	0.4524	5008	,	,		17724	0.3571		0.4901	False		,,,				2504	0.3589				p.G1004S		Atlas-SNP	.											.	FAT2	465	.	0			c.G3010A						PASS	.	T	SER/GLY	1713,2693	641.3+/-397.4	335,1043,825	44.0	37.0	39.0		3010	3.2	1.0	5	dbSNP_107	39	4496,4104	554.9+/-386.6	1181,2134,985	yes	missense	FAT2	NM_001447.2	56	1516,3177,1810	TT,TC,CC		47.7209,38.8788,47.7395	benign	1004/4350	150945483	6209,6797	2203	4300	6503	SO:0001583	missense	2196	exon1			TCCCACCATCACT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3010G>A	5.37:g.150945483C>T	ENSP00000261800:p.Gly1004Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	159	53	0.333333	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	935	0.4281135531135531	204	0.4146341463414634	161	0.4447513812154696	202	0.3531468531468531	368	0.48548812664907653	T	9.338	1.062294	0.19987	0.388788	0.522791	ENSG00000086570	ENST00000261800	T	0.50001	0.76	5.53	3.19	0.36642	Cadherin (4);Cadherin-like (1);	0.327956	0.30464	N	0.009564	T	0.00012	0.0000	L	0.39397	1.21	0.49798	P	1.7800000000001148E-4	B	0.06786	0.001	B	0.12156	0.007	T	0.47535	-0.9110	9	0.06236	T	0.91	.	4.9317	0.13921	0.0:0.3749:0.1616:0.4635	rs3734055;rs52828169;rs3734055	1004	Q9NYQ8	FAT2_HUMAN	S	1004	ENSP00000261800:G1004S	ENSP00000261800:G1004S	G	-	1	0	FAT2	150925676	0.146000	0.22672	0.999000	0.59377	0.963000	0.63663	0.364000	0.20325	0.402000	0.25451	-0.254000	0.11334	GGT	C|0.544;T|0.456	0.456	strong		0.597	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
KHNYN	23351	hgsc.bcm.edu	37	14	24901249	24901249	+	Missense_Mutation	SNP	A	A	C	rs3742520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24901249A>C	ENST00000251343.5	+	3	921	c.782A>C	c.(781-783)aAa>aCa	p.K261T	KHNYN_ENST00000553935.1_Missense_Mutation_p.K261T|KHNYN_ENST00000554268.1_5'Flank|CBLN3_ENST00000555436.1_5'Flank|KHNYN_ENST00000556842.1_Missense_Mutation_p.K261T|CBLN3_ENST00000267406.6_5'Flank			O15037	KHNYN_HUMAN	KH and NYN domain containing	261			K -> T (in dbSNP:rs3742520). {ECO:0000269|PubMed:9205841}.				RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						GAGGGAGGGAAACAGGGTGGT	0.617											OREG0022627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2029	0.405152	0.0552	0.5807	5008	,	,		19821	0.5208		0.5636	False		,,,				2504	0.4714				p.K261T		Atlas-SNP	.											KHNYN,rectum,carcinoma,0,1	KHNYN	46	1	0			c.A782C						PASS	.	A	THR/LYS	573,3833	252.4+/-258.8	39,495,1669	95.0	92.0	93.0		782	2.3	0.0	14	dbSNP_107	93	4661,3939	600.9+/-394.3	1282,2097,921	yes	missense	KHNYN	NM_015299.2	78	1321,2592,2590	CC,CA,AA		45.8023,13.005,40.243	possibly-damaging	261/679	24901249	5234,7772	2203	4300	6503	SO:0001583	missense	23351	exon3			GAGGGAAACAGGG	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.782A>C	14.37:g.24901249A>C	ENSP00000251343:p.Lys261Thr	Somatic	223	0	0	774	WXS	Illumina HiSeq	Phase_I	210	96	0.457143	NM_015299	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	37	CCDS32058.1	979	0.4482600732600733	43	0.08739837398373984	202	0.5580110497237569	301	0.5262237762237763	433	0.5712401055408971	A	5.982	0.365043	0.11296	0.13005	0.541977	ENSG00000100441	ENST00000251343;ENST00000556842;ENST00000553935	T;T;T	0.25414	1.8;1.8;1.8	4.7	2.28	0.28536	.	0.215138	0.14362	U	0.324384	T	0.00012	0.0000	L	0.27053	0.805	0.49915	P	1.6099999999996673E-4	B;B	0.18461	0.028;0.015	B;B	0.12156	0.007;0.007	T	0.39482	-0.9612	9	0.66056	D	0.02	.	3.8544	0.08968	0.711:0.0:0.1029:0.1861	rs3742520;rs57351660;rs3742520	302;261	D3DS77;O15037	.;KHNYN_HUMAN	T	261	ENSP00000251343:K261T;ENSP00000451106:K261T;ENSP00000450799:K261T	ENSP00000251343:K261T	K	+	2	0	KHNYN	23971089	0.887000	0.30362	0.048000	0.18961	0.168000	0.22595	1.941000	0.40233	0.182000	0.20032	0.460000	0.39030	AAA	A|0.599;C|0.401	0.401	strong		0.617	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
CLCA1	1179	hgsc.bcm.edu	37	1	86947975	86947975	+	Silent	SNP	A	A	T	rs1321694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86947975A>T	ENST00000234701.3	+	6	996	c.645A>T	c.(643-645)gtA>gtT	p.V215V	CLCA1_ENST00000394711.1_Silent_p.V215V			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	215					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		TCAATAAAGTAACAGGACTCT	0.398													A|||	1841	0.367612	0.2443	0.2939	5008	,	,		20995	0.505		0.3728	False		,,,				2504	0.4397				p.V215V		Atlas-SNP	.											.	CLCA1	109	.	0			c.A645T						PASS	.	A		1116,3290	398.8+/-331.0	140,836,1227	136.0	123.0	128.0		645	-2.2	0.1	1	dbSNP_88	128	3044,5556	467.7+/-367.1	534,1976,1790	no	coding-synonymous	CLCA1	NM_001285.3		674,2812,3017	TT,TA,AA		35.3953,25.3291,31.9852		215/915	86947975	4160,8846	2203	4300	6503	SO:0001819	synonymous_variant	1179	exon5			TAAAGTAACAGGA		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"""chloride channel, calcium activated, family member 1"", ""chloride channel regulator 1"""			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.645A>T	1.37:g.86947975A>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Silent	SNP	ENST00000234701.3	37	CCDS709.1																																																																																			T|0.353;N|0.000	0.353	strong		0.398	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	
ACAP1	9744	hgsc.bcm.edu	37	17	7245371	7245371	+	Silent	SNP	A	A	G	rs4796407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7245371A>G	ENST00000158762.3	+	3	422	c.216A>G	c.(214-216)ccA>ccG	p.P72P		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	72	BAR.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						TGGGTCCACCAGAGCCCATGA	0.632													A|||	1577	0.314896	0.3669	0.451	5008	,	,		20495	0.0486		0.4076	False		,,,				2504	0.3272				p.P72P		Atlas-SNP	.											.	ACAP1	66	.	0			c.A216G						PASS	.	A		1671,2735	508.1+/-366.9	305,1061,837	87.0	87.0	87.0		216	0.9	1.0	17	dbSNP_111	87	3622,4978	519.9+/-379.6	767,2088,1445	no	coding-synonymous	ACAP1	NM_014716.3		1072,3149,2282	GG,GA,AA		42.1163,37.9256,40.6966		72/741	7245371	5293,7713	2203	4300	6503	SO:0001819	synonymous_variant	9744	exon3			TCCACCAGAGCCC	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.216A>G	17.37:g.7245371A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_014716	Q53XN9	Silent	SNP	ENST00000158762.3	37	CCDS11101.1																																																																																			A|0.642;G|0.358	0.358	strong		0.632	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
ZIM3	114026	hgsc.bcm.edu	37	19	57648277	57648277	+	Missense_Mutation	SNP	A	A	T	rs4801200	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57648277A>T	ENST00000269834.1	-	4	590	c.205T>A	c.(205-207)Ttg>Atg	p.L69M	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		L -> M (in dbSNP:rs4801200).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TCTTCCTCCAACCATGGCTCC	0.517													A|||	2108	0.420927	0.267	0.4755	5008	,	,		18473	0.3621		0.5099	False		,,,				2504	0.5593				p.L69M		Atlas-SNP	.											.	ZIM3	107	.	0			c.T205A						PASS	.	A	MET/LEU	1367,3039	454.2+/-350.6	220,927,1056	284.0	193.0	224.0		205	-4.7	0.0	19	dbSNP_111	224	4554,4046	596.8+/-393.7	1230,2094,976	yes	missense	ZIM3	NM_052882.1	15	1450,3021,2032	TT,TA,AA		47.0465,31.0259,45.5251	benign	69/473	57648277	5921,7085	2203	4300	6503	SO:0001583	missense	114026	exon4			CCTCCAACCATGG	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"""Zinc fingers, C2H2-type"", ""-"""	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.205T>A	19.37:g.57648277A>T	ENSP00000269834:p.Leu69Met	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	258	120	0.465116	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	881	0.4033882783882784	118	0.23983739837398374	183	0.505524861878453	208	0.36363636363636365	372	0.49076517150395776	A	7.413	0.635215	0.14322	0.310259	0.529535	ENSG00000141946	ENST00000269834	T	0.04706	3.57	2.32	-4.65	0.03339	Krueppel-associated box (2);	.	.	.	.	T	0.00012	0.0000	N	0.01284	-0.91	0.80722	P	0.0	P	0.40144	0.704	B	0.35240	0.198	T	0.43702	-0.9375	8	0.02654	T	1	.	3.2755	0.06897	0.4533:0.0:0.1663:0.3804	rs4801200;rs52833722;rs4801200	69	Q96PE6	ZIM3_HUMAN	M	69	ENSP00000269834:L69M	ENSP00000269834:L69M	L	-	1	2	ZIM3	62340089	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.600000	0.02083	-1.311000	0.02309	0.260000	0.18958	TTG	A|0.564;T|0.436	0.436	strong		0.517	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
ALOX12	239	hgsc.bcm.edu	37	17	6905061	6905061	+	Silent	SNP	T	T	G	rs1042357	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6905061T>G	ENST00000251535.6	+	8	1145	c.1092T>G	c.(1090-1092)acT>acG	p.T364T	RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000574377.1_Intron|AC027763.2_ENST00000575727.1_Intron|AC027763.2_ENST00000399540.2_3'UTR	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	364	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						TGCTGAACACTCACCTGGTGG	0.532													T|||	2866	0.572284	0.5643	0.67	5008	,	,		18076	0.5238		0.5974	False		,,,				2504	0.5378				p.T364T		Atlas-SNP	.											.	ALOX12	49	.	0			c.T1092G						PASS	.	T		2496,1910	626.9+/-394.8	705,1086,412	107.0	93.0	97.0		1092	-9.8	0.2	17	dbSNP_86	97	4952,3648	623.8+/-397.5	1427,2098,775	no	coding-synonymous	ALOX12	NM_000697.2		2132,3184,1187	GG,GT,TT		42.4186,43.35,42.7341		364/664	6905061	7448,5558	2203	4300	6503	SO:0001819	synonymous_variant	239	exon8			GAACACTCACCTG	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.1092T>G	17.37:g.6905061T>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_000697	O95569|Q6ISF8|Q9UQM4	Silent	SNP	ENST00000251535.6	37	CCDS11084.1																																																																																			T|0.431;G|0.569	0.569	strong		0.532	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
MCTP1	79772	hgsc.bcm.edu	37	5	94050487	94050487	+	Silent	SNP	T	T	A	rs2636	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94050487T>A	ENST00000515393.1	-	20	2714	c.2715A>T	c.(2713-2715)atA>atT	p.I905I	ANKRD32_ENST00000493934.1_Intron|MCTP1_ENST00000514040.1_5'UTR|MCTP1_ENST00000429576.2_Silent_p.I598I|MCTP1_ENST00000312216.8_Silent_p.I684I|MCTP1_ENST00000505078.1_Silent_p.I421I	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	905					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		CTCACTTCTTTATCCTTTCGC	0.443													T|||	1988	0.396965	0.1853	0.4827	5008	,	,		17048	0.4345		0.4662	False		,,,				2504	0.5123				p.I905I		Atlas-SNP	.											.	MCTP1	110	.	0			c.A2715T						PASS	.	T	,	1030,3376	381.1+/-324.0	107,816,1280	207.0	199.0	201.0		2052,2715	0.1	1.0	5	dbSNP_36	201	3919,4681	547.9+/-385.3	881,2157,1262	no	coding-synonymous,coding-synonymous	MCTP1	NM_001002796.2,NM_024717.4	,	988,2973,2542	AA,AT,TT		45.5698,23.3772,38.0517	,	684/779,905/1000	94050487	4949,8057	2203	4300	6503	SO:0001819	synonymous_variant	79772	exon20			CTTCTTTATCCTT		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2715A>T	5.37:g.94050487T>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	37	CCDS34203.1																																																																																			T|0.597;N|0.000	.	strong		0.443	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	
MYBPHL	343263	hgsc.bcm.edu	37	1	109840169	109840169	+	Missense_Mutation	SNP	C	C	T	rs76186504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109840169C>T	ENST00000357155.1	-	3	354	c.305G>A	c.(304-306)cGg>cAg	p.R102Q	MYBPHL_ENST00000477962.1_Intron	NM_001010985.2|NM_001265613.1	NP_001010985.2|NP_001252542.1	A2RUH7	MBPHL_HUMAN	myosin binding protein H-like	102	Ig-like C2-type 1.									central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(2)	14		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)		CTCCCCATTCCGCACACTCAC	0.592													C|||	26	0.00519169	0.0015	0.0029	5008	,	,		20879	0.0		0.0219	False		,,,				2504	0.0				p.R102Q		Atlas-SNP	.											.	MYBPHL	28	.	0			c.G305A						PASS	.	C	GLN/ARG	24,4382	30.8+/-60.4	0,24,2179	95.0	85.0	88.0		305	3.2	1.0	1	dbSNP_131	88	180,8420	81.5+/-144.1	1,178,4121	yes	missense	MYBPHL	NM_001010985.2	43	1,202,6300	TT,TC,CC		2.093,0.5447,1.5685	possibly-damaging	102/355	109840169	204,12802	2203	4300	6503	SO:0001583	missense	343263	exon3			CCATTCCGCACAC	AK129834	CCDS30793.1	1p13	2013-02-11			ENSG00000221986	ENSG00000221986		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	30434	protein-coding gene	gene with protein product							Standard	NM_001010985		Approved		uc001dxk.1	A2RUH7	OTTHUMG00000012002	ENST00000357155.1:c.305G>A	1.37:g.109840169C>T	ENSP00000349678:p.Arg102Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	121	44	0.363636	NM_001265613	B7ZME5|Q5T2Z7	Missense_Mutation	SNP	ENST00000357155.1	37	CCDS30793.1	14	0.00641025641025641	0	0.0	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	C	18.88	3.718147	0.68844	0.005447	0.02093	ENSG00000221986	ENST00000357155	T	0.66995	-0.24	4.08	3.15	0.36227	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57257	0.2041	M	0.87971	2.92	0.42575	D	0.993196	B;P	0.39094	0.203;0.659	B;B	0.38803	0.031;0.282	T	0.61826	-0.6983	9	0.35671	T	0.21	.	10.526	0.44950	0.0:0.9022:0.0:0.0978	.	102;102	B7ZME5;A2RUH7	.;MBPHL_HUMAN	Q	102	ENSP00000349678:R102Q	ENSP00000349678:R102Q	R	-	2	0	MYBPHL	109641692	1.000000	0.71417	0.988000	0.46212	0.789000	0.44602	4.286000	0.58995	1.301000	0.44836	0.655000	0.94253	CGG	C|0.986;T|0.014	0.014	strong		0.592	MYBPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033197.1	NM_001010985	
HPS4	89781	hgsc.bcm.edu	37	22	26864577	26864577	+	Silent	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26864577G>C	ENST00000398145.2	-	8	1225	c.609C>G	c.(607-609)acC>acG	p.T203T	HPS4_ENST00000398141.1_Silent_p.T198T|HPS4_ENST00000336873.5_Silent_p.T203T|HPS4_ENST00000402105.3_Silent_p.T198T	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	203					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						GCGGGAGTTGGGTGCTGACAA	0.532									Hermansky-Pudlak syndrome																												p.T203T		Atlas-SNP	.											.	HPS4	123	.	0			c.C609G						PASS	.						96.0	77.0	83.0					22																	26864577		2203	4300	6503	SO:0001819	synonymous_variant	89781	exon8	Familial Cancer Database	HPS, HPS1-8	GAGTTGGGTGCTG		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.609C>G	22.37:g.26864577G>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Silent	SNP	ENST00000398145.2	37	CCDS13835.1																																																																																			.	.	none		0.532	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081	
UGT1A7	54577	hgsc.bcm.edu	37	2	234591205	234591205	+	Missense_Mutation	SNP	T	T	C	rs11692021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234591205T>C	ENST00000373426.3	+	1	622	c.622T>C	c.(622-624)Tgg>Cgg	p.W208R	UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A9_ENST00000354728.4_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	208			W -> R (in allele UGT1A7*3 and allele UGT1A7*4; dbSNP:rs11692021). {ECO:0000269|PubMed:11037804, ECO:0000269|PubMed:11434514, ECO:0000269|PubMed:19204906}.		cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	GGAGAGAGTATGGAACCACAT	0.453													T|||	1491	0.297724	0.2496	0.2637	5008	,	,		19491	0.1964		0.3598	False		,,,				2504	0.4274				p.W208R		Atlas-SNP	.											.	UGT1A7	74	.	0			c.T622C	GRCh37	CM004345	UGT1A7	M	rs11692021	PASS	.	T	,,ARG/TRP,	1211,3195	422.5+/-339.8	180,851,1172	176.0	185.0	182.0		,,622,	-8.3	0.0	2	dbSNP_120	182	3331,5269	496.2+/-374.2	653,2025,1622	no	intron,intron,missense,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A9	NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2	,,101,	833,2876,2794	CC,CT,TT		38.7326,27.4852,34.9223	,,,	,,208/531,	234591205	4542,8464	2203	4300	6503	SO:0001583	missense	54577	exon1			AGAGTATGGAACC	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.622T>C	2.37:g.234591205T>C	ENSP00000362525:p.Trp208Arg	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	360	196	0.544444	NM_019077	B8K293|O00473	Missense_Mutation	SNP	ENST00000373426.3	37	CCDS2506.1	636	0.29120879120879123	118	0.23983739837398374	113	0.31215469613259667	130	0.22727272727272727	275	0.3627968337730871	T	0.584	-0.835946	0.02713	0.274852	0.387326	ENSG00000244122	ENST00000373426	T	0.05786	3.39	4.16	-8.32	0.00996	.	.	.	.	.	T	0.00012	0.0000	N	0.20483	0.58	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.32268	-0.9913	8	0.36615	T	0.2	.	3.594	0.08000	0.4615:0.2944:0.1316:0.1125	rs11692021;rs17863779;rs57605148	208;208	Q5DSZ7;Q9HAW7	.;UD17_HUMAN	R	208	ENSP00000362525:W208R	ENSP00000362525:W208R	W	+	1	0	UGT1A7	234255944	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	-4.177000	0.00279	-4.859000	0.00029	-1.814000	0.00607	TGG	T|0.683;C|0.317	0.317	strong		0.453	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
C6orf165	154313	hgsc.bcm.edu	37	6	88173748	88173748	+	Missense_Mutation	SNP	G	G	A	rs139574881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:88173748G>A	ENST00000507897.1	+	13	1732	c.1649G>A	c.(1648-1650)cGc>cAc	p.R550H	C6ORF165_ENST00000369562.4_Missense_Mutation_p.R550H|C6orf165_ENST00000506888.1_3'UTR			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	550										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GCTAATTTGCGCCAGAAAGTT	0.358													.|||	4	0.000798722	0.0008	0.0	5008	,	,		18450	0.003		0.0	False		,,,				2504	0.0				p.R550H		Atlas-SNP	.											.	C6orf165	116	.	0			c.G1649A						PASS	.	G	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	39.0	40.0	40.0		1649	2.1	0.6	6	dbSNP_134	40	13,8587	9.8+/-36.6	0,13,4287	yes	missense	C6orf165	NM_001031743.2	29	0,16,6487	AA,AG,GG		0.1512,0.0681,0.123	possibly-damaging	550/623	88173748	16,12990	2203	4300	6503	SO:0001583	missense	154313	exon13			ATTTGCGCCAGAA	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.1649G>A	6.37:g.88173748G>A	ENSP00000426769:p.Arg550His	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	G	9.169	1.020606	0.19433	6.81E-4	0.001512	ENSG00000213204	ENST00000369562	T	0.38560	1.13	5.78	2.06	0.26882	.	0.152890	0.64402	N	0.000017	T	0.26448	0.0646	M	0.70842	2.15	0.36551	D	0.871855	D	0.57257	0.979	B	0.41666	0.363	T	0.13683	-1.0500	10	0.33940	T	0.23	.	14.1357	0.65287	0.1855:0.0:0.8145:0.0	.	550	Q8IYR0	CF165_HUMAN	H	550	ENSP00000358575:R550H	ENSP00000358575:R550H	R	+	2	0	C6orf165	88230467	0.998000	0.40836	0.619000	0.29118	0.204000	0.24138	2.447000	0.44917	0.089000	0.17243	-1.332000	0.01269	CGC	G|0.999;A|0.001	0.001	strong		0.358	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823	
KANK1	23189	hgsc.bcm.edu	37	9	712156	712156	+	Missense_Mutation	SNP	T	T	G	rs912174	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:712156T>G	ENST00000382303.1	+	7	2042	c.1390T>G	c.(1390-1392)Tcc>Gcc	p.S464A	KANK1_ENST00000382293.3_Missense_Mutation_p.S306A|KANK1_ENST00000382297.2_Missense_Mutation_p.S464A|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	464	Interaction with KIF21A.		S -> A (in dbSNP:rs912174). {ECO:0000269|PubMed:8724849}.		negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.S306A(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GACCATAGAATCCTTGAAGGA	0.473													G|||	1024	0.204473	0.2534	0.3084	5008	,	,		22325	0.1935		0.2137	False		,,,				2504	0.0665				p.S464A		Atlas-SNP	.											KANK1,NS,carcinoma,0,1	KANK1	231	1	1	Substitution - Missense(1)	stomach(1)	c.T1390G						PASS	.	G	ALA/SER,ALA/SER	1123,3283	717.7+/-408.7	143,837,1223	86.0	85.0	85.0		1390,916	5.5	0.9	9	dbSNP_86	85	1920,6680	727.5+/-406.6	234,1452,2614	yes	missense,missense	KANK1	NM_015158.2,NM_153186.3	99,99	377,2289,3837	GG,GT,TT		22.3256,25.488,23.3969	benign,benign	464/1353,306/1195	712156	3043,9963	2203	4300	6503	SO:0001583	missense	23189	exon7			ATAGAATCCTTGA	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1390T>G	9.37:g.712156T>G	ENSP00000371740:p.Ser464Ala	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	473	0.21657509157509158	108	0.21951219512195122	114	0.3149171270718232	96	0.16783216783216784	155	0.20448548812664907	G	3.902	-0.021755	0.07634	0.25488	0.223256	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.32023	1.47;1.47;1.48	5.52	5.52	0.82312	.	0.000000	0.56097	N	0.000029	T	0.00012	0.0000	N	0.00082	-2.215	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41305	-0.9516	9	0.02654	T	1	-14.5643	15.5859	0.76482	0.0:0.0:0.8609:0.1391	rs912174;rs52832305;rs61129314;rs912174	464;464	Q5W0W1;Q14678	.;KANK1_HUMAN	A	464;464;464;306	ENSP00000371740:S464A;ENSP00000371734:S464A;ENSP00000371730:S306A	ENSP00000346479:S464A	S	+	1	0	KANK1	702156	0.997000	0.39634	0.899000	0.35326	0.993000	0.82548	2.358000	0.44134	1.362000	0.46000	-0.121000	0.15023	TCC	T|0.781;G|0.219	0.219	strong		0.473	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
KRT76	51350	hgsc.bcm.edu	37	12	53166603	53166603	+	Silent	SNP	T	T	C	rs61730600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53166603T>C	ENST00000332411.2	-	4	989	c.936A>G	c.(934-936)acA>acG	p.T312T		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	312	Coil 1B.|Rod.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGACTTCATCTGTCAGGCTGT	0.507													T|||	112	0.0223642	0.0333	0.0303	5008	,	,		20414	0.0		0.0358	False		,,,				2504	0.0112				p.T312T		Atlas-SNP	.											.	KRT76	72	.	0			c.A936G						PASS	.	T		164,4242	109.5+/-147.8	6,152,2045	173.0	155.0	161.0		936	-9.2	0.0	12	dbSNP_129	161	326,8274	114.6+/-174.5	7,312,3981	no	coding-synonymous	KRT76	NM_015848.4		13,464,6026	CC,CT,TT		3.7907,3.7222,3.7675		312/639	53166603	490,12516	2203	4300	6503	SO:0001819	synonymous_variant	51350	exon4			TTCATCTGTCAGG	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.936A>G	12.37:g.53166603T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_015848	B4DRR3|Q7Z795	Silent	SNP	ENST00000332411.2	37	CCDS8838.1																																																																																			T|0.962;C|0.038	0.038	strong		0.507	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
RPS6KA2	6196	hgsc.bcm.edu	37	6	167271716	167271716	+	Missense_Mutation	SNP	T	T	C	rs9347162	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167271716T>C	ENST00000507747.1	-	8	465	c.466A>G	c.(466-468)Agc>Ggc	p.S156G	RPS6KA2_ENST00000503859.1_Missense_Mutation_p.E32G|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.E32G																							TGTGGTGGGCTCCACATCCAG	0.458													T|||	3043	0.607628	0.1551	0.732	5008	,	,		16674	0.875		0.7266	False		,,,				2504	0.7331				p.E32G		Atlas-SNP	.											.	RPS6KA2	212	.	0			c.A95G						PASS	.	T	GLY/GLU	1095,3311	391.0+/-327.9	142,811,1250	245.0	188.0	207.0		95	3.6	0.1	6	dbSNP_119	207	6467,2133	714.4+/-406.0	2441,1585,274	yes	missense	RPS6KA2	NM_001006932.1	98	2583,2396,1524	CC,CT,TT		24.8023,24.8525,41.8576	benign	32/742	167271716	7562,5444	2203	4300	6503	SO:0001583	missense	6196	exon2			GTGGGCTCCACAT																												ENST00000507747.1:c.466A>G	6.37:g.167271716T>C	ENSP00000426906:p.Ser156Gly	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	224	221	0.986607	NM_001006932		Missense_Mutation	SNP	ENST00000507747.1	37		1398|1398	0.6401098901098901|0.6401098901098901	64|64	0.13008130081300814|0.13008130081300814	261|261	0.7209944751381215|0.7209944751381215	511|511	0.8933566433566433|0.8933566433566433	562|562	0.741424802110818|0.741424802110818	T|T	6.515|6.515	0.463282|0.463282	0.12402|0.12402	0.248525|0.248525	0.751977|0.751977	ENSG00000071242|ENSG00000249141	ENST00000510118;ENST00000503859;ENST00000506565|ENST00000507747	T;T;T|.	0.70749|.	-0.5;-0.51;-0.38|.	4.74|4.74	3.56|3.56	0.40772|0.40772	.|.	1.018310|.	0.07931|.	U|.	0.977588|.	T|T	0.09555|0.09555	0.0235|0.0235	N|N	0.08118|0.08118	0|0	0.31438|0.31438	P|P	0.672304|0.672304	B;B|.	0.25272|.	0.0;0.122|.	B;B|.	0.22601|.	0.0;0.04|.	T|T	0.20538|0.20538	-1.0272|-1.0272	8|4	.|.	.|.	.|.	.|.	8.3166|8.3166	0.32104|0.32104	0.0:0.0:0.2007:0.7993|0.0:0.0:0.2007:0.7993	rs9347162;rs56893453|rs9347162;rs56893453	32;32|.	F2Z2J1;Q15349-3|.	.;.|.	G|G	32|156	ENSP00000422435:E32G;ENSP00000427015:E32G;ENSP00000425148:E32G|.	.|.	E|S	-|-	2|1	0|0	RPS6KA2|RP11-514O12.4	167191706|167191706	0.813000|0.813000	0.29090|0.29090	0.139000|0.139000	0.22197|0.22197	0.001000|0.001000	0.01503|0.01503	0.970000|0.970000	0.29383|0.29383	0.815000|0.815000	0.34398|0.34398	0.533000|0.533000	0.62120|0.62120	GAG|AGC	T|0.395;C|0.605	0.605	strong		0.458	RP11-514O12.4-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000362905.1		
ACTR8	93973	hgsc.bcm.edu	37	3	53906513	53906513	+	Silent	SNP	G	G	A	rs4687757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:53906513G>A	ENST00000335754.3	-	10	1300	c.1200C>T	c.(1198-1200)atC>atT	p.I400I	ACTR8_ENST00000482349.1_Silent_p.I289I|ACTR8_ENST00000231909.7_Silent_p.I105I|ACTR8_ENST00000488802.1_5'Flank	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	400					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		TCTGTCCAACGATTCCAAAAG	0.448													A|||	3457	0.690296	0.7118	0.6196	5008	,	,		19862	0.9444		0.4513	False		,,,				2504	0.6953				p.I400I		Atlas-SNP	.											.	ACTR8	56	.	0			c.C1200T						PASS	.	A		2956,1450	469.6+/-355.5	990,976,237	170.0	182.0	178.0		1200	-4.7	0.8	3	dbSNP_111	178	3769,4831	615.8+/-396.4	813,2143,1344	no	coding-synonymous	ACTR8	NM_022899.4		1803,3119,1581	AA,AG,GG		43.8256,32.9097,48.2931		400/625	53906513	6725,6281	2203	4300	6503	SO:0001819	synonymous_variant	93973	exon10			TCCAACGATTCCA		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"""INO80 complex subunits"""	14672	protein-coding gene	gene with protein product	"""INO80 complex subunit N"""		"""ARP8 (actin-related protein 8, yeast) homolog"""			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.1200C>T	3.37:g.53906513G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	143	63	0.440559	NM_022899	B3KSW7|Q8N566|Q9H663	Silent	SNP	ENST00000335754.3	37	CCDS2875.1	1452	0.6648351648351648	360	0.7317073170731707	223	0.6160220994475138	541	0.9458041958041958	328	0.43271767810026385	A	3.572	-0.087344	0.07097	0.670903	0.438256	ENSG00000113812	ENST00000486794	.	.	.	5.87	-4.73	0.03259	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.15263	-1.0443	3	.	.	.	-3.0714	15.7232	0.77732	0.3804:0.0:0.6196:0.0	rs4687757;rs17647352;rs17853087;rs56749948;rs4687757	.	.	.	L	154	.	.	S	-	2	0	ACTR8	53881553	0.952000	0.32445	0.754000	0.31244	0.256000	0.26092	0.244000	0.18124	-1.434000	0.01975	-0.972000	0.02603	TCG	G|0.411;A|0.589	0.589	strong		0.448	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899	
PRKCI	5584	hgsc.bcm.edu	37	3	169988286	169988286	+	Silent	SNP	C	C	T	rs56257047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:169988286C>T	ENST00000295797.4	+	6	833	c.528C>T	c.(526-528)ctC>ctT	p.L176L		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	176	Regulatory domain.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	ACTGCAAACTCTTGGTTCATA	0.403													C|||	378	0.0754792	0.0204	0.1225	5008	,	,		19057	0.0645		0.1541	False		,,,				2504	0.047				p.L176L		Atlas-SNP	.											.	PRKCI	82	.	0			c.C528T						PASS	.	C		176,4230	116.3+/-154.2	5,166,2032	115.0	106.0	109.0		528	-3.1	0.6	3	dbSNP_129	109	1299,7301	256.8+/-281.1	102,1095,3103	no	coding-synonymous	PRKCI	NM_002740.5		107,1261,5135	TT,TC,CC		15.1047,3.9946,11.3409		176/597	169988286	1475,11531	2203	4300	6503	SO:0001819	synonymous_variant	5584	exon6			CAAACTCTTGGTT		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.528C>T	3.37:g.169988286C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_002740	D3DNQ4|Q8WW06	Silent	SNP	ENST00000295797.4	37	CCDS3212.2																																																																																			C|0.886;T|0.114	0.114	strong		0.403	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740	
PTBP2	58155	hgsc.bcm.edu	37	1	97272456	97272456	+	Silent	SNP	A	A	G	rs6699932	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:97272456A>G	ENST00000426398.2	+	11	1156	c.1113A>G	c.(1111-1113)ttA>ttG	p.L371L	PTBP2_ENST00000370198.1_Silent_p.L376L|PTBP2_ENST00000394184.3_Silent_p.L387L|PTBP2_ENST00000541987.1_3'UTR|PTBP2_ENST00000370197.1_Silent_p.L376L|PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000609116.1_Silent_p.L371L	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	371	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177)	spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		TGAAGATTTTATACAATAAGA	0.358													G|||	1392	0.277955	0.5408	0.1499	5008	,	,		17431	0.2103		0.2117	False		,,,				2504	0.1513				p.L371L		Atlas-SNP	.											.	PTBP2	62	.	0			c.A1113G						PASS	.	G		2194,2212	590.6+/-387.4	547,1100,556	134.0	132.0	133.0		1113	3.3	1.0	1	dbSNP_116	133	1604,6996	743.0+/-407.2	133,1338,2829	no	coding-synonymous	PTBP2	NM_021190.2		680,2438,3385	GG,GA,AA		18.6512,49.7957,29.2019		371/532	97272456	3798,9208	2203	4300	6503	SO:0001819	synonymous_variant	58155	exon11			GATTTTATACAAT	AB051232	CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1	1p21.3	2013-07-16			ENSG00000117569	ENSG00000117569		"""RNA binding motif (RRM) containing"""	17662	protein-coding gene	gene with protein product		608449				11003644	Standard	XM_005271084		Approved	brPTB, nPTB, PTB, PTBLP	uc001drq.3	Q9UKA9	OTTHUMG00000010685	ENST00000426398.2:c.1113A>G	1.37:g.97272456A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Silent	SNP	ENST00000426398.2	37	CCDS754.1																																																																																			A|0.707;G|0.293	0.293	strong		0.358	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1		
IGSF10	285313	hgsc.bcm.edu	37	3	151154666	151154666	+	Silent	SNP	T	T	C	rs2172250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:151154666T>C	ENST00000282466.3	-	6	7682	c.7683A>G	c.(7681-7683)acA>acG	p.T2561T	IGSF10_ENST00000495443.1_5'UTR|MED12L_ENST00000474524.1_3'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2561	Ig-like C2-type 12.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCATCTCCCATGTGATTTCTG	0.517													C|||	4264	0.851438	0.8563	0.8285	5008	,	,		19464	0.8988		0.8539	False		,,,				2504	0.8098				p.T2561T		Atlas-SNP	.											.	IGSF10	279	.	0			c.A7683G						PASS	.	C	,,	3721,685	290.1+/-280.8	1573,575,55	74.0	68.0	70.0		1764,1620,7683	-9.2	0.5	3	dbSNP_96	70	7288,1312	257.3+/-281.4	3094,1100,106	yes	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	4667,1675,161	CC,CT,TT		15.2558,15.547,15.3545	,,	588/651,540/603,2561/2624	151154666	11009,1997	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			CTCCCATGTGATT	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.7683A>G	3.37:g.151154666T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			T|0.152;C|0.848	0.848	strong		0.517	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
KIF4B	285643	hgsc.bcm.edu	37	5	154395458	154395458	+	Missense_Mutation	SNP	G	G	A	rs17116710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:154395458G>A	ENST00000435029.4	+	1	2199	c.2039G>A	c.(2038-2040)cGt>cAt	p.R680H		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	680	Interaction with PRC1. {ECO:0000250}.		R -> H (in dbSNP:rs17116710). {ECO:0000269|PubMed:16201836}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GAACGAGACCGTAAGAGGCAA	0.428													G|||	896	0.178914	0.115	0.1268	5008	,	,		22477	0.2073		0.1879	False		,,,				2504	0.2638				p.R680H		Atlas-SNP	.											.	KIF4B	307	.	0			c.G2039A						PASS	.	G	HIS/ARG	523,3883	233.6+/-246.7	30,463,1710	125.0	128.0	127.0		2039	2.3	1.0	5	dbSNP_123	127	1573,7027	294.0+/-301.7	146,1281,2873	yes	missense	KIF4B	NM_001099293.1	29	176,1744,4583	AA,AG,GG		18.2907,11.8702,16.1156	probably-damaging	680/1235	154395458	2096,10910	2203	4300	6503	SO:0001583	missense	285643	exon1			GAGACCGTAAGAG	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.2039G>A	5.37:g.154395458G>A	ENSP00000387875:p.Arg680His	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	226	135	0.597345	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	361	0.1652930402930403	76	0.15447154471544716	47	0.1298342541436464	98	0.17132867132867133	140	0.18469656992084432	g	15.98	2.993690	0.54041	0.118702	0.182907	ENSG00000226650	ENST00000435029	T	0.22336	1.96	2.34	2.34	0.29019	.	.	.	.	.	T	0.00144	0.0004	M	0.86343	2.81	0.09310	P	0.999999688988	D	0.89917	1.0	D	0.75020	0.985	T	0.08432	-1.0722	8	0.72032	D	0.01	.	10.3246	0.43785	0.0:0.0:1.0:0.0	rs17116710;rs56483070;rs17116710	680	Q2VIQ3	KIF4B_HUMAN	H	680	ENSP00000387875:R680H	ENSP00000387875:R680H	R	+	2	0	KIF4B	154375651	1.000000	0.71417	0.966000	0.40874	0.758000	0.43043	5.842000	0.69417	1.330000	0.45394	0.563000	0.77884	CGT	G|0.829;A|0.171	0.171	strong		0.428	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
NLRP13	126204	hgsc.bcm.edu	37	19	56423254	56423254	+	Silent	SNP	G	G	A	rs304002	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56423254G>A	ENST00000342929.3	-	5	1928	c.1929C>T	c.(1927-1929)caC>caT	p.H643H	NLRP13_ENST00000588751.1_Silent_p.H643H	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	643							ATP binding (GO:0005524)	p.H643H(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CCTGGGACTCGTGTAGGCAGT	0.423													A|||	2756	0.550319	0.7133	0.366	5008	,	,		20512	0.5526		0.4563	False		,,,				2504	0.5552				p.H643H		Atlas-SNP	.											NLRP13,NS,carcinoma,0,1	NLRP13	220	1	1	Substitution - coding silent(1)	stomach(1)	c.C1929T						PASS	.	A		2963,1443	467.6+/-354.9	991,981,231	103.0	98.0	100.0		1929	-5.0	0.0	19	dbSNP_79	100	3970,4630	601.2+/-394.3	929,2112,1259	no	coding-synonymous	NLRP13	NM_176810.2		1920,3093,1490	AA,AG,GG		46.1628,32.7508,46.6938		643/1044	56423254	6933,6073	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon5			GGACTCGTGTAGG	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.1929C>T	19.37:g.56423254G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	187	94	0.502674	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			G|0.472;A|0.528	0.528	strong		0.423	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
NADSYN1	55191	hgsc.bcm.edu	37	11	71191817	71191817	+	Missense_Mutation	SNP	C	C	T	rs7121106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71191817C>T	ENST00000319023.2	+	11	1078	c.890C>T	c.(889-891)cCc>cTc	p.P297L	NADSYN1_ENST00000539574.1_Missense_Mutation_p.P37L|NADSYN1_ENST00000530055.1_5'UTR|NADSYN1_ENST00000526039.2_3'UTR	NM_018161.4	NP_060631.2	Q6IA69	NADE_HUMAN	NAD synthetase 1	297	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		P -> L (in dbSNP:rs7121106).		NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|NAD+ synthase (glutamine-hydrolyzing) activity (GO:0003952)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	25					L-Glutamine(DB00130)	AGGGCGAGCCCCTACCCCAGA	0.597													C|||	522	0.104233	0.1762	0.0346	5008	,	,		20234	0.0863		0.0646	False		,,,				2504	0.1155				p.P297L	Ovarian(79;763 1781 6490 50276)	Atlas-SNP	.											.	NADSYN1	48	.	0			c.C890T						PASS	.	C	LEU/PRO	601,3799	261.6+/-264.4	45,511,1644	76.0	68.0	71.0		890	5.2	1.0	11	dbSNP_116	71	441,8147	133.3+/-190.8	10,421,3863	yes	missense	NADSYN1	NM_018161.4	98	55,932,5507	TT,TC,CC		5.1351,13.6591,8.0228	benign	297/707	71191817	1042,11946	2200	4294	6494	SO:0001583	missense	55191	exon11			CGAGCCCCTACCC	AB091316	CCDS8201.1	11q13.4	2008-02-05				ENSG00000172890			29832	protein-coding gene	gene with protein product		608285				12547821	Standard	NM_018161		Approved	FLJ10631	uc001oqn.3	Q6IA69		ENST00000319023.2:c.890C>T	11.37:g.71191817C>T	ENSP00000326424:p.Pro297Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	90	56	0.622222	NM_018161	B3KUU4|Q86SN2|Q9HA25|Q9NVM8	Missense_Mutation	SNP	ENST00000319023.2	37	CCDS8201.1	200	0.09157509157509157	80	0.16260162601626016	18	0.049723756906077346	49	0.08566433566433566	53	0.06992084432717678	C	11.70	1.715946	0.30413	0.136591	0.051351	ENSG00000172890	ENST00000319023;ENST00000539574	T;T	0.21932	2.51;1.98	5.18	5.18	0.71444	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (1);	0.062078	0.64402	D	0.000003	T	0.00109	0.0003	M	0.78801	2.425	0.09310	P	0.999999851488	B;B	0.26935	0.164;0.04	B;B	0.23852	0.049;0.04	T	0.05370	-1.0889	9	0.33940	T	0.23	-26.9893	16.1854	0.81948	0.0:1.0:0.0:0.0	rs7121106	37;297	B3KUU4;Q6IA69	.;NADE_HUMAN	L	297;37	ENSP00000326424:P297L;ENSP00000443718:P37L	ENSP00000326424:P297L	P	+	2	0	NADSYN1	70869465	0.892000	0.30473	0.998000	0.56505	0.278000	0.26855	4.228000	0.58619	2.413000	0.81919	0.561000	0.74099	CCC	C|0.919;T|0.081	0.081	strong		0.597	NADSYN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394356.1	NM_018161	
ADAM20	8748	hgsc.bcm.edu	37	14	70990595	70990595	+	Missense_Mutation	SNP	C	C	T	rs143287090	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70990595C>T	ENST00000256389.3	-	2	1274	c.1030G>A	c.(1030-1032)Gat>Aat	p.D344N	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	294	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		TGTGCAACATCATGTTGTAGT	0.363													C|||	9	0.00179712	0.0045	0.0029	5008	,	,		23424	0.0		0.001	False		,,,				2504	0.0				p.D344N		Atlas-SNP	.											.	ADAM20	59	.	0			c.G1030A						PASS	.	C	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	176.0	105.0	129.0		1030	4.5	0.5	14	dbSNP_134	129	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADAM20	NM_003814.4	23	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	probably-damaging	344/777	70990595	3,13003	2203	4300	6503	SO:0001583	missense	8748	exon2			CAACATCATGTTG	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1030G>A	14.37:g.70990595C>T	ENSP00000256389:p.Asp344Asn	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	95	57	0.6	NM_003814	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	18.13	3.554445	0.65425	4.54E-4	1.16E-4	ENSG00000134007	ENST00000256389	T	0.17691	2.26	4.54	4.54	0.55810	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.37577	U	0.002034	T	0.40448	0.1117	M	0.91612	3.225	0.21184	N	0.999767	D	0.71674	0.998	D	0.77004	0.989	T	0.46498	-0.9187	10	0.87932	D	0	.	12.7261	0.57173	0.1646:0.8354:0.0:0.0	.	294	O43506	ADA20_HUMAN	N	344	ENSP00000256389:D344N	ENSP00000256389:D344N	D	-	1	0	ADAM20	70060348	0.965000	0.33210	0.539000	0.28077	0.095000	0.18619	3.277000	0.51654	2.222000	0.72286	0.557000	0.71058	GAT	C|0.998;T|0.002	0.002	strong		0.363	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2		
NLRP13	126204	hgsc.bcm.edu	37	19	56423893	56423893	+	Silent	SNP	G	G	A	rs303998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56423893G>A	ENST00000342929.3	-	5	1289	c.1290C>T	c.(1288-1290)acC>acT	p.T430T	NLRP13_ENST00000588751.1_Silent_p.T430T	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	430	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		AGGAACATACGGTCCAACACA	0.453													G|||	3249	0.648762	0.6853	0.5058	5008	,	,		20553	0.7302		0.5905	False		,,,				2504	0.6769				p.T430T		Atlas-SNP	.											NLRP13,NS,malignant_melanoma,-1,1	NLRP13	220	1	0			c.C1290T						PASS	.	G		2929,1477	678.6+/-403.6	990,949,264	95.0	98.0	97.0		1290	-3.9	0.0	19	dbSNP_79	97	5236,3364	642.6+/-399.8	1599,2038,663	no	coding-synonymous	NLRP13	NM_176810.2		2589,2987,927	AA,AG,GG		39.1163,33.5225,37.2213		430/1044	56423893	8165,4841	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon5			ACATACGGTCCAA	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.1290C>T	19.37:g.56423893G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			G|0.379;A|0.621	0.621	strong		0.453	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
FN3KRP	79672	hgsc.bcm.edu	37	17	80684784	80684784	+	Missense_Mutation	SNP	G	G	A	rs142718764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80684784G>A	ENST00000269373.6	+	6	740	c.667G>A	c.(667-669)Gta>Ata	p.V223I	RP11-388C12.5_ENST00000570919.1_lincRNA|FN3KRP_ENST00000535965.1_Missense_Mutation_p.V173I	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	223							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			GGGTGGAAACGTAGCAGAGGA	0.542													G|||	23	0.00459265	0.0008	0.0101	5008	,	,		18038	0.0		0.0139	False		,,,				2504	0.001				p.V223I		Atlas-SNP	.											FN3KRP,NS,lymphoid_neoplasm,0,2	FN3KRP	31	2	0			c.G667A						PASS	.	G	ILE/VAL	13,4393	20.2+/-43.8	0,13,2190	72.0	76.0	75.0		667	5.8	0.9	17	dbSNP_134	75	170,8430	78.6+/-141.3	2,166,4132	yes	missense	FN3KRP	NM_024619.3	29	2,179,6322	AA,AG,GG		1.9767,0.2951,1.407	probably-damaging	223/310	80684784	183,12823	2203	4300	6503	SO:0001583	missense	79672	exon6			GGAAACGTAGCAG	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.667G>A	17.37:g.80684784G>A	ENSP00000269373:p.Val223Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	137	85	0.620438	NM_024619	Q969F4|Q9H0U7	Missense_Mutation	SNP	ENST00000269373.6	37	CCDS11817.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	17.43	3.388490	0.61956	0.002951	0.019767	ENSG00000141560	ENST00000269373;ENST00000535965	T;T	0.39787	1.06;1.06	5.82	5.82	0.92795	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.27098	0.0664	L	0.58354	1.805	0.80722	D	1	P	0.50943	0.94	B	0.40375	0.327	T	0.15321	-1.0441	10	0.31617	T	0.26	-26.0305	19.6844	0.95976	0.0:0.0:1.0:0.0	.	223	Q9HA64	KT3K_HUMAN	I	223;173	ENSP00000269373:V223I;ENSP00000444994:V173I	ENSP00000269373:V223I	V	+	1	0	FN3KRP	78278073	1.000000	0.71417	0.931000	0.37212	0.091000	0.18340	7.773000	0.85462	2.761000	0.94854	0.655000	0.94253	GTA	G|0.987;A|0.013	0.013	strong		0.542	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619	
EDEM3	80267	hgsc.bcm.edu	37	1	184675814	184675814	+	Silent	SNP	G	G	A	rs1062994	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:184675814G>A	ENST00000318130.8	-	18	2432	c.2166C>T	c.(2164-2166)aaC>aaT	p.N722N	EDEM3_ENST00000367512.3_Silent_p.N679N|EDEM3_ENST00000466392.1_5'UTR	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	722	PA.				cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CATTCTGGATGTTGCGTGCCT	0.428													G|||	1756	0.350639	0.0257	0.3372	5008	,	,		16851	0.5784		0.3708	False		,,,				2504	0.544				p.N722N		Atlas-SNP	.											.	EDEM3	63	.	0			c.C2166T						PASS	.	G		391,4015	197.1+/-221.3	29,333,1841	167.0	118.0	135.0		2166	0.8	1.0	1	dbSNP_86	135	3309,5291	493.0+/-373.5	668,1973,1659	no	coding-synonymous	EDEM3	NM_025191.3		697,2306,3500	AA,AG,GG		38.4767,8.8743,28.4484		722/933	184675814	3700,9306	2203	4300	6503	SO:0001819	synonymous_variant	80267	exon18			CTGGATGTTGCGT	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"""chromosome 1 open reading frame 22"""	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.2166C>T	1.37:g.184675814G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Silent	SNP	ENST00000318130.8	37	CCDS1363.2																																																																																			G|0.693;A|0.307	0.307	strong		0.428	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191	
PABPN1L	390748	hgsc.bcm.edu	37	16	88932857	88932857	+	Missense_Mutation	SNP	T	T	C	rs139390142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88932857T>C	ENST00000419291.2	-	1	169	c.158A>G	c.(157-159)gAg>gGg	p.E53G	PABPN1L_ENST00000378358.4_Missense_Mutation_p.E53G|PABPN1L_ENST00000411789.2_Missense_Mutation_p.E53G|PABPN1L_ENST00000427766.1_Missense_Mutation_p.E53G	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	53						cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						atcctcttcctcctctttctc	0.607													t|||	11	0.00219649	0.0	0.0043	5008	,	,		19104	0.0		0.006	False		,,,				2504	0.002				p.E53G		Atlas-SNP	.											.	PABPN1L	25	.	0			c.A158G						PASS	.	T	GLY/GLU	3,3929		0,3,1963	51.0	57.0	55.0		158	-4.2	0.0	16	dbSNP_134	55	42,7942		0,42,3950	yes	missense	PABPN1L	NM_001080487.2	98	0,45,5913	CC,CT,TT		0.5261,0.0763,0.3776	benign	53/279	88932857	45,11871	1966	3992	5958	SO:0001583	missense	390748	exon1			TCTTCCTCCTCTT		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"""RNA binding motif (RRM) containing"""	37237	protein-coding gene	gene with protein product	"""embryonic poly(A) binding protein 2"""					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.158A>G	16.37:g.88932857T>C	ENSP00000408598:p.Glu53Gly	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_001080487	A1L3B3|A2VDI2	Missense_Mutation	SNP	ENST00000419291.2	37	CCDS45547.2	9	0.004120879120879121	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	5	0.006596306068601583	T	7.862	0.726328	0.15439	7.63E-4	0.005261	ENSG00000205022	ENST00000378358;ENST00000419291;ENST00000427766;ENST00000411789;ENST00000547152	T;T	0.19250	2.16;2.42	3.52	-4.19	0.03835	.	2.185190	0.02057	N	0.050477	T	0.11324	0.0276	N	0.24115	0.695	0.09310	N	1	B;B;B;P	0.46512	0.0;0.0;0.0;0.879	B;B;B;P	0.45998	0.0;0.001;0.0;0.5	T	0.18935	-1.0321	10	0.44086	T	0.13	.	4.3382	0.11097	0.1664:0.4546:0.0:0.379	.	53;53;53;53	A6NDY0;A6NDY0-4;C9JEK9;A6NDY0-2	EPAB2_HUMAN;.;.;.	G	53	ENSP00000367609:E53G;ENSP00000408598:E53G	ENSP00000367609:E53G	E	-	2	0	PABPN1L	87460358	0.314000	0.24563	0.000000	0.03702	0.026000	0.11368	0.515000	0.22801	-0.355000	0.08199	0.172000	0.16884	GAG	T|0.996;C|0.004	0.004	strong		0.607	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	
POTEF	728378	hgsc.bcm.edu	37	2	130877790	130877790	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130877790T>C	ENST00000409914.2	-	3	698	c.299A>G	c.(298-300)aAg>aGg	p.K100R	POTEF_ENST00000361163.4_Missense_Mutation_p.K100R|POTEF_ENST00000357462.5_Missense_Mutation_p.K100R|POTEF_ENST00000360967.5_Missense_Mutation_p.K100R	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	100					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GCAGCACCACTTGCCCATCTT	0.607																																					p.K100R		Atlas-SNP	.											POTEF,colon,carcinoma,-1,4	POTEF	140	4	0			c.A299G						scavenged	.						99.0	124.0	116.0					2																	130877790		2203	4296	6499	SO:0001583	missense	728378	exon3			CACCACTTGCCCA	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.299A>G	2.37:g.130877790T>C	ENSP00000386786:p.Lys100Arg	Somatic	411	0	0		WXS	Illumina HiSeq	Phase_I	506	5	0.00988142	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	10.84	1.462662	0.26248	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.79141	-1.24;-1.24;1.57;1.59	0.562	0.562	0.17290	.	.	.	.	.	T	0.62684	0.2448	L	0.46157	1.445	0.09310	N	1	P	0.42584	0.784	B	0.28638	0.092	T	0.55995	-0.8052	8	0.87932	D	0	.	.	.	.	.	100	A5A3E0	POTEF_HUMAN	R	100	ENSP00000350052:K100R;ENSP00000386786:K100R;ENSP00000354232:K100R;ENSP00000355012:K100R	ENSP00000350052:K100R	K	-	2	0	POTEF	130594260	0.001000	0.12720	0.078000	0.20375	0.098000	0.18820	-0.301000	0.08232	0.493000	0.27837	0.063000	0.15292	AAG	.	.	none		0.607	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
MUC4	4585	hgsc.bcm.edu	37	3	195515340	195515340	+	Silent	SNP	G	G	A	rs79661483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515340G>A	ENST00000463781.3	-	2	3570	c.3111C>T	c.(3109-3111)caC>caT	p.H1037H	MUC4_ENST00000475231.1_Silent_p.H1037H|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	469	Repeat.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGACGTGACCTGTGG	0.572													.|||	1003	0.20028	0.053	0.2075	5008	,	,		16071	0.37		0.2386	False		,,,				2504	0.18				p.H1037H		Atlas-SNP	.											.	MUC4	1505	.	0			c.C3111T						PASS	.						37.0	20.0	25.0					3																	195515340		692	1591	2283	SO:0001819	synonymous_variant	4585	exon2			GGTGACGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3111C>T	3.37:g.195515340G>A		Somatic	485	0	0		WXS	Illumina HiSeq	Phase_I	165	123	0.745455	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.628;A|0.372	0.372	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PELP1	27043	hgsc.bcm.edu	37	17	4576195	4576195	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576195C>T	ENST00000574876.1	-	16	2108	c.2091G>A	c.(2089-2091)tcG>tcA	p.S697S	PELP1_ENST00000301396.4_Silent_p.S841S|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Silent_p.S607S|PELP1_ENST00000572293.1_Silent_p.S747S|PELP1_ENST00000436683.2_Silent_p.S550S			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	697	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						CAGGGCGTGCCGAGGGCACAG	0.677																																					p.S697S		Atlas-SNP	.											PELP1_ENST00000301396,NS,carcinoma,-1,3	PELP1	102	3	0			c.G2091A						PASS	.						32.0	38.0	36.0					17																	4576195		1989	4144	6133	SO:0001819	synonymous_variant	27043	exon16			GCGTGCCGAGGGC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2091G>A	17.37:g.4576195C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	129	19	0.147287	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			.	.	none		0.677	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
Unknown	0	hgsc.bcm.edu	37	7	63680098	63680098	+	IGR	SNP	C	C	T	rs35920205|rs4479992	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:63680098C>T								GUSBP6 (68999 upstream) : ZNF679 (8753 downstream)																							AATCCTTTAACCACTCCTCAA	0.393													.|||	1119	0.223442	0.1551	0.2205	5008	,	,		19859	0.2679		0.2565	False		,,,				2504	0.2382				p.N223N		Atlas-SNP	.											.	.	.	.	0			c.C669T						PASS	.	C		216,1168		24,168,500	42.0	39.0	40.0		669	-0.5	0.0	7	dbSNP_111	40	780,2402		97,586,908	no	coding-synonymous	ZNF735	NM_001159524.1		121,754,1408	TT,TC,CC		24.5129,15.6069,21.8134		223/413	63680098	996,3570	692	1591	2283	SO:0001628	intergenic_variant	730291	exon4			CTTTAACCACTCC																													7.37:g.63680098C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_001159524		Silent	SNP		37																																																																																				C|0.803;T|0.197	0.197	strong	0	0.393								
SDK2	54549	hgsc.bcm.edu	37	17	71410891	71410891	+	Silent	SNP	C	C	T	rs12386051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:71410891C>T	ENST00000392650.3	-	18	2376	c.2376G>A	c.(2374-2376)acG>acA	p.T792T	SDK2_ENST00000388726.3_Silent_p.T792T	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	792					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CCGGAGGGACCGTGGGAACTA	0.612													C|||	1251	0.2498	0.0552	0.2205	5008	,	,		13989	0.4831		0.2495	False		,,,				2504	0.2935				p.T792T		Atlas-SNP	.											SDK2,NS,carcinoma,0,1	SDK2	219	1	0			c.G2376A						PASS	.	C		454,3952	212.5+/-232.4	38,378,1787	65.0	58.0	60.0		2376	-6.6	0.9	17	dbSNP_120	60	1958,6642	344.0+/-325.1	245,1468,2587	yes	coding-synonymous	SDK2	NM_001144952.1		283,1846,4374	TT,TC,CC		22.7674,10.3041,18.5453		792/2173	71410891	2412,10594	2203	4300	6503	SO:0001819	synonymous_variant	54549	exon18			AGGGACCGTGGGA	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.2376G>A	17.37:g.71410891C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1																																																																																			C|0.787;T|0.213	0.213	strong		0.612	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
TIAM1	7074	hgsc.bcm.edu	37	21	32493031	32493031	+	Silent	SNP	A	A	G	rs762194	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:32493031A>G	ENST00000286827.3	-	29	4902	c.4431T>C	c.(4429-4431)ggT>ggC	p.G1477G	TIAM1_ENST00000541036.1_Silent_p.G1417G	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1477					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CAGTGTCCCCACCACCGGGGG	0.567													A|||	2681	0.535343	0.531	0.598	5008	,	,		16126	0.7639		0.4712	False		,,,				2504	0.3272				p.G1477G		Atlas-SNP	.											.	TIAM1	522	.	0			c.T4431C						PASS	.	A		2288,2118	599.7+/-389.3	593,1102,508	64.0	63.0	64.0		4431	2.1	1.0	21	dbSNP_86	64	3950,4650	549.3+/-385.5	877,2196,1227	no	coding-synonymous	TIAM1	NM_003253.2		1470,3298,1735	GG,GA,AA		45.9302,48.0708,47.9625		1477/1592	32493031	6238,6768	2203	4300	6503	SO:0001819	synonymous_variant	7074	exon29			GTCCCCACCACCG		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.4431T>C	21.37:g.32493031A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																			A|0.482;G|0.518	0.518	strong		0.567	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
VARS	7407	hgsc.bcm.edu	37	6	31750509	31750509	+	Missense_Mutation	SNP	G	G	A	rs11531	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31750509G>A	ENST00000375663.3	-	15	2316	c.1876C>T	c.(1876-1878)Ccg>Tcg	p.P626S	VARS_ENST00000444930.2_Intron|VARS_ENST00000482996.1_5'Flank	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	626			P -> S (in dbSNP:rs11531).		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	AGGAAAGGCGGAGGCACATTG	0.627													G|||	269	0.0537141	0.0303	0.0432	5008	,	,		17926	0.121		0.0239	False		,,,				2504	0.0542				p.P626S		Atlas-SNP	.											.	VARS	76	.	0			c.C1876T						PASS	.	G	SER/PRO	93,2929		5,83,1423	38.0	37.0	38.0		1876	4.1	1.0	6	dbSNP_52	38	123,5293		0,123,2585	yes	missense	VARS	NM_006295.2	74	5,206,4008	AA,AG,GG		2.271,3.0774,2.5598	benign	626/1265	31750509	216,8222	1511	2708	4219	SO:0001583	missense	7407	exon15			AAGGCGGAGGCAC	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	12651	protein-coding gene	gene with protein product	"""valine tRNA ligase 1, cytoplasmic"""	192150	"""valyl-tRNA synthetase 2"""	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.1876C>T	6.37:g.31750509G>A	ENSP00000364815:p.Pro626Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	76	0.66087	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	37	CCDS34412.1	90	0.04120879120879121	14	0.028455284552845527	10	0.027624309392265192	51	0.08916083916083917	15	0.01978891820580475	G	14.02	2.409763	0.42715	0.030774	0.02271	ENSG00000204394	ENST00000375663	T	0.27890	1.64	4.92	4.05	0.47172	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.055131	0.64402	D	0.000001	T	0.18635	0.0447	L	0.38692	1.165	0.80722	D	1	P	0.34909	0.475	B	0.44044	0.439	T	0.04440	-1.0951	10	0.49607	T	0.09	-2.1775	11.1361	0.48375	0.0915:0.0:0.9085:0.0	rs11531;rs1135444;rs2273614;rs11540638;rs17207538;rs17354465;rs52832067;rs11531	626	P26640	SYVC_HUMAN	S	626	ENSP00000364815:P626S	ENSP00000364815:P626S	P	-	1	0	VARS	31858488	0.996000	0.38824	0.981000	0.43875	0.455000	0.32408	2.019000	0.41001	1.063000	0.40649	0.563000	0.77884	CCG	G|0.965;A|0.035	0.035	strong		0.627	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295	
TICRR	90381	hgsc.bcm.edu	37	15	90128966	90128966	+	Missense_Mutation	SNP	C	C	T	rs11629584	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90128966C>T	ENST00000268138.7	+	4	1309	c.1204C>T	c.(1204-1206)Cgg>Tgg	p.R402W	TICRR_ENST00000560985.1_Missense_Mutation_p.R401W|RP11-429B14.1_ENST00000559041.1_RNA			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	402			R -> W (in dbSNP:rs11629584).		cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R402W(1)									TGGTGAAGGCCGGCCCCCCAT	0.473													.|||	1811	0.361621	0.2905	0.3775	5008	,	,		17609	0.2331		0.5129	False		,,,				2504	0.4233				p.R402W		Atlas-SNP	.											C15orf42,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.C1204T						PASS	.	T	TRP/ARG	1299,2601		218,863,869	60.0	62.0	62.0		1204	5.2	1.0	15	dbSNP_120	62	4109,4153		1009,2091,1031	yes	missense	C15orf42	NM_152259.3	101	1227,2954,1900	TT,TC,CC		49.7337,33.3077,44.4664	benign	402/1911	90128966	5408,6754	1950	4131	6081	SO:0001583	missense	90381	exon4			GAAGGCCGGCCCC	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.1204C>T	15.37:g.90128966C>T	ENSP00000268138:p.Arg402Trp	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	196	99	0.505102	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	829	0.37957875457875456	134	0.27235772357723576	154	0.425414364640884	151	0.263986013986014	390	0.5145118733509235	T	13.50	2.255768	0.39896	0.333077	0.497337	ENSG00000140534	ENST00000268138	T	0.12465	2.68	5.25	5.25	0.73442	.	0.527164	0.19163	N	0.121136	T	0.00012	0.0000	N	0.00197	-1.87	0.49915	P	1.6099999999996673E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.36768	-0.9734	9	0.32370	T	0.25	-4.9882	9.9354	0.41548	0.0:0.0786:0.0:0.9214	rs11629584;rs59489744;rs11629584	402	Q7Z2Z1	TICRR_HUMAN	W	402	ENSP00000268138:R402W	ENSP00000268138:R402W	R	+	1	2	C15orf42	87929970	0.978000	0.34361	1.000000	0.80357	0.773000	0.43773	1.751000	0.38339	0.937000	0.37394	-0.312000	0.09012	CGG	C|0.601;T|0.399	0.399	strong		0.473	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
TUBA8	51807	hgsc.bcm.edu	37	22	18609703	18609703	+	Missense_Mutation	SNP	C	C	T	rs140202346		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:18609703C>T	ENST00000330423.3	+	4	1031	c.958C>T	c.(958-960)Cgg>Tgg	p.R320W	TUBA8_ENST00000316027.6_Missense_Mutation_p.R254W	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	320					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						CATGCTCTACCGGGGCGACGT	0.562													c|||	1	0.000199681	0.0	0.0	5008	,	,		20392	0.0		0.001	False		,,,				2504	0.0				p.R320W		Atlas-SNP	.											.	TUBA8	36	.	0			c.C958T						PASS	.	C	TRP/ARG,TRP/ARG	2,4404		0,2,2201	99.0	83.0	89.0		760,958	3.5	1.0	22	dbSNP_134	89	3,8597		0,3,4297	yes	missense,missense	TUBA8	NM_001193414.1,NM_018943.2	101,101	0,5,6498	TT,TC,CC		0.0349,0.0454,0.0384	probably-damaging,probably-damaging	254/384,320/450	18609703	5,13001	2203	4300	6503	SO:0001583	missense	51807	exon4			CTCTACCGGGGCG	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"""Tubulins"""	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.958C>T	22.37:g.18609703C>T	ENSP00000333326:p.Arg320Trp	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	174	96	0.551724	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	37	CCDS13751.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	16.41	3.115564	0.56505	4.54E-4	3.49E-4	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	D;D;D	0.84589	-1.87;-1.87;-1.87	5.67	3.48	0.39840	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95853	0.8650	H	0.99815	4.805	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95830	0.8857	10	0.87932	D	0	.	11.9598	0.53001	0.1374:0.7305:0.1321:0.0	.	254;344;320	B3KPW9;C9J2C0;Q9NY65	.;.;TBA8_HUMAN	W	254;320;344	ENSP00000318575:R254W;ENSP00000333326:R320W;ENSP00000412646:R344W	ENSP00000318575:R254W	R	+	1	2	TUBA8	16989703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.755000	0.62198	0.782000	0.33613	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.562	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943	
PLRG1	5356	hgsc.bcm.edu	37	4	155459194	155459194	+	Silent	SNP	A	A	T	rs7668818	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155459194A>T	ENST00000499023.2	-	13	1344	c.1218T>A	c.(1216-1218)atT>atA	p.I406I	PLRG1_ENST00000393905.2_Silent_p.I406I|PLRG1_ENST00000302078.5_Silent_p.I397I	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	406					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				AAAGATTTTGAATGAAACTTC	0.303													A|||	1155	0.230631	0.1498	0.1888	5008	,	,		15715	0.1438		0.325	False		,,,				2504	0.362				p.I406I		Atlas-SNP	.											.	PLRG1	43	.	0			c.T1218A						PASS	.	A	,	776,3624	294.7+/-283.3	70,636,1494	42.0	43.0	43.0		1191,1218	4.5	1.0	4	dbSNP_116	43	2813,5757	430.5+/-356.5	456,1901,1928	no	coding-synonymous,coding-synonymous	PLRG1	NM_001201564.1,NM_002669.3	,	526,2537,3422	TT,TA,AA		32.8238,17.6364,27.6715	,	397/506,406/515	155459194	3589,9381	2200	4285	6485	SO:0001819	synonymous_variant	5356	exon13			ATTTTGAATGAAA	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1218T>A	4.37:g.155459194A>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	213	213	1	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	37	CCDS34083.1																																																																																			A|0.748;T|0.252	0.252	strong		0.303	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
DEFB104A	140596	hgsc.bcm.edu	37	8	7694034	7694034	+	Missense_Mutation	SNP	A	A	G	rs202183310		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:7694034A>G	ENST00000314265.2	+	1	42	c.28A>G	c.(28-30)Att>Gtt	p.I10V		NM_080389.2	NP_525128.2	Q8WTQ1	D104A_HUMAN	defensin, beta 104A	10			I -> V (in dbSNP:rs2680507). {ECO:0000269|PubMed:11481241, ECO:0000269|PubMed:15489334}.		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.I10V(1)		liver(2)|pancreas(1)|skin(1)	4				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		GCTATTAGCCATTTCTCTTCT	0.502																																					p.I10V		Atlas-SNP	.											DEFB104A,NS,other,0,1	.	.	1	1	Substitution - Missense(1)	pancreas(1)	c.A28G						scavenged	.						10.0	11.0	11.0					8																	7694034		2052	4155	6207	SO:0001583	missense	503618	exon1			TTAGCCATTTCTC	AJ314835	CCDS34834.1	8p23.1	2011-03-29	2005-02-25	2005-02-25	ENSG00000176782	ENSG00000176782		"""Defensins, beta"""	18115	protein-coding gene	gene with protein product			"""defensin, beta 104"""	DEFB104			Standard	NM_080389		Approved	DEFB4, DEFB-4		Q8WTQ1	OTTHUMG00000150014	ENST00000314265.2:c.28A>G	8.37:g.7694034A>G	ENSP00000320813:p.Ile10Val	Somatic	2728	3	0.00109971		WXS	Illumina HiSeq	Phase_I	2137	424	0.198409	NM_001040702	Q496I2|Q496I3|Q496I4	Missense_Mutation	SNP	ENST00000314265.2	37	CCDS34834.1	621	0.28434065934065933	42	0.08536585365853659	128	0.35359116022099446	206	0.36013986013986016	245	0.3232189973614776	A	0.670	-0.802337	0.02841	.	.	ENSG00000176782	ENST00000314265	T	0.14144	2.53	1.69	-1.4	0.08968	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47761	-0.9092	5	0.32370	T	0.25	.	1.7865	0.03043	0.5325:0.0:0.1902:0.2773	.	.	.	.	V	10	ENSP00000320813:I10V	ENSP00000320813:I10V	I	+	1	0	DEFB104A	7731444	0.000000	0.05858	0.011000	0.14972	0.076000	0.17211	-0.448000	0.06820	-0.348000	0.08286	-0.641000	0.03968	ATT	A|0.250;G|0.750	0.750	weak		0.502	DEFB104A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315761.1	NM_080389	
SFTPD	6441	hgsc.bcm.edu	37	10	81706324	81706324	+	Missense_Mutation	SNP	A	A	G	rs721917	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:81706324A>G	ENST00000372292.3	-	2	132	c.92T>C	c.(91-93)aTg>aCg	p.M31T		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	31			M -> T (in dbSNP:rs721917). {ECO:0000269|PubMed:1339284, ECO:0000269|PubMed:19100526, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			AGCACTGGGCATTGTTCTGTG	0.617													g|||	2527	0.504593	0.4009	0.379	5008	,	,		20859	0.6151		0.4205	False		,,,				2504	0.7065				p.M31T		Atlas-SNP	.											SFTPD,NS,carcinoma,+1,1	SFTPD	43	1	0			c.T92C	GRCh37	CM021324	SFTPD	M	rs721917	PASS	.	G	THR/MET	1769,2637	643.9+/-397.9	376,1017,810	122.0	102.0	109.0		92	-1.4	0.0	10	dbSNP_86	109	3610,4990	626.4+/-397.8	761,2088,1451	yes	missense	SFTPD	NM_003019.4	81	1137,3105,2261	GG,GA,AA		41.9767,40.1498,41.3578	benign	31/376	81706324	5379,7627	2203	4300	6503	SO:0001583	missense	6441	exon2			CTGGGCATTGTTC	L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"""Collectins"""	10803	protein-coding gene	gene with protein product		178635	"""surfactant, pulmonary-associated protein D"""	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.92T>C	10.37:g.81706324A>G	ENSP00000361366:p.Met31Thr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	180	116	0.644444	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Missense_Mutation	SNP	ENST00000372292.3	37	CCDS7362.1	1021	0.4674908424908425	202	0.4105691056910569	149	0.4116022099447514	357	0.6241258741258742	313	0.4129287598944591	G	7.685	0.689886	0.15039	0.401498	0.419767	ENSG00000133661	ENST00000372292;ENST00000444384	D;D	0.91068	-2.62;-2.78	5.59	-1.35	0.09114	.	1.689840	0.03546	N	0.224694	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25779	-1.0122	9	0.10636	T	0.68	0.1384	6.1062	0.20075	0.576:0.0:0.3085:0.1155	rs721917;rs3750874;rs17887190;rs52794086;rs58664997;rs721917	31	P35247	SFTPD_HUMAN	T	31;44	ENSP00000361366:M31T;ENSP00000394325:M44T	ENSP00000361366:M31T	M	-	2	0	SFTPD	81696304	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.298000	0.08265	-0.475000	0.06852	-1.088000	0.02184	ATG	A|0.559;G|0.441	0.441	strong		0.617	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1		
DAGLB	221955	hgsc.bcm.edu	37	7	6456347	6456347	+	Silent	SNP	G	G	T	rs1055428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6456347G>T	ENST00000297056.6	-	11	1507	c.1338C>A	c.(1336-1338)ggC>ggA	p.G446G	DAGLB_ENST00000436575.1_Silent_p.G405G|DAGLB_ENST00000421761.2_Silent_p.G190G|DAGLB_ENST00000428902.2_Silent_p.G319G|DAGLB_ENST00000425398.2_Silent_p.G317G	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	446					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		CGGCCGCCCCGCCCCCGAGGC	0.637													G|||	761	0.151957	0.0348	0.1744	5008	,	,		14012	0.245		0.2097	False		,,,				2504	0.1391				p.G446G		Atlas-SNP	.											.	DAGLB	74	.	0			c.C1338A						PASS	.	G	,	330,4076	166.9+/-198.0	12,306,1885	35.0	39.0	38.0		951,1338	-9.5	0.0	7	dbSNP_86	38	1860,6740	320.0+/-314.4	222,1416,2662	no	coding-synonymous,coding-synonymous	DAGLB	NM_001142936.1,NM_139179.3	,	234,1722,4547	TT,TG,GG		21.6279,7.4898,16.8384	,	317/544,446/673	6456347	2190,10816	2203	4300	6503	SO:0001819	synonymous_variant	221955	exon11			CGCCCCGCCCCCG	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1338C>A	7.37:g.6456347G>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	52	40	0.769231	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Silent	SNP	ENST00000297056.6	37	CCDS5350.1																																																																																			G|0.843;T|0.157	0.157	strong		0.637	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
FSIP1	161835	hgsc.bcm.edu	37	15	39910404	39910404	+	Missense_Mutation	SNP	G	G	A	rs12908846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:39910404G>A	ENST00000350221.3	-	11	1440	c.1231C>T	c.(1231-1233)Ctt>Ttt	p.L411F		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	411			L -> F (in dbSNP:rs12908846).							NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCATCCAGAAGACACTTTAAC	0.353													G|||	788	0.157348	0.0333	0.1196	5008	,	,		19671	0.2907		0.1471	False		,,,				2504	0.2249				p.L411F		Atlas-SNP	.											.	FSIP1	53	.	0			c.C1231T						PASS	.	G	PHE/LEU	230,4164		3,224,1970	51.0	54.0	53.0		1231	5.1	1.0	15	dbSNP_121	53	1107,7475		65,977,3249	yes	missense	FSIP1	NM_152597.4	22	68,1201,5219	AA,AG,GG		12.8991,5.2344,10.3036	probably-damaging	411/582	39910404	1337,11639	2197	4291	6488	SO:0001583	missense	161835	exon11			CCAGAAGACACTT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1231C>T	15.37:g.39910404G>A	ENSP00000280236:p.Leu411Phe	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	349	0.15979853479853479	16	0.032520325203252036	48	0.13259668508287292	178	0.3111888111888112	107	0.14116094986807387	G	20.4	3.987146	0.74589	0.052344	0.128991	ENSG00000150667	ENST00000350221	T	0.35789	1.29	5.06	5.06	0.68205	.	0.104654	0.38217	N	0.001773	T	0.00012	0.0000	L	0.29908	0.895	0.27465	P	0.9530472	D	0.89917	1.0	D	0.91635	0.999	T	0.18808	-1.0325	8	.	.	.	-7.7703	17.1261	0.86714	0.0:0.0:1.0:0.0	rs12908846;rs59692160;rs12908846	411	Q8NA03	FSIP1_HUMAN	F	411	ENSP00000280236:L411F	.	L	-	1	0	FSIP1	37697696	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.542000	0.67218	2.785000	0.95823	0.655000	0.94253	CTT	G|0.862;A|0.138	0.138	strong		0.353	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
CTNNA2	1496	hgsc.bcm.edu	37	2	80646660	80646660	+	Silent	SNP	C	C	T	rs148134866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:80646660C>T	ENST00000402739.4	+	8	1229	c.1224C>T	c.(1222-1224)agC>agT	p.S408S	CTNNA2_ENST00000496558.1_Silent_p.S408S|CTNNA2_ENST00000541047.1_Silent_p.S408S|CTNNA2_ENST00000361291.4_Silent_p.S442S|CTNNA2_ENST00000540488.1_Silent_p.S408S|CTNNA2_ENST00000466387.1_Silent_p.S408S|CTNNA2_ENST00000343114.3_Silent_p.S87S	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	408					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CTGCAAAGAGCGGAAATGAAA	0.443													C|||	5	0.000998403	0.0023	0.0014	5008	,	,		15925	0.0		0.001	False		,,,				2504	0.0				p.S408S		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C1224T						PASS	.	C	,	27,4035		0,27,2004	117.0	116.0	116.0		1224,1224	-3.1	0.9	2	dbSNP_134	116	4,8432		0,4,4214	no	coding-synonymous,coding-synonymous	CTNNA2	NM_001164883.1,NM_004389.3	,	0,31,6218	TT,TC,CC		0.0474,0.6647,0.248	,	408/861,408/906	80646660	31,12467	2031	4218	6249	SO:0001819	synonymous_variant	1496	exon9			AAAGAGCGGAAAT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1224C>T	2.37:g.80646660C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																				C|0.998;T|0.002	0.002	strong		0.443	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
OR2W3	343171	hgsc.bcm.edu	37	1	248059712	248059712	+	Missense_Mutation	SNP	T	T	C	rs11204546	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248059712T>C	ENST00000360358.3	+	1	824	c.824T>C	c.(823-825)aTg>aCg	p.M275T	OR2W3_ENST00000537741.1_Missense_Mutation_p.M275T	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	275			M -> T (in dbSNP:rs11204546). {ECO:0000269|PubMed:17974005}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			ATGTTCCTCATGCTCTTCTAC	0.527													C|||	2403	0.479832	0.264	0.4568	5008	,	,		20442	0.5903		0.667	False		,,,				2504	0.4816				p.M275T		Atlas-SNP	.											.	OR2W3	113	.	0			c.T824C						PASS	.	C	THR/MET	1578,2828	667.6+/-401.9	287,1004,912	101.0	93.0	96.0		824	5.3	1.0	1	dbSNP_120	96	5617,2983	461.8+/-365.5	1826,1965,509	yes	missense	OR2W3	NM_001001957.2	81	2113,2969,1421	CC,CT,TT		34.686,35.8148,44.6794	benign	275/315	248059712	7195,5811	2203	4300	6503	SO:0001583	missense	343171	exon1			TCCTCATGCTCTT	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.824T>C	1.37:g.248059712T>C	ENSP00000353516:p.Met275Thr	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	256	150	0.585938	NM_001001957	Q6IF06|Q8NG86	Missense_Mutation	SNP	ENST00000360358.3	37	CCDS31099.1	1124	0.5146520146520146	143	0.29065040650406504	170	0.4696132596685083	308	0.5384615384615384	503	0.6635883905013192	C	0.028	-1.352137	0.01256	0.358148	0.65314	ENSG00000238243	ENST00000537741;ENST00000360358	T;T	0.00032	8.88;8.88	5.29	5.29	0.74685	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000007	T	0.00012	0.0000	N	0.00013	-2.94	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.09100	-1.0690	9	0.07325	T	0.83	.	13.2311	0.59945	0.0:0.9226:0.0:0.0774	rs11204546;rs52833163;rs60025695;rs11204546	275	Q7Z3T1	OR2W3_HUMAN	T	275	ENSP00000445853:M275T;ENSP00000353516:M275T	ENSP00000353516:M275T	M	+	2	0	OR2W3	246126335	0.000000	0.05858	0.999000	0.59377	0.383000	0.30230	0.343000	0.19944	1.488000	0.48433	-0.166000	0.13349	ATG	T|0.469;C|0.531	0.531	strong		0.527	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
DEPTOR	64798	hgsc.bcm.edu	37	8	120940652	120940652	+	Silent	SNP	C	C	T	rs16893299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:120940652C>T	ENST00000286234.5	+	2	265	c.135C>T	c.(133-135)caC>caT	p.H45H	DEPTOR_ENST00000523492.1_Intron	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	45	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						TCAGGCTGCACGAAGAAAAGG	0.373													T|||	1246	0.248802	0.379	0.1873	5008	,	,		19141	0.0367		0.2416	False		,,,				2504	0.3425				p.H45H		Atlas-SNP	.											.	DEPTOR	41	.	0			c.C135T						PASS	.	T		1585,2821	666.2+/-401.7	285,1015,903	91.0	93.0	92.0		135	2.3	1.0	8	dbSNP_123	92	2268,6332	708.0+/-405.6	292,1684,2324	no	coding-synonymous	DEPTOR	NM_022783.2		577,2699,3227	TT,TC,CC		26.3721,35.9737,29.6248		45/410	120940652	3853,9153	2203	4300	6503	SO:0001819	synonymous_variant	64798	exon2			GCTGCACGAAGAA		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"""DEP domain containing 6"""	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.135C>T	8.37:g.120940652C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Silent	SNP	ENST00000286234.5	37	CCDS6331.1																																																																																			C|0.743;T|0.257	0.257	strong		0.373	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783	
CCR6	1235	hgsc.bcm.edu	37	6	167550042	167550042	+	Silent	SNP	C	C	T	rs2071171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167550042C>T	ENST00000341935.5	+	3	876	c.324C>T	c.(322-324)acC>acT	p.T108T	CCR6_ENST00000349984.4_Silent_p.T108T|RP11-517H2.6_ENST00000609590.1_RNA|CCR6_ENST00000400926.2_Silent_p.T108T	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	108					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		GTCATGCCACCGGTGCGTGGG	0.498													C|||	2794	0.557907	0.4092	0.7075	5008	,	,		23045	0.5437		0.6203	False		,,,				2504	0.6033				p.T108T		Atlas-SNP	.											.	CCR6	36	.	0			c.C324T						PASS	.	C	,	1918,2488	546.9+/-377.1	407,1104,692	127.0	128.0	128.0		324,324	-9.7	0.0	6	dbSNP_96	128	5388,3212	651.2+/-400.8	1681,2026,593	no	coding-synonymous,coding-synonymous	CCR6	NM_004367.5,NM_031409.3	,	2088,3130,1285	TT,TC,CC		37.3488,43.5315,43.8259	,	108/375,108/375	167550042	7306,5700	2203	4300	6503	SO:0001819	synonymous_variant	1235	exon3			TGCCACCGGTGCG	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.324C>T	6.37:g.167550042C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_004367	E1P5C6|P78553|Q92846	Silent	SNP	ENST00000341935.5	37	CCDS5298.1																																																																																			C|0.443;T|0.557	0.557	strong		0.498	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1		
SRMS	6725	hgsc.bcm.edu	37	20	62173562	62173562	+	Silent	SNP	G	G	T	rs56130722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62173562G>T	ENST00000217188.1	-	5	940	c.900C>A	c.(898-900)atC>atA	p.I300I		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	300	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			GTTCCGTGACGATGTACACAG	0.672													G|||	1853	0.370008	0.0144	0.4784	5008	,	,		16702	0.9603		0.2167	False		,,,				2504	0.3231				p.I300I		Atlas-SNP	.											SRMS,caecum,carcinoma,0,1	SRMS	48	1	0			c.C900A						PASS	.	G		246,4154	141.9+/-177.2	6,234,1960	98.0	77.0	84.0		900	-0.2	1.0	20	dbSNP_129	84	1891,6709	336.0+/-321.7	213,1465,2622	no	coding-synonymous	SRMS	NM_080823.2		219,1699,4582	TT,TG,GG		21.9884,5.5909,16.4385		300/489	62173562	2137,10863	2200	4300	6500	SO:0001819	synonymous_variant	6725	exon5			CGTGACGATGTAC		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.900C>A	20.37:g.62173562G>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	193	98	0.507772	NM_080823		Silent	SNP	ENST00000217188.1	37	CCDS13525.1																																																																																			G|0.767;T|0.233	0.233	strong		0.672	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
OR51B4	79339	hgsc.bcm.edu	37	11	5322520	5322520	+	Silent	SNP	G	G	A	rs12283334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5322520G>A	ENST00000380224.1	-	1	706	c.657C>T	c.(655-657)ctC>ctT	p.L219L	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	219					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCACTGTCTTGAGGATTAGTA	0.373													G|||	986	0.196885	0.1354	0.2651	5008	,	,		21963	0.1458		0.2565	False		,,,				2504	0.2229				p.L219L		Atlas-SNP	.											.	OR51B4	64	.	0			c.C657T						PASS	.	G		631,3771	272.5+/-270.8	48,535,1618	72.0	69.0	70.0		657	-8.8	0.0	11	dbSNP_120	70	2408,6186	399.7+/-346.5	328,1752,2217	no	coding-synonymous	OR51B4	NM_033179.2		376,2287,3835	AA,AG,GG		28.0195,14.3344,23.3841		219/311	5322520	3039,9957	2201	4297	6498	SO:0001819	synonymous_variant	79339	exon1			TGTCTTGAGGATT	BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"""GPCR / Class A : Olfactory receptors"""	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.657C>T	11.37:g.5322520G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_033179	A7MAV5|Q6NTD7	Silent	SNP	ENST00000380224.1	37	CCDS7757.1																																																																																			G|0.775;A|0.225	0.225	strong		0.373	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179	
SMARCC2	6601	hgsc.bcm.edu	37	12	56559415	56559415	+	Silent	SNP	C	C	T	rs116595430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56559415C>T	ENST00000267064.4	-	26	2912	c.2826G>A	c.(2824-2826)gcG>gcA	p.A942A	SMARCC2_ENST00000394023.3_Silent_p.A973A|SMARCC2_ENST00000550164.1_Silent_p.A973A|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Silent_p.A973A	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	942				A -> P (in Ref. 1; AAC50694). {ECO:0000305}.	ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CCCTCATCTCCGCATACTTCA	0.587													C|||	26	0.00519169	0.0159	0.0072	5008	,	,		17950	0.0		0.0	False		,,,				2504	0.0				p.A973A		Atlas-SNP	.											.	SMARCC2	212	.	0			c.G2919A						PASS	.	C	,,	36,4370	40.8+/-73.8	1,34,2168	53.0	56.0	55.0		2919,2826,2919	-8.5	0.1	12	dbSNP_132	55	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	SMARCC2	NM_001130420.1,NM_003075.3,NM_139067.2	,,	1,41,6461	TT,TC,CC		0.0814,0.8171,0.3306	,,	973/1153,942/1215,973/1131	56559415	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	6601	exon27			CATCTCCGCATAC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.2826G>A	12.37:g.56559415C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Silent	SNP	ENST00000267064.4	37	CCDS8907.1																																																																																			C|0.996;T|0.004	0.004	strong		0.587	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
TCHH	7062	hgsc.bcm.edu	37	1	152083325	152083325	+	Missense_Mutation	SNP	A	A	T	rs11803731	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152083325A>T	ENST00000368804.1	-	2	2367	c.2368T>A	c.(2368-2370)Ttg>Atg	p.L790M		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	790			L -> M (in dbSNP:rs11803731).		keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCTCCCGCAATGGGGGCCTG	0.692													a|||	364	0.0726837	0.0045	0.0937	5008	,	,		13411	0.001		0.2286	False		,,,				2504	0.0634				p.L790M		Atlas-SNP	.											.	TCHH	275	.	0			c.T2368A						PASS	.		MET/LEU	145,3885		1,143,1871	24.0	30.0	28.0	http://omim.org/entry/139450|http://www.ncbi.nlm.nih.gov/pubmed?term	2368	-0.6	0.0	1	dbSNP_120	28	1494,6884		131,1232,2826	yes	missense	TCHH	NM_007113.2	15	132,1375,4697	TT,TA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	17.8324,3.598,13.2092	probably-damaging	790/1944	152083325	1639,10769	2015	4189	6204	SO:0001583	missense	7062	exon3			CCCGCAATGGGGG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.2368T>A	1.37:g.152083325A>T	ENSP00000357794:p.Leu790Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	222	0.10164835164835165	3	0.006097560975609756	51	0.1408839779005525	1	0.0017482517482517483	167	0.22031662269129287	a	0.520	-0.862595	0.02610	0.03598	0.178324	ENSG00000159450	ENST00000368804	T	0.08370	3.1	2.41	-0.583	0.11706	.	.	.	.	.	T	0.02929	0.0087	N	0.24115	0.695	0.80722	P	0.0	D	0.61080	0.989	P	0.53912	0.737	T	0.35624	-0.9781	8	0.51188	T	0.08	1.1016	1.5277	0.02529	0.4732:0.0:0.2233:0.3034	rs11803731;rs11803731	790	Q07283	TRHY_HUMAN	M	790	ENSP00000357794:L790M	ENSP00000357794:L790M	L	-	1	2	TCHH	150349949	0.000000	0.05858	0.003000	0.11579	0.034000	0.12701	-0.142000	0.10311	0.140000	0.18849	0.255000	0.18592	TTG	A|0.890;T|0.110	0.110	strong		0.692	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
FAM19A1	407738	hgsc.bcm.edu	37	3	68588002	68588002	+	Missense_Mutation	SNP	G	G	A	rs372722058		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:68588002G>A	ENST00000478136.1	+	4	845	c.355G>A	c.(355-357)Gca>Aca	p.A119T	FAM19A1_ENST00000496687.1_Missense_Mutation_p.A119T	NM_213609.3	NP_998774.2	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A1	119						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	7		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		ATGGATGTGCGCAACAGGCAA	0.428																																					p.A119T		Atlas-SNP	.											FAM19A1_ENST00000478136,colon,carcinoma,0,2	FAM19A1	58	2	0			c.G355A						scavenged	.	G	THR/ALA	0,3948		0,0,1974	127.0	126.0	127.0		355	4.1	0.6	3		127	2,8334		0,2,4166	no	missense	FAM19A1	NM_213609.2	58	0,2,6140	AA,AG,GG		0.024,0.0,0.0163	benign	119/134	68588002	2,12282	1974	4168	6142	SO:0001583	missense	407738	exon4			ATGTGCGCAACAG	AY325114	CCDS54606.1	3p14.1	2005-01-20			ENSG00000183662	ENSG00000183662			21587	protein-coding gene	gene with protein product						15028294	Standard	NM_213609		Approved	TAFA-1	uc003dnd.3	Q7Z5A9	OTTHUMG00000158745	ENST00000478136.1:c.355G>A	3.37:g.68588002G>A	ENSP00000418575:p.Ala119Thr	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	193	2	0.0103627	NM_213609	A8K0V3|Q8TCL8	Missense_Mutation	SNP	ENST00000478136.1	37	CCDS54606.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.915580	0.33815	0.0	2.4E-4	ENSG00000183662	ENST00000478136;ENST00000496687	.	.	.	5.01	4.13	0.48395	.	0.235146	0.45126	D	0.000387	T	0.16171	0.0389	N	0.11064	0.09	0.29503	N	0.854808	P	0.43750	0.816	B	0.32533	0.147	T	0.07966	-1.0745	9	0.10636	T	0.68	.	15.1166	0.72407	0.0:0.0:0.8572:0.1427	.	119	Q7Z5A9	F19A1_HUMAN	T	119	.	ENSP00000418575:A119T	A	+	1	0	FAM19A1	68670692	1.000000	0.71417	0.554000	0.28268	0.836000	0.47400	5.993000	0.70616	1.217000	0.43442	-0.175000	0.13238	GCA	.	.	weak		0.428	FAM19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352004.1	NM_213609	
MUC4	4585	hgsc.bcm.edu	37	3	195508500	195508500	+	Missense_Mutation	SNP	G	G	C	rs374619108		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508500G>C	ENST00000463781.3	-	2	10410	c.9951C>G	c.(9949-9951)gaC>gaG	p.D3317E	MUC4_ENST00000475231.1_Missense_Mutation_p.D3317E|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.D3317E(2)|p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)|p.S3317R(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGCGTCGGTGACAA	0.577																																					p.D3317E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,6	MUC4	1505	6	5	Substitution - Missense(3)|Deletion - In frame(2)	stomach(4)|kidney(1)	c.C9951G						scavenged	.						9.0	12.0	11.0					3																	195508500		600	1514	2114	SO:0001583	missense	4585	exon2			GGAAGCGTCGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9951C>G	3.37:g.195508500G>C	ENSP00000417498:p.Asp3317Glu	Somatic	105	6	0.0571429		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.278	0.419423	0.11928	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30981	1.61;1.51	0.423	0.423	0.16463	.	.	.	.	.	T	0.14141	0.0342	N	0.19112	0.55	0.09310	N	1	P	0.43352	0.804	B	0.33196	0.159	T	0.14144	-1.0483	7	.	.	.	.	.	.	.	.	3189	E7ESK3	.	E	3317	ENSP00000417498:D3317E;ENSP00000420243:D3317E	.	D	-	3	2	MUC4	196993279	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.672000	0.25187	0.494000	0.27859	0.089000	0.15464	GAC	.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
VPS54	51542	hgsc.bcm.edu	37	2	64124722	64124722	+	Missense_Mutation	SNP	C	C	A	rs11558741	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:64124722C>A	ENST00000272322.4	-	22	2890	c.2736G>T	c.(2734-2736)atG>atT	p.M912I	VPS54_ENST00000354504.3_Missense_Mutation_p.M759I|VPS54_ENST00000409558.4_Missense_Mutation_p.M900I			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	912			M -> I (in dbSNP:rs11558741).		growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						TTAAAAATAACATCTGAAAAA	0.254													C|||	691	0.137979	0.1611	0.1441	5008	,	,		16567	0.0813		0.164	False		,,,				2504	0.1339				p.M912I		Atlas-SNP	.											.	VPS54	57	.	0			c.G2736T						PASS	.	C	ILE/MET,ILE/MET	600,3794		38,524,1635	53.0	55.0	54.0		2700,2736	4.7	1.0	2	dbSNP_120	54	1292,7294		118,1056,3119	yes	missense,missense	VPS54	NM_001005739.1,NM_016516.2	10,10	156,1580,4754	AA,AC,CC		15.0478,13.655,14.5763	benign,benign	900/966,912/978	64124722	1892,11088	2197	4293	6490	SO:0001583	missense	51542	exon22			AAATAACATCTGA	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 164"""	614633	"""vacuolar protein sorting 54 (yeast)"""			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.2736G>T	2.37:g.64124722C>A	ENSP00000272322:p.Met912Ile	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	37	CCDS33208.1	328	0.15018315018315018	96	0.1951219512195122	45	0.12430939226519337	54	0.0944055944055944	133	0.17546174142480211	C	13.89	2.373226	0.42105	0.13655	0.150478	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T;T	0.33438	1.41;1.42;1.42	5.58	4.69	0.59074	.	0.038119	0.85682	D	0.000000	T	0.00039	0.0001	L	0.47716	1.5	0.21652	P	0.999607941	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.08055	0.001;0.0;0.003	T	0.10753	-1.0616	9	0.21540	T	0.41	.	9.7045	0.40207	0.1378:0.7903:0.0:0.072	rs11558741;rs17619976;rs60970434;rs17619976	759;912;900	Q9P1Q0-3;Q9P1Q0;Q9P1Q0-4	.;VPS54_HUMAN;.	I	759;912;900;900;912	ENSP00000346499:M759I;ENSP00000272322:M912I;ENSP00000386980:M900I	ENSP00000272322:M912I	M	-	3	0	VPS54	63978226	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.329000	0.52060	2.611000	0.88343	0.543000	0.68304	ATG	T|0.031;G|0.176	.	strong		0.254	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516	
SALL2	6297	hgsc.bcm.edu	37	14	21993638	21993638	+	Missense_Mutation	SNP	G	G	C	rs2242527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21993638G>C	ENST00000327430.3	-	2	518	c.224C>G	c.(223-225)tCt>tGt	p.S75C	SALL2_ENST00000450879.2_Missense_Mutation_p.S73C|SALL2_ENST00000538754.1_Missense_Mutation_p.S73C|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000317492.5_Missense_Mutation_p.S75C	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	75			S -> C (in dbSNP:rs2242527).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GGAGGCCGAAGAGTTGTTGGG	0.557													G|||	368	0.0734824	0.118	0.0576	5008	,	,		12336	0.0069		0.1153	False		,,,				2504	0.0501				p.S75C		Atlas-SNP	.											.	SALL2	95	.	0			c.C224G						PASS	.	G	CYS/SER	492,3914	229.1+/-243.8	31,430,1742	86.0	84.0	85.0		224	4.4	1.0	14	dbSNP_98	85	959,7641	209.4+/-250.6	47,865,3388	yes	missense	SALL2	NM_005407.1	112	78,1295,5130	CC,CG,GG		11.1512,11.1666,11.1564	probably-damaging	75/1008	21993638	1451,11555	2203	4300	6503	SO:0001583	missense	6297	exon2			GCCGAAGAGTTGT	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"""Zinc fingers, C2H2-type"""	10526	protein-coding gene	gene with protein product		602219	"""sal (Drosophila)-like 2"", ""sal-like 2 (Drosophila)"""			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.224C>G	14.37:g.21993638G>C	ENSP00000333537:p.Ser75Cys	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	264	124	0.469697	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Missense_Mutation	SNP	ENST00000327430.3	37	CCDS32045.1	172|172	0.07875457875457875|0.07875457875457875	52|52	0.10569105691056911|0.10569105691056911	24|24	0.06629834254143646|0.06629834254143646	4|4	0.006993006993006993|0.006993006993006993	92|92	0.12137203166226913|0.12137203166226913	G|G	14.69|14.69	2.610559|2.610559	0.46527|0.46527	0.111666|0.111666	0.111512|0.111512	ENSG00000165821|ENSG00000165821	ENST00000546363|ENST00000327430;ENST00000317492;ENST00000538754;ENST00000450879;ENST00000541876;ENST00000537235;ENST00000541965	.|T;T;T;T;T;T	.|0.44083	.|3.55;1.3;1.16;3.36;1.23;0.93	4.36|4.36	4.36|4.36	0.52297|0.52297	.|.	.|0.000000	.|0.38548	.|N	.|0.001650	T|T	0.01124|0.01124	0.0037|0.0037	L|L	0.55481|0.55481	1.735|1.735	0.45378|0.45378	P|P	0.0016359999999999708|0.0016359999999999708	.|D;D;D;D;D;D	.|0.89917	.|0.999;0.999;0.999;0.999;1.0;0.997	.|P;P;P;D;D;P	.|0.81914	.|0.908;0.908;0.908;0.995;0.991;0.887	T|T	0.33033|0.33033	-0.9884|-0.9884	4|9	.|0.66056	.|D	.|0.02	-13.033|-13.033	8.149|8.149	0.31130|0.31130	0.1078:0.0:0.8922:0.0|0.1078:0.0:0.8922:0.0	rs2242527;rs52815753;rs2242527|rs2242527;rs52815753;rs2242527	.|73;73;73;75;73;75	.|B4DK65;E7EW59;B4DFD9;F5GY43;Q8N656;Q9Y467	.|.;.;.;.;.;SALL2_HUMAN	V|C	69|75;75;73;73;75;73;13	.|ENSP00000333537:S75C;ENSP00000320536:S75C;ENSP00000445916:S73C;ENSP00000396773:S73C;ENSP00000438493:S73C;ENSP00000439654:S13C	.|ENSP00000320536:S75C	L|S	-|-	1|2	0|0	SALL2|SALL2	21063478|21063478	0.456000|0.456000	0.25744|0.25744	0.992000|0.992000	0.48379|0.48379	0.785000|0.785000	0.44390|0.44390	2.781000|2.781000	0.47750|0.47750	2.296000|2.296000	0.77279|0.77279	0.558000|0.558000	0.71614|0.71614	CTT|TCT	G|0.901;C|0.099	0.099	strong		0.557	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407	
USP10	9100	hgsc.bcm.edu	37	16	84796603	84796603	+	Silent	SNP	A	A	G	rs12932018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84796603A>G	ENST00000219473.7	+	9	1676	c.1563A>G	c.(1561-1563)caA>caG	p.Q521Q	USP10_ENST00000570191.1_Silent_p.Q525Q	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	521	USP.				autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						AGGGTCGACAAGAAGATGCTG	0.413													A|||	1315	0.26258	0.053	0.428	5008	,	,		19120	0.4087		0.2525	False		,,,				2504	0.2883				p.Q525Q		Atlas-SNP	.											.	USP10	51	.	0			c.A1575G						PASS	.	A		339,3455		5,329,1563	149.0	135.0	140.0		1563	-5.3	0.9	16	dbSNP_121	140	2207,6047		302,1603,2222	no	coding-synonymous	USP10	NM_005153.2		307,1932,3785	GG,GA,AA		26.7386,8.9352,21.1321		521/799	84796603	2546,9502	1897	4127	6024	SO:0001819	synonymous_variant	9100	exon10			TCGACAAGAAGAT	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.1563A>G	16.37:g.84796603A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			A|0.752;G|0.248	0.248	strong		0.413	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
ATP11A	23250	hgsc.bcm.edu	37	13	113481088	113481088	+	Silent	SNP	C	C	T	rs144248225	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:113481088C>T	ENST00000487903.1	+	12	1192	c.1104C>T	c.(1102-1104)gtC>gtT	p.V368V	ATP11A_ENST00000283558.8_Silent_p.V368V|ATP11A_ENST00000375630.2_Silent_p.V368V|ATP11A_ENST00000375645.3_Silent_p.V368V			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	368					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				ACGTCACGGTCGAGATGCAGA	0.542													C|||	15	0.00299521	0.0	0.0014	5008	,	,		22879	0.0		0.0109	False		,,,				2504	0.0031				p.V368V		Atlas-SNP	.											.	ATP11A	225	.	0			c.C1104T						PASS	.	C	,	13,4393	20.2+/-43.8	0,13,2190	142.0	123.0	129.0		1104,1104	-3.5	0.7	13	dbSNP_134	129	116,8484	61.3+/-123.2	0,116,4184	yes	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	0,129,6374	TT,TC,CC		1.3488,0.2951,0.9918	,	368/1135,368/1192	113481088	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	23250	exon12			CACGGTCGAGATG	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.1104C>T	13.37:g.113481088C>T		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	329	151	0.458967	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	C	2.788	-0.252040	0.05829	0.002951	0.013488	ENSG00000068650	ENST00000418678	.	.	.	5.37	-3.46	0.04767	.	.	.	.	.	T	0.38665	0.1049	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39881	-0.9592	4	.	.	.	.	4.6871	0.12762	0.1916:0.379:0.3387:0.0907	.	.	.	.	L	343	.	.	S	+	2	0	ATP11A	112529089	0.988000	0.35896	0.674000	0.29902	0.147000	0.21601	0.128000	0.15810	-0.335000	0.08451	-0.321000	0.08615	TCG	C|0.990;T|0.010	0.010	strong		0.542	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
PDPR	55066	hgsc.bcm.edu	37	16	70190570	70190570	+	Missense_Mutation	SNP	C	C	T	rs141395281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70190570C>T	ENST00000288050.4	+	19	3385	c.2428C>T	c.(2428-2430)Cgc>Tgc	p.R810C	PDPR_ENST00000542659.1_Missense_Mutation_p.R155C|RP11-296I10.3_ENST00000502126.1_RNA|RP11-296I10.3_ENST00000566989.1_RNA|PDPR_ENST00000398122.3_Missense_Mutation_p.R710C|PDPR_ENST00000567046.1_Missense_Mutation_p.R168C|PDPR_ENST00000568530.1_Missense_Mutation_p.R810C|PDPR_ENST00000562100.1_3'UTR	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	810					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		CAGCCTGGAGCGCCACGTTTG	0.537													C|||	21	0.00419329	0.0045	0.0058	5008	,	,		30988	0.0		0.006	False		,,,				2504	0.0051				p.R810C		Atlas-SNP	.											.	PDPR	66	.	0			c.C2428T						PASS	.	C	CYS/ARG	13,4167		0,13,2077	181.0	201.0	195.0		2428	6.0	1.0	16	dbSNP_134	195	58,8394		0,58,4168	yes	missense	PDPR	NM_017990.3	180	0,71,6245	TT,TC,CC		0.6862,0.311,0.5621	probably-damaging	810/880	70190570	71,12561	2090	4226	6316	SO:0001583	missense	55066	exon19			CTGGAGCGCCACG		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.2428C>T	16.37:g.70190570C>T	ENSP00000288050:p.Arg810Cys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	191	50	0.26178	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	13	0.005952380952380952	6	0.012195121951219513	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	12.41	1.928284	0.34002	0.00311	0.006862	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055;ENST00000542659	T;T;T	0.78364	-1.17;-1.17;-1.17	6.03	6.03	0.97812	Glycine cleavage T-protein, C-terminal barrel (1);	0.060606	0.64402	D	0.000002	T	0.73869	0.3642	N	0.17474	0.49	0.80722	D	1	D;B	0.89917	1.0;0.344	D;B	0.83275	0.996;0.108	T	0.78802	-0.2061	10	0.52906	T	0.07	.	14.4057	0.67081	0.1473:0.8526:0.0:0.0	.	477;810	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	C	810;710;477;155	ENSP00000288050:R810C;ENSP00000381190:R710C;ENSP00000441690:R155C	ENSP00000205055:R477C	R	+	1	0	PDPR	68748071	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	4.681000	0.61663	2.868000	0.98415	0.557000	0.71058	CGC	C|0.993;T|0.007	0.007	strong		0.537	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
OR2T4	127074	hgsc.bcm.edu	37	1	248525193	248525193	+	Missense_Mutation	SNP	C	C	T	rs28655275	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248525193C>T	ENST00000366475.1	+	1	311	c.311C>T	c.(310-312)gCg>gTg	p.A104V		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATGGACATGGCGTACATTTCT	0.498																																					p.A104V		Atlas-SNP	.											OR2T4,NS,carcinoma,-1,2	OR2T4	126	2	0			c.C311T						PASS	.	T	VAL/ALA	130,4276	811.1+/-416.0	3,124,2076	316.0	232.0	260.0		311	-3.2	0.2	1	dbSNP_125	260	1067,7529	759.6+/-407.6	51,965,3282	no	missense	OR2T4	NM_001004696.1	64	54,1089,5358	TT,TC,CC		12.4128,2.9505,9.2063	benign	104/349	248525193	1197,11805	2203	4298	6501	SO:0001583	missense	127074	exon1			ACATGGCGTACAT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.311C>T	1.37:g.248525193C>T	ENSP00000355431:p.Ala104Val	Somatic	1096	0	0		WXS	Illumina HiSeq	Phase_I	750	314	0.418667	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	440	0.20146520146520147	7	0.014227642276422764	74	0.20441988950276244	221	0.38636363636363635	138	0.1820580474934037	T	9.915	1.210607	0.22289	0.029505	0.124128	ENSG00000196944	ENST00000366475	T	0.78924	-1.22	3.48	-3.16	0.05217	GPCR, rhodopsin-like superfamily (1);	0.368836	0.23365	N	0.048969	T	0.00012	0.0000	N	0.10972	0.075	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28586	-1.0039	9	0.42905	T	0.14	.	6.5165	0.22250	0.0:0.3:0.2192:0.4808	rs28655275	104	Q8NH00	OR2T4_HUMAN	V	104	ENSP00000355431:A104V	ENSP00000355431:A104V	A	+	2	0	OR2T4	246591816	0.147000	0.22687	0.163000	0.22734	0.796000	0.44982	1.283000	0.33237	-0.481000	0.06792	-1.330000	0.01273	GCG	.	.	weak		0.498	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
FAM186A	121006	hgsc.bcm.edu	37	12	50745791	50745791	+	Silent	SNP	C	C	G	rs144970699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745791C>G	ENST00000327337.5	-	4	4823	c.4824G>C	c.(4822-4824)gcG>gcC	p.A1608A	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Silent_p.A1608A	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1608								p.A1608A(1)									CCTGAGCCTGCGCCTGCTGAG	0.672													c|||	2059	0.411142	0.3669	0.4611	5008	,	,		20931	0.4692		0.4404	False		,,,				2504	0.3456				p.A1608A	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - coding silent(1)	stomach(1)	c.G4824C						scavenged	.						9.0	9.0	9.0					12																	50745791		689	1587	2276	SO:0001819	synonymous_variant	121006	exon4			AGCCTGCGCCTGC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4824G>C	12.37:g.50745791C>G		Somatic	172	2	0.0116279		WXS	Illumina HiSeq	Phase_I	243	80	0.329218	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			C|0.737;G|0.263	0.263	strong		0.672	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
TSHZ1	10194	hgsc.bcm.edu	37	18	72999359	72999359	+	Missense_Mutation	SNP	T	T	C	rs55679337	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72999359T>C	ENST00000580243.1	+	2	2345	c.1997T>C	c.(1996-1998)cTg>cCg	p.L666P	TSHZ1_ENST00000322038.5_Missense_Mutation_p.L621P			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	666			L -> P (in dbSNP:rs55679337).		anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		AAGAGCTCCCTGGCCAAGGCT	0.557													C|||	1233	0.246206	0.1415	0.317	5008	,	,		19251	0.1726		0.3499	False		,,,				2504	0.3067				p.L621P		Atlas-SNP	.											.	TSHZ1	104	.	0			c.T1862C						PASS	.	C	PRO/LEU	734,3672	755.7+/-412.6	61,612,1530	97.0	86.0	89.0		1862	5.2	0.0	18	dbSNP_129	89	2862,5738	670.7+/-402.8	487,1888,1925	yes	missense	TSHZ1	NM_005786.4	98	548,2500,3455	CC,CT,TT		33.2791,16.6591,27.6488	benign	621/1033	72999359	3596,9410	2203	4300	6503	SO:0001583	missense	10194	exon2			GCTCCCTGGCCAA	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1997T>C	18.37:g.72999359T>C	ENSP00000464391:p.Leu666Pro	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	77	52	0.675325	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		560	0.2564102564102564	73	0.1483739837398374	132	0.36464088397790057	93	0.16258741258741258	262	0.34564643799472294	C	2.991	-0.208265	0.06180	0.166591	0.332791	ENSG00000179981	ENST00000322038	T	0.36878	1.23	5.22	5.22	0.72569	.	0.263906	0.33959	N	0.004384	T	0.00012	0.0000	N	0.00583	-1.355	0.51012	P	9.80000000000425E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.51919	-0.8644	9	0.31617	T	0.26	-23.6505	14.0235	0.64571	0.0:0.9269:0.0:0.0731	rs55679337	666	Q6ZSZ6	TSH1_HUMAN	P	621	ENSP00000323584:L621P	ENSP00000323584:L621P	L	+	2	0	TSHZ1	71128347	0.956000	0.32656	0.025000	0.17156	0.018000	0.09664	3.627000	0.54252	-1.181000	0.02730	-0.258000	0.10820	CTG	A|0.000;C|0.274;G|0.000;T|0.725	0.274	strong		0.557	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
MAMSTR	284358	hgsc.bcm.edu	37	19	49218111	49218111	+	Silent	SNP	G	G	T	rs33988101	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49218111G>T	ENST00000318083.6	-	6	543	c.480C>A	c.(478-480)ccC>ccA	p.P160P	MAMSTR_ENST00000377367.3_Silent_p.P57P|MAMSTR_ENST00000594582.1_Silent_p.P57P|MAMSTR_ENST00000356751.4_Silent_p.P57P|MAMSTR_ENST00000419611.1_Silent_p.P57P			Q6ZN01	MASTR_HUMAN	MEF2 activating motif and SAP domain containing transcriptional regulator	160	Pro-rich.				positive regulation of myotube differentiation (GO:0010831)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)			endometrium(1)|ovary(1)	2						TGTGTGGGGGGGGCGAGGGGC	0.587													G|||	1150	0.229633	0.152	0.3098	5008	,	,		13351	0.0208		0.492	False		,,,				2504	0.2229				p.P160P		Atlas-SNP	.											.	MAMSTR	36	.	0			c.C480A						PASS	.	G	,	963,3443	362.4+/-316.1	112,739,1352	65.0	67.0	67.0		480,171	-1.7	0.0	19	dbSNP_126	67	4531,4069	593.7+/-393.2	1185,2161,954	no	coding-synonymous,coding-synonymous	MAMSTR	NM_001130915.1,NM_182574.2	,	1297,2900,2306	TT,TG,GG		47.314,21.8566,42.242	,	160/416,57/313	49218111	5494,7512	2203	4300	6503	SO:0001819	synonymous_variant	284358	exon6			TGGGGGGGGCGAG	AK093389	CCDS12730.1, CCDS46137.1, CCDS74415.1	19q13.33	2009-07-09			ENSG00000176909	ENSG00000176909			26689	protein-coding gene	gene with protein product	"""MEF2-activating SAP transcriptional regulator"""	610349				16818234	Standard	NM_182574		Approved	MASTR, FLJ36070	uc002pkg.2	Q6ZN01		ENST00000318083.6:c.480C>A	19.37:g.49218111G>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	141	85	0.602837	NM_001130915	B7ZKX4|Q3KQU9|Q8N9Y3	Silent	SNP	ENST00000318083.6	37	CCDS46137.1																																																																																			G|0.621;T|0.379	0.379	strong		0.587	MAMSTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466179.1	NM_182574	
GPR153	387509	hgsc.bcm.edu	37	1	6313938	6313938	+	Missense_Mutation	SNP	C	C	T	rs12735670	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:6313938C>T	ENST00000377893.2	-	3	885	c.626G>A	c.(625-627)cGc>cAc	p.R209H		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	209			R -> H (in dbSNP:rs12735670). {ECO:0000269|PubMed:12679517, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		GAAGGCGCGGCGGTCGGCCTG	0.701													C|||	3501	0.699081	0.702	0.7939	5008	,	,		17470	0.6131		0.7117	False		,,,				2504	0.7035				p.R209H		Atlas-SNP	.											.	GPR153	44	.	0			c.G626A						PASS	.						31.0	33.0	32.0					1																	6313938		2199	4295	6494	SO:0001583	missense	387509	exon3			GCGCGGCGGTCGG	AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"""GPCR / Class A : Orphans"""	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.626G>A	1.37:g.6313938C>T	ENSP00000367125:p.Arg209His	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Missense_Mutation	SNP	ENST00000377893.2	37	CCDS64.1	1502	0.6877289377289377	339	0.6890243902439024	279	0.7707182320441989	338	0.5909090909090909	546	0.7203166226912929	C	5.326	0.245509	0.10077	.	.	ENSG00000158292	ENST00000377893	T	0.42513	0.97	4.9	2.03	0.26663	GPCR, rhodopsin-like superfamily (1);	0.292679	0.37095	N	0.002257	T	0.00012	0.0000	N	0.14661	0.345	0.32111	P	0.589358	B	0.15141	0.012	B	0.14578	0.011	T	0.26916	-1.0089	9	0.20046	T	0.44	-31.5101	7.4677	0.27330	0.0:0.5669:0.0:0.4331	rs12735670;rs58824924	209	Q6NV75	GP153_HUMAN	H	209	ENSP00000367125:R209H	ENSP00000367125:R209H	R	-	2	0	GPR153	6236525	0.995000	0.38212	0.331000	0.25455	0.025000	0.11179	0.366000	0.20365	0.147000	0.19030	-0.448000	0.05591	CGC	C|0.308;T|0.692	0.692	strong		0.701	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2		
SULT1A1	6817	hgsc.bcm.edu	37	16	28619920	28619920	+	Silent	SNP	A	A	G	rs1126446	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28619920A>G	ENST00000395607.1	-	3	426	c.153T>C	c.(151-153)acT>acC	p.T51T	SULT1A1_ENST00000395609.1_Silent_p.T51T|SULT1A1_ENST00000350842.4_Intron|SULT1A1_ENST00000569554.1_Silent_p.T51T|SULT1A1_ENST00000314752.7_Silent_p.T51T	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	51					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.T51T(1)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	TTACCCAGGTAGTGCCTGGAG	0.622													.|||	1456	0.290735	0.2292	0.4769	5008	,	,		24362	0.2669		0.335	False		,,,				2504	0.2209				p.T51T		Atlas-SNP	.											SULT1A1,caecum,carcinoma,-2,2	SULT1A1	53	2	1	Substitution - coding silent(1)	stomach(1)	c.T153C						scavenged	.	G	,,,,	856,3538		132,592,1473	101.0	71.0	81.0		153,153,153,153,	1.3	1.0	16	dbSNP_86	81	2798,5802		611,1576,2113	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	SULT1A1	NM_001055.3,NM_177529.2,NM_177530.2,NM_177534.2,NM_177536.3	,,,,	743,2168,3586	GG,GA,AA		32.5349,19.4811,28.1207	,,,,	51/296,51/296,51/296,51/296,	28619920	3654,9340	2197	4300	6497	SO:0001819	synonymous_variant	6817	exon2			CCAGGTAGTGCCT	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.153T>C	16.37:g.28619920A>G		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	642	185	0.288162	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Silent	SNP	ENST00000395607.1	37	CCDS32420.1																																																																																			A|0.735;G|0.265	0.265	strong		0.622	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
GALP	85569	hgsc.bcm.edu	37	19	56694505	56694505	+	Splice_Site	SNP	C	C	T	rs575756	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56694505C>T	ENST00000357330.2	+	5	301	c.219C>T	c.(217-219)gaC>gaT	p.D73D	GALP_ENST00000440823.1_3'UTR	NM_033106.3	NP_149097.1	Q9UBC7	GALP_HUMAN	galanin-like peptide	73					behavioral response to starvation (GO:0042595)|defense response to bacterium (GO:0042742)|neuropeptide signaling pathway (GO:0007218)|regulation of appetite (GO:0032098)|response to insulin (GO:0032868)	extracellular region (GO:0005576)				lung(4)	4		Colorectal(82;0.000147)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0507)		tgtttctAGACGGGCTCCCCT	0.488													C|||	1575	0.314497	0.1369	0.3617	5008	,	,		18590	0.3383		0.3529	False		,,,				2504	0.4571				p.D73D		Atlas-SNP	.											.	GALP	13	.	0			c.C219T						PASS	.	C	,	811,3595	324.8+/-298.8	96,619,1488	118.0	104.0	109.0		,219	-1.4	0.1	19	dbSNP_83	109	3287,5313	491.7+/-373.1	642,2003,1655	yes	utr-3,coding-synonymous-near-splice	GALP	NM_001145546.1,NM_033106.3	,	738,2622,3143	TT,TC,CC		38.2209,18.4067,31.5085	,	,73/117	56694505	4098,8908	2203	4300	6503	SO:0001630	splice_region_variant	85569	exon5			TCTAGACGGGCTC	AF188493	CCDS12940.1, CCDS46202.1	19q13.42	2013-02-26	2007-08-24			ENSG00000197487		"""Endogenous ligands"""	24840	protein-coding gene	gene with protein product		611178				10601261	Standard	NM_033106		Approved		uc002qmo.1	Q9UBC7		ENST00000357330.2:c.218-1C>T	19.37:g.56694505C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	258	116	0.449612	NM_033106	A1KXL3	Silent	SNP	ENST00000357330.2	37	CCDS12940.1																																																																																			C|0.685;N|0.001	.	strong		0.488	GALP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457832.1	NM_033106	Silent
SYT14	255928	hgsc.bcm.edu	37	1	210273710	210273710	+	Silent	SNP	A	A	G	rs376509952		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:210273710A>G	ENST00000472886.1	+	6	1082	c.1068A>G	c.(1066-1068)gaA>gaG	p.E356E	SYT14_ENST00000271745.7_Intron|SYT14_ENST00000367015.1_Silent_p.E318E|SYT14_ENST00000422431.1_Silent_p.E401E|SYT14_ENST00000367019.1_Silent_p.E356E|SYT14_ENST00000537238.1_Silent_p.E318E|SYT14_ENST00000534859.1_Silent_p.E356E|SYT14_ENST00000399639.2_Silent_p.E356E			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	356	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		TGAAAAAAGAAAAGATTGTGG	0.318													A|||	1	0.000199681	0.0	0.0	5008	,	,		19378	0.0		0.001	False		,,,				2504	0.0				p.E401E		Atlas-SNP	.											SYT14,NS,carcinoma,+2,1	SYT14	89	1	0			c.A1203G						scavenged	.	A	,,,	0,4406		0,0,2203	44.0	46.0	46.0		1203,1068,1203,1068	4.9	1.0	1		46	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYT14	NM_001146261.1,NM_001146262.1,NM_001146264.1,NM_153262.2	,,,	0,3,6500	GG,GA,AA		0.0349,0.0,0.0231	,,,	401/620,356/575,401/601,356/556	210273710	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	255928	exon7			AAAAGAAAAGATT	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"""Synaptotagmins"""	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.1068A>G	1.37:g.210273710A>G		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	272	4	0.0147059	NM_001146264	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Silent	SNP	ENST00000472886.1	37	CCDS31014.1																																																																																			.	.	none		0.318	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262	
ZNF587	84914	hgsc.bcm.edu	37	19	58370727	58370727	+	Missense_Mutation	SNP	T	T	G	rs77825740	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58370727T>G	ENST00000339656.5	+	3	1129	c.947T>G	c.(946-948)cTt>cGt	p.L316R	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000595295.1_Intron|ZNF587_ENST00000423137.1_Missense_Mutation_p.L315R|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF587_ENST00000419854.1_Missense_Mutation_p.L273R	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	316					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		AGCCATCAGCTTGTTCACACT	0.468													.|||	1445	0.288538	0.2421	0.3775	5008	,	,		19061	0.4087		0.2803	False		,,,				2504	0.1728				p.L316R	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.T947G						PASS	.						110.0	139.0	129.0					19																	58370727		2203	4300	6503	SO:0001583	missense	84914	exon3			ATCAGCTTGTTCA	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.947T>G	19.37:g.58370727T>G	ENSP00000345479:p.Leu316Arg	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	245	88	0.359184	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Missense_Mutation	SNP	ENST00000339656.5	37	CCDS12964.1	675	0.3090659340659341	103	0.20934959349593496	119	0.3287292817679558	263	0.4597902097902098	190	0.25065963060686014	.	0.001	-2.984521	0.00046	.	.	ENSG00000198466	ENST00000376209;ENST00000423137;ENST00000339656;ENST00000540851;ENST00000419854	T;T;T	0.12255	2.7;2.7;2.7	1.83	0.675	0.17952	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00855	-1.145	0.20638	N	0.999879	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42481	-0.9449	8	0.02654	T	1	.	5.2136	0.15331	0.1237:0.0:0.4481:0.4281	.	315;316	G3V0H5;Q96SQ5	.;ZN587_HUMAN	R	273;315;316;316;273	ENSP00000393865:L315R;ENSP00000345479:L316R;ENSP00000406999:L273R	ENSP00000345479:L316R	L	+	2	0	ZNF587	63062539	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.624000	0.00876	-1.268000	0.02439	-3.352000	0.00042	CTT	T|0.707;G|0.293	0.293	strong		0.468	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
ELP5	23587	hgsc.bcm.edu	37	17	7155861	7155861	+	Missense_Mutation	SNP	G	G	A	rs2521988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7155861G>A	ENST00000396628.2	+	1	257	c.40G>A	c.(40-42)Gag>Aag	p.E14K	CTDNEP1_ENST00000318988.6_5'Flank|ELP5_ENST00000396627.2_Missense_Mutation_p.E14K|CTDNEP1_ENST00000572043.1_5'Flank|RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000574255.1_Missense_Mutation_p.E14K|CTDNEP1_ENST00000574322.1_5'Flank|ELP5_ENST00000573657.1_Missense_Mutation_p.E14K|ELP5_ENST00000354429.2_Missense_Mutation_p.E14K|CTDNEP1_ENST00000573600.1_5'Flank|ELP5_ENST00000356683.2_Missense_Mutation_p.E14K|ELP5_ENST00000574993.1_Missense_Mutation_p.E14K	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5	14			E -> K (in dbSNP:rs2521988). {ECO:0000269|Ref.2}.		chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GACCGGACGCGAGTTGGAGAT	0.692													G|||	403	0.0804712	0.0068	0.049	5008	,	,		15804	0.0367		0.1421	False		,,,				2504	0.184				p.E14K		Atlas-SNP	.											.	.	.	.	0			c.G40A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	121,4285	90.2+/-128.9	3,115,2085	58.0	51.0	53.0		40,40,40,40	-6.9	0.0	17	dbSNP_100	53	1183,7417	238.2+/-269.8	77,1029,3194	yes	missense,missense,missense,missense	C17orf81	NM_015362.3,NM_203413.1,NM_203414.1,NM_203415.1	56,56,56,56	80,1144,5279	AA,AG,GG		13.7558,2.7463,10.0261	benign,benign,benign,benign	14/317,14/280,14/317,14/317	7155861	1304,11702	2203	4300	6503	SO:0001583	missense	23587	exon1			GGACGCGAGTTGG	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"""Elongator acetyltransferase complex subunits"""	30617	protein-coding gene	gene with protein product	"""dermal papilla derived protein 6"", ""S-phase 2 protein"""	615019	"""chromosome 17 open reading frame 81"""	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.40G>A	17.37:g.7155861G>A	ENSP00000379869:p.Glu14Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_203414	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Missense_Mutation	SNP	ENST00000396628.2	37	CCDS11094.1	161	0.07371794871794872	3	0.006097560975609756	17	0.04696132596685083	25	0.043706293706293704	116	0.15303430079155672	G	0.121	-1.125829	0.01770	0.027463	0.137558	ENSG00000170291	ENST00000354429;ENST00000396628;ENST00000396627;ENST00000356683	T;T;T;T	0.47869	1.49;1.49;1.49;0.83	3.48	-6.95	0.01628	.	4.253690	0.00357	N	0.000026	T	0.00144	0.0004	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.04178	-1.0971	9	0.30854	T	0.27	40.3597	1.568	0.02608	0.3587:0.327:0.1448:0.1695	rs2521988	14;14;14;14	Q8TE02-2;Q8TE02-3;A8K1M5;Q8TE02	.;.;.;DERP6_HUMAN	K	14	ENSP00000346412:E14K;ENSP00000379869:E14K;ENSP00000379868:E14K;ENSP00000349111:E14K	ENSP00000346412:E14K	E	+	1	0	C17orf81	7096585	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.798000	0.00363	-5.095000	0.00022	-1.040000	0.02373	GAG	G|0.906;A|0.094	0.094	strong		0.692	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362	
FOXA1	3169	hgsc.bcm.edu	37	14	38061742	38061742	+	Missense_Mutation	SNP	C	C	T	rs7144658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:38061742C>T	ENST00000250448.2	-	2	308	c.247G>A	c.(247-249)Gcc>Acc	p.A83T	FOXA1_ENST00000545425.2_5'UTR|FOXA1_ENST00000540786.1_Missense_Mutation_p.A50T	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	83			A -> T (in dbSNP:rs7144658). {ECO:0000269|PubMed:10899756}.		anatomical structure formation involved in morphogenesis (GO:0048646)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|epithelial cell maturation involved in prostate gland development (GO:0060743)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|glucose homeostasis (GO:0042593)|hormone metabolic process (GO:0042445)|lung epithelial cell differentiation (GO:0060487)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|prostate gland stromal morphogenesis (GO:0060741)|response to estradiol (GO:0032355)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)	microvillus (GO:0005902)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		GGCATGCCGGCTACTGCGCCG	0.692													C|||	2920	0.583067	0.3714	0.6614	5008	,	,		13014	0.8442		0.5825	False		,,,				2504	0.545				p.A83T		Atlas-SNP	.											.	FOXA1	56	.	0			c.G247A						PASS	.	C	THR/ALA	1897,2403		441,1015,694	44.0	49.0	47.0		247	3.0	0.7	14	dbSNP_116	47	4870,3392		1434,2002,695	yes	missense	FOXA1	NM_004496.2	58	1875,3017,1389	TT,TC,CC		41.0554,44.1163,46.1312	benign	83/473	38061742	6767,5795	2150	4131	6281	SO:0001583	missense	3169	exon2			TGCCGGCTACTGC	U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514		"""Forkhead boxes"""	5021	protein-coding gene	gene with protein product		602294	"""hepatocyte nuclear factor 3, alpha"""	HNF3A		9119385, 8652662	Standard	NM_004496		Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.247G>A	14.37:g.38061742C>T	ENSP00000250448:p.Ala83Thr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_004496	B2R9H6|B7ZAP5|Q9H2A0	Missense_Mutation	SNP	ENST00000250448.2	37	CCDS9665.1	1372	0.6282051282051282	195	0.39634146341463417	232	0.6408839779005525	500	0.8741258741258742	445	0.5870712401055409	C	15.22	2.770271	0.49680	0.441163	0.589446	ENSG00000129514	ENST00000250448;ENST00000540786	T;T	0.16196	2.36;2.36	3.88	2.96	0.34315	Fork-head N-terminal (1);	0.441828	0.21842	N	0.068316	T	0.00012	0.0000	L	0.31065	0.9	0.26212	P	0.9792839	B	0.14012	0.009	B	0.15484	0.013	T	0.18967	-1.0320	9	0.15499	T	0.54	.	5.555	0.17111	0.3523:0.5518:0.0:0.0958	rs7144658;rs57815362;rs7144658	83	P55317	FOXA1_HUMAN	T	83;50	ENSP00000250448:A83T;ENSP00000440178:A50T	ENSP00000250448:A83T	A	-	1	0	FOXA1	37131493	1.000000	0.71417	0.680000	0.29994	0.967000	0.64934	1.052000	0.30429	0.784000	0.33661	0.511000	0.50034	GCC	C|0.430;T|0.570	0.570	strong		0.692	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276735.1		
PRRC2A	7916	hgsc.bcm.edu	37	6	31599556	31599556	+	Silent	SNP	A	A	C	rs78503551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31599556A>C	ENST00000376033.2	+	16	3340	c.3106A>C	c.(3106-3108)Agg>Cgg	p.R1036R	PRRC2A_ENST00000376007.4_Silent_p.R1036R	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1036	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TGCCAGAGGGAGGGGTTTTCG	0.622													A|||	42	0.00838658	0.0068	0.0072	5008	,	,		12527	0.003		0.0099	False		,,,				2504	0.0153				p.R1036R		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A3106C						PASS	.	A	,	10,3000		0,10,1495	13.0	17.0	15.0		3106,3106	5.0	1.0	6	dbSNP_131	15	37,5373		0,37,2668	no	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	0,47,4163	CC,CA,AA		0.6839,0.3322,0.5582	,	1036/2158,1036/2158	31599556	47,8373	1505	2705	4210	SO:0001819	synonymous_variant	7916	exon16			AGAGGGAGGGGTT	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3106A>C	6.37:g.31599556A>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			A|0.995;C|0.005	0.005	strong		0.622	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
PTPRF	5792	hgsc.bcm.edu	37	1	44071221	44071221	+	Silent	SNP	G	G	A	rs631248	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:44071221G>A	ENST00000359947.4	+	19	3751	c.3411G>A	c.(3409-3411)gtG>gtA	p.V1137V	PTPRF_ENST00000372413.3_Silent_p.V1128V|PTPRF_ENST00000372414.3_Silent_p.V1137V|PTPRF_ENST00000422171.2_Silent_p.V485V|PTPRF_ENST00000438120.1_Silent_p.V1128V|PTPRF_ENST00000496447.1_3'UTR	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1137					cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TTGTTGTGGTGCCCATTGACC	0.632													G|||	3017	0.602436	0.4297	0.5418	5008	,	,		19963	0.7579		0.7376	False		,,,				2504	0.5798				p.V1137V		Atlas-SNP	.											.	PTPRF	172	.	0			c.G3411A						PASS	.	G	,	2084,2322	569.0+/-382.5	482,1120,601	142.0	110.0	121.0		3411,3384	0.3	1.0	1	dbSNP_83	121	6617,1983	722.9+/-406.4	2578,1461,261	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	3060,2581,862	AA,AG,GG		23.0581,47.2991,33.1001	,	1137/1908,1128/1899	44071221	8701,4305	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon19			TGTGGTGCCCATT	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3411G>A	1.37:g.44071221G>A		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	227	221	0.973568	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	1419|1419	0.6497252747252747|0.6497252747252747	200|200	0.4065040650406504|0.4065040650406504	223|223	0.6160220994475138|0.6160220994475138	425|425	0.743006993006993|0.743006993006993	571|571	0.7532981530343008|0.7532981530343008	G|G	9.594|9.594	1.126943|1.126943	0.20959|0.20959	0.472991|0.472991	0.769419|0.769419	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.18|5.18	0.259|0.259	0.15583|0.15583	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999852|0.9999999999999852	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.28396|0.28396	-1.0045|-1.0045	3|3	.|.	.|.	.|.	.|.	8.2819|8.2819	0.31906|0.31906	0.2442:0.113:0.6428:0.0|0.2442:0.113:0.6428:0.0	rs631248;rs1143703;rs17849107;rs631248|rs631248;rs1143703;rs17849107;rs631248	.|.	.|.	.|.	T|Y	510;551|783	.|.	.|.	A|C	+|+	1|2	0|0	PTPRF|PTPRF	43843808|43843808	0.976000|0.976000	0.34144|0.34144	1.000000|1.000000	0.80357|0.80357	0.930000|0.930000	0.56654|0.56654	0.308000|0.308000	0.19314|0.19314	0.169000|0.169000	0.19679|0.19679	-1.170000|-1.170000	0.01741|0.01741	GCC|TGC	A|0.648;C|0.002	0.648	strong		0.632	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
PDGFA	5154	hgsc.bcm.edu	37	7	552046	552046	+	Silent	SNP	A	A	G	rs1129401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:552046A>G	ENST00000354513.5	-	3	599	c.207T>C	c.(205-207)caT>caC	p.H69H	PDGFA_ENST00000426681.2_5'Flank|PDGFA_ENST00000402802.3_Silent_p.H69H	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	69					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		GCTTAGTGGCATGGACCCCGT	0.652													G|||	1244	0.248403	0.1271	0.2133	5008	,	,		16261	0.3234		0.2535	False		,,,				2504	0.3548				p.H69H		Atlas-SNP	.											.	PDGFA	34	.	0			c.T207C						PASS	.	G	,	710,3696	759.4+/-412.9	58,594,1551	65.0	62.0	63.0		207,207	-6.8	0.0	7	dbSNP_86	63	2246,6346	707.6+/-405.6	300,1646,2350	no	coding-synonymous,coding-synonymous	PDGFA	NM_002607.5,NM_033023.4	,	358,2240,3901	GG,GA,AA		26.1406,16.1144,22.742	,	69/212,69/197	552046	2956,10042	2203	4296	6499	SO:0001819	synonymous_variant	5154	exon3			AGTGGCATGGACC		CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"""PDGF A-chain"", ""platelet-derived growth factor alpha chain"""	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.207T>C	7.37:g.552046A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	155	67	0.432258	NM_002607	B5BU73	Silent	SNP	ENST00000354513.5	37	CCDS34578.1	536	0.2454212454212454	59	0.11991869918699187	84	0.23204419889502761	199	0.3479020979020979	194	0.2559366754617414	G	0.412	-0.912876	0.02415	0.161144	0.261406	ENSG00000197461	ENST00000400761	.	.	.	5.03	-6.84	0.01687	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.06197	-1.0840	3	.	.	.	-5.3505	17.1287	0.86721	0.6784:0.0:0.3216:0.0	rs1129401;rs1800816;rs2228457;rs3187241;rs17415666;rs61732882	.	.	.	R	76	.	.	C	-	1	0	PDGFA	518572	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.539000	0.06113	-1.968000	0.01006	-0.374000	0.07098	TGC	A|0.769;G|0.231	0.231	strong		0.652	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1		
SDC2	6383	hgsc.bcm.edu	37	8	97605800	97605800	+	Silent	SNP	C	C	T	rs1126681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:97605800C>T	ENST00000302190.4	+	2	1074	c.153C>T	c.(151-153)taC>taT	p.Y51Y	SDC2_ENST00000519914.1_Silent_p.Y22Y|SDC2_ENST00000522911.1_Silent_p.Y22Y|SDC2_ENST00000518385.1_Intron	NM_002998.3	NP_002989.2	P34741	SDC2_HUMAN	syndecan 2	51					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dendrite morphogenesis (GO:0048813)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|regulation of dendrite morphogenesis (GO:0048814)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)	p.Y51Y(2)		breast(1)|cervix(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|stomach(2)	16	Breast(36;3.41e-05)				Sargramostim(DB00020)	ACGATGACTACGCTTCTGCGT	0.473													C|||	1132	0.226038	0.0484	0.1628	5008	,	,		21516	0.3591		0.2217	False		,,,				2504	0.3783				p.Y51Y		Atlas-SNP	.											SDC2,NS,carcinoma,0,2	SDC2	33	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.C153T						PASS	.	C		362,4044	186.0+/-213.0	14,334,1855	142.0	108.0	119.0		153	-6.0	0.9	8	dbSNP_86	119	1894,6706	335.6+/-321.5	207,1480,2613	no	coding-synonymous	SDC2	NM_002998.3		221,1814,4468	TT,TC,CC		22.0233,8.2161,17.3458		51/202	97605800	2256,10750	2203	4300	6503	SO:0001819	synonymous_variant	6383	exon2			TGACTACGCTTCT	BC030133	CCDS6272.1	8q22-q23	2011-08-11	2007-02-15		ENSG00000169439	ENSG00000169439		"""Proteoglycans / Cell Surface : Syndecans"", ""CD molecules"""	10659	protein-coding gene	gene with protein product	"""syndecan proteoglycan 2"""	142460	"""heparan sulfate proteoglycan 1, cell surface-associated"""	HSPG, HSPG1		8187643	Standard	NM_002998		Approved	fibroglycan, SYND2, CD362	uc003yhv.1	P34741	OTTHUMG00000164689	ENST00000302190.4:c.153C>T	8.37:g.97605800C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_002998	B3KQA3|Q6PIS6|Q9H6V1	Silent	SNP	ENST00000302190.4	37	CCDS6272.1																																																																																			C|0.804;T|0.196	0.196	strong		0.473	SDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379750.1	NM_002998	
OTOL1	131149	hgsc.bcm.edu	37	3	161220819	161220819	+	Missense_Mutation	SNP	C	C	A	rs149127996	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:161220819C>A	ENST00000327928.4	+	4	523	c.523C>A	c.(523-525)Cct>Act	p.P175T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	175	Collagen-like 1.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						TTCAGGTGAACCTGGCCCTAA	0.398													C|||	14	0.00279553	0.0015	0.0043	5008	,	,		14597	0.0		0.0089	False		,,,				2504	0.0				p.P175T		Atlas-SNP	.											.	OTOL1	63	.	0			c.C523A						PASS	.	C	THR/PRO	4,3334		0,4,1665	7.0	6.0	6.0		523	1.9	1.0	3	dbSNP_134	6	28,7420		0,28,3696	yes	missense	OTOL1	NM_001080440.1	38	0,32,5361	AA,AC,CC		0.3759,0.1198,0.2967	benign	175/478	161220819	32,10754	1669	3724	5393	SO:0001583	missense	131149	exon4			GGTGAACCTGGCC		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.523C>A	3.37:g.161220819C>A	ENSP00000330808:p.Pro175Thr	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	184	77	0.418478	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	37	CCDS46948.1	11	0.005036630036630037	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	5.563	0.288736	0.10513	0.001198	0.003759	ENSG00000182447	ENST00000327928	D	0.96651	-4.08	4.94	1.94	0.25998	.	1.313780	0.05051	N	0.478274	D	0.90741	0.7094	L	0.41906	1.305	0.09310	N	1	B	0.20887	0.049	B	0.26693	0.072	T	0.81556	-0.0879	10	0.37606	T	0.19	.	2.6803	0.05091	0.2842:0.3954:0.2304:0.09	.	175	A6NHN0	OTOL1_HUMAN	T	175	ENSP00000330808:P175T	ENSP00000330808:P175T	P	+	1	0	OTOL1	162703513	0.004000	0.15560	0.987000	0.45799	0.976000	0.68499	0.410000	0.21098	0.462000	0.27095	0.557000	0.71058	CCT	C|0.995;A|0.005	0.005	strong		0.398	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
TOR1B	27348	hgsc.bcm.edu	37	9	132569553	132569553	+	Silent	SNP	C	C	T	rs36036025|rs1043178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:132569553C>T	ENST00000259339.2	+	3	612	c.552C>T	c.(550-552)ccC>ccT	p.P184P		NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	184					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				AATTGCACCCCGGGATCATTG	0.493													C|||	838	0.167332	0.0537	0.2839	5008	,	,		18896	0.0288		0.3161	False		,,,				2504	0.228				p.P184P		Atlas-SNP	.											.	TOR1B	20	.	0			c.C552T						PASS	.	C		373,4033	189.9+/-215.9	12,349,1842	191.0	179.0	183.0		552	-9.2	0.2	9	dbSNP_86	183	2872,5728	450.9+/-362.5	486,1900,1914	no	coding-synonymous	TOR1B	NM_014506.1		498,2249,3756	TT,TC,CC		33.3953,8.4657,24.95		184/337	132569553	3245,9761	2203	4300	6503	SO:0001819	synonymous_variant	27348	exon3			GCACCCCGGGATC	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.552C>T	9.37:g.132569553C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	210	110	0.52381	NM_014506		Silent	SNP	ENST00000259339.2	37	CCDS6929.1																																																																																			C|0.794;N|0.000	.	strong		0.493	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506	
THEM4	117145	hgsc.bcm.edu	37	1	151867528	151867528	+	Missense_Mutation	SNP	C	C	T	rs114800758	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151867528C>T	ENST00000368814.3	-	2	591	c.242G>A	c.(241-243)cGt>cAt	p.R81H	THEM4_ENST00000489410.1_Missense_Mutation_p.R81H	NM_053055.4	NP_444283.2	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	81					epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein kinase B signaling (GO:0043491)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	cell projection (GO:0042995)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(4)|lung(3)|urinary_tract(1)	9	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGTAGGTGTACGTTTATATGA	0.408													C|||	10	0.00199681	0.0	0.0	5008	,	,		18187	0.0		0.0099	False		,,,				2504	0.0				p.R81H		Atlas-SNP	.											.	THEM4	19	.	0			c.G242A						PASS	.	C	HIS/ARG	14,4392	21.2+/-45.6	0,14,2189	121.0	120.0	121.0		242	-6.8	0.0	1	dbSNP_132	121	82,8518	47.6+/-106.9	0,82,4218	yes	missense	THEM4	NM_053055.4	29	0,96,6407	TT,TC,CC		0.9535,0.3177,0.7381	benign	81/241	151867528	96,12910	2203	4300	6503	SO:0001583	missense	117145	exon2			GGTGTACGTTTAT	AJ313515	CCDS1006.1	1q21.3	2008-02-05			ENSG00000159445	ENSG00000159445			17947	protein-coding gene	gene with protein product	"""C-terminal modulator protein"""	606388				11598301	Standard	NM_053055		Approved	CTMP	uc001ezj.2	Q5T1C6	OTTHUMG00000013049	ENST00000368814.3:c.242G>A	1.37:g.151867528C>T	ENSP00000357804:p.Arg81His	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	149	100	0.671141	NM_053055	B2RBX2|Q96KR2	Missense_Mutation	SNP	ENST00000368814.3	37	CCDS1006.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	7.135	0.580580	0.13686	0.003177	0.009535	ENSG00000159445	ENST00000368814;ENST00000489410	T;T	0.24538	1.86;1.85	3.39	-6.77	0.01727	.	1.373530	0.04534	N	0.386920	T	0.04588	0.0125	L	0.50333	1.59	0.09310	N	1	B	0.31968	0.349	B	0.28916	0.096	T	0.20042	-1.0287	10	0.15952	T	0.53	6.1133	1.5837	0.02639	0.2296:0.1696:0.1141:0.4867	.	81	Q5T1C6	THEM4_HUMAN	H	81	ENSP00000357804:R81H;ENSP00000433304:R81H	ENSP00000357804:R81H	R	-	2	0	THEM4	150134152	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-3.893000	0.00340	-2.045000	0.00910	-0.157000	0.13467	CGT	C|0.994;T|0.006	0.006	strong		0.408	THEM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036615.1	NM_053055	
ZNF579	163033	hgsc.bcm.edu	37	19	56090076	56090076	+	Silent	SNP	G	G	T	rs34164618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56090076G>T	ENST00000325421.4	-	2	958	c.930C>A	c.(928-930)gcC>gcA	p.A310A	CTD-2537I9.5_ENST00000589396.1_lincRNA	NM_152600.2	NP_689813.2	Q8NAF0	ZN579_HUMAN	zinc finger protein 579	310					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.106)		GGAGGTAGGAGGCGAGGCGGA	0.741													G|||	1181	0.235823	0.2315	0.268	5008	,	,		8540	0.0754		0.2445	False		,,,				2504	0.3753				p.A310A		Atlas-SNP	.											.	ZNF579	21	.	0			c.C930A						PASS	.	G		1015,3381		117,781,1300	20.0	24.0	23.0		930	3.2	1.0	19	dbSNP_126	23	2010,6576		242,1526,2525	no	coding-synonymous	ZNF579	NM_152600.2		359,2307,3825	TT,TG,GG		23.4102,23.0892,23.3015		310/563	56090076	3025,9957	2198	4293	6491	SO:0001819	synonymous_variant	163033	exon2			GTAGGAGGCGAGG	AK092772	CCDS12927.1	19q13.42	2013-09-20			ENSG00000218891	ENSG00000218891		"""Zinc fingers, C2H2-type"""	26646	protein-coding gene	gene with protein product							Standard	NM_152600		Approved	FLJ35453	uc002qlh.3	Q8NAF0	OTTHUMG00000180857	ENST00000325421.4:c.930C>A	19.37:g.56090076G>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_152600		Silent	SNP	ENST00000325421.4	37	CCDS12927.1																																																																																			G|0.786;T|0.214	0.214	strong		0.741	ZNF579-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453348.1	NM_152600	
THSD1	55901	hgsc.bcm.edu	37	13	52952680	52952680	+	Silent	SNP	G	G	A	rs9536043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:52952680G>A	ENST00000258613.4	-	5	1603	c.1425C>T	c.(1423-1425)cgC>cgT	p.R475R	THSD1_ENST00000349258.4_Silent_p.R422R|THSD1_ENST00000544466.1_Silent_p.R96R	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	475					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		AGAAGCTCCCGCGCTGCTCGC	0.652													G|||	281	0.0561102	0.1135	0.0274	5008	,	,		14836	0.0079		0.0388	False		,,,				2504	0.0665				p.R475R		Atlas-SNP	.											THSD1,NS,carcinoma,-1,1	THSD1	89	1	0			c.C1425T						PASS	.	G	,	395,4011	195.0+/-219.7	16,363,1824	44.0	50.0	48.0		1425,1266	-12.1	0.0	13	dbSNP_119	48	442,8158	133.5+/-191.0	12,418,3870	no	coding-synonymous,coding-synonymous	THSD1	NM_018676.3,NM_199263.2	,	28,781,5694	AA,AG,GG		5.1395,8.965,6.4355	,	475/853,422/800	52952680	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	55901	exon5			GCTCCCGCGCTGC	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.1425C>T	13.37:g.52952680G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Silent	SNP	ENST00000258613.4	37	CCDS9432.1																																																																																			G|0.948;A|0.052	0.052	strong		0.652	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
PHLDB3	653583	hgsc.bcm.edu	37	19	43979589	43979589	+	Silent	SNP	G	G	T	rs1055099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:43979589G>T	ENST00000292140.5	-	16	2256	c.1896C>A	c.(1894-1896)acC>acA	p.T632T		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	632	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				CGTCAGCGGCGGTCACGATGA	0.672													T|||	2800	0.559105	0.6316	0.5086	5008	,	,		15307	0.6944		0.4165	False		,,,				2504	0.5041				p.T632T		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1896A						PASS	.	T		2074,1704		585,904,400	34.0	41.0	39.0		1896	-8.7	0.0	19	dbSNP_86	39	3402,4826		703,1996,1415	no	coding-synonymous	PHLDB3	NM_198850.3		1288,2900,1815	TT,TG,GG		41.3466,45.1032,45.6105		632/641	43979589	5476,6530	1889	4114	6003	SO:0001819	synonymous_variant	653583	exon16			AGCGGCGGTCACG		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1896C>A	19.37:g.43979589G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_198850	Q8N7Z4	Silent	SNP	ENST00000292140.5	37	CCDS12621.2																																																																																			G|0.453;T|0.547	0.547	strong		0.672	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
IRF2BPL	64207	hgsc.bcm.edu	37	14	77492891	77492891	+	Silent	SNP	G	G	A	rs879027	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:77492891G>A	ENST00000238647.3	-	1	2143	c.1245C>T	c.(1243-1245)taC>taT	p.Y415Y		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	415					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						GCTTCAATTCGTAGTCCATGC	0.587													G|||	1913	0.381989	0.0946	0.379	5008	,	,		14028	0.5238		0.5497	False		,,,				2504	0.454				p.Y415Y		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.C1245T						PASS	.	G		856,3550	331.2+/-301.9	90,676,1437	48.0	40.0	43.0		1245	2.0	1.0	14	dbSNP_86	43	4616,3984	595.6+/-393.5	1243,2130,927	no	coding-synonymous	IRF2BPL	NM_024496.2		1333,2806,2364	AA,AG,GG		46.3256,19.4281,42.0729		415/797	77492891	5472,7534	2203	4300	6503	SO:0001819	synonymous_variant	64207	exon1			CAATTCGTAGTCC	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"""enhanced at puberty 1"""	611720	"""chromosome 14 open reading frame 4"""	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.1245C>T	14.37:g.77492891G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			G|0.586;A|0.414	0.414	strong		0.587	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496	
AKAP13	11214	hgsc.bcm.edu	37	15	86124861	86124861	+	Missense_Mutation	SNP	C	C	A	rs371702364		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:86124861C>A	ENST00000394518.2	+	7	3657	c.3562C>A	c.(3562-3564)Ctg>Atg	p.L1188M	AKAP13_ENST00000361243.2_Missense_Mutation_p.L1188M|RP11-815J21.2_ENST00000561409.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1188					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						TCCTGTCCTACTGCAGCCTGT	0.582																																					p.L1188M	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C3562A						PASS	.	C	MET/LEU,MET/LEU	0,4404		0,0,2202	71.0	69.0	69.0		3562,3562	2.5	0.0	15		69	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	AKAP13	NM_006738.4,NM_007200.3	15,15	0,1,6500	AA,AC,CC		0.0116,0.0,0.0077	benign,benign	1188/2818,1188/2814	86124861	1,13001	2202	4299	6501	SO:0001583	missense	11214	exon7			GTCCTACTGCAGC	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.3562C>A	15.37:g.86124861C>A	ENSP00000378026:p.Leu1188Met	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	C	9.556	1.117178	0.20795	0.0	1.16E-4	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.16196	2.36;2.36	5.49	2.49	0.30216	.	.	.	.	.	T	0.09024	0.0223	N	0.14661	0.345	0.09310	N	0.999999	B;B	0.28291	0.028;0.206	B;B	0.27170	0.014;0.077	T	0.31916	-0.9926	9	0.45353	T	0.12	.	4.1054	0.10035	0.1653:0.5884:0.1595:0.0867	.	1188;1188	Q12802;Q12802-2	AKP13_HUMAN;.	M	1188;1188;1187;1187	ENSP00000354718:L1188M;ENSP00000378026:L1188M	ENSP00000354718:L1188M	L	+	1	2	AKAP13	83925865	0.001000	0.12720	0.000000	0.03702	0.217000	0.24651	1.161000	0.31773	0.236000	0.21180	0.650000	0.86243	CTG	.	.	weak		0.582	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
UGT1A6	54578	hgsc.bcm.edu	37	2	234652308	234652308	+	Intron	SNP	G	G	T	rs34622615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234652308G>T	ENST00000305139.6	+	2	1000				UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000406651.1_Intron|DNAJB3_ENST00000449667.1_RNA|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6						cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	ACTCGAAGGGGTCCTCGAAGG	0.637													G|||	117	0.0233626	0.0499	0.0115	5008	,	,		14048	0.003		0.0239	False		,,,				2504	0.0164				p.D85E		Atlas-SNP	.											.	.	.	.	0			c.C255A						PASS	.	G	GLU/ASP,,,,,,,,,	214,3700		12,190,1755	67.0	80.0	76.0		255,,,,,,,,,	1.6	0.9	2	dbSNP_126	76	257,8011		4,249,3881	yes	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3,DNAJB3	NM_001001394.3,NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	45,,,,,,,,,	16,439,5636	TT,TG,GG		3.1084,5.4676,3.8664	benign,,,,,,,,,	85/146,,,,,,,,,	234652308	471,11711	1957	4134	6091	SO:0001627	intron_variant	414061	exon1			GAAGGGGTCCTCG	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.862-23372G>T	2.37:g.234652308G>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	159	77	0.484277	NM_001001394	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1																																																																																			G|0.973;T|0.027	0.027	strong		0.637	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
USP24	23358	hgsc.bcm.edu	37	1	55538462	55538462	+	Silent	SNP	C	C	T	rs17410294	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55538462C>T	ENST00000294383.6	-	65	7598	c.7599G>A	c.(7597-7599)aaG>aaA	p.K2533K	USP24_ENST00000484447.1_5'UTR|USP24_ENST00000407756.1_Silent_p.K2373K	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2533					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						CAGTTACCTTCTTCTGTAGCC	0.428													C|||	326	0.0650958	0.0287	0.0764	5008	,	,		18938	0.003		0.161	False		,,,				2504	0.0716				p.K2533K		Atlas-SNP	.											.	USP24	323	.	0			c.G7599A						PASS	.	C		210,3656		8,194,1731	53.0	53.0	53.0		7599	3.1	1.0	1	dbSNP_123	53	1262,7030		107,1048,2991	no	coding-synonymous	USP24	NM_015306.2		115,1242,4722	TT,TC,CC		15.2195,5.432,12.1073		2533/2621	55538462	1472,10686	1933	4146	6079	SO:0001819	synonymous_variant	23358	exon65			TACCTTCTTCTGT	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.7599G>A	1.37:g.55538462C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			C|0.916;T|0.084	0.084	strong		0.428	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
GIMAP7	168537	hgsc.bcm.edu	37	7	150217309	150217309	+	Missense_Mutation	SNP	C	C	T	rs3735080	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150217309C>T	ENST00000313543.4	+	2	404	c.247C>T	c.(247-249)Cgc>Tgc	p.R83C		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	83	AIG1-type G.		R -> C (in dbSNP:rs3735080).		GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)	p.R83C(1)		breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGAAATCAGCCGCTGCATCAT	0.562													C|||	849	0.169529	0.0144	0.33	5008	,	,		19408	0.1587		0.2217	False		,,,				2504	0.2229				p.R83C		Atlas-SNP	.											GIMAP7,NS,carcinoma,0,1	GIMAP7	47	1	1	Substitution - Missense(1)	stomach(1)	c.C247T						PASS	.	C	CYS/ARG	218,4188	131.4+/-167.9	7,204,1992	48.0	49.0	49.0		247	-10.2	0.0	7	dbSNP_107	49	1961,6639	343.9+/-325.1	238,1485,2577	yes	missense	GIMAP7	NM_153236.3	180	245,1689,4569	TT,TC,CC		22.8023,4.9478,16.7538	probably-damaging	83/301	150217309	2179,10827	2203	4300	6503	SO:0001583	missense	168537	exon2			ATCAGCCGCTGCA	BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"""GTPases, IMAP"""	22404	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 7"""					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.247C>T	7.37:g.150217309C>T	ENSP00000315474:p.Arg83Cys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_153236		Missense_Mutation	SNP	ENST00000313543.4	37	CCDS5903.1	370	0.16941391941391942	12	0.024390243902439025	94	0.2596685082872928	83	0.1451048951048951	181	0.23878627968337732	C	12.26	1.884168	0.33255	0.049478	0.228023	ENSG00000179144	ENST00000313543	T	0.07444	3.19	5.09	-10.2	0.00374	AIG1 (1);	0.922232	0.09141	N	0.842960	T	0.00012	0.0000	M	0.91249	3.19	0.80722	P	0.0	D	0.89917	1.0	D	0.67103	0.949	T	0.34254	-0.9836	9	0.87932	D	0	.	16.2376	0.82384	0.7907:0.1247:0.0846:0.0	rs3735080;rs11554998;rs17469020;rs52825973;rs57588247;rs3735080	83	Q8NHV1	GIMA7_HUMAN	C	83	ENSP00000315474:R83C	ENSP00000315474:R83C	R	+	1	0	GIMAP7	149848242	0.000000	0.05858	0.004000	0.12327	0.023000	0.10783	-1.164000	0.03135	-1.798000	0.01250	-1.107000	0.02091	CGC	C|0.840;T|0.160	0.160	strong		0.562	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236	
THUMPD3	25917	hgsc.bcm.edu	37	3	9426224	9426224	+	Missense_Mutation	SNP	G	G	A	rs1129174	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:9426224G>A	ENST00000345094.3	+	10	1710	c.1376G>A	c.(1375-1377)cGa>cAa	p.R459Q	SETD5-AS1_ENST00000523354.1_RNA|SETD5-AS1_ENST00000519043.1_RNA|SETD5-AS1_ENST00000520629.1_RNA|THUMPD3_ENST00000452837.2_Missense_Mutation_p.R459Q|SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000515662.2_Missense_Mutation_p.R459Q|SETD5-AS1_ENST00000521609.1_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	459			R -> Q (in dbSNP:rs1129174). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		TCTGGAATGCGACACGTATGG	0.418													G|||	525	0.104832	0.0401	0.2248	5008	,	,		20841	0.0605		0.1879	False		,,,				2504	0.0675				p.R459Q		Atlas-SNP	.											THUMPD3,caecum,carcinoma,0,1	THUMPD3	46	1	0			c.G1376A						scavenged	.	G	GLN/ARG,GLN/ARG	290,4116	158.5+/-191.2	6,278,1919	388.0	344.0	359.0		1376,1376	4.8	1.0	3	dbSNP_86	359	1274,7326	254.7+/-279.9	85,1104,3111	yes	missense,missense	THUMPD3	NM_001114092.1,NM_015453.2	43,43	91,1382,5030	AA,AG,GG		14.814,6.5819,12.0252	benign,benign	459/508,459/508	9426224	1564,11442	2203	4300	6503	SO:0001583	missense	25917	exon10			GAATGCGACACGT	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.1376G>A	3.37:g.9426224G>A	ENSP00000339532:p.Arg459Gln	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Missense_Mutation	SNP	ENST00000345094.3	37	CCDS2573.1	293	0.13415750915750915	26	0.052845528455284556	82	0.2265193370165746	43	0.07517482517482517	142	0.18733509234828497	G	14.07	2.424325	0.43020	0.065819	0.14814	ENSG00000134077	ENST00000452837;ENST00000345094;ENST00000515662	T;T;T	0.42513	0.97;0.97;0.97	5.67	4.8	0.61643	Putative RNA methylase (1);	0.147419	0.64402	D	0.000009	T	0.00012	0.0000	N	0.04724	-0.175	0.35024	P	0.24185800000000002	B	0.21452	0.056	B	0.18561	0.022	T	0.16188	-1.0411	9	0.31617	T	0.26	-21.4693	14.2841	0.66235	0.072:0.0:0.928:0.0	rs1129174;rs3177483;rs3186769;rs3816407;rs52834451;rs61368596;rs1129174	459	Q9BV44	THUM3_HUMAN	Q	459	ENSP00000395893:R459Q;ENSP00000339532:R459Q;ENSP00000424064:R459Q	ENSP00000339532:R459Q	R	+	2	0	THUMPD3	9401224	1.000000	0.71417	0.996000	0.52242	0.254000	0.26022	5.388000	0.66249	1.415000	0.47037	0.555000	0.69702	CGA	G|0.880;A|0.120	0.120	strong		0.418	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453	
HK1	3098	hgsc.bcm.edu	37	10	71060610	71060610	+	Missense_Mutation	SNP	A	A	G	rs906220	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71060610A>G	ENST00000360289.2	+	5	519	c.20A>G	c.(19-21)cAt>cGt	p.H7R	HK1_ENST00000448642.2_Intron|HK1_ENST00000404387.2_Intron	NM_033497.2|NM_033498.2|NM_033500.2	NP_277032.1|NP_277033.1|NP_277035.2	P19367	HXK1_HUMAN	hexokinase 1	467	Hydrophobic.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						AGAGCCCTGcatgattttgta	0.388													G|||	4539	0.90635	0.8306	0.9107	5008	,	,		21549	0.994		0.9274	False		,,,				2504	0.8937				p.H7R		Atlas-SNP	.											.	HK1	170	.	0			c.A20G						PASS	.	G	,,ARG/HIS	3737,669	280.8+/-275.6	1576,585,42	59.0	61.0	60.0		,,20	-1.0	0.0	10	dbSNP_86	60	7932,668	167.8+/-219.5	3660,612,28	yes	intron,intron,missense	HK1	NM_033497.2,NM_033498.2,NM_033500.2	,,29	5236,1197,70	GG,GA,AA		7.7674,15.1838,10.2799	,,	,,7/906	71060610	11669,1337	2203	4300	6503	SO:0001583	missense	3098	exon5			CCCTGCATGATTT	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000360289.2:c.20A>G	10.37:g.71060610A>G	ENSP00000353433:p.His7Arg	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_033500	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000360289.2	37	CCDS7290.1	1985	0.9088827838827839	393	0.7987804878048781	314	0.8674033149171271	569	0.9947552447552448	709	0.9353562005277045	G	0.255	-1.003612	0.02128	0.848162	0.922326	ENSG00000156515	ENST00000360289;ENST00000421088	T;T	0.53423	0.62;0.62	0.51	-1.02	0.10135	.	.	.	.	.	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.14438	0.01	B	0.10450	0.005	T	0.24012	-1.0172	8	0.14656	T	0.56	.	2.7331	0.05232	0.2306:0.0:0.5078:0.2615	rs906220;rs52825217;rs60500903;rs906220	7	P19367-4	.	R	7	ENSP00000353433:H7R;ENSP00000398316:H7R	ENSP00000353433:H7R	H	+	2	0	HK1	70730616	0.006000	0.16342	0.001000	0.08648	0.011000	0.07611	-0.382000	0.07408	-1.388000	0.02092	-0.642000	0.03964	CAT	A|0.099;G|0.901	0.901	strong		0.388	HK1-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000188	
ALG14	199857	hgsc.bcm.edu	37	1	95538424	95538424	+	Missense_Mutation	SNP	C	C	T	rs34364382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:95538424C>T	ENST00000370205.5	-	1	77	c.31G>A	c.(31-33)Gca>Aca	p.A11T	ALG14_ENST00000495856.1_5'UTR	NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	11					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		ACAGCTCCTGCGGCCGCAGCT	0.582													C|||	9	0.00179712	0.0008	0.0029	5008	,	,		18389	0.0		0.005	False		,,,				2504	0.001				p.A11T		Atlas-SNP	.											.	ALG14	13	.	0			c.G31A						PASS	.	C	THR/ALA	6,4400	11.4+/-27.6	0,6,2197	79.0	77.0	78.0		31	3.3	0.0	1	dbSNP_126	78	101,8499	56.0+/-117.1	0,101,4199	yes	missense	ALG14	NM_144988.3	58	0,107,6396	TT,TC,CC		1.1744,0.1362,0.8227	possibly-damaging	11/217	95538424	107,12899	2203	4300	6503	SO:0001583	missense	199857	exon1			CTCCTGCGGCCGC		CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339			28287	protein-coding gene	gene with protein product		612866	"""asparagine-linked glycosylation 14 homolog (yeast)"", ""asparagine-linked glycosylation 14 homolog (S. cerevisiae)"""			15615718	Standard	NM_144988		Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.31G>A	1.37:g.95538424C>T	ENSP00000359224:p.Ala11Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_144988	A8K030	Missense_Mutation	SNP	ENST00000370205.5	37	CCDS752.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	14.66	2.600442	0.46423	0.001362	0.011744	ENSG00000172339	ENST00000370205	T	0.44083	0.93	5.21	3.34	0.38264	.	1.316220	0.04936	N	0.457681	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.06405	0.002	T	0.25502	-1.0130	10	0.22109	T	0.4	0.4063	9.4756	0.38869	0.0:0.8285:0.0:0.1715	rs34364382	11	Q96F25	ALG14_HUMAN	T	11	ENSP00000359224:A11T	ENSP00000359224:A11T	A	-	1	0	ALG14	95311012	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.652000	0.24888	0.772000	0.33382	0.591000	0.81541	GCA	C|0.994;T|0.006	0.006	strong		0.582	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988	
OR4M1	441670	hgsc.bcm.edu	37	14	20248828	20248828	+	Missense_Mutation	SNP	C	C	T	rs2635535	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20248828C>T	ENST00000315957.4	+	1	428	c.347C>T	c.(346-348)aCa>aTa	p.T116I		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	116			T -> I (in dbSNP:rs2635535).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTCTTGCTCACAGTGATGGCC	0.493													.|||	1274	0.254393	0.0847	0.3242	5008	,	,		27958	0.2937		0.3439	False		,,,				2504	0.3016				p.T116I		Atlas-SNP	.											.	OR4M1	104	.	0			c.C347T						PASS	.		ILE/THR	587,3819		18,551,1634	237.0	249.0	245.0		347	3.4	1.0	14	dbSNP_100	245	2790,5810		266,2258,1776	no	missense	OR4M1	NM_001005500.1	89	284,2809,3410	TT,TC,CC		32.4419,13.3227,25.9649	possibly-damaging	116/314	20248828	3377,9629	2203	4300	6503	SO:0001583	missense	441670	exon1			TGCTCACAGTGAT		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"""GPCR / Class A : Olfactory receptors"""	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.347C>T	14.37:g.20248828C>T	ENSP00000319654:p.Thr116Ile	Somatic	420	0	0		WXS	Illumina HiSeq	Phase_I	432	206	0.476852	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	CCDS32021.1	599	0.2742673992673993	40	0.08130081300813008	115	0.31767955801104975	169	0.29545454545454547	275	0.3627968337730871	.	11.72	1.723491	0.30593	0.133227	0.324419	ENSG00000176299	ENST00000315957	T	0.00380	7.64	4.33	3.43	0.39272	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000124	T	0.00012	0.0000	L	0.38649	1.16	0.36142	P	0.15317000000000003	B	0.18741	0.03	B	0.15052	0.012	T	0.03148	-1.1067	9	0.08599	T	0.76	-7.5579	9.9477	0.41621	0.0:0.8968:0.0:0.1032	rs2635535;rs52798113	116	Q8NGD0	OR4M1_HUMAN	I	116	ENSP00000319654:T116I	ENSP00000319654:T116I	T	+	2	0	OR4M1	19318668	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	1.306000	0.33505	2.407000	0.81776	0.506000	0.49869	ACA	C|0.736;T|0.264	0.264	strong		0.493	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1		
TBX4	9496	hgsc.bcm.edu	37	17	59560463	59560463	+	Silent	SNP	C	C	T	rs7218485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59560463C>T	ENST00000240335.1	+	8	1269	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D	TBX4_ENST00000393853.4_Silent_p.D409D|TBX4_ENST00000589449.1_Intron	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	408					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CTGGGGTGGACGACCTGCCCC	0.597													C|||	579	0.115615	0.1135	0.0764	5008	,	,		16721	0.1151		0.0994	False		,,,				2504	0.1636				p.D408D		Atlas-SNP	.											TBX4,colon,carcinoma,0,2	TBX4	69	2	0			c.C1224T						PASS	.	C		486,3920	227.2+/-242.5	24,438,1741	88.0	77.0	81.0		1224	-3.8	1.0	17	dbSNP_116	81	899,7701	200.2+/-244.0	47,805,3448	no	coding-synonymous	TBX4	NM_018488.2		71,1243,5189	TT,TC,CC		10.4535,11.0304,10.6489		408/546	59560463	1385,11621	2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			GGTGGACGACCTG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1224C>T	17.37:g.59560463C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			C|0.886;T|0.114	0.114	strong		0.597	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
PABPC1L	80336	hgsc.bcm.edu	37	20	43566787	43566787	+	Silent	SNP	A	A	G	rs11780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43566787A>G	ENST00000217073.2	+	13	1731	c.1731A>G	c.(1729-1731)tcA>tcG	p.S577S	PABPC1L_ENST00000372819.1_Silent_p.S131S|PABPC1L_ENST00000537323.1_3'UTR|PABPC1L_ENST00000372824.1_Silent_p.S131S|PABPC1L_ENST00000217075.2_Silent_p.S131S|PABPC1L_ENST00000255136.3_Silent_p.S577S|PABPC1L_ENST00000490798.1_Intron			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	577	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						TTGACAACTCAGAGCTGTTGC	0.592													G|||	2237	0.446685	0.6619	0.464	5008	,	,		20232	0.3631		0.3708	False		,,,				2504	0.3078				p.S577S		Atlas-SNP	.											.	PABPC1L	59	.	0			c.A1731G						PASS	.	G		1952,1184		616,720,232	66.0	59.0	61.0		1731	-2.5	1.0	20	dbSNP_52	61	2621,4543		483,1655,1444	yes	coding-synonymous	PABPC1L	NM_001124756.1		1099,2375,1676	GG,GA,AA		36.5857,37.7551,44.3981		577/615	43566787	4573,5727	1568	3582	5150	SO:0001819	synonymous_variant	80336	exon13			CAACTCAGAGCTG	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"""RNA binding motif (RRM) containing"""	15797	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 119"""	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.1731A>G	20.37:g.43566787A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_001124756	Q4VY17	Silent	SNP	ENST00000217073.2	37	CCDS42878.1	944	0.43223443223443225	310	0.6300813008130082	156	0.430939226519337	214	0.3741258741258741	264	0.3482849604221636	G	9.627	1.135406	0.21123	0.622449	0.365857	ENSG00000101104	ENST00000372821;ENST00000372826;ENST00000372822	.	.	.	4.72	-2.55	0.06288	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999627	.	.	.	.	.	.	T	0.41251	-0.9519	4	0.87932	D	0	.	2.7459	0.05267	0.4809:0.0918:0.2505:0.1768	rs11780;rs1132851;rs3171233;rs17406358;rs52822539;rs11780	.	.	.	R	159;113;100	.	ENSP00000361908:Q159R	Q	+	2	0	PABPC1L	43000201	0.000000	0.05858	0.990000	0.47175	0.981000	0.71138	-2.978000	0.00664	-0.298000	0.08921	-0.930000	0.02707	CAG	A|0.569;G|0.428	0.428	strong		0.592	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2		
EHD2	30846	hgsc.bcm.edu	37	19	48244194	48244194	+	Silent	SNP	A	A	G	rs7255434	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48244194A>G	ENST00000263277.3	+	6	1388	c.1137A>G	c.(1135-1137)ctA>ctG	p.L379L	EHD2_ENST00000540884.1_3'UTR|EHD2_ENST00000538399.1_Silent_p.L243L	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	379					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		CGAAGCTGCTAGAGGCACTGG	0.647													G|||	2494	0.498003	0.1346	0.5519	5008	,	,		17895	0.5605		0.672	False		,,,				2504	0.7076				p.L379L		Atlas-SNP	.											.	EHD2	59	.	0			c.A1137G						PASS	.	G		1054,3352	709.6+/-407.8	136,782,1285	47.0	40.0	43.0		1137	4.0	1.0	19	dbSNP_116	43	6005,2595	412.5+/-350.8	2081,1843,376	no	coding-synonymous	EHD2	NM_014601.3		2217,2625,1661	GG,GA,AA		30.1744,23.9219,45.725		379/544	48244194	7059,5947	2203	4300	6503	SO:0001819	synonymous_variant	30846	exon6			GCTGCTAGAGGCA	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.1137A>G	19.37:g.48244194A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1																																																																																			A|0.481;G|0.519	0.519	strong		0.647	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
SRGAP1	57522	hgsc.bcm.edu	37	12	64519806	64519806	+	Silent	SNP	T	T	C	rs789722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:64519806T>C	ENST00000355086.3	+	19	2798	c.2274T>C	c.(2272-2274)tcT>tcC	p.S758S	SRGAP1_ENST00000543397.1_Silent_p.S695S|SRGAP1_ENST00000357825.3_Silent_p.S735S	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	758	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TTGGGCGGTCTGCCAGAGAAC	0.522													t|||	2949	0.588858	0.6936	0.4683	5008	,	,		19833	0.6319		0.5398	False		,,,				2504	0.5389				p.S758S		Atlas-SNP	.											.	SRGAP1	146	.	0			c.T2274C						PASS	.	C		3054,1352	693.2+/-405.6	1050,954,199	146.0	123.0	131.0		2274	-9.5	0.7	12	dbSNP_86	131	4344,4256	580.3+/-391.0	1097,2150,1053	no	coding-synonymous	SRGAP1	NM_020762.2		2147,3104,1252	CC,CT,TT		49.4884,30.6854,43.1186		758/1086	64519806	7398,5608	2203	4300	6503	SO:0001819	synonymous_variant	57522	exon19			GCGGTCTGCCAGA	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2274T>C	12.37:g.64519806T>C		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	242	115	0.475207	NM_020762	Q9H8A3|Q9P2P2	Silent	SNP	ENST00000355086.3	37	CCDS8967.1																																																																																			T|0.405;C|0.595	0.595	strong		0.522	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
DBN1	1627	hgsc.bcm.edu	37	5	176894756	176894756	+	Silent	SNP	C	C	T	rs2545794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176894756C>T	ENST00000309007.5	-	4	537	c.318G>A	c.(316-318)gcG>gcA	p.A106A	DBN1_ENST00000393565.1_Silent_p.A106A|DBN1_ENST00000292385.5_Silent_p.A108A	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	106	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGAAGAACTCCGCCACCTTAG	0.657													a|||	1861	0.371605	0.4667	0.3617	5008	,	,		13785	0.2202		0.501	False		,,,				2504	0.273				p.A108A		Atlas-SNP	.											.	DBN1	122	.	0			c.G324A						PASS	.	G	,	1959,2345		449,1061,642	19.0	19.0	19.0		318,324	-10.5	0.4	5	dbSNP_100	19	4440,4014		1169,2102,956	no	coding-synonymous,coding-synonymous	DBN1	NM_004395.3,NM_080881.2	,	1618,3163,1598	TT,TC,CC		47.4805,45.5158,49.8432	,	106/650,108/652	176894756	6399,6359	2152	4227	6379	SO:0001819	synonymous_variant	1627	exon5			GAACTCCGCCACC		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.318G>A	5.37:g.176894756C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Silent	SNP	ENST00000309007.5	37	CCDS4420.1																																																																																			C|0.575;T|0.425	0.425	strong		0.657	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881	
PEF1	553115	hgsc.bcm.edu	37	1	32096265	32096265	+	Silent	SNP	A	A	G	rs1061770	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:32096265A>G	ENST00000373703.4	-	5	826	c.804T>C	c.(802-804)atT>atC	p.I268I	PEF1_ENST00000492061.1_5'Flank|HCRTR1_ENST00000373705.1_Intron	NM_012392.3	NP_036524.1	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1	268	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.|Required for interaction with PDCD6.				proteolysis (GO:0006508)|response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|poly(A) RNA binding (GO:0044822)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		AGCTGAGCCGAATGTTGCCTT	0.572													A|||	1787	0.356829	0.0794	0.4741	5008	,	,		2811	0.248		0.5676	False		,,,				2504	0.544				p.I268I		Atlas-SNP	.											.	PEF1	20	.	0			c.T804C						PASS	.	A		730,3676	301.0+/-286.6	77,576,1550	113.0	83.0	93.0		804	0.1	1.0	1	dbSNP_86	93	4811,3789	613.4+/-396.1	1352,2107,841	no	coding-synonymous	PEF1	NM_012392.3		1429,2683,2391	GG,GA,AA		44.0581,16.5683,42.6034		268/285	32096265	5541,7465	2203	4300	6503	SO:0001819	synonymous_variant	553115	exon5			GAGCCGAATGTTG		CCDS345.1	1p34	2013-01-10			ENSG00000162517	ENSG00000162517		"""EF-hand domain containing"""	30009	protein-coding gene	gene with protein product	"""peflin"""	610033				10486255, 11883899	Standard	NM_012392		Approved	PEF1A	uc001bth.2	Q9UBV8	OTTHUMG00000003877	ENST00000373703.4:c.804T>C	1.37:g.32096265A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	73	45	0.616438	NM_012392		Silent	SNP	ENST00000373703.4	37	CCDS345.1																																																																																			A|0.587;G|0.413	0.413	strong		0.572	PEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011046.1	NM_012392	
MUC6	4588	hgsc.bcm.edu	37	11	1017552	1017552	+	Missense_Mutation	SNP	T	T	C	rs35868469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1017552T>C	ENST00000421673.2	-	31	5299	c.5249A>G	c.(5248-5250)cAt>cGt	p.H1750R		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1750	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGTGTGTGAATGTAGGGATGT	0.552																																					p.H1750R		Atlas-SNP	.											.	MUC6	408	.	0			c.A5249G						PASS	.	T	ARG/HIS	159,4239		0,159,2040	833.0	788.0	803.0		5249	-4.9	0.0	11	dbSNP_126	803	695,7881		0,695,3593	no	missense	MUC6	NM_005961.2	29	0,854,5633	CC,CT,TT		8.104,3.6153,6.5824	probably-damaging	1750/2440	1017552	854,12120	2199	4288	6487	SO:0001583	missense	4588	exon31			TGTGAATGTAGGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5249A>G	11.37:g.1017552T>C	ENSP00000406861:p.His1750Arg	Somatic	1192	1	0.000838926		WXS	Illumina HiSeq	Phase_I	1211	188	0.155244	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	1.026	-0.683406	0.03353	0.036153	0.08104	ENSG00000184956	ENST00000421673	T	0.17691	2.26	2.44	-4.87	0.03123	.	.	.	.	.	T	0.00906	0.0030	L	0.43152	1.355	0.09310	N	1	D	0.54601	0.967	P	0.58210	0.835	T	0.01508	-1.1337	9	0.23891	T	0.37	.	3.5168	0.07727	0.4627:0.2884:0.0:0.2488	rs35868469	1750	Q6W4X9	MUC6_HUMAN	R	1750	ENSP00000406861:H1750R	ENSP00000406861:H1750R	H	-	2	0	MUC6	1007552	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.662000	0.00201	-1.333000	0.02247	-0.736000	0.03550	CAT	T|0.667;C|0.333	0.333	strong		0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
PRKCZ	5590	hgsc.bcm.edu	37	1	1987993	1987993	+	IGR	SNP	T	T	C	rs12184	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1987993T>C								RP11-547D24.3 (6484 upstream) : PRKCZ (16907 downstream)																							AGTGCAGGGATGAAGGCCTCA	0.627													C|||	3355	0.669928	0.8873	0.402	5008	,	,		14345	0.9454		0.3429	False		,,,				2504	0.6186				p.D88D		Atlas-SNP	.											.	PRKCZ	84	.	0			c.T264C						PASS	.	C		3609,797	317.4+/-295.1	1478,653,72	74.0	65.0	68.0		264	-3.4	0.6	1	dbSNP_52	68	2955,5645	667.1+/-402.4	516,1923,1861	no	coding-synonymous	PRKCZ	NM_002744.4		1994,2576,1933	CC,CT,TT		34.3605,18.089,49.531		88/593	1987993	6564,6442	2203	4300	6503	SO:0001628	intergenic_variant	5590	exon3			CAGGGATGAAGGC																													1.37:g.1987993T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	194	74	0.381443	NM_002744		Silent	SNP		37																																																																																				T|0.462;C|0.538	0.538	strong	0	0.627								
UBE4B	10277	hgsc.bcm.edu	37	1	10218472	10218472	+	Silent	SNP	T	T	C	rs114291761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:10218472T>C	ENST00000253251.8	+	21	3437	c.2598T>C	c.(2596-2598)caT>caC	p.H866H	UBE4B_ENST00000377157.3_Silent_p.H750H|UBE4B_ENST00000343090.6_Silent_p.H995H					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		TTCGCTATCATATTAGCACCA	0.423													C|||	31	0.0061901	0.0	0.0101	5008	,	,		19646	0.0		0.0219	False		,,,				2504	0.002				p.H995H		Atlas-SNP	.											.	UBE4B	233	.	0			c.T2985C						PASS	.	C	,	25,4381	824.1+/-416.5	0,25,2178	127.0	127.0	127.0		2985,2598	2.2	1.0	1	dbSNP_132	127	213,8387	809.8+/-407.1	2,209,4089	no	coding-synonymous,coding-synonymous	UBE4B	NM_001105562.2,NM_006048.4	,	2,234,6267	CC,CT,TT		2.4767,0.5674,1.8299	,	995/1303,866/1174	10218472	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	10277	exon22			CTATCATATTAGC	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2598T>C	1.37:g.10218472T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_001105562		Silent	SNP	ENST00000253251.8	37	CCDS110.1																																																																																			T|0.985;C|0.015	0.015	strong		0.423	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
ARAP3	64411	hgsc.bcm.edu	37	5	141051236	141051236	+	Silent	SNP	C	C	T	rs12514851	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141051236C>T	ENST00000239440.4	-	12	1820	c.1755G>A	c.(1753-1755)gcG>gcA	p.A585A	ARAP3_ENST00000508305.1_Silent_p.A507A|ARAP3_ENST00000513878.1_Silent_p.A247A	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	585	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GGCCAGGGGTCGCATCTGGAT	0.592													C|||	918	0.183307	0.1286	0.2925	5008	,	,		16224	0.1389		0.173	False		,,,				2504	0.2362				p.A585A		Atlas-SNP	.											.	ARAP3	139	.	0			c.G1755A						PASS	.	C		624,3782	266.2+/-267.1	45,534,1624	41.0	37.0	38.0		1755	-6.9	0.0	5	dbSNP_120	38	1270,7330	247.2+/-275.4	108,1054,3138	no	coding-synonymous	ARAP3	NM_022481.5		153,1588,4762	TT,TC,CC		14.7674,14.1625,14.5625		585/1545	141051236	1894,11112	2203	4300	6503	SO:0001819	synonymous_variant	64411	exon12			AGGGGTCGCATCT	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.1755G>A	5.37:g.141051236C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	199	58	0.291457	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																			C|0.849;T|0.151	0.151	strong		0.592	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
SCEL	8796	hgsc.bcm.edu	37	13	78216915	78216915	+	Silent	SNP	C	C	T	rs2813739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:78216915C>T	ENST00000349847.3	+	32	2106	c.2022C>T	c.(2020-2022)caC>caT	p.H674H	SCEL_ENST00000377246.3_Silent_p.H654H|SCEL_ENST00000535157.1_Silent_p.H632H	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	674	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AGACAATACACTGTGAACCTT	0.318													C|||	755	0.150759	0.1626	0.1556	5008	,	,		16708	0.1409		0.1252	False		,,,				2504	0.1677				p.H674H		Atlas-SNP	.											.	SCEL	85	.	0			c.C2022T						PASS	.	C	,,	750,3656	304.4+/-288.4	65,620,1518	106.0	106.0	106.0		1896,1962,2022	1.9	1.0	13	dbSNP_100	106	1240,7356	246.5+/-274.9	104,1032,3162	no	coding-synonymous,coding-synonymous,coding-synonymous	SCEL	NM_001160706.1,NM_003843.3,NM_144777.2	,,	169,1652,4680	TT,TC,CC		14.4253,17.0222,15.3053	,,	632/647,654/669,674/689	78216915	1990,11012	2203	4298	6501	SO:0001819	synonymous_variant	8796	exon32			AATACACTGTGAA	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.2022C>T	13.37:g.78216915C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Silent	SNP	ENST00000349847.3	37	CCDS9459.1																																																																																			C|0.851;T|0.149	0.149	strong		0.318	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	
USP29	57663	hgsc.bcm.edu	37	19	57642098	57642098	+	Silent	SNP	G	G	A	rs3764574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57642098G>A	ENST00000254181.4	+	4	2509	c.2055G>A	c.(2053-2055)gtG>gtA	p.V685V	USP29_ENST00000598197.1_Silent_p.V685V	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	685	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTCAAGAGGTGCCTCAACATC	0.448													G|||	2139	0.427117	0.289	0.4712	5008	,	,		21588	0.3611		0.5139	False		,,,				2504	0.5613				p.V685V		Atlas-SNP	.											.	USP29	186	.	0			c.G2055A						PASS	.	G		1443,2963	468.7+/-355.2	248,947,1008	70.0	65.0	67.0		2055	0.2	0.0	19	dbSNP_107	67	4573,4027	598.1+/-393.9	1243,2087,970	no	coding-synonymous	USP29	NM_020903.2		1491,3034,1978	AA,AG,GG		46.8256,32.7508,46.2556		685/923	57642098	6016,6990	2203	4300	6503	SO:0001819	synonymous_variant	57663	exon4			AGAGGTGCCTCAA		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"""Ubiquitin-specific peptidases"""	18563	protein-coding gene	gene with protein product		609546	"""ubiquitin specific protease 29"""			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.2055G>A	19.37:g.57642098G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	156	88	0.564103	NM_020903		Silent	SNP	ENST00000254181.4	37	CCDS33124.1																																																																																			G|0.565;A|0.435	0.435	strong		0.448	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1		
NIN	51199	hgsc.bcm.edu	37	14	51221341	51221341	+	Silent	SNP	C	C	T	rs45578537	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:51221341C>T	ENST00000382041.3	-	20	4864	c.4674G>A	c.(4672-4674)acG>acA	p.T1558T	NIN_ENST00000382043.4_Silent_p.T845T|NIN_ENST00000245441.5_Silent_p.T1558T|NIN_ENST00000453196.1_Silent_p.T1558T|NIN_ENST00000530997.2_Silent_p.T1558T|NIN_ENST00000324330.9_Silent_p.T1558T|NIN_ENST00000389868.3_Silent_p.T845T	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1558					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TTACAGTTTCCGTTTTTTGCC	0.279			T	PDGFRB	MPD								C|||	15	0.00299521	0.0008	0.0101	5008	,	,		18138	0.0		0.007	False		,,,				2504	0.0				p.T1558T		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.G4674A						PASS	.	C	,,,	10,4386	16.8+/-37.8	0,10,2188	70.0	67.0	68.0		2535,4674,4674,4674	2.0	1.0	14	dbSNP_127	68	141,8449	67.7+/-130.1	1,139,4155	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,,,	1,149,6343	TT,TC,CC		1.6414,0.2275,1.1628	,,,	845/1378,1558/2134,1558/2047,1558/2091	51221341	151,12835	2198	4295	6493	SO:0001819	synonymous_variant	51199	exon20			AGTTTCCGTTTTT	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.4674G>A	14.37:g.51221341C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	12	0.005494505494505495	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	5	0.006596306068601583	C	2.013	-0.426698	0.04701	0.002275	0.016414	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	4.77	2.01	0.26516	.	.	.	.	.	T	0.37972	0.1023	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34675	-0.9819	4	.	.	.	-4.709	6.3923	0.21593	0.0:0.0876:0.1572:0.7551	rs45578537;rs61743917	.	.	.	R	1049	.	.	G	-	1	0	NIN	50291091	0.998000	0.40836	0.997000	0.53966	0.467000	0.32768	0.243000	0.18106	0.774000	0.33427	-0.440000	0.05779	GGA	C|0.989;T|0.011	0.011	strong		0.279	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
ADPGK	83440	hgsc.bcm.edu	37	15	73052840	73052840	+	Missense_Mutation	SNP	T	T	C	rs8024644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:73052840T>C	ENST00000311669.8	-	4	644	c.551A>G	c.(550-552)aAg>aGg	p.K184R	ADPGK_ENST00000567733.1_5'UTR	NM_031284.4	NP_112574.3	Q9BRR6	ADPGK_HUMAN	ADP-dependent glucokinase	184	ADPK. {ECO:0000255|PROSITE- ProRule:PRU00584}.		K -> R (in dbSNP:rs8024644).		glycolytic process (GO:0006096)	extracellular region (GO:0005576)|membrane (GO:0016020)	ADP-specific glucokinase activity (GO:0043843)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	7						CTCATGTAGCTTTGGACCAAC	0.498													T|||	1033	0.20627	0.3404	0.1657	5008	,	,		19748	0.2252		0.1441	False		,,,				2504	0.0982				p.K184R		Atlas-SNP	.											.	ADPGK	19	.	0			c.A551G						PASS	.	T	ARG/LYS	1135,2845		173,789,1028	127.0	128.0	128.0		551	5.4	1.0	15	dbSNP_116	128	1114,7196		72,970,3113	yes	missense	ADPGK	NM_031284.4	26	245,1759,4141	CC,CT,TT		13.4055,28.5176,18.2994	possibly-damaging	184/497	73052840	2249,10041	1990	4155	6145	SO:0001583	missense	83440	exon4			TGTAGCTTTGGAC	AL136873	CCDS42057.1	15q24.1	2012-07-02			ENSG00000159322	ENSG00000159322			25250	protein-coding gene	gene with protein product		611861				11230166	Standard	NM_031284		Approved	DKFZp434B195, ADP-GK	uc002avf.4	Q9BRR6	OTTHUMG00000172777	ENST00000311669.8:c.551A>G	15.37:g.73052840T>C	ENSP00000312250:p.Lys184Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_031284	Q49AU7|Q8NBI1|Q8WZ90|Q96NF8|Q9H0A7	Missense_Mutation	SNP	ENST00000311669.8	37	CCDS42057.1	426	0.19505494505494506	153	0.31097560975609756	36	0.09944751381215469	135	0.23601398601398602	102	0.1345646437994723	T	19.22	3.785862	0.70337	0.285176	0.134055	ENSG00000159322	ENST00000311669;ENST00000443764;ENST00000331065	T	0.49720	0.77	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.52011	1.625	0.09310	P	1.0	P;P;P	0.48162	0.767;0.906;0.812	P;P;B	0.49561	0.615;0.615;0.355	T	0.22836	-1.0205	9	0.25106	T	0.35	-25.8753	15.5	0.75691	0.0:0.0:0.0:1.0	rs8024644	126;184;184	B4DG35;Q9BRR6;Q9BRR6-2	.;ADPGK_HUMAN;.	R	184;103;62	ENSP00000312250:K184R	ENSP00000312250:K184R	K	-	2	0	ADPGK	70839893	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.603000	0.82811	2.068000	0.61886	0.533000	0.62120	AAG	T|0.828;C|0.172	0.172	strong		0.498	ADPGK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420434.1	NM_031284	
TGM3	7053	hgsc.bcm.edu	37	20	2290333	2290333	+	Missense_Mutation	SNP	C	C	A	rs214803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2290333C>A	ENST00000381458.5	+	2	101	c.38C>A	c.(37-39)aCg>aAg	p.T13K		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	13			T -> K (in dbSNP:rs214803). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8099584, ECO:0000269|Ref.3, ECO:0000269|Ref.5, ECO:0000269|Ref.7}.		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)	p.T13M(1)		breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	AACTGGCAGACGGCCTTCAAC	0.522													C|||	3719	0.742612	0.41	0.8329	5008	,	,		21352	0.9246		0.838	False		,,,				2504	0.8425				p.T13K		Atlas-SNP	.											TGM3,caecum,carcinoma,-1,4	TGM3	105	4	1	Substitution - Missense(1)	large_intestine(1)	c.C38A						PASS	.	C	LYS/THR	2137,2269	580.0+/-385.0	504,1129,570	126.0	112.0	117.0		38	-1.1	0.0	20	dbSNP_79	117	7058,1542	746.8+/-407.3	2900,1258,142	yes	missense	TGM3	NM_003245.3	78	3404,2387,712	AA,AC,CC		17.9302,48.502,29.3019	benign	13/694	2290333	9195,3811	2203	4300	6503	SO:0001583	missense	7053	exon2			GGCAGACGGCCTT	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"""Transglutaminases"""	11779	protein-coding gene	gene with protein product	"""E polypeptide, protein-glutamine-gamma-glutamyltransferase"""	600238	"""transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.38C>A	20.37:g.2290333C>A	ENSP00000370867:p.Thr13Lys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	1675	0.766941391941392	211	0.42886178861788615	293	0.8093922651933702	539	0.9423076923076923	632	0.8337730870712401	C	9.284	1.048874	0.19827	0.48502	0.820698	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.84223	-1.82	5.53	-1.08	0.09936	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	1.443610	0.03527	N	0.221885	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	P	0.40681	0.727	B	0.24269	0.052	T	0.48375	-0.9041	9	0.28530	T	0.3	-12.1737	2.9077	0.05726	0.3045:0.2675:0.0:0.428	rs214803;rs3844903;rs52815802;rs60904394;rs214803	13	Q08188	TGM3_HUMAN	K	13	ENSP00000370867:T13K	ENSP00000370867:T13K	T	+	2	0	TGM3	2238333	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.742000	0.01835	-0.157000	0.11059	-0.367000	0.07326	ACG	T|0.002;G|0.003	.	strong		0.522	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245	
GIPC1	10755	hgsc.bcm.edu	37	19	14590236	14590236	+	Silent	SNP	C	C	T	rs3815715	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14590236C>T	ENST00000393033.4	-	7	1025	c.756G>A	c.(754-756)acG>acA	p.T252T	GIPC1_ENST00000393029.3_Silent_p.T155T|GIPC1_ENST00000345425.2_Silent_p.T252T|GIPC1_ENST00000586027.1_Silent_p.T252T|GIPC1_ENST00000591349.1_Silent_p.T155T|GIPC1_ENST00000393028.1_Silent_p.T155T	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	252					endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						GATCCTCCACCGTGGCGGGGC	0.622													c|||	1539	0.307308	0.1195	0.2536	5008	,	,		12956	0.6448		0.2555	False		,,,				2504	0.3047				p.T252T	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											GIPC1,NS,carcinoma,0,1	GIPC1	21	1	0			c.G756A						PASS	.	C	,,,,,	566,3768		50,466,1651	7.0	9.0	9.0		756,465,756,465,756,465	-8.1	0.9	19	dbSNP_107	9	2343,6163		364,1615,2274	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GIPC1	NM_005716.2,NM_202467.1,NM_202468.1,NM_202469.1,NM_202470.1,NM_202494.1	,,,,,	414,2081,3925	TT,TC,CC		27.5453,13.0595,22.6558	,,,,,	252/334,155/237,252/334,155/237,252/334,155/237	14590236	2909,9931	2167	4253	6420	SO:0001819	synonymous_variant	10755	exon6			CTCCACCGTGGCG	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"""chromosome 19 open reading frame 3"", ""regulator of G-protein signalling 19 interacting protein 1"""	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.756G>A	19.37:g.14590236C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Silent	SNP	ENST00000393033.4	37	CCDS12310.1																																																																																			C|0.678;T|0.322	0.322	strong		0.622	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		
SEMA4F	10505	hgsc.bcm.edu	37	2	74883750	74883750	+	Missense_Mutation	SNP	G	G	A	rs139676653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74883750G>A	ENST00000357877.2	+	2	384	c.235G>A	c.(235-237)Gtt>Att	p.V79I	SEMA4F_ENST00000339773.5_Missense_Mutation_p.V79I	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	79	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						CACACTTTATGTTGGCGCCCG	0.577													G|||	14	0.00279553	0.0	0.0043	5008	,	,		18054	0.0		0.0109	False		,,,				2504	0.0				p.V79I		Atlas-SNP	.											.	SEMA4F	89	.	0			c.G235A						PASS	.	G	ILE/VAL	4,4402	11.4+/-27.6	0,4,2199	121.0	108.0	112.0		235	3.1	1.0	2	dbSNP_134	112	66,8534	39.8+/-96.3	0,66,4234	yes	missense	SEMA4F	NM_004263.3	29	0,70,6433	AA,AG,GG		0.7674,0.0908,0.5382	probably-damaging	79/771	74883750	70,12936	2203	4300	6503	SO:0001583	missense	10505	exon2			CTTTATGTTGGCG	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"""Semaphorins"""	10734	protein-coding gene	gene with protein product	"""m-Sema M"""	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.235G>A	2.37:g.74883750G>A	ENSP00000350547:p.Val79Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_001271662	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	20	0.009157509157509158	1	0.0020325203252032522	3	0.008287292817679558	1	0.0017482517482517483	15	0.01978891820580475	G	12.16	1.855717	0.32791	9.08E-4	0.007674	ENSG00000135622	ENST00000357877;ENST00000339773;ENST00000434486;ENST00000453930	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	4.9	3.12	0.35913	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.176655	0.38164	N	0.001800	T	0.18509	0.0444	L	0.37697	1.125	0.21579	N	0.999638	B;B;B;D	0.55605	0.005;0.003;0.002;0.972	B;B;B;D	0.66716	0.015;0.01;0.007;0.946	T	0.03403	-1.1040	10	0.29301	T	0.29	.	7.4621	0.27302	0.1937:0.0:0.8063:0.0	.	79;79;79;79	B7Z931;C9K0A1;O95754-2;O95754	.;.;.;SEM4F_HUMAN	I	79	ENSP00000350547:V79I;ENSP00000342675:V79I;ENSP00000407698:V79I;ENSP00000409141:V79I	ENSP00000342675:V79I	V	+	1	0	SEMA4F	74737258	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	2.773000	0.47686	0.688000	0.31529	-0.143000	0.13931	GTT	G|0.993;A|0.007	0.007	strong		0.577	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263	
ZCCHC3	85364	hgsc.bcm.edu	37	20	278806	278806	+	Silent	SNP	C	C	T	rs1057189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:278806C>T	ENST00000382352.3	+	1	1070	c.579C>T	c.(577-579)tcC>tcT	p.S193S		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	193							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			TCCTGCGCTCCATCGGCATGG	0.662													C|||	853	0.170327	0.0098	0.1383	5008	,	,		12987	0.3294		0.2694	False		,,,				2504	0.1442				p.S193S		Atlas-SNP	.											.	ZCCHC3	20	.	0			c.C579T						PASS	.	C		178,3688		4,170,1759	21.0	22.0	22.0		579	3.0	1.0	20	dbSNP_86	22	2318,5894		336,1646,2124	no	coding-synonymous	ZCCHC3	NM_033089.6		340,1816,3883	TT,TC,CC		28.227,4.6042,20.6657		193/405	278806	2496,9582	1933	4106	6039	SO:0001819	synonymous_variant	85364	exon1			GCGCTCCATCGGC	AL034548	CCDS42844.1	20p13-p12.2	2014-04-10	2004-07-14	2004-07-14	ENSG00000177764	ENSG00000247315		"""Zinc fingers, CCHC domain containing"""	16230	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 99"""	C20orf99			Standard	NM_033089		Approved	dJ1103G7.7	uc002wdf.3	Q9NUD5	OTTHUMG00000188280	ENST00000382352.3:c.579C>T	20.37:g.278806C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_033089	Q3B7J3|Q6NT79	Silent	SNP	ENST00000382352.3	37	CCDS42844.1																																																																																			C|0.780;T|0.220	0.220	strong		0.662	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1		
DNAJB13	374407	hgsc.bcm.edu	37	11	73681135	73681135	+	Missense_Mutation	SNP	G	G	A	rs72982975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:73681135G>A	ENST00000339764.1	+	8	1678	c.927G>A	c.(925-927)atG>atA	p.M309I	RP11-167N4.2_ENST00000537019.1_RNA|DNAJB13_ENST00000537753.1_Missense_Mutation_p.M134I|DNAJB13_ENST00000543947.1_Missense_Mutation_p.M134I	NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	309					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					AGAAGCAGATGCTGCGCCAGG	0.622													g|||	1119	0.223442	0.1929	0.3473	5008	,	,		18231	0.1637		0.2575	False		,,,				2504	0.2035				p.M309I		Atlas-SNP	.											.	DNAJB13	28	.	0			c.G927A						PASS	.	G	ILE/MET	879,3521	342.8+/-307.3	76,727,1397	117.0	108.0	111.0		927	4.6	1.0	11	dbSNP_130	111	2234,6352	378.8+/-339.0	280,1674,2339	yes	missense	DNAJB13	NM_153614.2	10	356,2401,3736	AA,AG,GG		26.0191,19.9773,23.972	benign	309/317	73681135	3113,9873	2200	4293	6493	SO:0001583	missense	374407	exon8			GCAGATGCTGCGC	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"""Heat shock proteins / DNAJ (HSP40)"""	30718	protein-coding gene	gene with protein product	"""radial spoke 16 homolog A (Chlamydomonas)"""	610263	"""DnaJ (Hsp40) related, subfamily B, member 13"""				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.927G>A	11.37:g.73681135G>A	ENSP00000344431:p.Met309Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_153614	B3LEP4|Q8IZW5	Missense_Mutation	SNP	ENST00000339764.1	37	CCDS8227.1	521|521	0.23855311355311357|0.23855311355311357	104|104	0.21138211382113822|0.21138211382113822	118|118	0.3259668508287293|0.3259668508287293	94|94	0.16433566433566432|0.16433566433566432	205|205	0.2704485488126649|0.2704485488126649	G|G	16.13|16.13	3.036820|3.036820	0.54896|0.54896	0.199773|0.199773	0.260191|0.260191	ENSG00000187726|ENSG00000187726	ENST00000542350|ENST00000339764;ENST00000537753;ENST00000543947	.|T;T;T	.|0.39229	.|1.09;1.09;1.09	5.54|5.54	4.59|4.59	0.56863|0.56863	.|HSP40/DnaJ peptide-binding (1);	.|0.115848	.|0.64402	.|D	.|0.000011	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02708|0.02708	-0.52|-0.52	0.31243|0.31243	P|P	0.6949609999999999|0.6949609999999999	.|B	.|0.10296	.|0.003	.|B	.|0.16722	.|0.016	T|T	0.30851|0.30851	-0.9964|-0.9964	4|9	.|0.23891	.|T	.|0.37	.|.	13.1925|13.1925	0.59719|0.59719	0.0:0.2743:0.7257:0.0|0.0:0.2743:0.7257:0.0	.|.	.|309	.|P59910	.|DJB13_HUMAN	T|I	210|309;134;134	.|ENSP00000344431:M309I;ENSP00000439711:M134I;ENSP00000438576:M134I	.|ENSP00000344431:M309I	A|M	+|+	1|3	0|0	DNAJB13|DNAJB13	73358783|73358783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	2.898000|2.898000	0.48672|0.48672	2.619000|2.619000	0.88677|0.88677	0.644000|0.644000	0.83932|0.83932	GCT|ATG	G|0.759;A|0.241	0.241	strong		0.622	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614	
ATG10	83734	hgsc.bcm.edu	37	5	81549216	81549216	+	Missense_Mutation	SNP	C	C	T	rs1864183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:81549216C>T	ENST00000282185.3	+	7	929	c.635C>T	c.(634-636)aCg>aTg	p.T212M	ATG10_ENST00000458350.3_Missense_Mutation_p.T212M|ATG10_ENST00000514253.2_Intron	NM_031482.4	NP_113670.1	Q9H0Y0	ATG10_HUMAN	autophagy related 10	212			T -> M (in dbSNP:rs1864183). {ECO:0000269|PubMed:15489334}.		autophagy (GO:0006914)|autophagy in response to ER overload (GO:0034263)|positive regulation of protein modification process (GO:0031401)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	Atg12 ligase activity (GO:0019777)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(2)	9		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		GCCAAAGCAACGTCTCAGGAT	0.408													C|||	2608	0.520767	0.1747	0.5692	5008	,	,		22191	0.8909		0.4632	False		,,,				2504	0.6319				p.T212M		Atlas-SNP	.											.	ATG10	23	.	0			c.C635T						PASS	.	C	MET/THR,MET/THR	913,3493	350.0+/-310.6	111,691,1401	167.0	143.0	151.0		635,635	1.6	0.0	5	dbSNP_92	151	3996,4604	553.5+/-386.3	891,2214,1195	yes	missense,missense	ATG10	NM_001131028.1,NM_031482.4	81,81	1002,2905,2596	TT,TC,CC		46.4651,20.7217,37.7441	benign,benign	212/221,212/221	81549216	4909,8097	2203	4300	6503	SO:0001583	missense	83734	exon8			AAGCAACGTCTCA	AK024016	CCDS4057.1	5q14.1	2014-02-12	2012-06-06	2005-09-11	ENSG00000152348	ENSG00000152348			20315	protein-coding gene	gene with protein product		610800	"""APG10 autophagy 10-like (S. cerevisiae)"", ""ATG10 autophagy related 10 homolog (S. cerevisiae)"""	APG10L			Standard	NM_031482		Approved	DKFZP586I0418, FLJ13954	uc003khr.3	Q9H0Y0	OTTHUMG00000119041	ENST00000282185.3:c.635C>T	5.37:g.81549216C>T	ENSP00000282185:p.Thr212Met	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	NM_001131028	B2RE09|Q6PIX1|Q9H842	Missense_Mutation	SNP	ENST00000282185.3	37	CCDS4057.1	1177	0.5389194139194139	98	0.1991869918699187	191	0.5276243093922652	520	0.9090909090909091	368	0.48548812664907653	C	11.95	1.792911	0.31685	0.207217	0.464651	ENSG00000152348	ENST00000282185;ENST00000458350	T;T	0.22945	1.93;1.93	6.07	1.65	0.23941	.	1.104980	0.06687	N	0.768935	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.24882	0.113	B	0.11329	0.006	T	0.25467	-1.0131	9	0.39692	T	0.17	-20.7711	5.6695	0.17715	0.0:0.4901:0.2977:0.2122	rs1864183;rs17246167;rs17856117;rs17856773;rs57781122;rs1864183	212	Q9H0Y0	ATG10_HUMAN	M	212	ENSP00000282185:T212M;ENSP00000404938:T212M	ENSP00000282185:T212M	T	+	2	0	ATG10	81584972	0.000000	0.05858	0.000000	0.03702	0.132000	0.20833	-0.065000	0.11617	0.404000	0.25506	0.655000	0.94253	ACG	C|0.552;T|0.448	0.448	strong		0.408	ATG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239252.2	NM_001131028	
SNX15	29907	hgsc.bcm.edu	37	11	64799998	64799998	+	Silent	SNP	T	T	C	rs534236	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64799998T>C	ENST00000377244.3	+	3	361	c.231T>C	c.(229-231)ccT>ccC	p.P77P	RP11-399J13.3_ENST00000301886.3_3'UTR|SNX15_ENST00000352068.5_Silent_p.P77P	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	77	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						AGGAGTTCCCTGCTTTCCCCC	0.627													T|||	1876	0.374601	0.2148	0.6052	5008	,	,		17784	0.1825		0.6213	False		,,,				2504	0.3712				p.P77P	Esophageal Squamous(56;269 1304 3324 8253)	Atlas-SNP	.											.	SNX15	35	.	0			c.T231C						PASS	.	T	,	1272,3130	432.0+/-343.1	181,910,1110	65.0	55.0	59.0		231,231	-7.7	0.1	11	dbSNP_83	59	5552,3042	661.1+/-401.8	1775,2002,520	no	coding-synonymous,coding-synonymous	SNX15	NM_013306.4,NM_147777.3	,	1956,2912,1630	CC,CT,TT		35.3968,28.896,47.4915	,	77/343,77/257	64799998	6824,6172	2201	4297	6498	SO:0001819	synonymous_variant	29907	exon3			GTTCCCTGCTTTC	AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"""Sorting nexins"""	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.231T>C	11.37:g.64799998T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_147777	E5KQS6|Q9NRS5	Silent	SNP	ENST00000377244.3	37	CCDS8089.1	937	0.429029304029304	135	0.27439024390243905	223	0.6160220994475138	102	0.17832167832167833	477	0.6292875989445911	T	8.195	0.796932	0.16327	0.28896	0.646032	ENSG00000110025	ENST00000525648	.	.	.	4.89	-7.72	0.01250	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22745	P	0.99878566	.	.	.	.	.	.	T	0.45116	-0.9283	3	.	.	.	-21.2781	0.5102	0.00594	0.2697:0.1373:0.207:0.386	rs534236;rs17850569;rs534236	.	.	.	P	36	.	.	L	+	2	0	SNX15	64556574	0.000000	0.05858	0.061000	0.19648	0.029000	0.11900	-4.252000	0.00266	-1.237000	0.02539	-0.242000	0.12053	CTG	T|0.524;C|0.476	0.476	strong		0.627	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3		
CRTAC1	55118	hgsc.bcm.edu	37	10	99664456	99664456	+	Silent	SNP	T	T	C	rs7068503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:99664456T>C	ENST00000370597.3	-	7	1321	c.966A>G	c.(964-966)caA>caG	p.Q322Q	CRTAC1_ENST00000298819.4_Silent_p.Q322Q|CRTAC1_ENST00000370591.2_Silent_p.Q322Q	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	322						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GGGTGCTCATTTGCAGATAGA	0.572													C|||	491	0.0980431	0.1422	0.0476	5008	,	,		15318	0.0863		0.0527	False		,,,				2504	0.1329				p.Q322Q		Atlas-SNP	.											.	CRTAC1	86	.	0			c.A966G						PASS	.	C	,	600,3806	770.2+/-413.7	45,510,1648	100.0	101.0	101.0		966,966	3.1	1.0	10	dbSNP_116	101	632,7968	790.4+/-407.6	24,584,3692	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	69,1094,5340	CC,CT,TT		7.3488,13.6178,9.4726	,	322/646,322/662	99664456	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	55118	exon7			GCTCATTTGCAGA	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.966A>G	10.37:g.99664456T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																			T|0.914;C|0.086	0.086	strong		0.572	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
PTCHD2	57540	hgsc.bcm.edu	37	1	11561593	11561593	+	Missense_Mutation	SNP	G	G	A	rs2817580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11561593G>A	ENST00000294484.6	+	2	682	c.544G>A	c.(544-546)Ggc>Agc	p.G182S	PTCHD2_ENST00000389575.3_Missense_Mutation_p.G182S	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	182			G -> S (in dbSNP:rs2817580). {ECO:0000269|PubMed:10718198}.		cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CTCACTCGGTGGCCCAGGCCC	0.692													G|||	1862	0.371805	0.143	0.6311	5008	,	,		13855	0.2718		0.659	False		,,,				2504	0.3047				p.G182S		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G544A						PASS	.	G	SER/GLY	960,2852		150,660,1096	12.0	15.0	14.0		544	0.8	0.0	1	dbSNP_100	14	5214,3008		1659,1896,556	yes	missense	PTCHD2	NM_020780.1	56	1809,2556,1652	AA,AG,GG		36.5848,25.1836,48.6954	benign	182/1393	11561593	6174,5860	1906	4111	6017	SO:0001583	missense	57540	exon2			CTCGGTGGCCCAG	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.544G>A	1.37:g.11561593G>A	ENSP00000294484:p.Gly182Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	949	0.43452380952380953	71	0.1443089430894309	219	0.6049723756906077	157	0.2744755244755245	502	0.662269129287599	G	3.922	-0.017933	0.07681	0.251836	0.634152	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.21734	1.99;1.99	2.78	0.794	0.18638	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.13594	0.008	B	0.14578	0.011	T	0.33420	-0.9869	8	0.12430	T	0.62	.	6.4306	0.21794	0.2544:0.0:0.7456:0.0	rs2817580;rs3738160;rs2817580	182	Q9P2K9	PTHD2_HUMAN	S	182	ENSP00000294484:G182S;ENSP00000374226:G182S	ENSP00000294484:G182S	G	+	1	0	PTCHD2	11484180	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	0.106000	0.15354	0.058000	0.16222	0.561000	0.74099	GGC	G|0.586;A|0.414	0.414	strong		0.692	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
PABPC4	8761	hgsc.bcm.edu	37	1	40030823	40030823	+	Silent	SNP	C	C	T	rs12127094	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:40030823C>T	ENST00000372857.3	-	8	1992	c.1200G>A	c.(1198-1200)caG>caA	p.Q400Q	SNORA55_ENST00000364587.1_RNA|PABPC4_ENST00000372856.3_Silent_p.Q400Q|PABPC4_ENST00000372858.3_Silent_p.Q400Q|RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000372862.3_Silent_p.Q400Q	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	400					blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CAGGCTGGAACTGATTTAAGA	0.552													C|||	187	0.0373403	0.0061	0.0418	5008	,	,		18159	0.0179		0.1083	False		,,,				2504	0.0235				p.Q400Q		Atlas-SNP	.											.	PABPC4	56	.	0			c.G1200A						PASS	.	C	,,	82,4324	70.9+/-108.8	1,80,2122	70.0	62.0	64.0		1200,1200,1200	4.1	1.0	1	dbSNP_120	64	767,7833	182.3+/-230.8	35,697,3568	no	coding-synonymous,coding-synonymous,coding-synonymous	PABPC4	NM_001135653.1,NM_001135654.1,NM_003819.3	,,	36,777,5690	TT,TC,CC		8.9186,1.8611,6.5278	,,	400/661,400/632,400/645	40030823	849,12157	2203	4300	6503	SO:0001819	synonymous_variant	8761	exon8			CTGGAACTGATTT	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"""RNA binding motif (RRM) containing"""	8557	protein-coding gene	gene with protein product		603407	"""poly(A)-binding protein, cytoplasmic 4 (inducible form)"""			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.1200G>A	1.37:g.40030823C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	19	0.333333	NM_001135653	B1ANQ8|Q4VC03|Q6P0N3	Silent	SNP	ENST00000372857.3	37	CCDS438.1	112	0.05128205128205128	4	0.008130081300813009	22	0.06077348066298342	2	0.0034965034965034965	84	0.11081794195250659	C	9.118	1.008370	0.19199	0.018611	0.089186	ENSG00000090621	ENST00000421687;ENST00000527718	.	.	.	5.97	4.12	0.48240	.	.	.	.	.	T	0.03390	0.0098	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02037	-1.1225	4	.	.	.	.	12.8114	0.57641	0.0:0.8679:0.0:0.1321	rs12127094;rs12127094	.	.	.	N	302;127	.	.	S	-	2	0	PABPC4	39803410	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.716000	0.47219	0.867000	0.35654	-0.136000	0.14681	AGT	C|0.940;T|0.060	0.060	strong		0.552	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653	
RNPEP	6051	hgsc.bcm.edu	37	1	201969082	201969082	+	Silent	SNP	G	G	A	rs1130790	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201969082G>A	ENST00000295640.4	+	6	1186	c.1143G>A	c.(1141-1143)caG>caA	p.Q381Q	RP11-465N4.4_ENST00000419190.1_RNA|RNPEP_ENST00000471105.1_3'UTR|RNPEP_ENST00000367286.3_Silent_p.Q342Q|RP11-465N4.4_ENST00000415582.1_RNA	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	381					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)	p.Q381Q(1)		breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		TGCTGCGTCAGCACATGGACA	0.577											OREG0014093	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1545	0.308506	0.1558	0.438	5008	,	,		18265	0.3978		0.4284	False		,,,				2504	0.2076				p.Q381Q	GBM(19;39 479 7473 13131 19462)	Atlas-SNP	.											RNPEP,NS,carcinoma,0,2	RNPEP	39	2	1	Substitution - coding silent(1)	stomach(1)	c.G1143A						PASS	.	G		802,3604	320.2+/-296.5	72,658,1473	96.0	83.0	87.0		1143	4.3	1.0	1	dbSNP_86	87	3723,4877	529.8+/-381.7	795,2133,1372	no	coding-synonymous	RNPEP	NM_020216.3		867,2791,2845	AA,AG,GG		43.2907,18.2025,34.7916		381/651	201969082	4525,8481	2203	4300	6503	SO:0001819	synonymous_variant	6051	exon6			GCGTCAGCACATG	BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.1143G>A	1.37:g.201969082G>A		Somatic	166	0	0	2125	WXS	Illumina HiSeq	Phase_I	204	112	0.54902	NM_020216	Q9BVM9|Q9H1D4|Q9NPT7	Silent	SNP	ENST00000295640.4	37	CCDS1418.1																																																																																			G|0.652;A|0.348	0.348	strong		0.577	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216	
TRABD2A	129293	hgsc.bcm.edu	37	2	85059204	85059204	+	Missense_Mutation	SNP	C	C	T	rs201984217		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85059204C>T	ENST00000409520.2	-	5	1099	c.1057G>A	c.(1057-1059)Gcc>Acc	p.A353T	TRABD2A_ENST00000479944.1_5'UTR|TRABD2A_ENST00000335459.5_Missense_Mutation_p.A304T	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	353					head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										CCAGCAGGGGCGTGTTCTACC	0.562													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19756	0.0		0.0	False		,,,				2504	0.0				p.V304I		Atlas-SNP	.											.	.	.	.	0			c.G910A						PASS	.						135.0	134.0	134.0					2																	85059204		2027	4201	6228	SO:0001583	missense	129293	exon4			CAGGGGCGTGTTC	BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"""chromosome 2 open reading frame 89"""	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.1057G>A	2.37:g.85059204C>T	ENSP00000387075:p.Ala353Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_001080824	B4DKK8|I6UMB9	Missense_Mutation	SNP	ENST00000409520.2	37		.	.	.	.	.	.	.	.	.	.	C	0.676	-0.799962	0.02841	.	.	ENSG00000186854	ENST00000335459;ENST00000409520	T;T	0.19532	2.25;2.14	2.76	0.829	0.18847	.	0.419056	0.20863	N	0.084306	T	0.07503	0.0189	.	.	.	0.23492	N	0.997562	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.30534	-0.9975	9	0.10636	T	0.68	.	2.0163	0.03499	0.277:0.4522:0.0:0.2708	.	353;304	Q86V40;Q86V40-2	CB089_HUMAN;.	T	304;353	ENSP00000335004:A304T;ENSP00000387075:A353T	ENSP00000335004:A304T	A	-	1	0	C2orf89	84912715	1.000000	0.71417	0.990000	0.47175	0.749000	0.42624	0.750000	0.26334	0.465000	0.27167	0.462000	0.41574	GCC	C|0.998;T|0.002	0.002	weak		0.562	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824	
FOXO3	2309	hgsc.bcm.edu	37	6	108882915	108882915	+	Silent	SNP	C	C	T	rs150320900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:108882915C>T	ENST00000343882.6	+	2	808	c.504C>T	c.(502-504)cgC>cgT	p.R168R	FOXO3_ENST00000406360.1_Silent_p.R168R	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	168					antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		TGATCACCCGCGCCATCGAGA	0.657													C|||	12	0.00239617	0.0	0.0029	5008	,	,		13235	0.0		0.008	False		,,,				2504	0.002				p.R168R		Atlas-SNP	.											.	FOXO3	67	.	0			c.C504T						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	28.0	24.0	25.0		504,504	0.4	1.0	6	dbSNP_134	25	70,8530	42.2+/-99.7	0,70,4230	no	coding-synonymous,coding-synonymous	FOXO3	NM_001455.3,NM_201559.2	,	0,73,6430	TT,TC,CC		0.814,0.0681,0.5613	,	168/674,168/674	108882915	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	2309	exon1			CACCCGCGCCATC	AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"""Forkhead boxes"""	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.504C>T	6.37:g.108882915C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	127	65	0.511811	NM_001455	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Silent	SNP	ENST00000343882.6	37	CCDS5068.1																																																																																			C|0.995;T|0.005	0.005	strong		0.657	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2		
LAMA5	3911	hgsc.bcm.edu	37	20	60927412	60927412	+	Silent	SNP	G	G	A	rs624313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60927412G>A	ENST00000252999.3	-	4	639	c.573C>T	c.(571-573)tcC>tcT	p.S191S	RP11-157P1.5_ENST00000477848.1_RNA|RP11-157P1.5_ENST00000487421.1_RNA|LAMA5_ENST00000370692.3_Silent_p.S191S|LAMA5_ENST00000370677.3_Silent_p.S191S|RP11-157P1.5_ENST00000478167.1_RNA|RP11-157P1.5_ENST00000456721.2_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	191	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGTCCCTCTTGGAGGCTGCGG	0.692													g|||	2599	0.51897	0.1036	0.6369	5008	,	,		12934	0.7341		0.6581	False		,,,				2504	0.6319				p.S191S		Atlas-SNP	.											LAMA5,NS,carcinoma,0,2	LAMA5	268	2	0			c.C573T						PASS	.			906,3484	327.7+/-300.2	110,686,1399	36.0	34.0	35.0		573	2.9	1.0	20	dbSNP_83	35	5787,2797	655.1+/-401.2	1962,1863,467	no	coding-synonymous	LAMA5	NM_005560.3		2072,2549,1866	AA,AG,GG		32.5839,20.6378,48.4122		191/3696	60927412	6693,6281	2195	4292	6487	SO:0001819	synonymous_variant	3911	exon4			CCTCTTGGAGGCT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.573C>T	20.37:g.60927412G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	45	0.978261	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.486;A|0.514	0.514	strong		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
NRD1	4898	hgsc.bcm.edu	37	1	52266242	52266242	+	Silent	SNP	G	G	A	rs8375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:52266242G>A	ENST00000354831.7	-	23	2820	c.2631C>T	c.(2629-2631)ccC>ccT	p.P877P	NRD1_ENST00000485608.1_5'UTR|RP4-657D16.3_ENST00000586761.1_RNA|RP4-657D16.3_ENST00000588291.1_RNA|NRD1_ENST00000544028.1_Silent_p.P677P|RP4-657D16.6_ENST00000607338.1_RNA|NRD1_ENST00000539524.1_Silent_p.P745P|NRD1_ENST00000352171.7_Silent_p.P809P|RP4-657D16.3_ENST00000591675.1_RNA	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	808					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						CCAAAGTCTCGGGCTTGATGA	0.423													G|||	2449	0.489018	0.2224	0.5937	5008	,	,		20173	0.8234		0.5298	False		,,,				2504	0.3885				p.P877P		Atlas-SNP	.											.	NRD1	89	.	0			c.C2631T						PASS	.	G	,,	1228,3178	426.2+/-341.1	165,898,1140	181.0	171.0	174.0		2427,2235,2631	-4.1	1.0	1	dbSNP_52	174	4321,4279	579.3+/-390.9	1083,2155,1062	no	coding-synonymous,coding-synonymous,coding-synonymous	NRD1	NM_001101662.1,NM_001242361.1,NM_002525.2	,,	1248,3053,2202	AA,AG,GG		49.7558,27.8711,42.6649	,,	809/1152,745/1088,877/1220	52266242	5549,7457	2203	4300	6503	SO:0001819	synonymous_variant	4898	exon23			AGTCTCGGGCTTG	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.2631C>T	1.37:g.52266242G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	203	72	0.35468	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	37	CCDS559.1	1176	0.5384615384615384	114	0.23170731707317074	202	0.5580110497237569	466	0.8146853146853147	394	0.5197889182058048	G	6.926	0.540470	0.13250	0.278711	0.502442	ENSG00000078618	ENST00000440943	.	.	.	4.91	-4.12	0.03916	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999272099	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.6477	1.9029	0.03271	0.3099:0.0964:0.3421:0.2516	rs8375;rs1126997;rs2273199;rs3182412;rs10888734;rs11558620;rs17295088;rs17349599;rs17371636;rs17845186;rs17857996;rs56482093;rs60687281;rs10888734	.	.	.	X	224	.	.	R	-	1	2	NRD1	52038830	0.000000	0.05858	0.990000	0.47175	0.950000	0.60333	-3.991000	0.00318	-0.487000	0.06735	-2.102000	0.00361	CGA	T|0.088;G|0.434;C|0.096;A|0.382	0.382	strong		0.423	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
ULK2	9706	hgsc.bcm.edu	37	17	19729495	19729495	+	Silent	SNP	T	T	C	rs157397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:19729495T>C	ENST00000395544.4	-	11	1291	c.792A>G	c.(790-792)gcA>gcG	p.A264A	ULK2_ENST00000580130.1_Intron|ULK2_ENST00000361658.2_Silent_p.A264A	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	264	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					GGCTAAAAAATGCTTCTGTAA	0.303													T|||	3977	0.794129	0.7489	0.8948	5008	,	,		8576	0.5923		0.9642	False		,,,				2504	0.817				p.A264A		Atlas-SNP	.											.	ULK2	142	.	0			c.A792G						PASS	.	T	,	3511,895	735.5+/-410.7	1400,711,92	79.0	81.0	80.0		792,792	-3.1	1.0	17	dbSNP_79	80	8308,282	803.0+/-407.3	4021,266,8	no	coding-synonymous,coding-synonymous	ULK2	NM_001142610.1,NM_014683.3	,	5421,977,100	CC,CT,TT		3.2829,20.3132,9.0566	,	264/1037,264/1037	19729495	11819,1177	2203	4295	6498	SO:0001819	synonymous_variant	9706	exon11			AAAAAATGCTTCT	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"""unc-51 (C. elegans)-like kinase 2"", ""unc-51-like kinase 2 (C. elegans)"""			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.792A>G	17.37:g.19729495T>C		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	244	243	0.995902	NM_001142610	A8MY69|O75119	Silent	SNP	ENST00000395544.4	37	CCDS11213.1																																																																																			T|0.140;C|0.860	0.860	strong		0.303	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683	
IQCG	84223	hgsc.bcm.edu	37	3	197670652	197670652	+	Silent	SNP	G	G	A	rs3828371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:197670652G>A	ENST00000265239.6	-	4	703	c.279C>T	c.(277-279)tgC>tgT	p.C93C	IQCG_ENST00000453254.1_Silent_p.C93C|IQCG_ENST00000455191.1_Silent_p.C93C|IQCG_ENST00000480302.1_5'UTR	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	93						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		TCTATACCACGCAGATGCTCT	0.413													G|||	340	0.0678914	0.0961	0.0187	5008	,	,		20049	0.0526		0.0507	False		,,,				2504	0.0982				p.C93C		Atlas-SNP	.											.	IQCG	44	.	0			c.C279T						PASS	.	G	,	437,3969	212.5+/-232.4	26,385,1792	120.0	120.0	120.0		279,279	1.5	0.0	3	dbSNP_107	120	387,8213	125.6+/-184.2	9,369,3922	no	coding-synonymous,coding-synonymous	IQCG	NM_001134435.1,NM_032263.3	,	35,754,5714	AA,AG,GG		4.5,9.9183,6.3355	,	93/444,93/444	197670652	824,12182	2203	4300	6503	SO:0001819	synonymous_variant	84223	exon4			TACCACGCAGATG	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 9"""	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.279C>T	3.37:g.197670652G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	113	62	0.548673	NM_032263	Q9BST2|Q9HAG8	Silent	SNP	ENST00000265239.6	37	CCDS3331.1																																																																																			G|0.937;A|0.063	0.063	strong		0.413	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263	
VARS2	57176	hgsc.bcm.edu	37	6	30892322	30892322	+	Silent	SNP	C	C	T	rs2532942	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30892322C>T	ENST00000321897.5	+	25	3290	c.2658C>T	c.(2656-2658)ccC>ccT	p.P886P	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Silent_p.P746P|VARS2_ENST00000416670.2_Silent_p.P886P|VARS2_ENST00000541562.1_Silent_p.P916P			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	886					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CCCCCTACCCCAGCGCCTGCA	0.662													C|||	1112	0.222045	0.0983	0.2075	5008	,	,		12561	0.247		0.3559	False		,,,				2504	0.2362				p.P916P		Atlas-SNP	.											.	VARS2	60	.	0			c.C2748T						PASS	.	C	,,	442,2570		36,370,1100	15.0	19.0	17.0		2238,2748,2658	2.4	0.9	6	dbSNP_100	17	2048,3366		372,1304,1031	no	coding-synonymous,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	408,1674,2131	TT,TC,CC		37.8279,14.6746,29.5514	,,	746/924,916/1094,886/1064	30892322	2490,5936	1506	2707	4213	SO:0001819	synonymous_variant	57176	exon26			CTACCCCAGCGCC	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2658C>T	6.37:g.30892322C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	155	91	0.587097	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			C|0.739;T|0.261	0.261	strong		0.662	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
MAP7	9053	hgsc.bcm.edu	37	6	136687065	136687065	+	Missense_Mutation	SNP	C	C	T	rs35350783	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:136687065C>T	ENST00000354570.3	-	10	1491	c.1081G>A	c.(1081-1083)Gtc>Atc	p.V361I	MAP7_ENST00000544465.1_Missense_Mutation_p.V346I|MAP7_ENST00000432797.2_Missense_Mutation_p.V215I|MAP7_ENST00000438100.2_Missense_Mutation_p.V346I|MAP7_ENST00000454590.1_Missense_Mutation_p.V383I|RP3-406A7.3_ENST00000571188.1_RNA	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	361	Pro-rich.		V -> I (in dbSNP:rs35350783).		cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		GGGGGCCGGACCTGAGCAGGA	0.587													C|||	69	0.013778	0.0	0.0245	5008	,	,		16642	0.0		0.0398	False		,,,				2504	0.0123				p.V391I		Atlas-SNP	.											.	MAP7	63	.	0			c.G1171A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	25,4381	31.7+/-61.6	1,23,2179	67.0	69.0	68.0		1147,1171,1036,1147,1036,970,799,643,643,1081	0.8	0.1	6	dbSNP_126	68	312,8288	111.8+/-172.0	5,302,3993	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	MAP7	NM_001198608.1,NM_001198609.1,NM_001198611.1,NM_001198614.1,NM_001198615.1,NM_001198616.1,NM_001198617.1,NM_001198618.1,NM_001198619.1,NM_003980.4	29,29,29,29,29,29,29,29,29,29	6,325,6172	TT,TC,CC		3.6279,0.5674,2.5911	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	383/772,391/780,346/735,383/772,346/735,324/713,267/656,215/604,215/604,361/750	136687065	337,12669	2203	4300	6503	SO:0001583	missense	9053	exon10			GCCGGACCTGAGC	X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.1081G>A	6.37:g.136687065C>T	ENSP00000346581:p.Val361Ile	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	165	105	0.636364	NM_001198609	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Missense_Mutation	SNP	ENST00000354570.3	37	CCDS5178.1	45	0.020604395604395604	0	0.0	12	0.03314917127071823	0	0.0	33	0.04353562005277045	C	14.10	2.435414	0.43224	0.005674	0.036279	ENSG00000135525	ENST00000354570;ENST00000454590;ENST00000544465;ENST00000438100;ENST00000432797;ENST00000345567	T;T;T;T;T	0.08896	3.04;3.04;3.04;3.04;3.04	5.8	0.749	0.18381	.	1.589500	0.03691	N	0.247014	T	0.02193	0.0068	L	0.33485	1.01	0.09310	N	1	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.001;0.001;0.0	T	0.43637	-0.9379	10	0.38643	T	0.18	1.2411	6.2258	0.20708	0.0:0.3989:0.3265:0.2746	rs35350783	346;383;346;383;267;324;361	B7Z290;B7ZB64;F5H1E2;E9PCP3;F8W783;Q14244-2;Q14244	.;.;.;.;.;.;MAP7_HUMAN	I	361;383;346;346;215;267	ENSP00000346581:V361I;ENSP00000414712:V383I;ENSP00000445737:V346I;ENSP00000400790:V346I;ENSP00000414879:V215I	ENSP00000344217:V267I	V	-	1	0	MAP7	136728758	0.012000	0.17670	0.126000	0.21872	0.948000	0.59901	-0.066000	0.11598	0.100000	0.17581	0.650000	0.86243	GTC	T|0.028;G|0.000;C|0.972	0.028	strong		0.587	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980	
FERMT1	55612	hgsc.bcm.edu	37	20	6069723	6069723	+	Silent	SNP	G	G	A	rs35413391	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:6069723G>A	ENST00000217289.4	-	10	1941	c.1153C>T	c.(1153-1155)Cta>Tta	p.L385L	FERMT1_ENST00000536936.1_Silent_p.L128L|FERMT1_ENST00000478194.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	385	FERM.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						GCTTTTGGTAGTAACTTCTTG	0.358													g|||	159	0.0317492	0.0038	0.0749	5008	,	,		18431	0.0		0.0825	False		,,,				2504	0.0194				p.L385L		Atlas-SNP	.											.	FERMT1	106	.	0			c.C1153T						PASS	.	G		65,4341	61.7+/-98.7	0,65,2138	113.0	121.0	118.0		1153	-4.5	0.1	20	dbSNP_126	118	658,7942	165.7+/-217.8	20,618,3662	yes	coding-synonymous	FERMT1	NM_017671.4		20,683,5800	AA,AG,GG		7.6512,1.4753,5.559		385/678	6069723	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon10			TTGGTAGTAACTT	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1153C>T	20.37:g.6069723G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			G|0.949;A|0.051	0.051	strong		0.358	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
GATA4	2626	hgsc.bcm.edu	37	8	11614575	11614575	+	Missense_Mutation	SNP	A	A	G	rs3729856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11614575A>G	ENST00000335135.4	+	6	1687	c.1129A>G	c.(1129-1131)Agc>Ggc	p.S377G	GATA4_ENST00000532059.1_Missense_Mutation_p.S378G|GATA4_ENST00000528712.1_Missense_Mutation_p.S171G	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	377			S -> G (in dbSNP:rs3729856).		atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		CTACGGGCACAGCAGCTCCGT	0.657													A|||	215	0.0429313	0.0098	0.0677	5008	,	,		19680	0.001		0.1193	False		,,,				2504	0.0348				p.S377G		Atlas-SNP	.											.	GATA4	29	.	0			c.A1129G						PASS	.	A	GLY/SER	104,4302	82.4+/-120.9	2,100,2101	78.0	60.0	66.0		1129	0.9	1.0	8	dbSNP_107	66	1204,7396	240.7+/-271.3	100,1004,3196	yes	missense	GATA4	NM_002052.3	56	102,1104,5297	GG,GA,AA		14.0,2.3604,10.0569	benign	377/443	11614575	1308,11698	2203	4300	6503	SO:0001583	missense	2626	exon6			GGGCACAGCAGCT	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"""GATA zinc finger domain containing"""	4173	protein-coding gene	gene with protein product		600576	"""GATA-binding protein 4"""			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.1129A>G	8.37:g.11614575A>G	ENSP00000334458:p.Ser377Gly	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	295	140	0.474576	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Missense_Mutation	SNP	ENST00000335135.4	37	CCDS5983.1	134	0.06135531135531135	6	0.012195121951219513	29	0.08011049723756906	1	0.0017482517482517483	98	0.12928759894459102	A	11.91	1.779594	0.31502	0.023604	0.14	ENSG00000136574	ENST00000528712;ENST00000526716;ENST00000335135;ENST00000259090;ENST00000532059	D;D;D;D	0.98996	-5.31;-5.1;-4.73;-4.73	5.83	0.906	0.19314	.	0.470389	0.23169	N	0.051149	T	0.19485	0.0468	L	0.42245	1.32	0.32041	P	0.59825	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.73538	-0.3951	9	0.18710	T	0.47	-21.9862	1.7073	0.02884	0.4155:0.1484:0.3085:0.1276	rs3729856;rs3729856	378;377	B7ZKZ4;P43694	.;GATA4_HUMAN	G	171;171;377;376;378	ENSP00000435043:S171G;ENSP00000435347:S171G;ENSP00000334458:S377G;ENSP00000435712:S378G	ENSP00000259090:S376G	S	+	1	0	GATA4	11651984	0.849000	0.29639	0.991000	0.47740	0.550000	0.35303	0.243000	0.18106	0.140000	0.18849	-0.256000	0.11100	AGC	A|0.912;G|0.088	0.088	strong		0.657	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052	
PREX2	80243	hgsc.bcm.edu	37	8	69046409	69046409	+	Silent	SNP	G	G	A	rs3793379	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:69046409G>A	ENST00000288368.4	+	32	4159	c.3882G>A	c.(3880-3882)aaG>aaA	p.K1294K		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1294					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ACAACAGCAAGGAAAATGAGA	0.498													G|||	606	0.121006	0.0212	0.2003	5008	,	,		17557	0.1865		0.1153	False		,,,				2504	0.138				p.K1294K		Atlas-SNP	.											PREX2,colon,carcinoma,+1,1	PREX2	614	1	0			c.G3882A						scavenged	.	G		164,4242	110.4+/-148.6	2,160,2041	103.0	96.0	99.0		3882	2.0	1.0	8	dbSNP_107	99	1147,7453	235.0+/-267.7	74,999,3227	no	coding-synonymous	PREX2	NM_024870.2		76,1159,5268	AA,AG,GG		13.3372,3.7222,10.08		1294/1607	69046409	1311,11695	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon32			CAGCAAGGAAAAT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3882G>A	8.37:g.69046409G>A		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			G|0.894;A|0.106	0.106	strong		0.498	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
ELF1	1997	hgsc.bcm.edu	37	13	41515371	41515371	+	Silent	SNP	C	C	T	rs7987185	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:41515371C>T	ENST00000239882.3	-	8	1256	c.942G>A	c.(940-942)tcG>tcA	p.S314S	ELF1_ENST00000442101.1_Silent_p.S290S|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	314					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		ATGAAGATAGCGATGGATCTG	0.418													C|||	663	0.132388	0.2209	0.1282	5008	,	,		15035	0.0843		0.1362	False		,,,				2504	0.0613				p.S314S		Atlas-SNP	.											.	ELF1	65	.	0			c.G942A						PASS	.	C	,	973,3433	368.3+/-318.6	101,771,1331	112.0	123.0	119.0		870,942	-1.3	0.1	13	dbSNP_116	119	1486,7114	282.8+/-295.8	124,1238,2938	no	coding-synonymous,coding-synonymous	ELF1	NM_001145353.1,NM_172373.3	,	225,2009,4269	TT,TC,CC		17.2791,22.0835,18.9067	,	290/596,314/620	41515371	2459,10547	2203	4300	6503	SO:0001819	synonymous_variant	1997	exon8			AGATAGCGATGGA	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.942G>A	13.37:g.41515371C>T		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	97	95	0.979381	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Silent	SNP	ENST00000239882.3	37	CCDS9374.1																																																																																			C|0.830;T|0.170	0.170	strong		0.418	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
DSPP	1834	hgsc.bcm.edu	37	4	88536321	88536321	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536321G>A	ENST00000282478.7	+	4	2540	c.2507G>A	c.(2506-2508)aGc>aAc	p.S836N	DSPP_ENST00000399271.1_Missense_Mutation_p.S836N|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	836	Asp/Ser-rich.			S -> C (in Ref. 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		agcgatagcagcaacagcagt	0.498																																					p.S836N		Atlas-SNP	.											.	DSPP	174	.	0			c.G2507A						PASS	.						87.0	109.0	101.0					4																	88536321		1645	2951	4596	SO:0001583	missense	1834	exon5			ATAGCAGCAACAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2507G>A	4.37:g.88536321G>A	ENSP00000282478:p.Ser836Asn	Somatic	415	0	0		WXS	Illumina HiSeq	Phase_I	389	18	0.0462725	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	2.602	-0.292775	0.05568	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87412	-2.25;-2.25	0.918	0.918	0.19386	.	.	.	.	.	T	0.80623	0.4658	L	0.46157	1.445	0.09310	N	1	B	0.19817	0.039	B	0.20384	0.029	T	0.70281	-0.4915	9	0.54805	T	0.06	.	5.1892	0.15201	0.0:0.0:1.0:0.0	.	836	Q9NZW4	DSPP_HUMAN	N	836	ENSP00000382213:S836N;ENSP00000282478:S836N	ENSP00000282478:S836N	S	+	2	0	DSPP	88755345	0.550000	0.26489	0.027000	0.17364	0.003000	0.03518	0.902000	0.28459	0.792000	0.33850	0.165000	0.16767	AGC	.	.	none		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60021761	60021761	+	Missense_Mutation	SNP	C	C	T	rs35211496	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:60021761C>T	ENST00000586569.1	+	4	459	c.421C>T	c.(421-423)Cac>Tac	p.H141Y	TNFRSF11A_ENST00000269485.7_Missense_Mutation_p.H141Y	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	141			H -> Y (in dbSNP:rs35211496).		adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				GGGCGCCCAGCACCCGTGTAC	0.652													C|||	287	0.0573083	0.0038	0.0908	5008	,	,		16570	0.001		0.174	False		,,,				2504	0.044				p.H141Y		Atlas-SNP	.											TNFRSF11A,NS,carcinoma,0,1	TNFRSF11A	51	1	0			c.C421T						PASS	.	C	TYR/HIS	147,4137		4,139,1999	26.0	31.0	29.0		421	3.1	1.0	18	dbSNP_126	29	1506,6922		135,1236,2843	yes	missense	TNFRSF11A	NM_003839.2	83	139,1375,4842	TT,TC,CC		17.869,3.4314,13.0035	possibly-damaging	141/617	60021761	1653,11059	2142	4214	6356	SO:0001583	missense	8792	exon4			GCCCAGCACCCGT	AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11908	protein-coding gene	gene with protein product		603499	"""tumor necrosis factor receptor superfamily, member 11a, activator of NFKB"", ""Paget disease of bone 2"", ""loss of heterozygosity, 18, chromosomal region 1"""	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.421C>T	18.37:g.60021761C>T	ENSP00000465500:p.His141Tyr	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_001270951	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	37	CCDS11980.1	176	0.08058608058608059	3	0.006097560975609756	47	0.1298342541436464	1	0.0017482517482517483	125	0.16490765171503957	C	13.72	2.320014	0.41096	0.034314	0.17869	ENSG00000141655	ENST00000382790;ENST00000269485	T	0.62232	0.04	5.05	3.12	0.35913	TNFR/CD27/30/40/95 cysteine-rich region (1);	2.113090	0.02415	U	0.082057	T	0.00144	0.0004	L	0.36672	1.1	0.40234	P	0.022110999999999992	P;P	0.35700	0.516;0.461	B;B	0.23419	0.046;0.039	T	0.03910	-1.0993	8	.	.	.	-12.7549	9.9869	0.41847	0.153:0.6986:0.1483:0.0	rs35211496;rs61751990	163;141	Q59EP9;Q9Y6Q6	.;TNR11_HUMAN	Y	163;141	ENSP00000269485:H141Y	.	H	+	1	0	TNFRSF11A	58172741	0.867000	0.29959	0.999000	0.59377	0.998000	0.95712	1.907000	0.39897	1.239000	0.43787	0.650000	0.86243	CAC	C|0.883;T|0.117	0.117	strong		0.652	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2		
TCP10L2	401285	hgsc.bcm.edu	37	6	167592606	167592606	+	Silent	SNP	T	T	A	rs201866116	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167592606T>A	ENST00000366832.2	+	6	896	c.765T>A	c.(763-765)gtT>gtA	p.V255V		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	255										endometrium(1)|kidney(2)|lung(3)	6						CAGCCGGAGTTGCTGGTGAGC	0.577																																					p.V255V		Atlas-SNP	.											.	TCP10L2	41	.	0			c.T765A						PASS	.																																			SO:0001819	synonymous_variant	401285	exon6			CGGAGTTGCTGGT		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.765T>A	6.37:g.167592606T>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	108	22	0.203704	NM_001145121		Silent	SNP	ENST00000366832.2	37	CCDS47514.1																																																																																			T|0.927;A|0.073	0.073	strong		0.577	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
TEX26	122046	hgsc.bcm.edu	37	13	31543095	31543095	+	Silent	SNP	C	C	T	rs2274869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:31543095C>T	ENST00000380473.3	+	6	733	c.720C>T	c.(718-720)taC>taT	p.Y240Y	TEX26_ENST00000530916.1_Intron	NM_152325.1	NP_689538.1	Q8N6G2	TEX26_HUMAN	testis expressed 26	240																	AAAGTGACTACGACAAAACCT	0.428													C|||	965	0.192692	0.0726	0.317	5008	,	,		20151	0.126		0.2445	False		,,,				2504	0.2822				p.Y240Y		Atlas-SNP	.											.	.	.	.	0			c.C720T						PASS	.	C		458,3948	220.7+/-238.1	27,404,1772	177.0	173.0	174.0		720	-4.5	0.2	13	dbSNP_100	174	2265,6335	382.8+/-340.5	322,1621,2357	no	coding-synonymous	C13orf26	NM_152325.1		349,2025,4129	TT,TC,CC		26.3372,10.3949,20.9365		240/290	31543095	2723,10283	2203	4300	6503	SO:0001819	synonymous_variant	122046	exon6			TGACTACGACAAA	BC030277	CCDS9339.1	13q12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000175664	ENSG00000175664			28622	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 26"""	C13orf26		12477932	Standard	NM_152325		Approved	MGC40178	uc001uti.3	Q8N6G2	OTTHUMG00000016682	ENST00000380473.3:c.720C>T	13.37:g.31543095C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	141	82	0.58156	NM_152325		Silent	SNP	ENST00000380473.3	37	CCDS9339.1																																																																																			C|0.784;T|0.216	0.216	strong		0.428	TEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044380.2	NM_152325	
COL27A1	85301	hgsc.bcm.edu	37	9	116967405	116967405	+	Silent	SNP	G	G	T	rs13290696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:116967405G>T	ENST00000356083.3	+	8	2539	c.2148G>T	c.(2146-2148)ccG>ccT	p.P716P		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	716	Collagen-like 2.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						ATCCTGGACCGGCAGGGCACC	0.667													G|||	399	0.0796725	0.0416	0.0331	5008	,	,		17714	0.0208		0.0785	False		,,,				2504	0.226				p.P716P		Atlas-SNP	.											.	COL27A1	200	.	0			c.G2148T						PASS	.	G		222,4184	132.5+/-169.0	5,212,1986	66.0	53.0	57.0		2148	-10.1	0.0	9	dbSNP_121	57	821,7779	189.3+/-236.1	34,753,3513	no	coding-synonymous	COL27A1	NM_032888.2		39,965,5499	TT,TG,GG		9.5465,5.0386,8.0194		716/1861	116967405	1043,11963	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon8			TGGACCGGCAGGG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.2148G>T	9.37:g.116967405G>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			G|0.932;T|0.068	0.068	strong		0.667	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
ZNF606	80095	hgsc.bcm.edu	37	19	58490929	58490929	+	Silent	SNP	T	T	C	rs75971696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58490929T>C	ENST00000341164.4	-	7	1739	c.1119A>G	c.(1117-1119)aaA>aaG	p.K373K	ZNF606_ENST00000536132.1_Silent_p.K283K	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	373					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		ATTCATTGTATTTATACGCTT	0.338													T|||	163	0.0325479	0.0053	0.072	5008	,	,		10331	0.0		0.0805	False		,,,				2504	0.0256				p.K373K		Atlas-SNP	.											.	ZNF606	155	.	0			c.A1119G						PASS	.	T		76,4330	67.0+/-104.6	0,76,2127	115.0	98.0	104.0		1119	0.2	1.0	19	dbSNP_132	104	800,7800	186.9+/-234.3	41,718,3541	no	coding-synonymous	ZNF606	NM_025027.3		41,794,5668	CC,CT,TT		9.3023,1.7249,6.7354		373/793	58490929	876,12130	2203	4300	6503	SO:0001819	synonymous_variant	80095	exon7			ATTGTATTTATAC	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.1119A>G	19.37:g.58490929T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_025027	A8KAN2|Q8NE04|Q96JH5	Silent	SNP	ENST00000341164.4	37	CCDS12968.1																																																																																			T|0.934;C|0.066	0.066	strong		0.338	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027	
ITGA11	22801	hgsc.bcm.edu	37	15	68624290	68624290	+	Silent	SNP	G	G	A	rs2292745	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:68624290G>A	ENST00000315757.7	-	14	1763	c.1677C>T	c.(1675-1677)gaC>gaT	p.D559D	ITGA11_ENST00000423218.2_Silent_p.D559D	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	559					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CCACCACCACGTCATTGTAGG	0.542													G|||	1366	0.272764	0.0499	0.2882	5008	,	,		17674	0.5079		0.1869	False		,,,				2504	0.409				p.D559D		Atlas-SNP	.											.	ITGA11	110	.	0			c.C1677T						PASS	.	G		270,3692		7,256,1718	59.0	58.0	58.0		1677	0.6	1.0	15	dbSNP_100	58	1246,7058		101,1044,3007	no	coding-synonymous	ITGA11	NM_001004439.1		108,1300,4725	AA,AG,GG		15.0048,6.8147,12.3594		559/1189	68624290	1516,10750	1981	4152	6133	SO:0001819	synonymous_variant	22801	exon14			CACCACGTCATTG	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1677C>T	15.37:g.68624290G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	193	109	0.564767	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.757;A|0.242	0.242	strong		0.542	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
MOV10L1	54456	hgsc.bcm.edu	37	22	50555686	50555686	+	Missense_Mutation	SNP	A	A	C	rs760749	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50555686A>C	ENST00000262794.5	+	9	1443	c.1360A>C	c.(1360-1362)Att>Ctt	p.I454L	MOV10L1_ENST00000395858.3_Missense_Mutation_p.I454L|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Missense_Mutation_p.I454L|MOV10L1_ENST00000540615.1_Missense_Mutation_p.I434L	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	454			I -> L (in dbSNP:rs760749). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GGAGTCACTAATTGCTGCGCG	0.443													A|||	741	0.147963	0.0212	0.1182	5008	,	,		17252	0.2391		0.1849	False		,,,				2504	0.2086				p.I454L		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A1360C						PASS	.	A	LEU/ILE,LEU/ILE,LEU/ILE	175,4231	114.6+/-152.6	0,175,2028	89.0	85.0	86.0		1360,1300,1360	5.8	0.0	22	dbSNP_86	86	1389,7211	268.5+/-287.9	110,1169,3021	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	5,5,5	110,1344,5049	CC,CA,AA		16.1512,3.9719,12.0252	benign,benign,benign	454/1166,434/1166,454/1212	50555686	1564,11442	2203	4300	6503	SO:0001583	missense	54456	exon9			TCACTAATTGCTG	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1360A>C	22.37:g.50555686A>C	ENSP00000262794:p.Ile454Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	120	46	0.383333	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	342	0.1565934065934066	12	0.024390243902439025	62	0.1712707182320442	126	0.2202797202797203	142	0.18733509234828497	A	6.800	0.516669	0.12944	0.039719	0.161512	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;T;D	0.84730	-1.7;-1.7;-1.28;-1.89	5.76	5.76	0.90799	.	0.107622	0.64402	D	0.000007	T	0.00109	0.0003	L	0.32530	0.975	0.54753	P	1.399999999995849E-5	P;B;B;B	0.34837	0.472;0.097;0.059;0.059	B;B;B;B	0.27715	0.082;0.026;0.012;0.012	T	0.40997	-0.9533	9	0.05525	T	0.97	-17.816	10.326	0.43793	0.853:0.0:0.0:0.147	rs760749;rs5771173;rs17836613;rs59634867;rs760749	215;434;454;454	B7Z893;F5H403;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	L	454;454;454;434	ENSP00000438978:I454L;ENSP00000262794:I454L;ENSP00000379199:I454L;ENSP00000438542:I434L	ENSP00000262794:I454L	I	+	1	0	MOV10L1	48897813	0.291000	0.24352	0.048000	0.18961	0.040000	0.13550	0.754000	0.26390	2.193000	0.70182	0.528000	0.53228	ATT	A|0.868;C|0.132	0.132	strong		0.443	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
C20orf166	128826	hgsc.bcm.edu	37	20	61167883	61167883	+	Silent	SNP	G	G	A	rs6143064	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61167883G>A	ENST00000370527.3	+	4	1132	c.353G>A	c.(352-354)tGa>tAa	p.*118*	C20orf166_ENST00000370524.2_Silent_p.*100*|C20orf166_ENST00000370523.1_Silent_p.*100*	NM_178463.3	NP_848558.1			chromosome 20 open reading frame 166											endometrium(1)|kidney(1)|lung(2)	4	Breast(26;1.04e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)			AGCCACTGCTGAAGGGACTCC	0.582													G|||	1320	0.263578	0.0877	0.2968	5008	,	,		16708	0.1617		0.4016	False		,,,				2504	0.4407				p.X118X		Atlas-SNP	.											.	C20orf166	17	.	0			c.G353A						PASS	.	G		462,3564		31,400,1582	22.0	23.0	23.0		353	-0.5	0.0	20	dbSNP_114	23	3161,5151		590,1981,1585	no	coding-synonymous	C20orf166	NM_178463.3		621,2381,3167	AA,AG,GG		38.0294,11.4754,29.3646		118/118	61167883	3623,8715	2013	4156	6169	SO:0001819	synonymous_variant	128826	exon4			ACTGCTGAAGGGA	AL449263	CCDS46627.1	20q13.33	2014-01-21			ENSG00000174407	ENSG00000174407			16159	protein-coding gene	gene with protein product	"""MIR133A2 host gene"""						Standard	NM_178463		Approved	dJ353C17.1, MIR1-1HG, MIR133A2HG	uc011aaj.2	Q9H1L0	OTTHUMG00000048000	ENST00000370527.3:c.353G>A	20.37:g.61167883G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_178463		Silent	SNP	ENST00000370527.3	37	CCDS46627.1																																																																																			G|0.722;A|0.278	0.278	strong		0.582	C20orf166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109262.1	NM_178463	
SNCAIP	9627	hgsc.bcm.edu	37	5	121780312	121780312	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:121780312C>A	ENST00000261368.8	+	8	1739	c.1477C>A	c.(1477-1479)Ccc>Acc	p.P493T	SNCAIP_ENST00000379533.2_Missense_Mutation_p.P540T|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000542191.1_Missense_Mutation_p.P51T|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000261367.7_Missense_Mutation_p.P540T|SNCAIP_ENST00000503116.2_3'UTR|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000379538.3_Missense_Mutation_p.P127T|SNCAIP_ENST00000414317.2_Missense_Mutation_p.P95T|SNCAIP_ENST00000379536.2_Missense_Mutation_p.P433T|CTC-210G5.1_ENST00000505546.1_RNA|CTC-210G5.1_ENST00000509993.1_RNA|CTC-210G5.1_ENST00000503529.1_RNA	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	493					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TGGGGAAAAGCCCTCCCAGAG	0.547																																					p.P493T		Atlas-SNP	.											.	SNCAIP	308	.	0			c.C1477A						PASS	.						105.0	100.0	102.0					5																	121780312		2203	4300	6503	SO:0001583	missense	9627	exon8			GAAAAGCCCTCCC	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"""Ankyrin repeat domain containing"""	11139	protein-coding gene	gene with protein product	"""synphilin"""	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.1477C>A	5.37:g.121780312C>A	ENSP00000261368:p.Pro493Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	37	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.501545	0.85176	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854	T;T;T;T;T;T;T;T	0.70869	0.99;0.14;0.14;0.14;0.14;0.99;0.14;-0.52	5.66	5.66	0.87406	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.91126	0.7206	H	0.98276	4.19	0.53688	D	0.999971	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.998;0.999;0.997;0.988;0.999;0.988;0.996;0.993	D	0.94040	0.7308	10	0.72032	D	0.01	-20.578	19.7543	0.96284	0.0:1.0:0.0:0.0	.	433;121;95;433;127;127;540;493	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	T	51;433;493;540;433;127;540;95;133	ENSP00000441681:P51T;ENSP00000422106:P433T;ENSP00000261368:P493T;ENSP00000368848:P540T;ENSP00000368851:P433T;ENSP00000368854:P127T;ENSP00000261367:P540T;ENSP00000394392:P95T	ENSP00000261367:P540T	P	+	1	0	SNCAIP	121808211	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.903000	0.69877	2.680000	0.91292	0.561000	0.74099	CCC	.	.	none		0.547	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1		
NAGPA	51172	hgsc.bcm.edu	37	16	5075633	5075633	+	Missense_Mutation	SNP	G	G	A	rs7188856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:5075633G>A	ENST00000312251.3	-	10	1413	c.1394C>T	c.(1393-1395)aCt>aTt	p.T465I	RP11-165E7.1_ENST00000588778.1_RNA|NAGPA_ENST00000381955.3_Missense_Mutation_p.T431I	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	465			T -> I (in dbSNP:rs7188856). {ECO:0000269|PubMed:10551838}.		carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|lysosome organization (GO:0007040)|protein glycosylation (GO:0006486)|protein targeting to lysosome (GO:0006622)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity (GO:0003944)			endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1)	12					N-Acetyl-D-glucosamine(DB00141)	GTTTGCTGCAGTGCTGATCAG	0.642													G|||	1006	0.200879	0.0893	0.2997	5008	,	,		17690	0.1736		0.3419	False		,,,				2504	0.1646				p.T465I		Atlas-SNP	.											.	NAGPA	30	.	0			c.C1394T						PASS	.	G	ILE/THR	586,3806	257.4+/-261.8	30,526,1640	34.0	36.0	36.0		1394	-3.2	0.0	16	dbSNP_116	36	3005,5595	460.3+/-365.1	531,1943,1826	yes	missense	NAGPA	NM_016256.3	89	561,2469,3466	AA,AG,GG		34.9419,13.3424,27.6401	possibly-damaging	465/516	5075633	3591,9401	2196	4300	6496	SO:0001583	missense	51172	exon10			GCTGCAGTGCTGA	AF187072	CCDS10527.1	16p13.3	2008-02-05			ENSG00000103174	ENSG00000103174	3.1.4.45		17378	protein-coding gene	gene with protein product		607985				10551838, 12058031	Standard	NM_016256		Approved	APAA, UCE	uc002cyg.3	Q9UK23	OTTHUMG00000090515	ENST00000312251.3:c.1394C>T	16.37:g.5075633G>A	ENSP00000310998:p.Thr465Ile	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	242	116	0.479339	NM_016256	B2RAS1|Q96EJ8	Missense_Mutation	SNP	ENST00000312251.3	37	CCDS10527.1	498	0.22802197802197802	49	0.09959349593495935	99	0.27348066298342544	94	0.16433566433566432	256	0.33773087071240104	G	0.034	-1.317453	0.01331	0.133424	0.349419	ENSG00000103174	ENST00000312251;ENST00000381955	T;T	0.24151	2.28;1.87	5.18	-3.19	0.05171	.	1.101780	0.06824	N	0.792789	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.37430	-0.9706	9	0.52906	T	0.07	0.3722	11.7169	0.51659	0.5135:0.0:0.4865:0.0	rs7188856;rs17634473;rs7188856	465;431	Q9UK23;Q9UK23-2	NAGPA_HUMAN;.	I	465;431	ENSP00000310998:T465I;ENSP00000371381:T431I	ENSP00000310998:T465I	T	-	2	0	NAGPA	5015634	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.505000	0.02273	-1.423000	0.02002	-1.134000	0.01955	ACT	G|0.758;A|0.242	0.242	strong		0.642	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207003.1	NM_016256	
NIPA2	81614	hgsc.bcm.edu	37	15	23021238	23021238	+	Silent	SNP	C	C	T	rs145147241|rs7170838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:23021238C>T	ENST00000337451.3	-	4	711	c.99G>A	c.(97-99)aaG>aaA	p.K33K	NIPA2_ENST00000539711.2_Silent_p.K33K|NIPA2_ENST00000359727.4_Silent_p.K33K|NIPA2_ENST00000559571.1_5'Flank|NIPA2_ENST00000398014.2_Silent_p.K33K|NIPA2_ENST00000398013.3_Silent_p.K33K	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2	33						early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(4)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		GAAGGAGGCCCTTTTTTTTCA	0.448													T|||	1130	0.225639	0.2262	0.3112	5008	,	,		16677	0.2421		0.1799	False		,,,				2504	0.1943				p.K33K		Atlas-SNP	.											NIPA2,NS,adenoma,0,1	NIPA2	49	1	0			c.G99A						PASS	.	T	,,,,,	973,3433		120,733,1350	132.0	134.0	134.0		99,99,99,99,99,99	1.4	1.0	15	dbSNP_116	134	1372,7228		126,1120,3054	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NIPA2	NM_001008860.2,NM_001008892.2,NM_001008894.2,NM_001184888.1,NM_001184889.1,NM_030922.6	,,,,,	246,1853,4404	TT,TC,CC		15.9535,22.0835,18.0301	,,,,,	33/361,33/361,33/342,33/342,33/361,33/361	23021238	2345,10661	2203	4300	6503	SO:0001819	synonymous_variant	81614	exon6			GAGGCCCTTTTTT	AY732242	CCDS73693.1, CCDS73694.1	15q11.2	2008-02-05			ENSG00000140157	ENSG00000140157			17044	protein-coding gene	gene with protein product		608146				14508708	Standard	NM_001008860		Approved		uc001yuz.3	Q8N8Q9	OTTHUMG00000129101	ENST00000337451.3:c.99G>A	15.37:g.23021238C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	134	76	0.567164	NM_001184889	F8W7Y8|Q96F03|Q9BVS2	Silent	SNP	ENST00000337451.3	37	CCDS10010.1																																																																																			C|0.792;T|0.208	0.208	strong		0.448	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1	NM_030922	
C17orf77	146723	hgsc.bcm.edu	37	17	72588438	72588438	+	Nonsense_Mutation	SNP	G	G	T	rs79556281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72588438G>T	ENST00000392620.1	+	3	615	c.253G>T	c.(253-255)Gaa>Taa	p.E85*	CD300LD_ENST00000375352.1_5'Flank|C17orf77_ENST00000328023.2_Nonsense_Mutation_p.E85*	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	85						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						AAACCTACTCGAATCTCCTTC	0.453													g|||	23	0.00459265	0.0	0.0043	5008	,	,		22359	0.0		0.0179	False		,,,				2504	0.002				p.E85X		Atlas-SNP	.											.	C17orf77	31	.	0			c.G253T						PASS	.	A	stop/GLU	10,4396	16.8+/-37.8	0,10,2193	90.0	86.0	87.0		253	-8.1	0.0	17	dbSNP_131	87	85,8515	49.4+/-109.1	1,83,4216	yes	stop-gained	C17orf77	NM_152460.2		1,93,6409	TT,TG,GG		0.9884,0.227,0.7304		85/244	72588438	95,12911	2203	4300	6503	SO:0001587	stop_gained	146723	exon3			CTACTCGAATCTC		CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.253G>T	17.37:g.72588438G>T	ENSP00000376396:p.Glu85*	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	62	38	0.612903	NM_152460		Nonsense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	g	20.2	3.948429	0.73787	0.00227	0.009884	ENSG00000182352	ENST00000392620;ENST00000328023	.	.	.	4.07	-8.14	0.01069	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.7694	0.05329	0.489:0.2388:0.1618:0.1105	.	.	.	.	X	85	.	.	E	+	1	0	C17orf77	70100033	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.219000	0.02973	-1.873000	0.01135	-1.316000	0.01300	GAA	G|0.994;T|0.006	0.006	strong		0.453	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
WDFY4	57705	hgsc.bcm.edu	37	10	50186415	50186415	+	Missense_Mutation	SNP	C	C	T	rs2292584	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50186415C>T	ENST00000325239.5	+	59	9380	c.9353C>T	c.(9352-9354)cCg>cTg	p.P3118L	WDFY4_ENST00000465910.1_3'UTR|RP11-523O18.5_ENST00000428825.4_RNA|WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	3118				P -> L (in Ref. 3; AAH47574 and 5; BAB13433). {ECO:0000305}.		integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						GAGGAGCCCCCGGCTCAGCCT	0.617													C|||	2099	0.419129	0.3616	0.438	5008	,	,		19919	0.3512		0.4901	False		,,,				2504	0.4806				p.P3118L		Atlas-SNP	.											.	WDFY4	205	.	0			c.C9353T						PASS	.	C	LEU/PRO	521,863		105,311,276	67.0	75.0	72.0		9353	-1.0	0.0	10	dbSNP_100	72	1572,1610		400,772,419	yes	missense	WDFY4	NM_020945.1	98	505,1083,695	TT,TC,CC		49.4029,37.6445,45.8388	benign	3118/3185	50186415	2093,2473	692	1591	2283	SO:0001583	missense	57705	exon60			AGCCCCCGGCTCA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.9353C>T	10.37:g.50186415C>T	ENSP00000320563:p.Pro3118Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	871|871	0.39880952380952384|0.39880952380952384	162|162	0.32926829268292684|0.32926829268292684	163|163	0.45027624309392267|0.45027624309392267	171|171	0.29895104895104896|0.29895104895104896	375|375	0.4947229551451187|0.4947229551451187	C|C	0.687|0.687	-0.796110|-0.796110	0.02862|0.02862	0.376445|0.376445	0.494029|0.494029	ENSG00000128815|ENSG00000128815	ENST00000325239;ENST00000544136|ENST00000265453	T|.	0.55413|.	0.52|.	4.77|4.77	-0.999|-0.999	0.10208|0.10208	WD40 repeat-like-containing domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.47535|0.47535	-0.9110|-0.9110	7|4	.|.	.|.	.|.	.|.	2.2603|2.2603	0.04065|0.04065	0.1328:0.3971:0.2906:0.1794|0.1328:0.3971:0.2906:0.1794	rs2292584;rs58993406;rs2292584|rs2292584;rs58993406;rs2292584	3118|.	Q6ZS81|.	WDFY4_HUMAN|.	L|W	3118;581|1205	ENSP00000320563:P3118L|.	.|.	P|R	+|+	2|1	0|2	WDFY4|WDFY4	49856421|49856421	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.005000|0.005000	0.04900|0.04900	-0.189000|-0.189000	0.09629|0.09629	-0.062000|-0.062000	0.13088|0.13088	-0.254000|-0.254000	0.11334|0.11334	CCG|CGG	C|0.598;T|0.402	0.402	strong		0.617	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
MATN2	4147	hgsc.bcm.edu	37	8	98943446	98943446	+	Silent	SNP	T	T	C	rs2290470	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:98943446T>C	ENST00000520016.1	+	2	532	c.408T>C	c.(406-408)acT>acC	p.T136T	MATN2_ENST00000521689.1_Silent_p.T136T|MATN2_ENST00000524308.1_Silent_p.T136T|MATN2_ENST00000254898.5_Silent_p.T136T|MATN2_ENST00000522025.2_Intron			O00339	MATN2_HUMAN	matrilin 2	136	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			GCACCATGACTGGGCTGGCCA	0.577													G|||	2139	0.427117	0.2443	0.2896	5008	,	,		21591	0.7808		0.3419	False		,,,				2504	0.4949				p.T136T		Atlas-SNP	.											.	MATN2	165	.	0			c.T408C						PASS	.	G	,	1052,3166		160,732,1217	44.0	49.0	47.0		408,408	-11.9	0.2	8	dbSNP_100	47	2824,5676		470,1884,1896	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	630,2616,3113	CC,CT,TT		33.2235,24.9407,30.4765	,	136/957,136/938	98943446	3876,8842	2109	4250	6359	SO:0001819	synonymous_variant	4147	exon3			CATGACTGGGCTG	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.408T>C	8.37:g.98943446T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1																																																																																			C|0.399;T|0.601	0.399	strong		0.577	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
ADAM29	11086	hgsc.bcm.edu	37	4	175898994	175898994	+	Missense_Mutation	SNP	T	T	C	rs113485638	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175898994T>C	ENST00000359240.3	+	5	2988	c.2318T>C	c.(2317-2319)aTg>aCg	p.M773T	ADAM29_ENST00000445694.1_Missense_Mutation_p.M773T|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.M773T|ADAM29_ENST00000404450.4_Missense_Mutation_p.M773T	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	773	9 X 9 AA approximate repeats.			QPRVM -> HPQLT (in Ref. 1; AAF03777). {ECO:0000305}.	spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCTCGGGTGATGCCTTCTCAG	0.572													T|||	340	0.0678914	0.034	0.0663	5008	,	,		18552	0.0615		0.0964	False		,,,				2504	0.092				p.M773T	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											.	ADAM29	262	.	0			c.T2318C						PASS	.	T	THR/MET,THR/MET,THR/MET,THR/MET	1,4405		0,1,2202	177.0	157.0	164.0		2318,2318,2318,2318	-1.9	0.0	4	dbSNP_132	164	5,8595	818.9+/-406.8	0,5,4295	no	missense,missense,missense,missense	ADAM29	NM_014269.4,NM_001130705.1,NM_001130704.1,NM_001130703.1	81,81,81,81	0,6,6497	CC,CT,TT		0.0581,0.0227,0.0461	benign,benign,benign,benign	773/821,773/821,773/821,773/821	175898994	6,13000	2203	4300	6503	SO:0001583	missense	11086	exon4			GGGTGATGCCTTC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2318T>C	4.37:g.175898994T>C	ENSP00000352177:p.Met773Thr	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	211	39	0.184834	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.793535	0.00077	2.27E-4	5.81E-4	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01767	4.65;4.65;4.65;4.65	0.945	-1.89	0.07689	.	.	.	.	.	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48139	-0.9061	8	.	.	.	.	6.2442	0.20807	0.0:0.6365:0.0:0.3635	.	773	Q9UKF5	ADA29_HUMAN	T	773	ENSP00000352177:M773T;ENSP00000414544:M773T;ENSP00000384229:M773T;ENSP00000423517:M773T	.	M	+	2	0	ADAM29	176135569	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.420000	0.02457	-0.769000	0.04620	-0.639000	0.03973	ATG	T|0.500;C|0.500	0.500	weak		0.572	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
SAR1B	51128	hgsc.bcm.edu	37	5	133956668	133956668	+	Silent	SNP	G	G	A	rs11558540	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:133956668G>A	ENST00000402673.2	-	3	411	c.133C>T	c.(133-135)Cta>Tta	p.L45L	SAR1B_ENST00000507419.1_5'UTR|SAR1B_ENST00000439578.1_Silent_p.L45L	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	45					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|GTP catabolic process (GO:0006184)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			kidney(2)|lung(2)|urinary_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCATCTTTTAGCATGTGTAGC	0.358													G|||	841	0.167931	0.0303	0.0663	5008	,	,		19419	0.3135		0.1034	False		,,,				2504	0.3425				p.L45L		Atlas-SNP	.											.	SAR1B	19	.	0			c.C133T						PASS	.	G	,	206,4200	126.6+/-163.6	6,194,2003	343.0	292.0	310.0		133,133	3.7	1.0	5	dbSNP_120	310	1011,7589	216.6+/-255.6	52,907,3341	no	coding-synonymous,coding-synonymous	SAR1B	NM_001033503.2,NM_016103.3	,	58,1101,5344	AA,AG,GG		11.7558,4.6754,9.3572	,	45/199,45/199	133956668	1217,11789	2203	4300	6503	SO:0001819	synonymous_variant	51128	exon4			CTTTTAGCATGTG	AF092130	CCDS4177.1	5q31.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000152700	ENSG00000152700			10535	protein-coding gene	gene with protein product		607690	"""SAR1a gene homolog (S. cerevisiae) 2"", ""SAR1a gene homolog 2 (S. cerevisiae)"", ""SAR1 homolog B (S. cerevisiae)"""	SARA2			Standard	NM_001033503		Approved		uc003kzr.3	Q9Y6B6	OTTHUMG00000129114	ENST00000402673.2:c.133C>T	5.37:g.133956668G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	214	129	0.602804	NM_001033503	D3DQA4|Q567T4	Silent	SNP	ENST00000402673.2	37	CCDS4177.1																																																																																			G|0.886;A|0.114	0.114	strong		0.358	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103	
AMDHD1	144193	hgsc.bcm.edu	37	12	96346594	96346594	+	Silent	SNP	T	T	C	rs1982138	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:96346594T>C	ENST00000266736.2	+	2	343	c.237T>C	c.(235-237)atT>atC	p.I79I		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	79					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						GGAAATGTATTCTACCAGGTA	0.343													T|||	1275	0.254593	0.0923	0.1225	5008	,	,		16507	0.4673		0.2455	False		,,,				2504	0.3579				p.I79I		Atlas-SNP	.											.	AMDHD1	56	.	0			c.T237C						PASS	.	T		558,3848	238.0+/-249.6	31,496,1676	63.0	67.0	66.0		237	-0.1	1.0	12	dbSNP_92	66	2072,6522	353.4+/-329.1	245,1582,2470	no	coding-synonymous	AMDHD1	NM_152435.2		276,2078,4146	CC,CT,TT		24.1098,12.6645,20.2308		79/427	96346594	2630,10370	2203	4297	6500	SO:0001819	synonymous_variant	144193	exon2			ATGTATTCTACCA	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.237T>C	12.37:g.96346594T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_152435	A8K463|Q68CI8	Silent	SNP	ENST00000266736.2	37	CCDS9057.1																																																																																			T|0.779;C|0.221	0.221	strong		0.343	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435	
MUC4	4585	hgsc.bcm.edu	37	3	195505858	195505858	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195505858G>A	ENST00000463781.3	-	2	13052	c.12593C>T	c.(12592-12594)aCt>aTt	p.T4198I	MUC4_ENST00000475231.1_Missense_Mutation_p.T4198I|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGCTGAGGAAGTGTCGGTGAC	0.602																																					p.T4198I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	0			c.C12593T						scavenged	.						19.0	15.0	16.0					3																	195505858		689	1576	2265	SO:0001583	missense	4585	exon2			GAGGAAGTGTCGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12593C>T	3.37:g.195505858G>A	ENSP00000417498:p.Thr4198Ile	Somatic	238	3	0.012605		WXS	Illumina HiSeq	Phase_I	214	10	0.046729	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.623	0.115726	0.08831	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.38;1.3	.	.	.	.	.	.	.	.	T	0.19485	0.0468	N	0.14661	0.345	0.21105	N	0.999787	P	0.44090	0.826	B	0.40782	0.34	T	0.09975	-1.0650	7	.	.	.	.	6.6097	0.22745	2.0E-4:0.0:0.9998:0.0	.	4070	E7ESK3	.	I	4198	ENSP00000417498:T4198I;ENSP00000420243:T4198I	.	T	-	2	0	MUC4	196990637	0.000000	0.05858	0.017000	0.16124	0.032000	0.12392	0.289000	0.18957	0.452000	0.26830	0.074000	0.15403	ACT	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CTNNA3	29119	hgsc.bcm.edu	37	10	68040325	68040325	+	Missense_Mutation	SNP	C	C	T	rs4548513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:68040325C>T	ENST00000433211.2	-	13	1961	c.1787G>A	c.(1786-1788)aGc>aAc	p.S596N	CTNNA3_ENST00000373744.4_Missense_Mutation_p.S596N	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						ATTCAATGAGCTTTTGCTTAA	0.328													T|||	2429	0.485024	0.7269	0.4121	5008	,	,		17605	0.4187		0.3748	False		,,,				2504	0.3916				p.S596N		Atlas-SNP	.											.	CTNNA3	401	.	0			c.G1787A	GRCh37	CM074765	CTNNA3	M	rs4548513	PASS	.	T	ASN/SER,ASN/SER	2954,1452	454.7+/-350.8	1007,940,256	135.0	129.0	131.0		1787,1787	3.2	0.6	10	dbSNP_111	131	3114,5486	647.5+/-400.4	561,1992,1747	yes	missense,missense	CTNNA3	NM_001127384.1,NM_013266.2	46,46	1568,2932,2003	TT,TC,CC		36.2093,32.9551,46.6554	benign,benign	596/896,596/896	68040325	6068,6938	2203	4300	6503	SO:0001583	missense	29119	exon13			AATGAGCTTTTGC	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1787G>A	10.37:g.68040325C>T	ENSP00000389714:p.Ser596Asn	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	1032	0.4725274725274725	353	0.717479674796748	154	0.425414364640884	243	0.42482517482517484	282	0.3720316622691293	T	0.019	-1.454724	0.01071	0.670449	0.362093	ENSG00000183230	ENST00000433211;ENST00000373744	T;T	0.36157	1.27;1.27	5.54	3.16	0.36331	.	0.101185	0.42294	N	0.000735	T	0.00012	0.0000	N	0.00325	-1.645	0.23943	P	0.99639428	B	0.02656	0.0	B	0.04013	0.001	T	0.44112	-0.9349	9	0.02654	T	1	-13.3321	7.5116	0.27577	0.0:0.2511:0.0:0.7489	rs4548513;rs52832156;rs59069553;rs4548513	596	Q9UI47	CTNA3_HUMAN	N	596	ENSP00000389714:S596N;ENSP00000362849:S596N	ENSP00000362849:S596N	S	-	2	0	CTNNA3	67710331	0.992000	0.36948	0.635000	0.29338	0.424000	0.31475	0.882000	0.28186	0.069000	0.16605	-0.254000	0.11334	AGC	C|0.526;N|0.000	.	strong		0.328	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266	
FCGBP	8857	hgsc.bcm.edu	37	19	40392347	40392347	+	Missense_Mutation	SNP	C	C	G	rs139175656	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40392347C>G	ENST00000221347.6	-	16	8164	c.8157G>C	c.(8155-8157)caG>caC	p.Q2719H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2719				Q -> H (in Ref. 1; BAA19526). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)		p.Q2719H(2)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGGGCTCCACCTGGCCTCCAG	0.592													G|||	1513	0.302117	0.2708	0.4164	5008	,	,		15565	0.2103		0.3688	False		,,,				2504	0.2894				p.Q2719H		Atlas-SNP	.											FCGBP,NS,carcinoma,0,2	FCGBP	416	2	2	Substitution - Missense(2)	prostate(2)	c.G8157C						scavenged	.						17.0	16.0	17.0					19																	40392347		2135	4094	6229	SO:0001583	missense	8857	exon16			CTCCACCTGGCCT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8157G>C	19.37:g.40392347C>G	ENSP00000221347:p.Gln2719His	Somatic	211	2	0.00947867		WXS	Illumina HiSeq	Phase_I	369	34	0.0921409	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	0.582	-0.836839	0.02692	.	.	ENSG00000090920	ENST00000221347	T	0.76709	-1.04	2.02	-2.46	0.06461	Uncharacterised domain, cysteine-rich (2);	1.468830	0.04141	N	0.319631	T	0.53818	0.1820	N	0.04063	-0.285	0.09310	N	1	B	0.14012	0.009	B	0.20577	0.03	T	0.33904	-0.9850	10	0.37606	T	0.19	.	2.9179	0.05759	0.1094:0.305:0.4189:0.1668	.	2719	Q9Y6R7	FCGBP_HUMAN	H	2719	ENSP00000221347:Q2719H	ENSP00000221347:Q2719H	Q	-	3	2	FCGBP	45084187	0.000000	0.05858	0.060000	0.19600	0.366000	0.29705	-3.718000	0.00384	-0.933000	0.03737	-0.702000	0.03669	CAG	C|0.333;G|0.667	0.667	strong		0.592	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PUS10	150962	hgsc.bcm.edu	37	2	61175312	61175312	+	Silent	SNP	T	T	C	rs12479056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:61175312T>C	ENST00000316752.6	-	16	1578	c.1317A>G	c.(1315-1317)aaA>aaG	p.K439K	PUS10_ENST00000407787.1_Silent_p.K439K	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	439					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			TCTGGTCGATTTTTAAGTCCT	0.537													C|||	2281	0.455471	0.5696	0.5274	5008	,	,		18530	0.1687		0.6889	False		,,,				2504	0.3057				p.K439K		Atlas-SNP	.											.	PUS10	49	.	0			c.A1317G						PASS	.	C		2673,1733	517.2+/-369.4	828,1017,358	135.0	135.0	135.0		1317	4.4	1.0	2	dbSNP_120	135	5821,2779	440.9+/-359.6	1979,1863,458	no	coding-synonymous	PUS10	NM_144709.2		2807,2880,816	CC,CT,TT		32.314,39.3327,34.6917		439/530	61175312	8494,4512	2203	4300	6503	SO:0001819	synonymous_variant	150962	exon16			GTCGATTTTTAAG	AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"""coiled-coil domain containing 139"""	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.1317A>G	2.37:g.61175312T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_144709	Q5JPJ5|Q96MI8	Silent	SNP	ENST00000316752.6	37	CCDS1865.1																																																																																			T|0.412;C|0.588	0.588	strong		0.537	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709	
CKM	1158	hgsc.bcm.edu	37	19	45818835	45818835	+	Silent	SNP	A	A	G	rs1133190	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45818835A>G	ENST00000221476.3	-	4	543	c.369T>C	c.(367-369)ccT>ccC	p.P123P		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	123					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.P123P(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	GCACGTAGTTAGGGTCCAGGT	0.682													G|||	2039	0.407149	0.3011	0.3372	5008	,	,		15644	0.2381		0.6342	False		,,,				2504	0.5409				p.P123P		Atlas-SNP	.											CKM,colon,carcinoma,0,1	CKM	40	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T369C						PASS	.	G		1562,2844	658.0+/-400.3	276,1010,917	38.0	38.0	38.0		369	2.6	1.0	19	dbSNP_86	38	5416,3184	475.0+/-369.0	1738,1940,622	no	coding-synonymous	CKM	NM_001824.3		2014,2950,1539	GG,GA,AA		37.0233,35.4517,46.3478		123/382	45818835	6978,6028	2203	4300	6503	SO:0001819	synonymous_variant	1158	exon4			GTAGTTAGGGTCC	M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.369T>C	19.37:g.45818835A>G		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_001824	Q96QL9	Silent	SNP	ENST00000221476.3	37	CCDS12659.1																																																																																			A|0.522;G|0.478	0.478	strong		0.682	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
C4orf17	84103	hgsc.bcm.edu	37	4	100443784	100443784	+	Silent	SNP	C	C	G	rs200176388|rs36110345|rs386677740|rs61732380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100443784C>G	ENST00000326581.4	+	3	617	c.255C>G	c.(253-255)tcC>tcG	p.S85S	C4orf17_ENST00000514652.1_Silent_p.S85S|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	85			S -> P (in dbSNP:rs13119384). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		GTTACCCCTCCAGCACTGCAG	0.498													C|||	1057	0.211062	0.202	0.1888	5008	,	,		16686	0.1161		0.2744	False		,,,				2504	0.272				p.S85S		Atlas-SNP	.											.	C4orf17	42	.	0			c.C255G						PASS	.	C		90,4316		28,34,2141	112.0	104.0	107.0		255	1.6	0.1	4	dbSNP_129	107	186,8414		49,88,4163	no	coding-synonymous	C4orf17	NM_032149.2		77,122,6304	GG,GC,CC		2.1628,2.0427,2.1221		85/360	100443784	276,12730	2203	4300	6503	SO:0001819	synonymous_variant	84103	exon3			CCCCTCCAGCACT	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.255C>G	4.37:g.100443784C>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Silent	SNP	ENST00000326581.4	37	CCDS3649.1																																																																																			C|0.769;G|0.231	0.231	strong		0.498	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
SLC7A8	23428	hgsc.bcm.edu	37	14	23652004	23652004	+	Silent	SNP	G	G	A	rs1884545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:23652004G>A	ENST00000316902.7	-	1	845	c.120C>T	c.(118-120)atC>atT	p.I40I	SLC7A8_ENST00000469263.1_Silent_p.I40I|C14orf164_ENST00000399910.1_5'Flank	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	40					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	TGACCAATCCGATCTCTTTCT	0.597													G|||	284	0.0567093	0.0219	0.0807	5008	,	,		16034	0.004		0.1064	False		,,,				2504	0.09				p.I40I		Atlas-SNP	.											.	SLC7A8	54	.	0			c.C120T						PASS	.	G		216,4190	131.0+/-167.6	8,200,1995	130.0	111.0	117.0		120	1.8	1.0	14	dbSNP_92	117	1139,7461	236.0+/-268.3	72,995,3233	no	coding-synonymous	SLC7A8	NM_012244.2		80,1195,5228	AA,AG,GG		13.2442,4.9024,10.4183		40/536	23652004	1355,11651	2203	4300	6503	SO:0001819	synonymous_variant	23428	exon1			CAATCCGATCTCT	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"""Solute carriers"""	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.120C>T	14.37:g.23652004G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Silent	SNP	ENST00000316902.7	37	CCDS9590.1																																																																																			G|0.934;A|0.066	0.066	strong		0.597	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3		
BIRC7	79444	hgsc.bcm.edu	37	20	61869826	61869826	+	Silent	SNP	C	C	T	rs2273487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61869826C>T	ENST00000217169.3	+	3	742	c.528C>T	c.(526-528)tcC>tcT	p.S176S	BIRC7_ENST00000395306.1_Silent_p.S89S|MIR3196_ENST00000579556.1_RNA|BIRC7_ENST00000342412.6_Silent_p.S176S|NKAIN4_ENST00000466885.1_5'Flank	NM_139317.1	NP_647478.1	Q96CA5	BIRC7_HUMAN	baculoviral IAP repeat containing 7	176					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of natural killer cell apoptotic process (GO:0070247)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(9)|ovary(1)	12	all_cancers(38;2.72e-09)					TGCTGGGCTCCTGGGTGAGCG	0.622													C|||	2228	0.444888	0.3638	0.4798	5008	,	,		17002	0.4931		0.4404	False		,,,				2504	0.4847				p.S176S		Atlas-SNP	.											.	BIRC7	25	.	0			c.C528T						PASS	.	C	,	1666,2738	501.2+/-364.9	313,1040,849	57.0	61.0	59.0		528,528	3.6	1.0	20	dbSNP_100	59	3982,4618	549.6+/-385.6	952,2078,1270	no	coding-synonymous,coding-synonymous	BIRC7	NM_022161.2,NM_139317.1	,	1265,3118,2119	TT,TC,CC		46.3023,37.8292,43.4328	,	176/281,176/299	61869826	5648,7356	2202	4300	6502	SO:0001819	synonymous_variant	79444	exon3			GGGCTCCTGGGTG	AF301009	CCDS13512.1, CCDS13513.1	20q13.3	2011-01-25	2011-01-25		ENSG00000101197	ENSG00000101197		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	13702	protein-coding gene	gene with protein product	"""melanoma inhibitor of apoptosis protein"", ""kidney inhibitor of apoptosis protein"", ""livin inhibitor-of-apoptosis"", ""livin"""	605737	"""baculoviral IAP repeat-containing 7"""			11024045, 11162435	Standard	NM_139317		Approved	mliap, ML-IAP, KIAP, RNF50	uc002yej.3	Q96CA5	OTTHUMG00000032957	ENST00000217169.3:c.528C>T	20.37:g.61869826C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_139317	Q9BQV0|Q9H2A8|Q9HAP7	Silent	SNP	ENST00000217169.3	37	CCDS13513.1																																																																																			C|0.554;T|0.446	0.446	strong		0.622	BIRC7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080114.2	NM_139317	
RIN1	9610	hgsc.bcm.edu	37	11	66099987	66099987	+	Silent	SNP	C	C	T	rs1784029	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66099987C>T	ENST00000311320.4	-	10	2238	c.2112G>A	c.(2110-2112)gcG>gcA	p.A704A	RIN1_ENST00000530056.1_Silent_p.A538A|RIN1_ENST00000524804.1_5'Flank|RIN1_ENST00000424433.2_Intron|RP11-867G23.12_ENST00000526655.1_RNA	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	704	Ras and 14-3-3 protein binding region.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						CAGGCCACTCCGCCCGGCGGT	0.682													C|||	2808	0.560703	0.2209	0.7334	5008	,	,		15942	0.5595		0.662	False		,,,				2504	0.7945				p.A704A		Atlas-SNP	.											.	RIN1	64	.	0			c.G2112A						PASS	.	C		1295,3105	435.9+/-344.5	213,869,1118	83.0	92.0	89.0		2112	-3.0	1.0	11	dbSNP_89	89	5932,2658	682.8+/-403.8	2058,1816,421	no	coding-synonymous	RIN1	NM_004292.2		2271,2685,1539	TT,TC,CC		30.943,29.4318,44.3649		704/784	66099987	7227,5763	2200	4295	6495	SO:0001819	synonymous_variant	9610	exon10			CCACTCCGCCCGG	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.2112G>A	11.37:g.66099987C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_004292	O15010|Q00427|Q96CC8	Silent	SNP	ENST00000311320.4	37	CCDS31614.1																																																																																			C|0.445;T|0.555	0.555	strong		0.682	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
FCGBP	8857	hgsc.bcm.edu	37	19	40406029	40406029	+	Missense_Mutation	SNP	C	C	T	rs61735676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40406029C>T	ENST00000221347.6	-	10	4824	c.4817G>A	c.(4816-4818)cGg>cAg	p.R1606Q		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1606	Cys-rich.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCACTGCTGCCGACAGTTGTC	0.637													T|||	442	0.0882588	0.0741	0.0533	5008	,	,		20922	0.0635		0.0358	False		,,,				2504	0.2117				p.R1606Q		Atlas-SNP	.											.	FCGBP	416	.	0			c.G4817A						PASS	.	T	GLN/ARG	279,4123	757.8+/-412.8	25,229,1947	67.0	47.0	54.0		4817	-4.0	0.9	19	dbSNP_129	54	338,8258	769.6+/-407.6	16,306,3976	no	missense	FCGBP	NM_003890.2	43	41,535,5923	TT,TC,CC		3.9321,6.338,4.7469	benign	1606/5406	40406029	617,12381	2201	4298	6499	SO:0001583	missense	8857	exon10			TGCTGCCGACAGT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4817G>A	19.37:g.40406029C>T	ENSP00000221347:p.Arg1606Gln	Somatic	546	0	0		WXS	Illumina HiSeq	Phase_I	883	407	0.460929	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	122	0.055860805860805864	34	0.06910569105691057	18	0.049723756906077346	40	0.06993006993006994	30	0.0395778364116095	T	4.198	0.035391	0.08148	0.06338	0.039321	ENSG00000090920	ENST00000221347	T	0.04654	3.58	3.4	-4.03	0.04021	von Willebrand factor, type C (1);	.	.	.	.	T	0.00178	0.0005	N	0.02802	-0.49	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.47129	-0.9141	9	0.13108	T	0.6	.	6.3509	0.21375	0.0:0.4345:0.1532:0.4122	rs61735676	1606	Q9Y6R7	FCGBP_HUMAN	Q	1606	ENSP00000221347:R1606Q	ENSP00000221347:R1606Q	R	-	2	0	FCGBP	45097869	0.712000	0.27916	0.912000	0.35992	0.028000	0.11728	-0.806000	0.04525	-1.223000	0.02584	-2.161000	0.00327	CGG	C|0.948;T|0.052	0.052	strong		0.637	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SLC1A2	6506	hgsc.bcm.edu	37	11	35327748	35327748	+	Silent	SNP	C	C	T	rs752949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:35327748C>T	ENST00000278379.3	-	5	885	c.603G>A	c.(601-603)ccG>ccA	p.P201P	SLC1A2_ENST00000606205.1_Silent_p.P201P|SLC1A2_ENST00000395753.1_Silent_p.P192P|SLC1A2_ENST00000395750.1_Silent_p.P192P	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	201					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			CCTCCTCGTCCGGCGGTGGTG	0.502											OREG0020883	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	904	0.180511	0.1415	0.2464	5008	,	,		18901	0.1905		0.2624	False		,,,				2504	0.092				p.P201P	NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	Atlas-SNP	.											SLC1A2,NS,carcinoma,-1,1	SLC1A2	54	1	0			c.G603A						PASS	.	T	,	619,3785	768.6+/-413.6	45,529,1628	93.0	86.0	88.0		576,603	-3.3	0.0	11	dbSNP_92	88	2095,6501	717.2+/-406.2	251,1593,2454	no	coding-synonymous,coding-synonymous	SLC1A2	NM_001195728.1,NM_004171.3	,	296,2122,4082	TT,TC,CC		24.3718,14.0554,20.8769	,	192/566,201/575	35327748	2714,10286	2202	4298	6500	SO:0001819	synonymous_variant	6506	exon5			CTCGTCCGGCGGT	AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"""Solute carriers"""	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.603G>A	11.37:g.35327748C>T		Somatic	75	0	0	854	WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_004171	B4DQE9|Q14417|Q541G6|U3KQQ4	Silent	SNP	ENST00000278379.3	37	CCDS31459.1																																																																																			C|0.786;T|0.214	0.214	strong		0.502	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171	
TNC	3371	hgsc.bcm.edu	37	9	117835899	117835899	+	Missense_Mutation	SNP	C	C	T	rs1138545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:117835899C>T	ENST00000350763.4	-	10	3608	c.3197G>A	c.(3196-3198)cGt>cAt	p.R1066H	TNC_ENST00000346706.3_Missense_Mutation_p.R1066H|TNC_ENST00000341037.4_Missense_Mutation_p.R1066H|TNC_ENST00000345230.3_Missense_Mutation_p.R1066H|TNC_ENST00000423613.2_Missense_Mutation_p.R1066H|TNC_ENST00000537320.1_Missense_Mutation_p.R1066H|TNC_ENST00000535648.1_Missense_Mutation_p.R1066H|TNC_ENST00000542877.1_Missense_Mutation_p.R1066H|TNC_ENST00000340094.3_Missense_Mutation_p.R1066H	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1066	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.			R -> H (in Ref. 1; no nucleotide entry, 3; AAA88083 and 7; AAA52703). {ECO:0000305}.	bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TGCCTTCACACGTGCGGGCTT	0.542													C|||	592	0.118211	0.1513	0.0893	5008	,	,		20027	0.0952		0.1501	False		,,,				2504	0.0849				p.R1066H		Atlas-SNP	.											.	TNC	282	.	0			c.G3197A						PASS	.	C	HIS/ARG	566,3840	252.1+/-258.6	35,496,1672	116.0	104.0	108.0		3197	3.0	0.0	9	dbSNP_127	108	1243,7357	248.3+/-276.0	104,1035,3161	yes	missense	TNC	NM_002160.3	29	139,1531,4833	TT,TC,CC		14.4535,12.8461,13.909	benign	1066/2202	117835899	1809,11197	2203	4300	6503	SO:0001583	missense	3371	exon10			TTCACACGTGCGG		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.3197G>A	9.37:g.117835899C>T	ENSP00000265131:p.Arg1066His	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	152	83	0.546053	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	257	0.11767399267399267	65	0.13211382113821138	37	0.10220994475138122	32	0.055944055944055944	123	0.16226912928759896	C	5.666	0.307551	0.10733	0.128461	0.144535	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.53423	0.64;0.66;0.87;0.85;0.68;0.76;0.66;0.85;0.62	5.9	3.05	0.35203	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.342173	0.31963	N	0.006798	T	0.00178	0.0005	L	0.52573	1.65	0.58432	P	1.0000000000287557E-6	B;B	0.18013	0.025;0.001	B;B	0.13407	0.009;0.004	T	0.08953	-1.0697	9	0.25106	T	0.35	.	7.86	0.29504	0.0:0.644:0.1461:0.2099	rs45602433;rs61738260	1066;1066	E9PC84;P24821	.;TENA_HUMAN	H	1066	ENSP00000344400:R1066H;ENSP00000438152:R1066H;ENSP00000344555:R1066H;ENSP00000345861:R1066H;ENSP00000265131:R1066H;ENSP00000339553:R1066H;ENSP00000411406:R1066H;ENSP00000443478:R1066H;ENSP00000442242:R1066H	ENSP00000344400:R1066H	R	-	2	0	TNC	116875720	0.211000	0.23529	0.005000	0.12908	0.034000	0.12701	1.000000	0.29770	0.387000	0.25024	0.655000	0.94253	CGT	C|0.864;T|0.136	0.136	strong		0.542	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
FERMT1	55612	hgsc.bcm.edu	37	20	6064710	6064710	+	Silent	SNP	A	A	G	rs753927	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:6064710A>G	ENST00000217289.4	-	13	2483	c.1695T>C	c.(1693-1695)ttT>ttC	p.F565F	FERMT1_ENST00000536936.1_Silent_p.F308F|FERMT1_ENST00000478194.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	565	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						AGGTGAGGCCAAACTCAGGCA	0.542													G|||	1982	0.395767	0.3079	0.4568	5008	,	,		17470	0.6161		0.3588	False		,,,				2504	0.2822				p.F565F		Atlas-SNP	.											.	FERMT1	106	.	0			c.T1695C						PASS	.	G		1561,2845	667.1+/-401.8	291,979,933	73.0	57.0	63.0		1695	-2.6	1.0	20	dbSNP_86	63	3117,5483	656.9+/-401.4	557,2003,1740	no	coding-synonymous	FERMT1	NM_017671.4		848,2982,2673	GG,GA,AA		36.2442,35.429,35.968		565/678	6064710	4678,8328	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon13			GAGGCCAAACTCA	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1695T>C	20.37:g.6064710A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			A|0.615;G|0.385	0.385	strong		0.542	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
CSMD1	64478	hgsc.bcm.edu	37	8	3253768	3253768	+	Silent	SNP	C	C	T	rs3802303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:3253768C>T	ENST00000520002.1	-	18	3099	c.2544G>A	c.(2542-2544)ctG>ctA	p.L848L	CSMD1_ENST00000400186.3_Silent_p.L848L|CSMD1_ENST00000539096.1_Silent_p.L847L|CSMD1_ENST00000542608.1_Silent_p.L847L|CSMD1_ENST00000537824.1_Silent_p.L847L|CSMD1_ENST00000602723.1_Silent_p.L848L|CSMD1_ENST00000602557.1_Silent_p.L848L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	848	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CAGTGGTGAACAGCAGGTACA	0.597													T|||	1501	0.29972	0.3472	0.3386	5008	,	,		15559	0.0972		0.4235	False		,,,				2504	0.2894				p.L847L		Atlas-SNP	.											CSMD1_ENST00000537824,colon,carcinoma,0,2	CSMD1	1469	2	0			c.G2541A						PASS	.	T		1459,2877		278,903,987	34.0	45.0	42.0		2541	-9.9	0.0	8	dbSNP_107	42	3475,5079		732,2011,1534	no	coding-synonymous	CSMD1	NM_033225.5		1010,2914,2521	TT,TC,CC		40.6243,33.6485,38.2777		847/3565	3253768	4934,7956	2168	4277	6445	SO:0001819	synonymous_variant	64478	exon17			GGTGAACAGCAGG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2544G>A	8.37:g.3253768C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		687	0.31456043956043955	168	0.34146341463414637	133	0.3674033149171271	67	0.11713286713286714	319	0.420844327176781	T	0.026	-1.367594	0.01225	0.336485	0.406243	ENSG00000183117	ENST00000335551	.	.	.	4.93	-9.86	0.00473	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999776374	.	.	.	.	.	.	T	0.07065	-1.0792	3	.	.	.	.	5.1615	0.15064	0.136:0.4309:0.1698:0.2633	rs3802303;rs3802303	.	.	.	I	328	.	.	V	-	1	0	CSMD1	3241175	0.000000	0.05858	0.035000	0.18076	0.032000	0.12392	-3.102000	0.00603	-4.229000	0.00063	-4.636000	0.00004	GTT	C|0.663;T|0.337	0.337	strong		0.597	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SLC6A12	6539	hgsc.bcm.edu	37	12	319125	319125	+	Missense_Mutation	SNP	A	A	G	rs557881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:319125A>G	ENST00000428720.1	-	3	771	c.28T>C	c.(28-30)Tgt>Cgt	p.C10R	SLC6A12_ENST00000359674.4_Missense_Mutation_p.C10R|SLC6A12_ENST00000397296.2_Missense_Mutation_p.C10R|SLC6A12_ENST00000424061.2_Missense_Mutation_p.C10R|SLC6A12_ENST00000536824.1_Missense_Mutation_p.C10R	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	10			C -> R (in dbSNP:rs557881). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7589472}.	C -> Y (in Ref. 2; AAA66574). {ECO:0000305}.	amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			GGAGGCCCACACTCTTGCACT	0.622													G|||	2629	0.52496	0.7126	0.4308	5008	,	,		17088	0.3145		0.5229	False		,,,				2504	0.5573				p.C10R		Atlas-SNP	.											.	SLC6A12	60	.	0			c.T28C						PASS	.	G	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	3094,1312	443.1+/-346.9	1082,930,191	79.0	69.0	73.0		28,28,28,28	2.8	0.0	12	dbSNP_83	73	4550,4050	558.0+/-387.2	1194,2162,944	yes	missense,missense,missense,missense	SLC6A12	NM_001122847.2,NM_001122848.2,NM_001206931.1,NM_003044.4	180,180,180,180	2276,3092,1135	GG,GA,AA		47.093,29.7776,41.2271	benign,benign,benign,benign	10/615,10/615,10/615,10/615	319125	7644,5362	2203	4300	6503	SO:0001583	missense	6539	exon3			GCCCACACTCTTG	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.28T>C	12.37:g.319125A>G	ENSP00000388184:p.Cys10Arg	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	128	125	0.976562	NM_001122848	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	37	CCDS8501.1	1087	0.4977106227106227	359	0.7296747967479674	156	0.430939226519337	182	0.3181818181818182	390	0.5145118733509235	G	4.749	0.139228	0.09083	0.702224	0.52907	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824;ENST00000537793;ENST00000535347	T;T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;-0.35;0.79	5.63	2.81	0.32909	.	0.597438	0.15804	N	0.243826	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40813	-0.9543	9	0.21540	T	0.41	.	3.4038	0.07333	0.1178:0.4645:0.2717:0.146	rs557881;rs60807272;rs557881	10	P48065	S6A12_HUMAN	R	10	ENSP00000352702:C10R;ENSP00000380464:C10R;ENSP00000388184:C10R;ENSP00000399136:C10R;ENSP00000444268:C10R;ENSP00000439351:C10R;ENSP00000446082:C10R	ENSP00000352702:C10R	C	-	1	0	SLC6A12	189386	0.079000	0.21365	0.003000	0.11579	0.001000	0.01503	1.456000	0.35201	0.339000	0.23719	-0.213000	0.12676	TGT	A|0.466;G|0.534	0.534	strong		0.622	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
TGIF1	7050	hgsc.bcm.edu	37	18	3457607	3457607	+	Missense_Mutation	SNP	C	C	T	rs2229333	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:3457607C>T	ENST00000330513.5	+	3	1178	c.875C>T	c.(874-876)cCg>cTg	p.P292L	TGIF1_ENST00000472042.1_Missense_Mutation_p.P143L|TGIF1_ENST00000548489.2_Missense_Mutation_p.P177L|TGIF1_ENST00000401449.1_Missense_Mutation_p.P143L|TGIF1_ENST00000551541.1_Missense_Mutation_p.P143L|TGIF1_ENST00000345133.5_Missense_Mutation_p.P143L|TGIF1_ENST00000405385.3_Missense_Mutation_p.P143L|TGIF1_ENST00000343820.5_Missense_Mutation_p.P163L|TGIF1_ENST00000407501.2_Missense_Mutation_p.P163L|TGIF1_ENST00000400167.2_Missense_Mutation_p.P143L	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	292			P -> L (in dbSNP:rs2229333).|P -> S (in dbSNP:rs4468717). {ECO:0000269|PubMed:10764806, ECO:0000269|Ref.3}.		determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				CCGTCATCCCCGGGATCAGTT	0.532													C|||	389	0.0776757	0.0061	0.0461	5008	,	,		18746	0.1647		0.0596	False		,,,				2504	0.1258				p.P292L		Atlas-SNP	.											.	TGIF1	41	.	0			c.C875T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	54,4352	52.9+/-88.7	1,52,2150	55.0	51.0	52.0		488,875,530,488,428,428,428,428	4.4	0.5	18	dbSNP_98	52	521,8079	146.8+/-202.3	11,499,3790	no	missense,missense,missense,missense,missense,missense,missense,missense	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_173211.1,NM_174886.1	98,98,98,98,98,98,98,98	12,551,5940	TT,TC,CC		6.0581,1.2256,4.421	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	163/273,292/402,177/287,163/273,143/253,143/253,143/253,143/253	3457607	575,12431	2203	4300	6503	SO:0001583	missense	7050	exon3			CATCCCCGGGATC	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.875C>T	18.37:g.3457607C>T	ENSP00000327959:p.Pro292Leu	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	160	91	0.56875	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Missense_Mutation	SNP	ENST00000330513.5	37	CCDS11834.1	134	0.06135531135531135	4	0.008130081300813009	27	0.07458563535911603	62	0.10839160839160839	41	0.05408970976253298	C	8.345	0.829631	0.16749	0.012256	0.060581	ENSG00000177426	ENST00000552383;ENST00000401449;ENST00000548489;ENST00000549780;ENST00000405385;ENST00000343820;ENST00000407501;ENST00000551541;ENST00000345133;ENST00000330513;ENST00000549546;ENST00000400167;ENST00000472042	T;T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.17;0.38;0.28;-0.18;0.38;0.37;0.37;0.38;0.38;0.15;0.39;0.38;0.38	5.26	4.39	0.52855	.	0.000000	0.85682	D	0.000000	T	0.05227	0.0139	M	0.74258	2.255	0.09310	P	0.9999999869808	D;D;D	0.76494	0.999;0.982;0.997	P;P;D	0.63033	0.863;0.535;0.91	T	0.52049	-0.8627	9	0.36615	T	0.2	-21.8135	13.868	0.63600	0.0:0.926:0.0:0.074	rs2229333;rs3750274;rs17647302;rs52799550;rs2229333	292;163;177	Q15583;Q15583-2;F8VZB6	TGIF1_HUMAN;.;.	L	143;143;177;143;143;163;163;143;143;292;143;143;143	ENSP00000449287:P143L;ENSP00000385206:P143L;ENSP00000447747:P177L;ENSP00000448121:P143L;ENSP00000384970:P143L;ENSP00000339631:P163L;ENSP00000384133:P163L;ENSP00000450025:P143L;ENSP00000343969:P143L;ENSP00000327959:P292L;ENSP00000449580:P143L;ENSP00000383031:P143L;ENSP00000449501:P143L	ENSP00000327959:P292L	P	+	2	0	TGIF1	3447607	1.000000	0.71417	0.499000	0.27577	0.499000	0.33736	7.301000	0.78850	1.225000	0.43566	0.467000	0.42956	CCG	C|0.942;G|0.000;T|0.057	0.057	strong		0.532	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
ALPK2	115701	hgsc.bcm.edu	37	18	56204644	56204644	+	Silent	SNP	T	T	G	rs12963422	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204644T>G	ENST00000361673.3	-	5	2988	c.2775A>C	c.(2773-2775)gtA>gtC	p.V925V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	925						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GGCCAGCATGTACTGTGGAGG	0.488													T|||	1690	0.33746	0.0696	0.3184	5008	,	,		19240	0.5734		0.3221	False		,,,				2504	0.4857				p.V925V		Atlas-SNP	.											.	ALPK2	487	.	0			c.A2775C						PASS	.	T		551,3855	246.8+/-255.3	46,459,1698	49.0	52.0	51.0		2775	-8.2	0.0	18	dbSNP_121	51	3187,5413	482.5+/-370.9	600,1987,1713	no	coding-synonymous	ALPK2	NM_052947.3		646,2446,3411	GG,GT,TT		37.0581,12.5057,28.7406		925/2171	56204644	3738,9268	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			AGCATGTACTGTG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2775A>C	18.37:g.56204644T>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	78	47	0.602564	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			G|0.303;N|0.000	0.303	strong		0.488	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
CDH7	1005	hgsc.bcm.edu	37	18	63511176	63511176	+	Silent	SNP	T	T	C	rs2306675	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:63511176T>C	ENST00000397968.2	+	7	1536	c.1110T>C	c.(1108-1110)gaT>gaC	p.D370D	CDH7_ENST00000536984.2_Silent_p.D370D|CDH7_ENST00000323011.3_Silent_p.D370D	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	370	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		D -> E (in dbSNP:rs2306675).		adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D370D(1)		NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				TTGTGGAAGATGTAGATGAGC	0.502													T|||	932	0.186102	0.1528	0.2205	5008	,	,		12857	0.0377		0.3489	False		,,,				2504	0.1922				p.D370D		Atlas-SNP	.											CDH7,NS,carcinoma,0,1	CDH7	362	1	1	Substitution - coding silent(1)	stomach(1)	c.T1110C						PASS	.	T	,	856,3550	334.9+/-303.7	88,680,1435	188.0	156.0	167.0		1110,1110	-7.5	0.8	18	dbSNP_100	167	2914,5686	455.7+/-363.9	488,1938,1874	no	coding-synonymous,coding-synonymous	CDH7	NM_004361.2,NM_033646.1	,	576,2618,3309	CC,CT,TT		33.8837,19.4281,28.9866	,	370/786,370/786	63511176	3770,9236	2203	4300	6503	SO:0001819	synonymous_variant	1005	exon7			GGAAGATGTAGAT	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1110T>C	18.37:g.63511176T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_004361	Q9H157	Silent	SNP	ENST00000397968.2	37	CCDS11993.1																																																																																			T|0.756;C|0.244	0.244	strong		0.502	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
DTX3L	151636	hgsc.bcm.edu	37	3	122288210	122288210	+	Missense_Mutation	SNP	G	G	A	rs2332285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122288210G>A	ENST00000296161.4	+	3	1463	c.1274G>A	c.(1273-1275)aGg>aAg	p.R425K	DTX3L_ENST00000383661.3_Intron	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	425			R -> K (in dbSNP:rs2332285). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		TCCAAGGACAGGCAGGTAGAT	0.403													A|||	2734	0.545927	0.4644	0.5879	5008	,	,		22863	0.6597		0.5606	False		,,,				2504	0.4939				p.R425K		Atlas-SNP	.											.	DTX3L	59	.	0			c.G1274A						PASS	.	A	LYS/ARG	2165,2241	593.5+/-388.0	531,1103,569	99.0	95.0	96.0		1274	4.5	1.0	3	dbSNP_100	96	4915,3685	526.5+/-381.0	1421,2073,806	yes	missense	DTX3L	NM_138287.3	26	1952,3176,1375	AA,AG,GG		42.8488,49.1375,45.5636	benign	425/741	122288210	7080,5926	2203	4300	6503	SO:0001583	missense	151636	exon3			AGGACAGGCAGGT		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"""RING-type (C3HC4) zinc fingers"""	30323	protein-coding gene	gene with protein product	"""rhysin 2"""	613143	"""deltex 3-like (Drosophila)"""			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.1274G>A	3.37:g.122288210G>A	ENSP00000296161:p.Arg425Lys	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Missense_Mutation	SNP	ENST00000296161.4	37	CCDS3015.1	1241	0.5682234432234432	226	0.45934959349593496	208	0.574585635359116	383	0.6695804195804196	424	0.5593667546174143	A	3.449	-0.112492	0.06881	0.491375	0.571512	ENSG00000163840	ENST00000296161	T	0.24538	1.85	5.65	4.47	0.54385	.	0.101961	0.43747	N	0.000529	T	0.00012	0.0000	N	0.00119	-2.075	0.09310	P	0.999999999815924	B	0.02656	0.0	B	0.01281	0.0	T	0.44452	-0.9327	9	0.02654	T	1	-22.7409	8.3774	0.32451	0.8444:0.0:0.1556:0.0	rs2332285;rs17561454;rs52807756;rs60291555;rs2332285	425	Q8TDB6	DTX3L_HUMAN	K	425	ENSP00000296161:R425K	ENSP00000296161:R425K	R	+	2	0	DTX3L	123770900	0.118000	0.22208	0.965000	0.40720	0.469000	0.32828	1.192000	0.32150	0.542000	0.28846	-0.254000	0.11334	AGG	G|0.449;A|0.551	0.551	strong		0.403	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287	
ADAM28	10863	hgsc.bcm.edu	37	8	24167700	24167700	+	Silent	SNP	G	G	A	rs150620720	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:24167700G>A	ENST00000265769.4	+	4	362	c.252G>A	c.(250-252)acG>acA	p.T84T	ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000540823.1_5'UTR|ADAM28_ENST00000437154.2_Silent_p.T84T|RP11-624C23.1_ENST00000523700.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	84					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		CAGGCTACACGGAAACATATT	0.398													A|||	2	0.000399361	0.0	0.0	5008	,	,		18307	0.0		0.002	False		,,,				2504	0.0				p.T84T	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											ADAM28,NS,carcinoma,0,1	ADAM28	100	1	0			c.G252A						PASS	.	A	,	1,4405	825.4+/-416.5	0,1,2202	92.0	79.0	83.0		252,252	-9.1	0.0	8	dbSNP_134	83	1,8599	818.4+/-406.9	0,1,4299	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	84/776,84/541	24167700	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon4			CTACACGGAAACA	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.252G>A	8.37:g.24167700G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			G|1.000;A|0.000	0.000	strong		0.398	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
OR1A2	26189	hgsc.bcm.edu	37	17	3100827	3100827	+	Silent	SNP	T	T	C	rs2241093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3100827T>C	ENST00000381951.1	+	1	15	c.15T>C	c.(13-15)aaT>aaC	p.N5N		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	5					positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N5N(1)		breast(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						AGAAAGAAAATCAATCCTTTA	0.383													T|||	1460	0.291534	0.0613	0.2853	5008	,	,		20876	0.5605		0.3509	False		,,,				2504	0.2689				p.N5N		Atlas-SNP	.											OR1A2,NS,carcinoma,0,1	OR1A2	52	1	1	Substitution - coding silent(1)	stomach(1)	c.T15C						scavenged	.	T		513,3893	235.8+/-248.2	33,447,1723	89.0	86.0	87.0		15	-6.1	0.0	17	dbSNP_98	87	3184,5416	483.2+/-371.1	597,1990,1713	no	coding-synonymous	OR1A2	NM_012352.1		630,2437,3436	CC,CT,TT		37.0233,11.6432,28.4253		5/310	3100827	3697,9309	2203	4300	6503	SO:0001819	synonymous_variant	26189	exon1			AGAAAATCAATCC	AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"""GPCR / Class A : Olfactory receptors"""	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.15T>C	17.37:g.3100827T>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_012352	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Silent	SNP	ENST00000381951.1	37	CCDS11021.1																																																																																			T|0.693;C|0.307	0.307	strong		0.383	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352	
LRP5	4041	hgsc.bcm.edu	37	11	68192690	68192690	+	Silent	SNP	G	G	A	rs556442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:68192690G>A	ENST00000294304.7	+	15	3463	c.3357G>A	c.(3355-3357)gtG>gtA	p.V1119V		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1119	Beta-propeller 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCCTGGTGGTGGACAACACAC	0.672													G|||	2901	0.579273	0.1619	0.6758	5008	,	,		19306	0.7232		0.6899	False		,,,				2504	0.8129				p.V1119V		Atlas-SNP	.											.	LRP5	136	.	0			c.G3357A						PASS	.	G		1058,3342	385.4+/-325.7	126,806,1268	93.0	64.0	74.0		3357	-0.6	1.0	11	dbSNP_83	74	5780,2808	675.9+/-403.2	1967,1846,481	no	coding-synonymous	LRP5	NM_002335.2		2093,2652,1749	AA,AG,GG		32.6968,24.0455,47.3514		1119/1616	68192690	6838,6150	2200	4294	6494	SO:0001819	synonymous_variant	4041	exon15			GGTGGTGGACAAC	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3357G>A	11.37:g.68192690G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_002335	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																			G|0.460;A|0.540	0.540	strong		0.672	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
KHSRP	8570	hgsc.bcm.edu	37	19	6427408	6427408	+	5'Flank	SNP	G	G	A	rs3760750	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6427408G>A	ENST00000398148.3	-	0	0				SLC25A41_ENST00000321510.6_Silent_p.R243R	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein						gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						GCAGGTAGCCGCGGTAAAGGG	0.652													G|||	385	0.076877	0.003	0.0836	5008	,	,		17878	0.1438		0.0964	False		,,,				2504	0.0828				p.R243R	Colon(55;593 1006 2067 9135 22980)	Atlas-SNP	.											.	SLC25A41	26	.	0			c.C729T						PASS	.	G		99,4295		0,99,2098	30.0	37.0	35.0		729	-8.4	0.1	19	dbSNP_107	35	815,7777		32,751,3513	no	coding-synonymous	SLC25A41	NM_173637.3		32,850,5611	AA,AG,GG		9.4856,2.2531,7.0383		243/371	6427408	914,12072	2197	4296	6493	SO:0001631	upstream_gene_variant	284427	exon5			GTAGCCGCGGTAA	U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"""FUSE binding protein 2"""	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945			19.37:g.6427408G>A	Exception_encountered	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_173637	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Silent	SNP	ENST00000398148.3	37	CCDS45936.1																																																																																			G|0.908;A|0.092	0.092	strong		0.652	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1		
TOMM34	10953	hgsc.bcm.edu	37	20	43572217	43572217	+	Silent	SNP	T	T	C	rs1804644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43572217T>C	ENST00000372813.3	-	6	854	c.702A>G	c.(700-702)gcA>gcG	p.A234A	PABPC1L_ENST00000372819.1_Intron|PABPC1L_ENST00000490798.1_Intron	NM_006809.4	NP_006800.2	Q15785	TOM34_HUMAN	translocase of outer mitochondrial membrane 34	234					protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	11		Myeloproliferative disorder(115;0.0122)				AATAGCAGAGTGCTCTGAAGG	0.493													C|||	862	0.172125	0.4576	0.0706	5008	,	,		20481	0.1468		0.0318	False		,,,				2504	0.0286				p.A234A		Atlas-SNP	.											.	TOMM34	16	.	0			c.A702G						PASS	.	C		1729,2677	649.3+/-398.9	351,1027,825	113.0	103.0	106.0		702	-5.4	0.8	20	dbSNP_89	106	233,8367	809.2+/-407.2	7,219,4074	no	coding-synonymous	TOMM34	NM_006809.4		358,1246,4899	CC,CT,TT		2.7093,39.2419,15.0853		234/310	43572217	1962,11044	2203	4300	6503	SO:0001819	synonymous_variant	10953	exon6			GCAGAGTGCTCTG	U58970	CCDS13340.1	20q12-q13.1	2013-01-10			ENSG00000025772	ENSG00000025772		"""Tetratricopeptide (TTC) repeat domain containing"""	15746	protein-coding gene	gene with protein product	"""outer mitochondrial membrane translocase (34kD)"""					9324309	Standard	NM_006809		Approved	TOM34, HTOM34P	uc002xmy.3	Q15785	OTTHUMG00000032552	ENST00000372813.3:c.702A>G	20.37:g.43572217T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_006809	Q53GH9|Q6IBN7|Q9NTZ3	Silent	SNP	ENST00000372813.3	37	CCDS13340.1																																																																																			T|0.833;C|0.167	0.167	strong		0.493	TOMM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079390.3	NM_006809	
CPQ	10404	hgsc.bcm.edu	37	8	97847358	97847358	+	Silent	SNP	G	G	T	rs1864384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:97847358G>T	ENST00000220763.5	+	3	801	c.591G>T	c.(589-591)gtG>gtT	p.V197V		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	197					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										CTGCCAAGGTGGGGGCTTTGG	0.478													G|||	3051	0.609225	0.3177	0.6556	5008	,	,		17232	0.8829		0.6093	False		,,,				2504	0.6881				p.V197V		Atlas-SNP	.											.	.	.	.	0			c.G591T						PASS	.	G		1750,2656	521.5+/-370.6	339,1072,792	99.0	100.0	100.0		591	-7.0	0.5	8	dbSNP_92	100	5583,3017	663.8+/-402.1	1834,1915,551	no	coding-synonymous	PGCP	NM_016134.2		2173,2987,1343	TT,TG,GG		35.0814,39.7186,43.6183		197/473	97847358	7333,5673	2203	4300	6503	SO:0001819	synonymous_variant	10404	exon3			CAAGGTGGGGGCT	AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"""lysosomal dipeptidase"", ""Ser-Met dipeptidase"", ""plasma glutamate carboxypeptidase"""					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.591G>T	8.37:g.97847358G>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	216	214	0.990741	NM_016134	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Silent	SNP	ENST00000220763.5	37	CCDS6273.1																																																																																			G|0.413;T|0.587	0.587	strong		0.478	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134	
DXO	1797	hgsc.bcm.edu	37	6	31938412	31938412	+	Missense_Mutation	SNP	G	G	T	rs17207867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31938412G>T	ENST00000375349.3	-	4	1194	c.783C>A	c.(781-783)caC>caA	p.H261Q	STK19_ENST00000375333.2_5'Flank|DXO_ENST00000375356.3_Missense_Mutation_p.H261Q|DXO_ENST00000478221.1_5'UTR|DXO_ENST00000337523.5_Missense_Mutation_p.H261Q|STK19_ENST00000375331.2_5'Flank			O77932	DXO_HUMAN	decapping exoribonuclease	261			H -> Q (in dbSNP:rs17207867). {ECO:0000269|PubMed:14574404}.		metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										GGCCAGGGCTGTGCATCTCCT	0.602													G|||	594	0.11861	0.1694	0.0764	5008	,	,		17477	0.0347		0.0974	False		,,,				2504	0.1881				p.H261Q		Atlas-SNP	.											.	DOM3Z	20	.	0			c.C783A						PASS	.	G	GLN/HIS	444,2578		34,376,1101	72.0	75.0	74.0		783	3.6	1.0	6	dbSNP_123	74	496,4922		35,426,2248	yes	missense	DOM3Z	NM_005510.3	24	69,802,3349	TT,TG,GG		9.1547,14.6923,11.1374	benign	261/397	31938412	940,7500	1511	2709	4220	SO:0001583	missense	1797	exon4			AGGGCTGTGCATC	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"""DOM-3 (C. elegans) homolog Z"", ""dom-3 homolog Z (C. elegans)"""	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.783C>A	6.37:g.31938412G>T	ENSP00000364498:p.His261Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	64	0.627451	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Missense_Mutation	SNP	ENST00000375349.3	37	CCDS4732.1	220|220	0.10073260073260074|0.10073260073260074	94|94	0.1910569105691057|0.1910569105691057	26|26	0.0718232044198895|0.0718232044198895	22|22	0.038461538461538464|0.038461538461538464	78|78	0.10290237467018469|0.10290237467018469	G|G	14.38|14.38	2.518585|2.518585	0.44763|0.44763	0.146923|0.146923	0.091547|0.091547	ENSG00000204348|ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356|ENST00000495340	T;T;T|.	0.39787|.	1.06;1.06;1.06|.	4.46|4.46	3.59|3.59	0.41128|0.41128	RAI1-like (1);|.	0.109458|.	0.64402|.	D|.	0.000006|.	T|T	0.18383|0.18383	0.0441|0.0441	N|N	0.25426|0.25426	0.745|0.745	0.29311|0.29311	P|P	0.868011|0.868011	B|.	0.25272|.	0.122|.	B|.	0.18871|.	0.023|.	T|T	0.08994|0.08994	-1.0695|-1.0695	9|4	0.12430|.	T|.	0.62|.	-25.2902|-25.2902	6.6042|6.6042	0.22716|0.22716	0.0938:0.0:0.7283:0.1779|0.0938:0.0:0.7283:0.1779	rs17207867;rs59177784|rs17207867;rs59177784	261|.	O77932|.	DOM3Z_HUMAN|.	Q|K	261|68	ENSP00000337759:H261Q;ENSP00000364498:H261Q;ENSP00000364505:H261Q|.	ENSP00000337759:H261Q|.	H|T	-|-	3|2	2|0	DOM3Z|DOM3Z	32046391|32046391	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.570000|2.570000	0.45981|0.45981	1.088000|1.088000	0.41272|0.41272	0.561000|0.561000	0.74099|0.74099	CAC|ACA	A|0.000;C|0.000;G|0.895;T|0.105	0.105	strong		0.602	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3		
HIGD1C	613227	hgsc.bcm.edu	37	12	51354803	51354803	+	Silent	SNP	C	C	T	rs12306808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51354803C>T	ENST00000398455.3	+	2	224	c.147C>T	c.(145-147)taC>taT	p.Y49Y		NM_001109619.1	NP_001103089.1	A8MV81	HIG1C_HUMAN	HIG1 hypoxia inducible domain family, member 1C	49	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.					integral component of membrane (GO:0016021)				lung(1)	1						AGCTAAAGTACAGAAGAGATC	0.418													C|||	1318	0.263179	0.1793	0.1585	5008	,	,		19096	0.494		0.163	False		,,,				2504	0.316				p.Y49Y		Atlas-SNP	.											.	HIGD1C	4	.	0			c.C147T						PASS	.	C		621,3197		54,513,1342	94.0	94.0	94.0		147	3.6	1.0	12	dbSNP_120	94	1276,6968		105,1066,2951	no	coding-synonymous	HIGD1C	NM_001109619.1		159,1579,4293	TT,TC,CC		15.4779,16.2651,15.7271		49/98	51354803	1897,10165	1909	4122	6031	SO:0001819	synonymous_variant	613227	exon2			AAAGTACAGAAGA	DQ029494	CCDS44882.1	12q13.12	2011-09-16	2009-03-17		ENSG00000214511	ENSG00000214511			28044	protein-coding gene	gene with protein product			"""HIG1 domain family, member 1C"""				Standard	NM_001109619		Approved	Gm921	uc010smw.2	A8MV81	OTTHUMG00000169488	ENST00000398455.3:c.147C>T	12.37:g.51354803C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	235	128	0.544681	NM_001109619		Silent	SNP	ENST00000398455.3	37	CCDS44882.1																																																																																			C|0.758;T|0.242	0.242	strong		0.418	HIGD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404340.2	NM_001109619	
OR8U1	219417	hgsc.bcm.edu	37	11	56143715	56143715	+	Missense_Mutation	SNP	A	A	G	rs78460947|rs386753762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56143715A>G	ENST00000302270.1	+	1	616	c.616A>G	c.(616-618)Atg>Gtg	p.M206V		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	206			M -> I (in dbSNP:rs10896310).|M -> T (in dbSNP:rs10896309).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					TGCTGGTATCATGTTCATTTC	0.458													A|||	25	0.00499201	0.0008	0.0043	5008	,	,		24031	0.0		0.0199	False		,,,				2504	0.001				p.M206V		Atlas-SNP	.											.	OR8U1	59	.	0			c.A616G						PASS	.	A	VAL/MET	25,4075		0,25,2025	205.0	201.0	203.0		616	4.6	0.3	11	dbSNP_132	203	293,8135		4,285,3925	yes	missense	OR8U1	NM_001005204.1	21	4,310,5950	GG,GA,AA		3.4765,0.6098,2.5383	benign	206/310	56143715	318,12210	2050	4214	6264	SO:0001583	missense	219417	exon1			GGTATCATGTTCA	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"""GPCR / Class A : Olfactory receptors"""	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.616A>G	11.37:g.56143715A>G	ENSP00000304188:p.Met206Val	Somatic	613	0	0		WXS	Illumina HiSeq	Phase_I	666	298	0.447447	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	21	0.009615384615384616	0	0.0	3	0.008287292817679558	0	0.0	18	0.023746701846965697	A	1.804	-0.476378	0.04414	0.006098	0.034765	ENSG00000172199	ENST00000302270	T	0.00030	8.9	5.78	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.571004	0.16107	N	0.229286	T	0.00039	0.0001	N	0.03029	-0.43	0.09310	N	1	B	0.19935	0.04	B	0.25759	0.063	T	0.23368	-1.0190	10	0.49607	T	0.09	.	6.8208	0.23857	0.6374:0.1295:0.0:0.233	.	206	Q8NH10	OR8U1_HUMAN	V	206	ENSP00000304188:M206V	ENSP00000304188:M206V	M	+	1	0	OR8U1	55900291	0.000000	0.05858	0.256000	0.24389	0.003000	0.03518	-0.021000	0.12504	2.214000	0.71695	0.523000	0.50628	ATG	A|0.986;G|0.014	0.014	strong		0.458	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
OR13C2	392376	hgsc.bcm.edu	37	9	107367841	107367841	+	Missense_Mutation	SNP	A	A	T	rs10991326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107367841A>T	ENST00000542196.1	-	1	110	c.68T>A	c.(67-69)cTt>cAt	p.L23H		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	23						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GAGTAACTCAAGTCTTGGGTG	0.408													A|||	1868	0.373003	0.4342	0.2161	5008	,	,		20515	0.5645		0.1789	False		,,,				2504	0.4039				p.L23H		Atlas-SNP	.											OR13C2,NS,carcinoma,-1,1	OR13C2	46	1	0			c.T68A						PASS	.						31.0	35.0	33.0					9																	107367841		2181	4289	6470	SO:0001583	missense	392376	exon1			AACTCAAGTCTTG		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.68T>A	9.37:g.107367841A>T	ENSP00000438815:p.Leu23His	Somatic	523	0	0		WXS	Illumina HiSeq	Phase_I	526	212	0.403042	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	708	0.3241758241758242	184	0.37398373983739835	74	0.20441988950276244	319	0.5576923076923077	131	0.17282321899736147	A	10.73	1.431549	0.25813	.	.	ENSG00000257019	ENST00000542196	T	0.03413	3.94	3.39	3.39	0.38822	.	0.000000	0.33477	U	0.004878	T	0.00012	0.0000	M	0.78456	2.415	0.80722	P	0.0	D	0.76494	0.999	D	0.63033	0.91	T	0.36866	-0.9730	9	0.87932	D	0	.	9.8158	0.40851	1.0:0.0:0.0:0.0	rs10991326;rs60657466	23	Q8NGS9	O13C2_HUMAN	H	23	ENSP00000438815:L23H	ENSP00000438815:L23H	L	-	2	0	OR13C2	106407662	0.001000	0.12720	0.022000	0.16811	0.190000	0.23558	1.352000	0.34033	1.409000	0.46915	0.379000	0.24179	CTT	A|0.026;T|0.974	0.974	strong		0.408	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
TNFSF12	8742	hgsc.bcm.edu	37	17	7460517	7460517	+	Silent	SNP	G	G	C	rs3803798	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7460517G>C	ENST00000293825.6	+	7	863	c.600G>C	c.(598-600)gcG>gcC	p.A200A	TNFSF13_ENST00000338784.4_5'Flank|TNFSF13_ENST00000380535.4_5'Flank|TNFSF12-TNFSF13_ENST00000293826.4_Intron|TNFSF12_ENST00000557233.1_Intron|TNFSF12_ENST00000462811.1_3'UTR|TNFSF13_ENST00000396545.4_5'Flank|TNFSF13_ENST00000483039.1_5'Flank|TNFSF13_ENST00000349228.4_5'Flank|TNFSF13_ENST00000396542.1_5'Flank	NM_003809.2	NP_003800.1	O43508	TNF12_HUMAN	tumor necrosis factor (ligand) superfamily, member 12	200					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|endothelial cell migration (GO:0043542)|immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|receptor binding (GO:0005102)	p.A200A(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|prostate(2)	11		Prostate(122;0.157)				CCACTGCGGCGAGTTCCCTCG	0.662													G|||	2742	0.547524	0.4266	0.6167	5008	,	,		13631	0.6458		0.5139	False		,,,				2504	0.5951				p.A200A		Atlas-SNP	.											TNFSF12,colon,carcinoma,0,1	TNFSF12	20	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G600C						PASS	.	G	,	1994,2412	559.5+/-380.2	456,1082,665	78.0	62.0	67.0		600,	-7.7	0.0	17	dbSNP_107	67	4514,4086	591.8+/-392.9	1190,2134,976	no	coding-synonymous,intron	TNFSF12,TNFSF12-TNFSF13	NM_003809.2,NM_172089.3	,	1646,3216,1641	CC,CG,GG		47.5116,45.2565,49.9616	,	200/250,	7460517	6508,6498	2203	4300	6503	SO:0001819	synonymous_variant	8742	exon7			TGCGGCGAGTTCC	AF030099	CCDS11109.1	17p13.1	2008-02-01			ENSG00000239697	ENSG00000239697		"""Tumor necrosis factor (ligand) superfamily"""	11927	protein-coding gene	gene with protein product		602695				9405449, 9560343	Standard	NM_003809		Approved	TWEAK, DR3LG, APO3L		O43508	OTTHUMG00000108148	ENST00000293825.6:c.600G>C	17.37:g.7460517G>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_003809	Q8IZK7|Q8WUZ7	Silent	SNP	ENST00000293825.6	37	CCDS11109.1																																																																																			G|0.494;C|0.506	0.506	strong		0.662	TNFSF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226951.2	NM_003809	
MPPED1	758	hgsc.bcm.edu	37	22	43831056	43831056	+	Silent	SNP	C	C	T	rs4331615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43831056C>T	ENST00000417669.2	+	3	771	c.327C>T	c.(325-327)taC>taT	p.Y109Y	MPPED1_ENST00000538182.1_Silent_p.Y142Y|MPPED1_ENST00000414469.2_Silent_p.Y3Y|MPPED1_ENST00000542779.1_Silent_p.Y109Y|MPPED1_ENST00000443721.1_Silent_p.Y109Y|MPPED1_ENST00000439548.1_Intron			O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	109							hydrolase activity (GO:0016787)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|skin(1)	13		all_neural(38;0.0244)|Ovarian(80;0.0694)				AGATGCCGTACGGCGACGTGC	0.647													C|||	1780	0.355431	0.4206	0.3919	5008	,	,		17505	0.0873		0.4861	False		,,,				2504	0.3834				p.Y109Y		Atlas-SNP	.											.	MPPED1	59	.	0			c.C327T						PASS	.	C		1731,2497		374,983,757	92.0	105.0	100.0		327	-8.8	0.0	22	dbSNP_111	100	4393,4039		1147,2099,970	no	coding-synonymous	MPPED1	NM_001044370.1		1521,3082,1727	TT,TC,CC		47.9009,40.9413,48.3728		109/327	43831056	6124,6536	2114	4216	6330	SO:0001819	synonymous_variant	758	exon3			GCCGTACGGCGAC	U84894	CCDS46723.1	22q13.2	2013-09-20	2005-10-10	2005-10-10	ENSG00000186732	ENSG00000186732			1306	protein-coding gene	gene with protein product		602112	"""chromosome 22 open reading frame 1"""	C22orf1		9266672, 10591208	Standard	NM_001044370		Approved	239AB, FAM1A	uc011apv.2	O15442	OTTHUMG00000150566	ENST00000417669.2:c.327C>T	22.37:g.43831056C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001044370	A8K159|B7Z2S9|Q8N361	Silent	SNP	ENST00000417669.2	37	CCDS46723.1																																																																																			C|0.606;T|0.394	0.394	strong		0.647	MPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318938.2	NM_001044370	
SGIP1	84251	hgsc.bcm.edu	37	1	67109335	67109335	+	Missense_Mutation	SNP	A	A	G	rs7526812	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:67109335A>G	ENST00000371037.4	+	7	469	c.392A>G	c.(391-393)aAg>aGg	p.K131R	SGIP1_ENST00000371035.3_Missense_Mutation_p.K88R|SGIP1_ENST00000371036.3_Missense_Mutation_p.K106R|SGIP1_ENST00000468286.1_3'UTR|SGIP1_ENST00000371039.1_Missense_Mutation_p.K107R|SGIP1_ENST00000237247.6_Missense_Mutation_p.K135R	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	131			K -> R (in dbSNP:rs7526812). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.2}.		endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)	p.K131R(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						GACATTCTTAAGAATGCTGCA	0.368													A|||	1414	0.282348	0.4312	0.2867	5008	,	,		19950	0.2738		0.1402	False		,,,				2504	0.2331				p.K131R		Atlas-SNP	.											SGIP1,NS,carcinoma,0,1	SGIP1	272	1	1	Substitution - Missense(1)	stomach(1)	c.A392G						PASS	.	A	ARG/LYS	1612,2794	498.9+/-364.3	302,1008,893	149.0	145.0	147.0		392	5.3	1.0	1	dbSNP_116	147	1297,7303	256.3+/-280.9	107,1083,3110	yes	missense	SGIP1	NM_032291.2	26	409,2091,4003	GG,GA,AA		15.0814,36.5865,22.3666	possibly-damaging	131/829	67109335	2909,10097	2203	4300	6503	SO:0001583	missense	84251	exon7			TTCTTAAGAATGC	AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.392A>G	1.37:g.67109335A>G	ENSP00000360076:p.Lys131Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	121	74	0.61157	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Missense_Mutation	SNP	ENST00000371037.4	37	CCDS30744.1	573	0.2623626373626374	217	0.4410569105691057	71	0.19613259668508287	176	0.3076923076923077	109	0.1437994722955145	A	10.21	1.287897	0.23478	0.365865	0.150814	ENSG00000118473	ENST00000237247;ENST00000371039;ENST00000424320;ENST00000371035;ENST00000371038;ENST00000407289;ENST00000371036;ENST00000371037	T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26	5.3	5.3	0.74995	.	0.161255	0.56097	D	0.000032	T	0.06416	0.0165	L	0.47716	1.5	0.46416	P	9.649999999999936E-4	B	0.12630	0.006	B	0.08055	0.003	T	0.19418	-1.0306	9	0.18276	T	0.48	-13.2771	11.4888	0.50369	0.9272:0.0:0.0728:0.0	rs7526812;rs52830701;rs57004614;rs7526812	131	Q9BQI5	SGIP1_HUMAN	R	135;107;131;88;134;134;106;131	ENSP00000237247:K135R;ENSP00000360078:K107R;ENSP00000410439:K131R;ENSP00000360074:K88R;ENSP00000360075:K106R;ENSP00000360076:K131R	ENSP00000237247:K135R	K	+	2	0	SGIP1	66881923	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	3.063000	0.49978	2.126000	0.65437	0.533000	0.62120	AAG	A|0.749;G|0.251	0.251	strong		0.368	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291	
KNTC1	9735	hgsc.bcm.edu	37	12	123057792	123057792	+	Missense_Mutation	SNP	A	A	G	rs61751322	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123057792A>G	ENST00000333479.7	+	26	2420	c.2243A>G	c.(2242-2244)cAt>cGt	p.H748R	KNTC1_ENST00000450485.2_Missense_Mutation_p.H711R	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	748					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		ATGAGAGAACATGACTTGCAA	0.393													A|||	92	0.0183706	0.003	0.0331	5008	,	,		19334	0.0		0.0616	False		,,,				2504	0.0031				p.H748R		Atlas-SNP	.											.	KNTC1	182	.	0			c.A2243G						PASS	.	A	ARG/HIS	50,3634		0,50,1792	172.0	170.0	171.0		2243	5.7	0.6	12	dbSNP_129	171	531,7657		14,503,3577	yes	missense	KNTC1	NM_014708.4	29	14,553,5369	GG,GA,AA		6.4851,1.3572,4.8939	possibly-damaging	748/2210	123057792	581,11291	1842	4094	5936	SO:0001583	missense	9735	exon26			GAGAACATGACTT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.2243A>G	12.37:g.123057792A>G	ENSP00000328236:p.His748Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	70	0.03205128205128205	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	58	0.07651715039577836	A	13.54	2.268225	0.40095	0.013572	0.064851	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.24350	1.86;2.35	5.66	5.66	0.87406	.	0.104253	0.64402	D	0.000004	T	0.02119	0.0066	L	0.54323	1.7	0.80722	D	1	P;P	0.47106	0.89;0.827	P;B	0.49047	0.599;0.344	T	0.00048	-1.2206	10	0.41790	T	0.15	-13.7702	15.8843	0.79232	1.0:0.0:0.0:0.0	rs61751322	711;748	E7ES84;P50748	.;KNTC1_HUMAN	R	711;748	ENSP00000397992:H711R;ENSP00000328236:H748R	ENSP00000328236:H748R	H	+	2	0	KNTC1	121623745	1.000000	0.71417	0.614000	0.29051	0.255000	0.26057	7.838000	0.86804	2.164000	0.68074	0.533000	0.62120	CAT	A|0.962;G|0.038	0.038	strong		0.393	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
BSPRY	54836	hgsc.bcm.edu	37	9	116132334	116132334	+	Missense_Mutation	SNP	C	C	T	rs3088235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:116132334C>T	ENST00000374183.4	+	6	1160	c.1121C>T	c.(1120-1122)aCa>aTa	p.T374I	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	374	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		T -> I (in dbSNP:rs3088235). {ECO:0000269|PubMed:10978534, ECO:0000269|PubMed:14702039}.		calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						GCCTCCGGCACAGTGCTCTGT	0.632													C|||	630	0.125799	0.0068	0.0893	5008	,	,		18166	0.1448		0.1799	False		,,,				2504	0.2372				p.T374I		Atlas-SNP	.											.	BSPRY	21	.	0			c.C1121T						PASS	.	C	ILE/THR	147,3783		3,141,1821	45.0	49.0	47.0		1121	3.9	0.0	9	dbSNP_102	47	1606,6686		153,1300,2693	yes	missense	BSPRY	NM_017688.2	89	156,1441,4514	TT,TC,CC		19.3681,3.7405,14.343	benign	374/403	116132334	1753,10469	1965	4146	6111	SO:0001583	missense	54836	exon6			CCGGCACAGTGCT	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.1121C>T	9.37:g.116132334C>T	ENSP00000363298:p.Thr374Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	44	0.60274	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	37	CCDS43868.1	264	0.12087912087912088	4	0.008130081300813009	42	0.11602209944751381	73	0.12762237762237763	145	0.19129287598944592	C	1.512	-0.549115	0.04024	0.037405	0.193681	ENSG00000119411	ENST00000374183	T	0.70164	-0.46	5.69	3.86	0.44501	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.221215	0.49916	D	0.000124	T	0.00144	0.0004	L	0.58583	1.82	0.58432	P	1.0000000000287557E-6	P	0.40360	0.714	B	0.40782	0.34	T	0.09122	-1.0689	9	0.16420	T	0.52	-4.634	8.9651	0.35872	0.0:0.7749:0.0:0.2251	rs3088235;rs3750528;rs52790594;rs61234611;rs3088235	374	Q5W0U4	BSPRY_HUMAN	I	374	ENSP00000363298:T374I	ENSP00000363298:T374I	T	+	2	0	BSPRY	115172155	0.029000	0.19370	0.019000	0.16419	0.174000	0.22865	2.875000	0.48491	0.767000	0.33267	0.561000	0.74099	ACA	C|0.852;T|0.148	0.148	strong		0.632	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
DEPTOR	64798	hgsc.bcm.edu	37	8	120977542	120977542	+	Missense_Mutation	SNP	A	A	G	rs34068787	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:120977542A>G	ENST00000286234.5	+	4	626	c.496A>G	c.(496-498)Atg>Gtg	p.M166V	DEPTOR_ENST00000523492.1_Missense_Mutation_p.M65V	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	166	DEP 2. {ECO:0000255|PROSITE- ProRule:PRU00066}.			M -> V (in Ref. 2; BAB14054). {ECO:0000305}.	intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						GCGCACCTTCATGGCATCTGA	0.532													A|||	12	0.00239617	0.0	0.0043	5008	,	,		19723	0.0		0.0089	False		,,,				2504	0.0				p.M166V		Atlas-SNP	.											.	DEPTOR	41	.	0			c.A496G						PASS	.	A	VAL/MET	9,4397	15.5+/-35.6	1,7,2195	117.0	100.0	106.0		496	4.2	1.0	8	dbSNP_126	106	113,8487	59.8+/-121.6	0,113,4187	yes	missense	DEPTOR	NM_022783.2	21	1,120,6382	GG,GA,AA		1.314,0.2043,0.938	benign	166/410	120977542	122,12884	2203	4300	6503	SO:0001583	missense	64798	exon4			ACCTTCATGGCAT		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"""DEP domain containing 6"""	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.496A>G	8.37:g.120977542A>G	ENSP00000286234:p.Met166Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Missense_Mutation	SNP	ENST00000286234.5	37	CCDS6331.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	5.224	0.226749	0.09916	0.002043	0.01314	ENSG00000155792	ENST00000523492;ENST00000286234	T;T	0.19938	2.11;2.11	5.31	4.15	0.48705	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.096120	0.64402	N	0.000001	T	0.02494	0.0076	N	0.00112	-2.095	0.37297	D	0.908535	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.003	T	0.17471	-1.0368	10	0.13853	T	0.58	-26.3081	7.3916	0.26913	0.7492:0.0:0.2508:0.0	rs34068787	65;166	E7EV87;Q8TB45	.;DPTOR_HUMAN	V	65;166	ENSP00000430457:M65V;ENSP00000286234:M166V	ENSP00000286234:M166V	M	+	1	0	DEPTOR	121046723	1.000000	0.71417	1.000000	0.80357	0.320000	0.28249	3.112000	0.50368	0.866000	0.35629	0.533000	0.62120	ATG	A|0.993;G|0.007	0.007	strong		0.532	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783	
PTPRN	5798	hgsc.bcm.edu	37	2	220162129	220162129	+	Silent	SNP	C	C	T	rs144452294	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220162129C>T	ENST00000295718.2	-	14	2154	c.1914G>A	c.(1912-1914)acG>acA	p.T638T	PTPRN_ENST00000409251.3_Silent_p.T609T|PTPRN_ENST00000497977.1_5'Flank|PTPRN_ENST00000423636.2_Silent_p.T548T|AC114803.3_ENST00000417355.1_RNA	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	638					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		ACAAGGACTTCGTGGCCATGT	0.622													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		17782	0.0		0.007	False		,,,				2504	0.001				p.T638T		Atlas-SNP	.											PTPRN,colon,carcinoma,-1,1	PTPRN	138	1	0			c.G1914A						PASS	.	C	,,	9,4397	15.5+/-35.6	0,9,2194	53.0	56.0	55.0		1827,1644,1914	-4.2	1.0	2	dbSNP_134	55	78,8522	45.4+/-104.0	0,78,4222	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN	NM_001199763.1,NM_001199764.1,NM_002846.3	,,	0,87,6416	TT,TC,CC		0.907,0.2043,0.6689	,,	609/951,548/890,638/980	220162129	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	5798	exon14			GGACTTCGTGGCC		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1914G>A	2.37:g.220162129C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Silent	SNP	ENST00000295718.2	37	CCDS2440.1																																																																																			C|0.996;T|0.004	0.004	strong		0.622	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2		
TBC1D17	79735	hgsc.bcm.edu	37	19	50387729	50387729	+	Silent	SNP	C	C	T	rs35681527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50387729C>T	ENST00000221543.5	+	12	1556	c.1257C>T	c.(1255-1257)ggC>ggT	p.G419G	TBC1D17_ENST00000535102.2_Silent_p.G386G	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	419	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		ACGTCCAGGGCATGAGTGATC	0.642													C|||	536	0.107029	0.1876	0.0749	5008	,	,		15216	0.0		0.1163	False		,,,				2504	0.1217				p.G419G		Atlas-SNP	.											.	TBC1D17	39	.	0			c.C1257T						PASS	.	C	,	789,3617	316.3+/-294.6	67,655,1481	179.0	169.0	172.0		1158,1257	0.2	1.0	19	dbSNP_126	172	1031,7569	220.5+/-258.2	70,891,3339	no	coding-synonymous,coding-synonymous	TBC1D17	NM_001168222.1,NM_024682.2	,	137,1546,4820	TT,TC,CC		11.9884,17.9074,13.9935	,	386/616,419/649	50387729	1820,11186	2203	4300	6503	SO:0001819	synonymous_variant	79735	exon12			CCAGGGCATGAGT	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.1257C>T	19.37:g.50387729C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	37	CCDS12785.1																																																																																			C|0.873;G|0.000;T|0.127	0.127	strong		0.642	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
TIAM2	26230	hgsc.bcm.edu	37	6	155575607	155575607	+	Silent	SNP	G	G	A	rs3011895	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:155575607G>A	ENST00000461783.3	+	28	5641	c.4368G>A	c.(4366-4368)gaG>gaA	p.E1456E	TIAM2_ENST00000367174.2_Silent_p.E832E|TIAM2_ENST00000528391.2_Silent_p.E792E|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000275246.7_Silent_p.E381E|TIAM2_ENST00000318981.5_Silent_p.E1456E|TIAM2_ENST00000456144.1_Silent_p.E1485E|TIAM2_ENST00000456877.2_Silent_p.E768E|TIAM2_ENST00000360366.4_Silent_p.E1480E|TIAM2_ENST00000529824.2_Silent_p.E1485E			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1456	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TTCTGAGGGAGAACTTCAGGC	0.463													A|||	1279	0.255391	0.2806	0.245	5008	,	,		19017	0.0149		0.4284	False		,,,				2504	0.2986				p.E1456E		Atlas-SNP	.											.	TIAM2	161	.	0			c.G4368A						PASS	.	A	,	1293,3113	699.1+/-406.4	181,931,1091	143.0	125.0	131.0		1143,4368	-3.4	0.8	6	dbSNP_101	131	3574,5026	628.9+/-398.2	747,2080,1473	no	coding-synonymous,coding-synonymous	TIAM2	NM_001010927.2,NM_012454.3	,	928,3011,2564	AA,AG,GG		41.5581,29.3463,37.4212	,	381/627,1456/1702	155575607	4867,8139	2203	4300	6503	SO:0001819	synonymous_variant	26230	exon25			GAGGGAGAACTTC		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.4368G>A	6.37:g.155575607G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	191	90	0.471204	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																			G|0.666;A|0.334	0.334	strong		0.463	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
SLC41A1	254428	hgsc.bcm.edu	37	1	205779231	205779231	+	Silent	SNP	G	G	A	rs11240569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205779231G>A	ENST00000367137.3	-	2	1353	c.339C>T	c.(337-339)acC>acT	p.T113T		NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	113					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)	p.T113T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	17	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CAGCAGCCACGGTCCCAAAGC	0.607													G|||	1385	0.276558	0.0174	0.1873	5008	,	,		20273	0.5198		0.2883	False		,,,				2504	0.4274				p.T113T		Atlas-SNP	.											SLC41A1,NS,carcinoma,0,1	SLC41A1	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C339T						PASS	.	G		280,4126	156.3+/-189.4	12,256,1935	102.0	95.0	98.0		339	-11.2	0.4	1	dbSNP_120	98	2466,6134	406.9+/-349.0	350,1766,2184	no	coding-synonymous	SLC41A1	NM_173854.4		362,2022,4119	AA,AG,GG		28.6744,6.355,21.1133		113/514	205779231	2746,10260	2203	4300	6503	SO:0001819	synonymous_variant	254428	exon2			AGCCACGGTCCCA	AJ514402	CCDS30988.1	1q32.1	2013-07-17	2013-07-17		ENSG00000133065	ENSG00000133065		"""Solute carriers"""	19429	protein-coding gene	gene with protein product		610801				12810078, 18367447	Standard	NM_173854		Approved	MgtE	uc001hdh.1	Q8IVJ1	OTTHUMG00000036000	ENST00000367137.3:c.339C>T	1.37:g.205779231G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	160	66	0.4125	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Silent	SNP	ENST00000367137.3	37	CCDS30988.1																																																																																			G|0.761;A|0.239	0.239	strong		0.607	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1		
C4orf27	54969	hgsc.bcm.edu	37	4	170678993	170678993	+	Silent	SNP	T	T	C	rs11540095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:170678993T>C	ENST00000393381.2	-	1	111	c.36A>G	c.(34-36)ggA>ggG	p.G12G		NM_017867.2	NP_060337.2	Q9NWY4	CD027_HUMAN	chromosome 4 open reading frame 27	12						nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	12		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)		GCGGCCCCTCTCCGCCGGGCC	0.692													C|||	3893	0.777356	0.6899	0.7954	5008	,	,		12693	0.881		0.7843	False		,,,				2504	0.7689				p.G12G		Atlas-SNP	.											.	C4orf27	32	.	0			c.A36G						PASS	.	C		2972,1212		1062,848,182	5.0	6.0	6.0		36	1.7	0.7	4	dbSNP_120	6	6667,1561		2735,1197,182	no	coding-synonymous	C4orf27	NM_017867.2		3797,2045,364	CC,CT,TT		18.9718,28.9675,22.3413		12/347	170678993	9639,2773	2092	4114	6206	SO:0001819	synonymous_variant	54969	exon1			CCCCTCTCCGCCG	BC010367	CCDS3813.1	4q33	2011-01-25			ENSG00000056050	ENSG00000056050			26051	protein-coding gene	gene with protein product						11230166	Standard	NM_017867		Approved	FLJ20534	uc003isl.4	Q9NWY4	OTTHUMG00000160960	ENST00000393381.2:c.36A>G	4.37:g.170678993T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_017867		Silent	SNP	ENST00000393381.2	37	CCDS3813.1																																																																																			T|0.200;C|0.800	0.800	strong		0.692	C4orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363140.1	NM_017867	
TRAFD1	10906	hgsc.bcm.edu	37	12	112580071	112580071	+	Silent	SNP	C	C	T	rs7970397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:112580071C>T	ENST00000257604.5	+	6	1439	c.822C>T	c.(820-822)ggC>ggT	p.G274G	TRAFD1_ENST00000412615.2_Silent_p.G274G	NM_001143906.1	NP_001137378.1	O14545	TRAD1_HUMAN	TRAF-type zinc finger domain containing 1	274					negative regulation of innate immune response (GO:0045824)|response to cytokine (GO:0034097)		metal ion binding (GO:0046872)			kidney(5)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	17						AGTCTCATGGCGGTCCCAGGT	0.483													C|||	926	0.184904	0.2852	0.0778	5008	,	,		18497	0.2738		0.0944	False		,,,				2504	0.1268				p.G274G		Atlas-SNP	.											.	TRAFD1	42	.	0			c.C822T						PASS	.	C	,	1101,3305	397.6+/-330.5	123,855,1225	89.0	88.0	88.0		822,822	-2.9	0.0	12	dbSNP_116	88	800,7800	187.4+/-234.7	30,740,3530	no	coding-synonymous,coding-synonymous	TRAFD1	NM_001143906.1,NM_006700.2	,	153,1595,4755	TT,TC,CC		9.3023,24.9887,14.6163	,	274/583,274/583	112580071	1901,11105	2203	4300	6503	SO:0001819	synonymous_variant	10906	exon6			TCATGGCGGTCCC	AB007447	CCDS9160.1	12q24.13	2013-01-25			ENSG00000135148	ENSG00000135148			24808	protein-coding gene	gene with protein product		613197				12477932	Standard	NM_006700		Approved	FLN29	uc001ttp.3	O14545	OTTHUMG00000169640	ENST00000257604.5:c.822C>T	12.37:g.112580071C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	NM_001143906	A8K5L6|B4DI89	Silent	SNP	ENST00000257604.5	37	CCDS9160.1																																																																																			C|0.830;T|0.170	0.170	strong		0.483	TRAFD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405214.1	NM_006700	
TMEM201	199953	hgsc.bcm.edu	37	1	9670834	9670834	+	Missense_Mutation	SNP	C	C	T	rs4926472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:9670834C>T	ENST00000340381.6	+	9	1745	c.1736C>T	c.(1735-1737)cCg>cTg	p.P579L	TMEM201_ENST00000377376.4_Missense_Mutation_p.P555L	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	579					fibroblast migration (GO:0010761)|nuclear migration (GO:0007097)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				lung(3)|upper_aerodigestive_tract(1)	4	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)		CCCCGGAAGCCGCCCCTGCAG	0.706													C|||	3361	0.671126	0.5008	0.7651	5008	,	,		14631	0.6468		0.8022	False		,,,				2504	0.7249				p.P579L		Atlas-SNP	.											.	TMEM201	63	.	0			c.C1736T						PASS	.	C	LEU/PRO	773,611		235,303,154	21.0	28.0	26.0		1736	-10.4	0.0	1	dbSNP_111	26	2564,618		1033,498,60	yes	missense	TMEM201	NM_001130924.2	98	1268,801,214	TT,TC,CC		19.4217,44.1474,26.9163	benign	579/667	9670834	3337,1229	692	1591	2283	SO:0001583	missense	199953	exon9			GGAAGCCGCCCCT		CCDS30579.1, CCDS44055.1, CCDS44055.2	1p36.22	2009-11-06			ENSG00000188807	ENSG00000188807			33719	protein-coding gene	gene with protein product							Standard	NM_001130924		Approved	RP13-15M17.2, NET5	uc021ofy.1	Q5SNT2	OTTHUMG00000057457	ENST00000340381.6:c.1736C>T	1.37:g.9670834C>T	ENSP00000344503:p.Pro579Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	111	67	0.603604	NM_001130924	B9EH90|Q5SNT3	Missense_Mutation	SNP	ENST00000340381.6	37	CCDS44055.2	1492	0.6831501831501832	236	0.4796747967479675	279	0.7707182320441989	374	0.6538461538461539	603	0.7955145118733509	C	13.01	2.109353	0.37242	0.558526	0.805783	ENSG00000188807	ENST00000377376;ENST00000340381	.	.	.	5.19	-10.4	0.00318	.	1.272510	0.05129	N	0.492308	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.13145	0.007	B	0.09377	0.004	T	0.35871	-0.9771	8	0.41790	T	0.15	0.001	4.4328	0.11536	0.177:0.5096:0.1331:0.1804	rs4926472;rs9430384;rs17034216;rs57429272;rs4926472	555	E9PBR6	.	L	555;579	.	ENSP00000344503:P579L	P	+	2	0	TMEM201	9593421	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.403000	0.07214	-1.580000	0.01644	-0.397000	0.06425	CCG	C|0.322;T|0.678	0.678	strong		0.706	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87493737	87493737	+	Splice_Site	SNP	T	T	C	rs11648852	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:87493737T>C	ENST00000268616.4	-	2	377	c.160A>G	c.(160-162)Atc>Gtc	p.I54V		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	54			I -> V (in dbSNP:rs11648852).				nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CTTGGAGTGATCTGAGGGAAC	0.438													T|||	637	0.127196	0.0666	0.1182	5008	,	,		17397	0.2272		0.1183	False		,,,				2504	0.1217				p.I54V		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.A160G						PASS	.	T	VAL/ILE	406,3990	199.8+/-223.2	14,378,1806	113.0	109.0	110.0		160	-3.0	0.0	16	dbSNP_120	110	1110,7490	230.7+/-264.9	78,954,3268	yes	missense-near-splice	ZCCHC14	NM_015144.2	29	92,1332,5074	CC,CT,TT		12.907,9.2357,11.6651	benign	54/950	87493737	1516,11480	2198	4300	6498	SO:0001630	splice_region_variant	23174	exon2			GAGTGATCTGAGG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.160-1A>G	16.37:g.87493737T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	37	CCDS10961.1	321	0.14697802197802198	36	0.07317073170731707	50	0.13812154696132597	139	0.243006993006993	96	0.1266490765171504	T	0.041	-1.284746	0.01398	0.092357	0.12907	ENSG00000140948	ENST00000268616	T	0.15372	2.43	5.01	-3.02	0.05446	.	1.071750	0.07100	N	0.840201	T	0.00012	0.0000	N	0.00436	-1.5	0.58432	P	1.0000000000287557E-6	B	0.09022	0.002	B	0.06405	0.002	T	0.48068	-0.9067	9	0.14656	T	0.56	-10.8316	13.4733	0.61292	0.0:0.6866:0.0:0.3134	rs11648852;rs52791527;rs59463424;rs11648852	54	Q8WYQ9	ZCH14_HUMAN	V	54	ENSP00000268616:I54V	ENSP00000268616:I54V	I	-	1	0	ZCCHC14	86051238	0.967000	0.33354	0.020000	0.16555	0.005000	0.04900	0.450000	0.21762	-0.381000	0.07882	-0.290000	0.09829	ATC	T|0.873;C|0.127	0.127	strong		0.438	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	Missense_Mutation
RPP38	10557	hgsc.bcm.edu	37	10	15145948	15145948	+	Missense_Mutation	SNP	T	T	C	rs10242	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:15145948T>C	ENST00000378197.4	+	3	1149	c.635T>C	c.(634-636)aTt>aCt	p.I212T	RPP38_ENST00000451677.1_Intron|RPP38_ENST00000378202.5_Missense_Mutation_p.I212T|NMT2_ENST00000466201.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	212			I -> T (in dbSNP:rs10242).		RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)	8						CAAGACAGAATTGAAGATTCT	0.438													T|||	73	0.0145767	0.0038	0.0245	5008	,	,		19247	0.0		0.0427	False		,,,				2504	0.0082				p.I212T	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.T635C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE	21,4385	27.2+/-55.0	0,21,2182	66.0	69.0	68.0		635,635,635	-5.2	0.0	10	dbSNP_52	68	247,8353	98.6+/-160.1	3,241,4056	yes	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	89,89,89	3,262,6238	CC,CT,TT		2.8721,0.4766,2.0606	benign,benign,benign	212/284,212/284,212/284	15145948	268,12738	2203	4300	6503	SO:0001583	missense	10557	exon2			ACAGAATTGAAGA	U77664	CCDS7108.1	10p13	2012-05-21			ENSG00000152464	ENSG00000152464			30329	protein-coding gene	gene with protein product		606116				9037013, 9630247	Standard	NM_183005		Approved		uc001inx.5	P78345	OTTHUMG00000017728	ENST00000378197.4:c.635T>C	10.37:g.15145948T>C	ENSP00000367439:p.Ile212Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	37	CCDS7108.1	49	0.022435897435897436	5	0.01016260162601626	12	0.03314917127071823	0	0.0	32	0.04221635883905013	T	0.006	-2.026492	0.00414	0.004766	0.028721	ENSG00000152464	ENST00000378203;ENST00000378202;ENST00000378197	T;T;T	0.08546	3.08;3.08;3.08	5.35	-5.15	0.02866	.	0.941611	0.08925	N	0.873875	T	0.00440	0.0014	N	0.00289	-1.7	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	10	0.02654	T	1	-0.5777	15.1003	0.72269	0.0:0.5549:0.0:0.4451	rs10242;rs61037821;rs10242	212	P78345	RPP38_HUMAN	T	212	ENSP00000367445:I212T;ENSP00000367444:I212T;ENSP00000367439:I212T	ENSP00000367439:I212T	I	+	2	0	RPP38	15185954	0.000000	0.05858	0.000000	0.03702	0.263000	0.26337	-0.010000	0.12743	-0.767000	0.04633	-0.936000	0.02699	ATT	T|0.978;C|0.022	0.022	strong		0.438	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
ANO1	55107	hgsc.bcm.edu	37	11	70007392	70007392	+	Silent	SNP	A	A	G	rs2276067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:70007392A>G	ENST00000355303.5	+	17	2009	c.1704A>G	c.(1702-1704)gcA>gcG	p.A568A	ANO1_ENST00000316296.5_Silent_p.A510A|ANO1_ENST00000538023.1_Silent_p.A568A|ANO1_ENST00000530676.1_Silent_p.A422A|ANO1_ENST00000531349.1_Silent_p.A277A|ANO1_ENST00000398543.2_Silent_p.A422A	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	568					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CAGCCACCGCAGTCATCATCA	0.582													G|||	3296	0.658147	0.5893	0.6081	5008	,	,		21108	0.7798		0.6561	False		,,,				2504	0.6636				p.A568A		Atlas-SNP	.											.	ANO1	156	.	0			c.A1704G						PASS	.	G		2570,1794		758,1054,370	106.0	110.0	109.0		1704	-7.8	0.1	11	dbSNP_100	109	5677,2863		1906,1865,499	no	coding-synonymous	ANO1	NM_018043.5		2664,2919,869	GG,GA,AA		33.5246,41.1091,36.0896		568/987	70007392	8247,4657	2182	4270	6452	SO:0001819	synonymous_variant	55107	exon17			CACCGCAGTCATC	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.1704A>G	11.37:g.70007392A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	162	74	0.45679	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Silent	SNP	ENST00000355303.5	37	CCDS44663.1																																																																																			A|0.347;G|0.653	0.653	strong		0.582	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
MAMDC2	256691	hgsc.bcm.edu	37	9	72741247	72741247	+	Silent	SNP	C	C	T	rs2296772	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:72741247C>T	ENST00000377182.4	+	6	1433	c.816C>T	c.(814-816)taC>taT	p.Y272Y	MAMDC2-AS1_ENST00000591368.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	272	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						CTGGCCTTTACGAGGAAATCT	0.552													C|||	507	0.101238	0.0061	0.0331	5008	,	,		20940	0.2044		0.0825	False		,,,				2504	0.1912				p.Y272Y		Atlas-SNP	.											.	MAMDC2	55	.	0			c.C816T						PASS	.	C		75,4331	67.0+/-104.6	1,73,2129	66.0	59.0	61.0		816	-6.4	0.4	9	dbSNP_100	61	669,7931	169.3+/-220.7	26,617,3657	no	coding-synonymous	MAMDC2	NM_153267.4		27,690,5786	TT,TC,CC		7.7791,1.7022,5.7204		272/687	72741247	744,12262	2203	4300	6503	SO:0001819	synonymous_variant	256691	exon6			CCTTTACGAGGAA	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.816C>T	9.37:g.72741247C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	113	46	0.40708	NM_153267	Q5VW47|Q8WX43|Q96BM4	Silent	SNP	ENST00000377182.4	37	CCDS6631.1																																																																																			C|0.923;T|0.077	0.077	strong		0.552	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267	
OR13G1	441933	hgsc.bcm.edu	37	1	247836008	247836008	+	Silent	SNP	G	G	A	rs28555391	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247836008G>A	ENST00000359688.2	-	1	357	c.336C>T	c.(334-336)ttC>ttT	p.F112F	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CCATGGTGGTGAAGAGAACCA	0.468													G|||	1649	0.329273	0.2965	0.2392	5008	,	,		23332	0.376		0.3519	False		,,,				2504	0.3661				p.F112F		Atlas-SNP	.											.	OR13G1	78	.	0			c.C336T						PASS	.	G		1312,3094	441.0+/-346.2	188,936,1079	91.0	75.0	80.0		336	-1.3	0.0	1	dbSNP_125	80	3098,5502	474.3+/-368.8	562,1974,1764	no	coding-synonymous	OR13G1	NM_001005487.1		750,2910,2843	AA,AG,GG		36.0233,29.7776,33.9074		112/308	247836008	4410,8596	2203	4300	6503	SO:0001819	synonymous_variant	441933	exon1			GGTGGTGAAGAGA	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.336C>T	1.37:g.247836008G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	192	95	0.494792	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Silent	SNP	ENST00000359688.2	37	CCDS31094.1																																																																																			G|0.664;A|0.336	0.336	strong		0.468	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487	
ZNF485	220992	hgsc.bcm.edu	37	10	44111806	44111806	+	Silent	SNP	G	G	A	rs10899839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:44111806G>A	ENST00000361807.3	+	5	509	c.315G>A	c.(313-315)ctG>ctA	p.L105L	ZNF485_ENST00000374435.3_Silent_p.L105L|ZNF485_ENST00000374437.2_Silent_p.L14L	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	105					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						CATCTGTTCTGGGAGAGCGAA	0.418													G|||	1519	0.303315	0.534	0.2954	5008	,	,		19252	0.0417		0.2654	False		,,,				2504	0.3057				p.L105L		Atlas-SNP	.											.	ZNF485	102	.	0			c.G315A						PASS	.	G		2271,2135	596.9+/-388.7	596,1079,528	65.0	67.0	66.0		315	2.0	0.0	10	dbSNP_120	66	2579,6021	418.9+/-352.9	393,1793,2114	no	coding-synonymous	ZNF485	NM_145312.3		989,2872,2642	AA,AG,GG		29.9884,48.4567,37.2905		105/442	44111806	4850,8156	2203	4300	6503	SO:0001819	synonymous_variant	220992	exon5			TGTTCTGGGAGAG	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.315G>A	10.37:g.44111806G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_145312	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	37	CCDS7205.2																																																																																			G|0.681;A|0.319	0.319	strong		0.418	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
OR51A7	119687	hgsc.bcm.edu	37	11	4928866	4928866	+	Silent	SNP	C	C	T	rs7941509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4928866C>T	ENST00000359350.4	+	1	267	c.267C>T	c.(265-267)gcC>gcT	p.A89A	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTTCAATGCCATGGGAATTT	0.453													C|||	1995	0.398363	0.2625	0.3919	5008	,	,		21957	0.0804		0.6143	False		,,,				2504	0.6922				p.A89A		Atlas-SNP	.											OR51A7,rectum,carcinoma,0,1	OR51A7	86	1	0			c.C267T						PASS	.	C		1333,3069	445.7+/-347.8	197,939,1065	153.0	131.0	138.0		267	-2.3	0.2	11	dbSNP_116	138	5302,3294	646.7+/-400.3	1637,2028,633	no	coding-synonymous	OR51A7	NM_001004749.1		1834,2967,1698	TT,TC,CC		38.3201,30.2817,48.9537		89/313	4928866	6635,6363	2201	4298	6499	SO:0001819	synonymous_variant	119687	exon1			CAATGCCATGGGA	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"""GPCR / Class A : Olfactory receptors"""	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.267C>T	11.37:g.4928866C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_001004749	Q6IFH8	Silent	SNP	ENST00000359350.4	37	CCDS31364.1																																																																																			C|0.549;T|0.451	0.451	strong		0.453	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
KIAA0922	23240	hgsc.bcm.edu	37	4	154513627	154513627	+	Splice_Site	SNP	A	A	G	rs7669418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:154513627A>G	ENST00000409663.3	+	18	1862	c.1810A>G	c.(1810-1812)Atc>Gtc	p.I604V	KIAA0922_ENST00000440693.1_Intron|KIAA0922_ENST00000409959.3_Splice_Site_p.I605V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	604			I -> V (in dbSNP:rs7669418).			integral component of membrane (GO:0016021)		p.I457V(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TCACACCTAGATCAAGTACTT	0.498													G|||	1130	0.225639	0.1483	0.2147	5008	,	,		19400	0.2361		0.3072	False		,,,				2504	0.2434				p.I605V		Atlas-SNP	.											KIAA0922,NS,carcinoma,0,1	KIAA0922	214	1	1	Substitution - Missense(1)	stomach(1)	c.A1813G						PASS	.	G	VAL/ILE,VAL/ILE	794,3612	751.2+/-412.2	66,662,1475	124.0	104.0	111.0		1813,1810	3.5	1.0	4	dbSNP_116	111	2670,5930	684.2+/-403.9	426,1818,2056	yes	missense-near-splice,missense-near-splice	KIAA0922	NM_001131007.1,NM_015196.3	29,29	492,2480,3531	GG,GA,AA		31.0465,18.0209,26.6339	benign,benign	605/1611,604/1610	154513627	3464,9542	2203	4300	6503	SO:0001630	splice_region_variant	23240	exon18			ACCTAGATCAAGT	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.1810-1A>G	4.37:g.154513627A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	563	0.25778388278388276	67	0.13617886178861788	94	0.2596685082872928	157	0.2744755244755245	245	0.3232189973614776	G	0.015	-1.540589	0.00934	0.180209	0.310465	ENSG00000121210	ENST00000409663;ENST00000409959	T;T	0.12039	2.72;2.73	4.41	3.55	0.40652	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00380	-1.58	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43782	-0.9370	8	.	.	.	-6.4731	10.0083	0.41970	0.0758:0.138:0.7862:0.0	rs7669418;rs17370255;rs57147535;rs7669418	605;604	A2VDJ0-5;A2VDJ0	.;T131L_HUMAN	V	604;605	ENSP00000386574:I604V;ENSP00000386787:I605V	.	I	+	1	0	KIAA0922	154733077	1.000000	0.71417	0.992000	0.48379	0.002000	0.02628	6.044000	0.71012	0.596000	0.29794	-0.834000	0.03071	ATC	A|0.743;G|0.257	0.257	strong		0.498	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	Missense_Mutation
SMARCC2	6601	hgsc.bcm.edu	37	12	56563346	56563346	+	Silent	SNP	G	G	A	rs17852368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56563346G>A	ENST00000267064.4	-	24	2675	c.2589C>T	c.(2587-2589)gcC>gcT	p.A863A	SMARCC2_ENST00000394023.3_Silent_p.A894A|SMARCC2_ENST00000550164.1_Silent_p.A894A|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Silent_p.A894A	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	863	Poly-Ala.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			ccagggcggcggcagcagcgg	0.582													g|||	162	0.0323482	0.1127	0.0159	5008	,	,		16111	0.0		0.002	False		,,,				2504	0.0				p.A894A		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C2682T						PASS	.	G	,,	438,3968	213.5+/-233.1	28,382,1793	86.0	74.0	78.0		2682,2589,2682	-8.8	0.0	12	dbSNP_123	78	15,8585	11.9+/-42.8	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	SMARCC2	NM_001130420.1,NM_003075.3,NM_139067.2	,,	28,397,6078	AA,AG,GG		0.1744,9.941,3.483	,,	894/1153,863/1215,894/1131	56563346	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	6601	exon25			GGCGGCGGCAGCA	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.2589C>T	12.37:g.56563346G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	98	32	0.326531	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Silent	SNP	ENST00000267064.4	37	CCDS8907.1																																																																																			G|0.961;A|0.039	0.039	strong		0.582	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
TMEM119	338773	hgsc.bcm.edu	37	12	108985945	108985945	+	Missense_Mutation	SNP	A	A	G	rs7975237	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:108985945A>G	ENST00000392806.3	-	2	383	c.215T>C	c.(214-216)aTa>aCa	p.I72T		NM_181724.2	NP_859075.2	Q4V9L6	TM119_HUMAN	transmembrane protein 119	72			I -> T (in dbSNP:rs7975237). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:16303743}.		osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|skin(1)	7						CCCCAGGGTTATGGGCTGGGG	0.692													G|||	3283	0.655551	0.7542	0.4539	5008	,	,		14227	0.8532		0.4433	False		,,,				2504	0.68				p.I72T		Atlas-SNP	.											.	TMEM119	31	.	0			c.T215C						PASS	.	G	THR/ILE	3179,1227	419.8+/-338.8	1157,865,181	43.0	49.0	47.0		215	4.6	0.8	12	dbSNP_116	47	3865,4735	606.3+/-395.1	856,2153,1291	yes	missense	TMEM119	NM_181724.2	89	2013,3018,1472	GG,GA,AA		44.9419,27.8484,45.8404	benign	72/284	108985945	7044,5962	2203	4300	6503	SO:0001583	missense	338773	exon2			AGGGTTATGGGCT	AK075501	CCDS9119.1	12q23.3	2014-02-12				ENSG00000183160			27884	protein-coding gene	gene with protein product						12975309	Standard	NM_181724		Approved		uc001tng.3	Q4V9L6		ENST00000392806.3:c.215T>C	12.37:g.108985945A>G	ENSP00000376553:p.Ile72Thr	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	NM_181724	Q6UXE5|Q8N2F5	Missense_Mutation	SNP	ENST00000392806.3	37	CCDS9119.1	1326	0.6071428571428571	339	0.6890243902439024	174	0.48066298342541436	484	0.8461538461538461	329	0.4340369393139842	G	0.061	-1.223836	0.01530	0.721516	0.449419	ENSG00000183160	ENST00000392806;ENST00000433191;ENST00000549031	T;T	0.39406	1.1;1.08	4.59	4.59	0.56863	.	0.064020	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00104	-2.125	0.49915	P	1.6499999999997073E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.39375	-0.9617	9	0.02654	T	1	-2.8635	10.6585	0.45688	0.09:0.0:0.91:0.0	rs7975237;rs7975237	72	Q4V9L6	TM119_HUMAN	T	72;6;72	ENSP00000376553:I72T;ENSP00000448583:I72T	ENSP00000376553:I72T	I	-	2	0	TMEM119	107510074	0.997000	0.39634	0.758000	0.31321	0.008000	0.06430	1.977000	0.40589	1.089000	0.41292	-0.511000	0.04467	ATA	A|0.417;G|0.583	0.583	strong		0.692	TMEM119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403900.1	NM_181724	
CEP192	55125	hgsc.bcm.edu	37	18	13056682	13056682	+	Missense_Mutation	SNP	G	G	A	rs2282542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:13056682G>A	ENST00000325971.8	+	17	3898	c.2305G>A	c.(2305-2307)Gtg>Atg	p.V769M	CEP192_ENST00000506447.1_Missense_Mutation_p.V1365M|CEP192_ENST00000430049.2_Missense_Mutation_p.V890M			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	769			V -> M (in dbSNP:rs2282542). {ECO:0000269|PubMed:11230166}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GGATTCAGGAGTGACATCAGG	0.368													A|||	963	0.192292	0.1452	0.1225	5008	,	,		22185	0.3016		0.1262	False		,,,				2504	0.2607				p.V1365M		Atlas-SNP	.											.	CEP192	340	.	0			c.G4093A						PASS	.	A	MET/VAL	524,3880	736.1+/-410.7	28,468,1706	133.0	138.0	136.0		4093	-2.5	0.0	18	dbSNP_100	136	1096,7504	756.0+/-407.5	84,928,3288	yes	missense	CEP192	NM_032142.3	21	112,1396,4994	AA,AG,GG		12.7442,11.8983,12.4577	benign	1365/2538	13056682	1620,11384	2202	4300	6502	SO:0001583	missense	55125	exon19			TCAGGAGTGACAT	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.2305G>A	18.37:g.13056682G>A	ENSP00000317156:p.Val769Met	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	32	0.380952	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		373	0.1707875457875458	86	0.17479674796747968	46	0.1270718232044199	150	0.26223776223776224	91	0.12005277044854881	A	0.008	-1.890598	0.00527	0.118983	0.127442	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.05996	3.37;3.36;3.36	4.85	-2.49	0.06403	.	0.755012	0.12075	N	0.501841	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.12013	0.001;0.005;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.38499	-0.9658	9	0.02654	T	1	0.6872	2.1849	0.03884	0.4861:0.1183:0.2814:0.1143	rs2282542;rs52794837;rs59450390;rs2282542	890;1365;769	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	M	1365;769;769;890	ENSP00000427550:V1365M;ENSP00000317156:V769M;ENSP00000389190:V890M	ENSP00000317156:V769M	V	+	1	0	CEP192	13046682	0.000000	0.05858	0.010000	0.14722	0.640000	0.38277	-0.562000	0.05950	-0.770000	0.04614	-2.177000	0.00319	GTG	G|0.844;A|0.156	0.156	strong		0.368	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
ANKDD1A	348094	hgsc.bcm.edu	37	15	65235776	65235776	+	Missense_Mutation	SNP	A	A	G	rs34988193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:65235776A>G	ENST00000380230.3	+	11	1092	c.1063A>G	c.(1063-1065)Aag>Gag	p.K355E	ANKDD1A_ENST00000395720.1_Missense_Mutation_p.K355E|ANKDD1A_ENST00000395723.1_Missense_Mutation_p.K264E|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.K355E	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	355			K -> E (in dbSNP:rs34988193). {ECO:0000269|PubMed:15489334}.		signal transduction (GO:0007165)			p.K355E(1)		NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						CCTGAGAGATAAGGTACCTct	0.577													A|||	1233	0.246206	0.1263	0.232	5008	,	,		19679	0.127		0.336	False		,,,				2504	0.4489				p.K355E		Atlas-SNP	.											ANKDD1A,NS,carcinoma,0,1	ANKDD1A	47	1	1	Substitution - Missense(1)	prostate(1)	c.A1063G						PASS	.	A	GLU/LYS	757,3647	307.7+/-290.2	72,613,1517	155.0	145.0	148.0		1063	4.3	1.0	15	dbSNP_126	148	2971,5627	462.0+/-365.6	514,1943,1842	yes	missense	ANKDD1A	NM_182703.3	56	586,2556,3359	GG,GA,AA		34.5545,17.1889,28.6725	probably-damaging	355/523	65235776	3728,9274	2202	4299	6501	SO:0001583	missense	348094	exon11			AGAGATAAGGTAC		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"""Ankyrin repeat domain containing"""	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.1063A>G	15.37:g.65235776A>G	ENSP00000369579:p.Lys355Glu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	141	58	0.411348	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Missense_Mutation	SNP	ENST00000380230.3	37	CCDS10197.2	477	0.2184065934065934	73	0.1483739837398374	85	0.23480662983425415	75	0.13111888111888112	244	0.32189973614775724	A	20.9	4.071106	0.76301	0.171889	0.345545	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720;ENST00000395723	T;T;T;T	0.16196	2.38;2.38;2.38;2.36	5.42	4.27	0.50696	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000006	T	0.00012	0.0000	L	0.38649	1.16	0.09310	P	1.0	D	0.76494	0.999	D	0.68483	0.958	T	0.46105	-0.9215	9	0.36615	T	0.2	-48.4158	11.4729	0.50280	0.8492:0.1508:0.0:0.0	rs34988193;rs61079502;rs34988193	355	Q495B1	AKD1A_HUMAN	E	355;355;355;264	ENSP00000369579:K355E;ENSP00000350329:K355E;ENSP00000379070:K355E;ENSP00000379073:K264E	ENSP00000350329:K355E	K	+	1	0	ANKDD1A	63022829	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	8.227000	0.89787	1.046000	0.40249	0.533000	0.62120	AAG	A|0.742;G|0.258	0.258	strong		0.577	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	
FBXL18	80028	hgsc.bcm.edu	37	7	5541009	5541009	+	Silent	SNP	C	C	A	rs12667381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5541009C>A	ENST00000382368.3	-	3	1014	c.891G>T	c.(889-891)ctG>ctT	p.L297L	FBXL18_ENST00000453700.3_Silent_p.L297L	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	297									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		AGGACTTGGGCAGCTGCAGGG	0.607													C|||	841	0.167931	0.2428	0.1945	5008	,	,		19967	0.0308		0.1292	False		,,,				2504	0.229				p.L297L		Atlas-SNP	.											.	FBXL18	99	.	0			c.G891T						PASS	.	C		986,3308		109,768,1270	44.0	50.0	48.0		891	3.5	1.0	7	dbSNP_120	48	1035,7459		61,913,3273	no	coding-synonymous	FBXL18	NM_024963.4		170,1681,4543	AA,AC,CC		12.1851,22.9623,15.8039		297/719	5541009	2021,10767	2147	4247	6394	SO:0001819	synonymous_variant	80028	exon3			CTTGGGCAGCTGC	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"""F-boxes / Leucine-rich repeats"""	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.891G>T	7.37:g.5541009C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	48	0.585366	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Silent	SNP	ENST00000382368.3	37	CCDS43546.1	293	0.13415750915750915	112	0.22764227642276422	62	0.1712707182320442	17	0.02972027972027972	102	0.1345646437994723	C	6.268	0.417598	0.11870	0.229623	0.121851	ENSG00000155034	ENST00000458142	.	.	.	5.43	3.53	0.40419	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.04565	-1.0942	3	.	.	.	.	12.5126	0.56013	0.1286:0.7465:0.1249:0.0	rs12667381;rs12667381	.	.	.	F	181	.	.	C	-	2	0	FBXL18	5507535	0.986000	0.35501	1.000000	0.80357	0.950000	0.60333	0.258000	0.18387	2.553000	0.86117	0.650000	0.86243	TGC	C|0.861;A|0.139	0.139	strong		0.607	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963	
F13B	2165	hgsc.bcm.edu	37	1	197030201	197030201	+	Silent	SNP	T	T	C	rs5997	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197030201T>C	ENST00000367412.1	-	4	499	c.456A>G	c.(454-456)acA>acG	p.T152T		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	152	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						GAGCCAAACATGTTTCtaaaa	0.249													C|||	3925	0.783746	0.382	0.8804	5008	,	,		13344	1.0		0.9125	False		,,,				2504	0.9029				p.T152T		Atlas-SNP	.											.	F13B	137	.	0			c.A456G						PASS	.	C		2034,2372	592.9+/-387.9	477,1080,646	63.0	60.0	61.0		456	-3.1	1.0	1	dbSNP_52	61	7799,799	183.6+/-231.8	3536,727,36	no	coding-synonymous	F13B	NM_001994.2		4013,1807,682	CC,CT,TT		9.2929,46.1643,24.3848		152/662	197030201	9833,3171	2203	4299	6502	SO:0001819	synonymous_variant	2165	exon4			CAAACATGTTTCT	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.456A>G	1.37:g.197030201T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_001994	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	37	CCDS1388.1																																																																																			T|0.221;C|0.779	0.779	strong		0.249	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994	
APOPT1	84334	hgsc.bcm.edu	37	14	104029449	104029449	+	Silent	SNP	G	G	A	rs2274267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:104029449G>A	ENST00000409074.2	+	1	151	c.150G>A	c.(148-150)acG>acA	p.T50T	APOPT1_ENST00000247618.4_Silent_p.T37T|BAG5_ENST00000445922.2_5'Flank|RP11-73M18.2_ENST00000472726.2_Silent_p.T50T|BAG5_ENST00000299204.4_5'Flank|RP11-894P9.2_ENST00000556332.1_RNA|BAG5_ENST00000337322.4_5'Flank|APOPT1_ENST00000556253.2_Silent_p.T37T	NM_032374.3	NP_115750.2	Q96IL0	APOP1_HUMAN	apoptogenic 1, mitochondrial	50					intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)	mitochondrion (GO:0005739)											GCAGGGATACGGCGCCCAGCG	0.716													G|||	1108	0.221246	0.1074	0.3343	5008	,	,		12360	0.3512		0.2624	False		,,,				2504	0.1186				p.T50T		Atlas-SNP	.											.	.	.	.	0			c.G150A						PASS	.	G		557,3355		49,459,1448	4.0	6.0	5.0		150	-0.9	0.2	14	dbSNP_100	5	2012,5966		304,1404,2281	no	coding-synonymous	APOPT1	NM_032374.3		353,1863,3729	AA,AG,GG		25.2194,14.2382,21.6064		50/207	104029449	2569,9321	1956	3989	5945	SO:0001819	synonymous_variant	84334	exon1			GGATACGGCGCCC	BC007412	CCDS9983.2	14q32.33	2012-06-28	2012-06-28	2011-09-07	ENSG00000256053	ENSG00000256053			20492	protein-coding gene	gene with protein product	"""apoptogenic protein 1"""		"""chromosome 14 open reading frame 153"", ""apoptogenic 1"""	C14orf153		16782708, 18977203	Standard	NM_032374		Approved	MGC2562, APOP-1		Q96IL0	OTTHUMG00000153929	ENST00000409074.2:c.150G>A	14.37:g.104029449G>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	13	5	0.384615	NM_032374	Q53G28	Silent	SNP	ENST00000409074.2	37	CCDS9983.2	553	0.2532051282051282	49	0.09959349593495935	118	0.3259668508287293	189	0.3304195804195804	197	0.2598944591029024	G	6.245	0.413378	0.11812	0.142382	0.252194	ENSG00000256053	ENST00000440963	.	.	.	3.37	-0.865	0.10662	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53005	P	3.2999999999949736E-5	.	.	.	.	.	.	T	0.40213	-0.9575	4	0.09843	T	0.71	.	0.9102	0.01293	0.2249:0.1788:0.4131:0.1831	rs2274267;rs17095256;rs28362582	.	.	.	S	50	.	ENSP00000388067:G50S	G	+	1	0	C14orf153	103099202	0.296000	0.24398	0.214000	0.23707	0.083000	0.17756	-0.397000	0.07269	-0.499000	0.06623	-0.140000	0.14226	GGC	G|0.747;A|0.253	0.253	strong		0.716	APOPT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333060.2	NM_032374	
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775674	27775674	+	Missense_Mutation	SNP	A	A	G	rs200484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27775674A>G	ENST00000377401.2	-	1	35	c.11T>C	c.(10-12)cTg>cCg	p.L4P	HIST1H3H_ENST00000369163.2_5'Flank|HIST1H2AI_ENST00000358739.3_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	4			L -> P (in dbSNP:rs200484).		chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						AGACTTGGCCAGCTCGGGCAT	0.532													G|||	604	0.120607	0.2103	0.1412	5008	,	,		15542	0.0655		0.0865	False		,,,				2504	0.0767				p.L4P		Atlas-SNP	.											.	HIST1H2BL	48	.	0			c.T11C						PASS	.	G	PRO/LEU	831,3575		84,663,1456	62.0	67.0	66.0		11	4.3	0.5	6	dbSNP_79	66	955,7645		52,851,3397	yes	missense	HIST1H2BL	NM_003519.3	98	136,1514,4853	GG,GA,AA		11.1047,18.8606,13.7321	benign	4/127	27775674	1786,11220	2203	4300	6503	SO:0001583	missense	8340	exon1			TTGGCCAGCTCGG	Z83740	CCDS4625.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000185130	ENSG00000185130		"""Histones / Replication-dependent"""	4748	protein-coding gene	gene with protein product		602800	"""H2B histone family, member C"", ""histone 1, H2bl"""	H2BFC		9439656, 12408966	Standard	NM_003519		Approved	H2B/c, dJ97D16.4	uc003njl.3	Q99880	OTTHUMG00000014485	ENST00000377401.2:c.11T>C	6.37:g.27775674A>G	ENSP00000366618:p.Leu4Pro	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	269	127	0.472119	NM_003519	B2R5A3|Q52LW9	Missense_Mutation	SNP	ENST00000377401.2	37	CCDS4625.1	267	0.12225274725274725	99	0.20121951219512196	49	0.13535911602209943	50	0.08741258741258741	69	0.09102902374670185	.	0.044	-1.273737	0.01421	0.188606	0.111047	ENSG00000185130	ENST00000377401	T	0.17054	2.3	4.35	4.35	0.52113	.	.	.	.	.	T	0.01124	0.0037	N	0.00422	-1.515	0.26306	P	0.9778921	B	0.02656	0.0	B	0.01281	0.0	T	0.43909	-0.9362	8	0.02654	T	1	.	12.3065	0.54906	0.0843:0.0:0.9157:0.0	rs200484;rs684759;rs13205042;rs16868046;rs52805182;rs56710826;rs200484	4	Q99880	H2B1L_HUMAN	P	4	ENSP00000366618:L4P	ENSP00000366618:L4P	L	-	2	0	HIST1H2BL	27883653	0.997000	0.39634	0.497000	0.27552	0.012000	0.07955	2.724000	0.47285	1.126000	0.42016	-0.128000	0.14901	CTG	A|0.876;G|0.124	0.124	strong		0.532	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519	
MUC4	4585	hgsc.bcm.edu	37	3	195513173	195513173	+	Missense_Mutation	SNP	G	G	A	rs77448757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513173G>A	ENST00000463781.3	-	2	5737	c.5278C>T	c.(5278-5280)Cct>Tct	p.P1760S	MUC4_ENST00000475231.1_Missense_Mutation_p.P1760S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCCTGA	0.587																																					p.P1760S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C5278T						scavenged	.						53.0	49.0	50.0					3																	195513173		692	1591	2283	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5278C>T	3.37:g.195513173G>A	ENSP00000417498:p.Pro1760Ser	Somatic	484	2	0.00413223		WXS	Illumina HiSeq	Phase_I	620	96	0.154839	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	3.212	-0.161316	0.06502	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29142	1.58;1.58	.	.	.	.	.	.	.	.	T	0.08935	0.0221	N	0.02539	-0.55	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.27872	-1.0061	7	.	.	.	.	4.5334	0.12017	0.332:0.0:0.668:0.0	.	1760	E7ESK3	.	S	1760	ENSP00000417498:P1760S;ENSP00000420243:P1760S	.	P	-	1	0	MUC4	196997568	0.080000	0.21391	0.007000	0.13788	0.007000	0.05969	2.260000	0.43267	-1.764000	0.01305	-1.783000	0.00646	CCT	G|0.967;A|0.033	0.033	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LDLRAD1	388633	hgsc.bcm.edu	37	1	54480033	54480033	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:54480033G>A	ENST00000371360.1	-	3	95	c.78C>T	c.(76-78)ggC>ggT	p.G26G	LDLRAD1_ENST00000371362.3_Intron|LDLRAD1_ENST00000545928.1_Intron|LDLRAD1_ENST00000420619.1_Intron	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	26						integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						GGTGGCCGCCGCCTGCTGTGT	0.692																																					p.G26G		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.C78T						PASS	.						12.0	13.0	12.0					1																	54480033		1980	3842	5822	SO:0001819	synonymous_variant	388633	exon3			GCCGCCGCCTGCT		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 1"""				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.78C>T	1.37:g.54480033G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Silent	SNP	ENST00000371360.1	37	CCDS30725.1																																																																																			.	.	none		0.692	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978	
BNIP3	664	hgsc.bcm.edu	37	10	133786586	133786586	+	Silent	SNP	T	T	C	rs1050704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:133786586T>C	ENST00000368636.4	-	3	358	c.234A>G	c.(232-234)agA>agG	p.R78R	BNIP3_ENST00000540159.1_Silent_p.R78R	NM_004052.2	NP_004043.2	Q12983	BNIP3_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 3	78					apoptotic process (GO:0006915)|autophagic cell death (GO:0048102)|brown fat cell differentiation (GO:0050873)|cell death (GO:0008219)|cellular response to cobalt ion (GO:0071279)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|intrinsic apoptotic signaling pathway in response to hypoxia (GO:1990144)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrial protein catabolic process (GO:0035694)|negative regulation of apoptotic process (GO:0043066)|negative regulation of membrane potential (GO:0045837)|negative regulation of mitochondrial fusion (GO:0010637)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane permeability (GO:0046902)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTPase binding (GO:0051020)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|skin(1)	7		all_cancers(35;4e-11)|all_epithelial(44;5.07e-08)|Ovarian(717;2.61e-05)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Breast(234;0.023)|all_neural(114;0.0299)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)		Epithelial(32;1.59e-12)|all cancers(32;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(35;2.57e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TTTCAGAAGCTCTGTTGGTAT	0.423													T|||	362	0.0722843	0.0726	0.1081	5008	,	,		20538	0.0198		0.1233	False		,,,				2504	0.0481				p.R78R		Atlas-SNP	.											.	BNIP3	13	.	0			c.A234G						PASS	.	T		379,4027	190.5+/-216.4	19,341,1843	233.0	217.0	223.0		234	3.0	0.1	10	dbSNP_86	223	1186,7414	240.4+/-271.1	85,1016,3199	no	coding-synonymous	BNIP3	NM_004052.2		104,1357,5042	CC,CT,TT		13.7907,8.6019,12.0329		78/195	133786586	1565,11441	2203	4300	6503	SO:0001819	synonymous_variant	664	exon3			AGAAGCTCTGTTG	U15174	CCDS7663.1	10q26.3	2003-11-05	2002-08-29		ENSG00000176171	ENSG00000176171			1084	protein-coding gene	gene with protein product		603293	"""BCL2/adenovirus E1B 19kD-interacting protein 3"""			7954800	Standard	NM_004052		Approved	Nip3	uc001lkv.1	Q12983	OTTHUMG00000019278	ENST00000368636.4:c.234A>G	10.37:g.133786586T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_004052	O14620|Q96GP0	Silent	SNP	ENST00000368636.4	37	CCDS7663.1																																																																																			.	.	weak		0.423	BNIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051039.1		
CYP11B1	1584	hgsc.bcm.edu	37	8	143957738	143957738	+	Silent	SNP	C	C	T	rs34570566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143957738C>T	ENST00000292427.4	-	5	905	c.873G>A	c.(871-873)gcG>gcA	p.A291A	CYP11B1_ENST00000517471.1_Silent_p.A291A|CYP11B1_ENST00000377675.3_Silent_p.A362A	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	291					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	ACAGGAGCTCCGCCACGATGC	0.597									Familial Hyperaldosteronism type I				.|||	569	0.113618	0.2564	0.0375	5008	,	,		19264	0.0883		0.0408	False		,,,				2504	0.0757				p.A291A		Atlas-SNP	.											CYP11B1,NS,carcinoma,-1,1	CYP11B1	128	1	0			c.G873A						PASS	.	C	,	920,3486		104,712,1387	127.0	104.0	112.0		873,873	-8.2	0.0	8	dbSNP_126	112	211,8389		2,207,4091	no	coding-synonymous,coding-synonymous	CYP11B1	NM_000497.3,NM_001026213.1	,	106,919,5478	TT,TC,CC		2.4535,20.8806,8.696	,	291/504,291/438	143957738	1131,11875	2203	4300	6503	SO:0001819	synonymous_variant	1584	exon5	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GAGCTCCGCCACG	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.873G>A	8.37:g.143957738C>T		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	248	112	0.451613	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			C|0.910;T|0.090	0.090	strong		0.597	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
GPR144	347088	hgsc.bcm.edu	37	9	127215772	127215772	+	Missense_Mutation	SNP	C	C	G	rs72616654	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:127215772C>G	ENST00000334810.1	+	4	796	c.796C>G	c.(796-798)Cac>Gac	p.H266D				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	266	Pentaxin.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						CTCGGTGCGTCACGCCCTCAG	0.761													G|||	2623	0.523762	0.4834	0.6009	5008	,	,		6568	0.4494		0.5726	False		,,,				2504	0.5501				p.H266D		Atlas-SNP	.											.	GPR144	33	.	0			c.C796G						PASS	.						4.0	5.0	4.0					9																	127215772		654	1515	2169	SO:0001583	missense	347088	exon4			GTGCGTCACGCCC	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.796C>G	9.37:g.127215772C>G	ENSP00000335156:p.His266Asp	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	1149	0.5260989010989011	257	0.5223577235772358	216	0.5966850828729282	250	0.4370629370629371	426	0.5620052770448549	G	1.281	-0.610443	0.03690	.	.	ENSG00000180264	ENST00000334810	T	0.05996	3.36	3.81	2.9	0.33743	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.00012	0.0000	N	0.00707	-1.245	0.53688	P	2.2999999999995246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.21861	-1.0233	8	0.08837	T	0.75	.	7.5506	0.27796	0.0951:0.1682:0.7367:0.0	.	266	Q7Z7M1	GP144_HUMAN	D	266	ENSP00000335156:H266D	ENSP00000335156:H266D	H	+	1	0	GPR144	126255593	0.998000	0.40836	0.052000	0.19188	0.277000	0.26821	3.079000	0.50104	0.133000	0.18654	-0.647000	0.03941	CAC	C|0.491;G|0.509	0.509	strong		0.761	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
SEMA3C	10512	hgsc.bcm.edu	37	7	80427495	80427495	+	Silent	SNP	C	C	A	rs1880959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:80427495C>A	ENST00000265361.3	-	11	1605	c.1044G>T	c.(1042-1044)gtG>gtT	p.V348V	SEMA3C_ENST00000536800.1_Silent_p.V200V|SEMA3C_ENST00000544525.1_Silent_p.V366V|SEMA3C_ENST00000419255.2_Silent_p.V348V	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	348	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GCCCATTAAACACAGTCTGTA	0.393													C|||	237	0.0473243	0.0666	0.0504	5008	,	,		13404	0.001		0.0915	False		,,,				2504	0.0215				p.V348V		Atlas-SNP	.											SEMA3C,NS,carcinoma,-2,1	SEMA3C	106	1	0			c.G1044T						scavenged	.	C		375,4031	186.4+/-213.3	19,337,1847	60.0	60.0	60.0		1044	2.8	1.0	7	dbSNP_92	60	810,7790	186.3+/-233.8	28,754,3518	no	coding-synonymous	SEMA3C	NM_006379.3		47,1091,5365	AA,AC,CC		9.4186,8.5111,9.1112		348/752	80427495	1185,11821	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon11			ATTAAACACAGTC	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1044G>T	7.37:g.80427495C>A		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	143	67	0.468531	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			C|0.925;A|0.075	0.075	strong		0.393	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052981	33052981	+	Missense_Mutation	SNP	C	C	A	rs14362	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33052981C>A	ENST00000418931.2	+	3	735	c.619C>A	c.(619-621)Ctg>Atg	p.L207M		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	207	Beta-2.|Ig-like C1-type.		L -> M (in allele DPB1*04:02; dbSNP:rs14362).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GCACACCAGCCTGGATAGTCC	0.577													.|||	399	0.0796725	0.0076	0.2464	5008	,	,		19666	0.0367		0.1163	False		,,,				2504	0.0654				p.L207M		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.C619A						PASS	.	C	MET/LEU	87,2933		2,83,1425	78.0	82.0	80.0		619	4.0	1.0	6	dbSNP_52	80	597,4819		39,519,2150	yes	missense	HLA-DPB1	NM_002121.5	15	41,602,3575	AA,AC,CC		11.0229,2.8808,8.1081	probably-damaging	207/259	33052981	684,7752	1510	2708	4218	SO:0001583	missense	3115	exon3			ACCAGCCTGGATA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.619C>A	6.37:g.33052981C>A	ENSP00000408146:p.Leu207Met	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	313	167	0.533546	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	232	0.10622710622710622	6	0.012195121951219513	101	0.27900552486187846	30	0.05244755244755245	95	0.12532981530343007	C	15.53	2.861071	0.51482	0.028808	0.110229	ENSG00000223865	ENST00000418931;ENST00000411942;ENST00000422592;ENST00000428835	T;T	0.04758	3.56;3.56	4.04	4.04	0.47022	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.089667	0.47093	D	0.000258	T	0.12689	0.0308	M	0.91459	3.21	0.09310	P	1.0	P;B;B	0.40398	0.716;0.208;0.208	P;P;B	0.51101	0.659;0.489;0.443	T	0.00525	-1.1689	9	0.49607	T	0.09	.	14.0872	0.64964	0.0:1.0:0.0:0.0	rs14362;rs1042355;rs3176965;rs10947383;rs17358460;rs17398327;rs58897057	173;217;207	A2ALJ6;Q59GY1;P04440	.;.;DPB1_HUMAN	M	207;177;18;184	ENSP00000408146:L207M;ENSP00000412654:L184M	ENSP00000389210:L177M	L	+	1	2	HLA-DPB1	33160959	1.000000	0.71417	0.983000	0.44433	0.982000	0.71751	2.741000	0.47426	2.257000	0.74773	0.544000	0.68410	CTG	C|0.874;A|0.126	0.126	strong		0.577	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
LAMA4	3910	hgsc.bcm.edu	37	6	112435912	112435912	+	Silent	SNP	A	A	T	rs1050353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:112435912A>T	ENST00000230538.7	-	37	5557	c.5160T>A	c.(5158-5160)gtT>gtA	p.V1720V	LAMA4_ENST00000389463.4_Silent_p.V1713V|LAMA4_ENST00000424408.2_Silent_p.V1713V|LAMA4_ENST00000522006.1_Silent_p.V1713V	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1720	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GCTTGGGTGTAACTGAGGTGG	0.423													T|||	1411	0.281749	0.3419	0.2392	5008	,	,		17779	0.3571		0.2634	False		,,,				2504	0.1718				p.V1720V		Atlas-SNP	.											.	LAMA4	227	.	0			c.T5160A						PASS	.	T	,,	1477,2929	678.8+/-403.6	258,961,984	146.0	129.0	135.0		5160,5139,5139	-12.1	0.1	6	dbSNP_86	135	2489,6111	695.2+/-404.8	341,1807,2152	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	599,2768,3136	TT,TA,AA		28.9419,33.5225,30.4936	,,	1720/1824,1713/1817,1713/1817	112435912	3966,9040	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon37			GGGTGTAACTGAG		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.5160T>A	6.37:g.112435912A>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																			A|0.701;T|0.299	0.299	strong		0.423	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
MLXIPL	51085	hgsc.bcm.edu	37	7	73010754	73010754	+	Silent	SNP	C	C	T	rs61738649	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73010754C>T	ENST00000313375.3	-	12	1925	c.1878G>A	c.(1876-1878)ctG>ctA	p.L626L	MLXIPL_ENST00000429400.2_Silent_p.L626L|MLXIPL_ENST00000414749.2_Silent_p.L626L|MLXIPL_ENST00000395189.1_Silent_p.L533L|MLXIPL_ENST00000434326.1_Silent_p.L532L|MLXIPL_ENST00000354613.1_Silent_p.L626L	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	626					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				CACGGACGCTCAGAGTCCCAG	0.652													C|||	103	0.0205671	0.0015	0.0274	5008	,	,		11389	0.0		0.0716	False		,,,				2504	0.0102				p.L626L		Atlas-SNP	.											.	MLXIPL	54	.	0			c.G1878A						PASS	.	C	,,,	70,4336		1,68,2134	32.0	37.0	36.0		1878,1878,1878,1878	1.9	0.0	7	dbSNP_129	36	571,8029		19,533,3748	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MLXIPL	NM_032951.2,NM_032952.2,NM_032953.2,NM_032954.2	,,,	20,601,5882	TT,TC,CC		6.6395,1.5887,4.9285	,,,	626/853,626/834,626/851,626/832	73010754	641,12365	2203	4300	6503	SO:0001819	synonymous_variant	51085	exon12			GACGCTCAGAGTC	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"""carbohydrate response element binding protein"""	605678	"""Williams Beuren syndrome chromosome region 14"""	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.1878G>A	7.37:g.73010754C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Silent	SNP	ENST00000313375.3	37	CCDS5553.1																																																																																			C|0.957;T|0.043	0.043	strong		0.652	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951	
DSPP	1834	hgsc.bcm.edu	37	4	88536919	88536919	+	Silent	SNP	T	T	C	rs369387818		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536919T>C	ENST00000282478.7	+	4	3138	c.3105T>C	c.(3103-3105)gaT>gaC	p.D1035D	DSPP_ENST00000399271.1_Silent_p.D1035D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1035D(2)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgatagcagtgaca	0.517																																					p.D1035D		Atlas-SNP	.											DSPP,NS,carcinoma,0,3	DSPP	174	3	2	Substitution - coding silent(2)	kidney(2)	c.T3105C						scavenged	.						63.0	70.0	67.0					4																	88536919		1560	2747	4307	SO:0001819	synonymous_variant	1834	exon5			CAGCGATAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3105T>C	4.37:g.88536919T>C		Somatic	312	3	0.00961538		WXS	Illumina HiSeq	Phase_I	285	61	0.214035	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.517	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
NLRP1	22861	hgsc.bcm.edu	37	17	5436263	5436263	+	Missense_Mutation	SNP	C	C	T	rs2301582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5436263C>T	ENST00000572272.1	-	11	3174	c.3175G>A	c.(3175-3177)Gtg>Atg	p.V1059M	NLRP1_ENST00000577119.1_Missense_Mutation_p.V1029M|NLRP1_ENST00000354411.3_Missense_Mutation_p.V1029M|NLRP1_ENST00000345221.3_Missense_Mutation_p.V1059M|NLRP1_ENST00000269280.4_Missense_Mutation_p.V1059M|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000262467.5_Missense_Mutation_p.V1063M			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1059			V -> M (in dbSNP:rs2301582).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				GGAGAAGGCACGCACAAGAGT	0.607													C|||	923	0.184305	0.0787	0.3573	5008	,	,		17458	0.0228		0.3738	False		,,,				2504	0.1759				p.V1063M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G3187A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	567,3839	254.6+/-260.1	35,497,1671	89.0	78.0	82.0		3187,3175,3175,3085,3085	0.8	0.0	17	dbSNP_100	82	3421,5179	504.5+/-376.2	664,2093,1543	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	699,2590,3214	TT,TC,CC		39.7791,12.8688,30.6628	benign,benign,benign,benign,benign	1063/1376,1059/1430,1059/1474,1029/1444,1029/1400	5436263	3988,9018	2203	4300	6503	SO:0001583	missense	22861	exon11			AAGGCACGCACAA	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.3175G>A	17.37:g.5436263C>T	ENSP00000460475:p.Val1059Met	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_001033053	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	464	0.21245421245421245	46	0.09349593495934959	123	0.3397790055248619	16	0.027972027972027972	279	0.36807387862796836	C	8.966	0.971710	0.18736	0.128688	0.397791	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.71817	-0.6;-0.6;-0.58;-0.48;-0.58	3.94	0.836	0.18891	.	1.178250	0.06625	N	0.758189	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;P;P;P;P;B	0.42039	0.434;0.769;0.769;0.658;0.769;0.095	B;B;B;B;B;B	0.24701	0.055;0.037;0.037;0.017;0.037;0.01	T	0.17653	-1.0362	9	0.49607	T	0.09	.	6.2112	0.20630	0.1028:0.3672:0.53:0.0	rs2301582;rs17765850;rs52830015;rs56943859;rs2301582	325;1029;1029;1059;1059;1063	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	1063;1063;1059;1029;1059;325	ENSP00000442029:V1063M;ENSP00000262467:V1063M;ENSP00000269280:V1059M;ENSP00000346390:V1029M;ENSP00000324366:V1059M	ENSP00000262467:V1063M	V	-	1	0	NLRP1	5376987	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.977000	0.03782	0.255000	0.21593	-0.236000	0.12185	GTG	C|0.738;T|0.262	0.262	strong		0.607	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
LZTS3	9762	hgsc.bcm.edu	37	20	3147468	3147468	+	Silent	SNP	G	G	A	rs17853865	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:3147468G>A	ENST00000329152.3	-	1	1739	c.342C>T	c.(340-342)aaC>aaT	p.N114N	LZTS3_ENST00000337576.5_Silent_p.N114N|LZTS3_ENST00000360342.3_Silent_p.N114N			O60299	LZTS3_HUMAN		114						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											TGCCAACCACGTTGCCACAGA	0.647													G|||	700	0.139776	0.062	0.2003	5008	,	,		16794	0.0208		0.2256	False		,,,				2504	0.2362				p.N114N		Atlas-SNP	.											ProSAPiP1,NS,carcinoma,0,1	.	.	1	0			c.C342T						PASS	.	G		422,3984	209.2+/-230.0	21,380,1802	81.0	64.0	69.0		342	0.9	1.0	20	dbSNP_123	69	2030,6570	354.0+/-329.3	236,1558,2506	no	coding-synonymous	ProSAPiP1	NM_014731.2		257,1938,4308	AA,AG,GG		23.6047,9.5778,18.8528		114/674	3147468	2452,10554	2203	4300	6503	SO:0001819	synonymous_variant	0	exon1			AACCACGTTGCCA																												ENST00000329152.3:c.342C>T	20.37:g.3147468G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	Silent	SNP	ENST00000329152.3	37	CCDS13049.1																																																																																			G|0.830;A|0.170	0.170	strong		0.647	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2		
ANKRD36	375248	hgsc.bcm.edu	37	2	97883087	97883087	+	Silent	SNP	A	A	G	rs3927329		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97883087A>G	ENST00000461153.2	+	64	4075	c.3831A>G	c.(3829-3831)acA>acG	p.T1277T	ANKRD36_ENST00000420699.2_Silent_p.T1277T			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1277								p.T1277T(1)|p.T1081T(1)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						CAAGAATAACAGGCGGTTGGA	0.328																																					p.T1277T		Atlas-SNP	.											ANKRD36_ENST00000420699,NS,carcinoma,0,2	ANKRD36	170	2	2	Substitution - coding silent(2)	prostate(2)	c.A3831G						scavenged	.						156.0	119.0	130.0					2																	97883087		692	1591	2283	SO:0001819	synonymous_variant	375248	exon64			AATAACAGGCGGT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.3831A>G	2.37:g.97883087A>G		Somatic	786	2	0.00254453		WXS	Illumina HiSeq	Phase_I	887	280	0.315671	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Silent	SNP	ENST00000461153.2	37	CCDS54379.1																																																																																			A|0.850;G|0.149	0.149	strong		0.328	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
C21orf62	56245	hgsc.bcm.edu	37	21	34166343	34166343	+	Silent	SNP	C	C	T	rs2231390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:34166343C>T	ENST00000536776.1	-	2	530	c.390G>A	c.(388-390)gaG>gaA	p.E130E	C21orf62_ENST00000490358.1_Silent_p.E130E|C21orf49_ENST00000453404.1_Intron|C21orf49_ENST00000382377.3_Intron|C21orf62_ENST00000479548.1_Silent_p.E130E|C21orf49_ENST00000477513.1_Intron|C21orf62_ENST00000487113.1_Silent_p.E130E|C21orf49_ENST00000382375.4_Intron|C21orf49_ENST00000382378.1_Intron	NM_001162495.2|NM_001162496.2|NM_019596.5	NP_001155967.2|NP_001155968.2|NP_062542.5	Q9NYP8	CU062_HUMAN	chromosome 21 open reading frame 62	130										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	6		Myeloproliferative disorder(46;0.0255)				GATGCTTGGCCTCCATGTTGA	0.552													C|||	3643	0.727436	0.5287	0.8127	5008	,	,		21309	0.9157		0.7565	False		,,,				2504	0.7117				p.E130E		Atlas-SNP	.											.	C21orf62	26	.	0			c.G390A						PASS	.	C	,,	2504,1692		737,1030,331	89.0	86.0	87.0		390,390,390	1.9	0.9	21	dbSNP_98	87	6515,1955		2504,1507,224	no	coding-synonymous,coding-synonymous,coding-synonymous	C21orf62	NM_001162495.2,NM_001162496.2,NM_019596.5	,,	3241,2537,555	TT,TC,CC		23.0815,40.3241,28.7936	,,	130/220,130/220,130/220	34166343	9019,3647	2098	4235	6333	SO:0001819	synonymous_variant	56245	exon4			CTTGGCCTCCATG	AF231922	CCDS42919.1, CCDS42919.2	21q22.1	2011-02-24			ENSG00000205929	ENSG00000205929			1305	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 120"""	C21orf120			Standard	NM_001162495		Approved	B37, PRED81	uc011adu.2	Q9NYP8	OTTHUMG00000163477	ENST00000536776.1:c.390G>A	21.37:g.34166343C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_001162495	A8K4L8	Silent	SNP	ENST00000536776.1	37	CCDS42919.2																																																																																			C|0.240;T|0.760	0.760	strong		0.552	C21orf62-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139598.5	NM_019596	
RP1L1	94137	hgsc.bcm.edu	37	8	10469292	10469292	+	Silent	SNP	C	C	T	rs62490857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:10469292C>T	ENST00000382483.3	-	4	2539	c.2316G>A	c.(2314-2316)tcG>tcA	p.S772S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	772					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGGGGGCCGGCGAGCATGTCC	0.662													C|||	152	0.0303514	0.0023	0.0288	5008	,	,		16095	0.001		0.1083	False		,,,				2504	0.0194				p.S772S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G2316A						PASS	.	C		64,3840		0,64,1888	50.0	57.0	55.0		2316	-10.2	0.0	8	dbSNP_129	55	681,7581		25,631,3475	no	coding-synonymous	RP1L1	NM_178857.5		25,695,5363	TT,TC,CC		8.2426,1.6393,6.1236		772/2401	10469292	745,11421	1952	4131	6083	SO:0001819	synonymous_variant	94137	exon4			GGCCGGCGAGCAT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2316G>A	8.37:g.10469292C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	123	65	0.528455	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.945;T|0.055	0.055	strong		0.662	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
LINC00283	100874057	hgsc.bcm.edu	37	13	103394716	103394716	+	RNA	SNP	T	T	C	rs9585987	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103394716T>C	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		GAGAAATAGATGTGTAGGGAT	0.393													T|||	3479	0.694688	0.5431	0.7493	5008	,	,		20859	0.5913		0.826	False		,,,				2504	0.8323				p.T2777T		Atlas-SNP	.											.	.	.	.	0			c.A8331G						PASS	.	T		775,609		217,341,134	51.0	37.0	41.0		8331	-1.7	0.0	13	dbSNP_119	41	2541,639		1022,497,71	no	coding-synonymous	CCDC168	NM_001146197.1		1239,838,205	CC,CT,TT		20.0943,44.0029,27.3444		2777/7082	103394716	3316,1248	692	1590	2282			643677	exon4			AATAGATGTGTAG			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103394716T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	51	31	0.607843	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				T|0.305;C|0.695	0.695	strong		0.393	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
MUC16	94025	hgsc.bcm.edu	37	19	9072975	9072975	+	Missense_Mutation	SNP	G	G	A	rs17000816	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9072975G>A	ENST00000397910.4	-	3	14674	c.14471C>T	c.(14470-14472)aCg>aTg	p.T4824M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4826	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGAAGGATGCGTTGTCTCTAT	0.448													G|||	936	0.186901	0.0923	0.2536	5008	,	,		23617	0.3254		0.1322	False		,,,				2504	0.181				p.T4824M		Atlas-SNP	.											MUC16_ENST00000397910,rectum,carcinoma,0,3	MUC16	4315	3	0			c.C14471T						PASS	.		MET/THR	399,3763		17,365,1699	165.0	153.0	157.0		14471	-1.5	0.0	19	dbSNP_123	157	1164,7258		73,1018,3120	yes	missense	MUC16	NM_024690.2	81	90,1383,4819	AA,AG,GG		13.8209,9.5867,12.4205	benign	4824/14508	9072975	1563,11021	2081	4211	6292	SO:0001583	missense	94025	exon3			GGATGCGTTGTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14471C>T	19.37:g.9072975G>A	ENSP00000381008:p.Thr4824Met	Somatic	432	0	0		WXS	Illumina HiSeq	Phase_I	470	264	0.561702	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	439	0.20100732600732601	56	0.11382113821138211	80	0.22099447513812154	205	0.3583916083916084	98	0.12928759894459102	g	1.725	-0.495688	0.04291	0.095867	0.138209	ENSG00000181143	ENST00000397910	T	0.20332	2.08	2.02	-1.54	0.08584	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.46005	-0.9222	8	0.87932	D	0	.	5.65	0.17610	0.644:0.0:0.356:0.0	rs17000816;rs56515928;rs17000816	4824	B5ME49	.	M	4824	ENSP00000381008:T4824M	ENSP00000381008:T4824M	T	-	2	0	MUC16	8933975	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.495000	0.02294	-0.474000	0.06862	-0.692000	0.03713	ACG	G|0.810;A|0.190	0.190	strong		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87445839	87445839	+	Missense_Mutation	SNP	C	C	T	rs3748400	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:87445839C>T	ENST00000268616.4	-	12	2294	c.2077G>A	c.(2077-2079)Gtg>Atg	p.V693M		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	693			V -> M (in dbSNP:rs3748400). {ECO:0000269|PubMed:15489334}.				nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGGGGGCCCACTGGCATACTG	0.557													C|||	2311	0.461462	0.1135	0.5259	5008	,	,		14972	0.3115		0.7594	False		,,,				2504	0.7342				p.V693M		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.G2077A						PASS	.	C	MET/VAL	1058,3336		120,818,1259	45.0	55.0	51.0		2077	4.5	1.0	16	dbSNP_107	51	6540,2056		2478,1584,236	yes	missense	ZCCHC14	NM_015144.2	21	2598,2402,1495	TT,TC,CC		23.9181,24.0783,41.5089	probably-damaging	693/950	87445839	7598,5392	2197	4298	6495	SO:0001583	missense	23174	exon12			GGCCCACTGGCAT	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2077G>A	16.37:g.87445839C>T	ENSP00000268616:p.Val693Met	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	37	CCDS10961.1	1003	0.4592490842490842	64	0.13008130081300814	203	0.5607734806629834	167	0.291958041958042	569	0.7506596306068601	C	16.64	3.179118	0.57800	0.240783	0.760819	ENSG00000140948	ENST00000268616	T	0.25912	1.77	5.59	4.51	0.55191	.	0.000000	0.64402	D	0.000012	T	0.00012	0.0000	N	0.20986	0.625	0.30560	P	0.7645919999999999	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.03545	-1.1026	9	0.40728	T	0.16	-26.7455	12.1285	0.53930	0.0:0.8991:0.0:0.1009	rs3748400;rs61240224;rs3748400	693;693	Q8WYQ9-2;Q8WYQ9	.;ZCH14_HUMAN	M	693	ENSP00000268616:V693M	ENSP00000268616:V693M	V	-	1	0	ZCCHC14	86003340	0.790000	0.28787	1.000000	0.80357	0.967000	0.64934	1.327000	0.33746	1.107000	0.41642	0.563000	0.77884	GTG	C|0.484;T|0.516	0.516	strong		0.557	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
CYP17A1	1586	hgsc.bcm.edu	37	10	104596924	104596924	+	Silent	SNP	C	C	A	rs6163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:104596924C>A	ENST00000369887.3	-	1	366	c.195G>T	c.(193-195)tcG>tcT	p.S65S	CYP17A1_ENST00000489268.1_5'UTR|CYP17A1-AS1_ENST00000369884.4_RNA	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	65					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	CCATACGAACCGAATAGATGG	0.542													g|||	2055	0.410343	0.3268	0.4179	5008	,	,		19704	0.5873		0.3926	False		,,,				2504	0.3538				p.S65S		Atlas-SNP	.											CYP17A1,NS,carcinoma,-1,1	CYP17A1	48	1	0			c.G195T						PASS	.			1593,2813		292,1009,902	126.0	116.0	120.0		195	-0.5	0.0	10	dbSNP_52	120	3392,5208		663,2066,1571	no	coding-synonymous	CYP17A1	NM_000102.3		955,3075,2473	AA,AC,CC		39.4419,36.1552,38.3285		65/509	104596924	4985,8021	2203	4300	6503	SO:0001819	synonymous_variant	1586	exon1			ACGAACCGAATAG	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"""Cytochrome P450s"""	2593	protein-coding gene	gene with protein product	"""Steroid 17-alpha-monooxygenase"""	609300	"""cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"""	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.195G>T	10.37:g.104596924C>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_000102	Q5TZV7	Silent	SNP	ENST00000369887.3	37	CCDS7541.1																																																																																			C|0.605;A|0.390	0.390	strong		0.542	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102	
OR2H1	26716	hgsc.bcm.edu	37	6	29430170	29430170	+	Silent	SNP	T	T	C	rs2073148	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29430170T>C	ENST00000377136.1	+	4	1089	c.624T>C	c.(622-624)ccT>ccC	p.P208P	OR2H1_ENST00000396792.2_Silent_p.P208P|OR2H1_ENST00000377132.1_Silent_p.P208P|OR2H1_ENST00000442615.1_Silent_p.P208P|OR2H1_ENST00000377133.1_Silent_p.P208P|OR2H1_ENST00000473369.1_3'UTR			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						TGGTTGTGCCTCTCAGCCTCA	0.527													C|||	841	0.167931	0.3343	0.0893	5008	,	,		22416	0.1845		0.0408	False		,,,				2504	0.1125				p.P208P		Atlas-SNP	.											.	OR2H1	38	.	0			c.T624C						PASS	.	C		809,2213		105,599,807	198.0	184.0	189.0		624	-6.2	0.0	6	dbSNP_96	189	200,5218		5,190,2514	no	coding-synonymous	OR2H1	NM_030883.3		110,789,3321	CC,CT,TT		3.6914,26.7704,11.955		208/317	29430170	1009,7431	1511	2709	4220	SO:0001819	synonymous_variant	26716	exon3			TGTGCCTCTCAGC	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.624T>C	6.37:g.29430170T>C		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	266	141	0.530075	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	37	CCDS4660.1																																																																																			T|0.864;C|0.136	0.136	strong		0.527	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
TDRKH	11022	hgsc.bcm.edu	37	1	151747970	151747970	+	Silent	SNP	A	A	G	rs11204885	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151747970A>G	ENST00000368822.1	-	10	1965	c.1332T>C	c.(1330-1332)caT>caC	p.H444H	TDRKH_ENST00000368823.1_Silent_p.H440H|TDRKH_ENST00000368825.3_Silent_p.H399H|TDRKH_ENST00000368824.3_Silent_p.H444H|TDRKH_ENST00000458431.2_Silent_p.H444H|TDRKH_ENST00000440583.2_Silent_p.H220H|TDRKH_ENST00000368827.6_Silent_p.H444H			Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing	444					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	mitochondrion (GO:0005739)|pi-body (GO:0071546)|piP-body (GO:0071547)	RNA binding (GO:0003723)			breast(5)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGTCAGCACAATGAGTGAGTC	0.473																																					p.H444H		Atlas-SNP	.											.	TDRKH	45	.	0			c.T1332C						PASS	.	A	,,,	409,3479		19,371,1554	128.0	120.0	122.0		1332,1197,1332,1332	3.7	1.0	1	dbSNP_120	122	1816,6470		194,1428,2521	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TDRKH	NM_001083963.1,NM_001083964.1,NM_001083965.1,NM_006862.3	,,,	213,1799,4075	GG,GA,AA		21.9165,10.5195,18.2767	,,,	444/562,399/517,444/562,444/562	151747970	2225,9949	1944	4143	6087	SO:0001819	synonymous_variant	11022	exon10			AGCACAATGAGTG	AF227192	CCDS41394.1, CCDS41395.1	1q21	2013-01-23	2003-11-07		ENSG00000182134	ENSG00000182134		"""Tudor domain containing"""	11713	protein-coding gene	gene with protein product		609501	"""tudor and KH domain containing"""			10767542	Standard	NM_001083964		Approved	TDRD2	uc001eza.4	Q9Y2W6	OTTHUMG00000013062	ENST00000368822.1:c.1332T>C	1.37:g.151747970A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	224	134	0.598214	NM_001083965	D3DV24|Q5SZR3|Q5SZR5|Q8N582|Q9NYV5	Silent	SNP	ENST00000368822.1	37	CCDS41394.1																																																																																			A|0.773;G|0.227	0.227	strong		0.473	TDRKH-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000036648.2	NM_006862	
CMTR2	55783	hgsc.bcm.edu	37	16	71318001	71318001	+	Missense_Mutation	SNP	G	G	T	rs3096381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:71318001G>T	ENST00000338099.5	-	3	2159	c.1823C>A	c.(1822-1824)aCa>aAa	p.T608K	CMTR2_ENST00000434935.2_Missense_Mutation_p.T608K			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	608			T -> K (in dbSNP:rs3096381).		7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										GCTAAAAGTTGTGAGTTCAGC	0.423													G|||	566	0.113019	0.0651	0.1354	5008	,	,		19124	0.0288		0.1879	False		,,,				2504	0.1718				p.T608K		Atlas-SNP	.											.	FTSJD1	70	.	0			c.C1823A						PASS	.	G	LYS/THR,LYS/THR	346,4050	176.2+/-205.4	17,312,1869	52.0	51.0	52.0		1823,1823	2.7	0.1	16	dbSNP_103	52	1472,7128	277.2+/-292.7	133,1206,2961	yes	missense,missense	FTSJD1	NM_001099642.1,NM_018348.5	78,78	150,1518,4830	TT,TG,GG		17.1163,7.8708,13.9889	benign,benign	608/771,608/771	71318001	1818,11178	2198	4300	6498	SO:0001583	missense	55783	exon3			AAAGTTGTGAGTT	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1823C>A	16.37:g.71318001G>T	ENSP00000337512:p.Thr608Lys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	239	0.10943223443223443	36	0.07317073170731707	61	0.1685082872928177	17	0.02972027972027972	125	0.16490765171503957	G	1.669	-0.509532	0.04231	0.078708	0.171163	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.13778	2.56;2.56	6.04	2.66	0.31614	.	0.614618	0.17231	N	0.181921	T	0.00039	0.0001	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B	0.23735	0.09	B	0.15870	0.014	T	0.33954	-0.9848	9	0.45353	T	0.12	-12.7017	8.4422	0.32822	0.7783:0.0:0.2217:0.0	rs3096381;rs52829342;rs59344681;rs3096381	608	Q8IYT2	FTSJ1_HUMAN	K	608	ENSP00000337512:T608K;ENSP00000411148:T608K	ENSP00000337512:T608K	T	-	2	0	FTSJD1	69875502	0.506000	0.26139	0.080000	0.20451	0.220000	0.24768	1.210000	0.32370	0.204000	0.20548	-0.367000	0.07326	ACA	G|0.883;T|0.117	0.117	strong		0.423	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45258324	45258324	+	Missense_Mutation	SNP	C	C	T	rs2071762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45258324C>T	ENST00000389774.2	+	13	1385	c.1244C>T	c.(1243-1245)cCg>cTg	p.P415L	ARHGAP8_ENST00000517296.3_Missense_Mutation_p.P594L|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.P515L|ARHGAP8_ENST00000336963.4_3'UTR|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.P594L|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.P506L|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.P384L	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	415			P -> L (in dbSNP:rs2071762).		positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		TTCAGCACCCCGGAGGCACCT	0.622													C|||	1127	0.22504	0.0976	0.2493	5008	,	,		18510	0.3145		0.1759	False		,,,				2504	0.3384				p.P506L		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C1517T						PASS	.	C	LEU/PRO,,LEU/PRO,LEU/PRO	487,3919	227.2+/-242.5	24,439,1740	47.0	47.0	47.0		1244,,1517,1151	-7.3	0.0	22	dbSNP_96	47	1357,7243	263.8+/-285.2	106,1145,3049	yes	missense,utr-3,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	98,,98,98	130,1584,4789	TT,TC,CC		15.7791,11.0531,14.1781	benign,,benign,benign	415/465,,506/556,384/434	45258324	1844,11162	2203	4300	6503	SO:0001583	missense	553158	exon15			GCACCCCGGAGGC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1244C>T	22.37:g.45258324C>T	ENSP00000374424:p.Pro415Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	110	68	0.618182	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	467|467	0.21382783882783882|0.21382783882783882	45|45	0.09146341463414634|0.09146341463414634	94|94	0.2596685082872928|0.2596685082872928	202|202	0.3531468531468531|0.3531468531468531	126|126	0.1662269129287599|0.1662269129287599	C|C	7.606|7.606	0.673888|0.673888	0.14841|0.14841	0.110531|0.110531	0.157791|0.157791	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484|ENSG00000248405	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000356099|ENST00000515632	T;T;T;T;T;T|.	0.20332|.	2.16;2.15;2.15;2.16;2.08;2.08|.	3.67|3.67	-7.34|-7.34	0.01427|0.01427	Rho GTPase-activating protein domain (1);|.	1.549010|.	0.04584|.	N|.	0.395556|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.40543|0.40543	1.245|1.245	0.58432|0.58432	P|P	2.9999999999752447E-6|2.9999999999752447E-6	B;B;B;B;B|.	0.32071|.	0.084;0.043;0.146;0.355;0.207|.	B;B;B;B;B|.	0.20767|.	0.018;0.004;0.018;0.013;0.031|.	T|T	0.11916|0.11916	-1.0568|-1.0568	9|4	0.29301|.	T|.	0.29|.	.|.	9.2017|9.2017	0.37263|0.37263	0.2309:0.4889:0.2803:0.0|0.2309:0.4889:0.2803:0.0	rs2071762;rs56757666;rs2071762|rs2071762;rs56757666;rs2071762	437;420;415;594;515|.	B7ZMA4;A2RU51;P85298;B1AHC4;B1AHC3|.	.;.;RHG08_HUMAN;.;.|.	L|W	515;594;594;506;415;384|455	ENSP00000354732:P515L;ENSP00000262731:P594L;ENSP00000429240:P594L;ENSP00000374423:P506L;ENSP00000374424:P415L;ENSP00000348407:P384L|.	ENSP00000348407:P384L|.	P|R	+|+	2|1	0|2	PRR5-ARHGAP8;ARHGAP8|PRR5-ARHGAP8	43636988|43636988	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.175000|-1.175000	0.03102|0.03102	-2.296000|-2.296000	0.00662|0.00662	-1.014000|-1.014000	0.02459|0.02459	CCG|CGG	C|0.825;T|0.175	0.175	strong		0.622	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
TRIM16L	147166	hgsc.bcm.edu	37	17	18630995	18630995	+	Missense_Mutation	SNP	G	G	A	rs8075739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18630995G>A	ENST00000449552.2	+	4	1609	c.125G>A	c.(124-126)aGg>aAg	p.R42K	TRIM16L_ENST00000395672.2_Missense_Mutation_p.R42K|TRIM16L_ENST00000572555.1_Missense_Mutation_p.R42K|TRIM16L_ENST00000395902.3_Missense_Mutation_p.R96K|TRIM16L_ENST00000414850.2_Missense_Mutation_p.R42K|TRIM16L_ENST00000571708.1_Missense_Mutation_p.R42K|TRIM16L_ENST00000395671.4_Missense_Mutation_p.R42K			Q309B1	TR16L_HUMAN	tripartite motif containing 16-like	42				R -> K (in Ref. 2; BAG60964 and 4; AAI27828/AAI28592). {ECO:0000305}.		cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	9						CTGGAGTACAGGAGTGCCGAG	0.582													.|||	1635	0.326478	0.4433	0.389	5008	,	,		21725	0.2024		0.3976	False		,,,				2504	0.1789				p.R42K		Atlas-SNP	.											.	TRIM16L	15	.	0			c.G125A						PASS	.	G	LYS/ARG	1893,2513	541.7+/-375.8	376,1141,686	149.0	117.0	128.0		125	2.3	1.0	17	dbSNP_116	128	3374,5226	499.7+/-375.0	636,2102,1562	no	missense	TRIM16L	NM_001037330.1	26	1012,3243,2248	AA,AG,GG		39.2326,42.9641,40.4967	benign	42/349	18630995	5267,7739	2203	4300	6503	SO:0001583	missense	147166	exon2			AGTACAGGAGTGC	DQ232882	CCDS32588.1	17p11.2	2011-02-10	2011-01-25		ENSG00000108448	ENSG00000108448			32670	protein-coding gene	gene with protein product			"""tripartite motif-containing 16-like"""				Standard	XM_005256479		Approved	TRIM70	uc002gui.1	Q309B1	OTTHUMG00000059050	ENST00000449552.2:c.125G>A	17.37:g.18630995G>A	ENSP00000461386:p.Arg42Lys	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	221	106	0.479638	NM_001037330	A0PK10|B2RUW6|B4DQK2|B4DWQ8	Missense_Mutation	SNP	ENST00000449552.2	37	CCDS32588.1	765	0.35027472527472525	215	0.4369918699186992	139	0.3839779005524862	108	0.1888111888111888	303	0.3997361477572559	g	5.659	0.306187	0.10733	0.429641	0.392326	ENSG00000108448	ENST00000395902;ENST00000395672;ENST00000414850;ENST00000424146;ENST00000395671	T;T;T	0.67345	-0.24;-0.26;-0.26	3.25	2.26	0.28386	.	0.145649	0.40222	U	0.001157	T	0.00012	0.0000	L	0.27053	0.805	0.38401	P	0.05434499999999998	B;B;B;B	0.29805	0.106;0.257;0.145;0.257	B;B;B;B	0.25987	0.047;0.047;0.065;0.047	T	0.41875	-0.9484	9	0.38643	T	0.18	-18.4638	4.6102	0.12399	0.2727:0.0:0.7273:0.0	rs8075739;rs61676537	42;96;258;42	B4DWQ8;B4DE22;B3KMJ2;Q309B1	.;.;.;TR16L_HUMAN	K	96;42;42;42;42	ENSP00000379239:R96K;ENSP00000379031:R42K;ENSP00000379030:R42K	ENSP00000379030:R42K	R	+	2	0	TRIM16L	18571720	1.000000	0.71417	0.986000	0.45419	0.168000	0.22595	2.912000	0.48782	1.813000	0.52934	0.194000	0.17425	AGG	G|0.608;A|0.392	0.392	strong		0.582	TRIM16L-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130670.3	NM_001037330	
ZBED9	114821	hgsc.bcm.edu	37	6	28543264	28543264	+	Silent	SNP	C	C	T	rs17336532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28543264C>T	ENST00000452236.2	-	3	1835	c.1218G>A	c.(1216-1218)ttG>ttA	p.L406L	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						TTAATGACCGCAAAAAAGTTA	0.373													C|||	892	0.178115	0.1899	0.1729	5008	,	,		19492	0.1419		0.173	False		,,,				2504	0.2086				p.L406L		Atlas-SNP	.											.	SCAND3	156	.	0			c.G1218A						PASS	.	C		786,3614	288.1+/-279.7	64,658,1478	47.0	50.0	49.0		1218	3.5	1.0	6	dbSNP_123	49	1767,6833	311.6+/-310.4	184,1399,2717	no	coding-synonymous	SCAND3	NM_052923.1		248,2057,4195	TT,TC,CC		20.5465,17.8636,19.6385		406/1326	28543264	2553,10447	2200	4300	6500	SO:0001819	synonymous_variant	114821	exon3			TGACCGCAAAAAA																												ENST00000452236.2:c.1218G>A	6.37:g.28543264C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	72	45	0.625	NM_052923		Silent	SNP	ENST00000452236.2	37	CCDS34355.1																																																																																			C|0.820;T|0.180	0.180	strong		0.373	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3		
MRPL37	51253	hgsc.bcm.edu	37	1	54683856	54683856	+	Silent	SNP	C	C	G	rs15921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:54683856C>G	ENST00000360840.5	+	7	1283	c.1206C>G	c.(1204-1206)ggC>ggG	p.G402G	MRPL37_ENST00000605337.1_Intron|MRPL37_ENST00000336230.6_Silent_p.G271G	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	402					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						AACCTGTTGGCCCAGTTGGTT	0.448													G|||	2031	0.405551	0.3502	0.3545	5008	,	,		20898	0.5942		0.2078	False		,,,				2504	0.5256				p.G402G		Atlas-SNP	.											MRPL37,NS,carcinoma,0,2	MRPL37	36	2	0			c.C1206G						PASS	.	G		1355,3051	691.3+/-405.4	217,921,1065	199.0	208.0	205.0		1206	0.8	1.0	1	dbSNP_52	205	1862,6738	729.9+/-406.7	190,1482,2628	no	coding-synonymous	MRPL37	NM_016491.3		407,2403,3693	GG,GC,CC		21.6512,30.7535,24.7347		402/424	54683856	3217,9789	2203	4300	6503	SO:0001819	synonymous_variant	51253	exon7			TGTTGGCCCAGTT	AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"""Mitochondrial ribosomal proteins / large subunits"""	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.1206C>G	1.37:g.54683856C>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_016491	Q96Q67|Q9BWR1|Q9P0P3	Silent	SNP	ENST00000360840.5	37	CCDS589.1																																																																																			C|0.704;G|0.296	0.296	strong		0.448	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491	
AIPL1	23746	hgsc.bcm.edu	37	17	6330068	6330068	+	Silent	SNP	T	T	C	rs2292546	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6330068T>C	ENST00000381129.3	-	5	731	c.651A>G	c.(649-651)ccA>ccG	p.P217P	AIPL1_ENST00000576776.1_Intron|AIPL1_ENST00000575265.1_Silent_p.P217P|AIPL1_ENST00000570466.1_Silent_p.P195P|AIPL1_ENST00000574506.1_Silent_p.P205P|AIPL1_ENST00000571740.1_Silent_p.P209P|AIPL1_ENST00000250087.5_Silent_p.P154P|AIPL1_ENST00000576307.1_Silent_p.P157P	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	217					negative regulation of apoptotic process (GO:0043066)|phototransduction, visible light (GO:0007603)|protein farnesylation (GO:0018343)|protein folding (GO:0006457)|regulation of cGMP metabolic process (GO:0030823)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)	farnesylated protein binding (GO:0001918)|unfolded protein binding (GO:0051082)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	12				COAD - Colon adenocarcinoma(228;0.141)		GCACCTCCCATGGCTTCTCCT	0.617													C|||	3574	0.713658	0.73	0.745	5008	,	,		15613	0.6716		0.7614	False		,,,				2504	0.6636				p.P217P		Atlas-SNP	.											AIPL1,NS,carcinoma,0,1	AIPL1	34	1	0			c.A651G						PASS	.	C	,,	3182,1224	422.1+/-339.6	1155,872,176	90.0	65.0	73.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	462,471,651	-5.1	0.9	17	dbSNP_100	73	6425,2175	371.5+/-336.3	2386,1653,261	no	coding-synonymous,coding-synonymous,coding-synonymous	AIPL1	NM_001033054.1,NM_001033055.1,NM_014336.3	,,	3541,2525,437	CC,CT,TT		25.2907,27.7803,26.1341	,,	154/322,157/325,217/385	6330068	9607,3399	2203	4300	6503	SO:0001819	synonymous_variant	23746	exon5			CTCCCATGGCTTC	AF148864	CCDS11075.1, CCDS32539.1, CCDS32540.1, CCDS67130.1, CCDS67131.1, CCDS67132.1, CCDS67133.1	17p13.1	2013-01-08	2001-11-29		ENSG00000129221	ENSG00000129221			359	protein-coding gene	gene with protein product		604392	"""aryl hydrocarbon receptor-interacting protein-like 1"""	LCA4		10615133, 14555765, 15365173	Standard	NM_001285402		Approved		uc002gcp.3	Q9NZN9	OTTHUMG00000102043	ENST00000381129.3:c.651A>G	17.37:g.6330068T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Silent	SNP	ENST00000381129.3	37	CCDS11075.1																																																																																			T|0.262;C|0.738	0.738	strong		0.617	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336	
EBF4	57593	hgsc.bcm.edu	37	20	2686317	2686317	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2686317C>T	ENST00000609451.1	+	2	304	c.232C>T	c.(232-234)Cgg>Tgg	p.R78W	EBF4_ENST00000380648.4_Missense_Mutation_p.R74W			Q9BQW3	COE4_HUMAN	early B-cell factor 4	78					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CATGTACGACCGGCAGGGGCA	0.617																																					p.R74W		Atlas-SNP	.											.	.	.	.	0			c.C220T						PASS	.						75.0	77.0	76.0					20																	2686317		692	1591	2283	SO:0001583	missense	57593	exon3			TACGACCGGCAGG	BC019106	CCDS46573.1	20p13	2008-10-23			ENSG00000088881	ENSG00000088881			29278	protein-coding gene	gene with protein product		609935				10718198	Standard	NM_001110514		Approved	KIAA1442, COE4, RP5-860F19.3, O/E-4	uc002wgt.4	Q9BQW3	OTTHUMG00000031709	ENST00000609451.1:c.232C>T	20.37:g.2686317C>T	ENSP00000477023:p.Arg78Trp	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_001110514	Q1MTP7|Q5JY53|Q9NUB6|Q9P2A6	Missense_Mutation	SNP	ENST00000609451.1	37		.	.	.	.	.	.	.	.	.	.	C	19.44	3.827666	0.71143	.	.	ENSG00000088881	ENST00000380648;ENST00000342725	T;T	0.54071	0.59;0.59	4.64	4.64	0.57946	.	0.149754	0.31051	N	0.008358	T	0.70718	0.3256	M	0.70595	2.14	0.44798	D	0.997804	D	0.89917	1.0	D	0.73380	0.98	T	0.75077	-0.3445	10	0.87932	D	0	-8.4514	15.4209	0.75009	0.0:1.0:0.0:0.0	.	74	E9PEI2	.	W	74;78	ENSP00000370022:R74W;ENSP00000345030:R78W	ENSP00000345030:R78W	R	+	1	2	EBF4	2634317	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.065000	0.30592	2.301000	0.77427	0.485000	0.47835	CGG	.	.	none		0.617	EBF4-011	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471930.1	XM_938882	
OR2W3	343171	hgsc.bcm.edu	37	1	248059423	248059423	+	Missense_Mutation	SNP	C	C	T	rs10888267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248059423C>T	ENST00000360358.3	+	1	535	c.535C>T	c.(535-537)Cgt>Tgt	p.R179C	OR2W3_ENST00000537741.1_Missense_Mutation_p.R179C	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	179			R -> C (in dbSNP:rs10888267).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CCACTTCCTGCGTGAGATGCC	0.647													T|||	1948	0.388978	0.1422	0.3487	5008	,	,		19432	0.5714		0.5308	False		,,,				2504	0.4172				p.R179C		Atlas-SNP	.											.	OR2W3	113	.	0			c.C535T						PASS	.	T	CYS/ARG	1016,3390	729.4+/-410.0	133,750,1320	120.0	97.0	104.0		535	4.2	1.0	1	dbSNP_120	104	4576,4024	554.9+/-386.6	1218,2140,942	yes	missense	OR2W3	NM_001001957.2	180	1351,2890,2262	TT,TC,CC		46.7907,23.0595,42.9955	benign	179/315	248059423	5592,7414	2203	4300	6503	SO:0001583	missense	343171	exon1			TTCCTGCGTGAGA	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.535C>T	1.37:g.248059423C>T	ENSP00000353516:p.Arg179Cys	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	243	135	0.555556	NM_001001957	Q6IF06|Q8NG86	Missense_Mutation	SNP	ENST00000360358.3	37	CCDS31099.1	921	0.4217032967032967	86	0.17479674796747968	132	0.36464088397790057	297	0.5192307692307693	406	0.5356200527704486	T	4.582	0.108070	0.08780	0.230595	0.532093	ENSG00000238243	ENST00000537741;ENST00000360358	T;T	0.15256	2.44;2.44	5.28	4.15	0.48705	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00000	-3.96	0.43351	P	0.004589999999999983	B	0.06786	0.001	B	0.01281	0.0	T	0.47169	-0.9138	9	0.02654	T	1	.	8.1064	0.30887	0.0:0.0706:0.1354:0.7941	rs10888267;rs52823339;rs60024367;rs10888267	179	Q7Z3T1	OR2W3_HUMAN	C	179	ENSP00000445853:R179C;ENSP00000353516:R179C	ENSP00000353516:R179C	R	+	1	0	OR2W3	246126046	1.000000	0.71417	0.999000	0.59377	0.964000	0.63967	3.535000	0.53575	0.459000	0.27016	-0.326000	0.08463	CGT	C|0.582;T|0.418	0.418	strong		0.647	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
ST6GAL1	6480	hgsc.bcm.edu	37	3	186760533	186760533	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760533C>T	ENST00000169298.3	+	4	716	c.42C>T	c.(40-42)gtC>gtT	p.V14V	ST6GAL1_ENST00000448044.1_Silent_p.V14V|ST6GAL1_ENST00000457772.2_Intron	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	14					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		GCTGCTGCGTCCTGGTCTTTC	0.403																																					p.V14V		Atlas-SNP	.											.	ST6GAL1	36	.	0			c.C42T						PASS	.						165.0	161.0	162.0					3																	186760533		2203	4300	6503	SO:0001819	synonymous_variant	6480	exon3			CTGCGTCCTGGTC	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.42C>T	3.37:g.186760533C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	207	22	0.10628	NM_003032	A8KA14|B2R513|D3DNV3	Silent	SNP	ENST00000169298.3	37	CCDS3285.1																																																																																			.	.	none		0.403	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	
EDEM3	80267	hgsc.bcm.edu	37	1	184663537	184663537	+	Missense_Mutation	SNP	A	A	C	rs9425343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:184663537A>C	ENST00000318130.8	-	20	2725	c.2459T>G	c.(2458-2460)aTt>aGt	p.I820S	EDEM3_ENST00000367512.3_Missense_Mutation_p.I793S|EDEM3_ENST00000466392.1_5'Flank	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	820			I -> S (in dbSNP:rs9425343). {ECO:0000269|PubMed:17974005}.		cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ACTTGATGAAATCTGTTCACC	0.378													A|||	1770	0.353435	0.0356	0.3401	5008	,	,		19304	0.5784		0.3698	False		,,,				2504	0.544				p.I820S		Atlas-SNP	.											.	EDEM3	63	.	0			c.T2459G						PASS	.	A	SER/ILE	423,3983	201.8+/-224.7	32,359,1812	44.0	41.0	42.0		2459	1.1	0.0	1	dbSNP_119	42	3301,5297	480.9+/-370.5	665,1971,1663	yes	missense	EDEM3	NM_025191.3	142	697,2330,3475	CC,CA,AA		38.3926,9.6005,28.6373	benign	820/933	184663537	3724,9280	2203	4299	6502	SO:0001583	missense	80267	exon20			GATGAAATCTGTT	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"""chromosome 1 open reading frame 22"""	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.2459T>G	1.37:g.184663537A>C	ENSP00000318147:p.Ile820Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Missense_Mutation	SNP	ENST00000318130.8	37	CCDS1363.2	744	0.34065934065934067	28	0.056910569105691054	133	0.3674033149171271	299	0.5227272727272727	284	0.37467018469656993	A	0.946	-0.707891	0.03230	0.096005	0.383926	ENSG00000116406	ENST00000318130;ENST00000367512	T;T	0.73152	-0.65;-0.72	5.21	1.12	0.20585	.	1.040500	0.07490	N	0.905495	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.41342	-0.9514	9	0.09338	T	0.73	.	6.32	0.21213	0.6486:0.1384:0.213:0.0	rs9425343;rs52836910;rs58003524;rs9425343	820	Q9BZQ6	EDEM3_HUMAN	S	820;793	ENSP00000318147:I820S;ENSP00000356482:I793S	ENSP00000318147:I820S	I	-	2	0	EDEM3	182930160	0.003000	0.15002	0.008000	0.14137	0.342000	0.28953	0.294000	0.19047	0.295000	0.22570	0.533000	0.62120	ATT	A|0.687;C|0.313	0.313	strong		0.378	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191	
LSP1	4046	hgsc.bcm.edu	37	11	1902771	1902771	+	Silent	SNP	T	T	C	rs147746785	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1902771T>C	ENST00000311604.3	+	3	476	c.301T>C	c.(301-303)Ttg>Ctg	p.L101L	LSP1_ENST00000381775.1_Silent_p.L229L|LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000405957.2_Silent_p.L39L|LSP1_ENST00000406638.2_Silent_p.L39L	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	101				Missing (in Ref. 3; AAB29545). {ECO:0000305}.	cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GCAGGGCGCCTTGGACAGCGG	0.706													T|||	43	0.00858626	0.003	0.0058	5008	,	,		14079	0.0		0.0318	False		,,,				2504	0.0031				p.L229L		Atlas-SNP	.											.	LSP1	59	.	0			c.T685C						PASS	.	T	,,,	24,4298		0,24,2137	14.0	16.0	15.0		115,115,115,301	-6.3	0.0	11	dbSNP_134	15	214,8202		4,206,3998	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSP1	NM_001013253.1,NM_001013254.1,NM_001013255.1,NM_002339.2	,,,	4,230,6135	CC,CT,TT		2.5428,0.5553,1.8684	,,,	39/278,39/278,39/278,101/340	1902771	238,12500	2161	4208	6369	SO:0001819	synonymous_variant	4046	exon4			GGCGCCTTGGACA	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.301T>C	11.37:g.1902771T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	91	89	0.978022	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Silent	SNP	ENST00000311604.3	37	CCDS31334.1																																																																																			T|0.982;C|0.018	0.018	strong		0.706	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
RPGR	6103	hgsc.bcm.edu	37	X	38145021	38145021	+	Intron	SNP	A	A	T	rs62636730	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:38145021A>T	ENST00000339363.3	-	14	2688				RPGR_ENST00000309513.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.N1077K|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CCTGCCTTTCATTCTCTTCTT	0.408													A|||	34	0.00900662	0.0008	0.0086	3775	,	,		11742	0.0		0.0268	False		,,,				2504	0.0				p.N1077K		Atlas-SNP	.											.	RPGR	175	.	0			c.T3231A						PASS	.		,LYS/ASN	11,3822		0,11,0,1620,571	399.0	319.0	346.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,3231	1.5	0.0	X	dbSNP_129	346	197,6531		1,138,57,2289,1815	yes	intron,missense	RPGR	NM_000328.2,NM_001034853.1	,94	1,149,57,3909,2386	TT,TA,T,AA,A		2.9281,0.287,1.9695	,benign	,1077/1153	38145021	208,10353	2202	4300	6502	SO:0001627	intron_variant	6103	exon15			CCTTTCATTCTCT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+1325T>A	X.37:g.38145021A>T		Somatic	310	1	0.00322581		WXS	Illumina HiSeq	Phase_I	127	125	0.984252	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		27	0.0162748643761302	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	15	0.020161290322580645	a	10.05	1.243599	0.22796	0.00287	0.029281	ENSG00000156313	ENST00000378505	T	0.02323	4.34	2.84	1.55	0.23275	.	0.377608	0.18926	U	0.127352	T	0.00845	0.0028	L	0.29908	0.895	0.37470	P	0.08441799999999999	B	0.15141	0.012	B	0.09377	0.004	T	0.18398	-1.0338	9	0.87932	D	0	.	7.9343	0.29920	0.7932:0.2068:0.0:0.0	.	1077	E9PE28	.	K	1077	ENSP00000367766:N1077K	ENSP00000367766:N1077K	N	-	3	2	RPGR	38029965	0.000000	0.05858	0.008000	0.14137	0.559000	0.35586	0.335000	0.19806	0.162000	0.19483	0.278000	0.19347	AAT	A|0.983;T|0.017	0.017	strong		0.408	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
LRRC14	9684	hgsc.bcm.edu	37	8	145741765	145741765	+	5'Flank	SNP	G	G	A	rs4244613	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145741765G>A	ENST00000292524.1	+	0	0				RECQL4_ENST00000532237.1_5'UTR|RECQL4_ENST00000428558.2_Silent_p.S246S|CTD-2517M22.17_ENST00000580385.1_RNA|LRRC14_ENST00000529022.1_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCACACGGATGCTGACTTCTT	0.637													G|||	1853	0.370008	0.0885	0.4568	5008	,	,		16498	0.4831		0.4254	False		,,,				2504	0.5153				p.S246S		Atlas-SNP	.											.	RECQL4	75	.	0			c.C738T						PASS	.	G		631,3387		57,517,1435	17.0	19.0	18.0		738	-9.4	0.0	8	dbSNP_111	18	3557,4773		783,1991,1391	no	coding-synonymous	RECQL4	NM_004260.3		840,2508,2826	AA,AG,GG		42.7011,15.7043,33.9164		246/1209	145741765	4188,8160	2009	4165	6174	SO:0001631	upstream_gene_variant	9401	exon5			ACGGATGCTGACT	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		8.37:g.145741765G>A	Exception_encountered	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_004260	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			G|0.651;A|0.349	0.349	strong		0.637	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
RHNO1	83695	hgsc.bcm.edu	37	12	2997397	2997397	+	Silent	SNP	G	G	A	rs2907608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:2997397G>A	ENST00000489288.2	+	3	641	c.489G>A	c.(487-489)tcG>tcA	p.S163S	RHNO1_ENST00000461997.2_Silent_p.S149S|TULP3_ENST00000448120.2_5'Flank|TULP3_ENST00000397132.2_5'Flank|RHNO1_ENST00000464682.2_3'UTR	NM_001252499.2|NM_001257097.1|NM_001257098.1	NP_001239428.1|NP_001244026.1|NP_001244027.1	Q9BSD3	RHNO1_HUMAN	RAD9-HUS1-RAD1 interacting nuclear orphan 1	163					cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|positive regulation of G0 to G1 transition (GO:0070318)|recombinational repair (GO:0000725)	chromosome (GO:0005694)|nucleus (GO:0005634)											CAGAGTCATCGTCTGTGAAGG	0.507													G|||	2634	0.525958	0.5976	0.5706	5008	,	,		19325	0.6458		0.3489	False		,,,				2504	0.456				p.S163S		Atlas-SNP	.											.	.	.	.	0			c.G489A						PASS	.	G		2426,1980	618.6+/-393.2	660,1106,437	128.0	125.0	126.0			-9.9	0.0	12	dbSNP_101	126	2965,5635	461.8+/-365.5	516,1933,1851	no	intergenic				1176,3039,2288	AA,AG,GG		34.4767,44.9387,41.4501			2997397	5391,7615	2203	4300	6503	SO:0001819	synonymous_variant	83695	exon3			GTCATCGTCTGTG	AK021945	CCDS8518.1, CCDS58199.1	12p13.33	2012-08-23	2012-08-23	2012-08-23	ENSG00000171792	ENSG00000171792			28206	protein-coding gene	gene with protein product	"""Rad9, Rad1, Hus1 interacting nuclear orphan"""	614085	"""chromosome 12 open reading frame 32"""	C12orf32		20811708, 21659603	Standard	NM_001252499		Approved	HKMT1188, MGC13204, RHINO	uc031qfq.1	Q9BSD3	OTTHUMG00000158557	ENST00000489288.2:c.489G>A	12.37:g.2997397G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_001257098	B7Z989	Silent	SNP	ENST00000489288.2	37	CCDS8518.1																																																																																			G|0.532;A|0.468	0.468	strong		0.507	RHNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351286.2	NM_031465	
CAPS2	84698	hgsc.bcm.edu	37	12	75715330	75715330	+	Missense_Mutation	SNP	C	C	A	rs10879901	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:75715330C>A	ENST00000409445.3	-	6	571	c.375G>T	c.(373-375)ttG>ttT	p.L125F	CAPS2_ENST00000393284.3_5'UTR|CAPS2_ENST00000409799.1_Missense_Mutation_p.L75F|CAPS2_ENST00000442339.2_5'UTR	NM_032606.3	NP_115995.2	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	125			L -> F (in dbSNP:rs10879901).				calcium ion binding (GO:0005509)	p.L125F(1)		endometrium(2)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	10						TTGGTGCTGGCAAATTTTCAG	0.299													C|||	997	0.199081	0.1808	0.1686	5008	,	,		18696	0.2321		0.2535	False		,,,				2504	0.1554				p.L125F		Atlas-SNP	.											CAPS2_ENST00000409445,NS,carcinoma,0,1	CAPS2	96	1	1	Substitution - Missense(1)	kidney(1)	c.G375T						PASS	.						226.0	160.0	180.0					12																	75715330		692	1590	2282	SO:0001583	missense	84698	exon6			TGCTGGCAAATTT	AF251056	CCDS9008.2, CCDS66424.1, CCDS73497.1	12q14.1	2013-01-10	2005-05-09		ENSG00000180881	ENSG00000180881		"""EF-hand domain containing"""	16471	protein-coding gene	gene with protein product		607724	"""calcyphosphine 2"""			11846421	Standard	NM_032606		Approved		uc001sxk.4	Q9BXY5	OTTHUMG00000152787	ENST00000409445.3:c.375G>T	12.37:g.75715330C>A	ENSP00000386959:p.Leu125Phe	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_032606	Q6PH84|Q8N242|Q8NAY5	Missense_Mutation	SNP	ENST00000409445.3	37	CCDS9008.2	394	0.1804029304029304	55	0.11178861788617886	64	0.17679558011049723	104	0.18181818181818182	171	0.22559366754617413	C	15.49	2.848855	0.51164	.	.	ENSG00000180881	ENST00000409799;ENST00000409445;ENST00000552497;ENST00000436898	T;T;T;T	0.61627	1.14;0.55;0.15;0.09	5.15	-1.26	0.09376	.	0.137416	0.33040	N	0.005349	T	0.00039	0.0001	L	0.39245	1.2	0.09310	P	0.9999999999703258	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.12372	-1.0550	9	0.87932	D	0	0.013	5.7983	0.18399	0.1186:0.532:0.0:0.3495	rs10879901;rs52797522;rs56534596;rs61664370;rs10879901	125;75	Q9BXY5;B9A061	CAYP2_HUMAN;.	F	75;125;20;19	ENSP00000386977:L75F;ENSP00000386959:L125F;ENSP00000449797:L20F;ENSP00000411797:L19F	ENSP00000338474:L20F	L	-	3	2	CAPS2	74001597	0.960000	0.32886	0.960000	0.40013	0.620000	0.37586	-0.135000	0.10420	-0.482000	0.06782	-0.253000	0.11424	TTG	C|0.808;A|0.192	0.192	strong		0.299	CAPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327880.2		
TELO2	9894	hgsc.bcm.edu	37	16	1545448	1545448	+	Missense_Mutation	SNP	A	A	G	rs2235624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1545448A>G	ENST00000262319.6	+	3	716	c.437A>G	c.(436-438)cAg>cGg	p.Q146R		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	146			Q -> R (in dbSNP:rs2235624). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.6}.		regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				CAGCAGACGCAGCCCGGCTTC	0.682													A|||	2322	0.463658	0.2103	0.6556	5008	,	,		14106	0.5724		0.6153	False		,,,				2504	0.4018				p.Q146R		Atlas-SNP	.											.	TELO2	44	.	0			c.A437G						PASS	.	A	ARG/GLN	1135,3141		159,817,1162	15.0	14.0	14.0		437	-2.6	0.0	16	dbSNP_98	14	4963,3375		1519,1925,725	no	missense	TELO2	NM_016111.3	43	1678,2742,1887	GG,GA,AA		40.4773,26.5435,48.3431	benign	146/838	1545448	6098,6516	2138	4169	6307	SO:0001583	missense	9894	exon3			AGACGCAGCCCGG	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.437A>G	16.37:g.1545448A>G	ENSP00000262319:p.Gln146Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	1120	0.5128205128205128	99	0.20121951219512196	250	0.6906077348066298	310	0.541958041958042	461	0.6081794195250659	A	4.060	0.008978	0.07912	0.265435	0.595227	ENSG00000100726	ENST00000262319	D	0.83591	-1.74	5.33	-2.64	0.06114	.	1.263210	0.05448	N	0.549007	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.31910	0.346	B	0.24269	0.052	T	0.28744	-1.0034	9	0.18276	T	0.48	-10.9661	7.4525	0.27246	0.508:0.3423:0.1497:0.0	rs2235624;rs17845529;rs17858425;rs60202364;rs2235624	146	Q9Y4R8	TELO2_HUMAN	R	146	ENSP00000262319:Q146R	ENSP00000262319:Q146R	Q	+	2	0	TELO2	1485449	0.006000	0.16342	0.004000	0.12327	0.010000	0.07245	0.588000	0.23924	-0.281000	0.09141	-1.063000	0.02288	CAG	A|0.531;G|0.469	0.469	strong		0.682	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
EPHA3	2042	hgsc.bcm.edu	37	3	89521725	89521725	+	Silent	SNP	T	T	C	rs1054750	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:89521725T>C	ENST00000336596.2	+	16	3027	c.2802T>C	c.(2800-2802)ggT>ggC	p.G934G	EPHA3_ENST00000494014.1_Intron	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	934	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TCTTCACGGGTGTGGAGTACA	0.413										TSP Lung(6;0.00050)			C|||	649	0.129593	0.0688	0.1916	5008	,	,		19868	0.0813		0.2594	False		,,,				2504	0.0838				p.G934G		Atlas-SNP	.											EPHA3,NS,malignant_melanoma,+2,1	EPHA3	501	1	0			c.T2802C						PASS	.	C		390,4016	790.6+/-415.0	21,348,1834	115.0	105.0	109.0		2802	1.7	1.0	3	dbSNP_86	109	2040,6560	720.3+/-406.3	234,1572,2494	no	coding-synonymous	EPHA3	NM_005233.5		255,1920,4328	CC,CT,TT		23.7209,8.8516,18.6837		934/984	89521725	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	2042	exon16			CACGGGTGTGGAG	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2802T>C	3.37:g.89521725T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	143	67	0.468531	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																			T|0.835;C|0.165	0.165	strong		0.413	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
KIF2B	84643	hgsc.bcm.edu	37	17	51901385	51901385	+	Silent	SNP	C	C	T	rs3803826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:51901385C>T	ENST00000268919.4	+	1	1147	c.991C>T	c.(991-993)Ctg>Ttg	p.L331L		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	331	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CATTTATGCTCTGGTGGCACA	0.493													C|||	1675	0.334465	0.1074	0.4107	5008	,	,		22113	0.5863		0.3658	False		,,,				2504	0.2955				p.L331L		Atlas-SNP	.											.	KIF2B	254	.	0			c.C991T						PASS	.	C		656,3750	279.6+/-274.9	41,574,1588	107.0	108.0	107.0		991	-5.5	0.0	17	dbSNP_107	107	3075,5525	471.6+/-368.1	562,1951,1787	no	coding-synonymous	KIF2B	NM_032559.4		603,2525,3375	TT,TC,CC		35.7558,14.8888,28.6868		331/674	51901385	3731,9275	2203	4300	6503	SO:0001819	synonymous_variant	84643	exon1			TATGCTCTGGTGG	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.991C>T	17.37:g.51901385C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_032559	Q96MA2|Q9BXG6	Silent	SNP	ENST00000268919.4	37	CCDS32685.1																																																																																			C|0.677;T|0.323	0.323	strong		0.493	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
ODF2L	57489	hgsc.bcm.edu	37	1	86852621	86852621	+	Silent	SNP	A	A	G	rs2390096	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86852621A>G	ENST00000359242.3	-	2	371	c.90T>C	c.(88-90)tgT>tgC	p.C30C	ODF2L_ENST00000317336.7_Silent_p.C30C|ODF2L_ENST00000370567.1_Silent_p.C30C|ODF2L_ENST00000478286.2_Silent_p.C30C|ODF2L_ENST00000370566.3_Silent_p.C30C|ODF2L_ENST00000486215.1_Silent_p.C30C|ODF2L_ENST00000294678.2_Silent_p.C30C|ODF2L_ENST00000394731.1_5'UTR	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	30						centrosome (GO:0005813)		p.C30C(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TTTCACTGGTACACCGTGGTA	0.338													A|||	1576	0.314696	0.2352	0.2637	5008	,	,		12595	0.4167		0.3181	False		,,,				2504	0.3497				p.C30C		Atlas-SNP	.											ODF2L,NS,carcinoma,0,1	ODF2L	53	1	1	Substitution - coding silent(1)	stomach(1)	c.T90C						PASS	.	A	,,,	1182,3224	414.8+/-337.0	171,840,1192	118.0	127.0	124.0		90,90,90,90	1.5	0.0	1	dbSNP_100	124	2923,5677	455.7+/-363.9	464,1995,1841	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ODF2L	NM_001007022.2,NM_001184765.1,NM_001184766.1,NM_020729.2	,,,	635,2835,3033	GG,GA,AA		33.9884,26.8271,31.5624	,,,	30/637,30/621,30/592,30/621	86852621	4105,8901	2203	4300	6503	SO:0001819	synonymous_variant	57489	exon2			ACTGGTACACCGT		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.90T>C	1.37:g.86852621A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_001184766	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Silent	SNP	ENST00000359242.3	37	CCDS41354.2																																																																																			A|0.692;G|0.308	0.308	strong		0.338	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
PIGC	5279	hgsc.bcm.edu	37	1	172410967	172410967	+	Missense_Mutation	SNP	G	G	A	rs1063412	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:172410967G>A	ENST00000367728.1	-	1	2259	c.796C>T	c.(796-798)Cca>Tca	p.P266S	PIGC_ENST00000344529.4_Missense_Mutation_p.P266S|PIGC_ENST00000258324.1_Missense_Mutation_p.P266S|C1orf105_ENST00000367727.4_Intron|PIGC_ENST00000484368.1_Intron			Q92535	PIGC_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class C	266			P -> S (in dbSNP:rs1063412). {ECO:0000269|PubMed:9325057}.		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			breast(1)|endometrium(1)|kidney(1)|lung(1)	4						AGGTAGAATGGACACAGACAT	0.458													G|||	2275	0.454273	0.0605	0.536	5008	,	,		20245	0.6597		0.5994	False		,,,				2504	0.5675				p.P266S		Atlas-SNP	.											.	PIGC	24	.	0			c.C796T						PASS	.	G	SER/PRO,,SER/PRO	665,3741	282.5+/-276.6	54,557,1592	102.0	98.0	99.0		796,,796	4.2	1.0	1	dbSNP_86	99	4793,3807	613.4+/-396.1	1315,2163,822	yes	missense,intron,missense	PIGC,C1orf105	NM_002642.3,NM_139240.3,NM_153747.1	74,,74	1369,2720,2414	AA,AG,GG		44.2674,15.0931,41.9652	probably-damaging,,probably-damaging	266/298,,266/298	172410967	5458,7548	2203	4300	6503	SO:0001583	missense	5279	exon2			AGAATGGACACAG	BC006539	CCDS1302.1	1q23-q25	2013-02-26	2006-06-28		ENSG00000135845	ENSG00000135845	2.4.1.198	"""Phosphatidylinositol glycan anchor biosynthesis"""	8960	protein-coding gene	gene with protein product	"""phosphatidylinositol N-acetylglucosaminyltransferase"""	601730	"""phosphatidylinositol glycan, class C"""			8806613, 9325057	Standard	NM_153747		Approved		uc001gio.3	Q92535	OTTHUMG00000034751	ENST00000367728.1:c.796C>T	1.37:g.172410967G>A	ENSP00000356702:p.Pro266Ser	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	167	167	1	NM_153747	O14491	Missense_Mutation	SNP	ENST00000367728.1	37	CCDS1302.1	1092	0.5	47	0.09552845528455285	205	0.5662983425414365	377	0.6590909090909091	463	0.6108179419525066	G	21.0	4.083615	0.76642	0.150931	0.557326	ENSG00000135845	ENST00000344529;ENST00000367728;ENST00000258324	T;T;T	0.58060	0.36;0.36;0.36	5.16	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.53400	0.1794	L	0.48260	1.515	0.09310	P	1.0	D	0.89917	1.0	D	0.97110	1.0	T	0.57946	-0.7723	9	0.44086	T	0.13	0.0129	12.3206	0.54983	0.0826:0.0:0.9174:0.0	rs1063412;rs3170727;rs16844444;rs57213706;rs1063412	266	Q92535	PIGC_HUMAN	S	266	ENSP00000356701:P266S;ENSP00000356702:P266S;ENSP00000258324:P266S	ENSP00000258324:P266S	P	-	1	0	PIGC	170677590	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.034000	0.93747	1.157000	0.42530	0.655000	0.94253	CCA	G|0.552;A|0.448	0.448	strong		0.458	PIGC-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084068.1	NM_153747	
MUC16	94025	hgsc.bcm.edu	37	19	9076991	9076991	+	Silent	SNP	C	C	T	rs2591595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9076991C>T	ENST00000397910.4	-	3	10658	c.10455G>A	c.(10453-10455)gcG>gcA	p.A3485A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3486	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGACAGATGACGCAGAGCTTG	0.507													T|||	1243	0.248203	0.2005	0.2118	5008	,	,		24293	0.249		0.3121	False		,,,				2504	0.272				p.A3485A		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,-1,2	MUC16	4315	2	0			c.G10455A						PASS	.	T		875,3293		103,669,1312	117.0	113.0	115.0		10455	-3.9	0.0	19	dbSNP_100	115	2435,5991		350,1735,2128	no	coding-synonymous	MUC16	NM_024690.2		453,2404,3440	TT,TC,CC		28.8986,20.9933,26.2824		3485/14508	9076991	3310,9284	2084	4213	6297	SO:0001819	synonymous_variant	94025	exon3			AGATGACGCAGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10455G>A	19.37:g.9076991C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	220	99	0.45	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.750;T|0.250	0.250	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
HYKK	123688	hgsc.bcm.edu	37	15	78825562	78825562	+	Silent	SNP	C	C	T	rs12906951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78825562C>T	ENST00000569878.1	+	4	672	c.672C>T	c.(670-672)caC>caT	p.H224H	HYKK_ENST00000408962.2_Intron|HYKK_ENST00000563233.1_Intron|HYKK_ENST00000388988.4_Silent_p.H224H			A2RU49	HYKK_HUMAN	hydroxylysine kinase	224						cytoplasm (GO:0005737)	hydroxylysine kinase activity (GO:0047992)	p.H224H(2)									GTATCAATCACGGAGATCTTA	0.353													T|||	1183	0.236222	0.0998	0.2176	5008	,	,		19099	0.1528		0.3708	False		,,,				2504	0.3814				p.H224H		Atlas-SNP	.											AGPHD1,NS,carcinoma,0,1	AGPHD1	22	1	2	Substitution - coding silent(2)	prostate(2)	c.C672T						PASS	.	T	,	620,3032		59,502,1265	55.0	48.0	50.0		672,	-3.9	0.8	15	dbSNP_121	50	3377,4779		717,1943,1418	no	coding-synonymous,intron	AGPHD1	NM_001013619.2,NM_001083612.1	,	776,2445,2683	TT,TC,CC		41.4051,16.977,33.8499	,	224/374,	78825562	3997,7811	1826	4078	5904	SO:0001819	synonymous_variant	123688	exon5			CAATCACGGAGAT	BC132753, BC144383, BM045979	CCDS42063.1, CCDS45318.1	15q25.1	2013-06-11	2013-06-11	2013-06-11	ENSG00000188266	ENSG00000188266	2.7.1.81		34403	protein-coding gene	gene with protein product	"""5-hydroxylysine kinase"""	614681	"""aminoglycoside phosphotransferase domain containing 1"""	AGPHD1		18780872, 22241472	Standard	NM_001013619		Approved	LOC123688	uc010unc.2	A2RU49		ENST00000569878.1:c.672C>T	15.37:g.78825562C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_001013619	B7ZMA5|F8W6X5|Q6ZTN0	Silent	SNP	ENST00000569878.1	37	CCDS42063.1																																																																																			C|0.733;T|0.267	0.267	strong		0.353	HYKK-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435834.1	NM_001013619	
WWC2	80014	hgsc.bcm.edu	37	4	184192278	184192278	+	Missense_Mutation	SNP	G	G	T	rs11734376	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:184192278G>T	ENST00000403733.3	+	16	2645	c.2446G>T	c.(2446-2448)Gtt>Ttt	p.V816F	WWC2_ENST00000504005.1_Missense_Mutation_p.V498F|WWC2_ENST00000513834.1_Missense_Mutation_p.V767F|WWC2_ENST00000448232.2_Missense_Mutation_p.V816F	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	816			V -> F (in dbSNP:rs11734376). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TTCCAGTGAGGTTTTCACTCT	0.363													G|||	319	0.0636981	0.0083	0.1052	5008	,	,		15336	0.0		0.1431	False		,,,				2504	0.093				p.V816F		Atlas-SNP	.											.	WWC2	78	.	0			c.G2446T						PASS	.	G	PHE/VAL	138,4268	94.8+/-133.5	1,136,2066	48.0	46.0	47.0		2446	-2.0	1.0	4	dbSNP_120	47	1320,7280	251.2+/-277.8	112,1096,3092	yes	missense	WWC2	NM_024949.5	50	113,1232,5158	TT,TG,GG		15.3488,3.1321,11.2102	benign	816/1193	184192278	1458,11548	2203	4300	6503	SO:0001583	missense	80014	exon16			AGTGAGGTTTTCA	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2446G>T	4.37:g.184192278G>T	ENSP00000384222:p.Val816Phe	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	144	54	0.375	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	155	0.07097069597069597	6	0.012195121951219513	50	0.13812154696132597	0	0.0	99	0.13060686015831136	G	5.020	0.189364	0.09547	0.031321	0.153488	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.52	-2.0	0.07433	C2 calcium/lipid-binding domain, CaLB (1);	0.638313	0.15838	N	0.242183	T	0.00109	0.0003	L	0.31926	0.97	0.31401	P	0.6767179999999999	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.08055	0.003;0.002;0.002	T	0.24368	-1.0162	9	0.09338	T	0.73	-1.9517	6.7782	0.23630	0.4971:0.0:0.3839:0.119	rs11734376;rs17846520;rs17859593;rs52823830;rs57873564;rs11734376	816;816;767	Q6AWC2-6;Q6AWC2;Q6AWC2-4	.;WWC2_HUMAN;.	F	816;767;816;498	ENSP00000384222:V816F;ENSP00000425054:V767F;ENSP00000398577:V816F;ENSP00000427569:V498F	ENSP00000384222:V816F	V	+	1	0	WWC2	184429272	0.792000	0.28813	0.985000	0.45067	0.848000	0.48234	0.175000	0.16762	-0.093000	0.12396	-0.253000	0.11424	GTT	G|0.902;T|0.098	0.098	strong		0.363	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
MUS81	80198	hgsc.bcm.edu	37	11	65629934	65629934	+	Missense_Mutation	SNP	G	G	C	rs545500|rs386754402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65629934G>C	ENST00000308110.4	+	6	888	c.539G>C	c.(538-540)cGa>cCa	p.R180P	MUS81_ENST00000533035.1_Missense_Mutation_p.R105P|CFL1_ENST00000534769.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	180	Interaction with BLM.		R -> P (in dbSNP:rs545500). {ECO:0000269|PubMed:11741546, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		GGGAGTGCTCGACCCTGGCCA	0.617								Homologous recombination					G|||	2144	0.428115	0.2012	0.4063	5008	,	,		16101	0.3323		0.668	False		,,,				2504	0.6022				p.R180P		Atlas-SNP	.											.	MUS81	68	.	0			c.G539C						PASS	.	G	PRO/ARG	1124,3278	389.6+/-327.4	153,818,1230	75.0	62.0	66.0		539	-2.0	0.0	11	dbSNP_83	66	5713,2879	663.9+/-402.1	1894,1925,477	yes	missense	MUS81	NM_025128.4	103	2047,2743,1707	CC,CG,GG		33.5079,25.5338,47.3834	benign	180/552	65629934	6837,6157	2201	4296	6497	SO:0001583	missense	80198	exon6			GTGCTCGACCCTG		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.539G>C	11.37:g.65629934G>C	ENSP00000307853:p.Arg180Pro	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_025128	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	37	CCDS8115.1	974	0.445970695970696	117	0.23780487804878048	175	0.48342541436464087	174	0.3041958041958042	508	0.6701846965699209	G	15.14	2.746351	0.49257	0.255338	0.664921	ENSG00000172732	ENST00000533035;ENST00000308110;ENST00000437855;ENST00000525768	T;T;T	0.23147	2.47;2.7;1.92	5.29	-1.98	0.07480	.	0.645425	0.15248	N	0.272492	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P	0.39551	0.678	B	0.29077	0.098	T	0.36768	-0.9734	9	0.32370	T	0.25	-0.0236	10.1301	0.42674	0.5065:0.0:0.4935:0.0	rs545500;rs17850598	180	Q96NY9	MUS81_HUMAN	P	105;180;180;105	ENSP00000432287:R105P;ENSP00000307853:R180P;ENSP00000431478:R105P	ENSP00000307853:R180P	R	+	2	0	MUS81	65386510	0.000000	0.05858	0.000000	0.03702	0.810000	0.45777	-0.071000	0.11505	-0.236000	0.09753	-0.291000	0.09656	CGA	G|0.499;C|0.501	0.501	strong		0.617	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
CCS	9973	hgsc.bcm.edu	37	11	66373305	66373305	+	Silent	SNP	G	G	A	rs1127145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66373305G>A	ENST00000533244.1	+	8	1245	c.804G>A	c.(802-804)gcG>gcA	p.A268A	CCS_ENST00000310190.4_Silent_p.A249A	NM_005125.1	NP_005116.1	O14618	CCS_HUMAN	copper chaperone for superoxide dismutase	268					copper ion transmembrane transport (GO:0035434)|intracellular copper ion transport (GO:0015680)|positive regulation of oxidoreductase activity (GO:0051353)|removal of superoxide radicals (GO:0019430)|superoxide metabolic process (GO:0006801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|protein disulfide oxidoreductase activity (GO:0015035)|superoxide dismutase activity (GO:0004784)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|large_intestine(2)|lung(3)|stomach(1)	9						AGGAGTCAGCGCAGCCCCCTG	0.632													c|||	394	0.0786741	0.0098	0.0793	5008	,	,		18909	0.0208		0.1531	False		,,,				2504	0.1544				p.A268A		Atlas-SNP	.											CCS,NS,carcinoma,0,1	CCS	22	1	0			c.G804A						scavenged	.			145,4255		3,139,2058	42.0	40.0	41.0		804	-0.3	0.0	11	dbSNP_86	41	1374,7216		117,1140,3038	no	coding-synonymous	CCS	NM_005125.1		120,1279,5096	AA,AG,GG		15.9953,3.2955,11.6936		268/275	66373305	1519,11471	2200	4295	6495	SO:0001819	synonymous_variant	9973	exon8			GTCAGCGCAGCCC	AF002210	CCDS8146.1	11q13.2	2012-09-20			ENSG00000173992	ENSG00000173992			1613	protein-coding gene	gene with protein product		603864				9295278	Standard	NM_005125		Approved		uc001oir.3	O14618	OTTHUMG00000167238	ENST00000533244.1:c.804G>A	11.37:g.66373305G>A		Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	70	24	0.342857	NM_005125	Q2M366|Q8NEV0	Silent	SNP	ENST00000533244.1	37	CCDS8146.1																																																																																			A|0.102;C|0.000;G|0.897	0.102	strong		0.632	CCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393826.1	NM_005125	
CES1	1066	hgsc.bcm.edu	37	16	55862883	55862883	+	Splice_Site	SNP	C	C	A	rs3826190		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55862883C>A	ENST00000361503.4	-	2	183	c.53G>T	c.(52-54)gGg>gTg	p.G18V	CES1_ENST00000422046.2_Splice_Site_p.G18V|CES1_ENST00000566555.1_5'Flank|CES1_ENST00000360526.3_Missense_Mutation_p.G19V			P23141	EST1_HUMAN	carboxylesterase 1	18			G -> GA.		epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)	p.G19V(1)							all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	GGACGGATGCCCTGCTGGACA	0.522																																					p.G19V	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,NS,carcinoma,0,1	CES1	78	1	1	Substitution - Missense(1)	prostate(1)	c.G56T						PASS	.						38.0	29.0	32.0					16																	55862883		2198	4300	6498	SO:0001630	splice_region_variant	1066	exon2			GGATGCCCTGCTG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.53-1G>T	16.37:g.55862883C>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	17	0.293103	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	804	0.36813186813186816	220	0.44715447154471544	142	0.39226519337016574	112	0.1958041958041958	330	0.43535620052770446	.	18.35	3.604104	0.66445	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.66995	-0.24;-0.17;-0.17	4.48	3.52	0.40303	Carboxylesterase, type B (1);	8.429180	0.00357	N	0.000020	T	0.00012	0.0000	M	0.64080	1.96	0.58432	D	0.999993	D;D;D	0.63046	0.992;0.992;0.972	D;D;P	0.70487	0.969;0.958;0.891	T	0.53556	-0.8422	10	0.72032	D	0.01	.	9.5301	0.39189	0.0:0.8943:0.0:0.1057	rs3826190	18;18;19	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	V	19;18;18	ENSP00000353720:G19V;ENSP00000355193:G18V;ENSP00000390492:G18V	ENSP00000353720:G19V	G	-	2	0	CES1	54420384	0.940000	0.31905	0.780000	0.31762	0.099000	0.18886	1.881000	0.39638	2.051000	0.60960	0.393000	0.25936	GGG	C|0.632;A|0.368	0.368	strong		0.522	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	Missense_Mutation
RNF41	10193	hgsc.bcm.edu	37	12	56601998	56601998	+	Silent	SNP	G	G	A	rs17118378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56601998G>A	ENST00000345093.4	-	5	816	c.447C>T	c.(445-447)atC>atT	p.I149I	RNF41_ENST00000552656.1_Silent_p.I149I|RNF41_ENST00000394013.2_Silent_p.I78I|RNF41_ENST00000552244.1_Silent_p.I149I	NM_005785.3|NM_194359.2	NP_005776.1|NP_919340.1	Q9H4P4	RNF41_HUMAN	ring finger protein 41, E3 ubiquitin protein ligase	149					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|proteasomal protein catabolic process (GO:0010498)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|regulation of establishment of cell polarity (GO:2000114)|regulation of lymphocyte differentiation (GO:0045619)|regulation of MAPK cascade (GO:0043408)|regulation of myeloid cell differentiation (GO:0045637)|regulation of protein kinase B signaling (GO:0051896)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytosol (GO:0005829)	acid-amino acid ligase activity (GO:0016881)|protein tag (GO:0031386)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	11						CCAGCTCTGCGATGCGTGTCT	0.562													G|||	77	0.0153754	0.0424	0.0072	5008	,	,		19990	0.0		0.0	False		,,,				2504	0.0164				p.I149I		Atlas-SNP	.											.	RNF41	31	.	0			c.C447T						PASS	.	G	,,,	142,4264	101.6+/-140.2	6,130,2067	132.0	104.0	114.0		447,447,234,447	-4.0	0.9	12	dbSNP_123	114	9,8591	7.7+/-29.5	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNF41	NM_001242826.1,NM_005785.3,NM_194358.2,NM_194359.2	,,,	6,139,6358	AA,AG,GG		0.1047,3.2229,1.161	,,,	149/318,149/318,78/247,149/318	56601998	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	10193	exon5			CTCTGCGATGCGT	AF077599	CCDS8909.1, CCDS8910.1	12q13.13	2014-03-24	2014-03-24		ENSG00000181852	ENSG00000181852		"""RING-type (C3HC4) zinc fingers"""	18401	protein-coding gene	gene with protein product			"""ring finger protein 41"""				Standard	NM_005785		Approved	SBBI03, NRDP1	uc001skg.2	Q9H4P4	OTTHUMG00000170328	ENST00000345093.4:c.447C>T	12.37:g.56601998G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	214	96	0.448598	NM_005785	A6NFW0|B2RBT8|O75598	Silent	SNP	ENST00000345093.4	37	CCDS8909.1																																																																																			G|0.986;A|0.014	0.014	strong		0.562	RNF41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408525.1	NM_005785	
NYNRIN	57523	hgsc.bcm.edu	37	14	24883887	24883887	+	Missense_Mutation	SNP	G	G	A	rs8017377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24883887G>A	ENST00000382554.3	+	9	3250	c.2932G>A	c.(2932-2934)Gct>Act	p.A978T	NYNRIN_ENST00000554505.1_3'UTR	NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	978			A -> T (in dbSNP:rs8017377).		DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GAGTGATGACGCTGACTCTGG	0.557													G|||	1224	0.244409	0.1218	0.255	5008	,	,		20580	0.0496		0.4811	False		,,,				2504	0.3599				p.A978T		Atlas-SNP	.											.	NYNRIN	120	.	0			c.G2932A						PASS	.	G	THR/ALA	691,3709	274.6+/-272.0	68,555,1577	52.0	58.0	56.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2932	-9.1	0.0	14	dbSNP_116	56	3981,4583	539.9+/-383.7	948,2085,1249	yes	missense	NYNRIN	NM_025081.2	58	1016,2640,2826	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	46.4853,15.7045,36.0383	benign	978/1899	24883887	4672,8292	2200	4282	6482	SO:0001583	missense	57523	exon9			GATGACGCTGACT	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.2932G>A	14.37:g.24883887G>A	ENSP00000371994:p.Ala978Thr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	536	0.2454212454212454	60	0.12195121951219512	97	0.26795580110497236	31	0.05419580419580419	348	0.45910290237467016	G	10.03	1.239423	0.22711	0.157045	0.464853	ENSG00000205978	ENST00000382554	T	0.11169	2.8	4.54	-9.08	0.00720	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.47699	-0.9097	8	0.32370	T	0.25	.	0.3875	0.00405	0.375:0.1851:0.1579:0.2819	rs8017377;rs17795076;rs58497689;rs8017377	978	Q9P2P1	NYNRI_HUMAN	T	978	ENSP00000371994:A978T	ENSP00000371994:A978T	A	+	1	0	NYNRIN	23953727	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.409000	0.07160	-1.685000	0.01441	-1.824000	0.00597	GCT	G|0.753;A|0.247	0.247	strong		0.557	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
LILRB3	11025	hgsc.bcm.edu	37	19	54726816	54726816	+	Splice_Site	SNP	A	A	T	rs80332440		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54726816A>T	ENST00000391750.1	-	2	169	c.33T>A	c.(31-33)ctT>ctA	p.L11L	LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000346401.6_Splice_Site_p.L11L|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000424807.1_Splice_Site_p.L11L|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Splice_Site_p.L11L|LILRA6_ENST00000440558.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	11					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AAATCTCACCAAGGCAGAGCA	0.622																																					p.L11L		Atlas-SNP	.											LILRB3,NS,neuroblastoma,0,1	LILRB3	67	1	0			c.T33A						PASS	.						33.0	40.0	37.0					19																	54726816		2161	4254	6415	SO:0001630	splice_region_variant	11025	exon1			CTCACCAAGGCAG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.34+1T>A	19.37:g.54726816A>T		Somatic	341	1	0.00293255		WXS	Illumina HiSeq	Phase_I	369	116	0.314363	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			.	.	weak		0.622	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	Silent
SLC12A8	84561	hgsc.bcm.edu	37	3	124906162	124906162	+	Silent	SNP	G	G	A	rs34985183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:124906162G>A	ENST00000393469.4	-	3	358	c.309C>T	c.(307-309)agC>agT	p.S103S	SLC12A8_ENST00000423114.2_Silent_p.S132S|SLC12A8_ENST00000469902.1_Silent_p.S103S|SLC12A8_ENST00000314584.7_5'UTR	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	103					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						AGACGCCACCGCTGCCGATGC	0.652													G|||	127	0.0253594	0.0015	0.062	5008	,	,		17754	0.0089		0.0209	False		,,,				2504	0.0532				p.S103S		Atlas-SNP	.											.	SLC12A8	81	.	0			c.C309T						PASS	.	G	,	27,4329		0,27,2151	58.0	79.0	72.0		309,309	-8.0	0.4	3	dbSNP_126	72	219,8327		3,213,4057	yes	coding-synonymous,coding-synonymous	SLC12A8	NM_001195483.1,NM_024628.5	,	3,240,6208	AA,AG,GG		2.5626,0.6198,1.9067	,	103/715,103/715	124906162	246,12656	2178	4273	6451	SO:0001819	synonymous_variant	84561	exon4			GCCACCGCTGCCG		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.309C>T	3.37:g.124906162G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	195	99	0.507692	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Silent	SNP	ENST00000393469.4	37	CCDS43143.1	44	0.020146520146520148	3	0.006097560975609756	20	0.055248618784530384	5	0.008741258741258742	16	0.021108179419525065	G	14.65	2.599496	0.46318	0.006198	0.025626	ENSG00000221955	ENST00000479826	T	0.79141	-1.24	5.18	-7.97	0.01139	.	.	.	.	.	T	0.33673	0.0871	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73579	-0.3938	5	.	.	.	.	17.3163	0.87225	0.8063:0.0:0.1937:0.0	rs34985183	.	.	.	W	63	ENSP00000420197:R63W	.	R	-	1	2	SLC12A8	126388852	0.395000	0.25254	0.432000	0.26747	0.553000	0.35397	-0.177000	0.09796	-1.817000	0.01219	-1.138000	0.01928	CGG	G|0.974;A|0.026	0.026	strong		0.652	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
AK7	122481	hgsc.bcm.edu	37	14	96871104	96871104	+	Missense_Mutation	SNP	G	G	A	rs2275554	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:96871104G>A	ENST00000267584.4	+	3	349	c.305G>A	c.(304-306)cGa>cAa	p.R102Q	AK7_ENST00000554313.1_3'UTR	NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	102			R -> Q (in dbSNP:rs2275554). {ECO:0000269|PubMed:14702039}.		axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GCCATCTCTCGAGAAGACCTT	0.403													G|||	1069	0.213458	0.2269	0.1657	5008	,	,		18454	0.1944		0.2684	False		,,,				2504	0.1922				p.R102Q		Atlas-SNP	.											.	AK7	69	.	0			c.G305A						PASS	.	G	GLN/ARG	1009,3397	376.1+/-321.9	127,755,1321	94.0	87.0	89.0		305	4.5	0.2	14	dbSNP_100	89	2191,6409	372.7+/-336.7	309,1573,2418	yes	missense	AK7	NM_152327.2	43	436,2328,3739	AA,AG,GG		25.4767,22.9006,24.604	benign	102/724	96871104	3200,9806	2203	4300	6503	SO:0001583	missense	122481	exon3			TCTCTCGAGAAGA	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.305G>A	14.37:g.96871104G>A	ENSP00000267584:p.Arg102Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	42	0.385321	NM_152327	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	37	CCDS9945.1	427	0.1955128205128205	87	0.17682926829268292	55	0.15193370165745856	104	0.18181818181818182	181	0.23878627968337732	G	10.47	1.360434	0.24598	0.229006	0.254767	ENSG00000140057	ENST00000267584	T	0.41065	1.01	5.35	4.47	0.54385	.	0.200218	0.41097	N	0.000951	T	0.00012	0.0000	L	0.31476	0.935	0.09310	P	0.9999999999999996	B	0.26547	0.152	B	0.21917	0.037	T	0.18681	-1.0329	9	0.33940	T	0.23	-6.7224	12.998	0.58660	0.0794:0.0:0.9206:0.0	rs2275554;rs59019715;rs2275554	102	Q96M32	KAD7_HUMAN	Q	102	ENSP00000267584:R102Q	ENSP00000267584:R102Q	R	+	2	0	AK7	95940857	1.000000	0.71417	0.190000	0.23270	0.094000	0.18550	3.268000	0.51585	1.270000	0.44297	0.467000	0.42956	CGA	G|0.770;A|0.230	0.230	strong		0.403	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1		
WDR88	126248	hgsc.bcm.edu	37	19	33638586	33638586	+	Missense_Mutation	SNP	C	C	G	rs74994260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33638586C>G	ENST00000355868.3	+	4	588	c.512C>G	c.(511-513)gCc>gGc	p.A171G	WDR88_ENST00000361680.2_Missense_Mutation_p.A171G|WDR88_ENST00000592765.1_3'UTR	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	171								p.A171G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					ACAGTGAGGGCCTGGGACCTG	0.537													C|||	123	0.0245607	0.0038	0.0389	5008	,	,		17844	0.0		0.0586	False		,,,				2504	0.0327				p.A171G		Atlas-SNP	.											WDR88,lymph_node,lymphoid_neoplasm,0,1	WDR88	50	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C512G						PASS	.	C	GLY/ALA	52,4354	51.6+/-87.1	0,52,2151	116.0	98.0	104.0		512	2.0	0.6	19	dbSNP_132	104	581,8019	153.3+/-207.7	20,541,3739	yes	missense	WDR88	NM_173479.3	60	20,593,5890	GG,GC,CC		6.7558,1.1802,4.867	probably-damaging	171/473	33638586	633,12373	2203	4300	6503	SO:0001583	missense	126248	exon4			TGAGGGCCTGGGA	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.512C>G	19.37:g.33638586C>G	ENSP00000348129:p.Ala171Gly	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	37	CCDS12429.1	59	0.027014652014652016	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	40	0.052770448548812667	C	13.20	2.165364	0.38217	0.011802	0.067558	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.44881	0.91;0.91	5.32	2.01	0.26516	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	36.956400	0.00166	N	0.000002	T	0.06096	0.0158	L	0.29908	0.895	0.19945	N	0.999949	D	0.57571	0.98	P	0.55749	0.783	T	0.20840	-1.0263	10	0.72032	D	0.01	.	8.7474	0.34594	0.0:0.6806:0.0:0.3194	.	171	Q6ZMY6	WDR88_HUMAN	G	171	ENSP00000348129:A171G;ENSP00000355148:A171G	ENSP00000348129:A171G	A	+	2	0	WDR88	38330426	0.763000	0.28462	0.557000	0.28306	0.083000	0.17756	0.541000	0.23207	0.737000	0.32582	-0.136000	0.14681	GCC	C|0.953;G|0.047	0.047	strong		0.537	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
CEP83	51134	hgsc.bcm.edu	37	12	94761701	94761701	+	Silent	SNP	T	T	C	rs12426243	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:94761701T>C	ENST00000397809.5	-	11	1761	c.1212A>G	c.(1210-1212)agA>agG	p.R404R	CCDC41_ENST00000339839.5_Silent_p.R404R|CCDC41_ENST00000549352.1_5'Flank|CCDC41_ENST00000397807.2_Silent_p.R371R	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		396					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						AATCTGCTAATCTGTTCTCGA	0.353													T|||	396	0.0790735	0.0492	0.1311	5008	,	,		17366	0.0595		0.1183	False		,,,				2504	0.0624				p.R404R		Atlas-SNP	.											.	CCDC41	59	.	0			c.A1212G						PASS	.	T	,	181,3509		4,173,1668	147.0	128.0	134.0		1212,1212	5.8	1.0	12	dbSNP_120	134	930,7258		57,816,3221	no	coding-synonymous,coding-synonymous	CCDC41	NM_001042399.1,NM_016122.2	,	61,989,4889	CC,CT,TT		11.3581,4.9051,9.3534	,	404/702,404/702	94761701	1111,10767	1845	4094	5939	SO:0001819	synonymous_variant	51134	exon11			TGCTAATCTGTTC																												ENST00000397809.5:c.1212A>G	12.37:g.94761701T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	161	76	0.47205	NM_016122	A4FVB1|Q08AP1	Silent	SNP	ENST00000397809.5	37	CCDS41820.1																																																																																			T|0.891;C|0.109	0.109	strong		0.353	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3		
TMEM132C	92293	hgsc.bcm.edu	37	12	129189941	129189941	+	Missense_Mutation	SNP	G	G	A	rs12424159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:129189941G>A	ENST00000435159.2	+	9	2428	c.2428G>A	c.(2428-2430)Ggg>Agg	p.G810R	TMEM132C_ENST00000537538.1_Missense_Mutation_p.G195R|TMEM132C_ENST00000315208.8_Missense_Mutation_p.G426R	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	810			G -> R (in dbSNP:rs12424159).			integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						CAGCCCCGGCGGGGACTATGA	0.612													A|||	2445	0.488219	0.1838	0.6527	5008	,	,		18142	0.6042		0.5567	False		,,,				2504	0.593				p.G810R		Atlas-SNP	.											TMEM132C_ENST00000435159,caecum,carcinoma,0,2	TMEM132C	142	2	0			c.G2428A						PASS	.	A	ARG/GLY	321,1063		41,239,412	21.0	28.0	26.0		2428	-0.2	0.0	12	dbSNP_120	26	1817,1365		527,763,301	yes	missense	TMEM132C	NM_001136103.2	125	568,1002,713	AA,AG,GG		42.8975,23.1936,46.8244	benign	810/1109	129189941	2138,2428	692	1591	2283	SO:0001583	missense	92293	exon9			CCCGGCGGGGACT	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.2428G>A	12.37:g.129189941G>A	ENSP00000410852:p.Gly810Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_001136103	Q69YX8	Missense_Mutation	SNP	ENST00000435159.2	37		1095	0.5013736263736264	93	0.18902439024390244	220	0.6077348066298343	364	0.6363636363636364	418	0.5514511873350924	A	0.076	-1.192588	0.01607	0.231936	0.571025	ENSG00000181234	ENST00000435159;ENST00000315208;ENST00000537538	T;T;T	0.13307	2.6;2.6;2.6	4.61	-0.187	0.13268	.	1.704450	0.03531	N	0.222438	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.14805	0.011	B	0.11329	0.006	T	0.42865	-0.9426	9	0.15952	T	0.53	.	6.4763	0.22037	0.2546:0.2502:0.4952:0.0	rs12424159;rs59510636;rs12424159	810	Q8N3T6	T132C_HUMAN	R	810;426;195	ENSP00000410852:G810R;ENSP00000324458:G426R;ENSP00000438477:G195R	ENSP00000324458:G426R	G	+	1	0	TMEM132C	127755894	0.003000	0.15002	0.000000	0.03702	0.044000	0.14063	0.590000	0.23954	-0.288000	0.09051	-1.213000	0.01624	GGG	G|0.517;A|0.483	0.483	strong		0.612	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
MYO3A	53904	hgsc.bcm.edu	37	10	26355992	26355992	+	Missense_Mutation	SNP	A	A	G	rs3824699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:26355992A>G	ENST00000265944.5	+	11	1208	c.1042A>G	c.(1042-1044)Att>Gtt	p.I348V	MYO3A_ENST00000543632.1_Missense_Mutation_p.I348V	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	348	Myosin motor.		I -> V (in dbSNP:rs3824699). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AACCCTAGAAATTTTGGATGA	0.363													G|||	3319	0.66274	0.6929	0.6311	5008	,	,		17090	0.6181		0.7217	False		,,,				2504	0.6299				p.I348V		Atlas-SNP	.											.	MYO3A	371	.	0			c.A1042G						PASS	.	G	VAL/ILE	2996,1410	458.2+/-351.9	1009,978,216	76.0	70.0	72.0		1042	2.7	0.7	10	dbSNP_107	72	5881,2719	431.2+/-356.7	2037,1807,456	yes	missense	MYO3A	NM_017433.4	29	3046,2785,672	GG,GA,AA		31.6163,32.0018,31.7469	benign	348/1617	26355992	8877,4129	2203	4300	6503	SO:0001583	missense	53904	exon11			CTAGAAATTTTGG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1042A>G	10.37:g.26355992A>G	ENSP00000265944:p.Ile348Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	1455	0.6662087912087912	329	0.6686991869918699	223	0.6160220994475138	354	0.6188811188811189	549	0.7242744063324539	G	0.410	-0.913670	0.02415	0.679982	0.683837	ENSG00000095777	ENST00000265944;ENST00000543632	T;D	0.86956	-0.53;-2.19	5.56	2.73	0.32206	Myosin head, motor domain (2);	0.420315	0.27572	N	0.018770	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.45991	-0.9223	9	0.02654	T	1	.	9.6168	0.39696	0.2772:0.0:0.7228:0.0	rs3824699;rs60405423;rs3824699	348;348	F5H0U9;Q8NEV4	.;MYO3A_HUMAN	V	348	ENSP00000265944:I348V;ENSP00000445909:I348V	ENSP00000265944:I348V	I	+	1	0	MYO3A	26395998	1.000000	0.71417	0.708000	0.30435	0.733000	0.41908	2.019000	0.41001	0.067000	0.16545	-0.128000	0.14901	ATT	A|0.318;G|0.682	0.682	strong		0.363	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
MICA	100507436	hgsc.bcm.edu	37	6	31378928	31378928	+	Silent	SNP	C	C	T	rs41553614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31378928C>T	ENST00000449934.2	+	3	459	c.405C>T	c.(403-405)taC>taT	p.Y135Y	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				ATTTCTACTACGATGGGGAGC	0.552													c|||	77	0.0153754	0.0212	0.0245	5008	,	,		20471	0.003		0.0159	False		,,,				2504	0.0133				p.Y135Y		Atlas-SNP	.											.	MICA	21	.	0			c.C405T						PASS	.	C		38,1346		1,36,655	45.0	42.0	43.0		405	-3.0	0.0	6	dbSNP_127	43	49,3133		1,47,1543	no	coding-synonymous	MICA	NM_001177519.1		2,83,2198	TT,TC,CC		1.5399,2.7457,1.9054		135/333	31378928	87,4479	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon3			CTACTACGATGGG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.405C>T	6.37:g.31378928C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	221	113	0.511312	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.987;T|0.013	0.013	strong		0.552	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
PREX1	57580	hgsc.bcm.edu	37	20	47258763	47258763	+	Missense_Mutation	SNP	C	C	T	rs16993997	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:47258763C>T	ENST00000371941.3	-	29	3740	c.3718G>A	c.(3718-3720)Gtc>Atc	p.V1240I	PREX1_ENST00000496915.1_5'UTR|PREX1_ENST00000396220.1_Missense_Mutation_p.V1240I	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1240			V -> I (in dbSNP:rs16993997). {ECO:0000269|PubMed:17974005}.		actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CGGCTCATGACTGGCCCCTTG	0.582													.|||	755	0.150759	0.0182	0.2133	5008	,	,		16987	0.1528		0.1849	False		,,,				2504	0.2485				p.V1240I		Atlas-SNP	.											PREX1,NS,carcinoma,+2,1	PREX1	441	1	0			c.G3718A						PASS	.	C	ILE/VAL	251,4155	144.6+/-179.5	10,231,1962	91.0	87.0	88.0		3718	3.5	0.8	20	dbSNP_123	88	1623,6977	300.5+/-305.0	148,1327,2825	yes	missense	PREX1	NM_020820.3	29	158,1558,4787	TT,TC,CC		18.8721,5.6968,14.4087	benign	1240/1660	47258763	1874,11132	2203	4300	6503	SO:0001583	missense	57580	exon29			TCATGACTGGCCC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3718G>A	20.37:g.47258763C>T	ENSP00000361009:p.Val1240Ile	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	215	108	0.502326	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	313	0.1433150183150183	12	0.024390243902439025	81	0.22375690607734808	85	0.1486013986013986	135	0.17810026385224276	c	11.01	1.512329	0.27036	0.056968	0.188721	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.37235	1.21;1.21	5.4	3.47	0.39725	.	0.585620	0.14633	U	0.307705	T	0.00012	0.0000	N	0.17474	0.49	0.43334	P	0.0046279999999999655	B;B	0.12013	0.001;0.005	B;B	0.12837	0.003;0.008	T	0.15492	-1.0435	9	0.39692	T	0.17	.	10.6574	0.45684	0.0:0.7903:0.0:0.2097	rs16993997;rs16993997	1240;537	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	I	1240	ENSP00000361009:V1240I;ENSP00000379522:V1240I	ENSP00000361009:V1240I	V	-	1	0	PREX1	46692170	0.920000	0.31207	0.829000	0.32907	0.411000	0.31082	2.936000	0.48971	1.292000	0.44672	0.639000	0.83563	GTC	C|0.855;N|0.001	.	strong		0.582	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
C9orf72	203228	hgsc.bcm.edu	37	9	27556780	27556780	+	Silent	SNP	G	G	A	rs10122902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:27556780G>A	ENST00000380003.3	-	8	933	c.870C>T	c.(868-870)agC>agT	p.S290S	C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	290					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		GCAGCACAAAGCTTCCAGTTG	0.378													G|||	1134	0.226438	0.1513	0.2781	5008	,	,		20237	0.3016		0.162	False		,,,				2504	0.2802				p.S290S		Atlas-SNP	.											.	C9orf72	48	.	0			c.C870T						PASS	.	G		843,3563	333.1+/-302.8	79,685,1439	115.0	110.0	112.0		870	2.5	1.0	9	dbSNP_119	112	1709,6891	312.7+/-311.0	178,1353,2769	no	coding-synonymous	C9orf72	NM_018325.2		257,2038,4208	AA,AG,GG		19.8721,19.133,19.6217		290/482	27556780	2552,10454	2203	4300	6503	SO:0001819	synonymous_variant	203228	exon8			CACAAAGCTTCCA	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.870C>T	9.37:g.27556780G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	98	37	0.377551	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Silent	SNP	ENST00000380003.3	37	CCDS6522.1																																																																																			G|0.789;A|0.211	0.211	strong		0.378	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325	
TMEM129	92305	hgsc.bcm.edu	37	4	1719294	1719294	+	Silent	SNP	T	T	C	rs2236786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1719294T>C	ENST00000382936.3	-	3	1282	c.789A>G	c.(787-789)acA>acG	p.T263T	TMEM129_ENST00000303277.2_Intron|TMEM129_ENST00000536901.1_Silent_p.T263T	NM_001127266.1	NP_001120738.1	A0AVI4	TM129_HUMAN	transmembrane protein 129, E3 ubiquitin protein ligase	263					protein ubiquitination (GO:0016567)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			lung(2)	2			OV - Ovarian serous cystadenocarcinoma(23;0.00765)			GGGAGGCAAATGTCTCCAGGA	0.682													T|||	786	0.156949	0.0129	0.2651	5008	,	,		18069	0.1468		0.2137	False		,,,				2504	0.227				p.T263T		Atlas-SNP	.											.	TMEM129	10	.	0			c.A789G						PASS	.	T	,	48,1336		0,48,644	59.0	68.0	65.0		789,	-9.2	0.5	4	dbSNP_98	65	637,2545		57,523,1011	yes	coding-synonymous,intron	TMEM129	NM_001127266.1,NM_138385.3	,	57,571,1655	CC,CT,TT		20.0189,3.4682,15.0022	,	263/363,	1719294	685,3881	692	1591	2283	SO:0001819	synonymous_variant	92305	exon3			GGCAAATGTCTCC	BC009331	CCDS3351.1, CCDS46998.1	4p16.3	2014-07-25	2014-07-25		ENSG00000168936	ENSG00000168936			25137	protein-coding gene	gene with protein product		615975	"""transmembrane protein 129"""			24807418, 25030448	Standard	NM_138385		Approved	D4S2561E	uc003gdn.3	A0AVI4	OTTHUMG00000121150	ENST00000382936.3:c.789A>G	4.37:g.1719294T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_001127266	A6NH49|A6NI98|D3DVP8	Silent	SNP	ENST00000382936.3	37	CCDS46998.1																																																																																			T|0.851;C|0.149	0.149	strong		0.682	TMEM129-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350724.1	NM_138385	
XPO4	64328	hgsc.bcm.edu	37	13	21429874	21429874	+	Silent	SNP	T	T	C	rs61737207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:21429874T>C	ENST00000255305.6	-	4	419	c.348A>G	c.(346-348)ctA>ctG	p.L116L	XPO4_ENST00000490513.1_5'UTR|XPO4_ENST00000400602.2_Silent_p.L116L			Q9C0E2	XPO4_HUMAN	exportin 4	116					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		CTACTGCTAGTAGAATCTGTT	0.328													T|||	139	0.0277556	0.0318	0.0331	5008	,	,		16817	0.0		0.0447	False		,,,				2504	0.0297				p.L116L		Atlas-SNP	.											.	XPO4	153	.	0			c.A348G						PASS	.	T		92,3528		2,88,1720	126.0	116.0	119.0		348	-6.0	0.9	13	dbSNP_129	119	330,7824		7,316,3754	no	coding-synonymous	XPO4	NM_022459.4		9,404,5474	CC,CT,TT		4.0471,2.5414,3.5842		116/1152	21429874	422,11352	1810	4077	5887	SO:0001819	synonymous_variant	64328	exon4			TGCTAGTAGAATC	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"""Exportins"""	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.348A>G	13.37:g.21429874T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Silent	SNP	ENST00000255305.6	37	CCDS41872.1																																																																																			T|0.964;C|0.036	0.036	strong		0.328	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459	
STAB2	55576	hgsc.bcm.edu	37	12	104136316	104136316	+	Silent	SNP	C	C	T	rs2292688	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:104136316C>T	ENST00000388887.2	+	56	6219	c.6015C>T	c.(6013-6015)ttC>ttT	p.F2005F		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CGGGGAGATTCGGGCCTGATT	0.577													C|||	671	0.133986	0.0446	0.1787	5008	,	,		20976	0.252		0.0964	False		,,,				2504	0.1401				p.F2005F		Atlas-SNP	.											.	STAB2	370	.	0			c.C6015T						PASS	.	C		218,4188	134.1+/-170.4	6,206,1991	196.0	176.0	183.0		6015	0.7	1.0	12	dbSNP_100	183	865,7735	197.6+/-242.2	44,777,3479	no	coding-synonymous	STAB2	NM_017564.9		50,983,5470	TT,TC,CC		10.0581,4.9478,8.3269		2005/2552	104136316	1083,11923	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon56			GAGATTCGGGCCT	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.6015C>T	12.37:g.104136316C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	243	118	0.485597	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.892;T|0.108	0.108	strong		0.577	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
MDFI	4188	hgsc.bcm.edu	37	6	41621271	41621271	+	Silent	SNP	G	G	A	rs2230088	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41621271G>A	ENST00000373050.4	+	4	703	c.516G>A	c.(514-516)ctG>ctA	p.L172L				Q99750	MDFI_HUMAN	MyoD family inhibitor	233	Cys-rich.				activation of JUN kinase activity (GO:0007257)|cytoplasmic sequestering of transcription factor (GO:0042994)|dorsal/ventral axis specification (GO:0009950)|embryo development (GO:0009790)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|prostate(2)|skin(1)|urinary_tract(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.121)		Colorectal(64;0.0123)|COAD - Colon adenocarcinoma(64;0.0264)|KIRC - Kidney renal clear cell carcinoma(1;0.138)			CGGACTGCCTGGAGATCTGCA	0.667													G|||	326	0.0650958	0.0098	0.098	5008	,	,		16244	0.004		0.1471	False		,,,				2504	0.0951				p.L233L		Atlas-SNP	.											.	MDFI	19	.	0			c.G699A						PASS	.	G		168,4238	111.2+/-149.4	4,160,2039	90.0	91.0	91.0		699	3.1	1.0	6	dbSNP_98	91	1428,7172	274.1+/-291.0	128,1172,3000	no	coding-synonymous	MDFI	NM_005586.3		132,1332,5039	AA,AG,GG		16.6047,3.813,12.2713		233/247	41621271	1596,11410	2203	4300	6503	SO:0001819	synonymous_variant	4188	exon5			CTGCCTGGAGATC	U78313	CCDS4857.1, CCDS75451.1	6p21	2008-08-29			ENSG00000112559	ENSG00000112559			6967	protein-coding gene	gene with protein product	"""inhibitor of MyoD family a"""	604971				9250874, 17289077	Standard	NM_005586		Approved	I-mfa	uc003oqq.4	Q99750	OTTHUMG00000014681	ENST00000373050.4:c.516G>A	6.37:g.41621271G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_005586		Silent	SNP	ENST00000373050.4	37																																																																																				G|0.892;A|0.108	0.108	strong		0.667	MDFI-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000040519.2	NM_005586	
B3GNTL1	146712	hgsc.bcm.edu	37	17	80904844	80904844	+	Missense_Mutation	SNP	C	C	T	rs7225887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80904844C>T	ENST00000320865.3	-	12	1034	c.1021G>A	c.(1021-1023)Gcc>Acc	p.A341T	B3GNTL1_ENST00000576599.1_Missense_Mutation_p.A230T	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	341			A -> T (in dbSNP:rs7225887).				transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			TCCTCAAAGGCGCCCCCTGTG	0.622													C|||	781	0.15595	0.0582	0.2046	5008	,	,		14879	0.1577		0.2535	False		,,,				2504	0.1513				p.A341T		Atlas-SNP	.											B3GNTL1,NS,carcinoma,+2,1	B3GNTL1	40	1	0			c.G1021A						PASS	.	C	THR/ALA	319,4081		5,309,1886	56.0	47.0	50.0		1021	4.0	1.0	17	dbSNP_116	50	1806,6778		189,1428,2675	yes	missense	B3GNTL1	NM_001009905.1	58	194,1737,4561	TT,TC,CC		21.0391,7.25,16.3663	benign	341/362	80904844	2125,10859	2200	4292	6492	SO:0001583	missense	146712	exon12			CAAAGGCGCCCCC	AY634364	CCDS32778.1	17q25.3	2013-02-22	2004-01-13	2004-01-14	ENSG00000175711	ENSG00000175711		"""Glycosyltransferase family 2 domain containing"""	21727	protein-coding gene	gene with protein product		615337					Standard	NM_001009905		Approved	B3GNT8	uc002kgg.1	Q67FW5	OTTHUMG00000177788	ENST00000320865.3:c.1021G>A	17.37:g.80904844C>T	ENSP00000319979:p.Ala341Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_001009905	Q6GV30|Q8WUT3	Missense_Mutation	SNP	ENST00000320865.3	37	CCDS32778.1	380	0.17399267399267399	30	0.06097560975609756	76	0.20994475138121546	90	0.15734265734265734	184	0.24274406332453827	C	12.22	1.871294	0.33069	0.0725	0.210391	ENSG00000175711	ENST00000320865	T	0.41400	1.0	4.0	4.0	0.46444	.	0.419285	0.23201	N	0.050795	T	0.00012	0.0000	N	0.19112	0.55	0.36786	P	0.115429	B	0.15473	0.013	B	0.08055	0.003	T	0.17289	-1.0374	8	.	.	.	-14.9116	14.4067	0.67088	0.0:1.0:0.0:0.0	rs7225887;rs17344847;rs52802513;rs57810247;rs7225887	341	Q67FW5	B3GNL_HUMAN	T	341	ENSP00000319979:A341T	.	A	-	1	0	B3GNTL1	78498133	0.136000	0.22515	0.965000	0.40720	0.950000	0.60333	3.322000	0.52007	2.171000	0.68590	0.563000	0.77884	GCC	C|0.840;T|0.160	0.160	strong		0.622	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
FBXW5	54461	hgsc.bcm.edu	37	9	139838414	139838414	+	Missense_Mutation	SNP	C	C	T	rs200423543		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139838414C>T	ENST00000325285.3	-	2	201	c.122G>A	c.(121-123)cGg>cAg	p.R41Q	FBXW5_ENST00000483559.1_5'UTR|C8G_ENST00000224181.3_5'Flank	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	41	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GAACTCGTCCCGCGACACGGC	0.701																																					p.R41Q		Atlas-SNP	.											.	FBXW5	36	.	0			c.G122A						PASS	.		GLN/ARG	4,4272		0,4,2134	12.0	14.0	13.0		122	2.1	0.9	9		13	30,8458		0,30,4214	yes	missense	FBXW5	NM_018998.2	43	0,34,6348	TT,TC,CC		0.3534,0.0935,0.2664	probably-damaging	41/567	139838414	34,12730	2138	4244	6382	SO:0001583	missense	54461	exon2			TCGTCCCGCGACA	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13613	protein-coding gene	gene with protein product		609072	"""F-box and WD-40 domain protein 5"""				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.122G>A	9.37:g.139838414C>T	ENSP00000313034:p.Arg41Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	30	21	0.7	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	c	19.18	3.777882	0.70107	9.35E-4	0.003534	ENSG00000159069	ENST00000325285;ENST00000428398;ENST00000443788	T;T;T	0.66460	-0.21;-0.21;-0.21	4.02	2.08	0.27032	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.139015	0.47852	D	0.000201	T	0.67078	0.2855	L	0.35414	1.06	0.40830	D	0.983582	D	0.89917	1.0	D	0.68765	0.96	T	0.62334	-0.6876	10	0.33940	T	0.23	-1.4432	7.9151	0.29814	0.1841:0.6384:0.1775:0.0	.	41	Q969U6	FBXW5_HUMAN	Q	41	ENSP00000313034:R41Q;ENSP00000404829:R41Q;ENSP00000394011:R41Q	ENSP00000313034:R41Q	R	-	2	0	FBXW5	138958235	1.000000	0.71417	0.898000	0.35279	0.387000	0.30353	5.101000	0.64566	0.321000	0.23259	-0.529000	0.04317	CGG	.	.	weak		0.701	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
DROSHA	29102	hgsc.bcm.edu	37	5	31515657	31515657	+	Missense_Mutation	SNP	G	G	A	rs55656741	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:31515657G>A	ENST00000511367.2	-	6	1206	c.962C>T	c.(961-963)tCg>tTg	p.S321L	DROSHA_ENST00000344624.3_Missense_Mutation_p.S321L|DROSHA_ENST00000442743.1_Intron|DROSHA_ENST00000513349.1_Intron	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	321			S -> L (in dbSNP:rs55656741).		defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						aggaacaACCGATAAACCGTA	0.398													G|||	1412	0.281949	0.031	0.3559	5008	,	,		17973	0.1935		0.4513	False		,,,				2504	0.4857				p.S321L		Atlas-SNP	.											.	DROSHA	130	.	0			c.C962T						PASS	.	G	,LEU/SER	196,1682		10,176,753	27.0	30.0	29.0		,962	2.0	0.0	5	dbSNP_129	29	2054,2126		484,1086,520	yes	intron,missense	DROSHA	NM_001100412.1,NM_013235.4	,145	494,1262,1273	AA,AG,GG		49.1388,10.4366,37.141	,benign	,321/1375	31515657	2250,3808	939	2090	3029	SO:0001583	missense	29102	exon6			ACAACCGATAAAC	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.962C>T	5.37:g.31515657G>A	ENSP00000425979:p.Ser321Leu	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	611	0.27976190476190477	19	0.03861788617886179	137	0.3784530386740331	111	0.19405594405594406	344	0.45382585751978893	G	4.156	0.027468	0.08054	0.104366	0.491388	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000512302	T;T;T	0.44482	0.92;0.92;0.92	3.77	1.96	0.26148	.	1.219030	0.05901	N	0.629997	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	9	0.29301	T	0.29	3.4861	6.3598	0.21422	0.2284:0.0:0.7716:0.0	rs55656741;rs61748190	321	Q9NRR4	RNC_HUMAN	L	321;321;88	ENSP00000425979:S321L;ENSP00000339845:S321L;ENSP00000428782:S88L	ENSP00000339845:S321L	S	-	2	0	DROSHA	31551414	0.389000	0.25205	0.005000	0.12908	0.975000	0.68041	0.946000	0.29069	0.557000	0.29117	0.561000	0.74099	TCG	G|0.675;A|0.325	0.325	strong		0.398	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
AGR2	10551	hgsc.bcm.edu	37	7	16834597	16834597	+	Silent	SNP	A	A	G	rs6842	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:16834597A>G	ENST00000419304.2	-	7	593	c.441T>C	c.(439-441)aaT>aaC	p.N147N	AGR2_ENST00000419572.2_Silent_p.N167N|AGR2_ENST00000401412.1_Silent_p.N147N	NM_006408.3	NP_006399.1	O95994	AGR2_HUMAN	anterior gradient 2	147					lung goblet cell differentiation (GO:0060480)|mucus secretion (GO:0070254)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	dystroglycan binding (GO:0002162)			endometrium(2)|lung(1)|prostate(1)|skin(2)	6	Lung NSC(10;0.0376)|all_lung(11;0.0855)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		CATAGAGACGATTTGAATATC	0.418													A|||	1680	0.335463	0.1051	0.4957	5008	,	,		22739	0.2976		0.4672	False		,,,				2504	0.4366				p.N147N		Atlas-SNP	.											.	AGR2	14	.	0			c.T441C						PASS	.	A		733,3673	303.0+/-287.7	62,609,1532	150.0	120.0	130.0		441	-7.1	0.9	7	dbSNP_52	130	4273,4327	574.8+/-390.1	1044,2185,1071	no	coding-synonymous	AGR2	NM_006408.3		1106,2794,2603	GG,GA,AA		49.686,16.6364,38.4899		147/176	16834597	5006,8000	2203	4300	6503	SO:0001819	synonymous_variant	10551	exon7			GAGACGATTTGAA	AF038451	CCDS5364.1	7p21.3	2013-07-31	2013-07-31		ENSG00000106541	ENSG00000106541		"""Protein disulfide isomerases"""	328	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 17"""	606358	"""anterior gradient 2 homolog (Xenopus laevis)"""			9790916	Standard	NM_006408		Approved	XAG-2, HAG-2, AG2, PDIA17	uc003str.3	O95994	OTTHUMG00000023446	ENST00000419304.2:c.441T>C	7.37:g.16834597A>G		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	157	155	0.987261	NM_006408		Silent	SNP	ENST00000419304.2	37	CCDS5364.1																																																																																			T|0.132;G|0.313;C|0.057;A|0.498	0.313	strong		0.418	AGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207594.2	NM_006408	
CNTN6	27255	hgsc.bcm.edu	37	3	1424718	1424718	+	Silent	SNP	G	G	A	rs2291101	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:1424718G>A	ENST00000446702.2	+	18	2886	c.2259G>A	c.(2257-2259)gtG>gtA	p.V753V	CNTN6_ENST00000350110.2_Silent_p.V753V|CNTN6_ENST00000539053.1_Silent_p.V681V			Q9UQ52	CNTN6_HUMAN	contactin 6	753	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AGGAGAAAGTGTCATCTGTGG	0.453													A|||	2421	0.483427	0.3684	0.5476	5008	,	,		17324	0.6508		0.3917	False		,,,				2504	0.5153				p.V753V		Atlas-SNP	.											.	CNTN6	245	.	0			c.G2259A						PASS	.	A		1643,2763	660.5+/-400.7	293,1057,853	158.0	145.0	150.0		2259	-8.8	0.0	3	dbSNP_100	150	3654,4946	623.5+/-397.5	786,2082,1432	no	coding-synonymous	CNTN6	NM_014461.2		1079,3139,2285	AA,AG,GG		42.4884,37.2901,40.7274		753/1029	1424718	5297,7709	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon18			GAAAGTGTCATCT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2259G>A	3.37:g.1424718G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	201	96	0.477612	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			G|0.557;A|0.443	0.443	strong		0.453	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
PTPRQ	374462	hgsc.bcm.edu	37	12	80900397	80900397	+	Silent	SNP	C	C	G	rs12824064	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:80900397C>G	ENST00000266688.5	+	21	2493	c.2493C>G	c.(2491-2493)ctC>ctG	p.L831L				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	877	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						CTAGTACACTCAAAGGTGAAG	0.323													C|||	2306	0.460463	0.177	0.5764	5008	,	,		18892	0.3601		0.6451	False		,,,				2504	0.6748				p.L663L		Atlas-SNP	.											.	PTPRQ	119	.	0			c.C1989G						PASS	.	C		377,1007		60,257,375	152.0	138.0	142.0		2051	1.4	0.9	12	dbSNP_121	142	2115,1067		721,673,197	no	coding-synonymous	PTPRQ	NM_001145026.1		781,930,572	GG,GC,CC		33.5324,27.2399,45.4227		835/2300	80900397	2492,2074	692	1591	2283	SO:0001819	synonymous_variant	374462	exon13			TACACTCAAAGGT	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.2493C>G	12.37:g.80900397C>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001145026		Silent	SNP	ENST00000266688.5	37		966	0.4423076923076923	81	0.16463414634146342	193	0.5331491712707183	192	0.3356643356643357	500	0.6596306068601583	C	7.326	0.618031	0.14129	0.272399	0.664676	ENSG00000139304	ENST00000532722	.	.	.	5.44	1.37	0.22104	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.8721	0.05620	0.1715:0.3644:0.3202:0.144	rs12824064	.	.	.	X	532	.	.	S	+	2	0	PTPRQ	79424528	0.000000	0.05858	0.934000	0.37439	0.993000	0.82548	-1.699000	0.01906	0.319000	0.23209	0.591000	0.81541	TCA	C|0.556;G|0.444	0.444	strong		0.323	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
C1orf186	440712	hgsc.bcm.edu	37	1	206239403	206239403	+	Silent	SNP	C	C	T	rs28602496	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206239403C>T	ENST00000331555.5	-	6	1133	c.495G>A	c.(493-495)gcG>gcA	p.A165A		NM_001007544.1	NP_001007545.1	Q6ZWK4	CA186_HUMAN	chromosome 1 open reading frame 186	165						integral component of membrane (GO:0016021)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.0754)			GATCATATTCCGCTGGCTCAG	0.388													C|||	547	0.109225	0.1218	0.0764	5008	,	,		19829	0.0744		0.0626	False		,,,				2504	0.1994				p.A165A		Atlas-SNP	.											.	C1orf186	26	.	0			c.G495A						PASS	.	C		493,3913	228.1+/-243.1	28,437,1738	98.0	90.0	93.0		495	1.0	0.1	1	dbSNP_125	93	742,7858	179.3+/-228.5	44,654,3602	no	coding-synonymous	C1orf186	NM_001007544.1		72,1091,5340	TT,TC,CC		8.6279,11.1893,9.4956		165/173	206239403	1235,11771	2203	4300	6503	SO:0001819	synonymous_variant	440712	exon6			ATATTCCGCTGGC	AK122631	CCDS73014.1	1q32.1	2014-05-06			ENSG00000196533	ENSG00000263961			25341	protein-coding gene	gene with protein product							Standard	XM_005272738		Approved	FLJ16052	uc001hdt.2	Q6ZWK4	OTTHUMG00000184376	ENST00000331555.5:c.495G>A	1.37:g.206239403C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_001007544		Silent	SNP	ENST00000331555.5	37	CCDS30995.1																																																																																			C|0.907;T|0.093	0.093	strong		0.388	C1orf186-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088002.1	NM_001007544	
SCN8A	6334	hgsc.bcm.edu	37	12	52080965	52080965	+	Silent	SNP	C	C	T	rs4761829	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52080965C>T	ENST00000354534.6	+	5	754	c.576C>T	c.(574-576)gaC>gaT	p.D192D	SCN8A_ENST00000545061.1_Silent_p.D192D|SCN8A_ENST00000550891.1_Silent_p.D192D	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	192					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	TTTTACGGGACCCATGGAACT	0.418													T|||	3931	0.784944	0.6195	0.8948	5008	,	,		21327	0.994		0.8618	False		,,,				2504	0.636				p.D192D		Atlas-SNP	.											.	SCN8A	331	.	0			c.C576T						PASS	.	T	,	2588,1296		868,852,222	140.0	127.0	131.0		576,576	0.9	1.0	12	dbSNP_111	131	7177,1143		3082,1013,65	no	coding-synonymous,coding-synonymous	SCN8A	NM_001177984.1,NM_014191.2	,	3950,1865,287	TT,TC,CC		13.738,33.3677,19.9853	,	192/1940,192/1981	52080965	9765,2439	1942	4160	6102	SO:0001819	synonymous_variant	6334	exon5			ACGGGACCCATGG	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.576C>T	12.37:g.52080965C>T		Somatic	464	1	0.00215517		WXS	Illumina HiSeq	Phase_I	432	430	0.99537	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	37	CCDS44891.1																																																																																			C|0.176;T|0.824	0.824	strong		0.418	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
POU5F1	5460	hgsc.bcm.edu	37	6	31138107	31138107	+	Silent	SNP	G	G	A	rs1062630	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31138107G>A	ENST00000259915.8	-	1	363	c.291C>T	c.(289-291)ggC>ggT	p.G97G	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	97					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	CTCCTGCTTCGCCCTCAGGCT	0.672			T	EWSR1	sarcoma								G|||	847	0.169129	0.2678	0.1412	5008	,	,		15076	0.0377		0.2008	False		,,,				2504	0.1585				p.G97G		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	POU5F1,colon,carcinoma,0,2	POU5F1	25	2	0			c.C291T						PASS	.	G		809,2213		106,597,808	33.0	34.0	33.0		291	0.1	0.4	6	dbSNP_86	33	1252,4160		159,934,1613	no	coding-synonymous	POU5F1	NM_002701.4		265,1531,2421	AA,AG,GG		23.1338,26.7704,24.4368		97/361	31138107	2061,6373	1511	2706	4217	SO:0001819	synonymous_variant	5460	exon1			TGCTTCGCCCTCA	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.291C>T	6.37:g.31138107G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	157	155	0.987261	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Silent	SNP	ENST00000259915.8	37	CCDS34391.1																																																																																			G|0.784;A|0.216	0.216	strong		0.672	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
GPR111	222611	hgsc.bcm.edu	37	6	47646842	47646842	+	Missense_Mutation	SNP	A	A	G	rs6907125	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:47646842A>G	ENST00000296862.1	+	4	443	c.443A>G	c.(442-444)cAg>cGg	p.Q148R	GPR111_ENST00000507065.1_Missense_Mutation_p.Q80R|GPR111_ENST00000398742.2_Missense_Mutation_p.Q80R			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	148			Q -> R (in dbSNP:rs6907125).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GACACCTGCCAGACTCTTAAT	0.458													G|||	2589	0.516973	0.472	0.4366	5008	,	,		22238	0.3085		0.6272	False		,,,				2504	0.7362				p.Q80R		Atlas-SNP	.											.	GPR111	123	.	0			c.A239G						PASS	.	G	ARG/GLN	1885,2091		444,997,547	122.0	117.0	118.0		239	-1.8	0.0	6	dbSNP_116	118	5388,2946		1756,1876,535	yes	missense	GPR111	NM_153839.6	43	2200,2873,1082	GG,GA,AA		35.3492,47.4095,40.918	benign	80/643	47646842	7273,5037	1988	4167	6155	SO:0001583	missense	222611	exon5			CCTGCCAGACTCT	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.443A>G	6.37:g.47646842A>G	ENSP00000296862:p.Gln148Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	184	111	0.603261	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		1057	0.483974358974359	239	0.48577235772357724	178	0.49171270718232046	171	0.29895104895104896	469	0.6187335092348285	G	0.897	-0.723488	0.03158	0.474095	0.646508	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.35048	2.1;2.06;1.33	4.69	-1.76	0.08006	.	1.198910	0.06180	N	0.679354	T	0.03827	0.0108	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33343	-0.9872	9	0.38643	T	0.18	.	6.4296	0.21788	0.537:0.1727:0.2903:0.0	rs6907125;rs60689810;rs6907125	80;148	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	R	80;148;80	ENSP00000422934:Q80R;ENSP00000296862:Q148R;ENSP00000381727:Q80R	ENSP00000296862:Q148R	Q	+	2	0	GPR111	47754801	0.167000	0.22975	0.044000	0.18714	0.397000	0.30659	0.159000	0.16442	-0.415000	0.07484	-0.760000	0.03462	CAG	A|0.480;G|0.520	0.520	strong		0.458	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
KLHL32	114792	hgsc.bcm.edu	37	6	97562207	97562207	+	Silent	SNP	G	G	T	rs74787311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:97562207G>T	ENST00000369261.4	+	7	1539	c.1176G>T	c.(1174-1176)gtG>gtT	p.V392V	KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Silent_p.V323V|KLHL32_ENST00000536676.1_Silent_p.V356V	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	392										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		AGCATTTTGTGCTGGGTGCCA	0.542													G|||	92	0.0183706	0.0023	0.0375	5008	,	,		19608	0.001		0.0517	False		,,,				2504	0.0102				p.V392V		Atlas-SNP	.											.	KLHL32	85	.	0			c.G1176T						PASS	.	G		55,4349	52.3+/-87.9	1,53,2148	44.0	42.0	43.0		1176	2.5	1.0	6	dbSNP_132	43	590,8010	157.0+/-210.8	23,544,3733	no	coding-synonymous	KLHL32	NM_052904.3		24,597,5881	TT,TG,GG		6.8605,1.2489,4.96		392/621	97562207	645,12359	2202	4300	6502	SO:0001819	synonymous_variant	114792	exon7			TTTTGTGCTGGGT	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.1176G>T	6.37:g.97562207G>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	CCDS5038.1																																																																																			G|0.960;T|0.040	0.040	strong		0.542	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
MYPN	84665	hgsc.bcm.edu	37	10	69959242	69959242	+	Missense_Mutation	SNP	C	C	A	rs7079481	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:69959242C>A	ENST00000358913.5	+	17	3891	c.3403C>A	c.(3403-3405)Cca>Aca	p.P1135T	MYPN_ENST00000354393.2_Missense_Mutation_p.P860T|MYPN_ENST00000540630.1_Missense_Mutation_p.P1135T	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	1135	Ig-like 4.|Interaction with ACTN.		P -> T (in dbSNP:rs7079481). {ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						GCTCATTGACCCACTCACTCA	0.542													C|||	1704	0.340256	0.2163	0.402	5008	,	,		19149	0.2391		0.4841	False		,,,				2504	0.4202				p.P1135T		Atlas-SNP	.											.	MYPN	189	.	0			c.C3403A						PASS	.	C	THR/PRO	1163,3243	410.6+/-335.4	136,891,1176	126.0	102.0	110.0		3403	5.4	1.0	10	dbSNP_116	110	4116,4484	563.8+/-388.2	1033,2050,1217	yes	missense	MYPN	NM_032578.2	38	1169,2941,2393	AA,AC,CC		47.8605,26.3958,40.589	probably-damaging	1135/1321	69959242	5279,7727	2203	4300	6503	SO:0001583	missense	84665	exon17			ATTGACCCACTCA	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.3403C>A	10.37:g.69959242C>A	ENSP00000351790:p.Pro1135Thr	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	206	103	0.5	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	786	0.3598901098901099	117	0.23780487804878048	156	0.430939226519337	146	0.25524475524475526	367	0.4841688654353562	C	27.0	4.791076	0.90367	0.263958	0.478605	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.72394	-0.65;-0.65;-0.65	5.38	5.38	0.77491	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.35414	1.06	0.09310	P	0.999999999312082	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	T	0.44081	-0.9351	8	.	.	.	.	19.3311	0.94288	0.0:1.0:0.0:0.0	rs7079481;rs52819321;rs58442467;rs7079481	1135;860;1135	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	T	860;860;1135;1135	ENSP00000346369:P860T;ENSP00000351790:P1135T;ENSP00000441668:P1135T	.	P	+	1	0	MYPN	69629248	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	7.595000	0.82710	2.813000	0.96785	0.655000	0.94253	CCA	C|0.623;A|0.377	0.377	strong		0.542	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
NME8	51314	hgsc.bcm.edu	37	7	37934147	37934147	+	Silent	SNP	A	A	T	rs41276027|rs386712272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:37934147A>T	ENST00000199447.4	+	16	1851	c.1479A>T	c.(1477-1479)atA>atT	p.I493I	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Silent_p.I493I	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	493	NDK 3.		I -> T (in dbSNP:rs56128139). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										CTGAGCAAATAGAGAAAATTT	0.303													A|||	790	0.157748	0.0151	0.2291	5008	,	,		17450	0.1359		0.3419	False		,,,				2504	0.1329				p.I493I		Atlas-SNP	.											.	.	.	.	0			c.A1479T						PASS	.	A		2,4404		0,2,2201	59.0	61.0	61.0		1479	-3.0	0.0	7	dbSNP_127	61	47,8551		6,35,4258	no	coding-synonymous	TXNDC3	NM_016616.4		6,37,6459	TT,TA,AA		0.5466,0.0454,0.3768		493/589	37934147	49,12955	2203	4299	6502	SO:0001819	synonymous_variant	51314	exon16			GCAAATAGAGAAA	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1479A>T	7.37:g.37934147A>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	255	109	0.427451	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	37	CCDS5452.1																																																																																			A|0.761;T|0.239	0.239	strong		0.303	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
TREML2	79865	hgsc.bcm.edu	37	6	41166154	41166154	+	Missense_Mutation	SNP	G	G	C	rs77704965|rs35260020|rs71544266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41166154G>C	ENST00000483722.1	-	2	254	c.69C>G	c.(67-69)gaC>gaG	p.D23E		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	23	Ig-like V-type.			D -> G (in Ref. 5; AAI25080). {ECO:0000305}.	T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					TGTATACACTGTCAGCAGAGG	0.483													G|||	421	0.0840655	0.0091	0.0793	5008	,	,		21056	0.0843		0.1173	False		,,,				2504	0.1544				p.D23E		Atlas-SNP	.											.	TREML2	41	.	0			c.C69G						PASS	.	G	GLU/ASP	2,4404		1,0,2202	82.0	81.0	81.0		69	3.7	0.0	6	dbSNP_131	81	19,8571		9,1,4285	no	missense	TREML2	NM_024807.2	45	10,1,6487	CC,CG,GG		0.2212,0.0454,0.1616	benign	23/322	41166154	21,12975	2203	4295	6498	SO:0001583	missense	79865	exon2			TACACTGTCAGCA	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.69C>G	6.37:g.41166154G>C	ENSP00000418767:p.Asp23Glu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	125	0.05723443223443223	5	0.01016260162601626	32	0.08839779005524862	29	0.050699300699300696	59	0.07783641160949868	.	0.031	-1.332462	0.01298	4.54E-4	0.002212	ENSG00000112195	ENST00000483722	T	0.04119	3.7	4.55	3.67	0.42095	Immunoglobulin-like (1);	0.353337	0.23567	N	0.046784	T	0.00328	0.0010	N	0.00159	-1.955	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44360	-0.9333	10	0.02654	T	1	-4.7703	10.9551	0.47354	0.0:0.8056:0.1944:0.0	.	23	Q5T2D2	TRML2_HUMAN	E	23	ENSP00000418767:D23E	ENSP00000418767:D23E	D	-	3	2	TREML2	41274132	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.365000	0.20348	1.034000	0.39945	-0.256000	0.11100	GAC	G|0.956;C|0.044	0.044	strong		0.483	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
RGSL1	353299	hgsc.bcm.edu	37	1	182496829	182496829	+	Missense_Mutation	SNP	A	A	G	rs7535533	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:182496829A>G	ENST00000294854.8	+	11	2067	c.2047A>G	c.(2047-2049)Ata>Gta	p.I683V	RGSL1_ENST00000542961.1_Missense_Mutation_p.I718V|RGSL1_ENST00000456971.2_3'UTR	NM_001137669.1	NP_001131141.1	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1	683	RGS.			I -> V (in Ref. 6; BC121032/BC121033). {ECO:0000305}.	termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)				central_nervous_system(2)|skin(4)	6						GAAGATCAGTATAGAGACCAA	0.418													A|||	1563	0.312101	0.1914	0.2435	5008	,	,		20402	0.4315		0.3877	False		,,,				2504	0.3231				p.I683V	Ovarian(71;11 616 11292 12944 18021 32289 33994 41738 46526)	Atlas-SNP	.											.	RGSL1	111	.	0			c.A2047G						PASS	.	A	VAL/ILE	306,1078		39,228,425	98.0	84.0	88.0		2047	0.7	0.0	1	dbSNP_116	88	1180,2002		213,754,624	yes	missense	RGSL1	NM_001137669.1	29	252,982,1049	GG,GA,AA		37.0836,22.1098,32.5449	benign	683/1077	182496829	1486,3080	692	1591	2283	SO:0001583	missense	353299	exon11			ATCAGTATAGAGA	AF510428	CCDS58049.1	1q25	2013-04-02	2007-08-14		ENSG00000121446	ENSG00000121446			18636	protein-coding gene	gene with protein product		611012	"""regulator of G-protein signalling like 1"", ""regulator of G-protein signaling like 2"", ""regulator of G-protein signalling like 2"""	RGSL2		12801632	Standard	NM_001137669		Approved		uc009wxw.3	A5PLK6	OTTHUMG00000035217	ENST00000294854.8:c.2047A>G	1.37:g.182496829A>G	ENSP00000457748:p.Ile683Val	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	201	124	0.616915	NM_001137669	A2A2Z0|A6PVM2|A6PVM3|Q0VAJ4|Q0VAJ5|Q6ZRL0|Q86UV0|Q9H084	Missense_Mutation	SNP	ENST00000294854.8	37	CCDS58049.1																																																																																			A|0.661;G|0.339	0.339	strong		0.418	RGSL1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320710.3	NM_181572	
NRP1	8829	hgsc.bcm.edu	37	10	33474644	33474644	+	Silent	SNP	G	G	A	rs61760432	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:33474644G>A	ENST00000265371.4	-	16	2868	c.2343C>T	c.(2341-2343)ttC>ttT	p.F781F	NRP1_ENST00000374875.1_Silent_p.F593F|NRP1_ENST00000395995.1_Silent_p.F781F|NRP1_ENST00000374867.2_Silent_p.F781F			O14786	NRP1_HUMAN	neuropilin 1	781	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	TTTCGCCCTCGAAAATCACCT	0.393													G|||	95	0.0189696	0.0015	0.0346	5008	,	,		23197	0.001		0.0477	False		,,,				2504	0.0204				p.F781F	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.C2343T						PASS	.	G		32,4374	36.8+/-68.6	1,30,2172	94.0	85.0	88.0		2343	2.2	1.0	10	dbSNP_129	88	320,8280	113.1+/-173.2	7,306,3987	no	coding-synonymous	NRP1	NM_003873.5		8,336,6159	AA,AG,GG		3.7209,0.7263,2.7064		781/924	33474644	352,12654	2203	4300	6503	SO:0001819	synonymous_variant	8829	exon15			GCCCTCGAAAATC	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.2343C>T	10.37:g.33474644G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	178	78	0.438202	NM_003873	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	37	CCDS7177.1																																																																																			G|0.973;A|0.027	0.027	strong		0.393	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
CTTNBP2NL	55917	hgsc.bcm.edu	37	1	112999122	112999122	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:112999122T>C	ENST00000271277.6	+	6	1233	c.1008T>C	c.(1006-1008)ccT>ccC	p.P336P		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	336					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTGGGCTGCCTGGTCCTGCCA	0.478																																					p.P336P		Atlas-SNP	.											CTTNBP2NL,NS,carcinoma,+2,1	CTTNBP2NL	65	1	0			c.T1008C						scavenged	.						144.0	145.0	145.0					1																	112999122		2203	4300	6503	SO:0001819	synonymous_variant	55917	exon6			GCTGCCTGGTCCT	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.1008T>C	1.37:g.112999122T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	123	2	0.0162602	NM_018704	B3KMS5|Q96B40	Silent	SNP	ENST00000271277.6	37	CCDS845.1																																																																																			.	.	none		0.478	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704	
DNAH5	1767	hgsc.bcm.edu	37	5	13719022	13719022	+	Silent	SNP	T	T	G	rs30169	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13719022T>G	ENST00000265104.4	-	72	12572	c.12468A>C	c.(12466-12468)ggA>ggC	p.G4156G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4156	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTGCCCGGAGTCCTTGTGGAG	0.428									Kartagener syndrome				G|||	2099	0.419129	0.3858	0.4107	5008	,	,		17429	0.4405		0.3966	False		,,,				2504	0.4714				p.G4156G		Atlas-SNP	.											DNAH5,head_neck,malignant_melanoma,-2,1	DNAH5	868	1	0			c.A12468C						PASS	.	G		1713,2693	650.7+/-399.1	358,997,848	118.0	119.0	118.0		12468	2.8	1.0	5	dbSNP_76	118	3649,4951	623.3+/-397.4	759,2131,1410	no	coding-synonymous	DNAH5	NM_001369.2		1117,3128,2258	GG,GT,TT		42.4302,38.8788,41.2271		4156/4625	13719022	5362,7644	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon72	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCGGAGTCCTTGT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12468A>C	5.37:g.13719022T>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	251	131	0.521912	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.596;G|0.404	0.404	strong		0.428	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
HPR	3250	hgsc.bcm.edu	37	16	72110872	72110872	+	Silent	SNP	G	G	A	rs147707949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:72110872G>A	ENST00000540303.2	+	5	971	c.939G>A	c.(937-939)gcG>gcA	p.A313A	HPR_ENST00000356967.5_Silent_p.A313A|HPR_ENST00000228226.8_Silent_p.A350A|HPR_ENST00000561690.1_Missense_Mutation_p.G112S	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	313	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				CCTGGTACGCGGCTGGGATCC	0.547													G|||	8	0.00159744	0.0	0.0014	5008	,	,		25381	0.0		0.005	False		,,,				2504	0.002				p.A313A		Atlas-SNP	.											HPR,NS,carcinoma,+2,1	HPR	43	1	0			c.G939A						PASS	.	G		2,4190		0,2,2094	270.0	180.0	210.0		939	-0.2	1.0	16	dbSNP_134	210	21,8425		0,21,4202	no	coding-synonymous	HPR	NM_020995.3		0,23,6296	AA,AG,GG		0.2486,0.0477,0.182		313/349	72110872	23,12615	2096	4223	6319	SO:0001819	synonymous_variant	3250	exon5			GTACGCGGCTGGG	BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.939G>A	16.37:g.72110872G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	251	106	0.422311	NM_020995	Q7LE20|Q92658|Q92659|Q9ULB0	Silent	SNP	ENST00000540303.2	37	CCDS42193.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995	
BBS12	166379	hgsc.bcm.edu	37	4	123664204	123664204	+	Missense_Mutation	SNP	G	G	A	rs309370	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:123664204G>A	ENST00000314218.3	+	2	1350	c.1157G>A	c.(1156-1158)cGg>cAg	p.R386Q	BBS12_ENST00000542236.1_Missense_Mutation_p.R386Q	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	386			R -> Q (in dbSNP:rs309370). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						GATAGCATGCGGCTTCAAGAA	0.438									Bardet-Biedl syndrome				A|||	2536	0.50639	0.584	0.4726	5008	,	,		21101	0.6597		0.3191	False		,,,				2504	0.4601				p.R386Q		Atlas-SNP	.											.	BBS12	63	.	0			c.G1157A						PASS	.	A	GLN/ARG,GLN/ARG	2479,1927	548.5+/-377.6	698,1083,422	58.0	61.0	60.0		1157,1157	0.3	0.0	4	dbSNP_79	60	2903,5697	670.7+/-402.8	493,1917,1890	yes	missense,missense	BBS12	NM_001178007.1,NM_152618.2	43,43	1191,3000,2312	AA,AG,GG		33.7558,43.7358,41.3809	benign,benign	386/711,386/711	123664204	5382,7624	2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCATGCGGCTTCA	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1157G>A	4.37:g.123664204G>A	ENSP00000319062:p.Arg386Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	128	43	0.335938	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	1045	0.4784798534798535	272	0.5528455284552846	168	0.46408839779005523	362	0.6328671328671329	243	0.32058047493403696	A	3.101	-0.184690	0.06340	0.562642	0.337558	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.78924	-1.22;-1.22	5.68	0.337	0.15966	.	1.224000	0.05487	N	0.555912	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.41179	-0.9523	9	0.13470	T	0.59	-14.8675	2.2036	0.03930	0.3363:0.2377:0.3201:0.106	rs309370;rs17857449;rs52791731;rs56506272;rs59462913;rs309370	386	Q6ZW61	BBS12_HUMAN	Q	386	ENSP00000319062:R386Q;ENSP00000438273:R386Q	ENSP00000319062:R386Q	R	+	2	0	BBS12	123883654	0.000000	0.05858	0.000000	0.03702	0.390000	0.30446	-0.101000	0.10973	0.085000	0.17107	-0.269000	0.10298	CGG	G|0.542;A|0.458	0.458	strong		0.438	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
DMKN	93099	hgsc.bcm.edu	37	19	36002386	36002386	+	Missense_Mutation	SNP	C	C	T	rs56743379|rs117522133		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36002386C>T	ENST00000339686.3	-	5	1021	c.845G>A	c.(844-846)aGt>aAt	p.S282N	DMKN_ENST00000440396.1_Missense_Mutation_p.S282N|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.S282N|DMKN_ENST00000418261.1_Missense_Mutation_p.S282N|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.S282N|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.S282N	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	282	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			gctgccgccactgctgccgcc	0.632																																					p.S282N		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.G845A						PASS	.						26.0	20.0	22.0					19																	36002386		2190	4261	6451	SO:0001583	missense	93099	exon5			CCGCCACTGCTGC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.845G>A	19.37:g.36002386C>T	ENSP00000342012:p.Ser282Asn	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	79	22	0.278481	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	9.113	1.007164	0.19199	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	3.03	0.883	0.19177	.	1.984400	0.02204	N	0.062511	T	0.35098	0.0920	L	0.32530	0.975	0.09310	N	1	B;B;B;B;B	0.09022	0.002;0.002;0.002;0.002;0.001	B;B;B;B;B	0.10450	0.005;0.005;0.005;0.005;0.005	T	0.09862	-1.0655	10	0.12766	T	0.61	.	5.3636	0.16101	0.0:0.731:0.0:0.2689	.	282;282;282;282;282	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	N	282	ENSP00000342012:S282N;ENSP00000394908:S282N;ENSP00000415277:S282N;ENSP00000414743:S282N;ENSP00000388404:S282N;ENSP00000409513:S282N	ENSP00000342012:S282N	S	-	2	0	DMKN	40694226	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.157000	0.16402	0.352000	0.24053	-0.221000	0.12465	AGT	.	.	weak		0.632	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
HNF1A	6927	hgsc.bcm.edu	37	12	121437114	121437114	+	Silent	SNP	G	G	A	rs55834942	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	HNF1A_ENST00000541395.1_Silent_p.T515T|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Silent_p.T515T			P20823	HNF1A_HUMAN	HNF1 homeobox A	515					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACACCCACACGGGCCTGCTCC	0.677									Hepatic Adenoma, Familial Clustering of				.|||	315	0.0628994	0.0121	0.1095	5008	,	,		16172	0.001		0.1988	False		,,,				2504	0.0225				p.T515T		Atlas-SNP	.											HNF1A,brain,glioma,0,4	HNF1A	302	4	0			c.G1545A						PASS	.	G		175,4231	113.3+/-151.4	4,167,2032	68.0	70.0	70.0		1545	-7.7	0.9	12	dbSNP_129	70	1654,6944	303.3+/-306.4	156,1342,2801	yes	coding-synonymous	HNF1A	NM_000545.5		160,1509,4833	AA,AG,GG		19.237,3.9719,14.0649		515/632	121437114	1829,11175	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCACACGGGCCTG	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1545G>A	12.37:g.121437114G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	207	112	0.541063	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.860;A|0.140	0.140	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
MUC4	4585	hgsc.bcm.edu	37	3	195511403	195511403	+	Missense_Mutation	SNP	C	C	T	rs78846267|rs71627021		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195511403C>T	ENST00000463781.3	-	2	7507	c.7048G>A	c.(7048-7050)Gcc>Acc	p.A2350T	MUC4_ENST00000475231.1_Missense_Mutation_p.A2350T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.587																																					p.A2350T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G7048A						scavenged	.						11.0	12.0	12.0					3																	195511403		651	1555	2206	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7048G>A	3.37:g.195511403C>T	ENSP00000417498:p.Ala2350Thr	Somatic	164	7	0.0426829		WXS	Illumina HiSeq	Phase_I	269	56	0.208178	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	C	5.465	0.270947	0.10349	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.46;1.47	.	.	.	.	.	.	.	.	T	0.11665	0.0284	N	0.19112	0.55	0.09310	N	1	P	0.52463	0.953	B	0.34536	0.185	T	0.16512	-1.0400	7	.	.	.	.	2.1665	0.03838	0.3282:0.3412:0.3306:0.0	.	2350	E7ESK3	.	T	2350	ENSP00000417498:A2350T;ENSP00000420243:A2350T	.	A	-	1	0	MUC4	196995798	0.000000	0.05858	0.017000	0.16124	0.071000	0.16799	-2.347000	0.01095	-0.833000	0.04245	0.064000	0.15345	GCC	C|0.995;T|0.005	0.005	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CFP	5199	hgsc.bcm.edu	37	X	47483800	47483800	+	Silent	SNP	G	G	A	rs1048118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:47483800G>A	ENST00000396992.3	-	9	1404	c.1284C>T	c.(1282-1284)aaC>aaT	p.N428N	CFP_ENST00000247153.3_Silent_p.N428N	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin	428	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						AGAAGGTCACGTTCTTCTCGC	0.582													G|||	781	0.206887	0.205	0.1801	3775	,	,		12485	0.0169		0.1759	False		,,,				2504	0.1953				p.N428N		Atlas-SNP	.											.	CFP	43	.	0			c.C1284T						PASS	.	G	,	892,2943		76,596,144,960,427	174.0	113.0	134.0		1284,1284	-10.6	0.3	X	dbSNP_86	134	1624,5104		149,922,404,1357,1468	no	coding-synonymous,coding-synonymous	CFP	NM_001145252.1,NM_002621.2	,	225,1518,548,2317,1895	AA,AG,A,GG,G		24.1379,23.2595,23.819	,	428/470,428/470	47483800	2516,8047	2203	4300	6503	SO:0001819	synonymous_variant	5199	exon9			GGTCACGTTCTTC	M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"""Complement system"""	8864	protein-coding gene	gene with protein product		300383	"""properdin P factor, complement"""	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.1284C>T	X.37:g.47483800G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_001145252	O15134|O15135|O15136|O75826	Silent	SNP	ENST00000396992.3	37	CCDS14282.1																																																																																			G|0.777;0|0.004	.	strong		0.582	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056435.2	NM_002621	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383137	41383137	+	Silent	SNP	C	C	T	rs148915421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41383137C>T	ENST00000301146.4	-	7	1660	c.1119G>A	c.(1117-1119)agG>agA	p.R373R	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Silent_p.R322R	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	373						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTTTTTAACCCTGCGGGCCA	0.542													.|||	59	0.0117812	0.0	0.0144	5008	,	,		18858	0.002		0.0457	False		,,,				2504	0.001				p.R373R		Atlas-SNP	.											CYP2A7,NS,carcinoma,-1,1	CYP2A7	71	1	0			c.G1119A						PASS	.	C	,	23,4383	28.1+/-56.4	0,23,2180	103.0	91.0	95.0		1119,966	-1.3	0.0	19	dbSNP_134	95	283,8315	98.8+/-160.4	14,255,4030	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	14,278,6210	TT,TC,CC		3.2915,0.522,2.3531	,	373/495,322/444	41383137	306,12698	2203	4299	6502	SO:0001819	synonymous_variant	1549	exon7			TTTAACCCTGCGG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1119G>A	19.37:g.41383137C>T		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	258	115	0.445736	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			C|0.978;T|0.022	0.022	strong		0.542	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
MYO7A	4647	hgsc.bcm.edu	37	11	76895787	76895787	+	Intron	SNP	G	G	A	rs111033223|rs143953991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76895787G>A	ENST00000409709.3	+	27	3775				MYO7A_ENST00000458637.2_Intron|MYO7A_ENST00000409893.1_Missense_Mutation_p.R1177K|MYO7A_ENST00000409619.2_Intron	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA						actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GGGGACACCAGGGCCTGAAAG	0.602																																					p.R1177K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G3530A						PASS	.						13.0	15.0	14.0					11																	76895787		1872	3718	5590	SO:0001627	intron_variant	4647	exon27			ACACCAGGGCCTG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.3503+27G>A	11.37:g.76895787G>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	.	1.085	-0.665772	0.03428	.	.	ENSG00000137474	ENST00000409893	D	0.87729	-2.29	4.38	0.879	0.19155	.	.	.	.	.	T	0.68705	0.3030	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53851	-0.8380	8	.	.	.	.	3.7783	0.08669	0.2584:0.0:0.5575:0.1841	.	1177	B9A012	.	K	1177	ENSP00000386689:R1177K	.	R	+	2	0	MYO7A	76573435	0.001000	0.12720	0.009000	0.14445	0.011000	0.07611	0.416000	0.21198	0.304000	0.22809	-0.452000	0.05504	AGG	.	.	none		0.602	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
AIRE	326	hgsc.bcm.edu	37	21	45709568	45709568	+	Silent	SNP	C	C	T	rs1055311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45709568C>T	ENST00000291582.5	+	6	808	c.681C>T	c.(679-681)ggC>ggT	p.G227G	AIRE_ENST00000329347.4_5'Flank|AIRE_ENST00000355347.4_5'Flank	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	227	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		TCCAGGTTGGCGGGGAGTTCT	0.647									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				T|||	589	0.117612	0.0182	0.2248	5008	,	,		15544	0.005		0.2624	False		,,,				2504	0.1431				p.G227G		Atlas-SNP	.											.	AIRE	61	.	0			c.C681T						PASS	.	T		260,4146	783.2+/-414.6	5,250,1948	46.0	52.0	50.0		681	-3.1	0.6	21	dbSNP_86	50	2368,6230	690.4+/-404.4	338,1692,2269	no	coding-synonymous	AIRE	NM_000383.2		343,1942,4217	TT,TC,CC		27.5413,5.901,20.2092		227/546	45709568	2628,10376	2203	4299	6502	SO:0001819	synonymous_variant	326	exon6	Familial Cancer Database	APECED	GGTTGGCGGGGAG	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.681C>T	21.37:g.45709568C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	243	131	0.539095	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			C|0.833;T|0.167	0.167	strong		0.647	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
OR52H1	390067	hgsc.bcm.edu	37	11	5566112	5566112	+	Silent	SNP	C	C	T	rs1995156	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5566112C>T	ENST00000322653.4	-	1	667	c.642G>A	c.(640-642)acG>acA	p.T214T	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGAGATGACCGTCATGATGG	0.507													C|||	1924	0.384185	0.4614	0.5115	5008	,	,		24204	0.0853		0.5775	False		,,,				2504	0.2986				p.T214T		Atlas-SNP	.											.	OR52H1	46	.	0			c.G642A						PASS	.	C		2006,2396	560.0+/-380.4	473,1060,668	126.0	99.0	108.0		642	-10.7	0.1	11	dbSNP_92	108	5204,3390	640.2+/-399.6	1569,2066,662	no	coding-synonymous	OR52H1	NM_001005289.1		2042,3126,1330	TT,TC,CC		39.4461,45.5702,44.5214		214/321	5566112	7210,5786	2201	4297	6498	SO:0001819	synonymous_variant	390067	exon1			GATGACCGTCATG	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.642G>A	11.37:g.5566112C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_001005289	B9EH26|Q6IF79	Silent	SNP	ENST00000322653.4	37	CCDS31386.1																																																																																			C|0.517;T|0.483	0.483	strong		0.507	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
OR2A4	79541	hgsc.bcm.edu	37	6	132022419	132022419	+	Silent	SNP	G	G	A	rs201739285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:132022419G>A	ENST00000315453.2	-	1	216	c.123C>T	c.(121-123)aaC>aaT	p.N41N	ENPP3_ENST00000358229.5_Intron|ENPP3_ENST00000414305.1_Intron|ENPP3_ENST00000357639.3_Intron	NM_030908.1	NP_112170.1	O95047	OR2A4_HUMAN	olfactory receptor, family 2, subfamily A, member 4	41					positive regulation of cytokinesis (GO:0032467)|regulation of actin cytoskeleton organization (GO:0032956)	cleavage furrow (GO:0032154)|Flemming body (GO:0090543)|integral component of membrane (GO:0016021)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|ovary(1)|skin(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.018)|OV - Ovarian serous cystadenocarcinoma(155;0.041)		GTATGGTCCCGTTCCCCAGCA	0.577													g|||	1500	0.299521	0.5182	0.2291	5008	,	,		24864	0.3224		0.1024	False		,,,				2504	0.2331				p.N41N		Atlas-SNP	.											OR2A4,NS,carcinoma,0,1	OR2A4	17	1	0			c.C123T						scavenged	.						16.0	18.0	17.0					6																	132022419		2137	4202	6339	SO:0001819	synonymous_variant	79541	exon1			GGTCCCGTTCCCC	AC005587	CCDS5149.1	6q23	2012-08-09	2003-05-22		ENSG00000180658	ENSG00000180658		"""GPCR / Class A : Olfactory receptors"""	14729	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 10"""	OR2A10			Standard	NM_030908		Approved		uc011ecd.2	O95047	OTTHUMG00000016316	ENST00000315453.2:c.123C>T	6.37:g.132022419G>A		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	167	26	0.155689	NM_030908	Q0VAR3|Q6IF18|Q9NQN0	Silent	SNP	ENST00000315453.2	37	CCDS5149.1																																																																																			.	.	weak		0.577	OR2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109221.1	NM_030908	
KIF16B	55614	hgsc.bcm.edu	37	20	16486698	16486698	+	Silent	SNP	G	G	A	rs2295115	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:16486698G>A	ENST00000354981.2	-	8	994	c.837C>T	c.(835-837)ctC>ctT	p.L279L	KIF16B_ENST00000408042.1_Silent_p.L279L|KIF16B_ENST00000355755.3_Silent_p.L279L|KIF16B_ENST00000378003.2_5'UTR	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	279	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CCAGAGTCACGAGGGACTTGT	0.512													G|||	1206	0.240815	0.0582	0.2839	5008	,	,		16869	0.38		0.2843	False		,,,				2504	0.2689				p.L279L		Atlas-SNP	.											.	KIF16B	305	.	0			c.C837T						PASS	.	G	,,	458,3948	218.1+/-236.3	28,402,1773	114.0	106.0	109.0		837,837,837	-1.3	1.0	20	dbSNP_100	109	2639,5961	425.5+/-355.0	384,1871,2045	no	coding-synonymous,coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	,,	412,2273,3818	AA,AG,GG		30.686,10.3949,23.8121	,,	279/1267,279/1393,279/1318	16486698	3097,9909	2203	4300	6503	SO:0001819	synonymous_variant	55614	exon8			AGTCACGAGGGAC	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.837C>T	20.37:g.16486698G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			G|0.760;A|0.240	0.240	strong		0.512	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
C21orf58	54058	hgsc.bcm.edu	37	21	47734659	47734659	+	Missense_Mutation	SNP	G	G	A	rs13047478	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47734659G>A	ENST00000291691.7	-	5	1716	c.580C>T	c.(580-582)Cca>Tca	p.P194S	C21orf58_ENST00000397683.1_Missense_Mutation_p.P88S|C21orf58_ENST00000397682.3_Missense_Mutation_p.P88S|C21orf58_ENST00000397679.1_Missense_Mutation_p.P88S|C21orf58_ENST00000397680.1_Missense_Mutation_p.P88S	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	194										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		GGCGGGTCTGGGGCCAGCGGG	0.657													G|||	1442	0.287939	0.1263	0.4409	5008	,	,		14807	0.3115		0.33	False		,,,				2504	0.3303				p.P194S		Atlas-SNP	.											.	C21orf58	25	.	0			c.C580T						PASS	.	G	SER/PRO	649,3555		54,541,1507	16.0	15.0	15.0		580	4.7	0.1	21	dbSNP_121	15	2687,5655		448,1791,1932	yes	missense	C21orf58	NM_058180.3	74	502,2332,3439	AA,AG,GG		32.2105,15.4377,26.5901	benign	194/323	47734659	3336,9210	2102	4171	6273	SO:0001583	missense	54058	exon5			GGTCTGGGGCCAG		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.580C>T	21.37:g.47734659G>A	ENSP00000291691:p.Pro194Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	95	92	0.968421	NM_058180	B3KPI1	Missense_Mutation	SNP	ENST00000291691.7	37	CCDS13735.1	625	0.28617216117216115	67	0.13617886178861788	154	0.425414364640884	160	0.27972027972027974	244	0.32189973614775724	G	16.55	3.155161	0.57259	0.154377	0.322105	ENSG00000160298	ENST00000397683;ENST00000417060;ENST00000397682;ENST00000291691;ENST00000397679;ENST00000397680	T;T;T;T;T;T	0.60171	0.65;0.21;0.65;0.21;0.65;0.65	4.68	4.68	0.58851	.	0.162937	0.39475	N	0.001354	T	0.00012	0.0000	L	0.38175	1.15	0.09310	P	0.9999999999999938	D;D;D	0.67145	0.996;0.996;0.989	P;P;P	0.62813	0.848;0.907;0.848	T	0.42068	-0.9473	9	0.66056	D	0.02	-5.0994	13.4601	0.61223	0.0:0.0:1.0:0.0	rs13047478	194;88;194	P58505;Q8N7N9;P58505-2	CU058_HUMAN;.;.	S	88;156;88;194;88;88	ENSP00000380799:P88S;ENSP00000402356:P156S;ENSP00000380798:P88S;ENSP00000291691:P194S;ENSP00000380796:P88S;ENSP00000380797:P88S	ENSP00000291691:P194S	P	-	1	0	C21orf58	46559087	0.118000	0.22208	0.141000	0.22245	0.007000	0.05969	0.807000	0.27140	2.317000	0.78254	0.563000	0.77884	CCA	G|0.726;A|0.274	0.274	strong		0.657	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180	
MADCAM1	8174	hgsc.bcm.edu	37	19	501767	501767	+	Missense_Mutation	SNP	C	C	T	rs78245161		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:501767C>T	ENST00000215637.3	+	4	812	c.766C>T	c.(766-768)Cct>Tct	p.P256S	MADCAM1_ENST00000587541.1_Missense_Mutation_p.P37S|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	256	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCCAGGAGCCTCCCGACAC	0.726																																					p.P256S		Atlas-SNP	.											MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	0			c.C766T						PASS	.						31.0	35.0	33.0					19																	501767		2194	4286	6480	SO:0001583	missense	8174	exon4			CAGGAGCCTCCCG	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.766C>T	19.37:g.501767C>T	ENSP00000215637:p.Pro256Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	215	47	0.218605	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	c	5.207	0.223693	0.09863	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.09538	2.97	2.86	2.86	0.33363	.	.	.	.	.	T	0.06188	0.0160	N	0.12182	0.205	0.54753	D	0.999986	D	0.63046	0.992	P	0.45577	0.486	T	0.38045	-0.9679	9	0.08837	T	0.75	.	9.9622	0.41704	0.0:1.0:0.0:0.0	.	256	Q13477	MADCA_HUMAN	S	280;272;264;256	ENSP00000215637:P256S	ENSP00000215637:P256S	P	+	1	0	MADCAM1	452767	0.000000	0.05858	0.008000	0.14137	0.003000	0.03518	-0.228000	0.09114	1.548000	0.49413	0.638000	0.83543	CCT	C|0.500;T|0.500	0.500	weak		0.726	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
BTG2	7832	hgsc.bcm.edu	37	1	203274867	203274867	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:203274867G>T	ENST00000290551.4	+	1	204	c.133G>T	c.(133-135)Gca>Tca	p.A45S	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	45					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A45T(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTCCAGGAGGCACTCACAGG	0.706																																					p.A45S		Atlas-SNP	.											BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G133T						PASS	.						11.0	13.0	13.0					1																	203274867		2020	3950	5970	SO:0001583	missense	7832	exon1			CAGGAGGCACTCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"""B-cell translocation gene 2"", ""pheochromacytoma cell-3"", ""NGF-inducible anti-proliferative protein PC3"", ""nerve growth factor-inducible anti-proliferative"""	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.133G>T	1.37:g.203274867G>T	ENSP00000290551:p.Ala45Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	87	11	0.126437	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877798	0.51801	.	.	ENSG00000159388	ENST00000290551	T	0.23754	1.89	4.4	4.4	0.53042	Anti-proliferative protein (3);	0.078518	0.49916	D	0.000121	T	0.28928	0.0718	L	0.43152	1.355	0.43417	D	0.995564	B	0.15930	0.015	B	0.33521	0.165	T	0.09907	-1.0653	10	0.40728	T	0.16	-33.413	15.7078	0.77598	0.0:0.0:1.0:0.0	.	45	P78543	BTG2_HUMAN	S	45	ENSP00000290551:A45S	ENSP00000290551:A45S	A	+	1	0	BTG2	201541490	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.326000	0.59241	2.282000	0.76494	0.471000	0.43371	GCA	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
CKAP4	10970	hgsc.bcm.edu	37	12	106633569	106633569	+	Missense_Mutation	SNP	C	C	T	rs3088113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:106633569C>T	ENST00000378026.4	-	2	1178	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	CKAP4_ENST00000552828.1_5'Flank	NM_006825.3	NP_006816.2	Q07065	CKAP4_HUMAN	cytoskeleton-associated protein 4	348			A -> T (in dbSNP:rs3088113).			cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|pancreas(1)|urinary_tract(1)	20						GCCTGCAGGGCGAGCCGCTCC	0.637													C|||	1098	0.219249	0.0673	0.1513	5008	,	,		15611	0.5466		0.1372	False		,,,				2504	0.2198				p.A348T		Atlas-SNP	.											CKAP4,NS,carcinoma,+1,1	CKAP4	49	1	0			c.G1042A						PASS	.						23.0	25.0	24.0					12																	106633569		2203	4300	6503	SO:0001583	missense	10970	exon2			GCAGGGCGAGCCG	X69910	CCDS9103.1	12q23.3	2006-06-23				ENSG00000136026			16991	protein-coding gene	gene with protein product						8314870	Standard	NM_006825		Approved	P63, CLIMP-63, ERGIC-63	uc001tlk.3	Q07065		ENST00000378026.4:c.1042G>A	12.37:g.106633569C>T	ENSP00000367265:p.Ala348Thr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_006825	Q504S5|Q53ES6	Missense_Mutation	SNP	ENST00000378026.4	37	CCDS9103.1	511	0.23397435897435898	33	0.06707317073170732	53	0.1464088397790055	319	0.5576923076923077	106	0.13984168865435356	C	3.634	-0.074948	0.07184	.	.	ENSG00000136026	ENST00000378026	T	0.41758	0.99	5.82	4.79	0.61399	.	0.409690	0.28583	N	0.014839	T	0.00012	0.0000	N	0.11818	0.18	0.80722	P	0.0	B	0.15473	0.013	B	0.12156	0.007	T	0.46871	-0.9160	9	0.11182	T	0.66	-23.6109	2.5991	0.04862	0.3354:0.168:0.0:0.4965	rs3088113	348	Q07065	CKAP4_HUMAN	T	348	ENSP00000367265:A348T	ENSP00000367265:A348T	A	-	1	0	CKAP4	105157699	0.958000	0.32768	0.539000	0.28077	0.994000	0.84299	1.568000	0.36418	1.248000	0.43934	0.563000	0.77884	GCC	T|0.218;G|0.001;C|0.780	0.218	strong		0.637	CKAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407196.1		
PML	5371	hgsc.bcm.edu	37	15	74336633	74336633	+	Missense_Mutation	SNP	T	T	C	rs5742915	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:74336633T>C	ENST00000268058.3	+	9	2029	c.1933T>C	c.(1933-1935)Ttc>Ctc	p.F645L	PML_ENST00000565898.1_Missense_Mutation_p.F597L	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	645			F -> L (in dbSNP:rs5742915). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:1720570}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						GCCTGAAGCCTTCTTCAGCAT	0.602			T	"""RARA, PAX5"""	"""APL, ALL"""								T|||	963	0.192292	0.0454	0.2911	5008	,	,		18031	0.004		0.4384	False		,,,				2504	0.2618				p.F645L		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.T1933C						PASS	.	T	LEU/PHE	467,3929	221.7+/-238.7	25,417,1756	73.0	69.0	71.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1933	-3.3	0.0	15	dbSNP_114	71	3970,4624	549.1+/-385.5	921,2128,1248	yes	missense	PML	NM_033238.2	22	946,2545,3004	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	46.195,10.6233,34.157	benign	645/883	74336633	4437,8553	2198	4297	6495	SO:0001583	missense	5371	exon9			GAAGCCTTCTTCA	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1933T>C	15.37:g.74336633T>C	ENSP00000268058:p.Phe645Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_033238	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	37	CCDS10255.1	494	0.2261904761904762	26	0.052845528455284556	129	0.356353591160221	2	0.0034965034965034965	337	0.4445910290237467	T	3.535	-0.094924	0.07010	0.106233	0.46195	ENSG00000140464	ENST00000268058;ENST00000417341;ENST00000418568	T	0.41065	1.01	3.24	-3.26	0.05064	.	2.331610	0.02379	U	0.078638	T	0.00012	0.0000	N	0.08118	0	0.38303	P	0.056952	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.35724	-0.9777	9	0.02654	T	1	-0.5428	5.6012	0.17355	0.0:0.18:0.6082:0.2118	rs5742915;rs59256395;rs5742915	645;597	P29590;P29590-11	PML_HUMAN;.	L	645;206;645	ENSP00000268058:F645L	ENSP00000268058:F645L	F	+	1	0	PML	72123686	0.000000	0.05858	0.047000	0.18901	0.665000	0.39181	-0.220000	0.09215	-0.543000	0.06240	0.482000	0.46254	TTC	T|0.714;C|0.286	0.286	strong		0.602	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
RNMTL1	55178	hgsc.bcm.edu	37	17	695061	695061	+	Missense_Mutation	SNP	G	G	A	rs75658007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:695061G>A	ENST00000304478.4	+	4	1121	c.1015G>A	c.(1015-1017)Gtt>Att	p.V339I	RP11-676J12.8_ENST00000574560.1_RNA	NM_018146.2	NP_060616.1			RNA methyltransferase like 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)		TCATGTTGAGGTTCAGAGTTA	0.567													G|||	93	0.0185703	0.0008	0.0086	5008	,	,		19668	0.0446		0.0179	False		,,,				2504	0.0235				p.V339I		Atlas-SNP	.											.	RNMTL1	25	.	0			c.G1015A						PASS	.	G	ILE/VAL	11,4395	17.9+/-39.9	0,11,2192	63.0	65.0	64.0		1015	4.8	1.0	17	dbSNP_132	64	179,8421	81.5+/-144.1	4,171,4125	yes	missense	RNMTL1	NM_018146.2	29	4,182,6317	AA,AG,GG		2.0814,0.2497,1.4609	benign	339/421	695061	190,12816	2203	4300	6503	SO:0001583	missense	55178	exon4			GTTGAGGTTCAGA	AF177344	CCDS10997.1	17p13.3	2008-02-05			ENSG00000171861	ENSG00000171861			18485	protein-coding gene	gene with protein product		612600				12296377	Standard	NM_018146		Approved	FLJ10581, HC90	uc002frw.3	Q9HC36	OTTHUMG00000090285	ENST00000304478.4:c.1015G>A	17.37:g.695061G>A	ENSP00000306080:p.Val339Ile	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	106	64	0.603774	NM_018146		Missense_Mutation	SNP	ENST00000304478.4	37	CCDS10997.1	42	0.019230769230769232	1	0.0020325203252032522	3	0.008287292817679558	22	0.038461538461538464	16	0.021108179419525065	G	12.19	1.864312	0.32977	0.002497	0.020814	ENSG00000171861	ENST00000304478	T	0.18960	2.18	5.81	4.78	0.61160	tRNA/rRNA methyltransferase, SpoU (1);	0.417730	0.28214	N	0.016176	T	0.07638	0.0192	L	0.58510	1.815	0.29868	N	0.827053	B	0.25486	0.127	B	0.37989	0.262	T	0.02966	-1.1088	10	0.28530	T	0.3	-22.3486	15.4686	0.75422	0.0:0.1387:0.8613:0.0	.	339	Q9HC36	RMTL1_HUMAN	I	339	ENSP00000306080:V339I	ENSP00000306080:V339I	V	+	1	0	RNMTL1	641811	0.842000	0.29525	0.998000	0.56505	0.428000	0.31595	1.507000	0.35758	2.741000	0.93983	0.591000	0.81541	GTT	G|0.984;A|0.016	0.016	strong		0.567	RNMTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206611.1	NM_018146	
CDHR3	222256	hgsc.bcm.edu	37	7	105615426	105615426	+	Missense_Mutation	SNP	G	G	C	rs34426483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:105615426G>C	ENST00000317716.9	+	2	263	c.183G>C	c.(181-183)caG>caC	p.Q61H	CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000542731.1_Missense_Mutation_p.Q61H|CDHR3_ENST00000541203.1_Missense_Mutation_p.Q61H|CDHR3_ENST00000478080.1_Intron|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> H (in dbSNP:rs34426483).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						GATTTCCCCAGATAGTCAACT	0.463													G|||	806	0.160942	0.062	0.2133	5008	,	,		22218	0.2619		0.1789	False		,,,				2504	0.135				p.Q61H		Atlas-SNP	.											.	CDHR3	153	.	0			c.G183C						PASS	.	G	HIS/GLN	343,3425		17,309,1558	194.0	179.0	184.0		183	2.5	0.3	7	dbSNP_126	184	1634,6600		162,1310,2645	yes	missense	CDHR3	NM_152750.4	24	179,1619,4203	CC,CG,GG		19.8445,9.103,16.4723	benign	61/886	105615426	1977,10025	1884	4117	6001	SO:0001583	missense	222256	exon2			TCCCCAGATAGTC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.183G>C	7.37:g.105615426G>C	ENSP00000325954:p.Gln61His	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	219	88	0.401826	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	383	0.17536630036630035	36	0.07317073170731707	85	0.23480662983425415	126	0.2202797202797203	136	0.17941952506596306	G	5.960	0.361167	0.11296	0.09103	0.198445	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000541203	T;T;T	0.15256	2.44;2.44;2.44	5.4	2.47	0.30058	Cadherin (2);	1.214480	0.05938	N	0.636408	T	0.00012	0.0000	N	0.22421	0.69	0.43403	P	0.004468999999999945	B;B	0.26845	0.161;0.161	B;B	0.24541	0.054;0.054	T	0.40627	-0.9553	9	0.39692	T	0.17	0.5332	4.229	0.10594	0.076:0.1241:0.4259:0.3741	rs34426483;rs58941570	48;61	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	H	61	ENSP00000439766:Q61H;ENSP00000325954:Q61H;ENSP00000443733:Q61H	ENSP00000325954:Q61H	Q	+	3	2	CDHR3	105402662	0.359000	0.24955	0.254000	0.24359	0.314000	0.28054	0.535000	0.23114	0.825000	0.34637	0.655000	0.94253	CAG	G|0.824;C|0.176	0.176	strong		0.463	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
VPS13A	23230	hgsc.bcm.edu	37	9	79891006	79891006	+	Missense_Mutation	SNP	T	T	C	rs78048112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79891006T>C	ENST00000360280.3	+	26	2953	c.2693T>C	c.(2692-2694)gTt>gCt	p.V898A	VPS13A_ENST00000376634.4_Missense_Mutation_p.V898A|VPS13A_ENST00000357409.5_Missense_Mutation_p.V898A|VPS13A_ENST00000376636.3_Missense_Mutation_p.V898A	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	898			V -> A (in dbSNP:rs78048112). {ECO:0000269|PubMed:12404112}.		cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TATCACCTTGTTGGAGATTGT	0.328													T|||	58	0.0115815	0.003	0.0173	5008	,	,		14148	0.0		0.0298	False		,,,				2504	0.0123				p.V898A		Atlas-SNP	.											.	VPS13A	735	.	0			c.T2693C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	34,4370	38.4+/-70.7	0,34,2168	104.0	104.0	104.0		2693,2693,2693,2693	3.5	1.0	9	dbSNP_131	104	268,8332	103.3+/-164.5	3,262,4035	yes	missense,missense,missense,missense	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	64,64,64,64	3,296,6203	CC,CT,TT		3.1163,0.772,2.3224	benign,benign,benign,benign	898/3136,898/3070,898/3096,898/3175	79891006	302,12702	2202	4300	6502	SO:0001583	missense	23230	exon26			ACCTTGTTGGAGA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.2693T>C	9.37:g.79891006T>C	ENSP00000353422:p.Val898Ala	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	23	0.010531135531135532	4	0.008130081300813009	3	0.008287292817679558	0	0.0	16	0.021108179419525065	T	7.155	0.584540	0.13749	0.00772	0.031163	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.15372	2.43;2.43;2.43;2.43	5.82	3.46	0.39613	.	0.526409	0.18933	N	0.127162	T	0.03739	0.0106	L	0.51422	1.61	0.80722	D	1	B;B;B;B	0.24132	0.004;0.059;0.098;0.098	B;B;B;B	0.26969	0.012;0.034;0.075;0.075	T	0.09443	-1.0674	10	0.08179	T	0.78	.	3.0912	0.06295	0.3329:0.1342:0.0:0.5329	.	898;898;898;898	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	A	898	ENSP00000365821:V898A;ENSP00000365823:V898A;ENSP00000353422:V898A;ENSP00000349985:V898A	ENSP00000349985:V898A	V	+	2	0	VPS13A	79080826	0.993000	0.37304	1.000000	0.80357	0.981000	0.71138	0.929000	0.28844	0.994000	0.38892	0.460000	0.39030	GTT	T|0.980;C|0.020	0.020	strong		0.328	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
LAMA1	284217	hgsc.bcm.edu	37	18	7034508	7034508	+	Missense_Mutation	SNP	T	T	G	rs566655	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:7034508T>G	ENST00000389658.3	-	14	2114	c.2021A>C	c.(2020-2022)aAc>aCc	p.N674T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	674	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.		N -> T (in dbSNP:rs566655). {ECO:0000269|PubMed:1714537, ECO:0000269|PubMed:2049067}.		axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGAATTGTAGTTGGCTCTGAT	0.378													T|||	752	0.15016	0.1467	0.1974	5008	,	,		17017	0.1042		0.2247	False		,,,				2504	0.092				p.N674T		Atlas-SNP	.											.	LAMA1	458	.	0			c.A2021C						PASS	.	T	THR/ASN	724,3682	298.4+/-285.3	65,594,1544	115.0	111.0	113.0		2021	4.8	1.0	18	dbSNP_83	113	1987,6613	347.4+/-326.6	242,1503,2555	yes	missense	LAMA1	NM_005559.3	65	307,2097,4099	GG,GT,TT		23.1047,16.4321,20.8442	benign	674/3076	7034508	2711,10295	2203	4300	6503	SO:0001583	missense	284217	exon14			TTGTAGTTGGCTC	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2021A>C	18.37:g.7034508T>G	ENSP00000374309:p.Asn674Thr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	134	42	0.313433	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	382	0.1749084249084249	70	0.14227642276422764	65	0.17955801104972377	72	0.1258741258741259	175	0.23087071240105542	T	4.754	0.140128	0.09083	0.164321	0.231047	ENSG00000101680	ENST00000389658	T	0.29917	1.55	5.9	4.75	0.60458	Laminin B type IV (2);Laminin B, subgroup (1);	0.170205	0.51477	D	0.000090	T	0.00012	0.0000	N	0.05050	-0.12	0.32727	P	0.509567	P	0.41475	0.751	B	0.44315	0.446	T	0.13575	-1.0504	9	0.02654	T	1	.	9.7988	0.40751	0.0:0.1374:0.0:0.8626	rs566655;rs17442820;rs52791113;rs59387906;rs566655	674	P25391	LAMA1_HUMAN	T	674	ENSP00000374309:N674T	ENSP00000374309:N674T	N	-	2	0	LAMA1	7024508	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	0.256000	0.18351	1.067000	0.40740	0.533000	0.62120	AAC	T|0.807;G|0.193	0.193	strong		0.378	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
IRAK3	11213	hgsc.bcm.edu	37	12	66605228	66605228	+	Missense_Mutation	SNP	A	A	G	rs1152888|rs17854945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:66605228A>G	ENST00000261233.4	+	5	860	c.439A>G	c.(439-441)Ata>Gta	p.I147V	IRAK3_ENST00000457197.2_Missense_Mutation_p.I86V	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3											breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(28;0.0203)		TTCCTAAGGAATACTGCTTAA	0.343													A|||	3550	0.708866	0.4206	0.902	5008	,	,		18053	0.5794		0.9155	False		,,,				2504	0.8824				p.I147V		Atlas-SNP	.											.	IRAK3	75	.	0			c.A439G						PASS	.	A	VAL/ILE,VAL/ILE	2170,2234	565.0+/-381.6	527,1116,559	53.0	52.0	52.0		256,439	0.7	0.1	12	dbSNP_87	52	8022,574	787.8+/-407.6	3741,540,17	yes	missense,missense	IRAK3	NM_001142523.1,NM_007199.2	29,29	4268,1656,576	GG,GA,AA		6.6775,49.2734,21.6	benign,benign	86/536,147/597	66605228	10192,2808	2202	4298	6500	SO:0001583	missense	11213	exon5			TAAGGAATACTGC	AF113136	CCDS8975.1, CCDS44937.1	12q13.13	2008-05-02			ENSG00000090376	ENSG00000090376			17020	protein-coding gene	gene with protein product		604459				10383454	Standard	NM_001142523		Approved	IRAK-M	uc001sth.3	Q9Y616	OTTHUMG00000169002	ENST00000261233.4:c.439A>G	12.37:g.66605228A>G	ENSP00000261233:p.Ile147Val	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	230	229	0.995652	NM_007199		Missense_Mutation	SNP	ENST00000261233.4	37	CCDS8975.1	1569	0.7184065934065934	201	0.40853658536585363	326	0.9005524861878453	346	0.6048951048951049	696	0.9182058047493403	A	0.117	-1.130099	0.01756	0.492734	0.933225	ENSG00000090376	ENST00000261233;ENST00000457197	T;T	0.72394	-0.6;-0.65	5.94	0.744	0.18353	.	0.658167	0.16370	N	0.217378	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B	0.14438	0.01;0.001	B;B	0.12156	0.007;0.001	T	0.21690	-1.0238	8	.	.	.	-0.1899	4.8705	0.13629	0.6129:0.1485:0.2386:0.0	rs1152888;rs1732878;rs12827881;rs52818201;rs57154498;rs1152888	86;147	Q9Y616-2;Q9Y616	.;IRAK3_HUMAN	V	147;86	ENSP00000261233:I147V;ENSP00000409852:I86V	.	I	+	1	0	IRAK3	64891495	0.015000	0.18098	0.065000	0.19835	0.309000	0.27889	-0.341000	0.07811	-0.101000	0.12219	0.455000	0.32223	ATA	A|0.253;G|0.747	0.747	strong		0.343	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155219540	155219540	+	Missense_Mutation	SNP	C	C	A	rs141467714	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155219540C>A	ENST00000357232.4	-	18	4560	c.4561G>T	c.(4561-4563)Gct>Tct	p.A1521S		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1521	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GCACCAGAAGCCTCATCAGTC	0.483																																					p.A1521S		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4561T						PASS	.	C	SER/ALA	2,4404	4.2+/-10.8	0,2,2201	133.0	126.0	128.0		4561	0.8	0.0	4	dbSNP_134	128	33,8567	22.8+/-68.1	0,33,4267	yes	missense	DCHS2	NM_017639.3	99	0,35,6468	AA,AC,CC		0.3837,0.0454,0.2691	benign	1521/2917	155219540	35,12971	2203	4300	6503	SO:0001583	missense	54798	exon18			CAGAAGCCTCATC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4561G>T	4.37:g.155219540C>A	ENSP00000349768:p.Ala1521Ser	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	159	79	0.496855	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.010	-1.763380	0.00651	4.54E-4	0.003837	ENSG00000197410	ENST00000357232	T	0.49432	0.78	5.76	0.801	0.18679	Cadherin (4);Cadherin-like (1);	0.619653	0.16206	N	0.224698	T	0.19685	0.0473	N	0.11724	0.165	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.15925	-1.0420	10	0.09084	T	0.74	.	0.908	0.01288	0.3676:0.2927:0.1326:0.2071	.	1521	Q6V1P9	PCD23_HUMAN	S	1521	ENSP00000349768:A1521S	ENSP00000349768:A1521S	A	-	1	0	DCHS2	155438990	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	0.074000	0.14662	-0.106000	0.12110	0.650000	0.86243	GCT	C|0.998;A|0.002	0.002	strong		0.483	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
PREX1	57580	hgsc.bcm.edu	37	20	47267480	47267480	+	Silent	SNP	A	A	G	rs41283556	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:47267480A>G	ENST00000371941.3	-	23	2791	c.2769T>C	c.(2767-2769)tgT>tgC	p.C923C	PREX1_ENST00000396220.1_Silent_p.C923C	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	923					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCTTGGTGTCACAGATGTTGC	0.602													G|||	755	0.150759	0.0197	0.2118	5008	,	,		19772	0.1528		0.1849	False		,,,				2504	0.2474				p.C923C		Atlas-SNP	.											.	PREX1	441	.	0			c.T2769C						PASS	.	G		251,4155	803.7+/-415.7	10,231,1962	104.0	80.0	88.0		2769	-2.6	0.7	20	dbSNP_127	88	1624,6976	742.4+/-407.2	148,1328,2824	no	coding-synonymous	PREX1	NM_020820.3		158,1559,4786	GG,GA,AA		18.8837,5.6968,14.4164		923/1660	47267480	1875,11131	2203	4300	6503	SO:0001819	synonymous_variant	57580	exon23			GGTGTCACAGATG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2769T>C	20.37:g.47267480A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			A|0.851;G|0.149	0.149	strong		0.602	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
TSC22D2	9819	hgsc.bcm.edu	37	3	150128994	150128994	+	Silent	SNP	T	T	G	rs34647320	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:150128994T>G	ENST00000361875.3	+	1	2873	c.1857T>G	c.(1855-1857)ccT>ccG	p.P619P	TSC22D2_ENST00000361136.2_Silent_p.P619P	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	619					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TGAAGCCGCCTGTTGCAGATT	0.468													T|||	413	0.0824681	0.0386	0.0879	5008	,	,		18932	0.0317		0.172	False		,,,				2504	0.0982				p.P619P		Atlas-SNP	.											.	TSC22D2	42	.	0			c.T1857G						PASS	.	T		314,4092	166.9+/-198.0	10,294,1899	85.0	94.0	91.0		1857	1.2	1.0	3	dbSNP_126	91	1717,6883	311.8+/-310.5	165,1387,2748	no	coding-synonymous	TSC22D2	NM_014779.2		175,1681,4647	GG,GT,TT		19.9651,7.1266,15.6159		619/781	150128994	2031,10975	2203	4300	6503	SO:0001819	synonymous_variant	9819	exon1			GCCGCCTGTTGCA	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1857T>G	3.37:g.150128994T>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	194	79	0.407216	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	37	CCDS3149.1	203|203	0.09294871794871795|0.09294871794871795	15|15	0.03048780487804878|0.03048780487804878	33|33	0.09116022099447514|0.09116022099447514	29|29	0.050699300699300696|0.050699300699300696	126|126	0.1662269129287599|0.1662269129287599	T|T	8.025|8.025	0.760446|0.760446	0.15914|0.15914	0.071266|0.071266	0.199651|0.199651	ENSG00000196428|ENSG00000196428	ENST00000466814|ENST00000480589	.|.	.|.	.|.	5.05|5.05	1.23|1.23	0.21249|0.21249	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999991805|0.9999999999991805	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18967|0.18967	-1.0320|-1.0320	3|3	.|.	.|.	.|.	.|.	3.3184|3.3184	0.07041|0.07041	0.1903:0.3818:0.0:0.4278|0.1903:0.3818:0.0:0.4278	rs34647320|rs34647320	.|.	.|.	.|.	G|R	67|80	.|.	.|.	C|L	+|+	1|2	0|0	TSC22D2|TSC22D2	151611684|151611684	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	0.378000|0.378000	0.20569|0.20569	0.244000|0.244000	0.21351|0.21351	0.374000|0.374000	0.22700|0.22700	TGT|CTG	T|0.866;G|0.134;A|0.000	0.134	strong		0.468	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
NAT10	55226	hgsc.bcm.edu	37	11	34154641	34154641	+	Silent	SNP	C	C	T	rs2957518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34154641C>T	ENST00000257829.3	+	16	1892	c.1686C>T	c.(1684-1686)ccC>ccT	p.P562P	NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Silent_p.P490P	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	562	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TTCTGCCTCCCGTGCCCCCCA	0.562													C|||	4309	0.860423	0.5696	0.9553	5008	,	,		19974	1.0		0.9592	False		,,,				2504	0.9407				p.P562P		Atlas-SNP	.											NAT10,NS,carcinoma,+2,1	NAT10	78	1	0			c.C1686T						PASS	.	C	,	2807,1597	664.9+/-401.5	911,985,306	193.0	154.0	167.0		1470,1686	-11.3	0.4	11	dbSNP_101	167	8226,370	802.9+/-407.3	3937,352,9	no	coding-synonymous,coding-synonymous	NAT10	NM_001144030.1,NM_024662.2	,	4848,1337,315	TT,TC,CC		4.3043,36.2625,15.1308	,	490/954,562/1026	34154641	11033,1967	2202	4298	6500	SO:0001819	synonymous_variant	55226	exon16			GCCTCCCGTGCCC	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.1686C>T	11.37:g.34154641C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	37	CCDS7889.1																																																																																			C|0.152;T|0.848	0.848	strong		0.562	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662	
NOBOX	135935	hgsc.bcm.edu	37	7	144096068	144096068	+	Missense_Mutation	SNP	C	C	T	rs2525702	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:144096068C>T	ENST00000467773.1	-	8	1443	c.1444G>A	c.(1444-1446)Ggc>Agc	p.G482S	NOBOX_ENST00000483238.1_Missense_Mutation_p.G450S|NOBOX_ENST00000223140.5_Missense_Mutation_p.G365S	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	482	Pro-rich.		G -> S (in dbSNP:rs2525702). {ECO:0000269|PubMed:17701902}.		oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					CCACAGGGGCCGTCCTTGTGG	0.597													C|||	812	0.162141	0.2413	0.1124	5008	,	,		15514	0.0238		0.1561	False		,,,				2504	0.2393				p.G482S		Atlas-SNP	.											NOBOX_ENST00000467773,NS,carcinoma,0,2	NOBOX	130	2	0			c.G1444A						scavenged	.	C	SER/GLY	809,2975		105,599,1188	11.0	11.0	11.0		1444	3.3	0.2	7	dbSNP_100	11	1323,6897		126,1071,2913	yes	missense	NOBOX	NM_001080413.3	56	231,1670,4101	TT,TC,CC		16.0949,21.3795,17.7607	possibly-damaging	482/692	144096068	2132,9872	1892	4110	6002	SO:0001583	missense	135935	exon8			AGGGGCCGTCCTT			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1444G>A	7.37:g.144096068C>T	ENSP00000419457:p.Gly482Ser	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	212	77	0.363208	NM_001080413	A6NCD3|A8MZN5	Missense_Mutation	SNP	ENST00000467773.1	37		258	0.11813186813186813	91	0.18495934959349594	43	0.11878453038674033	4	0.006993006993006993	120	0.158311345646438	C	12.44	1.937408	0.34189	0.213795	0.160949	ENSG00000106410	ENST00000483238;ENST00000467773;ENST00000223140	T;T;T	0.32988	1.43;1.43;1.43	4.25	3.35	0.38373	.	0.765147	0.12242	N	0.486405	T	0.00039	0.0001	M	0.63843	1.955	0.58432	P	5.999999999950489E-6	B	0.26672	0.156	B	0.17098	0.017	T	0.11494	-1.0585	9	0.28530	T	0.3	-11.259	7.0702	0.25173	0.0:0.8736:0.0:0.1264	rs2525702;rs10370641;rs2525702	482	O60393	NOBOX_HUMAN	S	450;482;365	ENSP00000419565:G450S;ENSP00000419457:G482S;ENSP00000223140:G365S	ENSP00000223140:G365S	G	-	1	0	NOBOX	143727001	0.000000	0.05858	0.164000	0.22755	0.185000	0.23345	0.481000	0.22260	0.974000	0.38366	0.655000	0.94253	GGC	C|0.876;T|0.124	0.124	strong		0.597	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
ZNF350	59348	hgsc.bcm.edu	37	19	52468551	52468551	+	Silent	SNP	T	T	G	rs4986772	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52468551T>G	ENST00000243644.4	-	5	1382	c.1155A>C	c.(1153-1155)acA>acC	p.T385T	HCCAT3_ENST00000600253.1_RNA|ZNF350_ENST00000600703.1_5'Flank|HCCAT3_ENST00000595010.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	385					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		GCTTTTGCTTTGTGCTAAAGG	0.423													T|||	107	0.0213658	0.0008	0.0375	5008	,	,		22493	0.0		0.0457	False		,,,				2504	0.0348				p.T385T		Atlas-SNP	.											ZNF350,NS,carcinoma,-2,1	ZNF350	48	1	0			c.A1155C						scavenged	.	T		36,4370	40.8+/-73.8	0,36,2167	69.0	63.0	65.0		1155	-4.4	0.0	19	dbSNP_111	65	330,8270	113.9+/-173.9	13,304,3983	yes	coding-synonymous	ZNF350	NM_021632.3		13,340,6150	GG,GT,TT		3.8372,0.8171,2.8141		385/533	52468551	366,12640	2203	4300	6503	SO:0001819	synonymous_variant	59348	exon5			TTGCTTTGTGCTA	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"""Zinc fingers, C2H2-type"", ""-"""	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.1155A>C	19.37:g.52468551T>G		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	155	84	0.541936	NM_021632	Q96G73|Q9HAQ4	Silent	SNP	ENST00000243644.4	37	CCDS12845.1																																																																																			T|0.975;G|0.025	0.025	strong		0.423	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151151762	151151762	+	Silent	SNP	G	G	A	rs76807130	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:151151762G>A	ENST00000358517.2	+	15	1726	c.1515G>A	c.(1513-1515)ccG>ccA	p.P505P	PLEKHG1_ENST00000367328.1_Silent_p.P505P			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	505							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CAGCAAGGCCGTCTCCTGCCC	0.502													G|||	38	0.00758786	0.0	0.0101	5008	,	,		19194	0.001		0.0288	False		,,,				2504	0.001				p.P505P		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.G1515A						PASS	.	G		21,4385	28.1+/-56.4	0,21,2182	89.0	83.0	85.0		1515	-9.0	0.0	6	dbSNP_131	85	259,8341	101.4+/-162.7	3,253,4044	no	coding-synonymous	PLEKHG1	NM_001029884.1		3,274,6226	AA,AG,GG		3.0116,0.4766,2.1529		505/1386	151151762	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	57480	exon16			AAGGCCGTCTCCT	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.1515G>A	6.37:g.151151762G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																			G|0.980;A|0.020	0.020	strong		0.502	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
WDR90	197335	hgsc.bcm.edu	37	16	701656	701656	+	Missense_Mutation	SNP	C	C	T	rs11642546	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:701656C>T	ENST00000293879.4	+	8	749	c.749C>T	c.(748-750)cCg>cTg	p.P250L	AL022341.3_ENST00000455294.1_RNA|WDR90_ENST00000549091.1_Missense_Mutation_p.P250L			Q96KV7	WDR90_HUMAN	WD repeat domain 90	250			P -> L (in dbSNP:rs11642546). {ECO:0000269|PubMed:15489334}.							endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CTCCTGGGGCCGGGGCCACAG	0.657													c|||	2000	0.399361	0.2776	0.4006	5008	,	,		16039	0.6796		0.2594	False		,,,				2504	0.4182				p.P250L		Atlas-SNP	.											WDR90,NS,carcinoma,0,1	WDR90	107	1	0			c.C749T						scavenged	.		LEU/PRO	962,2982		117,728,1127	93.0	108.0	103.0		749	-7.5	0.0	16	dbSNP_120	103	1878,6428		203,1472,2478	yes	missense	WDR90	NM_145294.4	98	320,2200,3605	TT,TC,CC		22.6102,24.3915,23.1837	benign	250/1749	701656	2840,9410	1972	4153	6125	SO:0001583	missense	197335	exon8			TGGGGCCGGGGCC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.749C>T	16.37:g.701656C>T	ENSP00000293879:p.Pro250Leu	Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	852	0.3901098901098901	125	0.2540650406504065	142	0.39226519337016574	375	0.6555944055944056	210	0.2770448548812665	c	2.059	-0.415961	0.04766	0.243915	0.226102	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.28255	1.65;1.62	3.75	-7.51	0.01346	.	4.180590	0.01442	U	0.015155	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;B;B	0.35959	0.53;0.273;0.299	B;B;B	0.21708	0.036;0.013;0.035	T	0.42865	-0.9426	9	0.19590	T	0.45	.	2.8762	0.05631	0.3583:0.2309:0.3229:0.0879	rs11642546;rs11642546	250;250;250	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	L	250	ENSP00000448122:P250L;ENSP00000293879:P250L	ENSP00000293879:P250L	P	+	2	0	WDR90	641657	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.804000	0.01738	-1.506000	0.01805	0.506000	0.49869	CCG	C|0.651;T|0.349	0.349	strong		0.657	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
PER1	5187	hgsc.bcm.edu	37	17	8053344	8053344	+	Silent	SNP	G	G	A	rs35826160	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8053344G>A	ENST00000317276.4	-	4	711	c.474C>T	c.(472-474)cgC>cgT	p.R158R	PER1_ENST00000581082.1_Silent_p.R158R|PER1_ENST00000354903.5_Silent_p.R142R	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	158					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGGTCCCAGAGCGGCCCTTGC	0.642			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					G|||	43	0.00858626	0.0015	0.0202	5008	,	,		19428	0.0		0.0239	False		,,,				2504	0.0031				p.R158R		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.C474T						PASS	.	G		23,4383	28.1+/-56.4	1,21,2181	103.0	113.0	110.0		474	3.9	1.0	17	dbSNP_126	110	192,8408	82.9+/-145.4	2,188,4110	no	coding-synonymous	PER1	NM_002616.2		3,209,6291	AA,AG,GG		2.2326,0.522,1.6531		158/1291	8053344	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	5187	exon4			CCCAGAGCGGCCC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.474C>T	17.37:g.8053344G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_002616	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	37	CCDS11131.1																																																																																			G|0.984;A|0.016	0.016	strong		0.642	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
TCEB3B	51224	hgsc.bcm.edu	37	18	44561630	44561630	+	Silent	SNP	C	C	T	rs61746775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44561630C>T	ENST00000332567.4	-	1	358	c.6G>A	c.(4-6)gcG>gcA	p.A2A	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	2					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TGGACCCTGCCGCCATCTCAC	0.622													c|||	190	0.0379393	0.0499	0.0418	5008	,	,		16629	0.0069		0.0835	False		,,,				2504	0.0041				p.A2A		Atlas-SNP	.											.	TCEB3B	141	.	0			c.G6A						PASS	.	T	,	262,4140		9,244,1948	47.0	45.0	45.0		6,	-2.0	0.0	18	dbSNP_129	45	619,7975		24,571,3702	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	33,815,5650	TT,TC,CC		7.2027,5.9518,6.779	,	2/754,	44561630	881,12115	2201	4297	6498	SO:0001819	synonymous_variant	51224	exon1			CCCTGCCGCCATC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.6G>A	18.37:g.44561630C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			C|0.933;T|0.067	0.067	strong		0.622	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
GLYATL3	389396	hgsc.bcm.edu	37	6	49489397	49489397	+	Missense_Mutation	SNP	C	C	A	rs9369905	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:49489397C>A	ENST00000371197.4	+	5	466	c.353C>A	c.(352-354)gCc>gAc	p.A118D		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	118						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.A118D(3)		NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						AAAGCGGTTGCCAATTCAAAG	0.363													C|||	889	0.177516	0.0212	0.1931	5008	,	,		18692	0.2073		0.3439	False		,,,				2504	0.1759				p.A118D		Atlas-SNP	.											GLYATL3,NS,carcinoma,0,3	GLYATL3	19	3	3	Substitution - Missense(3)	kidney(2)|stomach(1)	c.C353A						PASS	.						209.0	173.0	184.0					6																	49489397		692	1591	2283	SO:0001583	missense	389396	exon5			CGGTTGCCAATTC		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.353C>A	6.37:g.49489397C>A	ENSP00000360240:p.Ala118Asp	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	137	52	0.379562	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	437	0.2000915750915751	15	0.03048780487804878	75	0.20718232044198895	97	0.16958041958041958	250	0.32981530343007914	C	15.38	2.816761	0.50633	.	.	ENSG00000203972	ENST00000371197;ENST00000545705	T;T	0.20738	2.05;2.05	5.9	5.9	0.94986	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	.	.	.	.	T	0.19644	0.0472	M	0.81341	2.54	0.27018	P	0.9645316	B	0.28470	0.213	B	0.32022	0.139	T	0.03335	-1.1047	8	0.36615	T	0.2	.	15.7685	0.78146	0.0:1.0:0.0:0.0	rs9369905;rs52815318;rs57040541;rs9369905	118	Q5SZD4	GLYL3_HUMAN	D	118	ENSP00000360240:A118D;ENSP00000440029:A118D	ENSP00000360240:A118D	A	+	2	0	GLYATL3	49597356	0.993000	0.37304	0.971000	0.41717	0.620000	0.37586	3.899000	0.56288	2.800000	0.96347	0.591000	0.81541	GCC	C|0.805;A|0.195	0.195	strong		0.363	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
DR1	1810	hgsc.bcm.edu	37	1	93826178	93826178	+	Missense_Mutation	SNP	A	A	T	rs3088371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:93826178A>T	ENST00000370272.4	+	3	1271	c.513A>T	c.(511-513)gaA>gaT	p.E171D	DR1_ENST00000481583.1_3'UTR|DR1_ENST00000370267.1_Missense_Mutation_p.E171D	NM_001938.2	NP_001929.1	Q01658	NC2B_HUMAN	down-regulator of transcription 1, TBP-binding (negative cofactor 2)	171			E -> D (in dbSNP:rs3088371).		chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)	4		all_lung(203;0.00252)|Lung NSC(277;0.011)|Melanoma(281;0.155)		all cancers(265;0.0032)|GBM - Glioblastoma multiforme(16;0.0165)|Epithelial(280;0.0977)		AGGATGAAGAAGATGATGATG	0.423													A|||	368	0.0734824	0.0666	0.0965	5008	,	,		17076	0.0268		0.0915	False		,,,				2504	0.0961				p.E171D		Atlas-SNP	.											.	DR1	10	.	0			c.A513T						PASS	.	A	ASP/GLU	304,4102	160.3+/-192.7	10,284,1909	71.0	70.0	70.0		513	-9.7	1.0	1	dbSNP_102	70	718,7882	175.5+/-225.5	29,660,3611	yes	missense	DR1	NM_001938.2	45	39,944,5520	TT,TA,AA		8.3488,6.8997,7.8579	benign	171/177	93826178	1022,11984	2203	4300	6503	SO:0001583	missense	1810	exon3			TGAAGAAGATGAT	M97388	CCDS744.1	1p22.1	2008-02-05			ENSG00000117505	ENSG00000117505			3017	protein-coding gene	gene with protein product		601482				1339312, 9040789	Standard	NM_001938		Approved	NC2, NC2-BETA	uc001dpu.3	Q01658	OTTHUMG00000010862	ENST00000370272.4:c.513A>T	1.37:g.93826178A>T	ENSP00000359295:p.Glu171Asp	Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	348	344	0.988506	NM_001938		Missense_Mutation	SNP	ENST00000370272.4	37	CCDS744.1	161	0.07371794871794872	25	0.0508130081300813	40	0.11049723756906077	15	0.026223776223776224	81	0.10686015831134564	A	14.91	2.677285	0.47886	0.068997	0.083488	ENSG00000117505	ENST00000370272;ENST00000370267	T;T	0.27557	1.66;1.66	5.5	-9.66	0.00534	.	0.309510	0.41001	N	0.000980	T	0.02119	0.0066	N	0.03608	-0.345	0.27155	P	0.9613185	B	0.02656	0.0	B	0.01281	0.0	T	0.33497	-0.9866	9	0.02654	T	1	-0.4113	11.3172	0.49399	0.1565:0.0866:0.0:0.7568	rs3088371;rs3202525;rs52822732;rs3088371	171	Q01658	NC2B_HUMAN	D	171	ENSP00000359295:E171D;ENSP00000359290:E171D	ENSP00000359290:E171D	E	+	3	2	DR1	93598766	0.498000	0.26075	0.953000	0.39169	0.994000	0.84299	-0.204000	0.09425	-1.172000	0.02762	-0.480000	0.04831	GAA	A|0.926;T|0.074	0.074	strong		0.423	DR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029976.2	NM_001938	
TRRAP	8295	hgsc.bcm.edu	37	7	98495408	98495408	+	Silent	SNP	G	G	C	rs55702649	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:98495408G>C	ENST00000359863.4	+	8	761	c.552G>C	c.(550-552)gtG>gtC	p.V184V	TRRAP_ENST00000355540.3_Silent_p.V184V|TRRAP_ENST00000446306.3_Silent_p.V184V	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	184					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AGAACACAGTGCCTCCCCCAG	0.423													G|||	63	0.0125799	0.003	0.0159	5008	,	,		18252	0.0		0.0427	False		,,,				2504	0.0051				p.V184V		Atlas-SNP	.											.	TRRAP	863	.	0			c.G552C						PASS	.	G		39,4367	42.3+/-75.8	1,37,2165	120.0	109.0	112.0		552	-1.0	1.0	7	dbSNP_129	112	356,8244	118.8+/-178.2	7,342,3951	no	coding-synonymous	TRRAP	NM_003496.3		8,379,6116	CC,CG,GG		4.1395,0.8852,3.0371		184/3831	98495408	395,12611	2203	4300	6503	SO:0001819	synonymous_variant	8295	exon8			CACAGTGCCTCCC	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.552G>C	7.37:g.98495408G>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1																																																																																			G|0.972;C|0.028	0.028	strong		0.423	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
LILRB5	10990	hgsc.bcm.edu	37	19	54759361	54759361	+	Missense_Mutation	SNP	T	T	C	rs12975366	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54759361T>C	ENST00000316219.5	-	5	847	c.740A>G	c.(739-741)gAt>gGt	p.D247G	LILRB5_ENST00000345866.6_Missense_Mutation_p.D147G|LILRB5_ENST00000450632.1_Missense_Mutation_p.D238G|LILRB5_ENST00000449561.2_Missense_Mutation_p.D247G	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	247	Ig-like C2-type 3.		D -> G (in dbSNP:rs12975366).		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ATAGCCGACATCAGAGCGACA	0.632													.|||	1356	0.270767	0.1483	0.3213	5008	,	,		15944	0.125		0.4344	False		,,,				2504	0.3824				p.D247G		Atlas-SNP	.											LILRB5_ENST00000450632,colon,carcinoma,0,4	LILRB5	176	4	0			c.A740G						scavenged	.	T	GLY/ASP,GLY/ASP,GLY/ASP	790,3616	317.7+/-295.3	61,668,1474	52.0	49.0	50.0		740,440,740	1.5	0.1	19	dbSNP_121	50	3529,5071	512.5+/-378.0	735,2059,1506	yes	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	94,94,94	796,2727,2980	CC,CT,TT		41.0349,17.9301,33.2078	probably-damaging,probably-damaging,probably-damaging	247/592,147/492,247/591	54759361	4319,8687	2203	4300	6503	SO:0001583	missense	10990	exon5			CCGACATCAGAGC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.740A>G	19.37:g.54759361T>C	ENSP00000320390:p.Asp247Gly	Somatic	228	2	0.00877193		WXS	Illumina HiSeq	Phase_I	283	126	0.44523	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	582	0.2664835164835165	91	0.18495934959349594	135	0.3729281767955801	44	0.07692307692307693	312	0.41160949868073876	T	13.84	2.356397	0.41700	0.179301	0.410349	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	2.62	1.52	0.23074	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.931743	0.08893	N	0.878354	T	0.00012	0.0000	M	0.78285	2.405	0.80722	P	0.0	D;D;D;D;D	0.89917	0.998;0.999;0.998;0.982;1.0	D;D;D;P;D	0.78314	0.988;0.959;0.961;0.9;0.991	T	0.39820	-0.9595	9	0.66056	D	0.02	.	5.5585	0.17129	0.0:0.0:0.2868:0.7132	rs12975366	238;138;147;247;247	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	G	247;238;247;147	ENSP00000320390:D247G;ENSP00000414225:D238G;ENSP00000406478:D247G;ENSP00000263430:D147G	ENSP00000320390:D247G	D	-	2	0	LILRB5	59451173	0.000000	0.05858	0.055000	0.19348	0.130000	0.20726	0.165000	0.16564	0.372000	0.24591	0.366000	0.22137	GAT	T|0.679;C|0.321	0.321	strong		0.632	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
NOC3L	64318	hgsc.bcm.edu	37	10	96104665	96104665	+	Missense_Mutation	SNP	T	T	G	rs3758526	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96104665T>G	ENST00000371361.3	-	12	1515	c.1415A>C	c.(1414-1416)gAg>gCg	p.E472A	NOC3L_ENST00000371350.1_Missense_Mutation_p.E472A|NOC3L_ENST00000463649.1_5'Flank|NOC3L_ENST00000543788.1_Missense_Mutation_p.E210A	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	472			E -> A (in dbSNP:rs3758526). {ECO:0000269|PubMed:14702039}.		fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				AAGCTCTCGCTCTAGTTTCTC	0.363													T|||	1036	0.206869	0.1657	0.0908	5008	,	,		18959	0.2937		0.1213	False		,,,				2504	0.3436				p.E472A		Atlas-SNP	.											.	NOC3L	67	.	0			c.A1415C						PASS	.	T	ALA/GLU	727,3677	298.4+/-285.3	62,603,1537	115.0	108.0	111.0		1415	4.9	1.0	10	dbSNP_107	111	1050,7548	221.2+/-258.7	65,920,3314	yes	missense	NOC3L	NM_022451.9	107	127,1523,4851	GG,GT,TT		12.2121,16.5077,13.6671	probably-damaging	472/801	96104665	1777,11225	2202	4299	6501	SO:0001583	missense	64318	exon12			TCTCGCTCTAGTT	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"""chromosome 10 open reading frame 117"""	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.1415A>C	10.37:g.96104665T>G	ENSP00000360412:p.Glu472Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	32	0.363636	NM_022451	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	400	0.18315018315018314	90	0.18292682926829268	38	0.10497237569060773	181	0.31643356643356646	91	0.12005277044854881	T	17.97	3.517429	0.64634	0.165077	0.122121	ENSG00000173145	ENST00000543788;ENST00000371361;ENST00000371350	T;T;T	0.17370	2.28;2.38;2.38	6.07	4.92	0.64577	.	0.140487	0.64402	D	0.000006	T	0.00012	0.0000	L	0.52823	1.66	0.24525	P	0.99414929	D	0.53745	0.962	P	0.50314	0.637	T	0.46830	-0.9163	9	0.34782	T	0.22	-19.9256	13.4707	0.61281	0.0:0.0:0.1307:0.8693	rs3758526;rs52826368;rs3758526	472	Q8WTT2	NOC3L_HUMAN	A	210;472;472	ENSP00000437838:E210A;ENSP00000360412:E472A;ENSP00000360401:E472A	ENSP00000360401:E472A	E	-	2	0	NOC3L	96094655	1.000000	0.71417	0.980000	0.43619	0.981000	0.71138	7.007000	0.76335	1.095000	0.41419	0.528000	0.53228	GAG	T|0.852;G|0.148	0.148	strong		0.363	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	
SPRR1B	6699	hgsc.bcm.edu	37	1	153004853	153004853	+	Missense_Mutation	SNP	C	C	T	rs3795382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:153004853C>T	ENST00000307098.4	+	2	97	c.32C>T	c.(31-33)aCc>aTc	p.T11I	SPRR1B_ENST00000392661.3_Missense_Mutation_p.T11I	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	11	2 X 12 AA approximate repeats.		T -> I (in dbSNP:rs3795382). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3133554, ECO:0000269|PubMed:8388378, ECO:0000269|Ref.4}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAGCCTTGCACCCCACCCCCT	0.552													T|||	2474	0.49401	0.4402	0.4251	5008	,	,		16011	0.5913		0.5099	False		,,,				2504	0.499				p.T11I		Atlas-SNP	.											SPRR1B,head_neck,carcinoma,0,1	SPRR1B	18	1	0			c.C32T						PASS	.	T	ILE/THR	2068,2338	570.8+/-382.9	482,1104,617	142.0	138.0	139.0		32	-0.1	0.0	1	dbSNP_107	139	4392,4208	584.4+/-391.7	1128,2136,1036	no	missense	SPRR1B	NM_003125.2	89	1610,3240,1653	TT,TC,CC		48.9302,46.936,49.6694	benign	11/90	153004853	6460,6546	2203	4300	6503	SO:0001583	missense	6699	exon2			CTTGCACCCCACC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.32C>T	1.37:g.153004853C>T	ENSP00000306461:p.Thr11Ile	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	353	205	0.580737	NM_003125	B2R5H7|P22529|P22530|Q5T524	Missense_Mutation	SNP	ENST00000307098.4	37	CCDS30863.1	1134	0.5192307692307693	228	0.4634146341463415	167	0.4613259668508287	355	0.6206293706293706	384	0.5065963060686016	c	1.477	-0.558376	0.03967	0.46936	0.510698	ENSG00000169469	ENST00000307098;ENST00000392661	T;T	0.14391	2.62;2.51	3.98	-0.059	0.13795	.	.	.	.	.	T	0.02418	0.0074	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47560	-0.9108	7	0.23891	T	0.37	-0.0032	8.0665	0.30663	0.0:0.5816:0.0:0.4184	rs3795382;rs17846538;rs17859612;rs17884771;rs52805231	11	P22528	SPR1B_HUMAN	I	11	ENSP00000306461:T11I;ENSP00000376429:T11I	ENSP00000306461:T11I	T	+	2	0	SPRR1B	151271477	0.005000	0.15991	0.000000	0.03702	0.408000	0.30992	-0.240000	0.08952	-0.338000	0.08413	-1.551000	0.00897	ACC	C|0.497;T|0.503	0.503	strong		0.552	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
PTX4	390667	hgsc.bcm.edu	37	16	1538464	1538464	+	Intron	SNP	C	C	T	rs2745103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1538464C>T	ENST00000447419.2	-	1	167				PTX4_ENST00000293922.1_Missense_Mutation_p.G2E|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GTTTCCACTCCCCATGACACT	0.652													C|||	1291	0.257788	0.1316	0.1945	5008	,	,		15785	0.497		0.2416	False		,,,				2504	0.2434				p.G2E		Atlas-SNP	.											.	PTX4	46	.	0			c.G5A						PASS	.	C	GLU/GLY	591,3807	258.6+/-262.5	37,517,1645	64.0	54.0	57.0		5	0.9	0.0	16	dbSNP_100	57	2187,6413	367.0+/-334.5	254,1679,2367	yes	missense	PTX4	NM_001013658.1	98	291,2196,4012	TT,TC,CC		25.4302,13.4379,21.3725	benign	2/474	1538464	2778,10220	2199	4300	6499	SO:0001627	intron_variant	390667	exon1			CCACTCCCCATGA		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.141+305G>A	16.37:g.1538464C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	225	110	0.488889	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		632	0.2893772893772894	57	0.11585365853658537	67	0.1850828729281768	309	0.5402097902097902	199	0.262532981530343	C	5.219	0.226002	0.09916	0.134379	0.254302	ENSG00000251692	ENST00000293922	T	0.07444	3.19	2.87	0.856	0.19019	.	1820.570000	0.00166	N	0.000000	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.27498	0.18	B	0.26310	0.068	T	0.46992	-0.9151	8	0.87932	D	0	.	4.118	0.10092	0.0:0.6175:0.2436:0.1389	rs2745103;rs58765039;rs2745103	2	Q96A99-2	.	E	2	ENSP00000293922:G2E	ENSP00000293922:G2E	G	-	2	0	PTX4	1478465	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	0.239000	0.18023	0.260000	0.21731	0.563000	0.77884	GGG	C|0.758;T|0.242	0.242	strong		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
OR7G1	125962	hgsc.bcm.edu	37	19	9225662	9225662	+	Missense_Mutation	SNP	T	T	C	rs138190811		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9225662T>C	ENST00000541538.1	-	1	777	c.778A>G	c.(778-780)Att>Gtt	p.I260V	OR7G1_ENST00000293614.1_Missense_Mutation_p.I260V	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						GCAGAACTAATGTACACCCCA	0.468													T|||	1	0.000199681	0.0	0.0	5008	,	,		18140	0.001		0.0	False		,,,				2504	0.0				p.I260V		Atlas-SNP	.											.	OR7G1	53	.	0			c.A778G						PASS	.	T	VAL/ILE	0,4406		0,0,2203	109.0	102.0	104.0		778	-7.6	0.0	19	dbSNP_134	104	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OR7G1	NM_001005192.2	29	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	benign	260/312	9225662	4,13002	2203	4300	6503	SO:0001583	missense	125962	exon1			AACTAATGTACAC		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"""GPCR / Class A : Olfactory receptors"""	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.778A>G	19.37:g.9225662T>C	ENSP00000444134:p.Ile260Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_001005192	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	.	.	.	.	.	.	.	.	.	.	t	9.233	1.036306	0.19669	0.0	4.65E-4	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.37058	1.22;1.22	3.78	-7.55	0.01327	GPCR, rhodopsin-like superfamily (1);	0.478549	0.15276	U	0.270958	T	0.18509	0.0444	N	0.25825	0.765	0.09310	N	1	B	0.16603	0.018	B	0.30943	0.122	T	0.22277	-1.0221	10	0.72032	D	0.01	.	2.0374	0.03542	0.2085:0.2559:0.3872:0.1484	.	260	Q8NGA0	OR7G1_HUMAN	V	260	ENSP00000293614:I260V;ENSP00000444134:I260V	ENSP00000293614:I260V	I	-	1	0	OR7G1	9086662	0.000000	0.05858	0.012000	0.15200	0.016000	0.09150	-2.649000	0.00858	-1.542000	0.01725	-0.539000	0.04255	ATT	T|0.999;C|0.001	0.001	strong		0.468	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1		
ZNF761	388561	hgsc.bcm.edu	37	19	53959343	53959343	+	RNA	SNP	G	G	A	rs2708742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53959343G>A	ENST00000454407.1	+	0	2035							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TAATGAGTGCGGCAAGACCTT	0.443													g|||	1820	0.363419	0.3306	0.5303	5008	,	,		22273	0.2401		0.3956	False		,,,				2504	0.3834				p.G528S		Atlas-SNP	.											.	ZNF761	104	.	0			c.G1582A						PASS	.	G	SER/GLY	1498,2908	477.0+/-357.8	254,990,959	104.0	101.0	102.0		1583	1.1	0.0	19	dbSNP_100	102	3492,5108	509.5+/-377.3	704,2084,1512	no	missense	ZNF761	NM_001008401.3	56	958,3074,2471	AA,AG,GG		40.6047,33.9991,38.3669	benign	528/747	53959343	4990,8016	2203	4300	6503			388561	exon7			GAGTGCGGCAAGA	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959343G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	75	46	0.613333	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																				G|0.635;A|0.365	0.365	strong		0.443	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74192791	74192791	+	Silent	SNP	C	C	T	rs10147537	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:74192791C>T	ENST00000286523.5	-	8	3212	c.2430G>A	c.(2428-2430)ctG>ctA	p.L810L	ELMSAN1_ENST00000394071.2_Silent_p.L810L	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	810	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GCTTCTTCAGCAGCAGCTTAT	0.597													T|||	99	0.0197684	0.0129	0.0231	5008	,	,		18392	0.0		0.0398	False		,,,				2504	0.0266				p.L810L		Atlas-SNP	.											.	.	.	.	0			c.G2430A						PASS	.	T	,	46,4358		1,44,2157	62.0	58.0	59.0		2430,2430	2.3	1.0	14	dbSNP_119	59	279,8315		6,267,4024	no	coding-synonymous,coding-synonymous	C14orf43	NM_001043318.1,NM_194278.3	,	7,311,6181	TT,TC,CC		3.2465,1.0445,2.5004	,	810/1046,810/1046	74192791	325,12673	2202	4297	6499	SO:0001819	synonymous_variant	91748	exon8			CTTCAGCAGCAGC	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.2430G>A	14.37:g.74192791C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	189	82	0.433862	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Silent	SNP	ENST00000286523.5	37	CCDS9819.1																																																																																			C|0.976;T|0.024	0.024	strong		0.597	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
NAPSA	9476	hgsc.bcm.edu	37	19	50863023	50863023	+	Silent	SNP	A	A	G	rs638294	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50863023A>G	ENST00000253719.2	-	6	973	c.765T>C	c.(763-765)ccT>ccC	p.P255P	NR1H2_ENST00000600978.1_Intron|NR1H2_ENST00000542413.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	255					membrane protein proteolysis (GO:0033619)|proteolysis (GO:0006508)|surfactant homeostasis (GO:0043129)	alveolar lamellar body (GO:0097208)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)|peptidase activity (GO:0008233)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		GCCAGTAGGCAGGGACCGTGA	0.652													a|||	1742	0.347843	0.4554	0.4049	5008	,	,		18656	0.1716		0.33	False		,,,				2504	0.362				p.P255P		Atlas-SNP	.											.	NAPSA	38	.	0			c.T765C						PASS	.	A		1913,2493	536.4+/-374.5	426,1061,716	61.0	66.0	64.0		765	-8.0	0.6	19	dbSNP_83	64	2863,5737	441.0+/-359.7	463,1937,1900	no	coding-synonymous	NAPSA	NM_004851.1		889,2998,2616	GG,GA,AA		33.2907,43.4181,36.7215		255/421	50863023	4776,8230	2203	4300	6503	SO:0001819	synonymous_variant	9476	exon6			GTAGGCAGGGACC	AF090386	CCDS12794.1	19q13.33	2011-08-25				ENSG00000131400			13395	protein-coding gene	gene with protein product	"""kidney-derived aspartic protease-like protein"""	605631					Standard	NM_004851		Approved	NAP1, NAPA, Kdap, KAP	uc002prx.3	O96009		ENST00000253719.2:c.765T>C	19.37:g.50863023A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	NM_004851	Q8WWD9	Silent	SNP	ENST00000253719.2	37	CCDS12794.1																																																																																			A|0.662;G|0.338	0.338	strong		0.652	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	NM_004851	
AOAH	313	hgsc.bcm.edu	37	7	36763672	36763672	+	Missense_Mutation	SNP	C	C	T	rs2228410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:36763672C>T	ENST00000258749.5	-	1	481	c.82G>A	c.(82-84)Gat>Aat	p.D28N	AOAH_ENST00000431169.1_Missense_Mutation_p.D28N|AOAH_ENST00000535891.1_Missense_Mutation_p.D28N	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	28			D -> N (in dbSNP:rs11976480). {ECO:0000269|PubMed:12690205, ECO:0000269|Ref.6}.		inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						GACTGGTCATCGTTGGCTGGA	0.502													C|||	1758	0.351038	0.1293	0.4294	5008	,	,		17607	0.5248		0.3569	False		,,,				2504	0.41				p.D28N		Atlas-SNP	.											.	AOAH	79	.	0			c.G82A	GRCh37	CM064972	AOAH	M	rs11976480	PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	668,3738	282.8+/-276.7	52,564,1587	56.0	60.0	58.0		82,82,82	-0.6	0.0	7	dbSNP_120	58	2805,5795	444.1+/-360.6	447,1911,1942	yes	missense,missense,missense	AOAH	NM_001177506.1,NM_001177507.1,NM_001637.3	23,23,23	499,2475,3529	TT,TC,CC		32.6163,15.1611,26.7031	benign,benign,benign	28/689,28/544,28/576	36763672	3473,9533	2203	4300	6503	SO:0001583	missense	313	exon1			GGTCATCGTTGGC	BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.82G>A	7.37:g.36763672C>T	ENSP00000258749:p.Asp28Asn	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001177507	A4D1Y5|B7Z490|Q53F13	Missense_Mutation	SNP	ENST00000258749.5	37	CCDS5448.1	771	0.35302197802197804	63	0.12804878048780488	136	0.3756906077348066	294	0.513986013986014	278	0.36675461741424803	C	5.549	0.286216	0.10513	0.151611	0.326163	ENSG00000136250	ENST00000535891;ENST00000258749;ENST00000431169;ENST00000544647;ENST00000435386	T;T;T;T	0.77620	1.63;-1.07;-1.11;0.66	4.18	-0.577	0.11727	.	3.465610	0.00944	N	0.002871	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.18968	0.0;0.032;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.29792	-1.0000	8	0.23891	T	0.37	-9.38	5.0497	0.14501	0.0:0.4354:0.1664:0.3982	rs11976480;rs52827163;rs58377668;rs11976480	28;28;28	B7Z490;C9J8T1;P28039	.;.;AOAH_HUMAN	N	28	ENSP00000441101:D28N;ENSP00000258749:D28N;ENSP00000405683:D28N;ENSP00000416051:D28N	ENSP00000258749:D28N	D	-	1	0	AOAH	36730197	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.187000	0.09656	-0.447000	0.07138	-2.449000	0.00209	GAT	C|0.697;T|0.303	0.303	strong		0.502	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
PLXNA3	55558	hgsc.bcm.edu	37	X	153693811	153693811	+	Silent	SNP	C	C	T	rs5945429	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153693811C>T	ENST00000369682.3	+	12	2464	c.2289C>T	c.(2287-2289)ttC>ttT	p.F763F		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	763					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AGCTGGACTTCTCCGTGGTCT	0.567													C|||	1438	0.380927	0.6687	0.0994	3775	,	,		13143	0.121		0.0855	False		,,,				2504	0.2832				p.F763F		Atlas-SNP	.											.	PLXNA3	156	.	0			c.C2289T						PASS	.	C		3032,803		1026,518,462,88,109	119.0	109.0	112.0		2289	2.7	1.0	X	dbSNP_114	112	891,5837		46,532,267,1850,1605	no	coding-synonymous	PLXNA3	NM_017514.3		1072,1050,729,1938,1714	TT,TC,T,CC,C		13.2432,20.9387,37.1391		763/1872	153693811	3923,6640	2203	4300	6503	SO:0001819	synonymous_variant	55558	exon12			GGACTTCTCCGTG	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.2289C>T	X.37:g.153693811C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_017514	Q5HY36	Silent	SNP	ENST00000369682.3	37	CCDS14752.1																																																																																			C|0.615;T|0.385	0.385	strong		0.567	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
KIF4B	285643	hgsc.bcm.edu	37	5	154395682	154395682	+	Missense_Mutation	SNP	G	G	A	rs41390849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:154395682G>A	ENST00000435029.4	+	1	2423	c.2263G>A	c.(2263-2265)Gtc>Atc	p.V755I		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	755	Interaction with PRC1. {ECO:0000250}.			V -> I (in Ref. 3; ABB92415). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TGAGGTTATGGTCAGTACTGA	0.458													G|||	621	0.124002	0.0053	0.0836	5008	,	,		20480	0.1895		0.1421	False		,,,				2504	0.227				p.V755I		Atlas-SNP	.											.	KIF4B	307	.	0			c.G2263A						PASS	.	G	ILE/VAL	125,4281	89.7+/-128.4	0,125,2078	86.0	83.0	84.0		2263	2.1	1.0	5	dbSNP_129	84	1247,7353	250.3+/-277.2	94,1059,3147	yes	missense	KIF4B	NM_001099293.1	29	94,1184,5225	AA,AG,GG		14.5,2.837,10.549	probably-damaging	755/1235	154395682	1372,11634	2203	4300	6503	SO:0001583	missense	285643	exon1			GTTATGGTCAGTA	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.2263G>A	5.37:g.154395682G>A	ENSP00000387875:p.Val755Ile	Somatic	306	2	0.00653595		WXS	Illumina HiSeq	Phase_I	321	218	0.679128	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	226	0.10347985347985347	4	0.008130081300813009	31	0.0856353591160221	88	0.15384615384615385	103	0.1358839050131926	g	11.04	1.523021	0.27211	0.02837	0.145	ENSG00000226650	ENST00000435029	T	0.69561	-0.41	2.14	2.14	0.27477	.	.	.	.	.	T	0.00496	0.0016	L	0.55017	1.72	0.09310	P	0.99999470196	B	0.20368	0.044	B	0.22386	0.039	T	0.21008	-1.0258	8	0.31617	T	0.26	.	10.3225	0.43775	0.0:0.0:1.0:0.0	rs56080630;rs61734293	755	Q2VIQ3	KIF4B_HUMAN	I	755	ENSP00000387875:V755I	ENSP00000387875:V755I	V	+	1	0	KIF4B	154375875	1.000000	0.71417	0.995000	0.50966	0.503000	0.33858	6.159000	0.71856	1.138000	0.42230	0.563000	0.77884	GTC	G|0.888;A|0.112	0.112	strong		0.458	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
CAGE1	285782	hgsc.bcm.edu	37	6	7374207	7374207	+	Missense_Mutation	SNP	T	T	G	rs2876098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:7374207T>G	ENST00000512086.1	-	5	1047	c.845A>C	c.(844-846)gAg>gCg	p.E282A	CAGE1_ENST00000338150.4_Missense_Mutation_p.E282A|CAGE1_ENST00000509324.1_5'UTR|CAGE1_ENST00000379918.4_Missense_Mutation_p.E282A|CAGE1_ENST00000296742.7_Missense_Mutation_p.E146A|CAGE1_ENST00000502583.1_Missense_Mutation_p.E282A			Q8TC20	CAGE1_HUMAN	cancer antigen 1	282			E -> A (in dbSNP:rs2876098).							breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					CTCACAGTTCTCCCGACATGC	0.458													T|||	513	0.102436	0.0703	0.1455	5008	,	,		19557	0.1062		0.1491	False		,,,				2504	0.0634				p.E282A		Atlas-SNP	.											.	CAGE1	165	.	0			c.A845C						PASS	.	T	ALA/GLU,ALA/GLU,ALA/GLU	360,3568		13,334,1617	99.0	96.0	97.0		845,845,437	3.2	0.0	6	dbSNP_101	97	1179,7115		106,967,3074	yes	missense,missense,missense	CAGE1	NM_001170692.1,NM_001170693.1,NM_205864.2	107,107,107	119,1301,4691	GG,GT,TT		14.2151,9.165,12.592	possibly-damaging,possibly-damaging,possibly-damaging	282/840,282/825,146/642	7374207	1539,10683	1964	4147	6111	SO:0001583	missense	285782	exon5			CAGTTCTCCCGAC	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"""cancer/testis antigen 95"""	608304	"""cancer/testis antigen 3"""	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.845A>C	6.37:g.7374207T>G	ENSP00000427583:p.Glu282Ala	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	241	109	0.452282	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	37		276	0.12637362637362637	42	0.08536585365853659	53	0.1464088397790055	63	0.11013986013986014	118	0.15567282321899736	T	16.25	3.071426	0.55646	0.09165	0.142151	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000296742;ENST00000512086;ENST00000338150;ENST00000542431;ENST00000512691	T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33	5.66	3.23	0.37069	.	0.542419	0.18024	N	0.154151	T	0.19446	0.0467	L	0.55481	1.735	0.80722	P	0.0	P;P;P	0.48294	0.908;0.775;0.86	B;B;P	0.44561	0.436;0.356;0.453	T	0.04635	-1.0937	9	0.54805	T	0.06	-0.3094	7.542	0.27744	0.0:0.1713:0.0:0.8287	rs2876098;rs17673083;rs60779509;rs2876098	282;282;282	Q8TC20-3;D6RCT9;Q8TC20	.;.;CAGE1_HUMAN	A	282;282;282;146;282;282;282;294	ENSP00000369250:E282A;ENSP00000425493:E282A;ENSP00000296742:E146A;ENSP00000427583:E282A;ENSP00000338107:E282A;ENSP00000423789:E294A	ENSP00000296742:E146A	E	-	2	0	CAGE1	7319206	0.008000	0.16893	0.001000	0.08648	0.005000	0.04900	0.785000	0.26830	0.410000	0.25675	0.482000	0.46254	GAG	T|0.882;G|0.118	0.118	strong		0.458	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745	
DNAJC13	23317	hgsc.bcm.edu	37	3	132221139	132221139	+	Missense_Mutation	SNP	C	C	T	rs55825559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:132221139C>T	ENST00000260818.6	+	40	4791	c.4543C>T	c.(4543-4545)Ccc>Tcc	p.P1515S		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1515			P -> S (in dbSNP:rs55825559).		osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TCAGAGTATTCCCCGCGTAGC	0.413													C|||	60	0.0119808	0.0	0.0245	5008	,	,		15388	0.0		0.0368	False		,,,				2504	0.0061				p.P1515S		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C4543T						PASS	.	C	SER/PRO	26,4380	32.6+/-62.9	0,26,2177	117.0	113.0	115.0		4543	5.8	1.0	3	dbSNP_129	115	239,8361	94.5+/-156.4	5,229,4066	yes	missense	DNAJC13	NM_015268.3	74	5,255,6243	TT,TC,CC		2.7791,0.5901,2.0375	benign	1515/2244	132221139	265,12741	2203	4300	6503	SO:0001583	missense	23317	exon40			AGTATTCCCCGCG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.4543C>T	3.37:g.132221139C>T	ENSP00000260818:p.Pro1515Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	144	50	0.347222	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	34	0.015567765567765568	0	0.0	9	0.024861878453038673	0	0.0	25	0.032981530343007916	C	14.92	2.678748	0.47886	0.005901	0.027791	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.52057	0.68	5.81	5.81	0.92471	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	M	0.69185	2.1	0.54753	D	0.999985	B	0.20368	0.044	B	0.15870	0.014	T	0.17653	-1.0362	10	0.40728	T	0.16	.	16.3288	0.82997	0.0:0.868:0.132:0.0	rs55825559;rs61748104	1515	O75165	DJC13_HUMAN	S	1515;162	ENSP00000260818:P1515S	ENSP00000260818:P1515S	P	+	1	0	DNAJC13	133703829	1.000000	0.71417	0.998000	0.56505	0.614000	0.37383	4.644000	0.61397	2.734000	0.93682	0.650000	0.86243	CCC	C|0.981;T|0.019	0.019	strong		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
MUC4	4585	hgsc.bcm.edu	37	3	195515038	195515038	+	Missense_Mutation	SNP	G	G	A	rs201206859		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515038G>A	ENST00000463781.3	-	2	3872	c.3413C>T	c.(3412-3414)cCt>cTt	p.P1138L	MUC4_ENST00000475231.1_Missense_Mutation_p.P1138L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	605					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P1138L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTCGGTGACAGGAAGAGAGGT	0.567																																					p.P1138L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.C3413T						scavenged	.																																			SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3413C>T	3.37:g.195515038G>A	ENSP00000417498:p.Pro1138Leu	Somatic	444	3	0.00675676		WXS	Illumina HiSeq	Phase_I	136	19	0.139706	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	5.066	0.197826	0.09652	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.39;1.39	0.814	0.814	0.18756	.	.	.	.	.	T	0.38108	0.1028	N	0.19112	0.55	0.09310	N	1	D	0.69078	0.997	D	0.74674	0.984	T	0.21280	-1.0250	8	.	.	.	.	7.6132	0.28142	0.0:0.0:1.0:0.0	.	1138	E7ESK3	.	L	1138	ENSP00000417498:P1138L;ENSP00000420243:P1138L	.	P	-	2	0	MUC4	196999433	0.002000	0.14202	0.001000	0.08648	0.065000	0.16274	1.050000	0.30404	0.776000	0.33473	0.064000	0.15345	CCT	.	.	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR2W3	343171	hgsc.bcm.edu	37	1	248059703	248059703	+	Missense_Mutation	SNP	T	T	A	rs11204545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248059703T>A	ENST00000360358.3	+	1	815	c.815T>A	c.(814-816)aTg>aAg	p.M272K	OR2W3_ENST00000537741.1_Missense_Mutation_p.M272K	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	272			M -> K (in dbSNP:rs11204545). {ECO:0000269|PubMed:17974005}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GACCAGGGCATGTTCCTCATG	0.532													A|||	2394	0.478035	0.2648	0.4553	5008	,	,		20492	0.5893		0.665	False		,,,				2504	0.4755				p.M272K		Atlas-SNP	.											.	OR2W3	113	.	0			c.T815A						PASS	.	A	LYS/MET	1574,2832	668.2+/-402.0	284,1006,913	110.0	101.0	104.0		815	5.3	1.0	1	dbSNP_120	104	5578,3022	465.7+/-366.6	1802,1974,524	yes	missense	OR2W3	NM_001001957.2	95	2086,2980,1437	AA,AT,TT		35.1395,35.724,45.01	benign	272/315	248059703	7152,5854	2203	4300	6503	SO:0001583	missense	343171	exon1			AGGGCATGTTCCT	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.815T>A	1.37:g.248059703T>A	ENSP00000353516:p.Met272Lys	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	262	151	0.576336	NM_001001957	Q6IF06|Q8NG86	Missense_Mutation	SNP	ENST00000360358.3	37	CCDS31099.1	1119	0.5123626373626373	143	0.29065040650406504	169	0.46685082872928174	307	0.5367132867132867	500	0.6596306068601583	A	0.060	-1.225422	0.01530	0.35724	0.648605	ENSG00000238243	ENST00000537741;ENST00000360358	T;T	0.00028	8.92;8.92	5.29	5.29	0.74685	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000005	T	0.00012	0.0000	N	0.00031	-2.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20438	-1.0275	9	0.02654	T	1	.	9.4446	0.38690	0.7171:0.0:0.0:0.2829	rs11204545;rs52819516;rs11204545	272	Q7Z3T1	OR2W3_HUMAN	K	272	ENSP00000445853:M272K;ENSP00000353516:M272K	ENSP00000353516:M272K	M	+	2	0	OR2W3	246126326	0.000000	0.05858	1.000000	0.80357	0.661000	0.39034	0.366000	0.20365	1.038000	0.40049	-0.311000	0.09066	ATG	T|0.459;A|0.541	0.541	strong		0.532	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
ZNF286B	729288	hgsc.bcm.edu	37	17	18565423	18565423	+	Missense_Mutation	SNP	G	G	A	rs9912852	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18565423G>A	ENST00000545289.1	-	5	1646	c.1396C>T	c.(1396-1398)Ccg>Tcg	p.P466S	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	466					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						CATTTGTACGGTTTCTTTCCA	0.393													.|||	1375	0.274561	0.2027	0.4496	5008	,	,		22033	0.1935		0.4066	False		,,,				2504	0.1953				p.P466S		Atlas-SNP	.											ZNF286B_ENST00000545289,colon,carcinoma,+2,2	ZNF286B	75	2	0			c.C1396T						PASS	.	G	SER/PRO	333,1051		41,251,400	137.0	131.0	133.0		1396	2.6	1.0	17	dbSNP_119	133	1243,1939		237,769,585	no	missense	ZNF286B	NM_001145045.1	74	278,1020,985	AA,AG,GG		39.0635,24.0607,34.516	probably-damaging	466/523	18565423	1576,2990	692	1591	2283	SO:0001583	missense	729288	exon5			TGTACGGTTTCTT		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1396C>T	17.37:g.18565423G>A	ENSP00000461413:p.Pro466Ser	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	260	122	0.469231	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.698;A|0.302	0.302	strong		0.393	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
CDH3	1001	hgsc.bcm.edu	37	16	68713823	68713823	+	Silent	SNP	C	C	A	rs2296408	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:68713823C>A	ENST00000264012.4	+	7	1357	c.813C>A	c.(811-813)acC>acA	p.T271T	CDH3_ENST00000429102.2_Silent_p.T271T|CDH3_ENST00000581171.1_Silent_p.T216T	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	271	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TCATGTTCACCATTCACCGGA	0.562													C|||	3044	0.607827	0.6679	0.5476	5008	,	,		18082	0.6141		0.6223	False		,,,				2504	0.5481				p.T271T		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.C813A						PASS	.	C		2957,1439	682.2+/-404.1	992,973,233	198.0	142.0	161.0		813	-10.6	0.0	16	dbSNP_100	161	5364,3236	650.6+/-400.7	1664,2036,600	no	coding-synonymous	CDH3	NM_001793.4		2656,3009,833	AA,AC,CC		37.6279,32.7343,35.9726		271/830	68713823	8321,4675	2198	4300	6498	SO:0001819	synonymous_variant	1001	exon7			GTTCACCATTCAC	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.813C>A	16.37:g.68713823C>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	124	122	0.983871	NM_001793	B2R6F4|Q05DI6	Silent	SNP	ENST00000264012.4	37	CCDS10868.1																																																																																			C|0.367;N|0.000	.	strong		0.562	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
USHBP1	83878	hgsc.bcm.edu	37	19	17373556	17373556	+	Silent	SNP	G	G	A	rs199682499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17373556G>A	ENST00000252597.3	-	4	620	c.447C>T	c.(445-447)ttC>ttT	p.F149F	USHBP1_ENST00000431146.2_Silent_p.F85F|USHBP1_ENST00000598570.1_5'UTR	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1									p.F149F(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						TTGTGCCTTCGAACTCCATCG	0.667													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17260	0.0		0.0	False		,,,				2504	0.0				p.F149F		Atlas-SNP	.											USHBP1,colon,carcinoma,0,1	USHBP1	85	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C447T						scavenged	.	C		1,4405		0,1,2202	56.0	56.0	56.0		447	-6.2	0.0	19		56	0,8598		0,0,4299	no	coding-synonymous	USHBP1	NM_031941.3		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		149/704	17373556	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	83878	exon4			GCCTTCGAACTCC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.447C>T	19.37:g.17373556G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	145	2	0.0137931	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			G|0.999;A|0.001	0.001	strong		0.667	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105897003	105897003	+	Silent	SNP	G	G	A	rs2241799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:105897003G>A	ENST00000393359.2	-	6	1725	c.1299C>T	c.(1297-1299)aaC>aaT	p.N433N	TGFBRAP1_ENST00000258449.1_Silent_p.N433N			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	433					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						TGCGGACCTCGTTCAGGTAGC	0.572													G|||	778	0.155351	0.0098	0.2176	5008	,	,		21326	0.1508		0.2117	False		,,,				2504	0.2546				p.N433N	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C1299T						PASS	.	G	,	186,4220	118.4+/-156.1	2,182,2019	156.0	130.0	139.0		1299,1299	-5.1	0.8	2	dbSNP_98	139	1767,6833	320.5+/-314.7	197,1373,2730	no	coding-synonymous,coding-synonymous	TGFBRAP1	NM_001142621.1,NM_004257.4	,	199,1555,4749	AA,AG,GG		20.5465,4.2215,15.0161	,	433/861,433/861	105897003	1953,11053	2203	4300	6503	SO:0001819	synonymous_variant	9392	exon6			GACCTCGTTCAGG	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.1299C>T	2.37:g.105897003G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	240	121	0.504167	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	37	CCDS2067.1																																																																																			G|0.853;A|0.147	0.147	strong		0.572	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
POLR2A	5430	hgsc.bcm.edu	37	17	7405937	7405937	+	Silent	SNP	C	C	T	rs2071504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7405937C>T	ENST00000322644.6	+	16	3072	c.2673C>T	c.(2671-2673)taC>taT	p.Y891Y		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	891					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				AGCTGCGCTACGGCGAAGACG	0.582													C|||	887	0.177117	0.1104	0.2334	5008	,	,		18438	0.1885		0.162	False		,,,				2504	0.2311				p.Y891Y		Atlas-SNP	.											.	POLR2A	157	.	0			c.C2673T						PASS	.	C		588,3818	259.8+/-263.3	47,494,1662	92.0	80.0	84.0		2673	-8.4	0.9	17	dbSNP_96	84	1264,7336	252.1+/-278.3	97,1070,3133	no	coding-synonymous	POLR2A	NM_000937.4		144,1564,4795	TT,TC,CC		14.6977,13.3454,14.2396		891/1971	7405937	1852,11154	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon16			GCGCTACGGCGAA			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.2673C>T	17.37:g.7405937C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			C|0.849;T|0.151	0.151	strong		0.582	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
HIGD1B	51751	hgsc.bcm.edu	37	17	42927721	42927721	+	Missense_Mutation	SNP	G	G	A	rs1071682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42927721G>A	ENST00000253410.2	+	3	508	c.257G>A	c.(256-258)aGc>aAc	p.S86N	HIGD1B_ENST00000591513.1_Missense_Mutation_p.S86N|EFTUD2_ENST00000426333.2_3'UTR|HIGD1B_ENST00000587021.1_Missense_Mutation_p.S41N	NM_016438.2	NP_057522.1	Q9P298	HIG1B_HUMAN	HIG1 hypoxia inducible domain family, member 1B	86	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.		S -> N (in dbSNP:rs1071682). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)	5		Prostate(33;0.109)				ACAATGTACAGCGATTACGTC	0.527													G|||	1128	0.22524	0.1959	0.2334	5008	,	,		19254	0.0843		0.3439	False		,,,				2504	0.2822				p.S86N		Atlas-SNP	.											.	HIGD1B	8	.	0			c.G257A						PASS	.	G	,,ASN/SER	971,3435	364.6+/-317.1	112,747,1344	107.0	99.0	102.0		,,257	4.2	1.0	17	dbSNP_86	102	3111,5489	470.9+/-367.9	578,1955,1767	yes	utr-3,utr-3,missense	EFTUD2,HIGD1B	NM_001142605.1,NM_004247.3,NM_016438.2	,,46	690,2702,3111	AA,AG,GG		36.1744,22.0381,31.3855	,,benign	,,86/100	42927721	4082,8924	2203	4300	6503	SO:0001583	missense	51751	exon4			TGTACAGCGATTA	AB038021	CCDS11488.1	17q21.31	2009-03-17	2009-03-17			ENSG00000131097			24318	protein-coding gene	gene with protein product			"""HIG1 domain family, member 1B"""			12477932	Standard	NM_016438		Approved	CLST11240, CLST11240-15	uc031rau.1	Q9P298		ENST00000253410.2:c.257G>A	17.37:g.42927721G>A	ENSP00000253410:p.Ser86Asn	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001271880	D3DX57|Q9P297	Missense_Mutation	SNP	ENST00000253410.2	37	CCDS11488.1	510	0.23351648351648352	104	0.21138211382113822	108	0.2983425414364641	46	0.08041958041958042	252	0.3324538258575198	G	8.023	0.760046	0.15846	0.220381	0.361744	ENSG00000131097	ENST00000253410	T	0.29917	1.55	5.24	4.23	0.50019	Hypoxia induced protein, domain (1);	0.358919	0.30201	N	0.010170	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999955091	B	0.02656	0.0	B	0.01281	0.0	T	0.42464	-0.9450	8	0.35671	T	0.21	-5.9784	7.5238	0.27643	0.2083:0.0:0.7917:0.0	rs1071682;rs2231649;rs3197382;rs3206868;rs11556249;rs17627800;rs52796922;rs61288939;rs1071682	86	Q9P298	HIG1B_HUMAN	N	86	ENSP00000253410:S86N	ENSP00000253410:S86N	S	+	2	0	HIGD1B	40283247	1.000000	0.71417	1.000000	0.80357	0.158000	0.22134	1.774000	0.38573	1.112000	0.41740	-0.466000	0.05196	AGC	G|0.720;A|0.280	0.280	strong		0.527	HIGD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448669.1	NM_016438	
TRIM59	286827	hgsc.bcm.edu	37	3	160156951	160156951	+	Silent	SNP	C	C	T	rs1141023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:160156951C>T	ENST00000309784.4	-	3	206	c.21G>A	c.(19-21)gaG>gaA	p.E7E	TRIM59_ENST00000543469.1_Silent_p.E7E|RP11-432B6.3_ENST00000483754.1_Silent_p.E7E	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	7					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GACAAGTTAACTCTTCCTCAA	0.328													C|||	412	0.0822684	0.0045	0.1009	5008	,	,		18066	0.0397		0.1839	False		,,,				2504	0.1135				p.E7E		Atlas-SNP	.											.	TRIM59	42	.	0			c.G21A						PASS	.	C		168,4236	101.2+/-139.8	4,160,2038	40.0	39.0	40.0		21	2.0	1.0	3	dbSNP_86	40	1742,6852	284.4+/-296.6	178,1386,2733	no	coding-synonymous	TRIM59	NM_173084.2		182,1546,4771	TT,TC,CC		20.27,3.8147,14.6946		7/404	160156951	1910,11088	2202	4297	6499	SO:0001819	synonymous_variant	286827	exon3			AGTTAACTCTTCC	AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	30834	protein-coding gene	gene with protein product			"""tripartite motif-containing 57"", ""tripartite motif-containing 59"""	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.21G>A	3.37:g.160156951C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	178	98	0.550562	NM_173084	A8K5G9|D3DNL9	Silent	SNP	ENST00000309784.4	37	CCDS3190.1																																																																																			C|0.882;T|0.118	0.118	strong		0.328	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084	
EPHA2	1969	hgsc.bcm.edu	37	1	16475126	16475126	+	Silent	SNP	C	C	T	rs6678618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16475126C>T	ENST00000358432.5	-	3	724	c.570G>A	c.(568-570)gcG>gcA	p.A190A	EPHA2_ENST00000461614.1_5'UTR	NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	190	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Mediates interaction with CLDN4.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	CGGAGAGCAGCGCCACACAGG	0.647													C|||	1135	0.226637	0.146	0.366	5008	,	,		19464	0.0308		0.3618	False		,,,				2504	0.2996				p.A190A		Atlas-SNP	.											EPHA2,NS,adenoma,0,1	EPHA2	102	1	0			c.G570A						PASS	.	C		734,3672	301.3+/-286.8	67,600,1536	63.0	61.0	62.0		570	-5.9	1.0	1	dbSNP_116	62	2971,5629	459.7+/-365.0	510,1951,1839	no	coding-synonymous	EPHA2	NM_004431.3		577,2551,3375	TT,TC,CC		34.5465,16.6591,28.4869		190/977	16475126	3705,9301	2203	4300	6503	SO:0001819	synonymous_variant	1969	exon3			GAGCAGCGCCACA	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.570G>A	1.37:g.16475126C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			C|0.748;T|0.252	0.252	strong		0.647	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
MSL1	339287	hgsc.bcm.edu	37	17	38285693	38285693	+	Silent	SNP	C	C	A	rs143879261	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38285693C>A	ENST00000398532.4	+	3	1503	c.1188C>A	c.(1186-1188)acC>acA	p.T396T	MSL1_ENST00000577454.1_Silent_p.T396T|MSL1_ENST00000578648.1_Silent_p.T396T|MSL1_ENST00000579565.1_Silent_p.T133T	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	396					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	7						CAGTGGACACCCCACCAAGAC	0.498													C|||	26	0.00519169	0.0008	0.0086	5008	,	,		16475	0.0		0.0159	False		,,,				2504	0.0031				p.T133T		Atlas-SNP	.											.	MSL1	21	.	0			c.C399A						PASS	.	C		17,3675		0,17,1829	50.0	52.0	52.0		399	6.0	1.0	17	dbSNP_134	52	182,8010		2,178,3916	no	coding-synonymous	MSL1	NM_001012241.1		2,195,5745	AA,AC,CC		2.2217,0.4605,1.6745		133/352	38285693	199,11685	1846	4096	5942	SO:0001819	synonymous_variant	339287	exon4			GGACACCCCACCA		CCDS45670.1	17q21.1	2011-03-21			ENSG00000188895	ENSG00000188895			27905	protein-coding gene	gene with protein product		614801				16227571, 16543150	Standard	NM_001012241		Approved	hMSL1, MSL-1, DKFZp686P24239	uc002hua.4	Q68DK7		ENST00000398532.4:c.1188C>A	17.37:g.38285693C>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	106	61	0.575472	NM_001012241	Q0VF46|Q69Z03	Silent	SNP	ENST00000398532.4	37																																																																																				C|0.992;A|0.008	0.008	strong		0.498	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241	
CCDC63	160762	hgsc.bcm.edu	37	12	111342558	111342558	+	Silent	SNP	G	G	T	rs34300256	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:111342558G>T	ENST00000308208.5	+	11	1751	c.1509G>T	c.(1507-1509)gtG>gtT	p.V503V	CCDC63_ENST00000545036.1_Silent_p.V463V|CCDC63_ENST00000552694.1_Silent_p.V424V	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	503										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						TCCCCCCAGTGCTGGGGGCTG	0.592													G|||	758	0.151358	0.1271	0.3516	5008	,	,		19331	0.002		0.2555	False		,,,				2504	0.089				p.V503V		Atlas-SNP	.											.	CCDC63	89	.	0			c.G1509T						PASS	.	G		640,3766	269.2+/-268.9	49,542,1612	58.0	58.0	58.0		1509	-0.4	0.0	12	dbSNP_126	58	2108,6492	352.9+/-328.9	260,1588,2452	no	coding-synonymous	CCDC63	NM_152591.1		309,2130,4064	TT,TG,GG		24.5116,14.5256,21.1287		503/564	111342558	2748,10258	2203	4300	6503	SO:0001819	synonymous_variant	160762	exon11			CCCAGTGCTGGGG	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"""outer row dynein assembly 5 homolog (Chlamydomonas)"""						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1509G>T	12.37:g.111342558G>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_152591	B4DY03|Q0P603|Q6P2E1	Silent	SNP	ENST00000308208.5	37	CCDS9151.1																																																																																			G|0.810;T|0.190	0.190	strong		0.592	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591	
TUBA8	51807	hgsc.bcm.edu	37	22	18609642	18609642	+	Silent	SNP	C	C	T	rs362203	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:18609642C>T	ENST00000330423.3	+	4	970	c.897C>T	c.(895-897)aaC>aaT	p.N299N	TUBA8_ENST00000316027.6_Silent_p.N233N	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	299					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						TTGAGCCCAACAGCCAGATGG	0.577													c|||	825	0.164736	0.0408	0.2421	5008	,	,		20969	0.4137		0.0358	False		,,,				2504	0.1534				p.N299N		Atlas-SNP	.											.	TUBA8	36	.	0			c.C897T						PASS	.	C	,	173,4233		5,163,2035	112.0	94.0	100.0		699,897	3.2	1.0	22	dbSNP_79	100	284,8316		3,278,4019	no	coding-synonymous,coding-synonymous	TUBA8	NM_001193414.1,NM_018943.2	,	8,441,6054	TT,TC,CC		3.3023,3.9265,3.5138	,	233/384,299/450	18609642	457,12549	2203	4300	6503	SO:0001819	synonymous_variant	51807	exon4			GCCCAACAGCCAG	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"""Tubulins"""	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.897C>T	22.37:g.18609642C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	190	96	0.505263	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Silent	SNP	ENST00000330423.3	37	CCDS13751.1																																																																																			C|0.928;T|0.072	0.072	strong		0.577	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943	
MYO1H	283446	hgsc.bcm.edu	37	12	109853349	109853349	+	Silent	SNP	A	A	G	rs73194218	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109853349A>G	ENST00000431443.2	+	14	1503	c.1503A>G	c.(1501-1503)ccA>ccG	p.P501P	MYO1H_ENST00000310903.5_Silent_p.P491P	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	501	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						TGGCTGGTCCAAAGGGCCGAA	0.522													A|||	138	0.0275559	0.0023	0.049	5008	,	,		17594	0.0		0.0785	False		,,,				2504	0.0225				p.P491P		Atlas-SNP	.											.	MYO1H	98	.	0			c.A1473G						PASS	.	A		51,3821		0,51,1885	47.0	48.0	48.0		1473	-11.0	0.0	12	dbSNP_130	48	551,7759		19,513,3623	no	coding-synonymous	MYO1H	NM_001101421.3		19,564,5508	GG,GA,AA		6.6306,1.3171,4.9417		491/1023	109853349	602,11580	1936	4155	6091	SO:0001819	synonymous_variant	283446	exon14			TGGTCCAAAGGGC		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.1503A>G	12.37:g.109853349A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				A|0.958;G|0.042	0.042	strong		0.522	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79059102	79059102	+	Missense_Mutation	SNP	C	C	T	rs148195966		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79059102C>T	ENST00000388820.4	-	19	3361	c.3151G>A	c.(3151-3153)Gag>Aag	p.E1051K	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1051					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						AGGTCCAGCTCTGGAGCCTCC	0.612																																					p.E1051K		Atlas-SNP	.											ADAMTS7,NS,neuroblastoma,0,1	ADAMTS7	142	1	0			c.G3151A						scavenged	.						17.0	21.0	20.0					15																	79059102		2128	4182	6310	SO:0001583	missense	11173	exon19			CCAGCTCTGGAGC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3151G>A	15.37:g.79059102C>T	ENSP00000373472:p.Glu1051Lys	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	83	3	0.0361446	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	c	11.90	1.776168	0.31411	.	.	ENSG00000136378	ENST00000388820	T	0.59083	0.29	4.12	3.16	0.36331	.	0.663295	0.12337	U	0.477850	T	0.42966	0.1226	L	0.36672	1.1	0.09310	N	1	B	0.15719	0.014	B	0.10450	0.005	T	0.23048	-1.0199	10	0.06757	T	0.87	.	11.4869	0.50358	0.0:0.7247:0.2753:0.0	.	1051	Q9UKP4	ATS7_HUMAN	K	1051	ENSP00000373472:E1051K	ENSP00000373472:E1051K	E	-	1	0	ADAMTS7	76846157	0.000000	0.05858	0.010000	0.14722	0.058000	0.15608	0.137000	0.15995	1.824000	0.53156	0.447000	0.29281	GAG	.	.	weak		0.612	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
NOS1AP	9722	hgsc.bcm.edu	37	1	162313735	162313735	+	Silent	SNP	C	C	T	rs3751284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:162313735C>T	ENST00000361897.5	+	6	966	c.564C>T	c.(562-564)agC>agT	p.S188S	NOS1AP_ENST00000530878.1_Silent_p.S183S|MIR556_ENST00000384996.1_RNA	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	188	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			ATGGAGAGAGCGAGAGGAACA	0.592													T|||	2158	0.430911	0.2829	0.451	5008	,	,		16087	0.6339		0.3549	False		,,,				2504	0.4857				p.S188S		Atlas-SNP	.											.	NOS1AP	139	.	0			c.C564T						PASS	.	T	,	1277,3129	700.4+/-406.6	188,901,1114	116.0	104.0	108.0		549,564	-8.2	0.1	1	dbSNP_107	108	3071,5529	661.4+/-401.9	550,1971,1779	no	coding-synonymous,coding-synonymous	NOS1AP	NM_001164757.1,NM_014697.2	,	738,2872,2893	TT,TC,CC		35.7093,28.9832,33.4307	,	183/502,188/507	162313735	4348,8658	2203	4300	6503	SO:0001819	synonymous_variant	9722	exon6			AGAGAGCGAGAGG	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"""C-terminal PDZ domain ligand of neuronal nitric oxide synthase"""	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.564C>T	1.37:g.162313735C>T		Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	470	271	0.576596	NM_014697	B7ZLF5|O43564|Q3T551|Q5VU95	Silent	SNP	ENST00000361897.5	37	CCDS1237.1																																																																																			C|0.642;T|0.358	0.358	strong		0.592	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697	
GAB2	9846	hgsc.bcm.edu	37	11	77930345	77930345	+	Silent	SNP	T	T	C	rs2450122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:77930345T>C	ENST00000361507.4	-	10	2089	c.2004A>G	c.(2002-2004)tcA>tcG	p.S668S	GAB2_ENST00000340149.2_Silent_p.S630S	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	668					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			TGGAAGGCTCTGAGGACTGCC	0.612													C|||	1325	0.264577	0.1989	0.3156	5008	,	,		19086	0.3978		0.1779	False		,,,				2504	0.2689				p.S668S		Atlas-SNP	.											.	GAB2	63	.	0			c.A2004G						PASS	.	C	,	794,3606	750.6+/-412.1	79,636,1485	112.0	93.0	100.0		1890,2004	-8.8	0.7	11	dbSNP_100	100	1387,7197	753.7+/-407.5	117,1153,3022	no	coding-synonymous,coding-synonymous	GAB2	NM_012296.3,NM_080491.2	,	196,1789,4507	CC,CT,TT		16.158,18.0455,16.7976	,	630/639,668/677	77930345	2181,10803	2200	4292	6492	SO:0001819	synonymous_variant	9846	exon10			AGGCTCTGAGGAC	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"""Pleckstrin homology (PH) domain containing"""	14458	protein-coding gene	gene with protein product	"""Grb2-associated binder 2"""	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.2004A>G	11.37:g.77930345T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			T|0.789;C|0.211	0.211	strong		0.612	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491	
CPT1B	1375	hgsc.bcm.edu	37	22	51011376	51011376	+	Missense_Mutation	SNP	G	G	C	rs8142477	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:51011376G>C	ENST00000360719.2	-	11	1417	c.1280C>G	c.(1279-1281)tCc>tGc	p.S427C	CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000312108.7_Missense_Mutation_p.S427C|CPT1B_ENST00000457250.1_Missense_Mutation_p.S393C|CPT1B_ENST00000440709.1_Intron|CPT1B_ENST00000405237.3_Missense_Mutation_p.S427C|CPT1B_ENST00000395650.2_Missense_Mutation_p.S427C|CPT1B_ENST00000434492.2_Missense_Mutation_p.S224C	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	427			S -> C (in dbSNP:rs8142477).		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		GGGGTCATAGGAGTAGGATTC	0.587													C|||	2118	0.422923	0.6679	0.2997	5008	,	,		18336	0.501		0.1143	False		,,,				2504	0.4162				p.S427C	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.C1280G						PASS	.	C	CYS/SER,CYS/SER,,CYS/SER,CYS/SER,CYS/SER,CYS/SER	2491,1915	547.2+/-377.2	718,1055,430	123.0	118.0	120.0		1178,1280,,1280,1280,1280,1280	-5.5	0.0	22	dbSNP_116	120	1004,7596	773.3+/-407.7	51,902,3347	yes	missense,missense,intron,missense,missense,missense,missense	CPT1B	NM_001145134.1,NM_001145135.1,NM_001145136.1,NM_001145137.1,NM_004377.3,NM_152245.2,NM_152246.2	112,112,,112,112,112,112	769,1957,3777	CC,CG,GG		11.6744,43.4635,26.8722	benign,benign,,benign,benign,benign,benign	393/739,427/773,,427/773,427/773,427/773,427/773	51011376	3495,9511	2203	4300	6503	SO:0001583	missense	1375	exon11			TCATAGGAGTAGG	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.1280C>G	22.37:g.51011376G>C	ENSP00000353945:p.Ser427Cys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	179	108	0.603352	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	37	CCDS14098.1	792	0.3626373626373626	315	0.6402439024390244	93	0.2569060773480663	291	0.5087412587412588	93	0.12269129287598944	C	3.878	-0.026487	0.07589	0.565365	0.116744	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000434492;ENST00000395650	D;D;D;D;D;D	0.89746	-2.56;-2.56;-2.56;-2.56;-2.56;-2.56	4.98	-5.54	0.02544	.	1.469010	0.04390	N	0.362247	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.005;0.003;0.003	T	0.17930	-1.0353	9	0.35671	T	0.21	0.3286	6.4139	0.21705	0.0:0.2947:0.318:0.3873	rs8142477;rs17836711;rs17848460;rs52832088;rs8142477	393;224;427	B7Z4U4;A2RRE8;Q92523	.;.;CPT1B_HUMAN	C	427;427;427;393;224;427	ENSP00000385486:S427C;ENSP00000312189:S427C;ENSP00000353945:S427C;ENSP00000409342:S393C;ENSP00000410966:S224C;ENSP00000379011:S427C	ENSP00000312189:S427C	S	-	2	0	CPT1B	49358242	0.027000	0.19231	0.000000	0.03702	0.001000	0.01503	0.686000	0.25392	-1.599000	0.01605	-2.174000	0.00321	TCC	G|0.699;C|0.301	0.301	strong		0.587	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318826	21318826	+	Missense_Mutation	SNP	G	G	A	rs142399667	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:21318826G>A	ENST00000583088.1	+	3	1067	c.172G>A	c.(172-174)Gcc>Acc	p.A58T	KCNJ12_ENST00000331718.5_Missense_Mutation_p.A58T	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	58					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CATTGAGTTCGCCAACATGGA	0.597										Prostate(3;0.18)																											p.A58T		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	0			c.G172A						scavenged	.	G	THR/ALA	69,4337	52.3+/-87.9	0,69,2134	197.0	131.0	153.0		172	5.3	1.0	17	dbSNP_134	153	62,8538	26.8+/-75.7	0,62,4238	yes	missense	KCNJ12	NM_021012.4	58	0,131,6372	AA,AG,GG		0.7209,1.566,1.0072	benign	58/434	21318826	131,12875	2203	4300	6503	SO:0001583	missense	100134444	exon3			GAGTTCGCCAACA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.172G>A	17.37:g.21318826G>A	ENSP00000463778:p.Ala58Thr	Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	259	45	0.173745	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692589	0.30052	0.01566	0.007209	ENSG00000184185	ENST00000331718	D	0.93859	-3.3	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.248894	0.40908	D	0.000997	T	0.77631	0.4159	N	0.16233	0.39	0.36661	D	0.877951	B	0.12630	0.006	B	0.18263	0.021	T	0.80009	-0.1562	10	0.32370	T	0.25	.	10.2342	0.43273	0.1224:0.0:0.8776:0.0	.	58	Q14500	IRK12_HUMAN	T	58	ENSP00000328150:A58T	ENSP00000328150:A58T	A	+	1	0	KCNJ12	21259419	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	2.230000	0.42999	2.506000	0.84524	0.591000	0.81541	GCC	G|0.993;A|0.007	0.007	strong		0.597	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
ANKRD61	100310846	hgsc.bcm.edu	37	7	6071060	6071060	+	Silent	SNP	G	G	A	rs4724769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6071060G>A	ENST00000409061.1	+	1	54	c.54G>A	c.(52-54)aaG>aaA	p.K18K	EIF2AK1_ENST00000536084.1_Intron|EIF2AK1_ENST00000199389.6_Intron	NM_001271700.1	NP_001258629.1	A6NGH8	ANR61_HUMAN	ankyrin repeat domain 61	18																	ACAGTGCCAAGTCCCTGGAAG	0.468													G|||	1691	0.33766	0.1679	0.4164	5008	,	,		19742	0.3641		0.4742	False		,,,				2504	0.3436				p.K18K		Atlas-SNP	.											.	.	.	.	0			c.G54A						PASS	.																																			SO:0001819	synonymous_variant	100310846	exon1			TGCCAAGTCCCTG		CCDS64590.1	7p22	2013-01-10			ENSG00000157999	ENSG00000157999		"""Ankyrin repeat domain containing"""	22467	protein-coding gene	gene with protein product							Standard	NM_001271700		Approved		uc031swn.1	A6NGH8	OTTHUMG00000154561	ENST00000409061.1:c.54G>A	7.37:g.6071060G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	171	87	0.508772	NM_001271700		Silent	SNP	ENST00000409061.1	37																																																																																				G|0.600;A|0.400	0.400	strong		0.468	ANKRD61-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000335991.1		
CBLB	868	hgsc.bcm.edu	37	3	105438957	105438957	+	Silent	SNP	T	T	G	rs2305036	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:105438957T>G	ENST00000264122.4	-	10	1662	c.1341A>C	c.(1339-1341)ctA>ctC	p.L447L	CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000405772.1_Silent_p.L447L|CBLB_ENST00000394027.3_Silent_p.L469L|CBLB_ENST00000403724.1_Silent_p.L447L	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	447					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						CGTCCAAGTCTAGCATCGGCA	0.463			Mis S		AML								G|||	1053	0.210264	0.1936	0.2968	5008	,	,		20280	0.2192		0.2376	False		,,,				2504	0.1339				p.L447L	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.A1341C						PASS	.	G		815,3591	749.3+/-412.0	76,663,1464	118.0	100.0	106.0		1341	0.9	1.0	3	dbSNP_100	106	1843,6757	730.6+/-406.8	207,1429,2664	no	coding-synonymous	CBLB	NM_170662.3		283,2092,4128	GG,GT,TT		21.4302,18.4975,20.4367		447/983	105438957	2658,10348	2203	4300	6503	SO:0001819	synonymous_variant	868	exon10			CAAGTCTAGCATC	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.1341A>C	3.37:g.105438957T>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	153	69	0.45098	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	37	CCDS2948.1																																																																																			T|0.786;G|0.214	0.214	strong		0.463	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
NPHP4	261734	hgsc.bcm.edu	37	1	5927169	5927169	+	Missense_Mutation	SNP	G	G	A	rs113445782	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:5927169G>A	ENST00000378156.4	-	25	3744	c.3479C>T	c.(3478-3480)cCg>cTg	p.P1160L	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	1160					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CATTCCCACCGGAGCACCTGG	0.572													G|||	29	0.00579073	0.0023	0.0144	5008	,	,		17891	0.0		0.0119	False		,,,				2504	0.0041				p.P1160L		Atlas-SNP	.											.	NPHP4	119	.	0			c.C3479T						PASS	.	G	LEU/PRO	11,4023		0,11,2006	43.0	50.0	48.0		3479	1.9	0.0	1	dbSNP_132	48	150,8204		2,146,4029	yes	missense	NPHP4	NM_015102.3	98	2,157,6035	AA,AG,GG		1.7955,0.2727,1.2996	benign	1160/1427	5927169	161,12227	2017	4177	6194	SO:0001583	missense	261734	exon25			CCCACCGGAGCAC	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.3479C>T	1.37:g.5927169G>A	ENSP00000367398:p.Pro1160Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	45	15	0.333333	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	15	0.006868131868131868	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	6	0.0079155672823219	G	3.745	-0.052840	0.07362	0.002727	0.017955	ENSG00000131697	ENST00000378156	D	0.87887	-2.31	5.91	1.9	0.25705	.	0.431232	0.23258	N	0.050170	T	0.67961	0.2949	L	0.50333	1.59	0.33276	D	0.561694	B;P	0.36587	0.167;0.559	B;B	0.32022	0.024;0.139	T	0.74340	-0.3697	10	0.49607	T	0.09	.	7.8011	0.29174	0.0619:0.3462:0.482:0.1099	.	102;1160	Q6ZSL3;O75161	.;NPHP4_HUMAN	L	1160	ENSP00000367398:P1160L	ENSP00000367398:P1160L	P	-	2	0	NPHP4	5849756	0.880000	0.30214	0.017000	0.16124	0.000000	0.00434	1.456000	0.35201	0.096000	0.17463	-2.702000	0.00136	CCG	G|0.992;A|0.008	0.008	strong		0.572	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
SLC38A9	153129	hgsc.bcm.edu	37	5	54960609	54960609	+	Silent	SNP	A	A	G	rs4865614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:54960609A>G	ENST00000396865.2	-	8	1200	c.609T>C	c.(607-609)ctT>ctC	p.L203L	SLC38A9_ENST00000515629.1_Silent_p.L140L|SLC38A9_ENST00000318672.3_Silent_p.L203L|SLC38A9_ENST00000416547.2_Silent_p.L79L|SLC38A9_ENST00000512595.1_Silent_p.L176L|SLC38A9_ENST00000539768.1_Silent_p.L203L	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	203					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				CCAAGGAGAAAAGGAGACTCG	0.368													A|||	2797	0.558506	0.4297	0.585	5008	,	,		13345	0.4613		0.661	False		,,,				2504	0.7086				p.L203L		Atlas-SNP	.											.	SLC38A9	50	.	0			c.T609C						PASS	.	A		2109,2297	572.2+/-383.3	499,1111,593	52.0	50.0	51.0		609	1.5	1.0	5	dbSNP_111	51	5624,2976	662.0+/-401.9	1832,1960,508	yes	coding-synonymous	SLC38A9	NM_173514.2		2331,3071,1101	GG,GA,AA		34.6047,47.8665,40.5428		203/562	54960609	7733,5273	2203	4300	6503	SO:0001819	synonymous_variant	153129	exon8			GGAGAAAAGGAGA		CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"""Solute carriers"""	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.609T>C	5.37:g.54960609A>G		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	271	140	0.516605	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Silent	SNP	ENST00000396865.2	37	CCDS3968.1																																																																																			A|0.433;G|0.567	0.567	strong		0.368	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514	
CLCA2	9635	hgsc.bcm.edu	37	1	86920904	86920904	+	Silent	SNP	A	A	G	rs2390057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86920904A>G	ENST00000370565.4	+	14	2688	c.2526A>G	c.(2524-2526)caA>caG	p.Q842Q		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	842					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)	p.Q842Q(1)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TCTCACCCCAAATTTCCACGA	0.393													A|||	1647	0.328874	0.2057	0.2435	5008	,	,		17291	0.4405		0.335	False		,,,				2504	0.4346				p.Q842Q	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											CLCA2,NS,carcinoma,0,1	CLCA2	102	1	1	Substitution - coding silent(1)	stomach(1)	c.A2526G						PASS	.	A		1085,3321	393.5+/-328.9	142,801,1260	110.0	104.0	106.0		2526	-1.1	0.0	1	dbSNP_100	106	2876,5724	451.3+/-362.6	470,1936,1894	no	coding-synonymous	CLCA2	NM_006536.5		612,2737,3154	GG,GA,AA		33.4419,24.6255,30.4552		842/944	86920904	3961,9045	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon14			ACCCCAAATTTCC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2526A>G	1.37:g.86920904A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			A|0.686;G|0.314	0.314	strong		0.393	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
TFF2	7032	hgsc.bcm.edu	37	21	43771047	43771047	+	Missense_Mutation	SNP	T	T	G	rs116946921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43771047T>G	ENST00000291526.4	-	1	190	c.20A>C	c.(19-21)cAg>cCg	p.Q7P	TFF2_ENST00000475297.1_5'UTR	NM_005423.4	NP_005414.1	Q03403	TFF2_HUMAN	trefoil factor 2	7				MGRRDAQLLAALLVLGLCA -> RHGTARRPAPGSAPRPGA MC (in Ref. 1). {ECO:0000305}.	calcium-mediated signaling (GO:0019722)|chemokine-mediated signaling pathway (GO:0070098)|digestion (GO:0007586)|negative regulation of gastric acid secretion (GO:0060455)|negative regulation of inflammatory response (GO:0050728)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				large_intestine(1)|pancreas(1)|urinary_tract(1)	3						TGCCAGGAGCTGGGCGTCTCG	0.557													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		18720	0.0		0.0099	False		,,,				2504	0.0031				p.Q7P		Atlas-SNP	.											.	TFF2	14	.	0			c.A20C						PASS	.	T	PRO/GLN	6,4400	9.9+/-24.2	0,6,2197	49.0	49.0	49.0		20	-0.5	0.0	21	dbSNP_132	49	76,8524	44.5+/-102.8	0,76,4224	yes	missense	TFF2	NM_005423.4	76	0,82,6421	GG,GT,TT		0.8837,0.1362,0.6305	benign	7/130	43771047	82,12924	2203	4300	6503	SO:0001583	missense	7032	exon1			AGGAGCTGGGCGT		CCDS13684.1	21q22.3	2008-07-28	2008-07-28		ENSG00000160181	ENSG00000160181			11756	protein-coding gene	gene with protein product		182590	"""spasmolytic protein 1"""	SML1		1505966, 9043862	Standard	NM_005423		Approved		uc002zaw.3	Q03403	OTTHUMG00000086797	ENST00000291526.4:c.20A>C	21.37:g.43771047T>G	ENSP00000291526:p.Gln7Pro	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	245	122	0.497959	NM_005423	Q15854	Missense_Mutation	SNP	ENST00000291526.4	37	CCDS13684.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	8.564	0.878447	0.17395	0.001362	0.008837	ENSG00000160181	ENST00000291526	T	0.29917	1.55	4.16	-0.498	0.12019	.	1.715760	0.03793	N	0.263260	T	0.12178	0.0296	N	0.13043	0.29	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15321	-1.0441	9	.	.	.	-5.8652	4.9546	0.14033	0.0:0.3079:0.4202:0.2719	.	7	Q03403	TFF2_HUMAN	P	7	ENSP00000291526:Q7P	.	Q	-	2	0	TFF2	42644116	0.000000	0.05858	0.001000	0.08648	0.317000	0.28152	-0.214000	0.09292	-0.341000	0.08376	0.379000	0.24179	CAG	T|0.994;G|0.006	0.006	strong		0.557	TFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195355.1	NM_005423	
ARSE	415	hgsc.bcm.edu	37	X	2856155	2856155	+	Missense_Mutation	SNP	C	C	T	rs35143646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2856155C>T	ENST00000381134.3	-	9	1336	c.1270G>A	c.(1270-1272)Ggc>Agc	p.G424S	ARSE_ENST00000545496.1_Missense_Mutation_p.G449S|ARSE_ENST00000540563.1_Missense_Mutation_p.G379S	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	424			G -> S (in dbSNP:rs35143646). {ECO:0000269|Ref.2}.		cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGCACCTCGCCGCCCGCCAGC	0.602													C|||	2169	0.57457	0.059	0.415	3775	,	,		11186	0.6786		0.5278	False		,,,				2504	0.6012				p.G424S		Atlas-SNP	.											.	ARSE	43	.	0			c.G1270A						PASS	.	C	SER/GLY	687,3144		65,474,83,1093,484	52.0	55.0	54.0		1270	3.5	0.0	X	dbSNP_126	54	4504,2211		1084,1066,1270,277,591	no	missense	ARSE	NM_000047.2	56	1149,1540,1353,1370,1075	TT,TC,T,CC,C		32.9263,17.9327,49.2225	benign	424/590	2856155	5191,5355	2199	4288	6487	SO:0001583	missense	415	exon9			CCTCGCCGCCCGC	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1270G>A	X.37:g.2856155C>T	ENSP00000370526:p.Gly424Ser	Somatic	395	0	0		WXS	Illumina HiSeq	Phase_I	132	130	0.984848	NM_000047	Q53FT2|Q53FU8	Missense_Mutation	SNP	ENST00000381134.3	37	CCDS14122.1	951	0.5732368896925859	22	0.046413502109704644	94	0.3671875	255	0.796875	275	0.5308880308880309	c	10.51	1.369388	0.24771	0.179327	0.670737	ENSG00000157399	ENST00000540563;ENST00000545496;ENST00000381134	D;D;D	0.93859	-3.3;-3.3;-3.3	3.46	3.46	0.39613	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.055865	0.64402	D	0.000001	T	0.00012	0.0000	L	0.56769	1.78	0.22424	P	0.999114817	P;P;P	0.50819	0.931;0.939;0.905	P;B;P	0.46299	0.511;0.41;0.49	T	0.48502	-0.9030	9	0.20519	T	0.43	.	14.3929	0.66991	0.0:1.0:0.0:0.0	rs35143646;rs60405351	379;449;424	F5H324;F5GYY5;P51690	.;.;ARSE_HUMAN	S	379;449;424	ENSP00000438198:G379S;ENSP00000441417:G449S;ENSP00000370526:G424S	ENSP00000370526:G424S	G	-	1	0	ARSE	2866155	1.000000	0.71417	0.017000	0.16124	0.005000	0.04900	6.335000	0.72949	1.355000	0.45865	0.540000	0.68198	GGC	C|0.503;T|0.497	0.497	strong		0.602	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
ALPK2	115701	hgsc.bcm.edu	37	18	56204977	56204977	+	Silent	SNP	C	C	T	rs3809971	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204977C>T	ENST00000361673.3	-	5	2655	c.2442G>A	c.(2440-2442)acG>acA	p.T814T	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	814						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TATCAAAACACGTTCCTTGGT	0.458													T|||	2024	0.404153	0.4312	0.4294	5008	,	,		22574	0.2361		0.5726	False		,,,				2504	0.3497				p.T814T		Atlas-SNP	.											.	ALPK2	487	.	0			c.G2442A						PASS	.	T		1983,2423	618.3+/-393.1	445,1093,665	121.0	112.0	115.0		2442	3.2	0.0	18	dbSNP_107	115	4589,4011	555.6+/-386.7	1236,2117,947	no	coding-synonymous	ALPK2	NM_052947.3		1681,3210,1612	TT,TC,CC		46.6395,45.0068,49.4695		814/2171	56204977	6572,6434	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			AAAACACGTTCCT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2442G>A	18.37:g.56204977C>T		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	187	68	0.363636	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.526;T|0.474	0.474	strong		0.458	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ARHGEF3	50650	hgsc.bcm.edu	37	3	56763619	56763619	+	Silent	SNP	A	A	G	rs6765444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:56763619A>G	ENST00000296315.3	-	10	1428	c.1260T>C	c.(1258-1260)aaT>aaC	p.N420N	ARHGEF3_ENST00000497267.1_Silent_p.N391N|ARHGEF3_ENST00000338458.4_Silent_p.N452N|ARHGEF3_ENST00000496106.1_Silent_p.N426N|ARHGEF3_ENST00000413728.2_Silent_p.N426N	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	420	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		TTTGGGATCCATTTTTGAAAC	0.403													G|||	1337	0.266973	0.2458	0.1124	5008	,	,		21392	0.3442		0.165	False		,,,				2504	0.4305				p.N452N		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.T1356C						PASS	.	G	,,	1080,3326	688.2+/-404.9	115,850,1238	84.0	89.0	87.0		1356,1278,1260	-3.0	1.0	3	dbSNP_116	87	1323,7277	748.0+/-407.3	97,1129,3074	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF3	NM_001128615.1,NM_001128616.1,NM_019555.2	,,	212,1979,4312	GG,GA,AA		15.3837,24.512,18.4761	,,	452/559,426/533,420/527	56763619	2403,10603	2203	4300	6503	SO:0001819	synonymous_variant	50650	exon13			GGATCCATTTTTG	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"""Rho guanine nucleotide exchange factors"""	683	protein-coding gene	gene with protein product	"""exchange factor found in platelets and leukemic and neuronal tissues, XPLN"", ""RhoGEF protein"""	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.1260T>C	3.37:g.56763619A>G		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	194	192	0.989691	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			A|0.787;G|0.213	0.213	strong		0.403	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
MTX3	345778	hgsc.bcm.edu	37	5	79282798	79282798	+	Missense_Mutation	SNP	G	G	C	rs9293796	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:79282798G>C	ENST00000512528.1	-	7	734	c.714C>G	c.(712-714)agC>agG	p.S238R	MTX3_ENST00000512560.1_Missense_Mutation_p.S177R|MTX3_ENST00000509852.1_Missense_Mutation_p.S238R			Q5HYI7	MTX3_HUMAN	metaxin 3	238			S -> R (in dbSNP:rs9293796).		protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(1)	7		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		TAAAATAACTGCTCAGGATGT	0.388													G|||	346	0.0690895	0.0204	0.0836	5008	,	,		16931	0.0079		0.1421	False		,,,				2504	0.1125				p.S238R		Atlas-SNP	.											.	MTX3	29	.	0			c.C714G						PASS	.	G	ARG/SER,ARG/SER	157,3587		5,147,1720	109.0	108.0	109.0		714,531	0.6	0.6	5	dbSNP_119	109	1193,7017		84,1025,2996	yes	missense,missense	MTX3	NM_001010891.4,NM_001167741.1	110,110	89,1172,4716	CC,CG,GG		14.5311,4.1934,11.2933	benign,benign	238/249,177/252	79282798	1350,10604	1872	4105	5977	SO:0001583	missense	345778	exon7			ATAACTGCTCAGG	BX538064	CCDS47239.1, CCDS47239.2, CCDS54872.1	5q14.1	2004-08-18				ENSG00000177034			24812	protein-coding gene	gene with protein product						15087125	Standard	NM_001010891		Approved		uc010jah.3	Q5HYI7		ENST00000512528.1:c.714C>G	5.37:g.79282798G>C	ENSP00000424798:p.Ser238Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	129	72	0.55814	NM_001010891	B4DL65|E9PB57|Q7Z380|Q8NB92	Missense_Mutation	SNP	ENST00000512528.1	37		161	0.07371794871794872	7	0.014227642276422764	40	0.11049723756906077	4	0.006993006993006993	110	0.14511873350923482	G	11.50	1.657008	0.29425	0.041934	0.145311	ENSG00000177034	ENST00000512560;ENST00000509852;ENST00000512528;ENST00000418095	T;T;T	0.47869	0.83;0.83;0.83	5.92	0.553	0.17235	Glutathione S-transferase, C-terminal-like (1);	.	.	.	.	T	0.00144	0.0004	N	0.25245	0.725	0.80722	P	0.0	B;B	0.17038	0.02;0.013	B;B	0.19946	0.023;0.027	T	0.15093	-1.0449	8	0.22706	T	0.39	.	5.7058	0.17907	0.4608:0.1366:0.4026:0.0	rs9293796;rs17196986;rs52831730;rs9293796	238;238	Q5HYI7-4;Q5HYI7	.;MTX3_HUMAN	R	177;238;238;238	ENSP00000423600:S177R;ENSP00000423302:S238R;ENSP00000424798:S238R	ENSP00000392181:S238R	S	-	3	2	MTX3	79318554	0.780000	0.28664	0.556000	0.28293	0.977000	0.68977	1.525000	0.35953	0.416000	0.25844	0.467000	0.42956	AGC	G|0.925;C|0.075	0.075	strong		0.388	MTX3-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372567.1	XM_293971	
DNAH2	146754	hgsc.bcm.edu	37	17	7682605	7682605	+	Silent	SNP	C	C	T	rs17806045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7682605C>T	ENST00000572933.1	+	36	7046	c.5586C>T	c.(5584-5586)atC>atT	p.I1862I	DNAH2_ENST00000389173.2_Silent_p.I1862I			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1862	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GCATCAACATCGAGGTGCTGT	0.557													c|||	358	0.0714856	0.0038	0.1527	5008	,	,		19154	0.001		0.169	False		,,,				2504	0.0777				p.I1862I		Atlas-SNP	.											.	DNAH2	498	.	0			c.C5586T						PASS	.	T		135,4271	97.1+/-135.8	3,129,2071	98.0	77.0	84.0		5586	-11.0	0.1	17	dbSNP_123	84	1239,7361	248.5+/-276.1	92,1055,3153	no	coding-synonymous	DNAH2	NM_020877.2		95,1184,5224	TT,TC,CC		14.407,3.064,10.5644		1862/4428	7682605	1374,11632	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon35			CAACATCGAGGTG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.5586C>T	17.37:g.7682605C>T		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	243	117	0.481481	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			C|0.910;T|0.090	0.090	strong		0.557	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
SRD5A1	6715	hgsc.bcm.edu	37	5	6652009	6652009	+	Silent	SNP	G	G	A	rs8192186	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:6652009G>A	ENST00000274192.5	+	2	582	c.348G>A	c.(346-348)gcG>gcA	p.A116A	SRD5A1_ENST00000537411.1_3'UTR|SRD5A1_ENST00000538824.1_Intron|SRD5A1_ENST00000504286.1_3'UTR	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	116					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)	p.A116A(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	CACTGTTGGCGTGTACAATGG	0.413													G|||	1463	0.292133	0.3328	0.3919	5008	,	,		18667	0.1587		0.3897	False		,,,				2504	0.2035				p.A116A		Atlas-SNP	.											SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	1	Substitution - coding silent(1)	stomach(1)	c.G348A						PASS	.	G		1441,2965	467.7+/-354.9	242,957,1004	178.0	154.0	162.0		348	-11.4	0.0	5	dbSNP_117	162	3219,5381	486.1+/-371.8	610,1999,1691	no	coding-synonymous	SRD5A1	NM_001047.2		852,2956,2695	AA,AG,GG		37.4302,32.7054,35.8296		116/260	6652009	4660,8346	2203	4300	6503	SO:0001819	synonymous_variant	6715	exon2			GTTGGCGTGTACA	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.348G>A	5.37:g.6652009G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	216	91	0.421296	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Silent	SNP	ENST00000274192.5	37	CCDS3870.1																																																																																			G|0.652;A|0.348	0.348	strong		0.413	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
INTS8	55656	hgsc.bcm.edu	37	8	95888307	95888307	+	Silent	SNP	C	C	T	rs1129152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95888307C>T	ENST00000523731.1	+	24	2827	c.2694C>T	c.(2692-2694)gcC>gcT	p.A898A	INTS8_ENST00000447247.1_Silent_p.A881A	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	898					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					TGTAGGTGGCCATTTTATGTC	0.299													C|||	2354	0.470048	0.2511	0.5288	5008	,	,		19137	0.6528		0.4573	False		,,,				2504	0.5491				p.A898A		Atlas-SNP	.											.	INTS8	92	.	0			c.C2694T						PASS	.	C		1206,3196	395.8+/-329.8	189,828,1184	88.0	93.0	91.0		2694	3.3	1.0	8	dbSNP_86	91	3547,5049	509.3+/-377.2	729,2089,1480	no	coding-synonymous	INTS8	NM_017864.2		918,2917,2664	TT,TC,CC		41.2634,27.3966,36.5672		898/996	95888307	4753,8245	2201	4298	6499	SO:0001819	synonymous_variant	55656	exon24			GGTGGCCATTTTA	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"""chromosome 8 open reading frame 52"""	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2694C>T	8.37:g.95888307C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	171	76	0.444444	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Silent	SNP	ENST00000523731.1	37	CCDS34925.1	1043	0.4775641025641026	139	0.28252032520325204	197	0.5441988950276243	360	0.6293706293706294	347	0.4577836411609499	C	8.736	0.917867	0.17982	0.273966	0.412634	ENSG00000164941	ENST00000520526	.	.	.	5.67	3.32	0.38043	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40701	-0.9549	3	.	.	.	-29.7653	3.4379	0.07453	0.5358:0.271:0.0717:0.1216	rs1129152;rs2290389;rs3186706;rs11538719;rs17411821;rs17663895;rs59844557;rs1129152	.	.	.	L	703	.	.	P	+	2	0	INTS8	95957483	0.840000	0.29493	1.000000	0.80357	0.984000	0.73092	-0.005000	0.12855	0.526000	0.28541	-0.467000	0.05162	CCA	C|0.581;T|0.419	0.419	strong		0.299	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864	
CHAF1A	10036	hgsc.bcm.edu	37	19	4442336	4442336	+	Missense_Mutation	SNP	C	C	T	rs9352	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4442336C>T	ENST00000301280.5	+	14	2869	c.2768C>T	c.(2767-2769)gCg>gTg	p.A923V		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	923	Binds to p60.		A -> V (in dbSNP:rs9352). {ECO:0000269|PubMed:11250073, ECO:0000269|PubMed:7600578}.		cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CCGGATGCTGCGGGTGAGAAG	0.582								Chromatin Structure					C|||	2844	0.567891	0.4191	0.7507	5008	,	,		21333	0.6657		0.5427	False		,,,				2504	0.5644				p.A923V		Atlas-SNP	.											.	CHAF1A	69	.	0			c.C2768T						PASS	.	C	VAL/ALA	1955,2451	528.2+/-372.3	441,1073,689	121.0	79.0	93.0		2768	0.1	0.9	19	dbSNP_52	93	4794,3806	579.9+/-391.0	1338,2118,844	yes	missense	CHAF1A	NM_005483.2	64	1779,3191,1533	TT,TC,CC		44.2558,44.3713,48.1086	possibly-damaging	923/957	4442336	6749,6257	2203	4300	6503	SO:0001583	missense	10036	exon14			ATGCTGCGGGTGA	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.2768C>T	19.37:g.4442336C>T	ENSP00000301280:p.Ala923Val	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	297	124	0.417508	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	37	CCDS32875.1	1255	0.5746336996336996	215	0.4369918699186992	259	0.7154696132596685	378	0.6608391608391608	403	0.5316622691292876	C	15.47	2.842317	0.51057	0.443713	0.557442	ENSG00000167670	ENST00000301280	T	0.22743	1.94	5.02	0.0919	0.14470	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.999999999406989	P	0.39250	0.665	B	0.26770	0.073	T	0.21245	-1.0251	8	0.87932	D	0	-22.3004	6.7886	0.23687	0.1666:0.5848:0.2486:0.0	rs9352;rs243381;rs1131237;rs2230634;rs3177927;rs11556316;rs52805653;rs57571457;rs9352	923	Q13111	CAF1A_HUMAN	V	923	ENSP00000301280:A923V	ENSP00000301280:A923V	A	+	2	0	CHAF1A	4393336	0.549000	0.26481	0.855000	0.33649	0.081000	0.17604	0.240000	0.18042	0.178000	0.19917	-0.311000	0.09066	GCG	C|0.465;T|0.535	0.535	strong		0.582	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483	
AHCTF1	25909	hgsc.bcm.edu	37	1	247053355	247053355	+	Missense_Mutation	SNP	G	G	C	rs116104791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247053355G>C	ENST00000391829.2	-	17	2180	c.2057C>G	c.(2056-2058)tCt>tGt	p.S686C	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000326225.3_Missense_Mutation_p.S695C|AHCTF1_ENST00000366508.1_Missense_Mutation_p.S721C			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	686	Necessary for cytoplasmic localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CAACTGCACAGAATCATCTAG	0.323													G|||	3	0.000599042	0.0	0.0014	5008	,	,		16361	0.0		0.002	False		,,,				2504	0.0				p.S695C	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C2084G						PASS	.	G	CYS/SER	3,4403	6.2+/-15.9	0,3,2200	98.0	105.0	102.0		2084	5.7	1.0	1	dbSNP_132	102	29,8571	19.8+/-62.0	0,29,4271	yes	missense	AHCTF1	NM_015446.4	112	0,32,6471	CC,CG,GG		0.3372,0.0681,0.246	benign	695/2276	247053355	32,12974	2203	4300	6503	SO:0001583	missense	25909	exon17			TGCACAGAATCAT		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.2057C>G	1.37:g.247053355G>C	ENSP00000375705:p.Ser686Cys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		.	.	.	.	.	.	.	.	.	.	G	13.35	2.211972	0.39102	6.81E-4	0.003372	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.33438	1.41;1.41;1.41	5.7	5.7	0.88788	.	0.285678	0.32852	N	0.005574	T	0.16727	0.0402	N	0.08118	0	0.22112	N	0.999352	B;B	0.27932	0.194;0.122	B;B	0.16289	0.015;0.007	T	0.15178	-1.0446	10	0.38643	T	0.18	-7.094	14.5479	0.68044	0.0:0.0:0.8186:0.1814	.	721;686	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	C	721;695;686	ENSP00000355464:S721C;ENSP00000355465:S695C;ENSP00000375705:S686C	ENSP00000355465:S695C	S	-	2	0	AHCTF1	245119978	0.999000	0.42202	1.000000	0.80357	0.821000	0.46438	2.896000	0.48656	2.675000	0.91044	0.591000	0.81541	TCT	G|0.997;C|0.003	0.003	strong		0.323	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
GDF9	2661	hgsc.bcm.edu	37	5	132198199	132198199	+	Silent	SNP	G	G	A	rs254286	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:132198199G>A	ENST00000378673.2	-	3	1313	c.447C>T	c.(445-447)acC>acT	p.T149T	GDF9_ENST00000296875.2_Silent_p.T149T|GDF9_ENST00000464378.1_5'UTR			O60383	GDF9_HUMAN	growth differentiation factor 9	149					female gamete generation (GO:0007292)|negative regulation of cell growth (GO:0030308)|oocyte growth (GO:0001555)|positive regulation of cell proliferation (GO:0008284)|regulation of progesterone secretion (GO:2000870)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(1)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	22		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGTGTTCAACGGTAGTAATGC	0.383													G|||	2283	0.455871	0.3313	0.4885	5008	,	,		19646	0.2897		0.5994	False		,,,				2504	0.6247				p.T149T		Atlas-SNP	.											.	GDF9	50	.	0			c.C447T	GRCh37	CM056327	GDF9	M	rs254286	PASS	.	G		1582,2820	454.2+/-350.6	287,1008,906	76.0	79.0	78.0		447	-4.7	0.0	5	dbSNP_79	78	4988,3612	615.5+/-396.4	1439,2110,751	no	coding-synonymous	GDF9	NM_005260.3		1726,3118,1657	AA,AG,GG		42.0,35.9382,49.4693		149/455	132198199	6570,6432	2201	4300	6501	SO:0001819	synonymous_variant	2661	exon2			TTCAACGGTAGTA		CCDS4162.1, CCDS75299.1	5q31.1	2014-01-30			ENSG00000164404	ENSG00000164404		"""Endogenous ligands"""	4224	protein-coding gene	gene with protein product		601918				7760846	Standard	NM_005260		Approved		uc003kxz.1	O60383	OTTHUMG00000059842	ENST00000378673.2:c.447C>T	5.37:g.132198199G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_005260	Q4VAW5	Silent	SNP	ENST00000378673.2	37	CCDS4162.1																																																																																			G|0.516;A|0.484	0.484	strong		0.383	GDF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133060.2	NM_005260	
OR10A2	341276	hgsc.bcm.edu	37	11	6891528	6891528	+	Silent	SNP	C	C	G	rs7117739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6891528C>G	ENST00000307322.4	+	1	605	c.543C>G	c.(541-543)ctC>ctG	p.L181L		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ACACAGCACTCTTTGAGATCT	0.512													-|||	1643	0.328075	0.2073	0.379	5008	,	,		21095	0.3135		0.3678	False		,,,				2504	0.4294				p.L181L		Atlas-SNP	.											.	OR10A2	55	.	0			c.C543G						PASS	.	G		898,3504		92,714,1395	221.0	171.0	188.0		543	0.9	0.4	11	dbSNP_116	188	3344,5248		664,2016,1616	yes	coding-synonymous	OR10A2	NM_001004460.1		756,2730,3011	GG,GC,CC		38.9199,20.3998,32.6458		181/304	6891528	4242,8752	2201	4296	6497	SO:0001819	synonymous_variant	341276	exon1			AGCACTCTTTGAG	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"""GPCR / Class A : Olfactory receptors"""	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.543C>G	11.37:g.6891528C>G		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	256	123	0.480469	NM_001004460	B2RNL9|Q6IFG9	Silent	SNP	ENST00000307322.4	37	CCDS31415.1																																																																																			C|0.680;G|0.320	0.320	strong		0.512	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460	
DTD2	112487	hgsc.bcm.edu	37	14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	rs17097904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:31926584G>A	ENST00000310850.4	-	1	132	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	DTD2_ENST00000356180.4_Missense_Mutation_p.R6W|RP11-176H8.1_ENST00000547378.1_Missense_Mutation_p.R6W	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	6			R -> W (in dbSNP:rs17097904).		D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R6W(1)									TGAGGAATCCGGCTACCCTCA	0.697																																					p.R6W		Atlas-SNP	.											C14orf126,third_ventricle,glioma,0,2	.	.	2	1	Substitution - Missense(1)	skin(1)	c.C16T						scavenged	.						12.0	12.0	12.0					14																	31926584		2183	4278	6461	SO:0001583	missense	112487	exon1			GAATCCGGCTACC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 126"""	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.16C>T	14.37:g.31926584G>A	ENSP00000312224:p.Arg6Trp	Somatic	108	2	0.0185185		WXS	Illumina HiSeq	Phase_I	87	5	0.0574713	NM_080664	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758136	0.69763	.	.	ENSG00000203546;ENSG00000129480;ENSG00000129480	ENST00000547378;ENST00000310850;ENST00000356180	T;T;T	0.55052	0.54;0.71;0.71	4.84	2.97	0.34412	D-Tyr tRNAtyr deacylase-like domain (1);	0.302778	0.30901	N	0.008651	T	0.52419	0.1733	M	0.69823	2.125	0.36855	D	0.888115	D	0.67145	0.996	B	0.43623	0.425	T	0.65220	-0.6221	10	0.87932	D	0	.	11.9711	0.53063	0.0:0.0:0.5428:0.4572	rs17097904	6	Q96FN9	DTD2_HUMAN	W	6	ENSP00000447056:R6W;ENSP00000312224:R6W;ENSP00000348503:R6W	ENSP00000312224:R6W	R	-	1	2	C14orf126;RP11-176H8.1	30996335	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	0.080000	0.14802	0.618000	0.30179	0.561000	0.74099	CGG	.	.	weak		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664	
PPP6R2	9701	hgsc.bcm.edu	37	22	50878196	50878196	+	Missense_Mutation	SNP	G	G	A	rs13057311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50878196G>A	ENST00000216061.5	+	21	2565	c.2195G>A	c.(2194-2196)aGg>aAg	p.R732K	PPP6R2_ENST00000395744.3_Missense_Mutation_p.R705K|PPP6R2_ENST00000359139.3_Missense_Mutation_p.R706K|PPP6R2_ENST00000395741.3_Missense_Mutation_p.R706K			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	732			R -> K (in dbSNP:rs13057311).			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						GGAGTGGTGAGGGACGTGGGT	0.602													G|||	970	0.19369	0.1059	0.2565	5008	,	,		20218	0.1419		0.2962	False		,,,				2504	0.2157				p.R732K		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G2195A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	567,3839	245.9+/-254.7	39,489,1675	69.0	58.0	62.0		2195,2117,2117,2114	1.5	0.0	22	dbSNP_121	62	2430,6170	398.7+/-346.2	358,1714,2228	no	missense,missense,missense,missense	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	26,26,26,26	397,2203,3903	AA,AG,GG		28.2558,12.8688,23.0432	benign,benign,benign,benign	732/960,706/934,706/928,705/933	50878196	2997,10009	2203	4300	6503	SO:0001583	missense	9701	exon20			TGGTGAGGGACGT	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.2195G>A	22.37:g.50878196G>A	ENSP00000216061:p.Arg732Lys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	174	57	0.327586	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	37		463	0.211996336996337	62	0.12601626016260162	96	0.26519337016574585	82	0.14335664335664336	223	0.2941952506596306	G	0.039	-1.293713	0.01375	0.128688	0.282558	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.83	1.46	0.22682	.	0.800541	0.12348	N	0.476819	T	0.00012	0.0000	N	0.22421	0.69	0.51482	P	7.500000000004725E-5	P;B;B;B;B;B	0.35174	0.488;0.113;0.069;0.113;0.113;0.191	B;B;B;B;B;B	0.26416	0.05;0.048;0.021;0.048;0.048;0.069	T	0.28396	-1.0045	9	0.05959	T	0.93	-2.4742	7.137	0.25533	0.1152:0.0:0.4072:0.4776	rs13057311;rs17183769;rs13057311	265;732;732;706;705;706	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	K	706;706;705;732	ENSP00000352051:R706K;ENSP00000379090:R706K;ENSP00000379093:R705K;ENSP00000216061:R732K	ENSP00000216061:R732K	R	+	2	0	PPP6R2	49225062	.	.	0.023000	0.16930	0.201000	0.24016	.	.	0.071000	0.16664	-0.291000	0.09656	AGG	G|0.783;A|0.217	0.217	strong		0.602	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	
ABCA12	26154	hgsc.bcm.edu	37	2	215901774	215901774	+	Silent	SNP	C	C	T	rs17501837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:215901774C>T	ENST00000272895.7	-	8	1107	c.888G>A	c.(886-888)gtG>gtA	p.V296V	AC072062.3_ENST00000437897.3_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	296					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.V296V(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AAACCTTCTGCACAACCAGCA	0.418													C|||	1119	0.223442	0.1354	0.2565	5008	,	,		17010	0.4127		0.2058	False		,,,				2504	0.1421				p.V296V	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											ABCA12,NS,carcinoma,0,1	ABCA12	368	1	1	Substitution - coding silent(1)	breast(1)	c.G888A						PASS	.	C		658,3748	279.6+/-274.9	49,560,1594	83.0	83.0	83.0		888	1.7	0.6	2	dbSNP_123	83	1810,6790	325.5+/-317.0	214,1382,2704	no	coding-synonymous	ABCA12	NM_173076.2		263,1942,4298	TT,TC,CC		21.0465,14.9342,18.9759		296/2596	215901774	2468,10538	2203	4300	6503	SO:0001819	synonymous_variant	26154	exon8			CTTCTGCACAACC	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.888G>A	2.37:g.215901774C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																			C|0.788;T|0.212	0.212	strong		0.418	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
IRF5	3663	hgsc.bcm.edu	37	7	128588712	128588712	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128588712C>T	ENST00000402030.2	+	9	1409	c.1337C>T	c.(1336-1338)tCa>tTa	p.S446L	IRF5_ENST00000357234.5_Missense_Mutation_p.S462L|IRF5_ENST00000249375.4_Missense_Mutation_p.S446L|IRF5_ENST00000473745.1_Missense_Mutation_p.S446L|IRF5_ENST00000477535.1_Missense_Mutation_p.S360L	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	446					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						CTACAGATCTCAAACCCAGAC	0.577																																					p.S462L		Atlas-SNP	.											.	IRF5	40	.	0			c.C1385T						PASS	.						123.0	128.0	126.0					7																	128588712		2203	4300	6503	SO:0001583	missense	3663	exon9			AGATCTCAAACCC		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.1337C>T	7.37:g.128588712C>T	ENSP00000385352:p.Ser446Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	99	16	0.161616	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	37	CCDS5808.1	.	.	.	.	.	.	.	.	.	.	C	33	5.274132	0.95459	.	.	ENSG00000128604	ENST00000357234;ENST00000477535;ENST00000402030;ENST00000249375;ENST00000473745;ENST00000412326	D;D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92;-3.92	5.88	5.88	0.94601	SMAD domain-like (1);SMAD/FHA domain (1);	0.000000	0.49916	D	0.000135	D	0.97445	0.9164	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.993;0.993;0.999	D	0.97569	1.0103	10	0.62326	D	0.03	-6.6903	17.7218	0.88353	0.0:1.0:0.0:0.0	.	360;446;462	E7EW54;Q13568;Q13568-2	.;IRF5_HUMAN;.	L	462;360;446;446;446;436	ENSP00000349770:S462L;ENSP00000419950:S360L;ENSP00000385352:S446L;ENSP00000249375:S446L;ENSP00000419149:S446L	ENSP00000249375:S446L	S	+	2	0	IRF5	128375948	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.487000	0.81328	2.778000	0.95560	0.655000	0.94253	TCA	.	.	none		0.577	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627	
SVIL	6840	hgsc.bcm.edu	37	10	29822159	29822159	+	Silent	SNP	T	T	C	rs7076239	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29822159T>C	ENST00000355867.4	-	8	1889	c.1137A>G	c.(1135-1137)ctA>ctG	p.L379L	SVIL_ENST00000375398.2_Silent_p.L379L|SVIL_ENST00000375400.3_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	379					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CTGGCGTCACTAGCTTGGCGG	0.562													C|||	1556	0.310703	0.3502	0.3862	5008	,	,		18887	0.0823		0.4274	False		,,,				2504	0.319				p.L379L		Atlas-SNP	.											SVIL,caecum,carcinoma,-2,1	SVIL	226	1	0			c.A1137G						PASS	.	C	,	1599,2807	665.1+/-401.5	298,1003,902	88.0	75.0	79.0		,1137	3.7	0.3	10	dbSNP_116	79	3839,4761	610.3+/-395.7	858,2123,1319	no	intron,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	1156,3126,2221	CC,CT,TT		44.6395,36.2914,41.8115	,	,379/2215	29822159	5438,7568	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			CGTCACTAGCTTG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1137A>G	10.37:g.29822159T>C		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	232	103	0.443966	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			T|0.634;C|0.366	0.366	strong		0.562	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
ADH4	127	hgsc.bcm.edu	37	4	100052733	100052733	+	Silent	SNP	C	C	A	rs1126670	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100052733C>A	ENST00000265512.7	-	6	839	c.765G>T	c.(763-765)ccG>ccT	p.P255P	ADH4_ENST00000505590.1_Silent_p.P274P|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000508393.1_Silent_p.P274P|ADH4_ENST00000423445.1_Silent_p.P274P	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	255					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		CTTCCTGGATCGGTTTATGTA	0.438													C|||	4243	0.847244	0.8608	0.7709	5008	,	,		19123	0.999		0.6978	False		,,,				2504	0.8804				p.P255P		Atlas-SNP	.											ADH4,NS,carcinoma,-1,1	ADH4	35	1	0			c.G765T						PASS	.	C		3626,780	752.9+/-412.3	1487,652,64	121.0	122.0	122.0		765	-0.6	0.2	4	dbSNP_86	122	5885,2715	682.6+/-403.8	1994,1897,409	no	coding-synonymous	ADH4	NM_000670.3		3481,2549,473	AA,AC,CC		31.5698,17.7031,26.8722		255/381	100052733	9511,3495	2203	4300	6503	SO:0001819	synonymous_variant	127	exon6			CTGGATCGGTTTA	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"""Alcohol dehydrogenases"""	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.765G>T	4.37:g.100052733C>A		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	184	184	1	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	37	CCDS34032.1																																																																																			C|0.217;A|0.783	0.783	strong		0.438	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	
AMH	268	hgsc.bcm.edu	37	19	2249634	2249634	+	Silent	SNP	G	G	A	rs61736575	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:2249634G>A	ENST00000221496.4	+	1	325	c.303G>A	c.(301-303)ggG>ggA	p.G101G	MIR4321_ENST00000592276.1_RNA	NM_000479.3	NP_000470	P03971	MIS_HUMAN	anti-Mullerian hormone	101			G -> V (in PMDS1). {ECO:0000269|PubMed:8162013}.		aging (GO:0007568)|cell-cell signaling (GO:0007267)|gonadal mesoderm development (GO:0007506)|Mullerian duct regression (GO:0001880)|positive regulation of gene expression (GO:0010628)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|preantral ovarian follicle growth (GO:0001546)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|urogenital system development (GO:0001655)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			lung(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCACCTTCGGGGTCTGCAACA	0.736									Persistant Mullerian Duct Syndrome (type I and II)				G|||	320	0.0638978	0.0174	0.062	5008	,	,		14660	0.129		0.0457	False		,,,				2504	0.0798				p.G101G		Atlas-SNP	.											.	AMH	12	.	0			c.G303A						PASS	.	G		75,3965		1,73,1946	4.0	5.0	5.0		303	-3.0	0.0	19	dbSNP_129	5	272,7712		4,264,3724	no	coding-synonymous	AMH	NM_000479.3		5,337,5670	AA,AG,GG		3.4068,1.8564,2.8859		101/561	2249634	347,11677	2020	3992	6012	SO:0001819	synonymous_variant	268	exon1	Familial Cancer Database	PMDS, Persistent Oviduct Syndrome	CTTCGGGGTCTGC	K03474	CCDS12085.1	19p13.3	2014-01-30				ENSG00000104899		"""Endogenous ligands"""	464	protein-coding gene	gene with protein product		600957				3754790, 18784351	Standard	NM_000479		Approved	MIS	uc002lvh.2	P03971		ENST00000221496.4:c.303G>A	19.37:g.2249634G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_000479	O75246|Q6GTN3	Silent	SNP	ENST00000221496.4	37	CCDS12085.1																																																																																			G|0.939;A|0.061	0.061	strong		0.736	AMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451276.3	NM_000479	
DAGLB	221955	hgsc.bcm.edu	37	7	6449496	6449496	+	Missense_Mutation	SNP	T	T	C	rs2303361	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6449496T>C	ENST00000297056.6	-	15	2160	c.1991A>G	c.(1990-1992)cAa>cGa	p.Q664R	DAGLB_ENST00000436575.1_Missense_Mutation_p.Q623R|DAGLB_ENST00000425398.2_Missense_Mutation_p.Q535R	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	664			Q -> R (in dbSNP:rs2303361). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GGAGACCCCTTGTGCTGGACA	0.587													T|||	816	0.162939	0.0545	0.1816	5008	,	,		17814	0.2669		0.2107	False		,,,				2504	0.1401				p.Q664R		Atlas-SNP	.											.	DAGLB	74	.	0			c.A1991G						PASS	.	T	ARG/GLN,ARG/GLN	414,3992		20,374,1809	62.0	59.0	60.0		1604,1991	-1.7	0.0	7	dbSNP_100	60	1889,6711		231,1427,2642	yes	missense,missense	DAGLB	NM_001142936.1,NM_139179.3	43,43	251,1801,4451	CC,CT,TT		21.9651,9.3963,17.7072	benign,benign	535/544,664/673	6449496	2303,10703	2203	4300	6503	SO:0001583	missense	221955	exon15			ACCCCTTGTGCTG	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1991A>G	7.37:g.6449496T>C	ENSP00000297056:p.Gln664Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	129	77	0.596899	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	37	CCDS5350.1	388	0.17765567765567766	30	0.06097560975609756	71	0.19613259668508287	124	0.21678321678321677	163	0.21503957783641162	.	5.573	0.290535	0.10567	0.093963	0.219651	ENSG00000164535	ENST00000297056;ENST00000425398;ENST00000436575	T;T;T	0.44083	0.94;0.93;0.94	5.79	-1.66	0.08265	.	1.121680	0.06392	N	0.717245	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	1.999999999946489E-6	B;B;B;B	0.13145	0.007;0.0;0.003;0.0	B;B;B;B	0.08055	0.003;0.001;0.001;0.0	T	0.25012	-1.0144	9	0.11182	T	0.66	-17.9873	6.5442	0.22397	0.0:0.2794:0.3284:0.3923	rs2303361;rs57945063;rs2303361	535;478;664;361	B4DQU0;B4DQQ6;Q8NCG7;B3KRA0	.;.;DGLB_HUMAN;.	R	664;535;623	ENSP00000297056:Q664R;ENSP00000391171:Q535R;ENSP00000404785:Q623R	ENSP00000297056:Q664R	Q	-	2	0	DAGLB	6416021	0.003000	0.15002	0.000000	0.03702	0.274000	0.26718	0.453000	0.21811	-0.549000	0.06191	-0.280000	0.10049	CAA	T|0.832;C|0.168	0.168	strong		0.587	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
POMGNT1	55624	hgsc.bcm.edu	37	1	46660295	46660295	+	Silent	SNP	T	T	C	rs2292487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46660295T>C	ENST00000371984.3	-	8	838	c.681A>G	c.(679-681)aaA>aaG	p.K227K	POMGNT1_ENST00000396420.3_Missense_Mutation_p.N188S|POMGNT1_ENST00000535522.1_Silent_p.K205K|POMGNT1_ENST00000371992.1_Silent_p.K227K|POMGNT1_ENST00000485714.1_5'Flank|POMGNT1_ENST00000371986.3_Silent_p.K227K	NM_017739.3	NP_060209	Q8WZA1	PMGT1_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)	227					protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)			breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(166;0.155)					GGGCAGGTGATTTAGAATGTT	0.587													C|||	1670	0.333466	0.3343	0.3963	5008	,	,		17783	0.1726		0.3549	False		,,,				2504	0.4315				p.K227K		Atlas-SNP	.											.	POMGNT1	96	.	0			c.A681G						PASS	.	C		1548,2858	670.9+/-402.4	266,1016,921	80.0	87.0	85.0		681	3.7	1.0	1	dbSNP_100	85	3000,5600	665.1+/-402.2	518,1964,1818	no	coding-synonymous	POMGNT1	NM_017739.3		784,2980,2739	CC,CT,TT		34.8837,35.1339,34.9685		227/661	46660295	4548,8458	2203	4300	6503	SO:0001819	synonymous_variant	55624	exon8			AGGTGATTTAGAA		CCDS531.1, CCDS57995.1	1p34.1	2014-09-17	2013-07-31		ENSG00000085998	ENSG00000085998	2.4.1.-	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	19139	protein-coding gene	gene with protein product	"""protein O-mannose beta-1,2-N-acetylglucosaminyltransferase"""	606822	"""muscle-eye-brain disease"", ""protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase"""	MEB		11742540, 12788071	Standard	NM_017739		Approved	FLJ20277, MGAT1.2, LGMD2O	uc001cpg.3	Q8WZA1	OTTHUMG00000007604	ENST00000371984.3:c.681A>G	1.37:g.46660295T>C		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_017739	D3DQ16|Q5VST2|Q5VST3|Q9BV55|Q9H9L8|Q9NXF9|Q9NYF7	Silent	SNP	ENST00000371984.3	37	CCDS531.1	654	0.29945054945054944	169	0.3434959349593496	123	0.3397790055248619	101	0.17657342657342656	261	0.34432717678100266	C	12.07	1.828845	0.32329	0.351339	0.348837	ENSG00000085998	ENST00000396420	.	.	.	5.93	3.73	0.42828	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47094	P	6.890000000000507E-4	.	.	.	.	.	.	T	0.29366	-1.0014	4	0.39692	T	0.17	-24.1574	10.3327	0.43831	0.0:0.703:0.0:0.297	rs2292487;rs59667023;rs2292487	.	.	.	S	188	.	ENSP00000379698:N188S	N	-	2	0	POMGNT1	46432882	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	0.575000	0.23729	0.844000	0.35094	-0.215000	0.12644	AAT	T|0.670;C|0.330	0.330	strong		0.587	POMGNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020146.1	NM_017739	
CCDC66	285331	hgsc.bcm.edu	37	3	56628031	56628031	+	Missense_Mutation	SNP	G	G	A	rs7637449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:56628031G>A	ENST00000394672.3	+	10	1449	c.1379G>A	c.(1378-1380)cGa>cAa	p.R460Q	CCDC66_ENST00000326595.7_Missense_Mutation_p.R426Q|CCDC66_ENST00000436465.2_Missense_Mutation_p.R460Q	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	460			R -> Q (in dbSNP:rs7637449). {ECO:0000269|PubMed:15489334}.		post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		CGAGACAGACGACGACAAAAA	0.378													G|||	1077	0.215056	0.0741	0.2839	5008	,	,		20188	0.0486		0.5388	False		,,,				2504	0.1953				p.R460Q		Atlas-SNP	.											.	CCDC66	145	.	0			c.G1379A						PASS	.	G	GLN/ARG,GLN/ARG	678,3728	287.2+/-279.2	66,546,1591	181.0	169.0	173.0		1277,1379	5.8	0.9	3	dbSNP_116	173	4621,3979	600.5+/-394.2	1241,2139,920	yes	missense,missense	CCDC66	NM_001012506.4,NM_001141947.1	43,43	1307,2685,2511	AA,AG,GG		46.2674,15.3881,40.7427	probably-damaging,probably-damaging	426/915,460/949	56628031	5299,7707	2203	4300	6503	SO:0001583	missense	285331	exon10			ACAGACGACGACA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1379G>A	3.37:g.56628031G>A	ENSP00000378167:p.Arg460Gln	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	191	84	0.439791	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	617	0.2825091575091575	42	0.08536585365853659	118	0.3259668508287293	34	0.05944055944055944	423	0.558047493403694	G	29.8	5.038495	0.93630	0.153881	0.537326	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.51521	-0.8695	9	0.72032	D	0.01	-9.6521	17.8518	0.88748	0.0:0.0:1.0:0.0	rs7637449;rs52797312;rs58163850;rs7637449	460	A2RUB6	CCD66_HUMAN	Q	416;460;426;460	ENSP00000401451:R416Q;ENSP00000378167:R460Q;ENSP00000326050:R426Q;ENSP00000404320:R460Q	ENSP00000326050:R426Q	R	+	2	0	CCDC66	56603071	0.998000	0.40836	0.875000	0.34327	0.968000	0.65278	4.880000	0.63107	2.739000	0.93911	0.585000	0.79938	CGA	G|0.660;A|0.340	0.340	strong		0.378	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
HYI	81888	hgsc.bcm.edu	37	1	43917637	43917637	+	Silent	SNP	G	G	A	rs2251802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43917637G>A	ENST00000372425.4	-	4	669	c.474C>T	c.(472-474)gaC>gaT	p.D158D	SZT2_ENST00000562955.1_3'UTR|HYI_ENST00000372426.1_Silent_p.D110D|HYI_ENST00000372434.1_Silent_p.D183D|HYI_ENST00000486909.1_Silent_p.D158D|HYI-AS1_ENST00000444386.1_RNA|HYI_ENST00000583037.1_Silent_p.D85D|HYI_ENST00000372432.1_Silent_p.D158D|SZT2_ENST00000372442.1_3'UTR			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)	158							hydroxypyruvate isomerase activity (GO:0008903)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	6	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				AGTACTGGGGGTCAGTGATGC	0.597													G|||	1117	0.223043	0.1884	0.389	5008	,	,		18026	0.0784		0.4215	False		,,,				2504	0.0971				p.D183D		Atlas-SNP	.											.	HYI	23	.	0			c.C549T						PASS	.	G	,,	1028,3378	378.5+/-322.9	108,812,1283	106.0	111.0	109.0		474,,474	2.5	1.0	1	dbSNP_100	109	3560,5040	516.2+/-378.8	760,2040,1500	no	coding-synonymous,utr-3,coding-synonymous	SZT2,HYI	NM_001190880.2,NM_015284.3,NM_031207.5	,,	868,2852,2783	AA,AG,GG		41.3953,23.3318,35.276	,,	158/278,,158/248	43917637	4588,8418	2203	4300	6503	SO:0001819	synonymous_variant	81888	exon5			CTGGGGGTCAGTG		CCDS488.1, CCDS488.2, CCDS53309.1, CCDS72771.1	1p34.2	2010-06-24	2010-06-24		ENSG00000178922	ENSG00000178922	5.3.1.22		26948	protein-coding gene	gene with protein product			"""hydroxypyruvate isomerase homolog (E. coli)"""			10561547	Standard	NM_031207		Approved	HT036	uc001cjo.3	Q5T013	OTTHUMG00000007502	ENST00000372425.4:c.474C>T	1.37:g.43917637G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	160	159	0.99375	NM_001243526	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Silent	SNP	ENST00000372425.4	37	CCDS53309.1	622	0.2847985347985348	103	0.20934959349593496	153	0.42265193370165743	46	0.08041958041958042	320	0.42216358839050133	G	9.510	1.105568	0.20632	0.233318	0.413953	ENSG00000178922	ENST00000470662;ENST00000487366	.	.	.	5.38	2.46	0.29980	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45948	-0.9226	3	.	.	.	.	4.5099	0.11906	0.2125:0.0:0.5195:0.268	rs2251802;rs3184210;rs17400088;rs17404673;rs17851702;rs2251802	.	.	.	I	77;82	.	.	T	-	2	0	HYI	43690224	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	0.684000	0.25364	0.334000	0.23590	0.462000	0.41574	ACC	G|0.679;A|0.321	0.321	strong		0.597	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207	
SORL1	6653	hgsc.bcm.edu	37	11	121448090	121448090	+	Silent	SNP	T	T	G	rs57514896|rs2070045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:121448090T>G	ENST00000260197.7	+	25	3690	c.3561T>G	c.(3559-3561)tcT>tcG	p.S1187S	SORL1_ENST00000525532.1_Silent_p.S131S|SORL1_ENST00000532694.1_Silent_p.S33S|SORL1_ENST00000534286.1_Silent_p.S97S	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1187	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)	p.S1187S(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		GGGACTGGTCTGATGAAGCCA	0.512													T|||	1707	0.340855	0.0787	0.438	5008	,	,		22094	0.5685		0.2406	False		,,,				2504	0.4949				p.S1187S		Atlas-SNP	.											SORL1,NS,carcinoma,0,1	SORL1	218	1	1	Substitution - coding silent(1)	stomach(1)	c.T3561G						PASS	.	T		448,3958	213.1+/-232.8	17,414,1772	186.0	167.0	173.0		3561	-1.3	1.0	11	dbSNP_96	173	1991,6607	350.6+/-327.9	222,1547,2530	no	coding-synonymous	SORL1	NM_003105.5		239,1961,4302	GG,GT,TT		23.1565,10.168,18.7558		1187/2215	121448090	2439,10565	2203	4299	6502	SO:0001819	synonymous_variant	6653	exon25			CTGGTCTGATGAA	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.3561T>G	11.37:g.121448090T>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	165	74	0.448485	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	37	CCDS8436.1																																																																																			T|0.760;G|0.240	0.240	strong		0.512	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
DCTN1	1639	hgsc.bcm.edu	37	2	74589828	74589828	+	Missense_Mutation	SNP	C	C	T	rs200834352		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74589828C>T	ENST00000361874.3	-	30	3875	c.3558G>A	c.(3556-3558)atG>atA	p.M1186I	DCTN1_ENST00000409240.1_Missense_Mutation_p.M1144I|DCTN1_ENST00000409438.1_Missense_Mutation_p.M1047I|DCTN1_ENST00000407639.2_Missense_Mutation_p.M1052I|RP11-287D1.3_ENST00000451608.2_Missense_Mutation_p.M99I|DCTN1_ENST00000394003.3_Missense_Mutation_p.M1179I|DCTN1_ENST00000409868.1_Missense_Mutation_p.M1164I|DCTN1_ENST00000409567.3_Missense_Mutation_p.M1161I	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	1186					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CCACTTGCTCCATAAGTTGGG	0.572																																					p.M1186I		Atlas-SNP	.											.	DCTN1	110	.	0			c.G3558A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	0,4406		0,0,2203	62.0	49.0	53.0		3483,3141,3432,3537,3558,3156	4.7	1.0	2		53	3,8597	2.2+/-6.3	0,3,4297	no	missense,missense,missense,missense,missense,missense	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	10,10,10,10,10,10	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign,benign,benign,benign	1161/1254,1047/1140,1144/1237,1179/1272,1186/1279,1052/1145	74589828	3,13003	2203	4300	6503	SO:0001583	missense	1639	exon30			TTGCTCCATAAGT		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.3558G>A	2.37:g.74589828C>T	ENSP00000354791:p.Met1186Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.269980	0.23221	0.0	3.49E-4	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	5.53	4.65	0.58169	.	0.185557	0.25978	N	0.027082	T	0.59702	0.2213	N	0.19112	0.55	0.34587	D	0.715042	B;B;B;B;B;B;B	0.09022	0.0;0.0;0.001;0.0;0.002;0.0;0.0	B;B;B;B;B;B;B	0.10450	0.0;0.0;0.0;0.0;0.005;0.001;0.001	T	0.61964	-0.6954	10	0.25751	T	0.34	-3.2341	13.1932	0.59723	0.0:0.9221:0.0:0.0779	.	1161;1144;1186;1179;1052;1047;1169	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4;A8MWX9	.;.;DCTN1_HUMAN;.;.;.;.	I	1186;1179;1169;1052;1047;1144;1164;1161	ENSP00000354791:M1186I;ENSP00000377571:M1179I;ENSP00000384844:M1052I;ENSP00000387270:M1047I;ENSP00000386406:M1144I;ENSP00000387327:M1164I;ENSP00000386843:M1161I	ENSP00000354791:M1186I	M	-	3	0	DCTN1	74443336	1.000000	0.71417	1.000000	0.80357	0.213000	0.24496	1.852000	0.39348	1.332000	0.45431	-0.218000	0.12543	ATG	C|0.999;T|0.001	0.001	weak		0.572	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
ERN1	2081	hgsc.bcm.edu	37	17	62121480	62121480	+	Silent	SNP	T	T	C	rs196912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:62121480T>C	ENST00000433197.3	-	22	2897	c.2802A>G	c.(2800-2802)acA>acG	p.T934T		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GGAAGCGAGATGTGAAGTAGC	0.617													T|||	2914	0.581869	0.2194	0.6009	5008	,	,		15693	0.6806		0.7515	False		,,,				2504	0.7822				p.T934T		Atlas-SNP	.											.	ERN1	102	.	0			c.A2802G						PASS	.	T		1315,2811		230,855,978	46.0	54.0	51.0		2802	-10.4	0.0	17	dbSNP_79	51	6424,2018		2457,1510,254	no	coding-synonymous	ERN1	NM_001433.3		2687,2365,1232	CC,CT,TT		23.9043,31.8711,38.423		934/978	62121480	7739,4829	2063	4221	6284	SO:0001819	synonymous_variant	2081	exon22			GCGAGATGTGAAG	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.2802A>G	17.37:g.62121480T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_001433		Silent	SNP	ENST00000433197.3	37	CCDS45762.1																																																																																			T|0.405;C|0.595	0.595	strong		0.617	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433	
IL17RB	55540	hgsc.bcm.edu	37	3	53886912	53886912	+	Silent	SNP	C	C	T	rs3733075	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:53886912C>T	ENST00000288167.3	+	5	378	c.369C>T	c.(367-369)taC>taT	p.Y123Y		NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B	123					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|regulation of cell growth (GO:0001558)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		CATTTTCCTACATCGGCTTCC	0.413													C|||	2150	0.429313	0.4281	0.3228	5008	,	,		21206	0.5913		0.3449	False		,,,				2504	0.4264				p.Y123Y		Atlas-SNP	.											.	IL17RB	27	.	0			c.C369T						PASS	.	C		1780,2626	526.2+/-371.8	345,1090,768	119.0	100.0	107.0		369	0.2	0.1	3	dbSNP_107	107	2828,5772	446.1+/-361.2	448,1932,1920	no	coding-synonymous	IL17RB	NM_018725.3		793,3022,2688	TT,TC,CC		32.8837,40.3995,35.4298		123/503	53886912	4608,8398	2203	4300	6503	SO:0001819	synonymous_variant	55540	exon5			TTCCTACATCGGC	AF212365	CCDS2874.1	3p21.1	2008-02-05		2003-07-09	ENSG00000056736	ENSG00000056736		"""Interleukins and interleukin receptors"""	18015	protein-coding gene	gene with protein product		605458	"""interleukin 17B receptor"""	IL17BR		10749887, 10815801	Standard	NM_018725		Approved	IL17RH1, EVI27, CRL4	uc003dha.3	Q9NRM6	OTTHUMG00000158280	ENST00000288167.3:c.369C>T	3.37:g.53886912C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	182	93	0.510989	NM_018725	Q9BPZ0|Q9NRL4|Q9NRM5	Silent	SNP	ENST00000288167.3	37	CCDS2874.1																																																																																			C|0.603;T|0.397	0.397	strong		0.413	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48258772	48258772	+	Silent	SNP	G	G	A	rs11083895	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48258772G>A	ENST00000246802.5	+	9	1259	c.1221G>A	c.(1219-1221)ggG>ggA	p.G407G	GLTSCR2_ENST00000598681.1_3'UTR|CTD-2571L23.6_ENST00000602048.1_RNA|SNORD23_ENST00000408876.1_RNA	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	407						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GAAGGCTGGGGCGGCTCAAGT	0.716													G|||	2618	0.522764	0.2315	0.5519	5008	,	,		7627	0.5575		0.672	False		,,,				2504	0.7065				p.G407G	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.G1221A						PASS	.	G		1117,1057		287,543,257	1.0	2.0	2.0		1221	2.9	1.0	19	dbSNP_120	2	4101,1193		1647,807,193	no	coding-synonymous	GLTSCR2	NM_015710.4		1934,1350,450	AA,AG,GG		22.5349,48.6201,30.1285		407/479	48258772	5218,2250	1087	2647	3734	SO:0001819	synonymous_variant	29997	exon9			GCTGGGGCGGCTC	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.1221G>A	19.37:g.48258772G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			G|0.469;A|0.531	0.531	strong		0.716	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
A1CF	29974	hgsc.bcm.edu	37	10	52595983	52595983	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:52595983A>G	ENST00000373993.1	-	4	499	c.455T>C	c.(454-456)aTc>aCc	p.I152T	A1CF_ENST00000374001.2_Missense_Mutation_p.I152T|A1CF_ENST00000395489.2_Missense_Mutation_p.I145T|A1CF_ENST00000395495.1_Missense_Mutation_p.I152T|A1CF_ENST00000373995.3_Missense_Mutation_p.I160T|A1CF_ENST00000373997.3_Missense_Mutation_p.I152T|A1CF_ENST00000282641.2_Missense_Mutation_p.I152T			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	152	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CTCCGATAAGATTTCTTCTCT	0.463																																					p.I160T		Atlas-SNP	.											A1CF_ENST00000373995,NS,carcinoma,+1,4	A1CF	190	4	0			c.T479C						scavenged	.						123.0	121.0	122.0					10																	52595983		2203	4300	6503	SO:0001583	missense	29974	exon7			GATAAGATTTCTT	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.455T>C	10.37:g.52595983A>G	ENSP00000363105:p.Ile152Thr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	149	4	0.0268456	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	37	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.481252	0.84747	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489;ENST00000414883	T;T;T;T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09;2.09;2.09;2.09	6.04	6.04	0.98038	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	H	0.94658	3.565	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.996	D;D;D;D	0.97110	1.0;0.999;1.0;0.999	T	0.69529	-0.5121	10	0.59425	D	0.04	-10.8777	14.5406	0.67990	1.0:0.0:0.0:0.0	.	145;152;152;160	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	T	152;152;152;160;152;152;135;145;152	ENSP00000363113:I152T;ENSP00000363105:I152T;ENSP00000363109:I152T;ENSP00000363107:I160T;ENSP00000282641:I152T;ENSP00000378873:I152T;ENSP00000378868:I145T;ENSP00000397953:I152T	ENSP00000282641:I152T	I	-	2	0	A1CF	52265989	1.000000	0.71417	0.991000	0.47740	0.910000	0.53928	9.233000	0.95337	2.317000	0.78254	0.460000	0.39030	ATC	.	.	none		0.463	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
EFCAB7	84455	hgsc.bcm.edu	37	1	64021096	64021096	+	Missense_Mutation	SNP	G	G	A	rs2273367	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:64021096G>A	ENST00000371088.4	+	9	1370	c.1124G>A	c.(1123-1125)aGg>aAg	p.R375K	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	375			R -> K (in dbSNP:rs2273367). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.				calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						ACTGGCTGTAGGCTGAGGAAA	0.358													G|||	701	0.139976	0.0673	0.1585	5008	,	,		15942	0.1855		0.1441	False		,,,				2504	0.1738				p.R375K		Atlas-SNP	.											EFCAB7,right_upper_lobe,carcinoma,-1,1	EFCAB7	45	1	0			c.G1124A						PASS	.	G	LYS/ARG	348,4058	179.7+/-208.2	8,332,1863	140.0	138.0	139.0		1124	4.0	1.0	1	dbSNP_100	139	1326,7274	260.9+/-283.5	93,1140,3067	yes	missense	EFCAB7	NM_032437.2	26	101,1472,4930	AA,AG,GG		15.4186,7.8983,12.871	benign	375/630	64021096	1674,11332	2203	4300	6503	SO:0001583	missense	84455	exon9			GCTGTAGGCTGAG	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.1124G>A	1.37:g.64021096G>A	ENSP00000360129:p.Arg375Lys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	150	60	0.4	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	315	0.14423076923076922	41	0.08333333333333333	61	0.1685082872928177	105	0.18356643356643357	108	0.1424802110817942	G	13.30	2.196337	0.38806	0.078983	0.154186	ENSG00000203965	ENST00000371088	T	0.44881	0.91	5.96	4.04	0.47022	.	0.214437	0.53938	N	0.000044	T	0.20618	0.0496	L	0.57536	1.79	0.09310	P	0.9999999999995571	B	0.06786	0.001	B	0.06405	0.002	T	0.05435	-1.0885	9	0.32370	T	0.25	-6.8388	10.965	0.47408	0.1579:0.0:0.8421:0.0	rs2273367;rs17851338;rs52834573;rs61180196;rs2273367	375	A8K855	EFCB7_HUMAN	K	375	ENSP00000360129:R375K	ENSP00000360129:R375K	R	+	2	0	EFCAB7	63793684	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.663000	0.61532	0.773000	0.33404	0.655000	0.94253	AGG	G|0.849;A|0.151	0.151	strong		0.358	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
SLC27A3	11000	hgsc.bcm.edu	37	1	153750738	153750738	+	Silent	SNP	G	G	C	rs34074094	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:153750738G>C	ENST00000368661.3	+	5	1469	c.1404G>C	c.(1402-1404)gtG>gtC	p.V468V	SLC27A3_ENST00000271857.2_Silent_p.V549V|SLC27A3_ENST00000484014.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	468					fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCCTGCAGGTGCTGGAGACAT	0.642													G|||	91	0.0181709	0.0378	0.0173	5008	,	,		15827	0.0		0.0199	False		,,,				2504	0.0092				p.V468V		Atlas-SNP	.											.	SLC27A3	42	.	0			c.G1404C						PASS	.	G		198,4208	123.3+/-160.7	5,188,2010	68.0	73.0	71.0		1404	2.1	1.0	1	dbSNP_126	71	189,8411	84.0+/-146.5	2,185,4113	no	coding-synonymous	SLC27A3	NM_024330.1		7,373,6123	CC,CG,GG		2.1977,4.4939,2.9755		468/731	153750738	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	11000	exon5			GCAGGTGCTGGAG	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.1404G>C	1.37:g.153750738G>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	88	52	0.590909	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Silent	SNP	ENST00000368661.3	37	CCDS1053.1	45	0.020604395604395604	26	0.052845528455284556	5	0.013812154696132596	0	0.0	14	0.018469656992084433	G	10.73	1.432809	0.25813	0.044939	0.021977	ENSG00000143554	ENST00000458027	.	.	.	5.13	2.09	0.27110	.	.	.	.	.	T	0.33089	0.0851	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22695	-1.0209	4	.	.	.	-20.2739	4.7481	0.13047	0.1985:0.312:0.4895:0.0	rs34074094	.	.	.	S	173	.	.	C	+	2	0	SLC27A3	152017362	0.002000	0.14202	1.000000	0.80357	0.988000	0.76386	-0.013000	0.12678	1.363000	0.46019	0.462000	0.41574	TGC	G|0.975;C|0.025	0.025	strong		0.642	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330	
OVCH1	341350	hgsc.bcm.edu	37	12	29604392	29604392	+	Missense_Mutation	SNP	C	C	G	rs1347570	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:29604392C>G	ENST00000318184.5	-	22	2640	c.2641G>C	c.(2641-2643)Gca>Cca	p.A881P	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	881	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.		P -> A (in dbSNP:rs1347570).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					ATACTGCTTGCTGAAACTCTG	0.423													G|||	2557	0.510583	0.621	0.3934	5008	,	,		15119	0.4008		0.5726	False		,,,				2504	0.4939				p.A881P		Atlas-SNP	.											.	OVCH1	195	.	0			c.G2641C						PASS	.	G	PRO/ALA	2456,1304		801,854,225	88.0	84.0	85.0		2641	2.4	0.1	12	dbSNP_88	85	4638,3586		1299,2040,773	yes	missense	OVCH1	NM_183378.2	27	2100,2894,998	GG,GC,CC		43.6041,34.6809,40.8044	probably-damaging	881/1135	29604392	7094,4890	1880	4112	5992	SO:0001583	missense	341350	exon22			TGCTTGCTGAAAC	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2641G>C	12.37:g.29604392C>G	ENSP00000326708:p.Ala881Pro	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	139	65	0.467626	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		1147	0.5251831501831502	313	0.6361788617886179	141	0.38950276243093923	260	0.45454545454545453	433	0.5712401055408971	G	1.388	-0.581633	0.03854	0.653191	0.563959	ENSG00000187950	ENST00000318184	T	0.16897	2.31	2.36	2.36	0.29203	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.40232	-0.9574	5	0.02654	T	1	.	7.1197	0.25437	0.0:0.2815:0.7185:0.0	rs1347570;rs52827123;rs1347570	.	.	.	P	881	ENSP00000326708:A881P	ENSP00000326708:A881P	A	-	1	0	OVCH1	29495659	0.014000	0.17966	0.096000	0.21009	0.611000	0.37282	1.469000	0.35343	0.572000	0.29383	-0.225000	0.12378	GCA	C|0.461;G|0.539	0.539	strong		0.423	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
CHRND	1144	hgsc.bcm.edu	37	2	233391306	233391306	+	Silent	SNP	G	G	A	rs55921262	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:233391306G>A	ENST00000258385.3	+	2	152	c.120G>A	c.(118-120)aaG>aaA	p.K40K	CHRND_ENST00000543200.1_Silent_p.K40K|CHRND_ENST00000457943.2_5'UTR|CHRND_ENST00000536614.1_Silent_p.K40K	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	40					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	GCTACAACAAGGAGCTCCGGC	0.632													G|||	77	0.0153754	0.0015	0.0259	5008	,	,		17569	0.0		0.0527	False		,,,				2504	0.0041				p.K40K		Atlas-SNP	.											.	CHRND	67	.	0			c.G120A						PASS	.	G		35,4371	40.8+/-73.8	0,35,2168	76.0	80.0	79.0		120	2.9	0.6	2	dbSNP_129	79	313,8287	110.8+/-171.2	7,299,3994	no	coding-synonymous	CHRND	NM_000751.1		7,334,6162	AA,AG,GG		3.6395,0.7944,2.6757		40/518	233391306	348,12658	2203	4300	6503	SO:0001819	synonymous_variant	1144	exon2			CAACAAGGAGCTC	X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1965	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, delta (muscle)"""	100720	"""cholinergic receptor, nicotinic, delta"""	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.120G>A	2.37:g.233391306G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	69	0.6	NM_000751	A8K661|B4DT92|Q52LH4	Silent	SNP	ENST00000258385.3	37	CCDS2494.1																																																																																			G|0.977;A|0.023	0.023	strong		0.632	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2		
RTP5	285093	hgsc.bcm.edu	37	2	242814009	242814009	+	Missense_Mutation	SNP	G	G	A	rs7420371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242814009G>A	ENST00000343216.3	+	2	330	c.302G>A	c.(301-303)gGg>gAg	p.G101E		NM_173821.2	NP_776182.2																					CCCGCACCCGGGGACTGCCAG	0.716													G|||	1361	0.271765	0.1051	0.2925	5008	,	,		15254	0.1925		0.4384	False		,,,				2504	0.3926				p.G101E		Atlas-SNP	.											.	.	.	.	0			c.G302A						PASS	.	G	GLU/GLY	551,3197		64,423,1387	7.0	9.0	9.0		302	-0.6	0.0	2	dbSNP_116	9	3443,4677		801,1841,1418	no	missense	C2orf85	NM_173821.2	98	865,2264,2805	AA,AG,GG		42.4015,14.7012,33.6535	probably-damaging	101/573	242814009	3994,7874	1874	4060	5934	SO:0001583	missense	285093	exon2			CACCCGGGGACTG																												ENST00000343216.3:c.302G>A	2.37:g.242814009G>A	ENSP00000345374:p.Gly101Glu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	21	14	0.666667	NM_173821		Missense_Mutation	SNP	ENST00000343216.3	37	CCDS42843.1	589	0.2696886446886447	50	0.1016260162601626	112	0.30939226519337015	87	0.1520979020979021	340	0.44854881266490765	.	7.227	0.598459	0.13939	0.147012	0.424015	ENSG00000188011	ENST00000343216	T	0.19532	2.14	2.67	-0.573	0.11742	.	.	.	.	.	T	0.00012	0.0000	N	0.00313	-1.665	0.80722	P	0.0	D	0.89917	1.0	D	0.75020	0.985	T	0.17048	-1.0382	8	0.02654	T	1	.	5.7222	0.17992	0.0:0.4141:0.3743:0.2115	rs7420371	101	Q14D33	CB085_HUMAN	E	101	ENSP00000345374:G101E	ENSP00000345374:G101E	G	+	2	0	C2orf85	242462682	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.950000	0.03889	-0.117000	0.11872	-0.552000	0.04208	GGG	G|0.729;A|0.271	0.271	strong		0.716	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
ADCK4	79934	hgsc.bcm.edu	37	19	41220529	41220529	+	Silent	SNP	C	C	T	rs11673492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41220529C>T	ENST00000324464.3	-	2	310	c.9G>A	c.(7-9)ctG>ctA	p.L3L	ADCK4_ENST00000450541.1_Silent_p.L3L|ITPKC_ENST00000263370.2_5'Flank|ADCK4_ENST00000243583.6_Silent_p.L3L	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	3						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CCCCCACCTTCAGCCACATTG	0.637													C|||	497	0.0992412	0.1324	0.0922	5008	,	,		12878	0.003		0.1978	False		,,,				2504	0.0573				p.L3L		Atlas-SNP	.											.	ADCK4	92	.	0			c.G9A						PASS	.	C	,	572,3834		42,488,1673	30.0	35.0	33.0		9,9	2.4	0.9	19	dbSNP_120	33	1656,6932		171,1314,2809	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	213,1802,4482	TT,TC,CC		19.2827,12.9823,17.1464	,	3/504,3/545	41220529	2228,10766	2203	4294	6497	SO:0001819	synonymous_variant	79934	exon2			CACCTTCAGCCAC	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.9G>A	19.37:g.41220529C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_001142555	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			C|0.854;T|0.146	0.146	strong		0.637	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
ATP2A1	487	hgsc.bcm.edu	37	16	28909622	28909622	+	Silent	SNP	G	G	A	rs12596913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28909622G>A	ENST00000357084.3	+	14	1881	c.1614G>A	c.(1612-1614)acG>acA	p.T538T	ATP2A1_ENST00000536376.1_Silent_p.T413T|ATP2A1_ENST00000395503.4_Silent_p.T538T	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	538					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						TGCCACTGACGGGGCCGGTGA	0.652													G|||	195	0.0389377	0.0174	0.0014	5008	,	,		17357	0.1567		0.0129	False		,,,				2504	0.0				p.T538T		Atlas-SNP	.											ATP2A1,NS,carcinoma,+1,1	ATP2A1	116	1	0			c.G1614A						scavenged	.	G	,	117,4277	89.2+/-127.9	3,111,2083	64.0	71.0	69.0		1614,1614	-10.9	0.0	16	dbSNP_120	69	52,8548	32.8+/-85.7	0,52,4248	no	coding-synonymous,coding-synonymous	ATP2A1	NM_004320.4,NM_173201.3	,	3,163,6331	AA,AG,GG		0.6047,2.6627,1.3006	,	538/995,538/1002	28909622	169,12825	2197	4300	6497	SO:0001819	synonymous_variant	487	exon14			ACTGACGGGGCCG		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.1614G>A	16.37:g.28909622G>A		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																			G|0.974;A|0.026	0.026	strong		0.652	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
SLC35G2	80723	hgsc.bcm.edu	37	3	136574521	136574521	+	Silent	SNP	C	C	T	rs1052620	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:136574521C>T	ENST00000446465.2	+	2	1847	c.1219C>T	c.(1219-1221)Cta>Tta	p.L407L	SLC35G2_ENST00000393079.3_Silent_p.L407L|RP11-85F14.5_ENST00000461864.1_RNA|RP11-85F14.5_ENST00000470236.1_RNA|RP11-85F14.5_ENST00000474250.1_RNA	NM_025246.2	NP_079522.2			solute carrier family 35, member G2																		CCAGGAAATACTAGACTCTCC	0.323													C|||	439	0.0876597	0.0098	0.0908	5008	,	,		16135	0.001		0.1889	False		,,,				2504	0.1759				p.L407L		Atlas-SNP	.											.	.	.	.	0			c.C1219T						PASS	.	C	,,	184,4222	116.7+/-154.6	6,172,2025	66.0	63.0	64.0		1219,1219,1219	3.0	1.0	3	dbSNP_86	64	2014,6586	339.1+/-323.0	232,1550,2518	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM22	NM_001097599.1,NM_001097600.1,NM_025246.2	,,	238,1722,4543	TT,TC,CC		23.4186,4.1761,16.8999	,,	407/413,407/413,407/413	136574521	2198,10808	2203	4300	6503	SO:0001819	synonymous_variant	80723	exon2			GAAATACTAGACT	BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"""Solute carriers"""	28480	protein-coding gene	gene with protein product			"""transmembrane protein 22"""	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.1219C>T	3.37:g.136574521C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	128	41	0.320312	NM_025246		Silent	SNP	ENST00000446465.2	37	CCDS3091.1																																																																																			C|0.857;T|0.143	0.143	strong		0.323	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246	
OR52D1	390066	hgsc.bcm.edu	37	11	5510341	5510341	+	Silent	SNP	C	C	T	rs404280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5510341C>T	ENST00000322641.5	+	1	427	c.405C>T	c.(403-405)taC>taT	p.Y135Y	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	135					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATTAAGGTACACAACCATTC	0.463													C|||	2631	0.525359	0.323	0.5836	5008	,	,		25054	0.6071		0.5944	False		,,,				2504	0.6022				p.Y135Y		Atlas-SNP	.											.	OR52D1	66	.	0			c.C405T						PASS	.	C		1689,2713	510.6+/-367.6	357,975,869	226.0	209.0	215.0		405	-2.0	0.1	11	dbSNP_80	215	5360,3234	650.5+/-400.7	1683,1994,620	no	coding-synonymous	OR52D1	NM_001005163.2		2040,2969,1489	TT,TC,CC		37.6309,38.3689,45.7602		135/319	5510341	7049,5947	2201	4297	6498	SO:0001819	synonymous_variant	390066	exon1			AAGGTACACAACC	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"""GPCR / Class A : Olfactory receptors"""	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.405C>T	11.37:g.5510341C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_001005163	B9EGY9|Q6IFI6	Silent	SNP	ENST00000322641.5	37	CCDS31384.1																																																																																			C|0.460;T|0.540	0.540	strong		0.463	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548522	32548522	+	Splice_Site	SNP	C	C	G	rs35121789	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32548522C>G	ENST00000360004.5	-	4	869		c.e4+1			NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AGGCTCCTCACCTTTCTGATT	0.527										Multiple Myeloma(14;0.17)																											.		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.763+1G>C						PASS	.						69.0	80.0	76.0					6																	32548522		1511	2709	4220	SO:0001630	splice_region_variant	3123	exon5			TCCTCACCTTTCT	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.763+1G>C	6.37:g.32548522C>G		Somatic	375	0	0		WXS	Illumina HiSeq	Phase_I	609	38	0.0623974	NM_002124	P01914|Q9MYF5	Splice_Site	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	c	14.08	2.428666	0.43122	.	.	ENSG00000196126	ENST00000360004	.	.	.	3.98	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9174	0.63908	0.0:1.0:0.0:0.0	rs35121789	.	.	.	.	-1	.	.	.	-	.	.	HLA-DRB1	32656500	1.000000	0.71417	0.945000	0.38365	0.570000	0.35934	4.495000	0.60353	1.943000	0.56356	0.453000	0.30009	.	C|0.983;G|0.018	0.018	strong		0.527	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	Intron
KAT6A	7994	hgsc.bcm.edu	37	8	41790866	41790866	+	Silent	SNP	G	G	C	rs2980901	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:41790866G>C	ENST00000396930.3	-	18	5415	c.4872C>G	c.(4870-4872)gtC>gtG	p.V1624V	KAT6A_ENST00000265713.2_Silent_p.V1624V|KAT6A_ENST00000406337.1_Silent_p.V1624V	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1624	Interaction with PML.|Interaction with RUNX1-2.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CAGCAGGCTGGACGCTGCTCT	0.642													G|||	182	0.0363419	0.1074	0.0159	5008	,	,		16184	0.0089		0.0089	False		,,,				2504	0.0112				p.V1624V		Atlas-SNP	.											.	.	.	.	0			c.C4872G						PASS	.	G	,,	386,4016		16,354,1831	29.0	26.0	27.0		4872,4872,4872	1.7	1.0	8	dbSNP_101	27	123,8469		0,123,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	KAT6A	NM_001099412.1,NM_001099413.1,NM_006766.3	,,	16,477,6004	CC,CG,GG		1.4316,8.7687,3.9172	,,	1624/2005,1624/2005,1624/2005	41790866	509,12485	2201	4296	6497	SO:0001819	synonymous_variant	7994	exon18			AGGCTGGACGCTG	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4872C>G	8.37:g.41790866G>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	37	CCDS6124.1																																																																																			G|0.964;C|0.036	0.036	strong		0.642	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
MAST3	23031	hgsc.bcm.edu	37	19	18245512	18245512	+	Silent	SNP	C	C	T	rs2270623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18245512C>T	ENST00000262811.6	+	15	1608	c.1608C>T	c.(1606-1608)atC>atT	p.I536I		NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	536	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						GAGAGTTCATCGACAAGCAGG	0.637													C|||	2660	0.53115	0.3222	0.5245	5008	,	,		15983	0.6726		0.503	False		,,,				2504	0.7014				p.I536I		Atlas-SNP	.											.	MAST3	83	.	0			c.C1608T						PASS	.	C		1450,2810		277,896,957	34.0	37.0	36.0		1608	-0.3	1.0	19	dbSNP_100	36	4444,4084		1188,2068,1008	no	coding-synonymous	MAST3	NM_015016.1		1465,2964,1965	TT,TC,CC		47.8893,34.0376,46.0901		536/1310	18245512	5894,6894	2130	4264	6394	SO:0001819	synonymous_variant	23031	exon15			GTTCATCGACAAG	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.1608C>T	19.37:g.18245512C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	150	71	0.473333	NM_015016	Q7LDZ8|Q9UPI0	Silent	SNP	ENST00000262811.6	37	CCDS46014.1																																																																																			C|0.501;T|0.499	0.499	strong		0.637	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150	
VWA2	340706	hgsc.bcm.edu	37	10	116050058	116050058	+	Missense_Mutation	SNP	G	G	C	rs45560935	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:116050058G>C	ENST00000392982.3	+	13	2432	c.2182G>C	c.(2182-2184)Gtc>Ctc	p.V728L				Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	728	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		GGGCAGCTGCGTCCTGCAGAA	0.602													G|||	6	0.00119808	0.0	0.0	5008	,	,		18275	0.0		0.006	False		,,,				2504	0.0				p.V728L		Atlas-SNP	.											.	VWA2	64	.	0			c.G2182C						PASS	.																																			SO:0001583	missense	340706	exon13			AGCTGCGTCCTGC	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.2182G>C	10.37:g.116050058G>C	ENSP00000376708:p.Val728Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	10.73	1.433111	0.25813	.	.	ENSG00000165816	ENST00000392982	D	0.92249	-3.0	5.65	-1.47	0.08772	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.461364	0.22065	N	0.065105	T	0.78591	0.4307	.	.	.	0.40475	D	0.980387	P	0.43857	0.819	B	0.38378	0.272	T	0.74553	-0.3627	9	0.16896	T	0.51	.	10.3483	0.43920	0.5818:0.0:0.4182:0.0	rs45560935	728	Q5GFL6	VWA2_HUMAN	L	728	ENSP00000376708:V728L	ENSP00000376708:V728L	V	+	1	0	VWA2	116040048	0.021000	0.18746	0.176000	0.23000	0.151000	0.21798	0.312000	0.19397	-0.137000	0.11455	-0.759000	0.03464	GTC	G|0.998;C|0.002	0.002	strong		0.602	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
TANC1	85461	hgsc.bcm.edu	37	2	160084473	160084473	+	Silent	SNP	A	A	C	rs2288110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160084473A>C	ENST00000263635.6	+	25	4284	c.4047A>C	c.(4045-4047)acA>acC	p.T1349T	TANC1_ENST00000454300.1_Silent_p.T1243T	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1349					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GAAGAAAAACAAATGTAAGCT	0.493													A|||	2398	0.478834	0.351	0.6009	5008	,	,		21388	0.6151		0.3718	False		,,,				2504	0.5348				p.T1349T		Atlas-SNP	.											.	TANC1	157	.	0			c.A4047C						PASS	.	A	,	1371,2477		252,867,805	89.0	89.0	89.0		4023,4047	-0.8	0.9	2	dbSNP_100	89	2888,5378		515,1858,1760	no	coding-synonymous,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	767,2725,2565	CC,CA,AA		34.9383,35.6289,35.1577	,	1341/1391,1349/1862	160084473	4259,7855	1924	4133	6057	SO:0001819	synonymous_variant	85461	exon25			AAAAACAAATGTA	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4047A>C	2.37:g.160084473A>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			A|0.566;C|0.434	0.434	strong		0.493	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
KMT2E	55904	hgsc.bcm.edu	37	7	104747899	104747899	+	Missense_Mutation	SNP	G	G	T	rs117986340	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:104747899G>T	ENST00000311117.3	+	22	3540	c.2995G>T	c.(2995-2997)Ggt>Tgt	p.G999C	CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334914.7_Missense_Mutation_p.G54C|KMT2E_ENST00000334877.4_Missense_Mutation_p.G999C|KMT2E_ENST00000257745.4_Missense_Mutation_p.G999C	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	999					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										AAAGACTATTGGTTATACGAG	0.433													G|||	77	0.0153754	0.0023	0.0274	5008	,	,		17573	0.0		0.0507	False		,,,				2504	0.0041				p.G999C		Atlas-SNP	.											.	MLL5	173	.	0			c.G2995T						PASS	.	G	CYS/GLY,CYS/GLY	28,4378	31.7+/-61.6	0,28,2175	83.0	87.0	85.0		2995,2995	6.0	1.0	7	dbSNP_132	85	399,8201	127.2+/-185.5	8,383,3909	yes	missense,missense	MLL5	NM_018682.3,NM_182931.2	159,159	8,411,6084	TT,TG,GG		4.6395,0.6355,3.2831	probably-damaging,probably-damaging	999/1859,999/1859	104747899	427,12579	2203	4300	6503	SO:0001583	missense	55904	exon21			ACTATTGGTTATA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2995G>T	7.37:g.104747899G>T	ENSP00000312379:p.Gly999Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	51	0.023351648351648352	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	40	0.052770448548812667	G	24.2	4.502636	0.85176	0.006355	0.046395	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.96168	-3.93;-3.11;-3.93;-0.21	6.03	6.03	0.97812	.	0.062767	0.64402	D	0.000006	D	0.85566	0.5726	L	0.29908	0.895	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	D	0.88825	0.3301	10	0.62326	D	0.03	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	999	Q8IZD2	MLL5_HUMAN	C	999;999;999;919;999;54	ENSP00000312379:G999C;ENSP00000335599:G999C;ENSP00000257745:G999C;ENSP00000333986:G54C	ENSP00000257745:G999C	G	+	1	0	MLL5	104535135	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.239000	0.78182	2.854000	0.98071	0.655000	0.94253	GGT	G|0.969;T|0.031	0.031	strong		0.433	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
TRMT2A	27037	hgsc.bcm.edu	37	22	20100158	20100158	+	Missense_Mutation	SNP	G	G	C	rs447017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20100158G>C	ENST00000252136.7	-	12	2194	c.1806C>G	c.(1804-1806)agC>agG	p.S602R	TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000404751.3_3'UTR|TRMT2A_ENST00000403707.3_Missense_Mutation_p.S602R|TRMT2A_ENST00000439169.2_Missense_Mutation_p.S620R|AC006547.8_ENST00000412713.1_RNA	NM_001257994.1|NM_022727.5|NM_182984.4	NP_001244923.1|NP_073564.3|NP_892029.2	Q8IZ69	TRM2A_HUMAN	tRNA methyltransferase 2 homolog A (S. cerevisiae)	602			S -> R (in dbSNP:rs447017).		RNA processing (GO:0006396)		nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)			breast(2)|endometrium(2)|lung(5)	9						GAGCTGGAGGGCTGTGGGGCC	0.612													G|||	88	0.0175719	0.0045	0.0159	5008	,	,		17101	0.0		0.0626	False		,,,				2504	0.0082				p.S602R		Atlas-SNP	.											.	TRMT2A	34	.	0			c.C1806G						PASS	.	G	ARG/SER,ARG/SER	51,4355	50.2+/-85.5	1,49,2153	59.0	60.0	60.0		1806,1806	-10.3	0.0	22	dbSNP_80	60	568,8032	152.7+/-207.2	24,520,3756	yes	missense,missense	TRMT2A	NM_022727.4,NM_182984.3	110,110	25,569,5909	CC,CG,GG		6.6047,1.1575,4.7593	benign,benign	602/626,602/626	20100158	619,12387	2203	4300	6503	SO:0001583	missense	27037	exon12			TGGAGGGCTGTGG	BC017184	CCDS13774.1, CCDS58793.1	22q11.21	2014-02-12	2012-06-12		ENSG00000099899	ENSG00000099899			24974	protein-coding gene	gene with protein product	"""HpaII tiny fragments locus 9C"""	611151				9417108, 18075473	Standard	NM_022727		Approved	HTF9C	uc002zrl.2	Q8IZ69	OTTHUMG00000150454	ENST00000252136.7:c.1806C>G	22.37:g.20100158G>C	ENSP00000252136:p.Ser602Arg	Somatic	501	1	0.00199601		WXS	Illumina HiSeq	Phase_I	475	213	0.448421	NM_022727	D3DX25|Q32P57|Q96ME6|Q9H732	Missense_Mutation	SNP	ENST00000252136.7	37	CCDS13774.1	59|59	0.027014652014652016|0.027014652014652016	3|3	0.006097560975609756|0.006097560975609756	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	47|47	0.06200527704485488|0.06200527704485488	G|G	8.529|8.529	0.870612|0.870612	0.17322|0.17322	0.011575|0.011575	0.066047|0.066047	ENSG00000099899|ENSG00000099899	ENST00000444256|ENST00000252136;ENST00000403707;ENST00000444845;ENST00000439169	.|T;T;T;T	.|0.43294	.|0.95;0.95;0.95;0.95	5.15|5.15	-10.3|-10.3	0.00346|0.00346	.|.	.|1.700760	.|0.03251	.|N	.|0.181881	T|T	0.00998|0.00998	0.0033|0.0033	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.05767|0.05767	-1.0865|-1.0865	5|10	.|0.16420	.|T	.|0.52	-2.108|-2.108	1.4172|1.4172	0.02304|0.02304	0.3734:0.091:0.167:0.3686|0.3734:0.091:0.167:0.3686	rs447017;rs695704;rs447017|rs447017;rs695704;rs447017	.|620;602	.|F2Z2W7;Q8IZ69	.|.;TRM2A_HUMAN	G|R	120|602;602;135;620	.|ENSP00000252136:S602R;ENSP00000385807:S602R;ENSP00000397744:S135R;ENSP00000395738:S620R	.|ENSP00000252136:S602R	A|S	-|-	2|3	0|2	TRMT2A|TRMT2A	18480158|18480158	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-0.716000|-0.716000	0.04991|0.04991	-1.738000|-1.738000	0.01348|0.01348	-1.272000|-1.272000	0.01410|0.01410	GCC|AGC	G|0.955;C|0.045	0.045	strong		0.612	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727	
PPL	5493	hgsc.bcm.edu	37	16	4935636	4935636	+	Missense_Mutation	SNP	G	G	A	rs2075639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4935636G>A	ENST00000345988.2	-	22	3109	c.3020C>T	c.(3019-3021)gCg>gTg	p.A1007V	PPL_ENST00000590782.2_Missense_Mutation_p.A1005V	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1007			A -> V (in dbSNP:rs2075639).		keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						GACCTCATCCGCCTGGGCCCT	0.697													G|||	598	0.119409	0.0061	0.1888	5008	,	,		17164	0.2242		0.0785	False		,,,				2504	0.1575				p.A1007V		Atlas-SNP	.											.	PPL	168	.	0			c.C3020T						PASS	.	G	VAL/ALA	108,4286	80.4+/-118.8	1,106,2090	76.0	79.0	78.0		3020	-2.7	0.0	16	dbSNP_96	78	701,7897	165.1+/-217.3	30,641,3628	yes	missense	PPL	NM_002705.4	64	31,747,5718	AA,AG,GG		8.1531,2.4579,6.2269	benign	1007/1757	4935636	809,12183	2197	4299	6496	SO:0001583	missense	5493	exon22			TCATCCGCCTGGG	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3020C>T	16.37:g.4935636G>A	ENSP00000340510:p.Ala1007Val	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	148	83	0.560811	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	258	0.11813186813186813	7	0.014227642276422764	61	0.1685082872928177	132	0.23076923076923078	58	0.07651715039577836	G	10.45	1.354545	0.24512	0.024579	0.081531	ENSG00000118898	ENST00000345988	T	0.46063	0.88	4.89	-2.67	0.06059	.	0.297452	0.31531	N	0.007490	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	5.000000000032756E-6	B	0.29253	0.239	B	0.14023	0.01	T	0.09164	-1.0687	9	0.51188	T	0.08	.	3.0003	0.06011	0.1392:0.1079:0.2588:0.4941	rs2075639;rs52834399;rs57621226;rs2075639	1007	O60437	PEPL_HUMAN	V	1007	ENSP00000340510:A1007V	ENSP00000340510:A1007V	A	-	2	0	PPL	4875637	0.970000	0.33590	0.020000	0.16555	0.202000	0.24057	1.726000	0.38085	-0.515000	0.06479	0.484000	0.47621	GCG	G|0.915;A|0.085	0.085	strong		0.697	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
GRAMD3	65983	hgsc.bcm.edu	37	5	125696140	125696140	+	Silent	SNP	G	G	A	rs11241887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:125696140G>A	ENST00000513040.1	+	1	317	c.117G>A	c.(115-117)ccG>ccA	p.P39P		NM_001146319.1	NP_001139791.1	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	0						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		CAGTGGGTCCGGACCTGGAAC	0.478													A|||	4652	0.928914	0.7874	0.964	5008	,	,		21515	1.0		0.9682	False		,,,				2504	0.9816				p.P39P		Atlas-SNP	.											.	GRAMD3	30	.	0			c.G117A						PASS	.	A		1131,253		458,215,19	97.0	93.0	94.0		117	0.1	0.0	5	dbSNP_120	94	3052,130		1465,122,4	no	coding-synonymous	GRAMD3	NM_001146319.1		1923,337,23	AA,AG,GG		4.0855,18.2803,8.3881		39/448	125696140	4183,383	692	1591	2283	SO:0001819	synonymous_variant	65983	exon1			GGGTCCGGACCTG	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000513040.1:c.117G>A	5.37:g.125696140G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Silent	SNP	ENST00000513040.1	37	CCDS54891.1																																																																																			G|0.069;A|0.931	0.931	strong		0.478	GRAMD3-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371350.1	NM_023927	
AEN	64782	hgsc.bcm.edu	37	15	89169614	89169614	+	Silent	SNP	A	A	G	rs3743476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89169614A>G	ENST00000332810.3	+	2	325	c.174A>G	c.(172-174)gaA>gaG	p.E58E	AEN_ENST00000379231.3_Silent_p.E58E	NM_022767.3	NP_073604.3	Q8WTP8	AEN_HUMAN	apoptosis enhancing nuclease	58					intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			NS(1)|kidney(1)|large_intestine(1)|lung(4)	7						TGCCTCCAGAACCAGGGTCCT	0.642													A|||	991	0.197883	0.0825	0.2061	5008	,	,		15751	0.1538		0.3618	False		,,,				2504	0.2249				p.E58E		Atlas-SNP	.											.	AEN	29	.	0			c.A174G						PASS	.	A		473,3925	207.8+/-229.1	25,423,1751	30.0	26.0	27.0		174	0.8	0.0	15	dbSNP_107	27	3014,5582	419.5+/-353.1	543,1928,1827	no	coding-synonymous	AEN	NM_022767.3		568,2351,3578	GG,GA,AA		35.0628,10.7549,26.8355		58/326	89169614	3487,9507	2199	4298	6497	SO:0001819	synonymous_variant	64782	exon2			TCCAGAACCAGGG	BC020988	CCDS10344.1	15q26.1	2008-07-15	2008-07-15	2008-07-15	ENSG00000181026	ENSG00000181026			25722	protein-coding gene	gene with protein product		610177	"""interferon stimulated exonuclease gene 20kDa-like 1"""	ISG20L1		18264133, 16171785	Standard	NM_022767		Approved	FLJ12484, FLJ12562	uc002bmt.2	Q8WTP8	OTTHUMG00000148681	ENST00000332810.3:c.174A>G	15.37:g.89169614A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_022767	C9J571|Q9BSA5|Q9H9X7	Silent	SNP	ENST00000332810.3	37	CCDS10344.1																																																																																			A|0.763;G|0.237	0.237	strong		0.642	AEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309071.1	NM_022767	
ANKRD61	100310846	hgsc.bcm.edu	37	7	6075823	6075823	+	Missense_Mutation	SNP	A	A	T	rs2302334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6075823A>T	ENST00000409061.1	+	3	1063	c.1063A>T	c.(1063-1065)Atg>Ttg	p.M355L	EIF2AK1_ENST00000536084.1_Intron|EIF2AK1_ENST00000199389.6_Intron	NM_001271700.1	NP_001258629.1	A6NGH8	ANR61_HUMAN	ankyrin repeat domain 61	355																	TGCAGGAATCATGCTACCAGA	0.418													A|||	1672	0.333866	0.1672	0.415	5008	,	,		20613	0.3631		0.4742	False		,,,				2504	0.3272				p.M355L		Atlas-SNP	.											.	.	.	.	0			c.A1063T						PASS	.																																			SO:0001583	missense	100310846	exon3			GGAATCATGCTAC		CCDS64590.1	7p22	2013-01-10			ENSG00000157999	ENSG00000157999		"""Ankyrin repeat domain containing"""	22467	protein-coding gene	gene with protein product							Standard	NM_001271700		Approved		uc031swn.1	A6NGH8	OTTHUMG00000154561	ENST00000409061.1:c.1063A>T	7.37:g.6075823A>T	ENSP00000386502:p.Met355Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_001271700		Missense_Mutation	SNP	ENST00000409061.1	37		846	0.3873626373626374	102	0.2073170731707317	151	0.4171270718232044	230	0.4020979020979021	363	0.4788918205804749	.	6.039	0.375551	0.11409	.	.	ENSG00000157999	ENST00000409061	T	0.30182	1.54	5.76	2.05	0.26809	.	0.365346	0.26855	N	0.022141	T	0.00012	0.0000	.	.	.	0.19945	P	0.9999419897	.	.	.	.	.	.	T	0.48433	-0.9036	6	0.27785	T	0.31	-26.0264	14.0786	0.64905	0.4441:0.5559:0.0:0.0	rs2302334;rs17344189;rs56650962;rs58351487;rs2302334	.	.	.	L	355	ENSP00000386502:M355L	ENSP00000386502:M355L	M	+	1	0	ANKRD61	6042349	0.995000	0.38212	0.895000	0.35142	0.954000	0.61252	1.107000	0.31110	0.380000	0.24823	0.460000	0.39030	ATG	A|0.619;T|0.381	0.381	strong		0.418	ANKRD61-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000335991.1		
SULT2B1	6820	hgsc.bcm.edu	37	19	49102399	49102399	+	Silent	SNP	C	C	T	rs1132054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49102399C>T	ENST00000201586.2	+	7	1012	c.834C>T	c.(832-834)tgC>tgT	p.C278C	SULT2B1_ENST00000323090.4_Silent_p.C263C|SULT2B1_ENST00000594274.1_3'UTR	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	278					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		CAGGGGTCTGCGGCGACTGGA	0.652													C|||	1814	0.36222	0.211	0.4222	5008	,	,		15383	0.2609		0.5149	False		,,,				2504	0.4714				p.C278C		Atlas-SNP	.											SULT2B1_ENST00000201586,NS,carcinoma,0,2	SULT2B1	72	2	0			c.C834T						PASS	.	C	,	1126,3268		144,838,1215	18.0	18.0	18.0		789,834	-6.4	0.0	19	dbSNP_86	18	4775,3813		1329,2117,848	no	coding-synonymous,coding-synonymous	SULT2B1	NM_004605.2,NM_177973.1	,	1473,2955,2063	TT,TC,CC		44.3992,25.6259,45.4552	,	263/351,278/366	49102399	5901,7081	2197	4294	6491	SO:0001819	synonymous_variant	6820	exon7			GGTCTGCGGCGAC	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.834C>T	19.37:g.49102399C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_177973	O00205|O75814	Silent	SNP	ENST00000201586.2	37	CCDS12723.1																																																																																			C|0.595;A|0.003	.	strong		0.652	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144069807	144069807	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:144069807C>T	ENST00000056217.5	+	9	4181	c.4007C>T	c.(4006-4008)tCg>tTg	p.S1336L	ARHGEF5_ENST00000471847.2_Missense_Mutation_p.S258L	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	1336	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					CCTGGCTCCTCGGAGGAGGCA	0.542																																					p.S1336L		Atlas-SNP	.											ARHGEF5,NS,carcinoma,-1,1	ARHGEF5	73	1	0			c.C4007T						scavenged	.						12.0	12.0	12.0					7																	144069807		2148	4221	6369	SO:0001583	missense	7984	exon9			GCTCCTCGGAGGA	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.4007C>T	7.37:g.144069807C>T	ENSP00000056217:p.Ser1336Leu	Somatic	881	2	0.00227015		WXS	Illumina HiSeq	Phase_I	587	114	0.194208	NM_005435	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.58|11.58	1.682337|1.682337	0.29872|0.29872	.|.	.|.	ENSG00000050327|ENSG00000050327	ENST00000474817|ENST00000056217;ENST00000344879;ENST00000471847	.|T;T	.|0.63913	.|-0.07;-0.07	5.1|5.1	5.1|5.1	0.69264|0.69264	.|Dbl homology (DH) domain (5);	.|0.925322	.|0.09085	.|N	.|0.850706	T|T	0.40448|0.40448	0.1117|0.1117	N|N	0.11255|0.11255	0.115|0.115	0.09310|0.09310	N|N	0.999996|0.999996	.|B;P	.|0.49307	.|0.0;0.922	.|B;B	.|0.36534	.|0.005;0.227	T|T	0.10451|0.10451	-1.0629|-1.0629	5|10	.|0.40728	.|T	.|0.16	0.254|0.254	9.6027|9.6027	0.39615|0.39615	0.0:0.9043:0.0:0.0957|0.0:0.9043:0.0:0.0957	.|.	.|191;1336	.|B3KQX6;Q12774	.|.;ARHG5_HUMAN	W|L	590|1336;191;258	.|ENSP00000056217:S1336L;ENSP00000418227:S258L	.|ENSP00000056217:S1336L	R|S	+|+	1|2	2|0	ARHGEF5|ARHGEF5	143700740|143700740	0.001000|0.001000	0.12720|0.12720	0.974000|0.974000	0.42286|0.42286	0.355000|0.355000	0.29361|0.29361	1.151000|1.151000	0.31651|0.31651	2.369000|2.369000	0.80426|0.80426	0.655000|0.655000	0.94253|0.94253	CGG|TCG	.	.	none		0.542	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
LPAR2	9170	hgsc.bcm.edu	37	19	19737686	19737686	+	Silent	SNP	C	C	T	rs33982830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19737686C>T	ENST00000542587.1	-	5	1310	c.408G>A	c.(406-408)gtG>gtA	p.V136V	LPAR2_ENST00000589311.1_5'Flank|LPAR2_ENST00000586703.1_Silent_p.V136V|LPAR2_ENST00000407877.3_Silent_p.V136V			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	136					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of Rho protein signal transduction (GO:0035025)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	10						TGTGCAGCTGCACGGCCATCA	0.706													C|||	868	0.173323	0.0204	0.1758	5008	,	,		14572	0.3323		0.2475	False		,,,				2504	0.138				p.V136V		Atlas-SNP	.											LPAR2,NS,carcinoma,0,1	LPAR2	28	1	0			c.G408A						PASS	.	C		239,4127		12,215,1956	15.0	13.0	14.0		408	0.7	1.0	19	dbSNP_126	14	2066,6496		231,1604,2446	no	coding-synonymous	LPAR2	NM_004720.5		243,1819,4402	TT,TC,CC		24.1299,5.4741,17.8295		136/352	19737686	2305,10623	2183	4281	6464	SO:0001819	synonymous_variant	9170	exon2			CAGCTGCACGGCC	AF011466	CCDS12407.1	19p12	2012-08-08	2008-04-11	2008-04-11		ENSG00000064547		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	3168	protein-coding gene	gene with protein product		605110	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4"""	EDG4		9525886, 9804623	Standard	NM_004720		Approved	EDG-4, LPA2	uc002nnb.4	Q9HBW0		ENST00000542587.1:c.408G>A	19.37:g.19737686C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_004720	O00543|O43431	Silent	SNP	ENST00000542587.1	37	CCDS12407.1																																																																																			C|0.828;T|0.172	0.172	strong		0.706	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720	
NBR1	4077	hgsc.bcm.edu	37	17	41361960	41361960	+	Missense_Mutation	SNP	A	A	G	rs8482	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41361960A>G	ENST00000422280.1	+	21	3227	c.2768A>G	c.(2767-2769)cAt>cGt	p.H923R	TMEM106A_ENST00000541594.1_5'Flank|NBR1_ENST00000542611.1_3'UTR|TMEM106A_ENST00000588659.1_5'Flank|TMEM106A_ENST00000331615.3_5'Flank|NBR1_ENST00000341165.6_Missense_Mutation_p.H923R|TMEM106A_ENST00000536052.1_5'Flank|NBR1_ENST00000590996.1_Missense_Mutation_p.H923R|NBR1_ENST00000389312.4_Missense_Mutation_p.H923R	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	923	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.		H -> R (in dbSNP:rs8482). {ECO:0000269|PubMed:11179671, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8069304}.		macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		CTGATGGCCCATCTCTTTGAA	0.378													A|||	1788	0.357029	0.2231	0.3775	5008	,	,		14549	0.373		0.3638	False		,,,				2504	0.5				p.H923R		Atlas-SNP	.											.	NBR1	55	.	0			c.A2768G						PASS	.	A	ARG/HIS,ARG/HIS,ARG/HIS	777,2359		89,599,880	32.0	29.0	30.0		2768,2768,2768	5.9	1.0	17	dbSNP_52	30	2371,4793		377,1617,1588	yes	missense,missense,missense	NBR1	NM_005899.3,NM_031858.2,NM_031862.2	29,29,29	466,2216,2468	GG,GA,AA		33.096,24.7768,30.5631	benign,benign,benign	923/967,923/967,923/967	41361960	3148,7152	1568	3582	5150	SO:0001583	missense	4077	exon21			TGGCCCATCTCTT	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"""membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"""	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.2768A>G	17.37:g.41361960A>G	ENSP00000411250:p.His923Arg	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	37	CCDS45694.1	714	0.3269230769230769	109	0.22154471544715448	143	0.39502762430939226	189	0.3304195804195804	273	0.36015831134564646	A	12.73	2.026576	0.35797	0.247768	0.33096	ENSG00000188554	ENST00000422280;ENST00000537493;ENST00000341165;ENST00000389312	T;T;T	0.39997	1.05;1.05;1.05	5.86	5.86	0.93980	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);UBA-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.60455	1.87	0.33132	P	0.45679400000000003	D	0.54772	0.968	B	0.42851	0.4	T	0.48222	-0.9054	8	0.14252	T	0.57	-16.1903	6.1609	0.20364	0.7757:0.0:0.0798:0.1445	rs8482;rs1054385;rs3194917	923	Q14596	NBR1_HUMAN	R	923;174;923;923	ENSP00000411250:H923R;ENSP00000343479:H923R;ENSP00000373963:H923R	ENSP00000343479:H923R	H	+	2	0	NBR1	38717486	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.466000	0.53071	2.241000	0.73720	0.533000	0.62120	CAT	A|0.671;G|0.329	0.329	strong		0.378	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899	
KCNN3	3782	hgsc.bcm.edu	37	1	154842244	154842244	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154842244A>T	ENST00000271915.4	-	1	512	c.197T>A	c.(196-198)cTt>cAt	p.L66H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	66	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	ctgctgctgaagctgcggagg	0.701																																					p.L66H		Atlas-SNP	.											KCNN3,NS,carcinoma,+1,3	KCNN3	141	3	0			c.T197A						scavenged	.																																			SO:0001583	missense	3782	exon1			TGCTGAAGCTGCG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.197T>A	1.37:g.154842244A>T	ENSP00000271915:p.Leu66His	Somatic	67	7	0.104478		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	a	9.986	1.229557	0.22542	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.58060	0.36	4.47	-1.06	0.10002	.	2.530250	0.01603	N	0.022141	T	0.17152	0.0412	N	0.08118	0	0.35103	D	0.765442	.	.	.	.	.	.	T	0.03807	-1.1002	8	0.72032	D	0.01	-1.1381	4.5154	0.11932	0.5982:0.0:0.2622:0.1396	.	.	.	.	H	66;161	ENSP00000271915:L66H	ENSP00000271915:L66H	L	-	2	0	KCNN3	153108868	0.001000	0.12720	0.839000	0.33178	0.980000	0.70556	0.019000	0.13444	0.013000	0.14918	0.460000	0.39030	CTT	.	.	none		0.701	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
PTGER1	5731	hgsc.bcm.edu	37	19	14583582	14583582	+	Silent	SNP	C	C	T	rs11668633	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14583582C>T	ENST00000292513.3	-	3	1116	c.999G>A	c.(997-999)ctG>ctA	p.L333L		NM_000955.2	NP_000946.2	P34995	PE2R1_HUMAN	prostaglandin E receptor 1 (subtype EP1), 42kDa	333					G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)									Alprostadil(DB00770)|Bimatoprost(DB00905)|Bupivacaine(DB00297)|Carboprost Tromethamine(DB00429)|Dinoprostone(DB00917)|Iloprost(DB01088)	CGGCCAGGAACAGTGGCCGCT	0.677													C|||	557	0.111222	0.0401	0.1527	5008	,	,		11945	0.0089		0.2495	False		,,,				2504	0.1411				p.L333L		Atlas-SNP	.											PTGER1,NS,carcinoma,0,1	PTGER1	5	1	0			c.G999A						PASS	.	C		324,4038		17,290,1874	20.0	18.0	19.0		999	-2.9	0.3	19	dbSNP_120	19	2357,6209		353,1651,2279	no	coding-synonymous	PTGER1	NM_000955.2		370,1941,4153	TT,TC,CC		27.5158,7.4278,20.7379		333/403	14583582	2681,10247	2181	4283	6464	SO:0001819	synonymous_variant	5731	exon3			CAGGAACAGTGGC		CCDS12309.1	19p13.1	2012-08-08	2002-08-29		ENSG00000160951	ENSG00000160951		"""GPCR / Class A : Prostanoid receptors"""	9593	protein-coding gene	gene with protein product		176802	"""prostaglandin E receptor 1 (subtype EP1), 42kD"""			8253813	Standard	NM_000955		Approved	EP1	uc002mys.3	P34995	OTTHUMG00000039610	ENST00000292513.3:c.999G>A	19.37:g.14583582C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_000955	Q5U5U4|Q86UH3|Q86VB5|Q8NHB2	Silent	SNP	ENST00000292513.3	37	CCDS12309.1																																																																																			C|0.862;T|0.138	0.138	strong		0.677	PTGER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095509.1		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067099	79067099	+	Silent	SNP	G	G	C	rs142017909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79067099G>C	ENST00000388820.4	-	12	1953	c.1743C>G	c.(1741-1743)cgC>cgG	p.R581R	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	581	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R581R(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GGAAGCGCTTGCGCTCACCCA	0.647																																					p.R581R		Atlas-SNP	.											ADAMTS7,NS,carcinoma,0,3	ADAMTS7	142	3	1	Substitution - coding silent(1)	large_intestine(1)	c.C1743G						PASS	.						69.0	79.0	76.0					15																	79067099		2196	4292	6488	SO:0001819	synonymous_variant	11173	exon12			GCGCTTGCGCTCA	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1743C>G	15.37:g.79067099G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	108	12	0.111111	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			G|0.970;C|0.030	0.030	strong		0.647	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
MUC16	94025	hgsc.bcm.edu	37	19	9020154	9020154	+	Silent	SNP	A	A	G	rs11882881|rs386806634	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9020154A>G	ENST00000397910.4	-	21	37544	c.37341T>C	c.(37339-37341)tcT>tcC	p.S12447S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12449	SEA 3. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATCCTTCTCAGACCTGGGGA	0.502													-|||	2236	0.446486	0.4138	0.5418	5008	,	,		19846	0.4623		0.3966	False		,,,				2504	0.4581				p.S12447S		Atlas-SNP	.											.	MUC16	4315	.	0			c.T37341C						PASS	.	T		1475,2351		288,899,726	93.0	81.0	85.0		37341	-6.4	0.0	19	dbSNP_120	85	3138,5116		570,1998,1559	no	coding-synonymous	MUC16	NM_024690.2		858,2897,2285	GG,GA,AA		38.0179,38.552,38.1871		12447/14508	9020154	4613,7467	1913	4127	6040	SO:0001819	synonymous_variant	94025	exon21			CTTCTCAGACCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37341T>C	19.37:g.9020154A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	192	100	0.520833	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			A|0.580;G|0.420	0.420	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FBXO46	23403	hgsc.bcm.edu	37	19	46216642	46216642	+	Missense_Mutation	SNP	G	G	T	rs11537711	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46216642G>T	ENST00000317683.3	-	2	245	c.112C>A	c.(112-114)Cct>Act	p.P38T		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	38										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		CCAGGCTCAGGGCAGGCTGAT	0.692													G|||	586	0.117013	0.1082	0.1441	5008	,	,		13636	0.0833		0.1123	False		,,,				2504	0.1493				p.P38T		Atlas-SNP	.											.	FBXO46	34	.	0			c.C112A						PASS	.	G	THR/PRO	465,3531		26,413,1559	20.0	25.0	23.0		112	-2.8	0.1	19	dbSNP_120	23	1016,7286		64,888,3199	yes	missense	FBXO46	NM_001080469.1	38	90,1301,4758	TT,TG,GG		12.238,11.6366,12.0426	benign	38/604	46216642	1481,10817	1998	4151	6149	SO:0001583	missense	23403	exon2			GCTCAGGGCAGGC	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"""F-boxes /  ""other"""""	25069	protein-coding gene	gene with protein product		609117	"""F-box only protein 34-like"""	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.112C>A	19.37:g.46216642G>T	ENSP00000410007:p.Pro38Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	96	54	0.5625	NM_001080469		Missense_Mutation	SNP	ENST00000317683.3	37	CCDS46116.1	211	0.09661172161172162	46	0.09349593495934959	43	0.11878453038674033	39	0.06818181818181818	83	0.10949868073878628	G	0.001	-3.274999	0.00020	0.116366	0.12238	ENSG00000177051	ENST00000317683	.	.	.	3.8	-2.8	0.05823	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.43977	P	0.003337999999999952	B	0.02656	0.0	B	0.04013	0.001	T	0.25916	-1.0118	7	0.16896	T	0.51	-1.5752	0.581	0.00712	0.3145:0.1558:0.3437:0.186	rs11537711;rs11537711	38	Q6PJ61	FBX46_HUMAN	T	38	.	ENSP00000410007:P38T	P	-	1	0	FBXO46	50908482	0.000000	0.05858	0.063000	0.19743	0.036000	0.12997	-0.721000	0.04963	-0.539000	0.06273	-0.266000	0.10368	CCT	G|0.898;T|0.102	0.102	strong		0.692	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179	
MYPOP	339344	hgsc.bcm.edu	37	19	46394187	46394187	+	Silent	SNP	C	C	T	rs62111265	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46394187C>T	ENST00000322217.5	-	3	980	c.894G>A	c.(892-894)ctG>ctA	p.L298L		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	298	Pro-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						GGGTTCCTGGCAGAAGGGGCA	0.711													C|||	628	0.125399	0.025	0.2161	5008	,	,		4314	0.0992		0.1779	False		,,,				2504	0.1697				p.L298L		Atlas-SNP	.											.	MYPOP	23	.	0			c.G894A						PASS	.	C		210,4064		8,194,1935	7.0	6.0	6.0		894	3.1	1.0	19	dbSNP_129	6	1360,7006		99,1162,2922	no	coding-synonymous	MYPOP	NM_001012643.2		107,1356,4857	TT,TC,CC		16.2563,4.9134,12.4209		298/400	46394187	1570,11070	2137	4183	6320	SO:0001819	synonymous_variant	339344	exon3			TCCTGGCAGAAGG	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"""p42 Myb-related transcription factor, partner of profilin"""					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.894G>A	19.37:g.46394187C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	26	25	0.961538	NM_001012643		Silent	SNP	ENST00000322217.5	37	CCDS33055.1																																																																																			C|0.872;G|0.000;T|0.128	0.128	strong		0.711	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111519740	111519740	+	Missense_Mutation	SNP	T	T	C	rs1560058	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:111519740T>C	ENST00000261486.5	-	18	1871	c.1595A>G	c.(1594-1596)aAc>aGc	p.N532S	EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	532						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		GGATCGCCTGTTGTTGGGGTC	0.428													T|||	3731	0.745008	0.5023	0.7954	5008	,	,		17099	0.9871		0.6938	False		,,,				2504	0.8405				p.N532S		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.A1595G						PASS	.	T	SER/ASN	2124,1612		593,938,337	190.0	171.0	177.0		1595	3.8	1.0	5	dbSNP_88	177	5694,2498		1993,1708,395	yes	missense	EPB41L4A	NM_022140.3	46	2586,2646,732	CC,CT,TT		30.4932,43.1478,34.4567	benign	532/687	111519740	7818,4110	1868	4096	5964	SO:0001583	missense	64097	exon18			CGCCTGTTGTTGG	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1595A>G	5.37:g.111519740T>C	ENSP00000261486:p.Asn532Ser	Somatic	426	0	0		WXS	Illumina HiSeq	Phase_I	465	222	0.477419	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	1643	0.7522893772893773	264	0.5365853658536586	277	0.7651933701657458	571	0.9982517482517482	531	0.7005277044854882	T	9.152	1.016401	0.19355	0.568522	0.695068	ENSG00000129595	ENST00000261486	D	0.81659	-1.52	6.17	3.77	0.43336	.	0.313230	0.35207	N	0.003373	T	0.00012	0.0000	N	0.14661	0.345	0.37088	P	0.10067099999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.44467	-0.9326	9	0.02654	T	1	.	10.7719	0.46327	0.0:0.1292:0.0:0.8708	rs1560058;rs4555873;rs17134211;rs52825505;rs59212360;rs1560058	532	Q9HCS5	E41LA_HUMAN	S	532	ENSP00000261486:N532S	ENSP00000261486:N532S	N	-	2	0	EPB41L4A	111547639	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.186000	0.42593	1.151000	0.42436	0.533000	0.62120	AAC	T|0.278;C|0.722	0.722	strong		0.428	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
SEC14L1	6397	hgsc.bcm.edu	37	17	75190962	75190962	+	Silent	SNP	C	C	T	rs674402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:75190962C>T	ENST00000413679.2	+	7	981	c.678C>T	c.(676-678)agC>agT	p.S226S	SEC14L1_ENST00000431431.2_Silent_p.S192S|SEC14L1_ENST00000585618.1_Silent_p.S226S|SEC14L1_ENST00000436233.4_Silent_p.S226S|SEC14L1_ENST00000430767.4_Silent_p.S226S|SEC14L1_ENST00000443798.4_Silent_p.S226S|SEC14L1_ENST00000392476.2_Silent_p.S226S|SEC14L1_ENST00000591437.1_Silent_p.S192S	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	226					transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						GCAGCCCCAGCGCACCTGAGC	0.622													C|||	1794	0.358227	0.3064	0.3329	5008	,	,		15446	0.3433		0.3559	False		,,,				2504	0.4642				p.S226S		Atlas-SNP	.											.	SEC14L1	81	.	0			c.C678T						PASS	.	C	,,,,,,	1390,3016	456.7+/-351.4	232,926,1045	65.0	64.0	64.0		678,678,678,576,678,678,678	-11.2	0.0	17	dbSNP_83	64	3214,5386	476.3+/-369.4	585,2044,1671	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEC14L1	NM_001039573.2,NM_001143998.1,NM_001143999.1,NM_001144001.1,NM_001204408.1,NM_001204410.1,NM_003003.3	,,,,,,	817,2970,2716	TT,TC,CC		37.3721,31.5479,35.399	,,,,,,	226/720,226/716,226/716,192/682,226/720,226/716,226/716	75190962	4604,8402	2203	4300	6503	SO:0001819	synonymous_variant	6397	exon9			CCCCAGCGCACCT	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"""SEC14 (S. cerevisiae)-like 1"""	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.678C>T	17.37:g.75190962C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Silent	SNP	ENST00000413679.2	37	CCDS11752.1																																																																																			C|0.643;T|0.357	0.357	strong		0.622	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	
TUBGCP2	10844	hgsc.bcm.edu	37	10	135112940	135112940	+	Silent	SNP	C	C	T	rs2298120	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:135112940C>T	ENST00000252936.3	-	3	486	c.447G>A	c.(445-447)acG>acA	p.T149T	TUBGCP2_ENST00000368563.2_Silent_p.T149T|TUBGCP2_ENST00000417178.2_Silent_p.T19T|TUBGCP2_ENST00000543663.1_Silent_p.T149T|TUBGCP2_ENST00000470829.1_5'UTR			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	149					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		CCTGCTGCAGCGTGGAGCCTG	0.637													C|||	703	0.140375	0.1891	0.1931	5008	,	,		17440	0.0486		0.1372	False		,,,				2504	0.135				p.T149T		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.G447A						PASS	.	C		840,3566	319.3+/-296.1	97,646,1460	39.0	34.0	36.0		447	-10.8	0.0	10	dbSNP_100	36	1179,7421	234.3+/-267.3	80,1019,3201	no	coding-synonymous	TUBGCP2	NM_006659.2		177,1665,4661	TT,TC,CC		13.7093,19.0649,15.5236		149/903	135112940	2019,10987	2203	4300	6503	SO:0001819	synonymous_variant	10844	exon4			CTGCAGCGTGGAG	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.447G>A	10.37:g.135112940C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_006659	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																			C|0.852;T|0.148	0.148	strong		0.637	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1		
NPHP1	4867	hgsc.bcm.edu	37	2	110922703	110922703	+	Silent	SNP	C	C	T	rs11675767	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:110922703C>T	ENST00000393272.3	-	7	751	c.654G>A	c.(652-654)gaG>gaA	p.E218E	NPHP1_ENST00000355301.4_Silent_p.E156E|NPHP1_ENST00000417665.1_Silent_p.E218E|NPHP1_ENST00000316534.4_Silent_p.E218E|NPHP1_ENST00000445609.2_Silent_p.E218E	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	218	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						CTTCACTTGACTCTTGGCCTT	0.383													T|||	2376	0.474441	0.5106	0.4193	5008	,	,		13896	0.5863		0.3032	False		,,,				2504	0.5256				p.E218E		Atlas-SNP	.											.	NPHP1	68	.	0			c.G654A						PASS	.	T	,,,	2153,2253	595.0+/-388.3	534,1085,584	191.0	177.0	182.0		654,654,468,654	-6.8	0.0	2	dbSNP_120	182	2774,5826	678.1+/-403.4	459,1856,1985	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPHP1	NM_000272.3,NM_001128178.1,NM_001128179.1,NM_207181.2	,,,	993,2941,2569	TT,TC,CC		32.2558,48.8652,37.8825	,,,	218/734,218/678,156/615,218/733	110922703	4927,8079	2203	4300	6503	SO:0001819	synonymous_variant	4867	exon7			ACTTGACTCTTGG	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"""nephrocystin-1"""	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.654G>A	2.37:g.110922703C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	177	177	1	NM_207181	O14837	Silent	SNP	ENST00000393272.3	37	CCDS46385.1																																																																																			C|0.575;T|0.425	0.425	strong		0.383	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272	
POTEF	728378	hgsc.bcm.edu	37	2	130832598	130832598	+	Missense_Mutation	SNP	C	C	T	rs3948036		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130832598C>T	ENST00000409914.2	-	17	2846	c.2447G>A	c.(2446-2448)cGc>cAc	p.R816H	POTEF_ENST00000357462.5_Missense_Mutation_p.R816H	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	816	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.R816H(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						CATCTTCTCGCGGTTGGCCTT	0.592																																					p.R816H		Atlas-SNP	.											POTEF,trunk,malignant_melanoma,0,3	POTEF	140	3	1	Substitution - Missense(1)	skin(1)	c.G2447A						scavenged	.						118.0	129.0	125.0					2																	130832598		2203	4300	6503	SO:0001583	missense	728378	exon17			TTCTCGCGGTTGG	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2447G>A	2.37:g.130832598C>T	ENSP00000386786:p.Arg816His	Somatic	504	2	0.00396825		WXS	Illumina HiSeq	Phase_I	604	67	0.110927	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	16.87	3.242651	0.58995	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.97066	-4.23;-4.23	.	.	.	Actin/actin-like conserved site (1);	.	.	.	.	D	0.98817	0.9601	H	0.99299	4.505	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	D	0.96667	0.9493	8	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	rs3948036	816	A5A3E0	POTEF_HUMAN	H	816	ENSP00000350052:R816H;ENSP00000386786:R816H	ENSP00000350052:R816H	R	-	2	0	POTEF	130549068	1.000000	0.71417	0.246000	0.24233	0.249000	0.25844	5.228000	0.65310	0.119000	0.18210	0.121000	0.15741	CGC	.	.	weak		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
ABCA7	10347	hgsc.bcm.edu	37	19	1052005	1052005	+	Silent	SNP	C	C	T	rs3764652	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1052005C>T	ENST00000263094.6	+	22	3258	c.3027C>T	c.(3025-3027)gcC>gcT	p.A1009A	ABCA7_ENST00000435683.2_Silent_p.A871A|ABCA7_ENST00000433129.1_Silent_p.A1009A	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1009	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCGTGTGGCCGTGGTGGCAG	0.667													C|||	1900	0.379393	0.326	0.4107	5008	,	,		14080	0.3353		0.4225	False		,,,				2504	0.4305				p.A1009A		Atlas-SNP	.											.	ABCA7	174	.	0			c.C3027T						PASS	.			1536,2848	465.5+/-354.2	257,1022,913	76.0	50.0	59.0		3027	-8.9	0.4	19	dbSNP_107	59	3664,4902	507.3+/-376.8	786,2092,1405	no	coding-synonymous	ABCA7	NM_019112.3		1043,3114,2318	TT,TC,CC		42.7738,35.0365,40.1544		1009/2147	1052005	5200,7750	2192	4283	6475	SO:0001819	synonymous_variant	10347	exon22			TGTGGCCGTGGTG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3027C>T	19.37:g.1052005C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			C|0.607;T|0.393	0.393	strong		0.667	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
LILRB3	11025	hgsc.bcm.edu	37	19	54725980	54725980	+	Silent	SNP	G	G	A	rs150024950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54725980G>A	ENST00000391750.1	-	5	514	c.378C>T	c.(376-378)ctC>ctT	p.L126L	LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000407860.2_Silent_p.L126L|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000346401.6_Silent_p.L126L|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000424807.1_Silent_p.L126L|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Silent_p.L126L|LILRA6_ENST00000440558.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	126	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.L126L(1)		endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCAGGGCTGAGAGGGTGGGTT	0.582													.|||	570	0.113818	0.0507	0.1037	5008	,	,		13484	0.0486		0.1471	False		,,,				2504	0.2393				p.L126L		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	1	Substitution - coding silent(1)	kidney(1)	c.C378T						scavenged	.						55.0	36.0	42.0					19																	54725980		2117	3871	5988	SO:0001819	synonymous_variant	11025	exon4			GGCTGAGAGGGTG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.378C>T	19.37:g.54725980G>A		Somatic	479	7	0.0146138		WXS	Illumina HiSeq	Phase_I	212	9	0.0424528	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			G|0.947;A|0.053	0.053	strong		0.582	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
ARSF	416	hgsc.bcm.edu	37	X	2990197	2990197	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2990197T>C	ENST00000381127.1	+	3	363	c.142T>C	c.(142-144)Tac>Cac	p.Y48H	ARSF_ENST00000537104.1_Missense_Mutation_p.Y48H|ARSF_ENST00000359361.2_Missense_Mutation_p.Y48H	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	48					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCTGGGCTGCTACGGCAATGA	0.517																																					p.Y48H		Atlas-SNP	.											.	ARSF	97	.	0			c.T142C						PASS	.						207.0	172.0	184.0					X																	2990197		2203	4300	6503	SO:0001583	missense	416	exon3			GGCTGCTACGGCA	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.142T>C	X.37:g.2990197T>C	ENSP00000370519:p.Tyr48His	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	83	4	0.0481928	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	t	12.11	1.838448	0.32513	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.95069	-3.6;-3.6;-3.6	2.46	2.46	0.29980	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.155495	0.44285	U	0.000472	D	0.96185	0.8756	M	0.89785	3.06	0.44862	D	0.997877	P	0.40000	0.698	P	0.50490	0.642	D	0.95657	0.8712	10	0.72032	D	0.01	.	9.9827	0.41824	0.0:0.0:0.0:1.0	.	48	P54793	ARSF_HUMAN	H	48	ENSP00000370519:Y48H;ENSP00000445594:Y48H;ENSP00000352319:Y48H	ENSP00000352319:Y48H	Y	+	1	0	ARSF	3000197	1.000000	0.71417	0.023000	0.16930	0.074000	0.17049	5.704000	0.68347	0.805000	0.34159	0.339000	0.21740	TAC	.	.	none		0.517	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
MED8	112950	hgsc.bcm.edu	37	1	43852667	43852667	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43852667C>T	ENST00000372457.4	-	4	316	c.273G>A	c.(271-273)cgG>cgA	p.R91R	SZT2_ENST00000562955.1_5'Flank|SZT2_ENST00000372450.4_5'Flank|RP1-92O14.6_ENST00000436713.1_RNA|MED8_ENST00000372455.4_Silent_p.R2R|SZT2_ENST00000310739.4_5'Flank|MED8_ENST00000290663.6_Silent_p.R91R	NM_001001653.2|NM_201542.3	NP_001001653.1|NP_963836.2	Q96G25	MED8_HUMAN	mediator complex subunit 8	91					gene expression (GO:0010467)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	9	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CTTCAGTCTGCCGCTGTAACA	0.478																																					p.R91R		Atlas-SNP	.											MED8_ENST00000290663,NS,carcinoma,-2,4	MED8	38	4	0			c.G273A						scavenged	.						150.0	137.0	142.0					1																	43852667		2203	4300	6503	SO:0001819	synonymous_variant	112950	exon4			AGTCTGCCGCTGT	AF521562, BC010543	CCDS486.2, CCDS487.2, CCDS60108.1	1p34.1	2008-02-05	2007-07-30		ENSG00000159479	ENSG00000159479			19971	protein-coding gene	gene with protein product		607956	"""mediator of RNA polymerase II transcription, subunit 8 homolog (S. cerevisiae)"""			12149480, 9671713	Standard	NM_052877		Approved	MGC17544, MGC19641, ARC32	uc001cje.2	Q96G25	OTTHUMG00000007421	ENST00000372457.4:c.273G>A	1.37:g.43852667C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	119	2	0.0168067	NM_201542	A9IZ91|A9IZ92|Q5JUY8|Q96FQ4	Silent	SNP	ENST00000372457.4	37	CCDS487.2																																																																																			.	.	none		0.478	MED8-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318959.1	NM_052877	
TBC1D32	221322	hgsc.bcm.edu	37	6	121642851	121642851	+	Missense_Mutation	SNP	C	C	T	rs7767455	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:121642851C>T	ENST00000398212.2	-	2	294	c.245G>A	c.(244-246)cGg>cAg	p.R82Q	TBC1D32_ENST00000275159.6_Missense_Mutation_p.R82Q	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	82			R -> Q (in dbSNP:rs7767455). {ECO:0000269|PubMed:14702039}.		cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										ACCCTGATTCCGATCAGATGT	0.373													C|||	983	0.196286	0.472	0.0893	5008	,	,		18797	0.1419		0.0577	False		,,,				2504	0.0982				p.R82Q		Atlas-SNP	.											.	C6orf170	146	.	0			c.G245A						PASS	.	C	GLN/ARG	1383,2365		276,831,767	249.0	226.0	233.0		245	4.3	0.9	6	dbSNP_116	233	527,7735		16,495,3620	yes	missense	C6orf170	NM_152730.4	43	292,1326,4387	TT,TC,CC		6.3786,36.8997,15.9034	benign	82/1258	121642851	1910,10100	1874	4131	6005	SO:0001583	missense	221322	exon2			TGATTCCGATCAG	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.245G>A	6.37:g.121642851C>T	ENSP00000381270:p.Arg82Gln	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	203	93	0.458128	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	385	0.1762820512820513	219	0.4451219512195122	37	0.10220994475138122	87	0.1520979020979021	42	0.055408970976253295	C	2.502	-0.314889	0.05422	0.368997	0.063786	ENSG00000146350	ENST00000275159;ENST00000398212;ENST00000422369	T;T;T	0.15372	2.43;2.43;2.43	5.44	4.27	0.50696	.	0.216710	0.41396	N	0.000886	T	0.00906	0.0030	N	0.00197	-1.87	0.46725	P	8.230000000000182E-4	B	0.06786	0.001	B	0.01281	0.0	T	0.45920	-0.9228	9	0.02654	T	1	-15.3945	11.4802	0.50320	0.0:0.071:0.0:0.929	rs7767455;rs59738942;rs7767455	82	Q96NH3	BROMI_HUMAN	Q	82	ENSP00000275159:R82Q;ENSP00000381270:R82Q;ENSP00000397993:R82Q	ENSP00000275159:R82Q	R	-	2	0	C6orf170	121684550	1.000000	0.71417	0.911000	0.35937	0.010000	0.07245	2.746000	0.47467	0.902000	0.36520	-0.355000	0.07637	CGG	C|0.826;T|0.174	0.174	strong		0.373	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
NCOR2	9612	hgsc.bcm.edu	37	12	124979789	124979789	+	Silent	SNP	T	T	G	rs872225	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124979789T>G	ENST00000405201.1	-	1	9	c.9A>C	c.(7-9)ggA>ggC	p.G3G	NCOR2_ENST00000397355.1_Silent_p.G3G|NCOR2_ENST00000429285.2_Silent_p.G3G|NCOR2_ENST00000404621.1_Silent_p.G3G|NCOR2_ENST00000356219.3_Silent_p.G3G|NCOR2_ENST00000404121.2_5'UTR			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	3					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GCTGTGTGGATCCCGACATGG	0.617													T|||	634	0.126597	0.0401	0.1182	5008	,	,		15508	0.1865		0.1849	False		,,,				2504	0.1278				p.G3G		Atlas-SNP	.											.	NCOR2	475	.	0			c.A9C						PASS	.	T	,,	239,3715		8,223,1746	29.0	33.0	32.0		9,9,9	-8.8	0.7	12	dbSNP_86	32	1432,6850		126,1180,2835	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	134,1403,4581	GG,GT,TT		17.2905,6.0445,13.6564	,,	3/2459,3/2505,3/2515	124979789	1671,10565	1977	4141	6118	SO:0001819	synonymous_variant	9612	exon3			TGTGGATCCCGAC	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.9A>C	12.37:g.124979789T>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	120	69	0.575	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			T|0.865;G|0.135	0.135	strong		0.617	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24261526	24261526	+	Missense_Mutation	SNP	A	A	G	rs3765124	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:24261526A>G	ENST00000256412.4	+	13	1551	c.1331A>G	c.(1330-1332)aAt>aGt	p.N444S	ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.N365S|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.N365S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	444	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.		N -> S (in dbSNP:rs3765124).		immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		GAGTGTACCAATCTCTGCTGT	0.438													A|||	1477	0.294928	0.0968	0.4553	5008	,	,		17229	0.2044		0.4284	False		,,,				2504	0.4049				p.N444S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A1331G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	677,3729	287.8+/-279.5	52,573,1578	218.0	186.0	197.0		1094,1094,1331	0.4	0.0	8	dbSNP_107	197	3804,4796	537.9+/-383.3	833,2138,1329	yes	missense,missense,missense	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	46,46,46	885,2711,2907	GG,GA,AA		44.2326,15.3654,34.4533	benign,benign,benign	365/392,365/392,444/471	24261526	4481,8525	2203	4300	6503	SO:0001583	missense	27299	exon13			GTACCAATCTCTG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.1331A>G	8.37:g.24261526A>G	ENSP00000256412:p.Asn444Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	643	0.2944139194139194	44	0.08943089430894309	152	0.4198895027624309	120	0.2097902097902098	327	0.4313984168865435	A	9.564	1.119311	0.20877	0.153654	0.442326	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.11604	2.76;2.76;2.76	5.6	0.414	0.16406	Blood coagulation inhibitor, Disintegrin (3);	0.558036	0.18286	N	0.145891	T	0.00012	0.0000	L	0.48986	1.54	0.80722	P	0.0	P	0.49862	0.929	P	0.44696	0.458	T	0.48603	-0.9021	9	0.22706	T	0.39	-7.4265	8.0431	0.30534	0.6671:0.0:0.3329:0.0	rs3765124;rs17737352;rs52806941;rs59180631;rs3765124	444	O15204	ADEC1_HUMAN	S	444;365;365	ENSP00000256412:N444S;ENSP00000442592:N365S;ENSP00000428993:N365S	ENSP00000256412:N444S	N	+	2	0	ADAMDEC1	24317471	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.317000	0.19487	-0.144000	0.11314	-0.388000	0.06559	AAT	A|0.687;G|0.313	0.313	strong		0.438	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
MPPED1	758	hgsc.bcm.edu	37	22	43830996	43830996	+	Silent	SNP	C	C	T	rs2413761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43830996C>T	ENST00000417669.2	+	3	711	c.267C>T	c.(265-267)taC>taT	p.Y89Y	MPPED1_ENST00000538182.1_Silent_p.Y122Y|MPPED1_ENST00000414469.2_5'UTR|MPPED1_ENST00000542779.1_Silent_p.Y89Y|MPPED1_ENST00000443721.1_Silent_p.Y89Y|MPPED1_ENST00000439548.1_Intron			O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	89							hydrolase activity (GO:0016787)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|skin(1)	13		all_neural(38;0.0244)|Ovarian(80;0.0694)				CTCCAGGCTACACCCGCTTCG	0.652													C|||	1776	0.354633	0.4206	0.3919	5008	,	,		17457	0.0873		0.4861	False		,,,				2504	0.3793				p.Y89Y		Atlas-SNP	.											.	MPPED1	59	.	0			c.C267T						PASS	.	C		1747,2561		379,989,786	108.0	125.0	119.0		267	4.8	1.0	22	dbSNP_100	119	4440,4044		1168,2104,970	no	coding-synonymous	MPPED1	NM_001044370.1		1547,3093,1756	TT,TC,CC		47.6662,40.5525,48.3662		89/327	43830996	6187,6605	2154	4242	6396	SO:0001819	synonymous_variant	758	exon3			AGGCTACACCCGC	U84894	CCDS46723.1	22q13.2	2013-09-20	2005-10-10	2005-10-10	ENSG00000186732	ENSG00000186732			1306	protein-coding gene	gene with protein product		602112	"""chromosome 22 open reading frame 1"""	C22orf1		9266672, 10591208	Standard	NM_001044370		Approved	239AB, FAM1A	uc011apv.2	O15442	OTTHUMG00000150566	ENST00000417669.2:c.267C>T	22.37:g.43830996C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001044370	A8K159|B7Z2S9|Q8N361	Silent	SNP	ENST00000417669.2	37	CCDS46723.1																																																																																			C|0.615;T|0.385	0.385	strong		0.652	MPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318938.2	NM_001044370	
SEMA3F	6405	hgsc.bcm.edu	37	3	50197097	50197097	+	Silent	SNP	C	C	T	rs1046953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50197097C>T	ENST00000002829.3	+	2	526	c.42C>T	c.(40-42)acC>acT	p.T14T	SEMA3F_ENST00000434342.1_Silent_p.T14T|SEMA3F_ENST00000413852.1_Intron	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	14					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CCCTACTGACCGGGGCCTGGC	0.617													T|||	1879	0.3752	0.3177	0.2983	5008	,	,		16725	0.1915		0.4026	False		,,,				2504	0.6687				p.T14T		Atlas-SNP	.											.	SEMA3F	62	.	0			c.C42T						PASS	.	T		1471,2935	677.1+/-403.3	252,967,984	60.0	57.0	58.0		42	-2.4	0.9	3	dbSNP_86	58	3510,5090	632.3+/-398.6	708,2094,1498	no	coding-synonymous	SEMA3F	NM_004186.3		960,3061,2482	TT,TC,CC		40.814,33.3863,38.2977		14/786	50197097	4981,8025	2203	4300	6503	SO:0001819	synonymous_variant	6405	exon2			ACTGACCGGGGCC	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10728	protein-coding gene	gene with protein product	"""sema IV"""	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.42C>T	3.37:g.50197097C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Silent	SNP	ENST00000002829.3	37	CCDS2811.1																																																																																			C|0.626;T|0.374	0.374	strong		0.617	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186	
ARHGEF17	9828	hgsc.bcm.edu	37	11	73076590	73076590	+	Silent	SNP	C	C	T	rs61749197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:73076590C>T	ENST00000263674.3	+	19	6056	c.5706C>T	c.(5704-5706)ccC>ccT	p.P1902P		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1902					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P1902P(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						TCACTCCTCCCGTGCACAGGA	0.577													C|||	162	0.0323482	0.0068	0.0418	5008	,	,		22002	0.003		0.0924	False		,,,				2504	0.0286				p.P1902P		Atlas-SNP	.											ARHGEF17,mucosal,malignant_melanoma,+1,2	ARHGEF17	117	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C5706T						PASS	.	C		81,4319	70.3+/-108.2	0,81,2119	140.0	107.0	118.0		5706	-11.6	0.5	11	dbSNP_129	118	788,7798	184.9+/-232.8	36,716,3541	no	coding-synonymous	ARHGEF17	NM_014786.3		36,797,5660	TT,TC,CC		9.1777,1.8409,6.6918		1902/2064	73076590	869,12117	2200	4293	6493	SO:0001819	synonymous_variant	9828	exon19			TCCTCCCGTGCAC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.5706C>T	11.37:g.73076590C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	169	96	0.568047	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	37	CCDS8221.1																																																																																			C|0.941;T|0.059	0.059	strong		0.577	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	
ANKRD53	79998	hgsc.bcm.edu	37	2	71212405	71212405	+	Missense_Mutation	SNP	T	T	C	rs61732279	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71212405T>C	ENST00000360589.3	+	6	1602	c.1568T>C	c.(1567-1569)cTg>cCg	p.L523P	AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000457410.1_Missense_Mutation_p.L489P|ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000272421.6_3'UTR	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	523				L -> P (in Ref. 1; BAC04181). {ECO:0000305}.				p.L523P(1)		endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						CTCCCCACCCTGCCCTCCCCA	0.562											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	742	0.148163	0.1316	0.1282	5008	,	,		13076	0.1617		0.2276	False		,,,				2504	0.089				p.L523P		Atlas-SNP	.											ANKRD53_ENST00000360589,NS,carcinoma,0,2	ANKRD53	55	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1568C						PASS	.	T	PRO/LEU,	187,1197		12,163,517	15.0	15.0	15.0		1568,	0.8	0.0	2	dbSNP_129	15	637,2545		75,487,1029	yes	missense,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	98,	87,650,1546	CC,CT,TT		20.0189,13.5116,18.0464	benign,	523/531,	71212405	824,3742	692	1591	2283	SO:0001583	missense	79998	exon6			CCACCCTGCCCTC	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1568T>C	2.37:g.71212405T>C	ENSP00000353796:p.Leu523Pro	Somatic	109	0	0	1128	WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_001115116	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	37	CCDS46321.1	375	0.1717032967032967	55	0.11178861788617886	49	0.13535911602209943	101	0.17657342657342656	170	0.22427440633245382	T	13.31	2.199486	0.38806	0.135116	0.200189	ENSG00000144031	ENST00000457410;ENST00000360589	T;T	0.75704	-0.83;-0.96	4.63	0.842	0.18927	.	0.443867	0.16837	N	0.197499	T	0.00039	0.0001	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B	0.25007	0.116	B	0.23852	0.049	T	0.04216	-1.0968	9	0.46703	T	0.11	-8.7589	1.2754	0.02030	0.1821:0.102:0.1894:0.5266	rs61732279	523	Q8N9V6	ANR53_HUMAN	P	489;523	ENSP00000407004:L489P;ENSP00000353796:L523P	ENSP00000353796:L523P	L	+	2	0	ANKRD53	71065913	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.054000	0.11826	0.139000	0.18822	0.533000	0.62120	CTG	T|0.841;C|0.159	0.159	strong		0.562	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
DHRS7C	201140	hgsc.bcm.edu	37	17	9676148	9676148	+	Silent	SNP	C	C	T	rs2280489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:9676148C>T	ENST00000330255.5	-	5	678	c.666G>A	c.(664-666)ccG>ccA	p.P222P	DHRS7C_ENST00000571134.1_Silent_p.P221P	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	222					regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						GGATGAAAGTCGGGCTCACGG	0.582													C|||	502	0.10024	0.112	0.0692	5008	,	,		19224	0.0992		0.1054	False		,,,				2504	0.1022				p.P222P		Atlas-SNP	.											.	DHRS7C	34	.	0			c.G666A						PASS	.	C	,	512,3890	208.5+/-229.5	40,432,1729	75.0	82.0	80.0		663,666	-9.1	0.0	17	dbSNP_100	80	912,7686	198.0+/-242.5	48,816,3435	no	coding-synonymous,coding-synonymous	DHRS7C	NM_001105571.2,NM_001220493.1	,	88,1248,5164	TT,TC,CC		10.6071,11.6311,10.9538	,	221/312,222/313	9676148	1424,11576	2201	4299	6500	SO:0001819	synonymous_variant	201140	exon5			GAAAGTCGGGCTC		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	32423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 32C, member 2"""					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.666G>A	17.37:g.9676148C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_001220493	B7ZW74|B9EJH3	Silent	SNP	ENST00000330255.5	37	CCDS56020.1																																																																																			T|0.103;C|0.897	0.103	strong		0.582	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912	
TEFM	79736	hgsc.bcm.edu	37	17	29226228	29226228	+	Missense_Mutation	SNP	T	T	C	rs2433	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29226228T>C	ENST00000581216.1	-	4	1663	c.1042A>G	c.(1042-1044)Att>Gtt	p.I348V	TEFM_ENST00000579183.1_5'Flank|TEFM_ENST00000580840.1_3'UTR	NM_024683.3	NP_078959.3	Q96QE5	TEFM_HUMAN	transcription elongation factor, mitochondrial	348			I -> V (in dbSNP:rs2433).		DNA metabolic process (GO:0006259)|oxidative phosphorylation (GO:0006119)|regulation of transcription, DNA-templated (GO:0006355)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	DNA polymerase processivity factor activity (GO:0030337)|poly(A) RNA binding (GO:0044822)										TAGAAGGCAATAGCTTGTAAT	0.348													T|||	724	0.144569	0.0719	0.1859	5008	,	,		21034	0.1369		0.1074	False		,,,				2504	0.2597				p.I348V		Atlas-SNP	.											.	.	.	.	0			c.A1042G						PASS	.	T	VAL/ILE	258,3424		11,236,1594	141.0	135.0	137.0		1042	-4.0	0.6	17	dbSNP_36	137	852,7322		35,782,3270	yes	missense	C17orf42	NM_024683.3	29	46,1018,4864	CC,CT,TT		10.4233,7.0071,9.3623	benign	348/361	29226228	1110,10746	1841	4087	5928	SO:0001583	missense	79736	exon4			AGGCAATAGCTTG		CCDS42291.1	17q11.2	2011-12-12	2011-12-12	2011-12-12	ENSG00000172171	ENSG00000172171			26223	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 42"""	C17orf42		11468690, 10843809, 21278163	Standard	NM_024683		Approved	FLJ22729	uc002hfu.2	Q96QE5		ENST00000581216.1:c.1042A>G	17.37:g.29226228T>C	ENSP00000462963:p.Ile348Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_024683	E1P655|Q6GPG5|Q6PJ19|Q96H04|Q9H5Z9	Missense_Mutation	SNP	ENST00000581216.1	37	CCDS42291.1	274	0.12545787545787546	45	0.09146341463414634	65	0.17955801104972377	92	0.16083916083916083	72	0.09498680738786279	T	2.302	-0.359837	0.05138	0.070071	0.104233	ENSG00000172171	ENST00000306049	.	.	.	6.16	-3.95	0.04118	Ribonuclease H-like (1);	0.444772	0.25487	N	0.030339	T	0.00039	0.0001	N	0.00890	-1.11	0.09310	P	0.9999999999999977	B	0.02656	0.0	B	0.01281	0.0	T	0.21793	-1.0235	8	0.02654	T	1	-19.1323	13.1694	0.59589	0.0:0.3869:0.0:0.6131	rs2433;rs52827271;rs58920644;rs2433	348	Q96QE5	TEFM_HUMAN	V	348	.	ENSP00000306574:I348V	I	-	1	0	C17orf42	26250354	0.001000	0.12720	0.568000	0.28447	0.929000	0.56500	-0.218000	0.09240	-0.961000	0.03609	-1.668000	0.00747	ATT	T|0.876;C|0.124	0.124	strong		0.348	TEFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444498.1	NM_024683	
THSD4	79875	hgsc.bcm.edu	37	15	71953045	71953045	+	Silent	SNP	G	G	A	rs62024298	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:71953045G>A	ENST00000355327.3	+	8	1463	c.1329G>A	c.(1327-1329)acG>acA	p.T443T	THSD4_ENST00000567838.1_3'UTR|THSD4_ENST00000357769.4_Silent_p.T83T|THSD4_ENST00000261862.6_Silent_p.T443T			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	443					elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TCAACATCACGGAGATGTACA	0.512													G|||	1688	0.337061	0.2027	0.2637	5008	,	,		18803	0.6706		0.2565	False		,,,				2504	0.3098				p.T443T		Atlas-SNP	.											.	THSD4	75	.	0			c.G1329A						PASS	.	G		754,3136		71,612,1262	85.0	88.0	87.0		1329	-9.1	0.7	15	dbSNP_129	87	1936,6356		229,1478,2439	no	coding-synonymous	THSD4	NM_024817.2		300,2090,3701	AA,AG,GG		23.3478,19.383,22.0818		443/1019	71953045	2690,9492	1945	4146	6091	SO:0001819	synonymous_variant	79875	exon7			CATCACGGAGATG	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.1329G>A	15.37:g.71953045G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Silent	SNP	ENST00000355327.3	37	CCDS10238.2																																																																																			G|0.678;A|0.322	0.322	strong		0.512	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817	
PPAT	5471	hgsc.bcm.edu	37	4	57273840	57273840	+	Silent	SNP	C	C	G	rs11538098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57273840C>G	ENST00000264220.2	-	2	308	c.171G>C	c.(169-171)tcG>tcC	p.S57S	AC068620.1_ENST00000598320.1_5'Flank|PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	57	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)	p.S57S(1)		cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	ATGTTGGCACCGAACTCCCAT	0.408													T|||	1303	0.260184	0.239	0.2795	5008	,	,		20452	0.0704		0.4016	False		,,,				2504	0.3252				p.S57S		Atlas-SNP	.											PPAT,NS,carcinoma,0,2	PPAT	41	2	1	Substitution - coding silent(1)	prostate(1)	c.G171C						PASS	.	T		1117,3289		127,863,1213	154.0	130.0	138.0		171	1.8	0.4	4	dbSNP_120	138	3585,5015		724,2137,1439	no	coding-synonymous	PPAT	NM_002703.4		851,3000,2652	GG,GC,CC		41.686,25.3518,36.1525		57/518	57273840	4702,8304	2203	4300	6503	SO:0001819	synonymous_variant	5471	exon2			TGGCACCGAACTC		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.171G>C	4.37:g.57273840C>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_002703		Silent	SNP	ENST00000264220.2	37	CCDS3505.1																																																																																			C|0.671;G|0.329	0.329	strong		0.408	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703	
BTNL2	56244	hgsc.bcm.edu	37	6	32363816	32363816	+	Splice_Site	SNP	T	T	C	rs2076530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32363816T>C	ENST00000374993.1	-	5	1077	c.1078A>G	c.(1078-1080)Agt>Ggt	p.S360G	BTNL2_ENST00000414363.1_Splice_Site_p.S150G|BTNL2_ENST00000540315.1_Splice_Site_p.S150G|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000454136.3_Splice_Site_p.S360G|BTNL2_ENST00000544175.1_Splice_Site_p.S83G|BTNL2_ENST00000374995.3_Splice_Site_p.S266G|BTNL2_ENST00000429232.2_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	360			S -> G (in dbSNP:rs2076530).			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						GAATTCTTACTTACCACCTTC	0.413													c|||	1938	0.386981	0.3275	0.4841	5008	,	,		19566	0.2917		0.4473	False		,,,				2504	0.4346				p.S360G		Atlas-SNP	.											.	BTNL2	50	.	0			c.A1078G						PASS	.		GLY/SER	974,2044		154,666,689	54.0	61.0	59.0	http://www.ncbi.nlm.nih.gov/omim/606000,612387|http://omim.org/entry/612387|http://omim.org/entry/606000#0001	1078	3.4	1.0	6	dbSNP_96	59	2375,3043		510,1355,844	yes	missense-near-splice	BTNL2	NM_019602.1	56	664,2021,1533	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	43.8354,32.273,39.6989	benign	360/456	32363816	3349,5087	1509	2709	4218	SO:0001630	splice_region_variant	56244	exon5			TCTTACTTACCAC	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.1078+1A>G	6.37:g.32363816T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	87	32	0.367816	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		824	0.3772893772893773	124	0.25203252032520324	179	0.494475138121547	192	0.3356643356643357	329	0.4340369393139842	c	0.492	-0.875000	0.02550	0.32273	0.438354	ENSG00000204290	ENST00000468270;ENST00000374995;ENST00000414363;ENST00000374993;ENST00000540315;ENST00000544175	T;T;T;T;T	0.03468	4.39;4.47;3.92;4.44;4.15	5.2	3.36	0.38483	.	0.328887	0.22150	N	0.063934	T	0.00271	0.0008	N	0.00134	-2.025	0.09310	P	0.9999999999998409	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36383	-0.9750	8	.	.	.	.	7.0015	0.24813	0.1401:0.7038:0.0:0.1562	rs2076530;rs7746551;rs17202463;rs56415813;rs60534273;rs2076530	150;360	Q9UIR0-4;Q9UIR0	.;BTNL2_HUMAN	G	360;266;150;360;150;83	ENSP00000364134:S266G;ENSP00000390512:S150G;ENSP00000364132:S360G;ENSP00000444714:S150G;ENSP00000443364:S83G	.	S	-	1	0	BTNL2	32471794	1.000000	0.71417	0.995000	0.50966	0.516000	0.34256	1.798000	0.38814	0.783000	0.33636	-1.371000	0.01190	AGT	T|0.628;C|0.372	0.372	strong		0.413	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	Missense_Mutation
MUC16	94025	hgsc.bcm.edu	37	19	9028373	9028373	+	Missense_Mutation	SNP	G	G	A	rs56396897	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9028373G>A	ENST00000397910.4	-	11	36622	c.36419C>T	c.(36418-36420)aCg>aTg	p.T12140M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12142	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATCCACTGCCGTGGCTGAGCT	0.532													G|||	1072	0.214058	0.0545	0.2075	5008	,	,		20524	0.2381		0.341	False		,,,				2504	0.2791				p.T12140M		Atlas-SNP	.											.	MUC16	4315	.	0			c.C36419T						PASS	.	G	MET/THR	444,3822		30,384,1719	139.0	145.0	143.0		36419	2.6	0.5	19	dbSNP_129	143	2674,5780		420,1834,1973	yes	missense	MUC16	NM_024690.2	81	450,2218,3692	AA,AG,GG		31.63,10.4079,24.5126	probably-damaging	12140/14508	9028373	3118,9602	2133	4227	6360	SO:0001583	missense	94025	exon11			ACTGCCGTGGCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36419C>T	19.37:g.9028373G>A	ENSP00000381008:p.Thr12140Met	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	194	77	0.396907	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	517	0.2367216117216117	22	0.044715447154471545	84	0.23204419889502761	151	0.263986013986014	260	0.34300791556728233	G	11.28	1.593164	0.28357	0.104079	0.3163	ENSG00000181143	ENST00000397910	T	0.39592	1.07	2.63	2.63	0.31362	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	D	0.89917	1.0	D	0.87578	0.998	T	0.18023	-1.0350	7	0.87932	D	0	.	8.8909	0.35432	0.0:0.0:1.0:0.0	rs56396897	12140	B5ME49	.	M	12140	ENSP00000381008:T12140M	ENSP00000381008:T12140M	T	-	2	0	MUC16	8889373	0.974000	0.33945	0.496000	0.27539	0.015000	0.08874	2.623000	0.46435	1.757000	0.51966	0.591000	0.81541	ACG	G|0.755;A|0.245	0.245	strong		0.532	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ULK4	54986	hgsc.bcm.edu	37	3	41996136	41996136	+	Missense_Mutation	SNP	T	T	C	rs2272007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:41996136T>C	ENST00000301831.4	-	2	578	c.116A>G	c.(115-117)aAa>aGa	p.K39R	ULK4_ENST00000420927.1_Missense_Mutation_p.K39R|ULK4_ENST00000414606.1_Missense_Mutation_p.K39R	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	39	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> R (in dbSNP:rs2272007). {ECO:0000269|PubMed:17344846}.		cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K39R(2)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TTCAGGCCTTTTGCACTTATC	0.433													T|||	3416	0.682109	0.2821	0.8098	5008	,	,		18273	0.8512		0.8091	False		,,,				2504	0.8272				p.K39R		Atlas-SNP	.											ULK4_ENST00000301831,NS,carcinoma,0,2	ULK4	150	2	2	Substitution - Missense(2)	prostate(2)	c.A116G						PASS	.	T	ARG/LYS	1352,2420		260,832,794	162.0	149.0	153.0		116	4.4	1.0	3	dbSNP_100	153	6790,1440		2805,1180,130	yes	missense	ULK4	NM_017886.2	26	3065,2012,924	CC,CT,TT		17.497,35.8431,32.1613	benign	39/1276	41996136	8142,3860	1886	4115	6001	SO:0001583	missense	54986	exon2			GGCCTTTTGCACT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.116A>G	3.37:g.41996136T>C	ENSP00000301831:p.Lys39Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	1523	0.6973443223443223	141	0.2865853658536585	291	0.8038674033149171	482	0.8426573426573427	609	0.8034300791556728	T	9.511	1.105636	0.20632	0.358431	0.82503	ENSG00000168038	ENST00000301831;ENST00000420927;ENST00000414606	T;T;T	0.66099	-0.19;-0.19;-0.19	5.56	4.4	0.53042	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.210177	0.49916	N	0.000131	T	0.00012	0.0000	N	0.02213	-0.635	0.27299	P	0.9576255	B;B	0.28258	0.022;0.205	B;B	0.31547	0.059;0.132	T	0.24728	-1.0152	9	0.21540	T	0.41	.	11.7026	0.51579	0.0:0.0693:0.0:0.9307	rs2272007;rs57004704;rs2272007	39;39	B4E2M4;Q96C45	.;ULK4_HUMAN	R	39	ENSP00000301831:K39R;ENSP00000412187:K39R;ENSP00000399382:K39R	ENSP00000301831:K39R	K	-	2	0	ULK4	41971140	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.866000	0.56040	1.058000	0.40530	0.456000	0.33151	AAA	T|0.314;C|0.686	0.686	strong		0.433	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
XIRP2	129446	hgsc.bcm.edu	37	2	168106803	168106803	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:168106803G>C	ENST00000409195.1	+	9	8990	c.8901G>C	c.(8899-8901)gaG>gaC	p.E2967D	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.E2967D|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.E2745D	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2792				S -> A (in Ref. 8; CAD91141). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGAAGCAGAGCCAAATAAAA	0.383																																					p.E2967D		Atlas-SNP	.											.	XIRP2	914	.	0			c.G8901C						PASS	.						90.0	88.0	88.0					2																	168106803		1822	4088	5910	SO:0001583	missense	129446	exon9			AGCAGAGCCAAAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8901G>C	2.37:g.168106803G>C	ENSP00000386840:p.Glu2967Asp	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	194	29	0.149485	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	9.715	1.158030	0.21454	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.03212	4.01;4.01;4.01	6.02	-1.98	0.07480	.	0.623038	0.17625	N	0.167595	T	0.02848	0.0085	L	0.40543	1.245	0.09310	N	0.999996	B;B;B	0.17667	0.013;0.023;0.023	B;B;B	0.18871	0.01;0.023;0.023	T	0.38134	-0.9675	10	0.40728	T	0.16	-11.4362	3.8151	0.08812	0.394:0.0974:0.4094:0.0991	.	2792;2792;2745	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	D	2967;2967;2745;381	ENSP00000386840:E2967D;ENSP00000295237:E2967D;ENSP00000387255:E2745D	ENSP00000295237:E2967D	E	+	3	2	XIRP2	167815049	0.595000	0.26857	0.958000	0.39756	0.978000	0.69477	-0.106000	0.10890	-0.277000	0.09193	-0.150000	0.13652	GAG	.	.	none		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
ZNF544	27300	hgsc.bcm.edu	37	19	58774094	58774094	+	Missense_Mutation	SNP	C	C	T	rs34914886	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58774094C>T	ENST00000596652.1	+	6	2356	c.2122C>T	c.(2122-2124)Cgg>Tgg	p.R708W	ZNF544_ENST00000596929.1_Intron|CTD-3138B18.5_ENST00000597230.1_RNA|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000600220.1_Missense_Mutation_p.R680W|ZNF544_ENST00000599953.1_Missense_Mutation_p.R566W|ZNF544_ENST00000415203.2_Missense_Mutation_p.R680W|ZNF544_ENST00000269829.4_Missense_Mutation_p.R708W|ZNF544_ENST00000600044.1_Missense_Mutation_p.R680W|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000596825.1_3'UTR			Q6NX49	ZN544_HUMAN	zinc finger protein 544	708					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		AGTGCATCGGCGGACACATAC	0.498													C|||	28	0.00559105	0.0008	0.0043	5008	,	,		21265	0.0		0.0209	False		,,,				2504	0.0031				p.R708W		Atlas-SNP	.											.	ZNF544	57	.	0			c.C2122T						PASS	.	C	TRP/ARG	9,4397	14.3+/-33.2	0,9,2194	128.0	131.0	130.0		2122	-4.5	0.0	19	dbSNP_126	130	152,8448	74.2+/-136.8	2,148,4150	yes	missense	ZNF544	NM_014480.2	101	2,157,6344	TT,TC,CC		1.7674,0.2043,1.2379	probably-damaging	708/716	58774094	161,12845	2203	4300	6503	SO:0001583	missense	27300	exon7			CATCGGCGGACAC	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"""Zinc fingers, C2H2-type"", ""-"""	16759	protein-coding gene	gene with protein product	"""zinc finger protein AF020591"""						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.2122C>T	19.37:g.58774094C>T	ENSP00000469635:p.Arg708Trp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	37	CCDS12973.1	20	0.009157509157509158	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	C	15.70	2.910460	0.52439	0.002043	0.017674	ENSG00000198131	ENST00000269829;ENST00000415203;ENST00000441758	T;T	0.36520	1.25;1.25	3.36	-4.51	0.03483	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39708	0.1088	M	0.91354	3.2	0.09310	N	0.999999	P;D;D	0.89917	0.559;1.0;1.0	B;D;D	0.73708	0.019;0.981;0.981	T	0.48625	-0.9019	9	0.87932	D	0	.	1.5063	0.02487	0.484:0.2002:0.1223:0.1935	rs34914886	680;680;708	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	W	708;680;260	ENSP00000269829:R708W;ENSP00000394341:R680W	ENSP00000269829:R708W	R	+	1	2	ZNF544	63465906	0.000000	0.05858	0.007000	0.13788	0.886000	0.51366	-3.023000	0.00641	-0.426000	0.07360	0.563000	0.77884	CGG	C|0.989;T|0.011	0.011	strong		0.498	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480	
REV3L	5980	hgsc.bcm.edu	37	6	111695268	111695268	+	Silent	SNP	C	C	T	rs455732	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:111695268C>T	ENST00000358835.3	-	14	4744	c.4290G>A	c.(4288-4290)gtG>gtA	p.V1430V	REV3L_ENST00000368805.1_Silent_p.V1430V|REV3L_ENST00000368802.3_Silent_p.V1430V|REV3L_ENST00000435970.1_Silent_p.V1352V			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1430					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CCGCTATGCACACAATCTGCT	0.413								DNA polymerases (catalytic subunits)					C|||	1773	0.354034	0.0461	0.4337	5008	,	,		19259	0.4187		0.496	False		,,,				2504	0.501				p.V1430V		Atlas-SNP	.											.	REV3L	386	.	0			c.G4290A						PASS	.	C		562,3844	247.5+/-255.7	57,448,1698	165.0	144.0	151.0		4290	2.9	1.0	6	dbSNP_80	151	4569,4029	597.6+/-393.8	1215,2139,945	no	coding-synonymous	REV3L	NM_002912.3		1272,2587,2643	TT,TC,CC		46.8597,12.7553,39.4571		1430/3131	111695268	5131,7873	2203	4299	6502	SO:0001819	synonymous_variant	5980	exon13			TATGCACACAATC	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.4290G>A	6.37:g.111695268C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	153	150	0.980392	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			C|0.621;T|0.379	0.379	strong		0.413	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
KMT2D	8085	hgsc.bcm.edu	37	12	49425978	49425978	+	Silent	SNP	T	T	C	rs3741622	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49425978T>C	ENST00000301067.7	-	39	12509	c.12510A>G	c.(12508-12510)ccA>ccG	p.P4170P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4170	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.P3900P(1)									TGGGAGGTTGTGGCCCTGTAT	0.592													T|||	1379	0.275359	0.0234	0.2363	5008	,	,		18835	0.4454		0.3022	False		,,,				2504	0.4407				p.P4170P		Atlas-SNP	.											MLL2,NS,carcinoma,0,1	MLL2	1173	1	1	Substitution - coding silent(1)	stomach(1)	c.A12510G						PASS	.	T		288,3676		10,268,1704	90.0	80.0	83.0		12510	1.8	1.0	12	dbSNP_107	83	2787,5517		480,1827,1845	no	coding-synonymous	MLL2	NM_003482.3		490,2095,3549	CC,CT,TT		33.5621,7.2654,25.0652		4170/5538	49425978	3075,9193	1982	4152	6134	SO:0001819	synonymous_variant	8085	exon39			AGGTTGTGGCCCT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.12510A>G	12.37:g.49425978T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	95	34	0.357895	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			T|0.725;C|0.275	0.275	strong		0.592	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
OVCH2	341277	hgsc.bcm.edu	37	11	7712523	7712523	+	RNA	SNP	G	G	A	rs4633461	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7712523G>A	ENST00000533663.1	-	0	334				OVCH2_ENST00000534193.2_RNA|OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		GAAGGAGACTGTAGCCTGAAA	0.488													G|||	843	0.168331	0.2791	0.1369	5008	,	,		18126	0.1577		0.1382	False		,,,				2504	0.0828				p.T539I		Atlas-SNP	.											.	OVCH2	47	.	0			c.C1616T						PASS	.	G	ILE/THR	949,2831		122,705,1063	64.0	63.0	63.0		1616	3.7	0.1	11	dbSNP_111	63	1208,7016		79,1050,2983	yes	missense	OVCH2	NM_198185.2	89	201,1755,4046	AA,AG,GG		14.6887,25.1058,17.969	possibly-damaging	539/565	7712523	2157,9847	1890	4112	6002			341277	exon15			GAGACTGTAGCCT	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"""ovochymase 2"""			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		11.37:g.7712523G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	66	0.52381	NM_198185		Missense_Mutation	SNP	ENST00000533663.1	37		376	0.17216117216117216	139	0.28252032520325204	55	0.15193370165745856	85	0.1486013986013986	97	0.1279683377308707	G	11.49	1.654456	0.29425	0.251058	0.146887	ENSG00000183378	ENST00000454689	T	0.19532	2.14	5.62	3.65	0.41850	CUB (5);	0.474783	0.16524	N	0.210649	T	0.00012	0.0000	M	0.74881	2.28	0.80722	P	0.0	B	0.24768	0.111	B	0.30495	0.116	T	0.19224	-1.0312	9	0.33940	T	0.23	-0.1036	10.1232	0.42634	0.0:0.1442:0.696:0.1598	rs4633461;rs59017984;rs4633461	539	Q7RTZ1	OVCH2_HUMAN	I	539	ENSP00000407158:T539I	ENSP00000407158:T539I	T	-	2	0	OVCH2	7669099	0.021000	0.18746	0.136000	0.22124	0.692000	0.40212	1.163000	0.31798	0.654000	0.30846	0.557000	0.71058	ACA	G|0.826;A|0.174	0.174	strong		0.488	OVCH2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000383928.1	NM_198185	
INCENP	3619	hgsc.bcm.edu	37	11	61897404	61897404	+	Silent	SNP	C	C	T	rs112218336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:61897404C>T	ENST00000394818.3	+	4	607	c.405C>T	c.(403-405)acC>acT	p.T135T	INCENP_ENST00000278849.4_Silent_p.T135T	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	135					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CCGCGGCTACCATGGCATTGG	0.632													C|||	25	0.00499201	0.0	0.0144	5008	,	,		15459	0.0		0.0149	False		,,,				2504	0.0				p.T135T		Atlas-SNP	.											.	INCENP	122	.	0			c.C405T						PASS	.	C	,	16,4382		0,16,2183	57.0	58.0	57.0		405,405	-6.1	0.0	11	dbSNP_132	57	125,8473		1,123,4175	no	coding-synonymous,coding-synonymous	INCENP	NM_001040694.1,NM_020238.2	,	1,139,6358	TT,TC,CC		1.4538,0.3638,1.0849	,	135/919,135/915	61897404	141,12855	2199	4299	6498	SO:0001819	synonymous_variant	3619	exon4			GGCTACCATGGCA	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.405C>T	11.37:g.61897404C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	37	CCDS44624.1																																																																																			C|0.991;G|0.000;T|0.009	0.009	strong		0.632	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
MFSD9	84804	hgsc.bcm.edu	37	2	103343356	103343356	+	Silent	SNP	A	A	C	rs34997861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:103343356A>C	ENST00000258436.5	-	4	418	c.375T>G	c.(373-375)ctT>ctG	p.L125L		NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	125					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						CTGCTCCGAGAAGGAGATAGC	0.493																																					p.L125L		Atlas-SNP	.											.	MFSD9	56	.	0			c.T375G						PASS	.	A		0,4406		0,0,2203	79.0	77.0	78.0		375	-4.7	0.1	2	dbSNP_126	78	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	MFSD9	NM_032718.3		0,8,6495	CC,CA,AA		0.093,0.0,0.0615		125/475	103343356	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	84804	exon4			TCCGAGAAGGAGA		CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.375T>G	2.37:g.103343356A>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	181	91	0.502762	NM_032718	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Silent	SNP	ENST00000258436.5	37	CCDS2063.1																																																																																			A|0.999;C|0.001	0.001	strong		0.493	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718	
ZNF106	64397	hgsc.bcm.edu	37	15	42734320	42734320	+	Silent	SNP	C	C	T	rs61753567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42734320C>T	ENST00000263805.4	-	7	3971	c.3645G>A	c.(3643-3645)gtG>gtA	p.V1215V	ZNF106_ENST00000565611.1_Silent_p.V400V|ZNF106_ENST00000565380.1_Silent_p.V443V	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	1215					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AGCTTGGTGGCACAGCATTCA	0.478													C|||	245	0.0489217	0.0045	0.0533	5008	,	,		19327	0.001		0.0716	False		,,,				2504	0.1319				p.V1215V		Atlas-SNP	.											.	ZFP106	117	.	0			c.G3645A						PASS	.	C		74,4332	64.1+/-101.4	1,72,2130	182.0	164.0	170.0		3645	1.2	0.6	15	dbSNP_129	170	604,7994	160.0+/-213.2	24,556,3719	no	coding-synonymous	ZFP106	NM_022473.1		25,628,5849	TT,TC,CC		7.0249,1.6795,5.2138		1215/1884	42734320	678,12326	2203	4299	6502	SO:0001819	synonymous_variant	64397	exon7			TGGTGGCACAGCA	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.3645G>A	15.37:g.42734320C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Silent	SNP	ENST00000263805.4	37	CCDS32208.1																																																																																			C|0.950;T|0.050	0.050	strong		0.478	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
SNCG	6623	hgsc.bcm.edu	37	10	88722398	88722398	+	Missense_Mutation	SNP	A	A	T	rs9864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88722398A>T	ENST00000372017.3	+	4	371	c.329A>T	c.(328-330)gAg>gTg	p.E110V	SNCG_ENST00000348795.4_Nonstop_Mutation_p.*127C|SNCG_ENST00000483064.1_3'UTR	NM_003087.2	NP_003078.2	O76070	SYUG_HUMAN	synuclein, gamma (breast cancer-specific protein 1)	110			E -> V (in dbSNP:rs9864). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9737786}.		adult locomotory behavior (GO:0008344)|aggressive behavior (GO:0002118)|cellular response to hydrostatic pressure (GO:0071464)|protein secretion (GO:0009306)|regulation of dopamine secretion (GO:0014059)|regulation of neurotransmitter secretion (GO:0046928)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				endometrium(1)|skin(1)	2						CAGGAGGGTGAGGCATCCAAA	0.612													a|||	1020	0.203674	0.1679	0.2233	5008	,	,		18772	0.0635		0.2336	False		,,,				2504	0.3517				p.E110V		Atlas-SNP	.											.	SNCG	8	.	0			c.A329T						PASS	.	A	VAL/GLU	824,3582	319.3+/-296.1	86,652,1465	87.0	103.0	98.0		329	2.6	0.0	10	dbSNP_52	98	2144,6456	358.5+/-331.2	247,1650,2403	yes	missense	SNCG	NM_003087.2	121	333,2302,3868	TT,TA,AA		24.9302,18.7018,22.8202	benign	110/128	88722398	2968,10038	2203	4300	6503	SO:0001583	missense	6623	exon4			AGGGTGAGGCATC	AF044311	CCDS7380.1	10q23.2-q23.3	2006-06-28			ENSG00000173267	ENSG00000173267			11141	protein-coding gene	gene with protein product	"""synoretin"""	602998				9044857, 9700196	Standard	NM_003087		Approved	BCSG1, SR, persyn	uc001keb.2	O76070	OTTHUMG00000018656	ENST00000372017.3:c.329A>T	10.37:g.88722398A>T	ENSP00000361087:p.Glu110Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	134	78	0.58209	NM_003087	O15104|Q96P61	Missense_Mutation	SNP	ENST00000372017.3	37	CCDS7380.1	398|398	0.18223443223443223|0.18223443223443223	82|82	0.16666666666666666|0.16666666666666666	94|94	0.2596685082872928|0.2596685082872928	38|38	0.06643356643356643|0.06643356643356643	184|184	0.24274406332453827|0.24274406332453827	A|A	5.966|5.966	0.362125|0.362125	0.11296|0.11296	0.187018|0.187018	0.249302|0.249302	ENSG00000173267|ENSG00000173267	ENST00000372017|ENST00000348795	D|.	0.84589|.	-1.87|.	3.81|3.81	2.63|2.63	0.31362|0.31362	.|.	1.114660|.	0.06941|.	N|.	0.812842|.	T|.	0.00012|.	0.0000|.	N|N	0.25647|0.25647	0.755|0.755	0.80722|0.80722	P|P	0.0|0.0	B|.	0.27286|.	0.174|.	B|.	0.30316|.	0.114|.	T|.	0.28073|.	-1.0055|.	9|.	0.36615|.	T|.	0.2|.	-0.49|-0.49	7.1573|7.1573	0.25645|0.25645	0.7705:0.2295:0.0:0.0|0.7705:0.2295:0.0:0.0	rs9864;rs1130096;rs3188626;rs9325593;rs11550196;rs17354005;rs17469989;rs60364371;rs9864|rs9864;rs1130096;rs3188626;rs9325593;rs11550196;rs17354005;rs17469989;rs60364371;rs9864	110|.	O76070|.	SYUG_HUMAN|.	V|C	110|127	ENSP00000361087:E110V|.	ENSP00000361087:E110V|.	E|X	+|+	2|3	0|0	SNCG|SNCG	88712378|88712378	0.082000|0.082000	0.21442|0.21442	0.003000|0.003000	0.11579|0.11579	0.453000|0.453000	0.32348|0.32348	1.097000|1.097000	0.30988|0.30988	0.791000|0.791000	0.33826|0.33826	0.482000|0.482000	0.46254|0.46254	GAG|TGA	A|0.789;T|0.211	0.211	strong		0.612	SNCG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049167.1		
COBLL1	22837	hgsc.bcm.edu	37	2	165551404	165551404	+	Missense_Mutation	SNP	G	G	A	rs17244632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:165551404G>A	ENST00000392717.2	-	13	2730	c.2726C>T	c.(2725-2727)aCt>aTt	p.T909I	COBLL1_ENST00000375458.2_Missense_Mutation_p.T833I|COBLL1_ENST00000342193.4_Missense_Mutation_p.T871I|COBLL1_ENST00000194871.6_Missense_Mutation_p.T938I|COBLL1_ENST00000409184.3_Missense_Mutation_p.T871I			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	909						extracellular vesicular exosome (GO:0070062)		p.T871I(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						AGCTGTGCCAGTGTCTCTTGT	0.448													G|||	264	0.0527157	0.0113	0.0519	5008	,	,		18589	0.0327		0.1581	False		,,,				2504	0.0215				p.T871I		Atlas-SNP	.											COBLL1,NS,carcinoma,0,1	COBLL1	122	1	1	Substitution - Missense(1)	stomach(1)	c.C2612T						PASS	.	G	ILE/THR	159,4247	107.8+/-146.2	5,149,2049	91.0	88.0	89.0		2612	0.6	0.3	2	dbSNP_123	89	1196,7404	242.9+/-272.7	80,1036,3184	yes	missense	COBLL1	NM_014900.3	89	85,1185,5233	AA,AG,GG		13.907,3.6087,10.4183	possibly-damaging	871/1167	165551404	1355,11651	2203	4300	6503	SO:0001583	missense	22837	exon12			GTGCCAGTGTCTC	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.2726C>T	2.37:g.165551404G>A	ENSP00000376478:p.Thr909Ile	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	134	73	0.544776	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		161	0.07371794871794872	7	0.014227642276422764	20	0.055248618784530384	19	0.033216783216783216	115	0.1517150395778364	G	9.264	1.043933	0.19748	0.036087	0.13907	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	6.17	0.63	0.17693	.	0.725118	0.13805	N	0.361548	T	0.00178	0.0005	L	0.51422	1.61	0.80722	P	0.0	P;P;P	0.50443	0.893;0.893;0.935	B;P;P	0.45610	0.383;0.486;0.487	T	0.06972	-1.0797	8	0.59425	D	0.04	-2.8783	1.7239	0.02918	0.1457:0.2523:0.3429:0.2591	rs17244632;rs52813009;rs17244632	909;938;871	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	I	833;871;871;909;938	.	ENSP00000194871:T938I	T	-	2	0	COBLL1	165259650	0.000000	0.05858	0.308000	0.25141	0.119000	0.20118	0.328000	0.19681	0.443000	0.26582	0.655000	0.94253	ACT	G|0.913;A|0.087	0.087	strong		0.448	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
C11orf45	219833	hgsc.bcm.edu	37	11	128772452	128772452	+	Silent	SNP	C	C	T	rs11221503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:128772452C>T	ENST00000524878.1	-	4	608	c.438G>A	c.(436-438)taG>taA	p.*146*	C11orf45_ENST00000310799.3_Silent_p.*146*|C11orf45_ENST00000530168.1_5'UTR|KCNJ5_ENST00000338350.4_Intron|KCNJ5_ENST00000529694.1_Intron			Q8TAV5	CK045_HUMAN	chromosome 11 open reading frame 45	0						extracellular region (GO:0005576)				endometrium(1)|kidney(1)|lung(2)|pancreas(1)|prostate(2)	7	all_hematologic(175;0.0641)	Lung NSC(97;0.00521)|Breast(109;0.00715)|all_lung(97;0.0111)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.00531)|LUSC - Lung squamous cell carcinoma(976;0.0193)|Lung(977;0.0195)		GGAGACAGGGCTAGTTAGGAC	0.602													C|||	589	0.117612	0.0151	0.1585	5008	,	,		18070	0.0903		0.2316	False		,,,				2504	0.138				p.X146X		Atlas-SNP	.											.	C11orf45	14	.	0			c.G438A						PASS	.	C	,	239,4161		12,215,1973	71.0	54.0	59.0		,438	1.6	0.0	11	dbSNP_120	59	1799,6795		216,1367,2714	no	intron,coding-synonymous	KCNJ5,C11orf45	NM_000890.3,NM_145013.1	,	228,1582,4687	TT,TC,CC		20.9332,5.4318,15.6842	,	,146/146	128772452	2038,10956	2200	4297	6497	SO:0001819	synonymous_variant	219833	exon4			ACAGGGCTAGTTA	AK125634	CCDS8478.1	11q24.3	2012-05-30			ENSG00000174370	ENSG00000174370			28584	protein-coding gene	gene with protein product							Standard	NM_001256088		Approved	MGC35558, FLJ43646	uc001qeu.3	Q8TAV5	OTTHUMG00000165796	ENST00000524878.1:c.438G>A	11.37:g.128772452C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_145013	B2RAD0	Silent	SNP	ENST00000524878.1	37	CCDS8478.1																																																																																			C|0.869;T|0.131	0.131	strong		0.602	C11orf45-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386243.1	NM_145013	
MCPH1	79648	hgsc.bcm.edu	37	8	6302154	6302154	+	Missense_Mutation	SNP	G	G	T	rs2083914	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:6302154G>T	ENST00000344683.5	+	8	987	c.911G>T	c.(910-912)aGa>aTa	p.R304I	MCPH1_ENST00000519480.1_Missense_Mutation_p.R304I|MCPH1_ENST00000522905.1_Missense_Mutation_p.R256I	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	304			R -> I (in dbSNP:rs2083914).		cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		AACTTGCAAAGAAATATTGCA	0.383													G|||	352	0.0702875	0.0295	0.0908	5008	,	,		20069	0.0298		0.159	False		,,,				2504	0.0613				p.R304I	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.G911T						PASS	.	G	ILE/ARG,ILE/ARG,ILE/ARG	147,3555		4,139,1708	50.0	46.0	47.0		911,767,911	-2.2	0.0	8	dbSNP_96	47	1256,6914		78,1100,2907	yes	missense,missense,missense	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	97,97,97	82,1239,4615	TT,TG,GG		15.3733,3.9708,11.8177	probably-damaging,probably-damaging,probably-damaging	304/611,256/563,304/836	6302154	1403,10469	1851	4085	5936	SO:0001583	missense	79648	exon8			TGCAAAGAAATAT	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.911G>T	8.37:g.6302154G>T	ENSP00000342924:p.Arg304Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	179	0.08195970695970696	14	0.028455284552845527	35	0.09668508287292818	18	0.03146853146853147	112	0.14775725593667546	G	17.30	3.353605	0.61293	0.039708	0.153733	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.13089	2.62;2.62;2.62	5.5	-2.24	0.06909	.	1.067020	0.07171	N	0.852328	T	0.00144	0.0004	M	0.69823	2.125	0.80722	P	0.0	D;D;D	0.67145	0.996;0.986;0.991	P;D;P	0.64321	0.852;0.924;0.793	T	0.12293	-1.0553	9	0.72032	D	0.01	-0.03	5.7841	0.18322	0.545:0.1472:0.3078:0.0	rs2083914;rs52808508;rs2083914	256;304;304	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	I	304;304;256	ENSP00000342924:R304I;ENSP00000430962:R304I;ENSP00000430768:R256I	ENSP00000342924:R304I	R	+	2	0	MCPH1	6289562	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.590000	0.05760	-0.261000	0.09405	0.655000	0.94253	AGA	G|0.900;T|0.100	0.100	strong		0.383	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
HLA-A	3105	hgsc.bcm.edu	37	6	29912373	29912373	+	Missense_Mutation	SNP	T	T	G	rs1137110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29912373T>G	ENST00000396634.1	+	7	1333	c.992T>G	c.(991-993)aTg>aGg	p.M331R	HLA-A_ENST00000376806.5_Missense_Mutation_p.M331R|HLA-A_ENST00000376809.5_Missense_Mutation_p.M331R|HLA-A_ENST00000376802.2_Intron			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	331					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCTGCCGTGATGTGGAGGAGG	0.582									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.M331R		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.T992G						scavenged	.						104.0	101.0	102.0					6																	29912373		1511	2705	4216	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCGTGATGTGGAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.992T>G	6.37:g.29912373T>G	ENSP00000379873:p.Met331Arg	Somatic	413	1	0.00242131		WXS	Illumina HiSeq	Phase_I	444	57	0.128378	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	261	0.11950549450549451	77	0.1565040650406504	51	0.1408839779005525	63	0.11013986013986014	70	0.09234828496042216	.	8.989	0.977328	0.18812	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00669	5.92;5.9;5.92	3.25	-0.0602	0.13790	.	0.665952	0.12732	U	0.443724	T	0.00412	0.0013	M	0.70275	2.135	0.80722	P	0.0	B;B;B;B;B	0.23185	0.0;0.0;0.081;0.0;0.0	B;B;B;B;B	0.23150	0.0;0.002;0.044;0.001;0.002	T	0.41052	-0.9530	9	0.87932	D	0	.	2.7323	0.05230	0.0:0.2692:0.2521:0.4788	rs2231114;rs3179292;rs9260190;rs41561813	210;331;331;331;331	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	R	331	ENSP00000379873:M331R;ENSP00000366002:M331R;ENSP00000366005:M331R	ENSP00000366002:M331R	M	+	2	0	HLA-A	30020352	0.000000	0.05858	0.006000	0.13384	0.804000	0.45430	-0.044000	0.12023	-0.116000	0.11893	-0.509000	0.04479	ATG	T|0.890;G|0.110	0.110	strong		0.582	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
IFT52	51098	hgsc.bcm.edu	37	20	42225114	42225114	+	Silent	SNP	G	G	A	rs2664519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:42225114G>A	ENST00000373030.3	+	3	289	c.159G>A	c.(157-159)gtG>gtA	p.V53V	IFT52_ENST00000373039.4_Silent_p.V53V	NM_016004.2	NP_057088.2	Q9Y366	IFT52_HUMAN	intraflagellar transport 52	53					cilium morphogenesis (GO:0060271)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube formation (GO:0001841)|regulation of protein processing (GO:0070613)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)	protein C-terminus binding (GO:0008022)			endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TAAATGGAGTGAAACTGTGGA	0.328													G|||	3728	0.744409	0.5915	0.7882	5008	,	,		19006	0.7927		0.826	False		,,,				2504	0.7863				p.V53V		Atlas-SNP	.											.	IFT52	40	.	0			c.G159A						PASS	.	G		2810,1596	661.6+/-400.9	902,1006,295	76.0	80.0	79.0		159	4.3	1.0	20	dbSNP_100	79	6841,1759	734.6+/-406.9	2722,1397,181	no	coding-synonymous	IFT52	NM_016004.2		3624,2403,476	AA,AG,GG		20.4535,36.2233,25.7958		53/438	42225114	9651,3355	2203	4300	6503	SO:0001819	synonymous_variant	51098	exon3			TGGAGTGAAACTG	AF151811	CCDS33470.1	20q12-q13.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000101052	ENSG00000101052		"""Intraflagellar transport homologs"""	15901	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 9"", ""intraflagellar transport 52 homolog (Chlamydomonas)"""	C20orf9		10810093	Standard	NM_016004		Approved	CGI-53, NGD5, dJ1028D15.1, NGD2	uc002xkw.3	Q9Y366	OTTHUMG00000032513	ENST00000373030.3:c.159G>A	20.37:g.42225114G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	209	96	0.45933	NM_016004	B3KMA1|E1P5W9|Q5H8Z0|Q9H1G3|Q9H1G4|Q9H1H2	Silent	SNP	ENST00000373030.3	37	CCDS33470.1																																																																																			G|0.265;A|0.735	0.735	strong		0.328	IFT52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079317.1	NM_016004	
TEX38	374973	hgsc.bcm.edu	37	1	47139103	47139103	+	Missense_Mutation	SNP	C	C	T	rs1025806	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:47139103C>T	ENST00000334122.4	+	2	703	c.596C>T	c.(595-597)gCc>gTc	p.A199V	ATPAF1_ENST00000525633.1_Intron|EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14-AS1_ENST00000442839.1_RNA|TEX38_ENST00000564373.1_Missense_Mutation_p.A145V|TEX38_ENST00000569393.1_Missense_Mutation_p.A253V|EFCAB14_ENST00000544071.1_Intron|TEX38_ENST00000415500.1_Missense_Mutation_p.A123V	NM_001145474.2	NP_001138946.1	Q6PEX7	TEX38_HUMAN	testis expressed 38	199			A -> V (in dbSNP:rs1025806). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)											AGCTTCAATGCCAAGCCTTTT	0.507													C|||	1333	0.266174	0.1785	0.3545	5008	,	,		20137	0.3353		0.2972	False		,,,				2504	0.2188				p.A199V		Atlas-SNP	.											ATPAF1-AS1_ENST00000569393,colon,carcinoma,0,2	.	.	2	0			c.C596T						PASS	.	C	VAL/ALA	258,1126		17,224,451	59.0	48.0	52.0		596	3.1	0.4	1	dbSNP_86	52	849,2333		97,655,839	yes	missense	ATPAF1-AS1	NM_001145474.2	64	114,879,1290	TT,TC,CC		26.6813,18.6416,24.2444	possibly-damaging	199/207	47139103	1107,3459	692	1591	2283	SO:0001583	missense	374973	exon2			TCAATGCCAAGCC		CCDS57999.1, CCDS72780.1, CCDS72781.1	1p33	2012-10-12	2012-10-12	2012-10-12	ENSG00000186118	ENSG00000186118			29589	protein-coding gene	gene with protein product	"""testis highly expressed protein 4"""		"""chromosome 1 open reading frame 223"", ""ATPAF1 antisense RNA 1 (non-protein coding)"", ""ATPAF1 antisense RNA 1"""	C1orf223, ATPAF1-AS1		12477932	Standard	XM_005270845		Approved	LOC374973, THEG4	uc001cqj.3	Q6PEX7	OTTHUMG00000007991	ENST00000334122.4:c.596C>T	1.37:g.47139103C>T	ENSP00000455854:p.Ala199Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_001145474	A1A4F8	Missense_Mutation	SNP	ENST00000334122.4	37	CCDS57999.1																																																																																			C|0.719;T|0.281	0.281	strong		0.507	TEX38-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000021929.2	NM_001145474	
TMEM132C	92293	hgsc.bcm.edu	37	12	129190266	129190266	+	Missense_Mutation	SNP	G	G	A	rs112818862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:129190266G>A	ENST00000435159.2	+	9	2753	c.2753G>A	c.(2752-2754)cGg>cAg	p.R918Q	TMEM132C_ENST00000537538.1_Missense_Mutation_p.R303Q|TMEM132C_ENST00000315208.8_Missense_Mutation_p.R534Q	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	918						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						CAGACTCCGCGGGGCCTGAGT	0.612													G|||	90	0.0179712	0.0	0.0029	5008	,	,		18120	0.0347		0.0149	False		,,,				2504	0.0389				p.R918Q		Atlas-SNP	.											.	TMEM132C	142	.	0			c.G2753A						PASS	.	G	GLN/ARG	1,1383		0,1,691	18.0	26.0	23.0		2753	1.7	0.0	12	dbSNP_132	23	25,3157		0,25,1566	yes	missense	TMEM132C	NM_001136103.2	43	0,26,2257	AA,AG,GG		0.7857,0.0723,0.5694	probably-damaging	918/1109	129190266	26,4540	692	1591	2283	SO:0001583	missense	92293	exon9			CTCCGCGGGGCCT	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.2753G>A	12.37:g.129190266G>A	ENSP00000410852:p.Arg918Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	93	56	0.602151	NM_001136103	Q69YX8	Missense_Mutation	SNP	ENST00000435159.2	37		27	0.012362637362637362	0	0.0	2	0.0055248618784530384	16	0.027972027972027972	9	0.011873350923482849	G	13.70	2.316102	0.40996	7.23E-4	0.007857	ENSG00000181234	ENST00000435159;ENST00000315208;ENST00000537538	T;T;T	0.25085	1.82;1.82;1.82	4.62	1.73	0.24493	.	0.338213	0.22633	N	0.057558	T	0.09069	0.0224	L	0.48935	1.535	0.09310	N	1	D	0.54397	0.966	P	0.48815	0.591	T	0.04621	-1.0938	10	0.30854	T	0.27	.	7.3314	0.26584	0.3464:0.0:0.6536:0.0	.	918	Q8N3T6	T132C_HUMAN	Q	918;534;303	ENSP00000410852:R918Q;ENSP00000324458:R534Q;ENSP00000438477:R303Q	ENSP00000324458:R534Q	R	+	2	0	TMEM132C	127756219	0.033000	0.19621	0.004000	0.12327	0.298000	0.27526	2.211000	0.42825	0.372000	0.24591	0.655000	0.94253	CGG	A|0.013;C|0.000;G|0.987	0.013	strong		0.612	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
HLA-G	3135	hgsc.bcm.edu	37	6	29796376	29796376	+	Missense_Mutation	SNP	C	C	A	rs12722477	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29796376C>A	ENST00000360323.6	+	3	424	c.400C>A	c.(400-402)Ctc>Atc	p.L134I	HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376828.2_Missense_Mutation_p.L139I|HLA-G_ENST00000428701.1_Missense_Mutation_p.L134I|HLA-G_ENST00000376818.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	134	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CGGACGCCTCCTCCGCGGGTA	0.667													c|||	1015	0.202676	0.2398	0.17	5008	,	,		14748	0.2857		0.0924	False		,,,				2504	0.2035				p.L134I		Atlas-SNP	.											.	HLA-G	90	.	0			c.C400A						PASS	.	C	ILE/LEU	660,2360		76,508,926	107.0	109.0	108.0		400	0.6	0.1	6	dbSNP_126	108	473,4945		23,427,2259	yes	missense	HLA-G	NM_002127.5	5	99,935,3185	AA,AC,CC		8.7302,21.8543,13.4274	benign	134/339	29796376	1133,7305	1510	2709	4219	SO:0001583	missense	3135	exon4			CGCCTCCTCCGCG		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.400C>A	6.37:g.29796376C>A	ENSP00000353472:p.Leu134Ile	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	188	109	0.579787	NM_002127		Missense_Mutation	SNP	ENST00000360323.6	37	CCDS4668.1	424	0.19413919413919414	95	0.19308943089430894	71	0.19613259668508287	192	0.3356643356643357	66	0.0870712401055409	.	12.81	2.050353	0.36181	0.218543	0.087302	ENSG00000204632	ENST00000376828;ENST00000428701;ENST00000360323	T;T;T	0.00010	9.42;9.42;9.42	1.72	0.563	0.17296	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	6.445200	0.02343	U	0.075118	T	0.00178	0.0005	M	0.89414	3.03	0.80722	P	0.0	B;D	0.58620	0.284;0.983	P;D	0.83275	0.475;0.996	T	0.50642	-0.8804	9	0.87932	D	0	.	5.3	0.15773	0.5224:0.4776:0.0:0.0	rs12722477;rs17225116;rs59771878	139;134	Q5RJ85;P17693	.;HLAG_HUMAN	I	139;134;134	ENSP00000366024:L139I;ENSP00000412927:L134I;ENSP00000353472:L134I	ENSP00000353472:L134I	L	+	1	0	HLA-G	29904355	0.000000	0.05858	0.062000	0.19696	0.038000	0.13279	-0.975000	0.03790	0.952000	0.37798	0.298000	0.19748	CTC	C|0.838;A|0.162	0.162	strong		0.667	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
PNMA3	29944	hgsc.bcm.edu	37	X	152226189	152226189	+	Silent	SNP	G	G	A	rs141778950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:152226189G>A	ENST00000370264.4	+	1	803	c.777G>A	c.(775-777)gaG>gaA	p.E259E	PNMA3_ENST00000447306.1_Silent_p.E259E|PNMA3_ENST00000370265.4_Silent_p.E259E			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	259					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					cctatcaggaggcaggagaga	0.488													G|||	4	0.0010596	0.0	0.0	3775	,	,		15718	0.0		0.004	False		,,,				2504	0.0				p.E259E		Atlas-SNP	.											.	PNMA3	81	.	0			c.G777A						PASS	.	G		3,3832		0,3,0,1629,571	166.0	157.0	160.0		777	-0.1	0.0	X	dbSNP_134	160	12,6716		0,10,2,2418,1870	no	coding-synonymous	PNMA3	NM_013364.4		0,13,2,4047,2441	AA,AG,A,GG,G		0.1784,0.0782,0.142		259/464	152226189	15,10548	2203	4300	6503	SO:0001819	synonymous_variant	29944	exon2			TCAGGAGGCAGGA	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"""Paraneoplastic Ma antigens"""	18742	protein-coding gene	gene with protein product	"""paraneoplastic cancer-testis-brain antigen"""	300675	"""paraneoplastic antigen MA3"""			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.777G>A	X.37:g.152226189G>A		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	110	108	0.981818	NM_013364	D3DWT7|Q9H0A4	Silent	SNP	ENST00000370264.4	37	CCDS35435.2																																																																																			G|0.999;A|0.001	0.001	strong		0.488	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364	
PCDHA3	56145	hgsc.bcm.edu	37	5	140181734	140181734	+	Missense_Mutation	SNP	A	A	G	rs3733708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140181734A>G	ENST00000522353.2	+	1	952	c.952A>G	c.(952-954)Atc>Gtc	p.I318V	PCDHA3_ENST00000532566.2_Missense_Mutation_p.I318V|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	318	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> V (in dbSNP:rs3733708).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCATATGAAATCCAGGTAGA	0.388													.|||	2631	0.525359	0.4788	0.5893	5008	,	,		23136	0.5317		0.5378	False		,,,				2504	0.5235				p.I318V		Atlas-SNP	.											.	PCDHA3	396	.	0			c.A952G						PASS	.	A	,,VAL/ILE,,VAL/ILE	2185,2221	585.5+/-386.3	533,1119,551	143.0	144.0	144.0		,,952,,952	3.5	1.0	5	dbSNP_107	144	4540,4060	594.4+/-393.3	1192,2156,952	yes	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,29,,29	1725,3275,1503	GG,GA,AA		47.2093,49.5915,48.2931	,,,,	,,318/951,,318/825	140181734	6725,6281	2203	4300	6503	SO:0001583	missense	56145	exon1			TATGAAATCCAGG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.952A>G	5.37:g.140181734A>G	ENSP00000429808:p.Ile318Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	117	25	0.213675	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	1163	0.5325091575091575	252	0.5121951219512195	194	0.5359116022099447	311	0.5437062937062938	406	0.5356200527704486	a	14.17	2.454859	0.43634	0.495915	0.527907	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.52526	0.66;0.66	4.79	3.54	0.40534	Cadherin (4);Cadherin-like (1);	0.000000	0.42172	U	0.000743	T	0.00012	0.0000	M	0.73430	2.235	0.39646	P	0.02960600000000002	P;P	0.35714	0.517;0.472	B;P	0.50825	0.359;0.651	T	0.53180	-0.8475	9	0.87932	D	0	.	10.5422	0.45039	0.7622:0.0:0.0:0.2378	rs3733708;rs13162484;rs17208250;rs17844256;rs52837026;rs57467015;rs3733708	318;318	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	V	318	ENSP00000429808:I318V;ENSP00000434086:I318V	ENSP00000429808:I318V	I	+	1	0	PCDHA3	140161918	0.000000	0.05858	0.985000	0.45067	0.953000	0.61014	-0.509000	0.06336	1.925000	0.55765	0.383000	0.25322	ATC	G|0.521;N|0.000	0.521	strong		0.388	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
TYRO3	7301	hgsc.bcm.edu	37	15	41862436	41862436	+	Splice_Site	SNP	A	A	G	rs201371674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41862436A>G	ENST00000263798.3	+	11	1606		c.e11-1		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GTTTTCCTTTAGGCAAGCCTT	0.587																																					.		Atlas-SNP	.											.	TYRO3	169	.	0			c.1383-2A>G						PASS	.																																			SO:0001630	splice_region_variant	7301	exon11			TCCTTTAGGCAAG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1383-1A>G	15.37:g.41862436A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	86	8	0.0930233	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862477	0.71949	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0491	0.58944	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39649728	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	7.007000	0.76335	2.208000	0.71279	0.533000	0.62120	.	A|0.986;G|0.014	0.014	strong		0.587	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron
CPAMD8	27151	hgsc.bcm.edu	37	19	17017878	17017878	+	Missense_Mutation	SNP	G	G	A	rs56408444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17017878G>A	ENST00000443236.1	-	30	4083	c.4052C>T	c.(4051-4053)gCg>gTg	p.A1351V	RN7SL835P_ENST00000579920.1_RNA	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1304						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GGCCAGGGGCGCAGCAGACTC	0.657													G|||	952	0.190096	0.025	0.3401	5008	,	,		12421	0.2431		0.2217	False		,,,				2504	0.2198				p.A1351V		Atlas-SNP	.											CPAMD8,NS,carcinoma,0,1	CPAMD8	192	1	0			c.C4052T						PASS	.	G	VAL/ALA	210,4100		8,194,1953	33.0	42.0	39.0		4052	-4.2	0.0	19	dbSNP_129	39	1662,6842		171,1320,2761	yes	missense	CPAMD8	NM_015692.2	64	179,1514,4714	AA,AG,GG		19.5437,4.8724,14.609	benign	1351/1933	17017878	1872,10942	2155	4252	6407	SO:0001583	missense	27151	exon30			AGGGGCGCAGCAG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.4052C>T	19.37:g.17017878G>A	ENSP00000402505:p.Ala1351Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	179	86	0.480447	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	436|436	0.19963369963369965|0.19963369963369965	15|15	0.03048780487804878|0.03048780487804878	121|121	0.3342541436464088|0.3342541436464088	134|134	0.23426573426573427|0.23426573426573427	166|166	0.21899736147757257|0.21899736147757257	G|G	0.607|0.607	-0.826442|-0.826442	0.02734|0.02734	0.048724|0.048724	0.195437|0.195437	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.07|3.07	-4.18|-4.18	0.03846|0.03846	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);|.	1.891200|.	0.04120|.	N|.	0.316189|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|.	0.22346|.	0.068|.	B|.	0.10450|.	0.005|.	T|T	0.44817|0.44817	-0.9303|-0.9303	8|4	0.02654|.	T|.	1|.	.|.	6.1572|6.1572	0.20344|0.20344	0.702:0.1636:0.1344:0.0|0.702:0.1636:0.1344:0.0	rs56408444;rs62128040|rs56408444;rs62128040	1304|.	Q8IZJ3|.	CPMD8_HUMAN|.	V|C	1351|1362	.|.	ENSP00000291440:A1351V|.	A|R	-|-	2|1	0|0	CPAMD8|CPAMD8	16878878|16878878	0.055000|0.055000	0.20627|0.20627	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	1.347000|1.347000	0.33975|0.33975	-0.651000|-0.651000	0.05415|0.05415	0.536000|0.536000	0.68110|0.68110	GCG|CGC	G|0.803;A|0.197	0.197	strong		0.657	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
FREM1	158326	hgsc.bcm.edu	37	9	14775859	14775859	+	Silent	SNP	G	G	A	rs10733289	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:14775859G>A	ENST00000380880.3	-	25	5568	c.4785C>T	c.(4783-4785)gcC>gcT	p.A1595A	FREM1_ENST00000486223.1_5'UTR|FREM1_ENST00000422223.2_Silent_p.A1595A|FREM1_ENST00000380881.4_Silent_p.A1596A|FREM1_ENST00000380894.1_Silent_p.A131A			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1595					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TCCCATCTGTGGCCATGAAAG	0.463													G|||	2087	0.416733	0.2905	0.4366	5008	,	,		19227	0.3294		0.5845	False		,,,				2504	0.4908				p.A1595A		Atlas-SNP	.											.	FREM1	261	.	0			c.C4785T						PASS	.	G	,	1401,2495		259,883,806	109.0	102.0	104.0		393,4785	4.9	1.0	9	dbSNP_120	104	4939,3377		1465,2009,684	no	coding-synonymous,coding-synonymous	FREM1	NM_001177704.1,NM_144966.5	,	1724,2892,1490	AA,AG,GG		40.6085,35.96,48.0839	,	131/716,1595/2180	14775859	6340,5872	1948	4158	6106	SO:0001819	synonymous_variant	158326	exon26			ATCTGTGGCCATG	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.4785C>T	9.37:g.14775859G>A		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	196	78	0.397959	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			G|0.593;A|0.407	0.407	strong		0.463	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
CACNA1E	777	hgsc.bcm.edu	37	1	181724381	181724381	+	Silent	SNP	C	C	T	rs41315709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:181724381C>T	ENST00000367573.2	+	28	3837	c.3837C>T	c.(3835-3837)ttC>ttT	p.F1279F	CACNA1E_ENST00000357570.5_Silent_p.F1230F|CACNA1E_ENST00000360108.3_Silent_p.F1260F|CACNA1E_ENST00000526775.1_Silent_p.F1260F|CACNA1E_ENST00000358338.5_Silent_p.F1211F|CACNA1E_ENST00000367567.4_Silent_p.F886F|CACNA1E_ENST00000367570.1_Silent_p.F1279F	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1279					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AGGCCGTCTTCGACTGCGTAG	0.512													C|||	4	0.000798722	0.0008	0.0	5008	,	,		21515	0.001		0.002	False		,,,				2504	0.0				p.F1279F		Atlas-SNP	.											CACNA1E_ENST00000367573,caecum,carcinoma,0,2	CACNA1E	778	2	0			c.C3837T						PASS	.	C	,,	0,4012		0,0,2006	120.0	116.0	118.0		3837,3837,3780	-5.9	0.9	1	dbSNP_127	118	7,8373		0,7,4183	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	,,	0,7,6189	TT,TC,CC		0.0835,0.0,0.0565	,,	1279/2271,1279/2314,1260/2252	181724381	7,12385	2006	4190	6196	SO:0001819	synonymous_variant	777	exon28			CGTCTTCGACTGC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3837C>T	1.37:g.181724381C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																			C|0.999;T|0.001	0.001	strong		0.512	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
ANKK1	255239	hgsc.bcm.edu	37	11	113268059	113268059	+	Missense_Mutation	SNP	G	G	A	rs11604671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:113268059G>A	ENST00000303941.3	+	6	1046	c.952G>A	c.(952-954)Ggg>Agg	p.G318R		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	318			G -> R (in dbSNP:rs11604671). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		GCGCCAGCCCGGGGAGGTGAG	0.607													C|||	1133	0.226238	0.0393	0.3026	5008	,	,		19688	0.0625		0.501	False		,,,				2504	0.3108				p.G318R		Atlas-SNP	.											.	ANKK1	83	.	0			c.G952A						PASS	.	C	ARG/GLY	514,3762		27,460,1651	39.0	46.0	44.0		952	0.5	0.0	11	dbSNP_120	44	4269,4221		1103,2063,1079	yes	missense	ANKK1	NM_178510.1	125	1130,2523,2730	AA,AG,GG		49.7173,12.0206,37.4667	benign	318/766	113268059	4783,7983	2138	4245	6383	SO:0001583	missense	255239	exon6			CAGCCCGGGGAGG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.952G>A	11.37:g.113268059G>A	ENSP00000306678:p.Gly318Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	82	28	0.341463	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	562	0.2573260073260073	29	0.05894308943089431	129	0.356353591160221	33	0.057692307692307696	371	0.4894459102902375	C	12.15	1.851560	0.32699	0.120206	0.502827	ENSG00000170209	ENST00000303941	T	0.73897	-0.79	4.58	0.519	0.17035	.	2.280460	0.02431	N	0.083550	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31447	-0.9943	9	0.14252	T	0.57	0.0976	2.5272	0.04694	0.1373:0.4149:0.2897:0.158	rs11604671;rs17600946;rs11604671	318	Q8NFD2	ANKK1_HUMAN	R	318	ENSP00000306678:G318R	ENSP00000306678:G318R	G	+	1	0	ANKK1	112773269	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.959000	0.01518	-0.309000	0.08779	-0.920000	0.02741	GGG	G|0.718;A|0.282	0.282	strong		0.607	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
BBS10	79738	hgsc.bcm.edu	37	12	76741341	76741341	+	Missense_Mutation	SNP	C	C	T	rs142863601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:76741341C>T	ENST00000393262.3	-	2	507	c.424G>A	c.(424-426)Gac>Aac	p.D142N		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	142			D -> N (in dbSNP:rs142863601). {ECO:0000269|PubMed:20120035}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|regulation of protein complex assembly (GO:0043254)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell projection (GO:0042995)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)	19						ATAATACCGTCTAATATTTGT	0.388									Bardet-Biedl syndrome				C|||	14	0.00279553	0.0008	0.0029	5008	,	,		19235	0.0		0.0109	False		,,,				2504	0.0				p.D142N		Atlas-SNP	.											.	BBS10	46	.	0			c.G424A						PASS	.	C	ASN/ASP	11,4395	17.9+/-39.9	0,11,2192	72.0	68.0	70.0		424	5.3	0.9	12	dbSNP_134	70	92,8508	51.9+/-112.3	1,90,4209	yes	missense	BBS10	NM_024685.3	23	1,101,6401	TT,TC,CC		1.0698,0.2497,0.7919	possibly-damaging	142/724	76741341	103,12903	2203	4300	6503	SO:0001583	missense	79738	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TACCGTCTAATAT	BC026355	CCDS9014.2	12q21.2	2014-06-17	2006-04-28	2006-04-28	ENSG00000179941	ENSG00000179941		"""Heat Shock Proteins / Chaperonins"""	26291	protein-coding gene	gene with protein product		610148	"""chromosome 12 open reading frame 58"""	C12orf58		16582908	Standard	NM_024685		Approved	FLJ23560	uc001syd.1	Q8TAM1	OTTHUMG00000147352	ENST00000393262.3:c.424G>A	12.37:g.76741341C>T	ENSP00000376946:p.Asp142Asn	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_024685	Q96CW2|Q9H5D2	Missense_Mutation	SNP	ENST00000393262.3	37	CCDS9014.2	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	C	25.9	4.683655	0.88639	0.002497	0.010698	ENSG00000179941	ENST00000393262;ENST00000547830	D	0.89050	-2.46	5.34	5.34	0.76211	.	0.128969	0.49916	D	0.000131	D	0.88948	0.6576	L	0.60455	1.87	0.40719	D	0.982642	D	0.58970	0.984	P	0.55303	0.773	D	0.89985	0.4103	10	0.56958	D	0.05	-8.0958	16.9217	0.86166	0.0:1.0:0.0:0.0	.	142	Q8TAM1	BBS10_HUMAN	N	142;76	ENSP00000376946:D142N	ENSP00000376946:D142N	D	-	1	0	BBS10	75265472	1.000000	0.71417	0.950000	0.38849	0.971000	0.66376	5.183000	0.65065	2.937000	0.99478	0.650000	0.86243	GAC	C|0.994;T|0.006	0.006	strong		0.388	BBS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303983.2	NM_024685	
RNF5	6048	hgsc.bcm.edu	37	6	32148031	32148031	+	Silent	SNP	A	A	G	rs1062070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32148031A>G	ENST00000375094.3	+	6	629	c.471A>G	c.(469-471)ccA>ccG	p.P157P	AGPAT1_ENST00000336984.6_5'Flank|AGPAT1_ENST00000490711.1_5'Flank|AGPAT1_ENST00000395497.1_5'Flank|RNF5_ENST00000427134.2_Intron|AGPAT1_ENST00000375104.2_5'Flank	NM_006913.3	NP_008844.1	Q99942	RNF5_HUMAN	ring finger protein 5, E3 ubiquitin protein ligase	157					cellular protein catabolic process (GO:0044257)|ER-associated misfolded protein catabolic process (GO:0071712)|negative regulation of autophagy (GO:0010507)|protein destabilization (GO:0031648)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of autophagic vacuole assembly (GO:2000785)|response to bacterium (GO:0009617)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(7)|urinary_tract(2)	10						AGGGTCACCCAGCCTCCAGCT	0.567													G|||	668	0.133387	0.1241	0.0865	5008	,	,		18465	0.0942		0.159	False		,,,				2504	0.1933				p.P157P		Atlas-SNP	.											.	RNF5	16	.	0			c.A471G						PASS	.	G		362,2660		23,316,1172	240.0	257.0	251.0		471	0.5	1.0	6	dbSNP_86	251	974,4444		83,808,1818	no	coding-synonymous	RNF5	NM_006913.3		106,1124,2990	GG,GA,AA		17.9771,11.9788,15.8294		157/181	32148031	1336,7104	1511	2709	4220	SO:0001819	synonymous_variant	6048	exon6			TCACCCAGCCTCC	U89336	CCDS4745.1	6p21.31	2013-01-09	2012-02-23			ENSG00000204308		"""RING-type (C3HC4) zinc fingers"""	10068	protein-coding gene	gene with protein product		602677	"""ring finger protein 5"""			9533025	Standard	NM_006913		Approved	NG2, G16, RING5, RMA1	uc031snv.1	Q99942	OTTHUMG00000031093	ENST00000375094.3:c.471A>G	6.37:g.32148031A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	87	26	0.298851	NM_006913	A2BFI6|B2R4K3|Q0VDB7|Q9UMQ2	Silent	SNP	ENST00000375094.3	37	CCDS4745.1																																																																																			A|0.860;G|0.140	0.140	strong		0.567	RNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076133.2	NM_006913	
SNTG1	54212	hgsc.bcm.edu	37	8	51571172	51571172	+	Silent	SNP	G	G	A	rs1911830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:51571172G>A	ENST00000522124.1	+	15	1648	c.987G>A	c.(985-987)acG>acA	p.T329T	SNTG1_ENST00000276467.5_Silent_p.T329T|SNTG1_ENST00000517473.1_Silent_p.T329T|SNTG1_ENST00000518864.1_Silent_p.T329T	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	329	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell communication (GO:0007154)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)|syntrophin complex (GO:0016013)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				GGGACTGGACGAGAGCAGAGA	0.323													g|||	2539	0.506989	0.2262	0.6153	5008	,	,		18668	0.6786		0.6909	False		,,,				2504	0.4438				p.T329T		Atlas-SNP	.											.	SNTG1	304	.	0			c.G987A						PASS	.	A		1353,3053	450.8+/-349.5	208,937,1058	107.0	91.0	97.0		987	-8.0	0.6	8	dbSNP_92	97	5833,2767	679.1+/-403.5	1980,1873,447	no	coding-synonymous	SNTG1	NM_018967.2		2188,2810,1505	AA,AG,GG		32.1744,30.7081,44.7486		329/518	51571172	7186,5820	2203	4300	6503	SO:0001819	synonymous_variant	54212	exon15			CTGGACGAGAGCA	AJ003030	CCDS6147.1, CCDS75737.1	8q11-q12	2008-07-03				ENSG00000147481			13740	protein-coding gene	gene with protein product		608714				10747910	Standard	NM_018967		Approved	SYN4, G1SYN	uc003xqs.1	Q9NSN8		ENST00000522124.1:c.987G>A	8.37:g.51571172G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_018967	Q2M3Q0|Q9NY98	Silent	SNP	ENST00000522124.1	37	CCDS6147.1																																																																																			G|0.449;A|0.551	0.551	strong		0.323	SNTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377964.1		
TMEM8A	58986	hgsc.bcm.edu	37	16	427784	427784	+	Silent	SNP	G	G	A	rs11641742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:427784G>A	ENST00000431232.2	-	2	346	c.186C>T	c.(184-186)taC>taT	p.Y62Y	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_De_novo_Start_OutOfFrame	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	62					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						TGGCACTGCCGTACCAGCTGT	0.677													G|||	2663	0.531749	0.6188	0.4712	5008	,	,		15053	0.2996		0.5378	False		,,,				2504	0.6902				p.Y62Y		Atlas-SNP	.											.	TMEM8A	49	.	0			c.C186T						PASS	.	G		2723,1635		850,1023,306	36.0	42.0	40.0		186	-8.8	0.7	16	dbSNP_120	40	4854,3714		1426,2002,856	no	coding-synonymous	TMEM8A	NM_021259.2		2276,3025,1162	AA,AG,GG		43.3473,37.5172,41.3817		62/772	427784	7577,5349	2179	4284	6463	SO:0001819	synonymous_variant	58986	exon2			ACTGCCGTACCAG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.186C>T	16.37:g.427784G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			G|0.455;A|0.545	0.545	strong		0.677	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
CNGA3	1261	hgsc.bcm.edu	37	2	98986510	98986510	+	Silent	SNP	T	T	C	rs6727412	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:98986510T>C	ENST00000272602.2	+	1	111	c.72T>C	c.(70-72)gaT>gaC	p.D24D	CNGA3_ENST00000393504.1_Silent_p.D24D|CNGA3_ENST00000436404.2_Silent_p.D24D			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	24					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						CAGACCGAGATCTCAATCGCG	0.507													T|||	450	0.0898562	0.084	0.1282	5008	,	,		18669	0.0099		0.166	False		,,,				2504	0.0746				p.D24D		Atlas-SNP	.											.	CNGA3	118	.	0			c.T72C						PASS	.	T	,	478,3928	225.2+/-241.2	23,432,1748	138.0	113.0	121.0		72,72	-6.6	0.0	2	dbSNP_116	121	1522,7078	288.1+/-298.6	130,1262,2908	no	coding-synonymous,coding-synonymous	CNGA3	NM_001079878.1,NM_001298.2	,	153,1694,4656	CC,CT,TT		17.6977,10.8488,15.3775	,	24/677,24/695	98986510	2000,11006	2203	4300	6503	SO:0001819	synonymous_variant	1261	exon2			CCGAGATCTCAAT	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.72T>C	2.37:g.98986510T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Silent	SNP	ENST00000272602.2	37	CCDS2034.1																																																																																			T|0.869;C|0.131	0.131	strong		0.507	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298	
PABPC4L	132430	hgsc.bcm.edu	37	4	135121368	135121368	+	Silent	SNP	G	G	T	rs2044116	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:135121368G>T	ENST00000421491.3	-	2	1063	c.807C>A	c.(805-807)gtC>gtA	p.V269V	PABPC4L_ENST00000529122.2_Silent_p.V327V			P0CB38	PAB4L_HUMAN	poly(A) binding protein, cytoplasmic 4-like	269							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)	3						CCTGTCGCTCGACTTTCTTTT	0.448													T|||	3190	0.636981	0.7186	0.5403	5008	,	,		17612	0.9841		0.329	False		,,,				2504	0.5542				p.V327V		Atlas-SNP	.											.	PABPC4L	60	.	0			c.C981A						PASS	.	T		925,459		310,305,77	75.0	61.0	65.0		981	-3.3	0.1	4	dbSNP_94	65	980,2202		142,696,753	no	coding-synonymous	PABPC4L	NM_001114734.1		452,1001,830	TT,TG,GG		30.7982,33.1647,41.7214		327/429	135121368	1905,2661	692	1591	2283	SO:0001819	synonymous_variant	132430	exon2			TCGCTCGACTTTC	AY672099		4q28.3	2013-02-12				ENSG00000254535		"""RNA binding motif (RRM) containing"""	31955	protein-coding gene	gene with protein product							Standard	NM_001114734		Approved		uc010ioe.3	P0CB38		ENST00000421491.3:c.807C>A	4.37:g.135121368G>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_001114734		Silent	SNP	ENST00000421491.3	37																																																																																				G|0.347;T|0.653	0.653	strong		0.448	PABPC4L-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364399.2	NM_001114734	
DEF6	50619	hgsc.bcm.edu	37	6	35288696	35288696	+	Silent	SNP	C	C	T	rs34278260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:35288696C>T	ENST00000316637.5	+	10	1622	c.1617C>T	c.(1615-1617)aaC>aaT	p.N539N	DEF6_ENST00000542066.1_Silent_p.N284N	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)	539						cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						CCAGCACCAACGTGAAACACT	0.552													C|||	103	0.0205671	0.053	0.013	5008	,	,		18342	0.002		0.0199	False		,,,				2504	0.002				p.N539N		Atlas-SNP	.											.	DEF6	36	.	0			c.C1617T						PASS	.	C		213,4193	126.1+/-163.2	5,203,1995	56.0	50.0	52.0		1617	-6.7	0.5	6	dbSNP_126	52	185,8415	80.1+/-142.7	2,181,4117	no	coding-synonymous	DEF6	NM_022047.3		7,384,6112	TT,TC,CC		2.1512,4.8343,3.0601		539/632	35288696	398,12608	2203	4300	6503	SO:0001819	synonymous_variant	50619	exon10			CACCAACGTGAAA	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"""Pleckstrin homology (PH) domain containing"""	2760	protein-coding gene	gene with protein product	"""SWAP-70-like adaptor protein of T cells"""	610094	"""differentially expressed in FDCP (mouse homolog) 6"""			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.1617C>T	6.37:g.35288696C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_022047	Q86VF4	Silent	SNP	ENST00000316637.5	37	CCDS4802.1																																																																																			C|0.970;T|0.030	0.030	strong		0.552	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047	
CEP350	9857	hgsc.bcm.edu	37	1	180010911	180010911	+	Missense_Mutation	SNP	A	A	G	rs16855164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180010911A>G	ENST00000367607.3	+	19	4754	c.4336A>G	c.(4336-4338)Aca>Gca	p.T1446A		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1446			T -> A (in dbSNP:rs16855164).		microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TCGCCTCACCACAGACGCAGC	0.448													A|||	552	0.110224	0.0923	0.0389	5008	,	,		15417	0.2153		0.0686	False		,,,				2504	0.1196				p.T1446A		Atlas-SNP	.											.	CEP350	418	.	0			c.A4336G						PASS	.	A	ALA/THR	406,4000	200.4+/-223.7	19,368,1816	56.0	52.0	54.0		4336	4.4	1.0	1	dbSNP_123	54	597,8003	157.3+/-211.0	17,563,3720	yes	missense	CEP350	NM_014810.4	58	36,931,5536	GG,GA,AA		6.9419,9.2147,7.7118	probably-damaging	1446/3118	180010911	1003,12003	2203	4300	6503	SO:0001583	missense	9857	exon19			CTCACCACAGACG	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.4336A>G	1.37:g.180010911A>G	ENSP00000356579:p.Thr1446Ala	Somatic	411	0	0		WXS	Illumina HiSeq	Phase_I	494	184	0.37247	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	244|244	0.11172161172161173|0.11172161172161173	46|46	0.09349593495934959|0.09349593495934959	17|17	0.04696132596685083|0.04696132596685083	129|129	0.22552447552447552|0.22552447552447552	52|52	0.06860158311345646|0.06860158311345646	A|A	12.00|12.00	1.807928|1.807928	0.31961|0.31961	0.092147|0.092147	0.069419|0.069419	ENSG00000135837|ENSG00000135837	ENST00000418229|ENST00000367607	.|T	.|0.49432	.|0.78	5.57|5.57	4.43|4.43	0.53597|0.53597	.|.	.|0.000000	.|0.48767	.|D	.|0.000179	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.28024|0.28024	P|P	0.9344136|0.9344136	.|B;B	.|0.31077	.|0.307;0.012	.|B;B	.|0.24701	.|0.055;0.011	T|T	0.24584|0.24584	-1.0156|-1.0156	4|8	.|.	.|.	.|.	.|.	10.4865|10.4865	0.44724|0.44724	0.8553:0.0:0.0:0.1447|0.8553:0.0:0.0:0.1447	rs16855164;rs52820945;rs16855164|rs16855164;rs52820945;rs16855164	.|1446;1446	.|E7EU22;Q5VT06	.|.;CE350_HUMAN	R|A	54|1446	.|ENSP00000356579:T1446A	.|.	H|T	+|+	2|1	0|0	CEP350|CEP350	178277534|178277534	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.170000|0.170000	0.22686|0.22686	2.028000|2.028000	0.41088|0.41088	0.911000|0.911000	0.36747|0.36747	0.482000|0.482000	0.46254|0.46254	CAC|ACA	A|0.905;G|0.095	0.095	strong		0.448	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
LSS	4047	hgsc.bcm.edu	37	21	47626602	47626602	+	Silent	SNP	G	G	A	rs111779817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47626602G>A	ENST00000397728.3	-	16	1626	c.1548C>T	c.(1546-1548)aaC>aaT	p.N516N	LSS_ENST00000522411.1_Silent_p.N505N|LSS_ENST00000457828.2_Silent_p.N436N|LSS_ENST00000356396.4_Silent_p.N516N	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	516					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					CCTCCGAGGGGTTCAGCAGCT	0.612													G|||	30	0.00599042	0.0	0.0072	5008	,	,		17554	0.0		0.007	False		,,,				2504	0.0184				p.N516N	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.C1548T						PASS	.	G	,,,	3,4403	6.2+/-15.9	0,3,2200	78.0	72.0	74.0		1548,1515,1308,1548	2.6	1.0	21	dbSNP_132	74	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	,,,	0,32,6471	AA,AG,GG		0.3372,0.0681,0.246	,,,	516/733,505/722,436/653,516/733	47626602	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	4047	exon16			CGAGGGGTTCAGC	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1548C>T	21.37:g.47626602G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	ENST00000397728.3	37	CCDS13733.1																																																																																			G|0.997;A|0.003	0.003	strong		0.612	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
ARFGEF2	10564	hgsc.bcm.edu	37	20	47630449	47630449	+	Silent	SNP	C	C	T	rs2281582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:47630449C>T	ENST00000371917.4	+	30	4131	c.4131C>T	c.(4129-4131)atC>atT	p.I1377I		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1377					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.I1377I(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TGTTCAGAATCGTGTTTCGGA	0.468													C|||	1044	0.208466	0.0416	0.2767	5008	,	,		21107	0.3938		0.1282	False		,,,				2504	0.2771				p.I1377I	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											ARFGEF2,NS,carcinoma,0,1	ARFGEF2	160	1	1	Substitution - coding silent(1)	stomach(1)	c.C4131T						PASS	.	C		293,4113	160.3+/-192.7	7,279,1917	158.0	133.0	141.0		4131	-4.5	0.9	20	dbSNP_100	141	1177,7423	239.9+/-270.8	85,1007,3208	no	coding-synonymous	ARFGEF2	NM_006420.2		92,1286,5125	TT,TC,CC		13.686,6.65,11.3025		1377/1786	47630449	1470,11536	2203	4300	6503	SO:0001819	synonymous_variant	10564	exon30			CAGAATCGTGTTT	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.4131C>T	20.37:g.47630449C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	123	61	0.495935	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			C|0.847;T|0.153	0.153	strong		0.468	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
MED15	51586	hgsc.bcm.edu	37	22	20922809	20922809	+	Splice_Site	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20922809T>C	ENST00000263205.7	+	8	1112	c.1043T>C	c.(1042-1044)gTc>gCc	p.V348A	MED15_ENST00000478831.1_3'UTR|MED15_ENST00000541476.1_Splice_Site_p.V322A|MED15_ENST00000406969.1_Splice_Site_p.V322A|MED15_ENST00000425759.2_Splice_Site_p.V237A|MED15_ENST00000292733.7_Splice_Site_p.V348A|MED15_ENST00000382974.2_Splice_Site_p.V277A|MED15_ENST00000542773.1_Splice_Site_p.V153A	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	348	Pro-rich.				gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			TCCCTCAAGGTCCGAGCTCCG	0.582																																					p.V348A		Atlas-SNP	.											.	MED15	68	.	0			c.T1043C						PASS	.						29.0	29.0	29.0					22																	20922809		2199	4297	6496	SO:0001630	splice_region_variant	51586	exon8			TCAAGGTCCGAGC	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.1042-1T>C	22.37:g.20922809T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Missense_Mutation	SNP	ENST00000263205.7	37	CCDS33602.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268558	0.40095	.	.	ENSG00000099917	ENST00000425759;ENST00000292733;ENST00000542773;ENST00000263205;ENST00000406969;ENST00000382974;ENST00000541476;ENST00000542312	T	0.41400	1.0	5.4	5.4	0.78164	Mediator complex, subunit Med15, metazoa (1);	0.481828	0.21991	N	0.066154	T	0.47116	0.1428	L	0.36672	1.1	0.42239	D	0.991925	D;D;P;P;D	0.53885	0.963;0.963;0.954;0.954;0.963	D;D;D;D;D	0.71414	0.973;0.973;0.954;0.954;0.973	T	0.40251	-0.9573	10	0.02654	T	1	.	11.7332	0.51750	0.0:0.0:0.0:1.0	.	294;367;322;348;348	B4DGD6;Q6PKB8;G3V1P5;Q96RN5-2;Q96RN5	.;.;.;.;MED15_HUMAN	A	237;348;153;348;322;277;322;294	ENSP00000263205:V348A	ENSP00000263205:V348A	V	+	2	0	MED15	19252809	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	3.611000	0.54132	2.274000	0.75844	0.533000	0.62120	GTC	.	.	none		0.582	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889	Missense_Mutation
C10orf71	118461	hgsc.bcm.edu	37	10	50532812	50532812	+	Missense_Mutation	SNP	A	A	G	rs11101093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50532812A>G	ENST00000374144.3	+	3	2510	c.2222A>G	c.(2221-2223)gAt>gGt	p.D741G	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	741			D -> G (in dbSNP:rs11101093).							endometrium(1)	1						GCCTCATTTGATGATCAGCAG	0.463													A|||	478	0.0954473	0.053	0.0663	5008	,	,		22000	0.122		0.1193	False		,,,				2504	0.1217				p.D741G		Atlas-SNP	.											.	C10orf71	179	.	0			c.A2222G						PASS	.	A	GLY/ASP,	76,1308		0,76,616	73.0	60.0	64.0		2222,	5.6	0.5	10	dbSNP_120	64	414,2768		24,366,1201	yes	missense,intron	C10orf71	NM_001135196.1,NM_199459.3	94,	24,442,1817	GG,GA,AA		13.0107,5.4913,10.7315	,	741/1436,	50532812	490,4076	692	1591	2283	SO:0001583	missense	118461	exon3			CATTTGATGATCA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.2222A>G	10.37:g.50532812A>G	ENSP00000363259:p.Asp741Gly	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	225	107	0.475556	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	211	0.09661172161172162	32	0.06504065040650407	30	0.08287292817679558	60	0.1048951048951049	89	0.11741424802110818	A	14.84	2.655166	0.47467	0.054913	0.130107	ENSG00000177354	ENST00000374144	T	0.05081	3.5	5.64	5.64	0.86602	.	0.732696	0.11145	U	0.594792	T	0.00073	0.0002	N	0.08118	0	0.36653	P	0.12250799999999995	.	.	.	.	.	.	T	0.39781	-0.9597	7	0.54805	T	0.06	.	6.769	0.23583	0.6973:0.1449:0.0:0.1579	rs11101093;rs57806961;rs11101093	.	.	.	G	741	ENSP00000363259:D741G	ENSP00000363259:D741G	D	+	2	0	C10orf71	50202818	0.988000	0.35896	0.520000	0.27837	0.940000	0.58332	3.080000	0.50112	2.160000	0.67779	0.482000	0.46254	GAT	A|0.908;G|0.092	0.092	strong		0.463	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
KNG1	3827	hgsc.bcm.edu	37	3	186440243	186440243	+	Silent	SNP	G	G	A	rs1469859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186440243G>A	ENST00000265023.4	+	3	536	c.324G>A	c.(322-324)acG>acA	p.T108T	KNG1_ENST00000287611.2_Silent_p.T108T|KNG1_ENST00000447445.1_Silent_p.T108T|RP11-573D15.8_ENST00000599314.1_RNA	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	108	Cystatin kininogen-type 1. {ECO:0000255|PROSITE-ProRule:PRU00979}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		GAGAATGCACGGCAACCGTGG	0.478													G|||	1222	0.24401	0.1551	0.3876	5008	,	,		17802	0.2133		0.335	False		,,,				2504	0.2004				p.T108T		Atlas-SNP	.											.	KNG1	129	.	0			c.G324A						PASS	.	G	,,	748,3658	305.2+/-288.9	71,606,1526	96.0	87.0	90.0		324,324,324	-8.6	0.1	3	dbSNP_88	90	2853,5747	445.6+/-361.0	504,1845,1951	no	coding-synonymous,coding-synonymous,coding-synonymous	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,,	575,2451,3477	AA,AG,GG		33.1744,16.9768,27.6872	,,	108/428,108/645,108/392	186440243	3601,9405	2203	4300	6503	SO:0001819	synonymous_variant	3827	exon3			ATGCACGGCAACC		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"""Endogenous ligands"""	6383	protein-coding gene	gene with protein product	"""alpha-2-thiol proteinase inhibitor"", ""bradykinin"""	612358	"""kininogen"""	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.324G>A	3.37:g.186440243G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_000893	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Silent	SNP	ENST00000265023.4	37	CCDS43183.1																																																																																			G|0.724;A|0.276	0.276	strong		0.478	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
TMEM63B	55362	hgsc.bcm.edu	37	6	44117664	44117664	+	Silent	SNP	C	C	T	rs4714762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44117664C>T	ENST00000259746.9	+	16	1665	c.1482C>T	c.(1480-1482)atC>atT	p.I494I	TMEM63B_ENST00000323267.6_Silent_p.I494I			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	494					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.I494I(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			TTCCCACCATCGTCTACTACT	0.612													C|||	528	0.105431	0.0061	0.0965	5008	,	,		20116	0.2321		0.0984	False		,,,				2504	0.1227				p.I494I		Atlas-SNP	.											TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	1	Substitution - coding silent(1)	stomach(1)	c.C1482T						PASS	.	C		108,4298	85.3+/-124.0	2,104,2097	205.0	144.0	165.0		1482	0.3	1.0	6	dbSNP_111	165	914,7686	201.8+/-245.2	53,808,3439	no	coding-synonymous	TMEM63B	NM_018426.1		55,912,5536	TT,TC,CC		10.6279,2.4512,7.8579		494/833	44117664	1022,11984	2203	4300	6503	SO:0001819	synonymous_variant	55362	exon16			CACCATCGTCTAC	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1482C>T	6.37:g.44117664C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	250	121	0.484	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	257	0.11767399267399267	2	0.0040650406504065045	38	0.10497237569060773	146	0.25524475524475526	71	0.09366754617414248	C	10.43	1.347414	0.24426	0.024512	0.106279	ENSG00000137216	ENST00000371893	.	.	.	4.42	0.341	0.15991	.	.	.	.	.	T	0.24547	0.0595	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.10706	-1.0618	3	.	.	.	.	8.5159	0.33246	0.0:0.4934:0.0:0.5066	rs4714762;rs57455510	.	.	.	L	423	.	.	S	+	2	0	TMEM63B	44225642	0.001000	0.12720	0.998000	0.56505	0.985000	0.73830	-1.277000	0.02812	-0.057000	0.13199	-0.437000	0.05841	TCG	C|0.910;G|0.000;T|0.089	0.089	strong		0.612	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
ZNF280A	129025	hgsc.bcm.edu	37	22	22868773	22868773	+	Silent	SNP	G	G	A	rs361737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22868773G>A	ENST00000302097.3	-	2	1434	c.1182C>T	c.(1180-1182)taC>taT	p.Y394Y		NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		CCTGGCACACGTAGGGCATTT	0.433													A|||	2379	0.47504	0.2405	0.7334	5008	,	,		19326	0.4137		0.7068	False		,,,				2504	0.4335				p.Y394Y		Atlas-SNP	.											ZNF280A,NS,adenoma,0,1	ZNF280A	67	1	0			c.C1182T						PASS	.	A		1356,3050	691.9+/-405.5	220,916,1067	124.0	103.0	110.0		1182	-2.9	0.1	22	dbSNP_79	110	5850,2746	436.8+/-358.4	2005,1840,453	no	coding-synonymous	ZNF280A	NM_080740.3		2225,2756,1520	AA,AG,GG		31.9451,30.7762,44.5778		394/543	22868773	7206,5796	2203	4298	6501	SO:0001819	synonymous_variant	129025	exon2			GCACACGTAGGGC	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.1182C>T	22.37:g.22868773G>A		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	284	132	0.464789	NM_080740		Silent	SNP	ENST00000302097.3	37	CCDS13800.1																																																																																			G|0.453;A|0.547	0.547	strong		0.433	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
CCDC74A	90557	hgsc.bcm.edu	37	2	132290464	132290464	+	Missense_Mutation	SNP	G	G	A	rs13660	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:132290464G>A	ENST00000295171.6	+	6	1042	c.904G>A	c.(904-906)Ggg>Agg	p.G302R	CCDC74A_ENST00000467992.2_3'UTR|CCDC74A_ENST00000409856.3_Missense_Mutation_p.G236R	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	302			G -> R (in dbSNP:rs13660).							endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CCTCCTGGAAGGGAGCCAGAG	0.687													g|||	615	0.122804	0.2965	0.085	5008	,	,		17235	0.004		0.1014	False		,,,				2504	0.0593				p.G302R		Atlas-SNP	.											CCDC74A,NS,carcinoma,-1,3	CCDC74A	44	3	0			c.G904A						PASS	.	G	ARG/GLY	1057,3349		80,897,1226	44.0	51.0	49.0		904	0.7	0.9	2	dbSNP_52	49	836,7764		21,794,3485	no	missense	CCDC74A	NM_138770.1	125	101,1691,4711	AA,AG,GG		9.7209,23.99,14.5548	probably-damaging	302/379	132290464	1893,11113	2203	4300	6503	SO:0001583	missense	90557	exon6			CTGGAAGGGAGCC		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.904G>A	2.37:g.132290464G>A	ENSP00000295171:p.Gly302Arg	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	251	109	0.434263	NM_138770	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	261	0.11950549450549451	152	0.3089430894308943	36	0.09944751381215469	2	0.0034965034965034965	71	0.09366754617414248	.	2.586	-0.296297	0.05532	0.2399	0.097209	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.34859	1.34;1.34	2.66	0.709	0.18150	.	0.449735	0.16074	U	0.230852	T	0.00012	0.0000	M	0.63428	1.95	0.36962	P	0.10658500000000004	B;B	0.14805	0.011;0.001	B;B	0.12156	0.007;0.004	T	0.19877	-1.0292	9	0.59425	D	0.04	.	6.2901	0.21054	0.2757:0.0:0.7243:0.0	.	236;302	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	R	302;236	ENSP00000295171:G302R;ENSP00000387009:G236R	ENSP00000295171:G302R	G	+	1	0	CCDC74A	132006934	0.360000	0.24964	0.927000	0.36925	0.165000	0.22458	0.204000	0.17335	-0.226000	0.09899	-1.050000	0.02344	GGG	G|0.866;A|0.134	0.134	strong		0.687	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
CCDC9	26093	hgsc.bcm.edu	37	19	47770032	47770032	+	Silent	SNP	C	C	T	rs60383222	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47770032C>T	ENST00000221922.6	+	8	1107	c.885C>T	c.(883-885)gcC>gcT	p.A295A		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	295							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		AGTGGGATGCCGAGAAGACCG	0.617													C|||	694	0.138578	0.1278	0.0865	5008	,	,		15709	0.0754		0.1471	False		,,,				2504	0.2464				p.A295A		Atlas-SNP	.											.	CCDC9	37	.	0			c.C885T						PASS	.	C		521,3881		34,453,1714	45.0	33.0	37.0		885	-8.6	0.1	19	dbSNP_129	37	1312,7288		110,1092,3098	no	coding-synonymous	CCDC9	NM_015603.2		144,1545,4812	TT,TC,CC		15.2558,11.8355,14.0978		295/532	47770032	1833,11169	2201	4300	6501	SO:0001819	synonymous_variant	26093	exon8			GGATGCCGAGAAG	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.885C>T	19.37:g.47770032C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	161	81	0.503106	NM_015603		Silent	SNP	ENST00000221922.6	37	CCDS12698.1																																																																																			C|0.880;T|0.120	0.120	strong		0.617	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
BOD1L1	259282	hgsc.bcm.edu	37	4	13601337	13601337	+	Missense_Mutation	SNP	G	G	A	rs3733557	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:13601337G>A	ENST00000040738.5	-	10	7322	c.7187C>T	c.(7186-7188)cCg>cTg	p.P2396L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2396			P -> L (in dbSNP:rs3733557). {ECO:0000269|PubMed:10718198}.			nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P2396L(1)									CACGGGACCCGGTTCTTTGCC	0.597													G|||	544	0.108626	0.0129	0.0908	5008	,	,		18586	0.1746		0.1352	False		,,,				2504	0.1554				p.P2396L		Atlas-SNP	.											BOD1L,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.C7187T						PASS	.	G	LEU/PRO	142,4264	98.9+/-137.6	2,138,2063	132.0	127.0	129.0		7187	-10.0	0.0	4	dbSNP_107	129	1281,7319	255.9+/-280.6	86,1109,3105	yes	missense	BOD1L	NM_148894.2	98	88,1247,5168	AA,AG,GG		14.8953,3.2229,10.9411	benign	2396/3052	13601337	1423,11583	2203	4300	6503	SO:0001583	missense	259282	exon10			GGACCCGGTTCTT	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.7187C>T	4.37:g.13601337G>A	ENSP00000040738:p.Pro2396Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	244	0.11172161172161173	10	0.02032520325203252	40	0.11049723756906077	98	0.17132867132867133	96	0.1266490765171504	G	8.783	0.928692	0.18131	0.032229	0.148953	ENSG00000038219	ENST00000040738	T	0.06218	3.33	4.98	-9.96	0.00443	.	5.307370	0.00843	N	0.001765	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40156	-0.9578	9	0.27082	T	0.32	.	3.1753	0.06566	0.1527:0.1914:0.4514:0.2045	rs3733557;rs17346523;rs52797579;rs61508626;rs3733557	2396	Q8NFC6	BOD1L_HUMAN	L	2396	ENSP00000040738:P2396L	ENSP00000040738:P2396L	P	-	2	0	BOD1L	13210435	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.906000	0.01590	-1.653000	0.01500	-0.459000	0.05422	CCG	G|0.894;A|0.106	0.106	strong		0.597	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
POM121L12	285877	hgsc.bcm.edu	37	7	53103554	53103554	+	Missense_Mutation	SNP	C	C	G	rs11238247	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:53103554C>G	ENST00000408890.4	+	1	206	c.190C>G	c.(190-192)Cag>Gag	p.Q64E		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	64			Q -> E (in dbSNP:rs11238247). {ECO:0000269|PubMed:14702039}.							endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GAGCCATATTCAGTACTTCCA	0.697													C|||	1680	0.335463	0.1921	0.4323	5008	,	,		12258	0.3095		0.4861	False		,,,				2504	0.3323				p.Q64E		Atlas-SNP	.											.	POM121L12	146	.	0			c.C190G						PASS	.	C	GLU/GLN	852,3038		105,642,1198	29.0	33.0	32.0		190	1.1	0.0	7	dbSNP_120	32	4217,4067		1064,2089,989	yes	missense	POM121L12	NM_182595.3	29	1169,2731,2187	GG,GC,CC		49.0946,21.9023,41.6379	possibly-damaging	64/297	53103554	5069,7105	1945	4142	6087	SO:0001583	missense	285877	exon1			CATATTCAGTACT		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.190C>G	7.37:g.53103554C>G	ENSP00000386133:p.Gln64Glu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	806	0.36904761904761907	102	0.2073170731707317	154	0.425414364640884	175	0.30594405594405594	375	0.4947229551451187	C	6.806	0.517760	0.13005	0.219023	0.509054	ENSG00000221900	ENST00000408890	T	0.23348	1.91	1.11	1.11	0.20524	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.43701	0.815	B	0.33690	0.168	T	0.43065	-0.9414	8	0.66056	D	0.02	.	5.5761	0.17225	0.0:1.0:0.0:0.0	rs11238247;rs52794294;rs11238247	64	Q8N7R1	P1L12_HUMAN	E	64	ENSP00000386133:Q64E	ENSP00000386133:Q64E	Q	+	1	0	POM121L12	53071048	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.130000	0.15850	0.903000	0.36546	0.313000	0.20887	CAG	C|0.588;G|0.412	0.412	strong		0.697	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
FAM129C	199786	hgsc.bcm.edu	37	19	17654182	17654182	+	Silent	SNP	G	G	A	rs76814516	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17654182G>A	ENST00000335393.4	+	12	1617	c.1479G>A	c.(1477-1479)acG>acA	p.T493T	FAM129C_ENST00000600871.1_Silent_p.T439T|FAM129C_ENST00000300971.2_Silent_p.T493T|FAM129C_ENST00000599124.1_Silent_p.T462T|FAM129C_ENST00000332386.5_Silent_p.T493T|FAM129C_ENST00000601861.1_Silent_p.T462T|FAM129C_ENST00000599164.1_Silent_p.T462T|FAM129C_ENST00000449408.2_Silent_p.T219T|FAM129C_ENST00000595684.1_Silent_p.T493T|FAM129C_ENST00000352727.3_Silent_p.T493T	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	493			T -> M (in dbSNP:rs45532635).							autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						GTCTGACGACGGCCCTCAACT	0.632													g|||	310	0.061901	0.0893	0.0432	5008	,	,		17131	0.0317		0.0417	False		,,,				2504	0.09				p.T493T		Atlas-SNP	.											.	FAM129C	110	.	0			c.G1479A						PASS	.	G	,	314,4092	167.3+/-198.3	15,284,1904	84.0	87.0	86.0		1479,1479	-9.8	0.0	19	dbSNP_132	86	448,8152	133.1+/-190.7	10,428,3862	no	coding-synonymous,coding-synonymous	FAM129C	NM_001098524.1,NM_173544.4	,	25,712,5766	AA,AG,GG		5.2093,7.1266,5.8588	,	493/652,493/698	17654182	762,12244	2203	4300	6503	SO:0001819	synonymous_variant	199786	exon12			GACGACGGCCCTC	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1479G>A	19.37:g.17654182G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	180	94	0.522222	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																			G|0.945;A|0.055	0.055	strong		0.632	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
KRT32	3882	hgsc.bcm.edu	37	17	39623431	39623431	+	Silent	SNP	C	C	T	rs117028403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39623431C>T	ENST00000225899.3	-	1	250	c.147G>A	c.(145-147)tcG>tcA	p.S49S	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	49	Head.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GCAGGCAGACCGAAGGCAGGC	0.662													C|||	75	0.014976	0.0008	0.0086	5008	,	,		17040	0.0		0.0318	False		,,,				2504	0.0368				p.S49S		Atlas-SNP	.											.	KRT32	57	.	0			c.G147A						PASS	.	C		28,4378	32.6+/-62.9	1,26,2176	36.0	39.0	38.0		147	-8.6	0.0	17	dbSNP_132	38	266,8334	98.8+/-160.4	6,254,4040	no	coding-synonymous	KRT32	NM_002278.3		7,280,6216	TT,TC,CC		3.093,0.6355,2.2605		49/449	39623431	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	3882	exon1			GCAGACCGAAGGC	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.147G>A	17.37:g.39623431C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_002278		Silent	SNP	ENST00000225899.3	37	CCDS11393.1																																																																																			C|0.981;T|0.019	0.019	strong		0.662	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
OSBPL1A	114876	hgsc.bcm.edu	37	18	21739725	21739725	+	IGR	SNP	T	T	C	rs1049684	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21739725T>C	ENST00000319481.3	-	0	4195				CABYR_ENST00000581397.1_Silent_p.P277P|CABYR_ENST00000327201.6_Silent_p.P179P|CABYR_ENST00000415309.2_Intron|CABYR_ENST00000399496.3_Silent_p.P277P|RP11-799B12.4_ENST00000583267.1_lincRNA|CABYR_ENST00000399499.1_Silent_p.P277P	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					AACCTCTTCCTGGACATGCTG	0.458													T|||	2360	0.471246	0.5605	0.3919	5008	,	,		22303	0.4444		0.3897	False		,,,				2504	0.5184				p.P277P		Atlas-SNP	.											.	CABYR	51	.	0			c.T831C						PASS	.	T	,,,,,	2437,1969	620.1+/-393.5	661,1115,427	89.0	89.0	89.0		,537,831,,831,	2.2	1.0	18	dbSNP_86	89	2998,5602	463.4+/-366.0	493,2012,1795	no	utr-3,coding-synonymous,coding-synonymous,utr-3,coding-synonymous,intron	CABYR	NM_012189.2,NM_138643.1,NM_138644.1,NM_153768.1,NM_153769.1,NM_153770.1	,,,,,	1154,3127,2222	CC,CT,TT		34.8605,44.6891,41.7884	,,,,,	,179/282,277/380,,277/380,	21739725	5435,7571	2203	4300	6503	SO:0001628	intergenic_variant	26256	exon5			TCTTCCTGGACAT	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944		18.37:g.21739725T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	80	78	0.975	NM_153769	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	37	CCDS11884.1																																																																																			T|0.561;C|0.439	0.439	strong		0.458	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
ZNF665	79788	hgsc.bcm.edu	37	19	53668697	53668697	+	Missense_Mutation	SNP	T	T	C	rs45499997	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53668697T>C	ENST00000600412.1	-	2	966	c.851A>G	c.(850-852)aAt>aGt	p.N284S	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Missense_Mutation_p.N349S			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		GCCACATTCATTACATTTGTA	0.438													T|||	140	0.0279553	0.003	0.1254	5008	,	,		22847	0.0		0.0457	False		,,,				2504	0.0031				p.N349S		Atlas-SNP	.											.	ZNF665	136	.	0			c.A1046G						PASS	.	T	SER/ASN	57,4349	57.4+/-93.9	2,53,2148	103.0	105.0	104.0		1046	-1.5	0.0	19	dbSNP_127	104	593,8007	156.4+/-210.3	17,559,3724	yes	missense	ZNF665	NM_024733.3	46	19,612,5872	CC,CT,TT		6.8953,1.2937,4.9977	benign	349/679	53668697	650,12356	2203	4300	6503	SO:0001583	missense	79788	exon4			CATTCATTACATT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.851A>G	19.37:g.53668697T>C	ENSP00000469154:p.Asn284Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	37		81	0.03708791208791209	2	0.0040650406504065045	42	0.11602209944751381	0	0.0	37	0.048812664907651716	T	8.778	0.927527	0.18056	0.012937	0.068953	ENSG00000197497	ENST00000396424	T	0.16324	2.35	2.94	-1.48	0.08745	.	.	.	.	.	T	0.00109	0.0003	N	0.01656	-0.775	0.09310	N	1	P	0.48911	0.917	P	0.52793	0.709	T	0.21690	-1.0238	9	0.27785	T	0.31	.	4.8859	0.13703	0.3:0.0:0.4479:0.2521	rs45499997	349	Q9H7R5-2	.	S	349	ENSP00000379702:N349S	ENSP00000379702:N349S	N	-	2	0	ZNF665	58360509	0.000000	0.05858	0.001000	0.08648	0.180000	0.23129	-4.075000	0.00300	-0.228000	0.09869	0.358000	0.22013	AAT	T|0.958;C|0.042	0.042	strong		0.438	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
ATP2B1	490	hgsc.bcm.edu	37	12	90028901	90028901	+	Silent	SNP	T	T	C	rs1050395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:90028901T>C	ENST00000428670.3	-	4	990	c.534A>G	c.(532-534)gaA>gaG	p.E178E	ATP2B1_ENST00000348959.3_Silent_p.E178E|ATP2B1_ENST00000359142.3_Silent_p.E178E|ATP2B1_ENST00000261173.2_Silent_p.E178E			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	178					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						TAAACTGTTTTTCCTTACTCC	0.438													T|||	605	0.120807	0.1505	0.1455	5008	,	,		17520	0.0317		0.1928	False		,,,				2504	0.0808				p.E178E		Atlas-SNP	.											.	ATP2B1	191	.	0			c.A534G						PASS	.	T	,	715,3691	296.7+/-284.4	51,613,1539	133.0	111.0	118.0		534,534	-0.9	1.0	12	dbSNP_86	118	1674,6926	304.6+/-307.0	164,1346,2790	no	coding-synonymous,coding-synonymous	ATP2B1	NM_001001323.1,NM_001682.2	,	215,1959,4329	CC,CT,TT		19.4651,16.2279,18.3684	,	178/1177,178/1221	90028901	2389,10617	2203	4300	6503	SO:0001819	synonymous_variant	490	exon3			CTGTTTTTCCTTA	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"""ATPases / P-type"""	814	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 1"""	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.534A>G	12.37:g.90028901T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Silent	SNP	ENST00000428670.3	37	CCDS9035.1																																																																																			T|0.837;C|0.163	0.163	strong		0.438	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	
POTEF	728378	hgsc.bcm.edu	37	2	130832389	130832389	+	Missense_Mutation	SNP	G	G	T	rs199761904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130832389G>T	ENST00000409914.2	-	17	3055	c.2656C>A	c.(2656-2658)Cct>Act	p.P886T	POTEF_ENST00000357462.5_Missense_Mutation_p.P886T	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	886	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						AGGTAGTCAGGCAGTTCCCGC	0.587																																					p.P886T		Atlas-SNP	.											POTEF,NS,carcinoma,0,1	POTEF	140	1	0			c.C2656A						scavenged	.						20.0	28.0	25.0					2																	130832389		1902	3994	5896	SO:0001583	missense	728378	exon17			AGTCAGGCAGTTC	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2656C>A	2.37:g.130832389G>T	ENSP00000386786:p.Pro886Thr	Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	439	48	0.109339	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	0.009	-1.840460	0.00573	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	T;T	0.04360	3.64;3.64	.	.	.	.	.	.	.	.	T	0.00241	0.0007	N	0.00000	-5.41	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59364	-0.7468	8	0.02654	T	1	.	4.0871	0.09951	0.0:1.0E-4:0.3502:0.6498	.	886	A5A3E0	POTEF_HUMAN	T	886	ENSP00000350052:P886T;ENSP00000386786:P886T	ENSP00000350052:P886T	P	-	1	0	POTEF	130548859	1.000000	0.71417	0.050000	0.19076	0.050000	0.14768	3.856000	0.55964	-2.076000	0.00875	-2.150000	0.00334	CCT	.	.	weak		0.587	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
GRIN3A	116443	hgsc.bcm.edu	37	9	104433235	104433235	+	Missense_Mutation	SNP	C	C	T	rs10989589	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:104433235C>T	ENST00000361820.3	-	3	2059	c.1459G>A	c.(1459-1461)Gga>Aga	p.G487R		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	487			G -> R (in dbSNP:rs10989589). {ECO:0000269|PubMed:11735224, ECO:0000269|PubMed:11880201}.		calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	ACAATCTTTCCCCCCTGCCAG	0.498													C|||	1329	0.265375	0.1097	0.3617	5008	,	,		18574	0.2262		0.4076	False		,,,				2504	0.3016				p.G487R		Atlas-SNP	.											GRIN3A,caecum,carcinoma,+1,1	GRIN3A	186	1	0			c.G1459A						PASS	.	C	ARG/GLY	741,3665	303.0+/-287.7	64,613,1526	166.0	161.0	163.0		1459	5.8	0.3	9	dbSNP_120	163	3549,5051	515.9+/-378.7	726,2097,1477	yes	missense	GRIN3A	NM_133445.2	125	790,2710,3003	TT,TC,CC		41.2674,16.818,32.9848	possibly-damaging	487/1116	104433235	4290,8716	2203	4300	6503	SO:0001583	missense	116443	exon3			TCTTTCCCCCCTG		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.1459G>A	9.37:g.104433235C>T	ENSP00000355155:p.Gly487Arg	Somatic	298	1	0.0033557		WXS	Illumina HiSeq	Phase_I	265	127	0.479245	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	618	0.28296703296703296	54	0.10975609756097561	147	0.40607734806629836	115	0.20104895104895104	302	0.39841688654353563	C	14.17	2.454432	0.43634	0.16818	0.412674	ENSG00000198785	ENST00000361820	T	0.11277	2.79	5.76	5.76	0.90799	.	0.135566	0.49305	D	0.000160	T	0.00012	0.0000	L	0.56396	1.775	0.09310	P	0.99999884003	P	0.52842	0.956	P	0.56474	0.799	T	0.52697	-0.8541	9	0.48119	T	0.1	.	13.5255	0.61593	0.0:0.9287:0.0:0.0713	rs10989589;rs52814301;rs10989589	487	Q8TCU5	NMD3A_HUMAN	R	487	ENSP00000355155:G487R	ENSP00000355155:G487R	G	-	1	0	GRIN3A	103473056	1.000000	0.71417	0.252000	0.24328	0.990000	0.78478	5.989000	0.70587	2.882000	0.98803	0.655000	0.94253	GGA	C|0.670;T|0.330	0.330	strong		0.498	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
C8orf48	157773	hgsc.bcm.edu	37	8	13424583	13424583	+	Missense_Mutation	SNP	C	C	T	rs13273355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:13424583C>T	ENST00000297324.4	+	1	232	c.83C>T	c.(82-84)tCt>tTt	p.S28F	RP11-145O15.3_ENST00000529018.1_RNA	NM_001007090.2	NP_001007091	Q96LL4	CH048_HUMAN	chromosome 8 open reading frame 48	28			S -> F (in dbSNP:rs13273355). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	5						TTGAAGAACTCTACTGATGAG	0.522													T|||	4067	0.812101	0.6921	0.8602	5008	,	,		18299	0.9673		0.8211	False		,,,				2504	0.771				p.S28F		Atlas-SNP	.											.	C8orf48	18	.	0			c.C83T						PASS	.	T	PHE/SER	1007,377		369,269,54	37.0	35.0	36.0		83	2.0	0.0	8	dbSNP_121	36	2605,577		1063,479,49	yes	missense	C8orf48	NM_001007090.2	155	1432,748,103	TT,TC,CC		18.1332,27.2399,20.8936	benign	28/320	13424583	3612,954	692	1591	2283	SO:0001583	missense	157773	exon1			AGAACTCTACTGA	AK058131	CCDS47809.1	8p22	2012-04-13			ENSG00000164743	ENSG00000164743			26345	protein-coding gene	gene with protein product						12477932	Standard	NM_001007090		Approved	FLJ25402	uc003wwp.3	Q96LL4	OTTHUMG00000165482	ENST00000297324.4:c.83C>T	8.37:g.13424583C>T	ENSP00000297324:p.Ser28Phe	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_001007090	Q96LJ9	Missense_Mutation	SNP	ENST00000297324.4	37	CCDS47809.1	1825	0.8356227106227107	340	0.6910569105691057	299	0.8259668508287292	560	0.9790209790209791	626	0.8258575197889182	T	0.066	-1.213849	0.01555	0.727601	0.818668	ENSG00000164743	ENST00000297324	T	0.28895	1.59	4.48	1.98	0.26296	.	1.374090	0.05297	N	0.522263	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26950	-1.0088	9	0.08837	T	0.75	0.3336	5.6094	0.17396	0.0:0.0966:0.3948:0.5086	rs13273355;rs17856923;rs52821396;rs57808930;rs13273355	28	Q96LL4	CH048_HUMAN	F	28	ENSP00000297324:S28F	ENSP00000297324:S28F	S	+	2	0	C8orf48	13468954	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.071000	0.11505	0.104000	0.17725	-0.254000	0.11334	TCT	C|0.183;N|0.000	.	strong		0.522	C8orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384400.1	NM_001007090	
MYOC	4653	hgsc.bcm.edu	37	1	171621525	171621525	+	Missense_Mutation	SNP	C	C	T	rs2234926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:171621525C>T	ENST00000037502.6	-	1	298	c.227G>A	c.(226-228)aGa>aAa	p.R76K		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	76			R -> K (in dbSNP:rs2234926). {ECO:0000269|PubMed:10798654, ECO:0000269|PubMed:10980537, ECO:0000269|PubMed:11004290, ECO:0000269|PubMed:12189160, ECO:0000269|PubMed:12356829, ECO:0000269|PubMed:12442283, ECO:0000269|PubMed:12872267, ECO:0000269|PubMed:15025728, ECO:0000269|PubMed:9863594}.		bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GCTGCTGTCTCTCTGTAAGTT	0.577													C|||	682	0.136182	0.0068	0.1023	5008	,	,		18797	0.0794		0.1412	False		,,,				2504	0.3885				p.R76K		Atlas-SNP	.											.	MYOC	69	.	0			c.G227A	GRCh37	CM085579	MYOC	M	rs2234926	PASS	.	C	LYS/ARG	122,4284	91.1+/-129.8	2,118,2083	130.0	102.0	111.0		227	3.4	1.0	1	dbSNP_98	111	1155,7445	237.1+/-269.0	76,1003,3221	yes	missense	MYOC	NM_000261.1	26	78,1121,5304	TT,TC,CC		13.4302,2.769,9.8185	probably-damaging	76/505	171621525	1277,11729	2203	4300	6503	SO:0001583	missense	4653	exon1			CTGTCTCTCTGTA	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.227G>A	1.37:g.171621525C>T	ENSP00000037502:p.Arg76Lys	Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	408	160	0.392157	NM_000261	B2RD84|O00620|Q7Z6Q9	Missense_Mutation	SNP	ENST00000037502.6	37	CCDS1297.1	175	0.08012820512820513	7	0.014227642276422764	31	0.0856353591160221	27	0.0472027972027972	110	0.14511873350923482	C	8.539	0.872785	0.17322	0.02769	0.134302	ENSG00000034971	ENST00000037502;ENST00000357746;ENST00000536591;ENST00000537133	T	0.60299	0.2	5.31	3.43	0.39272	.	0.072208	0.56097	N	0.000037	T	0.60274	0.2256	M	0.64997	1.995	0.43080	P	0.00526099999999996	D;B	0.58970	0.984;0.018	D;B	0.68192	0.956;0.012	T	0.65549	-0.6141	9	0.62326	D	0.03	.	11.2975	0.49286	0.0:0.8356:0.0:0.1644	rs2234926	76;76	B4DV44;Q99972	.;MYOC_HUMAN	K	76;76;9;76	ENSP00000037502:R76K	ENSP00000037502:R76K	R	-	2	0	MYOC	169888148	1.000000	0.71417	0.998000	0.56505	0.070000	0.16714	2.640000	0.46579	0.332000	0.23536	-0.797000	0.03246	AGA	C|0.909;T|0.091	0.091	strong		0.577	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261	
KIF2B	84643	hgsc.bcm.edu	37	17	51900729	51900729	+	Missense_Mutation	SNP	C	C	T	rs3803824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:51900729C>T	ENST00000268919.4	+	1	491	c.335C>T	c.(334-336)gCc>gTc	p.A112V		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	112			A -> V (in dbSNP:rs3803824). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CAGCGTACCGCCACGAAATGG	0.597													C|||	1053	0.210264	0.025	0.268	5008	,	,		15495	0.2034		0.3847	False		,,,				2504	0.2474				p.A112V		Atlas-SNP	.											KIF2B,NS,carcinoma,+1,3	KIF2B	254	3	0			c.C335T						PASS	.	C	VAL/ALA	377,4029	190.5+/-216.4	18,341,1844	77.0	83.0	81.0		335	4.0	0.0	17	dbSNP_107	81	3525,5075	513.5+/-378.2	730,2065,1505	yes	missense	KIF2B	NM_032559.4	64	748,2406,3349	TT,TC,CC		40.9884,8.5565,30.0015	benign	112/674	51900729	3902,9104	2203	4300	6503	SO:0001583	missense	84643	exon1			GTACCGCCACGAA	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.335C>T	17.37:g.51900729C>T	ENSP00000268919:p.Ala112Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	520	0.23809523809523808	16	0.032520325203252036	104	0.287292817679558	96	0.16783216783216784	304	0.40105540897097625	C	1.990	-0.432000	0.04669	0.085565	0.409884	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.75154	-0.91	4.99	4.02	0.46733	.	0.344162	0.20835	N	0.084805	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.12630	0.006	B	0.14023	0.01	T	0.30851	-0.9964	9	0.18276	T	0.48	.	7.5842	0.27982	0.0:0.811:0.0:0.189	rs3803824;rs17654285;rs52812737;rs61204455;rs3803824	112	Q8N4N8	KIF2B_HUMAN	V	112;35	ENSP00000268919:A112V	ENSP00000268919:A112V	A	+	2	0	KIF2B	49255728	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.532000	0.23067	1.446000	0.47643	0.655000	0.94253	GCC	C|0.741;T|0.259	0.259	strong		0.597	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
ACY3	91703	hgsc.bcm.edu	37	11	67414492	67414492	+	Missense_Mutation	SNP	C	C	T	rs948445	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67414492C>T	ENST00000255082.3	-	3	193	c.23G>A	c.(22-24)cGg>cAg	p.R8Q	ACY3_ENST00000529256.1_Intron	NM_080658.1	NP_542389.1	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	8	Hydrolytic domain. {ECO:0000250}.		R -> Q (in dbSNP:rs948445).		viral process (GO:0016032)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			endometrium(1)|lung(5)|prostate(2)	8					L-Aspartic Acid(DB00128)	CAGGGGCTCCCGGGGCACAGG	0.682													C|||	3605	0.719848	0.4009	0.8473	5008	,	,		17985	0.746		0.8121	False		,,,				2504	0.9387				p.R8Q	GBM(56;346 1011 27014 29495 46841)	Atlas-SNP	.											.	ACY3	27	.	0			c.G23A						PASS	.	C	GLN/ARG	2099,2197		525,1049,574	9.0	9.0	9.0		23	1.0	0.5	11	dbSNP_86	9	6979,1447		2922,1135,156	yes	missense	ACY3	NM_080658.1	43	3447,2184,730	TT,TC,CC		17.173,48.8594,28.6433	probably-damaging	8/320	67414492	9078,3644	2148	4213	6361	SO:0001583	missense	91703	exon3			GGCTCCCGGGGCA	BC008689	CCDS8175.1	11q13.2	2014-08-08			ENSG00000132744	ENSG00000132744			24104	protein-coding gene	gene with protein product		614413				14656720	Standard	NM_080658		Approved	HCBP1, MGC9740, ACY-3	uc001omq.3	Q96HD9	OTTHUMG00000167283	ENST00000255082.3:c.23G>A	11.37:g.67414492C>T	ENSP00000255082:p.Arg8Gln	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_080658		Missense_Mutation	SNP	ENST00000255082.3	37	CCDS8175.1	1600	0.7326007326007326	230	0.46747967479674796	312	0.861878453038674	439	0.7674825174825175	619	0.816622691292876	C	10.14	1.267576	0.23136	0.488594	0.82827	ENSG00000132744	ENST00000255082	D	0.96334	-3.98	4.03	1.04	0.20106	.	0.464005	0.21473	N	0.073978	T	0.00012	0.0000	N	0.08118	0	0.53688	P	2.8000000000028002E-5	B	0.21147	0.052	B	0.06405	0.002	T	0.43360	-0.9396	9	0.17369	T	0.5	.	7.6933	0.28579	0.0:0.6998:0.0:0.3002	rs948445;rs59605776;rs948445	8	Q96HD9	ACY3_HUMAN	Q	8	ENSP00000255082:R8Q	ENSP00000255082:R8Q	R	-	2	0	ACY3	67171068	0.000000	0.05858	0.458000	0.27068	0.788000	0.44548	0.195000	0.17155	0.003000	0.14656	0.462000	0.41574	CGG	C|0.295;T|0.705	0.705	strong		0.682	ACY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394002.1	NM_080658	
ERICH3	127254	hgsc.bcm.edu	37	1	75097426	75097426	+	Missense_Mutation	SNP	G	G	C	rs11210490	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:75097426G>C	ENST00000326665.5	-	7	1008	c.790C>G	c.(790-792)Cca>Gca	p.P264A	C1orf173_ENST00000420661.2_Missense_Mutation_p.P67A	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		264			P -> A (in dbSNP:rs11210490). {ECO:0000269|PubMed:14702039}.							NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						AAGCCATTTGGAGCAGTGGTT	0.368													G|||	1607	0.320887	0.2284	0.4741	5008	,	,		18825	0.1141		0.5268	False		,,,				2504	0.3384				p.P264A		Atlas-SNP	.											.	C1orf173	380	.	0			c.C790G						PASS	.	G	ALA/PRO	1399,3007	458.8+/-352.1	224,951,1028	171.0	154.0	160.0		790	3.5	1.0	1	dbSNP_120	160	4519,4081	592.4+/-393.0	1211,2097,992	yes	missense	C1orf173	NM_001002912.4	27	1435,3048,2020	CC,CG,GG		47.4535,31.7522,45.5021	probably-damaging	264/1531	75097426	5918,7088	2203	4300	6503	SO:0001583	missense	127254	exon7			CATTTGGAGCAGT																												ENST00000326665.5:c.790C>G	1.37:g.75097426G>C	ENSP00000322609:p.Pro264Ala	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	260	257	0.988462	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	741	0.3392857142857143	116	0.23577235772357724	178	0.49171270718232046	62	0.10839160839160839	385	0.5079155672823219	G	9.911	1.209431	0.22289	0.317522	0.525465	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.21932	2.43;1.98	5.39	3.49	0.39957	.	.	.	.	.	T	0.27169	0.0666	M	0.73598	2.24	0.27326	P	0.9569008	P;D	0.65815	0.944;0.995	P;P	0.61722	0.572;0.893	T	0.12268	-1.0554	8	0.54805	T	0.06	-7.5504	9.8566	0.41090	0.0729:0.0:0.7875:0.1396	rs11210490;rs11210490	67;264	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	A	264;67	ENSP00000322609:P264A;ENSP00000398581:P67A	ENSP00000322609:P264A	P	-	1	0	C1orf173	74870014	1.000000	0.71417	0.977000	0.42913	0.089000	0.18198	2.431000	0.44775	0.640000	0.30582	-0.142000	0.14014	CCA	G|0.588;C|0.412	0.412	strong		0.368	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
ABCC12	94160	hgsc.bcm.edu	37	16	48122582	48122582	+	Missense_Mutation	SNP	G	G	A	rs7193955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:48122582G>A	ENST00000311303.3	-	24	3694	c.3349C>T	c.(3349-3351)Cgt>Tgt	p.R1117C	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000532355.1_5'Flank|ABCC12_ENST00000448542.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	1117			R -> C (in dbSNP:rs7193955). {ECO:0000269|PubMed:11483364}.			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				ATCTCCCCACGGCTGGGCCAG	0.512													G|||	2961	0.591254	0.1112	0.5331	5008	,	,		18261	0.8889		0.7873	False		,,,				2504	0.773				p.R1117C		Atlas-SNP	.											ABCC12,colon,carcinoma,0,1	ABCC12	190	1	0			c.C3349T						PASS	.	G	CYS/ARG	1020,3382	375.4+/-321.6	124,772,1305	90.0	78.0	82.0		3349	2.7	0.5	16	dbSNP_116	82	6730,1870	729.2+/-406.7	2660,1410,230	yes	missense	ABCC12	NM_033226.2	180	2784,2182,1535	AA,AG,GG		21.7442,23.1713,40.3938	benign	1117/1360	48122582	7750,5252	2201	4300	6501	SO:0001583	missense	94160	exon24			CCCCACGGCTGGG	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.3349C>T	16.37:g.48122582G>A	ENSP00000311030:p.Arg1117Cys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	1384	0.6336996336996337	69	0.1402439024390244	197	0.5441988950276243	512	0.8951048951048951	606	0.7994722955145118	G	7.927	0.739832	0.15642	0.231713	0.782558	ENSG00000140798	ENST00000311303	D	0.90844	-2.74	5.87	2.67	0.31697	.	0.634955	0.17864	N	0.159431	T	0.00012	0.0000	L	0.60904	1.88	0.80722	P	0.0	B	0.11235	0.004	B	0.11329	0.006	T	0.34925	-0.9809	9	0.56958	D	0.05	.	3.9511	0.09369	0.0766:0.2455:0.4345:0.2434	rs7193955;rs52806630;rs60981757;rs7193955	1117	Q96J65	MRP9_HUMAN	C	1117	ENSP00000311030:R1117C	ENSP00000311030:R1117C	R	-	1	0	ABCC12	46680083	0.000000	0.05858	0.535000	0.28026	0.087000	0.18053	0.035000	0.13797	0.781000	0.33589	-0.150000	0.13652	CGT	G|0.395;A|0.605	0.605	strong		0.512	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
SERPINA9	327657	hgsc.bcm.edu	37	14	94933695	94933695	+	Missense_Mutation	SNP	G	G	A	rs17090921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94933695G>A	ENST00000380365.3	-	3	731	c.653C>T	c.(652-654)cCt>cTt	p.P218L	SERPINA9_ENST00000424550.2_Missense_Mutation_p.P87L|SERPINA9_ENST00000546329.1_Missense_Mutation_p.P200L|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000298845.7_Missense_Mutation_p.P136L|SERPINA9_ENST00000337425.5_Missense_Mutation_p.P236L|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000448305.2_Missense_Mutation_p.P138L			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	218			P -> L (in dbSNP:rs17090921). {ECO:0000269|PubMed:12975309}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TGTATATTCAGGGTGAAAGGG	0.468													G|||	1615	0.322484	0.146	0.3847	5008	,	,		21030	0.4643		0.3101	False		,,,				2504	0.3834				p.P236L		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C707T						PASS	.	G	LEU/PRO,LEU/PRO	622,3220		53,516,1352	66.0	63.0	64.0		407,707	1.9	0.0	14	dbSNP_123	64	2486,5780		375,1736,2022	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	98,98	428,2252,3374	AA,AG,GG		30.075,16.1895,25.669	benign,benign	136/336,236/436	94933695	3108,9000	1921	4133	6054	SO:0001583	missense	327657	exon3			TATTCAGGGTGAA	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.653C>T	14.37:g.94933695G>A	ENSP00000369723:p.Pro218Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	74	47	0.635135	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		721	0.3301282051282051	79	0.16056910569105692	127	0.35082872928176795	275	0.4807692307692308	240	0.316622691292876	G	10.74	1.435279	0.25813	0.161895	0.30075	ENSG00000170054	ENST00000448305;ENST00000298845;ENST00000424550;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01;-2.01	3.73	1.87	0.25490	Serpin domain (3);	34.778500	0.00166	N	0.000009	T	0.00012	0.0000	M	0.67517	2.055	0.80722	P	0.0	B;B;B;B;P	0.42203	0.168;0.44;0.391;0.386;0.773	B;B;B;B;B	0.39068	0.092;0.21;0.092;0.092;0.289	T	0.12066	-1.0562	9	0.48119	T	0.1	.	5.0016	0.14268	0.1832:0.0:0.6521:0.1647	rs17090921;rs52803409;rs17090921	200;218;138;236;136	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7;Q86WD7-2	.;SPA9_HUMAN;.;.;.	L	138;136;87;236;218;200	ENSP00000414092:P138L;ENSP00000298845:P136L;ENSP00000409012:P87L;ENSP00000337133:P236L;ENSP00000369723:P218L;ENSP00000445476:P200L	ENSP00000298845:P136L	P	-	2	0	SERPINA9	94003448	0.001000	0.12720	0.004000	0.12327	0.120000	0.20174	0.933000	0.28897	0.390000	0.25115	0.462000	0.41574	CCT	G|0.689;A|0.311	0.311	strong		0.468	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
MUC4	4585	hgsc.bcm.edu	37	3	195513826	195513826	+	Missense_Mutation	SNP	G	G	A	rs202029925		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513826G>A	ENST00000463781.3	-	2	5084	c.4625C>T	c.(4624-4626)cCt>cTt	p.P1542L	MUC4_ENST00000475231.1_Missense_Mutation_p.P1542L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.M1535_T1550delMPLPVTSPSSASTGDT(4)|p.P1542L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGCTGAGGAAGGGCTAGTGAC	0.592																																					p.P1542L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	5	Deletion - In frame(4)|Substitution - Missense(1)	stomach(4)|kidney(1)	c.C4625T						PASS	.																																			SO:0001583	missense	4585	exon2			GAGGAAGGGCTAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4625C>T	3.37:g.195513826G>A	ENSP00000417498:p.Pro1542Leu	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	144	30	0.208333	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	9.599	1.128178	0.20959	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26067	1.77;1.76	0.844	0.844	0.18943	.	.	.	.	.	T	0.21307	0.0513	N	0.19112	0.55	0.31987	N	0.6051	P	0.48350	0.909	P	0.52909	0.713	T	0.25779	-1.0122	8	.	.	.	.	5.3481	0.16020	1.0E-4:0.0:0.9999:0.0	.	1542	E7ESK3	.	L	1542	ENSP00000417498:P1542L;ENSP00000420243:P1542L	.	P	-	2	0	MUC4	196998221	0.000000	0.05858	0.010000	0.14722	0.010000	0.07245	-0.058000	0.11750	0.088000	0.17205	0.089000	0.15464	CCT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RNMTL1	55178	hgsc.bcm.edu	37	17	695062	695062	+	Missense_Mutation	SNP	T	T	A	rs80220493	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:695062T>A	ENST00000304478.4	+	4	1122	c.1016T>A	c.(1015-1017)gTt>gAt	p.V339D	RP11-676J12.8_ENST00000574560.1_RNA	NM_018146.2	NP_060616.1			RNA methyltransferase like 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)		CATGTTGAGGTTCAGAGTTAC	0.572													T|||	93	0.0185703	0.0008	0.0086	5008	,	,		19633	0.0446		0.0179	False		,,,				2504	0.0235				p.V339D		Atlas-SNP	.											.	RNMTL1	25	.	0			c.T1016A						PASS	.	T	ASP/VAL	11,4395	17.9+/-39.9	0,11,2192	64.0	65.0	65.0		1016	5.8	1.0	17	dbSNP_131	65	179,8421	81.2+/-143.8	4,171,4125	yes	missense	RNMTL1	NM_018146.2	152	4,182,6317	AA,AT,TT		2.0814,0.2497,1.4609	probably-damaging	339/421	695062	190,12816	2203	4300	6503	SO:0001583	missense	55178	exon4			TTGAGGTTCAGAG	AF177344	CCDS10997.1	17p13.3	2008-02-05			ENSG00000171861	ENSG00000171861			18485	protein-coding gene	gene with protein product		612600				12296377	Standard	NM_018146		Approved	FLJ10581, HC90	uc002frw.3	Q9HC36	OTTHUMG00000090285	ENST00000304478.4:c.1016T>A	17.37:g.695062T>A	ENSP00000306080:p.Val339Asp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	104	62	0.596154	NM_018146		Missense_Mutation	SNP	ENST00000304478.4	37	CCDS10997.1	42	0.019230769230769232	1	0.0020325203252032522	3	0.008287292817679558	22	0.038461538461538464	16	0.021108179419525065	T	16.77	3.215216	0.58452	0.002497	0.020814	ENSG00000171861	ENST00000304478	T	0.19806	2.12	5.81	5.81	0.92471	tRNA/rRNA methyltransferase, SpoU (1);	0.417730	0.28214	N	0.016176	T	0.09335	0.0230	L	0.46157	1.445	0.54753	D	0.999983	D	0.54964	0.969	P	0.62885	0.908	T	0.01127	-1.1443	10	0.27082	T	0.32	-22.3486	9.647	0.39875	0.0:0.0852:0.0:0.9148	.	339	Q9HC36	RMTL1_HUMAN	D	339	ENSP00000306080:V339D	ENSP00000306080:V339D	V	+	2	0	RNMTL1	641812	0.891000	0.30450	0.999000	0.59377	0.470000	0.32858	4.270000	0.58896	2.212000	0.71576	0.482000	0.46254	GTT	T|0.984;A|0.016	0.016	strong		0.572	RNMTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206611.1	NM_018146	
STAG3	10734	hgsc.bcm.edu	37	7	99778227	99778227	+	Missense_Mutation	SNP	G	G	T	rs11531577	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99778227G>T	ENST00000426455.1	+	2	455	c.48G>T	c.(46-48)ttG>ttT	p.L16F	STAG3_ENST00000394018.2_Missense_Mutation_p.L16F|STAG3_ENST00000317296.5_Missense_Mutation_p.L16F	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	16					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGAGGGCCTTGTCTGCATCTT	0.522													G|||	519	0.103634	0.0212	0.1081	5008	,	,		19180	0.0595		0.2296	False		,,,				2504	0.1278				p.L16F		Atlas-SNP	.											.	STAG3	121	.	0			c.G48T						PASS	.	G	PHE/LEU	279,4127	154.4+/-187.8	9,261,1933	209.0	191.0	197.0		48	-0.5	0.0	7	dbSNP_120	197	2016,6584	352.7+/-328.8	234,1548,2518	no	missense	STAG3	NM_012447.2	22	243,1809,4451	TT,TG,GG		23.4419,6.3323,17.6457	benign	16/1226	99778227	2295,10711	2203	4300	6503	SO:0001583	missense	10734	exon2			GGCCTTGTCTGCA	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.48G>T	7.37:g.99778227G>T	ENSP00000400359:p.Leu16Phe	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	261	0.11950549450549451	16	0.032520325203252036	34	0.09392265193370165	32	0.055944055944055944	179	0.23614775725593667	G	10.12	1.262754	0.23051	0.063323	0.234419	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000416412;ENST00000339784;ENST00000317296;ENST00000422690;ENST00000439782	T;T;T	0.29142	1.84;1.58;1.84	4.56	-0.534	0.11883	.	.	.	.	.	T	0.00012	0.0000	N	0.16656	0.425	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.001	T	0.40459	-0.9562	8	0.09338	T	0.73	0.4101	4.0076	0.09608	0.184:0.0:0.3413:0.4747	rs11531577;rs12234198	16;16	B4DZ10;Q9UJ98	.;STAG3_HUMAN	F	16	ENSP00000400359:L16F;ENSP00000377586:L16F;ENSP00000319318:L16F	ENSP00000319318:L16F	L	+	3	2	STAG3	99616163	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-0.075000	0.11431	0.002000	0.14630	0.313000	0.20887	TTG	G|0.839;T|0.161	0.161	strong		0.522	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
HEXIM1	10614	hgsc.bcm.edu	37	17	43227214	43227214	+	Silent	SNP	T	T	C	rs1044977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:43227214T>C	ENST00000332499.2	+	1	2531	c.657T>C	c.(655-657)gaT>gaC	p.D219D	AC002117.1_ENST00000589950.1_RNA|AC002117.1_ENST00000452741.1_RNA	NM_006460.2	NP_006451.1	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	219	Autoinhibitory acidic region; in absence of 7SK snRNA interacts with the basic region preventing interaction with P-TEFb and modulating subcellular localization.				heart development (GO:0007507)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)			breast(1)|kidney(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AGGAGCCGGATCTCAAAACCG	0.617											OREG0024474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	995	0.198682	0.0477	0.196	5008	,	,		14687	0.2183		0.2734	False		,,,				2504	0.3078				p.D219D		Atlas-SNP	.											.	HEXIM1	25	.	0			c.T657C						PASS	.	T		337,4069	167.6+/-198.6	6,325,1872	44.0	48.0	46.0		657	-1.8	1.0	17	dbSNP_86	46	2093,6507	346.0+/-326.0	243,1607,2450	no	coding-synonymous	HEXIM1	NM_006460.2		249,1932,4322	CC,CT,TT		24.3372,7.6487,18.6837		219/360	43227214	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	10614	exon1			GCCGGATCTCAAA	AB021179	CCDS11495.1	17q21.31	2006-03-28				ENSG00000186834			24953	protein-coding gene	gene with protein product		607328				12119119, 12832472	Standard	NM_006460		Approved	CLP-1, HIS1, MAQ1, EDG1	uc002iig.3	O94992		ENST00000332499.2:c.657T>C	17.37:g.43227214T>C		Somatic	83	0	0	914	WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_006460	B2R8Y5	Silent	SNP	ENST00000332499.2	37	CCDS11495.1																																																																																			T|0.817;C|0.183	0.183	strong		0.617	HEXIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449821.2	NM_006460	
GOLGA2	2801	hgsc.bcm.edu	37	9	131019738	131019738	+	Missense_Mutation	SNP	T	T	C	rs2240961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131019738T>C	ENST00000421699.2	-	25	2716	c.2704A>G	c.(2704-2706)Aga>Gga	p.R902G	AL590708.1_ENST00000408370.1_RNA|GOLGA2_ENST00000609374.1_Missense_Mutation_p.R890G	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	902			R -> G (in dbSNP:rs2240961).		mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						GCCAGGAATCTGCCATGCCAC	0.642													T|||	820	0.163738	0.2368	0.1412	5008	,	,		14312	0.1954		0.0586	False		,,,				2504	0.1564				p.R902G		Atlas-SNP	.											.	GOLGA2	69	.	0			c.A2704G						PASS	.	T	GLY/ARG	1005,3401	371.5+/-320.0	123,759,1321	46.0	46.0	46.0		2704	3.6	0.0	9	dbSNP_98	46	483,8117	139.7+/-196.3	16,451,3833	yes	missense	GOLGA2	NM_004486.4	125	139,1210,5154	CC,CT,TT		5.6163,22.8098,11.4409	possibly-damaging	902/1003	131019738	1488,11518	2203	4300	6503	SO:0001583	missense	2801	exon25			GGAATCTGCCATG	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.2704A>G	9.37:g.131019738T>C	ENSP00000416097:p.Arg902Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Missense_Mutation	SNP	ENST00000421699.2	37	CCDS6896.2	316	0.1446886446886447	117	0.23780487804878048	42	0.11602209944751381	114	0.1993006993006993	43	0.05672823218997362	t	18.20	3.571833	0.65765	0.228098	0.056163	ENSG00000167110	ENST00000421699;ENST00000342583	T	0.27104	1.69	4.8	3.62	0.41486	.	0.176961	0.47852	D	0.000215	T	0.00012	0.0000	L	0.54323	1.7	0.31698	P	0.641061	D;P	0.58620	0.983;0.734	P;P	0.56042	0.79;0.576	T	0.07731	-1.0757	9	0.72032	D	0.01	.	11.4254	0.50007	0.0:0.0:0.1516:0.8484	rs2240961;rs16912726	902;520	Q08379;Q08379-2	GOGA2_HUMAN;.	G	902;186	ENSP00000416097:R902G	ENSP00000342692:R186G	R	-	1	2	GOLGA2	130059559	0.642000	0.27260	0.003000	0.11579	0.016000	0.09150	3.762000	0.55250	0.647000	0.30713	0.454000	0.30748	AGA	T|0.875;C|0.125	0.125	strong		0.642	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486	
C14orf182	283551	hgsc.bcm.edu	37	14	50472405	50472405	+	Missense_Mutation	SNP	G	G	A	rs6572635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50472405G>A	ENST00000399206.1	-	1	1833	c.113C>T	c.(112-114)cCg>cTg	p.P38L	C14orf182_ENST00000529902.1_5'UTR	NM_001012706.1	NP_001012724.1	A1A4T8	CN182_HUMAN	chromosome 14 open reading frame 182	38			P -> L (in dbSNP:rs6572635).							large_intestine(2)|urinary_tract(1)	3						AAGACCTCTCGGTTCGTGAAT	0.537													G|||	1481	0.295727	0.3873	0.317	5008	,	,		18805	0.124		0.2773	False		,,,				2504	0.3528				p.P38L		Atlas-SNP	.											C14orf182,bladder,carcinoma,+1,1	C14orf182	8	1	0			c.C113T						scavenged	.	G	LEU/PRO	1523,2561		289,945,808	269.0	286.0	281.0		113	1.7	0.0	14	dbSNP_116	281	2240,6136		301,1638,2249	yes	missense	C14orf182	NM_001012706.1	98	590,2583,3057	AA,AG,GG		26.7431,37.2919,30.2006	probably-damaging	38/108	50472405	3763,8697	2042	4188	6230	SO:0001583	missense	283551	exon1			CCTCTCGGTTCGT	AK090420	CCDS41949.1	14q22.1	2009-02-24			ENSG00000214900	ENSG00000214900			27503	protein-coding gene	gene with protein product							Standard	NM_001012706		Approved		uc001wxi.1	A1A4T8		ENST00000399206.1:c.113C>T	14.37:g.50472405G>A	ENSP00000382157:p.Pro38Leu	Somatic	239	2	0.0083682		WXS	Illumina HiSeq	Phase_I	293	148	0.505119	NM_001012706	A8MYX4	Missense_Mutation	SNP	ENST00000399206.1	37	CCDS41949.1	555	0.2541208791208791	165	0.3353658536585366	106	0.292817679558011	79	0.1381118881118881	205	0.2704485488126649	G	10.57	1.385916	0.25031	0.372919	0.267431	ENSG00000214900	ENST00000399206	T	0.62639	0.01	3.63	1.72	0.24424	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.36412	0.552	B	0.28916	0.096	T	0.29427	-1.0012	7	0.87932	D	0	.	4.3609	0.11201	0.1184:0.0:0.6603:0.2213	rs6572635;rs56709337;rs6572635	38	A1A4T8-2	.	L	38	ENSP00000382157:P38L	ENSP00000382157:P38L	P	-	2	0	C14orf182	49542155	0.050000	0.20438	0.004000	0.12327	0.014000	0.08584	0.925000	0.28791	0.492000	0.27815	-0.263000	0.10527	CCG	G|0.739;A|0.261	0.261	strong		0.537	C14orf182-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395717.1	NM_001012706	
ZNF354C	30832	hgsc.bcm.edu	37	5	178503472	178503472	+	Silent	SNP	C	C	T	rs116407910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178503472C>T	ENST00000315475.6	+	3	360	c.54C>T	c.(52-54)gcC>gcT	p.A18A		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	18	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		GGGATGTGGCCGTGTTCTTCA	0.552													C|||	11	0.00219649	0.0	0.0072	5008	,	,		17713	0.0		0.006	False		,,,				2504	0.0				p.A18A		Atlas-SNP	.											ZNF354C,NS,carcinoma,+2,1	ZNF354C	77	1	0			c.C54T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	173.0	153.0	160.0		54	-5.6	0.3	5	dbSNP_132	160	40,8560	26.8+/-75.7	0,40,4260	no	coding-synonymous	ZNF354C	NM_014594.1		0,44,6459	TT,TC,CC		0.4651,0.0908,0.3383		18/555	178503472	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	30832	exon3			TGTGGCCGTGTTC		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.54C>T	5.37:g.178503472C>T		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	287	164	0.571429	NM_014594	Q6P4P9|Q8NFX1	Silent	SNP	ENST00000315475.6	37	CCDS4443.1																																																																																			C|0.996;T|0.004	0.004	strong		0.552	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
SEPT12	124404	hgsc.bcm.edu	37	16	4833970	4833970	+	Silent	SNP	C	C	T	rs759991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4833970C>T	ENST00000268231.8	-	5	737	c.474G>A	c.(472-474)gtG>gtA	p.V158V	SEPT12_ENST00000591861.1_5'Flank|SEPT12_ENST00000396693.5_Intron	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	158	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.V158V(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						CGCAGCAGTGCACCCGGGTGT	0.642													C|||	1568	0.313099	0.1989	0.3559	5008	,	,		16641	0.2966		0.3131	False		,,,				2504	0.454				p.V158V		Atlas-SNP	.											SEPT12,NS,carcinoma,0,1	SEPT12	40	1	1	Substitution - coding silent(1)	stomach(1)	c.G474A						PASS	.	C	,	899,3495	346.9+/-309.2	95,709,1393	136.0	124.0	128.0		,474	1.4	1.0	16	dbSNP_86	128	2295,6305	385.5+/-341.5	307,1681,2312	no	intron,coding-synonymous	SEPT12	NM_001154458.2,NM_144605.4	,	402,2390,3705	TT,TC,CC		26.686,20.4597,24.5806	,	,158/359	4833970	3194,9800	2197	4300	6497	SO:0001819	synonymous_variant	124404	exon5			GCAGTGCACCCGG	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.474G>A	16.37:g.4833970C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	CCDS10522.1																																																																																			C|0.728;T|0.272	0.272	strong		0.642	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
UGT2B15	7366	hgsc.bcm.edu	37	4	69512847	69512847	+	Missense_Mutation	SNP	T	T	G	rs4148269	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69512847T>G	ENST00000338206.5	-	6	1577	c.1568A>C	c.(1567-1569)aAa>aCa	p.K523T		NM_001076.3	NP_001067.2	P54855	UDB15_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B15	523			K -> T (in dbSNP:rs4148269). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15618667, ECO:0000269|PubMed:7835232, ECO:0000269|PubMed:8399210, ECO:0000269|PubMed:9295060}.		cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)									Acetaminophen(DB00316)|Dabigatran etexilate(DB06695)|Ezetimibe(DB00973)|Lorazepam(DB00186)|Morphine(DB00295)|Oxazepam(DB00842)|Valproic Acid(DB00313)	CTTCTTTCCTTTTTTGGCAAG	0.393													g|||	1841	0.367612	0.1263	0.5029	5008	,	,		18726	0.1895		0.6362	False		,,,				2504	0.5051				p.K523T		Atlas-SNP	.											.	UGT2B15	48	.	0			c.A1568C						PASS	.	G	THR/LYS	989,3417		127,735,1341	130.0	134.0	133.0		1568	-0.3	0.0	4	dbSNP_110	133	5436,3154		1764,1908,623	no	missense	UGT2B15	NM_001076.2	78	1891,2643,1964	GG,GT,TT		36.7171,22.4467,49.4383	benign	523/531	69512847	6425,6571	2203	4295	6498	SO:0001583	missense	7366	exon6			TTTCCTTTTTTGG	AF180322	CCDS3524.1	4q13	2008-02-05	2005-07-20		ENSG00000196620	ENSG00000196620		"""UDP glucuronosyltransferases"""	12546	protein-coding gene	gene with protein product		600069	"""UDP glycosyltransferase 2 family, polypeptide B15"""			7835904	Standard	NM_001076		Approved	UGT2B8	uc021xow.1	P54855	OTTHUMG00000161507	ENST00000338206.5:c.1568A>C	4.37:g.69512847T>G	ENSP00000341045:p.Lys523Thr	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	284	284	1	NM_001076	A6NDX0|A6NNJ4|A8K054|P23765|Q9UK63	Missense_Mutation	SNP	ENST00000338206.5	37	CCDS3524.1	713	0.32646520146520147	50	0.1016260162601626	165	0.4558011049723757	83	0.1451048951048951	415	0.5474934036939314	N	0.429	-0.904425	0.02453	0.224467	0.632829	ENSG00000196620	ENST00000338206	T	0.60797	0.16	2.96	-0.317	0.12736	.	0.654479	0.13025	N	0.419785	T	0.00012	0.0000	N	0.11698	0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45352	-0.9267	9	0.18710	T	0.47	.	5.4944	0.16795	0.1049:0.0:0.4116:0.4835	.	523	P54855	UDB15_HUMAN	T	523	ENSP00000341045:K523T	ENSP00000341045:K523T	K	-	2	0	UGT2B15	69195442	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.153000	0.01287	-0.289000	0.09038	-0.231000	0.12243	AAA	T|0.588;G|0.412	0.412	strong		0.393	UGT2B15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365172.1	NM_001076	
PLEC	5339	hgsc.bcm.edu	37	8	145007187	145007187	+	Missense_Mutation	SNP	G	G	A	rs11136336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145007187G>A	ENST00000322810.4	-	14	2091	c.1922C>T	c.(1921-1923)gCc>gTc	p.A641V	PLEC_ENST00000354589.3_Missense_Mutation_p.A504V|PLEC_ENST00000357649.2_Missense_Mutation_p.A508V|PLEC_ENST00000356346.3_Missense_Mutation_p.A490V|PLEC_ENST00000398774.2_Missense_Mutation_p.A472V|PLEC_ENST00000345136.3_Missense_Mutation_p.A504V|PLEC_ENST00000527096.1_Missense_Mutation_p.A527V|PLEC_ENST00000436759.2_Missense_Mutation_p.A531V|PLEC_ENST00000354958.2_Missense_Mutation_p.A482V	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	641	Globular 1.		A -> V (in dbSNP:rs11136336).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AGTCACCTGGGCCACCTGGGT	0.672													G|||	1159	0.23143	0.0605	0.2867	5008	,	,		15300	0.1399		0.4066	False		,,,				2504	0.3374				p.A641V		Atlas-SNP	.											.	PLEC	1144	.	0			c.C1922T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	410,3576		24,362,1607	13.0	18.0	16.0		1511,1523,1511,1415,1922,1445,1469,1592	3.9	0.7	8	dbSNP_120	16	3151,5161		610,1931,1615	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_201384.1,NM_201383.1,NM_201382.2,NM_201381.1,NM_201380.2,NM_201379.1,NM_201378.2,NM_000445.3	64,64,64,64,64,64,64,64	634,2293,3222	AA,AG,GG		37.909,10.286,28.9559	benign,benign,benign,benign,benign,benign,benign,benign	504/4548,508/4552,504/4548,472/4516,641/4685,482/4526,490/4534,531/4575	145007187	3561,8737	1993	4156	6149	SO:0001583	missense	5339	exon14			ACCTGGGCCACCT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.1922C>T	8.37:g.145007187G>A	ENSP00000323856:p.Ala641Val	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	524	0.23992673992673993	28	0.056910569105691054	104	0.287292817679558	89	0.1555944055944056	303	0.3997361477572559	G	9.379	1.072611	0.20147	0.10286	0.37909	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096;ENST00000528025	T;T;T;T;T;T;T;T;T;D	0.90069	-1.03;-1.04;-1.06;-1.06;-1.05;-1.03;-1.03;-1.03;-1.03;-2.61	4.87	3.92	0.45320	.	0.283995	0.25801	U	0.028215	T	0.00012	0.0000	N	0.02539	-0.55	0.48571	P	3.2200000000004447E-4	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.08289	-1.0729	9	0.45353	T	0.12	.	7.8835	0.29635	0.0914:0.1662:0.7424:0.0	rs11136336;rs11136336	531;490;482;641;472;504;508;504	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	V	504;508;504;472;641;482;490;531;527;548	ENSP00000344848:A504V;ENSP00000350277:A508V;ENSP00000346602:A504V;ENSP00000381756:A472V;ENSP00000323856:A641V;ENSP00000347044:A482V;ENSP00000348702:A490V;ENSP00000388180:A531V;ENSP00000434583:A527V;ENSP00000437303:A548V	ENSP00000323856:A641V	A	-	2	0	PLEC	145079175	1.000000	0.71417	0.707000	0.30419	0.197000	0.23852	1.952000	0.40343	2.261000	0.74972	0.643000	0.83706	GCC	G|0.772;A|0.228	0.228	strong		0.672	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
TNXB	7148	hgsc.bcm.edu	37	6	32049423	32049423	+	Missense_Mutation	SNP	C	C	T	rs12211410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32049423C>T	ENST00000375244.3	-	10	3965	c.3764G>A	c.(3763-3765)cGc>cAc	p.R1255H	TNXB_ENST00000375247.2_Missense_Mutation_p.R1255H			P22105	TENX_HUMAN	tenascin XB	1342	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GAACTCAGGGCGGGGGGGCTC	0.637													C|||	495	0.0988419	0.1127	0.0389	5008	,	,		14173	0.0347		0.0994	False		,,,				2504	0.1881				p.R1255H		Atlas-SNP	.											.	TNXB	553	.	0			c.G3764A						PASS	.	C	HIS/ARG	352,3382		18,316,1533	11.0	12.0	12.0		3764	-2.7	0.0	6	dbSNP_120	12	722,7478		43,636,3421	yes	missense	TNXB	NM_019105.6	29	61,952,4954	TT,TC,CC		8.8049,9.4269,8.9995	benign	1255/4243	32049423	1074,10860	1867	4100	5967	SO:0001583	missense	7148	exon10			TCAGGGCGGGGGG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.3764G>A	6.37:g.32049423C>T	ENSP00000364393:p.Arg1255His	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	194	107	0.551546	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		189	0.08653846153846154	75	0.1524390243902439	11	0.03038674033149171	22	0.038461538461538464	81	0.10686015831134564	C	6.644	0.487243	0.12641	0.094269	0.088049	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.55930	0.66;0.49	3.95	-2.69	0.06022	.	1.641460	0.04049	N	0.304352	T	0.11239	0.0274	N	0.03948	-0.315	0.80722	P	0.0	B	0.12013	0.005	B	0.04013	0.001	T	0.14783	-1.0460	9	0.41790	T	0.15	.	9.1549	0.36988	0.0:0.2512:0.0:0.7488	rs12211410;rs52822791;rs12211410	1255	P22105-3	.	H	1255	ENSP00000364393:R1255H;ENSP00000364396:R1255H	ENSP00000364393:R1255H	R	-	2	0	TNXB	32157401	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-3.560000	0.00431	-0.548000	0.06199	-0.501000	0.04562	CGC	C|0.904;T|0.096	0.096	strong		0.637	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
LARS	51520	hgsc.bcm.edu	37	5	145523105	145523105	+	Silent	SNP	G	G	A	rs11540217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145523105G>A	ENST00000394434.2	-	19	1913	c.1747C>T	c.(1747-1749)Ctg>Ttg	p.L583L	LARS_ENST00000545646.1_Silent_p.L537L|LARS_ENST00000510191.1_Silent_p.L529L|LARS_ENST00000274562.9_Silent_p.L556L	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	583					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	TCCCAAGGCAGGTGAGTGCCT	0.413													A|||	910	0.181709	0.0076	0.3775	5008	,	,		15082	0.1984		0.2525	False		,,,				2504	0.1881				p.L583L		Atlas-SNP	.											.	LARS	100	.	0			c.C1747T						PASS	.	A		265,4141	802.3+/-415.7	12,241,1950	98.0	97.0	97.0		1747	-0.3	0.9	5	dbSNP_120	97	2397,6203	699.0+/-405.1	352,1693,2255	no	coding-synonymous	LARS	NM_020117.9		364,1934,4205	AA,AG,GG		27.8721,6.0145,20.4675		583/1177	145523105	2662,10344	2203	4300	6503	SO:0001819	synonymous_variant	51520	exon19			AAGGCAGGTGAGT	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.1747C>T	5.37:g.145523105G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	60	18	0.3	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			G|0.794;A|0.206	0.206	strong		0.413	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
MUC16	94025	hgsc.bcm.edu	37	19	9085643	9085643	+	Missense_Mutation	SNP	A	A	G	rs1574479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9085643A>G	ENST00000397910.4	-	1	6375	c.6172T>C	c.(6172-6174)Tct>Cct	p.S2058P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2058	Ser-rich.|Thr-rich.		S -> P (in dbSNP:rs1574479).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGGGAGAGATGTAGTGAGG	0.478													A|||	952	0.190096	0.0711	0.2709	5008	,	,		21856	0.3036		0.172	False		,,,				2504	0.1953				p.S2058P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T6172C						PASS	.	A	PRO/SER	290,3690		5,280,1705	167.0	160.0	162.0		6172	0.7	0.0	19	dbSNP_88	162	1488,6820		127,1234,2793	yes	missense	MUC16	NM_024690.2	74	132,1514,4498	GG,GA,AA		17.9104,7.2864,14.4694	possibly-damaging	2058/14508	9085643	1778,10510	1990	4154	6144	SO:0001583	missense	94025	exon1			GGAGAGATGTAGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6172T>C	19.37:g.9085643A>G	ENSP00000381008:p.Ser2058Pro	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	a	2.263	-0.368789	0.05069	0.072864	0.179104	ENSG00000181143	ENST00000397910	T	0.02709	4.19	0.731	0.731	0.18277	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	P	0.42518	0.782	P	0.46110	0.504	T	0.51236	-0.8731	8	0.87932	D	0	.	3.8785	0.09068	1.0:0.0:0.0:0.0	rs1574479;rs52797107;rs1574479	2058	B5ME49	.	P	2058	ENSP00000381008:S2058P	ENSP00000381008:S2058P	S	-	1	0	MUC16	8946643	0.002000	0.14202	0.010000	0.14722	0.067000	0.16453	0.031000	0.13710	0.598000	0.29829	0.246000	0.17985	TCT	A|0.810;G|0.190	0.190	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CALD1	800	hgsc.bcm.edu	37	7	134618710	134618710	+	Missense_Mutation	SNP	A	A	G	rs6973420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:134618710A>G	ENST00000361675.2	+	5	1419	c.1190A>G	c.(1189-1191)cAt>cGt	p.H397R	CALD1_ENST00000361388.2_Intron|CALD1_ENST00000417172.1_Intron|CALD1_ENST00000361901.2_Intron|CALD1_ENST00000393118.2_Intron|CALD1_ENST00000495522.1_Intron|CALD1_ENST00000543443.1_Intron|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000422748.1_Intron			Q05682	CALD1_HUMAN	caldesmon 1	397			H -> R (in dbSNP:rs6973420). {ECO:0000269|PubMed:1555769}.		cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						GAGAAAAAACATGCCATGCAA	0.428													G|||	2546	0.508387	0.4357	0.366	5008	,	,		21799	0.8581		0.4821	False		,,,				2504	0.3742				p.H397R		Atlas-SNP	.											.	CALD1	150	.	0			c.A1190G						PASS	.	G	,,,,ARG/HIS	1958,2448	620.6+/-393.6	451,1056,696	113.0	122.0	119.0		,,,,1190	-4.5	0.0	7	dbSNP_116	119	3900,4700	605.5+/-395.0	906,2088,1306	yes	intron,intron,intron,intron,missense	CALD1	NM_004342.6,NM_033139.3,NM_033140.3,NM_033157.3,NM_033138.3	,,,,29	1357,3144,2002	GG,GA,AA		45.3488,44.4394,45.0408	,,,,benign	,,,,397/794	134618710	5858,7148	2203	4300	6503	SO:0001583	missense	800	exon5			AAAAACATGCCAT	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.1190A>G	7.37:g.134618710A>G	ENSP00000354826:p.His397Arg	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	228	101	0.442982	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	37	CCDS5835.1	1206	0.5521978021978022	210	0.4268292682926829	139	0.3839779005524862	490	0.8566433566433567	367	0.4841688654353562	G	0.040	-1.287969	0.01387	0.444394	0.453488	ENSG00000122786	ENST00000361675	T	0.28069	1.63	4.15	-4.5	0.03493	.	2.361110	0.01783	N	0.031867	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25882	-1.0119	8	.	.	.	12.5912	6.3213	0.21219	0.3306:0.2473:0.4222:0.0	rs6973420;rs17803435;rs59805101;rs6973420	397	Q05682	CALD1_HUMAN	R	397	ENSP00000354826:H397R	.	H	+	2	0	CALD1	134269250	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.464000	0.02359	-1.211000	0.02624	-2.371000	0.00235	CAT	A|0.502;G|0.496	0.496	strong		0.428	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138	
MYH13	8735	hgsc.bcm.edu	37	17	10223793	10223793	+	Silent	SNP	C	C	T	rs35783712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10223793C>T	ENST00000418404.3	-	24	3295	c.3132G>A	c.(3130-3132)caG>caA	p.Q1044Q	RP11-401O9.3_ENST00000577743.1_RNA|RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Silent_p.Q1044Q			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1044					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						GTTTCTTCTCCTGCTCTAAGG	0.493													C|||	87	0.0173722	0.0023	0.0274	5008	,	,		16884	0.001		0.0567	False		,,,				2504	0.0072				p.Q1044Q		Atlas-SNP	.											.	MYH13	533	.	0			c.G3132A						PASS	.	C		36,3646		0,36,1805	50.0	47.0	48.0		3132	2.8	1.0	17	dbSNP_126	48	466,7714		7,452,3631	no	coding-synonymous	MYH13	NM_003802.2		7,488,5436	TT,TC,CC		5.6968,0.9777,4.232		1044/1939	10223793	502,11360	1841	4090	5931	SO:0001819	synonymous_variant	8735	exon25			CTTCTCCTGCTCT	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3132G>A	17.37:g.10223793C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			C|0.970;T|0.030	0.030	strong		0.493	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
CSMD1	64478	hgsc.bcm.edu	37	8	3072107	3072107	+	Silent	SNP	G	G	C	rs73183587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:3072107G>C	ENST00000520002.1	-	31	5337	c.4782C>G	c.(4780-4782)ggC>ggG	p.G1594G	CSMD1_ENST00000400186.3_Silent_p.G1594G|CSMD1_ENST00000539096.1_Silent_p.G1593G|CSMD1_ENST00000542608.1_Silent_p.G1593G|CSMD1_ENST00000537824.1_Silent_p.G1593G|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Silent_p.G1594G|CSMD1_ENST00000602557.1_Silent_p.G1594G			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1594	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GAATCTTATAGCCAGAGTCAC	0.517													G|||	342	0.0682907	0.0076	0.085	5008	,	,		16384	0.0317		0.1551	False		,,,				2504	0.0869				p.G1593G		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C4779G						PASS	.	G		95,3973		0,95,1939	88.0	87.0	87.0		4779	-2.4	1.0	8	dbSNP_130	87	1086,7288		70,946,3171	no	coding-synonymous	CSMD1	NM_033225.5		70,1041,5110	CC,CG,GG		12.9687,2.3353,9.492		1593/3565	3072107	1181,11261	2034	4187	6221	SO:0001819	synonymous_variant	64478	exon30			CTTATAGCCAGAG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4782C>G	8.37:g.3072107G>C		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	213	90	0.422535	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		176	0.08058608058608059	1	0.0020325203252032522	37	0.10220994475138122	22	0.038461538461538464	116	0.15303430079155672	G	7.377	0.628068	0.14257	0.023353	0.129687	ENSG00000183117	ENST00000335551	.	.	.	5.39	-2.39	0.06602	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26503	-1.0101	3	.	.	.	.	2.2472	0.04034	0.1512:0.2441:0.3767:0.2281	.	.	.	.	V	1074	.	.	L	-	1	2	CSMD1	3059514	1.000000	0.71417	0.997000	0.53966	0.754000	0.42855	0.594000	0.24014	-0.047000	0.13423	0.591000	0.81541	CTA	G|0.909;C|0.091	0.091	strong		0.517	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
POLE	5426	hgsc.bcm.edu	37	12	133253995	133253995	+	Missense_Mutation	SNP	G	G	A	rs5744751	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133253995G>A	ENST00000320574.5	-	8	798	c.755C>T	c.(754-756)gCt>gTt	p.A252V	POLE_ENST00000535270.1_Missense_Mutation_p.A225V	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	252			A -> V (in dbSNP:rs5744751).		base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	TACCGGAAAAGCATTTCCTCG	0.423								DNA polymerases (catalytic subunits)					G|||	285	0.0569089	0.0045	0.0447	5008	,	,		20247	0.1052		0.1004	False		,,,				2504	0.0419				p.A252V		Atlas-SNP	.											.	POLE	416	.	0			c.C755T						PASS	.	G	VAL/ALA	70,4336	64.7+/-102.0	0,70,2133	115.0	109.0	111.0		755	5.6	1.0	12	dbSNP_114	111	923,7677	205.5+/-247.9	59,805,3436	yes	missense	POLE	NM_006231.2	64	59,875,5569	AA,AG,GG		10.7326,1.5887,7.6349	benign	252/2287	133253995	993,12013	2203	4300	6503	SO:0001583	missense	5426	exon8			GGAAAAGCATTTC		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.755C>T	12.37:g.133253995G>A	ENSP00000322570:p.Ala252Val	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	158	56	0.35443	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	157	0.07188644688644688	2	0.0040650406504065045	20	0.055248618784530384	57	0.09965034965034965	78	0.10290237467018469	G	12.78	2.041642	0.35989	0.015887	0.107326	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577	T;T;T;T	0.09911	2.93;2.93;2.93;2.93	5.64	5.64	0.86602	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.113409	0.64402	D	0.000009	T	0.00178	0.0005	N	0.16166	0.38	0.21950	P	0.999454457	B;B	0.13145	0.005;0.007	B;B	0.19946	0.016;0.027	T	0.47289	-0.9129	9	0.27082	T	0.32	.	19.7069	0.96076	0.0:0.0:1.0:0.0	rs5744751;rs52830930;rs60851699;rs5744751	225;252	F5H1D6;Q07864	.;DPOE1_HUMAN	V	252;263;225;32;187	ENSP00000322570:A252V;ENSP00000406383:A263V;ENSP00000445753:A225V;ENSP00000442519:A32V	ENSP00000322570:A252V	A	-	2	0	POLE	131764068	1.000000	0.71417	0.957000	0.39632	0.028000	0.11728	5.457000	0.66672	2.654000	0.90174	0.563000	0.77884	GCT	G|0.928;A|0.072	0.072	strong		0.423	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
FAM171B	165215	hgsc.bcm.edu	37	2	187626338	187626338	+	Silent	SNP	C	C	T	rs13026081	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:187626338C>T	ENST00000304698.5	+	8	1472	c.1269C>T	c.(1267-1269)gaC>gaT	p.D423D		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	423						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						AAGCTGAGGACAAGTCGCAGT	0.373													C|||	828	0.165335	0.0113	0.232	5008	,	,		16751	0.0456		0.3171	False		,,,				2504	0.2935				p.D423D		Atlas-SNP	.											.	FAM171B	146	.	0			c.C1269T						PASS	.	C		252,4154	139.2+/-174.8	17,218,1968	98.0	102.0	101.0		1269	2.0	1.0	2	dbSNP_121	101	2618,5978	419.7+/-353.2	399,1820,2079	no	coding-synonymous	FAM171B	NM_177454.3		416,2038,4047	TT,TC,CC		30.456,5.7195,22.0735		423/827	187626338	2870,10132	2203	4298	6501	SO:0001819	synonymous_variant	165215	exon8			TGAGGACAAGTCG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1269C>T	2.37:g.187626338C>T		Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	258	117	0.453488	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Silent	SNP	ENST00000304698.5	37	CCDS33347.1																																																																																			C|0.809;N|0.000	.	strong		0.373	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
MYO18B	84700	hgsc.bcm.edu	37	22	26164408	26164408	+	Silent	SNP	C	C	G	rs575271363		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26164408C>G	ENST00000407587.2	+	4	694	c.525C>G	c.(523-525)gcC>gcG	p.A175A	MYO18B_ENST00000335473.7_Silent_p.A175A|MYO18B_ENST00000536101.1_Silent_p.A175A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	175						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CCCATGACGCCCCCCCTTGCA	0.597													c|||	1	0.000199681	0.0	0.0	5008	,	,		13166	0.0		0.0	False		,,,				2504	0.001				p.A175A		Atlas-SNP	.											.	MYO18B	322	.	0			c.C525G						PASS	.						21.0	25.0	24.0					22																	26164408		1966	4142	6108	SO:0001819	synonymous_variant	84700	exon4			TGACGCCCCCCCT	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.525C>G	22.37:g.26164408C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				.	.	none		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
SLC18A2	6571	hgsc.bcm.edu	37	10	119003546	119003546	+	Silent	SNP	G	G	A	rs11568722		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:119003546G>A	ENST00000298472.5	+	3	329	c.186G>A	c.(184-186)acG>acA	p.T62T	RP11-501J20.5_ENST00000425264.1_RNA|SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	62					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	AAATCCAGACGGCCAGGCCAG	0.498																																					p.T62T		Atlas-SNP	.											SLC18A2,NS,carcinoma,+1,1	SLC18A2	58	1	0			c.G186A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	88.0	76.0	80.0		186	-11.6	0.0	10	dbSNP_126	80	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	SLC18A2	NM_003054.4		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		62/515	119003546	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	6571	exon3			CCAGACGGCCAGG	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.186G>A	10.37:g.119003546G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	99	55	0.555556	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	37	CCDS7599.1																																																																																			G|1.000;A|0.000	0.000	weak		0.498	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
HCRTR1	3061	hgsc.bcm.edu	37	1	32092525	32092525	+	Missense_Mutation	SNP	A	A	G	rs2271933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:32092525A>G	ENST00000373706.5	+	7	1375	c.1222A>G	c.(1222-1224)Atc>Gtc	p.I408V	HCRTR1_ENST00000468521.1_Intron|HCRTR1_ENST00000403528.2_Missense_Mutation_p.I408V|HCRTR1_ENST00000373705.1_Intron			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1	408			I -> V (in dbSNP:rs2271933). {ECO:0000269|PubMed:11723285, ECO:0000269|PubMed:14702039}.		feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|orexin receptor activity (GO:0016499)|peptide hormone binding (GO:0017046)			breast(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		CCGATGCTCCATCTCCAAAAT	0.652													G|||	2202	0.439696	0.2753	0.5086	5008	,	,		17417	0.244		0.6332	False		,,,				2504	0.6155				p.I408V		Atlas-SNP	.											HCRTR1,caecum,carcinoma,0,1	HCRTR1	20	1	0			c.A1222G	GRCh37	CM056598	HCRTR1	M	rs2271933	scavenged	.	G	VAL/ILE	1364,3042	689.8+/-405.2	202,960,1041	106.0	105.0	106.0		1222	3.8	1.0	1	dbSNP_100	106	5281,3319	494.6+/-373.8	1643,1995,662	yes	missense	HCRTR1	NM_001525.2	29	1845,2955,1703	GG,GA,AA		38.593,30.9578,48.9082	benign	408/426	32092525	6645,6361	2203	4300	6503	SO:0001583	missense	3061	exon9			TGCTCCATCTCCA	AF041243	CCDS344.1	1p33	2012-08-08			ENSG00000121764	ENSG00000121764		"""GPCR / Class A : Hypocretin (orexin) receptors"""	4848	protein-coding gene	gene with protein product		602392				9491897	Standard	NM_001525		Approved	OX1R	uc009vtx.2	O43613	OTTHUMG00000003876	ENST00000373706.5:c.1222A>G	1.37:g.32092525A>G	ENSP00000362810:p.Ile408Val	Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	NM_001525	A8K3A6|Q9HBV6	Missense_Mutation	SNP	ENST00000373706.5	37	CCDS344.1	939	0.42994505494505497	127	0.258130081300813	192	0.5303867403314917	148	0.25874125874125875	472	0.6226912928759895	G	0.922	-0.715416	0.03206	0.309578	0.61407	ENSG00000121764	ENST00000403528;ENST00000373706	T;T	0.58797	0.31;0.31	4.7	3.78	0.43462	.	0.156920	0.41938	N	0.000795	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45644	-0.9247	9	0.02654	T	1	.	8.2159	0.31511	0.1904:0.0:0.8096:0.0	rs2271933;rs17444652;rs59309008;rs2271933	408	O43613	OX1R_HUMAN	V	408	ENSP00000384387:I408V;ENSP00000362810:I408V	ENSP00000362810:I408V	I	+	1	0	HCRTR1	31865112	0.962000	0.33011	0.965000	0.40720	0.914000	0.54420	1.595000	0.36708	0.690000	0.31570	-0.735000	0.03563	ATC	A|0.531;G|0.469	0.469	strong		0.652	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	NM_001525	
TRIM31	11074	hgsc.bcm.edu	37	6	30078330	30078330	+	Silent	SNP	C	C	T	rs2239529	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30078330C>T	ENST00000376734.3	-	4	764	c.639G>A	c.(637-639)gcG>gcA	p.A213A	TRIM31_ENST00000540829.1_Silent_p.A213A|TRIM31_ENST00000485864.1_5'UTR|TRIM31-AS1_ENST00000440874.1_RNA	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	213					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						AGTGTTTCCCCGCTTCCGTTC	0.512													C|||	317	0.0632987	0.0121	0.1138	5008	,	,		19102	0.0486		0.1193	False		,,,				2504	0.0542				p.A213A		Atlas-SNP	.											TRIM31,trunk,malignant_melanoma,-2,2	TRIM31	40	2	0			c.G639A						PASS	.	C		161,4245	107.3+/-145.7	5,151,2047	192.0	172.0	179.0		639	-2.6	0.0	6	dbSNP_98	179	1207,7393	243.9+/-273.3	75,1057,3168	yes	coding-synonymous	TRIM31	NM_007028.3		80,1208,5215	TT,TC,CC		14.0349,3.6541,10.5182		213/426	30078330	1368,11638	2203	4300	6503	SO:0001819	synonymous_variant	11074	exon4			TTTCCCCGCTTCC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.639G>A	6.37:g.30078330C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	233	109	0.467811	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			C|0.907;T|0.093	0.093	strong		0.512	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
AGT	183	hgsc.bcm.edu	37	1	230845977	230845977	+	Missense_Mutation	SNP	G	G	A	rs4762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:230845977G>A	ENST00000366667.4	-	2	834	c.620C>T	c.(619-621)aCg>aTg	p.T207M	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	207			T -> M (associated with hypertension; dbSNP:rs4762). {ECO:0000269|PubMed:1394429}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCCCACCACCGTGGACAGCAG	0.662													G|||	509	0.101637	0.0545	0.1268	5008	,	,		19740	0.1071		0.1302	False		,,,				2504	0.1125				p.T207M		Atlas-SNP	.											.	AGT	62	.	0			c.C620T	GRCh37	CM920009	AGT	M	rs4762	PASS	.	G	MET/THR	291,4115	151.8+/-185.6	13,265,1925	32.0	33.0	33.0		620	4.1	0.8	1	dbSNP_52	33	1130,7470	222.9+/-259.8	71,988,3241	yes	missense	AGT	NM_000029.3	81	84,1253,5166	AA,AG,GG		13.1395,6.6046,10.9257	probably-damaging	207/486	230845977	1421,11585	2203	4300	6503	SO:0001583	missense	183	exon2			ACCACCGTGGACA	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"""Serine (or cysteine) peptidase inhibitors"", ""Endogenous ligands"""	333	protein-coding gene	gene with protein product	"""alpha-1 antiproteinase, antitrypsin"""	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.620C>T	1.37:g.230845977G>A	ENSP00000355627:p.Thr207Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	227	0.10393772893772894	17	0.034552845528455285	45	0.12430939226519337	58	0.10139860139860139	107	0.14116094986807387	G	11.57	1.679313	0.29783	0.066046	0.131395	ENSG00000135744	ENST00000366667	D	0.84223	-1.82	5.01	4.08	0.47627	Serpin domain (3);	0.157526	0.56097	D	0.000038	T	0.05960	0.0155	M	0.66939	2.045	0.26682	P	0.9715215	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.997	T	0.65364	-0.6186	9	0.72032	D	0.01	.	4.3912	0.11341	0.081:0.121:0.5566:0.2414	rs4762;rs3182294;rs16852387;rs52830531;rs60395225;rs4762	207;207;207	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	M	207	ENSP00000355627:T207M	ENSP00000355627:T207M	T	-	2	0	AGT	228912600	0.992000	0.36948	0.834000	0.33040	0.033000	0.12548	2.300000	0.43620	1.201000	0.43203	0.591000	0.81541	ACG	G|0.900;A|0.100	0.100	strong		0.662	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
PCNXL3	399909	hgsc.bcm.edu	37	11	65384727	65384727	+	Silent	SNP	C	C	T	rs12790427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65384727C>T	ENST00000355703.3	+	3	887	c.348C>T	c.(346-348)ccC>ccT	p.P116P		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	116						integral component of membrane (GO:0016021)		p.P116P(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CCAGGGACCCCGGAGTGGAGA	0.542													C|||	1482	0.295927	0.2648	0.4236	5008	,	,		20205	0.4226		0.1968	False		,,,				2504	0.2188				p.P116P		Atlas-SNP	.											PCNXL3_ENST00000355703,NS,carcinoma,0,1	PCNXL3	140	1	1	Substitution - coding silent(1)	stomach(1)	c.C348T						PASS	.	C		958,3066		117,724,1171	35.0	38.0	37.0		348	-4.4	1.0	11	dbSNP_121	37	1638,6686		156,1326,2680	no	coding-synonymous	PCNXL3	NM_032223.2		273,2050,3851	TT,TC,CC		19.678,23.8072,21.0236		116/2035	65384727	2596,9752	2012	4162	6174	SO:0001819	synonymous_variant	399909	exon3			GGACCCCGGAGTG	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.348C>T	11.37:g.65384727C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			C|0.719;T|0.281	0.281	strong		0.542	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
TCEB3B	51224	hgsc.bcm.edu	37	18	44561619	44561619	+	Missense_Mutation	SNP	G	G	C	rs61738602	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44561619G>C	ENST00000332567.4	-	1	369	c.17C>G	c.(16-18)aCt>aGt	p.T6S	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	6	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GTGCAGCGTAGTGGACCCTGC	0.617													g|||	190	0.0379393	0.0499	0.0418	5008	,	,		16517	0.0069		0.0835	False		,,,				2504	0.0041				p.T6S		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C17G						PASS	.	C	SER/THR,	263,4141		9,245,1948	49.0	48.0	48.0		17,	-0.4	0.0	18	dbSNP_129	48	621,7977		28,565,3706	no	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	58,	37,810,5654	CC,CG,GG		7.2226,5.9718,6.799	possibly-damaging,	6/754,	44561619	884,12118	2202	4299	6501	SO:0001583	missense	51224	exon1			AGCGTAGTGGACC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.17C>G	18.37:g.44561619G>C	ENSP00000331302:p.Thr6Ser	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	121	0.0554029304029304	32	0.06504065040650407	17	0.04696132596685083	6	0.01048951048951049	66	0.0870712401055409	g	0.001	-3.777083	0.00004	0.059718	0.072226	ENSG00000206181	ENST00000332567	T	0.05025	3.51	0.195	-0.39	0.12450	Transcription factor IIS, N-terminal (2);	14.105800	0.01474	N	0.016384	T	0.00073	0.0002	N	0.00788	-1.185	0.80722	P	0.0	B	0.15141	0.012	B	0.08055	0.003	T	0.36601	-0.9741	8	0.02654	T	1	1.0064	.	.	.	rs61738602	6	Q8IYF1	ELOA2_HUMAN	S	6	ENSP00000331302:T6S	ENSP00000331302:T6S	T	-	2	0	TCEB3B	42815617	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.886000	0.01619	-2.617000	0.00442	-2.620000	0.00156	ACT	C|0.074;G|0.926;T|0.000	0.074	strong		0.617	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418260	105418260	+	Silent	SNP	T	T	A	rs56330864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105418260T>A	ENST00000333244.5	-	7	3647	c.3528A>T	c.(3526-3528)tcA>tcT	p.S1176S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1176						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGCCTGGGGCTGACGCCCCGA	0.612													.|||	39	0.00778754	0.0023	0.0101	5008	,	,		18682	0.001		0.0189	False		,,,				2504	0.0092				p.S1176S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A3528T						PASS	.	T		640,3216		101,438,1389	165.0	165.0	165.0		3528	-8.8	0.0	14	dbSNP_129	165	4427,3805		1384,1659,1073	no	coding-synonymous	AHNAK2	NM_138420.2		1485,2097,2462	AA,AT,TT		46.2221,16.5975,41.9176		1176/5796	105418260	5067,7021	1928	4116	6044	SO:0001819	synonymous_variant	113146	exon7			TGGGGCTGACGCC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3528A>T	14.37:g.105418260T>A		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	337	202	0.599407	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.617;C|0.006;T|0.377	0.617	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MTUS1	57509	hgsc.bcm.edu	37	8	17503612	17503612	+	Silent	SNP	C	C	G	rs61733704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17503612C>G	ENST00000262102.6	-	15	3860	c.3636G>C	c.(3634-3636)tcG>tcC	p.S1212S	MTUS1_ENST00000519263.1_Silent_p.S1158S|MTUS1_ENST00000381869.3_Silent_p.S1158S|MTUS1_ENST00000297488.6_Silent_p.S378S|MTUS1_ENST00000381861.3_Silent_p.S459S|MTUS1_ENST00000544260.1_Silent_p.S357S|MTUS1_ENST00000400046.1_Silent_p.S284S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1212					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		CCTTCTCCAGCGACTCTTGCA	0.448													C|||	77	0.0153754	0.0015	0.0115	5008	,	,		14078	0.0		0.0388	False		,,,				2504	0.0286				p.S1212S		Atlas-SNP	.											.	MTUS1	144	.	0			c.G3636C						PASS	.	C	,,,,	21,3729		0,21,1854	38.0	39.0	39.0		3636,3474,1377,1071,1134	-8.9	0.0	8	dbSNP_129	39	329,7903		2,325,3789	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2,NM_001001931.2,NM_001166393.1,NM_020749.4	,,,,	2,346,5643	GG,GC,CC		3.9966,0.56,2.921	,,,,	1212/1271,1158/1217,459/518,357/416,378/437	17503612	350,11632	1875	4116	5991	SO:0001819	synonymous_variant	57509	exon15			CTCCAGCGACTCT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.3636G>C	8.37:g.17503612C>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			C|0.956;G|0.044	0.044	strong		0.448	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
ASCC3	10973	hgsc.bcm.edu	37	6	101296389	101296389	+	Missense_Mutation	SNP	G	G	A	rs9390698	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:101296389G>A	ENST00000369162.2	-	4	780	c.436C>T	c.(436-438)Ctt>Ttt	p.L146F	ASCC3_ENST00000522650.1_Missense_Mutation_p.L146F	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	146			L -> F (in dbSNP:rs9390698). {ECO:0000269|PubMed:17974005}.		cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.L146F(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AGAGCAGTAAGATCATCTTGA	0.368													G|||	1229	0.245407	0.0628	0.415	5008	,	,		20467	0.2331		0.4493	False		,,,				2504	0.1748				p.L146F		Atlas-SNP	.											ASCC3,NS,carcinoma,0,1	ASCC3	205	1	1	Substitution - Missense(1)	stomach(1)	c.C436T						PASS	.	G	PHE/LEU	638,3768	272.2+/-270.6	53,532,1618	64.0	57.0	59.0		436	5.0	1.0	6	dbSNP_119	59	3920,4680	545.3+/-384.8	913,2094,1293	yes	missense	ASCC3	NM_006828.2	22	966,2626,2911	AA,AG,GG		45.5814,14.4803,35.0454	possibly-damaging	146/2203	101296389	4558,8448	2203	4300	6503	SO:0001583	missense	10973	exon4			CAGTAAGATCATC	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.436C>T	6.37:g.101296389G>A	ENSP00000358159:p.Leu146Phe	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	141	51	0.361702	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	666	0.30494505494505497	36	0.07317073170731707	131	0.36187845303867405	153	0.2674825174825175	346	0.45646437994722955	G	13.66	2.302375	0.40694	0.144803	0.455814	ENSG00000112249	ENST00000369162;ENST00000522650;ENST00000324723	T;T;T	0.59224	0.37;0.28;0.7	5.85	4.97	0.65823	.	0.069655	0.64402	D	0.000013	T	0.42337	0.1198	L	0.59436	1.845	0.09310	P	1.0	B;B;B	0.19583	0.037;0.037;0.001	B;B;B	0.17433	0.018;0.018;0.004	T	0.46345	-0.9198	9	0.51188	T	0.08	.	16.8624	0.86021	0.0:0.1284:0.8715:0.0	rs9390698;rs17616305;rs52799794;rs9390698	146;146;146	Q4G1A0;E7EW23;Q8N3C0	.;.;HELC1_HUMAN	F	146	ENSP00000358159:L146F;ENSP00000430769:L146F;ENSP00000320777:L146F	ENSP00000320777:L146F	L	-	1	0	ASCC3	101403110	0.999000	0.42202	0.987000	0.45799	0.995000	0.86356	2.523000	0.45580	1.438000	0.47492	0.655000	0.94253	CTT	G|0.688;A|0.312	0.312	strong		0.368	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
MCM7	4176	hgsc.bcm.edu	37	7	99693078	99693078	+	Silent	SNP	G	G	A	rs12267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99693078G>A	ENST00000303887.5	-	12	2256	c.1611C>T	c.(1609-1611)atC>atT	p.I537I	MIR25_ENST00000384816.1_RNA|MIR93_ENST00000385024.1_RNA|MCM7_ENST00000343023.6_Intron|MIR106B_ENST00000385301.1_RNA|MCM7_ENST00000354230.3_Silent_p.I361I	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	537	Interaction with RAD17.|MCM.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCACATAGGTGATGTGCTGGG	0.577													G|||	1302	0.259984	0.0628	0.3545	5008	,	,		18118	0.4048		0.2565	False		,,,				2504	0.3139				p.I537I		Atlas-SNP	.											.	MCM7	136	.	0			c.C1611T						PASS	.	G	,	429,3977	207.2+/-228.6	20,389,1794	56.0	46.0	50.0		1611,1083	4.4	1.0	7	dbSNP_52	50	2124,6476	360.0+/-331.8	275,1574,2451	no	coding-synonymous,coding-synonymous	MCM7	NM_005916.3,NM_182776.1	,	295,1963,4245	AA,AG,GG		24.6977,9.7367,19.6294	,	537/720,361/544	99693078	2553,10453	2203	4300	6503	SO:0001819	synonymous_variant	4176	exon12			ATAGGTGATGTGC		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 104"""	600592	"""minichromosome maintenance deficient (S. cerevisiae) 7"", ""MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"""	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1611C>T	7.37:g.99693078G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Silent	SNP	ENST00000303887.5	37	CCDS5683.1																																																																																			G|0.778;A|0.222	0.222	strong		0.577	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3		
KIAA0408	9729	hgsc.bcm.edu	37	6	127768472	127768472	+	Missense_Mutation	SNP	G	G	A	rs2236026	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:127768472G>A	ENST00000483725.3	-	5	1328	c.992C>T	c.(991-993)tCg>tTg	p.S331L	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	331			S -> L (in dbSNP:rs2236026).							endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		ACCATCTTTCGAAGTTTTCCC	0.418													g|||	1094	0.21845	0.0227	0.304	5008	,	,		20780	0.6835		0.0855	False		,,,				2504	0.0798				p.S331L		Atlas-SNP	.											.	KIAA0408	61	.	0			c.C992T						PASS	.	G	,LEU/SER	135,4271	96.7+/-135.4	1,133,2069	124.0	119.0	120.0		,992	1.3	0.9	6	dbSNP_98	120	660,7940	167.5+/-219.3	30,600,3670	yes	utr-3,missense	KIAA0408,C6orf174	NM_001012279.2,NM_014702.4	,145	31,733,5739	AA,AG,GG		7.6744,3.064,6.1126	,benign	,331/695	127768472	795,12211	2203	4300	6503	SO:0001583	missense	9729	exon5			TCTTTCGAAGTTT	AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.992C>T	6.37:g.127768472G>A	ENSP00000435150:p.Ser331Leu	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	150	93	0.62	NM_014702	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Missense_Mutation	SNP	ENST00000483725.3	37	CCDS34531.1	542	0.24816849816849818	14	0.028455284552845527	85	0.23480662983425415	384	0.6713286713286714	59	0.07783641160949868	g	0.007	-1.937173	0.00484	0.03064	0.076744	ENSG00000189367	ENST00000483725	T	0.25749	1.78	5.23	1.28	0.21552	.	0.670270	0.11331	N	0.575017	T	0.01092	0.0036	N	0.00182	-1.905	0.51012	P	9.199999999998099E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.47058	-0.9146	9	0.06099	T	0.92	4.0E-4	5.3764	0.16168	0.5996:0.2392:0.1613:0.0	rs2236026;rs52805967;rs57655122;rs2236026	331	Q6ZU52	K0408_HUMAN	L	331	ENSP00000435150:S331L	ENSP00000435150:S331L	S	-	2	0	KIAA0408	127810165	0.979000	0.34478	0.905000	0.35620	0.039000	0.13416	1.004000	0.29822	0.309000	0.22966	-0.285000	0.09966	TCG	G|0.855;A|0.145	0.145	strong		0.418	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702	
PERP	64065	hgsc.bcm.edu	37	6	138413333	138413333	+	Missense_Mutation	SNP	G	G	C	rs648802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138413333G>C	ENST00000421351.3	-	3	598	c.428C>G	c.(427-429)cCt>cGt	p.P143R		NM_022121.4	NP_071404.2	Q96FX8	PERP_HUMAN	PERP, TP53 apoptosis effector	143			P -> R (in dbSNP:rs648802). {ECO:0000269|PubMed:12752121, ECO:0000269|PubMed:16303743}.		activation of cysteine-type endopeptidase activity (GO:0097202)|amelogenesis (GO:0097186)|desmosome organization (GO:0002934)|heterotypic cell-cell adhesion (GO:0034113)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of proteolysis (GO:0045862)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(1)|lung(1)|prostate(1)	5	Breast(32;0.0799)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000878)|OV - Ovarian serous cystadenocarcinoma(155;0.000997)		AGTGACAGCAGGGTTGGCATG	0.507													G|||	3161	0.63119	0.5507	0.5274	5008	,	,		19485	0.7222		0.5775	False		,,,				2504	0.7751				p.P143R		Atlas-SNP	.											.	PERP	15	.	0			c.C428G						PASS	.	G	ARG/PRO	2339,2067	606.9+/-390.8	626,1087,490	94.0	90.0	91.0		428	-2.6	0.0	6	dbSNP_83	91	4745,3855	609.1+/-395.5	1309,2127,864	yes	missense	PERP	NM_022121.4	103	1935,3214,1354	CC,CG,GG		44.8256,46.9133,45.5328	possibly-damaging	143/194	138413333	7084,5922	2203	4300	6503	SO:0001583	missense	64065	exon3			ACAGCAGGGTTGG	AF317550	CCDS5188.1	6q24	2014-04-29			ENSG00000112378	ENSG00000112378			17637	protein-coding gene	gene with protein product	"""keratinocyte associated protein 1"""	609301				11062687	Standard	NM_022121		Approved	PIGPC1, dJ496H19.1, KCP1, THW, KRTCAP1	uc003qht.2	Q96FX8	OTTHUMG00000015668	ENST00000421351.3:c.428C>G	6.37:g.138413333G>C	ENSP00000397157:p.Pro143Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_022121	B2RB73|E1P590|Q8IWS3|Q8N1J6|Q8NC16|Q9H1C5|Q9H230	Missense_Mutation	SNP	ENST00000421351.3	37	CCDS5188.1	1262	0.5778388278388278	254	0.516260162601626	195	0.5386740331491713	384	0.6713286713286714	429	0.5659630606860159	G	5.215	0.225135	0.09916	0.530867	0.551744	ENSG00000112378	ENST00000421351;ENST00000265603	D	0.88975	-2.45	5.1	-2.56	0.06268	.	1.226220	0.05769	N	0.606299	T	0.56140	0.1965	N	0.22421	0.69	0.80722	P	0.0	B	0.20550	0.046	B	0.22601	0.04	T	0.48790	-0.9004	9	0.11182	T	0.66	0.2946	2.0754	0.03623	0.3902:0.122:0.3634:0.1244	rs648802;rs17090835;rs52818511;rs60547415;rs648802	143	Q96FX8	PERP_HUMAN	R	143;125	ENSP00000397157:P143R	ENSP00000265603:P125R	P	-	2	0	PERP	138455026	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-0.125000	0.10579	-0.508000	0.06540	0.561000	0.74099	CCT	G|0.435;C|0.565	0.565	strong		0.507	PERP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042423.2	NM_022121	
OR51A2	401667	hgsc.bcm.edu	37	11	4976447	4976447	+	Missense_Mutation	SNP	C	C	G	rs77497717	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4976447C>G	ENST00000380371.1	-	1	496	c.497G>C	c.(496-498)aGa>aCa	p.R166T	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTCAAGCTTCTTAAAGTGAA	0.418													C|||	435	0.086861	0.112	0.0865	5008	,	,		14020	0.0069		0.1243	False		,,,				2504	0.0971				p.R166T		Atlas-SNP	.											.	OR51A2	40	.	0			c.G497C						PASS	.		THR/ARG	642,3510		222,198,1656	152.0	132.0	139.0		497	-0.6	0.0	11	dbSNP_131	139	1811,6107		680,451,2828	no	missense	OR51A2	NM_001004748.1	71	902,649,4484	GG,GC,CC		22.8719,15.4624,20.3231	possibly-damaging	166/314	4976447	2453,9617	2076	3959	6035	SO:0001583	missense	401667	exon1			AAGCTTCTTAAAG	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.497G>C	11.37:g.4976447C>G	ENSP00000369729:p.Arg166Thr	Somatic	543	0	0		WXS	Illumina HiSeq	Phase_I	384	345	0.898438	NM_001004748		Missense_Mutation	SNP	ENST00000380371.1	37	CCDS31368.1	213	0.09752747252747253	40	0.08130081300813008	46	0.1270718232044199	3	0.005244755244755245	124	0.16358839050131926	-	7.414	0.635312	0.14322	0.154624	0.228719	ENSG00000205496	ENST00000380371	T	0.71817	-0.6	3.13	-0.611	0.11601	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.45051	1.395	0.80722	P	0.0	B	0.23249	0.082	B	0.24701	0.055	T	0.09400	-1.0676	8	0.66056	D	0.02	.	7.4986	0.27505	0.0:0.3281:0.0:0.6719	.	166	Q8NGJ7	O51A2_HUMAN	T	166	ENSP00000369729:R166T	ENSP00000369729:R166T	R	-	2	0	OR51A2	4933023	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-2.709000	0.00819	0.017000	0.15025	-0.512000	0.04463	AGA	C|0.897;G|0.103	0.103	strong		0.418	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
VARS2	57176	hgsc.bcm.edu	37	6	30882634	30882634	+	Silent	SNP	C	C	T	rs1264302	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30882634C>T	ENST00000321897.5	+	1	653	c.21C>T	c.(19-21)gcC>gcT	p.A7A	VARS2_ENST00000542001.1_Intron|VARS2_ENST00000416670.2_Silent_p.A7A|VARS2_ENST00000541562.1_Silent_p.A37A			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	7					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TGCCTCTCGCCTCTTTTCGAC	0.562													C|||	1112	0.222045	0.0983	0.2075	5008	,	,		19658	0.247		0.3559	False		,,,				2504	0.2362				p.A37A		Atlas-SNP	.											.	VARS2	60	.	0			c.C111T						PASS	.	C	,,	439,2579		33,373,1103	52.0	57.0	55.0		,111,21	-0.9	0.0	6	dbSNP_87	55	2036,3380		362,1312,1034	no	intron,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	395,1685,2137	TT,TC,CC		37.5923,14.5461,29.3455	,,	,37/1094,7/1064	30882634	2475,5959	1509	2708	4217	SO:0001819	synonymous_variant	57176	exon2			TCTCGCCTCTTTT	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.21C>T	6.37:g.30882634C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	76	0.608	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			C|0.733;T|0.267	0.267	strong		0.562	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
ARSD	414	hgsc.bcm.edu	37	X	2836060	2836060	+	Silent	SNP	G	G	A	rs113318393		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836060G>A	ENST00000381154.1	-	5	723	c.648C>T	c.(646-648)gcC>gcT	p.A216A	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	216					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGGTCTGGCCGGCAGCCAGGG	0.652																																					p.A216A		Atlas-SNP	.											.	ARSD	47	.	0			c.C648T						PASS	.						16.0	20.0	18.0					X																	2836060		2201	4294	6495	SO:0001819	synonymous_variant	414	exon5			CTGGCCGGCAGCC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.648C>T	X.37:g.2836060G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			G|0.930;A|0.070	0.070	strong		0.652	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
PALB2	79728	hgsc.bcm.edu	37	16	23646191	23646191	+	Missense_Mutation	SNP	T	T	C	rs152451|rs587780206	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23646191T>C	ENST00000261584.4	-	4	1828	c.1676A>G	c.(1675-1677)cAa>cGa	p.Q559R		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	559	DNA-binding (with the preference D loop > dsDNA > ssDNA).		Q -> R (in dbSNP:rs152451). {ECO:0000269|PubMed:21618343}.		DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		ACCTTTCACTTGAATAAATAA	0.348			"""F, N, Mis"""			"""Wilms tumor, medulloblastoma, AML ,breast"""		Involved in tolerance or repair of DNA crosslinks					C|||	755	0.150759	0.2405	0.0908	5008	,	,		15292	0.1786		0.0934	False		,,,				2504	0.1022				p.Q559R		Atlas-SNP	.	yes	Rec		"""Fanconi anaemia N, breast cancer susceptibility """	16	16p12.1	79728	partner and localizer of BRCA2		"""L, O, E"""	.	PALB2	108	.	0			c.A1676G						PASS	.	C	ARG/GLN	970,3424	730.4+/-410.2	103,764,1330	62.0	55.0	58.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1676	-2.7	0.0	16	dbSNP_79	58	782,7818	782.1+/-407.6	36,710,3554	yes	missense	PALB2	NM_024675.3	43	139,1474,4884	CC,CT,TT		9.093,22.0756,13.4831	benign	559/1187	23646191	1752,11242	2197	4300	6497	SO:0001583	missense	79728	exon4			TTCACTTGAATAA		CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"""Fanconi anemia, complementation groups"""	26144	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group N"""	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.1676A>G	16.37:g.23646191T>C	ENSP00000261584:p.Gln559Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	320	0.14652014652014653	114	0.23170731707317074	29	0.08011049723756906	104	0.18181818181818182	73	0.09630606860158311	C	0.029	-1.346517	0.01266	0.220756	0.09093	ENSG00000083093	ENST00000261584	T	0.14640	2.49	4.55	-2.73	0.05950	.	2.630300	0.01492	N	0.017104	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35276	-0.9795	9	0.02654	T	1	1.0893	5.6066	0.17383	0.0:0.2275:0.4044:0.3682	rs152451;rs463585;rs3743974	559	Q86YC2	PALB2_HUMAN	R	559	ENSP00000261584:Q559R	ENSP00000261584:Q559R	Q	-	2	0	PALB2	23553692	0.011000	0.17503	0.001000	0.08648	0.003000	0.03518	0.401000	0.20948	-0.613000	0.05694	-1.082000	0.02213	CAA	T|0.856;C|0.144	0.144	strong		0.348	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497914	32497914	+	Missense_Mutation	SNP	C	C	T	rs76748970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32497914C>T	ENST00000374975.3	-	1	150	c.88G>A	c.(88-90)Ggg>Agg	p.G30R		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CGGGTGTCCCCAGCCAAAGCC	0.547																																					p.G30R		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.G88A						PASS	.						103.0	105.0	104.0					6																	32497914		2203	4300	6503	SO:0001583	missense	3127	exon1			TGTCCCCAGCCAA		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.88G>A	6.37:g.32497914C>T	ENSP00000364114:p.Gly30Arg	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	376	115	0.305851	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	404	0.184981684981685	40	0.08130081300813008	78	0.2154696132596685	126	0.2202797202797203	160	0.21108179419525067	.	5.421	0.262764	0.10294	.	.	ENSG00000198502	ENST00000374975	T	0.00220	8.52	4.54	2.07	0.26955	MHC classes I/II-like antigen recognition protein (1);	1.862590	0.02449	N	0.085362	T	0.00039	0.0001	N	0.03903	-0.33	0.80722	P	0.0	B	0.15719	0.014	B	0.25987	0.065	T	0.12016	-1.0564	9	0.02654	T	1	.	5.9769	0.19385	0.0:0.2201:0.0:0.7799	.	30	Q30154	DRB5_HUMAN	R	30	ENSP00000364114:G30R	ENSP00000364114:G30R	G	-	1	0	HLA-DRB5	32605892	0.227000	0.23707	0.001000	0.08648	0.062000	0.15995	0.527000	0.22987	0.253000	0.21552	-0.350000	0.07774	GGG	C|0.842;T|0.158	0.158	strong		0.547	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
ST6GALNAC1	55808	hgsc.bcm.edu	37	17	74625686	74625686	+	Missense_Mutation	SNP	A	A	G	rs8077382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74625686A>G	ENST00000156626.7	-	2	438	c.239T>C	c.(238-240)gTg>gCg	p.V80A	ST6GALNAC1_ENST00000590878.1_5'UTR	NM_018414.3	NP_060884.1	Q9NSC7	SIA7A_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	80			V -> A (in dbSNP:rs8077382). {ECO:0000269|PubMed:12975309}.		oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	22						GTTCTCTGGCACTGGCTCTGC	0.577													G|||	398	0.0794728	0.1392	0.062	5008	,	,		18833	0.001		0.0924	False		,,,				2504	0.0787				p.V80A		Atlas-SNP	.											.	ST6GALNAC1	42	.	0			c.T239C						PASS	.	G	ALA/VAL	600,3806	770.8+/-413.8	41,518,1644	165.0	146.0	152.0		239	-7.4	0.0	17	dbSNP_116	152	856,7744	780.5+/-407.7	39,778,3483	yes	missense	ST6GALNAC1	NM_018414.3	64	80,1296,5127	GG,GA,AA		9.9535,13.6178,11.1948	benign	80/601	74625686	1456,11550	2203	4300	6503	SO:0001583	missense	55808	exon2			TCTGGCACTGGCT	Y11339	CCDS11748.1	17q25.3	2013-03-01	2005-02-07	2005-02-07	ENSG00000070526	ENSG00000070526		"""Sialyltransferases"""	23614	protein-coding gene	gene with protein product		610138	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) A"""	SIAT7A			Standard	NM_001289107		Approved	ST6GalNAcI	uc002jsh.3	Q9NSC7	OTTHUMG00000180369	ENST00000156626.7:c.239T>C	17.37:g.74625686A>G	ENSP00000156626:p.Val80Ala	Somatic	552	0	0		WXS	Illumina HiSeq	Phase_I	556	553	0.994604	NM_018414	Q6UW90|Q9NSC6	Missense_Mutation	SNP	ENST00000156626.7	37	CCDS11748.1	156	0.07142857142857142	55	0.11178861788617886	26	0.0718232044198895	0	0.0	75	0.09894459102902374	G	0.015	-1.552182	0.00918	0.136178	0.099535	ENSG00000070526	ENST00000156626;ENST00000359088	T;T	0.23147	1.96;1.92	3.72	-7.44	0.01379	.	.	.	.	.	T	0.00039	0.0001	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.19128	-1.0315	8	0.07325	T	0.83	0.9285	3.5529	0.07853	0.3065:0.1162:0.4618:0.1155	rs8077382;rs52828162;rs60500971;rs8077382	80	Q9NSC7	SIA7A_HUMAN	A	80	ENSP00000156626:V80A;ENSP00000351991:V80A	ENSP00000156626:V80A	V	-	2	0	ST6GALNAC1	72137281	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-4.894000	0.00173	-2.119000	0.00827	-3.716000	0.00023	GTG	A|0.898;G|0.102	0.102	strong		0.577	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450974.1	NM_018414	
ALK	238	hgsc.bcm.edu	37	2	29940529	29940529	+	Silent	SNP	A	A	T	rs2246745	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29940529A>T	ENST00000389048.3	-	2	1608	c.702T>A	c.(700-702)ccT>ccA	p.P234P	ALK_ENST00000431873.1_Silent_p.P234P	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	234					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GAGAAGGAGAAGGCATGTTTG	0.408			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				A|||	2951	0.589257	0.1513	0.6902	5008	,	,		20442	0.7827		0.7913	False		,,,				2504	0.7025				p.P234P		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,NS,carcinoma,-1,1	ALK	533	1	0			c.T702A						PASS	.	A		1172,3234	409.7+/-335.1	157,858,1188	165.0	142.0	150.0		702	1.8	0.9	2	dbSNP_100	150	6983,1617	742.8+/-407.2	2840,1303,157	no	coding-synonymous	ALK	NM_004304.4		2997,2161,1345	TT,TA,AA		18.8023,26.6001,37.2982		234/1621	29940529	8155,4851	2203	4300	6503	SO:0001819	synonymous_variant	238	exon2	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AGGAGAAGGCATG	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.702T>A	2.37:g.29940529A>T		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	247	247	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			A|0.355;T|0.645	0.645	strong		0.408	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
ZNRF1	84937	hgsc.bcm.edu	37	16	75146357	75146357	+	IGR	SNP	T	T	G	rs372986804		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:75146357T>G	ENST00000335325.4	+	0	4620				LDHD_ENST00000450168.2_Missense_Mutation_p.Q451P|LDHD_ENST00000300051.4_Missense_Mutation_p.Q474P|RP11-252E2.1_ENST00000499110.1_RNA	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase						proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						CTGCAGCAGCTGCCGCTTGCC	0.667																																					p.Q474P		Atlas-SNP	.											.	LDHD	34	.	0			c.A1421C						PASS	.	T	PRO/GLN,PRO/GLN	0,4396		0,0,2198	27.0	28.0	28.0		1421,1352	4.2	1.0	16		28	2,8598		0,2,4298	no	missense,missense	LDHD	NM_153486.3,NM_194436.2	76,76	0,2,6496	GG,GT,TT		0.0233,0.0,0.0154	benign,benign	474/508,451/485	75146357	2,12994	2198	4300	6498	SO:0001628	intergenic_variant	197257	exon11			AGCAGCTGCCGCT	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"""RING-type (C3HC4) zinc fingers"""	18452	protein-coding gene	gene with protein product		612060	"""zinc and ring finger 1"""				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606		16.37:g.75146357T>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_153486	D3DUJ9|Q9H083	Missense_Mutation	SNP	ENST00000335325.4	37	CCDS10912.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.636542	0.47049	0.0	2.33E-4	ENSG00000166816	ENST00000450168;ENST00000300051	D;D	0.87179	-2.22;-2.22	5.27	4.16	0.48862	Vanillyl-alcohol oxidase, C-terminal subdomain 2 (1);FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.450708	0.22902	N	0.054258	T	0.79741	0.4498	N	0.13003	0.285	0.30172	N	0.801213	P;P	0.41546	0.579;0.754	B;P	0.48089	0.43;0.566	T	0.74275	-0.3718	10	0.33141	T	0.24	-16.5283	6.5485	0.22420	0.2656:0.0:0.138:0.5963	.	451;474	Q86WU2-2;Q86WU2	.;LDHD_HUMAN	P	451;474	ENSP00000417011:Q451P;ENSP00000300051:Q474P	ENSP00000300051:Q474P	Q	-	2	0	LDHD	73703858	0.800000	0.28916	1.000000	0.80357	0.974000	0.67602	1.415000	0.34748	0.821000	0.34540	0.460000	0.39030	CAG	.	.	weak		0.667	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2		
PLD1	5337	hgsc.bcm.edu	37	3	171404478	171404478	+	Missense_Mutation	SNP	C	C	A	rs2290480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:171404478C>A	ENST00000351298.4	-	16	1990	c.1864G>T	c.(1864-1866)Gct>Tct	p.A622S	PLD1_ENST00000356327.5_Intron|PLD1_ENST00000340989.4_Missense_Mutation_p.A622S|PLD1_ENST00000342215.6_Intron	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	622	Catalytic.		A -> S (in dbSNP:rs2290480).		chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	TACTTACCAGCATGAGGTCTA	0.438													C|||	829	0.165535	0.1384	0.1052	5008	,	,		17750	0.13		0.1988	False		,,,				2504	0.2474				p.A622S	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											PLD1,NS,carcinoma,0,2	PLD1	134	2	0			c.G1864T						PASS	.	C	,SER/ALA	564,3842	252.4+/-258.8	34,496,1673	132.0	136.0	135.0		,1864	-8.8	0.0	3	dbSNP_100	135	1762,6838	319.1+/-314.0	195,1372,2733	yes	intron,missense	PLD1	NM_001130081.2,NM_002662.4	,99	229,1868,4406	AA,AC,CC		20.4884,12.8007,17.8841	,benign	,622/1075	171404478	2326,10680	2203	4300	6503	SO:0001583	missense	5337	exon16			TACCAGCATGAGG	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1864G>T	3.37:g.171404478C>A	ENSP00000342793:p.Ala622Ser	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	245	97	0.395918	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	37	CCDS3216.1	326	0.14926739926739926	65	0.13211382113821138	42	0.11602209944751381	67	0.11713286713286714	152	0.20052770448548812	C	6.267	0.417295	0.11870	0.128007	0.204884	ENSG00000075651	ENST00000351298;ENST00000340989	T;T	0.06528	3.43;3.29	5.46	-8.81	0.00813	.	3.181240	0.00582	N	0.000327	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38950	-0.9637	9	0.07482	T	0.82	.	9.5572	0.39346	0.095:0.3045:0.0:0.6005	rs2290480;rs2290480	622	Q13393	PLD1_HUMAN	S	622	ENSP00000342793:A622S;ENSP00000340326:A622S	ENSP00000340326:A622S	A	-	1	0	PLD1	172887172	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-3.644000	0.00405	-2.053000	0.00901	0.557000	0.71058	GCT	C|0.841;A|0.159	0.159	strong		0.438	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
IDO2	169355	hgsc.bcm.edu	37	8	39840234	39840234	+	Missense_Mutation	SNP	A	A	G	rs4736794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:39840234A>G	ENST00000389060.4	+	4	379	c.379A>G	c.(379-381)Atc>Gtc	p.I127V	IDO2_ENST00000343295.4_3'UTR|IDO2_ENST00000502986.2_Missense_Mutation_p.I140V|RP11-44K6.3_ENST00000517623.1_RNA			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	127					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						GCTCCCTCCTATCCTGGTCCA	0.463													A|||	800	0.159744	0.0227	0.2118	5008	,	,		17762	0.3343		0.1014	False		,,,				2504	0.1881				p.I140V		Atlas-SNP	.											.	IDO2	78	.	0			c.A418G						PASS	.	A	VAL/ILE	115,3659		3,109,1775	66.0	66.0	66.0		418	5.3	1.0	8	dbSNP_111	66	780,7436		28,724,3356	yes	missense	IDO2	NM_194294.2	29	31,833,5131	GG,GA,AA		9.4937,3.0472,7.4646	probably-damaging	140/421	39840234	895,11095	1887	4108	5995	SO:0001583	missense	169355	exon5			CCTCCTATCCTGG	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.379A>G	8.37:g.39840234A>G	ENSP00000426447:p.Ile127Val	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	127	43	0.338583	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		358	0.16391941391941392	10	0.02032520325203252	67	0.1850828729281768	207	0.3618881118881119	74	0.09762532981530343	A	20.8	4.056992	0.76074	0.030472	0.094937	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.41758	0.99;0.99	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.37850	1.14	0.25863	P	0.9838042	D	0.76494	0.999	D	0.83275	0.996	T	0.38757	-0.9646	8	.	.	.	.	11.6398	0.51227	1.0:0.0:0.0:0.0	rs4736794;rs52790922;rs57148239;rs4736794	140	F5H5G0	.	V	140;127	ENSP00000443432:I140V;ENSP00000426447:I127V	.	I	+	1	0	IDO2	39959391	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	6.903000	0.75703	2.009000	0.58944	0.377000	0.23210	ATC	A|0.845;G|0.155	0.155	strong		0.463	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145273366	145273366	+	Nonsense_Mutation	SNP	C	C	T	rs140871032	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145273366C>T	ENST00000369340.3	+	4	664	c.220C>T	c.(220-222)Cga>Tga	p.R74*	RP11-458D21.5_ENST00000468030.1_Nonsense_Mutation_p.R74*|NOTCH2NL_ENST00000344859.3_Nonsense_Mutation_p.R74*|NOTCH2NL_ENST00000362074.6_Nonsense_Mutation_p.R74*			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	74	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.R74*(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						CTTTGTGTCTCGACCTTGCCT	0.547																																					p.R74X		Atlas-SNP	.											NOTCH2NL_ENST00000362074,NS,haematopoietic_neoplasm,0,2	NOTCH2NL	100	2	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C220T						PASS	.	C	stop/ARG	30,4376	27.2+/-55.0	0,30,2173	503.0	457.0	473.0		220	2.8	0.8	1	dbSNP_134	473	104,8496	44.9+/-103.4	0,104,4196	no	stop-gained	NOTCH2NL	NM_203458.3		0,134,6369	TT,TC,CC		1.2093,0.6809,1.0303		74/237	145273366	134,12872	2203	4300	6503	SO:0001587	stop_gained	388677	exon3			GTGTCTCGACCTT		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.220C>T	1.37:g.145273366C>T	ENSP00000358346:p.Arg74*	Somatic	1988	1	0.000503018		WXS	Illumina HiSeq	Phase_I	2315	385	0.166307	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Nonsense_Mutation	SNP	ENST00000369340.3	37	CCDS909.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373173	0.82573	0.006809	0.012093	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	.	.	.	2.75	2.75	0.32379	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	11.2552	0.49050	0.0:1.0:0.0:0.0	.	.	.	.	X	74	.	ENSP00000344557:R74X	R	+	1	2	NOTCH2NL	143984723	0.982000	0.34865	0.838000	0.33150	0.100000	0.18952	5.568000	0.67385	1.532000	0.49169	0.394000	0.25966	CGA	C|0.964;T|0.036	0.036	strong		0.547	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458	
OR51I1	390063	hgsc.bcm.edu	37	11	5461930	5461930	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5461930G>A	ENST00000380211.1	-	1	814	c.815C>T	c.(814-816)cCt>cTt	p.P272L	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	272					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGAACAACAGGTGGAGCACT	0.473																																					p.P272L		Atlas-SNP	.											OR51I1,neck,malignant_melanoma,0,1	OR51I1	66	1	0			c.C815T						scavenged	.						143.0	125.0	131.0					11																	5461930		2201	4297	6498	SO:0001583	missense	390063	exon1			ACAACAGGTGGAG	BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"""GPCR / Class A : Olfactory receptors"""	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.815C>T	11.37:g.5461930G>A	ENSP00000369559:p.Pro272Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	158	3	0.0189873	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.405321	0.25378	.	.	ENSG00000167359	ENST00000321307;ENST00000380211	T	0.00207	8.55	5.47	1.22	0.21188	GPCR, rhodopsin-like superfamily (1);	0.841724	0.10412	N	0.677770	T	0.00178	0.0005	L	0.53780	1.695	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.45041	-0.9288	10	0.62326	D	0.03	.	1.4672	0.02408	0.1648:0.1432:0.3975:0.2945	.	272	Q9H343	O51I1_HUMAN	L	269;272	ENSP00000369559:P272L	ENSP00000439622:P269L	P	-	2	0	OR51I1	5418506	0.000000	0.05858	0.666000	0.29783	0.673000	0.39480	0.025000	0.13577	0.667000	0.31107	0.551000	0.68910	CCT	.	.	none		0.473	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288	
UGGT2	55757	hgsc.bcm.edu	37	13	96555149	96555149	+	Missense_Mutation	SNP	C	C	T	rs33949518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:96555149C>T	ENST00000376747.3	-	21	2531	c.2461G>A	c.(2461-2463)Gct>Act	p.A821T		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	821			A -> T (in dbSNP:rs33949518). {ECO:0000269|PubMed:10694380}.		cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						GAGTAAATAGCTGTAGCAATT	0.328													C|||	576	0.115016	0.1399	0.1167	5008	,	,		17475	0.0526		0.1819	False		,,,				2504	0.0757				p.A821T		Atlas-SNP	.											.	UGGT2	127	.	0			c.G2461A						PASS	.	C	THR/ALA	604,3798	256.7+/-261.4	43,518,1640	93.0	101.0	99.0		2461	4.8	1.0	13	dbSNP_126	99	1397,7199	268.2+/-287.7	123,1151,3024	yes	missense	UGGT2	NM_020121.3	58	166,1669,4664	TT,TC,CC		16.2517,13.721,15.3947	benign	821/1517	96555149	2001,10997	2201	4298	6499	SO:0001583	missense	55757	exon21			AAATAGCTGTAGC	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.2461G>A	13.37:g.96555149C>T	ENSP00000365938:p.Ala821Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	292	0.1336996336996337	77	0.1565040650406504	57	0.1574585635359116	25	0.043706293706293704	133	0.17546174142480211	C	12.92	2.081586	0.36758	0.13721	0.162517	ENSG00000102595	ENST00000376747	T	0.08634	3.07	5.66	4.81	0.61882	.	0.435762	0.25408	N	0.030896	T	0.00039	0.0001	M	0.76328	2.33	0.24946	P	0.99182671	B	0.20887	0.049	B	0.19946	0.027	T	0.28839	-1.0031	9	0.15952	T	0.53	-15.4287	12.3074	0.54910	0.1409:0.7379:0.1212:0.0	rs33949518;rs58131245;rs33949518	821	Q9NYU1	UGGG2_HUMAN	T	821	ENSP00000365938:A821T	ENSP00000365938:A821T	A	-	1	0	UGGT2	95353150	1.000000	0.71417	0.992000	0.48379	0.826000	0.46750	2.713000	0.47194	1.384000	0.46424	-0.172000	0.13284	GCT	C|0.858;T|0.142	0.142	strong		0.328	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
IMPDH1	3614	hgsc.bcm.edu	37	7	128038555	128038555	+	Silent	SNP	C	C	G	rs2288550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128038555C>G	ENST00000480861.1	-	7	794	c.717G>C	c.(715-717)ctG>ctC	p.L239L	IMPDH1_ENST00000419067.2_Silent_p.L296L|IMPDH1_ENST00000354269.5_Silent_p.L319L|IMPDH1_ENST00000343214.4_Silent_p.L219L|IMPDH1_ENST00000378717.4_Silent_p.L260L|IMPDH1_ENST00000470772.1_Silent_p.L243L|IMPDH1_ENST00000338791.6_Silent_p.L329L|IMPDH1_ENST00000496200.1_Silent_p.L219L|IMPDH1_ENST00000348127.6_Silent_p.L293L	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						CCCCACAGAGCAGCTGCTTCT	0.607											OREG0018292	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	652	0.130192	0.0537	0.1023	5008	,	,		18094	0.121		0.1789	False		,,,				2504	0.2127				p.L329L		Atlas-SNP	.											.	IMPDH1	38	.	0			c.G987C						PASS	.	C	,,,,,,	337,4069	171.6+/-201.8	11,315,1877	57.0	63.0	61.0		987,957,732,717,657,888,879	3.5	1.0	7	dbSNP_100	61	1469,7131	266.4+/-286.7	115,1239,2946	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IMPDH1	NM_000883.3,NM_001102605.1,NM_001142573.1,NM_001142574.1,NM_001142575.1,NM_001142576.1,NM_183243.2	,,,,,,	126,1554,4823	GG,GC,CC		17.0814,7.6487,13.8859	,,,,,,	329/600,319/590,244/515,239/510,219/490,296/567,293/564	128038555	1806,11200	2203	4300	6503	SO:0001819	synonymous_variant	3614	exon10			ACAGAGCAGCTGC		CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"""retinitis pigmentosa 10 (autosomal dominant)"", ""IMP (inosine monophosphate) dehydrogenase 1"""	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.717G>C	7.37:g.128038555C>G		Somatic	144	0	0	1561	WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_000883		Silent	SNP	ENST00000480861.1	37	CCDS55161.1																																																																																			C|0.868;G|0.132	0.132	strong		0.607	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883	
PDPR	55066	hgsc.bcm.edu	37	16	70172890	70172890	+	Missense_Mutation	SNP	C	C	T	rs112617700		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70172890C>T	ENST00000288050.4	+	11	2236	c.1279C>T	c.(1279-1281)Cgc>Tgc	p.R427C	PDPR_ENST00000398122.3_Missense_Mutation_p.R327C|PDPR_ENST00000568530.1_Missense_Mutation_p.R427C|PDPR_ENST00000562100.1_3'UTR	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	427					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)	p.R427C(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		CCAGAGCAGCCGCACCTTTCT	0.512																																					p.R427C		Atlas-SNP	.											PDPR,colon,carcinoma,-1,2	PDPR	66	2	1	Substitution - Missense(1)	stomach(1)	c.C1279T						scavenged	.						20.0	21.0	21.0					16																	70172890		1801	4043	5844	SO:0001583	missense	55066	exon11			AGCAGCCGCACCT		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1279C>T	16.37:g.70172890C>T	ENSP00000288050:p.Arg427Cys	Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	290	55	0.189655	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	287	0.13141025641025642	69	0.1402439024390244	43	0.11878453038674033	51	0.08916083916083917	124	0.16358839050131926	C	29.1	4.978510	0.92982	.	.	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	D;D	0.85773	-2.03;-2.03	4.42	4.42	0.53409	.	0.119515	0.64402	D	0.000017	T	0.03136	0.0092	M	0.77406	2.37	0.80722	D	1	D;D	0.89917	1.0;0.998	P;P	0.56216	0.794;0.676	T	0.26087	-1.0113	10	0.72032	D	0.01	.	16.0044	0.80349	0.0:1.0:0.0:0.0	.	155;427	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	C	427;327;155	ENSP00000288050:R427C;ENSP00000381190:R327C	ENSP00000205055:R155C	R	+	1	0	PDPR	68730391	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	7.645000	0.83430	1.985000	0.57927	0.455000	0.32223	CGC	C|0.870;T|0.130	0.130	strong		0.512	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
CBX2	84733	hgsc.bcm.edu	37	17	77758653	77758653	+	Missense_Mutation	SNP	C	C	G	rs141957173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:77758653C>G	ENST00000310942.4	+	5	1515	c.1411C>G	c.(1411-1413)Ccc>Gcc	p.P471A		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	471					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GGACTCCGACCCCGACTCCGC	0.667													C|||	6	0.00119808	0.0	0.0	5008	,	,		15360	0.0		0.006	False		,,,				2504	0.0				p.P471A		Atlas-SNP	.											.	CBX2	50	.	0			c.C1411G						PASS	.	C	ALA/PRO	3,4403	6.2+/-15.9	0,3,2200	38.0	36.0	37.0		1411	5.4	1.0	17	dbSNP_134	37	87,8513	47.6+/-106.9	0,87,4213	yes	missense	CBX2	NM_005189.2	27	0,90,6413	GG,GC,CC		1.0116,0.0681,0.692	possibly-damaging	471/533	77758653	90,12916	2203	4300	6503	SO:0001583	missense	84733	exon5			TCCGACCCCGACT	BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.1411C>G	17.37:g.77758653C>G	ENSP00000308750:p.Pro471Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_005189	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	9.419	1.082569	0.20309	6.81E-4	0.010116	ENSG00000173894	ENST00000310942	.	.	.	5.45	5.45	0.79879	.	1.949320	0.02055	N	0.050337	T	0.46347	0.1388	L	0.36672	1.1	0.80722	D	1	B	0.34015	0.435	B	0.27262	0.078	T	0.30208	-0.9986	9	0.54805	T	0.06	13.4368	14.9645	0.71182	0.1433:0.8567:0.0:0.0	.	471	Q14781	CBX2_HUMAN	A	471	.	ENSP00000308750:P471A	P	+	1	0	CBX2	75373248	1.000000	0.71417	0.987000	0.45799	0.018000	0.09664	5.777000	0.68931	2.568000	0.86640	0.650000	0.86243	CCC	C|0.996;G|0.004	0.004	strong		0.667	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
ADH4	127	hgsc.bcm.edu	37	4	100045616	100045616	+	Splice_Site	SNP	C	C	T	rs1126673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100045616C>T	ENST00000265512.7	-	9	1194	c.1120G>A	c.(1120-1122)Gtc>Atc	p.V374I	ADH4_ENST00000505590.1_Splice_Site_p.V393I|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000508393.1_Splice_Site_p.V393I|ADH4_ENST00000423445.1_Splice_Site_p.V393I	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	374			V -> I (in dbSNP:rs1126673). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		ATTGTTCGGACGCTGTTAATA	0.318													C|||	4243	0.847244	0.8608	0.7709	5008	,	,		16198	0.999		0.6978	False		,,,				2504	0.8804				p.V374I		Atlas-SNP	.											.	ADH4	35	.	0			c.G1120A						PASS	.	C	ILE/VAL	3623,781	729.6+/-410.1	1487,649,66	32.0	33.0	33.0		1120	0.6	1.0	4	dbSNP_86	33	5868,2728	666.1+/-402.3	1986,1896,416	yes	missense-near-splice	ADH4	NM_000670.3	29	3473,2545,482	TT,TC,CC		31.7357,17.7339,26.9923	benign	374/381	100045616	9491,3509	2202	4298	6500	SO:0001630	splice_region_variant	127	exon9			TTCGGACGCTGTT	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"""Alcohol dehydrogenases"""	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.1119-1G>A	4.37:g.100045616C>T		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	208	208	1	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	37	CCDS34032.1	1792	0.8205128205128205	414	0.8414634146341463	274	0.7569060773480663	572	1.0	532	0.7018469656992085	C	0.007	-1.995442	0.00435	0.822661	0.682643	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590	T;T;T;T	0.02916	4.11;4.11;4.11;4.11	3.16	0.629	0.17687	GroES-like (1);	0.170390	0.35525	N	0.003142	T	0.00012	0.0000	N	0.02751	-0.505	0.49213	P	2.3099999999998122E-4	B;B	0.11235	0.004;0.0	B;B	0.08055	0.003;0.001	T	0.30794	-0.9966	9	0.02654	T	1	-3.5331	3.5916	0.07990	0.0:0.1249:0.2267:0.6484	rs1126673;rs1540055;rs3181820;rs17410005;rs17856657;rs52807892;rs57345384;rs1126673	393;374	P08319-2;P08319	.;ADH4_HUMAN	I	393;374;393;393	ENSP00000424630:V393I;ENSP00000265512:V374I;ENSP00000397939:V393I;ENSP00000425416:V393I	ENSP00000265512:V374I	V	-	1	0	ADH4	100264639	0.998000	0.40836	0.985000	0.45067	0.282000	0.26991	0.511000	0.22739	0.133000	0.18654	-0.294000	0.09567	GTC	C|0.225;T|0.775	0.775	strong		0.318	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	Missense_Mutation
ZNF45	7596	hgsc.bcm.edu	37	19	44418693	44418693	+	Missense_Mutation	SNP	T	T	C	rs388706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44418693T>C	ENST00000269973.5	-	10	1985	c.895A>G	c.(895-897)Act>Gct	p.T299A	ZNF45_ENST00000589703.1_Missense_Mutation_p.T299A|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	299			T -> A (in dbSNP:rs388706). {ECO:0000269|PubMed:15057824}.		gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						TTCTTTCCAGTGTGAACTTTC	0.463													C|||	2631	0.525359	0.3336	0.6499	5008	,	,		21442	0.7996		0.5169	False		,,,				2504	0.4223				p.T299A		Atlas-SNP	.											.	ZNF45	51	.	0			c.A895G						PASS	.	C	ALA/THR	1578,2828	666.6+/-401.7	293,992,918	92.0	78.0	83.0		895	-2.2	0.0	19	dbSNP_80	83	4351,4249	573.5+/-389.9	1118,2115,1067	yes	missense	ZNF45	NM_003425.3	58	1411,3107,1985	CC,CT,TT		49.407,35.8148,45.5867	benign	299/683	44418693	5929,7077	2203	4300	6503	SO:0001583	missense	7596	exon10			TTCCAGTGTGAAC	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"""Zinc fingers, C2H2-type"", ""-"""	13111	protein-coding gene	gene with protein product		194554	"""zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)"", ""zinc finger protein 13"""	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.895A>G	19.37:g.44418693T>C	ENSP00000269973:p.Thr299Ala	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	1255	0.5746336996336996	187	0.3800813008130081	209	0.5773480662983426	470	0.8216783216783217	389	0.5131926121372031	C	2.197	-0.383998	0.04966	0.358148	0.50593	ENSG00000124459	ENST00000269973;ENST00000328762	T	0.26518	1.73	3.07	-2.16	0.07080	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	2.708020	0.01708	N	0.027547	T	0.00012	0.0000	L	0.47078	1.49	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.48490	-0.9031	9	0.52906	T	0.07	5.6738	6.2967	0.21089	0.1154:0.2785:0.0:0.6061	rs388706;rs17712977;rs52790068;rs61572009;rs388706	299	Q02386	ZNF45_HUMAN	A	299	ENSP00000269973:T299A	ENSP00000269973:T299A	T	-	1	0	ZNF45	49110533	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.211000	0.09332	-1.254000	0.02485	-2.985000	0.00079	ACT	T|0.488;C|0.512	0.512	strong		0.463	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
CR2	1380	hgsc.bcm.edu	37	1	207648173	207648173	+	Silent	SNP	T	T	C	rs61735651	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207648173T>C	ENST00000367058.3	+	13	2340	c.2151T>C	c.(2149-2151)atT>atC	p.I717I	CR2_ENST00000367057.3_Silent_p.I776I|CR2_ENST00000367059.3_Silent_p.I717I|CR2_ENST00000458541.2_Silent_p.I690I	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	717	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CTGCAGTTATTCACTGTCACC	0.413													T|||	317	0.0632987	0.1203	0.0447	5008	,	,		19682	0.001		0.0865	False		,,,				2504	0.0399				p.I776I		Atlas-SNP	.											.	CR2	164	.	0			c.T2328C						PASS	.	T	,	429,3973		30,369,1802	76.0	84.0	81.0		2328,2151	2.3	0.4	1	dbSNP_129	81	899,7701		39,821,3440	no	coding-synonymous,coding-synonymous	CR2	NM_001006658.2,NM_001877.4	,	69,1190,5242	CC,CT,TT		10.4535,9.7456,10.2138	,	776/1093,717/1034	207648173	1328,11674	2201	4300	6501	SO:0001819	synonymous_variant	1380	exon14			AGTTATTCACTGT	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2151T>C	1.37:g.207648173T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Silent	SNP	ENST00000367058.3	37	CCDS1478.1																																																																																			T|0.917;C|0.083	0.083	strong		0.413	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
CDHR5	53841	hgsc.bcm.edu	37	11	617537	617537	+	Silent	SNP	C	C	T	rs2740380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:617537C>T	ENST00000358353.3	-	16	2674	c.2352G>A	c.(2350-2352)ccG>ccA	p.P784P	CDHR5_ENST00000397542.2_Silent_p.P784P|IRF7_ENST00000525445.1_5'Flank|IRF7_ENST00000397570.1_5'Flank|CDHR5_ENST00000349570.7_Silent_p.P590P|IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000348655.6_5'Flank|IRF7_ENST00000397566.1_5'Flank|IRF7_ENST00000330243.5_5'Flank|IRF7_ENST00000397574.2_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	784					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						ACCCGCCCTCCGGCCGCCGCT	0.721													C|||	2428	0.484824	0.1876	0.4625	5008	,	,		9843	0.7044		0.5596	False		,,,				2504	0.5992				p.P784P		Atlas-SNP	.											.	CDHR5	77	.	0			c.G2352A						PASS	.	C	,,	1118,3260		166,786,1237	24.0	26.0	25.0		2334,2352,1770	-7.9	0.0	11	dbSNP_100	25	4661,3909		1301,2059,925	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	1467,2845,2162	TT,TC,CC		45.6126,25.5368,44.6324	,,	778/840,784/846,590/652	617537	5779,7169	2189	4285	6474	SO:0001819	synonymous_variant	53841	exon15			GCCCTCCGGCCGC	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2352G>A	11.37:g.617537C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																			C|0.534;T|0.466	0.466	strong		0.721	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
POM121L12	285877	hgsc.bcm.edu	37	7	53103946	53103946	+	Silent	SNP	G	G	C	rs12113170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:53103946G>C	ENST00000408890.4	+	1	598	c.582G>C	c.(580-582)ggG>ggC	p.G194G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	194										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGTTCGACGGGCCGTTGTGGT	0.682													G|||	1647	0.328874	0.1725	0.4308	5008	,	,		12550	0.3026		0.4871	False		,,,				2504	0.3323				p.G194G		Atlas-SNP	.											.	POM121L12	146	.	0			c.G582C						PASS	.	G		802,3142		90,622,1260	48.0	55.0	53.0		582	-4.4	0.0	7	dbSNP_120	53	4189,4093		1054,2081,1006	no	coding-synonymous	POM121L12	NM_182595.3		1144,2703,2266	CC,CG,GG		49.4204,20.3347,40.8228		194/297	53103946	4991,7235	1972	4141	6113	SO:0001819	synonymous_variant	285877	exon1			CGACGGGCCGTTG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.582G>C	7.37:g.53103946G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.631;C|0.369	0.369	strong		0.682	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
FDFT1	2222	hgsc.bcm.edu	37	8	11667179	11667179	+	Silent	SNP	C	C	T	rs8417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11667179C>T	ENST00000220584.4	+	3	423	c.201C>T	c.(199-201)aaC>aaT	p.N67N	FDFT1_ENST00000530664.1_Silent_p.N3N|FDFT1_ENST00000528643.1_5'UTR|FDFT1_ENST00000528812.1_Silent_p.N3N|FDFT1_ENST00000525777.1_5'UTR|FDFT1_ENST00000443614.2_Silent_p.N67N|FDFT1_ENST00000538689.1_5'UTR|FDFT1_ENST00000446331.2_Intron|FDFT1_ENST00000525900.1_Silent_p.N60N	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	67					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		TTTACAGCAACGCAGTGTGCA	0.393													C|||	1191	0.237819	0.0923	0.2406	5008	,	,		20475	0.4474		0.1918	False		,,,				2504	0.2638				p.N67N		Atlas-SNP	.											.	FDFT1	25	.	0			c.C201T						PASS	.	C		514,3892	235.8+/-248.2	25,464,1714	74.0	70.0	72.0		201	-2.9	0.5	8	dbSNP_52	72	1652,6948	305.2+/-307.3	168,1316,2816	no	coding-synonymous	FDFT1	NM_004462.3		193,1780,4530	TT,TC,CC		19.2093,11.6659,16.6539		67/418	11667179	2166,10840	2203	4300	6503	SO:0001819	synonymous_variant	2222	exon3			CAGCAACGCAGTG	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.201C>T	8.37:g.11667179C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Silent	SNP	ENST00000220584.4	37	CCDS5985.1																																																																																			C|0.809;T|0.191	0.191	strong		0.393	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
HJURP	55355	hgsc.bcm.edu	37	2	234752863	234752863	+	Missense_Mutation	SNP	C	C	T	rs140874442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234752863C>T	ENST00000411486.2	-	7	627	c.562G>A	c.(562-564)Gtg>Atg	p.V188M	HJURP_ENST00000432087.1_Missense_Mutation_p.V134M|HJURP_ENST00000441687.1_Missense_Mutation_p.V103M|HJURP_ENST00000434039.1_Intron	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	188					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		GGGGCAGGCACGGCAGGTGAG	0.532													C|||	4	0.000798722	0.0008	0.0014	5008	,	,		21900	0.0		0.002	False		,,,				2504	0.0				p.V188M		Atlas-SNP	.											.	HJURP	72	.	0			c.G562A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	101.0	98.0	99.0		562	-4.4	0.0	2	dbSNP_134	99	36,8564	24.0+/-70.4	0,36,4264	yes	missense	HJURP	NM_018410.3	21	0,37,6466	TT,TC,CC		0.4186,0.0227,0.2845	benign	188/749	234752863	37,12969	2203	4300	6503	SO:0001583	missense	55355	exon7			CAGGCACGGCAGG		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.562G>A	2.37:g.234752863C>T	ENSP00000414109:p.Val188Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	7.453	0.642993	0.14451	2.27E-4	0.004186	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924;ENST00000454020	T;T;T;T;T	0.32023	3.25;3.24;3.22;2.91;1.47	4.09	-4.38	0.03622	.	2.541040	0.01846	N	0.035607	T	0.09291	0.0229	N	0.00538	-1.39	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.27020	-1.0086	10	0.44086	T	0.13	0.4745	6.3534	0.21389	0.0:0.4492:0.1535:0.3973	.	103;134;188	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	M	188;134;103;103;147	ENSP00000414109:V188M;ENSP00000407208:V134M;ENSP00000401944:V103M;ENSP00000393253:V103M;ENSP00000414051:V147M	ENSP00000414109:V188M	V	-	1	0	HJURP	234417602	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.680000	0.05197	-0.832000	0.04251	-1.085000	0.02201	GTG	C|0.998;T|0.002	0.002	strong		0.532	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
ELOVL2	54898	hgsc.bcm.edu	37	6	11005776	11005776	+	Silent	SNP	C	C	T	rs559223553		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:11005776C>T	ENST00000354666.3	-	3	167	c.84G>A	c.(82-84)ggG>ggA	p.G28G		NM_017770.3	NP_060240.3	Q9NXB9	ELOV2_HUMAN	ELOVL fatty acid elongase 2	28					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	fatty acid elongase activity (GO:0009922)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(2)	14	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)			ACATGAACCACCCTCTGACTC	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		23355	0.0		0.0	False		,,,				2504	0.001				p.G28G		Atlas-SNP	.											.	ELOVL2	40	.	0			c.G84A						PASS	.						107.0	82.0	90.0					6																	11005776		2203	4300	6503	SO:0001819	synonymous_variant	54898	exon3			GAACCACCCTCTG	AK000341	CCDS4518.1	6p24.1	2011-05-25	2011-05-25		ENSG00000197977	ENSG00000197977			14416	protein-coding gene	gene with protein product		611814	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2"""			12371743, 16564093	Standard	NM_017770		Approved	Ssc2	uc003mzp.4	Q9NXB9	OTTHUMG00000014252	ENST00000354666.3:c.84G>A	6.37:g.11005776C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_017770	Q6P9E1|Q86W94	Silent	SNP	ENST00000354666.3	37	CCDS4518.1																																																																																			.	.	none		0.408	ELOVL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039849.1		
HACE1	57531	hgsc.bcm.edu	37	6	105198267	105198267	+	Silent	SNP	A	A	G	rs7752614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:105198267A>G	ENST00000262903.4	-	20	2568	c.2292T>C	c.(2290-2292)ttT>ttC	p.F764F	HACE1_ENST00000517995.1_5'UTR|HACE1_ENST00000369125.2_Silent_p.F549F	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	764	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		TGAACATATGAAAGCCCTGTA	0.383													A|||	871	0.173922	0.3699	0.1398	5008	,	,		15848	0.003		0.1481	False		,,,				2504	0.136				p.F764F		Atlas-SNP	.											HACE1,NS,adenoma,0,1	HACE1	96	1	0			c.T2292C						PASS	.	A		1549,2857	484.8+/-360.1	263,1023,917	111.0	105.0	107.0		2292	2.5	1.0	6	dbSNP_116	107	1403,7197	268.5+/-287.9	114,1175,3011	no	coding-synonymous	HACE1	NM_020771.3		377,2198,3928	GG,GA,AA		16.314,35.1566,22.6972		764/910	105198267	2952,10054	2203	4300	6503	SO:0001819	synonymous_variant	57531	exon20			CATATGAAAGCCC	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"""Ankyrin repeat domain containing"""	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.2292T>C	6.37:g.105198267A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	93	61	0.655914	NM_020771	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Silent	SNP	ENST00000262903.4	37	CCDS5050.1																																																																																			A|0.805;G|0.195	0.195	strong		0.383	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095	
ARMC4	55130	hgsc.bcm.edu	37	10	28250610	28250610	+	Missense_Mutation	SNP	C	C	A	rs147175768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:28250610C>A	ENST00000305242.5	-	10	1365	c.1273G>T	c.(1273-1275)Gat>Tat	p.D425Y	ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000239715.3_Missense_Mutation_p.D282Y|ARMC4_ENST00000545014.1_5'UTR|ARMC4_ENST00000537576.1_Missense_Mutation_p.D117Y	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	425					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.D425Y(3)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						GAGGAGCTATCGCTAACAGTT	0.413																																					p.D425Y		Atlas-SNP	.											ARMC4,NS,malignant_melanoma,0,3	ARMC4	177	3	3	Substitution - Missense(3)	skin(2)|NS(1)	c.G1273T						scavenged	.						68.0	63.0	65.0					10																	28250610		2203	4295	6498	SO:0001583	missense	55130	exon10			AGCTATCGCTAAC	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1273G>T	10.37:g.28250610C>A	ENSP00000306410:p.Asp425Tyr	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	194	23	0.118557	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	90	0.04120879120879121	20	0.04065040650406504	16	0.04419889502762431	10	0.017482517482517484	44	0.05804749340369393	C	12.66	2.005911	0.35415	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.4	5.4	0.78164	.	0.268930	0.40640	N	0.001048	T	0.02970	0.0088	L	0.50333	1.59	0.50813	D	0.999894	P	0.45569	0.861	B	0.37267	0.245	T	0.00956	-1.1501	10	0.72032	D	0.01	-9.8277	18.3066	0.90184	0.0:1.0:0.0:0.0	.	425	Q5T2S8	ARMC4_HUMAN	Y	117;425;117;319;282	ENSP00000443208:D117Y;ENSP00000306410:D425Y;ENSP00000398155:D319Y;ENSP00000239715:D282Y	ENSP00000239715:D282Y	D	-	1	0	ARMC4	28290616	1.000000	0.71417	0.912000	0.35992	0.024000	0.10985	5.087000	0.64480	2.677000	0.91161	0.650000	0.86243	GAT	.	.	weak		0.413	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	
NPAS1	4861	hgsc.bcm.edu	37	19	47543774	47543774	+	Silent	SNP	G	G	A	rs3745615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47543774G>A	ENST00000602212.1	+	9	1255	c.1035G>A	c.(1033-1035)caG>caA	p.Q345Q	NPAS1_ENST00000449844.2_Silent_p.Q345Q|NPAS1_ENST00000602189.1_Silent_p.Q170Q|NPAS1_ENST00000439365.2_Silent_p.Q169Q			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	345	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		TCCACGGACAGGACGCCACGA	0.662													G|||	2878	0.574681	0.3177	0.6556	5008	,	,		12848	0.7192		0.7237	False		,,,				2504	0.5624				p.Q345Q		Atlas-SNP	.											NPAS1,rectum,carcinoma,0,1	NPAS1	32	1	0			c.G1035A						PASS	.	G		1638,2764		305,1028,868	45.0	38.0	40.0		1035	4.1	1.0	19	dbSNP_107	40	6193,2401		2239,1715,343	no	coding-synonymous	NPAS1	NM_002517.2		2544,2743,1211	AA,AG,GG		27.9381,37.2104,39.743		345/591	47543774	7831,5165	2201	4297	6498	SO:0001819	synonymous_variant	4861	exon8			CGGACAGGACGCC	U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"""Basic helix-loop-helix proteins"""	7894	protein-coding gene	gene with protein product	"""neuronal PAS1"", ""member of PAS superfamily 5"""	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.1035G>A	19.37:g.47543774G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	234	109	0.465812	NM_002517	B4DR69|Q99632|Q9BY83	Silent	SNP	ENST00000602212.1	37	CCDS12694.1																																																																																			G|0.412;A|0.588	0.588	strong		0.662	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1	NM_002517	
TRIM5	85363	hgsc.bcm.edu	37	11	5701074	5701074	+	Missense_Mutation	SNP	C	C	A	rs11601507	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5701074C>A	ENST00000380034.3	-	2	590	c.334G>T	c.(334-336)Gtc>Ttc	p.V112F	TRIM5_ENST00000396853.4_Missense_Mutation_p.V112F|TRIM5_ENST00000396847.3_Missense_Mutation_p.V112F|TRIM5_ENST00000396855.3_Missense_Mutation_p.V112F|TRIM5_ENST00000380027.1_Missense_Mutation_p.V112F|TRIM5_ENST00000483835.1_5'UTR|TRIM5_ENST00000305836.5_Missense_Mutation_p.V112F	NM_033034.2|NM_033092.2	NP_149023.2|NP_149083.2	Q9C035	TRIM5_HUMAN	tripartite motif containing 5	112			V -> F (in dbSNP:rs11601507). {ECO:0000269|Ref.9}.		activation of innate immune response (GO:0002218)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|signaling pattern recognition receptor activity (GO:0008329)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		CAGCAAATGACCTTCCCGTCC	0.552													C|||	432	0.086262	0.0061	0.0634	5008	,	,		19619	0.0873		0.0676	False		,,,				2504	0.229				p.V112F		Atlas-SNP	.											TRIM5_ENST00000380034,rectum,NS,+2,2	TRIM5	111	2	0			c.G334T						PASS	.	C	PHE/VAL,PHE/VAL,PHE/VAL	72,4330	62.3+/-99.4	2,68,2131	173.0	151.0	158.0		334,334,334	-3.1	0.0	11	dbSNP_120	158	684,7910	170.4+/-221.6	23,638,3636	no	missense,missense,missense	TRIM5	NM_033034.2,NM_033092.2,NM_033093.2	50,50,50	25,706,5767	AA,AC,CC		7.959,1.6356,5.8172	benign,benign,benign	112/494,112/348,112/327	5701074	756,12240	2201	4297	6498	SO:0001583	missense	85363	exon2			AAATGACCTTCCC	AF220025	CCDS31392.1, CCDS31393.1, CCDS31394.1	11p15	2014-06-03	2011-01-25		ENSG00000132256	ENSG00000132256		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16276	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM5"", ""tripartite motif protein TRIM"""	608487	"""tripartite motif-containing 5"""			11331580	Standard	NM_033034		Approved	RNF88, TRIM5alpha	uc001mbm.2	Q9C035	OTTHUMG00000066893	ENST00000380034.3:c.334G>T	11.37:g.5701074C>A	ENSP00000369373:p.Val112Phe	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	156	76	0.487179	NM_033093	A6NGQ1|A8WFA8|D3DQS8|D3DQS9|G3GJY1|Q2MLV4|Q2MLV8|Q2MLV9|Q2MLW1|Q2MLW3|Q2MLW4|Q2MLW6|Q2MLW7|Q2MLX1|Q2MLX2|Q2MLX3|Q2MLX5|Q2MLY3|Q2MLY4|Q2V6Q6|Q6GX26|Q8WU46|Q96SR5|Q9C031|Q9C032|Q9C033|Q9C034	Missense_Mutation	SNP	ENST00000380034.3	37	CCDS31393.1	128	0.05860805860805861	7	0.014227642276422764	19	0.052486187845303865	59	0.10314685314685315	43	0.05672823218997362	C	8.021	0.759613	0.15846	0.016356	0.07959	ENSG00000132256	ENST00000396855;ENST00000305836;ENST00000380034;ENST00000380027;ENST00000396847;ENST00000396853;ENST00000412903	T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98	4.07	-3.14	0.05250	Zinc finger, B-box (3);	0.963521	0.08539	N	0.930864	T	0.01061	0.0035	L	0.52266	1.64	0.09310	N	0.999999	P;B;P	0.36438	0.553;0.077;0.529	B;B;B	0.44163	0.414;0.067;0.443	T	0.24693	-1.0153	10	0.87932	D	0	.	1.6214	0.02714	0.128:0.3735:0.2511:0.2474	rs11601507;rs52811710;rs56896272;rs11601507	112;112;112	Q9C035-3;Q9C035-4;Q9C035	.;.;TRIM5_HUMAN	F	112	ENSP00000380064:V112F;ENSP00000307031:V112F;ENSP00000369373:V112F;ENSP00000369366:V112F;ENSP00000380058:V112F;ENSP00000380062:V112F;ENSP00000388031:V112F	ENSP00000307031:V112F	V	-	1	0	TRIM5	5657650	0.000000	0.05858	0.009000	0.14445	0.277000	0.26821	-4.570000	0.00214	-0.593000	0.05844	-0.157000	0.13467	GTC	C|0.933;A|0.067	0.067	strong		0.552	TRIM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143360.3	NM_033034	
CST2	1470	hgsc.bcm.edu	37	20	23805955	23805955	+	Silent	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23805955C>A	ENST00000304725.2	-	2	304	c.234G>T	c.(232-234)gtG>gtT	p.V78V		NM_001322.2	NP_001313.1	P09228	CYTT_HUMAN	cystatin SA	78					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|cervix(1)|large_intestine(1)|liver(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	10						TCACCCCGCCCACGATCTACA	0.537																																					p.V78V	Pancreas(193;496 3017 22514 29918)	Atlas-SNP	.											CST2,colon,carcinoma,-2,1	CST2	39	1	0			c.G234T						scavenged	.						221.0	172.0	189.0					20																	23805955		2203	4300	6503	SO:0001819	synonymous_variant	1470	exon2			CCCGCCCACGATC	M19671	CCDS13161.1	20p11.2	2007-11-29			ENSG00000170369	ENSG00000170369			2474	protein-coding gene	gene with protein product	"""cystatin 2"""	123856					Standard	NM_001322		Approved		uc002wtq.1	P09228	OTTHUMG00000032086	ENST00000304725.2:c.234G>T	20.37:g.23805955C>A		Somatic	142	2	0.0140845		WXS	Illumina HiSeq	Phase_I	150	6	0.04	NM_001322	Q9UCQ7	Silent	SNP	ENST00000304725.2	37	CCDS13161.1																																																																																			.	.	none		0.537	CST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078352.2		
VWA2	340706	hgsc.bcm.edu	37	10	116046066	116046066	+	Missense_Mutation	SNP	C	C	T	rs141860499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:116046066C>T	ENST00000392982.3	+	11	1616	c.1366C>T	c.(1366-1368)Cac>Tac	p.H456Y	VWA2_ENST00000603594.1_Missense_Mutation_p.H456Y			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	456	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CACTGAGTCACACTCCGAGGA	0.682													C|||	22	0.00439297	0.0	0.0173	5008	,	,		18291	0.0		0.0099	False		,,,				2504	0.0				p.H456Y		Atlas-SNP	.											.	VWA2	64	.	0			c.C1366T						PASS	.	C	TYR/HIS	12,4394	19.1+/-41.9	0,12,2191	75.0	62.0	67.0		1366	1.1	0.0	10	dbSNP_134	67	74,8524	44.5+/-102.8	0,74,4225	yes	missense	VWA2	NM_198496.1	83	0,86,6416	TT,TC,CC		0.8607,0.2724,0.6613	benign	456/726	116046066	86,12918	2203	4299	6502	SO:0001583	missense	340706	exon11			GAGTCACACTCCG	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1366C>T	10.37:g.116046066C>T	ENSP00000376708:p.His456Tyr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	8.267	0.812548	0.16537	0.002724	0.008607	ENSG00000165816	ENST00000392982;ENST00000298715	D	0.82893	-1.66	5.6	1.12	0.20585	von Willebrand factor, type A (3);	1.027200	0.07698	N	0.939799	T	0.61974	0.2390	N	0.19112	0.55	0.09310	N	1	B;B;B	0.29378	0.107;0.243;0.205	B;B;B	0.34536	0.053;0.185;0.116	T	0.52917	-0.8511	10	0.06099	T	0.92	.	7.9215	0.29848	0.4955:0.2971:0.2075:0.0	.	152;456;456	Q5GFL6-3;Q5GFL6;Q5GFL6-2	.;VWA2_HUMAN;.	Y	456	ENSP00000376708:H456Y	ENSP00000298715:H456Y	H	+	1	0	VWA2	116036056	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	1.083000	0.30815	0.628000	0.30357	0.563000	0.77884	CAC	C|0.993;T|0.007	0.007	strong		0.682	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
PIP5KL1	138429	hgsc.bcm.edu	37	9	130690412	130690412	+	Silent	SNP	G	G	C	rs10760515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:130690412G>C	ENST00000388747.4	-	4	410	c.366C>G	c.(364-366)gcC>gcG	p.A122A	PIP5KL1_ENST00000490773.1_5'UTR|PIP5KL1_ENST00000300432.3_5'Flank	NM_001135219.1	NP_001128691.1	Q5T9C9	PI5L1_HUMAN	phosphatidylinositol-4-phosphate 5-kinase-like 1	122	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|skin(1)	8						CGGGGCCCAGGGCAGCCTGAT	0.711													C|||	3874	0.773562	0.708	0.902	5008	,	,		13179	0.6528		0.9195	False		,,,				2504	0.7454				p.A122A		Atlas-SNP	.											.	PIP5KL1	38	.	0			c.C366G						PASS	.	C		2275,781		854,567,107	10.0	12.0	11.0		366	-6.2	0.1	9	dbSNP_120	11	6438,608		2949,540,34	no	coding-synonymous	PIP5KL1	NM_001135219.1		3803,1107,141	CC,CG,GG		8.629,25.5563,13.7498		122/395	130690412	8713,1389	1528	3523	5051	SO:0001819	synonymous_variant	138429	exon4			GCCCAGGGCAGCC	BC042184	CCDS6885.1, CCDS48030.1	9q34.13	2008-02-05			ENSG00000167103	ENSG00000167103			28711	protein-coding gene	gene with protein product		612865				12477932	Standard	NM_001135219		Approved	bA203J24.5, MGC46424	uc011mao.2	Q5T9C9	OTTHUMG00000020719	ENST00000388747.4:c.366C>G	9.37:g.130690412G>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_001135219	Q8IVS3	Silent	SNP	ENST00000388747.4	37	CCDS48030.1																																																																																			G|0.237;C|0.763	0.763	strong		0.711	PIP5KL1-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054289.2	NM_173492	
UBB	7314	hgsc.bcm.edu	37	17	16285611	16285611	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:16285611C>T	ENST00000395837.1	+	2	571	c.390C>T	c.(388-390)cgC>cgT	p.R130R	UBB_ENST00000395839.1_Silent_p.R130R|UBB_ENST00000302182.3_Silent_p.R130R|UBB_ENST00000578649.1_Intron|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000535788.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	130	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AAGATGGCCGCACTCTTTCTG	0.542																																					p.R130R	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,rectum,carcinoma,+2,2	UBB	30	2	0			c.C390T						scavenged	.																																			SO:0001819	synonymous_variant	7314	exon2			TGGCCGCACTCTT		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.390C>T	17.37:g.16285611C>T		Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	229	6	0.0262009	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			.	.	none		0.542	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
CCDC77	84318	hgsc.bcm.edu	37	12	547683	547683	+	Missense_Mutation	SNP	T	T	C	rs735295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:547683T>C	ENST00000239830.4	+	10	1183	c.1004T>C	c.(1003-1005)aTg>aCg	p.M335T	CCDC77_ENST00000422000.1_Missense_Mutation_p.M303T|CCDC77_ENST00000412006.2_Missense_Mutation_p.M303T|CCDC77_ENST00000540180.1_Missense_Mutation_p.M303T	NM_032358.3	NP_115734.1	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77	335			M -> T (in dbSNP:rs735295).			centrosome (GO:0005813)|membrane (GO:0016020)				cervix(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			TTGCCCGTTATGCATGAGAGT	0.348													t|||	1617	0.322883	0.2943	0.4107	5008	,	,		20941	0.3433		0.2594	False		,,,				2504	0.3436				p.M335T		Atlas-SNP	.											.	CCDC77	35	.	0			c.T1004C						PASS	.		THR/MET,THR/MET,THR/MET,THR/MET	1275,3131	434.9+/-344.1	188,899,1116	107.0	113.0	111.0		908,908,908,1004	-0.7	0.0	12	dbSNP_86	111	2262,6338	381.6+/-340.1	327,1608,2365	yes	missense,missense,missense,missense	CCDC77	NM_001130146.1,NM_001130147.1,NM_001130148.1,NM_032358.3	81,81,81,81	515,2507,3481	CC,CT,TT		26.3023,28.9378,27.1951	benign,benign,benign,benign	303/457,303/457,303/457,335/489	547683	3537,9469	2203	4300	6503	SO:0001583	missense	84318	exon10			CCGTTATGCATGA	AK027638	CCDS8503.1, CCDS44781.1	12p13.33	2006-02-16			ENSG00000120647	ENSG00000120647			28203	protein-coding gene	gene with protein product						12477932	Standard	NM_001130148		Approved	MGC13183	uc001qig.3	Q9BR77	OTTHUMG00000129214	ENST00000239830.4:c.1004T>C	12.37:g.547683T>C	ENSP00000239830:p.Met335Thr	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	172	80	0.465116	NM_032358	B4DDE8	Missense_Mutation	SNP	ENST00000239830.4	37	CCDS8503.1	656	0.30036630036630035	135	0.27439024390243905	131	0.36187845303867405	210	0.36713286713286714	180	0.23746701846965698	t	1.210	-0.629996	0.03610	0.289378	0.263023	ENSG00000120647	ENST00000540180;ENST00000422000;ENST00000543504;ENST00000239830;ENST00000412006	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.04	-0.73	0.11154	.	1.631020	0.03648	N	0.240587	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.36962	-0.9726	9	0.14252	T	0.57	1.6004	1.8436	0.03155	0.3208:0.0781:0.3264:0.2747	rs735295;rs3764877;rs56454173;rs59893558;rs735295	335	Q9BR77	CCD77_HUMAN	T	303;303;303;335;303	ENSP00000440554:M303T;ENSP00000391870:M303T;ENSP00000445873:M303T;ENSP00000239830:M335T;ENSP00000412925:M303T	ENSP00000239830:M335T	M	+	2	0	CCDC77	417944	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.569000	0.05902	0.008000	0.14787	-0.438000	0.05819	ATG	C|0.291;N|0.001	0.291	strong		0.348	CCDC77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251296.1	NM_032358	
POU5F1	5460	hgsc.bcm.edu	37	6	31138377	31138377	+	Silent	SNP	C	C	T	rs2077010	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31138377C>T	ENST00000259915.8	-	1	93	c.21G>A	c.(19-21)tcG>tcA	p.S7S	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	7					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	AGGCGAAATCCGAAGCCAGGT	0.672			T	EWSR1	sarcoma								C|||	2113	0.421925	0.4478	0.4726	5008	,	,		12960	0.3859		0.4105	False		,,,				2504	0.3998				p.S7S		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	.	POU5F1	25	.	0			c.G21A						PASS	.	C		1050,1698		242,566,566	4.0	4.0	4.0		21	-7.4	0.8	6	dbSNP_96	4	1810,3054		399,1012,1021	no	coding-synonymous	POU5F1	NM_002701.4		641,1578,1587	TT,TC,CC		37.2122,38.2096,37.5723		7/361	31138377	2860,4752	1374	2432	3806	SO:0001819	synonymous_variant	5460	exon1			GAAATCCGAAGCC	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.21G>A	6.37:g.31138377C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	88	0.977778	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Silent	SNP	ENST00000259915.8	37	CCDS34391.1																																																																																			C|0.592;T|0.408	0.408	strong		0.672	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
CNP	1267	hgsc.bcm.edu	37	17	40125864	40125864	+	Silent	SNP	G	G	A	rs2070106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:40125864G>A	ENST00000393892.3	+	4	1332	c.1188G>A	c.(1186-1188)ggG>ggA	p.G396G	CNP_ENST00000393888.1_Silent_p.G376G|CNP_ENST00000472031.1_3'UTR|CNP_ENST00000591072.1_Silent_p.G161G	NM_033133.4	NP_149124.3	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	396					adult locomotory behavior (GO:0008344)|aging (GO:0007568)|axonogenesis (GO:0007409)|cyclic nucleotide catabolic process (GO:0009214)|microtubule cytoskeleton organization (GO:0000226)|oligodendrocyte differentiation (GO:0048709)|regulation of mitochondrial membrane permeability (GO:0046902)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule (GO:0005874)|microvillus (GO:0005902)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|myelin sheath abaxonal region (GO:0035748)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity (GO:0004113)|cyclic nucleotide binding (GO:0030551)|RNA binding (GO:0003723)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	9		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		TCTTCACGGGGTACTACGGGA	0.597													G|||	1378	0.27516	0.0756	0.2406	5008	,	,		15024	0.4157		0.2843	False		,,,				2504	0.4151				p.G396G		Atlas-SNP	.											.	CNP	58	.	0			c.G1188A						PASS	.	G		406,3668		17,372,1648	34.0	39.0	37.0		1188	-10.4	0.1	17	dbSNP_96	37	2688,5692		438,1812,1940	no	coding-synonymous	CNP	NM_033133.4		455,2184,3588	AA,AG,GG		32.0764,9.9656,24.8434		396/422	40125864	3094,9360	2037	4190	6227	SO:0001819	synonymous_variant	1267	exon4			CACGGGGTACTAC		CCDS11414.2	17q21	2008-02-05			ENSG00000173786	ENSG00000173786	3.1.4.37		2158	protein-coding gene	gene with protein product		123830				1322358	Standard	XM_006721701		Approved		uc002hyl.1	P09543	OTTHUMG00000133502	ENST00000393892.3:c.1188G>A	17.37:g.40125864G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_033133		Silent	SNP	ENST00000393892.3	37	CCDS11414.2																																																																																			G|0.731;A|0.269	0.269	strong		0.597	CNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257443.2		
ZDBF2	57683	hgsc.bcm.edu	37	2	207172627	207172627	+	Silent	SNP	A	A	G	rs7582864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:207172627A>G	ENST00000374423.3	+	5	3761	c.3375A>G	c.(3373-3375)caA>caG	p.Q1125Q		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1125							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						TTTCTGTCCAATCTGTGGCTG	0.343													a|||	2293	0.457867	0.326	0.6066	5008	,	,		19868	0.3571		0.5636	False		,,,				2504	0.5256				p.Q1125Q		Atlas-SNP	.											ZDBF2_ENST00000374423,NS,carcinoma,0,2	ZDBF2	531	2	0			c.A3375G						PASS	.	G		1460,2232		300,860,686	50.0	47.0	48.0		3375	-4.3	0.0	2	dbSNP_116	48	4868,3302		1450,1968,667	no	coding-synonymous	ZDBF2	NM_020923.1		1750,2828,1353	GG,GA,AA		40.4162,39.545,46.6532		1125/2355	207172627	6328,5534	1846	4085	5931	SO:0001819	synonymous_variant	57683	exon5			TGTCCAATCTGTG	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.3375A>G	2.37:g.207172627A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			A|0.540;G|0.460	0.460	strong		0.343	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
ALPK2	115701	hgsc.bcm.edu	37	18	56204945	56204945	+	Missense_Mutation	SNP	C	C	G	rs3809972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204945C>G	ENST00000361673.3	-	5	2687	c.2474G>C	c.(2473-2475)aGa>aCa	p.R825T	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	825			R -> T (in dbSNP:rs3809972). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						ATCAACTGGTCTCCCAACAAG	0.418													G|||	2024	0.404153	0.4312	0.4294	5008	,	,		22836	0.2361		0.5726	False		,,,				2504	0.3497				p.R825T		Atlas-SNP	.											.	ALPK2	487	.	0			c.G2474C						PASS	.	G	THR/ARG	1984,2422	618.1+/-393.1	446,1092,665	97.0	93.0	94.0		2474	1.3	0.0	18	dbSNP_107	94	4589,4011	555.2+/-386.6	1237,2115,948	yes	missense	ALPK2	NM_052947.3	71	1683,3207,1613	GG,GC,CC		46.6395,45.0295,49.4618	benign	825/2171	56204945	6573,6433	2203	4300	6503	SO:0001583	missense	115701	exon5			ACTGGTCTCCCAA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2474G>C	18.37:g.56204945C>G	ENSP00000354991:p.Arg825Thr	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	155	60	0.387097	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	955	0.43727106227106227	189	0.38414634146341464	184	0.5082872928176796	137	0.2395104895104895	445	0.5870712401055409	G	0.989	-0.694484	0.03303	0.450295	0.533605	ENSG00000198796	ENST00000361673	T	0.38887	1.11	5.57	1.3	0.21679	.	1.325910	0.04699	N	0.415427	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45264	-0.9273	9	0.22109	T	0.4	-0.0267	5.5085	0.16868	0.3499:0.1423:0.5078:0.0	rs3809972;rs17309802;rs52836407;rs3809972	825;825	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	T	825	ENSP00000354991:R825T	ENSP00000354991:R825T	R	-	2	0	ALPK2	54355925	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.435000	0.06931	0.072000	0.16694	-0.901000	0.02856	AGA	C|0.531;G|0.469	0.469	strong		0.418	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971162	45971162	+	Silent	SNP	C	C	T	rs199922020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45971162C>T	ENST00000391621.1	-	1	226	c.180G>A	c.(178-180)gcG>gcA	p.A60A	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	60	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GCTCACAGGCCGCCTGGCAGC	0.706																																					p.A60A		Atlas-SNP	.											KRTAP10-2,colon,carcinoma,0,1	KRTAP10-2	21	1	0			c.G180A						scavenged	.																																			SO:0001819	synonymous_variant	386679	exon1			ACAGGCCGCCTGG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.180G>A	21.37:g.45971162C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	106	36	0.339623	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			.	.	weak		0.706	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
FERMT1	55612	hgsc.bcm.edu	37	20	6100088	6100088	+	Silent	SNP	A	A	G	rs10373	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:6100088A>G	ENST00000217289.4	-	2	902	c.114T>C	c.(112-114)caT>caC	p.H38H	FERMT1_ENST00000536936.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	38					cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						CTCCTCCAACATGAAGGTCTC	0.458													A|||	2627	0.524561	0.5325	0.4928	5008	,	,		21047	0.377		0.5616	False		,,,				2504	0.6503				p.H38H		Atlas-SNP	.											.	FERMT1	106	.	0			c.T114C						PASS	.	A		2348,2058	607.1+/-390.9	642,1064,497	234.0	162.0	186.0		114	-1.6	0.0	20	dbSNP_52	186	4576,4024	597.1+/-393.7	1206,2164,930	no	coding-synonymous	FERMT1	NM_017671.4		1848,3228,1427	GG,GA,AA		46.7907,46.709,46.763		38/678	6100088	6924,6082	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon2			TCCAACATGAAGG	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.114T>C	20.37:g.6100088A>G		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	213	108	0.507042	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			A|0.466;G|0.534	0.534	strong		0.458	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
RAB11FIP5	26056	hgsc.bcm.edu	37	2	73315683	73315683	+	Missense_Mutation	SNP	G	G	T	rs538411572		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:73315683G>T	ENST00000258098.6	-	3	1303	c.1063C>A	c.(1063-1065)Cgc>Agc	p.R355S	RAB11FIP5_ENST00000493523.2_5'UTR	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	355					cellular response to acidic pH (GO:0071468)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|regulation of protein localization to cell surface (GO:2000008)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)			biliary_tract(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	23						ATGGAGCTGCGGTGCCGCACA	0.627																																					p.R355S		Atlas-SNP	.											RAB11FIP5,NS,carcinoma,+1,1	RAB11FIP5	66	1	0			c.C1063A						scavenged	.						27.0	32.0	30.0					2																	73315683		2203	4300	6503	SO:0001583	missense	26056	exon3			AGCTGCGGTGCCG	AF334812	CCDS1923.1	2p13	2008-02-05			ENSG00000135631	ENSG00000135631			24845	protein-coding gene	gene with protein product		605536				10048485, 11163216	Standard	NM_015470		Approved	GAF1, KIAA0857, RIP11, pp75	uc002sis.4	Q9BXF6	OTTHUMG00000129779	ENST00000258098.6:c.1063C>A	2.37:g.73315683G>T	ENSP00000258098:p.Arg355Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	112	3	0.0267857	NM_015470	O94939|Q9P0M1	Missense_Mutation	SNP	ENST00000258098.6	37	CCDS1923.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.598133	0.46318	.	.	ENSG00000135631	ENST00000258098	T	0.44881	0.91	4.19	4.19	0.49359	.	0.321554	0.25717	N	0.028774	T	0.34803	0.0910	L	0.59436	1.845	0.33109	D	0.540242	B;B	0.22604	0.072;0.072	B;B	0.22152	0.038;0.038	T	0.37033	-0.9723	10	0.19590	T	0.45	-15.6313	8.0872	0.30780	0.1098:0.0:0.8902:0.0	.	355;355	Q9BXF6;Q2Z1P3	RFIP5_HUMAN;.	S	355	ENSP00000258098:R355S	ENSP00000258098:R355S	R	-	1	0	RAB11FIP5	73169191	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.400000	0.34577	2.335000	0.79485	0.462000	0.41574	CGC	.	.	none		0.627	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470	
ANXA6	309	hgsc.bcm.edu	37	5	150518988	150518988	+	Silent	SNP	G	G	A	rs2228458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150518988G>A	ENST00000354546.5	-	4	357	c.130C>T	c.(130-132)Ctg>Ttg	p.L44L	ANXA6_ENST00000521512.1_Silent_p.L44L|ANXA6_ENST00000356496.5_Silent_p.L44L|ANXA6_ENST00000377751.5_Silent_p.L44L|ANXA6_ENST00000523714.1_Silent_p.L12L	NM_001155.4	NP_001146.2	P08133	ANXA6_HUMAN	annexin A6	44					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|protein homooligomerization (GO:0051260)|regulation of muscle contraction (GO:0006937)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|cholesterol binding (GO:0015485)|GTP binding (GO:0005525)|ligand-gated ion channel activity (GO:0015276)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|lung(9)	12		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTATGTCCAGTATGGCCTCC	0.587													G|||	1390	0.277556	0.0144	0.3069	5008	,	,		20093	0.4454		0.2177	False		,,,				2504	0.501				p.L44L		Atlas-SNP	.											.	ANXA6	102	.	0			c.C130T						PASS	.	G	,	282,3922		10,262,1830	111.0	121.0	118.0		130,34	1.0	1.0	5	dbSNP_98	118	1978,6488		230,1518,2485	no	coding-synonymous,coding-synonymous	ANXA6	NM_001155.4,NM_001193544.1	,	240,1780,4315	AA,AG,GG		23.364,6.7079,17.8374	,	44/674,12/642	150518988	2260,10410	2102	4233	6335	SO:0001819	synonymous_variant	309	exon4			TGTCCAGTATGGC	J03578	CCDS47315.1, CCDS54941.1	5q33.1	2008-02-05			ENSG00000197043	ENSG00000197043		"""Annexins"""	544	protein-coding gene	gene with protein product		114070		ANX6		3258820	Standard	NM_001155		Approved		uc003ltl.2	P08133	OTTHUMG00000164179	ENST00000354546.5:c.130C>T	5.37:g.150518988G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	170	52	0.305882	NM_001155	B7Z8A7|D3DQH4|E9PGK1|Q6ZT79	Silent	SNP	ENST00000354546.5	37	CCDS47315.1																																																																																			G|0.752;N|0.000	.	strong		0.587	ANXA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377668.2	NM_001155	
HERC1	8925	hgsc.bcm.edu	37	15	63918307	63918307	+	Silent	SNP	G	G	C	rs1140422	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63918307G>C	ENST00000443617.2	-	71	13239	c.13152C>G	c.(13150-13152)ccC>ccG	p.P4384P		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4384					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCCCATACTGGGGGGGCACTG	0.557													G|||	368	0.0734824	0.0189	0.1873	5008	,	,		19519	0.003		0.161	False		,,,				2504	0.0491				p.P4384P		Atlas-SNP	.											.	HERC1	624	.	0			c.C13152G						PASS	.	G		169,3791		3,163,1814	38.0	40.0	39.0		13152	-7.7	0.6	15	dbSNP_86	39	1430,6864		129,1172,2846	no	coding-synonymous	HERC1	NM_003922.3		132,1335,4660	CC,CG,GG		17.2414,4.2677,13.0488		4384/4862	63918307	1599,10655	1980	4147	6127	SO:0001819	synonymous_variant	8925	exon71			ATACTGGGGGGGC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13152C>G	15.37:g.63918307G>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																			G|0.899;C|0.101	0.101	strong		0.557	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
TBC1D8	11138	hgsc.bcm.edu	37	2	101624471	101624471	+	Missense_Mutation	SNP	T	T	C	rs746924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:101624471T>C	ENST00000376840.4	-	20	3234	c.3235A>G	c.(3235-3237)Agg>Ggg	p.R1079G	RPL31_ENST00000409028.4_Intron|RPL31_ENST00000409038.1_Intron|RPL31_ENST00000409650.1_Intron|TBC1D8_ENST00000409318.1_Missense_Mutation_p.R1094G			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	1079			R -> G (in dbSNP:rs746924). {ECO:0000269|PubMed:14702039}.		blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						GTCCAGTCCCTTTCTGCCGCC	0.502													C|||	2576	0.514377	0.4667	0.5706	5008	,	,		17486	0.2946		0.6819	False		,,,				2504	0.593				p.R1079G		Atlas-SNP	.											.	TBC1D8	169	.	0			c.A3235G						PASS	.	C	,GLY/ARG	1975,1833		514,947,443	59.0	61.0	60.0		,3235	5.1	1.0	2	dbSNP_86	60	5494,2728		1844,1806,461	yes	intron,missense	RPL31,TBC1D8	NM_001098577.2,NM_001102426.1	,125	2358,2753,904	CC,CT,TT		33.1793,48.1355,37.9135	,benign	,1079/1141	101624471	7469,4561	1904	4111	6015	SO:0001583	missense	11138	exon20			AGTCCCTTTCTGC	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.3235A>G	2.37:g.101624471T>C	ENSP00000366036:p.Arg1079Gly	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	192	105	0.546875	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation	SNP	ENST00000376840.4	37	CCDS46375.1	1189	0.5444139194139194	231	0.4695121951219512	235	0.649171270718232	205	0.3583916083916084	518	0.683377308707124	C	0.227	-1.023717	0.02061	0.518645	0.668207	ENSG00000204634	ENST00000376840;ENST00000409318	T;T	0.02974	4.09;4.09	5.14	5.14	0.70334	.	0.109676	0.40728	N	0.001032	T	0.00012	0.0000	N	0.02296	-0.605	0.53688	P	2.5000000000052758E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.02610	-1.1134	9	0.15952	T	0.53	-19.7693	13.5418	0.61679	0.0:0.9236:0.0:0.0764	rs746924;rs1057581;rs3739012;rs61100269;rs746924	1079	O95759	TBCD8_HUMAN	G	1079;1094	ENSP00000366036:R1079G;ENSP00000386856:R1094G	ENSP00000366036:R1079G	R	-	1	2	TBC1D8	100990903	0.844000	0.29557	0.976000	0.42696	0.160000	0.22226	1.224000	0.32539	1.143000	0.42306	-0.186000	0.12905	AGG	C|0.538;N|0.000	0.538	strong		0.502	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
TSC2	7249	hgsc.bcm.edu	37	16	2114407	2114407	+	Silent	SNP	C	C	T	rs137854246|rs34012042	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2114407C>T	ENST00000219476.3	+	15	2208	c.1578C>T	c.(1576-1578)agC>agT	p.S526S	TSC2_ENST00000568454.1_Silent_p.S537S|TSC2_ENST00000401874.2_Silent_p.S526S|TSC2_ENST00000439673.2_Silent_p.S489S|TSC2_ENST00000382538.6_Silent_p.S477S|TSC2_ENST00000353929.4_Silent_p.S526S|TSC2_ENST00000350773.4_Silent_p.S526S	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	526					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				ACTTCAACAGCCTGCTGGACA	0.632			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				C|||	176	0.0351438	0.0023	0.0461	5008	,	,		18873	0.0		0.0726	False		,,,				2504	0.0695				p.S526S		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.C1578T						PASS	.	C	,,	67,4329	61.1+/-98.1	0,67,2131	73.0	74.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1578,1578,1578	-5.3	0.6	16	dbSNP_126	74	600,8000	158.2+/-211.7	21,558,3721	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	21,625,5852	TT,TC,CC		6.9767,1.5241,5.1323	,,	526/1808,526/1741,526/1785	2114407	667,12329	2198	4300	6498	SO:0001819	synonymous_variant	7249	exon15	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CAACAGCCTGCTG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.1578C>T	16.37:g.2114407C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	166	71	0.427711	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			C|0.949;T|0.051	0.051	strong		0.632	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
LTN1	26046	hgsc.bcm.edu	37	21	30332911	30332911	+	Missense_Mutation	SNP	C	C	T	rs34635840	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:30332911C>T	ENST00000361371.5	-	12	2360	c.2281G>A	c.(2281-2283)Gta>Ata	p.V761I	LTN1_ENST00000389194.2_Missense_Mutation_p.V807I			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	761			V -> I (in dbSNP:rs34635840).		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TCTGAAGATACCCTGGATTCC	0.383													C|||	168	0.0335463	0.0023	0.0504	5008	,	,		17429	0.0		0.1123	False		,,,				2504	0.0174				p.V807I		Atlas-SNP	.											.	LTN1	141	.	0			c.G2419A						PASS	.	C	ILE/VAL	101,4305	82.4+/-120.9	0,101,2102	110.0	97.0	101.0		2419	0.8	0.0	21	dbSNP_126	101	893,7707	201.3+/-244.8	47,799,3454	yes	missense	LTN1	NM_015565.2	29	47,900,5556	TT,TC,CC		10.3837,2.2923,7.6426	benign	807/1813	30332911	994,12012	2203	4300	6503	SO:0001583	missense	26046	exon12			AAGATACCCTGGA	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.2281G>A	21.37:g.30332911C>T	ENSP00000354977:p.Val761Ile	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	169	66	0.390533	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		109	0.04990842490842491	2	0.0040650406504065045	24	0.06629834254143646	0	0.0	83	0.10949868073878628	C	6.116	0.389733	0.11581	0.022923	0.103837	ENSG00000198862	ENST00000389194;ENST00000361371	T;T	0.17691	2.26;2.26	4.84	0.791	0.18619	.	1.354920	0.04516	N	0.383793	T	0.00144	0.0004	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33828	-0.9853	9	0.11794	T	0.64	.	3.9996	0.09574	0.1326:0.5939:0.1282:0.1454	rs34635840	761	O94822	LTN1_HUMAN	I	807;761	ENSP00000373846:V807I;ENSP00000354977:V761I	ENSP00000354977:V761I	V	-	1	0	LTN1	29254782	0.000000	0.05858	0.000000	0.03702	0.322000	0.28314	-0.140000	0.10342	0.039000	0.15632	-0.282000	0.10007	GTA	C|0.926;T|0.074	0.074	strong		0.383	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
LRRN2	10446	hgsc.bcm.edu	37	1	204589066	204589066	+	Missense_Mutation	SNP	C	C	T	rs36012907	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204589066C>T	ENST00000367175.1	-	1	2267	c.55G>A	c.(55-57)Gct>Act	p.A19T	LRRN2_ENST00000496057.1_5'UTR|LRRN2_ENST00000367176.3_Missense_Mutation_p.A19T|LRRN2_ENST00000367177.3_Missense_Mutation_p.A19T			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	19			A -> T (in dbSNP:rs36012907). {ECO:0000269|PubMed:12975309}.		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			ACGGGCACAGCGGCAGTGGCA	0.647													C|||	122	0.024361	0.0015	0.0576	5008	,	,		17470	0.0		0.0726	False		,,,				2504	0.0072				p.A19T		Atlas-SNP	.											.	LRRN2	81	.	0			c.G55A						PASS	.	C	THR/ALA,THR/ALA	87,4313		1,85,2114	19.0	22.0	21.0		55,55	1.6	0.2	1	dbSNP_126	21	824,7774		39,746,3514	yes	missense,missense	LRRN2	NM_201630.1,NM_006338.2	58,58	40,831,5628	TT,TC,CC		9.5836,1.9773,7.0088	benign,benign	19/714,19/714	204589066	911,12087	2200	4299	6499	SO:0001583	missense	10446	exon3			GCACAGCGGCAGT	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.55G>A	1.37:g.204589066C>T	ENSP00000356143:p.Ala19Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	78	0.03571428571428571	1	0.0020325203252032522	28	0.07734806629834254	0	0.0	49	0.06464379947229551	C	9.501	1.103266	0.20632	0.019773	0.095836	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.60424	0.19;0.19;0.19	5.79	1.63	0.23807	.	0.748708	0.11411	N	0.566775	T	0.01092	0.0036	N	0.22421	0.69	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.03287	-1.1052	10	0.21540	T	0.41	.	5.964	0.19315	0.0:0.6342:0.1354:0.2304	rs36012907	19	O75325	LRRN2_HUMAN	T	19	ENSP00000356144:A19T;ENSP00000356145:A19T;ENSP00000356143:A19T	ENSP00000356143:A19T	A	-	1	0	LRRN2	202855689	0.198000	0.23374	0.196000	0.23383	0.976000	0.68499	0.673000	0.25203	0.352000	0.24053	0.650000	0.86243	GCT	C|0.942;T|0.058	0.058	strong		0.647	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
CTCFL	140690	hgsc.bcm.edu	37	20	56090807	56090807	+	Silent	SNP	A	A	G	rs6025601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:56090807A>G	ENST00000608263.1	-	5	1804	c.1143T>C	c.(1141-1143)gaT>gaC	p.D381D	CTCFL_ENST00000502686.2_Silent_p.D119D|CTCFL_ENST00000608440.1_Silent_p.D381D|CTCFL_ENST00000609232.1_Silent_p.D381D|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000429804.3_Silent_p.D381D|CTCFL_ENST00000243914.3_Silent_p.D381D|CTCFL_ENST00000371196.2_Silent_p.D381D|CTCFL_ENST00000423479.3_Silent_p.D381D|CTCFL_ENST00000433949.3_Silent_p.D176D|CTCFL_ENST00000539382.1_Silent_p.D176D|CTCFL_ENST00000608425.1_Silent_p.D381D|CTCFL_ENST00000422869.2_Silent_p.D381D|CTCFL_ENST00000608903.1_Silent_p.D119D	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	381					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GCTTGTAGGTATCTCTGCTGG	0.473													G|||	1645	0.328474	0.4092	0.33	5008	,	,		18536	0.369		0.2097	False		,,,				2504	0.2986				p.D381D		Atlas-SNP	.											CTCFL,bladder,carcinoma,-2,2	CTCFL	97	2	0			c.T1143C						PASS	.	G		1579,2827	666.5+/-401.7	259,1061,883	176.0	166.0	170.0		1143	2.9	1.0	20	dbSNP_114	170	1675,6925	739.7+/-407.1	172,1331,2797	no	coding-synonymous	CTCFL	NM_080618.2		431,2392,3680	GG,GA,AA		19.4767,35.8375,25.0192		381/664	56090807	3254,9752	2203	4300	6503	SO:0001819	synonymous_variant	140690	exon5			GTAGGTATCTCTG		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1143T>C	20.37:g.56090807A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Silent	SNP	ENST00000608263.1	37	CCDS13459.1																																																																																			A|0.717;G|0.283	0.283	strong		0.473	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
OR51A2	401667	hgsc.bcm.edu	37	11	4976077	4976077	+	Missense_Mutation	SNP	T	T	G	rs2570573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4976077T>G	ENST00000380371.1	-	1	866	c.867A>C	c.(865-867)aaA>aaC	p.K289N	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	289			K -> N (in dbSNP:rs2570573).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAACAATTGGTTTCATCAGCG	0.418																																					p.K289N		Atlas-SNP	.											OR51A2,NS,carcinoma,-2,1	OR51A2	40	1	0			c.A867C						scavenged	.		ASN/LYS	597,3473		223,151,1661	84.0	67.0	73.0		867	-4.2	0.9	11	dbSNP_100	73	1533,5907		543,447,2730	yes	missense	OR51A2	NM_001004748.1	94	766,598,4391	GG,GT,TT		20.6048,14.6683,18.5056	benign	289/314	4976077	2130,9380	2035	3720	5755	SO:0001583	missense	401667	exon1			AATTGGTTTCATC	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.867A>C	11.37:g.4976077T>G	ENSP00000369729:p.Lys289Asn	Somatic	500	1	0.002		WXS	Illumina HiSeq	Phase_I	35	33	0.942857	NM_001004748		Missense_Mutation	SNP	ENST00000380371.1	37	CCDS31368.1	.	.	.	.	.	.	.	.	.	.	-	0.004	-2.278436	0.00254	0.146683	0.206048	ENSG00000205496	ENST00000380371	T	0.49139	0.79	3.45	-4.21	0.03812	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00000	-4.29	0.49389	P	2.1099999999996122E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.39482	-0.9612	8	0.02654	T	1	.	9.3539	0.38155	0.2085:0.0:0.6632:0.1283	rs2570573;rs2959192;rs61436556;rs2570573	289	Q8NGJ7	O51A2_HUMAN	N	289	ENSP00000369729:K289N	ENSP00000369729:K289N	K	-	3	2	OR51A2	4932653	0.112000	0.22096	0.886000	0.34754	0.012000	0.07955	-0.640000	0.05440	-1.567000	0.01671	-1.260000	0.01463	AAA	T|0.952;G|0.048	0.048	strong		0.418	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
ZNF646	9726	hgsc.bcm.edu	37	16	31088347	31088347	+	Silent	SNP	G	G	A	rs749671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31088347G>A	ENST00000394979.2	+	1	1125	c.702G>A	c.(700-702)gaG>gaA	p.E234E	ZNF668_ENST00000300849.4_5'Flank|ZNF646_ENST00000300850.5_Silent_p.E234E|ZNF668_ENST00000564456.1_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CTCCTGCTGAGGAGGAGCGGC	0.597													G|||	1770	0.353435	0.0545	0.4035	5008	,	,		18624	0.8849		0.3817	False		,,,				2504	0.1452				p.E234E		Atlas-SNP	.											.	ZNF646	133	.	0			c.G702A						PASS	.	G		504,3890	230.1+/-244.4	33,438,1726	50.0	51.0	51.0		702	4.8	1.0	16	dbSNP_86	51	3413,5187	500.9+/-375.3	670,2073,1557	no	coding-synonymous	ZNF646	NM_014699.3		703,2511,3283	AA,AG,GG		39.686,11.4702,30.1447		234/1833	31088347	3917,9077	2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			TGCTGAGGAGGAG	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.702G>A	16.37:g.31088347G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	93	57	0.612903	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																				G|0.646;A|0.354	0.354	strong		0.597	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
DES	1674	hgsc.bcm.edu	37	2	220286142	220286142	+	Silent	SNP	G	G	A	rs1058284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220286142G>A	ENST00000373960.3	+	6	1190	c.1104G>A	c.(1102-1104)gcG>gcA	p.A368A		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	368	Coil 2B.|Rod.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		ACAACATTGCGCGCCTGGAGG	0.597													G|||	1671	0.333666	0.4607	0.3429	5008	,	,		17124	0.1835		0.3648	False		,,,				2504	0.2781				p.A368A		Atlas-SNP	.											DES,right_upper_lobe,carcinoma,+1,1	DES	53	1	0			c.G1104A						PASS	.	G		1945,2461	551.7+/-378.3	442,1061,700	60.0	59.0	60.0		1104	-10.2	0.0	2	dbSNP_86	60	3055,5545	469.1+/-367.5	567,1921,1812	no	coding-synonymous	DES	NM_001927.3		1009,2982,2512	AA,AG,GG		35.5233,44.1443,38.4438		368/471	220286142	5000,8006	2203	4300	6503	SO:0001819	synonymous_variant	1674	exon6			CATTGCGCGCCTG	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.1104G>A	2.37:g.220286142G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Silent	SNP	ENST00000373960.3	37	CCDS33383.1																																																																																			G|0.640;A|0.360	0.360	strong		0.597	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
LY6G6F	259215	hgsc.bcm.edu	37	6	31677953	31677953	+	Missense_Mutation	SNP	G	G	A	rs61740977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31677953G>A	ENST00000375832.4	+	4	819	c.797G>A	c.(796-798)gGc>gAc	p.G266D	LY6G6F_ENST00000556581.1_Missense_Mutation_p.G266D|XXbac-BPG32J3.20_ENST00000461287.1_Intron|MEGT1_ENST00000503322.1_Missense_Mutation_p.G266D	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						GGGGCTCCAGGCAGAGGTGAG	0.632													G|||	42	0.00838658	0.0068	0.0072	5008	,	,		19569	0.003		0.0099	False		,,,				2504	0.0153				p.G266D		Atlas-SNP	.											LY6G6F,colon,carcinoma,+1,1	LY6G6F	23	1	0			c.G797A						scavenged	.	G	ASP/GLY	10,3012		0,10,1501	60.0	62.0	61.0		797	-0.1	0.0	6	dbSNP_129	61	41,5373		0,41,2666	yes	missense	LY6G6F	NM_001003693.1	94	0,51,4167	AA,AG,GG		0.7573,0.3309,0.6046	probably-damaging	266/298	31677953	51,8385	1511	2707	4218	SO:0001583	missense	259215	exon4			CTCCAGGCAGAGG		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"""Immunoglobulin superfamily / V-set domain containing"""	13933	protein-coding gene	gene with protein product		611404	"""chromosome 6 open reading frame 21"""	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.797G>A	6.37:g.31677953G>A	ENSP00000364992:p.Gly266Asp	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_001003693	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	G	8.620	0.891217	0.17613	0.003309	0.007573	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.16196	2.52;2.36;2.52	5.25	-0.08	0.13708	.	0.971401	0.08471	N	0.940953	T	0.01627	0.0052	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.47560	-0.9108	10	0.27785	T	0.31	0.4188	5.858	0.18730	0.353:0.0:0.5128:0.1342	rs61740977	266;266	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	D	266	ENSP00000452432:G266D;ENSP00000364992:G266D;ENSP00000421232:G266D	ENSP00000364992:G266D	G	+	2	0	XXbac-BPG32J3.19;LY6G6F	31785932	0.007000	0.16637	0.020000	0.16555	0.036000	0.12997	0.191000	0.17076	-0.177000	0.10690	-1.491000	0.00971	GGC	G|0.994;A|0.006	0.006	strong		0.632	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693	
MOB3A	126308	hgsc.bcm.edu	37	19	2078176	2078176	+	Silent	SNP	C	C	T	rs35452475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:2078176C>T	ENST00000357066.3	-	3	763	c.384G>A	c.(382-384)gcG>gcA	p.A128A	MOB3A_ENST00000592143.1_Intron|MOB3A_ENST00000592280.1_Silent_p.A128A	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	128						intracellular (GO:0005622)	metal ion binding (GO:0046872)										TGTTGATCTGCGCCTCGATCC	0.597													C|||	173	0.0345447	0.0023	0.0274	5008	,	,		17349	0.001		0.0616	False		,,,				2504	0.09				p.A128A		Atlas-SNP	.											MOBKL2A,caecum,carcinoma,-1,1	.	.	1	0			c.G384A						PASS	.	C		64,4342	57.4+/-93.9	1,62,2140	72.0	53.0	59.0		384	-4.4	0.4	19	dbSNP_126	59	573,8027	154.6+/-208.8	16,541,3743	no	coding-synonymous	MOB3A	NM_130807.2		17,603,5883	TT,TC,CC		6.6628,1.4526,4.8977		128/218	2078176	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			GATCTGCGCCTCG	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.384G>A	19.37:g.2078176C>T		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	269	125	0.464684	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			C|0.956;T|0.044	0.044	strong		0.597	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
ZNF880	400713	hgsc.bcm.edu	37	19	52888210	52888210	+	Silent	SNP	T	T	C	rs56151179	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52888210T>C	ENST00000422689.2	+	4	1392	c.1377T>C	c.(1375-1377)acT>acC	p.T459T		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	459					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GATTTCATACTGGAGAGAAAC	0.388																																					p.T459T		Atlas-SNP	.											.	ZNF880	45	.	0			c.T1377C						PASS	.	T		529,855		102,325,265	74.0	70.0	71.0		1377	2.0	0.9	19	dbSNP_129	71	1217,1965		222,773,596	no	coding-synonymous	ZNF880	NM_001145434.1		324,1098,861	CC,CT,TT		38.2464,38.2225,38.2392		459/578	52888210	1746,2820	692	1591	2283	SO:0001819	synonymous_variant	400713	exon4			TCATACTGGAGAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1377T>C	19.37:g.52888210T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_001145434	B4DNA6	Silent	SNP	ENST00000422689.2	37	CCDS46164.1																																																																																			T|0.633;C|0.367	0.367	strong		0.388	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331128	28331128	+	Missense_Mutation	SNP	A	A	C	rs13201753|rs371085669	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28331128A>C	ENST00000377255.3	+	5	896	c.599A>C	c.(598-600)aAa>aCa	p.K200T	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.K52T|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.K200T	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	200			K -> A (requires 2 nucleotide substitutions; dbSNP:rs13201752). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.|K -> E (in dbSNP:rs45505399). {ECO:0000269|PubMed:14702039}.|K -> T (in dbSNP:rs13201753).		autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						AGAGAAGATAAAGTGGTAGCT	0.537													C|||	1952	0.389776	0.5825	0.3213	5008	,	,		16779	0.2986		0.2843	False		,,,				2504	0.3804				p.K200T		Atlas-SNP	.											ZKSCAN3,NS,other,-1,1	ZKSCAN3	50	1	0			c.A599C						PASS	.	C	THR/LYS,THR/LYS,THR/LYS	2170,2236		549,1072,582	97.0	83.0	88.0		599,155,599	-0.1	0.0	6	dbSNP_121	88	2534,6066		400,1734,2166	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	78,78,78	949,2806,2748	CC,CA,AA		29.4651,49.251,36.1679	benign,benign,benign	200/539,52/391,200/539	28331128	4704,8302	2203	4300	6503	SO:0001583	missense	80317	exon4			AAGATAAAGTGGT	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.599A>C	6.37:g.28331128A>C	ENSP00000366465:p.Lys200Thr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	121	48	0.396694	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	579	0.2651098901098901	199	0.40447154471544716	101	0.27900552486187846	129	0.22552447552447552	150	0.19788918205804748	.	0.016	-1.538627	0.00942	0.49251	0.294651	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.14022	2.54;2.54;2.54	2.99	-0.126	0.13515	.	.	.	.	.	T	0.01353	0.0044	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49418	-0.8942	8	0.19147	T	0.46	.	6.7841	0.23664	0.3054:0.3751:0.3196:0.0	rs13201753;rs58899552;rs13201753	200	Q9BRR0	ZKSC3_HUMAN	T	200;52;200	ENSP00000252211:K200T;ENSP00000341883:K52T;ENSP00000366465:K200T	ENSP00000252211:K200T	K	+	2	0	ZKSCAN3	28439107	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.151000	0.10175	-0.315000	0.08703	-1.122000	0.02009	AAA	.	.	alt		0.537	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
WDR72	256764	hgsc.bcm.edu	37	15	53994493	53994493	+	Silent	SNP	A	A	G	rs6416452	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:53994493A>G	ENST00000396328.1	-	12	1646	c.1407T>C	c.(1405-1407)taT>taC	p.Y469Y	WDR72_ENST00000557913.1_Silent_p.Y466Y|WDR72_ENST00000559418.1_Silent_p.Y479Y|WDR72_ENST00000360509.5_Silent_p.Y469Y	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	469										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		GACCATGTGGATAGAGTAATG	0.383													G|||	3204	0.639776	0.702	0.6628	5008	,	,		13602	0.8016		0.505	False		,,,				2504	0.5112				p.Y469Y		Atlas-SNP	.											.	WDR72	177	.	0			c.T1407C						PASS	.	G		3018,1370	454.0+/-350.5	1029,960,205	123.0	117.0	119.0		1407	-2.0	0.2	15	dbSNP_116	119	4285,4301	577.9+/-390.6	1059,2167,1067	yes	coding-synonymous	WDR72	NM_182758.2		2088,3127,1272	GG,GA,AA		49.9068,31.2215,43.7105		469/1103	53994493	7303,5671	2194	4293	6487	SO:0001819	synonymous_variant	256764	exon12			ATGTGGATAGAGT	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.1407T>C	15.37:g.53994493A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_182758	Q7Z3I3|Q8N8X2	Silent	SNP	ENST00000396328.1	37	CCDS10151.1																																																																																			A|0.403;G|0.597	0.597	strong		0.383	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971299	45971299	+	Missense_Mutation	SNP	T	T	C	rs233240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45971299T>C	ENST00000391621.1	-	1	89	c.43A>G	c.(43-45)Aac>Gac	p.N15D	KRTAP10-2_ENST00000498210.1_5'UTR|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	15			N -> D (in dbSNP:rs233240). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)		p.N15D(1)		large_intestine(1)|lung(4)|skin(1)	6						TGCCAGGAGTTGGTGCAGGCG	0.667													T|||	1085	0.216653	0.1725	0.1527	5008	,	,		17203	0.371		0.2068	False		,,,				2504	0.1728				p.N15D		Atlas-SNP	.											KRTAP10-2,bladder,carcinoma,0,3	KRTAP10-2	21	3	1	Substitution - Missense(1)	large_intestine(1)	c.A43G						PASS	.	T	,ASP/ASN	761,3645	309.4+/-291.0	65,631,1507	81.0	86.0	84.0		,43	-1.0	0.0	21	dbSNP_79	84	1692,6908	310.1+/-309.7	158,1376,2766	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,23	223,2007,4273	CC,CT,TT		19.6744,17.2719,18.8605	,benign	,15/256	45971299	2453,10553	2203	4300	6503	SO:0001583	missense	386679	exon1			AGGAGTTGGTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.43A>G	21.37:g.45971299T>C	ENSP00000375479:p.Asn15Asp	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	183	95	0.519126	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	531	0.24313186813186813	81	0.16463414634146342	60	0.16574585635359115	218	0.3811188811188811	172	0.22691292875989447	t	0.005	-2.231254	0.00280	0.172719	0.196744	ENSG00000205445	ENST00000391621	T	0.14640	2.49	3.46	-1.05	0.10036	.	.	.	.	.	T	0.00012	0.0000	N	0.00355	-1.605	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38457	-0.9660	8	0.02654	T	1	.	3.6264	0.08114	0.0:0.4225:0.1919:0.3855	rs233240;rs620443;rs59814995	15	P60368	KR102_HUMAN	D	15	ENSP00000375479:N15D	ENSP00000375479:N15D	N	-	1	0	KRTAP10-2	44795727	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.100000	0.15231	-0.801000	0.04427	-0.814000	0.03130	AAC	T|0.767;C|0.233	0.233	strong		0.667	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
NRAP	4892	hgsc.bcm.edu	37	10	115370254	115370254	+	Silent	SNP	A	A	G	rs12243176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115370254A>G	ENST00000359988.3	-	31	3811	c.3567T>C	c.(3565-3567)atT>atC	p.I1189I	NRAP_ENST00000369360.3_Silent_p.I1162I|NRAP_ENST00000360478.3_Silent_p.I1154I|NRAP_ENST00000369358.4_Silent_p.I1197I	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TCCTCCCTTCAATCTCTAACG	0.418													A|||	2351	0.469449	0.354	0.4669	5008	,	,		17753	0.6032		0.4652	False		,,,				2504	0.4939				p.I1189I		Atlas-SNP	.											.	NRAP	208	.	0			c.T3567C						PASS	.	A	,	1587,2819	495.5+/-363.3	300,987,916	178.0	150.0	160.0		3462,3567	-5.9	0.8	10	dbSNP_120	160	4166,4434	567.6+/-388.9	1004,2158,1138	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	1304,3145,2054	GG,GA,AA		48.4419,36.0191,44.2334	,	1154/1696,1189/1731	115370254	5753,7253	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon31			CCCTTCAATCTCT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3567T>C	10.37:g.115370254A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			A|0.547;G|0.453	0.453	strong		0.418	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
TULP4	56995	hgsc.bcm.edu	37	6	158924595	158924595	+	Silent	SNP	A	A	G	rs3749853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:158924595A>G	ENST00000367097.3	+	13	5257	c.3900A>G	c.(3898-3900)caA>caG	p.Q1300Q	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	1300					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CCGACCTCCAAAGCCACTTGG	0.612													A|||	726	0.144968	0.1672	0.1037	5008	,	,		16677	0.1389		0.1889	False		,,,				2504	0.1053				p.Q1300Q		Atlas-SNP	.											.	TULP4	137	.	0			c.A3900G						PASS	.	A	,	705,3701	286.9+/-279.0	60,585,1558	55.0	59.0	58.0		,3900	-3.0	1.0	6	dbSNP_107	58	1684,6916	298.2+/-303.8	162,1360,2778	no	intron,coding-synonymous	TULP4	NM_001007466.1,NM_020245.3	,	222,1945,4336	GG,GA,AA		19.5814,16.0009,18.3684	,	,1300/1544	158924595	2389,10617	2203	4300	6503	SO:0001819	synonymous_variant	56995	exon13			CCTCCAAAGCCAC		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.3900A>G	6.37:g.158924595A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Silent	SNP	ENST00000367097.3	37	CCDS34561.1																																																																																			A|0.827;G|0.173	0.173	strong		0.612	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
TTLL5	23093	hgsc.bcm.edu	37	14	76330181	76330181	+	Silent	SNP	G	G	A	rs3742764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:76330181G>A	ENST00000298832.9	+	29	3703	c.3498G>A	c.(3496-3498)ctG>ctA	p.L1166L	TTLL5_ENST00000554510.1_Silent_p.L675L|TTLL5_ENST00000557636.1_Silent_p.L1181L|TTLL5_ENST00000556893.1_Silent_p.L717L	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1166					fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		GGCAGCTCCTGGACCAGAGTC	0.453													G|||	1094	0.21845	0.2769	0.0634	5008	,	,		15378	0.4137		0.0885	False		,,,				2504	0.182				p.L1166L		Atlas-SNP	.											.	TTLL5	102	.	0			c.G3498A						PASS	.	G		984,3422	368.6+/-318.7	98,788,1317	64.0	69.0	67.0		3498	3.5	1.0	14	dbSNP_107	67	722,7878	176.0+/-226.0	30,662,3608	no	coding-synonymous	TTLL5	NM_015072.4		128,1450,4925	AA,AG,GG		8.3953,22.3332,13.117		1166/1282	76330181	1706,11300	2203	4300	6503	SO:0001819	synonymous_variant	23093	exon29			GCTCCTGGACCAG	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.3498G>A	14.37:g.76330181G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	137	42	0.306569	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Silent	SNP	ENST00000298832.9	37	CCDS32124.1																																																																																			G|0.824;A|0.176	0.176	strong		0.453	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
PPP5C	5536	hgsc.bcm.edu	37	19	46878989	46878989	+	Silent	SNP	G	G	A	rs4239538	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46878989G>A	ENST00000012443.4	+	3	595	c.492G>A	c.(490-492)tcG>tcA	p.S164S	PPP5C_ENST00000391919.1_Silent_p.S58S	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	164					cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		TGGTGGACTCGCTGGACATCG	0.597													G|||	699	0.139577	0.0794	0.1931	5008	,	,		19732	0.0357		0.3022	False		,,,				2504	0.1227				p.S164S		Atlas-SNP	.											.	PPP5C	44	.	0			c.G492A						PASS	.	G	,	545,3857		36,473,1692	38.0	32.0	34.0		492,492	-6.1	0.1	19	dbSNP_111	34	2474,6124		316,1842,2141	no	coding-synonymous,coding-synonymous	PPP5C	NM_001204284.1,NM_006247.3	,	352,2315,3833	AA,AG,GG		28.7741,12.3807,23.2231	,	164/478,164/500	46878989	3019,9981	2201	4299	6500	SO:0001819	synonymous_variant	5536	exon3			GGACTCGCTGGAC		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.492G>A	19.37:g.46878989G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	190	86	0.452632	NM_006247	Q16722|Q53XV2	Silent	SNP	ENST00000012443.4	37	CCDS12684.1																																																																																			G|0.628;A|0.372	0.372	strong		0.597	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247	
TGM5	9333	hgsc.bcm.edu	37	15	43527819	43527819	+	Missense_Mutation	SNP	T	T	C	rs35985214	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43527819T>C	ENST00000220420.5	-	10	1569	c.1562A>G	c.(1561-1563)cAg>cGg	p.Q521R	TGM5_ENST00000349114.4_Missense_Mutation_p.Q439R	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	521			Q -> R (in dbSNP:rs35985214).		cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	GCATATATCCTGGCCCATGTT	0.577													T|||	28	0.00559105	0.0008	0.0086	5008	,	,		21464	0.0		0.0179	False		,,,				2504	0.0031				p.Q521R		Atlas-SNP	.											TGM5,rectum,carcinoma,-1,1	TGM5	88	1	0			c.A1562G						PASS	.	T	ARG/GLN,ARG/GLN	17,4389	23.3+/-48.9	0,17,2186	99.0	81.0	87.0		1316,1562	1.7	1.0	15	dbSNP_126	87	146,8452	70.7+/-133.2	1,144,4154	yes	missense,missense	TGM5	NM_004245.3,NM_201631.3	43,43	1,161,6340	CC,CT,TT		1.6981,0.3858,1.2535	benign,benign	439/639,521/721	43527819	163,12841	2203	4299	6502	SO:0001583	missense	9333	exon10			ATATCCTGGCCCA	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.1562A>G	15.37:g.43527819T>C	ENSP00000220420:p.Gln521Arg	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	160	59	0.36875	NM_201631	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	7.086	0.571152	0.13623	0.003858	0.016981	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.69561	-0.41;-0.41	5.58	1.73	0.24493	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.134279	0.47852	D	0.000201	T	0.37919	0.1021	L	0.50333	1.59	0.27114	N	0.962306	B;B	0.12630	0.004;0.006	B;B	0.19666	0.013;0.026	T	0.39502	-0.9611	10	0.42905	T	0.14	-8.616	4.8757	0.13655	0.1649:0.1715:0.0:0.6635	rs35985214	439;521	O43548-2;O43548	.;TGM5_HUMAN	R	521;439;520	ENSP00000220420:Q521R;ENSP00000220419:Q439R	ENSP00000220420:Q521R	Q	-	2	0	TGM5	41315111	1.000000	0.71417	0.997000	0.53966	0.029000	0.11900	1.138000	0.31491	0.387000	0.25024	-0.274000	0.10170	CAG	T|0.988;C|0.012	0.012	strong		0.577	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
GDA	9615	hgsc.bcm.edu	37	9	74865703	74865703	+	3'UTR	SNP	C	C	T	rs41310055	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:74865703C>T	ENST00000358399.3	+	0	3903				GDA_ENST00000238018.4_Missense_Mutation_p.P467S|GDA_ENST00000376986.1_Missense_Mutation_p.P389S|GDA_ENST00000376989.3_Missense_Mutation_p.P406S	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase						guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		CTCACCCCATCCTCCACCATT	0.348													C|||	56	0.0111821	0.0023	0.0259	5008	,	,		19901	0.0		0.0338	False		,,,				2504	0.001				p.P467S		Atlas-SNP	.											.	GDA	113	.	0			c.C1399T						PASS	.	C	SER/PRO,,,	5,1747		0,5,871	183.0	176.0	178.0		1399,,,	-4.2	0.0	9	dbSNP_127	178	114,3868		3,108,1880	yes	missense,utr-3,utr-3,utr-3	GDA	NM_001242505.1,NM_001242506.1,NM_001242507.1,NM_004293.3	74,,,	3,113,2751	TT,TC,CC		2.8629,0.2854,2.0753	,,,	467/472,,,	74865703	119,5615	876	1991	2867	SO:0001624	3_prime_UTR_variant	9615	exon15			CCCCATCCTCCAC	AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.*2445C>T	9.37:g.74865703C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_001242505	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Missense_Mutation	SNP	ENST00000358399.3	37	CCDS6641.1	38	0.0173992673992674	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	22	0.029023746701846966	C	11.23	1.578328	0.28180	0.002854	0.028629	ENSG00000119125	ENST00000238018;ENST00000376989;ENST00000376986;ENST00000436438	.	.	.	5.63	-4.16	0.03869	.	0.435749	0.10633	U	0.651951	T	0.03348	0.0097	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18429	-1.0337	9	0.87932	D	0	.	0.8379	0.01143	0.2342:0.2716:0.1157:0.3785	rs41310055	389;467	Q5SZC6;Q9Y2T3-3	.;.	S	467;406;389;175	.	ENSP00000238018:P467S	P	+	1	0	GDA	74055523	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.992000	0.01476	-0.594000	0.05836	-0.140000	0.14226	CCT	C|0.979;T|0.021	0.021	strong		0.348	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1		
MUC16	94025	hgsc.bcm.edu	37	19	9077436	9077436	+	Missense_Mutation	SNP	G	G	A	rs1862462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9077436G>A	ENST00000397910.4	-	3	10213	c.10010C>T	c.(10009-10011)tCa>tTa	p.S3337L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3338	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTTGTCTTTGAAACCAGTTC	0.502													G|||	1243	0.248203	0.1997	0.2118	5008	,	,		21495	0.249		0.3121	False		,,,				2504	0.273				p.S3337L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C10010T						PASS	.	G	LEU/SER	834,3080		98,638,1221	144.0	134.0	137.0		10010	-0.1	0.0	19	dbSNP_92	137	2394,5932		347,1700,2116	yes	missense	MUC16	NM_024690.2	145	445,2338,3337	AA,AG,GG		28.7533,21.3081,26.3725	benign	3337/14508	9077436	3228,9012	1957	4163	6120	SO:0001583	missense	94025	exon3			GTCTTTGAAACCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10010C>T	19.37:g.9077436G>A	ENSP00000381008:p.Ser3337Leu	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	241	117	0.485477	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	552	0.25274725274725274	108	0.21951219512195122	88	0.2430939226519337	124	0.21678321678321677	232	0.30606860158311344	g	3.953	-0.011966	0.07727	0.213081	0.287533	ENSG00000181143	ENST00000397910	T	0.02656	4.21	2.13	-0.123	0.13527	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.06405	0.002	T	0.47459	-0.9116	8	0.87932	D	0	.	4.6935	0.12791	0.3344:0.0:0.6656:0.0	rs1862462;rs17516250;rs56508237;rs58424799;rs1862462	3337	B5ME49	.	L	3337	ENSP00000381008:S3337L	ENSP00000381008:S3337L	S	-	2	0	MUC16	8938436	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.053000	0.11846	0.035000	0.15519	-1.054000	0.02325	TCA	G|0.749;A|0.251	0.251	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MTERF2	80298	hgsc.bcm.edu	37	12	107372277	107372277	+	Silent	SNP	C	C	T	rs1043156	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:107372277C>T	ENST00000552029.1	-	2	2284	c.216G>A	c.(214-216)gaG>gaA	p.E72E	MTERFD3_ENST00000240050.4_Silent_p.E72E|MTERFD3_ENST00000392830.2_Silent_p.E72E|C12orf23_ENST00000551237.1_3'UTR			Q49AM1	MTEF2_HUMAN		72					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						AGGTTTCATCCTCTAAAAGTA	0.383													C|||	588	0.117412	0.149	0.0922	5008	,	,		19062	0.0099		0.1252	False		,,,				2504	0.1953				p.E72E		Atlas-SNP	.											.	MTERFD3	32	.	0			c.G216A						PASS	.	C	,	620,3786	267.1+/-267.6	48,524,1631	118.0	115.0	116.0		216,216	1.6	0.4	12	dbSNP_86	116	1129,7471	232.1+/-265.8	63,1003,3234	no	coding-synonymous,coding-synonymous	MTERFD3	NM_001033050.1,NM_025198.3	,	111,1527,4865	TT,TC,CC		13.1279,14.0717,13.4476	,	72/386,72/386	107372277	1749,11257	2203	4300	6503	SO:0001819	synonymous_variant	80298	exon3			TTCATCCTCTAAA																												ENST00000552029.1:c.216G>A	12.37:g.107372277C>T		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_001033050	Q53HM2|Q9H4L6|Q9H7Y9	Silent	SNP	ENST00000552029.1	37	CCDS9111.1																																																																																			C|0.884;T|0.116	0.116	strong		0.383	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1		
LRRCC1	85444	hgsc.bcm.edu	37	8	86021932	86021932	+	Missense_Mutation	SNP	T	T	A	rs16913589	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:86021932T>A	ENST00000360375.3	+	2	356	c.207T>A	c.(205-207)caT>caA	p.H69Q	LRRCC1_ENST00000414626.2_Missense_Mutation_p.H49Q	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	69			H -> Q (in dbSNP:rs16913589).		mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ATTTACAACATCTAGATCTGT	0.323													T|||	110	0.0219649	0.0408	0.0288	5008	,	,		15529	0.0		0.0239	False		,,,				2504	0.0123				p.H69Q		Atlas-SNP	.											.	LRRCC1	212	.	0			c.T207A						PASS	.	T	GLN/HIS	130,3552		1,128,1712	65.0	58.0	60.0		207	3.4	1.0	8	dbSNP_123	60	371,7801		7,357,3722	yes	missense	LRRCC1	NM_033402.4	24	8,485,5434	AA,AT,TT		4.5399,3.5307,4.2264	probably-damaging	69/1033	86021932	501,11353	1841	4086	5927	SO:0001583	missense	85444	exon2			ACAACATCTAGAT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.207T>A	8.37:g.86021932T>A	ENSP00000353538:p.His69Gln	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	162	89	0.549383	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	51	0.023351648351648352	19	0.03861788617886179	12	0.03314917127071823	0	0.0	20	0.026385224274406333	T	19.27	3.794981	0.70452	0.035307	0.045399	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.22945	1.93;1.93	5.79	3.4	0.38934	.	0.000000	0.42053	D	0.000766	T	0.08758	0.0217	L	0.51422	1.61	0.50813	D	0.999899	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.988	T	0.00282	-1.1850	10	0.31617	T	0.26	-19.0196	9.2669	0.37647	0.0:0.28:0.0:0.72	rs16913589;rs52817898;rs16913589	49;69	Q9C099-2;Q9C099	.;LRCC1_HUMAN	Q	69;49	ENSP00000353538:H69Q;ENSP00000394695:H49Q	ENSP00000353538:H69Q	H	+	3	2	LRRCC1	86209184	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	1.317000	0.33631	0.453000	0.26858	0.482000	0.46254	CAT	T|0.969;A|0.031	0.031	strong		0.323	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
KHK	3795	hgsc.bcm.edu	37	2	27315252	27315252	+	Missense_Mutation	SNP	G	G	A	rs2304681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:27315252G>A	ENST00000260599.6	+	2	658	c.145G>A	c.(145-147)Gtt>Att	p.V49I	KHK_ENST00000490823.1_3'UTR|KHK_ENST00000260598.5_Missense_Mutation_p.V49I	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	49			V -> I (in dbSNP:rs2304681). {ECO:0000269|PubMed:7833921}.		carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCTGCACCGTTCTCTCCCT	0.632													G|||	1660	0.33147	0.3033	0.5043	5008	,	,		19742	0.2312		0.3767	False		,,,				2504	0.3037				p.V49I		Atlas-SNP	.											KHK_ENST00000260598,colon,carcinoma,0,2	KHK	60	2	0			c.G145A						PASS	.	G	ILE/VAL,ILE/VAL	1399,3007	459.0+/-352.1	230,939,1034	76.0	63.0	67.0		145,145	2.7	0.0	2	dbSNP_100	67	3231,5369	486.6+/-371.9	622,1987,1691	yes	missense,missense	KHK	NM_000221.2,NM_006488.2	29,29	852,2926,2725	AA,AG,GG		37.5698,31.7522,35.599	benign,benign	49/299,49/299	27315252	4630,8376	2203	4300	6503	SO:0001583	missense	3795	exon2			TGCACCGTTCTCT		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.145G>A	2.37:g.27315252G>A	ENSP00000260599:p.Val49Ile	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	70	44	0.628571	NM_006488	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	37	CCDS1734.1	745	0.3411172161172161	156	0.3170731707317073	172	0.47513812154696133	150	0.26223776223776224	267	0.35224274406332456	G	19.83	3.900193	0.72754	0.317522	0.375698	ENSG00000138030	ENST00000260599;ENST00000260598;ENST00000429697	T;T;T	0.77877	-1.13;-1.13;-1.13	5.5	2.71	0.32032	Carbohydrate/purine kinase (1);	0.183501	0.47852	N	0.000205	T	0.00012	0.0000	M	0.69185	2.1	0.24585	P	0.99385471	B;P;B	0.35821	0.045;0.523;0.045	B;B;B	0.32393	0.012;0.145;0.012	T	0.43734	-0.9373	9	0.18710	T	0.47	-18.5598	7.773	0.29019	0.336:0.0:0.664:0.0	rs2304681;rs13006404;rs17845083;rs17847238;rs17857867;rs57123139;rs2304681	49;49;49	Q6IBK2;P50053-2;P50053	.;.;KHK_HUMAN	I	49	ENSP00000260599:V49I;ENSP00000260598:V49I;ENSP00000404741:V49I	ENSP00000260598:V49I	V	+	1	0	KHK	27168756	1.000000	0.71417	0.013000	0.15412	0.966000	0.64601	4.090000	0.57693	0.701000	0.31803	0.462000	0.41574	GTT	G|0.649;A|0.351	0.351	strong		0.632	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1		
C9orf40	55071	hgsc.bcm.edu	37	9	77567335	77567335	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:77567335C>T	ENST00000376854.5	-	1	467	c.193G>A	c.(193-195)Gag>Aag	p.E65K	RP11-197P3.4_ENST00000455609.1_RNA	NM_017998.2	NP_060468.2	Q8IXQ3	CI040_HUMAN	chromosome 9 open reading frame 40	65										lung(2)|stomach(1)	3						GCCGAGGGCTCTGCCATGGTC	0.706																																					p.E65K		Atlas-SNP	.											.	C9orf40	5	.	0			c.G193A						PASS	.						11.0	11.0	11.0					9																	77567335		2086	4155	6241	SO:0001583	missense	55071	exon1			AGGGCTCTGCCAT	AK000972	CCDS6648.1	9q21.31	2012-03-15			ENSG00000135045	ENSG00000135045			23433	protein-coding gene	gene with protein product							Standard	NM_017998		Approved	FLJ10110	uc004ajo.4	Q8IXQ3	OTTHUMG00000020031	ENST00000376854.5:c.193G>A	9.37:g.77567335C>T	ENSP00000366050:p.Glu65Lys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_017998	Q9NWD3	Missense_Mutation	SNP	ENST00000376854.5	37	CCDS6648.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930235	0.73327	.	.	ENSG00000135045	ENST00000376854	.	.	.	5.21	4.25	0.50352	.	0.327978	0.21929	N	0.067058	T	0.50769	0.1635	M	0.61703	1.905	0.23620	N	0.997277	P	0.50156	0.932	P	0.53450	0.726	T	0.44034	-0.9354	9	0.56958	D	0.05	-11.2091	10.2293	0.43245	0.1977:0.8023:0.0:0.0	.	65	Q8IXQ3	CI040_HUMAN	K	65	.	ENSP00000366050:E65K	E	-	1	0	C9orf40	76757155	0.160000	0.22878	0.496000	0.27539	0.498000	0.33706	1.673000	0.37534	2.447000	0.82792	0.305000	0.20034	GAG	.	.	none		0.706	C9orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052702.1	NM_017998	
C16orf89	146556	hgsc.bcm.edu	37	16	5097947	5097947	+	Missense_Mutation	SNP	A	A	G	rs1127920	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:5097947A>G	ENST00000315997.5	-	7	1088	c.887T>C	c.(886-888)tTa>tCa	p.L296S	C16orf89_ENST00000474471.3_Missense_Mutation_p.L328S|C16orf89_ENST00000350219.4_Missense_Mutation_p.L334S|C16orf89_ENST00000422873.1_Missense_Mutation_p.L334S|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000472572.3_Missense_Mutation_p.L296S	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	296			L -> S (in dbSNP:rs1127920). {ECO:0000269|PubMed:15489334}.			cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	12						AGCTTTAGATAATTCTTCATC	0.328													A|||	1132	0.226038	0.0325	0.4337	5008	,	,		18221	0.2034		0.3678	False		,,,				2504	0.2178				p.L296S		Atlas-SNP	.											.	C16orf89	64	.	0			c.T887C						PASS	.	A	SER/LEU,SER/LEU	324,3282		13,298,1492	63.0	56.0	58.0		887,887	-2.8	0.0	16	dbSNP_86	58	2784,5348		479,1826,1761	yes	missense,missense	C16orf89	NM_001098514.2,NM_152459.4	145,145	492,2124,3253	GG,GA,AA		34.2351,8.985,26.4781	possibly-damaging,possibly-damaging	296/362,296/403	5097947	3108,8630	1803	4066	5869	SO:0001583	missense	146556	exon7			TTAGATAATTCTT		CCDS42116.1, CCDS45404.1, CCDS42116.2, CCDS45404.2	16p13.3	2011-12-12			ENSG00000153446	ENSG00000153446			28687	protein-coding gene	gene with protein product						12975309, 20578903	Standard	NM_001098514		Approved	MGC45438	uc010bud.3	Q6UX73	OTTHUMG00000159314	ENST00000315997.5:c.887T>C	16.37:g.5097947A>G	ENSP00000324672:p.Leu296Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Missense_Mutation	SNP	ENST00000315997.5	37	CCDS42116.2	558	0.2554945054945055	21	0.042682926829268296	141	0.38950276243093923	113	0.19755244755244755	283	0.3733509234828496	A	14.34	2.506853	0.44558	0.08985	0.342351	ENSG00000153446	ENST00000474471;ENST00000472572;ENST00000477550;ENST00000422873;ENST00000350219;ENST00000315997	T;T;T;T	0.40225	1.17;1.04;1.04;1.17	3.59	-2.84	0.05751	.	1.396170	0.04946	N	0.459453	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P;P	0.38922	0.651;0.617	B;B	0.42282	0.212;0.382	T	0.18745	-1.0327	9	0.56958	D	0.05	-23.7719	1.8854	0.03237	0.269:0.1639:0.4064:0.1607	rs1127920;rs3210909;rs9674145;rs11558485;rs17846054;rs17859047;rs52830272;rs9674145	296;334	Q6UX73;G3V0F0	CP089_HUMAN;.	S	328;296;296;334;334;328	ENSP00000417158:L328S;ENSP00000420566:L296S;ENSP00000390402:L334S;ENSP00000283478:L334S	ENSP00000324672:L328S	L	-	2	0	C16orf89	5037948	0.000000	0.05858	0.000000	0.03702	0.621000	0.37620	-0.056000	0.11787	-0.796000	0.04456	0.459000	0.35465	TTA	T|0.086;G|0.260	0.260	strong		0.328	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459	
BCL2	596	hgsc.bcm.edu	37	18	60985879	60985879	+	Silent	SNP	T	T	C	rs1801018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:60985879T>C	ENST00000398117.1	-	1	1482	c.21A>G	c.(19-21)acA>acG	p.T7T	BCL2_ENST00000333681.4_Silent_p.T7T|BCL2_ENST00000444484.1_Silent_p.T7T|BCL2_ENST00000589955.1_Silent_p.T7T	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	7			T -> S. {ECO:0000269|PubMed:2834197, ECO:0000269|PubMed:3285301}.		actin filament organization (GO:0007015)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|axonogenesis (GO:0007409)|B cell homeostasis (GO:0001782)|B cell lineage commitment (GO:0002326)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|behavioral fear response (GO:0001662)|branching involved in ureteric bud morphogenesis (GO:0001658)|CD8-positive, alpha-beta T cell lineage commitment (GO:0043375)|cell aging (GO:0007569)|cell growth (GO:0016049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to organic substance (GO:0071310)|cochlear nucleus development (GO:0021747)|defense response to virus (GO:0051607)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|ear development (GO:0043583)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|female pregnancy (GO:0007565)|focal adhesion assembly (GO:0048041)|gland morphogenesis (GO:0022612)|glomerulus development (GO:0032835)|hair follicle morphogenesis (GO:0031069)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|melanin metabolic process (GO:0006582)|melanocyte differentiation (GO:0030318)|mesenchymal cell development (GO:0014031)|metanephros development (GO:0001656)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of autophagy (GO:0010507)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cellular pH reduction (GO:0032848)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of retinal cell programmed cell death (GO:0046671)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oocyte development (GO:0048599)|organ growth (GO:0035265)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pigment granule organization (GO:0048753)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell growth (GO:0030307)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron maturation (GO:0014042)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smooth muscle cell migration (GO:0014911)|post-embryonic development (GO:0009791)|protein dephosphorylation (GO:0006470)|protein polyubiquitination (GO:0000209)|reactive oxygen species metabolic process (GO:0072593)|regulation of calcium ion transport (GO:0051924)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glycoprotein biosynthetic process (GO:0010559)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|regulation of protein stability (GO:0031647)|regulation of transmembrane transporter activity (GO:0022898)|regulation of viral genome replication (GO:0045069)|release of cytochrome c from mitochondria (GO:0001836)|renal system process (GO:0003014)|response to acid chemical (GO:0001101)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to iron ion (GO:0010039)|response to ischemia (GO:0002931)|response to nicotine (GO:0035094)|response to radiation (GO:0009314)|response to toxic substance (GO:0009636)|response to UV-B (GO:0010224)|single organismal cell-cell adhesion (GO:0016337)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|channel inhibitor activity (GO:0016248)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(106)|kidney(1)|large_intestine(1)|lung(3)	113		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Ibuprofen(DB01050)|Paclitaxel(DB01229)|Rasagiline(DB01367)	TATCGTACCCTGTTCTCCCAG	0.627			T	IGH@	"""NHL, CLL"""								T|||	1218	0.243211	0.0318	0.389	5008	,	,		14585	0.0923		0.4751	False		,,,				2504	0.3425				p.T7T		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	BCL2_ENST00000444484,brain,glioma,0,15	BCL2	272	15	0			c.A21G						PASS	.	T	,	337,3577		16,305,1636	67.0	74.0	71.0		21,21	0.5	0.9	18	dbSNP_89	71	3402,4728		707,1988,1370	no	coding-synonymous,coding-synonymous	BCL2	NM_000633.2,NM_000657.2	,	723,2293,3006	CC,CT,TT		41.845,8.6101,31.0445	,	7/240,7/206	60985879	3739,8305	1957	4065	6022	SO:0001819	synonymous_variant	596	exon2			GTACCCTGTTCTC	M14745	CCDS11981.1, CCDS45882.1	18q21.3	2014-03-07			ENSG00000171791	ENSG00000171791		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	990	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 50"""	151430					Standard	XM_006722523		Approved	Bcl-2, PPP1R50	uc002lit.1	P10415	OTTHUMG00000132791	ENST00000398117.1:c.21A>G	18.37:g.60985879T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	59	17	0.288136	NM_000633	C9JHD5|P10416|Q13842|Q16197	Silent	SNP	ENST00000398117.1	37	CCDS11981.1																																																																																			T|0.720;C|0.280	0.280	strong		0.627	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657	
OR8D4	338662	hgsc.bcm.edu	37	11	123777412	123777412	+	Missense_Mutation	SNP	A	A	G	rs17127950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123777412A>G	ENST00000321355.2	+	1	304	c.274A>G	c.(274-276)Atc>Gtc	p.I92V		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	92			I -> V (in dbSNP:rs17127950).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		AGATAGATCCATCTCCTATTC	0.403													A|||	934	0.186502	0.2844	0.1455	5008	,	,		22333	0.0933		0.1829	False		,,,				2504	0.183				p.I92V		Atlas-SNP	.											.	OR8D4	62	.	0			c.A274G						PASS	.	A	VAL/ILE	1081,3323	392.1+/-328.4	140,801,1261	260.0	262.0	261.0		274	3.5	0.1	11	dbSNP_123	261	1635,6963	303.0+/-306.2	164,1307,2828	yes	missense	OR8D4	NM_001005197.1	29	304,2108,4089	GG,GA,AA		19.0161,24.5459,20.8891	possibly-damaging	92/315	123777412	2716,10286	2202	4299	6501	SO:0001583	missense	338662	exon1			AGATCCATCTCCT	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.274A>G	11.37:g.123777412A>G	ENSP00000325381:p.Ile92Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	162	72	0.444444	NM_001005197	Q6IFE9	Missense_Mutation	SNP	ENST00000321355.2	37	CCDS31698.1	406	0.1858974358974359	133	0.2703252032520325	57	0.1574585635359116	75	0.13111888111888112	141	0.18601583113456466	A	7.674	0.687645	0.14973	0.245459	0.190161	ENSG00000181518	ENST00000321355	T	0.05580	3.42	5.81	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.138719	0.32901	N	0.005516	T	0.00012	0.0000	M	0.78637	2.42	0.37613	P	0.07899100000000003	B	0.16802	0.019	B	0.21151	0.033	T	0.25222	-1.0138	9	0.72032	D	0.01	.	7.8258	0.29313	0.769:0.0:0.231:0.0	rs17127950;rs52791176;rs58181468;rs17127950	92	Q8NGM9	OR8D4_HUMAN	V	92	ENSP00000325381:I92V	ENSP00000325381:I92V	I	+	1	0	OR8D4	123282622	0.963000	0.33076	0.072000	0.20136	0.270000	0.26580	3.218000	0.51192	0.480000	0.27534	-0.250000	0.11733	ATC	A|0.800;G|0.200	0.200	strong		0.403	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
AP1M1	8907	hgsc.bcm.edu	37	19	16339715	16339715	+	Silent	SNP	C	C	T	rs3752797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:16339715C>T	ENST00000291439.3	+	9	1472	c.1023C>T	c.(1021-1023)atC>atT	p.I341I	AP1M1_ENST00000444449.2_Silent_p.I353I|AP1M1_ENST00000429941.2_Intron|AP1M1_ENST00000541844.1_Silent_p.I269I|AP1M1_ENST00000590756.1_Silent_p.I269I	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	341	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						ACAGCGAGATCGTGTGGTCCA	0.612													C|||	2264	0.452077	0.177	0.585	5008	,	,		19833	0.3641		0.7008	False		,,,				2504	0.5644				p.I353I		Atlas-SNP	.											.	AP1M1	48	.	0			c.C1059T						PASS	.	C	,	1123,3283	401.7+/-332.1	156,811,1236	235.0	137.0	171.0		1059,1023	-3.5	1.0	19	dbSNP_107	171	6136,2464	696.5+/-404.9	2200,1736,364	no	coding-synonymous,coding-synonymous	AP1M1	NM_001130524.1,NM_032493.3	,	2356,2547,1600	TT,TC,CC		28.6512,25.488,44.1873	,	353/436,341/424	16339715	7259,5747	2203	4300	6503	SO:0001819	synonymous_variant	8907	exon10			CGAGATCGTGTGG		CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.1023C>T	19.37:g.16339715C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_001130524	Q4TTY5	Silent	SNP	ENST00000291439.3	37	CCDS12342.1																																																																																			C|0.486;T|0.514	0.514	strong		0.612	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493	
PHC2	1912	hgsc.bcm.edu	37	1	33790496	33790496	+	Silent	SNP	G	G	A	rs11554674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33790496G>A	ENST00000257118.5	-	14	2600	c.2547C>T	c.(2545-2547)taC>taT	p.Y849Y	RP11-415J8.3_ENST00000588828.1_RNA|PHC2_ENST00000431992.1_Silent_p.Y820Y|PHC2_ENST00000373422.3_Silent_p.Y455Y|PHC2_ENST00000373418.3_Silent_p.Y314Y|PHC2_ENST00000485928.1_5'UTR|RP11-415J8.3_ENST00000587696.1_RNA|PHC2_ENST00000419414.2_Silent_p.Y850Y|RP11-415J8.3_ENST00000457957.2_RNA	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	849	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TGATGCGGGCGTAGATCTTCA	0.627													G|||	866	0.172923	0.0182	0.1715	5008	,	,		17074	0.2113		0.2416	False		,,,				2504	0.273				p.Y849Y		Atlas-SNP	.											.	PHC2	78	.	0			c.C2547T						PASS	.	G	,	227,4179	134.9+/-171.1	5,217,1981	76.0	69.0	71.0		942,2547	-5.7	0.3	1	dbSNP_120	71	2126,6474	364.7+/-333.6	253,1620,2427	no	coding-synonymous,coding-synonymous	PHC2	NM_004427.3,NM_198040.2	,	258,1837,4408	AA,AG,GG		24.7209,5.1521,18.0917	,	314/324,849/859	33790496	2353,10653	2203	4300	6503	SO:0001819	synonymous_variant	1912	exon14			GCGGGCGTAGATC	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.2547C>T	1.37:g.33790496G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Silent	SNP	ENST00000257118.5	37	CCDS378.1																																																																																			G|0.830;A|0.170	0.170	strong		0.627	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
CFHR2	3080	hgsc.bcm.edu	37	1	196876458	196876458	+	Intron	SNP	A	A	G	rs7417769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:196876458A>G	ENST00000367421.3	+	2	135				CFHR4_ENST00000251424.4_Intron|CFHR4_ENST00000367416.2_Missense_Mutation_p.N209S|CFHR4_ENST00000608469.1_Intron|CFHR4_ENST00000367418.2_Intron			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						TCTTCAGAAAACTGTGGGCCT	0.383													A|||	2950	0.589058	0.2095	0.7305	5008	,	,		15001	0.8304		0.6839	False		,,,				2504	0.6554				p.N210S		Atlas-SNP	.											.	CFHR4	141	.	0			c.A629G						PASS	.																																			SO:0001627	intron_variant	10877	exon5			CAGAAAACTGTGG	X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367421.3:c.59-42127A>G	1.37:g.196876458A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	212	121	0.570755	NM_001201550	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367421.3	37		1376	0.63003663003663	126	0.25609756097560976	254	0.7016574585635359	472	0.8251748251748252	524	0.6912928759894459	.	8.504	0.864967	0.17250	.	.	ENSG00000134365	ENST00000367416	T	0.31510	1.49	3.65	1.13	0.20643	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34625	-0.9821	7	0.06494	T	0.89	.	3.1655	0.06534	0.6708:0.0:0.1234:0.2058	rs7417769;rs58790632;rs7417769	209;210	C9J7J7;Q5DVJ7	.;.	S	209	ENSP00000356386:N209S	ENSP00000356386:N209S	N	+	2	0	CFHR4	195143081	0.000000	0.05858	0.003000	0.11579	0.022000	0.10575	0.164000	0.16542	-0.002000	0.14469	0.438000	0.28831	AAC	A|0.364;G|0.636	0.636	strong		0.383	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666	
MYO1G	64005	hgsc.bcm.edu	37	7	45005795	45005795	+	Silent	SNP	G	G	A	rs2269969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45005795G>A	ENST00000258787.7	-	16	2170	c.2034C>T	c.(2032-2034)caC>caT	p.H678H		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	678	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						CCTGCAGCCCGTGCTGCTCCA	0.632													G|||	555	0.110823	0.0461	0.1671	5008	,	,		17924	0.0942		0.2197	False		,,,				2504	0.0634				p.H678H		Atlas-SNP	.											.	MYO1G	86	.	0			c.C2034T						PASS	.	G		310,4096	162.5+/-194.5	12,286,1905	53.0	48.0	50.0		2034	-5.9	0.7	7	dbSNP_100	50	1721,6879	308.9+/-309.1	176,1369,2755	no	coding-synonymous	MYO1G	NM_033054.2		188,1655,4660	AA,AG,GG		20.0116,7.0359,15.6159		678/1019	45005795	2031,10975	2203	4300	6503	SO:0001819	synonymous_variant	64005	exon16			CAGCCCGTGCTGC	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.2034C>T	7.37:g.45005795G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Silent	SNP	ENST00000258787.7	37	CCDS34629.1																																																																																			G|0.848;A|0.152	0.152	strong		0.632	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
SPTBN5	51332	hgsc.bcm.edu	37	15	42149506	42149506	+	Missense_Mutation	SNP	G	G	C	rs12442525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42149506G>C	ENST00000320955.6	-	51	8778	c.8551C>G	c.(8551-8553)Cag>Gag	p.Q2851E		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2851					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		ACAAAGGCCTGGGCCTGGCCC	0.662													G|||	2358	0.470847	0.0598	0.5951	5008	,	,		17472	0.9454		0.4712	False		,,,				2504	0.4489				p.Q2816E		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C8446G						PASS	.	G	GLU/GLN	544,3628		65,414,1607	12.0	14.0	13.0		8446	3.5	0.2	15	dbSNP_120	13	3960,4476		982,1996,1240	yes	missense	SPTBN5	NM_016642.2	29	1047,2410,2847	CC,CG,GG		46.9417,13.0393,35.7234	benign	2816/3640	42149506	4504,8104	2086	4218	6304	SO:0001583	missense	51332	exon51			AGGCCTGGGCCTG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8551C>G	15.37:g.42149506G>C	ENSP00000317790:p.Gln2851Glu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		1164	0.532967032967033	35	0.07113821138211382	214	0.5911602209944752	542	0.9475524475524476	373	0.4920844327176781	.	8.517	0.867948	0.17250	0.130393	0.469417	ENSG00000137877	ENST00000320955	T	0.33216	1.42	4.53	3.54	0.40534	.	0.549056	0.16416	N	0.215395	T	0.00012	0.0000	L	0.50919	1.6	0.80722	P	0.0	B	0.33777	0.425	B	0.31290	0.127	T	0.21724	-1.0237	9	0.59425	D	0.04	.	13.9202	0.63926	0.0:0.1531:0.8469:0.0	rs12442525;rs60096193	2851	Q9NRC6	SPTN5_HUMAN	E	2851	ENSP00000317790:Q2851E	ENSP00000317790:Q2851E	Q	-	1	0	SPTBN5	39936798	0.997000	0.39634	0.208000	0.23602	0.897000	0.52465	2.774000	0.47694	2.063000	0.61619	0.467000	0.42956	CAG	G|0.462;C|0.538	0.538	strong		0.662	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
DNAH8	1769	hgsc.bcm.edu	37	6	38729511	38729511	+	Missense_Mutation	SNP	T	T	C	rs61748600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38729511T>C	ENST00000359357.3	+	9	1152	c.898T>C	c.(898-900)Tat>Cat	p.Y300H	DNAH8_ENST00000441566.1_Missense_Mutation_p.Y300H|DNAH8_ENST00000449981.2_Missense_Mutation_p.Y517H			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	300					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ATGTAAAGCATATATTACTGA	0.264													T|||	420	0.0838658	0.0469	0.2334	5008	,	,		14654	0.0198		0.1372	False		,,,				2504	0.0389				p.Y517H		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T1549C						PASS	.	T	HIS/TYR	279,4127	155.5+/-188.7	8,263,1932	82.0	85.0	84.0		1549	6.0	1.0	6	dbSNP_129	84	1313,7285	257.7+/-281.7	96,1121,3082	yes	missense	DNAH8	NM_001206927.1	83	104,1384,5014	CC,CT,TT		15.271,6.3323,12.2424	benign	517/4708	38729511	1592,11412	2203	4299	6502	SO:0001583	missense	1769	exon11			AAAGCATATATTA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.898T>C	6.37:g.38729511T>C	ENSP00000352312:p.Tyr300His	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	208	83	0.399038	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		226	0.10347985347985347	26	0.052845528455284556	78	0.2154696132596685	14	0.024475524475524476	108	0.1424802110817942	T	21.2	4.114753	0.77210	0.063323	0.15271	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.58210	0.35;0.35;0.35	6.0	6.0	0.97389	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.46870	0.1415	L	0.58428	1.81	0.09310	P	0.99999613319	B	0.33857	0.429	P	0.44772	0.46	T	0.51857	-0.8652	9	0.35671	T	0.21	.	14.0315	0.64617	0.0:0.0:0.0:1.0	rs61748600	300	Q96JB1	DYH8_HUMAN	H	505;505;300;300	ENSP00000333363:Y505H;ENSP00000352312:Y300H;ENSP00000402294:Y300H	ENSP00000333363:Y505H	Y	+	1	0	DNAH8	38837489	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	4.287000	0.59001	2.297000	0.77311	0.519000	0.50382	TAT	T|0.879;C|0.121	0.121	strong		0.264	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
TRIM77	390231	hgsc.bcm.edu	37	11	89443808	89443808	+	Silent	SNP	A	A	C	rs11018745	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:89443808A>C	ENST00000398290.3	+	1	342	c.342A>C	c.(340-342)ctA>ctC	p.L114L		NM_001146162.1	NP_001139634.1	I1YAP6	TRI77_HUMAN	tripartite motif containing 77	114						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										TGTGTTTTCTATGCTCTCAAT	0.443													C|||	1300	0.259585	0.1188	0.281	5008	,	,		17154	0.3264		0.3738	False		,,,				2504	0.2485				p.L114L		Atlas-SNP	.											.	.	.	.	0			c.A342C						PASS	.						51.0	42.0	45.0					11																	89443808		692	1589	2281	SO:0001819	synonymous_variant	390231	exon1			TTTTCTATGCTCT		CCDS60929.1	11q14.3	2014-02-17	2013-01-14	2013-01-14	ENSG00000214414	ENSG00000214414		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	34228	protein-coding gene	gene with protein product			"""tripartite motif-containing 77"", ""tripartite motif containing 77, pseudogene"""	TRIM77P			Standard	NM_001146162		Approved		uc010rtw.2	I1YAP6	OTTHUMG00000167624	ENST00000398290.3:c.342A>C	11.37:g.89443808A>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_001146162		Silent	SNP	ENST00000398290.3	37																																																																																				A|0.705;C|0.295	0.295	strong		0.443	TRIM77-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146162	
BNIP2	663	hgsc.bcm.edu	37	15	59963488	59963488	+	Silent	SNP	A	A	G	rs1135148	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:59963488A>G	ENST00000607373.1	-	7	803	c.601T>C	c.(601-603)Tta>Cta	p.L201L	BNIP2_ENST00000267859.3_Silent_p.L322L|BNIP2_ENST00000478981.1_5'Flank|AC092755.4_ENST00000441746.1_RNA|BNIP2_ENST00000415213.2_Silent_p.L263L	NM_004330.2	NP_004321.2	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 2	201	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|positive regulation of GTPase activity (GO:0043547)|positive regulation of muscle cell differentiation (GO:0051149)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)			NS(1)|large_intestine(2)|lung(5)|ovary(1)	9						TCTGCTACTAATAGCTCCAAA	0.338													A|||	1663	0.332069	0.1029	0.3847	5008	,	,		16327	0.5615		0.3519	False		,,,				2504	0.3476				p.L322L	Ovarian(174;1936 1978 6671 8240 38212)	Atlas-SNP	.											.	BNIP2	27	.	0			c.T964C						PASS	.	A		669,3709		56,557,1576	60.0	54.0	56.0		964	3.6	1.0	15	dbSNP_86	56	2929,5643		518,1893,1875	no	coding-synonymous	BNIP2	NM_004330.2		574,2450,3451	GG,GA,AA		34.1694,15.281,27.7838		322/436	59963488	3598,9352	2189	4286	6475	SO:0001819	synonymous_variant	663	exon7			CTACTAATAGCTC	U15173	CCDS10174.2	15q21.3	2008-07-18	2002-08-29		ENSG00000140299	ENSG00000140299			1083	protein-coding gene	gene with protein product		603292	"""BCL2/adenovirus E1B 19kD-interacting protein 2"""			7954800	Standard	NM_004330		Approved	Nip2, BNIP-2	uc010uhc.2	Q12982	OTTHUMG00000132727	ENST00000607373.1:c.601T>C	15.37:g.59963488A>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	44	16	0.363636	NM_004330	B4DS94	Silent	SNP	ENST00000607373.1	37																																																																																				A|0.703;G|0.297	0.297	strong		0.338	BNIP2-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470740.1	NM_004330	
SMC5	23137	hgsc.bcm.edu	37	9	72897440	72897440	+	Missense_Mutation	SNP	T	T	C	rs1180117	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:72897440T>C	ENST00000361138.5	+	7	980	c.922T>C	c.(922-924)Tgt>Cgt	p.C308R		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	308			C -> R (in dbSNP:rs1180117). {ECO:0000269|PubMed:11408570, ECO:0000269|PubMed:15489334}.		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						TCCTGTAACATGTCGAATTGA	0.353													C|||	1232	0.246006	0.2655	0.1542	5008	,	,		17121	0.2659		0.1928	False		,,,				2504	0.319				p.C308R		Atlas-SNP	.											.	SMC5	96	.	0			c.T922C						PASS	.	C	ARG/CYS	1071,3335	722.2+/-409.3	126,819,1258	93.0	90.0	91.0		922	2.6	0.0	9	dbSNP_87	91	1730,6870	736.5+/-407.0	180,1370,2750	yes	missense	SMC5	NM_015110.3	180	306,2189,4008	CC,CT,TT		20.1163,24.3078,21.5362	benign	308/1102	72897440	2801,10205	2203	4300	6503	SO:0001583	missense	23137	exon7			GTAACATGTCGAA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.922T>C	9.37:g.72897440T>C	ENSP00000354957:p.Cys308Arg	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	276	134	0.485507	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	491	0.22481684981684982	142	0.2886178861788618	56	0.15469613259668508	146	0.25524475524475526	147	0.19393139841688653	C	0.018	-1.486534	0.01018	0.243078	0.201163	ENSG00000198887	ENST00000361138	T	0.15952	2.38	5.61	2.61	0.31194	RecF/RecN/SMC (1);	0.675701	0.15131	N	0.278842	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46735	-0.9170	9	0.14252	T	0.57	1.4368	3.2463	0.06798	0.3592:0.4049:0.1067:0.1292	rs1180117;rs57413829;rs1180117	308	Q8IY18	SMC5_HUMAN	R	308	ENSP00000354957:C308R	ENSP00000354957:C308R	C	+	1	0	SMC5	72087260	0.000000	0.05858	0.000000	0.03702	0.626000	0.37791	0.328000	0.19681	0.076000	0.16826	-0.128000	0.14901	TGT	T|0.778;C|0.222	0.222	strong		0.353	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
OBP2A	29991	hgsc.bcm.edu	37	9	138440562	138440562	+	Missense_Mutation	SNP	C	C	T	rs3178137	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:138440562C>T	ENST00000539850.1	+	5	423	c.397C>T	c.(397-399)Cct>Tct	p.P133S	OBP2A_ENST00000342114.4_Missense_Mutation_p.P110S|OBP2A_ENST00000371776.1_Missense_Mutation_p.P133S|OBP2A_ENST00000340780.3_Silent_p.I154I			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	133			P -> S (in dbSNP:rs3178137).		response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		AGGTAGGAATCCTAATACCAA	0.582													.|||	913	0.182308	0.1604	0.1398	5008	,	,		15740	0.1567		0.2525	False		,,,				2504	0.1963				p.P133S		Atlas-SNP	.											.	OBP2A	21	.	0			c.C397T						PASS	.	T	SER/PRO	799,3607	320.2+/-296.5	77,645,1481	83.0	76.0	79.0		397	0.5	0.0	9	dbSNP_105	79	2274,6326	381.9+/-340.2	304,1666,2330	yes	missense	OBP2A	NM_014582.2	74	381,2311,3811	TT,TC,CC		26.4419,18.1344,23.6276	benign	133/171	138440562	3073,9933	2203	4300	6503	SO:0001583	missense	29991	exon5			AGGAATCCTAATA	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.397C>T	9.37:g.138440562C>T	ENSP00000441028:p.Pro133Ser	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	167	76	0.45509	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	423	0.1936813186813187	84	0.17073170731707318	63	0.17403314917127072	83	0.1451048951048951	193	0.2546174142480211	c	10.69	1.420551	0.25639	0.181344	0.264419	ENSG00000122136	ENST00000342114;ENST00000371776;ENST00000539850	T;T;T	0.11495	2.77;2.96;2.96	2.49	0.488	0.16848	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.00012	0.0000	L	0.41573	1.285	0.80722	P	0.0	P;B	0.44734	0.842;0.054	P;B	0.47981	0.563;0.175	T	0.45323	-0.9269	8	0.42905	T	0.14	-0.5946	5.0378	0.14443	0.0:0.6868:0.0:0.3132	rs3178137;rs7855089	110;133	Q5T8A4;Q9NY56	.;OBP2A_HUMAN	S	110;133;133	ENSP00000340950:P110S;ENSP00000360841:P133S;ENSP00000441028:P133S	ENSP00000340950:P110S	P	+	1	0	OBP2A	137580383	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.113000	0.10774	0.126000	0.18424	-0.359000	0.07587	CCT	C|0.781;T|0.219	0.219	strong		0.582	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	
SERPINB5	5268	hgsc.bcm.edu	37	18	61170782	61170782	+	Missense_Mutation	SNP	A	A	G	rs1455555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:61170782A>G	ENST00000382771.4	+	7	1247	c.955A>G	c.(955-957)Atc>Gtc	p.I319V		NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	319			I -> V (in dbSNP:rs1455555). {ECO:0000269|PubMed:17974005}.		cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						ATCAAATGTTATCCACAAAGT	0.458													A|||	1827	0.364816	0.1884	0.4092	5008	,	,		19831	0.4871		0.4662	False		,,,				2504	0.3415				p.I319V		Atlas-SNP	.											.	SERPINB5	35	.	0			c.A955G						PASS	.	A	VAL/ILE	1023,3383	378.5+/-322.9	133,757,1313	92.0	76.0	81.0		955	0.5	0.4	18	dbSNP_88	81	4244,4356	573.4+/-389.9	1069,2106,1125	yes	missense	SERPINB5	NM_002639.4	29	1202,2863,2438	GG,GA,AA		49.3488,23.2183,40.4967	benign	319/376	61170782	5267,7739	2203	4300	6503	SO:0001583	missense	5268	exon7			AATGTTATCCACA	U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"""Serine (or cysteine) peptidase inhibitors"""	8949	protein-coding gene	gene with protein product	"""protease inhibitor 5 (maspin)"""	154790	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"""	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.955A>G	18.37:g.61170782A>G	ENSP00000372221:p.Ile319Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	130	44	0.338462	NM_002639	B2R6Y4|Q6N0B4|Q8WW89	Missense_Mutation	SNP	ENST00000382771.4	37	CCDS32839.1	872	0.3992673992673993	82	0.16666666666666666	155	0.4281767955801105	263	0.4597902097902098	372	0.49076517150395776	A	0.603	-0.828305	0.02734	0.232183	0.493488	ENSG00000206075	ENST00000382771	D	0.83075	-1.68	5.95	0.527	0.17084	Serpin domain (3);	0.270437	0.36409	N	0.002601	T	0.00012	0.0000	N	0.20357	0.565	0.23271	P	0.99800098	B	0.02656	0.0	B	0.06405	0.002	T	0.24728	-1.0152	9	0.02654	T	1	.	9.8568	0.41090	0.723:0.0:0.277:0.0	rs1455555;rs3744947;rs52802635;rs60882957;rs1455555	319	P36952	SPB5_HUMAN	V	319	ENSP00000372221:I319V	ENSP00000372221:I319V	I	+	1	0	SERPINB5	59321762	0.957000	0.32711	0.446000	0.26920	0.819000	0.46315	1.402000	0.34600	0.088000	0.17205	-0.290000	0.09829	ATC	A|0.611;G|0.389	0.389	strong		0.458	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639	
CAMK2B	816	hgsc.bcm.edu	37	7	44259706	44259706	+	Silent	SNP	G	G	A	rs1065359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:44259706G>A	ENST00000395749.2	-	23	2032	c.1956C>T	c.(1954-1956)aaC>aaT	p.N652N	CAMK2B_ENST00000346990.4_Silent_p.N435N|CAMK2B_ENST00000347193.4_Silent_p.N478N|CAMK2B_ENST00000350811.3_Silent_p.N528N|CAMK2B_ENST00000457475.1_Silent_p.N504N|CAMK2B_ENST00000502837.2_3'UTR|CAMK2B_ENST00000353625.4_Silent_p.N465N|CAMK2B_ENST00000358707.3_Silent_p.N489N|CAMK2B_ENST00000395747.2_Silent_p.N504N|CAMK2B_ENST00000258682.6_Silent_p.N503N|CAMK2B_ENST00000489429.1_5'UTR|CAMK2B_ENST00000440254.2_Silent_p.N528N	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	652					activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						GGAAGTGCACGTTCTGCCACT	0.672													G|||	1698	0.339058	0.1596	0.3213	5008	,	,		16451	0.3879		0.4085	False		,,,				2504	0.4724				p.N652N		Atlas-SNP	.											.	CAMK2B	56	.	0			c.C1956T						PASS	.	G	,,,,,,,	971,3429		119,733,1348	29.0	27.0	28.0		1956,1584,1512,1509,1467,1434,1395,1305	-5.0	0.9	7	dbSNP_86	28	3589,5009		743,2103,1453	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2B	NM_001220.4,NM_172078.2,NM_172079.2,NM_172080.2,NM_172081.2,NM_172082.2,NM_172083.2,NM_172084.2	,,,,,,,	862,2836,2801	AA,AG,GG		41.7423,22.0682,35.0823	,,,,,,,	652/667,528/543,504/519,503/518,489/504,478/493,465/480,435/450	44259706	4560,8438	2200	4299	6499	SO:0001819	synonymous_variant	816	exon23			GTGCACGTTCTGC	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"""CaM-kinase II beta chain"", ""calcium/calmodulin-dependent protein kinase type II beta chain"", ""CaM kinase II beta subunit"", ""proline rich calmodulin-dependent protein kinase"""	607707	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"""	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.1956C>T	7.37:g.44259706G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_001220	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Silent	SNP	ENST00000395749.2	37	CCDS5483.1																																																																																			G|0.654;A|0.346	0.346	strong		0.672	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370657	26370657	+	Missense_Mutation	SNP	A	A	G	rs71544290|rs9358936	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26370657A>G	ENST00000356386.2	+	5	729	c.541A>G	c.(541-543)Aac>Gac	p.N181D	BTN3A2_ENST00000527422.1_Missense_Mutation_p.N181D|BTN3A2_ENST00000377708.2_Missense_Mutation_p.N181D|BTN3A2_ENST00000508906.2_Missense_Mutation_p.N139D|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000396948.1_Missense_Mutation_p.N181D|BTN3A2_ENST00000396934.3_Missense_Mutation_p.N158D	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	181			N -> D (in dbSNP:rs9358936). {ECO:0000269|PubMed:14702039}.		interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						ACAGTGGAGCAACGCCAAGGG	0.542													G|||	409	0.0816693	0.0287	0.0403	5008	,	,		18132	0.0992		0.1123	False		,,,				2504	0.1329				p.N181D		Atlas-SNP	.											.	BTN3A2	44	.	0			c.A541G						PASS	.	G	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	168,4238		2,164,2037	130.0	115.0	120.0		541,541,472,415,541	-4.1	0.0	6	dbSNP_119	120	940,7660		51,838,3411	no	missense,missense,missense,missense,missense	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	23,23,23,23,23	53,1002,5448	GG,GA,AA		10.9302,3.813,8.5191	benign,benign,benign,benign,benign	181/335,181/335,158/312,139/293,181/335	26370657	1108,11898	2203	4300	6503	SO:0001583	missense	11118	exon3			TGGAGCAACGCCA	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.541A>G	6.37:g.26370657A>G	ENSP00000348751:p.Asn181Asp	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	268	125	0.466418	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	158	0.07234432234432235	22	0.044715447154471545	14	0.03867403314917127	40	0.06993006993006994	82	0.10817941952506596	N	0.006	-2.031555	0.00410	0.03813	0.109302	ENSG00000186470	ENST00000532865;ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T;T	0.75260	-0.92;4.32;4.32;4.16;4.32;4.32;4.73	2.31	-4.07	0.03975	Immunoglobulin-like fold (1);	.	.	.	.	T	0.11324	0.0276	N	0.01109	-1.01	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.01393	-1.1366	8	0.02654	T	1	.	5.8415	0.18637	0.5502:0.1453:0.3045:0.0	rs9358936	158;181	F8W6E0;P78410	.;BT3A2_HUMAN	D	139;181;181;181;158;181;181;139	ENSP00000435952:N139D;ENSP00000432138:N181D;ENSP00000348751:N181D;ENSP00000380140:N158D;ENSP00000366937:N181D;ENSP00000380152:N181D;ENSP00000442687:N139D	ENSP00000348751:N181D	N	+	1	0	BTN3A2	26478636	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.022000	0.01439	-2.079000	0.00871	-2.510000	0.00188	AAC	A|0.926;G|0.074	0.074	strong		0.542	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
C4orf17	84103	hgsc.bcm.edu	37	4	100443720	100443720	+	Missense_Mutation	SNP	G	G	A	rs13143848	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100443720G>A	ENST00000326581.4	+	3	553	c.191G>A	c.(190-192)gGa>gAa	p.G64E	C4orf17_ENST00000514652.1_Missense_Mutation_p.G64E|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	64			G -> E (in dbSNP:rs13143848). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.					p.G64E(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		ACATTGTGGGGAGTTGGCCAG	0.428													G|||	1574	0.314297	0.3449	0.219	5008	,	,		18112	0.2361		0.2992	False		,,,				2504	0.4366				p.G64E		Atlas-SNP	.											C4orf17,NS,carcinoma,0,1	C4orf17	42	1	1	Substitution - Missense(1)	prostate(1)	c.G191A						PASS	.	G	GLU/GLY	1479,2927	475.7+/-357.4	239,1001,963	178.0	155.0	163.0		191	1.2	0.0	4	dbSNP_121	163	2649,5951	425.6+/-355.0	408,1833,2059	yes	missense	C4orf17	NM_032149.2	98	647,2834,3022	AA,AG,GG		30.8023,33.5679,31.7392	probably-damaging	64/360	100443720	4128,8878	2203	4300	6503	SO:0001583	missense	84103	exon3			TGTGGGGAGTTGG	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.191G>A	4.37:g.100443720G>A	ENSP00000322582:p.Gly64Glu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	565	0.2586996336996337	172	0.34959349593495936	84	0.23204419889502761	91	0.1590909090909091	218	0.287598944591029	G	7.485	0.649475	0.14516	0.335679	0.308023	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.16743	2.33;2.32	5.18	1.2	0.21068	.	1.209900	0.05571	N	0.571058	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.28850	0.225	B	0.27380	0.079	T	0.44847	-0.9301	9	0.15066	T	0.55	1.6219	3.2821	0.06918	0.3038:0.0:0.5128:0.1834	rs13143848;rs58148455;rs13143848	64	Q53FE4	CD017_HUMAN	E	64	ENSP00000322582:G64E;ENSP00000427663:G64E	ENSP00000322582:G64E	G	+	2	0	C4orf17	100662743	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.097000	0.15168	0.332000	0.23536	0.585000	0.79938	GGA	G|0.699;A|0.301	0.301	strong		0.428	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
MEIG1	644890	hgsc.bcm.edu	37	10	15008493	15008493	+	Missense_Mutation	SNP	A	A	C	rs4750568	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:15008493A>C	ENST00000378240.1	+	1	56	c.26A>C	c.(25-27)aAa>aCa	p.K9T	MEIG1_ENST00000407572.1_Missense_Mutation_p.K9T			Q5JSS6	MEIG1_HUMAN	meiosis/spermiogenesis associated 1	9			K -> T (in dbSNP:rs4750568).		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)				kidney(1)|ovary(1)|prostate(1)	3						GTAAAACCAAAATCAGTAAGT	0.333													.|||	3061	0.611222	0.5439	0.732	5008	,	,		17640	0.4802		0.668	False		,,,				2504	0.6933				p.K9T		Atlas-SNP	.											.	MEIG1	11	.	0			c.A26C						PASS	.	A	THR/LYS	2577,1829	635.5+/-396.4	735,1107,361	69.0	67.0	67.0		26	5.7	1.0	10	dbSNP_111	67	5918,2682	682.3+/-403.8	2060,1798,442	yes	missense	MEIG1	NM_001080836.2	78	2795,2905,803	CC,CA,AA		31.186,41.5116,34.684	probably-damaging	9/89	15008493	8495,4511	2203	4300	6503	SO:0001583	missense	644890	exon2			AACCAAAATCAGT		CCDS31151.1	10p13	2013-08-05	2013-08-05		ENSG00000197889	ENSG00000197889			23429	protein-coding gene	gene with protein product	"""spermatogenesis associated 39"""	614174	"""meiosis expressed gene 1 homolog (mouse)"""			23258628	Standard	NM_001080836		Approved	bA2K17.3, SPATA39	uc009xjk.1	Q5JSS6	OTTHUMG00000017717	ENST00000378240.1:c.26A>C	10.37:g.15008493A>C	ENSP00000367486:p.Lys9Thr	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	223	222	0.995516	NM_001080836		Missense_Mutation	SNP	ENST00000378240.1	37	CCDS31151.1	1270	0.5815018315018315	247	0.5020325203252033	262	0.7237569060773481	260	0.45454545454545453	501	0.6609498680738787	a	17.27	3.347870	0.61183	0.584884	0.68814	ENSG00000197889	ENST00000407572;ENST00000378240	T;T	0.51574	0.7;0.7	5.68	5.68	0.88126	.	0.053548	0.64402	D	0.000001	T	0.00012	0.0000	.	.	.	0.21256	P	0.999741864	D	0.61697	0.99	P	0.52793	0.709	T	0.37244	-0.9714	8	0.28530	T	0.3	-19.9629	15.5945	0.76569	1.0:0.0:0.0:0.0	rs4750568;rs9794105;rs52794549;rs4750568	9	Q5JSS6	MEIG1_HUMAN	T	9	ENSP00000384334:K9T;ENSP00000367486:K9T	ENSP00000367486:K9T	K	+	2	0	MEIG1	15048499	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	5.750000	0.68712	2.155000	0.67459	0.460000	0.39030	AAA	A|0.380;C|0.620	0.620	strong		0.333	MEIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046942.1	XM_927975	
LIPC	3990	hgsc.bcm.edu	37	15	58860963	58860963	+	Silent	SNP	C	C	A	rs6074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:58860963C>A	ENST00000356113.6	+	11	2052	c.1437C>A	c.(1435-1437)acC>acA	p.T479T	LIPC_ENST00000299022.5_Silent_p.T479T|LIPC_ENST00000433326.2_Silent_p.T418T			P11150	LIPC_HUMAN	lipase, hepatic	479	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		TTCGCCCAACCCAGGAAAAAA	0.348													C|||	1009	0.201478	0.0817	0.196	5008	,	,		19374	0.249		0.1561	False		,,,				2504	0.365				p.T479T		Atlas-SNP	.											.	LIPC	56	.	0			c.C1437A						PASS	.	C		432,3952	207.2+/-228.6	27,378,1787	85.0	80.0	81.0		1437	4.6	1.0	15	dbSNP_52	81	1220,7364	244.0+/-273.4	88,1044,3160	no	coding-synonymous	LIPC	NM_000236.2		115,1422,4947	AA,AC,CC		14.2125,9.854,12.739		479/500	58860963	1652,11316	2192	4292	6484	SO:0001819	synonymous_variant	3990	exon9			CCCAACCCAGGAA		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.1437C>A	15.37:g.58860963C>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	40	0.555556	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Silent	SNP	ENST00000356113.6	37	CCDS10166.1																																																																																			C|0.856;A|0.144	0.144	strong		0.348	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1		
GPR87	53836	hgsc.bcm.edu	37	3	151011969	151011969	+	Silent	SNP	G	G	A	rs1048408	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:151011969G>A	ENST00000260843.4	-	3	1529	c.1065C>T	c.(1063-1065)taC>taT	p.Y355Y	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	355					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACACATCAGTGTAATCATAAT	0.348													A|||	2482	0.495607	0.4561	0.5692	5008	,	,		19851	0.5139		0.4642	False		,,,				2504	0.5102				p.Y355Y		Atlas-SNP	.											.	GPR87	52	.	0			c.C1065T						PASS	.	A	,	1921,2485	625.9+/-394.6	393,1135,675	136.0	137.0	137.0		1065,	-5.0	0.1	3	dbSNP_86	137	4040,4560	595.3+/-393.4	941,2158,1201	no	coding-synonymous,intron	GPR87,MED12L	NM_023915.3,NM_053002.4	,	1334,3293,1876	AA,AG,GG		46.9767,43.5996,45.8327	,	355/359,	151011969	5961,7045	2203	4300	6503	SO:0001819	synonymous_variant	53836	exon3			ATCAGTGTAATCA	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"""GPCR / Class A : Orphans"""	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.1065C>T	3.37:g.151011969G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Silent	SNP	ENST00000260843.4	37	CCDS3157.1																																																																																			G|0.533;A|0.467	0.467	strong		0.348	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		
MUC4	4585	hgsc.bcm.edu	37	3	195506987	195506987	+	Missense_Mutation	SNP	T	T	C	rs200157887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506987T>C	ENST00000463781.3	-	2	11923	c.11464A>G	c.(11464-11466)Acc>Gcc	p.T3822A	MUC4_ENST00000475231.1_Missense_Mutation_p.T3822A|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3822A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGTGTCACCTGTG	0.582													.|||	203	0.0405351	0.0537	0.0476	5008	,	,		9489	0.0188		0.0368	False		,,,				2504	0.044				p.T3822A		Atlas-SNP	.											MUC4_ENST00000463781,extremity,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	skin(2)	c.A11464G						scavenged	.																																			SO:0001583	missense	4585	exon2			GGGTGGTGTCACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11464A>G	3.37:g.195506987T>C	ENSP00000417498:p.Thr3822Ala	Somatic	62	4	0.0645161		WXS	Illumina HiSeq	Phase_I	170	25	0.147059	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	t	2.846	-0.239335	0.05944	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.52;1.5	.	.	.	.	.	.	.	.	T	0.12305	0.0299	N	0.19112	0.55	0.09310	N	1	P	0.37985	0.613	B	0.25140	0.058	T	0.15838	-1.0423	7	.	.	.	.	2.8304	0.05498	3.0E-4:2.0E-4:0.4983:0.5012	.	3694	E7ESK3	.	A	3822	ENSP00000417498:T3822A;ENSP00000420243:T3822A	.	T	-	1	0	MUC4	196991766	0.069000	0.21087	0.113000	0.21522	0.113000	0.19764	1.804000	0.38873	0.056000	0.16144	0.055000	0.15244	ACC	T|0.816;C|0.185	0.185	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ANO9	338440	hgsc.bcm.edu	37	11	433867	433867	+	Missense_Mutation	SNP	G	G	A	rs12575508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:433867G>A	ENST00000332826.6	-	3	236	c.152C>T	c.(151-153)gCg>gTg	p.A51V		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	51					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						TTGCTGCCGCGCCTGCCGGGG	0.692													g|||	995	0.198682	0.2557	0.1369	5008	,	,		12471	0.1766		0.2058	False		,,,				2504	0.181				p.A51V		Atlas-SNP	.											.	ANO9	61	.	0			c.C152T						PASS	.		VAL/ALA	1085,3235		141,803,1216	22.0	20.0	21.0		152	-4.1	0.0	11	dbSNP_120	21	1540,6976		156,1228,2874	yes	missense	ANO9	NM_001012302.2	64	297,2031,4090	AA,AG,GG		18.0836,25.1157,20.4503	benign	51/783	433867	2625,10211	2160	4258	6418	SO:0001583	missense	338440	exon3			TGCCGCGCCTGCC	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	20679	protein-coding gene	gene with protein product			"""tumor protein p53 inducible protein 5"", ""transmembrane protein 16J"""	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.152C>T	11.37:g.433867G>A	ENSP00000332788:p.Ala51Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	37	CCDS31326.1	438	0.20054945054945056	123	0.25	55	0.15193370165745856	108	0.1888111888111888	152	0.20052770448548812	g	5.863	0.343456	0.11069	0.251157	0.180836	ENSG00000185101	ENST00000332826	T	0.66099	-0.19	2.88	-4.12	0.03916	.	2.537780	0.02195	N	0.061777	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.03051	-1.1078	9	0.39692	T	0.17	.	1.7666	0.03003	0.295:0.2625:0.322:0.1204	rs12575508;rs12575508	51	A1A5B4	ANO9_HUMAN	V	51	ENSP00000332788:A51V	ENSP00000332788:A51V	A	-	2	0	ANO9	423867	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.861000	0.00177	-1.354000	0.02188	-0.565000	0.04167	GCG	G|0.785;A|0.215	0.215	strong		0.692	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302	
CHRNA3	1136	hgsc.bcm.edu	37	15	78893787	78893787	+	Silent	SNP	G	G	A	rs56403513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78893787G>A	ENST00000326828.5	-	5	1581	c.1197C>T	c.(1195-1197)gaC>gaT	p.D399D	CHRNA3_ENST00000348639.3_Silent_p.D399D	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	399					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	CACACATCCCGTCCTGGCAGG	0.542													G|||	5	0.000998403	0.0008	0.0	5008	,	,		19435	0.001		0.003	False		,,,				2504	0.0				p.D399D		Atlas-SNP	.											.	CHRNA3	56	.	0			c.C1197T						PASS	.	G	,	2,4390	4.2+/-10.8	0,2,2194	104.0	93.0	97.0		1197,1197	-12.0	0.0	15	dbSNP_129	97	33,8553	22.8+/-68.1	0,33,4260	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	0,35,6454	AA,AG,GG		0.3843,0.0455,0.2697	,	399/506,399/490	78893787	35,12943	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			CATCCCGTCCTGG		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.1197C>T	15.37:g.78893787G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	243	115	0.473251	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			G|0.996;A|0.004	0.004	strong		0.542	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
FHDC1	85462	hgsc.bcm.edu	37	4	153886104	153886104	+	Silent	SNP	G	G	A	rs2018007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:153886104G>A	ENST00000511601.1	+	9	1265	c.1077G>A	c.(1075-1077)ttG>ttA	p.L359L	FHDC1_ENST00000260008.3_Silent_p.L359L			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	359	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.								ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					CAGAAAAATTGCATCATGTTC	0.303													G|||	113	0.0225639	0.0749	0.0086	5008	,	,		18165	0.0		0.005	False		,,,				2504	0.0031				p.L359L		Atlas-SNP	.											.	FHDC1	102	.	0			c.G1077A						PASS	.	G		277,4129	152.2+/-185.9	13,251,1939	75.0	81.0	79.0		1077	0.9	0.0	4	dbSNP_92	79	37,8557	24.6+/-71.5	1,35,4261	no	coding-synonymous	FHDC1	NM_033393.2		14,286,6200	AA,AG,GG		0.4305,6.2869,2.4154		359/1144	153886104	314,12686	2203	4297	6500	SO:0001819	synonymous_variant	85462	exon8			AAAATTGCATCAT	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.1077G>A	4.37:g.153886104G>A		Somatic	359	0	0		WXS	Illumina HiSeq	Phase_I	401	183	0.456359	NM_033393		Silent	SNP	ENST00000511601.1	37	CCDS34081.1																																																																																			G|0.973;A|0.027	0.027	strong		0.303	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393	
OR2C3	81472	hgsc.bcm.edu	37	1	247694949	247694949	+	Missense_Mutation	SNP	G	G	C	rs6702693	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247694949G>C	ENST00000366487.3	-	2	1226	c.865C>G	c.(865-867)Ctt>Gtt	p.L289V	GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000366490.3_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	289			L -> V (in dbSNP:rs6702693).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			GTGTAAATAAGTGGGTTCAGC	0.532													G|||	712	0.142173	0.1029	0.098	5008	,	,		21698	0.1042		0.173	False		,,,				2504	0.2342				p.L289V		Atlas-SNP	.											.	OR2C3	92	.	0			c.C865G						PASS	.	G	VAL/LEU	485,3921	226.5+/-242.0	30,425,1748	95.0	83.0	87.0		865	0.8	0.0	1	dbSNP_116	87	1362,7238	266.0+/-286.5	99,1164,3037	yes	missense	OR2C3	NM_198074.4	32	129,1589,4785	CC,CG,GG		15.8372,11.0077,14.2011	possibly-damaging	289/321	247694949	1847,11159	2203	4300	6503	SO:0001583	missense	81472	exon2			AAATAAGTGGGTT	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"""GPCR / Class A : Olfactory receptors"""	15005	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily C, member 4"""	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.865C>G	1.37:g.247694949G>C	ENSP00000355443:p.Leu289Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	172	75	0.436047	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Missense_Mutation	SNP	ENST00000366487.3	37	CCDS1634.2	277	0.12683150183150182	52	0.10569105691056911	40	0.11049723756906077	52	0.09090909090909091	133	0.17546174142480211	G	6.291	0.421715	0.11928	0.110077	0.158372	ENSG00000196242	ENST00000366487	T	0.39592	1.07	3.91	0.788	0.18601	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31392	U	0.007725	T	0.00039	0.0001	N	0.21097	0.63	0.80722	P	0.0	B	0.16603	0.018	B	0.19666	0.026	T	0.09079	-1.0691	9	0.59425	D	0.04	.	5.0558	0.14531	0.2966:0.0:0.558:0.1455	rs6702693	289	Q8N628	OR2C3_HUMAN	V	289	ENSP00000355443:L289V	ENSP00000355443:L289V	L	-	1	0	OR2C3	245761572	0.000000	0.05858	0.006000	0.13384	0.001000	0.01503	-2.875000	0.00718	-0.174000	0.10743	-0.797000	0.03246	CTT	G|0.854;C|0.146	0.146	strong		0.532	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074	
RNF43	54894	hgsc.bcm.edu	37	17	56436109	56436109	+	Missense_Mutation	SNP	C	C	T	rs34523089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56436109C>T	ENST00000584437.1	-	8	2983	c.1028G>A	c.(1027-1029)cGc>cAc	p.R343H	RNF43_ENST00000583753.1_Missense_Mutation_p.R302H|RNF43_ENST00000407977.2_Missense_Mutation_p.R343H|RNF43_ENST00000577625.1_Missense_Mutation_p.R216H|RNF43_ENST00000500597.2_Missense_Mutation_p.R302H|RNF43_ENST00000577716.1_Missense_Mutation_p.R343H|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Missense_Mutation_p.R216H			Q68DV7	RNF43_HUMAN	ring finger protein 43	343			R -> H (in dbSNP:rs34523089).		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGGATGCTGGCGAATGAGGTG	0.597													C|||	327	0.0652955	0.0091	0.1167	5008	,	,		18742	0.001		0.163	False		,,,				2504	0.0706				p.R343H		Atlas-SNP	.											RNF43,NS,carcinoma,0,1	RNF43	157	1	0			c.G1028A						PASS	.	C	HIS/ARG	159,4239		3,153,2043	17.0	18.0	18.0		1028	2.7	1.0	17	dbSNP_126	18	1360,7218		135,1090,3064	yes	missense	RNF43	NM_017763.4	29	138,1243,5107	TT,TC,CC		15.8545,3.6153,11.7062	probably-damaging	343/784	56436109	1519,11457	2199	4289	6488	SO:0001583	missense	54894	exon9			TGCTGGCGAATGA		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1028G>A	17.37:g.56436109C>T	ENSP00000463069:p.Arg343His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	166	0.076007326007326	3	0.006097560975609756	44	0.12154696132596685	1	0.0017482517482517483	118	0.15567282321899736	C	16.21	3.058842	0.55325	0.036153	0.158545	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.09350	3.14;2.99	3.66	2.69	0.31865	.	0.421385	0.24485	N	0.038106	T	0.00073	0.0002	L	0.27053	0.805	0.31011	P	0.71922	B;D;D	0.89917	0.007;1.0;0.999	B;D;D	0.79108	0.005;0.992;0.981	T	0.17258	-1.0375	9	0.45353	T	0.12	-21.2099	8.7609	0.34674	0.0:0.8913:0.0:0.1087	rs34523089	302;343;343	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	H	343;302	ENSP00000385328:R343H;ENSP00000441969:R302H	ENSP00000385328:R343H	R	-	2	0	RNF43	53791108	1.000000	0.71417	0.999000	0.59377	0.937000	0.57800	2.096000	0.41738	0.886000	0.36113	0.400000	0.26472	CGC	C|0.912;T|0.088	0.088	strong		0.597	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
SCN3A	6328	hgsc.bcm.edu	37	2	165987772	165987772	+	Silent	SNP	T	T	G	rs62174900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:165987772T>G	ENST00000360093.3	-	16	3038	c.2547A>C	c.(2545-2547)gtA>gtC	p.V849V	SCN3A_ENST00000283254.7_Silent_p.V849V|SCN3A_ENST00000409101.3_Silent_p.V800V	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	849					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGATCGCAGTACAGACAATC	0.333													T|||	910	0.181709	0.0234	0.1787	5008	,	,		11002	0.2728		0.1968	False		,,,				2504	0.2883				p.V849V		Atlas-SNP	.											.	SCN3A	544	.	0			c.A2547C						PASS	.	T	,,	284,4122	155.9+/-189.0	13,258,1932	103.0	100.0	101.0		2400,2400,2547	-1.7	1.0	2	dbSNP_129	101	1835,6765	328.5+/-318.3	208,1419,2673	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN3A	NM_001081676.1,NM_001081677.1,NM_006922.3	,,	221,1677,4605	GG,GT,TT		21.3372,6.4458,16.2925	,,	800/1952,800/1952,849/2001	165987772	2119,10887	2203	4300	6503	SO:0001819	synonymous_variant	6328	exon16			TCGCAGTACAGAC	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2547A>C	2.37:g.165987772T>G		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	176	82	0.465909	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																				T|0.828;G|0.172	0.172	strong		0.333	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
DEFA3	1668	hgsc.bcm.edu	37	8	6873603	6873603	+	Missense_Mutation	SNP	T	T	G	rs145076681		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:6873603T>G	ENST00000327857.2	-	3	285	c.194A>C	c.(193-195)gAc>gCc	p.D65A	DEFA1B_ENST00000535841.1_Intron	NM_005217.3	NP_005208.1	P59666	DEF3_HUMAN	defensin, alpha 3, neutrophil-specific	65					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular estrogen receptor signaling pathway (GO:0030520)|killing of cells of other organism (GO:0031640)	azurophil granule lumen (GO:0035578)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.D65A(1)		endometrium(1)|prostate(2)	3				COAD - Colon adenocarcinoma(149;0.0561)|READ - Rectum adenocarcinoma(644;0.118)		GCAATAGCAGTCCATGTTTTT	0.498																																					p.D65A		Atlas-SNP	.											DEFA3,NS,carcinoma,0,1	DEFA3	7	1	1	Substitution - Missense(1)	prostate(1)	c.A194C						scavenged	.						156.0	118.0	130.0					8																	6873603		1957	4128	6085	SO:0001583	missense	1668	exon3			TAGCAGTCCATGT	M23281	CCDS5962.1	8p23.1	2009-08-05			ENSG00000239839	ENSG00000239839		"""Defensins, alpha"""	2762	protein-coding gene	gene with protein product		604522		DEF3		8477861, 17214878, 15944200	Standard	NM_005217		Approved	HNP-3		P59666	OTTHUMG00000090381	ENST00000327857.2:c.194A>C	8.37:g.6873603T>G	ENSP00000328359:p.Asp65Ala	Somatic	646	23	0.0356037		WXS	Illumina HiSeq	Phase_I	416	40	0.0961538	NM_005217	P11479|Q14125	Missense_Mutation	SNP	ENST00000327857.2	37	CCDS5962.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.042516	0.00402	.	.	ENSG00000239839	ENST00000327857	T	0.41400	1.0	1.01	-2.03	0.07365	.	.	.	.	.	T	0.15046	0.0363	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24154	-1.0168	7	0.08179	T	0.78	.	0.1742	0.00116	0.3008:0.2168:0.2655:0.217	.	65	P59666	DEF3_HUMAN	A	65	ENSP00000328359:D65A	ENSP00000328359:D65A	D	-	2	0	DEFA3	6861013	0.002000	0.14202	0.000000	0.03702	0.011000	0.07611	-0.189000	0.09629	-1.937000	0.01047	-0.806000	0.03193	GAC	T|0.167;G|0.833	0.833	strong		0.498	DEFA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206753.2	NM_005217	
USP32	84669	hgsc.bcm.edu	37	17	58288421	58288421	+	Missense_Mutation	SNP	C	C	T	rs146577219	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:58288421C>T	ENST00000300896.4	-	21	2571	c.2377G>A	c.(2377-2379)Gaa>Aaa	p.E793K	USP32_ENST00000592339.1_Missense_Mutation_p.E463K	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	793	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CTCCAAAGTTCCTGCACTAAA	0.358																																					p.E793K		Atlas-SNP	.											USP32,NS,carcinoma,0,5	USP32	128	5	0			c.G2377A						scavenged	.						27.0	27.0	27.0					17																	58288421		2203	4296	6499	SO:0001583	missense	84669	exon21			AAAGTTCCTGCAC	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"""Ubiquitin-specific peptidases"", ""EF-hand domain containing"""	19143	protein-coding gene	gene with protein product		607740	"""ubiquitin specific protease 32"""			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.2377G>A	17.37:g.58288421C>T	ENSP00000300896:p.Glu793Lys	Somatic	621	1	0.00161031		WXS	Illumina HiSeq	Phase_I	695	153	0.220144	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	C	33	5.220205	0.95139	.	.	ENSG00000170832	ENST00000300896	T	0.29917	1.55	5.26	5.26	0.73747	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	N	0.25286	0.73	0.80722	D	1	B	0.30021	0.265	B	0.36959	0.237	T	0.05273	-1.0895	10	0.29301	T	0.29	.	19.2198	0.93791	0.0:1.0:0.0:0.0	.	793	Q8NFA0	UBP32_HUMAN	K	793	ENSP00000300896:E793K	ENSP00000300896:E793K	E	-	1	0	USP32	55643203	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.697000	0.84279	2.615000	0.88500	0.655000	0.94253	GAA	C|0.926;T|0.073	0.073	strong		0.358	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582	
HLA-C	3107	hgsc.bcm.edu	37	6	31239506	31239506	+	Silent	SNP	C	C	G	rs1050414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31239506C>G	ENST00000376228.5	-	2	227	c.213G>C	c.(211-213)ccG>ccC	p.P71P	HLA-C_ENST00000383329.3_Silent_p.P71P	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	71	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACGGCGCCCGCGGCTCCCCTC	0.697													c|||	583	0.116414	0.112	0.0548	5008	,	,		12243	0.126		0.1143	False		,,,				2504	0.1585				p.P71P		Atlas-SNP	.											.	HLA-C	92	.	0			c.G213C						PASS	.	C		431,2589		33,365,1112	39.0	41.0	40.0		213	1.0	1.0	6	dbSNP_86	40	548,4866		29,490,2188	no	coding-synonymous	HLA-C	NM_002117.5		62,855,3300	GG,GC,CC		10.1219,14.2715,11.6078		71/367	31239506	979,7455	1510	2707	4217	SO:0001819	synonymous_variant	3107	exon2			CGCCCGCGGCTCC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.213G>C	6.37:g.31239506C>G		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	225	117	0.52	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	226	0.10347985347985347	72	0.14634146341463414	16	0.04419889502762431	42	0.07342657342657342	96	0.1266490765171504	-	10.21	1.287402	0.23478	0.142715	0.101219	ENSG00000204525	ENST00000415537	.	.	.	2.81	0.985	0.19779	.	.	.	.	.	T	0.15609	0.0376	.	.	.	0.09310	P	0.9999999999259963	.	.	.	.	.	.	T	0.15435	-1.0437	3	.	.	.	.	5.0842	0.14673	0.0:0.7063:0.0:0.2937	rs1050414;rs2308552;rs3173348;rs16895973;rs28732105	.	.	.	P	71	.	.	A	-	1	0	HLA-C	31347485	0.002000	0.14202	1.000000	0.80357	0.145000	0.21501	-0.755000	0.04782	0.251000	0.21505	0.305000	0.20034	GCG	C|0.891;G|0.109	0.109	strong		0.697	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
KLHL14	57565	hgsc.bcm.edu	37	18	30349691	30349691	+	Silent	SNP	C	C	T	rs17851892	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:30349691C>T	ENST00000359358.4	-	2	1302	c.864G>A	c.(862-864)ccG>ccA	p.P288P	AC012123.1_ENST00000426194.1_5'Flank|KLHL14_ENST00000358095.4_Silent_p.P288P	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	288						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						TCTGGCAGACCGGGTCGGTTC	0.622													c|||	1634	0.326278	0.177	0.3977	5008	,	,		10617	0.3452		0.337	False		,,,				2504	0.4468				p.P288P		Atlas-SNP	.											.	KLHL14	92	.	0			c.G864A						PASS	.			839,3565		83,673,1446	47.0	49.0	48.0		864	-3.5	1.0	18	dbSNP_123	48	3044,5554		538,1968,1793	no	coding-synonymous	KLHL14	NM_020805.1		621,2641,3239	TT,TC,CC		35.4036,19.0509,29.8646		288/629	30349691	3883,9119	2202	4299	6501	SO:0001819	synonymous_variant	57565	exon2			GCAGACCGGGTCG	AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"""Kelch-like"", ""BTB/POZ domain containing"""	29266	protein-coding gene	gene with protein product	"""printor"""	613772	"""kelch-like 14 (Drosophila)"""			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.864G>A	18.37:g.30349691C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	143	83	0.58042	NM_020805	A6NNW1|B4DHA0|Q8WU41	Silent	SNP	ENST00000359358.4	37	CCDS32813.1																																																																																			C|0.695;T|0.305	0.305	strong		0.622	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1		
PARP15	165631	hgsc.bcm.edu	37	3	122354792	122354792	+	Missense_Mutation	SNP	G	G	A	rs12489170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122354792G>A	ENST00000464300.2	+	12	1948	c.1882G>A	c.(1882-1884)Gga>Aga	p.G628R	PARP15_ENST00000483793.1_Missense_Mutation_p.G433R|PARP15_ENST00000310366.4_Missense_Mutation_p.G394R|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000493645.1_Missense_Mutation_p.G325R	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	628	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.		G -> R (in dbSNP:rs12489170).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		CTTCACAAAGGGACGTGCAGG	0.478													G|||	1110	0.221645	0.0983	0.2478	5008	,	,		19992	0.4881		0.1322	False		,,,				2504	0.1871				p.G628R		Atlas-SNP	.											.	PARP15	115	.	0			c.G1882A						PASS	.	G	ARG/GLY,ARG/GLY	511,3895	236.1+/-248.4	28,455,1720	164.0	134.0	144.0		1882,1180	4.0	0.0	3	dbSNP_120	144	1138,7462	233.7+/-266.9	91,956,3253	yes	missense,missense	PARP15	NM_001113523.1,NM_152615.1	125,125	119,1411,4973	AA,AG,GG		13.2326,11.5978,12.6788	probably-damaging,probably-damaging	628/679,394/445	122354792	1649,11357	2203	4300	6503	SO:0001583	missense	165631	exon12			ACAAAGGGACGTG	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1882G>A	3.37:g.122354792G>A	ENSP00000417214:p.Gly628Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	512	0.23443223443223443	48	0.0975609756097561	82	0.2265193370165746	281	0.49125874125874125	101	0.13324538258575197	G	20.7	4.030508	0.75504	0.115978	0.132326	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	T;T;T;T	0.16457	2.34;2.34;2.34;2.34	3.99	3.99	0.46301	Poly(ADP-ribose) polymerase, catalytic domain (2);	.	.	.	.	T	0.00012	0.0000	M	0.93594	3.435	0.09310	P	0.99999999239116	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.48502	-0.9030	8	0.62326	D	0.03	.	14.7995	0.69903	0.0:0.0:1.0:0.0	rs12489170;rs60932120;rs12489170	325;394;375;433;606	B7ZL48;Q460N3-2;F5H8I1;C9J7L3;Q460N3	.;.;.;.;PAR15_HUMAN	R	628;433;375;394;325	ENSP00000417214:G628R;ENSP00000417785:G433R;ENSP00000308436:G394R;ENSP00000419488:G325R	ENSP00000308436:G394R	G	+	1	0	PARP15	123837482	1.000000	0.71417	0.030000	0.17652	0.002000	0.02628	9.647000	0.98478	2.058000	0.61347	0.650000	0.86243	GGA	G|0.823;A|0.177	0.177	strong		0.478	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
BTN2A1	11120	hgsc.bcm.edu	37	6	26468637	26468637	+	Missense_Mutation	SNP	G	G	A	rs142664900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26468637G>A	ENST00000312541.5	+	8	1692	c.1444G>A	c.(1444-1446)Gtg>Atg	p.V482M	BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000541522.1_Missense_Mutation_p.V421M|BTN2A1_ENST00000429381.1_3'UTR	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	482	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						AGCCTTTTCCGTGCCTGTGAG	0.577																																					p.V482M		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G1444A						PASS	.	G	MET/VAL,,MET/VAL,	2,4404	4.2+/-10.8	0,2,2201	173.0	135.0	148.0		1261,,1444,	1.8	0.1	6	dbSNP_134	148	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,missense,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	21,,21,	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	possibly-damaging,,possibly-damaging,	421/467,,482/528,	26468637	3,13003	2203	4300	6503	SO:0001583	missense	11120	exon8			TTTTCCGTGCCTG	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1444G>A	6.37:g.26468637G>A	ENSP00000312158:p.Val482Met	Somatic	347	1	0.00288184		WXS	Illumina HiSeq	Phase_I	515	263	0.51068	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.773|7.773	0.707775|0.707775	0.15239|0.15239	4.54E-4|4.54E-4	1.16E-4|1.16E-4	ENSG00000112763|ENSG00000112763	ENST00000265424|ENST00000312541;ENST00000541522	.|T;T	.|0.60920	.|0.15;0.15	2.72|2.72	1.84|1.84	0.25277|0.25277	.|Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.|.	.|.	.|.	.|.	.|T	.|0.45617	.|0.1351	L|L	0.61218|0.61218	1.895|1.895	0.09310|0.09310	N|N	1|1	.|D	.|0.58620	.|0.983	.|P	.|0.51055	.|0.657	.|T	.|0.23655	.|-1.0182	.|9	.|0.59425	.|D	.|0.04	.|.	8.0041|8.0041	0.30315|0.30315	0.1317:0.0:0.8683:0.0|0.1317:0.0:0.8683:0.0	.|.	.|482	.|Q7KYR7	.|BT2A1_HUMAN	.|M	-1|482;421	.|ENSP00000312158:V482M;ENSP00000443909:V421M	.|ENSP00000312158:V482M	.|V	+|+	.|1	.|0	BTN2A1|BTN2A1	26576616|26576616	0.006000|0.006000	0.16342|0.16342	0.051000|0.051000	0.19133|0.19133	0.003000|0.003000	0.03518|0.03518	1.564000|1.564000	0.36375|0.36375	0.712000|0.712000	0.32039|0.32039	-0.424000|-0.424000	0.05967|0.05967	.|GTG	G|0.999;A|0.001	0.001	strong		0.577	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
HCN4	10021	hgsc.bcm.edu	37	15	73660505	73660505	+	Missense_Mutation	SNP	C	C	T	rs143090627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:73660505C>T	ENST00000261917.3	-	1	1100	c.107G>A	c.(106-108)gGg>gAg	p.G36E		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	36					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GCCCCCGGCCCCCTCCTCCTC	0.746													C|||	125	0.0249601	0.0068	0.0447	5008	,	,		7263	0.0		0.0696	False		,,,				2504	0.0153				p.G36E		Atlas-SNP	.											.	HCN4	150	.	0			c.G107A						PASS	.	C	GLU/GLY	27,3487		0,27,1730	3.0	4.0	3.0		107	2.0	0.5	15	dbSNP_134	3	378,7070		3,372,3349	yes	missense	HCN4	NM_005477.2	98	3,399,5079	TT,TC,CC		5.0752,0.7684,3.6946	probably-damaging	36/1204	73660505	405,10557	1757	3724	5481	SO:0001583	missense	10021	exon1			CCGGCCCCCTCCT	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.107G>A	15.37:g.73660505C>T	ENSP00000261917:p.Gly36Glu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	95	0.043498168498168496	4	0.008130081300813009	20	0.055248618784530384	19	0.033216783216783216	52	0.06860158311345646	C	11.44	1.638041	0.29157	0.007684	0.050752	ENSG00000138622	ENST00000261917	D	0.98044	-4.68	2.89	1.96	0.26148	.	.	.	.	.	T	0.60051	0.2239	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.75875	-0.3163	9	0.41790	T	0.15	.	6.7141	0.23294	0.0:0.8562:0.0:0.1438	.	36	Q9Y3Q4	HCN4_HUMAN	E	36	ENSP00000261917:G36E	ENSP00000261917:G36E	G	-	2	0	HCN4	71447558	0.002000	0.14202	0.512000	0.27736	0.852000	0.48524	0.620000	0.24403	0.419000	0.25927	0.298000	0.19748	GGG	C|0.957;T|0.043	0.043	strong		0.746	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
LAMA5	3911	hgsc.bcm.edu	37	20	60927349	60927349	+	Silent	SNP	C	C	T	rs483876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60927349C>T	ENST00000252999.3	-	4	702	c.636G>A	c.(634-636)gcG>gcA	p.A212A	RP11-157P1.5_ENST00000477848.1_RNA|RP11-157P1.5_ENST00000487421.1_RNA|LAMA5_ENST00000370692.3_Silent_p.A212A|LAMA5_ENST00000370677.3_Silent_p.A212A|RP11-157P1.5_ENST00000478167.1_RNA|RP11-157P1.5_ENST00000456721.2_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	212	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGCAGATGGCCGCGTCGTCCC	0.697													c|||	3762	0.751198	0.4213	0.8026	5008	,	,		12422	0.9405		0.9215	False		,,,				2504	0.7904				p.A212A		Atlas-SNP	.											LAMA5,NS,carcinoma,0,2	LAMA5	268	2	0			c.G636A						PASS	.			2318,2084	595.7+/-388.5	604,1110,487	71.0	63.0	66.0		636	-8.1	0.0	20	dbSNP_83	66	7985,607	789.1+/-407.6	3711,563,22	no	coding-synonymous	LAMA5	NM_005560.3		4315,1673,509	TT,TC,CC		7.0647,47.3421,20.7096		212/3696	60927349	10303,2691	2201	4296	6497	SO:0001819	synonymous_variant	3911	exon4			GATGGCCGCGTCG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.636G>A	20.37:g.60927349C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			C|0.206;T|0.794	0.794	strong		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
CTAGE5	4253	hgsc.bcm.edu	37	14	39818028	39818028	+	Missense_Mutation	SNP	A	A	G	rs1140952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:39818028A>G	ENST00000280083.3	+	23	2409	c.2095A>G	c.(2095-2097)Atc>Gtc	p.I699V	CTAGE5_ENST00000396158.2_Missense_Mutation_p.I704V|CTAGE5_ENST00000556148.1_Missense_Mutation_p.I624V|CTAGE5_ENST00000553352.1_Missense_Mutation_p.I670V|CTAGE5_ENST00000396165.4_Missense_Mutation_p.I670V|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.I670V|CTAGE5_ENST00000557038.1_Missense_Mutation_p.I619V|CTAGE5_ENST00000341502.5_Missense_Mutation_p.I699V|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.I1234V|CTAGE5_ENST00000553383.1_3'UTR|CTAGE5_ENST00000348007.3_Missense_Mutation_p.I656V|CTAGE5_ENST00000341749.3_Missense_Mutation_p.I687V			O15320	CTGE5_HUMAN	CTAGE family, member 5	699	Pro-rich.		I -> V (in dbSNP:rs1140952). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9356211}.		positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TCTTGCTCCAATCAGAGGTCC	0.493													A|||	1926	0.384585	0.2519	0.3415	5008	,	,		16436	0.5923		0.4115	False		,,,				2504	0.3528				p.I704V		Atlas-SNP	.											CTAGE5,rectum,carcinoma,0,1	CTAGE5	75	1	0			c.A2110G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1173,3233	412.2+/-336.0	151,871,1181	191.0	199.0	196.0		2095,2059,1966,2008	-2.0	0.0	14	dbSNP_86	196	3395,5205	500.7+/-375.3	671,2053,1576	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	29,29,29,29	822,2924,2757	GG,GA,AA		39.4767,26.6228,35.1223	benign,benign,benign,benign	699/805,687/793,656/762,670/776	39818028	4568,8438	2203	4300	6503	SO:0001583	missense	4253	exon23			GCTCCAATCAGAG	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.2095A>G	14.37:g.39818028A>G	ENSP00000280083:p.Ile699Val	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	255	143	0.560784	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	937	0.429029304029304	131	0.266260162601626	136	0.3756906077348066	359	0.6276223776223776	311	0.4102902374670185	A	0.004	-2.297832	0.00243	0.266228	0.394767	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.06528	3.49;3.33;3.33;3.29;3.55;3.58;3.58;3.33;3.83;3.29	5.41	-2.01	0.07410	.	1.206650	0.06423	N	0.722732	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.002;0.004;0.002;0.004;0.002	T	0.32241	-0.9914	8	.	.	.	.	8.1094	0.30905	0.1281:0.1851:0.6868:0.0	rs1140952;rs3204972;rs17846661;rs17859758;rs1140952	704;656;699;627;687	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	V	1234;687;619;670;699;704;699;624;656;670	ENSP00000452252:I1234V;ENSP00000343897:I687V;ENSP00000450869:I619V;ENSP00000379468:I670V;ENSP00000339286:I699V;ENSP00000379462:I704V;ENSP00000280083:I699V;ENSP00000452562:I624V;ENSP00000343912:I656V;ENSP00000450449:I670V	.	I	+	1	0	CTAGE5;RP11-407N17.3	38887779	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-1.436000	0.02421	-0.792000	0.04480	-0.316000	0.08728	ATC	A|0.632;G|0.368	0.368	strong		0.493	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
FOLH1	2346	hgsc.bcm.edu	37	11	49208267	49208267	+	Missense_Mutation	SNP	G	G	A	rs75940285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49208267G>A	ENST00000256999.2	-	5	828	c.568C>T	c.(568-570)Cgg>Tgg	p.R190W	FOLH1_ENST00000343844.4_De_novo_Start_InFrame|FOLH1_ENST00000340334.7_Missense_Mutation_p.R175W|FOLH1_ENST00000356696.3_Missense_Mutation_p.R190W|FOLH1_ENST00000533034.1_Missense_Mutation_p.R175W	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	190					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)	p.R190W(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TTCATGTCCCGTTCCAATTTA	0.348																																					p.R190W		Atlas-SNP	.											FOLH1,NS,carcinoma,+1,2	FOLH1	141	2	1	Substitution - Missense(1)	NS(1)	c.C568T						PASS	.						80.0	84.0	82.0					11																	49208267		2201	4296	6497	SO:0001583	missense	2346	exon5			TGTCCCGTTCCAA	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.568C>T	11.37:g.49208267G>A	ENSP00000256999:p.Arg190Trp	Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	441	71	0.160998	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889502	0.52014	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	3.05	0.979	0.19745	Protease-associated domain, PA (1);	0.000000	0.48286	D	0.000192	T	0.59985	0.2234	M	0.82056	2.57	0.80722	D	1	D;D;D;P	0.76494	0.999;0.998;0.987;0.941	D;P;P;B	0.70016	0.967;0.821;0.742;0.422	T	0.60250	-0.7300	10	0.87932	D	0	.	8.9034	0.35507	0.0:0.0:0.3751:0.6249	.	175;175;190;190	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	W	190;190;175;175;190	ENSP00000256999:R190W;ENSP00000349129:R190W;ENSP00000344131:R175W;ENSP00000431463:R175W	ENSP00000256999:R190W	R	-	1	2	FOLH1	49164843	0.953000	0.32496	0.991000	0.47740	0.964000	0.63967	1.623000	0.37008	0.120000	0.18254	0.430000	0.28490	CGG	G|0.877;A|0.123	0.123	strong		0.348	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
KRT6C	286887	hgsc.bcm.edu	37	12	52867190	52867190	+	Missense_Mutation	SNP	C	C	T	rs394598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52867190C>T	ENST00000252250.6	-	1	379	c.332G>A	c.(331-333)gGt>gAt	p.G111D		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	111	Head.			G -> D (in Ref. 1; AAC41770/AAC41769). {ECO:0000305}.	intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		ACCACCCAGACCAAAGCCAAT	0.647																																					p.G111D		Atlas-SNP	.											KRT6C,brain,glioma,0,1	KRT6C	55	1	0			c.G332A						scavenged	.						4.0	4.0	4.0					12																	52867190		1761	2940	4701	SO:0001583	missense	286887	exon1			CCCAGACCAAAGC	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.332G>A	12.37:g.52867190C>T	ENSP00000252250:p.Gly111Asp	Somatic	459	0	0		WXS	Illumina HiSeq	Phase_I	377	76	0.201592	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	.	.	.	.	.	.	.	.	.	.	c	9.356	1.066808	0.20067	.	.	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.97941	-4.62	2.61	2.61	0.31194	.	0.000000	0.50627	D	0.000103	D	0.98121	0.9380	M	0.93328	3.405	0.28954	P	0.890213	D	0.64830	0.994	P	0.51516	0.672	D	0.99897	1.1151	9	0.52906	T	0.07	.	10.5791	0.45244	0.193:0.807:0.0:0.0	rs394598;rs1707772;rs2885244	111	P48668	K2C6C_HUMAN	D	111;96	ENSP00000252250:G111D	ENSP00000252250:G111D	G	-	2	0	KRT6C	51153457	.	.	0.999000	0.59377	0.138000	0.21146	.	.	1.770000	0.52166	0.508000	0.49915	GGT	C|0.500;T|0.500	0.500	weak		0.647	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057417	46057417	+	Missense_Mutation	SNP	A	A	C	rs114653592|rs386819192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46057417A>C	ENST00000380095.1	+	1	145	c.83A>C	c.(82-84)gAg>gCg	p.E28A	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	28	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						AGCTGCTGCGAGCCCTGCTGC	0.687													A|||	1444	0.288339	0.2337	0.2075	5008	,	,		16132	0.253		0.3101	False		,,,				2504	0.4335				p.E28A		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.A83C						PASS	.	A	,ALA/GLU	262,4144		115,32,2056	65.0	70.0	68.0		,83	3.5	1.0	21	dbSNP_132	68	726,7872		327,72,3900	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,107	442,104,5956	CC,CA,AA		8.4438,5.9464,7.5977	,probably-damaging	,28/252	46057417	988,12016	2203	4299	6502	SO:0001583	missense	353333	exon1			GCTGCGAGCCCTG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.83A>C	21.37:g.46057417A>C	ENSP00000369438:p.Glu28Ala	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	145	74	0.510345	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	473	0.21657509157509158	80	0.16260162601626016	68	0.1878453038674033	129	0.22552447552447552	196	0.25857519788918204	a	11.78	1.742087	0.30865	0.059464	0.084438	ENSG00000221859	ENST00000380095	T	0.14766	2.48	3.52	3.52	0.40303	.	.	.	.	.	T	0.00012	0.0000	M	0.73372	2.23	0.39648	P	0.029576000000000047	P	0.46987	0.888	B	0.38985	0.287	T	0.40403	-0.9565	8	0.41790	T	0.15	.	10.2769	0.43515	1.0:0.0:0.0:0.0	.	28	P60014	KR10A_HUMAN	A	28	ENSP00000369438:E28A	ENSP00000369438:E28A	E	+	2	0	KRTAP10-10	44881845	0.642000	0.27260	0.987000	0.45799	0.009000	0.06853	1.008000	0.29872	1.358000	0.45922	0.383000	0.25322	GAG	A|0.757;C|0.243	0.243	strong		0.687	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
TTC24	164118	hgsc.bcm.edu	37	1	156551848	156551848	+	Missense_Mutation	SNP	A	A	G	rs6682716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156551848A>G	ENST00000368237.3	+	1	692	c.692A>G	c.(691-693)gAg>gGg	p.E231G	TTC24_ENST00000368236.3_Missense_Mutation_p.E231G			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	231			E -> G (in dbSNP:rs6682716).							breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGGAGCACTGAGAGGCGACTG	0.627													A|||	1753	0.35004	0.0825	0.4553	5008	,	,		17940	0.2877		0.7018	False		,,,				2504	0.3395				p.E231G		Atlas-SNP	.											TTC24,NS,carcinoma,0,1	TTC24	46	1	0			c.A692G						PASS	.	A	GLY/GLU	267,1113		36,195,459	9.0	10.0	10.0		692	3.4	0.0	1	dbSNP_116	10	2284,898		832,620,139	yes	missense	TTC24	NM_001105669.2	98	868,815,598	GG,GA,AA		28.2212,19.3478,44.0815		231/583	156551848	2551,2011	690	1591	2281	SO:0001583	missense	164118	exon2			GCACTGAGAGGCG		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"""Tetratricopeptide (TTC) repeat domain containing"""	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.692A>G	1.37:g.156551848A>G	ENSP00000357220:p.Glu231Gly	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	922|922	0.42216117216117216|0.42216117216117216	47|47	0.09552845528455285|0.09552845528455285	178|178	0.49171270718232046|0.49171270718232046	166|166	0.2902097902097902|0.2902097902097902	531|531	0.7005277044854882|0.7005277044854882	A|A	13.36|13.36	2.213651|2.213651	0.39102|0.39102	0.193478|0.193478	0.717788|0.717788	ENSG00000187862|ENSG00000187862	ENST00000368236;ENST00000368237|ENST00000340086	T;T|.	0.76060|.	-0.99;-0.99|.	4.58|4.58	3.41|3.41	0.39046|0.39046	.|.	0.524885|.	0.16286|.	N|.	0.221131|.	T|T	0.17238|0.17238	0.0414|0.0414	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.07121|0.07121	-1.0789|-1.0789	6|4	.|.	.|.	.|.	-8.3235|-8.3235	9.4528|9.4528	0.38736|0.38736	0.9114:0.0:0.0886:0.0|0.9114:0.0:0.0886:0.0	rs6682716;rs52791705;rs58971631;rs6682716|rs6682716;rs52791705;rs58971631;rs6682716	.|.	.|.	.|.	G|G	231|4	ENSP00000357219:E231G;ENSP00000357220:E231G|.	.|.	E|R	+|+	2|1	0|2	TTC24|TTC24	154818472|154818472	0.024000|0.024000	0.19004|0.19004	0.019000|0.019000	0.16419|0.16419	0.077000|0.077000	0.17291|0.17291	2.290000|2.290000	0.43531|0.43531	1.933000|1.933000	0.56026|0.56026	0.374000|0.374000	0.22700|0.22700	GAG|AGA	A|0.624;G|0.376	0.376	strong		0.627	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384	
MTFR1	9650	hgsc.bcm.edu	37	8	66620359	66620359	+	Intron	SNP	G	G	A	rs13274205	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:66620359G>A	ENST00000262146.4	+	7	1059				MTFR1_ENST00000458689.2_Intron	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1						aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			AAAGGGAGGTGATACAGGATT	0.413													G|||	1389	0.277356	0.3215	0.3156	5008	,	,		19512	0.0		0.5348	False		,,,				2504	0.2117				p.X349X		Atlas-SNP	.											.	MTFR1	26	.	0			c.G1046A						PASS	.	G	,,	472,912		83,306,303	46.0	38.0	41.0		,1046,	-0.1	0.0	8	dbSNP_121	41	1761,1421		480,801,310	no	intron,coding-synonymous,intron	MTFR1	NM_001145838.1,NM_001145839.1,NM_014637.3	,,	563,1107,613	AA,AG,GG		44.6574,34.104,48.9049	,,	,349/349,	66620359	2233,2333	692	1591	2283	SO:0001627	intron_variant	9650	exon7			GGAGGTGATACAG		CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"""likely ortholog of chicken chondrocyte protein with a poly proline region"""					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.933+113G>A	8.37:g.66620359G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_001145839	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Silent	SNP	ENST00000262146.4	37	CCDS6182.1																																																																																			G|0.693;A|0.307	0.307	strong		0.413	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637	
VNN2	8875	hgsc.bcm.edu	37	6	133077063	133077063	+	Silent	SNP	T	T	C	rs1883613	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:133077063T>C	ENST00000326499.6	-	3	580	c.456A>G	c.(454-456)acA>acG	p.T152T	VNN2_ENST00000525289.1_Silent_p.T152T|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000526192.1_5'UTR|VNN2_ENST00000525270.1_Silent_p.T99T	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	152	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TAGGAGGACATGTGGAGTCAC	0.453													T|||	1582	0.315895	0.261	0.4395	5008	,	,		15412	0.2351		0.34	False		,,,				2504	0.3609				p.T152T		Atlas-SNP	.											.	VNN2	83	.	0			c.A456G						PASS	.	T	,,	1281,3125	434.9+/-344.1	177,927,1099	153.0	130.0	138.0		456,456,297	-10.1	0.0	6	dbSNP_92	138	3002,5598	464.2+/-366.2	489,2024,1787	no	coding-synonymous,coding-synonymous,coding-synonymous	VNN2	NM_001242350.1,NM_004665.2,NM_078488.1	,,	666,2951,2886	CC,CT,TT		34.907,29.074,32.931	,,	152/300,152/521,99/468	133077063	4283,8723	2203	4300	6503	SO:0001819	synonymous_variant	8875	exon3			AGGACATGTGGAG	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"""Vanins"""	12706	protein-coding gene	gene with protein product	"""pantetheinase"""	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.456A>G	6.37:g.133077063T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	102	39	0.382353	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																			T|0.682;C|0.318	0.318	strong		0.453	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2		
PRIM1	5557	hgsc.bcm.edu	37	12	57146069	57146069	+	Missense_Mutation	SNP	T	T	G	rs2277339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57146069T>G	ENST00000338193.6	-	1	50	c.14A>C	c.(13-15)gAc>gCc	p.D5A	PRIM1_ENST00000552408.1_5'Flank|HSD17B6_ENST00000554643.1_5'Flank|HSD17B6_ENST00000555805.1_5'UTR|HSD17B6_ENST00000555159.1_5'UTR|HSD17B6_ENST00000554150.1_5'Flank	NM_000946.2	NP_000937.1	P49642	PRI1_HUMAN	primase, DNA, polypeptide 1 (49kDa)	5			D -> A (in dbSNP:rs2277339).		DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			kidney(1)|lung(6)|prostate(1)	8						CTCGGTGGGGTCAAACGTCTC	0.597													T|||	743	0.148363	0.1989	0.1268	5008	,	,		13687	0.2063		0.1113	False		,,,				2504	0.0736				p.D5A		Atlas-SNP	.											.	PRIM1	22	.	0			c.A14C						PASS	.	T	ALA/ASP	705,3193		71,563,1315	31.0	33.0	33.0	http://www.ncbi.nlm.nih.gov/pubmed?term	14	4.7	1.0	12	dbSNP_100	33	784,7498		38,708,3395	yes	missense	PRIM1	NM_000946.2	126	109,1271,4710	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	9.4663,18.0862,12.225	possibly-damaging	5/421	57146069	1489,10691	1949	4141	6090	SO:0001583	missense	5557	exon1			GTGGGGTCAAACG	BC005266	CCDS44926.1	12q13.3	2007-06-19	2007-06-19			ENSG00000198056			9369	protein-coding gene	gene with protein product		176635				8530050	Standard	NM_000946		Approved		uc001smd.3	P49642	OTTHUMG00000170034	ENST00000338193.6:c.14A>C	12.37:g.57146069T>G	ENSP00000350491:p.Asp5Ala	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_000946		Missense_Mutation	SNP	ENST00000338193.6	37	CCDS44926.1	353	0.16163003663003664	86	0.17479674796747968	51	0.1408839779005525	136	0.23776223776223776	80	0.10554089709762533	T	26.0	4.690245	0.88735	0.180862	0.094663	ENSG00000198056	ENST00000537418;ENST00000338193;ENST00000550770	T;T	0.50277	0.75;0.78	4.72	4.72	0.59763	.	0.055012	0.64402	D	0.000002	T	0.00039	0.0001	L	0.58583	1.82	0.09310	P	1.0	P;D	0.63046	0.936;0.992	P;P	0.55713	0.757;0.782	T	0.04078	-1.0979	9	0.59425	D	0.04	-10.75	12.1181	0.53875	0.0:0.0:0.0:1.0	rs2277339;rs60784893;rs2277339	5;5	F8VSB2;P49642	.;PRI1_HUMAN	A	5	ENSP00000350491:D5A;ENSP00000450185:D5A	ENSP00000350491:D5A	D	-	2	0	PRIM1	55432336	1.000000	0.71417	0.993000	0.49108	0.934000	0.57294	6.955000	0.76007	2.124000	0.65301	0.459000	0.35465	GAC	T|0.845;G|0.155	0.155	strong		0.597	PRIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406956.1	NM_000946	
F5	2153	hgsc.bcm.edu	37	1	169521849	169521849	+	Silent	SNP	T	T	C	rs6035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169521849T>C	ENST00000367797.3	-	8	1443	c.1242A>G	c.(1240-1242)aaA>aaG	p.K414K	F5_ENST00000367796.3_Silent_p.K414K|F5_ENST00000546081.1_Silent_p.K277K	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	414	F5/8 type A 2.|Plastocyanin-like 3.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TCCCATCTTCTTTCATATTGG	0.348													T|||	416	0.0830671	0.0847	0.0735	5008	,	,		15504	0.0714		0.0865	False		,,,				2504	0.0961				p.K414K		Atlas-SNP	.											.	F5	301	.	0			c.A1242G	GRCh37	CM070088	F5	M	rs6035	PASS	.	T		399,4007	197.7+/-221.8	30,339,1834	154.0	153.0	154.0		1242	0.8	0.0	1	dbSNP_52	154	743,7857	179.5+/-228.6	42,659,3599	no	coding-synonymous	F5	NM_000130.4		72,998,5433	CC,CT,TT		8.6395,9.0558,8.7806		414/2225	169521849	1142,11864	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon8			ATCTTCTTTCATA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1242A>G	1.37:g.169521849T>C		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	249	127	0.51004	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			T|0.917;C|0.083	0.083	strong		0.348	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
NEUROD4	58158	hgsc.bcm.edu	37	12	55420785	55420785	+	Missense_Mutation	SNP	G	G	A	rs151143558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:55420785G>A	ENST00000242994.3	+	2	940	c.562G>A	c.(562-564)Gat>Aat	p.D188N		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	188					amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						GAAGCACGAGGATAAATCTCC	0.517													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18905	0.0		0.003	False		,,,				2504	0.0				p.D188N		Atlas-SNP	.											.	NEUROD4	87	.	0			c.G562A						PASS	.	G	ASN/ASP	0,4406		0,0,2203	77.0	81.0	80.0		562	5.6	1.0	12	dbSNP_134	80	39,8561	24.6+/-71.5	0,39,4261	yes	missense	NEUROD4	NM_021191.2	23	0,39,6464	AA,AG,GG		0.4535,0.0,0.2999	benign	188/332	55420785	39,12967	2203	4300	6503	SO:0001583	missense	58158	exon2			CACGAGGATAAAT	AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"""Basic helix-loop-helix proteins"""	13802	protein-coding gene	gene with protein product		611635	"""neurogenic differentiation 4"""				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.562G>A	12.37:g.55420785G>A	ENSP00000242994:p.Asp188Asn	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_021191	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	37	CCDS8886.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	20.4	3.977793	0.74360	0.0	0.004535	ENSG00000123307	ENST00000242994	T	0.65178	-0.14	5.56	5.56	0.83823	Neurogenic differentiation factor, domain of unknown function (1);	0.214698	0.47455	D	0.000236	T	0.67739	0.2925	L	0.41492	1.28	0.37808	D	0.927932	B	0.24317	0.101	B	0.43809	0.432	T	0.70414	-0.4878	10	0.72032	D	0.01	-37.9711	17.4011	0.87459	0.0:0.0:1.0:0.0	.	188	Q9HD90	NDF4_HUMAN	N	188	ENSP00000242994:D188N	ENSP00000242994:D188N	D	+	1	0	NEUROD4	53707052	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.774000	0.75012	2.774000	0.95407	0.655000	0.94253	GAT	G|0.997;A|0.003	0.003	strong		0.517	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1		
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1814391	1814391	+	Silent	SNP	T	T	C	rs2294618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1814391T>C	ENST00000250894.4	+	19	2365	c.2208T>C	c.(2206-2208)gaT>gaC	p.D736D	MAPK8IP3_ENST00000356010.5_Silent_p.D730D	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	736					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						CAGGCCGCGATCCCCTGACCT	0.682													T|||	764	0.152556	0.0378	0.0908	5008	,	,		16007	0.2847		0.1531	False		,,,				2504	0.2147				p.D736D		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.T2208C						PASS	.	T	,	172,3964		3,166,1899	16.0	22.0	20.0		2190,2208	2.9	1.0	16	dbSNP_100	20	1059,7343		64,931,3206	no	coding-synonymous,coding-synonymous	MAPK8IP3	NM_001040439.1,NM_015133.3	,	67,1097,5105	CC,CT,TT		12.6041,4.1586,9.8182	,	730/1331,736/1337	1814391	1231,11307	2068	4201	6269	SO:0001819	synonymous_variant	23162	exon19			CCGCGATCCCCTG	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.2208T>C	16.37:g.1814391T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	37	CCDS10442.2																																																																																			T|0.839;C|0.161	0.161	strong		0.682	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
CARD14	79092	hgsc.bcm.edu	37	17	78157995	78157995	+	Silent	SNP	G	G	A	rs4889990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:78157995G>A	ENST00000573882.1	+	6	1169	c.633G>A	c.(631-633)gaG>gaA	p.E211E	CARD14_ENST00000570421.1_Silent_p.E211E|CARD14_ENST00000392434.2_5'UTR|CARD14_ENST00000344227.2_Silent_p.E211E			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	211					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CGCTGCAGGAGAAGGAGCTGG	0.652													G|||	1738	0.347045	0.4198	0.2939	5008	,	,		19510	0.2212		0.3618	False		,,,				2504	0.4008				p.E211E		Atlas-SNP	.											.	CARD14	98	.	0			c.G633A						PASS	.	G		1790,2568		388,1014,777	19.0	15.0	17.0		633	0.8	1.0	17	dbSNP_111	17	3203,5351		655,1893,1729	no	coding-synonymous	CARD14	NM_024110.3		1043,2907,2506	AA,AG,GG		37.4445,41.0739,38.6695		211/1005	78157995	4993,7919	2179	4277	6456	SO:0001819	synonymous_variant	79092	exon4			GCAGGAGAAGGAG	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.633G>A	17.37:g.78157995G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			G|0.641;A|0.359	0.359	strong		0.652	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
PRG2	5553	hgsc.bcm.edu	37	11	57155288	57155288	+	Silent	SNP	T	T	C	rs630396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57155288T>C	ENST00000311862.5	-	5	622	c.549A>G	c.(547-549)gcA>gcG	p.A183A	PRG2_ENST00000525955.1_Silent_p.A183A|PRG2_ENST00000533605.1_Silent_p.A172A	NM_001243245.1|NM_002728.4	NP_001230174.1|NP_002719.3	P13727	PRG2_HUMAN	proteoglycan 2, bone marrow (natural killer cell activator, eosinophil granule major basic protein)	183	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Sargramostim(DB00020)	CAGCCCAGTATGCAAAGTTCC	0.627													C|||	4713	0.941094	0.7973	0.9784	5008	,	,		16838	0.996		0.999	False		,,,				2504	0.9928				p.A183A		Atlas-SNP	.											PRG2_ENST00000311862,colon,carcinoma,-1,1	PRG2	65	1	0			c.A549G						PASS	.	C		3691,705		1541,609,48	20.0	20.0	20.0		549	-9.8	0.0	11	dbSNP_83	20	8562,12		4275,12,0	no	coding-synonymous	PRG2	NM_002728.4		5816,621,48	CC,CT,TT		0.14,16.0373,5.5281		183/223	57155288	12253,717	2198	4287	6485	SO:0001819	synonymous_variant	5553	exon5			CCAGTATGCAAAG	BC005929	CCDS7955.1, CCDS58133.1	11q12	2005-11-25				ENSG00000186652			9362	protein-coding gene	gene with protein product		605601				1565101	Standard	NM_001243245		Approved	MBP, BMPG		P13727		ENST00000311862.5:c.549A>G	11.37:g.57155288T>C		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_002728	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000311862.5	37	CCDS7955.1																																																																																			C|0.935;T|0.065	0.935	strong		0.627	PRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392468.1	NM_002728	
GNB1L	54584	hgsc.bcm.edu	37	22	19808769	19808769	+	Missense_Mutation	SNP	C	C	T	rs5748449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:19808769C>T	ENST00000329517.6	-	3	346	c.110G>A	c.(109-111)cGc>cAc	p.R37H	GNB1L_ENST00000405009.1_Missense_Mutation_p.R37H|GNB1L_ENST00000460402.1_Intron|GNB1L_ENST00000403325.1_Missense_Mutation_p.R37H	NM_053004.2	NP_443730.1	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	37			R -> H (in dbSNP:rs5748449).		G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|social behavior (GO:0035176)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)				breast(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	12	Colorectal(54;0.0993)					GAGGAGCGGGCGCCCCTGAGC	0.677													C|||	721	0.14397	0.0197	0.1758	5008	,	,		17191	0.0913		0.1968	False		,,,				2504	0.2894				p.R37H		Atlas-SNP	.											.	GNB1L	34	.	0			c.G110A						PASS	.	C	HIS/ARG	238,4168	134.9+/-171.1	10,218,1975	46.0	57.0	53.0		110	-4.6	0.0	22	dbSNP_114	53	1733,6867	305.6+/-307.5	180,1373,2747	yes	missense	GNB1L	NM_053004.2	29	190,1591,4722	TT,TC,CC		20.1512,5.4017,15.1545	benign	37/328	19808769	1971,11035	2203	4300	6503	SO:0001583	missense	54584	exon3			AGCGGGCGCCCCT	AF238328	CCDS13768.1	22q11.2	2013-05-21			ENSG00000185838	ENSG00000185838		"""WD repeat domain containing"""	4397	protein-coding gene	gene with protein product		610778				11072084	Standard	NM_053004		Approved	GY2, WDR14	uc002zqf.1	Q9BYB4	OTTHUMG00000150279	ENST00000329517.6:c.110G>A	22.37:g.19808769C>T	ENSP00000331313:p.Arg37His	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_053004	Q9H2S2|Q9H4M4	Missense_Mutation	SNP	ENST00000329517.6	37	CCDS13768.1	280	0.1282051282051282	14	0.028455284552845527	70	0.19337016574585636	51	0.08916083916083917	145	0.19129287598944592	C	3.185	-0.167019	0.06461	0.054017	0.201512	ENSG00000185838	ENST00000329517;ENST00000403325;ENST00000405009;ENST00000453108	T;T;T;T	0.35789	2.16;2.16;5.02;1.29	4.9	-4.57	0.03421	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.391610	0.05331	N	0.528250	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23190	-1.0195	9	0.16420	T	0.52	-17.5463	4.561	0.12160	0.1736:0.5063:0.1196:0.2006	rs5748449;rs5748449	37	Q9BYB4	GNB1L_HUMAN	H	37	ENSP00000331313:R37H;ENSP00000385154:R37H;ENSP00000384626:R37H;ENSP00000389412:R37H	ENSP00000331313:R37H	R	-	2	0	GNB1L	18188769	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-2.766000	0.00782	-0.600000	0.05790	-0.752000	0.03492	CGC	C|0.860;T|0.140	0.140	strong		0.677	GNB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075202.1		
VARS2	57176	hgsc.bcm.edu	37	6	30888161	30888161	+	Missense_Mutation	SNP	T	T	C	rs2249464	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30888161T>C	ENST00000321897.5	+	13	1977	c.1345T>C	c.(1345-1347)Tgg>Cgg	p.W449R	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Missense_Mutation_p.W309R|VARS2_ENST00000416670.2_Missense_Mutation_p.W449R|VARS2_ENST00000541562.1_Missense_Mutation_p.W479R			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	449			W -> R (in dbSNP:rs2249464). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						GCTGAGTGAATGGGGCCTGTT	0.507													C|||	3086	0.616214	0.3593	0.6297	5008	,	,		16650	0.8413		0.5596	False		,,,				2504	0.7802				p.W479R		Atlas-SNP	.											.	VARS2	60	.	0			c.T1435C						PASS	.	C	ARG/TRP,ARG/TRP,ARG/TRP	1639,2767	657.5+/-400.2	284,1071,848	47.0	50.0	49.0		925,1435,1345	4.3	1.0	6	dbSNP_100	49	4645,3955	549.6+/-385.6	1242,2161,897	yes	missense,missense,missense	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	101,101,101	1526,3232,1745	CC,CT,TT		45.9884,37.1993,48.3162	benign,benign,benign	309/924,479/1094,449/1064	30888161	6284,6722	2203	4300	6503	SO:0001583	missense	57176	exon14			AGTGAATGGGGCC	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1345T>C	6.37:g.30888161T>C	ENSP00000316092:p.Trp449Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	1260	0.5769230769230769	149	0.30284552845528456	217	0.5994475138121547	458	0.8006993006993007	436	0.575197889182058	C	0.043	-1.278043	0.01410	0.371993	0.540116	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.33216	1.42;1.42;1.42;1.42	4.27	4.27	0.50696	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.262247	0.36002	N	0.002851	T	0.01092	0.0036	N	0.00039	-2.505	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40869	-0.9540	9	0.07175	T	0.84	-15.0648	5.8387	0.18621	0.1888:0.7098:0.0:0.1013	rs2249464;rs17195977;rs52836674;rs58710343;rs2249464	479;449	F5GXJ0;Q5ST30	.;SYVM_HUMAN	R	449;449;309;479	ENSP00000316092:W449R;ENSP00000394802:W449R;ENSP00000438200:W309R;ENSP00000441000:W479R	ENSP00000316092:W449R	W	+	1	0	VARS2	30996140	0.844000	0.29557	0.999000	0.59377	0.258000	0.26162	1.299000	0.33424	0.943000	0.37553	-0.355000	0.07637	TGG	T|0.471;C|0.529	0.529	strong		0.507	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
ALPP	250	hgsc.bcm.edu	37	2	233244930	233244930	+	Missense_Mutation	SNP	G	G	C	rs1048988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:233244930G>C	ENST00000392027.2	+	6	961	c.692G>C	c.(691-693)cGc>cCc	p.R231P	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	231			R -> P (in dbSNP:rs1048988). {ECO:0000269|PubMed:3512548}.		dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		TACATGTTTCGCATGGGAACC	0.617													C|||	704	0.140575	0.0393	0.183	5008	,	,		17811	0.0327		0.2952	False		,,,				2504	0.1994				p.R231P		Atlas-SNP	.											.	ALPP	53	.	0			c.G692C						PASS	.	G	PRO/ARG	288,4118		13,262,1928	120.0	101.0	107.0		692	0.3	0.2	2	dbSNP_86	107	2180,6414		313,1554,2430	no	missense	ALPP	NM_001632.3	103	326,1816,4358	CC,CG,GG		25.3665,6.5365,18.9846	benign	231/536	233244930	2468,10532	2203	4297	6500	SO:0001583	missense	250	exon6			TGTTTCGCATGGG	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.692G>C	2.37:g.233244930G>C	ENSP00000375881:p.Arg231Pro	Somatic	418	0	0		WXS	Illumina HiSeq	Phase_I	449	448	0.997773	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	315	0.14423076923076922	37	0.07520325203252033	71	0.19613259668508287	31	0.05419580419580419	176	0.23218997361477572	.	0.004	-2.332974	0.00227	0.065365	0.253665	ENSG00000163283	ENST00000392027	D	0.94723	-3.5	2.31	0.318	0.15867	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.107337	0.64402	N	0.000004	T	0.00039	0.0001	N	0.00001	-3.68	0.38425	P	0.05372900000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.58165	-0.7684	9	0.02654	T	1	.	12.9635	0.58472	0.0:0.8242:0.1758:0.0	rs1048988;rs2678510;rs3189061;rs17412784;rs1048988	231	P05187	PPB1_HUMAN	P	231	ENSP00000375881:R231P	ENSP00000375881:R231P	R	+	2	0	ALPP	232953174	0.991000	0.36638	0.168000	0.22838	0.172000	0.22775	3.488000	0.53229	-0.072000	0.12864	-0.735000	0.03563	CGC	G|0.823;C|0.177	0.177	strong		0.617	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
MTTP	4547	hgsc.bcm.edu	37	4	100504566	100504566	+	Missense_Mutation	SNP	G	G	C	rs61733139	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100504566G>C	ENST00000265517.5	+	3	488	c.285G>C	c.(283-285)caG>caC	p.Q95H	MTTP_ENST00000457717.1_Missense_Mutation_p.Q95H|MTTP_ENST00000511045.1_Missense_Mutation_p.Q122H|MTTP_ENST00000422897.2_Missense_Mutation_p.Q95H			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	95	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		Q -> H (in dbSNP:rs61733139). {ECO:0000269|PubMed:11792722}.		cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	TGAATCAGCAGAGAGGAGAGA	0.378													G|||	183	0.0365415	0.0477	0.0274	5008	,	,		17237	0.0		0.0547	False		,,,				2504	0.047				p.Q95H		Atlas-SNP	.											.	MTTP	127	.	0			c.G285C						PASS	.	G	HIS/GLN	225,4179	131.4+/-167.9	6,213,1983	111.0	120.0	117.0		285	1.4	1.0	4	dbSNP_129	117	470,8128	138.7+/-195.5	10,450,3839	yes	missense	MTTP	NM_000253.2	24	16,663,5822	CC,CG,GG		5.4664,5.109,5.3453	benign	95/895	100504566	695,12307	2202	4299	6501	SO:0001583	missense	4547	exon4			TCAGCAGAGAGGA		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.285G>C	4.37:g.100504566G>C	ENSP00000265517:p.Gln95His	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	276	127	0.460145	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	65	0.02976190476190476	20	0.04065040650406504	7	0.019337016574585635	0	0.0	38	0.05013192612137203	G	11.33	1.607846	0.28623	0.05109	0.054664	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000422897;ENST00000538053	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	5.71	1.39	0.22231	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.292720	0.36665	N	0.002474	T	0.02533	0.0077	N	0.14661	0.345	0.09310	N	1	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.12156	0.002;0.002;0.007	T	0.06197	-1.0840	10	0.14656	T	0.56	-4.0E-4	0.8566	0.01184	0.2979:0.2486:0.3084:0.1451	rs61733139	122;95;95	E9PBP6;P55157;Q6P5T3	.;MTP_HUMAN;.	H	105;122;95;95;95;95	ENSP00000426755:Q105H;ENSP00000427679:Q122H;ENSP00000400821:Q95H;ENSP00000265517:Q95H;ENSP00000407350:Q95H	ENSP00000265517:Q95H	Q	+	3	2	MTTP	100723589	0.855000	0.29742	0.986000	0.45419	0.975000	0.68041	-0.174000	0.09839	0.701000	0.31803	0.655000	0.94253	CAG	G|0.952;C|0.048	0.048	strong		0.378	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
MADCAM1	8174	hgsc.bcm.edu	37	19	501695	501695	+	Missense_Mutation	SNP	C	C	T	rs77685069		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:501695C>T	ENST00000215637.3	+	4	740	c.694C>T	c.(694-696)Cct>Tct	p.P232S	MADCAM1_ENST00000587541.1_Missense_Mutation_p.P13S|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	232	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCCCGGAGCCTCCCGACAC	0.657																																					p.P232S		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C694T						PASS	.						33.0	45.0	41.0					19																	501695		2203	4299	6502	SO:0001583	missense	8174	exon4			CCGGAGCCTCCCG	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.694C>T	19.37:g.501695C>T	ENSP00000215637:p.Pro232Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	215	23	0.106977	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	c	10.73	1.433068	0.25813	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.12039	2.72	4.13	1.79	0.24919	.	3.587270	0.01390	N	0.013211	T	0.08133	0.0203	N	0.14661	0.345	0.09310	N	1	B	0.34103	0.437	B	0.31495	0.131	T	0.27262	-1.0079	10	0.15066	T	0.55	.	5.1333	0.14922	0.371:0.5267:0.0:0.1022	.	232	Q13477	MADCA_HUMAN	S	256;248;240;232	ENSP00000215637:P232S	ENSP00000215637:P232S	P	+	1	0	MADCAM1	452695	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.138000	0.16016	0.385000	0.24970	0.603000	0.83216	CCT	C|0.500;T|0.500	0.500	weak		0.657	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
ZNF526	116115	hgsc.bcm.edu	37	19	42729121	42729121	+	Missense_Mutation	SNP	C	C	T	rs150807158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:42729121C>T	ENST00000301215.3	+	3	791	c.566C>T	c.(565-567)cCa>cTa	p.P189L		NM_133444.1	NP_597701.1	Q8TF50	ZN526_HUMAN	zinc finger protein 526	189					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(3)	22		Prostate(69;0.0704)				CCTTCTCCCCCATCCGAAGTC	0.597													C|||	13	0.00259585	0.0008	0.0	5008	,	,		19799	0.0		0.006	False		,,,				2504	0.0061				p.P189L		Atlas-SNP	.											.	ZNF526	51	.	0			c.C566T						PASS	.	C	LEU/PRO	9,4397	15.5+/-35.6	0,9,2194	135.0	127.0	130.0		566	4.4	0.1	19	dbSNP_134	130	124,8476	64.9+/-127.2	2,120,4178	yes	missense	ZNF526	NM_133444.1	98	2,129,6372	TT,TC,CC		1.4419,0.2043,1.0226	possibly-damaging	189/671	42729121	133,12873	2203	4300	6503	SO:0001583	missense	116115	exon3			CTCCCCCATCCGA	AB075831	CCDS12598.1	19q13.31	2013-01-08				ENSG00000167625		"""Zinc fingers, C2H2-type"""	29415	protein-coding gene	gene with protein product		614387				11853319	Standard	NM_133444		Approved	KIAA1951, MGC4267	uc002osz.1	Q8TF50		ENST00000301215.3:c.566C>T	19.37:g.42729121C>T	ENSP00000301215:p.Pro189Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_133444	B3KV29|Q69YI2|Q96E24	Missense_Mutation	SNP	ENST00000301215.3	37	CCDS12598.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	6.077	0.382572	0.11524	0.002043	0.014419	ENSG00000167625	ENST00000437878;ENST00000301215	T	0.08634	3.07	4.4	4.4	0.53042	.	0.555420	0.16362	N	0.217738	T	0.06096	0.0158	L	0.44542	1.39	0.33667	D	0.61049	B	0.12013	0.005	B	0.10450	0.005	T	0.02683	-1.1124	10	0.72032	D	0.01	-4.7579	9.9765	0.41786	0.0:0.9038:0.0:0.0962	.	189	Q8TF50	ZN526_HUMAN	L	45;189	ENSP00000301215:P189L	ENSP00000301215:P189L	P	+	2	0	ZNF526	47420961	0.022000	0.18835	0.057000	0.19452	0.395000	0.30598	2.169000	0.42434	2.449000	0.82847	0.467000	0.42956	CCA	C|0.991;T|0.009	0.009	strong		0.597	ZNF526-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463681.2	XM_057401	
ZNF33B	7582	hgsc.bcm.edu	37	10	43089965	43089965	+	Missense_Mutation	SNP	G	G	A	rs210280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43089965G>A	ENST00000359467.3	-	5	547	c.433C>T	c.(433-435)Cgt>Tgt	p.R145C	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	145			R -> C (in dbSNP:rs210280). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8464732}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						CTCATTCCACGTGAGTCATAC	0.338													a|||	3641	0.727037	0.5348	0.7767	5008	,	,		9575	0.873		0.835	False		,,,				2504	0.6902				p.R145C	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.C433T						PASS	.	A	CYS/ARG	2741,1663	505.1+/-366.0	841,1059,302	77.0	74.0	75.0		433	-0.5	0.0	10	dbSNP_79	75	7303,1293	254.0+/-279.5	3104,1095,99	yes	missense	ZNF33B	NM_006955.1	180	3945,2154,401	AA,AG,GG		15.0419,37.7611,22.7385	benign	145/779	43089965	10044,2956	2202	4298	6500	SO:0001583	missense	7582	exon5			TTCCACGTGAGTC	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"""Zinc fingers, C2H2-type"", ""-"""	13097	protein-coding gene	gene with protein product		194522	"""zinc finger protein 33b (KOX 31)"", ""zinc finger protein 11B"""	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.433C>T	10.37:g.43089965G>A	ENSP00000352444:p.Arg145Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	1679	0.7687728937728938	262	0.532520325203252	284	0.7845303867403315	498	0.8706293706293706	635	0.837730870712401	A	0.311	-0.967615	0.02232	0.622389	0.849581	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.05025	3.51	2.14	-0.499	0.12015	.	1.297520	0.05632	N	0.581834	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	9	0.09084	T	0.74	.	3.6316	0.08134	0.5384:0.1977:0.2639:0.0	rs210280;rs482460;rs17846436;rs17859485;rs52831158;rs59394808;rs210280	145	Q06732	ZN33B_HUMAN	C	145;111	ENSP00000352444:R145C	ENSP00000352444:R145C	R	-	1	0	ZNF33B	42409971	0.118000	0.22208	0.000000	0.03702	0.001000	0.01503	-0.232000	0.09055	-0.496000	0.06650	-0.970000	0.02610	CGT	G|0.236;A|0.764	0.764	strong		0.338	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106685448	106685448	+	Silent	SNP	G	G	T	rs75385144	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:106685448G>T	ENST00000265717.4	+	1	355	c.96G>T	c.(94-96)gcG>gcT	p.A32A		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	32	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TGGAGTTCGCGCTGCAGCACT	0.701													G|||	1434	0.286342	0.0197	0.4164	5008	,	,		6544	0.3433		0.3579	False		,,,				2504	0.4223				p.A32A		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G96T						PASS	.	G		271,3937		14,243,1847	6.0	8.0	7.0		96	2.0	1.0	7	dbSNP_131	7	2493,5831		437,1619,2106	no	coding-synonymous	PRKAR2B	NM_002736.2		451,1862,3953	TT,TG,GG		29.9495,6.4401,22.0555		32/419	106685448	2764,9768	2104	4162	6266	SO:0001819	synonymous_variant	5577	exon1			GTTCGCGCTGCAG		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.96G>T	7.37:g.106685448G>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.707;T|0.293	0.293	strong		0.701	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
HMMR	3161	hgsc.bcm.edu	37	5	162901156	162901156	+	Missense_Mutation	SNP	G	G	A	rs2303078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:162901156G>A	ENST00000358715.3	+	10	1031	c.995G>A	c.(994-996)cGt>cAt	p.R332H	HMMR_ENST00000432118.2_Missense_Mutation_p.R246H|HMMR_ENST00000353866.3_Missense_Mutation_p.R317H|HMMR_ENST00000393915.4_Missense_Mutation_p.R333H			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	332			R -> H (in dbSNP:rs2303078).	QER -> REH (in Ref. 1; AAC52049). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	CAACAGGAACGTGAAAAGCTT	0.308													G|||	124	0.0247604	0.003	0.0303	5008	,	,		19680	0.0437		0.0398	False		,,,				2504	0.0153				p.R333H		Atlas-SNP	.											.	HMMR	64	.	0			c.G998A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	55,4351	53.6+/-89.4	0,55,2148	78.0	77.0	78.0		998,737,995,950	-1.0	0.0	5	dbSNP_100	78	435,8163	132.6+/-190.3	10,415,3874	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	29,29,29,29	10,470,6022	AA,AG,GG		5.0593,1.2483,3.7681	benign,benign,benign,benign	333/726,246/639,332/725,317/710	162901156	490,12514	2203	4299	6502	SO:0001583	missense	3161	exon10			AGGAACGTGAAAA	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.995G>A	5.37:g.162901156G>A	ENSP00000351554:p.Arg332His	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	304	106	0.348684	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	83	0.038003663003663	4	0.008130081300813009	11	0.03038674033149171	34	0.05944055944055944	34	0.044854881266490766	G	0.149	-1.093091	0.01858	0.012483	0.050593	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000434157;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.06528	3.29;3.29;3.29;3.29;3.29	5.77	-1.02	0.10135	.	0.810444	0.11726	N	0.535412	T	0.00210	0.0006	N	0.00707	-1.245	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.46925	-0.9156	10	0.15499	T	0.54	3.3839	4.9511	0.14015	0.5844:0.0:0.2898:0.1258	rs2303078;rs52835383;rs2303078	246;333;317;332	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	H	218;317;317;333;309;246;332	ENSP00000400527:R218H;ENSP00000185942:R317H;ENSP00000377492:R333H;ENSP00000402673:R246H;ENSP00000351554:R332H	ENSP00000185942:R317H	R	+	2	0	HMMR	162833734	0.880000	0.30214	0.001000	0.08648	0.018000	0.09664	0.462000	0.21956	-0.301000	0.08882	-1.093000	0.02169	CGT	G|0.961;A|0.039	0.039	strong		0.308	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
CFHR5	81494	hgsc.bcm.edu	37	1	196953220	196953220	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:196953220C>T	ENST00000256785.4	+	3	492	c.383C>T	c.(382-384)tCg>tTg	p.S128L	CFHR5_ENST00000367414.5_Missense_Mutation_p.S152L			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	128	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						AAAAACATTTCGTGTGTAGAA	0.378																																					p.S128L		Atlas-SNP	.											CFHR5_ENST00000367414,NS,malignant_melanoma,0,6	CFHR5	150	6	0			c.C383T						PASS	.						96.0	86.0	89.0					1																	196953220		2203	4300	6503	SO:0001583	missense	81494	exon3			ACATTTCGTGTGT	AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"""Complement system"""	24668	protein-coding gene	gene with protein product	"""factor H related protein 5"""	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.383C>T	1.37:g.196953220C>T	ENSP00000256785:p.Ser128Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	11	0.115789	NM_030787	Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.912751	0.33721	.	.	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.63580	-0.05;-0.05	3.89	0.396	0.16309	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.44767	0.1309	L	0.36672	1.1	0.09310	N	1	B	0.26363	0.147	B	0.26202	0.067	T	0.26155	-1.0111	9	0.19590	T	0.45	.	4.7535	0.13071	0.3661:0.5179:0.0:0.116	.	128	Q9BXR6	FHR5_HUMAN	L	152;128	ENSP00000356384:S152L;ENSP00000256785:S128L	ENSP00000256785:S128L	S	+	2	0	CFHR5	195219843	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.282000	0.08445	0.212000	0.20703	0.467000	0.42956	TCG	.	.	none		0.378	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787	
ZBTB2	57621	hgsc.bcm.edu	37	6	151686905	151686905	+	Silent	SNP	C	C	T	rs11155787	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:151686905C>T	ENST00000325144.4	-	3	1436	c.1296G>A	c.(1294-1296)gaG>gaA	p.E432E		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	432					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		GACTCCCTTCCTCAAATGTGC	0.493													C|||	2123	0.423922	0.3517	0.5447	5008	,	,		21385	0.2778		0.6382	False		,,,				2504	0.3661				p.E432E		Atlas-SNP	.											.	ZBTB2	30	.	0			c.G1296A						PASS	.	C		1735,2671	516.8+/-369.3	352,1031,820	161.0	131.0	141.0		1296	5.4	1.0	6	dbSNP_120	141	5477,3123	657.0+/-401.4	1757,1963,580	yes	coding-synonymous	ZBTB2	NM_020861.1		2109,2994,1400	TT,TC,CC		36.314,39.3781,44.5487		432/515	151686905	7212,5794	2203	4300	6503	SO:0001819	synonymous_variant	57621	exon3			CCCTTCCTCAAAT	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.1296G>A	6.37:g.151686905C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	281	279	0.992883	NM_020861	A8K7C7|Q5SZ81|Q9P245	Silent	SNP	ENST00000325144.4	37	CCDS5231.1																																																																																			C|0.495;T|0.505	0.505	strong		0.493	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140772427	140772427	+	Missense_Mutation	SNP	T	T	G	rs726684	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140772427T>G	ENST00000398604.2	+	1	47	c.47T>G	c.(46-48)cTg>cGg	p.L16R	PCDHGA7_ENST00000518325.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	16			L -> R (in dbSNP:rs726684).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGATCCTGCTGTGCGCGCTG	0.557													.|||	822	0.164137	0.1021	0.3329	5008	,	,		17243	0.1319		0.1909	False		,,,				2504	0.1339				p.L16R		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.T47G						PASS	.	T	,ARG/LEU,,,,,,,,,,,ARG/LEU	450,3766		27,396,1685	17.0	21.0	20.0		,47,,,,,,,,,,,47	5.0	1.0	5	dbSNP_86	20	1470,7050		116,1238,2906	yes	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,102,,,,,,,,,,,102	143,1634,4591	GG,GT,TT		17.2535,10.6736,15.0754	,,,,,,,,,,,,	,16/821,,,,,,,,,,,16/933	140772427	1920,10816	2108	4260	6368	SO:0001583	missense	9708	exon1			TCCTGCTGTGCGC	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.47T>G	5.37:g.140772427T>G	ENSP00000381605:p.Leu16Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	19	0.267606	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	375	0.1717032967032967	41	0.08333333333333333	112	0.30939226519337015	73	0.12762237762237763	149	0.19656992084432717	.	15.59	2.878362	0.51801	0.106736	0.172535	ENSG00000253767	ENST00000398604	T	0.53206	0.63	5.04	5.04	0.67666	.	.	.	.	.	T	0.00012	0.0000	M	0.89353	3.025	0.39240	P	0.03616600000000003	D;P	0.71674	0.998;0.908	D;P	0.65233	0.933;0.799	T	0.14062	-1.0486	8	0.72032	D	0.01	.	10.3989	0.44218	0.1465:0.0:0.0:0.8535	rs726684;rs17603060;rs58099825;rs726684	16;16	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	R	16	ENSP00000381605:L16R	ENSP00000381605:L16R	L	+	2	0	PCDHGA8	140752611	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	4.361000	0.59461	1.910000	0.55303	0.533000	0.62120	CTG	T|0.847;G|0.153	0.153	strong		0.557	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
NAT2	10	hgsc.bcm.edu	37	8	18258103	18258103	+	Missense_Mutation	SNP	G	G	A	rs1799930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:18258103G>A	ENST00000286479.3	+	2	697	c.590G>A	c.(589-591)cGa>cAa	p.R197Q	NAT2_ENST00000520116.1_Missense_Mutation_p.R67Q	NM_000015.2	NP_000006.2	P11245	ARY2_HUMAN	N-acetyltransferase 2 (arylamine N-acetyltransferase)	197			R -> Q (in allele NAT2*5E, allele NAT2*6A, allele NAT2*6B, allele NAT2*6C, allele NAT2*6D and allele NAT2*14D; a slow acetylator; dbSNP:rs1799930). {ECO:0000269|PubMed:1381364, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16416399, ECO:0000269|Ref.14, ECO:0000269|Ref.8}.		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	arylamine N-acetyltransferase activity (GO:0004060)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(2)	12				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)	Acetaminophen(DB00316)|Clonazepam(DB01068)|Dapsone(DB00250)|Ezogabine(DB04953)|Isoniazid(DB00951)|Sulfamethoxazole(DB01015)	CTTGAACCTCGAACAATTGAA	0.363									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				G|||	1327	0.264976	0.2375	0.1715	5008	,	,		18802	0.256		0.2823	False		,,,				2504	0.3599				p.R197Q		Atlas-SNP	.											.	NAT2	34	.	0			c.G590A	GRCh37	CM910270	NAT2	M	rs1799930	PASS	.	G	GLN/ARG	1171,3235	388.6+/-327.0	169,833,1201	87.0	93.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	590	2.5	1.0	8	dbSNP_89	91	2497,6103	403.0+/-347.6	356,1785,2159	yes	missense	NAT2	NM_000015.2	43	525,2618,3360	AA,AG,GG		29.0349,26.5774,28.2024	probably-damaging	197/291	18258103	3668,9338	2203	4300	6503	SO:0001583	missense	10	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	AACCTCGAACAAT	D90042	CCDS6008.1	8p22	2012-01-18			ENSG00000156006	ENSG00000156006	2.3.1.5		7646	protein-coding gene	gene with protein product		612182		AAC2		7773298	Standard	NM_000015		Approved		uc003wyw.1	P11245	OTTHUMG00000130826	ENST00000286479.3:c.590G>A	8.37:g.18258103G>A	ENSP00000286479:p.Arg197Gln	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_000015	O43637|O60654|O60655|Q13146|Q16697|Q2MLE4|Q2MLF5|Q2MLG8|Q2MLJ6|Q2MLK4|Q2MLK6|Q2MLN7|Q6LET4|Q86XS0|Q86XS1|Q96KY8|Q96T64|Q96T65|Q9H220	Missense_Mutation	SNP	ENST00000286479.3	37	CCDS6008.1	535	0.24496336996336995	130	0.26422764227642276	65	0.17955801104972377	129	0.22552447552447552	211	0.2783641160949868	G	13.33	2.204474	0.38905	0.265774	0.290349	ENSG00000156006	ENST00000286479;ENST00000520116	T;T	0.02140	4.43;4.43	2.51	2.51	0.30379	.	0.074179	0.53938	D	0.000041	T	0.00012	0.0000	M	0.76328	2.33	0.23010	P	0.99843819	D	0.89917	1.0	D	0.78314	0.991	T	0.44050	-0.9353	9	0.51188	T	0.08	.	8.6215	0.33864	0.0:0.0:1.0:0.0	rs1799930;rs4646269;rs17517027;rs17856496;rs60190029;rs1799930	197	A4Z6T7	.	Q	197;67	ENSP00000286479:R197Q;ENSP00000428416:R67Q	ENSP00000286479:R197Q	R	+	2	0	NAT2	18302383	0.068000	0.21057	0.990000	0.47175	0.021000	0.10359	1.291000	0.33330	1.706000	0.51276	0.436000	0.28706	CGA	G|0.742;A|0.258	0.258	strong		0.363	NAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253380.1	NM_000015	
GLP1R	2740	hgsc.bcm.edu	37	6	39048491	39048491	+	Silent	SNP	A	A	C	rs1126476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:39048491A>C	ENST00000373256.4	+	12	1243	c.1200A>C	c.(1198-1200)atA>atC	p.I400I		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	400					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)			breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	TGGTGGCCATATTATACTGCT	0.572													C|||	2459	0.491014	0.4856	0.5375	5008	,	,		20236	0.4593		0.504	False		,,,				2504	0.4847				p.I400I		Atlas-SNP	.											.	GLP1R	64	.	0			c.A1200C						PASS	.	C		2279,2127	578.7+/-384.7	592,1095,516	136.0	125.0	129.0		1200	4.5	0.9	6	dbSNP_86	129	4400,4200	570.8+/-389.4	1128,2144,1028	no	coding-synonymous	GLP1R	NM_002062.3		1720,3239,1544	CC,CA,AA		48.8372,48.2751,48.6468		400/464	39048491	6679,6327	2203	4300	6503	SO:0001819	synonymous_variant	2740	exon12			GGCCATATTATAC		CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"""GPCR / Class B : Glucagon receptors"""	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.1200A>C	6.37:g.39048491A>C		Somatic	236	2	0.00847458		WXS	Illumina HiSeq	Phase_I	284	284	1	NM_002062	Q2M229|Q99669	Silent	SNP	ENST00000373256.4	37	CCDS4839.1																																																																																			A|0.489;C|0.511	0.511	strong		0.572	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1		
MDH1B	130752	hgsc.bcm.edu	37	2	207603234	207603234	+	Splice_Site	SNP	T	T	G	rs2287631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:207603234T>G	ENST00000374412.3	-	12	1805	c.1530A>C	c.(1528-1530)gaA>gaC	p.E510D	MDH1B_ENST00000454776.2_Splice_Site_p.E509D|MDH1B_ENST00000449792.1_Splice_Site_p.E412D	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	510			E -> D (in dbSNP:rs2287631).		carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		TGCCTTCAAATTCTGTAAAAG	0.274													G|||	2092	0.417732	0.5961	0.3617	5008	,	,		19969	0.5347		0.1412	False		,,,				2504	0.3804				p.E510D	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.A1530C						PASS	.	G	ASP/GLU	2223,2181	573.3+/-383.5	552,1119,531	78.0	80.0	80.0		1530	-3.1	0.0	2	dbSNP_100	80	1278,7314	752.3+/-407.4	97,1084,3115	yes	missense-near-splice	MDH1B	NM_001039845.1	45	649,2203,3646	GG,GT,TT		14.8743,49.5232,26.9391	benign	510/519	207603234	3501,9495	2202	4296	6498	SO:0001630	splice_region_variant	130752	exon12			TTCAAATTCTGTA		CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.1529-1A>C	2.37:g.207603234T>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	157	59	0.375796	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	832	0.38095238095238093	296	0.6016260162601627	120	0.3314917127071823	322	0.5629370629370629	94	0.12401055408970976	G	0.026	-1.375286	0.01214	0.504768	0.148743	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.34072	1.41;1.38;1.4	4.44	-3.1	0.05315	.	0.872837	0.09496	N	0.794337	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45026	-0.9289	9	0.02654	T	1	.	0.4693	0.00529	0.2913:0.1262:0.1992:0.3834	rs2287631;rs52818171;rs60689609;rs2287631	509;510	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	D	510;412;509	ENSP00000363533:E510D;ENSP00000416577:E412D;ENSP00000389916:E509D	ENSP00000363533:E510D	E	-	3	2	MDH1B	207311479	0.000000	0.05858	0.015000	0.15790	0.001000	0.01503	-1.583000	0.02115	-0.964000	0.03595	-2.042000	0.00416	GAA	T|0.683;G|0.317	0.317	strong		0.274	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	Missense_Mutation
SLC31A2	1318	hgsc.bcm.edu	37	9	115925104	115925104	+	Silent	SNP	C	C	T	rs3810906	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:115925104C>T	ENST00000259392.3	+	4	472	c.339C>T	c.(337-339)gcC>gcT	p.A113A		NM_001860.2	NP_001851.1	O15432	COPT2_HUMAN	solute carrier family 31 (copper transporter), member 2	113					cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|regulation of copper ion transmembrane transport (GO:1902311)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)	p.A113A(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	7					Carboplatin(DB00958)|Cisplatin(DB00515)	TCATGCTGGCCGTAATGTCCT	0.483													C|||	1560	0.311502	0.2103	0.3919	5008	,	,		18268	0.4067		0.2465	False		,,,				2504	0.3599				p.A113A		Atlas-SNP	.											SLC31A2,NS,carcinoma,0,1	SLC31A2	11	1	1	Substitution - coding silent(1)	stomach(1)	c.C339T						PASS	.	C		903,3159		112,679,1240	287.0	280.0	283.0		339	-3.8	0.2	9	dbSNP_107	283	2113,6263		273,1567,2348	no	coding-synonymous	SLC31A2	NM_001860.2		385,2246,3588	TT,TC,CC		25.2268,22.2304,24.2483		113/144	115925104	3016,9422	2031	4188	6219	SO:0001819	synonymous_variant	1318	exon4			GCTGGCCGTAATG		CCDS6788.1	9q32	2013-07-17	2013-07-17		ENSG00000136867	ENSG00000136867		"""Solute carriers"""	11017	protein-coding gene	gene with protein product	"""copper transporter 2"""	603088		COPT2		9207117	Standard	NM_001860		Approved	hCTR2, CTR2	uc004bgq.3	O15432	OTTHUMG00000021037	ENST00000259392.3:c.339C>T	9.37:g.115925104C>T		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	245	109	0.444898	NM_001860		Silent	SNP	ENST00000259392.3	37	CCDS6788.1																																																																																			C|0.696;T|0.304	0.304	strong		0.483	SLC31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055509.2	NM_001860	
DEFB108B	245911	hgsc.bcm.edu	37	11	71548520	71548520	+	Missense_Mutation	SNP	A	A	T	rs12285495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71548520A>T	ENST00000328698.1	+	2	134	c.134A>T	c.(133-135)cAt>cTt	p.H45L	DEFB108B_ENST00000529157.1_3'UTR	NM_001002035.1	NP_001002035.1	Q8NET1	D108B_HUMAN	defensin, beta 108B	45			H -> L (in dbSNP:rs12285495).		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|kidney(1)|lung(2)|skin(1)	5						ACAGAAATCCATGTTGGGAGA	0.468													.|||	2256	0.450479	0.3427	0.3732	5008	,	,		15708	0.3631		0.5984	False		,,,				2504	0.589				p.H45L		Atlas-SNP	.											.	DEFB108B	6	.	0			c.A134T						PASS	.	A	LEU/HIS	1682,2718		316,1050,834	105.0	112.0	110.0		134	0.2	0.1	11	dbSNP_120	110	5213,3373		1581,2051,661	no	missense	DEFB108B	NM_001002035.1	99	1897,3101,1495	TT,TA,AA		39.2849,38.2273,46.9044	possibly-damaging	45/74	71548520	6895,6091	2200	4293	6493	SO:0001583	missense	245911	exon2			AAATCCATGTTGG	AF529416	CCDS31631.1	11q13.4	2011-03-29			ENSG00000184276	ENSG00000184276		"""Defensins, beta"""	29966	protein-coding gene	gene with protein product							Standard	NM_001002035		Approved		uc010rqr.2	Q8NET1	OTTHUMG00000167533	ENST00000328698.1:c.134A>T	11.37:g.71548520A>T	ENSP00000333234:p.His45Leu	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	293	289	0.986348	NM_001002035		Missense_Mutation	SNP	ENST00000328698.1	37	CCDS31631.1	1030	0.4716117216117216	192	0.3902439024390244	158	0.43646408839779005	214	0.3741258741258741	466	0.6147757255936676	.	10.86	1.470492	0.26423	0.382273	0.607151	ENSG00000184276	ENST00000328698	T	0.10668	2.85	1.51	0.238	0.15480	.	0.755014	0.10839	N	0.628422	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.33394	-0.9870	8	0.72032	D	0.01	.	3.4459	0.07481	0.6409:0.0:0.0:0.3591	rs12285495;rs59318528	45	Q8NET1	D108B_HUMAN	L	45	ENSP00000333234:H45L	ENSP00000333234:H45L	H	+	2	0	DEFB108B	71226168	0.003000	0.15002	0.126000	0.21872	0.339000	0.28857	0.195000	0.17155	0.055000	0.16094	0.329000	0.21502	CAT	A|0.486;T|0.514	0.514	strong		0.468	DEFB108B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394945.1	NM_001002035	
OPN1SW	611	hgsc.bcm.edu	37	7	128415195	128415195	+	Silent	SNP	T	T	G	rs1799922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128415195T>G	ENST00000249389.2	-	2	365	c.366A>C	c.(364-366)ggA>ggC	p.G122G		NM_001708.2	NP_001699.1	P03999	OPSB_HUMAN	opsin 1 (cone pigments), short-wave-sensitive	122					phototransduction (GO:0007602)|phototransduction, visible light (GO:0007603)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)|receptor activity (GO:0004872)	p.G122G(1)		NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|stomach(1)	19						CCAGTGACCATCCTGTAACCA	0.567													G|||	937	0.187101	0.112	0.2291	5008	,	,		21414	0.0675		0.4095	False		,,,				2504	0.1534				p.G122G		Atlas-SNP	.											OPN1SW,NS,carcinoma,0,1	OPN1SW	52	1	1	Substitution - coding silent(1)	stomach(1)	c.A366C						PASS	.	G		651,3755	765.7+/-413.4	47,557,1599	65.0	52.0	56.0		366	0.8	1.0	7	dbSNP_89	56	3471,5129	634.5+/-398.9	706,2059,1535	no	coding-synonymous	OPN1SW	NM_001708.2		753,2616,3134	GG,GT,TT		40.3605,14.7753,31.6931		122/349	128415195	4122,8884	2203	4300	6503	SO:0001819	synonymous_variant	611	exon2			TGACCATCCTGTA	U53874	CCDS5806.1	7q31.3-q32	2013-01-08	2008-04-16		ENSG00000128617	ENSG00000128617		"""GPCR / Class A : Opsin receptors"""	1012	protein-coding gene	gene with protein product	"""color blindness, tritan"", ""blue-sensitive opsin"""	613522	"""blue cone photoreceptor pigment"""	BCP		2937147, 8270261	Standard	NM_001708		Approved	BOP, CBT	uc003vnt.4	P03999	OTTHUMG00000158311	ENST00000249389.2:c.366A>C	7.37:g.128415195T>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_001708	Q13877	Silent	SNP	ENST00000249389.2	37	CCDS5806.1																																																																																			T|0.710;G|0.290	0.290	strong		0.567	OPN1SW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350655.1	NM_001708	
NRDE2	55051	hgsc.bcm.edu	37	14	90745422	90745422	+	Missense_Mutation	SNP	T	T	C	rs3737035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:90745422T>C	ENST00000354366.3	-	13	3585	c.3353A>G	c.(3352-3354)aAt>aGt	p.N1118S	NRDE2_ENST00000357904.3_Missense_Mutation_p.N887S	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	1118			N -> S (in dbSNP:rs3737035). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.														CCAAGGGCAATTCTGAAGTGC	0.473													T|||	1624	0.324281	0.0825	0.3012	5008	,	,		22906	0.5099		0.3946	False		,,,				2504	0.4039				p.N1118S		Atlas-SNP	.											.	.	.	.	0			c.A3353G						PASS	.	T	SER/ASN,SER/ASN	636,3770	274.3+/-271.8	46,544,1613	247.0	228.0	235.0		3353,2660	-3.0	0.0	14	dbSNP_107	235	3432,5168	506.3+/-376.6	679,2074,1547	yes	missense,missense	C14orf102	NM_017970.3,NM_199043.1	46,46	725,2618,3160	CC,CT,TT		39.907,14.4349,31.2779	benign,benign	1118/1165,887/934	90745422	4068,8938	2203	4300	6503	SO:0001583	missense	55051	exon13			GGGCAATTCTGAA	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 102"""	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.3353A>G	14.37:g.90745422T>C	ENSP00000346335:p.Asn1118Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	37	CCDS9890.1	765	0.35027472527472525	46	0.09349593495934959	118	0.3259668508287293	292	0.5104895104895105	309	0.4076517150395778	T	0.014	-1.577019	0.00887	0.144349	0.39907	ENSG00000119720	ENST00000354366;ENST00000357904	T;T	0.24723	1.84;1.84	5.04	-3.03	0.05429	.	0.354677	0.30762	N	0.008933	T	0.00012	0.0000	N	0.05031	-0.125	0.51482	P	7.699999999999374E-5	B;B	0.11235	0.001;0.004	B;B	0.09377	0.001;0.004	T	0.38929	-0.9638	9	0.07644	T	0.81	-7.8744	6.781	0.23646	0.1283:0.4457:0.0:0.4259	rs3737035;rs17188668;rs58956807;rs3737035	887;1118	E9PBK4;Q9H7Z3	.;CN102_HUMAN	S	1118;887	ENSP00000346335:N1118S;ENSP00000350579:N887S	ENSP00000346335:N1118S	N	-	2	0	C14orf102	89815175	1.000000	0.71417	0.034000	0.17996	0.013000	0.08279	1.427000	0.34881	-0.493000	0.06678	-0.379000	0.06801	AAT	T|0.672;C|0.328	0.328	strong		0.473	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970	
SLC1A7	6512	hgsc.bcm.edu	37	1	53600078	53600078	+	Silent	SNP	A	A	G	rs3737989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:53600078A>G	ENST00000371494.4	-	2	286	c.159T>C	c.(157-159)ccT>ccC	p.P53P	SLC1A7_ENST00000371491.4_Silent_p.P53P	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	53					dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		GGAGCTCTCCAGGGAACTGGA	0.507													A|||	942	0.188099	0.1293	0.3718	5008	,	,		20833	0.2907		0.159	False		,,,				2504	0.0613				p.P53P	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											.	SLC1A7	65	.	0			c.T159C						PASS	.	A		614,3792	266.5+/-267.3	40,534,1629	74.0	68.0	70.0		159	-3.0	1.0	1	dbSNP_107	70	1445,7155	274.2+/-291.1	103,1239,2958	no	coding-synonymous	SLC1A7	NM_006671.4		143,1773,4587	GG,GA,AA		16.8023,13.9355,15.8312		53/561	53600078	2059,10947	2203	4300	6503	SO:0001819	synonymous_variant	6512	exon2			CTCTCCAGGGAAC	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"""Solute carriers"""	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.159T>C	1.37:g.53600078A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Silent	SNP	ENST00000371494.4	37	CCDS574.1																																																																																			A|0.820;G|0.180	0.180	strong		0.507	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671	
REPIN1	29803	hgsc.bcm.edu	37	7	150068371	150068371	+	Missense_Mutation	SNP	T	T	C	rs3735165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150068371T>C	ENST00000425389.2	+	1	119	c.41T>C	c.(40-42)cTg>cCg	p.L14P	REPIN1_ENST00000518462.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000444957.1_Missense_Mutation_p.L14P|REPIN1_ENST00000489432.2_Missense_Mutation_p.L71P|REPIN1_ENST00000540729.1_Missense_Mutation_p.L14P|REPIN1_ENST00000466559.1_Missense_Mutation_p.W32R|REPIN1_ENST00000518514.1_Silent_p.P62P|REPIN1_ENST00000397281.2_Missense_Mutation_p.L14P|REPIN1_ENST00000479668.1_Missense_Mutation_p.W113R|REPIN1_ENST00000482680.1_Missense_Mutation_p.W113R	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	14			L -> P (in dbSNP:rs3735165). {ECO:0000269|Ref.2}.		DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			GCCATGGGCCTGGCCCAGCCC	0.652													C|||	2164	0.432109	0.5484	0.2248	5008	,	,		17092	0.4673		0.3171	False		,,,				2504	0.5041				p.L71P		Atlas-SNP	.											REPIN1_ENST00000489432,NS,carcinoma,0,2	REPIN1	74	2	0			c.T212C						PASS	.	C	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	1918,1844		507,904,470	11.0	15.0	14.0		212,41,41,41	3.4	0.3	7	dbSNP_107	14	2545,5649		428,1689,1980	yes	missense,missense,missense,missense	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	98,98,98,98	935,2593,2450	CC,CT,TT		31.0593,49.0165,37.3285	benign,benign,benign,benign	71/625,14/568,14/568,14/568	150068371	4463,7493	1881	4097	5978	SO:0001583	missense	29803	exon3			TGGGCCTGGCCCA	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.41T>C	7.37:g.150068371T>C	ENSP00000388287:p.Leu14Pro	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Missense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	904|904	0.4139194139194139|0.4139194139194139	272|272	0.5528455284552846|0.5528455284552846	88|88	0.2430939226519337|0.2430939226519337	281|281	0.49125874125874125|0.49125874125874125	263|263	0.3469656992084433|0.3469656992084433	C|C	1.773|1.773	-0.483945|-0.483945	0.04383|0.04383	0.509835|0.509835	0.310593|0.310593	ENSG00000214022|ENSG00000214022	ENST00000519397;ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000461637;ENST00000425389|ENST00000479668;ENST00000466559;ENST00000482680	T;T;T;T;T;T;T;T|.	0.06687|.	5.54;3.29;3.29;3.29;3.27;3.53;3.43;3.29|.	5.2|5.2	3.4|3.4	0.38934|0.38934	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.21579|0.21579	P|P	0.999634327|0.999634327	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.42068|0.42068	-0.9473|-0.9473	8|5	0.48119|0.87932	T|D	0.1|0	-3.7114|-3.7114	7.7378|7.7378	0.28825|0.28825	0.0:0.7341:0.0:0.2659|0.0:0.7341:0.0:0.2659	rs3735165;rs11553625;rs59736478|rs3735165;rs11553625;rs59736478	71;14|.	C9J3L7;Q9BWE0|.	.;REPI1_HUMAN|.	P|R	14;14;14;14;71;73;74;71;14|113;32;113	ENSP00000428562:L14P;ENSP00000445016:L14P;ENSP00000380451:L14P;ENSP00000407714:L14P;ENSP00000417291:L71P;ENSP00000419789:L73P;ENSP00000419872:L74P;ENSP00000388287:L14P|.	ENSP00000380451:L14P|ENSP00000418507:W32R	L|W	+|+	2|1	0|0	REPIN1|REPIN1	149699304|149699304	0.040000|0.040000	0.19996|0.19996	0.294000|0.294000	0.24946|0.24946	0.559000|0.559000	0.35586|0.35586	0.888000|0.888000	0.28268|0.28268	0.217000|0.217000	0.20800|0.20800	-1.403000|-1.403000	0.01137|0.01137	CTG|TGG	T|0.578;C|0.422	0.422	strong		0.652	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
NLRP4	147945	hgsc.bcm.edu	37	19	56392875	56392875	+	Silent	SNP	T	T	G	rs302456	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56392875T>G	ENST00000301295.6	+	10	3329	c.2907T>G	c.(2905-2907)ctT>ctG	p.L969L	NLRP4_ENST00000346986.5_Silent_p.L913L|NLRP4_ENST00000587891.1_Silent_p.L894L	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	969					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.L969L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CCCAGGCACTTCTGACGGCTG	0.428													T|||	1257	0.250998	0.3525	0.2839	5008	,	,		18541	0.2063		0.2326	False		,,,				2504	0.1554				p.L969L		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,+2,2	NLRP4	331	2	1	Substitution - coding silent(1)	stomach(1)	c.T2907G						scavenged	.	T		1455,2951	470.5+/-355.8	231,993,979	72.0	60.0	64.0		2907	-4.7	0.0	19	dbSNP_79	64	2382,6218	396.3+/-345.4	311,1760,2229	no	coding-synonymous	NLRP4	NM_134444.4		542,2753,3208	GG,GT,TT		27.6977,33.0232,29.5018		969/995	56392875	3837,9169	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon10			GGCACTTCTGACG	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2907T>G	19.37:g.56392875T>G		Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	51	18	0.352941	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			T|0.716;G|0.284	0.284	strong		0.428	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
KPNA7	402569	hgsc.bcm.edu	37	7	98782750	98782750	+	Silent	SNP	C	C	T	rs10953283	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:98782750C>T	ENST00000327442.6	-	7	975	c.936G>A	c.(934-936)acG>acA	p.T312T		NM_001145715.1	NP_001139187.1	A9QM74	IMA8_HUMAN	karyopherin alpha 7 (importin alpha 8)	312					cytokine-mediated signaling pathway (GO:0019221)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(3)|endometrium(2)|kidney(1)|prostate(1)|skin(1)	8						CATCTGTGCCCGTGACAATGT	0.542													C|||	2244	0.448083	0.1044	0.5951	5008	,	,		17110	0.6746		0.6024	False		,,,				2504	0.4162				p.T312T		Atlas-SNP	.											.	KPNA7	31	.	0			c.G936A						PASS	.	C		247,1137		22,203,467	41.0	37.0	38.0		936	-11.1	0.0	7	dbSNP_120	38	1998,1184		638,722,231	no	coding-synonymous	KPNA7	NM_001145715.1		660,925,698	TT,TC,CC		37.2093,17.8468,49.1678		312/517	98782750	2245,2321	692	1591	2283	SO:0001819	synonymous_variant	402569	exon7			TGTGCCCGTGACA		CCDS47651.1	7q22.1	2013-02-14			ENSG00000185467	ENSG00000185467		"""Importins"", ""Armadillo repeat containing"""	21839	protein-coding gene	gene with protein product		614107					Standard	NM_001145715		Approved		uc010lft.2	A9QM74	OTTHUMG00000154412	ENST00000327442.6:c.936G>A	7.37:g.98782750C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_001145715	A4D277	Silent	SNP	ENST00000327442.6	37	CCDS47651.1																																																																																			C|0.511;N|0.000	.	strong		0.542	KPNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335118.1	NM_001145715	
MUC16	94025	hgsc.bcm.edu	37	19	9002597	9002597	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9002597C>T	ENST00000397910.4	-	51	40422	c.40219G>A	c.(40219-40221)Gac>Aac	p.D13407N	MUC16_ENST00000380951.5_Missense_Mutation_p.D48N	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13409	SEA 9. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CGCTCTCTGTCCAGTCCAGGG	0.592																																					p.D13407N		Atlas-SNP	.											MUC16_ENST00000397910,NS,lymphoid_neoplasm,0,2	MUC16	4315	2	0			c.G40219A						scavenged	.																																			SO:0001583	missense	94025	exon51			CTCTGTCCAGTCC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.40219G>A	19.37:g.9002597C>T	ENSP00000381008:p.Asp13407Asn	Somatic	282	15	0.0531915		WXS	Illumina HiSeq	Phase_I	311	31	0.0996785	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	11.51|11.51	1.659878|1.659878	0.29515|0.29515	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T;T|.	0.45668|.	0.89;0.89|.	2.75|2.75	-0.839|-0.839	0.10759|0.10759	SEA (1);|.	.|.	.|.	.|.	.|.	T|.	0.43344|.	0.1243|.	L|L	0.52759|0.52759	1.655|1.655	.|.	.|.	.|.	B;D|.	0.60575|.	0.007;0.988|.	B;D|.	0.75020|.	0.014;0.985|.	T|.	0.51236|.	-0.8731|.	8|.	0.54805|.	T|.	0.06|.	-11.8857|-11.8857	6.8102|6.8102	0.23801|0.23801	0.0:0.8029:0.0:0.1971|0.0:0.8029:0.0:0.1971	.|.	21052;13407|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	N|X	13407;48|246	ENSP00000381008:D13407N;ENSP00000370338:D48N|.	ENSP00000370338:D48N|.	D|W	-|-	1|3	0|0	MUC16|MUC16	8863597|8863597	0.045000|0.045000	0.20229|0.20229	0.003000|0.003000	0.11579|0.11579	0.000000|0.000000	0.00434|0.00434	1.258000|1.258000	0.32944|0.32944	-0.029000|-0.029000	0.13827|0.13827	-3.921000|-3.921000	0.00016|0.00016	GAC|TGG	.	.	none		0.592	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
RGS6	9628	hgsc.bcm.edu	37	14	72945012	72945012	+	Silent	SNP	T	T	C	rs2302143	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:72945012T>C	ENST00000553530.1	+	12	1036	c.829T>C	c.(829-831)Ttg>Ctg	p.L277L	RGS6_ENST00000434263.2_Silent_p.L208L|RGS6_ENST00000404301.2_Silent_p.L277L|RGS6_ENST00000402788.2_Silent_p.L277L|RGS6_ENST00000343854.6_Silent_p.L277L|RGS6_ENST00000553525.1_Silent_p.L277L|RGS6_ENST00000355512.6_Silent_p.L277L|RGS6_ENST00000406236.4_Silent_p.L277L|RGS6_ENST00000554782.1_Silent_p.L138L|RGS6_ENST00000407322.4_Silent_p.L277L|RGS6_ENST00000556437.1_Silent_p.L277L|RGS6_ENST00000555571.1_Silent_p.L277L	NM_001204417.1|NM_001204418.1|NM_001204420.1|NM_001204421.1|NM_001204422.1|NM_004296.5	NP_001191346.1|NP_001191347.1|NP_001191349.1|NP_001191350.1|NP_001191351.1|NP_004287.3	P49758	RGS6_HUMAN	regulator of G-protein signaling 6	277	G protein gamma.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		CAGACATTGTTTGAAAATGTC	0.338													T|||	630	0.125799	0.0567	0.2219	5008	,	,		21617	0.0675		0.1262	False		,,,				2504	0.2106				p.L277L	Ovarian(143;1926 2468 21071 48641)	Atlas-SNP	.											RGS6_ENST00000553525,NS,carcinoma,-2,2	RGS6	92	2	0			c.T829C						PASS	.	T	,,,,,,,,,	321,4085	171.2+/-201.5	12,297,1894	123.0	120.0	121.0		829,829,829,829,829,829,829,724,829,829	5.6	1.0	14	dbSNP_100	121	1037,7561	219.0+/-257.2	65,907,3327	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RGS6	NM_001204416.1,NM_001204417.1,NM_001204418.1,NM_001204419.1,NM_001204420.1,NM_001204421.1,NM_001204422.1,NM_001204423.1,NM_001204424.1,NM_004296.5	,,,,,,,,,	77,1204,5221	CC,CT,TT		12.0609,7.2855,10.4429	,,,,,,,,,	277/491,277/486,277/468,277/454,277/436,277/449,277/431,242/438,277/491,277/473	72945012	1358,11646	2203	4299	6502	SO:0001819	synonymous_variant	9628	exon12			CATTGTTTGAAAA	AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732		"""Regulators of G-protein signaling"""	10002	protein-coding gene	gene with protein product		603894	"""regulator of G-protein signalling 6"""			10083744, 14734556	Standard	NM_004296		Approved		uc010ttn.2	P49758		ENST00000553530.1:c.829T>C	14.37:g.72945012T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001204424	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Silent	SNP	ENST00000553530.1	37	CCDS9808.1																																																																																			T|0.889;C|0.111	0.111	strong		0.338	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2		
MLX	6945	hgsc.bcm.edu	37	17	40722162	40722162	+	Silent	SNP	G	G	A	rs1474040	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:40722162G>A	ENST00000246912.4	+	7	854	c.801G>A	c.(799-801)gcG>gcA	p.A267A	MLX_ENST00000435881.2_Silent_p.A213A|MLX_ENST00000346833.4_Silent_p.A183A	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	267					energy reserve metabolic process (GO:0006112)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|positive regulation of cellular metabolic process (GO:0031325)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(3)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	10		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		AGCTGTCAGCGTGTGTCTTCA	0.532													G|||	484	0.0966454	0.0113	0.1816	5008	,	,		21738	0.0		0.2783	False		,,,				2504	0.0644				p.A267A	GBM(121;657 1601 4665 24731 34640)	Atlas-SNP	.											MLX,colon,carcinoma,+1,1	MLX	17	1	0			c.G801A						PASS	.	G	,,	207,4199	127.8+/-164.7	6,195,2002	109.0	91.0	97.0		801,639,549	-4.0	0.9	17	dbSNP_88	97	2264,6336	384.5+/-341.1	295,1674,2331	no	coding-synonymous,coding-synonymous,coding-synonymous	MLX	NM_170607.2,NM_198204.1,NM_198205.1	,,	301,1869,4333	AA,AG,GG		26.3256,4.6981,18.9989	,,	267/299,213/245,183/215	40722162	2471,10535	2203	4300	6503	SO:0001819	synonymous_variant	6945	exon7			GTCAGCGTGTGTC	AF213668	CCDS11430.1, CCDS42341.1, CCDS45687.1	17q21.1	2013-05-21	2012-11-15	2005-02-11		ENSG00000108788		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	11645	protein-coding gene	gene with protein product		602976	"""transcription factor-like 4"", ""MAX-like protein X"""	TCFL4		8973301	Standard	NM_170607		Approved	MAD7, MXD7, bHLHd13	uc002iag.3	Q9UH92		ENST00000246912.4:c.801G>A	17.37:g.40722162G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	214	115	0.537383	NM_170607	A8K2J3|B2RAV8|B2RD73|Q53XM6|Q96FL2|Q9H2V0|Q9H2V1|Q9H2V2|Q9NXN3	Silent	SNP	ENST00000246912.4	37	CCDS11430.1																																																																																			G|0.827;A|0.173	0.173	strong		0.532	MLX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450415.1	NM_170607	
UGT2B28	54490	hgsc.bcm.edu	37	4	70152499	70152499	+	Silent	SNP	T	T	A	rs41292341	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70152499T>A	ENST00000335568.5	+	3	902	c.900T>A	c.(898-900)ggT>ggA	p.G300G	UGT2B28_ENST00000511240.1_Silent_p.G300G	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	300					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						AGAGCTCTGGTGAAAATGGTG	0.413													t|||	142	0.0283546	0.0371	0.036	5008	,	,		10829	0.004		0.0388	False		,,,				2504	0.0256				p.G300G		Atlas-SNP	.											UGT2B28,caecum,carcinoma,0,1	UGT2B28	101	1	0			c.T900A						scavenged	.	A	,	93,4047		15,63,1992	140.0	158.0	152.0		900,900	0.7	1.0	4	dbSNP_127	152	305,8197		44,217,3990	no	coding-synonymous,coding-synonymous	UGT2B28	NM_001207004.1,NM_053039.1	,	59,280,5982	AA,AT,TT		3.5874,2.2464,3.1482	,	300/336,300/530	70152499	398,12244	2070	4251	6321	SO:0001819	synonymous_variant	54490	exon3			CTCTGGTGAAAAT	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.900T>A	4.37:g.70152499T>A		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	121	3	0.0247934	NM_053039	B5BUM0|Q9BY62|Q9BY63	Silent	SNP	ENST00000335568.5	37	CCDS3528.1																																																																																			T|0.972;A|0.028	0.028	strong		0.413	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
FAM186A	121006	hgsc.bcm.edu	37	12	50745858	50745858	+	Missense_Mutation	SNP	T	T	G	rs34602257|rs374020295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745858T>G	ENST00000327337.5	-	4	4756	c.4757A>C	c.(4756-4758)gAa>gCa	p.E1586A	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Missense_Mutation_p.E1586A	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1586								p.E1586A(1)									GATCCCCAGTTCCTGCGCCTG	0.662													t|||	1384	0.276358	0.2262	0.3055	5008	,	,		21922	0.3244		0.2992	False		,,,				2504	0.2505				p.E1586A	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,caecum,carcinoma,0,3	FAM186A	181	3	1	Substitution - Missense(1)	stomach(1)	c.A4757C						scavenged	.						5.0	6.0	6.0					12																	50745858		680	1568	2248	SO:0001583	missense	121006	exon4			CCCAGTTCCTGCG		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4757A>C	12.37:g.50745858T>G	ENSP00000329995:p.Glu1586Ala	Somatic	230	4	0.0173913		WXS	Illumina HiSeq	Phase_I	253	89	0.351779	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	t	0.818	-0.749490	0.03065	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.03745	3.82;3.82	4.11	-8.22	0.01037	.	.	.	.	.	T	0.01320	0.0043	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43925	-0.9361	8	0.02654	T	1	.	11.0464	0.47861	0.1288:0.0:0.1797:0.6915	.	1586;1586	F5GYN0;A6NE01	.;F186A_HUMAN	A	1586	ENSP00000441337:E1586A;ENSP00000329995:E1586A	ENSP00000329995:E1586A	E	-	2	0	FAM186A	49032125	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.314000	0.02715	-2.575000	0.00465	-4.006000	0.00013	GAA	.	.	weak		0.662	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
PPP1R18	170954	hgsc.bcm.edu	37	6	30652781	30652781	+	Missense_Mutation	SNP	C	C	T	rs9262143	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30652781C>T	ENST00000274853.3	-	1	2891	c.1015G>A	c.(1015-1017)Ggg>Agg	p.G339R	PPP1R18_ENST00000488324.1_Intron|PPP1R18_ENST00000399199.3_Missense_Mutation_p.G339R	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	339			G -> R (in dbSNP:rs9262143). {ECO:0000269|PubMed:14574404}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CGAGCCTTCCCGGAGTTCAGG	0.567													C|||	97	0.019369	0.0023	0.0202	5008	,	,		14981	0.0		0.0795	False		,,,				2504	0.0				p.G339R		Atlas-SNP	.											.	.	.	.	0			c.G1015A						PASS	.	C	ARG/GLY,ARG/GLY	54,2818		1,52,1383	120.0	143.0	135.0		1015,1015	5.1	1.0	6	dbSNP_118	135	551,4765		32,487,2139	yes	missense,missense	KIAA1949	NM_001134870.1,NM_133471.3	125,125	33,539,3522	TT,TC,CC		10.3649,1.8802,7.3889	probably-damaging,probably-damaging	339/614,339/614	30652781	605,7583	1436	2658	4094	SO:0001583	missense	170954	exon2			CCTTCCCGGAGTT	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29413	protein-coding gene	gene with protein product	"""protein phosphatase 1 F-actin cytoskeleton targeting subunit"""	610990	"""KIAA1949"""	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.1015G>A	6.37:g.30652781C>T	ENSP00000274853:p.Gly339Arg	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	225	85	0.377778	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	79	0.036172161172161175	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	66	0.0870712401055409	C	20.5	4.006971	0.74932	0.018802	0.103649	ENSG00000146112	ENST00000274853;ENST00000399199	T;T	0.55588	0.51;0.51	5.1	5.1	0.69264	.	0.378221	0.21808	N	0.068801	T	0.50837	0.1639	L	0.32530	0.975	0.38584	D	0.950265	D	0.76494	0.999	D	0.64595	0.927	T	0.45101	-0.9284	10	0.28530	T	0.3	-24.1078	17.2657	0.87086	0.0:1.0:0.0:0.0	rs9262143;rs17189267;rs52821119;rs57338511;rs9262143	339	Q6NYC8	PPR18_HUMAN	R	339	ENSP00000274853:G339R;ENSP00000382150:G339R	ENSP00000274853:G339R	G	-	1	0	KIAA1949	30760760	0.995000	0.38212	1.000000	0.80357	0.967000	0.64934	3.624000	0.54231	2.369000	0.80426	0.561000	0.74099	GGG	C|0.942;T|0.058	0.058	strong		0.567	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471	
RRBP1	6238	hgsc.bcm.edu	37	20	17610535	17610535	+	Silent	SNP	C	C	T	rs11551701	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:17610535C>T	ENST00000377813.1	-	9	2985	c.2682G>A	c.(2680-2682)acG>acA	p.T894T	RRBP1_ENST00000246043.4_Silent_p.T894T|RRBP1_ENST00000377807.2_Silent_p.T461T|RRBP1_ENST00000360807.4_Silent_p.T461T|RRBP1_ENST00000455029.2_Silent_p.T235T			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	894					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						GGCTGCTCTGCGTGTGGCACA	0.716													C|||	384	0.0766773	0.0991	0.049	5008	,	,		13649	0.0655		0.0835	False		,,,				2504	0.0706				p.T461T		Atlas-SNP	.											.	RRBP1	157	.	0			c.G1383A						PASS	.	C	,	388,4018	175.9+/-205.1	27,334,1842	27.0	28.0	27.0		1383,1383	-8.8	0.0	20	dbSNP_120	27	659,7935	161.1+/-214.1	34,591,3672	no	coding-synonymous,coding-synonymous	RRBP1	NM_001042576.1,NM_004587.2	,	61,925,5514	TT,TC,CC		7.6681,8.8062,8.0538	,	461/978,461/978	17610535	1047,11953	2203	4297	6500	SO:0001819	synonymous_variant	6238	exon9			GCTCTGCGTGTGG	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"""ribosome binding protein 1 (dog 180kD homolog)"", ""ribosome binding protein 1 homolog 180kDa (dog)"""			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.2682G>A	20.37:g.17610535C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	59	43	0.728814	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Silent	SNP	ENST00000377813.1	37																																																																																				C|0.925;T|0.075	0.075	strong		0.716	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576	
PTPRG	5793	hgsc.bcm.edu	37	3	61975382	61975382	+	Missense_Mutation	SNP	T	T	C	rs62620047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:61975382T>C	ENST00000474889.1	+	3	651	c.274T>C	c.(274-276)Tat>Cat	p.Y92H	PTPRG_ENST00000295874.10_Missense_Mutation_p.Y92H	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	92	Alpha-carbonic anhydrase.		Y -> H (in dbSNP:rs62620047). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8833149}.		brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TTTAGACCAGTATGCGCGTGT	0.488													T|||	440	0.0878594	0.0696	0.0879	5008	,	,		18472	0.002		0.1441	False		,,,				2504	0.1431				p.Y92H		Atlas-SNP	.											.	PTPRG	153	.	0			c.T274C						PASS	.	T	HIS/TYR	337,4069	178.0+/-206.8	14,309,1880	115.0	105.0	108.0		274	4.1	1.0	3	dbSNP_129	108	1225,7375	247.4+/-275.4	96,1033,3171	yes	missense	PTPRG	NM_002841.3	83	110,1342,5051	CC,CT,TT		14.2442,7.6487,12.0098	benign	92/1446	61975382	1562,11444	2203	4300	6503	SO:0001583	missense	5793	exon3			GACCAGTATGCGC	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.274T>C	3.37:g.61975382T>C	ENSP00000418112:p.Tyr92His	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	138	67	0.485507	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	191	0.08745421245421245	26	0.052845528455284556	41	0.1132596685082873	2	0.0034965034965034965	122	0.16094986807387862	T	9.548	1.115287	0.20795	0.076487	0.142442	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.66099	-0.19;-0.19	5.92	4.14	0.48551	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.415282	0.27705	N	0.018194	T	0.00178	0.0005	N	0.11131	0.1	0.51012	P	9.80000000000425E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03534	-1.1027	9	0.38643	T	0.18	.	7.6336	0.28253	0.133:0.7303:0.0:0.1366	rs62620047	92;92	P23470-2;P23470	.;PTPRG_HUMAN	H	92	ENSP00000418112:Y92H;ENSP00000295874:Y92H	ENSP00000295874:Y92H	Y	+	1	0	PTPRG	61950422	0.141000	0.22595	1.000000	0.80357	0.983000	0.72400	0.550000	0.23345	0.846000	0.35142	-0.132000	0.14878	TAT	T|0.887;C|0.113	0.113	strong		0.488	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
MAGEB16	139604	hgsc.bcm.edu	37	X	35820795	35820795	+	Missense_Mutation	SNP	A	A	G	rs5973488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:35820795A>G	ENST00000399989.1	+	2	761	c.482A>G	c.(481-483)cAc>cGc	p.H161R	MAGEB16_ENST00000399985.1_Missense_Mutation_p.H161R|MAGEB16_ENST00000399987.1_Missense_Mutation_p.H161R|MAGEB16_ENST00000399992.1_Missense_Mutation_p.H193R|MAGEB16_ENST00000399988.1_Missense_Mutation_p.H161R	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	161	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		H -> R (in dbSNP:rs5973488).					p.H328R(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						GCTTCTGAGCACCTAGAGATG	0.468													G|||	2341	0.620132	0.447	0.4121	3775	,	,		15447	0.5704		0.4185	False		,,,				2504	0.4785				p.H161R		Atlas-SNP	.											.	MAGEB16	64	.	1	Substitution - Missense(1)	stomach(1)	c.A482G						PASS	.	G	ARG/HIS	2084,1484		545,687,307,267,263	86.0	84.0	84.0		482	0.8	0.0	X	dbSNP_114	84	3521,3056		694,1180,953,510,856	yes	missense	MAGEB16	NM_001099921.1	29	1239,1867,1260,777,1119	GG,GA,G,AA,A		46.465,41.5919,44.7511	benign	161/325	35820795	5605,4540	2069	4193	6262	SO:0001583	missense	139604	exon2			CTGAGCACCTAGA		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.482A>G	X.37:g.35820795A>G	ENSP00000382871:p.His161Arg	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	1014	0.6112115732368897	151	0.4415204678362573	102	0.4146341463414634	212	0.5792349726775956	230	0.3885135135135135	G	1.483	-0.556608	0.03967	0.584081	0.53535	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04454	3.62;3.62;3.62;3.62;3.62	3.13	0.77	0.18497	.	0.765519	0.12495	N	0.463915	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.14023	0.01	T	0.17992	-1.0351	9	0.13108	T	0.6	.	6.2305	0.20732	0.3889:0.0:0.6111:0.0	rs5973488;rs17311186;rs52793468;rs56743553;rs5973488	161	A2A368	MAGBG_HUMAN	R	161;193;161;161;161	ENSP00000382870:H161R;ENSP00000382874:H193R;ENSP00000382869:H161R;ENSP00000382871:H161R;ENSP00000382867:H161R	ENSP00000382867:H161R	H	+	2	0	MAGEB16	35730716	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.027000	0.03592	-0.170000	0.10816	-0.265000	0.10407	CAC	A|0.361;0|0.032	.	strong		0.468	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
LSM3	27258	hgsc.bcm.edu	37	3	14223120	14223120	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14223120C>T	ENST00000306024.3	+	2	585	c.82C>T	c.(82-84)Cga>Tga	p.R28*	XPC_ENST00000285021.7_5'Flank	NM_014463.2	NP_055278.1	P62310	LSM3_HUMAN	LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)	28					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|large_intestine(2)|ovary(1)	4						CCTAGATGAGCGAATTTATGT	0.403																																					p.R28X		Atlas-SNP	.											LSM3,colon,carcinoma,-1,1	LSM3	13	1	0			c.C82T						scavenged	.						125.0	133.0	130.0					3																	14223120		2203	4300	6503	SO:0001587	stop_gained	27258	exon2			GATGAGCGAATTT	AF182289	CCDS2619.1	3p25.1	2012-08-15			ENSG00000170860	ENSG00000170860			17874	protein-coding gene	gene with protein product		607283				10369684	Standard	NM_014463		Approved	YLR438C, SMX4, USS2	uc003byn.3	P62310	OTTHUMG00000129838	ENST00000306024.3:c.82C>T	3.37:g.14223120C>T	ENSP00000302160:p.Arg28*	Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	349	4	0.0114613	NM_014463	Q6IAH0|Q9Y4Z1	Nonsense_Mutation	SNP	ENST00000306024.3	37	CCDS2619.1	.	.	.	.	.	.	.	.	.	.	C	41	8.879668	0.98988	.	.	ENSG00000170860	ENST00000306024	.	.	.	5.5	3.71	0.42584	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.4679	12.0216	0.53346	0.0:0.8578:0.0:0.1422	.	.	.	.	X	28	.	ENSP00000302160:R28X	R	+	1	2	LSM3	14198124	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	1.247000	0.32815	0.690000	0.31570	-0.150000	0.13652	CGA	.	.	none		0.403	LSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252078.3	NM_014463	
LGR6	59352	hgsc.bcm.edu	37	1	202287206	202287206	+	Missense_Mutation	SNP	T	T	C	rs788795|rs113146160	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202287206T>C	ENST00000367278.3	+	18	1864	c.1775T>C	c.(1774-1776)gTc>gCc	p.V592A	LGR6_ENST00000255432.7_Missense_Mutation_p.V540A|LGR6_ENST00000439764.2_Missense_Mutation_p.V453A	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	592			V -> A (in dbSNP:rs788795). {ECO:0000269|PubMed:12975309, ECO:0000269|Ref.5}.		G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						GGCGGGCCTGTCCCCCTGCCC	0.622													T|||	3055	0.610024	0.3381	0.7219	5008	,	,		18029	0.7679		0.6392	False		,,,				2504	0.7055				p.V592A		Atlas-SNP	.											.	LGR6	102	.	0			c.T1775C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	1627,2779	496.4+/-363.5	295,1037,871	87.0	75.0	79.0		1775,1358,1619	-5.2	0.0	1	dbSNP_86	79	5242,3358	638.1+/-399.3	1602,2038,660	yes	missense,missense,missense	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	64,64,64	1897,3075,1531	CC,CT,TT		39.0465,36.9269,47.1859	benign,benign,benign	592/968,453/829,540/916	202287206	6869,6137	2203	4300	6503	SO:0001583	missense	59352	exon18			GGCCTGTCCCCCT	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.1775T>C	1.37:g.202287206T>C	ENSP00000356247:p.Val592Ala	Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	166	163	0.981928	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	37	CCDS30971.1	1344	0.6153846153846154	178	0.3617886178861789	248	0.6850828729281768	430	0.7517482517482518	488	0.6437994722955145	T	0.093	-1.164466	0.01673	0.369269	0.609535	ENSG00000133067	ENST00000367278;ENST00000255432;ENST00000439764	D;D;D	0.89050	-2.46;-2.46;-2.46	5.5	-5.15	0.02866	.	0.896444	0.09814	N	0.752423	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.001;0.002	T	0.33523	-0.9865	9	0.09590	T	0.72	.	10.3915	0.44171	0.0:0.3053:0.3827:0.3121	rs788795	453;540;592	Q9HBX8-1;Q9HBX8-2;Q9HBX8	.;.;LGR6_HUMAN	A	592;540;453	ENSP00000356247:V592A;ENSP00000255432:V540A;ENSP00000387869:V453A	ENSP00000255432:V540A	V	+	2	0	LGR6	200553829	0.000000	0.05858	0.000000	0.03702	0.406000	0.30931	0.118000	0.15605	-0.551000	0.06175	0.397000	0.26171	GTC	T|0.451;C|0.549	0.549	strong		0.622	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
ALG11	440138	hgsc.bcm.edu	37	13	52598799	52598799	+	Silent	SNP	G	G	A	rs61958802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:52598799G>A	ENST00000521508.1	+	3	938	c.933G>A	c.(931-933)ccG>ccA	p.P311P	ALG11_ENST00000523764.1_Intron|UTP14C_ENST00000521776.2_5'Flank|ALG11_ENST00000519151.1_3'UTR	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	311					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		AGTTTAGGCCGGAAAAGAATC	0.433													g|||	151	0.0301518	0.0068	0.0231	5008	,	,		20807	0.0079		0.0388	False		,,,				2504	0.0808				p.P311P		Atlas-SNP	.											.	ALG11	39	.	0			c.G933A						PASS	.	A		73,4333	65.8+/-103.3	1,71,2131	80.0	77.0	78.0		933	-9.9	0.8	13	dbSNP_129	78	398,8202	127.7+/-186.0	9,380,3911	no	coding-synonymous	ALG11	NM_001004127.2		10,451,6042	AA,AG,GG		4.6279,1.6568,3.6214		311/493	52598799	471,12535	2203	4300	6503	SO:0001819	synonymous_variant	440138	exon3			TAGGCCGGAAAAG	AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"""Glycosyltransferase group 1 domain containing"""	32456	protein-coding gene	gene with protein product	"""GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"""	613666	"""asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"""			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.933G>A	13.37:g.52598799G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	193	83	0.430052	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Silent	SNP	ENST00000521508.1	37	CCDS31977.1																																																																																			G|0.967;A|0.033	0.033	strong		0.433	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127	
C2orf73	129852	hgsc.bcm.edu	37	2	54562012	54562012	+	Missense_Mutation	SNP	C	C	A	rs55714450	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:54562012C>A	ENST00000398634.2	+	2	127	c.85C>A	c.(85-87)Cac>Aac	p.H29N	C2orf73_ENST00000405749.1_Intron|C2orf73_ENST00000491538.1_Intron	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	29			H -> N (in dbSNP:rs55714450).							breast(2)	2						AGAAATTAAACACGAAGAAAA	0.303													C|||	1021	0.203874	0.1619	0.2954	5008	,	,		18549	0.0456		0.3419	False		,,,				2504	0.2168				p.H29N		Atlas-SNP	.											.	C2orf73	17	.	0			c.C85A						PASS	.	C	ASN/HIS	671,2967		80,511,1228	62.0	52.0	55.0		85	0.3	1.0	2	dbSNP_129	55	2761,5371		485,1791,1790	yes	missense	C2orf73	NM_001100396.1	68	565,2302,3018	AA,AC,CC		33.9523,18.4442,29.1589	benign	29/288	54562012	3432,8338	1819	4066	5885	SO:0001583	missense	129852	exon2			ATTAAACACGAAG	BC031669, AK097617	CCDS46285.1	2p16.2	2008-07-07			ENSG00000177994	ENSG00000177994			26861	protein-coding gene	gene with protein product						14702039	Standard	NM_001100396		Approved	FLJ40298	uc002rxt.1	Q8N5S3	OTTHUMG00000151826	ENST00000398634.2:c.85C>A	2.37:g.54562012C>A	ENSP00000381631:p.His29Asn	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	255	119	0.466667	NM_001100396	A0AV79|A0AV81|Q8N7V4	Missense_Mutation	SNP	ENST00000398634.2	37	CCDS46285.1	481	0.22023809523809523	78	0.15853658536585366	107	0.2955801104972376	22	0.038461538461538464	274	0.36147757255936674	C	1.011	-0.687753	0.03328	0.184442	0.339523	ENSG00000177994	ENST00000486488;ENST00000398634	T;T	0.31247	1.5;1.5	4.5	0.334	0.15948	.	0.885835	0.09662	N	0.772356	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.299999999996974E-5	B	0.09022	0.002	B	0.10450	0.005	T	0.46400	-0.9194	9	0.35671	T	0.21	-24.6075	1.7904	0.03050	0.1957:0.3112:0.3535:0.1395	rs55714450;rs62141760	29	Q8N5S3	CB073_HUMAN	N	35;29	ENSP00000417971:H35N;ENSP00000381631:H29N	ENSP00000381631:H29N	H	+	1	0	C2orf73	54415516	0.249000	0.23941	0.972000	0.41901	0.150000	0.21749	-0.629000	0.05508	0.169000	0.19679	-0.300000	0.09419	CAC	C|0.747;A|0.253	0.253	strong		0.303	C2orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324075.2	NM_001100396	
NEB	4703	hgsc.bcm.edu	37	2	152527572	152527572	+	Missense_Mutation	SNP	C	C	T	rs7426114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:152527572C>T	ENST00000172853.10	-	38	4618	c.4471G>A	c.(4471-4473)Gtg>Atg	p.V1491M	NEB_ENST00000409198.1_Missense_Mutation_p.V1491M|NEB_ENST00000397345.3_Missense_Mutation_p.V1491M|NEB_ENST00000604864.1_Missense_Mutation_p.V1491M|NEB_ENST00000603639.1_Missense_Mutation_p.V1491M|NEB_ENST00000427231.2_Missense_Mutation_p.V1491M			P20929	NEBU_HUMAN	nebulin	1491			V -> M (in dbSNP:rs7426114). {ECO:0000269|PubMed:7739042}.		muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGAGCCAACACCATGCCCATG	0.483													C|||	2670	0.533147	0.1959	0.8357	5008	,	,		22583	0.379		0.8231	False		,,,				2504	0.635				p.V1491M		Atlas-SNP	.											.	NEB	1697	.	0			c.G4471A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	1356,2878		226,904,987	152.0	149.0	150.0		4471,4471,4471	5.4	1.0	2	dbSNP_116	150	7030,1414		2942,1146,134	yes	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	21,21,21	3168,2050,1121	TT,TC,CC		16.7456,32.0265,33.8539	probably-damaging,probably-damaging,probably-damaging	1491/8526,1491/8526,1491/6670	152527572	8386,4292	2117	4222	6339	SO:0001583	missense	4703	exon38			CCAACACCATGCC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.4471G>A	2.37:g.152527572C>T	ENSP00000172853:p.Val1491Met	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	291	291	1	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		1244	0.5695970695970696	101	0.20528455284552846	290	0.8011049723756906	224	0.3916083916083916	629	0.8298153034300791	C	22.3	4.270470	0.80469	0.320265	0.832544	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.07114	3.22;3.31;3.31;3.28	5.42	5.42	0.78866	.	0.139163	0.48286	D	0.000183	T	0.00012	0.0000	L	0.53561	1.675	0.09310	P	1.0	P	0.43885	0.82	B	0.43445	0.42	T	0.00677	-1.1614	9	0.56958	D	0.05	.	14.7853	0.69800	0.0:0.9289:0.0:0.0711	rs7426114;rs52833662;rs58843632;rs7426114	1491	P20929	NEBU_HUMAN	M	1491	ENSP00000386259:V1491M;ENSP00000380505:V1491M;ENSP00000416578:V1491M;ENSP00000172853:V1491M	ENSP00000172853:V1491M	V	-	1	0	NEB	152235818	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.696000	0.47052	2.691000	0.91804	0.655000	0.94253	GTG	C|0.461;N|0.000	.	strong		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
L1TD1	54596	hgsc.bcm.edu	37	1	62676284	62676284	+	Missense_Mutation	SNP	C	C	T	rs549166182|rs2886644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:62676284C>T	ENST00000498273.1	+	4	2133	c.1838C>T	c.(1837-1839)aCa>aTa	p.T613I	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	613			T -> I (in dbSNP:rs2886644).							breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						acagaggaaacagaagaaaac	0.363																																					p.T613I		Atlas-SNP	.											.	L1TD1	114	.	0			c.C1838T						PASS	.	C	ILE/THR,ILE/THR	686,3720	267.7+/-268.0	52,582,1569	30.0	29.0	29.0		1838,1838	2.2	0.1	1	dbSNP_101	29	2329,6269	357.1+/-330.6	331,1667,2301	yes	missense,missense	L1TD1	NM_001164835.1,NM_019079.4	89,89	383,2249,3870	TT,TC,CC		27.0877,15.5697,23.1852	possibly-damaging,possibly-damaging	613/866,613/866	62676284	3015,9989	2203	4299	6502	SO:0001583	missense	54596	exon5			AGGAAACAGAAGA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1838C>T	1.37:g.62676284C>T	ENSP00000419901:p.Thr613Ile	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	340	0.15567765567765568	61	0.12398373983739837	64	0.17679558011049723	29	0.050699300699300696	186	0.24538258575197888	C	10.60	1.394345	0.25205	0.155697	0.270877	ENSG00000240563	ENST00000498273	T	0.15139	2.45	3.09	2.18	0.27775	.	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.25850	0.136	B	0.34038	0.174	T	0.38520	-0.9657	8	0.35671	T	0.21	.	6.4075	0.21672	0.0:0.86:0.0:0.14	rs2886644;rs52837192;rs2886644	613	Q5T7N2	LITD1_HUMAN	I	613	ENSP00000419901:T613I	ENSP00000419901:T613I	T	+	2	0	L1TD1	62448872	0.005000	0.15991	0.110000	0.21437	0.224000	0.24922	0.402000	0.20965	0.893000	0.36288	-0.444000	0.05651	ACA	C|0.809;T|0.191	0.191	strong		0.363	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
CEP170B	283638	hgsc.bcm.edu	37	14	105344293	105344293	+	Silent	SNP	C	C	T	rs61995995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105344293C>T	ENST00000414716.3	+	4	495	c.267C>T	c.(265-267)ttC>ttT	p.F89F	CEP170B_ENST00000453495.1_Silent_p.F89F|CEP170B_ENST00000556508.1_Silent_p.F19F|CEP170B_ENST00000418279.1_Silent_p.F19F	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	89						cytoplasm (GO:0005737)|microtubule (GO:0005874)											TCATCCGCTTCGGCTACGATA	0.597													C|||	1772	0.353834	0.1339	0.5159	5008	,	,		13855	0.1994		0.5716	False		,,,				2504	0.4714				p.F89F		Atlas-SNP	.											.	.	.	.	0			c.C267T						PASS	.	C	,	873,3325		116,641,1342	48.0	55.0	53.0		267,57	-2.1	1.0	14	dbSNP_129	53	4853,3587		1408,2037,775	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	1524,2678,2117	TT,TC,CC		42.5,20.7956,45.3078	,	89/1555,19/1520	105344293	5726,6912	2099	4220	6319	SO:0001819	synonymous_variant	283638	exon4			CCGCTTCGGCTAC	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.267C>T	14.37:g.105344293C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	91	30	0.32967	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																			C|0.592;T|0.408	0.408	strong		0.597	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
AP5Z1	9907	hgsc.bcm.edu	37	7	4827330	4827330	+	Silent	SNP	C	C	T	rs17135128	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4827330C>T	ENST00000348624.4	+	11	1471	c.1377C>T	c.(1375-1377)gaC>gaT	p.D459D	AP5Z1_ENST00000401897.1_Silent_p.D459D|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	459					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCCTGGTGGACGCTGGCACAG	0.692													C|||	408	0.0814696	0.0401	0.036	5008	,	,		15883	0.0496		0.0736	False		,,,				2504	0.2106				p.D459D		Atlas-SNP	.											KIAA0415_ENST00000450194,rectum,carcinoma,0,2	.	.	2	0			c.C1377T						PASS	.	C		189,3981		5,179,1901	25.0	31.0	29.0		1377	-3.7	0.0	7	dbSNP_123	29	532,7742		19,494,3624	no	coding-synonymous	KIAA0415	NM_014855.2		24,673,5525	TT,TC,CC		6.4298,4.5324,5.794		459/808	4827330	721,11723	2085	4137	6222	SO:0001819	synonymous_variant	9907	exon11			GGTGGACGCTGGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1377C>T	7.37:g.4827330C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	100	60	0.6	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			C|0.943;T|0.057	0.057	strong		0.692	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
PCDHB8	56128	hgsc.bcm.edu	37	5	140559914	140559914	+	Missense_Mutation	SNP	T	T	C	rs2740583	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140559914T>C	ENST00000239444.2	+	1	2544	c.2299T>C	c.(2299-2301)Ttc>Ctc	p.F767L	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	767			F -> L (in dbSNP:rs2740583). {ECO:0000269|PubMed:11322959, ECO:0000269|PubMed:15489334}.		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAGTTCCAGTTCCTGAAACC	0.502													T|||	973	0.194289	0.0197	0.2939	5008	,	,		16792	0.1171		0.3449	False		,,,				2504	0.2843				p.F767L		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T2299C						PASS	.	T	LEU/PHE	301,4105	162.9+/-194.8	17,267,1919	99.0	102.0	101.0		2299	4.5	0.3	5	dbSNP_100	101	2995,5605	464.0+/-366.1	532,1931,1837	yes	missense	PCDHB8	NM_019120.3	22	549,2198,3756	CC,CT,TT		34.8256,6.8316,25.3421	benign	767/802	140559914	3296,9710	2203	4300	6503	SO:0001583	missense	56128	exon1			TTCCAGTTCCTGA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.2299T>C	5.37:g.140559914T>C	ENSP00000239444:p.Phe767Leu	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	178	51	0.286517	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	467	0.21382783882783882	13	0.026422764227642278	121	0.3342541436464088	71	0.12412587412587413	262	0.34564643799472294	T	22.2	4.258002	0.80246	0.068316	0.348256	ENSG00000120322	ENST00000239444	T	0.18657	2.2	4.53	4.53	0.55603	.	.	.	.	.	T	0.00012	0.0000	M	0.88105	2.93	0.36688	P	0.12056599999999995	B	0.24132	0.098	B	0.29942	0.109	T	0.23190	-1.0195	8	0.66056	D	0.02	.	13.5476	0.61713	0.0:0.0:0.0:1.0	rs2740583;rs17697117;rs17844510;rs61661593;rs2740583	767	Q9UN66	PCDB8_HUMAN	L	767	ENSP00000239444:F767L	ENSP00000239444:F767L	F	+	1	0	PCDHB8	140540098	0.998000	0.40836	0.332000	0.25469	0.020000	0.10135	3.378000	0.52432	1.673000	0.50895	0.455000	0.32223	TTC	A|0.000;C|0.223;N|0.000;T|0.776	0.223	strong		0.502	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
TF	7018	hgsc.bcm.edu	37	3	133474328	133474328	+	Silent	SNP	G	G	A	rs12769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:133474328G>A	ENST00000402696.3	+	5	1109	c.624G>A	c.(622-624)tcG>tcA	p.S208S	TFP1_ENST00000460564.1_RNA|TF_ENST00000264998.3_Silent_p.S81S	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	208	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	TCGGCTACTCGGGAGCCTTCA	0.582													G|||	1559	0.311302	0.087	0.3775	5008	,	,		19938	0.4454		0.3211	False		,,,				2504	0.4192				p.S208S		Atlas-SNP	.											.	TF	116	.	0			c.G624A						PASS	.	G		592,3814	260.4+/-263.7	34,524,1645	77.0	66.0	70.0		624	-10.2	0.0	3	dbSNP_52	70	2787,5813	442.2+/-360.0	473,1841,1986	no	coding-synonymous	TF	NM_001063.3		507,2365,3631	AA,AG,GG		32.407,13.4362,25.9803		208/699	133474328	3379,9627	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon5			CTACTCGGGAGCC		CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.624G>A	3.37:g.133474328G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			G|0.727;A|0.273	0.273	strong		0.582	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
SLC34A3	142680	hgsc.bcm.edu	37	9	140127725	140127725	+	Silent	SNP	C	C	T	rs34796681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140127725C>T	ENST00000538474.1	+	7	849	c.625C>T	c.(625-627)Ctg>Ttg	p.L209L	SLC34A3_ENST00000361134.2_Silent_p.L209L	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	209					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		CCTGCTGCCACTGGAGAGCGC	0.682													c|||	2	0.000399361	0.0	0.0014	5008	,	,		11300	0.0		0.001	False		,,,				2504	0.0				p.L209L		Atlas-SNP	.											.	SLC34A3	32	.	0			c.C625T						PASS	.		,,	8,4304		0,8,2148	14.0	15.0	15.0		625,625,625	2.7	0.6	9	dbSNP_126	15	59,8433		0,59,4187	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC34A3	NM_001177316.1,NM_001177317.1,NM_080877.2	,,	0,67,6335	TT,TC,CC		0.6948,0.1855,0.5233	,,	209/600,209/600,209/600	140127725	67,12737	2156	4246	6402	SO:0001819	synonymous_variant	142680	exon7			CTGCCACTGGAGA	AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"""Solute carriers"""	20305	protein-coding gene	gene with protein product		609826	"""solute carrier family 34 (sodium phosphate), member 3"""			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.625C>T	9.37:g.140127725C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_001177317	A2BFA1	Silent	SNP	ENST00000538474.1	37	CCDS7038.1																																																																																			C|0.993;T|0.007	0.007	strong		0.682	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877	
HELB	92797	hgsc.bcm.edu	37	12	66696410	66696410	+	Silent	SNP	C	C	T	rs3741604	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:66696410C>T	ENST00000247815.4	+	1	86	c.27C>T	c.(25-27)cgC>cgT	p.R9R		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	9					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		CGTACCTGCGCCAACTTCAGG	0.557													C|||	1519	0.303315	0.143	0.3256	5008	,	,		16059	0.1825		0.5308	False		,,,				2504	0.3947				p.R9R		Atlas-SNP	.											.	HELB	90	.	0			c.C27T						PASS	.	C		948,3458	360.9+/-315.4	100,748,1355	79.0	74.0	76.0		27	-5.0	0.0	12	dbSNP_107	76	4659,3941	604.2+/-394.8	1279,2101,920	no	coding-synonymous	HELB	NM_033647.2		1379,2849,2275	TT,TC,CC		45.8256,21.5161,43.1109		9/1088	66696410	5607,7399	2203	4300	6503	SO:0001819	synonymous_variant	92797	exon1			CCTGCGCCAACTT	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.27C>T	12.37:g.66696410C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	167	96	0.57485	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	37	CCDS8976.1																																																																																			C|0.620;T|0.380	0.380	strong		0.557	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
MUC16	94025	hgsc.bcm.edu	37	19	9069892	9069892	+	Missense_Mutation	SNP	A	A	C	rs1862460	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9069892A>C	ENST00000397910.4	-	3	17757	c.17554T>G	c.(17554-17556)Ttt>Gtt	p.F5852V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5854	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCTGTTACAAAAGGAAAAGTG	0.478													C|||	1275	0.254593	0.2905	0.2911	5008	,	,		21340	0.3264		0.169	False		,,,				2504	0.1943				p.F5852V		Atlas-SNP	.											.	MUC16	4315	.	0			c.T17554G						PASS	.	C	VAL/PHE	1008,2846		132,744,1051	207.0	193.0	198.0		17554	-0.7	0.0	19	dbSNP_92	198	1514,6724		138,1238,2743	yes	missense	MUC16	NM_024690.2	50	270,1982,3794	CC,CA,AA		18.3782,26.1546,20.8568	benign	5852/14508	9069892	2522,9570	1927	4119	6046	SO:0001583	missense	94025	exon3			TTACAAAAGGAAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.17554T>G	19.37:g.9069892A>C	ENSP00000381008:p.Phe5852Val	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	267	154	0.576779	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	549	0.25137362637362637	125	0.2540650406504065	93	0.2569060773480663	205	0.3583916083916084	126	0.1662269129287599	c	3.417	-0.118983	0.06838	0.261546	0.183782	ENSG00000181143	ENST00000397910	T	0.02682	4.2	1.74	-0.715	0.11215	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.44997	-0.9291	8	0.87932	D	0	.	2.8277	0.05490	0.4787:0.3557:0.0:0.1656	rs1862460;rs52808057;rs57945851;rs1862460	5852	B5ME49	.	V	5852	ENSP00000381008:F5852V	ENSP00000381008:F5852V	F	-	1	0	MUC16	8930892	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.147000	0.01293	-0.452000	0.07087	-0.729000	0.03580	TTT	A|0.755;C|0.245	0.245	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DTNB	1838	hgsc.bcm.edu	37	2	25655772	25655772	+	Silent	SNP	T	T	C	rs7583475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:25655772T>C	ENST00000406818.3	-	14	1689	c.1440A>G	c.(1438-1440)gcA>gcG	p.A480A	DTNB_ENST00000407186.1_Silent_p.A450A|DTNB_ENST00000288642.8_Silent_p.A480A|DTNB_ENST00000407038.3_Silent_p.A450A|DTNB_ENST00000407661.3_Silent_p.A480A|DTNB_ENST00000496972.2_Silent_p.A423A|DTNB_ENST00000545439.1_Silent_p.A276A|DTNB_ENST00000405222.1_Silent_p.A450A|DTNB_ENST00000404103.3_Silent_p.A480A	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	480						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCGCAGCTCTGCCAGCAGCG	0.567													T|||	1199	0.239417	0.3298	0.2104	5008	,	,		19600	0.005		0.3489	False		,,,				2504	0.2669				p.A480A		Atlas-SNP	.											.	DTNB	43	.	0			c.A1440G						PASS	.	T	,,,,	1405,2935		240,925,1005	23.0	28.0	27.0		1440,1440,1350,1440,1350	-9.0	0.9	2	dbSNP_116	27	2850,5716		493,1864,1926	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	,,,,	733,2789,2931	CC,CT,TT		33.2711,32.3733,32.9692	,,,,	480/628,480/598,450/568,480/610,450/561	25655772	4255,8651	2170	4283	6453	SO:0001819	synonymous_variant	1838	exon14			CAGCTCTGCCAGC	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.1440A>G	2.37:g.25655772T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Silent	SNP	ENST00000406818.3	37	CCDS46237.1																																																																																			T|0.743;C|0.257	0.257	strong		0.567	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147	
ZNF528	84436	hgsc.bcm.edu	37	19	52909200	52909200	+	Missense_Mutation	SNP	A	A	G	rs370656674		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52909200A>G	ENST00000360465.3	+	5	482	c.56A>G	c.(55-57)cAg>cGg	p.Q19R	ZNF528_ENST00000598192.1_Missense_Mutation_p.Q19R|ZNF528_ENST00000391788.2_Missense_Mutation_p.Q9R|ZNF528_ENST00000594530.1_Missense_Mutation_p.Q19R	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	19	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		GAGTTCTCTCAGGAAGAGTGG	0.468																																					p.Q19R		Atlas-SNP	.											.	ZNF528	95	.	0			c.A56G						PASS	.	A	ARG/GLN	0,4406		0,0,2203	182.0	179.0	180.0		56	-0.7	0.0	19		180	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF528	NM_032423.2	43	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	19/629	52909200	1,13005	2203	4300	6503	SO:0001583	missense	84436	exon5			TCTCTCAGGAAGA	AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"""Zinc fingers, C2H2-type"", ""-"""	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.56A>G	19.37:g.52909200A>G	ENSP00000353652:p.Gln19Arg	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	200	96	0.48	NM_032423	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.438395	0.25900	0.0	1.16E-4	ENSG00000167555	ENST00000391788;ENST00000391787;ENST00000360465	T;T;T	0.01963	4.53;4.53;4.53	1.93	-0.733	0.11144	Krueppel-associated box (4);	.	.	.	.	T	0.05777	0.0151	L	0.53729	1.69	0.19775	N	0.999957	D	0.76494	0.999	D	0.72338	0.977	T	0.35151	-0.9800	9	0.45353	T	0.12	.	0.995	0.01465	0.2762:0.3854:0.1474:0.1911	.	19	Q3MIS6	ZN528_HUMAN	R	9;19;19	ENSP00000375665:Q9R;ENSP00000375664:Q19R;ENSP00000353652:Q19R	ENSP00000353652:Q19R	Q	+	2	0	ZNF528	57601012	0.001000	0.12720	0.015000	0.15790	0.517000	0.34286	-0.590000	0.05760	-0.452000	0.07087	0.402000	0.26972	CAG	.	.	weak		0.468	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423	
UPF3A	65110	hgsc.bcm.edu	37	13	115067419	115067419	+	Silent	SNP	G	G	A	rs146464930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:115067419G>A	ENST00000375299.3	+	9	1277	c.1221G>A	c.(1219-1221)ccG>ccA	p.P407P	UPF3A_ENST00000475218.2_3'UTR|UPF3A_ENST00000351487.5_Silent_p.P374P	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	407					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleocytoplasmic transport (GO:0006913)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GCGGGGCTCCGGGGGAGGCCA	0.567													G|||	14	0.00279553	0.0008	0.0043	5008	,	,		19212	0.0		0.0099	False		,,,				2504	0.0				p.P407P		Atlas-SNP	.											.	UPF3A	47	.	0			c.G1221A						PASS	.	G	,	13,4359		0,13,2173	14.0	19.0	17.0		1221,1122	-9.9	0.0	13	dbSNP_134	17	156,8366		2,152,4107	no	coding-synonymous,coding-synonymous	UPF3A	NM_023011.3,NM_080687.2	,	2,165,6280	AA,AG,GG		1.8306,0.2973,1.3107	,	407/477,374/444	115067419	169,12725	2186	4261	6447	SO:0001819	synonymous_variant	65110	exon9			GGCTCCGGGGGAG	AF318575	CCDS9543.1, CCDS9544.1	13q34	2010-04-30			ENSG00000169062	ENSG00000169062			20332	protein-coding gene	gene with protein product		605530				11113196, 11163187	Standard	NM_023011		Approved	RENT3A, UPF3, HUPF3A	uc001vup.3	Q9H1J1	OTTHUMG00000017403	ENST00000375299.3:c.1221G>A	13.37:g.115067419G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Silent	SNP	ENST00000375299.3	37	CCDS9543.1																																																																																			G|0.991;A|0.009	0.009	strong		0.567	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		
MCM9	254394	hgsc.bcm.edu	37	6	119137011	119137011	+	Missense_Mutation	SNP	G	G	A	rs35917528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:119137011G>A	ENST00000316316.6	-	13	2694	c.2408C>T	c.(2407-2409)cCa>cTa	p.P803L		NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	803					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		TGTCTCTCCTGGTGATGGAAG	0.468													G|||	245	0.0489217	0.0265	0.072	5008	,	,		20834	0.0		0.1133	False		,,,				2504	0.047				p.P803L		Atlas-SNP	.											.	MCM9	73	.	0			c.C2408T						PASS	.																																			SO:0001583	missense	254394	exon12			TCTCCTGGTGATG	BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"""minichromosome maintenance deficient domain containing 1"", ""chromosome 6 open reading frame 61"""	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.2408C>T	6.37:g.119137011G>A	ENSP00000314505:p.Pro803Leu	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	21	5	0.238095	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	134	0.06135531135531135	20	0.04065040650406504	34	0.09392265193370165	0	0.0	80	0.10554089709762533	G	11.85	1.763174	0.31228	.	.	ENSG00000111877	ENST00000316316;ENST00000243218	T	0.03689	3.84	6.17	3.26	0.37387	.	0.238047	0.43416	D	0.000564	T	0.01387	0.0045	L	0.57536	1.79	0.47407	P	5.889999999999507E-4	P	0.38922	0.651	B	0.27887	0.084	T	0.53287	-0.8460	9	0.25106	T	0.35	.	10.9587	0.47372	0.0:0.1264:0.6107:0.2629	rs35917528	803	Q9NXL9	MCM9_HUMAN	L	803;422	ENSP00000314505:P803L	ENSP00000243218:P422L	P	-	2	0	MCM9	119243714	0.661000	0.27430	0.192000	0.23308	0.096000	0.18686	0.747000	0.26290	0.880000	0.35969	0.655000	0.94253	CCA	G|0.926;A|0.074	0.074	strong		0.468	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
ACP6	51205	hgsc.bcm.edu	37	1	147131103	147131103	+	Silent	SNP	C	C	T	rs11800736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:147131103C>T	ENST00000369238.6	-	4	978	c.531G>A	c.(529-531)ctG>ctA	p.L177L	ACP6_ENST00000392988.2_Silent_p.L177L	NM_016361.3	NP_057445.4	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	177					dephosphorylation (GO:0016311)|lysobisphosphatidic acid metabolic process (GO:2001311)|phospholipid metabolic process (GO:0006644)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	acid phosphatase activity (GO:0003993)|lysophosphatidic acid phosphatase activity (GO:0052642)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(4)|prostate(1)	16	all_hematologic(923;0.0276)					AAAGCCCAGCCAGCAAACAAC	0.443													C|||	92	0.0183706	0.0023	0.0245	5008	,	,		19397	0.0		0.0457	False		,,,				2504	0.0266				p.L177L		Atlas-SNP	.											.	ACP6	36	.	0			c.G531A						PASS	.	C		39,4367	43.8+/-77.6	0,39,2164	129.0	132.0	131.0		531	3.6	1.0	1	dbSNP_120	131	474,8126	138.9+/-195.6	18,438,3844	no	coding-synonymous	ACP6	NM_016361.3		18,477,6008	TT,TC,CC		5.5116,0.8852,3.9443		177/429	147131103	513,12493	2203	4300	6503	SO:0001819	synonymous_variant	51205	exon4			CCCAGCCAGCAAA	BC009965	CCDS928.1	1q21	2008-02-05			ENSG00000162836	ENSG00000162836			29609	protein-coding gene	gene with protein product		611471				12010880, 10506173	Standard	NM_016361		Approved	LPAP, ACPL1	uc001epr.2	Q9NPH0	OTTHUMG00000014019	ENST00000369238.6:c.531G>A	1.37:g.147131103C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	259	143	0.552124	NM_016361	Q59G61|Q5T490|Q6IAQ3|Q7LG81|Q9UIG6	Silent	SNP	ENST00000369238.6	37	CCDS928.1																																																																																			C|0.966;T|0.034	0.034	strong		0.443	ACP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039420.2	NM_016361	
CDH19	28513	hgsc.bcm.edu	37	18	64176365	64176365	+	Silent	SNP	G	G	T	rs1055335	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:64176365G>T	ENST00000262150.2	-	11	1987	c.1695C>A	c.(1693-1695)acC>acA	p.T565T	CDH19_ENST00000540086.1_Intron	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	1840	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				GGATGGTAAGGGTGTTTGTAC	0.453													G|||	1264	0.252396	0.0651	0.2795	5008	,	,		16004	0.2331		0.3529	False		,,,				2504	0.4029				p.T565T		Atlas-SNP	.											.	CDH19	141	.	0			c.C1695A						PASS	.	G		529,3877	240.3+/-251.1	34,461,1708	212.0	179.0	190.0		1695	-0.1	1.0	18	dbSNP_86	190	3261,5339	489.9+/-372.7	632,1997,1671	no	coding-synonymous	CDH19	NM_021153.2		666,2458,3379	TT,TG,GG		37.9186,12.0064,29.1404		565/773	64176365	3790,9216	2203	4300	6503	SO:0001819	synonymous_variant	28513	exon11			GGTAAGGGTGTTT	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.1695C>A	18.37:g.64176365G>T		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	183	176	0.961749	NM_021153	O15098	Silent	SNP	ENST00000262150.2	37	CCDS11994.1																																																																																			G|0.731;T|0.269	0.269	strong		0.453	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
HACL1	26061	hgsc.bcm.edu	37	3	15637914	15637914	+	Silent	SNP	G	G	A	rs74506826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:15637914G>A	ENST00000321169.5	-	3	571	c.204C>T	c.(202-204)tcC>tcT	p.S68S	HACL1_ENST00000451445.2_Silent_p.S68S|HACL1_ENST00000457447.2_Silent_p.S68S|HACL1_ENST00000456194.2_Silent_p.S68S|HACL1_ENST00000435217.2_Intron	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	68					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						ATCCAATCGCGGAGGCAGCAT	0.358													G|||	48	0.00958466	0.0	0.0144	5008	,	,		16549	0.0		0.0348	False		,,,				2504	0.0031				p.S68S		Atlas-SNP	.											.	HACL1	33	.	0			c.C204T						PASS	.	G		21,4385	29.0+/-57.7	1,19,2183	76.0	67.0	70.0		204	-11.4	0.0	3	dbSNP_132	70	224,8376	92.6+/-154.6	5,214,4081	no	coding-synonymous	HACL1	NM_012260.2		6,233,6264	AA,AG,GG		2.6047,0.4766,1.8837		68/579	15637914	245,12761	2203	4300	6503	SO:0001819	synonymous_variant	26061	exon3			AATCGCGGAGGCA	AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"""2-hydroxyphytanoyl-CoA lyase"""	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.204C>T	3.37:g.15637914G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	294	125	0.42517	NM_012260	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Silent	SNP	ENST00000321169.5	37	CCDS2627.1																																																																																			G|0.982;A|0.018	0.018	strong		0.358	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260	
WDR35	57539	hgsc.bcm.edu	37	2	20131079	20131079	+	Missense_Mutation	SNP	T	T	C	rs1191778	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:20131079T>C	ENST00000345530.3	-	25	3063	c.2948A>G	c.(2947-2949)gAa>gGa	p.E983G	WDR35_ENST00000281405.4_Missense_Mutation_p.E972G|WDR35_ENST00000416055.2_Missense_Mutation_p.E456G	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	983			E -> G (in dbSNP:rs1191778). {ECO:0000269|PubMed:14702039}.		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCATCTGTTCATGGTATTG	0.358													T|||	1164	0.232428	0.1097	0.3588	5008	,	,		16337	0.1171		0.4443	False		,,,				2504	0.2096				p.E983G		Atlas-SNP	.											WDR35,NS,carcinoma,-1,1	WDR35	92	1	0			c.A2948G						PASS	.	T	GLY/GLU,GLY/GLU	709,3697	293.8+/-282.8	52,605,1546	166.0	159.0	161.0		2948,2915	4.8	0.0	2	dbSNP_87	161	3463,5137	508.0+/-377.0	689,2085,1526	yes	missense,missense	WDR35	NM_001006657.1,NM_020779.3	98,98	741,2690,3072	CC,CT,TT		40.2674,16.0917,32.0775	benign,benign	983/1182,972/1171	20131079	4172,8834	2203	4300	6503	SO:0001583	missense	57539	exon25			ATCTGTTCATGGT	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2948A>G	2.37:g.20131079T>C	ENSP00000314444:p.Glu983Gly	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	201	89	0.442786	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	611	0.27976190476190477	53	0.10772357723577236	139	0.3839779005524862	87	0.1520979020979021	332	0.43799472295514513	T	12.10	1.837657	0.32513	0.160917	0.402674	ENSG00000118965	ENST00000345530;ENST00000281405;ENST00000416055	T;T;T	0.74526	-0.23;-0.23;-0.85	4.82	4.82	0.62117	.	0.210756	0.48767	D	0.000173	T	0.00012	0.0000	M	0.76002	2.32	0.40456	P	0.01980599999999999	B;B;P	0.42692	0.348;0.073;0.787	B;B;P	0.46758	0.156;0.066;0.526	T	0.17806	-1.0357	9	0.54805	T	0.06	-18.7985	13.8697	0.63610	0.0:0.0:0.0:1.0	rs1191778;rs1658525;rs52827575;rs61210615;rs1191778	972;983;456	Q9P2L0-2;Q9P2L0;B3KR94	.;WDR35_HUMAN;.	G	983;972;456	ENSP00000314444:E983G;ENSP00000281405:E972G;ENSP00000399159:E456G	ENSP00000281405:E972G	E	-	2	0	WDR35	19994560	0.992000	0.36948	0.019000	0.16419	0.680000	0.39746	3.878000	0.56130	1.933000	0.56026	0.482000	0.46254	GAA	T|0.710;C|0.290	0.290	strong		0.358	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
ZNF419	79744	hgsc.bcm.edu	37	19	58002964	58002964	+	Splice_Site	SNP	G	G	C	rs1135692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58002964G>C	ENST00000221735.7	+	3	384	c.198G>C	c.(196-198)ctG>ctC	p.L66L	ZNF419_ENST00000424930.2_Splice_Site_p.L67L|ZNF419_ENST00000354197.4_Splice_Site_p.L54L|ZNF419_ENST00000518999.1_Splice_Site_p.L67L|ZNF419_ENST00000415379.2_Splice_Site_p.L53L|ZNF419_ENST00000426954.2_Splice_Site_p.L54L|ZNF419_ENST00000520540.1_Splice_Site_p.L54L|ZNF419_ENST00000442920.2_Splice_Site_p.L53L|AC003005.4_ENST00000601674.1_Splice_Site_p.L53L|ZNF419_ENST00000347466.6_Splice_Site_p.L67L			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		TGGCCTCTCTGGGTAAGGTTC	0.542													G|||	1310	0.261581	0.2761	0.2608	5008	,	,		20364	0.1181		0.3638	False		,,,				2504	0.2853				p.L67L		Atlas-SNP	.											.	ZNF419	134	.	0			c.G201C						PASS	.	G	,,,,,,	1262,3144	428.7+/-342.0	179,904,1120	67.0	69.0	69.0		201,162,159,201,162,159,198	-0.9	0.2	19	dbSNP_116	69	3010,5588	464.4+/-366.2	498,2014,1787	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	,,,,,,	677,2918,2907	CC,CG,GG		35.0081,28.6428,32.8514	,,,,,,	67/512,54/499,53/498,67/479,54/466,53/465,66/511	58002964	4272,8732	2203	4299	6502	SO:0001630	splice_region_variant	79744	exon3			CTCTCTGGGTAAG	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.199+1G>C	19.37:g.58002964G>C		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	229	105	0.458515	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																			G|0.730;C|0.270	0.270	strong		0.542	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	Silent
FAM26F	441168	hgsc.bcm.edu	37	6	116783330	116783330	+	Missense_Mutation	SNP	G	G	A	rs1057192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116783330G>A	ENST00000368605.1	+	2	333	c.238G>A	c.(238-240)Gga>Aga	p.G80R	RP1-93H18.6_ENST00000476099.1_RNA|FAM26F_ENST00000368606.3_Intron	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	80			G -> R (in dbSNP:rs1057192).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(1)	3				GBM - Glioblastoma multiforme(226;0.0402)|all cancers(137;0.0627)|OV - Ovarian serous cystadenocarcinoma(136;0.0655)|Epithelial(106;0.231)		CCTGCTCACCGGATGCTGCTC	0.721													G|||	1200	0.239617	0.0628	0.17	5008	,	,		13100	0.3651		0.2485	False		,,,				2504	0.3896				p.E80K		Atlas-SNP	.											.	FAM26F	12	.	0			c.G238A						PASS	.	G	ARG/GLY	285,3437		11,263,1587	4.0	4.0	4.0		238	4.2	1.0	6	dbSNP_86	4	1331,5787		122,1087,2350	yes	missense	FAM26F	NM_001010919.1	125	133,1350,3937	AA,AG,GG		18.6991,7.6572,14.9077	probably-damaging	80/316	116783330	1616,9224	1861	3559	5420	SO:0001583	missense	441168	exon2			CTCACCGGATGCT	AF086130	CCDS34519.1, CCDS64506.1	6q22.1	2007-06-20			ENSG00000188820	ENSG00000188820			33391	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 187"""	C6orf187			Standard	NM_001010919		Approved	RP1-93H18.5, OTTHUMP00000017061, OTTHUMP00000017062, dJ93H18.5	uc003pwv.4	Q5R3K3	OTTHUMG00000015438	ENST00000368605.1:c.238G>A	6.37:g.116783330G>A	ENSP00000357594:p.Gly80Arg	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	11	7	0.636364	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	492	0.22527472527472528	23	0.046747967479674794	64	0.17679558011049723	209	0.36538461538461536	196	0.25857519788918204	G	19.26	3.793370	0.70452	0.076572	0.186991	ENSG00000188820	ENST00000368605	T	0.24908	1.83	5.1	4.22	0.49857	.	0.060943	0.64402	D	0.000004	T	0.45498	0.1345	M	0.83223	2.63	0.09310	P	0.999999384292	D	0.89917	1.0	D	0.79784	0.993	T	0.59150	-0.7508	9	0.87932	D	0	-20.7189	15.7243	0.77743	0.0:0.137:0.863:0.0	rs1057192;rs3173147	80	Q5R3K3	FA26F_HUMAN	R	80	ENSP00000357594:G80R	ENSP00000357594:G80R	G	+	1	0	FAM26F	116890023	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	4.925000	0.63425	1.372000	0.46190	0.491000	0.48974	GGA	.	.	weak		0.721	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919	
MUC16	94025	hgsc.bcm.edu	37	19	9065632	9065632	+	Missense_Mutation	SNP	T	T	C	rs1867691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9065632T>C	ENST00000397910.4	-	3	22017	c.21814A>G	c.(21814-21816)Att>Gtt	p.I7272V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7274	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTAGCACCAATGGACACTTCA	0.488													t|||	1081	0.215855	0.0802	0.2061	5008	,	,		21790	0.249		0.3111	False		,,,				2504	0.274				p.I7272V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A21814G						PASS	.	T	VAL/ILE	473,3545		28,417,1564	141.0	134.0	136.0		21814	-2.7	0.0	19	dbSNP_92	136	2385,5961		340,1705,2128	yes	missense	MUC16	NM_024690.2	29	368,2122,3692	CC,CT,TT		28.5766,11.772,23.1155	benign	7272/14508	9065632	2858,9506	2009	4173	6182	SO:0001583	missense	94025	exon3			CACCAATGGACAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21814A>G	19.37:g.9065632T>C	ENSP00000381008:p.Ile7272Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	494	0.2261904761904762	53	0.10772357723577236	87	0.24033149171270718	122	0.21328671328671328	232	0.30606860158311344	t	2.759	-0.258393	0.05791	0.11772	0.285766	ENSG00000181143	ENST00000397910	T	0.02236	4.38	2.82	-2.74	0.05932	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	.	.	.	B	0.06786	0.001	B	0.09377	0.004	T	0.47724	-0.9095	8	0.87932	D	0	.	0.9168	0.01306	0.1569:0.2308:0.1592:0.4531	rs1867691;rs2547061;rs17515635;rs59475496;rs1867691	7272	B5ME49	.	V	7272	ENSP00000381008:I7272V	ENSP00000381008:I7272V	I	-	1	0	MUC16	8926632	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.502000	0.06390	-1.196000	0.02676	-1.120000	0.02017	ATT	T|0.778;C|0.222	0.222	strong		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CMC2	56942	hgsc.bcm.edu	37	16	81010073	81010073	+	Missense_Mutation	SNP	C	C	T	rs1127390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81010073C>T	ENST00000219400.3	-	4	572	c.157G>A	c.(157-159)Gta>Ata	p.V53I	CMC2_ENST00000564174.1_Missense_Mutation_p.V29I|CMC2_ENST00000565108.1_Missense_Mutation_p.V29I|CMC2_ENST00000564249.1_Missense_Mutation_p.V53I|CMC2_ENST00000565925.1_3'UTR|CMC2_ENST00000565914.1_Missense_Mutation_p.V53I|CMC2_ENST00000566231.1_5'UTR|CMC2_ENST00000486645.1_3'UTR|CMC2_ENST00000570195.1_3'UTR|CMC2_ENST00000562713.1_3'UTR	NM_020188.3	NP_064573.1	Q9NRP2	COXM2_HUMAN	C-x(9)-C motif containing 2	53						mitochondrion (GO:0005739)											CTGTTTTCTACGTACTGAAAA	0.343													T|||	1994	0.398163	0.6694	0.366	5008	,	,		16380	0.4454		0.2296	False		,,,				2504	0.1789				p.V53I		Atlas-SNP	.											.	.	.	.	0			c.G157A						PASS	.	T	ILE/VAL	2534,1872	527.8+/-372.2	739,1056,408	42.0	45.0	44.0		157	-4.7	0.0	16	dbSNP_86	44	1847,6753	725.8+/-406.6	212,1423,2665	yes	missense	C16orf61	NM_020188.3	29	951,2479,3073	TT,TC,CC		21.4767,42.4875,33.6845	benign	53/80	81010073	4381,8625	2203	4300	6503	SO:0001583	missense	56942	exon4			TTTCTACGTACTG	BC032631	CCDS10930.1	16q23.2	2013-10-18	2013-10-18	2012-02-14	ENSG00000103121	ENSG00000103121			24447	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 61"", ""COX assembly mitochondrial protein 2 homolog (S. cerevisiae)"""	C16orf61		20220131	Standard	NM_020188		Approved	DC13, MGC45036	uc002ffu.3	Q9NRP2	OTTHUMG00000137625	ENST00000219400.3:c.157G>A	16.37:g.81010073C>T	ENSP00000219400:p.Val53Ile	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_020188	D3DUK6	Missense_Mutation	SNP	ENST00000219400.3	37	CCDS10930.1	882	0.40384615384615385	327	0.6646341463414634	132	0.36464088397790057	251	0.4388111888111888	172	0.22691292875989447	T	2.211	-0.380614	0.05000	0.575125	0.214767	ENSG00000103121	ENST00000219400	T	0.42131	0.98	4.68	-4.67	0.03319	.	1.480890	0.03549	N	0.225217	T	0.00012	0.0000	.	.	.	0.50313	P	1.32000000000021E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.39722	-0.9600	8	0.28530	T	0.3	.	4.4894	0.11806	0.1311:0.5137:0.1334:0.2218	rs9304	53	Q9NRP2	CP061_HUMAN	I	53	ENSP00000219400:V53I	ENSP00000219400:V53I	V	-	1	0	C16orf61	79567574	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.722000	0.04958	-1.468000	0.01892	-0.321000	0.08615	GTA	.	.	weak		0.343	CMC2-001	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269047.1	NM_020188	
MYBPC1	4604	hgsc.bcm.edu	37	12	102045163	102045163	+	Missense_Mutation	SNP	C	C	G	rs3817552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:102045163C>G	ENST00000550270.1	+	14	1443	c.1443C>G	c.(1441-1443)caC>caG	p.H481Q	MYBPC1_ENST00000547405.1_Missense_Mutation_p.H455Q|MYBPC1_ENST00000361466.2_Missense_Mutation_p.H506Q|MYBPC1_ENST00000392934.3_Missense_Mutation_p.H468Q|MYBPC1_ENST00000547509.1_Missense_Mutation_p.H467Q|MYBPC1_ENST00000550501.1_Intron|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000452455.2_Missense_Mutation_p.H481Q|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000441232.1_Missense_Mutation_p.H481Q|MYBPC1_ENST00000360610.2_Missense_Mutation_p.H481Q|MYBPC1_ENST00000361685.2_Missense_Mutation_p.H506Q|MYBPC1_ENST00000536007.1_Missense_Mutation_p.H462Q|MYBPC1_ENST00000541119.1_Missense_Mutation_p.H469Q|MYBPC1_ENST00000545503.2_Missense_Mutation_p.H481Q|MYBPC1_ENST00000551300.1_Missense_Mutation_p.H382Q|MYBPC1_ENST00000553190.1_Missense_Mutation_p.H481Q|MYBPC1_ENST00000549145.1_Missense_Mutation_p.H494Q			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	481	Ig-like C2-type 4.		H -> Q (in dbSNP:rs3817552).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						AGGTGGTTCACAAGGGAAGGT	0.428													C|||	857	0.171126	0.1278	0.0893	5008	,	,		20876	0.2986		0.1501	False		,,,				2504	0.1779				p.H506Q		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C1518G	GRCh37	CM065330	MYBPC1	M	rs3817552	PASS	.	C	GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS	571,3835	253.7+/-259.5	31,509,1663	112.0	115.0	114.0		1518,1518,1443,1443	3.6	1.0	12	dbSNP_107	114	1273,7327	253.7+/-279.3	101,1071,3128	yes	missense,missense,missense,missense	MYBPC1	NM_002465.2,NM_206819.1,NM_206820.1,NM_206821.1	24,24,24,24	132,1580,4791	GG,GC,CC		14.8023,12.9596,14.1781	probably-damaging,probably-damaging,probably-damaging,probably-damaging	506/1172,506/1149,481/1142,481/1124	102045163	1844,11162	2203	4300	6503	SO:0001583	missense	4604	exon16			GGTTCACAAGGGA		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7549	protein-coding gene	gene with protein product		160794	"""myosin-binding protein C, slow-type"""			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.1443C>G	12.37:g.102045163C>G	ENSP00000449702:p.His481Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	385	0.1762820512820513	63	0.12804878048780488	36	0.09944751381215469	167	0.291958041958042	119	0.15699208443271767	C	16.76	3.211904	0.58452	0.129596	0.148023	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.48	3.63	0.41609	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000059	T	0.00012	0.0000	L	0.48986	1.54	0.19575	P	0.9999645718	P;D;D;D;D;D;D;D;D;D;D	0.89917	0.947;1.0;1.0;0.999;0.999;0.976;0.999;0.999;0.997;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.93;0.999;0.998;0.998;0.997;0.949;0.997;0.999;0.986;0.998;0.999	T	0.15206	-1.0445	9	0.87932	D	0	.	5.075	0.14626	0.158:0.6341:0.0:0.2079	rs3817552;rs52790499;rs3817552	462;469;481;481;468;455;481;481;506;506;494	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	Q	455;481;481;481;468;467;506;494;481;506;481;462;469;506;382;481	ENSP00000448175:H455Q;ENSP00000400908:H481Q;ENSP00000388989:H481Q;ENSP00000353822:H481Q;ENSP00000376665:H468Q;ENSP00000447362:H467Q;ENSP00000354845:H506Q;ENSP00000447660:H494Q;ENSP00000447900:H481Q;ENSP00000440034:H481Q;ENSP00000446128:H462Q;ENSP00000442847:H469Q;ENSP00000354849:H506Q;ENSP00000447116:H382Q;ENSP00000449702:H481Q	ENSP00000353822:H481Q	H	+	3	2	MYBPC1	100569294	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	2.317000	0.43770	1.289000	0.44618	0.655000	0.94253	CAC	C|0.844;G|0.156	0.156	strong		0.428	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
OR2M7	391196	hgsc.bcm.edu	37	1	248487016	248487016	+	Silent	SNP	C	C	T	rs4451579	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248487016C>T	ENST00000317965.2	-	1	883	c.855G>A	c.(853-855)ctG>ctA	p.L285L		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	285						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGAGAGGATTCAGCATGGGAG	0.433													.|||	1070	0.213658	0.0091	0.245	5008	,	,		19077	0.3641		0.172	False		,,,				2504	0.3558				p.L285L		Atlas-SNP	.											.	OR2M7	84	.	0			c.G855A						PASS	.	C		194,4212	120.8+/-158.4	4,186,2013	100.0	93.0	96.0		855	-1.1	0.7	1	dbSNP_111	96	1451,7149	277.8+/-293.0	125,1201,2974	no	coding-synonymous	OR2M7	NM_001004691.1		129,1387,4987	TT,TC,CC		16.8721,4.4031,12.648		285/313	248487016	1645,11361	2203	4300	6503	SO:0001819	synonymous_variant	391196	exon1			AGGATTCAGCATG	BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"""GPCR / Class A : Olfactory receptors"""	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.855G>A	1.37:g.248487016C>T		Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	295	146	0.494915	NM_001004691	B2RNL0|Q6IEX6	Silent	SNP	ENST00000317965.2	37	CCDS31111.1																																																																																			C|0.847;T|0.153	0.153	strong		0.433	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691	
ACACB	32	hgsc.bcm.edu	37	12	109665242	109665242	+	Missense_Mutation	SNP	G	G	A	rs60293430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109665242G>A	ENST00000338432.7	+	28	4068	c.3949G>A	c.(3949-3951)Ggc>Agc	p.G1317S	ACACB_ENST00000377854.5_Missense_Mutation_p.G1247S|ACACB_ENST00000377848.3_Missense_Mutation_p.G1317S			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1317					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GCTCCCGGACGGCACCTGCGT	0.577													G|||	259	0.0517173	0.1074	0.0548	5008	,	,		17197	0.002		0.0586	False		,,,				2504	0.0184				p.G1317S		Atlas-SNP	.											.	ACACB	330	.	0			c.G3949A						PASS	.	G	SER/GLY	456,3950	214.8+/-234.0	23,410,1770	53.0	45.0	47.0		3949	5.4	1.0	12	dbSNP_129	47	522,8078	144.3+/-200.2	19,484,3797	yes	missense	ACACB	NM_001093.3	56	42,894,5567	AA,AG,GG		6.0698,10.3495,7.5196	benign	1317/2459	109665242	978,12028	2203	4300	6503	SO:0001583	missense	32	exon27			CCGGACGGCACCT	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.3949G>A	12.37:g.109665242G>A	ENSP00000341044:p.Gly1317Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	105	0.04807692307692308	45	0.09146341463414634	22	0.06077348066298342	0	0.0	38	0.05013192612137203	G	16.13	3.034855	0.54896	0.103495	0.060698	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.44881	0.91;0.91;0.91	5.38	5.38	0.77491	Acetyl-CoA carboxylase, central domain (1);	0.053759	0.85682	D	0.000000	T	0.02342	0.0072	L	0.55213	1.73	0.09310	P	1.0	D	0.65815	0.995	P	0.62813	0.907	T	0.04128	-1.0975	9	0.17832	T	0.49	.	14.364	0.66792	0.0:0.0:0.852:0.148	rs60293430;rs61752506	1317	O00763	ACACB_HUMAN	S	1317;1317;1247;548	ENSP00000341044:G1317S;ENSP00000367079:G1317S;ENSP00000367085:G1247S	ENSP00000341044:G1317S	G	+	1	0	ACACB	108149625	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	4.727000	0.61993	2.679000	0.91253	0.655000	0.94253	GGC	G|0.932;A|0.068	0.068	strong		0.577	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
IGFN1	91156	hgsc.bcm.edu	37	1	201195119	201195119	+	Missense_Mutation	SNP	C	C	T	rs3738270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201195119C>T	ENST00000335211.4	+	22	10784	c.10654C>T	c.(10654-10656)Cac>Tac	p.H3552Y	RP11-567E21.3_ENST00000453155.1_RNA|IGFN1_ENST00000295591.8_3'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1095						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CGACCGCATCCACACCAACCG	0.657													C|||	2843	0.567692	0.1989	0.5893	5008	,	,		17777	0.8313		0.7038	False		,,,				2504	0.6391				p.H3552Y		Atlas-SNP	.											IGFN1_ENST00000335211,caecum,carcinoma,0,6	IGFN1	220	6	0			c.C10654T						PASS	.	C	TYR/HIS	1280,3126	433.7+/-343.7	181,918,1104	87.0	67.0	74.0		10654	3.1	1.0	1	dbSNP_107	74	5752,2848	672.2+/-402.9	1914,1924,462	yes	missense	IGFN1	NM_001164586.1	83	2095,2842,1566	TT,TC,CC		33.1163,29.0513,45.9326	benign	3552/3709	201195119	7032,5974	2203	4300	6503	SO:0001583	missense	91156	exon22			CGCATCCACACCA	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.10654C>T	1.37:g.201195119C>T	ENSP00000334714:p.His3552Tyr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	142	81	0.570423	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	1336|1336	0.6117216117216118|0.6117216117216118	107|107	0.21747967479674796|0.21747967479674796	220|220	0.6077348066298343|0.6077348066298343	472|472	0.8251748251748252|0.8251748251748252	537|537	0.7084432717678101|0.7084432717678101	C|C	0.236|0.236	-1.017435|-1.017435	0.02078|0.02078	0.290513|0.290513	0.668837|0.668837	ENSG00000163395|ENSG00000163395	ENST00000335211|ENST00000412892	T|.	0.57436|.	0.4|.	5.0|5.0	3.09|3.09	0.35607|0.35607	.|.	0.331149|.	0.33199|.	N|.	0.005165|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	P|P	0.9999999999098946|0.9999999999098946	B|.	0.22851|.	0.076|.	B|.	0.30029|.	0.11|.	T|T	0.18650|0.18650	-1.0330|-1.0330	9|4	0.42905|.	T|.	0.14|.	.|.	6.5506|6.5506	0.22431|0.22431	0.0:0.6864:0.0:0.3136|0.0:0.6864:0.0:0.3136	rs3738270;rs17424416;rs52823855;rs61528795;rs3738270|rs3738270;rs17424416;rs52823855;rs61528795;rs3738270	3552|.	F8WAI1|.	.|.	Y|L	3552|969	ENSP00000334714:H3552Y|.	ENSP00000334714:H3552Y|.	H|P	+|+	1|2	0|0	IGFN1|IGFN1	199461742|199461742	1.000000|1.000000	0.71417|0.71417	0.971000|0.971000	0.41717|0.41717	0.516000|0.516000	0.34256|0.34256	2.889000|2.889000	0.48601|0.48601	1.344000|1.344000	0.45657|0.45657	-0.258000|-0.258000	0.10820|0.10820	CAC|CCA	C|0.435;T|0.565	0.565	strong		0.657	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
RPAP1	26015	hgsc.bcm.edu	37	15	41813279	41813279	+	Silent	SNP	C	C	T	rs3743031	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41813279C>T	ENST00000304330.4	-	22	3221	c.3105G>A	c.(3103-3105)agG>agA	p.R1035R	RPAP1_ENST00000561603.1_Intron	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	1035	Leu-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		ACCGAGGGACCCTGCTGCTTC	0.602													C|||	1495	0.298522	0.1256	0.3285	5008	,	,		17963	0.2758		0.4324	False		,,,				2504	0.3967				p.R1035R		Atlas-SNP	.											RPAP1,NS,carcinoma,0,1	RPAP1	111	1	0			c.G3105A						PASS	.	C		794,3612		79,636,1488	45.0	49.0	47.0		3105	3.9	0.0	15	dbSNP_107	47	3684,4914		816,2052,1431	no	coding-synonymous	RPAP1	NM_015540.2		895,2688,2919	TT,TC,CC		42.8472,18.0209,34.4356		1035/1394	41813279	4478,8526	2203	4299	6502	SO:0001819	synonymous_variant	26015	exon22			AGGGACCCTGCTG	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.3105G>A	15.37:g.41813279C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	176	65	0.369318	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	37	CCDS10079.1																																																																																			C|0.680;T|0.320	0.320	strong		0.602	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
NPHP4	261734	hgsc.bcm.edu	37	1	5937168	5937168	+	Silent	SNP	G	G	A	rs3747992	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:5937168G>A	ENST00000378156.4	-	20	3067	c.2802C>T	c.(2800-2802)cgC>cgT	p.R934R	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	934					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CGCTCGTCCCGCGCCGGCCCA	0.637													G|||	2271	0.453474	0.2859	0.4597	5008	,	,		16650	0.7341		0.4225	False		,,,				2504	0.4182				p.R934R		Atlas-SNP	.											NPHP4,NS,carcinoma,0,2	NPHP4	119	2	0			c.C2802T						PASS	.	G		1224,2996		180,864,1066	14.0	18.0	17.0		2802	-0.8	0.0	1	dbSNP_107	17	3227,5183		649,1929,1627	no	coding-synonymous	NPHP4	NM_015102.3		829,2793,2693	AA,AG,GG		38.371,29.0047,35.2415		934/1427	5937168	4451,8179	2110	4205	6315	SO:0001819	synonymous_variant	261734	exon20			CGTCCCGCGCCGG	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2802C>T	1.37:g.5937168G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	186	81	0.435484	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			G|0.536;A|0.464	0.464	strong		0.637	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
SPTB	6710	hgsc.bcm.edu	37	14	65253749	65253749	+	Silent	SNP	C	C	T	rs72724498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:65253749C>T	ENST00000389721.5	-	15	2966	c.2934G>A	c.(2932-2934)gaG>gaA	p.E978E	SPTB_ENST00000556626.1_Silent_p.E978E|SPTB_ENST00000542895.1_Silent_p.E978E|SPTB_ENST00000389720.3_Silent_p.E978E|SPTB_ENST00000389722.3_Silent_p.E978E	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	978					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CTTTTGTGGACTCCACTACCT	0.612													c|||	31	0.0061901	0.0023	0.0115	5008	,	,		18897	0.0		0.0199	False		,,,				2504	0.0				p.E978E		Atlas-SNP	.											.	SPTB	378	.	0			c.G2934A						PASS	.		,	19,4387	26.2+/-53.5	0,19,2184	84.0	79.0	81.0		2934,2934	5.1	1.0	14	dbSNP_130	81	194,8406	85.8+/-148.2	0,194,4106	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	0,213,6290	TT,TC,CC		2.2558,0.4312,1.6377	,	978/2138,978/2329	65253749	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon15			TGTGGACTCCACT		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.2934G>A	14.37:g.65253749C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			C|0.988;T|0.012	0.012	strong		0.612	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
MTBP	27085	hgsc.bcm.edu	37	8	121463425	121463425	+	Silent	SNP	T	T	C	rs61753755	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:121463425T>C	ENST00000305949.1	+	4	333	c.288T>C	c.(286-288)gaT>gaC	p.D96D		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	96					cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			GTAGTTCTGATTGGCAAGAGA	0.269													T|||	189	0.0377396	0.0847	0.0144	5008	,	,		15992	0.0		0.0288	False		,,,				2504	0.0389				p.D96D		Atlas-SNP	.											.	MTBP	77	.	0			c.T288C						PASS	.	T		360,4046	178.0+/-206.8	12,336,1855	60.0	61.0	61.0		288	-0.1	1.0	8	dbSNP_129	61	181,8409	80.9+/-143.5	2,177,4116	no	coding-synonymous	MTBP	NM_022045.3		14,513,5971	CC,CT,TT		2.1071,8.1707,4.1628		96/905	121463425	541,12455	2203	4295	6498	SO:0001819	synonymous_variant	27085	exon4			TTCTGATTGGCAA		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"""MDM2 (mouse double minute 2)-binding protein, 104kD"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"""			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.288T>C	8.37:g.121463425T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_022045	B4DUR5|Q9HA89	Silent	SNP	ENST00000305949.1	37	CCDS6333.1																																																																																			T|0.966;C|0.034	0.034	strong		0.269	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045	
NYAP1	222950	hgsc.bcm.edu	37	7	100086246	100086246	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100086246G>A	ENST00000300179.2	+	4	1061	c.902G>A	c.(901-903)cGc>cAc	p.R301H	NYAP1_ENST00000423930.1_Missense_Mutation_p.R301H|NYAP1_ENST00000454988.1_Missense_Mutation_p.R244H	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	301	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CATGCCCACCGCCGCCCAGCT	0.692																																					p.R301H		Atlas-SNP	.											.	.	.	.	0			c.G902A						PASS	.						46.0	49.0	48.0					7																	100086246		2203	4296	6499	SO:0001583	missense	222950	exon4			CCCACCGCCGCCC	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"""chromosome 7 open reading frame 51"", ""KIAA1486-like"""	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.902G>A	7.37:g.100086246G>A	ENSP00000300179:p.Arg301His	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	91	13	0.142857	NM_173564	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	37	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	G	7.182	0.589872	0.13812	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.32988	1.43;1.43;1.45	4.9	4.02	0.46733	.	0.133388	0.34802	N	0.003671	T	0.21921	0.0528	L	0.34521	1.04	0.43719	D	0.996195	P;P	0.40834	0.68;0.73	B;B	0.38500	0.214;0.275	T	0.02371	-1.1169	10	0.33940	T	0.23	-13.797	9.197	0.37235	0.1022:0.0:0.8978:0.0	.	244;301	C9JS30;Q6ZVC0	.;CG051_HUMAN	H	301;301;244	ENSP00000300179:R301H;ENSP00000411861:R301H;ENSP00000394424:R244H	ENSP00000300179:R301H	R	+	2	0	C7orf51	99924182	0.929000	0.31497	0.990000	0.47175	0.190000	0.23558	1.581000	0.36558	1.055000	0.40461	0.407000	0.27541	CGC	.	.	none		0.692	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564	
TLE3	7090	hgsc.bcm.edu	37	15	70346923	70346923	+	Silent	SNP	C	C	T	rs2228178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:70346923C>T	ENST00000558939.1	-	16	3066	c.1689G>A	c.(1687-1689)tcG>tcA	p.S563S	TLE3_ENST00000560589.1_Silent_p.S507S|TLE3_ENST00000539550.1_Silent_p.S490S|TLE3_ENST00000559191.1_Silent_p.S144S|TLE3_ENST00000557997.1_Silent_p.S555S|TLE3_ENST00000559048.1_Silent_p.S563S|TLE3_ENST00000557907.1_Silent_p.S555S|TLE3_ENST00000442299.2_Silent_p.S555S|TLE3_ENST00000451782.2_Silent_p.S560S|TLE3_ENST00000558379.1_Silent_p.S558S|TLE3_ENST00000440567.3_Silent_p.S553S|TLE3_ENST00000559929.1_Silent_p.S573S|TLE3_ENST00000558201.1_Silent_p.S569S|TLE3_ENST00000560939.1_Silent_p.S565S|TLE3_ENST00000317509.8_Silent_p.S551S	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	563					Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GGGGCGTGGGCGAGGCCAGGT	0.657													C|||	1816	0.36262	0.2284	0.4726	5008	,	,		18079	0.255		0.4781	False		,,,				2504	0.4581				p.S563S		Atlas-SNP	.											TLE3,bladder,carcinoma,-1,1	TLE3	104	1	0			c.G1689A						PASS	.	C	,,	1199,3183		179,841,1171	30.0	35.0	33.0		1680,1689,1653	-9.1	0.7	15	dbSNP_98	33	4037,4549		969,2099,1225	no	coding-synonymous,coding-synonymous,coding-synonymous	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	,,	1148,2940,2396	TT,TC,CC		47.0184,27.3619,40.3763	,,	560/770,563/773,551/761	70346923	5236,7732	2191	4293	6484	SO:0001819	synonymous_variant	7090	exon16			CGTGGGCGAGGCC	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.1689G>A	15.37:g.70346923C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Silent	SNP	ENST00000558939.1	37	CCDS45293.1																																																																																			C|0.629;T|0.371	0.371	strong		0.657	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
STX8	9482	hgsc.bcm.edu	37	17	9471711	9471711	+	Silent	SNP	T	T	G	rs1133295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:9471711T>G	ENST00000306357.4	-	2	521	c.94A>C	c.(94-96)Aga>Cga	p.R32R	STX8_ENST00000573373.1_5'UTR|STX8_ENST00000574431.1_Intron	NM_004853.2	NP_004844.1	Q9UNK0	STX8_HUMAN	syntaxin 8	32					endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|transport (GO:0006810)|vesicle fusion (GO:0006906)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(1)	12						TCACCTTTTCTTTCATATTGA	0.373													T|||	3406	0.680112	0.2806	0.8372	5008	,	,		19476	0.9891		0.8002	False		,,,				2504	0.6667				p.R32R		Atlas-SNP	.											.	STX8	28	.	0			c.A94C						PASS	.	T		1581,2825	489.7+/-361.6	293,995,915	189.0	142.0	158.0		94	3.2	1.0	17	dbSNP_86	158	6731,1869	726.6+/-406.6	2635,1461,204	no	coding-synonymous	STX8	NM_004853.2		2928,2456,1119	GG,GT,TT		21.7326,35.8829,36.091		32/237	9471711	8312,4694	2203	4300	6503	SO:0001819	synonymous_variant	9482	exon2			CTTTTCTTTCATA	AF115323	CCDS32565.1	17p13.1	2012-05-25			ENSG00000170310	ENSG00000170310			11443	protein-coding gene	gene with protein product		604203				9852078, 10198254	Standard	NM_004853		Approved	CARB	uc002glx.3	Q9UNK0	OTTHUMG00000177844	ENST00000306357.4:c.94A>C	17.37:g.9471711T>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	131	63	0.480916	NM_004853	O60712|Q53XT8	Silent	SNP	ENST00000306357.4	37	CCDS32565.1																																																																																			T|0.339;G|0.661	0.661	strong		0.373	STX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439206.3	NM_004853	
C10orf90	118611	hgsc.bcm.edu	37	10	128193400	128193400	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:128193400C>T	ENST00000284694.7	-	3	489	c.369G>A	c.(367-369)ccG>ccA	p.P123P	C10orf90_ENST00000544758.1_Silent_p.P220P|C10orf90_ENST00000392694.1_Silent_p.P76P|C10orf90_ENST00000454341.1_Silent_p.P123P|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000356858.3_Silent_p.P76P	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	123	Required for interaction with HDAC1. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		CCTCTTTGGGCGGCAGCTCTG	0.647											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P123P		Atlas-SNP	.											C10orf90,colon,carcinoma,0,1	C10orf90	121	1	0			c.G369A						scavenged	.																																			SO:0001819	synonymous_variant	118611	exon3			TTTGGGCGGCAGC	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.369G>A	10.37:g.128193400C>T		Somatic	115	0	0	1563	WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	37	CCDS31310.1																																																																																			.	.	none		0.647	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
GLYATL3	389396	hgsc.bcm.edu	37	6	49479750	49479750	+	Missense_Mutation	SNP	T	T	C	rs13193063	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:49479750T>C	ENST00000371197.4	+	2	160	c.47T>C	c.(46-48)aTg>aCg	p.M16T		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	16						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.M16T(1)		NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						CTGGAGAAAATGTTGAAGAGT	0.318													T|||	912	0.182109	0.0537	0.1931	5008	,	,		11526	0.2044		0.333	False		,,,				2504	0.1697				p.M16T		Atlas-SNP	.											GLYATL3,NS,carcinoma,0,1	GLYATL3	19	1	1	Substitution - Missense(1)	kidney(1)	c.T47C						PASS	.						237.0	204.0	214.0					6																	49479750		692	1591	2283	SO:0001583	missense	389396	exon2			AGAAAATGTTGAA		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.47T>C	6.37:g.49479750T>C	ENSP00000360240:p.Met16Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	438	0.20054945054945056	29	0.05894308943089431	73	0.20165745856353592	94	0.16433566433566432	242	0.31926121372031663	T	11.00	1.509980	0.27036	.	.	ENSG00000203972	ENST00000371197;ENST00000545705	T;T	0.13538	2.58;2.58	5.8	5.8	0.92144	Glycine N-acyltransferase, N-terminal (1);	0.349316	0.32970	N	0.005433	T	0.06142	0.0159	L	0.48986	1.54	0.36788	P	0.11531100000000005	B	0.31459	0.324	B	0.31390	0.129	T	0.25467	-1.0131	9	0.19590	T	0.45	-1.7855	12.5278	0.56096	0.0:0.0:0.0:1.0	rs13193063;rs17663633;rs13193063	16	Q5SZD4	GLYL3_HUMAN	T	16	ENSP00000360240:M16T;ENSP00000440029:M16T	ENSP00000360240:M16T	M	+	2	0	GLYATL3	49587709	0.923000	0.31300	0.746000	0.31095	0.992000	0.81027	1.779000	0.38624	2.215000	0.71742	0.472000	0.43445	ATG	C|0.179;N|0.000	0.179	strong		0.318	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
B3GNT3	10331	hgsc.bcm.edu	37	19	17922666	17922666	+	Missense_Mutation	SNP	G	G	A	rs77134098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17922666G>A	ENST00000318683.6	+	3	1001	c.854G>A	c.(853-855)cGt>cAt	p.R285H	B3GNT3_ENST00000595387.1_Missense_Mutation_p.R285H	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	285					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)|galactosyltransferase activity (GO:0008378)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						GCCCTGCGCCGTGCTGCCCAT	0.597													G|||	55	0.0109824	0.0076	0.0173	5008	,	,		19507	0.001		0.0278	False		,,,				2504	0.0041				p.R285H		Atlas-SNP	.											B3GNT3,extremity,malignant_melanoma,+1,1	B3GNT3	40	1	0			c.G854A						PASS	.	G	HIS/ARG	64,4342	59.9+/-96.7	2,60,2141	109.0	94.0	100.0		854	5.2	0.7	19	dbSNP_131	100	169,8431	78.6+/-141.3	1,167,4132	yes	missense	B3GNT3	NM_014256.3	29	3,227,6273	AA,AG,GG		1.9651,1.4526,1.7915	benign	285/373	17922666	233,12773	2203	4300	6503	SO:0001583	missense	10331	exon3			TGCGCCGTGCTGC	AB015630	CCDS12364.1	19p13.1	2013-02-19				ENSG00000179913		"""Beta 3-glycosyltransferases"""	13528	protein-coding gene	gene with protein product	"""putative type II membrane protein"", ""beta-1,3-N-acetylglucosaminyltransferase bGnT-3"", ""transmembrane protein 3"""	605863		TMEM3		10072769, 11042166	Standard	NM_014256		Approved	B3GN-T3, beta3Gn-T3, HP10328, B3GNT-3	uc002nhl.1	Q9Y2A9		ENST00000318683.6:c.854G>A	19.37:g.17922666G>A	ENSP00000321874:p.Arg285His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_014256	B2RAS4|Q6NWU9|Q6NXU9|Q8WWR6|Q9C0J2	Missense_Mutation	SNP	ENST00000318683.6	37	CCDS12364.1	35	0.016025641025641024	5	0.01016260162601626	9	0.024861878453038673	1	0.0017482517482517483	20	0.026385224274406333	G	6.204	0.405851	0.11754	0.014526	0.019651	ENSG00000179913	ENST00000318683	T	0.42900	0.96	5.23	5.23	0.72850	.	0.280431	0.32719	N	0.005724	T	0.15349	0.0370	L	0.53729	1.69	0.36827	D	0.886692	B	0.18166	0.026	B	0.16722	0.016	T	0.18745	-1.0327	10	0.30854	T	0.27	.	9.8407	0.40998	0.0942:0.0:0.9058:0.0	.	285	Q9Y2A9	B3GN3_HUMAN	H	285	ENSP00000321874:R285H	ENSP00000321874:R285H	R	+	2	0	B3GNT3	17783666	0.000000	0.05858	0.656000	0.29637	0.011000	0.07611	0.363000	0.20301	2.452000	0.82932	0.561000	0.74099	CGT	G|0.983;A|0.017	0.017	strong		0.597	B3GNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466877.1	NM_014256	
CDKL1	8814	hgsc.bcm.edu	37	14	50799126	50799126	+	Missense_Mutation	SNP	G	G	C	rs7161563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50799126G>C	ENST00000395834.1	-	8	850	c.823C>G	c.(823-825)Caa>Gaa	p.Q275E	ATP5S_ENST00000358473.1_Intron|CDKL1_ENST00000216378.2_3'UTR	NM_004196.3	NP_004187.2	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				heart development (GO:0007507)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.Q275E(1)		endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12	all_epithelial(31;0.000746)|Breast(41;0.0102)					GTCAGCCTTTGAGTAGGGTCC	0.353													C|||	2914	0.581869	0.5961	0.5908	5008	,	,		20516	0.6181		0.5606	False		,,,				2504	0.5409				p.Q275E		Atlas-SNP	.											CDKL1_ENST00000395834,NS,adenoma,0,2	CDKL1	50	2	1	Substitution - Missense(1)	stomach(1)	c.C823G						PASS	.	C	GLU/GLN	2566,1840	535.9+/-374.3	754,1058,391	140.0	133.0	136.0		823	4.2	0.9	14	dbSNP_116	136	4865,3735	532.2+/-382.1	1390,2085,825	yes	missense	CDKL1	NM_004196.3	29	2144,3143,1216	CC,CG,GG		43.4302,41.7612,42.8648		275/359	50799126	7431,5575	2203	4300	6503	SO:0001583	missense	8814	exon8			GCCTTTGAGTAGG	AF390028	CCDS9699.1, CCDS73637.1	14q21.3	2011-11-04			ENSG00000100490	ENSG00000100490		"""Cyclin-dependent kinases"""	1781	protein-coding gene	gene with protein product		603441				1639063, 7595554	Standard	XM_005268157		Approved	KKIALRE	uc010anu.2	Q00532	OTTHUMG00000140290	ENST00000395834.1:c.823C>G	14.37:g.50799126G>C	ENSP00000379176:p.Gln275Glu	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	225	111	0.493333	NM_004196	Q2M3A4|Q6QUA0|Q8WXQ5	Missense_Mutation	SNP	ENST00000395834.1	37	CCDS9699.1	1259|1259	0.5764652014652014|0.5764652014652014	284|284	0.5772357723577236|0.5772357723577236	205|205	0.5662983425414365|0.5662983425414365	345|345	0.6031468531468531|0.6031468531468531	425|425	0.5606860158311345|0.5606860158311345	C|C	0.191|0.191	-1.053298|-1.053298	0.01965|0.01965	0.582388|0.582388	0.565698|0.565698	ENSG00000100490|ENSG00000100490	ENST00000395834|ENST00000534267	T|.	0.64260|.	-0.09|.	6.06|6.06	4.21|4.21	0.49690|0.49690	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	P|P	0.9999999999999891|0.9999999999999891	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|.	0.44667|.	-0.9313|.	8|.	0.12766|.	T|.	0.61|.	.|.	8.3926|8.3926	0.32537|0.32537	0.0:0.6359:0.2378:0.1263|0.0:0.6359:0.2378:0.1263	rs7161563;rs17122413;rs7161563|rs7161563;rs17122413;rs7161563	274|.	Q00532|.	CDKL1_HUMAN|.	E|X	275|88	ENSP00000379176:Q275E|.	ENSP00000379176:Q275E|.	Q|S	-|-	1|2	0|0	CDKL1|CDKL1	49868876|49868876	0.870000|0.870000	0.30015|0.30015	0.940000|0.940000	0.37924|0.37924	0.185000|0.185000	0.23345|0.23345	1.719000|1.719000	0.38011|0.38011	0.880000|0.880000	0.35969|0.35969	-0.120000|-0.120000	0.15030|0.15030	CAA|TCA	G|0.424;C|0.576	0.576	strong		0.353	CDKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276872.2		
LMX1B	4010	hgsc.bcm.edu	37	9	129453229	129453229	+	Silent	SNP	A	A	G	rs2277158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:129453229A>G	ENST00000373474.4	+	3	448	c.441A>G	c.(439-441)gaA>gaG	p.E147E	LMX1B_ENST00000561065.1_Silent_p.E124E|LMX1B_ENST00000355497.5_Silent_p.E147E|LMX1B_ENST00000526117.1_Silent_p.E147E|LMX1B_ENST00000425646.2_Silent_p.E124E			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	147	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						GCGTGTGTGAACGGCAGCTAC	0.627									Nail-Patella Syndrome				G|||	2404	0.480032	0.5454	0.4092	5008	,	,		21001	0.5585		0.4394	False		,,,				2504	0.4029				p.E147E	Pancreas(110;1796 2278 18357 20466)	Atlas-SNP	.											.	LMX1B	86	.	0			c.A441G						PASS	.	G	,,	2312,2094	570.5+/-382.9	612,1088,503	82.0	63.0	70.0		441,441,441	3.1	1.0	9	dbSNP_100	70	3704,4896	618.9+/-396.8	801,2102,1397	no	coding-synonymous,coding-synonymous,coding-synonymous	LMX1B	NM_001174146.1,NM_001174147.1,NM_002316.3	,,	1413,3190,1900	GG,GA,AA		43.0698,47.5261,46.2556	,,	147/407,147/403,147/396	129453229	6016,6990	2203	4300	6503	SO:0001819	synonymous_variant	4010	exon3	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	GTGTGAACGGCAG	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"""Homeoboxes / LIM class"""	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.441A>G	9.37:g.129453229A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001174146	F8W7W6|O75463|Q5JU95|Q6ISC9	Silent	SNP	ENST00000373474.4	37	CCDS55342.1																																																																																			A|0.530;G|0.470	0.470	strong		0.627	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2		
KLC3	147700	hgsc.bcm.edu	37	19	45849909	45849909	+	Silent	SNP	A	A	G	rs9749618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45849909A>G	ENST00000391946.2	+	3	468	c.366A>G	c.(364-366)gaA>gaG	p.E122E	KLC3_ENST00000470402.1_Silent_p.E136E|KLC3_ENST00000585434.1_Silent_p.E122E	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	122					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TGCGGGAGGAACTGGAGGAGA	0.701													A|||	983	0.196286	0.0809	0.1873	5008	,	,		11388	0.0873		0.334	False		,,,				2504	0.3292				p.E122E		Atlas-SNP	.											KLC3,colon,carcinoma,0,1	KLC3	37	1	0			c.A366G						PASS	.	A		444,3498		44,356,1571	5.0	7.0	6.0		366	1.9	1.0	19	dbSNP_119	6	2326,5724		403,1520,2102	no	coding-synonymous	KLC3	NM_177417.2		447,1876,3673	GG,GA,AA		28.8944,11.2633,23.0987		122/505	45849909	2770,9222	1971	4025	5996	SO:0001819	synonymous_variant	147700	exon3			GGAGGAACTGGAG	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.366A>G	19.37:g.45849909A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	34	11	0.323529	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Silent	SNP	ENST00000391946.2	37	CCDS12660.2																																																																																			A|0.790;G|0.210	0.210	strong		0.701	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
ZNF805	390980	hgsc.bcm.edu	37	19	57760018	57760018	+	Missense_Mutation	SNP	G	G	A	rs2014572	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57760018G>A	ENST00000414468.2	+	3	203	c.203G>A	c.(202-204)gGg>gAg	p.G68E	ZNF805_ENST00000354309.4_5'UTR|ZNF805_ENST00000535550.1_5'UTR	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	68	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		G -> E (in dbSNP:rs2014572).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(3)|lung(1)|stomach(1)	9						CTAGAGCATGGGCAGGAGCCA	0.542													.|||	1845	0.368411	0.2481	0.4496	5008	,	,		20344	0.1815		0.5746	False		,,,				2504	0.454				p.G68E		Atlas-SNP	.											.	ZNF805	30	.	0			c.G203A						PASS	.	A	GLU/GLY,	382,1002		52,278,362	70.0	63.0	65.0	http://www.ncbi.nlm.nih.gov/pubmed?term	203,	0.0	0.0	19	dbSNP_92	65	1648,1534		430,788,373	yes	missense,utr-5	ZNF805	NM_001023563.3,NM_001145078.1	98,	482,1066,735	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	48.2087,27.6012,44.459	benign,	68/628,	57760018	2030,2536	692	1591	2283	SO:0001583	missense	390980	exon3			AGCATGGGCAGGA	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.203G>A	19.37:g.57760018G>A	ENSP00000412999:p.Gly68Glu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_001023563	B4DNM5	Missense_Mutation	SNP	ENST00000414468.2	37	CCDS46207.1	852	0.3901098901098901	129	0.2621951219512195	175	0.48342541436464087	115	0.20104895104895104	433	0.5712401055408971	A	11.87	1.767179	0.31320	0.276012	0.517913	ENSG00000204524	ENST00000414468	T	0.00892	5.57	4.67	-0.00356	0.14025	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	L	0.37850	1.14	0.58432	P	1.999999999946489E-6	P	0.39665	0.682	B	0.32864	0.154	T	0.00304	-1.1832	8	0.26408	T	0.33	.	10.9728	0.47448	0.2482:0.0:0.7518:0.0	rs2014572;rs3746232;rs52814311;rs60463144;rs2014572	68	Q5CZA5	ZN805_HUMAN	E	68	ENSP00000412999:G68E	ENSP00000412999:G68E	G	+	2	0	ZNF805	62451830	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.261000	0.18442	-0.048000	0.13401	-1.004000	0.02495	GGG	G|0.625;A|0.375	0.375	strong		0.542	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563	
NQO2	4835	hgsc.bcm.edu	37	6	3015865	3015865	+	Silent	SNP	C	C	T	rs4149367	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:3015865C>T	ENST00000338130.2	+	8	1117	c.405C>T	c.(403-405)tcC>tcT	p.S135S	NQO2_ENST00000380455.4_Silent_p.S135S|NQO2_ENST00000380454.4_Intron|NQO2_ENST00000380441.1_Intron|NQO2_ENST00000380430.1_Silent_p.S135S			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	135					memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	TCTACGATTCCGGTTTGCTCC	0.512													c|||	898	0.179313	0.3608	0.1037	5008	,	,		21076	0.1567		0.0696	False		,,,				2504	0.1237				p.S135S		Atlas-SNP	.											.	NQO2	21	.	0			c.C405T						PASS	.	T		1359,3047	450.6+/-349.4	202,955,1046	99.0	95.0	96.0		405	-5.8	0.0	6	dbSNP_110	96	594,8006	158.2+/-211.7	16,562,3722	no	coding-synonymous	NQO2	NM_000904.3		218,1517,4768	TT,TC,CC		6.907,30.8443,15.0161		135/232	3015865	1953,11053	2203	4300	6503	SO:0001819	synonymous_variant	4835	exon5			CGATTCCGGTTTG	U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"""NAD(P)H menadione oxidoreductase 2, dioxin-inducible"""	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.405C>T	6.37:g.3015865C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_000904	B2R492|Q5TD04	Silent	SNP	ENST00000338130.2	37	CCDS4481.1																																																																																			C|0.841;T|0.159	0.159	strong		0.512	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		
OR5AR1	219493	hgsc.bcm.edu	37	11	56431216	56431216	+	Nonsense_Mutation	SNP	C	C	T	rs11228710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56431216C>T	ENST00000302969.2	+	1	79	c.55C>T	c.(55-57)Cag>Tag	p.Q19*		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						GGGCATCACCCAGGACCCTCA	0.403													C|||	3120	0.623003	0.2716	0.7406	5008	,	,		16067	0.7857		0.6879	False		,,,				2504	0.7802				p.Q19X		Atlas-SNP	.											.	OR5AR1	68	.	0			c.C55T						PASS	.	C	stop/GLN	1487,2915	476.3+/-357.6	256,975,970	205.0	192.0	196.0		55	5.3	1.0	11	dbSNP_120	196	5924,2668	684.6+/-404.0	2045,1834,417	yes	stop-gained	OR5AR1	NM_001004730.1		2301,2809,1387	TT,TC,CC		31.0521,33.7801,42.966		19/311	56431216	7411,5583	2201	4296	6497	SO:0001587	stop_gained	219493	exon1			ATCACCCAGGACC	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"""GPCR / Class A : Olfactory receptors"""	15260	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AR, member 1"""				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.55C>T	11.37:g.56431216C>T	ENSP00000302639:p.Gln19*	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	211	123	0.582938	NM_001004730	Q6IF61	Nonsense_Mutation	SNP	ENST00000302969.2	37	CCDS31535.1	1363	0.6240842490842491	119	0.241869918699187	272	0.7513812154696132	457	0.798951048951049	515	0.679419525065963	C	19.48	3.834831	0.71373	0.337801	0.689479	ENSG00000172459	ENST00000302969	.	.	.	5.33	5.33	0.75918	.	0.000000	0.45126	D	0.000387	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	14.4814	0.67585	0.0:0.8417:0.1583:0.0	rs11228710;rs52820413;rs58540799;rs11228710	.	.	.	X	19	.	ENSP00000302639:Q19X	Q	+	1	0	OR5AR1	56187792	0.005000	0.15991	0.997000	0.53966	0.952000	0.60782	0.906000	0.28517	2.780000	0.95670	0.637000	0.83480	CAG	C|0.411;N|0.000	.	strong		0.403	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730	
OR12D3	81797	hgsc.bcm.edu	37	6	29342825	29342825	+	Silent	SNP	G	G	A	rs3749970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29342825G>A	ENST00000396806.3	-	1	243	c.240C>T	c.(238-240)ctC>ctT	p.L80L	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						CGAGGTTTACGAGCAGCTTGG	0.448													G|||	1437	0.286941	0.0651	0.3646	5008	,	,		19264	0.255		0.494	False		,,,				2504	0.3517				p.L80L		Atlas-SNP	.											OR12D3,NS,carcinoma,0,1	OR12D3	55	1	0			c.C240T						PASS	.	G		394,2624		22,350,1137	58.0	60.0	59.0		240	-8.4	0.0	6	dbSNP_107	59	2592,2826		632,1328,749	no	coding-synonymous	OR12D3	NM_030959.2		654,1678,1886	AA,AG,GG		47.8405,13.055,35.3959		80/317	29342825	2986,5450	1509	2709	4218	SO:0001819	synonymous_variant	81797	exon1			GTTTACGAGCAGC		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"""GPCR / Class A : Olfactory receptors"""	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.240C>T	6.37:g.29342825G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Silent	SNP	ENST00000396806.3	37	CCDS4658.1																																																																																			G|0.667;A|0.333	0.333	strong		0.448	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
FAM136A	84908	hgsc.bcm.edu	37	2	70524577	70524577	+	Silent	SNP	G	G	A	rs2618235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:70524577G>A	ENST00000037869.3	-	3	339	c.261C>T	c.(259-261)aaC>aaT	p.N87N	FAM136A_ENST00000430566.1_Silent_p.N194N|FAM136A_ENST00000450256.1_3'UTR	NM_032822.2	NP_116211.2	Q96C01	F136A_HUMAN	family with sequence similarity 136, member A	87						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						TGGCTTTGTCGTTGCAATGCA	0.512													G|||	1321	0.263778	0.1339	0.2075	5008	,	,		18619	0.3829		0.3141	False		,,,				2504	0.3047				p.N87N		Atlas-SNP	.											FAM136A,right_upper_lobe,carcinoma,-2,1	FAM136A	14	1	0			c.C261T						PASS	.	G		732,3674	301.5+/-286.9	64,604,1535	98.0	91.0	94.0		261	-10.0	0.3	2	dbSNP_100	94	2716,5884	424.1+/-354.6	408,1900,1992	no	coding-synonymous	FAM136A	NM_032822.2		472,2504,3527	AA,AG,GG		31.5814,16.6137,26.5108		87/139	70524577	3448,9558	2203	4300	6503	SO:0001819	synonymous_variant	84908	exon3			TTTGTCGTTGCAA	BC014975	CCDS1904.1	2p14	2014-02-12	2007-07-10		ENSG00000035141	ENSG00000035141			25911	protein-coding gene	gene with protein product	"""hypothetical protein FLJ14668"""					12477932	Standard	NM_032822		Approved	FLJ14668	uc002sgq.4	Q96C01	OTTHUMG00000129668	ENST00000037869.3:c.261C>T	2.37:g.70524577G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	107	39	0.364486	NM_032822	Q96SS3	Silent	SNP	ENST00000037869.3	37	CCDS1904.1																																																																																			G|0.748;A|0.252	0.252	strong		0.512	FAM136A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251869.2	NM_032822	
HLA-A	3105	hgsc.bcm.edu	37	6	29910759	29910759	+	Missense_Mutation	SNP	T	T	C	rs1071742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29910759T>C	ENST00000396634.1	+	4	640	c.299T>C	c.(298-300)gTg>gCg	p.V100A	HLA-A_ENST00000376806.5_Missense_Mutation_p.V100A|HLA-A_ENST00000376809.5_Missense_Mutation_p.V100A|HLA-A_ENST00000376802.2_Missense_Mutation_p.V100A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	100	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ACTGACCGAGTGGACCTGGGG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	774	0.154553	0.1445	0.1225	5008	,	,		10249	0.0704		0.1928	False		,,,				2504	0.2382				p.V100A		Atlas-SNP	.											HLA-A,rectum,carcinoma,0,1	HLA-A	89	1	0			c.T299C						PASS	.	C	ALA/VAL	656,3732		158,340,1696	60.0	64.0	63.0		299	-6.7	0.0	6	dbSNP_86	63	2286,6282		597,1092,2595	yes	missense	HLA-A	NM_002116.7	64	755,1432,4291	CC,CT,TT		26.6807,14.9499,22.7076	benign	100/366	29910759	2942,10014	2194	4284	6478	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ACCGAGTGGACCT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.299T>C	6.37:g.29910759T>C	ENSP00000379873:p.Val100Ala	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	214	77	0.359813	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	5.521	0.280982	0.10458	0.149499	0.266807	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00792	5.69;5.69;5.69;5.69	3.33	-6.67	0.01783	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	15.776400	0.01836	N	0.034989	T	0.00300	0.0009	M	0.67625	2.065	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.09377	0.004;0.003;0.002;0.001;0.004	T	0.46289	-0.9202	9	0.38643	T	0.18	.	0.4643	0.00521	0.2856:0.2905:0.146:0.2778	rs1071742;rs2231002;rs3129019;rs3173422;rs3200152;rs3200155;rs9256981;rs17423971;rs41551313	100;100;100;100;100	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	A	100	ENSP00000379873:V100A;ENSP00000366002:V100A;ENSP00000366005:V100A;ENSP00000365998:V100A	ENSP00000348012:V100A	V	+	2	0	HLA-A	30018738	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.538000	0.00938	-1.834000	0.01193	-3.111000	0.00062	GTG	A|0.129;C|0.082;T|0.790	0.082	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
PIEZO1	9780	hgsc.bcm.edu	37	16	88782079	88782079	+	Silent	SNP	G	G	A	rs1061228	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88782079G>A	ENST00000301015.9	-	51	7746	c.7500C>T	c.(7498-7500)taC>taT	p.Y2500Y	PIEZO1_ENST00000327397.7_Missense_Mutation_p.R356C|MIR4722_ENST00000578292.1_RNA|RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2500					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						TGAGCTTGGCGTACAACTCCT	0.617													G|||	432	0.086262	0.0159	0.1369	5008	,	,		15983	0.126		0.1193	False		,,,				2504	0.0706				p.Y2500Y		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C7500T						PASS	.						73.0	66.0	68.0					16																	88782079		692	1589	2281	SO:0001819	synonymous_variant	9780	exon51			CTTGGCGTACAAC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.7500C>T	16.37:g.88782079G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	246	0.11263736263736264	10	0.02032520325203252	51	0.1408839779005525	94	0.16433566433566432	91	0.12005277044854881	G	10.73	1.432739	0.25813	.	.	ENSG00000103335	ENST00000451779;ENST00000327397	T	0.69926	-0.44	4.74	-2.49	0.06403	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.37292	P	0.091696	B	0.06786	0.001	B	0.04013	0.001	T	0.08700	-1.0709	7	0.87932	D	0	-15.9375	10.3786	0.44096	0.5308:0.0:0.4692:0.0	rs1061228;rs17845148;rs17857952	356	E7EUT2	.	C	2446;356	ENSP00000333704:R356C	ENSP00000333704:R356C	R	-	1	0	FAM38A	87309580	0.994000	0.37717	0.102000	0.21198	0.973000	0.67179	0.261000	0.18442	-0.670000	0.05282	-0.258000	0.10820	CGC	T|0.000;G|0.884;C|0.000;A|0.115	0.115	strong		0.617	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
GPR162	27239	hgsc.bcm.edu	37	12	6935955	6935955	+	Silent	SNP	T	T	C	rs35717080	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6935955T>C	ENST00000311268.3	+	5	2140	c.1353T>C	c.(1351-1353)ggT>ggC	p.G451G	LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000428545.2_Silent_p.G167G|LEPREL2_ENST00000251761.8_RNA|GPR162_ENST00000382315.3_Silent_p.G147G	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	451						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						CCCTCGGGGGTCCTCCTGAGT	0.617													T|||	230	0.0459265	0.0068	0.0519	5008	,	,		15124	0.001		0.1302	False		,,,				2504	0.0542				p.G451G		Atlas-SNP	.											.	GPR162	55	.	0			c.T1353C						PASS	.	T	,	103,4303	76.8+/-115.0	4,95,2104	45.0	54.0	51.0		501,1353	-0.2	0.9	12	dbSNP_126	51	969,7631	208.3+/-249.8	60,849,3391	no	coding-synonymous,coding-synonymous	GPR162	NM_014449.1,NM_019858.1	,	64,944,5495	CC,CT,TT		11.2674,2.3377,8.2423	,	167/305,451/589	6935955	1072,11934	2203	4300	6503	SO:0001819	synonymous_variant	27239	exon5			CGGGGGTCCTCCT	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"""GPCR / Class A : Orphans"""	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.1353T>C	12.37:g.6935955T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_019858	Q16664|Q59EH5|Q66K56	Silent	SNP	ENST00000311268.3	37	CCDS8563.1																																																																																			T|0.912;C|0.088	0.088	strong		0.617	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
SEC14L3	266629	hgsc.bcm.edu	37	22	30857373	30857373	+	Missense_Mutation	SNP	A	A	C	rs2240345	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30857373A>C	ENST00000215812.4	-	11	1095	c.1005T>G	c.(1003-1005)gaT>gaG	p.D335E	SEC14L3_ENST00000415957.2_Missense_Mutation_p.D276E|SEC14L3_ENST00000403066.1_Missense_Mutation_p.D276E|SEC14L3_ENST00000539629.1_Missense_Mutation_p.D276E|SEC14L3_ENST00000540910.1_Missense_Mutation_p.D258E|SEC14L3_ENST00000401751.1_Missense_Mutation_p.D276E|SEC14L3_ENST00000402286.1_Missense_Mutation_p.D258E	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	335	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.		D -> E (in dbSNP:rs2240345). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.D335E(1)		NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	TGGGTAGAACATCTGTCATCT	0.602													C|||	3889	0.776558	0.9009	0.5735	5008	,	,		17898	0.8601		0.6123	False		,,,				2504	0.8354				p.D335E	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											SEC14L3,NS,lymphoid_neoplasm,0,1	SEC14L3	46	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1005G						PASS	.	C	GLU/ASP	3763,643	276.0+/-272.9	1594,575,34	79.0	73.0	75.0		1005	3.5	1.0	22	dbSNP_98	75	5242,3358	499.3+/-375.0	1586,2070,644	yes	missense	SEC14L3	NM_174975.4	45	3180,2645,678	CC,CA,AA		39.0465,14.5937,30.7627	benign	335/401	30857373	9005,4001	2203	4300	6503	SO:0001583	missense	266629	exon11			TAGAACATCTGTC	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.1005T>G	22.37:g.30857373A>C	ENSP00000215812:p.Asp335Glu	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	196	97	0.494898	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	1644	0.7527472527472527	441	0.8963414634146342	239	0.6602209944751382	497	0.8688811188811189	467	0.6160949868073878	C	2.064	-0.414758	0.04766	0.854063	0.609535	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.38240	1.15;1.15;1.15;1.15;1.15;1.15;1.15	5.67	3.55	0.40652	GOLD (2);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00150	-1.985	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37384	-0.9708	9	0.02654	T	1	-30.8806	7.9705	0.30124	0.1292:0.7284:0.0:0.1424	rs2240345;rs17737891;rs57401803;rs2240345	258;335	E9PE57;Q9UDX4	.;S14L3_HUMAN	E	276;276;335;258;276;276;258	ENSP00000385941:D276E;ENSP00000401864:D276E;ENSP00000215812:D335E;ENSP00000385004:D258E;ENSP00000383896:D276E;ENSP00000444691:D276E;ENSP00000439752:D258E	ENSP00000215812:D335E	D	-	3	2	SEC14L3	29187373	0.990000	0.36364	0.952000	0.39060	0.340000	0.28889	0.355000	0.20163	0.322000	0.23283	-0.701000	0.03672	GAT	A|0.265;C|0.735	0.735	strong		0.602	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
ZNF618	114991	hgsc.bcm.edu	37	9	116770776	116770776	+	Silent	SNP	C	C	T	rs3748183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:116770776C>T	ENST00000374126.5	+	9	795	c.696C>T	c.(694-696)gtC>gtT	p.V232V	ZNF618_ENST00000288466.7_Silent_p.V200V			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	232					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						ACCAAGGTGTCGTGGCCACGG	0.657													C|||	1519	0.303315	0.062	0.2565	5008	,	,		17346	0.5962		0.3439	False		,,,				2504	0.319				p.V200V		Atlas-SNP	.											.	ZNF618	184	.	0			c.C600T						PASS	.	C		424,3478		25,374,1552	49.0	57.0	55.0		600	-5.7	0.8	9	dbSNP_107	55	2698,5554		451,1796,1879	no	coding-synonymous	ZNF618	NM_133374.2		476,2170,3431	TT,TC,CC		32.6951,10.8662,25.687		200/862	116770776	3122,9032	1951	4126	6077	SO:0001819	synonymous_variant	114991	exon8			AGGTGTCGTGGCC	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.696C>T	9.37:g.116770776C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				C|0.649;T|0.351	0.351	strong		0.657	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978592	45978592	+	Missense_Mutation	SNP	T	T	C	rs452472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45978592T>C	ENST00000391620.1	-	1	51	c.7A>G	c.(7-9)Acg>Gcg	p.T3A	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	3			T -> A (in dbSNP:rs452472). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						ATGGTAGACGTGGCCATGCTG	0.642													.|||	1067	0.213059	0.1483	0.2594	5008	,	,		17698	0.1964		0.337	False		,,,				2504	0.1575				p.T3A		Atlas-SNP	.											KRTAP10-3,rectum,carcinoma,0,1	KRTAP10-3	17	1	0			c.A7G						PASS	.	T	,ALA/THR	730,3676	732.5+/-410.4	60,610,1533	59.0	59.0	59.0		,7	-3.7	0.0	21	dbSNP_80	59	2840,5760	661.1+/-401.8	475,1890,1935	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,58	535,2500,3468	CC,CT,TT		33.0233,16.5683,27.4489	,benign	,3/222	45978592	3570,9436	2203	4300	6503	SO:0001583	missense	386682	exon1			TAGACGTGGCCAT	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.7A>G	21.37:g.45978592T>C	ENSP00000375478:p.Thr3Ala	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	198	95	0.479798	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	482	0.2206959706959707	65	0.13211382113821138	91	0.2513812154696133	102	0.17832167832167833	224	0.2955145118733509	c	0.001	-2.986087	0.00046	0.165683	0.330233	ENSG00000212935	ENST00000391620	T	0.02863	4.13	3.32	-3.69	0.04450	.	.	.	.	.	T	0.00012	0.0000	N	0.00128	-2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36720	-0.9736	8	0.02654	T	1	.	3.4126	0.07364	0.1224:0.5648:0.1215:0.1914	rs452472	3	P60369	KR103_HUMAN	A	3	ENSP00000375478:T3A	ENSP00000375478:T3A	T	-	1	0	KRTAP10-3	44803020	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.871000	0.04223	-1.132000	0.02907	-2.541000	0.00179	ACG	T|0.735;C|0.265	0.265	strong		0.642	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
NSFL1C	55968	hgsc.bcm.edu	37	20	1426393	1426393	+	Missense_Mutation	SNP	C	C	T	rs9575	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1426393C>T	ENST00000216879.4	-	8	1735	c.868G>A	c.(868-870)Gac>Aac	p.D290N	NSFL1C_ENST00000381658.4_Missense_Mutation_p.D179N|NSFL1C_ENST00000353088.2_Missense_Mutation_p.D259N|NSFL1C_ENST00000350991.4_Missense_Mutation_p.D292N|NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000476071.1_Missense_Mutation_p.D292N	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	290			D -> N (in dbSNP:rs9575). {ECO:0000269|PubMed:11042152}.			chromosome (GO:0005694)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						TCTGATTCGTCGATTAAGATG	0.537													C|||	2336	0.466454	0.2534	0.5115	5008	,	,		19949	0.7887		0.4076	False		,,,				2504	0.4509				p.D290N		Atlas-SNP	.											NSFL1C,colon,carcinoma,+2,2	NSFL1C	38	2	0			c.G868A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	1221,3185	423.4+/-340.1	169,883,1151	200.0	195.0	197.0		874,868,775	-1.4	0.1	20	dbSNP_52	197	3519,5081	514.1+/-378.3	735,2049,1516	yes	missense,missense,missense	NSFL1C	NM_001206736.1,NM_016143.4,NM_018839.4	23,23,23	904,2932,2667	TT,TC,CC		40.9186,27.7122,36.4447	benign,benign,benign	292/373,290/371,259/340	1426393	4740,8266	2203	4300	6503	SO:0001583	missense	55968	exon8			ATTCGTCGATTAA	AF112211	CCDS13015.1, CCDS13016.1, CCDS56175.1	20p13	2011-06-28			ENSG00000088833	ENSG00000088833		"""UBX domain containing"""	15912	protein-coding gene	gene with protein product	"""SHP1 homolog (S. cerevisiae)"", ""UBX domain protein 2C"""	606610				11042152	Standard	NM_016143		Approved	dJ776F14.1, p47, UBXD10, UBX1, UBXN2C	uc002wfc.3	Q9UNZ2	OTTHUMG00000031665	ENST00000216879.4:c.868G>A	20.37:g.1426393C>T	ENSP00000216879:p.Asp290Asn	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	243	102	0.419753	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	37	CCDS13015.1	1054	0.4826007326007326	117	0.23780487804878048	172	0.47513812154696133	439	0.7674825174825175	326	0.43007915567282323	C	15.62	2.888671	0.52014	0.277122	0.409186	ENSG00000088833	ENST00000353088;ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	4.53	-1.35	0.09114	UBX (1);	0.224720	0.44688	N	0.000435	T	0.00012	0.0000	L	0.52759	1.655	0.20403	P	0.9999006895	B;B;B	0.20671	0.027;0.047;0.013	B;B;B	0.17433	0.007;0.017;0.018	T	0.27468	-1.0073	9	0.49607	T	0.09	-3.2202	9.1604	0.37019	0.0:0.65:0.0:0.35	rs9575;rs3171294;rs17719623;rs9575	259;179;290	Q9UNZ2-4;Q9UNZ2-6;Q9UNZ2	.;.;NSF1C_HUMAN	N	259;292;290;179;292	ENSP00000338643:D259N;ENSP00000418529:D292N;ENSP00000216879:D290N;ENSP00000371074:D179N;ENSP00000202584:D292N	ENSP00000216879:D290N	D	-	1	0	NSFL1C	1374393	0.977000	0.34250	0.137000	0.22149	0.916000	0.54674	1.085000	0.30840	-0.271000	0.09272	-0.367000	0.07326	GAC	C|0.589;T|0.411	0.411	strong		0.537	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143	
ARHGAP12	94134	hgsc.bcm.edu	37	10	32141460	32141460	+	Silent	SNP	T	T	C	rs2799021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:32141460T>C	ENST00000344936.2	-	6	1389	c.1155A>G	c.(1153-1155)gaA>gaG	p.E385E	ARHGAP12_ENST00000311380.4_Silent_p.E338E|ARHGAP12_ENST00000375250.5_Silent_p.E385E|ARHGAP12_ENST00000375245.4_Silent_p.E338E|ARHGAP12_ENST00000396144.4_Silent_p.E385E	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	385	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				GCAATTCCCATTCTGACCGAG	0.333													T|||	1161	0.231829	0.0545	0.2954	5008	,	,		15238	0.4127		0.2048	False		,,,				2504	0.2679				p.E385E		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.A1155G						PASS	.	T		371,4035	187.8+/-214.3	16,339,1848	100.0	99.0	99.0		1155	2.1	1.0	10	dbSNP_100	99	1826,6774	327.9+/-318.0	191,1444,2665	no	coding-synonymous	ARHGAP12	NM_018287.5		207,1783,4513	CC,CT,TT		21.2326,8.4203,16.8922		385/847	32141460	2197,10809	2203	4300	6503	SO:0001819	synonymous_variant	94134	exon6			TTCCCATTCTGAC	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1155A>G	10.37:g.32141460T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	154	71	0.461039	NM_001270696	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Silent	SNP	ENST00000344936.2	37	CCDS7170.1	505	0.23122710622710624	28	0.056910569105691054	89	0.24585635359116023	219	0.38286713286713286	169	0.22295514511873352	T	9.049	0.991719	0.18966	0.084203	0.212326	ENSG00000165322	ENST00000454919	.	.	.	5.85	2.14	0.27477	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38672	-0.9650	3	.	.	.	.	10.3205	0.43762	0.0:0.2537:0.0:0.7463	rs2799021;rs17572817;rs56514703;rs2799021	.	.	.	V	61	.	.	M	-	1	0	ARHGAP12	32181466	0.998000	0.40836	0.997000	0.53966	0.961000	0.63080	0.386000	0.20702	0.108000	0.17862	0.455000	0.32223	ATG	T|0.798;C|0.202	0.202	strong		0.333	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
CPNE1	8904	hgsc.bcm.edu	37	20	34214723	34214723	+	Silent	SNP	T	T	C	rs2425068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:34214723T>C	ENST00000317619.3	-	17	1633	c.1239A>G	c.(1237-1239)caA>caG	p.Q413Q	CPNE1_ENST00000397442.1_Silent_p.Q413Q|CPNE1_ENST00000397446.1_Silent_p.Q413Q|CPNE1_ENST00000317677.5_Silent_p.Q418Q|CPNE1_ENST00000397443.1_Silent_p.Q413Q|CPNE1_ENST00000397445.1_Silent_p.Q413Q|CPNE1_ENST00000352393.4_Silent_p.Q413Q			Q99829	CPNE1_HUMAN	copine I	413	VWFA.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GCATGAAGTATTGCTGGGGAC	0.547													T|||	152	0.0303514	0.0023	0.0908	5008	,	,		20706	0.002		0.0517	False		,,,				2504	0.0327				p.Q418Q		Atlas-SNP	.											.	CPNE1	44	.	0			c.A1254G						PASS	.	T	,,,,,	52,4354	52.9+/-88.7	0,52,2151	118.0	84.0	96.0		,1254,1239,1239,1239,1239	4.2	1.0	20	dbSNP_100	96	630,7970	162.3+/-215.1	27,576,3697	yes	splice-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	,,,,,	27,628,5848	CC,CT,TT		7.3256,1.1802,5.2437	,,,,,	,418/543,413/538,413/538,413/538,413/538	34214723	682,12324	2203	4300	6503	SO:0001819	synonymous_variant	8904	exon15			GAAGTATTGCTGG	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.1239A>G	20.37:g.34214723T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Silent	SNP	ENST00000317619.3	37	CCDS13260.1	71|71	0.03250915750915751|0.03250915750915751	3|3	0.006097560975609756|0.006097560975609756	28|28	0.07734806629834254|0.07734806629834254	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	T|T	17.42|17.42	3.384943|3.384943	0.61956|0.61956	0.011802|0.011802	0.073256|0.073256	ENSG00000214078|ENSG00000214078	ENST00000437340|ENST00000415920	.|.	.|.	.|.	5.27|5.27	4.18|4.18	0.49190|0.49190	.|.	.|.	.|.	.|.	.|.	.|T	.|0.10078	.|0.0247	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.37150	.|-0.9718	.|5	.|0.87932	.|D	.|0	.|-2.5493	10.073|10.073	0.42345|0.42345	0.0:0.0798:0.0:0.9202|0.0:0.0798:0.0:0.9202	rs2425068;rs2425068|rs2425068;rs2425068	.|.	.|.	.|.	.|S	-1|52	.|.	.|ENSP00000386067:N421S	.|N	-|-	.|2	.|0	CPNE1|CPNE1	33678137|33678137	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.961000|0.961000	0.63080|0.63080	4.993000|4.993000	0.63895|0.63895	1.032000|1.032000	0.39892|0.39892	0.460000|0.460000	0.39030|0.39030	.|AAT	T|0.956;C|0.044	0.044	strong		0.547	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
CDHR2	54825	hgsc.bcm.edu	37	5	176011889	176011889	+	Silent	SNP	G	G	A	rs4868660	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176011889G>A	ENST00000510636.1	+	19	2881	c.2607G>A	c.(2605-2607)gcG>gcA	p.A869A	CDHR2_ENST00000261944.5_Silent_p.A869A|CDHR2_ENST00000506348.1_Silent_p.A869A	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	869	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						TCTCAGTGGCGGCCAACGGCT	0.607													G|||	1023	0.204273	0.1021	0.402	5008	,	,		19243	0.0278		0.4145	False		,,,				2504	0.1677				p.A869A		Atlas-SNP	.											.	CDHR2	152	.	0			c.G2607A						PASS	.	G	,	707,3699	291.3+/-281.4	53,601,1549	64.0	53.0	57.0		2607,2607	-1.2	0.0	5	dbSNP_111	57	3675,4925	519.3+/-379.4	779,2117,1404	no	coding-synonymous,coding-synonymous	CDHR2	NM_001171976.1,NM_017675.4	,	832,2718,2953	AA,AG,GG		42.7326,16.0463,33.6921	,	869/1311,869/1311	176011889	4382,8624	2203	4300	6503	SO:0001819	synonymous_variant	54825	exon19			AGTGGCGGCCAAC	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.2607G>A	5.37:g.176011889G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	213	67	0.314554	NM_017675	A1L3U4|A6NC80|Q9NXP8	Silent	SNP	ENST00000510636.1	37	CCDS34297.1																																																																																			G|0.727;A|0.273	0.273	strong		0.607	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
TMEM254	80195	hgsc.bcm.edu	37	10	81841692	81841692	+	Silent	SNP	G	G	T	rs1932574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:81841692G>T	ENST00000372281.3	+	2	213	c.183G>T	c.(181-183)ctG>ctT	p.L61L	TMEM254_ENST00000372274.1_Silent_p.L61L|TMEM254_ENST00000372277.3_Silent_p.L61L|TMEM254_ENST00000372275.1_Silent_p.L61L|TMEM254_ENST00000467529.1_3'UTR	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254	61						integral component of membrane (GO:0016021)											ACACCCTCCTGTGCAATGGGT	0.547													.|||	2109	0.421126	0.2345	0.3372	5008	,	,		15872	0.6865		0.4125	False		,,,				2504	0.4683				p.C93F		Atlas-SNP	.											.	TMEM254	1	.	0			c.G278T						PASS	.	G		1179,3227	414.8+/-337.0	170,839,1194	96.0	96.0	96.0		183	1.3	0.1	10	dbSNP_92	96	3678,4922	526.1+/-380.9	779,2120,1401	no	coding-synonymous	C10orf57	NM_025125.2		949,2959,2595	TT,TG,GG		42.7674,26.759,37.3443		61/124	81841692	4857,8149	2203	4300	6503	SO:0001819	synonymous_variant	80195	exon3			CCTCCTGTGCAAT	BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 57"""	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.183G>T	10.37:g.81841692G>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_001270371	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	37	CCDS7363.1	925|925	0.42353479853479853|0.42353479853479853	102|102	0.2073170731707317|0.2073170731707317	119|119	0.3287292817679558|0.3287292817679558	391|391	0.6835664335664335|0.6835664335664335	313|313	0.4129287598944591|0.4129287598944591	G|G	3.937|3.937	-0.014996|-0.014996	0.07681|0.07681	0.26759|0.26759	0.427674|0.427674	ENSG00000133678|ENSG00000133678	ENST00000372273|ENST00000450179	.|.	.|.	.|.	5.34|5.34	1.28|1.28	0.21552|0.21552	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.48135|0.48135	P|P	4.0200000000001346E-4|4.0200000000001346E-4	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39961|0.39961	-0.9588|-0.9588	3|3	.|.	.|.	.|.	-19.6002|-19.6002	8.5308|8.5308	0.33333|0.33333	0.3419:0.0:0.6581:0.0|0.3419:0.0:0.6581:0.0	rs1932574;rs11559166;rs1932574|rs1932574;rs11559166;rs1932574	.|.	.|.	.|.	F|L	82|39	.|.	.|.	C|V	+|+	2|1	0|0	C10orf57|C10orf57	81831672|81831672	0.000000|0.000000	0.05858|0.05858	0.062000|0.062000	0.19696|0.19696	0.682000|0.682000	0.39822|0.39822	-0.437000|-0.437000	0.06914|0.06914	0.318000|0.318000	0.23185|0.23185	0.655000|0.655000	0.94253|0.94253	TGT|GTG	G|0.607;T|0.393	0.393	strong		0.547	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1	NM_025125	
ADCK1	57143	hgsc.bcm.edu	37	14	78374172	78374172	+	Silent	SNP	C	C	T	rs34272020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:78374172C>T	ENST00000238561.5	+	7	867	c.768C>T	c.(766-768)tcC>tcT	p.S256S	ADCK1_ENST00000341211.5_Silent_p.S188S	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	263	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		GGGACCTGTCCACGGAGCGGG	0.572													C|||	383	0.0764776	0.1014	0.0994	5008	,	,		21271	0.001		0.1322	False		,,,				2504	0.047				p.S256S		Atlas-SNP	.											.	ADCK1	81	.	0			c.C768T						PASS	.	C	,	531,3875	240.9+/-251.5	41,449,1713	83.0	70.0	74.0		564,768	1.9	1.0	14	dbSNP_126	74	992,7608	213.8+/-253.6	58,876,3366	no	coding-synonymous,coding-synonymous	ADCK1	NM_001142545.1,NM_020421.3	,	99,1325,5079	TT,TC,CC		11.5349,12.0517,11.71	,	188/456,256/524	78374172	1523,11483	2203	4300	6503	SO:0001819	synonymous_variant	57143	exon7			CCTGTCCACGGAG	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.768C>T	14.37:g.78374172C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Silent	SNP	ENST00000238561.5	37	CCDS9869.1																																																																																			C|0.893;T|0.107	0.107	strong		0.572	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
OR2G3	81469	hgsc.bcm.edu	37	1	247769217	247769217	+	Silent	SNP	T	T	G	rs61750030	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247769217T>G	ENST00000320002.2	+	1	362	c.330T>G	c.(328-330)acT>acG	p.T110T	RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TGGGCTCCACTGAATGTATCC	0.493													T|||	184	0.0367412	0.0121	0.0447	5008	,	,		21698	0.0		0.1074	False		,,,				2504	0.0297				p.T110T		Atlas-SNP	.											OR2G3,NS,carcinoma,+2,1	OR2G3	108	1	0			c.T330G						PASS	.	T		123,4283	91.1+/-129.8	2,119,2082	273.0	239.0	251.0		330	-7.4	0.1	1	dbSNP_129	251	844,7756	193.9+/-239.5	49,746,3505	no	coding-synonymous	OR2G3	NM_001001914.1		51,865,5587	GG,GT,TT		9.814,2.7916,7.435		110/310	247769217	967,12039	2203	4300	6503	SO:0001819	synonymous_variant	81469	exon1			CTCCACTGAATGT	BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"""GPCR / Class A : Olfactory receptors"""	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.330T>G	1.37:g.247769217T>G		Somatic	354	1	0.00282486		WXS	Illumina HiSeq	Phase_I	339	170	0.501475	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Silent	SNP	ENST00000320002.2	37	CCDS31093.1																																																																																			T|0.934;G|0.066	0.066	strong		0.493	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1		
FBXL18	80028	hgsc.bcm.edu	37	7	5521468	5521468	+	Silent	SNP	G	G	A	rs10951956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5521468G>A	ENST00000382368.3	-	5	2218	c.2095C>T	c.(2095-2097)Ctg>Ttg	p.L699L	AC092171.4_ENST00000444210.2_lincRNA	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	0									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		ATCTCATCCAGGTGCACCAGG	0.632													G|||	751	0.14996	0.1339	0.1844	5008	,	,		15625	0.0387		0.1312	False		,,,				2504	0.2812				p.L699L		Atlas-SNP	.											.	FBXL18	99	.	0			c.C2095T						PASS	.	G		553,3527		39,475,1526	94.0	105.0	101.0		2095	3.9	1.0	7	dbSNP_120	101	1097,7273		70,957,3158	no	coding-synonymous	FBXL18	NM_024963.4		109,1432,4684	AA,AG,GG		13.1063,13.5539,13.253		699/719	5521468	1650,10800	2040	4185	6225	SO:0001819	synonymous_variant	80028	exon5			CATCCAGGTGCAC	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"""F-boxes / Leucine-rich repeats"""	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.2095C>T	7.37:g.5521468G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Silent	SNP	ENST00000382368.3	37	CCDS43546.1	255	0.11675824175824176	71	0.1443089430894309	61	0.1685082872928177	20	0.03496503496503497	103	0.1358839050131926	G	10.44	1.349523	0.24426	0.135539	0.131063	ENSG00000155034	ENST00000297035	.	.	.	4.83	3.93	0.45458	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20009	-1.0288	4	0.87932	D	0	.	5.4219	0.16405	0.2723:0.0:0.7277:0.0	rs10951956;rs52819283;rs58984836;rs10951956	.	.	.	L	258	.	ENSP00000297035:P258L	P	-	2	0	FBXL18	5487994	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.448000	0.60027	2.384000	0.81235	0.511000	0.50034	CCT	G|0.878;A|0.122	0.122	strong		0.632	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963	
SLC9A4	389015	hgsc.bcm.edu	37	2	103149100	103149100	+	Missense_Mutation	SNP	G	G	A	rs1014286	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:103149100G>A	ENST00000295269.4	+	12	2807	c.2350G>A	c.(2350-2352)Ggc>Agc	p.G784S		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	784				G -> S (in Ref. 1; CAH10500/CAH10600). {ECO:0000305}.	epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCATGGACACGGCAGGGACCA	0.498													G|||	3117	0.622404	0.6657	0.6816	5008	,	,		19648	0.5308		0.675	False		,,,				2504	0.5624				p.G784S		Atlas-SNP	.											.	SLC9A4	115	.	0			c.G2350A						PASS	.	G	SER/GLY	2825,1581	665.2+/-401.5	907,1011,285	67.0	46.0	53.0		2350	-11.0	0.0	2	dbSNP_86	53	5463,3137	654.0+/-401.1	1739,1985,576	yes	missense	SLC9A4	NM_001011552.3	56	2646,2996,861	AA,AG,GG		36.4767,35.8829,36.2756	benign	784/799	103149100	8288,4718	2203	4300	6503	SO:0001583	missense	389015	exon12			GGACACGGCAGGG		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.2350G>A	2.37:g.103149100G>A	ENSP00000295269:p.Gly784Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	1414	0.6474358974358975	342	0.6951219512195121	254	0.7016574585635359	304	0.5314685314685315	514	0.6781002638522428	G	4.238	0.043156	0.08196	0.641171	0.635233	ENSG00000180251	ENST00000295269	T	0.39592	1.07	5.52	-11.0	0.00169	.	1.038380	0.07474	N	0.902670	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.35992	-0.9766	9	0.15952	T	0.53	.	9.557	0.39346	0.1824:0.0984:0.6218:0.0973	rs1014286;rs52798704;rs57201061;rs1014286	784	Q6AI14	SL9A4_HUMAN	S	784	ENSP00000295269:G784S	ENSP00000295269:G784S	G	+	1	0	SLC9A4	102515532	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.514000	0.06298	-2.116000	0.00830	-1.084000	0.02203	GGC	G|0.366;N|0.000	.	strong		0.498	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
DSCR4	10281	hgsc.bcm.edu	37	21	39493232	39493232	+	Missense_Mutation	SNP	G	G	A	rs61731605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:39493232G>A	ENST00000328264.3	-	1	222	c.118C>T	c.(118-120)Cct>Tct	p.P40S	DSCR8_ENST00000400477.3_5'Flank|DSCR4_ENST00000398948.1_Missense_Mutation_p.P40S|DSCR8_ENST00000357704.4_5'Flank	NM_005867.2	NP_005858.1	P56555	DSCR4_HUMAN	Down syndrome critical region gene 4	40										large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	6						ctgtggagaggagaagctgag	0.512													G|||	51	0.0101837	0.0	0.0245	5008	,	,		17151	0.002		0.0278	False		,,,				2504	0.0041				p.P40S		Atlas-SNP	.											.	DSCR4	20	.	0			c.C118T						PASS	.	G		30,4376	35.2+/-66.4	0,30,2173	75.0	69.0	71.0			1.3	0.0	21	dbSNP_129	71	256,8344	98.8+/-160.4	3,250,4047	yes	intergenic				3,280,6220	AA,AG,GG		2.9767,0.6809,2.199			39493232	286,12720	2203	4300	6503	SO:0001583	missense	10281	exon1			GGAGAGGAGAAGC	AB000099	CCDS33554.1	21q22.2	2012-04-19			ENSG00000184029	ENSG00000184029			3045	protein-coding gene	gene with protein product		604829				9455479	Standard	NM_005867		Approved	DCRB	uc002ywp.3	P56555	OTTHUMG00000086673	ENST00000328264.3:c.118C>T	21.37:g.39493232G>A	ENSP00000328676:p.Pro40Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_005867	Q4VB31	Missense_Mutation	SNP	ENST00000328264.3	37	CCDS33554.1	37	0.01694139194139194	0	0.0	12	0.03314917127071823	2	0.0034965034965034965	23	0.030343007915567283	G	9.758	1.169279	0.21621	0.006809	0.029767	ENSG00000184029	ENST00000398948;ENST00000328264	.	.	.	1.33	1.33	0.21861	.	.	.	.	.	T	0.30355	0.0762	.	.	.	0.09310	N	1	D	0.65815	0.995	D	0.65323	0.934	T	0.13098	-1.0522	7	0.87932	D	0	.	6.0593	0.19828	0.0:0.0:1.0:0.0	rs61731605	40	P56555	DSCR4_HUMAN	S	40	.	ENSP00000328676:P40S	P	-	1	0	DSCR4	38415102	0.006000	0.16342	0.011000	0.14972	0.058000	0.15608	0.196000	0.17176	1.058000	0.40530	0.313000	0.20887	CCT	G|0.980;A|0.020	0.020	strong		0.512	DSCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000194834.1	NM_005867	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720673	135720673	+	Silent	SNP	T	T	C	rs9872542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:135720673T>C	ENST00000264977.3	+	2	950	c.333T>C	c.(331-333)gaT>gaC	p.D111D	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	111					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ACTTAAAGGATATTGCAGGAG	0.423													C|||	936	0.186901	0.202	0.1455	5008	,	,		21751	0.0288		0.2783	False		,,,				2504	0.2648				p.D111D		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T333C						PASS	.	C	,	954,3452	727.3+/-409.8	99,756,1348	42.0	43.0	43.0		,333	5.8	1.0	3	dbSNP_119	43	2713,5885	678.3+/-403.4	417,1879,2003	no	intron,coding-synonymous	PPP2R3A	NM_001190447.1,NM_002718.4	,	516,2635,3351	CC,CT,TT		31.5538,21.6523,28.199	,	,111/1151	135720673	3667,9337	2203	4299	6502	SO:0001819	synonymous_variant	5523	exon2			AAAGGATATTGCA	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.333T>C	3.37:g.135720673T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	37	CCDS3087.1																																																																																			T|0.802;C|0.198	0.198	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
P2RX7	5027	hgsc.bcm.edu	37	12	121605355	121605355	+	Missense_Mutation	SNP	G	G	A	rs7958311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121605355G>A	ENST00000546057.1	+	8	952	c.809G>A	c.(808-810)cGt>cAt	p.R270H	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000541446.1_Intron|P2RX7_ENST00000328963.5_Missense_Mutation_p.R100H|P2RX7_ENST00000377162.2_Intron|P2RX7_ENST00000535250.1_Missense_Mutation_p.R180H	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	270			R -> C (in dbSNP:rs16950860).|R -> H (in dbSNP:rs7958311). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15896293, ECO:0000269|PubMed:9038151}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)	p.R270H(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CATCACTGCCGTCCCAAATAC	0.522													G|||	1281	0.255791	0.2708	0.2968	5008	,	,		17536	0.3958		0.2296	False		,,,				2504	0.089				p.R270H		Atlas-SNP	.											P2RX7,NS,carcinoma,0,1	P2RX7	53	1	1	Substitution - Missense(1)	stomach(1)	c.G809A						PASS	.	G	HIS/ARG	1054,3352	385.4+/-325.7	138,778,1287	213.0	157.0	176.0		809	1.0	0.8	12	dbSNP_116	176	2128,6472	367.3+/-334.7	263,1602,2435	yes	missense	P2RX7	NM_002562.5	29	401,2380,3722	AA,AG,GG		24.7442,23.9219,24.4656	possibly-damaging	270/596	121605355	3182,9824	2203	4300	6503	SO:0001583	missense	5027	exon8			ACTGCCGTCCCAA	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.809G>A	12.37:g.121605355G>A	ENSP00000442349:p.Arg270His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	135	59	0.437037	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	631	0.2889194139194139	114	0.23170731707317074	106	0.292817679558011	237	0.4143356643356643	174	0.22955145118733508	G	13.79	2.342889	0.41498	0.239219	0.247442	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250	T;T;T	0.04234	3.67;3.67;3.67	6.04	0.975	0.19721	.	0.458332	0.22674	N	0.057023	T	0.00012	0.0000	L	0.45698	1.435	0.58432	P	1.0000000000287557E-6	D;D;D	0.58970	0.975;0.98;0.984	B;P;P	0.49332	0.387;0.472;0.607	T	0.37009	-0.9724	9	0.11182	T	0.66	.	5.6648	0.17689	0.3333:0.0:0.5471:0.1196	rs7958311;rs17855427;rs7958311	100;180;270	F8W951;F5H7E8;Q99572	.;.;P2RX7_HUMAN	H	270;100;180	ENSP00000442349:R270H;ENSP00000330696:R100H;ENSP00000442572:R180H	ENSP00000330696:R100H	R	+	2	0	P2RX7	120089738	0.013000	0.17824	0.832000	0.32986	0.974000	0.67602	0.757000	0.26433	0.124000	0.18369	0.563000	0.77884	CGT	A|0.265;G|0.735;N|0.000	0.265	strong		0.522	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
FLT4	2324	hgsc.bcm.edu	37	5	180046344	180046344	+	Missense_Mutation	SNP	G	G	C	rs448012	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:180046344G>C	ENST00000261937.6	-	19	2748	c.2670C>G	c.(2668-2670)caC>caG	p.H890Q	FLT4_ENST00000502649.1_Missense_Mutation_p.H890Q|FLT4_ENST00000393347.3_Missense_Mutation_p.H890Q|FLT4_ENST00000424276.2_5'Flank	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	890	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		H -> Q (in dbSNP:rs448012). {ECO:0000269|PubMed:11807987, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8386825, ECO:0000269|Ref.7}.		blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCAGCGCGCGGTGCTCGCTGG	0.697													G|||	2918	0.582668	0.5144	0.7464	5008	,	,		9644	0.497		0.6531	False		,,,				2504	0.5746				p.H890Q	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											FLT4_ENST00000261937,NS,carcinoma,0,2	FLT4	356	2	0			c.C2670G						PASS	.	G	GLN/HIS,GLN/HIS	2398,1998	588.0+/-386.8	655,1088,455	38.0	35.0	36.0		2670,2670	1.2	1.0	5	dbSNP_80	36	5356,3236	622.5+/-397.3	1691,1974,631	no	missense,missense	FLT4	NM_002020.4,NM_182925.4	24,24	2346,3062,1086	CC,CG,GG		37.6629,45.4504,40.2987	benign,benign	890/1299,890/1364	180046344	7754,5234	2198	4296	6494	SO:0001583	missense	2324	exon19			CGCGCGGTGCTCG	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.2670C>G	5.37:g.180046344G>C	ENSP00000261937:p.His890Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	1150	0.5265567765567766	227	0.4613821138211382	233	0.643646408839779	251	0.4388111888111888	439	0.579155672823219	G	16.09	3.023122	0.54683	0.545496	0.623371	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649	D;D;D	0.81821	-1.54;-1.54;-1.54	4.0	1.22	0.21188	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.04018	-0.295	0.18873	P	0.9999871816	B;B	0.27498	0.18;0.18	B;B	0.38921	0.285;0.285	T	0.48080	-0.9066	8	0.29301	T	0.29	.	8.8325	0.35093	0.2491:0.0:0.7509:0.0	rs448012;rs1130377;rs2447732	890;890	E9PD35;P35916	.;VGFR3_HUMAN	Q	890	ENSP00000261937:H890Q;ENSP00000377016:H890Q;ENSP00000426057:H890Q	ENSP00000261937:H890Q	H	-	3	2	FLT4	179978950	1.000000	0.71417	0.987000	0.45799	0.929000	0.56500	3.431000	0.52814	0.126000	0.18424	0.455000	0.32223	CAC	G|0.426;C|0.574	0.574	strong		0.697	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
HSD17B14	51171	hgsc.bcm.edu	37	19	49334991	49334991	+	Silent	SNP	C	C	T	rs62127966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49334991C>T	ENST00000263278.4	-	5	569	c.303G>A	c.(301-303)gaG>gaA	p.E101E	HSD17B14_ENST00000599157.1_Intron	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	101					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GGGCAGAGGTCTCCTCAGGCC	0.642													C|||	329	0.0656949	0.0076	0.0951	5008	,	,		14585	0.0		0.2048	False		,,,				2504	0.0481				p.E101E		Atlas-SNP	.											.	HSD17B14	25	.	0			c.G303A						PASS	.	C		191,4215	116.3+/-154.2	8,175,2020	51.0	54.0	53.0		303	2.0	1.0	19	dbSNP_129	53	1740,6860	307.2+/-308.3	163,1414,2723	no	coding-synonymous	HSD17B14	NM_016246.2		171,1589,4743	TT,TC,CC		20.2326,4.335,14.847		101/271	49334991	1931,11075	2203	4300	6503	SO:0001819	synonymous_variant	51171	exon5			AGAGGTCTCCTCA	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.303G>A	19.37:g.49334991C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	172	87	0.505814	NM_016246	Q9UKU3	Silent	SNP	ENST00000263278.4	37	CCDS12736.1																																																																																			C|0.873;T|0.127	0.127	strong		0.642	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
POLQ	10721	hgsc.bcm.edu	37	3	121258368	121258368	+	Silent	SNP	G	G	A	rs36065146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121258368G>A	ENST00000264233.5	-	4	671	c.543C>T	c.(541-543)ttC>ttT	p.F181F		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	181	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CCAATGAAGAGAAATGCCTTG	0.398								DNA polymerases (catalytic subunits)					G|||	127	0.0253594	0.0008	0.0591	5008	,	,		18627	0.001		0.0537	False		,,,				2504	0.0307				p.F181F	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C543T						PASS	.	G		47,4359	48.2+/-83.0	0,47,2156	129.0	124.0	126.0		543	0.1	1.0	3	dbSNP_126	126	458,8142	137.5+/-194.4	12,434,3854	no	coding-synonymous	POLQ	NM_199420.3		12,481,6010	AA,AG,GG		5.3256,1.0667,3.8828		181/2591	121258368	505,12501	2203	4300	6503	SO:0001819	synonymous_variant	10721	exon4			TGAAGAGAAATGC	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.543C>T	3.37:g.121258368G>A		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	237	126	0.531646	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																			G|0.962;A|0.038	0.038	strong		0.398	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
DNHD1	144132	hgsc.bcm.edu	37	11	6585007	6585007	+	Missense_Mutation	SNP	G	G	A	rs11040923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6585007G>A	ENST00000527990.2	+	29	9937	c.9937G>A	c.(9937-9939)Gat>Aat	p.D3313N	DNHD1_ENST00000254579.6_Missense_Mutation_p.D3313N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3313					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AGGTATGGACGATGCAGCCCT	0.572													G|||	2182	0.435703	0.0734	0.4654	5008	,	,		20999	0.7212		0.4742	False		,,,				2504	0.5706				p.D3313N		Atlas-SNP	.											.	DNHD1	198	.	0			c.G9937A						PASS	.	G	ASN/ASP	193,1191		8,177,507	51.0	47.0	48.0		9937	1.9	0.0	11	dbSNP_120	48	1552,1630		380,792,419	yes	missense	DNHD1	NM_144666.2	23	388,969,926	AA,AG,GG		48.7744,13.9451,38.2173	benign	3313/4754	6585007	1745,2821	692	1591	2283	SO:0001583	missense	144132	exon31			ATGGACGATGCAG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.9937G>A	11.37:g.6585007G>A	ENSP00000436180:p.Asp3313Asn	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	972	0.44505494505494503	49	0.09959349593495935	169	0.46685082872928174	386	0.6748251748251748	368	0.48548812664907653	G	6.557	0.471037	0.12461	0.139451	0.487744	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000526486	T;T	0.74106	-0.81;-0.81	4.87	1.89	0.25635	Dynein heavy chain, coiled coil stalk (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18863	0.031	B	0.18871	0.023	T	0.42649	-0.9439	8	0.40728	T	0.16	.	4.8015	0.13299	0.1976:0.1778:0.6246:0.0	rs11040923;rs17245815;rs58851054;rs11040923	3313	Q96M86	DNHD1_HUMAN	N	3313;3313;225	ENSP00000254579:D3313N;ENSP00000436180:D3313N	ENSP00000254579:D3313N	D	+	1	0	DNHD1	6541583	0.088000	0.21588	0.001000	0.08648	0.071000	0.16799	1.110000	0.31147	0.108000	0.17862	0.313000	0.20887	GAT	G|0.573;A|0.427	0.427	strong		0.572	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
HORMAD2	150280	hgsc.bcm.edu	37	22	30489945	30489945	+	Missense_Mutation	SNP	G	G	A	rs34150968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30489945G>A	ENST00000336726.6	+	2	359	c.4G>A	c.(4-6)Gcc>Acc	p.A2T	HORMAD2_ENST00000403975.1_Missense_Mutation_p.A2T	NM_152510.2	NP_689723.1	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2	2			A -> T (in dbSNP:rs34150968).		meiotic nuclear division (GO:0007126)|meiotic sister chromatid cohesion (GO:0051177)	chromosome (GO:0005694)|nucleus (GO:0005634)				large_intestine(1)|lung(1)	2			Epithelial(10;0.125)			TCCTACAATGGCCACTGCTCA	0.328													G|||	16	0.00319489	0.0	0.0043	5008	,	,		15203	0.0		0.0129	False		,,,				2504	0.0				p.A2T		Atlas-SNP	.											.	HORMAD2	12	.	0			c.G4A						PASS	.	G	THR/ALA	7,3711		0,7,1852	74.0	66.0	69.0		4	1.6	1.0	22	dbSNP_126	69	94,8134		0,94,4020	yes	missense	HORMAD2	NM_152510.2	58	0,101,5872	AA,AG,GG		1.1424,0.1883,0.8455	possibly-damaging	2/308	30489945	101,11845	1859	4114	5973	SO:0001583	missense	150280	exon2			ACAATGGCCACTG	AK098703	CCDS46683.1	22q12.2	2014-01-21			ENSG00000176635	ENSG00000176635			28383	protein-coding gene	gene with protein product						12477932	Standard	NM_152510		Approved	MGC26710, CT46.2	uc003agy.3	Q8N7B1	OTTHUMG00000150881	ENST00000336726.6:c.4G>A	22.37:g.30489945G>A	ENSP00000336984:p.Ala2Thr	Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	249	110	0.441767	NM_152510	B5MEB2|Q8NHR2	Missense_Mutation	SNP	ENST00000336726.6	37	CCDS46683.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	11.81	1.748595	0.30955	0.001883	0.011424	ENSG00000176635	ENST00000336726;ENST00000403975	T;T	0.35973	1.28;1.28	5.02	1.62	0.23740	.	0.497968	0.20580	N	0.089551	T	0.25827	0.0629	M	0.74881	2.28	0.31316	N	0.686633	B	0.23540	0.087	B	0.17433	0.018	T	0.28933	-1.0028	10	0.56958	D	0.05	-7.1149	5.765	0.18221	0.0917:0.0:0.577:0.3313	rs34150968	2	Q8N7B1	HORM2_HUMAN	T	2	ENSP00000336984:A2T;ENSP00000385055:A2T	ENSP00000336984:A2T	A	+	1	0	HORMAD2	28819945	1.000000	0.71417	1.000000	0.80357	0.379000	0.30106	1.781000	0.38644	0.340000	0.23745	0.491000	0.48974	GCC	G|0.993;A|0.007	0.007	strong		0.328	HORMAD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320416.2	NM_152510	
Unknown	0	hgsc.bcm.edu	37	13	103410914	103410914	+	IGR	SNP	A	A	T	rs12855785	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103410914A>T								LINC00283 (13340 upstream) : TEX30 (7425 downstream)																							CTTTTGGGGCAACTGTCTTCC	0.284													A|||	1910	0.38139	0.1044	0.5029	5008	,	,		16341	0.4097		0.5089	False		,,,				2504	0.5092				p.C82S		Atlas-SNP	.											.	.	.	.	0			c.T244A						PASS	.	A	SER/CYS	262,1122		28,206,458	49.0	42.0	44.0		244	0.8	0.0	13	dbSNP_121	44	1592,1586		410,772,407	yes	missense	CCDC168	NM_001146197.1	112	438,978,865	TT,TA,AA		49.9056,18.9306,40.6401		82/7082	103410914	1854,2708	692	1589	2281	SO:0001628	intergenic_variant	643677	exon2			TGGGGCAACTGTC																													13.37:g.103410914A>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	32	0.395062	NM_001146197		Missense_Mutation	SNP		37																																																																																				A|0.627;T|0.373	0.373	strong	0	0.284								
AGGF1	55109	hgsc.bcm.edu	37	5	76332530	76332530	+	Silent	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:76332530T>G	ENST00000312916.7	+	4	1048	c.666T>G	c.(664-666)ggT>ggG	p.G222G		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	222					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		ACAGCACTGGTTTCTATTATG	0.423																																					p.G222G		Atlas-SNP	.											AGGF1,NS,carcinoma,+2,1	AGGF1	71	1	0			c.T666G						scavenged	.						48.0	49.0	49.0					5																	76332530		2203	4300	6503	SO:0001819	synonymous_variant	55109	exon4			CACTGGTTTCTAT	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.666T>G	5.37:g.76332530T>G		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	201	6	0.0298507	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Silent	SNP	ENST00000312916.7	37	CCDS4035.1																																																																																			.	.	none		0.423	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
DISC1	27185	hgsc.bcm.edu	37	1	231903010	231903010	+	Silent	SNP	C	C	T	rs3738402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:231903010C>T	ENST00000602281.1	+	5	1446	c.1393C>T	c.(1393-1395)Cta>Tta	p.L465L	DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000439617.2_Silent_p.L465L|DISC1_ENST00000366633.3_Silent_p.L465L|DISC1_ENST00000366636.4_Silent_p.L465L|DISC1_ENST00000539444.1_Silent_p.L465L|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000535983.1_Silent_p.L465L|DISC1_ENST00000602873.1_Silent_p.L115L|DISC1_ENST00000537876.1_Silent_p.L465L	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	465	Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.|Required for localization to punctate cytoplasmic foci.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				AAAGCAGCAGCTACAGGTGAG	0.512													C|||	496	0.0990415	0.0575	0.1383	5008	,	,		17514	0.2044		0.0268	False		,,,				2504	0.093				p.L497L		Atlas-SNP	.											.	DISC1	207	.	0			c.C1489T						PASS	.	C	,,,,,,,,,,,,,,,	198,4208	125.3+/-162.5	6,186,2011	77.0	69.0	72.0		1393,1393,1489,1393,1393,,1393,1393,1393,1393,1393,1393,1393,1393,343,1393	-7.6	0.0	1	dbSNP_107	72	265,8335	102.3+/-163.5	1,263,4036	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DISC1	NM_001012957.1,NM_001012959.1,NM_001164537.1,NM_001164538.1,NM_001164539.1,NM_001164540.1,NM_001164541.1,NM_001164542.1,NM_001164544.1,NM_001164545.1,NM_001164546.1,NM_001164547.1,NM_001164548.1,NM_001164549.1,NM_001164556.1,NM_018662.2	,,,,,,,,,,,,,,,	7,449,6047	TT,TC,CC		3.0814,4.4939,3.5599	,,,,,,,,,,,,,,,	465/833,465/679,497/887,465/804,465/756,,465/696,465/682,465/663,465/580,465/560,465/560,465/552,465/548,115/202,465/855	231903010	463,12543	2203	4300	6503	SO:0001819	synonymous_variant	27185	exon6			CAGCAGCTACAGG	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1393C>T	1.37:g.231903010C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Silent	SNP	ENST00000602281.1	37	CCDS59205.1																																																																																			C|0.937;T|0.063	0.063	strong		0.512	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
EVC	2121	hgsc.bcm.edu	37	4	5721021	5721021	+	Missense_Mutation	SNP	A	A	C	rs2291157	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:5721021A>C	ENST00000264956.6	+	2	405	c.221A>C	c.(220-222)cAg>cCg	p.Q74P	EVC_ENST00000509451.1_Missense_Mutation_p.Q74P|EVC_ENST00000382674.2_Missense_Mutation_p.Q74P	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	74			Q -> P (in dbSNP:rs2291157). {ECO:0000269|PubMed:10700184}.		cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				TCTAATGCGCAGACCCCCTCG	0.478													A|||	522	0.104233	0.031	0.1254	5008	,	,		19446	0.1597		0.0954	False		,,,				2504	0.1401				p.Q74P		Atlas-SNP	.											.	EVC	90	.	0			c.A221C						PASS	.	A	PRO/GLN	223,4183	134.9+/-171.1	6,211,1986	198.0	198.0	198.0		221	-0.1	0.0	4	dbSNP_100	198	792,7808	185.5+/-233.2	36,720,3544	yes	missense	EVC	NM_153717.2	76	42,931,5530	CC,CA,AA		9.2093,5.0613,7.8041	probably-damaging	74/993	5721021	1015,11991	2203	4300	6503	SO:0001583	missense	2121	exon2			ATGCGCAGACCCC	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.221A>C	4.37:g.5721021A>C	ENSP00000264956:p.Gln74Pro	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	252	0.11538461538461539	23	0.046747967479674794	55	0.15193370165745856	105	0.18356643356643357	69	0.09102902374670185	A	13.15	2.150749	0.37923	0.050613	0.092093	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.54479	0.57;0.57;0.65	3.99	-0.0931	0.13652	.	0.500397	0.20474	N	0.091627	T	0.00109	0.0003	L	0.57536	1.79	0.80722	P	0.0	B	0.14805	0.011	B	0.10450	0.005	T	0.03773	-1.1005	9	0.45353	T	0.12	.	4.6228	0.12463	0.4996:0.3919:0.1085:0.0	rs2291157;rs61234179;rs2291157	74	P57679	EVC_HUMAN	P	74	ENSP00000264956:Q74P;ENSP00000372120:Q74P;ENSP00000426774:Q74P	ENSP00000264956:Q74P	Q	+	2	0	EVC	5771922	0.290000	0.24343	0.006000	0.13384	0.016000	0.09150	1.862000	0.39448	-0.072000	0.12864	-0.460000	0.05396	CAG	A|0.908;C|0.092	0.092	strong		0.478	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
ADAM7	8756	hgsc.bcm.edu	37	8	24339679	24339679	+	Missense_Mutation	SNP	G	G	A	rs13255694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:24339679G>A	ENST00000175238.6	+	9	813	c.730G>A	c.(730-732)Gtg>Atg	p.V244M	ADAM7_ENST00000520720.1_Missense_Mutation_p.V16M|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000380789.1_Missense_Mutation_p.V244M	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	244	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.		V -> M (in dbSNP:rs13255694).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		AAACATCCATGTGACGTTGGT	0.294													G|||	1309	0.261382	0.1006	0.428	5008	,	,		18287	0.1875		0.3032	False		,,,				2504	0.3937				p.V244M		Atlas-SNP	.											.	ADAM7	165	.	0			c.G730A						PASS	.	G	MET/VAL	560,3846	247.5+/-255.7	38,484,1681	86.0	84.0	85.0		730	5.6	1.0	8	dbSNP_121	85	2833,5763	443.1+/-360.3	474,1885,1939	yes	missense	ADAM7	NM_003817.2	21	512,2369,3620	AA,AG,GG		32.9572,12.7099,26.096	probably-damaging	244/755	24339679	3393,9609	2203	4298	6501	SO:0001583	missense	8756	exon9			ATCCATGTGACGT	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.730G>A	8.37:g.24339679G>A	ENSP00000175238:p.Val244Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	539	0.2467948717948718	47	0.09552845528455285	149	0.4116022099447514	109	0.19055944055944055	234	0.3087071240105541	G	17.31	3.357026	0.61293	0.127099	0.329572	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.72942	-0.7;-0.7;-0.7	5.63	5.63	0.86233	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.49305	D	0.000147	T	0.00012	0.0000	H	0.94886	3.595	0.19945	P	0.9999442786	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.01630	-1.1308	9	0.87932	D	0	.	15.176	0.72913	0.0:0.0:1.0:0.0	rs13255694;rs17811530;rs52806960;rs61591583;rs13255694	16;244	E5RK87;Q9H2U9	.;ADAM7_HUMAN	M	244;244;16;59	ENSP00000175238:V244M;ENSP00000370166:V244M;ENSP00000430400:V16M	ENSP00000175238:V244M	V	+	1	0	ADAM7	24395569	1.000000	0.71417	0.990000	0.47175	0.429000	0.31625	4.064000	0.57506	2.652000	0.90054	0.655000	0.94253	GTG	G|0.755;A|0.245	0.245	strong		0.294	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
ITGB2	3689	hgsc.bcm.edu	37	21	46330674	46330674	+	Silent	SNP	C	C	A	rs11088969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46330674C>A	ENST00000397850.2	-	3	476	c.24G>T	c.(22-24)ctG>ctT	p.L8L	ITGB2_ENST00000397857.1_Silent_p.L8L|ITGB2_ENST00000523126.1_5'Flank|ITGB2_ENST00000397852.1_Silent_p.L8L|ITGB2_ENST00000397846.3_Silent_p.L8L|ITGB2_ENST00000302347.5_Silent_p.L8L|ITGB2_ENST00000397854.3_Silent_p.L8L|ITGB2_ENST00000355153.4_Silent_p.L8L			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	8					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	CCAGGGCGAGCAGTGGGGGGC	0.667													C|||	1067	0.213059	0.2383	0.1383	5008	,	,		19421	0.0595		0.2127	False		,,,				2504	0.3906				p.L8L		Atlas-SNP	.											.	ITGB2	107	.	0			c.G24T						PASS	.	C	,	983,3421	360.6+/-315.3	114,755,1333	38.0	42.0	41.0		24,24	-0.6	0.0	21	dbSNP_120	41	1841,6759	321.5+/-315.1	206,1429,2665	no	coding-synonymous,coding-synonymous	ITGB2	NM_000211.3,NM_001127491.1	,	320,2184,3998	AA,AC,CC		21.407,22.3206,21.7164	,	8/770,8/770	46330674	2824,10180	2202	4300	6502	SO:0001819	synonymous_variant	3689	exon2			GGCGAGCAGTGGG	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.24G>T	21.37:g.46330674C>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	37	CCDS13716.1																																																																																			C|0.796;A|0.204	0.204	strong		0.667	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
NUP54	53371	hgsc.bcm.edu	37	4	77057501	77057501	+	Silent	SNP	A	A	G	rs11558468	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:77057501A>G	ENST00000264883.3	-	4	500	c.360T>C	c.(358-360)acT>acC	p.T120T	NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000458189.2_Intron|NUP54_ENST00000515460.1_5'UTR|NUP54_ENST00000514987.1_Silent_p.T72T	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	120	9 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						GAGCACTCGCAGTATTTATCA	0.433													A|||	776	0.154952	0.0567	0.1282	5008	,	,		16678	0.3512		0.1312	False		,,,				2504	0.1288				p.T120T		Atlas-SNP	.											.	NUP54	48	.	0			c.T360C						PASS	.	A		308,4098	166.2+/-197.5	15,278,1910	92.0	94.0	93.0		360	3.2	1.0	4	dbSNP_120	93	1299,7301	257.3+/-281.4	101,1097,3102	no	coding-synonymous	NUP54	NM_017426.2		116,1375,5012	GG,GA,AA		15.1047,6.9905,12.3558		120/508	77057501	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon4			ACTCGCAGTATTT	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.360T>C	4.37:g.77057501A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	160	92	0.575	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			A|0.865;G|0.135	0.135	strong		0.433	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
PLXNC1	10154	hgsc.bcm.edu	37	12	94673277	94673277	+	Silent	SNP	G	G	A	rs2230760	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:94673277G>A	ENST00000258526.4	+	22	3876	c.3627G>A	c.(3625-3627)ccG>ccA	p.P1209P	PLXNC1_ENST00000545312.1_5'UTR|RP11-1105G2.3_ENST00000547927.1_5'Flank|RP11-1105G2.3_ENST00000551941.1_Intron|RP11-1105G2.4_ENST00000550111.1_RNA|PLXNC1_ENST00000547057.1_Silent_p.P256P	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1209					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.P1209P(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AAAAAATCCCGGAAAACGAGA	0.388													G|||	530	0.105831	0.062	0.1441	5008	,	,		15979	0.1696		0.1282	False		,,,				2504	0.0491				p.P1209P		Atlas-SNP	.											PLXNC1,NS,carcinoma,0,1	PLXNC1	135	1	1	Substitution - coding silent(1)	stomach(1)	c.G3627A						PASS	.	G		268,4138	153.7+/-187.2	6,256,1941	92.0	88.0	89.0		3627	-4.1	1.0	12	dbSNP_116	89	1036,7564	219.2+/-257.4	64,908,3328	no	coding-synonymous	PLXNC1	NM_005761.2		70,1164,5269	AA,AG,GG		12.0465,6.0826,10.0261		1209/1569	94673277	1304,11702	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon22			AATCCCGGAAAAC	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.3627G>A	12.37:g.94673277G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	75	29	0.386667	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			G|0.888;A|0.112	0.112	strong		0.388	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
TXK	7294	hgsc.bcm.edu	37	4	48069696	48069696	+	Silent	SNP	G	G	C	rs2230594	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:48069696G>C	ENST00000264316.4	-	15	1627	c.1542C>G	c.(1540-1542)gcC>gcG	p.A514A	TXK_ENST00000507351.1_Silent_p.A169A	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	514	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						GCAGCAGCTCGGCAAATGTAG	0.488													G|||	2174	0.434105	0.2874	0.5692	5008	,	,		16804	0.4306		0.5229	False		,,,				2504	0.4489				p.A514A		Atlas-SNP	.											.	TXK	58	.	0			c.C1542G						PASS	.	G		1438,2968	465.9+/-354.3	247,944,1012	100.0	106.0	104.0		1542	-0.6	0.9	4	dbSNP_98	104	4524,4076	594.0+/-393.2	1201,2122,977	no	coding-synonymous	TXK	NM_003328.2		1448,3066,1989	CC,CG,GG		47.3953,32.6373,45.8404		514/528	48069696	5962,7044	2203	4300	6503	SO:0001819	synonymous_variant	7294	exon15			CAGCTCGGCAAAT	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"""SH2 domain containing"""	12434	protein-coding gene	gene with protein product		600058	"""PTK4 protein tyrosine kinase 4"""	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.1542C>G	4.37:g.48069696G>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	183	83	0.453552	NM_003328	Q14220	Silent	SNP	ENST00000264316.4	37	CCDS3480.1																																																																																			G|0.528;C|0.472	0.472	strong		0.488	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328	
FLNC	2318	hgsc.bcm.edu	37	7	128484816	128484816	+	Silent	SNP	A	A	G	rs3734973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128484816A>G	ENST00000325888.8	+	21	3558	c.3297A>G	c.(3295-3297)gtA>gtG	p.V1099V	FLNC_ENST00000346177.6_Silent_p.V1099V	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1099					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GGCTGACCGTAGAGGGCCCCT	0.637													G|||	1903	0.379992	0.6082	0.2248	5008	,	,		19215	0.4891		0.1551	False		,,,				2504	0.3006				p.V1099V		Atlas-SNP	.											FLNC,caecum,carcinoma,+2,1	FLNC	339	1	0			c.A3297G						PASS	.	G	,	2140,1996		574,992,502	57.0	66.0	63.0		3297,3297	2.7	1.0	7	dbSNP_107	63	1392,7054		94,1204,2925	yes	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	668,2196,3427	GG,GA,AA		16.4812,48.2592,28.0718	,	1099/2693,1099/2726	128484816	3532,9050	2068	4223	6291	SO:0001819	synonymous_variant	2318	exon21			GACCGTAGAGGGC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3297A>G	7.37:g.128484816A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			A|0.663;G|0.337	0.337	strong		0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
TTC12	54970	hgsc.bcm.edu	37	11	113194168	113194168	+	Missense_Mutation	SNP	A	A	C	rs723077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:113194168A>C	ENST00000529221.1	+	3	322	c.217A>C	c.(217-219)Atg>Ctg	p.M73L	TTC12_ENST00000314756.3_Missense_Mutation_p.M73L|TTC12_ENST00000393020.1_Missense_Mutation_p.M73L|TTC12_ENST00000483239.2_Missense_Mutation_p.M73L	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	73			M -> L (in dbSNP:rs723077). {ECO:0000269|PubMed:15489334}.					p.M73L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		ACAAACTGCTATGAAGGTTTC	0.423													A|||	1796	0.358626	0.1172	0.3963	5008	,	,		15190	0.4018		0.4831	False		,,,				2504	0.4857				p.M73L		Atlas-SNP	.											TTC12,NS,adenoma,0,2	TTC12	66	2	1	Substitution - Missense(1)	stomach(1)	c.A217C						PASS	.	A	LEU/MET	852,3550	336.3+/-304.3	90,672,1439	125.0	122.0	123.0		217	-8.6	0.0	11	dbSNP_86	123	4339,4253	580.4+/-391.1	1128,2083,1085	yes	missense	TTC12	NM_017868.3	15	1218,2755,2524	CC,CA,AA		49.4995,19.3548,39.9492	benign	73/706	113194168	5191,7803	2201	4296	6497	SO:0001583	missense	54970	exon3			ACTGCTATGAAGG	AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"""Tetratricopeptide (TTC) repeat domain containing"""	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.217A>C	11.37:g.113194168A>C	ENSP00000433757:p.Met73Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_017868	Q8N5H9|Q9NWY3	Missense_Mutation	SNP	ENST00000529221.1	37	CCDS8360.2	803	0.3676739926739927	64	0.13008130081300814	161	0.4447513812154696	216	0.3776223776223776	362	0.47757255936675463	A	7.380	0.628627	0.14257	0.193548	0.505005	ENSG00000149292	ENST00000529221;ENST00000429951;ENST00000442859;ENST00000531164;ENST00000529850;ENST00000314756;ENST00000525965;ENST00000393020;ENST00000455306;ENST00000483239	T;T;T;T;T;T;T;T;T;T	0.39997	2.64;1.06;1.64;1.64;1.05;2.62;1.06;2.61;1.63;2.63	4.3	-8.61	0.00885	Armadillo-type fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37361	-0.9709	8	0.18710	T	0.47	1.4877	5.3935	0.16257	0.3277:0.1029:0.4681:0.1013	rs723077;rs11540307;rs17514567;rs17845996;rs17858980;rs60933940;rs723077	73;73	A8K8G6;Q9H892	.;TTC12_HUMAN	L	73;73;73;48;73;73;73;73;73;73	ENSP00000433757:M73L;ENSP00000413335:M73L;ENSP00000400039:M73L;ENSP00000433916:M48L;ENSP00000431806:M73L;ENSP00000315160:M73L;ENSP00000435308:M73L;ENSP00000376743:M73L;ENSP00000402004:M73L;ENSP00000419652:M73L	ENSP00000315160:M73L	M	+	1	0	TTC12	112699378	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-1.431000	0.02432	-2.455000	0.00540	-1.125000	0.01998	ATG	A|0.618;C|0.382	0.382	strong		0.423	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868	
ZC3H12A	80149	hgsc.bcm.edu	37	1	37948912	37948912	+	Silent	SNP	C	C	T	rs41267299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:37948912C>T	ENST00000373087.6	+	6	1616	c.1500C>T	c.(1498-1500)gcC>gcT	p.A500A		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GTGTCCCTGCCGACTACCCAC	0.637													C|||	207	0.0413339	0.0038	0.0461	5008	,	,		15525	0.0486		0.0865	False		,,,				2504	0.0348				p.A500A		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.C1500T						PASS	.	C		65,4341	59.9+/-96.7	0,65,2138	79.0	91.0	87.0		1500	-9.6	0.6	1	dbSNP_127	87	726,7874	175.6+/-225.6	32,662,3606	no	coding-synonymous	ZC3H12A	NM_025079.2		32,727,5744	TT,TC,CC		8.4419,1.4753,6.0818		500/600	37948912	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	80149	exon6			CCCTGCCGACTAC		CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"""Zinc fingers, CCCH-type domain containing"""	26259	protein-coding gene	gene with protein product	"""MCP induced protein 1"""	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.1500C>T	1.37:g.37948912C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	169	55	0.325444	NM_025079		Silent	SNP	ENST00000373087.6	37	CCDS417.1																																																																																			C|0.943;T|0.057	0.057	strong		0.637	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079	
SCN8A	6334	hgsc.bcm.edu	37	12	52184271	52184271	+	Silent	SNP	T	T	C	rs303815	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52184271T>C	ENST00000354534.6	+	25	4687	c.4509T>C	c.(4507-4509)ccT>ccC	p.P1503P	SCN8A_ENST00000545061.1_Silent_p.P1462P	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1503					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	CACAGAAACCTATTCCCCGCC	0.473													T|||	2523	0.503794	0.3003	0.7493	5008	,	,		20978	0.5724		0.7306	False		,,,				2504	0.3006				p.P1503P		Atlas-SNP	.											.	SCN8A	331	.	0			c.T4509C						PASS	.	T	,	1494,2532		292,910,811	49.0	49.0	49.0		4386,4509	2.8	1.0	12	dbSNP_79	49	6296,2130		2347,1602,264	no	coding-synonymous,coding-synonymous	SCN8A	NM_001177984.1,NM_014191.2	,	2639,2512,1075	CC,CT,TT		25.2789,37.1088,37.4398	,	1462/1940,1503/1981	52184271	7790,4662	2013	4213	6226	SO:0001819	synonymous_variant	6334	exon25			GAAACCTATTCCC	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.4509T>C	12.37:g.52184271T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	37	CCDS44891.1																																																																																			T|0.438;C|0.562	0.562	strong		0.473	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
MYH8	4626	hgsc.bcm.edu	37	17	10296486	10296486	+	Silent	SNP	G	G	A	rs33969260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10296486G>A	ENST00000403437.2	-	36	5302	c.5208C>T	c.(5206-5208)gaC>gaT	p.D1736D	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1736					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GTTGGGAAACGTCATTTTCTA	0.378									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				G|||	478	0.0954473	0.0212	0.1383	5008	,	,		19575	0.002		0.2942	False		,,,				2504	0.0573				p.D1736D		Atlas-SNP	.											.	MYH8	346	.	0			c.C5208T						PASS	.	G		239,4167	140.8+/-176.2	7,225,1971	267.0	240.0	249.0		5208	1.8	1.0	17	dbSNP_126	249	2099,6501	362.3+/-332.7	268,1563,2469	no	coding-synonymous	MYH8	NM_002472.2		275,1788,4440	AA,AG,GG		24.407,5.4244,17.9763		1736/1938	10296486	2338,10668	2203	4300	6503	SO:0001819	synonymous_variant	4626	exon36	Familial Cancer Database	Carney Complex Variant	GGAAACGTCATTT		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.5208C>T	17.37:g.10296486G>A		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	268	138	0.514925	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			G|0.826;A|0.174	0.174	strong		0.378	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
SPAG17	200162	hgsc.bcm.edu	37	1	118535211	118535211	+	Missense_Mutation	SNP	T	T	C	rs35290515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:118535211T>C	ENST00000336338.5	-	36	5304	c.5239A>G	c.(5239-5241)Aaa>Gaa	p.K1747E		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1747						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ACTAGCTGTTTGGACTCAATG	0.448													T|||	65	0.0129792	0.0008	0.0288	5008	,	,		15614	0.0		0.0318	False		,,,				2504	0.0123				p.K1747E		Atlas-SNP	.											.	SPAG17	263	.	0			c.A5239G						PASS	.	T	GLU/LYS	26,4380	32.6+/-62.9	0,26,2177	92.0	90.0	91.0		5239	-1.9	0.0	1	dbSNP_126	91	285,8315	105.4+/-166.3	4,277,4019	yes	missense	SPAG17	NM_206996.2	56	4,303,6196	CC,CT,TT		3.314,0.5901,2.3912	probably-damaging	1747/2224	118535211	311,12695	2203	4300	6503	SO:0001583	missense	200162	exon36			GCTGTTTGGACTC		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5239A>G	1.37:g.118535211T>C	ENSP00000337804:p.Lys1747Glu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	181	75	0.414365	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	35	0.016025641025641024	0	0.0	13	0.03591160220994475	0	0.0	22	0.029023746701846966	T	12.87	2.068360	0.36470	0.005901	0.03314	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.21734	1.99	5.6	-1.87	0.07737	.	0.536654	0.20400	N	0.093080	T	0.10465	0.0256	M	0.61703	1.905	0.09310	N	1	P	0.38078	0.617	B	0.37144	0.242	T	0.25328	-1.0135	10	0.49607	T	0.09	.	15.5645	0.76281	0.0:0.0:0.5819:0.4181	rs35290515	1747	Q6Q759	SPG17_HUMAN	E	1747;227	ENSP00000337804:K1747E	ENSP00000337804:K1747E	K	-	1	0	SPAG17	118336734	0.176000	0.23096	0.004000	0.12327	0.059000	0.15707	0.839000	0.27586	0.049000	0.15920	-0.313000	0.08912	AAA	T|0.979;C|0.021	0.021	strong		0.448	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
ANKRD66	100287718	hgsc.bcm.edu	37	6	46726500	46726500	+	Missense_Mutation	SNP	C	C	A	rs9472839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46726500C>A	ENST00000565422.1	+	5	603	c.598C>A	c.(598-600)Cag>Aag	p.Q200K	ANKRD66_ENST00000536046.1_Missense_Mutation_p.Q171K|RP11-268F1.3_ENST00000438738.1_lincRNA	NM_001162435.2	NP_001155907.2	B4E2M5	ANR66_HUMAN	ankyrin repeat domain 66	200																	CGCTGCCCAGCAGAAGGGGCT	0.537													C|||	506	0.101038	0.2148	0.0865	5008	,	,		17497	0.0		0.1074	False		,,,				2504	0.0552				p.Q200K		Atlas-SNP	.											.	.	.	.	0			c.C598A						PASS	.	C	LYS/GLN	214,1170		15,184,493	38.0	37.0	38.0		598	4.7	0.0	6	dbSNP_119	38	385,2797		31,323,1237	yes	missense	LOC100287718	NM_001162435.2	53	46,507,1730	AA,AC,CC		12.0993,15.4624,13.1187	benign	200/252	46726500	599,3967	692	1591	2283	SO:0001583	missense	100287718	exon5			GCCCAGCAGAAGG	AK304342	CCDS59024.1	6p12.3	2013-01-11			ENSG00000230062	ENSG00000230062		"""Ankyrin repeat domain containing"""	44669	protein-coding gene	gene with protein product							Standard	NM_001162435		Approved		uc011dwf.2	B4E2M5	OTTHUMG00000014791	ENST00000565422.1:c.598C>A	6.37:g.46726500C>A	ENSP00000454770:p.Gln200Lys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	21	0.333333	NM_001162435		Missense_Mutation	SNP	ENST00000565422.1	37	CCDS59024.1																																																																																			C|0.903;A|0.097	0.097	strong		0.537	ANKRD66-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432045.1	NM_001162435	
BCL6	604	hgsc.bcm.edu	37	3	187446211	187446211	+	Missense_Mutation	SNP	C	C	T	rs2229362	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:187446211C>T	ENST00000406870.2	-	6	1843	c.1477G>A	c.(1477-1479)Gct>Act	p.A493T	BCL6_ENST00000450123.2_Missense_Mutation_p.A493T|RP11-211G3.3_ENST00000437407.1_Intron|RP11-211G3.3_ENST00000449623.1_Intron|BCL6_ENST00000232014.4_Missense_Mutation_p.A493T	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	493			A -> T (in dbSNP:rs2229362).		actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		GTGGGGCCAGCGGTGTGGAGG	0.597			"""T, Mis"""	"""IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"""	"""NHL, CLL"""								C|||	927	0.185104	0.4092	0.1282	5008	,	,		20036	0.0784		0.1392	False		,,,				2504	0.0798				p.A493T		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.G1477A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	1784,2622	516.8+/-369.3	376,1032,795	65.0	55.0	59.0		1477,1477,1477	-0.8	0.0	3	dbSNP_98	59	1308,7292	252.1+/-278.3	101,1106,3093	yes	missense,missense,missense	BCL6	NM_001130845.1,NM_001134738.1,NM_001706.4	58,58,58	477,2138,3888	TT,TC,CC		15.2093,40.4902,23.7736	benign,benign,benign	493/707,493/651,493/707	187446211	3092,9914	2203	4300	6503	SO:0001583	missense	604	exon5			GGCCAGCGGTGTG		CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1001	protein-coding gene	gene with protein product		109565	"""zinc finger protein 51"""	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.1477G>A	3.37:g.187446211C>T	ENSP00000384371:p.Ala493Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	197	112	0.568528	NM_001134738	A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	37	CCDS3289.1	385	0.1762820512820513	196	0.3983739837398374	48	0.13259668508287292	40	0.06993006993006994	101	0.13324538258575197	C	6.427	0.446850	0.12223	0.404902	0.152093	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123	T;T;T	0.08458	3.13;3.13;3.09	4.98	-0.824	0.10812	.	0.434279	0.29165	N	0.012957	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.11235	0.0;0.004	B;B	0.04013	0.0;0.001	T	0.45716	-0.9242	9	0.13470	T	0.59	.	2.4249	0.04457	0.1124:0.23:0.395:0.2626	rs2229362;rs2272149;rs9870212;rs58593171;rs2229362	493;493	B8PSA7;P41182	.;BCL6_HUMAN	T	493	ENSP00000384371:A493T;ENSP00000232014:A493T;ENSP00000413122:A493T	ENSP00000232014:A493T	A	-	1	0	BCL6	188928905	0.155000	0.22806	0.000000	0.03702	0.923000	0.55619	0.433000	0.21477	0.013000	0.14918	0.561000	0.74099	GCT	C|0.782;T|0.218	0.218	strong		0.597	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931	
EPN3	55040	hgsc.bcm.edu	37	17	48616271	48616271	+	Silent	SNP	C	C	T	rs72835715	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48616271C>T	ENST00000268933.3	+	4	1287	c.708C>T	c.(706-708)gaC>gaT	p.D236D	EPN3_ENST00000541226.1_Intron|RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000537145.1_Intron	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	236						clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CCCACAGGGACGAGGACCTGC	0.677													C|||	64	0.0127796	0.0008	0.0144	5008	,	,		17972	0.0		0.0437	False		,,,				2504	0.0092				p.D236D		Atlas-SNP	.											.	EPN3	32	.	0			c.C708T						PASS	.	C		46,4360	46.0+/-80.4	1,44,2158	33.0	30.0	31.0		708	-5.9	0.8	17	dbSNP_130	31	395,8205	121.0+/-180.1	12,371,3917	no	coding-synonymous	EPN3	NM_017957.2		13,415,6075	TT,TC,CC		4.593,1.044,3.3907		236/633	48616271	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	55040	exon4			CAGGGACGAGGAC	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.708C>T	17.37:g.48616271C>T		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	271	142	0.523985	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Silent	SNP	ENST00000268933.3	37	CCDS11570.1																																																																																			C|0.973;T|0.027	0.027	strong		0.677	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
LMNTD2	256329	hgsc.bcm.edu	37	11	557989	557989	+	Silent	SNP	C	C	T	rs7129811	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:557989C>T	ENST00000329451.3	-	5	512	c.450G>A	c.(448-450)caG>caA	p.Q150Q	RASSF7_ENST00000397582.3_5'Flank|RP11-496I9.1_ENST00000527620.1_RNA|RASSF7_ENST00000431809.1_5'Flank|RP11-496I9.1_ENST00000527113.1_RNA	NM_173573.2	NP_775844.2	Q8IXW0	LMTD2_HUMAN		150										NS(1)|breast(1)|central_nervous_system(1)|lung(4)|pancreas(1)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCTCCATCTCCTGGAGCGTGC	0.657													C|||	2363	0.471845	0.152	0.4366	5008	,	,		16039	0.6696		0.5746	False		,,,				2504	0.6196				p.Q150Q		Atlas-SNP	.											.	C11orf35	22	.	0			c.G450A						PASS	.	C		958,3446		110,738,1354	27.0	29.0	29.0		450	3.7	0.6	11	dbSNP_116	29	4814,3782		1350,2114,834	no	coding-synonymous	C11orf35	NM_173573.2		1460,2852,2188	TT,TC,CC		43.9972,21.753,44.4		150/635	557989	5772,7228	2202	4298	6500	SO:0001819	synonymous_variant	256329	exon5			CATCTCCTGGAGC																												ENST00000329451.3:c.450G>A	11.37:g.557989C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_173573		Silent	SNP	ENST00000329451.3	37	CCDS7701.1																																																																																			C|0.559;T|0.441	0.441	strong		0.657	C11orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254973.2		
ARHGAP28	79822	hgsc.bcm.edu	37	18	6889973	6889973	+	Silent	SNP	A	A	G	rs4239328	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:6889973A>G	ENST00000383472.4	+	13	1727	c.1623A>G	c.(1621-1623)ccA>ccG	p.P541P	ARHGAP28_ENST00000400091.2_Silent_p.P541P|ARHGAP28_ENST00000314319.3_Silent_p.P382P|ARHGAP28_ENST00000532996.1_Silent_p.P364P|ARHGAP28_ENST00000531294.1_Silent_p.P377P|ARHGAP28_ENST00000418986.1_Silent_p.P382P|ARHGAP28_ENST00000262227.3_Silent_p.P489P|ARHGAP28_ENST00000419673.2_Silent_p.P382P			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	541	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				TGATGGCACCAAACCTTTTCT	0.403													A|||	2809	0.560903	0.5545	0.5331	5008	,	,		21051	0.6052		0.5736	False		,,,				2504	0.5307				p.P382P		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.A1146G						PASS	.	A		2503,1903	628.0+/-395.0	689,1125,389	146.0	142.0	143.0		1146	-1.0	1.0	18	dbSNP_111	143	4919,3681	621.9+/-397.2	1384,2151,765	no	coding-synonymous	ARHGAP28	NM_001010000.2		2073,3276,1154	GG,GA,AA		42.8023,43.1911,42.934		382/571	6889973	7422,5584	2203	4300	6503	SO:0001819	synonymous_variant	79822	exon12			GGCACCAAACCTT	BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1623A>G	18.37:g.6889973A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Silent	SNP	ENST00000383472.4	37																																																																																				A|0.424;G|0.576	0.576	strong		0.403	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
MUC4	4585	hgsc.bcm.edu	37	3	195512287	195512287	+	Missense_Mutation	SNP	G	G	A	rs113602668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195512287G>A	ENST00000463781.3	-	2	6623	c.6164C>T	c.(6163-6165)tCc>tTc	p.S2055F	MUC4_ENST00000475231.1_Missense_Mutation_p.S2055F|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGATACTGAGGAAAGGCTGGT	0.572																																					p.S2055F		Atlas-SNP	.											.	MUC4	1505	.	0			c.C6164T						PASS	.						18.0	18.0	18.0					3																	195512287		686	1573	2259	SO:0001583	missense	4585	exon2			ACTGAGGAAAGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6164C>T	3.37:g.195512287G>A	ENSP00000417498:p.Ser2055Phe	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	417	99	0.23741	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	5.081	0.200645	0.09652	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32988	1.43;1.43	.	.	.	.	.	.	.	.	T	0.14056	0.0340	N	0.19112	0.55	0.09310	N	1	P	0.35139	0.486	B	0.22601	0.04	T	0.15752	-1.0426	6	.	.	.	.	.	.	.	.	2055	E7ESK3	.	F	2055	ENSP00000417498:S2055F;ENSP00000420243:S2055F	.	S	-	2	0	MUC4	196996682	.	.	0.002000	0.10522	0.014000	0.08584	.	.	0.488000	0.27723	0.064000	0.15345	TCC	G|0.843;A|0.157	0.157	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EPB41L3	23136	hgsc.bcm.edu	37	18	5397383	5397383	+	Missense_Mutation	SNP	G	G	A	rs61736460	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:5397383G>A	ENST00000341928.2	-	18	2855	c.2515C>T	c.(2515-2517)Ccc>Tcc	p.P839S	EPB41L3_ENST00000542146.1_Missense_Mutation_p.P144S|EPB41L3_ENST00000544123.1_Missense_Mutation_p.P670S|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000427684.2_Missense_Mutation_p.P136S|EPB41L3_ENST00000540638.2_Missense_Mutation_p.P617S|EPB41L3_ENST00000400111.3_Missense_Mutation_p.P617S|EPB41L3_ENST00000342933.3_Missense_Mutation_p.P839S	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	839	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TGCACGGTGGGTTCCGTCTCT	0.542													G|||	39	0.00778754	0.0015	0.0159	5008	,	,		18323	0.0		0.0239	False		,,,				2504	0.002				p.P839S		Atlas-SNP	.											.	EPB41L3	222	.	0			c.C2515T						PASS	.	G	SER/PRO	18,4388	22.3+/-47.3	0,18,2185	61.0	64.0	63.0		2515	-8.3	0.0	18	dbSNP_129	63	232,8368	94.5+/-156.4	2,228,4070	yes	missense	EPB41L3	NM_012307.2	74	2,246,6255	AA,AG,GG		2.6977,0.4085,1.9222	benign	839/1088	5397383	250,12756	2203	4300	6503	SO:0001583	missense	23136	exon18			CGGTGGGTTCCGT	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2515C>T	18.37:g.5397383G>A	ENSP00000343158:p.Pro839Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	26	0.011904761904761904	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	19	0.025065963060686015	G	2.825	-0.243973	0.05906	0.004085	0.026977	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	T;T;T;T;T;D	0.81579	-1.29;-1.43;0.09;0.09;-1.29;-1.51	5.83	-8.32	0.00996	.	10.205300	0.00424	N	0.000061	T	0.24699	0.0599	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B;B;B	0.11235	0.0;0.002;0.004;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.12837	0.001;0.004;0.008;0.001;0.0;0.002;0.001;0.001	T	0.52975	-0.8503	10	0.06099	T	0.92	.	2.0165	0.03499	0.1619:0.32:0.2699:0.2482	.	670;136;144;231;508;617;839;74	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	S	839;508;670;508;136;144;839;617	ENSP00000343158:P839S;ENSP00000441174:P670S;ENSP00000392195:P136S;ENSP00000442233:P144S;ENSP00000341138:P839S;ENSP00000382981:P617S	ENSP00000343158:P839S	P	-	1	0	EPB41L3	5387383	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.488000	0.02308	-1.086000	0.03084	0.591000	0.81541	CCC	G|0.984;A|0.016	0.016	strong		0.542	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
SLCO4C1	353189	hgsc.bcm.edu	37	5	101631761	101631761	+	Missense_Mutation	SNP	T	T	C	rs76381196	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:101631761T>C	ENST00000310954.6	-	1	492	c.206A>G	c.(205-207)aAt>aGt	p.N69S		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TTCGGAGACATTGGGAGGGGC	0.577													T|||	137	0.0273562	0.003	0.0418	5008	,	,		15737	0.0238		0.0586	False		,,,				2504	0.0215				p.N69S		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.A206G						PASS	.	T	SER/ASN	43,4363	45.3+/-79.5	0,43,2160	88.0	90.0	89.0		206	0.0	0.0	5	dbSNP_132	89	450,8150	136.2+/-193.3	16,418,3866	yes	missense	SLCO4C1	NM_180991.4	46	16,461,6026	CC,CT,TT		5.2326,0.9759,3.7906	benign	69/725	101631761	493,12513	2203	4300	6503	SO:0001583	missense	353189	exon1			GAGACATTGGGAG	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.206A>G	5.37:g.101631761T>C	ENSP00000309741:p.Asn69Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_180991		Missense_Mutation	SNP	ENST00000310954.6	37	CCDS34205.1	73	0.033424908424908424	0	0.0	17	0.04696132596685083	23	0.04020979020979021	33	0.04353562005277045	T	0.489	-0.876175	0.02550	0.009759	0.052326	ENSG00000173930	ENST00000310954	T	0.37411	1.2	3.03	0.0173	0.14112	.	1.779600	0.03597	N	0.232787	T	0.03477	0.0100	N	0.25647	0.755	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07443	-1.0772	10	0.09843	T	0.71	.	3.8277	0.08861	0.1318:0.0:0.4638:0.4045	.	69	Q6ZQN7	SO4C1_HUMAN	S	69	ENSP00000309741:N69S	ENSP00000309741:N69S	N	-	2	0	SLCO4C1	101659660	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.523000	0.22925	-0.021000	0.14009	-0.438000	0.05819	AAT	T|0.966;C|0.034	0.034	strong		0.577	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
FAM186A	121006	hgsc.bcm.edu	37	12	50746917	50746917	+	Missense_Mutation	SNP	A	A	G	rs10876023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50746917A>G	ENST00000327337.5	-	4	3697	c.3698T>C	c.(3697-3699)cTt>cCt	p.L1233P	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Missense_Mutation_p.L1233P	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1233			L -> P (in dbSNP:rs10876023).					p.L1233P(1)									GGCCTGCTGAAGGGTTAGAGT	0.632													G|||	3051	0.609225	0.5045	0.732	5008	,	,		20432	0.744		0.664	False		,,,				2504	0.4683				p.L1233P	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - Missense(1)	kidney(1)	c.T3698C						scavenged	.						20.0	18.0	18.0					12																	50746917		692	1590	2282	SO:0001583	missense	121006	exon4			TGCTGAAGGGTTA		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.3698T>C	12.37:g.50746917A>G	ENSP00000329995:p.Leu1233Pro	Somatic	245	11	0.044898		WXS	Illumina HiSeq	Phase_I	260	132	0.507692	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	1429	0.6543040293040293	244	0.4959349593495935	268	0.7403314917127072	412	0.7202797202797203	505	0.6662269129287599	G	0.013	-1.620429	0.00828	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.04234	3.67;3.67	4.36	1.47	0.22746	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.11235	0.004;0.0	B;B	0.10450	0.005;0.0	T	0.27054	-1.0085	8	0.02654	T	1	.	3.6574	0.08226	0.3638:0.0:0.4711:0.1651	rs10876023;rs52789832;rs58944222;rs10876023	1233;1233	F5GYN0;A6NE01	.;F186A_HUMAN	P	1233	ENSP00000441337:L1233P;ENSP00000329995:L1233P	ENSP00000329995:L1233P	L	-	2	0	FAM186A	49033184	0.000000	0.05858	0.002000	0.10522	0.052000	0.14988	-0.822000	0.04448	-0.020000	0.14032	-1.288000	0.01363	CTT	A|0.349;G|0.651	0.651	strong		0.632	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
PCTP	58488	hgsc.bcm.edu	37	17	53851228	53851228	+	Silent	SNP	C	C	T	rs2960062	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:53851228C>T	ENST00000268896.5	+	4	608	c.483C>T	c.(481-483)atC>atT	p.I161I	PCTP_ENST00000573500.1_Silent_p.I161I|PCTP_ENST00000576221.1_3'UTR|PCTP_ENST00000576183.1_Silent_p.I161I|PCTP_ENST00000325214.6_Silent_p.I89I	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	161	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			GCCTGGCGATCGAGAGTGACG	0.627													C|||	3896	0.777955	0.3691	0.8487	5008	,	,		21413	0.9405		0.9612	False		,,,				2504	0.9243				p.I161I		Atlas-SNP	.											.	PCTP	17	.	0			c.C483T						PASS	.	C	,	2173,2233	578.0+/-384.6	551,1071,581	64.0	50.0	55.0		267,483	-5.8	0.1	17	dbSNP_101	55	8338,262	800.2+/-407.4	4043,252,5	no	coding-synonymous,coding-synonymous	PCTP	NM_001102402.2,NM_021213.3	,	4594,1323,586	TT,TC,CC		3.0465,49.3191,19.1835	,	89/143,161/215	53851228	10511,2495	2203	4300	6503	SO:0001819	synonymous_variant	58488	exon4			GGCGATCGAGAGT	AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"""StAR-related lipid transfer (START) domain containing"""	8752	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 2"""	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.483C>T	17.37:g.53851228C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_021213	Q9BSC9|Q9UIT3|Q9UKW7	Silent	SNP	ENST00000268896.5	37	CCDS11588.1																																																																																			C|0.205;T|0.795	0.795	strong		0.627	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2	NM_021213	
LARS	51520	hgsc.bcm.edu	37	5	145508340	145508340	+	Silent	SNP	A	A	G	rs2895647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145508340A>G	ENST00000394434.2	-	27	2941	c.2775T>C	c.(2773-2775)acT>acC	p.T925T	LARS_ENST00000545646.1_Silent_p.T879T|LARS_ENST00000510191.1_Silent_p.T871T|LARS_ENST00000274562.9_Silent_p.T898T	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	925					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	GTTGTTTGTCAGTCTTCTAGA	0.433													A|||	910	0.181709	0.0076	0.3775	5008	,	,		17138	0.1984		0.2525	False		,,,				2504	0.1881				p.T925T		Atlas-SNP	.											.	LARS	100	.	0			c.T2775C						PASS	.	A		265,4141	149.2+/-183.4	12,241,1950	181.0	175.0	177.0		2775	3.1	1.0	5	dbSNP_101	177	2398,6202	398.9+/-346.3	352,1694,2254	no	coding-synonymous	LARS	NM_020117.9		364,1935,4204	GG,GA,AA		27.8837,6.0145,20.4752		925/1177	145508340	2663,10343	2203	4300	6503	SO:0001819	synonymous_variant	51520	exon27			TTTGTCAGTCTTC	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2775T>C	5.37:g.145508340A>G		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	282	84	0.297872	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			A|0.799;G|0.201	0.201	strong		0.433	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
MEFV	4210	hgsc.bcm.edu	37	16	3293888	3293888	+	Silent	SNP	C	C	T	rs1231122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3293888C>T	ENST00000219596.1	-	9	1803	c.1764G>A	c.(1762-1764)ccG>ccA	p.P588P	MEFV_ENST00000339854.4_Silent_p.P408P|MEFV_ENST00000541159.1_Missense_Mutation_p.G436R|MEFV_ENST00000536379.1_Silent_p.P377P	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	588	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CAATCAGCTCCGGAACTACGG	0.507													T|||	1771	0.353634	0.3306	0.3746	5008	,	,		19051	0.3958		0.4423	False		,,,				2504	0.2352				p.G436R		Atlas-SNP	.											MEFV,rectum,carcinoma,-1,1	MEFV	170	1	0			c.G1306A						PASS	.	T	,ARG/GLY	1501,2893	671.9+/-402.5	244,1013,940	45.0	47.0	46.0		1764,1306	-0.2	0.2	16	dbSNP_87	46	4003,4597	597.6+/-393.8	956,2091,1253	yes	coding-synonymous,missense	MEFV	NM_000243.2,NM_001198536.1	,125	1200,3104,2193	TT,TC,CC		46.5465,34.1602,42.358	,	588/782,436/446	3293888	5504,7490	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon8			CAGCTCCGGAACT	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1764G>A	16.37:g.3293888C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	142	64	0.450704	NM_001198536	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	37	CCDS10498.1	836	0.38278388278388276	143	0.29065040650406504	135	0.3729281767955801	222	0.3881118881118881	336	0.44327176781002636	T	0.649	-0.810459	0.02798	0.341602	0.465465	ENSG00000103313	ENST00000541159	T	0.65549	-0.16	4.83	-0.232	0.13082	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.42120	-0.9470	5	0.31617	T	0.26	-22.9385	0.9747	0.01423	0.1487:0.2594:0.1541:0.4377	rs1231122;rs1801180;rs3843145;rs1231122	.	.	.	R	436	ENSP00000438711:G436R	ENSP00000438711:G436R	G	-	1	0	MEFV	3233889	0.338000	0.24775	0.175000	0.22980	0.018000	0.09664	0.169000	0.16641	-0.445000	0.07159	-0.972000	0.02603	GGA	C|0.608;T|0.392	0.392	strong		0.507	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
ASAP3	55616	hgsc.bcm.edu	37	1	23763449	23763449	+	Silent	SNP	G	G	A	rs115515935	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:23763449G>A	ENST00000336689.3	-	15	1475	c.1431C>T	c.(1429-1431)cgC>cgT	p.R477R	ASAP3_ENST00000437606.2_Silent_p.R468R|ASAP3_ENST00000495646.1_5'Flank	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	477	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						GTGACTGCATGCGCGAAAAGC	0.652													G|||	250	0.0499201	0.0121	0.0605	5008	,	,		11498	0.0		0.1044	False		,,,				2504	0.089				p.R477R		Atlas-SNP	.											.	ASAP3	65	.	0			c.C1431T						PASS	.	G	,	118,4286		4,110,2088	20.0	22.0	21.0		1404,1431	2.5	1.0	1	dbSNP_132	21	841,7755		39,763,3496	no	coding-synonymous,coding-synonymous	ASAP3	NM_001143778.1,NM_017707.3	,	43,873,5584	AA,AG,GG		9.7836,2.6794,7.3769	,	468/895,477/904	23763449	959,12041	2202	4298	6500	SO:0001819	synonymous_variant	55616	exon15			CTGCATGCGCGAA	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	14987	protein-coding gene	gene with protein product	"""centaurin, beta 6"""		"""development and differentiation enhancing factor-like 1"""	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.1431C>T	1.37:g.23763449G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	66	45	0.681818	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Silent	SNP	ENST00000336689.3	37	CCDS235.1																																																																																			G|0.932;A|0.068	0.068	strong		0.652	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707	
DSPP	1834	hgsc.bcm.edu	37	4	88536451	88536451	+	Silent	SNP	C	C	T	rs111205176|rs149201255		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536451C>T	ENST00000282478.7	+	4	2670	c.2637C>T	c.(2635-2637)agC>agT	p.S879S	DSPP_ENST00000399271.1_Silent_p.S879S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	879	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgacagcagtgatagca	0.493																																					p.S879S		Atlas-SNP	.											DSPP,colon,carcinoma,0,1	DSPP	174	1	0			c.C2637T						PASS	.						71.0	84.0	80.0					4																	88536451		1629	2928	4557	SO:0001819	synonymous_variant	1834	exon5			TGACAGCAGTGAT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2637C>T	4.37:g.88536451C>T		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	308	31	0.100649	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.493	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
FAM129C	199786	hgsc.bcm.edu	37	19	17650053	17650053	+	Silent	SNP	G	G	A	rs74546231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17650053G>A	ENST00000335393.4	+	7	921	c.783G>A	c.(781-783)gtG>gtA	p.V261V	FAM129C_ENST00000600871.1_Silent_p.V207V|FAM129C_ENST00000300971.2_Silent_p.V261V|FAM129C_ENST00000599124.1_Silent_p.V230V|FAM129C_ENST00000332386.5_Silent_p.V261V|FAM129C_ENST00000601861.1_Silent_p.V230V|FAM129C_ENST00000599164.1_Silent_p.V230V|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000595684.1_Silent_p.V261V|FAM129C_ENST00000352727.3_Silent_p.V261V	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	261										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						ACGACGACGTGACCCTAGGCT	0.726													g|||	95	0.0189696	0.0023	0.0274	5008	,	,		12413	0.0		0.0636	False		,,,				2504	0.0092				p.V261V		Atlas-SNP	.											FAM129C_ENST00000332386,NS,carcinoma,0,2	FAM129C	110	2	0			c.G783A						PASS	.	G	,	67,4321		1,65,2128	19.0	19.0	19.0		783,783	0.5	1.0	19	dbSNP_132	19	594,7986		21,552,3717	no	coding-synonymous,coding-synonymous	FAM129C	NM_001098524.1,NM_173544.4	,	22,617,5845	AA,AG,GG		6.9231,1.5269,5.0972	,	261/652,261/698	17650053	661,12307	2194	4290	6484	SO:0001819	synonymous_variant	199786	exon7			CGACGTGACCCTA	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.783G>A	19.37:g.17650053G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	38	23	0.605263	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																			G|0.962;A|0.038	0.038	strong		0.726	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
UQCRFS1	7386	hgsc.bcm.edu	37	19	29699033	29699033	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:29699033T>C	ENST00000304863.4	-	2	669	c.247A>G	c.(247-249)Atc>Gtc	p.I83V		NM_006003.2	NP_005994.2	P47985	UCRI_HUMAN	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	83					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)	p.I83V(4)		endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Breast(6;0.0545)|Esophageal squamous(110;0.239)		Lung(7;0.092)			GGCACCTTGATGTCTGTGTGG	0.423																																					p.I83V		Atlas-SNP	.											UQCRFS1,NS,carcinoma,0,4	UQCRFS1	23	4	4	Substitution - Missense(4)	endometrium(2)|kidney(2)	c.A247G						scavenged	.						53.0	59.0	57.0					19																	29699033		2203	4299	6502	SO:0001583	missense	7386	exon2			CCTTGATGTCTGT	BC010035	CCDS12415.1	19q12	2011-07-04			ENSG00000169021	ENSG00000169021	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12587	protein-coding gene	gene with protein product	"""cytochrome b-c1 complex subunit 5"""	191327				8088805	Standard	NM_006003		Approved	RIS1, RIP1, UQCR5, RISP	uc002nsd.2	P47985		ENST00000304863.4:c.247A>G	19.37:g.29699033T>C	ENSP00000306397:p.Ile83Val	Somatic	63	4	0.0634921		WXS	Illumina HiSeq	Phase_I	67	8	0.119403	NM_006003	A8K519|Q6NVX5|Q9UPH2	Missense_Mutation	SNP	ENST00000304863.4	37	CCDS12415.1	.	.	.	.	.	.	.	.	.	.	t	0.014	-1.596233	0.00857	.	.	ENSG00000169021	ENST00000304863	T	0.42131	0.98	5.42	-4.98	0.03019	Ubiquinol cytochrome reductase, transmembrane domain (3);	0.618499	0.17385	N	0.176150	T	0.22360	0.0539	N	0.16862	0.45	0.20764	N	0.999851	B	0.02656	0.0	B	0.14578	0.011	T	0.23976	-1.0173	10	0.08837	T	0.75	.	17.2071	0.86921	0.0:0.6778:0.0:0.3222	.	83	P47985	UCRI_HUMAN	V	83	ENSP00000306397:I83V	ENSP00000306397:I83V	I	-	1	0	UQCRFS1	34390873	0.987000	0.35691	0.084000	0.20598	0.009000	0.06853	0.184000	0.16939	-1.243000	0.02519	-3.117000	0.00062	ATC	.	.	none		0.423	UQCRFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458563.1	NM_006003	
CECR5	27440	hgsc.bcm.edu	37	22	17630486	17630486	+	Silent	SNP	C	C	A	rs1034859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:17630486C>A	ENST00000336737.4	-	2	301	c.276G>T	c.(274-276)ggG>ggT	p.G92G	CECR5_ENST00000155674.5_Silent_p.G62G|CECR5_ENST00000399852.3_Intron|CECR5_ENST00000480451.1_5'UTR	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	92						mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				GTAAGATGTTCCCAGCATTTG	0.592													C|||	2676	0.534345	0.3759	0.6744	5008	,	,		17538	0.6796		0.5447	False		,,,				2504	0.4888				p.G92G		Atlas-SNP	.											.	CECR5	46	.	0			c.G276T						PASS	.	C	,	1707,2699	514.7+/-368.7	324,1059,820	100.0	100.0	100.0		186,276	1.5	1.0	22	dbSNP_86	100	4584,4016	596.6+/-393.6	1224,2136,940	no	coding-synonymous,coding-synonymous	CECR5	NM_017829.5,NM_033070.2	,	1548,3195,1760	AA,AC,CC		46.6977,38.7426,48.37	,	62/394,92/424	17630486	6291,6715	2203	4300	6503	SO:0001819	synonymous_variant	27440	exon2			GATGTTCCCAGCA	AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.276G>T	22.37:g.17630486C>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_033070	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Silent	SNP	ENST00000336737.4	37	CCDS33595.1																																																																																			C|0.487;A|0.513	0.513	strong		0.592	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829	
REPIN1	29803	hgsc.bcm.edu	37	7	150068620	150068620	+	Missense_Mutation	SNP	C	C	T	rs17173703	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150068620C>T	ENST00000425389.2	+	1	368	c.290C>T	c.(289-291)gCc>gTc	p.A97V	REPIN1_ENST00000518462.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000444957.1_Missense_Mutation_p.A97V|REPIN1_ENST00000489432.2_Missense_Mutation_p.A154V|REPIN1_ENST00000540729.1_Missense_Mutation_p.A97V|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000518514.1_3'UTR|REPIN1_ENST00000397281.2_Missense_Mutation_p.A97V|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000482680.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	97			A -> V (in dbSNP:rs17173703).		DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			TTTCGCCATGCCCCCTTCTTA	0.687													C|||	1164	0.232428	0.0227	0.1527	5008	,	,		14808	0.3988		0.2793	False		,,,				2504	0.3528				p.A154V		Atlas-SNP	.											.	REPIN1	74	.	0			c.C461T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	212,4040		8,196,1922	20.0	23.0	22.0		461,290,290,290	3.6	1.0	7	dbSNP_123	22	2231,6223		284,1663,2280	yes	missense,missense,missense,missense	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	64,64,64,64	292,1859,4202	TT,TC,CC		26.3899,4.9859,19.2271	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	154/625,97/568,97/568,97/568	150068620	2443,10263	2126	4227	6353	SO:0001583	missense	29803	exon3			GCCATGCCCCCTT	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.290C>T	7.37:g.150068620C>T	ENSP00000388287:p.Ala97Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Missense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	546	0.25	15	0.03048780487804878	63	0.17403314917127072	243	0.42482517482517484	225	0.29683377308707126	C	16.32	3.091429	0.55968	0.049859	0.263899	ENSG00000214022	ENST00000519397;ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000461637;ENST00000425389	T;T;T;T;T;T;T;T	0.52754	0.65;2.45;2.45;2.45;2.45;2.45;2.45;2.45	5.54	3.63	0.41609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	.	.	.	.	T	0.00012	0.0000	L	0.39566	1.225	0.33306	P	0.43454800000000005	P;P	0.38745	0.645;0.645	P;B	0.46975	0.533;0.405	T	0.46693	-0.9173	8	0.48119	T	0.1	-8.9286	7.3226	0.26536	0.0:0.6246:0.2862:0.0892	rs17173703	154;97	C9J3L7;Q9BWE0	.;REPI1_HUMAN	V	97;97;97;97;154;156;157;154;97	ENSP00000428562:A97V;ENSP00000445016:A97V;ENSP00000380451:A97V;ENSP00000407714:A97V;ENSP00000417291:A154V;ENSP00000419789:A156V;ENSP00000419872:A157V;ENSP00000388287:A97V	ENSP00000380451:A97V	A	+	2	0	REPIN1	149699553	0.814000	0.29104	0.999000	0.59377	0.982000	0.71751	0.878000	0.28126	1.340000	0.45581	0.462000	0.41574	GCC	C|0.765;T|0.235	0.235	strong		0.687	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
GBP4	115361	hgsc.bcm.edu	37	1	89652097	89652097	+	Missense_Mutation	SNP	C	C	T	rs1142886	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89652097C>T	ENST00000355754.6	-	10	1723	c.1626G>A	c.(1624-1626)atG>atA	p.M542I	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	542			M -> I (in dbSNP:rs1142886).	YM -> NI (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		CCATTTGGGCCATGTATTCCT	0.473													C|||	1801	0.359625	0.1445	0.3141	5008	,	,		18628	0.3998		0.4891	False		,,,				2504	0.5082				p.M542I		Atlas-SNP	.											.	GBP4	89	.	0			c.G1626A						PASS	.	C	ILE/MET	446,3960		119,208,1876	168.0	105.0	126.0		1626	-7.4	0.0	1	dbSNP_86	126	2956,5644		1064,828,2408	no	missense	GBP4	NM_052941.4	10	1183,1036,4284	TT,TC,CC		34.3721,10.1226,26.1572	benign	542/641	89652097	3402,9604	2203	4300	6503	SO:0001583	missense	115361	exon10			TTGGGCCATGTAT	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1626G>A	1.37:g.89652097C>T	ENSP00000359490:p.Met542Ile	Somatic	468	0	0		WXS	Illumina HiSeq	Phase_I	137	135	0.985401	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	617	0.2825091575091575	38	0.07723577235772358	113	0.31215469613259667	182	0.3181818181818182	284	0.37467018469656993	C	0.034	-1.318603	0.01320	0.101226	0.343721	ENSG00000162654	ENST00000355754	T	0.49432	0.78	4.29	-7.4	0.01397	Guanylate-binding protein, C-terminal (3);	1.121610	0.06584	N	0.750755	T	0.02083	0.0065	N	0.00256	-1.76	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.21518	-1.0243	9	0.02654	T	1	.	5.4902	0.16771	0.2068:0.3872:0.0:0.4059	rs1142886;rs3180072;rs3206368;rs34488490	542	Q96PP9	GBP4_HUMAN	I	542	ENSP00000359490:M542I	ENSP00000359490:M542I	M	-	3	0	GBP4	89424685	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-4.744000	0.00191	-1.145000	0.02858	-1.326000	0.01283	ATG	C|0.619;T|0.381	0.381	strong		0.473	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
PHIP	55023	hgsc.bcm.edu	37	6	79656562	79656562	+	Silent	SNP	A	A	T	rs2275291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:79656562A>T	ENST00000275034.4	-	37	4403	c.4236T>A	c.(4234-4236)gcT>gcA	p.A1412A	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1412					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CTTCAAAGAAAGCAGACAGGC	0.333													A|||	1205	0.240615	0.2564	0.2853	5008	,	,		15350	0.1845		0.3211	False		,,,				2504	0.1626				p.A1412A		Atlas-SNP	.											.	PHIP	177	.	0			c.T4236A						PASS	.	A		1206,3200	399.2+/-331.1	160,886,1157	66.0	68.0	67.0		4236	4.4	1.0	6	dbSNP_100	67	2591,6009	415.3+/-351.7	410,1771,2119	no	coding-synonymous	PHIP	NM_017934.5		570,2657,3276	TT,TA,AA		30.1279,27.3718,29.1942		1412/1822	79656562	3797,9209	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon37			AAAGAAAGCAGAC	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4236T>A	6.37:g.79656562A>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			A|0.719;T|0.281	0.281	strong		0.333	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
FAM186A	121006	hgsc.bcm.edu	37	12	50745783	50745783	+	Missense_Mutation	SNP	T	T	A	rs373687267		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745783T>A	ENST00000327337.5	-	4	4831	c.4832A>T	c.(4831-4833)cAg>cTg	p.Q1611L	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Missense_Mutation_p.Q1611L	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1611								p.Q1611L(1)									AGGGATCCCCTGAGCCTGCGC	0.677																																					p.Q1611L	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - Missense(1)	stomach(1)	c.A4832T						scavenged	.						12.0	11.0	12.0					12																	50745783		692	1590	2282	SO:0001583	missense	121006	exon4			ATCCCCTGAGCCT		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4832A>T	12.37:g.50745783T>A	ENSP00000329995:p.Gln1611Leu	Somatic	170	2	0.0117647		WXS	Illumina HiSeq	Phase_I	257	87	0.338521	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	T	0.158	-1.083821	0.01888	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.04406	3.63;3.63	3.66	-7.33	0.01431	.	.	.	.	.	T	0.02230	0.0069	N	0.17082	0.46	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43180	-0.9407	9	0.12103	T	0.63	.	5.6207	0.17455	0.2461:0.2677:0.0:0.4862	.	1611;1611	F5GYN0;A6NE01	.;F186A_HUMAN	L	1611	ENSP00000441337:Q1611L;ENSP00000329995:Q1611L	ENSP00000329995:Q1611L	Q	-	2	0	FAM186A	49032050	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-8.288000	0.00022	-3.000000	0.00276	-1.250000	0.01514	CAG	.	.	weak		0.677	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
IGFN1	91156	hgsc.bcm.edu	37	1	201181920	201181920	+	Silent	SNP	G	G	T	rs12060924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201181920G>T	ENST00000335211.4	+	12	8029	c.7899G>T	c.(7897-7899)ggG>ggT	p.G2633G	IGFN1_ENST00000451870.2_Intron|IGFN1_ENST00000295591.8_5'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	0						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						AAAACCAGGGGTTTAGCCAAG	0.577													g|||	1537	0.306909	0.1853	0.3141	5008	,	,		18307	0.3105		0.3499	False		,,,				2504	0.4182				p.G2633G		Atlas-SNP	.											.	IGFN1	220	.	0			c.G7899T						PASS	.			272,1112		28,216,448	26.0	30.0	29.0		7899	1.0	0.0	1	dbSNP_120	29	1062,2120		180,702,709	no	coding-synonymous	IGFN1	NM_001164586.1		208,918,1157	TT,TG,GG		33.3752,19.6532,29.2159		2633/3709	201181920	1334,3232	692	1591	2283	SO:0001819	synonymous_variant	91156	exon12			CCAGGGGTTTAGC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.7899G>T	1.37:g.201181920G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	672	0.3076923076923077	104	0.21138211382113822	113	0.31215469613259667	191	0.3339160839160839	264	0.3482849604221636	g	3.553	-0.091204	0.07053	0.196532	0.333752	ENSG00000163395	ENST00000412892	.	.	.	3.15	1.04	0.20106	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53688	P	2.1000000000048757E-5	.	.	.	.	.	.	T	0.40117	-0.9580	3	.	.	.	.	4.9669	0.14094	0.1306:0.2162:0.6532:0.0	rs12060924	.	.	.	F	51	.	.	V	+	1	0	IGFN1	199448543	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	0.052000	0.14163	-0.135000	0.11495	0.306000	0.20318	GTT	G|0.691;T|0.309	0.309	strong		0.577	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
TRIM38	10475	hgsc.bcm.edu	37	6	25983777	25983777	+	Silent	SNP	C	C	T	rs17528178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:25983777C>T	ENST00000357085.3	+	8	1736	c.1260C>T	c.(1258-1260)gcC>gcT	p.A420A	U91328.21_ENST00000608931.1_RNA|TRIM38_ENST00000349458.3_Silent_p.A420A	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	420	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						ACTATGAGGCCGGAGTTGTAT	0.473													C|||	161	0.0321486	0.0514	0.0403	5008	,	,		18020	0.0		0.0646	False		,,,				2504	0.0				p.A420A		Atlas-SNP	.											.	TRIM38	50	.	0			c.C1260T						PASS	.	C		247,4159	144.2+/-179.2	6,235,1962	87.0	85.0	86.0		1260	-8.5	0.0	6	dbSNP_123	86	634,7966	163.3+/-215.9	22,590,3688	no	coding-synonymous	TRIM38	NM_006355.2		28,825,5650	TT,TC,CC		7.3721,5.606,6.7738		420/466	25983777	881,12125	2203	4300	6503	SO:0001819	synonymous_variant	10475	exon8			TGAGGCCGGAGTT	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10059	protein-coding gene	gene with protein product			"""ring finger protein 15"", ""tripartite motif-containing 38"""	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.1260C>T	6.37:g.25983777C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	203	112	0.551724	NM_006355	B2R862	Silent	SNP	ENST00000357085.3	37	CCDS4568.1																																																																																			C|0.942;G|0.000;T|0.058	0.058	strong		0.473	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2		
MCPH1	79648	hgsc.bcm.edu	37	8	6296550	6296550	+	Missense_Mutation	SNP	G	G	T	rs2442513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:6296550G>T	ENST00000344683.5	+	6	589	c.513G>T	c.(511-513)agG>agT	p.R171S	MCPH1_ENST00000519480.1_Missense_Mutation_p.R171S|MCPH1_ENST00000522905.1_Intron	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	171			R -> S (in dbSNP:rs2442513). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.5}.		cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		TTAATAGTAGGCACCACAGCG	0.323													T|||	4592	0.916933	0.7405	0.9827	5008	,	,		17356	0.9851		0.9871	False		,,,				2504	0.9663				p.R171S	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.G513T						PASS	.	T	SER/ARG,,SER/ARG	2997,761		1202,593,84	94.0	86.0	88.0		513,,513	-4.6	0.0	8	dbSNP_100	88	8080,136		3972,136,0	yes	missense,intron,missense	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	110,,110	5174,729,84	TT,TG,GG		1.6553,20.2501,7.4912	benign,,benign	171/611,,171/836	6296550	11077,897	1879	4108	5987	SO:0001583	missense	79648	exon6			TAGTAGGCACCAC	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.513G>T	8.37:g.6296550G>T	ENSP00000342924:p.Arg171Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	2028	0.9285714285714286	354	0.7195121951219512	355	0.9806629834254144	568	0.993006993006993	751	0.9907651715039578	T	2.476	-0.320674	0.05386	0.797499	0.983447	ENSG00000147316	ENST00000344683;ENST00000519480	T;T	0.05319	3.78;3.46	3.64	-4.59	0.03400	.	1.218780	0.05906	N	0.630898	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18871	-1.0323	9	0.07990	T	0.79	-1.184	5.881	0.18856	0.0:0.2768:0.3872:0.3361	rs2442513;rs17855554;rs52799955;rs60616014;rs2442513	171;171	Q8NEM0;E9PGU5	MCPH1_HUMAN;.	S	171	ENSP00000342924:R171S;ENSP00000430962:R171S	ENSP00000342924:R171S	R	+	3	2	MCPH1	6283958	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.292000	0.08332	-1.007000	0.03408	-0.346000	0.07831	AGG	G|0.081;T|0.919	0.919	strong		0.323	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
F8	2157	hgsc.bcm.edu	37	X	154158201	154158201	+	Silent	SNP	T	T	G	rs1800292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:154158201T>G	ENST00000360256.4	-	14	4064	c.3864A>C	c.(3862-3864)tcA>tcC	p.S1288S		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1288	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CCCCTTTTTTTGAGAAATGAG	0.378													T|||	606	0.16053	0.0499	0.1484	3775	,	,		13873	0.1359		0.0527	False		,,,				2504	0.2526				p.S1288S		Atlas-SNP	.											.	F8	646	.	0			c.A3864C	GRCh37	CI992004	F8	I	rs1800292	PASS	.	T		238,3597		7,188,36,1437,535	164.0	141.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3864	2.5	0.1	X	dbSNP_89	149	608,6119		22,381,183,2025,1688	no	coding-synonymous	F8	NM_000132.3		29,569,219,3462,2223	GG,GT,G,TT,T		9.0382,6.206,8.0098		1288/2352	154158201	846,9716	2203	4299	6502	SO:0001819	synonymous_variant	2157	exon14			TTTTTTTGAGAAA	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"""Factor VIIIF8B"", ""hemophilia A"""	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3864A>C	X.37:g.154158201T>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_000132	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	37	CCDS35457.1																																																																																			T|0.888;0|0.022	.	strong		0.378	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
SULF2	55959	hgsc.bcm.edu	37	20	46365636	46365636	+	Missense_Mutation	SNP	C	C	T	rs56218501	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:46365636C>T	ENST00000359930.4	-	3	1077	c.226G>A	c.(226-228)Gcg>Acg	p.A76T	SULF2_ENST00000484875.1_Missense_Mutation_p.A76T|SULF2_ENST00000361612.4_Missense_Mutation_p.A76T|SULF2_ENST00000478766.1_5'UTR|SULF2_ENST00000467815.1_Missense_Mutation_p.A76T	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	76			A -> T (in dbSNP:rs56218501). {ECO:0000269|PubMed:10574462}.		bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						ATGAAGTGCGCCCCGCCCTGC	0.607													C|||	389	0.0776757	0.0061	0.1354	5008	,	,		18064	0.001		0.2167	False		,,,				2504	0.0695				p.A76T		Atlas-SNP	.											SULF2,colon,carcinoma,+2,3	SULF2	131	3	0			c.G226A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	168,4238	110.8+/-149.0	8,152,2043	206.0	164.0	178.0		226,226,226	5.4	1.0	20	dbSNP_129	178	1848,6752	331.5+/-319.7	219,1410,2671	yes	missense,missense,missense	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	58,58,58	227,1562,4714	TT,TC,CC		21.4884,3.813,15.5005	benign,benign,benign	76/871,76/871,76/868	46365636	2016,10990	2203	4300	6503	SO:0001583	missense	55959	exon3			AGTGCGCCCCGCC	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.226G>A	20.37:g.46365636C>T	ENSP00000353007:p.Ala76Thr	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	250	142	0.568	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	218	0.09981684981684982	2	0.0040650406504065045	60	0.16574585635359115	0	0.0	156	0.20580474934036938	C	13.86	2.362478	0.41902	0.03813	0.214884	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815;ENST00000437955	D;D;D;D;D	0.98455	-4.94;-4.94;-4.94;-4.94;-4.94	5.44	5.44	0.79542	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.103148	0.64402	D	0.000002	T	0.00754	0.0025	N	0.05534	-0.03	0.23809	P	0.99678531	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.09377	0.002;0.002;0.004	T	0.55405	-0.8146	9	0.27785	T	0.31	-14.4645	8.5077	0.33197	0.1539:0.7697:0.0:0.0764	rs56218501;rs61741658	76;76;76	G3XAE6;Q8IWU5-2;Q8IWU5	.;.;SULF2_HUMAN	T	76	ENSP00000353007:A76T;ENSP00000418290:A76T;ENSP00000354662:A76T;ENSP00000418442:A76T;ENSP00000410026:A76T	ENSP00000353007:A76T	A	-	1	0	SULF2	45799043	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	2.973000	0.49264	2.559000	0.86315	0.561000	0.74099	GCG	C|0.856;G|0.000;T|0.144	0.144	strong		0.607	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
GPC2	221914	hgsc.bcm.edu	37	7	99768957	99768957	+	Silent	SNP	C	C	T	rs75779608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99768957C>T	ENST00000292377.2	-	9	1580	c.1413G>A	c.(1411-1413)cgG>cgA	p.R471R	GAL3ST4_ENST00000360039.4_5'Flank|GPC2_ENST00000471050.1_5'UTR|GAL3ST4_ENST00000423751.1_5'Flank	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2	471					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuron differentiation (GO:0030182)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	anchored component of membrane (GO:0031225)|endoplasmic reticulum (GO:0005783)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.R471R(1)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(3)	18	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGAGCTGTAGCCGACGCCGCC	0.706													C|||	492	0.0982428	0.0182	0.1052	5008	,	,		8610	0.0556		0.2157	False		,,,				2504	0.1247				p.R471R		Atlas-SNP	.											GPC2,NS,haematopoietic_neoplasm,0,1	GPC2	49	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1413A						PASS	.	C		228,3912		9,210,1851	7.0	9.0	8.0		1413	0.2	0.8	7	dbSNP_131	8	1612,6562		145,1322,2620	no	coding-synonymous	GPC2	NM_152742.1		154,1532,4471	TT,TC,CC		19.7211,5.5072,14.9423		471/580	99768957	1840,10474	2070	4087	6157	SO:0001819	synonymous_variant	221914	exon9			CTGTAGCCGACGC	BX375153	CCDS5689.1	7q22.1	2007-02-16	2007-02-15		ENSG00000213420	ENSG00000213420		"""Proteoglycans / Cell Surface : Glypicans"""	4450	protein-coding gene	gene with protein product	"""glypican proteoglycan 2, cerebroglycan proteoglycan"""		"""glypican 2 (cerebroglycan)"""			8294498	Standard	NM_152742		Approved	cerebroglycan, FLJ38962, DKFZp547M109	uc003utv.3	Q8N158	OTTHUMG00000154894	ENST00000292377.2:c.1413G>A	7.37:g.99768957C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	99	62	0.626263	NM_152742	A4D2A7	Silent	SNP	ENST00000292377.2	37	CCDS5689.1																																																																																			C|0.885;T|0.115	0.115	strong		0.706	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337556.1	NM_152742	
C2orf61	285051	hgsc.bcm.edu	37	2	47378611	47378611	+	Missense_Mutation	SNP	T	T	C	rs71423949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:47378611T>C	ENST00000445927.2	-	3	311	c.185A>G	c.(184-186)gAa>gGa	p.E62G	RP11-761B3.1_ENST00000422269.1_3'UTR|C2orf61_ENST00000294947.2_Missense_Mutation_p.E62G	NM_001163561.1	NP_001157033.1	Q8N801	CB061_HUMAN	chromosome 2 open reading frame 61	62								p.0?(2)		endometrium(1)|kidney(1)|lung(2)	4		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			TAGGGATTCTTCAATAAAAGT	0.348													T|||	42	0.00838658	0.0045	0.0115	5008	,	,		18052	0.0		0.0199	False		,,,				2504	0.0082				p.E62G		Atlas-SNP	.											C2orf61_ENST00000445927,NS,carcinoma,-1,2	C2orf61	31	2	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A185G						PASS	.	T	GLY/GLU,GLY/GLU	28,4378	32.6+/-62.9	0,28,2175	114.0	113.0	113.0		185,185	5.1	1.0	2	dbSNP_130	113	198,8402	83.4+/-145.9	2,194,4104	yes	missense,missense	C2orf61	NM_001163561.1,NM_173649.2	98,98	2,222,6279	CC,CT,TT		2.3023,0.6355,1.7377	possibly-damaging,possibly-damaging	62/249,62/178	47378611	226,12780	2203	4300	6503	SO:0001583	missense	285051	exon3			GATTCTTCAATAA	AK097491	CCDS1831.1, CCDS54356.1	2p21	2008-02-05			ENSG00000239605	ENSG00000239605			26850	protein-coding gene	gene with protein product							Standard	NM_173649		Approved	FLJ40172	uc010yog.2	Q8N801	OTTHUMG00000128851	ENST00000445927.2:c.185A>G	2.37:g.47378611T>C	ENSP00000408527:p.Glu62Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	166	91	0.548193	NM_173649	H7C2Z2	Missense_Mutation	SNP	ENST00000445927.2	37	CCDS54356.1	27	0.012362637362637362	4	0.008130081300813009	5	0.013812154696132596	0	0.0	18	0.023746701846965697	T	20.6	4.021562	0.75275	0.006355	0.023023	ENSG00000239605	ENST00000445927;ENST00000294947	T;T	0.37058	1.22;1.24	5.12	5.12	0.69794	.	0.121832	0.36972	N	0.002320	T	0.38612	0.1047	M	0.62723	1.935	0.34185	D	0.671394	D	0.71674	0.998	D	0.66979	0.948	T	0.65298	-0.6202	10	0.66056	D	0.02	-0.3057	13.137	0.59415	0.0:0.0:0.0:1.0	.	62	Q8N801	CB061_HUMAN	G	62	ENSP00000408527:E62G;ENSP00000294947:E62G	ENSP00000294947:E62G	E	-	2	0	C2orf61	47232115	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.211000	0.65219	1.930000	0.55929	0.383000	0.25322	GAA	T|0.983;C|0.017	0.017	strong		0.348	C2orf61-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173649	
AKR1C3	8644	hgsc.bcm.edu	37	10	5138747	5138747	+	Missense_Mutation	SNP	A	A	G	rs11551177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:5138747A>G	ENST00000380554.3	+	2	882	c.230A>G	c.(229-231)gAa>gGa	p.E77G	AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.E54G	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	77			E -> G (in dbSNP:rs41306308).		arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	GTGAAGAGAGAAGACATATTC	0.423													A|||	184	0.0367412	0.028	0.0663	5008	,	,		22113	0.001		0.0825	False		,,,				2504	0.0174				p.E77G		Atlas-SNP	.											.	AKR1C3	21	.	0			c.A230G						PASS	.	A	GLY/GLU	111,4295	86.8+/-125.4	0,111,2092	175.0	138.0	151.0		230	2.0	0.5	10	dbSNP_120	151	543,8053	149.5+/-204.6	13,517,3768	no	missense	AKR1C3	NM_003739.4	98	13,628,5860	GG,GA,AA		6.3169,2.5193,5.03	benign	77/324	5138747	654,12348	2203	4298	6501	SO:0001583	missense	8644	exon2			AGAGAGAAGACAT	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.230A>G	10.37:g.5138747A>G	ENSP00000369927:p.Glu77Gly	Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	328	157	0.478659	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	103	0.04716117216117216	14	0.028455284552845527	25	0.06906077348066299	1	0.0017482517482517483	63	0.08311345646437995	A	17.28	3.349582	0.61183	0.025193	0.063169	ENSG00000196139	ENST00000380554	T	0.56611	0.45	2.0	2.0	0.26442	NADP-dependent oxidoreductase domain (3);	0.103283	0.39544	N	0.001339	T	0.04861	0.0131	M	0.78637	2.42	0.80722	D	1	B;B	0.20780	0.029;0.048	B;B	0.29598	0.096;0.104	T	0.36138	-0.9760	10	0.87932	D	0	.	7.9207	0.29843	1.0:0.0:0.0:0.0	rs41306308	77;77	B4DKT3;P42330	.;AK1C3_HUMAN	G	77	ENSP00000369927:E77G	ENSP00000369927:E77G	E	+	2	0	AKR1C3	5128747	1.000000	0.71417	0.478000	0.27316	0.756000	0.42949	6.896000	0.75665	1.168000	0.42723	0.260000	0.18958	GAA	A|0.950;G|0.050	0.050	strong		0.423	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28358320	28358320	+	Intron	SNP	A	A	G	rs1361385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28358320A>G	ENST00000361028.1	-	4	1840				ZSCAN12_ENST00000396827.3_Intron			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						CACTCTTTACATACATAGGTA	0.428													A|||	1935	0.386382	0.5582	0.3271	5008	,	,		21437	0.2996		0.2893	False		,,,				2504	0.3855				p.C583R		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.T1747C						PASS	.	A	ARG/CYS	645,739		147,351,194	298.0	257.0	269.0		1747	2.4	0.2	6	dbSNP_88	269	1003,2179		161,681,749	yes	missense	ZSCAN12	NM_001163391.1	180	308,1032,943	GG,GA,AA		31.5211,46.604,36.0929		583/612	28358320	1648,2918	692	1591	2283	SO:0001627	intron_variant	9753	exon4			CTTTACATACATA	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.1694+52T>C	6.37:g.28358320A>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	251	98	0.390438	NM_001163391	O43724	Missense_Mutation	SNP	ENST00000361028.1	37																																																																																				A|0.632;G|0.368	0.368	strong		0.428	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
CNTRL	11064	hgsc.bcm.edu	37	9	123929770	123929770	+	Silent	SNP	C	C	T	rs61745682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:123929770C>T	ENST00000373855.1	+	37	5919	c.5659C>T	c.(5659-5661)Ctg>Ttg	p.L1887L	CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000373850.1_Silent_p.L1335L|CNTRL_ENST00000238341.5_Silent_p.L1887L			Q7Z7A1	CNTRL_HUMAN	centriolin	1887					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						CCTAAAGGACCTGCTTCACAC	0.453													C|||	637	0.127196	0.0174	0.1945	5008	,	,		19467	0.1746		0.1431	False		,,,				2504	0.1626				p.L1887L		Atlas-SNP	.											.	CNTRL	161	.	0			c.C5659T						PASS	.	C		160,4246	107.3+/-145.7	1,158,2044	60.0	48.0	52.0		5659	4.2	0.9	9	dbSNP_129	52	1234,7366	244.3+/-273.6	91,1052,3157	no	coding-synonymous	CNTRL	NM_007018.4		92,1210,5201	TT,TC,CC		14.3488,3.6314,10.7181		1887/2326	123929770	1394,11612	2203	4300	6503	SO:0001819	synonymous_variant	11064	exon35			AAGGACCTGCTTC	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.5659C>T	9.37:g.123929770C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	190	105	0.552632	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Silent	SNP	ENST00000373855.1	37	CCDS35118.1																																																																																			C|0.881;T|0.119	0.119	strong		0.453	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
ECM1	1893	hgsc.bcm.edu	37	1	150483355	150483355	+	Missense_Mutation	SNP	C	C	T	rs3737240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:150483355C>T	ENST00000369047.4	+	6	514	c.389C>T	c.(388-390)aCg>aTg	p.T130M	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Missense_Mutation_p.T157M|ECM1_ENST00000346569.6_Missense_Mutation_p.T130M	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	130			T -> M (in dbSNP:rs3737240). {ECO:0000269|PubMed:12603844, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			ATTCCAGGAACGCCAGCTCCA	0.597													C|||	1121	0.223842	0.0325	0.2493	5008	,	,		17844	0.2371		0.3757	False		,,,				2504	0.2945				p.T157M	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											ECM1_ENST00000369049,NS,carcinoma,0,2	ECM1	96	2	0			c.C470T						PASS	.	C	MET/THR,MET/THR,MET/THR	418,3954		29,360,1797	53.0	54.0	53.0		470,389,389	-5.2	0.0	1	dbSNP_107	53	3405,5143		706,1993,1575	yes	missense,missense,missense	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	81,81,81	735,2353,3372	TT,TC,CC		39.8339,9.5608,29.5898	benign,benign,benign	157/568,130/541,130/416	150483355	3823,9097	2186	4274	6460	SO:0001583	missense	1893	exon6			CAGGAACGCCAGC	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.389C>T	1.37:g.150483355C>T	ENSP00000358043:p.Thr130Met	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	193	80	0.414508	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Missense_Mutation	SNP	ENST00000369047.4	37	CCDS953.1	533	0.24404761904761904	15	0.03048780487804878	106	0.292817679558011	134	0.23426573426573427	278	0.36675461741424803	C	9.009	0.981920	0.18812	0.095608	0.398339	ENSG00000143369	ENST00000369049;ENST00000369047;ENST00000346569	T;T;T	0.75821	-0.97;-0.97;-0.97	4.86	-5.22	0.02806	.	0.733388	0.12158	N	0.494295	T	0.38506	0.1043	L	0.29908	0.895	0.80722	P	0.0	D;B;B;B;B	0.64830	0.994;0.02;0.11;0.0;0.136	P;B;B;B;B	0.47744	0.556;0.005;0.01;0.0;0.023	T	0.25710	-1.0124	9	0.35671	T	0.21	-2.6117	1.2462	0.01973	0.2141:0.1373:0.1627:0.4858	rs3737240;rs11541581;rs17852141;rs3737240	59;157;130;130;130	Q16610-3;Q16610-4;C8CHS3;Q16610-2;Q16610	.;.;.;.;ECM1_HUMAN	M	157;130;130	ENSP00000358045:T157M;ENSP00000358043:T130M;ENSP00000271630:T130M	ENSP00000271630:T130M	T	+	2	0	ECM1	148749979	0.189000	0.23263	0.001000	0.08648	0.001000	0.01503	-0.279000	0.08479	-0.716000	0.04962	-2.727000	0.00130	ACG	C|0.728;T|0.272	0.272	strong		0.597	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
EIF3A	8661	hgsc.bcm.edu	37	10	120828969	120828969	+	Silent	SNP	A	A	G	rs7908387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:120828969A>G	ENST00000369144.3	-	6	1066	c.939T>C	c.(937-939)gaT>gaC	p.D313D	EIF3A_ENST00000541549.1_Silent_p.D279D	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		TTTGCATCTCATCTTGTGTGA	0.338													A|||	3959	0.790535	0.3949	0.9193	5008	,	,		22304	0.8829		0.9692	False		,,,				2504	0.955				p.D313D		Atlas-SNP	.											.	EIF3A	142	.	0			c.T939C						PASS	.	A		2267,2139	596.9+/-388.7	586,1095,522	86.0	79.0	82.0		939	0.5	1.0	10	dbSNP_116	82	8372,228	807.9+/-407.2	4076,220,4	no	coding-synonymous	EIF3A	NM_003750.2		4662,1315,526	GG,GA,AA		2.6512,48.5474,18.1993		313/1383	120828969	10639,2367	2203	4300	6503	SO:0001819	synonymous_variant	8661	exon6			CATCTCATCTTGT	U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"""eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"""	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.939T>C	10.37:g.120828969A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	Silent	SNP	ENST00000369144.3	37	CCDS7608.1																																																																																			A|0.196;G|0.804	0.804	strong		0.338	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750	
SLC5A12	159963	hgsc.bcm.edu	37	11	26705310	26705310	+	Silent	SNP	A	A	G	rs3924551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:26705310A>G	ENST00000396005.3	-	11	1611	c.1302T>C	c.(1300-1302)aaT>aaC	p.N434N		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	434					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						TTACCTTCCAATTCACAAAAG	0.512													G|||	2179	0.435104	0.3185	0.3689	5008	,	,		17943	0.3472		0.6342	False		,,,				2504	0.5256				p.N434N		Atlas-SNP	.											SLC5A12,NS,carcinoma,0,1	SLC5A12	134	1	0			c.T1302C						PASS	.	G		1423,2351		277,869,741	61.0	58.0	59.0		1302	5.6	1.0	11	dbSNP_108	59	5099,3155		1582,1935,610	no	coding-synonymous	SLC5A12	NM_178498.3		1859,2804,1351	GG,GA,AA		38.2239,37.7054,45.7765		434/619	26705310	6522,5506	1887	4127	6014	SO:0001819	synonymous_variant	159963	exon11			CTTCCAATTCACA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"""Solute carriers"""	28750	protein-coding gene	gene with protein product		612455	"""solute carrier family 5 (sodium/glucose cotransporter), member 12"""			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1302T>C	11.37:g.26705310A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			A|0.542;G|0.458	0.458	strong		0.512	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
GALNT9	50614	hgsc.bcm.edu	37	12	132862868	132862868	+	Silent	SNP	G	G	A	rs78370891	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:132862868G>A	ENST00000328957.8	-	2	386	c.387C>T	c.(385-387)ctC>ctT	p.L129L		NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	129					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		TGCTCCGATCGAGGGAGATGC	0.667													C|||	257	0.0513179	0.0386	0.0793	5008	,	,		9703	0.0		0.1213	False		,,,				2504	0.0297				p.L129L	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.C387T						PASS	.	C		51,1333		0,51,641	54.0	61.0	59.0		387	2.7	1.0	12	dbSNP_132	59	302,2880		22,258,1311	no	coding-synonymous	GALNT9	NM_001122636.1		22,309,1952	AA,AG,GG		9.4909,3.685,7.7311		129/360	132862868	353,4213	692	1591	2283	SO:0001819	synonymous_variant	50614	exon2			CCGATCGAGGGAG	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.387C>T	12.37:g.132862868G>A		Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	359	178	0.495822	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37																																																																																				G|0.934;A|0.066	0.066	strong		0.667	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
CLRN2	645104	hgsc.bcm.edu	37	4	17528570	17528570	+	Silent	SNP	G	G	C	rs2597792	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:17528570G>C	ENST00000511148.2	+	3	666	c.564G>C	c.(562-564)tcG>tcC	p.S188S	snoU13_ENST00000459186.1_RNA	NM_001079827.2	NP_001073296.1	A0PK11	CLRN2_HUMAN	clarin 2	188						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|upper_aerodigestive_tract(1)	15						ATGAAGAGTCGTTTTGGATCT	0.517													G|||	307	0.0613019	0.1452	0.0346	5008	,	,		19019	0.0		0.0338	False		,,,				2504	0.0583				p.S188S		Atlas-SNP	.											.	CLRN2	40	.	0			c.G564C						PASS	.	G		545,3759		31,483,1638	111.0	120.0	117.0		564	-11.5	0.0	4	dbSNP_100	117	333,8169		6,321,3924	no	coding-synonymous	CLRN2	NM_001079827.2		37,804,5562	CC,CG,GG		3.9167,12.6626,6.8562		188/233	17528570	878,11928	2152	4251	6403	SO:0001819	synonymous_variant	645104	exon3			AGAGTCGTTTTGG		CCDS47032.1	4p15.32	2008-01-17			ENSG00000249581	ENSG00000249581			33939	protein-coding gene	gene with protein product						12080385	Standard	NM_001079827		Approved		uc003gpg.1	A0PK11	OTTHUMG00000160273	ENST00000511148.2:c.564G>C	4.37:g.17528570G>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	169	86	0.508876	NM_001079827		Silent	SNP	ENST00000511148.2	37	CCDS47032.1																																																																																			G|0.952;C|0.048	0.048	strong		0.517	CLRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359990.2	NM_001079827	
MAP4K3	8491	hgsc.bcm.edu	37	2	39507417	39507417	+	Silent	SNP	T	T	A	rs3755176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:39507417T>A	ENST00000263881.3	-	23	2034	c.1710A>T	c.(1708-1710)acA>acT	p.T570T	MAP4K3_ENST00000341681.5_Silent_p.T549T|MAP4K3_ENST00000536018.1_Silent_p.T123T|MAP4K3_ENST00000437545.1_Silent_p.T486T	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	570	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				TACTACCTCTTGTATCTGGGT	0.333													T|||	3141	0.627196	0.2012	0.7363	5008	,	,		13635	0.7966		0.8549	False		,,,				2504	0.7168				p.T570T		Atlas-SNP	.											.	MAP4K3	109	.	0			c.A1710T						PASS	.	T		1421,2985	460.5+/-352.6	241,939,1023	74.0	69.0	71.0		1710	0.1	1.0	2	dbSNP_107	71	7236,1360	752.8+/-407.4	3055,1126,117	no	coding-synonymous	MAP4K3	NM_003618.2		3296,2065,1140	AA,AT,TT		15.8213,32.2515,33.4179		570/895	39507417	8657,4345	2203	4298	6501	SO:0001819	synonymous_variant	8491	exon23			ACCTCTTGTATCT	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1710A>T	2.37:g.39507417T>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Silent	SNP	ENST00000263881.3	37	CCDS1803.1																																																																																			T|0.326;A|0.674	0.674	strong		0.333	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	
ZFP69B	65243	hgsc.bcm.edu	37	1	40923019	40923019	+	Missense_Mutation	SNP	G	G	A	rs2272994	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:40923019G>A	ENST00000411995.2	+	5	719	c.344G>A	c.(343-345)tGt>tAt	p.C115Y	ZFP69B_ENST00000484445.1_Missense_Mutation_p.M86I|ZFP69B_ENST00000361584.3_Missense_Mutation_p.C13Y	NM_023070.2	NP_075558.2	Q9UJL9	ZF69B_HUMAN	ZFP69 zinc finger protein B	115	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		C -> Y (in dbSNP:rs2272994).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TAAGCAGGATGTCAGCTTTCC	0.443													G|||	1110	0.221645	0.0212	0.3516	5008	,	,		20074	0.2986		0.2366	False		,,,				2504	0.3057				p.C115Y		Atlas-SNP	.											.	.	.	.	0			c.G344A						PASS	.	G	TYR/CYS	278,4128		6,266,1931	105.0	95.0	98.0		344	1.0	1.0	1	dbSNP_100	98	1873,6727		221,1431,2648	yes	missense	ZNF643	NM_023070.2	194	227,1697,4579	AA,AG,GG		21.7791,6.3096,16.5385	benign	115/535	40923019	2151,10855	2203	4300	6503	SO:0001583	missense	65243	exon4			CAGGATGTCAGCT	BC017498	CCDS452.1, CCDS452.2	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187801	ENSG00000187801		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	28053	protein-coding gene	gene with protein product			"""zinc finger protein 643"""	ZNF643			Standard	NM_023070		Approved	ZKSCAN23B, FLJ34293, ZSCAN54B	uc001cfn.2	Q9UJL9	OTTHUMG00000007302	ENST00000411995.2:c.344G>A	1.37:g.40923019G>A	ENSP00000399664:p.Cys115Tyr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	107	34	0.317757	NM_023070	Q5QPL4	Missense_Mutation	SNP	ENST00000411995.2	37	CCDS452.2	484|484	0.2216117216117216|0.2216117216117216	13|13	0.026422764227642278|0.026422764227642278	116|116	0.32044198895027626|0.32044198895027626	181|181	0.31643356643356646|0.31643356643356646	174|174	0.22955145118733508|0.22955145118733508	.|.	11.27|11.27	1.588414|1.588414	0.28357|0.28357	0.063096|0.063096	0.217791|0.217791	ENSG00000187801|ENSG00000187801	ENST00000411995;ENST00000361584|ENST00000431552;ENST00000484445	T;T|.	0.00730|.	5.77;5.77|.	3.4|3.4	0.988|0.988	0.19796|0.19796	Krueppel-associated box (3);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03881|0.03881	-0.34|-0.34	0.50813|0.50813	P|P	1.0399999999999299E-4|1.0399999999999299E-4	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.40608|0.40608	-0.9554|-0.9554	8|5	0.31617|0.66056	T|D	0.26|0.02	.|.	4.1937|4.1937	0.10433|0.10433	0.7155:0.0:0.1063:0.1782|0.7155:0.0:0.1063:0.1782	rs2272994;rs52813536;rs58074442;rs2272994|rs2272994;rs52813536;rs58074442;rs2272994	115|.	Q9UJL9|.	ZN643_HUMAN|.	Y|I	115;13|46;86	ENSP00000399664:C115Y;ENSP00000354547:C13Y|.	ENSP00000354547:C13Y|ENSP00000400051:M46I	C|M	+|+	2|3	0|0	ZNF643|ZNF643	40695606|40695606	0.002000|0.002000	0.14202|0.14202	0.987000|0.987000	0.45799|0.45799	0.679000|0.679000	0.39708|0.39708	-0.085000|-0.085000	0.11250|0.11250	0.174000|0.174000	0.19809|0.19809	-0.294000|-0.294000	0.09567|0.09567	TGT|ATG	G|0.815;A|0.185	0.185	strong		0.443	ZFP69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019078.2	NM_023070	
RFX5	5993	hgsc.bcm.edu	37	1	151315287	151315287	+	Missense_Mutation	SNP	G	G	C	rs2233854	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151315287G>C	ENST00000290524.4	-	11	1404	c.1226C>G	c.(1225-1227)cCc>cGc	p.P409R	RP11-126K1.8_ENST00000422153.1_RNA|RFX5_ENST00000452513.2_Missense_Mutation_p.P369R|RFX5_ENST00000478564.1_5'Flank|RFX5_ENST00000368870.2_Missense_Mutation_p.P409R|RFX5_ENST00000452671.2_Missense_Mutation_p.P409R	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	409			P -> R (in dbSNP:rs2233854).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TGTGCCCCGGGGCTGAGTGAG	0.577													G|||	318	0.0634984	0.003	0.0994	5008	,	,		17803	0.0		0.171	False		,,,				2504	0.0746				p.P409R		Atlas-SNP	.											.	RFX5	69	.	0			c.C1226G						PASS	.	G	ARG/PRO,ARG/PRO	154,4252	106.0+/-144.5	0,154,2049	145.0	153.0	150.0		1226,1226	3.3	0.3	1	dbSNP_98	150	1392,7208	268.7+/-288.0	111,1170,3019	yes	missense,missense	RFX5	NM_000449.3,NM_001025603.1	103,103	111,1324,5068	CC,CG,GG		16.186,3.4952,11.8868	benign,benign	409/617,409/617	151315287	1546,11460	2203	4300	6503	SO:0001583	missense	5993	exon11			CCCCGGGGCTGAG		CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.1226C>G	1.37:g.151315287G>C	ENSP00000290524:p.Pro409Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	140	51	0.364286	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	37	CCDS994.1	173	0.07921245421245421	1	0.0020325203252032522	37	0.10220994475138122	0	0.0	135	0.17810026385224276	G	10.08	1.252305	0.22880	0.034952	0.16186	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000452671;ENST00000452513;ENST00000392746	T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32	5.11	3.26	0.37387	.	0.513188	0.18988	N	0.125669	T	0.13798	0.0334	L	0.50333	1.59	0.40855	P	0.016218999999999983	B;P	0.39216	0.435;0.664	B;B	0.30782	0.12;0.109	T	0.04767	-1.0928	9	0.87932	D	0	-2.0525	8.7495	0.34607	0.175:0.0:0.825:0.0	rs2233854;rs52795020;rs2233854	369;409	B7Z848;P48382	.;RFX5_HUMAN	R	409;409;409;369;409	ENSP00000290524:P409R;ENSP00000357864:P409R;ENSP00000389130:P409R;ENSP00000398388:P369R;ENSP00000376502:P409R	ENSP00000290524:P409R	P	-	2	0	RFX5	149581911	0.809000	0.29036	0.256000	0.24389	0.663000	0.39108	1.746000	0.38288	0.749000	0.32854	0.491000	0.48974	CCC	G|0.896;C|0.104	0.104	strong		0.577	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449	
SULT1A1	6817	hgsc.bcm.edu	37	16	28617485	28617485	+	Missense_Mutation	SNP	C	C	T	rs1801030	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28617485C>T	ENST00000395607.1	-	7	940	c.667G>A	c.(667-669)Gtg>Atg	p.V223M	SULT1A1_ENST00000395609.1_Missense_Mutation_p.V223M|SULT1A1_ENST00000350842.4_Missense_Mutation_p.V145M|SULT1A1_ENST00000569554.1_Missense_Mutation_p.V223M|SULT1A1_ENST00000314752.7_Missense_Mutation_p.V223M	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	223			V -> M (in dbSNP:rs1801030). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:7581483, ECO:0000269|PubMed:7695643, ECO:0000269|PubMed:7864863, ECO:0000269|PubMed:8033246, ECO:0000269|PubMed:8363592, ECO:0000269|PubMed:8423770, ECO:0000269|PubMed:8484775, ECO:0000269|PubMed:8912648, ECO:0000269|PubMed:8924211, ECO:0000269|PubMed:9345314, ECO:0000269|PubMed:9855620, ECO:0000269|Ref.11, ECO:0000269|Ref.12}.		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)			endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	TGCTGAACCACGAAGTCCACG	0.562																																					p.V223M		Atlas-SNP	.											.	SULT1A1	53	.	0			c.G667A						PASS	.	T	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	2759,1633		1113,533,550	90.0	36.0	54.0		667,667,667,667,433	2.2	0.0	16	dbSNP_89	54	8576,18		4282,12,3	no	missense,missense,missense,missense,missense	SULT1A1	NM_001055.3,NM_177529.2,NM_177530.2,NM_177534.2,NM_177536.3	21,21,21,21,21	5395,545,553	TT,TC,CC		0.2094,37.1812,12.7137	benign,benign,benign,benign,benign	223/296,223/296,223/296,223/296,145/218	28617485	11335,1651	2196	4297	6493	SO:0001583	missense	6817	exon6			GAACCACGAAGTC	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.667G>A	16.37:g.28617485C>T	ENSP00000378971:p.Val223Met	Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	881	877	0.99546	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Missense_Mutation	SNP	ENST00000395607.1	37	CCDS32420.1	1948	0.891941391941392	310	0.6300813008130082	345	0.9530386740331491	563	0.9842657342657343	730	0.9630606860158312	t	3.010	-0.204037	0.06180	0.628188	0.997906	ENSG00000196502	ENST00000314752;ENST00000350842;ENST00000395609;ENST00000395607	T;T;T;T	0.01963	4.53;4.53;4.53;4.53	2.18	2.18	0.27775	Sulfotransferase domain (1);	0.076082	0.53938	N	0.000057	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B;B	0.22683	0.036;0.073	B;B	0.27887	0.011;0.084	T	0.18461	-1.0336	9	0.49607	T	0.09	.	5.7389	0.18081	0.0:0.1486:0.0:0.8514	rs45543439	145;223	P50225-2;P50225	.;ST1A1_HUMAN	M	223;145;223;223	ENSP00000321988:V223M;ENSP00000329399:V145M;ENSP00000378972:V223M;ENSP00000378971:V223M	ENSP00000321988:V223M	V	-	1	0	SULT1A1	28524986	0.983000	0.35010	0.017000	0.16124	0.220000	0.24768	2.112000	0.41892	0.299000	0.22661	-0.848000	0.03037	GTG	C|0.083;T|0.917	0.917	strong		0.562	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
HEATR4	399671	hgsc.bcm.edu	37	14	73987627	73987627	+	Missense_Mutation	SNP	C	C	T	rs551858976		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:73987627C>T	ENST00000553558.1	-	4	1319	c.998G>A	c.(997-999)cGc>cAc	p.R333H	HEATR4_ENST00000560393.1_Missense_Mutation_p.R286H|RP3-414A15.11_ENST00000553394.1_RNA|RP3-414A15.2_ENST00000555972.2_RNA|HEATR4_ENST00000334988.2_Missense_Mutation_p.R333H	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	333										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		AGTCACCTGGCGAAAGTAGCT	0.522													C|||	1	0.000199681	0.0	0.0	5008	,	,		19594	0.001		0.0	False		,,,				2504	0.0				p.R333H		Atlas-SNP	.											HEATR4_ENST00000553558,NS,carcinoma,-1,2	HEATR4	126	2	0			c.G998A						scavenged	.						159.0	144.0	149.0					14																	73987627		2203	4300	6503	SO:0001583	missense	399671	exon3			ACCTGGCGAAAGT	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.998G>A	14.37:g.73987627C>T	ENSP00000450444:p.Arg333His	Somatic	395	0	0		WXS	Illumina HiSeq	Phase_I	401	4	0.00997506	NM_203309	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660359	0.29515	.	.	ENSG00000187105	ENST00000553558;ENST00000334988	T	0.43294	0.95	5.39	2.45	0.29901	.	0.153060	0.29806	N	0.011148	T	0.25158	0.0611	N	0.20986	0.625	0.09310	N	1	B	0.13594	0.008	B	0.10450	0.005	T	0.16837	-1.0389	10	0.59425	D	0.04	-4.0133	5.2798	0.15668	0.1603:0.6635:0.0:0.1762	.	333	Q86WZ0	HEAT4_HUMAN	H	333;286	ENSP00000450444:R333H	ENSP00000335447:R286H	R	-	2	0	HEATR4	73057380	0.002000	0.14202	0.021000	0.16686	0.008000	0.06430	-0.033000	0.12246	0.598000	0.29829	-0.137000	0.14449	CGC	.	.	none		0.522	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
FCGBP	8857	hgsc.bcm.edu	37	19	40392360	40392360	+	Missense_Mutation	SNP	G	G	A	rs200977347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40392360G>A	ENST00000221347.6	-	16	8151	c.8144C>T	c.(8143-8145)gCa>gTa	p.A2715V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2715						extracellular vesicular exosome (GO:0070062)		p.A2715V(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCTCCAGCTGCCTGGCAAGC	0.587													G|||	1248	0.249201	0.1619	0.3876	5008	,	,		13881	0.1935		0.33	False		,,,				2504	0.2434				p.A2715V		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	large_intestine(1)	c.C8144T						scavenged	.						5.0	6.0	6.0					19																	40392360		1980	3956	5936	SO:0001583	missense	8857	exon16			CCAGCTGCCTGGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8144C>T	19.37:g.40392360G>A	ENSP00000221347:p.Ala2715Val	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	343	18	0.0524781	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082846	0.36758	.	.	ENSG00000090920	ENST00000221347	T	0.77620	-1.11	2.58	-0.163	0.13363	Uncharacterised domain, cysteine-rich (2);	0.292022	0.32244	N	0.006362	D	0.82323	0.5012	M	0.76574	2.34	0.23331	N	0.997894	D	0.76494	0.999	D	0.79108	0.992	T	0.69347	-0.5169	10	0.33940	T	0.23	.	5.3676	0.16123	0.0:0.1728:0.3161:0.5111	.	2715	Q9Y6R7	FCGBP_HUMAN	V	2715	ENSP00000221347:A2715V	ENSP00000221347:A2715V	A	-	2	0	FCGBP	45084200	0.000000	0.05858	0.984000	0.44739	0.668000	0.39293	-0.272000	0.08560	0.383000	0.24910	0.298000	0.19748	GCA	.	.	weak		0.587	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
WARS	7453	hgsc.bcm.edu	37	14	100808845	100808845	+	Silent	SNP	G	G	A	rs9453	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:100808845G>A	ENST00000355338.2	-	9	1621	c.1003C>T	c.(1003-1005)Ctg>Ttg	p.L335L	WARS_ENST00000557135.1_Silent_p.L335L|RP11-638I2.8_ENST00000557226.1_RNA|RP11-638I2.9_ENST00000556212.1_RNA|WARS_ENST00000392882.2_Silent_p.L335L|WARS_ENST00000556645.1_Silent_p.L294L|WARS_ENST00000358655.4_Silent_p.L294L|WARS_ENST00000344102.5_Silent_p.L294L	NM_173701.1	NP_776049.1	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase	335					angiogenesis (GO:0001525)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|regulation of angiogenesis (GO:0045765)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	GTGGAGTGCAGCAGGGCTGGT	0.597													G|||	3469	0.692692	0.4372	0.8372	5008	,	,		17386	0.755		0.7644	False		,,,				2504	0.7975				p.L335L		Atlas-SNP	.											.	WARS	37	.	0			c.C1003T						PASS	.	G	,,,	2166,2240	583.8+/-385.9	530,1106,567	88.0	82.0	84.0		1003,1003,880,880	5.0	1.0	14	dbSNP_52	84	6399,2201	710.6+/-405.8	2390,1619,291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WARS	NM_004184.3,NM_173701.1,NM_213645.1,NM_213646.1	,,,	2920,2725,858	AA,AG,GG		25.593,49.1602,34.1458	,,,	335/472,335/472,294/431,294/431	100808845	8565,4441	2203	4300	6503	SO:0001819	synonymous_variant	7453	exon9			AGTGCAGCAGGGC	M61715	CCDS9960.1, CCDS9961.1	14q32.2	2014-03-19			ENSG00000140105	ENSG00000140105	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12729	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 1, cytoplasmic"""	191050		IFI53		1537332, 1763065	Standard	NM_004184		Approved	IFP53	uc001yhl.1	P23381	OTTHUMG00000171572	ENST00000355338.2:c.1003C>T	14.37:g.100808845G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	200	199	0.995	NM_004184	A6NGN1|A6NID3|P78535|Q502Y0|Q53XB6|Q9UDI5|Q9UDL3	Silent	SNP	ENST00000355338.2	37	CCDS9960.1																																																																																			G|0.333;A|0.667	0.667	strong		0.597	WARS-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414236.1	NM_004184	
TRIM31	11074	hgsc.bcm.edu	37	6	30078275	30078275	+	Missense_Mutation	SNP	C	C	T	rs2523989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30078275C>T	ENST00000376734.3	-	4	819	c.694G>A	c.(694-696)Gtt>Att	p.V232I	TRIM31_ENST00000540829.1_Missense_Mutation_p.V232I|TRIM31_ENST00000485864.1_5'UTR|TRIM31-AS1_ENST00000440874.1_RNA	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	232			V -> I (in dbSNP:rs2523989). {ECO:0000269|PubMed:14574404}.	ASTEPQLNDLKKLVDSLK -> EIPLMPTVERSQEARCYP (in Ref. 6; CAA69165). {ECO:0000305}.	innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						AGGGAATCAACGAGCTTCTTG	0.552													T|||	374	0.0746805	0.0492	0.1239	5008	,	,		18612	0.0486		0.1203	False		,,,				2504	0.0542				p.V232I		Atlas-SNP	.											.	TRIM31	40	.	0			c.G694A						PASS	.	T	ILE/VAL	296,4110	799.7+/-415.5	11,274,1918	199.0	180.0	186.0		694	0.4	0.0	6	dbSNP_100	186	1207,7393	763.5+/-407.6	76,1055,3169	yes	missense	TRIM31	NM_007028.3	29	87,1329,5087	TT,TC,CC		14.0349,6.7181,11.5562	benign	232/426	30078275	1503,11503	2203	4300	6503	SO:0001583	missense	11074	exon4			AATCAACGAGCTT	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.694G>A	6.37:g.30078275C>T	ENSP00000365924:p.Val232Ile	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	223	93	0.41704	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Missense_Mutation	SNP	ENST00000376734.3	37	CCDS34374.1	199	0.09111721611721611	14	0.028455284552845527	53	0.1464088397790055	38	0.06643356643356643	94	0.12401055408970976	T	0.019	-1.464264	0.01053	0.067181	0.140349	ENSG00000204616	ENST00000376734;ENST00000376728;ENST00000540829	T;T	0.61980	0.06;0.06	3.26	0.419	0.16438	.	.	.	.	.	T	0.07728	0.0194	N	0.01874	-0.695	0.80722	P	0.0	B	0.19583	0.037	B	0.11329	0.006	T	0.22173	-1.0224	8	0.02654	T	1	.	3.1145	0.06370	0.0:0.3495:0.2401:0.4104	rs2523989;rs6457153;rs17389049;rs17851467;rs52820560;rs56648206;rs58929461;rs2523989	232	Q9BZY9	TRI31_HUMAN	I	232	ENSP00000365924:V232I;ENSP00000444311:V232I	ENSP00000365918:V232I	V	-	1	0	TRIM31	30186254	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	0.141000	0.16076	0.013000	0.14918	-0.891000	0.02926	GTT	C|0.898;T|0.102	0.102	strong		0.552	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
ALKBH3	221120	hgsc.bcm.edu	37	11	43940602	43940602	+	Missense_Mutation	SNP	C	C	G	rs1130290	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:43940602C>G	ENST00000302708.4	+	9	1095	c.684C>G	c.(682-684)gaC>gaG	p.D228E	ALKBH3-AS1_ENST00000499194.1_RNA|RP11-613D13.4_ENST00000526408.1_RNA|ALKBH3-AS1_ENST00000534287.1_RNA|ALKBH3-AS1_ENST00000528285.1_RNA|ALKBH3-AS1_ENST00000527960.1_RNA|ALKBH3_ENST00000532410.1_3'UTR	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	228	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.		D -> E (in dbSNP:rs2434470). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)	p.D228E(1)		endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	AGAATGGAGACTACACATATG	0.413								Direct reversal of damage					C|||	696	0.138978	0.0802	0.1398	5008	,	,		24051	0.0933		0.2575	False		,,,				2504	0.1431				p.D228E		Atlas-SNP	.											ALKBH3,NS,carcinoma,0,1	ALKBH3	33	1	1	Substitution - Missense(1)	prostate(1)	c.C684G						PASS	.	C	GLU/ASP	431,3975	209.8+/-230.5	22,387,1794	179.0	152.0	161.0		684	5.9	1.0	11	dbSNP_100	161	2245,6355	379.7+/-339.4	291,1663,2346	yes	missense	ALKBH3	NM_139178.3	45	313,2050,4140	GG,GC,CC		26.1047,9.7821,20.5751	probably-damaging	228/287	43940602	2676,10330	2203	4300	6503	SO:0001583	missense	221120	exon9			TGGAGACTACACA	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"""Alkylation repair homologs"""	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.684C>G	11.37:g.43940602C>G	ENSP00000302232:p.Asp228Glu	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Missense_Mutation	SNP	ENST00000302708.4	37	CCDS7906.1	350|350	0.16025641025641027|0.16025641025641027	48|48	0.0975609756097561|0.0975609756097561	56|56	0.15469613259668508|0.15469613259668508	48|48	0.08391608391608392|0.08391608391608392	198|198	0.2612137203166227|0.2612137203166227	C|C	25.6|25.6	4.658695|4.658695	0.88154|0.88154	0.097821|0.097821	0.261047|0.261047	ENSG00000166199|ENSG00000166199	ENST00000302708|ENST00000532129	T|.	0.13538|.	2.58|.	5.91|5.91	5.91|5.91	0.95273|0.95273	Oxoglutarate/iron-dependent oxygenase (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00039|0.00039	0.0001|0.0001	M|M	0.68593|0.68593	2.085|2.085	0.09310|0.09310	P|P	1.0|1.0	P|.	0.47604|.	0.898|.	P|.	0.55577|.	0.779|.	T|T	0.00085|0.00085	-1.2098|-1.2098	9|4	0.72032|.	D|.	0.01|.	-24.4655|-24.4655	15.7986|15.7986	0.78433|0.78433	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2434470;rs3740986;rs17565250;rs52822276;rs56569355;rs2434470|rs2434470;rs3740986;rs17565250;rs52822276;rs56569355;rs2434470	228|.	Q96Q83|.	ALKB3_HUMAN|.	E|V	228|98	ENSP00000302232:D228E|.	ENSP00000302232:D228E|.	D|L	+|+	3|1	2|2	ALKBH3|ALKBH3	43897178|43897178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	2.591000|2.591000	0.46163|0.46163	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	GAC|CTA	C|0.827;G|0.173	0.173	strong		0.413	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178	
AKAP11	11215	hgsc.bcm.edu	37	13	42873782	42873782	+	Silent	SNP	G	G	A	rs9525605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:42873782G>A	ENST00000025301.2	+	8	1075	c.900G>A	c.(898-900)tcG>tcA	p.S300S		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	300	Ser-rich.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		CATTTTTTTCGTCTTCTCCTG	0.363													G|||	104	0.0207668	0.0023	0.0375	5008	,	,		20846	0.001		0.0497	False		,,,				2504	0.0245				p.S300S		Atlas-SNP	.											.	AKAP11	146	.	0			c.G900A						PASS	.	G		58,4348	55.5+/-91.7	2,54,2147	63.0	65.0	65.0		900	-3.4	0.7	13	dbSNP_119	65	533,8065	146.6+/-202.2	10,513,3776	no	coding-synonymous	AKAP11	NM_016248.3		12,567,5923	AA,AG,GG		6.1991,1.3164,4.5448		300/1902	42873782	591,12413	2203	4299	6502	SO:0001819	synonymous_variant	11215	exon8			TTTTTCGTCTTCT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.900G>A	13.37:g.42873782G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			G|0.960;A|0.040	0.040	strong		0.363	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
TNC	3371	hgsc.bcm.edu	37	9	117846570	117846570	+	Silent	SNP	C	C	T	rs2274836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:117846570C>T	ENST00000350763.4	-	4	2460	c.2049G>A	c.(2047-2049)gaG>gaA	p.E683E	TNC_ENST00000346706.3_Silent_p.E683E|TNC_ENST00000341037.4_Silent_p.E683E|TNC_ENST00000345230.3_Silent_p.E683E|TNC_ENST00000423613.2_Silent_p.E683E|TNC_ENST00000537320.1_Silent_p.E683E|TNC_ENST00000535648.1_Silent_p.E683E|TNC_ENST00000542877.1_Silent_p.E683E|TNC_ENST00000340094.3_Silent_p.E683E	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	683	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CCACACCAGGCTCCAGCTCCT	0.567													C|||	2324	0.464058	0.3933	0.3573	5008	,	,		18928	0.5942		0.4354	False		,,,				2504	0.5307				p.E683E		Atlas-SNP	.											TNC,NS,malignant_melanoma,-2,1	TNC	282	1	0			c.G2049A						PASS	.	C		1815,2591	533.1+/-373.6	373,1069,761	97.0	92.0	94.0		2049	3.9	1.0	9	dbSNP_100	94	3901,4699	545.6+/-384.8	898,2105,1297	no	coding-synonymous	TNC	NM_002160.3		1271,3174,2058	TT,TC,CC		45.3605,41.1938,43.9489		683/2202	117846570	5716,7290	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon4			ACCAGGCTCCAGC		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.2049G>A	9.37:g.117846570C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	133	131	0.984962	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																			C|0.552;T|0.448	0.448	strong		0.567	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
MSLN	10232	hgsc.bcm.edu	37	16	813650	813650	+	Silent	SNP	G	G	A	rs3765319	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:813650G>A	ENST00000382862.3	+	4	233	c.138G>A	c.(136-138)gcG>gcA	p.A46A	MSLN_ENST00000545450.2_Silent_p.A46A|MSLN_ENST00000563941.1_Silent_p.A46A|MSLN_ENST00000566549.1_Silent_p.A46A	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	46					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				AGGAGGCTGCGCCCCTGGACG	0.662													G|||	724	0.144569	0.0477	0.1153	5008	,	,		11642	0.3006		0.1501	False		,,,				2504	0.1299				p.A46A		Atlas-SNP	.											.	MSLN	109	.	0			c.G138A						PASS	.	G	,,	299,4089	156.6+/-189.7	11,277,1906	37.0	34.0	35.0		138,138,138	-3.2	0.0	16	dbSNP_107	35	1605,6979	289.3+/-299.2	158,1289,2845	no	coding-synonymous,coding-synonymous,coding-synonymous	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	,,	169,1566,4751	AA,AG,GG		18.6976,6.814,14.6778	,,	46/623,46/623,46/631	813650	1904,11068	2194	4292	6486	SO:0001819	synonymous_variant	10232	exon5			GGCTGCGCCCCTG	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.138G>A	16.37:g.813650G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Silent	SNP	ENST00000382862.3	37	CCDS32356.1																																																																																			A|0.146;G|0.854;T|0.000	0.146	strong		0.662	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
PER1	5187	hgsc.bcm.edu	37	17	8053916	8053916	+	Missense_Mutation	SNP	G	G	A	rs72845601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8053916G>A	ENST00000317276.4	-	2	346	c.109C>T	c.(109-111)Cca>Tca	p.P37S	PER1_ENST00000581082.1_Missense_Mutation_p.P37S|PER1_ENST00000354903.5_Missense_Mutation_p.P21S	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	37	Interaction with BTRC. {ECO:0000269|PubMed:15917222}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CTGGGGCCTGGGCAAGGCCGG	0.652			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					G|||	27	0.00539137	0.0	0.0029	5008	,	,		18923	0.0		0.0169	False		,,,				2504	0.0082				p.P37S		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.C109T						PASS	.	G	SER/PRO	11,4395	17.9+/-39.9	0,11,2192	78.0	79.0	79.0		109	4.3	1.0	17	dbSNP_130	79	164,8436	76.9+/-139.5	4,156,4140	yes	missense	PER1	NM_002616.2	74	4,167,6332	AA,AG,GG		1.907,0.2497,1.3455	possibly-damaging	37/1291	8053916	175,12831	2203	4300	6503	SO:0001583	missense	5187	exon2			GGCCTGGGCAAGG	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.109C>T	17.37:g.8053916G>A	ENSP00000314420:p.Pro37Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	131	63	0.480916	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	19.30	3.801532	0.70682	0.002497	0.01907	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.36878	2.61;1.23	4.33	4.33	0.51752	.	0.236029	0.30011	N	0.010625	T	0.22085	0.0532	N	0.08118	0	0.36954	D	0.893014	D;D;D	0.76494	0.999;0.997;0.993	D;D;D	0.75484	0.982;0.986;0.979	T	0.44190	-0.9344	10	0.51188	T	0.08	-9.4022	12.2034	0.54339	0.0:0.0:1.0:0.0	.	37;21;37	Q6IN51;B4DI49;O15534	.;.;PER1_HUMAN	S	37;21	ENSP00000314420:P37S;ENSP00000346979:P21S	ENSP00000314420:P37S	P	-	1	0	PER1	7994641	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	1.568000	0.36418	2.253000	0.74438	0.563000	0.77884	CCA	G|0.988;A|0.012	0.012	strong		0.652	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
KIAA0895L	653319	hgsc.bcm.edu	37	16	67213950	67213950	+	Silent	SNP	G	G	A	rs61733768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:67213950G>A	ENST00000290881.7	-	3	1490	c.564C>T	c.(562-564)atC>atT	p.I188I	KIAA0895L_ENST00000563831.2_Intron|KIAA0895L_ENST00000563902.1_Silent_p.I188I|KIAA0895L_ENST00000561621.1_Silent_p.I188I			Q68EN5	K895L_HUMAN	KIAA0895-like	188										breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						TGACCTGATGGATGAACTGTC	0.587													G|||	150	0.0299521	0.0242	0.0173	5008	,	,		17548	0.0		0.0288	False		,,,				2504	0.0787				p.I188I		Atlas-SNP	.											.	KIAA0895L	32	.	0			c.C564T						PASS	.	G		98,3918		0,98,1910	84.0	86.0	85.0		564	-0.5	1.0	16	dbSNP_129	85	261,8081		3,255,3913	no	coding-synonymous	KIAA0895L	NM_001040715.1		3,353,5823	AA,AG,GG		3.1287,2.4402,2.905		188/472	67213950	359,11999	2008	4171	6179	SO:0001819	synonymous_variant	653319	exon2			CTGATGGATGAAC	AK092303	CCDS42177.1	16q22.1	2008-11-27				ENSG00000196123			34408	protein-coding gene	gene with protein product							Standard	NM_001040715		Approved	LOC653319	uc002ert.3	Q68EN5		ENST00000290881.7:c.564C>T	16.37:g.67213950G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	NM_001040715	A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Silent	SNP	ENST00000290881.7	37	CCDS42177.1																																																																																			G|0.978;A|0.022	0.022	strong		0.587	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715	
PADI3	51702	hgsc.bcm.edu	37	1	17609448	17609448	+	Silent	SNP	G	G	T	rs2293920	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17609448G>T	ENST00000375460.3	+	16	1909	c.1869G>T	c.(1867-1869)ccG>ccT	p.P623P		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	623					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	TGCTGGAGCCGCTGGGCCTCC	0.597													G|||	2028	0.404952	0.1725	0.415	5008	,	,		20108	0.623		0.4374	False		,,,				2504	0.454				p.P623P		Atlas-SNP	.											.	PADI3	81	.	0			c.G1869T						PASS	.	G		1019,3387	376.6+/-322.1	112,795,1296	91.0	76.0	81.0		1869	-1.0	1.0	1	dbSNP_100	81	3806,4794	537.9+/-383.3	855,2096,1349	no	coding-synonymous	PADI3	NM_016233.2		967,2891,2645	TT,TG,GG		44.2558,23.1276,37.0983		623/665	17609448	4825,8181	2203	4300	6503	SO:0001819	synonymous_variant	51702	exon16			GGAGCCGCTGGGC	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"""Peptidyl arginine deiminases"""	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.1869G>T	1.37:g.17609448G>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	146	64	0.438356	NM_016233	Q58EY7|Q70SX5	Silent	SNP	ENST00000375460.3	37	CCDS179.1																																																																																			G|0.602;T|0.398	0.398	strong		0.597	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1		
ZIC4	84107	hgsc.bcm.edu	37	3	147108756	147108756	+	Silent	SNP	C	C	G	rs17509456	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:147108756C>G	ENST00000383075.3	-	4	1478	c.966G>C	c.(964-966)tcG>tcC	p.S322S	ZIC4_ENST00000472749.2_5'UTR|ZIC4_ENST00000425731.3_Silent_p.S360S|ZIC4_ENST00000484399.1_Silent_p.S322S|ZIC4_ENST00000491672.1_Silent_p.S116S|ZIC4_ENST00000525172.2_Silent_p.S372S|ZIC4_ENST00000473123.1_Silent_p.S322S	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	322						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S322S(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						CCACCGCCGCCGAGGAGGCCA	0.721													C|||	87	0.0173722	0.0038	0.0245	5008	,	,		14138	0.0		0.0577	False		,,,				2504	0.0072				p.S372S		Atlas-SNP	.											ZIC4_ENST00000525172,NS,carcinoma,0,2	ZIC4	174	2	1	Substitution - coding silent(1)	lung(1)	c.G1116C						PASS	.	C	,,	30,4006		0,30,1988	16.0	20.0	18.0		1116,1080,966	-2.5	0.9	3	dbSNP_123	18	369,7951		7,355,3798	no	coding-synonymous,coding-synonymous,coding-synonymous	ZIC4	NM_001168378.1,NM_001168379.1,NM_032153.5	,,	7,385,5786	GG,GC,CC		4.4351,0.7433,3.2292	,,	372/385,360/373,322/335	147108756	399,11957	2018	4160	6178	SO:0001819	synonymous_variant	84107	exon4			CGCCGCCGAGGAG	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"""Zinc fingers, C2H2-type"""	20393	protein-coding gene	gene with protein product		608948	"""zinc finger protein of the cerebellum 4"""				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.966G>C	3.37:g.147108756C>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_001168378	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Silent	SNP	ENST00000383075.3	37	CCDS43160.1																																																																																			C|0.975;G|0.025	0.025	strong		0.721	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1		
TCEB3B	51224	hgsc.bcm.edu	37	18	44560038	44560038	+	Missense_Mutation	SNP	C	C	A	rs72921303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44560038C>A	ENST00000332567.4	-	1	1950	c.1598G>T	c.(1597-1599)tGt>tTt	p.C533F	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	533	Activation domain. {ECO:0000250}.|Interacting with Elongin BC complex. {ECO:0000250}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CACCTGGGCACACTGCTGGCG	0.622													C|||	38	0.00758786	0.0008	0.0101	5008	,	,		17015	0.006		0.0209	False		,,,				2504	0.0031				p.C533F		Atlas-SNP	.											.	TCEB3B	141	.	0			c.G1598T						PASS	.	C	PHE/CYS,	18,4388	23.3+/-48.9	0,18,2185	66.0	71.0	69.0		1598,	1.6	0.0	18	dbSNP_130	69	125,8475	60.2+/-122.0	0,125,4175	yes	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	205,	0,143,6360	AA,AC,CC		1.4535,0.4085,1.0995	probably-damaging,	533/754,	44560038	143,12863	2203	4300	6503	SO:0001583	missense	51224	exon1			TGGGCACACTGCT	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1598G>T	18.37:g.44560038C>A	ENSP00000331302:p.Cys533Phe	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	25	0.011446886446886446	1	0.0020325203252032522	4	0.011049723756906077	5	0.008741258741258742	15	0.01978891820580475	C	12.62	1.991813	0.35131	0.004085	0.014535	ENSG00000206181	ENST00000332567	T	0.38722	1.12	1.65	1.65	0.23941	.	0.893166	0.09517	N	0.791534	T	0.45498	0.1345	M	0.77616	2.38	0.24516	N	0.994185	D	0.89917	1.0	D	0.91635	0.999	T	0.32295	-0.9912	10	0.87932	D	0	-3.3489	6.7906	0.23697	0.0:1.0:0.0:0.0	.	533	Q8IYF1	ELOA2_HUMAN	F	533	ENSP00000331302:C533F	ENSP00000331302:C533F	C	-	2	0	TCEB3B	42814036	1.000000	0.71417	0.001000	0.08648	0.001000	0.01503	1.461000	0.35255	1.258000	0.44101	0.609000	0.83330	TGT	C|0.988;A|0.012	0.012	strong		0.622	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
MDN1	23195	hgsc.bcm.edu	37	6	90372574	90372574	+	Missense_Mutation	SNP	A	A	C	rs36040566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90372574A>C	ENST00000369393.3	-	86	14464	c.14349T>G	c.(14347-14349)gaT>gaG	p.D4783E	MDN1_ENST00000428876.1_Missense_Mutation_p.D4783E			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4783			D -> E (in dbSNP:rs36040566).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		cttcctcctcatcATCATCAC	0.458													A|||	445	0.0888578	0.0053	0.085	5008	,	,		19674	0.0476		0.1551	False		,,,				2504	0.1789				p.D4783E		Atlas-SNP	.											.	MDN1	478	.	0			c.T14349G						PASS	.	A	GLU/ASP	124,4282	89.2+/-127.9	5,114,2084	301.0	254.0	270.0		14349	-7.0	0.0	6	dbSNP_126	270	1240,7360	248.5+/-276.1	101,1038,3161	yes	missense	MDN1	NM_014611.1	45	106,1152,5245	CC,CA,AA		14.4186,2.8143,10.4875	benign	4783/5597	90372574	1364,11642	2203	4300	6503	SO:0001583	missense	23195	exon86			CTCCTCATCATCA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14349T>G	6.37:g.90372574A>C	ENSP00000358400:p.Asp4783Glu	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	246	110	0.447154	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	164	0.07509157509157509	4	0.008130081300813009	27	0.07458563535911603	24	0.04195804195804196	109	0.1437994722955145	A	9.175	1.022246	0.19433	0.028143	0.144186	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03272	3.99;3.99	4.53	-6.99	0.01605	.	0.354569	0.28214	N	0.016166	T	0.00328	0.0010	N	0.04335	-0.225	0.51767	P	6.799999999995698E-5	B	0.09022	0.002	B	0.09377	0.004	T	0.42832	-0.9428	9	0.08381	T	0.77	.	1.0429	0.01563	0.229:0.2875:0.2771:0.2064	rs36040566	4783	Q9NU22	MDN1_HUMAN	E	4783	ENSP00000358400:D4783E;ENSP00000413970:D4783E	ENSP00000358400:D4783E	D	-	3	2	MDN1	90429295	0.000000	0.05858	0.007000	0.13788	0.866000	0.49608	-2.338000	0.01103	-0.797000	0.04450	-0.250000	0.11733	GAT	A|0.909;C|0.091	0.091	strong		0.458	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ANO3	63982	hgsc.bcm.edu	37	11	26677947	26677947	+	Silent	SNP	C	C	T	rs10835051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:26677947C>T	ENST00000256737.3	+	26	3534	c.2682C>T	c.(2680-2682)ccC>ccT	p.P894P	ANO3_ENST00000537978.1_Silent_p.P878P|ANO3_ENST00000531568.1_Silent_p.P748P|ANO3_ENST00000525139.1_Silent_p.P878P	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	894					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						GAGGCCCGCCCTGGAGTTCCA	0.413													T|||	2797	0.558506	0.3268	0.5519	5008	,	,		16117	0.5655		0.666	False		,,,				2504	0.7587				p.P894P		Atlas-SNP	.											ANO3,right_upper_lobe,carcinoma,+2,1	ANO3	145	1	0			c.C2682T						PASS	.	T		1590,2816	664.5+/-401.4	287,1016,900	153.0	155.0	154.0		2682	2.8	1.0	11	dbSNP_120	154	5706,2892	453.1+/-363.1	1888,1930,481	no	coding-synonymous	ANO3	NM_031418.2		2175,2946,1381	TT,TC,CC		33.6357,36.0872,43.8942		894/982	26677947	7296,5708	2203	4299	6502	SO:0001819	synonymous_variant	63982	exon26			CCCGCCCTGGAGT	AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	14004	protein-coding gene	gene with protein product	"""transmembrane protein 16C (eight membrane-spanning domains)"""	610110	"""chromosome 11 open reading frame 25"", ""transmembrane protein 16C"""	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.2682C>T	11.37:g.26677947C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	195	195	1	NM_031418	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																			C|0.448;N|0.000	.	strong		0.413	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418	
CCDC173	129881	hgsc.bcm.edu	37	2	170510651	170510651	+	Missense_Mutation	SNP	C	C	T	rs61741435	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170510651C>T	ENST00000447353.1	-	6	998	c.893G>A	c.(892-894)aGa>aAa	p.R298K		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	298																	GATGAATTTTCTCATCTTTTC	0.333													C|||	170	0.0339457	0.0008	0.0086	5008	,	,		18886	0.1081		0.0298	False		,,,				2504	0.0245				p.R298K		Atlas-SNP	.											.	.	.	.	0			c.G893A						PASS	.	C	LYS/ARG	25,3599		0,25,1787	118.0	103.0	108.0		893	4.9	1.0	2	dbSNP_129	108	283,7895		3,277,3809	yes	missense	C2orf77	NM_001085447.1	26	3,302,5596	TT,TC,CC		3.4605,0.6898,2.6097	probably-damaging	298/553	170510651	308,11494	1812	4089	5901	SO:0001583	missense	129881	exon6			AATTTTCTCATCT	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"""hypothetical LOC129881"""		"""chromosome 2 open reading frame 77"""	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.893G>A	2.37:g.170510651C>T	ENSP00000391504:p.Arg298Lys	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	234	102	0.435897	NM_001085447	Q6PJF6	Missense_Mutation	SNP	ENST00000447353.1	37	CCDS46445.1	86	0.039377289377289376	1	0.0020325203252032522	5	0.013812154696132596	58	0.10139860139860139	22	0.029023746701846966	C	21.0	4.083951	0.76642	0.006898	0.034605	ENSG00000154479	ENST00000447353	T	0.09445	2.98	4.95	4.95	0.65309	.	1.631700	0.03934	N	0.285878	T	0.00496	0.0016	M	0.65975	2.015	0.31260	P	0.6930339999999999	P	0.43750	0.816	B	0.43155	0.41	T	0.36792	-0.9733	9	0.09843	T	0.71	.	16.0319	0.80585	0.0:1.0:0.0:0.0	.	298	Q0VFZ6	CB077_HUMAN	K	298	ENSP00000391504:R298K	ENSP00000391504:R298K	R	-	2	0	C2orf77	170218897	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	2.063000	0.41423	2.450000	0.82876	0.585000	0.79938	AGA	C|0.960;T|0.040	0.040	strong		0.333	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447	
SLC46A2	57864	hgsc.bcm.edu	37	9	115652881	115652881	+	Silent	SNP	G	G	T	rs3802491	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:115652881G>T	ENST00000374228.4	-	1	312	c.81C>A	c.(79-81)gcC>gcA	p.A27A		NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	27					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						CCTGGGACGAGGCCACCACGG	0.672													G|||	2094	0.418131	0.1906	0.4798	5008	,	,		14846	0.746		0.327	False		,,,				2504	0.4376				p.A27A		Atlas-SNP	.											.	SLC46A2	30	.	0			c.C81A						PASS	.	G		909,3497	332.3+/-302.4	90,729,1384	35.0	38.0	37.0		81	2.1	0.9	9	dbSNP_107	37	2962,5638	442.0+/-360.0	524,1914,1862	no	coding-synonymous	SLC46A2	NM_033051.3		614,2643,3246	TT,TG,GG		34.4419,20.631,29.7632		27/476	115652881	3871,9135	2203	4300	6503	SO:0001819	synonymous_variant	57864	exon1			GGACGAGGCCACC	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"""Solute carriers"""	16055	protein-coding gene	gene with protein product		608956	"""thymic stromal co-transporter"""	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.81C>A	9.37:g.115652881G>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	37	CCDS6786.1																																																																																			G|0.667;T|0.333	0.333	strong		0.672	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051	
ENPP5	59084	hgsc.bcm.edu	37	6	46135489	46135489	+	Missense_Mutation	SNP	T	T	C	rs6926570	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46135489T>C	ENST00000371383.2	-	3	771	c.511A>G	c.(511-513)Att>Gtt	p.I171V	ENPP5_ENST00000492313.1_5'Flank|ENPP5_ENST00000230565.3_Missense_Mutation_p.I171V					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						AACCATTCAATAATTTTGGCA	0.423													T|||	2226	0.444489	0.1899	0.4467	5008	,	,		20698	0.4494		0.5308	False		,,,				2504	0.6933				p.I171V		Atlas-SNP	.											.	ENPP5	44	.	0			c.A511G						PASS	.	T	VAL/ILE	1041,3365	374.9+/-321.4	125,791,1287	89.0	98.0	95.0		511	5.3	1.0	6	dbSNP_116	95	4556,4044	593.5+/-393.2	1205,2146,949	yes	missense	ENPP5	NM_021572.4	29	1330,2937,2236	CC,CT,TT		47.0233,23.6269,43.034	benign	171/478	46135489	5597,7409	2203	4300	6503	SO:0001583	missense	59084	exon2			ATTCAATAATTTT	AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.511A>G	6.37:g.46135489T>C	ENSP00000360436:p.Ile171Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_021572		Missense_Mutation	SNP	ENST00000371383.2	37	CCDS4915.1	908	0.4157509157509158	95	0.19308943089430894	178	0.49171270718232046	231	0.40384615384615385	404	0.5329815303430079	T	15.67	2.903331	0.52333	0.236269	0.529767	ENSG00000112796	ENST00000371383;ENST00000230565	T;T	0.72505	-0.66;-0.66	5.33	5.33	0.75918	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	L	0.35644	1.08	0.23681	P	0.99712777	B	0.32653	0.379	B	0.37091	0.241	T	0.52268	-0.8598	9	0.19147	T	0.46	-26.7479	15.6241	0.76840	0.0:0.0:0.0:1.0	rs6926570;rs57037284;rs6926570	171	Q9UJA9	ENPP5_HUMAN	V	171	ENSP00000360436:I171V;ENSP00000230565:I171V	ENSP00000230565:I171V	I	-	1	0	ENPP5	46243448	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.618000	0.83043	2.145000	0.66743	0.533000	0.62120	ATT	C|0.421;N|0.000	0.421	strong		0.423	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
SPTY2D1	144108	hgsc.bcm.edu	37	11	18633971	18633971	+	Silent	SNP	G	G	A	rs11605097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18633971G>A	ENST00000336349.5	-	4	2011	c.1776C>T	c.(1774-1776)gaC>gaT	p.D592D	SPTY2D1-AS1_ENST00000501599.2_RNA	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	592	Poly-Asp.									breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						CATCATCATCGTCATCTTCCT	0.363													G|||	1544	0.308307	0.0794	0.451	5008	,	,		16806	0.3472		0.4195	False		,,,				2504	0.362				p.D592D		Atlas-SNP	.											.	SPTY2D1	72	.	0			c.C1776T						PASS	.	G		607,3791	263.8+/-265.7	42,523,1634	131.0	124.0	126.0		1776	-3.7	1.0	11	dbSNP_120	126	3953,4633	550.2+/-385.7	931,2091,1271	no	coding-synonymous	SPTY2D1	NM_194285.2		973,2614,2905	AA,AG,GG		46.0401,13.8017,35.1201		592/686	18633971	4560,8424	2199	4293	6492	SO:0001819	synonymous_variant	144108	exon4			ATCATCGTCATCT	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1776C>T	11.37:g.18633971G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	207	101	0.487923	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Silent	SNP	ENST00000336349.5	37	CCDS31441.1																																																																																			G|0.668;A|0.332	0.332	strong		0.363	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285	
KLHL38	340359	hgsc.bcm.edu	37	8	124664167	124664167	+	Missense_Mutation	SNP	T	T	C	rs11784192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:124664167T>C	ENST00000325995.7	-	1	1023	c.1000A>G	c.(1000-1002)Atc>Gtc	p.I334V	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	334			I -> V (in dbSNP:rs11784192). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.							breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						AGCACATAGATGCTGCGGTGC	0.572													t|||	3637	0.726238	0.6641	0.7118	5008	,	,		20956	0.7113		0.8579	False		,,,				2504	0.7004				p.I334V		Atlas-SNP	.											.	KLHL38	81	.	0			c.A1000G						PASS	.	C	VAL/ILE	2898,1134		1044,810,162	60.0	62.0	61.0		1000	-3.0	0.0	8	dbSNP_120	61	7078,1278		3011,1056,111	yes	missense	KLHL38	NM_001081675.2	29	4055,1866,273	CC,CT,TT		15.2944,28.125,19.4705	benign	334/582	124664167	9976,2412	2016	4178	6194	SO:0001583	missense	340359	exon1			CATAGATGCTGCG		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1000A>G	8.37:g.124664167T>C	ENSP00000321475:p.Ile334Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	1633	0.7477106227106227	319	0.6483739837398373	264	0.7292817679558011	400	0.6993006993006993	650	0.8575197889182058	t	0.005	-2.190054	0.00302	0.71875	0.847056	ENSG00000175946	ENST00000325995	T	0.68331	-0.32	5.18	-2.96	0.05547	Kelch-type beta propeller (1);	0.548943	0.20780	N	0.085808	T	0.00012	0.0000	N	0.25332	0.735	0.80722	P	0.0	B	0.02656	0.0	B	0.12156	0.007	T	0.44436	-0.9328	9	0.05525	T	0.97	.	14.8205	0.70068	0.0:0.3447:0.0:0.6553	rs11784192;rs52803268;rs56938667;rs11784192	334	Q2WGJ6	KLH38_HUMAN	V	334	ENSP00000321475:I334V	ENSP00000321475:I334V	I	-	1	0	KLHL38	124733348	0.002000	0.14202	0.027000	0.17364	0.111000	0.19643	-1.023000	0.03607	-1.421000	0.02007	-2.192000	0.00311	ATC	T|0.234;C|0.766	0.766	strong		0.572	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
IRX2	153572	hgsc.bcm.edu	37	5	2749057	2749057	+	Missense_Mutation	SNP	C	C	A	rs76906087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:2749057C>A	ENST00000382611.6	-	3	1013	c.765G>T	c.(763-765)gaG>gaT	p.E255D	IRX2_ENST00000302057.5_Missense_Mutation_p.E255D|IRX2_ENST00000502957.1_5'UTR	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	255					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26				GBM - Glioblastoma multiforme(108;0.204)		TGTCCTTGCACTCCGAGCCCG	0.692													C|||	586	0.117013	0.0098	0.0706	5008	,	,		9506	0.0913		0.1421	False		,,,				2504	0.2955				p.E255D		Atlas-SNP	.											IRX2,NS,carcinoma,0,1	IRX2	60	1	0			c.G765T						PASS	.	C	ASP/GLU,ASP/GLU	129,4265		4,121,2072	22.0	22.0	22.0		765,765	4.9	1.0	5	dbSNP_132	22	1318,7260		122,1074,3093	yes	missense,missense	IRX2	NM_001134222.1,NM_033267.4	45,45	126,1195,5165	AA,AC,CC		15.3649,2.9358,11.1548	benign,benign	255/472,255/472	2749057	1447,11525	2197	4289	6486	SO:0001583	missense	153572	exon3			CTTGCACTCCGAG	AF319967	CCDS3868.1	5p15.33	2011-06-20	2007-07-13		ENSG00000170561	ENSG00000170561		"""Homeoboxes / TALE class"""	14359	protein-coding gene	gene with protein product		606198				11435706	Standard	NM_033267		Approved		uc003jdb.3	Q9BZI1	OTTHUMG00000090377	ENST00000382611.6:c.765G>T	5.37:g.2749057C>A	ENSP00000372056:p.Glu255Asp	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_001134222	Q68A19|Q7Z2I7	Missense_Mutation	SNP	ENST00000382611.6	37	CCDS3868.1	190	0.08699633699633699	9	0.018292682926829267	28	0.07734806629834254	43	0.07517482517482517	110	0.14511873350923482	C	13.71	2.316921	0.40996	0.029358	0.153649	ENSG00000170561	ENST00000382611;ENST00000302057;ENST00000502957	T;T;T	0.66280	-0.18;-0.18;-0.2	4.87	4.87	0.63330	.	0.516800	0.20691	N	0.087452	T	0.00496	0.0016	L	0.50333	1.59	0.21184	P	0.999760849	D	0.58268	0.982	P	0.46718	0.525	T	0.15723	-1.0427	9	0.34782	T	0.22	-20.8591	11.5223	0.50558	0.0:0.9174:0.0:0.0826	.	255	Q9BZI1	IRX2_HUMAN	D	255;255;162	ENSP00000372056:E255D;ENSP00000307006:E255D;ENSP00000426151:E162D	ENSP00000307006:E255D	E	-	3	2	IRX2	2802057	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	0.585000	0.23879	2.248000	0.74166	0.563000	0.77884	GAG	C|0.891;A|0.109	0.109	strong		0.692	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2		
CHUK	1147	hgsc.bcm.edu	37	10	101964312	101964312	+	Silent	SNP	G	G	A	rs17880383	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:101964312G>A	ENST00000370397.7	-	13	1544	c.1458C>T	c.(1456-1458)agC>agT	p.S486S		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	486					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CAAGCTGAATGCTTTTGTGAA	0.363													G|||	133	0.0265575	0.0023	0.0519	5008	,	,		18766	0.001		0.0785	False		,,,				2504	0.0143				p.S486S	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.C1458T						PASS	.	G		46,4360	48.2+/-83.0	0,46,2157	156.0	140.0	145.0		1458	4.0	1.0	10	dbSNP_124	145	528,8072	148.0+/-203.3	21,486,3793	no	coding-synonymous	CHUK	NM_001278.3		21,532,5950	AA,AG,GG		6.1395,1.044,4.4133		486/746	101964312	574,12432	2203	4300	6503	SO:0001819	synonymous_variant	1147	exon13			CTGAATGCTTTTG	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1458C>T	10.37:g.101964312G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	178	88	0.494382	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Silent	SNP	ENST00000370397.7	37	CCDS7488.1																																																																																			G|0.953;A|0.047	0.047	strong		0.363	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278	
EPX	8288	hgsc.bcm.edu	37	17	56270442	56270442	+	Missense_Mutation	SNP	A	A	G	rs11079339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56270442A>G	ENST00000225371.5	+	2	230	c.120A>G	c.(118-120)atA>atG	p.I40M		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	40			I -> M (in dbSNP:rs11079339). {ECO:0000269|Ref.2}.		defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	GAGACTGCATAGCAGAGGCCA	0.612													A|||	611	0.122005	0.1233	0.1412	5008	,	,		19426	0.0992		0.1531	False		,,,				2504	0.0982				p.I40M		Atlas-SNP	.											.	EPX	95	.	0			c.A120G						PASS	.	A	MET/ILE	623,3783	271.6+/-270.3	38,547,1618	118.0	118.0	118.0		120	-6.1	0.2	17	dbSNP_120	118	1212,7388	244.6+/-273.7	97,1018,3185	yes	missense	EPX	NM_000502.4	10	135,1565,4803	GG,GA,AA		14.093,14.1398,14.1089	benign	40/716	56270442	1835,11171	2203	4300	6503	SO:0001583	missense	8288	exon2			CTGCATAGCAGAG	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.120A>G	17.37:g.56270442A>G	ENSP00000225371:p.Ile40Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	86	51	0.593023	NM_000502	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	37	CCDS11602.1	270	0.12362637362637363	58	0.11788617886178862	44	0.12154696132596685	46	0.08041958041958042	122	0.16094986807387862	A	14.04	2.415976	0.42817	0.141398	0.14093	ENSG00000121053	ENST00000225371	T	0.72167	-0.63	5.13	-6.08	0.02151	.	0.590152	0.18122	N	0.151005	T	0.00210	0.0006	N	0.20445	0.575	0.48901	P	2.769999999999717E-4	B	0.12630	0.006	B	0.06405	0.002	T	0.02232	-1.1191	9	0.26408	T	0.33	-3.6705	4.1458	0.10215	0.1691:0.5197:0.1921:0.1191	rs11079339;rs56469108;rs60296065;rs11079339	40	P11678	PERE_HUMAN	M	40	ENSP00000225371:I40M	ENSP00000225371:I40M	I	+	3	3	EPX	53625441	0.000000	0.05858	0.194000	0.23346	0.907000	0.53573	-0.651000	0.05372	-0.983000	0.03511	0.444000	0.29173	ATA	A|0.876;G|0.124	0.124	strong		0.612	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802768	31802768	+	Missense_Mutation	SNP	G	G	A	rs2226548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:31802768G>A	ENST00000334068.2	+	1	197	c.175G>A	c.(175-177)Gcc>Acc	p.A59T		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	59	4 X 10 AA approximate repeats.		A -> T (in dbSNP:rs2226548). {ECO:0000269|PubMed:15489334}.			intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						CTGGGAGCCCGCCAGCTGCCA	0.622													-|||	2760	0.551118	0.6452	0.6427	5008	,	,		17651	0.2758		0.5736	False		,,,				2504	0.6196				p.A59T	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.G175A						PASS	.	A	THR/ALA	2801,1605		880,1041,282	59.0	59.0	59.0		175	-2.5	0.0	21	dbSNP_96	59	5047,3553		1483,2081,736	yes	missense	KRTAP13-4	NM_181600.1	58	2363,3122,1018	AA,AG,GG		41.314,36.4276,39.6586	benign	59/161	31802768	7848,5158	2203	4300	6503	SO:0001583	missense	284827	exon1			GAGCCCGCCAGCT	AP001708	CCDS13592.1	21q22.1	2006-03-13			ENSG00000186971	ENSG00000186971		"""Keratin associated proteins"""	18926	protein-coding gene	gene with protein product						12359730	Standard	NM_181600		Approved	KAP13.4	uc011acw.2	Q3LI77	OTTHUMG00000057770	ENST00000334068.2:c.175G>A	21.37:g.31802768G>A	ENSP00000334834:p.Ala59Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	175	173	0.988571	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	37	CCDS13592.1	1146	0.5247252747252747	325	0.6605691056910569	234	0.6464088397790055	167	0.291958041958042	420	0.554089709762533	-	0.010	-1.772617	0.00640	0.635724	0.58686	ENSG00000186971	ENST00000334068	T	0.02498	4.27	4.95	-2.5	0.06384	.	1.375280	0.05046	N	0.477219	T	0.00012	0.0000	N	0.00056	-2.365	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.47736	-0.9094	9	0.02654	T	1	.	0.6398	0.00809	0.4482:0.1285:0.1727:0.2506	rs2226548	59	Q3LI77	KR134_HUMAN	T	59	ENSP00000334834:A59T	ENSP00000334834:A59T	A	+	1	0	KRTAP13-4	30724639	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.656000	0.05342	-0.445000	0.07159	-0.988000	0.02552	GCC	G|0.411;A|0.589	0.589	strong		0.622	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
OR10H1	26539	hgsc.bcm.edu	37	19	15918802	15918802	+	Missense_Mutation	SNP	C	C	G	rs4808383	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15918802C>G	ENST00000334920.2	-	1	134	c.46G>C	c.(46-48)Ggc>Cgc	p.G16R		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	16			G -> R (in dbSNP:rs4808383).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						ACAGAGAAGCCGACGAGGATG	0.557													.|||	766	0.152955	0.1331	0.1124	5008	,	,		20065	0.12		0.1779	False		,,,				2504	0.2168				p.G16R		Atlas-SNP	.											.	OR10H1	59	.	0			c.G46C						PASS	.	C	ARG/GLY	612,3794	266.2+/-267.1	52,508,1643	153.0	145.0	148.0		46	2.3	0.3	19	dbSNP_111	148	1695,6905	311.7+/-310.5	175,1345,2780	yes	missense	OR10H1	NM_013940.2	125	227,1853,4423	GG,GC,CC		19.7093,13.8901,17.738	probably-damaging	16/319	15918802	2307,10699	2203	4300	6503	SO:0001583	missense	26539	exon1			AGAAGCCGACGAG	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.46G>C	19.37:g.15918802C>G	ENSP00000335596:p.Gly16Arg	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	275	136	0.494545	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	318	0.14560439560439561	66	0.13414634146341464	36	0.09944751381215469	77	0.1346153846153846	139	0.18337730870712401	c	13.00	2.105991	0.37145	0.138901	0.197093	ENSG00000186723	ENST00000334920	T	0.00659	5.94	4.47	2.28	0.28536	.	0.000000	0.50627	D	0.000103	T	0.00012	0.0000	M	0.93939	3.475	0.30892	P	0.730259	D	0.89917	1.0	D	0.70716	0.97	T	0.15150	-1.0447	9	0.72032	D	0.01	.	6.9577	0.24580	0.1726:0.7323:0.0:0.0952	rs4808383;rs52830115;rs4808383	16	Q9Y4A9	O10H1_HUMAN	R	16	ENSP00000335596:G16R	ENSP00000335596:G16R	G	-	1	0	OR10H1	15779802	0.285000	0.24296	0.320000	0.25306	0.003000	0.03518	1.939000	0.40213	0.323000	0.23307	0.643000	0.83706	GGC	C|0.832;G|0.168	0.168	strong		0.557	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
STK11IP	114790	hgsc.bcm.edu	37	2	220473355	220473355	+	Missense_Mutation	SNP	G	G	A	rs673951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220473355G>A	ENST00000456909.1	+	15	1744	c.1654G>A	c.(1654-1656)Gta>Ata	p.V552I	STK11IP_ENST00000295641.10_Missense_Mutation_p.V563I			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	563	Glu-rich.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCTGAGGGCGTACGGGGCAG	0.602													G|||	1755	0.350439	0.0272	0.3919	5008	,	,		17351	0.6825		0.3598	False		,,,				2504	0.4059				p.V563I		Atlas-SNP	.											.	STK11IP	152	.	0			c.G1687A						PASS	.	G	ILE/VAL	292,3702		11,270,1716	52.0	57.0	55.0		1687	0.5	0.0	2	dbSNP_83	55	2801,5485		461,1879,1803	yes	missense	STK11IP	NM_052902.2	29	472,2149,3519	AA,AG,GG		33.804,7.311,25.1873	benign	563/1100	220473355	3093,9187	1997	4143	6140	SO:0001583	missense	114790	exon15			GAGGGCGTACGGG	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.1654G>A	2.37:g.220473355G>A	ENSP00000389383:p.Val552Ile	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	280	141	0.503571	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	37		840	0.38461538461538464	18	0.036585365853658534	136	0.3756906077348066	407	0.7115384615384616	279	0.36807387862796836	G	2.879	-0.232288	0.05983	0.07311	0.33804	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.05081	3.5;3.5	4.5	0.456	0.16655	.	0.943966	0.08791	N	0.893239	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.33022	0.035;0.394	B;B	0.28465	0.009;0.09	T	0.19582	-1.0301	9	0.20519	T	0.43	-1.1691	4.1782	0.10362	0.0846:0.2921:0.4728:0.1505	rs673951;rs734848;rs17853278;rs60175423;rs673951	563;563	Q8N1F8-2;Q8N1F8	.;S11IP_HUMAN	I	552;531;563	ENSP00000389383:V552I;ENSP00000295641:V563I	ENSP00000295641:V563I	V	+	1	0	STK11IP	220181599	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-0.183000	0.09712	-0.102000	0.12197	-0.219000	0.12488	GTA	G|0.643;A|0.357	0.357	strong		0.602	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
DMKN	93099	hgsc.bcm.edu	37	19	36003962	36003962	+	Missense_Mutation	SNP	T	T	C	rs7247001	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36003962T>C	ENST00000339686.3	-	1	592	c.416A>G	c.(415-417)aAt>aGt	p.N139S	DMKN_ENST00000440396.1_Missense_Mutation_p.N139S|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000429837.1_Missense_Mutation_p.N139S|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.N139S|DMKN_ENST00000418261.1_Missense_Mutation_p.N139S|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Missense_Mutation_p.N139S|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.N139S|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.N139S	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	139	Gly-rich.		N -> S (in dbSNP:rs7247001). {ECO:0000269|PubMed:12975309}.			extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CCAAGCACCATTGTGGCCAGG	0.592													t|||	526	0.105032	0.2443	0.0432	5008	,	,		17026	0.006		0.0755	False		,,,				2504	0.093				p.N139S		Atlas-SNP	.											.	DMKN	116	.	0			c.A416G						PASS	.	C	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	932,3474	354.4+/-312.6	110,712,1381	63.0	70.0	68.0		416,416,416,416,416,416,416	0.9	0.0	19	dbSNP_116	68	593,8007	157.0+/-210.8	27,539,3734	yes	missense,missense,missense,missense,missense,missense,missense	DMKN	NM_001126056.2,NM_001126057.2,NM_001126058.2,NM_001190347.1,NM_001190348.1,NM_001190349.1,NM_033317.4	46,46,46,46,46,46,46	137,1251,5115	CC,CT,TT		6.8953,21.153,11.7254	benign,benign,benign,benign,benign,benign,benign	139/466,139/399,139/387,139/450,139/437,139/370,139/477	36003962	1525,11481	2203	4300	6503	SO:0001583	missense	93099	exon1			GCACCATTGTGGC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.416A>G	19.37:g.36003962T>C	ENSP00000342012:p.Asn139Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	210	0.09615384615384616	126	0.25609756097560976	22	0.06077348066298342	1	0.0017482517482517483	61	0.08047493403693931	t	7.215	0.596162	0.13875	0.21153	0.068953	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000429837;ENST00000419602;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T;T;T	0.17054	2.8;2.58;2.6;2.32;2.33;2.31;2.31;2.3	2.97	0.85	0.18980	.	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;B;B;B;B;B;B	0.32573	0.376;0.055;0.055;0.376;0.376;0.376;0.376	B;B;B;B;B;B;B	0.34301	0.179;0.01;0.01;0.179;0.179;0.179;0.179	T	0.42865	-0.9426	8	0.21540	T	0.41	.	4.4909	0.11813	0.0:0.3033:0.0:0.6967	rs7247001;rs60468030;rs7247001	139;139;139;139;139;139;139	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;C9J4P6;Q6E0U4-4;Q6E0U4	.;.;.;.;.;.;DMKN_HUMAN	S	139	ENSP00000342012:N139S;ENSP00000405503:N139S;ENSP00000391036:N139S;ENSP00000394908:N139S;ENSP00000415277:N139S;ENSP00000414743:N139S;ENSP00000388404:N139S;ENSP00000409513:N139S	ENSP00000342012:N139S	N	-	2	0	DMKN	40695802	0.000000	0.05858	0.017000	0.16124	0.009000	0.06853	-1.055000	0.03493	0.388000	0.25054	-0.489000	0.04712	AAT	T|0.885;C|0.115	0.115	strong		0.592	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
OR2T2	401992	hgsc.bcm.edu	37	1	248616764	248616764	+	Silent	SNP	C	C	T	rs376553658		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248616764C>T	ENST00000342927.3	+	1	688	c.666C>T	c.(664-666)atC>atT	p.I222I		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	222						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACACGCACATCCTCCTGACTG	0.542																																					p.I222I		Atlas-SNP	.											OR2T2,NS,carcinoma,0,1	OR2T2	73	1	0			c.C666T						scavenged	.						182.0	125.0	144.0					1																	248616764		2186	4264	6450	SO:0001819	synonymous_variant	401992	exon1			GCACATCCTCCTG	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.666C>T	1.37:g.248616764C>T		Somatic	541	0	0		WXS	Illumina HiSeq	Phase_I	329	21	0.0638298	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			C|0.500;T|0.500	0.500	strong		0.542	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
SLC16A13	201232	hgsc.bcm.edu	37	17	6943266	6943266	+	Silent	SNP	G	G	A	rs4796576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6943266G>A	ENST00000308027.6	+	4	1574	c.1266G>A	c.(1264-1266)ggG>ggA	p.G422G		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	422						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CCAAGGAGGGGCTGGAAGAGG	0.542													G|||	2803	0.559704	0.4213	0.4784	5008	,	,		17379	0.7758		0.667	False		,,,				2504	0.4714				p.G422G		Atlas-SNP	.											.	SLC16A13	28	.	0			c.G1266A						PASS	.	G		2011,2395	559.3+/-380.2	486,1039,678	90.0	97.0	95.0		1266	-4.1	0.0	17	dbSNP_111	95	5765,2835	674.0+/-403.1	1954,1857,489	no	coding-synonymous	SLC16A13	NM_201566.2		2440,2896,1167	AA,AG,GG		32.9651,45.6423,40.2122		422/427	6943266	7776,5230	2203	4300	6503	SO:0001819	synonymous_variant	201232	exon4			GGAGGGGCTGGAA	BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"""Solute carriers"""	31037	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 13"""		"""solute carrier family 16 (monocarboxylic acid transporters), member 13"""				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.1266G>A	17.37:g.6943266G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_201566	A3KMG3|A5PKU5|Q2VP92	Silent	SNP	ENST00000308027.6	37	CCDS11085.1																																																																																			G|0.412;A|0.588	0.588	strong		0.542	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2		
ZNF415	55786	hgsc.bcm.edu	37	19	53612720	53612720	+	De_novo_Start_OutOfFrame	SNP	T	T	C	rs1560099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53612720T>C	ENST00000601493.1	-	0	543				ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.Y193C|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000500065.4_Missense_Mutation_p.Y193C|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000421033.1_Missense_Mutation_p.Y205C|ZNF415_ENST00000440291.1_Missense_Mutation_p.Y180C|ZNF415_ENST00000455735.2_Missense_Mutation_p.Y241C|ZNF415_ENST00000448501.1_Missense_Mutation_p.Y241C			Q09FC8	ZN415_HUMAN	zinc finger protein 415						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		ATCAGTCCCATATTTATTAGA	0.363													T|||	834	0.166534	0.0219	0.2911	5008	,	,		21572	0.3363		0.1769	False		,,,				2504	0.0879				p.Y193C		Atlas-SNP	.											.	ZNF415	68	.	0			c.A578G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	208,4198	128.6+/-165.4	5,198,2000	106.0	96.0	99.0		578,578,578	-5.5	0.0	19	dbSNP_88	99	1385,7215	267.2+/-287.2	114,1157,3029	yes	missense,missense,missense	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	194,194,194	119,1355,5029	CC,CT,TT		16.1047,4.7208,12.2482	benign,benign,benign	193/556,193/556,193/556	53612720	1593,11413	2203	4300	6503			55786	exon4			GTCCCATATTTAT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000601493.1:c.-113A>G	19.37:g.53612720T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000601493.1	37		421	0.19276556776556777	7	0.014227642276422764	88	0.2430939226519337	199	0.3479020979020979	127	0.16754617414248021	T	4.759	0.141173	0.09083	0.047208	0.161047	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.03831	3.79;3.79;3.79;3.79;3.79;3.79	2.74	-5.49	0.02584	.	.	.	.	.	T	0.00012	0.0000	N	0.00599	-1.345	0.80722	P	0.0	B;B;D;B;B	0.76494	0.0;0.0;0.999;0.0;0.003	B;B;D;B;B	0.79784	0.0;0.0;0.993;0.0;0.004	T	0.20739	-1.0266	8	0.02654	T	1	.	5.1664	0.15088	0.1316:0.6504:0.0:0.218	rs1560099;rs3170111;rs52796533;rs56818125;rs1560099	193;241;193;180;205	F5H287;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;ZN415_HUMAN;.;.;.	C	193;193;241;205;241;180	ENSP00000243643:Y193C;ENSP00000439435:Y193C;ENSP00000396492:Y241C;ENSP00000395055:Y205C;ENSP00000388787:Y241C;ENSP00000414601:Y180C	ENSP00000243643:Y193C	Y	-	2	0	ZNF415	58304532	0.000000	0.05858	0.000000	0.03702	0.202000	0.24057	-1.377000	0.02558	-1.636000	0.01533	0.260000	0.18958	TAT	T|0.843;C|0.157	0.157	strong		0.363	ZNF415-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000464038.1	NM_018355	
CEBPB	1051	hgsc.bcm.edu	37	20	48808011	48808011	+	Silent	SNP	C	C	T	rs4253439	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:48808011C>T	ENST00000303004.3	+	1	636	c.441C>T	c.(439-441)gcC>gcT	p.A147A		NM_005194.3	NP_005185.2	P17676	CEBPB_HUMAN	CCAAT/enhancer binding protein (C/EBP), beta	147					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cellular response to amino acid stimulus (GO:0071230)|embryonic placenta development (GO:0001892)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mammary gland epithelial cell differentiation (GO:0060644)|mammary gland epithelial cell proliferation (GO:0033598)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|response to lipopolysaccharide (GO:0032496)|transcription from RNA polymerase II promoter (GO:0006366)	condensed chromosome, centromeric region (GO:0000779)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|lung(1)	2			BRCA - Breast invasive adenocarcinoma(9;5.72e-08)|STAD - Stomach adenocarcinoma(23;0.19)			GCCTGGGGGCCGCCAAGGGCG	0.741													C|||	1852	0.369808	0.1944	0.3977	5008	,	,		3841	0.4752		0.4344	False		,,,				2504	0.4121				p.A147A		Atlas-SNP	.											.	CEBPB	5	.	0			c.C441T						PASS	.	C		875,3041		180,515,1263	3.0	3.0	3.0		441	2.0	1.0	20	dbSNP_111	3	3024,4628		751,1522,1553	no	coding-synonymous	CEBPB	NM_005194.2		931,2037,2816	TT,TC,CC		39.5191,22.3442,33.705		147/346	48808011	3899,7669	1958	3826	5784	SO:0001819	synonymous_variant	1051	exon1			GGGGGCCGCCAAG	AY193834	CCDS13429.1	20q13.1	2013-01-10			ENSG00000172216	ENSG00000172216		"""basic leucine zipper proteins"""	1834	protein-coding gene	gene with protein product	"""liver-enriched transcriptional activator protein"", ""nuclear factor of interleukin 6"", ""interleukin 6-dependent DNA-binding protein"""	189965		TCF5		1535333, 1840554	Standard	NM_005194		Approved	LAP, CRP2, NFIL6, IL6DBP, C/EBP-beta	uc002xvi.2	P17676	OTTHUMG00000032715	ENST00000303004.3:c.441C>T	20.37:g.48808011C>T		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_005194	A8K671|Q96IH2|Q9H4Z5	Silent	SNP	ENST00000303004.3	37	CCDS13429.1																																																																																			C|0.638;T|0.362	0.362	strong		0.741	CEBPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079672.1	NM_005194	
OR52I1	390037	hgsc.bcm.edu	37	11	4615508	4615508	+	Silent	SNP	C	C	G	rs2010719	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4615508C>G	ENST00000530443.2	+	1	240	c.240C>G	c.(238-240)tcC>tcG	p.S80S	OR52I1_ENST00000450052.2_Silent_p.S104S	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCCTCCTCCGTGGTACCCA	0.507													G|||	3065	0.612021	0.5303	0.7046	5008	,	,		21113	0.5595		0.659	False		,,,				2504	0.6626				p.S80S		Atlas-SNP	.											OR52I1,NS,carcinoma,+1,1	OR52I1	29	1	0			c.C240G						PASS	.	G		2031,2371		664,703,834	166.0	141.0	149.0		240	-9.8	0.0	11	dbSNP_92	149	5255,3337		1955,1345,996	no	coding-synonymous	OR52I1	NM_001005169.1		2619,2048,1830	GG,GC,CC		38.8385,46.1381,43.928		80/325	4615508	7286,5708	2201	4296	6497	SO:0001819	synonymous_variant	390037	exon1			CTCCTCCGTGGTA	BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"""GPCR / Class A : Olfactory receptors"""	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.240C>G	11.37:g.4615508C>G		Somatic	432	0	0		WXS	Illumina HiSeq	Phase_I	315	314	0.996825	NM_001005169	Q6IF91	Silent	SNP	ENST00000530443.2	37	CCDS59223.1																																																																																			C|0.416;G|0.584	0.584	strong		0.507	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
MAPK11	5600	hgsc.bcm.edu	37	22	50704028	50704028	+	Missense_Mutation	SNP	C	C	T	rs33932986	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50704028C>T	ENST00000330651.6	-	10	924	c.824G>A	c.(823-825)cGt>cAt	p.R275H	MAPK11_ENST00000495277.1_5'Flank	NM_002751.5	NP_002742.3	Q15759	MK11_HUMAN	mitogen-activated protein kinase 11	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs33932986). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.9}.		activation of MAPK activity (GO:0000187)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|lung(4)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Regorafenib(DB08896)	GTTGGCTCCACGGAAGATGCT	0.642													C|||	83	0.0165735	0.0151	0.0331	5008	,	,		16651	0.0		0.0219	False		,,,				2504	0.0184				p.R275H	GBM(9;634 739 50668)	Atlas-SNP	.											.	MAPK11	23	.	0			c.G824A						PASS	.	C	HIS/ARG	44,4362	45.3+/-79.5	0,44,2159	46.0	46.0	46.0		824	-5.0	0.1	22	dbSNP_126	46	167,8433	75.4+/-138.0	0,167,4133	yes	missense	MAPK11	NM_002751.5	29	0,211,6292	TT,TC,CC		1.9419,0.9986,1.6223	benign	275/365	50704028	211,12795	2203	4300	6503	SO:0001583	missense	5600	exon10			GCTCCACGGAAGA	Y14440	CCDS14090.1	22q13.33	2011-06-09			ENSG00000185386	ENSG00000185386	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6873	protein-coding gene	gene with protein product		602898		PRKM11		9218798	Standard	NM_002751		Approved	p38-2, p38Beta, SAPK2	uc003bkr.3	Q15759	OTTHUMG00000150226	ENST00000330651.6:c.824G>A	22.37:g.50704028C>T	ENSP00000333685:p.Arg275His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	102	29	0.284314	NM_002751	A8K730|B0LPG1|B7Z630|E7ETQ1|L7RT27|O00284|O15472|Q2XNF2	Missense_Mutation	SNP	ENST00000330651.6	37	CCDS14090.1	37	0.01694139194139194	7	0.014227642276422764	16	0.04419889502762431	0	0.0	14	0.018469656992084433	C	11.81	1.750982	0.31046	0.009986	0.019419	ENSG00000185386	ENST00000330651	T	0.14022	2.54	4.29	-4.97	0.03029	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.391142	0.24262	N	0.040077	T	0.01765	0.0056	L	0.28504	0.86	0.36446	D	0.865812	B	0.09022	0.002	B	0.11329	0.006	T	0.13361	-1.0512	10	0.33141	T	0.24	.	14.0629	0.64810	0.0:0.8033:0.0:0.1967	rs33932986	275	Q15759	MK11_HUMAN	H	275	ENSP00000333685:R275H	ENSP00000333685:R275H	R	-	2	0	MAPK11	49046155	0.000000	0.05858	0.122000	0.21767	0.970000	0.65996	-1.513000	0.02256	-0.973000	0.03555	-0.458000	0.05436	CGT	C|0.985;T|0.015	0.015	strong		0.642	MAPK11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316900.1		
COL6A3	1293	hgsc.bcm.edu	37	2	238249717	238249717	+	Silent	SNP	G	G	A	rs34558385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238249717G>A	ENST00000295550.4	-	38	8294	c.7842C>T	c.(7840-7842)agC>agT	p.S2614S	COL6A3_ENST00000472056.1_Silent_p.S2007S|COL6A3_ENST00000409809.1_Silent_p.S2408S|COL6A3_ENST00000346358.4_Silent_p.S2414S|COL6A3_ENST00000347401.3_Silent_p.S2413S|COL6A3_ENST00000353578.4_Silent_p.S2408S	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2614	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGTCCACATCGCTCCCTGCCG	0.522													G|||	218	0.0435304	0.003	0.0432	5008	,	,		16652	0.0089		0.1133	False		,,,				2504	0.0624				p.S2614S		Atlas-SNP	.											.	COL6A3	608	.	0			c.C7842T						PASS	.	G	,,	80,4326	70.9+/-108.8	1,78,2124	150.0	149.0	150.0		7842,6021,7224	-2.4	0.1	2	dbSNP_126	150	856,7744	194.9+/-240.2	43,770,3487	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	44,848,5611	AA,AG,GG		9.9535,1.8157,7.1967	,,	2614/3178,2007/2571,2408/2972	238249717	936,12070	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			CACATCGCTCCCT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7842C>T	2.37:g.238249717G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	257	135	0.525292	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.929;A|0.071	0.071	strong		0.522	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
GABRD	2563	hgsc.bcm.edu	37	1	1959699	1959699	+	Missense_Mutation	SNP	G	G	A	rs41307846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1959699G>A	ENST00000378585.4	+	6	742	c.659G>A	c.(658-660)cGc>cAc	p.R220H		NM_000815.4	NP_000806.2	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	220			R -> C (in a GEFS+ family; does not affect receptor current amplitudes; unknown pathological significance; dbSNP:rs139300921). {ECO:0000269|PubMed:15115768}.|R -> H (associated with susceptibility to EIG10 and EJM7; reduced receptor current amplitudes; dbSNP:rs41307846). {ECO:0000269|PubMed:15115768, ECO:0000269|Ref.1}.		signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(2)|endometrium(3)|kidney(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ACCAGCTACCGCTTCACCACG	0.637													G|||	29	0.00579073	0.0008	0.0043	5008	,	,		12527	0.0		0.0179	False		,,,				2504	0.0072				p.R220H		Atlas-SNP	.											.	GABRD	49	.	0			c.G659A	GRCh37	CM041768	GABRD	M	rs41307846	PASS	.	G	HIS/ARG	20,4380	26.2+/-53.5	0,20,2180	89.0	65.0	73.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	659	1.5	1.0	1	dbSNP_127	73	197,8403	86.1+/-148.5	2,193,4105	yes	missense	GABRD	NM_000815.4	29	2,213,6285	AA,AG,GG		2.2907,0.4545,1.6692	benign	220/453	1959699	217,12783	2200	4300	6500	SO:0001583	missense	2563	exon6			GCTACCGCTTCAC	BC033801	CCDS36.1	1p36.3	2012-06-22			ENSG00000187730	ENSG00000187730		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4084	protein-coding gene	gene with protein product	"""GABA(A) receptor, delta"""	137163				2176788, 10965146	Standard	NM_000815		Approved		uc001aip.2	O14764	OTTHUMG00000041064	ENST00000378585.4:c.659G>A	1.37:g.1959699G>A	ENSP00000367848:p.Arg220His	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	137	76	0.554745	NM_000815	Q8N4N9	Missense_Mutation	SNP	ENST00000378585.4	37	CCDS36.1	21	0.009615384615384616	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	18	0.023746701846965697	G	5.326	0.245486	0.10077	0.004545	0.022907	ENSG00000187730	ENST00000378585	T	0.79141	-1.24	3.47	1.47	0.22746	Neurotransmitter-gated ion-channel ligand-binding (3);	0.209202	0.40222	N	0.001149	T	0.40372	0.1114	N	0.17838	0.53	0.44956	D	0.997978	B	0.17268	0.021	B	0.12837	0.008	T	0.25641	-1.0126	10	0.19147	T	0.46	-6.1993	6.1947	0.20544	0.3642:0.0:0.6358:0.0	rs41307846	220	O14764	GBRD_HUMAN	H	220	ENSP00000367848:R220H	ENSP00000367848:R220H	R	+	2	0	GABRD	1949559	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.308000	0.43690	0.753000	0.32945	0.561000	0.74099	CGC	G|0.985;A|0.015	0.015	strong		0.637	GABRD-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098493.1	NM_000815	
DNASE2B	58511	hgsc.bcm.edu	37	1	84867610	84867610	+	Missense_Mutation	SNP	G	G	A	rs3754274	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:84867610G>A	ENST00000370665.3	+	2	185	c.152G>A	c.(151-153)aGa>aAa	p.R51K		NM_021233.2	NP_067056.2	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta	51			R -> K (in dbSNP:rs3754274).		apoptotic DNA fragmentation (GO:0006309)	extracellular region (GO:0005576)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)			endometrium(1)|lung(4)|skin(1)	6				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)		TTACCTAAAAGACAAAACAAG	0.363													G|||	1125	0.224641	0.0401	0.245	5008	,	,		19494	0.369		0.2744	False		,,,				2504	0.2597				p.R51K	Pancreas(54;788 1175 11852 16034 30034)	Atlas-SNP	.											.	DNASE2B	40	.	0			c.G152A						PASS	.	G	LYS/ARG	272,3414		15,242,1586	57.0	54.0	55.0		152	-0.4	0.3	1	dbSNP_107	55	2296,5876		345,1606,2135	yes	missense	DNASE2B	NM_021233.2	26	360,1848,3721	AA,AG,GG		28.0959,7.3793,21.6563	benign	51/362	84867610	2568,9290	1843	4086	5929	SO:0001583	missense	58511	exon2			CTAAAAGACAAAA	AF274571	CCDS694.1, CCDS44167.1	1p22.3	2008-02-05			ENSG00000137976	ENSG00000137976			28875	protein-coding gene	gene with protein product		608057				12594037, 11376952	Standard	NM_021233		Approved	DLAD	uc001djt.1	Q8WZ79	OTTHUMG00000009860	ENST00000370665.3:c.152G>A	1.37:g.84867610G>A	ENSP00000359699:p.Arg51Lys	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_021233	Q5VXD0|Q5VXD1|Q8WZ80|Q9NQW3	Missense_Mutation	SNP	ENST00000370665.3	37	CCDS44167.1	497	0.22756410256410256	27	0.054878048780487805	75	0.20718232044198895	194	0.33916083916083917	201	0.26517150395778366	G	1.945	-0.442542	0.04604	0.073793	0.280959	ENSG00000137976	ENST00000370665	T	0.13089	2.62	5.12	-0.372	0.12520	.	0.704957	0.14608	N	0.309222	T	0.01592	0.0051	N	0.20401	0.57	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.46555	-0.9183	9	0.16420	T	0.52	-4.2137	0.9403	0.01354	0.3681:0.1525:0.3227:0.1567	rs3754274;rs17479583;rs52827493;rs60174659;rs3754274	51	Q8WZ79	DNS2B_HUMAN	K	51	ENSP00000359699:R51K	ENSP00000359699:R51K	R	+	2	0	DNASE2B	84640198	0.000000	0.05858	0.278000	0.24718	0.985000	0.73830	-0.068000	0.11561	0.060000	0.16281	0.467000	0.42956	AGA	G|0.773;A|0.227	0.227	strong		0.363	DNASE2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027248.1	NM_021233	
GRAMD1B	57476	hgsc.bcm.edu	37	11	123480981	123480981	+	Silent	SNP	T	T	C	rs10893053	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123480981T>C	ENST00000529750.1	+	13	1752	c.1425T>C	c.(1423-1425)caT>caC	p.H475H	GRAMD1B_ENST00000456860.2_Silent_p.H482H|GRAMD1B_ENST00000450171.2_Silent_p.H166H|GRAMD1B_ENST00000322282.7_Silent_p.H475H	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	475						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		TGCCCTACCATGACTACTTCT	0.562													T|||	1211	0.241813	0.0719	0.2392	5008	,	,		18260	0.1746		0.3141	False		,,,				2504	0.4683				p.H475H		Atlas-SNP	.											.	GRAMD1B	122	.	0			c.T1425C						PASS	.	T		415,3697		19,377,1660	123.0	120.0	121.0		1425	-0.9	1.0	11	dbSNP_120	121	2739,5661		460,1819,1921	yes	coding-synonymous	GRAMD1B	NM_020716.1		479,2196,3581	CC,CT,TT		32.6071,10.0924,25.2078		475/739	123480981	3154,9358	2056	4200	6256	SO:0001819	synonymous_variant	57476	exon13			CTACCATGACTAC	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.1425T>C	11.37:g.123480981T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_020716	Q6UW85|Q9ULL9	Silent	SNP	ENST00000529750.1	37	CCDS53720.1																																																																																			T|0.767;C|0.233	0.233	strong		0.562	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660	
ZNF280A	129025	hgsc.bcm.edu	37	22	22869548	22869548	+	Missense_Mutation	SNP	T	T	C	rs362011	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22869548T>C	ENST00000302097.3	-	2	659	c.407A>G	c.(406-408)aAt>aGt	p.N136S	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	136			N -> S (in dbSNP:rs362011). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9074928}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		ATCTGAGTAATTGGGAGAAAC	0.478													T|||	2373	0.473842	0.239	0.7334	5008	,	,		17220	0.4147		0.7038	False		,,,				2504	0.4315				p.N136S		Atlas-SNP	.											.	ZNF280A	67	.	0			c.A407G						PASS	.	T	SER/ASN	1345,3061	434.9+/-344.1	219,907,1077	67.0	65.0	65.0		407	0.6	0.0	22	dbSNP_79	65	5839,2761	664.8+/-402.2	2006,1827,467	yes	missense	ZNF280A	NM_080740.3	46	2225,2734,1544	CC,CT,TT		32.1047,30.5266,44.764	benign	136/543	22869548	7184,5822	2203	4300	6503	SO:0001583	missense	129025	exon2			GAGTAATTGGGAG	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.407A>G	22.37:g.22869548T>C	ENSP00000302855:p.Asn136Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	1155	0.5288461538461539	126	0.25609756097560976	254	0.7016574585635359	244	0.42657342657342656	531	0.7005277044854882	T	2.586	-0.296399	0.05532	0.305266	0.678953	ENSG00000169548	ENST00000302097	T	0.23754	1.89	3.7	0.624	0.17659	.	.	.	.	.	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B	0.19200	0.034	B	0.21708	0.036	T	0.36648	-0.9739	8	0.08837	T	0.75	0.0192	5.8027	0.18422	0.0:0.3143:0.0:0.6857	rs362011;rs695787;rs17857437;rs61246623;rs362011	136	P59817	Z280A_HUMAN	S	136	ENSP00000302855:N136S	ENSP00000302855:N136S	N	-	2	0	ZNF280A	21199548	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.116000	0.10724	0.049000	0.15920	0.528000	0.53228	AAT	T|0.479;C|0.521	0.521	strong		0.478	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702726	27702726	+	Silent	SNP	G	G	A	rs11015753	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:27702726G>A	ENST00000438700.3	-	1	571	c.454C>T	c.(454-456)Ctg>Ttg	p.L152L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	152			L -> P (in dbSNP:rs6482626). {ECO:0000269|PubMed:15489334}.		spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						CCGGTGCCCAGCGCGGCTGTC	0.672													G|||	848	0.169329	0.0787	0.1844	5008	,	,		12710	0.0089		0.3062	False		,,,				2504	0.3057				p.L152L		Atlas-SNP	.											.	PTCHD3	140	.	0			c.C454T						PASS	.	G		412,3994	197.1+/-221.3	17,378,1808	61.0	70.0	67.0		454	3.6	0.0	10	dbSNP_120	67	2628,5972	414.5+/-351.5	435,1758,2107	no	coding-synonymous	PTCHD3	NM_001034842.3		452,2136,3915	AA,AG,GG		30.5581,9.3509,23.3738		152/768	27702726	3040,9966	2203	4300	6503	SO:0001819	synonymous_variant	374308	exon1			TGCCCAGCGCGGC	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.454C>T	10.37:g.27702726G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	57	0.670588	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			G|0.786;A|0.214	0.214	strong		0.672	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
CSPG4	1464	hgsc.bcm.edu	37	15	75980112	75980112	+	Silent	SNP	A	A	G	rs4414463	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75980112A>G	ENST00000308508.5	-	3	3386	c.3294T>C	c.(3292-3294)gcT>gcC	p.A1098A		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1098	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						AGCCACGGTCAGCCCCTGAGT	0.647													G|||	2210	0.441294	0.4024	0.5548	5008	,	,		19871	0.3145		0.5229	False		,,,				2504	0.4601				p.A1098A		Atlas-SNP	.											.	CSPG4	175	.	0			c.T3294C						PASS	.	G		1868,2526		388,1092,717	62.0	60.0	61.0		3294	-7.1	0.5	15	dbSNP_111	61	4735,3849		1329,2077,886	no	coding-synonymous	CSPG4	NM_001897.4		1717,3169,1603	GG,GA,AA		44.8392,42.5125,49.1216		1098/2323	75980112	6603,6375	2197	4292	6489	SO:0001819	synonymous_variant	1464	exon3			ACGGTCAGCCCCT	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.3294T>C	15.37:g.75980112A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	178	84	0.47191	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			A|0.524;G|0.476	0.476	strong		0.647	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
MYPN	84665	hgsc.bcm.edu	37	10	69934258	69934258	+	Missense_Mutation	SNP	C	C	G	rs3814182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:69934258C>G	ENST00000358913.5	+	11	2897	c.2409C>G	c.(2407-2409)agC>agG	p.S803R	MYPN_ENST00000354393.2_Missense_Mutation_p.S528R|MYPN_ENST00000540630.1_Missense_Mutation_p.S803R	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	803	Pro-rich.		S -> R (in dbSNP:rs3814182). {ECO:0000269|PubMed:11309420, ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CCATCCCCAGCGGAAACCAGT	0.542													C|||	2361	0.471446	0.447	0.4597	5008	,	,		18659	0.3512		0.5666	False		,,,				2504	0.5389				p.S803R		Atlas-SNP	.											.	MYPN	189	.	0			c.C2409G						PASS	.	C	ARG/SER	2064,2342	568.8+/-382.5	495,1074,634	111.0	98.0	103.0		2409	-9.6	0.3	10	dbSNP_107	103	4738,3862	609.4+/-395.5	1314,2110,876	yes	missense	MYPN	NM_032578.2	110	1809,3184,1510	GG,GC,CC		44.907,46.8452,47.7011	benign	803/1321	69934258	6802,6204	2203	4300	6503	SO:0001583	missense	84665	exon11			CCCCAGCGGAAAC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2409C>G	10.37:g.69934258C>G	ENSP00000351790:p.Ser803Arg	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	191	81	0.424084	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	1046	0.47893772893772896	240	0.4878048780487805	182	0.5027624309392266	195	0.3409090909090909	429	0.5659630606860159	C	12.78	2.039690	0.35989	0.468452	0.55093	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.58506	0.33;0.38;0.36	5.8	-9.63	0.00544	.	0.277370	0.41823	D	0.000815	T	0.00012	0.0000	L	0.46157	1.445	0.38615	P	0.04899699999999996	P;P;P	0.46512	0.879;0.773;0.664	B;B;B	0.43360	0.397;0.417;0.12	T	0.08269	-1.0730	8	.	.	.	.	19.5953	0.95535	0.0:0.7212:0.0:0.2788	rs3814182;rs59227755;rs3814182	803;528;803	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	R	528;528;803;803	ENSP00000346369:S528R;ENSP00000351790:S803R;ENSP00000441668:S803R	.	S	+	3	2	MYPN	69604264	0.000000	0.05858	0.265000	0.24526	0.876000	0.50452	-3.502000	0.00449	-1.913000	0.01079	-0.136000	0.14681	AGC	C|0.500;G|0.500	0.500	strong		0.542	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
FASN	2194	hgsc.bcm.edu	37	17	80040450	80040450	+	Missense_Mutation	SNP	C	C	T	rs145688025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80040450C>T	ENST00000306749.2	-	34	6090	c.5872G>A	c.(5872-5874)Gag>Aag	p.E1958K	FASN_ENST00000579758.1_5'UTR	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1958	Beta-ketoacyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	TGCGCCGCCTCGGCAATGAGG	0.697													.|||	9	0.00179712	0.0	0.0014	5008	,	,		14596	0.0		0.008	False		,,,				2504	0.0				p.E1958K	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											FASN,NS,carcinoma,0,1	FASN	154	1	0			c.G5872A						PASS	.	C	LYS/GLU	5,4381		0,5,2188	18.0	23.0	21.0		5872	4.6	0.8	17	dbSNP_134	21	50,8532		0,50,4241	yes	missense	FASN	NM_004104.4	56	0,55,6429	TT,TC,CC		0.5826,0.114,0.4241	probably-damaging	1958/2512	80040450	55,12913	2193	4291	6484	SO:0001583	missense	2194	exon34			CCGCCTCGGCAAT	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.5872G>A	17.37:g.80040450C>T	ENSP00000304592:p.Glu1958Lys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	22.1	4.246059	0.80024	0.00114	0.005826	ENSG00000169710	ENST00000306749	T	0.44083	0.93	4.62	4.62	0.57501	Polyketide synthase/Fatty acid synthase, KR (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	L	0.48174	1.505	0.80722	D	1	D	0.76494	0.999	D	0.65684	0.937	T	0.49925	-0.8887	10	0.36615	T	0.2	-40.4636	17.6281	0.88098	0.0:1.0:0.0:0.0	.	1958	P49327	FAS_HUMAN	K	1958	ENSP00000304592:E1958K	ENSP00000304592:E1958K	E	-	1	0	FASN	77633739	1.000000	0.71417	0.762000	0.31397	0.063000	0.16089	5.699000	0.68310	2.398000	0.81561	0.462000	0.41574	GAG	C|0.997;T|0.003	0.003	strong		0.697	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
OR5AK2	390181	hgsc.bcm.edu	37	11	56756516	56756516	+	Missense_Mutation	SNP	G	G	C	rs12420424	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56756516G>C	ENST00000326855.2	+	1	170	c.128G>C	c.(127-129)aGt>aCt	p.S43T		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	43			S -> T (in dbSNP:rs12420424).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						ATGGGTAATAGTGGAATAATC	0.373													C|||	298	0.0595048	0.0227	0.121	5008	,	,		20007	0.002		0.0825	False		,,,				2504	0.1012				p.S43T		Atlas-SNP	.											.	OR5AK2	45	.	0			c.G128C						PASS	.	C	THR/SER	162,4240	810.9+/-416.0	5,152,2044	126.0	115.0	119.0		128	1.3	0.1	11	dbSNP_120	119	679,7913	786.9+/-407.6	31,617,3648	no	missense	OR5AK2	NM_001005323.1	58	36,769,5692	CC,CG,GG		7.9027,3.6801,6.4722	benign	43/310	56756516	841,12153	2201	4296	6497	SO:0001583	missense	390181	exon1			GTAATAGTGGAAT	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.128G>C	11.37:g.56756516G>C	ENSP00000322784:p.Ser43Thr	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	301	142	0.471761	NM_001005323	B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	CCDS31538.1	117	0.05357142857142857	9	0.018292682926829267	41	0.1132596685082873	2	0.0034965034965034965	65	0.08575197889182058	C	1.888	-0.456271	0.04540	0.036801	0.079027	ENSG00000181273	ENST00000326855	T	0.00438	7.42	3.66	1.29	0.21616	GPCR, rhodopsin-like superfamily (1);	0.682371	0.12010	N	0.507981	T	0.00012	0.0000	N	0.03891	-0.335	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29336	-1.0015	9	0.62326	D	0.03	-9.7249	4.4129	0.11441	0.0:0.325:0.1707:0.5043	rs12420424	43	Q8NH90	O5AK2_HUMAN	T	43	ENSP00000322784:S43T	ENSP00000322784:S43T	S	+	2	0	OR5AK2	56513092	0.000000	0.05858	0.085000	0.20634	0.153000	0.21895	0.588000	0.23924	-0.114000	0.11936	-1.041000	0.02371	AGT	G|0.938;C|0.062	0.062	strong		0.373	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
SORBS1	10580	hgsc.bcm.edu	37	10	97174269	97174269	+	Silent	SNP	C	C	T	rs11188316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:97174269C>T	ENST00000361941.3	-	7	818	c.792G>A	c.(790-792)acG>acA	p.T264T	SORBS1_ENST00000371227.4_Silent_p.T264T|SORBS1_ENST00000354106.3_Silent_p.T255T|SORBS1_ENST00000371246.2_Silent_p.T264T|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371247.2_Silent_p.T264T|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000371245.3_Silent_p.T195T|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000353505.5_Silent_p.T195T|SORBS1_ENST00000371249.2_Silent_p.T232T|SORBS1_ENST00000393949.1_Silent_p.T255T|SORBS1_ENST00000277982.5_Silent_p.T264T	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1									p.G196*(1)|p.G265*(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		AAACAGCTCCCGTGAGGTCAG	0.597													C|||	137	0.0273562	0.0076	0.036	5008	,	,		20165	0.0		0.0696	False		,,,				2504	0.0327				p.T264T		Atlas-SNP	.											.	SORBS1	185	.	2	Substitution - Nonsense(2)	lung(2)	c.G792A						PASS	.	C	,,,,,,	82,4324		3,76,2124	43.0	45.0	44.0		792,792,585,,,696,	2.4	1.0	10	dbSNP_120	44	737,7863		39,659,3602	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	42,735,5726	TT,TC,CC		8.5698,1.8611,6.2971	,,,,,,	264/1293,264/1152,195/906,,,232/817,	97174269	819,12187	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon7			AGCTCCCGTGAGG	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.792G>A	10.37:g.97174269C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	145	58	0.4	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			C|0.952;T|0.048	0.048	strong		0.597	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
PKP3	11187	hgsc.bcm.edu	37	11	403980	403980	+	Silent	SNP	G	G	A	rs11748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:403980G>A	ENST00000331563.2	+	11	2191	c.2115G>A	c.(2113-2115)ccG>ccA	p.P705P		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	705					desmosome assembly (GO:0002159)|establishment of protein localization to plasma membrane (GO:0090002)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|desmosome (GO:0030057)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)			breast(1)|central_nervous_system(1)|endometrium(3)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGAAGCTGCCGGGCAGCGTGG	0.672													g|||	2559	0.510982	0.5212	0.6066	5008	,	,		17443	0.3651		0.5606	False		,,,				2504	0.5286				p.P705P		Atlas-SNP	.											.	PKP3	36	.	0			c.G2115A						PASS	.	G		2320,2030	583.5+/-385.8	626,1068,481	30.0	34.0	33.0		2115	-7.9	0.8	11	dbSNP_52	33	4812,3748	599.7+/-394.1	1358,2096,826	no	coding-synonymous	PKP3	NM_007183.2		1984,3164,1307	AA,AG,GG		43.785,46.6667,44.756		705/798	403980	7132,5778	2175	4280	6455	SO:0001819	synonymous_variant	11187	exon11			GCTGCCGGGCAGC	Z98265	CCDS7695.1	11p15	2013-02-14			ENSG00000184363	ENSG00000184363		"""Armadillo repeat containing"""	9025	protein-coding gene	gene with protein product		605561				10374265	Standard	XM_005252760		Approved		uc001lpc.3	Q9Y446	OTTHUMG00000119068	ENST00000331563.2:c.2115G>A	11.37:g.403980G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	96	94	0.979167	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	37	CCDS7695.1																																																																																			G|0.467;A|0.533	0.533	strong		0.672	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183	
FABP9	646480	hgsc.bcm.edu	37	8	82370894	82370894	+	Silent	SNP	T	T	C	rs139486050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:82370894T>C	ENST00000379071.2	-	3	346	c.291A>G	c.(289-291)aaA>aaG	p.K97K	RP11-157I4.4_ENST00000524085.2_RNA	NM_001080526.1	NP_001073995.1	Q0Z7S8	FABP9_HUMAN	fatty acid binding protein 9, testis	97					acrosome assembly (GO:0001675)	acrosomal vesicle (GO:0001669)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	6			Epithelial(68;0.186)			TGCCAAGCCATTTTTGGACGT	0.328													T|||	2	0.000399361	0.0	0.0014	5008	,	,		18485	0.0		0.001	False		,,,				2504	0.0				p.K97K		Atlas-SNP	.											.	FABP9	15	.	0			c.A291G						PASS	.	T		5,4397	9.9+/-24.2	0,5,2196	103.0	95.0	98.0		291	2.7	1.0	8	dbSNP_134	98	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	FABP9	NM_001080526.1		0,25,6476	CC,CT,TT		0.2326,0.1136,0.1923		97/133	82370894	25,12977	2201	4300	6501	SO:0001819	synonymous_variant	646480	exon3			AAGCCATTTTTGG			8q21.13	2013-03-01			ENSG00000205186	ENSG00000205186		"""Fatty acid binding protein family"""	3563	protein-coding gene	gene with protein product						7958448	Standard	NM_001080526		Approved	PERF, T-FABP, PERF15	uc011lfo.2	Q0Z7S8	OTTHUMG00000164601	ENST00000379071.2:c.291A>G	8.37:g.82370894T>C		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	254	127	0.5	NM_001080526		Silent	SNP	ENST00000379071.2	37																																																																																				T|0.999;C|0.001	0.001	strong		0.328	FABP9-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379367.2	NM_001080526	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377918	49377918	+	Missense_Mutation	SNP	G	G	T	rs35087747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49377918G>T	ENST00000200453.5	+	2	1697	c.1428G>T	c.(1426-1428)agG>agT	p.R476S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	476	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.		R -> S (in dbSNP:rs35087747). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CGGACCAGAGGGCCCACTTCA	0.572													T|||	421	0.0840655	0.087	0.0793	5008	,	,		17447	0.003		0.164	False		,,,				2504	0.0849				p.R476S		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1428T						PASS	.	T	SER/ARG	578,3828	771.4+/-413.8	35,508,1660	71.0	70.0	70.0		1428	-5.6	0.0	19	dbSNP_126	70	1549,7051	745.0+/-407.3	129,1291,2880	yes	missense	PPP1R15A	NM_014330.3	110	164,1799,4540	TT,TG,GG		18.0116,13.1185,16.354	benign	476/675	49377918	2127,10879	2203	4300	6503	SO:0001583	missense	23645	exon2			CCAGAGGGCCCAC	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1428G>T	19.37:g.49377918G>T	ENSP00000200453:p.Arg476Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	198	0.09065934065934066	45	0.09146341463414634	30	0.08287292817679558	1	0.0017482517482517483	122	0.16094986807387862	T	0.463	-0.888184	0.02511	0.131185	0.180116	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05139	3.49	4.19	-5.56	0.02529	.	0.890365	0.09631	N	0.776241	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34925	-0.9809	9	0.02654	T	1	2.4026	3.0039	0.06023	0.2444:0.4426:0.1244:0.1886	rs35087747	476	O75807	PR15A_HUMAN	S	476;316;434	ENSP00000200453:R476S	ENSP00000200453:R476S	R	+	3	2	PPP1R15A	54069730	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.597000	0.00894	-1.820000	0.01215	-1.089000	0.02181	AGG	A|0.000;C|0.000;G|0.864;T|0.136	0.136	strong		0.572	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
ZNF416	55659	hgsc.bcm.edu	37	19	58084930	58084930	+	Silent	SNP	G	G	A	rs3746222	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58084930G>A	ENST00000196489.3	-	4	564	c.342C>T	c.(340-342)acC>acT	p.T114T		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	114					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		GCAAAATGTCGGTCAGGAATG	0.507													G|||	839	0.167532	0.202	0.1369	5008	,	,		20042	0.0942		0.2078	False		,,,				2504	0.1769				p.T114T		Atlas-SNP	.											.	ZNF416	50	.	0			c.C342T						PASS	.	G		852,3554	334.4+/-303.4	76,700,1427	121.0	104.0	110.0		342	-2.1	0.0	19	dbSNP_107	110	1661,6939	307.2+/-308.3	153,1355,2792	no	coding-synonymous	ZNF416	NM_017879.1		229,2055,4219	AA,AG,GG		19.314,19.3373,19.3219		114/595	58084930	2513,10493	2203	4300	6503	SO:0001819	synonymous_variant	55659	exon4			AATGTCGGTCAGG	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"""Zinc fingers, C2H2-type"", ""-"""	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.342C>T	19.37:g.58084930G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	217	90	0.414747	NM_017879	Q9NWW8	Silent	SNP	ENST00000196489.3	37	CCDS12954.1																																																																																			G|0.828;A|0.172	0.172	strong		0.507	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879	
OR2J2	26707	hgsc.bcm.edu	37	6	29141849	29141849	+	Missense_Mutation	SNP	T	T	C	rs3116856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29141849T>C	ENST00000377167.2	+	1	539	c.437T>C	c.(436-438)gTt>gCt	p.V146A		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	146			A -> V (in allele 6M1-6*02 and allele 6M1-6*03; dbSNP:rs3116856). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						CACTTGTTGGTTGCGGCTTCT	0.463													C|||	1893	0.377995	0.112	0.451	5008	,	,		21396	0.378		0.5477	False		,,,				2504	0.5112				p.V146A		Atlas-SNP	.											.	OR2J2	51	.	0			c.T437C						PASS	.	C	ALA/VAL	748,3250		75,598,1326	301.0	276.0	284.0		437	2.3	0.4	6	dbSNP_103	284	4513,3831		1237,2039,896	no	missense	OR2J2	NM_030905.2	64	1312,2637,2222	CC,CT,TT		45.9132,18.7094,42.6268	probably-damaging	146/313	29141849	5261,7081	1999	4172	6171	SO:0001583	missense	26707	exon1			TGTTGGTTGCGGC		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.437T>C	6.37:g.29141849T>C	ENSP00000366372:p.Val146Ala	Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	539	315	0.584416	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	37	CCDS43434.1	870	0.3983516483516483	59	0.11991869918699187	166	0.4585635359116022	209	0.36538461538461536	436	0.575197889182058	C	0	-2.819406	0.00072	0.187094	0.540868	ENSG00000204700	ENST00000377167	T	0.39056	1.1	2.3	2.3	0.28687	.	.	.	.	.	T	0.05364	0.0142	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.36163	-0.9759	5	0.02654	T	1	.	7.9731	0.30138	0.0:0.8633:0.0:0.1367	rs3116856;rs17737530;rs52793747;rs3116856	.	.	.	A	146	ENSP00000366372:V146A	ENSP00000366372:V146A	V	+	2	0	OR2J2	29249828	0.000000	0.05858	0.369000	0.25952	0.019000	0.09904	-0.161000	0.10026	0.290000	0.22444	-0.971000	0.02607	GTT	T|0.566;C|0.434	0.434	strong		0.463	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2		
FBXO2	26232	hgsc.bcm.edu	37	1	11710561	11710561	+	Missense_Mutation	SNP	T	T	G	rs9614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11710561T>G	ENST00000354287.4	-	2	694	c.353A>C	c.(352-354)aAg>aCg	p.K118T	FBXO2_ENST00000475961.1_5'Flank	NM_012168.5	NP_036300.2	Q9UK22	FBX2_HUMAN	F-box protein 2	118	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.		K -> T (in dbSNP:rs9614). {ECO:0000269|Ref.2}.		cellular protein modification process (GO:0006464)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of protein ubiquitination (GO:0031396)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|SCF ubiquitin ligase complex (GO:0019005)	beta-amyloid binding (GO:0001540)|carbohydrate binding (GO:0030246)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|large_intestine(1)|lung(4)	6	Ovarian(185;0.249)	Lung NSC(185;9.37e-06)|all_lung(284;1.39e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|BRCA - Breast invasive adenocarcinoma(304;1.88e-06)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|Lung(427;0.0146)|LUSC - Lung squamous cell carcinoma(448;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		GCGGCGCCGCTTGCTCAGGAA	0.687													T|||	1220	0.24361	0.143	0.2565	5008	,	,		14310	0.4494		0.1759	False		,,,				2504	0.228				p.K118T		Atlas-SNP	.											.	FBXO2	25	.	0			c.A353C						PASS	.	T	THR/LYS	730,3668		53,624,1522	20.0	25.0	23.0		353	3.9	1.0	1	dbSNP_52	23	1653,6943		160,1333,2805	yes	missense	FBXO2	NM_012168.5	78	213,1957,4327	GG,GT,TT		19.2299,16.5985,18.3392	probably-damaging	118/297	11710561	2383,10611	2199	4298	6497	SO:0001583	missense	26232	exon2			CGCCGCTTGCTCA	AF174594	CCDS130.1	1p36.21	2010-04-21	2004-06-15		ENSG00000116661	ENSG00000116661		"""F-boxes /  ""other"""""	13581	protein-coding gene	gene with protein product		607112	"""F-box only protein 2"", ""organ of Corti protein 1"""	OCP1		10531035, 10531037	Standard	NM_012168		Approved	FBX2, Nfb42, Fbs1, Fbg1	uc001asj.3	Q9UK22	OTTHUMG00000002072	ENST00000354287.4:c.353A>C	1.37:g.11710561T>G	ENSP00000346240:p.Lys118Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	66	40	0.606061	NM_012168	B2R7K7|Q5TGY0|Q6FGJ7|Q8TB29|Q9UKC6	Missense_Mutation	SNP	ENST00000354287.4	37	CCDS130.1	537	0.24587912087912087	73	0.1483739837398374	84	0.23204419889502761	249	0.4353146853146853	131	0.17282321899736147	T	22.7	4.326899	0.81690	0.165985	0.192299	ENSG00000116661	ENST00000354287;ENST00000452872	T	0.32272	1.46	5.06	3.91	0.45181	Galactose-binding domain-like (1);F-box domain, Skp2-like (1);F-box associated (FBA) domain (2);	0.334286	0.29286	N	0.012596	T	0.00012	0.0000	L	0.58101	1.795	0.28577	P	0.9103149	D;D	0.71674	0.986;0.998	D;D	0.87578	0.926;0.998	T	0.47045	-0.9147	9	0.49607	T	0.09	.	9.0059	0.36111	0.0:0.0874:0.0:0.9126	rs9614;rs1055561;rs3170621;rs17342213;rs17349907;rs60441174;rs9614	118;118	A6NNP0;Q9UK22	.;FBX2_HUMAN	T	118	ENSP00000346240:K118T	ENSP00000346240:K118T	K	-	2	0	FBXO2	11633148	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.091000	0.41691	1.891000	0.54761	0.459000	0.35465	AAG	T|0.788;G|0.212	0.212	strong		0.687	FBXO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005764.1	NM_012168	
PRG4	10216	hgsc.bcm.edu	37	1	186276411	186276411	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:186276411G>A	ENST00000445192.2	+	7	1605	c.1560G>A	c.(1558-1560)aaG>aaA	p.K520K	PRG4_ENST00000367483.4_Silent_p.K479K|PRG4_ENST00000367485.4_Silent_p.K427K|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Silent_p.K477K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	520	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCACTCCCAAGGAGCCTGCAC	0.632																																					p.K520K		Atlas-SNP	.											PRG4,NS,malignant_melanoma,0,1	PRG4	259	1	0			c.G1560A						scavenged	.						129.0	118.0	122.0					1																	186276411		2203	4299	6502	SO:0001819	synonymous_variant	10216	exon7			TCCCAAGGAGCCT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1560G>A	1.37:g.186276411G>A		Somatic	179	7	0.0391061		WXS	Illumina HiSeq	Phase_I	250	6	0.024	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			.	.	none		0.632	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
ADCY1	107	hgsc.bcm.edu	37	7	45701762	45701762	+	Silent	SNP	C	C	T	rs61729596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45701762C>T	ENST00000297323.7	+	8	1576	c.1554C>T	c.(1552-1554)ttC>ttT	p.F518F	ADCY1_ENST00000432715.1_Silent_p.F293F	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	518	Interaction with calmodulin. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GGAAAATGTTCAAGGCCGAGA	0.542													C|||	50	0.00998403	0.0	0.0101	5008	,	,		19969	0.0		0.0239	False		,,,				2504	0.0194				p.F518F		Atlas-SNP	.											.	ADCY1	187	.	0			c.C1554T						PASS	.	C		20,4386	27.2+/-55.0	0,20,2183	84.0	70.0	75.0		1554	3.9	1.0	7	dbSNP_129	75	175,8425	79.2+/-141.9	3,169,4128	no	coding-synonymous	ADCY1	NM_021116.2		3,189,6311	TT,TC,CC		2.0349,0.4539,1.4993		518/1120	45701762	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	107	exon8			AATGTTCAAGGCC	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"""Adenylate cyclases"""	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1554C>T	7.37:g.45701762C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	37	CCDS34631.1																																																																																			C|0.986;T|0.014	0.014	strong		0.542	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116	
WDR81	124997	hgsc.bcm.edu	37	17	1637074	1637074	+	Silent	SNP	A	A	G	rs587780504|rs3809871	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1637074A>G	ENST00000409644.1	+	7	4743	c.4743A>G	c.(4741-4743)ccA>ccG	p.P1581P	WDR81_ENST00000545662.1_Silent_p.P212P|WDR81_ENST00000419248.1_Silent_p.P354P|WDR81_ENST00000309182.5_Silent_p.P530P|WDR81_ENST00000446363.1_Silent_p.P220P|WDR81_ENST00000437219.2_Silent_p.P378P|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1581					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ACCCCGGACCACTGGGCCCCA	0.697													G|||	2702	0.539537	0.5522	0.5	5008	,	,		14420	0.7312		0.5149	False		,,,				2504	0.3783				p.P1581P		Atlas-SNP	.											WDR81_ENST00000437219,NS,carcinoma,0,3	WDR81	180	3	0			c.A4743G						PASS	.	G	,,,	2418,1984		673,1072,456	21.0	25.0	23.0		1134,4743,1062,1590	-10.4	0.0	17	dbSNP_107	23	4389,4195		1137,2115,1040	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	1810,3187,1496	GG,GA,AA		48.87,45.0704,47.582	,,,	378/739,1581/1942,354/715,530/891	1637074	6807,6179	2201	4292	6493	SO:0001819	synonymous_variant	124997	exon7			CGGACCACTGGGC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.4743A>G	17.37:g.1637074A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	23	0.348485	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			A|0.448;G|0.552	0.552	strong		0.697	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
COG1	9382	hgsc.bcm.edu	37	17	71192873	71192873	+	Silent	SNP	A	A	G	rs11544800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:71192873A>G	ENST00000299886.4	+	2	623	c.543A>G	c.(541-543)gcA>gcG	p.A181A	RP11-143K11.5_ENST00000580671.1_RNA	NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	181					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			GGCAGGTGGCAGCCGCCAGCC	0.572													A|||	2260	0.451278	0.2451	0.4755	5008	,	,		13936	0.6181		0.5457	False		,,,				2504	0.4438				p.A181A		Atlas-SNP	.											COG1,NS,carcinoma,+2,1	COG1	46	1	0			c.A543G						scavenged	.	A		1226,3180		186,854,1163	29.0	31.0	30.0		543	-0.1	0.9	17	dbSNP_120	30	4610,3990		1268,2074,958	no	coding-synonymous	COG1	NM_018714.2		1454,2928,2121	GG,GA,AA		46.3953,27.8257,44.8716		181/981	71192873	5836,7170	2203	4300	6503	SO:0001819	synonymous_variant	9382	exon2			GGTGGCAGCCGCC		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.543A>G	17.37:g.71192873A>G		Somatic	71	2	0.028169		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_018714	Q9NPV9|Q9P2G6	Silent	SNP	ENST00000299886.4	37	CCDS11692.1																																																																																			A|0.504;G|0.496	0.496	strong		0.572	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
CCDC159	126075	hgsc.bcm.edu	37	19	11465316	11465316	+	Missense_Mutation	SNP	G	G	C	rs6887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11465316G>C	ENST00000588790.1	+	12	1280	c.833G>C	c.(832-834)tGt>tCt	p.C278S	CCDC159_ENST00000458408.1_Missense_Mutation_p.C278S|DKFZP761J1410_ENST00000251473.5_5'Flank|DKFZP761J1410_ENST00000591608.1_5'Flank			P0C7I6	CC159_HUMAN	coiled-coil domain containing 159	393										endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	5						GACTCCGACTGTGACCAGGAC	0.642													C|||	1886	0.376597	0.4486	0.3718	5008	,	,		15852	0.2788		0.4533	False		,,,				2504	0.3047				p.C278S		Atlas-SNP	.											.	CCDC159	35	.	0			c.G833C						PASS	.	C	SER/CYS	1954,2438		433,1088,675	32.0	39.0	36.0		833	0.3	0.0	19	dbSNP_52	36	3992,4592		955,2082,1255	yes	missense	CCDC159	NM_001080503.2	112	1388,3170,1930	CC,CG,GG		46.5051,44.49,45.8231	benign	278/298	11465316	5946,7030	2196	4292	6488	SO:0001583	missense	126075	exon10			CCGACTGTGACCA	BC038439	CCDS45976.1	19p13.2	2010-02-17			ENSG00000183401	ENSG00000183401			26996	protein-coding gene	gene with protein product							Standard	NM_001080503		Approved		uc010xlt.2	P0C7I6		ENST00000588790.1:c.833G>C	19.37:g.11465316G>C	ENSP00000468232:p.Cys278Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	145	67	0.462069	NM_001080503	B4DEG3|B4DWR8|B4E133|B7ZAM4	Missense_Mutation	SNP	ENST00000588790.1	37	CCDS45976.1	849	0.38873626373626374	219	0.4451219512195122	143	0.39502762430939226	143	0.25	344	0.45382585751978893	C	0.343	-0.949288	0.02304	0.4449	0.465051	ENSG00000183401	ENST00000458408;ENST00000427879	T	0.39406	1.08	4.13	0.299	0.15771	.	.	.	.	.	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47156	-0.9139	8	0.08381	T	0.77	4.0E-4	8.6764	0.34181	0.1452:0.2636:0.5912:0.0	rs6887;rs3167723;rs17702516;rs59712669;rs6887	393;278	P0C7I6;P0C7I6-2	CC159_HUMAN;.	S	278;393	ENSP00000402239:C278S	ENSP00000390400:C393S	C	+	2	0	CCDC159	11326316	0.001000	0.12720	0.000000	0.03702	0.069000	0.16628	-0.055000	0.11807	0.121000	0.18284	-0.322000	0.08575	TGT	G|0.619;C|0.381	0.381	strong		0.642	CCDC159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458761.1	NM_001080503	
HHIPL1	84439	hgsc.bcm.edu	37	14	100129327	100129327	+	Silent	SNP	G	G	A	rs34890784	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:100129327G>A	ENST00000330710.5	+	6	1715	c.1617G>A	c.(1615-1617)ccG>ccA	p.P539P	HHIPL1_ENST00000357223.2_Silent_p.P539P	NM_001127258.1	NP_001120730.1	Q96JK4	HIPL1_HUMAN	HHIP-like 1	539					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|skin(2)	15		Melanoma(154;0.128)				ACTACTACCCGTACATCATCT	0.602													G|||	162	0.0323482	0.0045	0.0346	5008	,	,		20779	0.005		0.0785	False		,,,				2504	0.0491				p.P539P		Atlas-SNP	.											HHIPL1,NS,malignant_melanoma,+2,1	HHIPL1	86	1	0			c.G1617A						PASS	.	G	,	74,4332	65.3+/-102.7	2,70,2131	110.0	91.0	98.0		1617,1617	-9.8	0.3	14	dbSNP_126	98	741,7859	178.9+/-228.2	33,675,3592	no	coding-synonymous,coding-synonymous	HHIPL1	NM_001127258.1,NM_032425.4	,	35,745,5723	AA,AG,GG		8.6163,1.6795,6.2663	,	539/783,539/609	100129327	815,12191	2203	4300	6503	SO:0001819	synonymous_variant	84439	exon6			CTACCCGTACATC	AB058725	CCDS9953.1, CCDS45162.1	14q32	2008-01-16	2008-01-16	2008-01-16		ENSG00000182218			19710	protein-coding gene	gene with protein product			"""KIAA1822"""	KIAA1822			Standard	NM_032425		Approved		uc010avs.3	Q96JK4		ENST00000330710.5:c.1617G>A	14.37:g.100129327G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	144	60	0.416667	NM_032425	A2RUF8|B2RN09|Q6UXX2	Silent	SNP	ENST00000330710.5	37	CCDS45162.1																																																																																			G|0.944;A|0.056	0.056	strong		0.602	HHIPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413811.1	XM_041566	
CARD10	29775	hgsc.bcm.edu	37	22	37900762	37900762	+	Silent	SNP	G	G	A	rs3817805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:37900762G>A	ENST00000403299.1	-	9	1614	c.1398C>T	c.(1396-1398)tcC>tcT	p.S466S	CARD10_ENST00000406271.3_Silent_p.S180S|CARD10_ENST00000251973.5_Silent_p.S466S			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	466					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					ACAGGGAATGGGAGGAGGCAC	0.622													G|||	657	0.13119	0.0197	0.1441	5008	,	,		18194	0.2708		0.1064	False		,,,				2504	0.1544				p.S466S		Atlas-SNP	.											.	CARD10	55	.	0			c.C1398T						PASS	.	G		88,4318	70.9+/-108.8	1,86,2116	53.0	40.0	45.0		1398	3.3	1.0	22	dbSNP_107	45	914,7686	200.4+/-244.2	28,858,3414	no	coding-synonymous	CARD10	NM_014550.3		29,944,5530	AA,AG,GG		10.6279,1.9973,7.7041		466/1033	37900762	1002,12004	2203	4300	6503	SO:0001819	synonymous_variant	29775	exon8			GGAATGGGAGGAG	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1398C>T	22.37:g.37900762G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			G|0.894;A|0.106	0.106	strong		0.622	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
PDPR	55066	hgsc.bcm.edu	37	16	70170222	70170222	+	Missense_Mutation	SNP	G	G	T	rs59034887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70170222G>T	ENST00000288050.4	+	10	2080	c.1123G>T	c.(1123-1125)Gtg>Ttg	p.V375L	PDPR_ENST00000398122.3_Missense_Mutation_p.V275L|PDPR_ENST00000568530.1_Missense_Mutation_p.V375L|PDPR_ENST00000562100.1_3'UTR	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	375					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)	p.V375L(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GTCTCCTGCAGTGCAGGGCTA	0.512																																					p.V375L		Atlas-SNP	.											PDPR,NS,carcinoma,0,1	PDPR	66	1	1	Substitution - Missense(1)	stomach(1)	c.G1123T						PASS	.	G	LEU/VAL	599,3339		0,599,1370	76.0	78.0	77.0		1123	4.4	0.0	16	dbSNP_129	77	1136,7204		0,1136,3034	no	missense	PDPR	NM_017990.3	32	0,1735,4404	TT,TG,GG		13.6211,15.2108,14.131	benign	375/880	70170222	1735,10543	1969	4170	6139	SO:0001583	missense	55066	exon10			CCTGCAGTGCAGG		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1123G>T	16.37:g.70170222G>T	ENSP00000288050:p.Val375Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	230	55	0.23913	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	298	0.13644688644688643	88	0.17886178861788618	45	0.12430939226519337	50	0.08741258741258741	115	0.1517150395778364	G	12.75	2.030632	0.35797	0.152108	0.136211	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	D;D	0.85258	-1.96;-1.96	4.42	4.42	0.53409	FAD dependent oxidoreductase (1);	0.130868	0.51477	D	0.000085	T	0.00328	0.0010	N	0.16066	0.365	0.80722	D	1	B;B	0.11235	0.004;0.001	B;B	0.16289	0.01;0.015	T	0.03695	-1.1012	10	0.07644	T	0.81	.	11.9828	0.53129	0.0:0.1751:0.8249:0.0	rs59034887	103;375	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	L	375;275;103	ENSP00000288050:V375L;ENSP00000381190:V275L	ENSP00000205055:V103L	V	+	1	0	PDPR	68727723	1.000000	0.71417	0.039000	0.18376	0.977000	0.68977	7.777000	0.85628	1.985000	0.57927	0.455000	0.32223	GTG	G|0.870;T|0.130	0.130	strong		0.512	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
NEK10	152110	hgsc.bcm.edu	37	3	27332820	27332820	+	Missense_Mutation	SNP	A	A	G	rs10510592	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:27332820A>G	ENST00000429845.2	-	19	1900	c.1538T>C	c.(1537-1539)tTg>tCg	p.L513S	NEK10_ENST00000341435.5_Missense_Mutation_p.L513S|NEK10_ENST00000357467.2_5'UTR			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	513			L -> S (in dbSNP:rs10510592). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:17974005}.		positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TATATATTTCAAAGGAGCTTT	0.353													G|||	1059	0.211462	0.1203	0.353	5008	,	,		18497	0.1002		0.2744	False		,,,				2504	0.2843				p.L513S		Atlas-SNP	.											.	NEK10	271	.	0			c.T1538C						PASS	.	G	SER/LEU	528,2608		48,432,1088	145.0	133.0	137.0		1538	2.8	1.0	3	dbSNP_119	137	1932,5232		282,1368,1932	yes	missense	NEK10	NM_199347.2	145	330,1800,3020	GG,GA,AA		26.9682,16.8367,23.8835	benign	513/713	27332820	2460,7840	1568	3582	5150	SO:0001583	missense	152110	exon19			TATTTCAAAGGAG	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1538T>C	3.37:g.27332820A>G	ENSP00000395849:p.Leu513Ser	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	299	164	0.548495	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	SNP	ENST00000429845.2	37		465|465	0.2129120879120879|0.2129120879120879	64|64	0.13008130081300814|0.13008130081300814	132|132	0.36464088397790057|0.36464088397790057	58|58	0.10139860139860139|0.10139860139860139	211|211	0.2783641160949868|0.2783641160949868	G|G	0.517|0.517	-0.863737|-0.863737	0.02590|0.02590	0.168367|0.168367	0.269682|0.269682	ENSG00000163491|ENSG00000163491	ENST00000341435;ENST00000396636|ENST00000424275	T|.	0.39787|.	1.06|.	5.55|5.55	2.77|2.77	0.32553|0.32553	Protein kinase-like domain (1);|.	0.444912|.	0.23237|.	N|.	0.050389|.	T|.	0.00012|.	0.0000|.	N|N	0.03084|0.03084	-0.415|-0.415	0.09310|0.09310	P|P	0.99999999496892|0.99999999496892	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|.	0.46638|.	-0.9177|.	9|.	0.05620|.	T|.	0.96|.	.|.	7.4239|7.4239	0.27088|0.27088	0.2038:0.1204:0.6758:0.0|0.2038:0.1204:0.6758:0.0	rs10510592;rs17630275;rs52817784;rs61064099;rs10510592|rs10510592;rs17630275;rs52817784;rs61064099;rs10510592	513|.	Q6ZWH5|.	NEK10_HUMAN|.	S|R	513|46	ENSP00000343847:L513S|.	ENSP00000343847:L513S|.	L|X	-|-	2|1	0|0	NEK10|NEK10	27307824|27307824	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.960000|0.960000	0.62799|0.62799	2.318000|2.318000	0.43779|0.43779	0.039000|0.039000	0.15632|0.15632	-0.784000|-0.784000	0.03344|0.03344	TTG|TGA	A|0.824;G|0.176	0.176	strong		0.353	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	
AKNAD1	254268	hgsc.bcm.edu	37	1	109391662	109391662	+	Missense_Mutation	SNP	G	G	C	rs11580913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109391662G>C	ENST00000370001.3	-	4	1322	c.1054C>G	c.(1054-1056)Ctc>Gtc	p.L352V	AKNAD1_ENST00000369995.3_Missense_Mutation_p.L352V|AKNAD1_ENST00000357393.4_Missense_Mutation_p.L59V|AKNAD1_ENST00000369994.1_Missense_Mutation_p.L352V	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	352			L -> V (in dbSNP:rs11580913).			cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						AACTTAGAGAGACTTGCCTCA	0.373													G|||	311	0.0621006	0.1452	0.0519	5008	,	,		15155	0.0		0.0676	False		,,,				2504	0.0153				p.L352V		Atlas-SNP	.											AKNAD1,colon,carcinoma,0,1	AKNAD1	83	1	0			c.C1054G						PASS	.	G	VAL/LEU	622,3784	268.6+/-268.5	42,538,1623	91.0	95.0	93.0		1054	-1.5	0.0	1	dbSNP_120	93	720,7880	175.6+/-225.6	24,672,3604	yes	missense	AKNAD1	NM_152763.3	32	66,1210,5227	CC,CG,GG		8.3721,14.1171,10.3183	benign	352/837	109391662	1342,11664	2203	4300	6503	SO:0001583	missense	254268	exon4			TAGAGAGACTTGC	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.1054C>G	1.37:g.109391662G>C	ENSP00000359018:p.Leu352Val	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	42	12	0.285714	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	140	0.0641025641025641	64	0.13008130081300814	20	0.055248618784530384	0	0.0	56	0.07387862796833773	G	6.686	0.495208	0.12762	0.141171	0.083721	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	5.31	-1.53	0.08611	.	0.914520	0.09282	N	0.823651	T	0.06735	0.0172	N	0.17082	0.46	0.09310	N	1	P;P	0.42993	0.797;0.725	P;B	0.45428	0.48;0.364	T	0.14062	-1.0486	10	0.27785	T	0.31	0.6087	1.9987	0.03462	0.2509:0.3571:0.2753:0.1167	rs11580913;rs52794458;rs11580913	59;352	B4DET8;Q5T1N1	.;AKND1_HUMAN	V	352;59;352;352	ENSP00000359018:L352V;ENSP00000349968:L59V;ENSP00000359011:L352V;ENSP00000359012:L352V	ENSP00000349968:L59V	L	-	1	0	AKNAD1	109193185	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-0.297000	0.08276	0.044000	0.15775	0.561000	0.74099	CTC	G|0.910;C|0.090	0.090	strong		0.373	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
NLRP8	126205	hgsc.bcm.edu	37	19	56473460	56473460	+	Silent	SNP	T	T	C	rs6509975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56473460T>C	ENST00000291971.3	+	4	2141	c.2070T>C	c.(2068-2070)cgT>cgC	p.R690R	NLRP8_ENST00000590542.1_Silent_p.R690R	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	690					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		GGCTGCATCGTTGGTGGCAAG	0.483													C|||	1724	0.344249	0.4092	0.3646	5008	,	,		19927	0.2827		0.2972	False		,,,				2504	0.3538				p.R690R		Atlas-SNP	.											NLRP8_ENST00000291971,rectum,carcinoma,+1,2	NLRP8	225	2	0			c.T2070C						scavenged	.	C		1776,2630	638.5+/-396.9	357,1062,784	198.0	171.0	180.0		2070	-0.6	0.0	19	dbSNP_116	180	2593,6007	688.2+/-404.3	407,1779,2114	no	coding-synonymous	NLRP8	NM_176811.2		764,2841,2898	CC,CT,TT		30.1512,40.3087,33.5922		690/1049	56473460	4369,8637	2203	4300	6503	SO:0001819	synonymous_variant	126205	exon4			GCATCGTTGGTGG	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2070T>C	19.37:g.56473460T>C		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																			C|0.330;N|0.000	0.330	strong		0.483	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
NPC1	4864	hgsc.bcm.edu	37	18	21120444	21120444	+	Missense_Mutation	SNP	T	T	C	rs1805082	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21120444T>C	ENST00000269228.5	-	17	3126	c.2572A>G	c.(2572-2574)Att>Gtt	p.I858V	NPC1_ENST00000412552.2_Missense_Mutation_p.I540V|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	858			I -> V (common polymorphism in Japanese; dbSNP:rs1805082). {ECO:0000269|PubMed:10480349, ECO:0000269|PubMed:11479732, ECO:0000269|PubMed:11754101, ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:15774455, ECO:0000269|PubMed:16098014}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCCAATCCAATATCTACTTTG	0.338													T|||	2433	0.485823	0.3646	0.611	5008	,	,		19289	0.6111		0.4583	False		,,,				2504	0.4601				p.I858V		Atlas-SNP	.											.	NPC1	114	.	0			c.A2572G						PASS	.	T	VAL/ILE	1711,2695	515.2+/-368.8	312,1087,804	109.0	96.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2572	6.1	1.0	18	dbSNP_89	101	4047,4553	556.5+/-386.9	938,2171,1191	yes	missense	NPC1	NM_000271.4	29	1250,3258,1995	CC,CT,TT		47.0581,38.8334,44.2719	benign	858/1279	21120444	5758,7248	2203	4300	6503	SO:0001583	missense	4864	exon17			ATCCAATATCTAC	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2572A>G	18.37:g.21120444T>C	ENSP00000269228:p.Ile858Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	1100	0.5036630036630036	179	0.3638211382113821	201	0.5552486187845304	367	0.6416083916083916	353	0.4656992084432718	T	17.17	3.321358	0.60634	0.388334	0.470581	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.94000	-3.33;-3.33	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.33485	1.01	0.09310	P	0.999999999248751	B;B	0.20671	0.044;0.047	B;B	0.21360	0.034;0.021	T	0.41215	-0.9521	9	0.16420	T	0.52	-30.843	16.6288	0.85011	0.0:0.0:0.0:1.0	rs1805082;rs17797474;rs1805082	869;858	Q59GR1;O15118	.;NPC1_HUMAN	V	858;540;703	ENSP00000269228:I858V;ENSP00000408606:I540V	ENSP00000269228:I858V	I	-	1	0	NPC1	19374442	1.000000	0.71417	0.985000	0.45067	0.934000	0.57294	4.947000	0.63583	2.326000	0.78906	0.533000	0.62120	ATT	T|0.533;C|0.467	0.467	strong		0.338	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
CMYA5	202333	hgsc.bcm.edu	37	5	79025592	79025592	+	Missense_Mutation	SNP	C	C	T	rs114648445	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:79025592C>T	ENST00000446378.2	+	2	1035	c.1004C>T	c.(1003-1005)aCa>aTa	p.T335I		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	335					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CTAAATGCCACATCTGCATTG	0.463													C|||	13	0.00259585	0.0008	0.0029	5008	,	,		21455	0.0		0.0099	False		,,,				2504	0.0				p.T335I		Atlas-SNP	.											.	CMYA5	643	.	0			c.C1004T						PASS	.	C	ILE/THR	3,3987		0,3,1992	68.0	65.0	66.0		1004	3.4	0.0	5	dbSNP_132	66	56,8284		0,56,4114	yes	missense	CMYA5	NM_153610.3	89	0,59,6106	TT,TC,CC		0.6715,0.0752,0.4785	possibly-damaging	335/4070	79025592	59,12271	1995	4170	6165	SO:0001583	missense	202333	exon2			ATGCCACATCTGC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.1004C>T	5.37:g.79025592C>T	ENSP00000394770:p.Thr335Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	171	76	0.444444	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	10.74	1.435181	0.25813	7.52E-4	0.006715	ENSG00000164309	ENST00000446378	T	0.43688	0.94	5.15	3.36	0.38483	.	1.320480	0.05114	N	0.489480	T	0.19406	0.0466	N	0.14661	0.345	0.09310	N	1	B	0.30763	0.294	B	0.27887	0.084	T	0.25813	-1.0121	10	0.87932	D	0	.	3.333	0.07091	0.2023:0.565:0.0:0.2327	.	335	Q8N3K9	CMYA5_HUMAN	I	335	ENSP00000394770:T335I	ENSP00000394770:T335I	T	+	2	0	CMYA5	79061348	0.000000	0.05858	0.012000	0.15200	0.079000	0.17450	0.580000	0.23803	0.729000	0.32403	-0.181000	0.13052	ACA	C|0.997;T|0.003	0.003	strong		0.463	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
MEGF6	1953	hgsc.bcm.edu	37	1	3411235	3411235	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:3411235G>A	ENST00000356575.4	-	31	4168	c.3942C>T	c.(3940-3942)caC>caT	p.H1314H	MEGF6_ENST00000294599.4_Silent_p.H1079H	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1314	EGF-like 24. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		CGTTGCTGGCGTGGCACAGGC	0.701																																					p.H1314H	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C3942T						PASS	.						9.0	13.0	12.0					1																	3411235		2003	4143	6146	SO:0001819	synonymous_variant	1953	exon31			GCTGGCGTGGCAC	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.3942C>T	1.37:g.3411235G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	28	17	0.607143	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	g	0.020	-1.445500	0.01089	.	.	ENSG00000162591	ENST00000491842	.	.	.	3.72	-0.402	0.12404	.	.	.	.	.	T	0.57519	0.2059	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51841	-0.8654	4	.	.	.	-25.4103	10.398	0.44211	0.3477:0.0:0.6523:0.0	.	.	.	.	M	88	.	.	T	-	2	0	MEGF6	3401095	0.001000	0.12720	0.046000	0.18839	0.039000	0.13416	0.019000	0.13444	-0.178000	0.10672	-1.295000	0.01343	ACG	.	.	none		0.701	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
STAB2	55576	hgsc.bcm.edu	37	12	104153004	104153004	+	Missense_Mutation	SNP	C	C	G	rs2271637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:104153004C>G	ENST00000388887.2	+	65	7405	c.7201C>G	c.(7201-7203)Ctg>Gtg	p.L2401V	RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GCAAACGAGGCTGGGAAGCAA	0.537													C|||	1629	0.32528	0.1286	0.317	5008	,	,		19970	0.5238		0.2535	False		,,,				2504	0.4663				p.L2401V		Atlas-SNP	.											.	STAB2	370	.	0			c.C7201G						PASS	.	C	VAL/LEU	641,3765	275.2+/-272.4	47,547,1609	123.0	100.0	108.0		7201	3.8	1.0	12	dbSNP_100	108	2301,6299	388.9+/-342.7	280,1741,2279	yes	missense	STAB2	NM_017564.9	32	327,2288,3888	GG,GC,CC		26.7558,14.5483,22.6203	benign	2401/2552	104153004	2942,10064	2203	4300	6503	SO:0001583	missense	55576	exon65			ACGAGGCTGGGAA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.7201C>G	12.37:g.104153004C>G	ENSP00000373539:p.Leu2401Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	637	0.2916666666666667	53	0.10772357723577236	109	0.3011049723756906	283	0.49475524475524474	192	0.2532981530343008	C	12.05	1.822038	0.32237	0.145483	0.267558	ENSG00000136011	ENST00000388887	D	0.90620	-2.7	4.77	3.8	0.43715	FAS1 domain (4);	0.273443	0.30093	N	0.010439	T	0.00012	0.0000	M	0.78916	2.43	0.28695	P	0.9043705	P	0.47604	0.898	P	0.45167	0.472	T	0.11717	-1.0576	9	0.31617	T	0.26	.	11.0836	0.48074	0.311:0.689:0.0:0.0	rs2271637;rs52828564;rs2271637	2401	Q8WWQ8	STAB2_HUMAN	V	2401	ENSP00000373539:L2401V	ENSP00000373539:L2401V	L	+	1	2	STAB2	102677134	1.000000	0.71417	0.992000	0.48379	0.390000	0.30446	2.061000	0.41403	2.340000	0.79590	0.655000	0.94253	CTG	C|0.734;G|0.266	0.266	strong		0.537	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
ST5	6764	hgsc.bcm.edu	37	11	8724191	8724191	+	Missense_Mutation	SNP	A	A	G	rs113126215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8724191A>G	ENST00000534127.1	-	17	3033	c.2648T>C	c.(2647-2649)gTg>gCg	p.V883A	ST5_ENST00000530991.1_Missense_Mutation_p.V355A|ST5_ENST00000526099.1_Missense_Mutation_p.V396A|ST5_ENST00000313726.6_Missense_Mutation_p.V883A|ST5_ENST00000357665.1_Missense_Mutation_p.V883A|ST5_ENST00000526757.1_Missense_Mutation_p.V463A|ST5_ENST00000530438.1_Missense_Mutation_p.V463A|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000534278.1_Missense_Mutation_p.V74A	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	883	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		GAGCTGGCGCACACTGAGGCA	0.582													a|||	8	0.00159744	0.0008	0.0014	5008	,	,		19188	0.0		0.005	False		,,,				2504	0.001				p.V883A		Atlas-SNP	.											.	ST5	85	.	0			c.T2648C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	9,4393	15.5+/-35.6	0,9,2192	86.0	79.0	81.0		2648,1388,2648	4.7	1.0	11	dbSNP_132	81	48,8544	31.2+/-83.2	0,48,4248	yes	missense,missense,missense	ST5	NM_005418.3,NM_139157.2,NM_213618.1	64,64,64	0,57,6440	GG,GA,AA		0.5587,0.2045,0.4387	benign,benign,benign	883/1138,463/718,883/1138	8724191	57,12937	2201	4296	6497	SO:0001583	missense	6764	exon17			TGGCGCACACTGA	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.2648T>C	11.37:g.8724191A>G	ENSP00000433528:p.Val883Ala	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	a	16.30	3.083512	0.55861	0.002045	0.005587	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000534278;ENST00000530438;ENST00000533081	T;T;T;T;T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71	4.72	4.72	0.59763	DENN (3);	0.000000	0.85682	D	0.000000	T	0.19406	0.0466	M	0.78801	2.425	0.53005	D	0.999961	B;B;B	0.28026	0.023;0.012;0.198	B;B;B	0.38755	0.202;0.038;0.281	T	0.05699	-1.0869	10	0.87932	D	0	-10.884	14.2346	0.65916	1.0:0.0:0.0:0.0	.	396;463;883	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	A	463;883;883;355;883;396;74;463;73	ENSP00000435097:V463A;ENSP00000433528:V883A;ENSP00000319678:V883A;ENSP00000432887:V355A;ENSP00000350294:V883A;ENSP00000436808:V396A;ENSP00000433349:V74A;ENSP00000436802:V463A;ENSP00000436067:V73A	ENSP00000319678:V883A	V	-	2	0	ST5	8680767	0.990000	0.36364	1.000000	0.80357	0.992000	0.81027	7.573000	0.82421	1.760000	0.52011	0.398000	0.26397	GTG	A|0.996;G|0.004	0.004	strong		0.582	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
LIPA	3988	hgsc.bcm.edu	37	10	91007339	91007339	+	Missense_Mutation	SNP	C	C	T	rs1051339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:91007339C>T	ENST00000336233.5	-	2	389	c.67G>A	c.(67-69)Gga>Aga	p.G23R	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000456827.1_Missense_Mutation_p.G23R			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	23			G -> R (in dbSNP:rs1051339). {ECO:0000269|PubMed:8725147}.		cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cytokine production (GO:0001816)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|lung development (GO:0030324)|tissue remodeling (GO:0048771)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	lipase activity (GO:0016298)|sterol esterase activity (GO:0004771)			endometrium(1)|large_intestine(2)|lung(3)	6		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		AGTTTCCCTCCAGACCCCTCA	0.398													C|||	601	0.120008	0.2345	0.085	5008	,	,		11955	0.0625		0.1024	False		,,,				2504	0.0675				p.G23R		Atlas-SNP	.											.	LIPA	29	.	0			c.G67A						PASS	.	C	ARG/GLY,ARG/GLY	997,3409	372.7+/-320.5	118,761,1324	107.0	104.0	105.0		67,67	-4.1	0.0	10	dbSNP_86	105	912,7688	203.0+/-246.1	50,812,3438	yes	missense,missense	LIPA	NM_000235.2,NM_001127605.1	125,125	168,1573,4762	TT,TC,CC		10.6047,22.6282,14.6778	benign,benign	23/400,23/400	91007339	1909,11097	2203	4300	6503	SO:0001583	missense	3988	exon2			TCCCTCCAGACCC	M74775	CCDS7401.1, CCDS73160.1	10q23.2-q23.3	2012-07-13	2008-08-01		ENSG00000107798	ENSG00000107798	3.1.1.13		6617	protein-coding gene	gene with protein product	"""Wolman disease"""	613497				8432549	Standard	NM_000235		Approved	LAL, CESD	uc009xtq.3	P38571	OTTHUMG00000018716	ENST00000336233.5:c.67G>A	10.37:g.91007339C>T	ENSP00000337354:p.Gly23Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_000235	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Missense_Mutation	SNP	ENST00000336233.5	37	CCDS7401.1	246	0.11263736263736264	93	0.18902439024390244	37	0.10220994475138122	43	0.07517482517482517	73	0.09630606860158311	C	7.820	0.717659	0.15372	0.226282	0.106047	ENSG00000107798	ENST00000336233;ENST00000371829;ENST00000541980;ENST00000456827;ENST00000542307;ENST00000428800;ENST00000282673	T;T;T;T	0.75938	-0.37;-0.37;-0.24;-0.98	4.93	-4.06	0.03986	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.03910	-1.0993	8	0.23891	T	0.37	0.2204	2.6021	0.04868	0.1488:0.4308:0.1524:0.268	rs1051339;rs2229253;rs3191716;rs6586179;rs17383331;rs52795430;rs59958870;rs6586179	23	P38571	LICH_HUMAN	R	23	ENSP00000337354:G23R;ENSP00000413019:G23R;ENSP00000388415:G23R;ENSP00000282673:G23R	ENSP00000282673:G23R	G	-	1	0	LIPA	90997319	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.955000	0.03869	-0.446000	0.07149	-0.378000	0.06908	GGA	T|0.109;G|0.167	0.109	strong		0.398	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235	
OR6M1	390261	hgsc.bcm.edu	37	11	123676231	123676231	+	Missense_Mutation	SNP	G	G	T	rs4936845	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123676231G>T	ENST00000309154.2	-	1	864	c.827C>A	c.(826-828)aCa>aAa	p.T276K		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	276			T -> K (in dbSNP:rs4936845).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		GGTCACCACTGTGATGAGGAC	0.478													G|||	1219	0.243411	0.1029	0.317	5008	,	,		17328	0.2946		0.2853	False		,,,				2504	0.2853				p.T276K		Atlas-SNP	.											OR6M1,colon,carcinoma,0,1	OR6M1	60	1	0			c.C827A						PASS	.	G	LYS/THR	540,3864	243.4+/-253.1	44,452,1706	127.0	120.0	122.0		827	3.5	0.3	11	dbSNP_111	122	2568,6030	420.5+/-353.4	389,1790,2120	yes	missense	OR6M1	NM_001005325.1	78	433,2242,3826	TT,TG,GG		29.8674,12.2616,23.904	possibly-damaging	276/314	123676231	3108,9894	2202	4299	6501	SO:0001583	missense	390261	exon1			ACCACTGTGATGA	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"""GPCR / Class A : Olfactory receptors"""	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.827C>A	11.37:g.123676231G>T	ENSP00000311038:p.Thr276Lys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	157	79	0.503185	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	526	0.24084249084249085	54	0.10975609756097561	94	0.2596685082872928	161	0.28146853146853146	217	0.2862796833773087	G	13.48	2.251267	0.39797	0.122616	0.298674	ENSG00000196099	ENST00000309154	T	0.00265	8.39	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34200	U	0.004164	T	0.00012	0.0000	M	0.92970	3.365	0.80722	P	0.0	P	0.41188	0.741	P	0.53809	0.735	T	0.04153	-1.0973	9	0.87932	D	0	.	6.5789	0.22583	0.1324:0.0:0.8676:0.0	rs4936845;rs52810786;rs56873896;rs4936845	276	Q8NGM8	OR6M1_HUMAN	K	276	ENSP00000311038:T276K	ENSP00000311038:T276K	T	-	2	0	OR6M1	123181441	0.010000	0.17322	0.295000	0.24960	0.731000	0.41821	1.794000	0.38774	1.754000	0.51921	0.655000	0.94253	ACA	G|0.763;T|0.237	0.237	strong		0.478	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325	
GPR55	9290	hgsc.bcm.edu	37	2	231774844	231774844	+	Silent	SNP	G	G	A	rs2396777	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231774844G>A	ENST00000392040.1	-	2	1026	c.834C>T	c.(832-834)aaC>aaT	p.N278N	AC012507.4_ENST00000454890.1_RNA|GPR55_ENST00000392039.2_Silent_p.N278N	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	278					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)	p.N278N(1)		endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		AGCAGTTGACGTTGGAGAAAC	0.507													G|||	1731	0.345647	0.6815	0.1686	5008	,	,		23399	0.2331		0.1471	False		,,,				2504	0.3374				p.N278N		Atlas-SNP	.											GPR55,NS,carcinoma,0,1	GPR55	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C834T						PASS	.	G		2555,1851	633.8+/-396.1	754,1047,402	107.0	105.0	106.0		834	0.4	0.4	2	dbSNP_100	106	1442,7158	275.3+/-291.7	135,1172,2993	no	coding-synonymous	GPR55	NM_005683.3		889,2219,3395	AA,AG,GG		16.7674,42.0109,30.732		278/320	231774844	3997,9009	2203	4300	6503	SO:0001819	synonymous_variant	9290	exon2			GTTGACGTTGGAG	AF096786	CCDS2480.1	2q37	2012-08-21			ENSG00000135898	ENSG00000135898		"""GPCR / Class A : Orphans"""	4511	protein-coding gene	gene with protein product		604107				9931487	Standard	NM_005683		Approved		uc002vrg.3	Q9Y2T6	OTTHUMG00000133224	ENST00000392040.1:c.834C>T	2.37:g.231774844G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	123	61	0.495935	NM_005683	Q8N580	Silent	SNP	ENST00000392040.1	37	CCDS2480.1																																																																																			G|0.690;N|0.000	.	strong		0.507	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683	
ADAM28	10863	hgsc.bcm.edu	37	8	24171051	24171051	+	Silent	SNP	C	C	T	rs6996616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:24171051C>T	ENST00000265769.4	+	6	644	c.534C>T	c.(532-534)caC>caT	p.H178H	ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000540823.1_Intron|ADAM28_ENST00000437154.2_Silent_p.H178H|RP11-624C23.1_ENST00000523700.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	178					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGTGGGCCCACGATTTGCAGC	0.448													T|||	932	0.186102	0.152	0.0965	5008	,	,		16774	0.3621		0.1571	False		,,,				2504	0.1442				p.H178H	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.C534T						PASS	.	T	,	754,3652	755.8+/-412.6	65,624,1514	208.0	181.0	190.0		534,534	0.0	0.0	8	dbSNP_116	190	1315,7285	758.0+/-407.5	104,1107,3089	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	169,1731,4603	TT,TC,CC		15.2907,17.113,15.908	,	178/776,178/541	24171051	2069,10937	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon6			GGCCCACGATTTG	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.534C>T	8.37:g.24171051C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	249	139	0.558233	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			C|0.809;T|0.191	0.191	strong		0.448	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
ZC3H4	23211	hgsc.bcm.edu	37	19	47572395	47572395	+	Silent	SNP	C	C	T	rs202116030	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47572395C>T	ENST00000253048.5	-	14	2389	c.2352G>A	c.(2350-2352)gcG>gcA	p.A784A	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	784							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		CCAGCCTCCTCGCTCTCTCCT	0.692													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		17200	0.0		0.0	False		,,,				2504	0.0				p.A784A		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G2352A						PASS	.	C		3,4171		0,3,2084	68.0	80.0	76.0		2352	-2.5	1.0	19		76	4,8412		0,4,4204	no	coding-synonymous	ZC3H4	NM_015168.1		0,7,6288	TT,TC,CC		0.0475,0.0719,0.0556		784/1304	47572395	7,12583	2087	4208	6295	SO:0001819	synonymous_variant	23211	exon14			CCTCCTCGCTCTC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2352G>A	19.37:g.47572395C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			C|1.000;T|0.000	0.000	strong		0.692	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
TAS1R2	80834	hgsc.bcm.edu	37	1	19181393	19181393	+	Missense_Mutation	SNP	T	T	C	rs35874116	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19181393T>C	ENST00000375371.3	-	3	592	c.571A>G	c.(571-573)Atc>Gtc	p.I191V	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	191			I -> V (in dbSNP:rs35874116). {ECO:0000269|PubMed:11917125}.		detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ATGGCCTCGATGTGGTGGTCG	0.612													C|||	1337	0.266973	0.3389	0.2695	5008	,	,		20996	0.1042		0.3241	False		,,,				2504	0.2771				p.I191V		Atlas-SNP	.											TAS1R2,NS,carcinoma,0,1	TAS1R2	134	1	0			c.A571G						PASS	.	C	VAL/ILE	1349,3057	684.6+/-404.4	206,937,1060	42.0	42.0	42.0		571	-4.1	0.0	1	dbSNP_126	42	2845,5755	666.6+/-402.4	461,1923,1916	yes	missense	TAS1R2	NM_152232.2	29	667,2860,2976	CC,CT,TT		33.0814,30.6173,32.2467	benign	191/840	19181393	4194,8812	2203	4300	6503	SO:0001583	missense	80834	exon3			CCTCGATGTGGTG		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.571A>G	1.37:g.19181393T>C	ENSP00000364520:p.Ile191Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	581	0.266025641025641	167	0.3394308943089431	112	0.30939226519337015	57	0.09965034965034965	245	0.3232189973614776	C	0.004	-2.354529	0.00217	0.306173	0.330814	ENSG00000179002	ENST00000375371	D	0.82526	-1.62	4.9	-4.08	0.03963	Extracellular ligand-binding receptor (1);	1.331270	0.05169	N	0.499177	T	0.00012	0.0000	N	0.04245	-0.25	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.10405	-1.0631	9	0.02654	T	1	.	10.7064	0.45958	0.0:0.5932:0.1201:0.2867	rs35874116	191	Q8TE23	TS1R2_HUMAN	V	191	ENSP00000364520:I191V	ENSP00000364520:I191V	I	-	1	0	TAS1R2	19053980	0.000000	0.05858	0.012000	0.15200	0.008000	0.06430	-0.421000	0.07053	-1.020000	0.03354	-2.680000	0.00142	ATC	T|0.700;C|0.300	0.300	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
PHLDB1	23187	hgsc.bcm.edu	37	11	118514625	118514625	+	Silent	SNP	C	C	T	rs11216938	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118514625C>T	ENST00000361417.2	+	15	3396	c.2985C>T	c.(2983-2985)agC>agT	p.S995S	PHLDB1_ENST00000527898.1_Silent_p.S31S|PHLDB1_ENST00000524713.1_Silent_p.S138S|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000356063.5_Silent_p.S948S	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	995										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		ccCAGCTCAGCGTGGCTACCC	0.692													C|||	1104	0.220447	0.1082	0.2118	5008	,	,		13682	0.2302		0.2157	False		,,,				2504	0.3732				p.S995S		Atlas-SNP	.											PHLDB1,rectum,carcinoma,0,1	PHLDB1	103	1	0			c.C2985T						PASS	.	C	,,	533,3867	223.3+/-239.8	32,469,1699	25.0	29.0	28.0		2985,2844,2985	-1.7	1.0	11	dbSNP_120	28	1851,6737	307.6+/-308.5	197,1457,2640	no	coding-synonymous,coding-synonymous,coding-synonymous	PHLDB1	NM_001144758.1,NM_001144759.1,NM_015157.2	,,	229,1926,4339	TT,TC,CC		21.5533,12.1136,18.3554	,,	995/1378,948/1320,995/1378	118514625	2384,10604	2200	4294	6494	SO:0001819	synonymous_variant	23187	exon14			GCTCAGCGTGGCT		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.2985C>T	11.37:g.118514625C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	37	CCDS8401.1																																																																																			C|0.822;T|0.178	0.178	strong		0.692	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157	
CYP3A7	1551	hgsc.bcm.edu	37	7	99306685	99306685	+	Missense_Mutation	SNP	C	C	G	rs2257401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99306685C>G	ENST00000336374.2	-	11	1228	c.1226G>C	c.(1225-1227)aGa>aCa	p.R409T		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	409			R -> T (in dbSNP:rs2257401). {ECO:0000269|PubMed:11137287, ECO:0000269|PubMed:11266076, ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2722762, ECO:0000269|PubMed:2786707, ECO:0000269|Ref.5}.		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CTCAGGCTCTCTCCAGTACTT	0.493													G|||	3353	0.669529	0.3835	0.8069	5008	,	,		18828	0.7123		0.9274	False		,,,				2504	0.6493				p.R409T		Atlas-SNP	.											.	CYP3A7	59	.	0			c.G1226C						PASS	.	G	THR/ARG	2107,2299		509,1089,605	140.0	142.0	142.0		1226	1.5	0.4	7	dbSNP_100	142	7829,771		3570,689,41	no	missense	CYP3A7	NM_000765.3	71	4079,1778,646	GG,GC,CC		8.9651,47.8212,23.6045	benign	409/504	99306685	9936,3070	2203	4300	6503	SO:0001583	missense	1551	exon11			GGCTCTCTCCAGT	AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"""Cytochrome P450s"""	2640	protein-coding gene	gene with protein product		605340	"""cytochrome P450, subfamily IIIA, polypeptide 7"""			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.1226G>C	7.37:g.99306685C>G	ENSP00000337450:p.Arg409Thr	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	236	235	0.995763	NM_000765	A4D288|Q9H241	Missense_Mutation	SNP	ENST00000336374.2	37	CCDS5673.1	1595	0.7303113553113553	192	0.3902439024390244	287	0.7928176795580111	409	0.715034965034965	707	0.9327176781002638	N	3.772	-0.047459	0.07407	0.478212	0.910349	ENSG00000160870	ENST00000292414;ENST00000336374	T	0.67698	-0.28	3.46	1.54	0.23209	.	0.609497	0.17651	N	0.166665	T	0.00012	0.0000	N	0.00327	-1.64	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.28170	-1.0052	9	0.40728	T	0.16	.	4.6922	0.12786	0.2276:0.1844:0.588:0.0	rs2257401;rs11536558;rs57389434;rs2257401	409	P24462	CP3A7_HUMAN	T	409	ENSP00000337450:R409T	ENSP00000292414:R409T	R	-	2	0	CYP3A7	99144621	0.994000	0.37717	0.373000	0.26003	0.361000	0.29550	2.950000	0.49081	0.114000	0.18032	-0.676000	0.03789	AGA	C|0.254;G|0.746	0.746	strong		0.493	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1		
SLC6A5	9152	hgsc.bcm.edu	37	11	20648380	20648380	+	Missense_Mutation	SNP	G	G	A	rs1805091	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:20648380G>A	ENST00000525748.1	+	8	1660	c.1387G>A	c.(1387-1389)Gat>Aat	p.D463N		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	463			D -> N (in dbSNP:rs1805091). {ECO:0000269|PubMed:10606742}.		glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	GAAACTCACGGATGCCACGGT	0.552													G|||	815	0.16274	0.1165	0.1787	5008	,	,		16566	0.0883		0.2505	False		,,,				2504	0.2004				p.D463N		Atlas-SNP	.											SLC6A5,caecum,carcinoma,0,1	SLC6A5	151	1	0			c.G1387A						PASS	.	G	ASN/ASP	551,3855	247.5+/-255.7	35,481,1687	108.0	102.0	104.0		1387	6.0	1.0	11	dbSNP_89	104	2470,6130	406.1+/-348.7	352,1766,2182	yes	missense	SLC6A5	NM_004211.3	23	387,2247,3869	AA,AG,GG		28.7209,12.5057,23.2277	possibly-damaging	463/798	20648380	3021,9985	2203	4300	6503	SO:0001583	missense	9152	exon8			CTCACGGATGCCA	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1387G>A	11.37:g.20648380G>A	ENSP00000434364:p.Asp463Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	395	0.18086080586080586	82	0.16666666666666666	75	0.20718232044198895	52	0.09090909090909091	186	0.24538258575197888	G	21.1	4.096148	0.76870	0.125057	0.287209	ENSG00000165970	ENST00000525748	T	0.74526	-0.85	6.04	6.04	0.98038	.	0.087926	0.85682	D	0.000000	T	0.00012	0.0000	L	0.35288	1.05	0.09310	P	0.9999999999330931	B	0.23937	0.094	B	0.32393	0.145	T	0.01743	-1.1283	9	0.38643	T	0.18	.	20.1743	0.98175	0.0:0.0:1.0:0.0	rs1805091;rs3740871;rs45629968;rs52834191;rs59290674;rs1805091	463	Q9Y345	SC6A5_HUMAN	N	463	ENSP00000434364:D463N	ENSP00000434364:D463N	D	+	1	0	SLC6A5	20604956	1.000000	0.71417	0.993000	0.49108	0.966000	0.64601	9.869000	0.99810	2.873000	0.98535	0.561000	0.74099	GAT	G|0.790;A|0.210	0.210	strong		0.552	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
PEX6	5190	hgsc.bcm.edu	37	6	42932200	42932200	+	Missense_Mutation	SNP	G	G	T	rs386700658|rs1129187	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:42932200G>T	ENST00000304611.8	-	17	2885	c.2816C>A	c.(2815-2817)cCa>cAa	p.P939Q	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	939			P -> Q (in dbSNP:rs1129187). {ECO:0000269|PubMed:11355018, ECO:0000269|PubMed:19105186}.		ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			TGAGCTACCTGGCTCCAGCCC	0.632													G|||	1660	0.33147	0.3699	0.3516	5008	,	,		18582	0.1012		0.4622	False		,,,				2504	0.3681				p.P939Q		Atlas-SNP	.											PEX6,colon,carcinoma,0,1	PEX6	44	1	0			c.C2816A						PASS	.	G	GLN/PRO	1720,2686	496.0+/-363.4	332,1056,815	48.0	45.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2816	0.6	0.0	6	dbSNP_86	46	3832,4768	515.8+/-378.7	834,2164,1302	yes	missense	PEX6	NM_000287.3	76	1166,3220,2117	TT,TG,GG		44.5581,39.0377,42.688	benign	939/981	42932200	5552,7454	2203	4300	6503	SO:0001583	missense	5190	exon17			CTACCTGGCTCCA	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"""ATPases / AAA-type"""	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2816C>A	6.37:g.42932200G>T	ENSP00000303511:p.Pro939Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	157	67	0.426752	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	719	0.3292124542124542	169	0.3434959349593496	130	0.35911602209944754	71	0.12412587412587413	349	0.4604221635883905	G	12.52	1.963729	0.34659	0.390377	0.445581	ENSG00000124587	ENST00000304611	D	0.94758	-3.51	5.96	0.549	0.17213	.	0.978492	0.08443	N	0.945108	T	0.82116	0.4967	L	0.48362	1.52	0.09310	P	1.0	B	0.11235	0.004	B	0.11329	0.006	T	0.63989	-0.6512	9	0.37606	T	0.19	-1.1722	2.5906	0.04841	0.2743:0.1118:0.4992:0.1148	rs1129187;rs3186790;rs9471979;rs17415506;rs59470433;rs1129187	939	Q13608	PEX6_HUMAN	Q	939	ENSP00000303511:P939Q	ENSP00000303511:P939Q	P	-	2	0	PEX6	43040178	0.000000	0.05858	0.008000	0.14137	0.910000	0.53928	0.232000	0.17891	-0.182000	0.10602	0.650000	0.86243	CCA	G|0.617;T|0.383	0.383	strong		0.632	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	
NME8	51314	hgsc.bcm.edu	37	7	37934146	37934146	+	Missense_Mutation	SNP	T	T	C	rs56128139|rs386712272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:37934146T>C	ENST00000199447.4	+	16	1850	c.1478T>C	c.(1477-1479)aTa>aCa	p.I493T	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Missense_Mutation_p.I493T	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	493	NDK 3.		I -> T (in dbSNP:rs56128139). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										CCTGAGCAAATAGAGAAAATT	0.303													T|||	790	0.157748	0.0151	0.2291	5008	,	,		17475	0.1359		0.3419	False		,,,				2504	0.1329				p.I493T		Atlas-SNP	.											.	.	.	.	0			c.T1478C						PASS	.	T	THR/ILE	5,4401		2,1,2200	61.0	63.0	63.0		1478	1.1	0.0	7	dbSNP_129	63	77,8521		12,53,4234	yes	missense	TXNDC3	NM_016616.4	89	14,54,6434	CC,CT,TT		0.8956,0.1135,0.6306	benign	493/589	37934146	82,12922	2203	4299	6502	SO:0001583	missense	51314	exon16			AGCAAATAGAGAA	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1478T>C	7.37:g.37934146T>C	ENSP00000199447:p.Ile493Thr	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	257	112	0.435798	NM_016616	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	343	0.15705128205128205	11	0.022357723577235773	73	0.20165745856353592	70	0.12237762237762238	189	0.24934036939313983	T	6.406	0.442939	0.12164	0.001135	0.008956	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.43688	0.94;0.94	4.05	1.11	0.20524	.	0.568879	0.14595	N	0.310022	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.14438	0.01	B	0.23275	0.045	T	0.26360	-1.0105	9	0.52906	T	0.07	-4.655	5.9615	0.19303	0.0:0.6617:0.0:0.3383	rs56128139;rs62001871	493	Q8N427	TXND3_HUMAN	T	493	ENSP00000199447:I493T;ENSP00000397063:I493T	ENSP00000199447:I493T	I	+	2	0	TXNDC3	37900671	0.012000	0.17670	0.000000	0.03702	0.002000	0.02628	0.098000	0.15189	0.265000	0.21872	-0.621000	0.04028	ATA	T|0.761;C|0.239	0.239	strong		0.303	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
ZNF697	90874	hgsc.bcm.edu	37	1	120166453	120166453	+	Silent	SNP	G	G	C	rs76236163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120166453G>C	ENST00000421812.2	-	3	632	c.513C>G	c.(511-513)gcC>gcG	p.A171A		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		CGAGGTCCACGGCCATGGGGT	0.697													G|||	190	0.0379393	0.003	0.0677	5008	,	,		11125	0.002		0.0974	False		,,,				2504	0.0399				p.A171A		Atlas-SNP	.											.	ZNF697	26	.	0			c.C513G						PASS	.	G		69,3871		2,65,1903	6.0	8.0	8.0		513	1.2	0.2	1	dbSNP_132	8	797,7353		36,725,3314	no	coding-synonymous	ZNF697	NM_001080470.1		38,790,5217	CC,CG,GG		9.7791,1.7513,7.1629		171/546	120166453	866,11224	1970	4075	6045	SO:0001819	synonymous_variant	90874	exon3			GTCCACGGCCATG	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"""Zinc fingers, C2H2-type"""	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.513C>G	1.37:g.120166453G>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	37	CCDS44202.1																																																																																			G|0.949;C|0.051	0.051	strong		0.697	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	
MADCAM1	8174	hgsc.bcm.edu	37	19	501762	501762	+	Missense_Mutation	SNP	A	A	C	rs200007467		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:501762A>C	ENST00000215637.3	+	4	807	c.761A>C	c.(760-762)cAg>cCg	p.Q254P	MADCAM1_ENST00000587541.1_Missense_Mutation_p.Q35P|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	254	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.			Q -> P (in Ref. 1; AAC13661). {ECO:0000305}.	aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)	p.Q254P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCACCTCCCAGGAGCCTCCC	0.721																																					p.Q254P		Atlas-SNP	.											MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	1	Substitution - Missense(1)	kidney(1)	c.A761C						scavenged	.						31.0	36.0	34.0					19																	501762		2194	4290	6484	SO:0001583	missense	8174	exon4			CCTCCCAGGAGCC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.761A>C	19.37:g.501762A>C	ENSP00000215637:p.Gln254Pro	Somatic	164	5	0.0304878		WXS	Illumina HiSeq	Phase_I	223	75	0.336323	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	N	5.739	0.320845	0.10845	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.09073	3.02	2.86	-5.72	0.02406	.	.	.	.	.	T	0.01940	0.0061	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40869	-0.9540	9	0.02654	T	1	.	3.6031	0.08032	0.3032:0.5048:0.0:0.192	.	254	Q13477	MADCA_HUMAN	P	278;270;262;254	ENSP00000215637:Q254P	ENSP00000215637:Q254P	Q	+	2	0	MADCAM1	452762	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.356000	0.00247	-1.159000	0.02807	-1.988000	0.00451	CAG	.	.	weak		0.721	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
NAA38	84316	hgsc.bcm.edu	37	17	7760704	7760704	+	Silent	SNP	A	A	G	rs8522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7760704A>G	ENST00000335155.5	-	1	77	c.78T>C	c.(76-78)gcT>gcC	p.A26A	CYB5D1_ENST00000570446.1_5'Flank|CYB5D1_ENST00000571846.1_5'Flank|LSMD1_ENST00000576861.1_Intron|LSMD1_ENST00000575208.1_Intron|CYB5D1_ENST00000332439.4_5'Flank|LSMD1_ENST00000570555.1_5'Flank|LSMD1_ENST00000576384.1_5'Flank|LSMD1_ENST00000575771.1_5'UTR|LSMD1_ENST00000333775.5_Missense_Mutation_p.L13P|LSMD1_ENST00000575071.1_5'UTR			Q9BRA0	LSMD1_HUMAN		26					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|lung(2)|ovary(1)	4		all_cancers(10;0.11)|Prostate(122;0.219)				TGCTAACCCCAGCACTGGAGC	0.637													G|||	2185	0.436302	0.388	0.3905	5008	,	,		15269	0.7956		0.1948	False		,,,				2504	0.4121				p.L13P	GBM(66;626 1401 29924 42527)	Atlas-SNP	.											.	LSMD1	8	.	0			c.T38C						PASS	.	G	PRO/LEU	1544,2862	641.0+/-397.4	272,1000,931	42.0	52.0	49.0		38	-5.0	0.9	17	dbSNP_52	49	1882,6718	711.5+/-405.8	209,1464,2627	yes	missense	LSMD1	NM_032356.3	98	481,2464,3558	GG,GA,AA		21.8837,35.0431,26.3417	benign	13/174	7760704	3426,9580	2203	4300	6503	SO:0001819	synonymous_variant	84316	exon1			AACCCCAGCACTG																												ENST00000335155.5:c.78T>C	17.37:g.7760704A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	141	56	0.397163	NM_032356	Q8N4M0	Missense_Mutation	SNP	ENST00000335155.5	37		874	0.4001831501831502	148	0.3008130081300813	127	0.35082872928176795	465	0.8129370629370629	134	0.17678100263852242	G	0.844	-0.740751	0.03088	0.350431	0.218837	ENSG00000183011	ENST00000333775	T	0.56444	0.46	5.65	-5.02	0.02982	.	0.196677	0.25469	N	0.030450	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999877715	B	0.02656	0.0	B	0.01281	0.0	T	0.32161	-0.9917	8	0.11794	T	0.64	.	3.8358	0.08893	0.5487:0.1141:0.2209:0.1162	rs8522;rs1129549;rs3826332;rs11551746;rs17855012;rs52822583;rs58072623;rs8522	13	Q9BRA0-2	.	P	13	ENSP00000332103:L13P	ENSP00000332103:L13P	L	-	2	0	LSMD1	7701429	0.911000	0.30947	0.947000	0.38551	0.581000	0.36288	-0.339000	0.07832	-0.670000	0.05282	-0.916000	0.02749	CTG	A|0.678;G|0.322	0.322	strong		0.637	LSMD1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
KIAA1211	57482	hgsc.bcm.edu	37	4	57180473	57180473	+	Missense_Mutation	SNP	C	C	A	rs6823339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57180473C>A	ENST00000504228.1	+	6	910	c.805C>A	c.(805-807)Ctc>Atc	p.L269I	KIAA1211_ENST00000264229.6_Missense_Mutation_p.L269I|KIAA1211_ENST00000541073.1_Missense_Mutation_p.L262I			Q6ZU35	K1211_HUMAN	KIAA1211	269	Glu-rich.		L -> I (in dbSNP:rs6823339).							endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AAGGCAGGAGCTCTTGGAGGA	0.657													C|||	1472	0.29393	0.3616	0.2839	5008	,	,		13368	0.0675		0.4095	False		,,,				2504	0.3241				p.L269I		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C805A						PASS	.	C	ILE/LEU	1223,2587		219,785,901	12.0	15.0	14.0		805	3.0	1.0	4	dbSNP_116	14	3113,4891		682,1749,1571	yes	missense	KIAA1211	NM_020722.1	5	901,2534,2472	AA,AC,CC		38.8931,32.0997,36.7022	possibly-damaging	269/1234	57180473	4336,7478	1905	4002	5907	SO:0001583	missense	57482	exon8			CAGGAGCTCTTGG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.805C>A	4.37:g.57180473C>A	ENSP00000423366:p.Leu269Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	644	0.2948717948717949	180	0.36585365853658536	114	0.3149171270718232	33	0.057692307692307696	317	0.4182058047493404	C	12.18	1.859468	0.32884	0.320997	0.388931	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.12672	2.67;2.67;2.66	4.77	3.02	0.34903	.	.	.	.	.	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;P;P	0.51537	0.946;0.86;0.86	B;B;B	0.43052	0.406;0.328;0.328	T	0.41592	-0.9500	8	0.16420	T	0.52	-7.7337	2.6747	0.05078	0.1513:0.5402:0.1465:0.162	rs6823339	262;262;269	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	I	269;269;262;179	ENSP00000264229:L269I;ENSP00000423366:L269I;ENSP00000444006:L262I	ENSP00000264229:L269I	L	+	1	0	KIAA1211	56875230	0.004000	0.15560	0.975000	0.42487	0.959000	0.62525	0.877000	0.28106	0.428000	0.26173	0.462000	0.41574	CTC	C|0.703;A|0.297	0.297	strong		0.657	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
CFAP74	85452	hgsc.bcm.edu	37	1	1900186	1900186	+	IGR	SNP	T	T	C	rs35269416	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1900186T>C								TMEM52 (49474 upstream) : C1orf222 (19376 downstream)																							GGGATGCTGTTTCTTCCTCTT	0.547													t|||	771	0.153954	0.0847	0.219	5008	,	,		19340	0.1101		0.1938	False		,,,				2504	0.2055				p.K378R		Atlas-SNP	.											.	KIAA1751	92	.	0			c.A1133G						PASS	.	T	ARG/LYS	326,3778		8,310,1734	179.0	189.0	186.0		1133	-3.6	0.0	1	dbSNP_126	186	1712,6668		171,1370,2649	yes	missense	KIAA1751	NM_001080484.1	26	179,1680,4383	CC,CT,TT		20.4296,7.9435,16.3249	benign	378/763	1900186	2038,10446	2052	4190	6242	SO:0001628	intergenic_variant	85452	exon11			TGCTGTTTCTTCC																													1.37:g.1900186T>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	172	84	0.488372	NM_001080484		Missense_Mutation	SNP		37		318	0.14560439560439561	43	0.08739837398373984	70	0.19337016574585636	65	0.11363636363636363	140	0.18469656992084432	t	5.253	0.232159	0.09969	0.079435	0.204296	ENSG00000142609	ENST00000270720	.	.	.	3.67	-3.57	0.04612	.	1.650180	0.03416	N	0.205639	T	0.00039	0.0001	N	0.17474	0.49	0.58432	P	1.0000000000287557E-6	B;B	0.23990	0.095;0.012	B;B	0.18871	0.023;0.007	T	0.12477	-1.0546	8	0.16896	T	0.51	-2.4306	6.9556	0.24570	0.0:0.5071:0.1548:0.3381	rs35269416;rs61745134	378;378	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	R	378	.	ENSP00000270720:K378R	K	-	2	0	C1orf222	1890046	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.230000	0.09083	-0.890000	0.03945	0.454000	0.30748	AAA	T|0.833;C|0.167	0.167	strong	0	0.547								
CYP2C19	1557	hgsc.bcm.edu	37	10	96602622	96602622	+	Silent	SNP	C	C	T	rs3758580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96602622C>T	ENST00000371321.3	+	7	1072	c.990C>T	c.(988-990)gtC>gtT	p.V330V	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	330					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)	p.V330V(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	TTGAACGTGTCGTTGGCAGAA	0.507													c|||	1108	0.221246	0.1702	0.1037	5008	,	,		19622	0.3125		0.1451	False		,,,				2504	0.3579				p.V330V		Atlas-SNP	.											CYP2C19,colon,carcinoma,0,1	CYP2C19	88	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C990T						PASS	.	G		731,3675		61,609,1533	164.0	145.0	152.0		990	-1.4	0.0	10	dbSNP_107	152	1274,7326		95,1084,3121	no	coding-synonymous	CYP2C19	NM_000769.1		156,1693,4654	TT,TC,CC		14.814,16.591,15.416		330/491	96602622	2005,11001	2203	4300	6503	SO:0001819	synonymous_variant	1557	exon7			ACGTGTCGTTGGC	M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.990C>T	10.37:g.96602622C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	182	88	0.483516	NM_000769	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Silent	SNP	ENST00000371321.3	37	CCDS7436.1																																																																																			C|0.826;T|0.174	0.174	strong		0.507	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	
OR8B3	390271	hgsc.bcm.edu	37	11	124266927	124266927	+	Silent	SNP	A	A	G	rs142812088		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124266927A>G	ENST00000354597.3	-	1	337	c.321T>C	c.(319-321)ttT>ttC	p.F107F		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CAGAGATGACAAAAAAGAGAA	0.388																																					p.F107F		Atlas-SNP	.											OR8B3,NS,carcinoma,0,1	OR8B3	36	1	0			c.T321C						scavenged	.						78.0	76.0	77.0					11																	124266927		2201	4299	6500	SO:0001819	synonymous_variant	390271	exon1			GATGACAAAAAAG	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.321T>C	11.37:g.124266927A>G		Somatic	309	17	0.0550162		WXS	Illumina HiSeq	Phase_I	339	22	0.0648968	NM_001005467	Q6IFQ8|Q8NGH1	Silent	SNP	ENST00000354597.3	37	CCDS31709.1																																																																																			A|1.000;G|0.000	0.000	weak		0.388	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
C10orf71	118461	hgsc.bcm.edu	37	10	50533463	50533463	+	Missense_Mutation	SNP	T	T	A	rs10857470	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50533463T>A	ENST00000374144.3	+	3	3161	c.2873T>A	c.(2872-2874)tTc>tAc	p.F958Y	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	958			F -> Y (in dbSNP:rs10857470).							endometrium(1)	1						AAGGGGAATTTCCCATCTATG	0.617													T|||	478	0.0954473	0.053	0.0663	5008	,	,		17494	0.122		0.1193	False		,,,				2504	0.1217				p.F958Y		Atlas-SNP	.											.	C10orf71	179	.	0			c.T2873A						PASS	.	T	TYR/PHE,	71,1313		0,71,621	18.0	21.0	20.0		2873,	1.0	0.0	10	dbSNP_120	20	408,2774		25,358,1208	yes	missense,intron	C10orf71	NM_001135196.1,NM_199459.3	22,	25,429,1829	AA,AT,TT		12.8221,5.1301,10.4906	,	958/1436,	50533463	479,4087	692	1591	2283	SO:0001583	missense	118461	exon3			GGAATTTCCCATC	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.2873T>A	10.37:g.50533463T>A	ENSP00000363259:p.Phe958Tyr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	108	62	0.574074	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	211	0.09661172161172162	32	0.06504065040650407	30	0.08287292817679558	60	0.1048951048951049	89	0.11741424802110818	T	11.57	1.677426	0.29783	0.051301	0.128221	ENSG00000177354	ENST00000374144	T	0.04551	3.6	5.06	0.982	0.19762	.	0.774300	0.10520	U	0.665098	T	0.00073	0.0002	N	0.19112	0.55	0.80722	P	0.0	.	.	.	.	.	.	T	0.47209	-0.9135	7	0.54805	T	0.06	.	8.8382	0.35126	0.0:0.2548:0.0:0.7452	rs10857470;rs10857470	.	.	.	Y	958	ENSP00000363259:F958Y	ENSP00000363259:F958Y	F	+	2	0	C10orf71	50203469	0.001000	0.12720	0.000000	0.03702	0.166000	0.22503	0.596000	0.24044	0.288000	0.22398	-0.483000	0.04790	TTC	T|0.906;A|0.094	0.094	strong		0.617	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
SLC6A12	6539	hgsc.bcm.edu	37	12	319111	319111	+	Silent	SNP	T	T	C	rs526690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:319111T>C	ENST00000428720.1	-	3	785	c.42A>G	c.(40-42)gcA>gcG	p.A14A	SLC6A12_ENST00000359674.4_Silent_p.A14A|SLC6A12_ENST00000397296.2_Silent_p.A14A|SLC6A12_ENST00000424061.2_Silent_p.A14A|SLC6A12_ENST00000536824.1_Silent_p.A14A	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	14					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			CCCAGGAGACTGCAGGAGGCC	0.617													C|||	2650	0.529153	0.7284	0.4366	5008	,	,		17247	0.3075		0.5268	False		,,,				2504	0.5562				p.A14A		Atlas-SNP	.											.	SLC6A12	60	.	0			c.A42G						PASS	.	C	,,,	3130,1276	435.9+/-344.5	1113,904,186	96.0	84.0	88.0		42,42,42,42	1.2	0.2	12	dbSNP_83	88	4598,4002	554.1+/-386.4	1219,2160,921	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC6A12	NM_001122847.2,NM_001122848.2,NM_001206931.1,NM_003044.4	,,,	2332,3064,1107	CC,CT,TT		46.5349,28.9605,40.5813	,,,	14/615,14/615,14/615,14/615	319111	7728,5278	2203	4300	6503	SO:0001819	synonymous_variant	6539	exon3			GGAGACTGCAGGA	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.42A>G	12.37:g.319111T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	137	132	0.963504	NM_001122848	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	37	CCDS8501.1																																																																																			T|0.434;C|0.566	0.566	strong		0.617	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
ARSD	414	hgsc.bcm.edu	37	X	2833628	2833628	+	Silent	SNP	A	A	C	rs373216270		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2833628A>C	ENST00000381154.1	-	6	1044	c.969T>G	c.(967-969)ggT>ggG	p.G323G	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	323					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CCACATTATCACCATATAAGC	0.507																																					p.G323G		Atlas-SNP	.											.	ARSD	47	.	0			c.T969G						PASS	.						240.0	161.0	188.0					X																	2833628		2203	4300	6503	SO:0001819	synonymous_variant	414	exon6			ATTATCACCATAT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.969T>G	X.37:g.2833628A>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	87	20	0.229885	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			.	.	weak		0.507	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
ZNF490	57474	hgsc.bcm.edu	37	19	12692001	12692001	+	Silent	SNP	G	G	A	rs3745651	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12692001G>A	ENST00000311437.6	-	5	1010	c.888C>T	c.(886-888)caC>caT	p.H296H	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	296					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						GAGTCCTTTCGTGGGTTAGAA	0.428													G|||	1033	0.20627	0.0386	0.2983	5008	,	,		20580	0.0536		0.5099	False		,,,				2504	0.2127				p.H296H		Atlas-SNP	.											.	ZNF490	42	.	0			c.C888T						PASS	.	G		460,3946	216.8+/-235.3	28,404,1771	76.0	75.0	75.0		888	-2.0	0.1	19	dbSNP_107	75	4390,4210	581.3+/-391.2	1121,2148,1031	yes	coding-synonymous	ZNF490	NM_020714.2		1149,2552,2802	AA,AG,GG		48.9535,10.4403,37.2905		296/530	12692001	4850,8156	2203	4300	6503	SO:0001819	synonymous_variant	57474	exon5			CCTTTCGTGGGTT	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.888C>T	19.37:g.12692001G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	56	34	0.607143	NM_020714		Silent	SNP	ENST00000311437.6	37	CCDS12272.1																																																																																			G|0.688;A|0.312	0.312	strong		0.428	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714	
MAN2B1	4125	hgsc.bcm.edu	37	19	12772090	12772090	+	Missense_Mutation	SNP	C	C	T	rs1133330	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12772090C>T	ENST00000456935.2	-	7	1050	c.1010G>A	c.(1009-1011)cGg>cAg	p.R337Q	MAN2B1_ENST00000221363.4_Missense_Mutation_p.R337Q|MAN2B1_ENST00000495617.1_5'Flank	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	337			R -> Q (in dbSNP:rs1133330). {ECO:0000269|PubMed:22161967, ECO:0000269|PubMed:9915946}.		cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ATTTACCAGCCGGATGAGCTT	0.552													C|||	1244	0.248403	0.3086	0.255	5008	,	,		20976	0.0615		0.3926	False		,,,				2504	0.2065				p.R337Q		Atlas-SNP	.											MAN2B1,NS,meningioma,0,1	MAN2B1	91	1	0			c.G1010A						PASS	.	C	GLN/ARG,GLN/ARG	1379,3027	455.9+/-351.1	215,949,1039	221.0	174.0	190.0		1010,1010	-5.3	0.3	19	dbSNP_86	190	3431,5169	504.3+/-376.1	668,2095,1537	yes	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	43,43	883,3044,2576	TT,TC,CC		39.8953,31.2982,36.9829	benign,benign	337/1012,337/1011	12772090	4810,8196	2203	4300	6503	SO:0001583	missense	4125	exon7			ACCAGCCGGATGA		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.1010G>A	19.37:g.12772090C>T	ENSP00000395473:p.Arg337Gln	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_001173498	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	566	0.2591575091575092	140	0.2845528455284553	106	0.292817679558011	30	0.05244755244755245	290	0.38258575197889183	C	12.08	1.830324	0.32329	0.312982	0.398953	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	T;T	0.79454	-1.27;-1.27	5.51	-5.32	0.02722	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	1.735930	0.03031	N	0.152116	T	0.00012	0.0000	N	0.05510	-0.035	0.46849	P	7.770000000000277E-4	B;B	0.20550	0.022;0.046	B;B	0.15052	0.007;0.012	T	0.03840	-1.0999	9	0.29301	T	0.29	-13.1141	13.4528	0.61180	0.0:0.3494:0.0:0.6506	rs1133330;rs2070087;rs3195023;rs17421598;rs56909861;rs1133330	337;337	G5E928;O00754	.;MA2B1_HUMAN	Q	337;276;337	ENSP00000395473:R337Q;ENSP00000221363:R337Q	ENSP00000221363:R337Q	R	-	2	0	MAN2B1	12633090	0.013000	0.17824	0.311000	0.25182	0.842000	0.47809	-0.041000	0.12084	-0.929000	0.03757	-0.291000	0.09656	CGG	C|0.675;T|0.325	0.325	strong		0.552	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
PDE2A	5138	hgsc.bcm.edu	37	11	72289291	72289291	+	Silent	SNP	T	T	C	rs1135029	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:72289291T>C	ENST00000334456.5	-	30	2846	c.2601A>G	c.(2599-2601)gcA>gcG	p.A867A	PDE2A_ENST00000540345.1_Silent_p.A858A|PDE2A_ENST00000544570.1_Silent_p.A860A|PDE2A_ENST00000376450.3_Silent_p.A611A|PDE2A_ENST00000418754.2_Silent_p.A752A|PDE2A_ENST00000444035.2_Silent_p.A858A	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	867	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	AGATGGGCATTGCAATGTGCT	0.562													T|||	1494	0.298323	0.0885	0.3213	5008	,	,		22174	0.245		0.5298	False		,,,				2504	0.3824				p.A867A		Atlas-SNP	.											PDE2A,caecum,carcinoma,-1,2	PDE2A	156	2	0			c.A2601G						PASS	.	T	,,	773,3627	312.5+/-292.6	70,633,1497	196.0	160.0	172.0		2580,2574,2601	-11.2	0.4	11	dbSNP_86	172	4604,3982	601.4+/-394.4	1236,2132,925	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE2A	NM_001143839.3,NM_001146209.2,NM_002599.4	,,	1306,2765,2422	CC,CT,TT		46.3778,17.5682,41.4061	,,	860/935,858/933,867/942	72289291	5377,7609	2200	4293	6493	SO:0001819	synonymous_variant	5138	exon30			GGGCATTGCAATG	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"""Phosphodiesterases"""	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.2601A>G	11.37:g.72289291T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_002599	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Silent	SNP	ENST00000334456.5	37	CCDS8216.1																																																																																			T|0.638;C|0.362	0.362	strong		0.562	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	
CCL14	6358	hgsc.bcm.edu	37	17	34311387	34311387	+	Missense_Mutation	SNP	T	T	C	rs16971802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34311387T>C	ENST00000394509.4	-	2	289	c.181A>G	c.(181-183)Aag>Gag	p.K61E	CTB-186H2.3_ENST00000593057.1_Intron|CTB-186H2.3_ENST00000591669.1_5'Flank|CCL14_ENST00000536149.1_Missense_Mutation_p.K77E|CCL16_ENST00000293275.3_5'Flank|CCL14_ENST00000480944.2_Missense_Mutation_p.K83E|CCL15-CCL14_ENST00000481427.2_3'UTR|CCL14_ENST00000435911.2_Missense_Mutation_p.K77E|CCL14_ENST00000586216.1_Missense_Mutation_p.K61E			Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14	61			K -> E (in dbSNP:rs16971802).		cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)	extracellular space (GO:0005615)				large_intestine(1)|lung(6)	7		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATTCCGGGCTTGGAGCACTGG	0.577													T|||	318	0.0634984	0.1536	0.0576	5008	,	,		20801	0.0		0.0537	False		,,,				2504	0.0215				p.K77E		Atlas-SNP	.											.	CCL14	22	.	0			c.A229G						PASS	.	T	GLU/LYS,GLU/LYS	595,3811	263.1+/-265.3	42,511,1650	102.0	87.0	92.0		229,181	4.1	0.7	17	dbSNP_123	92	449,8151	135.4+/-192.6	7,435,3858	yes	missense,missense	CCL14	NM_032962.4,NM_032963.3	56,56	49,946,5508	CC,CT,TT		5.2209,13.5043,8.0271	possibly-damaging,possibly-damaging	77/110,61/94	34311387	1044,11962	2203	4300	6503	SO:0001583	missense	6358	exon3			CGGGCTTGGAGCA	Z49270	CCDS32624.1, CCDS45652.1	17q11.2	2014-04-10	2002-08-22	2002-08-23	ENSG00000213494	ENSG00000276409		"""Chemokine ligands"", ""Endogenous ligands"""	10612	protein-coding gene	gene with protein product		601392	"""small inducible cytokine subfamily A (Cys-Cys), member 14"""	SCYA14		8661057	Standard	NM_032963		Approved	HCC-1, HCC-3, NCC-2, SCYL2, CKb1, MCIF	uc010wcq.1	Q16627	OTTHUMG00000188403	ENST00000394509.4:c.181A>G	17.37:g.34311387T>C	ENSP00000378017:p.Lys61Glu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_032962	E1P649|E1P650|Q13954	Missense_Mutation	SNP	ENST00000394509.4	37	CCDS32624.1	133	0.060897435897435896	79	0.16056910569105692	19	0.052486187845303865	0	0.0	35	0.04617414248021108	T	16.19	3.052917	0.55218	0.135043	0.052209	ENSG00000213494	ENST00000394509;ENST00000536149;ENST00000435911	T;T;T	0.05447	3.44;3.44;3.44	5.14	4.05	0.47172	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.192216	0.31358	U	0.007781	T	0.00073	0.0002	.	.	.	0.51482	P	7.40000000000185E-5	P;D	0.56035	0.943;0.974	P;P	0.54544	0.755;0.641	T	0.11397	-1.0589	8	0.66056	D	0.02	.	9.4164	0.38523	0.0:0.0:0.1787:0.8213	rs16971802;rs56435289;rs16971802	61;77	Q16627;Q16627-2	CCL14_HUMAN;.	E	61;77;77	ENSP00000378017:K61E;ENSP00000441771:K77E;ENSP00000409197:K77E	ENSP00000378017:K61E	K	-	1	0	CCL14	31335500	0.304000	0.24472	0.688000	0.30117	0.690000	0.40134	0.521000	0.22893	0.863000	0.35553	0.460000	0.39030	AAG	T|0.925;C|0.075	0.075	strong		0.577	CCL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272892.2	NM_032962	
IP6K2	51447	hgsc.bcm.edu	37	3	48732480	48732480	+	Intron	SNP	T	T	C	rs17080319	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:48732480T>C	ENST00000328631.5	-	2	426				IP6K2_ENST00000443964.1_Missense_Mutation_p.D141G|IP6K2_ENST00000446860.1_Missense_Mutation_p.D140G|IP6K2_ENST00000413298.1_Intron|IP6K2_ENST00000432678.2_Intron|IP6K2_ENST00000340879.4_Intron|IP6K2_ENST00000450045.1_Intron|IP6K2_ENST00000449610.1_Missense_Mutation_p.D82G|IP6K2_ENST00000417896.1_Missense_Mutation_p.D82G|IP6K2_ENST00000453202.1_Missense_Mutation_p.D82G|IP6K2_ENST00000436134.1_Intron|IP6K2_ENST00000431721.2_Missense_Mutation_p.D137G	NM_001005909.2|NM_016291.3	NP_001005909.1|NP_057375.2	Q9UHH9	IP6K2_HUMAN	inositol hexakisphosphate kinase 2						cytokine-mediated signaling pathway (GO:0019221)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell growth (GO:0030308)|phosphate ion transport (GO:0006817)|phosphatidylinositol phosphorylation (GO:0046854)|positive regulation of apoptotic process (GO:0043065)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	15						ATCTCTCACATCTCCTCGCCA	0.597													T|||	604	0.120607	0.2549	0.0893	5008	,	,		18551	0.0486		0.1243	False		,,,				2504	0.0317				p.D140G		Atlas-SNP	.											.	IP6K2	63	.	0			c.A419G						PASS	.	T	,,,,,GLY/ASP,GLY/ASP,	956,3450	362.1+/-316.0	92,772,1339	48.0	45.0	46.0		,,,,,410,419,	-1.1	0.0	3	dbSNP_123	46	1077,7523	225.4+/-261.5	69,939,3292	yes	intron,intron,intron,intron,intron,missense,missense,intron	IP6K2	NM_001005909.2,NM_001005910.2,NM_001005911.2,NM_001146178.2,NM_001146179.2,NM_001190316.1,NM_001190317.1,NM_016291.3	,,,,,94,94,	161,1711,4631	CC,CT,TT		12.5233,21.6977,15.6312	,,,,,,,	,,,,,137/186,140/189,	48732480	2033,10973	2203	4300	6503	SO:0001627	intron_variant	51447	exon3			CTCACATCTCCTC	AF177145	CCDS2777.1, CCDS33752.1, CCDS54579.1, CCDS54580.1, CCDS54581.1	3p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000068745	ENSG00000068745			17313	protein-coding gene	gene with protein product		606992	"""inositol hexaphosphate kinase 2"""	IHPK2		10574768	Standard	NM_016291		Approved		uc003cup.3	Q9UHH9	OTTHUMG00000133543	ENST00000328631.5:c.202+42A>G	3.37:g.48732480T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001190317	A8K3B1|B4E3G6|G8JLL6|Q6P0N8|Q9BSZ6|Q9BUW3|Q9H4P7|Q9NT63|Q9UFU6	Missense_Mutation	SNP	ENST00000328631.5	37	CCDS2777.1	289	0.13232600732600733	122	0.24796747967479674	33	0.09116022099447514	38	0.06643356643356643	96	0.1266490765171504	T	14.24	2.475785	0.44044	0.216977	0.125233	ENSG00000068745	ENST00000431721;ENST00000449610;ENST00000446860;ENST00000417896;ENST00000443964;ENST00000453202	T;T;T;T;T;T	0.55234	0.53;0.58;0.53;0.58;0.53;0.58	4.55	-1.12	0.09808	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.003;0.003	T	0.23762	-1.0179	8	0.56958	D	0.05	.	0.4297	0.00469	0.1829:0.2606:0.1888:0.3677	rs17080319;rs17080319	140;136;137	B4E3G6;A8K636;A8K3B1	.;.;.	G	137;82;140;82;141;82	ENSP00000414139:D137G;ENSP00000393077:D82G;ENSP00000399052:D140G;ENSP00000388116:D82G;ENSP00000410950:D141G;ENSP00000387394:D82G	ENSP00000388116:D82G	D	-	2	0	IP6K2	48707484	0.000000	0.05858	0.000000	0.03702	0.521000	0.34408	-0.250000	0.08830	-0.036000	0.13669	0.164000	0.16699	GAT	A|0.000;C|0.134;T|0.866	0.134	strong		0.597	IP6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257521.2	NM_016291	
ZNF180	7733	hgsc.bcm.edu	37	19	44981375	44981375	+	Silent	SNP	T	T	C	rs954314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44981375T>C	ENST00000221327.4	-	5	1604	c.1323A>G	c.(1321-1323)caA>caG	p.Q441Q	ZNF180_ENST00000391956.4_Silent_p.Q416Q|ZNF180_ENST00000592529.1_Silent_p.Q414Q|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				ACTTTCCACATTGATTGCATT	0.393													T|||	804	0.160543	0.1513	0.1729	5008	,	,		19777	0.002		0.338	False		,,,				2504	0.1452				p.Q441Q	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											ZNF180,caecum,carcinoma,0,1	ZNF180	103	1	0			c.A1323G						PASS	.	T		872,3534	333.6+/-303.0	88,696,1419	75.0	77.0	76.0		1323	-5.9	0.9	19	dbSNP_86	76	2776,5824	439.2+/-359.1	460,1856,1984	no	coding-synonymous	ZNF180	NM_013256.3		548,2552,3403	CC,CT,TT		32.2791,19.7912,28.0486		441/693	44981375	3648,9358	2203	4300	6503	SO:0001819	synonymous_variant	7733	exon5			TCCACATTGATTG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1323A>G	19.37:g.44981375T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																			T|0.760;C|0.240	0.240	strong		0.393	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
HIST1H4H	8365	hgsc.bcm.edu	37	6	26285560	26285560	+	Silent	SNP	A	A	G	rs2393592	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26285560A>G	ENST00000377727.1	-	1	177	c.168T>C	c.(166-168)cgT>cgC	p.R56R	HIST1H4H_ENST00000289352.1_Silent_p.R56R	NM_003543.3	NP_003534.1	P62805	H4_HUMAN	histone cluster 1, H4h	56					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(2)|ovary(2)|upper_aerodigestive_tract(3)	7						TCAGAACACCACGAGTCTCCT	0.547										HNSCC(76;0.23)			G|||	3100	0.61901	0.3449	0.6412	5008	,	,		20118	0.8929		0.5547	False		,,,				2504	0.7577				p.R56R		Atlas-SNP	.											.	HIST1H4H	16	.	0			c.T168C						PASS	.	G		1662,2744		331,1000,872	166.0	138.0	147.0		168	0.4	1.0	6	dbSNP_100	147	4630,3970		1250,2130,920	no	coding-synonymous	HIST1H4H	NM_003543.3		1581,3130,1792	GG,GA,AA		46.1628,37.7213,48.3777		56/104	26285560	6292,6714	2203	4300	6503	SO:0001819	synonymous_variant	8365	exon1			AACACCACGAGTC	X60487	CCDS4604.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158406	ENSG00000158406		"""Histones / Replication-dependent"""	4788	protein-coding gene	gene with protein product		602828	"""H4 histone family, member H"", ""histone 1, H4h"""	H4FH		9119399, 12408966	Standard	NM_003543		Approved	H4/h	uc003nhm.2	P62805	OTTHUMG00000014454	ENST00000377727.1:c.168T>C	6.37:g.26285560A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	267	144	0.539326	NM_003543	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377727.1	37	CCDS4604.1																																																																																			A|0.445;G|0.555	0.555	strong		0.547	HIST1H4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040119.1	NM_003543	
NOTCH2	4853	hgsc.bcm.edu	37	1	120458122	120458122	+	Missense_Mutation	SNP	A	A	T	rs35586704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120458122A>T	ENST00000256646.2	-	34	7442	c.7223T>A	c.(7222-7224)cTc>cAc	p.L2408H		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2408					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCACCCTGGAGGTGACCACT	0.567			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				A|||	4	0.000798722	0.0	0.0	5008	,	,		21639	0.0		0.004	False		,,,				2504	0.0				p.L2408H		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.T7223A						PASS	.	A	HIS/LEU	5,4401	9.9+/-24.2	0,5,2198	123.0	108.0	113.0		7223	5.3	1.0	1	dbSNP_126	113	22,8578	16.6+/-54.9	0,22,4278	yes	missense	NOTCH2	NM_024408.3	99	0,27,6476	TT,TA,AA		0.2558,0.1135,0.2076	probably-damaging	2408/2472	120458122	27,12979	2203	4300	6503	SO:0001583	missense	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CCCTGGAGGTGAC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.7223T>A	1.37:g.120458122A>T	ENSP00000256646:p.Leu2408His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	124	73	0.58871	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	15.05	2.717318	0.48622	0.001135	0.002558	ENSG00000134250	ENST00000256646	T	0.77489	-1.1	5.35	5.35	0.76521	Domain of unknown function DUF3454, notch (1);	0.000000	0.32769	U	0.005675	T	0.79375	0.4435	L	0.43923	1.385	0.34826	D	0.739179	D	0.76494	0.999	D	0.70487	0.969	D	0.83604	0.0130	10	0.87932	D	0	.	14.5066	0.67758	1.0:0.0:0.0:0.0	rs35586704	2408	Q04721	NOTC2_HUMAN	H	2408	ENSP00000256646:L2408H	ENSP00000256646:L2408H	L	-	2	0	NOTCH2	120259645	0.946000	0.32159	1.000000	0.80357	0.958000	0.62258	2.431000	0.44775	2.027000	0.59764	0.482000	0.46254	CTC	A|0.998;T|0.002	0.002	strong		0.567	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
XIRP1	165904	hgsc.bcm.edu	37	3	39228774	39228774	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:39228774G>A	ENST00000340369.3	-	2	2391	c.2163C>T	c.(2161-2163)ccC>ccT	p.P721P	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Silent_p.P721P	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	721					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CAGAACCCGCGGGGATGGACC	0.582																																					p.P721P		Atlas-SNP	.											.	XIRP1	173	.	0			c.C2163T						PASS	.						52.0	55.0	54.0					3																	39228774		2203	4300	6503	SO:0001819	synonymous_variant	165904	exon2			ACCCGCGGGGATG	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.2163C>T	3.37:g.39228774G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	105	39	0.371429	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																			.	.	none		0.582	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
FAM170B	170370	hgsc.bcm.edu	37	10	50339925	50339925	+	Silent	SNP	G	G	A	rs12765281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50339925G>A	ENST00000311787.5	-	2	674	c.585C>T	c.(583-585)gaC>gaT	p.D195D	FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	195										central_nervous_system(1)|endometrium(1)|skin(1)	3						TGACCAGCCAGTCCGGCGGCT	0.687													G|||	1228	0.245208	0.118	0.3444	5008	,	,		15830	0.3075		0.2684	False		,,,				2504	0.2587				p.D195D		Atlas-SNP	.											.	FAM170B	20	.	0			c.C585T						PASS	.						7.0	11.0	10.0					10																	50339925		684	1579	2263	SO:0001819	synonymous_variant	170370	exon2			CAGCCAGTCCGGC		CCDS53536.1	10q11.23	2008-11-06	2008-06-12	2008-06-12	ENSG00000172538	ENSG00000172538			19736	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 73"""	C10orf73			Standard	NM_001164484		Approved	Em:AC084727.4	uc001jhj.3	A6NMN3	OTTHUMG00000018187	ENST00000311787.5:c.585C>T	10.37:g.50339925G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_001164484	Q86WY6|Q8N6K8	Silent	SNP	ENST00000311787.5	37	CCDS53536.1																																																																																			G|0.768;A|0.232	0.232	strong		0.687	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
WRN	7486	hgsc.bcm.edu	37	8	30973957	30973957	+	Silent	SNP	G	G	T	rs1800392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:30973957G>T	ENST00000298139.5	+	20	2610	c.2361G>T	c.(2359-2361)ctG>ctT	p.L787L		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	787	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTAGGAAACTGAATCTATCCT	0.383			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				G|||	2360	0.471246	0.4175	0.5764	5008	,	,		18469	0.624		0.4493	False		,,,				2504	0.3344				p.L787L	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.G2361T						PASS	.	G		1810,2596	531.1+/-373.1	364,1082,757	126.0	116.0	119.0		2361	3.8	0.6	8	dbSNP_89	119	4019,4581	556.1+/-386.8	928,2163,1209	yes	coding-synonymous	WRN	NM_000553.4		1292,3245,1966	TT,TG,GG		46.7326,41.0803,44.8178		787/1433	30973957	5829,7177	2203	4300	6503	SO:0001819	synonymous_variant	7486	exon20	Familial Cancer Database	WS, Adult Progeria	GAAACTGAATCTA		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.2361G>T	8.37:g.30973957G>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	37	CCDS6082.1																																																																																			G|0.509;T|0.491	0.491	strong		0.383	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
PQLC2	54896	hgsc.bcm.edu	37	1	19652874	19652874	+	Missense_Mutation	SNP	G	G	A	rs41264079	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19652874G>A	ENST00000375153.3	+	5	1158	c.518G>A	c.(517-519)gGc>gAc	p.G173D	PQLC2_ENST00000375155.3_Missense_Mutation_p.G173D|PQLC2_ENST00000400548.2_Missense_Mutation_p.G108D	NM_001040125.1	NP_001035214.1	Q6ZP29	LAAT1_HUMAN	PQ loop repeat containing 2	173				G -> D (in Ref. 1; BAG54217). {ECO:0000305}.	amino acid homeostasis (GO:0080144)|arginine transport (GO:0015809)|lysine transport (GO:0015819)	integral component of organelle membrane (GO:0031301)|lysosomal membrane (GO:0005765)	arginine transmembrane transporter activity (GO:0015181)|basic amino acid transmembrane transporter activity (GO:0015174)|L-lysine transmembrane transporter activity (GO:0015189)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTGGAGTCGGGCAGCAAGGTG	0.701													G|||	248	0.0495208	0.0061	0.0447	5008	,	,		15617	0.0089		0.1243	False		,,,				2504	0.0767				p.G173D		Atlas-SNP	.											PQLC2,NS,carcinoma,0,2	PQLC2	34	2	0			c.G518A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY	82,4324		3,76,2124	22.0	24.0	23.0		518,323,518	1.0	0.0	1	dbSNP_127	23	954,7644		51,852,3396	yes	missense,missense,missense	PQLC2	NM_001040125.1,NM_001040126.1,NM_017765.2	94,94,94	54,928,5520	AA,AG,GG		11.0956,1.8611,7.9668	possibly-damaging,possibly-damaging,possibly-damaging	173/292,108/227,173/292	19652874	1036,11968	2203	4299	6502	SO:0001583	missense	54896	exon5			AGTCGGGCAGCAA	BC015324	CCDS195.2, CCDS30618.1	1p36.13	2013-10-11			ENSG00000040487	ENSG00000040487			26001	protein-coding gene	gene with protein product		614760				23169667	Standard	XM_005245915		Approved	FLJ20320	uc001bby.3	Q6ZP29	OTTHUMG00000002521	ENST00000375153.3:c.518G>A	1.37:g.19652874G>A	ENSP00000364295:p.Gly173Asp	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	30	12	0.4	NM_001040125	B3KWQ5|Q6ZMJ3|Q6ZP27|Q9NXC7	Missense_Mutation	SNP	ENST00000375153.3	37	CCDS195.2	123	0.05631868131868132	6	0.012195121951219513	19	0.052486187845303865	1	0.0017482517482517483	97	0.1279683377308707	G	9.751	1.167406	0.21621	0.018611	0.110956	ENSG00000040487	ENST00000375155;ENST00000375153;ENST00000400548;ENST00000432465	T;T	0.44482	0.92;0.92	5.34	1.03	0.20045	.	0.587200	0.19101	N	0.122716	T	0.00300	0.0009	L	0.46947	1.48	0.09310	N	1	B	0.19445	0.036	B	0.14578	0.011	T	0.08973	-1.0696	10	0.10636	T	0.68	-11.0629	6.7836	0.23662	0.1716:0.2965:0.5319:0.0	rs41264079	173	Q6ZP29	PQLC2_HUMAN	D	173;173;108;78	ENSP00000364297:G173D;ENSP00000364295:G173D	ENSP00000364295:G173D	G	+	2	0	PQLC2	19525461	0.006000	0.16342	0.008000	0.14137	0.252000	0.25951	0.561000	0.23515	0.623000	0.30267	0.462000	0.41574	GGC	G|0.938;A|0.062	0.062	strong		0.701	PQLC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007255.1	NM_017765	
PRRC2A	7916	hgsc.bcm.edu	37	6	31600430	31600430	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31600430G>A	ENST00000376033.2	+	16	4214	c.3980G>A	c.(3979-3981)aGc>aAc	p.S1327N	PRRC2A_ENST00000376007.4_Missense_Mutation_p.S1327N	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1327	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GCATCAGAGAGCAGTGACTTC	0.602																																					p.S1327N		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G3980A						PASS	.						76.0	79.0	78.0					6																	31600430		1509	2709	4218	SO:0001583	missense	7916	exon16			CAGAGAGCAGTGA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3980G>A	6.37:g.31600430G>A	ENSP00000365201:p.Ser1327Asn	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	156	91	0.583333	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.584062	0.28268	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.04234	3.67;3.67	5.22	5.22	0.72569	.	0.084158	0.52532	D	0.000067	T	0.11537	0.0281	L	0.60067	1.865	0.45747	D	0.99864	D	0.67145	0.996	P	0.62740	0.906	T	0.00717	-1.1596	10	0.87932	D	0	-14.4073	17.7172	0.88341	0.0:0.0:1.0:0.0	.	1327	P48634	PRC2A_HUMAN	N	1321;1310;1327;1327;552	ENSP00000365175:S1327N;ENSP00000365201:S1327N	ENSP00000365175:S1327N	S	+	2	0	PRRC2A	31708409	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.369000	0.79578	2.714000	0.92807	0.561000	0.74099	AGC	.	.	none		0.602	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377873	49377873	+	Silent	SNP	G	G	A	rs35023389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49377873G>A	ENST00000200453.5	+	2	1652	c.1383G>A	c.(1381-1383)ttG>ttA	p.L461L		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	461	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		AAGCAGCCTTGGGAGAAGCTG	0.562													G|||	419	0.0836661	0.0877	0.0793	5008	,	,		18197	0.003		0.164	False		,,,				2504	0.0818				p.L461L		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1383A						PASS	.	G		576,3830	255.2+/-260.5	35,506,1662	73.0	74.0	73.0		1383	0.6	0.0	19	dbSNP_126	73	1549,7051	290.4+/-299.8	128,1293,2879	no	coding-synonymous	PPP1R15A	NM_014330.3		163,1799,4541	AA,AG,GG		18.0116,13.0731,16.3386		461/675	49377873	2125,10881	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon2			AGCCTTGGGAGAA	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1383G>A	19.37:g.49377873G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			G|0.860;A|0.140	0.140	strong		0.562	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
ASB2	51676	hgsc.bcm.edu	37	14	94405616	94405616	+	Silent	SNP	G	G	A	rs140791740		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94405616G>A	ENST00000315988.4	-	6	1799	c.1311C>T	c.(1309-1311)gcC>gcT	p.A437A	ASB2_ENST00000555019.1_Silent_p.A485A|ASB2_ENST00000556337.1_5'Flank|RP11-131H24.4_ENST00000557646.1_5'Flank	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	437					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		GGCACTTCATGGCGAACATGA	0.667													G|||	1	0.000199681	0.0	0.0014	5008	,	,		15940	0.0		0.0	False		,,,				2504	0.0				p.A485A		Atlas-SNP	.											.	ASB2	71	.	0			c.C1455T						PASS	.	G	,	0,4406		0,0,2203	55.0	56.0	56.0		1455,1311	5.1	1.0	14	dbSNP_134	56	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	ASB2	NM_001202429.1,NM_016150.4	,	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,	485/636,437/588	94405616	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	51676	exon8			CTTCATGGCGAAC	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.1311C>T	14.37:g.94405616G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	37	CCDS9915.1																																																																																			G|1.000;A|0.000	0.000	strong		0.667	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
CES1	1066	hgsc.bcm.edu	37	16	55862691	55862691	+	Missense_Mutation	SNP	G	G	A	rs62028647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55862691G>A	ENST00000361503.4	-	2	375	c.245C>T	c.(244-246)tCg>tTg	p.S82L	CES1_ENST00000422046.2_Missense_Mutation_p.S82L|CES1_ENST00000566555.1_5'Flank|CES1_ENST00000360526.3_Missense_Mutation_p.S83L			P23141	EST1_HUMAN	carboxylesterase 1	82					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	AGGAGGGTACGAGGTGGCATT	0.542																																					p.S83L	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.C248T						PASS	.						106.0	104.0	105.0					16																	55862691		2198	4300	6498	SO:0001583	missense	1066	exon2			GGGTACGAGGTGG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.245C>T	16.37:g.55862691G>A	ENSP00000355193:p.Ser82Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	122	31	0.254098	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	824	0.3772893772893773	224	0.45528455284552843	145	0.4005524861878453	117	0.20454545454545456	338	0.44591029023746703	.	12.07	1.827253	0.32329	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.68765	-0.35;-0.35;-0.35	4.48	4.48	0.54585	Carboxylesterase, type B (1);	0.146929	0.31472	N	0.007582	T	0.00012	0.0000	M	0.82823	2.61	0.36044	D	0.840328	D;D;P	0.53312	0.959;0.959;0.949	P;P;B	0.46253	0.509;0.509;0.375	T	0.34900	-0.9810	10	0.87932	D	0	.	14.6933	0.69101	0.0:0.0:1.0:0.0	rs62028647	82;82;83	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	L	83;82;82	ENSP00000353720:S83L;ENSP00000355193:S82L;ENSP00000390492:S82L	ENSP00000353720:S83L	S	-	2	0	CES1	54420192	0.941000	0.31946	0.984000	0.44739	0.053000	0.15095	3.676000	0.54612	2.051000	0.60960	0.393000	0.25936	TCG	G|0.622;A|0.378	0.378	strong		0.542	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
LRRFIP2	9209	hgsc.bcm.edu	37	3	37151157	37151157	+	Missense_Mutation	SNP	T	T	C	rs36068826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37151157T>C	ENST00000336686.4	-	10	631	c.551A>G	c.(550-552)tAt>tGt	p.Y184C	LRRFIP2_ENST00000421307.1_Missense_Mutation_p.Y184C|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000396428.2_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	184	DVL3-binding.|Ser-rich.				Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						GTCACTCTTATATGTTGCCAG	0.373													T|||	40	0.00798722	0.0	0.0159	5008	,	,		19407	0.0		0.0199	False		,,,				2504	0.0092				p.Y184C		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.A551G						PASS	.	T	,CYS/TYR,	24,4382	31.7+/-61.6	0,24,2179	113.0	116.0	115.0		,551,	4.6	0.9	3	dbSNP_126	115	267,8333	102.9+/-164.1	5,257,4038	yes	intron,missense,intron	LRRFIP2	NM_001134369.1,NM_006309.2,NM_017724.2	,194,	5,281,6217	CC,CT,TT		3.1047,0.5447,2.2374	,benign,	,184/722,	37151157	291,12715	2203	4300	6503	SO:0001583	missense	9209	exon11			CTCTTATATGTTG	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.551A>G	3.37:g.37151157T>C	ENSP00000338727:p.Tyr184Cys	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	119	47	0.394958	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	26	0.011904761904761904	0	0.0	10	0.027624309392265192	0	0.0	16	0.021108179419525065	T	11.05	1.525899	0.27299	0.005447	0.031047	ENSG00000093167	ENST00000421307;ENST00000336686	T;T	0.44083	0.93;0.93	5.49	4.61	0.57282	.	0.515838	0.20832	N	0.084875	T	0.09905	0.0243	N	0.08118	0	0.23747	N	0.99696	B	0.24368	0.102	B	0.27262	0.078	T	0.16719	-1.0393	10	0.62326	D	0.03	3.6533	13.2958	0.60296	0.0:0.0:0.7078:0.2922	rs36068826	184	Q9Y608	LRRF2_HUMAN	C	184	ENSP00000392217:Y184C;ENSP00000338727:Y184C	ENSP00000338727:Y184C	Y	-	2	0	LRRFIP2	37126161	0.998000	0.40836	0.900000	0.35374	0.700000	0.40528	2.142000	0.42177	1.550000	0.49438	-0.168000	0.13345	TAT	T|0.980;C|0.020	0.020	strong		0.373	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	
TRIP12	9320	hgsc.bcm.edu	37	2	230668858	230668858	+	Silent	SNP	T	T	C	rs13018957	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:230668858T>C	ENST00000283943.5	-	18	2689	c.2511A>G	c.(2509-2511)acA>acG	p.T837T	TRIP12_ENST00000389045.3_Silent_p.T567T|TRIP12_ENST00000389044.4_Silent_p.T885T|TRIP12_ENST00000543084.1_Intron	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	837					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.T837T(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CACCAAATAATGTCTTAATAA	0.383													T|||	1757	0.350839	0.1589	0.438	5008	,	,		16773	0.3581		0.5089	False		,,,				2504	0.3783				p.T837T		Atlas-SNP	.											TRIP12,NS,carcinoma,0,1	TRIP12	207	1	1	Substitution - coding silent(1)	stomach(1)	c.A2511G						PASS	.	T		940,3466	353.1+/-312.0	109,722,1372	84.0	90.0	88.0		2511	-6.9	0.6	2	dbSNP_121	88	4135,4465	563.9+/-388.2	999,2137,1164	no	coding-synonymous	TRIP12	NM_004238.1		1108,2859,2536	CC,CT,TT		48.0814,21.3345,39.0205		837/1993	230668858	5075,7931	2203	4300	6503	SO:0001819	synonymous_variant	9320	exon18			AAATAATGTCTTA	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.2511A>G	2.37:g.230668858T>C		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	276	128	0.463768	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	37	CCDS33391.1																																																																																			T|0.611;C|0.389	0.389	strong		0.383	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	
KIF15	56992	hgsc.bcm.edu	37	3	44871505	44871505	+	Missense_Mutation	SNP	A	A	T	rs11710339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:44871505A>T	ENST00000326047.4	+	25	3135	c.2986A>T	c.(2986-2988)Aca>Tca	p.T996S	KIF15_ENST00000425755.1_Missense_Mutation_p.T631S	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	996			T -> S (in dbSNP:rs11710339). {ECO:0000269|PubMed:12747765, ECO:0000269|PubMed:17974005}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		GGAGCTAAGAACATCGGTCTG	0.373													A|||	316	0.063099	0.0159	0.0836	5008	,	,		13014	0.0		0.2197	False		,,,				2504	0.0164				p.T996S		Atlas-SNP	.											.	KIF15	103	.	0			c.A2986T						PASS	.	A	SER/THR	198,4208	123.3+/-160.7	4,190,2009	117.0	106.0	110.0		2986	-4.0	0.0	3	dbSNP_120	110	1794,6806	324.6+/-316.5	174,1446,2680	yes	missense	KIF15	NM_020242.2	58	178,1636,4689	TT,TA,AA		20.8605,4.4939,15.316	benign	996/1389	44871505	1992,11014	2203	4300	6503	SO:0001583	missense	56992	exon25			CTAAGAACATCGG	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.2986A>T	3.37:g.44871505A>T	ENSP00000324020:p.Thr996Ser	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	146	84	0.575342	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	37	CCDS33744.1	200	0.09157509157509157	7	0.014227642276422764	28	0.07734806629834254	0	0.0	165	0.21767810026385223	A	9.425	1.084041	0.20309	0.044939	0.208605	ENSG00000163808	ENST00000326047;ENST00000396031;ENST00000425755	T;T	0.40756	1.02;1.02	5.61	-4.04	0.04010	.	0.730438	0.12092	N	0.500355	T	0.00012	0.0000	N	0.20685	0.6	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.13407	0.009	T	0.31668	-0.9935	9	0.08381	T	0.77	.	6.5448	0.22400	0.443:0.0:0.3782:0.1788	rs11710339;rs17631234;rs11710339	996	Q9NS87	KIF15_HUMAN	S	996;995;631	ENSP00000324020:T996S;ENSP00000389982:T631S	ENSP00000324020:T996S	T	+	1	0	KIF15	44846509	0.500000	0.26091	0.031000	0.17742	0.989000	0.77384	0.083000	0.14871	-0.345000	0.08325	0.482000	0.46254	ACA	A|0.868;T|0.132	0.132	strong		0.373	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
ZSCAN20	7579	hgsc.bcm.edu	37	1	33957130	33957130	+	Silent	SNP	C	C	A	rs3795419	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33957130C>A	ENST00000361328.3	+	6	1425	c.1272C>A	c.(1270-1272)gcC>gcA	p.A424A	ZSCAN20_ENST00000373413.2_Silent_p.A370A	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	424					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A424A(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CAGGAGAGGCCGTGGCACTTC	0.612													C|||	974	0.194489	0.0204	0.2104	5008	,	,		17850	0.3651		0.162	False		,,,				2504	0.2761				p.A424A		Atlas-SNP	.											ZSCAN20,NS,carcinoma,0,1	ZSCAN20	107	1	1	Substitution - coding silent(1)	stomach(1)	c.C1272A						PASS	.	C		175,3689		2,171,1759	59.0	66.0	64.0		1272	-8.6	0.0	1	dbSNP_107	64	1422,6836		136,1150,2843	no	coding-synonymous	ZSCAN20	NM_145238.3		138,1321,4602	AA,AC,CC		17.2197,4.529,13.1744		424/1044	33957130	1597,10525	1932	4129	6061	SO:0001819	synonymous_variant	7579	exon6			AGAGGCCGTGGCA	X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"""-"", ""Zinc fingers, C2H2-type"""	13093	protein-coding gene	gene with protein product		611315	"""zinc finger protein 31 (KOX 29)"", ""zinc finger protein 31"""	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.1272C>A	1.37:g.33957130C>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	37	CCDS41300.1																																																																																			C|0.824;A|0.176	0.176	strong		0.612	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238	
NLRP13	126204	hgsc.bcm.edu	37	19	56423728	56423728	+	Silent	SNP	A	A	G	rs303999	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56423728A>G	ENST00000342929.3	-	5	1454	c.1455T>C	c.(1453-1455)agT>agC	p.S485S	NLRP13_ENST00000588751.1_Silent_p.S485S	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	485	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CTATGGCCAGACTGCAGAGGG	0.493													A|||	3327	0.664337	0.733	0.5086	5008	,	,		19405	0.7292		0.5915	False		,,,				2504	0.6902				p.S485S		Atlas-SNP	.											.	NLRP13	220	.	0			c.T1455C						PASS	.	A		3112,1294	694.9+/-405.9	1104,904,195	52.0	53.0	53.0		1455	-1.3	0.0	19	dbSNP_79	53	5236,3364	637.9+/-399.3	1600,2036,664	no	coding-synonymous	NLRP13	NM_176810.2		2704,2940,859	GG,GA,AA		39.1163,29.369,35.8142		485/1044	56423728	8348,4658	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon5			GGCCAGACTGCAG	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.1455T>C	19.37:g.56423728A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			A|0.367;G|0.633	0.633	strong		0.493	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
KDM3A	55818	hgsc.bcm.edu	37	2	86705072	86705072	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:86705072A>G	ENST00000409556.1	+	14	2377	c.2012A>G	c.(2011-2013)aAc>aGc	p.N671S	KDM3A_ENST00000542128.1_Missense_Mutation_p.N619S|KDM3A_ENST00000312912.5_Missense_Mutation_p.N671S|KDM3A_ENST00000409064.1_Missense_Mutation_p.N671S			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	671					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.N671S(2)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						ACCATCTTCAACCTGCACTGG	0.478																																					p.N671S	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											KDM3A_ENST00000409556,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,2	KDM3A	179	2	2	Substitution - Missense(2)	central_nervous_system(2)	c.A2012G						scavenged	.						248.0	220.0	230.0					2																	86705072		2203	4300	6503	SO:0001583	missense	55818	exon13			TCTTCAACCTGCA	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.2012A>G	2.37:g.86705072A>G	ENSP00000386660:p.Asn671Ser	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	297	3	0.010101	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	37	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.426019	0.83667	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58	5.84	4.69	0.59074	.	0.000000	0.85682	D	0.000000	D	0.94228	0.8147	M	0.85197	2.74	0.47584	D	0.999466	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.93976	0.7254	10	0.62326	D	0.03	.	11.1342	0.48365	0.9282:0.0:0.0718:0.0	.	619;671	F5H070;Q9Y4C1	.;KDM3A_HUMAN	S	671;671;671;671;619	ENSP00000386660:N671S;ENSP00000323659:N671S;ENSP00000386516:N671S;ENSP00000438324:N619S	ENSP00000323659:N671S	N	+	2	0	KDM3A	86558583	1.000000	0.71417	0.994000	0.49952	0.987000	0.75469	9.339000	0.96797	1.044000	0.40200	0.533000	0.62120	AAC	.	.	none		0.478	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133918420	133918420	+	Silent	SNP	G	G	A	rs11146177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:133918420G>A	ENST00000298622.4	+	1	246	c.108G>A	c.(106-108)caG>caA	p.Q36Q		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	36						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		CAGACATCCAGATCGAGCTGC	0.662													G|||	809	0.161542	0.1293	0.1081	5008	,	,		16530	0.2014		0.2008	False		,,,				2504	0.1616				p.Q36Q		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.G108A						PASS	.	G		506,3668		31,444,1612	19.0	24.0	23.0		108	2.9	1.0	10	dbSNP_120	23	1569,6871		158,1253,2809	no	coding-synonymous	JAKMIP3	NM_001105521.2		189,1697,4421	AA,AG,GG		18.59,12.1227,16.45		36/845	133918420	2075,10539	2087	4220	6307	SO:0001819	synonymous_variant	282973	exon1			CATCCAGATCGAG	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.108G>A	10.37:g.133918420G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	162	76	0.469136	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			G|0.837;A|0.163	0.163	strong		0.662	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
RPS6KA1	6195	hgsc.bcm.edu	37	1	26883511	26883511	+	Missense_Mutation	SNP	A	A	C	rs2229712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:26883511A>C	ENST00000374168.2	+	13	1158	c.1004A>C	c.(1003-1005)aAg>aCg	p.K335T	RPS6KA1_ENST00000374162.2_Missense_Mutation_p.K243T|RPS6KA1_ENST00000530003.1_Missense_Mutation_p.K319T|MIR1976_ENST00000459548.1_RNA|RPS6KA1_ENST00000526792.1_Missense_Mutation_p.K243T|RPS6KA1_ENST00000531382.1_Missense_Mutation_p.K344T|RPS6KA1_ENST00000374166.4_Missense_Mutation_p.K324T|RPS6KA1_ENST00000488985.1_3'UTR	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	335	AGC-kinase C-terminal.		K -> T (in dbSNP:rs2229712). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8141249}.		axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		CGTGAGATCAAGCCACCCTTC	0.577													A|||	806	0.160942	0.0083	0.2651	5008	,	,		19808	0.1855		0.1938	False		,,,				2504	0.2342				p.K344T		Atlas-SNP	.											.	RPS6KA1	65	.	0			c.A1031C						PASS	.	A	THR/LYS,THR/LYS	209,4197	126.1+/-163.2	5,199,1999	229.0	162.0	185.0		1031,1004	5.5	1.0	1	dbSNP_98	185	2051,6549	357.5+/-330.8	257,1537,2506	yes	missense,missense	RPS6KA1	NM_001006665.1,NM_002953.3	78,78	262,1736,4505	CC,CA,AA		23.8488,4.7435,17.3766	benign,benign	344/745,335/736	26883511	2260,10746	2203	4300	6503	SO:0001583	missense	6195	exon12			AGATCAAGCCACC	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"""ribosomal protein S6 kinase, 90kD, polypeptide 1"""			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.1004A>C	1.37:g.26883511A>C	ENSP00000363283:p.Lys335Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_001006665	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Missense_Mutation	SNP	ENST00000374168.2	37	CCDS284.1	364	0.16666666666666666	7	0.014227642276422764	96	0.26519337016574585	112	0.1958041958041958	149	0.19656992084432717	A	15.44	2.834313	0.50951	0.047435	0.238488	ENSG00000117676	ENST00000374168;ENST00000374166;ENST00000526792;ENST00000374162;ENST00000530003;ENST00000374164;ENST00000531382	T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63	5.49	5.49	0.81192	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.090341	0.85682	D	0.000000	T	0.00012	0.0000	L	0.37897	1.145	0.09310	P	0.999999877667	B;B;B	0.30793	0.088;0.031;0.295	B;B;B	0.29598	0.104;0.012;0.055	T	0.19353	-1.0308	9	0.49607	T	0.09	.	10.011	0.41986	0.9244:0.0:0.0756:0.0	rs2229712;rs3816540;rs11546002;rs58836104;rs3816540	319;344;335	B7Z2K7;Q15418-2;Q15418	.;.;KS6A1_HUMAN	T	335;324;243;243;319;55;344	ENSP00000363283:K335T;ENSP00000363281:K324T;ENSP00000431651:K243T;ENSP00000363277:K243T;ENSP00000432281:K319T;ENSP00000435412:K344T	ENSP00000363277:K243T	K	+	2	0	RPS6KA1	26756098	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.218000	0.77991	2.093000	0.63338	0.533000	0.62120	AAG	A|0.833;C|0.167	0.167	strong		0.577	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953	
TRPM5	29850	hgsc.bcm.edu	37	11	2432964	2432964	+	Silent	SNP	T	T	C	rs2074234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:2432964T>C	ENST00000155858.6	-	17	2516	c.2508A>G	c.(2506-2508)acA>acG	p.T836T	TRPM5_ENST00000452833.1_Silent_p.T838T|TRPM5_ENST00000533060.1_Silent_p.T836T|TRPM5_ENST00000528453.1_Silent_p.T836T	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		TGGCGAGGACTGTGCGGCCAG	0.632													T|||	1658	0.33107	0.2027	0.366	5008	,	,		16312	0.4643		0.3509	False		,,,				2504	0.3221				p.T836T	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.A2508G						PASS	.	T		1061,3343	380.6+/-323.8	126,809,1267	59.0	57.0	58.0		2508	-8.6	0.0	11	dbSNP_96	58	3014,5584	461.1+/-365.4	542,1930,1827	no	coding-synonymous	TRPM5	NM_014555.3		668,2739,3094	CC,CT,TT		35.0547,24.0917,31.3413		836/1166	2432964	4075,8927	2202	4299	6501	SO:0001819	synonymous_variant	29850	exon17			GAGGACTGTGCGG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.2508A>G	11.37:g.2432964T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	89	30	0.337079	NM_014555		Silent	SNP	ENST00000155858.6	37	CCDS31340.1																																																																																			C|0.328;N|0.001;T|0.671	0.328	strong		0.632	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
ARAP3	64411	hgsc.bcm.edu	37	5	141059158	141059158	+	Missense_Mutation	SNP	C	C	G	rs1031904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141059158C>G	ENST00000239440.4	-	4	717	c.652G>C	c.(652-654)Gac>Cac	p.D218H	ARAP3_ENST00000508305.1_Missense_Mutation_p.D140H	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	218			D -> H (in dbSNP:rs1031904).		cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TCTCTTCTGTCGGGGGCTCCT	0.587													C|||	442	0.0882588	0.0159	0.1023	5008	,	,		16997	0.0813		0.1173	False		,,,				2504	0.1534				p.D218H		Atlas-SNP	.											.	ARAP3	139	.	0			c.G652C						PASS	.	C	HIS/ASP	161,4245	109.1+/-147.4	3,155,2045	81.0	75.0	77.0		652	2.2	0.8	5	dbSNP_86	77	1035,7565	218.3+/-256.7	64,907,3329	yes	missense	ARAP3	NM_022481.5	81	67,1062,5374	GG,GC,CC		12.0349,3.6541,9.1958	benign	218/1545	141059158	1196,11810	2203	4300	6503	SO:0001583	missense	64411	exon4			TTCTGTCGGGGGC	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.652G>C	5.37:g.141059158C>G	ENSP00000239440:p.Asp218His	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	151	55	0.364238	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	187	0.08562271062271062	5	0.01016260162601626	40	0.11049723756906077	52	0.09090909090909091	90	0.11873350923482849	C	10.54	1.377946	0.24944	0.036541	0.120349	ENSG00000120318	ENST00000522690;ENST00000508305;ENST00000239440;ENST00000504448	T;T;T	0.18174	2.5;3.2;2.23	5.41	2.22	0.28083	.	0.556823	0.18323	N	0.144753	T	0.00178	0.0005	N	0.19112	0.55	0.09310	P	0.9999975802	P;B	0.41524	0.753;0.435	B;B	0.42851	0.4;0.159	T	0.20107	-1.0285	9	0.46703	T	0.11	.	7.8362	0.29371	0.0:0.6942:0.0:0.3058	rs1031904	140;218	G5E9Y3;Q8WWN8	.;ARAP3_HUMAN	H	140;140;218;218	ENSP00000421826:D140H;ENSP00000239440:D218H;ENSP00000421148:D218H	ENSP00000239440:D218H	D	-	1	0	ARAP3	141039342	0.251000	0.23961	0.765000	0.31456	0.092000	0.18411	0.576000	0.23744	0.665000	0.31066	0.462000	0.41574	GAC	C|0.908;G|0.092	0.092	strong		0.587	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
ZNF20	7568	hgsc.bcm.edu	37	19	12244656	12244656	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12244656C>T	ENST00000334213.5	-	4	569	c.345G>A	c.(343-345)acG>acA	p.T115T	ZNF20_ENST00000485451.1_5'UTR|ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000600335.1_Intron	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	115					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						ATGAATGACCCGTGCCAACTT	0.423																																					p.T115T		Atlas-SNP	.											.	ZNF20	86	.	0			c.G345A						PASS	.						259.0	260.0	259.0					19																	12244656		2117	4252	6369	SO:0001819	synonymous_variant	7568	exon4			ATGACCCGTGCCA	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"""Zinc fingers, C2H2-type"", ""-"""	12992	protein-coding gene	gene with protein product		194557	"""zinc finger protein 20 (KOX 13)"""				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.345G>A	19.37:g.12244656C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	210	112	0.533333	NM_021143	Q8N457|Q9UG41	Silent	SNP	ENST00000334213.5	37	CCDS45986.1																																																																																			.	.	none		0.423	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143	
MUC4	4585	hgsc.bcm.edu	37	3	195513772	195513772	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513772G>A	ENST00000463781.3	-	2	5138	c.4679C>T	c.(4678-4680)tCa>tTa	p.S1560L	MUC4_ENST00000475231.1_Missense_Mutation_p.S1560L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTGGATACTGAGGAAGCGTC	0.577																																					p.S1560L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C4679T						PASS	.						16.0	12.0	13.0					3																	195513772		686	1568	2254	SO:0001583	missense	4585	exon2			GATACTGAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4679C>T	3.37:g.195513772G>A	ENSP00000417498:p.Ser1560Leu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	267	18	0.0674157	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	4.658	0.122338	0.08931	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.57;1.56	.	.	.	.	.	.	.	.	T	0.15305	0.0369	N	0.19112	0.55	0.09310	N	1	B	0.22480	0.07	B	0.14023	0.01	T	0.28004	-1.0057	7	.	.	.	.	4.7275	0.12948	1.0E-4:0.0:0.6493:0.3506	.	1560	E7ESK3	.	L	1560	ENSP00000417498:S1560L;ENSP00000420243:S1560L	.	S	-	2	0	MUC4	196998167	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	0.230000	0.17852	0.064000	0.16427	0.064000	0.15345	TCA	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DDX23	9416	hgsc.bcm.edu	37	12	49230035	49230035	+	Silent	SNP	T	T	G	rs1057908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49230035T>G	ENST00000308025.3	-	11	1330	c.1251A>C	c.(1249-1251)atA>atC	p.I417I	DDX23_ENST00000553182.1_5'Flank	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	417					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						CCTGACGCTGTATAGGTGTTG	0.512													G|||	2366	0.472444	0.4319	0.4323	5008	,	,		20474	0.62		0.4851	False		,,,				2504	0.3906				p.I417I		Atlas-SNP	.											.	DDX23	82	.	0			c.A1251C						PASS	.	G		1841,2565	634.4+/-396.2	378,1085,740	165.0	157.0	160.0		1251	4.6	1.0	12	dbSNP_86	160	4202,4398	585.3+/-391.9	1029,2144,1127	no	coding-synonymous	DDX23	NM_004818.2		1407,3229,1867	GG,GT,TT		48.8605,41.7839,46.4632		417/821	49230035	6043,6963	2203	4300	6503	SO:0001819	synonymous_variant	9416	exon11			ACGCTGTATAGGT	AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"""DEAD-boxes"""	17347	protein-coding gene	gene with protein product		612172	"""PRP28 homolog, yeast"""			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.1251A>C	12.37:g.49230035T>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	223	108	0.484305	NM_004818	B2R600|B4DH15|O43188	Silent	SNP	ENST00000308025.3	37	CCDS8770.1																																																																																			T|0.526;G|0.474	0.474	strong		0.512	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818	
MMD2	221938	hgsc.bcm.edu	37	7	4959807	4959807	+	Silent	SNP	G	G	A	rs932061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4959807G>A	ENST00000404774.3	-	3	479	c.285C>T	c.(283-285)caC>caT	p.H95H	MMD2_ENST00000401401.3_Silent_p.H95H|MMD2_ENST00000406755.1_Silent_p.H95H	NM_001100600.1	NP_001094070.1	Q8IY49	PAQRA_HUMAN	monocyte to macrophage differentiation-associated 2	95						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(11)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		GGCACCTGAGGTGGCTCTTCT	0.657													G|||	2212	0.441693	0.618	0.5951	5008	,	,		16463	0.2996		0.4085	False		,,,				2504	0.2751				p.H95H		Atlas-SNP	.											.	MMD2	63	.	0			c.C285T						PASS	.	G	,	2135,1691		630,875,408	19.0	21.0	20.0		285,285	1.5	1.0	7	dbSNP_86	20	3359,4821		740,1879,1471	yes	coding-synonymous,coding-synonymous	MMD2	NM_001100600.1,NM_198403.3	,	1370,2754,1879	AA,AG,GG		41.0636,44.1976,45.7605	,	95/271,95/247	4959807	5494,6512	1913	4090	6003	SO:0001819	synonymous_variant	221938	exon3			CCTGAGGTGGCTC	BC037881	CCDS47529.1, CCDS47530.1, CCDS59047.1	7p22	2004-06-23			ENSG00000136297	ENSG00000136297			30133	protein-coding gene	gene with protein product		614581				12477932	Standard	NM_198403		Approved	PAQR10	uc003sno.4	Q8IY49	OTTHUMG00000151844	ENST00000404774.3:c.285C>T	7.37:g.4959807G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_198403	B5MBW4|Q6NVU5|Q6TCH0	Silent	SNP	ENST00000404774.3	37	CCDS47529.1																																																																																			G|0.545;A|0.455	0.455	strong		0.657	MMD2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324136.1	NM_198403	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50660064	50660064	+	Silent	SNP	C	C	T	rs140491142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50660064C>T	ENST00000248846.5	-	16	2828	c.2724G>A	c.(2722-2724)ccG>ccA	p.P908P	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Silent_p.P908P			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	908					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TCTGCACGGACGGCTCAGCCC	0.677																																					p.P908P		Atlas-SNP	.											TUBGCP6,NS,carcinoma,0,1	TUBGCP6	132	1	0			c.G2724A						scavenged	.	C		0,4406		0,0,2203	42.0	38.0	39.0		2724	-2.5	0.0	22	dbSNP_134	39	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	TUBGCP6	NM_020461.3		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		908/1820	50660064	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	85378	exon16			CACGGACGGCTCA	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.2724G>A	22.37:g.50660064C>T		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	220	89	0.404545	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			C|0.999;T|0.001	0.001	strong		0.677	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
ALPK2	115701	hgsc.bcm.edu	37	18	56203891	56203891	+	Silent	SNP	G	G	T	rs3809978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56203891G>T	ENST00000361673.3	-	5	3741	c.3528C>A	c.(3526-3528)ccC>ccA	p.P1176P	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1176						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TAGAGCTTGCGGGTGAGTGGG	0.577													T|||	3364	0.671725	0.4675	0.6772	5008	,	,		19124	0.7966		0.7674	False		,,,				2504	0.7168				p.P1176P		Atlas-SNP	.											.	ALPK2	487	.	0			c.C3528A						PASS	.	T		2276,2130	578.0+/-384.6	597,1082,524	89.0	79.0	82.0		3528	-6.0	0.0	18	dbSNP_107	82	6606,1994	347.7+/-326.7	2550,1506,244	no	coding-synonymous	ALPK2	NM_052947.3		3147,2588,768	TT,TG,GG		23.186,48.3432,31.7084		1176/2171	56203891	8882,4124	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			GCTTGCGGGTGAG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3528C>A	18.37:g.56203891G>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			T|0.684;G|0.316;A|0.000	0.684	strong		0.577	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
CBLB	868	hgsc.bcm.edu	37	3	105439026	105439026	+	Silent	SNP	G	G	A	rs2305035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:105439026G>A	ENST00000264122.4	-	10	1593	c.1272C>T	c.(1270-1272)gaC>gaT	p.D424D	CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000405772.1_Silent_p.D424D|CBLB_ENST00000394027.3_Silent_p.D446D|CBLB_ENST00000403724.1_Silent_p.D424D	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	424					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						GATCAAAGGGGTCCACGATTA	0.478			Mis S		AML								G|||	1052	0.210064	0.1929	0.2983	5008	,	,		18868	0.2183		0.2376	False		,,,				2504	0.1339				p.D424D	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.C1272T						PASS	.	G		812,3594	324.5+/-298.6	75,662,1466	100.0	87.0	91.0		1272	0.4	1.0	3	dbSNP_100	91	1845,6755	329.3+/-318.7	205,1435,2660	no	coding-synonymous	CBLB	NM_170662.3		280,2097,4126	AA,AG,GG		21.4535,18.4294,20.429		424/983	105439026	2657,10349	2203	4300	6503	SO:0001819	synonymous_variant	868	exon10			AAAGGGGTCCACG	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.1272C>T	3.37:g.105439026G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	169	75	0.443787	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	37	CCDS2948.1																																																																																			G|0.787;A|0.213	0.213	strong		0.478	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
COL6A2	1292	hgsc.bcm.edu	37	21	47545913	47545913	+	Silent	SNP	G	G	A	rs2839114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47545913G>A	ENST00000300527.4	+	26	2288	c.2184G>A	c.(2182-2184)gtG>gtA	p.V728V	COL6A2_ENST00000357838.4_Silent_p.V728V|COL6A2_ENST00000310645.5_Silent_p.V728V|COL6A2_ENST00000409416.1_Silent_p.V728V|COL6A2_ENST00000397763.1_Silent_p.V728V	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	728	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGTTTGCGGTGGTCATCACGG	0.652													G|||	1613	0.322085	0.1067	0.5548	5008	,	,		14926	0.4226		0.3837	False		,,,				2504	0.2812				p.V728V		Atlas-SNP	.											.	COL6A2	351	.	0			c.G2184A						PASS	.	G	,,	584,3822	256.7+/-261.4	47,490,1666	80.0	77.0	78.0		2184,2184,2184	3.1	1.0	21	dbSNP_100	78	3208,5392	483.3+/-371.1	614,1980,1706	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	661,2470,3372	AA,AG,GG		37.3023,13.2547,29.1558	,,	728/1020,728/919,728/829	47545913	3792,9214	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			TGCGGTGGTCATC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2184G>A	21.37:g.47545913G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	148	62	0.418919	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			G|0.690;A|0.310	0.310	strong		0.652	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
OR5M11	219487	hgsc.bcm.edu	37	11	56310222	56310222	+	Missense_Mutation	SNP	C	C	T	rs628524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56310222C>T	ENST00000528616.2	-	1	535	c.512G>A	c.(511-513)aGt>aAt	p.S171N		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	171			S -> N (in dbSNP:rs628524). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						GTTGATGACACTGGATCTACA	0.483													T|||	3475	0.69389	0.3608	0.7651	5008	,	,		18202	0.875		0.7455	False		,,,				2504	0.8538				p.S171N		Atlas-SNP	.											.	OR5M11	60	.	0			c.G512A						PASS	.	T	ASN/SER	1839,2345		413,1013,666	45.0	47.0	47.0		512	4.0	1.0	11	dbSNP_83	47	6323,2135		2382,1559,288	yes	missense	OR5M11	NM_001005245.1	46	2795,2572,954	TT,TC,CC		25.2424,43.9532,35.4374	benign	171/306	56310222	8162,4480	2092	4229	6321	SO:0001583	missense	219487	exon1			ATGACACTGGATC	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"""GPCR / Class A : Olfactory receptors"""	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.512G>A	11.37:g.56310222C>T	ENSP00000432417:p.Ser171Asn	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_001005245	B2RNL5|B2RNL7	Missense_Mutation	SNP	ENST00000528616.2	37	CCDS53629.1	1477	0.6762820512820513	142	0.2886178861788618	282	0.7790055248618785	498	0.8706293706293706	555	0.7321899736147758	T	1.011	-0.688012	0.03328	0.439532	0.747576	ENSG00000255223	ENST00000528616	T	0.00020	9.04	5.1	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00023	-2.71	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.29792	-1.0000	8	0.02654	T	1	.	8.6362	0.33950	0.0:0.1576:0.0:0.8424	rs628524;rs52808983;rs628524	171	Q96RB7	OR5MB_HUMAN	N	171	ENSP00000432417:S171N	ENSP00000432417:S171N	S	-	2	0	OR5M11	56066798	0.001000	0.12720	1.000000	0.80357	0.900000	0.52787	-0.108000	0.10857	0.447000	0.26695	-0.285000	0.09966	AGT	T|0.660;G|0.007	0.660	strong		0.483	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245	
AGRN	375790	hgsc.bcm.edu	37	1	984302	984302	+	Silent	SNP	T	T	C	rs9442391	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:984302T>C	ENST00000379370.2	+	24	4211	c.4161T>C	c.(4159-4161)acT>acC	p.T1387T		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1387	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		CCTTCCCCACTCTCCGCGCCT	0.687													t|||	2733	0.545727	0.2405	0.6614	5008	,	,		7123	0.8294		0.5636	False		,,,				2504	0.5654				p.T1387T		Atlas-SNP	.											.	AGRN	110	.	0			c.T4161C						PASS	.	C		1203,3103		200,803,1150	7.0	7.0	7.0		4161	-7.4	0.2	1	dbSNP_119	7	4672,3832		1339,1994,919	no	coding-synonymous	AGRN	NM_198576.3		1539,2797,2069	CC,CT,TT		45.0611,27.9378,45.8626		1387/2046	984302	5875,6935	2153	4252	6405	SO:0001819	synonymous_variant	375790	exon24			CCCCACTCTCCGC	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.4161T>C	1.37:g.984302T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			T|0.431;C|0.569	0.569	strong		0.687	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
TRAK2	66008	hgsc.bcm.edu	37	2	202252539	202252539	+	Missense_Mutation	SNP	G	G	A	rs2244438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:202252539G>A	ENST00000332624.3	-	13	2011	c.1583C>T	c.(1582-1584)aCa>aTa	p.T528I		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	528			T -> I (in dbSNP:rs2244438). {ECO:0000269|PubMed:11161814}.		protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						AAGGCTCTCTGTCGGGGTGAC	0.493													G|||	1197	0.239018	0.2095	0.3905	5008	,	,		17694	0.2431		0.3141	False		,,,				2504	0.09				p.T528I		Atlas-SNP	.											.	TRAK2	62	.	0			c.C1583T						PASS	.	G	ILE/THR	1027,3379	380.4+/-323.7	126,775,1302	105.0	100.0	102.0		1583	4.1	0.4	2	dbSNP_100	102	2617,5983	423.0+/-354.2	382,1853,2065	yes	missense	TRAK2	NM_015049.2	89	508,2628,3367	AA,AG,GG		30.4302,23.3091,28.0178	probably-damaging	528/915	202252539	3644,9362	2203	4300	6503	SO:0001583	missense	66008	exon13			CTCTCTGTCGGGG	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.1583C>T	2.37:g.202252539G>A	ENSP00000328875:p.Thr528Ile	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	37	CCDS2347.1	633	0.28983516483516486	111	0.22560975609756098	145	0.4005524861878453	145	0.2534965034965035	232	0.30606860158311344	G	8.488	0.861341	0.17178	0.233091	0.304302	ENSG00000115993	ENST00000332624;ENST00000542292	T	0.45276	0.9	4.94	4.07	0.47477	Trafficking kinesin-binding protein domain (1);	0.566917	0.19621	N	0.109919	T	0.00012	0.0000	M	0.66939	2.045	0.32117	P	0.5885210000000001	B	0.23249	0.082	B	0.20577	0.03	T	0.32134	-0.9918	9	0.72032	D	0.01	.	10.4782	0.44678	0.1554:0.0:0.8446:0.0	rs2244438;rs52836839;rs60941354;rs2244438	528	O60296	TRAK2_HUMAN	I	528;434	ENSP00000328875:T528I	ENSP00000328875:T528I	T	-	2	0	TRAK2	201960784	0.036000	0.19791	0.398000	0.26321	0.143000	0.21401	1.979000	0.40608	1.334000	0.45468	0.655000	0.94253	ACA	G|0.722;A|0.278	0.278	strong		0.493	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
FAT2	2196	hgsc.bcm.edu	37	5	150946436	150946436	+	Missense_Mutation	SNP	A	A	G	rs9324700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150946436A>G	ENST00000261800.5	-	1	2069	c.2057T>C	c.(2056-2058)tTt>tCt	p.F686S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	686			F -> S (in dbSNP:rs9324700).		epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGCCCAATAAAGTGGAGGAT	0.408													G|||	2103	0.419928	0.4418	0.4539	5008	,	,		22865	0.3571		0.4901	False		,,,				2504	0.3589				p.F686S		Atlas-SNP	.											.	FAT2	465	.	0			c.T2057C						PASS	.	G	SER/PHE	1965,2441	619.5+/-393.4	426,1113,664	113.0	108.0	110.0		2057	4.7	0.0	5	dbSNP_119	110	4503,4097	561.2+/-387.7	1184,2135,981	yes	missense	FAT2	NM_001447.2	155	1610,3248,1645	GG,GA,AA		47.6395,44.5983,49.7309	benign	686/4350	150946436	6468,6538	2203	4300	6503	SO:0001583	missense	2196	exon1			CCAATAAAGTGGA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2057T>C	5.37:g.150946436A>G	ENSP00000261800:p.Phe686Ser	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	219	76	0.347032	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	969	0.44368131868131866	238	0.483739837398374	162	0.44751381215469616	201	0.3513986013986014	368	0.48548812664907653	G	0.018	-1.477988	0.01035	0.445983	0.523605	ENSG00000086570	ENST00000261800	T	0.39592	1.07	5.57	4.68	0.58851	.	0.188706	0.38164	N	0.001787	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44205	-0.9343	9	0.05833	T	0.94	.	11.0521	0.47896	0.0668:0.0:0.804:0.1292	rs9324700;rs17717795;rs58284682;rs9324700	686	Q9NYQ8	FAT2_HUMAN	S	686	ENSP00000261800:F686S	ENSP00000261800:F686S	F	-	2	0	FAT2	150926629	0.995000	0.38212	0.004000	0.12327	0.587000	0.36485	4.410000	0.59774	0.816000	0.34421	-0.119000	0.15052	TTT	A|0.534;G|0.466	0.466	strong		0.408	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
PTPRD	5789	hgsc.bcm.edu	37	9	8518052	8518052	+	Missense_Mutation	SNP	G	G	C	rs10977171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:8518052G>C	ENST00000381196.4	-	18	1882	c.1339C>G	c.(1339-1341)Cag>Gag	p.Q447E	PTPRD_ENST00000356435.5_Missense_Mutation_p.Q447E|PTPRD_ENST00000397606.3_Missense_Mutation_p.Q437E|PTPRD_ENST00000397611.3_Missense_Mutation_p.Q444E|PTPRD_ENST00000537002.1_Missense_Mutation_p.Q444E|PTPRD_ENST00000360074.4_Missense_Mutation_p.Q434E|PTPRD_ENST00000358503.5_Missense_Mutation_p.Q434E|PTPRD_ENST00000355233.5_Missense_Mutation_p.Q447E|PTPRD_ENST00000486161.1_Missense_Mutation_p.Q447E|PTPRD_ENST00000397617.3_Missense_Mutation_p.Q437E|PTPRD_ENST00000540109.1_Missense_Mutation_p.Q447E	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	447	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> E (in dbSNP:rs10977171).		heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.Q447E(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CCTTGGATCTGTCCATTTGGC	0.458										TSP Lung(15;0.13)			G|||	255	0.0509185	0.0015	0.0504	5008	,	,		19554	0.121		0.0348	False		,,,				2504	0.0624				p.Q447E		Atlas-SNP	.											PTPRD,NS,carcinoma,0,1	PTPRD	1348	1	1	Substitution - Missense(1)	stomach(1)	c.C1339G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN	36,4370	40.8+/-73.8	0,36,2167	280.0	253.0	262.0		1330,1309,1339,1339,1339,1321	5.3	1.0	9	dbSNP_120	262	385,8215	125.6+/-184.2	9,367,3924	yes	missense,missense,missense,missense,missense,missense	PTPRD	NM_001040712.2,NM_001171025.1,NM_002839.3,NM_130391.3,NM_130392.3,NM_130393.3	29,29,29,29,29,29	9,403,6091	CC,CG,GG		4.4767,0.8171,3.237	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	444/1503,437/1506,447/1913,447/1506,447/1507,441/1497	8518052	421,12585	2203	4300	6503	SO:0001583	missense	5789	exon10			GGATCTGTCCATT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1339C>G	9.37:g.8518052G>C	ENSP00000370593:p.Gln447Glu	Somatic	342	1	0.00292398		WXS	Illumina HiSeq	Phase_I	274	92	0.335766	NM_130392	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	118	0.05402930402930403	1	0.0020325203252032522	16	0.04419889502762431	75	0.13111888111888112	26	0.03430079155672823	G	5.702	0.314073	0.10789	0.008171	0.044767	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44	5.31	5.31	0.75309	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.02342	0.0072	L	0.38649	1.16	0.09310	P	0.9999999202626	P;P;P;P;B;P;P;D;P	0.62365	0.778;0.894;0.88;0.778;0.001;0.938;0.892;0.991;0.613	P;P;P;P;B;P;P;D;B	0.79784	0.639;0.728;0.522;0.639;0.006;0.702;0.551;0.993;0.271	T	0.22173	-1.0224	8	.	.	.	.	18.9787	0.92747	0.0:0.0:1.0:0.0	rs10977171;rs52821081;rs10977171	437;441;447;447;444;444;434;447;447	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	E	447;447;434;434;447;437;444;444;447;447;447;437	ENSP00000370593:Q447E;ENSP00000348812:Q447E;ENSP00000353187:Q434E;ENSP00000351293:Q434E;ENSP00000347373:Q447E;ENSP00000380741:Q437E;ENSP00000380735:Q444E;ENSP00000440515:Q444E;ENSP00000438164:Q447E;ENSP00000417093:Q447E;ENSP00000380731:Q437E	.	Q	-	1	0	PTPRD	8508052	1.000000	0.71417	1.000000	0.80357	0.043000	0.13939	9.807000	0.99171	2.484000	0.83849	0.467000	0.42956	CAG	G|0.951;C|0.049	0.049	strong		0.458	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
SEMA5B	54437	hgsc.bcm.edu	37	3	122642590	122642590	+	Silent	SNP	G	G	A	rs2276778	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122642590G>A	ENST00000357599.3	-	10	1532	c.1146C>T	c.(1144-1146)atC>atT	p.I382I	SEMA5B_ENST00000195173.4_Silent_p.I382I|SEMA5B_ENST00000451055.2_Silent_p.I436I	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	382	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		CAGAAGCCGCGATGCTGTTTC	0.582													G|||	2085	0.416334	0.1861	0.4366	5008	,	,		19040	0.3006		0.6511	False		,,,				2504	0.591				p.I436I		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C1308T						PASS	.	G		1172,3234	408.4+/-334.6	172,828,1203	97.0	94.0	95.0		1146	-10.8	0.0	3	dbSNP_100	95	5751,2849	674.6+/-403.1	1930,1891,479	no	coding-synonymous	SEMA5B	NM_001031702.2		2102,2719,1682	AA,AG,GG		33.1279,26.6001,46.7707		382/1152	122642590	6923,6083	2203	4300	6503	SO:0001819	synonymous_variant	54437	exon10			AGCCGCGATGCTG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1146C>T	3.37:g.122642590G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1																																																																																			G|0.514;A|0.486	0.486	strong		0.582	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
ARSD	414	hgsc.bcm.edu	37	X	2836211	2836211	+	Missense_Mutation	SNP	A	A	T	rs73632977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836211A>T	ENST00000381154.1	-	5	572	c.497T>A	c.(496-498)cTg>cAg	p.L166Q	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	166					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.L166Q(1)		large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCCGTGGTTCAGGGGGTGGTG	0.572																																					p.L166Q		Atlas-SNP	.											.	ARSD	47	.	1	Substitution - Missense(1)	large_intestine(1)	c.T497A						PASS	.						34.0	20.0	25.0					X																	2836211		2200	4289	6489	SO:0001583	missense	414	exon5			TGGTTCAGGGGGT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.497T>A	X.37:g.2836211A>T	ENSP00000370546:p.Leu166Gln	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	142	0.08559373116335142	33	0.07432432432432433	27	0.07988165680473373	33	0.06111111111111111	59	0.081267217630854	a	10.90	1.480007	0.26598	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.94184	-3.37	3.47	3.47	0.39725	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.183165	0.37304	U	0.002147	T	0.65186	0.2667	M	0.79805	2.47	0.80722	P	0.0	D;D	0.61080	0.98;0.989	D;D	0.64877	0.93;0.917	T	0.81662	-0.0831	9	0.62326	D	0.03	.	7.379	0.26845	0.8026:0.0:0.0:0.1974	.	166;166	E9PAW5;P51689	.;ARSD_HUMAN	Q	166	ENSP00000370546:L166Q	ENSP00000217890:L166Q	L	-	2	0	ARSD	2846211	0.026000	0.19158	0.027000	0.17364	0.309000	0.27889	2.195000	0.42677	1.132000	0.42129	0.343000	0.21770	CTG	A|0.913;T|0.087	0.087	strong		0.572	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
LY6D	8581	hgsc.bcm.edu	37	8	143867905	143867905	+	Missense_Mutation	SNP	C	C	T	rs2572925	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143867905C>T	ENST00000301263.4	-	1	103	c.28G>A	c.(28-30)Gcc>Acc	p.A10T	LY6D_ENST00000518434.1_5'UTR|RP11-706C16.8_ENST00000510610.2_RNA	NM_003695.2	NP_003686.1	Q14210	LY6D_HUMAN	lymphocyte antigen 6 complex, locus D	10			A -> T (in dbSNP:rs2572925). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9366413}.		cell adhesion (GO:0007155)|lymphocyte differentiation (GO:0030098)|response to stilbenoid (GO:0035634)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|membrane (GO:0016020)|plasma membrane (GO:0005886)				large_intestine(1)|lung(3)|prostate(1)	5	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					ACAGCCAGGGCTGCAAGGAGC	0.662													C|||	1812	0.361821	0.4841	0.4049	5008	,	,		226	0.1865		0.3996	False		,,,				2504	0.3078				p.A10T		Atlas-SNP	.											.	LY6D	10	.	0			c.G28A						PASS	.	C	THR/ALA	1754,2194		417,920,637	16.0	14.0	15.0		28	-0.7	0.0	8	dbSNP_100	15	2774,4930		553,1668,1631	yes	missense	LY6D	NM_003695.2	58	970,2588,2268	TT,TC,CC		36.0073,44.4276,38.8603	possibly-damaging	10/129	143867905	4528,7124	1974	3852	5826	SO:0001583	missense	8581	exon1			CCAGGGCTGCAAG	U66837	CCDS6390.1	8q24	2004-07-06			ENSG00000167656	ENSG00000167656			13348	protein-coding gene	gene with protein product		606204				7790363, 9551972	Standard	NM_003695		Approved	E48	uc003yxf.1	Q14210	OTTHUMG00000164693	ENST00000301263.4:c.28G>A	8.37:g.143867905C>T	ENSP00000301263:p.Ala10Thr	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	127	122	0.96063	NM_003695	B2R5F1|D3DWJ0|O43783|Q6GTV9|Q8TBD4|Q92933	Missense_Mutation	SNP	ENST00000301263.4	37	CCDS6390.1	784	0.358974358974359	235	0.47764227642276424	130	0.35911602209944754	129	0.22552447552447552	290	0.38258575197889183	c	7.205	0.594206	0.13875	0.444276	0.360073	ENSG00000167656	ENST00000301263	T	0.26518	1.73	3.32	-0.69	0.11309	.	2.614030	0.02032	N	0.048634	T	0.00012	0.0000	M	0.65498	2.005	0.80722	P	0.0	P	0.37525	0.598	B	0.34301	0.179	T	0.44205	-0.9343	9	0.30078	T	0.28	-8.6153	8.2882	0.31941	0.0:0.5788:0.0:0.4212	rs2572925;rs11553465;rs17852948;rs57621469;rs2572925	10	Q14210	LY6D_HUMAN	T	10	ENSP00000301263:A10T	ENSP00000301263:A10T	A	-	1	0	LY6D	143864907	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.314000	0.01125	-0.442000	0.07190	-1.688000	0.00730	GCC	C|0.637;T|0.363	0.363	strong		0.662	LY6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379774.1	NM_003695	
QRICH2	84074	hgsc.bcm.edu	37	17	74290008	74290008	+	Missense_Mutation	SNP	G	G	T	rs62621822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74290008G>T	ENST00000262765.5	-	4	481	c.302C>A	c.(301-303)cCa>cAa	p.P101Q		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	101										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CTCAATACTTGGTTGCTTGGT	0.527													G|||	37	0.00738818	0.0	0.0101	5008	,	,		18679	0.0		0.0278	False		,,,				2504	0.002				p.P101Q		Atlas-SNP	.											.	QRICH2	143	.	0			c.C302A						PASS	.	G	GLN/PRO	25,4381	31.7+/-61.6	0,25,2178	104.0	104.0	104.0		302	0.7	0.0	17	dbSNP_129	104	252,8348	100.8+/-162.1	1,250,4049	yes	missense	QRICH2	NM_032134.1	76	1,275,6227	TT,TG,GG		2.9302,0.5674,2.1298	probably-damaging	101/1664	74290008	277,12729	2203	4300	6503	SO:0001583	missense	84074	exon4			ATACTTGGTTGCT	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.302C>A	17.37:g.74290008G>T	ENSP00000262765:p.Pro101Gln	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	G	11.32	1.603688	0.28534	0.005674	0.029302	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.09630	2.96	3.74	0.655	0.17839	.	.	.	.	.	T	0.06781	0.0173	M	0.66939	2.045	0.09310	N	1	D;P	0.58268	0.982;0.899	P;P	0.54889	0.763;0.571	T	0.06625	-1.0816	9	0.72032	D	0.01	-0.0019	5.8311	0.18581	0.3459:0.0:0.6541:0.0	rs62621822	101;101	B5MD94;Q9H0J4	.;QRIC2_HUMAN	Q	101	ENSP00000262765:P101Q	ENSP00000262765:P101Q	P	-	2	0	QRICH2	71801603	0.000000	0.05858	0.000000	0.03702	0.147000	0.21601	0.394000	0.20834	0.197000	0.20387	-0.251000	0.11542	CCA	G|0.982;T|0.018	0.018	strong		0.527	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
NRXN3	9369	hgsc.bcm.edu	37	14	79270093	79270093	+	Silent	SNP	G	G	A	rs2288140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:79270093G>A	ENST00000554719.1	+	6	1547	c.1056G>A	c.(1054-1056)acG>acA	p.T352T	NRXN3_ENST00000335750.5_Silent_p.T352T	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	129					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TGGTGGCTACGACCTCCAGGG	0.552													G|||	573	0.114417	0.1543	0.0879	5008	,	,		17640	0.1101		0.0517	False		,,,				2504	0.1483				p.T352T		Atlas-SNP	.											NRXN3,colon,carcinoma,+1,1	NRXN3	342	1	0			c.G1056A						PASS	.	G		584,3822	256.7+/-261.4	42,500,1661	150.0	112.0	125.0		1056	-12.3	0.0	14	dbSNP_100	125	324,8276	113.7+/-173.7	4,316,3980	no	coding-synonymous	NRXN3	NM_004796.4		46,816,5641	AA,AG,GG		3.7674,13.2547,6.9814		352/1062	79270093	908,12098	2203	4300	6503	SO:0001819	synonymous_variant	9369	exon6			GGCTACGACCTCC	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"""chromosome 14 open reading frame 60"""	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.1056G>A	14.37:g.79270093G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Silent	SNP	ENST00000554719.1	37	CCDS9870.1																																																																																			G|0.920;A|0.080	0.080	strong		0.552	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250	
TMA16	55319	hgsc.bcm.edu	37	4	164435265	164435265	+	Missense_Mutation	SNP	A	A	C	rs2304802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:164435265A>C	ENST00000358572.5	+	4	535	c.194A>C	c.(193-195)cAa>cCa	p.Q65P	TMA16_ENST00000511562.1_3'UTR|TMA16_ENST00000513272.1_Missense_Mutation_p.Q65P|TMA16_ENST00000508268.1_Missense_Mutation_p.Q65P|TMA16_ENST00000513134.1_Missense_Mutation_p.Q65P	NM_018352.2	NP_060822.2	Q96EY4	TMA16_HUMAN	translation machinery associated 16 homolog (S. cerevisiae)	65			Q -> P (in dbSNP:rs2304802). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)		p.Q65P(2)									CTTGATCCCCAAAAAAAGAGA	0.358													A|||	1903	0.379992	0.2504	0.6009	5008	,	,		19903	0.3423		0.4682	False		,,,				2504	0.3466				p.Q65P		Atlas-SNP	.											C4orf43,NS,carcinoma,0,2	.	.	2	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.A194C						PASS	.	A	PRO/GLN	977,2675		145,687,994	95.0	86.0	89.0		194	3.0	0.1	4	dbSNP_100	89	3823,4325		962,1899,1213	yes	missense	C4orf43	NM_018352.2	76	1107,2586,2207	CC,CA,AA		46.9195,26.7525,40.678	benign	65/204	164435265	4800,7000	1826	4074	5900	SO:0001583	missense	55319	exon4			ATCCCCAAAAAAA		CCDS43278.1	4q32.3	2012-03-02	2012-03-02	2012-03-02	ENSG00000198498	ENSG00000198498			25638	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 43"""	C4orf43		12477932	Standard	NM_018352		Approved	FLJ11184	uc003iqq.4	Q96EY4	OTTHUMG00000161528	ENST00000358572.5:c.194A>C	4.37:g.164435265A>C	ENSP00000351380:p.Gln65Pro	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_018352	Q0P6E4|Q0P6J1|Q9NUR7	Missense_Mutation	SNP	ENST00000358572.5	37	CCDS43278.1	901	0.4125457875457875	124	0.25203252032520324	216	0.5966850828729282	197	0.34440559440559443	364	0.48021108179419525	A	6.442	0.449727	0.12223	0.267525	0.469195	ENSG00000198498	ENST00000358572;ENST00000513272;ENST00000513134;ENST00000508268	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.39	2.96	0.34315	.	0.787793	0.12848	N	0.434179	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40608	-0.9554	9	0.37606	T	0.19	-0.3681	8.7145	0.34403	0.8405:0.0:0.1595:0.0	rs2304802;rs3207214;rs17576322;rs17850804;rs52811362;rs2304802	65	Q96EY4	CD043_HUMAN	P	65	ENSP00000351380:Q65P;ENSP00000426933:Q65P;ENSP00000423901:Q65P;ENSP00000423375:Q65P	ENSP00000351380:Q65P	Q	+	2	0	C4orf43	164654715	0.002000	0.14202	0.068000	0.19968	0.570000	0.35934	1.401000	0.34589	0.978000	0.38470	0.528000	0.53228	CAA	C|0.418;N|0.000	0.418	strong		0.358	TMA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365208.1	NM_018352	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232596728	232596728	+	Silent	SNP	G	G	A	rs74807360	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:232596728G>A	ENST00000366630.1	-	9	3358	c.3000C>T	c.(2998-3000)gcC>gcT	p.A1000A	SIPA1L2_ENST00000262861.4_Silent_p.A1000A|SIPA1L2_ENST00000308942.4_Silent_p.A74A			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1000	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GGGTCAGAGTGGCCACGGCTA	0.572													G|||	137	0.0273562	0.0023	0.0519	5008	,	,		19230	0.001		0.0785	False		,,,				2504	0.0184				p.A1000A		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C3000T						PASS	.	G		55,4351	49.6+/-84.7	0,55,2148	45.0	49.0	47.0		3000	4.7	1.0	1	dbSNP_132	47	610,7990	153.4+/-207.8	21,568,3711	no	coding-synonymous	SIPA1L2	NM_020808.3		21,623,5859	AA,AG,GG		7.093,1.2483,5.113		1000/1723	232596728	665,12341	2203	4300	6503	SO:0001819	synonymous_variant	57568	exon8			CAGAGTGGCCACG	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.3000C>T	1.37:g.232596728G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	139	57	0.410072	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			G|0.947;A|0.053	0.053	strong		0.572	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
SPTBN5	51332	hgsc.bcm.edu	37	15	42162713	42162713	+	Silent	SNP	G	G	A	rs61753871	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42162713G>A	ENST00000320955.6	-	30	5720	c.5493C>T	c.(5491-5493)caC>caT	p.H1831H		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1831					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTCGGAGCGCGTGGCCTCGGG	0.657													G|||	151	0.0301518	0.0008	0.0533	5008	,	,		17035	0.0129		0.0378	False		,,,				2504	0.0634				p.H1796H		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C5388T						PASS	.	G		29,4053		0,29,2012	64.0	69.0	67.0		5388	-1.9	0.0	15	dbSNP_129	67	323,8039		10,303,3868	no	coding-synonymous	SPTBN5	NM_016642.2		10,332,5880	AA,AG,GG		3.8627,0.7104,2.8287		1796/3640	42162713	352,12092	2041	4181	6222	SO:0001819	synonymous_variant	51332	exon30			GAGCGCGTGGCCT	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.5493C>T	15.37:g.42162713G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_016642		Silent	SNP	ENST00000320955.6	37																																																																																				G|0.968;A|0.032	0.032	strong		0.657	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
CYP19A1	1588	hgsc.bcm.edu	37	15	51529112	51529112	+	Silent	SNP	T	T	C	rs700518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:51529112T>C	ENST00000396402.1	-	3	393	c.240A>G	c.(238-240)gtA>gtG	p.V80V	CYP19A1_ENST00000396404.4_Silent_p.V80V|CYP19A1_ENST00000557858.1_Silent_p.V80V|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000405913.3_Silent_p.V80V|CYP19A1_ENST00000559878.1_Silent_p.V80V|CYP19A1_ENST00000260433.2_Silent_p.V80V	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	80					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.V80V(1)		endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	ATTCTCCATATACCCGGTTGT	0.488													C|||	1632	0.325879	0.1619	0.3156	5008	,	,		18329	0.4385		0.4692	False		,,,				2504	0.2914				p.V80V	Melanoma(142;1016 1807 39614 48966 51721)	Atlas-SNP	.											CYP19A1,NS,adenoma,0,2	CYP19A1	75	2	1	Substitution - coding silent(1)	stomach(1)	c.A240G						PASS	.	C	,	941,3451	735.8+/-410.7	111,719,1366	130.0	125.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	240,240	4.1	1.0	15	dbSNP_86	126	4310,4276	575.0+/-390.2	1068,2174,1051	no	coding-synonymous,coding-synonymous	CYP19A1	NM_000103.3,NM_031226.2	,	1179,2893,2417	CC,CT,TT		49.802,21.4253,40.4608	,	80/504,80/504	51529112	5251,7727	2196	4293	6489	SO:0001819	synonymous_variant	1588	exon4			TCCATATACCCGG	D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"""Cytochrome P450s"""	2594	protein-coding gene	gene with protein product		107910	"""cytochrome P450, subfamily XIX (aromatization of androgens)"""	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.240A>G	15.37:g.51529112T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_031226	Q16731|Q3B764|Q58FA0|Q8IYJ7	Silent	SNP	ENST00000396402.1	37	CCDS10139.1																																																																																			T|0.612;C|0.388	0.388	strong		0.488	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254669.1		
MRGPRX3	117195	hgsc.bcm.edu	37	11	18159669	18159669	+	Nonsense_Mutation	SNP	G	G	A	rs386751136|rs78408237	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18159669G>A	ENST00000396275.2	+	3	1281	c.920G>A	c.(919-921)tGg>tAg	p.W307*		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	307				W -> Q (in Ref. 5; AAH67292). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GGTGGAGGGTGGCTTCCTCAG	0.572													.|||	170	0.0339457	0.0083	0.0591	5008	,	,		19533	0.0079		0.0855	False		,,,				2504	0.0245				p.W307X		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.G920A						PASS	.	G	stop/TRP	55,4345		1,53,2146	40.0	43.0	42.0		920	0.3	0.0	11	dbSNP_131	42	649,7937		39,571,3683	no	stop-gained	MRGPRX3	NM_054031.3		40,624,5829	AA,AG,GG		7.5588,1.25,5.4212		307/323	18159669	704,12282	2200	4293	6493	SO:0001587	stop_gained	117195	exon3			GAGGGTGGCTTCC		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.920G>A	11.37:g.18159669G>A	ENSP00000379571:p.Trp307*	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Nonsense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	88	0.040293040293040296	5	0.01016260162601626	25	0.06906077348066299	5	0.008741258741258742	53	0.06992084432717678	G	16.34	3.094591	0.56075	0.0125	0.075588	ENSG00000179826	ENST00000396275	.	.	.	1.3	0.321	0.15883	.	1.239230	0.05408	N	0.541893	.	.	.	.	.	.	0.49798	P	1.7400000000000748E-4	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	3.9345	0.09299	0.2529:0.0:0.7471:0.0	.	.	.	.	X	307	.	ENSP00000379571:W307X	W	+	2	0	MRGPRX3	18116245	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.096000	0.11059	0.105000	0.17753	-1.112000	0.02068	TGG	G|0.948;A|0.052	0.052	strong		0.572	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
CATSPER3	347732	hgsc.bcm.edu	37	5	134345062	134345062	+	Splice_Site	SNP	A	A	G	rs72800379	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:134345062A>G	ENST00000282611.6	+	6	904	c.818A>G	c.(817-819)gAc>gGc	p.D273G		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	273					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACTCTCTAGGACTCCATCAGA	0.562													A|||	2	0.000399361	0.0	0.0	5008	,	,		21912	0.0		0.002	False		,,,				2504	0.0				p.D273G		Atlas-SNP	.											.	CATSPER3	38	.	0			c.A818G						PASS	.	A	GLY/ASP	3,4403	8.1+/-20.4	0,3,2200	131.0	121.0	125.0		818	2.6	1.0	5	dbSNP_130	125	26,8574	19.2+/-60.6	0,26,4274	yes	missense-near-splice	CATSPER3	NM_178019.2	94	0,29,6474	GG,GA,AA		0.3023,0.0681,0.223	probably-damaging	273/399	134345062	29,12977	2203	4300	6503	SO:0001630	splice_region_variant	347732	exon6			TCTAGGACTCCAT	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.817-1A>G	5.37:g.134345062A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	96	61	0.635417	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	8.757	0.922728	0.18056	6.81E-4	0.003023	ENSG00000152705	ENST00000282611	D	0.97256	-4.31	5.18	2.63	0.31362	.	0.441063	0.21510	N	0.073389	D	0.94440	0.8211	L	0.59436	1.845	0.32616	N	0.523999	P	0.46987	0.888	B	0.42062	0.374	D	0.92979	0.6404	10	0.59425	D	0.04	-12.8622	5.9345	0.19158	0.6619:0.1727:0.0:0.1654	.	273	Q86XQ3	CTSR3_HUMAN	G	273	ENSP00000282611:D273G	ENSP00000282611:D273G	D	+	2	0	CATSPER3	134372961	0.982000	0.34865	0.995000	0.50966	0.200000	0.23975	1.330000	0.33781	0.430000	0.26230	0.533000	0.62120	GAC	A|0.998;G|0.002	0.002	strong		0.562	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	Missense_Mutation
DSPP	1834	hgsc.bcm.edu	37	4	88536472	88536472	+	Silent	SNP	C	C	T	rs561406193		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536472C>T	ENST00000282478.7	+	4	2691	c.2658C>T	c.(2656-2658)aaC>aaT	p.N886N	DSPP_ENST00000399271.1_Silent_p.N886N|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	886	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcaacgaaagcagca	0.493																																					p.N886N		Atlas-SNP	.											.	DSPP	174	.	0			c.C2658T						PASS	.						72.0	87.0	82.0					4																	88536472		1623	2913	4536	SO:0001819	synonymous_variant	1834	exon5			CAGCAACGAAAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2658C>T	4.37:g.88536472C>T		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	293	21	0.0716724	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.493	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
OR4N2	390429	hgsc.bcm.edu	37	14	20296010	20296010	+	Missense_Mutation	SNP	G	G	C	rs17114261	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20296010G>C	ENST00000315947.1	+	1	403	c.403G>C	c.(403-405)Gtc>Ctc	p.V135L	OR4N2_ENST00000568211.1_Missense_Mutation_p.V135L	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	135			V -> L (in dbSNP:rs17114261).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTATCCTACTGTCATGAACCC	0.522																																					p.V135L		Atlas-SNP	.											.	OR4N2	125	.	0			c.G403C						PASS	.	G	LEU/VAL	1121,3285		87,947,1169	209.0	221.0	217.0		403	-0.6	0.4	14	dbSNP_123	217	1852,6748		73,1706,2521	no	missense	OR4N2	NM_001004723.1	32	160,2653,3690	CC,CG,GG		21.5349,25.4426,22.8587	benign	135/308	20296010	2973,10033	2203	4300	6503	SO:0001583	missense	390429	exon1			CCTACTGTCATGA		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.403G>C	14.37:g.20296010G>C	ENSP00000319601:p.Val135Leu	Somatic	395	1	0.00253165		WXS	Illumina HiSeq	Phase_I	429	205	0.477855	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	419	0.19184981684981686	136	0.2764227642276423	62	0.1712707182320442	67	0.11713286713286714	154	0.20316622691292877	.	8.615	0.889998	0.17540	0.254426	0.215349	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.01092	5.35;5.35	4.53	-0.609	0.11608	GPCR, rhodopsin-like superfamily (1);	0.151669	0.30800	N	0.008845	T	0.00012	0.0000	N	0.02830	-0.485	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.12156	0.007	T	0.48536	-0.9027	9	0.66056	D	0.02	-16.9757	4.4754	0.11733	0.4631:0.1668:0.3701:0.0	rs17114261	135	Q8NGD1	OR4N2_HUMAN	L	135	ENSP00000452022:V135L;ENSP00000319601:V135L	ENSP00000319601:V135L	V	+	1	0	OR4N2	19365850	0.000000	0.05858	0.387000	0.26183	0.524000	0.34500	-0.609000	0.05635	-0.010000	0.14271	0.591000	0.81541	GTC	G|0.824;C|0.176	0.176	strong		0.522	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
SEC16B	89866	hgsc.bcm.edu	37	1	177902387	177902387	+	Missense_Mutation	SNP	C	C	A	rs61745560	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177902387C>A	ENST00000308284.6	-	22	2874	c.2785G>T	c.(2785-2787)Gct>Tct	p.A929S	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	929				A -> S (in Ref. 4; CAI46016). {ECO:0000305}.	COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						TCGTCTCCAGCGGGGGATGCG	0.592													A|||	1139	0.227436	0.2655	0.2608	5008	,	,		17935	0.1052		0.2604	False		,,,				2504	0.2444				p.A929S		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2785T						PASS	.	A	SER/ALA	1116,2828		153,810,1009	29.0	35.0	33.0		2785	2.7	0.3	1	dbSNP_129	33	1952,6404		231,1490,2457	yes	missense	SEC16B	NM_033127.2	99	384,2300,3466	AA,AC,CC		23.3605,28.2961,24.9431	benign	929/1061	177902387	3068,9232	1972	4178	6150	SO:0001583	missense	89866	exon22			CTCCAGCGGGGGA	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2785G>T	1.37:g.177902387C>A	ENSP00000308339:p.Ala929Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	113	60	0.530973	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	484	0.2216117216117216	114	0.23170731707317074	95	0.26243093922651933	73	0.12762237762237763	202	0.26649076517150394	A	9.107	1.005487	0.19199	0.282961	0.233605	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.13089	2.62	5.19	2.68	0.31781	.	0.478491	0.19860	N	0.104444	T	0.00012	0.0000	N	0.00325	-1.645	0.49483	P	2.0299999999995322E-4	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.43360	-0.9396	9	0.10636	T	0.68	-11.2487	4.9398	0.13960	0.4842:0.1644:0.0:0.3515	rs61745560	484;930;929;626	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	S	929;613;644	ENSP00000308339:A929S	ENSP00000239472:A644S	A	-	1	0	AL359075.1	176169010	0.563000	0.26594	0.314000	0.25224	0.002000	0.02628	0.987000	0.29603	0.287000	0.22375	-0.256000	0.11100	GCT	C|0.774;A|0.226	0.226	strong		0.592	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
HIST3H3	8290	hgsc.bcm.edu	37	1	228612838	228612838	+	Silent	SNP	G	G	T	rs2230656	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228612838G>T	ENST00000366696.1	-	1	188	c.189C>A	c.(187-189)atC>atA	p.I63I		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	63					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				GCAACTTGCGGATTAGCAGCT	0.657													g|||	3457	0.690296	0.3116	0.8977	5008	,	,		16875	0.6895		0.8847	False		,,,				2504	0.8558				p.I63I		Atlas-SNP	.											.	HIST3H3	20	.	0			c.C189A						PASS	.	G		1838,2568	535.0+/-374.1	365,1108,730	85.0	88.0	87.0		189	-0.3	1.0	1	dbSNP_98	87	7613,987	774.0+/-407.7	3366,881,53	no	coding-synonymous	HIST3H3	NM_003493.2		3731,1989,783	TT,TG,GG		11.4767,41.7158,27.3335		63/137	228612838	9451,3555	2203	4300	6503	SO:0001819	synonymous_variant	8290	exon1			CTTGCGGATTAGC	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"""Histones / Replication-dependent"""	4778	protein-coding gene	gene with protein product		602820	"""H3 histone family, member T"", ""histone 3, H3"""	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.189C>A	1.37:g.228612838G>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	166	166	1	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			G|0.291;T|0.709	0.709	strong		0.657	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493	
APOBR	55911	hgsc.bcm.edu	37	16	28507644	28507644	+	Missense_Mutation	SNP	C	C	G	rs180743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28507644C>G	ENST00000431282.1	+	3	1265	c.1255C>G	c.(1255-1257)Ccc>Gcc	p.P419A	CLN3_ENST00000567160.1_5'Flank|CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000564831.1_Missense_Mutation_p.P428A|APOBR_ENST00000328423.5_Missense_Mutation_p.P419A			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	419	Glu-rich.		P -> A (in dbSNP:rs180743). {ECO:0000269|PubMed:10852956, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15830122}.		cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)	p.P419A(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						CCCCAAACAGCCCCAGGTCCT	0.612													G|||	1508	0.301118	0.4107	0.4308	5008	,	,		17646	0.1042		0.3479	False		,,,				2504	0.2157				p.P428A		Atlas-SNP	.											APOBR,NS,carcinoma,0,1	APOBR	89	1	1	Substitution - Missense(1)	stomach(1)	c.C1282G						PASS	.	G	ALA/PRO	1629,2351		356,917,717	37.0	42.0	40.0		1255	0.5	0.1	16	dbSNP_79	40	3245,5083		660,1925,1579	yes	missense	APOBR	NM_018690.3	27	1016,2842,2296	GG,GC,CC		38.9649,40.9296,39.6003	benign	419/1089	28507644	4874,7434	1990	4164	6154	SO:0001583	missense	55911	exon2			AAACAGCCCCAGG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1255C>G	16.37:g.28507644C>G	ENSP00000416094:p.Pro419Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		622	0.2847985347985348	173	0.3516260162601626	125	0.3453038674033149	63	0.11013986013986014	261	0.34432717678100266	G	9.659	1.143564	0.21205	0.409296	0.389649	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.41758	0.99;0.99	4.07	0.489	0.16854	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.43147	-0.9409	5	0.06891	T	0.86	0.1921	4.273	0.10796	0.2827:0.3855:0.3317:0.0	rs180743;rs181201;rs180743	.	.	.	A	419	ENSP00000327669:P419A;ENSP00000416094:P419A	ENSP00000327669:P419A	P	+	1	0	APOBR	28415145	0.000000	0.05858	0.097000	0.21041	0.649000	0.38597	-0.438000	0.06905	-0.054000	0.13266	-0.291000	0.09656	CCC	C|0.698;G|0.302	0.302	strong		0.612	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
ABCB4	5244	hgsc.bcm.edu	37	7	87082292	87082292	+	Silent	SNP	G	G	A	rs1202283	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:87082292G>A	ENST00000265723.4	-	6	615	c.504C>T	c.(502-504)aaC>aaT	p.N168N	ABCB4_ENST00000358400.3_Silent_p.N168N|ABCB4_ENST00000359206.3_Silent_p.N168N|ABCB4_ENST00000545634.1_Silent_p.N168N|ABCB4_ENST00000453593.1_Silent_p.N168N	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	168	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	CAGTGGTGTCGTTGATGTCAA	0.373													G|||	1742	0.347843	0.0189	0.4885	5008	,	,		18668	0.3839		0.5527	False		,,,				2504	0.4448				p.N168N		Atlas-SNP	.											.	ABCB4	177	.	0			c.C504T						PASS	.	G	,,	541,3865	246.2+/-254.9	34,473,1696	121.0	110.0	113.0		504,504,504	-11.5	0.0	7	dbSNP_87	113	4715,3885	607.6+/-395.3	1299,2117,884	yes	coding-synonymous,coding-synonymous,coding-synonymous	ABCB4	NM_000443.3,NM_018849.2,NM_018850.2	,,	1333,2590,2580	AA,AG,GG		45.1744,12.2787,40.4121	,,	168/1280,168/1287,168/1233	87082292	5256,7750	2203	4300	6503	SO:0001819	synonymous_variant	5244	exon6			GGTGTCGTTGATG	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.504C>T	7.37:g.87082292G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	37	CCDS5606.1																																																																																			G|0.614;A|0.386	0.386	strong		0.373	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443	
MYOM2	9172	hgsc.bcm.edu	37	8	2054171	2054171	+	Silent	SNP	C	C	T	rs3817705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:2054171C>T	ENST00000262113.4	+	22	3015	c.2874C>T	c.(2872-2874)atC>atT	p.I958I	MYOM2_ENST00000523438.1_Silent_p.I383I	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	958	Ig-like C2-type 3.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GGTTTAAAATCGAAACCGTGG	0.448													C|||	1277	0.254992	0.1006	0.3098	5008	,	,		17185	0.2282		0.4135	False		,,,				2504	0.2894				p.I958I		Atlas-SNP	.											.	MYOM2	251	.	0			c.C2874T						PASS	.	C		679,3727	285.7+/-278.4	50,579,1574	100.0	99.0	100.0		2874	-8.0	0.0	8	dbSNP_107	100	3484,5116	510.1+/-377.4	715,2054,1531	no	coding-synonymous	MYOM2	NM_003970.2		765,2633,3105	TT,TC,CC		40.5116,15.4108,32.0083		958/1466	2054171	4163,8843	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon22			TAAAATCGAAACC		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2874C>T	8.37:g.2054171C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			C|0.707;T|0.293	0.293	strong		0.448	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
ALOX12	239	hgsc.bcm.edu	37	17	6902743	6902743	+	Silent	SNP	G	G	A	rs1042356	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6902743G>A	ENST00000251535.6	+	6	818	c.765G>A	c.(763-765)tcG>tcA	p.S255S	RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000574377.1_3'UTR|AC027763.2_ENST00000575727.1_3'UTR	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	255	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						TGCTGCCCTCGGGGATGGAAG	0.557													G|||	3014	0.601837	0.6793	0.67	5008	,	,		18855	0.5208		0.5984	False		,,,				2504	0.5358				p.S255S		Atlas-SNP	.											.	ALOX12	49	.	0			c.G765A						PASS	.	G		2904,1502	675.6+/-403.1	953,998,252	124.0	103.0	110.0		765	-10.3	0.0	17	dbSNP_86	110	4969,3631	624.6+/-397.6	1437,2095,768	no	coding-synonymous	ALOX12	NM_000697.2		2390,3093,1020	AA,AG,GG		42.2209,34.0899,39.4664		255/664	6902743	7873,5133	2203	4300	6503	SO:0001819	synonymous_variant	239	exon6			GCCCTCGGGGATG	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.765G>A	17.37:g.6902743G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	161	78	0.484472	NM_000697	O95569|Q6ISF8|Q9UQM4	Silent	SNP	ENST00000251535.6	37	CCDS11084.1																																																																																			G|0.402;A|0.598	0.598	strong		0.557	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
MUC4	4585	hgsc.bcm.edu	37	3	195515134	195515134	+	Missense_Mutation	SNP	G	G	T	rs374418206		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515134G>T	ENST00000463781.3	-	2	3776	c.3317C>A	c.(3316-3318)cCt>cAt	p.P1106H	MUC4_ENST00000475231.1_Missense_Mutation_p.P1106H|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	538					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P1106H(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTCGGTGACAGGAAGAGAGGT	0.572																																					p.P1106H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	2	Substitution - Missense(2)	skin(2)	c.C3317A						scavenged	.						8.0	7.0	7.0					3																	195515134		649	1454	2103	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3317C>A	3.37:g.195515134G>T	ENSP00000417498:p.Pro1106His	Somatic	361	1	0.00277008		WXS	Illumina HiSeq	Phase_I	205	19	0.0926829	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	4.963	0.178958	0.09443	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34072	1.38;1.38	0.814	0.814	0.18756	.	.	.	.	.	T	0.38427	0.1040	N	0.19112	0.55	0.09310	N	1	D	0.76494	0.999	D	0.77557	0.99	T	0.21655	-1.0239	8	.	.	.	.	7.6132	0.28142	0.0:0.0:1.0:0.0	.	1106	E7ESK3	.	H	1106	ENSP00000417498:P1106H;ENSP00000420243:P1106H	.	P	-	2	0	MUC4	196999529	0.103000	0.21917	0.003000	0.11579	0.286000	0.27126	3.387000	0.52501	0.776000	0.33473	0.064000	0.15345	CCT	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
QRFPR	84109	hgsc.bcm.edu	37	4	122301595	122301595	+	Missense_Mutation	SNP	C	C	A	rs55693553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:122301595C>A	ENST00000394427.2	-	1	619	c.208G>T	c.(208-210)Gtg>Ttg	p.V70L	QRFPR_ENST00000334383.5_Missense_Mutation_p.V70L	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	70					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						CTGCGGGTCACCACGTAGAAC	0.612													C|||	38	0.00758786	0.0008	0.0187	5008	,	,		15467	0.0		0.0239	False		,,,				2504	0.0				p.V70L		Atlas-SNP	.											.	QRFPR	65	.	0			c.G208T						PASS	.						93.0	74.0	81.0					4																	122301595		2203	4300	6503	SO:0001583	missense	84109	exon1			GGGTCACCACGTA	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.208G>T	4.37:g.122301595C>A	ENSP00000377948:p.Val70Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	180	94	0.522222	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	26.5	4.740826	0.89573	.	.	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.35048	1.33;1.33	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.054824	0.64402	D	0.000001	T	0.24236	0.0587	L	0.46947	1.48	0.58432	D	0.999997	P;P;P	0.47841	0.626;0.901;0.88	B;P;P	0.45610	0.233;0.487;0.47	T	0.04078	-1.0979	10	0.34782	T	0.22	.	18.2778	0.90088	0.0:1.0:0.0:0.0	rs55693553;rs61741355	70;70;70	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	L	70	ENSP00000377948:V70L;ENSP00000335610:V70L	ENSP00000335610:V70L	V	-	1	0	QRFPR	122521045	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.614000	0.46359	2.383000	0.81215	0.467000	0.42956	GTG	C|0.987;A|0.013	0.013	strong		0.612	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
IL1RN	3557	hgsc.bcm.edu	37	2	113887207	113887207	+	Silent	SNP	T	T	C	rs419598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113887207T>C	ENST00000409930.3	+	2	235	c.171T>C	c.(169-171)gcT>gcC	p.A57A	IL1RN_ENST00000259206.5_Silent_p.A60A|IL1RN_ENST00000361779.3_Silent_p.A23A|IL1RN_ENST00000409052.1_Silent_p.A23A|IL1RN_ENST00000354115.2_Silent_p.A39A	NM_173842.2	NP_776214.1	P18510	IL1RA_HUMAN	interleukin 1 receptor antagonist	57					acute-phase response (GO:0006953)|carboxylic acid metabolic process (GO:0019752)|chronic inflammatory response to antigenic stimulus (GO:0002439)|female pregnancy (GO:0007565)|fever generation (GO:0001660)|immune response (GO:0006955)|insulin secretion (GO:0030073)|lipid metabolic process (GO:0006629)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of membrane potential (GO:0045837)|positive regulation of JUN kinase activity (GO:0043507)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	interleukin-1 receptor antagonist activity (GO:0005152)|interleukin-1 receptor binding (GO:0005149)|interleukin-1 Type I receptor antagonist activity (GO:0045352)|interleukin-1 Type II receptor antagonist activity (GO:0045353)|interleukin-1, Type I receptor binding (GO:0005150)|interleukin-1, Type II receptor binding (GO:0005151)			breast(1)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	10					Rilonacept(DB06372)	AACTAGTTGCTGGATACTTGC	0.478									Lichen Sclerosis et Atrophicus, Familial Clustering of				T|||	960	0.191693	0.0333	0.3314	5008	,	,		24639	0.0942		0.2922	False		,,,				2504	0.3037				p.A60A		Atlas-SNP	.											.	IL1RN	30	.	0			c.T180C	GRCh37	CM025329	IL1RN	M	rs419598	PASS	.	T	,,,	283,4123	157.0+/-190.0	6,271,1926	170.0	154.0	159.0		117,180,171,69	-1.5	0.9	2	dbSNP_80	159	2398,6202	397.8+/-345.9	355,1688,2257	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL1RN	NM_000577.4,NM_173841.2,NM_173842.2,NM_173843.2	,,,	361,1959,4183	CC,CT,TT		27.8837,6.4231,20.6136	,,,	39/160,60/181,57/178,23/144	113887207	2681,10325	2203	4300	6503	SO:0001819	synonymous_variant	3557	exon4	Familial Cancer Database	Lichen Sclerosis, Familial	AGTTGCTGGATAC	M55646	CCDS2113.1, CCDS2114.1, CCDS2115.1, CCDS46396.1	2q14.2	2014-09-17			ENSG00000136689	ENSG00000136689		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	6000	protein-coding gene	gene with protein product	"""interleukin-1 receptor antagonist protein"", ""intracellular interleukin-1 receptor antagonist"""	147679				1386337, 8432529	Standard	NM_000577		Approved	IL1RA, ICIL-1RA, IL1F3, IRAP, IL-1RN, MGC10430	uc002tjb.3	P18510	OTTHUMG00000131341	ENST00000409930.3:c.171T>C	2.37:g.113887207T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_173841	A8K4G1|Q14628|Q53SC2|Q7RTZ4|Q96GD6|Q9UPC0	Silent	SNP	ENST00000409930.3	37	CCDS46396.1																																																																																			T|0.816;C|0.184	0.184	strong		0.478	IL1RN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330802.1	NM_173841	
WDR74	54663	hgsc.bcm.edu	37	11	62602983	62602983	+	Silent	SNP	A	A	G	rs2298636	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62602983A>G	ENST00000525239.1	-	7	1075	c.538T>C	c.(538-540)Ttg>Ctg	p.L180L	WDR74_ENST00000529106.1_Silent_p.L180L|WDR74_ENST00000278856.4_Silent_p.L180L|WDR74_ENST00000525752.1_Silent_p.L123L|WDR74_ENST00000540620.1_5'UTR|WDR74_ENST00000311713.7_Silent_p.L180L|RP11-727F15.9_ENST00000535867.1_RNA|RP11-727F15.9_ENST00000535817.1_RNA			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	180					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						GGAACCCGCAAGTCCAGCCAG	0.597													g|||	563	0.11242	0.1634	0.0548	5008	,	,		18010	0.1558		0.0437	False		,,,				2504	0.1104				p.L180L		Atlas-SNP	.											.	WDR74	36	.	0			c.T538C						PASS	.			520,3442		35,450,1496	73.0	79.0	77.0		538	3.6	1.0	11	dbSNP_100	77	466,7868		17,432,3718	no	coding-synonymous	WDR74	NM_018093.2		52,882,5214	GG,GA,AA		5.5916,13.1247,8.0189		180/386	62602983	986,11310	1981	4167	6148	SO:0001819	synonymous_variant	54663	exon7			CCCGCAAGTCCAG		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"""WD repeat domain containing"""	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.538T>C	11.37:g.62602983A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Silent	SNP	ENST00000525239.1	37	CCDS44630.1																																																																																			A|0.902;G|0.098	0.098	strong		0.597	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093	
GOLIM4	27333	hgsc.bcm.edu	37	3	167747707	167747707	+	Missense_Mutation	SNP	C	C	T	rs140974195	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167747707C>T	ENST00000470487.1	-	10	1983	c.1294G>A	c.(1294-1296)Gaa>Aaa	p.E432K	GOLIM4_ENST00000309027.4_Missense_Mutation_p.E404K	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	432	Gln-rich.|Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						tgcaaagcttcctggtgttcc	0.587													C|||	6	0.00119808	0.0	0.0043	5008	,	,		15802	0.0		0.003	False		,,,				2504	0.0				p.E432K		Atlas-SNP	.											.	GOLIM4	71	.	0			c.G1294A						PASS	.	C	LYS/GLU	0,4406		0,0,2203	71.0	65.0	67.0		1294	4.7	0.9	3	dbSNP_134	67	19,8581	14.0+/-48.4	0,19,4281	yes	missense	GOLIM4	NM_014498.3	56	0,19,6484	TT,TC,CC		0.2209,0.0,0.1461	possibly-damaging	432/697	167747707	19,12987	2203	4300	6503	SO:0001583	missense	27333	exon10			AAGCTTCCTGGTG	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"""golgi phosphoprotein 4"""	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1294G>A	3.37:g.167747707C>T	ENSP00000417354:p.Glu432Lys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	118	40	0.338983	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	6	0.0027472527472527475	0	0.0	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	28.6	4.935733	0.92458	0.0	0.002209	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	5.65	4.74	0.60224	.	0.188818	0.56097	D	0.000034	T	0.62768	0.2455	M	0.71581	2.175	0.33996	D	0.64974	D;P	0.54397	0.966;0.941	P;P	0.56216	0.794;0.731	T	0.76069	-0.3094	9	0.45353	T	0.12	-10.4908	16.3164	0.82930	0.0:0.868:0.132:0.0	.	404;432	F8W785;O00461	.;GOLI4_HUMAN	K	432;404	.	ENSP00000309893:E404K	E	-	1	0	GOLIM4	169230401	1.000000	0.71417	0.950000	0.38849	0.833000	0.47200	4.851000	0.62896	2.694000	0.91930	0.555000	0.69702	GAA	C|0.998;T|0.002	0.002	strong		0.587	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2		
DDX39B	7919	hgsc.bcm.edu	37	6	31503219	31503219	+	Silent	SNP	G	G	A	rs55799418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31503219G>A	ENST00000396172.1	-	6	1290	c.660C>T	c.(658-660)caC>caT	p.H220H	DDX39B_ENST00000458640.1_Silent_p.H220H|DDX39B_ENST00000453105.2_Silent_p.H173H|DDX39B_ENST00000376177.2_Silent_p.H220H|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR|DDX39B_ENST00000417556.2_Silent_p.H235H|DDX39B_ENST00000415382.2_Silent_p.H142H|SNORD117_ENST00000364915.1_RNA	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	220	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						CCTGCTTCTCGTGGGGGGTCA	0.443													G|||	46	0.0091853	0.0098	0.0086	5008	,	,		19144	0.003		0.0089	False		,,,				2504	0.0153				p.H220H		Atlas-SNP	.											.	DDX39B	38	.	0			c.C660T						PASS	.	G	,	18,3004		0,18,1493	190.0	151.0	165.0		660,660	-3.5	1.0	6	dbSNP_129	165	45,5373		0,45,2664	no	coding-synonymous,coding-synonymous	DDX39B	NM_004640.6,NM_080598.5	,	0,63,4157	AA,AG,GG		0.8306,0.5956,0.7464	,	220/429,220/429	31503219	63,8377	1511	2709	4220	SO:0001819	synonymous_variant	7919	exon6			CTTCTCGTGGGGG	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"""DEAD-boxes"""	13917	protein-coding gene	gene with protein product	"""U2AF65-associated protein 56"""	142560	"""HLA-B associated transcript 1"""	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.660C>T	6.37:g.31503219G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Silent	SNP	ENST00000396172.1	37	CCDS4697.1																																																																																			G|0.993;A|0.007	0.007	strong		0.443	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640	
PARP8	79668	hgsc.bcm.edu	37	5	50057729	50057729	+	Silent	SNP	G	G	A	rs282547	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:50057729G>A	ENST00000281631.5	+	6	578	c.420G>A	c.(418-420)ggG>ggA	p.G140G	PARP8_ENST00000505554.1_Silent_p.G119G|PARP8_ENST00000514342.2_5'UTR|PARP8_ENST00000514067.2_Silent_p.G140G|PARP8_ENST00000505697.2_Silent_p.G140G|PARP8_ENST00000503750.2_Silent_p.G140G|PARP8_ENST00000511363.2_3'UTR	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	140						intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				ATTACGGAGGGCAGGTAAGGA	0.388													G|||	2343	0.467851	0.1619	0.5778	5008	,	,		15057	0.6687		0.6272	False		,,,				2504	0.4325				p.G140G		Atlas-SNP	.											.	PARP8	93	.	0			c.G420A						PASS	.	G	,,	1116,3290		192,732,1279	74.0	72.0	73.0		420,420,420	2.9	1.0	5	dbSNP_79	73	5688,2912		1999,1690,611	yes	coding-synonymous,coding-synonymous,coding-synonymous	PARP8	NM_001178055.1,NM_001178056.1,NM_024615.3	,,	2191,2422,1890	AA,AG,GG		33.8605,25.3291,47.6857	,,	140/855,140/813,140/855	50057729	6804,6202	2203	4300	6503	SO:0001819	synonymous_variant	79668	exon6			CGGAGGGCAGGTA	AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"""Poly (ADP-ribose) polymerases"""	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.420G>A	5.37:g.50057729G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	187	83	0.44385	NM_001178056	Q3KRB7|Q6DHZ1|Q9H754	Silent	SNP	ENST00000281631.5	37	CCDS3954.1																																																																																			T|0.010;G|0.455;A|0.534	0.534	strong		0.388	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615	
BRCA1	672	hgsc.bcm.edu	37	17	41244435	41244435	+	Missense_Mutation	SNP	T	T	C	rs80357920|rs16941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41244435T>C	ENST00000357654.3	-	10	3231	c.3113A>G	c.(3112-3114)gAa>gGa	p.E1038G	BRCA1_ENST00000354071.3_Missense_Mutation_p.E1038G|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.E742G|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.E991G|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.E1038G|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.E1038G|BRCA1_ENST00000468300.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1038			E -> G (common polymorphism; dbSNP:rs16941). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7894493, ECO:0000269|Ref.6}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TGAGCTGGCTTCTTTAAAAAC	0.358			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			T|||	1681	0.335663	0.1573	0.3646	5008	,	,		20076	0.371		0.3569	False		,,,				2504	0.498				p.E1038G		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.A3113G	GRCh37	CM032861	BRCA1	M	rs16941	PASS	.	T	GLY/GLU,GLY/GLU,,,GLY/GLU	830,3576	326.4+/-299.6	76,678,1449	128.0	122.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3113,2972,,,3113	-1.0	0.5	17	dbSNP_60	124	2799,5801	440.8+/-359.6	444,1911,1945	yes	missense,missense,intron,intron,missense	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	98,98,,,98	520,2589,3394	CC,CT,TT		32.5465,18.8379,27.9025	benign,benign,,,benign	1038/1864,991/1817,,,1038/1885	41244435	3629,9377	2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		CTGGCTTCTTTAA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.3113A>G	17.37:g.41244435T>C	ENSP00000350283:p.Glu1038Gly	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	214	112	0.523364	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	662	0.3031135531135531	63	0.12804878048780488	139	0.3839779005524862	189	0.3304195804195804	271	0.3575197889182058	T	11.99	1.803390	0.31869	0.188379	0.325465	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24;-1.24	5.23	-0.974	0.10293	.	0.514353	0.17997	N	0.155009	T	0.00012	0.0000	M	0.81341	2.54	0.80722	P	0.0	B;B;B;B;P;B	0.50528	0.012;0.034;0.112;0.237;0.936;0.058	B;B;B;B;P;B	0.49301	0.006;0.006;0.118;0.177;0.606;0.065	T	0.04593	-1.0940	9	0.59425	D	0.04	-1.0083	6.1615	0.20366	0.1188:0.3513:0.0:0.5299	rs16941;rs16941	1038;997;1038;1038;1038;1038	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	G	1038;1038;1038;1038;742;1038;991	ENSP00000350283:E1038G;ENSP00000326002:E1038G;ENSP00000246907:E1038G;ENSP00000310938:E742G;ENSP00000418960:E1038G;ENSP00000418775:E991G	ENSP00000310938:E742G	E	-	2	0	BRCA1	38497961	0.000000	0.05858	0.509000	0.27700	0.856000	0.48823	-0.480000	0.06559	0.112000	0.17975	0.455000	0.32223	GAA	T|0.716;C|0.284	0.284	strong		0.358	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
OSBPL6	114880	hgsc.bcm.edu	37	2	179201048	179201048	+	Silent	SNP	G	G	T	rs16866263	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179201048G>T	ENST00000190611.4	+	9	1054	c.678G>T	c.(676-678)ccG>ccT	p.P226P	OSBPL6_ENST00000315022.2_Silent_p.P205P|OSBPL6_ENST00000409631.1_Silent_p.P226P|OSBPL6_ENST00000392505.2_Silent_p.P226P|OSBPL6_ENST00000359685.3_Silent_p.P226P|OSBPL6_ENST00000357080.4_Silent_p.P226P|OSBPL6_ENST00000409045.3_Silent_p.P226P	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	226					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			ACAGCTTTCCGTGGCAGTCCC	0.443													G|||	350	0.0698882	0.0499	0.0548	5008	,	,		21802	0.0278		0.0567	False		,,,				2504	0.1646				p.P226P		Atlas-SNP	.											OSBPL6_ENST00000392505,mucosal,malignant_melanoma,+2,2	OSBPL6	178	2	0			c.G678T						PASS	.	G	,,,,	218,4188	132.5+/-169.0	6,206,1991	217.0	215.0	216.0		678,678,678,678,615	-11.1	0.2	2	dbSNP_123	216	368,8232	121.8+/-180.9	7,354,3939	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL6	NM_001201480.1,NM_001201481.1,NM_001201482.1,NM_032523.3,NM_145739.2	,,,,	13,560,5930	TT,TG,GG		4.2791,4.9478,4.5056	,,,,	226/960,226/904,226/899,226/935,205/939	179201048	586,12420	2203	4300	6503	SO:0001819	synonymous_variant	114880	exon9			CTTTCCGTGGCAG	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.678G>T	2.37:g.179201048G>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																			G|0.955;T|0.045	0.045	strong		0.443	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
AHRR	57491	hgsc.bcm.edu	37	5	422955	422955	+	Missense_Mutation	SNP	C	C	G	rs2292596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:422955C>G	ENST00000505113.1	+	6	609	c.565C>G	c.(565-567)Ccc>Gcc	p.P189A	AHRR_ENST00000316418.5_Missense_Mutation_p.P189A|AHRR_ENST00000512529.1_Missense_Mutation_p.P35A|AHRR_ENST00000506456.1_Missense_Mutation_p.P45A	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	189			P -> A (in dbSNP:rs2292596). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.5}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			GTTTGGGCAGCCCCCGCCCTT	0.592																																					p.P189A		Atlas-SNP	.											AHRR,brain,glioma,0,2	AHRR	67	2	0			c.C565G	GRCh37	CM057935	AHRR	M	rs2292596	PASS	.	C	ALA/PRO,ALA/PRO	593,3451		43,507,1472	43.0	50.0	47.0		565,565	3.1	0.3	5	dbSNP_100	47	3154,5190		622,1910,1640	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	27,27	665,2417,3112	GG,GC,CC		37.7996,14.6637,30.247	benign,benign	189/702,189/720	422955	3747,8641	2022	4172	6194	SO:0001583	missense	57491	exon6			GGGCAGCCCCCGC	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.565C>G	5.37:g.422955C>G	ENSP00000424601:p.Pro189Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	110	71	0.645455	NM_001242412	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	672	0.3076923076923077	62	0.12601626016260162	109	0.3011049723756906	229	0.40034965034965037	272	0.35883905013192613	C	4.514	0.095307	0.08681	0.146637	0.377996	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456	T;T;T;T	0.22134	2.24;2.24;1.98;1.97	4.9	3.08	0.35506	.	0.186887	0.46442	D	0.000291	T	0.00012	0.0000	M	0.71581	2.175	0.45284	P	0.001715000000000022	P;B;B	0.50156	0.932;0.067;0.036	P;B;B	0.50659	0.647;0.012;0.061	T	0.44757	-0.9307	9	0.22109	T	0.4	.	4.6477	0.12580	0.0:0.614:0.182:0.2039	rs2292596;rs2292596	45;189;189	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	A	189;189;35;45	ENSP00000424601:P189A;ENSP00000323816:P189A;ENSP00000424880:P35A;ENSP00000426932:P45A	ENSP00000323816:P189A	P	+	1	0	AHRR	475955	0.543000	0.26434	0.279000	0.24732	0.048000	0.14542	1.157000	0.31724	0.450000	0.26774	0.655000	0.94253	CCC	C|0.670;G|0.330	0.330	strong		0.592	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
MREG	55686	hgsc.bcm.edu	37	2	216878008	216878008	+	Missense_Mutation	SNP	C	C	G	rs1864253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:216878008C>G	ENST00000263268.6	-	1	338	c.43G>C	c.(43-45)Ggg>Cgg	p.G15R		NM_018000.2	NP_060470.2	Q8N565	MREG_HUMAN	melanoregulin	15	Cys-rich.		G -> R (in dbSNP:rs1864253). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			plasma membrane (GO:0005886)				large_intestine(1)|lung(2)	3		Renal(323;0.0328)		Epithelial(149;4.64e-07)|all cancers(144;5.56e-05)|LUSC - Lung squamous cell carcinoma(224;0.00832)|Lung(261;0.0111)		CACTCGCACCCGCAGCAGCAG	0.741													G|||	3391	0.677117	0.7277	0.7248	5008	,	,		9620	0.6806		0.6402	False		,,,				2504	0.6094				p.G15R		Atlas-SNP	.											MREG,NS,carcinoma,0,2	MREG	10	2	0			c.G43C						PASS	.	G	ARG/GLY	2469,879		941,587,146	6.0	12.0	10.0		43	3.7	0.4	2	dbSNP_92	10	4315,2363		1483,1349,507	yes	missense	MREG	NM_018000.2	125	2424,1936,653	GG,GC,CC		35.3848,26.2545,32.3359	benign	15/215	216878008	6784,3242	1674	3339	5013	SO:0001583	missense	55686	exon1			CGCACCCGCAGCA	AK000978	CCDS46513.1	2q35	2013-09-27			ENSG00000118242	ENSG00000118242			25478	protein-coding gene	gene with protein product		609207				19240024, 22275436	Standard	NM_018000		Approved	FLJ10116, DSU, WDT2	uc002vfo.3	Q8N565	OTTHUMG00000154828	ENST00000263268.6:c.43G>C	2.37:g.216878008C>G	ENSP00000263268:p.Gly15Arg	Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_018000	Q53R89|Q53TC1|Q5XKB6|Q9NWC9|Q9P1S1	Missense_Mutation	SNP	ENST00000263268.6	37	CCDS46513.1	1470	0.6730769230769231	342	0.6951219512195121	245	0.6767955801104972	395	0.6905594405594405	488	0.6437994722955145	G	8.163	0.789879	0.16258	0.737455	0.646152	ENSG00000118242	ENST00000236976;ENST00000263268	T	0.41758	0.99	3.71	3.71	0.42584	.	0.926591	0.08911	N	0.875791	T	0.00012	0.0000	N	0.22421	0.69	0.19300	P	0.9999702094	B	0.02656	0.0	B	0.01281	0.0	T	0.39921	-0.9590	9	0.31617	T	0.26	-0.2072	9.3886	0.38359	0.0:0.2186:0.7814:0.0	rs1864253;rs1864253	15	Q8N565	MREG_HUMAN	R	15	ENSP00000263268:G15R	ENSP00000236976:G15R	G	-	1	0	MREG	216586253	0.018000	0.18449	0.389000	0.26208	0.149000	0.21700	0.005000	0.13129	0.914000	0.36822	-0.357000	0.07601	GGG	C|0.317;G|0.683	0.683	strong		0.741	MREG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337297.1	NM_018000	
NMB	4828	hgsc.bcm.edu	37	15	85200520	85200520	+	Missense_Mutation	SNP	G	G	T	rs1051168	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85200520G>T	ENST00000360476.3	-	2	612	c.217C>A	c.(217-219)Ccc>Acc	p.P73T	WDR73_ENST00000398528.3_5'Flank|WDR73_ENST00000434634.2_5'Flank|NMB_ENST00000394588.3_Missense_Mutation_p.P73T			P08949	NMB_HUMAN	neuromedin B	73			P -> T (in dbSNP:rs1051168). {ECO:0000269|PubMed:15489334}.	PLGTAPHTS -> HWGQLPTPP (in Ref. 1; AAA59934). {ECO:0000305}.	arachidonic acid secretion (GO:0050482)|cell-cell signaling (GO:0007267)|glucose homeostasis (GO:0042593)|negative regulation of hormone secretion (GO:0046888)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hormone secretion (GO:0046887)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|neuron projection (GO:0043005)	hormone activity (GO:0005179)			endometrium(1)	1				all cancers(203;3.5e-06)		GAGGTGTGGGGAGCTGTCCCC	0.607													G|||	693	0.138379	0.0136	0.1816	5008	,	,		18979	0.1359		0.2584	False		,,,				2504	0.1554				p.P73T		Atlas-SNP	.											.	NMB	14	.	0			c.C217A	GRCh37	CM045181	NMB	M	rs1051168	PASS	.	G	THR/PRO,THR/PRO	228,4176		8,212,1982	33.0	26.0	28.0		217,217	-1.4	0.0	15	dbSNP_86	28	2288,6310		281,1726,2292	yes	missense,missense	NMB	NM_021077.3,NM_205858.1	38,38	289,1938,4274	TT,TG,GG		26.6108,5.1771,19.3509	possibly-damaging,possibly-damaging	73/122,73/155	85200520	2516,10486	2202	4299	6501	SO:0001583	missense	4828	exon2			TGTGGGGAGCTGT		CCDS10332.1, CCDS42076.1	15q25.2-q25.3	2013-09-19			ENSG00000197696	ENSG00000197696			7842	protein-coding gene	gene with protein product		162340				2458345	Standard	NM_021077		Approved	MGC2277, MGC3936, MGC17211	uc002bla.3	P08949	OTTHUMG00000148666	ENST00000360476.3:c.217C>A	15.37:g.85200520G>T	ENSP00000353664:p.Pro73Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	141	78	0.553191	NM_205858	Q96A06|Q96HH5	Missense_Mutation	SNP	ENST00000360476.3	37	CCDS10332.1	358	0.16391941391941392	5	0.01016260162601626	73	0.20165745856353592	81	0.14160839160839161	199	0.262532981530343	G	10.58	1.388808	0.25118	0.051771	0.266108	ENSG00000197696	ENST00000360476;ENST00000394588	T;T	0.47528	0.93;0.84	5.11	-1.37	0.09056	.	0.759821	0.12773	N	0.440331	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B	0.22346	0.068;0.041	B;B	0.23419	0.046;0.021	T	0.23511	-1.0186	9	0.02654	T	1	-8.7065	4.2642	0.10756	0.4384:0.0:0.4065:0.1551	rs1051168;rs3191563;rs17850187;rs17850193;rs17857977;rs1051168	73;73	P08949-2;P08949	.;NMB_HUMAN	T	73	ENSP00000353664:P73T;ENSP00000378089:P73T	ENSP00000353664:P73T	P	-	1	0	NMB	83001524	0.077000	0.21312	0.001000	0.08648	0.943000	0.58893	0.191000	0.17076	0.065000	0.16485	-0.137000	0.14449	CCC	G|0.833;T|0.167	0.167	strong		0.607	NMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308995.1	NM_021077	
FYCO1	79443	hgsc.bcm.edu	37	3	46007823	46007823	+	Missense_Mutation	SNP	G	G	T	rs13079478|rs71622515|rs199842602	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46007823G>T	ENST00000296137.2	-	8	3208	c.3003C>A	c.(3001-3003)aaC>aaA	p.N1001K	FYCO1_ENST00000535325.1_Missense_Mutation_p.N1001K	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1001			N -> D (in dbSNP:rs13059238).		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		ACTTGAGGGTGTTGAGCTCCT	0.612													G|||	527	0.105232	0.0053	0.0591	5008	,	,		19406	0.004		0.1223	False		,,,				2504	0.3599				p.N1001K		Atlas-SNP	.											.	FYCO1	115	.	0			c.C3003A						PASS	.	G	LYS/ASN	0,4406		0,0,2203	97.0	84.0	89.0		3003	1.4	0.3	3	dbSNP_121	89	12,8588		1,10,4289	yes	missense	FYCO1	NM_024513.2	94	1,10,6492	TT,TG,GG		0.1395,0.0,0.0923	benign	1001/1479	46007823	12,12994	2203	4300	6503	SO:0001583	missense	79443	exon8			GAGGGTGTTGAGC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.3003C>A	3.37:g.46007823G>T	ENSP00000296137:p.Asn1001Lys	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	159	62	0.389937	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	129	0.059065934065934064	3	0.006097560975609756	19	0.052486187845303865	0	0.0	107	0.14116094986807387	G	9.521	1.108394	0.20714	0.0	0.001395	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.79940	-1.32;-1.32	5.49	1.44	0.22558	.	0.437095	0.25572	N	0.029755	T	0.00580	0.0019	N	0.14661	0.345	0.80722	P	0.0	B;B	0.15719	0.014;0.008	B;B	0.15484	0.013;0.008	T	0.03534	-1.1027	9	0.06891	T	0.86	-17.5834	3.5326	0.07782	0.4252:0.0:0.4016:0.1732	rs13079478	1001;1001	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	K	1001	ENSP00000296137:N1001K;ENSP00000441178:N1001K	ENSP00000296137:N1001K	N	-	3	2	FYCO1	45982827	0.033000	0.19621	0.300000	0.25030	0.997000	0.91878	0.297000	0.19101	0.281000	0.22233	0.655000	0.94253	AAC	GTT|0.500;TTC|0.500	.	alt		0.612	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
KRT40	125115	hgsc.bcm.edu	37	17	39135089	39135089	+	Missense_Mutation	SNP	G	G	A	rs11649834	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39135089G>A	ENST00000398486.2	-	8	1323	c.1163C>T	c.(1162-1164)aCg>aTg	p.T388M	KRT40_ENST00000377755.4_Missense_Mutation_p.T388M|AC004231.2_ENST00000418393.1_RNA	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	388	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GCCCCAGTACGTGTTGATCTC	0.572													G|||	338	0.067492	0.0098	0.0965	5008	,	,		15927	0.0556		0.1272	False		,,,				2504	0.0757				p.T388M		Atlas-SNP	.											.	KRT40	27	.	0			c.C1163T						PASS	.	G	MET/THR	131,4275	93.4+/-132.2	2,127,2074	70.0	78.0	75.0		1163	5.6	0.6	17	dbSNP_120	75	1174,7418	235.0+/-267.7	77,1020,3199	yes	missense	KRT40	NM_182497.3	81	79,1147,5273	AA,AG,GG		13.6639,2.9732,10.04	probably-damaging	388/432	39135089	1305,11693	2203	4296	6499	SO:0001583	missense	125115	exon8			CAGTACGTGTTGA	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1163C>T	17.37:g.39135089G>A	ENSP00000381500:p.Thr388Met	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	167	0.07646520146520147	5	0.01016260162601626	36	0.09944751381215469	27	0.0472027972027972	99	0.13060686015831136	G	12.67	2.006968	0.35415	0.029732	0.136639	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.91996	-2.95;-2.95	5.56	5.56	0.83823	Filament (1);	0.000000	0.34676	N	0.003774	T	0.27241	0.0668	M	0.92507	3.315	0.32698	P	0.5133220000000001	D	0.89917	1.0	D	0.79108	0.992	T	0.57831	-0.7743	9	0.72032	D	0.01	.	15.3367	0.74263	0.0:0.0:0.86:0.14	rs11649834	388	Q6A162	K1C40_HUMAN	M	388	ENSP00000366984:T388M;ENSP00000381500:T388M	ENSP00000366984:T388M	T	-	2	0	KRT40	36388615	0.030000	0.19436	0.625000	0.29200	0.067000	0.16453	1.408000	0.34668	2.784000	0.95788	0.655000	0.94253	ACG	G|0.922;A|0.078	0.078	strong		0.572	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
ZNF468	90333	hgsc.bcm.edu	37	19	53352388	53352388	+	Silent	SNP	A	A	G	rs536376293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53352388A>G	ENST00000595646.1	-	3	214	c.94T>C	c.(94-96)Tta>Cta	p.L32L	ZNF468_ENST00000390651.4_5'UTR|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_5'UTR|ZNF468_ENST00000243639.4_Silent_p.L32L			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	32	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L32L(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		TCCCTGTATAAAGTCCTCTGA	0.468													-|||	32	0.00638978	0.0129	0.0	5008	,	,		18523	0.001		0.0099	False		,,,				2504	0.0041				p.L32L		Atlas-SNP	.											ZNF468,colon,carcinoma,0,1	ZNF468	46	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T94C						scavenged	.						147.0	149.0	149.0					19																	53352388		2203	4300	6503	SO:0001819	synonymous_variant	90333	exon3			TGTATAAAGTCCT	AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"""Zinc fingers, C2H2-type"", ""-"""	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.94T>C	19.37:g.53352388A>G		Somatic	58	2	0.0344828		WXS	Illumina HiSeq	Phase_I	50	5	0.1	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Silent	SNP	ENST00000595646.1	37	CCDS33094.1																																																																																			.	.	none		0.468	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
AGAP11	119385	hgsc.bcm.edu	37	10	88768423	88768423	+	RNA	SNP	A	A	G	rs2641562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88768423A>G	ENST00000444431.1	+	0	3023				RP11-96C23.10_ENST00000451760.1_RNA|RP11-96C23.5_ENST00000433214.2_RNA|RP11-96C23.14_ENST00000444180.3_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										GGCTGAAGACATGGAAAAAGA	0.453													A|||	2007	0.400759	0.2073	0.2723	5008	,	,		21664	0.6925		0.4513	False		,,,				2504	0.4008				p.T138T		Atlas-SNP	.											.	.	.	.	0			c.A414G						PASS	.	A		1098,3280		149,800,1240	153.0	169.0	164.0		414	0.1	0.2	10	dbSNP_100	164	3521,5039		712,2097,1471	no	coding-synonymous	AGAP11	NM_133447.1		861,2897,2711	GG,GA,AA		41.1332,25.0799,35.701		138/551	88768423	4619,8319	2189	4280	6469			119385	exon12			GAAGACATGGAAA			10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		10.37:g.88768423A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	224	113	0.504464	NM_133447	B9EIP7|D3DWE4	Silent	SNP	ENST00000444431.1	37																																																																																				A|0.567;G|0.433	0.433	strong		0.453	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447	
TRIM69	140691	hgsc.bcm.edu	37	15	45047134	45047134	+	Missense_Mutation	SNP	G	G	A	rs2470911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45047134G>A	ENST00000559390.1	+	3	971	c.43G>A	c.(43-45)Gac>Aac	p.D15N	TRIM69_ENST00000560442.1_Intron|TRIM69_ENST00000561043.1_Intron|TRIM69_ENST00000558173.1_5'UTR|TRIM69_ENST00000558329.1_Intron|TRIM69_ENST00000329464.4_Missense_Mutation_p.D15N|TRIM69_ENST00000338264.4_Intron			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	15	Necessary for nuclear localization. {ECO:0000250}.		D -> N (in dbSNP:rs2470911). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		CGATCCAGGCGACTATGTTGA	0.418													g|||	2819	0.562899	0.4826	0.6484	5008	,	,		21630	0.5813		0.7256	False		,,,				2504	0.4243				p.D15N	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											.	TRIM69	47	.	0			c.G43A						PASS	.	A	,ASN/ASP	2392,2004	613.5+/-392.2	647,1098,453	133.0	124.0	127.0		,43	2.7	0.0	15	dbSNP_100	127	6158,2438	698.1+/-405.0	2209,1740,349	yes	intron,missense	TRIM69	NM_080745.3,NM_182985.3	,23	2856,2838,802	AA,AG,GG		28.362,45.5869,34.1903	,benign	,15/501	45047134	8550,4442	2198	4298	6496	SO:0001583	missense	140691	exon2			CCAGGCGACTATG	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	17857	protein-coding gene	gene with protein product			"""ring finger protein 36"", ""tripartite motif-containing 69"""	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.43G>A	15.37:g.45047134G>A	ENSP00000453177:p.Asp15Asn	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	187	91	0.486631	NM_182985	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Missense_Mutation	SNP	ENST00000559390.1	37	CCDS32220.1	1409	0.6451465201465202	250	0.508130081300813	238	0.6574585635359116	369	0.6451048951048951	552	0.7282321899736148	g	0.650	-0.810047	0.02798	0.544131	0.71638	ENSG00000185880	ENST00000329464	T	0.38560	1.13	5.07	2.73	0.32206	.	0.341802	0.25503	N	0.030238	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39375	-0.9617	9	0.06891	T	0.86	.	7.1239	0.25461	0.7852:0.0:0.2148:0.0	rs2470911;rs11565463;rs17516997;rs17857344;rs52822668;rs58269664;rs2470911	15	Q86WT6	TRI69_HUMAN	N	15	ENSP00000332284:D15N	ENSP00000332284:D15N	D	+	1	0	TRIM69	42834426	0.000000	0.05858	0.004000	0.12327	0.022000	0.10575	0.419000	0.21247	0.416000	0.25844	-1.344000	0.01245	GAC	G|0.361;A|0.639	0.639	strong		0.418	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		
TMEM173	340061	hgsc.bcm.edu	37	5	138861146	138861146	+	Silent	SNP	C	C	G	rs7447927	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:138861146C>G	ENST00000330794.4	-	3	477	c.144G>C	c.(142-144)gtG>gtC	p.V48V	TMEM173_ENST00000511850.1_5'UTR	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	48					activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTAGGTGGAGCACCAGGTACC	0.632													C|||	2146	0.428514	0.0787	0.5058	5008	,	,		18387	0.375		0.6859	False		,,,				2504	0.637				p.V48V		Atlas-SNP	.											.	TMEM173	19	.	0			c.G144C						PASS	.	C		812,3594	322.3+/-297.6	76,660,1467	54.0	57.0	56.0		144	-0.2	0.0	5	dbSNP_116	56	6202,2398	699.6+/-405.1	2251,1700,349	no	coding-synonymous	TMEM173	NM_198282.2		2327,2360,1816	GG,GC,CC		27.8837,18.4294,46.071		48/380	138861146	7014,5992	2203	4300	6503	SO:0001819	synonymous_variant	340061	exon3			GTGGAGCACCAGG		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.144G>C	5.37:g.138861146C>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	170	115	0.676471	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Silent	SNP	ENST00000330794.4	37	CCDS4215.1																																																																																			C|0.484;G|0.516	0.516	strong		0.632	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
MUC16	94025	hgsc.bcm.edu	37	19	9072875	9072875	+	Silent	SNP	G	G	A	rs73009098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9072875G>A	ENST00000397910.4	-	3	14774	c.14571C>T	c.(14569-14571)gtC>gtT	p.V4857V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4859	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTGGAGATGTGACTTTAGATG	0.438													G|||	935	0.186701	0.0923	0.2536	5008	,	,		24451	0.3254		0.1322	False		,,,				2504	0.18				p.V4857V		Atlas-SNP	.											.	MUC16	4315	.	0			c.C14571T						PASS	.			389,3697		16,357,1670	186.0	175.0	179.0		14571	-1.3	0.0	19	dbSNP_130	179	1160,7216		73,1014,3101	no	coding-synonymous	MUC16	NM_024690.2		89,1371,4771	AA,AG,GG		13.8491,9.5203,12.4298		4857/14508	9072875	1549,10913	2043	4188	6231	SO:0001819	synonymous_variant	94025	exon3			AGATGTGACTTTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14571C>T	19.37:g.9072875G>A		Somatic	529	0	0		WXS	Illumina HiSeq	Phase_I	487	237	0.486653	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.809;A|0.191	0.191	strong		0.438	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CYP4F2	8529	hgsc.bcm.edu	37	19	15990431	15990431	+	Missense_Mutation	SNP	C	C	T	rs2108622	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15990431C>T	ENST00000221700.6	-	11	1392	c.1297G>A	c.(1297-1299)Gtg>Atg	p.V433M		NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TCCGGCCACACAGCTGGGTTG	0.577													.|||	1186	0.236821	0.0825	0.2378	5008	,	,		18423	0.2143		0.2903	False		,,,				2504	0.4131				p.V433M		Atlas-SNP	.											.	CYP4F2	97	.	0			c.G1297A	GRCh37	CM074767	CYP4F2	M	rs2108622	PASS	.	C	MET/VAL	428,3978	208.5+/-229.5	23,382,1798	110.0	118.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1297	1.7	0.9	19	dbSNP_96	115	2504,6096	410.8+/-350.3	379,1746,2175	yes	missense	CYP4F2	NM_001082.3	21	402,2128,3973	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	29.1163,9.714,22.5434	probably-damaging	433/521	15990431	2932,10074	2203	4300	6503	SO:0001583	missense	8529	exon11			GCCACACAGCTGG	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.1297G>A	19.37:g.15990431C>T	ENSP00000221700:p.Val433Met	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	37	CCDS12336.1	470	0.21520146520146521	42	0.08536585365853659	103	0.2845303867403315	118	0.2062937062937063	207	0.27308707124010556	c	14.01	2.407803	0.42715	0.09714	0.291163	ENSG00000186115	ENST00000221700;ENST00000392846	T	0.70749	-0.51	2.78	1.72	0.24424	.	0.000000	0.56097	U	0.000026	T	0.00039	0.0001	M	0.90019	3.08	0.09310	P	1.0	D	0.89917	1.0	D	0.73380	0.98	T	0.02156	-1.1204	9	0.72032	D	0.01	.	7.54	0.27733	0.0:0.8612:0.0:0.1388	rs2108622;rs52819608;rs57319528;rs2108622	433	P78329	CP4F2_HUMAN	M	433;284	ENSP00000221700:V433M	ENSP00000221700:V433M	V	-	1	0	CYP4F2	15851431	0.942000	0.31987	0.926000	0.36857	0.526000	0.34562	1.995000	0.40767	0.476000	0.27440	0.491000	0.48974	GTG	C|0.779;T|0.221	0.221	strong		0.577	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
SLC7A2	6542	hgsc.bcm.edu	37	8	17396380	17396380	+	Intron	SNP	G	G	A	rs13259948	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17396380G>A	ENST00000494857.1	+	3	196				SLC7A2_ENST00000004531.10_Missense_Mutation_p.R16Q|SLC7A2_ENST00000470360.1_Missense_Mutation_p.R16Q|SLC7A2_ENST00000398090.3_Missense_Mutation_p.R16Q|SLC7A2_ENST00000522656.1_Intron	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2						amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	CTAATTTGTCGAGGGTTTATT	0.418													g|||	298	0.0595048	0.0098	0.0937	5008	,	,		17361	0.0		0.1869	False		,,,				2504	0.0327				p.R16Q		Atlas-SNP	.											.	SLC7A2	157	.	0			c.G47A						PASS	.	A	,GLN/ARG,GLN/ARG	134,3584		3,128,1728	109.0	99.0	102.0		,47,47	0.6	0.0	8	dbSNP_121	102	1578,6608		168,1242,2683	yes	intron,missense,missense	SLC7A2	NM_001008539.3,NM_003046.5,NM_001164771.1	,43,43	171,1370,4411	AA,AG,GG		19.2768,3.6041,14.3817	,benign,benign	,16/698,16/699	17396380	1712,10192	1859	4093	5952	SO:0001627	intron_variant	6542	exon1			TTTGTCGAGGGTT	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.-22-4447G>A	8.37:g.17396380G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	85	51	0.6	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	37	CCDS34852.1	175	0.08012820512820513	5	0.01016260162601626	39	0.10773480662983426	0	0.0	131	0.17282321899736147	g	11.79	1.743855	0.30865	0.036041	0.192768	ENSG00000003989	ENST00000470360;ENST00000004531;ENST00000398090	D;D;D	0.88818	-2.43;-2.29;-2.43	3.34	0.559	0.17272	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.34079	-0.9843	7	0.87932	D	0	.	5.4713	0.16672	0.3777:0.0:0.6223:0.0	rs13259948;rs17504833;rs56458067;rs13259948	16;16	P52569-3;P52569-2	.;.	Q	16	ENSP00000419873:R16Q;ENSP00000004531:R16Q;ENSP00000381164:R16Q	ENSP00000004531:R16Q	R	+	2	0	SLC7A2	17440759	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.782000	0.26788	0.106000	0.17784	-0.355000	0.07637	CGA	G|0.897;A|0.103	0.103	strong		0.418	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
ZNF626	199777	hgsc.bcm.edu	37	19	20808414	20808414	+	Missense_Mutation	SNP	C	C	T	rs8110802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20808414C>T	ENST00000601440.1	-	4	415	c.269G>A	c.(268-270)aGc>aAc	p.S90N	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	90			S -> N (in dbSNP:rs8110802).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						ATCTTTCATGCTCTGCTCTGG	0.323													N|||	363	0.072484	0.2436	0.0259	5008	,	,		17039	0.0		0.0139	False		,,,				2504	0.0092				p.S90N		Atlas-SNP	.											.	ZNF626	121	.	0			c.G269A						PASS	.	C	ASN/SER	774,3566		90,594,1486	51.0	57.0	55.0		269	1.1	0.0	19	dbSNP_116	55	84,8476		3,78,4199	no	missense	ZNF626	NM_001076675.2	46	93,672,5685	TT,TC,CC		0.9813,17.8341,6.6512	benign	90/529	20808414	858,12042	2170	4280	6450	SO:0001583	missense	199777	exon4			TTCATGCTCTGCT	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.269G>A	19.37:g.20808414C>T	ENSP00000469958:p.Ser90Asn	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	122	50	0.409836	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	140	0.0641025641025641	119	0.241869918699187	10	0.027624309392265192	0	0.0	11	0.014511873350923483	N	2.780	-0.253612	0.05829	0.178341	0.009813	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	1.08	1.08	0.20341	.	.	.	.	.	T	0.00012	0.0000	N	0.20574	0.59	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.33752	-0.9856	7	0.14656	T	0.56	.	3.4203	0.07391	0.0:0.703:0.0:0.297	rs8110802;rs16996433;rs8110802	90	Q68DY1	ZN626_HUMAN	N	90;14;90	.	ENSP00000445201:S90N	S	-	2	0	ZNF626	20600254	0.000000	0.05858	0.012000	0.15200	0.263000	0.26337	-0.331000	0.07914	0.503000	0.28060	0.289000	0.19496	AGC	C|0.961;T|0.039	0.039	strong		0.323	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
OPN4	94233	hgsc.bcm.edu	37	10	88414569	88414569	+	Missense_Mutation	SNP	C	C	T	rs2675703	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88414569C>T	ENST00000241891.5	+	1	196	c.29C>T	c.(28-30)cCg>cTg	p.P10L	OPN4_ENST00000372071.2_Missense_Mutation_p.P10L	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	10			P -> L (in dbSNP:rs2675703). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CCAAGAGTCCCGCCCAGCCCA	0.642													C|||	392	0.0782748	0.0227	0.1196	5008	,	,		16004	0.0446		0.1511	False		,,,				2504	0.0838				p.P10L		Atlas-SNP	.											OPN4,NS,carcinoma,0,1	OPN4	61	1	0			c.C29T						PASS	.	C	LEU/PRO,LEU/PRO	176,4230	115.9+/-153.8	6,164,2033	66.0	67.0	67.0		29,29	-2.1	0.0	10	dbSNP_100	67	1161,7439	236.8+/-268.9	69,1023,3208	yes	missense,missense	OPN4	NM_001030015.2,NM_033282.3	98,98	75,1187,5241	TT,TC,CC		13.5,3.9946,10.2799	possibly-damaging,possibly-damaging	10/490,10/479	88414569	1337,11669	2203	4300	6503	SO:0001583	missense	94233	exon1			GAGTCCCGCCCAG	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.29C>T	10.37:g.88414569C>T	ENSP00000241891:p.Pro10Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_033282	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	37	CCDS7376.1	209	0.09569597069597069	17	0.034552845528455285	52	0.143646408839779	30	0.05244755244755245	110	0.14511873350923482	C	2.718	-0.267266	0.05754	0.039946	0.135	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.66460	-0.16;0.21;-0.21	4.65	-2.14	0.07123	.	0.680336	0.12954	N	0.425615	T	0.00241	0.0007	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.10296	0.001;0.002;0.003	B;B;B	0.06405	0.001;0.001;0.002	T	0.09618	-1.0666	9	0.02654	T	1	.	4.4654	0.11687	0.1568:0.3542:0.0:0.4889	rs2675703;rs3824747;rs2675703	10;10;10	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	L	10	ENSP00000361141:P10L;ENSP00000241891:P10L;ENSP00000393132:P10L	ENSP00000241891:P10L	P	+	2	0	OPN4	88404549	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.773000	0.04689	-0.273000	0.09246	-0.137000	0.14449	CCG	C|0.900;T|0.100	0.100	strong		0.642	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
STK36	27148	hgsc.bcm.edu	37	2	219562675	219562675	+	Missense_Mutation	SNP	G	G	A	rs1863704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219562675G>A	ENST00000295709.3	+	25	3287	c.3008G>A	c.(3007-3009)gGt>gAt	p.G1003D	STK36_ENST00000440309.1_Missense_Mutation_p.G1003D|STK36_ENST00000392105.3_Missense_Mutation_p.G982D|STK36_ENST00000392106.2_Missense_Mutation_p.G982D	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CTCCTTATAGGTGTCTTGGCC	0.557													G|||	950	0.189696	0.0212	0.3285	5008	,	,		21184	0.0556		0.3757	False		,,,				2504	0.2658				p.G1003D		Atlas-SNP	.											STK36,rectum,carcinoma,0,1	STK36	111	1	0			c.G3008A						PASS	.	G	ASP/GLY	336,4070	178.7+/-207.4	11,314,1878	149.0	131.0	137.0		3008	2.0	0.0	2	dbSNP_92	137	3284,5316	492.8+/-373.4	656,1972,1672	yes	missense	STK36	NM_015690.4	94	667,2286,3550	AA,AG,GG		38.186,7.626,27.8333	possibly-damaging	1003/1316	219562675	3620,9386	2203	4300	6503	SO:0001583	missense	27148	exon25			TTATAGGTGTCTT	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3008G>A	2.37:g.219562675G>A	ENSP00000295709:p.Gly1003Asp	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	217	92	0.423963	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	454|454	0.2078754578754579|0.2078754578754579	23|23	0.046747967479674794|0.046747967479674794	112|112	0.30939226519337015|0.30939226519337015	36|36	0.06293706293706294|0.06293706293706294	283|283	0.3733509234828496|0.3733509234828496	G|G	0.208|0.208	-1.039006|-1.039006	0.02013|0.02013	0.07626|0.07626	0.38186|0.38186	ENSG00000163482|ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309|ENST00000431040	T;T;T;T|.	0.69561|.	-0.4;-0.4;-0.41;-0.4|.	5.82|5.82	2.01|2.01	0.26516|0.26516	.|.	0.790460|.	0.11084|.	N|.	0.601535|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	B;P;B|.	0.39424|.	0.001;0.673;0.179|.	B;B;B|.	0.36464|.	0.001;0.225;0.077|.	T|T	0.47699|0.47699	-0.9097|-0.9097	9|4	0.32370|.	T|.	0.25|.	-0.0347|-0.0347	6.8511|6.8511	0.24014|0.24014	0.3342:0.0:0.5491:0.1167|0.3342:0.0:0.5491:0.1167	rs1863704;rs56519430;rs57906514;rs1863704|rs1863704;rs56519430;rs57906514;rs1863704	982;982;1003|.	A8MU99;Q9NRP7-2;Q9NRP7|.	.;.;STK36_HUMAN|.	D|M	1003;982;982;1003|196	ENSP00000295709:G1003D;ENSP00000375955:G982D;ENSP00000375954:G982D;ENSP00000394095:G1003D|.	ENSP00000295709:G1003D|.	G|V	+|+	2|1	0|0	STK36|STK36	219270919|219270919	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.823000|0.823000	0.27366|0.27366	0.122000|0.122000	0.18314|0.18314	-0.797000|-0.797000	0.03246|0.03246	GGT|GTG	G|0.767;A|0.233	0.233	strong		0.557	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
ZNF770	54989	hgsc.bcm.edu	37	15	35273760	35273760	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:35273760G>A	ENST00000356321.4	-	3	2220	c.1876C>T	c.(1876-1878)Cga>Tga	p.R626*		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	626					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R626*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		ACACTGCATCGGTACAGGAAG	0.423																																					p.R626X		Atlas-SNP	.											ZNF770,NS,carcinoma,0,1	ZNF770	64	1	1	Substitution - Nonsense(1)	endometrium(1)	c.C1876T						scavenged	.						135.0	127.0	130.0					15																	35273760		2201	4298	6499	SO:0001587	stop_gained	54989	exon3			TGCATCGGTACAG	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"""Zinc fingers, C2H2-type"""	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.1876C>T	15.37:g.35273760G>A	ENSP00000348673:p.Arg626*	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	157	2	0.0127389	NM_014106	Q6ZMZ6|Q9NWV2	Nonsense_Mutation	SNP	ENST00000356321.4	37	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	G	37	6.020666	0.97211	.	.	ENSG00000198146	ENST00000356321	.	.	.	5.36	4.46	0.54185	.	0.276725	0.30159	N	0.010272	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-1.7595	9.1343	0.36863	0.0731:0.0:0.7816:0.1454	.	.	.	.	X	626	.	ENSP00000348673:R626X	R	-	1	2	ZNF770	33061052	.	.	1.000000	0.80357	0.277000	0.26821	.	.	1.513000	0.48852	-0.253000	0.11424	CGA	.	.	none		0.423	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106	
FRMD3	257019	hgsc.bcm.edu	37	9	85863091	85863091	+	Silent	SNP	A	A	G	rs10114696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:85863091A>G	ENST00000304195.3	-	14	1742	c.1536T>C	c.(1534-1536)taT>taC	p.Y512Y	FRMD3_ENST00000376434.1_Silent_p.Y318Y|FRMD3_ENST00000328788.1_Silent_p.Y169Y|FRMD3_ENST00000376438.1_Silent_p.Y512Y|FRMD3_ENST00000465485.1_5'UTR	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	512						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						TCAGAATGTCATAGCTCCACG	0.507													.|||	1404	0.280351	0.1415	0.2767	5008	,	,		19160	0.2014		0.3936	False		,,,				2504	0.4356				p.Y512Y		Atlas-SNP	.											.	FRMD3	96	.	0			c.T1536C						PASS	.	A		696,3268		61,574,1347	80.0	83.0	82.0		1536	4.6	1.0	9	dbSNP_119	82	3451,4897		728,1995,1451	no	coding-synonymous	FRMD3	NM_174938.4		789,2569,2798	GG,GA,AA		41.3392,17.558,33.6826		512/598	85863091	4147,8165	1982	4174	6156	SO:0001819	synonymous_variant	257019	exon14			AATGTCATAGCTC	AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159			24125	protein-coding gene	gene with protein product		607619				12601556	Standard	NM_174938		Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.1536T>C	9.37:g.85863091A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_174938	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	Silent	SNP	ENST00000304195.3	37	CCDS43840.1																																																																																			A|0.685;G|0.315	0.315	strong		0.507	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157355.1	NM_174938	
MUC16	94025	hgsc.bcm.edu	37	19	9056989	9056989	+	Missense_Mutation	SNP	C	C	G	rs4804381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9056989C>G	ENST00000397910.4	-	3	30660	c.30457G>C	c.(30457-30459)Gag>Cag	p.E10153Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10155	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCTGTGGTCTCAAAATTAGCA	0.463													C|||	932	0.186102	0.0666	0.281	5008	,	,		22984	0.3313		0.167	False		,,,				2504	0.1503				p.E10153Q		Atlas-SNP	.											.	MUC16	4315	.	0			c.G30457C						PASS	.	C	GLN/GLU	314,3536		14,286,1625	76.0	73.0	74.0		30457	-0.7	0.0	19	dbSNP_111	74	1506,6768		136,1234,2767	yes	missense	MUC16	NM_024690.2	29	150,1520,4392	GG,GC,CC		18.2016,8.1558,15.0115	possibly-damaging	10153/14508	9056989	1820,10304	1925	4137	6062	SO:0001583	missense	94025	exon3			TGGTCTCAAAATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30457G>C	19.37:g.9056989C>G	ENSP00000381008:p.Glu10153Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	462	0.21153846153846154	35	0.07113821138211382	93	0.2569060773480663	208	0.36363636363636365	126	0.1662269129287599	c	4.952	0.176786	0.09443	0.081558	0.182016	ENSG00000181143	ENST00000397910	T	0.40756	1.02	2.85	-0.7	0.11273	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	.	.	.	P	0.41041	0.736	B	0.40636	0.335	T	0.37596	-0.9699	8	0.87932	D	0	.	4.9506	0.14011	0.0:0.4393:0.4299:0.1308	rs4804381;rs4804381	10153	B5ME49	.	Q	10153	ENSP00000381008:E10153Q	ENSP00000381008:E10153Q	E	-	1	0	MUC16	8917989	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.107000	0.10873	-0.044000	0.13491	-0.300000	0.09419	GAG	C|0.780;G|0.220	0.220	strong		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CACNA1H	8912	hgsc.bcm.edu	37	16	1268979	1268979	+	Missense_Mutation	SNP	C	C	T	rs72552054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1268979C>T	ENST00000348261.5	+	34	6145	c.5897C>T	c.(5896-5898)gCc>gTc	p.A1966V	CACNA1H_ENST00000358590.4_Missense_Mutation_p.A1960V|CACNA1H_ENST00000565831.1_Missense_Mutation_p.A1960V	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1966					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GGCTCCGTTGCCTCTGTGCAC	0.682													c|||	46	0.0091853	0.0	0.0058	5008	,	,		11402	0.0		0.0149	False		,,,				2504	0.0276				p.A1966V		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5897T						PASS	.		VAL/ALA,VAL/ALA	16,3352		0,16,1668	7.0	10.0	9.0		5879,5897	3.5	0.0	16	dbSNP_130	9	133,6457		1,131,3163	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	64,64	1,147,4831	TT,TC,CC		2.0182,0.4751,1.4963	benign,benign	1960/2348,1966/2354	1268979	149,9809	1684	3295	4979	SO:0001583	missense	8912	exon34			CCGTTGCCTCTGT	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5897C>T	16.37:g.1268979C>T	ENSP00000334198:p.Ala1966Val	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	194	96	0.494845	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	c	11.79	1.743384	0.30865	0.004751	0.020182	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96554	-4.05;-3.99	4.43	3.48	0.39840	.	4.554490	0.01645	U	0.024250	D	0.87672	0.6236	N	0.24115	0.695	0.09310	N	1	B;B;B	0.24368	0.004;0.102;0.001	B;B;B	0.24541	0.004;0.054;0.004	T	0.80993	-0.1134	10	0.15952	T	0.53	.	9.8436	0.41013	0.0:0.9043:0.0:0.0957	.	712;1960;1966	A2SX38;O95180-2;O95180	.;.;CAC1H_HUMAN	V	1966;1960	ENSP00000334198:A1966V;ENSP00000351401:A1960V	ENSP00000334198:A1966V	A	+	2	0	CACNA1H	1208980	0.003000	0.15002	0.003000	0.11579	0.002000	0.02628	1.611000	0.36879	1.109000	0.41680	-0.394000	0.06481	GCC	C|0.992;T|0.008	0.008	strong		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
CIT	11113	hgsc.bcm.edu	37	12	120156141	120156141	+	Silent	SNP	G	G	A	rs278102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:120156141G>A	ENST00000261833.7	-	31	4003	c.3951C>T	c.(3949-3951)tcC>tcT	p.S1317S	CIT_ENST00000392521.2_Silent_p.S1359S|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1317					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GCACGATGGCGGACATGGCGA	0.642													G|||	914	0.182508	0.2383	0.1916	5008	,	,		13978	0.0109		0.2843	False		,,,				2504	0.1728				p.S1359S		Atlas-SNP	.											.	CIT	535	.	0			c.C4077T						PASS	.	G	,	1056,3350	385.6+/-325.8	134,788,1281	69.0	79.0	76.0		4077,3951	-8.0	0.9	12	dbSNP_79	76	2485,6113	407.8+/-349.3	358,1769,2172	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	492,2557,3453	AA,AG,GG		28.9021,23.9673,27.2301	,	1359/2070,1317/2028	120156141	3541,9463	2203	4299	6502	SO:0001819	synonymous_variant	11113	exon32			GATGGCGGACATG	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3951C>T	12.37:g.120156141G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	409	0.18727106227106227	115	0.23373983739837398	73	0.20165745856353592	5	0.008741258741258742	216	0.2849604221635884	G	11.45	1.641188	0.29157	0.239673	0.289021	ENSG00000122966	ENST00000392520	.	.	.	5.74	-8.01	0.01122	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17410	-1.0370	3	.	.	.	.	8.9636	0.35863	0.439:0.1088:0.4522:0.0	rs278102;rs17409026;rs278102	.	.	.	L	930	.	.	P	-	2	0	CIT	118640524	0.307000	0.24500	0.876000	0.34364	0.986000	0.74619	-0.263000	0.08670	-1.770000	0.01295	-0.345000	0.07892	CCG	G|0.760;A|0.240	0.240	strong		0.642	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
ATP6V0A2	23545	hgsc.bcm.edu	37	12	124209332	124209332	+	Silent	SNP	T	T	C	rs1139789	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124209332T>C	ENST00000330342.3	+	4	674	c.426T>C	c.(424-426)aaT>aaC	p.N142N		NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	142					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		TGAAACGCAATGTTGAGGTAC	0.383													C|||	3761	0.750998	0.7027	0.7723	5008	,	,		14701	0.9474		0.6282	False		,,,				2504	0.7249				p.N142N		Atlas-SNP	.											.	ATP6V0A2	68	.	0			c.T426C						PASS	.	C		2994,1412	462.3+/-353.2	1034,926,243	120.0	119.0	119.0		426	-7.5	0.0	12	dbSNP_86	119	5416,3184	482.8+/-371.0	1723,1970,607	no	coding-synonymous	ATP6V0A2	NM_012463.3		2757,2896,850	CC,CT,TT		37.0233,32.0472,35.3375		142/857	124209332	8410,4596	2203	4300	6503	SO:0001819	synonymous_variant	23545	exon4			ACGCAATGTTGAG	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"""ATPases / V-type"""	18481	protein-coding gene	gene with protein product	"""infantile malignant osteopetrosis"""	611716	"""infantile malignant osteopetrosis"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 2"", ""ATPase, H+ transporting, lysosomal V0 subunit A2"""			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.426T>C	12.37:g.124209332T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_012463	A8K026|Q6NUM0	Silent	SNP	ENST00000330342.3	37	CCDS9254.1																																																																																			T|0.317;G|0.037	.	strong		0.383	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463	
ALPK2	115701	hgsc.bcm.edu	37	18	56247180	56247180	+	Silent	SNP	T	T	C	rs9958735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56247180T>C	ENST00000361673.3	-	4	1041	c.828A>G	c.(826-828)ctA>ctG	p.L276L	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	276						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TTGCCTCAGATAGCGGGAGGC	0.493											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2555	0.510184	0.4289	0.4856	5008	,	,		20176	0.6022		0.5	False		,,,				2504	0.5532				p.L276L		Atlas-SNP	.											.	ALPK2	487	.	0			c.A828G						PASS	.	C		1924,2482	623.9+/-394.2	432,1060,711	114.0	106.0	109.0		828	-0.8	0.0	18	dbSNP_119	109	4310,4290	577.4+/-390.6	1113,2084,1103	no	coding-synonymous	ALPK2	NM_052947.3		1545,3144,1814	CC,CT,TT		49.8837,43.6677,47.9317		276/2171	56247180	6234,6772	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon4			CTCAGATAGCGGG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.828A>G	18.37:g.56247180T>C		Somatic	279	0	0	1014	WXS	Illumina HiSeq	Phase_I	278	277	0.996403	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			T|0.502;C|0.498	0.498	strong		0.493	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
PCDH1	5097	hgsc.bcm.edu	37	5	141243646	141243646	+	Silent	SNP	A	A	G	rs3797054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141243646A>G	ENST00000394536.3	-	3	2389	c.2250T>C	c.(2248-2250)gcT>gcC	p.A750A	PCDH1_ENST00000287008.3_Silent_p.A750A|PCDH1_ENST00000456271.1_Silent_p.A738A|PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000511044.1_5'UTR|PCDH1_ENST00000536585.1_Silent_p.A728A	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	750	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		AGATCAGCTCAGCATTGACAC	0.567													A|||	2107	0.420727	0.2935	0.3357	5008	,	,		21673	0.5784		0.3469	False		,,,				2504	0.5665				p.A750A	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.T2250C						PASS	.	A	,	1376,3030	454.2+/-350.6	207,962,1034	62.0	59.0	60.0		2250,2250	-8.3	1.0	5	dbSNP_107	60	3019,5581	463.9+/-366.1	551,1917,1832	no	coding-synonymous,coding-synonymous	PCDH1	NM_002587.3,NM_032420.2	,	758,2879,2866	GG,GA,AA		35.1047,31.2301,33.7921	,	750/1061,750/1238	141243646	4395,8611	2203	4300	6503	SO:0001819	synonymous_variant	5097	exon3			CAGCTCAGCATTG	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"""Cadherins / Protocadherins : Non-clustered"""	8655	protein-coding gene	gene with protein product		603626	"""protocadherin 1 (cadherin-like 1)"""			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.2250T>C	5.37:g.141243646A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	101	62	0.613861	NM_032420	Q8IUP2	Silent	SNP	ENST00000394536.3	37	CCDS43375.1																																																																																			A|0.640;G|0.360	0.360	strong		0.567	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49967981	49967981	+	Silent	SNP	T	T	G	rs11558188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49967981T>G	ENST00000293350.4	+	12	1693	c.1530T>G	c.(1528-1530)gtT>gtG	p.V510V	CTD-3148I10.9_ENST00000599536.1_3'UTR|ALDH16A1_ENST00000433981.2_Silent_p.V345V|ALDH16A1_ENST00000540132.1_Silent_p.V347V|ALDH16A1_ENST00000455361.2_Silent_p.V459V	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	510						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		GCCTCGCTGTTCCCTCAACCC	0.612													T|||	1051	0.209864	0.3396	0.2277	5008	,	,		14798	0.005		0.335	False		,,,				2504	0.1043				p.V510V		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.T1530G						PASS	.	T	,	1368,3038	451.4+/-349.7	214,940,1049	126.0	132.0	130.0		1377,1530	-9.3	0.0	19	dbSNP_120	130	3014,5586	465.2+/-366.4	527,1960,1813	yes	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	741,2900,2862	GG,GT,TT		35.0465,31.0486,33.6921	,	459/752,510/803	49967981	4382,8624	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon12			CGCTGTTCCCTCA	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1530T>G	19.37:g.49967981T>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			T|0.692;G|0.308	0.308	strong		0.612	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
PAPPA2	60676	hgsc.bcm.edu	37	1	176809368	176809368	+	Silent	SNP	C	C	T	rs12118034	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:176809368C>T	ENST00000367662.3	+	22	6426	c.5262C>T	c.(5260-5262)gaC>gaT	p.D1754D		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1754					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GCCACTATGACGGGGGAGACT	0.532													C|||	479	0.095647	0.0045	0.0821	5008	,	,		19455	0.002		0.2117	False		,,,				2504	0.2055				p.D1754D		Atlas-SNP	.											.	PAPPA2	665	.	0			c.C5262T						PASS	.	C		141,3847		4,133,1857	143.0	141.0	142.0		5262	-2.1	0.9	1	dbSNP_120	142	1495,6813		138,1219,2797	no	coding-synonymous	PAPPA2	NM_020318.2		142,1352,4654	TT,TC,CC		17.9947,3.5356,13.3051		1754/1792	176809368	1636,10660	1994	4154	6148	SO:0001819	synonymous_variant	60676	exon22			CTATGACGGGGGA	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.5262C>T	1.37:g.176809368C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	37	CCDS41438.1																																																																																			C|0.879;T|0.121	0.121	strong		0.532	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
ZNF519	162655	hgsc.bcm.edu	37	18	14105770	14105770	+	Missense_Mutation	SNP	T	T	C	rs61730995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:14105770T>C	ENST00000590202.1	-	3	921	c.769A>G	c.(769-771)Ata>Gta	p.I257V	ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	257					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						GTGTTAATTATCTTATGTCCC	0.328													T|||	7	0.00139776	0.0008	0.0014	5008	,	,		18546	0.0		0.004	False		,,,				2504	0.001				p.I257V		Atlas-SNP	.											.	ZNF519	53	.	0			c.A769G						PASS	.	T	VAL/ILE	5,4399	9.9+/-24.2	0,5,2197	43.0	48.0	46.0		769	0.6	0.0	18	dbSNP_129	46	72,8524	41.7+/-99.0	1,70,4227	no	missense	ZNF519	NM_145287.3	29	1,75,6424	CC,CT,TT		0.8376,0.1135,0.5923	benign	257/541	14105770	77,12923	2202	4298	6500	SO:0001583	missense	162655	exon3			TAATTATCTTATG	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.769A>G	18.37:g.14105770T>C	ENSP00000464872:p.Ile257Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	T	0.378	-0.930146	0.02359	0.001135	0.008376	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	.	.	.	.	.	T	0.19087	0.0458	N	0.25890	0.77	0.09310	N	0.999993	B	0.13594	0.008	B	0.08055	0.003	T	0.16041	-1.0416	8	0.39692	T	0.17	.	5.6281	0.17495	0.0:1.0E-4:0.0:0.9999	.	257	Q8TB69	ZN519_HUMAN	V	257	.	ENSP00000307908:I257V	I	-	1	0	ZNF519	14095770	0.000000	0.05858	0.005000	0.12908	0.342000	0.28953	-0.164000	0.09983	0.552000	0.29026	0.076000	0.15429	ATA	T|0.996;C|0.004	0.004	strong		0.328	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
CXorf58	254158	hgsc.bcm.edu	37	X	23928489	23928489	+	Missense_Mutation	SNP	C	C	T	rs2707164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:23928489C>T	ENST00000379211.3	+	2	619	c.70C>T	c.(70-72)Cgc>Tgc	p.R24C	APOO_ENST00000379220.3_5'Flank|APOO_ENST00000379226.4_5'Flank	NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	24			R -> C (in dbSNP:rs2707164). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						ACAAAAAGTTCGCAGAGTACA	0.373													C|||	1397	0.370066	0.1505	0.4294	3775	,	,		15069	0.2381		0.5139	False		,,,				2504	0.1462				p.R24C		Atlas-SNP	.											.	CXorf58	53	.	0			c.C70T						PASS	.	C	CYS/ARG,CYS/ARG	942,2893		112,572,146,948,425	131.0	96.0	108.0		70,70	-0.7	0.0	X	dbSNP_100	108	4745,1983		1222,987,1314,219,558	yes	missense,missense	CXorf58	NM_001169574.1,NM_152761.2	180,180	1334,1559,1460,1167,983	TT,TC,T,CC,C		29.4738,24.5632,46.1611	probably-damaging,probably-damaging	24/331,24/333	23928489	5687,4876	2203	4300	6503	SO:0001583	missense	254158	exon2			AAAGTTCGCAGAG	AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.70C>T	X.37:g.23928489C>T	ENSP00000368511:p.Arg24Cys	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_152761		Missense_Mutation	SNP	ENST00000379211.3	37	CCDS14209.1	772	0.4653405666063894	69	0.15065502183406113	104	0.4126984126984127	99	0.21153846153846154	260	0.49429657794676807	C	6.635	0.485625	0.12641	0.245632	0.705262	ENSG00000165182	ENST00000379211	T	0.32753	1.44	3.44	-0.668	0.11392	.	1.597720	0.03958	N	0.289533	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.67145	0.996	P	0.47573	0.55	T	0.42932	-0.9422	9	0.37606	T	0.19	10.0265	6.5671	0.22519	0.0:0.3254:0.5532:0.1214	rs2707164;rs17322469;rs52793631;rs58445345;rs2707164	24	Q96LI9	CX058_HUMAN	C	24	ENSP00000368511:R24C	ENSP00000368511:R24C	R	+	1	0	CXorf58	23838410	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.158000	0.16422	-0.274000	0.09232	0.600000	0.82982	CGC	0|0.003;T|0.491	0.491	strong		0.373	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761	
NTNG2	84628	hgsc.bcm.edu	37	9	135073877	135073877	+	Silent	SNP	C	C	T	rs3824574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135073877C>T	ENST00000393229.3	+	3	1514	c.738C>T	c.(736-738)ttC>ttT	p.F246F	NTNG2_ENST00000393228.4_Silent_p.F246F|NTNG2_ENST00000372179.3_Silent_p.F246F|NTNG2_ENST00000360670.3_Silent_p.F246F	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	246	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		TCAAGGAGTTCTTCACCCTCA	0.647													C|||	1454	0.290335	0.1936	0.2493	5008	,	,		18045	0.378		0.3211	False		,,,				2504	0.3282				p.F246F		Atlas-SNP	.											NTNG2,NS,carcinoma,0,1	NTNG2	66	1	0			c.C738T						PASS	.	C		847,3559		86,675,1442	49.0	53.0	52.0		738	2.1	1.0	9	dbSNP_107	52	2736,5860		441,1854,2003	no	coding-synonymous	NTNG2	NM_032536.2		527,2529,3445	TT,TC,CC		31.8288,19.2238,27.5573		246/531	135073877	3583,9419	2203	4298	6501	SO:0001819	synonymous_variant	84628	exon3			GGAGTTCTTCACC	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"""Netrins"""	14288	protein-coding gene	gene with protein product	"""Netrin-G2"""		"""netrin G1"""	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.738C>T	9.37:g.135073877C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	143	72	0.503497	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Silent	SNP	ENST00000393229.3	37	CCDS6946.1																																																																																			C|0.711;T|0.289	0.289	strong		0.647	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536	
ITPA	3704	hgsc.bcm.edu	37	20	3204084	3204084	+	Silent	SNP	G	G	A	rs9101	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:3204084G>A	ENST00000380113.3	+	8	753	c.561G>A	c.(559-561)gaG>gaA	p.E187E	ITPA_ENST00000399838.3_Silent_p.E146E|ITPA_ENST00000455664.2_Silent_p.E170E|ITPA_ENST00000483354.1_3'UTR	NM_033453.3|NM_181493.2	NP_258412.1|NP_852470.1			inosine triphosphatase (nucleoside triphosphate pyrophosphatase)											autonomic_ganglia(1)|large_intestine(3)|ovary(1)|stomach(1)	6						AGCTGCAGGAGTACTTTGGCA	0.632													G|||	1705	0.340455	0.0832	0.2781	5008	,	,		18199	0.5089		0.3091	False		,,,				2504	0.591				p.E187E		Atlas-SNP	.											ITPA,NS,carcinoma,0,1	ITPA	16	1	0			c.G561A						scavenged	.	G	,	495,3911	227.8+/-242.9	31,433,1739	50.0	40.0	43.0		561,510	-5.4	0.2	20	dbSNP_52	43	2458,6142	401.9+/-347.3	377,1704,2219	no	coding-synonymous,coding-synonymous	ITPA	NM_033453.2,NM_181493.1	,	408,2137,3958	AA,AG,GG		28.5814,11.2347,22.7049	,	187/195,170/178	3204084	2953,10053	2203	4300	6503	SO:0001819	synonymous_variant	3704	exon8			GCAGGAGTACTTT	AF026816	CCDS13051.1, CCDS46576.1, CCDS58762.1	20p	2002-02-01			ENSG00000125877	ENSG00000125877	3.6.1.19		6176	protein-coding gene	gene with protein product		147520		C20orf37		11278832	Standard	NM_033453		Approved	HLC14-06-P, dJ794I6.3	uc002wid.4	Q9BY32	OTTHUMG00000031738	ENST00000380113.3:c.561G>A	20.37:g.3204084G>A		Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_033453		Silent	SNP	ENST00000380113.3	37	CCDS13051.1																																																																																			G|0.729;A|0.271	0.271	strong		0.632	ITPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077719.2		
ZNF417	147687	hgsc.bcm.edu	37	19	58420682	58420682	+	Missense_Mutation	SNP	T	T	C	rs202194085		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58420682T>C	ENST00000312026.5	-	3	1128	c.964A>G	c.(964-966)Agg>Ggg	p.R322G	ZNF417_ENST00000595559.1_Missense_Mutation_p.R321G|ZNF417_ENST00000536263.1_Missense_Mutation_p.R123G|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	322					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		TCATAAGGCCTTTCTCCAGTG	0.463																																					p.R322G		Atlas-SNP	.											.	ZNF417	44	.	0			c.A964G						PASS	.						183.0	154.0	164.0					19																	58420682		2203	4300	6503	SO:0001583	missense	147687	exon3			AAGGCCTTTCTCC	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.964A>G	19.37:g.58420682T>C	ENSP00000311319:p.Arg322Gly	Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	332	43	0.129518	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	.	.	.	.	.	.	.	.	.	.	.	11.04	1.521531	0.27211	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.19938	2.11;2.11	2.21	1.15	0.20763	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25606	0.0623	M	0.80847	2.515	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.23547	-1.0185	9	0.52906	T	0.07	.	7.8867	0.29655	0.0:0.1347:0.0:0.8653	.	322	Q8TAU3	ZN417_HUMAN	G	322;123	ENSP00000311319:R322G;ENSP00000442760:R123G	ENSP00000311319:R322G	R	-	1	2	ZNF417	63112494	0.000000	0.05858	0.014000	0.15608	0.105000	0.19272	0.832000	0.27490	-0.231000	0.09825	-0.665000	0.03846	AGG	.	.	weak		0.463	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
OR4K1	79544	hgsc.bcm.edu	37	14	20404614	20404614	+	Missense_Mutation	SNP	C	C	A	rs34608158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20404614C>A	ENST00000285600.4	+	1	848	c.789C>A	c.(787-789)agC>agA	p.S263R		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, member 1	263						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		GGCCTTTTAGCAGACTTCCTG	0.418													C|||	886	0.176917	0.0408	0.1628	5008	,	,		25688	0.128		0.3032	False		,,,				2504	0.2914				p.S263R		Atlas-SNP	.											.	OR4K1	108	.	0			c.C789A						PASS	.	C	ARG/SER	353,4053		10,333,1860	125.0	130.0	128.0		789	2.2	1.0	14	dbSNP_126	128	2270,6330		212,1846,2242	yes	missense	OR4K1	NM_001004063.2	110	222,2179,4102	AA,AC,CC		26.3953,8.0118,20.1676	benign	263/312	20404614	2623,10383	2203	4300	6503	SO:0001583	missense	79544	exon1			TTTTAGCAGACTT		CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"""GPCR / Class A : Olfactory receptors"""	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.789C>A	14.37:g.20404614C>A	ENSP00000285600:p.Ser263Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	29	0.358025	NM_001004063	B9EKV9|Q8NGD6|Q96R73	Missense_Mutation	SNP	ENST00000285600.4	37	CCDS32025.1	413	0.1891025641025641	24	0.04878048780487805	72	0.19889502762430938	75	0.13111888111888112	242	0.31926121372031663	.	11.03	1.519819	0.27211	0.080118	0.263953	ENSG00000155249	ENST00000285600	T	0.00272	8.36	5.09	2.23	0.28157	GPCR, rhodopsin-like superfamily (1);	0.182279	0.39615	N	0.001304	T	0.00012	0.0000	M	0.64676	1.99	0.80722	P	0.0	B	0.23990	0.095	B	0.30105	0.111	T	0.25293	-1.0136	9	0.51188	T	0.08	.	7.3716	0.26804	0.0:0.6596:0.0:0.3404	rs34608158	263	Q8NGD4	OR4K1_HUMAN	R	263	ENSP00000285600:S263R	ENSP00000285600:S263R	S	+	3	2	OR4K1	19474454	0.000000	0.05858	0.997000	0.53966	0.817000	0.46193	-0.033000	0.12246	0.731000	0.32448	0.655000	0.94253	AGC	C|0.801;A|0.199	0.199	strong		0.418	OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1		
PNN	5411	hgsc.bcm.edu	37	14	39644498	39644498	+	Silent	SNP	G	G	A	rs11558738|rs1061583	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:39644498G>A	ENST00000216832.4	+	1	82	c.15G>A	c.(13-15)gtG>gtA	p.V5V	RP11-407N17.4_ENST00000556537.1_lincRNA|PNN_ENST00000553331.1_Silent_p.V5V|PNN_ENST00000556530.1_Silent_p.V5V	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	5	Necessary for interaction with RNPS1.|Necessary for interactions with KRT8, KRT18 and KRT19.|Necessary for mediating alternative 5' splicing.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		CGGTCGCCGTGAGAACTTTGC	0.602													G|||	935	0.186701	0.0091	0.2017	5008	,	,		14330	0.2321		0.2783	False		,,,				2504	0.2751				p.V5V		Atlas-SNP	.											PNN,right_upper_lobe,carcinoma,+2,1	PNN	67	1	0			c.G15A						PASS	.	G		228,4178	133.7+/-170.0	6,216,1981	53.0	45.0	48.0		15	5.2	1.0	14	dbSNP_86	48	2255,6345	377.2+/-338.5	290,1675,2335	no	coding-synonymous	PNN	NM_002687.3		296,1891,4316	AA,AG,GG		26.2209,5.1748,19.0912		5/718	39644498	2483,10523	2203	4300	6503	SO:0001819	synonymous_variant	5411	exon1			CGCCGTGAGAACT	U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.15G>A	14.37:g.39644498G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_002687	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Silent	SNP	ENST00000216832.4	37	CCDS9671.1																																																																																			G|0.804;A|0.196	0.196	strong		0.602	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687	
HSPG2	3339	hgsc.bcm.edu	37	1	22160020	22160020	+	Missense_Mutation	SNP	C	C	T	rs17459097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22160020C>T	ENST00000374695.3	-	79	10997	c.10918G>A	c.(10918-10920)Gtc>Atc	p.V3640I	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3640	Ig-like C2-type 22.		V -> I (in dbSNP:rs17459097).		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCGGTGCAGACGTAGGTACCT	0.612													C|||	109	0.0217652	0.0023	0.036	5008	,	,		19039	0.0		0.0765	False		,,,				2504	0.0041				p.V3640I		Atlas-SNP	.											.	HSPG2	311	.	0			c.G10918A						PASS	.	C	ILE/VAL	45,4361	48.9+/-83.8	1,43,2159	65.0	52.0	56.0		10918	1.0	1.0	1	dbSNP_123	56	466,8134	136.5+/-193.6	14,438,3848	yes	missense	HSPG2	NM_005529.5	29	15,481,6007	TT,TC,CC		5.4186,1.0213,3.929	benign	3640/4392	22160020	511,12495	2203	4300	6503	SO:0001583	missense	3339	exon79			TGCAGACGTAGGT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10918G>A	1.37:g.22160020C>T	ENSP00000363827:p.Val3640Ile	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	173	55	0.317919	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	73	0.033424908424908424	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	53	0.06992084432717678	C	8.812	0.935451	0.18206	0.010213	0.054186	ENSG00000142798	ENST00000374695	T	0.72394	-0.65	4.0	1.02	0.19986	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.222705	0.22729	N	0.056358	T	0.06781	0.0173	N	0.21545	0.675	0.29968	N	0.818844	B;B	0.18461	0.028;0.01	B;B	0.21360	0.034;0.015	T	0.06935	-1.0799	10	0.18710	T	0.47	.	8.9569	0.35823	0.0:0.7217:0.0:0.2783	rs17459097;rs52804667;rs17459097	1580;3640	Q59EG0;P98160	.;PGBM_HUMAN	I	3640	ENSP00000363827:V3640I	ENSP00000363827:V3640I	V	-	1	0	HSPG2	22032607	0.800000	0.28916	0.990000	0.47175	0.330000	0.28571	1.468000	0.35332	0.438000	0.26450	0.313000	0.20887	GTC	C|0.962;T|0.038	0.038	strong		0.612	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161019040	161019040	+	Missense_Mutation	SNP	G	G	C	rs3813609	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161019040G>C	ENST00000368013.3	-	12	2091	c.1771C>G	c.(1771-1773)Ctg>Gtg	p.L591V	ARHGAP30_ENST00000368015.1_Missense_Mutation_p.L414V|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.L591V	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	591			L -> V (in dbSNP:rs3813609). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GCGGAGTCCAGGGAACAGCAG	0.567													G|||	1983	0.395966	0.1815	0.4654	5008	,	,		21362	0.3333		0.6292	False		,,,				2504	0.4611				p.L591V		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.C1771G						PASS	.	G	VAL/LEU,VAL/LEU	1158,3248	410.6+/-335.4	145,868,1190	94.0	101.0	99.0		1771,1771	1.1	0.5	1	dbSNP_107	99	5222,3378	640.6+/-399.6	1560,2102,638	yes	missense,missense	ARHGAP30	NM_001025598.1,NM_181720.2	32,32	1705,2970,1828	CC,CG,GG		39.2791,26.2823,49.0543	benign,benign	591/1102,591/891	161019040	6380,6626	2203	4300	6503	SO:0001583	missense	257106	exon12			AGTCCAGGGAACA	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1771C>G	1.37:g.161019040G>C	ENSP00000356992:p.Leu591Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	CCDS30918.1	939	0.42994505494505497	101	0.20528455284552846	173	0.47790055248618785	191	0.3339160839160839	474	0.6253298153034301	G	9.123	1.009373	0.19277	0.262823	0.607209	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.35421	2.92;2.84;1.31	5.18	1.1	0.20463	.	1.038190	0.07683	N	0.937368	T	0.10594	0.0259	L	0.59436	1.845	0.58432	P	1.999999999946489E-6	B;P	0.41848	0.361;0.763	B;B	0.39027	0.081;0.288	T	0.18935	-1.0321	9	0.10902	T	0.67	.	1.7083	0.02887	0.2435:0.1391:0.4746:0.1429	rs3813609;rs52800561;rs3813609	591;591	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	V	591;591;443;414	ENSP00000356995:L591V;ENSP00000356992:L591V;ENSP00000356994:L414V	ENSP00000356992:L591V	L	-	1	2	ARHGAP30	159285664	0.983000	0.35010	0.518000	0.27811	0.941000	0.58515	2.269000	0.43346	-0.047000	0.13423	-0.266000	0.10368	CTG	G|0.539;C|0.461	0.461	strong		0.567	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
OR1I1	126370	hgsc.bcm.edu	37	19	15198606	15198606	+	Missense_Mutation	SNP	C	C	T	rs73008812	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198606C>T	ENST00000209540.2	+	1	816	c.730C>T	c.(730-732)Cac>Tac	p.H244Y		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						CTGTGGCTTACACCTCACTGT	0.527													C|||	912	0.182109	0.0242	0.219	5008	,	,		22596	0.2371		0.17	False		,,,				2504	0.3252				p.H244Y		Atlas-SNP	.											.	OR1I1	58	.	0			c.C730T						PASS	.	C	TYR/HIS	203,4203	126.1+/-163.2	3,197,2003	141.0	105.0	117.0		730	4.6	0.9	19	dbSNP_130	117	1454,7146	278.0+/-293.2	108,1238,2954	yes	missense	OR1I1	NM_001004713.1	83	111,1435,4957	TT,TC,CC		16.907,4.6074,12.7403	probably-damaging	244/356	15198606	1657,11349	2203	4300	6503	SO:0001583	missense	126370	exon1			GGCTTACACCTCA	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.730C>T	19.37:g.15198606C>T	ENSP00000209540:p.His244Tyr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	351	0.16071428571428573	17	0.034552845528455285	76	0.20994475138121546	119	0.20804195804195805	139	0.18337730870712401	C	15.83	2.950495	0.53186	0.046074	0.16907	ENSG00000094661	ENST00000209540	T	0.00314	8.14	4.6	4.6	0.57074	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33534	U	0.004803	T	0.00012	0.0000	H	0.98133	4.155	0.24052	P	0.99604909	D	0.89917	1.0	D	0.91635	0.999	T	0.22556	-1.0213	9	0.87932	D	0	.	15.022	0.71637	0.0:1.0:0.0:0.0	.	244	O60431	OR1I1_HUMAN	Y	244	ENSP00000209540:H244Y	ENSP00000209540:H244Y	H	+	1	0	OR1I1	15059606	0.954000	0.32549	0.941000	0.38009	0.174000	0.22865	2.196000	0.42686	2.419000	0.82065	0.549000	0.68633	CAC	C|0.866;T|0.134	0.134	strong		0.527	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
MYH14	79784	hgsc.bcm.edu	37	19	50771609	50771609	+	Silent	SNP	G	G	A	rs3745504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50771609G>A	ENST00000596571.1	+	21	2895	c.2895G>A	c.(2893-2895)ctG>ctA	p.L965L	MYH14_ENST00000262269.8_Silent_p.L1006L|MYH14_ENST00000440075.2_Silent_p.L1006L|MYH14_ENST00000425460.1_Silent_p.L973L|MYH14_ENST00000376970.2_Silent_p.L998L|MYH14_ENST00000601313.1_Silent_p.L1006L|MYH14_ENST00000598205.1_Silent_p.L973L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	965					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		AGAAGAGGCTGCAGCAGCACA	0.607													G|||	2426	0.484425	0.4221	0.6873	5008	,	,		15070	0.3829		0.5905	False		,,,				2504	0.4202				p.L1006L		Atlas-SNP	.											.	MYH14	261	.	0			c.G3018A						PASS	.	G	,,	1972,2276		477,1018,629	32.0	43.0	40.0		2919,3018,2895	3.9	1.0	19	dbSNP_107	40	4782,3680		1368,2046,817	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	1845,3064,1446	AA,AG,GG		43.4885,46.4218,46.8607	,,	973/2004,1006/2037,965/1996	50771609	6754,5956	2124	4231	6355	SO:0001819	synonymous_variant	79784	exon24			GAGGCTGCAGCAG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2895G>A	19.37:g.50771609G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			G|0.514;A|0.486	0.486	strong		0.607	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
ADCYAP1	116	hgsc.bcm.edu	37	18	907675	907675	+	Silent	SNP	G	G	A	rs8192597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:907675G>A	ENST00000579794.1	+	2	404	c.126G>A	c.(124-126)gcG>gcA	p.A42A	RP11-672L10.2_ENST00000577358.1_RNA|RP11-672L10.3_ENST00000582554.1_RNA|ADCYAP1_ENST00000450565.3_Silent_p.A42A|RP11-672L10.2_ENST00000581719.2_RNA|RP11-672L10.2_ENST00000580612.1_RNA	NM_001117.3	NP_001108.2	P18509	PACA_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary)	42					activation of adenylate cyclase activity (GO:0007190)|ATP metabolic process (GO:0046034)|behavioral fear response (GO:0001662)|cAMP-mediated signaling (GO:0019933)|cell-cell signaling (GO:0007267)|cellular response to glucocorticoid stimulus (GO:0071385)|female pregnancy (GO:0007565)|histamine secretion (GO:0001821)|negative regulation of acute inflammatory response to antigenic stimulus (GO:0002865)|negative regulation of acute inflammatory response to non-antigenic stimulus (GO:0002878)|negative regulation of cell cycle (GO:0045786)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of Rho GTPase activity (GO:0034259)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|pituitary gland development (GO:0021983)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of somatostatin secretion (GO:0090274)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)|regulation of postsynaptic membrane potential (GO:0060078)|regulation of protein localization (GO:0032880)|response to ethanol (GO:0045471)|response to starvation (GO:0042594)|sensory perception of pain (GO:0019233)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|terminal bouton (GO:0043195)	neuropeptide hormone activity (GO:0005184)|peptide hormone receptor binding (GO:0051428)|pituitary adenylate cyclase activating polypeptide activity (GO:0016521)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						AGGAAGAGGCGTACGGCGAGG	0.726													G|||	3516	0.702077	0.5061	0.7622	5008	,	,		8604	0.8492		0.6889	False		,,,				2504	0.7863				p.A42A		Atlas-SNP	.											ADCYAP1,NS,carcinoma,0,1	ADCYAP1	24	1	0			c.G126A						PASS	.	G	,	2350,1996		679,992,502	9.0	11.0	11.0		126,126	-3.4	1.0	18	dbSNP_117	11	6028,2476		2167,1694,391	no	coding-synonymous,coding-synonymous	ADCYAP1	NM_001099733.1,NM_001117.3	,	2846,2686,893	AA,AG,GG		29.1157,45.9273,34.8016	,	42/177,42/177	907675	8378,4472	2173	4252	6425	SO:0001819	synonymous_variant	116	exon3			AGAGGCGTACGGC	S83513	CCDS11825.1	18p11	2013-02-28			ENSG00000141433	ENSG00000141433		"""Endogenous ligands"""	241	protein-coding gene	gene with protein product	"""prepro-PACAP"""	102980				1730060	Standard	NM_001099733		Approved	PACAP	uc010dkh.4	P18509	OTTHUMG00000131479	ENST00000579794.1:c.126G>A	18.37:g.907675G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	11	10	0.909091	NM_001099733	B2R7N4|Q52LQ0	Silent	SNP	ENST00000579794.1	37	CCDS11825.1																																																																																			G|0.306;A|0.694	0.694	strong		0.726	ADCYAP1-003	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440765.3	NM_001117	
B3GALNT1	8706	hgsc.bcm.edu	37	3	160804167	160804167	+	Missense_Mutation	SNP	C	C	T	rs2231257	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:160804167C>T	ENST00000392781.2	-	8	1123	c.376G>A	c.(376-378)Gac>Aac	p.D126N	B3GALNT1_ENST00000392779.2_Missense_Mutation_p.D126N|B3GALNT1_ENST00000392780.1_Missense_Mutation_p.D126N|B3GALNT1_ENST00000417187.1_Intron|B3GALNT1_ENST00000473285.1_Missense_Mutation_p.D126N|B3GALNT1_ENST00000488170.1_Missense_Mutation_p.D126N|B3GALNT1_ENST00000320474.4_Missense_Mutation_p.D126N	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	126			D -> N (in dbSNP:rs2231257). {ECO:0000269|Ref.8}.		oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			AACATTTTGTCTTCCTTTTCA	0.393													C|||	260	0.0519169	0.0038	0.0591	5008	,	,		20257	0.0417		0.0298	False		,,,				2504	0.1452				p.D126N		Atlas-SNP	.											.	B3GALNT1	34	.	0			c.G376A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	49,4357	48.9+/-83.8	1,47,2155	107.0	103.0	105.0		376,376,376,376,376	5.7	1.0	3	dbSNP_98	105	290,8310	107.8+/-168.5	3,284,4013	yes	missense,missense,missense,missense,missense	B3GALNT1	NM_001038628.1,NM_003781.3,NM_033167.2,NM_033168.2,NM_033169.2	23,23,23,23,23	4,331,6168	TT,TC,CC		3.3721,1.1121,2.6065	benign,benign,benign,benign,benign	126/332,126/332,126/332,126/332,126/332	160804167	339,12667	2203	4300	6503	SO:0001583	missense	8706	exon8			TTTTGTCTTCCTT	Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"""Blood group antigens"", ""Beta 3-glycosyltransferases"""	918	protein-coding gene	gene with protein product	"""globoside synthase"", ""P antigen synthase"""	603094	"""UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)"", ""UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"""	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.376G>A	3.37:g.160804167C>T	ENSP00000376532:p.Asp126Asn	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	26	0.366197	NM_001038628	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Missense_Mutation	SNP	ENST00000392781.2	37	CCDS3193.1	58	0.026556776556776556	4	0.008130081300813009	14	0.03867403314917127	22	0.038461538461538464	18	0.023746701846965697	C	9.800	1.180328	0.21787	0.011121	0.033721	ENSG00000169255	ENST00000320474;ENST00000392779;ENST00000392780;ENST00000392781;ENST00000473285;ENST00000488170	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.73	5.73	0.89815	.	1.905830	0.02222	N	0.064124	T	0.27169	0.0666	L	0.31476	0.935	0.40277	D	0.978357	D	0.71674	0.998	D	0.63113	0.911	T	0.35773	-0.9775	10	0.38643	T	0.18	.	18.8796	0.92351	0.0:1.0:0.0:0.0	rs2231257;rs52824161;rs2231257	126	O75752	B3GL1_HUMAN	N	126	ENSP00000323479:D126N;ENSP00000376530:D126N;ENSP00000376531:D126N;ENSP00000376532:D126N;ENSP00000418226:D126N;ENSP00000420163:D126N	ENSP00000323479:D126N	D	-	1	0	B3GALNT1	162286861	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	4.898000	0.63238	2.701000	0.92244	0.561000	0.74099	GAC	C|0.973;T|0.027	0.027	strong		0.393	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167	
UBQLN3	50613	hgsc.bcm.edu	37	11	5528918	5528918	+	Missense_Mutation	SNP	C	C	T	rs2227271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5528918C>T	ENST00000311659.4	-	2	2018	c.1871G>A	c.(1870-1872)cGg>cAg	p.R624Q	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_5'Flank|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_5'Flank	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	624	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.		R -> Q (in dbSNP:rs2227271).							NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCCCATGGACCGCAGTTGCTC	0.547													C|||	921	0.183906	0.0552	0.3329	5008	,	,		19586	0.0516		0.3698	False		,,,				2504	0.1973				p.R624Q	Ovarian(72;684 1260 12332 41642 52180)	Atlas-SNP	.											UBQLN3,NS,carcinoma,0,4	UBQLN3	107	4	0			c.G1871A						PASS	.	C	GLN/ARG	447,3955	211.5+/-231.7	32,383,1786	68.0	71.0	70.0		1871	1.2	0.2	11	dbSNP_98	70	3262,5332	490.0+/-372.7	625,2012,1660	yes	missense	UBQLN3	NM_017481.2	43	657,2395,3446	TT,TC,CC		37.9567,10.1545,28.5396	possibly-damaging	624/656	5528918	3709,9287	2201	4297	6498	SO:0001583	missense	50613	exon2			ATGGACCGCAGTT	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"""Ubiquilin family"""	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1871G>A	11.37:g.5528918C>T	ENSP00000347997:p.Arg624Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	124	122	0.983871	NM_017481	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	37	CCDS7758.1	484	0.2216117216117216	44	0.08943089430894309	124	0.3425414364640884	40	0.06993006993006994	276	0.3641160949868074	C	9.298	1.052279	0.19827	0.101545	0.379567	ENSG00000175520	ENST00000311659	T	0.25085	1.82	5.14	1.23	0.21249	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.173706	0.28653	N	0.014599	T	0.00012	0.0000	L	0.33093	0.98	0.80722	P	0.0	B	0.20459	0.045	B	0.19391	0.025	T	0.44436	-0.9328	9	0.59425	D	0.04	-23.0576	6.8446	0.23980	0.0:0.5539:0.0:0.4461	rs2227271;rs17370824;rs52825586;rs2227271	624	Q9H347	UBQL3_HUMAN	Q	624	ENSP00000347997:R624Q	ENSP00000347997:R624Q	R	-	2	0	UBQLN3	5485494	0.001000	0.12720	0.213000	0.23690	0.979000	0.70002	0.537000	0.23144	0.429000	0.26202	0.655000	0.94253	CGG	C|0.756;T|0.244	0.244	strong		0.547	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481	
FAM154B	283726	hgsc.bcm.edu	37	15	82574461	82574461	+	Splice_Site	SNP	C	C	T	rs76375505	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:82574461C>T	ENST00000339465.5	+	3	324	c.255C>T	c.(253-255)gaC>gaT	p.D85D	FAM154B_ENST00000427381.2_Splice_Site_p.D70D|FAM154B_ENST00000565501.1_3'UTR	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	85										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						ATTTTCAAGACGATTATAGAG	0.333													C|||	132	0.0263578	0.003	0.0144	5008	,	,		19292	0.0605		0.0229	False		,,,				2504	0.0348				p.D85D		Atlas-SNP	.											.	FAM154B	50	.	0			c.C255T						PASS	.	C		15,4379		0,15,2182	53.0	58.0	56.0		255	2.4	1.0	15	dbSNP_131	56	192,8404		4,184,4110	no	coding-synonymous-near-splice	FAM154B	NM_001008226.1		4,199,6292	TT,TC,CC		2.2336,0.3414,1.5935		85/399	82574461	207,12783	2197	4298	6495	SO:0001630	splice_region_variant	283726	exon3			TCAAGACGATTAT	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.254-1C>T	15.37:g.82574461C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_001008226	B4E2M2	Silent	SNP	ENST00000339465.5	37	CCDS32310.1																																																																																			C|0.977;T|0.023	0.023	strong		0.333	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226	Silent
NOS2	4843	hgsc.bcm.edu	37	17	26105932	26105932	+	Silent	SNP	G	G	A	rs1137933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:26105932G>A	ENST00000313735.6	-	10	1388	c.1155C>T	c.(1153-1155)gaC>gaT	p.D385D		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	385					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	AGCGCTGGACGTCACAGAAGT	0.627													G|||	974	0.194489	0.1815	0.1974	5008	,	,		13055	0.1736		0.2445	False		,,,				2504	0.18				p.D385D		Atlas-SNP	.											.	NOS2	113	.	0			c.C1155T	GRCh37	CM041814	NOS2	M	rs1137933	PASS	.	G		824,3582	327.5+/-300.1	76,672,1455	80.0	79.0	79.0		1155	-8.7	0.0	17	dbSNP_86	79	1940,6660	341.2+/-323.9	259,1422,2619	no	coding-synonymous	NOS2	NM_000625.4		335,2094,4074	AA,AG,GG		22.5581,18.7018,21.2517		385/1154	26105932	2764,10242	2203	4300	6503	SO:0001819	synonymous_variant	4843	exon10			CTGGACGTCACAG	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1155C>T	17.37:g.26105932G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			G|0.794;N|0.002	.	strong		0.627	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
ATP2C2	9914	hgsc.bcm.edu	37	16	84402275	84402275	+	Silent	SNP	G	G	C	rs62048787	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84402275G>C	ENST00000262429.4	+	1	143	c.54G>C	c.(52-54)ggG>ggC	p.G18G	ATP2C2_ENST00000416219.2_Silent_p.G18G	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	18					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.G18G(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TCTCGGGCGGGGGCCGCCAGT	0.706													G|||	2092	0.417732	0.5499	0.4856	5008	,	,		12564	0.4841		0.2714	False		,,,				2504	0.273				p.G18G		Atlas-SNP	.											ATP2C2,rectum,carcinoma,0,3	ATP2C2	75	3	2	Substitution - coding silent(2)	prostate(2)	c.G54C						PASS	.	G		1340,2286		254,832,727	7.0	12.0	11.0		54	-6.1	0.0	16	dbSNP_129	11	1685,6367		219,1247,2560	no	coding-synonymous	ATP2C2	NM_014861.2		473,2079,3287	CC,CG,GG		20.9265,36.9553,25.9034		18/947	84402275	3025,8653	1813	4026	5839	SO:0001819	synonymous_variant	9914	exon1			GGGCGGGGGCCGC	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.54G>C	16.37:g.84402275G>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Silent	SNP	ENST00000262429.4	37	CCDS42207.1																																																																																			G|0.597;C|0.403	0.403	strong		0.706	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
MRPL4	51073	hgsc.bcm.edu	37	19	10363251	10363251	+	Missense_Mutation	SNP	A	A	C	rs113197610	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10363251A>C	ENST00000253099.6	+	3	436	c.149A>C	c.(148-150)aAa>aCa	p.K50T	MRPL4_ENST00000393733.2_Missense_Mutation_p.K50T|MRPL4_ENST00000307422.5_Missense_Mutation_p.K50T|MRPL4_ENST00000590669.1_Missense_Mutation_p.K50T|CTD-2369P2.5_ENST00000592893.1_RNA|MRPL4_ENST00000588502.1_Missense_Mutation_p.K49T	NM_015956.2|NM_146388.1	NP_057040.2|NP_666500.1	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4	50					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)		GTGCTGCGCAAAGTCGAGCTC	0.692													A|||	60	0.0119808	0.0023	0.0144	5008	,	,		15483	0.0		0.0189	False		,,,				2504	0.0286				p.K50T		Atlas-SNP	.											.	MRPL4	22	.	0			c.A149C						PASS	.	A	THR/LYS,THR/LYS,THR/LYS	17,4389		0,17,2186	37.0	41.0	40.0		149,149,149	-1.5	0.0	19	dbSNP_132	40	171,8429		2,167,4131	yes	missense,missense,missense	MRPL4	NM_015956.2,NM_146387.1,NM_146388.1	78,78,78	2,184,6317	CC,CA,AA		1.9884,0.3858,1.4455	benign,benign,benign	50/312,50/312,50/264	10363251	188,12818	2203	4300	6503	SO:0001583	missense	51073	exon4			TGCGCAAAGTCGA	AB049635	CCDS12230.1, CCDS42499.1	19p13.2	2012-11-14			ENSG00000105364	ENSG00000105364		"""Mitochondrial ribosomal proteins / large subunits"""	14276	protein-coding gene	gene with protein product		611823					Standard	NM_015956		Approved	CGI-28	uc002mnn.3	Q9BYD3	OTTHUMG00000180400	ENST00000253099.6:c.149A>C	19.37:g.10363251A>C	ENSP00000253099:p.Lys50Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_146387	A6NNV7|Q9BW07|Q9H4N2|Q9Y317	Missense_Mutation	SNP	ENST00000253099.6	37	CCDS12230.1	21	0.009615384615384616	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	12	0.0158311345646438	A	13.37	2.215716	0.39102	0.003858	0.019884	ENSG00000105364	ENST00000253099;ENST00000307422;ENST00000393733	.	.	.	4.89	-1.47	0.08772	.	0.573531	0.17229	N	0.182001	T	0.13628	0.0330	L	0.38175	1.15	0.09310	N	1	B;B	0.21071	0.051;0.01	B;B	0.20767	0.031;0.005	T	0.09100	-1.0690	9	0.37606	T	0.19	-7.6469	4.889	0.13717	0.4132:0.285:0.3018:0.0	.	50;50	Q9BYD3-2;Q9BYD3	.;RM04_HUMAN	T	50	.	ENSP00000253099:K50T	K	+	2	0	MRPL4	10224251	0.000000	0.05858	0.001000	0.08648	0.028000	0.11728	-1.091000	0.03369	-0.458000	0.07023	0.454000	0.30748	AAA	A|0.988;C|0.012	0.012	strong		0.692	MRPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451197.1		
LGR5	8549	hgsc.bcm.edu	37	12	71977427	71977427	+	Splice_Site	SNP	G	G	A	rs200272164		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:71977427G>A	ENST00000266674.5	+	18	1948	c.1637G>A	c.(1636-1638)gGc>gAc	p.G546D	LGR5_ENST00000540815.2_Splice_Site_p.G522D|LGR5_ENST00000536515.1_Splice_Site_p.G474D|RP11-186F10.2_ENST00000546601.1_RNA			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	546					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						GGACTTCTAGGCCCCTTCAAA	0.423													G|||	1	0.000199681	0.0	0.0	5008	,	,		22325	0.0		0.001	False		,,,				2504	0.0				p.G546D		Atlas-SNP	.											.	LGR5	103	.	0			c.G1637A						PASS	.						180.0	173.0	176.0					12																	71977427		2203	4300	6503	SO:0001630	splice_region_variant	8549	exon18			TTCTAGGCCCCTT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"""GPCR / Class A : Orphans"""	4504	protein-coding gene	gene with protein product		606667	"""G protein-coupled receptor 49"", ""leucine-rich repeat-containing G protein-coupled receptor 5"""	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1637-1G>A	12.37:g.71977427G>A		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	268	123	0.458955	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation	SNP	ENST00000266674.5	37	CCDS9000.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	25.7	4.663054	0.88251	.	.	ENSG00000139292	ENST00000266674;ENST00000451585;ENST00000536515;ENST00000540815	D;D;D	0.90563	-2.69;-2.69;-2.69	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000005	D	0.92570	0.7640	L	0.31065	0.9	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.99;0.998	D	0.91262	0.5037	9	.	.	.	.	19.812	0.96551	0.0:0.0:1.0:0.0	.	522;546	O75473-2;O75473	.;LGR5_HUMAN	D	546;546;474;522	ENSP00000266674:G546D;ENSP00000443033:G474D;ENSP00000441035:G522D	.	G	+	2	0	LGR5	70263694	1.000000	0.71417	0.991000	0.47740	0.940000	0.58332	9.807000	0.99171	2.685000	0.91497	0.655000	0.94253	GGC	G|1.000;A|0.000	0.000	strong		0.423	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667	Missense_Mutation
DCAF8L1	139425	hgsc.bcm.edu	37	X	27999146	27999146	+	Silent	SNP	C	C	T	rs41311803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:27999146C>T	ENST00000441525.1	-	1	420	c.306G>A	c.(304-306)gaG>gaA	p.E102E		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	102	Glu-rich.									NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						cttcttcttcctcctccCTTT	0.502													C|||	347	0.0919205	0.1074	0.0403	3775	,	,		15425	0.0387		0.0676	False		,,,				2504	0.0716				p.E102E		Atlas-SNP	.											.	DCAF8L1	121	.	0			c.G306A						PASS	.	C		530,3303		44,376,66,1211,505	154.0	96.0	116.0		306	0.8	0.6	X	dbSNP_127	116	538,6190		20,352,146,2056,1726	no	coding-synonymous	DCAF8L1	NM_001017930.1		64,728,212,3267,2231	TT,TC,T,CC,C		7.9964,13.8273,10.1127		102/601	27999146	1068,9493	2202	4300	6502	SO:0001819	synonymous_variant	139425	exon1			TTCTTCCTCCTCC		CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"""WD repeat domain containing"""	31810	protein-coding gene	gene with protein product			"""WD repeat domain 42B"""	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.306G>A	X.37:g.27999146C>T		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_001017930	B3KXX1	Silent	SNP	ENST00000441525.1	37	CCDS35222.1																																																																																			C|0.904;T|0.096	0.096	strong		0.502	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690	
SCARF1	8578	hgsc.bcm.edu	37	17	1542153	1542153	+	Silent	SNP	G	G	A	rs2272012	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1542153G>A	ENST00000263071.4	-	8	1360	c.1311C>T	c.(1309-1311)ggC>ggT	p.G437G	SCARF1_ENST00000348987.3_Silent_p.G351G|SCARF1_ENST00000574545.1_5'Flank|SCARF1_ENST00000571272.1_Silent_p.G437G	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	437	Poly-Leu.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGCAGGCAAGGCCCAGGAAGA	0.667													G|||	3234	0.645767	0.4244	0.6902	5008	,	,		13734	0.877		0.6332	False		,,,				2504	0.6881				p.G437G		Atlas-SNP	.											.	SCARF1	46	.	0			c.C1311T						PASS	.	G	,,	2047,2357	547.5+/-377.3	490,1067,645	43.0	44.0	44.0		1311,1311,1053	4.5	0.9	17	dbSNP_100	44	5338,3262	637.9+/-399.3	1633,2072,595	no	coding-synonymous,coding-synonymous,coding-synonymous	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	,,	2123,3139,1240	AA,AG,GG		37.9302,46.4805,43.2098	,,	437/831,437/570,351/745	1542153	7385,5619	2202	4300	6502	SO:0001819	synonymous_variant	8578	exon8			GGCAAGGCCCAGG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1311C>T	17.37:g.1542153G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	224	223	0.995536	NM_145350	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Silent	SNP	ENST00000263071.4	37	CCDS11007.1																																																																																			G|0.403;A|0.597	0.597	strong		0.667	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
LAMC3	10319	hgsc.bcm.edu	37	9	133962930	133962930	+	Missense_Mutation	SNP	C	C	T	rs7024108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133962930C>T	ENST00000361069.4	+	26	4431	c.4298C>T	c.(4297-4299)aCg>aTg	p.T1433M	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1433	Domain II and I.			T -> M (in Ref. 3; BAD92124). {ECO:0000305}.	astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		ACCAGCCAGACGCAAGCCACG	0.647													C|||	1112	0.222045	0.2148	0.2075	5008	,	,		17990	0.1855		0.337	False		,,,				2504	0.1616				p.T1433M		Atlas-SNP	.											.	LAMC3	167	.	0			c.C4298T						PASS	.	C	MET/THR	1003,3403	371.0+/-319.8	108,787,1308	72.0	77.0	75.0		4298	2.9	0.2	9	dbSNP_116	75	2925,5675	455.5+/-363.8	473,1979,1848	yes	missense	LAMC3	NM_006059.3	81	581,2766,3156	TT,TC,CC		34.0116,22.7644,30.2014	benign	1433/1576	133962930	3928,9078	2203	4300	6503	SO:0001583	missense	10319	exon26			GCCAGACGCAAGC	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.4298C>T	9.37:g.133962930C>T	ENSP00000354360:p.Thr1433Met	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	553|553	0.2532051282051282|0.2532051282051282	112|112	0.22764227642276422|0.22764227642276422	79|79	0.21823204419889503|0.21823204419889503	111|111	0.19405594405594406|0.19405594405594406	251|251	0.3311345646437995|0.3311345646437995	C|C	11.05|11.05	1.523552|1.523552	0.27299|0.27299	0.227644|0.227644	0.340116|0.340116	ENSG00000050555|ENSG00000050555	ENST00000355452|ENST00000361069;ENST00000355048	.|T	.|0.27890	.|1.64	4.74|4.74	2.92|2.92	0.33932|0.33932	.|.	.|0.640244	.|0.15728	.|N	.|0.247567	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	P|P	0.0|0.0	.|P	.|0.38020	.|0.615	.|B	.|0.27608	.|0.081	T|T	0.40059|0.40059	-0.9583|-0.9583	4|9	.|0.46703	.|T	.|0.11	.|.	7.0722|7.0722	0.25185|0.25185	0.0:0.797:0.0:0.203|0.0:0.797:0.0:0.203	rs7024108;rs7024108|rs7024108;rs7024108	.|1433	.|Q9Y6N6	.|LAMC3_HUMAN	C|M	115|1433;1445	.|ENSP00000354360:T1433M	.|ENSP00000347156:T1445M	R|T	+|+	1|2	0|0	LAMC3|LAMC3	132952751|132952751	0.111000|0.111000	0.22076|0.22076	0.228000|0.228000	0.23943|0.23943	0.045000|0.045000	0.14185|0.14185	1.156000|1.156000	0.31712|0.31712	0.621000|0.621000	0.30232|0.30232	-0.251000|-0.251000	0.11542|0.11542	CGC|ACG	C|0.725;T|0.275	0.275	strong		0.647	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
UGT1A3	54659	hgsc.bcm.edu	37	2	234638580	234638580	+	Missense_Mutation	SNP	A	A	G	rs45449995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234638580A>G	ENST00000482026.1	+	1	827	c.808A>G	c.(808-810)Atg>Gtg	p.M270V	UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000609767.1_Missense_Mutation_p.M270V|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	270			M -> V (in dbSNP:rs45449995). {ECO:0000269|PubMed:19204906}.		cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	CAGGCCAATCATGCCCAACAT	0.498													A|||	121	0.0241613	0.0522	0.013	5008	,	,		17408	0.003		0.0239	False		,,,				2504	0.0164				p.M270V		Atlas-SNP	.											.	UGT1A3	91	.	0			c.A808G						PASS	.	A	,,,,,,VAL/MET,,	239,4167	141.1+/-176.5	8,223,1972	144.0	144.0	144.0		,,,,,,808,,	4.0	1.0	2	dbSNP_127	144	267,8333	103.1+/-164.3	4,259,4037	yes	intron,intron,intron,intron,intron,intron,missense,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,21,,	12,482,6009	GG,GA,AA		3.1047,5.4244,3.8905	,,,,,,,,	,,,,,,270/535,,	234638580	506,12500	2203	4300	6503	SO:0001583	missense	54659	exon1			CCAATCATGCCCA	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"""UDP glucuronosyltransferases"""	12535	other	complex locus constituent		606428	"""UDP glycosyltransferase 1 family, polypeptide A3"""			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.808A>G	2.37:g.234638580A>G	ENSP00000418532:p.Met270Val	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	229	109	0.475983	NM_019093	B8K287	Missense_Mutation	SNP	ENST00000482026.1	37	CCDS2509.1	57	0.0260989010989011	29	0.05894308943089431	9	0.024861878453038673	0	0.0	19	0.025065963060686015	a	21.0	4.089494	0.76756	0.054244	0.031047	ENSG00000243135	ENST00000482026	T	0.59906	0.23	4.0	4.0	0.46444	.	.	.	.	.	T	0.25005	0.0607	M	0.79011	2.435	0.42150	D	0.991559	P;P	0.47191	0.891;0.891	P;P	0.57720	0.826;0.826	T	0.59193	-0.7500	9	0.56958	D	0.05	.	12.938	0.58327	1.0:0.0:0.0:0.0	rs45449995;rs61734925	270;270	Q5DT01;P35503	.;UD13_HUMAN	V	270	ENSP00000418532:M270V	ENSP00000418532:M270V	M	+	1	0	UGT1A3	234303319	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.456000	0.80751	1.457000	0.47850	0.373000	0.22412	ATG	A|0.962;G|0.038	0.038	strong		0.498	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093	
UBE2O	63893	hgsc.bcm.edu	37	17	74392249	74392249	+	Silent	SNP	G	G	A	rs76110889	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74392249G>A	ENST00000319380.7	-	14	2833	c.2769C>T	c.(2767-2769)agC>agT	p.S923S	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	923					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						CGCCCTTGGCGCTGGTGAAGG	0.642													G|||	16	0.00319489	0.0	0.0058	5008	,	,		17280	0.0		0.0119	False		,,,				2504	0.0				p.S923S		Atlas-SNP	.											.	UBE2O	207	.	0			c.C2769T						PASS	.	G		12,4394	17.9+/-39.9	0,12,2191	40.0	43.0	42.0		2769	-0.5	1.0	17	dbSNP_132	42	106,8494	59.1+/-120.7	0,106,4194	no	coding-synonymous	UBE2O	NM_022066.3		0,118,6385	AA,AG,GG		1.2326,0.2724,0.9073		923/1293	74392249	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	63893	exon14			CTTGGCGCTGGTG	AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.2769C>T	17.37:g.74392249G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	37	CCDS32742.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066	
PCSK1	5122	hgsc.bcm.edu	37	5	95728898	95728898	+	Missense_Mutation	SNP	C	C	G	rs6235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:95728898C>G	ENST00000311106.3	-	14	2306	c.2069G>C	c.(2068-2070)aGt>aCt	p.S690T	PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.S643T	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	690			S -> T (in dbSNP:rs6235). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:17595246}.		cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GAGCTTTGCACTTGGGGACTT	0.483													C|||	1221	0.24381	0.1263	0.2305	5008	,	,		19208	0.3591		0.2594	False		,,,				2504	0.2771				p.S690T		Atlas-SNP	.											.	PCSK1	93	.	0			c.G2069C						PASS	.	C	THR/SER,THR/SER,THR/SER	702,3704	291.5+/-281.6	53,596,1554	115.0	121.0	119.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2069,1928,1139	4.0	1.0	5	dbSNP_52	119	2389,6211	397.4+/-345.7	301,1787,2212	yes	missense,missense,missense	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	58,58,58	354,2383,3766	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	27.7791,15.9328,23.766	benign,benign,benign	690/754,643/707,380/444	95728898	3091,9915	2203	4300	6503	SO:0001583	missense	5122	exon14			TTTGCACTTGGGG		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.2069G>C	5.37:g.95728898C>G	ENSP00000308024:p.Ser690Thr	Somatic	439	0	0		WXS	Illumina HiSeq	Phase_I	444	199	0.448198	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	538	0.24633699633699635	51	0.10365853658536585	83	0.2292817679558011	196	0.34265734265734266	208	0.27440633245382584	C	8.948	0.967513	0.18659	0.159328	0.277791	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.66280	-0.05;-0.2	5.76	3.95	0.45737	.	0.280490	0.40554	N	0.001078	T	0.00012	0.0000	L	0.50333	1.59	0.48696	P	3.0399999999997096E-4	B;B	0.10296	0.003;0.001	B;B	0.09377	0.004;0.002	T	0.13308	-1.0514	9	0.14656	T	0.56	-7.0802	9.5219	0.39140	0.0:0.8156:0.0:0.1844	rs6235;rs52800779;rs6235	643;690	E9PHA1;P29120	.;NEC1_HUMAN	T	690;643	ENSP00000308024:S690T;ENSP00000421600:S643T	ENSP00000308024:S690T	S	-	2	0	PCSK1	95754654	0.131000	0.22433	0.983000	0.44433	0.308000	0.27856	0.893000	0.28336	2.713000	0.92767	0.655000	0.94253	AGT	C|0.756;G|0.244	0.244	strong		0.483	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
CDH3	1001	hgsc.bcm.edu	37	16	68712730	68712730	+	Silent	SNP	C	C	A	rs8049247	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:68712730C>A	ENST00000264012.4	+	6	1156	c.612C>A	c.(610-612)atC>atA	p.I204I	CDH3_ENST00000429102.2_Silent_p.I204I|CDH3_ENST00000581171.1_Silent_p.I149I	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	204	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TCTCCATCATCGTGACCGACC	0.577													C|||	700	0.139776	0.32	0.0865	5008	,	,		18836	0.002		0.1471	False		,,,				2504	0.0685				p.I204I		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.C612A						PASS	.	C		1252,3144	428.9+/-342.0	161,930,1107	64.0	51.0	55.0		612	-6.3	0.1	16	dbSNP_116	55	1216,7384	245.6+/-274.3	82,1052,3166	no	coding-synonymous	CDH3	NM_001793.4		243,1982,4273	AA,AC,CC		14.1395,28.4804,18.9905		204/830	68712730	2468,10528	2198	4300	6498	SO:0001819	synonymous_variant	1001	exon6			CATCATCGTGACC	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.612C>A	16.37:g.68712730C>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	130	52	0.4	NM_001793	B2R6F4|Q05DI6	Silent	SNP	ENST00000264012.4	37	CCDS10868.1																																																																																			C|0.825;A|0.175	0.175	strong		0.577	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
ADHFE1	137872	hgsc.bcm.edu	37	8	67369355	67369355	+	Silent	SNP	G	G	C	rs2555588	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:67369355G>C	ENST00000396623.3	+	12	1147	c.1116G>C	c.(1114-1116)acG>acC	p.T372T	ADHFE1_ENST00000496501.1_3'UTR|ADHFE1_ENST00000415254.1_Silent_p.T324T	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	372					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|molecular hydrogen transport (GO:0015993)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacid-oxoacid transhydrogenase activity (GO:0047988)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	29		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			TCACTTTCACGGCCCAGATGT	0.552													G|||	682	0.136182	0.2141	0.1542	5008	,	,		15377	0.0		0.2078	False		,,,				2504	0.0849				p.T372T		Atlas-SNP	.											.	ADHFE1	83	.	0			c.G1116C						PASS	.	G		1003,3403	374.9+/-321.4	125,753,1325	165.0	154.0	157.0		1116	-11.7	0.0	8	dbSNP_100	157	1562,7038	292.6+/-300.9	143,1276,2881	no	coding-synonymous	ADHFE1	NM_144650.2		268,2029,4206	CC,CG,GG		18.1628,22.7644,19.7217		372/468	67369355	2565,10441	2203	4300	6503	SO:0001819	synonymous_variant	137872	exon12			TTTCACGGCCCAG	AK056992	CCDS6190.2	8q12.3	2013-05-21			ENSG00000147576	ENSG00000147576	1.1.99.24	"""Alcohol dehydrogenases"""	16354	protein-coding gene	gene with protein product	"""hydroxyacid-oxoacid transhydrogenase"""	611083				12592711	Standard	NM_144650		Approved	ADHFe1, FLJ32430	uc003xwb.4	Q8IWW8	OTTHUMG00000150215	ENST00000396623.3:c.1116G>C	8.37:g.67369355G>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	96	33	0.34375	NM_144650	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Silent	SNP	ENST00000396623.3	37	CCDS6190.2																																																																																			G|0.827;C|0.173	0.173	strong		0.552	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650	
ZNF862	643641	hgsc.bcm.edu	37	7	149558409	149558409	+	Silent	SNP	G	G	C	rs2240361	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149558409G>C	ENST00000223210.4	+	7	2405	c.2160G>C	c.(2158-2160)ctG>ctC	p.L720L	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	720					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CGCAGCTGCTGCCTGTCCACT	0.647													G|||	1906	0.380591	0.2405	0.4741	5008	,	,		18325	0.3284		0.5865	False		,,,				2504	0.3456				p.L720L		Atlas-SNP	.											.	ZNF862	97	.	0			c.G2160C						PASS	.	G		1404,2736		251,902,917	26.0	28.0	27.0		2160	4.4	1.0	7	dbSNP_98	27	5043,3367		1539,1965,701	no	coding-synonymous	ZNF862	NM_001099220.1		1790,2867,1618	CC,CG,GG		40.0357,33.913,48.6295		720/1170	149558409	6447,6103	2070	4205	6275	SO:0001819	synonymous_variant	643641	exon7			GCTGCTGCCTGTC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.2160G>C	7.37:g.149558409G>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																			G|0.536;C|0.464	0.464	strong		0.647	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
SORBS1	10580	hgsc.bcm.edu	37	10	97141523	97141523	+	Silent	SNP	G	G	A	rs2274490	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:97141523G>A	ENST00000361941.3	-	16	1598	c.1572C>T	c.(1570-1572)gaC>gaT	p.D524D	SORBS1_ENST00000371227.4_Silent_p.D478D|SORBS1_ENST00000354106.3_Silent_p.D494D|SORBS1_ENST00000371246.2_Silent_p.D546D|SORBS1_ENST00000371239.1_Silent_p.D323D|SORBS1_ENST00000371247.2_Silent_p.D524D|SORBS1_ENST00000306402.6_Silent_p.D355D|SORBS1_ENST00000347291.4_Silent_p.D392D|SORBS1_ENST00000607232.1_Silent_p.D313D|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000371245.3_Silent_p.D409D|SORBS1_ENST00000371241.1_Silent_p.D314D|SORBS1_ENST00000353505.5_Silent_p.D409D|SORBS1_ENST00000371249.2_Silent_p.D446D|SORBS1_ENST00000393949.1_Silent_p.D494D|SORBS1_ENST00000277982.5_Silent_p.D546D	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		ATTTTCTTGTGTCTACTTTCT	0.413													A|||	2992	0.597444	0.4289	0.7233	5008	,	,		18584	0.6498		0.6024	False		,,,				2504	0.6769				p.D546D		Atlas-SNP	.											.	SORBS1	185	.	0			c.C1638T						PASS	.	A	,,,,,,	2024,2382	613.3+/-392.2	452,1120,631	180.0	178.0	179.0		1572,1638,1227,942,942,1338,1065	4.9	1.0	10	dbSNP_100	179	5076,3524	512.8+/-378.0	1496,2084,720	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	1948,3204,1351	AA,AG,GG		40.9767,45.9374,45.4098	,,,,,,	524/1293,546/1152,409/906,314/741,314/685,446/817,355/782	97141523	7100,5906	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon16			TCTTGTGTCTACT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.1572C>T	10.37:g.97141523G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			G|0.436;A|0.564	0.564	strong		0.413	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
ITGBL1	9358	hgsc.bcm.edu	37	13	102366825	102366825	+	Silent	SNP	A	A	G	rs2281991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:102366825A>G	ENST00000376180.3	+	10	1536	c.1317A>G	c.(1315-1317)gaA>gaG	p.E439E	RP11-397O8.7_ENST00000606869.1_lincRNA|ITGBL1_ENST00000376162.3_Silent_p.E346E|ITGBL1_ENST00000545560.2_Silent_p.E298E	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	439	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTTCTGCTGAAGAGTGGTATA	0.393													A|||	1071	0.213858	0.0847	0.1614	5008	,	,		21448	0.4058		0.1521	False		,,,				2504	0.2914				p.E439E		Atlas-SNP	.											.	ITGBL1	83	.	0			c.A1317G						PASS	.	A		416,3990	205.5+/-227.4	23,370,1810	424.0	393.0	403.0		1317	1.7	0.2	13	dbSNP_100	403	1183,7417	241.3+/-271.7	84,1015,3201	no	coding-synonymous	ITGBL1	NM_004791.1		107,1385,5011	GG,GA,AA		13.7558,9.4417,12.2943		439/495	102366825	1599,11407	2203	4300	6503	SO:0001819	synonymous_variant	9358	exon10			TGCTGAAGAGTGG	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"""ten integrin EGF-like repeat domains protein"", ""ITGBL1, integrin beta-like 1"""	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.1317A>G	13.37:g.102366825A>G		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	237	123	0.518987	NM_004791	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Silent	SNP	ENST00000376180.3	37	CCDS9499.1																																																																																			A|0.829;G|0.171	0.171	strong		0.393	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791	
CDS1	1040	hgsc.bcm.edu	37	4	85530633	85530633	+	Missense_Mutation	SNP	G	G	T	rs36068434	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:85530633G>T	ENST00000295887.5	+	3	720	c.297G>T	c.(295-297)ttG>ttT	p.L99F		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		TGATCTCGTTGTTTTTCCTGA	0.338													G|||	153	0.0305511	0.0371	0.0144	5008	,	,		16462	0.001		0.0378	False		,,,				2504	0.0562				p.L99F		Atlas-SNP	.											.	CDS1	58	.	0			c.G297T						PASS	.	G	PHE/LEU	146,4260	100.3+/-138.9	3,140,2060	294.0	272.0	279.0		297	3.6	1.0	4	dbSNP_126	279	349,8251	117.9+/-177.5	10,329,3961	yes	missense	CDS1	NM_001263.3	22	13,469,6021	TT,TG,GG		4.0581,3.3137,3.8059	benign	99/462	85530633	495,12511	2203	4300	6503	SO:0001583	missense	1040	exon3			CTCGTTGTTTTTC	U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.297G>T	4.37:g.85530633G>T	ENSP00000295887:p.Leu99Phe	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	191	98	0.513089	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000295887.5	37	CCDS3608.1	58	0.026556776556776556	19	0.03861788617886179	4	0.011049723756906077	1	0.0017482517482517483	34	0.044854881266490766	G	11.26	1.587007	0.28268	0.033137	0.040581	ENSG00000163624	ENST00000295887	T	0.44482	0.92	5.6	3.57	0.40892	.	0.464146	0.22320	N	0.061608	T	0.03305	0.0096	N	0.02158	-0.66	0.26328	N	0.977566	B	0.02656	0.0	B	0.10450	0.005	T	0.09037	-1.0693	10	0.28530	T	0.3	-3.1211	5.5994	0.17345	0.0988:0.1442:0.6186:0.1384	rs36068434	99	Q92903	CDS1_HUMAN	F	99	ENSP00000295887:L99F	ENSP00000295887:L99F	L	+	3	2	CDS1	85749657	0.637000	0.27216	0.985000	0.45067	0.711000	0.40976	0.423000	0.21313	1.329000	0.45376	0.650000	0.86243	TTG	G|0.964;T|0.036	0.036	strong		0.338	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2		
MUC16	94025	hgsc.bcm.edu	37	19	9060656	9060656	+	Silent	SNP	C	C	T	rs2216663	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9060656C>T	ENST00000397910.4	-	3	26993	c.26790G>A	c.(26788-26790)gaG>gaA	p.E8930E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8932	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.E8930E(2)|p.E4563E(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCTGAATTGCCTCTGTCTCCA	0.493													c|||	1050	0.209665	0.0628	0.2003	5008	,	,		21414	0.249		0.3101	False		,,,				2504	0.271				p.E8930E		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,3	MUC16	4315	3	3	Substitution - coding silent(3)	stomach(3)	c.G26790A						PASS	.	C		425,3671		24,377,1647	180.0	170.0	173.0		26790	-0.2	0.0	19	dbSNP_96	173	2415,6013		342,1731,2141	no	coding-synonymous	MUC16	NM_024690.2		366,2108,3788	TT,TC,CC		28.6545,10.376,22.6765		8930/14508	9060656	2840,9684	2048	4214	6262	SO:0001819	synonymous_variant	94025	exon3			AATTGCCTCTGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.26790G>A	19.37:g.9060656C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	174	100	0.574713	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.788;T|0.212	0.212	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ADAM29	11086	hgsc.bcm.edu	37	4	175898913	175898913	+	Missense_Mutation	SNP	C	C	T	rs142711835		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175898913C>T	ENST00000359240.3	+	5	2907	c.2237C>T	c.(2236-2238)aCg>aTg	p.T746M	ADAM29_ENST00000445694.1_Missense_Mutation_p.T746M|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.T746M|ADAM29_ENST00000404450.4_Missense_Mutation_p.T746M	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	746	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T746M(2)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCTCCTGTGACGCCTTCCCAG	0.537																																					p.T746M	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,rectum,carcinoma,0,22	ADAM29	262	22	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	c.C2237T						scavenged	.						149.0	132.0	138.0					4																	175898913		2203	4300	6503	SO:0001583	missense	11086	exon4			CTGTGACGCCTTC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2237C>T	4.37:g.175898913C>T	ENSP00000352177:p.Thr746Met	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	202	21	0.10396	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	8.511	0.866447	0.17250	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.02015	4.5;4.5;4.5;4.5	1.54	0.582	0.17412	.	.	.	.	.	T	0.01558	0.0050	N	0.08118	0	0.09310	N	1	D	0.62365	0.991	P	0.45998	0.5	T	0.53005	-0.8499	8	.	.	.	.	6.1783	0.20457	0.0:0.802:0.0:0.198	.	746	Q9UKF5	ADA29_HUMAN	M	746	ENSP00000352177:T746M;ENSP00000414544:T746M;ENSP00000384229:T746M;ENSP00000423517:T746M	.	T	+	2	0	ADAM29	176135488	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.798000	0.04565	-0.059000	0.13154	0.478000	0.44815	ACG	.	.	weak		0.537	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
EMR2	30817	hgsc.bcm.edu	37	19	14875388	14875388	+	Missense_Mutation	SNP	G	G	A	rs35612307	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14875388G>A	ENST00000315576.3	-	11	1392	c.941C>T	c.(940-942)gCc>gTc	p.A314V	EMR2_ENST00000392967.2_Missense_Mutation_p.A314V|EMR2_ENST00000353005.1_Missense_Mutation_p.A172V|EMR2_ENST00000594294.1_Missense_Mutation_p.A265V|EMR2_ENST00000353876.1_Missense_Mutation_p.A221V|EMR2_ENST00000596991.2_Missense_Mutation_p.A314V|EMR2_ENST00000595839.1_Missense_Mutation_p.A172V|EMR2_ENST00000601345.1_Missense_Mutation_p.A314V|EMR2_ENST00000392965.3_Missense_Mutation_p.A314V|EMR2_ENST00000392964.3_Missense_Mutation_p.A53V|EMR2_ENST00000346057.1_Missense_Mutation_p.A265V|EMR2_ENST00000594076.1_Missense_Mutation_p.A221V	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	314			A -> V (in dbSNP:rs35612307).		cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						GTCCCCAGGGGCCTCCAGCAG	0.622													G|||	951	0.189896	0.0946	0.3458	5008	,	,		15749	0.1667		0.2813	False		,,,				2504	0.138				p.A314V		Atlas-SNP	.											.	EMR2	99	.	0			c.C941T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	517,3887	233.9+/-246.9	37,443,1722	39.0	37.0	38.0		941,794,662,515,941,794,662	-3.3	0.0	19	dbSNP_126	38	2549,6049	406.2+/-348.7	385,1779,2135	yes	missense,missense,missense,missense,missense,missense,missense	EMR2	NM_013447.2,NM_152916.1,NM_152917.1,NM_152918.1,NM_152919.1,NM_152920.1,NM_152921.1	64,64,64,64,64,64,64	422,2222,3857	AA,AG,GG		29.6464,11.7393,23.581	benign,benign,benign,benign,benign,benign,benign	314/824,265/775,221/731,172/682,314/813,265/764,221/720	14875388	3066,9936	2202	4299	6501	SO:0001583	missense	30817	exon10			CCAGGGGCCTCCA	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.941C>T	19.37:g.14875388G>A	ENSP00000319883:p.Ala314Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	147	78	0.530612	NM_001271052	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	508	0.2326007326007326	54	0.10975609756097561	125	0.3453038674033149	124	0.21678321678321677	205	0.2704485488126649	G	14.59	2.579958	0.46006	0.117393	0.296464	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965;ENST00000392964;ENST00000392962	T;T;T;T;T;T;T;T	0.78707	-0.91;-1.05;-0.44;0.35;1.1;-1.2;1.48;-1.09	3.77	-3.32	0.04973	.	.	.	.	.	T	0.00012	0.0000	L	0.43923	1.385	0.80722	P	0.0	B;B;B;B;B;B	0.30763	0.294;0.08;0.004;0.027;0.016;0.171	B;B;B;B;B;B	0.28011	0.057;0.027;0.002;0.037;0.01;0.085	T	0.11155	-1.0599	8	0.38643	T	0.18	.	2.2231	0.03977	0.1072:0.1584:0.2526:0.4818	rs35612307;rs62122625	314;221;172;265;314;314	E7ESD7;Q9UHX3-4;Q9UHX3-5;Q9UHX3-3;Q9UHX3;Q9UHX3-2	.;.;.;.;EMR2_HUMAN;.	V	314;314;265;221;172;314;53;265	ENSP00000319883:A314V;ENSP00000376694:A314V;ENSP00000263380:A265V;ENSP00000319454:A221V;ENSP00000319838:A172V;ENSP00000376692:A314V;ENSP00000376691:A53V;ENSP00000376689:A265V	ENSP00000319883:A314V	A	-	2	0	EMR2	14736388	0.000000	0.05858	0.000000	0.03702	0.472000	0.32918	-0.787000	0.04618	-0.240000	0.09696	0.508000	0.49915	GCC	G|0.765;A|0.235	0.235	strong		0.622	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		
OR10H2	26538	hgsc.bcm.edu	37	19	15839174	15839174	+	Silent	SNP	C	C	T	rs2285956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15839174C>T	ENST00000305899.3	+	1	341	c.321C>T	c.(319-321)ttC>ttT	p.F107F		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					CCTTCAGCTTCGGCTTCACCC	0.642																																					p.F107F		Atlas-SNP	.											.	OR10H2	59	.	0			c.C321T						PASS	.						60.0	56.0	58.0					19																	15839174		2202	4277	6479	SO:0001819	synonymous_variant	26538	exon1			CAGCTTCGGCTTC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.321C>T	19.37:g.15839174C>T		Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	318	117	0.367925	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			T|1.000;|0.000	1.000	weak		0.642	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
UTP6	55813	hgsc.bcm.edu	37	17	30222002	30222002	+	Missense_Mutation	SNP	T	T	C	rs3760454	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:30222002T>C	ENST00000261708.4	-	3	343	c.206A>G	c.(205-207)cAg>cGg	p.Q69R	UTP6_ENST00000490218.2_5'UTR	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	69			Q -> R (in dbSNP:rs3760454). {ECO:0000269|PubMed:12097419, ECO:0000269|PubMed:15489334}.		rRNA processing (GO:0006364)	nucleolus (GO:0005730)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				TCTTCTTCTCTGGATCAGCTC	0.313													T|||	1780	0.355431	0.0257	0.3242	5008	,	,		16787	0.6458		0.4523	False		,,,				2504	0.4243				p.Q69R		Atlas-SNP	.											.	UTP6	46	.	0			c.A206G						PASS	.	T	ARG/GLN	404,3996	189.2+/-215.4	23,358,1819	74.0	60.0	65.0		206	5.3	1.0	17	dbSNP_107	65	3895,4697	516.9+/-378.9	861,2173,1262	yes	missense	UTP6	NM_018428.2	43	884,2531,3081	CC,CT,TT		45.3329,9.1818,33.0896	benign	69/598	30222002	4299,8693	2200	4296	6496	SO:0001583	missense	55813	exon3			CTTCTCTGGATCA	AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651			18279	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated antigen 66"""		"""chromosome 17 open reading frame 40"""	C17orf40		10843809, 16138909	Standard	NM_018428		Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.206A>G	17.37:g.30222002T>C	ENSP00000261708:p.Gln69Arg	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	217	85	0.391705	NM_018428	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	37	CCDS11269.1	866	0.3965201465201465	17	0.034552845528455285	130	0.35911602209944754	376	0.6573426573426573	343	0.4525065963060686	T	11.32	1.603617	0.28534	0.091818	0.453329	ENSG00000108651	ENST00000261708	T	0.27720	1.65	5.31	5.31	0.75309	U3 small nucleolar RNA-associated protein 6 (1);	0.203490	0.50627	D	0.000108	T	0.00012	0.0000	N	0.00864	-1.135	0.30342	P	0.785656	B	0.22800	0.075	B	0.20384	0.029	T	0.33266	-0.9875	9	0.02654	T	1	-10.493	13.7773	0.63062	0.0:0.0:0.0:1.0	rs3760454;rs11550098;rs56475503;rs60232137;rs3760454	69	Q9NYH9	UTP6_HUMAN	R	69	ENSP00000261708:Q69R	ENSP00000261708:Q69R	Q	-	2	0	UTP6	27246115	1.000000	0.71417	0.999000	0.59377	0.716000	0.41182	4.609000	0.61148	2.118000	0.64928	0.533000	0.62120	CAG	T|0.638;C|0.362	0.362	strong		0.313	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428	
MTOR	2475	hgsc.bcm.edu	37	1	11205058	11205058	+	Silent	SNP	C	C	T	rs1057079	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11205058C>T	ENST00000361445.4	-	33	4807	c.4731G>A	c.(4729-4731)gcG>gcA	p.A1577A	MTOR_ENST00000495435.1_5'UTR|MTOR-AS1_ENST00000445982.1_RNA|MTOR-AS1_ENST00000420480.1_RNA	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1577	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CTCCTGCCATCGCAGTTAATT	0.463													C|||	2742	0.547524	0.0635	0.7017	5008	,	,		19784	0.8165		0.7356	False		,,,				2504	0.6217				p.A1577A		Atlas-SNP	.											.	MTOR	327	.	0			c.G4731A						PASS	.	C		779,3627	314.7+/-293.7	82,615,1506	125.0	109.0	115.0		4731	-5.2	0.8	1	dbSNP_86	115	6321,2279	707.3+/-405.6	2334,1653,313	no	coding-synonymous	MTOR	NM_004958.3		2416,2268,1819	TT,TC,CC		26.5,17.6804,45.4098		1577/2550	11205058	7100,5906	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon33			TGCCATCGCAGTT	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.4731G>A	1.37:g.11205058C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			C|0.437;T|0.563	0.563	strong		0.463	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
OVGP1	5016	hgsc.bcm.edu	37	1	111957592	111957592	+	Missense_Mutation	SNP	A	A	G	rs56294468|rs376377993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111957592A>G	ENST00000369732.3	-	11	1586	c.1531T>C	c.(1531-1533)Tct>Cct	p.S511P		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	511				S -> P (in Ref. 2; AAB04126). {ECO:0000305}.	binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TAACCCACAGAGGTCAGGGTC	0.572													a|||	1118	0.223243	0.1989	0.1715	5008	,	,		18021	0.1587		0.2763	False		,,,				2504	0.3047				p.S511P		Atlas-SNP	.											OVGP1_ENST00000369728,NS,malignant_melanoma,+1,2	OVGP1	177	2	0			c.T1531C						PASS	.	A	PRO/SER	774,3610	297.3+/-284.7	91,592,1509	64.0	61.0	62.0		1531	-5.5	0.0	1	dbSNP_129	62	2579,6021	404.8+/-348.3	388,1803,2109	yes	missense	OVGP1	NM_002557.3	74	479,2395,3618	GG,GA,AA		29.9884,17.6551,25.8241	benign	511/679	111957592	3353,9631	2192	4300	6492	SO:0001583	missense	5016	exon11			CCACAGAGGTCAG	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1531T>C	1.37:g.111957592A>G	ENSP00000358747:p.Ser511Pro	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	94	92	0.978723	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	440	0.20146520146520147	91	0.18495934959349594	70	0.19337016574585636	77	0.1346153846153846	202	0.26649076517150394	a	3.357	-0.131299	0.06753	0.176551	0.299884	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.03386	3.95	2.76	-5.52	0.02560	.	.	.	.	.	T	0.00356	0.0011	N	0.01576	-0.805	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46359	-0.9197	8	0.25751	T	0.34	.	4.3367	0.11090	0.4549:0.0:0.3888:0.1564	rs56294468;rs61742540	511;575	Q12889;Q59HH5	OVGP1_HUMAN;.	P	511;575;319	ENSP00000358747:S511P	ENSP00000358743:S575P	S	-	1	0	OVGP1	111759115	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.421000	0.07053	-1.460000	0.01911	-0.621000	0.04028	TCT	A|0.767;G|0.233	0.233	strong		0.572	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
PREX1	57580	hgsc.bcm.edu	37	20	47273726	47273726	+	Splice_Site	SNP	C	C	T	rs55904123	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:47273726C>T	ENST00000371941.3	-	18	1997	c.1975G>A	c.(1975-1977)Gtg>Atg	p.V659M	PREX1_ENST00000396220.1_Splice_Site_p.V659M	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	659	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.		V -> M (in dbSNP:rs55904123). {ECO:0000269|PubMed:17974005}.		actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGGCCAGCCACCTGGGTAGGG	0.572											OREG0026010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	803	0.160343	0.0363	0.2133	5008	,	,		21050	0.1587		0.1839	False		,,,				2504	0.2679				p.V659M		Atlas-SNP	.											PREX1_ENST00000396220,NS,adenoma,0,2	PREX1	441	2	0			c.G1975A						PASS	.	T	MET/VAL	341,4065	792.8+/-415.2	13,315,1875	75.0	58.0	64.0		1975	2.8	1.0	20	dbSNP_129	64	1617,6983	740.3+/-407.1	147,1323,2830	yes	missense-near-splice	PREX1	NM_020820.3	21	160,1638,4705	TT,TC,CC		18.8023,7.7394,15.0546	benign	659/1660	47273726	1958,11048	2203	4300	6503	SO:0001630	splice_region_variant	57580	exon18			CAGCCACCTGGGT	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1975-1G>A	20.37:g.47273726C>T		Somatic	52	0	0	945	WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	325	0.1488095238095238	21	0.042682926829268296	81	0.22375690607734808	88	0.15384615384615385	135	0.17810026385224276	T	0.007	-1.987474	0.00443	0.077394	0.188023	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.17213	2.29;2.29	5.12	2.8	0.32819	PDZ/DHR/GLGF (3);	0.079540	0.51477	N	0.000100	T	0.00012	0.0000	N	0.01352	-0.895	0.33382	P	0.42501999999999995	B	0.02656	0.0	B	0.04013	0.001	T	0.46400	-0.9194	9	0.02654	T	1	.	8.5258	0.33304	0.0:0.1263:0.1111:0.7626	rs55904123;rs62621373	659	Q8TCU6	PREX1_HUMAN	M	659	ENSP00000361009:V659M;ENSP00000379522:V659M	ENSP00000361009:V659M	V	-	1	0	PREX1	46707133	1.000000	0.71417	0.981000	0.43875	0.047000	0.14425	3.541000	0.53618	-0.281000	0.09141	-2.680000	0.00142	GTG	C|0.849;T|0.151	0.151	strong		0.572	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	Missense_Mutation
LILRB3	11025	hgsc.bcm.edu	37	19	54725930	54725930	+	Missense_Mutation	SNP	C	C	T	rs61480095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54725930C>T	ENST00000391750.1	-	5	564	c.428G>A	c.(427-429)cGa>cAa	p.R143Q	LILRA6_ENST00000270464.5_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000407860.2_Missense_Mutation_p.R143Q|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000346401.6_Missense_Mutation_p.R143Q|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000424807.1_Missense_Mutation_p.R143Q|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.R143Q|LILRA6_ENST00000440558.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	143	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R143Q(11)		endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGAGCCACATCGGAGGGTCAT	0.582													.|||	2249	0.449081	0.2776	0.4769	5008	,	,		13331	0.626		0.4751	False		,,,				2504	0.4519				p.R143Q		Atlas-SNP	.											LILRB3,NS,carcinoma,0,11	LILRB3	67	11	11	Substitution - Missense(11)	kidney(11)	c.G428A						PASS	.						28.0	19.0	22.0					19																	54725930		2090	3824	5914	SO:0001583	missense	11025	exon4			CCACATCGGAGGG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.428G>A	19.37:g.54725930C>T	ENSP00000375630:p.Arg143Gln	Somatic	577	0	0		WXS	Illumina HiSeq	Phase_I	256	147	0.574219	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	0.024	-1.388513	0.01185	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65;5.75	2.87	-3.69	0.04450	Immunoglobulin-like fold (1);	0.513077	0.18054	N	0.153187	T	0.02047	0.0064	N	0.01109	-1.01	0.80722	P	0.0	B;B;B;B;B	0.25609	0.014;0.007;0.13;0.034;0.037	B;B;B;B;B	0.16722	0.016;0.002;0.003;0.003;0.002	T	0.30563	-0.9974	9	0.02654	T	1	.	1.113	0.01708	0.1765:0.3576:0.1802:0.2857	rs61480095;rs62133096	143;143;143;143;143	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	Q	143	ENSP00000375630:R143Q;ENSP00000412771:R143Q;ENSP00000345184:R143Q;ENSP00000245620:R143Q;ENSP00000384274:R143Q;ENSP00000388199:R143Q	ENSP00000245620:R143Q	R	-	2	0	LILRB3	59417742	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-6.718000	0.00056	-1.014000	0.03379	-0.350000	0.07774	CGA	.	.	weak		0.582	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
DMXL2	23312	hgsc.bcm.edu	37	15	51914662	51914662	+	Silent	SNP	G	G	A	rs2278990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:51914662G>A	ENST00000251076.5	-	1	368	c.81C>T	c.(79-81)ccC>ccT	p.P27P	DMXL2_ENST00000543779.2_Silent_p.P27P|DMXL2_ENST00000449909.3_Silent_p.P27P	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	27						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TCACCGTGAAGGGGACATCCC	0.687													G|||	2061	0.411542	0.3616	0.4856	5008	,	,		15280	0.3333		0.5149	False		,,,				2504	0.4008				p.P27P		Atlas-SNP	.											.	DMXL2	262	.	0			c.C81T						PASS	.	G	,,	1606,2748		323,960,894	22.0	19.0	20.0		81,81,81	-1.4	1.0	15	dbSNP_100	20	4126,4396		1079,1968,1214	no	coding-synonymous,coding-synonymous,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	1402,2928,2108	AA,AG,GG		48.4159,36.8856,44.5169	,,	27/3038,27/2401,27/3037	51914662	5732,7144	2177	4261	6438	SO:0001819	synonymous_variant	23312	exon1			CGTGAAGGGGACA	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.81C>T	15.37:g.51914662G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	160	68	0.425	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			G|0.567;A|0.433	0.433	strong		0.687	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
SEMG1	6406	hgsc.bcm.edu	37	20	43837052	43837052	+	Missense_Mutation	SNP	C	C	A	rs199672858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43837052C>A	ENST00000372781.3	+	2	1171	c.1114C>A	c.(1114-1116)Cgc>Agc	p.R372S	SEMG1_ENST00000244069.6_Missense_Mutation_p.R312S	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	372	2 X 60 AA tandem repeats, type 1.|Repeat-rich region. {ECO:0000250}.		R -> L (in dbSNP:rs2233887). {ECO:0000269|PubMed:14629036}.		insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				TGTATCCCAACGCAGTATTTA	0.418																																					p.R372S		Atlas-SNP	.											SEMG1,bladder,carcinoma,0,3	SEMG1	71	3	0			c.C1114A						scavenged	.						77.0	71.0	73.0					20																	43837052		2203	4300	6503	SO:0001583	missense	6406	exon2			TCCCAACGCAGTA		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.1114C>A	20.37:g.43837052C>A	ENSP00000361867:p.Arg372Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	183	2	0.010929	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.712711	0.00712	.	.	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.03951	3.75;3.75	0.951	-1.9	0.07665	.	.	.	.	.	T	0.00754	0.0025	N	0.00082	-2.215	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34079	-0.9843	9	0.09590	T	0.72	.	0.297	0.00267	0.2228:0.2395:0.2981:0.2396	.	312;372	P04279-2;P04279	.;SEMG1_HUMAN	S	312;372	ENSP00000244069:R312S;ENSP00000361867:R372S	ENSP00000244069:R312S	R	+	1	0	SEMG1	43270466	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.965000	0.03829	-2.064000	0.00888	-1.625000	0.00788	CGC	C|1.000;T|0.000	.	alt		0.418	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
HLA-A	3105	hgsc.bcm.edu	37	6	29910371	29910371	+	Missense_Mutation	SNP	C	C	T	rs2230954|rs41548119	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29910371C>T	ENST00000396634.1	+	3	382	c.41C>T	c.(40-42)tCg>tTg	p.S14L	HLA-A_ENST00000376806.5_Missense_Mutation_p.S14L|HLA-A_ENST00000376809.5_Missense_Mutation_p.S14L|HLA-A_ENST00000376802.2_Missense_Mutation_p.S14L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	14					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CTGCTACTCTCGGGGGCCCTG	0.711									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.S14L		Atlas-SNP	.											.	HLA-A	89	.	0			c.C41T						PASS	.	C	LEU/SER	731,3667		28,675,1496	30.0	33.0	32.0		41	-1.4	0.0	6	dbSNP_126	32	907,7689		24,859,3415	no	missense	HLA-A	NM_002116.7	145	52,1534,4911	TT,TC,CC		10.5514,16.6212,12.6058	possibly-damaging	14/366	29910371	1638,11356	2199	4298	6497	SO:0001583	missense	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TACTCTCGGGGGC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.41C>T	6.37:g.29910371C>T	ENSP00000379873:p.Ser14Leu	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	291	128	0.439863	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	296	0.13553113553113552	84	0.17073170731707318	57	0.1574585635359116	78	0.13636363636363635	77	0.10158311345646438	.	11.29	1.596221	0.28445	0.166212	0.105514	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00637	6.06;6.05;6.06;6.06	3.72	-1.38	0.09027	.	1.975200	0.04193	U	0.328582	T	0.00524	0.0017	N	0.14661	0.345	0.80722	P	0.0	D;B;D;B	0.76494	0.999;0.001;0.997;0.002	D;B;D;B	0.73380	0.974;0.002;0.98;0.004	T	0.52756	-0.8533	9	0.87932	D	0	.	7.2758	0.26283	0.0:0.414:0.0:0.586	rs2230954;rs3115639;rs3173431;rs41545915	14;14;14;14	Q5SRN7;P16188;Q5SRN5;P04439	.;1A30_HUMAN;.;1A03_HUMAN	L	14	ENSP00000379873:S14L;ENSP00000366002:S14L;ENSP00000366005:S14L;ENSP00000365998:S14L	ENSP00000348012:S14L	S	+	2	0	HLA-A	30018350	0.000000	0.05858	0.000000	0.03702	0.293000	0.27360	-4.415000	0.00237	-0.164000	0.10927	0.478000	0.44815	TCG	C|0.872;T|0.128	0.128	strong		0.711	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ZNF131	7690	hgsc.bcm.edu	37	5	43161351	43161351	+	Splice_Site	SNP	G	G	A	rs71627581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:43161351G>A	ENST00000399534.1	+	5	416	c.372G>A	c.(370-372)agG>agA	p.R124R	ZNF131_ENST00000505606.2_Splice_Site_p.R124R|ZNF131_ENST00000509931.1_Intron|ZNF131_ENST00000509156.1_Splice_Site_p.R124R|ZNF131_ENST00000306938.4_Splice_Site_p.R124R|ZNF131_ENST00000509634.1_Splice_Site_p.R124R			P52739	ZN131_HUMAN	zinc finger protein 131	124					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	17						TGTATTTCAGGAACAAAGAAA	0.323													G|||	180	0.0359425	0.003	0.0591	5008	,	,		18963	0.002		0.1193	False		,,,				2504	0.0133				p.R124R		Atlas-SNP	.											.	ZNF131	51	.	0			c.G372A						PASS	.	G		79,3525		0,79,1723	63.0	59.0	60.0		372	0.6	1.0	5	dbSNP_130	60	851,7277		44,763,3257	yes	coding-synonymous-near-splice	ZNF131	NM_003432.1		44,842,4980	AA,AG,GG		10.47,2.192,7.927		124/590	43161351	930,10802	1802	4064	5866	SO:0001630	splice_region_variant	7690	exon5			TTTCAGGAACAAA	U09410	CCDS43313.1	5p12	2013-01-09	2006-06-13		ENSG00000172262	ENSG00000172262		"""Zinc fingers, C2H2-type"", ""-"", ""BTB/POZ domain containing"""	12915	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 35"""	604073	"""zinc finger protein 131 (clone pHZ-10)"""				Standard	XM_005248359		Approved	ZBTB35, pHZ-10	uc003jnk.3	P52739	OTTHUMG00000162223	ENST00000399534.1:c.372-1G>A	5.37:g.43161351G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_003432	B4DRL3|Q6PIF0	Silent	SNP	ENST00000399534.1	37																																																																																				G|0.937;A|0.063	0.063	strong		0.323	ZNF131-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000367982.1	NM_003432	Silent
FAM221A	340277	hgsc.bcm.edu	37	7	23728931	23728931	+	Missense_Mutation	SNP	T	T	C	rs35495590	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:23728931T>C	ENST00000344962.4	+	3	372	c.283T>C	c.(283-285)Tgc>Cgc	p.C95R	FAM221A_ENST00000409653.1_Missense_Mutation_p.C37R|FAM221A_ENST00000409994.3_Missense_Mutation_p.C37R|FAM221A_ENST00000409192.3_Missense_Mutation_p.C95R	NM_199136.3	NP_954587.2	A4D161	F221A_HUMAN	family with sequence similarity 221, member A	95			C -> R (in dbSNP:rs35495590).														TCCTCAGCAGTGCCCCATTGA	0.438													C|||	441	0.0880591	0.056	0.072	5008	,	,		16139	0.1359		0.0746	False		,,,				2504	0.1074				p.C95R		Atlas-SNP	.											.	.	.	.	0			c.T283C						PASS	.	C	ARG/CYS,ARG/CYS,ARG/CYS	233,4173	805.3+/-415.8	7,219,1977	88.0	83.0	85.0		283,109,283	2.9	1.0	7	dbSNP_126	85	614,7986	791.7+/-407.5	23,568,3709	yes	missense,missense,missense	C7orf46	NM_001127364.1,NM_001127365.1,NM_199136.3	180,180,180	30,787,5686	CC,CT,TT		7.1395,5.2882,6.5124	benign,benign,benign	95/263,37/205,95/299	23728931	847,12159	2203	4300	6503	SO:0001583	missense	340277	exon3			CAGCAGTGCCCCA		CCDS5385.1, CCDS47561.1, CCDS47562.1, CCDS75570.1	7p15.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000188732	ENSG00000188732			27977	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 46"""	C7orf46		12477932	Standard	XR_242080		Approved	FLJ45875, MGC72075, DKFZp686F0810	uc003swo.4	A4D161	OTTHUMG00000128463	ENST00000344962.4:c.283T>C	7.37:g.23728931T>C	ENSP00000342576:p.Cys95Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_199136	Q05CG4|Q4G0Q7|Q6P519	Missense_Mutation	SNP	ENST00000344962.4	37	CCDS5385.1	196	0.08974358974358974	19	0.03861788617886179	21	0.058011049723756904	94	0.16433566433566432	62	0.08179419525065963	C	0.012	-1.668178	0.00765	0.052882	0.071395	ENSG00000188732	ENST00000409192;ENST00000344962;ENST00000409653;ENST00000409994	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.71	2.86	0.33363	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00053	-2.39	0.32951	P	0.480306	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35919	-0.9769	9	0.02654	T	1	-3.8104	5.4147	0.16368	0.2389:0.5669:0.0:0.1942	rs35495590	37;95;95	A4D161-3;A4D161-2;A4D161	.;.;CG046_HUMAN	R	95;95;37;37	ENSP00000386927:C95R;ENSP00000342576:C95R;ENSP00000386900:C37R;ENSP00000386631:C37R	ENSP00000342576:C95R	C	+	1	0	C7orf46	23695456	0.996000	0.38824	1.000000	0.80357	0.206000	0.24218	1.261000	0.32980	0.345000	0.23873	-0.865000	0.03005	TGC	T|0.923;C|0.077	0.077	strong		0.438	FAM221A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250261.1	NM_199136	
CFAP53	220136	hgsc.bcm.edu	37	18	47777244	47777244	+	Missense_Mutation	SNP	C	C	T	rs35193847	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:47777244C>T	ENST00000398545.4	-	5	997	c.880G>A	c.(880-882)Gag>Aag	p.E294K		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		TCTATCCTCTCTTGTAGGGCT	0.418													C|||	969	0.19349	0.1036	0.1787	5008	,	,		20837	0.0625		0.3926	False		,,,				2504	0.2556				p.E294K		Atlas-SNP	.											.	CCDC11	59	.	0			c.G880A						PASS	.	C	LYS/GLU	542,3210		43,456,1377	385.0	342.0	356.0		880	4.9	0.8	18	dbSNP_126	356	3112,5114		618,1876,1619	yes	missense	CCDC11	NM_145020.3	56	661,2332,2996	TT,TC,CC		37.8313,14.4456,30.5059	possibly-damaging	294/515	47777244	3654,8324	1876	4113	5989	SO:0001583	missense	220136	exon5			TCCTCTCTTGTAG																												ENST00000398545.4:c.880G>A	18.37:g.47777244C>T	ENSP00000381553:p.Glu294Lys	Somatic	448	0	0		WXS	Illumina HiSeq	Phase_I	362	144	0.39779	NM_145020		Missense_Mutation	SNP	ENST00000398545.4	37	CCDS11940.2	441	0.20192307692307693	49	0.09959349593495935	74	0.20441988950276244	39	0.06818181818181818	279	0.36807387862796836	C	12.00	1.807417	0.31961	0.144456	0.378313	ENSG00000172361	ENST00000398545	T	0.11821	2.74	5.81	4.94	0.65067	.	0.524458	0.21054	N	0.080955	T	0.00012	0.0000	L	0.46157	1.445	0.53688	P	2.8000000000028002E-5	P	0.37061	0.58	B	0.37550	0.253	T	0.43669	-0.9377	9	0.11794	T	0.64	-5.5184	8.4953	0.33125	0.0:0.7651:0.1536:0.0813	rs35193847;rs56682575	294	Q96M91	CCD11_HUMAN	K	294	ENSP00000381553:E294K	ENSP00000381553:E294K	E	-	1	0	CCDC11	46031242	0.587000	0.26791	0.806000	0.32338	0.006000	0.05464	2.060000	0.41394	1.471000	0.48121	0.655000	0.94253	GAG	C|0.738;T|0.262	0.262	strong		0.418	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
ATP8B2	57198	hgsc.bcm.edu	37	1	154310048	154310048	+	Silent	SNP	C	C	G	rs1760795	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154310048C>G	ENST00000368487.3	+	12	1249	c.1062C>G	c.(1060-1062)ctC>ctG	p.L354L	ATP8B2_ENST00000426445.1_Intron|ATP8B2_ENST00000341822.2_Intron|RNU7-57P_ENST00000459540.1_RNA|ATP8B2_ENST00000368489.3_Intron	NM_001005855.1	NP_001005855.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	372					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CCTGGGGTCTCTCCAGGGAGT	0.468													C|||	2153	0.429912	0.1551	0.4957	5008	,	,		20687	0.624		0.4523	False		,,,				2504	0.5317				p.L354L		Atlas-SNP	.											.	ATP8B2	158	.	0			c.C1062G						PASS	.	C	,	933,3473	355.1+/-312.9	92,749,1362	214.0	201.0	206.0		1062,	2.4	0.0	1	dbSNP_89	206	4062,4538	559.7+/-387.5	963,2136,1201	no	coding-synonymous,intron	ATP8B2	NM_001005855.1,NM_020452.3	,	1055,2885,2563	GG,GC,CC		47.2326,21.1757,38.4054	,	354/388,	154310048	4995,8011	2203	4300	6503	SO:0001819	synonymous_variant	57198	exon12			GGGTCTCTCCAGG	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"""ATPases / P-type"""	13534	protein-coding gene	gene with protein product		605867	"""ATPase, class I, type 8B, member 2"""			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368487.3:c.1062C>G	1.37:g.154310048C>G		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	314	127	0.404459	NM_001005855	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368487.3	37	CCDS41405.1																																																																																			C|0.542;G|0.458	0.458	strong		0.468	ATP8B2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087903.2	NM_020452	
NELFA	7469	hgsc.bcm.edu	37	4	2010507	2010507	+	Silent	SNP	C	C	T	rs373321225		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2010507C>T	ENST00000411638.2	-	1	195	c.180G>A	c.(178-180)acG>acA	p.T60T	NELFA_ENST00000542778.1_5'UTR|NELFA_ENST00000382882.3_Silent_p.T71T	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	60					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)										GGAGGTGCAGCGTCCCGAGTA	0.672																																					p.T71T		Atlas-SNP	.											WHSC2,NS,carcinoma,0,1	.	.	1	0			c.G213A						scavenged	.	C		0,4406		0,0,2203	53.0	42.0	46.0		213	-2.4	0.9	4		46	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	WHSC2	NM_005663.4		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		71/540	2010507	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	7469	exon1			GTGCAGCGTCCCG	AF101434	CCDS3358.2	4p16.3	2013-01-31	2013-01-31	2013-01-31	ENSG00000185049	ENSG00000185049			12768	protein-coding gene	gene with protein product		606026	"""Wolf-Hirschhorn syndrome candidate 2"""	WHSC2		10409432	Standard	NM_005663		Approved	NELF-A	uc003gem.3	Q9H3P2	OTTHUMG00000089967	ENST00000411638.2:c.180G>A	4.37:g.2010507C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	150	3	0.02	NM_005663	A2A2T1|O95392	Silent	SNP	ENST00000411638.2	37		.	.	.	.	.	.	.	.	.	.	C	3.482	-0.105649	0.06924	0.0	1.16E-4	ENSG00000185049	ENST00000411649	.	.	.	3.45	-2.41	0.06562	.	.	.	.	.	T	0.51975	0.1706	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47611	-0.9104	4	.	.	.	-20.0299	8.3305	0.32184	0.0:0.3582:0.4797:0.1621	.	.	.	.	H	19	.	.	R	-	2	0	WHSC2	1980305	1.000000	0.71417	0.891000	0.34965	0.008000	0.06430	1.068000	0.30629	-0.329000	0.08527	-0.438000	0.05819	CGC	.	.	weak		0.672	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663	
FOLH1	2346	hgsc.bcm.edu	37	11	49207398	49207398	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49207398C>T	ENST00000256999.2	-	6	909	c.649G>A	c.(649-651)Gcc>Acc	p.A217T	FOLH1_ENST00000343844.4_Intron|FOLH1_ENST00000340334.7_Missense_Mutation_p.A202T|FOLH1_ENST00000356696.3_Missense_Mutation_p.A217T|FOLH1_ENST00000533034.1_Missense_Mutation_p.A202T	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	217					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	GCCAGCTGGGCATTTTTAACC	0.418																																					p.A217T		Atlas-SNP	.											.	FOLH1	141	.	0			c.G649A						PASS	.						37.0	44.0	42.0					11																	49207398		2201	4296	6497	SO:0001583	missense	2346	exon6			GCTGGGCATTTTT	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.649G>A	11.37:g.49207398C>T	ENSP00000256999:p.Ala217Thr	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	206	31	0.150485	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737168	0.69304	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63	3.01	2.06	0.26882	Protease-associated domain, PA (1);	0.126165	0.35407	N	0.003233	D	0.87822	0.6274	H	0.97516	4.02	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.993;0.999	D	0.88363	0.2989	10	0.87932	D	0	.	9.7982	0.40748	0.0:0.7869:0.2131:0.0	.	202;202;217;217	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	T	217;217;202;202;217	ENSP00000256999:A217T;ENSP00000349129:A217T;ENSP00000344131:A202T;ENSP00000431463:A202T	ENSP00000256999:A217T	A	-	1	0	FOLH1	49163974	1.000000	0.71417	0.992000	0.48379	0.974000	0.67602	5.974000	0.70465	0.593000	0.29745	0.400000	0.26472	GCC	.	.	none		0.418	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16534646	16534646	+	Missense_Mutation	SNP	C	C	G	rs221058	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16534646C>G	ENST00000270747.3	-	3	623	c.487G>C	c.(487-489)Ggc>Cgc	p.G163R	ARHGEF19_ENST00000478117.1_5'Flank	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	163			G -> R (in dbSNP:rs221058). {ECO:0000269|PubMed:14702039}.		regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		ACTACCTGGCCAGGCTCTAGG	0.657													C|||	1222	0.24401	0.0862	0.3948	5008	,	,		16480	0.1528		0.2654	False		,,,				2504	0.4223				p.G163R		Atlas-SNP	.											ARHGEF19,colon,carcinoma,0,1	ARHGEF19	49	1	0			c.G487C						PASS	.	C	ARG/GLY	453,3953	209.2+/-230.0	35,383,1785	56.0	61.0	59.0		487	2.1	1.0	1	dbSNP_79	59	2233,6367	370.2+/-335.8	295,1643,2362	yes	missense	ARHGEF19	NM_153213.3	125	330,2026,4147	GG,GC,CC		25.9651,10.2814,20.652	benign	163/803	16534646	2686,10320	2203	4300	6503	SO:0001583	missense	128272	exon3			CCTGGCCAGGCTC	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.487G>C	1.37:g.16534646C>G	ENSP00000270747:p.Gly163Arg	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	176	68	0.386364	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	450	0.20604395604395603	47	0.09552845528455285	118	0.3259668508287293	74	0.12937062937062938	211	0.2783641160949868	C	10.83	1.459937	0.26248	0.102814	0.259651	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.50001	0.76;0.76	5.21	2.13	0.27403	.	1.238380	0.05817	N	0.615075	T	0.00012	0.0000	L	0.32530	0.975	0.45390	P	0.001623000000000041	B	0.15719	0.014	B	0.14578	0.011	T	0.31138	-0.9954	9	0.30078	T	0.28	.	6.6718	0.23072	0.0:0.6669:0.0:0.3331	rs221058;rs221058	163	Q8IW93	ARHGJ_HUMAN	R	163	ENSP00000270747:G163R;ENSP00000396001:G163R	ENSP00000270747:G163R	G	-	1	0	ARHGEF19	16407233	0.296000	0.24398	0.967000	0.41034	0.118000	0.20060	0.673000	0.25203	0.220000	0.20860	0.561000	0.74099	GGC	C|0.794;G|0.206	0.206	strong		0.657	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
CYB5D1	124637	hgsc.bcm.edu	37	17	7761512	7761512	+	Missense_Mutation	SNP	C	C	A	rs12453250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7761512C>A	ENST00000332439.4	+	1	212	c.60C>A	c.(58-60)ttC>ttA	p.F20L	CYB5D1_ENST00000570446.1_Missense_Mutation_p.F20L|CYB5D1_ENST00000571846.1_Missense_Mutation_p.F20L|LSMD1_ENST00000576861.1_Intron|LSMD1_ENST00000575208.1_5'Flank|LSMD1_ENST00000570555.1_Intron|LSMD1_ENST00000576384.1_5'Flank|LSMD1_ENST00000575771.1_5'Flank|LSMD1_ENST00000335155.5_5'Flank|LSMD1_ENST00000333775.5_5'Flank|LSMD1_ENST00000575071.1_5'Flank	NM_144607.4	NP_653208.2	Q6P9G0	CB5D1_HUMAN	cytochrome b5 domain containing 1	20	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.		F -> L (in dbSNP:rs12453250).				heme binding (GO:0020037)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(2)|skin(2)	6		all_cancers(10;0.11)|Prostate(122;0.219)				GTCGCTATTTCACGCCGGCGG	0.582											OREG0024147	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1284	0.25639	0.3472	0.2867	5008	,	,		17307	0.2728		0.0934	False		,,,				2504	0.2628				p.F20L		Atlas-SNP	.											.	CYB5D1	16	.	0			c.C60A						PASS	.	C	LEU/PHE	1332,3074	443.7+/-347.1	202,928,1073	77.0	82.0	80.0		60	1.3	1.0	17	dbSNP_120	80	958,7642	210.0+/-251.0	47,864,3389	yes	missense	CYB5D1	NM_144607.4	22	249,1792,4462	AA,AC,CC		11.1395,30.2315,17.6073	probably-damaging	20/229	7761512	2290,10716	2203	4300	6503	SO:0001583	missense	124637	exon1			CTATTTCACGCCG	AK057061	CCDS11123.1	17p13.1	2006-01-12	2006-01-12						26516	protein-coding gene	gene with protein product						12477932	Standard	NM_144607		Approved	FLJ32499	uc002gjb.4	Q6P9G0		ENST00000332439.4:c.60C>A	17.37:g.7761512C>A	ENSP00000331479:p.Phe20Leu	Somatic	87	0	0	644	WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_144607	D3DTQ8|Q96DM7	Missense_Mutation	SNP	ENST00000332439.4	37	CCDS11123.1	407	0.18635531135531136	130	0.26422764227642276	85	0.23480662983425415	132	0.23076923076923078	60	0.079155672823219	C	18.52	3.640753	0.67244	0.302315	0.111395	ENSG00000182224	ENST00000332439;ENST00000541486	D	0.82081	-1.57	5.41	1.28	0.21552	Cytochrome b5 (4);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.39326	1.205	0.40772	P	0.016907000000000005	P;D	0.54047	0.945;0.964	P;P	0.51297	0.641;0.665	T	0.02766	-1.1113	9	0.62326	D	0.03	-4.3159	9.3842	0.38333	0.0:0.7044:0.0:0.2956	rs12453250;rs61658971;rs12453250	20;20	Q6P9G0-2;Q6P9G0	.;CB5D1_HUMAN	L	20	ENSP00000331479:F20L	ENSP00000331479:F20L	F	+	3	2	CYB5D1	7702237	1.000000	0.71417	0.996000	0.52242	0.926000	0.56050	1.582000	0.36568	0.139000	0.18822	0.561000	0.74099	TTC	C|0.814;A|0.186	0.186	strong		0.582	CYB5D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440841.1	NM_144607	
MUC2	4583	hgsc.bcm.edu	37	11	1103296	1103296	+	Silent	SNP	T	T	C	rs7126405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1103296T>C	ENST00000441003.2	+	46	8073	c.8046T>C	c.(8044-8046)ttT>ttC	p.F2682F		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5044					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCCCCAACTTTGATGCCAGCA	0.597													C|||	833	0.166334	0.4259	0.0778	5008	,	,		18842	0.0357		0.1123	False		,,,				2504	0.0685				p.F2678F		Atlas-SNP	.											.	MUC2	614	.	0			c.T8034C						PASS	.	C		1439,2763		236,967,898	124.0	132.0	129.0		8031	-1.3	0.0	11	dbSNP_116	129	864,7562		36,792,3385	no	coding-synonymous	MUC2	NM_002457.2		272,1759,4283	CC,CT,TT		10.254,34.2456,18.2373		2677/2813	1103296	2303,10325	2101	4213	6314	SO:0001819	synonymous_variant	4583	exon47			CAACTTTGATGCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8046T>C	11.37:g.1103296T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	196	94	0.479592	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.845;C|0.155	0.155	strong		0.597	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZNF623	9831	hgsc.bcm.edu	37	8	144732450	144732450	+	Silent	SNP	G	G	A	rs3750204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144732450G>A	ENST00000501748.2	+	1	497	c.408G>A	c.(406-408)tcG>tcA	p.S136S	ZNF623_ENST00000526926.1_Silent_p.S96S|ZNF623_ENST00000458270.2_Silent_p.S96S	NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S136S(1)		endometrium(2)|kidney(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CGTTTAATTCGGACCTAGTTA	0.483													g|||	1545	0.308506	0.3563	0.3141	5008	,	,		23243	0.3651		0.2266	False		,,,				2504	0.2658				p.S136S		Atlas-SNP	.											ZNF623,NS,carcinoma,0,1	ZNF623	63	1	1	Substitution - coding silent(1)	stomach(1)	c.G408A						PASS	.	A	,	1402,3004	458.6+/-352.0	204,994,1005	115.0	103.0	107.0		288,408	-8.0	0.0	8	dbSNP_107	107	1917,6683	340.0+/-323.4	220,1477,2603	no	coding-synonymous,coding-synonymous	ZNF623	NM_001082480.1,NM_014789.3	,	424,2471,3608	AA,AG,GG		22.2907,31.8202,25.519	,	96/497,136/537	144732450	3319,9687	2203	4300	6503	SO:0001819	synonymous_variant	9831	exon1			TAATTCGGACCTA	AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309		"""Zinc fingers, C2H2-type"""	29084	protein-coding gene	gene with protein product						9734811	Standard	NM_014789		Approved	KIAA0628	uc003yzd.2	O75123		ENST00000501748.2:c.408G>A	8.37:g.144732450G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	164	84	0.512195	NM_014789	A4FU80|B4DGP3|E7ENV5	Silent	SNP	ENST00000501748.2	37	CCDS34957.1																																																																																			G|0.722;A|0.278	0.278	strong		0.483	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382522.3	NM_014789	
OR2T3	343173	hgsc.bcm.edu	37	1	248637416	248637416	+	Silent	SNP	G	G	C	rs75924848	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248637416G>C	ENST00000359594.2	+	1	790	c.765G>C	c.(763-765)ctG>ctC	p.L255L		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TAGTGCTGCTGCTCTTCGGTG	0.547													.|||	1453	0.290136	0.2572	0.2853	5008	,	,		31570	0.3661		0.2097	False		,,,				2504	0.3425				p.L255L		Atlas-SNP	.											.	OR2T3	79	.	0			c.G765C						PASS	.						263.0	237.0	246.0					1																	248637416		2203	4300	6503	SO:0001819	synonymous_variant	343173	exon1			GCTGCTGCTCTTC		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.765G>C	1.37:g.248637416G>C		Somatic	937	0	0		WXS	Illumina HiSeq	Phase_I	929	254	0.273412	NM_001005495	B2RNJ1	Silent	SNP	ENST00000359594.2	37	CCDS31117.1																																																																																			G|0.887;C|0.113	0.113	strong		0.547	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
PHTF2	57157	hgsc.bcm.edu	37	7	77569559	77569559	+	Silent	SNP	C	C	T	rs1064040	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:77569559C>T	ENST00000248550.7	+	13	1756	c.1680C>T	c.(1678-1680)cgC>cgT	p.R560R	PHTF2_ENST00000275575.7_Silent_p.R522R|PHTF2_ENST00000416283.2_Silent_p.R526R|PHTF2_ENST00000307305.8_Silent_p.R522R|PHTF2_ENST00000422959.2_Silent_p.R526R|PHTF2_ENST00000424760.1_Silent_p.R522R			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	560					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						TTGTGGTTCGCGTGTCTCTTG	0.343													C|||	80	0.0159744	0.0098	0.0317	5008	,	,		15147	0.001		0.0298	False		,,,				2504	0.0143				p.R526R		Atlas-SNP	.											.	PHTF2	104	.	0			c.C1578T						PASS	.	C	,,	53,3615		0,53,1781	169.0	155.0	159.0		1578,1566,1566	-1.6	1.0	7	dbSNP_86	159	272,7908		3,266,3821	no	coding-synonymous,coding-synonymous,coding-synonymous	PHTF2	NM_001127357.1,NM_001127358.1,NM_020432.4	,,	3,319,5602	TT,TC,CC		3.3252,1.4449,2.7431	,,	526/752,522/748,522/748	77569559	325,11523	1834	4090	5924	SO:0001819	synonymous_variant	57157	exon12			GGTTCGCGTGTCT	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1680C>T	7.37:g.77569559C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Silent	SNP	ENST00000248550.7	37																																																																																				C|0.980;T|0.020	0.020	strong		0.343	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432	
SKA3	221150	hgsc.bcm.edu	37	13	21729252	21729252	+	3'UTR	SNP	T	T	C	rs11147976	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:21729252T>C	ENST00000314759.5	-	0	1400				SKA3_ENST00000400018.3_Missense_Mutation_p.K386R	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)		p.K386R(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TCATCTCATTTTGTTCAGTTT	0.353																																					p.K386R		Atlas-SNP	.											.	SKA3	76	.	1	Substitution - Missense(1)	endometrium(1)	c.A1157G						PASS	.						143.0	152.0	149.0					13																	21729252		2202	4300	6502	SO:0001624	3_prime_UTR_variant	221150	exon8			CTCATTTTGTTCA	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.*37A>G	13.37:g.21729252T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	175	35	0.2	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	285	0.1304945054945055	12	0.024390243902439025	53	0.1464088397790055	123	0.21503496503496503	97	0.1279683377308707	C	14.23	2.472714	0.43942	.	.	ENSG00000165480	ENST00000400018	T	0.23950	1.88	4.03	1.2	0.21068	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34576	-0.9823	8	0.02654	T	1	.	6.6402	0.22904	0.0:0.549:0.0:0.451	rs11147976;rs52803875;rs56923931;rs11147976	386	Q8IX90-3	.	R	386	ENSP00000382896:K386R	ENSP00000382896:K386R	K	-	2	0	SKA3	20627252	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.064000	0.14437	-0.005000	0.14395	-1.473000	0.01005	AAA	T|0.889;C|0.111	0.111	strong		0.353	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
MAPK6	5597	hgsc.bcm.edu	37	15	52353498	52353498	+	Missense_Mutation	SNP	C	C	G	rs17853426|rs35697691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:52353498C>G	ENST00000261845.5	+	5	1675	c.868C>G	c.(868-870)Ctg>Gtg	p.L290V	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> V (in dbSNP:rs35697691). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)	p.L290V(2)		breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CTCTGCAGCACTGGATTTCCT	0.358													C|||	164	0.0327476	0.0061	0.0735	5008	,	,		18672	0.0		0.0875	False		,,,				2504	0.0174				p.L290V		Atlas-SNP	.											MAPK6,face,carcinoma,0,5	MAPK6	70	5	2	Substitution - Missense(2)	lung(1)|skin(1)	c.C868G						PASS	.	C	VAL/LEU	100,4290	77.8+/-116.1	4,92,2099	93.0	89.0	91.0		868	5.1	1.0	15	dbSNP_126	91	794,7792	182.5+/-230.9	35,724,3534	yes	missense	MAPK6	NM_002748.3	32	39,816,5633	GG,GC,CC		9.2476,2.2779,6.8896	probably-damaging	290/722	52353498	894,12082	2195	4293	6488	SO:0001583	missense	5597	exon5			GCAGCACTGGATT	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"""Mitogen-activated protein kinase cascade / Kinases"""	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.868C>G	15.37:g.52353498C>G	ENSP00000261845:p.Leu290Val	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	257	121	0.470817	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	37	CCDS10147.1	93	0.042582417582417584	4	0.008130081300813009	25	0.06906077348066299	0	0.0	64	0.08443271767810026	C	16.84	3.233417	0.58886	0.022779	0.092476	ENSG00000069956	ENST00000261845	T	0.66099	-0.19	5.13	5.13	0.70059	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.07007	0.0178	N	0.17379	0.485	0.09310	P	0.999999574787	D	0.69078	0.997	D	0.79108	0.992	T	0.47341	-0.9125	9	0.37606	T	0.19	-0.3463	18.5662	0.91118	0.0:1.0:0.0:0.0	rs35697691	290	Q16659	MK06_HUMAN	V	290	ENSP00000261845:L290V	ENSP00000261845:L290V	L	+	1	2	MAPK6	50140790	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.015000	0.40961	2.399000	0.81585	0.585000	0.79938	CTG	C|0.939;G|0.061	0.061	strong		0.358	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748	
OR8D4	338662	hgsc.bcm.edu	37	11	123777861	123777861	+	Silent	SNP	T	T	C	rs61748875	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123777861T>C	ENST00000321355.2	+	1	753	c.723T>C	c.(721-723)tgT>tgC	p.C241C		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C241C(1)		large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		TTAGCACCTGTAGCTCCCACC	0.458													T|||	818	0.163339	0.2005	0.1398	5008	,	,		18173	0.0933		0.1819	False		,,,				2504	0.183				p.C241C		Atlas-SNP	.											OR8D4,NS,carcinoma,0,1	OR8D4	62	1	1	Substitution - coding silent(1)	stomach(1)	c.T723C						PASS	.	T		857,3547	336.5+/-304.4	88,681,1433	114.0	114.0	114.0		723	3.6	1.0	11	dbSNP_129	114	1634,6964	303.0+/-306.2	164,1306,2829	no	coding-synonymous	OR8D4	NM_001005197.1		252,1987,4262	CC,CT,TT		19.0044,19.4596,19.1586		241/315	123777861	2491,10511	2202	4299	6501	SO:0001819	synonymous_variant	338662	exon1			CACCTGTAGCTCC	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.723T>C	11.37:g.123777861T>C		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	245	124	0.506122	NM_001005197	Q6IFE9	Silent	SNP	ENST00000321355.2	37	CCDS31698.1																																																																																			T|0.815;C|0.185	0.185	strong		0.458	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
GSE1	23199	hgsc.bcm.edu	37	16	85702028	85702028	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:85702028A>G	ENST00000253458.7	+	14	3589	c.3413A>G	c.(3412-3414)gAa>gGa	p.E1138G	GSE1_ENST00000405402.2_Missense_Mutation_p.E1034G|GSE1_ENST00000393243.1_Missense_Mutation_p.E1065G	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	1138																	GAACACATAGAAGGTAAGGGG	0.547																																					p.E1138G		Atlas-SNP	.											KIAA0182,NS,carcinoma,+1,1	.	.	1	0			c.A3413G						scavenged	.						27.0	31.0	29.0					16																	85702028		2196	4300	6496	SO:0001583	missense	23199	exon14			ACATAGAAGGTAA	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.3413A>G	16.37:g.85702028A>G	ENSP00000253458:p.Glu1138Gly	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	25	7	0.28	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	37	CCDS10952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.4|21.4	4.142274|4.142274	0.77775|0.77775	.|.	.|.	ENSG00000131149|ENSG00000131149	ENST00000405402;ENST00000253458;ENST00000393243|ENST00000412692;ENST00000438180	T;T;T|.	0.34472|.	1.36;1.36;1.36|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71091|0.71091	0.3299|0.3299	M|M	0.64997|0.64997	1.995|1.995	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D|.	0.89917|.	0.999;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.995;0.999;0.999;0.998|.	T|T	0.70930|0.70930	-0.4738|-0.4738	10|5	0.72032|.	D|.	0.01|.	-11.1152|-11.1152	14.9832|14.9832	0.71327|0.71327	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	901;1034;1065;1138|.	Q59GZ0;Q14687-2;Q14687-3;Q14687|.	.;.;.;GSE1_HUMAN|.	G|E	1034;1138;1065|907;340	ENSP00000384839:E1034G;ENSP00000253458:E1138G;ENSP00000376934:E1065G|.	ENSP00000253458:E1138G|.	E|K	+|+	2|1	0|0	KIAA0182|KIAA0182	84259529|84259529	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.603000|0.603000	0.37013|0.37013	8.832000|8.832000	0.92079|0.92079	1.951000|1.951000	0.56629|0.56629	0.459000|0.459000	0.35465|0.35465	GAA|AAG	.	.	none		0.547	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	
ARID4A	5926	hgsc.bcm.edu	37	14	58831142	58831142	+	Missense_Mutation	SNP	A	A	G	rs1051858|rs386777941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:58831142A>G	ENST00000355431.3	+	20	2708	c.2335A>G	c.(2335-2337)Aca>Gca	p.T779A	ARID4A_ENST00000395168.3_Missense_Mutation_p.T779A|ARID4A_ENST00000348476.3_Missense_Mutation_p.T779A|ARID4A_ENST00000431317.2_Missense_Mutation_p.T779A	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	779			T -> A (in dbSNP:rs1051858). {ECO:0000269|PubMed:8414517}.		erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AATGGAAAAAACAGAAGAAGT	0.328													G|||	1750	0.349441	0.3434	0.2291	5008	,	,		15678	0.5169		0.34	False		,,,				2504	0.2802				p.T779A		Atlas-SNP	.											.	ARID4A	222	.	0			c.A2335G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR	1506,2898		247,1012,943	38.0	43.0	41.0		2335,2335,2335	1.5	0.0	14	dbSNP_86	41	2835,5745		450,1935,1905	yes	missense,missense,missense	ARID4A	NM_002892.3,NM_023000.2,NM_023001.2	58,58,58	697,2947,2848	GG,GA,AA		33.042,34.1962,33.4335	benign,benign,benign	779/1258,779/1204,779/1189	58831142	4341,8643	2202	4290	6492	SO:0001583	missense	5926	exon20			GAAAAAACAGAAG	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2335A>G	14.37:g.58831142A>G	ENSP00000347602:p.Thr779Ala	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	839	0.3841575091575092	157	0.31910569105691056	99	0.27348066298342544	306	0.534965034965035	277	0.3654353562005277	G	0.733	-0.779318	0.02929	0.341962	0.33042	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.13778	2.59;2.58;2.58;2.58;2.56	5.46	1.52	0.23074	.	1.543180	0.03203	N	0.174991	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.45293	-0.9271	9	0.09338	T	0.73	-0.0033	2.1538	0.03807	0.3574:0.1167:0.4062:0.1196	rs1051858;rs17214268;rs52814271;rs57783039;rs1051858	779;779;779	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	A	779;779;779;779;457	ENSP00000347602:T779A;ENSP00000344556:T779A;ENSP00000378597:T779A;ENSP00000397368:T779A;ENSP00000416053:T457A	ENSP00000344556:T779A	T	+	1	0	ARID4A	57900895	0.001000	0.12720	0.007000	0.13788	0.872000	0.50106	-0.111000	0.10807	-0.195000	0.10382	-0.128000	0.14901	ACA	A|0.645;G|0.354	0.354	strong		0.328	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
SEC23IP	11196	hgsc.bcm.edu	37	10	121685559	121685559	+	Silent	SNP	G	G	A	rs12771873	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:121685559G>A	ENST00000369075.3	+	13	2205	c.2133G>A	c.(2131-2133)gcG>gcA	p.A711A	SEC23IP_ENST00000543134.1_Silent_p.A500A	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	711					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A711A(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		AAAAAGCAGCGTCAGAAAAGA	0.408													G|||	597	0.119209	0.0023	0.0274	5008	,	,		16652	0.2113		0.0537	False		,,,				2504	0.3149				p.A711A		Atlas-SNP	.											SEC23IP,NS,carcinoma,0,1	SEC23IP	100	1	1	Substitution - coding silent(1)	stomach(1)	c.G2133A						PASS	.	G		38,4368	43.8+/-77.6	0,38,2165	46.0	45.0	45.0		2133	-7.8	0.0	10	dbSNP_121	45	475,8125	138.7+/-195.5	9,457,3834	no	coding-synonymous	SEC23IP	NM_007190.3		9,495,5999	AA,AG,GG		5.5233,0.8625,3.9443		711/1001	121685559	513,12493	2203	4300	6503	SO:0001819	synonymous_variant	11196	exon13			AGCAGCGTCAGAA	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"""Sterile alpha motif (SAM) domain containing"""	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.2133G>A	10.37:g.121685559G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Silent	SNP	ENST00000369075.3	37	CCDS7618.1																																																																																			G|0.937;A|0.063	0.063	strong		0.408	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1		
PLEC	5339	hgsc.bcm.edu	37	8	144997656	144997656	+	Silent	SNP	C	C	T	rs7016416	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144997656C>T	ENST00000322810.4	-	31	7021	c.6852G>A	c.(6850-6852)gcG>gcA	p.A2284A	PLEC_ENST00000354589.3_Silent_p.A2147A|PLEC_ENST00000357649.2_Silent_p.A2151A|PLEC_ENST00000356346.3_Silent_p.A2133A|PLEC_ENST00000398774.2_Silent_p.A2115A|PLEC_ENST00000345136.3_Silent_p.A2147A|PLEC_ENST00000527096.1_Silent_p.A2170A|PLEC_ENST00000436759.2_Silent_p.A2174A|PLEC_ENST00000354958.2_Silent_p.A2125A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2284	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GTGCCCGCCGCGCCGCCTCTT	0.692													C|||	1153	0.230232	0.028	0.2954	5008	,	,		12031	0.1429		0.4245	False		,,,				2504	0.3476				p.A2284A		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	0			c.G6852A						scavenged	.	C	,,,,,,,	329,3527		26,277,1625	8.0	11.0	10.0		6522,6399,6375,6852,6345,6441,6453,6441	-7.4	0.0	8	dbSNP_116	10	3097,4915		616,1865,1525	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	642,2142,3150	TT,TC,CC		38.6545,8.5322,28.8675	,,,,,,,	2174/4575,2133/4534,2125/4526,2284/4685,2115/4516,2147/4548,2151/4552,2147/4548	144997656	3426,8442	1928	4006	5934	SO:0001819	synonymous_variant	5339	exon31			CCGCCGCGCCGCC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.6852G>A	8.37:g.144997656C>T		Somatic	29	1	0.0344828		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			C|0.718;T|0.282	0.282	strong		0.692	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
FBXO7	25793	hgsc.bcm.edu	37	22	32871383	32871383	+	Intron	SNP	T	T	G	rs8137714	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:32871383T>G	ENST00000266087.7	+	1	449				FBXO7_ENST00000382058.3_Missense_Mutation_p.L12R|FBXO7_ENST00000397426.1_5'UTR	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7						cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGTCCCCTCCTCGGTGAGTCA	0.617													T|||	776	0.154952	0.1233	0.2161	5008	,	,		12429	0.1567		0.1928	False		,,,				2504	0.1135				p.L12R		Atlas-SNP	.											FBXO7_ENST00000382058,NS,carcinoma,0,1	FBXO7	131	1	0			c.T35G						PASS	.	T	ARG/LEU,	537,3099		39,459,1320	25.0	31.0	29.0		35,	-6.1	0.0	22	dbSNP_116	29	1668,6478		161,1346,2566	yes	missense,intron	FBXO7	NM_001033024.1,NM_012179.3	102,	200,1805,3886	GG,GT,TT		20.4763,14.769,18.715	,	12/444,	32871383	2205,9577	1818	4073	5891	SO:0001627	intron_variant	25793	exon1			CCCTCCTCGGTGA	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.122+272T>G	22.37:g.32871383T>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_001033024	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	37	CCDS13907.1	383	0.17536630036630035	53	0.10772357723577236	85	0.23480662983425415	95	0.1660839160839161	150	0.19788918205804748	T	4.156	0.027415	0.08054	0.14769	0.204763	ENSG00000100225	ENST00000452138;ENST00000382058	T;T	0.65364	0.81;-0.15	3.07	-6.13	0.02118	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09015	-1.0694	8	0.40728	T	0.16	.	0.5836	0.00716	0.3068:0.276:0.1109:0.3063	rs8137714;rs11538370	12	Q9Y3I1-2	.	R	12	ENSP00000388547:L12R;ENSP00000371490:L12R	ENSP00000371490:L12R	L	+	2	0	FBXO7	31201383	0.003000	0.15002	0.002000	0.10522	0.001000	0.01503	-0.257000	0.08745	-1.638000	0.01529	-0.441000	0.05720	CTC	A|0.000;C|0.000;G|0.179;T|0.820	0.179	strong		0.617	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
NPEPL1	79716	hgsc.bcm.edu	37	20	57290347	57290347	+	Missense_Mutation	SNP	C	C	G	rs6026468	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57290347C>G	ENST00000356091.6	+	12	1825	c.1537C>G	c.(1537-1539)Ctg>Gtg	p.L513V	NPEPL1_ENST00000525967.1_Missense_Mutation_p.L485V|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525817.1_Missense_Mutation_p.L465V	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	513			L -> V (in dbSNP:rs6026468). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			GGAGGGGGACCTGGGGAGGGA	0.602																																					p.L513V		Atlas-SNP	.											.	NPEPL1	36	.	0			c.C1537G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU	3293,899		1299,695,102	26.0	31.0	30.0		1453,1393,1537	-10.5	0.0	20	dbSNP_114	30	5109,3307		1563,1983,662	yes	missense,missense,missense	NPEPL1	NM_001204872.1,NM_001204873.1,NM_024663.3	32,32,32	2862,2678,764	GG,GC,CC		39.2942,21.4456,33.3598	benign,benign,benign	485/496,465/476,513/524	57290347	8402,4206	2096	4208	6304	SO:0001583	missense	79716	exon12			GGGGACCTGGGGA	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.1537C>G	20.37:g.57290347C>G	ENSP00000348395:p.Leu513Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	37	CCDS46621.1	1252	0.5732600732600732	407	0.8272357723577236	154	0.425414364640884	255	0.4458041958041958	436	0.575197889182058	G	0.010	-1.760425	0.00657	0.785544	0.607058	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.29917	1.55;1.57;1.57	5.26	-10.5	0.00291	.	0.744268	0.13195	N	0.406447	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45131	-0.9282	9	0.02654	T	1	-0.0092	1.4758	0.02425	0.4214:0.1455:0.2645:0.1686	rs6026468;rs6026468	513;465;485	Q8NDH3;G5EA34;E9PN47	PEPL1_HUMAN;.;.	V	485;465;513	ENSP00000434810:L485V;ENSP00000437112:L465V;ENSP00000348395:L513V	ENSP00000348395:L513V	L	+	1	2	NPEPL1	56723754	0.000000	0.05858	0.000000	0.03702	0.217000	0.24651	-0.623000	0.05546	-3.969000	0.00086	-1.773000	0.00660	CTG	C|0.422;G|0.578	0.578	strong		0.602	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
NLRP14	338323	hgsc.bcm.edu	37	11	7091569	7091569	+	Missense_Mutation	SNP	C	C	T	rs17280682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7091569C>T	ENST00000299481.4	+	11	3374	c.3028C>T	c.(3028-3030)Ctt>Ttt	p.L1010F		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	1010			L -> F (in dbSNP:rs17280682). {ECO:0000269|PubMed:16931801}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		CTCCTCTGCTCTTATCTGCAA	0.358													C|||	481	0.0960463	0.0666	0.1297	5008	,	,		19436	0.0169		0.2147	False		,,,				2504	0.0716				p.L1010F		Atlas-SNP	.											.	NLRP14	187	.	0			c.C3028T						PASS	.	C	PHE/LEU	368,4034	189.9+/-215.9	10,348,1843	108.0	103.0	105.0		3028	4.1	0.1	11	dbSNP_123	105	1848,6744	330.3+/-319.2	205,1438,2653	yes	missense	NLRP14	NM_176822.3	22	215,1786,4496	TT,TC,CC		21.5084,8.3598,17.054	probably-damaging	1010/1094	7091569	2216,10778	2201	4296	6497	SO:0001583	missense	338323	exon11			TCTGCTCTTATCT	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.3028C>T	11.37:g.7091569C>T	ENSP00000299481:p.Leu1010Phe	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	246	0.11263736263736264	24	0.04878048780487805	48	0.13259668508287292	13	0.022727272727272728	161	0.21240105540897097	C	14.57	2.575489	0.45902	0.083598	0.215084	ENSG00000158077	ENST00000299481	T	0.61859	0.07	4.13	4.13	0.48395	.	0.000000	0.37095	N	0.002246	T	0.00073	0.0002	M	0.74881	2.28	0.47547	P	5.450000000000177E-4	P	0.40197	0.706	B	0.43838	0.433	T	0.07539	-1.0767	9	0.51188	T	0.08	.	12.1948	0.54290	0.0:1.0:0.0:0.0	rs17280682;rs58608223;rs17280682	1010	Q86W24	NAL14_HUMAN	F	1010	ENSP00000299481:L1010F	ENSP00000299481:L1010F	L	+	1	0	NLRP14	7048145	0.901000	0.30685	0.091000	0.20842	0.027000	0.11550	2.377000	0.44300	2.602000	0.87976	0.557000	0.71058	CTT	C|0.850;T|0.150	0.150	strong		0.358	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
CD248	57124	hgsc.bcm.edu	37	11	66083782	66083782	+	Silent	SNP	G	G	A	rs3741368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66083782G>A	ENST00000311330.3	-	1	733	c.717C>T	c.(715-717)aaC>aaT	p.N239N	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	239					anatomical structure regression (GO:0060033)|cell migration (GO:0016477)|lymph node development (GO:0048535)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	26						CGCAGCCCCCGTTGTCAGGGC	0.682													G|||	1279	0.255391	0.0378	0.5303	5008	,	,		17523	0.2272		0.4463	False		,,,				2504	0.1871				p.N239N		Atlas-SNP	.											CD248,NS,carcinoma,0,1	CD248	69	1	0			c.C717T						PASS	.	G		443,3957		27,389,1784	28.0	38.0	35.0		717	0.1	1.0	11	dbSNP_107	35	3830,4754		857,2116,1319	no	coding-synonymous	CD248	NM_020404.2		884,2505,3103	AA,AG,GG		44.6179,10.0682,32.9097		239/758	66083782	4273,8711	2200	4292	6492	SO:0001819	synonymous_variant	57124	exon1			GCCCCCGTTGTCA	AF279142	CCDS8134.1	11q13	2006-04-12	2006-03-28	2005-02-11	ENSG00000174807	ENSG00000174807		"""CD molecules"""	18219	protein-coding gene	gene with protein product	"""endosialin"", ""tumor endothelial marker 1"""	606064	"""CD164 sialomucin-like 1"", ""CD248 antigen, endosialin"""	CD164L1		10947988, 11084048	Standard	NM_020404		Approved	TEM1	uc001ohm.1	Q9HCU0	OTTHUMG00000167073	ENST00000311330.3:c.717C>T	11.37:g.66083782G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_020404	Q2M2V5|Q3SX55|Q96KB6	Silent	SNP	ENST00000311330.3	37	CCDS8134.1																																																																																			G|0.702;A|0.298	0.298	strong		0.682	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404	
TANGO2	128989	hgsc.bcm.edu	37	22	20043504	20043504	+	Missense_Mutation	SNP	G	G	A	rs142442293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20043504G>A	ENST00000327374.4	+	6	597	c.419G>A	c.(418-420)cGa>cAa	p.R140Q	TANGO2_ENST00000401886.1_Intron|TANGO2_ENST00000434570.2_Missense_Mutation_p.R181Q|TANGO2_ENST00000401833.1_Missense_Mutation_p.R181Q|TANGO2_ENST00000432883.1_Intron|TANGO2_ENST00000447208.2_Missense_Mutation_p.R140Q|TANGO2_ENST00000420290.2_Missense_Mutation_p.R42Q|TANGO2_ENST00000456048.1_Missense_Mutation_p.R145Q|TANGO2_ENST00000398042.2_Intron	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	140																	TATGGGAACCGAGGGGAGCCT	0.582													G|||	10	0.00199681	0.0	0.0043	5008	,	,		18456	0.0		0.007	False		,,,				2504	0.0				p.R140Q		Atlas-SNP	.											.	TANGO2	4	.	0			c.G419A						PASS	.	G	GLN/ARG	8,4398	14.3+/-33.2	0,8,2195	146.0	122.0	130.0		419	4.5	1.0	22	dbSNP_134	130	66,8534	40.3+/-97.0	0,66,4234	yes	missense	C22orf25	NM_152906.4	43	0,74,6429	AA,AG,GG		0.7674,0.1816,0.569	probably-damaging	140/277	20043504	74,12932	2203	4300	6503	SO:0001583	missense	128989	exon6			GGAACCGAGGGGA		CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 25"""	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.419G>A	22.37:g.20043504G>A	ENSP00000332721:p.Arg140Gln	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_152906	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	37	CCDS13772.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	17.39	3.377251	0.61735	0.001816	0.007674	ENSG00000183597	ENST00000447208;ENST00000450664;ENST00000327374;ENST00000401833;ENST00000434168;ENST00000434570;ENST00000420290;ENST00000456048	T;T;T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93	4.52	4.52	0.55395	.	0.140989	0.50627	D	0.000103	T	0.23649	0.0572	M	0.86097	2.795	0.40039	D	0.975622	P;P;P;P;P;B	0.45531	0.807;0.657;0.86;0.458;0.513;0.372	B;B;B;B;B;B	0.37198	0.131;0.227;0.243;0.067;0.046;0.029	T	0.29610	-1.0006	10	0.36615	T	0.2	-34.711	12.9432	0.58357	0.0:0.0:1.0:0.0	.	140;181;42;181;145;140	B7Z9Q5;B7Z730;B7Z583;B7WNV6;C9JC99;Q6ICL3	.;.;.;.;.;CV025_HUMAN	Q	140;140;140;181;140;181;42;145	ENSP00000389797:R140Q;ENSP00000415450:R140Q;ENSP00000332721:R140Q;ENSP00000384827:R181Q;ENSP00000411602:R140Q;ENSP00000391262:R181Q;ENSP00000396182:R42Q;ENSP00000403645:R145Q	ENSP00000332721:R140Q	R	+	2	0	C22orf25	18423504	0.999000	0.42202	0.995000	0.50966	0.614000	0.37383	2.511000	0.45476	2.499000	0.84300	0.563000	0.77884	CGA	G|0.996;A|0.004	0.004	strong		0.582	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906	
TTC17	55761	hgsc.bcm.edu	37	11	43472746	43472746	+	Silent	SNP	C	C	T	rs11551137	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:43472746C>T	ENST00000039989.4	+	21	2975	c.2961C>T	c.(2959-2961)ctC>ctT	p.L987L		NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	987					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						TACAAAATCTCGGCAAAGACC	0.423													C|||	416	0.0830671	0.0023	0.2579	5008	,	,		19439	0.0317		0.0954	False		,,,				2504	0.1084				p.L987L		Atlas-SNP	.											.	TTC17	112	.	0			c.C2961T						PASS	.	C		96,4310	77.8+/-116.1	0,96,2107	99.0	91.0	94.0		2961	0.3	1.0	11	dbSNP_120	94	764,7836	182.2+/-230.7	33,698,3569	no	coding-synonymous	TTC17	NM_018259.5		33,794,5676	TT,TC,CC		8.8837,2.1788,6.6123		987/1142	43472746	860,12146	2203	4300	6503	SO:0001819	synonymous_variant	55761	exon21			AAATCTCGGCAAA	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"""Tetratricopeptide (TTC) repeat domain containing"""	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.2961C>T	11.37:g.43472746C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	39	0.6	NM_018259	G3XAB3|Q8NEC0	Silent	SNP	ENST00000039989.4	37	CCDS31466.1	179	0.08195970695970696	2	0.0040650406504065045	85	0.23480662983425415	18	0.03146853146853147	74	0.09762532981530343	C	9.492	1.100985	0.20552	0.021788	0.088837	ENSG00000052841	ENST00000418561	.	.	.	5.84	0.274	0.15654	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20240	-1.0281	3	.	.	.	-11.7732	6.2318	0.20738	0.0:0.1449:0.3789:0.4762	rs11551137;rs12420769;rs17594421;rs11551137	.	.	.	L	6	.	.	S	+	2	0	TTC17	43429322	0.906000	0.30813	1.000000	0.80357	0.985000	0.73830	-0.334000	0.07883	0.109000	0.17891	-0.300000	0.09419	TCG	C|0.929;T|0.071	0.071	strong		0.423	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259	
CCL25	6370	hgsc.bcm.edu	37	19	8122737	8122737	+	Silent	SNP	G	G	A	rs2303164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8122737G>A	ENST00000390669.3	+	4	428	c.378G>A	c.(376-378)tcG>tcA	p.S126S	CCL25_ENST00000315626.4_Missense_Mutation_p.V82I|CCL25_ENST00000253451.4_Silent_p.S125S			O15444	CCL25_HUMAN	chemokine (C-C motif) ligand 25	126					cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of cell-matrix adhesion (GO:0001954)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR10 chemokine receptor binding (GO:0031735)|chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|hormone activity (GO:0005179)			NS(1)|endometrium(1)|lung(1)|skin(1)|urinary_tract(1)	5						agttatcatcgtccaagttta	0.453													G|||	3238	0.646565	0.5499	0.451	5008	,	,		20326	0.7679		0.6392	False		,,,				2504	0.7986				p.S126S		Atlas-SNP	.											.	CCL25	12	.	0			c.G378A						PASS	.	G	,	2252,1724		623,1006,359	138.0	128.0	131.0		375,378	0.1	0.0	19	dbSNP_100	131	5437,2891		1779,1879,506	no	coding-synonymous,coding-synonymous	CCL25	NM_001201359.1,NM_005624.3	,	2402,2885,865	AA,AG,GG		34.7142,43.3602,37.5081	,	125/150,126/151	8122737	7689,4615	1988	4164	6152	SO:0001819	synonymous_variant	6370	exon5			ATCATCGTCCAAG	U86358	CCDS12194.1, CCDS56080.1	19p13.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000131142	ENSG00000131142		"""Chemokine ligands"", ""Endogenous ligands"""	10624	protein-coding gene	gene with protein product	"""Ck beta-15"", ""thymus expressed chemokine"", ""TECKvar"""	602565	"""small inducible cytokine subfamily A (Cys-Cys), member 25"""	SCYA25		9285413, 9722960	Standard	NM_005624		Approved	TECK, Ckb15	uc002mjd.3	O15444	OTTHUMG00000141287	ENST00000390669.3:c.378G>A	19.37:g.8122737G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	195	195	1	NM_005624	A1L4J4|A6NI52|A8K9E7|B5MCA5|Q96KJ7	Silent	SNP	ENST00000390669.3	37	CCDS12194.1	1372	0.6282051282051282	290	0.5894308943089431	176	0.4861878453038674	421	0.736013986013986	485	0.6398416886543535	G	2.091	-0.408462	0.04832	0.566398	0.652858	ENSG00000131142	ENST00000315626	T	0.49432	0.78	1.17	0.0884	0.14455	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.29862	0.259	B	0.12156	0.007	T	0.43147	-0.9409	7	0.02654	T	1	1.4409	3.3495	0.07147	0.2896:0.0:0.7104:0.0	rs2303164;rs58375834;rs2303164	82	C9JDZ7	.	I	82	ENSP00000324756:V82I	ENSP00000324756:V82I	V	+	1	0	CCL25	8028737	0.001000	0.12720	0.003000	0.11579	0.030000	0.12068	0.375000	0.20518	0.070000	0.16634	0.305000	0.20034	GTC	G|0.360;A|0.640	0.640	strong		0.453	CCL25-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280522.1	NM_005624	
ZNF211	10520	hgsc.bcm.edu	37	19	58144715	58144715	+	Start_Codon_SNP	SNP	A	A	G	rs9749449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58144715A>G	ENST00000347302.3	+	1	180	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	ZNF211_ENST00000420680.1_Intron|ZNF211_ENST00000240731.4_Start_Codon_SNP_p.M1V|ZNF211_ENST00000544273.1_5'UTR|ZNF211_ENST00000391703.3_Intron|ZNF211_ENST00000541801.1_Intron|ZNF211_ENST00000299871.5_Start_Codon_SNP_p.M1V|ZNF211_ENST00000254182.7_Intron	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	1					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GGGGATAGCGATGCTCGGGTT	0.716													G|||	1074	0.214457	0.2337	0.1311	5008	,	,		11638	0.3204		0.161	False		,,,				2504	0.1933				p.M1V		Atlas-SNP	.											ZNF211,colon,carcinoma,0,1	ZNF211	78	1	0			c.A1G						scavenged	.	G	VAL/MET,VAL/MET	795,3479		74,647,1416	6.0	9.0	8.0		1,1	-0.4	0.0	19	dbSNP_119	8	1174,7234		74,1026,3104	no	missense,missense	ZNF211	NM_006385.3,NM_198855.2	21,21	148,1673,4520	GG,GA,AA		13.9629,18.6008,15.5259	benign,benign	1/578,1/565	58144715	1969,10713	2137	4204	6341	SO:0001582	initiator_codon_variant	10520	exon1			ATAGCGATGCTCG	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1A>G	19.37:g.58144715A>G	ENSP00000339562:p.Met1Val	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	20	6	0.3	NM_198855	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	483	0.22115384615384615	135	0.27439024390243905	52	0.143646408839779	179	0.3129370629370629	117	0.15435356200527706	G	8.877	0.950688	0.18431	0.186008	0.139629	ENSG00000121417	ENST00000347302;ENST00000299871;ENST00000240731	T;T;T	0.05580	3.44;3.42;3.43	0.929	-0.423	0.12325	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	4.000000000004E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43750	-0.9372	7	0.06757	T	0.87	.	2.7262	0.05214	0.2557:0.3686:0.3758:0.0	rs9749449;rs9749449	1;1;1	F8WDV2;Q13398;B9ZVW1	.;ZN211_HUMAN;.	V	1	ENSP00000339562:M1V;ENSP00000299871:M1V;ENSP00000240731:M1V	ENSP00000240731:M1V	M	+	1	0	ZNF211	62836527	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.769000	0.04710	-0.659000	0.05359	-0.227000	0.12334	ATG	A|0.783;G|0.217	0.217	strong		0.716	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		Missense_Mutation
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274069	39274069	+	Missense_Mutation	SNP	G	G	C	rs349771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39274069G>C	ENST00000391413.2	-	1	537	c.499C>G	c.(499-501)Cga>Gga	p.R167G		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	167				R -> G (in Ref. 1; CAC27583 and 3; AAI26132/AAI30563). {ECO:0000305}.		keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGGAGACTCGGCCACAGACT	0.662													g|||	2320	0.463259	0.4365	0.487	5008	,	,		17612	0.252		0.661	False		,,,				2504	0.4969				p.R167G		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.C499G						PASS	.						35.0	39.0	38.0					17																	39274069		692	1590	2282	SO:0001583	missense	653240	exon1			AGACTCGGCCACA	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.499C>G	17.37:g.39274069G>C	ENSP00000375232:p.Arg167Gly	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	163	162	0.993865	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	994	0.4551282051282051	207	0.42073170731707316	186	0.5138121546961326	136	0.23776223776223776	465	0.6134564643799473	.	12.44	1.937647	0.34189	.	.	ENSG00000212721	ENST00000391413	T	0.00622	6.16	3.95	2.95	0.34219	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.44643	P	0.0023760000000000447	B	0.29646	0.253	B	0.28305	0.088	T	0.00202	-1.1925	8	0.51188	T	0.08	.	11.1465	0.48434	0.0:0.0:0.8133:0.1867	rs349771;rs62066327	167	Q9BYQ6	KR411_HUMAN	G	167	ENSP00000375232:R167G	ENSP00000375232:R167G	R	-	1	2	KRTAP4-11	36527595	0.116000	0.22171	0.948000	0.38648	0.879000	0.50718	2.143000	0.42187	0.934000	0.37316	0.609000	0.83330	CGA	G|0.750;C|0.250	0.250	weak		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
TBC1D2B	23102	hgsc.bcm.edu	37	15	78369815	78369815	+	Silent	SNP	G	G	A	rs9047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78369815G>A	ENST00000300584.3	-	1	179	c.180C>T	c.(178-180)ttC>ttT	p.F60F	TBC1D2B_ENST00000409931.3_Silent_p.F60F|SH2D7_ENST00000409568.2_5'Flank	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	60	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rab GTPase activator activity (GO:0005097)			breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						GGCGCGCGTCGAACACGAACC	0.687													G|||	899	0.179513	0.0424	0.1542	5008	,	,		8310	0.3363		0.1869	False		,,,				2504	0.2137				p.F60F		Atlas-SNP	.											.	TBC1D2B	104	.	0			c.C180T						PASS	.						4.0	9.0	7.0					15																	78369815		618	1485	2103	SO:0001819	synonymous_variant	23102	exon1			CGCGTCGAACACG	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.180C>T	15.37:g.78369815G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Silent	SNP	ENST00000300584.3	37	CCDS45314.1																																																																																			G|0.810;A|0.190	0.190	strong		0.687	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	
MUC4	4585	hgsc.bcm.edu	37	3	195515414	195515414	+	Missense_Mutation	SNP	T	T	C	rs200193644|rs71180964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515414T>C	ENST00000463781.3	-	2	3496	c.3037A>G	c.(3037-3039)Agc>Ggc	p.S1013G	MUC4_ENST00000475231.1_Missense_Mutation_p.S1013G|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGGGCTGGTGACAGGA	0.577													.|||	808	0.161342	0.152	0.1124	5008	,	,		17653	0.2321		0.1352	False		,,,				2504	0.1626				p.S1013G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	6	Deletion - In frame(4)|Substitution - Missense(2)	stomach(6)	c.A3037G						scavenged	.						54.0	29.0	36.0					3																	195515414		687	1591	2278	SO:0001583	missense	4585	exon2			AAGGGCTGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3037A>G	3.37:g.195515414T>C	ENSP00000417498:p.Ser1013Gly	Somatic	605	2	0.00330579		WXS	Illumina HiSeq	Phase_I	182	48	0.263736	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	0.269	-0.994094	0.02145	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.42;1.41	0.814	-1.63	0.08345	.	.	.	.	.	T	0.11623	0.0283	N	0.19112	0.55	0.09310	N	1	P	0.42584	0.784	B	0.28638	0.092	T	0.12041	-1.0563	8	.	.	.	.	2.4902	0.04608	0.3389:0.3247:0.0:0.3364	.	1013	E7ESK3	.	G	1013	ENSP00000417498:S1013G;ENSP00000420243:S1013G	.	S	-	1	0	MUC4	196999809	.	.	0.000000	0.03702	0.012000	0.07955	.	.	-3.949000	0.00088	-2.075000	0.00382	AGC	T|0.963;C|0.037	0.037	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EID2	163126	hgsc.bcm.edu	37	19	40030654	40030654	+	Silent	SNP	G	G	C	rs76765165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40030654G>C	ENST00000390658.2	-	1	216	c.66C>G	c.(64-66)gtC>gtG	p.V22V		NM_153232.3	NP_694964.3			EP300 interacting inhibitor of differentiation 2											large_intestine(2)|lung(1)|urinary_tract(1)	4	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;3.2e-25)|all cancers(26;8.83e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			CCGCCTGCGGGACGTCTCTGT	0.731													.|||	1153	0.230232	0.1853	0.2507	5008	,	,		9909	0.2937		0.2614	False		,,,				2504	0.1789				p.V22V		Atlas-SNP	.											EID2,NS,carcinoma,0,1	EID2	14	1	0			c.C66G						scavenged	.						19.0	22.0	21.0					19																	40030654		1398	2975	4373	SO:0001819	synonymous_variant	163126	exon1			CTGCGGGACGTCT	BC030137	CCDS12540.2	19q13.2	2008-10-24	2006-10-12	2006-10-12	ENSG00000176396	ENSG00000176396			28292	protein-coding gene	gene with protein product		609773	"""CREBBP/EP300 inhibitory protein 2"", ""CREBBP/EP300 inhibitor 2"""	CRI2		14585496	Standard	NM_153232		Approved	EID-2, MGC20452	uc002oma.3	Q8N6I1	OTTHUMG00000074073	ENST00000390658.2:c.66C>G	19.37:g.40030654G>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_153232		Silent	SNP	ENST00000390658.2	37	CCDS12540.2																																																																																			G|0.786;C|0.214	0.214	strong		0.731	EID2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157251.1	NM_153232	
POU2F1	5451	hgsc.bcm.edu	37	1	167381251	167381251	+	Silent	SNP	A	A	G	rs2229284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:167381251A>G	ENST00000541643.3	+	15	1704	c.1542A>G	c.(1540-1542)ccA>ccG	p.P514P	POU2F1_ENST00000420254.3_Silent_p.P514P|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000367862.5_Silent_p.P526P|POU2F1_ENST00000429375.2_Silent_p.P474P|POU2F1_ENST00000367866.2_Silent_p.P537P			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	514					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						CAGCGCCTCCAGCTTCCTCAG	0.532													A|||	76	0.0151757	0.0008	0.0403	5008	,	,		20882	0.0		0.0388	False		,,,				2504	0.0082				p.P537P		Atlas-SNP	.											.	POU2F1	120	.	0			c.A1611G						PASS	.	A	,,	16,4390	23.3+/-48.9	0,16,2187	88.0	84.0	85.0		1578,1422,1611	-11.0	0.0	1	dbSNP_134	85	233,8367	95.9+/-157.7	3,227,4070	no	coding-synonymous,coding-synonymous,coding-synonymous	POU2F1	NM_001198783.1,NM_001198786.1,NM_002697.3	,,	3,243,6257	GG,GA,AA		2.7093,0.3631,1.9145	,,	526/756,474/704,537/767	167381251	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	5451	exon14			GCCTCCAGCTTCC	BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"""Homeoboxes / POU class"""	9212	protein-coding gene	gene with protein product		164175	"""POU domain class 2, transcription factor 1"""	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.1542A>G	1.37:g.167381251A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	149	55	0.369128	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Silent	SNP	ENST00000541643.3	37																																																																																				A|0.978;G|0.022	0.022	strong		0.532	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697	
MACROD1	28992	hgsc.bcm.edu	37	11	63885305	63885305	+	Intron	SNP	C	C	T	rs3824854	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:63885305C>T	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.P522P	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						ATGAGACACCCGTGTGTGCCA	0.607													C|||	729	0.145567	0.0673	0.3055	5008	,	,		21232	0.1815		0.174	False		,,,				2504	0.0716				p.P522P		Atlas-SNP	.											.	FLRT1	46	.	0			c.C1566T						PASS	.	C	,	389,4013	195.0+/-219.7	15,359,1827	111.0	83.0	92.0		1566,	-6.3	0.7	11	dbSNP_107	92	1496,7098	283.6+/-296.2	136,1224,2937	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	151,1583,4764	TT,TC,CC		17.4075,8.8369,14.5045	,	522/675,	63885305	1885,11111	2201	4297	6498	SO:0001627	intron_variant	23769	exon2			GACACCCGTGTGT	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+33405G>A	11.37:g.63885305C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	212	120	0.566038	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			C|0.855;T|0.145	0.145	strong		0.607	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
KLRC4	8302	hgsc.bcm.edu	37	12	10562025	10562025	+	Silent	SNP	C	C	T	rs1841957	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10562025C>T	ENST00000309384.1	-	1	331	c.150G>A	c.(148-150)tcG>tcA	p.S50S	KLRC4-KLRK1_ENST00000539300.1_Missense_Mutation_p.G42R	NM_013431.2	NP_038459.1	O43908	NKG2F_HUMAN	killer cell lectin-like receptor subfamily C, member 4	50					cellular defense response (GO:0006968)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						CTTGATGATCCGAAGAAGCAT	0.353													C|||	2474	0.49401	0.208	0.6311	5008	,	,		19873	0.5605		0.663	False		,,,				2504	0.5409				p.S50S		Atlas-SNP	.											.	KLRC4	23	.	0			c.G150A						PASS	.	C	,	1273,3131	433.1+/-343.5	199,875,1128	191.0	182.0	185.0		,150	-0.4	0.0	12	dbSNP_92	185	5831,2769	677.8+/-403.4	2002,1827,471	no	intron,coding-synonymous	KLRC4,KLRC4-KLRK1	NM_001199805.1,NM_013431.2	,	2201,2702,1599	TT,TC,CC		32.1977,28.9055,45.3707	,	,50/159	10562025	7104,5900	2202	4300	6502	SO:0001819	synonymous_variant	8302	exon1			ATGATCCGAAGAA	U96846	CCDS8624.1	12p13.2-p12.3	2008-08-05			ENSG00000183542	ENSG00000183542		"""Killer cell lectin-like receptors"""	6377	protein-coding gene	gene with protein product		602893				9598306	Standard	NM_013431		Approved	NKG2-F	uc001qye.3	O43908	OTTHUMG00000168575	ENST00000309384.1:c.150G>A	12.37:g.10562025C>T		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	338	337	0.997041	NM_013431	O60851	Silent	SNP	ENST00000309384.1	37	CCDS8624.1																																																																																			C|0.461;T|0.539	0.539	strong		0.353	KLRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400108.1	NM_013431	
CA6	765	hgsc.bcm.edu	37	1	9009444	9009444	+	Missense_Mutation	SNP	A	A	C	rs2274328	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:9009444A>C	ENST00000377443.2	+	2	206	c.202A>C	c.(202-204)Atg>Ctg	p.M68L	CA6_ENST00000377436.3_Missense_Mutation_p.M68L|CA6_ENST00000480186.3_Missense_Mutation_p.M68L|CA6_ENST00000476083.1_Intron|CA6_ENST00000377442.2_Intron	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	68			M -> L (in dbSNP:rs2274328).		bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	GGGGCTCAATATGACAGGCTA	0.607													C|||	2511	0.501398	0.5598	0.4712	5008	,	,		20063	0.4127		0.5358	False		,,,				2504	0.5				p.M68L		Atlas-SNP	.											CA6_ENST00000319474,brain,glioma,0,2	CA6	47	2	0			c.A202C						PASS	.	C	LEU/MET	2403,2003	559.0+/-380.1	666,1071,466	59.0	49.0	52.0		202	2.4	0.0	1	dbSNP_100	52	4505,4095	560.6+/-387.6	1192,2121,987	yes	missense	CA6	NM_001215.2	15	1858,3192,1453	CC,CA,AA		47.6163,45.4607,46.8861	benign	68/309	9009444	6908,6098	2203	4300	6503	SO:0001583	missense	765	exon2			CTCAATATGACAG	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.202A>C	1.37:g.9009444A>C	ENSP00000366662:p.Met68Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	87	29	0.333333	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Missense_Mutation	SNP	ENST00000377443.2	37	CCDS30578.1	1079	0.49404761904761907	264	0.5365853658536586	182	0.5027624309392266	243	0.42482517482517484	390	0.5145118733509235	C	1.753	-0.488725	0.04352	0.545393	0.523837	ENSG00000131686	ENST00000319474;ENST00000377443;ENST00000377436	T;T;T	0.61859	0.07;0.07;0.07	5.32	2.4	0.29515	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.080431	0.52532	N	0.000076	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45086	-0.9285	8	.	.	.	.	4.5988	0.12343	0.3068:0.5279:0.0:0.1653	rs2274328;rs60130913;rs2274328	68	P23280	CAH6_HUMAN	L	68	ENSP00000325786:M68L;ENSP00000366662:M68L;ENSP00000366654:M68L	.	M	+	1	0	CA6	8932031	0.188000	0.23250	0.001000	0.08648	0.006000	0.05464	0.497000	0.22514	0.058000	0.16222	-0.121000	0.15023	ATG	A|0.488;C|0.511	0.511	strong		0.607	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
VPS13A	23230	hgsc.bcm.edu	37	9	79897117	79897117	+	Silent	SNP	G	G	A	rs11145366	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79897117G>A	ENST00000360280.3	+	29	3305	c.3045G>A	c.(3043-3045)ccG>ccA	p.P1015P	VPS13A_ENST00000376634.4_Silent_p.P1015P|VPS13A_ENST00000357409.5_Silent_p.P1015P|VPS13A_ENST00000423463.2_3'UTR|VPS13A_ENST00000376636.3_Silent_p.P1015P	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1015					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ATATCCTTCCGCAATCAGAGG	0.318													G|||	420	0.0838658	0.1165	0.0677	5008	,	,		13503	0.0327		0.1213	False		,,,				2504	0.0654				p.P1015P		Atlas-SNP	.											VPS13A_ENST00000376634,NS,carcinoma,+1,3	VPS13A	735	3	0			c.G3045A						PASS	.	G	,,,	507,3899	226.5+/-242.0	23,461,1719	58.0	63.0	61.0		3045,3045,3045,3045	-0.3	0.4	9	dbSNP_120	61	956,7642	209.0+/-250.3	58,840,3401	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	81,1301,5120	AA,AG,GG		11.1189,11.507,11.2504	,,,	1015/3136,1015/3070,1015/3096,1015/3175	79897117	1463,11541	2203	4299	6502	SO:0001819	synonymous_variant	23230	exon29			CCTTCCGCAATCA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.3045G>A	9.37:g.79897117G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	223	121	0.542601	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			G|0.898;A|0.102	0.102	strong		0.318	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
SRSF6	6431	hgsc.bcm.edu	37	20	42088708	42088708	+	Silent	SNP	G	G	A	rs61733949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:42088708G>A	ENST00000244020.3	+	4	523	c.417G>A	c.(415-417)gcG>gcA	p.A139A		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	139	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						TAACCTATGCGGATGCCCACA	0.413													G|||	157	0.0313498	0.0023	0.0461	5008	,	,		20861	0.0169		0.0716	False		,,,				2504	0.0337				p.A139A		Atlas-SNP	.											.	SRSF6	37	.	0			c.G417A						PASS	.	G		50,4356	51.6+/-87.1	0,50,2153	123.0	123.0	123.0		417	-1.5	1.0	20	dbSNP_129	123	549,8051	150.4+/-205.3	13,523,3764	no	coding-synonymous	SRSF6	NM_006275.5		13,573,5917	AA,AG,GG		6.3837,1.1348,4.6056		139/345	42088708	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	6431	exon4			CTATGCGGATGCC	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10788	protein-coding gene	gene with protein product	"""pre-mRNA splicing factor SRP55"", ""SR splicing factor 6"""	601944	"""splicing factor, arginine/serine-rich 6"""	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.417G>A	20.37:g.42088708G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	135	59	0.437037	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Silent	SNP	ENST00000244020.3	37	CCDS13318.1																																																																																			G|0.956;A|0.044	0.044	strong		0.413	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275	
XYLT2	64132	hgsc.bcm.edu	37	17	48431197	48431197	+	Silent	SNP	C	C	T	rs739989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48431197C>T	ENST00000017003.2	+	2	391	c.342C>T	c.(340-342)ccC>ccT	p.P114P	XYLT2_ENST00000507602.1_Silent_p.P114P	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	114					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					CTGCCCCACCCCCGGAAGCCC	0.721													C|||	663	0.132388	0.0424	0.2795	5008	,	,		12892	0.0794		0.2147	False		,,,				2504	0.1196				p.P114P		Atlas-SNP	.											.	XYLT2	51	.	0			c.C342T						PASS	.	C		259,3883		12,235,1824	5.0	7.0	7.0		342	3.4	1.0	17	dbSNP_86	7	1678,6588		167,1344,2622	no	coding-synonymous	XYLT2	NM_022167.2		179,1579,4446	TT,TC,CC		20.3,6.253,15.6109		114/866	48431197	1937,10471	2071	4133	6204	SO:0001819	synonymous_variant	64132	exon2			CCCACCCCCGGAA	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.342C>T	17.37:g.48431197C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_022167	Q6UY41|Q86V00	Silent	SNP	ENST00000017003.2	37	CCDS11563.1																																																																																			C|0.856;T|0.144	0.144	strong		0.721	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
GJA8	2703	hgsc.bcm.edu	37	1	147380886	147380886	+	Silent	SNP	C	C	T	rs3766503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:147380886C>T	ENST00000369235.1	+	1	804	c.804C>T	c.(802-804)ctC>ctT	p.L268L	GJA8_ENST00000240986.4_Silent_p.L268L			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	268					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)	p.L268L(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GCTATCAGCTCCTAGAAGAAG	0.542													.|||	246	0.0491214	0.0628	0.013	5008	,	,		18214	0.0476		0.0358	False		,,,				2504	0.0716				p.L268L	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											GJA8,NS,carcinoma,0,1	GJA8	108	1	1	Substitution - coding silent(1)	stomach(1)	c.C804T						PASS	.	C		341,4065	174.8+/-204.3	20,301,1882	54.0	56.0	55.0		804	-1.7	0.9	1	dbSNP_107	55	360,8240	118.5+/-177.9	7,346,3947	no	coding-synonymous	GJA8	NM_005267.4		27,647,5829	TT,TC,CC		4.186,7.7394,5.3898		268/434	147380886	701,12305	2203	4300	6503	SO:0001819	synonymous_variant	2703	exon2			TCAGCTCCTAGAA	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"""Ion channels / Gap junction proteins (connexins)"""	4281	protein-coding gene	gene with protein product	"""connexin 50"""	600897	"""gap junction protein, alpha 8, 50kD (connexin 50)"", ""gap junction protein, alpha 8, 50kDa (connexin 50)"""	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.804C>T	1.37:g.147380886C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	37	CCDS30834.1																																																																																			C|0.948;T|0.052	0.052	strong		0.542	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267	
DENND1B	163486	hgsc.bcm.edu	37	1	197480927	197480927	+	IGR	SNP	C	C	T	rs12142127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197480927C>T								CRB1 (33342 upstream) : DENND1B (40457 downstream)																							CCAGCTTCCCCTGATCTGAGC	0.383													C|||	1150	0.229633	0.1415	0.2622	5008	,	,		15737	0.2212		0.3062	False		,,,				2504	0.2556				p.Q582Q		Atlas-SNP	.											.	DENND1B	108	.	0			c.G1746A						PASS	.	C		729,3677	297.8+/-285.0	61,607,1535	96.0	95.0	96.0		1746	-0.8	1.0	1	dbSNP_120	96	2910,5690	450.7+/-362.5	500,1910,1890	no	coding-synonymous	DENND1B	NM_001195215.1		561,2517,3425	TT,TC,CC		33.8372,16.5456,27.9794		582/776	197480927	3639,9367	2203	4300	6503	SO:0001628	intergenic_variant	163486	exon22			CTTCCCCTGATCT																													1.37:g.197480927C>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	298	126	0.422819	NM_001195215		Silent	SNP		37																																																																																				C|0.754;T|0.246	0.246	strong	0	0.383								
MIOS	54468	hgsc.bcm.edu	37	7	7646687	7646687	+	Silent	SNP	A	A	G	rs4222	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:7646687A>G	ENST00000340080.4	+	13	3013	c.2592A>G	c.(2590-2592)acA>acG	p.T864T	MIOS_ENST00000405785.1_Silent_p.T864T	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	864						lysosomal membrane (GO:0005765)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGGATACAACAGGGAATCTGG	0.428													A|||	3462	0.691294	0.5575	0.7954	5008	,	,		15926	0.7381		0.7734	False		,,,				2504	0.6656				p.T864T		Atlas-SNP	.											.	MIOS	68	.	0			c.A2592G						PASS	.	A		2358,1456		724,910,273	79.0	77.0	77.0		2592	5.1	1.0	7	dbSNP_36	77	6480,1766		2550,1380,193	no	coding-synonymous	MIOS	NM_019005.3		3274,2290,466	GG,GA,AA		21.4164,38.1751,26.7164		864/876	7646687	8838,3222	1907	4123	6030	SO:0001819	synonymous_variant	54468	exon13			TACAACAGGGAAT		CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"""WD repeat-containing protein mio"""	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.2592A>G	7.37:g.7646687A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_019005	B2RTV6|O75216|Q7L551|Q9H092	Silent	SNP	ENST00000340080.4	37	CCDS43554.1																																																																																			G|0.722;N|0.000	0.722	strong		0.428	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005	
MUC16	94025	hgsc.bcm.edu	37	19	9072221	9072221	+	Silent	SNP	G	G	A	rs66498329	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9072221G>A	ENST00000397910.4	-	3	15428	c.15225C>T	c.(15223-15225)ggC>ggT	p.G5075G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5077	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCTTCACTAGGCCAGAGGTGA	0.468													G|||	1007	0.201078	0.0946	0.2824	5008	,	,		21007	0.3254		0.167	False		,,,				2504	0.1943				p.G5075G		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	0			c.C15225T						PASS	.			401,3443		18,365,1539	153.0	138.0	143.0		15225	-3.4	0.0	19	dbSNP_130	143	1503,6757		136,1231,2763	no	coding-synonymous	MUC16	NM_024690.2		154,1596,4302	AA,AG,GG		18.1961,10.4318,15.7303		5075/14508	9072221	1904,10200	1922	4130	6052	SO:0001819	synonymous_variant	94025	exon3			CACTAGGCCAGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15225C>T	19.37:g.9072221G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	111	49	0.441441	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.787;A|0.213	0.213	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
WDR43	23160	hgsc.bcm.edu	37	2	29152456	29152456	+	Silent	SNP	A	A	G	rs1140697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29152456A>G	ENST00000407426.3	+	11	1373	c.1317A>G	c.(1315-1317)gaA>gaG	p.E439E	Y_RNA_ENST00000410292.1_RNA|SNORD53_ENST00000579969.1_RNA|SNORD53_SNORD92_ENST00000577887.1_RNA	NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	439						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					TTAGCATTGAAGAACGTCTGG	0.348													A|||	2092	0.417732	0.3601	0.4265	5008	,	,		16718	0.0704		0.6889	False		,,,				2504	0.5685				p.E439E		Atlas-SNP	.											WDR43,NS,carcinoma,+2,1	WDR43	38	1	0			c.A1317G						PASS	.	A		1579,2091		342,895,598	83.0	80.0	81.0		1317	3.5	1.0	2	dbSNP_86	81	5890,2302		2106,1678,312	no	coding-synonymous	WDR43	NM_015131.1		2448,2573,910	GG,GA,AA		28.1006,43.0245,37.0342		439/678	29152456	7469,4393	1835	4096	5931	SO:0001819	synonymous_variant	23160	exon11			CATTGAAGAACGT	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"""WD repeat domain containing"""	28945	protein-coding gene	gene with protein product	"""UTP5, small subunit (SSU) processome component, homolog (yeast)"""					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.1317A>G	2.37:g.29152456A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	191	191	1	NM_015131	Q15395|Q92577	Silent	SNP	ENST00000407426.3	37	CCDS46251.1																																																																																			A|0.564;G|0.436	0.436	strong		0.348	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089	
ABCG8	64241	hgsc.bcm.edu	37	2	44099433	44099433	+	Missense_Mutation	SNP	C	C	A	rs4148217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:44099433C>A	ENST00000272286.2	+	8	1289	c.1199C>A	c.(1198-1200)aCg>aAg	p.T400K		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	400			T -> K (in dbSNP:rs4148217). {ECO:0000269|PubMed:11452359, ECO:0000269|PubMed:11668628, ECO:0000269|PubMed:12111378}.		ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	CAGCAGTTTACGACGCTGATC	0.502													C|||	1080	0.215655	0.2912	0.3228	5008	,	,		18266	0.1141		0.2008	False		,,,				2504	0.1575				p.T400K		Atlas-SNP	.											ABCG8,colon,carcinoma,0,1	ABCG8	98	1	0			c.C1199A	GRCh37	CM042913	ABCG8	M	rs4148217	PASS	.	C	LYS/THR	1202,3204	413.7+/-336.6	178,846,1179	46.0	44.0	45.0		1199	3.9	0.0	2	dbSNP_110	45	1647,6953	300.6+/-305.0	162,1323,2815	yes	missense	ABCG8	NM_022437.2	78	340,2169,3994	AA,AC,CC		19.1512,27.281,21.9053	benign	400/674	44099433	2849,10157	2203	4300	6503	SO:0001583	missense	64241	exon8			AGTTTACGACGCT	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.1199C>A	2.37:g.44099433C>A	ENSP00000272286:p.Thr400Lys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_022437	Q53QN8	Missense_Mutation	SNP	ENST00000272286.2	37	CCDS1815.1	476	0.21794871794871795	154	0.3130081300813008	117	0.32320441988950277	60	0.1048951048951049	145	0.19129287598944592	C	9.876	1.200333	0.22121	0.27281	0.191512	ENSG00000143921	ENST00000272286	T	0.69806	-0.43	4.81	3.93	0.45458	ABC-2 type transporter (1);	0.400469	0.29451	N	0.012101	T	0.00012	0.0000	N	0.17474	0.49	0.58432	P	1.999999999946489E-6	B;B	0.21688	0.009;0.059	B;B	0.23419	0.016;0.046	T	0.19647	-1.0299	9	0.27785	T	0.31	.	9.9542	0.41657	0.0:0.9036:0.0:0.0964	rs4148217;rs59591548;rs4148217	399;400	Q9H221-2;Q9H221	.;ABCG8_HUMAN	K	400	ENSP00000272286:T400K	ENSP00000272286:T400K	T	+	2	0	ABCG8	43952937	0.001000	0.12720	0.011000	0.14972	0.089000	0.18198	1.368000	0.34216	1.015000	0.39444	0.591000	0.81541	ACG	A|0.212;C|0.788	0.212	strong		0.502	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
UGT1A7	54577	hgsc.bcm.edu	37	2	234590975	234590975	+	Missense_Mutation	SNP	G	G	A	rs17868324|rs397726009|rs66534818|rs386656364|rs71405712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234590975G>A	ENST00000373426.3	+	1	392	c.392G>A	c.(391-393)cGa>cAa	p.R131Q	UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A9_ENST00000354728.4_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	131			R -> K (in allele UGT1A7*2 and allele UGT1A7*3). {ECO:0000269|PubMed:11037804, ECO:0000269|PubMed:11434514, ECO:0000269|PubMed:19204906, ECO:0000269|Ref.3}.|R -> Q (in dbSNP:rs17868324).		cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	TTTAATGACCGAAAATTAGTA	0.368													A|||	2886	0.576278	0.6097	0.5072	5008	,	,		19096	0.4385		0.6034	False		,,,				2504	0.6943				p.R131Q		Atlas-SNP	.											.	UGT1A7	74	.	0			c.G392A						PASS	.						69.0	76.0	74.0					2																	234590975		2201	4296	6497	SO:0001583	missense	54577	exon1			ATGACCGAAAATT	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.392G>A	2.37:g.234590975G>A	ENSP00000362525:p.Arg131Gln	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	129	46	0.356589	NM_019077	B8K293|O00473	Missense_Mutation	SNP	ENST00000373426.3	37	CCDS2506.1	992	0.4542124542124542	234	0.47560975609756095	176	0.4861878453038674	207	0.3618881118881119	375	0.4947229551451187	A	6.902	0.535926	0.13188	.	.	ENSG00000244122	ENST00000373426	T	0.59906	0.23	4.51	-9.01	0.00744	.	.	.	.	.	T	0.00012	0.0000	N	0.11870	0.19	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30090	-0.9990	8	0.27082	T	0.32	.	5.8774	0.18836	0.6524:0.0972:0.1839:0.0666	rs17868324	131;131	Q5DSZ7;Q9HAW7	.;UD17_HUMAN	Q	131	ENSP00000362525:R131Q	ENSP00000362525:R131Q	R	+	2	0	UGT1A7	234255714	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.670000	0.05256	-2.128000	0.00818	-1.305000	0.01319	CGA	.	.	weak		0.368	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
PRR3	80742	hgsc.bcm.edu	37	6	30530203	30530203	+	Silent	SNP	A	A	G	rs61748658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30530203A>G	ENST00000376560.3	+	4	957	c.498A>G	c.(496-498)aaA>aaG	p.K166K	PRR3_ENST00000376557.3_Silent_p.K145K|PRR3_ENST00000498336.1_3'UTR	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	166							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						ATTTTGCCAAAAAGGGCCACT	0.473													.|||	189	0.0377396	0.0628	0.0029	5008	,	,		20081	0.0595		0.003	False		,,,				2504	0.0419				p.K166K		Atlas-SNP	.											.	PRR3	5	.	0			c.A498G						PASS	.	A	,	167,3853		4,159,1847	206.0	203.0	204.0		435,498	4.1	1.0	6	dbSNP_129	204	42,8368		0,42,4163	no	coding-synonymous,coding-synonymous	PRR3	NM_001077497.2,NM_025263.3	,	4,201,6010	GG,GA,AA		0.4994,4.1542,1.6814	,	145/168,166/189	30530203	209,12221	2010	4205	6215	SO:0001819	synonymous_variant	80742	exon4			TGCCAAAAAGGGC	AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576		"""Zinc fingers, CCCH-type domain containing"""	21149	protein-coding gene	gene with protein product			"""proline-rich polpeptide 3"""				Standard	NM_025263		Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.498A>G	6.37:g.30530203A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Silent	SNP	ENST00000376560.3	37	CCDS43440.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263	
ZBTB46	140685	hgsc.bcm.edu	37	20	62378364	62378364	+	Silent	SNP	C	C	T	rs12625387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62378364C>T	ENST00000245663.4	-	5	1839	c.1689G>A	c.(1687-1689)gcG>gcA	p.A563A	ZBTB46_ENST00000302995.2_Silent_p.A563A|ZBTB46_ENST00000395104.1_Silent_p.A563A|RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	563					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CCTTGTCGTCCGCCAACAGCG	0.721													C|||	1350	0.269569	0.1392	0.3804	5008	,	,		10252	0.3452		0.3499	False		,,,				2504	0.2065				p.A563A		Atlas-SNP	.											ZBTB46,rectum,carcinoma,0,1	ZBTB46	72	1	0			c.G1689A						PASS	.	C		746,3652		73,600,1526	30.0	29.0	29.0		1689	-0.2	0.3	20	dbSNP_120	29	2911,5675		480,1951,1862	no	coding-synonymous	ZBTB46	NM_025224.3		553,2551,3388	TT,TC,CC		33.904,16.9623,28.1654		563/590	62378364	3657,9327	2199	4293	6492	SO:0001819	synonymous_variant	140685	exon5			GTCGTCCGCCAAC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1689G>A	20.37:g.62378364C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	23	17	0.73913	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.724;T|0.276	0.276	strong		0.721	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
RSU1	6251	hgsc.bcm.edu	37	10	16796919	16796919	+	Silent	SNP	C	C	A	rs1049632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:16796919C>A	ENST00000377921.3	-	4	652	c.351G>T	c.(349-351)acG>acT	p.T117T	RSU1_ENST00000464074.2_5'UTR|RSU1_ENST00000602389.1_Silent_p.T64T|RSU1_ENST00000345264.5_Silent_p.T117T			Q15404	RSU1_HUMAN	Ras suppressor protein 1	117					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		AGTTGTTGTACGTCAAGTCCA	0.448													A|||	2090	0.417332	0.736	0.2911	5008	,	,		15063	0.4028		0.2624	False		,,,				2504	0.2505				p.T117T		Atlas-SNP	.											.	RSU1	31	.	0			c.G351T						PASS	.	A	,	2881,1525	481.9+/-359.3	945,991,267	84.0	93.0	90.0		351,192	2.8	1.0	10	dbSNP_86	90	2149,6451	714.3+/-406.0	268,1613,2419	no	coding-synonymous,coding-synonymous	RSU1	NM_012425.3,NM_152724.2	,	1213,2604,2686	AA,AC,CC		24.9884,34.6119,38.6745	,	117/278,64/225	16796919	5030,7976	2203	4300	6503	SO:0001819	synonymous_variant	6251	exon5			GTTGTACGTCAAG	AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.351G>T	10.37:g.16796919C>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_012425	A8KA46|D3DRU3|Q6FI17	Silent	SNP	ENST00000377921.3	37	CCDS7112.1																																																																																			C|0.598;A|0.402	0.402	strong		0.448	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724	
APLF	200558	hgsc.bcm.edu	37	2	68794483	68794483	+	Missense_Mutation	SNP	C	C	A	rs36021078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:68794483C>A	ENST00000303795.4	+	9	1468	c.1297C>A	c.(1297-1299)Cag>Aag	p.Q433K	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	433					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GAAGAATCCCCAGCACAAGAT	0.318													C|||	134	0.0267572	0.003	0.0144	5008	,	,		15806	0.0317		0.0408	False		,,,				2504	0.0481				p.Q433K		Atlas-SNP	.											APLF,NS,carcinoma,-1,1	APLF	69	1	0			c.C1297A						PASS	.	C	LYS/GLN	25,4381	27.2+/-55.0	0,25,2178	63.0	63.0	63.0		1297	5.0	1.0	2	dbSNP_126	63	319,8277	107.2+/-168.0	8,303,3987	yes	missense	APLF	NM_173545.2	53	8,328,6165	AA,AC,CC		3.711,0.5674,2.6457	probably-damaging	433/512	68794483	344,12658	2203	4298	6501	SO:0001583	missense	200558	exon9			AATCCCCAGCACA	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1297C>A	2.37:g.68794483C>A	ENSP00000307004:p.Gln433Lys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	256	121	0.472656	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	54	0.024725274725274724	2	0.0040650406504065045	5	0.013812154696132596	18	0.03146853146853147	29	0.03825857519788918	C	22.1	4.241121	0.79912	0.005674	0.03711	ENSG00000169621	ENST00000303795	T	0.26660	1.72	4.99	4.99	0.66335	Zinc finger, C2H2, APLF-like (1);	0.067342	0.64402	D	0.000005	T	0.17195	0.0413	M	0.64170	1.965	0.38110	D	0.937548	D	0.69078	0.997	D	0.83275	0.996	T	0.18903	-1.0322	10	0.62326	D	0.03	.	13.9502	0.64111	0.0:1.0:0.0:0.0	rs36021078	433	Q8IW19	APLF_HUMAN	K	433	ENSP00000307004:Q433K	ENSP00000307004:Q433K	Q	+	1	0	APLF	68647987	0.997000	0.39634	0.998000	0.56505	0.948000	0.59901	3.381000	0.52455	2.739000	0.93911	0.585000	0.79938	CAG	C|0.973;A|0.027	0.027	strong		0.318	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
ADRA2B	151	hgsc.bcm.edu	37	2	96780863	96780863	+	Silent	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:96780863C>G	ENST00000409345.3	-	1	1121	c.1026G>C	c.(1024-1026)ctG>ctC	p.L342L		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	342					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)			endometrium(2)|large_intestine(2)|lung(9)|ovary(3)	16					Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CGCCCCTGCCCAGGAGCACCT	0.701																																					p.L342L		Atlas-SNP	.											.	ADRA2B	115	.	0			c.G1026C						PASS	.																																			SO:0001819	synonymous_variant	151	exon1			CCTGCCCAGGAGC	M34041	CCDS56129.1	2q11.1	2014-05-06	2012-05-09		ENSG00000222040	ENSG00000274286		"""GPCR / Class A : Adrenoceptors : alpha"""	282	protein-coding gene	gene with protein product		104260	"""adrenergic, alpha-2B-, receptor"""	ADRA2L1, ADRA2RL1		2164221	Standard	NM_000682		Approved	ADRARL1	uc021vlh.1	P18089	OTTHUMG00000188276	ENST00000409345.3:c.1026G>C	2.37:g.96780863C>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_000682	Q4TUH9|Q53RF2|Q9BZK0	Silent	SNP	ENST00000409345.3	37	CCDS56129.1																																																																																			.	.	none		0.701	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1		
EEA1	8411	hgsc.bcm.edu	37	12	93258665	93258665	+	Silent	SNP	A	A	G	rs17194451	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:93258665A>G	ENST00000322349.8	-	3	480	c.216T>C	c.(214-216)caT>caC	p.H72H	EEA1_ENST00000547833.1_5'UTR	NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	72					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						ACTCTCCTCCATGACCTGAGT	0.373													A|||	855	0.170727	0.1876	0.1599	5008	,	,		17058	0.0218		0.3191	False		,,,				2504	0.1564				p.H72H		Atlas-SNP	.											.	EEA1	104	.	0			c.T216C						PASS	.	A		928,3478	356.1+/-313.4	111,706,1386	119.0	105.0	110.0		216	0.3	1.0	12	dbSNP_123	110	2657,5943	427.4+/-355.6	414,1829,2057	no	coding-synonymous	EEA1	NM_003566.3		525,2535,3443	GG,GA,AA		30.8953,21.0622,27.5642		72/1412	93258665	3585,9421	2203	4300	6503	SO:0001819	synonymous_variant	8411	exon3			TCCTCCATGACCT	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.216T>C	12.37:g.93258665A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	87	56	0.643678	NM_003566	Q14221	Silent	SNP	ENST00000322349.8	37	CCDS31874.1																																																																																			A|0.756;G|0.244	0.244	strong		0.373	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
METTL3	56339	hgsc.bcm.edu	37	14	21971694	21971694	+	Silent	SNP	C	C	G	rs11540964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21971694C>G	ENST00000298717.4	-	3	496	c.345G>C	c.(343-345)ggG>ggC	p.G115G	METTL3_ENST00000538267.1_Silent_p.G115G	NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	115					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		GGCTTTCTACCCCATCTTGAG	0.478													C|||	2	0.000399361	0.0	0.0	5008	,	,		23416	0.0		0.002	False		,,,				2504	0.0				p.G115G		Atlas-SNP	.											.	METTL3	48	.	0			c.G345C						PASS	.	C		0,4406		0,0,2203	60.0	56.0	57.0		345	-4.0	0.9	14	dbSNP_120	57	25,8575	16.6+/-54.9	0,25,4275	no	coding-synonymous	METTL3	NM_019852.3		0,25,6478	GG,GC,CC		0.2907,0.0,0.1922		115/581	21971694	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	56339	exon3			TTCTACCCCATCT	AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"""N6-adenosine-methyltransferase 70 kDa subunit"""	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.345G>C	14.37:g.21971694C>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_019852	O14736|Q86V05|Q9HB32	Silent	SNP	ENST00000298717.4	37	CCDS32044.1																																																																																			C|0.998;G|0.002	0.002	strong		0.478	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852	
POLN	353497	hgsc.bcm.edu	37	4	2181080	2181080	+	Silent	SNP	T	T	C	rs6830513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2181080T>C	ENST00000511885.2	-	8	1487	c.1134A>G	c.(1132-1134)acA>acG	p.T378T	POLN_ENST00000382865.1_Silent_p.T378T|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	378					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			TCACTTTAACTGTAATGGATT	0.343								DNA polymerases (catalytic subunits)					C|||	1612	0.321885	0.5703	0.2435	5008	,	,		18801	0.373		0.1243	False		,,,				2504	0.1922				p.T378T		Atlas-SNP	.											.	POLN	82	.	0			c.A1134G						PASS	.	C		2220,2186	585.3+/-386.2	581,1058,564	98.0	104.0	102.0		1134	-7.4	0.0	4	dbSNP_116	102	993,7607	772.9+/-407.7	59,875,3366	no	coding-synonymous	POLN	NM_181808.2		640,1933,3930	CC,CT,TT		11.5465,49.6142,24.704		378/901	2181080	3213,9793	2203	4300	6503	SO:0001819	synonymous_variant	353497	exon6			TTTAACTGTAATG	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.1134A>G	4.37:g.2181080T>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	157	69	0.43949	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Silent	SNP	ENST00000511885.2	37	CCDS3360.1	678	0.31043956043956045	282	0.573170731707317	91	0.2513812154696133	210	0.36713286713286714	95	0.12532981530343007	C	3.609	-0.079915	0.07141	0.503858	0.115465	ENSG00000130997	ENST00000511098	.	.	.	5.61	-7.45	0.01374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44742	-0.9308	3	.	.	.	-1.9205	1.6768	0.02823	0.3622:0.1352:0.0925:0.4101	rs6830513;rs56712967;rs6830513	.	.	.	R	12	.	.	Q	-	2	0	POLN	2150878	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.832000	0.04400	-1.657000	0.01492	-4.471000	0.00005	CAG	T|0.715;C|0.285	0.285	strong		0.343	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
ITGA3	3675	hgsc.bcm.edu	37	17	48151353	48151353	+	Silent	SNP	T	T	C	rs2285524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48151353T>C	ENST00000320031.8	+	8	1560	c.1230T>C	c.(1228-1230)ctT>ctC	p.L410L	ITGA3_ENST00000007722.7_Silent_p.L410L|ITGA3_ENST00000544892.1_Silent_p.L185L	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	410					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						AGGGGCTCCTTAGACAGCCCC	0.557													C|||	1529	0.305312	0.4402	0.33	5008	,	,		16810	0.3085		0.0954	False		,,,				2504	0.318				p.L410L		Atlas-SNP	.											.	ITGA3	128	.	0			c.T1230C						PASS	.	C	,	1797,2609	641.1+/-397.4	338,1121,744	71.0	75.0	73.0		1230,1230	3.8	0.6	17	dbSNP_100	73	1034,7566	771.7+/-407.7	61,912,3327	no	coding-synonymous,coding-synonymous	ITGA3	NM_002204.2,NM_005501.2	,	399,2033,4071	CC,CT,TT		12.0233,40.7853,21.7669	,	410/1052,410/1067	48151353	2831,10175	2203	4300	6503	SO:0001819	synonymous_variant	3675	exon8			GCTCCTTAGACAG	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.1230T>C	17.37:g.48151353T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	37	CCDS11558.1																																																																																			T|0.775;C|0.225	0.225	strong		0.557	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
GNG4	2786	hgsc.bcm.edu	37	1	235715523	235715523	+	Silent	SNP	A	A	G	rs14326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:235715523A>G	ENST00000366598.4	-	3	329	c.114T>C	c.(112-114)gcT>gcC	p.A38A	GNG4_ENST00000450593.1_Silent_p.A38A|GNG4_ENST00000366597.1_Silent_p.A38A|GNG4_ENST00000391854.2_Silent_p.A38A|GNG4_ENST00000484517.1_5'UTR			P50150	GBG4_HUMAN	guanine nucleotide binding protein (G protein), gamma 4	38					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of cell growth (GO:0030308)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)			GGAGGTCCGCAGCTGCCTGGG	0.562													A|||	3161	0.63119	0.5893	0.6599	5008	,	,		19704	0.8383		0.495	False		,,,				2504	0.5941				p.A38A		Atlas-SNP	.											.	GNG4	18	.	0			c.T114C						PASS	.	A	,,	2636,1770	644.4+/-398.0	795,1046,362	90.0	91.0	91.0		114,114,114	-9.5	0.0	1	dbSNP_52	91	4376,4224	583.3+/-391.5	1110,2156,1034	no	coding-synonymous,coding-synonymous,coding-synonymous	GNG4	NM_001098721.1,NM_001098722.1,NM_004485.3	,,	1905,3202,1396	GG,GA,AA		49.1163,40.1725,46.0864	,,	38/76,38/76,38/76	235715523	7012,5994	2203	4300	6503	SO:0001819	synonymous_variant	2786	exon3			GTCCGCAGCTGCC	BC022485	CCDS1607.1	1q42.3	2008-02-05			ENSG00000168243	ENSG00000168243			4407	protein-coding gene	gene with protein product		604388				7665596	Standard	NM_001098721		Approved		uc001hxh.4	P50150	OTTHUMG00000040740	ENST00000366598.4:c.114T>C	1.37:g.235715523A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_004485		Silent	SNP	ENST00000366598.4	37	CCDS1607.1																																																																																			A|0.429;G|0.571	0.571	strong		0.562	GNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097906.1	NM_004485	
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417718	138417718	+	Silent	SNP	A	A	G	rs3807154	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:138417718A>G	ENST00000310018.2	-	17	2094	c.1812T>C	c.(1810-1812)caT>caC	p.H604H	ATP6V0A4_ENST00000393054.1_Silent_p.H604H|ATP6V0A4_ENST00000353492.4_Silent_p.H604H	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	604			H -> Q (in dbSNP:rs3807154).		ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GCTGAGATACATGGACGTCAA	0.423													A|||	3393	0.677516	0.4236	0.7824	5008	,	,		16443	0.8472		0.7237	False		,,,				2504	0.7239				p.H604H		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.T1812C						PASS	.	A	,,	2049,2357	567.3+/-382.1	480,1089,634	141.0	129.0	133.0		1812,1812,1812	0.5	0.0	7	dbSNP_107	133	6185,2415	699.3+/-405.1	2233,1719,348	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	,,	2713,2808,982	GG,GA,AA		28.0814,46.5048,36.6908	,,	604/841,604/841,604/841	138417718	8234,4772	2203	4300	6503	SO:0001819	synonymous_variant	50617	exon16			AGATACATGGACG	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1812T>C	7.37:g.138417718A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_130841	A4D1R4|A8KA80|Q32M47	Silent	SNP	ENST00000310018.2	37	CCDS5849.1																																																																																			A|0.340;G|0.660	0.660	strong		0.423	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
ATAD5	79915	hgsc.bcm.edu	37	17	29161845	29161845	+	Missense_Mutation	SNP	G	G	A	rs17826219	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29161845G>A	ENST00000321990.4	+	2	1124	c.746G>A	c.(745-747)aGa>aAa	p.R249K	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	249			R -> K (in dbSNP:rs17826219).		cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				GCAAACTCTAGAGATAACGTA	0.338													G|||	722	0.144169	0.0711	0.1859	5008	,	,		19724	0.1359		0.1074	False		,,,				2504	0.2597				p.R249K		Atlas-SNP	.											.	ATAD5	150	.	0			c.G746A						PASS	.	G	LYS/ARG	324,4080	156.3+/-189.4	14,296,1892	77.0	81.0	79.0		746	3.3	0.0	17	dbSNP_123	79	895,7705	192.1+/-238.2	36,823,3441	yes	missense	ATAD5	NM_024857.3	26	50,1119,5333	AA,AG,GG		10.407,7.3569,9.374	benign	249/1845	29161845	1219,11785	2202	4300	6502	SO:0001583	missense	79915	exon2			ACTCTAGAGATAA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.746G>A	17.37:g.29161845G>A	ENSP00000313171:p.Arg249Lys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	274	0.12545787545787546	45	0.09146341463414634	65	0.17955801104972377	92	0.16083916083916083	72	0.09498680738786279	G	2.450	-0.326665	0.05350	0.073569	0.10407	ENSG00000176208	ENST00000321990	T	0.16073	2.37	5.31	3.3	0.37823	.	1.326570	0.04476	N	0.376900	T	0.00039	0.0001	L	0.56769	1.78	0.80722	P	0.0	B;B	0.32467	0.372;0.156	B;B	0.25140	0.058;0.026	T	0.22836	-1.0205	9	0.27082	T	0.32	.	7.9332	0.29914	0.2753:0.0:0.7247:0.0	rs17826219;rs52827508;rs60889029;rs17826219	249;249	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	K	249	ENSP00000313171:R249K	ENSP00000313171:R249K	R	+	2	0	ATAD5	26185971	0.494000	0.26043	0.003000	0.11579	0.239000	0.25481	2.594000	0.46189	1.378000	0.46305	-0.150000	0.13652	AGA	G|0.889;A|0.111	0.111	strong		0.338	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
PDHB	5162	hgsc.bcm.edu	37	3	58410554	58410554	+	IGR	SNP	C	C	T	rs34579268	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58410554C>T	ENST00000302746.6	-	0	1527				PXK_ENST00000302779.5_Missense_Mutation_p.A518V|PXK_ENST00000356151.2_Missense_Mutation_p.A535V|PXK_ENST00000479241.1_Silent_p.G528G|PXK_ENST00000463280.1_3'UTR|PXK_ENST00000536660.1_Missense_Mutation_p.A398V|PXK_ENST00000383716.3_Missense_Mutation_p.A502V	NM_000925.3|NM_001173468.1	NP_000916.2|NP_001166939.1	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta						acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	9				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	Pyruvic acid(DB00119)	AGCACCGAGGCACCTGCCCAG	0.567													C|||	1029	0.205471	0.2141	0.2839	5008	,	,		17867	0.001		0.3777	False		,,,				2504	0.1718				p.A535V		Atlas-SNP	.											PXK_ENST00000356151,brain,glioma,0,1	PXK	89	1	0			c.C1604T						PASS	.	C	VAL/ALA	952,3454	360.4+/-315.2	97,758,1348	61.0	48.0	53.0		1604	-5.2	0.0	3	dbSNP_126	53	3205,5395	482.5+/-370.9	615,1975,1710	yes	missense	PXK	NM_017771.3	64	712,2733,3058	TT,TC,CC		37.2674,21.6069,31.9622	benign	535/579	58410554	4157,8849	2203	4300	6503	SO:0001628	intergenic_variant	54899	exon18			CCGAGGCACCTGC		CCDS2890.1, CCDS54602.1	3p21.1-p14.2	1995-12-20			ENSG00000168291	ENSG00000168291	1.2.4.1		8808	protein-coding gene	gene with protein product		179060					Standard	NR_033384		Approved		uc003dkf.4	P11177	OTTHUMG00000159157		3.37:g.58410554C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	196	94	0.479592	NM_017771	B2R7L0|B4DDD7|Q6FH45|Q9BQ27|Q9UFK3	Missense_Mutation	SNP	ENST00000302746.6	37	CCDS2890.1	521|521	0.23855311355311357|0.23855311355311357	131|131	0.266260162601626|0.266260162601626	111|111	0.30662983425414364|0.30662983425414364	2|2	0.0034965034965034965|0.0034965034965034965	277|277	0.3654353562005277|0.3654353562005277	C|C	8.525|8.525	0.869609|0.869609	0.17322|0.17322	0.216069|0.216069	0.372674|0.372674	ENSG00000168297|ENSG00000168297	ENST00000356151;ENST00000302779;ENST00000383716;ENST00000536660|ENST00000479134	T;T;T;T|.	0.19250|.	2.16;2.16;2.17;2.17|.	6.03|6.03	-5.16|-5.16	0.02857|0.02857	.|.	1.260030|.	0.05066|.	N|.	0.480815|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.16478|0.16478	0.41|0.41	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.35301|0.35301	-0.9794|-0.9794	9|4	0.37606|.	T|.	0.19|.	2.213|2.213	11.2739|11.2739	0.49155|0.49155	0.0:0.2675:0.0935:0.639|0.0:0.2675:0.0935:0.639	rs34579268;rs58363342|rs34579268;rs58363342	502;535|.	Q7Z7A4-6;Q7Z7A4|.	.;PXK_HUMAN|.	V|Y	535;518;502;398|269	ENSP00000348472:A535V;ENSP00000305045:A518V;ENSP00000373222:A502V;ENSP00000438356:A398V|.	ENSP00000305045:A518V|.	A|H	+|+	2|1	0|0	PXK|PXK	58385594|58385594	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.334000|0.334000	0.28698|0.28698	-1.086000|-1.086000	0.03386|0.03386	-0.924000|-0.924000	0.03780|0.03780	-0.140000|-0.140000	0.14226|0.14226	GCA|CAC	C|0.691;T|0.309	0.309	strong		0.567	PDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353558.1		
CFHR1	3078	hgsc.bcm.edu	37	1	196794680	196794680	+	Silent	SNP	G	G	A	rs41315553		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:196794680G>A	ENST00000320493.5	+	2	220	c.132G>A	c.(130-132)caG>caA	p.Q44Q	CFHR2_ENST00000367421.3_Intron|CFHR1_ENST00000367424.4_Silent_p.Q44Q	NM_002113.2	NP_002104.2	Q03591	FHR1_HUMAN	complement factor H-related 1	44	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|kidney(1)|large_intestine(2)|lung(7)	11						CATTTTCCCAGGTTCCTACAG	0.333																																					p.Q44Q		Atlas-SNP	.											CFHR1,NS,carcinoma,0,1	CFHR1	47	1	0			c.G132A						scavenged	.						48.0	57.0	54.0					1																	196794680		1839	4112	5951	SO:0001819	synonymous_variant	3078	exon2			TTCCCAGGTTCCT	M65292	CCDS1386.1	1q32	2014-09-17	2004-08-09	2006-02-28	ENSG00000244414	ENSG00000244414		"""Complement system"""	4888	protein-coding gene	gene with protein product		134371	"""H factor (complement)-like 1"", ""complement factor H-related 1 pseudogene"", ""H factor (complement)-like 2"""	HFL1, CFHL1, CFHR1P, HFL2, CFHL1P		1711047, 1826708	Standard	NM_002113		Approved	H36-1, FHR1, CFHL, H36-2		Q03591	OTTHUMG00000036276	ENST00000320493.5:c.132G>A	1.37:g.196794680G>A		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	201	3	0.0149254	NM_002113	A8K465|Q3B774|Q9UJ17	Silent	SNP	ENST00000320493.5	37	CCDS1386.1																																																																																			.	.	weak		0.333	CFHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088251.2	NM_002113	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057806	46057806	+	Missense_Mutation	SNP	G	G	A	rs4818950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46057806G>A	ENST00000380095.1	+	1	534	c.472G>A	c.(472-474)Gtg>Atg	p.V158M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	158	15 X 5 AA repeats of C-C-X(3).		V -> M (in dbSNP:rs4818950).			keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CGTCTGCTATGTGCCTGTGTG	0.617													G|||	3022	0.603435	0.4342	0.6671	5008	,	,		21756	0.6667		0.6928	False		,,,				2504	0.6299				p.V158M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G472A						PASS	.	G	,MET/VAL	2058,2348	567.7+/-382.2	480,1098,625	281.0	254.0	263.0		,472	-0.3	0.0	21	dbSNP_111	263	5738,2862	672.4+/-402.9	1911,1916,473	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,21	2391,3014,1098	AA,AG,GG		33.2791,46.709,40.0584	,benign	,158/252	46057806	7796,5210	2203	4300	6503	SO:0001583	missense	353333	exon1			TGCTATGTGCCTG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.472G>A	21.37:g.46057806G>A	ENSP00000369438:p.Val158Met	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	188	105	0.558511	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	1354	0.61996336996337	221	0.4491869918699187	241	0.6657458563535912	369	0.6451048951048951	523	0.6899736147757256	g	0.902	-0.721876	0.03182	0.46709	0.667209	ENSG00000221859	ENST00000380095	T	0.01414	4.92	3.13	-0.278	0.12894	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.38677	0.642	P	0.48334	0.574	T	0.05402	-1.0887	8	0.48119	T	0.1	.	3.0811	0.06262	0.5855:0.0:0.2299:0.1845	rs4818950;rs17004668;rs57325201;rs4818950	158	P60014	KR10A_HUMAN	M	158	ENSP00000369438:V158M	ENSP00000369438:V158M	V	+	1	0	KRTAP10-10	44882234	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.385000	0.02540	-0.309000	0.08779	0.306000	0.20318	GTG	G|0.392;A|0.608	0.608	strong		0.617	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
SCLY	51540	hgsc.bcm.edu	37	2	238990388	238990388	+	Missense_Mutation	SNP	G	G	A	rs3210400	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238990388G>A	ENST00000555827.1	+	5	587	c.523G>A	c.(523-525)Gca>Aca	p.A175T	SCLY_ENST00000429612.2_Intron|SCLY_ENST00000373332.3_Missense_Mutation_p.A93T|SCLY_ENST00000422984.2_Missense_Mutation_p.A81T|SCLY_ENST00000409736.2_Missense_Mutation_p.A175T|SCLY_ENST00000254663.6_Missense_Mutation_p.A183T			Q96I15	SCLY_HUMAN	selenocysteine lyase	175			A -> T (in dbSNP:rs3210400). {ECO:0000269|PubMed:15489334}.		cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GAGCGGGCAGGCAGAGGTGGA	0.572													G|||	1272	0.253994	0.0393	0.438	5008	,	,		18735	0.2321		0.4563	False		,,,				2504	0.228				p.A183T	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											.	SCLY	51	.	0			c.G547A						PASS	.	G	THR/ALA	415,3991	203.1+/-225.7	18,379,1806	109.0	95.0	99.0		547	5.0	0.0	2	dbSNP_105	99	3642,4958	523.6+/-380.4	794,2054,1452	yes	missense	SCLY	NM_016510.5	58	812,2433,3258	AA,AG,GG		42.3488,9.419,31.1933	benign	183/454	238990388	4057,8949	2203	4300	6503	SO:0001583	missense	51540	exon5			GGGCAGGCAGAGG	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.523G>A	2.37:g.238990388G>A	ENSP00000450613:p.Ala175Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	37		647|647	0.29624542124542125|0.29624542124542125	21|21	0.042682926829268296|0.042682926829268296	156|156	0.430939226519337|0.430939226519337	122|122	0.21328671328671328|0.21328671328671328	348|348	0.45910290237467016|0.45910290237467016	G|G	13.64|13.64	2.296062|2.296062	0.40594|0.40594	0.09419|0.09419	0.423488|0.423488	ENSG00000132330|ENSG00000132330	ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965|ENST00000437134	T;T;T;D;T;T;T|.	0.86627|.	1.98;1.98;1.56;-2.15;1.56;1.98;1.56|.	5.84|5.84	4.96|4.96	0.65561|0.65561	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);|.	0.522273|.	0.21381|.	N|.	0.075472|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43152|0.43152	1.355|1.355	0.24182|0.24182	P|P	0.9955825700000001|0.9955825700000001	P;B;P|.	0.42296|.	0.775;0.452;0.696|.	P;B;B|.	0.48873|.	0.593;0.314;0.281|.	T|T	0.50923|0.50923	-0.8770|-0.8770	9|4	0.87932|.	D|.	0|.	-21.4942|-21.4942	10.0151|10.0151	0.42010|0.42010	0.1556:0.0:0.8444:0.0|0.1556:0.0:0.8444:0.0	rs3210400;rs3739052;rs52837213;rs60128375;rs3210400|rs3210400;rs3739052;rs52837213;rs60128375;rs3210400	81;175;175|.	E7ESG3;Q96I15;Q96I15-2|.	.;SCLY_HUMAN;.|.	T|D	183;175;93;89;175;81;5|18	ENSP00000254663:A183T;ENSP00000450613:A175T;ENSP00000362429:A93T;ENSP00000414165:A89T;ENSP00000387162:A175T;ENSP00000416865:A81T;ENSP00000414053:A5T|.	ENSP00000254663:A175T|.	A|G	+|+	1|2	0|0	SCLY|SCLY	238655127|238655127	1.000000|1.000000	0.71417|0.71417	0.008000|0.008000	0.14137|0.14137	0.123000|0.123000	0.20343|0.20343	4.874000|4.874000	0.63064|0.63064	1.464000|1.464000	0.47987|0.47987	0.655000|0.655000	0.94253|0.94253	GCA|GGC	G|0.715;A|0.285	0.285	strong		0.572	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
TMPO	7112	hgsc.bcm.edu	37	12	98938307	98938307	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:98938307G>A	ENST00000556029.1	+	6	1227	c.871G>A	c.(871-873)Gaa>Aaa	p.E291K	TMPO_ENST00000393053.2_Intron|TMPO_ENST00000343315.5_Missense_Mutation_p.E251K|TMPO_ENST00000548223.1_3'UTR	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	291	Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TTCAAGCAACGAATCCTTAGT	0.348																																					p.E291K		Atlas-SNP	.											TMPO,colon,carcinoma,0,1	TMPO	111	1	0			c.G871A						scavenged	.						35.0	36.0	36.0					12																	98938307		2203	4299	6502	SO:0001583	missense	7112	exon6			AGCAACGAATCCT		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"""LEM domain containing 4"""	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.871G>A	12.37:g.98938307G>A	ENSP00000450627:p.Glu291Lys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	131	4	0.0305344	NM_001032283	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.991297	0.35131	.	.	ENSG00000120802	ENST00000556029;ENST00000343315	T;T	0.60299	0.25;0.2	5.82	4.93	0.64822	.	.	.	.	.	T	0.45617	0.1351	L	0.44542	1.39	0.80722	D	1	B	0.10296	0.003	B	0.04013	0.001	T	0.35798	-0.9774	9	0.27785	T	0.31	.	7.5849	0.27987	0.1433:0.1367:0.72:0.0	.	291	P42167	LAP2B_HUMAN	K	291;251	ENSP00000450627:E291K;ENSP00000340251:E251K	ENSP00000340251:E291K	E	+	1	0	TMPO	97462438	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.250000	0.32850	1.461000	0.47929	0.591000	0.81541	GAA	.	.	none		0.348	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276	
NBPF7	343505	hgsc.bcm.edu	37	1	120387120	120387120	+	IGR	SNP	G	G	A	rs12405228	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120387120G>A								REG4 (32837 upstream) : ADAM30 (49035 downstream)																							TGGCAGAAGAGGTGGAGCCAG	0.488											OREG0013730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	1793	0.358027	0.0416	0.4827	5008	,	,		19791	0.3641		0.5835	False		,,,				2504	0.4591				p.T13T		Atlas-SNP	.											.	NBPF7	46	.	0			c.C39T						PASS	.	G		529,3737		49,431,1653	79.0	86.0	84.0		39	0.7	0.4	1	dbSNP_120	84	4846,3696		1390,2066,815	no	coding-synonymous	NBPF7	NM_001047980.1		1439,2497,2468	AA,AG,GG		43.2686,12.4004,41.966		13/422	120387120	5375,7433	2133	4271	6404	SO:0001628	intergenic_variant	343505	exon1			AGAAGAGGTGGAG																													1.37:g.120387120G>A		Somatic	78	0	0	1503	WXS	Illumina HiSeq	Phase_I	75	26	0.346667	NM_001047980		Silent	SNP		37																																																																																				G|0.564;A|0.436	0.436	strong	0	0.488								
LPCAT1	79888	hgsc.bcm.edu	37	5	1494909	1494909	+	Silent	SNP	C	C	T	rs3733796	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:1494909C>T	ENST00000283415.3	-	3	531	c.399G>A	c.(397-399)gcG>gcA	p.A133A		NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	133					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		ACGAGTGAGGCGCGAGCGTGA	0.647													C|||	1490	0.297524	0.3086	0.2262	5008	,	,		15040	0.4028		0.1869	False		,,,				2504	0.3384				p.A133A		Atlas-SNP	.											LPCAT1,NS,carcinoma,-1,1	LPCAT1	70	1	0			c.G399A						PASS	.	C		1267,3139	432.0+/-343.1	178,911,1114	83.0	72.0	76.0		399	-10.0	0.1	5	dbSNP_107	76	1609,6991	298.7+/-304.1	159,1291,2850	no	coding-synonymous	LPCAT1	NM_024830.3		337,2202,3964	TT,TC,CC		18.7093,28.7562,22.1129		133/535	1494909	2876,10130	2203	4300	6503	SO:0001819	synonymous_variant	79888	exon3			GTGAGGCGCGAGC	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"""EF-hand domain containing"""	25718	protein-coding gene	gene with protein product		610472	"""acyltransferase like 2"""	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.399G>A	5.37:g.1494909C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	110	64	0.581818	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	37	CCDS3864.1																																																																																			C|0.755;T|0.245	0.245	strong		0.647	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	
CDK5RAP3	80279	hgsc.bcm.edu	37	17	46053334	46053334	+	Silent	SNP	A	A	G	rs202125432	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46053334A>G	ENST00000338399.4	+	8	859	c.753A>G	c.(751-753)gaA>gaG	p.E251E	CDK5RAP3_ENST00000536708.2_Silent_p.E276E|RP11-6N17.9_ENST00000582262.1_RNA	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	251					brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)	p.E251E(1)		NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						CTGTGGTGGAACGACCCCACC	0.602																																					p.E251E		Atlas-SNP	.											CDK5RAP3,NS,carcinoma,0,2	CDK5RAP3	38	2	1	Substitution - coding silent(1)	prostate(1)	c.A753G						scavenged	.																																			SO:0001819	synonymous_variant	80279	exon8			GGTGGAACGACCC	AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465			18673	protein-coding gene	gene with protein product	"""ischemic heart CDK5 activator-binding protein C53"", ""LXXLL/leucine-zipper-containing ARFbinding protein"""	608202				10721722	Standard	NM_176096		Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.753A>G	17.37:g.46053334A>G		Somatic	63	3	0.047619		WXS	Illumina HiSeq	Phase_I	88	6	0.0681818	NM_176096	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	Silent	SNP	ENST00000338399.4	37	CCDS42356.1																																																																																			A|0.949;G|0.051	0.051	strong		0.602	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442913.1	NM_176096	
KIAA0195	9772	hgsc.bcm.edu	37	17	73493874	73493874	+	Silent	SNP	G	G	C	rs12949173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73493874G>C	ENST00000314256.7	+	27	3814	c.3420G>C	c.(3418-3420)ctG>ctC	p.L1140L	AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000579208.1_Silent_p.L791L|KIAA0195_ENST00000375248.5_Silent_p.L1150L	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	1140						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCTCTCTGCTGGGGAAGCCCC	0.522													G|||	302	0.0603035	0.0068	0.0994	5008	,	,		18836	0.0		0.1889	False		,,,				2504	0.0348				p.L1140L		Atlas-SNP	.											.	KIAA0195	102	.	0			c.G3420C						PASS	.	G		171,4235	112.9+/-151.0	2,167,2034	87.0	74.0	79.0		3420	3.7	1.0	17	dbSNP_121	79	1884,6716	335.6+/-321.5	217,1450,2633	no	coding-synonymous	KIAA0195	NM_014738.4		219,1617,4667	CC,CG,GG		21.907,3.8811,15.8004		1140/1357	73493874	2055,10951	2203	4300	6503	SO:0001819	synonymous_variant	9772	exon27			TCTGCTGGGGAAG		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.3420G>C	17.37:g.73493874G>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_014738	O75536|Q86XF1	Silent	SNP	ENST00000314256.7	37	CCDS32732.1																																																																																			G|0.863;C|0.137	0.137	strong		0.522	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
MACF1	23499	hgsc.bcm.edu	37	1	39748921	39748921	+	Silent	SNP	G	G	A	rs2275188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39748921G>A	ENST00000372915.3	+	7	858	c.771G>A	c.(769-771)caG>caA	p.Q257Q	MACF1_ENST00000539005.1_Silent_p.Q257Q|MACF1_ENST00000361689.2_Silent_p.Q257Q|MACF1_ENST00000545844.1_Silent_p.Q257Q|MACF1_ENST00000317713.7_Silent_p.Q257Q|MACF1_ENST00000564288.1_Silent_p.Q252Q|MACF1_ENST00000567887.1_Silent_p.Q289Q			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	257	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ATCTGGAACAGGCTTTTGAAG	0.478													G|||	2975	0.59405	0.2685	0.6657	5008	,	,		19182	0.6498		0.7167	False		,,,				2504	0.7996				p.Q257Q		Atlas-SNP	.											.	MACF1	909	.	0			c.G771A						PASS	.	G		1560,2846	489.7+/-361.6	277,1006,920	93.0	88.0	90.0		771	1.7	1.0	1	dbSNP_100	90	5955,2645	685.6+/-404.1	2078,1799,423	no	coding-synonymous	MACF1	NM_012090.4		2355,2805,1343	AA,AG,GG		30.7558,35.4063,42.219		257/5431	39748921	7515,5491	2203	4300	6503	SO:0001819	synonymous_variant	23499	exon9			GGAACAGGCTTTT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.771G>A	1.37:g.39748921G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																				G|0.422;A|0.578	0.578	strong		0.478	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
FMNL2	114793	hgsc.bcm.edu	37	2	153405594	153405594	+	Silent	SNP	G	G	A	rs1155779	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:153405594G>A	ENST00000288670.9	+	4	709	c.342G>A	c.(340-342)ttG>ttA	p.L114L		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	114	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						AAATTTCTTTGAGAACTAACC	0.343													A|||	3267	0.652356	0.4902	0.6715	5008	,	,		13509	0.7976		0.5865	False		,,,				2504	0.7761				p.L114L		Atlas-SNP	.											.	FMNL2	75	.	0			c.G342A						PASS	.	A		1794,1830		449,896,467	71.0	65.0	67.0		342	5.9	1.0	2	dbSNP_87	67	4816,3328		1406,2004,662	no	coding-synonymous	FMNL2	NM_052905.3		1855,2900,1129	AA,AG,GG		40.8644,49.5033,43.8307		114/1093	153405594	6610,5158	1812	4072	5884	SO:0001819	synonymous_variant	114793	exon4			TTCTTTGAGAACT	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.342G>A	2.37:g.153405594G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																			G|0.375;A|0.625	0.625	strong		0.343	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
KRT6B	3854	hgsc.bcm.edu	37	12	52844246	52844246	+	Silent	SNP	A	A	G	rs28542657	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52844246A>G	ENST00000252252.3	-	2	746	c.699T>C	c.(697-699)ggT>ggC	p.G233G		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	233	Coil 1B.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)	p.G233G(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		AGTCCAGACGACCCCGTTCCC	0.557													G|||	394	0.0786741	0.0061	0.0821	5008	,	,		23280	0.1875		0.0875	False		,,,				2504	0.0532				p.G233G		Atlas-SNP	.											KRT6B,NS,carcinoma,0,1	KRT6B	90	1	1	Substitution - coding silent(1)	ovary(1)	c.T699C						scavenged	.						210.0	184.0	193.0					12																	52844246		2203	4300	6503	SO:0001819	synonymous_variant	3854	exon2			CAGACGACCCCGT	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.699T>C	12.37:g.52844246A>G		Somatic	343	6	0.0174927		WXS	Illumina HiSeq	Phase_I	506	107	0.211462	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			.	.	weak		0.557	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
NACA	4666	hgsc.bcm.edu	37	12	57108203	57108203	+	Silent	SNP	A	A	G	rs4902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57108203A>G	ENST00000454682.1	-	5	6047	c.5766T>C	c.(5764-5766)atT>atC	p.I1922I	NACA_ENST00000552540.1_Silent_p.I59I|NACA_ENST00000356769.3_Silent_p.I59I|NACA_ENST00000550952.1_Silent_p.I769I|NACA_ENST00000548563.1_5'UTR|NACA_ENST00000393891.4_Silent_p.I59I|NACA_ENST00000546392.1_Silent_p.I59I|NACA_ENST00000551793.1_5'UTR	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1922					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.I59I(1)|p.I1922I(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GTTCTTCATCAATTTCAGCTG	0.398			T	BCL6	NHL								A|||	3043	0.607628	0.3343	0.6657	5008	,	,		20870	0.7401		0.6252	False		,,,				2504	0.7812				p.I769I		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	NACA_ENST00000454682,NS,carcinoma,0,2	NACA	131	2	2	Substitution - coding silent(2)	prostate(2)	c.T2307C						PASS	.	A	,,,	1820,2586	533.6+/-373.7	369,1082,752	99.0	89.0	93.0		177,177,2307,177	-0.8	1.0	12	dbSNP_52	93	5345,3255	649.4+/-400.6	1667,2011,622	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,,	2036,3093,1374	GG,GA,AA		37.8488,41.3073,44.91	,,,	59/216,59/216,769/926,59/216	57108203	7165,5841	2203	4300	6503	SO:0001819	synonymous_variant	4666	exon7			TTCATCAATTTCA	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.5766T>C	12.37:g.57108203A>G		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	234	233	0.995726	NM_001113203		Silent	SNP	ENST00000454682.1	37																																																																																				T|0.000;G|0.576;C|0.000;A|0.424	0.576	strong		0.398	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
MUC16	94025	hgsc.bcm.edu	37	19	9048421	9048421	+	Silent	SNP	T	T	C	rs56194405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9048421T>C	ENST00000397910.4	-	5	33413	c.33210A>G	c.(33208-33210)acA>acG	p.T11070T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11072	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCATTGAAGGTGTGGTTTCTA	0.502													T|||	927	0.185104	0.062	0.2752	5008	,	,		23344	0.3363		0.167	False		,,,				2504	0.1503				p.T11070T		Atlas-SNP	.											.	MUC16	4315	.	0			c.A33210G						PASS	.			301,3533		14,273,1630	84.0	76.0	78.0		33210	-0.6	0.0	19	dbSNP_129	78	1505,6751		139,1227,2762	no	coding-synonymous	MUC16	NM_024690.2		153,1500,4392	CC,CT,TT		18.2292,7.8508,14.938		11070/14508	9048421	1806,10284	1917	4128	6045	SO:0001819	synonymous_variant	94025	exon5			TGAAGGTGTGGTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33210A>G	19.37:g.9048421T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.792;C|0.208	0.208	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TMEM261	90871	hgsc.bcm.edu	37	9	7799653	7799653	+	Missense_Mutation	SNP	G	G	T	rs1127430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:7799653G>T	ENST00000358227.4	-	1	414	c.82C>A	c.(82-84)Ccc>Acc	p.P28T	TMEM261_ENST00000484082.1_Intron	NM_033428.1	NP_219500.1	Q96GE9	TM261_HUMAN	transmembrane protein 261	28			P -> T (in dbSNP:rs1127430).			integral component of membrane (GO:0016021)											GTAGCTGGGGGCGCAGGTTTG	0.662													g|||	1874	0.374201	0.264	0.5375	5008	,	,		9632	0.371		0.3926	False		,,,				2504	0.3916				p.P28T		Atlas-SNP	.											.	C9orf123	7	.	0			c.C82A						PASS	.	G	THR/PRO	1224,3182		178,868,1157	22.0	26.0	25.0		82	3.5	0.0	9	dbSNP_86	25	3382,5218		663,2056,1581	no	missense	C9orf123	NM_033428.1	38	841,2924,2738	TT,TG,GG		39.3256,27.7803,35.4144	probably-damaging	28/113	7799653	4606,8400	2203	4300	6503	SO:0001583	missense	90871	exon1			CTGGGGGCGCAGG	BC009510	CCDS34989.1	9p24.1	2014-02-21	2013-09-11	2013-09-11	ENSG00000137038	ENSG00000137038			30536	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 123"""	C9orf123		21666724	Standard	NM_033428		Approved	MGC4730	uc003zkj.3	Q96GE9	OTTHUMG00000019539	ENST00000358227.4:c.82C>A	9.37:g.7799653G>T	ENSP00000350961:p.Pro28Thr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_033428	A8K9B7|Q5T6Y9|Q9NT74	Missense_Mutation	SNP	ENST00000358227.4	37	CCDS34989.1	819	0.375	137	0.2784552845528455	198	0.5469613259668509	197	0.34440559440559443	287	0.3786279683377309	g	17.75	3.467238	0.63625	0.277803	0.393256	ENSG00000137038	ENST00000358227	T	0.52526	0.66	5.34	3.45	0.39498	.	0.309163	0.24041	N	0.042086	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	P;P	0.46512	0.717;0.879	B;P	0.45639	0.243;0.488	T	0.48547	-0.9026	9	0.72032	D	0.01	-4.188	8.6511	0.34035	0.0:0.166:0.6616:0.1724	rs1127430;rs3183396	28;28	Q96GE9-2;Q96GE9	.;CI123_HUMAN	T	28	ENSP00000350961:P28T	ENSP00000350961:P28T	P	-	1	0	C9orf123	7789653	0.000000	0.05858	0.003000	0.11579	0.139000	0.21198	-0.242000	0.08928	0.773000	0.33404	0.645000	0.84053	CCC	G|0.647;T|0.353	0.353	strong		0.662	TMEM261-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051705.1	NM_033428	
SPRR3	6707	hgsc.bcm.edu	37	1	152975763	152975763	+	Silent	SNP	C	C	A	rs1977734	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152975763C>A	ENST00000295367.4	+	2	309	c.267C>A	c.(265-267)ggC>ggA	p.G89G	SPRR3_ENST00000542696.1_Silent_p.G89G|SPRR3_ENST00000331860.3_Silent_p.G89G	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	89	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGAGCCAGGCTGTACCAAGG	0.602													T|||	2627	0.524561	0.5	0.4323	5008	,	,		17476	0.6319		0.5318	False		,,,				2504	0.5051				p.G89G		Atlas-SNP	.											.	SPRR3	45	.	0			c.C267A						PASS	.	C	,	2311,2095		594,1123,486	72.0	60.0	64.0		267,267	1.5	0.0	1	dbSNP_92	64	4670,3928		1279,2112,908	no	coding-synonymous,coding-synonymous	SPRR3	NM_001097589.1,NM_005416.2	,	1873,3235,1394	AA,AC,CC		45.685,47.5488,46.3165	,	89/170,89/170	152975763	6981,6023	2203	4299	6502	SO:0001819	synonymous_variant	6707	exon2			GCCAGGCTGTACC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.267C>A	1.37:g.152975763C>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			T|0.000;C|0.476;A|0.524	0.524	strong		0.602	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858421	27858421	+	Silent	SNP	A	A	G	rs200973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27858421A>G	ENST00000359303.2	-	1	149	c.150T>C	c.(148-150)cgT>cgC	p.R50R	HIST1H3J_ENST00000479986.1_5'UTR|HIST1H2BO_ENST00000303806.4_5'Flank	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	50					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						GGCGGATCTCACGCAAGGCCA	0.612													G|||	722	0.144169	0.2095	0.1542	5008	,	,		15341	0.0714		0.1461	False		,,,				2504	0.1217				p.R50R		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.T150C						PASS	.	G		883,3523	732.2+/-410.3	90,703,1410	47.0	49.0	48.0		150	3.1	1.0	6	dbSNP_79	48	1387,7213	744.2+/-407.2	114,1159,3027	no	coding-synonymous	HIST1H3J	NM_003535.2		204,1862,4437	GG,GA,AA		16.1279,20.0409,17.4535		50/137	27858421	2270,10736	2203	4300	6503	SO:0001819	synonymous_variant	8356	exon1			GATCTCACGCAAG	Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153		"""Histones / Replication-dependent"""	4774	protein-coding gene	gene with protein product		602817	"""H3 histone family, member J"", ""histone 1, H3j"""	H3FJ		9439656, 12408966	Standard	NM_003535		Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000359303.2:c.150T>C	6.37:g.27858421A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000359303.2	37	CCDS4638.1																																																																																			A|0.839;G|0.161	0.161	strong		0.612	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535	
OR51A2	401667	hgsc.bcm.edu	37	11	4976659	4976659	+	Silent	SNP	A	A	T	rs3986369	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4976659A>T	ENST00000380371.1	-	1	284	c.285T>A	c.(283-285)tcT>tcA	p.S95S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	95						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGGCACTAGAAGAAGTTTCAG	0.438													a|||	717	0.143171	0.0968	0.1931	5008	,	,		13905	0.2312		0.172	False		,,,				2504	0.0501				p.S95S		Atlas-SNP	.											OR51A2,NS,carcinoma,0,1	OR51A2	40	1	0			c.T285A						scavenged	.						137.0	106.0	117.0					11																	4976659		1865	3319	5184	SO:0001819	synonymous_variant	401667	exon1			ACTAGAAGAAGTT	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.285T>A	11.37:g.4976659A>T		Somatic	658	0	0		WXS	Illumina HiSeq	Phase_I	341	5	0.0146628	NM_001004748		Silent	SNP	ENST00000380371.1	37	CCDS31368.1																																																																																			A|0.689;T|0.311	0.311	strong		0.438	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
OTOGL	283310	hgsc.bcm.edu	37	12	80765800	80765800	+	Splice_Site	SNP	A	A	G	rs1551122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:80765800A>G	ENST00000547103.1	+	56	6680	c.6674A>G	c.(6673-6675)aAt>aGt	p.N2225S	OTOGL_ENST00000546620.1_Splice_Site_p.N256S|OTOGL_ENST00000458043.2_Splice_Site_p.N2237S			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2225				N -> S (in Ref. 2; BAC11376 and 3; AAI01018/AAI01019). {ECO:0000305}.	L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TCTTTCTAGAATGAAGGGATT	0.303													A|||	2424	0.484026	0.1051	0.4798	5008	,	,		14369	0.7024		0.6461	False		,,,				2504	0.6074				p.N2237S		Atlas-SNP	.											.	OTOGL	235	.	0			c.A6710G						PASS	.	A	SER/ASN	948,3458	360.1+/-315.1	104,740,1359	105.0	98.0	100.0		6710	6.0	1.0	12	dbSNP_88	100	5509,3089	654.7+/-401.2	1769,1971,559	yes	missense-near-splice	OTOGL	NM_173591.3	46	1873,2711,1918	GG,GA,AA		35.927,21.5161,49.654	probably-damaging	2237/2345	80765800	6457,6547	2203	4299	6502	SO:0001630	splice_region_variant	283310	exon56			TCTAGAATGAAGG	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6673-1A>G	12.37:g.80765800A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		1123|1123	0.5141941391941391|0.5141941391941391	69|69	0.1402439024390244|0.1402439024390244	178|178	0.49171270718232046|0.49171270718232046	389|389	0.6800699300699301|0.6800699300699301	487|487	0.6424802110817942|0.6424802110817942	A|A	19.24|19.24	3.789085|3.789085	0.70337|0.70337	0.215161|0.215161	0.64073|0.64073	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043;ENST00000546620	.|T;T;T	.|0.17213	.|2.38;2.38;2.29	5.98|5.98	5.98|5.98	0.97165|0.97165	.|.	.|0.126953	.|0.50627	.|D	.|0.000109	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.70595|0.70595	2.14|2.14	0.33264|0.33264	P|P	0.439929|0.439929	.|D	.|0.65815	.|0.995	.|D	.|0.63033	.|0.91	T|T	0.33471|0.33471	-0.9867|-0.9867	4|9	.|0.25751	.|T	.|0.34	.|.	16.143|16.143	0.81539|0.81539	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs1551122;rs52790105;rs59532812;rs1551122|rs1551122;rs52790105;rs59532812;rs1551122	.|602	.|Q3ZCN5	.|OTOGL_HUMAN	V|S	645|2225;2237;256	.|ENSP00000447211:N2225S;ENSP00000400895:N2237S;ENSP00000449094:N256S	.|ENSP00000400895:N2237S	M|N	+|+	1|2	0|0	OTOGL|OTOGL	79289931|79289931	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	5.331000|5.331000	0.65905|0.65905	2.289000|2.289000	0.77006|0.77006	0.482000|0.482000	0.46254|0.46254	ATG|AAT	A|0.518;G|0.482	0.482	strong		0.303	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	Missense_Mutation
CHD9	80205	hgsc.bcm.edu	37	16	53262964	53262964	+	Silent	SNP	C	C	T	rs35198193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:53262964C>T	ENST00000398510.3	+	7	2325	c.2238C>T	c.(2236-2238)atC>atT	p.I746I	CHD9_ENST00000564845.1_Silent_p.I746I|CHD9_ENST00000447540.1_Silent_p.I746I|CHD9_ENST00000566029.1_Silent_p.I746I			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	746	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				AGCAGAAAATCAAACGATTCA	0.318													C|||	681	0.135982	0.0658	0.0533	5008	,	,		14516	0.1944		0.1282	False		,,,				2504	0.2372				p.I746I		Atlas-SNP	.											.	CHD9	203	.	0			c.C2238T						PASS	.	C		257,3355		12,233,1561	35.0	31.0	33.0		2238	2.4	1.0	16	dbSNP_126	33	1021,7131		71,879,3126	no	coding-synonymous	CHD9	NM_025134.4		83,1112,4687	TT,TC,CC		12.5245,7.1152,10.8637		746/2882	53262964	1278,10486	1806	4076	5882	SO:0001819	synonymous_variant	80205	exon8			GAAAATCAAACGA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.2238C>T	16.37:g.53262964C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	120	50	0.416667	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	37																																																																																				C|0.864;T|0.136	0.136	strong		0.318	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
FAM45A	404636	hgsc.bcm.edu	37	10	120896027	120896027	+	Silent	SNP	G	G	A	rs11198799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:120896027G>A	ENST00000361432.2	+	9	968	c.942G>A	c.(940-942)ccG>ccA	p.P314P	FAM45A_ENST00000489988.1_3'UTR|FAM45A_ENST00000535029.1_3'UTR|FAM45A_ENST00000544016.1_Silent_p.P163P	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	314										breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		ACCTAGCACCGTTTTCAGAAG	0.353													G|||	4519	0.902356	0.7194	0.9236	5008	,	,		20105	0.9534		0.9911	False		,,,				2504	0.9908				p.P314P		Atlas-SNP	.											.	FAM45A	30	.	0			c.G942A						PASS	.						56.0	60.0	59.0					10																	120896027		2201	4297	6498	SO:0001819	synonymous_variant	404636	exon9			AGCACCGTTTTCA	AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979			31793	protein-coding gene	gene with protein product							Standard	NM_207009		Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.942G>A	10.37:g.120896027G>A		Somatic	654	2	0.0030581		WXS	Illumina HiSeq	Phase_I	628	566	0.901274	NM_207009	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	Silent	SNP	ENST00000361432.2	37	CCDS7609.1																																																																																			.	.	weak		0.353	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050623.1	NM_207009	
NAV1	89796	hgsc.bcm.edu	37	1	201777250	201777250	+	Missense_Mutation	SNP	C	C	T	rs2820289	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201777250C>T	ENST00000367296.4	+	18	4238	c.3818C>T	c.(3817-3819)tCg>tTg	p.S1273L	NAV1_ENST00000367297.4_Missense_Mutation_p.S1265L|NAV1_ENST00000367300.3_Missense_Mutation_p.S1213L|MIR1231_ENST00000408101.1_RNA|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367295.1_Missense_Mutation_p.S879L|NAV1_ENST00000295624.6_Missense_Mutation_p.S1270L|NAV1_ENST00000367302.1_Missense_Mutation_p.S1226L	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1273			S -> L (in dbSNP:rs2820289). {ECO:0000269|PubMed:12079279}.		microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						TCCTCCACCTCGTCCTCCGTG	0.562													c|||	429	0.0856629	0.0023	0.1398	5008	,	,		19061	0.1756		0.0636	False		,,,				2504	0.09				p.S1273L		Atlas-SNP	.											NAV1,NS,carcinoma,-1,1	NAV1	143	1	0			c.C3818T						PASS	.		LEU/SER,LEU/SER	79,4327	70.3+/-108.2	1,77,2125	122.0	114.0	117.0		2636,3818	4.4	0.5	1	dbSNP_100	117	632,7968	163.9+/-216.4	23,586,3691	yes	missense,missense	NAV1	NM_001167738.1,NM_020443.4	145,145	24,663,5816	TT,TC,CC		7.3488,1.793,5.4667	probably-damaging,probably-damaging	879/1484,1273/1878	201777250	711,12295	2203	4300	6503	SO:0001583	missense	89796	exon18			CCACCTCGTCCTC	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.3818C>T	1.37:g.201777250C>T	ENSP00000356265:p.Ser1273Leu	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	289	288	0.99654	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	205	0.09386446886446886	3	0.006097560975609756	26	0.0718232044198895	118	0.2062937062937063	58	0.07651715039577836	c	24.6	4.545266	0.86022	0.01793	0.073488	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000367295	D;D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82;-3.82	5.33	4.42	0.53409	.	0.143822	0.47093	D	0.000248	T	0.01489	0.0048	L	0.60455	1.87	0.21553	P	0.999645964	D;P	0.67145	0.996;0.939	P;B	0.56127	0.792;0.406	T	0.00000	-1.2953	9	0.87932	D	0	-5.7771	13.6033	0.62033	0.0:0.9243:0.0:0.0757	rs2820289;rs52802753;rs57412406;rs2820289	879;1270	Q8NEY1-5;Q8NEY1-3	.;.	L	1226;1273;1270;1265;1213;879	ENSP00000356271:S1226L;ENSP00000356265:S1273L;ENSP00000295624:S1270L;ENSP00000356266:S1265L;ENSP00000356269:S1213L;ENSP00000356264:S879L	ENSP00000295624:S1270L	S	+	2	0	NAV1	200043873	1.000000	0.71417	0.489000	0.27452	0.642000	0.38348	4.617000	0.61204	1.257000	0.44085	0.552000	0.68991	TCG	C|0.922;T|0.078	0.078	strong		0.562	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443	
RNF175	285533	hgsc.bcm.edu	37	4	154631563	154631563	+	Missense_Mutation	SNP	T	T	C	rs1339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:154631563T>C	ENST00000347063.4	-	9	1317	c.945A>G	c.(943-945)atA>atG	p.I315M		NM_173662.2	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	315			I -> M (in dbSNP:rs1339).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	13	all_hematologic(180;0.093)	Renal(120;0.118)				GAACTATTCCTATCACCACAG	0.448													T|||	772	0.154153	0.0121	0.1369	5008	,	,		17106	0.3026		0.2276	False		,,,				2504	0.1299				p.I315M		Atlas-SNP	.											.	RNF175	40	.	0			c.A945G						PASS	.	T	MET/ILE	170,3686		5,160,1763	73.0	67.0	69.0		945	-4.4	1.0	4	dbSNP_36	69	1714,6552		189,1336,2608	yes	missense	RNF175	NM_173662.2	10	194,1496,4371	CC,CT,TT		20.7355,4.4087,15.542	possibly-damaging	315/329	154631563	1884,10238	1928	4133	6061	SO:0001583	missense	285533	exon9			TATTCCTATCACC	BC034385	CCDS47149.1	4q31.3	2008-02-05			ENSG00000145428	ENSG00000145428		"""RING-type (C3HC4) zinc fingers"""	27735	protein-coding gene	gene with protein product							Standard	NM_173662		Approved	FLJ34190	uc003int.3	Q8N4F7	OTTHUMG00000161557	ENST00000347063.4:c.945A>G	4.37:g.154631563T>C	ENSP00000340979:p.Ile315Met	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_173662	C9JL66|Q8NB61	Missense_Mutation	SNP	ENST00000347063.4	37	CCDS47149.1	377	0.17261904761904762	7	0.014227642276422764	61	0.1685082872928177	147	0.256993006993007	162	0.21372031662269128	T	17.50	3.404071	0.62288	0.044087	0.207355	ENSG00000145428	ENST00000347063	T	0.24538	1.85	4.26	-4.42	0.03579	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.45581	1.43	0.09310	P	0.9999999999999412	D	0.63880	0.993	D	0.66351	0.943	T	0.07158	-1.0787	9	0.44086	T	0.13	-9.2525	1.9222	0.03310	0.4798:0.0848:0.2356:0.1998	rs1339;rs52816039;rs57786176;rs1339	315	Q8N4F7	RN175_HUMAN	M	315	ENSP00000340979:I315M	ENSP00000340979:I315M	I	-	3	3	RNF175	154851013	0.339000	0.24784	0.965000	0.40720	0.998000	0.95712	-0.465000	0.06680	-0.675000	0.05246	0.533000	0.62120	ATA	T|0.834;C|0.166	0.166	strong		0.448	RNF175-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365286.1	NM_173662	
PCDH9	5101	hgsc.bcm.edu	37	13	67801532	67801532	+	Silent	SNP	A	A	G	rs45527937	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:67801532A>G	ENST00000377865.2	-	1	1175	c.1041T>C	c.(1039-1041)aaT>aaC	p.N347N	PCDH9_ENST00000456367.1_Silent_p.N347N|PCDH9_ENST00000544246.1_Silent_p.N347N|PCDH9_ENST00000328454.5_Silent_p.N347N|PCDH9_ENST00000377861.3_Silent_p.N347N			Q9HC56	PCDH9_HUMAN	protocadherin 9	347	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CATCGGTGACATTGATGGTAA	0.453													A|||	48	0.00958466	0.0015	0.0115	5008	,	,		18124	0.0		0.0318	False		,,,				2504	0.0061				p.N347N		Atlas-SNP	.											.	PCDH9	252	.	0			c.T1041C						PASS	.	A	,	17,4389	25.3+/-52.1	1,15,2187	139.0	135.0	136.0		1041,1041	3.8	1.0	13	dbSNP_127	136	233,8367	95.2+/-157.0	7,219,4074	no	coding-synonymous,coding-synonymous	PCDH9	NM_020403.4,NM_203487.2	,	8,234,6261	GG,GA,AA		2.7093,0.3858,1.9222	,	347/1204,347/1238	67801532	250,12756	2203	4300	6503	SO:0001819	synonymous_variant	5101	exon2			GGTGACATTGATG	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1041T>C	13.37:g.67801532A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	CCDS9444.1																																																																																			A|0.981;G|0.019	0.019	strong		0.453	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
RFXANK	8625	hgsc.bcm.edu	37	19	19307817	19307817	+	Missense_Mutation	SNP	G	G	A	rs375541634		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19307817G>A	ENST00000303088.4	+	4	707	c.233G>A	c.(232-234)cGa>cAa	p.R78Q	RFXANK_ENST00000407360.3_Missense_Mutation_p.R78Q|RFXANK_ENST00000456252.3_Missense_Mutation_p.R78Q|RFXANK_ENST00000353145.1_Missense_Mutation_p.R77Q|RFXANK_ENST00000392324.4_Missense_Mutation_p.R77Q	NM_003721.2	NP_003712.1	O14593	RFXK_HUMAN	regulatory factor X-associated ankyrin-containing protein	78					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			NS(1)|breast(1)|endometrium(1)|lung(8)|ovary(2)|prostate(1)	14			Epithelial(12;0.00228)			AACCGGCAGCGAGGGAACGAG	0.617																																					p.R78Q		Atlas-SNP	.											.	RFXANK	31	.	0			c.G233A						PASS	.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	81.0	76.0	77.0		233,230	4.1	1.0	19		77	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RFXANK	NM_003721.2,NM_134440.1	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	78/261,77/238	19307817	1,13005	2203	4300	6503	SO:0001583	missense	8625	exon4			GGCAGCGAGGGAA	AF094760	CCDS12395.1, CCDS12396.1, CCDS62611.1	19p12	2014-09-17			ENSG00000064490	ENSG00000064490		"""Ankyrin repeat domain containing"""	9987	protein-coding gene	gene with protein product	"""ankyrin repeat-containing regulatory factor X-associated protein"", ""regulatory factor X subunit B"", ""RFX-Bdelta4"", ""DNA-binding protein RFXANK"""	603200				9806546, 10072068	Standard	NM_003721		Approved	BLS, RFX-B, ANKRA1, F14150_1, MGC138628	uc002nls.3	O14593	OTTHUMG00000169224	ENST00000303088.4:c.233G>A	19.37:g.19307817G>A	ENSP00000305071:p.Arg78Gln	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_003721	O95839|Q24JQ1|Q6FGA8	Missense_Mutation	SNP	ENST00000303088.4	37	CCDS12395.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492551	0.84962	0.0	1.16E-4	ENSG00000064490	ENST00000353145;ENST00000456252;ENST00000303088;ENST00000407360;ENST00000543652;ENST00000540981;ENST00000541873;ENST00000392324;ENST00000535017	T;T;T;T;T;T;T;T	0.70869	-0.52;1.01;1.1;1.03;1.7;-0.28;-0.52;-0.28	5.16	4.13	0.48395	.	0.054459	0.85682	N	0.000000	T	0.80391	0.4614	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.996	T	0.78275	-0.2267	10	0.09338	T	0.73	-18.4611	11.3832	0.49770	0.0888:0.0:0.9112:0.0	.	78;78;77;78	Q6IB23;Q24JQ1;O14593-2;O14593	.;.;.;RFXK_HUMAN	Q	77;78;78;77;78;78;77;77;43	ENSP00000262804:R77Q;ENSP00000409138:R78Q;ENSP00000305071:R78Q;ENSP00000384572:R77Q;ENSP00000439581:R78Q;ENSP00000440325:R78Q;ENSP00000376138:R77Q;ENSP00000444280:R43Q	ENSP00000305071:R78Q	R	+	2	0	RFXANK	19168817	1.000000	0.71417	0.968000	0.41197	0.456000	0.32438	9.574000	0.98184	1.184000	0.42957	0.561000	0.74099	CGA	.	.	weak		0.617	RFXANK-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402923.2	NM_003721	
GSDMB	55876	hgsc.bcm.edu	37	17	38064469	38064469	+	Silent	SNP	T	T	C	rs11078928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38064469T>C	ENST00000394179.1	-	6	802	c.672A>G	c.(670-672)ttA>ttG	p.L224L	GSDMB_ENST00000418519.1_Splice_Site|GSDMB_ENST00000360317.3_Splice_Site|GSDMB_ENST00000520542.1_Splice_Site|GSDMB_ENST00000394175.2_Intron|GSDMB_ENST00000309481.7_Intron			Q8TAX9	GSDMB_HUMAN	gasdermin B	224						cytoplasm (GO:0005737)		p.?(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						AATGAATATCTAAACCAGCAC	0.433													T|||	1430	0.285543	0.1036	0.3357	5008	,	,		15743	0.2817		0.4652	False		,,,				2504	0.3149				.		Atlas-SNP	.											GSDMB_ENST00000418519,NS,carcinoma,0,1	GSDMB	87	1	1	Unknown(1)	stomach(1)	c.662-2A>G						PASS	.	T	,,,	186,1198		10,166,516	78.0	64.0	68.0		,,,	2.1	0.0	17	dbSNP_120	68	1391,1791		295,801,495	yes	intron,splice-3,splice-3,intron	GSDMB	NM_001042471.1,NM_001165958.1,NM_001165959.1,NM_018530.2	,,,	305,967,1011	CC,CT,TT		43.7146,13.4393,34.5379	,,,	,,,	38064469	1577,2989	692	1591	2283	SO:0001819	synonymous_variant	55876	exon7			AATATCTAAACCA	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"""gasdermin-like"""	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.672A>G	17.37:g.38064469T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	76	74	0.973684	NM_001165958	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Splice_Site	SNP	ENST00000394179.1	37		713	0.32646520146520147	51	0.10365853658536585	124	0.3425414364640884	180	0.3146853146853147	358	0.47229551451187335	T	2.921	-0.223260	0.06061	0.134393	0.437146	ENSG00000073605	ENST00000420491;ENST00000520542;ENST00000418519	.	.	.	3.19	2.11	0.27256	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3471	0.32279	0.0:0.0:0.1986:0.8014	rs11078928;rs17852277	.	.	.	.	-1	.	.	.	-	.	.	GSDMB	35317995	0.022000	0.18835	0.001000	0.08648	0.003000	0.03518	0.732000	0.26072	0.144000	0.18951	-1.524000	0.00929	.	T|0.651;C|0.349	0.349	strong		0.433	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	
ASPM	259266	hgsc.bcm.edu	37	1	197112533	197112533	+	Silent	SNP	G	G	A	rs6677082	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197112533G>A	ENST00000367409.4	-	3	1105	c.849C>T	c.(847-849)tcC>tcT	p.S283S	ASPM_ENST00000294732.7_Silent_p.S283S	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	283					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TAACATTTACGGAATTAAAGG	0.333													.|||	3784	0.755591	0.295	0.8746	5008	,	,		18038	0.9831		0.9095	False		,,,				2504	0.9008				p.S283S		Atlas-SNP	.											.	ASPM	444	.	0			c.C849T						PASS	.	G	,	1706,2700	502.4+/-365.2	345,1016,842	82.0	80.0	81.0		849,849	-2.4	0.0	1	dbSNP_116	81	7797,801	777.7+/-407.7	3536,725,38	no	coding-synonymous,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	3881,1741,880	AA,AG,GG		9.3161,38.7199,26.9225	,	283/1893,283/3478	197112533	9503,3501	2203	4299	6502	SO:0001819	synonymous_variant	259266	exon3			ATTTACGGAATTA	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.849C>T	1.37:g.197112533G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			G|0.240;A|0.760	0.760	strong		0.333	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
RYR1	6261	hgsc.bcm.edu	37	19	38981284	38981284	+	Silent	SNP	A	A	G	rs2228068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38981284A>G	ENST00000359596.3	+	37	6039	c.6039A>G	c.(6037-6039)aaA>aaG	p.K2013K	RYR1_ENST00000355481.4_Silent_p.K2013K|RYR1_ENST00000360985.3_Silent_p.K2013K			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2013	6 X approximate repeats.		K -> Q (in MHS1). {ECO:0000269|PubMed:20681998}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGCAATTCAAAGATGGTACAG	0.453													A|||	376	0.0750799	0.0219	0.0677	5008	,	,		22272	0.0079		0.0974	False		,,,				2504	0.1984				p.K2013K		Atlas-SNP	.											.	RYR1	708	.	0			c.A6039G						PASS	.	A	,	155,4251	105.6+/-144.1	4,147,2052	120.0	103.0	109.0		6039,6039	4.2	1.0	19	dbSNP_98	109	844,7756	192.1+/-238.2	45,754,3501	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	49,901,5553	GG,GA,AA		9.814,3.5179,7.6811	,	2013/5039,2013/5034	38981284	999,12007	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon37			ATTCAAAGATGGT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6039A>G	19.37:g.38981284A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			A|0.927;G|0.073	0.073	strong		0.453	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
LLGL2	3993	hgsc.bcm.edu	37	17	73566561	73566561	+	Silent	SNP	G	G	A	rs2305525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73566561G>A	ENST00000392550.3	+	16	2124	c.2007G>A	c.(2005-2007)ccG>ccA	p.P669P	LLGL2_ENST00000577200.1_Silent_p.P669P|LLGL2_ENST00000167462.5_Silent_p.P669P	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	669					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			AGCGGCACCCGGCTGGCCCCC	0.711													G|||	561	0.112021	0.0151	0.1383	5008	,	,		13691	0.1498		0.1839	False		,,,				2504	0.1115				p.P669P		Atlas-SNP	.											.	LLGL2	155	.	0			c.G2007A						PASS	.	G	,	222,4008		28,166,1921	8.0	9.0	9.0		2007,2007	-7.3	0.0	17	dbSNP_100	9	1904,6478		280,1344,2567	no	coding-synonymous,coding-synonymous	LLGL2	NM_001031803.1,NM_004524.2	,	308,1510,4488	AA,AG,GG		22.7153,5.2482,16.857	,	669/1021,669/1016	73566561	2126,10486	2115	4191	6306	SO:0001819	synonymous_variant	3993	exon16			GCACCCGGCTGGC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2007G>A	17.37:g.73566561G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			G|0.868;A|0.132	0.132	strong		0.711	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
NLRP5	126206	hgsc.bcm.edu	37	19	56539240	56539240	+	Silent	SNP	C	C	T	rs397977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56539240C>T	ENST00000390649.3	+	7	1641	c.1641C>T	c.(1639-1641)gaC>gaT	p.D547D		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	547	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.D547D(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CAGTGTTTGACGGTGACGACC	0.547													C|||	1740	0.347444	0.1316	0.4366	5008	,	,		18759	0.3571		0.4235	False		,,,				2504	0.4877				p.D547D		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - coding silent(1)	stomach(1)	c.C1641T						PASS	.	C		816,3442		98,620,1411	59.0	62.0	61.0		1641	-4.4	0.0	19	dbSNP_80	61	3833,4665		889,2055,1305	no	coding-synonymous	NLRP5	NM_153447.4		987,2675,2716	TT,TC,CC		45.1047,19.1639,36.4456		547/1201	56539240	4649,8107	2129	4249	6378	SO:0001819	synonymous_variant	126206	exon7			GTTTGACGGTGAC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1641C>T	19.37:g.56539240C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			C|0.671;N|0.000	.	strong		0.547	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
TDRD6	221400	hgsc.bcm.edu	37	6	46658905	46658905	+	Missense_Mutation	SNP	C	C	G	rs9381472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46658905C>G	ENST00000316081.6	+	1	3040	c.3040C>G	c.(3040-3042)Cag>Gag	p.Q1014E	TDRD6_ENST00000544460.1_Missense_Mutation_p.Q1014E	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1014			Q -> E (in dbSNP:rs9381472). {ECO:0000269|PubMed:14702039}.		germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TATTTTAGAACAGTTGTCATG	0.343													C|||	2092	0.417732	0.3631	0.4323	5008	,	,		19636	0.3492		0.329	False		,,,				2504	0.6431				p.Q1014E		Atlas-SNP	.											.	TDRD6	205	.	0			c.C3040G						PASS	.	C	GLU/GLN,GLU/GLN	1684,2722	490.4+/-361.8	322,1040,841	47.0	52.0	50.0		3040,3040	3.5	1.0	6	dbSNP_119	50	2856,5744	442.8+/-360.2	504,1848,1948	yes	missense,missense	TDRD6	NM_001010870.2,NM_001168359.1	29,29	826,2888,2789	GG,GC,CC		33.2093,38.2206,34.907	possibly-damaging,possibly-damaging	1014/2097,1014/2067	46658905	4540,8466	2203	4300	6503	SO:0001583	missense	221400	exon1			TTAGAACAGTTGT	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.3040C>G	6.37:g.46658905C>G	ENSP00000346065:p.Gln1014Glu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	786	0.3598901098901099	180	0.36585365853658536	148	0.4088397790055249	202	0.3531468531468531	256	0.33773087071240104	C	8.698	0.908949	0.17833	0.382206	0.332093	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.08370	3.1;3.1	5.36	3.52	0.40303	Maternal tudor protein (1);	1.417590	0.03640	N	0.239271	T	0.02083	0.0065	L	0.28608	0.87	0.42236	P	0.008086999999999955	B;B	0.12013	0.004;0.005	B;B	0.18561	0.013;0.022	T	0.43861	-0.9365	9	0.09338	T	0.73	-21.7981	10.0578	0.42255	0.2788:0.5867:0.1345:0.0	rs9381472;rs56926189;rs9381472	1014;1014	F5H5M3;O60522	.;TDRD6_HUMAN	E	1014	ENSP00000443299:Q1014E;ENSP00000346065:Q1014E	ENSP00000346065:Q1014E	Q	+	1	0	TDRD6	46766864	0.930000	0.31532	0.992000	0.48379	0.871000	0.50021	1.590000	0.36654	0.576000	0.29452	0.655000	0.94253	CAG	C|0.649;G|0.351	0.351	strong		0.343	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
UBR3	130507	hgsc.bcm.edu	37	2	170789504	170789504	+	Silent	SNP	C	C	T	rs73015765	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170789504C>T	ENST00000272793.5	+	19	2699	c.2649C>T	c.(2647-2649)gaC>gaT	p.D883D	UBR3_ENST00000418381.1_Silent_p.D883D			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	883					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						CTGCAATGGACAGATATACTG	0.353													C|||	137	0.0273562	0.0197	0.0274	5008	,	,		15979	0.0		0.0567	False		,,,				2504	0.0358				p.D883D		Atlas-SNP	.											.	UBR3	182	.	0			c.C2649T						PASS	.	C		42,1342		1,40,651	125.0	109.0	114.0		2649	5.1	1.0	2	dbSNP_130	114	176,3006		5,166,1420	no	coding-synonymous	UBR3	NM_172070.3		6,206,2071	TT,TC,CC		5.5311,3.0347,4.7744		883/1889	170789504	218,4348	692	1591	2283	SO:0001819	synonymous_variant	130507	exon19			AATGGACAGATAT	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.2649C>T	2.37:g.170789504C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	157	83	0.528662	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				C|0.961;T|0.039	0.039	strong		0.353	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
ZNF880	400713	hgsc.bcm.edu	37	19	52888050	52888050	+	Missense_Mutation	SNP	A	A	G	rs76053634	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52888050A>G	ENST00000422689.2	+	4	1232	c.1217A>G	c.(1216-1218)cAa>cGa	p.Q406R		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	406					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						ACGGGAGAGCAACCTTACAAA	0.398																																					p.Q406R		Atlas-SNP	.											ZNF880,colon,carcinoma,0,2	ZNF880	45	2	0			c.A1217G						PASS	.						70.0	64.0	66.0					19																	52888050		1568	3582	5150	SO:0001583	missense	400713	exon4			GAGAGCAACCTTA	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1217A>G	19.37:g.52888050A>G	ENSP00000406318:p.Gln406Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	13	0.309524	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	A	4.567	0.105370	0.08731	.	.	ENSG00000221923	ENST00000422689	T	0.15718	2.4	1.84	1.84	0.25277	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04182	0.0116	N	0.00392	-1.555	0.19775	N	0.999952	B	0.17667	0.023	B	0.23150	0.044	T	0.43360	-0.9396	8	.	.	.	.	8.4442	0.32833	1.0:0.0:0.0:0.0	.	406	Q6PDB4	ZN880_HUMAN	R	406	ENSP00000406318:Q406R	.	Q	+	2	0	ZNF880	57579862	0.002000	0.14202	0.418000	0.26571	0.177000	0.22998	0.149000	0.16243	0.834000	0.34852	0.450000	0.29827	CAA	A|0.867;G|0.133	0.133	strong		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ANP32D	23519	hgsc.bcm.edu	37	12	48866585	48866585	+	Missense_Mutation	SNP	A	A	C	rs7956679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48866585A>C	ENST00000266594.1	+	1	138	c.138A>C	c.(136-138)ttA>ttC	p.L46F		NM_012404.2	NP_036536.2	O95626	AN32D_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member D	46			L -> F (in dbSNP:rs7956679).			nuclear matrix (GO:0016363)				central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	9						AACTGGAATTATTAAATACAA	0.418													c|||	1454	0.290335	0.1604	0.3357	5008	,	,		18340	0.6548		0.0815	False		,,,				2504	0.273				p.L46F		Atlas-SNP	.											ANP32D,colon,carcinoma,+1,1	ANP32D	15	1	0			c.A138C						PASS	.	C	PHE/LEU	683,3723	761.6+/-413.1	51,581,1571	125.0	127.0	126.0		138	0.6	0.0	12	dbSNP_116	126	555,8045	794.3+/-407.5	18,519,3763	yes	missense	ANP32D	NM_012404.2	22	69,1100,5334	CC,CA,AA		6.4535,15.5016,9.5187	benign	46/132	48866585	1238,11768	2203	4300	6503	SO:0001583	missense	23519	exon1			GGAATTATTAAAT	U71084	CCDS31788.1	12q13.12	2008-08-04			ENSG00000139223	ENSG00000139223		"""ANP32 acidic nuclear phosphoproteins"""	16676	protein-coding gene	gene with protein product	"""pp32 related 2"""	606878				10086381, 10400610	Standard	NM_012404		Approved	PP32R2	uc010slt.2	O95626	OTTHUMG00000162681	ENST00000266594.1:c.138A>C	12.37:g.48866585A>C	ENSP00000266594:p.Leu46Phe	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	189	102	0.539683	NM_012404	Q6NTC4	Missense_Mutation	SNP	ENST00000266594.1	37	CCDS31788.1	607	0.27793040293040294	71	0.1443089430894309	110	0.30386740331491713	359	0.6276223776223776	67	0.08839050131926121	c	0.007	-2.006770	0.00426	0.155016	0.064535	ENSG00000139223	ENST00000266594	T	0.00022	9.01	1.57	0.58	0.17402	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00237	-1.79	0.47037	P	7.099999999999884E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.48293	-0.9048	9	0.02654	T	1	.	2.0895	0.03654	0.2523:0.4031:0.0:0.3447	rs7956679;rs52790622;rs7956679	46	O95626	AN32D_HUMAN	F	46	ENSP00000266594:L46F	ENSP00000266594:L46F	L	+	3	2	ANP32D	47152852	1.000000	0.71417	0.008000	0.14137	0.043000	0.13939	1.160000	0.31761	-0.422000	0.07405	-2.030000	0.00424	TTA	A|0.837;C|0.163	0.163	strong		0.418	ANP32D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370058.1	NM_012404	
ECM1	1893	hgsc.bcm.edu	37	1	150485839	150485839	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:150485839G>A	ENST00000369047.4	+	10	1644	c.1519G>A	c.(1519-1521)Gtg>Atg	p.V507M	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Missense_Mutation_p.V534M|LINC00568_ENST00000416894.1_lincRNA|ECM1_ENST00000346569.6_Missense_Mutation_p.V382M	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	507					angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)	p.V507L(1)|p.V534L(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			TCTGAGGAACGTGGCTCTAGT	0.552																																					p.V534M	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											ECM1,NS,carcinoma,0,1	ECM1	96	1	2	Substitution - Missense(2)	endometrium(2)	c.G1600A						scavenged	.						115.0	105.0	109.0					1																	150485839		2203	4300	6503	SO:0001583	missense	1893	exon10			AGGAACGTGGCTC	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.1519G>A	1.37:g.150485839G>A	ENSP00000358043:p.Val507Met	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	235	3	0.012766	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Missense_Mutation	SNP	ENST00000369047.4	37	CCDS953.1	.	.	.	.	.	.	.	.	.	.	G	18.28	3.588108	0.66105	.	.	ENSG00000143369	ENST00000369049;ENST00000369047;ENST00000346569	T;T;T	0.80994	-1.44;-1.44;-1.44	4.85	3.93	0.45458	.	0.096378	0.38436	N	0.001698	T	0.81346	0.4803	M	0.62723	1.935	0.21933	N	0.999464	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.73802	-0.3868	10	0.87932	D	0	-10.5547	9.1075	0.36707	0.0996:0.0:0.9004:0.0	.	534;382;507	Q16610-4;Q16610-2;Q16610	.;.;ECM1_HUMAN	M	534;507;382	ENSP00000358045:V534M;ENSP00000358043:V507M;ENSP00000271630:V382M	ENSP00000271630:V382M	V	+	1	0	ECM1	148752463	1.000000	0.71417	0.938000	0.37757	0.904000	0.53231	4.171000	0.58236	1.254000	0.44035	0.563000	0.77884	GTG	.	.	none		0.552	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
TRDN	10345	hgsc.bcm.edu	37	6	123703291	123703291	+	Splice_Site	SNP	A	A	C	rs200706450		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:123703291A>C	ENST00000398178.3	-	15	1158	c.1137T>G	c.(1135-1137)gaT>gaG	p.D379E	TRDN_ENST00000334268.4_Splice_Site_p.D379E	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	379					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		TTTTCTTGGAATCTGAAAACA	0.284																																					p.D380E		Atlas-SNP	.											.	TRDN	88	.	0			c.T1140G						PASS	.						21.0	19.0	20.0					6																	123703291		1645	3752	5397	SO:0001630	splice_region_variant	10345	exon15			CTTGGAATCTGAA	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1136-1T>G	6.37:g.123703291A>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.809011	0.31961	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.21361	2.02;2.01	4.42	1.95	0.26073	.	0.317399	0.28420	N	0.015417	T	0.02230	0.0069	N	0.14661	0.345	0.80722	D	1	B;B;B	0.17667	0.023;0.023;0.023	B;B;B	0.12837	0.008;0.008;0.008	T	0.43669	-0.9377	10	0.02654	T	1	.	3.799	0.08751	0.7097:0.0:0.1035:0.1868	.	379;380;379	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	E	379;381;379	ENSP00000381240:D379E;ENSP00000333984:D379E	ENSP00000333984:D379E	D	-	3	2	TRDN	123744990	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.025000	0.30090	0.297000	0.22615	0.377000	0.23210	GAT	.	.	weak		0.284	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Missense_Mutation
DNAJC30	84277	hgsc.bcm.edu	37	7	73097082	73097082	+	Silent	SNP	A	A	G	rs79849491	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73097082A>G	ENST00000395176.2	-	1	701	c.672T>C	c.(670-672)ttT>ttC	p.F224F	WBSCR22_ENST00000423497.1_5'Flank|WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000265758.2_5'Flank	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	224						mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(1)	4						ATTAAATATAAAAGCCGATGA	0.512													A|||	125	0.0249601	0.0439	0.0202	5008	,	,		15128	0.0		0.0328	False		,,,				2504	0.0204				p.F224F		Atlas-SNP	.											.	DNAJC30	12	.	0			c.T672C						PASS	.	A		164,4242	86.8+/-125.4	2,160,2041	41.0	49.0	46.0		672	2.8	0.2	7	dbSNP_132	46	314,8286	95.4+/-157.2	8,298,3994	no	coding-synonymous	DNAJC30	NM_032317.2		10,458,6035	GG,GA,AA		3.6512,3.7222,3.6752		224/227	73097082	478,12528	2203	4300	6503	SO:0001819	synonymous_variant	84277	exon1			AATATAAAAGCCG	AF412025	CCDS5556.1	7q11.23	2011-09-02	2008-06-17	2008-06-17	ENSG00000176410	ENSG00000176410		"""Heat shock proteins / DNAJ (HSP40)"""	16410	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 18"""	WBSCR18		12073013	Standard	NM_032317		Approved		uc003tys.1	Q96LL9	OTTHUMG00000023290	ENST00000395176.2:c.672T>C	7.37:g.73097082A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_032317	Q9BSG8	Silent	SNP	ENST00000395176.2	37	CCDS5556.1																																																																																			A|0.966;G|0.034	0.034	strong		0.512	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2		
STRAP	11171	hgsc.bcm.edu	37	12	16042908	16042908	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:16042908C>T	ENST00000419869.2	+	3	608	c.295C>T	c.(295-297)Cat>Tat	p.H99Y	STRAP_ENST00000538352.1_Missense_Mutation_p.H5Y|STRAP_ENST00000025399.6_Missense_Mutation_p.H112Y	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	99					maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|spliceosomal snRNP assembly (GO:0000387)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	15		Hepatocellular(102;0.121)				GACCCTGGCTCATAAACACAT	0.338																																					p.H99Y		Atlas-SNP	.											.	STRAP	33	.	0			c.C295T						PASS	.						112.0	105.0	107.0					12																	16042908		2203	4300	6503	SO:0001583	missense	11171	exon3			CTGGCTCATAAAC	AB024327	CCDS8676.1	12p13.1	2013-01-10			ENSG00000023734	ENSG00000023734		"""WD repeat domain containing"""	30796	protein-coding gene	gene with protein product	"""Unr-interacting protein"""	605986					Standard	NM_007178		Approved	UNRIP, pt-wd, MAWD	uc001rdc.4	Q9Y3F4	OTTHUMG00000168791	ENST00000419869.2:c.295C>T	12.37:g.16042908C>T	ENSP00000392270:p.His99Tyr	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	325	45	0.138462	NM_007178	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Missense_Mutation	SNP	ENST00000419869.2	37	CCDS8676.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221170	0.79464	.	.	ENSG00000023734	ENST00000538352;ENST00000025399;ENST00000419869	T;T;T	0.81415	-1.49;-1.49;-1.49	4.69	3.78	0.43462	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.047356	0.85682	D	0.000000	D	0.91429	0.7295	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93213	0.6602	10	0.87932	D	0	-16.9887	14.0735	0.64874	0.1519:0.8481:0.0:0.0	.	112;99	B4DNJ6;Q9Y3F4	.;STRAP_HUMAN	Y	5;112;99	ENSP00000439761:H5Y;ENSP00000025399:H112Y;ENSP00000392270:H99Y	ENSP00000025399:H112Y	H	+	1	0	STRAP	15934175	1.000000	0.71417	0.965000	0.40720	0.996000	0.88848	5.453000	0.66645	1.143000	0.42306	0.655000	0.94253	CAT	.	.	none		0.338	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178	
SLC4A8	9498	hgsc.bcm.edu	37	12	51856159	51856159	+	Silent	SNP	C	C	T	rs71449805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51856159C>T	ENST00000453097.2	+	10	1384	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SLC4A8_ENST00000514353.3_Silent_p.F336F|SLC4A8_ENST00000358657.3_Silent_p.F416F|SLC4A8_ENST00000535225.2_Silent_p.F336F|SLC4A8_ENST00000394856.1_Silent_p.F336F	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TTGATGAGTTCCTAGACCAGG	0.473													C|||	48	0.00958466	0.0015	0.0187	5008	,	,		18122	0.0		0.0278	False		,,,				2504	0.0051				p.F389F		Atlas-SNP	.											.	SLC4A8	292	.	0			c.C1167T						PASS	.	C	,	36,4370	41.6+/-74.8	0,36,2167	123.0	118.0	120.0		1167,1167	4.3	1.0	12	dbSNP_130	120	351,8249	118.5+/-177.9	5,341,3954	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	5,377,6121	TT,TC,CC		4.0814,0.8171,2.9755	,	389/1094,389/1045	51856159	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon10			TGAGTTCCTAGAC	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1167C>T	12.37:g.51856159C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
SLC12A5	57468	hgsc.bcm.edu	37	20	44680493	44680493	+	Silent	SNP	G	G	A	rs17344810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:44680493G>A	ENST00000454036.2	+	18	2479	c.2430G>A	c.(2428-2430)acG>acA	p.T810T	SLC12A5_ENST00000243964.3_Silent_p.T787T	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	810					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	ATCATCAGACGTGGAGGAACT	0.617													G|||	461	0.0920527	0.0688	0.0634	5008	,	,		11640	0.0149		0.1183	False		,,,				2504	0.1963				p.T810T		Atlas-SNP	.											.	SLC12A5	181	.	0			c.G2430A						PASS	.	G	,	382,4024	191.6+/-217.2	21,340,1842	45.0	48.0	47.0		2430,2361	-6.7	1.0	20	dbSNP_123	47	960,7640	204.9+/-247.5	48,864,3388	no	coding-synonymous,coding-synonymous	SLC12A5	NM_001134771.1,NM_020708.4	,	69,1204,5230	AA,AG,GG		11.1628,8.67,10.3183	,	810/1140,787/1117	44680493	1342,11664	2203	4300	6503	SO:0001819	synonymous_variant	57468	exon18			TCAGACGTGGAGG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.2430G>A	20.37:g.44680493G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	37	CCDS46610.1																																																																																			G|0.909;A|0.091	0.091	strong		0.617	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
KIF1C	10749	hgsc.bcm.edu	37	17	4926882	4926882	+	Silent	SNP	A	A	G	rs346828	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4926882A>G	ENST00000320785.5	+	23	3105	c.2748A>G	c.(2746-2748)ccA>ccG	p.P916P		NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	916					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						CCCCCTCGCCACCACTGTCAA	0.677													A|||	3381	0.67512	0.5204	0.7392	5008	,	,		12936	0.6627		0.7107	False		,,,				2504	0.8149				p.P916P	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											KIF1C,NS,carcinoma,0,1	KIF1C	70	1	0			c.A2748G						scavenged	.	A		2475,1923		723,1029,447	30.0	29.0	29.0		2748	-9.8	0.2	17	dbSNP_79	29	6147,2433		2260,1627,403	no	coding-synonymous	KIF1C	NM_006612.5		2983,2656,850	GG,GA,AA		28.3566,43.7244,33.5645		916/1104	4926882	8622,4356	2199	4290	6489	SO:0001819	synonymous_variant	10749	exon23			CTCGCCACCACTG	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.2748A>G	17.37:g.4926882A>G		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	143	61	0.426573	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			A|0.339;G|0.661	0.661	strong		0.677	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
MYH15	22989	hgsc.bcm.edu	37	3	108189627	108189627	+	Missense_Mutation	SNP	C	C	T	rs4299484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108189627C>T	ENST00000273353.3	-	14	1417	c.1361G>A	c.(1360-1362)cGg>cAg	p.R454Q		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	454	Myosin motor.		R -> Q (in dbSNP:rs4299484).			cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R454Q(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CCTGTTGATCCGTGCCACTAG	0.458													C|||	505	0.100839	0.0098	0.1873	5008	,	,		14327	0.0		0.2932	False		,,,				2504	0.0685				p.R454Q		Atlas-SNP	.											MYH15,NS,carcinoma,0,1	MYH15	223	1	1	Substitution - Missense(1)	prostate(1)	c.G1361A						PASS	.	C	GLN/ARG	222,3770		8,206,1782	94.0	89.0	90.0		1361	2.6	0.0	3	dbSNP_111	90	2495,5801		374,1747,2027	yes	missense	MYH15	NM_014981.1	43	382,1953,3809	TT,TC,CC		30.0747,5.5611,22.111	probably-damaging	454/1947	108189627	2717,9571	1996	4148	6144	SO:0001583	missense	22989	exon14			TTGATCCGTGCCA	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1361G>A	3.37:g.108189627C>T	ENSP00000273353:p.Arg454Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	71	0.563492	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	318	0.14560439560439561	10	0.02032520325203252	79	0.21823204419889503	0	0.0	229	0.3021108179419525	C	23.4	4.411069	0.83340	0.055611	0.300747	ENSG00000144821	ENST00000273353	D	0.88431	-2.38	5.77	2.58	0.30949	Myosin head, motor domain (2);	.	.	.	.	T	0.00039	0.0001	M	0.88181	2.935	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00015	-1.2392	8	0.87932	D	0	.	7.0191	0.24904	0.1319:0.6992:0.0:0.1689	rs4299484;rs17538845;rs52826675;rs56656800;rs4299484	454	Q9Y2K3	MYH15_HUMAN	Q	454	ENSP00000273353:R454Q	ENSP00000273353:R454Q	R	-	2	0	MYH15	109672317	0.000000	0.05858	0.001000	0.08648	0.977000	0.68977	0.405000	0.21015	0.557000	0.29117	0.650000	0.86243	CGG	C|0.833;T|0.167	0.167	strong		0.458	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
FAM166B	730112	hgsc.bcm.edu	37	9	35563361	35563361	+	Missense_Mutation	SNP	G	G	A	rs75679360	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35563361G>A	ENST00000399742.2	-	2	158	c.88C>T	c.(88-90)Cgg>Tgg	p.R30W	FAM166B_ENST00000492890.1_Intron	NM_001099951.2|NM_001164310.1	NP_001093421.1|NP_001157782.1	A8MTA8	F166B_HUMAN	family with sequence similarity 166, member B	30										kidney(3)|large_intestine(1)|lung(4)|ovary(1)	9						ACGCTGAACCGAAGTAGTGGG	0.637													G|||	167	0.0333466	0.0424	0.0144	5008	,	,		17983	0.003		0.0616	False		,,,				2504	0.0368				p.R30W		Atlas-SNP	.											.	FAM166B	19	.	0			c.C88T						PASS	.	G	TRP/ARG,TRP/ARG	145,4119		2,141,1989	28.0	34.0	32.0		88,88	3.8	1.0	9	dbSNP_131	32	416,8064		7,402,3831	yes	missense,missense	FAM166B	NM_001099951.2,NM_001164310.1	101,101	9,543,5820	AA,AG,GG		4.9057,3.4006,4.4021	possibly-damaging,possibly-damaging	30/217,30/276	35563361	561,12183	2132	4240	6372	SO:0001583	missense	730112	exon2			TGAACCGAAGTAG	BC129999	CCDS47963.1, CCDS56572.1	9p13.3	2008-06-10			ENSG00000215187	ENSG00000215187			34242	protein-coding gene	gene with protein product							Standard	NM_001099951		Approved		uc010mkr.3	A8MTA8	OTTHUMG00000019858	ENST00000399742.2:c.88C>T	9.37:g.35563361G>A	ENSP00000382646:p.Arg30Trp	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_001099951	A1L3B2|B7ZBJ0	Missense_Mutation	SNP	ENST00000399742.2	37	CCDS56572.1	75	0.034340659340659344	16	0.032520325203252036	3	0.008287292817679558	3	0.005244755244755245	53	0.06992084432717678	G	19.57	3.852417	0.71719	0.034006	0.049057	ENSG00000215187	ENST00000399742;ENST00000537504	T	0.48201	0.82	5.76	3.77	0.43336	.	0.238348	0.18353	U	0.143808	T	0.10809	0.0264	M	0.71036	2.16	0.35253	D	0.778862	D;D;D;D	0.76494	0.999;0.999;0.998;0.999	P;P;P;P	0.60886	0.88;0.88;0.861;0.862	T	0.53788	-0.8389	9	.	.	.	-16.4912	9.9346	0.41543	0.0:0.16:0.6944:0.1455	.	30;30;30;30	B7ZW33;B7ZW26;A8MTA8;A8MTA8-2	.;.;F166B_HUMAN;.	W	30	ENSP00000382646:R30W	.	R	-	1	2	FAM166B	35553361	0.999000	0.42202	1.000000	0.80357	0.969000	0.65631	1.531000	0.36018	1.393000	0.46605	0.561000	0.74099	CGG	G|0.963;A|0.037	0.037	strong		0.637	FAM166B-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336563.1	NM_001099951	
PSTPIP2	9050	hgsc.bcm.edu	37	18	43573649	43573649	+	Silent	SNP	A	A	G	rs116067668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:43573649A>G	ENST00000409746.5	-	10	734	c.663T>C	c.(661-663)tgT>tgC	p.C221C	PSTPIP2_ENST00000589328.1_Silent_p.C221C|PSTPIP2_ENST00000588801.1_Intron	NM_024430.3	NP_077748.3	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting protein 2	221						cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)				endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	17						TTATTCGTTCACATTCTTGAG	0.408													A|||	202	0.0403355	0.0189	0.0159	5008	,	,		22713	0.0198		0.0318	False		,,,				2504	0.1166				p.C221C		Atlas-SNP	.											.	PSTPIP2	65	.	0			c.T663C						PASS	.	A		82,4324	70.3+/-108.2	1,80,2122	148.0	115.0	126.0		663	4.3	1.0	18	dbSNP_132	126	219,8381	91.1+/-153.3	2,215,4083	no	coding-synonymous	PSTPIP2	NM_024430.3		3,295,6205	GG,GA,AA		2.5465,1.8611,2.3143		221/335	43573649	301,12705	2203	4300	6503	SO:0001819	synonymous_variant	9050	exon10			TCGTTCACATTCT		CCDS32820.2	18q12	2008-07-28			ENSG00000152229	ENSG00000152229			9581	protein-coding gene	gene with protein product						9804817	Standard	NM_024430		Approved		uc002lbp.4	Q9H939	OTTHUMG00000152674	ENST00000409746.5:c.663T>C	18.37:g.43573649A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	143	49	0.342657	NM_024430		Silent	SNP	ENST00000409746.5	37	CCDS32820.2																																																																																			A|0.976;G|0.024	0.024	strong		0.408	PSTPIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327522.1		
ULK1	8408	hgsc.bcm.edu	37	12	132396603	132396603	+	Silent	SNP	C	C	T	rs11616018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:132396603C>T	ENST00000321867.4	+	13	1416	c.1065C>T	c.(1063-1065)gaC>gaT	p.D355D		NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	355	Interaction with GABARAP and GABARAPL2.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		GTGACACAGACGACTTCGTCA	0.647													C|||	2763	0.551717	0.298	0.7363	5008	,	,		18650	0.3343		0.829	False		,,,				2504	0.7025				p.D355D		Atlas-SNP	.											ULK1,NS,carcinoma,0,1	ULK1	92	1	0			c.C1065T						PASS	.	C		1626,2774	488.0+/-361.1	308,1010,882	49.0	39.0	42.0		1065	-6.5	0.2	12	dbSNP_120	42	7075,1521	739.0+/-407.1	2927,1221,150	no	coding-synonymous	ULK1	NM_003565.2		3235,2231,1032	TT,TC,CC		17.6943,36.9545,33.0486		355/1051	132396603	8701,4295	2200	4298	6498	SO:0001819	synonymous_variant	8408	exon13			CACAGACGACTTC	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.1065C>T	12.37:g.132396603C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			C|0.397;T|0.603	0.603	strong		0.647	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
DLC1	10395	hgsc.bcm.edu	37	8	12958145	12958145	+	Silent	SNP	T	T	G	rs61757612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:12958145T>G	ENST00000276297.4	-	9	2110	c.1701A>C	c.(1699-1701)ccA>ccC	p.P567P	DLC1_ENST00000512044.2_Silent_p.P164P|DLC1_ENST00000520226.1_Silent_p.P56P|DLC1_ENST00000358919.2_Silent_p.P130P	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	567					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GGGAGTCGTCTGGGGACCCAG	0.607													T|||	84	0.0167732	0.0061	0.0144	5008	,	,		14689	0.001		0.0586	False		,,,				2504	0.0061				p.P567P		Atlas-SNP	.											.	DLC1	411	.	0			c.A1701C						PASS	.	T	,,	44,4362	45.3+/-79.5	0,44,2159	36.0	41.0	39.0		168,390,1701	-4.4	0.8	8	dbSNP_129	39	413,8187	125.0+/-183.6	13,387,3900	no	coding-synonymous,coding-synonymous,coding-synonymous	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	,,	13,431,6059	GG,GT,TT		4.8023,0.9986,3.5138	,,	56/1018,130/1092,567/1529	12958145	457,12549	2203	4300	6503	SO:0001819	synonymous_variant	10395	exon9			GTCGTCTGGGGAC	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1701A>C	8.37:g.12958145T>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1	54	0.024725274725274724	4	0.008130081300813009	7	0.019337016574585635	0	0.0	43	0.05672823218997362	T	3.617	-0.078362	0.07184	0.009986	0.048023	ENSG00000164741	ENST00000503161	.	.	.	5.22	-4.36	0.03645	.	.	.	.	.	T	0.09379	0.0231	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32025	-0.9922	4	.	.	.	.	7.0159	0.24887	0.0:0.1819:0.3865:0.4317	rs61757612	.	.	.	P	39	.	.	Q	-	2	0	DLC1	13002516	0.007000	0.16637	0.829000	0.32907	0.208000	0.24298	-0.369000	0.07533	-0.819000	0.04323	-0.912000	0.02778	CAG	T|0.969;G|0.031	0.031	strong		0.607	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
SSPO	23145	hgsc.bcm.edu	37	7	149484798	149484798	+	RNA	SNP	C	C	T	rs62490656	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149484798C>T	ENST00000378016.2	+	0	3620							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CGCTGTGGGGCGCTGCTGCAG	0.667													C|||	832	0.166134	0.0234	0.2147	5008	,	,		16879	0.1518		0.2495	False		,,,				2504	0.2536				p.A1207V		Atlas-SNP	.											.	.	.	.	0			c.C3620T						PASS	.	C		177,3887		1,175,1856	7.0	10.0	9.0		3624	-2.7	0.0	7	dbSNP_129	9	1883,6435		211,1461,2487	no	coding-notMod3	SSPO	NM_198455.2		212,1636,4343	TT,TC,CC		22.6377,4.3553,16.6371			149484798	2060,10322	2032	4159	6191			23145	exon25			GTGGGGCGCTGCT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149484798C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	38	23	0.605263	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.826;T|0.174	0.174	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
MYLK	4638	hgsc.bcm.edu	37	3	123452838	123452838	+	Silent	SNP	G	G	A	rs4678047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:123452838G>A	ENST00000475616.1	-	7	1004	c.1005C>T	c.(1003-1005)acC>acT	p.T335T	MYLK_ENST00000346322.5_Silent_p.T335T|MYLK_ENST00000360304.3_Silent_p.T335T|MYLK_ENST00000359169.1_Silent_p.T335T|MYLK_ENST00000360772.3_Silent_p.T335T			Q15746	MYLK_HUMAN	myosin light chain kinase	335					actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		GAAGGACCGGGGTCTGCGGGG	0.642													G|||	3169	0.632788	0.3623	0.7262	5008	,	,		15445	0.9375		0.6491	False		,,,				2504	0.6012				p.T335T		Atlas-SNP	.											.	MYLK	224	.	0			c.C1005T						PASS	.	G	,,,	1727,2679	507.6+/-366.7	336,1055,812	54.0	59.0	57.0		1005,1005,1005,1005	0.3	0.0	3	dbSNP_111	57	5743,2857	663.9+/-402.1	1923,1897,480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	2259,2952,1292	AA,AG,GG		33.2209,39.1966,42.565	,,,	335/1915,335/1846,335/1864,335/1795	123452838	7470,5536	2203	4300	6503	SO:0001819	synonymous_variant	4638	exon10			GACCGGGGTCTGC	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.1005C>T	3.37:g.123452838G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	37	CCDS46896.1																																																																																			A|0.608;G|0.392	0.608	strong		0.642	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
BPIFB2	80341	hgsc.bcm.edu	37	20	31596472	31596472	+	Missense_Mutation	SNP	A	A	T	rs6088066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:31596472A>T	ENST00000170150.3	+	2	287	c.92A>T	c.(91-93)aAg>aTg	p.K31M		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	31			K -> M (in dbSNP:rs6088066).			extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CGACTCAACAAGGCAGCATTG	0.602													A|||	685	0.136781	0.1641	0.1527	5008	,	,		20203	0.0089		0.2406	False		,,,				2504	0.1135				p.K31M		Atlas-SNP	.											.	.	.	.	0			c.A92T						PASS	.	A	MET/LYS	801,3605	297.3+/-284.7	74,653,1476	67.0	54.0	58.0		92	-0.2	0.2	20	dbSNP_114	58	1920,6678	305.7+/-307.6	206,1508,2585	yes	missense	BPIFB2	NM_025227.1	95	280,2161,4061	TT,TA,AA		22.3308,18.1798,20.9243	possibly-damaging	31/459	31596472	2721,10283	2203	4299	6502	SO:0001583	missense	80341	exon2			TCAACAAGGCAGC	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.92A>T	20.37:g.31596472A>T	ENSP00000170150:p.Lys31Met	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	37	CCDS13210.1	336	0.15384615384615385	87	0.17682926829268292	66	0.18232044198895028	3	0.005244755244755245	180	0.23746701846965698	A	17.05	3.290903	0.59976	0.181798	0.223308	ENSG00000078898	ENST00000170150	T	0.05447	3.44	5.17	-0.229	0.13094	.	1.213840	0.05841	N	0.619432	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.26002	0.139	B	0.19946	0.027	T	0.48445	-0.9035	9	0.31617	T	0.26	-0.6592	3.7776	0.08667	0.5174:0.0:0.3235:0.1591	rs6088066;rs17372659;rs52836575;rs6088066	31	Q8N4F0	BPIB2_HUMAN	M	31	ENSP00000170150:K31M	ENSP00000170150:K31M	K	+	2	0	BPIFB2	31060133	0.259000	0.24043	0.152000	0.22495	0.471000	0.32888	0.371000	0.20450	-0.154000	0.11118	0.528000	0.53228	AAG	A|0.820;T|0.180	0.180	strong		0.602	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
HLA-A	3105	hgsc.bcm.edu	37	6	29911272	29911272	+	Missense_Mutation	SNP	T	T	G	rs76185201	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29911272T>G	ENST00000396634.1	+	5	912	c.571T>G	c.(571-573)Tgg>Ggg	p.W191G	HLA-A_ENST00000376806.5_Missense_Mutation_p.W191G|HLA-A_ENST00000376809.5_Missense_Mutation_p.W191G|HLA-A_ENST00000376802.2_Missense_Mutation_p.W191G			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	191	Alpha-2.		EW -> DG (in allele A*31:05).		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GTGCGTGGAGTGGCTCCGCAG	0.677									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	1062	0.212061	0.1672	0.2075	5008	,	,		13907	0.2173		0.2058	False		,,,				2504	0.2771				p.W191G		Atlas-SNP	.											HLA-A,colon,carcinoma,0,1	HLA-A	89	1	0			c.T571G						scavenged	.						49.0	39.0	43.0					6																	29911272		1510	2705	4215	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTGGAGTGGCTCC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.571T>G	6.37:g.29911272T>G	ENSP00000379873:p.Trp191Gly	Somatic	252	2	0.00793651		WXS	Illumina HiSeq	Phase_I	370	77	0.208108	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	418	0.19139194139194138	56	0.11382113821138211	77	0.212707182320442	139	0.243006993006993	146	0.19261213720316622	.	8.499	0.863893	0.17250	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00014	9.21;9.21;9.21;9.21	3.78	-2.67	0.06059	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	2.778300	0.01729	U	0.028724	T	0.00039	0.0001	M	0.83483	2.645	0.80722	P	0.0	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.001;0.0;0.001;0.001	T	0.37979	-0.9682	9	0.59425	D	0.04	.	4.7021	0.12832	0.0:0.188:0.3051:0.5069	rs3098019;rs9260161;rs41558617;rs52818888	70;191;191;191;191;191;191	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	G	191	ENSP00000379873:W191G;ENSP00000366002:W191G;ENSP00000366005:W191G;ENSP00000365998:W191G	ENSP00000365998:W191G	W	+	1	0	HLA-A	30019251	0.737000	0.28175	0.000000	0.03702	0.112000	0.19704	0.741000	0.26202	-0.555000	0.06142	0.397000	0.26171	TGG	A|0.001;G|0.178;T|0.821	0.178	strong		0.677	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
IKBIP	121457	hgsc.bcm.edu	37	12	99007623	99007623	+	Missense_Mutation	SNP	C	C	T	rs1048906	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:99007623C>T	ENST00000342502.2	-	3	1204	c.793G>A	c.(793-795)Ggt>Agt	p.G265S	IKBIP_ENST00000420861.1_Missense_Mutation_p.G159S|IKBIP_ENST00000393042.3_3'UTR	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	265			G -> S (in dbSNP:rs1048906).		response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						GCTCTGTCACCTTCTAAGCTT	0.358													T|||	1956	0.390575	0.5295	0.3329	5008	,	,		19240	0.3492		0.2982	False		,,,				2504	0.3814				p.G265S		Atlas-SNP	.											.	IKBIP	46	.	0			c.G793A						PASS	.	T	SER/GLY,	2199,2205	588.1+/-386.8	566,1067,569	127.0	131.0	129.0		793,	1.9	1.0	12	dbSNP_86	129	2699,5899	681.8+/-403.7	424,1851,2024	yes	missense,utr-3	IKBIP	NM_201612.1,NM_201613.1	56,	990,2918,2593	TT,TC,CC		31.391,49.9319,37.6711	,	265/351,	99007623	4898,8104	2202	4299	6501	SO:0001583	missense	121457	exon3			TGTCACCTTCTAA	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"""I kappa B kinase interacting protein"""	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.793G>A	12.37:g.99007623C>T	ENSP00000343471:p.Gly265Ser	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	193	87	0.450777	NM_201612	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Missense_Mutation	SNP	ENST00000342502.2	37	CCDS9067.1	779	0.3566849816849817	243	0.49390243902439024	120	0.3314917127071823	187	0.3269230769230769	229	0.3021108179419525	T	1.750	-0.489406	0.04352	0.499319	0.31391	ENSG00000166130	ENST00000342502;ENST00000420861	T;T	0.38077	1.16;1.3	5.54	1.86	0.25419	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.50632	P	1.1099999999997223E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.47837	-0.9086	8	0.02654	T	1	.	9.8834	0.41247	0.0:0.3942:0.0:0.6058	rs1048906;rs3168530;rs17846476;rs17859535;rs59586369;rs1048906	265	Q70UQ0	IKIP_HUMAN	S	265;159	ENSP00000343471:G265S;ENSP00000398023:G159S	ENSP00000343471:G265S	G	-	1	0	IKBIP	97531754	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	1.688000	0.37690	0.061000	0.16311	-1.213000	0.01624	GGT	C|0.625;T|0.374	0.374	strong		0.358	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687	
EPHA2	1969	hgsc.bcm.edu	37	1	16451767	16451767	+	Silent	SNP	G	G	A	rs3754334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16451767G>A	ENST00000358432.5	-	17	3028	c.2874C>T	c.(2872-2874)atC>atT	p.I958I		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	958	Negatively regulates interaction with ARHGEF16.|SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	GGCTGTAGGCGATGCGCTTCT	0.642													G|||	1185	0.236621	0.1135	0.3141	5008	,	,		12121	0.1548		0.3161	False		,,,				2504	0.3507				p.I958I		Atlas-SNP	.											.	EPHA2	102	.	0			c.C2874T						PASS	.	G		545,3861	244.3+/-253.7	32,481,1690	61.0	47.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2874	-6.9	0.8	1	dbSNP_107	52	2419,6181	396.7+/-345.5	344,1731,2225	yes	coding-synonymous	EPHA2	NM_004431.3		376,2212,3915	AA,AG,GG		28.1279,12.3695,22.7895		958/977	16451767	2964,10042	2203	4300	6503	SO:0001819	synonymous_variant	1969	exon17			GTAGGCGATGCGC	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.2874C>T	1.37:g.16451767G>A		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	301	109	0.362126	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			G|0.777;A|0.223	0.223	strong		0.642	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
ZNF208	7757	hgsc.bcm.edu	37	19	22155918	22155918	+	Missense_Mutation	SNP	T	T	C	rs10425763	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:22155918T>C	ENST00000397126.4	-	4	2066	c.1918A>G	c.(1918-1920)Aaa>Gaa	p.K640E	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	640			K -> E (in dbSNP:rs10425763).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				CCACATTCTTTACATTTGTAG	0.403													t|||	1741	0.347644	0.2685	0.4078	5008	,	,		21273	0.504		0.4602	False		,,,				2504	0.135				p.K640E		Atlas-SNP	.											.	ZNF208	817	.	0			c.A1918G						PASS	.	T	GLU/LYS	1226,3030		180,866,1082	93.0	97.0	96.0		1918	-5.0	0.0	19	dbSNP_119	96	3592,4920		757,2078,1421	no	missense	ZNF208	NM_007153.3	56	937,2944,2503	CC,CT,TT		42.1992,28.8064,37.735	benign	640/1281	22155918	4818,7950	2128	4256	6384	SO:0001583	missense	7757	exon4			ATTCTTTACATTT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1918A>G	19.37:g.22155918T>C	ENSP00000380315:p.Lys640Glu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	905	0.4143772893772894	127	0.258130081300813	137	0.3784530386740331	288	0.5034965034965035	353	0.4656992084432718	T	0.043	-1.277267	0.01410	0.288064	0.421992	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.18810	2.19	2.49	-4.98	0.03019	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.22983	0.078	B	0.23716	0.048	T	0.39781	-0.9597	7	0.02654	T	1	.	2.1959	0.03911	0.1165:0.1577:0.1996:0.5263	rs10425763	540	O43345	ZN208_HUMAN	E	640;540	ENSP00000380315:K640E	ENSP00000380315:K640E	K	-	1	0	ZNF208	21947758	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	-4.448000	0.00232	-2.224000	0.00725	-1.193000	0.01689	AAA	T|0.500;C|0.500	0.500	strong		0.403	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
COL6A5	256076	hgsc.bcm.edu	37	3	130124989	130124989	+	Silent	SNP	C	C	T	rs4688761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130124989C>T	ENST00000432398.2	+	16	4889	c.4395C>T	c.(4393-4395)gaC>gaT	p.D1465D	COL6A5_ENST00000265379.6_Silent_p.D1465D	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1465	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GTCATGGAGACGATGGGATTG	0.403													C|||	2048	0.408946	0.2867	0.4625	5008	,	,		18935	0.1796		0.7256	False		,,,				2504	0.4468				p.D1465D		Atlas-SNP	.											.	COL6A5	205	.	0			c.C4395T						PASS	.	C		506,878		95,316,281	156.0	125.0	134.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4395	-11.7	0.0	3	dbSNP_111	134	2259,923		807,645,139	no	coding-synonymous	COL6A5	NM_153264.5		902,961,420	TT,TC,CC		29.0069,36.5607,39.4437		1465/2527	130124989	2765,1801	692	1591	2283	SO:0001819	synonymous_variant	256076	exon16			TGGAGACGATGGG	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.4395C>T	3.37:g.130124989C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				C|0.577;T|0.423	0.423	strong		0.403	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
CR2	1380	hgsc.bcm.edu	37	1	207646898	207646898	+	Intron	SNP	T	T	C	rs4308977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207646898T>C	ENST00000367058.3	+	11	2167				CR2_ENST00000367057.3_Missense_Mutation_p.S663P|CR2_ENST00000367059.3_Intron|CR2_ENST00000458541.2_Intron	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2						B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						AGGCTGCCAGTCACCTCCTGG	0.458													C|||	1450	0.289537	0.5356	0.2089	5008	,	,		20506	0.1091		0.2913	False		,,,				2504	0.1984				p.S663P		Atlas-SNP	.											.	CR2	164	.	0			c.T1987C						PASS	.	C	PRO/SER,	2188,2218	590.7+/-387.4	541,1106,556	109.0	112.0	111.0		1987,	1.2	0.0	1	dbSNP_111	111	2716,5884	682.0+/-403.8	426,1864,2010	yes	missense,intron	CR2	NM_001006658.2,NM_001877.4	74,	967,2970,2566	CC,CT,TT		31.5814,49.6596,37.7057	,	663/1093,	207646898	4904,8102	2203	4300	6503	SO:0001627	intron_variant	1380	exon11			TGCCAGTCACCTC	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1979-248T>C	1.37:g.207646898T>C		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	216	216	1	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	649	0.29716117216117216	265	0.5386178861788617	94	0.2596685082872928	65	0.11363636363636363	225	0.29683377308707126	C	0.854	-0.737638	0.03111	0.496596	0.315814	ENSG00000117322	ENST00000367057	T	0.63096	-0.02	4.58	1.19	0.21007	.	.	.	.	.	T	0.00012	0.0000	N	0.00656	-1.285	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47341	-0.9125	8	0.24483	T	0.36	.	7.633	0.28251	0.0:0.4107:0.4919:0.0974	rs4308977;rs52823425;rs59151132;rs4308977	663	P20023-3	.	P	663	ENSP00000356024:S663P	ENSP00000356024:S663P	S	+	1	0	CR2	205713521	0.197000	0.23362	0.011000	0.14972	0.471000	0.32888	-0.081000	0.11321	0.087000	0.17167	-0.119000	0.15052	TCA	T|0.664;C|0.336	0.336	strong		0.458	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
CNTN1	1272	hgsc.bcm.edu	37	12	41312471	41312471	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:41312471T>C	ENST00000551295.2	+	4	242	c.125T>C	c.(124-126)aTt>aCt	p.I42T	CNTN1_ENST00000348761.2_Missense_Mutation_p.I31T|CNTN1_ENST00000547702.1_Missense_Mutation_p.I42T|CNTN1_ENST00000547849.1_Missense_Mutation_p.I42T|CNTN1_ENST00000347616.1_Missense_Mutation_p.I42T|CNTN1_ENST00000360099.3_Missense_Mutation_p.I42T	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	42	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TTTGGACCAATTTTTGAAGAG	0.378																																					p.I42T		Atlas-SNP	.											.	CNTN1	207	.	0			c.T125C						PASS	.						73.0	79.0	77.0					12																	41312471		2203	4300	6503	SO:0001583	missense	1272	exon4			GACCAATTTTTGA	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.125T>C	12.37:g.41312471T>C	ENSP00000447006:p.Ile42Thr	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	205	34	0.165854	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.707931	0.89018	.	.	ENSG00000018236	ENST00000547702;ENST00000551424;ENST00000551295;ENST00000548005;ENST00000552248;ENST00000547849;ENST00000552913;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T;T;T	0.65178	-0.14;0.25;1.05;1.05;-0.14;0.25;-0.14;0.18	5.36	5.36	0.76844	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.059649	0.64402	D	0.000003	T	0.63331	0.2502	N	0.25957	0.775	0.41091	D	0.985594	P;P;P	0.50156	0.9;0.917;0.932	B;P;P	0.57009	0.39;0.637;0.811	T	0.60576	-0.7236	10	0.25106	T	0.35	.	15.6713	0.77279	0.0:0.0:0.0:1.0	.	42;31;42	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	T	42;42;42;42;42;42;42;42;42;31	ENSP00000448004:I42T;ENSP00000447006:I42T;ENSP00000447862:I42T;ENSP00000447860:I42T;ENSP00000448653:I42T;ENSP00000325660:I42T;ENSP00000353213:I42T;ENSP00000261160:I31T	ENSP00000325660:I42T	I	+	2	0	CNTN1	39598738	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.314000	0.78988	2.167000	0.68274	0.477000	0.44152	ATT	.	.	none		0.378	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843	
FGA	2243	hgsc.bcm.edu	37	4	155507225	155507225	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155507225A>G	ENST00000302053.3	-	5	1434	c.1356T>C	c.(1354-1356)ggT>ggC	p.G452G	FGA_ENST00000403106.3_Silent_p.G452G	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	452					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	TGGTTGTGCTACCAGAGGTGA	0.463																																					p.G452G	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											FGA,NS,carcinoma,-1,1	FGA	179	1	0			c.T1356C						scavenged	.						218.0	226.0	223.0					4																	155507225		2203	4300	6503	SO:0001819	synonymous_variant	2243	exon5			TGTGCTACCAGAG		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1356T>C	4.37:g.155507225A>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	257	3	0.0116732	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Silent	SNP	ENST00000302053.3	37	CCDS3787.1																																																																																			.	.	none		0.463	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
KPRP	448834	hgsc.bcm.edu	37	1	152732436	152732436	+	Silent	SNP	G	G	C	rs4845480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152732436G>C	ENST00000606109.1	+	1	400	c.372G>C	c.(370-372)gcG>gcC	p.A124A	KPRP_ENST00000368773.1_Silent_p.A124A			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	124	Gln-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTGCGAAGCGTCACAACCTG	0.502													C|||	2456	0.490415	0.5787	0.4914	5008	,	,		23278	0.4187		0.5159	False		,,,				2504	0.4182				p.A124A		Atlas-SNP	.											KPRP,NS,carcinoma,+1,1	KPRP	152	1	0			c.G372C						PASS	.	C		2439,1967	554.9+/-379.1	676,1087,440	259.0	245.0	250.0		372	-0.8	0.0	1	dbSNP_111	250	4322,4278	575.7+/-390.3	1096,2130,1074	no	coding-synonymous	KPRP	NM_001025231.1		1772,3217,1514	CC,CG,GG		49.7442,44.6437,48.0163		124/580	152732436	6761,6245	2203	4300	6503	SO:0001819	synonymous_variant	448834	exon2			CGAAGCGTCACAA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.372G>C	1.37:g.152732436G>C		Somatic	286	1	0.0034965		WXS	Illumina HiSeq	Phase_I	312	312	1	NM_001025231		Silent	SNP	ENST00000606109.1	37	CCDS30862.1																																																																																			G|0.490;C|0.510	0.510	strong		0.502	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
MUC16	94025	hgsc.bcm.edu	37	19	9057721	9057721	+	Missense_Mutation	SNP	C	C	T	rs2216662	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9057721C>T	ENST00000397910.4	-	3	29928	c.29725G>A	c.(29725-29727)Gtc>Atc	p.V9909I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9911	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCATGGAGACTTCAGTAGTA	0.473													C|||	2214	0.442093	0.2852	0.4856	5008	,	,		21011	0.5635		0.4732	False		,,,				2504	0.4663				p.V9909I		Atlas-SNP	.											.	MUC16	4315	.	0			c.G29725A						PASS	.	C	ILE/VAL	1183,2755		177,829,963	163.0	154.0	157.0		29725	-4.8	0.0	19	dbSNP_96	157	3906,4392		938,2030,1181	yes	missense	MUC16	NM_024690.2	29	1115,2859,2144	TT,TC,CC		47.0716,30.0406,41.5904	benign	9909/14508	9057721	5089,7147	1969	4149	6118	SO:0001583	missense	94025	exon3			TGGAGACTTCAGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29725G>A	19.37:g.9057721C>T	ENSP00000381008:p.Val9909Ile	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	252	249	0.988095	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	1006	0.4606227106227106	148	0.3008130081300813	179	0.494475138121547	324	0.5664335664335665	355	0.4683377308707124	c	5.518	0.280553	0.10458	0.300406	0.470716	ENSG00000181143	ENST00000397910	T	0.02421	4.3	2.42	-4.85	0.03142	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	.	.	.	B	0.20988	0.05	B	0.15870	0.014	T	0.39440	-0.9614	8	0.87932	D	0	.	0.3447	0.00339	0.2945:0.1667:0.2933:0.2456	rs2216662;rs56626879;rs2216662	9909	B5ME49	.	I	9909	ENSP00000381008:V9909I	ENSP00000381008:V9909I	V	-	1	0	MUC16	8918721	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.382000	0.02546	-1.826000	0.01205	0.557000	0.71058	GTC	C|0.565;T|0.435	0.435	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GEMIN4	50628	hgsc.bcm.edu	37	17	649984	649984	+	Silent	SNP	G	G	A	rs147516197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:649984G>A	ENST00000319004.5	-	2	1417	c.1299C>T	c.(1297-1299)ttC>ttT	p.F433F	GEMIN4_ENST00000437269.1_3'UTR|GEMIN4_ENST00000576778.1_Silent_p.F422F	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	433					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		ACTCGTCCGAGAAGGCCCACT	0.547													G|||	46	0.0091853	0.0	0.0043	5008	,	,		19907	0.0149		0.0089	False		,,,				2504	0.0194				p.F433F		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C1299T						PASS	.	G		1,3955		0,1,1977	53.0	55.0	55.0		1299	5.1	1.0	17	dbSNP_134	55	86,8214		1,84,4065	no	coding-synonymous	GEMIN4	NM_015721.2		1,85,6042	AA,AG,GG		1.0361,0.0253,0.7099		433/1059	649984	87,12169	1978	4150	6128	SO:0001819	synonymous_variant	50628	exon2			GTCCGAGAAGGCC	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.1299C>T	17.37:g.649984G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			G|0.991;A|0.009	0.009	strong		0.547	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
NPY	4852	hgsc.bcm.edu	37	7	24325009	24325009	+	Silent	SNP	G	G	A	rs5573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:24325009G>A	ENST00000407573.1	+	3	440	c.150G>A	c.(148-150)tcG>tcA	p.S50S	NPY_ENST00000405982.1_Silent_p.S50S|NPY_ENST00000242152.2_Silent_p.S50S			P01303	NPY_HUMAN	neuropeptide Y	50					adult feeding behavior (GO:0008343)|behavior (GO:0007610)|blood circulation (GO:0008015)|calcium ion transport (GO:0006816)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of appetite (GO:0032100)|regulation of blood pressure (GO:0008217)|synaptic transmission (GO:0007268)	cell (GO:0005623)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			breast(1)|kidney(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	9						GATACTACTCGGCGCTGCGAC	0.677													G|||	2574	0.513978	0.3555	0.6643	5008	,	,		16319	0.6379		0.507	False		,,,				2504	0.501				p.S50S		Atlas-SNP	.											NPY,colon,carcinoma,0,1	NPY	25	1	0			c.G150A						PASS	.	G		1644,2762	501.0+/-364.9	315,1014,874	75.0	55.0	62.0		150	-8.2	0.4	7	dbSNP_52	62	4301,4299	574.9+/-390.1	1052,2197,1051	no	coding-synonymous	NPY	NM_000905.3		1367,3211,1925	AA,AG,GG		49.9884,37.3128,45.7097		50/98	24325009	5945,7061	2203	4300	6503	SO:0001819	synonymous_variant	4852	exon2			CTACTCGGCGCTG	K01911	CCDS5387.1	7p15.3	2013-02-26			ENSG00000122585	ENSG00000122585		"""Endogenous ligands"""	7955	protein-coding gene	gene with protein product	"""prepro-neuropeptide Y"""	162640					Standard	NM_000905		Approved	PYY4	uc003sww.2	P01303	OTTHUMG00000022973	ENST00000407573.1:c.150G>A	7.37:g.24325009G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	NM_000905		Silent	SNP	ENST00000407573.1	37	CCDS5387.1																																																																																			A|0.483;C|0.000;G|0.517;T|0.000	0.483	strong		0.677	NPY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326748.1	NM_000905	
SMARCC2	6601	hgsc.bcm.edu	37	12	56578682	56578682	+	Silent	SNP	T	T	C	rs7136420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56578682T>C	ENST00000267064.4	-	5	524	c.438A>G	c.(436-438)ccA>ccG	p.P146P	SMARCC2_ENST00000394023.3_Silent_p.P146P|SMARCC2_ENST00000550164.1_Silent_p.P146P|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Silent_p.P146P|SMARCC2_ENST00000550859.1_5'UTR	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	146					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			GCTCAATTTCTGGGCACAGAA	0.408													T|||	176	0.0351438	0.1225	0.0173	5008	,	,		21553	0.0		0.002	False		,,,				2504	0.0				p.P146P		Atlas-SNP	.											.	SMARCC2	212	.	0			c.A438G						PASS	.	T	,,	467,3939	223.3+/-239.8	28,411,1764	151.0	137.0	141.0		438,438,438	-0.7	1.0	12	dbSNP_116	141	14,8586	11.2+/-40.8	0,14,4286	no	coding-synonymous,coding-synonymous,coding-synonymous	SMARCC2	NM_001130420.1,NM_003075.3,NM_139067.2	,,	28,425,6050	CC,CT,TT		0.1628,10.5992,3.6983	,,	146/1153,146/1215,146/1131	56578682	481,12525	2203	4300	6503	SO:0001819	synonymous_variant	6601	exon5			AATTTCTGGGCAC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.438A>G	12.37:g.56578682T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Silent	SNP	ENST00000267064.4	37	CCDS8907.1																																																																																			T|0.956;C|0.044	0.044	strong		0.408	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
UBASH3A	53347	hgsc.bcm.edu	37	21	43863521	43863521	+	Silent	SNP	A	A	G	rs386818914|rs868092	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43863521A>G	ENST00000319294.6	+	13	1762	c.1731A>G	c.(1729-1731)ccA>ccG	p.P577P	UBASH3A_ENST00000398367.1_Intron|UBASH3A_ENST00000291535.6_Silent_p.P539P	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	577	Phosphatase-like.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						ACACCTGTCCACAGGACAGTA	0.552													G|||	3089	0.616813	0.59	0.6556	5008	,	,		19473	0.5169		0.6879	False		,,,				2504	0.6554				p.P577P		Atlas-SNP	.											.	UBASH3A	72	.	0			c.A1731G						PASS	.	G	,	2768,1638	484.6+/-360.1	858,1052,293	65.0	47.0	53.0		1617,1731	-3.9	0.0	21	dbSNP_86	53	6298,2302	371.3+/-336.2	2315,1668,317	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	3173,2720,610	GG,GA,AA		26.7674,37.1766,30.2937	,	539/624,577/662	43863521	9066,3940	2203	4300	6503	SO:0001819	synonymous_variant	53347	exon13			CTGTCCACAGGAC	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.1731A>G	21.37:g.43863521A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			A|0.359;G|0.641	0.641	strong		0.552	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
CDH3	1001	hgsc.bcm.edu	37	16	68713730	68713730	+	Silent	SNP	G	G	A	rs2296409	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:68713730G>A	ENST00000264012.4	+	7	1264	c.720G>A	c.(718-720)acG>acA	p.T240T	CDH3_ENST00000429102.2_Silent_p.T240T|CDH3_ENST00000581171.1_Silent_p.T185T	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	240	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TGACAGCCACGGATGAGGATG	0.498													G|||	3044	0.607827	0.6679	0.5476	5008	,	,		17511	0.6141		0.6223	False		,,,				2504	0.5481				p.T240T		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G720A						PASS	.	G		2957,1439	682.2+/-404.1	992,973,233	157.0	115.0	129.0		720	-10.1	0.6	16	dbSNP_100	129	5363,3237	650.4+/-400.7	1663,2037,600	no	coding-synonymous	CDH3	NM_001793.4		2655,3010,833	AA,AG,GG		37.6395,32.7343,35.9803		240/830	68713730	8320,4676	2198	4300	6498	SO:0001819	synonymous_variant	1001	exon7			AGCCACGGATGAG	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.720G>A	16.37:g.68713730G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_001793	B2R6F4|Q05DI6	Silent	SNP	ENST00000264012.4	37	CCDS10868.1																																																																																			G|0.368;A|0.632	0.632	strong		0.498	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
SPAG17	200162	hgsc.bcm.edu	37	1	118565953	118565953	+	Missense_Mutation	SNP	G	G	A	rs10923472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:118565953G>A	ENST00000336338.5	-	28	4108	c.4043C>T	c.(4042-4044)cCa>cTa	p.P1348L		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1348			P -> L (in dbSNP:rs10923472).			cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		AATCTCAGATGGTATCGTTTC	0.383													G|||	1439	0.28734	0.1551	0.4107	5008	,	,		15600	0.1567		0.4314	False		,,,				2504	0.365				p.P1348L		Atlas-SNP	.											.	SPAG17	263	.	0			c.C4043T						PASS	.	G	LEU/PRO	897,3509	347.5+/-309.5	89,719,1395	118.0	109.0	112.0		4043	5.6	0.1	1	dbSNP_120	112	3857,4743	540.4+/-383.8	875,2107,1318	yes	missense	SPAG17	NM_206996.2	98	964,2826,2713	AA,AG,GG		44.8488,20.3586,36.5524	probably-damaging	1348/2224	118565953	4754,8252	2203	4300	6503	SO:0001583	missense	200162	exon28			TCAGATGGTATCG		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4043C>T	1.37:g.118565953G>A	ENSP00000337804:p.Pro1348Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	634	0.2902930402930403	73	0.1483739837398374	156	0.430939226519337	71	0.12412587412587413	334	0.44063324538258575	G	18.18	3.566922	0.65651	0.203586	0.448488	ENSG00000155761	ENST00000336338	T	0.20463	2.07	5.63	5.63	0.86233	.	0.431247	0.25529	N	0.030042	T	0.37100	0.0991	M	0.66939	2.045	0.30462	P	0.774151	D	0.89917	1.0	D	0.87578	0.998	T	0.16541	-1.0399	9	0.72032	D	0.01	.	15.1893	0.73032	0.0:0.0:1.0:0.0	rs10923472;rs17257687;rs52828260;rs57051065;rs10923472	1348	Q6Q759	SPG17_HUMAN	L	1348	ENSP00000337804:P1348L	ENSP00000337804:P1348L	P	-	2	0	SPAG17	118367476	0.936000	0.31750	0.132000	0.22025	0.085000	0.17905	2.084000	0.41625	2.669000	0.90835	0.591000	0.81541	CCA	G|0.682;A|0.318	0.318	strong		0.383	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
NAALADL2	254827	hgsc.bcm.edu	37	3	175189447	175189447	+	Silent	SNP	G	G	A	rs9290555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:175189447G>A	ENST00000454872.1	+	9	1682	c.1554G>A	c.(1552-1554)caG>caA	p.Q518Q	NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	518						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		AGGTTCTTCAGAAAAATGTTG	0.353													G|||	2740	0.547125	0.3434	0.6585	5008	,	,		13171	0.6756		0.6402	False		,,,				2504	0.5153				p.Q518Q		Atlas-SNP	.											.	NAALADL2	86	.	0			c.G1554A						PASS	.	G		1294,2306		233,828,739	67.0	56.0	59.0		1554	-0.4	1.0	3	dbSNP_119	59	5110,3042		1603,1904,569	no	coding-synonymous	NAALADL2	NM_207015.2		1836,2732,1308	AA,AG,GG		37.316,35.9444,45.5071		518/796	175189447	6404,5348	1800	4076	5876	SO:0001819	synonymous_variant	254827	exon9			TCTTCAGAAAAAT		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.1554G>A	3.37:g.175189447G>A		Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	247	247	1	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Silent	SNP	ENST00000454872.1	37	CCDS46960.1																																																																																			G|0.456;A|0.544	0.544	strong		0.353	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
SLC9A3	6550	hgsc.bcm.edu	37	5	475104	475104	+	Missense_Mutation	SNP	A	A	G	rs2247114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:475104A>G	ENST00000264938.3	-	16	2404	c.2395T>C	c.(2395-2397)Tgc>Cgc	p.C799R	CTD-2228K2.7_ENST00000606319.1_RNA|SLC9A3_ENST00000514375.1_Missense_Mutation_p.C790R|CTD-2228K2.5_ENST00000510714.1_5'Flank|CTD-2228K2.5_ENST00000510604.1_5'Flank|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.5_ENST00000342584.3_5'Flank|CTD-2228K2.7_ENST00000607286.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	799			C -> R (in dbSNP:rs2247114). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7631746}.		ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			ATCAGGCGGCAGAAGGTGCCG	0.726																																					p.C799R		Atlas-SNP	.											.	SLC9A3	89	.	0			c.T2395C						PASS	.	G	ARG/CYS	3848,554		1687,474,40	19.0	23.0	22.0		2395	3.8	1.0	5	dbSNP_100	22	7474,1118		3271,932,93	yes	missense	SLC9A3	NM_004174.2	180	4958,1406,133	GG,GA,AA		13.0121,12.5852,12.8675	benign	799/835	475104	11322,1672	2201	4296	6497	SO:0001583	missense	6550	exon16			GGCGGCAGAAGGT		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2395T>C	5.37:g.475104A>G	ENSP00000264938:p.Cys799Arg	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	143	79	0.552448	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	37	CCDS3855.1	1628	0.7454212454212454	420	0.8536585365853658	273	0.7541436464088398	289	0.5052447552447552	646	0.8522427440633246	G	0.012	-1.648975	0.00785	0.874148	0.869879	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.68025	-0.3;-0.3	4.81	3.84	0.44239	.	0.750230	0.12381	N	0.473899	T	0.00012	0.0000	N	0.00095	-2.16	0.29718	P	0.838892	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39781	-0.9597	9	0.02654	T	1	.	7.296	0.26393	0.0992:0.0:0.6732:0.2276	rs2247114;rs58623748;rs2247114	790;799	E9PF67;P48764	.;SL9A3_HUMAN	R	799;790	ENSP00000264938:C799R;ENSP00000422983:C790R	ENSP00000264938:C799R	C	-	1	0	SLC9A3	528104	0.999000	0.42202	0.994000	0.49952	0.308000	0.27856	1.936000	0.40183	1.045000	0.40225	-0.355000	0.07637	TGC	A|0.191;G|0.809	0.809	strong		0.726	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
ACTR3B	57180	hgsc.bcm.edu	37	7	152497656	152497656	+	Silent	SNP	T	T	C	rs201991209		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:152497656T>C	ENST00000256001.8	+	3	275	c.141T>C	c.(139-141)gcT>gcC	p.A47A	ACTR3B_ENST00000377776.3_Silent_p.A47A|ACTR3B_ENST00000397282.2_5'UTR|ACTR3B_ENST00000537264.1_Intron	NM_020445.5	NP_065178.1	Q9P1U1	ARP3B_HUMAN	ARP3 actin-related protein 3 homolog B (yeast)	47						cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	13		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)		TTGACCAAGCTCAAAGGAGAG	0.383																																					p.A47A		Atlas-SNP	.											ACTR3B,NS,carcinoma,+1,1	ACTR3B	50	1	0			c.T141C						scavenged	.						134.0	124.0	128.0					7																	152497656		2203	4300	6503	SO:0001819	synonymous_variant	57180	exon3			CCAAGCTCAAAGG		CCDS5934.1, CCDS34782.1	7q36.1	2010-07-20			ENSG00000133627	ENSG00000133627			17256	protein-coding gene	gene with protein product						10806390	Standard	NM_001040135		Approved	ARP11, ARP3beta	uc003wle.2	Q9P1U1	OTTHUMG00000151463	ENST00000256001.8:c.141T>C	7.37:g.152497656T>C		Somatic	119	2	0.0168067		WXS	Illumina HiSeq	Phase_I	152	29	0.190789	NM_020445	A8MTG1|B4DFW4|Q7Z526|Q96BT2	Silent	SNP	ENST00000256001.8	37	CCDS5934.1																																																																																			.	.	weak		0.383	ACTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322803.1	NM_020445	
ARSD	414	hgsc.bcm.edu	37	X	2833631	2833631	+	Silent	SNP	A	A	G	rs377542415		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2833631A>G	ENST00000381154.1	-	6	1041	c.966T>C	c.(964-966)taT>taC	p.Y322Y	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	322					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CATTATCACCATATAAGCCAT	0.507																																					p.Y322Y		Atlas-SNP	.											.	ARSD	47	.	0			c.T966C						PASS	.						236.0	159.0	185.0					X																	2833631		2203	4300	6503	SO:0001819	synonymous_variant	414	exon6			ATCACCATATAAG	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.966T>C	X.37:g.2833631A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	93	20	0.215054	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			.	.	weak		0.507	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
LRRC16A	55604	hgsc.bcm.edu	37	6	25605091	25605091	+	Missense_Mutation	SNP	G	G	A	rs1012899	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:25605091G>A	ENST00000329474.6	+	34	3972	c.3604G>A	c.(3604-3606)Ggc>Agc	p.G1202S		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1202				G -> S (in Ref. 1; ACI49709). {ECO:0000305}.	actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						AGCTTTGAGCGGCGTAGAACG	0.493													A|||	4013	0.801318	0.7867	0.7695	5008	,	,		18971	0.869		0.7445	False		,,,				2504	0.8323				p.G1202S		Atlas-SNP	.											.	LRRC16A	168	.	0			c.G3604A						PASS	.	A	SER/GLY,SER/GLY	1395,357		551,293,32	17.0	16.0	16.0		3604,3604	4.4	0.1	6	dbSNP_86	16	3038,944		1176,686,129	yes	missense,missense	LRRC16A	NM_001173977.1,NM_017640.5	56,56	1727,979,161	AA,AG,GG		23.7067,20.3767,22.6892	benign,benign	1202/1366,1202/1372	25605091	4433,1301	876	1991	2867	SO:0001583	missense	55604	exon34			TTGAGCGGCGTAG	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.3604G>A	6.37:g.25605091G>A	ENSP00000331983:p.Gly1202Ser	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	1732	0.793040293040293	367	0.7459349593495935	285	0.787292817679558	513	0.8968531468531469	567	0.7480211081794196	A	0.098	-1.156985	0.01686	0.796233	0.762933	ENSG00000079691	ENST00000329474	T	0.14022	2.54	5.54	4.39	0.52855	.	0.631229	0.16948	N	0.193031	T	0.01320	0.0043	N	0.03115	-0.41	0.35739	P	0.18147999999999997	B	0.02656	0.0	B	0.01281	0.0	T	0.45848	-0.9233	9	0.05833	T	0.94	-5.83	8.4206	0.32698	0.8476:0.0:0.1524:0.0	rs1012899;rs17492218;rs52813055;rs56587110;rs61195207;rs1012899	1202	Q5VZK9	LR16A_HUMAN	S	1202	ENSP00000331983:G1202S	ENSP00000331983:G1202S	G	+	1	0	LRRC16A	25713070	0.738000	0.28186	0.074000	0.20217	0.046000	0.14306	1.280000	0.33202	0.927000	0.37143	-0.381000	0.06696	GGC	G|0.197;A|0.803	0.803	strong		0.493	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
TM7SF3	51768	hgsc.bcm.edu	37	12	27143508	27143508	+	Missense_Mutation	SNP	G	G	A	rs10771314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:27143508G>A	ENST00000343028.4	-	6	968	c.743C>T	c.(742-744)cCg>cTg	p.P248L	TM7SF3_ENST00000542667.1_Intron	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	248			P -> L (in dbSNP:rs10771314).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	18	Colorectal(261;0.0847)					ACCTTGTCCCGGGAGGGAGGA	0.428													G|||	244	0.048722	0.0144	0.0807	5008	,	,		19155	0.0595		0.0775	False		,,,				2504	0.0317				p.P248L		Atlas-SNP	.											.	TM7SF3	41	.	0			c.C743T						PASS	.	G	LEU/PRO	125,4281	93.4+/-132.2	1,123,2079	122.0	110.0	114.0		743	-1.8	0.0	12	dbSNP_120	114	879,7721	198.5+/-242.8	44,791,3465	yes	missense	TM7SF3	NM_016551.2	98	45,914,5544	AA,AG,GG		10.2209,2.837,7.7195	benign	248/571	27143508	1004,12002	2203	4300	6503	SO:0001583	missense	51768	exon6			TGTCCCGGGAGGG	AB032470	CCDS8710.1	12q11-q12	2012-08-10			ENSG00000064115	ENSG00000064115			23049	protein-coding gene	gene with protein product		605181				10828615	Standard	NM_016551		Approved		uc010sjl.2	Q9NS93	OTTHUMG00000169243	ENST00000343028.4:c.743C>T	12.37:g.27143508G>A	ENSP00000342322:p.Pro248Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	146	145	0.993151	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	37	CCDS8710.1	130|130	0.05952380952380952|0.05952380952380952	4|4	0.008130081300813009|0.008130081300813009	27|27	0.07458563535911603|0.07458563535911603	41|41	0.07167832167832168|0.07167832167832168	58|58	0.07651715039577836|0.07651715039577836	G|G	11.88|11.88	1.769765|1.769765	0.31320|0.31320	0.02837|0.02837	0.102209|0.102209	ENSG00000064115|ENSG00000064115	ENST00000343028;ENST00000543655;ENST00000535819|ENST00000545303	T;T;T|.	0.45668|.	1.42;0.89;0.89|.	5.0|5.0	-1.78|-1.78	0.07957|0.07957	.|.	0.288766|.	0.38897|.	N|.	0.001531|.	T|T	0.02047|0.02047	0.0064|0.0064	L|L	0.42245|0.42245	1.32|1.32	0.58432|0.58432	D|D	0.999996|0.999996	B|.	0.32653|.	0.379|.	B|.	0.17979|.	0.02|.	T|T	0.05209|0.05209	-1.0899|-1.0899	10|5	0.35671|.	T|.	0.21|.	7.0E-4|7.0E-4	9.1426|9.1426	0.36912|0.36912	0.0849:0.1585:0.6733:0.0832|0.0849:0.1585:0.6733:0.0832	rs10771314;rs52837696;rs60050366;rs10771314|rs10771314;rs52837696;rs60050366;rs10771314	248|.	Q9NS93|.	TM7S3_HUMAN|.	L|W	248;39;39|29	ENSP00000342322:P248L;ENSP00000441924:P39L;ENSP00000445156:P39L|.	ENSP00000342322:P248L|.	P|R	-|-	2|1	0|2	TM7SF3|TM7SF3	27034775|27034775	0.993000|0.993000	0.37304|0.37304	0.026000|0.026000	0.17262|0.17262	0.878000|0.878000	0.50629|0.50629	1.827000|1.827000	0.39102|0.39102	-0.105000|-0.105000	0.12132|0.12132	-0.237000|-0.237000	0.12165|0.12165	CCG|CGG	G|0.933;A|0.067	0.067	strong		0.428	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551	
TMEM133	83935	hgsc.bcm.edu	37	11	100863096	100863096	+	Silent	SNP	A	A	G	rs515552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100863096A>G	ENST00000303130.2	+	1	286	c.57A>G	c.(55-57)gaA>gaG	p.E19E		NM_032021.2	NP_114410.1	Q9H2Q1	TM133_HUMAN	transmembrane protein 133	19						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(1)|lung(1)|prostate(1)	5		Acute lymphoblastic leukemia(157;0.000869)|all_hematologic(158;0.014)		BRCA - Breast invasive adenocarcinoma(274;0.0675)		CAGGTCACGAAAAAGAACACA	0.433													A|||	1944	0.388179	0.1248	0.3977	5008	,	,		21672	0.7579		0.2028	False		,,,				2504	0.547				p.E19E		Atlas-SNP	.											.	TMEM133	9	.	0			c.A57G						PASS	.	A		592,3814	250.0+/-257.2	44,504,1655	88.0	83.0	85.0		57	-0.3	0.0	11	dbSNP_83	85	1808,6792	314.1+/-311.6	200,1408,2692	no	coding-synonymous	TMEM133	NM_032021.2		244,1912,4347	GG,GA,AA		21.0233,13.4362,18.453		19/130	100863096	2400,10606	2203	4300	6503	SO:0001819	synonymous_variant	83935	exon1			TCACGAAAAAGAA	AF247167	CCDS8309.1	11q22.1	2006-03-09				ENSG00000170647			24033	protein-coding gene	gene with protein product						12477932	Standard	NM_032021		Approved	AD031	uc001pgf.3	Q9H2Q1		ENST00000303130.2:c.57A>G	11.37:g.100863096A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_032021		Silent	SNP	ENST00000303130.2	37	CCDS8309.1																																																																																			A|0.773;G|0.227	0.227	strong		0.433	TMEM133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395137.1	NM_032021	
ANKRD53	79998	hgsc.bcm.edu	37	2	71212129	71212129	+	Missense_Mutation	SNP	A	A	T	rs3796100	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71212129A>T	ENST00000360589.3	+	6	1326	c.1292A>T	c.(1291-1293)cAc>cTc	p.H431L	AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000457410.1_Missense_Mutation_p.H397L|ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000272421.6_3'UTR	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	431			H -> L (in dbSNP:rs3796100). {ECO:0000269|PubMed:14702039}.							endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						CCTGATGGGCACGGCGGTGCG	0.677											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	686	0.136981	0.09	0.1254	5008	,	,		13552	0.1627		0.2276	False		,,,				2504	0.089				p.H431L		Atlas-SNP	.											.	ANKRD53	55	.	0			c.A1292T						PASS	.	A	LEU/HIS,	144,1230		9,126,552	8.0	11.0	10.0		1292,	-1.7	0.0	2	dbSNP_107	10	633,2521		60,513,1004	yes	missense,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	99,	69,639,1556	TT,TA,AA		20.0698,10.4803,17.1599	benign,	431/531,	71212129	777,3751	687	1577	2264	SO:0001583	missense	79998	exon6			ATGGGCACGGCGG	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1292A>T	2.37:g.71212129A>T	ENSP00000353796:p.His431Leu	Somatic	72	0	0	1128	WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_001115116	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	37	CCDS46321.1	368	0.1684981684981685	48	0.0975609756097561	48	0.13259668508287292	102	0.17832167832167833	170	0.22427440633245382	A	12.74	2.027947	0.35797	0.104803	0.200698	ENSG00000144031	ENST00000457410;ENST00000360589	T;T	0.62941	0.08;-0.01	5.56	-1.67	0.08238	.	1.290300	0.05084	N	0.484000	T	0.00039	0.0001	N	0.24115	0.695	0.80722	P	0.0	.	.	.	.	.	.	T	0.04400	-1.0954	7	0.46703	T	0.11	-3.7831	1.365	0.02200	0.4359:0.2765:0.1541:0.1335	rs3796100;rs17664715;rs3796100	.	.	.	L	397;431	ENSP00000407004:H397L;ENSP00000353796:H431L	ENSP00000353796:H431L	H	+	2	0	ANKRD53	71065637	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.183000	0.16919	-0.421000	0.07416	0.459000	0.35465	CAC	A|0.828;T|0.172	0.172	strong		0.677	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68053802	68053802	+	Silent	SNP	T	T	C	rs734028	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:68053802T>C	ENST00000329153.5	+	29	4077	c.3945T>C	c.(3943-3945)gcT>gcC	p.A1315A	PLEKHH1_ENST00000417684.2_Missense_Mutation_p.Y257H	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	1315	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		TTGCAGAAGCTACCTTCATCA	0.498													T|||	2781	0.555312	0.2057	0.6614	5008	,	,		18444	0.6617		0.673	False		,,,				2504	0.7219				p.A1315A		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.T3945C						PASS	.	T		1217,2721		202,813,954	57.0	62.0	60.0		3945	-8.9	0.4	14	dbSNP_86	60	5536,2764		1861,1814,475	no	coding-synonymous	PLEKHH1	NM_020715.2		2063,2627,1429	CC,CT,TT		33.3012,30.904,44.8194		1315/1365	68053802	6753,5485	1969	4150	6119	SO:0001819	synonymous_variant	57475	exon29			AGAAGCTACCTTC	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.3945T>C	14.37:g.68053802T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	192	86	0.447917	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Silent	SNP	ENST00000329153.5	37	CCDS45128.1	1257	0.5755494505494505	112	0.22764227642276422	238	0.6574585635359116	392	0.6853146853146853	515	0.679419525065963	T	14.49	2.551989	0.45487	0.30904	0.666988	ENSG00000054690	ENST00000417684	.	.	.	5.53	-8.85	0.00799	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.899999999996574E-5	B	0.10296	0.003	B	0.08055	0.003	T	0.44952	-0.9294	6	0.02654	T	1	.	1.8549	0.03177	0.2609:0.2673:0.3379:0.134	rs734028;rs17782377;rs57181795;rs734028	257	E7ESY2	.	H	257	.	ENSP00000397712:Y257H	Y	+	1	0	PLEKHH1	67123555	0.893000	0.30496	0.390000	0.26220	0.977000	0.68977	-0.101000	0.10973	-1.411000	0.02032	0.528000	0.53228	TAC	T|0.452;C|0.548	0.548	strong		0.498	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
OR13D1	286365	hgsc.bcm.edu	37	9	107456933	107456933	+	Silent	SNP	C	C	T	rs12347076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107456933C>T	ENST00000318763.5	+	1	274	c.231C>T	c.(229-231)ctC>ctT	p.L77L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	77						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						ATAGCCTCCTCATTATCATCA	0.448													C|||	1354	0.270367	0.1657	0.183	5008	,	,		20502	0.4821		0.1909	False		,,,				2504	0.3374				p.L77L		Atlas-SNP	.											.	OR13D1	42	.	0			c.C231T						PASS	.	C		789,3617	319.1+/-295.9	75,639,1489	208.0	208.0	208.0		231	0.3	0.2	9	dbSNP_120	208	1824,6776	328.2+/-318.2	224,1376,2700	no	coding-synonymous	OR13D1	NM_001004484.1		299,2015,4189	TT,TC,CC		21.2093,17.9074,20.0907		77/347	107456933	2613,10393	2203	4300	6503	SO:0001819	synonymous_variant	286365	exon1			CCTCCTCATTATC		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"""GPCR / Class A : Olfactory receptors"""	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.231C>T	9.37:g.107456933C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	220	96	0.436364	NM_001004484	B9EIS1|Q6IFL1	Silent	SNP	ENST00000318763.5	37	CCDS35094.1																																																																																			C|0.771;T|0.229	0.229	strong		0.448	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
BTBD11	121551	hgsc.bcm.edu	37	12	108051406	108051406	+	Missense_Mutation	SNP	G	G	A	rs12303478	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:108051406G>A	ENST00000280758.5	+	17	3754	c.3226G>A	c.(3226-3228)Ggc>Agc	p.G1076S	BTBD11_ENST00000420571.2_Missense_Mutation_p.G957S|BTBD11_ENST00000357167.4_Missense_Mutation_p.G613S|BTBD11_ENST00000494235.2_Missense_Mutation_p.G155S	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	1076			G -> S (in dbSNP:rs12303478).			integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TGAAGGGACCGGCCAGGATGT	0.478													G|||	525	0.104832	0.1989	0.0692	5008	,	,		20662	0.001		0.0964	False		,,,				2504	0.1186				p.G1076S		Atlas-SNP	.											.	BTBD11	122	.	0			c.G3226A						PASS	.	G	SER/GLY,SER/GLY	721,3685	299.0+/-285.6	45,631,1527	123.0	112.0	116.0		1837,3226	5.6	1.0	12	dbSNP_120	116	808,7792	189.3+/-236.1	37,734,3529	yes	missense,missense	BTBD11	NM_001017523.1,NM_001018072.1	56,56	82,1365,5056	AA,AG,GG		9.3953,16.364,11.7561	benign,benign	613/642,1076/1105	108051406	1529,11477	2203	4300	6503	SO:0001583	missense	121551	exon17			GGGACCGGCCAGG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.3226G>A	12.37:g.108051406G>A	ENSP00000280758:p.Gly1076Ser	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	201	95	0.472637	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	181	0.08287545787545787	80	0.16260162601626016	33	0.09116022099447514	1	0.0017482517482517483	67	0.08839050131926121	G	16.12	3.031635	0.54790	0.16364	0.093953	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000357167;ENST00000494235	T;T;T;T	0.39056	1.28;1.46;1.1;1.26	5.6	5.6	0.85130	.	0.095314	0.64402	D	0.000001	T	0.00178	0.0005	L	0.46157	1.445	0.20307	P	0.9999127565	B;B	0.25312	0.123;0.123	B;B	0.12837	0.008;0.008	T	0.02668	-1.1126	9	0.26408	T	0.33	.	19.6296	0.95694	0.0:0.0:1.0:0.0	rs12303478;rs52798261;rs57558542;rs12303478	613;1076	E9PHS4;A6QL63	.;BTBDB_HUMAN	S	1076;957;613;155	ENSP00000280758:G1076S;ENSP00000413889:G957S;ENSP00000349690:G613S;ENSP00000448322:G155S	ENSP00000280758:G1076S	G	+	1	0	BTBD11	106575536	1.000000	0.71417	0.971000	0.41717	0.758000	0.43043	3.360000	0.52299	2.644000	0.89710	0.655000	0.94253	GGC	G|0.891;A|0.109	0.109	strong		0.478	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
ZNF184	7738	hgsc.bcm.edu	37	6	27425185	27425185	+	Missense_Mutation	SNP	C	C	A	rs386698292|rs1883216	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27425185C>A	ENST00000211936.6	-	4	363	c.79G>T	c.(79-81)Gcg>Tcg	p.A27S	ZNF184_ENST00000377419.1_Missense_Mutation_p.A27S	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	27			A -> S (in dbSNP:rs1883216). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9073517}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						AAAGTCACCGCTTCCTGAAAT	0.423													A|||	3096	0.618211	0.531	0.6715	5008	,	,		18470	0.5774		0.6451	False		,,,				2504	0.7127				p.A27S		Atlas-SNP	.											ZNF184,NS,carcinoma,+2,1	ZNF184	89	1	0			c.G79T						PASS	.	A	SER/ALA	2355,2051	567.0+/-382.0	623,1109,471	101.0	100.0	101.0		79	3.2	1.0	6	dbSNP_92	101	5454,3146	477.8+/-369.7	1755,1944,601	yes	missense	ZNF184	NM_007149.2	99	2378,3053,1072	AA,AC,CC		36.5814,46.5502,39.9585	benign	27/752	27425185	7809,5197	2203	4300	6503	SO:0001583	missense	7738	exon4			TCACCGCTTCCTG	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"""Zinc fingers, C2H2-type"", ""-"""	12975	protein-coding gene	gene with protein product		602277	"""zinc finger protein 184 (Kruppel-like)"""				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.79G>T	6.37:g.27425185C>A	ENSP00000211936:p.Ala27Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_007149	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	37	CCDS4624.1	1288	0.5897435897435898	253	0.5142276422764228	237	0.6546961325966851	315	0.5506993006993007	483	0.637203166226913	A	2.806	-0.248095	0.05867	0.534498	0.634186	ENSG00000096654	ENST00000211936;ENST00000377419;ENST00000341087	T;T	0.00730	5.77;5.77	4.32	3.17	0.36434	Krueppel-associated box (1);	0.000000	0.39407	N	0.001372	T	0.00073	0.0002	N	0.00661	-1.28	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16778	-1.0391	9	0.02654	T	1	.	3.7677	0.08629	0.6192:0.1894:0.1913:0.0	rs1883216;rs17845715;rs17858663;rs52830797;rs58634439;rs1883216	27	Q99676	ZN184_HUMAN	S	27	ENSP00000211936:A27S;ENSP00000366636:A27S	ENSP00000211936:A27S	A	-	1	0	ZNF184	27533164	0.914000	0.31030	0.996000	0.52242	0.963000	0.63663	1.456000	0.35201	0.449000	0.26747	-0.256000	0.11100	GCG	C|0.387;A|0.613	0.613	strong		0.423	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149	
SLCO4A1	28231	hgsc.bcm.edu	37	20	61288038	61288038	+	Missense_Mutation	SNP	G	G	A	rs1047099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61288038G>A	ENST00000370507.1	+	1	328	c.232G>A	c.(232-234)Gtc>Atc	p.V78I	SLCO4A1_ENST00000217159.1_Missense_Mutation_p.V78I			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	78			V -> I (in dbSNP:rs1047099). {ECO:0000269|PubMed:14702039}.		sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GGTGCGGTACGTCTCGGCCGG	0.701													G|||	744	0.148562	0.0121	0.1585	5008	,	,		16019	0.1677		0.2903	False		,,,				2504	0.1605				p.V78I	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											.	SLCO4A1	65	.	0			c.G232A						PASS	.	G	ILE/VAL	234,4150		8,218,1966	18.0	16.0	17.0		232	1.8	0.0	20	dbSNP_86	17	2304,6278		304,1696,2291	yes	missense	SLCO4A1	NM_016354.3	29	312,1914,4257	AA,AG,GG		26.8469,5.3376,19.5743	benign	78/723	61288038	2538,10428	2192	4291	6483	SO:0001583	missense	28231	exon2			CGGTACGTCTCGG	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"""Solute carriers"""	10953	protein-coding gene	gene with protein product		612436	"""solute carrier family 21 (organic anion transporter), member 12"""	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.232G>A	20.37:g.61288038G>A	ENSP00000359538:p.Val78Ile	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Missense_Mutation	SNP	ENST00000370507.1	37	CCDS13501.1	395	0.18086080586080586	7	0.014227642276422764	70	0.19337016574585636	108	0.1888111888111888	210	0.2770448548812665	G	11.68	1.711049	0.30322	0.053376	0.268469	ENSG00000101187	ENST00000217159;ENST00000370512;ENST00000370507;ENST00000342674	T;T	0.43294	0.95;0.95	3.79	1.77	0.24775	.	2.616690	0.01796	N	0.032622	T	0.00012	0.0000	L	0.39020	1.185	0.80722	P	0.0	B	0.21071	0.051	B	0.09377	0.004	T	0.14615	-1.0466	9	0.27082	T	0.32	.	5.8169	0.18497	0.1864:0.1584:0.6552:0.0	rs1047099;rs17845471;rs17858350	78	Q96BD0	SO4A1_HUMAN	I	78	ENSP00000217159:V78I;ENSP00000359538:V78I	ENSP00000217159:V78I	V	+	1	0	SLCO4A1	60758483	0.000000	0.05858	0.002000	0.10522	0.366000	0.29705	0.676000	0.25247	0.256000	0.21614	0.462000	0.41574	GTC	A|0.172;C|0.010	0.172	strong		0.701	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	
AGBL2	79841	hgsc.bcm.edu	37	11	47701528	47701528	+	Missense_Mutation	SNP	C	C	A	rs12286721	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:47701528C>A	ENST00000525123.1	-	13	2298	c.2013G>T	c.(2011-2013)atG>atT	p.M671I	AGBL2_ENST00000357610.3_Missense_Mutation_p.M671I|AGBL2_ENST00000298861.4_Missense_Mutation_p.M671I|AGBL2_ENST00000528244.1_Missense_Mutation_p.M633I|AGBL2_ENST00000529712.1_5'UTR	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	671			M -> I (in dbSNP:rs12286721). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						TTTTTACCTTCATTTGGTCAG	0.458													C|||	2908	0.580671	0.6377	0.6657	5008	,	,		16917	0.5694		0.5666	False		,,,				2504	0.4693				p.M671I		Atlas-SNP	.											.	AGBL2	73	.	0			c.G2013T						PASS	.	C	ILE/MET	2709,1693	653.4+/-399.6	826,1057,318	101.0	97.0	98.0		2013	0.6	1.0	11	dbSNP_120	98	4694,3902	606.3+/-395.1	1288,2118,892	yes	missense	AGBL2	NM_024783.3	10	2114,3175,1210	AA,AC,CC		45.3932,38.4598,43.0451	benign	671/903	47701528	7403,5595	2201	4298	6499	SO:0001583	missense	79841	exon13			TACCTTCATTTGG		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"""cytoplasmic carboxypeptidase 2"""					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.2013G>T	11.37:g.47701528C>A	ENSP00000435582:p.Met671Ile	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Missense_Mutation	SNP	ENST00000525123.1	37	CCDS7944.1	1333	0.6103479853479854	297	0.6036585365853658	232	0.6408839779005525	372	0.6503496503496503	432	0.5699208443271768	C	10.68	1.417560	0.25552	0.615402	0.546068	ENSG00000165923	ENST00000528609;ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244	T;T;T;T	0.09163	3.01;3.01;3.01;3.01	5.26	0.549	0.17213	.	0.341660	0.33854	N	0.004484	T	0.00012	0.0000	N	0.08118	0	0.46222	P	0.0010630000000000361	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.21042	-1.0257	9	0.42905	T	0.14	-3.5842	6.0447	0.19753	0.0763:0.117:0.5704:0.2363	rs12286721;rs52811031;rs56521901;rs60342826;rs12286721	633;633;671	F6U0I4;B4DZS1;Q5U5Z8	.;.;CBPC2_HUMAN	I	54;671;671;671;633	ENSP00000435582:M671I;ENSP00000350228:M671I;ENSP00000298861:M671I;ENSP00000436630:M633I	ENSP00000298861:M671I	M	-	3	0	AGBL2	47658104	0.988000	0.35896	1.000000	0.80357	0.734000	0.41952	0.469000	0.22067	0.212000	0.20703	-1.211000	0.01629	ATG	C|0.420;A|0.580	0.580	strong		0.458	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783	
MS4A14	84689	hgsc.bcm.edu	37	11	60184277	60184277	+	Missense_Mutation	SNP	A	A	C	rs73481226	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60184277A>C	ENST00000300187.6	+	5	2113	c.1836A>C	c.(1834-1836)caA>caC	p.Q612H	MS4A14_ENST00000531783.1_Missense_Mutation_p.Q645H|MS4A14_ENST00000395005.2_Missense_Mutation_p.Q595H|MS4A14_ENST00000531787.1_Missense_Mutation_p.Q500H	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	612	Gln-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						AGCCGGCCCAAGAGAAGAAAT	0.448													A|||	458	0.0914537	0.0363	0.0389	5008	,	,		20824	0.247		0.0169	False		,,,				2504	0.1196				p.Q645H		Atlas-SNP	.											.	MS4A14	120	.	0			c.A1935C						PASS	.	A	HIS/GLN,HIS/GLN	150,4256	103.4+/-141.9	2,146,2055	52.0	46.0	48.0		1785,1836	1.1	0.0	11	dbSNP_130	48	164,8436	75.4+/-138.0	0,164,4136	yes	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	24,24	2,310,6191	CC,CA,AA		1.907,3.4044,2.4143	possibly-damaging,possibly-damaging	595/663,612/680	60184277	314,12692	2203	4300	6503	SO:0001583	missense	84689	exon6			GGCCCAAGAGAAG	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"""membrane-spanning 4-domains, subfamily A, member 16"""	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1836A>C	11.37:g.60184277A>C	ENSP00000300187:p.Gln612His	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	167	0.07646520146520147	10	0.02032520325203252	12	0.03314917127071823	133	0.23251748251748253	12	0.0158311345646438	A	12.64	1.998171	0.35226	0.034044	0.01907	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.35236	1.32;2.54;1.33;2.89	3.52	1.15	0.20763	.	10.332000	0.00166	N	0.000000	T	0.00039	0.0001	L	0.54323	1.7	0.54753	P	1.6000000000016E-5	D;D	0.64830	0.994;0.989	P;P	0.61940	0.896;0.79	T	0.04178	-1.0971	9	0.28530	T	0.3	2.6708	1.8542	0.03175	0.5153:0.0:0.236:0.2487	.	595;612	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	H	500;612;595;645	ENSP00000437222:Q500H;ENSP00000300187:Q612H;ENSP00000378453:Q595H;ENSP00000433761:Q645H	ENSP00000300187:Q612H	Q	+	3	2	MS4A14	59940853	0.016000	0.18221	0.003000	0.11579	0.216000	0.24613	0.380000	0.20602	0.483000	0.27608	0.460000	0.39030	CAA	A|0.960;C|0.040	0.040	strong		0.448	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
PHC2	1912	hgsc.bcm.edu	37	1	33820134	33820134	+	Missense_Mutation	SNP	C	C	T	rs12026290	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33820134C>T	ENST00000257118.5	-	8	1476	c.1423G>A	c.(1423-1425)Gtg>Atg	p.V475M	PHC2_ENST00000373416.1_De_novo_Start_InFrame|PHC2_ENST00000419414.2_Missense_Mutation_p.V476M|PHC2_ENST00000373422.3_Missense_Mutation_p.V81M|PHC2_ENST00000431992.1_Missense_Mutation_p.V446M|RP11-415J8.5_ENST00000432703.1_RNA	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	475			V -> M (in dbSNP:rs12026290). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CCTGGTGCCACTTCTTTCCAG	0.567													C|||	859	0.171526	0.0182	0.17	5008	,	,		19765	0.2113		0.2346	False		,,,				2504	0.274				p.V475M		Atlas-SNP	.											.	PHC2	78	.	0			c.G1423A						PASS	.	C	MET/VAL	224,4182	133.7+/-170.0	5,214,1984	66.0	57.0	60.0		1423	3.9	0.4	1	dbSNP_120	60	2079,6521	358.6+/-331.2	243,1593,2464	yes	missense	PHC2	NM_198040.2	21	248,1807,4448	TT,TC,CC		24.1744,5.084,17.7072	benign	475/859	33820134	2303,10703	2203	4300	6503	SO:0001583	missense	1912	exon8			GTGCCACTTCTTT	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.1423G>A	1.37:g.33820134C>T	ENSP00000257118:p.Val475Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	41	0.401961	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	367	0.16804029304029305	17	0.034552845528455285	62	0.1712707182320442	113	0.19755244755244755	175	0.23087071240105542	C	8.589	0.884024	0.17467	0.05084	0.241744	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000373422;ENST00000419414	T;T;T;T	0.47869	1.8;1.37;0.83;1.74	5.82	3.93	0.45458	.	1.073430	0.07142	N	0.847566	T	0.00012	0.0000	L	0.44542	1.39	0.23879	P	0.99658715	B;B	0.33448	0.412;0.412	B;B	0.33890	0.172;0.172	T	0.09422	-1.0675	9	0.62326	D	0.03	-0.3209	9.1642	0.37041	0.0:0.8283:0.0:0.1717	rs12026290;rs17474465;rs52827989;rs59603087;rs12026290	476;475	A8KA40;Q8IXK0	.;PHC2_HUMAN	M	446;475;81;476	ENSP00000389436:V446M;ENSP00000257118:V475M;ENSP00000362521:V81M;ENSP00000391440:V476M	ENSP00000257118:V475M	V	-	1	0	PHC2	33592721	0.024000	0.19004	0.429000	0.26710	0.123000	0.20343	0.612000	0.24283	1.457000	0.47850	0.563000	0.77884	GTG	C|0.834;N|0.000	.	strong		0.567	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
CRIP3	401262	hgsc.bcm.edu	37	6	43273604	43273604	+	3'UTR	SNP	A	A	G	rs2242416	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43273604A>G	ENST00000274990.4	-	0	758				CRIP3_ENST00000372569.3_Missense_Mutation_p.I188T|ZNF318_ENST00000607252.1_5'Flank			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3						T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			CACATCGCCAATGTTCACACC	0.542													A|||	2088	0.416933	0.0719	0.4035	5008	,	,		20332	0.621		0.5765	False		,,,				2504	0.5184				p.I188T		Atlas-SNP	.											.	CRIP3	30	.	0			c.T563C						PASS	.	A	THR/ILE	705,3685		55,595,1545	76.0	80.0	79.0		563	5.8	1.0	6	dbSNP_98	79	5031,3559		1445,2141,709	yes	missense	CRIP3	NM_206922.2	89	1500,2736,2254	GG,GA,AA		41.4319,16.0592,44.1911	benign	188/205	43273604	5736,7244	2195	4295	6490	SO:0001624	3_prime_UTR_variant	401262	exon8			TCGCCAATGTTCA	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.*100T>C	6.37:g.43273604A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	150	87	0.58	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	37		1000	0.45787545787545786	30	0.06097560975609756	157	0.43370165745856354	371	0.6486013986013986	442	0.58311345646438	A	10.18	1.279807	0.23392	0.160592	0.585681	ENSG00000146215	ENST00000372569	D	0.92397	-3.03	5.77	5.77	0.91146	.	.	.	.	.	T	0.78400	0.4277	.	.	.	0.09310	P	1.0	B	0.23891	0.093	B	0.23574	0.047	T	0.72997	-0.4121	7	0.12766	T	0.61	.	14.039	0.64663	1.0:0.0:0.0:0.0	rs2242416;rs17287893;rs56983690;rs2242416	188	Q6Q6R5-3	.	T	188	ENSP00000361650:I188T	ENSP00000361650:I188T	I	-	2	0	CRIP3	43381582	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.562000	0.60816	2.200000	0.70718	0.533000	0.62120	ATT	G|0.469;N|0.000	0.469	strong		0.542	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1		
USP24	23358	hgsc.bcm.edu	37	1	55541174	55541174	+	Missense_Mutation	SNP	A	A	G	rs487230	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55541174A>G	ENST00000294383.6	-	63	7402	c.7403T>C	c.(7402-7404)gTa>gCa	p.V2468A	USP24_ENST00000484447.1_5'Flank|USP24_ENST00000407756.1_Missense_Mutation_p.V2308A	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2468			V -> A (in dbSNP:rs487230). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:14702039}.		ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						GACTCGCTCTACTTGTATAGG	0.338													A|||	3467	0.692292	0.2648	0.8473	5008	,	,		20294	0.9187		0.7714	False		,,,				2504	0.8456				p.V2468A		Atlas-SNP	.											.	USP24	323	.	0			c.T7403C						PASS	.	A	ALA/VAL	1310,2362		241,828,767	77.0	65.0	69.0	http://omim.org/entry/606852	7403	4.2	1.0	1	dbSNP_83	69	6284,1908		2425,1434,237	yes	missense	USP24	NM_015306.2	64	2666,2262,1004	GG,GA,AA		23.291,35.6754,35.9912	benign	2468/2621	55541174	7594,4270	1836	4096	5932	SO:0001583	missense	23358	exon63			CGCTCTACTTGTA	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.7403T>C	1.37:g.55541174A>G	ENSP00000294383:p.Val2468Ala	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	171	64	0.374269	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	1534	0.7023809523809523	149	0.30284552845528456	298	0.8232044198895028	512	0.8951048951048951	575	0.758575197889182	A	12.49	1.954963	0.34471	0.356754	0.76709	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.02103	4.45;4.46	5.35	4.22	0.49857	.	0.150023	0.43260	D	0.000591	T	0.00012	0.0000	N	0.04508	-0.205	0.34397	P	0.30518900000000004	B	0.02656	0.0	B	0.04013	0.001	T	0.21449	-1.0245	9	0.06891	T	0.86	.	11.4124	0.49933	0.9296:0.0:0.0704:0.0	rs487230;rs1165279;rs1752393;rs2297565;rs52832643;rs61200868;rs487230	2308	B7WPF4	.	A	2468;2308	ENSP00000294383:V2468A;ENSP00000385700:V2308A	ENSP00000294383:V2468A	V	-	2	0	USP24	55313762	1.000000	0.71417	0.984000	0.44739	0.993000	0.82548	5.139000	0.64801	1.158000	0.42547	0.533000	0.62120	GTA	T|0.008;G|0.677	0.677	strong		0.338	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
OR51S1	119692	hgsc.bcm.edu	37	11	4870298	4870298	+	Silent	SNP	T	T	G	rs11601065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4870298T>G	ENST00000322101.2	-	1	216	c.141A>C	c.(139-141)gcA>gcC	p.A47A	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CATTTCCCAGTGCAGAGAGAA	0.562													T|||	844	0.16853	0.0227	0.1441	5008	,	,		19755	0.0675		0.2555	False		,,,				2504	0.3978				p.A47A		Atlas-SNP	.											.	OR51S1	83	.	0			c.A141C						PASS	.	T		234,4168	137.3+/-173.1	8,218,1975	105.0	86.0	93.0		141	-0.3	0.7	11	dbSNP_120	93	2515,6081	412.0+/-350.7	363,1789,2146	no	coding-synonymous	OR51S1	NM_001004758.1		371,2007,4121	GG,GT,TT		29.2578,5.3158,21.1494		47/324	4870298	2749,10249	2201	4298	6499	SO:0001819	synonymous_variant	119692	exon1			TCCCAGTGCAGAG	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.141A>C	11.37:g.4870298T>G		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	316	155	0.490506	NM_001004758	B9EGZ1|Q6IFI2	Silent	SNP	ENST00000322101.2	37	CCDS31362.1																																																																																			T|0.828;G|0.172	0.172	strong		0.562	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
ALDH3B2	222	hgsc.bcm.edu	37	11	67430762	67430762	+	Missense_Mutation	SNP	T	T	C	rs1551886	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67430762T>C	ENST00000349015.3	-	10	1520	c.1082A>G	c.(1081-1083)cAc>cGc	p.H361R	ALDH3B2_ENST00000530069.1_Missense_Mutation_p.H361R	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	361			H -> R (in dbSNP:rs1551886). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7484374, ECO:0000269|PubMed:8890755}.		alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						GGGTGGGTAGTGGATCTCCTT	0.637													C|||	4347	0.868011	0.7179	0.9193	5008	,	,		18312	0.9097		0.8877	False		,,,				2504	0.9714				p.H361R		Atlas-SNP	.											.	ALDH3B2	46	.	0			c.A1082G						PASS	.	C	ARG/HIS,ARG/HIS	3314,1086	393.3+/-328.8	1244,826,130	90.0	85.0	86.0		1082,1082	-6.3	0.0	11	dbSNP_88	86	7731,857	195.4+/-240.6	3476,779,39	yes	missense,missense	ALDH3B2	NM_000695.3,NM_001031615.1	29,29	4720,1605,169	CC,CT,TT		9.979,24.6818,14.96	benign,benign	361/386,361/386	67430762	11045,1943	2200	4294	6494	SO:0001583	missense	222	exon10			GGGTAGTGGATCT	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"""Aldehyde dehydrogenases"""	411	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 8"", ""acetaldehyde dehydrogenase 8"""	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.1082A>G	11.37:g.67430762T>C	ENSP00000255084:p.His361Arg	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	184	183	0.994565	NM_001031615	Q53Y98|Q8NAL5|Q96IB2	Missense_Mutation	SNP	ENST00000349015.3	37	CCDS31622.1	1927|1927	0.8823260073260073|0.8823260073260073	384|384	0.7804878048780488|0.7804878048780488	328|328	0.9060773480662984|0.9060773480662984	537|537	0.9388111888111889|0.9388111888111889	678|678	0.8944591029023746|0.8944591029023746	C|C	1.528|1.528	-0.545187|-0.545187	0.04024|0.04024	0.753182|0.753182	0.90021|0.90021	ENSG00000132746|ENSG00000132746	ENST00000530069;ENST00000349015|ENST00000531248	T;T|.	0.77620|.	-1.11;-1.11|.	3.75|3.75	-6.26|-6.26	0.02033|0.02033	.|.	0.063229|.	0.64402|.	N|.	0.000004|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01352|0.01352	-0.895|-0.895	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.17930|0.17930	-1.0353|-1.0353	9|4	0.02654|.	T|.	1|.	.|.	2.2306|2.2306	0.03995|0.03995	0.1907:0.4973:0.0939:0.2181|0.1907:0.4973:0.0939:0.2181	rs1551886;rs3741173;rs52819527;rs56879940;rs1551886|rs1551886;rs3741173;rs52819527;rs56879940;rs1551886	361|.	P48448|.	AL3B2_HUMAN|.	R|A	361|90	ENSP00000431595:H361R;ENSP00000255084:H361R|.	ENSP00000255084:H361R|.	H|T	-|-	2|1	0|0	ALDH3B2|ALDH3B2	67187338|67187338	0.641000|0.641000	0.27251|0.27251	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	0.410000|0.410000	0.21098|0.21098	-2.051000|-2.051000	0.00904|0.00904	-0.320000|-0.320000	0.08662|0.08662	CAC|ACT	T|0.136;C|0.864	0.864	strong		0.637	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695	
DHRSX	207063	hgsc.bcm.edu	37	X	2139186	2139186	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2139186C>T	ENST00000334651.5	-	7	941	c.889G>A	c.(889-891)Gag>Aag	p.E297K		NM_145177.2	NP_660160.2	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked	297			E -> K (in dbSNP:rs12010). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.				oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)	16		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GTCTCTTTCTCGTTGTATAGG	0.532													.|||	2361	0.471446	0.3109	0.4207	5008	,	,		20703	0.754		0.3588	False		,,,				2504	0.5491				p.E297K		Atlas-SNP	.											.	DHRSX	24	.	0			c.G889A						PASS	.	C	LYS/GLU	1299,3107		189,921,1093	295.0	255.0	269.0		889	2.3	0.8	X	dbSNP_134	269	2288,6304		312,1664,2320	yes	missense	DHRSX	NM_145177.2	56	501,2585,3413	TT,TC,CC		26.6294,29.4825,27.5966	probably-damaging	297/331	2139186	3587,9411	2203	4296	6499	SO:0001583	missense	207063	exon7			CTTTCTCGTTGTA	AJ293620	CCDS35195.1	Xp22.33 and Yp11.2	2014-05-07	2003-09-12		ENSG00000169084	ENSG00000169084		"""Pseudoautosomal regions / PAR1"""	18399	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 6"", ""short chain dehydrogenase/reductase family 46C, member 1"", ""dehydrogenase/reductase (SDR family) Y-linked"""		"""dehydrogenase/reductase (SDR family) X chromosome"""			11731500, 19027726	Standard	NM_145177		Approved	DHRS5X, DHRSXY, DHRSY, DHRS5Y, SDR46C1, SDR7C6	uc004cqf.4	Q8N5I4	OTTHUMG00000021068	ENST00000334651.5:c.889G>A	X.37:g.2139186C>T	ENSP00000334113:p.Glu297Lys	Somatic	535	2	0.00373832		WXS	Illumina HiSeq	Phase_I	574	277	0.482578	NM_145177	Q6UWC7|Q8WUS4|Q96GR8|Q9NTF6	Missense_Mutation	SNP	ENST00000334651.5	37	CCDS35195.1	991	0.45375457875457875	150	0.3048780487804878	135	0.3729281767955801	440	0.7692307692307693	266	0.35092348284960423	c	10.28	1.307322	0.23821	0.294825	0.266294	ENSG00000169084	ENST00000334651	T	0.63255	-0.03	2.32	2.32	0.28847	NAD(P)-binding domain (1);	0.182908	0.36134	U	0.002778	T	0.00012	0.0000	N	0.25060	0.705	0.09310	N	1	P	0.45348	0.856	B	0.33295	0.161	T	0.48570	-0.9024	10	0.52906	T	0.07	.	11.6281	0.51158	0.0:1.0:0.0:0.0	.	297	Q8N5I4	DHRSX_HUMAN	K	297	ENSP00000334113:E297K	ENSP00000334113:E297K	E	-	1	0	DHRSX	2149186	1.000000	0.71417	0.760000	0.31359	0.329000	0.28539	3.943000	0.56621	0.956000	0.37904	0.124000	0.15798	GAG	C|0.714;T|0.286	0.286	strong		0.532	DHRSX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055617.3	NM_145177	
GABRA1	2554	hgsc.bcm.edu	37	5	161281245	161281245	+	Silent	SNP	T	T	C	rs1129647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:161281245T>C	ENST00000428797.2	+	4	511	c.156T>C	c.(154-156)ggT>ggC	p.G52G	GABRA1_ENST00000393943.4_Silent_p.G52G|GABRA1_ENST00000444819.1_Silent_p.G52G|GABRA1_ENST00000437025.2_Silent_p.G52G|GABRA1_ENST00000420560.1_Silent_p.G52G|GABRA1_ENST00000023897.6_Silent_p.G52G	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	52					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	TCCTAGATGGTTATGACAATC	0.363													T|||	1146	0.228834	0.1067	0.2161	5008	,	,		16450	0.2937		0.2883	False		,,,				2504	0.2751				p.G52G		Atlas-SNP	.											.	GABRA1	132	.	0			c.T156C						PASS	.	T	,,,,,,	573,3833	251.5+/-258.2	51,471,1681	102.0	105.0	104.0		156,156,156,156,156,156,156	0.3	1.0	5	dbSNP_126	104	2340,6260	390.7+/-343.4	298,1744,2258	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRA1	NM_000806.5,NM_001127643.1,NM_001127644.1,NM_001127645.1,NM_001127646.1,NM_001127647.1,NM_001127648.1	,,,,,,	349,2215,3939	CC,CT,TT		27.2093,13.005,22.3974	,,,,,,	52/457,52/457,52/457,52/457,52/457,52/457,52/457	161281245	2913,10093	2203	4300	6503	SO:0001819	synonymous_variant	2554	exon4			AGATGGTTATGAC		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4075	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 1"""	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.156T>C	5.37:g.161281245T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	84	30	0.357143	NM_001127643	D3DQK6|Q8N629	Silent	SNP	ENST00000428797.2	37	CCDS4357.1																																																																																			T|0.776;C|0.224	0.224	strong		0.363	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161017556	161017556	+	Silent	SNP	C	C	T	rs2774279	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161017556C>T	ENST00000368013.3	-	12	3575	c.3255G>A	c.(3253-3255)agG>agA	p.R1085R	USF1_ENST00000368021.3_5'Flank|USF1_ENST00000435396.1_5'Flank|ARHGAP30_ENST00000368015.1_Silent_p.R908R|ARHGAP30_ENST00000368016.3_Silent_p.R874R|USF1_ENST00000368020.1_5'Flank	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	1085					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			ATGCATATGACCTGCGCTGAG	0.552													C|||	1093	0.218251	0.1422	0.2003	5008	,	,		20077	0.1389		0.333	False		,,,				2504	0.2975				p.R1085R		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.G3255A						PASS	.	C	,	846,3560	333.3+/-302.9	80,686,1437	87.0	87.0	87.0		3255,2622	-1.2	0.0	1	dbSNP_100	87	2856,5744	448.2+/-361.8	460,1936,1904	no	coding-synonymous,coding-synonymous	ARHGAP30	NM_001025598.1,NM_181720.2	,	540,2622,3341	TT,TC,CC		33.2093,19.2011,28.4638	,	1085/1102,874/891	161017556	3702,9304	2203	4300	6503	SO:0001819	synonymous_variant	257106	exon12			ATATGACCTGCGC	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.3255G>A	1.37:g.161017556C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	37	CCDS30918.1																																																																																			C|0.752;T|0.248	0.248	strong		0.552	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
ANKRD36	375248	hgsc.bcm.edu	37	2	97877440	97877440	+	Missense_Mutation	SNP	T	T	C	rs35711845	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97877440T>C	ENST00000461153.2	+	58	3675	c.3431T>C	c.(3430-3432)aTg>aCg	p.M1144T	ANKRD36_ENST00000420699.2_Missense_Mutation_p.M1144T			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1144										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GTTCCGAATATGGCCACGGAA	0.338													.|||	1324	0.264377	0.0885	0.3602	5008	,	,		25668	0.1964		0.5129	False		,,,				2504	0.2485				p.M1144T		Atlas-SNP	.											.	ANKRD36	170	.	0			c.T3431C						PASS	.	T	THR/MET	250,1134		3,244,445	149.0	140.0	143.0		3431	-2.3	0.0	2	dbSNP_126	143	1583,1599		99,1385,107	yes	missense	ANKRD36	NM_001164315.1	81	102,1629,552	CC,CT,TT		49.7486,18.0636,40.1445	benign	1144/1942	97877440	1833,2733	692	1591	2283	SO:0001583	missense	375248	exon58			CGAATATGGCCAC	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.3431T>C	2.37:g.97877440T>C	ENSP00000419530:p.Met1144Thr	Somatic	530	1	0.00188679		WXS	Illumina HiSeq	Phase_I	733	318	0.433834	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	1.894	-0.454824	0.04540	0.180636	0.497486	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000461694	T;T	0.77229	-1.08;-1.08	1.17	-2.3	0.06785	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39941	-0.9589	8	0.23891	T	0.37	.	1.5487	0.02570	0.4242:0.0:0.2415:0.3342	rs35711845;rs62156172	1144	A6QL64	AN36A_HUMAN	T	1144;1144;404	ENSP00000419530:M1144T;ENSP00000391950:M1144T	ENSP00000391950:M1144T	M	+	2	0	ANKRD36	97241167	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.779000	0.26746	-0.591000	0.05859	-0.727000	0.03589	ATG	T|0.500;C|0.500	0.500	strong		0.338	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
XYLB	9942	hgsc.bcm.edu	37	3	38404472	38404472	+	Missense_Mutation	SNP	C	C	A	rs17118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38404472C>A	ENST00000207870.3	+	4	345	c.255C>A	c.(253-255)gaC>gaA	p.D85E	XYLB_ENST00000542835.1_Intron	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	85			D -> E (in dbSNP:rs17118). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9763671, ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		CGGGCTTCGACTTCTCTCAAG	0.532													C|||	1177	0.235024	0.1051	0.304	5008	,	,		16920	0.2857		0.3469	False		,,,				2504	0.1943				p.D85E		Atlas-SNP	.											XYLB,caecum,carcinoma,+2,1	XYLB	50	1	0			c.C255A						PASS	.	C	GLU/ASP	626,3780	270.4+/-269.6	53,520,1630	121.0	121.0	121.0		255	0.7	1.0	3	dbSNP_60	121	3031,5569	466.4+/-366.8	547,1937,1816	yes	missense	XYLB	NM_005108.3	45	600,2457,3446	AA,AC,CC		35.2442,14.2079,28.1178	possibly-damaging	85/537	38404472	3657,9349	2203	4300	6503	SO:0001583	missense	9942	exon4			CTTCGACTTCTCT	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"""xylulokinase (H. influenzae) homolog"""			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.255C>A	3.37:g.38404472C>A	ENSP00000207870:p.Asp85Glu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	37	CCDS2678.1	572	0.2619047619047619	70	0.14227642276422764	105	0.2900552486187845	144	0.2517482517482518	253	0.3337730870712401	C	18.21	3.573801	0.65765	0.142079	0.352442	ENSG00000093217	ENST00000207870	T	0.46819	0.86	4.93	0.69	0.18039	Carbohydrate kinase, FGGY, N-terminal (1);	0.700768	0.14941	N	0.289492	T	0.00012	0.0000	M	0.67953	2.075	0.09310	P	0.999999999768008	B	0.31318	0.319	P	0.46339	0.513	T	0.37103	-0.9720	9	0.48119	T	0.1	.	4.3919	0.11344	0.0:0.4086:0.3182:0.2732	rs17118;rs151612;rs574507;rs17037616;rs17854790;rs56462081;rs57457746;rs17118	85	O75191	XYLB_HUMAN	E	85	ENSP00000207870:D85E	ENSP00000207870:D85E	D	+	3	2	XYLB	38379476	0.986000	0.35501	0.984000	0.44739	0.933000	0.57130	0.155000	0.16362	0.198000	0.20407	0.455000	0.32223	GAC	C|0.731;A|0.269	0.269	strong		0.532	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998004	72998004	+	Silent	SNP	T	T	C	rs3744908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72998004T>C	ENST00000580243.1	+	2	990	c.642T>C	c.(640-642)taT>taC	p.Y214Y	TSHZ1_ENST00000322038.5_Silent_p.Y169Y			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	214					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		CGTCCTCGTATGGGCTGCTTC	0.632													C|||	1381	0.275759	0.1293	0.3545	5008	,	,		13589	0.1687		0.4085	False		,,,				2504	0.3916				p.Y169Y		Atlas-SNP	.											.	TSHZ1	104	.	0			c.T507C						PASS	.	C		742,3664	750.0+/-412.1	66,610,1527	47.0	37.0	40.0		507	-1.8	1.0	18	dbSNP_107	40	3449,5151	630.5+/-398.4	690,2069,1541	no	coding-synonymous	TSHZ1	NM_005786.4		756,2679,3068	CC,CT,TT		40.1047,16.8407,32.2236		169/1033	72998004	4191,8815	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			CTCGTATGGGCTG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.642T>C	18.37:g.72998004T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				T|0.690;C|0.310	0.310	strong		0.632	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
SLC16A7	9194	hgsc.bcm.edu	37	12	60173356	60173356	+	Missense_Mutation	SNP	A	A	T	rs3763980	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:60173356A>T	ENST00000261187.4	+	5	1497	c.1333A>T	c.(1333-1335)Acc>Tcc	p.T445S	SLC16A7_ENST00000552432.1_Missense_Mutation_p.T445S|SLC16A7_ENST00000543448.1_Missense_Mutation_p.T346S|SLC16A7_ENST00000547379.1_Missense_Mutation_p.T445S|SLC16A7_ENST00000552024.1_Missense_Mutation_p.T445S	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	445			T -> S (in dbSNP:rs3763980). {ECO:0000269|Ref.2}.		lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	AAGGCAGAAGACCAGAGAATC	0.423													A|||	1227	0.245008	0.2088	0.1801	5008	,	,		15272	0.3175		0.3002	False		,,,				2504	0.2086				p.T445S		Atlas-SNP	.											.	SLC16A7	82	.	0			c.A1333T						PASS	.	A	SER/THR	934,3472	351.1+/-311.1	92,750,1361	96.0	82.0	87.0		1333	-2.5	0.0	12	dbSNP_107	87	2055,6545	355.9+/-330.1	263,1529,2508	yes	missense	SLC16A7	NM_004731.3	58	355,2279,3869	TT,TA,AA		23.8953,21.1984,22.9817	benign	445/479	60173356	2989,10017	2203	4300	6503	SO:0001583	missense	9194	exon6			CAGAAGACCAGAG	AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"""Solute carriers"""	10928	protein-coding gene	gene with protein product		603654	"""solute carrier family 16 (monocarboxylic acid transporters), member 7"""			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.1333A>T	12.37:g.60173356A>T	ENSP00000261187:p.Thr445Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001270622	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	602	0.27564102564102566	105	0.21341463414634146	86	0.23756906077348067	191	0.3339160839160839	220	0.29023746701846964	A	0.008	-1.902371	0.00512	0.211984	0.238953	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000261187;ENST00000543448	T;T;T;T;T	0.16196	2.49;2.49;2.49;2.49;2.36	1.88	-2.51	0.06365	.	1.506430	0.03748	N	0.256134	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.44436	-0.9328	8	.	.	.	.	2.9296	0.05795	0.393:0.2573:0.3497:0.0	rs3763980;rs17571543;rs56973174;rs3763980	445	O60669	MOT2_HUMAN	S	445;445;445;445;346	ENSP00000449547:T445S;ENSP00000448071:T445S;ENSP00000448742:T445S;ENSP00000261187:T445S;ENSP00000443731:T346S	.	T	+	1	0	SLC16A7	58459623	0.503000	0.26115	0.000000	0.03702	0.010000	0.07245	1.138000	0.31491	-0.635000	0.05531	-0.456000	0.05471	ACC	T|0.245;N|0.000	0.245	strong		0.423	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731	
FRY	10129	hgsc.bcm.edu	37	13	32811607	32811607	+	Missense_Mutation	SNP	G	G	A	rs2806639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:32811607G>A	ENST00000380250.3	+	44	6398	c.5902G>A	c.(5902-5904)Ggc>Agc	p.G1968S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1968			G -> S (in dbSNP:rs2806639).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		AACCACCAGCGGCAACACCGC	0.532													G|||	1081	0.215855	0.3487	0.2392	5008	,	,		17080	0.004		0.3091	False		,,,				2504	0.1421				p.G1968S		Atlas-SNP	.											.	FRY	312	.	0			c.G5902A						PASS	.	G	SER/GLY	1295,2733		197,901,916	61.0	69.0	66.0		5902	6.2	1.0	13	dbSNP_100	66	2626,5758		412,1802,1978	yes	missense	FRY	NM_023037.2	56	609,2703,2894	AA,AG,GG		31.3216,32.15,31.5904	benign	1968/3014	32811607	3921,8491	2014	4192	6206	SO:0001583	missense	10129	exon44			ACCAGCGGCAACA	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.5902G>A	13.37:g.32811607G>A	ENSP00000369600:p.Gly1968Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	71	44	0.619718	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	492	0.22527472527472528	155	0.3150406504065041	89	0.24585635359116023	4	0.006993006993006993	244	0.32189973614775724	G	4.136	0.023614	0.08006	0.3215	0.313216	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.21361	2.01	6.17	6.17	0.99709	.	0.227868	0.40554	N	0.001075	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46735	-0.9170	9	0.18710	T	0.47	.	15.9457	0.79792	0.0657:0.0:0.9343:0.0	rs2806639;rs52798355;rs61692237;rs2806639	1968	Q5TBA9	FRY_HUMAN	S	1968;805	ENSP00000369600:G1968S	ENSP00000369600:G1968S	G	+	1	0	FRY	31709607	0.986000	0.35501	0.993000	0.49108	0.081000	0.17604	1.858000	0.39408	2.941000	0.99782	0.655000	0.94253	GGC	G|0.755;A|0.245	0.245	strong		0.532	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
ASXL1	171023	hgsc.bcm.edu	37	20	31024274	31024274	+	Silent	SNP	T	T	C	rs4911231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:31024274T>C	ENST00000375687.4	+	13	4183	c.3759T>C	c.(3757-3759)agT>agC	p.S1253S	ASXL1_ENST00000306058.5_Silent_p.S1248S	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1253					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CACAGGACAGTAATTCAAATG	0.448			"""F, N, Mis"""		"""MDS, CMML"""								T|||	2032	0.405751	0.1664	0.4294	5008	,	,		21767	0.7411		0.3499	False		,,,				2504	0.4243				p.S1253S		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.T3759C						PASS	.	T		847,3559	335.5+/-303.9	85,677,1441	96.0	90.0	92.0		3759	0.7	0.4	20	dbSNP_111	92	3316,5284	494.0+/-373.7	630,2056,1614	no	coding-synonymous	ASXL1	NM_015338.5		715,2733,3055	CC,CT,TT		38.5581,19.2238,32.0083		1253/1542	31024274	4163,8843	2203	4300	6503	SO:0001819	synonymous_variant	171023	exon12			GGACAGTAATTCA	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3759T>C	20.37:g.31024274T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																			T|0.653;C|0.347	0.347	strong		0.448	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
MDGA1	266727	hgsc.bcm.edu	37	6	37626142	37626142	+	Silent	SNP	C	C	T	rs2273110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:37626142C>T	ENST00000434837.3	-	3	1439	c.261G>A	c.(259-261)tcG>tcA	p.S87S	MDGA1_ENST00000505425.1_Silent_p.S87S|MDGA1_ENST00000297153.7_Silent_p.S87S	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	87	Ig-like 1.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CGTTGAACACCGATGTCTCCT	0.647													C|||	681	0.135982	0.0454	0.1499	5008	,	,		17612	0.1627		0.1988	False		,,,				2504	0.1564				p.S87S		Atlas-SNP	.											.	MDGA1	104	.	0			c.G261A						PASS	.	C		294,3960		12,270,1845	86.0	95.0	92.0		261	-4.2	0.8	6	dbSNP_100	92	1645,6795		162,1321,2737	no	coding-synonymous	MDGA1	NM_153487.3		174,1591,4582	TT,TC,CC		19.4905,6.9111,15.2749		87/956	37626142	1939,10755	2127	4220	6347	SO:0001819	synonymous_variant	266727	exon3			GAACACCGATGTC	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.261G>A	6.37:g.37626142C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_153487	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	37	CCDS47417.1																																																																																			C|0.849;T|0.151	0.151	strong		0.647	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
OR13C2	392376	hgsc.bcm.edu	37	9	107367008	107367008	+	Missense_Mutation	SNP	T	T	C	rs10156474	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107367008T>C	ENST00000542196.1	-	1	943	c.901A>G	c.(901-903)Aag>Gag	p.K301E		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	301			K -> E (in dbSNP:rs10156474).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						TTCACATCCTTGTTTCTAAGA	0.373													T|||	2155	0.430312	0.6256	0.2248	5008	,	,		20518	0.5774		0.1789	False		,,,				2504	0.4192				p.K301E		Atlas-SNP	.											.	OR13C2	46	.	0			c.A901G						PASS	.	T	GLU/LYS	2508,1894	629.6+/-395.3	759,990,452	163.0	161.0	162.0		901	3.5	1.0	9	dbSNP_119	162	1668,6932	307.4+/-308.4	183,1302,2815	no	missense	OR13C2	NM_001004481.1	56	942,2292,3267	CC,CT,TT		19.3953,43.0259,32.1181	probably-damaging	301/319	107367008	4176,8826	2201	4300	6501	SO:0001583	missense	392376	exon1			CATCCTTGTTTCT		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.901A>G	9.37:g.107367008T>C	ENSP00000438815:p.Lys301Glu	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	247	104	0.421053	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	826	0.3782051282051282	284	0.5772357723577236	79	0.21823204419889503	331	0.5786713286713286	132	0.1741424802110818	T	13.90	2.373626	0.42105	0.569741	0.193953	ENSG00000257019	ENST00000542196	T	0.44083	0.93	3.53	3.53	0.40419	.	0.000000	0.38436	U	0.001685	T	0.00012	0.0000	M	0.87038	2.855	0.39415	P	0.03319000000000005	P	0.39883	0.693	B	0.38500	0.275	T	0.48433	-0.9036	9	0.87932	D	0	.	6.7989	0.23740	0.0:0.0:0.2401:0.7599	rs10156474;rs59534843	301	Q8NGS9	O13C2_HUMAN	E	301	ENSP00000438815:K301E	ENSP00000438815:K301E	K	-	1	0	OR13C2	106406829	0.437000	0.25593	0.996000	0.52242	0.867000	0.49689	1.835000	0.39181	1.475000	0.48197	0.379000	0.24179	AAG	T|0.639;C|0.361	0.361	strong		0.373	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
FAM65C	140876	hgsc.bcm.edu	37	20	49214188	49214188	+	Silent	SNP	C	C	T	rs35976890	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:49214188C>T	ENST00000327979.2	-	14	2118	c.1707G>A	c.(1705-1707)gaG>gaA	p.E569E	FAM65C_ENST00000535356.1_Silent_p.E573E|FAM65C_ENST00000045083.2_Silent_p.E569E			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	569										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGGCGAAGCTCTCCAGGATGC	0.652													C|||	122	0.024361	0.0023	0.036	5008	,	,		15258	0.001		0.0765	False		,,,				2504	0.0164				p.E569E		Atlas-SNP	.											.	FAM65C	87	.	0			c.G1707A						PASS	.	C		76,4328	65.8+/-103.3	1,74,2127	73.0	56.0	62.0		1707	-0.2	1.0	20	dbSNP_126	62	648,7952	156.4+/-210.3	20,608,3672	no	coding-synonymous	FAM65C	NM_080829.2		21,682,5799	TT,TC,CC		7.5349,1.7257,5.5675		569/947	49214188	724,12280	2202	4300	6502	SO:0001819	synonymous_variant	140876	exon14			GAAGCTCTCCAGG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 175"", ""chromosome 20 open reading frame 176"""	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1707G>A	20.37:g.49214188C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_080829	Q5QPB6|Q9NQQ2	Silent	SNP	ENST00000327979.2	37	CCDS13431.2																																																																																			C|0.957;T|0.043	0.043	strong		0.652	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1		
TANC1	85461	hgsc.bcm.edu	37	2	160086653	160086653	+	Silent	SNP	C	C	T	rs67270488|rs4664277|rs4664276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160086653C>T	ENST00000263635.6	+	27	4953	c.4716C>T	c.(4714-4716)gcC>gcT	p.A1572A	TANC1_ENST00000454300.1_Silent_p.A1466A	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1572					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GAATCGCTGCCACTCCTGCTG	0.562													C|||	2459	0.491014	0.3949	0.6037	5008	,	,		20482	0.6161		0.3718	False		,,,				2504	0.5348				p.A1572A		Atlas-SNP	.											.	TANC1	157	.	0			c.C4716T						PASS	.	C	,	1418,2472		287,844,814	54.0	60.0	58.0		,4716	-11.5	0.0	2	dbSNP_111	58	2746,5536		523,1700,1918	no	utr-3,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	810,2544,2732	TT,TC,CC		33.1562,36.4524,34.2097	,	,1572/1862	160086653	4164,8008	1945	4141	6086	SO:0001819	synonymous_variant	85461	exon27			CGCTGCCACTCCT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4716C>T	2.37:g.160086653C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			.	.	alt		0.562	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
DNHD1	144132	hgsc.bcm.edu	37	11	6568213	6568213	+	Missense_Mutation	SNP	T	T	C	rs58186801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6568213T>C	ENST00000527990.2	+	19	6044	c.6044T>C	c.(6043-6045)aTg>aCg	p.M2015T	DNHD1_ENST00000254579.6_Missense_Mutation_p.M2015T			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2015					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CTGGCAGCCATGGAGGACACC	0.617													T|||	698	0.139377	0.0129	0.2118	5008	,	,		14803	0.1597		0.2465	False		,,,				2504	0.1278				p.M2015T		Atlas-SNP	.											.	DNHD1	198	.	0			c.T6044C						PASS	.	T	THR/MET	56,1328		2,52,638	13.0	16.0	15.0		6044	-1.0	0.3	11	dbSNP_129	15	711,2469		89,533,968	yes	missense	DNHD1	NM_144666.2	81	91,585,1606	CC,CT,TT		22.3585,4.0462,16.8054	benign	2015/4754	6568213	767,3797	692	1590	2282	SO:0001583	missense	144132	exon21			CAGCCATGGAGGA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.6044T>C	11.37:g.6568213T>C	ENSP00000436180:p.Met2015Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	64	41	0.640625	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	368	0.1684981684981685	8	0.016260162601626018	85	0.23480662983425415	93	0.16258741258741258	182	0.24010554089709762	T	0.016	-1.519073	0.00967	0.040462	0.223585	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000533649	T;T	0.26957	1.7;1.7	4.6	-1.05	0.10036	.	0.747484	0.12991	N	0.422447	T	0.00012	0.0000	N	0.25647	0.755	0.50313	P	1.36000000000025E-4	B	0.06786	0.001	B	0.08055	0.003	T	0.43180	-0.9407	9	0.15952	T	0.53	.	5.1027	0.14768	0.0:0.266:0.293:0.4409	rs58186801;rs61743369	2015	Q96M86	DNHD1_HUMAN	T	2015;2015;306	ENSP00000254579:M2015T;ENSP00000436180:M2015T	ENSP00000254579:M2015T	M	+	2	0	DNHD1	6524789	0.562000	0.26586	0.328000	0.25416	0.406000	0.30931	-0.235000	0.09016	-0.014000	0.14175	0.533000	0.62120	ATG	T|0.825;C|0.175	0.175	strong		0.617	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
MPRIP	23164	hgsc.bcm.edu	37	17	17062241	17062241	+	Silent	SNP	C	C	G	rs11551189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17062241C>G	ENST00000341712.4	+	14	1971	c.1971C>G	c.(1969-1971)gcC>gcG	p.A657A	MPRIP_ENST00000395804.3_Silent_p.A657A|MPRIP_ENST00000395811.5_Silent_p.A657A|MPRIP_ENST00000444976.1_Silent_p.A619A			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	657	Interaction with RHOA.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						TGCCCATCGCCCCCGTCCACC	0.597													C|||	2269	0.453075	0.0756	0.5231	5008	,	,		18084	0.7113		0.5417	False		,,,				2504	0.5562				p.A657A		Atlas-SNP	.											MPRIP,caecum,carcinoma,+2,2	MPRIP	87	2	0			c.C1971G						PASS	.	C	,	631,3763		57,517,1623	29.0	31.0	31.0		1971,1971	1.0	0.9	17	dbSNP_120	31	4622,3960		1278,2066,947	yes	coding-synonymous,coding-synonymous	MPRIP	NM_015134.3,NM_201274.3	,	1335,2583,2570	GG,GC,CC		46.1431,14.3605,40.4824	,	657/1039,657/1026	17062241	5253,7723	2197	4291	6488	SO:0001819	synonymous_variant	23164	exon14			CATCGCCCCCGTC	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.1971C>G	17.37:g.17062241C>G		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	174	75	0.431034	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Silent	SNP	ENST00000341712.4	37	CCDS32578.1	1050	0.4807692307692308	42	0.08536585365853659	182	0.5027624309392266	396	0.6923076923076923	430	0.5672823218997362	C	0.225	-1.025905	0.02045	0.143605	0.538569	ENSG00000133030	ENST00000423885	.	.	.	5.38	0.988	0.19796	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.39014	-0.9634	3	.	.	.	.	8.5409	0.33393	0.0:0.4901:0.3176:0.1923	rs11551189	.	.	.	R	144	.	.	P	+	2	0	MPRIP	17002966	0.574000	0.26684	0.872000	0.34217	0.019000	0.09904	0.224000	0.17738	-0.232000	0.09811	-2.698000	0.00137	CCC	C|0.576;G|0.424	0.424	strong		0.597	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	
RIPK4	54101	hgsc.bcm.edu	37	21	43164232	43164232	+	Silent	SNP	C	C	A	rs2277789	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43164232C>A	ENST00000352483.2	-	8	1213	c.1149G>T	c.(1147-1149)ctG>ctT	p.L383L	RIPK4_ENST00000542057.1_Silent_p.L272L|RIPK4_ENST00000544709.1_Silent_p.L272L|RIPK4_ENST00000332512.3_Silent_p.L335L|AP001615.9_ENST00000423276.1_RNA			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	383					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GCTGTGAGAGCAGCTCGGAGA	0.642													C|||	1924	0.384185	0.233	0.4193	5008	,	,		17674	0.4772		0.4573	False		,,,				2504	0.3926				p.L335L		Atlas-SNP	.											.	RIPK4	151	.	0			c.G1005T						PASS	.	C		1194,3212		159,876,1168	19.0	23.0	22.0		1005	1.0	1.0	21	dbSNP_100	22	3526,5074		751,2024,1525	no	coding-synonymous	RIPK4	NM_020639.2		910,2900,2693	AA,AC,CC		41.0,27.0994,36.2909		335/785	43164232	4720,8286	2203	4300	6503	SO:0001819	synonymous_variant	54101	exon7			TGAGAGCAGCTCG	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1149G>T	21.37:g.43164232C>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				C|0.623;A|0.377	0.377	strong		0.642	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
TTN	7273	hgsc.bcm.edu	37	2	179583317	179583317	+	Silent	SNP	G	G	A	rs72648978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179583317G>A	ENST00000591111.1	-	83	23789	c.23565C>T	c.(23563-23565)acC>acT	p.T7855T	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.T6928T|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Silent_p.T8172T			Q8WZ42	TITIN_HUMAN	titin	12043	Ig-like 61.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTCACAAAGGTGGCTGGTT	0.413													G|||	368	0.0734824	0.0802	0.0692	5008	,	,		20597	0.0198		0.0944	False		,,,				2504	0.1012				p.T8172T		Atlas-SNP	.											.	TTN	18412	.	0			c.C24516T						PASS	.	G	,,,	267,3461		15,237,1612	53.0	50.0	51.0		,20784,,	-1.7	1.0	2	dbSNP_130	51	907,7331		66,775,3278	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	81,1012,4890	AA,AG,GG		11.01,7.162,9.8111	,,,	,6928/33424,,	179583317	1174,10792	1864	4119	5983	SO:0001819	synonymous_variant	7273	exon85			CACAAAGGTGGCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.23565C>T	2.37:g.179583317G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.927;A|0.073	0.073	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NUP54	53371	hgsc.bcm.edu	37	4	77065580	77065580	+	Silent	SNP	T	T	C	rs11558469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:77065580T>C	ENST00000264883.3	-	2	254	c.114A>G	c.(112-114)gcA>gcG	p.A38A	NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000515460.1_5'UTR|NUP54_ENST00000514987.1_Silent_p.A38A	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	38	9 X 2 AA repeats of F-G.|Gly-rich.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)	p.A38A(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						AAAAGCTGAATGCAGAACCTG	0.358													t|||	776	0.154952	0.0567	0.1282	5008	,	,		16392	0.3512		0.1312	False		,,,				2504	0.1288				p.A38A		Atlas-SNP	.											NUP54,NS,carcinoma,0,1	NUP54	48	1	1	Substitution - coding silent(1)	stomach(1)	c.A114G						PASS	.	C		308,4098	166.2+/-197.5	15,278,1910	91.0	89.0	90.0		114	-8.4	0.8	4	dbSNP_120	90	1299,7301	257.2+/-281.3	101,1097,3102	no	coding-synonymous	NUP54	NM_017426.2		116,1375,5012	CC,CT,TT		15.1047,6.9905,12.3558		38/508	77065580	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon2			GCTGAATGCAGAA	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.114A>G	4.37:g.77065580T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	169	95	0.56213	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			T|0.865;C|0.135	0.135	strong		0.358	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
SLC38A9	153129	hgsc.bcm.edu	37	5	54960673	54960673	+	Missense_Mutation	SNP	C	C	G	rs4865615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:54960673C>G	ENST00000396865.2	-	8	1136	c.545G>C	c.(544-546)aGc>aCc	p.S182T	SLC38A9_ENST00000515629.1_Missense_Mutation_p.S119T|SLC38A9_ENST00000318672.3_Missense_Mutation_p.S182T|SLC38A9_ENST00000416547.2_Missense_Mutation_p.S58T|SLC38A9_ENST00000512595.1_Missense_Mutation_p.S155T|SLC38A9_ENST00000539768.1_Missense_Mutation_p.S182T	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	182			S -> T (in dbSNP:rs4865615). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				ATATTCCCAGCTAGTGGTATC	0.373													G|||	2797	0.558506	0.4297	0.585	5008	,	,		13278	0.4613		0.661	False		,,,				2504	0.7086				p.S182T		Atlas-SNP	.											SLC38A9,colon,carcinoma,0,1	SLC38A9	50	1	0			c.G545C						PASS	.	G	THR/SER	2107,2299	594.1+/-388.1	499,1109,595	37.0	34.0	35.0		545	-1.4	0.0	5	dbSNP_111	35	5617,2983	455.3+/-363.7	1827,1963,510	yes	missense	SLC38A9	NM_173514.2	58	2326,3072,1105	GG,GC,CC		34.686,47.8212,40.612	benign	182/562	54960673	7724,5282	2203	4300	6503	SO:0001583	missense	153129	exon8			TCCCAGCTAGTGG		CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"""Solute carriers"""	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.545G>C	5.37:g.54960673C>G	ENSP00000380074:p.Ser182Thr	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	228	102	0.447368	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Missense_Mutation	SNP	ENST00000396865.2	37	CCDS3968.1	1199	0.548992673992674	216	0.43902439024390244	222	0.6132596685082873	271	0.4737762237762238	490	0.6464379947229552	G	0.253	-1.005234	0.02112	0.478212	0.65314	ENSG00000177058	ENST00000396865;ENST00000318672;ENST00000539768;ENST00000515629;ENST00000416547;ENST00000512595;ENST00000511233;ENST00000512208	T;T;T;T;T;T;T;T	0.02345	4.33;4.33;4.33;4.33;4.33;4.33;4.33;4.33	5.6	-1.44	0.08856	.	0.495662	0.23918	N	0.043265	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.33111	-0.9881	9	0.06891	T	0.86	-3.509	1.2864	0.02052	0.2207:0.2588:0.343:0.1774	rs4865615;rs58959124;rs4865615	155;182	B3KXV1;Q8NBW4	.;S38A9_HUMAN	T	182;182;182;119;58;155;182;119	ENSP00000380074:S182T;ENSP00000316596:S182T;ENSP00000437771:S182T;ENSP00000420934:S119T;ENSP00000397429:S58T;ENSP00000427335:S155T;ENSP00000423219:S182T;ENSP00000426413:S119T	ENSP00000316596:S182T	S	-	2	0	SLC38A9	54996430	1.000000	0.71417	0.005000	0.12908	0.215000	0.24574	1.201000	0.32259	-0.186000	0.10533	-0.752000	0.03492	AGC	C|0.435;G|0.565	0.565	strong		0.373	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514	
APOBEC1	339	hgsc.bcm.edu	37	12	7805236	7805236	+	Missense_Mutation	SNP	C	C	G	rs2302515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7805236C>G	ENST00000229304.4	-	3	260	c.240G>C	c.(238-240)atG>atC	p.M80I		NM_001644.3	NP_001635.2	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	80			M -> I (in dbSNP:rs2302515). {ECO:0000269|PubMed:8078915, ECO:0000269|PubMed:8208612, ECO:0000269|PubMed:9186903, ECO:0000269|PubMed:9479499}.		cellular response to insulin stimulus (GO:0032869)|cytidine deamination (GO:0009972)|cytidine to uridine editing (GO:0016554)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|gene expression (GO:0010467)|lipid metabolic process (GO:0006629)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein transport (GO:0042953)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to osmotic stress (GO:0006970)|response to zinc ion (GO:0010043)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	AU-rich element binding (GO:0017091)|cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						TGGAGCAGCTCATGGATGGGT	0.478													G|||	3301	0.659145	0.4962	0.6225	5008	,	,		-128	0.5565		0.8946	False		,,,				2504	0.7689				p.M80I	Pancreas(135;929 1826 4531 10527 41012)	Atlas-SNP	.											APOBEC1,NS,carcinoma,-1,1	APOBEC1	43	1	0			c.G240C						PASS	.	G	ILE/MET	2470,1936	550.5+/-378.0	689,1092,422	45.0	44.0	44.0		240	2.6	0.1	12	dbSNP_100	44	7658,942	207.3+/-249.1	3421,816,63	yes	missense	APOBEC1	NM_001644.3	10	4110,1908,485	GG,GC,CC		10.9535,43.9401,22.1282	benign	80/237	7805236	10128,2878	2203	4300	6503	SO:0001583	missense	339	exon3			GCAGCTCATGGAT	U72891	CCDS8579.1	12p13.1	2007-02-01			ENSG00000111701	ENSG00000111701		"""Apolipoprotein B mRNA editing enzymes"""	604	protein-coding gene	gene with protein product		600130					Standard	XM_005253355		Approved	BEDP, CDAR1, APOBEC-1, HEPR	uc001qtb.3	P41238	OTTHUMG00000141288	ENST00000229304.4:c.240G>C	12.37:g.7805236C>G	ENSP00000229304:p.Met80Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_001644	Q9UE64|Q9UM71	Missense_Mutation	SNP	ENST00000229304.4	37	CCDS8579.1	1518	0.695054945054945	265	0.5386178861788617	253	0.6988950276243094	327	0.5716783216783217	673	0.8878627968337731	G	0.882	-0.728398	0.03135	0.560599	0.890465	ENSG00000111701	ENST00000229304	T	0.63255	-0.03	4.48	2.61	0.31194	APOBEC-like, N-terminal (1);APOBEC/CMP deaminase, zinc-binding (1);	1.098920	0.06892	N	0.804464	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37197	-0.9716	9	0.33141	T	0.24	-0.1288	4.4167	0.11459	0.2061:0.1881:0.6058:0.0	rs2302515;rs3181612;rs52811404;rs59440410;rs2302515	80	P41238	ABEC1_HUMAN	I	80	ENSP00000229304:M80I	ENSP00000229304:M80I	M	-	3	0	APOBEC1	7696503	0.000000	0.05858	0.068000	0.19968	0.290000	0.27261	-0.218000	0.09240	0.468000	0.27243	-0.357000	0.07601	ATG	C|0.248;G|0.752	0.752	strong		0.478	APOBEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280523.1	NM_001644	
CBR3	874	hgsc.bcm.edu	37	21	37507501	37507501	+	Missense_Mutation	SNP	G	G	A	rs8133052	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:37507501G>A	ENST00000290354.5	+	1	292	c.11G>A	c.(10-12)tGc>tAc	p.C4Y	CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000453159.1_RNA|CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000608622.1_RNA|CBR3-AS1_ENST00000413862.1_RNA	NM_001236.3	NP_001227.1	O75828	CBR3_HUMAN	carbonyl reductase 3	4			C -> Y (in dbSNP:rs8133052). {ECO:0000269|Ref.5}.		cognition (GO:0050890)|phylloquinone catabolic process (GO:0042376)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	3-keto sterol reductase activity (GO:0000253)|carbonyl reductase (NADPH) activity (GO:0004090)|NADPH binding (GO:0070402)			kidney(1)|large_intestine(1)|lung(1)	3					Doxorubicin(DB00997)	ATGTCGTCCTGCAGCCGCGTG	0.721													G|||	1837	0.366813	0.2451	0.4856	5008	,	,		13383	0.4335		0.4523	False		,,,				2504	0.2904				p.C4Y		Atlas-SNP	.											CBR3,NS,carcinoma,0,1	CBR3	11	1	0			c.G11A						PASS	.	G	TYR/CYS	1102,2986		201,700,1143	7.0	6.0	6.0		11	2.5	1.0	21	dbSNP_116	6	3407,4617		811,1785,1416	no	missense	CBR3	NM_001236.3	194	1012,2485,2559	AA,AG,GG		42.4601,26.9569,37.2275	benign	4/278	37507501	4509,7603	2044	4012	6056	SO:0001583	missense	874	exon1			CGTCCTGCAGCCG	AB004854	CCDS13642.1	21q22.2	2011-09-14			ENSG00000159231	ENSG00000159231	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	1549	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 21C, member 2"""	603608				9740676, 19027726	Standard	NM_001236		Approved	SDR21C2	uc002yve.3	O75828	OTTHUMG00000086617	ENST00000290354.5:c.11G>A	21.37:g.37507501G>A	ENSP00000290354:p.Cys4Tyr	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	13	10	0.769231	NM_001236	Q6FHP2	Missense_Mutation	SNP	ENST00000290354.5	37	CCDS13642.1	882	0.40384615384615385	131	0.266260162601626	163	0.45027624309392267	247	0.4318181818181818	341	0.449868073878628	G	11.21	1.572033	0.28092	0.269569	0.424601	ENSG00000159231	ENST00000290354	T	0.69040	-0.37	5.32	2.52	0.30459	.	0.598172	0.18584	N	0.136957	T	0.00012	0.0000	N	0.04508	-0.205	0.26140	P	0.9802905	B	0.02656	0.0	B	0.06405	0.002	T	0.44787	-0.9305	9	0.28530	T	0.3	-9.6105	8.715	0.34405	0.2964:0.0:0.7036:0.0	rs8133052;rs17283714;rs57678090;rs8133052	4	O75828	CBR3_HUMAN	Y	4	ENSP00000290354:C4Y	ENSP00000290354:C4Y	C	+	2	0	CBR3	36429371	0.244000	0.23889	1.000000	0.80357	0.995000	0.86356	-0.042000	0.12063	0.375000	0.24679	0.655000	0.94253	TGC	G|0.602;A|0.398	0.398	strong		0.721	CBR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194632.1		
OR4C11	219429	hgsc.bcm.edu	37	11	55371807	55371807	+	Missense_Mutation	SNP	A	A	T	rs11230346	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55371807A>T	ENST00000302231.4	-	1	67	c.43T>A	c.(43-45)Tta>Ata	p.L15I		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	15			L -> I (in dbSNP:rs11230346). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						TCCTGTGTTAATCCTAACAGT	0.353													a|||	1161	0.231829	0.1354	0.3401	5008	,	,		11921	0.2173		0.2922	False		,,,				2504	0.2382				p.L15I		Atlas-SNP	.											OR4C11,colon,carcinoma,0,1	OR4C11	73	1	0			c.T43A						PASS	.	A	ILE/LEU	666,3680		123,420,1630	66.0	61.0	63.0		43	-3.7	0.0	11	dbSNP_120	63	2382,5626		698,986,2320	yes	missense	OR4C11	NM_001004700.2	5	821,1406,3950	TT,TA,AA		29.7453,15.3244,24.6722	probably-damaging	15/311	55371807	3048,9306	2173	4004	6177	SO:0001583	missense	219429	exon1			GTGTTAATCCTAA	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"""GPCR / Class A : Olfactory receptors"""	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.43T>A	11.37:g.55371807A>T	ENSP00000306651:p.Leu15Ile	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	168	76	0.452381	NM_001004700	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	37	CCDS31503.1	546	0.25	46	0.09349593495934959	126	0.34806629834254144	139	0.243006993006993	235	0.3100263852242744	A	9.510	1.105539	0.20632	0.153244	0.297453	ENSG00000172188	ENST00000302231	T	0.00335	8.06	4.43	-3.74	0.04385	.	0.000000	0.38272	U	0.001741	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	P	0.44241	0.829	B	0.33254	0.16	T	0.48581	-0.9023	9	0.62326	D	0.03	.	5.2332	0.15434	0.277:0.0:0.4447:0.2784	rs11230346	15	Q6IEV9	OR4CB_HUMAN	I	15	ENSP00000306651:L15I	ENSP00000306651:L15I	L	-	1	2	OR4C11	55128383	0.000000	0.05858	0.019000	0.16419	0.041000	0.13682	-0.968000	0.03817	-0.563000	0.06078	0.448000	0.29417	TTA	A|0.734;T|0.266	0.266	strong		0.353	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700	
PADI2	11240	hgsc.bcm.edu	37	1	17405809	17405809	+	Silent	SNP	G	G	A	rs2057096	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17405809G>A	ENST00000375486.4	-	11	1323	c.1260C>T	c.(1258-1260)aaC>aaT	p.N420N	PADI2_ENST00000466151.1_5'UTR|PADI2_ENST00000444885.2_Silent_p.N304N|PADI2_ENST00000375481.1_Silent_p.N420N	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	420					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	ATGTCTTGCCGTTCACGGTCA	0.592													G|||	2176	0.434505	0.295	0.5259	5008	,	,		14866	0.3879		0.5726	False		,,,				2504	0.4642				p.N420N		Atlas-SNP	.											.	PADI2	72	.	0			c.C1260T						PASS	.	G		1593,2813	495.1+/-363.2	275,1043,885	64.0	65.0	64.0		1260	-5.9	1.0	1	dbSNP_94	64	4972,3628	624.5+/-397.6	1423,2126,751	no	coding-synonymous	PADI2	NM_007365.2		1698,3169,1636	AA,AG,GG		42.186,36.1552,49.5233		420/666	17405809	6565,6441	2203	4300	6503	SO:0001819	synonymous_variant	11240	exon11			CTTGCCGTTCACG	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1260C>T	1.37:g.17405809G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	CCDS177.1																																																																																			G|0.520;A|0.480	0.480	strong		0.592	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
PPP6C	5537	hgsc.bcm.edu	37	9	127951863	127951863	+	Intron	SNP	G	G	A	rs466994	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:127951863G>A	ENST00000373547.4	-	1	175				PPP6C_ENST00000451402.1_Silent_p.F45F|PPP6C_ENST00000373546.3_Intron|PPP6C_ENST00000415905.1_Intron	NM_002721.4	NP_002712.1	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit						G1/S transition of mitotic cell cycle (GO:0000082)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(3)	14						CTGGAGAAAGGAAgggccggc	0.697													G|||	2279	0.455072	0.4682	0.3473	5008	,	,		12046	0.5417		0.4513	False		,,,				2504	0.4284				p.F45F		Atlas-SNP	.											PPP6C_ENST00000451402,NS,carcinoma,0,1	PPP6C	108	1	0			c.C135T						PASS	.						8.0	13.0	11.0					9																	127951863		685	1565	2250	SO:0001627	intron_variant	5537	exon1			AGAAAGGAAGGGC	AF035158	CCDS6861.1, CCDS48018.1, CCDS48019.1	9q33.3	2010-03-17			ENSG00000119414	ENSG00000119414		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9323	protein-coding gene	gene with protein product		612725				9143513	Standard	NM_002721		Approved	PP6	uc004bpg.4	O00743	OTTHUMG00000020671	ENST00000373547.4:c.75+59C>T	9.37:g.127951863G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_001123355	B2R5V6|B7Z2W9|B7Z5K9|Q5U0A2|Q9UIC9	Silent	SNP	ENST00000373547.4	37	CCDS6861.1																																																																																			G|0.563;A|0.437	0.437	strong		0.697	PPP6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054060.1	NM_016294	
SERPINA9	327657	hgsc.bcm.edu	37	14	94931105	94931105	+	Missense_Mutation	SNP	A	A	G	rs11628722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94931105A>G	ENST00000380365.3	-	4	1067	c.989T>C	c.(988-990)gTc>gCc	p.V330A	SERPINA9_ENST00000424550.2_Missense_Mutation_p.V199A|SERPINA9_ENST00000546329.1_Missense_Mutation_p.V312A|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000298845.7_Missense_Mutation_p.V248A|SERPINA9_ENST00000337425.5_Missense_Mutation_p.V348A|SERPINA9_ENST00000448305.2_Missense_Mutation_p.V250A			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	330			V -> A (in dbSNP:rs11628722). {ECO:0000269|PubMed:12819018, ECO:0000269|PubMed:12975309}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TTTGTCAAAGACATTTTGGAT	0.423													G|||	3386	0.676118	0.3759	0.7507	5008	,	,		20168	0.6468		0.8529	False		,,,				2504	0.8773				p.V348A		Atlas-SNP	.											SERPINA9_ENST00000337425,colon,carcinoma,0,4	SERPINA9	105	4	0			c.T1043C						PASS	.	G	ALA/VAL,ALA/VAL	1705,1969		382,941,514	111.0	96.0	101.0		743,1043	2.1	0.0	14	dbSNP_120	101	6820,1360		2830,1160,100	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	64,64	3212,2101,614	GG,GA,AA		16.6259,46.4072,28.0833	benign,benign	248/336,348/436	94931105	8525,3329	1837	4090	5927	SO:0001583	missense	327657	exon4			TCAAAGACATTTT	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.989T>C	14.37:g.94931105A>G	ENSP00000369723:p.Val330Ala	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		1512	0.6923076923076923	212	0.43089430894308944	272	0.7513812154696132	379	0.6625874125874126	649	0.8562005277044855	G	0.018	-1.473840	0.01044	0.464072	0.833741	ENSG00000170054	ENST00000448305;ENST00000298845;ENST00000424550;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	3.96	2.06	0.26882	Serpin domain (3);	0.225717	0.30911	N	0.008627	T	0.00012	0.0000	N	0.04245	-0.25	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.001	B;B;B;B;B	0.14578	0.001;0.011;0.0;0.004;0.001	T	0.39482	-0.9612	9	0.09843	T	0.71	.	5.2002	0.15260	0.3287:0.0:0.5323:0.1391	rs11628722;rs52823758;rs59098222;rs11628722	312;330;250;348;248	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7;Q86WD7-2	.;SPA9_HUMAN;.;.;.	A	250;248;199;348;330;312	ENSP00000414092:V250A;ENSP00000298845:V248A;ENSP00000409012:V199A;ENSP00000337133:V348A;ENSP00000369723:V330A;ENSP00000445476:V312A	ENSP00000298845:V248A	V	-	2	0	SERPINA9	94000858	0.004000	0.15560	0.004000	0.12327	0.001000	0.01503	1.074000	0.30703	-0.106000	0.12110	-2.420000	0.00218	GTC	A|0.315;G|0.685	0.685	strong		0.423	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
GPR153	387509	hgsc.bcm.edu	37	1	6314822	6314822	+	Silent	SNP	T	T	C	rs11590458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:6314822T>C	ENST00000377893.2	-	2	403	c.144A>G	c.(142-144)acA>acG	p.T48T		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		TGGCCGCGAGTGTACACAGCA	0.637													t|||	3663	0.73143	0.8086	0.8012	5008	,	,		20359	0.6181		0.7127	False		,,,				2504	0.7137				p.T48T		Atlas-SNP	.											.	GPR153	44	.	0			c.A144G						PASS	.	T		3485,921	738.4+/-411.0	1390,705,108	84.0	83.0	83.0		144	-6.1	0.0	1	dbSNP_120	83	6033,2567	690.9+/-404.5	2128,1777,395	no	coding-synonymous	GPR153	NM_207370.2		3518,2482,503	CC,CT,TT		29.8488,20.9033,26.8184		48/610	6314822	9518,3488	2203	4300	6503	SO:0001819	synonymous_variant	387509	exon2			CGCGAGTGTACAC	AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"""GPCR / Class A : Orphans"""	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.144A>G	1.37:g.6314822T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	138	45	0.326087	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Silent	SNP	ENST00000377893.2	37	CCDS64.1																																																																																			T|0.282;C|0.718	0.718	strong		0.637	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2		
OR8J3	81168	hgsc.bcm.edu	37	11	55904382	55904382	+	Missense_Mutation	SNP	A	A	C	rs17150102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55904382A>C	ENST00000301529.1	-	1	812	c.813T>G	c.(811-813)gaT>gaG	p.D271E		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	271			D -> E (in dbSNP:rs17150102).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D271E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					AAGCCATCTTATCAGTATCCA	0.408													A|||	518	0.103435	0.0499	0.098	5008	,	,		18145	0.1438		0.1213	False		,,,				2504	0.1196				p.D271E		Atlas-SNP	.											OR8J3,NS,carcinoma,0,1	OR8J3	112	1	1	Substitution - Missense(1)	stomach(1)	c.T813G						PASS	.	A	GLU/ASP	240,4162	140.8+/-176.2	7,226,1968	136.0	134.0	135.0		813	0.7	1.0	11	dbSNP_123	135	1007,7585	216.4+/-255.5	54,899,3343	yes	missense	OR8J3	NM_001004064.1	45	61,1125,5311	CC,CA,AA		11.7202,5.4521,9.5967	probably-damaging	271/316	55904382	1247,11747	2201	4296	6497	SO:0001583	missense	81168	exon1			CATCTTATCAGTA		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.813T>G	11.37:g.55904382A>C	ENSP00000301529:p.Asp271Glu	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	208	101	0.485577	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	253	0.11584249084249085	32	0.06504065040650407	33	0.09116022099447514	88	0.15384615384615385	100	0.13192612137203166	A	15.45	2.837998	0.50951	0.054521	0.117202	ENSG00000167822	ENST00000301529	T	0.00227	8.5	3.27	0.672	0.17935	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	L	0.52011	1.625	0.80722	P	0.0	D	0.69078	0.997	D	0.74348	0.983	T	0.53892	-0.8374	9	0.44086	T	0.13	.	1.7242	0.02918	0.3404:0.0:0.3678:0.2918	rs17150102;rs52801432;rs17150102	271	Q8NGG0	OR8J3_HUMAN	E	271	ENSP00000301529:D271E	ENSP00000301529:D271E	D	-	3	2	OR8J3	55660958	0.000000	0.05858	0.996000	0.52242	0.699000	0.40488	-0.398000	0.07259	1.272000	0.44329	0.247000	0.18012	GAT	A|0.900;C|0.100	0.100	strong		0.408	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
OR13C9	286362	hgsc.bcm.edu	37	9	107380215	107380215	+	Missense_Mutation	SNP	T	T	A	rs993658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107380215T>A	ENST00000259362.1	-	1	270	c.271A>T	c.(271-273)Acc>Tcc	p.T91S		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	91			T -> S (in dbSNP:rs993658).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AAGGAAATGGTCTTTCTTTCT	0.502													T|||	1753	0.35004	0.351	0.2104	5008	,	,		20373	0.5645		0.1779	False		,,,				2504	0.4039				p.T91S		Atlas-SNP	.											OR13C9,colon,carcinoma,+2,1	OR13C9	42	1	0			c.A271T						PASS	.	T	SER/THR	1362,3044	451.8+/-349.8	223,916,1064	134.0	139.0	137.0		271	2.2	1.0	9	dbSNP_86	137	1654,6946	306.2+/-307.8	181,1292,2827	no	missense	OR13C9	NM_001001956.1	58	404,2208,3891	AA,AT,TT		19.2326,30.9124,23.1893	probably-damaging	91/319	107380215	3016,9990	2203	4300	6503	SO:0001583	missense	286362	exon1			AAATGGTCTTTCT		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.271A>T	9.37:g.107380215T>A	ENSP00000259362:p.Thr91Ser	Somatic	621	1	0.00161031		WXS	Illumina HiSeq	Phase_I	623	310	0.497592	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	684	0.3131868131868132	156	0.3170731707317073	74	0.20441988950276244	322	0.5629370629370629	132	0.1741424802110818	T	11.45	1.641969	0.29157	0.309124	0.192326	ENSG00000136839	ENST00000259362	T	0.01422	4.91	4.78	2.2	0.27929	GPCR, rhodopsin-like superfamily (1);	0.282386	0.25256	N	0.031997	T	0.00012	0.0000	N	0.17764	0.52	0.54753	P	1.6000000000016E-5	B	0.06786	0.001	B	0.10450	0.005	T	0.09271	-1.0682	9	0.33141	T	0.24	.	8.3632	0.32372	0.3107:0.0:0.0:0.6893	rs993658;rs52822852;rs993658	91	Q8NGT0	O13C9_HUMAN	S	91	ENSP00000259362:T91S	ENSP00000259362:T91S	T	-	1	0	OR13C9	106420036	0.000000	0.05858	1.000000	0.80357	0.973000	0.67179	-0.033000	0.12246	0.809000	0.34255	0.519000	0.50382	ACC	T|0.743;A|0.257	0.257	strong		0.502	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609965	32609965	+	Missense_Mutation	SNP	C	C	A	rs7990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32609965C>A	ENST00000343139.5	+	3	650	c.548C>A	c.(547-549)gCt>gAt	p.A183D	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.A183D|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.A183D	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	182	Alpha-2.|Ig-like C1-type.		E -> D (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*01:07, allele DQA1*02:01, allele DQA1*03:01, allele DQA1*03:02, allele DQA1*03:03, allele DQA1*04:01, allele DQA1*04:02, allele DQA1*04:04, allele DQA1*06:01 and allele DQA1*06:02; dbSNP:rs707963).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CTCCCTTCTGCTGATGAGATT	0.468													.|||	500	0.0998403	0.084	0.1095	5008	,	,		14318	0.2173		0.0686	False		,,,				2504	0.0256				p.A183D		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C548A						PASS	.	C	ASP/ALA	234,2786		13,208,1289	102.0	101.0	101.0		548	-2.0	0.9	6	dbSNP_52	101	456,4952		25,406,2273	no	missense	HLA-DQA1	NM_002122.3	126	38,614,3562	AA,AC,CC		8.432,7.7483,8.187	benign	183/256	32609965	690,7738	1510	2704	4214	SO:0001583	missense	3117	exon3			CTTCTGCTGATGA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.548C>A	6.37:g.32609965C>A	ENSP00000339398:p.Ala183Asp	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	181	97	0.535912	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	218|218	0.09981684981684982|0.09981684981684982	21|21	0.042682926829268296|0.042682926829268296	18|18	0.049723756906077346|0.049723756906077346	128|128	0.22377622377622378|0.22377622377622378	51|51	0.06728232189973615|0.06728232189973615	.|.	1.937|1.937	-0.444604|-0.444604	0.04604|0.04604	0.077483|0.077483	0.08432|0.08432	ENSG00000196735|ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949|ENST00000486548	T;T;T;T|.	0.02890|.	4.12;4.12;4.12;4.12|.	4.1|4.1	-2.03|-2.03	0.07365|0.07365	.|.	0.720175|.	0.12796|.	N|.	0.438420|.	T|T	0.16128|0.16128	0.0388|0.0388	N|N	0.21097|0.21097	0.63|0.63	0.44890|0.44890	P|P	0.0020940000000000403|0.0020940000000000403	B;B|.	0.09022|.	0.002;0.0|.	B;B|.	0.09377|.	0.004;0.002|.	T|T	0.18493|0.18493	-1.0335|-1.0335	9|4	0.19147|.	T|.	0.46|.	.|.	10.57|10.57	0.45194|0.45194	0.7148:0.1765:0.1087:0.0|0.7148:0.1765:0.1087:0.0	rs7990;rs1048263;rs2308886;rs3188280|rs7990;rs1048263;rs2308886;rs3188280	189;183|.	Q59F33;G4XQK2|.	.;.|.	D|M	183|156	ENSP00000339398:A183D;ENSP00000378767:A183D;ENSP00000437302:A183D;ENSP00000364087:A183D|.	ENSP00000339398:A183D|.	A|L	+|+	2|1	0|2	HLA-DQA1|HLA-DQA1	32717943|32717943	0.000000|0.000000	0.05858|0.05858	0.883000|0.883000	0.34634|0.34634	0.706000|0.706000	0.40770|0.40770	-1.379000|-1.379000	0.02554|0.02554	-0.572000|-0.572000	0.06006|0.06006	-0.182000|-0.182000	0.12963|0.12963	GCT|CTG	C|0.928;A|0.072	0.072	strong		0.468	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
PLAT	5327	hgsc.bcm.edu	37	8	42044954	42044954	+	Silent	SNP	G	G	A	rs1058720	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:42044954G>A	ENST00000220809.4	-	6	757	c.501C>T	c.(499-501)gaC>gaT	p.D167D	PLAT_ENST00000352041.3_Silent_p.D121D|PLAT_ENST00000429089.2_Silent_p.D167D|PLAT_ENST00000519510.1_Intron|PLAT_ENST00000429710.2_Intron|PLAT_ENST00000270189.6_Silent_p.D167D|PLAT_ENST00000524009.1_Intron	NM_000930.3	NP_000921.1	P00750	TPA_HUMAN	plasminogen activator, tissue	167	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|fibrinolysis (GO:0042730)|negative regulation of proteolysis (GO:0045861)|plasminogen activation (GO:0031639)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of ovulation (GO:0060279)|proteolysis (GO:0006508)|regulation of synaptic plasticity (GO:0048167)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|smooth muscle cell migration (GO:0014909)|synaptic transmission, glutamatergic (GO:0035249)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|synapse (GO:0045202)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|skin(1)|soft_tissue(1)|urinary_tract(1)	27	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Aminocaproic Acid(DB00513)|Ibuprofen(DB01050)|Iloprost(DB01088)|Urokinase(DB00013)	GCCTGATGGCGTCTGGCCTCC	0.642													G|||	2558	0.510783	0.348	0.5735	5008	,	,		20228	0.504		0.5855	False		,,,				2504	0.6166				p.D167D		Atlas-SNP	.											.	PLAT	62	.	0			c.C501T						PASS	.	G	,	1782,2624	523.5+/-371.1	364,1054,785	44.0	44.0	44.0		501,363	-11.9	0.0	8	dbSNP_86	44	4799,3801	612.7+/-396.0	1356,2087,857	yes	coding-synonymous,coding-synonymous	PLAT	NM_000930.3,NM_033011.2	,	1720,3141,1642	AA,AG,GG		44.1977,40.4448,49.4003	,	167/563,121/517	42044954	6581,6425	2203	4300	6503	SO:0001819	synonymous_variant	5327	exon6			GATGGCGTCTGGC		CCDS6126.1, CCDS6127.1	8p11.21	2012-10-02			ENSG00000104368	ENSG00000104368			9051	protein-coding gene	gene with protein product		173370					Standard	NM_033011		Approved		uc003xos.2	P00750	OTTHUMG00000164072	ENST00000220809.4:c.501C>T	8.37:g.42044954G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_000930	A8K022|B2R8E8|Q15103|Q503B0|Q6PJA5|Q7Z7N2|Q86YK8|Q9BU99|Q9BZW1	Silent	SNP	ENST00000220809.4	37	CCDS6126.1																																																																																			G|0.488;A|0.512	0.512	strong		0.642	PLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377100.1	NM_000930	
SAMD9	54809	hgsc.bcm.edu	37	7	92735154	92735154	+	Missense_Mutation	SNP	G	G	A	rs147157740	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:92735154G>A	ENST00000379958.2	-	3	526	c.257C>T	c.(256-258)tCt>tTt	p.S86F		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	86						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TCCCATCTTAGATGTCTGAAT	0.383													G|||	15	0.00299521	0.0	0.0072	5008	,	,		18338	0.0		0.0099	False		,,,				2504	0.0				p.S86F		Atlas-SNP	.											.	SAMD9	239	.	0			c.C257T						PASS	.	G	PHE/SER,PHE/SER	7,4399	12.9+/-30.5	0,7,2196	171.0	169.0	170.0		257,257	-2.1	0.0	7	dbSNP_134	170	58,8542	36.4+/-91.3	0,58,4242	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	155,155	0,65,6438	AA,AG,GG		0.6744,0.1589,0.4998	benign,benign	86/1590,86/1590	92735154	65,12941	2203	4300	6503	SO:0001583	missense	54809	exon2			ATCTTAGATGTCT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.257C>T	7.37:g.92735154G>A	ENSP00000369292:p.Ser86Phe	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	217	105	0.483871	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	9.731	1.162254	0.21538	0.001589	0.006744	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.25250	1.81;2.63	4.6	-2.08	0.07254	.	1.711930	0.03721	N	0.251921	T	0.11922	0.0290	L	0.27053	0.805	0.09310	N	1	B	0.32653	0.379	B	0.30782	0.12	T	0.20605	-1.0270	10	0.62326	D	0.03	.	4.2849	0.10850	0.0861:0.4566:0.2508:0.2066	.	86	Q5K651	SAMD9_HUMAN	F	86	ENSP00000369292:S86F;ENSP00000414529:S86F	ENSP00000369292:S86F	S	-	2	0	SAMD9	92573090	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.011000	0.12721	-0.530000	0.06349	-1.368000	0.01194	TCT	G|0.995;A|0.005	0.005	strong		0.383	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
TMEM2	23670	hgsc.bcm.edu	37	9	74349846	74349846	+	Missense_Mutation	SNP	A	A	T	rs25695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:74349846A>T	ENST00000377044.4	-	6	1808	c.1269T>A	c.(1267-1269)gaT>gaA	p.D423E	TMEM2_ENST00000377066.5_Intron	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	423			D -> E (in dbSNP:rs25695).		multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		AACTACTAACATCATCTAGCA	0.408													A|||	406	0.0810703	0.0386	0.0476	5008	,	,		17399	0.0198		0.0815	False		,,,				2504	0.2249				p.D423E		Atlas-SNP	.											.	TMEM2	112	.	0			c.T1269A						PASS	.	A	,GLU/ASP	173,4233	113.3+/-151.4	6,161,2036	198.0	188.0	191.0		,1269	-7.4	0.7	9	dbSNP_72	191	724,7876	176.3+/-226.2	31,662,3607	yes	intron,missense	TMEM2	NM_001135820.1,NM_013390.2	,45	37,823,5643	TT,TA,AA		8.4186,3.9265,6.8968	,benign	,423/1384	74349846	897,12109	2203	4300	6503	SO:0001583	missense	23670	exon6			ACTAACATCATCT		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1269T>A	9.37:g.74349846A>T	ENSP00000366243:p.Asp423Glu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	172	84	0.488372	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	123	0.05631868131868132	27	0.054878048780487805	21	0.058011049723756904	13	0.022727272727272728	62	0.08179419525065963	A	11.46	1.646357	0.29246	0.039265	0.084186	ENSG00000135048	ENST00000377044	T	0.80123	-1.34	6.08	-7.36	0.01417	Pectin lyase fold/virulence factor (1);	0.146554	0.64402	D	0.000012	T	0.17704	0.0425	M	0.81497	2.545	0.80722	D	1	B	0.32245	0.361	B	0.30029	0.11	T	0.54289	-0.8316	10	0.41790	T	0.15	.	18.5272	0.90976	0.4864:0.0:0.5136:0.0	rs25695;rs17476197;rs25695	423	Q9UHN6	TMEM2_HUMAN	E	423	ENSP00000366243:D423E	ENSP00000366243:D423E	D	-	3	2	TMEM2	73539666	0.011000	0.17503	0.663000	0.29738	0.318000	0.28184	-0.689000	0.05144	-1.738000	0.01348	-1.139000	0.01908	GAT	A|0.936;T|0.064	0.064	strong		0.408	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
C3orf14	57415	hgsc.bcm.edu	37	3	62319048	62319048	+	Missense_Mutation	SNP	A	A	G	rs114729571	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:62319048A>G	ENST00000494481.1	+	6	685	c.371A>G	c.(370-372)aAt>aGt	p.N124S	C3orf14_ENST00000542214.1_Missense_Mutation_p.N124S|PTPRG-AS1_ENST00000490916.1_RNA|PTPRG-AS1_ENST00000495542.1_RNA|C3orf14_ENST00000232519.5_Missense_Mutation_p.N124S|C3orf14_ENST00000462069.1_Missense_Mutation_p.N124S			Q9HBI5	CC014_HUMAN	chromosome 3 open reading frame 14	124										central_nervous_system(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.00023)|KIRC - Kidney renal clear cell carcinoma(15;0.00877)|Kidney(15;0.0101)		ACCATTCAAAATGAGGCACAG	0.343													A|||	87	0.0173722	0.003	0.0173	5008	,	,		18616	0.001		0.0487	False		,,,				2504	0.0215				p.N124S		Atlas-SNP	.											.	C3orf14	10	.	0			c.A371G						PASS	.	A	SER/ASN	27,4379	34.3+/-65.2	0,27,2176	86.0	83.0	84.0		371	0.2	0.0	3	dbSNP_132	84	279,8321	103.1+/-164.3	5,269,4026	yes	missense	C3orf14	NM_020685.3	46	5,296,6202	GG,GA,AA		3.2442,0.6128,2.3528	benign	124/129	62319048	306,12700	2203	4300	6503	SO:0001583	missense	57415	exon5			TTCAAAATGAGGC	AF236158	CCDS2896.1	3p14.2	2011-11-29			ENSG00000114405	ENSG00000114405			25024	protein-coding gene	gene with protein product						12477932	Standard	XM_005265338		Approved	HT021	uc003dlg.3	Q9HBI5	OTTHUMG00000158704	ENST00000494481.1:c.371A>G	3.37:g.62319048A>G	ENSP00000418086:p.Asn124Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	45	28	0.622222	NM_020685	B2R9U0	Missense_Mutation	SNP	ENST00000494481.1	37	CCDS2896.1	47	0.02152014652014652	2	0.0040650406504065045	7	0.019337016574585635	1	0.0017482517482517483	37	0.048812664907651716	A	8.480	0.859662	0.17178	0.006128	0.032442	ENSG00000114405	ENST00000462069;ENST00000232519;ENST00000494481;ENST00000542214	.	.	.	6.16	0.165	0.14995	.	1.152020	0.06270	N	0.695574	T	0.03959	0.0111	N	0.16478	0.41	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.15150	-1.0447	9	0.19147	T	0.46	-8.852	5.0634	0.14568	0.5368:0.2746:0.1885:0.0	.	124	Q9HBI5	CC014_HUMAN	S	124	.	ENSP00000232519:N124S	N	+	2	0	C3orf14	62294088	0.008000	0.16893	0.000000	0.03702	0.378000	0.30076	0.756000	0.26419	-0.175000	0.10725	-0.256000	0.11100	AAT	A|0.977;G|0.023	0.023	strong		0.343	C3orf14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351807.1	NM_020685	
PCDHB7	56129	hgsc.bcm.edu	37	5	140554606	140554606	+	Silent	SNP	T	T	C	rs11741863	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140554606T>C	ENST00000231137.3	+	1	2364	c.2190T>C	c.(2188-2190)ttT>ttC	p.F730F	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	730					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGGCCCCTTTCCACGACATC	0.647													T|||	1352	0.269968	0.0484	0.3055	5008	,	,		22194	0.5278		0.2296	False		,,,				2504	0.32				p.F730F		Atlas-SNP	.											PCDHB7,caecum,carcinoma,0,1	PCDHB7	231	1	0			c.T2190C						PASS	.	T		219,4187		9,201,1993	82.0	130.0	114.0		2190	-3.4	0.5	5	dbSNP_120	114	1407,7193		209,989,3102	no	coding-synonymous	PCDHB7	NM_018940.2		218,1190,5095	CC,CT,TT		16.3605,4.9705,12.5019		730/794	140554606	1626,11380	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			CCCCTTTCCACGA	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2190T>C	5.37:g.140554606T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	265	99	0.373585	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			T|0.805;C|0.195	0.195	strong		0.647	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
SLC28A2	9153	hgsc.bcm.edu	37	15	45554267	45554267	+	Missense_Mutation	SNP	C	C	A	rs1060896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45554267C>A	ENST00000347644.3	+	4	290	c.225C>A	c.(223-225)agC>agA	p.S75R	CTD-2651B20.3_ENST00000561404.1_RNA|CTD-2651B20.3_ENST00000560344.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	75			S -> R (in dbSNP:rs1060896). {ECO:0000269|PubMed:10087507, ECO:0000269|PubMed:15861032, ECO:0000269|PubMed:17700367}.		nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Mercaptopurine(DB01033)	CACACGCCAGCTTGTTCAAGA	0.403													C|||	1568	0.313099	0.1082	0.3905	5008	,	,		19707	0.1181		0.6322	False		,,,				2504	0.408				p.S75R	NSCLC(92;493 1501 26361 28917 47116)	Atlas-SNP	.											SLC28A2,NS,carcinoma,+1,1	SLC28A2	64	1	0			c.C225A						PASS	.	C	ARG/SER	861,3535	337.3+/-304.8	91,679,1428	179.0	163.0	169.0		225	-3.7	0.0	15	dbSNP_86	169	5714,2882	672.0+/-402.9	1872,1970,456	yes	missense	SLC28A2	NM_004212.3	110	1963,2649,1884	AA,AC,CC		33.5272,19.586,49.3919	benign	75/659	45554267	6575,6417	2198	4298	6496	SO:0001583	missense	9153	exon4			CGCCAGCTTGTTC	U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"""Solute carriers"""	11002	protein-coding gene	gene with protein product		606208	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"""			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.225C>A	15.37:g.45554267C>A	ENSP00000315006:p.Ser75Arg	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	157	76	0.484076	NM_004212	A8K7F9|O43239|Q52LZ0	Missense_Mutation	SNP	ENST00000347644.3	37	CCDS10121.1	746	0.3415750915750916	58	0.11788617886178862	157	0.43370165745856354	37	0.06468531468531469	494	0.6517150395778364	C	6.322	0.427502	0.11987	0.19586	0.664728	ENSG00000137860	ENST00000347644	T	0.80909	-1.43	5.64	-3.67	0.04476	.	1.450760	0.03631	N	0.237861	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39643	-0.9604	9	0.14252	T	0.57	4.8993	1.2998	0.02077	0.4269:0.1862:0.2244:0.1625	rs1060896;rs17215647;rs17532209;rs52828213;rs58568974;rs1060896	75	O43868	S28A2_HUMAN	R	75	ENSP00000315006:S75R	ENSP00000315006:S75R	S	+	3	2	SLC28A2	43341559	0.000000	0.05858	0.016000	0.15963	0.768000	0.43524	-1.600000	0.02083	-0.195000	0.10382	-0.488000	0.04728	AGC	C|0.608;A|0.391	0.391	strong		0.403	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212	
EMR1	2015	hgsc.bcm.edu	37	19	6921868	6921868	+	Missense_Mutation	SNP	G	G	A	rs7256147	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6921868G>A	ENST00000312053.4	+	14	1802	c.1765G>A	c.(1765-1767)Gtt>Att	p.V589I	EMR1_ENST00000250572.8_Missense_Mutation_p.V589I|EMR1_ENST00000450315.3_Missense_Mutation_p.V412I|EMR1_ENST00000381404.4_Missense_Mutation_p.V537I|EMR1_ENST00000381407.5_Missense_Mutation_p.V448I	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	589	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.|Ser/Thr-rich.		V -> I (in dbSNP:rs7256147). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					AAATCTTGCCGTTATCATGGC	0.458													G|||	1132	0.226038	0.2534	0.1758	5008	,	,		20422	0.2024		0.2177	False		,,,				2504	0.2577				p.V589I		Atlas-SNP	.											.	EMR1	153	.	0			c.G1765A						PASS	.	G	ILE/VAL	1017,3389	378.3+/-322.8	119,779,1305	168.0	142.0	151.0		1765	-2.5	0.2	19	dbSNP_116	151	1720,6880	313.7+/-311.4	152,1416,2732	yes	missense	EMR1	NM_001974.3	29	271,2195,4037	AA,AG,GG		20.0,23.0822,21.0441	benign	589/887	6921868	2737,10269	2203	4300	6503	SO:0001583	missense	2015	exon14			CTTGCCGTTATCA	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.1765G>A	19.37:g.6921868G>A	ENSP00000311545:p.Val589Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	142	56	0.394366	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	440	0.20146520146520147	144	0.2926829268292683	51	0.1408839779005525	92	0.16083916083916083	153	0.20184696569920843	G	0.088	-1.171130	0.01660	0.230822	0.2	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4;-0.4	4.43	-2.52	0.06346	GPS domain (3);	.	.	.	.	T	0.00012	0.0000	N	0.04387	-0.21	0.58432	P	6.999999999979245E-6	B;B;B;B	0.22604	0.012;0.017;0.072;0.021	B;B;B;B	0.17722	0.006;0.011;0.019;0.011	T	0.10567	-1.0624	8	0.02654	T	1	.	11.3457	0.49559	0.4153:0.0:0.5847:0.0	rs7256147;rs17855005;rs52793961;rs60313628;rs7256147	412;589;537;589	E7EPX9;Q14246-2;E9PD45;Q14246	.;.;.;EMR1_HUMAN	I	589;589;537;589;448;412	ENSP00000311545:V589I;ENSP00000370811:V537I;ENSP00000250572:V589I;ENSP00000370814:V448I;ENSP00000405974:V412I	ENSP00000250572:V589I	V	+	1	0	EMR1	6872868	0.001000	0.12720	0.158000	0.22627	0.004000	0.04260	-0.809000	0.04510	-0.787000	0.04510	-0.811000	0.03165	GTT	G|0.783;A|0.217	0.217	strong		0.458	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
RGAG4	340526	hgsc.bcm.edu	37	X	71349774	71349774	+	Silent	SNP	T	T	C	rs12393722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:71349774T>C	ENST00000545866.1	-	1	1984	c.1617A>G	c.(1615-1617)ggA>ggG	p.G539G	NHSL2_ENST00000540800.1_Intron|RGAG4_ENST00000609883.1_Silent_p.G539G	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	539										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					CTTGGCGTTGTCCTAAACGAC	0.592													C|||	1454	0.385166	0.1021	0.4193	3775	,	,		13966	0.119		0.5964	False		,,,				2504	0.3149				p.G539G		Atlas-SNP	.											.	RGAG4	63	.	0			c.A1617G						PASS	.	C	,	813,2507		106,477,124,792,446	46.0	49.0	48.0		,1617	2.2	0.9	X	dbSNP_120	48	5125,1342		1484,736,1421,120,366	no	intron,coding-synonymous	RGAG4,NHSL2	NM_001013627.2,NM_001024455.3	,	1590,1213,1545,912,812	CC,CT,C,TT,T		20.7515,24.488,39.3277	,	,539/570	71349774	5938,3849	1945	4127	6072	SO:0001819	synonymous_variant	340526	exon1			GCGTTGTCCTAAA	AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.1617A>G	X.37:g.71349774T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Silent	SNP	ENST00000545866.1	37	CCDS55446.1																																																																																			T|0.599;C|0.401	0.401	strong		0.592	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
EYS	346007	hgsc.bcm.edu	37	6	66005888	66005888	+	Missense_Mutation	SNP	C	C	T	rs9342464	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:66005888C>T	ENST00000370621.3	-	12	2417	c.1891G>A	c.(1891-1893)Ggt>Agt	p.G631S	EYS_ENST00000370616.2_Missense_Mutation_p.G631S|EYS_ENST00000503581.1_Missense_Mutation_p.G631S			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	631			G -> S (in dbSNP:rs9342464). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTTTGCAGACCGCTACAGTTA	0.433													C|||	2980	0.595048	0.2209	0.7161	5008	,	,		13425	0.8948		0.5924	False		,,,				2504	0.7086				p.G631S		Atlas-SNP	.											.	EYS	527	.	0			c.G1891A						PASS	.	C	SER/GLY	416,968		70,276,346	155.0	120.0	131.0		1891	1.7	0.0	6	dbSNP_119	131	1856,1326		535,786,270	yes	missense	EYS	NM_001142800.1	56	605,1062,616	TT,TC,CC		41.6719,30.0578,49.7591	benign	631/3145	66005888	2272,2294	692	1591	2283	SO:0001583	missense	346007	exon12			GCAGACCGCTACA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1891G>A	6.37:g.66005888C>T	ENSP00000359655:p.Gly631Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	103	99	0.961165	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		1323	0.6057692307692307	107	0.21747967479674796	254	0.7016574585635359	523	0.9143356643356644	439	0.579155672823219	.	3.705	-0.060638	0.07317	0.300578	0.583281	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.81163	-1.46;-1.46;-1.46	5.48	1.71	0.24356	.	.	.	.	.	T	0.41050	0.1142	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.05289	-1.0894	8	0.72032	D	0.01	.	6.0161	0.19603	0.5668:0.157:0.0:0.2762	rs9342464;rs17411829;rs9342464	631	Q5T1H1-1	.	S	631	ENSP00000424243:G631S;ENSP00000359655:G631S;ENSP00000359650:G631S	ENSP00000359650:G631S	G	-	1	0	EYS	66062609	0.005000	0.15991	0.025000	0.17156	0.010000	0.07245	2.140000	0.42159	0.054000	0.16065	-1.556000	0.00890	GGT	C|0.404;T|0.596	0.596	strong		0.433	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
CHPF2	54480	hgsc.bcm.edu	37	7	150934975	150934975	+	Silent	SNP	C	C	G	rs2487154	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150934975C>G	ENST00000035307.2	+	4	3040	c.1527C>G	c.(1525-1527)gcC>gcG	p.A509A	CHPF2_ENST00000495645.1_Silent_p.A501A|RP4-548D19.3_ENST00000607902.1_RNA|MIR671_ENST00000390183.1_RNA	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	509					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TCCTCGAGGCCTTTGCAGCCA	0.602													C|||	2171	0.433506	0.2685	0.4164	5008	,	,		17374	0.7153		0.4503	False		,,,				2504	0.3609				p.A509A		Atlas-SNP	.											.	CHPF2	52	.	0			c.C1527G						PASS	.	C		1305,3099		204,897,1101	34.0	33.0	33.0		1527	5.0	1.0	7	dbSNP_100	33	3510,5088		712,2086,1501	no	coding-synonymous	CHPF2	NM_019015.1		916,2983,2602	GG,GC,CC		40.8234,29.6322,37.0328		509/773	150934975	4815,8187	2202	4299	6501	SO:0001819	synonymous_variant	54480	exon4			CGAGGCCTTTGCA	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.1527C>G	7.37:g.150934975C>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Silent	SNP	ENST00000035307.2	37	CCDS34779.1																																																																																			C|0.595;G|0.405	0.405	strong		0.602	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
MCM9	254394	hgsc.bcm.edu	37	6	119136759	119136759	+	Missense_Mutation	SNP	A	A	C	rs65685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:119136759A>C	ENST00000316316.6	-	13	2946	c.2660T>G	c.(2659-2661)aTg>aGg	p.M887R		NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	887					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		TGAGTCCAGCATTCTGTCTGG	0.532													A|||	454	0.090655	0.034	0.1037	5008	,	,		19843	0.0605		0.1262	False		,,,				2504	0.1524				p.M887R		Atlas-SNP	.											.	MCM9	73	.	0			c.T2660G						PASS	.																																			SO:0001583	missense	254394	exon12			TCCAGCATTCTGT	BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"""minichromosome maintenance deficient domain containing 1"", ""chromosome 6 open reading frame 61"""	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.2660T>G	6.37:g.119136759A>C	ENSP00000314505:p.Met887Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	192	0.08791208791208792	20	0.04065040650406504	43	0.11878453038674033	34	0.05944055944055944	95	0.12532981530343007	A	6.329	0.428846	0.11987	.	.	ENSG00000111877	ENST00000316316;ENST00000243218	T	0.03301	3.98	6.03	-12.1	0.00011	.	.	.	.	.	T	0.00241	0.0007	N	0.01352	-0.895	0.80722	P	0.0	.	.	.	.	.	.	T	0.49615	-0.8921	6	0.13470	T	0.59	.	0.0368	0.00007	0.2851:0.2236:0.2089:0.2823	rs65685;rs3751443;rs17235356;rs60968013;rs65685	.	.	.	R	887;506	ENSP00000314505:M887R	ENSP00000243218:M506R	M	-	2	0	MCM9	119243462	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.254000	0.02874	-2.074000	0.00877	-0.177000	0.13119	ATG	A|0.878;C|0.085	0.085	strong		0.532	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
DEPTOR	64798	hgsc.bcm.edu	37	8	121013770	121013770	+	Missense_Mutation	SNP	A	A	G	rs2271900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:121013770A>G	ENST00000286234.5	+	5	741	c.611A>G	c.(610-612)aAc>aGc	p.N204S	DEPTOR_ENST00000523492.1_Missense_Mutation_p.N103S|DEPTOR_ENST00000518057.1_3'UTR	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	204	DEP 2. {ECO:0000255|PROSITE- ProRule:PRU00066}.		N -> S (in dbSNP:rs2271900). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						CCAGTGTCCAACAAGCACCCA	0.512													A|||	3211	0.641174	0.4743	0.7219	5008	,	,		16927	0.7093		0.7296	False		,,,				2504	0.6483				p.N204S		Atlas-SNP	.											.	DEPTOR	41	.	0			c.A611G						PASS	.	A	SER/ASN	2247,2159	594.5+/-388.2	578,1091,534	47.0	48.0	48.0		611	3.6	1.0	8	dbSNP_100	48	6210,2390	700.8+/-405.2	2234,1742,324	yes	missense	DEPTOR	NM_022783.2	46	2812,2833,858	GG,GA,AA		27.7907,49.0014,34.9762	benign	204/410	121013770	8457,4549	2203	4300	6503	SO:0001583	missense	64798	exon5			TGTCCAACAAGCA		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"""DEP domain containing 6"""	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.611A>G	8.37:g.121013770A>G	ENSP00000286234:p.Asn204Ser	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	30	17	0.566667	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Missense_Mutation	SNP	ENST00000286234.5	37	CCDS6331.1	1475	0.6753663003663004	228	0.4634146341463415	266	0.7348066298342542	419	0.7325174825174825	562	0.741424802110818	A	13.80	2.345632	0.41498	0.509986	0.722093	ENSG00000155792	ENST00000523492;ENST00000286234	T;T	0.14640	2.49;2.49	6.03	3.58	0.41010	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.081277	0.85682	D	0.000000	T	0.00012	0.0000	L	0.38838	1.175	0.19575	P	0.9999677986	P;B	0.35527	0.507;0.015	B;B	0.40702	0.338;0.02	T	0.02081	-1.1217	9	0.22706	T	0.39	-45.1096	8.909	0.35541	0.8077:0.127:0.0654:0.0	rs2271900;rs17852241;rs17858161;rs52812290;rs56851525;rs2271900	103;204	E7EV87;Q8TB45	.;DPTOR_HUMAN	S	103;204	ENSP00000430457:N103S;ENSP00000286234:N204S	ENSP00000286234:N204S	N	+	2	0	DEPTOR	121082951	1.000000	0.71417	1.000000	0.80357	0.390000	0.30446	4.774000	0.62339	1.112000	0.41740	0.533000	0.62120	AAC	A|0.344;G|0.656	0.656	strong		0.512	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783	
PEAR1	375033	hgsc.bcm.edu	37	1	156883493	156883493	+	Missense_Mutation	SNP	G	G	A	rs11264581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156883493G>A	ENST00000338302.3	+	22	2879	c.2654G>A	c.(2653-2655)cGc>cAc	p.R885H	PEAR1_ENST00000292357.7_Missense_Mutation_p.R885H			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	885	Pro-rich.		R -> H (in dbSNP:rs11264581).		recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGGAGCAGCCGCCTGGACCGA	0.612													G|||	1161	0.231829	0.0469	0.2954	5008	,	,		16121	0.4732		0.1759	False		,,,				2504	0.2454				p.R885H		Atlas-SNP	.											.	PEAR1	118	.	0			c.G2654A						PASS	.	G	HIS/ARG	293,4113	159.6+/-192.1	7,279,1917	37.0	38.0	38.0		2654	-3.7	0.7	1	dbSNP_120	38	1577,7023	291.1+/-300.1	149,1279,2872	yes	missense	PEAR1	NM_001080471.1	29	156,1558,4789	AA,AG,GG		18.3372,6.65,14.378	benign	885/1038	156883493	1870,11136	2203	4300	6503	SO:0001583	missense	375033	exon21			GCAGCCGCCTGGA	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.2654G>A	1.37:g.156883493G>A	ENSP00000344465:p.Arg885His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	125	76	0.608	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	488	0.22344322344322345	26	0.052845528455284556	79	0.21823204419889503	251	0.4388111888111888	132	0.1741424802110818	G	13.25	2.182510	0.38511	0.0665	0.183372	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.88975	-2.45;-2.45	5.78	-3.72	0.04411	.	0.543959	0.15501	N	0.259052	T	0.45975	0.1369	N	0.03608	-0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.28396	-1.0045	9	0.15066	T	0.55	.	5.0929	0.14718	0.2315:0.0:0.3078:0.4608	rs11264581;rs59112747;rs11264581	885	Q5VY43	PEAR1_HUMAN	H	885	ENSP00000344465:R885H;ENSP00000292357:R885H	ENSP00000292357:R885H	R	+	2	0	PEAR1	155150117	0.000000	0.05858	0.737000	0.30932	0.740000	0.42216	-0.451000	0.06795	-0.439000	0.07222	0.563000	0.77884	CGC	G|0.832;A|0.168	0.168	strong		0.612	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
SYNE1	23345	hgsc.bcm.edu	37	6	152683413	152683413	+	Silent	SNP	G	G	T	rs4407724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152683413G>T	ENST00000367255.5	-	64	10792	c.10191C>A	c.(10189-10191)ggC>ggA	p.G3397G	SYNE1_ENST00000265368.4_Silent_p.G3397G|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000448038.1_Silent_p.G3404G|SYNE1_ENST00000423061.1_Silent_p.G3404G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3397					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ACTGTCGAACGCCATCCTGAT	0.468										HNSCC(10;0.0054)			G|||	3301	0.659145	0.5764	0.6859	5008	,	,		20411	0.7927		0.6799	False		,,,				2504	0.593				p.G3404G		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C10212A						PASS	.	G	,	2576,1830	637.5+/-396.8	751,1074,378	129.0	118.0	122.0		10212,10191	-5.7	0.3	6	dbSNP_111	122	5853,2747	680.2+/-403.6	1995,1863,442	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	2746,2937,820	TT,TG,GG		31.9419,41.5343,35.1915	,	3404/8750,3397/8798	152683413	8429,4577	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon64			TCGAACGCCATCC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.10191C>A	6.37:g.152683413G>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	234	105	0.448718	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			G|0.332;T|0.668	0.668	strong		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SBF2	81846	hgsc.bcm.edu	37	11	9879838	9879838	+	Missense_Mutation	SNP	C	C	T	rs7102464	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:9879838C>T	ENST00000256190.8	-	18	2172	c.2035G>A	c.(2035-2037)Gaa>Aaa	p.E679K	RP11-1H15.2_ENST00000533659.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	679			E -> K (in dbSNP:rs7102464).		cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		CGAACCTGTTCCTGCACTGCA	0.468													C|||	164	0.0327476	0.0023	0.0519	5008	,	,		19098	0.0		0.1163	False		,,,				2504	0.0082				p.E679K		Atlas-SNP	.											.	SBF2	146	.	0			c.G2035A						PASS	.	C	LYS/GLU	102,4300	81.9+/-120.4	1,100,2100	211.0	191.0	198.0		2035	4.3	1.0	11	dbSNP_116	198	918,7670	203.8+/-246.7	64,790,3440	yes	missense	SBF2	NM_030962.3	56	65,890,5540	TT,TC,CC		10.6893,2.3171,7.8522	benign	679/1850	9879838	1020,11970	2201	4294	6495	SO:0001583	missense	81846	exon18			CCTGTTCCTGCAC	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	2135	protein-coding gene	gene with protein product	"""myotubularin related 13"""	607697	"""Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)"", ""DENN/MADD domain containing 7B"""	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.2035G>A	11.37:g.9879838C>T	ENSP00000256190:p.Glu679Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	37	CCDS31427.1	122|122	0.055860805860805864|0.055860805860805864	3|3	0.006097560975609756|0.006097560975609756	20|20	0.055248618784530384|0.055248618784530384	0|0	0.0|0.0	99|99	0.13060686015831136|0.13060686015831136	C|C	10.67|10.67	1.415362|1.415362	0.25552|0.25552	0.023171|0.023171	0.106893|0.106893	ENSG00000133812|ENSG00000133812	ENST00000256190|ENST00000420722	T|.	0.41400|.	1.0|.	5.36|5.36	4.34|4.34	0.51931|0.51931	.|.	0.157913|.	0.56097|.	D|.	0.000034|.	T|T	0.00144|0.00144	0.0004|0.0004	N|N	0.01705|0.01705	-0.755|-0.755	0.35399|0.35399	D|D	0.791393|0.791393	B|.	0.02656|.	0.0|.	B|.	0.09377|.	0.004|.	T|T	0.26883|0.26883	-1.0090|-1.0090	10|5	0.09084|.	T|.	0.74|.	.|.	3.53|3.53	0.07773|0.07773	0.0:0.6334:0.0:0.3666|0.0:0.6334:0.0:0.3666	rs7102464;rs17354351;rs52819750;rs61100799;rs7102464|rs7102464;rs17354351;rs52819750;rs61100799;rs7102464	679|.	Q86WG5|.	MTMRD_HUMAN|.	K|E	679|285	ENSP00000256190:E679K|.	ENSP00000256190:E679K|.	E|G	-|-	1|2	0|0	SBF2|SBF2	9836414|9836414	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.946000|4.946000	0.63576|0.63576	2.523000|2.523000	0.85059|0.85059	0.552000|0.552000	0.68991|0.68991	GAA|GGA	C|0.933;T|0.067	0.067	strong		0.468	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962	
CARS2	79587	hgsc.bcm.edu	37	13	111340342	111340342	+	Silent	SNP	G	G	A	rs2304767	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:111340342G>A	ENST00000257347.4	-	4	480	c.417C>T	c.(415-417)ctC>ctT	p.L139L	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	139					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	AAAGACTGGCGAGGGAAGCGG	0.527													G|||	741	0.147963	0.0151	0.2176	5008	,	,		18287	0.12		0.325	False		,,,				2504	0.1247				p.L139L		Atlas-SNP	.											.	CARS2	37	.	0			c.C417T						PASS	.	G		301,4105	164.4+/-196.0	13,275,1915	68.0	61.0	63.0		417	-9.4	0.0	13	dbSNP_100	63	2879,5721	449.7+/-362.2	494,1891,1915	no	coding-synonymous	CARS2	NM_024537.2		507,2166,3830	AA,AG,GG		33.4767,6.8316,24.4503		139/565	111340342	3180,9826	2203	4300	6503	SO:0001819	synonymous_variant	79587	exon4			ACTGGCGAGGGAA	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.417C>T	13.37:g.111340342G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_024537	Q8NI84|Q96IV4	Silent	SNP	ENST00000257347.4	37	CCDS9514.1																																																																																			G|0.791;A|0.209	0.209	strong		0.527	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	
FLYWCH1	84256	hgsc.bcm.edu	37	16	2983138	2983138	+	Silent	SNP	C	C	T	rs2074363	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2983138C>T	ENST00000253928.9	+	5	1209	c.804C>T	c.(802-804)gcC>gcT	p.A268A	FLYWCH1_ENST00000416288.2_Silent_p.A267A|FLYWCH1_ENST00000399667.2_Silent_p.A268A			Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1	268						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|lung(3)	4						TAGGACAGGCCCGGCCCCTCG	0.627													.|||	532	0.10623	0.1725	0.1009	5008	,	,		16167	0.0625		0.1143	False		,,,				2504	0.0573				p.A267A		Atlas-SNP	.											.	FLYWCH1	27	.	0			c.C801T						PASS	.	C	,	495,3431		39,417,1507	24.0	27.0	26.0		801,801	0.9	0.0	16	dbSNP_96	26	837,7425		44,749,3338	no	coding-synonymous,coding-synonymous	FLYWCH1	NM_020912.1,NM_032296.2	,	83,1166,4845	TT,TC,CC		10.1307,12.6083,10.9288	,	267/704,267/716	2983138	1332,10856	1963	4131	6094	SO:0001819	synonymous_variant	84256	exon5			ACAGGCCCGGCCC	AL136585	CCDS45390.1	16p13.3	2013-01-10	2007-06-21	2007-06-21	ENSG00000059122	ENSG00000059122		"""Zinc fingers"""	25404	protein-coding gene	gene with protein product						11230166, 10997877	Standard	XM_006720959		Approved	DKFZp761A132	uc002csc.3	Q4VC44		ENST00000253928.9:c.804C>T	16.37:g.2983138C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	38	37	0.973684	NM_020912	D3DUA1|Q6ZSQ1|Q8WV62|Q9BQG6|Q9BUS5|Q9HCM0	Silent	SNP	ENST00000253928.9	37																																																																																				C|0.877;T|0.123	0.123	strong		0.627	FLYWCH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000436479.1	NM_032296	
MFSD3	113655	hgsc.bcm.edu	37	8	145737816	145737816	+	IGR	SNP	C	C	T	rs4251691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145737816C>T	ENST00000301327.4	+	0	1548				RECQL4_ENST00000532237.1_5'UTR|RECQL4_ENST00000428558.2_Missense_Mutation_p.R1005Q|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GCAGAGAGCCCGCCGCACAGA	0.667													C|||	1925	0.384385	0.0635	0.4899	5008	,	,		17898	0.4762		0.4543	False		,,,				2504	0.5767				p.R1005Q		Atlas-SNP	.											RECQL4,rectum,carcinoma,0,1	RECQL4	75	1	0			c.G3014A						PASS	.	C	GLN/ARG	543,3685		54,435,1625	22.0	31.0	28.0		3015	0.3	0.1	8	dbSNP_111	28	3802,4678		875,2052,1313	no	missense	RECQL4	NM_004260.3	43	929,2487,2938	TT,TC,CC		44.8349,12.843,34.1911	benign	1005/1209	145737816	4345,8363	2114	4240	6354	SO:0001628	intergenic_variant	9401	exon18			AGAGCCCGCCGCA		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		8.37:g.145737816C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_004260		Missense_Mutation	SNP	ENST00000301327.4	37	CCDS6431.1																																																																																			C|0.624;T|0.376	0.376	strong		0.667	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
C1orf68	100129271	hgsc.bcm.edu	37	1	152692074	152692074	+	Missense_Mutation	SNP	G	G	C	rs1332500	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152692074G>C	ENST00000368775.2	+	1	77	c.77G>C	c.(76-78)aGc>aCc	p.S26T		NM_001024679.2	NP_001019850.1	Q5T750	XP32_HUMAN	chromosome 1 open reading frame 68	26			S -> T (in dbSNP:rs1332500).		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)		p.S26T(1)		NS(1)|breast(1)|lung(2)|prostate(1)|stomach(3)	8						GGGCAGGGTAGCAATGGTGCC	0.522													C|||	1749	0.349241	0.5461	0.3804	5008	,	,		17303	0.1716		0.3608	False		,,,				2504	0.2321				p.S26T		Atlas-SNP	.											C1orf68,NS,carcinoma,0,1	C1orf68	19	1	1	Substitution - Missense(1)	stomach(1)	c.G77C						PASS	.						102.0	100.0	101.0					1																	152692074		692	1591	2283	SO:0001583	missense	100129271	exon1			AGGGTAGCAATGG	AF005081	CCDS44226.1	1q21.3	2014-05-30			ENSG00000198854	ENSG00000198854			29468	protein-coding gene	gene with protein product						11698679	Standard	NM_001024679		Approved	LEP7	uc010pdu.2	Q5T750	OTTHUMG00000012401	ENST00000368775.2:c.77G>C	1.37:g.152692074G>C	ENSP00000357764:p.Ser26Thr	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	207	204	0.985507	NM_001024679	O14634	Missense_Mutation	SNP	ENST00000368775.2	37	CCDS44226.1	767	0.35119047619047616	259	0.5264227642276422	137	0.3784530386740331	103	0.18006993006993008	268	0.35356200527704484	C	0.012	-1.673937	0.00758	.	.	ENSG00000198854	ENST00000362017;ENST00000368775	T;T	0.23950	1.88;1.88	3.86	0.885	0.19188	.	0.835692	0.10039	N	0.723727	T	0.01835	0.0058	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44065	-0.9352	9	0.02654	T	1	3.1982	2.9191	0.05762	0.1703:0.3719:0.3561:0.1017	rs1332500;rs1332500	26	Q5T750	XP32_HUMAN	T	26	ENSP00000354769:S26T;ENSP00000357764:S26T	ENSP00000354769:S26T	S	+	2	0	C1orf68	150958698	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.412000	0.21131	-0.012000	0.14223	-0.908000	0.02827	AGC	G|0.655;C|0.345	0.345	strong		0.522	C1orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034521.2	NM_001024679	
DSC1	1823	hgsc.bcm.edu	37	18	28720147	28720147	+	Missense_Mutation	SNP	C	C	T	rs17800159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:28720147C>T	ENST00000257198.5	-	10	1639	c.1378G>A	c.(1378-1380)Gtt>Att	p.V460I	DSC1_ENST00000257197.3_Missense_Mutation_p.V460I|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	460	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> I (in dbSNP:rs17800159).		homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V460I(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			ATAATTTTAACGGTGACAGTT	0.453													C|||	933	0.186302	0.0091	0.232	5008	,	,		14951	0.4792		0.1332	False		,,,				2504	0.1462				p.V460I		Atlas-SNP	.											DSC1_ENST00000257198,NS,carcinoma,0,2	DSC1	240	2	2	Substitution - Missense(2)	stomach(2)	c.G1378A						scavenged	.	C	ILE/VAL,ILE/VAL	110,4296	86.3+/-125.0	2,106,2095	107.0	101.0	103.0		1378,1378	5.8	1.0	18	dbSNP_123	103	1108,7492	230.7+/-264.9	80,948,3272	yes	missense,missense	DSC1	NM_004948.3,NM_024421.2	29,29	82,1054,5367	TT,TC,CC		12.8837,2.4966,9.3649	possibly-damaging,possibly-damaging	460/841,460/895	28720147	1218,11788	2203	4300	6503	SO:0001583	missense	1823	exon10			TTTTAACGGTGAC	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1378G>A	18.37:g.28720147C>T	ENSP00000257198:p.Val460Ile	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	136	53	0.389706	NM_004948	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	454	0.2078754578754579	11	0.022357723577235773	75	0.20718232044198895	279	0.48776223776223776	89	0.11741424802110818	C	14.76	2.631257	0.46944	0.024966	0.128837	ENSG00000134765	ENST00000257197;ENST00000257198	T;T	0.64260	-0.09;-0.09	5.83	5.83	0.93111	Cadherin (4);Cadherin-like (1);	0.000000	0.47852	D	0.000201	T	0.00012	0.0000	L	0.51914	1.62	0.24227	P	0.99541603	D;D	0.76494	0.999;0.997	D;P	0.81914	0.995;0.766	T	0.44682	-0.9312	9	0.14656	T	0.56	.	17.9032	0.88911	0.0:1.0:0.0:0.0	rs17800159;rs52809488;rs17800159	460;460	Q08554;Q9HB00	DSC1_HUMAN;.	I	460	ENSP00000257197:V460I;ENSP00000257198:V460I	ENSP00000257197:V460I	V	-	1	0	DSC1	26974145	1.000000	0.71417	0.996000	0.52242	0.261000	0.26267	3.858000	0.55979	2.761000	0.94854	0.650000	0.86243	GTT	C|0.860;T|0.140	0.140	strong		0.453	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
SPATA31A3	727830	hgsc.bcm.edu	37	9	40702760	40702760	+	Missense_Mutation	SNP	T	T	G	rs192661010	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:40702760T>G	ENST00000356699.5	+	4	446	c.417T>G	c.(415-417)caT>caG	p.H139Q	RP11-395E19.5_ENST00000432614.1_lincRNA|SPATA31A3_ENST00000463536.1_3'UTR	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	139	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGTCCTCTCATGAGCCTATGG	0.597													T|||	514	0.102636	0.0885	0.1009	5008	,	,		20141	0.003		0.2286	False		,,,				2504	0.0961				p.H139Q		Atlas-SNP	.											FAM75A3_ENST00000356699,NS,carcinoma,+2,2	.	.	2	0			c.T417G						scavenged	.	T	GLN/HIS	382,3416		13,356,1530	53.0	63.0	60.0		417	-3.7	0.0	9	dbSNP_134	60	1741,6417		82,1577,2420	no	missense	FAM75A3	NM_001083124.1	24	95,1933,3950	GG,GT,TT		21.341,10.0579,17.7568	possibly-damaging	139/1348	40702760	2123,9833	1899	4079	5978	SO:0001583	missense	727830	exon4			CTCTCATGAGCCT			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A3"""	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.417T>G	9.37:g.40702760T>G	ENSP00000349132:p.His139Gln	Somatic	832	0	0		WXS	Illumina HiSeq	Phase_I	787	279	0.354511	NM_001083124		Missense_Mutation	SNP	ENST00000356699.5	37	CCDS47969.1	.	.	.	.	.	.	.	.	.	.	T	1.786	-0.480697	0.04383	0.100579	0.21341	ENSG00000147926	ENST00000356699	T	0.03889	3.77	1.86	-3.73	0.04398	.	1.943840	0.02631	N	0.104336	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.45760	-0.9239	9	0.25106	T	0.35	0.3542	0.1983	0.00142	0.2674:0.2166:0.2878:0.2282	.	139	Q5VYP0	F75A3_HUMAN	Q	139	ENSP00000349132:H139Q	ENSP00000349132:H139Q	H	+	3	2	FAM75A3	40692760	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.285000	0.02791	-1.013000	0.03383	-0.836000	0.03065	CAT	T|0.744;G|0.256	0.256	strong		0.597	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124	
PER3	8863	hgsc.bcm.edu	37	1	7890026	7890026	+	Missense_Mutation	SNP	A	A	G	rs199947375|rs57875989		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7890026A>G	ENST00000361923.2	+	18	3167	c.2992A>G	c.(2992-2994)Aag>Gag	p.K998E	PER3_ENST00000377532.3_Missense_Mutation_p.K1007E|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	998	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.K998E(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTCCCATGAAGAATCCATC	0.587																																					p.K998E		Atlas-SNP	.											PER3,NS,carcinoma,0,4	PER3	95	4	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2992G						PASS	.						84.0	69.0	74.0					1																	7890026		1999	3897	5896	SO:0001583	missense	8863	exon18			CCCATGAAGAATC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2992A>G	1.37:g.7890026A>G	ENSP00000355031:p.Lys998Glu	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	106	20	0.188679	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.434686	0.00182	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.13538	2.58;2.58	.	.	.	Period circadian-like, C-terminal (1);	5.912170	0.01354	N	0.012011	T	0.04724	0.0128	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.26503	-1.0101	8	0.02654	T	1	.	.	.	.	.	998;1007;1007;998	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	E	1007;998	ENSP00000366755:K1007E;ENSP00000355031:K998E	ENSP00000355031:K998E	K	+	1	0	PER3	7812613	0.002000	0.14202	0.013000	0.15412	0.014000	0.08584	-0.844000	0.04345	-0.911000	0.03843	-0.891000	0.02926	AAG	.	.	weak		0.587	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
ETS2	2114	hgsc.bcm.edu	37	21	40191431	40191431	+	Silent	SNP	T	T	G	rs457705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:40191431T>G	ENST00000360214.3	+	9	1276	c.816T>G	c.(814-816)acT>acG	p.T272T	ETS2_ENST00000360938.3_Silent_p.T272T	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	272					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				TGCCAGGGACTCCCAAAGACC	0.547													G|||	2910	0.58107	0.5628	0.5778	5008	,	,		18814	0.4563		0.838	False		,,,				2504	0.4724				p.T412T		Atlas-SNP	.											ETS2_ENST00000360214,NS,carcinoma,0,2	ETS2	87	2	0			c.T1236G						scavenged	.	G		2739,1667	509.6+/-367.3	872,995,336	71.0	64.0	66.0		816	-0.9	0.1	21	dbSNP_80	66	7292,1308	257.6+/-281.6	3085,1122,93	no	coding-synonymous	ETS2	NM_005239.4		3957,2117,429	GG,GT,TT		15.2093,37.8348,22.8741		272/470	40191431	10031,2975	2203	4300	6503	SO:0001819	synonymous_variant	2114	exon9			AGGGACTCCCAAA		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.816T>G	21.37:g.40191431T>G		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001256295	A6NM68|D3DSH6|Q53Y89	Silent	SNP	ENST00000360214.3	37	CCDS13659.1																																																																																			T|0.298;G|0.702	0.702	strong		0.547	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
OR51E1	143503	hgsc.bcm.edu	37	11	4674575	4674575	+	Missense_Mutation	SNP	G	G	A	rs3817098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4674575G>A	ENST00000530215.1	+	2	190	c.149G>A	c.(148-150)cGc>cAc	p.R50H	OR51E1_ENST00000396952.5_Silent_p.P273P			Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	0						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|skin(1)|stomach(2)	30		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGACTCTCCGCTGCCCGTCA	0.493													C|||	1470	0.29353	0.2012	0.4179	5008	,	,		19913	0.0556		0.499	False		,,,				2504	0.364				p.P273P		Atlas-SNP	.											.	OR51E1	67	.	0			c.G819A						PASS	.	C		1066,3336		145,776,1280	176.0	166.0	170.0		819	-0.3	1.0	11	dbSNP_107	170	4662,3934		1269,2124,905	no	coding-synonymous	OR51E1	NM_152430.3		1414,2900,2185	AA,AG,GG		45.7655,24.2163,44.0683		273/319	4674575	5728,7270	2201	4298	6499	SO:0001583	missense	143503	exon2			CTCTCCGCTGCCC	AY775731	CCDS31358.2	11p15.4	2012-08-22	2004-11-03	2004-11-06	ENSG00000180785	ENSG00000180785		"""GPCR / Class A : Olfactory receptors"""	15194	protein-coding gene	gene with protein product		611267	"""olfactory receptor, family 51, subfamily E, member 1 pseudogene"""	OR51E1P, OR52A3P, GPR164			Standard	NM_152430		Approved	GPR136	uc001lzi.4	Q8TCB6	OTTHUMG00000157024	ENST00000530215.1:c.149G>A	11.37:g.4674575G>A	ENSP00000431593:p.Arg50His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_152430	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Silent	SNP	ENST00000530215.1	37		667	0.30540293040293043	104	0.21138211382113822	156	0.430939226519337	38	0.06643356643356643	369	0.4868073878627968	C	12.62	1.992606	0.35131	0.242163	0.542345	ENSG00000180785	ENST00000530215	T	0.37058	1.22	4.77	-0.309	0.12769	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44922	-0.9296	5	0.34782	T	0.22	.	2.4516	0.04519	0.1184:0.434:0.2315:0.2162	rs3817098;rs17224511;rs56919705;rs3817098	.	.	.	H	50	ENSP00000431593:R50H	ENSP00000431593:R50H	R	+	2	0	OR51E1	4631151	0.000000	0.05858	0.952000	0.39060	0.220000	0.24768	-1.771000	0.01789	-0.131000	0.11578	-0.120000	0.15030	CGC	G|0.615;A|0.385	0.385	strong		0.493	OR51E1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000385957.1	NM_152430	
CPN2	1370	hgsc.bcm.edu	37	3	194061826	194061826	+	Missense_Mutation	SNP	C	C	T	rs11711157	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:194061826C>T	ENST00000323830.3	-	2	1695	c.1606G>A	c.(1606-1608)Gtg>Atg	p.V536M	CPN2_ENST00000429275.1_Missense_Mutation_p.V536M	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	536			V -> M (in dbSNP:rs11711157). {ECO:0000269|PubMed:2378615}.		protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		TCGATAGACACGGTGAGCCGC	0.652													C|||	1425	0.284545	0.1702	0.245	5008	,	,		18251	0.3175		0.3121	False		,,,				2504	0.4049				p.V536M		Atlas-SNP	.											.	CPN2	56	.	0			c.G1606A						PASS	.	C	MET/VAL	822,3584	309.7+/-291.2	73,676,1454	32.0	33.0	32.0		1606	2.8	0.7	3	dbSNP_120	32	2409,6191	388.8+/-342.7	344,1721,2235	yes	missense	CPN2	NM_001080513.2	21	417,2397,3689	TT,TC,CC		28.0116,18.6564,24.8424	probably-damaging	536/546	194061826	3231,9775	2203	4300	6503	SO:0001583	missense	1370	exon2			TAGACACGGTGAG	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"""carboxypeptidase N, polypeptide 2, 83kD"""	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.1606G>A	3.37:g.194061826C>T	ENSP00000319464:p.Val536Met	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	653	0.298992673992674	77	0.1565040650406504	109	0.3011049723756906	210	0.36713286713286714	257	0.3390501319261214	C	13.41	2.229251	0.39399	0.186564	0.280116	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.57752	0.38;0.38	5.7	2.79	0.32731	.	0.250032	0.20930	N	0.083110	T	0.00012	0.0000	L	0.29908	0.895	0.35207	P	0.225221	P	0.48998	0.918	B	0.25759	0.063	T	0.39502	-0.9611	9	0.87932	D	0	.	10.2345	0.43275	0.0:0.6763:0.2528:0.0709	rs11711157;rs58446504;rs11711157	536	P22792	CPN2_HUMAN	M	536	ENSP00000319464:V536M;ENSP00000402232:V536M	ENSP00000319464:V536M	V	-	1	0	CPN2	195543521	0.427000	0.25514	0.727000	0.30756	0.083000	0.17756	0.955000	0.29188	0.871000	0.35750	-0.140000	0.14226	GTG	C|0.732;T|0.268	0.268	strong		0.652	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513	
FAM189A1	23359	hgsc.bcm.edu	37	15	29544656	29544656	+	Silent	SNP	T	T	C	rs4583203	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:29544656T>C	ENST00000261275.4	-	3	302	c.303A>G	c.(301-303)gcA>gcG	p.A101A		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	101						integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						TTACACACACTGCAGAAAGCA	0.398													T|||	2500	0.499201	0.2231	0.4885	5008	,	,		17356	0.6339		0.5835	False		,,,				2504	0.6544				p.A101A		Atlas-SNP	.											FAM189A1,NS,carcinoma,-1,1	FAM189A1	20	1	0			c.A303G						PASS	.	T		379,1005		53,273,366	143.0	112.0	121.0		303	-5.2	0.6	15	dbSNP_111	121	1907,1275		566,775,250	no	coding-synonymous	FAM189A1	NM_015307.1		619,1048,616	CC,CT,TT		40.0691,27.3844,49.9343		101/540	29544656	2286,2280	692	1591	2283	SO:0001819	synonymous_variant	23359	exon3			ACACACTGCAGAA		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.303A>G	15.37:g.29544656T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	241	240	0.995851	NM_015307	A0PK09	Silent	SNP	ENST00000261275.4	37	CCDS45198.1																																																																																			T|0.529;C|0.471	0.471	strong		0.398	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
MYO15A	51168	hgsc.bcm.edu	37	17	18023897	18023897	+	Missense_Mutation	SNP	G	G	A	rs2955365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18023897G>A	ENST00000205890.5	+	2	2121	c.1783G>A	c.(1783-1785)Gcc>Acc	p.A595T		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	595				A -> T (in Ref. 2; AAF05903/AF051976). {ECO:0000305}.	inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CAGCCAGAAGGCCCGGGCGGG	0.701													G|||	2772	0.553514	0.503	0.4741	5008	,	,		7970	0.6567		0.3708	False		,,,				2504	0.7597				p.A595T		Atlas-SNP	.											.	MYO15A	268	.	0			c.G1783A						PASS	.	G	THR/ALA	1422,1900		345,732,584	5.0	6.0	6.0		1783	3.6	1.0	17	dbSNP_101	6	2198,5272		395,1408,1932	yes	missense	MYO15A	NM_016239.3	58	740,2140,2516	AA,AG,GG		29.4244,42.8055,33.5434	probably-damaging	595/3531	18023897	3620,7172	1661	3735	5396	SO:0001583	missense	51168	exon2			CAGAAGGCCCGGG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.1783G>A	17.37:g.18023897G>A	ENSP00000205890:p.Ala595Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	1075	0.49221611721611724	267	0.5426829268292683	160	0.4419889502762431	374	0.6538461538461539	274	0.36147757255936674	G	12.28	1.890897	0.33348	0.428055	0.294244	ENSG00000091536	ENST00000205890	D	0.89123	-2.47	4.63	3.58	0.41010	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.9999999881489	P	0.39809	0.689	B	0.34590	0.186	T	0.48937	-0.8990	8	0.56958	D	0.05	.	12.164	0.54119	0.0:0.0:0.8282:0.1718	rs2955365;rs2955365	595	Q9UKN7	MYO15_HUMAN	T	595	ENSP00000205890:A595T	ENSP00000205890:A595T	A	+	1	0	MYO15A	17964622	0.906000	0.30813	0.973000	0.42090	0.175000	0.22909	1.488000	0.35551	2.122000	0.65172	0.448000	0.29417	GCC	G|0.485;A|0.515	0.515	strong		0.701	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
PCDHGC5	56097	hgsc.bcm.edu	37	5	140869003	140869003	+	Silent	SNP	T	T	C	rs1002519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140869003T>C	ENST00000252087.1	+	1	196	c.196T>C	c.(196-198)Ttg>Ctg	p.L66L	PCDHGA7_ENST00000518325.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	66	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGCTGCAATTGGGCTCTGA	0.542													T|||	966	0.192891	0.1225	0.366	5008	,	,		17242	0.129		0.2296	False		,,,				2504	0.1933				p.L66L		Atlas-SNP	.											PCDHGC5_ENST00000252087,NS,carcinoma,-1,2	PCDHGC5	199	2	0			c.T196C						PASS	.	T	,,,,,,,,,,,,,,,,,,,,,,,,	625,3781	271.0+/-269.9	43,539,1621	94.0	97.0	96.0		,,,,,,,,,,,,,,,,,,,,196,,,,196	-5.2	0.2	5	dbSNP_86	96	1947,6653	344.7+/-325.5	210,1527,2563	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,coding-synonymous	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGC5,PCDHGC4,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_018928.2,NM_018929.2,NM_032088.1,NM_032092.1,NM_032403.1,NM_032407.1	,,,,,,,,,,,,,,,,,,,,,,,,	253,2066,4184	CC,CT,TT		22.6395,14.1852,19.7755	,,,,,,,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,,,66/945,,,,66/879	140869003	2572,10434	2203	4300	6503	SO:0001819	synonymous_variant	56097	exon1			CTGCAATTGGGCT	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"""Cadherins / Protocadherins : Clustered"""	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.196T>C	5.37:g.140869003T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	104	37	0.355769	NM_018929	Q9Y5C2	Silent	SNP	ENST00000252087.1	37	CCDS4263.1																																																																																			T|0.810;C|0.190	0.190	strong		0.542	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929	
RANBP2	5903	hgsc.bcm.edu	37	2	109367844	109367844	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:109367844T>G	ENST00000283195.6	+	10	1524	c.1398T>G	c.(1396-1398)caT>caG	p.H466Q		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	466					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.H466Q(6)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATTTGCCCCATGAAACCTCAA	0.358																																					p.H466Q		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,6	RANBP2	488	6	6	Substitution - Missense(6)	endometrium(6)	c.T1398G						scavenged	.						69.0	78.0	75.0					2																	109367844		1510	2703	4213	SO:0001583	missense	5903	exon10			GCCCCATGAAACC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.1398T>G	2.37:g.109367844T>G	ENSP00000283195:p.His466Gln	Somatic	1913	54	0.0282279		WXS	Illumina HiSeq	Phase_I	1701	28	0.0164609	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	2.180	-0.387877	0.04932	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	D	0.82526	-1.62	5.25	2.44	0.29823	.	.	.	.	.	T	0.43545	0.1252	N	0.00197	-1.87	0.20563	N	0.999888	B	0.02656	0.0	B	0.01281	0.0	T	0.50039	-0.8874	9	0.02654	T	1	-0.0972	5.4961	0.16804	0.3195:0.0:0.5396:0.1409	.	466	P49792	RBP2_HUMAN	Q	466	ENSP00000283195:H466Q	ENSP00000283195:H466Q	H	+	3	2	RANBP2	108734276	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.307000	0.43682	0.319000	0.23209	-0.127000	0.14921	CAT	.	.	weak		0.358	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
ARMC1	55156	hgsc.bcm.edu	37	8	66525548	66525548	+	Silent	SNP	T	T	C	rs11559265	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:66525548T>C	ENST00000276569.3	-	4	640	c.396A>G	c.(394-396)caA>caG	p.Q132Q	ARMC1_ENST00000523384.1_5'Flank|ARMC1_ENST00000458464.2_Intron	NM_018120.4	NP_060590.1	Q9NVT9	ARMC1_HUMAN	armadillo repeat containing 1	132					metal ion transport (GO:0030001)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(1)|lung(8)|skin(1)	14			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			CCAGAAAAAATTGAGCTTTCC	0.393													C|||	1283	0.25619	0.0877	0.3228	5008	,	,		19145	0.379		0.3002	False		,,,				2504	0.2648				p.Q132Q		Atlas-SNP	.											.	ARMC1	22	.	0			c.A396G						PASS	.	C		542,3864	776.6+/-414.2	34,474,1695	152.0	140.0	144.0		396	5.9	1.0	8	dbSNP_120	144	2698,5902	682.6+/-403.8	398,1902,2000	no	coding-synonymous	ARMC1	NM_018120.4		432,2376,3695	CC,CT,TT		31.3721,12.3014,24.9116		132/283	66525548	3240,9766	2203	4300	6503	SO:0001819	synonymous_variant	55156	exon4			AAAAAATTGAGCT	BC011607	CCDS6181.1, CCDS69490.1	8q12.3	2013-02-14			ENSG00000104442	ENSG00000104442		"""Armadillo repeat containing"""	17684	protein-coding gene	gene with protein product							Standard	XM_005251264		Approved	FLJ10511, Arcp	uc003xvl.3	Q9NVT9	OTTHUMG00000164374	ENST00000276569.3:c.396A>G	8.37:g.66525548T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	158	61	0.386076	NM_018120	B4E2W7|Q9H018|Q9H820	Silent	SNP	ENST00000276569.3	37	CCDS6181.1																																																																																			T|0.731;C|0.269	0.269	strong		0.393	ARMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378480.1	NM_018120	
TOP3A	7156	hgsc.bcm.edu	37	17	18193941	18193941	+	Silent	SNP	G	G	A	rs2230154	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18193941G>A	ENST00000321105.5	-	13	1741	c.1527C>T	c.(1525-1527)gaC>gaT	p.D509D	TOP3A_ENST00000542570.1_Silent_p.D414D|TOP3A_ENST00000540524.1_Silent_p.D39D	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	509					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)	p.D509D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TGGTCTCCCCGTCCACCATCT	0.582													g|||	896	0.178914	0.1611	0.2421	5008	,	,		20534	0.0605		0.3062	False		,,,				2504	0.1493				p.D509D		Atlas-SNP	.											TOP3A,NS,carcinoma,0,1	TOP3A	85	1	1	Substitution - coding silent(1)	stomach(1)	c.C1527T						PASS	.	A		901,3505	348.5+/-309.9	83,735,1385	88.0	62.0	71.0		1527	-6.1	1.0	17	dbSNP_98	71	2600,6000	422.0+/-353.9	383,1834,2083	no	coding-synonymous	TOP3A	NM_004618.3		466,2569,3468	AA,AG,GG		30.2326,20.4494,26.9183		509/1002	18193941	3501,9505	2203	4300	6503	SO:0001819	synonymous_variant	7156	exon13			CTCCCCGTCCACC	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.1527C>T	17.37:g.18193941G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	120	41	0.341667	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	37	CCDS11194.1																																																																																			G|0.757;A|0.243	0.243	strong		0.582	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
BMP8B	656	hgsc.bcm.edu	37	1	40229368	40229368	+	Intron	SNP	A	A	G	rs2463260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:40229368A>G	ENST00000372827.3	-	5	1324				PPIE_ENST00000372830.1_3'UTR|PPIE_ENST00000356511.2_Missense_Mutation_p.E282G|BMP8B_ENST00000397360.2_Missense_Mutation_p.S347P	NM_001720.3	NP_001711.2	P34820	BMP8B_HUMAN	bone morphogenetic protein 8b						cartilage development (GO:0051216)|cell differentiation (GO:0030154)|growth (GO:0040007)|ossification (GO:0001503)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)				endometrium(1)|liver(1)|ovary(1)|urinary_tract(1)	4	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CAGAAACAAGAAGAGTCAGCA	0.498													G|||	1832	0.365815	0.2625	0.3559	5008	,	,		13491	0.3075		0.4473	False		,,,				2504	0.4888				p.E282G		Atlas-SNP	.											.	PPIE	33	.	0			c.A845G						PASS	.						47.0	42.0	44.0					1																	40229368		2192	4271	6463	SO:0001627	intron_variant	10450	exon10			AACAAGAAGAGTC	BC023526	CCDS444.1	1p35-p32	2014-01-30	2008-05-22	2003-10-22	ENSG00000116985	ENSG00000116985		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1075	protein-coding gene	gene with protein product	"""osteogenic protein 2"""	602284	"""bone morphogenetic protein 8 (osteogenic protein 2)"""	BMP8		1460021, 9070944	Standard	NM_001720		Approved	OP-2	uc001cdz.1	P34820	OTTHUMG00000009247	ENST00000372827.3:c.948+15T>C	1.37:g.40229368A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_203456	E7EMY8|Q32NE5|Q53ZM7|Q9NUF0	Missense_Mutation	SNP	ENST00000372827.3	37	CCDS444.1	784|784	0.358974358974359|0.358974358974359	129|129	0.2621951219512195|0.2621951219512195	135|135	0.3729281767955801|0.3729281767955801	197|197	0.34440559440559443|0.34440559440559443	323|323	0.4261213720316623|0.4261213720316623	G|G	6.531|6.531	0.466132|0.466132	0.12402|0.12402	.|.	.|.	ENSG00000084072|ENSG00000116985	ENST00000356511|ENST00000397360	T|T	0.39056|0.61980	1.1|0.06	3.17|3.17	-6.03|-6.03	0.02185|0.02185	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.20739|0.20739	-1.0266|-1.0266	7|7	0.02654|0.06625	T|T	1|0.88	.|.	7.4386|7.4386	0.27171|0.27171	0.5734:0.1177:0.3089:0.0|0.5734:0.1177:0.3089:0.0	rs2463260;rs2745498;rs11810813|rs2463260;rs2745498;rs11810813	282|347	Q9UNP9-2|E7EMY8	.|.	G|P	282|347	ENSP00000348904:E282G|ENSP00000380518:S347P	ENSP00000348904:E282G|ENSP00000380518:S347P	E|S	+|-	2|1	0|0	PPIE|BMP8B	40001955|40001955	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-0.266000|-0.266000	0.08631|0.08631	-1.798000|-1.798000	0.01250|0.01250	-0.746000|-0.746000	0.03513|0.03513	GAA|TCT	A|0.500;G|0.500	0.500	strong		0.498	BMP8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025641.1	NM_001720	
VARS2	57176	hgsc.bcm.edu	37	6	30893941	30893941	+	Missense_Mutation	SNP	G	G	A	rs4678	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30893941G>A	ENST00000321897.5	+	29	3778	c.3146G>A	c.(3145-3147)cGg>cAg	p.R1049Q	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Missense_Mutation_p.R909Q|VARS2_ENST00000416670.2_Missense_Mutation_p.R1049Q|VARS2_ENST00000541562.1_Missense_Mutation_p.R1079Q			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	1049			R -> Q (in dbSNP:rs4678). {ECO:0000269|PubMed:11572484, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TCTCACCTCCGGCAGCTGATG	0.557													G|||	453	0.0904553	0.0968	0.0663	5008	,	,		19166	0.0258		0.1551	False		,,,				2504	0.0992				p.R1079Q		Atlas-SNP	.											.	VARS2	60	.	0			c.G3236A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	367,2653		15,337,1158	53.0	57.0	56.0		2726,3236,3146	-8.5	0.1	6	dbSNP_52	56	1047,4367		94,859,1754	yes	missense,missense,missense	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	43,43,43	109,1196,2912	AA,AG,GG		19.3388,12.1523,16.7655	benign,benign,benign	909/924,1079/1094,1049/1064	30893941	1414,7020	1510	2707	4217	SO:0001583	missense	57176	exon30			ACCTCCGGCAGCT	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.3146G>A	6.37:g.30893941G>A	ENSP00000316092:p.Arg1049Gln	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	316	145	0.458861	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	246	0.11263736263736264	71	0.1443089430894309	27	0.07458563535911603	20	0.03496503496503497	128	0.16886543535620052	G	4.681	0.126566	0.08931	0.121523	0.193388	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.8	-8.54	0.00912	.	1.356270	0.04712	N	0.417762	T	0.02929	0.0087	N	0.11845	0.185	0.80722	P	0.0	B;B;B;B	0.22983	0.078;0.0;0.0;0.0	B;B;B;B	0.16722	0.016;0.0;0.001;0.0	T	0.14699	-1.0463	9	0.02654	T	1	-4.8705	8.5559	0.33480	0.3693:0.0:0.5217:0.109	rs4678;rs1043490;rs3173376;rs6929532;rs16898111;rs17189642;rs52796175;rs56648004;rs60218550;rs4678	487;1047;1079;1049	Q5ST30-2;B7ZL25;F5GXJ0;Q5ST30	.;.;.;SYVM_HUMAN	Q	1049;1049;909;1079	ENSP00000316092:R1049Q;ENSP00000394802:R1049Q;ENSP00000438200:R909Q;ENSP00000441000:R1079Q	ENSP00000316092:R1049Q	R	+	2	0	VARS2	31001920	0.057000	0.20700	0.058000	0.19502	0.721000	0.41392	-1.020000	0.03618	-1.624000	0.01556	-0.150000	0.13652	CGG	G|0.856;A|0.144	0.144	strong		0.557	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
GATA5	140628	hgsc.bcm.edu	37	20	61048549	61048549	+	Silent	SNP	G	G	A	rs41305803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61048549G>A	ENST00000252997.2	-	3	670	c.609C>T	c.(607-609)gaC>gaT	p.D203D		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	203					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			GGCCGGTGCCGTCTCGGCGCC	0.647													G|||	1944	0.388179	0.4501	0.438	5008	,	,		12093	0.3403		0.4404	False		,,,				2504	0.2648				p.D203D		Atlas-SNP	.											.	GATA5	22	.	0			c.C609T						PASS	.	G		1860,2530		391,1078,726	44.0	37.0	39.0		609	-3.5	0.2	20	dbSNP_127	39	3733,4861		818,2097,1382	no	coding-synonymous	GATA5	NM_080473.4		1209,3175,2108	AA,AG,GG		43.4373,42.369,43.0761		203/398	61048549	5593,7391	2195	4297	6492	SO:0001819	synonymous_variant	140628	exon3			GGTGCCGTCTCGG	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"""GATA zinc finger domain containing"""	15802	protein-coding gene	gene with protein product		611496	"""GATA-binding protein 5"""			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.609C>T	20.37:g.61048549G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			G|0.568;A|0.432	0.432	strong		0.647	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473	
FNDC8	54752	hgsc.bcm.edu	37	17	33454415	33454415	+	Silent	SNP	C	C	A	rs2306508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:33454415C>A	ENST00000158009.5	+	2	679	c.564C>A	c.(562-564)acC>acA	p.T188T		NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	188	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	11		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)		TTGAGCACACCGTCAACAATT	0.542													C|||	2226	0.444489	0.1044	0.5447	5008	,	,		21013	0.7123		0.4354	False		,,,				2504	0.5665				p.T188T		Atlas-SNP	.											.	FNDC8	28	.	0			c.C564A						PASS	.	C		702,3704	283.1+/-276.9	67,568,1568	103.0	92.0	95.0		564	-7.7	1.0	17	dbSNP_100	95	3647,4953	525.0+/-380.7	779,2089,1432	no	coding-synonymous	FNDC8	NM_017559.2		846,2657,3000	AA,AC,CC		42.407,15.9328,33.4384		188/325	33454415	4349,8657	2203	4300	6503	SO:0001819	synonymous_variant	54752	exon2			GCACACCGTCAAC	BC024002	CCDS11290.1	17q12	2013-02-11			ENSG00000073598	ENSG00000073598		"""Fibronectin type III domain containing"""	25286	protein-coding gene	gene with protein product						12477932	Standard	XM_005257993		Approved	DKFZp434H2215	uc002hix.3	Q8TC99	OTTHUMG00000132932	ENST00000158009.5:c.564C>A	17.37:g.33454415C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_017559	B2R9G6|Q9UFC2	Silent	SNP	ENST00000158009.5	37	CCDS11290.1																																																																																			C|0.608;A|0.392	0.392	strong		0.542	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559	
TMEM132B	114795	hgsc.bcm.edu	37	12	125834395	125834395	+	Silent	SNP	T	T	C	rs3803155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:125834395T>C	ENST00000299308.3	+	2	458	c.450T>C	c.(448-450)agT>agC	p.S150S	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	150						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		GGGATGACAGTGACCTTACGG	0.537													C|||	3311	0.661142	0.3154	0.8055	5008	,	,		19657	0.8105		0.7435	False		,,,				2504	0.7873				p.S150S		Atlas-SNP	.											.	TMEM132B	207	.	0			c.T450C						PASS	.	C		1752,2274		391,970,652	117.0	116.0	116.0		450	-8.6	0.0	12	dbSNP_107	116	6298,2086		2355,1588,249	no	coding-synonymous	TMEM132B	NM_052907.2		2746,2558,901	CC,CT,TT		24.8807,43.5171,35.133		150/1079	125834395	8050,4360	2013	4192	6205	SO:0001819	synonymous_variant	114795	exon2			TGACAGTGACCTT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.450T>C	12.37:g.125834395T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	191	92	0.481675	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			T|0.332;C|0.668	0.668	strong		0.537	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
BDP1	55814	hgsc.bcm.edu	37	5	70798541	70798541	+	Missense_Mutation	SNP	A	A	G	rs36009281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:70798541A>G	ENST00000358731.4	+	15	2427	c.2164A>G	c.(2164-2166)Aaa>Gaa	p.K722E	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	722			K -> E (in dbSNP:rs36009281).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TGCTGAAAGAAAAGAAATTCT	0.423													A|||	163	0.0325479	0.003	0.0432	5008	,	,		16266	0.0		0.0885	False		,,,				2504	0.0409				p.K722E		Atlas-SNP	.											.	BDP1	204	.	0			c.A2164G						PASS	.	A	GLU/LYS	56,3666		0,56,1805	96.0	89.0	91.0		2164	4.7	1.0	5	dbSNP_126	91	682,7490		30,622,3434	yes	missense	BDP1	NM_018429.2	56	30,678,5239	GG,GA,AA		8.3456,1.5046,6.2048	probably-damaging	722/2625	70798541	738,11156	1861	4086	5947	SO:0001583	missense	55814	exon15			GAAAGAAAAGAAA	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.2164A>G	5.37:g.70798541A>G	ENSP00000351575:p.Lys722Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	72	0.03296703296703297	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	55	0.07255936675461741	A	15.94	2.980560	0.53827	0.015046	0.083456	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000451951;ENST00000444711	T	0.12255	2.7	4.7	4.7	0.59300	.	0.083784	0.51477	D	0.000094	T	0.01765	0.0056	M	0.64997	1.995	0.80722	D	1	D;D;D	0.71674	0.974;0.998;0.997	P;D;D	0.80764	0.869;0.994;0.946	T	0.00023	-1.2334	10	0.66056	D	0.02	.	10.7286	0.46083	1.0:0.0:0.0:0.0	rs36009281	722;722;722	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	E	722;722;302;722	ENSP00000351575:K722E	ENSP00000351575:K722E	K	+	1	0	BDP1	70834297	0.999000	0.42202	0.993000	0.49108	0.108000	0.19459	1.185000	0.32065	2.109000	0.64355	0.402000	0.26972	AAA	A|0.949;G|0.051	0.051	strong		0.423	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
FAM13A	10144	hgsc.bcm.edu	37	4	89950630	89950630	+	Silent	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:89950630C>G	ENST00000264344.5	-	2	405	c.198G>C	c.(196-198)gtG>gtC	p.V66V	FAM13A_ENST00000509094.1_Silent_p.V66V|FAM13A_ENST00000515600.1_Silent_p.V66V|FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000511976.1_5'UTR	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	66	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						TCAAATATTCCACTATATTCC	0.393																																					p.V66V		Atlas-SNP	.											.	FAM13A	181	.	0			c.G198C						PASS	.						158.0	152.0	154.0					4																	89950630		2203	4300	6503	SO:0001819	synonymous_variant	10144	exon2			ATATTCCACTATA	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.198G>C	4.37:g.89950630C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	137	17	0.124088	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	37	CCDS34029.1																																																																																			.	.	none		0.393	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
ADAMTS13	11093	hgsc.bcm.edu	37	9	136301982	136301982	+	Missense_Mutation	SNP	C	C	G	rs2301612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136301982C>G	ENST00000371929.3	+	12	1786	c.1342C>G	c.(1342-1344)Caa>Gaa	p.Q448E	ADAMTS13_ENST00000356589.2_Missense_Mutation_p.Q417E|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.Q448E|ADAMTS13_ENST00000536611.1_Missense_Mutation_p.Q120E|ADAMTS13_ENST00000485925.1_Intron|ADAMTS13_ENST00000371916.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	448	Cysteine-rich.		Q -> E (does not affect protein secretion; normal proteolytic activity; dbSNP:rs2301612). {ECO:0000269|PubMed:11586351, ECO:0000269|PubMed:12181489, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14512317, ECO:0000269|PubMed:14563640, ECO:0000269|PubMed:17003922, ECO:0000269|PubMed:19055667, ECO:0000269|Ref.6}.		cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GTTCATGTCGCAACAGTGCGC	0.697													G|||	1360	0.271565	0.0408	0.389	5008	,	,		12424	0.1835		0.4254	False		,,,				2504	0.4325				p.Q448E		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C1342G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN	421,3969		32,357,1806	15.0	12.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1342,1249,1342	4.2	0.6	9	dbSNP_100	13	3485,5089		725,2035,1527	yes	missense,missense,missense	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	29,29,29	757,2392,3333	GG,GC,CC		40.6461,9.59,30.1296	benign,benign,benign	448/1428,417/1341,448/1372	136301982	3906,9058	2195	4287	6482	SO:0001583	missense	11093	exon12			ATGTCGCAACAGT	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.1342C>G	9.37:g.136301982C>G	ENSP00000360997:p.Gln448Glu	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	228	111	0.486842	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	600	0.27472527472527475	28	0.056910569105691054	132	0.36464088397790057	108	0.1888111888111888	332	0.43799472295514513	G	0.692	-0.794038	0.02862	0.0959	0.406461	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589;ENST00000536611	T;T;T;T	0.67345	-0.21;-0.26;-0.23;3.91	5.17	4.25	0.50352	.	.	.	.	.	T	0.00012	0.0000	N	0.00754	-1.215	0.53005	P	3.2999999999949736E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35992	-0.9766	8	0.02654	T	1	.	13.5897	0.61953	0.0:0.297:0.703:0.0	rs2301612;rs17662628;rs36220238;rs2301612	448;417;448	Q76LX8;Q76LX8-3;Q76LX8-2	ATS13_HUMAN;.;.	E	448;448;417;120	ENSP00000360997:Q448E;ENSP00000347927:Q448E;ENSP00000348997:Q417E;ENSP00000444504:Q120E	ENSP00000347927:Q448E	Q	+	1	0	ADAMTS13	135291803	1.000000	0.71417	0.600000	0.28864	0.317000	0.28152	3.711000	0.54868	0.678000	0.31325	-0.223000	0.12442	CAA	C|0.735;G|0.265	0.265	strong		0.697	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
SLC22A4	6583	hgsc.bcm.edu	37	5	131676320	131676320	+	Missense_Mutation	SNP	C	C	T	rs1050152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:131676320C>T	ENST00000200652.3	+	9	1681	c.1507C>T	c.(1507-1509)Ctc>Ttc	p.L503F	AC034220.3_ENST00000417795.1_RNA|AC034220.3_ENST00000437091.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	503			L -> F (reduces the ability to transport carnitine; dbSNP:rs1050152). {ECO:0000269|PubMed:15107849, ECO:0000269|PubMed:9426230}.		body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	GATTGGAATCCTCACCCTTTT	0.423													C|||	673	0.134385	0.0212	0.2435	5008	,	,		18689	0.001		0.3867	False		,,,				2504	0.0879				p.L503F		Atlas-SNP	.											SLC22A4,NS,carcinoma,-2,1	SLC22A4	45	1	0			c.C1507T	GRCh37	CM041074	SLC22A4	M	rs1050152	PASS	.	C	PHE/LEU	367,4039	183.6+/-211.2	22,323,1858	237.0	218.0	225.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1507	-4.6	0.5	5	dbSNP_86	225	3607,4993	522.2+/-380.1	747,2113,1440	yes	missense	SLC22A4	NM_003059.2	22	769,2436,3298	TT,TC,CC		41.9419,8.3296,30.5551	benign	503/552	131676320	3974,9032	2203	4300	6503	SO:0001583	missense	6583	exon9			GGAATCCTCACCC	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.1507C>T	5.37:g.131676320C>T	ENSP00000200652:p.Leu503Phe	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	202	67	0.331683	NM_003059	O14546	Missense_Mutation	SNP	ENST00000200652.3	37	CCDS4153.1	403	0.18452380952380953	15	0.03048780487804878	105	0.2900552486187845	0	0.0	283	0.3733509234828496	C	9.415	1.081608	0.20309	0.083296	0.419419	ENSG00000197208	ENST00000200652	T	0.74526	-0.85	5.22	-4.62	0.03370	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.782657	0.12072	N	0.502162	T	0.00012	0.0000	L	0.52206	1.635	0.42947	P	0.005637000000000003	B	0.12630	0.006	B	0.23419	0.046	T	0.35176	-0.9799	9	0.54805	T	0.06	.	6.0229	0.19638	0.1479:0.2382:0.5244:0.0894	rs1050152;rs17680807;rs52829495;rs57045625;rs1050152	503	Q9H015	S22A4_HUMAN	F	503	ENSP00000200652:L503F	ENSP00000200652:L503F	L	+	1	0	SLC22A4	131704219	0.001000	0.12720	0.543000	0.28128	0.313000	0.28021	-0.079000	0.11357	-0.729000	0.04875	-0.388000	0.06559	CTC	C|0.748;T|0.252	0.252	strong		0.423	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059	
RLN1	6013	hgsc.bcm.edu	37	9	5335590	5335590	+	Silent	SNP	T	T	G	rs35426888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:5335590T>G	ENST00000223862.1	-	2	345	c.219A>C	c.(217-219)gtA>gtC	p.V73V	RLN1_ENST00000223858.4_Missense_Mutation_p.Y107S|RLN1_ENST00000487557.2_5'UTR	NM_006911.2	NP_008842.1	P04808	REL1_HUMAN	relaxin 1	73					female pregnancy (GO:0007565)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			large_intestine(1)|lung(4)	5	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.02)|Lung(218;0.0984)		TGAAGGATGGTACAATTTCTG	0.363													T|||	37	0.00738818	0.0	0.0173	5008	,	,		20846	0.0		0.0109	False		,,,				2504	0.0143				p.V73V		Atlas-SNP	.											.	RLN1	16	.	0			c.A219C						PASS	.						46.0	48.0	47.0					9																	5335590		2202	4300	6502	SO:0001819	synonymous_variant	6013	exon2			GGATGGTACAATT		CCDS6462.1	9p24.1	2013-02-26	2004-11-15		ENSG00000107018	ENSG00000107018		"""Endogenous ligands"""	10026	protein-coding gene	gene with protein product	"""prorelaxin H1"""	179730	"""relaxin 1 (H1)"""				Standard	NM_006911		Approved	H1	uc003zjb.2	P04808	OTTHUMG00000019495	ENST00000223862.1:c.219A>C	9.37:g.5335590T>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_006911	Q99936|Q9UQJ1	Silent	SNP	ENST00000223862.1	37	CCDS6462.1	.	.	.	.	.	.	.	.	.	.	T	2.574	-0.298894	0.05532	.	.	ENSG00000107018	ENST00000223858	T	0.23348	1.91	2.21	0.163	0.14986	.	.	.	.	.	T	0.10035	0.0246	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34527	-0.9825	6	0.12430	T	0.62	.	3.1868	0.06603	0.2517:0.5914:0.0:0.1569	rs35426888;rs61758132	.	.	.	S	107	ENSP00000223858:Y107S	ENSP00000223858:Y107S	Y	-	2	0	RLN1	5325590	0.000000	0.05858	0.009000	0.14445	0.005000	0.04900	-0.303000	0.08210	0.053000	0.16036	-1.550000	0.00899	TAC	C|0.005;G|0.002;T|0.993	0.002	strong		0.363	RLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051617.1		
PCMT1	5110	hgsc.bcm.edu	37	6	150114745	150114745	+	Missense_Mutation	SNP	G	G	A	rs4816	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:150114745G>A	ENST00000367380.5	+	5	565	c.358G>A	c.(358-360)Gta>Ata	p.V120I	PCMT1_ENST00000367378.1_Missense_Mutation_p.V178I|PCMT1_ENST00000464889.1_Missense_Mutation_p.V178I|PCMT1_ENST00000544496.1_Missense_Mutation_p.V85I|RP11-350J20.5_ENST00000455607.2_RNA|PCMT1_ENST00000367384.2_Missense_Mutation_p.V178I	NM_001252049.1|NM_001252050.1|NM_001252051.1|NM_001252052.1|NM_005389.2	NP_001238978.1|NP_001238979.1|NP_001238980.1|NP_001238981.1|NP_005380.2	P22061	PIMT_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase	120			V -> I (in dbSNP:rs4816). {ECO:0000269|PubMed:10496068, ECO:0000269|PubMed:1339271, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1998518, ECO:0000269|PubMed:21269460, ECO:0000269|Ref.11}.		protein methylation (GO:0006479)|protein repair (GO:0030091)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		AGATGACTCAGTAAATAATGT	0.368													A|||	3342	0.667332	0.9009	0.6715	5008	,	,		15072	0.8343		0.3678	False		,,,				2504	0.4847				p.V178I		Atlas-SNP	.											.	PCMT1	27	.	0			c.G532A	GRCh37	CM060415	PCMT1	M	rs4816	PASS	.	A	ILE/VAL	3507,899	344.9+/-308.3	1410,687,106	74.0	78.0	77.0		532	4.6	1.0	6	dbSNP_52	77	3210,5388	651.0+/-400.8	590,2030,1679	yes	missense	PCMT1	NM_005389.2	29	2000,2717,1785	AA,AG,GG		37.3343,20.404,48.3467	benign	178/286	150114745	6717,6287	2203	4299	6502	SO:0001583	missense	5110	exon5			GACTCAGTAAATA		CCDS5219.1, CCDS5219.2, CCDS59041.1, CCDS75533.1, CCDS75534.1	6q22.3-q24	2008-02-05			ENSG00000120265	ENSG00000120265	2.1.1.77		8728	protein-coding gene	gene with protein product		176851				1478665, 10343128	Standard	NM_005389		Approved		uc003qne.3	P22061	OTTHUMG00000015794	ENST00000367380.5:c.358G>A	6.37:g.150114745G>A	ENSP00000356350:p.Val120Ile	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	150	80	0.533333	NM_005389	A8K109|J3KP72|Q14661|Q16556|Q5VYC1|Q5VYC2|Q93061|Q96II9|Q99625|Q9BQV7|Q9BQV8|Q9NP03	Missense_Mutation	SNP	ENST00000367380.5	37		1392	0.6373626373626373	437	0.8882113821138211	227	0.6270718232044199	460	0.8041958041958042	268	0.35356200527704484	A	11.22	1.575546	0.28092	0.79596	0.373343	ENSG00000120265	ENST00000367384;ENST00000367378;ENST00000464889;ENST00000367380;ENST00000544496;ENST00000495487	T;T;T;T;T;T	0.41758	1.0;1.0;1.0;1.0;0.99;1.98	5.77	4.61	0.57282	.	0.077718	0.85682	N	0.000000	T	0.06735	0.0172	N	0.02379	-0.575	0.53688	P	2.599999999997049E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.21245	-1.0251	9	0.22706	T	0.39	-15.8427	10.4629	0.44590	0.868:0.0:0.132:0.0	rs4816;rs1050644;rs3190977;rs11155687;rs17856263;rs52803050;rs58532082;rs4816	85;120;120	B7Z972;P22061-2;P22061	.;.;PIMT_HUMAN	I	178;178;178;120;85;89	ENSP00000356354:V178I;ENSP00000356348:V178I;ENSP00000420813:V178I;ENSP00000356350:V120I;ENSP00000438247:V85I;ENSP00000418881:V89I	ENSP00000356348:V178I	V	+	1	0	PCMT1	150156438	0.980000	0.34600	1.000000	0.80357	0.990000	0.78478	2.084000	0.41625	0.453000	0.26858	-0.332000	0.08345	GTA	G|0.418;A|0.582	0.582	strong		0.368	PCMT1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
PNPLA3	80339	hgsc.bcm.edu	37	22	44328832	44328832	+	Silent	SNP	C	C	T	rs34179073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:44328832C>T	ENST00000216180.3	+	4	734	c.561C>T	c.(559-561)ttC>ttT	p.F187F	PNPLA3_ENST00000423180.2_Silent_p.F183F|PNPLA3_ENST00000478713.1_3'UTR	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	187					acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				TGTCCCCCTTCTATGGGGAGT	0.493													C|||	175	0.0349441	0.0061	0.062	5008	,	,		22791	0.0		0.0865	False		,,,				2504	0.0378				p.F187F		Atlas-SNP	.											.	PNPLA3	53	.	0			c.C561T						PASS	.	C		88,4318	73.6+/-111.7	1,86,2116	218.0	174.0	189.0		561	3.5	0.9	22	dbSNP_126	189	821,7779	190.4+/-236.9	47,727,3526	no	coding-synonymous	PNPLA3	NM_025225.2		48,813,5642	TT,TC,CC		9.5465,1.9973,6.9891		187/482	44328832	909,12097	2203	4300	6503	SO:0001819	synonymous_variant	80339	exon4			CCCCTTCTATGGG		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.561C>T	22.37:g.44328832C>T		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	263	168	0.638783	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Silent	SNP	ENST00000216180.3	37	CCDS14054.1																																																																																			C|0.935;G|0.000;T|0.064	0.064	strong		0.493	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225	
EGR4	1961	hgsc.bcm.edu	37	2	73518867	73518867	+	Silent	SNP	G	G	A	rs7558708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:73518867G>A	ENST00000545030.1	-	2	1562	c.1488C>T	c.(1486-1488)cgC>cgT	p.R496R	EGR4_ENST00000436467.2_Silent_p.R393R	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	496					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GCTCGTCGGAGCGCGCAAAGC	0.682													G|||	1425	0.284545	0.4554	0.2046	5008	,	,		13798	0.3998		0.0636	False		,,,				2504	0.2188				p.R496R		Atlas-SNP	.											.	EGR4	52	.	0			c.C1488T						PASS	.	G		1740,2666	513.7+/-368.4	332,1076,795	44.0	40.0	41.0		1488	3.9	1.0	2	dbSNP_116	41	532,8068	146.8+/-202.3	13,506,3781	no	coding-synonymous	EGR4	NM_001965.3		345,1582,4576	AA,AG,GG		6.186,39.4916,17.4689		496/590	73518867	2272,10734	2203	4300	6503	SO:0001819	synonymous_variant	1961	exon2			GTCGGAGCGCGCA		CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"""Zinc fingers, C2H2-type"""	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.1488C>T	2.37:g.73518867G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Silent	SNP	ENST00000545030.1	37	CCDS1925.2																																																																																			G|0.791;A|0.209	0.209	strong		0.682	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965	
MYO3A	53904	hgsc.bcm.edu	37	10	26446312	26446312	+	Missense_Mutation	SNP	G	G	A	rs3758449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:26446312G>A	ENST00000265944.5	+	26	3033	c.2867G>A	c.(2866-2868)aGt>aAt	p.S956N	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	956	Myosin motor.		S -> N (in dbSNP:rs3758449). {ECO:0000269|PubMed:17344846}.|S -> R (in an ovarian serous carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S956N(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AAACCAAATAGTGAGCGTCAG	0.393													A|||	2280	0.455272	0.4304	0.451	5008	,	,		15843	0.3552		0.5646	False		,,,				2504	0.4826				p.S956N		Atlas-SNP	.											MYO3A,rectum,carcinoma,0,6	MYO3A	371	6	1	Substitution - Missense(1)	stomach(1)	c.G2867A						PASS	.	A	ASN/SER	2054,2352	608.8+/-391.2	487,1080,636	140.0	133.0	135.0		2867	4.2	1.0	10	dbSNP_107	135	4723,3877	543.7+/-384.4	1325,2073,902	yes	missense	MYO3A	NM_017433.4	46	1812,3153,1538	AA,AG,GG		45.0814,46.6182,47.8933	benign	956/1617	26446312	6777,6229	2203	4300	6503	SO:0001583	missense	53904	exon26			CAAATAGTGAGCG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2867G>A	10.37:g.26446312G>A	ENSP00000265944:p.Ser956Asn	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	182	95	0.521978	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	1001	0.4583333333333333	198	0.4024390243902439	154	0.425414364640884	217	0.3793706293706294	432	0.5699208443271768	A	6.877	0.531306	0.13127	0.466182	0.549186	ENSG00000095777	ENST00000265944	T	0.71341	-0.56	5.31	4.17	0.49024	Myosin head, motor domain (2);	0.041772	0.85682	N	0.000000	T	0.00012	0.0000	N	0.02412	-0.56	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41592	-0.9500	9	0.07175	T	0.84	.	9.5203	0.39131	0.8561:0.0:0.1439:0.0	rs3758449;rs17666875;rs56712933;rs3758449	956	Q8NEV4	MYO3A_HUMAN	N	956	ENSP00000265944:S956N	ENSP00000265944:S956N	S	+	2	0	MYO3A	26486318	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.327000	0.65881	0.961000	0.38030	-0.254000	0.11334	AGT	G|0.512;N|0.000	.	strong		0.393	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
LAMC3	10319	hgsc.bcm.edu	37	9	133927878	133927878	+	Splice_Site	SNP	A	A	G	rs10901333	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133927878A>G	ENST00000361069.4	+	10	1764	c.1631A>G	c.(1630-1632)gAg>gGg	p.E544G	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	544	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.		E -> G (in dbSNP:rs10901333). {ECO:0000269|PubMed:10225960, ECO:0000269|Ref.3}.		astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		TTGTCTTCAGAGAAGTTCCTG	0.483											OREG0019556	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2360	0.471246	0.5499	0.3314	5008	,	,		17410	0.4325		0.497	False		,,,				2504	0.4775				p.E544G		Atlas-SNP	.											.	LAMC3	167	.	0			c.A1631G						PASS	.	A	GLY/GLU	2322,2084	601.5+/-389.7	619,1084,500	83.0	94.0	90.0		1631	4.2	1.0	9	dbSNP_120	90	4116,4484	562.7+/-388.0	1012,2092,1196	yes	missense-near-splice	LAMC3	NM_006059.3	98	1631,3176,1696	GG,GA,AA		47.8605,47.2991,49.5002	probably-damaging	544/1576	133927878	6438,6568	2203	4300	6503	SO:0001630	splice_region_variant	10319	exon10			CTTCAGAGAAGTT	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.1631-1A>G	9.37:g.133927878A>G		Somatic	98	0	0	1606	WXS	Illumina HiSeq	Phase_I	92	92	1	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	964	0.4413919413919414	257	0.5223577235772358	122	0.3370165745856354	228	0.3986013986013986	357	0.470976253298153	A	11.61	1.691384	0.30052	0.527009	0.478605	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.38560	1.13	5.42	4.25	0.50352	Laminin B type IV (2);	0.208574	0.49916	D	0.000121	T	0.00012	0.0000	L	0.56769	1.78	0.29596	P	0.8480449999999999	B	0.17465	0.022	B	0.26614	0.071	T	0.45454	-0.9260	8	.	.	.	.	6.6242	0.22820	0.7655:0.154:0.0805:0.0	rs10901333;rs52796473;rs57407531;rs10901333	544	Q9Y6N6	LAMC3_HUMAN	G	544	ENSP00000354360:E544G	.	E	+	2	0	LAMC3	132917699	1.000000	0.71417	0.993000	0.49108	0.229000	0.25112	1.458000	0.35223	0.859000	0.35456	0.459000	0.35465	GAG	A|0.520;G|0.480	0.480	strong		0.483	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	Missense_Mutation
PRKRA	8575	hgsc.bcm.edu	37	2	179300979	179300979	+	Missense_Mutation	SNP	A	A	T	rs77419724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179300979A>T	ENST00000325748.4	-	7	877	c.677T>A	c.(676-678)aTc>aAc	p.I226N	AC009948.5_ENST00000454488.1_RNA|AC009948.5_ENST00000436616.2_RNA|AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000438687.3_Missense_Mutation_p.I113N|PRKRA_ENST00000432031.2_Missense_Mutation_p.I215N|PRKRA_ENST00000487082.1_Missense_Mutation_p.I201N	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	226	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.I226N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CAGTAAGTTGATCTTTTCACC	0.353																																					p.I226N	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											PRKRA,NS,carcinoma,0,1	PRKRA	56	1	1	Substitution - Missense(1)	pancreas(1)	c.T677A						PASS	.	A	ASN/ILE,ASN/ILE,ASN/ILE	226,4180		0,226,1977	157.0	179.0	172.0		644,602,677	5.9	1.0	2	dbSNP_132	172	835,7765		0,835,3465	yes	missense,missense,missense	PRKRA	NM_001139517.1,NM_001139518.1,NM_003690.4	149,149,149	0,1061,5442	TT,TA,AA		9.7093,5.1294,8.1578	probably-damaging,probably-damaging,probably-damaging	215/303,201/289,226/314	179300979	1061,11945	2203	4300	6503	SO:0001583	missense	8575	exon7			AAGTTGATCTTTT	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.677T>A	2.37:g.179300979A>T	ENSP00000318176:p.Ile226Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	129	51	0.395349	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Missense_Mutation	SNP	ENST00000325748.4	37	CCDS2279.1	256	0.11721611721611722	26	0.052845528455284556	59	0.16298342541436464	51	0.08916083916083917	120	0.158311345646438	A	25.3	4.621990	0.87460	0.051294	0.097093	ENSG00000180228	ENST00000325748;ENST00000438687;ENST00000487082;ENST00000432031	T;T;T;T	0.79247	-1.18;-1.25;-1.11;-1.17	5.92	5.92	0.95590	.	0.196115	0.42053	N	0.000775	T	0.01421	0.0046	L	0.50333	1.59	0.42971	D	0.994437	D;B	0.67145	0.996;0.138	D;B	0.64595	0.927;0.037	T	0.23797	-1.0178	10	0.72032	D	0.01	.	13.9014	0.63806	1.0:0.0:0.0:0.0	.	226;215	O75569;O75569-2	PRKRA_HUMAN;.	N	226;113;201;215	ENSP00000318176:I226N;ENSP00000398980:I113N;ENSP00000430604:I201N;ENSP00000393883:I215N	ENSP00000318176:I226N	I	-	2	0	PRKRA	179009225	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.644000	0.83416	2.277000	0.76020	0.528000	0.53228	ATC	A|0.879;T|0.121	0.121	strong		0.353	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	
ANKK1	255239	hgsc.bcm.edu	37	11	113270160	113270160	+	Missense_Mutation	SNP	A	A	G	rs2734849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:113270160A>G	ENST00000303941.3	+	8	1563	c.1469A>G	c.(1468-1470)cAt>cGt	p.H490R		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	490			H -> R (in dbSNP:rs2734849). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		CCCAACCTGCATGAGGCTGAG	0.597													A|||	1227	0.245008	0.1044	0.3098	5008	,	,		19763	0.0625		0.504	False		,,,				2504	0.3108				p.H490R		Atlas-SNP	.											.	ANKK1	83	.	0			c.A1469G	GRCh37	CM085118	ANKK1	M	rs2734849	PASS	.	A	ARG/HIS	665,3379		50,565,1407	16.0	18.0	17.0		1469	-9.3	0.0	11	dbSNP_100	17	4205,4177		1089,2027,1075	yes	missense	ANKK1	NM_178510.1	29	1139,2592,2482	GG,GA,AA		49.833,16.4441,39.192	benign	490/766	113270160	4870,7556	2022	4191	6213	SO:0001583	missense	255239	exon8			ACCTGCATGAGGC	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.1469A>G	11.37:g.113270160A>G	ENSP00000306678:p.His490Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	598	0.27380952380952384	59	0.11991869918699187	131	0.36187845303867405	33	0.057692307692307696	375	0.4947229551451187	A	0.017	-1.494949	0.01009	0.164441	0.50167	ENSG00000170209	ENST00000303941	T	0.14893	2.47	4.66	-9.31	0.00646	Ankyrin repeat-containing domain (3);	1.164800	0.06415	N	0.721278	T	0.00012	0.0000	N	0.00188	-1.89	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.48490	-0.9031	9	0.08837	T	0.75	1.1889	17.9493	0.89047	0.871:0.0:0.129:0.0	rs2734849;rs52793977;rs59959221;rs2734849	490	Q8NFD2	ANKK1_HUMAN	R	490	ENSP00000306678:H490R	ENSP00000306678:H490R	H	+	2	0	ANKK1	112775370	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.114000	0.10757	-2.467000	0.00532	-0.379000	0.06801	CAT	A|0.725;G|0.275	0.275	strong		0.597	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
CYP2C8	1558	hgsc.bcm.edu	37	10	96798749	96798749	+	Missense_Mutation	SNP	T	T	C	rs10509681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96798749T>C	ENST00000371270.3	-	8	1290	c.1196A>G	c.(1195-1197)aAa>aGa	p.K399R	CYP2C8_ENST00000535898.1_Missense_Mutation_p.K297R	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	399			K -> R (in allele CYP2C8*3; dbSNP:rs10509681). {ECO:0000269|PubMed:11668219, ECO:0000269|PubMed:12429347, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:2216732, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	AGGAAATTCTTTGTCATCATG	0.383													T|||	229	0.0457268	0.0083	0.0994	5008	,	,		22146	0.001		0.1183	False		,,,				2504	0.0297				p.K399R		Atlas-SNP	.											.	CYP2C8	73	.	0			c.A1196G	GRCh37	CM014701	CYP2C8	M	rs10509681	PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	108,4298	83.9+/-122.4	2,104,2097	133.0	124.0	127.0		1196,986,890,986	-1.4	0.0	10	dbSNP_119	127	1003,7597	215.5+/-254.8	67,869,3364	yes	missense,missense,missense,missense	CYP2C8	NM_000770.3,NM_001198853.1,NM_001198854.1,NM_001198855.1	26,26,26,26	69,973,5461	CC,CT,TT		11.6628,2.4512,8.5422	benign,benign,benign,benign	399/491,329/421,297/389,329/421	96798749	1111,11895	2203	4300	6503	SO:0001583	missense	1558	exon8			AATTCTTTGTCAT	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"""Cytochrome P450s"""	2622	protein-coding gene	gene with protein product		601129	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"""			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.1196A>G	10.37:g.96798749T>C	ENSP00000360317:p.Lys399Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	111	46	0.414414	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	141	0.06456043956043957	6	0.012195121951219513	46	0.1270718232044199	2	0.0034965034965034965	87	0.11477572559366754	T	10.51	1.369107	0.24771	0.024512	0.116628	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898	T;T	0.70516	-0.49;-0.49	3.96	-1.44	0.08856	.	0.504809	0.19644	U	0.109394	T	0.01061	0.0035	M	0.62016	1.91	0.80722	P	0.0	B;B;B	0.17268	0.02;0.021;0.021	B;B;B	0.27380	0.079;0.063;0.078	T	0.15752	-1.0426	9	0.46703	T	0.11	.	4.629	0.12491	0.0:0.2844:0.1588:0.5567	rs10509681;rs17522568;rs56435423;rs61450273;rs10509681	297;367;399	B7Z1F6;B7Z8S1;P10632	.;.;CP2C8_HUMAN	R	399;366;297	ENSP00000360317:K399R;ENSP00000445062:K297R	ENSP00000360317:K399R	K	-	2	0	CYP2C8	96788739	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-0.030000	0.12308	-0.368000	0.08040	0.402000	0.26972	AAA	T|0.946;C|0.054	0.054	strong		0.383	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
CES1	1066	hgsc.bcm.edu	37	16	55862836	55862836	+	Silent	SNP	G	G	A	rs3826191		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55862836G>A	ENST00000361503.4	-	2	230	c.100C>T	c.(100-102)Ctg>Ttg	p.L34L	CES1_ENST00000422046.2_Silent_p.L34L|CES1_ENST00000566555.1_5'Flank|CES1_ENST00000360526.3_Silent_p.L35L			P23141	EST1_HUMAN	carboxylesterase 1	34					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	AACTTCCCCAGCACTTTGCCA	0.557																																					p.L35L	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,colon,carcinoma,0,1	CES1	78	1	0			c.C103T						PASS	.						64.0	50.0	55.0					16																	55862836		2198	4300	6498	SO:0001819	synonymous_variant	1066	exon2			TCCCCAGCACTTT	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.100C>T	16.37:g.55862836G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	20	0.190476	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																			G|0.500;A|0.500	0.500	strong		0.557	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
OTOF	9381	hgsc.bcm.edu	37	2	26695500	26695500	+	Missense_Mutation	SNP	A	A	C	rs41288773	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:26695500A>C	ENST00000272371.2	-	30	3877	c.3751T>G	c.(3751-3753)Tgc>Ggc	p.C1251G	OTOF_ENST00000338581.6_Intron|OTOF_ENST00000339598.3_Intron|OTOF_ENST00000402415.3_Missense_Mutation_p.C561G|OTOF_ENST00000403946.3_Missense_Mutation_p.C1251G	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1251					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCACACGGCAGCGCCGGAGA	0.582													A|||	34	0.00678914	0.0008	0.0058	5008	,	,		19683	0.0		0.0239	False		,,,				2504	0.0051				p.C1251G	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.T3751G						PASS	.	A	,GLY/CYS,GLY/CYS,	13,4391	20.2+/-43.8	0,13,2189	45.0	40.0	42.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,3751,1681,	-4.8	0.0	2	dbSNP_127	42	170,8430	77.5+/-140.1	1,168,4131	yes	intron,missense,missense,intron	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,159,159,	1,181,6320	CC,CA,AA		1.9767,0.2952,1.4073	,benign,benign,	,1251/1998,561/1308,	26695500	183,12821	2202	4300	6502	SO:0001583	missense	9381	exon30			CACGGCAGCGCCG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3751T>G	2.37:g.26695500A>C	ENSP00000272371:p.Cys1251Gly	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	20	0.009157509157509158	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	16	0.021108179419525065	A	0.467	-0.886171	0.02511	0.002952	0.019767	ENSG00000115155	ENST00000402415;ENST00000272371;ENST00000403946	T;T;T	0.79454	-1.01;-1.27;-1.27	4.93	-4.82	0.03171	C2 calcium/lipid-binding domain, CaLB (1);	0.765022	0.12579	N	0.456624	T	0.39118	0.1066	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31558	-0.9939	9	.	.	.	-3.1649	6.7555	0.23512	0.4907:0.2258:0.2835:0.0	rs41288773	1251;561	Q9HC10;Q9HC10-3	OTOF_HUMAN;.	G	561;1251;1251	ENSP00000383906:C561G;ENSP00000272371:C1251G;ENSP00000385255:C1251G	.	C	-	1	0	OTOF	26549004	0.958000	0.32768	0.002000	0.10522	0.031000	0.12232	1.434000	0.34958	-0.392000	0.07751	0.459000	0.35465	TGC	A|0.986;C|0.014	0.014	strong		0.582	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
DSPP	1834	hgsc.bcm.edu	37	4	88537035	88537035	+	Missense_Mutation	SNP	A	A	G	rs202210195		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88537035A>G	ENST00000282478.7	+	4	3254	c.3221A>G	c.(3220-3222)gAc>gGc	p.D1074G	DSPP_ENST00000399271.1_Missense_Mutation_p.D1074G|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1074	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagtgacagcagcgac	0.542																																					p.D1074G		Atlas-SNP	.											DSPP,NS,carcinoma,-1,1	DSPP	174	1	0			c.A3221G						scavenged	.						58.0	65.0	62.0					4																	88537035		1567	2848	4415	SO:0001583	missense	1834	exon5			GCAGTGACAGCAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3221A>G	4.37:g.88537035A>G	ENSP00000282478:p.Asp1074Gly	Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	295	81	0.274576	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	a	3.083	-0.188481	0.06299	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	1.51	1.51	0.23008	.	.	.	.	.	D	0.83468	0.5261	L	0.34521	1.04	0.58432	P	4.000000000004E-6	D	0.58620	0.983	P	0.48598	0.583	T	0.81771	-0.0780	8	0.48119	T	0.1	.	5.1866	0.15187	1.0:0.0:0.0:0.0	.	1074	Q9NZW4	DSPP_HUMAN	G	1074	ENSP00000382213:D1074G;ENSP00000282478:D1074G	ENSP00000282478:D1074G	D	+	2	0	DSPP	88756059	0.407000	0.25352	0.138000	0.22173	0.004000	0.04260	1.380000	0.34351	0.963000	0.38082	0.242000	0.17961	GAC	.	.	weak		0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39909394	39909394	+	Silent	SNP	C	C	T	rs146672674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39909394C>T	ENST00000409794.3	+	10	1954	c.1104C>T	c.(1102-1104)agC>agT	p.S368S	PLEKHG2_ENST00000458508.2_Silent_p.S309S|PLEKHG2_ENST00000378550.1_Silent_p.S368S|PLEKHG2_ENST00000409797.2_Silent_p.S368S|PLEKHG2_ENST00000425673.1_Silent_p.S368S	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	368	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TGAGCGTGAGCGAGAGTCCCC	0.577													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18474	0.0		0.0	False		,,,				2504	0.0				p.S368S		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C1104T						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	230.0	231.0	231.0		1104	-3.3	1.0	19	dbSNP_134	231	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	PLEKHG2	NM_022835.2		0,12,6491	TT,TC,CC		0.0698,0.1362,0.0923		368/1387	39909394	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	64857	exon10			CGTGAGCGAGAGT	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1104C>T	19.37:g.39909394C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.421	1.082999	0.20309	0.001362	6.98E-4	ENSG00000090924	ENST00000205135	.	.	.	4.4	-3.26	0.05064	.	.	.	.	.	T	0.48537	0.1505	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44406	-0.9330	4	.	.	.	.	6.3348	0.21291	0.1262:0.3477:0.0:0.5261	.	.	.	.	V	265	.	.	A	+	2	0	PLEKHG2	44601234	0.000000	0.05858	0.990000	0.47175	0.799000	0.45148	-4.066000	0.00302	-0.329000	0.08527	0.462000	0.41574	GCG	C|0.999;T|0.001	0.001	strong		0.577	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
OR4X1	390113	hgsc.bcm.edu	37	11	48285906	48285906	+	Missense_Mutation	SNP	C	C	T	rs16905753	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:48285906C>T	ENST00000320048.1	+	1	494	c.494C>T	c.(493-495)cCg>cTg	p.P165L		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	165			P -> L (in dbSNP:rs16905753).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P165L(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						TTCCAGCTCCCGTTCTGTGGC	0.562													C|||	915	0.182708	0.3185	0.1268	5008	,	,		21065	0.1627		0.1252	False		,,,				2504	0.1186				p.P165L		Atlas-SNP	.											OR4X1,NS,adenoma,-1,2	OR4X1	75	2	1	Substitution - Missense(1)	stomach(1)	c.C494T						scavenged	.	C	LEU/PRO	1261,3141	431.2+/-342.8	191,879,1131	104.0	92.0	96.0		494	4.3	0.9	11	dbSNP_123	96	1155,7441	236.4+/-268.6	77,1001,3220	yes	missense	OR4X1	NM_001004726.1	98	268,1880,4351	TT,TC,CC		13.4365,28.6461,18.5875	benign	165/306	48285906	2416,10582	2201	4298	6499	SO:0001583	missense	390113	exon1			AGCTCCCGTTCTG	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"""GPCR / Class A : Olfactory receptors"""	14854	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily X, member 1"""				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.494C>T	11.37:g.48285906C>T	ENSP00000321506:p.Pro165Leu	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_001004726	Q6IF74	Missense_Mutation	SNP	ENST00000320048.1	37	CCDS31487.1	368	0.1684981684981685	134	0.27235772357723576	45	0.12430939226519337	93	0.16258741258741258	96	0.1266490765171504	C	16.41	3.116671	0.56505	0.286461	0.134365	ENSG00000176567	ENST00000320048	T	0.00158	8.65	4.28	4.28	0.50868	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.84683	2.71	0.37564	P	0.08081799999999995	P	0.37663	0.604	B	0.39419	0.299	T	0.44528	-0.9322	8	0.87932	D	0	.	14.7726	0.69691	0.0:1.0:0.0:0.0	rs16905753;rs52801988;rs16905753	165	Q8NH49	OR4X1_HUMAN	L	165	ENSP00000321506:P165L	ENSP00000321506:P165L	P	+	2	0	OR4X1	48242482	0.044000	0.20184	0.948000	0.38648	0.688000	0.40055	3.311000	0.51919	2.404000	0.81709	0.539000	0.68188	CCG	C|0.822;T|0.178	0.178	strong		0.562	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726	
NPR3	4883	hgsc.bcm.edu	37	5	32786389	32786389	+	Missense_Mutation	SNP	A	A	G	rs2270915	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:32786389A>G	ENST00000265074.8	+	8	1907	c.1564A>G	c.(1564-1566)Aac>Gac	p.N522D	NPR3_ENST00000415685.2_Missense_Mutation_p.N305D|NPR3_ENST00000415167.2_Missense_Mutation_p.N521D|NPR3_ENST00000434067.2_Missense_Mutation_p.N306D|AC026703.1_ENST00000326958.1_5'Flank	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	522				N -> D (in Ref. 4; BAG61896). {ECO:0000305}.	adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	AGAAGAAAGTAACCTTGGAAA	0.403													A|||	979	0.195487	0.0991	0.2147	5008	,	,		18620	0.2024		0.1879	False		,,,				2504	0.3129				p.N522D		Atlas-SNP	.											.	NPR3	65	.	0			c.A1564G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN	428,3234		33,362,1436	78.0	73.0	74.0		1561,1564,913	5.0	0.7	5	dbSNP_100	74	1649,6519		159,1331,2594	yes	missense,missense,missense	NPR3	NM_000908.3,NM_001204375.1,NM_001204376.1	23,23,23	192,1693,4030	GG,GA,AA		20.1885,11.6876,17.5571	benign,benign,benign	521/541,522/542,305/325	32786389	2077,9753	1831	4084	5915	SO:0001583	missense	4883	exon8			GAAAGTAACCTTG		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"""guanylate cyclase C"""	108962	"""chromosome 5 open reading frame 23"", ""atrionatriuretic peptide receptor C"", ""natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)"", ""natriuretic peptide receptor C"""	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.1564A>G	5.37:g.32786389A>G	ENSP00000265074:p.Asn522Asp	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	223	117	0.524664	NM_001204375	A2RRD1|B4DT84|E7EPG9	Missense_Mutation	SNP	ENST00000265074.8	37	CCDS56357.1	388	0.17765567765567766	47	0.09552845528455285	68	0.1878453038674033	122	0.21328671328671328	151	0.19920844327176782	A	12.56	1.975892	0.34848	0.116876	0.201885	ENSG00000113389	ENST00000434067;ENST00000415685;ENST00000265074;ENST00000415167	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	6.17	5.0	0.66597	.	0.198485	0.53938	D	0.000058	T	0.00012	0.0000	N	0.08118	0	0.27179	P	0.9607229	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.002;0.003	T	0.10268	-1.0637	9	0.33940	T	0.23	-14.8784	13.7445	0.62868	0.8716:0.1283:0.0:0.0	rs2270915;rs52798471;rs59552869;rs2270915	305;522;521	E7EPG9;P17342;Q60I31	.;ANPRC_HUMAN;.	D	306;305;522;521	ENSP00000388408:N306D;ENSP00000402490:N305D;ENSP00000265074:N522D;ENSP00000398028:N521D	ENSP00000265074:N522D	N	+	1	0	NPR3	32822146	1.000000	0.71417	0.741000	0.31004	0.983000	0.72400	4.122000	0.57910	1.137000	0.42214	0.533000	0.62120	AAC	A|0.833;G|0.167	0.167	strong		0.403	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908	
NEFH	4744	hgsc.bcm.edu	37	22	29886354	29886354	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29886354G>A	ENST00000310624.6	+	4	2758	c.2725G>A	c.(2725-2727)Gag>Aag	p.E909K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	915	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CCCAGAGAAGGAGGCTCCTGC	0.502																																					p.E909K		Atlas-SNP	.											.	NEFH	178	.	0			c.G2725A						PASS	.						57.0	62.0	60.0					22																	29886354		2203	4300	6503	SO:0001583	missense	4744	exon4			GAGAAGGAGGCTC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2725G>A	22.37:g.29886354G>A	ENSP00000311997:p.Glu909Lys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.442446	0.25987	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.84223	-1.82	5.48	4.4	0.53042	.	0.270105	0.26719	N	0.022846	T	0.79633	0.4479	L	0.59436	1.845	0.41319	D	0.98716	P	0.38020	0.615	B	0.33121	0.158	T	0.79137	-0.1927	10	0.40728	T	0.16	.	10.1869	0.43002	0.0756:0.1391:0.7853:0.0	.	915	P12036	NFH_HUMAN	K	860;909	ENSP00000311997:E909K	ENSP00000311997:E909K	E	+	1	0	NEFH	28216354	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	3.431000	0.52814	2.739000	0.93911	0.655000	0.94253	GAG	.	.	none		0.502	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
PAPD7	11044	hgsc.bcm.edu	37	5	6748659	6748659	+	Silent	SNP	T	T	C	rs274681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:6748659T>C	ENST00000230859.6	+	8	921	c.792T>C	c.(790-792)gcT>gcC	p.A264A		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	494					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)	p.A264A(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TCAGCCATGCTGTGTCACCGC	0.552													C|||	2828	0.564696	0.4047	0.5836	5008	,	,		20718	0.5754		0.6759	False		,,,				2504	0.6421				p.A264A	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											PAPD7,colon,carcinoma,0,2	PAPD7	69	2	1	Substitution - coding silent(1)	stomach(1)	c.T792C						PASS	.	C	,,	1950,2456	622.9+/-394.0	429,1092,682	302.0	263.0	276.0		792,252,792	-4.9	0.6	5	dbSNP_79	276	6056,2544	414.3+/-351.4	2144,1768,388	no	coding-synonymous,coding-synonymous,coding-synonymous	PAPD7	NM_001171805.1,NM_001171806.1,NM_006999.4	,,	2573,2860,1070	CC,CT,TT		29.5814,44.2578,38.4438	,,	264/542,84/363,264/543	6748659	8006,5000	2203	4300	6503	SO:0001819	synonymous_variant	11044	exon8			CCATGCTGTGTCA	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"""topoisomerase-related function protein 4-1"", ""polymerase (DNA-directed) sigma"", ""DNA polymerase kappa"", ""TUTase5"""	605198	"""polymerase (DNA directed) sigma"""	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.792T>C	5.37:g.6748659T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	264	92	0.348485	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Silent	SNP	ENST00000230859.6	37	CCDS3871.1																																																																																			T|0.392;C|0.608	0.608	strong		0.552	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999	
FOLH1	2346	hgsc.bcm.edu	37	11	49227620	49227620	+	Splice_Site	SNP	A	A	G	rs202676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49227620A>G	ENST00000256999.2	-	2	483	c.223T>C	c.(223-225)Tat>Cat	p.Y75H	FOLH1_ENST00000343844.4_5'UTR|FOLH1_ENST00000340334.7_Splice_Site_p.Y60H|FOLH1_ENST00000356696.3_Splice_Site_p.Y75H|FOLH1_ENST00000533034.1_Splice_Site_p.Y60H	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	75			Y -> H (in dbSNP:rs202676). {ECO:0000269|PubMed:9838072}.		folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGTACTTACTATAAGAACTTC	0.294													A|||	1935	0.386382	0.6021	0.2896	5008	,	,		16366	0.3155		0.2256	False		,,,				2504	0.4018				p.Y75H		Atlas-SNP	.											.	FOLH1	141	.	0			c.T223C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR,,HIS/TYR	2305,2095	599.3+/-389.2	593,1119,488	68.0	68.0	68.0		223,178,178,,223	1.9	0.9	11	dbSNP_79	68	1924,6662	337.1+/-322.1	206,1512,2575	yes	missense-near-splice,missense-near-splice,missense-near-splice,utr-5,missense-near-splice	FOLH1	NM_001014986.1,NM_001193471.1,NM_001193472.1,NM_001193473.1,NM_004476.1	83,83,83,,83	799,2631,3063	GG,GA,AA		22.4086,47.6136,32.5658	benign,benign,benign,,benign	75/720,60/736,60/705,,75/751	49227620	4229,8757	2200	4293	6493	SO:0001630	splice_region_variant	2346	exon2			CTTACTATAAGAA	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.224+1T>C	11.37:g.49227620A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	90	35	0.388889	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	755	0.3456959706959707	288	0.5853658536585366	96	0.26519337016574585	197	0.34440559440559443	174	0.22955145118733508	A	0.951	-0.706256	0.03255	0.523864	0.224086	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724;ENST00000529117	T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1	4.29	1.93	0.25924	.	0.293789	0.24436	N	0.038558	T	0.00012	0.0000	N	0.11724	0.165	0.09310	P	0.9999999999994258	B;B;B;B;B	0.13145	0.007;0.0;0.0;0.004;0.0	B;B;B;B;B	0.17722	0.019;0.002;0.0;0.012;0.0	T	0.43163	-0.9408	9	0.41790	T	0.15	.	7.8033	0.29187	0.7216:0.0:0.2784:0.0	rs202676;rs7937199;rs52836105;rs58342698;rs202676	60;60;60;75;75	Q04609-9;Q04609-7;A4UU13;Q04609-8;Q04609	.;.;.;.;FOLH1_HUMAN	H	75;75;60;60;75;18	ENSP00000256999:Y75H;ENSP00000349129:Y75H;ENSP00000344131:Y60H;ENSP00000431463:Y60H;ENSP00000431577:Y18H	ENSP00000256999:Y75H	Y	-	1	0	FOLH1	49184196	0.800000	0.28916	0.906000	0.35671	0.393000	0.30537	0.183000	0.16919	0.011000	0.14865	-1.186000	0.01703	TAT	A|0.657;G|0.343	0.343	strong		0.294	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	Missense_Mutation
GOLGB1	2804	hgsc.bcm.edu	37	3	121415610	121415610	+	Missense_Mutation	SNP	G	G	A	rs33988592	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121415610G>A	ENST00000340645.5	-	13	3870	c.3745C>T	c.(3745-3747)Cca>Tca	p.P1249S	GOLGB1_ENST00000393667.3_Missense_Mutation_p.P1254S	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1249			P -> S (in dbSNP:rs33988592).		Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TCTGTGCTTGGGAGTTTTCCG	0.438													G|||	736	0.146965	0.1286	0.1383	5008	,	,		21254	0.0923		0.2833	False		,,,				2504	0.0941				p.P1254S		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C3760T						PASS	.	G	SER/PRO	667,3739	282.8+/-276.7	50,567,1586	203.0	182.0	189.0		3745	1.9	0.0	3	dbSNP_126	189	2468,6132	405.4+/-348.5	368,1732,2200	yes	missense	GOLGB1	NM_004487.3	74	418,2299,3786	AA,AG,GG		28.6977,15.1384,24.1043	benign	1249/3260	121415610	3135,9871	2203	4300	6503	SO:0001583	missense	2804	exon13			TGCTTGGGAGTTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.3745C>T	3.37:g.121415610G>A	ENSP00000341848:p.Pro1249Ser	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	384	181	0.471354	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	377	0.17261904761904762	65	0.13211382113821138	48	0.13259668508287292	55	0.09615384615384616	209	0.2757255936675462	G	0.041	-1.284513	0.01398	0.151384	0.286977	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	T;T;T	0.22539	2.56;2.54;1.95	6.07	1.91	0.25777	.	0.655467	0.14262	N	0.330719	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B;B;B;B;B	0.12630	0.006;0.006;0.006;0.006;0.006	B;B;B;B;B	0.10450	0.005;0.005;0.003;0.003;0.003	T	0.41395	-0.9511	9	0.09843	T	0.71	.	2.4289	0.04466	0.1581:0.1242:0.4626:0.2551	rs33988592	1174;1213;1254;1254;1249	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.;.;.;.;GOGB1_HUMAN	S	1249;1254;1213	ENSP00000341848:P1249S;ENSP00000377275:P1254S;ENSP00000418231:P1213S	ENSP00000341848:P1249S	P	-	1	0	GOLGB1	122898300	0.000000	0.05858	0.004000	0.12327	0.083000	0.17756	-0.819000	0.04462	0.410000	0.25675	0.655000	0.94253	CCA	G|0.780;A|0.220	0.220	strong		0.438	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
CCDC169	728591	hgsc.bcm.edu	37	13	36801415	36801415	+	Missense_Mutation	SNP	C	C	T	rs9546785	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:36801415C>T	ENST00000503173.1	-	8	678	c.649G>A	c.(649-651)Gga>Aga	p.G217R	SOHLH2_ENST00000554962.1_Intron|CCDC169_ENST00000239860.6_Missense_Mutation_p.G117R|CCDC169-SOHLH2_ENST00000511166.1_Intron|CCDC169_ENST00000491049.2_Missense_Mutation_p.G115R|CCDC169_ENST00000379864.2_Missense_Mutation_p.G115R	NM_001198908.1	NP_001185837.1	A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	0										breast(1)|endometrium(1)	2						GCTTTTTGTCCGAGGCATGTC	0.493													C|||	1891	0.377596	0.2231	0.4755	5008	,	,		14885	0.3819		0.4712	False		,,,				2504	0.4162				p.G217R		Atlas-SNP	.											.	CCDC169	20	.	0			c.G649A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,	368,1016		51,266,375	96.0	81.0	86.0		343,343,349,649,	0.2	0.0	13	dbSNP_119	86	1513,1669		358,797,436	yes	missense,missense,missense,missense,intron	CCDC169,CCDC169-SOHLH2	NM_001144982.2,NM_001144983.2,NM_001144984.2,NM_001198908.1,NM_001198910.1	125,125,125,125,	409,1063,811	TT,TC,CC		47.5487,26.5896,41.1958	,,,,	115/140,115/140,117/142,217/242,	36801415	1881,2685	692	1591	2283	SO:0001583	missense	728591	exon8			TTTGTCCGAGGCA		CCDS45027.1, CCDS45028.1, CCDS45029.1, CCDS53863.1, CCDS55897.1	13q13.3	2011-08-09	2011-08-09	2011-08-09	ENSG00000242715	ENSG00000242715			34361	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 38"""	C13orf38			Standard	NM_001144981		Approved	RP11-251J8.1, LOC728591		A6NNP5	OTTHUMG00000016731	ENST00000503173.1:c.649G>A	13.37:g.36801415C>T	ENSP00000426174:p.Gly217Arg	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	279	134	0.480287	NM_001198908	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Missense_Mutation	SNP	ENST00000503173.1	37	CCDS55897.1	830	0.38003663003663	110	0.22357723577235772	166	0.4585635359116022	207	0.3618881118881119	347	0.4577836411609499	C	6.816	0.519730	0.13005	0.265896	0.475487	ENSG00000242715	ENST00000491049;ENST00000503173;ENST00000239860;ENST00000379864	T;T;T;T	0.59083	0.33;0.48;0.29;0.33	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.73380	0.98;0.98;0.98	T	0.46484	-0.9188	7	0.87932	D	0	.	.	.	.	rs9546785;rs52798169;rs9546785	217;117;115	A6NNP5-4;B7ZW49;A6NNP5-3	.;.;.	R	115;217;117;115	ENSP00000425252:G115R;ENSP00000426174:G217R;ENSP00000239860:G117R;ENSP00000369193:G115R	ENSP00000239860:G117R	G	-	1	0	CCDC169	35699415	0.002000	0.14202	0.004000	0.12327	0.004000	0.04260	0.305000	0.19254	0.308000	0.22923	0.313000	0.20887	GGA	C|0.624;T|0.376	0.376	strong		0.493	CCDC169-012	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368253.1	NM_001144981	
OR10H2	26538	hgsc.bcm.edu	37	19	15839459	15839459	+	Silent	SNP	G	G	A	rs11669315	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15839459G>A	ENST00000305899.3	+	1	626	c.606G>A	c.(604-606)ttG>ttA	p.L202L		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					GCGTGGGCTTGGTATGTATCA	0.517													G|||	764	0.152556	0.1278	0.121	5008	,	,		23239	0.123		0.17	False		,,,				2504	0.2209				p.L202L		Atlas-SNP	.											.	OR10H2	59	.	0			c.G606A						PASS	.	G		612,3794		46,520,1637	223.0	182.0	196.0		606	2.3	0.0	19	dbSNP_120	196	1652,6948		179,1294,2827	no	coding-synonymous	OR10H2	NM_013939.2		225,1814,4464	AA,AG,GG		19.2093,13.8901,17.4074		202/316	15839459	2264,10742	2203	4300	6503	SO:0001819	synonymous_variant	26538	exon1			GGGCTTGGTATGT	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.606G>A	19.37:g.15839459G>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	238	114	0.478992	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			G|0.839;A|0.161	0.161	strong		0.517	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
COL23A1	91522	hgsc.bcm.edu	37	5	177675217	177675217	+	Silent	SNP	C	C	T	rs2913851	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:177675217C>T	ENST00000390654.3	-	20	1545	c.1188G>A	c.(1186-1188)gcG>gcA	p.A396A		NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	396	Gly-rich.				collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		GGCTGTCAGACGCCGACTCCC	0.652													C|||	1518	0.303115	0.0991	0.4409	5008	,	,		17329	0.2192		0.4771	False		,,,				2504	0.3885				p.A396A		Atlas-SNP	.											COL23A1,colon,carcinoma,0,1	COL23A1	47	1	0			c.G1188A						PASS	.	C		594,3400		53,488,1456	57.0	58.0	58.0		1188	-8.7	0.0	5	dbSNP_101	58	4140,4186		1038,2064,1061	no	coding-synonymous	COL23A1	NM_173465.3		1091,2552,2517	TT,TC,CC		49.7238,14.8723,38.4253		396/541	177675217	4734,7586	1997	4163	6160	SO:0001819	synonymous_variant	91522	exon20			GTCAGACGCCGAC	AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"""Collagens"""	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.1188G>A	5.37:g.177675217C>T		Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	306	89	0.29085	NM_173465	Q8IVR4|Q9NT93	Silent	SNP	ENST00000390654.3	37	CCDS4436.1																																																																																			C|0.668;T|0.332	0.332	strong		0.652	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465	
CLIC3	9022	hgsc.bcm.edu	37	9	139890105	139890105	+	Silent	SNP	C	C	G	rs141765089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139890105C>G	ENST00000494426.1	-	2	397	c.138G>C	c.(136-138)acG>acC	p.T46T	CLIC3_ENST00000480181.1_5'UTR	NM_004669.2	NP_004660.2	O95833	CLIC3_HUMAN	chloride intracellular channel 3	46	GST N-terminal.|Required for insertion into the membrane. {ECO:0000250}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|signal transduction (GO:0007165)	chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			lung(1)|skin(1)	2	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CTCACCTGCGCGTGTCCACCG	0.706													C|||	21	0.00419329	0.0015	0.0058	5008	,	,		10979	0.0		0.0149	False		,,,				2504	0.0				p.T46T		Atlas-SNP	.											.	CLIC3	13	.	0			c.G138C						PASS	.	C		19,4383	25.3+/-52.1	0,19,2182	40.0	37.0	38.0		138	-7.4	0.0	9	dbSNP_134	38	162,8434	69.4+/-131.9	2,158,4138	no	coding-synonymous	CLIC3	NM_004669.2		2,177,6320	GG,GC,CC		1.8846,0.4316,1.3925		46/237	139890105	181,12817	2201	4298	6499	SO:0001819	synonymous_variant	9022	exon2			CCTGCGCGTGTCC	AF102166	CCDS7021.1	9q34.3	2012-09-26			ENSG00000169583	ENSG00000169583		"""Ion channels / Chloride channels : Intracellular"""	2064	protein-coding gene	gene with protein product		606533				9880541	Standard	NM_004669		Approved		uc004ckj.1	O95833	OTTHUMG00000020954	ENST00000494426.1:c.138G>C	9.37:g.139890105C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	44	0.647059	NM_004669	Q5SPZ7	Silent	SNP	ENST00000494426.1	37	CCDS7021.1																																																																																			C|0.991;G|0.009	0.009	strong		0.706	CLIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055173.2	NM_004669	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108135	17108135	+	Missense_Mutation	SNP	C	C	T	rs3745340	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17108135C>T	ENST00000443236.1	-	11	1053	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	CPAMD8_ENST00000388925.4_Missense_Mutation_p.R294Q	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	294						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GTCGAAGTCCCGGGAGCCGAG	0.607													c|||	1649	0.329273	0.1649	0.353	5008	,	,		19240	0.5		0.3976	False		,,,				2504	0.2883				p.R341Q		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G1022A						PASS	.	C	GLN/ARG	795,3235		79,637,1299	13.0	15.0	14.0		1022	-3.8	0.8	19	dbSNP_107	14	3138,5204		619,1900,1652	no	missense	CPAMD8	NM_015692.2	43	698,2537,2951	TT,TC,CC		37.6169,19.727,31.7895	possibly-damaging	341/1933	17108135	3933,8439	2015	4171	6186	SO:0001583	missense	27151	exon11			AAGTCCCGGGAGC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1022G>A	19.37:g.17108135C>T	ENSP00000402505:p.Arg341Gln	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	172	161	0.936047	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	815|815	0.3731684981684982|0.3731684981684982	87|87	0.17682926829268292|0.17682926829268292	147|147	0.40607734806629836|0.40607734806629836	276|276	0.4825174825174825|0.4825174825174825	305|305	0.4023746701846966|0.4023746701846966	c|c	9.619|9.619	1.133286|1.133286	0.21041|0.21041	0.19727|0.19727	0.376169|0.376169	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440;ENST00000388925	.|T;T	.|0.51325	.|0.71;0.72	3.0|3.0	-3.79|-3.79	0.04320|0.04320	.|.	.|0.186387	.|0.32488	.|N	.|0.006027	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00707|0.00707	-1.245|-1.245	0.51767|0.51767	P|P	6.799999999995698E-5|6.799999999995698E-5	.|B	.|0.06786	.|0.001	.|B	.|0.01281	.|0.0	T|T	0.47315|0.47315	-0.9127|-0.9127	4|9	.|0.25751	.|T	.|0.34	.|.	6.6288|6.6288	0.22845|0.22845	0.0:0.38:0.371:0.2489|0.0:0.38:0.371:0.2489	rs3745340;rs57931423;rs3745340|rs3745340;rs57931423;rs3745340	.|294	.|Q8IZJ3	.|CPMD8_HUMAN	R|Q	352|341;294	.|ENSP00000291440:R341Q;ENSP00000373577:R294Q	.|ENSP00000291440:R341Q	G|R	-|-	1|2	0|0	CPAMD8|CPAMD8	16969135|16969135	0.997000|0.997000	0.39634|0.39634	0.786000|0.786000	0.31890|0.31890	0.743000|0.743000	0.42351|0.42351	2.354000|2.354000	0.44098|0.44098	-0.514000|-0.514000	0.06488|0.06488	-0.417000|-0.417000	0.06048|0.06048	GGG|CGG	C|0.647;T|0.353	0.353	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
FXYD4	53828	hgsc.bcm.edu	37	10	43871158	43871158	+	Missense_Mutation	SNP	G	G	A	rs41307500	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43871158G>A	ENST00000476166.1	+	7	522	c.188G>A	c.(187-189)tGc>tAc	p.C63Y	FXYD4_ENST00000480834.1_3'UTR	NM_173160.2	NP_775183.1	P59646	FXYD4_HUMAN	FXYD domain containing ion transport regulator 4	63				C -> Y (in Ref. 1; AAQ88947). {ECO:0000305}.	ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)			NS(1)|large_intestine(1)|lung(3)	5						AAATGCAAATGCAAGAGCAGC	0.617													G|||	129	0.0257588	0.0008	0.013	5008	,	,		16005	0.0407		0.0368	False		,,,				2504	0.0419				p.C63Y	GBM(173;880 2047 13035 42390 49655)	Atlas-SNP	.											.	FXYD4	9	.	0			c.G188A						PASS	.	G	TYR/CYS	27,4379	33.5+/-64.1	0,27,2176	82.0	86.0	85.0		188	4.3	1.0	10	dbSNP_127	85	325,8275	113.5+/-173.5	10,305,3985	yes	missense	FXYD4	NM_173160.2	194	10,332,6161	AA,AG,GG		3.7791,0.6128,2.7064	possibly-damaging	63/90	43871158	352,12654	2203	4300	6503	SO:0001583	missense	53828	exon7			GCAAATGCAAGAG		CCDS7203.1	10q11.21	2008-02-01	2002-01-14		ENSG00000150201	ENSG00000150201			4028	protein-coding gene	gene with protein product			"""FXYD domain-containing ion transport regulator 4"""			10950925, 12763854	Standard	NM_001184963		Approved	CHIF	uc001jaq.1	P59646	OTTHUMG00000018027	ENST00000476166.1:c.188G>A	10.37:g.43871158G>A	ENSP00000473361:p.Cys63Tyr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_001184963	Q6UWZ1|Q7Z4M5	Missense_Mutation	SNP	ENST00000476166.1	37	CCDS7203.1	63	0.028846153846153848	1	0.0020325203252032522	5	0.013812154696132596	25	0.043706293706293704	32	0.04221635883905013	G	16.78	3.218240	0.58560	0.006128	0.037791	ENSG00000150201	ENST00000374451;ENST00000458363	.	.	.	4.32	4.32	0.51571	.	0.057884	0.64402	D	0.000001	T	0.41650	0.1168	.	.	.	0.33287	D	0.563011	D	0.69078	0.997	D	0.70487	0.969	T	0.71533	-0.4564	8	0.66056	D	0.02	-4.7309	12.6074	0.56531	0.0:0.0:1.0:0.0	rs41307500;rs61860880	63	P59646	FXYD4_HUMAN	Y	63	.	ENSP00000363575:C63Y	C	+	2	0	FXYD4	43191164	1.000000	0.71417	0.999000	0.59377	0.716000	0.41182	3.340000	0.52143	2.701000	0.92244	0.655000	0.94253	TGC	G|0.972;A|0.028	0.028	strong		0.617	FXYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047698.2	NM_173160	
OR1I1	126370	hgsc.bcm.edu	37	19	15198292	15198292	+	Missense_Mutation	SNP	C	C	G	rs8104843	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198292C>G	ENST00000209540.2	+	1	502	c.416C>G	c.(415-417)cCt>cGt	p.P139R		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	139			P -> R (in dbSNP:rs8104843).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						ATGTGCTCCCCTGTCTGTGGG	0.572													G|||	3364	0.671725	0.3767	0.7723	5008	,	,		22072	0.622		0.829	False		,,,				2504	0.8885				p.P139R		Atlas-SNP	.											.	OR1I1	58	.	0			c.C416G						PASS	.	G	ARG/PRO	1930,2476		414,1102,687	84.0	71.0	76.0		416	-1.2	0.0	19	dbSNP_116	76	7253,1347		3055,1143,102	yes	missense	OR1I1	NM_001004713.1	103	3469,2245,789	GG,GC,CC		15.6628,43.8039,29.3941	benign	139/356	15198292	9183,3823	2203	4300	6503	SO:0001583	missense	126370	exon1			GCTCCCCTGTCTG	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.416C>G	19.37:g.15198292C>G	ENSP00000209540:p.Pro139Arg	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	1453	0.6652930402930403	189	0.38414634146341464	283	0.7817679558011049	350	0.6118881118881119	631	0.8324538258575198	N	0.001	-3.041142	0.00039	0.438039	0.843372	ENSG00000094661	ENST00000209540	T	0.31247	1.5	4.8	-1.19	0.09585	GPCR, rhodopsin-like superfamily (1);	0.571765	0.13123	N	0.412065	T	0.00012	0.0000	N	0.00252	-1.77	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27706	-1.0066	9	0.02654	T	1	.	5.8812	0.18856	0.4821:0.1357:0.3821:0.0	rs8104843;rs52819707;rs8104843	139	O60431	OR1I1_HUMAN	R	139	ENSP00000209540:P139R	ENSP00000209540:P139R	P	+	2	0	OR1I1	15059292	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.900000	0.04097	-0.498000	0.06632	-0.909000	0.02823	CCT	C|0.301;G|0.699	0.699	strong		0.572	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
KCNN3	3782	hgsc.bcm.edu	37	1	154842330	154842330	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154842330T>C	ENST00000271915.4	-	1	426	c.111A>G	c.(109-111)caA>caG	p.Q37Q	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	37	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gctgctgctgttgctgctgct	0.677																																					p.Q37Q		Atlas-SNP	.											KCNN3,rectum,carcinoma,0,1	KCNN3	141	1	0			c.A111G						PASS	.						8.0	8.0	8.0					1																	154842330		1936	3838	5774	SO:0001819	synonymous_variant	3782	exon1			CTGCTGTTGCTGC	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.111A>G	1.37:g.154842330T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	7	0.0958904	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	37	CCDS30880.1																																																																																			.	.	none		0.677	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
C19orf71	100128569	hgsc.bcm.edu	37	19	3543397	3543397	+	Missense_Mutation	SNP	C	C	T	rs12608919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:3543397C>T	ENST00000329493.5	+	2	272	c.248C>T	c.(247-249)cCg>cTg	p.P83L	MFSD12_ENST00000389395.3_Intron|AC005786.7_ENST00000589360.1_RNA|MFSD12_ENST00000398558.4_Intron	NM_001135580.1	NP_001129052.1	A6NCJ1	CS071_HUMAN	chromosome 19 open reading frame 71	83			P -> L (in dbSNP:rs12608919).							endometrium(2)	2						CCACGGGCCCCGGCCAGCCCC	0.692													C|||	1839	0.367212	0.0159	0.4986	5008	,	,		12289	0.7986		0.334	False		,,,				2504	0.3384				p.P83L		Atlas-SNP	.											C19orf71,colon,carcinoma,0,1	C19orf71	12	1	0			c.C248T						PASS	.						10.0	23.0	19.0					19																	3543397		678	1557	2235	SO:0001583	missense	100128569	exon2			GGGCCCCGGCCAG		CCDS45918.1	19p13.3	2012-10-26			ENSG00000183397	ENSG00000183397			34496	protein-coding gene	gene with protein product							Standard	NM_001135580		Approved	LOC100128569	uc010xhm.2	A6NCJ1		ENST00000329493.5:c.248C>T	19.37:g.3543397C>T	ENSP00000327950:p.Pro83Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	70	44	0.628571	NM_001135580		Missense_Mutation	SNP	ENST00000329493.5	37	CCDS45918.1	904	0.4139194139194139	18	0.036585365853658534	162	0.44751381215469616	464	0.8111888111888111	260	0.34300791556728233	C	1.241	-0.621326	0.03636	.	.	ENSG00000183397	ENST00000329493	T	0.25085	1.82	4.51	-6.94	0.01633	.	0.989975	0.08196	N	0.983046	T	0.00012	0.0000	N	0.05031	-0.125	0.80722	P	0.0	B	0.14805	0.011	B	0.10450	0.005	T	0.38222	-0.9671	9	0.02654	T	1	.	13.7342	0.62807	0.0:0.7188:0.0:0.2812	rs12608919;rs12608919	83	A6NCJ1	CS071_HUMAN	L	83	ENSP00000327950:P83L	ENSP00000327950:P83L	P	+	2	0	C19orf71	3494397	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.787000	0.00769	-1.520000	0.01773	-0.657000	0.03884	CCG	C|0.611;T|0.389	0.389	strong		0.692	C19orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452943.1	NM_001135580	
CCDC88A	55704	hgsc.bcm.edu	37	2	55615950	55615950	+	Silent	SNP	T	T	C	rs147639776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:55615950T>C	ENST00000436346.1	-	3	1078	c.237A>G	c.(235-237)ctA>ctG	p.L79L	CCDC88A_ENST00000263630.8_Silent_p.L79L|CCDC88A_ENST00000336838.6_Silent_p.L79L|CCDC88A_ENST00000413716.2_Silent_p.L79L	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	79					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						CCAAAATGGATAGATTGTGCA	0.269													T|||	3	0.000599042	0.0	0.0029	5008	,	,		12742	0.0		0.001	False		,,,				2504	0.0				p.L79L		Atlas-SNP	.											.	CCDC88A	336	.	0			c.A237G						PASS	.	T	,	2,4400	4.2+/-10.8	0,2,2199	69.0	74.0	72.0		237,237	-11.9	0.1	2	dbSNP_134	72	23,8531	17.3+/-56.4	0,23,4254	no	coding-synonymous,coding-synonymous	CCDC88A	NM_001135597.1,NM_018084.4	,	0,25,6453	CC,CT,TT		0.2689,0.0454,0.193	,	79/1871,79/1844	55615950	25,12931	2201	4277	6478	SO:0001819	synonymous_variant	55704	exon3			AATGGATAGATTG	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"""Galpha-interacting vesicle-associated protein"", ""Akt-phosphorylation enhancer"", ""girdin"", ""girders of actin filaments"""	609736	"""KIAA1212"""	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.237A>G	2.37:g.55615950T>C		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	304	141	0.463816	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Silent	SNP	ENST00000436346.1	37																																																																																				T|0.998;C|0.002	0.002	strong		0.269	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571	
CYP2A6	1548	hgsc.bcm.edu	37	19	41354533	41354533	+	Missense_Mutation	SNP	A	A	T	rs1801272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41354533A>T	ENST00000301141.5	-	3	499	c.479T>A	c.(478-480)cTc>cAc	p.L160H	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	160			L -> H (in allele CYP2A6*2; unable to catalyze 7-hydroxylation of coumarin; causes switching from coumarin 7- hydroxylation to 3-hydroxylation; dbSNP:rs1801272). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2322567, ECO:0000269|PubMed:2748347, ECO:0000269|Ref.6}.		coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	AGTGCCCCGGAGGGCGTCGAT	0.701													.|||	46	0.0091853	0.0008	0.0072	5008	,	,		12445	0.0		0.0338	False		,,,				2504	0.0061				p.L160H		Atlas-SNP	.											.	CYP2A6	69	.	0			c.T479A	GRCh37	CM980517	CYP2A6	M	rs1801272	PASS	.	A	HIS/LEU	20,4386		0,20,2183	35.0	38.0	37.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	479	2.8	0.0	19	dbSNP_89	37	212,8386		5,202,4092	no	missense	CYP2A6	NM_000762.5	99	5,222,6275	TT,TA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	2.4657,0.4539,1.7841	benign	160/495	41354533	232,12772	2203	4299	6502	SO:0001583	missense	1548	exon3			CCCCGGAGGGCGT	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.479T>A	19.37:g.41354533A>T	ENSP00000301141:p.Leu160His	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	28	0.01282051282051282	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	24	0.0316622691292876	-	15.37	2.814794	0.50527	0.004539	0.024657	ENSG00000255974	ENST00000301141	T	0.74632	-0.86	2.77	2.77	0.32553	.	0.336308	0.29676	U	0.011482	T	0.73908	0.3647	M	0.91406	3.205	0.09310	N	1	B	0.23937	0.094	P	0.52109	0.69	T	0.77640	-0.2512	10	0.87932	D	0	.	9.861	0.41114	1.0:0.0:0.0:0.0	rs1801272;rs4986890;rs17791931;rs56844942;rs1801272	160	P11509	CP2A6_HUMAN	H	160	ENSP00000301141:L160H	ENSP00000301141:L160H	L	-	2	0	CYP2A6	46046373	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	1.474000	0.35398	1.140000	0.42260	0.318000	0.21364	CTC	A|0.983;T|0.017	0.017	strong		0.701	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
PTK2B	2185	hgsc.bcm.edu	37	8	27308585	27308585	+	Missense_Mutation	SNP	A	A	C	rs751019	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27308585A>C	ENST00000397501.1	+	31	3321	c.2513A>C	c.(2512-2514)aAg>aCg	p.K838T	PTK2B_ENST00000346049.5_Missense_Mutation_p.K838T|PTK2B_ENST00000338238.4_Missense_Mutation_p.K796T|PTK2B_ENST00000420218.2_Missense_Mutation_p.K796T|PTK2B_ENST00000544172.1_Missense_Mutation_p.K838T|PTK2B_ENST00000397497.4_Missense_Mutation_p.K542T|PTK2B_ENST00000517339.1_Missense_Mutation_p.K796T	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	838	Interaction with TGFB1I1. {ECO:0000250}.|Pro-rich.		K -> T (in dbSNP:rs751019). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:19369195}.		activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	ATGAATGATAAGTCCCCATTG	0.567													A|||	1826	0.364617	0.2413	0.4092	5008	,	,		17939	0.3601		0.4573	False		,,,				2504	0.409				p.K838T		Atlas-SNP	.											.	PTK2B	304	.	0			c.A2513C						PASS	.	A	THR/LYS,THR/LYS,THR/LYS,THR/LYS	1239,3167	425.9+/-341.0	185,869,1149	96.0	99.0	98.0		2513,2513,2387,2513	4.3	1.0	8	dbSNP_86	98	3995,4605	553.5+/-386.3	952,2091,1257	yes	missense,missense,missense,missense	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	78,78,78,78	1137,2960,2406	CC,CA,AA		46.4535,28.1207,40.243	benign,benign,benign,benign	838/1010,838/1010,796/968,838/1010	27308585	5234,7772	2203	4300	6503	SO:0001583	missense	2185	exon31			ATGATAAGTCCCC	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.2513A>C	8.37:g.27308585A>C	ENSP00000380638:p.Lys838Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Missense_Mutation	SNP	ENST00000397501.1	37	CCDS6057.1	819	0.375	128	0.2601626016260163	158	0.43646408839779005	192	0.3356643356643357	341	0.449868073878628	A	8.485	0.860694	0.17178	0.281207	0.464535	ENSG00000120899	ENST00000397501;ENST00000338238;ENST00000544172;ENST00000346049;ENST00000420218;ENST00000517339;ENST00000397497	T;T;T;T;T;T;T	0.74421	-0.83;-0.8;-0.83;-0.83;-0.8;-0.8;-0.84	5.42	4.26	0.50523	.	0.417504	0.28279	N	0.015930	T	0.00012	0.0000	N	0.11560	0.145	0.36516	P	0.130135	B;B	0.15719	0.003;0.014	B;B	0.08055	0.003;0.003	T	0.40739	-0.9547	9	0.30854	T	0.27	.	8.0735	0.30704	0.9079:0.0:0.0921:0.0	rs751019;rs60668946;rs751019	796;838	Q14289-2;Q14289	.;FAK2_HUMAN	T	838;796;838;838;796;796;542	ENSP00000380638:K838T;ENSP00000342242:K796T;ENSP00000440926:K838T;ENSP00000332816:K838T;ENSP00000391995:K796T;ENSP00000427931:K796T;ENSP00000380634:K542T	ENSP00000342242:K796T	K	+	2	0	PTK2B	27364502	1.000000	0.71417	0.993000	0.49108	0.632000	0.37999	3.193000	0.50997	0.890000	0.36211	-0.256000	0.11100	AAG	A|0.601;C|0.399	0.399	strong		0.567	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
TRIM51	84767	hgsc.bcm.edu	37	11	55652963	55652963	+	Missense_Mutation	SNP	A	A	G	rs2063276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55652963A>G	ENST00000449290.2	+	2	151	c.59A>G	c.(58-60)aAc>aGc	p.N20S	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	20						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										ATCTGCATGAACTACTTCCTA	0.502													N|||	3414	0.681709	0.6452	0.683	5008	,	,		18043	0.7649		0.6153	False		,,,				2504	0.7127				p.N20S		Atlas-SNP	.											.	.	.	.	0			c.A59G						PASS	.	A	SER/ASN	897,487		308,281,103	21.0	18.0	19.0		59	0.8	0.0	11	dbSNP_94	19	1962,1198		615,732,233	no	missense	SPRYD5	NM_032681.3	46	923,1013,336	GG,GA,AA		37.9114,35.1879,37.0819	possibly-damaging	20/453	55652963	2859,1685	692	1580	2272	SO:0001583	missense	84767	exon2			GCATGAACTACTT	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.59A>G	11.37:g.55652963A>G	ENSP00000395086:p.Asn20Ser	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	296	139	0.469595	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37		1411	0.6460622710622711	304	0.6178861788617886	235	0.649171270718232	421	0.736013986013986	451	0.5949868073878628	.	6.155	0.396776	0.11638	0.648121	0.620886	ENSG00000124900	ENST00000449290	D	0.83914	-1.78	0.803	0.803	0.18691	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	.	.	.	.	T	0.00012	0.0000	N	0.16266	0.395	0.36627	P	0.12391600000000003	P	0.44429	0.835	P	0.49477	0.612	T	0.42155	-0.9468	8	0.59425	D	0.04	.	5.8508	0.18691	0.9999:0.0:1.0E-4:0.0	rs2063276	20	Q9BSJ1	SPRY5_HUMAN	S	20	ENSP00000395086:N20S	ENSP00000395086:N20S	N	+	2	0	SPRYD5	55409539	0.831000	0.29352	0.005000	0.12908	0.120000	0.20174	1.010000	0.29898	0.624000	0.30286	0.128000	0.15822	AAC	A|0.360;G|0.640	0.640	strong		0.502	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
SLC5A8	160728	hgsc.bcm.edu	37	12	101587518	101587518	+	Missense_Mutation	SNP	C	C	T	rs1709189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:101587518C>T	ENST00000536262.2	-	5	1135	c.577G>A	c.(577-579)Gtt>Att	p.V193I		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						ATGATCCCAACTTGAAAAACA	0.398													C|||	1399	0.279353	0.2224	0.1268	5008	,	,		20280	0.5437		0.2475	False		,,,				2504	0.2249				p.V193I	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.G577A						PASS	.	C	ILE/VAL	819,3587	325.9+/-299.3	76,667,1460	178.0	164.0	168.0		577	3.6	1.0	12	dbSNP_89	168	1930,6670	340.5+/-323.6	205,1520,2575	yes	missense	SLC5A8	NM_145913.3	29	281,2187,4035	TT,TC,CC		22.4419,18.5883,21.1364	benign	193/611	101587518	2749,10257	2203	4300	6503	SO:0001583	missense	160728	exon5			TCCCAACTTGAAA	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"""Solute carriers"""	19119	protein-coding gene	gene with protein product		608044	"""solute carrier family 5 (iodide transporter), member 8"""			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.577G>A	12.37:g.101587518C>T	ENSP00000445340:p.Val193Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_145913		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	640	0.29304029304029305	108	0.21951219512195122	54	0.14917127071823205	300	0.5244755244755245	178	0.23482849604221637	C	14.47	2.544870	0.45280	0.185883	0.224419	ENSG00000256870	ENST00000536262	D	0.87809	-2.3	5.44	3.6	0.41247	.	0.121777	0.56097	D	0.000039	T	0.00012	0.0000	N	0.17800	0.525	0.26000	P	0.9821381	B	0.02656	0.0	B	0.12837	0.008	T	0.40459	-0.9562	9	0.42905	T	0.14	.	12.0769	0.53649	0.0:0.858:0.0:0.142	rs1709189;rs52793799;rs60134232;rs1709189	193	Q8N695	SC5A8_HUMAN	I	193	ENSP00000445340:V193I	ENSP00000445340:V193I	V	-	1	0	SLC5A8	100111649	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.947000	0.40293	1.291000	0.44653	0.655000	0.94253	GTT	C|0.745;T|0.255	0.255	strong		0.398	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913	
ATAD5	79915	hgsc.bcm.edu	37	17	29161358	29161358	+	Missense_Mutation	SNP	C	C	T	rs3816780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29161358C>T	ENST00000321990.4	+	2	637	c.259C>T	c.(259-261)Cct>Tct	p.P87S	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	87			P -> S (in dbSNP:rs3816780).		cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				GATAAAGTCACCTGAATCAGT	0.358													T|||	864	0.172524	0.1762	0.1902	5008	,	,		16716	0.1359		0.1074	False		,,,				2504	0.2597				p.P87S		Atlas-SNP	.											.	ATAD5	150	.	0			c.C259T						PASS	.	T	SER/PRO	730,3676	747.1+/-411.8	59,612,1532	94.0	94.0	94.0		259	1.4	0.0	17	dbSNP_107	94	902,7696	769.2+/-407.6	37,828,3434	yes	missense	ATAD5	NM_024857.3	74	96,1440,4966	TT,TC,CC		10.4908,16.5683,12.55	benign	87/1845	29161358	1632,11372	2203	4299	6502	SO:0001583	missense	79915	exon2			AAGTCACCTGAAT		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.259C>T	17.37:g.29161358C>T	ENSP00000313171:p.Pro87Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	321	0.14697802197802198	89	0.18089430894308944	68	0.1878453038674033	92	0.16083916083916083	72	0.09498680738786279	T	0.979	-0.697651	0.03279	0.165683	0.104908	ENSG00000176208	ENST00000321990	T	0.16073	2.37	6.07	1.36	0.22044	.	1.112970	0.06461	N	0.729421	T	0.00012	0.0000	N	0.00128	-2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40572	-0.9556	9	0.02654	T	1	.	5.2567	0.15552	0.0:0.2929:0.2688:0.4383	rs3816780;rs61505672;rs3816780	87	Q96QE3	ATAD5_HUMAN	S	87	ENSP00000313171:P87S	ENSP00000313171:P87S	P	+	1	0	ATAD5	26185484	0.000000	0.05858	0.003000	0.11579	0.126000	0.20510	-0.341000	0.07811	-0.279000	0.09167	-0.254000	0.11334	CCT	C|0.859;T|0.141	0.141	strong		0.358	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
CTBS	1486	hgsc.bcm.edu	37	1	85031630	85031630	+	Silent	SNP	G	G	A	rs2994953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:85031630G>A	ENST00000370630.5	-	4	639	c.591C>T	c.(589-591)atC>atT	p.I197I	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	197					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		AAGCATCTGCGATTCCAGTAT	0.368													G|||	1486	0.296725	0.3404	0.2637	5008	,	,		10897	0.2341		0.2455	False		,,,				2504	0.3783				p.I197I		Atlas-SNP	.											.	CTBS	24	.	0			c.C591T						PASS	.	G		1434,2972	466.0+/-354.4	232,970,1001	97.0	91.0	93.0		591	1.6	1.0	1	dbSNP_101	93	2234,6366	378.1+/-338.8	299,1636,2365	no	coding-synonymous	CTBS	NM_004388.2		531,2606,3366	AA,AG,GG		25.9767,32.5465,28.2024		197/386	85031630	3668,9338	2203	4300	6503	SO:0001819	synonymous_variant	1486	exon4			ATCTGCGATTCCA	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.591C>T	1.37:g.85031630G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	186	100	0.537634	NM_004388	Q5VX50	Silent	SNP	ENST00000370630.5	37	CCDS698.1																																																																																			G|0.720;A|0.280	0.280	strong		0.368	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
CREBZF	58487	hgsc.bcm.edu	37	11	85374993	85374993	+	Silent	SNP	C	C	T	rs1192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:85374993C>T	ENST00000527447.1	-	1	1153	c.927G>A	c.(925-927)ccG>ccA	p.P309P	CREBZF_ENST00000398294.2_Silent_p.P227P|CREBZF_ENST00000534224.1_Intron|CREBZF_ENST00000531515.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	309					negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				GCTTTCCCACCGGCAGAGCGT	0.642											OREG0021274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1041	0.207867	0.118	0.2867	5008	,	,		15506	0.2847		0.0984	False		,,,				2504	0.3067				p.P309P	NSCLC(172;674 2044 9050 18334 41735)	Atlas-SNP	.											.	CREBZF	26	.	0			c.G927A						PASS	.	C		477,3473		23,431,1521	59.0	63.0	62.0		927	-6.4	0.4	11	dbSNP_36	62	782,7516		39,704,3406	no	coding-synonymous	CREBZF	NM_001039618.2		62,1135,4927	TT,TC,CC		9.424,12.0759,10.2792		309/355	85374993	1259,10989	1975	4149	6124	SO:0001819	synonymous_variant	58487	exon1			TCCCACCGGCAGA	AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"""basic leucine zipper proteins"""	24905	protein-coding gene	gene with protein product	"""Zhangfei"""	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.927G>A	11.37:g.85374993C>T		Somatic	118	0	0	1236	WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_001039618	B2R8Q9|Q0P5U9|Q52LT3	Silent	SNP	ENST00000527447.1	37	CCDS41697.1																																																																																			C|0.837;T|0.163	0.163	strong		0.642	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390191.2	NM_001039618	
TAS2R8	50836	hgsc.bcm.edu	37	12	10958896	10958896	+	Missense_Mutation	SNP	T	T	G	rs143804727	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10958896T>G	ENST00000240615.2	-	1	996	c.684A>C	c.(682-684)gaA>gaC	p.E228D		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	228					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TCACATGAACTTCTGTGCTGG	0.333													T|||	42	0.00838658	0.0	0.0231	5008	,	,		18097	0.002		0.0129	False		,,,				2504	0.0112				p.E228D		Atlas-SNP	.											TAS2R8,colon,carcinoma,0,1	TAS2R8	42	1	0			c.A684C						PASS	.	T	ASP/GLU	14,4392	21.2+/-45.6	0,14,2189	82.0	86.0	84.0		684	-1.8	0.0	12	dbSNP_134	84	197,8401	84.8+/-147.2	2,193,4104	yes	missense	TAS2R8	NM_023918.1	45	2,207,6293	GG,GT,TT		2.2912,0.3177,1.6226	possibly-damaging	228/310	10958896	211,12793	2203	4299	6502	SO:0001583	missense	50836	exon1			ATGAACTTCTGTG	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.684A>C	12.37:g.10958896T>G	ENSP00000240615:p.Glu228Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_023918	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	37	CCDS8632.1	14	0.00641025641025641	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	5	0.006596306068601583	T	11.29	1.595797	0.28445	0.003177	0.022912	ENSG00000121314	ENST00000240615	T	0.37752	1.18	5.38	-1.83	0.07833	GPCR, rhodopsin-like superfamily (1);	0.488214	0.16827	U	0.197913	T	0.35098	0.0920	M	0.80332	2.49	0.09310	N	1	D	0.63046	0.992	D	0.65573	0.936	T	0.36089	-0.9762	10	0.72032	D	0.01	.	5.7484	0.18132	0.1379:0.3212:0.0:0.5409	.	228	Q9NYW2	TA2R8_HUMAN	D	228	ENSP00000240615:E228D	ENSP00000240615:E228D	E	-	3	2	TAS2R8	10850163	0.000000	0.05858	0.032000	0.17829	0.008000	0.06430	-3.643000	0.00405	-0.700000	0.05070	-0.904000	0.02843	GAA	T|0.987;G|0.013	0.013	strong		0.333	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
TTC3	7267	hgsc.bcm.edu	37	21	38563725	38563725	+	Splice_Site	SNP	G	G	A	rs2835655	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:38563725G>A	ENST00000399017.2	+	40	7862	c.5115G>A	c.(5113-5115)aaG>aaA	p.K1705K	TTC3-AS1_ENST00000424733.1_RNA|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Splice_Site_p.K1705K|TTC3_ENST00000355666.1_Splice_Site_p.K1705K	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1705					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AGAAAGCAAAGGTAAGTTGTA	0.318													G|||	2007	0.400759	0.3033	0.268	5008	,	,		14083	0.5238		0.3439	False		,,,				2504	0.5583				p.K1705K	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.G5115A						PASS	.	G	,	1406,2998		233,940,1029	34.0	34.0	34.0		5115,5115	2.3	0.4	21	dbSNP_100	34	2626,5944		431,1764,2090	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	TTC3	NM_001001894.1,NM_003316.3	,	664,2704,3119	AA,AG,GG		30.6418,31.9255,31.0775	,	1705/2026,1705/2026	38563725	4032,8942	2202	4285	6487	SO:0001630	splice_region_variant	7267	exon40			AGCAAAGGTAAGT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5115+1G>A	21.37:g.38563725G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	231	99	0.428571	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	807	0.3695054945054945	154	0.3130081300813008	98	0.27071823204419887	302	0.527972027972028	253	0.3337730870712401	G	10.31	1.314981	0.23908	0.319255	0.306418	ENSG00000182670	ENST00000428693	.	.	.	5.31	2.28	0.28536	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999886898	.	.	.	.	.	.	T	0.47114	-0.9142	3	.	.	.	-1.6023	4.3185	0.11005	0.2078:0.0:0.5966:0.1956	rs2835655;rs17284336;rs60772137;rs2835655	.	.	.	S	31	.	.	G	+	1	0	TTC3	37485595	1.000000	0.71417	0.353000	0.25747	0.753000	0.42808	1.881000	0.39638	0.223000	0.20920	-0.355000	0.07637	GGT	G|0.653;A|0.347	0.347	strong		0.318	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		Silent
TET2	54790	hgsc.bcm.edu	37	4	106183003	106183003	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106183003C>A	ENST00000540549.1	+	8	4902	c.4042C>A	c.(4042-4044)Cag>Aag	p.Q1348K	TET2_ENST00000513237.1_Missense_Mutation_p.Q1369K|TET2_ENST00000380013.4_Missense_Mutation_p.Q1348K|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1348					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ATATAATAATCAGGTAAGTTT	0.308			"""Mis N, F"""		MDS																																p.Q1348K		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.C4042A						PASS	.						66.0	58.0	60.0					4																	106183003		692	1587	2279	SO:0001583	missense	54790	exon8			AATAATCAGGTAA	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.4042C>A	4.37:g.106183003C>A	ENSP00000442788:p.Gln1348Lys	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	253	28	0.110672	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148220	0.94603	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.14266	2.52;2.52;2.52	5.36	5.36	0.76844	TET cysteine-rich domain (1);	.	.	.	.	T	0.45034	0.1322	M	0.86268	2.805	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	T	0.50566	-0.8813	9	0.87932	D	0	-11.679	19.0905	0.93225	0.0:1.0:0.0:0.0	.	1369;1348	E7EQS8;Q6N021	.;TET2_HUMAN	K	1348;1369;1348	ENSP00000442788:Q1348K;ENSP00000425443:Q1369K;ENSP00000369351:Q1348K	ENSP00000369351:Q1348K	Q	+	1	0	TET2	106402452	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.585000	0.82584	2.526000	0.85167	0.555000	0.69702	CAG	.	.	none		0.308	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
STRA8	346673	hgsc.bcm.edu	37	7	134925411	134925411	+	Silent	SNP	G	G	A	rs7805859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:134925411G>A	ENST00000275764.3	+	2	201	c.201G>A	c.(199-201)gcG>gcA	p.A67A		NM_182489.1	NP_872295.1			stimulated by retinoic acid 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(1)	16						CCCTGGCAGCGCTCTTCAACA	0.617													G|||	1957	0.390775	0.3487	0.4063	5008	,	,		15246	0.2133		0.4553	False		,,,				2504	0.5532				p.A67A		Atlas-SNP	.											.	STRA8	39	.	0			c.G201A						PASS	.	G		1629,2777	497.1+/-363.7	302,1025,876	58.0	60.0	59.0		201	-2.2	0.2	7	dbSNP_116	59	3858,4742	537.5+/-383.2	890,2078,1332	no	coding-synonymous	STRA8	NM_182489.1		1192,3103,2208	AA,AG,GG		44.8605,36.9723,42.1882		67/331	134925411	5487,7519	2203	4300	6503	SO:0001819	synonymous_variant	346673	exon2			GGCAGCGCTCTTC	AF513502	CCDS5839.1	7q33	2012-12-07	2012-12-07		ENSG00000146857	ENSG00000146857			30653	protein-coding gene	gene with protein product		609987	"""stimulated by retinoic acid gene 8 homolog (mouse)"", ""stimulated by retinoic acid 8 homolog (mouse)"""			12489526	Standard	NM_182489		Approved		uc011kpx.2	Q7Z7C7	OTTHUMG00000155415	ENST00000275764.3:c.201G>A	7.37:g.134925411G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	246	108	0.439024	NM_182489		Silent	SNP	ENST00000275764.3	37	CCDS5839.1																																																																																			G|0.591;A|0.409	0.409	strong		0.617	STRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340028.1	NM_182489	
MTMR3	8897	hgsc.bcm.edu	37	22	30415983	30415983	+	Missense_Mutation	SNP	C	C	T	rs61737780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30415983C>T	ENST00000401950.2	+	17	2677	c.2335C>T	c.(2335-2337)Ctc>Ttc	p.L779F	MTMR3_ENST00000351488.3_Missense_Mutation_p.L779F|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000333027.3_Missense_Mutation_p.L779F|MTMR3_ENST00000406629.1_Missense_Mutation_p.L779F|CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000323630.5_Missense_Mutation_p.L643F	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	779					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			CCTCAGTTCTCTCCAGGTCCC	0.552													C|||	17	0.00339457	0.0	0.0043	5008	,	,		18968	0.0		0.0139	False		,,,				2504	0.0				p.L779F		Atlas-SNP	.											.	MTMR3	106	.	0			c.C2335T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU	7,4399	12.9+/-30.5	0,7,2196	73.0	77.0	76.0		2335,2335,2335	3.7	0.9	22	dbSNP_129	76	99,8501	55.2+/-116.2	0,99,4201	yes	missense,missense,missense	MTMR3	NM_021090.3,NM_153050.2,NM_153051.2	22,22,22	0,106,6397	TT,TC,CC		1.1512,0.1589,0.815	possibly-damaging,possibly-damaging,possibly-damaging	779/1199,779/1171,779/1162	30415983	106,12900	2203	4300	6503	SO:0001583	missense	8897	exon17			AGTTCTCTCCAGG	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.2335C>T	22.37:g.30415983C>T	ENSP00000384651:p.Leu779Phe	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	161	70	0.434783	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	37	CCDS13870.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	2.316	-0.356778	0.05138	0.001589	0.011512	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.93763	-3.08;-3.05;-3.28;-3.1;-3.05	4.73	3.66	0.41972	.	1.991870	0.01826	N	0.034355	D	0.84826	0.5558	N	0.19112	0.55	0.09310	N	1	P;B;P	0.37636	0.603;0.257;0.603	B;B;B	0.36186	0.219;0.109;0.219	T	0.76208	-0.3043	10	0.10111	T	0.7	.	12.5279	0.56098	0.3353:0.6647:0.0:0.0	rs61737780	779;779;779	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	F	779;779;643;779;779	ENSP00000384651:L779F;ENSP00000331649:L779F;ENSP00000318070:L643F;ENSP00000307271:L779F;ENSP00000384077:L779F	ENSP00000318070:L643F	L	+	1	0	MTMR3	28745983	0.000000	0.05858	0.924000	0.36721	0.812000	0.45895	-0.164000	0.09983	2.448000	0.82819	0.462000	0.41574	CTC	C|0.992;T|0.008	0.008	strong		0.552	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552039	32552039	+	Missense_Mutation	SNP	C	C	T	rs150747106		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32552039C>T	ENST00000360004.5	-	2	322	c.217G>A	c.(217-219)Gtg>Atg	p.V73M		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	73	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AACTCCCCCACGTCGCTGTCG	0.632										Multiple Myeloma(14;0.17)																											p.V73M		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G217A						PASS	.						37.0	38.0	37.0					6																	32552039		2197	4292	6489	SO:0001583	missense	3123	exon2			CCCCCACGTCGCT	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.217G>A	6.37:g.32552039C>T	ENSP00000353099:p.Val73Met	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	120	22	0.183333	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	368	0.1684981684981685	37	0.07520325203252033	75	0.20718232044198895	112	0.1958041958041958	144	0.18997361477572558	.	12.23	1.876883	0.33162	.	.	ENSG00000196126	ENST00000360004	T	0.00402	7.56	3.52	0.0987	0.14499	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	0.657385	0.14883	N	0.292848	T	0.00695	0.0023	H	0.95679	3.705	0.32016	N	0.601387	D	0.89917	1.0	D	0.85130	0.997	T	0.33343	-0.9872	10	0.72032	D	0.01	.	6.8224	0.23864	0.3354:0.4996:0.1649:0.0	.	73	P01911	2B1F_HUMAN	M	73	ENSP00000353099:V73M	ENSP00000353099:V73M	V	-	1	0	HLA-DRB1	32660017	0.053000	0.20554	0.990000	0.47175	0.053000	0.15095	-0.110000	0.10824	0.237000	0.21200	0.453000	0.30009	GTG	C|0.831;T|0.169	0.169	strong		0.632	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
HBS1L	10767	hgsc.bcm.edu	37	6	135287597	135287597	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:135287597C>T	ENST00000367837.5	-	17	2119	c.1913G>A	c.(1912-1914)gGc>gAc	p.G638D	HBS1L_ENST00000367826.2_Missense_Mutation_p.G596D|HBS1L_ENST00000445176.2_Missense_Mutation_p.G362D|HBS1L_ENST00000415177.2_Missense_Mutation_p.G573D|HBS1L_ENST00000367824.4_Missense_Mutation_p.G474D|HBS1L_ENST00000527578.1_Missense_Mutation_p.G474D	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	638					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		TGCATTCTGGCCTTTAGTCAA	0.328																																					p.G638D		Atlas-SNP	.											.	HBS1L	75	.	0			c.G1913A						PASS	.						106.0	105.0	106.0					6																	135287597		2203	4300	6503	SO:0001583	missense	10767	exon17			TTCTGGCCTTTAG	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.1913G>A	6.37:g.135287597C>T	ENSP00000356811:p.Gly638Asp	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	37	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145634	0.77888	.	.	ENSG00000112339	ENST00000367837;ENST00000527578;ENST00000415177;ENST00000367826;ENST00000367824;ENST00000533274;ENST00000445176	T;T;T;T;T;T;T	0.69561	-0.38;-0.38;-0.34;-0.4;-0.38;-0.41;0.71	5.96	5.96	0.96718	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation elongation factor EFTu/EF1A, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	M	0.73319	2.225	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.967;0.992	T	0.80279	-0.1449	10	0.87932	D	0	-8.0087	20.4008	0.98991	0.0:1.0:0.0:0.0	.	596;638	Q9Y450-4;Q9Y450	.;HBS1L_HUMAN	D	638;474;573;596;474;508;362	ENSP00000356811:G638D;ENSP00000436256:G474D;ENSP00000389826:G573D;ENSP00000356800:G596D;ENSP00000356798:G474D;ENSP00000434533:G508D;ENSP00000415305:G362D	ENSP00000356798:G474D	G	-	2	0	HBS1L	135329290	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.265000	0.78442	2.826000	0.97356	0.655000	0.94253	GGC	.	.	none		0.328	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
LIG1	3978	hgsc.bcm.edu	37	19	48626236	48626236	+	Silent	SNP	A	A	G	rs116999747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48626236A>G	ENST00000263274.7	-	23	2606	c.2187T>C	c.(2185-2187)gtT>gtC	p.V729V	CTC-453G23.5_ENST00000596839.1_RNA|CTC-453G23.5_ENST00000596563.1_RNA|LIG1_ENST00000536218.1_Silent_p.V661V|LIG1_ENST00000427526.2_Silent_p.V698V	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	729					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	AGGTGGCATCAACATCCAGGG	0.617								Nucleotide excision repair (NER)					A|||	6	0.00119808	0.0	0.0029	5008	,	,		18483	0.0		0.004	False		,,,				2504	0.0				p.V729V		Atlas-SNP	.											.	LIG1	151	.	0			c.T2187C						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	166.0	149.0	155.0		2187	-9.9	0.1	19	dbSNP_132	155	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	LIG1	NM_000234.1		0,37,6466	GG,GA,AA		0.407,0.0454,0.2845		729/920	48626236	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	3978	exon23			GGCATCAACATCC		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.2187T>C	19.37:g.48626236A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_000234	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	37	CCDS12711.1																																																																																			A|0.997;G|0.003	0.003	strong		0.617	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
KCNH6	81033	hgsc.bcm.edu	37	17	61623052	61623052	+	Missense_Mutation	SNP	C	C	T	rs35819807	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:61623052C>T	ENST00000583023.1	+	14	2785	c.2774C>T	c.(2773-2775)aCg>aTg	p.T925M	KCNH6_ENST00000314672.5_Missense_Mutation_p.T889M|KCNH6_ENST00000581784.1_Missense_Mutation_p.T836M|KCNH6_ENST00000456941.2_Missense_Mutation_p.T836M	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	925			T -> M (in dbSNP:rs35819807). {ECO:0000269|PubMed:14702039}.		potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GCTGTGGCAACGGACAAAACT	0.567													C|||	701	0.139976	0.1626	0.1052	5008	,	,		18935	0.0367		0.2485	False		,,,				2504	0.1288				p.T925M		Atlas-SNP	.											.	KCNH6	122	.	0			c.C2774T						PASS	.	C	MET/THR,MET/THR	723,3683	298.4+/-285.3	64,595,1544	102.0	91.0	95.0		2774,2507	-7.6	0.0	17	dbSNP_126	95	2122,6478	366.0+/-334.1	277,1568,2455	yes	missense,missense	KCNH6	NM_030779.2,NM_173092.1	81,81	341,2163,3999	TT,TC,CC		24.6744,16.4094,21.8745	benign,benign	925/995,836/906	61623052	2845,10161	2203	4300	6503	SO:0001583	missense	81033	exon14			TGGCAACGGACAA	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2774C>T	17.37:g.61623052C>T	ENSP00000463533:p.Thr925Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	113	60	0.530973	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	343	0.15705128205128205	86	0.17479674796747968	45	0.12430939226519337	22	0.038461538461538464	190	0.25065963060686014	C	9.316	1.056938	0.19907	0.164094	0.246744	ENSG00000173826	ENST00000314672;ENST00000456941	D	0.99220	-5.58	5.02	-7.62	0.01294	.	1.666530	0.04760	N	0.426110	T	0.00356	0.0011	N	0.16478	0.41	0.80722	P	0.0	B;B;B	0.14012	0.007;0.003;0.009	B;B;B	0.09377	0.003;0.004;0.002	T	0.73575	-0.3939	9	0.30078	T	0.28	.	6.9583	0.24583	0.0995:0.493:0.2976:0.1098	rs35819807	889;836;925	B4DKC0;Q9H252-2;Q9H252	.;.;KCNH6_HUMAN	M	925;836	ENSP00000396900:T836M	ENSP00000318212:T925M	T	+	2	0	KCNH6	58976784	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.188000	0.17018	-1.025000	0.03334	-1.092000	0.02172	ACG	C|0.804;T|0.196	0.196	strong		0.567	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
CC2D1A	54862	hgsc.bcm.edu	37	19	14038791	14038791	+	Missense_Mutation	SNP	C	C	T	rs2305777	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14038791C>T	ENST00000318003.7	+	23	2643	c.2402C>T	c.(2401-2403)aCg>aTg	p.T801M	CC2D1A_ENST00000589606.1_Missense_Mutation_p.T801M	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	801			T -> M (in dbSNP:rs2305777).		positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			CAGTTGGAGACGACGACAGAG	0.657													c|||	626	0.125	0.0174	0.1816	5008	,	,		15054	0.0615		0.2644	False		,,,				2504	0.1524				p.T801M		Atlas-SNP	.											.	CC2D1A	67	.	0			c.C2402T						PASS	.	C	MET/THR	181,3953		5,171,1891	70.0	81.0	78.0		2402	5.2	0.9	19	dbSNP_100	78	2245,6157		296,1653,2252	yes	missense	CC2D1A	NM_017721.4	81	301,1824,4143	TT,TC,CC		26.7198,4.3783,19.3523	probably-damaging	801/952	14038791	2426,10110	2067	4201	6268	SO:0001583	missense	54862	exon23			TGGAGACGACGAC	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.2402C>T	19.37:g.14038791C>T	ENSP00000313601:p.Thr801Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	330	0.1510989010989011	15	0.03048780487804878	71	0.19613259668508287	39	0.06818181818181818	205	0.2704485488126649	c	16.38	3.105779	0.56291	0.043783	0.267198	ENSG00000132024	ENST00000318003;ENST00000254346	T	0.21932	1.98	5.22	5.22	0.72569	.	0.208969	0.40469	N	0.001085	T	0.00012	0.0000	L	0.39020	1.185	0.25790	P	0.9846208	P;D;D	0.89917	0.627;1.0;1.0	B;D;D	0.79108	0.09;0.992;0.951	T	0.25257	-1.0137	9	0.40728	T	0.16	-21.6206	13.3122	0.60386	0.0:0.8407:0.1593:0.0	rs2305777;rs52806822;rs56704254;rs2305777	423;801;801	Q9NX28;Q6P1N0-2;Q6P1N0	.;.;C2D1A_HUMAN	M	801;424	ENSP00000313601:T801M	ENSP00000254346:T424M	T	+	2	0	CC2D1A	13899791	0.998000	0.40836	0.940000	0.37924	0.665000	0.39181	3.945000	0.56637	2.447000	0.82792	0.491000	0.48974	ACG	C|0.836;T|0.164	0.164	strong		0.657	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
SAMD4B	55095	hgsc.bcm.edu	37	19	39876556	39876556	+	IGR	SNP	C	C	T	rs117151141	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39876556C>T	ENST00000314471.6	+	0	4519				PAF1_ENST00000595564.1_Silent_p.*486*|PAF1_ENST00000221266.7_Silent_p.*463*|PAF1_ENST00000221265.3_3'UTR	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			GTGAAAGGCTCACAAACAGAC	0.478													N|||	72	0.014377	0.0136	0.0216	5008	,	,		18878	0.001		0.0278	False		,,,				2504	0.0102				p.X486X		Atlas-SNP	.											.	PAF1	43	.	0			c.G1457A						PASS	.																																			SO:0001628	intergenic_variant	54623	exon13			AAGGCTCACAAAC		CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"""Sterile alpha motif (SAM) domain containing"""	25492	protein-coding gene	gene with protein product	"""smaug homolog B (Drosophila)"""					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9			19.37:g.39876556C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_001256826	A5Z0M6|Q6P194	Silent	SNP	ENST00000314471.6	37	CCDS33020.1																																																																																			C|0.981;T|0.019	0.019	strong		0.478	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028	
SPOCK3	50859	hgsc.bcm.edu	37	4	167656073	167656073	+	Silent	SNP	C	C	T	rs1057377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:167656073C>T	ENST00000357154.3	-	12	1447	c.1310G>A	c.(1309-1311)tGa>tAa	p.*437*	SPOCK3_ENST00000502330.1_Silent_p.*437*|SPOCK3_ENST00000510741.1_Silent_p.*394*|SPOCK3_ENST00000511531.1_Silent_p.*437*|SPOCK3_ENST00000504953.1_Silent_p.*434*|SPOCK3_ENST00000421836.2_Silent_p.*386*|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Silent_p.*434*|SPOCK3_ENST00000534949.1_Silent_p.*341*|SPOCK3_ENST00000541637.1_Silent_p.*339*|SPOCK3_ENST00000541354.1_Silent_p.*317*|SPOCK3_ENST00000506886.1_Silent_p.*437*|SPOCK3_ENST00000535728.1_Silent_p.*305*|SPOCK3_ENST00000511269.1_Silent_p.*434*|SPOCK3_ENST00000512681.1_Silent_p.*339*	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	0					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		tgtcatcaatcaaatgtatac	0.294													C|||	646	0.128994	0.0113	0.1167	5008	,	,		14599	0.001		0.2565	False		,,,				2504	0.2975				p.X437X		Atlas-SNP	.											.	SPOCK3	90	.	0			c.G1310A						PASS	.	C	,,,,,,,	179,4227	113.8+/-151.8	6,167,2030	134.0	129.0	130.0		1301,1157,950,1034,1022,1181,1181,1310	5.0	0.8	4	dbSNP_86	130	2290,6310	379.2+/-339.2	309,1672,2319	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPOCK3	NM_001040159.1,NM_001204352.1,NM_001204353.1,NM_001204354.1,NM_001204355.1,NM_001204356.1,NM_001204357.1,NM_016950.2	,,,,,,,	315,1839,4349	TT,TC,CC		26.6279,4.0626,18.9835	,,,,,,,	434/434,386/386,317/317,345/345,341/341,394/394,394/394,437/437	167656073	2469,10537	2203	4300	6503	SO:0001819	synonymous_variant	50859	exon12			ATCAATCAAATGT	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1310G>A	4.37:g.167656073C>T		Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	426	201	0.471831	NM_016950	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Silent	SNP	ENST00000357154.3	37	CCDS54817.1																																																																																			C|0.843;T|0.157	0.157	strong		0.294	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1		
MLC1	23209	hgsc.bcm.edu	37	22	50515843	50515843	+	Missense_Mutation	SNP	C	C	A	rs6010260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50515843C>A	ENST00000311597.5	-	6	1118	c.512G>T	c.(511-513)tGc>tTc	p.C171F	MLC1_ENST00000450140.2_Missense_Mutation_p.C119F|MLC1_ENST00000395876.2_Missense_Mutation_p.C171F|MLC1_ENST00000538737.1_Missense_Mutation_p.C137F|MLC1_ENST00000535444.1_Missense_Mutation_p.C92F|MLC1_ENST00000431262.2_Missense_Mutation_p.C141F	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	171			C -> F (in dbSNP:rs6010260).		caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CTTTTTCTTGCAGTCCTCCTC	0.632													C|||	609	0.121605	0.0514	0.1571	5008	,	,		17517	0.0913		0.1153	False		,,,				2504	0.229				p.C171F		Atlas-SNP	.											.	MLC1	48	.	0			c.G512T						PASS	.	C	PHE/CYS,PHE/CYS	312,4094	166.2+/-197.5	14,284,1905	79.0	59.0	66.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	512,512	3.3	0.2	22	dbSNP_114	66	1019,7581	218.4+/-256.8	56,907,3337	yes	missense,missense	MLC1	NM_015166.3,NM_139202.2	205,205	70,1191,5242	AA,AC,CC		11.8488,7.0813,10.2337	possibly-damaging,possibly-damaging	171/378,171/378	50515843	1331,11675	2203	4300	6503	SO:0001583	missense	23209	exon6			TTCTTGCAGTCCT	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.512G>T	22.37:g.50515843C>A	ENSP00000310375:p.Cys171Phe	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	126	96	0.761905	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	220	0.10073260073260074	32	0.06504065040650407	49	0.13535911602209943	55	0.09615384615384616	84	0.11081794195250659	C	13.23	2.175120	0.38413	0.070813	0.118488	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140;ENST00000442311	D;D;D;D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25;-2.25;-2.25;-2.25	4.38	3.27	0.37495	.	0.197522	0.56097	D	0.000035	T	0.02727	0.0082	L	0.51422	1.61	0.09310	P	0.999999533183	B;B;B;B	0.30439	0.279;0.178;0.218;0.178	B;B;B;B	0.30495	0.116;0.116;0.116;0.116	T	0.60321	-0.7286	9	0.59425	D	0.04	-25.8857	10.5524	0.45097	0.1929:0.8071:0.0:0.0	rs6010260;rs52803331;rs6010260	137;141;119;171	F5H1B9;B7Z659;B7Z1X1;Q15049	.;.;.;MLC1_HUMAN	F	171;171;137;141;92;119;141	ENSP00000379216:C171F;ENSP00000310375:C171F;ENSP00000445805:C137F;ENSP00000415877:C141F;ENSP00000438910:C92F;ENSP00000412448:C119F;ENSP00000401385:C141F	ENSP00000310375:C171F	C	-	2	0	MLC1	48857970	0.967000	0.33354	0.237000	0.24090	0.736000	0.42039	2.112000	0.41892	2.124000	0.65301	0.655000	0.94253	TGC	C|0.898;A|0.102	0.102	strong		0.632	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
C15orf48	84419	hgsc.bcm.edu	37	15	45725175	45725175	+	Silent	SNP	C	C	G	rs149677351	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45725175C>G	ENST00000344300.3	+	4	403	c.213C>G	c.(211-213)ccC>ccG	p.P71P	MIR147B_ENST00000390185.1_RNA|RP11-519G16.5_ENST00000559553.1_RNA|C15orf48_ENST00000396650.2_Silent_p.P71P	NM_032413.3	NP_115789.1	Q9C002	NMES1_HUMAN	chromosome 15 open reading frame 48	71						mitochondrion (GO:0005739)|nucleus (GO:0005634)				large_intestine(1)|lung(2)|ovary(1)	4		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.67e-16)|GBM - Glioblastoma multiforme(94;1.71e-06)		AATGGAAACCCATTGAAGAGT	0.363													C|||	9	0.00179712	0.0	0.0029	5008	,	,		16966	0.0		0.006	False		,,,				2504	0.001				p.P71P		Atlas-SNP	.											.	C15orf48	9	.	0			c.C213G						PASS	.	C	,	5,4391	8.1+/-20.4	0,5,2193	65.0	68.0	67.0		213,213	-6.1	0.7	15	dbSNP_134	67	66,8530	40.3+/-97.0	0,66,4232	no	coding-synonymous,coding-synonymous	C15orf48	NM_032413.2,NM_197955.1	,	0,71,6425	GG,GC,CC		0.7678,0.1137,0.5465	,	71/84,71/84	45725175	71,12921	2198	4298	6496	SO:0001819	synonymous_variant	84419	exon5			GAAACCCATTGAA		CCDS10124.1	15q21.1	2014-05-29			ENSG00000166920	ENSG00000166920			29898	protein-coding gene	gene with protein product	"""normal mucosa of esophagus specific 1"""	608409				12209954	Standard	NM_032413		Approved	NMES1	uc001zvh.4	Q9C002	OTTHUMG00000131424	ENST00000344300.3:c.213C>G	15.37:g.45725175C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	53	36	0.679245	NM_197955		Silent	SNP	ENST00000344300.3	37	CCDS10124.1																																																																																			C|0.996;G|0.004	0.004	strong		0.363	C15orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254217.2	NM_032413	
OR6N1	128372	hgsc.bcm.edu	37	1	158735691	158735691	+	Missense_Mutation	SNP	T	T	C	rs857825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158735691T>C	ENST00000335094.2	-	1	801	c.782A>G	c.(781-783)cAg>cGg	p.Q261R		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	261			Q -> R (in dbSNP:rs857825). {ECO:0000269|PubMed:12213199}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					CTTCTTCAGCTGCACATACAT	0.542													C|||	3345	0.667931	0.7784	0.7839	5008	,	,		20920	0.6171		0.7217	False		,,,				2504	0.4335				p.Q261R		Atlas-SNP	.											OR6N1,NS,adenoma,0,1	OR6N1	96	1	0			c.A782G						PASS	.	C	ARG/GLN	3436,970	365.1+/-317.3	1329,778,96	179.0	168.0	172.0		782	4.7	0.9	1	dbSNP_86	172	6162,2438	402.3+/-347.4	2217,1728,355	yes	missense	OR6N1	NM_001005185.1	43	3546,2506,451	CC,CT,TT		28.3488,22.0154,26.2033	benign	261/313	158735691	9598,3408	2203	4300	6503	SO:0001583	missense	128372	exon1			TTCAGCTGCACAT	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.782A>G	1.37:g.158735691T>C	ENSP00000335535:p.Gln261Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	1561	0.7147435897435898	376	0.7642276422764228	286	0.7900552486187845	344	0.6013986013986014	555	0.7321899736147758	C	0.006	-2.029825	0.00410	0.779846	0.716512	ENSG00000197403	ENST00000335094	T	0.36520	1.25	4.74	4.74	0.60224	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	N	0.000859	T	0.03220	0.0094	N	0.00811	-1.165	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33471	-0.9867	9	0.02654	T	1	-6.156	12.1889	0.54257	0.0:0.9155:0.0:0.0845	rs857825;rs17652404;rs52821209;rs857825	261	Q8NGY5	OR6N1_HUMAN	R	261	ENSP00000335535:Q261R	ENSP00000335535:Q261R	Q	-	2	0	OR6N1	157002315	0.001000	0.12720	0.945000	0.38365	0.113000	0.19764	1.410000	0.34691	1.211000	0.43351	-0.119000	0.15052	CAG	T|0.285;C|0.715	0.715	strong		0.542	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
SEMA4D	10507	hgsc.bcm.edu	37	9	92003679	92003679	+	Missense_Mutation	SNP	C	C	T	rs11526468	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:92003679C>T	ENST00000450295.1	-	11	1755	c.979G>A	c.(979-981)Gcc>Acc	p.A327T	SEMA4D_ENST00000455551.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000343780.4_Missense_Mutation_p.A327T|SEMA4D_ENST00000356444.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000420987.1_Missense_Mutation_p.A327T|SEMA4D_ENST00000438547.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000339861.4_Missense_Mutation_p.A327T|SEMA4D_ENST00000422704.2_Missense_Mutation_p.A327T			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	327	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		A -> T (in dbSNP:rs11526468).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AGGTTGTAGGCGCACACTGCC	0.627													C|||	1128	0.22524	0.0174	0.2723	5008	,	,		19441	0.3294		0.3072	False		,,,				2504	0.2812				p.A327T		Atlas-SNP	.											.	SEMA4D	81	.	0			c.G979A						PASS	.	C	THR/ALA,THR/ALA	278,4128	153.7+/-187.2	11,256,1936	76.0	61.0	66.0		979,979	4.0	1.0	9	dbSNP_120	66	2486,6114	407.8+/-349.3	349,1788,2163	yes	missense,missense	SEMA4D	NM_001142287.1,NM_006378.3	58,58	360,2044,4099	TT,TC,CC		28.907,6.3096,21.2517	probably-damaging,probably-damaging	327/739,327/863	92003679	2764,10242	2203	4300	6503	SO:0001583	missense	10507	exon13			TGTAGGCGCACAC	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.979G>A	9.37:g.92003679C>T	ENSP00000416523:p.Ala327Thr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_006378	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	573	0.2623626373626374	13	0.026422764227642278	107	0.2955801104972376	218	0.3811188811188811	235	0.3100263852242744	C	25.8	4.678510	0.88542	0.063096	0.28907	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52;2.52;2.52;2.52	4.96	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.092834	0.85682	D	0.000000	T	0.00012	0.0000	H	0.94886	3.595	0.09310	P	0.999991156	D;D	0.89917	0.997;1.0	P;D	0.73380	0.871;0.98	T	0.33854	-0.9852	9	0.41790	T	0.15	.	14.4731	0.67529	0.1481:0.8519:0.0:0.0	rs11526468	327;327	Q92854-2;Q92854	.;SEM4D_HUMAN	T	327	ENSP00000344923:A327T;ENSP00000391733:A327T;ENSP00000411981:A327T;ENSP00000343418:A327T;ENSP00000416523:A327T;ENSP00000405102:A327T;ENSP00000348822:A327T;ENSP00000388768:A327T	ENSP00000344923:A327T	A	-	1	0	SEMA4D	91193499	1.000000	0.71417	0.985000	0.45067	0.882000	0.50991	5.521000	0.67086	1.250000	0.43966	0.561000	0.74099	GCC	C|0.774;T|0.226	0.226	strong		0.627	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
CYP2E1	1571	hgsc.bcm.edu	37	10	135351362	135351362	+	Silent	SNP	T	T	C	rs2515641	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:135351362T>C	ENST00000463117.2	+	10	1535	c.1263T>C	c.(1261-1263)ttT>ttC	p.F421F	SPRN_ENST00000541506.1_Intron|CYP2E1_ENST00000252945.3_Silent_p.F421F			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	421					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	ATGGAAAGTTTAAGTACAGTG	0.443									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				.|||	3510	0.700879	0.3389	0.8213	5008	,	,		21002	0.7946		0.8718	False		,,,				2504	0.8323				p.F421F		Atlas-SNP	.											.	CYP2E1	69	.	0			c.T1263C						PASS	.	C		1750,2656	646.6+/-398.4	326,1098,779	96.0	85.0	89.0		1263	3.4	1.0	10	dbSNP_100	89	7591,1009	216.3+/-255.4	3330,931,39	no	coding-synonymous	CYP2E1	NM_000773.3		3656,2029,818	CC,CT,TT		11.7326,39.7186,28.1793		421/494	135351362	9341,3665	2203	4300	6503	SO:0001819	synonymous_variant	1571	exon8	Familial Cancer Database	incl.: Familial Head and Neck Cancer	AAAGTTTAAGTAC	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"""Cytochrome P450s"""	2631	protein-coding gene	gene with protein product		124040	"""cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"""	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.1263T>C	10.37:g.135351362T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_000773	Q5VZD5|Q6NWT9|Q9UK47	Silent	SNP	ENST00000463117.2	37	CCDS7686.1																																																																																			T|0.288;C|0.712	0.712	strong		0.443	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773	
GCC1	79571	hgsc.bcm.edu	37	7	127222521	127222521	+	Silent	SNP	G	G	A	rs33973710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:127222521G>A	ENST00000321407.2	-	2	2299	c.1875C>T	c.(1873-1875)ggC>ggT	p.G625G	GCC1_ENST00000497650.1_5'Flank	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	625					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CCCCAGGACCGCCACCACCCA	0.587													G|||	627	0.1252	0.208	0.121	5008	,	,		20979	0.0417		0.162	False		,,,				2504	0.0644				p.G625G		Atlas-SNP	.											.	GCC1	83	.	0			c.C1875T						PASS	.	G		906,3500	348.7+/-310.1	85,736,1382	78.0	79.0	79.0		1875	-1.8	0.0	7	dbSNP_126	79	1262,7338	251.2+/-277.8	97,1068,3135	no	coding-synonymous	GCC1	NM_024523.5		182,1804,4517	AA,AG,GG		14.6744,20.5629,16.6692		625/776	127222521	2168,10838	2203	4300	6503	SO:0001819	synonymous_variant	79571	exon2			AGGACCGCCACCA	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"""golgi coiled-coil 1"""			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.1875C>T	7.37:g.127222521G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_024523	Q9H6N7	Silent	SNP	ENST00000321407.2	37	CCDS5796.1																																																																																			G|0.837;A|0.163	0.163	strong		0.587	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523	
KRT75	9119	hgsc.bcm.edu	37	12	52827608	52827608	+	Missense_Mutation	SNP	C	C	T	rs2232387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52827608C>T	ENST00000252245.5	-	1	701	c.481G>A	c.(481-483)Gcc>Acc	p.A161T		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	161	Coil 1A.|Rod.		A -> T (common polymorphism; may increase risk to develop PFB; the variant is disruptive at late stages of filament assembly compromising the aggregation of keratin molecules into intermediate filaments; dbSNP:rs2232387). {ECO:0000269|PubMed:15086549}.		hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		ATGAAGGAGGCGAACTTATTG	0.562													C|||	717	0.143171	0.1891	0.2089	5008	,	,		18897	0.0754		0.1213	False		,,,				2504	0.1268				p.A161T		Atlas-SNP	.											.	KRT75	75	.	0			c.G481A	GRCh37	CM041106	KRT75	M	rs2232387	PASS	.	C	THR/ALA	789,3617	317.2+/-295.0	75,639,1489	154.0	154.0	154.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	481	5.7	1.0	12	dbSNP_98	154	958,7642	209.7+/-250.8	56,846,3398	yes	missense	KRT75	NM_004693.2	58	131,1485,4887	TT,TC,CC		11.1395,17.9074,13.4323	probably-damaging	161/552	52827608	1747,11259	2203	4300	6503	SO:0001583	missense	9119	exon1			AGGAGGCGAACTT	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.481G>A	12.37:g.52827608C>T	ENSP00000252245:p.Ala161Thr	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	220	107	0.486364	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	293	0.13415750915750915	103	0.20934959349593496	66	0.18232044198895028	36	0.06293706293706294	88	0.11609498680738786	C	35	5.441892	0.96187	0.179074	0.111395	ENSG00000170454	ENST00000252245	D	0.95205	-3.64	5.74	5.74	0.90152	Filament (1);	0.000000	0.53938	D	0.000053	T	0.06325	0.0163	H	0.99261	4.49	0.09310	P	0.99999974983	D	0.89917	1.0	D	0.91635	0.999	T	0.00077	-1.2117	9	0.87932	D	0	.	19.9197	0.97082	0.0:1.0:0.0:0.0	rs2232387;rs58159352;rs2232387	161	O95678	K2C75_HUMAN	T	161	ENSP00000252245:A161T	ENSP00000252245:A161T	A	-	1	0	KRT75	51113875	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	4.955000	0.63638	2.702000	0.92279	0.655000	0.94253	GCC	C|0.864;T|0.136	0.136	strong		0.562	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
GJA9	81025	hgsc.bcm.edu	37	1	39340282	39340282	+	Missense_Mutation	SNP	C	C	T	rs880303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39340282C>T	ENST00000360786.3	-	1	1741	c.1489G>A	c.(1489-1491)Gta>Ata	p.V497I	MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000454994.2_Intron|RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA|GJA9_ENST00000357771.3_Missense_Mutation_p.V497I|MYCBP_ENST00000397572.2_5'Flank			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	497			V -> I (in dbSNP:rs880303). {ECO:0000269|Ref.1}.		cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			AGGGACACTACGTGATTTGGA	0.433													C|||	1557	0.310903	0.1452	0.4813	5008	,	,		19898	0.2718		0.4523	False		,,,				2504	0.3088				p.V497I		Atlas-SNP	.											.	GJA9	55	.	0			c.G1489A						PASS	.	C	ILE/VAL	827,3579	328.0+/-300.3	81,665,1457	93.0	90.0	91.0		1489	-4.7	0.0	1	dbSNP_86	91	3914,4686	546.7+/-385.0	880,2154,1266	yes	missense	GJA9	NM_030772.4	29	961,2819,2723	TT,TC,CC		45.5116,18.7699,36.4524	benign	497/516	39340282	4741,8265	2203	4300	6503	SO:0001583	missense	81025	exon2			ACACTACGTGATT	AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"""Ion channels / Gap junction proteins (connexins)"""	19155	protein-coding gene	gene with protein product	"""connexin 59"""	611923	"""gap junction protein, alpha 10, 59kDa"""	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.1489G>A	1.37:g.39340282C>T	ENSP00000354020:p.Val497Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000360786.3	37	CCDS432.1	756	0.34615384615384615	74	0.15040650406504066	171	0.4723756906077348	168	0.2937062937062937	343	0.4525065963060686	C	8.017	0.758789	0.15846	0.187699	0.455116	ENSG00000131233	ENST00000357771;ENST00000360786	D;D	0.97378	-4.36;-4.36	4.16	-4.7	0.03288	.	672.406000	0.00649	N	0.000558	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50808	-0.8784	9	0.19590	T	0.45	.	1.938	0.03341	0.1411:0.4103:0.1402:0.3084	rs880303;rs17499686;rs52793287;rs58889690;rs880303	497	P57773	CXA9_HUMAN	I	497	ENSP00000350415:V497I;ENSP00000354020:V497I	ENSP00000350415:V497I	V	-	1	0	GJA9	39112869	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.499000	0.22546	-0.846000	0.04174	-0.471000	0.05019	GTA	C|0.662;N|0.000	.	strong		0.433	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
KCNQ4	9132	hgsc.bcm.edu	37	1	41285087	41285087	+	Silent	SNP	T	T	C	rs4660468	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:41285087T>C	ENST00000347132.5	+	5	859	c.777T>C	c.(775-777)gcT>gcC	p.A259A	KCNQ4_ENST00000509682.2_Silent_p.A259A|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	259					inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	TCTACCTGGCTGAGAAGGACG	0.652													C|||	2821	0.563299	0.5348	0.562	5008	,	,		12798	0.4683		0.6978	False		,,,				2504	0.5624				p.A259A		Atlas-SNP	.											.	KCNQ4	58	.	0			c.T777C						PASS	.	C	,	2545,1861	537.5+/-374.7	747,1051,405	130.0	103.0	112.0		777,777	-6.7	1.0	1	dbSNP_111	112	6251,2349	391.6+/-343.7	2273,1705,322	no	coding-synonymous,coding-synonymous	KCNQ4	NM_004700.3,NM_172163.2	,	3020,2756,727	CC,CT,TT		27.314,42.2379,32.3697	,	259/696,259/642	41285087	8796,4210	2203	4300	6503	SO:0001819	synonymous_variant	9132	exon5			CCTGGCTGAGAAG	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.777T>C	1.37:g.41285087T>C		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	186	106	0.569892	NM_004700	O96025	Silent	SNP	ENST00000347132.5	37	CCDS456.1	1227	0.5618131868131868	255	0.5182926829268293	211	0.5828729281767956	242	0.4230769230769231	519	0.6846965699208444	C	12.34	1.909646	0.33721	0.577621	0.72686	ENSG00000117013	ENST00000443478	.	.	.	5.08	-6.66	0.01789	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999997505	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.6808	5.1521	0.15015	0.0883:0.1615:0.5323:0.2179	rs4660468;rs60368714;rs4660468	.	.	.	R	155	.	.	X	+	1	0	KCNQ4	41057674	0.000000	0.05858	0.983000	0.44433	0.971000	0.66376	-4.231000	0.00269	-0.695000	0.05105	-1.109000	0.02080	TGA	C|0.623;N|0.000	0.623	strong		0.652	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
MYO1H	283446	hgsc.bcm.edu	37	12	109835590	109835590	+	Silent	SNP	A	A	G	rs11611358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109835590A>G	ENST00000431443.2	+	4	495	c.495A>G	c.(493-495)aaA>aaG	p.K165K	MYO1H_ENST00000310903.5_Silent_p.K165K	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	165	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						GATTTGGGAAATACATGGATA	0.453													A|||	1264	0.252396	0.0651	0.4524	5008	,	,		18134	0.3552		0.3052	False		,,,				2504	0.2035				p.K165K		Atlas-SNP	.											MYO1H,colon,carcinoma,0,1	MYO1H	98	1	0			c.A495G						PASS	.	A		411,3381		29,353,1514	79.0	74.0	76.0		495	-0.5	1.0	12	dbSNP_120	76	2477,5837		351,1775,2031	no	coding-synonymous	MYO1H	NM_001101421.3		380,2128,3545	GG,GA,AA		29.7931,10.8386,23.8559		165/1023	109835590	2888,9218	1896	4157	6053	SO:0001819	synonymous_variant	283446	exon4			TGGGAAATACATG		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.495A>G	12.37:g.109835590A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				A|0.742;G|0.258	0.258	strong		0.453	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
IL2RA	3559	hgsc.bcm.edu	37	10	6067969	6067969	+	Silent	SNP	C	C	T	rs2228150	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:6067969C>T	ENST00000379959.3	-	2	257	c.84G>A	c.(82-84)ccG>ccA	p.P28P	IL2RA_ENST00000379954.1_Silent_p.P28P|RP11-536K7.5_ENST00000440436.1_RNA|IL2RA_ENST00000256876.6_Silent_p.P28P	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	28	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)			endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	GGATCTCTGGCGGGTCATCGT	0.463													C|||	410	0.081869	0.2322	0.0317	5008	,	,		18681	0.001		0.0229	False		,,,				2504	0.0583				p.P28P		Atlas-SNP	.											.	IL2RA	37	.	0			c.G84A						PASS	.	C		900,3506	348.5+/-309.9	88,724,1391	101.0	88.0	92.0		84	-7.8	0.0	10	dbSNP_98	92	236,8364	95.4+/-157.2	4,228,4068	no	coding-synonymous	IL2RA	NM_000417.2		92,952,5459	TT,TC,CC		2.7442,20.4267,8.7344		28/273	6067969	1136,11870	2203	4300	6503	SO:0001819	synonymous_variant	3559	exon2			CTCTGGCGGGTCA	X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"""Interleukins and interleukin receptors"", ""CD molecules"""	6008	protein-coding gene	gene with protein product		147730	"""insulin-dependent diabetes mellitus 10"""	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.84G>A	10.37:g.6067969C>T		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	238	102	0.428571	NM_000417	Q5W007	Silent	SNP	ENST00000379959.3	37	CCDS7076.1																																																																																			T|0.080;G|0.006	0.080	strong		0.463	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417	
TDG	6996	hgsc.bcm.edu	37	12	104376608	104376608	+	Silent	SNP	G	G	A	rs61937629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:104376608G>A	ENST00000392872.3	+	5	744	c.510G>A	c.(508-510)gaG>gaA	p.E170E	TDG_ENST00000544861.1_Silent_p.E27E|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_5'UTR|TDG_ENST00000266775.9_Silent_p.E166E	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	170					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)	p.E170E(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		GGCTCAGTGAGGTCCAGCTGA	0.443								Base excision repair (BER), DNA glycosylases																													p.E170E		Atlas-SNP	.											TDG,NS,carcinoma,0,1	TDG	43	1	1	Substitution - coding silent(1)	stomach(1)	c.G510A						PASS	.						124.0	116.0	118.0					12																	104376608		2203	4300	6503	SO:0001819	synonymous_variant	6996	exon5			CAGTGAGGTCCAG	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.510G>A	12.37:g.104376608G>A		Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	379	41	0.108179	NM_003211	Q8IUZ6|Q8IZM3	Silent	SNP	ENST00000392872.3	37	CCDS9095.1																																																																																			G|0.924;A|0.076	0.076	strong		0.443	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
NXPE4	54827	hgsc.bcm.edu	37	11	114441936	114441936	+	Silent	SNP	A	A	G	rs12421748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:114441936A>G	ENST00000375478.3	-	6	1539	c.1359T>C	c.(1357-1359)aaT>aaC	p.N453N	NXPE4_ENST00000424261.2_Silent_p.N169N	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	453						extracellular vesicular exosome (GO:0070062)											CTTTGTGGACATTGAGGGCCC	0.418													A|||	516	0.103035	0.0091	0.2017	5008	,	,		17881	0.0		0.1292	False		,,,				2504	0.2393				p.N453N		Atlas-SNP	.											.	.	.	.	0			c.T1359C						PASS	.	A	,	114,3654		4,106,1774	136.0	124.0	128.0		1359,507	-3.8	0.0	11	dbSNP_120	128	1110,7108		86,938,3085	no	coding-synonymous,coding-synonymous	FAM55D	NM_001077639.1,NM_017678.2	,	90,1044,4859	GG,GA,AA		13.5069,3.0255,10.2119	,	453/545,169/261	114441936	1224,10762	1884	4109	5993	SO:0001819	synonymous_variant	54827	exon6			GTGGACATTGAGG	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1359T>C	11.37:g.114441936A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	220	114	0.518182	NM_001077639	Q6QDB4|Q9NXP5	Silent	SNP	ENST00000375478.3	37	CCDS41718.1																																																																																			A|0.894;G|0.106	0.106	strong		0.418	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
ZNF142	7701	hgsc.bcm.edu	37	2	219507302	219507302	+	Missense_Mutation	SNP	C	C	T	rs3821033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219507302C>T	ENST00000449707.1	-	8	4358	c.3937G>A	c.(3937-3939)Gca>Aca	p.A1313T	ZNF142_ENST00000411696.2_Missense_Mutation_p.A1313T	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	1313			A -> T (in dbSNP:rs3821033).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GCAGGCTGTGCAGGCTCGGGG	0.647													C|||	410	0.081869	0.143	0.0274	5008	,	,		17415	0.122		0.0258	False		,,,				2504	0.0542				p.A1313T	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.G3937A						PASS	.	C	THR/ALA	474,3754		24,426,1664	24.0	29.0	27.0		3937	-7.2	0.0	2	dbSNP_107	27	270,8206		4,262,3972	yes	missense	ZNF142	NM_001105537.1	58	28,688,5636	TT,TC,CC		3.1855,11.211,5.8564	benign	1313/1688	219507302	744,11960	2114	4238	6352	SO:0001583	missense	7701	exon8			GCTGTGCAGGCTC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.3937G>A	2.37:g.219507302C>T	ENSP00000408643:p.Ala1313Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	45	0.391304	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	173	0.07921245421245421	63	0.12804878048780488	12	0.03314917127071823	81	0.14160839160839161	17	0.022427440633245383	C	0.385	-0.926578	0.02377	0.11211	0.031855	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.11712	2.75;2.75	5.48	-7.18	0.01505	Zinc finger, C2H2 (1);	0.685815	0.13935	N	0.352638	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43829	-0.9367	9	0.07325	T	0.83	0.0932	9.4842	0.38919	0.1026:0.6279:0.1038:0.1658	rs3821033;rs52823395;rs3821033	1313;1150	P52746;A8MWU9	ZN142_HUMAN;.	T	1313	ENSP00000408643:A1313T;ENSP00000398798:A1313T	ENSP00000398798:A1313T	A	-	1	0	ZNF142	219215546	0.000000	0.05858	0.000000	0.03702	0.508000	0.34012	-2.699000	0.00825	-1.190000	0.02698	-0.320000	0.08662	GCA	C|0.924;T|0.076	0.076	strong		0.647	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
KATNAL1	84056	hgsc.bcm.edu	37	13	30784566	30784566	+	Silent	SNP	A	A	G	rs11617724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:30784566A>G	ENST00000380615.3	-	10	1328	c.1161T>C	c.(1159-1161)gcT>gcC	p.A387A	KATNAL1_ENST00000380617.3_Silent_p.A387A	NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1											autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		TCAGAAGCTCAGCTCTTCCTT	0.378													a|||	224	0.0447284	0.1233	0.036	5008	,	,		18073	0.0		0.0328	False		,,,				2504	0.0031				p.A387A		Atlas-SNP	.											.	KATNAL1	53	.	0			c.T1161C						PASS	.	A	,	483,3923	226.9+/-242.2	30,423,1750	181.0	170.0	174.0		1161,1161	-11.5	0.3	13	dbSNP_120	174	319,8281	113.3+/-173.4	3,313,3984	no	coding-synonymous,coding-synonymous	KATNAL1	NM_001014380.1,NM_032116.3	,	33,736,5734	GG,GA,AA		3.7093,10.9623,6.1664	,	387/491,387/491	30784566	802,12204	2203	4300	6503	SO:0001819	synonymous_variant	84056	exon10			AAGCTCAGCTCTT	AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781		"""ATPases / AAA-type"""	28361	protein-coding gene	gene with protein product		614764				12477932	Standard	NM_001014380		Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.1161T>C	13.37:g.30784566A>G		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	209	206	0.985646	NM_001014380		Silent	SNP	ENST00000380615.3	37	CCDS31956.1																																																																																			A|0.940;G|0.060	0.060	strong		0.378	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116	
HEATR5B	54497	hgsc.bcm.edu	37	2	37230734	37230734	+	Silent	SNP	C	C	T	rs17497654	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:37230734C>T	ENST00000233099.5	-	31	5096	c.5001G>A	c.(4999-5001)caG>caA	p.Q1667Q	HEATR5B_ENST00000354531.2_Silent_p.Q1667Q	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1667						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				CTCTTACTATCTGTTGTACAA	0.378													C|||	652	0.130192	0.2345	0.1326	5008	,	,		15144	0.0238		0.1461	False		,,,				2504	0.0808				p.Q1667Q		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G5001A						PASS	.	C		921,3485	353.6+/-312.2	97,727,1379	84.0	84.0	84.0		5001	4.6	1.0	2	dbSNP_123	84	1401,7199	271.2+/-289.4	120,1161,3019	no	coding-synonymous	HEATR5B	NM_019024.1		217,1888,4398	TT,TC,CC		16.2907,20.9033,17.8533		1667/2072	37230734	2322,10684	2203	4300	6503	SO:0001819	synonymous_variant	54497	exon31			TACTATCTGTTGT	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.5001G>A	2.37:g.37230734C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			C|0.834;T|0.166	0.166	strong		0.378	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
RSU1	6251	hgsc.bcm.edu	37	10	16794623	16794623	+	Silent	SNP	C	C	T	rs10445	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:16794623C>T	ENST00000377921.3	-	6	814	c.513G>A	c.(511-513)tcG>tcA	p.S171S	RSU1_ENST00000464074.2_5'UTR|RSU1_ENST00000602389.1_Silent_p.S118S|RSU1_ENST00000345264.5_Silent_p.S171S			Q15404	RSU1_HUMAN	Ras suppressor protein 1	171					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		CCTTAGGCAGCGAGATCAGGT	0.478													C|||	518	0.103435	0.0113	0.1599	5008	,	,		19626	0.1538		0.1581	False		,,,				2504	0.0798				p.S171S		Atlas-SNP	.											.	RSU1	31	.	0			c.G513A						PASS	.	C	,	129,4277	93.9+/-132.6	5,119,2079	102.0	96.0	98.0		513,354	-1.4	1.0	10	dbSNP_52	98	1242,7358	249.2+/-276.5	90,1062,3148	no	coding-synonymous,coding-synonymous	RSU1	NM_012425.3,NM_152724.2	,	95,1181,5227	TT,TC,CC		14.4419,2.9278,10.5413	,	171/278,118/225	16794623	1371,11635	2203	4300	6503	SO:0001819	synonymous_variant	6251	exon7			AGGCAGCGAGATC	AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.513G>A	10.37:g.16794623C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_012425	A8KA46|D3DRU3|Q6FI17	Silent	SNP	ENST00000377921.3	37	CCDS7112.1																																																																																			C|0.887;T|0.113	0.113	strong		0.478	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724	
ADIRF	10974	hgsc.bcm.edu	37	10	88730312	88730312	+	Silent	SNP	T	T	C	rs4869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88730312T>C	ENST00000372013.3	+	3	557	c.204T>C	c.(202-204)atT>atC	p.I68I	ADIRF-AS1_ENST00000440490.1_RNA|RP11-96C23.15_ENST00000609363.1_RNA|ADIRF-AS1_ENST00000609111.1_RNA|RP11-96C23.5_ENST00000433214.2_RNA|ADIRF-AS1_ENST00000418273.2_RNA	NM_006829.2	NP_006820.1	Q15847	ADIRF_HUMAN	adipogenesis regulatory factor	68					cell differentiation (GO:0030154)|cellular response to cisplatin (GO:0072719)|cellular response to radiation (GO:0071478)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of response to drug (GO:2001023)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.I68I(1)									TCTCTGGGATTGGGAAAAAAT	0.587													N|||	2640	0.527157	0.3585	0.4308	5008	,	,		17157	0.8095		0.6014	False		,,,				2504	0.456				p.I68I		Atlas-SNP	.											C10orf116,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.T204C						PASS	.	C		1662,2744	652.1+/-399.3	341,980,882	77.0	70.0	72.0	http://omim.org/entry/178500	204	-8.6	0.0	10	dbSNP_52	72	4610,3990	546.5+/-385.0	1229,2152,919	no	coding-synonymous	C10orf116	NM_006829.2		1570,3132,1801	CC,CT,TT		46.3953,37.7213,48.2239		68/77	88730312	6272,6734	2203	4300	6503	SO:0001819	synonymous_variant	10974	exon3			TGGGATTGGGAAA	BC004471	CCDS7381.1	10q23.31	2013-02-20	2013-02-20	2013-02-20	ENSG00000148671	ENSG00000148671			24043	protein-coding gene	gene with protein product	"""adipose specific 2"", ""adipose most abundant gene transcript 2"", ""adipogenesis factor rich in obesity"""		"""chromosome 10 open reading frame 116"""	C10orf116		8619847, 23239344	Standard	NM_006829		Approved	APM2, AFRO	uc001ked.2	Q15847	OTTHUMG00000018668	ENST00000372013.3:c.204T>C	10.37:g.88730312T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	170	75	0.441176	NM_006829		Silent	SNP	ENST00000372013.3	37	CCDS7381.1																																																																																			T|0.489;C|0.511	0.511	strong		0.587	ADIRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049194.1	NM_006829	
KCNJ11	3767	hgsc.bcm.edu	37	11	17409069	17409069	+	Silent	SNP	G	G	A	rs5218	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:17409069G>A	ENST00000339994.4	-	1	1137	c.570C>T	c.(568-570)gcC>gcT	p.A190A	KCNJ11_ENST00000526747.1_5'Flank|KCNJ11_ENST00000528731.1_Silent_p.A103A	NM_000525.3	NP_000516.3	Q14654	KCJ11_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 11	190					cellular response to glucose stimulus (GO:0071333)|cellular response to nicotine (GO:0071316)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|negative regulation of insulin secretion (GO:0046676)|neurological system process (GO:0050877)|positive regulation of cation channel activity (GO:2001259)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ischemia (GO:0002931)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	ATP-sensitive potassium channel complex (GO:0008282)|axolemma (GO:0030673)|cell body fiber (GO:0070852)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|ion channel binding (GO:0044325)|potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(3)|skin(2)	16				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)	Diazoxide(DB01119)|Glimepiride(DB00222)|Glyburide(DB01016)|Ibutilide(DB00308)|Levosimendan(DB00922)|Thiamylal(DB01154)|Verapamil(DB00661)|Yohimbine(DB01392)	CGTGGCGCAGGGCGATCACCG	0.587											OREG0020810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1139	0.227436	0.0257	0.1816	5008	,	,		21810	0.5129		0.3221	False		,,,				2504	0.1411				p.A190A		Atlas-SNP	.											.	KCNJ11	39	.	0			c.C570T	GRCh37	CM035697	KCNJ11	M	rs5218	PASS	.	G	,	331,4069	170.1+/-200.6	16,299,1885	61.0	43.0	49.0		570,309	-0.1	0.7	11	dbSNP_52	49	2563,6023	408.6+/-349.5	388,1787,2118	no	coding-synonymous,coding-synonymous	KCNJ11	NM_000525.3,NM_001166290.1	,	404,2086,4003	AA,AG,GG		29.8509,7.5227,22.2855	,	190/391,103/304	17409069	2894,10092	2200	4293	6493	SO:0001819	synonymous_variant	3767	exon1			GCGCAGGGCGATC	D50582	CCDS31436.1, CCDS53606.1	11p15.1	2011-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6257	protein-coding gene	gene with protein product		600937				7502040, 16382105	Standard	NM_001166290		Approved	Kir6.2, BIR	uc001mna.3	Q14654		ENST00000339994.4:c.570C>T	11.37:g.17409069G>A		Somatic	63	0	0	717	WXS	Illumina HiSeq	Phase_I	55	55	1	NM_000525	B4DWI4|E9PNK0|Q2M1H7|Q58EX3|Q8IW96	Silent	SNP	ENST00000339994.4	37	CCDS31436.1																																																																																			G|0.773;A|0.227	0.227	strong		0.587	KCNJ11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387037.1	NM_000525	
HK2	3099	hgsc.bcm.edu	37	2	75107651	75107651	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:75107651G>A	ENST00000290573.2	+	10	2125	c.1525G>A	c.(1525-1527)Gtc>Atc	p.V509I	HK2_ENST00000409174.1_Missense_Mutation_p.V481I	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	509	Catalytic.|Hexokinase type-1 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.V509I(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CAGTGCCCCCGTCAAGATGCT	0.597																																					p.V509I		Atlas-SNP	.											HK2,NS,carcinoma,0,1	HK2	85	1	2	Substitution - Missense(2)	lung(2)	c.G1525A						PASS	.						74.0	73.0	73.0					2																	75107651		2203	4300	6503	SO:0001583	missense	3099	exon10			GCCCCCGTCAAGA		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.1525G>A	2.37:g.75107651G>A	ENSP00000290573:p.Val509Ile	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	203	22	0.108374	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.358474	0.61403	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.98345	-4.88;-4.88	4.99	4.99	0.66335	Hexokinase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98270	0.9427	L	0.51853	1.615	0.80722	D	1	D	0.61697	0.99	D	0.73380	0.98	D	0.97702	1.0185	10	0.35671	T	0.21	-40.4869	16.1435	0.81544	0.0:0.0:1.0:0.0	.	509	P52789	HXK2_HUMAN	I	509;509;481	ENSP00000290573:V509I;ENSP00000387140:V481I	ENSP00000290573:V509I	V	+	1	0	HK2	74961159	1.000000	0.71417	0.963000	0.40424	0.607000	0.37147	7.613000	0.82986	2.756000	0.94617	0.655000	0.94253	GTC	.	.	none		0.597	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
LARP1	23367	hgsc.bcm.edu	37	5	154092616	154092616	+	Missense_Mutation	SNP	C	C	T	rs148235669	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:154092616C>T	ENST00000336314.4	+	1	155	c.131C>T	c.(130-132)gCc>gTc	p.A44V		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	62					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTGGCAGCTGCCCCGAGGAAG	0.602													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		17738	0.0		0.0	False		,,,				2504	0.001				p.A44V		Atlas-SNP	.											.	LARP1	187	.	0			c.C131T						PASS	.	C	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	53.0	53.0	53.0		131	2.9	0.8	5	dbSNP_134	53	22,8578	16.0+/-53.3	0,22,4278	yes	missense	LARP1	NM_015315.3	64	0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		44/1020	154092616	24,12982	2203	4300	6503	SO:0001583	missense	23367	exon1			CAGCTGCCCCGAG	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"""La ribonucleoprotein domain containing"""	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.131C>T	5.37:g.154092616C>T	ENSP00000336721:p.Ala44Val	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	269	90	0.334572	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.	.	.	.	.	.	.	.	.	.	C	6.440	0.449233	0.12223	4.54E-4	0.002558	ENSG00000155506	ENST00000336314	T	0.25085	1.82	3.81	2.94	0.34122	.	.	.	.	.	T	0.17577	0.0422	.	.	.	0.19300	N	0.999973	B	0.27997	0.197	B	0.29176	0.099	T	0.19484	-1.0304	8	0.30078	T	0.28	.	8.8895	0.35425	0.2222:0.7778:0.0:0.0	.	44	Q6PKG0-3	.	V	44	ENSP00000336721:A44V	ENSP00000336721:A44V	A	+	2	0	LARP1	154072809	0.960000	0.32886	0.823000	0.32752	0.013000	0.08279	2.833000	0.48159	1.182000	0.42928	-0.310000	0.09108	GCC	C|0.998;T|0.002	0.002	strong		0.602	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551	
ZNF469	84627	hgsc.bcm.edu	37	16	88495654	88495654	+	Silent	SNP	A	A	G	rs12927001	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88495654A>G	ENST00000437464.1	+	1	1776	c.1776A>G	c.(1774-1776)ccA>ccG	p.P592P	ZNF469_ENST00000565624.1_Silent_p.P592P	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	592	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GCGAGTCCCCACTGCCGTCAC	0.697													A|||	4381	0.8748	0.6725	0.9438	5008	,	,		10399	0.9157		0.9453	False		,,,				2504	0.9847				p.P592P		Atlas-SNP	.											.	ZNF469	121	.	0			c.A1776G						PASS	.						8.0	13.0	11.0					16																	88495654		683	1579	2262	SO:0001819	synonymous_variant	84627	exon1			GTCCCCACTGCCG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.1776A>G	16.37:g.88495654A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			A|0.134;G|0.866	0.866	strong		0.697	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
HECW1	23072	hgsc.bcm.edu	37	7	43506158	43506158	+	Silent	SNP	T	T	C	rs2304328	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43506158T>C	ENST00000395891.2	+	15	3509	c.2904T>C	c.(2902-2904)caT>caC	p.H968H	HECW1_ENST00000453890.1_Silent_p.H934H	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	968					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CTGTGCTACATGCCAATTATG	0.493													C|||	2243	0.447883	0.5189	0.4035	5008	,	,		14738	0.3492		0.4284	False		,,,				2504	0.5051				p.H968H		Atlas-SNP	.											.	HECW1	540	.	0			c.T2904C						PASS	.	C		1791,2049		426,939,555	96.0	89.0	91.0		2904	-11.6	0.0	7	dbSNP_100	91	3399,4853		680,2039,1407	no	coding-synonymous	HECW1	NM_015052.3		1106,2978,1962	CC,CT,TT		41.19,46.6406,42.9209		968/1607	43506158	5190,6902	1920	4126	6046	SO:0001819	synonymous_variant	23072	exon15			GCTACATGCCAAT	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.2904T>C	7.37:g.43506158T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	54	34	0.62963	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			T|0.570;C|0.430	0.430	strong		0.493	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
ADAMTS8	11095	hgsc.bcm.edu	37	11	130281488	130281488	+	Missense_Mutation	SNP	G	G	A	rs2131535	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130281488G>A	ENST00000257359.6	-	6	2280	c.1574C>T	c.(1573-1575)gCa>gTa	p.A525V		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	525	Disintegrin.			A -> V (in Ref. 1; AAD48081). {ECO:0000305}.	negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		GCCTCCATCTGCCACGGGCTG	0.587													A|||	3726	0.74401	0.705	0.8012	5008	,	,		19014	0.8304		0.7694	False		,,,				2504	0.6411				p.A525V		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.C1574T						PASS	.	A	VAL/ALA	2869,1165		1020,829,168	47.0	50.0	49.0		1574	5.9	0.9	11	dbSNP_96	49	6308,2058		2366,1576,241	yes	missense	ADAMTS8	NM_007037.4	64	3386,2405,409	AA,AG,GG		24.5996,28.8795,25.9919	benign	525/890	130281488	9177,3223	2017	4183	6200	SO:0001583	missense	11095	exon6			CCATCTGCCACGG	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.1574C>T	11.37:g.130281488G>A	ENSP00000257359:p.Ala525Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_007037	Q9NZS0	Missense_Mutation	SNP	ENST00000257359.6	37	CCDS41732.1	1692	0.7747252747252747	347	0.7052845528455285	291	0.8038674033149171	471	0.8234265734265734	583	0.7691292875989446	A	5.884	0.347222	0.11126	0.711205	0.754004	ENSG00000134917	ENST00000257359;ENST00000414575	T	0.58506	0.33	5.87	5.87	0.94306	.	0.054880	0.64402	N	0.000001	T	0.00012	0.0000	N	0.08118	0	0.48901	P	2.7200000000005E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	9	0.02654	T	1	.	8.2543	0.31746	0.8153:0.0:0.0657:0.1191	rs2131535;rs52791263;rs59108290;rs2131535	525	Q9UP79	ATS8_HUMAN	V	525;554	ENSP00000257359:A525V	ENSP00000257359:A525V	A	-	2	0	ADAMTS8	129786698	0.995000	0.38212	0.945000	0.38365	0.705000	0.40729	4.831000	0.62752	1.051000	0.40369	-0.352000	0.07741	GCA	G|0.243;A|0.757	0.757	strong		0.587	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	
COL4A2	1284	hgsc.bcm.edu	37	13	111102042	111102042	+	Silent	SNP	G	G	A	rs76425569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:111102042G>A	ENST00000360467.5	+	19	1401	c.1095G>A	c.(1093-1095)ccG>ccA	p.P365P		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	365	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GAGGTGACCCGGGATTCCCAG	0.597													G|||	1195	0.238618	0.093	0.1844	5008	,	,		17674	0.2718		0.3539	False		,,,				2504	0.3211				p.P365P		Atlas-SNP	.											.	COL4A2	178	.	0			c.G1095A						PASS	.	G		364,2636		16,332,1152	18.0	19.0	19.0		1095	-7.1	0.9	13	dbSNP_131	19	2142,4392		336,1470,1461	no	coding-synonymous	COL4A2	NM_001846.2		352,1802,2613	AA,AG,GG		32.7824,12.1333,26.2849		365/1713	111102042	2506,7028	1500	3267	4767	SO:0001819	synonymous_variant	1284	exon19			TGACCCGGGATTC	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1095G>A	13.37:g.111102042G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			G|0.729;A|0.271	0.271	strong		0.597	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
ERBB4	2066	hgsc.bcm.edu	37	2	212251864	212251864	+	Silent	SNP	T	T	C	rs3748962	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:212251864T>C	ENST00000342788.4	-	27	3505	c.3195A>G	c.(3193-3195)gtA>gtG	p.V1065V	ERBB4_ENST00000436443.1_Silent_p.V1049V|ERBB4_ENST00000402597.1_Silent_p.V1055V	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1065					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	CATCTCGGTATACAAACTGGT	0.433										TSP Lung(8;0.080)			T|||	1117	0.223043	0.0756	0.2983	5008	,	,		18765	0.2887		0.2992	False		,,,				2504	0.2229				p.V1065V		Atlas-SNP	.											.	ERBB4	480	.	0			c.A3195G						PASS	.	T	,	444,3962	214.5+/-233.7	29,386,1788	110.0	113.0	112.0		3147,3195	-8.9	0.3	2	dbSNP_107	112	2843,5757	447.9+/-361.7	499,1845,1956	no	coding-synonymous,coding-synonymous	ERBB4	NM_001042599.1,NM_005235.2	,	528,2231,3744	CC,CT,TT		33.0581,10.0772,25.273	,	1049/1293,1065/1309	212251864	3287,9719	2203	4300	6503	SO:0001819	synonymous_variant	2066	exon27			TCGGTATACAAAC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3195A>G	2.37:g.212251864T>C		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	266	137	0.515038	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1																																																																																			T|0.756;C|0.244	0.244	strong		0.433	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
SLC35G5	83650	hgsc.bcm.edu	37	8	11188743	11188743	+	Missense_Mutation	SNP	C	C	T	rs13260331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11188743C>T	ENST00000382435.4	+	1	347	c.128C>T	c.(127-129)gCc>gTc	p.A43V		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	43						integral component of membrane (GO:0016021)											CTGCTGGTGGCCCTGCTGGGT	0.682													C|||	1588	0.317093	0.0197	0.3401	5008	,	,		16598	0.5833		0.3588	False		,,,				2504	0.3855				p.A43V		Atlas-SNP	.											.	.	.	.	0			c.C128T						PASS	.	C	VAL/ALA	384,4022	190.2+/-216.2	20,344,1839	50.0	56.0	54.0		128	0.3	0.8	8	dbSNP_121	54	3350,5250	496.3+/-374.2	674,2002,1624	no	missense	SLC35G5	NM_054028.1	64	694,2346,3463	TT,TC,CC		38.9535,8.7154,28.7098	possibly-damaging	43/339	11188743	3734,9272	2203	4300	6503	SO:0001583	missense	83650	exon1			TGGTGGCCCTGCT	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.128C>T	8.37:g.11188743C>T	ENSP00000371872:p.Ala43Val	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	126	68	0.539683	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	730	0.3342490842490842	15	0.03048780487804878	118	0.3259668508287293	332	0.5804195804195804	265	0.3496042216358839	C	11.44	1.638949	0.29157	0.087154	0.389535	ENSG00000177710	ENST00000382435	T	0.31510	1.49	0.34	0.34	0.15985	.	0.000000	0.44688	D	0.000436	T	0.00012	0.0000	L	0.29908	0.895	0.33612	P	0.39624499999999996	D	0.69078	0.997	D	0.75020	0.985	T	0.43686	-0.9376	9	0.18710	T	0.47	-8.3892	2.848	0.05549	0.0:0.5979:0.0:0.4021	rs13260331;rs59076275	43	Q96KT7	S35G5_HUMAN	V	43	ENSP00000371872:A43V	ENSP00000371872:A43V	A	+	2	0	SLC35G5	11226153	0.799000	0.28903	0.849000	0.33467	0.193000	0.23685	0.269000	0.18589	0.426000	0.26116	0.089000	0.15464	GCC	C|0.705;T|0.295	0.295	strong		0.682	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
HIVEP3	59269	hgsc.bcm.edu	37	1	41990461	41990461	+	Silent	SNP	G	G	A	rs35122733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:41990461G>A	ENST00000372583.1	-	6	6213	c.5328C>T	c.(5326-5328)caC>caT	p.H1776H	HIVEP3_ENST00000372584.1_Silent_p.H1776H|HIVEP3_ENST00000460604.1_Intron|HIVEP3_ENST00000247584.5_Silent_p.H1776H|HIVEP3_ENST00000429157.2_Silent_p.H1776H	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1776	ZAS2.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GGACGTCAGTGTGGGTGCGGA	0.547													G|||	244	0.048722	0.0144	0.1124	5008	,	,		20915	0.004		0.0417	False		,,,				2504	0.1033				p.H1776H		Atlas-SNP	.											.	HIVEP3	235	.	0			c.C5328T						PASS	.	G	,	125,4281	92.0+/-130.7	3,119,2081	162.0	128.0	139.0		5328,5328	4.1	1.0	1	dbSNP_126	139	469,8131	138.3+/-195.1	10,449,3841	no	coding-synonymous,coding-synonymous	HIVEP3	NM_001127714.2,NM_024503.4	,	13,568,5922	AA,AG,GG		5.4535,2.837,4.5671	,	1776/2406,1776/2407	41990461	594,12412	2203	4300	6503	SO:0001819	synonymous_variant	59269	exon6			GTCAGTGTGGGTG	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5328C>T	1.37:g.41990461G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	140	83	0.592857	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																			G|0.956;A|0.044	0.044	strong		0.547	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
TBX15	6913	hgsc.bcm.edu	37	1	119427454	119427454	+	Silent	SNP	G	G	A	rs12569041	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:119427454G>A	ENST00000369429.3	-	8	1719	c.1710C>T	c.(1708-1710)agC>agT	p.S570S	TBX15_ENST00000207157.3_Silent_p.S464S			Q96SF7	TBX15_HUMAN	T-box 15	570					embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		TGGGTGAAGGGCTAATCATGT	0.537													G|||	374	0.0746805	0.0265	0.0663	5008	,	,		18368	0.1171		0.1193	False		,,,				2504	0.0562				p.S464S		Atlas-SNP	.											TBX15,right_lower_lobe,carcinoma,-1,1	TBX15	95	1	0			c.C1392T						PASS	.	G		167,4239	112.1+/-150.2	2,163,2038	90.0	83.0	85.0		1392	3.5	1.0	1	dbSNP_120	85	1028,7572	219.1+/-257.3	61,906,3333	no	coding-synonymous	TBX15	NM_152380.2		63,1069,5371	AA,AG,GG		11.9535,3.7903,9.1881		464/497	119427454	1195,11811	2203	4300	6503	SO:0001819	synonymous_variant	6913	exon8			TGAAGGGCTAATC	AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"""T-boxes"""	11594	protein-coding gene	gene with protein product		604127	"""T-box 14"""	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.1710C>T	1.37:g.119427454G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	181	176	0.972376	NM_152380	Q08E76|Q5JT54|Q5T9S7	Silent	SNP	ENST00000369429.3	37																																																																																				G|0.913;A|0.087	0.087	strong		0.537	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380	
PIGB	9488	hgsc.bcm.edu	37	15	55619796	55619796	+	Missense_Mutation	SNP	T	T	C	rs2290344	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:55619796T>C	ENST00000164305.5	+	4	776	c.485T>C	c.(484-486)aTg>aCg	p.M162T	PIGB_ENST00000539642.1_Intron	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	162			M -> T (in dbSNP:rs2290344).		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		TACTCATTAATGAAGCAACTA	0.388													T|||	1152	0.230032	0.0189	0.2118	5008	,	,		15519	0.5635		0.1203	False		,,,				2504	0.2975				p.M162T		Atlas-SNP	.											.	PIGB	36	.	0			c.T485C						PASS	.	T	THR/MET	144,3558		1,142,1708	93.0	87.0	89.0		485	3.2	1.0	15	dbSNP_100	89	889,7313		59,771,3271	yes	missense	PIGB	NM_004855.4	81	60,913,4979	CC,CT,TT		10.8388,3.8898,8.6778	benign	162/555	55619796	1033,10871	1851	4101	5952	SO:0001583	missense	9488	exon4			CATTAATGAAGCA	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8959	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 3"", ""dol-P-Man dependent GPI mannosyltransferase"""	604122	"""phosphatidylinositol glycan, class B"""			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.485T>C	15.37:g.55619796T>C	ENSP00000164305:p.Met162Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_004855	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	37		454	0.2078754578754579	8	0.016260162601626018	73	0.20165745856353592	292	0.5104895104895105	81	0.10686015831134564	T	10.78	1.446235	0.25987	0.038898	0.108388	ENSG00000069943	ENST00000164305	T	0.63580	-0.05	5.57	3.23	0.37069	.	0.408765	0.30392	N	0.009732	T	0.00012	0.0000	N	0.00237	-1.79	0.09310	P	0.9999999999999959	B	0.02656	0.0	B	0.06405	0.002	T	0.44513	-0.9323	9	0.23302	T	0.38	-6.9731	8.8825	0.35382	0.0:0.1556:0.0:0.8444	rs2290344;rs52791382;rs59002340;rs2290344	162	Q92521	PIGB_HUMAN	T	162	ENSP00000164305:M162T	ENSP00000164305:M162T	M	+	2	0	PIGB	53407088	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	2.727000	0.47311	0.912000	0.36772	0.533000	0.62120	ATG	T|0.805;C|0.195	0.195	strong		0.388	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855	
MACROD1	28992	hgsc.bcm.edu	37	11	63884027	63884027	+	Intron	SNP	C	C	T	rs614035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:63884027C>T	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.A96A	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						TCAACAACGCCGGCATCCCCC	0.567													C|||	2034	0.40615	0.1475	0.5519	5008	,	,		21458	0.3254		0.6968	False		,,,				2504	0.4366				p.A96A		Atlas-SNP	.											.	FLRT1	46	.	0			c.C288T						PASS	.	C	,	1018,3384	376.1+/-321.9	114,790,1297	85.0	67.0	73.0		288,	-11.1	0.0	11	dbSNP_83	73	5873,2721	680.9+/-403.7	2026,1821,450	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	2140,2611,1747	TT,TC,CC		31.6616,23.1259,46.976	,	96/675,	63884027	6891,6105	2201	4297	6498	SO:0001627	intron_variant	23769	exon2			CAACGCCGGCATC	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34683G>A	11.37:g.63884027C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			C|0.521;T|0.479	0.479	strong		0.567	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
SVIL	6840	hgsc.bcm.edu	37	10	29839798	29839798	+	Silent	SNP	A	A	G	rs17834991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29839798A>G	ENST00000355867.4	-	6	1307	c.555T>C	c.(553-555)taT>taC	p.Y185Y	SVIL_ENST00000375398.2_Silent_p.Y185Y|SVIL_ENST00000375400.3_Silent_p.Y185Y	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	185					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.Y185Y(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CATGGAGGGCATAGTCCTTGG	0.572													A|||	791	0.157947	0.0348	0.2839	5008	,	,		18876	0.1637		0.2147	False		,,,				2504	0.1708				p.Y185Y		Atlas-SNP	.											SVIL,NS,carcinoma,0,1	SVIL	226	1	1	Substitution - coding silent(1)	stomach(1)	c.T555C						PASS	.	A	,	282,4124	157.0+/-190.0	10,262,1931	93.0	94.0	94.0		555,555	-0.5	0.0	10	dbSNP_123	94	1734,6866	315.8+/-312.4	180,1374,2746	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	190,1636,4677	GG,GA,AA		20.1628,6.4004,15.5005	,	185/1789,185/2215	29839798	2016,10990	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			GAGGGCATAGTCC	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.555T>C	10.37:g.29839798A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			A|0.839;G|0.161;T|0.000	0.161	strong		0.572	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
SPTLC3	55304	hgsc.bcm.edu	37	20	13071816	13071816	+	Silent	SNP	C	C	T	rs6109692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:13071816C>T	ENST00000399002.2	+	5	967	c.693C>T	c.(691-693)ttC>ttT	p.F231F	SPTLC3_ENST00000378194.4_Silent_p.F231F	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	231					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						GGATGGGATTCGCAACTAACT	0.413													C|||	371	0.0740815	0.0567	0.0836	5008	,	,		20998	0.0694		0.1054	False		,,,				2504	0.0634				p.F231F		Atlas-SNP	.											.	SPTLC3	78	.	0			c.C693T						PASS	.	C		250,3606		4,242,1682	140.0	140.0	140.0		693	0.8	1.0	20	dbSNP_114	140	888,7366		44,800,3283	no	coding-synonymous	SPTLC3	NM_018327.2		48,1042,4965	TT,TC,CC		10.7584,6.4834,9.3972		231/553	13071816	1138,10972	1928	4127	6055	SO:0001819	synonymous_variant	55304	exon5			GGGATTCGCAACT	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.693C>T	20.37:g.13071816C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	193	88	0.455959	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Silent	SNP	ENST00000399002.2	37	CCDS13115.2																																																																																			C|0.913;T|0.087	0.087	strong		0.413	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
MTMR4	9110	hgsc.bcm.edu	37	17	56585593	56585593	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56585593C>T	ENST00000323456.5	-	8	718	c.594G>A	c.(592-594)tgG>tgA	p.W198*	MTMR4_ENST00000579925.1_Nonsense_Mutation_p.W198*	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	198	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGTCAGTGATCCACACAGGAA	0.557																																					p.W198X		Atlas-SNP	.											.	MTMR4	91	.	0			c.G594A						PASS	.						79.0	74.0	75.0					17																	56585593		2203	4300	6503	SO:0001587	stop_gained	9110	exon8			AGTGATCCACACA	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.594G>A	17.37:g.56585593C>T	ENSP00000325285:p.Trp198*	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	4	0.0952381	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Nonsense_Mutation	SNP	ENST00000323456.5	37	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	C	36	5.881577	0.97062	.	.	ENSG00000108389	ENST00000323456	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8095	0.92053	0.0:1.0:0.0:0.0	.	.	.	.	X	198	.	ENSP00000325285:W198X	W	-	3	0	MTMR4	53940592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.942000	0.70203	2.775000	0.95449	0.650000	0.86243	TGG	.	.	none		0.557	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687	
GDF3	9573	hgsc.bcm.edu	37	12	7842932	7842932	+	Missense_Mutation	SNP	C	C	T	rs12819884	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7842932C>T	ENST00000329913.3	-	2	684	c.637G>A	c.(637-639)Ggg>Agg	p.G213R		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	213			G -> R (in dbSNP:rs12819884). {ECO:0000269|PubMed:15489334}.		endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)	p.G213R(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						AAATTCACCCCTGAGTCTCTA	0.493													C|||	1128	0.22524	0.1762	0.1671	5008	,	,		-128	0.1488		0.326	False		,,,				2504	0.3078				p.G213R		Atlas-SNP	.											GDF3,NS,adenoma,0,2	GDF3	68	2	1	Substitution - Missense(1)	stomach(1)	c.G637A						PASS	.	C	ARG/GLY	813,3593	322.9+/-297.8	84,645,1474	80.0	81.0	81.0		637	1.6	0.0	12	dbSNP_121	81	2656,5944	427.0+/-355.5	411,1834,2055	yes	missense	GDF3	NM_020634.1	125	495,2479,3529	TT,TC,CC		30.8837,18.4521,26.6723	benign	213/365	7842932	3469,9537	2203	4300	6503	SO:0001583	missense	9573	exon2			TCACCCCTGAGTC	AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"""Endogenous ligands"""	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.637G>A	12.37:g.7842932C>T	ENSP00000331745:p.Gly213Arg	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_020634	Q8NEJ4	Missense_Mutation	SNP	ENST00000329913.3	37	CCDS8581.1	541	0.24771062271062272	98	0.1991869918699187	75	0.20718232044198895	111	0.19405594405594406	257	0.3390501319261214	C	9.738	1.164021	0.21538	0.184521	0.308837	ENSG00000184344	ENST00000329913	T	0.64803	-0.12	4.61	1.64	0.23874	Transforming growth factor-beta, N-terminal (1);	1.057280	0.07259	N	0.867224	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.06786	0.001	B	0.12156	0.007	T	0.28459	-1.0043	9	0.13853	T	0.58	.	5.3922	0.16249	0.0:0.6309:0.1708:0.1983	rs12819884;rs17845938;rs17858918;rs52806074;rs12819884	213	Q9NR23	GDF3_HUMAN	R	213	ENSP00000331745:G213R	ENSP00000331745:G213R	G	-	1	0	GDF3	7734199	0.000000	0.05858	0.000000	0.03702	0.440000	0.31957	-0.091000	0.11146	0.471000	0.27319	-0.291000	0.09656	GGG	C|0.752;T|0.248	0.248	strong		0.493	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1		
TCTE1	202500	hgsc.bcm.edu	37	6	44268371	44268371	+	5'Flank	SNP	T	T	C	rs325008	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44268371T>C	ENST00000371505.4	-	0	0				TMEM151B_ENST00000438774.2_Intron|AARS2_ENST00000491573.1_5'UTR|TCTE1_ENST00000371503.3_5'Flank|AARS2_ENST00000244571.4_Silent_p.S957S|RP11-444E17.6_ENST00000505802.1_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1											breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCACCACTCGTGAGCCCCACG	0.627													C|||	4354	0.869409	0.5976	0.9496	5008	,	,		19229	0.998		0.9612	False		,,,				2504	0.953				p.S957S		Atlas-SNP	.											.	AARS2	77	.	0			c.A2871G						PASS	.	C		3022,1384	457.1+/-351.5	1045,932,226	83.0	71.0	75.0		2871	-8.7	0.0	6	dbSNP_79	75	8308,292	107.4+/-168.2	4010,288,2	no	coding-synonymous	AARS2	NM_020745.2		5055,1220,228	CC,CT,TT		3.3953,31.4117,12.8864		957/986	44268371	11330,1676	2203	4300	6503	SO:0001631	upstream_gene_variant	57505	exon22			CACTCGTGAGCCC	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763		6.37:g.44268371T>C	Exception_encountered	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_020745	B4DX59|Q8IYS6	Silent	SNP	ENST00000371505.4	37	CCDS4910.1																																																																																			T|0.130;C|0.870	0.870	strong		0.627	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
C11orf30	56946	hgsc.bcm.edu	37	11	76257215	76257215	+	Silent	SNP	T	T	C	rs3753051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76257215T>C	ENST00000529032.1	+	19	3648	c.3648T>C	c.(3646-3648)acT>acC	p.T1216T	C11orf30_ENST00000334736.3_Silent_p.T1216T|C11orf30_ENST00000524767.1_Silent_p.T1231T|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000525919.1_Silent_p.T1217T|C11orf30_ENST00000524490.1_Silent_p.T1118T|C11orf30_ENST00000525038.1_Silent_p.T1217T|C11orf30_ENST00000533248.1_Silent_p.T1125T			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	1216					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.T1216T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						GTCCATCCACTGTTGGCTCTT	0.512													T|||	1036	0.206869	0.1815	0.1729	5008	,	,		19992	0.1379		0.3131	False		,,,				2504	0.227				p.T1216T		Atlas-SNP	.											C11orf30,NS,carcinoma,0,1	C11orf30	123	1	1	Substitution - coding silent(1)	stomach(1)	c.T3648C						PASS	.	T		959,3441	361.9+/-315.9	108,743,1349	86.0	88.0	87.0		3648	4.9	1.0	11	dbSNP_107	87	2758,5826	439.0+/-359.1	454,1850,1988	no	coding-synonymous	C11orf30	NM_020193.3		562,2593,3337	CC,CT,TT		32.1295,21.7955,28.6275		1216/1323	76257215	3717,9267	2200	4292	6492	SO:0001819	synonymous_variant	56946	exon20			ATCCACTGTTGGC	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.3648T>C	11.37:g.76257215T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Silent	SNP	ENST00000529032.1	37	CCDS8244.1	466	0.21336996336996336	78	0.15853658536585366	68	0.1878453038674033	83	0.1451048951048951	237	0.31266490765171506	T	3.579	-0.086042	0.07097	0.217955	0.321295	ENSG00000158636	ENST00000531793	.	.	.	6.06	4.87	0.63330	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.39313	-0.9620	3	.	.	.	-2.2619	7.4136	0.27032	0.129:0.0687:0.0:0.8023	rs3753051;rs17749636;rs3753051	.	.	.	P	75	.	.	L	+	2	0	C11orf30	75934863	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	0.886000	0.28241	2.322000	0.78497	0.528000	0.53228	CTG	T|0.755;C|0.245	0.245	strong		0.512	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
GCNT1	2650	hgsc.bcm.edu	37	9	79118329	79118329	+	Silent	SNP	G	G	A	rs1057406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79118329G>A	ENST00000376730.4	+	4	1515	c.1032G>A	c.(1030-1032)ctG>ctA	p.L344L	GCNT1_ENST00000536223.1_Silent_p.L344L|GCNT1_ENST00000442371.1_Silent_p.L344L|GCNT1_ENST00000444201.2_Silent_p.L344L	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	344	Catalytic. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						AGTATGATCTGTCTGACATGC	0.547													G|||	1180	0.235623	0.239	0.2493	5008	,	,		20510	0.1974		0.2276	False		,,,				2504	0.2689				p.L344L		Atlas-SNP	.											.	GCNT1	52	.	0			c.G1032A						PASS	.	G	,,,,	972,3434	364.6+/-317.1	126,720,1357	84.0	78.0	80.0		1032,1032,1032,1032,1032	3.1	1.0	9	dbSNP_86	80	1849,6751	329.3+/-318.7	192,1465,2643	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	,,,,	318,2185,4000	AA,AG,GG		21.5,22.0608,21.69	,,,,	344/429,344/429,344/429,344/429,344/429	79118329	2821,10185	2203	4300	6503	SO:0001819	synonymous_variant	2650	exon4			TGATCTGTCTGAC	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.1032G>A	9.37:g.79118329G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	283	116	0.409894	NM_001490	Q6DJZ4	Silent	SNP	ENST00000376730.4	37	CCDS6653.1																																																																																			G|0.774;A|0.226	0.226	strong		0.547	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
CYP39A1	51302	hgsc.bcm.edu	37	6	46609905	46609905	+	Missense_Mutation	SNP	C	C	T	rs2277119	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46609905C>T	ENST00000275016.2	-	2	511	c.308G>A	c.(307-309)cGt>cAt	p.R103H		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	103			R -> H (in dbSNP:rs2277119).		bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						TTTACCTGTACGATAAACGAT	0.328													C|||	1291	0.257788	0.2436	0.1844	5008	,	,		18906	0.2183		0.2505	False		,,,				2504	0.3773				p.R103H		Atlas-SNP	.											.	CYP39A1	41	.	0			c.G308A						PASS	.	C	HIS/ARG	1071,3335	379.7+/-323.4	112,847,1244	65.0	67.0	67.0		308	-8.9	0.0	6	dbSNP_100	67	1960,6632	343.5+/-324.9	230,1500,2566	yes	missense	CYP39A1	NM_016593.3	29	342,2347,3810	TT,TC,CC		22.8119,24.3078,23.319	benign	103/470	46609905	3031,9967	2203	4296	6499	SO:0001583	missense	51302	exon2			CCTGTACGATAAA	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.308G>A	6.37:g.46609905C>T	ENSP00000275016:p.Arg103His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	494	0.2261904761904762	121	0.2459349593495935	64	0.17679558011049723	114	0.1993006993006993	195	0.25725593667546176	C	1.557	-0.537807	0.04082	0.243078	0.228119	ENSG00000146233	ENST00000275016	T	0.68624	-0.34	4.7	-8.93	0.00771	.	1.369710	0.04860	N	0.443911	T	0.15696	0.0378	N	0.01751	-0.74	0.80722	P	0.0	B;B	0.19445	0.036;0.001	B;B	0.10450	0.005;0.002	T	0.11717	-1.0576	9	0.10636	T	0.68	3.4561	19.749	0.96260	0.0:0.1868:0.0:0.8132	rs2277119;rs17216701;rs60948107;rs2277119	103;103	B7Z786;Q9NYL5	.;CP39A_HUMAN	H	103	ENSP00000275016:R103H	ENSP00000275016:R103H	R	-	2	0	CYP39A1	46717864	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.459000	0.06728	-2.709000	0.00395	-1.119000	0.02030	CGT	C|0.767;T|0.232	0.232	strong		0.328	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
TNK1	8711	hgsc.bcm.edu	37	17	7287992	7287992	+	Silent	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7287992C>A	ENST00000576812.1	+	7	1425	c.1056C>A	c.(1054-1056)ctC>ctA	p.L352L	TNK1_ENST00000311668.2_Silent_p.L352L|TNK1_ENST00000570896.1_Silent_p.L352L	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				CCAGGGCCCTCTACTCCCTCG	0.711																																					p.L352L		Atlas-SNP	.											.	TNK1	31	.	0			c.C1056A						PASS	.						16.0	20.0	19.0					17																	7287992		1951	4129	6080	SO:0001819	synonymous_variant	8711	exon7			GGCCCTCTACTCC	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.1056C>A	17.37:g.7287992C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_003985		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			.	.	none		0.711	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	
RB1CC1	9821	hgsc.bcm.edu	37	8	53586706	53586706	+	Missense_Mutation	SNP	A	A	G	rs17337252	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:53586706A>G	ENST00000025008.5	-	7	1224	c.701T>C	c.(700-702)aTg>aCg	p.M234T	RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Missense_Mutation_p.M234T|RB1CC1_ENST00000435644.2_Missense_Mutation_p.M234T	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	234			M -> T (in dbSNP:rs17337252). {ECO:0000269|PubMed:11850849, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9039502}.		autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				GGATCTTTTCATCTCAGCTTT	0.423													A|||	2519	0.502995	0.2088	0.6095	5008	,	,		19241	0.8393		0.5	False		,,,				2504	0.4816				p.M234T	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.T701C	GRCh37	CM063091	RB1CC1	M	rs17337252	PASS	.	A	THR/MET,THR/MET	1122,3284	402.4+/-332.3	143,836,1224	246.0	232.0	237.0		701,701	3.0	0.9	8	dbSNP_123	237	4211,4389	570.8+/-389.4	1034,2143,1123	yes	missense,missense	RB1CC1	NM_001083617.1,NM_014781.4	81,81	1177,2979,2347	GG,GA,AA		48.9651,25.4653,41.0042	benign,benign	234/1592,234/1595	53586706	5333,7673	2203	4300	6503	SO:0001583	missense	9821	exon7			CTTTTCATCTCAG	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.701T>C	8.37:g.53586706A>G	ENSP00000025008:p.Met234Thr	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	221	109	0.493213	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	1195	0.5471611721611722	112	0.22764227642276422	214	0.5911602209944752	481	0.8409090909090909	388	0.5118733509234829	A	9.138	1.013096	0.19277	0.254653	0.489651	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.12984	2.63;2.63;2.63	5.36	2.99	0.34606	.	0.681941	0.14591	N	0.310238	T	0.00012	0.0000	N	0.02011	-0.69	0.39175	P	0.037321999999999966	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18272	-1.0342	9	0.10902	T	0.67	-2.1882	3.6785	0.08301	0.5558:0.0:0.1717:0.2725	rs17337252;rs17851535;rs58549444;rs17337252	234;234	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	T	234	ENSP00000025008:M234T;ENSP00000396067:M234T;ENSP00000445960:M234T	ENSP00000025008:M234T	M	-	2	0	RB1CC1	53749259	0.485000	0.25972	0.893000	0.35052	0.803000	0.45373	2.354000	0.44098	0.976000	0.38417	0.383000	0.25322	ATG	A|0.533;G|0.467	0.467	strong		0.423	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
C5orf60	285679	hgsc.bcm.edu	37	5	179071892	179071892	+	Missense_Mutation	SNP	C	C	T	rs4990389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:179071892C>T	ENST00000448248.2	-	1	155	c.130G>A	c.(130-132)Gtt>Att	p.V44I	C5orf60_ENST00000506142.1_Intron	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	44						integral component of membrane (GO:0016021)		p.V44I(2)		NS(1)|breast(1)|kidney(5)	7						CTGAACACAACAAAGAGGACG	0.517													-|||	83	0.0165735	0.0575	0.0058	5008	,	,		23834	0.0		0.002	False		,,,				2504	0.001				p.V44I		Atlas-SNP	.											C5orf60,NS,carcinoma,0,2	C5orf60	24	2	2	Substitution - Missense(2)	kidney(2)	c.G130A						scavenged	.						91.0	85.0	87.0					5																	179071892		692	1591	2283	SO:0001583	missense	285679	exon1			ACACAACAAAGAG	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.130G>A	5.37:g.179071892C>T	ENSP00000404583:p.Val44Ile	Somatic	194	4	0.0206186		WXS	Illumina HiSeq	Phase_I	219	8	0.0365297	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	14	0.00641025641025641	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	N	0.001	-2.963530	0.00049	.	.	ENSG00000204661	ENST00000448248	T	0.23552	1.9	0.526	-1.05	0.10036	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27262	-1.0079	8	0.10902	T	0.67	.	.	.	.	rs4990389;rs7731272	44;44	A6NFR6-2;A6NFR6-4	.;.	I	44	ENSP00000404583:V44I	ENSP00000404583:V44I	V	-	1	0	C5orf60	179004498	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.627000	0.02033	-2.544000	0.00483	-2.140000	0.00339	GTT	C|0.994;T|0.006	0.006	strong		0.517	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
OR4D2	124538	hgsc.bcm.edu	37	17	56247101	56247101	+	Missense_Mutation	SNP	C	C	A	rs60994383	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56247101C>A	ENST00000545221.1	+	1	85	c.85C>A	c.(85-87)Cta>Ata	p.L29I		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	29			L -> I (in dbSNP:rs60994383).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						TTTCCTGTTTCTAATGTTCCT	0.483													C|||	1178	0.235224	0.3775	0.1599	5008	,	,		20152	0.1657		0.2147	False		,,,				2504	0.1892				p.L29I		Atlas-SNP	.											.	OR4D2	48	.	0			c.C85A						PASS	.	C	ILE/LEU	1567,2839	490.4+/-361.8	275,1017,911	159.0	141.0	147.0		85	-5.0	0.9	17	dbSNP_129	147	1963,6637	346.7+/-326.3	234,1495,2571	yes	missense	OR4D2	NM_001004707.3	5	509,2512,3482	AA,AC,CC		22.8256,35.5651,27.1413	benign	29/308	56247101	3530,9476	2203	4300	6503	SO:0001583	missense	124538	exon1			CTGTTTCTAATGT		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"""GPCR / Class A : Olfactory receptors"""	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.85C>A	17.37:g.56247101C>A	ENSP00000441354:p.Leu29Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	179	83	0.463687	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	37	CCDS32688.1	498	0.22802197802197802	178	0.3617886178861789	66	0.18232044198895028	90	0.15734265734265734	164	0.21635883905013192	C	4.031	0.003271	0.07866	0.355651	0.228256	ENSG00000255713	ENST00000545221	T	0.00272	8.36	5.4	-5.02	0.02982	.	0.596543	0.13642	N	0.372932	T	0.00012	0.0000	L	0.28014	0.82	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.31475	-0.9942	9	0.42905	T	0.14	-0.2109	2.2874	0.04130	0.2069:0.334:0.3064:0.1527	rs60994383;rs62083702	29	P58180	OR4D2_HUMAN	I	29	ENSP00000441354:L29I	ENSP00000441354:L29I	L	+	1	2	OR4D2	53602100	0.000000	0.05858	0.947000	0.38551	0.016000	0.09150	-2.547000	0.00931	-0.561000	0.06094	-1.610000	0.00802	CTA	C|0.745;A|0.255	0.255	strong		0.483	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1		
SH3D21	79729	hgsc.bcm.edu	37	1	36773405	36773405	+	Silent	SNP	T	T	G	rs35343437	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36773405T>G	ENST00000426732.2	+	5	408	c.123T>G	c.(121-123)ccT>ccG	p.P41P	SH3D21_ENST00000453908.2_Silent_p.P157P|SH3D21_ENST00000505871.1_Silent_p.P46P|SH3D21_ENST00000312808.4_5'UTR			A4FU49	SH321_HUMAN	SH3 domain containing 21	41						extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						CAGTCAGCCCTGGTCCCCAGC	0.582													T|||	2109	0.421126	0.1241	0.562	5008	,	,		19550	0.7192		0.4443	False		,,,				2504	0.3916				p.P157P		Atlas-SNP	.											.	SH3D21	73	.	0			c.T471G						PASS	.	T	,	257,1127		20,217,455	89.0	78.0	81.0		471,138	-2.8	0.0	1	dbSNP_126	81	1567,1615		371,825,395	no	coding-synonymous,coding-synonymous	SH3D21	NM_001162530.1,NM_024676.4	,	391,1042,850	GG,GT,TT		49.2458,18.5694,39.9474	,	157/757,46/646	36773405	1824,2742	692	1591	2283	SO:0001819	synonymous_variant	79729	exon6			CAGCCCTGGTCCC	AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 113"""	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.123T>G	1.37:g.36773405T>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	170	66	0.388235	NM_001162530	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Silent	SNP	ENST00000426732.2	37																																																																																				T|0.555;G|0.445	0.445	strong		0.582	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676	
CEP350	9857	hgsc.bcm.edu	37	1	179989584	179989584	+	Missense_Mutation	SNP	G	G	C	rs6692219	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:179989584G>C	ENST00000367607.3	+	12	3093	c.2675G>C	c.(2674-2676)aGa>aCa	p.R892T		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	892			R -> T (in dbSNP:rs6692219).		microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TTCTCTGCCAGAATTCAGAAG	0.428													G|||	238	0.047524	0.0484	0.0187	5008	,	,		22095	0.0526		0.0348	False		,,,				2504	0.0746				p.R892T		Atlas-SNP	.											.	CEP350	418	.	0			c.G2675C						PASS	.	G	THR/ARG	205,4201	128.2+/-165.1	2,201,2000	101.0	99.0	100.0		2675	6.0	1.0	1	dbSNP_116	100	297,8303	109.0+/-169.6	6,285,4009	yes	missense	CEP350	NM_014810.4	71	8,486,6009	CC,CG,GG		3.4535,4.6527,3.8598	probably-damaging	892/3118	179989584	502,12504	2203	4300	6503	SO:0001583	missense	9857	exon12			CTGCCAGAATTCA	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.2675G>C	1.37:g.179989584G>C	ENSP00000356579:p.Arg892Thr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	122	41	0.336066	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	88	0.040293040293040296	24	0.04878048780487805	10	0.027624309392265192	26	0.045454545454545456	28	0.036939313984168866	G	17.43	3.388508	0.61956	0.046527	0.034535	ENSG00000135837	ENST00000367607	T	0.24908	1.83	6.02	6.02	0.97574	.	0.000000	0.43110	D	0.000603	T	0.08980	0.0222	L	0.34521	1.04	0.44816	D	0.997825	D;D	0.76494	0.999;0.969	D;P	0.63488	0.915;0.603	T	0.00104	-1.2058	9	.	.	.	.	20.1358	0.98028	0.0:0.0:1.0:0.0	rs6692219;rs52804555;rs6692219	892;892	E7EU22;Q5VT06	.;CE350_HUMAN	T	892	ENSP00000356579:R892T	.	R	+	2	0	CEP350	178256207	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.337000	0.79256	2.865000	0.98341	0.655000	0.94253	AGA	G|0.963;C|0.037	0.037	strong		0.428	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
GRB14	2888	hgsc.bcm.edu	37	2	165476253	165476253	+	Missense_Mutation	SNP	A	A	T	rs61748245	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:165476253A>T	ENST00000263915.3	-	2	806	c.268T>A	c.(268-270)Ttt>Att	p.F90I		NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	90			F -> I (in dbSNP:rs61748245). {ECO:0000269|PubMed:21220648, ECO:0000269|PubMed:8647858}.		blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						ACAGATGTAAATGGAGAACAG	0.348													A|||	2219	0.443091	0.1838	0.7392	5008	,	,		14271	0.3571		0.6769	False		,,,				2504	0.4315				p.F90I		Atlas-SNP	.											GRB14,trunk,malignant_melanoma,+1,1	GRB14	73	1	0			c.T268A						PASS	.	A	ILE/PHE	1177,3229	412.6+/-336.2	166,845,1192	141.0	142.0	142.0		268	4.3	1.0	2	dbSNP_129	142	5636,2964	666.6+/-402.4	1883,1870,547	yes	missense	GRB14	NM_004490.2	21	2049,2715,1739	TT,TA,AA		34.4651,26.7136,47.6165	benign	90/541	165476253	6813,6193	2203	4300	6503	SO:0001583	missense	2888	exon2			ATGTAAATGGAGA		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.268T>A	2.37:g.165476253A>T	ENSP00000263915:p.Phe90Ile	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	242	241	0.995868	NM_004490	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	37	CCDS2222.1	1083	0.4958791208791209	109	0.22154471544715448	253	0.6988950276243094	208	0.36363636363636365	513	0.6767810026385225	A	11.79	1.743698	0.30865	0.267136	0.655349	ENSG00000115290	ENST00000263915;ENST00000446413;ENST00000424693	T;T;T	0.41400	2.02;1.61;1.0	5.45	4.3	0.51218	.	0.195453	0.36932	N	0.002332	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.999999999999769	B	0.17465	0.022	B	0.19946	0.027	T	0.33929	-0.9849	9	0.20519	T	0.43	-2.7772	8.9411	0.35731	0.9131:0.0:0.0869:0.0	rs61748245	90	Q14449	GRB14_HUMAN	I	90;45;32	ENSP00000263915:F90I;ENSP00000416786:F45I;ENSP00000401702:F32I	ENSP00000263915:F90I	F	-	1	0	GRB14	165184499	0.975000	0.34042	1.000000	0.80357	0.999000	0.98932	1.690000	0.37711	0.913000	0.36797	0.533000	0.62120	TTT	A|0.485;T|0.515	0.515	strong		0.348	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2		
ZNF236	7776	hgsc.bcm.edu	37	18	74680259	74680259	+	Silent	SNP	C	C	T	rs657066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:74680259C>T	ENST00000253159.8	+	31	5700	c.5502C>T	c.(5500-5502)gcC>gcT	p.A1834A	ZNF236_ENST00000320610.9_Silent_p.A1836A	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1834					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		TGCAGGAGGCCGCCGGCGAGT	0.582													c|||	4468	0.892173	0.6778	0.9424	5008	,	,		16023	0.9772		0.9672	False		,,,				2504	0.9816				p.A1834A		Atlas-SNP	.											.	ZNF236	325	.	0			c.C5502T						PASS	.	T		2908,1084		1082,744,170	68.0	81.0	77.0		5502	-9.8	0.0	18	dbSNP_83	77	8132,208		3963,206,1	no	coding-synonymous	ZNF236	NM_007345.3		5045,950,171	TT,TC,CC		2.494,27.1543,10.4768		1834/1846	74680259	11040,1292	1996	4170	6166	SO:0001819	synonymous_variant	7776	exon31			GGAGGCCGCCGGC	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.5502C>T	18.37:g.74680259C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	26	0.351351	NM_007345	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	CCDS42447.1																																																																																			C|0.073;T|0.927	0.927	strong		0.582	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
TRABD2B	388630	hgsc.bcm.edu	37	1	48459907	48459907	+	Silent	SNP	C	C	T	rs3814006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:48459907C>T	ENST00000606738.2	-	2	570	c.465G>A	c.(463-465)gcG>gcA	p.A155A	TRABD2B_ENST00000435576.2_5'Flank	NM_001194986.1	NP_001181915.1	A6NFA1	TIKI2_HUMAN	TraB domain containing 2B	155					metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										CCCAGTTGCCCGCGATGGCAT	0.612													C|||	830	0.165735	0.0144	0.2233	5008	,	,		19246	0.253		0.2793	False		,,,				2504	0.1227				p.A155A		Atlas-SNP	.											RP11-543D5.3,NS,carcinoma,0,1	.	.	1	0			c.G465A						PASS	.																																			SO:0001819	synonymous_variant	388630	exon2			GTTGCCCGCGATG		CCDS58000.1	1p33	2012-07-04			ENSG00000204018				44200	protein-coding gene	gene with protein product		614913					Standard	NM_001194986		Approved		uc021ong.1	A6NFA1	OTTHUMG00000007960	ENST00000606738.2:c.465G>A	1.37:g.48459907C>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_001194986	I6U4Y0	Silent	SNP	ENST00000606738.2	37	CCDS58000.1																																																																																			C|0.817;T|0.183	0.183	strong		0.612	TRABD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021842.3	NM_001194986	
CSN1S1	1446	hgsc.bcm.edu	37	4	70807771	70807771	+	Missense_Mutation	SNP	C	C	T	rs10030475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70807771C>T	ENST00000246891.4	+	13	399	c.350C>T	c.(349-351)gCc>gTc	p.A117V	CSN1S1_ENST00000507772.1_Missense_Mutation_p.A109V|CSN1S1_ENST00000444405.3_Missense_Mutation_p.A108V|CSN1S1_ENST00000505782.1_Missense_Mutation_p.A101V|CSN1S1_ENST00000507763.1_Missense_Mutation_p.A108V	NM_001890.1	NP_001881.1	P47710	CASA1_HUMAN	casein alpha s1	117			A -> V (in dbSNP:rs10030475). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)|extracellular space (GO:0005615)	transporter activity (GO:0005215)			lung(5)|prostate(1)|upper_aerodigestive_tract(1)	7						TAGCAAGCTGCCCATGCCCAG	0.294													T|||	1885	0.376398	0.3018	0.4568	5008	,	,		14991	0.2887		0.4085	False		,,,				2504	0.4775				p.A117V		Atlas-SNP	.											.	CSN1S1	20	.	0			c.C350T						PASS	.	T	VAL/ALA,VAL/ALA	1107,2457		211,685,886	23.0	22.0	23.0		323,350	-4.5	0.0	4	dbSNP_119	23	3160,4868		699,1762,1553	yes	missense,missense	CSN1S1	NM_001025104.1,NM_001890.1	64,64	910,2447,2439	TT,TC,CC		39.3622,31.0606,36.8099	benign,benign	108/177,117/186	70807771	4267,7325	1782	4014	5796	SO:0001583	missense	1446	exon13			AAGCTGCCCATGC	X78416	CCDS47067.1, CCDS54769.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000126545	ENSG00000126545			2445	protein-coding gene	gene with protein product		115450	"""casein, alpha"""	CASA, CSN1		9050925, 7619062	Standard	NM_001890		Approved		uc003hep.1	P47710	OTTHUMG00000160843	ENST00000246891.4:c.350C>T	4.37:g.70807771C>T	ENSP00000246891:p.Ala117Val	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	282	277	0.98227	NM_001890	A1A510|A1A511|E9PB60|Q4PNR5	Missense_Mutation	SNP	ENST00000246891.4	37	CCDS47067.1	755	0.3456959706959707	141	0.2865853658536585	155	0.4281767955801105	143	0.25	316	0.41688654353562005	T	0.289	-0.981317	0.02197	0.310606	0.393622	ENSG00000126545	ENST00000246891;ENST00000444405;ENST00000507763;ENST00000507772;ENST00000505782	T;T;T;T;T	0.42131	1.05;0.98;0.98;0.98;0.99	4.61	-4.5	0.03493	.	.	.	.	.	T	0.00012	0.0000	N	0.11927	0.2	0.20489	P	0.9999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35425	-0.9789	8	0.02654	T	1	.	7.9829	0.30194	0.1153:0.4677:0.0:0.4171	rs10030475;rs52817786;rs58475257;rs10030475	109;108;117	E9PDQ1;E9PB60;P47710	.;.;CASA1_HUMAN	V	117;108;108;109;101	ENSP00000246891:A117V;ENSP00000413157:A108V;ENSP00000422611:A108V;ENSP00000427490:A109V;ENSP00000426684:A101V	ENSP00000246891:A117V	A	+	2	0	CSN1S1	70842360	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.097000	0.03349	-1.313000	0.02303	-3.067000	0.00067	GCC	C|0.659;T|0.341	0.341	strong		0.294	CSN1S1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362629.1		
TRIML1	339976	hgsc.bcm.edu	37	4	189061106	189061106	+	Missense_Mutation	SNP	G	G	A	rs13131525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:189061106G>A	ENST00000332517.3	+	1	534	c.394G>A	c.(394-396)Gag>Aag	p.E132K	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	132			E -> K (in dbSNP:rs13131525).		multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		CAGCGAGGCTGAGGAGCATCA	0.582													G|||	1280	0.255591	0.1157	0.4942	5008	,	,		19109	0.0655		0.4672	False		,,,				2504	0.2536				p.E132K	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.G394A						PASS	.	G	LYS/GLU	785,3621	296.4+/-284.2	64,657,1482	45.0	42.0	43.0		394	4.8	1.0	4	dbSNP_121	43	4305,4295	549.9+/-385.6	1094,2117,1089	yes	missense	TRIML1	NM_178556.3	56	1158,2774,2571	AA,AG,GG		49.9419,17.8166,39.1358	benign	132/469	189061106	5090,7916	2203	4300	6503	SO:0001583	missense	339976	exon1			GAGGCTGAGGAGC	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.394G>A	4.37:g.189061106G>A	ENSP00000327738:p.Glu132Lys	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	308	308	1	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	635	0.2907509157509158	55	0.11178861788617886	176	0.4861878453038674	50	0.08741258741258741	354	0.46701846965699206	G	13.27	2.187911	0.38609	0.178166	0.500581	ENSG00000184108	ENST00000332517	T	0.61980	0.06	4.85	4.85	0.62838	.	0.325925	0.24472	N	0.038231	T	0.00012	0.0000	L	0.57536	1.79	0.26359	P	0.9770894999999999	D	0.61697	0.99	P	0.60068	0.868	T	0.49072	-0.8977	9	0.72032	D	0.01	-29.3586	14.1946	0.65662	0.0:0.0:1.0:0.0	rs13131525;rs60211754;rs13131525	132	Q8N9V2	TRIML_HUMAN	K	132	ENSP00000327738:E132K	ENSP00000327738:E132K	E	+	1	0	TRIML1	189298100	0.298000	0.24417	1.000000	0.80357	0.256000	0.26092	2.607000	0.46300	2.625000	0.88918	0.561000	0.74099	GAG	G|0.670;A|0.330	0.330	strong		0.582	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556	
PELI1	57162	hgsc.bcm.edu	37	2	64335394	64335394	+	Silent	SNP	A	A	G	rs17753351	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:64335394A>G	ENST00000358912.4	-	2	493	c.51T>C	c.(49-51)taT>taC	p.Y17Y	PELI1_ENST00000466177.2_5'UTR	NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	17					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						TGAGTTCACCATATTTTACTG	0.373													A|||	96	0.0191693	0.0015	0.0231	5008	,	,		18324	0.0		0.0517	False		,,,				2504	0.0266				p.Y17Y		Atlas-SNP	.											.	PELI1	34	.	0			c.T51C						PASS	.	A		37,4369	40.8+/-73.8	0,37,2166	194.0	181.0	185.0		51	4.3	1.0	2	dbSNP_123	185	410,8190	129.2+/-187.3	8,394,3898	no	coding-synonymous	PELI1	NM_020651.3		8,431,6064	GG,GA,AA		4.7674,0.8398,3.4369		17/419	64335394	447,12559	2203	4300	6503	SO:0001819	synonymous_variant	57162	exon2			TTCACCATATTTT		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"""Pellino homologs"""	8827	protein-coding gene	gene with protein product		614797	"""pellino (Drosophila) homolog 1"", ""pellino homolog 1 (Drosophila)"""			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.51T>C	2.37:g.64335394A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_020651	Q96SM0|Q9GZY5|Q9HCX0	Silent	SNP	ENST00000358912.4	37	CCDS1876.1																																																																																			A|0.965;G|0.035	0.035	strong		0.373	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651	
GIMAP6	474344	hgsc.bcm.edu	37	7	150325175	150325175	+	Missense_Mutation	SNP	C	C	T	rs13234724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150325175C>T	ENST00000328902.5	-	3	727	c.511G>A	c.(511-513)Ggc>Agc	p.G171S	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	171	AIG1-type G.		G -> S (in dbSNP:rs13234724). {ECO:0000269|PubMed:14702039}.			cytosol (GO:0005829)	GTP binding (GO:0005525)	p.G171S(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCCAGGGAGCCGCCAGCCAGG	0.612													C|||	900	0.179712	0.0651	0.3141	5008	,	,		16739	0.1944		0.1948	False		,,,				2504	0.2086				p.G241S		Atlas-SNP	.											GIMAP6,NS,carcinoma,+2,2	GIMAP6	60	2	1	Substitution - Missense(1)	lung(1)	c.G721A						PASS	.	C	SER/GLY	382,4024	192.6+/-218.0	17,348,1838	109.0	111.0	110.0		511	3.4	0.0	7	dbSNP_121	110	1755,6845	316.2+/-312.6	188,1379,2733	yes	missense	GIMAP6	NM_024711.5	56	205,1727,4571	TT,TC,CC		20.407,8.67,16.4309	possibly-damaging	171/293	150325175	2137,10869	2203	4300	6503	SO:0001583	missense	474344	exon3			GGGAGCCGCCAGC	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"""GTPases, IMAP"""	21918	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 6"""					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.511G>A	7.37:g.150325175C>T	ENSP00000330374:p.Gly171Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	371	0.16987179487179488	36	0.07317073170731707	84	0.23204419889502761	94	0.16433566433566432	157	0.20712401055408972	C	16.63	3.175495	0.57692	0.0867	0.20407	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.05319	3.46	4.29	3.39	0.38822	AIG1 (1);	1.131570	0.06429	N	0.723757	T	0.00012	0.0000	L	0.43554	1.36	0.47905	P	4.5600000000001195E-4	P;D	0.54964	0.704;0.969	B;B	0.41088	0.218;0.347	T	0.41520	-0.9504	9	0.13108	T	0.6	.	10.0873	0.42425	0.0:0.7967:0.2033:0.0	rs13234724;rs52799454;rs60245186;rs13234724	171;91	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	S	171;232	ENSP00000330374:G171S	ENSP00000330374:G171S	G	-	1	0	GIMAP6	149956108	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.478000	0.22212	1.008000	0.39264	0.561000	0.74099	GGC	C|0.832;G|0.000;T|0.168	0.168	strong		0.612	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711	
SCO2	9997	hgsc.bcm.edu	37	22	50962259	50962259	+	Silent	SNP	G	G	A	rs131811	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50962259G>A	ENST00000543927.1	-	2	788	c.582C>T	c.(580-582)tcC>tcT	p.S194S	SCO2_ENST00000535425.1_Silent_p.S194S|SCO2_ENST00000395693.3_Silent_p.S194S|CTA-384D8.36_ENST00000608319.1_RNA|SCO2_ENST00000252785.3_Silent_p.S194S	NM_001169109.1	NP_001162580.1	O43819	SCO2_HUMAN	SCO2 cytochrome c oxidase assembly protein	194	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|eye development (GO:0001654)|in utero embryonic development (GO:0001701)|muscle system process (GO:0003012)|oxidation-reduction process (GO:0055114)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			endometrium(1)|lung(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCTGTTTGGTGGAGCCGGTCA	0.587													G|||	129	0.0257588	0.003	0.0533	5008	,	,		19707	0.001		0.0815	False		,,,				2504	0.0051				p.S194S		Atlas-SNP	.											.	SCO2	38	.	0			c.C582T						PASS	.	G	,,,,,	72,4334	65.3+/-102.7	0,72,2131	119.0	104.0	109.0		582,582,582,,582,	-7.8	0.0	22	dbSNP_78	109	604,7996	159.4+/-212.7	22,560,3718	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous,utr-3	SCO2,NCAPH2	NM_001169109.1,NM_001169110.1,NM_001169111.1,NM_001185011.1,NM_005138.2,NM_152299.3	,,,,,	22,632,5849	AA,AG,GG		7.0233,1.6341,5.1976	,,,,,	194/267,194/267,194/267,,194/267,	50962259	676,12330	2203	4300	6503	SO:0001819	synonymous_variant	9997	exon2			TTTGGTGGAGCCG	AL021683	CCDS14095.1	22q13.33	2014-01-30	2012-10-15		ENSG00000130489	ENSG00000130489		"""Mitochondrial respiratory chain complex assembly factors"""	10604	protein-coding gene	gene with protein product		604272	"""SCO (cytochrome oxidase deficient, yeast) homolog 2"", ""SCO cytochrome oxidase deficient homolog 2 (yeast)"", ""myopia 6"""	MYP6		10218584, 16091356, 23643385	Standard	NM_005138		Approved	SCO1L	uc003bma.3	O43819	OTTHUMG00000150251	ENST00000543927.1:c.582C>T	22.37:g.50962259G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	93	60	0.645161	NM_001169111	Q3T1B5|Q9UK87	Silent	SNP	ENST00000543927.1	37	CCDS14095.1																																																																																			G|0.958;A|0.042	0.042	strong		0.587	SCO2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317091.1	NM_005138	
CAPN7	23473	hgsc.bcm.edu	37	3	15259992	15259992	+	Missense_Mutation	SNP	G	G	A	rs35247476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:15259992G>A	ENST00000253693.2	+	4	635	c.382G>A	c.(382-384)Gct>Act	p.A128T		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	128					positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						TTATGAAACTGCTGATAAAGT	0.343													G|||	156	0.0311502	0.0008	0.0461	5008	,	,		18876	0.0159		0.0736	False		,,,				2504	0.0337				p.A128T		Atlas-SNP	.											.	CAPN7	63	.	0			c.G382A						PASS	.	G	THR/ALA	60,4346	57.4+/-93.9	1,58,2144	112.0	115.0	114.0		382	5.2	1.0	3	dbSNP_126	114	550,8050	151.8+/-206.5	21,508,3771	yes	missense	CAPN7	NM_014296.2	58	22,566,5915	AA,AG,GG		6.3953,1.3618,4.6901	benign	128/814	15259992	610,12396	2203	4300	6503	SO:0001583	missense	23473	exon4			GAAACTGCTGATA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"""calpain like protease"", ""homolog of Aspergillus Nidulans PALB"""	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.382G>A	3.37:g.15259992G>A	ENSP00000253693:p.Ala128Thr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_014296		Missense_Mutation	SNP	ENST00000253693.2	37	CCDS2624.1	87	0.03983516483516483	0	0.0	21	0.058011049723756904	10	0.017482517482517484	56	0.07387862796833773	G	14.38	2.517035	0.44763	0.013618	0.063953	ENSG00000131375	ENST00000253693	T	0.69435	-0.4	6.17	5.23	0.72850	MIT (2);	0.537430	0.20175	N	0.097659	T	0.03827	0.0108	N	0.02011	-0.69	0.36115	P	0.15490499999999996	B	0.12013	0.005	B	0.14578	0.011	T	0.16660	-1.0395	9	0.17832	T	0.49	-21.0893	14.1249	0.65213	0.0:0.0:0.7858:0.2142	rs35247476	128	Q9Y6W3	CAN7_HUMAN	T	128	ENSP00000253693:A128T	ENSP00000253693:A128T	A	+	1	0	CAPN7	15234996	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.339000	0.52135	2.941000	0.99782	0.655000	0.94253	GCT	G|0.954;A|0.046	0.046	strong		0.343	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296	
LAMA5	3911	hgsc.bcm.edu	37	20	60921643	60921643	+	Missense_Mutation	SNP	T	T	C	rs4925229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60921643T>C	ENST00000252999.3	-	9	1267	c.1201A>G	c.(1201-1203)Acc>Gcc	p.T401A	LAMA5_ENST00000370692.3_Missense_Mutation_p.T401A|LAMA5_ENST00000370677.3_Missense_Mutation_p.T401A	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	401	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.		T -> A (in dbSNP:rs4925229). {ECO:0000269|PubMed:11821406}.		angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TTGACGCCGGTGGTGTGGTGC	0.687													T|||	4304	0.859425	0.6142	0.853	5008	,	,		16028	0.9613		0.9771	False		,,,				2504	0.9693				p.T401A		Atlas-SNP	.											.	LAMA5	268	.	0			c.A1201G						PASS	.	T	ALA/THR	3005,1363		1026,953,205	62.0	71.0	68.0		1201	4.6	1.0	20	dbSNP_111	68	8375,201		4094,187,7	yes	missense	LAMA5	NM_005560.3	58	5120,1140,212	CC,CT,TT		2.3438,31.2042,12.0828	possibly-damaging	401/3696	60921643	11380,1564	2184	4288	6472	SO:0001583	missense	3911	exon9			CGCCGGTGGTGTG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.1201A>G	20.37:g.60921643T>C	ENSP00000252999:p.Thr401Ala	Somatic	320	1	0.003125		WXS	Illumina HiSeq	Phase_I	253	253	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	1919	0.8786630036630036	316	0.6422764227642277	308	0.850828729281768	554	0.9685314685314685	741	0.9775725593667546	T	6.423	0.446120	0.12164	0.687958	0.976562	ENSG00000130702	ENST00000252999;ENST00000370692;ENST00000370677	T;T;T	0.60797	0.16;0.16;0.16	4.63	4.63	0.57726	EGF-like, laminin (4);	0.163601	0.53938	D	0.000046	T	0.00012	0.0000	L	0.31065	0.9	0.28501	P	0.9140366	B	0.33171	0.4	B	0.30251	0.113	T	0.42783	-0.9431	9	0.21540	T	0.41	.	7.1385	0.25541	0.0:0.1731:0.0:0.8269	rs4925229;rs60371886;rs4925229	401	O15230	LAMA5_HUMAN	A	401	ENSP00000252999:T401A;ENSP00000359726:T401A;ENSP00000359711:T401A	ENSP00000252999:T401A	T	-	1	0	LAMA5	60355038	0.765000	0.28485	0.996000	0.52242	0.201000	0.24016	1.064000	0.30579	1.719000	0.51432	0.459000	0.35465	ACC	T|0.137;C|0.863	0.863	strong		0.687	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SLC22A25	387601	hgsc.bcm.edu	37	11	62984868	62984868	+	Missense_Mutation	SNP	T	T	C	rs11231409	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62984868T>C	ENST00000306494.6	-	4	747	c.748A>G	c.(748-750)Agc>Ggc	p.S250G	SLC22A25_ENST00000403374.2_Missense_Mutation_p.S84G|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						AAAGCCAGGCTTCCCAGGGTT	0.443													C|||	2145	0.428315	0.2859	0.451	5008	,	,		21477	0.5288		0.3966	False		,,,				2504	0.5337				p.S250G		Atlas-SNP	.											.	SLC22A25	87	.	0			c.A748G						PASS	.	C	GLY/SER	1399,3003	687.4+/-404.8	208,983,1010	138.0	127.0	131.0		748	0.3	0.0	11	dbSNP_120	131	3259,5337	648.8+/-400.5	642,1975,1681	yes	missense	SLC22A25	NM_199352.3	56	850,2958,2691	CC,CT,TT		37.913,31.781,35.8363	benign	250/548	62984868	4658,8340	2201	4298	6499	SO:0001583	missense	387601	exon4			CCAGGCTTCCCAG	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.748A>G	11.37:g.62984868T>C	ENSP00000307443:p.Ser250Gly	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	894	0.40934065934065933	135	0.27439024390243905	136	0.3756906077348066	333	0.5821678321678322	290	0.38258575197889183	C	0.015	-1.546617	0.00926	0.31781	0.37913	ENSG00000196600	ENST00000306494;ENST00000403374	T;T	0.58060	0.44;0.36	3.49	0.346	0.16017	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.787064	0.10545	N	0.662245	T	0.00012	0.0000	N	0.00019	-2.785	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.002	T	0.45338	-0.9268	9	0.02654	T	1	.	6.9208	0.24387	0.0:0.5361:0.0:0.4639	rs11231409;rs52819103;rs60604366;rs11231409	248;250	A4IF29;Q6T423	.;S22AP_HUMAN	G	250;84	ENSP00000307443:S250G;ENSP00000384208:S84G	ENSP00000307443:S250G	S	-	1	0	SLC22A25	62741444	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.206000	0.17375	-0.224000	0.09928	-0.270000	0.10280	AGC	T|0.610;C|0.390	0.390	strong		0.443	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
PGM5	5239	hgsc.bcm.edu	37	9	70999315	70999315	+	Splice_Site	SNP	T	T	C	rs17081271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:70999315T>C	ENST00000396396.1	+	3	655	c.426T>C	c.(424-426)ggT>ggC	p.G142G	PGM5_ENST00000396392.1_Splice_Site_p.G142G|PGM5_ENST00000604870.2_3'UTR	NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN	phosphoglucomutase 5	142					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)	cell-cell adherens junction (GO:0005913)|costamere (GO:0043034)|cytoplasmic side of plasma membrane (GO:0009898)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|sarcolemma (GO:0042383)|spot adherens junction (GO:0005914)|stress fiber (GO:0001725)|Z disc (GO:0030018)	intramolecular transferase activity, phosphotransferases (GO:0016868)|magnesium ion binding (GO:0000287)|structural molecule activity (GO:0005198)			endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						ACATTTTAGGTCCTGCACCCG	0.408													t|||	1598	0.319089	0.3585	0.4236	5008	,	,		21750	0.3095		0.3181	False		,,,				2504	0.2025				p.G142G		Atlas-SNP	.											.	PGM5	80	.	0			c.T426C						PASS	.	T		1516,2890		265,986,952	89.0	81.0	84.0		426	2.1	1.0	9	dbSNP_123	84	2685,5913		446,1793,2060	no	coding-synonymous-near-splice	PGM5	NM_021965.3		711,2779,3012	CC,CT,TT		31.2282,34.4076,32.3054		142/568	70999315	4201,8803	2203	4299	6502	SO:0001630	splice_region_variant	5239	exon3			TTTAGGTCCTGCA	L40933	CCDS6622.2	9q13	2008-02-05			ENSG00000154330	ENSG00000154330			8908	protein-coding gene	gene with protein product	"""phosphoglucomutase-related protein"""	600981				8586438, 8631316	Standard	NM_021965		Approved	PGMRP	uc004agr.3	Q15124	OTTHUMG00000019966	ENST00000396396.1:c.425-1T>C	9.37:g.70999315T>C		Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	297	125	0.420875	NM_021965	B1AM46|B4DLQ6|Q5VYV3|Q8N527|Q9UDH4	Silent	SNP	ENST00000396396.1	37	CCDS6622.2																																																																																			T|0.680;C|0.320	0.320	strong		0.408	PGM5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052548.2	NM_021965	Silent
CXorf40A	91966	hgsc.bcm.edu	37	X	148628490	148628490	+	Silent	SNP	A	A	T	rs12116111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:148628490A>T	ENST00000441248.1	+	4	2046	c.459A>T	c.(457-459)ccA>ccT	p.P153P	CXorf40A_ENST00000450602.2_Silent_p.P153P|CXorf40A_ENST00000423421.1_Silent_p.P153P|CXorf40A_ENST00000359293.5_Silent_p.P153P|CXorf40A_ENST00000434353.2_Intron|CXorf40A_ENST00000428236.1_Silent_p.P91P|RP5-937E21.8_ENST00000431993.1_RNA|CXorf40A_ENST00000423540.2_Silent_p.P153P|CXorf40A_ENST00000422892.2_Intron|CXorf40A_ENST00000393985.3_Silent_p.P153P|CXorf40A_ENST00000514208.1_Intron			Q8TE69	CX04A_HUMAN	chromosome X open reading frame 40A	153										breast(1)|endometrium(3)|large_intestine(1)|lung(2)	7	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					ACCTGATCCCATTGGGGCATG	0.493													T|||	3558	0.942517	0.5998	0.7464	3775	,	,		6278	0.7579		0.7604	False		,,,				2504	0.7342				p.P153P		Atlas-SNP	.											.	CXorf40A	15	.	0			c.A459T						PASS	.						55.0	23.0	33.0					X																	148628490		2203	4283	6486	SO:0001819	synonymous_variant	91966	exon5			GATCCCATTGGGG	AF011889	CCDS14687.1, CCDS55522.1	Xq28	2010-03-16	2005-09-13	2005-09-13	ENSG00000197620	ENSG00000197620			28089	protein-coding gene	gene with protein product	"""endothelial-overexpressed lipopolysaccharide-associated factor 1"""		"""chromosome X open reading frame 40"""	CXorf40		8717057, 9147653, 16383041	Standard	XM_005278212		Approved	EOLA1	uc004fdg.3	Q8TE69	OTTHUMG00000022622	ENST00000441248.1:c.459A>T	X.37:g.148628490A>T		Somatic	687	1	0.0014556		WXS	Illumina HiSeq	Phase_I	176	174	0.988636	NM_178124	A8K784|B7Z6H6|B7ZL96|D6RA72|E7ENU3|Q2M3E9	Silent	SNP	ENST00000441248.1	37	CCDS14687.1																																																																																			.	.	weak		0.493	CXorf40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058699.3	NM_178124	
OR10A2	341276	hgsc.bcm.edu	37	11	6891758	6891758	+	Missense_Mutation	SNP	A	A	C	rs7926083	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6891758A>C	ENST00000307322.4	+	1	835	c.773A>C	c.(772-774)aAg>aCg	p.K258T		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	258			K -> T (in dbSNP:rs7926083).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCTGAGGGCAAGAAGCTGCTA	0.433													-|||	1625	0.324481	0.2073	0.3732	5008	,	,		23923	0.3135		0.3569	False		,,,				2504	0.4264				p.K258T		Atlas-SNP	.											.	OR10A2	55	.	0			c.A773C						PASS	.	A	THR/LYS	885,3517	341.8+/-306.9	89,707,1405	190.0	178.0	182.0		773	4.2	0.9	11	dbSNP_116	182	3205,5387	485.4+/-371.6	604,1997,1695	yes	missense	OR10A2	NM_001004460.1	78	693,2704,3100	CC,CA,AA		37.3021,20.1045,31.4761	probably-damaging	258/304	6891758	4090,8904	2201	4296	6497	SO:0001583	missense	341276	exon1			AGGGCAAGAAGCT	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"""GPCR / Class A : Olfactory receptors"""	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.773A>C	11.37:g.6891758A>C	ENSP00000303862:p.Lys258Thr	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	152	79	0.519737	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	37	CCDS31415.1	671	0.30723443223443225	97	0.19715447154471544	128	0.35359116022099446	176	0.3076923076923077	270	0.3562005277044855	a	11.50	1.657657	0.29425	0.201045	0.373021	ENSG00000170790	ENST00000307322	T	0.00115	8.71	4.18	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	0.107611	0.41605	D	0.000850	T	0.00012	0.0000	L	0.27053	0.805	0.35398	P	0.208611	D	0.76494	0.999	D	0.79784	0.993	T	0.65869	-0.6063	9	0.72032	D	0.01	.	11.568	0.50818	1.0:0.0:0.0:0.0	rs7926083;rs52825481;rs60681363;rs7926083	258	Q9H208	O10A2_HUMAN	T	258	ENSP00000303862:K258T	ENSP00000303862:K258T	K	+	2	0	OR10A2	6848334	0.004000	0.15560	0.887000	0.34795	0.039000	0.13416	2.229000	0.42990	1.908000	0.55244	0.529000	0.55759	AAG	A|0.685;C|0.315	0.315	strong		0.433	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460	
CLU	1191	hgsc.bcm.edu	37	8	27462481	27462481	+	Silent	SNP	A	A	G	rs7982	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27462481A>G	ENST00000316403.10	-	5	1194	c.789T>C	c.(787-789)caT>caC	p.H263H	CLU_ENST00000546343.1_Silent_p.H274H|CLU_ENST00000405140.3_Silent_p.H263H|CLU_ENST00000560366.1_Silent_p.H315H|CLU_ENST00000523500.1_Silent_p.H263H			P10909	CLUS_HUMAN	clusterin	263					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		AGGCCGGGCTATGGAAGTGGA	0.557													G|||	3328	0.664537	0.5749	0.6556	5008	,	,		15953	0.7887		0.6143	False		,,,				2504	0.7157				p.H263H		Atlas-SNP	.											.	CLU	54	.	0			c.T789C						PASS	.	G		2590,1816	532.6+/-373.5	738,1114,351	108.0	108.0	108.0		789	-0.9	0.0	8	dbSNP_52	108	5186,3414	503.4+/-375.9	1573,2040,687	no	coding-synonymous	CLU	NM_203339.2		2311,3154,1038	GG,GA,AA		39.6977,41.2165,40.2122		263/450	27462481	7776,5230	2203	4300	6503	SO:0001819	synonymous_variant	1191	exon5			CGGGCTATGGAAG	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.789T>C	8.37:g.27462481A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1	1422	0.6510989010989011	270	0.5487804878048781	232	0.6408839779005525	461	0.8059440559440559	459	0.6055408970976254	G	4.591	0.109767	0.08780	0.587835	0.603023	ENSG00000120885	ENST00000522098	.	.	.	3.68	-0.917	0.10485	.	.	.	.	.	.	.	.	.	.	.	0.54753	P	1.3000000000040757E-5	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.6694	4.8125	0.13351	0.4259:0.1521:0.422:0.0	rs7982;rs1049263;rs1532280;rs3189370;rs17349487;rs17850671;rs17851750;rs60199999	.	.	.	Q	126	.	.	X	-	1	0	CLU	27518398	0.001000	0.12720	0.003000	0.11579	0.190000	0.23558	-0.719000	0.04974	-0.708000	0.05015	-0.213000	0.12676	TAG	G|0.610;C|0.000;A|0.390	0.610	strong		0.557	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
ADH7	131	hgsc.bcm.edu	37	4	100341861	100341861	+	Silent	SNP	C	C	T	rs971074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100341861C>T	ENST00000209665.4	-	6	930	c.690G>A	c.(688-690)agG>agA	p.R230R	ADH7_ENST00000476959.1_Silent_p.R238R|ADH7_ENST00000482593.1_Silent_p.R161R|ADH7_ENST00000437033.2_Silent_p.R218R	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	230					ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		TCCCAATGATCCTAGATGCAC	0.517													C|||	600	0.119808	0.1422	0.1268	5008	,	,		19050	0.12		0.1183	False		,,,				2504	0.0859				p.R238R		Atlas-SNP	.											.	ADH7	76	.	0			c.G714A						PASS	.	C	,	747,3659	306.9+/-289.7	68,611,1524	151.0	130.0	137.0	http://www.ncbi.nlm.nih.gov/pubmed?term	690,714	1.1	0.2	4	dbSNP_86	137	1042,7558	221.3+/-258.8	74,894,3332	yes	coding-synonymous,coding-synonymous	ADH7	NM_000673.4,NM_001166504.1	,	142,1505,4856	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	12.1163,16.9542,13.7552	,	230/387,238/395	100341861	1789,11217	2203	4300	6503	SO:0001819	synonymous_variant	131	exon6			AATGATCCTAGAT	X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"""Alcohol dehydrogenases"""	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.690G>A	4.37:g.100341861C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	NM_001166504	A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Silent	SNP	ENST00000209665.4	37	CCDS34034.1																																																																																			C|0.862;T|0.138	0.138	strong		0.517	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673	
CRB2	286204	hgsc.bcm.edu	37	9	126132919	126132919	+	Silent	SNP	G	G	A	rs33984675	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126132919G>A	ENST00000373631.3	+	7	1588	c.1587G>A	c.(1585-1587)gcG>gcA	p.A529A	CRB2_ENST00000373629.2_Silent_p.A197A|CRB2_ENST00000359999.3_Silent_p.A529A	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	529	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						TCCATCTAGCGACCCTGGAGC	0.642													G|||	990	0.197684	0.059	0.1758	5008	,	,		19807	0.252		0.2753	False		,,,				2504	0.2648				p.A529A		Atlas-SNP	.											.	CRB2	86	.	0			c.G1587A						PASS	.	G		383,4023	192.3+/-217.7	17,349,1837	72.0	66.0	68.0		1587	3.0	0.5	9	dbSNP_126	68	2696,5904	430.3+/-356.5	430,1836,2034	no	coding-synonymous	CRB2	NM_173689.5		447,2185,3871	AA,AG,GG		31.3488,8.6927,23.6737		529/1286	126132919	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon7			TCTAGCGACCCTG	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.1587G>A	9.37:g.126132919G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			G|0.766;A|0.234	0.234	strong		0.642	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100814570	100814570	+	Silent	SNP	A	A	G	rs543146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100814570A>G	ENST00000298815.8	+	10	1017	c.1014A>G	c.(1012-1014)cgA>cgG	p.R338R	ARHGAP42_ENST00000524892.2_Silent_p.R304R	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	338	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGACAAACGATTCTGCTTTG	0.328													A|||	2058	0.410942	0.1362	0.4308	5008	,	,		17776	0.7312		0.2565	False		,,,				2504	0.5971				p.R338R		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A1014G						PASS	.	A		276,1108		24,228,440	120.0	97.0	104.0		1014	-1.1	1.0	11	dbSNP_83	104	911,2271		127,657,807	no	coding-synonymous	ARHGAP42	NM_152432.2		151,885,1247	GG,GA,AA		28.6298,19.9422,25.9965		338/875	100814570	1187,3379	692	1591	2283	SO:0001819	synonymous_variant	143872	exon10			CAAACGATTCTGC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.1014A>G	11.37:g.100814570A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.643;G|0.357	0.357	strong		0.328	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
SPINK5	11005	hgsc.bcm.edu	37	5	147505116	147505116	+	Intron	SNP	G	G	A	rs3764930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147505116G>A	ENST00000256084.7	+	29	2781				SPINK5_ENST00000359874.3_Silent_p.A923A	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5						anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAATGAAGCGGAGGATGCAA	0.463													G|||	2270	0.453275	0.1876	0.6225	5008	,	,		19509	0.4821		0.5915	False		,,,				2504	0.5204				p.A923A		Atlas-SNP	.											.	SPINK5	245	.	0			c.G2769A						PASS	.	G	,	824,2312		112,600,856	73.0	64.0	67.0		2769,	-6.9	0.0	5	dbSNP_107	67	4393,2771		1319,1755,508	no	coding-synonymous,intron	SPINK5	NM_001127698.1,NM_006846.3	,	1431,2355,1364	AA,AG,GG		38.6795,26.2755,49.3495	,	923/1095,	147505116	5217,5083	1568	3582	5150	SO:0001627	intron_variant	11005	exon29			TGAAGCGGAGGAT	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.2740-170G>A	5.37:g.147505116G>A		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	264	264	1	NM_001127698	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			G|0.545;A|0.455	0.455	strong		0.463	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
RFPL1	5988	hgsc.bcm.edu	37	22	29837537	29837537	+	Missense_Mutation	SNP	T	T	C	rs3804076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29837537T>C	ENST00000354373.2	+	2	589	c.380T>C	c.(379-381)aTg>aCg	p.M127T	RFPL1S_ENST00000461286.3_RNA|RFPL1S_ENST00000539579.1_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	127	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		M -> T (in dbSNP:rs3804076). {ECO:0000269|PubMed:10508838, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.				zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						ACAGTGGATATGACCTTGGAT	0.488													-|||	1157	0.23103	0.0356	0.4006	5008	,	,		20603	0.1091		0.4384	False		,,,				2504	0.2873				p.M127T		Atlas-SNP	.											RFPL1,colon,carcinoma,0,1	RFPL1	43	1	0			c.T380C						PASS	.	T	THR/MET	403,4003		19,365,1819	105.0	93.0	97.0		380	1.1	0.3	22	dbSNP_107	97	3740,4860		821,2098,1381	no	missense	RFPL1	NM_021026.2	81	840,2463,3200	CC,CT,TT		43.4884,9.1466,31.8545	possibly-damaging	127/318	29837537	4143,8863	2203	4300	6503	SO:0001583	missense	5988	exon2			TGGATATGACCTT	AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250		"""RING-type (C3HC4) zinc fingers"""	9977	protein-coding gene	gene with protein product		605968				10508838	Standard	NM_021026		Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.380T>C	22.37:g.29837537T>C	ENSP00000346342:p.Met127Thr	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	323	129	0.399381	NM_021026	Q6IC06|Q9UJ97	Missense_Mutation	SNP	ENST00000354373.2	37	CCDS13857.2	571	0.26144688644688646	26	0.052845528455284556	141	0.38950276243093923	73	0.12762237762237763	331	0.4366754617414248	-	14.91	2.676780	0.47886	0.091466	0.434884	ENSG00000128250	ENST00000354373	T	0.10477	2.87	1.1	1.1	0.20463	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00012	0.0000	M	0.88570	2.965	0.41774	P	0.010213999999999945	D	0.58268	0.982	D	0.87578	0.998	T	0.39981	-0.9587	8	0.59425	D	0.04	.	6.3123	0.21171	0.0:0.0:0.0:1.0	rs3804076;rs3804076	127	O75677	RFPL1_HUMAN	T	127	ENSP00000346342:M127T	ENSP00000346342:M127T	M	+	2	0	RFPL1	28167537	0.939000	0.31865	0.345000	0.25642	0.354000	0.29330	3.478000	0.53158	0.744000	0.32741	0.348000	0.21847	ATG	T|0.702;C|0.298	0.298	strong		0.488	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318719.1	NM_021026	
IQCE	23288	hgsc.bcm.edu	37	7	2649777	2649777	+	Missense_Mutation	SNP	C	C	T	rs1061566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2649777C>T	ENST00000402050.2	+	22	2253	c.2069C>T	c.(2068-2070)aCg>aTg	p.T690M	IQCE_ENST00000438376.2_Missense_Mutation_p.T674M|IQCE_ENST00000325979.7_Missense_Mutation_p.T625M|IQCE_ENST00000404984.1_Missense_Mutation_p.T639M	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	690			T -> M (in dbSNP:rs1061566). {ECO:0000269|PubMed:10470851}.			mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		TCTCTGCCCACGAAGAACTTT	0.557													C|||	310	0.061901	0.0053	0.0865	5008	,	,		21817	0.003		0.1342	False		,,,				2504	0.1074				p.T690M		Atlas-SNP	.											.	IQCE	66	.	0			c.C2069T						PASS	.	C	MET/THR,MET/THR	141,4079		4,133,1973	101.0	102.0	101.0		2021,2069	-3.2	0.0	7	dbSNP_86	101	1311,7151		107,1097,3027	yes	missense,missense	IQCE	NM_001100390.1,NM_152558.3	81,81	111,1230,5000	TT,TC,CC		15.4928,3.3412,11.4493	probably-damaging,probably-damaging	674/680,690/696	2649777	1452,11230	2110	4231	6341	SO:0001583	missense	23288	exon22			TGCCCACGAAGAA	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.2069C>T	7.37:g.2649777C>T	ENSP00000385597:p.Thr690Met	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	141	0.06456043956043957	6	0.012195121951219513	29	0.08011049723756906	0	0.0	106	0.13984168865435356	C	12.12	1.842166	0.32513	0.033412	0.154928	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979	T;T;T;T	0.11604	2.77;2.76;2.77;2.77	4.63	-3.23	0.05109	.	1.412350	0.04877	N	0.447051	T	0.00039	0.0001	L	0.28274	0.84	0.80722	P	0.0	B;B	0.20887	0.029;0.049	B;B	0.11329	0.003;0.006	T	0.43393	-0.9394	9	0.48119	T	0.1	.	5.2101	0.15312	0.0:0.1865:0.4057:0.4078	rs1061566;rs1061566	690;674	Q6IPM2;Q6IPM2-4	IQCE_HUMAN;.	M	690;639;674;625	ENSP00000385597:T690M;ENSP00000385945:T639M;ENSP00000396178:T674M;ENSP00000313772:T625M	ENSP00000313772:T625M	T	+	2	0	IQCE	2616303	0.003000	0.15002	0.000000	0.03702	0.005000	0.04900	-0.450000	0.06803	-0.358000	0.08162	-0.367000	0.07326	ACG	C|0.919;T|0.081	0.081	strong		0.557	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
ZNF45	7596	hgsc.bcm.edu	37	19	44418544	44418544	+	Silent	SNP	A	A	G	rs425221	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44418544A>G	ENST00000269973.5	-	10	2134	c.1044T>C	c.(1042-1044)aaT>aaC	p.N348N	ZNF45_ENST00000589703.1_Silent_p.N348N|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	348					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						TACAATGAATATTAAGGTGTG	0.478													G|||	2632	0.525559	0.3343	0.6499	5008	,	,		22417	0.7996		0.5169	False		,,,				2504	0.4223				p.N348N		Atlas-SNP	.											.	ZNF45	51	.	0			c.T1044C						PASS	.	G		1580,2826	666.5+/-401.7	293,994,916	71.0	66.0	68.0		1044	1.4	0.3	19	dbSNP_80	68	4353,4247	573.4+/-389.9	1119,2115,1066	no	coding-synonymous	ZNF45	NM_003425.3		1412,3109,1982	GG,GA,AA		49.3837,35.8602,45.6174		348/683	44418544	5933,7073	2203	4300	6503	SO:0001819	synonymous_variant	7596	exon10			ATGAATATTAAGG	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"""Zinc fingers, C2H2-type"", ""-"""	13111	protein-coding gene	gene with protein product		194554	"""zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)"", ""zinc finger protein 13"""	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.1044T>C	19.37:g.44418544A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	152	82	0.539474	NM_003425	P17016|P78472|Q9P1U9	Silent	SNP	ENST00000269973.5	37	CCDS12632.1																																																																																			A|0.488;G|0.512	0.512	strong		0.478	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
CCDC180	100499483	hgsc.bcm.edu	37	9	100070351	100070351	+	Silent	SNP	G	G	C	rs12683119	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100070351G>C	ENST00000357054.1	+	16	1490	c.555G>C	c.(553-555)tcG>tcC	p.S185S	CCDC180_ENST00000529487.1_Silent_p.S46S|CCDC180_ENST00000411667.2_Silent_p.S46S|CCDC180_ENST00000395220.1_Silent_p.S185S|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_Silent_p.S46S			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	185						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CCAAGATGTCGTCAGTGGGGA	0.592													G|||	687	0.137181	0.0356	0.2003	5008	,	,		14826	0.0575		0.2038	False		,,,				2504	0.2434				p.S46S		Atlas-SNP	.											.	.	.	.	0			c.G138C						PASS	.	G		320,4086	170.5+/-200.9	14,292,1897	72.0	65.0	67.0		138	-6.0	0.0	9	dbSNP_120	67	2362,6238	393.9+/-344.5	312,1738,2250	no	coding-synonymous	C9orf174	NM_020893.2		326,2030,4147	CC,CG,GG		27.4651,7.2628,20.6213		46/1702	100070351	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			GATGTCGTCAGTG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.555G>C	9.37:g.100070351G>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	121	50	0.413223	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				G|0.813;C|0.187	0.187	strong		0.592	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
C2orf71	388939	hgsc.bcm.edu	37	2	29297068	29297068	+	Silent	SNP	C	C	T	rs35929540	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29297068C>T	ENST00000331664.5	-	1	59	c.60G>A	c.(58-60)caG>caA	p.Q20Q		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	20					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TTTTCAAGAACTGAATGCCAC	0.473													C|||	584	0.116613	0.0303	0.1585	5008	,	,		21773	0.123		0.2137	False		,,,				2504	0.0971				p.Q20Q		Atlas-SNP	.											.	C2orf71	146	.	0			c.G60A						PASS	.	C		274,3694		9,256,1719	93.0	87.0	89.0		60	5.0	1.0	2	dbSNP_126	89	1859,6489		189,1481,2504	no	coding-synonymous	C2orf71	NM_001029883.1		198,1737,4223	TT,TC,CC		22.2688,6.9052,17.3189		20/1289	29297068	2133,10183	1984	4174	6158	SO:0001819	synonymous_variant	388939	exon1			CAAGAACTGAATG		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.60G>A	2.37:g.29297068C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			C|0.822;T|0.178	0.178	strong		0.473	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
HTN3	3347	hgsc.bcm.edu	37	4	70898907	70898907	+	Silent	SNP	C	C	T	rs1849937	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70898907C>T	ENST00000530128.1	+	5	201	c.126C>T	c.(124-126)ggC>ggT	p.G42G	HTN3_ENST00000526767.1_Silent_p.G42G|HTN3_ENST00000381057.3_Silent_p.G32G			P15516	HIS3_HUMAN	histatin 3	42					biomineral tissue development (GO:0031214)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)	p.G42G(1)		breast(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	8						CACATCGAGGCTATAGATCAA	0.368													C|||	563	0.11242	0.0151	0.1614	5008	,	,		19306	0.2024		0.1143	False		,,,				2504	0.1145				p.G42G		Atlas-SNP	.											HTN3,NS,carcinoma,0,1	HTN3	16	1	1	Substitution - coding silent(1)	prostate(1)	c.C126T						PASS	.	C		151,4255	103.8+/-142.4	5,141,2057	140.0	125.0	130.0		126	-2.2	0.0	4	dbSNP_92	130	831,7769	191.0+/-237.3	44,743,3513	no	coding-synonymous	HTN3	NM_000200.2		49,884,5570	TT,TC,CC		9.6628,3.4271,7.5504		42/52	70898907	982,12024	2203	4300	6503	SO:0001819	synonymous_variant	3347	exon5			TCGAGGCTATAGA		CCDS33999.1	4q13	2008-08-29							5284	protein-coding gene	gene with protein product		142702					Standard	NM_000200		Approved	HIS2	uc003hew.2	P15516		ENST00000530128.1:c.126C>T	4.37:g.70898907C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	161	67	0.416149	NM_000200	Q16243|Q502Z1	Silent	SNP	ENST00000530128.1	37	CCDS33999.1																																																																																			C|0.911;T|0.089	0.089	strong		0.368	HTN3-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387375.1	NM_000200	
FAF2	23197	hgsc.bcm.edu	37	5	175919324	175919324	+	Silent	SNP	G	G	A	rs78597771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:175919324G>A	ENST00000261942.6	+	5	527	c.474G>A	c.(472-474)acG>acA	p.T158T		NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	158					lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						ACCAGGGAACGTACAGCCAGG	0.493													G|||	42	0.00838658	0.0015	0.0144	5008	,	,		20504	0.0		0.0288	False		,,,				2504	0.001				p.T158T		Atlas-SNP	.											.	FAF2	38	.	0			c.G474A						PASS	.	G		27,4379	32.6+/-62.9	0,27,2176	62.0	57.0	59.0		474	0.4	1.0	5	dbSNP_132	59	286,8314	107.0+/-167.8	4,278,4018	no	coding-synonymous	FAF2	NM_014613.2		4,305,6194	AA,AG,GG		3.3256,0.6128,2.4066		158/446	175919324	313,12693	2203	4300	6503	SO:0001819	synonymous_variant	23197	exon5			GGGAACGTACAGC	BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"""UBX domain containing"""	24666	protein-coding gene	gene with protein product	"""expressed in T cells and eosinophils in atopic dermatitis"", ""UBX domain protein 3B"""		"""UBX domain containing 8"""	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.474G>A	5.37:g.175919324G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	27	0.355263	NM_014613	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Silent	SNP	ENST00000261942.6	37	CCDS34296.1																																																																																			G|0.978;A|0.022	0.022	strong		0.493	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613	
HERC2	8924	hgsc.bcm.edu	37	15	28517492	28517492	+	Missense_Mutation	SNP	C	C	A	rs77399744		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28517492C>A	ENST00000261609.7	-	9	1060	c.952G>T	c.(952-954)Gac>Tac	p.D318Y		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GCCCCGCTGTCCCACAGCTGA	0.478																																					p.D318Y		Atlas-SNP	.											.	HERC2	501	.	0			c.G952T						PASS	.						49.0	40.0	43.0					15																	28517492		2203	4300	6503	SO:0001583	missense	8924	exon9			CGCTGTCCCACAG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.952G>T	15.37:g.28517492C>A	ENSP00000261609:p.Asp318Tyr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	121	21	0.173554	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.803213	0.90623	.	.	ENSG00000128731	ENST00000261609	T	0.48836	0.8	5.58	5.58	0.84498	.	0.062950	0.64402	D	0.000003	T	0.50718	0.1632	L	0.59436	1.845	0.80722	D	1	P	0.44090	0.826	B	0.41088	0.347	T	0.56884	-0.7905	10	0.72032	D	0.01	.	19.5567	0.95351	0.0:1.0:0.0:0.0	.	318	O95714	HERC2_HUMAN	Y	318	ENSP00000261609:D318Y	ENSP00000261609:D318Y	D	-	1	0	HERC2	26191087	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.761000	0.85260	2.641000	0.89580	0.650000	0.86243	GAC	C|0.500;A|0.500	0.500	weak		0.478	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
PTPRQ	374462	hgsc.bcm.edu	37	12	80899901	80899901	+	Missense_Mutation	SNP	C	C	A	rs11114486	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:80899901C>A	ENST00000266688.5	+	20	2359	c.2359C>A	c.(2359-2361)Caa>Aaa	p.Q787K				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	833	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)	p.Q787K(1)		breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						TGGAATCATACAAAAATATAC	0.328													C|||	2137	0.426717	0.0582	0.5591	5008	,	,		15623	0.3601		0.6451	False		,,,				2504	0.6748				p.Q619K		Atlas-SNP	.											PTPRQ,NS,carcinoma,0,1	PTPRQ	119	1	1	Substitution - Missense(1)	kidney(1)	c.C1855A						PASS	.						49.0	35.0	40.0					12																	80899901		692	1578	2270	SO:0001583	missense	374462	exon12			ATCATACAAAAAT	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.2359C>A	12.37:g.80899901C>A	ENSP00000266688:p.Gln787Lys	Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	155	152	0.980645	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		927|927	0.42445054945054944|0.42445054945054944	49|49	0.09959349593495935|0.09959349593495935	186|186	0.5138121546961326|0.5138121546961326	192|192	0.3356643356643357|0.3356643356643357	500|500	0.6596306068601583|0.6596306068601583	C|C	2.762|2.762	-0.257704|-0.257704	0.05791|0.05791	.|.	.|.	ENSG00000139304|ENSG00000139304	ENST00000266688|ENST00000532722	T|.	0.56444|.	0.46|.	5.87|5.87	4.96|4.96	0.65561|0.65561	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.38654|0.38654	P|P	0.048077000000000036|0.048077000000000036	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.47623|.	-0.9103|.	5|.	0.05620|.	T|.	0.96|.	.|.	11.0804|11.0804	0.48057|0.48057	0.1349:0.6044:0.2607:0.0|0.1349:0.6044:0.2607:0.0	rs11114486;rs52817843;rs61576764;rs11114486|rs11114486;rs52817843;rs61576764;rs11114486	.|.	.|.	.|.	K|X	787|487	ENSP00000266688:Q787K|.	ENSP00000266688:Q787K|.	Q|Y	+|+	1|3	0|2	PTPRQ|PTPRQ	79424032|79424032	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.841000|0.841000	0.27613|0.27613	1.437000|1.437000	0.47472|0.47472	0.585000|0.585000	0.79938|0.79938	CAA|TAC	C|0.608;A|0.392	0.392	strong		0.328	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390469	208390469	+	Missense_Mutation	SNP	C	C	T	rs3748735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:208390469C>T	ENST00000367033.3	-	2	1556	c.799G>A	c.(799-801)Gcc>Acc	p.A267T		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	267	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		A -> T (in dbSNP:rs3748735).		axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GAGTTGATGGCCACACCCTCA	0.577													C|||	699	0.139577	0.0673	0.1715	5008	,	,		19639	0.1458		0.1988	False		,,,				2504	0.1472				p.A267T		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G799A						PASS	.	C	THR/ALA	386,4020	195.3+/-220.0	19,348,1836	115.0	114.0	114.0		799	4.9	1.0	1	dbSNP_107	114	1686,6914	308.6+/-309.0	189,1308,2803	yes	missense	PLXNA2	NM_025179.3	58	208,1656,4639	TT,TC,CC		19.6047,8.7608,15.9311	benign	267/1895	208390469	2072,10934	2203	4300	6503	SO:0001583	missense	5362	exon2			TGATGGCCACACC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.799G>A	1.37:g.208390469C>T	ENSP00000356000:p.Ala267Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	308	0.14102564102564102	34	0.06910569105691057	55	0.15193370165745856	80	0.13986013986013987	139	0.18337730870712401	C	14.10	2.434528	0.43224	0.087608	0.196047	ENSG00000076356	ENST00000367033	T	0.10860	2.83	5.84	4.91	0.64330	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.472859	0.22674	N	0.057027	T	0.00012	0.0000	N	0.08118	0	0.25798	P	0.9845479	P;B	0.38827	0.649;0.053	B;B	0.41510	0.359;0.13	T	0.42464	-0.9450	9	0.07325	T	0.83	.	14.0881	0.64971	0.3283:0.6717:0.0:0.0	rs3748735;rs57678694;rs3748735	321;267	O75051-2;O75051	.;PLXA2_HUMAN	T	267	ENSP00000356000:A267T	ENSP00000356000:A267T	A	-	1	0	PLXNA2	206457092	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.531000	0.53546	1.433000	0.47394	0.655000	0.94253	GCC	C|0.850;T|0.150	0.150	strong		0.577	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
NLRP13	126204	hgsc.bcm.edu	37	19	56423668	56423668	+	Silent	SNP	G	G	A	rs304001	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56423668G>A	ENST00000342929.3	-	5	1514	c.1515C>T	c.(1513-1515)atC>atT	p.I505I	NLRP13_ENST00000588751.1_Silent_p.I505I	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	505	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CCAGGCCCTCGATCTCAGTGT	0.478													G|||	3247	0.648363	0.6861	0.5014	5008	,	,		19699	0.7302		0.5905	False		,,,				2504	0.6769				p.I505I		Atlas-SNP	.											.	NLRP13	220	.	0			c.C1515T						PASS	.	G		2928,1478	678.2+/-403.5	988,952,263	56.0	56.0	56.0		1515	-3.3	0.0	19	dbSNP_79	56	5236,3364	642.3+/-399.8	1597,2042,661	no	coding-synonymous	NLRP13	NM_176810.2		2585,2994,924	AA,AG,GG		39.1163,33.5452,37.229		505/1044	56423668	8164,4842	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon5			GCCCTCGATCTCA	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.1515C>T	19.37:g.56423668G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	123	71	0.577236	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			G|0.373;A|0.627	0.627	strong		0.478	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
EXD1	161829	hgsc.bcm.edu	37	15	41488231	41488231	+	Missense_Mutation	SNP	G	G	C	rs139947718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41488231G>C	ENST00000314992.5	-	6	555	c.365C>G	c.(364-366)gCc>gGc	p.A122G	EXD1_ENST00000458580.2_Missense_Mutation_p.A180G	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	122	3'-5' exonuclease.						3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						GCAATTTGTGGCCACCTACAA	0.383													G|||	8	0.00159744	0.0	0.0043	5008	,	,		19008	0.0		0.004	False		,,,				2504	0.001				p.A122G		Atlas-SNP	.											.	EXD1	52	.	0			c.C365G						PASS	.	G	GLY/ALA	5,4401	4.2+/-10.8	0,5,2198	46.0	47.0	47.0		365	5.7	1.0	15	dbSNP_134	47	48,8552	26.3+/-74.7	0,48,4252	yes	missense	EXD1	NM_152596.2	60	0,53,6450	CC,CG,GG		0.5581,0.1135,0.4075	probably-damaging	122/515	41488231	53,12953	2203	4300	6503	SO:0001583	missense	161829	exon6			TTTGTGGCCACCT	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.365C>G	15.37:g.41488231G>C	ENSP00000321029:p.Ala122Gly	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_152596	A8K909|B7Z839|Q6ZW94	Missense_Mutation	SNP	ENST00000314992.5	37	CCDS10072.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	21.6	4.173271	0.78452	0.001135	0.005581	ENSG00000178997	ENST00000314992;ENST00000458580	T;T	0.61742	0.08;0.08	5.65	5.65	0.86999	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	0.062205	0.64402	D	0.000008	T	0.63885	0.2549	L	0.46885	1.475	0.50813	D	0.999899	D;D	0.71674	0.998;0.998	D;D	0.74023	0.982;0.982	T	0.67887	-0.5554	10	0.52906	T	0.07	-8.9912	17.4865	0.87689	0.0:0.0:1.0:0.0	.	180;122	B7Z839;Q8NHP7	.;EXD1_HUMAN	G	122;180	ENSP00000321029:A122G;ENSP00000415056:A180G	ENSP00000321029:A122G	A	-	2	0	EXD1	39275523	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.633000	0.67825	2.665000	0.90641	0.462000	0.41574	GCC	G|0.996;C|0.004	0.004	strong		0.383	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596	
ZNF594	84622	hgsc.bcm.edu	37	17	5085893	5085893	+	Silent	SNP	C	C	T	rs4115657	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5085893C>T	ENST00000399604.4	-	1	1799	c.1659G>A	c.(1657-1659)gaG>gaA	p.E553E	ZNF594_ENST00000575779.1_Silent_p.E553E			Q96JF6	ZN594_HUMAN	zinc finger protein 594	553					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CCCTAAGCTCCTCATCCTGGC	0.483													C|||	1613	0.322085	0.1369	0.5994	5008	,	,		20721	0.1746		0.6034	False		,,,				2504	0.2382				p.E553E		Atlas-SNP	.											.	ZNF594	89	.	0			c.G1659A						PASS	.	C		1057,3007		136,785,1111	139.0	122.0	127.0		1659	-2.3	0.0	17	dbSNP_108	127	5409,3037		1738,1933,552	no	coding-synonymous	ZNF594	NM_032530.1		1874,2718,1663	TT,TC,CC		35.9578,26.0089,48.3133		553/808	5085893	6466,6044	2032	4223	6255	SO:0001819	synonymous_variant	84622	exon2			AAGCTCCTCATCC	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1659G>A	17.37:g.5085893C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			C|0.545;T|0.455	0.455	strong		0.483	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
MSGN1	343930	hgsc.bcm.edu	37	2	17998331	17998331	+	Silent	SNP	T	T	C	rs13001625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:17998331T>C	ENST00000281047.3	+	1	569	c.546T>C	c.(544-546)ctT>ctC	p.L182L		NM_001105569.1	NP_001099039.1	A6NI15	MSGN1_HUMAN	mesogenin 1	182					cell differentiation (GO:0030154)|segment specification (GO:0007379)|somitogenesis (GO:0001756)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CAGACCTCCTTAACCGCGGCA	0.572													C|||	1475	0.294529	0.2027	0.3501	5008	,	,		18695	0.0278		0.5378	False		,,,				2504	0.4039				p.L182L	Melanoma(127;325 1712 14802 40657 49130)	Atlas-SNP	.											.	MSGN1	39	.	0			c.T546C						PASS	.	C		1054,3016		144,766,1125	37.0	40.0	39.0		546	3.0	1.0	2	dbSNP_121	39	4775,3595		1379,2017,789	no	coding-synonymous	MSGN1	NM_001105569.1		1523,2783,1914	CC,CT,TT		42.951,25.8968,46.8569		182/194	17998331	5829,6611	2035	4185	6220	SO:0001819	synonymous_variant	343930	exon1			CCTCCTTAACCGC		CCDS42657.1	2p24.2	2007-07-23			ENSG00000151379	ENSG00000151379			14907	protein-coding gene	gene with protein product	"""paraxial mesogenin"""	612209				10837126	Standard	NM_001105569		Approved	pMesogenin1	uc010yjt.2	A6NI15	OTTHUMG00000159089	ENST00000281047.3:c.546T>C	2.37:g.17998331T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_001105569		Silent	SNP	ENST00000281047.3	37	CCDS42657.1																																																																																			T|0.585;C|0.415	0.415	strong		0.572	MSGN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353253.1	XM_292850	
NBPF14	25832	hgsc.bcm.edu	37	1	148009349	148009349	+	Missense_Mutation	SNP	A	A	G	rs141981140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:148009349A>G	ENST00000369219.1	-	16	1974	c.1958T>C	c.(1957-1959)aTg>aCg	p.M653T				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	653	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					CTCACCATCCATGTCAACAGC	0.478																																					p.M653T		Atlas-SNP	.											NBPF14,NS,carcinoma,0,1	NBPF14	107	1	0			c.T1958C						scavenged	.	A	THR/MET	416,2396		0,416,990	65.0	116.0	103.0		1958			1	dbSNP_134	103	1178,6834		2,1174,2830	no	missense	NBPF14	NM_015383.1	81	2,1590,3820	GG,GA,AA		14.7029,14.7937,14.7265	possibly-damaging	653/922	148009349	1594,9230	1406	4006	5412	SO:0001583	missense	25832	exon16			CCATCCATGTCAA	AK092351		1q21.1	2013-01-17			ENSG00000122497			"""neuroblastoma breakpoint family"""	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1958T>C	1.37:g.148009349A>G	ENSP00000358221:p.Met653Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	232	14	0.0603448	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	7.065|7.065	0.567077|0.567077	0.13560|0.13560	0.147937|0.147937	0.147029|0.147029	ENSG00000122497|ENSG00000122497	ENST00000369219;ENST00000434489|ENST00000310701	T|.	0.06528|.	3.29|.	.|.	.|.	.|.	DUF1220 (2);|.	.|.	.|.	.|.	.|.	T|T	0.22704|0.22704	0.0548|0.0548	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	B;P|.	0.38395|.	0.214;0.629|.	B;P|.	0.48982|.	0.117;0.597|.	T|T	0.21449|0.21449	-1.0245|-1.0245	6|2	0.30078|.	T|.	0.28|.	.|.	.|.	.|.	.|.	.|.	1;653|.	F8WEX8;Q5TI25|.	.;NBPFE_HUMAN|.	T|R	653;243|659	ENSP00000358221:M653T|.	ENSP00000358221:M653T|.	M|W	-|-	2|1	0|0	NBPF14|NBPF14	146475973|146475973	0.596000|0.596000	0.26866|0.26866	.|.	.|.	.|.	.|.	0.724000|0.724000	0.25954|0.25954	.|.	.|.	.|.	.|.	ATG|TGG	A|0.941;G|0.059	0.059	strong		0.478	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383	
PCDH12	51294	hgsc.bcm.edu	37	5	141337225	141337225	+	Silent	SNP	A	A	G	rs164077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141337225A>G	ENST00000231484.3	-	1	1402	c.192T>C	c.(190-192)gcT>gcC	p.A64A	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	64	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGGAAGGCAGCCCCAGCTT	0.617													A|||	3768	0.752396	0.4675	0.8401	5008	,	,		16713	0.9732		0.7763	False		,,,				2504	0.8231				p.A64A		Atlas-SNP	.											.	PCDH12	133	.	0			c.T192C						PASS	.	A		2294,2112	593.8+/-388.1	607,1080,516	57.0	57.0	57.0		192	2.4	0.2	5	dbSNP_79	57	6890,1710	726.7+/-406.6	2771,1348,181	no	coding-synonymous	PCDH12	NM_016580.2		3378,2428,697	GG,GA,AA		19.8837,47.9346,29.3864		64/1185	141337225	9184,3822	2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			GAAGGCAGCCCCA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.192T>C	5.37:g.141337225A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	CCDS4269.1																																																																																			A|0.273;G|0.727	0.727	strong		0.617	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
PARVB	29780	hgsc.bcm.edu	37	22	44489896	44489896	+	Splice_Site	SNP	T	T	C	rs738479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:44489896T>C	ENST00000338758.7	+	2	264	c.201T>C	c.(199-201)ctT>ctC	p.L67L	PARVB_ENST00000477795.1_3'UTR|PARVB_ENST00000404989.1_Splice_Site_p.L30L|PARVB_ENST00000406477.3_Splice_Site_p.L100L	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	67					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				ACACCCAGCTTGGTACGGGGG	0.577													C|||	3233	0.645567	0.6014	0.6484	5008	,	,		16384	0.8462		0.5487	False		,,,				2504	0.5961				p.L100L		Atlas-SNP	.											.	PARVB	44	.	0			c.T300C						PASS	.	C	,	2574,1832	533.3+/-373.7	746,1082,375	71.0	71.0	71.0		300,201	-8.6	0.8	22	dbSNP_86	71	5002,3598	520.1+/-379.6	1472,2058,770	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PARVB	NM_001003828.2,NM_013327.4	,	2218,3140,1145	CC,CT,TT		41.8372,41.5797,41.75	,	100/398,67/365	44489896	7576,5430	2203	4300	6503	SO:0001630	splice_region_variant	29780	exon3			CCAGCTTGGTACG	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.202+1T>C	22.37:g.44489896T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Silent	SNP	ENST00000338758.7	37	CCDS14056.1																																																																																			T|0.386;C|0.614	0.614	strong		0.577	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	Silent
OR8S1	341568	hgsc.bcm.edu	37	12	48920006	48920006	+	Missense_Mutation	SNP	G	G	A	rs12425518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48920006G>A	ENST00000310194.1	+	1	592	c.592G>A	c.(592-594)Gcc>Acc	p.A198T	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	198				A -> V (in Ref. 1; BAC05832). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						AAGCCTCATCGCCTTGCTCTG	0.478													g|||	1737	0.346845	0.4304	0.3991	5008	,	,		22317	0.5407		0.0755	False		,,,				2504	0.2761				p.A198T		Atlas-SNP	.											.	OR8S1	47	.	0			c.G592A						PASS	.	C	THR/ALA	1660,2746	507.1+/-366.6	292,1076,835	183.0	149.0	161.0		592	-1.3	0.0	12	dbSNP_120	161	590,8010	156.1+/-210.0	22,546,3732	yes	missense	OR8S1	NM_001005203.2	58	314,1622,4567	AA,AG,GG		6.8605,37.6759,17.2997	benign	198/360	48920006	2250,10756	2203	4300	6503	SO:0001583	missense	341568	exon1			CTCATCGCCTTGC		CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"""GPCR / Class A : Olfactory receptors"""	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.592G>A	12.37:g.48920006G>A	ENSP00000310632:p.Ala198Thr	Somatic	428	0	0		WXS	Illumina HiSeq	Phase_I	427	196	0.459016	NM_001005203		Missense_Mutation	SNP	ENST00000310194.1	37	CCDS31789.1	690	0.3159340659340659	194	0.3943089430894309	130	0.35911602209944754	306	0.534965034965035	60	0.079155672823219	G	9.699	1.154072	0.21371	0.376759	0.068605	ENSG00000197376	ENST00000310194	T	0.37235	1.21	4.88	-1.34	0.09143	GPCR, rhodopsin-like superfamily (1);	2.019960	0.02772	N	0.119764	T	0.00012	0.0000	N	0.17872	0.535	0.80722	P	0.0	B	0.23937	0.094	B	0.25884	0.064	T	0.47368	-0.9123	9	0.51188	T	0.08	-47.3227	4.8362	0.13466	0.4087:0.2843:0.307:0.0	rs12425518;rs58634382;rs12425518	198	Q8NH09	OR8S1_HUMAN	T	198	ENSP00000310632:A198T	ENSP00000310632:A198T	A	+	1	0	OR8S1	47206273	0.000000	0.05858	0.000000	0.03702	0.700000	0.40528	-0.478000	0.06575	-0.135000	0.11495	-0.121000	0.15023	GCC	G|0.750;A|0.250	0.250	strong		0.478	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
KRT75	9119	hgsc.bcm.edu	37	12	52824352	52824352	+	Silent	SNP	G	G	A	rs395623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52824352G>A	ENST00000252245.5	-	5	1228	c.1008C>T	c.(1006-1008)gcC>gcT	p.A336A	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	336	Coil 2.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		ACTCAGCCTCGGCCCGGCTGC	0.552													G|||	1214	0.242412	0.0272	0.232	5008	,	,		19985	0.4494		0.3708	False		,,,				2504	0.1953				p.A336A		Atlas-SNP	.											.	KRT75	75	.	0			c.C1008T						PASS	.	G		317,4089	170.9+/-201.2	15,287,1901	178.0	160.0	166.0		1008	-11.5	0.1	12	dbSNP_80	166	3227,5373	487.3+/-372.1	610,2007,1683	no	coding-synonymous	KRT75	NM_004693.2		625,2294,3584	AA,AG,GG		37.5233,7.1947,27.249		336/552	52824352	3544,9462	2203	4300	6503	SO:0001819	synonymous_variant	9119	exon5			AGCCTCGGCCCGG	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.1008C>T	12.37:g.52824352G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	193	94	0.487047	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																			G|0.709;A|0.291	0.291	strong		0.552	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
ABCA8	10351	hgsc.bcm.edu	37	17	66871837	66871837	+	Missense_Mutation	SNP	C	C	T	rs35403175	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:66871837C>T	ENST00000269080.2	-	34	4425	c.4288G>A	c.(4288-4290)Ggt>Agt	p.G1430S	ABCA8_ENST00000586539.1_Missense_Mutation_p.G1470S|ABCA8_ENST00000430352.2_Missense_Mutation_p.G1470S	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1430	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		G -> S (in dbSNP:rs35403175).		transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					AGGAGGGCACCCCTTTCCGTG	0.502													C|||	316	0.063099	0.1051	0.0303	5008	,	,		18648	0.0516		0.0189	False		,,,				2504	0.0869				p.G1430S		Atlas-SNP	.											.	ABCA8	213	.	0			c.G4288A						PASS	.	C	SER/GLY	385,4021	194.3+/-219.2	16,353,1834	85.0	66.0	72.0		4288	3.4	0.9	17	dbSNP_126	72	131,8469	66.3+/-128.7	1,129,4170	yes	missense	ABCA8	NM_007168.2	56	17,482,6004	TT,TC,CC		1.5233,8.7381,3.9674	possibly-damaging	1430/1582	66871837	516,12490	2203	4300	6503	SO:0001583	missense	10351	exon34			GGGCACCCCTTTC	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.4288G>A	17.37:g.66871837C>T	ENSP00000269080:p.Gly1430Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	40	0.37037	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	85	0.03891941391941392	37	0.07520325203252033	15	0.04143646408839779	19	0.033216783216783216	14	0.018469656992084433	C	23.8	4.462244	0.84425	0.087381	0.015233	ENSG00000141338	ENST00000269080;ENST00000430352	D;D	0.95171	-3.63;-3.63	4.36	3.38	0.38709	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.116383	0.38381	N	0.001705	T	0.36717	0.0977	N	0.05351	-0.065	0.48341	D	0.999634	D;P;D	0.67145	0.996;0.939;0.996	P;P;P	0.62813	0.907;0.779;0.907	T	0.73655	-0.3914	10	0.07325	T	0.83	.	11.4474	0.50131	0.0:0.9118:0.0:0.0881	rs35403175	1470;1470;1430	A1L3U3;C9JQE6;O94911	.;.;ABCA8_HUMAN	S	1430;1470	ENSP00000269080:G1430S;ENSP00000402814:G1470S	ENSP00000269080:G1430S	G	-	1	0	ABCA8	64383432	0.917000	0.31117	0.933000	0.37362	0.855000	0.48748	5.579000	0.67457	1.195000	0.43115	0.650000	0.86243	GGT	C|0.961;T|0.039	0.039	strong		0.502	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
CCDC54	84692	hgsc.bcm.edu	37	3	107097346	107097346	+	Silent	SNP	C	C	A	rs3811061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:107097346C>A	ENST00000261058.1	+	1	1159	c.912C>A	c.(910-912)acC>acA	p.T304T		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	304										NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						TGAGCTTGACCACAATCTGTC	0.433													C|||	346	0.0690895	0.0204	0.0692	5008	,	,		19322	0.0357		0.1272	False		,,,				2504	0.1094				p.T304T		Atlas-SNP	.											.	CCDC54	56	.	0			c.C912A						PASS	.	C		158,4216		3,152,2032	88.0	91.0	90.0		912	0.3	1.0	3	dbSNP_107	90	940,7644		53,834,3405	no	coding-synonymous	CCDC54	NM_032600.2		56,986,5437	AA,AC,CC		10.9506,3.6123,8.4735		304/329	107097346	1098,11860	2187	4292	6479	SO:0001819	synonymous_variant	84692	exon1			CTTGACCACAATC	AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"""sperm protein 17"""					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.912C>A	3.37:g.107097346C>A		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	297	164	0.552189	NM_032600	Q96A43	Silent	SNP	ENST00000261058.1	37	CCDS2949.1																																																																																			C|0.914;A|0.086	0.086	strong		0.433	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600	
LRRC61	65999	hgsc.bcm.edu	37	7	150034378	150034378	+	Missense_Mutation	SNP	A	A	G	rs3735169	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150034378A>G	ENST00000359623.4	+	3	1016	c.428A>G	c.(427-429)aAc>aGc	p.N143S	LRRC61_ENST00000323078.7_Missense_Mutation_p.N143S|LRRC61_ENST00000493307.1_Missense_Mutation_p.N143S	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	143	LRRCT.		N -> S (in dbSNP:rs3735169). {ECO:0000269|PubMed:14702039}.							endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			CTCTGTGCCAACCCCTCCTAC	0.657													G|||	1294	0.258387	0.2625	0.1571	5008	,	,		18703	0.2897		0.2455	False		,,,				2504	0.3057				p.N143S		Atlas-SNP	.											.	LRRC61	17	.	0			c.A428G						PASS	.	G	SER/ASN,SER/ASN	1076,3330	719.7+/-409.0	128,820,1255	57.0	57.0	57.0		428,428	0.7	0.1	7	dbSNP_107	57	2198,6402	709.9+/-405.7	286,1626,2388	yes	missense,missense	LRRC61	NM_001142928.1,NM_023942.2	46,46	414,2446,3643	GG,GA,AA		25.5581,24.4212,25.173	benign,benign	143/260,143/260	150034378	3274,9732	2203	4300	6503	SO:0001583	missense	65999	exon2			GTGCCAACCCCTC	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.428A>G	7.37:g.150034378A>G	ENSP00000352642:p.Asn143Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_023942	B3KUW0|D3DWY8	Missense_Mutation	SNP	ENST00000359623.4	37	CCDS5901.1	572	0.2619047619047619	118	0.23983739837398374	66	0.18232044198895028	182	0.3181818181818182	206	0.2717678100263852	G	0.012	-1.649709	0.00785	0.244212	0.255581	ENSG00000127399	ENST00000323078;ENST00000359623;ENST00000493307	T;T;T	0.22945	1.93;1.93;1.93	3.82	0.741	0.18336	.	0.276635	0.36591	N	0.002504	T	0.00012	0.0000	N	0.02158	-0.66	0.48452	P	3.429999999999822E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.48352	-0.9043	9	0.18710	T	0.47	-7.5883	7.2278	0.26026	0.4766:0.0:0.5234:0.0	rs3735169;rs57401595;rs3735169	143	Q9BV99	LRC61_HUMAN	S	143	ENSP00000339047:N143S;ENSP00000352642:N143S;ENSP00000420560:N143S	ENSP00000339047:N143S	N	+	2	0	LRRC61	149665311	0.000000	0.05858	0.095000	0.20976	0.498000	0.33706	-0.123000	0.10611	-0.314000	0.08716	-0.665000	0.03846	AAC	A|0.744;G|0.256	0.256	strong		0.657	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942	
TTC28	23331	hgsc.bcm.edu	37	22	28504258	28504258	+	Silent	SNP	A	A	G	rs9625409	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:28504258A>G	ENST00000397906.2	-	7	1716	c.1575T>C	c.(1573-1575)aaT>aaC	p.N525N		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	525					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						TGCCCAGGGCATTGTAGGCAT	0.572													A|||	297	0.0593051	0.0598	0.0677	5008	,	,		18711	0.002		0.0755	False		,,,				2504	0.0951				p.N525N		Atlas-SNP	.											.	TTC28	84	.	0			c.T1575C						PASS	.	A		96,1288		1,94,597	82.0	75.0	77.0		1575	-10.4	0.3	22	dbSNP_119	77	264,2918		15,234,1342	no	coding-synonymous	TTC28	NM_001145418.1		16,328,1939	GG,GA,AA		8.2967,6.9364,7.8844		525/2482	28504258	360,4206	692	1591	2283	SO:0001819	synonymous_variant	23331	exon7			CAGGGCATTGTAG	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.1575T>C	22.37:g.28504258A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			A|0.942;G|0.058	0.058	strong		0.572	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
UBD	10537	hgsc.bcm.edu	37	6	29523957	29523957	+	Silent	SNP	A	A	G	rs404240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29523957A>G	ENST00000377050.4	-	2	421	c.198T>C	c.(196-198)taT>taC	p.Y66Y	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	66	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.				aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TGTCAATGCCATAAGATGAGA	0.498													A|||	90	0.0179712	0.0023	0.0187	5008	,	,		21228	0.0		0.0736	False		,,,				2504	0.0				p.Y66Y		Atlas-SNP	.											.	UBD	13	.	0			c.T198C						PASS	.	A		61,2961		0,61,1450	62.0	62.0	62.0		198	-3.2	0.3	6	dbSNP_80	62	501,4917		26,449,2234	no	coding-synonymous	UBD	NM_006398.3		26,510,3684	GG,GA,AA		9.247,2.0185,6.6588		66/166	29523957	562,7878	1511	2709	4220	SO:0001819	synonymous_variant	10537	exon2			AATGCCATAAGAT	Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.198T>C	6.37:g.29523957A>G		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	241	92	0.381743	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Silent	SNP	ENST00000377050.4	37	CCDS4662.1																																																																																			A|0.947;G|0.053	0.053	strong		0.498	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3		
ACTR8	93973	hgsc.bcm.edu	37	3	53905308	53905308	+	Silent	SNP	T	T	C	rs1046677	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:53905308T>C	ENST00000335754.3	-	11	1618	c.1518A>G	c.(1516-1518)ggA>ggG	p.G506G	ACTR8_ENST00000482349.1_Silent_p.G395G|ACTR8_ENST00000231909.7_Silent_p.G211G|ACTR8_ENST00000488802.1_5'Flank	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	506					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		CCAGGGCTTTTCCTTCAAACA	0.547													C|||	3467	0.692292	0.7186	0.6196	5008	,	,		19990	0.9444		0.4523	False		,,,				2504	0.6953				p.G506G		Atlas-SNP	.											ACTR8_ENST00000231909,NS,carcinoma,-2,2	ACTR8	56	2	0			c.A1518G						PASS	.	C		2977,1429	464.5+/-353.9	1009,959,235	103.0	100.0	101.0		1518	-2.5	0.9	3	dbSNP_86	101	3771,4829	614.9+/-396.3	814,2143,1343	no	coding-synonymous	ACTR8	NM_022899.4		1823,3102,1578	CC,CT,TT		43.8488,32.433,48.1163		506/625	53905308	6748,6258	2203	4300	6503	SO:0001819	synonymous_variant	93973	exon11			GGCTTTTCCTTCA		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"""INO80 complex subunits"""	14672	protein-coding gene	gene with protein product	"""INO80 complex subunit N"""		"""ARP8 (actin-related protein 8, yeast) homolog"""			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.1518A>G	3.37:g.53905308T>C		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	270	130	0.481481	NM_022899	B3KSW7|Q8N566|Q9H663	Silent	SNP	ENST00000335754.3	37	CCDS2875.1	1456	0.6666666666666666	363	0.7378048780487805	223	0.6160220994475138	541	0.9458041958041958	329	0.4340369393139842	C	9.636	1.137708	0.21123	0.67567	0.438488	ENSG00000113812	ENST00000486794	.	.	.	5.67	-2.54	0.06307	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.19976	-1.0289	3	.	.	.	-11.7537	7.8427	0.29408	0.0:0.2982:0.3936:0.3082	rs1046677;rs17641862;rs17846012;rs17858996;rs57230247;rs1046677	.	.	.	G	260	.	.	E	-	2	0	ACTR8	53880348	0.916000	0.31088	0.936000	0.37596	0.958000	0.62258	-0.016000	0.12613	-0.796000	0.04456	-1.551000	0.00897	GAA	T|0.410;C|0.590	0.590	strong		0.547	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899	
ACPP	55	hgsc.bcm.edu	37	3	132068831	132068831	+	Silent	SNP	C	C	T	rs2228402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:132068831C>T	ENST00000336375.5	+	8	939	c.849C>T	c.(847-849)ctC>ctT	p.L283L	ACPP_ENST00000351273.7_Silent_p.L283L|ACPP_ENST00000475741.1_Silent_p.L250L	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	283					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						ACAAAAAACTCATCATGTATT	0.353													T|||	1981	0.395567	0.3585	0.4841	5008	,	,		21077	0.1171		0.5378	False		,,,				2504	0.5235				p.L283L		Atlas-SNP	.											.	ACPP	118	.	0			c.C849T						PASS	.	T	,	1706,2700	651.9+/-399.3	337,1032,834	138.0	123.0	128.0		849,849	-7.9	0.0	3	dbSNP_98	128	4801,3799	537.8+/-383.3	1332,2137,831	no	coding-synonymous,coding-synonymous	ACPP	NM_001099.4,NM_001134194.1	,	1669,3169,1665	TT,TC,CC		44.1744,38.7199,49.9692	,	283/387,283/419	132068831	6507,6499	2203	4300	6503	SO:0001819	synonymous_variant	55	exon8			AAAACTCATCATG		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.849C>T	3.37:g.132068831C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	142	62	0.43662	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Silent	SNP	ENST00000336375.5	37	CCDS3073.1																																																																																			C|0.529;T|0.471	0.471	strong		0.353	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099	
TCP10	6953	hgsc.bcm.edu	37	6	167786686	167786686	+	Missense_Mutation	SNP	C	C	T	rs140649985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167786686C>T	ENST00000397829.4	-	8	1119	c.952G>A	c.(952-954)Gct>Act	p.A318T	TCP10_ENST00000366827.2_Intron	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	345						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		CTGGAGGGAGCGGCGTGCAGA	0.532																																					p.A318T		Atlas-SNP	.											.	TCP10	35	.	0			c.G952A						PASS	.	C	THR/ALA	5,3699		0,5,1847	86.0	91.0	89.0		952	-3.3	0.0	6	dbSNP_134	89	45,8151		0,45,4053	no	missense	TCP10	NM_004610.3	58	0,50,5900	TT,TC,CC		0.549,0.135,0.4202	probably-damaging	318/327	167786686	50,11850	1852	4098	5950	SO:0001583	missense	6953	exon8			AGGGAGCGGCGTG	U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"""t-complex 10 (a murine tcp homolog)"", ""t-complex 10 (mouse)"", ""t-complex 10 homolog (mouse)"""			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.952G>A	6.37:g.167786686C>T	ENSP00000380929:p.Ala318Thr	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	188	49	0.260638	NM_004610	Q5JR60|Q6P4F4	Missense_Mutation	SNP	ENST00000397829.4	37	CCDS43527.1	18	0.008241758241758242	2	0.0040650406504065045	1	0.0027624309392265192	5	0.008741258741258742	10	0.013192612137203167	c	13.11	2.137893	0.37728	0.00135	0.00549	ENSG00000203690	ENST00000397829	T	0.27890	1.64	1.64	-3.29	0.05017	.	.	.	.	.	T	0.03178	0.0093	N	0.14661	0.345	0.09310	N	0.999998	P	0.45126	0.851	B	0.24848	0.056	T	0.23547	-1.0185	9	0.87932	D	0	.	4.2044	0.10481	0.3777:0.3043:0.3179:0.0	.	345	Q12799	TCP10_HUMAN	T	318	ENSP00000380929:A318T	ENSP00000380929:A318T	A	-	1	0	TCP10	167706676	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.523000	0.06230	-1.547000	0.01715	0.467000	0.42956	GCT	C|0.994;T|0.006	0.006	strong		0.532	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134943	32134943	+	Missense_Mutation	SNP	A	A	G	rs10771894	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32134943A>G	ENST00000312561.4	+	4	1468	c.1054A>G	c.(1054-1056)Agt>Ggt	p.S352G	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	352			S -> G (in dbSNP:rs10771894). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039}.														GCCTTTTAACAGTCCCATTAG	0.373													a|||	1754	0.35024	0.4047	0.3862	5008	,	,		21305	0.3135		0.3588	False		,,,				2504	0.2802				p.S352G		Atlas-SNP	.											.	.	.	.	0			c.A1054G						PASS	.	A	GLY/SER	1825,2581	530.8+/-373.0	376,1073,754	82.0	82.0	82.0		1054	0.4	0.0	12	dbSNP_120	82	3212,5388	483.4+/-371.1	588,2036,1676	yes	missense	C12orf35	NM_018169.3	56	964,3109,2430	GG,GA,AA		37.3488,41.4208,38.7283	benign	352/1748	32134943	5037,7969	2203	4300	6503	SO:0001583	missense	55196	exon4			TTTAACAGTCCCA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1054A>G	12.37:g.32134943A>G	ENSP00000310338:p.Ser352Gly	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	804	0.36813186813186816	213	0.4329268292682927	137	0.3784530386740331	178	0.3111888111888112	276	0.3641160949868074	a	10.49	1.364702	0.24684	0.414208	0.373488	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.05925	4.01;3.37	5.45	0.438	0.16560	.	1.541240	0.03671	N	0.243908	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47045	-0.9147	8	.	.	.	.	2.3617	0.04308	0.1959:0.14:0.5207:0.1434	rs10771894;rs17511162;rs61657460;rs10771894	352	Q9HCM1	CL035_HUMAN	G	352	ENSP00000310338:S352G;ENSP00000370442:S352G	.	S	+	1	0	C12orf35	32026210	0.024000	0.19004	0.001000	0.08648	0.001000	0.01503	1.074000	0.30703	0.187000	0.20147	-0.253000	0.11424	AGT	A|0.620;G|0.380	0.380	strong		0.373	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
OR10H5	284433	hgsc.bcm.edu	37	19	15905289	15905289	+	Missense_Mutation	SNP	G	G	T	rs61754873	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15905289G>T	ENST00000308940.8	+	1	529	c.431G>T	c.(430-432)cGg>cTg	p.R144L		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						TGCACCTGCCGGGTGGGCTGC	0.622													.|||	470	0.0938498	0.0938	0.1081	5008	,	,		19943	0.0635		0.1312	False		,,,				2504	0.0767				p.R144L		Atlas-SNP	.											.	OR10H5	49	.	0			c.G431T						PASS	.	T	LEU/ARG	412,3994		25,362,1816	94.0	81.0	85.0		431	3.4	0.0	19	dbSNP_129	85	1160,7440		78,1004,3218	no	missense	OR10H5	NM_001004466.1	102	103,1366,5034	TT,TG,GG		13.4884,9.3509,12.0867	benign	144/316	15905289	1572,11434	2203	4300	6503	SO:0001583	missense	284433	exon1			CCTGCCGGGTGGG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.431G>T	19.37:g.15905289G>T	ENSP00000310704:p.Arg144Leu	Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	221	104	0.470588	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	229	0.10485347985347986	45	0.09146341463414634	47	0.1298342541436464	42	0.07342657342657342	95	0.12532981530343007	.	0.011	-1.700170	0.00725	0.093509	0.134884	ENSG00000172519	ENST00000308940	T	0.29917	1.55	3.36	3.36	0.38483	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39020	N	0.001494	T	0.00039	0.0001	N	0.00003	-3.435	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27297	-1.0078	9	0.02654	T	1	.	6.7711	0.23594	0.0:0.0:0.2415:0.7585	rs61754873	144	Q8NGA6	O10H5_HUMAN	L	144	ENSP00000310704:R144L	ENSP00000310704:R144L	R	+	2	0	OR10H5	15766289	0.016000	0.18221	0.009000	0.14445	0.406000	0.30931	2.214000	0.42853	0.487000	0.27698	-0.346000	0.07831	CGG	G|0.875;T|0.125	0.125	strong		0.622	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
REXO4	57109	hgsc.bcm.edu	37	9	136277482	136277482	+	Missense_Mutation	SNP	T	T	C	rs2285487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136277482T>C	ENST00000371942.3	-	4	1046	c.847A>G	c.(847-849)Act>Gct	p.T283A	REXO4_ENST00000478037.1_5'UTR|REXO4_ENST00000371935.2_Intron	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	283	Exonuclease.		T -> A (in dbSNP:rs2285487). {ECO:0000269|PubMed:9325058}.		regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		ACGGGCTCAGTTGGTTTGACG	0.562													T|||	168	0.0335463	0.0083	0.0403	5008	,	,		20922	0.0198		0.0825	False		,,,				2504	0.0266				p.T283A		Atlas-SNP	.											.	REXO4	27	.	0			c.A847G						PASS	.	T	ALA/THR	93,4313	75.7+/-113.9	1,91,2111	241.0	221.0	228.0		847	-0.3	0.0	9	dbSNP_100	228	731,7869	176.3+/-226.2	37,657,3606	yes	missense	REXO4	NM_020385.2	58	38,748,5717	CC,CT,TT		8.5,2.1108,6.3355	probably-damaging	283/423	136277482	824,12182	2203	4300	6503	SO:0001583	missense	57109	exon4			GCTCAGTTGGTTT	AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"""Xenopus prevents mitotic catatrophe 2 homolog"", ""XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"""	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.847A>G	9.37:g.136277482T>C	ENSP00000361010:p.Thr283Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Missense_Mutation	SNP	ENST00000371942.3	37	CCDS6969.1	101	0.04624542124542125	7	0.014227642276422764	16	0.04419889502762431	12	0.02097902097902098	66	0.0870712401055409	T	10.27	1.304442	0.23736	0.021108	0.085	ENSG00000148300	ENST00000453165;ENST00000371942	T;T	0.30182	1.54;1.54	5.03	-0.329	0.12686	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.102758	0.64402	N	0.000003	T	0.00754	0.0025	L	0.58101	1.795	0.09310	P	0.9999999824378	B	0.17038	0.02	B	0.21151	0.033	T	0.24728	-1.0152	9	0.11485	T	0.65	-13.7982	5.2666	0.15603	0.0:0.243:0.1399:0.6171	rs2285487;rs41506846;rs59923134;rs2285487	283	Q9GZR2	REXO4_HUMAN	A	268;283	ENSP00000403272:T268A;ENSP00000361010:T283A	ENSP00000361010:T283A	T	-	1	0	REXO4	135267303	0.939000	0.31865	0.002000	0.10522	0.158000	0.22134	1.523000	0.35932	-0.290000	0.09025	0.459000	0.35465	ACT	T|0.944;C|0.056	0.056	strong		0.562	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1		
SLC23A3	151295	hgsc.bcm.edu	37	2	220034377	220034377	+	Silent	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220034377C>A	ENST00000409878.3	-	2	218	c.186G>T	c.(184-186)ctG>ctT	p.L62L	SLC23A3_ENST00000396775.3_Silent_p.L4L|SLC23A3_ENST00000455516.2_Silent_p.L62L|SLC23A3_ENST00000295738.7_Silent_p.L62L	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	62					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGACACAGAGCAGAGAAGCCA	0.532																																					p.L62L		Atlas-SNP	.											.	SLC23A3	60	.	0			c.G186T						PASS	.						57.0	76.0	69.0					2																	220034377		2091	4226	6317	SO:0001819	synonymous_variant	151295	exon2			ACAGAGCAGAGAA	BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901		"""Solute carriers"""	20601	protein-coding gene	gene with protein product							Standard	NM_144712		Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	Q6PIS1	OTTHUMG00000154616	ENST00000409878.3:c.186G>T	2.37:g.220034377C>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	105	5	0.047619	NM_001144890	B7Z512|Q2PYN6|Q96NA6	Silent	SNP	ENST00000409878.3	37	CCDS46518.1																																																																																			.	.	none		0.532	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626571	140626571	+	Silent	SNP	C	C	A	rs652104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140626571C>A	ENST00000231173.3	+	1	1425	c.1425C>A	c.(1423-1425)gcC>gcA	p.A475A		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	475	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A475A(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTGTCAGCGCCACAGACAGAG	0.657													C|||	1264	0.252396	0.0113	0.2911	5008	,	,		14631	0.5258		0.2316	False		,,,				2504	0.2904				p.A475A		Atlas-SNP	.											PCDHB15,NS,carcinoma,0,1	PCDHB15	138	1	1	Substitution - coding silent(1)	stomach(1)	c.C1425A						PASS	.						68.0	76.0	73.0					5																	140626571		2203	4289	6492	SO:0001819	synonymous_variant	56121	exon1			CAGCGCCACAGAC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1425C>A	5.37:g.140626571C>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	171	118	0.690058	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			C|0.766;A|0.234	0.234	strong		0.657	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
MUC4	4585	hgsc.bcm.edu	37	3	195510827	195510827	+	Missense_Mutation	SNP	C	C	T	rs413807	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195510827C>T	ENST00000463781.3	-	2	8083	c.7624G>A	c.(7624-7626)Gcc>Acc	p.A2542T	MUC4_ENST00000475231.1_Missense_Mutation_p.A2542T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACGTGTG	0.582													.|||	177	0.0353435	0.1293	0.0058	5008	,	,		17991	0.001		0.0	False		,,,				2504	0.001				p.A2542T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G7624A						PASS	.						179.0	144.0	154.0					3																	195510827		652	1591	2243	SO:0001583	missense	4585	exon2			AGGTGGCGTGACG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7624G>A	3.37:g.195510827C>T	ENSP00000417498:p.Ala2542Thr	Somatic	465	0	0		WXS	Illumina HiSeq	Phase_I	723	351	0.485477	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	9.405	1.079094	0.20227	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.43;1.42	.	.	.	.	.	.	.	.	T	0.09113	0.0225	N	0.08118	0	0.52099	P	5.999999999994898E-5	P	0.52463	0.953	B	0.28991	0.097	T	0.23404	-1.0189	6	.	.	.	.	4.4363	0.11552	0.0:0.666:0.0:0.334	rs413807	2542	E7ESK3	.	T	2542	ENSP00000417498:A2542T;ENSP00000420243:A2542T	.	A	-	1	0	MUC4	196995222	0.040000	0.19996	0.000000	0.03702	0.000000	0.00434	-1.533000	0.02215	-0.000000	0.14550	0.000000	0.15137	GCC	C|0.500;T|0.500	0.500	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HAGHL	84264	hgsc.bcm.edu	37	16	778820	778820	+	Silent	SNP	G	G	A	rs12448432	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:778820G>A	ENST00000341413.4	+	7	806	c.525G>A	c.(523-525)acG>acA	p.T175T	HAGHL_ENST00000549114.1_Missense_Mutation_p.A202T|HAGHL_ENST00000564537.1_Missense_Mutation_p.A202T|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000561546.1_Silent_p.T175T|HAGHL_ENST00000389703.3_Silent_p.T175T|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000564545.1_Missense_Mutation_p.A84T			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	175							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				ACGAGCACACGCTTAGCAACC	0.667													G|||	1975	0.394369	0.1573	0.4625	5008	,	,		9189	0.7569		0.2376	False		,,,				2504	0.454				p.T175T	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											.	HAGHL	18	.	0			c.G525A						PASS	.	G		563,3815	238.7+/-250.0	32,499,1658	26.0	27.0	26.0		525	-8.2	0.0	16	dbSNP_120	26	1796,6786	299.9+/-304.7	197,1402,2692	no	coding-synonymous	HAGHL	NM_032304.2		229,1901,4350	AA,AG,GG		20.9275,12.8598,18.2022		175/283	778820	2359,10601	2189	4291	6480	SO:0001819	synonymous_variant	84264	exon6			GCACACGCTTAGC	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.525G>A	16.37:g.778820G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	113	60	0.530973	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37		865	0.39606227106227104	82	0.16666666666666666	148	0.4088397790055249	436	0.7622377622377622	199	0.262532981530343	G	15.03	2.712967	0.48517	0.128598	0.209275	ENSG00000103253	ENST00000549114;ENST00000389701	D	0.87103	-2.21	4.27	-8.21	0.01041	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999590043	B	0.11235	0.004	B	0.12837	0.008	T	0.34551	-0.9824	6	.	.	.	-20.0695	1.828	0.03125	0.4147:0.1648:0.2828:0.1376	rs12448432;rs61367184;rs12448432	202	Q6PII5-3	.	T	202;203	ENSP00000447170:A202T	.	A	+	1	0	HAGHL	718821	0.002000	0.14202	0.002000	0.10522	0.426000	0.31534	-1.023000	0.03607	-1.455000	0.01923	-0.258000	0.10820	GCT	G|0.733;A|0.267	0.267	strong		0.667	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
KMT2C	58508	hgsc.bcm.edu	37	7	151970797	151970797	+	Silent	SNP	A	A	T	rs141993954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151970797A>T	ENST00000262189.6	-	7	1223	c.1005T>A	c.(1003-1005)ccT>ccA	p.P335P	KMT2C_ENST00000355193.2_Silent_p.P335P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	335					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TACATCTTTCAGGAGCTTGGT	0.388																																					p.P335P		Atlas-SNP	.											MLL3_ENST00000355193,NS,adenoma,0,4	MLL3	1564	4	0			c.T1005A						PASS	.	A		49,4357	29.0+/-57.7	0,49,2154	236.0	218.0	224.0		1005	2.3	1.0	7	dbSNP_134	224	176,8424	61.0+/-122.8	0,176,4124	no	coding-synonymous	MLL3	NM_170606.2		0,225,6278	TT,TA,AA		2.0465,1.1121,1.73		335/4912	151970797	225,12781	2203	4300	6503	SO:0001819	synonymous_variant	58508	exon7			TCTTTCAGGAGCT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1005T>A	7.37:g.151970797A>T		Somatic	751	0	0		WXS	Illumina HiSeq	Phase_I	745	87	0.116779	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			A|0.985;T|0.015	0.015	strong		0.388	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
MUC4	4585	hgsc.bcm.edu	37	3	195514948	195514948	+	Missense_Mutation	SNP	G	G	A	rs200751227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195514948G>A	ENST00000463781.3	-	2	3962	c.3503C>T	c.(3502-3504)cCt>cTt	p.P1168L	MUC4_ENST00000475231.1_Missense_Mutation_p.P1168L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	646	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P1168L(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GACAGGAAGAGGGGTGGCCTG	0.567													.|||	2	0.000399361	0.0	0.0	5008	,	,		10668	0.0		0.0	False		,,,				2504	0.002				p.P1168L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	stomach(2)	c.C3503T						PASS	.						3.0	2.0	3.0					3																	195514948		529	1152	1681	SO:0001583	missense	4585	exon2			GGAAGAGGGGTGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3503C>T	3.37:g.195514948G>A	ENSP00000417498:p.Pro1168Leu	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	118	96	0.813559	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	8.096	0.775646	0.16051	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.3;1.3	0.534	0.534	0.17127	.	.	.	.	.	T	0.15912	0.0383	N	0.19112	0.55	0.80722	P	0.0	P	0.42584	0.784	B	0.28849	0.095	T	0.17623	-1.0363	7	.	.	.	.	6.9921	0.24761	1.0E-4:0.0:0.9999:0.0	.	1168	E7ESK3	.	L	1168	ENSP00000417498:P1168L;ENSP00000420243:P1168L	.	P	-	2	0	MUC4	196999343	.	.	0.016000	0.15963	0.034000	0.12701	.	.	0.582000	0.29556	0.064000	0.15345	CCT	G|0.819;A|0.181	0.181	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HIF1AN	55662	hgsc.bcm.edu	37	10	102295836	102295836	+	Missense_Mutation	SNP	C	C	G	rs2295778	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:102295836C>G	ENST00000299163.6	+	1	221	c.121C>G	c.(121-123)Ccc>Gcc	p.P41A		NM_017902.2	NP_060372.2	Q9NWT6	HIF1N_HUMAN	hypoxia inducible factor 1, alpha subunit inhibitor	41	Interaction with VHL.		P -> A (in dbSNP:rs2295778). {ECO:0000269|Ref.4}.		cellular response to hypoxia (GO:0071456)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|oxidation-reduction process (GO:0055114)|peptidyl-asparagine hydroxylation (GO:0042265)|peptidyl-aspartic acid hydroxylation (GO:0042264)|peptidyl-histidine hydroxylation (GO:0036138)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of vasculogenesis (GO:2001214)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ankyrin repeat binding (GO:0071532)|carboxylic acid binding (GO:0031406)|cofactor binding (GO:0048037)|iron ion binding (GO:0005506)|NF-kappaB binding (GO:0051059)|Notch binding (GO:0005112)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-asparagine 3-dioxygenase activity (GO:0036140)|peptidyl-histidine dioxygenase activity (GO:0036139)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(1)|prostate(2)|urinary_tract(1)	10		Colorectal(252;0.234)		Epithelial(162;6.75e-10)|all cancers(201;4.88e-08)		CCCGACTAGGCCCATTCCGCG	0.657											OREG0020442	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	905	0.180711	0.0182	0.2147	5008	,	,		13350	0.253		0.2694	False		,,,				2504	0.2106				p.P41A		Atlas-SNP	.											HIF1AN,NS,carcinoma,0,1	HIF1AN	41	1	0			c.C121G	GRCh37	CM065271	HIF1AN	M	rs2295778	PASS	.	C	ALA/PRO	218,4164		5,208,1978	14.0	16.0	16.0		121	4.1	1.0	10	dbSNP_100	16	2193,6363		302,1589,2387	yes	missense	HIF1AN	NM_017902.2	27	307,1797,4365	GG,GC,CC		25.6311,4.9749,18.635	benign	41/350	102295836	2411,10527	2191	4278	6469	SO:0001583	missense	55662	exon1			ACTAGGCCCATTC	AK000622	CCDS7498.1	10q24	2008-12-18	2008-12-02		ENSG00000166135	ENSG00000166135	1.14.11.16		17113	protein-coding gene	gene with protein product	"""Peptide-aspartate beta-dioxygenase"""	606615				11641274	Standard	NM_017902		Approved	FLJ20615, DKFZp762F1811, FLJ22027, FIH1	uc001krj.4	Q9NWT6	OTTHUMG00000018911	ENST00000299163.6:c.121C>G	10.37:g.102295836C>G	ENSP00000299163:p.Pro41Ala	Somatic	115	0	0	1365	WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_017902	D3DR69|Q5W147|Q969Q7|Q9NPV5	Missense_Mutation	SNP	ENST00000299163.6	37	CCDS7498.1	435	0.19917582417582416	10	0.02032520325203252	85	0.23480662983425415	135	0.23601398601398602	205	0.2704485488126649	C	10.95	1.496867	0.26861	0.049749	0.256311	ENSG00000166135	ENST00000299163;ENST00000442724	T	0.70399	-0.48	5.08	4.13	0.48395	.	0.118844	0.64402	D	0.000018	T	0.00012	0.0000	L	0.34521	1.04	0.23754	P	0.99693669	B	0.09022	0.002	B	0.01281	0.0	T	0.03619	-1.1019	9	0.41790	T	0.15	-10.1627	15.7617	0.78087	0.0:0.8642:0.1358:0.0	rs2295778;rs52817205;rs2295778	41	Q9NWT6	HIF1N_HUMAN	A	41;74	ENSP00000299163:P41A	ENSP00000299163:P41A	P	+	1	0	HIF1AN	102285826	1.000000	0.71417	1.000000	0.80357	0.351000	0.29236	2.861000	0.48380	2.646000	0.89796	0.650000	0.86243	CCC	C|0.806;G|0.194	0.194	strong		0.657	HIF1AN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049865.5	NM_017902	
UNC79	57578	hgsc.bcm.edu	37	14	94103602	94103602	+	Silent	SNP	G	G	A	rs4905082	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94103602G>A	ENST00000393151.2	+	33	5874	c.5874G>A	c.(5872-5874)acG>acA	p.T1958T	UNC79_ENST00000555664.1_Silent_p.T1919T|UNC79_ENST00000256339.4_Silent_p.T1781T|UNC79_ENST00000553484.1_Silent_p.T1980T			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1958					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						acgtgccaacgtgcctaaacc	0.483													G|||	2530	0.505192	0.3472	0.6585	5008	,	,		19782	0.3849		0.674	False		,,,				2504	0.5603				p.T1781T		Atlas-SNP	.											UNC79,colon,carcinoma,+1,2	UNC79	366	2	0			c.G5343A						PASS	.	G		1698,2708	514.4+/-368.6	338,1022,843	155.0	113.0	127.0		5343	-0.5	0.9	14	dbSNP_111	127	5819,2781	678.3+/-403.5	1954,1911,435	no	coding-synonymous	UNC79	NM_020818.3		2292,2933,1278	AA,AG,GG		32.3372,38.5384,42.2036		1781/2459	94103602	7517,5489	2203	4300	6503	SO:0001819	synonymous_variant	57578	exon33			GCCAACGTGCCTA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.5874G>A	14.37:g.94103602G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																				G|0.450;A|0.550	0.550	strong		0.483	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
ZNF561	93134	hgsc.bcm.edu	37	19	9721401	9721401	+	Silent	SNP	A	A	T	rs28445940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9721401A>T	ENST00000302851.3	-	6	1299	c.936T>A	c.(934-936)acT>acA	p.T312T	ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000424629.1_Silent_p.T243T|ZNF561_ENST00000495503.1_5'Flank|ZNF561_ENST00000354661.4_Silent_p.T176T	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						TCCCACAGTAAGTACACTTGT	0.378													T|||	1411	0.281749	0.5	0.3775	5008	,	,		22239	0.0665		0.2107	False		,,,				2504	0.2137				p.T312T		Atlas-SNP	.											.	ZNF561	64	.	0			c.T936A						PASS	.	T		1828,2578	637.6+/-396.8	377,1074,752	134.0	124.0	128.0		936	-2.2	0.0	19	dbSNP_125	128	1704,6896	737.5+/-407.0	170,1364,2766	no	coding-synonymous	ZNF561	NM_152289.2		547,2438,3518	TT,TA,AA		19.814,41.4889,27.1567		312/487	9721401	3532,9474	2203	4300	6503	SO:0001819	synonymous_variant	93134	exon6			ACAGTAAGTACAC	AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"""Zinc fingers, C2H2-type"", ""-"""	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.936T>A	19.37:g.9721401A>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	168	80	0.47619	NM_152289	B4E2Q8|Q6PJS0	Silent	SNP	ENST00000302851.3	37	CCDS12216.2																																																																																			A|0.733;T|0.267	0.267	strong		0.378	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289	
ZNF625	90589	hgsc.bcm.edu	37	19	12256358	12256358	+	Silent	SNP	T	T	G	rs12972621	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12256358T>G	ENST00000355738.1	-	4	1024	c.675A>C	c.(673-675)cgA>cgC	p.R225R	ZNF625-ZNF20_ENST00000430024.1_Intron|ZNF625_ENST00000542938.1_Silent_p.R225R|ZNF625_ENST00000455799.1_3'UTR|CTC-359D24.3_ENST00000472362.1_RNA|ZNF625_ENST00000439556.2_Silent_p.R291R			Q96I27	ZN625_HUMAN	zinc finger protein 625	225					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|large_intestine(6)|lung(4)|skin(2)	14						TTTCATGATATCGAACGGAAT	0.453													T|||	2003	0.39996	0.0295	0.3862	5008	,	,		22544	0.6369		0.4533	False		,,,				2504	0.6115				p.R291R		Atlas-SNP	.											ZNF625,trunk,malignant_melanoma,-2,1	ZNF625	37	1	0			c.A873C						PASS	.	T		433,3973	210.2+/-230.7	24,385,1794	123.0	117.0	119.0		873	0.9	0.0	19	dbSNP_121	119	4008,4592	554.9+/-386.6	928,2152,1220	no	coding-synonymous	ZNF625	NM_145233.3		952,2537,3014	GG,GT,TT		46.6047,9.8275,34.1458		291/373	12256358	4441,8565	2203	4300	6503	SO:0001819	synonymous_variant	90589	exon4			ATGATATCGAACG	BC007868	CCDS12269.1, CCDS12269.2	19p13.2	2013-01-08			ENSG00000257591	ENSG00000257591		"""Zinc fingers, C2H2-type"", ""-"""	30571	protein-coding gene	gene with protein product						12477932	Standard	NM_145233		Approved		uc010dyo.2	Q96I27	OTTHUMG00000156407	ENST00000355738.1:c.675A>C	19.37:g.12256358T>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	117	64	0.547009	NM_145233	A4FU45|I3L0E9	Silent	SNP	ENST00000355738.1	37																																																																																				G|0.365;N|0.000	0.365	strong		0.453	ZNF625-201	KNOWN	basic	protein_coding	protein_coding		NM_145233	
ANKLE2	23141	hgsc.bcm.edu	37	12	133306710	133306710	+	Missense_Mutation	SNP	C	C	T	rs78905764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133306710C>T	ENST00000357997.5	-	11	2127	c.2038G>A	c.(2038-2040)Gag>Aag	p.E680K	ANKLE2_ENST00000542657.1_Missense_Mutation_p.E35K|ANKLE2_ENST00000542374.1_Intron|ANKLE2_ENST00000539605.1_Missense_Mutation_p.E618K|ANKLE2_ENST00000542282.1_Missense_Mutation_p.E35K	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	680				E -> K (in Ref. 1; BAG52720). {ECO:0000305}.	mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GCCTCCTGCTCCAAGGGGAAG	0.572													c|||	264	0.0527157	0.0015	0.0447	5008	,	,		15971	0.1002		0.0785	False		,,,				2504	0.0521				p.E680K		Atlas-SNP	.											.	ANKLE2	76	.	0			c.G2038A						PASS	.		LYS/GLU	43,3885		0,43,1921	58.0	63.0	61.0		2038	4.7	0.1	12	dbSNP_131	61	593,7689		25,543,3573	yes	missense	ANKLE2	NM_015114.1	56	25,586,5494	TT,TC,CC		7.1601,1.0947,5.2088	possibly-damaging	680/939	133306710	636,11574	1964	4141	6105	SO:0001583	missense	23141	exon11			CCTGCTCCAAGGG	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.2038G>A	12.37:g.133306710C>T	ENSP00000350686:p.Glu680Lys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	CCDS41869.1	137	0.06272893772893773	2	0.0040650406504065045	18	0.049723756906077346	60	0.1048951048951049	57	0.07519788918205805	C	16.07	3.018310	0.54576	0.010947	0.071601	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000542282;ENST00000542657;ENST00000538766	T;T;T;T;T	0.51071	1.8;1.78;0.73;0.73;0.72	5.53	4.65	0.58169	.	0.525762	0.23266	N	0.050080	T	0.01421	0.0046	L	0.46157	1.445	0.09310	P	0.99999999986259	P	0.48640	0.913	B	0.41813	0.367	T	0.17228	-1.0376	9	0.38643	T	0.18	-11.1214	14.6753	0.68975	0.0:0.9301:0.0:0.0699	.	680	Q86XL3	ANKL2_HUMAN	K	618;680;35;35;35	ENSP00000446268:E618K;ENSP00000350686:E680K;ENSP00000437807:E35K;ENSP00000438551:E35K;ENSP00000445760:E35K	ENSP00000350686:E680K	E	-	1	0	ANKLE2	131816783	0.526000	0.26298	0.080000	0.20451	0.057000	0.15508	4.268000	0.58883	1.483000	0.48342	0.651000	0.88453	GAG	C|0.934;T|0.066	0.066	strong		0.572	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
CUBN	8029	hgsc.bcm.edu	37	10	16949550	16949550	+	Silent	SNP	T	T	C	rs3740165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:16949550T>C	ENST00000377833.4	-	49	7727	c.7662A>G	c.(7660-7662)ccA>ccG	p.P2554P		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2554	CUB 18. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGCCGCCATATGGCCTGGATC	0.448													T|||	533	0.10643	0.2073	0.0346	5008	,	,		18553	0.1508		0.0358	False		,,,				2504	0.0481				p.P2554P		Atlas-SNP	.											.	CUBN	515	.	0			c.A7662G						PASS	.	T		757,3649	308.6+/-290.6	59,639,1505	93.0	79.0	84.0		7662	-6.1	1.0	10	dbSNP_107	84	306,8294	110.4+/-170.8	5,296,3999	no	coding-synonymous	CUBN	NM_001081.3		64,935,5504	CC,CT,TT		3.5581,17.1811,8.1732		2554/3624	16949550	1063,11943	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon49			GCCATATGGCCTG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.7662A>G	10.37:g.16949550T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			T|0.911;C|0.089	0.089	strong		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
PAXIP1	22976	hgsc.bcm.edu	37	7	154760666	154760666	+	Silent	SNP	C	C	T	rs61752011	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:154760666C>T	ENST00000404141.1	-	7	1399	c.1245G>A	c.(1243-1245)ccG>ccA	p.P415P	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Silent_p.P415P			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	415	Gln-rich.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		GGTGTAAAACCGGGtgctgct	0.562													C|||	1110	0.221645	0.0484	0.3588	5008	,	,		16758	0.2133		0.2922	False		,,,				2504	0.2945				p.P415P		Atlas-SNP	.											PAXIP1_ENST00000397192,NS,carcinoma,0,2	PAXIP1	150	2	0			c.G1245A						PASS	.	C		272,3634		8,256,1689	22.0	22.0	22.0		1245	-9.9	0.0	7	dbSNP_129	22	1762,5876		184,1394,2241	no	coding-synonymous	PAXIP1	NM_007349.3		192,1650,3930	TT,TC,CC		23.0689,6.9636,17.6195		415/1070	154760666	2034,9510	1953	3819	5772	SO:0001819	synonymous_variant	22976	exon7			TAAAACCGGGTGC	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1245G>A	7.37:g.154760666C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Silent	SNP	ENST00000404141.1	37	CCDS47753.1																																																																																			C|0.784;T|0.216	0.216	strong		0.562	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
DNAH5	1767	hgsc.bcm.edu	37	5	13780991	13780991	+	Silent	SNP	C	C	T	rs111995400	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13780991C>T	ENST00000265104.4	-	53	9002	c.8898G>A	c.(8896-8898)acG>acA	p.T2966T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2966	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AAGCCAACCTCGTCAGGCTCT	0.463									Kartagener syndrome				C|||	52	0.0103834	0.0015	0.0101	5008	,	,		18879	0.0		0.0398	False		,,,				2504	0.0031				p.T2966T		Atlas-SNP	.											.	DNAH5	868	.	0			c.G8898A						PASS	.	C		22,4384	30.8+/-60.4	0,22,2181	94.0	80.0	85.0		8898	-11.1	0.7	5	dbSNP_132	85	272,8328	104.0+/-165.0	3,266,4031	no	coding-synonymous	DNAH5	NM_001369.2		3,288,6212	TT,TC,CC		3.1628,0.4993,2.2605		2966/4625	13780991	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon53	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAACCTCGTCAGG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8898G>A	5.37:g.13780991C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			C|0.979;T|0.021	0.021	strong		0.463	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133961494	133961494	+	Silent	SNP	C	C	T	rs2818384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:133961494C>T	ENST00000298622.4	+	13	1926	c.1788C>T	c.(1786-1788)caC>caT	p.H596H	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	596						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GGCTCAGACACGAGGTGCAGG	0.557													C|||	2131	0.425519	0.2821	0.7233	5008	,	,		19908	0.3065		0.5895	False		,,,				2504	0.362				p.H596H		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.C1788T						PASS	.			1524,2878	470.5+/-355.8	250,1024,927	120.0	95.0	104.0		1788	-6.3	0.5	10	dbSNP_100	104	5208,3380	622.9+/-397.4	1603,2002,689	no	coding-synonymous	JAKMIP3	NM_001105521.2		1853,3026,1616	TT,TC,CC		39.3572,34.6206,48.1755		596/845	133961494	6732,6258	2201	4294	6495	SO:0001819	synonymous_variant	282973	exon13			CAGACACGAGGTG	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1788C>T	10.37:g.133961494C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			C|0.514;T|0.486	0.486	strong		0.557	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
CFAP46	54777	hgsc.bcm.edu	37	10	134682855	134682855	+	Silent	SNP	C	C	T	rs7908950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134682855C>T	ENST00000368586.5	-	33	4633	c.4533G>A	c.(4531-4533)gaG>gaA	p.E1511E		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCAGCTTCAGCTCGGAGCACG	0.657													C|||	1568	0.313099	0.1256	0.5173	5008	,	,		14842	0.2649		0.3877	False		,,,				2504	0.3947				p.E1511E		Atlas-SNP	.											.	TTC40	100	.	0			c.G4533A						PASS	.																																			SO:0001819	synonymous_variant	54777	exon33			CTTCAGCTCGGAG																												ENST00000368586.5:c.4533G>A	10.37:g.134682855C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			C|0.713;T|0.287	0.287	strong		0.657	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
SMG6	23293	hgsc.bcm.edu	37	17	2203175	2203175	+	Missense_Mutation	SNP	C	C	G	rs1885986	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:2203175C>G	ENST00000263073.6	-	2	922	c.872G>C	c.(871-873)cGa>cCa	p.R291P	SMG6_ENST00000544865.1_Missense_Mutation_p.R260P	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	291	Interaction with telomeric DNA.		R -> P (in dbSNP:rs1885986). {ECO:0000269|PubMed:9872452}.		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTTCTTCAGTCGTGGCCTCTC	0.552													C|||	925	0.184704	0.0318	0.4222	5008	,	,		17225	0.0893		0.3569	False		,,,				2504	0.1442				p.R291P	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G872C						PASS	.	C	PRO/ARG,PRO/ARG	321,4085	169.4+/-200.1	15,291,1897	84.0	74.0	78.0		779,872	5.3	1.0	17	dbSNP_92	78	3091,5509	473.3+/-368.6	554,1983,1763	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	103,103	569,2274,3660	GG,GC,CC		35.9419,7.2855,26.234	probably-damaging,probably-damaging	260/1389,291/1420	2203175	3412,9594	2203	4300	6503	SO:0001583	missense	23293	exon2			TTCAGTCGTGGCC	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.872G>C	17.37:g.2203175C>G	ENSP00000263073:p.Arg291Pro	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	169	83	0.491124	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	512	0.23443223443223443	21	0.042682926829268296	155	0.4281767955801105	75	0.13111888111888112	261	0.34432717678100266	C	15.57	2.871802	0.51695	0.072855	0.359419	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.10288	2.89;2.89	5.35	5.35	0.76521	.	0.282865	0.34245	N	0.004131	T	0.00012	0.0000	L	0.29908	0.895	0.46011	P	0.0011879999999999669	D	0.71674	0.998	D	0.64042	0.921	T	0.55283	-0.8165	9	0.54805	T	0.06	-3.0807	19.0567	0.93069	0.0:1.0:0.0:0.0	rs1885986;rs3744273;rs1885986	291	Q86US8	EST1A_HUMAN	P	291;260	ENSP00000263073:R291P;ENSP00000443920:R260P	ENSP00000263073:R291P	R	-	2	0	SMG6	2149925	0.963000	0.33076	0.997000	0.53966	0.976000	0.68499	3.931000	0.56529	2.490000	0.84030	0.655000	0.94253	CGA	C|0.743;G|0.257	0.257	strong		0.552	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
IVL	3713	hgsc.bcm.edu	37	1	152882981	152882981	+	Silent	SNP	A	A	T	rs62637699	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152882981A>T	ENST00000368764.3	+	2	772	c.708A>T	c.(706-708)ccA>ccT	p.P236P	IVL_ENST00000392667.2_Silent_p.P90P			P07476	INVO_HUMAN	involucrin	236	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		P -> S (in dbSNP:rs17855670). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2873896}.		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			tggagctcccacagcagcagg	0.677																																					p.P236P		Atlas-SNP	.											IVL,colon,carcinoma,+2,2	IVL	100	2	0			c.A708T						scavenged	.						3.0	4.0	3.0					1																	152882981		1601	3431	5032	SO:0001819	synonymous_variant	3713	exon2			GCTCCCACAGCAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.708A>T	1.37:g.152882981A>T		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	159	39	0.245283	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			A|0.696;T|0.304	0.304	strong		0.677	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
SHROOM2	357	hgsc.bcm.edu	37	X	9863112	9863112	+	Silent	SNP	A	A	G	rs6530341	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:9863112A>G	ENST00000380913.3	+	4	1254	c.1164A>G	c.(1162-1164)ccA>ccG	p.P388P		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	388					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				CGGGCTGCCCACAGGAGGCCC	0.677													A|||	786	0.208212	0.1672	0.1974	3775	,	,		10580	0.2669		0.0905	False		,,,				2504	0.0695				p.P388P		Atlas-SNP	.											.	SHROOM2	139	.	0			c.A1164G						PASS	.	A		865,2957		89,557,130,984,432	19.0	16.0	17.0		1164	-8.6	0.0	X	dbSNP_116	17	928,5788		49,587,243,1791,1619	no	coding-synonymous	SHROOM2	NM_001649.2		138,1144,373,2775,2051	GG,GA,G,AA,A		13.8177,22.6321,17.0146		388/1617	9863112	1793,8745	2192	4289	6481	SO:0001819	synonymous_variant	357	exon4			CTGCCCACAGGAG	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.1164A>G	X.37:g.9863112A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_001649	B9EIQ7	Silent	SNP	ENST00000380913.3	37	CCDS14135.1																																																																																			A|0.805;0|0.004	.	strong		0.677	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
GPR116	221395	hgsc.bcm.edu	37	6	46827073	46827073	+	Missense_Mutation	SNP	A	A	G	rs547499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46827073A>G	ENST00000283296.7	-	17	2855	c.2567T>C	c.(2566-2568)aTg>aCg	p.M856T	GPR116_ENST00000265417.7_Missense_Mutation_p.M856T|GPR116_ENST00000362015.4_Missense_Mutation_p.M856T|GPR116_ENST00000456426.2_Missense_Mutation_p.M714T|GPR116_ENST00000545669.1_Missense_Mutation_p.M285T	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	856			M -> T (in dbSNP:rs547499). {ECO:0000269|PubMed:10048485, ECO:0000269|PubMed:15489334}.		energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CTTGATTACCATGCTGCTCAT	0.453													A|||	2556	0.510383	0.149	0.6225	5008	,	,		20276	0.63		0.7227	False		,,,				2504	0.5777				p.M856T	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											GPR116,caecum,carcinoma,0,1	GPR116	133	1	0			c.T2567C						PASS	.	A	THR/MET,THR/MET	1025,3381	379.0+/-323.1	130,765,1308	66.0	62.0	63.0		2567,2567	5.6	0.9	6	dbSNP_83	63	6228,2372	702.4+/-405.3	2263,1702,335	no	missense,missense	GPR116	NM_001098518.1,NM_015234.4	81,81	2393,2467,1643	GG,GA,AA		27.5814,23.2637,44.2334	possibly-damaging,possibly-damaging	856/1347,856/1347	46827073	7253,5753	2203	4300	6503	SO:0001583	missense	221395	exon17			ATTACCATGCTGC	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2567T>C	6.37:g.46827073A>G	ENSP00000283296:p.Met856Thr	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	288	114	0.395833	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	1193	0.5462454212454212	85	0.17276422764227642	223	0.6160220994475138	344	0.6013986013986014	541	0.7137203166226913	A	2.044	-0.419264	0.04766	0.232637	0.724186	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84	5.58	5.58	0.84498	.	0.344395	0.29178	N	0.012912	T	0.22936	0.0554	L	0.60455	1.87	0.52501	P	4.499999999996174E-5	B;P;B;P	0.35656	0.007;0.514;0.005;0.514	B;B;B;B	0.33521	0.013;0.165;0.03;0.165	T	0.21177	-1.0253	9	0.27785	T	0.31	-22.9312	6.2135	0.20642	0.7824:0.0:0.0747:0.1428	rs547499;rs547499	285;856;714;856	F5GWK9;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;GP116_HUMAN	T	856;856;856;714;227;856;285	ENSP00000283296:M856T;ENSP00000354563:M856T;ENSP00000412866:M714T;ENSP00000265417:M856T;ENSP00000441581:M285T	ENSP00000265417:M856T	M	-	2	0	GPR116	46935032	0.003000	0.15002	0.941000	0.38009	0.671000	0.39405	1.833000	0.39161	2.126000	0.65437	0.454000	0.30748	ATG	A|0.452;G|0.548	0.548	strong		0.453	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
LOXL4	84171	hgsc.bcm.edu	37	10	100013438	100013438	+	Silent	SNP	C	C	T	rs17524355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:100013438C>T	ENST00000260702.3	-	11	1857	c.1707G>A	c.(1705-1707)gcG>gcA	p.A569A	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	569	Lysyl-oxidase like.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		CCATGTGATCCGCAGACTTGG	0.592													C|||	659	0.131589	0.1528	0.1484	5008	,	,		18566	0.0288		0.2207	False		,,,				2504	0.1053				p.A569A		Atlas-SNP	.											LOXL4,caecum,carcinoma,-1,2	LOXL4	60	2	0			c.G1707A						PASS	.	C		767,3639	311.1+/-291.9	75,617,1511	110.0	99.0	102.0		1707	-8.3	0.6	10	dbSNP_123	102	1841,6759	330.9+/-319.4	193,1455,2652	no	coding-synonymous	LOXL4	NM_032211.6		268,2072,4163	TT,TC,CC		21.407,17.4081,20.0523		569/757	100013438	2608,10398	2203	4300	6503	SO:0001819	synonymous_variant	84171	exon11			GTGATCCGCAGAC	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1707G>A	10.37:g.100013438C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Silent	SNP	ENST00000260702.3	37	CCDS7473.1																																																																																			C|0.826;T|0.174	0.174	strong		0.592	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
NUAK2	81788	hgsc.bcm.edu	37	1	205273040	205273040	+	Silent	SNP	G	G	A	rs56069742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205273040G>A	ENST00000367157.3	-	7	1551	c.1425C>T	c.(1423-1425)ggC>ggT	p.G475G		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CAAACACGTCGCCTGCGTCCA	0.582													G|||	11	0.00219649	0.0	0.0072	5008	,	,		16957	0.001		0.005	False		,,,				2504	0.0				p.G475G		Atlas-SNP	.											.	NUAK2	107	.	0			c.C1425T						PASS	.	G		12,4394	16.8+/-37.8	0,12,2191	35.0	34.0	34.0		1425	-9.7	0.0	1	dbSNP_129	34	132,8468	66.7+/-129.0	0,132,4168	no	coding-synonymous	NUAK2	NM_030952.1		0,144,6359	AA,AG,GG		1.5349,0.2724,1.1072		475/629	205273040	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	81788	exon7			CACGTCGCCTGCG	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1425C>T	1.37:g.205273040G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_030952		Silent	SNP	ENST00000367157.3	37	CCDS1453.1																																																																																			G|0.992;A|0.008	0.008	strong		0.582	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
DNAH9	1770	hgsc.bcm.edu	37	17	11757556	11757556	+	Silent	SNP	C	C	G	rs12449553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11757556C>G	ENST00000262442.4	+	50	9812	c.9744C>G	c.(9742-9744)ccC>ccG	p.P3248P	DNAH9_ENST00000454412.2_Silent_p.P3248P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3248	Stalk. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.P3248P(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TGCAAGACCCCGAGTTCAATC	0.488													C|||	2021	0.403554	0.3336	0.5893	5008	,	,		19390	0.3403		0.4245	False		,,,				2504	0.41				p.P3248P		Atlas-SNP	.											DNAH9,NS,carcinoma,0,1	DNAH9	695	1	1	Substitution - coding silent(1)	stomach(1)	c.C9744G						PASS	.	C		1483,2923	474.6+/-357.0	250,983,970	150.0	139.0	143.0		9744	-11.1	0.0	17	dbSNP_120	143	3668,4932	525.7+/-380.8	801,2066,1433	no	coding-synonymous	DNAH9	NM_001372.3		1051,3049,2403	GG,GC,CC		42.6512,33.6586,39.6048		3248/4487	11757556	5151,7855	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon50			AGACCCCGAGTTC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.9744C>G	17.37:g.11757556C>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.605;G|0.395	0.395	strong		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
OR10A2	341276	hgsc.bcm.edu	37	11	6891605	6891605	+	Missense_Mutation	SNP	A	A	G	rs10839631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6891605A>G	ENST00000307322.4	+	1	682	c.620A>G	c.(619-621)cAc>cGc	p.H207R		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	207			H -> R (in dbSNP:rs10839631). {ECO:0000269|PubMed:12213199}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TCCTATACTCACATTGCTGCT	0.463													-|||	1625	0.324481	0.2073	0.3732	5008	,	,		23826	0.3135		0.3569	False		,,,				2504	0.4264				p.H207R		Atlas-SNP	.											.	OR10A2	55	.	0			c.A620G						PASS	.	G	ARG/HIS	885,3517		89,707,1405	274.0	213.0	233.0		620	-2.8	0.0	11	dbSNP_120	233	3204,5388		604,1996,1696	no	missense	OR10A2	NM_001004460.1	29	693,2703,3101	GG,GA,AA		37.2905,20.1045,31.4684	benign	207/304	6891605	4089,8905	2201	4296	6497	SO:0001583	missense	341276	exon1			ATACTCACATTGC	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"""GPCR / Class A : Olfactory receptors"""	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.620A>G	11.37:g.6891605A>G	ENSP00000303862:p.His207Arg	Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	304	164	0.539474	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	37	CCDS31415.1	642	0.29395604395604397	90	0.18292682926829268	125	0.3453038674033149	169	0.29545454545454547	258	0.3403693931398417	N	0.001	-3.294832	0.00019	0.201045	0.372905	ENSG00000170790	ENST00000307322	T	0.00063	8.78	4.18	-2.84	0.05751	GPCR, rhodopsin-like superfamily (1);	0.330770	0.26525	N	0.023888	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.36504	-0.9745	9	0.02654	T	1	.	4.3458	0.11133	0.3087:0.0:0.3224:0.3689	rs10839631;rs10839631	207	Q9H208	O10A2_HUMAN	R	207	ENSP00000303862:H207R	ENSP00000303862:H207R	H	+	2	0	OR10A2	6848181	0.000000	0.05858	0.004000	0.12327	0.110000	0.19582	-2.861000	0.00726	-1.081000	0.03105	-3.683000	0.00024	CAC	A|0.689;G|0.311	0.311	strong		0.463	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460	
FDFT1	2222	hgsc.bcm.edu	37	8	11689119	11689119	+	Silent	SNP	G	G	C	rs9205	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11689119G>C	ENST00000220584.4	+	7	1194	c.972G>C	c.(970-972)ctG>ctC	p.L324L	FDFT1_ENST00000528812.1_Silent_p.L260L|FDFT1_ENST00000525777.1_Silent_p.L239L|FDFT1_ENST00000528643.1_Silent_p.L239L|FDFT1_ENST00000538689.1_Silent_p.L213L|FDFT1_ENST00000443614.2_Silent_p.L281L|FDFT1_ENST00000525900.1_Silent_p.L317L|FDFT1_ENST00000530664.1_Silent_p.L260L|FDFT1_ENST00000446331.2_3'UTR	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	324					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		CAGTGACCCTGATGATGGATG	0.443													G|||	1537	0.306909	0.084	0.2824	5008	,	,		19543	0.7252		0.2097	False		,,,				2504	0.2945				p.L324L		Atlas-SNP	.											.	FDFT1	25	.	0			c.G972C						PASS	.	G		506,3900	234.2+/-247.1	20,466,1717	212.0	198.0	203.0		972	-9.1	0.2	8	dbSNP_52	203	1801,6799	324.6+/-316.5	208,1385,2707	no	coding-synonymous	FDFT1	NM_004462.3		228,1851,4424	CC,CG,GG		20.9419,11.4843,17.738		324/418	11689119	2307,10699	2203	4300	6503	SO:0001819	synonymous_variant	2222	exon7			GACCCTGATGATG	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.972G>C	8.37:g.11689119G>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	102	40	0.392157	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Silent	SNP	ENST00000220584.4	37	CCDS5985.1																																																																																			G|0.773;C|0.227	0.227	strong		0.443	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
SMIM3	85027	hgsc.bcm.edu	37	5	150175109	150175109	+	Missense_Mutation	SNP	C	C	T	rs61736140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150175109C>T	ENST00000526627.1	+	2	1145	c.107C>T	c.(106-108)tCg>tTg	p.S36L	AC010441.1_ENST00000600109.1_3'UTR	NM_032947.4	NP_116565.3	Q9BZL3	SMIM3_HUMAN	small integral membrane protein 3	36						integral component of membrane (GO:0016021)											ATCATGACCTCGTTGTTGCTG	0.547													C|||	10	0.00199681	0.0	0.0029	5008	,	,		22069	0.0		0.008	False		,,,				2504	0.0				p.S36L		Atlas-SNP	.											.	.	.	.	0			c.C107T						PASS	.																																			SO:0001583	missense	85027	exon2			TGACCTCGTTGTT	AF313413	CCDS47312.1, CCDS47312.2	5q33.1	2012-10-01	2012-10-01	2012-10-01	ENSG00000256235	ENSG00000256235			30248	protein-coding gene	gene with protein product		608324	"""chromosome 5 open reading frame 62"""	C5orf62		11288140	Standard	NM_032947		Approved	MSTP150, NID67	uc003lsw.3	Q9BZL3	OTTHUMG00000163646	ENST00000526627.1:c.107C>T	5.37:g.150175109C>T	ENSP00000436897:p.Ser36Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	40	0.689655	NM_032947	Q3MIG3|Q6ZUV4	Missense_Mutation	SNP	ENST00000526627.1	37	CCDS47312.2	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	18.98	3.737622	0.69304	.	.	ENSG00000256235	ENST00000526627	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	T	0.65554	0.2702	.	.	.	0.38915	D	0.957602	.	.	.	.	.	.	T	0.69514	-0.5125	4	.	.	.	.	16.8482	0.85986	0.0:1.0:0.0:0.0	rs61736140	.	.	.	L	36	.	.	S	+	2	0	C5orf62	150155302	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.723000	0.54955	2.768000	0.95171	0.491000	0.48974	TCG	C|0.996;T|0.004	0.004	strong		0.547	SMIM3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374647.2	NM_032947	
DMD	1756	hgsc.bcm.edu	37	X	31697636	31697636	+	Silent	SNP	A	A	G	rs1801188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:31697636A>G	ENST00000357033.4	-	53	7934	c.7728T>C	c.(7726-7728)aaT>aaC	p.N2576N	DMD_ENST00000378707.3_Silent_p.N116N|DMD_ENST00000474231.1_Silent_p.N116N|DMD_ENST00000343523.2_Silent_p.N116N|DMD_ENST00000378677.2_Silent_p.N2572N|DMD_ENST00000359836.1_Silent_p.N116N|DMD_ENST00000541735.1_Silent_p.N116N	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2576					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTAACATTTCATTCAACTGTT	0.413													A|||	684	0.181192	0.0711	0.1182	3775	,	,		11946	0.2887		0.1193	False		,,,				2504	0.0992				p.N2576N		Atlas-SNP	.											.	DMD	2127	.	0			c.T7728C						PASS	.	A	,,,,,,,,,,,	409,3424		15,323,56,1293,515	177.0	144.0	155.0		7704,7728,7359,7716,7359,3705,3696,348,348,348,348,348	3.5	1.0	X	dbSNP_89	155	1364,5364		109,765,381,1554,1491	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3,NM_004011.3,NM_004012.3,NM_004013.2,NM_004020.3,NM_004021.2,NM_004022.2,NM_004023.2	,,,,,,,,,,,	124,1088,437,2847,2006	GG,GA,G,AA,A		20.2735,10.6705,16.7882	,,,,,,,,,,,	2568/3678,2576/3686,2453/3563,2572/3682,2453/3563,1235/2345,1232/2342,116/1226,116/1116,116/1244,116/1231,116/1134	31697636	1773,8788	2202	4300	6502	SO:0001819	synonymous_variant	1756	exon53			CATTTCATTCAAC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.7728T>C	X.37:g.31697636A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1	332	0.2001205545509343	21	0.04375	25	0.0748502994011976	118	0.2610619469026549	67	0.0938375350140056	A	9.387	1.074424	0.20227	0.106705	0.202735	ENSG00000198947	ENST00000465285	.	.	.	5.89	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999795826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.9442	0.09341	0.5906:0.0:0.1497:0.2597	rs1801188;rs17338646;rs1801188	.	.	.	R	305	.	.	X	-	1	0	DMD	31607557	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.065000	0.30592	0.833000	0.34828	0.441000	0.28932	TGA	0|0.002;G|0.185	0.185	strong		0.413	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CACNA1A	773	hgsc.bcm.edu	37	19	13397324	13397324	+	Silent	SNP	G	G	A	rs16029	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:13397324G>A	ENST00000360228.5	-	20	3545	c.3546C>T	c.(3544-3546)gtC>gtT	p.V1182V	CACNA1A_ENST00000573710.2_Silent_p.V1183V	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1183					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CACCTTGTACGACGGTGTGGT	0.632													G|||	47	0.00938498	0.0008	0.0144	5008	,	,		12386	0.0		0.0258	False		,,,				2504	0.0102				p.V1183V		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C3549T						PASS	.	G	,,,,	12,3930		0,12,1959	29.0	30.0	29.0		3558,3549,3546,3549,3558	-4.6	0.8	19	dbSNP_54	29	175,8105		1,173,3966	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	1,185,5925	AA,AG,GG		2.1135,0.3044,1.53	,,,,	1186/2267,1183/2262,1182/2507,1183/2264,1186/2513	13397324	187,12035	1971	4140	6111	SO:0001819	synonymous_variant	773	exon20			TTGTACGACGGTG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3546C>T	19.37:g.13397324G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	172	63	0.366279	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			G|0.987;A|0.013	0.013	strong		0.632	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751544	19751544	+	Silent	SNP	C	C	T	rs2297224	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:19751544C>T	ENST00000400113.3	-	4	683	c.579G>A	c.(577-579)acG>acA	p.T193T		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	193					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		GTTCCAGGGTCGTGTGGGTGG	0.552													C|||	1446	0.288738	0.2171	0.2824	5008	,	,		20432	0.3671		0.2674	False		,,,				2504	0.3313				p.T193T		Atlas-SNP	.											.	TUBA3C	166	.	0			c.G579A						PASS	.	C		895,3511	345.7+/-308.6	108,679,1416	149.0	146.0	147.0		579	-1.0	1.0	13	dbSNP_100	147	2078,6518	360.1+/-331.8	261,1556,2481	no	coding-synonymous	TUBA3C	NM_006001.2		369,2235,3897	TT,TC,CC		24.174,20.3132,22.8657		193/451	19751544	2973,10029	2203	4298	6501	SO:0001819	synonymous_variant	7278	exon4			CAGGGTCGTGTGG	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.579G>A	13.37:g.19751544C>T		Somatic	529	1	0.00189036		WXS	Illumina HiSeq	Phase_I	522	287	0.549808	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			C|0.737;T|0.263	0.263	strong		0.552	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
MPP2	4355	hgsc.bcm.edu	37	17	41960343	41960343	+	Silent	SNP	T	T	C	rs124719	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41960343T>C	ENST00000461854.1	-	6	538	c.453A>G	c.(451-453)acA>acG	p.T151T	MPP2_ENST00000473246.1_5'UTR|MPP2_ENST00000520305.1_5'UTR|MPP2_ENST00000518766.1_Silent_p.T172T|MPP2_ENST00000269095.4_Silent_p.T127T|MPP2_ENST00000377184.3_Silent_p.T144T|MPP2_ENST00000536246.1_Silent_p.T116T|MPP2_ENST00000523501.1_Silent_p.T116T			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	151					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(4)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		GGTTGCTGAATGTAGGGTCCA	0.627													t|||	4138	0.826278	0.587	0.9006	5008	,	,		13497	1.0		0.838	False		,,,				2504	0.9059				p.T127T		Atlas-SNP	.											.	MPP2	67	.	0			c.A381G						PASS	.	T		2780,1626	660.3+/-400.7	884,1012,307	74.0	75.0	75.0		381	-5.3	0.5	17	dbSNP_79	75	7363,1237	760.6+/-407.6	3151,1061,88	no	coding-synonymous	MPP2	NM_005374.3		4035,2073,395	CC,CT,TT		14.3837,36.9042,22.0129		127/553	41960343	10143,2863	2203	4300	6503	SO:0001819	synonymous_variant	4355	exon5			GCTGAATGTAGGG		CCDS11471.1, CCDS62206.1, CCDS62207.1, CCDS62208.1, CCDS62209.1, CCDS62210.1	17q12-q21	2008-07-18			ENSG00000108852	ENSG00000108852			7220	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 2"", ""discs large, homolog 2"""	600723		DLG2		7590743	Standard	NM_001278370		Approved	DKFZp761D0712	uc002ieo.1	Q14168	OTTHUMG00000133840	ENST00000461854.1:c.453A>G	17.37:g.41960343T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	126	124	0.984127	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000461854.1	37																																																																																				T|0.208;C|0.792	0.792	strong		0.627	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374	
HIVEP1	3096	hgsc.bcm.edu	37	6	12124855	12124855	+	Missense_Mutation	SNP	G	G	A	rs2228213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:12124855G>A	ENST00000379388.2	+	4	5159	c.4827G>A	c.(4825-4827)atG>atA	p.M1609I	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1609			M -> I (in dbSNP:rs2228213). {ECO:0000269|PubMed:2108316}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M1609I(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTGACAGCATGTCTAATTCGC	0.458													G|||	1087	0.217053	0.0628	0.245	5008	,	,		22560	0.2232		0.333	False		,,,				2504	0.2802				p.M1609I		Atlas-SNP	.											HIVEP1,NS,carcinoma,0,1	HIVEP1	242	1	1	Substitution - Missense(1)	prostate(1)	c.G4827A						PASS	.	G	ILE/MET	375,3739		21,333,1703	127.0	127.0	127.0		4827	1.5	0.0	6	dbSNP_98	127	2879,5513		496,1887,1813	yes	missense	HIVEP1	NM_002114.2	10	517,2220,3516	AA,AG,GG		34.3065,9.1152,26.0195	benign	1609/2719	12124855	3254,9252	2057	4196	6253	SO:0001583	missense	3096	exon4			CAGCATGTCTAAT	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.4827G>A	6.37:g.12124855G>A	ENSP00000368698:p.Met1609Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	194	192	0.989691	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	513	0.2348901098901099	42	0.08536585365853659	87	0.24033149171270718	134	0.23426573426573427	250	0.32981530343007914	G	8.067	0.769364	0.15983	0.091152	0.343065	ENSG00000095951	ENST00000379388	T	0.08282	3.11	5.77	1.51	0.23008	.	.	.	.	.	T	0.02848	0.0085	L	0.47716	1.5	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.36114	-0.9761	7	.	.	.	0.3363	12.2002	0.54321	0.2588:0.0:0.7412:0.0	rs2228213;rs3823451;rs17609202;rs52803833;rs58502243;rs2228213	1609	P15822	ZEP1_HUMAN	I	1609	ENSP00000368698:M1609I	.	M	+	3	0	HIVEP1	12232841	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.624000	0.24462	0.369000	0.24510	0.650000	0.86243	ATG	G|0.757;A|0.241	0.241	strong		0.458	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
SPINK5	11005	hgsc.bcm.edu	37	5	147480027	147480027	+	Missense_Mutation	SNP	G	G	A	rs2303063	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147480027G>A	ENST00000256084.7	+	13	1145	c.1103G>A	c.(1102-1104)aGt>aAt	p.S368N	SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000398454.1_Missense_Mutation_p.S368N|SPINK5_ENST00000359874.3_Missense_Mutation_p.S368N	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	368	Kazal-like 6. {ECO:0000255|PROSITE- ProRule:PRU00798}.		S -> N (in dbSNP:rs2303063). {ECO:0000269|PubMed:10419450, ECO:0000269|PubMed:10835624, ECO:0000269|PubMed:16374478}.		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCTTTGCAGTGAATATCGA	0.443													G|||	2161	0.43151	0.1982	0.611	5008	,	,		17590	0.4831		0.4861	False		,,,				2504	0.5102				p.S368N		Atlas-SNP	.											.	SPINK5	245	.	0			c.G1103A	GRCh37	CM013814	SPINK5	M	rs2303063	PASS	.	G	ASN/SER,ASN/SER,ASN/SER	960,2862		118,724,1069	120.0	107.0	111.0		1103,1103,1103	2.3	0.1	5	dbSNP_100	111	4223,4041		1072,2079,981	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	46,46,46	1190,2803,2050	AA,AG,GG		48.8988,25.1177,42.8843	benign,benign,benign	368/1095,368/917,368/1065	147480027	5183,6903	1911	4132	6043	SO:0001583	missense	11005	exon13			TTTGCAGTGAATA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1103G>A	5.37:g.147480027G>A	ENSP00000256084:p.Ser368Asn	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	935	0.4281135531135531	111	0.22560975609756098	213	0.5883977900552486	263	0.4597902097902098	348	0.45910290237467016	G	2.157	-0.393140	0.04899	0.251177	0.511012	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.07800	3.16;3.16;3.16;3.16	4.6	2.35	0.29111	Proteinase inhibitor I1, Kazal (1);	0.506378	0.16574	N	0.208519	T	0.00012	0.0000	N	0.21508	0.67	0.52501	P	4.899999999996574E-5	B;B;B	0.13145	0.007;0.004;0.007	B;B;B	0.17433	0.018;0.008;0.018	T	0.26849	-1.0091	9	0.15952	T	0.53	-1.5338	5.9604	0.19297	0.3001:0.0:0.6999:0.0	rs2303063;rs17718582;rs17860504;rs52815597;rs2303063	368;368;368	Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;ISK5_HUMAN;.	N	368;368;349;368	ENSP00000381472:S368N;ENSP00000352936:S368N;ENSP00000421519:S349N;ENSP00000256084:S368N	ENSP00000256084:S368N	S	+	2	0	SPINK5	147460220	0.005000	0.15991	0.108000	0.21378	0.231000	0.25187	0.036000	0.13819	0.432000	0.26286	0.591000	0.81541	AGT	G|0.573;A|0.427	0.427	strong		0.443	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
PKN2	5586	hgsc.bcm.edu	37	1	89271574	89271574	+	Splice_Site	SNP	T	T	C	rs786906	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89271574T>C	ENST00000370521.3	+	12	2036	c.1677T>C	c.(1675-1677)agT>agC	p.S559S	PKN2_ENST00000544045.1_Splice_Site_p.S233S|PKN2_ENST00000370505.3_Splice_Site_p.S402S|PKN2_ENST00000370513.5_Splice_Site_p.S511S|PKN2_ENST00000316005.7_3'UTR	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	559					apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		CTTCTATAAGTGATTCTACAG	0.338													T|||	2562	0.511581	0.3563	0.4856	5008	,	,		17131	0.4702		0.5676	False		,,,				2504	0.7249				p.S559S		Atlas-SNP	.											.	PKN2	109	.	0			c.T1677C						PASS	.	T		1495,2133		310,875,629	65.0	60.0	61.0		1677	4.6	1.0	1	dbSNP_86	61	4571,3605		1268,2035,785	yes	coding-synonymous-near-splice	PKN2	NM_006256.2		1578,2910,1414	CC,CT,TT		44.0925,41.2073,48.6106		559/985	89271574	6066,5738	1814	4088	5902	SO:0001630	splice_region_variant	5586	exon12			TATAAGTGATTCT	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1677-1T>C	1.37:g.89271574T>C		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	170	167	0.982353	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Silent	SNP	ENST00000370521.3	37	CCDS714.1																																																																																			T|0.475;G|0.005	.	strong		0.338	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	Silent
FAM175B	23172	hgsc.bcm.edu	37	10	126517989	126517989	+	Silent	SNP	G	G	A	rs2303611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:126517989G>A	ENST00000298492.5	+	7	651	c.606G>A	c.(604-606)gtG>gtA	p.V202V		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	202					cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						AGGATGGAGTGATGAAAGACA	0.373													G|||	2419	0.483027	0.1694	0.5663	5008	,	,		18460	0.5873		0.5457	False		,,,				2504	0.6759				p.V202V		Atlas-SNP	.											.	FAM175B	39	.	0			c.G606A						PASS	.	G		1043,3363	382.1+/-324.3	130,783,1290	175.0	165.0	168.0		606	-11.7	0.0	10	dbSNP_100	168	4905,3695	620.3+/-397.0	1403,2099,798	no	coding-synonymous	FAM175B	NM_032182.3		1533,2882,2088	AA,AG,GG		42.9651,23.6723,45.7327		202/416	126517989	5948,7058	2203	4300	6503	SO:0001819	synonymous_variant	23172	exon7			TGGAGTGATGAAA	D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"""Abraxas brother"""	611144	"""KIAA0157"""	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.606G>A	10.37:g.126517989G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	202	202	1	NM_032182	B4DKR2|Q96H11	Silent	SNP	ENST00000298492.5	37	CCDS31308.2																																																																																			G|0.534;A|0.466	0.466	strong		0.373	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182	
ELN	2006	hgsc.bcm.edu	37	7	73470714	73470714	+	Missense_Mutation	SNP	G	G	A	rs2071307	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73470714G>A	ENST00000252034.7	+	20	1663	c.1264G>A	c.(1264-1266)Ggt>Agt	p.G422S	ELN_ENST00000380575.4_Missense_Mutation_p.G412S|ELN_ENST00000380562.4_Missense_Mutation_p.G422S|ELN_ENST00000357036.5_Missense_Mutation_p.G427S|ELN_ENST00000380576.5_Missense_Mutation_p.G422S|ELN_ENST00000320399.6_Missense_Mutation_p.G422S|ELN_ENST00000320492.7_Intron|ELN_ENST00000445912.1_Missense_Mutation_p.G422S|ELN_ENST00000380584.4_Missense_Mutation_p.G408S|ELN_ENST00000429192.1_Missense_Mutation_p.G427S|ELN_ENST00000458204.1_Missense_Mutation_p.G412S|ELN_ENST00000414324.1_Missense_Mutation_p.G417S|ELN_ENST00000380553.4_Missense_Mutation_p.G305S|ELN_ENST00000358929.4_Missense_Mutation_p.G422S	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.		G -> S (in dbSNP:rs2071307). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2831431, ECO:0000269|PubMed:3039501, ECO:0000269|PubMed:3171221, ECO:0000269|PubMed:8689688, ECO:0000269|PubMed:9215670}.		blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)	p.G422S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				AGGTGTCCCTGGTGTCGGAGG	0.617			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""						A|||	1104	0.220447	0.1339	0.2464	5008	,	,		15486	0.1081		0.4205	False		,,,				2504	0.229				p.G427S		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	ELN,NS,carcinoma,0,1	ELN	81	1	1	Substitution - Missense(1)	stomach(1)	c.G1279A						PASS	.	A	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	779,3627	753.3+/-412.4	72,635,1496	110.0	108.0	108.0		1264,1279,1279,1234,1264	1.2	0.0	7	dbSNP_96	108	3551,5049	630.5+/-398.4	728,2095,1477	yes	missense,missense,missense,missense,missense	ELN	NM_001081755.1,NM_001081754.1,NM_001081753.1,NM_001081752.1,NM_000501.2	56,56,56,56,56	800,2730,2973	AA,AG,GG		41.2907,17.6804,33.2923	benign,benign,benign,benign,benign	422/706,427/712,427/693,412/678,422/725	73470714	4330,8676	2203	4300	6503	SO:0001583	missense	2006	exon20			GTCCCTGGTGTCG		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1264G>A	7.37:g.73470714G>A	ENSP00000252034:p.Gly422Ser	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	306	147	0.480392	NM_001081753	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	37	CCDS5562.2	559	0.25595238095238093	74	0.15040650406504066	108	0.2983425414364641	78	0.13636363636363635	299	0.3944591029023747	A	10.41	1.343509	0.24339	0.176804	0.412907	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000442462;ENST00000380553;ENST00000380576;ENST00000320399	T;T;T;T;T;T;T;T;T;T;T;T;T	0.58652	1.13;1.16;0.32;1.18;1.14;1.25;1.38;1.14;1.11;1.27;1.31;1.28;1.16	2.18	1.2	0.21068	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B;B;B	0.15141	0.012;0.012;0.012;0.012;0.007;0.012;0.012;0.012;0.012;0.012;0.012;0.012	B;B;B;B;B;B;B;B;B;B;B;B	0.06405	0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002	T	0.36237	-0.9756	7	0.49607	T	0.09	.	7.3905	0.26907	0.1691:0.0:0.8309:0.0	rs2071307;rs11567855;rs17855987;rs58147333;rs2071307	422;391;417;412;422;412;427;427;422;305;408;422	E7ENM0;E9PBM4;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.	S	422;422;422;417;422;412;408;412;427;427;391;305;422;422	ENSP00000389857:G422S;ENSP00000252034:G422S;ENSP00000351807:G422S;ENSP00000392575:G417S;ENSP00000369936:G422S;ENSP00000369949:G412S;ENSP00000369958:G408S;ENSP00000403162:G412S;ENSP00000349540:G427S;ENSP00000391129:G427S;ENSP00000369926:G305S;ENSP00000369950:G422S;ENSP00000313565:G422S	ENSP00000252034:G422S	G	+	1	0	ELN	73108650	0.111000	0.22076	0.002000	0.10522	0.002000	0.02628	0.532000	0.23067	-0.267000	0.09325	-1.446000	0.01064	GGT	G|0.704;A|0.296	0.296	strong		0.617	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
C5orf64	285668	hgsc.bcm.edu	37	5	60982841	60982841	+	Missense_Mutation	SNP	G	G	A	rs16893687	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:60982841G>A	ENST00000505642.1	+	3	244	c.169G>A	c.(169-171)Gct>Act	p.A57T	RP11-2O17.2_ENST00000513386.1_RNA|C5orf64_ENST00000313303.7_Missense_Mutation_p.A57T|RP11-2O17.2_ENST00000505623.1_RNA|RP11-2O17.2_ENST00000507264.1_RNA|C5orf64_ENST00000510414.1_Intron	NM_173667.2	NP_775938.1	Q2M2E5	CE064_HUMAN	chromosome 5 open reading frame 64	57			A -> T (in dbSNP:rs16893687). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				breast(1)	1						GGATCTGACCGCTGAAGTTTA	0.438													A|||	2482	0.495607	0.4486	0.4914	5008	,	,		19731	0.6458		0.336	False		,,,				2504	0.5716				p.A57T		Atlas-SNP	.											.	C5orf64	9	.	0			c.G169A						PASS	.	A	THR/ALA	1678,2180		378,922,629	152.0	147.0	149.0		169	0.9	0.7	5	dbSNP_123	149	2665,5593		425,1815,1889	yes	missense	C5orf64	NM_173667.2	58	803,2737,2518	AA,AG,GG		32.2717,43.494,35.8452	benign	57/131	60982841	4343,7773	1929	4129	6058	SO:0001583	missense	285668	exon3			CTGACCGCTGAAG		CCDS54860.1	5q12.1	2014-02-12	2011-05-05		ENSG00000178722	ENSG00000178722			26744	protein-coding gene	gene with protein product							Standard	NM_173667		Approved	FLJ37543	uc003jst.1	Q2M2E5	OTTHUMG00000162412	ENST00000505642.1:c.169G>A	5.37:g.60982841G>A	ENSP00000423157:p.Ala57Thr	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	251	106	0.422311	NM_173667	Q2M2H1|Q8N1U8	Missense_Mutation	SNP	ENST00000505642.1	37	CCDS54860.1	1015	0.46474358974358976	208	0.42276422764227645	155	0.4281767955801105	398	0.6958041958041958	254	0.33509234828496043	A	7.117	0.577093	0.13686	0.43494	0.322717	ENSG00000178722	ENST00000505642;ENST00000313303	T;T	0.38401	1.14;1.14	4.92	0.845	0.18950	.	0.559392	0.13523	N	0.381575	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42498	-0.9448	9	0.02654	T	1	-3.1044	3.2402	0.06778	0.3489:0.4296:0.0825:0.1391	rs16893687;rs52816625;rs56445660;rs16893687	57	Q2M2E5	CE064_HUMAN	T	57	ENSP00000423157:A57T;ENSP00000318395:A57T	ENSP00000318395:A57T	A	+	1	0	C5orf64	61018598	0.010000	0.17322	0.713000	0.30519	0.827000	0.46813	0.102000	0.15272	-0.253000	0.09514	-0.254000	0.11334	GCT	G|0.539;A|0.461	0.461	strong		0.438	C5orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368790.1	NM_173667	
BBS12	166379	hgsc.bcm.edu	37	4	123664256	123664256	+	Silent	SNP	G	G	A	rs17006092	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:123664256G>A	ENST00000314218.3	+	2	1402	c.1209G>A	c.(1207-1209)gtG>gtA	p.V403V	BBS12_ENST00000542236.1_Silent_p.V403V	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	403					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TGTTACAGGTGTTAATCCAGT	0.403									Bardet-Biedl syndrome				A|||	173	0.0345447	0.1006	0.0259	5008	,	,		22653	0.0		0.0219	False		,,,				2504	0.0				p.V403V		Atlas-SNP	.											.	BBS12	63	.	0			c.G1209A						PASS	.	A	,	352,4054	793.3+/-415.2	13,326,1864	69.0	74.0	72.0		1209,1209	-4.9	0.0	4	dbSNP_123	72	168,8432	812.0+/-407.1	2,164,4134	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	15,490,5998	AA,AG,GG		1.9535,7.9891,3.9982	,	403/711,403/711	123664256	520,12486	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	ACAGGTGTTAATC	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1209G>A	4.37:g.123664256G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	150	58	0.386667	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			G|0.961;A|0.039	0.039	strong		0.403	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
PANX3	116337	hgsc.bcm.edu	37	11	124481558	124481558	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124481558C>T	ENST00000284288.2	+	1	173	c.106C>T	c.(106-108)Cgg>Tgg	p.R36W		NM_052959.2	NP_443191.1	Q96QZ0	PANX3_HUMAN	pannexin 3	36					cell-cell signaling (GO:0007267)|ion transport (GO:0006811)|protein hexamerization (GO:0034214)|transmembrane transport (GO:0055085)	gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|urinary_tract(1)	26	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		GCCCCTGGACCGGATAGTCAA	0.592																																					p.R36W		Atlas-SNP	.											PANX3,NS,carcinoma,-1,1	PANX3	52	1	0			c.C106T						scavenged	.						91.0	93.0	92.0					11																	124481558		2201	4299	6500	SO:0001583	missense	116337	exon1			CTGGACCGGATAG	AF406650	CCDS8447.1	11q24.2	2011-12-02			ENSG00000154143	ENSG00000154143		"""Ion channels / Pannexins"""	20573	protein-coding gene	gene with protein product		608422					Standard	NM_052959		Approved	Px3	uc001qah.3	Q96QZ0	OTTHUMG00000165925	ENST00000284288.2:c.106C>T	11.37:g.124481558C>T	ENSP00000284288:p.Arg36Trp	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	219	3	0.0136986	NM_052959		Missense_Mutation	SNP	ENST00000284288.2	37	CCDS8447.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.335636	0.60853	.	.	ENSG00000154143	ENST00000284288	T	0.31247	1.5	4.88	2.56	0.30785	.	0.316678	0.33938	N	0.004415	T	0.40815	0.1132	L	0.53249	1.67	0.27435	N	0.953887	D	0.65815	0.995	P	0.53490	0.727	T	0.37174	-0.9717	10	0.87932	D	0	-3.1069	13.356	0.60627	0.3798:0.6202:0.0:0.0	.	36	Q96QZ0	PANX3_HUMAN	W	36	ENSP00000284288:R36W	ENSP00000284288:R36W	R	+	1	2	PANX3	123986768	1.000000	0.71417	0.346000	0.25655	0.783000	0.44284	3.912000	0.56386	0.361000	0.24292	-0.182000	0.12963	CGG	.	.	none		0.592	PANX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387064.1		
AP4B1	10717	hgsc.bcm.edu	37	1	114444444	114444444	+	Silent	SNP	T	T	G	rs34751342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:114444444T>G	ENST00000369569.1	-	3	682	c.402A>C	c.(400-402)tcA>tcC	p.S134S	AP4B1_ENST00000369566.3_Intron|AP4B1_ENST00000256658.4_Silent_p.S134S|AP4B1_ENST00000369567.1_Intron|AP4B1-AS1_ENST00000419536.1_RNA	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	134					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCTGACATATGAAGCCTTAT	0.453													T|||	108	0.0215655	0.0023	0.0389	5008	,	,		20112	0.0		0.0239	False		,,,				2504	0.0552				p.S134S		Atlas-SNP	.											.	AP4B1	72	.	0			c.A402C						PASS	.	T		27,4379	35.2+/-66.4	0,27,2176	175.0	145.0	155.0		402	-10.9	0.0	1	dbSNP_126	155	361,8239	122.2+/-181.2	3,355,3942	no	coding-synonymous	AP4B1	NM_006594.2		3,382,6118	GG,GT,TT		4.1977,0.6128,2.9832		134/740	114444444	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	10717	exon4			GACATATGAAGCC	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"""beta 4 subunit of AP-4"""	607245	"""spastic paraplegia 47"""	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.402A>C	1.37:g.114444444T>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	160	54	0.3375	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Silent	SNP	ENST00000369569.1	37	CCDS865.1																																																																																			T|0.971;G|0.029	0.029	strong		0.453	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594	
LAMA5	3911	hgsc.bcm.edu	37	20	60920887	60920887	+	Silent	SNP	G	G	A	rs11204472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60920887G>A	ENST00000252999.3	-	11	1530	c.1464C>T	c.(1462-1464)gcC>gcT	p.A488A	LAMA5_ENST00000370692.3_Silent_p.A488A|LAMA5_ENST00000370677.3_Silent_p.A488A	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	488					angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CAATCTGGCCGGCTGGCAGCA	0.627													G|||	2617	0.522564	0.1059	0.6412	5008	,	,		15783	0.7401		0.667	False		,,,				2504	0.6288				p.A488A		Atlas-SNP	.											.	LAMA5	268	.	0			c.C1464T						PASS	.	G		988,3304		150,688,1308	44.0	39.0	41.0		1464	-3.7	0.5	20	dbSNP_120	41	5847,2541		2114,1619,461	no	coding-synonymous	LAMA5	NM_005560.3		2264,2307,1769	AA,AG,GG		30.2933,23.0196,46.0962		488/3696	60920887	6835,5845	2146	4194	6340	SO:0001819	synonymous_variant	3911	exon11			CTGGCCGGCTGGC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.1464C>T	20.37:g.60920887G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.487;A|0.513	0.513	strong		0.627	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
UTS2	10911	hgsc.bcm.edu	37	1	7913445	7913445	+	5'Flank	SNP	C	C	T	rs13306061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7913445C>T	ENST00000361696.5	-	0	0				UTS2_ENST00000054668.5_Missense_Mutation_p.R16Q|UTS2_ENST00000377516.2_5'UTR	NM_006786.3	NP_006777.1	O95399	UTS2_HUMAN	urotensin 2						muscle contraction (GO:0006936)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell differentiation (GO:0045597)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of heart rate (GO:0010460)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to testosterone (GO:0033574)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			kidney(1)|lung(4)|urinary_tract(1)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		TTTATGAGTCCGAGCAGAAGT	0.413													C|||	426	0.0850639	0.0719	0.0994	5008	,	,		19428	0.0357		0.1829	False		,,,				2504	0.0429				p.R16Q		Atlas-SNP	.											.	UTS2	18	.	0			c.G47A						PASS	.	C	GLN/ARG	366,4040	186.4+/-213.3	11,344,1848	167.0	154.0	158.0		47	2.8	0.0	1	dbSNP_121	158	1525,7075	287.5+/-298.3	139,1247,2914	yes	missense	UTS2	NM_021995.2	43	150,1591,4762	TT,TC,CC		17.7326,8.3069,14.5394	benign	16/140	7913445	1891,11115	2203	4300	6503	SO:0001631	upstream_gene_variant	10911	exon1			TGAGTCCGAGCAG	AF104118	CCDS90.1, CCDS91.1	1p36	2013-02-28			ENSG00000049247	ENSG00000049247		"""Endogenous ligands"""	12636	protein-coding gene	gene with protein product	"""prepro U-II"""	604097				9861051, 10499587	Standard	NM_021995		Approved	UII, U-II, UCN2, PRO1068	uc001aos.3	O95399	OTTHUMG00000001218		1.37:g.7913445C>T	Exception_encountered	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	160	98	0.6125	NM_021995	Q5H8X7|Q6UXF6|Q9UKP7	Missense_Mutation	SNP	ENST00000361696.5	37	CCDS91.1	236	0.10805860805860806	34	0.06910569105691057	45	0.12430939226519337	18	0.03146853146853147	139	0.18337730870712401	C	8.886	0.952879	0.18431	0.083069	0.177326	ENSG00000049247	ENST00000054668	T	0.35605	1.3	4.68	2.75	0.32379	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	P	0.49961	0.93	B	0.39904	0.313	T	0.15150	-1.0447	7	0.22706	T	0.39	.	6.634	0.22874	0.0:0.5915:0.0:0.4085	rs13306061	16	O95399-2	.	Q	16	ENSP00000054668:R16Q	ENSP00000054668:R16Q	R	-	2	0	UTS2	7836032	0.001000	0.12720	0.012000	0.15200	0.020000	0.10135	-0.074000	0.11450	0.465000	0.27167	0.655000	0.94253	CGG	C|0.870;T|0.130	0.130	strong		0.413	UTS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003612.1	NM_006786	
FAM24B	196792	hgsc.bcm.edu	37	10	124610027	124610027	+	Missense_Mutation	SNP	G	G	A	rs1891110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124610027G>A	ENST00000368898.3	-	3	295	c.5C>T	c.(4-6)cCt>cTt	p.P2L	FAM24B_ENST00000368896.1_Missense_Mutation_p.P2L|CUZD1_ENST00000545804.1_Intron|CUZD1_ENST00000368904.1_5'UTR|FAM24B_ENST00000462859.1_Intron	NM_152644.2	NP_689857.2	Q8N5W8	FA24B_HUMAN	family with sequence similarity 24, member B	2			P -> L (in dbSNP:rs1891110). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.136)|COAD - Colon adenocarcinoma(40;0.141)		AGCGATGACAGGCATAATCAC	0.502													A|||	2516	0.502396	0.4834	0.4597	5008	,	,		20107	0.4931		0.5785	False		,,,				2504	0.4898				p.P2L		Atlas-SNP	.											.	FAM24B	9	.	0			c.C5T						PASS	.	A	LEU/PRO,LEU/PRO	2292,2114	576.7+/-384.3	610,1072,521	185.0	154.0	164.0		5,5	3.0	0.0	10	dbSNP_92	164	4772,3828	541.1+/-383.9	1323,2126,851	yes	missense,missense	FAM24B	NM_152644.2,NM_001204364.1	98,98	1933,3198,1372	AA,AG,GG		44.5116,47.98,45.6866	benign,benign	2/95,2/95	124610027	7064,5942	2203	4300	6503	SO:0001583	missense	196792	exon3			ATGACAGGCATAA	BC031343	CCDS31303.1	10q26.13	2004-05-27			ENSG00000213185	ENSG00000213185			23475	protein-coding gene	gene with protein product						12477932	Standard	NM_152644		Approved	MGC45962, AC073585.2	uc021qai.1	Q8N5W8	OTTHUMG00000019194	ENST00000368898.3:c.5C>T	10.37:g.124610027G>A	ENSP00000357894:p.Pro2Leu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	176	96	0.545455	NM_001204364	Q5JPG1	Missense_Mutation	SNP	ENST00000368898.3	37	CCDS31303.1	1150	0.5265567765567766	252	0.5121951219512195	162	0.44751381215469616	298	0.5209790209790209	438	0.5778364116094987	A	0.055	-1.238180	0.01493	0.5202	0.554884	ENSG00000213185	ENST00000368898;ENST00000368896	T;T	0.39056	1.1;1.1	3.0	3.0	0.34707	.	0.970919	0.08370	U	0.956308	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	8	0.33940	T	0.23	.	5.0762	0.14632	0.8615:0.0:0.1385:0.0	rs1891110;rs17653026;rs17845954;rs17858936;rs57906451;rs1891110	2	Q8N5W8	FA24B_HUMAN	L	2	ENSP00000357894:P2L;ENSP00000357892:P2L	ENSP00000357892:P2L	P	-	2	0	FAM24B	124600017	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	1.235000	0.32671	0.555000	0.29079	-0.516000	0.04426	CCT	G|0.475;A|0.525	0.525	strong		0.502	FAM24B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050825.1	NM_152644	
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107531152	107531152	+	Missense_Mutation	SNP	G	G	C	rs10761084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107531152G>C	ENST00000374762.3	+	3	351	c.280G>C	c.(280-282)Gct>Cct	p.A94P	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	94			A -> P (in dbSNP:rs10761084). {ECO:0000269|PubMed:14702039}.					p.A94P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						AGATAATTTTGCTCATCGAGC	0.358													.|||	890	0.177716	0.0257	0.1455	5008	,	,		15655	0.2857		0.1769	False		,,,				2504	0.2955				p.A94P		Atlas-SNP	.											NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	1	Substitution - Missense(1)	stomach(1)	c.G280C						PASS	.	G	PRO/ALA	199,4207	124.5+/-161.8	6,187,2010	62.0	59.0	60.0		280	3.8	1.0	9	dbSNP_120	60	1633,6967	301.6+/-305.5	171,1291,2838	yes	missense	NIPSNAP3B	NM_018376.2	27	177,1478,4848	CC,CG,GG		18.9884,4.5166,14.0858	possibly-damaging	94/248	107531152	1832,11174	2203	4300	6503	SO:0001583	missense	55335	exon3			AATTTTGCTCATC	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.280G>C	9.37:g.107531152G>C	ENSP00000363894:p.Ala94Pro	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	147	78	0.530612	NM_018376	Q5VX30|Q9NUM2	Missense_Mutation	SNP	ENST00000374762.3	37	CCDS6761.1	357	0.16346153846153846	15	0.03048780487804878	60	0.16574585635359115	146	0.25524475524475526	136	0.17941952506596306	G	17.64	3.439372	0.63067	0.045166	0.189884	ENSG00000165028	ENST00000374762	T	0.50813	0.73	3.77	3.77	0.43336	Dimeric alpha-beta barrel (1);	0.060953	0.64402	U	0.000004	T	0.00039	0.0001	M	0.81239	2.535	0.20821	P	0.999845625	D	0.63880	0.993	D	0.70487	0.969	T	0.04281	-1.0963	9	0.30854	T	0.27	-6.9526	12.9916	0.58622	0.0:0.0:1.0:0.0	rs10761084;rs56447258;rs10761084	94	Q9BS92	NPS3B_HUMAN	P	94	ENSP00000363894:A94P	ENSP00000363894:A94P	A	+	1	0	NIPSNAP3B	106570973	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.087000	0.50167	2.088000	0.63022	0.650000	0.86243	GCT	G|0.846;C|0.154	0.154	strong		0.358	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376	
REP15	387849	hgsc.bcm.edu	37	12	27849795	27849795	+	Silent	SNP	C	C	T	rs929948|rs386761425	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:27849795C>T	ENST00000310791.2	+	1	368	c.300C>T	c.(298-300)tcC>tcT	p.S100S	RP11-1060J15.4_ENST00000536317.1_RNA|RP11-1060J15.4_ENST00000542660.1_RNA|RP11-1060J15.4_ENST00000536922.1_RNA	NM_001029874.1	NP_001025045.1	Q6BDI9	REP15_HUMAN	RAB15 effector protein	100					receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	endosome membrane (GO:0010008)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)				breast(1)|cervix(1)|large_intestine(2)|lung(4)|ovary(1)	9	Lung SC(9;0.0873)					TTTGGGGATCCAACAAGCAAA	0.488													C|||	2985	0.596046	0.6399	0.6888	5008	,	,		20554	0.5268		0.6262	False		,,,				2504	0.5112				p.S100S		Atlas-SNP	.											.	REP15	13	.	0			c.C300T						PASS	.	C		2775,1631	661.2+/-400.9	873,1029,301	83.0	80.0	81.0		300	-9.8	0.0	12	dbSNP_86	81	5305,3295	646.4+/-400.3	1624,2057,619	no	coding-synonymous	REP15	NM_001029874.1		2497,3086,920	TT,TC,CC		38.314,37.0177,37.8748		100/237	27849795	8080,4926	2203	4300	6503	SO:0001819	synonymous_variant	387849	exon1			GGGATCCAACAAG	BC140921	CCDS31762.1	12p11.22	2010-09-02			ENSG00000174236	ENSG00000174236			33748	protein-coding gene	gene with protein product		610848				16195351	Standard	NM_001029874		Approved	RAB15EP	uc001rig.1	Q6BDI9		ENST00000310791.2:c.300C>T	12.37:g.27849795C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001029874	B2RU16	Silent	SNP	ENST00000310791.2	37	CCDS31762.1																																																																																			C|0.408;T|0.592	0.592	strong		0.488	REP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402894.1	NM_001029874	
CCDC146	57639	hgsc.bcm.edu	37	7	76891535	76891535	+	Nonsense_Mutation	SNP	C	C	T	rs371350411		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76891535C>T	ENST00000285871.4	+	9	1211	c.1084C>T	c.(1084-1086)Cga>Tga	p.R362*	CCDC146_ENST00000431197.1_Nonsense_Mutation_p.R108*|CCDC146_ENST00000415740.2_3'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	362										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				ACGAGATTTTCGAAATTTAAG	0.423																																					p.R362X		Atlas-SNP	.											CCDC146,NS,carcinoma,0,2	CCDC146	87	2	0			c.C1084T						PASS	.	C	stop/ARG	0,4406		0,0,2203	99.0	98.0	98.0		1084	4.8	1.0	7		98	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	CCDC146	NM_020879.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		362/956	76891535	1,13005	2203	4300	6503	SO:0001587	stop_gained	57639	exon9			GATTTTCGAAATT	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.1084C>T	7.37:g.76891535C>T	ENSP00000285871:p.Arg362*	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	102	13	0.127451	NM_020879	A8K8X6|Q9P223	Nonsense_Mutation	SNP	ENST00000285871.4	37	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	C	38	6.998870	0.97990	0.0	1.16E-4	ENSG00000135205	ENST00000285871;ENST00000431197	.	.	.	5.78	4.82	0.62117	.	0.207319	0.41823	D	0.000813	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.9971	13.1907	0.59709	0.2483:0.7517:0.0:0.0	.	.	.	.	X	362;108	.	ENSP00000285871:R362X	R	+	1	2	AC007000.1	76729471	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	1.811000	0.38942	2.744000	0.94065	0.563000	0.77884	CGA	.	.	weak		0.423	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
NPY4R	5540	hgsc.bcm.edu	37	10	47087609	47087609	+	Missense_Mutation	SNP	G	G	A	rs386743380|rs79871698	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:47087609G>A	ENST00000395716.1	+	2	911	c.826G>A	c.(826-828)Gtg>Atg	p.V276M	NPY4R_ENST00000374312.1_Missense_Mutation_p.V276M			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	276					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										GGCCTTTGCTGTGCTCTGGCT	0.582													G|||	597	0.119209	0.0734	0.1383	5008	,	,		42725	0.0923		0.1571	False		,,,				2504	0.1564				p.V276M		Atlas-SNP	.											.	PPYR1	54	.	0			c.G826A						PASS	.	G	MET/VAL	42,4364	29.9+/-59.1	0,42,2161	157.0	113.0	128.0		826	-0.1	0.1	10	dbSNP_131	128	118,8482	29.0+/-79.6	0,118,4182	yes	missense	PPYR1	NM_005972.4	21	0,160,6343	AA,AG,GG		1.3721,0.9532,1.2302	probably-damaging	276/376	47087609	160,12846	2203	4300	6503	SO:0001583	missense	5540	exon3			TTTGCTGTGCTCT		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.826G>A	10.37:g.47087609G>A	ENSP00000379066:p.Val276Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	133	25	0.18797	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	37	CCDS31193.1	.	.	.	.	.	.	.	.	.	.	G	8.854	0.945253	0.18356	0.009532	0.013721	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.69561	-0.41;-0.41	5.18	-0.0452	0.13852	GPCR, rhodopsin-like superfamily (1);	0.423733	0.23312	N	0.049560	T	0.71821	0.3385	M	0.90650	3.135	0.33790	D	0.625383	D	0.53885	0.963	P	0.60345	0.873	T	0.77335	-0.2626	10	0.72032	D	0.01	.	5.2927	0.15735	0.3143:0.2575:0.4282:0.0	.	276	P50391	NPY4R_HUMAN	M	276	ENSP00000363431:V276M;ENSP00000379066:V276M	ENSP00000363431:V276M	V	+	1	0	PPYR1	46507615	0.341000	0.24801	0.064000	0.19789	0.123000	0.20343	0.930000	0.28858	0.034000	0.15491	-0.136000	0.14681	GTG	G|0.938;A|0.062	0.062	strong		0.582	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
BBS12	166379	hgsc.bcm.edu	37	4	123664457	123664457	+	Silent	SNP	C	C	T	rs13135445	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:123664457C>T	ENST00000314218.3	+	2	1603	c.1410C>T	c.(1408-1410)tgC>tgT	p.C470C	BBS12_ENST00000542236.1_Silent_p.C470C	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	470					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						ACGGGGTCTGCGTGACCTTCT	0.478									Bardet-Biedl syndrome				T|||	606	0.121006	0.1293	0.1297	5008	,	,		19655	0.0		0.2346	False		,,,				2504	0.1115				p.C470C		Atlas-SNP	.											.	BBS12	63	.	0			c.C1410T						PASS	.	T	,	599,3807	770.2+/-413.7	38,523,1642	80.0	78.0	79.0		1410,1410	-0.7	0.0	4	dbSNP_121	79	2108,6492	716.6+/-406.1	255,1598,2447	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	293,2121,4089	TT,TC,CC		24.5116,13.5951,20.8135	,	470/711,470/711	123664457	2707,10299	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGTCTGCGTGACC	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1410C>T	4.37:g.123664457C>T		Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	177	91	0.514124	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			C|0.818;T|0.182	0.182	strong		0.478	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
NLRP5	126206	hgsc.bcm.edu	37	19	56538723	56538723	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56538723C>T	ENST00000390649.3	+	7	1124	c.1124C>T	c.(1123-1125)aCa>aTa	p.T375I		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	375	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		AACAATGACACAAAGCTCTGC	0.557																																					p.T375I		Atlas-SNP	.											.	NLRP5	217	.	0			c.C1124T						PASS	.						45.0	46.0	46.0					19																	56538723		2075	4215	6290	SO:0001583	missense	126206	exon7			ATGACACAAAGCT	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1124C>T	19.37:g.56538723C>T	ENSP00000375063:p.Thr375Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	11	0.229167	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	C	3.198	-0.164275	0.06502	.	.	ENSG00000171487	ENST00000390649	T	0.73897	-0.79	3.35	-6.71	0.01760	NACHT nucleoside triphosphatase (1);	5.357820	0.00397	N	0.000045	T	0.50973	0.1647	N	0.17082	0.46	0.09310	N	1	B	0.15719	0.014	B	0.21708	0.036	T	0.44375	-0.9332	10	0.17832	T	0.49	.	0.8494	0.01169	0.2606:0.2256:0.11:0.4037	.	375	P59047	NALP5_HUMAN	I	375	ENSP00000375063:T375I	ENSP00000375063:T375I	T	+	2	0	NLRP5	61230535	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.527000	0.00441	-2.083000	0.00867	0.655000	0.94253	ACA	.	.	none		0.557	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
UFSP1	402682	hgsc.bcm.edu	37	7	100486754	100486754	+	Missense_Mutation	SNP	G	G	C	rs12666989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100486754G>C	ENST00000388761.2	-	1	585	c.139C>G	c.(139-141)Ctg>Gtg	p.L47V		NM_001015072.3	NP_001015072.2	Q6NVU6	UFSP1_HUMAN	UFM1-specific peptidase 1 (non-functional)	47			L -> V (in dbSNP:rs12666989). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:14702039}.			extracellular vesicular exosome (GO:0070062)	thiolester hydrolase activity (GO:0016790)|UFM1 hydrolase activity (GO:0071567)			lung(1)|stomach(1)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGCCTCTCCAGCTCCCCGTGC	0.692													G|||	443	0.0884585	0.0416	0.1023	5008	,	,		14356	0.0308		0.1829	False		,,,				2504	0.1043				p.L47V		Atlas-SNP	.											.	UFSP1	8	.	0			c.C139G						PASS	.	G	VAL/LEU	248,4154		6,236,1959	28.0	29.0	28.0	http://www.ncbi.nlm.nih.gov/pubmed?term	139	2.5	0.1	7	dbSNP_120	28	1532,7068		151,1230,2919	yes	missense	UFSP1	NM_001015072.3	32	157,1466,4878	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	17.814,5.6338,13.6902	benign	47/143	100486754	1780,11222	2201	4300	6501	SO:0001583	missense	402682	exon1			TCTCCAGCTCCCC	AF312032	CCDS34710.1	7q22.1	2008-03-25			ENSG00000176125	ENSG00000176125			33821	protein-coding gene	gene with protein product		611481				17182609, 18321862	Standard	NM_001015072		Approved	UFSP	uc003uxc.4	Q6NVU6	OTTHUMG00000159662	ENST00000388761.2:c.139C>G	7.37:g.100486754G>C	ENSP00000373413:p.Leu47Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001015072	A4D2E4|A8K8V2|B6ZDG6|Q9BXP6	Missense_Mutation	SNP	ENST00000388761.2	37	CCDS34710.1	231	0.10576923076923077	21	0.042682926829268296	43	0.11878453038674033	19	0.033216783216783216	148	0.19525065963060687	G	0.030	-1.339530	0.01277	0.056338	0.17814	ENSG00000176125	ENST00000388761	T	0.29655	1.56	4.43	2.54	0.30619	.	0.545587	0.15337	N	0.267700	T	0.00012	0.0000	N	0.17872	0.535	0.48901	P	2.769999999999717E-4	P	0.42078	0.77	B	0.41299	0.353	T	0.20940	-1.0260	9	0.12430	T	0.62	-22.0861	7.534	0.27700	0.0963:0.1689:0.7348:0.0	rs12666989;rs17880260;rs12666989	47	Q6NVU6	UFSP1_HUMAN	V	47	ENSP00000373413:L47V	ENSP00000373413:L47V	L	-	1	2	UFSP1	100324690	0.022000	0.18835	0.111000	0.21465	0.010000	0.07245	0.527000	0.22987	0.567000	0.29293	0.484000	0.47621	CTG	G|0.879;C|0.121	0.121	strong		0.692	UFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356751.1	NM_001015072	
PRUNE2	158471	hgsc.bcm.edu	37	9	79322068	79322068	+	Missense_Mutation	SNP	G	G	T	rs683866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79322068G>T	ENST00000376718.3	-	8	5245	c.5122C>A	c.(5122-5124)Cac>Aac	p.H1708N	PRUNE2_ENST00000428286.1_Missense_Mutation_p.H1349N	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1708					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TCAGCAACGTGGCAGTTGGCC	0.453													G|||	2512	0.501597	0.3419	0.6427	5008	,	,		20074	0.4454		0.5984	False		,,,				2504	0.5757				p.H1708N		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C5122A						PASS	.	G	ASN/HIS	1278,1858		256,766,546	94.0	80.0	84.0		5122	5.2	0.0	9	dbSNP_83	84	4415,2749		1366,1683,533	yes	missense	PRUNE2	NM_015225.2	68	1622,2449,1079	TT,TG,GG		38.3724,40.7526,44.7282	benign	1708/3089	79322068	5693,4607	1568	3582	5150	SO:0001583	missense	158471	exon8			CAACGTGGCAGTT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.5122C>A	9.37:g.79322068G>T	ENSP00000365908:p.His1708Asn	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	173	93	0.537572	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	1097|1097	0.5022893772893773|0.5022893772893773	175|175	0.3556910569105691|0.3556910569105691	227|227	0.6270718232044199|0.6270718232044199	257|257	0.4493006993006993|0.4493006993006993	438|438	0.5778364116094987|0.5778364116094987	G|G	0.044|0.044	-1.274175|-1.274175	0.01421|0.01421	0.407526|0.407526	0.616276|0.616276	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.39229|.	1.1;1.09|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.803539|.	0.10810|.	N|.	0.631677|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.24087|0.24087	P|P	0.99592952|0.99592952	B|.	0.12013|.	0.005|.	B|.	0.06405|.	0.002|.	T|T	0.45249|0.45249	-0.9274|-0.9274	9|4	0.15952|.	T|.	0.53|.	0.0184|0.0184	11.5076|11.5076	0.50476|0.50476	0.0:0.0:0.8083:0.1917|0.0:0.0:0.8083:0.1917	rs683866;rs1831233;rs17180788;rs52815496;rs61647805;rs683866|rs683866;rs1831233;rs17180788;rs52815496;rs61647805;rs683866	1708|.	Q8WUY3|.	PRUN2_HUMAN|.	N|Q	1708;1349;1707|1029	ENSP00000365908:H1708N;ENSP00000397425:H1349N|.	ENSP00000365908:H1708N|.	H|P	-|-	1|2	0|0	PRUNE2|PRUNE2	78511888|78511888	0.104000|0.104000	0.21937|0.21937	0.044000|0.044000	0.18714|0.18714	0.022000|0.022000	0.10575|0.10575	0.848000|0.848000	0.27710|0.27710	2.413000|2.413000	0.81919|0.81919	0.655000|0.655000	0.94253|0.94253	CAC|CCA	G|0.498;T|0.502	0.502	strong		0.453	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
OTOGL	283310	hgsc.bcm.edu	37	12	80735771	80735771	+	Silent	SNP	T	T	C	rs10778727	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:80735771T>C	ENST00000547103.1	+	43	5037	c.5031T>C	c.(5029-5031)aaT>aaC	p.N1677N	RN7SKP261_ENST00000410948.1_RNA|OTOGL_ENST00000458043.2_Silent_p.N1689N			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1677	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						GGATGCAAAATGGCACAATTA	0.318													T|||	2478	0.494808	0.1823	0.4885	5008	,	,		17652	0.6935		0.6451	False		,,,				2504	0.5624				p.N1689N		Atlas-SNP	.											OTOGL_ENST00000458043,NS,carcinoma,+1,3	OTOGL	235	3	0			c.T5067C						PASS	.	T		1039,2599		147,745,927	44.0	42.0	43.0		5067	2.7	1.0	12	dbSNP_120	43	5221,2963		1668,1885,539	no	coding-synonymous	OTOGL	NM_173591.3		1815,2630,1466	CC,CT,TT		36.2048,28.5596,47.0479		1689/2345	80735771	6260,5562	1819	4092	5911	SO:0001819	synonymous_variant	283310	exon43			GCAAAATGGCACA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5031T>C	12.37:g.80735771T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Silent	SNP	ENST00000547103.1	37		1157	0.5297619047619048	101	0.20528455284552846	182	0.5027624309392266	388	0.6783216783216783	486	0.6411609498680739	T	8.902	0.956673	0.18507	0.285596	0.637952	ENSG00000165899	ENST00000298820	.	.	.	5.06	2.69	0.31865	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999928	.	.	.	.	.	.	T	0.38693	-0.9649	3	.	.	.	.	5.3719	0.16144	0.0:0.4091:0.0:0.5909	rs10778727;rs10778727	.	.	.	T	132	.	.	M	+	2	0	OTOGL	79259902	0.997000	0.39634	1.000000	0.80357	0.991000	0.79684	0.264000	0.18497	0.875000	0.35847	0.528000	0.53228	ATG	T|0.487;C|0.513	0.513	strong		0.318	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
ANKMY1	51281	hgsc.bcm.edu	37	2	241463595	241463595	+	Missense_Mutation	SNP	T	T	C	rs35996697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:241463595T>C	ENST00000272972.3	-	7	1486	c.1272A>G	c.(1270-1272)atA>atG	p.I424M	ANKMY1_ENST00000403283.1_Missense_Mutation_p.I362M|ANKMY1_ENST00000401804.1_Missense_Mutation_p.I513M|ANKMY1_ENST00000391987.1_Missense_Mutation_p.I424M|ANKMY1_ENST00000373320.4_Missense_Mutation_p.I194M|ANKMY1_ENST00000361678.4_Missense_Mutation_p.I283M|ANKMY1_ENST00000373318.2_Missense_Mutation_p.I283M|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000405523.3_Missense_Mutation_p.I283M|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000405002.1_Missense_Mutation_p.I194M|ANKMY1_ENST00000536462.1_Missense_Mutation_p.I236M	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	424			I -> M (in dbSNP:rs35996697). {ECO:0000269|Ref.1}.				metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		TCCTGTGGTCTATGGACCCCC	0.647													C|||	598	0.119409	0.1891	0.134	5008	,	,		17123	0.0089		0.1779	False		,,,				2504	0.0685				p.I424M		Atlas-SNP	.											ANKMY1_ENST00000361678,colon,carcinoma,0,2	ANKMY1	112	2	0			c.A1272G						PASS	.	C	MET/ILE,MET/ILE	872,3534	742.8+/-411.4	81,710,1412	60.0	60.0	60.0		1272,849	-2.5	0.0	2	dbSNP_126	60	1485,7115	748.5+/-407.3	132,1221,2947	yes	missense,missense	ANKMY1	NM_016552.2,NM_017844.2	10,10	213,1931,4359	CC,CT,TT		17.2674,19.7912,18.1224	benign,benign	424/942,283/718	241463595	2357,10649	2203	4300	6503	SO:0001583	missense	51281	exon7			GTGGTCTATGGAC	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1272A>G	2.37:g.241463595T>C	ENSP00000272972:p.Ile424Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	266	0.12179487179487179	87	0.17682926829268292	52	0.143646408839779	5	0.008741258741258742	122	0.16094986807387862	C	4.697	0.129512	0.08981	0.197912	0.172674	ENSG00000144504	ENST00000373318;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T	0.55760	2.92;0.52;2.25;0.52;4.39;2.48;0.5;2.23;2.23;2.5	2.39	-2.55	0.06288	Ankyrin repeat-containing domain (1);	12.913800	0.00166	N	0.000017	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B;B	0.15473	0.013;0.0;0.01;0.0;0.001;0.013	B;B;B;B;B;B	0.13407	0.004;0.0;0.009;0.0;0.003;0.004	T	0.06058	-1.0848	9	0.34782	T	0.22	-35.69	6.204	0.20591	0.0:0.4656:0.2359:0.2984	rs35996697	424;236;194;283;283;424	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;Q9P2S6-2;Q9P2S6	.;.;.;.;.;ANKY1_HUMAN	M	283;424;283;424;194;362;513;236;283;194	ENSP00000362415:I283M;ENSP00000272972:I424M;ENSP00000355097:I283M;ENSP00000375847:I424M;ENSP00000362417:I194M;ENSP00000383968:I362M;ENSP00000385887:I513M;ENSP00000444707:I236M;ENSP00000385635:I283M;ENSP00000385145:I194M	ENSP00000272972:I424M	I	-	3	3	ANKMY1	241112268	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.660000	0.00400	-1.112000	0.02984	-1.140000	0.01884	ATA	T|0.828;C|0.172	0.172	strong		0.647	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
PRRT4	401399	hgsc.bcm.edu	37	7	127991133	127991133	+	Missense_Mutation	SNP	G	G	A	rs891215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:127991133G>A	ENST00000446477.2	-	6	2790	c.2477C>T	c.(2476-2478)cCg>cTg	p.P826L	PRRT4_ENST00000435512.1_Missense_Mutation_p.P620L|PRRT4_ENST00000489835.2_3'UTR|PRRT4_ENST00000535159.1_Missense_Mutation_p.P826L	NM_001174164.1	NP_001167635.1	C9JH25	PRRT4_HUMAN	proline-rich transmembrane protein 4	826	Ser-rich.					integral component of membrane (GO:0016021)				endometrium(4)|prostate(1)	5						AGGGCAGCGCGGGGGCCTGTC	0.706													G|||	2185	0.436302	0.1831	0.6153	5008	,	,		13888	0.3462		0.667	False		,,,				2504	0.5072				p.P826L		Atlas-SNP	.											.	PRRT4	31	.	0			c.C2477T						PASS	.						3.0	5.0	4.0					7																	127991133		611	1519	2130	SO:0001583	missense	401399	exon6			CAGCGCGGGGGCC	BC063892	CCDS47698.1, CCDS47698.2, CCDS55160.1	7q32.1	2011-10-10			ENSG00000224940	ENSG00000224940		"""Proline-rich transmembrane proteins"""	37280	protein-coding gene	gene with protein product							Standard	NM_001114726		Approved		uc022aky.1	C9JH25	OTTHUMG00000157714	ENST00000446477.2:c.2477C>T	7.37:g.127991133G>A	ENSP00000415026:p.Pro826Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_001174164	A4D0Z9|C9JVW7	Missense_Mutation	SNP	ENST00000446477.2	37	CCDS55160.1	1075	0.49221611721611724	127	0.258130081300813	224	0.6187845303867403	205	0.3583916083916084	519	0.6846965699208444	G	2.056	-0.416618	0.04766	.	.	ENSG00000224940	ENST00000446477;ENST00000480290;ENST00000535159;ENST00000435512	.	.	.	4.16	3.28	0.37604	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.26935	0.164	B	0.22152	0.038	T	0.36792	-0.9733	7	0.48119	T	0.1	-4.7215	7.8142	0.29249	0.1141:0.0:0.8859:0.0	rs891215	826	C9JH25	PRRT4_HUMAN	L	826;355;826;620	.	ENSP00000410779:P620L	P	-	2	0	PRRT4	127778369	0.000000	0.05858	0.486000	0.27416	0.948000	0.59901	0.352000	0.20113	1.112000	0.41740	0.462000	0.41574	CCG	G|0.505;A|0.495	0.495	strong		0.706	PRRT4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001114726	
LCE3D	84648	hgsc.bcm.edu	37	1	152552285	152552285	+	Missense_Mutation	SNP	C	C	A	rs512208	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152552285C>A	ENST00000368787.3	-	2	184	c.128G>T	c.(127-129)gGc>gTc	p.G43V		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	43			G -> V (in dbSNP:rs512208). {ECO:0000269|PubMed:15489334}.		keratinization (GO:0031424)			p.G43V(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		AGGGCCACAGCCCCCAGAGCT	0.662													C|||	1386	0.276757	0.1384	0.2853	5008	,	,		15854	0.3264		0.3827	False		,,,				2504	0.2975				p.G43V		Atlas-SNP	.											LCE3D,NS,carcinoma,0,1	LCE3D	28	1	1	Substitution - Missense(1)	stomach(1)	c.G128T						PASS	.	C	VAL/GLY	789,3617	316.1+/-294.4	78,633,1492	57.0	66.0	63.0		128	0.3	0.6	1	dbSNP_83	63	3138,5454	473.4+/-368.6	598,1942,1756	no	missense	LCE3D	NM_032563.1	109	676,2575,3248	AA,AC,CC		36.5223,17.9074,30.2123	benign	43/93	152552285	3927,9071	2203	4296	6499	SO:0001583	missense	84648	exon2			CCACAGCCCCCAG	BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"""Late cornified envelopes"""	16615	protein-coding gene	gene with protein product		612616	"""small proline rich-like (epidermal differentiation complex) 6B"""	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.128G>T	1.37:g.152552285C>A	ENSP00000357776:p.Gly43Val	Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	314	304	0.968153	NM_032563	Q3MIL1	Missense_Mutation	SNP	ENST00000368787.3	37	CCDS1014.1	655	0.2999084249084249	68	0.13821138211382114	103	0.2845303867403315	188	0.32867132867132864	296	0.39050131926121373	C	0.190	-1.053864	0.01965	0.179074	0.365223	ENSG00000163202	ENST00000368787	T	0.03982	3.74	3.63	0.259	0.15583	.	.	.	.	.	T	0.01222	0.0040	.	.	.	0.48135	P	4.089999999999927E-4	B	0.34181	0.44	B	0.33750	0.169	T	0.50294	-0.8845	7	0.34782	T	0.22	.	6.4364	0.21825	0.1979:0.4157:0.3864:0.0	rs512208	43	Q9BYE3	LCE3D_HUMAN	V	43	ENSP00000357776:G43V	ENSP00000357776:G43V	G	-	2	0	LCE3D	150818909	0.111000	0.22076	0.642000	0.29436	0.005000	0.04900	0.010000	0.13242	0.318000	0.23185	-0.929000	0.02709	GGC	C|0.986;A|0.014	0.014	weak		0.662	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563	
MUC17	140453	hgsc.bcm.edu	37	7	100696348	100696348	+	Silent	SNP	G	G	T	rs200413820		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100696348G>T	ENST00000306151.4	+	10	13249	c.13185G>T	c.(13183-13185)gtG>gtT	p.V4395V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4395					cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ACGGCCTCGTGGGGGCAGGGG	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		17902	0.0		0.001	False		,,,				2504	0.0				p.V4395V		Atlas-SNP	.											MUC17,right_lower_lobe,carcinoma,0,1	MUC17	804	1	0			c.G13185T						PASS	.						91.0	77.0	82.0					7																	100696348		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon10			CCTCGTGGGGGCA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.13185G>T	7.37:g.100696348G>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	112	43	0.383929	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|1.000;T|0.000	0.000	strong		0.597	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
COG5	10466	hgsc.bcm.edu	37	7	106897237	106897237	+	Intron	SNP	A	A	C	rs17349904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:106897237A>C	ENST00000347053.3	-	15	1830				COG5_ENST00000297135.3_Silent_p.V594V|COG5_ENST00000393603.2_Silent_p.V594V	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5						intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						GACTGGAAACAACCTAGAACA	0.338													A|||	650	0.129792	0.0136	0.121	5008	,	,		16049	0.1587		0.2028	False		,,,				2504	0.1881				p.V594V		Atlas-SNP	.											.	COG5	78	.	0			c.T1782G						PASS	.	A	,,	220,4186	131.0+/-167.6	6,208,1989	78.0	78.0	78.0		1782,1782,	-3.4	1.0	7	dbSNP_123	78	1847,6753	326.9+/-317.6	207,1433,2660	no	coding-synonymous,coding-synonymous,intron	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	,,	213,1641,4649	CC,CA,AA		21.4767,4.9932,15.8927	,,	594/824,594/861,	106897237	2067,10939	2203	4300	6503	SO:0001627	intron_variant	10466	exon16			GGAAACAACCTAG	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1779+1480T>G	7.37:g.106897237A>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Silent	SNP	ENST00000347053.3	37	CCDS5743.1																																																																																			A|0.851;C|0.149	0.149	strong		0.338	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
TRPC1	7220	hgsc.bcm.edu	37	3	142523349	142523349	+	Silent	SNP	G	G	A	rs3821647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:142523349G>A	ENST00000476941.1	+	12	2517	c.2031G>A	c.(2029-2031)acG>acA	p.T677T	TRPC1_ENST00000273482.6_Silent_p.T643T	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	677					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.T643T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						ACAAATGTACGTTACCTCCAC	0.368													G|||	972	0.194089	0.2186	0.1354	5008	,	,		16060	0.2391		0.2038	False		,,,				2504	0.1462				p.T677T		Atlas-SNP	.											TRPC1,NS,carcinoma,0,1	TRPC1	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G2031A						PASS	.	G		928,3478	352.6+/-311.8	97,734,1372	100.0	95.0	97.0		1929	-3.1	1.0	3	dbSNP_107	97	1578,7022	294.8+/-302.1	163,1252,2885	no	coding-synonymous	TRPC1	NM_003304.4		260,1986,4257	AA,AG,GG		18.3488,21.0622,19.268		643/760	142523349	2506,10500	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon12			ATGTACGTTACCT	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2031G>A	3.37:g.142523349G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	234	120	0.512821	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			G|0.806;A|0.194	0.194	strong		0.368	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
ART4	420	hgsc.bcm.edu	37	12	14993608	14993608	+	Silent	SNP	G	G	A	rs3088189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:14993608G>A	ENST00000228936.4	-	2	1005	c.624C>T	c.(622-624)ctC>ctT	p.L208L	RP11-233G1.4_ENST00000444324.2_RNA|C12orf60_ENST00000527783.1_Intron	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	208					arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)	p.L208L(1)		large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						GGGATGTGGAGAGGAATTGGC	0.493													G|||	1466	0.292732	0.2685	0.3746	5008	,	,		19894	0.0982		0.3728	False		,,,				2504	0.3855				p.L208L		Atlas-SNP	.											ART4,NS,adenoma,0,2	ART4	27	2	1	Substitution - coding silent(1)	stomach(1)	c.C624T						PASS	.	G		1231,3175	425.9+/-341.0	176,879,1148	101.0	101.0	101.0		624	-0.1	0.3	12	dbSNP_102	101	3398,5202	501.4+/-375.5	699,2000,1601	no	coding-synonymous	ART4	NM_021071.2		875,2879,2749	AA,AG,GG		39.5116,27.9392,35.5913		208/315	14993608	4629,8377	2203	4300	6503	SO:0001819	synonymous_variant	420	exon2			TGTGGAGAGGAAT	X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"""CD molecules"", ""Blood group antigens"""	726	protein-coding gene	gene with protein product		110600	"""Dombrock blood group"", ""ADP-ribosyltransferase 4 (DO blood group)"", ""ADP-ribosyltransferase 4"""	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.624C>T	12.37:g.14993608G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_021071	Q9BZ50|Q9BZ51|Q9HB06	Silent	SNP	ENST00000228936.4	37	CCDS8668.1																																																																																			G|0.677;A|0.323	0.323	strong		0.493	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071	
ASPM	259266	hgsc.bcm.edu	37	1	197070815	197070815	+	Silent	SNP	T	T	C	rs1412640|rs386638268	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197070815T>C	ENST00000367409.4	-	18	7822	c.7566A>G	c.(7564-7566)ttA>ttG	p.L2522L	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2522					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTTCTCTTTGTAATTTTGCAG	0.333													c|||	4086	0.815895	0.497	0.8934	5008	,	,		19634	1.0		0.9125	False		,,,				2504	0.9029				p.L2522L		Atlas-SNP	.											.	ASPM	444	.	0			c.A7566G						PASS	.		,	2429,1977	542.5+/-376.0	668,1093,442	79.0	80.0	80.0		,7566	-0.0	1.0	1	dbSNP_88	80	7801,793	184.0+/-232.1	3540,721,36	no	intron,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	4208,1814,478	CC,CT,TT		9.2274,44.8706,21.3077	,	,2522/3478	197070815	10230,2770	2203	4297	6500	SO:0001819	synonymous_variant	259266	exon18			TCTTTGTAATTTT	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.7566A>G	1.37:g.197070815T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	150	83	0.553333	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			T|0.189;C|0.811	0.811	strong		0.333	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
GALNTL5	168391	hgsc.bcm.edu	37	7	151684256	151684256	+	Missense_Mutation	SNP	A	A	G	rs61729490	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151684256A>G	ENST00000392800.2	+	5	802	c.548A>G	c.(547-549)gAa>gGa	p.E183G	GALNTL5_ENST00000431418.2_Missense_Mutation_p.E183G	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	183	Catalytic subdomain A.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GATTTGAAAGAAAAACTAGAC	0.343													A|||	1105	0.220647	0.2587	0.2334	5008	,	,		17777	0.2063		0.16	False		,,,				2504	0.2372				p.E183G		Atlas-SNP	.											.	GALNTL5	87	.	0			c.A548G						PASS	.	A	GLY/GLU	988,3418	345.4+/-308.5	118,752,1333	39.0	42.0	41.0		548	-2.6	0.1	7	dbSNP_129	41	1372,7228	253.6+/-279.2	116,1140,3044	yes	missense	GALNTL5	NM_145292.3	98	234,1892,4377	GG,GA,AA		15.9535,22.424,18.1455	benign	183/444	151684256	2360,10646	2203	4300	6503	SO:0001583	missense	168391	exon5			TGAAAGAAAAACT	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"""Glycosyltransferase family 2 domain containing"""	21725	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 5"""	615133	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"""	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.548A>G	7.37:g.151684256A>G	ENSP00000376548:p.Glu183Gly	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	452	0.20695970695970695	129	0.2621951219512195	89	0.24585635359116023	109	0.19055944055944055	125	0.16490765171503957	a	10.49	1.364965	0.24684	0.22424	0.159535	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.63744	-0.06;-0.06	4.3	-2.57	0.06248	Glycosyl transferase, family 2 (1);	0.713546	0.11949	N	0.513859	T	0.00012	0.0000	L	0.31157	0.91	0.58432	P	1.0000000000287557E-6	B	0.15719	0.014	B	0.17722	0.019	T	0.16660	-1.0395	9	0.21540	T	0.41	.	5.0715	0.14609	0.4889:0.2522:0.2588:0.0	rs61729490	183	Q7Z4T8	GLTL5_HUMAN	G	183	ENSP00000392582:E183G;ENSP00000376548:E183G	ENSP00000376548:E183G	E	+	2	0	GALNTL5	151315189	1.000000	0.71417	0.068000	0.19968	0.914000	0.54420	2.000000	0.40816	-0.301000	0.08882	0.454000	0.30748	GAA	A|0.814;G|0.186	0.186	strong		0.343	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292	
CFAP46	54777	hgsc.bcm.edu	37	10	134736052	134736052	+	Missense_Mutation	SNP	G	G	T	rs4880287	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134736052G>T	ENST00000368586.5	-	12	1517	c.1417C>A	c.(1417-1419)Cgt>Agt	p.R473S	TTC40_ENST00000368582.2_Missense_Mutation_p.R473S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GTGCACAGACGCAGCCGGGTG	0.701													G|||	1799	0.359225	0.2821	0.4986	5008	,	,		15449	0.3274		0.3459	False		,,,				2504	0.411				p.R473S		Atlas-SNP	.											.	TTC40	100	.	0			c.C1417A						PASS	.																																			SO:0001583	missense	54777	exon12			ACAGACGCAGCCG																												ENST00000368586.5:c.1417C>A	10.37:g.134736052G>T	ENSP00000357575:p.Arg473Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	785	0.35943223443223443	161	0.32723577235772355	164	0.4530386740331492	194	0.33916083916083917	266	0.35092348284960423	G	7.319	0.616533	0.14129	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.44083	2.92;0.93	3.28	3.28	0.37604	.	0.909396	0.09144	N	0.842524	T	0.00012	0.0000	.	.	.	0.50632	P	1.1200000000000099E-4	.	.	.	.	.	.	T	0.47484	-0.9114	6	0.66056	D	0.02	-7.2575	9.937	0.41556	0.0:0.0:0.7961:0.2039	rs4880287	.	.	.	S	473	ENSP00000357575:R473S;ENSP00000357571:R473S	ENSP00000357571:R473S	R	-	1	0	C10orf93	134586042	0.004000	0.15560	0.873000	0.34254	0.025000	0.11179	1.261000	0.32980	1.859000	0.53934	0.462000	0.41574	CGT	G|0.640;T|0.360	0.360	strong		0.701	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
FAM186A	121006	hgsc.bcm.edu	37	12	50754563	50754563	+	Missense_Mutation	SNP	T	T	G	rs12303082	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50754563T>G	ENST00000327337.5	-	3	558	c.559A>C	c.(559-561)Aag>Cag	p.K187Q	FAM186A_ENST00000543111.1_Missense_Mutation_p.K187Q	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	187			K -> Q (in dbSNP:rs12303082). {ECO:0000269|PubMed:17974005}.														TGTTTCTTCTTTTCGTCGAGG	0.338													T|||	3032	0.605431	0.4985	0.7334	5008	,	,		20047	0.7431		0.659	False		,,,				2504	0.4622				p.K187Q	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.A559C						PASS	.						106.0	80.0	88.0					12																	50754563		692	1591	2283	SO:0001583	missense	121006	exon3			TCTTCTTTTCGTC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.559A>C	12.37:g.50754563T>G	ENSP00000329995:p.Lys187Gln	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	1421	0.6506410256410257	239	0.48577235772357724	266	0.7348066298342542	412	0.7202797202797203	504	0.6649076517150396	T	13.74	2.327934	0.41197	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.11277	2.79;2.79	4.72	4.72	0.59763	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.28454	P	0.9161856	D	0.63046	0.992	D	0.63381	0.914	T	0.00090	-1.2087	8	0.35671	T	0.21	.	10.7886	0.46419	0.0:0.0:0.0:1.0	rs12303082;rs52816822;rs60816360;rs12303082	187	A6NE01	F186A_HUMAN	Q	187	ENSP00000441337:K187Q;ENSP00000329995:K187Q	ENSP00000329995:K187Q	K	-	1	0	FAM186A	49040830	0.549000	0.26481	0.018000	0.16275	0.008000	0.06430	3.184000	0.50926	2.134000	0.65973	0.528000	0.53228	AAG	T|0.371;G|0.629	0.629	strong		0.338	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
TSHZ2	128553	hgsc.bcm.edu	37	20	51870336	51870336	+	Missense_Mutation	SNP	G	G	C	rs739869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:51870336G>C	ENST00000371497.5	+	2	1226	c.339G>C	c.(337-339)agG>agC	p.R113S	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Missense_Mutation_p.R110S|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R110S	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	113			R -> S (in dbSNP:rs739869). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CTCACGTCAGGCTTCCAAACG	0.532													G|||	264	0.0527157	0.0514	0.0591	5008	,	,		22214	0.0		0.1262	False		,,,				2504	0.0286				p.R113S		Atlas-SNP	.											.	TSHZ2	209	.	0			c.G339C						PASS	.	G	SER/ARG,SER/ARG	258,4148	148.0+/-182.4	5,248,1950	83.0	72.0	75.0		330,339	1.1	0.4	20	dbSNP_86	75	1023,7577	219.9+/-257.8	63,897,3340	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	110,110	68,1145,5290	CC,CG,GG		11.8953,5.8557,9.8493	benign,benign	110/1032,113/1035	51870336	1281,11725	2203	4300	6503	SO:0001583	missense	128553	exon2			CGTCAGGCTTCCA	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.339G>C	20.37:g.51870336G>C	ENSP00000360552:p.Arg113Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	135	0.061813186813186816	20	0.04065040650406504	26	0.0718232044198895	0	0.0	89	0.11741424802110818	G	0.268	-0.994872	0.02145	0.058557	0.118953	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.12774	2.65;2.65	5.7	1.09	0.20402	.	0.141334	0.64402	D	0.000008	T	0.00109	0.0003	N	0.14661	0.345	0.53005	P	3.6999999999953737E-5	B	0.12630	0.006	B	0.14023	0.01	T	0.38564	-0.9655	9	0.23302	T	0.38	-30.2724	7.7223	0.28740	0.5865:0.0:0.4135:0.0	rs739869;rs52792789;rs739869	113	Q9NRE2	TSH2_HUMAN	S	113;110	ENSP00000360552:R113S;ENSP00000333114:R110S	ENSP00000333114:R110S	R	+	3	2	TSHZ2	51303743	0.899000	0.30636	0.370000	0.25965	0.020000	0.10135	0.479000	0.22228	0.285000	0.22329	0.643000	0.83706	AGG	G|0.921;C|0.079	0.079	strong		0.532	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
ADCK1	57143	hgsc.bcm.edu	37	14	78390880	78390880	+	Silent	SNP	T	T	C	rs2302944	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:78390880T>C	ENST00000238561.5	+	8	1038	c.939T>C	c.(937-939)aaT>aaC	p.N313N	ADCK1_ENST00000556560.1_3'UTR|ADCK1_ENST00000341211.5_Silent_p.N245N	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	320	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		ACCCCGGCAATGTACTGGTGC	0.572													T|||	1175	0.234625	0.1626	0.196	5008	,	,		18266	0.2798		0.2127	False		,,,				2504	0.3354				p.N313N		Atlas-SNP	.											.	ADCK1	81	.	0			c.T939C						PASS	.	T	,	775,3631	314.9+/-293.9	66,643,1494	97.0	90.0	92.0		735,939	-8.7	0.6	14	dbSNP_100	92	1829,6771	328.0+/-318.1	187,1455,2658	no	coding-synonymous,coding-synonymous	ADCK1	NM_001142545.1,NM_020421.3	,	253,2098,4152	CC,CT,TT		21.2674,17.5897,20.0215	,	245/456,313/524	78390880	2604,10402	2203	4300	6503	SO:0001819	synonymous_variant	57143	exon8			CGGCAATGTACTG	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.939T>C	14.37:g.78390880T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Silent	SNP	ENST00000238561.5	37	CCDS9869.1																																																																																			T|0.791;C|0.209	0.209	strong		0.572	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
ZNF189	7743	hgsc.bcm.edu	37	9	104170350	104170350	+	Silent	SNP	A	A	G	rs1047968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:104170350A>G	ENST00000339664.2	+	3	429	c.300A>G	c.(298-300)acA>acG	p.T100T	ZNF189_ENST00000259395.4_Silent_p.T58T|ZNF189_ENST00000374861.3_Silent_p.T86T	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	100					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				GTAGAGAAACATTTGAACTTG	0.383													a|||	312	0.0623003	0.0265	0.0893	5008	,	,		18241	0.002		0.1153	False		,,,				2504	0.0992				p.T100T		Atlas-SNP	.											.	ZNF189	79	.	0			c.A300G						PASS	.	A	,	173,4233	112.9+/-151.0	1,171,2031	87.0	82.0	84.0		300,174	-0.3	1.0	9	dbSNP_86	84	925,7675	205.9+/-248.2	54,817,3429	no	coding-synonymous,coding-synonymous	ZNF189	NM_003452.2,NM_197977.1	,	55,988,5460	GG,GA,AA		10.7558,3.9265,8.4423	,	100/627,58/585	104170350	1098,11908	2203	4300	6503	SO:0001819	synonymous_variant	7743	exon3			AGAAACATTTGAA	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.300A>G	9.37:g.104170350A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	174	76	0.436782	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	37	CCDS6754.1																																																																																			A|0.931;G|0.069	0.069	strong		0.383	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
FBXO32	114907	hgsc.bcm.edu	37	8	124525483	124525483	+	Silent	SNP	C	C	T	rs3739287	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:124525483C>T	ENST00000517956.1	-	6	797	c.606G>A	c.(604-606)acG>acA	p.T202T	FBXO32_ENST00000443022.2_Intron	NM_058229.3|NM_148177.2	NP_478136.1|NP_680482.1	Q969P5	FBX32_HUMAN	F-box protein 32	202					cellular response to dexamethasone stimulus (GO:0071549)|protein ubiquitination (GO:0016567)|response to denervation involved in regulation of muscle adaptation (GO:0014894)	nucleolus (GO:0005730)|Z disc (GO:0030018)				autonomic_ganglia(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)|stomach(1)	21	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AGTGGAGAATCGTCTCCATCC	0.557													C|||	1019	0.203474	0.1808	0.1772	5008	,	,		17984	0.4673		0.0895	False		,,,				2504	0.0982				p.T202T		Atlas-SNP	.											.	FBXO32	39	.	0			c.G606A						PASS	.	C	,,	784,3622	317.4+/-295.1	66,652,1485	129.0	106.0	114.0		,606,171	-9.0	0.3	8	dbSNP_107	114	802,7798	186.7+/-234.1	43,716,3541	no	intron,coding-synonymous,coding-synonymous	FBXO32	NM_001242463.1,NM_058229.3,NM_148177.2	,,	109,1368,5026	TT,TC,CC		9.3256,17.7939,12.1944	,,	,202/356,57/211	124525483	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	114907	exon6			GAGAATCGTCTCC	AJ420108	CCDS6345.1, CCDS56553.1	8q24.13	2008-01-28	2004-06-15		ENSG00000156804	ENSG00000156804		"""F-boxes /  ""other"""""	16731	protein-coding gene	gene with protein product		606604	"""F-box only protein 32"""			11679633, 11717410	Standard	NM_058229		Approved	MAFbx, ATROGIN1, Fbx32	uc003yqr.3	Q969P5	OTTHUMG00000164981	ENST00000517956.1:c.606G>A	8.37:g.124525483C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	160	82	0.5125	NM_058229	A4KYM0	Silent	SNP	ENST00000517956.1	37	CCDS6345.1																																																																																			C|0.843;T|0.157	0.157	strong		0.557	FBXO32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381281.1		
OR8A1	390275	hgsc.bcm.edu	37	11	124440362	124440362	+	Missense_Mutation	SNP	C	C	G	rs55861866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124440362C>G	ENST00000284287.3	+	1	470	c.398C>G	c.(397-399)aCa>aGa	p.T133R		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	133			T -> R (in dbSNP:rs55861866).		axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		TACATGCTGACAGTGATGGCC	0.478													C|||	1363	0.272165	0.0726	0.3847	5008	,	,		24437	0.2659		0.3598	False		,,,				2504	0.3783				p.T133R		Atlas-SNP	.											OR8A1,colon,carcinoma,+1,1	OR8A1	61	1	0			c.C398G						PASS	.	C	ARG/THR	578,3824	257.7+/-262.0	42,494,1665	174.0	146.0	156.0		398	3.2	0.6	11	dbSNP_129	156	2985,5613	463.4+/-366.0	530,1925,1844	yes	missense	OR8A1	NM_001005194.1	71	572,2419,3509	GG,GC,CC		34.7174,13.1304,27.4077	probably-damaging	133/327	124440362	3563,9437	2201	4299	6500	SO:0001583	missense	390275	exon1			TGCTGACAGTGAT	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"""GPCR / Class A : Olfactory receptors"""	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.398C>G	11.37:g.124440362C>G	ENSP00000284287:p.Thr133Arg	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	178	176	0.988764	NM_001005194	Q6IEW7|Q96RC6	Missense_Mutation	SNP	ENST00000284287.3	37	CCDS31712.1	609	0.27884615384615385	43	0.08739837398373984	136	0.3756906077348066	163	0.28496503496503495	267	0.35224274406332456	C	18.12	3.552723	0.65425	0.131304	0.347174	ENSG00000196119	ENST00000284287	T	0.01359	4.98	5.03	3.17	0.36434	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000211	T	0.00012	0.0000	H	0.95187	3.635	0.27424	P	0.9542106	P	0.52842	0.956	P	0.58266	0.836	T	0.33059	-0.9883	9	0.87932	D	0	.	7.485	0.27427	0.0:0.7083:0.1377:0.154	rs55861866;rs56775161;rs61748725	133	Q8NGG7	OR8A1_HUMAN	R	133	ENSP00000284287:T133R	ENSP00000284287:T133R	T	+	2	0	OR8A1	123945572	0.734000	0.28142	0.646000	0.29493	0.982000	0.71751	3.401000	0.52601	0.707000	0.31934	0.650000	0.86243	ACA	C|0.718;G|0.282	0.282	strong		0.478	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194	
USP40	55230	hgsc.bcm.edu	37	2	234432017	234432017	+	Missense_Mutation	SNP	A	A	G	rs838543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234432017A>G	ENST00000427112.2	-	15	2032	c.1997T>C	c.(1996-1998)gTc>gCc	p.V666A	USP40_ENST00000450966.1_Missense_Mutation_p.V678A|USP40_ENST00000251722.6_Missense_Mutation_p.V666A			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	666			V -> A (in dbSNP:rs838543).		ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		AGCTGGAAAGACATGTGGAGA	0.468													A|||	902	0.180112	0.2284	0.134	5008	,	,		19676	0.1458		0.2435	False		,,,				2504	0.1176				p.V678A		Atlas-SNP	.											.	USP40	174	.	0			c.T2033C						PASS	.	A	ALA/VAL	848,3170		86,676,1247	179.0	169.0	172.0		2033	5.6	0.9	2	dbSNP_86	172	1761,6597		188,1385,2606	yes	missense	USP40	NM_018218.2	64	274,2061,3853	GG,GA,AA		21.0696,21.105,21.0811	benign	678/1248	234432017	2609,9767	2009	4179	6188	SO:0001583	missense	55230	exon15			GGAAAGACATGTG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1997T>C	2.37:g.234432017A>G	ENSP00000387898:p.Val666Ala	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	178	93	0.522472	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	410	0.18772893772893773	121	0.2459349593495935	48	0.13259668508287292	66	0.11538461538461539	175	0.23087071240105542	A	12.61	1.989024	0.35131	0.21105	0.210696	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.53206	0.63;0.63;0.63	5.57	5.57	0.84162	.	.	.	.	.	T	0.00012	0.0000	L	0.55103	1.725	0.25118	P	0.99066606	B;B	0.24618	0.036;0.107	B;B	0.18871	0.01;0.023	T	0.05419	-1.0886	8	0.44086	T	0.13	.	14.3088	0.66403	1.0:0.0:0.0:0.0	rs838543;rs17669447;rs52822056;rs61311513;rs838543	666;678	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	A	678;666;666	ENSP00000415434:V678A;ENSP00000251722:V666A;ENSP00000387898:V666A	ENSP00000251722:V666A	V	-	2	0	USP40	234096756	0.966000	0.33281	0.948000	0.38648	0.956000	0.61745	2.928000	0.48908	2.119000	0.64992	0.533000	0.62120	GTC	T|0.001;G|0.188	0.188	strong		0.468	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
RPS6KA2	6196	hgsc.bcm.edu	37	6	166826255	166826255	+	Silent	SNP	G	G	A	rs909631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:166826255G>A	ENST00000265678.4	-	21	2420	c.2197C>T	c.(2197-2199)Ctg>Ttg	p.L733L	RPS6KA2_ENST00000503859.1_Silent_p.L741L|RPS6KA2_ENST00000509742.1_5'UTR|RPS6KA2_ENST00000481261.2_Silent_p.L644L|RPS6KA2_ENST00000510118.1_Silent_p.L758L|RPS6KA2_ENST00000405189.3_Silent_p.L644L	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	733					axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		ACCCGCTACAGCCGCGTGGAC	0.662													A|||	3106	0.620208	0.3101	0.6643	5008	,	,		13038	0.7431		0.6571	False		,,,				2504	0.8436				p.L741L		Atlas-SNP	.											.	RPS6KA2	212	.	0			c.C2221T						PASS	.	A	,	1676,2720		324,1028,846	29.0	26.0	27.0		2221,2197	-2.0	0.2	6	dbSNP_86	27	5839,2755		2001,1837,459	no	coding-synonymous,coding-synonymous	RPS6KA2	NM_001006932.1,NM_021135.4	,	2325,2865,1305	AA,AG,GG		32.0572,38.1256,42.1478	,	741/742,733/734	166826255	7515,5475	2198	4297	6495	SO:0001819	synonymous_variant	6196	exon22			GCTACAGCCGCGT	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"""ribosomal protein S6 kinase, 90kD, polypeptide 2"""			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.2197C>T	6.37:g.166826255G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	27	19	0.703704	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Silent	SNP	ENST00000265678.4	37	CCDS5294.1																																																																																			G|0.419;A|0.581	0.581	strong		0.662	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
OR2T34	127068	hgsc.bcm.edu	37	1	248737348	248737348	+	Silent	SNP	G	G	A	rs61833442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248737348G>A	ENST00000328782.2	-	1	732	c.711C>T	c.(709-711)gcC>gcT	p.A237A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTGCGGCCGGCGGCAGAAT	0.567													g|||	1625	0.324481	0.5098	0.2349	5008	,	,		20077	0.251		0.2107	False		,,,				2504	0.3303				p.A237A		Atlas-SNP	.											OR2T34,NS,carcinoma,-2,1	OR2T34	72	1	0			c.C711T						PASS	.						110.0	124.0	119.0					1																	248737348		2176	4300	6476	SO:0001819	synonymous_variant	127068	exon1			GCGGCCGGCGGCA	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.711C>T	1.37:g.248737348G>A		Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	434	50	0.115207	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Silent	SNP	ENST00000328782.2	37	CCDS31120.1																																																																																			G|0.787;A|0.213	0.213	strong		0.567	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
SYTL5	94122	hgsc.bcm.edu	37	X	37932886	37932886	+	Silent	SNP	A	A	G	rs4827330	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:37932886A>G	ENST00000357972.5	+	5	1035	c.489A>G	c.(487-489)gcA>gcG	p.A163A	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000297875.2_Silent_p.A163A|SYTL5_ENST00000456733.2_Silent_p.A163A			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	163					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						GCCAGGATGCAGAAAAGTCAG	0.453													G|||	1220	0.323179	0.3593	0.2738	3775	,	,		13562	0.0615		0.1948	False		,,,				2504	0.3037				p.A163A		Atlas-SNP	.											.	SYTL5	72	.	0			c.A489G						PASS	.	G	,,	1618,2215		302,777,237,552,334	68.0	56.0	60.0		489,489,489	-5.9	0.0	X	dbSNP_111	60	1661,5067		144,903,470,1381,1402	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL5	NM_001163334.1,NM_001163335.1,NM_138780.2	,,	446,1680,707,1933,1736	GG,GA,G,AA,A		24.6879,42.2124,31.0482	,,	163/753,163/731,163/731	37932886	3279,7282	2202	4300	6502	SO:0001819	synonymous_variant	94122	exon4			GGATGCAGAAAAG		CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.489A>G	X.37:g.37932886A>G		Somatic	361	1	0.00277008		WXS	Illumina HiSeq	Phase_I	212	208	0.981132	NM_001163334	A2RRF2	Silent	SNP	ENST00000357972.5	37	CCDS14244.1																																																																																			A|0.684;0|0.003	.	strong		0.453	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780	
TNR	7143	hgsc.bcm.edu	37	1	175324651	175324651	+	Silent	SNP	A	A	G	rs2228359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:175324651A>G	ENST00000367674.2	-	17	3945	c.3237T>C	c.(3235-3237)gaT>gaC	p.D1079D	TNR_ENST00000263525.2_Silent_p.D1079D			Q92752	TENR_HUMAN	tenascin R	1079	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TGCGGCTTCCATCGGTGGATT	0.498													G|||	3334	0.665735	0.5197	0.7104	5008	,	,		21729	0.7946		0.6819	False		,,,				2504	0.682				p.D1079D		Atlas-SNP	.											TNR,colon,carcinoma,-2,1	TNR	399	1	0			c.T3237C						PASS	.	G		2366,2040	566.0+/-381.8	629,1108,466	83.0	83.0	83.0		3237	0.2	0.8	1	dbSNP_98	83	5899,2701	432.9+/-357.3	2025,1849,426	no	coding-synonymous	TNR	NM_003285.2		2654,2957,892	GG,GA,AA		31.407,46.3005,36.4524		1079/1359	175324651	8265,4741	2203	4300	6503	SO:0001819	synonymous_variant	7143	exon17			GCTTCCATCGGTG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3237T>C	1.37:g.175324651A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																			A|0.349;G|0.651	0.651	strong		0.498	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
GNA14	9630	hgsc.bcm.edu	37	9	80040566	80040566	+	Silent	SNP	C	C	T	rs1801259	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:80040566C>T	ENST00000341700.6	-	6	1302	c.789G>A	c.(787-789)tcG>tcA	p.S263S	GNA14_ENST00000464095.1_5'UTR	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	263					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						AAATCACAGACGAATTCAGAA	0.373													c|||	426	0.0850639	0.1172	0.0677	5008	,	,		20020	0.0308		0.1233	False		,,,				2504	0.0706				p.S263S		Atlas-SNP	.											.	GNA14	50	.	0			c.G789A						PASS	.	T		499,3907	229.8+/-244.2	23,453,1727	111.0	116.0	114.0		789	-4.2	0.9	9	dbSNP_89	114	956,7644	210.1+/-251.1	58,840,3402	no	coding-synonymous	GNA14	NM_004297.3		81,1293,5129	TT,TC,CC		11.1163,11.3255,11.1871		263/356	80040566	1455,11551	2203	4300	6503	SO:0001819	synonymous_variant	9630	exon6			CACAGACGAATTC	AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.789G>A	9.37:g.80040566C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	NM_004297	B1ALW3	Silent	SNP	ENST00000341700.6	37	CCDS6657.1																																																																																			C|0.894;T|0.106	0.106	strong		0.373	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75969335	75969335	+	Missense_Mutation	SNP	C	C	T	rs77237106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75969335C>T	ENST00000308508.5	-	10	5617	c.5525G>A	c.(5524-5526)cGg>cAg	p.R1842Q	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1842	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TCGGGTGAGCCGGAGTGGGAC	0.662													C|||	274	0.0547125	0.0076	0.0821	5008	,	,		17011	0.0		0.1759	False		,,,				2504	0.0307				p.R1842Q		Atlas-SNP	.											.	CSPG4	175	.	0			c.G5525A						PASS	.	C	GLN/ARG	123,4079		2,119,1980	14.0	15.0	15.0		5525	3.2	0.1	15	dbSNP_131	15	1331,7005		123,1085,2960	yes	missense	CSPG4	NM_001897.4	43	125,1204,4940	TT,TC,CC		15.9669,2.9272,11.5967	possibly-damaging	1842/2323	75969335	1454,11084	2101	4168	6269	SO:0001583	missense	1464	exon10			GTGAGCCGGAGTG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.5525G>A	15.37:g.75969335C>T	ENSP00000312506:p.Arg1842Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	45	0.652174	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	162	0.07417582417582418	4	0.008130081300813009	34	0.09392265193370165	0	0.0	124	0.16358839050131926	C	10.22	1.288895	0.23478	0.029272	0.159669	ENSG00000173546	ENST00000308508	T	0.19250	2.16	5.29	3.16	0.36331	.	0.295925	0.29087	N	0.013188	T	0.00039	0.0001	N	0.25647	0.755	0.31038	P	0.7166239999999999	B	0.15719	0.014	B	0.06405	0.002	T	0.30563	-0.9974	9	0.11182	T	0.66	.	6.6071	0.22731	0.0:0.6128:0.0:0.3872	.	1842	Q6UVK1	CSPG4_HUMAN	Q	1842	ENSP00000312506:R1842Q	ENSP00000312506:R1842Q	R	-	2	0	CSPG4	73756390	0.015000	0.18098	0.125000	0.21846	0.776000	0.43924	-0.059000	0.11731	1.222000	0.43521	0.561000	0.74099	CGG	C|0.919;T|0.081	0.081	strong		0.662	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
MAP4K5	11183	hgsc.bcm.edu	37	14	50901768	50901768	+	Missense_Mutation	SNP	G	G	A	rs17780143	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50901768G>A	ENST00000013125.4	-	26	2216	c.1898C>T	c.(1897-1899)aCg>aTg	p.T633M		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	633	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.		T -> M (in dbSNP:rs17780143). {ECO:0000269|PubMed:17344846}.		activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					TTTATGTCCCGTGTAAGGGTT	0.348													G|||	268	0.0535144	0.0008	0.134	5008	,	,		16465	0.0298		0.0408	False		,,,				2504	0.1053				p.T633M		Atlas-SNP	.											MAP4K5,lymph_node,lymphoid_neoplasm,0,1	MAP4K5	48	1	0			c.C1898T						PASS	.	G	MET/THR,MET/THR	50,3562		1,48,1757	59.0	57.0	58.0		1898,1898	5.7	1.0	14	dbSNP_123	58	484,7678		15,454,3612	yes	missense,missense	MAP4K5	NM_006575.4,NM_198794.2	81,81	16,502,5369	AA,AG,GG		5.9299,1.3843,4.5354	probably-damaging,probably-damaging	633/847,633/847	50901768	534,11240	1806	4081	5887	SO:0001583	missense	11183	exon26			TGTCCCGTGTAAG	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.1898C>T	14.37:g.50901768G>A	ENSP00000013125:p.Thr633Met	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	37		95	0.043498168498168496	0	0.0	47	0.1298342541436464	16	0.027972027972027972	32	0.04221635883905013	G	28.4	4.916578	0.92249	0.013843	0.059299	ENSG00000012983	ENST00000013125	T	0.04706	3.57	5.65	5.65	0.86999	Citron-like (3);	0.047448	0.85682	D	0.000000	T	0.00210	0.0006	M	0.72894	2.215	0.09310	P	0.999999999387087	D;D	0.76494	0.989;0.999	P;P	0.60345	0.832;0.873	T	0.00026	-1.2314	9	0.72032	D	0.01	.	19.7256	0.96162	0.0:0.0:1.0:0.0	rs17780143;rs52820828;rs56883224;rs17780143	633;633	B2R928;Q9Y4K4	.;M4K5_HUMAN	M	633	ENSP00000013125:T633M	ENSP00000013125:T633M	T	-	2	0	MAP4K5	49971518	1.000000	0.71417	0.986000	0.45419	0.924000	0.55760	9.807000	0.99171	2.667000	0.90743	0.585000	0.79938	ACG	G|0.951;A|0.049	0.049	strong		0.348	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575	
PTX4	390667	hgsc.bcm.edu	37	16	1536535	1536535	+	Missense_Mutation	SNP	C	C	T	rs2745098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1536535C>T	ENST00000447419.2	-	3	867	c.842G>A	c.(841-843)aGg>aAg	p.R281K	PTX4_ENST00000293922.1_Missense_Mutation_p.R276K|PTX4_ENST00000440447.2_Missense_Mutation_p.G133R			Q96A99	PTX4_HUMAN	pentraxin 4, long	281	Pentaxin.		R -> K (in dbSNP:rs2745098).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GACCACGTTCCTGGTGGAGGC	0.657													T|||	2486	0.496406	0.7474	0.3228	5008	,	,		18995	0.5238		0.3738	False		,,,				2504	0.3783				p.R276K		Atlas-SNP	.											.	PTX4	46	.	0			c.G827A						PASS	.	T	LYS/ARG	2968,1430	459.2+/-352.2	993,982,224	51.0	52.0	52.0		827	4.5	0.0	16	dbSNP_100	52	3169,5431	648.3+/-400.5	558,2053,1689	yes	missense	PTX4	NM_001013658.1	26	1551,3035,1913	TT,TC,CC		36.8488,32.5148,47.215	benign	276/474	1536535	6137,6861	2199	4300	6499	SO:0001583	missense	390667	exon3			ACGTTCCTGGTGG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.842G>A	16.37:g.1536535C>T	ENSP00000445277:p.Arg281Lys	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		1079	0.49404761904761907	342	0.6951219512195121	116	0.32044198895027626	321	0.5611888111888111	300	0.39577836411609496	T	6.812	0.518886	0.13005	0.674852	0.368488	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.62364	0.03;0.03	5.58	4.48	0.54585	.	0.658399	0.15448	N	0.261830	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46816	-0.9164	9	0.02654	T	1	.	6.1276	0.20187	0.1495:0.0796:0.0:0.7709	rs2745098;rs56885857;rs2745098	276	Q96A99-2	.	K	281;276	ENSP00000445277:R281K;ENSP00000293922:R276K	ENSP00000293922:R276K	R	-	2	0	PTX4	1476536	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	0.247000	0.18179	0.396000	0.25283	-0.254000	0.11334	AGG	C|0.507;T|0.493	0.493	strong		0.657	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
CTC1	80169	hgsc.bcm.edu	37	17	8138569	8138569	+	Missense_Mutation	SNP	C	C	G	rs62624978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8138569C>G	ENST00000315684.8	-	8	1248	c.1241G>C	c.(1240-1242)gGg>gCg	p.G414A	CTC1_ENST00000581671.1_5'Flank	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	414					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						TCTTGTCCCCCCTCCCACTGA	0.582													c|||	38	0.00758786	0.0015	0.0202	5008	,	,		19351	0.0		0.0189	False		,,,				2504	0.0031				p.G414A		Atlas-SNP	.											.	CTC1	75	.	0			c.G1241C						PASS	.		ALA/GLY	19,4083		1,17,2033	45.0	52.0	50.0		1241	5.0	1.0	17	dbSNP_129	50	171,8241		1,169,4036	yes	missense	CTC1	NM_025099.5	60	2,186,6069	GG,GC,CC		2.0328,0.4632,1.5183	probably-damaging	414/1218	8138569	190,12324	2051	4206	6257	SO:0001583	missense	80169	exon8			GTCCCCCCTCCCA	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.1241G>C	17.37:g.8138569C>G	ENSP00000313759:p.Gly414Ala	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	39	11	0.282051	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	37	CCDS42259.1	23	0.010531135531135532	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	13	0.017150395778364115	c	8.551	0.875454	0.17395	0.004632	0.020328	ENSG00000178971	ENST00000315684;ENST00000449476	D;D	0.83591	-1.74;-1.74	5.04	5.04	0.67666	.	0.190660	0.34025	N	0.004338	T	0.77445	0.4131	L	0.50919	1.6	0.36741	D	0.88221	D	0.89917	1.0	D	0.91635	0.999	T	0.79600	-0.1736	10	0.06757	T	0.87	-11.1032	13.7672	0.63002	0.0:1.0:0.0:0.0	rs62624978	414	Q2NKJ3	CTC1_HUMAN	A	414;379	ENSP00000313759:G414A;ENSP00000396018:G379A	ENSP00000313759:G414A	G	-	2	0	CTC1	8079294	0.737000	0.28175	1.000000	0.80357	0.987000	0.75469	1.980000	0.40618	2.629000	0.89072	0.598000	0.82781	GGG	C|0.987;G|0.013	0.013	strong		0.582	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
SULT6B1	391365	hgsc.bcm.edu	37	2	37406680	37406680	+	Missense_Mutation	SNP	C	C	G	rs10205833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:37406680C>G	ENST00000535679.1	-	4	449	c.450G>C	c.(448-450)ttG>ttC	p.L150F	SULT6B1_ENST00000260637.3_Missense_Mutation_p.L112F|SULT6B1_ENST00000407963.1_Missense_Mutation_p.L112F|SULT6B1_ENST00000379149.2_Intron			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	150			L -> F (in dbSNP:rs10205833). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				TGTGGAAATGCAAAAAAGATA	0.368													G|||	2128	0.42492	0.2277	0.4207	5008	,	,		19419	0.8016		0.2614	False		,,,				2504	0.4744				p.L112F		Atlas-SNP	.											.	SULT6B1	46	.	0			c.G336C						PASS	.	G	PHE/LEU	1090,3316	720.1+/-409.0	140,810,1253	139.0	132.0	134.0		336	0.4	1.0	2	dbSNP_119	134	2158,6442	712.8+/-405.9	299,1560,2441	yes	missense	SULT6B1	NM_001032377.1	22	439,2370,3694	GG,GC,CC		25.093,24.739,24.9731	benign	112/266	37406680	3248,9758	2203	4300	6503	SO:0001583	missense	391365	exon4			GAAATGCAAAAAA	AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"""Sulfotransferases, cytosolic"""	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.450G>C	2.37:g.37406680C>G	ENSP00000444081:p.Leu150Phe	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_001032377	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	37		906	0.41483516483516486	102	0.2073170731707317	139	0.3839779005524862	455	0.7954545454545454	210	0.2770448548812665	G	0.417	-0.910131	0.02434	0.24739	0.25093	ENSG00000138068	ENST00000535679;ENST00000260637;ENST00000407963	D;D;D	0.81908	-1.55;-1.55;-1.55	4.27	0.367	0.16140	Sulfotransferase domain (1);	0.110564	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00010	-3.05	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.42783	-0.9431	9	0.02654	T	1	.	5.2867	0.15706	0.4262:0.1476:0.4262:0.0	rs10205833;rs10205833	150	Q6IMI4	ST6B1_HUMAN	F	150;112;112	ENSP00000444081:L150F;ENSP00000260637:L112F;ENSP00000384950:L112F	ENSP00000260637:L112F	L	-	3	2	SULT6B1	37260184	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	0.681000	0.25320	-0.041000	0.13558	-0.216000	0.12614	TTG	C|0.686;G|0.314	0.314	strong		0.368	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377	
SSPO	23145	hgsc.bcm.edu	37	7	149489491	149489491	+	RNA	SNP	C	C	T	rs1076277	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149489491C>T	ENST00000378016.2	+	0	5644							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCCTGGGCAACGCATCAAGGC	0.706													C|||	259	0.0517173	0.0068	0.0504	5008	,	,		15236	0.0962		0.0666	False		,,,				2504	0.0521				p.R1882C		Atlas-SNP	.											.	.	.	.	0			c.C5644T						PASS	.	C		51,4223		0,51,2086	14.0	22.0	19.0		5648	5.0	0.2	7	dbSNP_86	19	535,7911		22,491,3710	yes	coding-notMod3	SSPO	NM_198455.2		22,542,5796	TT,TC,CC		6.3344,1.1933,4.6069			149489491	586,12134	2137	4223	6360			23145	exon37			GGGCAACGCATCA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149489491C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.942;T|0.058	0.058	strong		0.706	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
TMEM260	54916	hgsc.bcm.edu	37	14	57052511	57052511	+	Silent	SNP	G	G	T	rs3737171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:57052511G>T	ENST00000261556.6	+	3	347	c.225G>T	c.(223-225)acG>acT	p.T75T	TMEM260_ENST00000538838.1_Silent_p.T75T|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	75						integral component of membrane (GO:0016021)											CTTTGTTCACGCTGGTGGCTA	0.448													G|||	1619	0.323283	0.0227	0.5346	5008	,	,		18852	0.4732		0.4254	False		,,,				2504	0.32				p.T75T		Atlas-SNP	.											.	.	.	.	0			c.G225T						PASS	.	G		390,4016	194.0+/-219.0	19,352,1832	250.0	213.0	226.0		225	-10.3	0.9	14	dbSNP_107	226	3527,5073	514.1+/-378.3	733,2061,1506	no	coding-synonymous	C14orf101	NM_017799.3		752,2413,3338	TT,TG,GG		41.0116,8.8516,30.1169		75/708	57052511	3917,9089	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			GTTCACGCTGGTG	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 101"""	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.225G>T	14.37:g.57052511G>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	238	109	0.457983	NM_017799	A8KAN4|B3KPF5|Q86XE1	Silent	SNP	ENST00000261556.6	37	CCDS9727.2																																																																																			G|0.674;T|0.326	0.326	strong		0.448	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799	
ZNF439	90594	hgsc.bcm.edu	37	19	11979164	11979164	+	Missense_Mutation	SNP	T	T	C	rs10500209	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11979164T>C	ENST00000304030.2	+	3	1480	c.1280T>C	c.(1279-1281)tTg>tCg	p.L427S	ZNF439_ENST00000455282.1_Missense_Mutation_p.L291S|ZNF439_ENST00000592534.1_Intron	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	427			L -> S (in dbSNP:rs10500209). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						AATCTTCAATTGCATGGTAGG	0.453													-|||	502	0.10024	0.0091	0.2017	5008	,	,		19620	0.004		0.2604	False		,,,				2504	0.0859				p.L427S		Atlas-SNP	.											.	ZNF439	67	.	0			c.T1280C						PASS	.	T	SER/LEU	234,4172	138.4+/-174.2	3,228,1972	71.0	66.0	68.0		1280	-0.7	0.0	19	dbSNP_119	68	2358,6242	392.9+/-344.2	303,1752,2245	no	missense	ZNF439	NM_152262.2	145	306,1980,4217	CC,CT,TT		27.4186,5.3109,19.9293	benign	427/500	11979164	2592,10414	2203	4300	6503	SO:0001583	missense	90594	exon3			TTCAATTGCATGG	AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"""Zinc fingers, C2H2-type"", ""-"""	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.1280T>C	19.37:g.11979164T>C	ENSP00000305077:p.Leu427Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	295	0.13507326007326007	9	0.018292682926829267	76	0.20994475138121546	4	0.006993006993006993	206	0.2717678100263852	t	0.012	-1.684349	0.00745	0.053109	0.274186	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.07021	3.23;3.23	0.575	-0.71	0.11234	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.03253	-0.375	0.80722	P	0.0	B	0.26602	0.154	B	0.31101	0.124	T	0.45644	-0.9247	8	0.10636	T	0.68	.	3.2351	0.06762	0.0:0.4434:0.2616:0.295	rs10500209;rs17705609;rs17855566;rs52803841;rs56466712;rs59470711;rs10500209	427	Q8NDP4	ZN439_HUMAN	S	291;427	ENSP00000395632:L291S;ENSP00000305077:L427S	ENSP00000305077:L427S	L	+	2	0	ZNF439	11840164	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-10.396000	0.00006	-0.375000	0.07955	0.163000	0.16589	TTG	T|0.842;C|0.158	0.158	strong		0.453	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		
ACACB	32	hgsc.bcm.edu	37	12	109577735	109577735	+	Silent	SNP	C	C	T	rs2878960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109577735C>T	ENST00000338432.7	+	2	644	c.525C>T	c.(523-525)tcC>tcT	p.S175S	ACACB_ENST00000377848.3_Silent_p.S175S|ACACB_ENST00000377854.5_Silent_p.S175S			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	175					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	ACTACTCCTCCGACGAGGACT	0.577													C|||	1992	0.397764	0.2564	0.3977	5008	,	,		16869	0.2589		0.6879	False		,,,				2504	0.4335				p.S175S		Atlas-SNP	.											.	ACACB	330	.	0			c.C525T						PASS	.	C		1326,3080	441.6+/-346.4	195,936,1072	81.0	83.0	82.0		525	-4.1	0.1	12	dbSNP_101	82	5769,2831	668.1+/-402.5	1928,1913,459	no	coding-synonymous	ACACB	NM_001093.3		2123,2849,1531	TT,TC,CC		32.9186,30.0953,45.4483		175/2459	109577735	7095,5911	2203	4300	6503	SO:0001819	synonymous_variant	32	exon1			CTCCTCCGACGAG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.525C>T	12.37:g.109577735C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.511;T|0.489	0.489	strong		0.577	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
GPR78	27201	hgsc.bcm.edu	37	4	8582742	8582742	+	Silent	SNP	C	C	T	rs17844776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:8582742C>T	ENST00000382487.4	+	1	450	c.33C>T	c.(31-33)ctC>ctT	p.L11L	GPR78_ENST00000509216.1_Intron	NM_080819.4	NP_543009.2	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	11					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(4)|kidney(4)|large_intestine(1)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26						TGGCGGGTCTCCTGGTGATGG	0.682													C|||	696	0.138978	0.0325	0.2161	5008	,	,		14310	0.0228		0.3231	False		,,,				2504	0.1585				p.L11L		Atlas-SNP	.											.	GPR78	58	.	0			c.C33T						PASS	.	C		355,4047		18,319,1864	18.0	22.0	20.0		33	-1.7	0.0	4	dbSNP_123	20	2876,5710		495,1886,1912	no	coding-synonymous	GPR78	NM_080819.2		513,2205,3776	TT,TC,CC		33.4964,8.0645,24.8768		11/364	8582742	3231,9757	2201	4293	6494	SO:0001819	synonymous_variant	27201	exon1			GGGTCTCCTGGTG	AF411107	CCDS3403.1	4p16.1	2012-08-21			ENSG00000155269	ENSG00000155269		"""GPCR / Class A : Orphans"""	4528	protein-coding gene	gene with protein product		606921				11574155	Standard	NM_080819		Approved		uc003glk.4	Q96P69	OTTHUMG00000128483	ENST00000382487.4:c.33C>T	4.37:g.8582742C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_080819	Q8NGV3	Silent	SNP	ENST00000382487.4	37	CCDS3403.1																																																																																			C|0.811;T|0.189	0.189	strong		0.682	GPR78-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359201.1		
VWA2	340706	hgsc.bcm.edu	37	10	116020974	116020974	+	Silent	SNP	C	C	G	rs71484937	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:116020974C>G	ENST00000392982.3	+	5	541	c.291C>G	c.(289-291)tcC>tcG	p.S97S	VWA2_ENST00000603594.1_Silent_p.S97S			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	97	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		AGTTCAGTTCCACTCCTCATC	0.483													C|||	159	0.0317492	0.0015	0.0749	5008	,	,		20305	0.0		0.0964	False		,,,				2504	0.0082				p.S97S		Atlas-SNP	.											.	VWA2	64	.	0			c.C291G						PASS	.	C		86,4320	73.6+/-111.7	0,86,2117	115.0	106.0	109.0		291	-9.0	0.0	10	dbSNP_130	109	679,7921	170.4+/-221.6	22,635,3643	no	coding-synonymous	VWA2	NM_198496.1		22,721,5760	GG,GC,CC		7.8953,1.9519,5.8819		97/726	116020974	765,12241	2203	4300	6503	SO:0001819	synonymous_variant	340706	exon5			CAGTTCCACTCCT	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.291C>G	10.37:g.116020974C>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	184	75	0.407609	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	37																																																																																				C|0.943;G|0.057	0.057	strong		0.483	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
TSSK2	23617	hgsc.bcm.edu	37	22	19119545	19119545	+	Silent	SNP	C	C	T	rs45604134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:19119545C>T	ENST00000399635.2	+	1	1225	c.633C>T	c.(631-633)tgC>tgT	p.C211C	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	211	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					TCATGGTCTGCGGCTCCATGC	0.597													C|||	815	0.16274	0.1195	0.134	5008	,	,		20404	0.125		0.173	False		,,,				2504	0.2699				p.C211C		Atlas-SNP	.											.	TSSK2	29	.	0			c.C633T						PASS	.	C	,	489,3917	228.1+/-243.1	30,429,1744	94.0	89.0	91.0		,633	-8.6	0.9	22	dbSNP_127	91	1589,7011	292.7+/-301.0	165,1259,2876	yes	utr-3,coding-synonymous	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,	195,1688,4620	TT,TC,CC		18.4767,11.0985,15.9772	,	,211/359	19119545	2078,10928	2203	4300	6503	SO:0001819	synonymous_variant	23617	exon1			GGTCTGCGGCTCC	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"""serine/threonine kinase 22B (spermiogenesis associated)"""	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.633C>T	22.37:g.19119545C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_053006	Q8IY55	Silent	SNP	ENST00000399635.2	37	CCDS13755.1																																																																																			C|0.846;T|0.154	0.154	strong		0.597	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
PSMD5	5711	hgsc.bcm.edu	37	9	123583192	123583192	+	Silent	SNP	A	A	G	rs1060817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:123583192A>G	ENST00000210313.3	-	9	1256	c.1182T>C	c.(1180-1182)gaT>gaC	p.D394D	PSMD5_ENST00000604848.1_Silent_p.D51D|PSMD5_ENST00000373904.5_Silent_p.D351D	NM_001270427.1|NM_005047.3	NP_001257356.1|NP_005038.1	Q16401	PSMD5_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	394					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|protein folding (GO:0006457)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)				endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)	10						GCTCCAGTGGATCCCGAGATA	0.453													A|||	2446	0.488419	0.1626	0.6571	5008	,	,		21160	0.4673		0.5895	False		,,,				2504	0.727				p.D394D		Atlas-SNP	.											.	PSMD5	34	.	0			c.T1182C						PASS	.	A		1017,3389	375.9+/-321.8	109,799,1295	86.0	87.0	87.0		1182	1.0	0.9	9	dbSNP_86	87	5113,3487	633.9+/-398.8	1514,2085,701	no	coding-synonymous	PSMD5	NM_005047.2		1623,2884,1996	GG,GA,AA		40.5465,23.0822,47.1321		394/505	123583192	6130,6876	2203	4300	6503	SO:0001819	synonymous_variant	5711	exon9			CAGTGGATCCCGA	AK001065	CCDS6824.1, CCDS59143.1	9q34.11	2008-02-05			ENSG00000095261	ENSG00000095261		"""Proteasome (prosome, macropain) subunits"""	9563	protein-coding gene	gene with protein product		604452				7559544	Standard	NM_005047		Approved	S5B, KIAA0072	uc004bko.4	Q16401	OTTHUMG00000020573	ENST00000210313.3:c.1182T>C	9.37:g.123583192A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	25	0.367647	NM_005047	B4DZM8|Q15045|Q4VXG8	Silent	SNP	ENST00000210313.3	37	CCDS6824.1																																																																																			A|0.532;G|0.468	0.468	strong		0.453	PSMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053825.2	NM_005047	
MUC16	94025	hgsc.bcm.edu	37	19	9072313	9072313	+	Missense_Mutation	SNP	A	A	G	rs2121133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9072313A>G	ENST00000397910.4	-	3	15336	c.15133T>C	c.(15133-15135)Tcc>Ccc	p.S5045P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5047	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCAGGTGAGGACAGAAAGGAA	0.478													A|||	1054	0.210463	0.0628	0.2046	5008	,	,		20061	0.249		0.3101	False		,,,				2504	0.272				p.S5045P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T15133C						PASS	.		PRO/SER	401,3505		23,355,1575	83.0	80.0	81.0		15133	-3.2	0.0	19	dbSNP_96	81	2393,5903		341,1711,2096	yes	missense	MUC16	NM_024690.2	74	364,2066,3671	GG,GA,AA		28.8452,10.2663,22.8979	benign	5045/14508	9072313	2794,9408	1953	4148	6101	SO:0001583	missense	94025	exon3			GTGAGGACAGAAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15133T>C	19.37:g.9072313A>G	ENSP00000381008:p.Ser5045Pro	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	488	0.22344322344322345	47	0.09552845528455285	87	0.24033149171270718	122	0.21328671328671328	232	0.30606860158311344	a	4.940	0.174556	0.09391	0.102663	0.288452	ENSG00000181143	ENST00000397910	T	0.29142	1.58	1.59	-3.18	0.05186	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	.	.	.	B	0.09022	0.002	B	0.04013	0.001	T	0.40251	-0.9573	8	0.87932	D	0	.	3.207	0.06670	0.4598:0.2227:0.3175:0.0	rs2121133;rs2121133	5045	B5ME49	.	P	5045	ENSP00000381008:S5045P	ENSP00000381008:S5045P	S	-	1	0	MUC16	8933313	0.004000	0.15560	0.000000	0.03702	0.265000	0.26407	0.008000	0.13197	-1.081000	0.03105	0.234000	0.17832	TCC	A|0.771;G|0.229	0.229	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ETV1	2115	hgsc.bcm.edu	37	7	13978809	13978809	+	Missense_Mutation	SNP	T	T	C	rs9639168	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:13978809T>C	ENST00000430479.1	-	7	965	c.298A>G	c.(298-300)Agc>Ggc	p.S100G	ETV1_ENST00000405218.2_Missense_Mutation_p.S100G|ETV1_ENST00000403527.1_Missense_Mutation_p.S60G|ETV1_ENST00000405358.4_Missense_Mutation_p.S114G|ETV1_ENST00000420159.2_Missense_Mutation_p.S42G|ETV1_ENST00000242066.5_Missense_Mutation_p.S82G|ETV1_ENST00000476720.2_5'UTR|ETV1_ENST00000343495.5_Missense_Mutation_p.S82G|ETV1_ENST00000399357.3_Missense_Mutation_p.S60G|ETV1_ENST00000403685.1_Missense_Mutation_p.S82G|ETV1_ENST00000405192.2_Missense_Mutation_p.S100G	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	100			S -> G (in dbSNP:rs9639168). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						CAGGCAGAGCTGATTTCTGAA	0.403			T	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""	"""Ewing sarcoma, prostate"""								C|||	1599	0.319289	0.18	0.3458	5008	,	,		17089	0.4187		0.3439	False		,,,				2504	0.3609				p.S100G		Atlas-SNP	.		Dom	yes		7	7p22	2115	ets variant gene 1		"""M, E"""	ETV1_ENST00000403527,NS,meningioma,0,2	ETV1	138	2	0			c.A298G						PASS	.	C	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	727,3007		85,557,1225	151.0	139.0	143.0		298,244,244,178,124,178,298	4.6	1.0	7	dbSNP_119	143	2766,5426		472,1822,1802	yes	missense,missense,missense,missense,missense,missense,missense	ETV1	NM_001163147.1,NM_001163148.1,NM_001163149.1,NM_001163150.1,NM_001163151.1,NM_001163152.1,NM_004956.4	56,56,56,56,56,56,56	557,2379,3027	CC,CT,TT		33.7646,19.4697,29.2889	benign,benign,benign,benign,benign,benign,benign	100/455,82/460,82/460,60/438,42/420,60/375,100/478	13978809	3493,8433	1867	4096	5963	SO:0001583	missense	2115	exon7			CAGAGCTGATTTC		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"""ets variant gene 1"""			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.298A>G	7.37:g.13978809T>C	ENSP00000405327:p.Ser100Gly	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_004956	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	CCDS55088.1	696	0.31868131868131866	100	0.2032520325203252	140	0.3867403314917127	212	0.3706293706293706	244	0.32189973614775724	C	10.04	1.242238	0.22796	0.194697	0.337646	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000399357;ENST00000405192;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956;ENST00000443608;ENST00000421381	T;T;T;T;T;T;T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96	5.45	4.57	0.56435	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.255451	0.47093	N	0.000255	T	0.00012	0.0000	N	0.17474	0.49	0.48341	P	3.649999999999487E-4	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.48080	-0.9066	9	0.13108	T	0.6	.	8.696	0.34296	0.0:0.713:0.0:0.287	rs9639168;rs52830566;rs58087404;rs9639168	82;114;42;60;60;100	P50549-2;B5MCT2;F5GXR2;B7Z9P2;E9PHB1;P50549	.;.;.;.;.;ETV1_HUMAN	G	100;82;82;42;60;100;114;60;100;82;42;60;100	ENSP00000405327:S100G;ENSP00000242066:S82G;ENSP00000340853:S82G;ENSP00000411626:S42G;ENSP00000382293:S60G;ENSP00000385381:S100G;ENSP00000384085:S114G;ENSP00000384138:S60G;ENSP00000385551:S100G;ENSP00000385686:S82G;ENSP00000393078:S42G;ENSP00000394710:S60G;ENSP00000391043:S100G	ENSP00000242066:S82G	S	-	1	0	ETV1	13945334	0.980000	0.34600	0.998000	0.56505	0.987000	0.75469	0.877000	0.28106	0.791000	0.33826	-0.119000	0.15052	AGC	C|0.302;N|0.000	0.302	strong		0.403	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956	
DLEC1	9940	hgsc.bcm.edu	37	3	38151731	38151731	+	Silent	SNP	T	T	C	rs12630114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38151731T>C	ENST00000308059.6	+	23	3423	c.3402T>C	c.(3400-3402)taT>taC	p.Y1134Y	DLEC1_ENST00000346219.3_Silent_p.Y1134Y|DLEC1_ENST00000452631.2_Silent_p.Y1137Y					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		AGTTTGAGTATTTCGGGAGCC	0.542													C|||	2292	0.457668	0.5673	0.451	5008	,	,		18060	0.6131		0.3628	False		,,,				2504	0.2515				p.Y1134Y		Atlas-SNP	.											.	DLEC1	278	.	0			c.T3402C						PASS	.	C	,	2082,1840		556,970,435	99.0	108.0	105.0		3402,3402	4.2	0.7	3	dbSNP_120	105	3052,5276		592,1868,1704	no	coding-synonymous,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	1148,2838,2139	CC,CT,TT		36.6475,46.9148,41.9102	,	1134/1756,1134/1779	38151731	5134,7116	1961	4164	6125	SO:0001819	synonymous_variant	9940	exon23			TGAGTATTTCGGG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.3402T>C	3.37:g.38151731T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	56	18	0.321429	NM_007337		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			C|0.467;N|0.000	0.467	strong		0.542	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
OR4C11	219429	hgsc.bcm.edu	37	11	55371381	55371381	+	Nonsense_Mutation	SNP	G	G	A	rs75423534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55371381G>A	ENST00000302231.4	-	1	493	c.469C>T	c.(469-471)Cag>Tag	p.Q157*		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q157K(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						AGGATAATCTGAGCTGTAGAG	0.458													g|||	346	0.0690895	0.003	0.1225	5008	,	,		14125	0.005		0.1322	False		,,,				2504	0.1217				p.Q157X		Atlas-SNP	.											OR4C11,rectum,carcinoma,0,1	OR4C11	73	1	1	Substitution - Missense(1)	large_intestine(1)	c.C469T						PASS	.	G	stop/GLN	126,4232		19,88,2072	69.0	60.0	63.0		469	4.3	0.2	11	dbSNP_131	63	1094,6920		260,574,3173	yes	stop-gained	OR4C11	NM_001004700.2		279,662,5245	AA,AG,GG		13.6511,2.8912,9.861		157/311	55371381	1220,11152	2179	4007	6186	SO:0001587	stop_gained	219429	exon1			TAATCTGAGCTGT	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"""GPCR / Class A : Olfactory receptors"""	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.469C>T	11.37:g.55371381G>A	ENSP00000306651:p.Gln157*	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	164	104	0.634146	NM_001004700	B9EIL4|Q8NGL8	Nonsense_Mutation	SNP	ENST00000302231.4	37	CCDS31503.1	161	0.07371794871794872	1	0.0020325203252032522	41	0.1132596685082873	4	0.006993006993006993	115	0.1517150395778364	G	9.320	1.057753	0.19907	0.028912	0.136511	ENSG00000172188	ENST00000302231	.	.	.	4.34	4.34	0.51931	.	0.000000	0.46442	U	0.000300	.	.	.	.	.	.	0.09310	P	0.9999999999999756	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	15.9533	0.79861	0.0:0.0:1.0:0.0	.	.	.	.	X	157	.	ENSP00000306651:Q157X	Q	-	1	0	OR4C11	55127957	0.001000	0.12720	0.213000	0.23690	0.004000	0.04260	0.160000	0.16462	2.425000	0.82216	0.478000	0.44815	CAG	G|0.926;A|0.074	0.074	strong		0.458	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700	
PLCB3	5331	hgsc.bcm.edu	37	11	64034866	64034866	+	Silent	SNP	G	G	A	rs7938380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64034866G>A	ENST00000540288.1	+	31	3646	c.3543G>A	c.(3541-3543)gcG>gcA	p.A1181A	PLCB3_ENST00000279230.6_Silent_p.A1181A|PLCB3_ENST00000325234.5_Silent_p.A1114A	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	1181					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						AGCAGCGGGCGAGGCTCCCCC	0.721													G|||	449	0.0896565	0.0234	0.1239	5008	,	,		11929	0.1052		0.165	False		,,,				2504	0.0613				p.A1181A		Atlas-SNP	.											.	PLCB3	103	.	0			c.G3543A						PASS	.	G	,	196,4070		8,180,1945	7.0	8.0	8.0		3543,3342	-9.0	0.4	11	dbSNP_116	8	1218,7094		97,1024,3035	no	coding-synonymous,coding-synonymous	PLCB3	NM_000932.2,NM_001184883.1	,	105,1204,4980	AA,AG,GG		14.6535,4.5945,11.2419	,	1181/1235,1114/1168	64034866	1414,11164	2133	4156	6289	SO:0001819	synonymous_variant	5331	exon31			GCGGGCGAGGCTC	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.3543G>A	11.37:g.64034866G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																			G|0.888;A|0.112	0.112	strong		0.721	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
N4BP2	55728	hgsc.bcm.edu	37	4	40103767	40103767	+	Missense_Mutation	SNP	G	G	T	rs17511668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:40103767G>T	ENST00000261435.6	+	4	718	c.302G>T	c.(301-303)aGt>aTt	p.S101I		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	101			S -> I (in dbSNP:rs17511668).		nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TCTTCACAAAGTTTCGTTGCT	0.338													G|||	570	0.113818	0.0106	0.255	5008	,	,		16258	0.0208		0.2217	False		,,,				2504	0.138				p.S101I		Atlas-SNP	.											.	N4BP2	166	.	0			c.G302T						PASS	.	G	ILE/SER	214,4192	128.2+/-165.1	10,194,1999	79.0	78.0	78.0		302	1.3	0.0	4	dbSNP_123	78	1978,6622	343.7+/-325.0	234,1510,2556	yes	missense	N4BP2	NM_018177.4	142	244,1704,4555	TT,TG,GG		23.0,4.857,16.8538	benign	101/1771	40103767	2192,10814	2203	4300	6503	SO:0001583	missense	55728	exon4			CACAAAGTTTCGT	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.302G>T	4.37:g.40103767G>T	ENSP00000261435:p.Ser101Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	286	0.13095238095238096	6	0.012195121951219513	97	0.26795580110497236	10	0.017482517482517484	173	0.22823218997361477	G	7.215	0.596153	0.13875	0.04857	0.23	ENSG00000078177	ENST00000261435;ENST00000381804;ENST00000515550	T;T	0.33438	2.16;1.41	6.08	1.32	0.21799	.	1.086440	0.06897	N	0.805379	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P;B	0.34724	0.465;0.335	B;B	0.33521	0.165;0.08	T	0.33085	-0.9882	9	0.72032	D	0.01	-0.0785	1.7256	0.02921	0.2058:0.3217:0.3069:0.1656	rs17511668;rs17511668	101;101	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	I	101;21;21	ENSP00000261435:S101I;ENSP00000422057:S21I	ENSP00000261435:S101I	S	+	2	0	N4BP2	39780162	0.000000	0.05858	0.001000	0.08648	0.313000	0.28021	-0.144000	0.10280	-0.065000	0.13021	0.591000	0.81541	AGT	G|0.859;T|0.141	0.141	strong		0.338	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
WWTR1	25937	hgsc.bcm.edu	37	3	149290781	149290781	+	Silent	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:149290781T>G	ENST00000465804.1	-	4	694	c.438A>C	c.(436-438)atA>atC	p.I146I	WWTR1_ENST00000360632.3_Silent_p.I146I|WWTR1_ENST00000467467.1_Silent_p.I146I	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	146	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TGATTTTTTCTATGTGACTAA	0.388			T	CAMTA1	epitheliod hemangioendothelioma																																p.I146I		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	.	WWTR1	42	.	0			c.A438C						PASS	.						125.0	118.0	120.0					3																	149290781		2203	4300	6503	SO:0001819	synonymous_variant	25937	exon4			TTTTTCTATGTGA	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.438A>C	3.37:g.149290781T>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	95	15	0.157895	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Silent	SNP	ENST00000465804.1	37	CCDS3144.1																																																																																			.	.	none		0.388	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472	
RBM19	9904	hgsc.bcm.edu	37	12	114261053	114261053	+	Silent	SNP	G	G	A	rs11066773	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:114261053G>A	ENST00000545145.2	-	24	2937	c.2859C>T	c.(2857-2859)agC>agT	p.S953S	RBM19_ENST00000392561.3_Silent_p.S953S|RBM19_ENST00000261741.5_Silent_p.S953S	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	953					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TCTGCTCCTCGCTGTCGCTGT	0.642													G|||	656	0.13099	0.0484	0.1182	5008	,	,		15453	0.1528		0.1024	False		,,,				2504	0.2587				p.S953S		Atlas-SNP	.											.	RBM19	117	.	0			c.C2859T						PASS	.	G	,,	286,4120	157.4+/-190.3	11,264,1928	49.0	43.0	45.0		2859,2859,2859	-4.5	0.0	12	dbSNP_120	45	1129,7471	230.5+/-264.8	90,949,3261	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	101,1213,5189	AA,AG,GG		13.1279,6.4911,10.8796	,,	953/961,953/961,953/961	114261053	1415,11591	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon24			CTCCTCGCTGTCG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.2859C>T	12.37:g.114261053G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.894;A|0.106	0.106	strong		0.642	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
ONECUT1	3175	hgsc.bcm.edu	37	15	53081859	53081859	+	Missense_Mutation	SNP	G	G	C	rs74805019	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:53081859G>C	ENST00000305901.5	-	1	350	c.223C>G	c.(223-225)Cct>Gct	p.P75A	ONECUT1_ENST00000561401.2_Intron	NM_004498.2	NP_004489.1	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	75			P -> A (in dbSNP:rs74805019). {ECO:0000269|PubMed:10491763}.		B cell differentiation (GO:0030183)|cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|endoderm development (GO:0007492)|epithelial cell development (GO:0002064)|glucose metabolic process (GO:0006006)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription, DNA-templated (GO:0006355)|spleen development (GO:0048536)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	17				all cancers(107;0.0708)		CTGTGCTCAGGGGCCCGGTGG	0.716													G|||	50	0.00998403	0.0015	0.0101	5008	,	,		12439	0.0		0.0378	False		,,,				2504	0.0031				p.P75A		Atlas-SNP	.											.	ONECUT1	48	.	0			c.C223G						PASS	.	G	ALA/PRO	35,4353		0,35,2159	24.0	24.0	24.0		223	3.2	1.0	15	dbSNP_133	24	277,8301		2,273,4014	yes	missense	ONECUT1	NM_004498.1	27	2,308,6173	CC,CG,GG		3.2292,0.7976,2.4063	benign	75/466	53081859	312,12654	2194	4289	6483	SO:0001583	missense	3175	exon1			GCTCAGGGGCCCG	U77975	CCDS10150.1	15q21.3	2012-03-09	2007-07-16		ENSG00000169856	ENSG00000169856		"""Homeoboxes / CUT class"""	8138	protein-coding gene	gene with protein product		604164	"""one cut domain, family member 1"""	HNF6, HNF6A		8887657, 8790352	Standard	NM_004498		Approved	HNF-6	uc002aci.2	Q9UBC0	OTTHUMG00000131899	ENST00000305901.5:c.223C>G	15.37:g.53081859G>C	ENSP00000302630:p.Pro75Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	23	0.338235	NM_004498	B2RTV4|Q99744|Q9UMR6	Missense_Mutation	SNP	ENST00000305901.5	37	CCDS10150.1	35	0.016025641025641024	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	31	0.040897097625329816	G	11.42	1.634918	0.29068	0.007976	0.032292	ENSG00000169856	ENST00000305901	T	0.43294	0.95	4.17	3.22	0.36961	.	0.294433	0.33382	N	0.004964	T	0.17238	0.0414	L	0.40543	1.245	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.14699	-1.0463	10	0.07813	T	0.8	-6.8106	12.3608	0.55203	0.0:0.1719:0.8281:0.0	.	75	Q9UBC0	HNF6_HUMAN	A	75	ENSP00000302630:P75A	ENSP00000302630:P75A	P	-	1	0	ONECUT1	50869151	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	3.362000	0.52314	0.905000	0.36596	0.436000	0.28706	CCT	G|0.981;C|0.019	0.019	strong		0.716	ONECUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254849.2		
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150167	39150167	+	Silent	SNP	G	G	A	rs12452295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39150167G>A	ENST00000391586.1	-	1	218	c.183C>T	c.(181-183)tgC>tgT	p.C61C		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	61						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.C61C(1)		lung(2)|prostate(2)	4		Breast(137;0.00043)				AGGTGGGCACGCAGGGCTGAG	0.632													G|||	1210	0.241613	0.0567	0.3141	5008	,	,		18403	0.3234		0.2823	False		,,,				2504	0.3139				p.C61C		Atlas-SNP	.											KRTAP3-3,NS,carcinoma,0,1	KRTAP3-3	11	1	1	Substitution - coding silent(1)	prostate(1)	c.C183T						PASS	.	G		407,3999	201.8+/-224.7	22,363,1818	106.0	77.0	87.0		183	3.5	1.0	17	dbSNP_120	87	2540,6048	415.2+/-351.7	370,1800,2124	no	coding-synonymous	KRTAP3-3	NM_033185.2		392,2163,3942	AA,AG,GG		29.5762,9.2374,22.6797		61/99	39150167	2947,10047	2203	4294	6497	SO:0001819	synonymous_variant	85293	exon1			GGGCACGCAGGGC	AJ406933	CCDS32643.1	17q21.2	2013-06-25			ENSG00000212899	ENSG00000212899		"""Keratin associated proteins"""	18890	protein-coding gene	gene with protein product						11279113	Standard	NM_033185		Approved	KAP3.3	uc002hvr.1	Q9BYR6	OTTHUMG00000133591	ENST00000391586.1:c.183C>T	17.37:g.39150167G>A		Somatic	494	0	0		WXS	Illumina HiSeq	Phase_I	372	370	0.994624	NM_033185	Q52LP0|Q6NTD4	Silent	SNP	ENST00000391586.1	37	CCDS32643.1																																																																																			G|0.777;A|0.223	0.223	strong		0.632	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75981976	75981976	+	Missense_Mutation	SNP	C	C	T	rs200493777		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75981976C>T	ENST00000308508.5	-	3	1522	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	477	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.			RH -> HY (in Ref. 1; CAA65529). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.R477H(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTCGCCATGGCGTGCCCCTCG	0.637																																					p.R477H		Atlas-SNP	.											CSPG4,NS,carcinoma,0,2	CSPG4	175	2	1	Substitution - Missense(1)	kidney(1)	c.G1430A						scavenged	.						67.0	61.0	63.0					15																	75981976		2197	4291	6488	SO:0001583	missense	1464	exon3			CCATGGCGTGCCC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1430G>A	15.37:g.75981976C>T	ENSP00000312506:p.Arg477His	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	185	11	0.0594595	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	9.517	1.107225	0.20714	.	.	ENSG00000173546	ENST00000308508	T	0.19532	2.14	5.12	4.19	0.49359	.	0.096704	0.44483	D	0.000447	T	0.17746	0.0426	L	0.57536	1.79	0.27465	N	0.953023	P	0.35628	0.513	B	0.27380	0.079	T	0.14783	-1.0460	10	0.41790	T	0.15	.	9.3594	0.38186	0.0:0.8315:0.0:0.1685	.	477	Q6UVK1	CSPG4_HUMAN	H	477	ENSP00000312506:R477H	ENSP00000312506:R477H	R	-	2	0	CSPG4	73769031	0.038000	0.19896	0.145000	0.22337	0.035000	0.12851	1.407000	0.34657	2.375000	0.81037	0.555000	0.69702	CGC	C|0.999;T|0.001	0.001	weak		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
HS3ST1	9957	hgsc.bcm.edu	37	4	11401087	11401087	+	Silent	SNP	A	A	G	rs1047389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:11401087A>G	ENST00000002596.5	-	2	1717	c.543T>C	c.(541-543)gaT>gaC	p.D181D		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	181					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						TGAGCCTGCCATCGCGCACCA	0.582													G|||	1262	0.251997	0.3192	0.1945	5008	,	,		19159	0.1885		0.1978	False		,,,				2504	0.3231				p.D181D		Atlas-SNP	.											.	HS3ST1	41	.	0			c.T543C						PASS	.	G		1287,3119	700.4+/-406.6	196,895,1112	83.0	76.0	78.0		543	0.1	0.8	4	dbSNP_86	78	1820,6780	731.5+/-406.8	189,1442,2669	no	coding-synonymous	HS3ST1	NM_005114.2		385,2337,3781	GG,GA,AA		21.1628,29.2102,23.889		181/308	11401087	3107,9899	2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			CCTGCCATCGCGC	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.543T>C	4.37:g.11401087A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	37	CCDS3408.1																																																																																			G|0.241;N|0.000	0.241	strong		0.582	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114	
TATDN1	83940	hgsc.bcm.edu	37	8	125528135	125528135	+	Silent	SNP	G	G	A	rs11542673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:125528135G>A	ENST00000276692.6	-	5	376	c.339C>T	c.(337-339)tgC>tgT	p.C113C	TATDN1_ENST00000605953.1_Silent_p.C113C|TATDN1_ENST00000519548.1_Silent_p.C66C|TATDN1_ENST00000521546.1_5'UTR|TATDN1_ENST00000517678.1_Silent_p.C59C	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1	113					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CACCAAGTCCGCATTCTCCTA	0.353													A|||	774	0.154553	0.1248	0.0504	5008	,	,		16843	0.1915		0.0338	False		,,,				2504	0.3548				p.C113C		Atlas-SNP	.											.	TATDN1	29	.	0			c.C339T						PASS	.	A	,	482,3924	781.9+/-414.5	26,430,1747	116.0	110.0	112.0		198,339	5.6	1.0	8	dbSNP_120	112	437,8163	799.7+/-407.4	12,413,3875	no	coding-synonymous,coding-synonymous	TATDN1	NM_001146160.1,NM_032026.3	,	38,843,5622	AA,AG,GG		5.0814,10.9396,7.066	,	66/251,113/298	125528135	919,12087	2203	4300	6503	SO:0001819	synonymous_variant	83940	exon5			AAGTCCGCATTCT	AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068	ENST00000276692.6:c.339C>T	8.37:g.125528135G>A		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	258	128	0.496124	NM_032026	B2R5J0|Q8TD02|Q9BY40	Silent	SNP	ENST00000276692.6	37	CCDS6351.1	207	0.09478021978021978	58	0.11788617886178862	17	0.04696132596685083	106	0.1853146853146853	26	0.03430079155672823	A	2.848	-0.238970	0.05944	0.109396	0.050814	ENSG00000147687	ENST00000519232	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14615	-1.0466	3	.	.	.	-8.7102	8.8495	0.35190	0.8556:0.0:0.1444:0.0	rs11542673	.	.	.	W	143	.	.	R	-	1	2	TATDN1	125597316	1.000000	0.71417	1.000000	0.80357	0.348000	0.29142	4.268000	0.58883	0.950000	0.37743	-0.360000	0.07572	CGG	G|0.918;A|0.082	0.082	strong		0.353	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026	
FAM160A2	84067	hgsc.bcm.edu	37	11	6239139	6239139	+	Silent	SNP	A	A	G	rs11040809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6239139A>G	ENST00000449352.2	-	9	1940	c.1677T>C	c.(1675-1677)cgT>cgC	p.R559R	FAM160A2_ENST00000265978.4_Silent_p.R573R|FAM160A2_ENST00000524416.1_Silent_p.R559R|FAM160A2_ENST00000529360.1_5'Flank			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	559					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCACACCACGACGTGCCTCAC	0.642													A|||	547	0.109225	0.0106	0.1167	5008	,	,		11293	0.0456		0.2336	False		,,,				2504	0.1748				p.R573R		Atlas-SNP	.											.	FAM160A2	100	.	0			c.T1719C						PASS	.	A	,	207,4195	127.0+/-164.0	7,193,2001	65.0	61.0	62.0		1677,1719	1.6	1.0	11	dbSNP_120	62	2176,6416	366.5+/-334.3	280,1616,2400	no	coding-synonymous,coding-synonymous	FAM160A2	NM_001098794.1,NM_032127.3	,	287,1809,4401	GG,GA,AA		25.3259,4.7024,18.3392	,	559/973,573/987	6239139	2383,10611	2201	4296	6497	SO:0001819	synonymous_variant	84067	exon9			ACCACGACGTGCC		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 56"""	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.1677T>C	11.37:g.6239139A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Silent	SNP	ENST00000449352.2	37	CCDS44530.1																																																																																			A|0.841;G|0.159;N|0.000;T|0.000	0.159	strong		0.642	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
EGFL8	80864	hgsc.bcm.edu	37	6	32134510	32134510	+	Missense_Mutation	SNP	G	G	A	rs3096697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32134510G>A	ENST00000395512.1	+	4	362	c.257G>A	c.(256-258)aGg>aAg	p.R86K	EGFL8_ENST00000333845.6_Missense_Mutation_p.R86K|AGPAT1_ENST00000490711.1_5'Flank|PPT2-EGFL8_ENST00000422437.1_3'UTR			Q99944	EGFL8_HUMAN	EGF-like-domain, multiple 8	86	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.		R -> K (in dbSNP:rs3096697). {ECO:0000269|PubMed:14574404}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	10						CGGGAGGTGAGGCGGGAGGTT	0.652													G|||	777	0.155152	0.2095	0.1023	5008	,	,		15949	0.0367		0.2008	False		,,,				2504	0.1943				p.R86K		Atlas-SNP	.											.	EGFL8	15	.	0			c.G257A						PASS	.	G	LYS/ARG	825,3581	316.1+/-294.4	77,671,1455	45.0	54.0	51.0		257	3.4	1.0	6	dbSNP_103	51	1861,6739	322.8+/-315.7	197,1467,2636	yes	missense	EGFL8	NM_030652.3	26	274,2138,4091	AA,AG,GG		21.6395,18.7245,20.652	benign	86/294	32134510	2686,10320	2203	4300	6503	SO:0001583	missense	80864	exon4			AGGTGAGGCGGGA	U89336	CCDS4743.1	6p21	2010-06-25	2003-05-21	2003-05-23	ENSG00000241404	ENSG00000241404			13944	protein-coding gene	gene with protein product		609897	"""chromosome 6 open reading frame 8"""	C6orf8			Standard	NM_030652		Approved	NG3		Q99944	OTTHUMG00000031222	ENST00000395512.1:c.257G>A	6.37:g.32134510G>A	ENSP00000378888:p.Arg86Lys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	120	48	0.4	NM_030652	B0S884|G5E9Q0|Q5JP23|Q5SSX3|Q8IV30	Missense_Mutation	SNP	ENST00000395512.1	37	CCDS4743.1	311	0.1423992673992674	105	0.21341463414634146	33	0.09116022099447514	23	0.04020979020979021	150	0.19788918205804748	G	9.290	1.050493	0.19827	0.187245	0.216395	ENSG00000241404	ENST00000333845;ENST00000395512;ENST00000432129	T;T;T	0.40225	1.04;1.04;1.04	6.08	3.38	0.38709	EMI domain (2);	.	.	.	.	T	0.08268	0.0206	N	0.11560	0.145	0.43421	P	0.004430000000000045	B	0.09022	0.002	B	0.08055	0.003	T	0.26780	-1.0093	8	0.19590	T	0.45	-9.8585	8.4318	0.32761	0.2396:0.0:0.7604:0.0	rs3096697;rs17421868;rs58410180;rs3096697	86	Q99944	EGFL8_HUMAN	K	86	ENSP00000333380:R86K;ENSP00000378888:R86K;ENSP00000401694:R86K	ENSP00000333380:R86K	R	+	2	0	EGFL8	32242488	0.002000	0.14202	0.990000	0.47175	0.990000	0.78478	0.683000	0.25349	0.474000	0.27392	-0.136000	0.14681	AGG	G|0.830;A|0.170	0.170	strong		0.652	EGFL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076463.3	NM_030652	
FNDC1	84624	hgsc.bcm.edu	37	6	159672455	159672455	+	Silent	SNP	C	C	T	rs294899	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:159672455C>T	ENST00000297267.9	+	17	5156	c.4956C>T	c.(4954-4956)gaC>gaT	p.D1652D	FNDC1_ENST00000340366.6_Silent_p.D1589D	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1652					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AGAAGAGTGACCTGCCTCCCC	0.552													C|||	2256	0.450479	0.1914	0.6297	5008	,	,		21692	0.3036		0.7087	False		,,,				2504	0.5593				p.D1652D		Atlas-SNP	.											.	FNDC1	250	.	0			c.C4956T						PASS	.	C		1217,2957		186,845,1056	77.0	75.0	75.0		4956	-0.8	0.1	6	dbSNP_79	75	5864,2564		2030,1804,380	no	coding-synonymous	FNDC1	NM_032532.2		2216,2649,1436	TT,TC,CC		30.4224,29.1567,43.8105		1652/1895	159672455	7081,5521	2087	4214	6301	SO:0001819	synonymous_variant	84624	exon17			GAGTGACCTGCCT	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.4956C>T	6.37:g.159672455C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	1053	0.48214285714285715	96	0.1951219512195122	241	0.6657458563535912	169	0.29545454545454547	547	0.7216358839050132	C	6.772	0.511325	0.12944	0.291567	0.695776	ENSG00000164694	ENST00000329629	.	.	.	5.51	-0.76	0.11041	.	.	.	.	.	T	0.18964	0.0455	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.15780	-1.0425	3	.	.	.	-9.2865	6.4635	0.21970	0.0:0.3086:0.3078:0.3836	rs294899;rs3814446;rs17290583;rs294899	.	.	.	S	1548	.	.	P	+	1	0	FNDC1	159592445	0.002000	0.14202	0.053000	0.19242	0.940000	0.58332	-0.658000	0.05329	-0.055000	0.13244	0.585000	0.79938	CCT	C|0.523;T|0.477	0.477	strong		0.552	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
JMJD1C	221037	hgsc.bcm.edu	37	10	64927837	64927837	+	Missense_Mutation	SNP	C	C	T	rs71508957	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:64927837C>T	ENST00000399262.2	-	26	7809	c.7591G>A	c.(7591-7593)Gag>Aag	p.E2531K	JMJD1C_ENST00000402544.1_Missense_Mutation_p.E2294K|JMJD1C_ENST00000542921.1_Missense_Mutation_p.E2349K|JMJD1C_ENST00000399251.1_3'UTR	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2531					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					ACTTCATCCTCGTGTATCTTC	0.333													C|||	10	0.00199681	0.0008	0.0	5008	,	,		18116	0.0		0.004	False		,,,				2504	0.0051				p.E2531K		Atlas-SNP	.											.	JMJD1C	347	.	0			c.G7591A						PASS	.	C	LYS/GLU,LYS/GLU	6,3716		0,6,1855	181.0	163.0	169.0		6880,7591	5.4	1.0	10	dbSNP_130	169	82,8102		1,80,4011	yes	missense,missense	JMJD1C	NM_004241.2,NM_032776.1	56,56	1,86,5866	TT,TC,CC		1.002,0.1612,0.7391	probably-damaging,probably-damaging	2294/2304,2531/2541	64927837	88,11818	1861	4092	5953	SO:0001583	missense	221037	exon26			CATCCTCGTGTAT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.7591G>A	10.37:g.64927837C>T	ENSP00000382204:p.Glu2531Lys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.89	3.499039	0.64298	0.001612	0.01002	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.67698	-0.28;-0.28;-0.28	5.42	5.42	0.78866	.	0.128349	0.53938	D	0.000055	T	0.62502	0.2433	L	0.34521	1.04	0.80722	D	1	D;B	0.69078	0.997;0.403	P;B	0.53450	0.726;0.17	T	0.70306	-0.4908	10	0.62326	D	0.03	-21.4168	19.2123	0.93760	0.0:1.0:0.0:0.0	.	2531;2349	Q15652;A0T124	JHD2C_HUMAN;.	K	2531;2294;2349	ENSP00000382204:E2531K;ENSP00000384990:E2294K;ENSP00000444682:E2349K	ENSP00000382204:E2531K	E	-	1	0	JMJD1C	64597843	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.593000	0.46180	2.528000	0.85240	0.591000	0.81541	GAG	C|0.998;T|0.002	0.002	strong		0.333	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
C12orf71	728858	hgsc.bcm.edu	37	12	27235279	27235279	+	Silent	SNP	G	G	A	rs12228215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:27235279G>A	ENST00000429849.2	-	1	168	c.138C>T	c.(136-138)tcC>tcT	p.S46S		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	46										endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						AAGGACCCTTGGAAGGTGCAT	0.542													G|||	126	0.0251597	0.0045	0.0216	5008	,	,		18205	0.0288		0.0676	False		,,,				2504	0.0082				p.S46S		Atlas-SNP	.											.	C12orf71	20	.	0			c.C138T						PASS	.	G		76,3790		0,76,1857	56.0	55.0	55.0		138	-3.6	0.0	12	dbSNP_120	55	763,7493		39,685,3404	no	coding-synonymous	C12orf71	NM_001080406.1		39,761,5261	AA,AG,GG		9.2418,1.9659,6.9213		46/270	27235279	839,11283	1933	4128	6061	SO:0001819	synonymous_variant	728858	exon1			ACCCTTGGAAGGT		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.138C>T	12.37:g.27235279G>A		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	305	303	0.993443	NM_001080406		Silent	SNP	ENST00000429849.2	37	CCDS44851.1																																																																																			G|0.955;A|0.045	0.045	strong		0.542	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
HTR4	3360	hgsc.bcm.edu	37	5	147929740	147929740	+	Silent	SNP	G	G	A	rs17706743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147929740G>A	ENST00000377888.3	-	3	250	c.112C>T	c.(112-114)Ctg>Ttg	p.L38L	HTR4_ENST00000517929.1_Silent_p.L38L|HTR4_ENST00000354217.2_Silent_p.L38L|HTR4_ENST00000521735.1_Silent_p.L38L|HTR4_ENST00000362016.2_Silent_p.L38L|HTR4_ENST00000360693.3_Silent_p.L38L|HTR4_ENST00000314512.6_Silent_p.L38L|HTR4_ENST00000521530.1_Silent_p.L38L|HTR4_ENST00000519495.1_5'UTR|HTR4_ENST00000520514.1_Silent_p.L38L	NM_000870.5	NP_000861.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	38					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|regulation of appetite (GO:0032098)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cinitapride(DB08810)|Cisapride(DB00604)|Ergoloid mesylate(DB01049)|Metoclopramide(DB01233)|Ondansetron(DB00904)	ATCACCAGCAGGTTCCCCAAG	0.557													G|||	137	0.0273562	0.0038	0.036	5008	,	,		17288	0.001		0.0388	False		,,,				2504	0.0685				p.L38L	GBM(120;370 1604 14007 17804 41573)	Atlas-SNP	.											.	HTR4	161	.	0			c.C112T						PASS	.	G	,,,,	36,4370	41.6+/-74.8	0,36,2167	128.0	91.0	103.0		112,112,112,112,112	4.5	1.0	5	dbSNP_123	103	371,8229	122.4+/-181.4	6,359,3935	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HTR4	NM_000870.5,NM_001040169.2,NM_001040172.2,NM_001040173.2,NM_199453.3	,,,,	6,395,6102	AA,AG,GG		4.314,0.8171,3.1293	,,,,	38/389,38/388,38/361,38/429,38/379	147929740	407,12599	2203	4300	6503	SO:0001819	synonymous_variant	3360	exon2			CCAGCAGGTTCCC	Y08756	CCDS4291.1, CCDS34270.1, CCDS34271.1, CCDS34272.1, CCDS34273.1, CCDS34273.2, CCDS75353.1	5q31-q33	2012-08-08	2012-02-03		ENSG00000164270	ENSG00000164270		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5299	protein-coding gene	gene with protein product		602164	"""5-hydroxytryptamine (serotonin) receptor 4"""			9371406, 9276448	Standard	NM_199453		Approved	5-HT4	uc021yfj.1	Q13639	OTTHUMG00000129931	ENST00000377888.3:c.112C>T	5.37:g.147929740G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_001040169	C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Silent	SNP	ENST00000377888.3	37	CCDS4291.1																																																																																			G|0.970;A|0.030	0.030	strong		0.557	HTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252187.2	NM_000870	
ABCA8	10351	hgsc.bcm.edu	37	17	66873743	66873743	+	Silent	SNP	G	G	A	rs8068987	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:66873743G>A	ENST00000269080.2	-	31	4133	c.3996C>T	c.(3994-3996)ccC>ccT	p.P1332P	ABCA8_ENST00000586539.1_Silent_p.P1372P|ABCA8_ENST00000430352.2_Silent_p.P1372P	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1332	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CTGTCAGGTTGGGCCACAGCG	0.607													G|||	774	0.154553	0.2292	0.111	5008	,	,		16794	0.0952		0.1243	False		,,,				2504	0.1769				p.P1332P		Atlas-SNP	.											.	ABCA8	213	.	0			c.C3996T						PASS	.	G		939,3467	360.1+/-315.1	90,759,1354	145.0	125.0	132.0		3996	2.2	1.0	17	dbSNP_116	132	966,7634	210.3+/-251.2	55,856,3389	no	coding-synonymous	ABCA8	NM_007168.2		145,1615,4743	AA,AG,GG		11.2326,21.3118,14.6471		1332/1582	66873743	1905,11101	2203	4300	6503	SO:0001819	synonymous_variant	10351	exon31			CAGGTTGGGCCAC	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3996C>T	17.37:g.66873743G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	195	91	0.466667	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																			G|0.860;A|0.140	0.140	strong		0.607	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
CCDC102B	79839	hgsc.bcm.edu	37	18	66504351	66504351	+	Silent	SNP	G	G	A	rs637051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:66504351G>A	ENST00000360242.5	+	2	468	c.351G>A	c.(349-351)agG>agA	p.R117R	CCDC102B_ENST00000584156.1_Silent_p.R117R|CCDC102B_ENST00000319445.6_Silent_p.R117R|CCDC102B_ENST00000358653.5_Silent_p.R117R|CCDC102B_ENST00000577772.1_3'UTR	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	117										breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				ACAGTGCCAGGGAGGAAGGAA	0.468													G|||	1033	0.20627	0.1929	0.2839	5008	,	,		19812	0.006		0.4165	False		,,,				2504	0.1595				p.R117R		Atlas-SNP	.											CCDC102B,NS,carcinoma,+1,1	CCDC102B	92	1	0			c.G351A						PASS	.	G	,	841,3021		88,665,1178	90.0	88.0	89.0		351,351	1.3	1.0	18	dbSNP_83	89	3363,4903		679,2005,1449	no	coding-synonymous,coding-synonymous	CCDC102B	NM_001093729.1,NM_024781.2	,	767,2670,2627	AA,AG,GG		40.6847,21.7763,34.6636	,	117/514,117/514	66504351	4204,7924	1931	4133	6064	SO:0001819	synonymous_variant	79839	exon4			TGCCAGGGAGGAA	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.351G>A	18.37:g.66504351G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Silent	SNP	ENST00000360242.5	37	CCDS11996.2																																																																																			G|0.744;A|0.256	0.256	strong		0.468	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
DMPK	1760	hgsc.bcm.edu	37	19	46275976	46275976	+	Missense_Mutation	SNP	G	G	C	rs527221	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46275976G>C	ENST00000291270.4	-	10	1392	c.1267C>G	c.(1267-1269)Ctg>Gtg	p.L423V	AC074212.6_ENST00000586251.1_RNA|AC074212.6_ENST00000591530.1_RNA|AC074212.6_ENST00000590076.1_RNA|DMPK_ENST00000354227.5_Missense_Mutation_p.L418V|DMPK_ENST00000447742.2_Missense_Mutation_p.L418V|AC074212.5_ENST00000592217.2_RNA|DMPK_ENST00000600757.1_Missense_Mutation_p.L428V|DMPK_ENST00000458663.2_Missense_Mutation_p.L418V|DMPK_ENST00000343373.4_Missense_Mutation_p.L433V|AC074212.6_ENST00000586498.1_RNA|DMPK_ENST00000595361.1_5'Flank	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	423			L -> V (in dbSNP:rs527221). {ECO:0000269|PubMed:1310900, ECO:0000269|PubMed:7905855, ECO:0000269|PubMed:8469976, ECO:0000269|PubMed:8499920}.		cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		TCGGCCTCCAGTTCCATGGGT	0.627													G|||	727	0.145168	0.053	0.1902	5008	,	,		18162	0.1796		0.1113	False		,,,				2504	0.2372				p.L433V	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											DMPK_ENST00000343373,NS,carcinoma,0,2	DMPK	74	2	0			c.C1297G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	296,4110	160.0+/-192.4	4,288,1911	42.0	43.0	43.0		1252,1252,1297,1267	3.9	1.0	19	dbSNP_83	43	971,7629	208.4+/-249.9	58,855,3387	yes	missense,missense,missense,missense	DMPK	NM_001081560.1,NM_001081562.1,NM_001081563.1,NM_004409.3	32,32,32,32	62,1143,5298	CC,CG,GG		11.2907,6.7181,9.7417	benign,benign,benign,benign	418/625,418/626,433/640,423/630	46275976	1267,11739	2203	4300	6503	SO:0001583	missense	1760	exon9			CCTCCAGTTCCAT	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"""dystrophia myotonica 1"", ""DM protein kinase"", ""myotonin protein kinase A"", ""myotonic dystrophy associated protein kinase"", ""thymopoietin homolog"""	605377	"""dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"""	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.1267C>G	19.37:g.46275976G>C	ENSP00000291270:p.Leu423Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_001081563	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	37	CCDS12674.1	268	0.1227106227106227	28	0.056910569105691054	56	0.15469613259668508	98	0.17132867132867133	86	0.11345646437994723	g	14.92	2.680756	0.47886	0.067181	0.112907	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.67865	-0.29;-0.23;-0.26;-0.24;-0.18	3.87	3.87	0.44632	AGC-kinase, C-terminal (1);	0.000000	0.33854	N	0.004494	T	0.00496	0.0016	L	0.55481	1.735	0.09310	P	1.0	B;D;D;D;D;D;D;D	0.76494	0.34;0.998;0.999;0.999;0.996;0.999;0.997;0.999	B;D;D;D;P;D;P;D	0.71414	0.108;0.913;0.973;0.918;0.82;0.94;0.906;0.945	T	0.29518	-1.0009	9	0.13108	T	0.6	.	11.5239	0.50569	0.0:0.0:1.0:0.0	rs527221;rs1042156;rs3170161;rs17423419;rs527221	418;423;449;418;418;423;465;433	Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;DMPK_HUMAN;.;.	V	418;449;423;418;418;433;433;418	ENSP00000401753:L418V;ENSP00000291270:L423V;ENSP00000413417:L418V;ENSP00000345997:L433V;ENSP00000346168:L418V	ENSP00000291270:L423V	L	-	1	2	DMPK	50967816	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.365000	0.59486	2.157000	0.67596	0.561000	0.74099	CTG	G|0.900;C|0.100	0.100	strong		0.627	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409	
OR2AG2	338755	hgsc.bcm.edu	37	11	6790106	6790106	+	Missense_Mutation	SNP	T	T	C	rs7102536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6790106T>C	ENST00000338569.2	-	1	180	c.83A>G	c.(82-84)tAt>tGt	p.Y28C		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	28			Y -> C (in dbSNP:rs7102536).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AAATGTAGCATAGAGCAGTTC	0.507													C|||	4393	0.877196	0.9002	0.8415	5008	,	,		19437	0.9286		0.8141	False		,,,				2504	0.8834				p.Y28C		Atlas-SNP	.											.	OR2AG2	55	.	0			c.A83G						PASS	.	C	CYS/TYR	3969,433	208.2+/-229.3	1786,397,18	105.0	101.0	102.0		83	3.4	0.8	11	dbSNP_116	102	7152,1440	276.3+/-292.2	2990,1172,134	yes	missense	OR2AG2	NM_001004490.1	194	4776,1569,152	CC,CT,TT		16.7598,9.8364,14.4143	benign	28/317	6790106	11121,1873	2201	4296	6497	SO:0001583	missense	338755	exon1			GTAGCATAGAGCA	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.83A>G	11.37:g.6790106T>C	ENSP00000342697:p.Tyr28Cys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	168	167	0.994048	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	1897	0.8685897435897436	442	0.8983739837398373	303	0.8370165745856354	532	0.9300699300699301	620	0.8179419525065963	C	1.145	-0.648419	0.03506	0.901636	0.832402	ENSG00000188124	ENST00000338569	T	0.03212	4.01	4.28	3.36	0.38483	.	0.115660	0.39834	N	0.001242	T	0.00012	0.0000	N	0.19112	0.55	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.17745	-1.0359	9	0.27082	T	0.32	.	5.4004	0.16293	0.3556:0.5503:0.0:0.0941	rs7102536;rs17179069;rs52820109;rs58664598;rs7102536	28	A6NM03	O2AG2_HUMAN	C	28	ENSP00000342697:Y28C	ENSP00000342697:Y28C	Y	-	2	0	OR2AG2	6746682	0.066000	0.20996	0.833000	0.33012	0.327000	0.28475	0.488000	0.22371	0.749000	0.32854	-0.119000	0.15052	TAT	T|0.137;C|0.863	0.863	strong		0.507	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
DNAJC6	9829	hgsc.bcm.edu	37	1	65855119	65855119	+	Silent	SNP	G	G	A	rs148673423		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:65855119G>A	ENST00000395325.3	+	10	1360	c.1203G>A	c.(1201-1203)acG>acA	p.T401T	DNAJC6_ENST00000263441.7_Silent_p.T388T|DNAJC6_ENST00000371069.4_Silent_p.T458T	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	401					cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)	p.T401T(1)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						ATCAAGATACGCTGGCCTTAG	0.413																																					p.T458T		Atlas-SNP	.											DNAJC6,NS,carcinoma,+1,2	DNAJC6	104	2	1	Substitution - coding silent(1)	lung(1)	c.G1374A						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	134.0	116.0	122.0		1203	-2.3	0.8	1	dbSNP_134	122	0,8600		0,0,4300	no	coding-synonymous	DNAJC6	NM_014787.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		401/914	65855119	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9829	exon10			AGATACGCTGGCC	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"""Heat shock proteins / DNAJ (HSP40)"""	15469	protein-coding gene	gene with protein product	"""auxilin"""	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.1203G>A	1.37:g.65855119G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	129	2	0.0155039	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Silent	SNP	ENST00000395325.3	37	CCDS30739.1																																																																																			G|1.000;A|0.000	0.000	weak		0.413	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1		
CEP250	11190	hgsc.bcm.edu	37	20	34092076	34092076	+	Missense_Mutation	SNP	G	G	A	rs56259282	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:34092076G>A	ENST00000397527.1	+	30	6599	c.5879G>A	c.(5878-5880)cGg>cAg	p.R1960Q	CEP250_ENST00000342580.4_Missense_Mutation_p.R1904Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1960	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GAGGCTGCCCGGGCCCGGGCT	0.657													G|||	24	0.00479233	0.0008	0.0115	5008	,	,		18767	0.0		0.0119	False		,,,				2504	0.0031				p.R1960Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G5879A						PASS	.	G	GLN/ARG	9,4369		0,9,2180	9.0	11.0	10.0		5879	-4.0	0.0	20	dbSNP_129	10	103,8479		2,99,4190	yes	missense	CEP250	NM_007186.3	43	2,108,6370	AA,AG,GG		1.2002,0.2056,0.8642	benign	1960/2443	34092076	112,12848	2189	4291	6480	SO:0001583	missense	11190	exon30			CTGCCCGGGCCCG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.5879G>A	20.37:g.34092076G>A	ENSP00000380661:p.Arg1960Gln	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	15	0.006868131868131868	0	0.0	8	0.022099447513812154	0	0.0	7	0.009234828496042216	G	2.257	-0.370208	0.05069	0.002056	0.012002	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.41065	3.05;3.04;1.01	4.95	-4.04	0.04010	.	1.940040	0.02640	N	0.105311	T	0.11836	0.0288	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.05550	-1.0878	10	0.12430	T	0.62	.	0.1713	0.00113	0.3233:0.1493:0.21:0.3175	rs56259282	1960	Q9BV73	CP250_HUMAN	Q	1960;1904;448	ENSP00000380661:R1960Q;ENSP00000341541:R1904Q;ENSP00000395992:R448Q	ENSP00000341541:R1904Q	R	+	2	0	CEP250	33555490	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.281000	0.08456	-0.484000	0.06763	-0.733000	0.03571	CGG	G|0.993;A|0.007	0.007	strong		0.657	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
CYP2A13	1553	hgsc.bcm.edu	37	19	41600311	41600311	+	Missense_Mutation	SNP	A	A	C	rs115698903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41600311A>C	ENST00000330436.3	+	7	1135	c.1135A>C	c.(1135-1137)Aag>Cag	p.K379Q		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	379					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	CAAGGACACCAAGTTTCGGGA	0.567													a|||	83	0.0165735	0.0061	0.0	5008	,	,		19775	0.0069		0.008	False		,,,				2504	0.0613				p.K379Q		Atlas-SNP	.											CYP2A13,NS,carcinoma,-1,1	CYP2A13	90	1	0			c.A1135C						PASS	.	A	GLN/LYS	19,4387		0,19,2184	116.0	106.0	110.0		1135	2.2	1.0	19	dbSNP_132	110	46,8554		0,46,4254	yes	missense	CYP2A13	NM_000766.3	53	0,65,6438	CC,CA,AA		0.5349,0.4312,0.4998	benign	379/495	41600311	65,12941	2203	4300	6503	SO:0001583	missense	1553	exon7			GACACCAAGTTTC	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"""Cytochrome P450s"""	2608	protein-coding gene	gene with protein product		608055	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"""			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.1135A>C	19.37:g.41600311A>C	ENSP00000332679:p.Lys379Gln	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	213	108	0.507042	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	12	0.005494505494505495	6	0.012195121951219513	0	0.0	1	0.0017482517482517483	5	0.006596306068601583	.	7.352	0.623028	0.14193	0.004312	0.005349	ENSG00000197838	ENST00000330436	T	0.70164	-0.46	4.36	2.18	0.27775	.	0.237828	0.34652	N	0.003790	T	0.35537	0.0935	N	0.17764	0.52	0.21652	N	0.99961	B	0.12630	0.006	B	0.12837	0.008	T	0.14476	-1.0471	10	0.30078	T	0.28	.	4.1933	0.10431	0.6726:0.0:0.1762:0.1512	.	379	Q16696	CP2AD_HUMAN	Q	379	ENSP00000332679:K379Q	ENSP00000332679:K379Q	K	+	1	0	CYP2A13	46292151	0.000000	0.05858	0.974000	0.42286	0.188000	0.23474	-0.232000	0.09055	0.193000	0.20303	0.397000	0.26171	AAG	A|0.995;C|0.005	0.005	strong		0.567	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766	
PAN2	9924	hgsc.bcm.edu	37	12	56716948	56716948	+	Missense_Mutation	SNP	A	A	C	rs34404784	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56716948A>C	ENST00000425394.2	-	17	2779	c.2403T>G	c.(2401-2403)atT>atG	p.I801M	PAN2_ENST00000440411.3_Missense_Mutation_p.I797M|PAN2_ENST00000257931.5_Missense_Mutation_p.I800M|PAN2_ENST00000548043.1_Missense_Mutation_p.I801M	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	TCAACTCCTCAATGGAGGGAC	0.468													A|||	11	0.00219649	0.0	0.0043	5008	,	,		18669	0.0		0.008	False		,,,				2504	0.0				p.I801M		Atlas-SNP	.											.	PAN2	107	.	0			c.T2403G						PASS	.	A	MET/ILE,MET/ILE,MET/ILE	5,4401	9.9+/-24.2	0,5,2198	176.0	166.0	169.0		2403,2400,2391	-6.7	0.9	12	dbSNP_126	169	53,8547	33.8+/-87.4	1,51,4248	yes	missense,missense,missense	PAN2	NM_001127460.2,NM_001166279.1,NM_014871.4	10,10,10	1,56,6446	CC,CA,AA		0.6163,0.1135,0.4459	benign,benign,benign	801/1203,800/1202,797/1199	56716948	58,12948	2203	4300	6503	SO:0001583	missense	9924	exon17			CTCCTCAATGGAG	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"""Ubiquitin-specific peptidases"""	20074	protein-coding gene	gene with protein product	"""PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"""		"""ubiquitin specific protease 52"", ""ubiquitin specific peptidase 52"", ""PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.2403T>G	12.37:g.56716948A>C	ENSP00000401721:p.Ile801Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	121	66	0.545455	NM_001127460		Missense_Mutation	SNP	ENST00000425394.2	37	CCDS44922.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	A	8.670	0.902555	0.17760	0.001135	0.006163	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	5.09	-6.65	0.01795	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.496933	0.21063	N	0.080782	T	0.04048	0.0113	N	0.08118	0	0.32354	N	0.558059	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.002;0.002;0.004	T	0.07888	-1.0749	10	0.34782	T	0.22	-0.1515	2.3962	0.04390	0.2285:0.426:0.1369:0.2086	rs34404784	800;797;801	Q504Q3-3;Q504Q3-2;Q504Q3	.;.;PAN2_HUMAN	M	801;797;800;801	ENSP00000401721:I801M;ENSP00000388231:I797M;ENSP00000257931:I800M;ENSP00000449861:I801M	ENSP00000257931:I800M	I	-	3	3	PAN2	55003215	0.165000	0.22948	0.944000	0.38274	0.799000	0.45148	-0.543000	0.06084	-0.954000	0.03640	-0.444000	0.05651	ATT	A|0.994;C|0.006	0.006	strong		0.468	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871	
PRDM9	56979	hgsc.bcm.edu	37	5	23527385	23527385	+	Missense_Mutation	SNP	A	A	C	rs572984210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:23527385A>C	ENST00000296682.3	+	11	2370	c.2188A>C	c.(2188-2190)Agc>Cgc	p.S730R		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	730					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GCGGGGCTTTAGCAATAAGTC	0.592										HNSCC(3;0.000094)			A|||	2	0.000399361	0.0	0.0	5008	,	,		18107	0.0		0.001	False		,,,				2504	0.001				p.S730R		Atlas-SNP	.											PRDM9,rectum,carcinoma,-2,1	PRDM9	344	1	0			c.A2188C						scavenged	.						23.0	25.0	24.0					5																	23527385		2061	4175	6236	SO:0001583	missense	56979	exon11			GGCTTTAGCAATA	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2188A>C	5.37:g.23527385A>C	ENSP00000296682:p.Ser730Arg	Somatic	221	7	0.0316742		WXS	Illumina HiSeq	Phase_I	255	4	0.0156863	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	A	1.456	-0.563682	0.03939	.	.	ENSG00000164256	ENST00000296682	T	0.19669	2.13	2.88	2.88	0.33553	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12390	0.0301	L	0.27944	0.81	0.09310	N	1	P	0.47350	0.894	B	0.38880	0.284	T	0.11324	-1.0592	9	0.44086	T	0.13	.	5.3589	0.16077	0.7466:0.0:0.0:0.2534	.	730	Q9NQV7	PRDM9_HUMAN	R	730	ENSP00000296682:S730R	ENSP00000296682:S730R	S	+	1	0	PRDM9	23563142	0.001000	0.12720	0.030000	0.17652	0.002000	0.02628	0.832000	0.27490	1.549000	0.49425	0.454000	0.30748	AGC	.	.	none		0.592	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
OR2D2	120776	hgsc.bcm.edu	37	11	6913290	6913290	+	Missense_Mutation	SNP	A	A	G	rs1965209	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6913290A>G	ENST00000299459.2	-	1	540	c.442T>C	c.(442-444)Tca>Cca	p.S148P		NM_003700.1	NP_003691.1	Q9H210	OR2D2_HUMAN	olfactory receptor, family 2, subfamily D, member 2	148			S -> P (in dbSNP:rs1965209).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	18		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTGGTCCATGATCCTGTTGCC	0.493													A|||	745	0.148762	0.0333	0.2637	5008	,	,		21896	0.1399		0.1918	False		,,,				2504	0.1881				p.S148P		Atlas-SNP	.											.	OR2D2	52	.	0			c.T442C						PASS	.		PRO/SER	270,4132	151.4+/-185.3	10,250,1941	136.0	103.0	114.0		442	5.1	1.0	11	dbSNP_92	114	1924,6668	341.0+/-323.9	240,1444,2612	yes	missense	OR2D2	NM_003700.1	74	250,1694,4553	GG,GA,AA		22.3929,6.1336,16.8847	probably-damaging	148/309	6913290	2194,10800	2201	4296	6497	SO:0001583	missense	120776	exon1			TCCATGATCCTGT	AB065824	CCDS31416.1	11p15.4	2012-08-09			ENSG00000166368	ENSG00000166368		"""GPCR / Class A : Olfactory receptors"""	8244	protein-coding gene	gene with protein product		608494		OR2D1		9787077	Standard	NM_003700		Approved	OR11-610, hg27	uc010rau.2	Q9H210	OTTHUMG00000165741	ENST00000299459.2:c.442T>C	11.37:g.6913290A>G	ENSP00000299459:p.Ser148Pro	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	165	81	0.490909	NM_003700	B9EIL5|O95224|Q6IF28|Q8NGH4|Q96R52	Missense_Mutation	SNP	ENST00000299459.2	37	CCDS31416.1	329	0.15064102564102563	21	0.042682926829268296	86	0.23756906077348067	78	0.13636363636363635	144	0.18997361477572558	a	15.32	2.798883	0.50208	0.061336	0.223929	ENSG00000166368	ENST00000299459	T	0.38887	1.11	5.12	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	0.189334	0.25922	N	0.027422	T	0.00039	0.0001	M	0.73319	2.225	0.35634	P	0.18953299999999995	D	0.63880	0.993	P	0.60541	0.876	T	0.02661	-1.1127	9	0.87932	D	0	-10.3945	13.2293	0.59933	1.0:0.0:0.0:0.0	rs1965209;rs17275325;rs52825166;rs57705655;rs1965209	148	Q9H210	OR2D2_HUMAN	P	148	ENSP00000299459:S148P	ENSP00000299459:S148P	S	-	1	0	OR2D2	6869866	0.996000	0.38824	0.997000	0.53966	0.979000	0.70002	3.944000	0.56629	2.291000	0.77112	0.524000	0.50904	TCA	A|0.840;G|0.160	0.160	strong		0.493	OR2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385986.1	NM_003700	
MUC4	4585	hgsc.bcm.edu	37	3	195508526	195508526	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508526G>C	ENST00000463781.3	-	2	10384	c.9925C>G	c.(9925-9927)Cac>Gac	p.H3309D	MUC4_ENST00000475231.1_Missense_Mutation_p.H3309D|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H3309D(2)|p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGAGTGGCGTGACCTGTGGAT	0.567																																					p.H3309D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	4	Substitution - Missense(2)|Deletion - In frame(2)	stomach(4)	c.C9925G						scavenged	.						20.0	18.0	19.0					3																	195508526		666	1526	2192	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9925C>G	3.37:g.195508526G>C	ENSP00000417498:p.His3309Asp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	111	31	0.279279	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.405	0.074889	0.08485	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27720	1.65;1.66	0.743	0.743	0.18347	.	.	.	.	.	T	0.12987	0.0315	N	0.19112	0.55	0.09310	N	1	P	0.38110	0.618	B	0.25759	0.063	T	0.15607	-1.0431	8	.	.	.	.	4.7007	0.12825	0.0:0.0:1.0:0.0	.	3181	E7ESK3	.	D	3309	ENSP00000417498:H3309D;ENSP00000420243:H3309D	.	H	-	1	0	MUC4	196993305	0.000000	0.05858	0.027000	0.17364	0.027000	0.11550	-4.092000	0.00297	0.088000	0.17205	0.089000	0.15464	CAC	.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TPST2	8459	hgsc.bcm.edu	37	22	26937198	26937198	+	Silent	SNP	C	C	G	rs140525210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26937198C>G	ENST00000338754.4	-	3	669	c.399G>C	c.(397-399)ctG>ctC	p.L133L	TPST2_ENST00000398110.2_Silent_p.L133L|TPST2_ENST00000403880.1_Silent_p.L133L	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	133					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						TGGCGGCGTCCAGCACCTCAT	0.662													C|||	32	0.00638978	0.0	0.0029	5008	,	,		14224	0.0		0.0189	False		,,,				2504	0.0112				p.L133L		Atlas-SNP	.											.	TPST2	23	.	0			c.G399C						PASS	.	C	,	20,4386	25.3+/-52.1	0,20,2183	43.0	34.0	37.0		399,399	3.2	1.0	22	dbSNP_134	37	182,8416	80.6+/-143.3	1,180,4118	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	1,200,6301	GG,GC,CC		2.1168,0.4539,1.5534	,	133/378,133/378	26937198	202,12802	2203	4299	6502	SO:0001819	synonymous_variant	8459	exon3			GGCGTCCAGCACC	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12021	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog B (Drosophila)"""	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.399G>C	22.37:g.26937198C>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			C|0.985;G|0.015	0.015	strong		0.662	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
YLPM1	56252	hgsc.bcm.edu	37	14	75248652	75248652	+	Missense_Mutation	SNP	C	C	G	rs45617140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:75248652C>G	ENST00000552421.1	+	4	2030	c.1906C>G	c.(1906-1908)Cct>Gct	p.P636A	YLPM1_ENST00000325680.7_Missense_Mutation_p.P636A|YLPM1_ENST00000238571.3_Missense_Mutation_p.P441A			P49750	YLPM1_HUMAN	YLP motif containing 1	0					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		AATACCTCCCCCTGGAGTTCC	0.557													C|||	217	0.0433307	0.0045	0.0418	5008	,	,		18860	0.001		0.0994	False		,,,				2504	0.0828				p.P636A		Atlas-SNP	.											.	YLPM1	298	.	0			c.C1906G						PASS	.	C	ALA/PRO	67,3957		1,65,1946	87.0	91.0	89.0		1906	6.1	1.0	14	dbSNP_127	89	799,7543		35,729,3407	yes	missense	YLPM1	NM_019589.2	27	36,794,5353	GG,GC,CC		9.578,1.665,7.0031	possibly-damaging	636/2147	75248652	866,11500	2012	4171	6183	SO:0001583	missense	56252	exon4			CCTCCCCCTGGAG	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.1906C>G	14.37:g.75248652C>G	ENSP00000447921:p.Pro636Ala	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	249	127	0.51004	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	37		111	0.050824175824175824	5	0.01016260162601626	19	0.052486187845303865	1	0.0017482517482517483	86	0.11345646437994723	C	12.49	1.954788	0.34471	0.01665	0.09578	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680	.	.	.	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000002	T	0.00875	0.0029	L	0.43152	1.355	0.31358	P	0.6816800000000001	P	0.47191	0.891	P	0.45610	0.487	T	0.07083	-1.0791	8	0.07175	T	0.84	-9.5661	11.8778	0.52558	0.0:0.8913:0.0:0.1087	rs45617140	636	P49750-4	.	A	636;636;441;349	.	ENSP00000238571:P441A	P	+	1	0	YLPM1	74318405	0.621000	0.27077	1.000000	0.80357	0.843000	0.47879	1.279000	0.33191	2.894000	0.99253	0.591000	0.81541	CCT	C|0.936;G|0.064	0.064	strong		0.557	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589	
DDI1	414301	hgsc.bcm.edu	37	11	103908735	103908735	+	Silent	SNP	G	G	A	rs1052313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:103908735G>A	ENST00000302259.3	+	1	1428	c.1185G>A	c.(1183-1185)gaG>gaA	p.E395E	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	395							aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		GACGAAAAGAGCATTAAAGCA	0.423													G|||	1847	0.36881	0.1082	0.5807	5008	,	,		20665	0.3988		0.4751	False		,,,				2504	0.4305				p.E395E		Atlas-SNP	.											.	DDI1	222	.	0			c.G1185A						PASS	.	G	,,	774,3608		80,614,1497	43.0	43.0	43.0		1185,,	4.3	0.2	11	dbSNP_86	43	4005,4579		933,2139,1220	no	coding-synonymous,intron,intron	PDGFD,DDI1	NM_001001711.2,NM_025208.4,NM_033135.3	,,	1013,2753,2717	AA,AG,GG		46.6566,17.6632,36.8579	,,	395/397,,	103908735	4779,8187	2191	4292	6483	SO:0001819	synonymous_variant	414301	exon1			AAAAGAGCATTAA		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"""				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.1185G>A	11.37:g.103908735G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_001001711	Q7Z4U6|Q8WTS3	Silent	SNP	ENST00000302259.3	37	CCDS31660.1																																																																																			G|0.625;A|0.374	0.374	strong		0.423	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711	
KRT76	51350	hgsc.bcm.edu	37	12	53162638	53162638	+	Silent	SNP	G	G	A	rs2280479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53162638G>A	ENST00000332411.2	-	9	1829	c.1776C>T	c.(1774-1776)tcC>tcT	p.S592S		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	592	Tail.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.S592S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGTGGCTCACGGAGATGCTAC	0.622													g|||	803	0.160343	0.0908	0.196	5008	,	,		16084	0.3502		0.0467	False		,,,				2504	0.1503				p.S592S		Atlas-SNP	.											KRT76,NS,carcinoma,0,1	KRT76	72	1	1	Substitution - coding silent(1)	stomach(1)	c.C1776T						PASS	.	A		375,4031	188.8+/-215.1	17,341,1845	66.0	59.0	61.0		1776	-7.0	0.0	12	dbSNP_100	61	402,8198	128.2+/-186.4	11,380,3909	no	coding-synonymous	KRT76	NM_015848.4		28,721,5754	AA,AG,GG		4.6744,8.5111,5.9742		592/639	53162638	777,12229	2203	4300	6503	SO:0001819	synonymous_variant	51350	exon9			GCTCACGGAGATG	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.1776C>T	12.37:g.53162638G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_015848	B4DRR3|Q7Z795	Silent	SNP	ENST00000332411.2	37	CCDS8838.1																																																																																			G|0.897;A|0.103	0.103	strong		0.622	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
PCDHA8	56140	hgsc.bcm.edu	37	5	140222157	140222157	+	Missense_Mutation	SNP	A	A	C	rs3733705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140222157A>C	ENST00000531613.1	+	1	1251	c.1251A>C	c.(1249-1251)agA>agC	p.R417S	PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.R417S|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	417	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R417S(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCGCGAGAGAGTGTCGGCCT	0.627													.|||	1920	0.383387	0.1331	0.4611	5008	,	,		16149	0.5268		0.4036	False		,,,				2504	0.498				p.R417S		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,0,2	PCDHA8	366	2	2	Substitution - Missense(2)	stomach(2)	c.A1251C						PASS	.	C	,,,,,,,SER/ARG,,,SER/ARG	767,3623		99,569,1527	123.0	106.0	111.0		,,,,,,,1251,,,1251	-2.1	0.0	5	dbSNP_107	111	3386,5140		885,1616,1762	no	intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,missense	PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031856.1	,,,,,,,110,,,110	984,2185,3289	CC,CA,AA		39.7138,17.4715,32.1539	,,,,,,,,,,	,,,,,,,417/951,,,417/815	140222157	4153,8763	2195	4263	6458	SO:0001583	missense	56140	exon1			CGAGAGAGTGTCG	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1251A>C	5.37:g.140222157A>C	ENSP00000434655:p.Arg417Ser	Somatic	379	0	0		WXS	Illumina HiSeq	Phase_I	354	101	0.285311	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	694	0.31776556776556775	54	0.10975609756097561	113	0.31215469613259667	276	0.4825174825174825	251	0.3311345646437995	C	0.003	-2.540342	0.00143	0.174715	0.397138	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.01584	4.75;4.75	3.57	-2.11	0.07187	Cadherin (4);Cadherin-like (1);	0.554866	0.14808	N	0.297205	T	0.00012	0.0000	N	0.16266	0.395	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.002	T	0.38802	-0.9644	9	0.02654	T	1	.	1.3206	0.02116	0.2073:0.3617:0.1129:0.3181	rs3733705;rs11744680;rs17844318	417;417	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	S	417	ENSP00000434655:R417S;ENSP00000367363:R417S	ENSP00000367363:R417S	R	+	3	2	PCDHA8	140202341	0.000000	0.05858	0.002000	0.10522	0.027000	0.11550	-2.436000	0.01019	-0.413000	0.07507	-0.672000	0.03802	AGA	A|0.649;C|0.351	0.351	strong		0.627	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
LTA	4049	hgsc.bcm.edu	37	6	31541086	31541086	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31541086C>T	ENST00000454783.1	+	4	492	c.234C>T	c.(232-234)ctC>ctT	p.L78L	TNF_ENST00000449264.2_5'Flank|LTA_ENST00000418386.2_Silent_p.L78L	NM_001159740.2	NP_001153212.1	P01374	TNFB_HUMAN	lymphotoxin alpha	78					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|humoral immune response (GO:0006959)|lymph node development (GO:0048535)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of interferon-gamma production (GO:0032729)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|membrane (GO:0016020)	receptor binding (GO:0005102)			endometrium(2)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9					Etanercept(DB00005)	ACTCACTGCTCTGGAGAGCAA	0.562																																					p.L78L		Atlas-SNP	.											.	LTA	18	.	0			c.C234T						PASS	.						73.0	63.0	67.0					6																	31541086		2203	4300	6503	SO:0001819	synonymous_variant	4049	exon4			ACTGCTCTGGAGA	X01393	CCDS4701.1	6p21.3	2013-05-22	2013-05-22		ENSG00000226979	ENSG00000226979		"""Tumor necrosis factor (ligand) superfamily"""	6709	protein-coding gene	gene with protein product	"""TNF superfamily member 1"""	153440	"""lymphotoxin alpha (TNF superfamily, member 1)"""	TNFB		2995927, 3001529	Standard	NM_001159740		Approved	TNFSF1, LT	uc011dnu.2	P01374	OTTHUMG00000031135	ENST00000454783.1:c.234C>T	6.37:g.31541086C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	157	50	0.318471	NM_001159740	Q8N4C3|Q9UKS8	Silent	SNP	ENST00000454783.1	37	CCDS4701.1																																																																																			.	.	none		0.562	LTA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259097.1		
MSH6	2956	hgsc.bcm.edu	37	2	48018081	48018081	+	Silent	SNP	A	A	G	rs1800932	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:48018081A>G	ENST00000234420.5	+	2	428	c.276A>G	c.(274-276)ccA>ccG	p.P92P	MSH6_ENST00000540021.1_Intron|MSH6_ENST00000538136.1_5'UTR|FBXO11_ENST00000405808.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	92	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACTTCTCACCAGGAGATTTGG	0.423			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	434	0.0866613	0.084	0.121	5008	,	,		19522	0.0		0.1789	False		,,,				2504	0.0603				p.P92P		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A276G						PASS	.	A		513,3893	237.1+/-249.0	33,447,1723	86.0	81.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	276	0.2	1.0	2	dbSNP_89	83	1636,6964	302.2+/-305.8	165,1306,2829	no	coding-synonymous	MSH6	NM_000179.2		198,1753,4552	GG,GA,AA		19.0233,11.6432,16.5231		92/1361	48018081	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	2956	exon2	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTCACCAGGAGAT	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.276A>G	2.37:g.48018081A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	37	CCDS1836.1																																																																																			A|0.864;G|0.136	0.136	strong		0.423	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
ZNF536	9745	hgsc.bcm.edu	37	19	31038995	31038995	+	Silent	SNP	T	T	C	rs1469705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:31038995T>C	ENST00000355537.3	+	4	2616	c.2469T>C	c.(2467-2469)gaT>gaC	p.D823D		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	823					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					ACCACAAGGATGAGATGTCAA	0.562													C|||	1892	0.377796	0.5053	0.3718	5008	,	,		16699	0.3185		0.3111	False		,,,				2504	0.3395				p.D823D		Atlas-SNP	.											.	ZNF536	424	.	0			c.T2469C						PASS	.	C		2155,2251	594.5+/-388.2	532,1091,580	74.0	82.0	79.0		2469	-6.6	0.6	19	dbSNP_88	79	2310,6290	704.2+/-405.4	303,1704,2293	no	coding-synonymous	ZNF536	NM_014717.1		835,2795,2873	CC,CT,TT		26.8605,48.9106,34.3303		823/1301	31038995	4465,8541	2203	4300	6503	SO:0001819	synonymous_variant	9745	exon4			CAAGGATGAGATG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.2469T>C	19.37:g.31038995T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																			T|0.646;C|0.354	0.354	strong		0.562	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
PRPH	5630	hgsc.bcm.edu	37	12	49689009	49689009	+	Missense_Mutation	SNP	G	G	A	rs57451017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49689009G>A	ENST00000257860.4	+	1	1525	c.26G>A	c.(25-27)cGg>cAg	p.R9Q	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						TCGGGCCTCCGGGCCGGCTTC	0.692													G|||	73	0.0145767	0.0008	0.0101	5008	,	,		14471	0.0139		0.0169	False		,,,				2504	0.0348				p.R9Q		Atlas-SNP	.											.	PRPH	26	.	0			c.G26A						PASS	.	G	GLN/ARG	15,4377		0,15,2181	14.0	15.0	15.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	26	3.7	1.0	12	dbSNP_129	15	99,8473		0,99,4187	yes	missense	PRPH	NM_006262.3	43	0,114,6368	AA,AG,GG		1.1549,0.3415,0.8794	possibly-damaging	9/471	49689009	114,12850	2196	4286	6482	SO:0001583	missense	5630	exon1			GCCTCCGGGCCGG		CCDS8783.1	12q12-q13	2013-01-16						"""Intermediate filaments type III"""	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.26G>A	12.37:g.49689009G>A	ENSP00000257860:p.Arg9Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_006262	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000257860.4	37	CCDS8783.1	33	0.01510989010989011	2	0.0040650406504065045	5	0.013812154696132596	14	0.024475524475524476	12	0.0158311345646438	G	23.8	4.454808	0.84209	0.003415	0.011549	ENSG00000135406	ENST00000257860	D	0.83673	-1.75	4.55	3.66	0.41972	.	0.000000	0.34531	N	0.003900	T	0.49983	0.1589	N	0.19112	0.55	0.39071	D	0.96072	P	0.36495	0.556	B	0.24394	0.053	T	0.62364	-0.6870	10	0.39692	T	0.17	.	10.2584	0.43412	0.0974:0.0:0.9026:0.0	rs57451017	9	P41219	PERI_HUMAN	Q	9	ENSP00000257860:R9Q	ENSP00000257860:R9Q	R	+	2	0	PRPH	47975276	.	.	1.000000	0.80357	0.776000	0.43924	.	.	1.129000	0.42072	0.563000	0.77884	CGG	G|0.986;A|0.014	0.014	strong		0.692	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262	
OR5AK2	390181	hgsc.bcm.edu	37	11	56756399	56756399	+	Missense_Mutation	SNP	G	G	T	rs10896563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56756399G>T	ENST00000326855.2	+	1	53	c.11G>T	c.(10-12)gGa>gTa	p.G4V		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	4			G -> V (in dbSNP:rs10896563).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						ATGACACTAGGAAACAGCACT	0.398													G|||	684	0.136581	0.025	0.0778	5008	,	,		18225	0.3879		0.0746	False		,,,				2504	0.1339				p.G4V		Atlas-SNP	.											.	OR5AK2	45	.	0			c.G11T						PASS	.	G	VAL/GLY	112,4290	85.8+/-124.5	1,110,2090	124.0	121.0	122.0		11	-4.2	0.0	11	dbSNP_120	122	608,7984	158.2+/-211.7	27,554,3715	yes	missense	OR5AK2	NM_001005323.1	109	28,664,5805	TT,TG,GG		7.0764,2.5443,5.541	benign	4/310	56756399	720,12274	2201	4296	6497	SO:0001583	missense	390181	exon1			CACTAGGAAACAG	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.11G>T	11.37:g.56756399G>T	ENSP00000322784:p.Gly4Val	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	258	135	0.523256	NM_001005323	B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	CCDS31538.1	295	0.13507326007326007	15	0.03048780487804878	18	0.049723756906077346	211	0.3688811188811189	51	0.06728232189973615	G	3.646	-0.072519	0.07228	0.025443	0.070764	ENSG00000181273	ENST00000326855	T	0.00484	7.08	3.85	-4.16	0.03869	.	1.353690	0.05313	N	0.525229	T	0.00012	0.0000	L	0.37897	1.145	0.58432	P	1.999999999946489E-6	B	0.29936	0.262	B	0.35039	0.194	T	0.04165	-1.0972	9	0.39692	T	0.17	2.4039	6.529	0.22316	0.6307:0.0:0.2311:0.1382	rs10896563;rs52794870	4	Q8NH90	O5AK2_HUMAN	V	4	ENSP00000322784:G4V	ENSP00000322784:G4V	G	+	2	0	OR5AK2	56512975	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.403000	0.01046	-1.062000	0.03181	0.194000	0.17425	GGA	G|0.918;T|0.082	0.082	strong		0.398	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
FAM186A	121006	hgsc.bcm.edu	37	12	50744119	50744119	+	Missense_Mutation	SNP	G	G	A	rs7296291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50744119G>A	ENST00000327337.5	-	4	6495	c.6496C>T	c.(6496-6498)Cat>Tat	p.H2166Y	FAM186A_ENST00000543096.1_Missense_Mutation_p.H177Y|FAM186A_ENST00000543111.1_Missense_Mutation_p.H2166Y	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2166			H -> Y (in dbSNP:rs7296291).														TACCTGGCATGCTGGATCAGC	0.373													A|||	3031	0.605232	0.4985	0.732	5008	,	,		18932	0.7431		0.659	False		,,,				2504	0.4622				p.H2166Y	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.C6496T						PASS	.	A	TYR/HIS	712,672		178,356,158	94.0	72.0	78.0		6496	-2.2	0.9	12	dbSNP_116	78	2067,1115		704,659,228	yes	missense	FAM186A	NM_001145475.1	83	882,1015,386	AA,AG,GG		35.0409,48.5549,39.1371	benign	2166/2352	50744119	2779,1787	692	1591	2283	SO:0001583	missense	121006	exon4			TGGCATGCTGGAT		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6496C>T	12.37:g.50744119G>A	ENSP00000329995:p.His2166Tyr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	71	0.568	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	1421	0.6506410256410257	239	0.48577235772357724	266	0.7348066298342542	412	0.7202797202797203	504	0.6649076517150396	A	0.010	-1.787780	0.00628	0.514451	0.649591	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.41065	1.01;1.01;1.01	3.84	-2.21	0.06973	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42965	-0.9420	8	0.02654	T	1	.	1.6118	0.02695	0.1828:0.1163:0.3728:0.3281	rs7296291;rs52835323;rs61530368;rs7296291	2166;2166	F5GYN0;A6NE01	.;F186A_HUMAN	Y	2166;177;2166	ENSP00000441337:H2166Y;ENSP00000443703:H177Y;ENSP00000329995:H2166Y	ENSP00000329995:H2166Y	H	-	1	0	FAM186A	49030386	0.618000	0.27051	0.857000	0.33713	0.517000	0.34286	-0.050000	0.11904	-0.493000	0.06678	-1.853000	0.00566	CAT	G|0.365;A|0.635	0.635	strong		0.373	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
MAS1L	116511	hgsc.bcm.edu	37	6	29455599	29455599	+	Silent	SNP	A	A	G	rs17184114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29455599A>G	ENST00000377127.3	-	1	139	c.81T>C	c.(79-81)tgT>tgC	p.C27C		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	27					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						GACAAAGGCTACATGAGAGAG	0.512													A|||	614	0.122604	0.2655	0.0648	5008	,	,		21863	0.126		0.0268	False		,,,				2504	0.0654				p.C27C	NSCLC(153;755 1987 3859 11251 32945)	Atlas-SNP	.											.	MAS1L	66	.	0			c.T81C						PASS	.	A		957,3449	361.4+/-315.7	97,763,1343	80.0	82.0	81.0		81	-1.0	0.0	6	dbSNP_123	81	224,8376	93.5+/-155.5	4,216,4080	no	coding-synonymous	MAS1L	NM_052967.1		101,979,5423	GG,GA,AA		2.6047,21.7204,9.0804		27/379	29455599	1181,11825	2203	4300	6503	SO:0001819	synonymous_variant	116511	exon1			AAGGCTACATGAG	S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"""GPCR / Class A : Orphans"""	13961	protein-coding gene	gene with protein product		607235	"""MAS1 oncogene-like"""				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.81T>C	6.37:g.29455599A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_052967	Q5SUN5	Silent	SNP	ENST00000377127.3	37	CCDS4661.1																																																																																			A|0.893;G|0.107	0.107	strong		0.512	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967	
SIRPG	55423	hgsc.bcm.edu	37	20	1617069	1617069	+	Silent	SNP	A	A	G	rs2277761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1617069A>G	ENST00000303415.3	-	3	577	c.513T>C	c.(511-513)caT>caC	p.H171H	RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000216927.4_Silent_p.H171H|SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000381583.2_Silent_p.H171H|SIRPG_ENST00000381580.1_Silent_p.H138H|RP11-77C3.3_ENST00000437384.1_RNA	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	171	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GAGAGAAGCCATGGGACTCAC	0.557													a|||	1148	0.229233	0.1619	0.366	5008	,	,		19683	0.2103		0.2376	False		,,,				2504	0.2342				p.H171H		Atlas-SNP	.											SIRPG,NS,carcinoma,-1,1	SIRPG	61	1	0			c.T513C						PASS	.	A	,,	726,3680		54,618,1531	149.0	133.0	138.0		513,513,	-4.2	0.0	20	dbSNP_100	138	2134,6466		266,1602,2432	no	coding-synonymous,coding-synonymous,intron	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	320,2220,3963	GG,GA,AA		24.814,16.4775,21.9899	,,	171/277,171/388,	1617069	2860,10146	2203	4300	6503	SO:0001819	synonymous_variant	55423	exon3			GAAGCCATGGGAC	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.513T>C	20.37:g.1617069A>G		Somatic	451	1	0.00221729		WXS	Illumina HiSeq	Phase_I	411	409	0.995134	NM_001039508	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			A|0.776;G|0.224	0.224	strong		0.557	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
ARRDC5	645432	hgsc.bcm.edu	37	19	4902754	4902754	+	Silent	SNP	G	G	A	rs2779168	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4902754G>A	ENST00000381781.2	-	1	125	c.126C>T	c.(124-126)atC>atT	p.I42I	UHRF1_ENST00000592666.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	42										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		TCAGGGTTAAGATCACCTGCC	0.557													G|||	648	0.129393	0.059	0.17	5008	,	,		18274	0.0		0.3181	False		,,,				2504	0.135				p.I42I		Atlas-SNP	.											.	ARRDC5	19	.	0			c.C126T						PASS	.	G		388,3418		24,340,1539	134.0	123.0	127.0		126	-5.8	0.1	19	dbSNP_100	127	2801,5437		475,1851,1793	no	coding-synonymous	ARRDC5	NM_001080523.1		499,2191,3332	AA,AG,GG		34.001,10.1944,26.4779		42/343	4902754	3189,8855	1903	4119	6022	SO:0001819	synonymous_variant	645432	exon1			GGTTAAGATCACC		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.126C>T	19.37:g.4902754G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	272	97	0.356618	NM_001080523		Silent	SNP	ENST00000381781.2	37	CCDS45929.1																																																																																			G|0.806;A|0.194	0.194	strong		0.557	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803	
FCGBP	8857	hgsc.bcm.edu	37	19	40366240	40366240	+	Missense_Mutation	SNP	G	G	A	rs62106922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40366240G>A	ENST00000221347.6	-	30	14001	c.13994C>T	c.(13993-13995)cCg>cTg	p.P4665L		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4665	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCAGGCGTCCGGGCCGCCGAA	0.731													G|||	415	0.0828674	0.0545	0.0562	5008	,	,		13056	0.0645		0.0358	False		,,,				2504	0.2076				p.P4665L		Atlas-SNP	.											.	FCGBP	416	.	0			c.C13994T						PASS	.	G	LEU/PRO	250,4148		9,232,1958	24.0	34.0	31.0		13994	4.1	0.0	19	dbSNP_129	31	320,8270		6,308,3981	no	missense	FCGBP	NM_003890.2	98	15,540,5939	AA,AG,GG		3.7253,5.6844,4.3887	probably-damaging	4665/5406	40366240	570,12418	2199	4295	6494	SO:0001583	missense	8857	exon30			GCGTCCGGGCCGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13994C>T	19.37:g.40366240G>A	ENSP00000221347:p.Pro4665Leu	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	132	0.06043956043956044	36	0.07317073170731707	22	0.06077348066298342	43	0.07517482517482517	31	0.040897097625329816	G	8.850	0.944289	0.18356	0.056844	0.037253	ENSG00000090920	ENST00000221347	T	0.18502	2.21	4.12	4.12	0.48240	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.843602	0.10156	U	0.708977	T	0.00637	0.0021	L	0.58510	1.815	0.09310	N	1	P	0.39181	0.663	B	0.32533	0.147	T	0.16600	-1.0397	10	0.10111	T	0.7	.	5.3258	0.15905	0.1043:0.0:0.692:0.2036	rs62106922	4665	Q9Y6R7	FCGBP_HUMAN	L	4665	ENSP00000221347:P4665L	ENSP00000221347:P4665L	P	-	2	0	FCGBP	45058080	0.001000	0.12720	0.042000	0.18584	0.198000	0.23893	1.068000	0.30629	2.289000	0.77006	0.305000	0.20034	CCG	G|0.948;A|0.052	0.052	strong		0.731	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CYP1B1	1545	hgsc.bcm.edu	37	2	38298203	38298203	+	Missense_Mutation	SNP	C	C	G	rs1056836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:38298203C>G	ENST00000260630.3	-	3	1695	c.1294G>C	c.(1294-1296)Gtg>Ctg	p.V432L	CYP1B1_ENST00000494864.1_5'UTR|CYP1B1_ENST00000407341.1_Missense_Mutation_p.V432L	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	432			L -> V (in allele CYP1B1*3, allele CYP1B1*5, allele CYP1B1*6 and allele CYP1B1*7; 1.6-fold increase in 17beta- estradiol 4-hydroxylation activity but no change in 17beta-estradiol 2- hydroxylation activity; 2-fold reduction in testosterone 6beta-hydroxylation activity and 3-fold reduction in testosterone affinity; 6-fold and 4-fold increase in progesterone 6beta- and 16alpha-hydroxylation activity, respectively and 7-fold reduction in progesterone affinity; dbSNP:rs1056836). {ECO:0000269|PubMed:10655546, ECO:0000269|PubMed:10739169, ECO:0000269|PubMed:11527932, ECO:0000269|PubMed:11774072, ECO:0000269|PubMed:11854439, ECO:0000269|PubMed:11980847, ECO:0000269|PubMed:12036985, ECO:0000269|PubMed:12525557, ECO:0000269|PubMed:14635112, ECO:0000269|PubMed:15342693, ECO:0000269|PubMed:15475877, ECO:0000269|PubMed:16688110, ECO:0000269|PubMed:9497261, ECO:0000269|PubMed:9823305, ECO:0000269|Ref.5}.		angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	GGCCACTTCACTGGGTCATGA	0.493													C|||	3079	0.614816	0.1831	0.7233	5008	,	,		19209	0.9087		0.6024	False		,,,				2504	0.8313				p.V432L		Atlas-SNP	.											CYP1B1,caecum,carcinoma,0,1	CYP1B1	39	1	0			c.G1294C	GRCh37	CM004465	CYP1B1	M	rs1056836	PASS	.	C	LEU/VAL	1014,3392	374.9+/-321.4	137,740,1326	73.0	64.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1294	5.9	0.0	2	dbSNP_86	67	4781,3819	612.4+/-396.0	1344,2093,863	yes	missense	CYP1B1	NM_000104.3	32	1481,2833,2189	GG,GC,CC		44.407,23.0141,44.5564	benign	432/544	38298203	5795,7211	2203	4300	6503	SO:0001583	missense	1545	exon3			ACTTCACTGGGTC	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.1294G>C	2.37:g.38298203C>G	ENSP00000260630:p.Val432Leu	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	NM_000104	Q5TZW8|Q93089|Q9H316	Missense_Mutation	SNP	ENST00000260630.3	37	CCDS1793.1	1340	0.6135531135531136	95	0.19308943089430894	249	0.6878453038674033	517	0.9038461538461539	479	0.6319261213720316	C	9.985	1.229235	0.22542	0.230141	0.55593	ENSG00000138061	ENST00000260630;ENST00000407341	T;T	0.68025	-0.3;-0.3	5.95	5.95	0.96441	.	1.219440	0.05416	N	0.543299	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.53041	-0.8494	8	0.27785	T	0.31	.	13.4692	0.61273	0.0:0.8433:0.1567:0.0	rs1056836;rs3731848;rs17405323;rs52802961;rs59494749;rs1056836	432	Q53TK1	.	L	432	ENSP00000260630:V432L;ENSP00000384972:V432L	ENSP00000260630:V432L	V	-	1	0	CYP1B1	38151707	0.000000	0.05858	0.033000	0.17914	0.966000	0.64601	0.163000	0.16520	2.824000	0.97209	0.655000	0.94253	GTG	C|0.487;G|0.513	0.513	strong		0.493	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
UCK1	83549	hgsc.bcm.edu	37	9	134401335	134401335	+	Silent	SNP	C	C	T	rs2296957	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:134401335C>T	ENST00000372215.4	-	6	726	c.633G>A	c.(631-633)ccG>ccA	p.P211P	UCK1_ENST00000459858.1_5'UTR|UCK1_ENST00000372208.3_Missense_Mutation_p.A180T|UCK1_ENST00000372210.3_Silent_p.P202P|UCK1_ENST00000372211.3_Silent_p.P216P	NM_001261450.1|NM_001261451.1|NM_031432.2	NP_001248379.1|NP_001248380.1|NP_113620.1	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1	211					CTP salvage (GO:0044211)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		CCACTCCTCGCGGGATGATCA	0.537													C|||	4066	0.811901	0.5227	0.8127	5008	,	,		17601	0.9236		0.9215	False		,,,				2504	0.9744				p.A180T	Melanoma(42;523 1129 28385 43975 48113)	Atlas-SNP	.											UCK1_ENST00000372211,NS,lymphoid_neoplasm,0,4	UCK1	29	4	0			c.G538A						PASS	.	C	THR/ALA,	2635,1771	641.0+/-397.4	789,1057,357	134.0	120.0	124.0		538,633	-5.1	0.9	9	dbSNP_100	124	8164,436	792.6+/-407.5	3876,412,12	yes	missense,coding-synonymous	UCK1	NM_001135954.1,NM_031432.2	58,	4665,1469,369	TT,TC,CC		5.0698,40.1952,16.9691	,	180/202,211/278	134401335	10799,2207	2203	4300	6503	SO:0001819	synonymous_variant	83549	exon5			TCCTCGCGGGATG	AF237290	CCDS6944.1, CCDS48046.1, CCDS59151.1, CCDS59152.1	9q34.1	2008-02-05			ENSG00000130717	ENSG00000130717	2.7.1.48		14859	protein-coding gene	gene with protein product		609328				11306702	Standard	NM_031432		Approved	URK1, FLJ12255	uc031tfj.1	Q9HA47	OTTHUMG00000020823	ENST00000372215.4:c.633G>A	9.37:g.134401335C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_001135954	Q5JT09|Q5JT10|Q5JT12|Q5JT13|Q6IA74|Q96BJ0	Missense_Mutation	SNP	ENST00000372215.4	37	CCDS6944.1	1798	0.8232600732600732	257	0.5223577235772358	307	0.8480662983425414	525	0.9178321678321678	709	0.9353562005277045	C	11.93	1.785333	0.31593	0.598048	0.949302	ENSG00000130717	ENST00000372208	.	.	.	4.97	-5.08	0.02929	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.24483	0.104	B	0.15870	0.014	T	0.29579	-1.0007	6	0.87932	D	0	-6.2537	8.4369	0.32793	0.1735:0.394:0.4325:0.0	rs2296957;rs13293644;rs17148018;rs60126285;rs2296957	180	Q9HA47-2	.	T	180	.	ENSP00000361282:A180T	A	-	1	0	UCK1	133391156	0.001000	0.12720	0.908000	0.35775	0.175000	0.22909	-1.779000	0.01777	-1.075000	0.03129	-0.397000	0.06425	GCG	T|0.818;C|0.181;N|0.000;A|0.001	0.818	strong		0.537	UCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054726.1	NM_031432	
PTPRR	5801	hgsc.bcm.edu	37	12	71155380	71155380	+	Silent	SNP	A	A	G	rs10506608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:71155380A>G	ENST00000283228.2	-	4	950	c.498T>C	c.(496-498)ttT>ttC	p.F166F	PTPRR_ENST00000342084.4_Silent_p.F54F	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	166					ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		TGGGAGACACAAACAGTTCAA	0.328													A|||	238	0.047524	0.034	0.0403	5008	,	,		18047	0.002		0.0875	False		,,,				2504	0.0767				p.F166F		Atlas-SNP	.											.	PTPRR	109	.	0			c.T498C						PASS	.	A	,	203,4203	125.3+/-162.5	4,195,2004	114.0	112.0	112.0		162,498	4.3	1.0	12	dbSNP_119	112	762,7838	181.9+/-230.5	31,700,3569	no	coding-synonymous,coding-synonymous	PTPRR	NM_001207015.1,NM_002849.3	,	35,895,5573	GG,GA,AA		8.8605,4.6074,7.4197	,	54/546,166/658	71155380	965,12041	2203	4300	6503	SO:0001819	synonymous_variant	5801	exon4			AGACACAAACAGT	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.498T>C	12.37:g.71155380A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	146	49	0.335616	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Silent	SNP	ENST00000283228.2	37	CCDS8998.1																																																																																			A|0.948;G|0.052	0.052	strong		0.328	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
PCLO	27445	hgsc.bcm.edu	37	7	82582846	82582846	+	Missense_Mutation	SNP	C	C	T	rs10954696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82582846C>T	ENST00000333891.9	-	5	7760	c.7423G>A	c.(7423-7425)Gtt>Att	p.V2475I	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.V2475I	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATTCTTGTAACAGGTAATCCA	0.443													C|||	1604	0.320288	0.1021	0.389	5008	,	,		12115	0.4425		0.3608	False		,,,				2504	0.3988				p.V2475I		Atlas-SNP	.											.	PCLO	1506	.	0			c.G7423A						PASS	.	C	ILE/VAL,ILE/VAL	536,3374		40,456,1459	128.0	126.0	127.0		7423,7423	2.6	0.5	7	dbSNP_120	127	2995,5295		544,1907,1694	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	29,29	584,2363,3153	TT,TC,CC		36.1279,13.7084,28.9426	benign,benign	2475/5143,2475/4936	82582846	3531,8669	1955	4145	6100	SO:0001583	missense	27445	exon5			TTGTAACAGGTAA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.7423G>A	7.37:g.82582846C>T	ENSP00000334319:p.Val2475Ile	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	711	0.32554945054945056	46	0.09349593495934959	135	0.3729281767955801	253	0.4423076923076923	277	0.3654353562005277	C	0.307	-0.970320	0.02232	0.137084	0.361279	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16196	2.37;2.36	4.52	2.62	0.31277	.	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.22457	P	0.999085595	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.41928	-0.9481	8	0.87932	D	0	.	8.8003	0.34905	0.0:0.7328:0.0:0.2672	rs10954696;rs58069415;rs10954696	2475;2475	Q9Y6V0-5;Q9Y6V0-6	.;.	I	2406;2475;2475	ENSP00000334319:V2475I;ENSP00000388393:V2475I	ENSP00000334319:V2475I	V	-	1	0	PCLO	82420782	0.000000	0.05858	0.546000	0.28166	0.091000	0.18340	-0.776000	0.04674	0.847000	0.35167	0.484000	0.47621	GTT	C|0.674;T|0.326	0.326	strong		0.443	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047857	46047857	+	Missense_Mutation	SNP	C	C	T	rs9980129	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46047857C>T	ENST00000397911.3	+	1	818	c.769C>T	c.(769-771)Cgc>Tgc	p.R257C	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	257			R -> C (in dbSNP:rs9980129). {ECO:0000269|PubMed:14962103, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CACCTCCTCCCGCCAGCCCAG	0.692													T|||	3138	0.626597	0.5076	0.6744	5008	,	,		18439	0.6488		0.7068	False		,,,				2504	0.6483				p.R257C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.C769T						PASS	.	T	,CYS/ARG	2317,2085	528.4+/-372.4	626,1065,510	61.0	78.0	72.0		,769	1.2	1.0	21	dbSNP_119	72	5788,2798	430.3+/-356.5	1953,1882,458	yes	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,180	2579,2947,968	TT,TC,CC		32.5879,47.3648,37.5962	,benign	,257/293	46047857	8105,4883	2201	4293	6494	SO:0001583	missense	386676	exon1			TCCTCCCGCCAGC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.769C>T	21.37:g.46047857C>T	ENSP00000381009:p.Arg257Cys	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	227	123	0.54185	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	1384	0.6336996336996337	252	0.5121951219512195	245	0.6767955801104972	353	0.6171328671328671	534	0.7044854881266491	t	0.033	-1.322386	0.01320	0.526352	0.674121	ENSG00000221837	ENST00000397911	T	0.00635	6.06	2.6	1.24	0.21308	.	.	.	.	.	T	0.00012	0.0000	N	0.00043	-2.465	0.36089	P	0.15666400000000003	B	0.20052	0.041	B	0.18871	0.023	T	0.06935	-1.0799	7	.	.	.	.	3.9932	0.09546	0.0:0.1389:0.2108:0.6503	rs9980129	257	P60411	KR109_HUMAN	C	257	ENSP00000381009:R257C	.	R	+	1	0	KRTAP10-9	44872285	0.190000	0.23276	0.997000	0.53966	0.734000	0.41952	0.165000	0.16564	0.229000	0.21039	-0.360000	0.07572	CGC	C|0.352;T|0.648	0.648	strong		0.692	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
CERS4	79603	hgsc.bcm.edu	37	19	8326944	8326944	+	Missense_Mutation	SNP	G	G	A	rs17160349	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8326944G>A	ENST00000251363.5	+	12	1436	c.1136G>A	c.(1135-1137)cGg>cAg	p.R379Q	CERS4_ENST00000558331.1_Missense_Mutation_p.R328Q|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559336.1_Missense_Mutation_p.R291Q|CERS4_ENST00000559450.1_Missense_Mutation_p.R379Q	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	379			R -> Q (in dbSNP:rs17160349). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GATGGCCCTCGGAGCCGGGTG	0.682													G|||	627	0.1252	0.1241	0.1744	5008	,	,		11860	0.0863		0.162	False		,,,				2504	0.0941				p.R379Q		Atlas-SNP	.											LASS4,NS,carcinoma,0,1	.	.	1	0			c.G1136A						PASS	.	G	GLN/ARG	551,3801		44,463,1669	8.0	11.0	10.0		1136	3.6	0.6	19	dbSNP_123	10	1323,7159		127,1069,3045	yes	missense	CERS4	NM_024552.2	43	171,1532,4714	AA,AG,GG		15.5977,12.6608,14.6018	probably-damaging	379/395	8326944	1874,10960	2176	4241	6417	SO:0001583	missense	79603	exon12			GCCCTCGGAGCCG		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.1136G>A	19.37:g.8326944G>A	ENSP00000251363:p.Arg379Gln	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	37	CCDS12197.1	317	0.14514652014652016	77	0.1565040650406504	69	0.19060773480662985	41	0.07167832167832168	130	0.17150395778364116	G	21.6	4.172695	0.78452	0.126608	0.155977	ENSG00000090661	ENST00000251363	T	0.05855	3.38	4.61	3.57	0.40892	.	46.516500	0.00166	N	0.000000	T	0.00039	0.0001	M	0.66506	2.035	0.80722	P	0.0	D;D	0.71674	0.998;0.998	P;P	0.54346	0.665;0.749	T	0.15065	-1.0450	9	0.18710	T	0.47	-47.2197	8.9184	0.35596	0.1066:0.0:0.8934:0.0	rs17160349;rs17855413;rs17160349	379;379	Q53HF9;Q9HA82	.;CERS4_HUMAN	Q	379	ENSP00000251363:R379Q	ENSP00000251363:R379Q	R	+	2	0	CERS4	8232944	0.988000	0.35896	0.556000	0.28293	0.023000	0.10783	2.081000	0.41596	1.067000	0.40740	0.491000	0.48974	CGG	A|0.139;C|0.000;G|0.860	0.139	strong		0.682	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
RPS14	6208	hgsc.bcm.edu	37	5	149826526	149826526	+	Splice_Site	SNP	C	C	T	rs4841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:149826526C>T	ENST00000401695.3	-	3	196	c.150G>A	c.(148-150)aaG>aaA	p.K50K	RPS14_ENST00000312037.5_Splice_Site_p.K50K|RPS14_ENST00000407193.1_Splice_Site_p.K50K			P62263	RS14_HUMAN	ribosomal protein S14	50					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|maturation of SSU-rRNA (GO:0030490)|mRNA metabolic process (GO:0016071)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|ribosomal small subunit assembly (GO:0000028)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)			central_nervous_system(1)|lung(1)|skin(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGATGGTTTCCCTGGGGACAA	0.517													T|||	1344	0.268371	0.2027	0.2161	5008	,	,		20873	0.2669		0.2575	False		,,,				2504	0.407				p.K50K		Atlas-SNP	.											.	RPS14	11	.	0			c.G150A						PASS	.	T	,,	947,3459	736.7+/-410.8	96,755,1352	98.0	86.0	90.0		150,150,150	2.0	1.0	5	dbSNP_52	90	2293,6307	705.7+/-405.5	285,1723,2292	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	RPS14	NM_001025070.1,NM_001025071.1,NM_005617.3	,,	381,2478,3644	TT,TC,CC		26.6628,21.4934,24.9116	,,	50/152,50/152,50/152	149826526	3240,9766	2203	4300	6503	SO:0001630	splice_region_variant	6208	exon3			GGTTTCCCTGGGG		CCDS4307.1	5q31-q33	2012-10-02			ENSG00000164587	ENSG00000164587		"""S ribosomal proteins"""	10387	protein-coding gene	gene with protein product	"""emetine resistance"", ""40S ribosomal protein S14"""	130620				3785212, 1549121	Standard	XM_006714790		Approved	EMTB, S14	uc003lsj.3	P62263	OTTHUMG00000130080	ENST00000401695.3:c.150-1G>A	5.37:g.149826526C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	66	0.673469	NM_001025071	B2R5G5|D3DQG5|P06366|Q5BJI0	Silent	SNP	ENST00000401695.3	37	CCDS4307.1																																																																																			T|0.198;G|0.151;C|0.606;A|0.044	0.198	strong		0.517	RPS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252373.1	NM_001025071	Silent
ANPEP	290	hgsc.bcm.edu	37	15	90349461	90349461	+	Silent	SNP	G	G	A	rs41276922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90349461G>A	ENST00000300060.6	-	2	667	c.354C>T	c.(352-354)gaC>gaT	p.D118D		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	118	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	TGATGATGACGTCAGTGGCCT	0.607													G|||	213	0.0425319	0.0424	0.0403	5008	,	,		18904	0.001		0.0885	False		,,,				2504	0.0399				p.D118D	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C354T						PASS	.	G		201,4199	123.7+/-161.0	5,191,2004	105.0	84.0	91.0		354	-4.1	0.0	15	dbSNP_127	91	673,7925	169.0+/-220.4	25,623,3651	no	coding-synonymous	ANPEP	NM_001150.2		30,814,5655	AA,AG,GG		7.8274,4.5682,6.7241		118/968	90349461	874,12124	2200	4299	6499	SO:0001819	synonymous_variant	290	exon2			GATGACGTCAGTG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.354C>T	15.37:g.90349461G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	37	CCDS10356.1																																																																																			G|0.939;A|0.061	0.061	strong		0.607	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
ANXA9	8416	hgsc.bcm.edu	37	1	150958836	150958836	+	Missense_Mutation	SNP	A	A	G	rs267733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:150958836A>G	ENST00000368947.4	+	8	973	c.497A>G	c.(496-498)gAc>gGc	p.D166G		NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	166			D -> G (in dbSNP:rs267733). {ECO:0000269|PubMed:10899159, ECO:0000269|PubMed:9742942, ECO:0000269|Ref.5}.		single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCTGTGGATGACATCACATCT	0.567													A|||	318	0.0634984	0.0424	0.0735	5008	,	,		19507	0.0258		0.1382	False		,,,				2504	0.047				p.D166G		Atlas-SNP	.											.	ANXA9	28	.	0			c.A497G						PASS	.	A	GLY/ASP	271,4135	152.9+/-186.6	5,261,1937	81.0	69.0	73.0		497	5.1	1.0	1	dbSNP_79	73	1332,7268	261.3+/-283.8	112,1108,3080	yes	missense	ANXA9	NM_003568.2	94	117,1369,5017	GG,GA,AA		15.4884,6.1507,12.3251	probably-damaging	166/346	150958836	1603,11403	2203	4300	6503	SO:0001583	missense	8416	exon8			TGGATGACATCAC	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"""Annexins"""	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.497A>G	1.37:g.150958836A>G	ENSP00000357943:p.Asp166Gly	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	174	76	0.436782	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	37	CCDS975.2	173	0.07921245421245421	21	0.042682926829268296	29	0.08011049723756906	19	0.033216783216783216	104	0.13720316622691292	A	14.34	2.507144	0.44558	0.061507	0.154884	ENSG00000143412	ENST00000368947	T	0.08634	3.07	5.1	5.1	0.69264	.	0.061224	0.64402	D	0.000005	T	0.24160	0.0585	M	0.91300	3.195	0.23589	P	0.99734447	D	0.61697	0.99	D	0.67231	0.95	T	0.27262	-1.0079	9	0.72032	D	0.01	.	11.5488	0.50708	1.0:0.0:0.0:0.0	rs267733;rs579783;rs17356291;rs17610363;rs61138212;rs267733	166	O76027	ANXA9_HUMAN	G	166	ENSP00000357943:D166G	ENSP00000357943:D166G	D	+	2	0	ANXA9	149225460	1.000000	0.71417	1.000000	0.80357	0.134000	0.20937	5.151000	0.64875	2.049000	0.60858	0.379000	0.24179	GAC	A|0.906;G|0.094	0.094	strong		0.567	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568	
ASPM	259266	hgsc.bcm.edu	37	1	197091537	197091537	+	Silent	SNP	A	A	T	rs4915337	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197091537A>T	ENST00000367409.4	-	14	3835	c.3579T>A	c.(3577-3579)tcT>tcA	p.S1193S	ASPM_ENST00000294732.7_Silent_p.S1193S|ASPM_ENST00000367408.1_Silent_p.S443S	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1193	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						ATGCTTTAAGAGACATATCCA	0.383													a|||	3919	0.782548	0.379	0.8804	5008	,	,		18581	1.0		0.9125	False		,,,				2504	0.9008				p.S1193S		Atlas-SNP	.											.	ASPM	444	.	0			c.T3579A						PASS	.	T	,	2012,2394	560.0+/-380.4	464,1084,655	75.0	71.0	72.0		3579,3579	0.6	0.1	1	dbSNP_111	72	7804,796	781.7+/-407.6	3540,724,36	no	coding-synonymous,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	4004,1808,691	TT,TA,AA		9.2558,45.665,24.5271	,	1193/1893,1193/3478	197091537	9816,3190	2203	4300	6503	SO:0001819	synonymous_variant	259266	exon14			TTTAAGAGACATA	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3579T>A	1.37:g.197091537A>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	154	80	0.519481	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			A|0.212;T|0.788	0.788	strong		0.383	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
NLRP9	338321	hgsc.bcm.edu	37	19	56249672	56249672	+	Silent	SNP	A	A	G	rs56211941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56249672A>G	ENST00000332836.2	-	1	96	c.69T>C	c.(67-69)ttT>ttC	p.F23F	RN7SKP109_ENST00000410592.1_RNA	NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	23	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		TAAATTTCCAAAACTCTTCCT	0.448													A|||	953	0.190296	0.0121	0.2349	5008	,	,		15384	0.1786		0.2068	False		,,,				2504	0.3947				p.F23F		Atlas-SNP	.											NLRP9,colon,carcinoma,0,1	NLRP9	163	1	0			c.T69C						PASS	.	A		162,4244	106.5+/-144.9	0,162,2041	120.0	128.0	125.0		69	0.5	0.4	19	dbSNP_129	125	1760,6840	316.8+/-312.9	191,1378,2731	no	coding-synonymous	NLRP9	NM_176820.2		191,1540,4772	GG,GA,AA		20.4651,3.6768,14.7778		23/992	56249672	1922,11084	2203	4300	6503	SO:0001819	synonymous_variant	338321	exon1			TTTCCAAAACTCT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22941	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"""	609663	"""NACHT, leucine rich repeat and PYD containing 9"""	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.69T>C	19.37:g.56249672A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	150	71	0.473333	NM_176820	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	37	CCDS12934.1																																																																																			A|0.852;G|0.148	0.148	strong		0.448	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820	
USP24	23358	hgsc.bcm.edu	37	1	55589175	55589175	+	Silent	SNP	C	C	T	rs145599916		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55589175C>T	ENST00000294383.6	-	36	4220	c.4221G>A	c.(4219-4221)gcG>gcA	p.A1407A	USP24_ENST00000407756.1_Silent_p.A1247A	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1407					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						AAGCCTCTCCCGCAATCAGCG	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		17947	0.0		0.001	False		,,,				2504	0.0				p.A1407A		Atlas-SNP	.											.	USP24	323	.	0			c.G4221A						PASS	.	C		1,3863		0,1,1931	64.0	63.0	63.0		4221	-10.2	0.3	1	dbSNP_134	63	11,8251		0,11,4120	no	coding-synonymous	USP24	NM_015306.2		0,12,6051	TT,TC,CC		0.1331,0.0259,0.099		1407/2621	55589175	12,12114	1932	4131	6063	SO:0001819	synonymous_variant	23358	exon36			CTCTCCCGCAATC	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.4221G>A	1.37:g.55589175C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			C|1.000;T|0.000	0.000	strong		0.507	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
ANPEP	290	hgsc.bcm.edu	37	15	90347783	90347783	+	Silent	SNP	C	C	T	rs17240240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90347783C>T	ENST00000300060.6	-	5	1276	c.963G>A	c.(961-963)acG>acA	p.T321T	ANPEP_ENST00000558177.1_5'Flank	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	321	Interaction with HCoV-229E.|Metalloprotease.		T -> M (in dbSNP:rs8179199).		angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GGATGGGGCCCGTCACGTTCA	0.602													C|||	200	0.0399361	0.028	0.0389	5008	,	,		16692	0.001		0.0895	False		,,,				2504	0.046				p.T321T	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											ANPEP,NS,carcinoma,-1,1	ANPEP	124	1	0			c.G963A						scavenged	.	C		153,4247	103.4+/-141.9	4,145,2051	91.0	94.0	93.0		963	-3.6	0.7	15	dbSNP_123	93	667,7931	168.4+/-220.0	24,619,3656	no	coding-synonymous	ANPEP	NM_001150.2		28,764,5707	TT,TC,CC		7.7576,3.4773,6.3087		321/968	90347783	820,12178	2200	4299	6499	SO:0001819	synonymous_variant	290	exon5			GGGGCCCGTCACG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.963G>A	15.37:g.90347783C>T		Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	37	CCDS10356.1																																																																																			C|0.942;T|0.058	0.058	strong		0.602	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
KIAA0141	9812	hgsc.bcm.edu	37	5	141309824	141309824	+	Missense_Mutation	SNP	G	G	A	rs351260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141309824G>A	ENST00000432126.2	+	7	873	c.739G>A	c.(739-741)Gct>Act	p.A247T	KIAA0141_ENST00000194118.4_Missense_Mutation_p.A247T	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	247			A -> T (in dbSNP:rs351260). {ECO:0000269|PubMed:15489334}.		extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTTTCCATCGCTTTCAACTT	0.463													G|||	817	0.163139	0.0234	0.2161	5008	,	,		20734	0.1329		0.3062	False		,,,				2504	0.1984				p.A247T		Atlas-SNP	.											.	KIAA0141	44	.	0			c.G739A						PASS	.	G	THR/ALA,THR/ALA	320,4086	168.0+/-198.9	14,292,1897	63.0	62.0	62.0		739,739	4.0	1.0	5	dbSNP_79	62	2900,5700	453.4+/-363.2	481,1938,1881	yes	missense,missense	KIAA0141	NM_001142603.1,NM_014773.3	58,58	495,2230,3778	AA,AG,GG		33.7209,7.2628,24.7578	benign,benign	247/516,247/516	141309824	3220,9786	2203	4300	6503	SO:0001583	missense	9812	exon7			TCCATCGCTTTCA	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.739G>A	5.37:g.141309824G>A	ENSP00000396225:p.Ala247Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	155	91	0.587097	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	411	0.18818681318681318	21	0.042682926829268296	90	0.24861878453038674	75	0.13111888111888112	225	0.29683377308707126	G	13.51	2.258234	0.39896	0.072628	0.337209	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	T;T;T	0.62232	0.53;0.53;0.04	4.86	3.97	0.46021	Tetratricopeptide-like helical (1);	0.219160	0.39544	N	0.001326	T	0.00012	0.0000	M	0.91972	3.26	0.40341	P	0.020966999999999958	P	0.41214	0.742	B	0.36534	0.227	T	0.09509	-1.0671	9	0.44086	T	0.13	-3.5127	9.3661	0.38226	0.0989:0.0:0.9011:0.0	rs351260;rs17850264;rs17850666;rs17850731;rs52801955;rs56492989;rs61460168;rs351260	247	Q14154	DELE_HUMAN	T	247	ENSP00000396225:A247T;ENSP00000194118:A247T;ENSP00000422686:A247T	ENSP00000194118:A247T	A	+	1	0	KIAA0141	141290008	0.998000	0.40836	0.999000	0.59377	0.991000	0.79684	2.644000	0.46613	1.243000	0.43853	0.455000	0.32223	GCT	G|0.771;T|0.005	.	strong		0.463	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
PNRC1	10957	hgsc.bcm.edu	37	6	89793894	89793894	+	Silent	SNP	G	G	C	rs1130809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:89793894G>C	ENST00000336032.3	+	2	1080	c.963G>C	c.(961-963)acG>acC	p.T321T	PNRC1_ENST00000354922.3_Silent_p.T136T|PNRC1_ENST00000369472.1_Silent_p.T136T	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		ACTTAAAAACGCTCCTCAAAG	0.398										Multiple Myeloma(7;0.094)			G|||	1747	0.348842	0.2443	0.4006	5008	,	,		16481	0.6696		0.167	False		,,,				2504	0.3098				p.T321T		Atlas-SNP	.											.	PNRC1	17	.	0			c.G963C						PASS	.	G		989,3417	357.6+/-314.0	117,755,1331	58.0	57.0	57.0		963	3.4	1.0	6	dbSNP_86	57	1363,7235	255.9+/-280.6	110,1143,3046	no	coding-synonymous	PNRC1	NM_006813.2		227,1898,4377	CC,CG,GG		15.8525,22.4467,18.0867		321/328	89793894	2352,10652	2203	4299	6502	SO:0001819	synonymous_variant	10957	exon2			AAAAACGCTCCTC	U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"""proline rich 2"""	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.963G>C	6.37:g.89793894G>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	126	71	0.563492	NM_006813	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Silent	SNP	ENST00000336032.3	37	CCDS5018.1																																																																																			G|0.746;C|0.254	0.254	strong		0.398	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813	
EHMT1	79813	hgsc.bcm.edu	37	9	140638534	140638534	+	Missense_Mutation	SNP	G	G	A	rs11137198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140638534G>A	ENST00000460843.1	+	6	1189	c.1162G>A	c.(1162-1164)Gcc>Acc	p.A388T	EHMT1_ENST00000462484.1_Missense_Mutation_p.A388T|EHMT1_ENST00000334856.6_Missense_Mutation_p.A357T|EHMT1_ENST00000371394.2_3'UTR	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	388			A -> T (in dbSNP:rs11137198).		chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GGCTGATCGCGCCCAGAAGGT	0.567													G|||	34	0.00678914	0.0008	0.0058	5008	,	,		16838	0.0		0.0199	False		,,,				2504	0.0092				p.A388T		Atlas-SNP	.											.	EHMT1	196	.	0			c.G1162A						PASS	.	G	THR/ALA,THR/ALA	16,4390	23.3+/-48.9	0,16,2187	60.0	63.0	62.0		1162,1162	-0.3	0.0	9	dbSNP_120	62	187,8413	84.2+/-146.7	3,181,4116	yes	missense,missense	EHMT1	NM_001145527.1,NM_024757.4	58,58	3,197,6303	AA,AG,GG		2.1744,0.3631,1.5608	benign,benign	388/809,388/1299	140638534	203,12803	2203	4300	6503	SO:0001583	missense	79813	exon6			GATCGCGCCCAGA	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1162G>A	9.37:g.140638534G>A	ENSP00000417980:p.Ala388Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	37	CCDS7050.2	19	0.0086996336996337	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	17	0.022427440633245383	G	4.068	0.010439	0.07912	0.003631	0.021744	ENSG00000181090	ENST00000334856;ENST00000371400;ENST00000462484;ENST00000460843	T;T;T	0.69685	1.67;0.91;-0.42	5.25	-0.306	0.12780	.	0.794414	0.11854	N	0.523050	T	0.26304	0.0642	N	0.22421	0.69	0.09310	N	0.999992	B;B;B	0.14012	0.002;0.009;0.009	B;B;B	0.13407	0.001;0.009;0.009	T	0.14952	-1.0454	10	0.09084	T	0.74	.	4.0512	0.09796	0.3854:0.0:0.3682:0.2464	rs11137198;rs11137198	388;357;388	Q9H9B1;Q9H9B1-2;Q9H9B1-4	EHMT1_HUMAN;.;.	T	357;357;388;388	ENSP00000334476:A357T;ENSP00000417328:A388T;ENSP00000417980:A388T	ENSP00000334476:A357T	A	+	1	0	EHMT1	139758355	0.022000	0.18835	0.021000	0.16686	0.026000	0.11368	0.074000	0.14662	-0.417000	0.07461	-1.036000	0.02392	GCC	G|0.986;A|0.014	0.014	strong		0.567	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
PRR5L	79899	hgsc.bcm.edu	37	11	36422701	36422701	+	Silent	SNP	C	C	T	rs78731804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:36422701C>T	ENST00000378867.3	+	3	385	c.30C>T	c.(28-30)ccC>ccT	p.P10P	PRR5L_ENST00000389693.3_Intron|PRR5L_ENST00000527487.1_Silent_p.P10P|PRR5L_ENST00000530639.1_Silent_p.P10P|PRR5L_ENST00000311599.5_5'UTR	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	10					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)	p.P10P(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						CCATTCTGCCCGTCGAGTTCC	0.612													C|||	463	0.0924521	0.0908	0.1066	5008	,	,		17325	0.1171		0.0596	False		,,,				2504	0.093				p.P10P		Atlas-SNP	.											PRR5L,caecum,carcinoma,0,1	PRR5L	35	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C30T						PASS	.	C	,,,	400,4004	195.7+/-220.2	23,354,1825	53.0	46.0	49.0		30,,30,30	-0.0	0.0	11	dbSNP_131	49	482,8114	140.8+/-197.2	13,456,3829	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	PRR5L	NM_001160167.1,NM_001160168.1,NM_001160169.1,NM_024841.4	,,,	36,810,5654	TT,TC,CC		5.6073,9.0827,6.7846	,,,	10/369,,10/206,10/369	36422701	882,12118	2202	4298	6500	SO:0001819	synonymous_variant	79899	exon3			TCTGCCCGTCGAG		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"""protein observed with Rictor-2"""	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.30C>T	11.37:g.36422701C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Silent	SNP	ENST00000378867.3	37	CCDS31463.1																																																																																			C|0.930;T|0.070	0.070	strong		0.612	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841	
SPTBN1	6711	hgsc.bcm.edu	37	2	54858664	54858664	+	Silent	SNP	C	C	T	rs2229503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:54858664C>T	ENST00000356805.4	+	16	3761	c.3480C>T	c.(3478-3480)aaC>aaT	p.N1160N	SPTBN1_ENST00000333896.5_Silent_p.N1147N	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1160					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			TGTGGGAGAACAGACAAAATC	0.547													C|||	578	0.115415	0.1339	0.0951	5008	,	,		19822	0.0813		0.174	False		,,,				2504	0.0798				p.N1160N		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C3480T						PASS	.	C	,	573,3833	257.0+/-261.6	33,507,1663	101.0	100.0	100.0		3480,3441	3.5	1.0	2	dbSNP_98	100	1594,7006	297.1+/-303.3	160,1274,2866	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	193,1781,4529	TT,TC,CC		18.5349,13.005,16.6615	,	1160/2365,1147/2156	54858664	2167,10839	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon16			GGAGAACAGACAA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3480C>T	2.37:g.54858664C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.857;T|0.143	0.143	strong		0.547	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
SPP1	6696	hgsc.bcm.edu	37	4	88902851	88902851	+	Silent	SNP	T	T	C	rs35382133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88902851T>C	ENST00000395080.3	+	6	568	c.441T>C	c.(439-441)acT>acC	p.T147T	SPP1_ENST00000360804.4_Silent_p.T120T|SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000237623.7_Silent_p.T133T	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	147					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		AAGTTTTCACTCCAGTTGTCC	0.473													T|||	89	0.0177716	0.0061	0.013	5008	,	,		19392	0.0		0.0239	False		,,,				2504	0.0491				p.T160T		Atlas-SNP	.											.	SPP1	35	.	0			c.T480C						PASS	.	T	,,	33,4373	37.6+/-69.7	0,33,2170	181.0	166.0	171.0		399,441,360	-4.7	0.0	4	dbSNP_126	171	165,8435	77.5+/-140.1	1,163,4136	no	coding-synonymous,coding-synonymous,coding-synonymous	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	,,	1,196,6306	CC,CT,TT		1.9186,0.749,1.5224	,,	133/301,147/315,120/288	88902851	198,12808	2203	4300	6503	SO:0001819	synonymous_variant	6696	exon7			TTTCACTCCAGTT		CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"""Endogenous ligands"""	11255	protein-coding gene	gene with protein product	"""early T-lymphocyte activation 1"""	166490	"""osteopontin"", ""bone sialoprotein I"""	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.441T>C	4.37:g.88902851T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	210	89	0.42381	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	37	CCDS43250.1																																																																																			T|0.985;C|0.015	0.015	strong		0.473	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
IKBKAP	8518	hgsc.bcm.edu	37	9	111653574	111653574	+	Silent	SNP	C	C	G	rs1063110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:111653574C>G	ENST00000374647.5	-	28	3376	c.3069G>C	c.(3067-3069)ctG>ctC	p.L1023L	IKBKAP_ENST00000537196.1_Silent_p.L674L|IKBKAP_ENST00000467959.1_5'Flank	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	1023					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TGCCACATGTCAGAAAGGCTG	0.562													C|||	1580	0.315495	0.0477	0.4553	5008	,	,		16868	0.4762		0.4523	False		,,,				2504	0.272				p.L1023L		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G3069C						PASS	.	C		494,3912	227.5+/-242.7	36,422,1745	89.0	84.0	86.0		3069	3.9	1.0	9	dbSNP_86	86	3914,4686	546.6+/-385.0	907,2100,1293	no	coding-synonymous	IKBKAP	NM_003640.3		943,2522,3038	GG,GC,CC		45.5116,11.212,33.892		1023/1333	111653574	4408,8598	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon28			ACATGTCAGAAAG	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.3069G>C	9.37:g.111653574C>G		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			G|0.357;C|0.643	0.357	strong		0.562	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
AJAP1	55966	hgsc.bcm.edu	37	1	4772717	4772717	+	Missense_Mutation	SNP	G	G	A	rs242056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:4772717G>A	ENST00000378191.4	+	2	1168	c.787G>A	c.(787-789)Ggg>Agg	p.G263R	AJAP1_ENST00000378190.3_Missense_Mutation_p.G263R	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	263			G -> R (in dbSNP:rs242056). {ECO:0000269|PubMed:16410724}.		cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		CAGCAACAACGGGGAAGTCAC	0.607													G|||	1807	0.360823	0.1664	0.3761	5008	,	,		16220	0.2728		0.6431	False		,,,				2504	0.4131				p.G263R		Atlas-SNP	.											.	AJAP1	68	.	0			c.G787A						PASS	.	G	ARG/GLY,ARG/GLY	1097,3309	384.9+/-325.5	150,797,1256	71.0	78.0	76.0		787,787	4.8	0.0	1	dbSNP_79	76	5719,2881	663.8+/-402.1	1889,1941,470	yes	missense,missense	AJAP1	NM_001042478.1,NM_018836.3	125,125	2039,2738,1726	AA,AG,GG		33.5,24.8979,47.5934	probably-damaging,probably-damaging	263/412,263/412	4772717	6816,6190	2203	4300	6503	SO:0001583	missense	55966	exon2			AACAACGGGGAAG	AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"""transmembrane protein SHREW1"""	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.787G>A	1.37:g.4772717G>A	ENSP00000367433:p.Gly263Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_018836	Q9Y229	Missense_Mutation	SNP	ENST00000378191.4	37	CCDS54.1	888	0.4065934065934066	100	0.2032520325203252	157	0.43370165745856354	150	0.26223776223776224	481	0.6345646437994723	G	10.14	1.268191	0.23136	0.248979	0.665	ENSG00000196581	ENST00000378190;ENST00000378191	T;T	0.45276	0.9;0.9	4.76	4.76	0.60689	.	0.236408	0.34750	N	0.003703	T	0.00012	0.0000	N	0.19112	0.55	0.35888	P	0.17056800000000005	D	0.76494	0.999	P	0.61658	0.892	T	0.25847	-1.0120	9	0.27082	T	0.32	-14.0393	13.2654	0.60131	0.0:0.0:1.0:0.0	rs242056;rs487066;rs58701997;rs242056	263	Q9UKB5	AJAP1_HUMAN	R	263	ENSP00000367432:G263R;ENSP00000367433:G263R	ENSP00000367432:G263R	G	+	1	0	AJAP1	4672577	0.858000	0.29795	0.012000	0.15200	0.038000	0.13279	3.781000	0.55394	2.179000	0.69175	0.467000	0.42956	GGG	G|0.523;A|0.477	0.477	strong		0.607	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836	
RNF123	63891	hgsc.bcm.edu	37	3	49758302	49758302	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49758302C>T	ENST00000327697.6	+	37	3857	c.3713C>T	c.(3712-3714)tCt>tTt	p.S1238F	AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000480687.1_3'UTR|RNF123_ENST00000433785.1_Missense_Mutation_p.S350F|RNF123_ENST00000497099.1_3'UTR|GMPPB_ENST00000308375.6_3'UTR|AMIGO3_ENST00000535833.1_5'UTR	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	1238	Poly-Ala.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		ACCTCTGCATCTGCCCAGGCA	0.572																																					p.S1238F		Atlas-SNP	.											RNF123,NS,carcinoma,0,1	RNF123	100	1	0			c.C3713T						scavenged	.						115.0	114.0	114.0					3																	49758302		2203	4300	6503	SO:0001583	missense	63891	exon37			CTGCATCTGCCCA	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.3713C>T	3.37:g.49758302C>T	ENSP00000328287:p.Ser1238Phe	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	153	4	0.0261438	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488875	0.84962	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000433785	T	0.73789	-0.78	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.80854	0.4703	M	0.67953	2.075	0.54753	D	0.999986	D	0.61080	0.989	P	0.53912	0.737	T	0.82566	-0.0393	10	0.52906	T	0.07	-16.3458	16.5221	0.84320	0.0:1.0:0.0:0.0	.	1238	Q5XPI4	RN123_HUMAN	F	1238;1238;350	ENSP00000328287:S1238F	ENSP00000328287:S1238F	S	+	2	0	RNF123	49733306	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.282000	0.58971	2.481000	0.83766	0.561000	0.74099	TCT	.	.	none		0.572	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
GAREM	64762	hgsc.bcm.edu	37	18	30050356	30050356	+	Silent	SNP	C	C	T	rs11664566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:30050356C>T	ENST00000269209.6	-	1	39	c.36G>A	c.(34-36)aaG>aaA	p.K12K	GAREM_ENST00000399218.4_Silent_p.K12K			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	12	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										ACTTCACATCCTTGAGGCTGC	0.726													c|||	1280	0.255591	0.298	0.2161	5008	,	,		8443	0.3869		0.162	False		,,,				2504	0.1871				p.K12K		Atlas-SNP	.											.	.	.	.	0			c.G36A						PASS	.		,	1195,3201		164,867,1167	16.0	18.0	17.0		36,36	3.5	1.0	18	dbSNP_120	17	1361,7229		122,1117,3056	no	coding-synonymous,coding-synonymous	FAM59A	NM_001242409.1,NM_022751.2	,	286,1984,4223	TT,TC,CC		15.844,27.1838,19.6827	,	12/877,12/876	30050356	2556,10430	2198	4295	6493	SO:0001819	synonymous_variant	64762	exon1			CACATCCTTGAGG	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.36G>A	18.37:g.30050356C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	53	18	0.339623	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																			C|0.784;T|0.216	0.216	strong		0.726	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751	
TTC30A	92104	hgsc.bcm.edu	37	2	178482594	178482594	+	Missense_Mutation	SNP	G	G	T	rs61742858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:178482594G>T	ENST00000355689.5	-	1	1100	c.836C>A	c.(835-837)cCc>cAc	p.P279H	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	279				P -> H (in Ref. 1; BAF85084). {ECO:0000305}.	cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			CTCTGCCCTGGGTGGCATGTC	0.502													G|||	395	0.0788738	0.0068	0.1542	5008	,	,		21302	0.001		0.2346	False		,,,				2504	0.0429				p.P279H		Atlas-SNP	.											.	TTC30A	60	.	0			c.C836A						PASS	.	G	HIS/PRO	186,4220	118.8+/-156.5	3,180,2020	127.0	138.0	134.0		836	4.9	0.6	2	dbSNP_129	134	1891,6709	334.7+/-321.1	209,1473,2618	no	missense	TTC30A	NM_152275.3	77	212,1653,4638	TT,TG,GG		21.9884,4.2215,15.9696	probably-damaging	279/666	178482594	2077,10929	2203	4300	6503	SO:0001583	missense	92104	exon1			GCCCTGGGTGGCA	AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"""Tetratricopeptide (TTC) repeat domain containing"""	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.836C>A	2.37:g.178482594G>T	ENSP00000347915:p.Pro279His	Somatic	492	0	0		WXS	Illumina HiSeq	Phase_I	553	547	0.98915	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	37	CCDS2276.1	254	0.1163003663003663	5	0.01016260162601626	58	0.16022099447513813	0	0.0	191	0.2519788918205805	G	15.69	2.908034	0.52333	0.042215	0.219884	ENSG00000197557	ENST00000355689	T	0.22945	1.93	5.78	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.93016	3.37	0.09310	P	0.99999999776138	D	0.89917	1.0	D	0.97110	1.0	T	0.03662	-1.1015	9	0.87932	D	0	.	14.871	0.70456	0.0686:0.0:0.9314:0.0	.	279	Q86WT1	TT30A_HUMAN	H	279	ENSP00000347915:P279H	ENSP00000347915:P279H	P	-	2	0	TTC30A	178190840	1.000000	0.71417	0.625000	0.29200	0.995000	0.86356	4.219000	0.58561	1.472000	0.48140	0.549000	0.68633	CCC	G|0.847;T|0.153	0.153	strong		0.502	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275	
HRH4	59340	hgsc.bcm.edu	37	18	22056766	22056766	+	Missense_Mutation	SNP	C	C	T	rs11665084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:22056766C>T	ENST00000256906.4	+	3	513	c.413C>T	c.(412-414)gCc>gTc	p.A138V	HRH4_ENST00000426880.2_Intron	NM_001160166.1|NM_021624.3	NP_001153638.1|NP_067637.2	Q9H3N8	HRH4_HUMAN	histamine receptor H4	138			A -> V (in dbSNP:rs11665084). {ECO:0000269|PubMed:10973974}.		inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of MAPK cascade (GO:0043408)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Amitriptyline(DB00321)|Amoxapine(DB00543)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Mianserin(DB06148)|Olanzapine(DB00334)	CTGATGGTGGCCGTTTGGGTG	0.393													C|||	286	0.0571086	0.0106	0.134	5008	,	,		21696	0.0347		0.0964	False		,,,				2504	0.0481				p.A138V		Atlas-SNP	.											.	HRH4	46	.	0			c.C413T						PASS	.	C	,,VAL/ALA	112,4294	86.8+/-125.4	1,110,2092	199.0	186.0	191.0		,,413	4.9	0.9	18	dbSNP_120	191	839,7761	192.7+/-238.6	42,755,3503	yes	intron,utr-3,missense	HRH4	NM_001143828.1,NM_001160166.1,NM_021624.3	,,64	43,865,5595	TT,TC,CC		9.7558,2.542,7.312	,,probably-damaging	,,138/391	22056766	951,12055	2203	4300	6503	SO:0001583	missense	59340	exon3			TGGTGGCCGTTTG	AF312230	CCDS11887.1, CCDS45841.1	18q11.2	2012-08-08			ENSG00000134489	ENSG00000134489		"""GPCR / Class A : Histamine receptors"""	17383	protein-coding gene	gene with protein product		606792				11118334, 10973974	Standard	NM_021624		Approved	H4R, HH4R, AXOR35, GPCR105, GPRv53	uc002kvi.3	Q9H3N8	OTTHUMG00000131945	ENST00000256906.4:c.413C>T	18.37:g.22056766C>T	ENSP00000256906:p.Ala138Val	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	216	90	0.416667	NM_021624	B0YJ19|B2KJ48|Q4G0I6|Q9GZQ0	Missense_Mutation	SNP	ENST00000256906.4	37	CCDS11887.1	146	0.06684981684981685	3	0.006097560975609756	41	0.1132596685082873	28	0.04895104895104895	74	0.09762532981530343	C	14.63	2.593668	0.46214	0.02542	0.097558	ENSG00000134489	ENST00000256906	T	0.36878	1.23	5.79	4.9	0.64082	GPCR, rhodopsin-like superfamily (1);	0.213135	0.40640	N	0.001050	T	0.00496	0.0016	L	0.45352	1.415	0.09310	P	0.9999999999999928	B	0.27068	0.167	B	0.30716	0.119	T	0.08452	-1.0721	9	0.02654	T	1	-9.9961	9.3701	0.38248	0.0:0.7796:0.1457:0.0747	rs11665084;rs17203335;rs52834131;rs60698202;rs11665084	138	Q9H3N8	HRH4_HUMAN	V	138	ENSP00000256906:A138V	ENSP00000256906:A138V	A	+	2	0	HRH4	20310764	0.727000	0.28069	0.917000	0.36280	0.864000	0.49448	1.414000	0.34736	1.405000	0.46838	0.655000	0.94253	GCC	C|0.930;T|0.070	0.070	strong		0.393	HRH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254904.1		
LRRC27	80313	hgsc.bcm.edu	37	10	134161517	134161517	+	Missense_Mutation	SNP	C	C	T	rs2474329	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134161517C>T	ENST00000368614.3	+	6	688	c.583C>T	c.(583-585)Cgt>Tgt	p.R195C	LRRC27_ENST00000368610.3_Missense_Mutation_p.R133C|LRRC27_ENST00000368615.3_Missense_Mutation_p.R195C|LRRC27_ENST00000368612.1_Missense_Mutation_p.R133C|LRRC27_ENST00000344079.5_Missense_Mutation_p.R195C|LRRC27_ENST00000392638.2_Missense_Mutation_p.R195C|LRRC27_ENST00000432555.2_Missense_Mutation_p.R68C|LRRC27_ENST00000368613.4_Missense_Mutation_p.R195C|LRRC27_ENST00000356571.4_3'UTR	NM_030626.2	NP_085129.1	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27	195			R -> C (in dbSNP:rs2474329).							breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	18		all_cancers(35;6.28e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;9.12e-05)|Epithelial(32;0.000116)|all cancers(32;0.000145)|BRCA - Breast invasive adenocarcinoma(275;0.218)		GATGACCCTCCGTGACCTCCC	0.547													c|||	385	0.076877	0.0522	0.1138	5008	,	,		16281	0.0		0.1859	False		,,,				2504	0.0511				p.R195C		Atlas-SNP	.											.	LRRC27	64	.	0			c.C583T						PASS	.	T	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	302,4104	163.6+/-195.4	11,280,1912	103.0	109.0	107.0		583,583,583,583	-0.6	0.0	10	dbSNP_100	107	1941,6659	334.5+/-321.0	230,1481,2589	yes	missense,missense,missense,missense	LRRC27	NM_001143757.1,NM_001143758.1,NM_001143759.1,NM_030626.2	180,180,180,180	241,1761,4501	TT,TC,CC		22.5698,6.8543,17.2459	benign,benign,benign,benign	195/531,195/384,195/384,195/531	134161517	2243,10763	2203	4300	6503	SO:0001583	missense	80313	exon6			ACCCTCCGTGACC	AB051461	CCDS31316.1, CCDS44496.1	10q26.3	2013-09-20			ENSG00000148814	ENSG00000148814			29346	protein-coding gene	gene with protein product						11214970	Standard	NM_030626		Approved	KIAA1674	uc010quw.1	Q9C0I9	OTTHUMG00000019284	ENST00000368614.3:c.583C>T	10.37:g.134161517C>T	ENSP00000357603:p.Arg195Cys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	134	50	0.373134	NM_001143757	A6NE72|A6NJB4|A6NKD3|D3DRH0|Q5SZH6|Q5SZH8|Q5SZH9|Q86XT5|Q8N7C8|Q8NA21	Missense_Mutation	SNP	ENST00000368614.3	37	CCDS31316.1	220	0.10073260073260074	28	0.056910569105691054	54	0.14917127071823205	0	0.0	138	0.1820580474934037	c	8.082	0.772591	0.16051	0.068543	0.225698	ENSG00000148814	ENST00000368615;ENST00000392638;ENST00000344079;ENST00000368614;ENST00000368613;ENST00000368612;ENST00000368610;ENST00000432555	T;T;T;T;T;T;T;T	0.46451	2.52;2.44;2.44;2.46;2.46;4.22;4.22;0.87	3.09	-0.645	0.11475	.	2.145260	0.01775	N	0.031386	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;P;B;B;B	0.44044	0.002;0.825;0.002;0.0;0.004	B;B;B;B;B	0.34722	0.001;0.188;0.001;0.0;0.001	T	0.07829	-1.0752	9	0.37606	T	0.19	0.7324	4.7016	0.12830	0.3686:0.4544:0.0:0.177	rs2474329;rs52823335;rs59594126;rs2474329	195;68;133;195;195	Q9C0I9-4;B4DW88;Q9C0I9-2;Q9C0I9;Q9C0I9-3	.;.;.;LRC27_HUMAN;.	C	195;195;195;195;195;133;133;68	ENSP00000357604:R195C;ENSP00000376413:R195C;ENSP00000342641:R195C;ENSP00000357603:R195C;ENSP00000357602:R195C;ENSP00000357601:R133C;ENSP00000357599:R133C;ENSP00000407949:R68C	ENSP00000342641:R195C	R	+	1	0	LRRC27	134011507	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.072000	0.11486	-0.125000	0.11703	-1.068000	0.02270	CGT	C|0.864;T|0.136	0.136	strong		0.547	LRRC27-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051058.2	XM_290462	
NOL11	25926	hgsc.bcm.edu	37	17	65735660	65735660	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:65735660A>G	ENST00000253247.4	+	16	1986	c.1871A>G	c.(1870-1872)tAc>tGc	p.Y624C	SNORA38B_ENST00000363524.1_RNA|NOL11_ENST00000535137.1_Missense_Mutation_p.Y442C	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	624					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			TATTTCCTGTACCTGAAGTGT	0.348																																					p.Y624C		Atlas-SNP	.											NOL11,NS,lymphoid_neoplasm,+1,1	NOL11	48	1	0			c.A1871G						scavenged	.						101.0	99.0	99.0					17																	65735660		2203	4300	6503	SO:0001583	missense	25926	exon16			TCCTGTACCTGAA	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1871A>G	17.37:g.65735660A>G	ENSP00000253247:p.Tyr624Cys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	196	2	0.0102041	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Missense_Mutation	SNP	ENST00000253247.4	37	CCDS11671.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.369215	0.61624	.	.	ENSG00000130935	ENST00000253247;ENST00000535137	T	0.51574	0.7	5.0	5.0	0.66597	.	0.124523	0.56097	D	0.000027	T	0.67287	0.2877	M	0.76328	2.33	0.45822	D	0.998693	D	0.89917	1.0	D	0.85130	0.997	T	0.71583	-0.4549	10	0.87932	D	0	-10.0984	12.5796	0.56383	1.0:0.0:0.0:0.0	.	624	Q9H8H0	NOL11_HUMAN	C	624;442	ENSP00000253247:Y624C	ENSP00000253247:Y624C	Y	+	2	0	NOL11	63166122	1.000000	0.71417	0.998000	0.56505	0.847000	0.48162	6.223000	0.72257	2.013000	0.59113	0.472000	0.43445	TAC	.	.	none		0.348	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462	
TMX4	56255	hgsc.bcm.edu	37	20	7980390	7980390	+	Silent	SNP	C	C	T	rs1012891	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:7980390C>T	ENST00000246024.2	-	4	671	c.456G>A	c.(454-456)ccG>ccA	p.P152P	TMX4_ENST00000530935.1_5'UTR	NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	152					cell redox homeostasis (GO:0045454)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(2)|lung(11)|skin(1)	17						TTAGAGAAGCCGGGGATTTCC	0.418													C|||	1756	0.350639	0.2602	0.2939	5008	,	,		16262	0.3562		0.3111	False		,,,				2504	0.5481				p.P152P		Atlas-SNP	.											.	TMX4	39	.	0			c.G456A						PASS	.	C		1202,3204	414.1+/-336.7	160,882,1161	45.0	47.0	46.0		456	-11.5	0.2	20	dbSNP_86	46	2524,6076	411.6+/-350.5	359,1806,2135	no	coding-synonymous	TMX4	NM_021156.2		519,2688,3296	TT,TC,CC		29.3488,27.281,28.6483		152/350	7980390	3726,9280	2203	4300	6503	SO:0001819	synonymous_variant	56255	exon4			AGAAGCCGGGGAT		CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827		"""Protein disulfide isomerases"""	25237	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 14"""		"""thioredoxin domain containing 13"""	TXNDC13			Standard	NM_021156		Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.456G>A	20.37:g.7980390C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Silent	SNP	ENST00000246024.2	37	CCDS13101.1																																																																																			C|0.691;T|0.308	0.308	strong		0.418	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118231360	118231360	+	Missense_Mutation	SNP	G	G	A	rs386747984|rs386747985|rs10736251|rs539127048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:118231360G>A	ENST00000369230.3	+	10	1287	c.1141G>A	c.(1141-1143)Gtt>Att	p.V381I		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	381	PLAT.		V -> I (in dbSNP:rs10736251). {ECO:0000269|PubMed:15489334}.		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		AGGCGGGGCAGTTAGGAAAAC	0.483														4828	0.964058	0.8691	0.9899	5008	,	,		14283	1.0		1.0	False		,,,				2504	1.0				p.V381I		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.G1141A						PASS	.	A	ILE/VAL	3914,492	229.1+/-243.8	1763,388,52	134.0	143.0	140.0		1141	-7.4	0.0	10	dbSNP_120	140	8589,11	8.4+/-32.0	4289,11,0	yes	missense	PNLIPRP3	NM_001011709.2	29	6052,399,52	AA,AG,GG		0.1279,11.1666,3.8674	benign	381/468	118231360	12503,503	2203	4300	6503	SO:0001583	missense	119548	exon10			GGGGCAGTTAGGA	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1141G>A	10.37:g.118231360G>A	ENSP00000358232:p.Val381Ile	Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	175	174	0.994286	NM_001011709		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	2123	0.9720695970695971	435	0.8841463414634146	358	0.988950276243094	572	1.0	758	1.0	A	9.741	1.164824	0.21538	0.888334	0.998721	ENSG00000203837	ENST00000369230	T	0.64260	-0.09	4.18	-7.38	0.01407	Lipoxygenase, LH2 (2);Lipase/lipooxygenase, PLAT/LH2 (1);	1.834040	0.03541	N	0.223884	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	9	0.38643	T	0.18	.	10.3058	0.43680	0.2386:0.2238:0.5376:0.0	rs10736251;rs57869460;rs10736251	381	Q17RR3	LIPR3_HUMAN	I	381	ENSP00000358232:V381I	ENSP00000358232:V381I	V	+	1	0	PNLIPRP3	118221350	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.311000	0.08124	-2.252000	0.00699	-1.460000	0.01027	GTT	G|0.030;A|0.970	0.970	strong		0.483	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
ADRA1B	147	hgsc.bcm.edu	37	5	159344446	159344446	+	Silent	SNP	C	C	T	rs3730284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:159344446C>T	ENST00000306675.3	+	1	657	c.534C>T	c.(532-534)atC>atT	p.I178I		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	178					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)			endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	TCATCTCCATCGGGCCTCTCC	0.617													C|||	70	0.0139776	0.0091	0.0144	5008	,	,		18780	0.0		0.0408	False		,,,				2504	0.0072				p.I178I		Atlas-SNP	.											.	ADRA1B	39	.	0			c.C534T						PASS	.	C		61,4345	58.1+/-94.6	1,59,2143	81.0	77.0	78.0		534	-2.5	1.0	5	dbSNP_107	78	292,8308	107.2+/-168.0	5,282,4013	no	coding-synonymous	ADRA1B	NM_000679.3		6,341,6156	TT,TC,CC		3.3953,1.3845,2.7141		178/521	159344446	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	147	exon1			CTCCATCGGGCCT	L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"""GPCR / Class A : Adrenoceptors : alpha"""	278	protein-coding gene	gene with protein product		104220	"""adrenergic, alpha-1B-, receptor"""				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.534C>T	5.37:g.159344446C>T		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	191	127	0.664921	NM_000679	B0LPE1	Silent	SNP	ENST00000306675.3	37	CCDS4347.1																																																																																			C|0.976;T|0.024	0.024	strong		0.617	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1		
GLB1L3	112937	hgsc.bcm.edu	37	11	134147600	134147600	+	Silent	SNP	T	T	C	rs76849136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:134147600T>C	ENST00000431683.2	+	3	156	c.156T>C	c.(154-156)aaT>aaC	p.N52N	GLB1L3_ENST00000389887.5_Silent_p.N52N	NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	52					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		CCAGGTTTAATTGGTCTCATC	0.562													T|||	51	0.0101837	0.0015	0.0101	5008	,	,		17048	0.003		0.0368	False		,,,				2504	0.002				p.N52N		Atlas-SNP	.											.	GLB1L3	102	.	0			c.T156C						PASS	.	T		37,4025		0,37,1994	29.0	31.0	30.0		156	-10.1	0.0	11	dbSNP_132	30	221,8203		1,219,3992	no	coding-synonymous	GLB1L3	NM_001080407.2		1,256,5986	CC,CT,TT		2.6235,0.9109,2.0663		52/654	134147600	258,12228	2031	4212	6243	SO:0001819	synonymous_variant	112937	exon3			GTTTAATTGGTCT		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.156T>C	11.37:g.134147600T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Silent	SNP	ENST00000431683.2	37	CCDS44780.1																																																																																			T|0.981;C|0.019	0.019	strong		0.562	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416	
CBWD3	445571	hgsc.bcm.edu	37	9	70871836	70871836	+	Splice_Site	SNP	C	C	G	rs376362566		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:70871836C>G	ENST00000360171.6	+	5	981		c.e5-1		CBWD3_ENST00000377342.5_Intron	NM_201453.2	NP_958861.2	Q5JTY5	CBWD3_HUMAN	COBW domain containing 3								ATP binding (GO:0005524)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TATATTTTCACGTGCAGTGGC	0.289																																					.		Atlas-SNP	.											CBWD3,rectum,carcinoma,-1,1	CBWD3	10	1	0			c.431-1C>G						scavenged	.						25.0	31.0	29.0					9																	70871836		2190	4250	6440	SO:0001630	splice_region_variant	445571	exon5			TTTTCACGTGCAG	BC069006	CCDS35038.1, CCDS35038.2	9q13	2014-05-06			ENSG00000196873	ENSG00000196873			18519	protein-coding gene	gene with protein product		611080				15233989, 12421752	Standard	XM_005277637		Approved	bA561O23.1	uc004aga.4	Q5JTY5	OTTHUMG00000184383	ENST00000360171.6:c.431-1C>G	9.37:g.70871836C>G		Somatic	560	4	0.00714286		WXS	Illumina HiSeq	Phase_I	445	10	0.0224719	NM_201453	B4DNG9|Q6VB91	Splice_Site	SNP	ENST00000360171.6	37	CCDS35038.1	.	.	.	.	.	.	.	.	.	.	c	14.78	2.637800	0.47049	.	.	ENSG00000196873	ENST00000360171;ENST00000447896;ENST00000455061;ENST00000455820;ENST00000377344	.	.	.	3.38	3.38	0.38709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.714	0.51641	0.0:0.1812:0.8188:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CBWD3	70061656	1.000000	0.71417	0.991000	0.47740	0.802000	0.45316	7.061000	0.76699	0.543000	0.28864	-0.676000	0.03789	.	C|0.500;G|0.500	0.500	weak		0.289	CBWD3-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052526.1	NM_201453	Intron
VSIG10L	147645	hgsc.bcm.edu	37	19	51841417	51841417	+	Missense_Mutation	SNP	C	C	T	rs34380065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51841417C>T	ENST00000335624.4	-	6	1774	c.1775G>A	c.(1774-1776)cGg>cAg	p.R592Q	CTD-2616J11.16_ENST00000594311.1_RNA|CTD-2616J11.16_ENST00000601148.1_RNA	NM_001163922.1	NP_001157394.1	Q86VR7	VS10L_HUMAN	V-set and immunoglobulin domain containing 10 like	592			R -> Q (in dbSNP:rs34380065). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)	4						CTCCCCCAACCGTGTCTCTGC	0.652													C|||	2851	0.569289	0.4644	0.4654	5008	,	,		13538	0.6151		0.5636	False		,,,				2504	0.7434				p.R592Q		Atlas-SNP	.											.	VSIG10L	40	.	0			c.G1775A						PASS	.	C	GLN/ARG	659,717		171,317,200	6.0	7.0	7.0		1775	-8.4	0.0	19	dbSNP_126	7	1876,1278		588,700,289	yes	missense	VSIG10L	NM_001163922.1	43	759,1017,489	TT,TC,CC		40.52,47.8924,44.0397	benign	592/868	51841417	2535,1995	688	1577	2265	SO:0001583	missense	147645	exon6			CCCAACCGTGTCT		CCDS54300.1	19q13.41	2013-01-11				ENSG00000186806		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27111	protein-coding gene	gene with protein product						12477932	Standard	NM_001163922		Approved		uc002pwf.3	Q86VR7		ENST00000335624.4:c.1775G>A	19.37:g.51841417C>T	ENSP00000335623:p.Arg592Gln	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_001163922		Missense_Mutation	SNP	ENST00000335624.4	37	CCDS54300.1	1153	0.5279304029304029	224	0.45528455284552843	162	0.44751381215469616	352	0.6153846153846154	415	0.5474934036939314	C	8.276	0.814392	0.16607	0.478924	0.5948	ENSG00000186806	ENST00000335624	T	0.27890	1.64	5.12	-8.41	0.00961	.	0.956791	0.08552	N	0.928865	T	0.00012	0.0000	L	0.41027	1.25	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.49341	-0.8950	9	0.13853	T	0.58	-4.3012	2.0607	0.03592	0.1109:0.2745:0.1805:0.4341	rs34380065;rs58868085	592	Q86VR7	VS10L_HUMAN	Q	592	ENSP00000335623:R592Q	ENSP00000335623:R592Q	R	-	2	0	VSIG10L	56533229	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.742000	0.01835	-0.736000	0.04831	-0.367000	0.07326	CGG	C|0.464;T|0.536	0.536	strong		0.652	VSIG10L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464535.1	NM_001163922	
EYS	346007	hgsc.bcm.edu	37	6	66044927	66044927	+	Missense_Mutation	SNP	T	T	C	rs61753610	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:66044927T>C	ENST00000370621.3	-	11	2238	c.1712A>G	c.(1711-1713)cAa>cGa	p.Q571R	EYS_ENST00000370618.3_Missense_Mutation_p.Q571R|EYS_ENST00000393380.2_Missense_Mutation_p.Q571R|EYS_ENST00000342421.5_Missense_Mutation_p.Q571R|EYS_ENST00000370616.2_Missense_Mutation_p.Q571R|EYS_ENST00000503581.1_Missense_Mutation_p.Q571R			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	571	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.		Q -> R (in dbSNP:rs61753610). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTCATTTTCTTGATCATCAGT	0.348													T|||	622	0.124201	0.0083	0.1902	5008	,	,		17073	0.121		0.17	False		,,,				2504	0.1902				p.Q571R		Atlas-SNP	.											.	EYS	527	.	0			c.A1712G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN	148,4258	101.6+/-140.2	0,148,2055	177.0	162.0	167.0		1712,1712,1712	2.2	0.0	6	dbSNP_129	167	1485,7115	282.1+/-295.4	143,1199,2958	yes	missense,missense,missense	EYS	NM_198283.1,NM_001142801.1,NM_001142800.1	43,43,43	143,1347,5013	CC,CT,TT		17.2674,3.3591,12.5557	benign,benign,benign	571/595,571/620,571/3145	66044927	1633,11373	2203	4300	6503	SO:0001583	missense	346007	exon11			TTTTCTTGATCAT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1712A>G	6.37:g.66044927T>C	ENSP00000359655:p.Gln571Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	170	75	0.441176	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		263	0.12042124542124542	6	0.012195121951219513	63	0.17403314917127072	66	0.11538461538461539	128	0.16886543535620052	t	8.268	0.812815	0.16537	0.033591	0.172674	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99	3.47	2.23	0.28157	.	.	.	.	.	T	0.02533	0.0077	N	0.08118	0	0.80722	P	0.0	B;B;B	0.32829	0.218;0.386;0.267	B;B;B	0.28139	0.058;0.086;0.039	T	0.47086	-0.9144	8	0.19147	T	0.46	.	6.7297	0.23377	0.0:0.0:0.2425:0.7575	rs61753610	571;571;571	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	R	571	ENSP00000424243:Q571R;ENSP00000359655:Q571R;ENSP00000359650:Q571R;ENSP00000377042:Q571R;ENSP00000341818:Q571R;ENSP00000359652:Q571R	ENSP00000341818:Q571R	Q	-	2	0	EYS	66101648	0.995000	0.38212	0.008000	0.14137	0.032000	0.12392	1.502000	0.35704	0.326000	0.23384	0.402000	0.26972	CAA	T|0.875;C|0.125	0.125	strong		0.348	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
MAGEC3	139081	hgsc.bcm.edu	37	X	140983127	140983127	+	Missense_Mutation	SNP	G	G	A	rs176026	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:140983127G>A	ENST00000298296.1	+	5	982	c.982G>A	c.(982-984)Gca>Aca	p.A328T	MAGEC3_ENST00000544766.1_5'UTR|MAGEC3_ENST00000409007.1_5'Flank|MAGEC3_ENST00000443323.2_Intron|MAGEC3_ENST00000536088.1_Intron|MAGEC3_ENST00000448920.1_Missense_Mutation_p.A80T|MAGEC3_ENST00000483584.1_3'UTR	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	328	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.		A -> T (in dbSNP:rs176026).							NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					AGGACCTGAAGCATTTTGCGA	0.597													-|||	2328	0.616689	0.326	0.5202	3775	,	,		7453	0.3681		0.7018	False		,,,				2504	0.4693				p.A328T		Atlas-SNP	.											.	MAGEC3	228	.	0			c.G982A						PASS	.	G	THR/ALA,	1962,1872		455,769,283,408,287	128.0	113.0	118.0		982,	0.7	0.0	X	dbSNP_79	118	6251,477		2087,325,1752,16,120	yes	missense,utr-5	MAGEC3	NM_138702.1,NM_177456.2	58,	2542,1094,2035,424,407	AA,AG,A,GG,G		7.0898,48.8263,22.2401	probably-damaging,	328/644,	140983127	8213,2349	2202	4300	6502	SO:0001583	missense	139081	exon5			CCTGAAGCATTTT	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.982G>A	X.37:g.140983127G>A	ENSP00000298296:p.Ala328Thr	Somatic	319	1	0.0031348		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	1121	0.675708257986739	126	0.3181818181818182	134	0.6090909090909091	139	0.32175925925925924	375	0.8680555555555556	N	8.760	0.923358	0.18056	0.511737	0.929102	ENSG00000165509	ENST00000298296;ENST00000448920	T;T	0.41065	3.78;1.01	0.684	0.684	0.18003	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	D	0.57571	0.98	P	0.57009	0.811	T	0.37009	-0.9724	7	0.19147	T	0.46	.	.	.	.	rs176026;rs423893;rs863553;rs1183812;rs58520044;rs176026	328	Q8TD91	MAGC3_HUMAN	T	328;80	ENSP00000298296:A328T;ENSP00000395092:A80T	ENSP00000298296:A328T	A	+	1	0	MAGEC3	140810793	0.001000	0.12720	0.003000	0.11579	0.005000	0.04900	0.475000	0.22164	0.623000	0.30267	0.165000	0.16767	GCA	G|0.294;A|0.706	0.706	strong		0.597	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
ATG2A	23130	hgsc.bcm.edu	37	11	64680819	64680819	+	Silent	SNP	G	G	A	rs618006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64680819G>A	ENST00000377264.3	-	5	757	c.645C>T	c.(643-645)gaC>gaT	p.D215D	ATG2A_ENST00000421419.2_Silent_p.D215D	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	215					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GCTGATGCACGTCCACCGGCG	0.682													G|||	2763	0.551717	0.4054	0.4697	5008	,	,		16265	0.5427		0.7217	False		,,,				2504	0.6421				p.D215D		Atlas-SNP	.											.	ATG2A	133	.	0			c.C645T						PASS	.	G		2063,2335		508,1047,644	19.0	21.0	20.0		645	-4.5	0.9	11	dbSNP_83	20	6239,2351		2263,1713,319	no	coding-synonymous	ATG2A	NM_015104.2		2771,2760,963	AA,AG,GG		27.369,46.9077,36.0795		215/1939	64680819	8302,4686	2199	4295	6494	SO:0001819	synonymous_variant	23130	exon5			ATGCACGTCCACC		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.645C>T	11.37:g.64680819G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	37	CCDS31602.1	1277	0.5847069597069597	217	0.4410569105691057	187	0.5165745856353591	310	0.541958041958042	563	0.7427440633245382	g	9.117	1.008019	0.19199	0.469077	0.72631	ENSG00000110046	ENST00000418259	.	.	.	3.97	-4.51	0.03483	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999987508	.	.	.	.	.	.	T	0.21895	-1.0232	3	.	.	.	.	12.4469	0.55654	0.7808:0.0:0.2192:0.0	rs618006;rs618006	.	.	.	C	17	.	.	R	-	1	0	ATG2A	64437395	0.713000	0.27926	0.949000	0.38748	0.809000	0.45718	-0.239000	0.08965	-0.852000	0.04141	0.450000	0.29827	CGT	G|0.401;A|0.599	0.599	strong		0.682	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
SGOL2	151246	hgsc.bcm.edu	37	2	201437048	201437048	+	Missense_Mutation	SNP	A	A	G	rs17532665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:201437048A>G	ENST00000357799.4	+	7	2077	c.1979A>G	c.(1978-1980)aAc>aGc	p.N660S		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	660			N -> S (in dbSNP:rs17532665). {ECO:0000269|Ref.1}.		meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						ATCTCTGAAAACATAGAAGTT	0.353													A|||	343	0.0684904	0.0454	0.0677	5008	,	,		17373	0.002		0.1501	False		,,,				2504	0.0849				p.N660S		Atlas-SNP	.											.	SGOL2	126	.	0			c.A1979G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	205,3409		4,197,1606	55.0	55.0	55.0		1979,1979,1979	4.1	0.0	2	dbSNP_123	55	1245,6869		95,1055,2907	yes	missense,missense,missense	SGOL2	NM_001160033.1,NM_001160046.1,NM_152524.5	46,46,46	99,1252,4513	GG,GA,AA		15.3439,5.6724,12.3636	probably-damaging,probably-damaging,probably-damaging	660/1261,660/1262,660/1266	201437048	1450,10278	1807	4057	5864	SO:0001583	missense	151246	exon7			CTGAAAACATAGA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1979A>G	2.37:g.201437048A>G	ENSP00000350447:p.Asn660Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	176	89	0.505682	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	164	0.07509157509157509	26	0.052845528455284556	26	0.0718232044198895	1	0.0017482517482517483	111	0.14643799472295516	A	8.418	0.845831	0.16963	0.056724	0.153439	ENSG00000163535	ENST00000357799	T	0.14640	2.49	5.25	4.09	0.47781	.	0.000000	0.56097	D	0.000027	T	0.00073	0.0002	L	0.60455	1.87	0.48087	P	4.1800000000002946E-4	P;P;P	0.46277	0.875;0.875;0.875	B;B;B	0.40825	0.341;0.341;0.341	T	0.23119	-1.0197	9	0.37606	T	0.19	-6.109	7.7712	0.29010	0.9071:0.0:0.0929:0.0	rs17532665;rs17532665	660;660;660	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	S	660	ENSP00000350447:N660S	ENSP00000350447:N660S	N	+	2	0	SGOL2	201145293	0.436000	0.25586	0.010000	0.14722	0.022000	0.10575	2.484000	0.45242	1.126000	0.42016	0.477000	0.44152	AAC	A|0.914;G|0.086	0.086	strong		0.353	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
HCLS1	3059	hgsc.bcm.edu	37	3	121354583	121354583	+	Splice_Site	SNP	G	G	A	rs3772126	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121354583G>A	ENST00000314583.3	-	9	781	c.690C>T	c.(688-690)gcC>gcT	p.A230A	HCLS1_ENST00000428394.2_Splice_Site_p.A193A|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	230					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		AAGCCTCACCGGCTTCTATGG	0.507													G|||	1093	0.218251	0.0507	0.1571	5008	,	,		19404	0.4802		0.2505	False		,,,				2504	0.1851				p.A230A		Atlas-SNP	.											.	HCLS1	78	.	0			c.C690T						PASS	.	G		329,4077	172.7+/-202.6	12,305,1886	127.0	130.0	129.0		690	2.2	1.0	3	dbSNP_107	129	2112,6488	365.1+/-333.8	278,1556,2466	yes	coding-synonymous-near-splice	HCLS1	NM_005335.4		290,1861,4352	AA,AG,GG		24.5581,7.4671,18.7683		230/487	121354583	2441,10565	2203	4300	6503	SO:0001630	splice_region_variant	3059	exon9			CTCACCGGCTTCT		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.691+1C>T	3.37:g.121354583G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	144	78	0.541667	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Silent	SNP	ENST00000314583.3	37	CCDS3003.1																																																																																			G|0.788;A|0.212	0.212	strong		0.507	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	Silent
SLC14A2	8170	hgsc.bcm.edu	37	18	43262359	43262359	+	Missense_Mutation	SNP	G	G	A	rs3745009	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:43262359G>A	ENST00000255226.6	+	20	3454	c.2638G>A	c.(2638-2640)Gcc>Acc	p.A880T	SLC14A2_ENST00000589658.1_Missense_Mutation_p.A357T|SLC14A2_ENST00000586448.1_Missense_Mutation_p.A880T|RP11-116O18.3_ENST00000589510.1_RNA	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	880			A -> T (in dbSNP:rs3745009). {ECO:0000269|PubMed:15489334}.		transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)	p.A880T(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAATAACCCCGCCATCTACAA	0.527													G|||	2142	0.427716	0.4024	0.3761	5008	,	,		19225	0.3869		0.4404	False		,,,				2504	0.5276				p.A880T		Atlas-SNP	.											SLC14A2,NS,carcinoma,0,2	SLC14A2	121	2	1	Substitution - Missense(1)	prostate(1)	c.G2638A	GRCh37	CM013794	SLC14A2	M	rs3745009	PASS	.	G	THR/ALA,THR/ALA	1720,2686	517.8+/-369.5	354,1012,837	271.0	262.0	265.0		2638,2638	5.1	1.0	18	dbSNP_107	265	3870,4730	544.3+/-384.6	862,2146,1292	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	58,58	1216,3158,2129	AA,AG,GG		45.0,39.0377,42.9802	benign,benign	880/921,880/921	43262359	5590,7416	2203	4300	6503	SO:0001583	missense	8170	exon21			AACCCCGCCATCT	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.2638G>A	18.37:g.43262359G>A	ENSP00000255226:p.Ala880Thr	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	211	126	0.597156	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	880	0.40293040293040294	196	0.3983739837398374	127	0.35082872928176795	223	0.38986013986013984	334	0.44063324538258575	G	15.21	2.766981	0.49574	0.390377	0.45	ENSG00000132874	ENST00000255226	T	0.51071	0.72	5.14	5.14	0.70334	.	0.110360	0.39687	N	0.001291	T	0.00012	0.0000	L	0.48877	1.53	0.09310	P	0.9999999999999103	B	0.16396	0.017	B	0.19148	0.024	T	0.43360	-0.9396	9	0.23302	T	0.38	-11.6177	18.2166	0.89887	0.0:0.0:1.0:0.0	rs3745009;rs52819242;rs58066525;rs3745009	880	Q15849	UT2_HUMAN	T	880	ENSP00000255226:A880T	ENSP00000255226:A880T	A	+	1	0	SLC14A2	41516357	0.978000	0.34361	0.967000	0.41034	0.993000	0.82548	1.970000	0.40520	2.390000	0.81377	0.561000	0.74099	GCC	G|0.573;A|0.427	0.427	strong		0.527	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
C11orf40	143501	hgsc.bcm.edu	37	11	4594648	4594648	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4594648C>G	ENST00000307616.1	-	2	195	c.196G>C	c.(196-198)Gat>Cat	p.D66H		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	66										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		ATGAACACATCCTTATCTAAG	0.433																																					p.D66H		Atlas-SNP	.											C11orf40,NS,carcinoma,0,1	C11orf40	37	1	0			c.G196C						PASS	.						164.0	146.0	152.0					11																	4594648		2201	4298	6499	SO:0001583	missense	143501	exon2			ACACATCCTTATC		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.196G>C	11.37:g.4594648C>G	ENSP00000302918:p.Asp66His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	37	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	C	5.540	0.284501	0.10513	.	.	ENSG00000171987	ENST00000307616	T	0.57107	0.42	1.49	-1.98	0.07480	.	.	.	.	.	T	0.30634	0.0771	N	0.08118	0	0.09310	N	1	D	0.58268	0.982	P	0.47603	0.551	T	0.17592	-1.0364	9	0.87932	D	0	.	1.9732	0.03410	0.2617:0.3567:0.0:0.3816	.	66	Q8WZ69	CK040_HUMAN	H	66	ENSP00000302918:D66H	ENSP00000302918:D66H	D	-	1	0	C11orf40	4551224	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-1.399000	0.02506	-0.671000	0.05274	0.563000	0.77884	GAT	.	.	none		0.433	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
CECR6	27439	hgsc.bcm.edu	37	22	17600420	17600420	+	Missense_Mutation	SNP	C	C	A	rs184892903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:17600420C>A	ENST00000331437.3	-	1	1723	c.1598G>T	c.(1597-1599)gGc>gTc	p.G533V	CECR6_ENST00000399875.1_Missense_Mutation_p.G178V|AC006946.15_ENST00000441544.1_5'Flank	NM_031890.3	NP_114096.1	Q9BXQ6	CECR6_HUMAN	cat eye syndrome chromosome region, candidate 6	533										haematopoietic_and_lymphoid_tissue(1)	1		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.221)		AGCACCGTAGCCCCCTCTGGC	0.706													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		11413	0.0		0.001	False		,,,				2504	0.0				p.G533V		Atlas-SNP	.											.	CECR6	11	.	0			c.G1598T						PASS	.	C	VAL/GLY,VAL/GLY	2,4254		0,2,2126	9.0	9.0	9.0		533,1598	3.2	0.3	22		9	20,8360		0,20,4170	no	missense,missense	CECR6	NM_001163079.1,NM_031890.3	109,109	0,22,6296	AA,AC,CC		0.2387,0.047,0.1741	probably-damaging,probably-damaging	178/224,533/579	17600420	22,12614	2128	4190	6318	SO:0001583	missense	27439	exon1			CCGTAGCCCCCTC	AF307451	CCDS13740.1, CCDS54494.1	22q11.2	2008-06-12			ENSG00000183307	ENSG00000183307			1844	protein-coding gene	gene with protein product						11381032	Standard	NM_031890		Approved		uc002zmb.2	Q9BXQ6	OTTHUMG00000030471	ENST00000331437.3:c.1598G>T	22.37:g.17600420C>A	ENSP00000329318:p.Gly533Val	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	15	11	0.733333	NM_031890	A8MYY1	Missense_Mutation	SNP	ENST00000331437.3	37	CCDS13740.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.331834	0.24167	4.7E-4	0.002387	ENSG00000183307	ENST00000399875;ENST00000331437	.	.	.	4.26	3.22	0.36961	.	0.421699	0.17930	U	0.157200	T	0.33059	0.0850	N	0.19112	0.55	0.34394	D	0.6945	P	0.37207	0.587	B	0.37989	0.262	T	0.50189	-0.8857	9	0.59425	D	0.04	.	10.2222	0.43203	0.0:0.7984:0.2016:0.0	.	533	Q9BXQ6	CECR6_HUMAN	V	178;533	.	ENSP00000329318:G533V	G	-	2	0	CECR6	15980420	0.943000	0.32029	0.307000	0.25127	0.185000	0.23345	2.249000	0.43169	1.119000	0.41883	0.561000	0.74099	GGC	.	.	weak		0.706	CECR6-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075359.4	NM_031890	
HSD3B7	80270	hgsc.bcm.edu	37	16	30999462	30999462	+	Silent	SNP	T	T	C	rs2305880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:30999462T>C	ENST00000297679.5	+	7	1161	c.1068T>C	c.(1066-1068)cgT>cgC	p.R356R	HSD3B7_ENST00000353250.5_3'UTR|AC135048.1_ENST00000602217.1_5'Flank|HSD3B7_ENST00000262520.6_3'UTR	NM_025193.3	NP_079469.2	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	356					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity (GO:0047016)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GCCGGACCCGTACCATTCTCT	0.652													C|||	2468	0.492812	0.2027	0.5692	5008	,	,		18355	0.9058		0.6362	False		,,,				2504	0.2577				p.R356R		Atlas-SNP	.											.	HSD3B7	33	.	0			c.T1068C						PASS	.	C	,,	1272,3122		184,904,1109	23.0	21.0	22.0		,,1068	2.1	1.0	16	dbSNP_100	22	5542,3058		1804,1934,562	no	utr-3,utr-3,coding-synonymous	HSD3B7	NM_001142777.1,NM_001142778.1,NM_025193.3	,,	1988,2838,1671	CC,CT,TT		35.5581,28.9486,47.5604	,,	,,356/370	30999462	6814,6180	2197	4300	6497	SO:0001819	synonymous_variant	80270	exon7			GACCCGTACCATT	AF277719	CCDS10698.1, CCDS45466.1	16p11.2	2011-09-14			ENSG00000099377	ENSG00000099377	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	18324	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 3"""	607764				11067870, 19027726	Standard	NM_001142777		Approved	C(27)-3BETA-HSD, SDR11E3	uc002eaf.2	Q9H2F3	OTTHUMG00000132417	ENST00000297679.5:c.1068T>C	16.37:g.30999462T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_025193	Q96M28|Q9BSN9	Silent	SNP	ENST00000297679.5	37	CCDS10698.1																																																																																			T|0.454;C|0.546	0.546	strong		0.652	HSD3B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255554.2		
GPR98	84059	hgsc.bcm.edu	37	5	89979698	89979698	+	Missense_Mutation	SNP	C	C	T	rs4916685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:89979698C>T	ENST00000405460.2	+	28	6056	c.5960C>T	c.(5959-5961)cCt>cTt	p.P1987L		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1987	Calx-beta 14. {ECO:0000255}.		P -> L (in dbSNP:rs4916685). {ECO:0000269|PubMed:14740321}.		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.P1987L(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AAAAACAGACCTGTTAAAGTT	0.388													C|||	1689	0.33726	0.261	0.5086	5008	,	,		19224	0.375		0.3201	False		,,,				2504	0.2975				p.P1987L		Atlas-SNP	.											GPR98,NS,carcinoma,0,1	GPR98	605	1	1	Substitution - Missense(1)	stomach(1)	c.C5960T						PASS	.	C	LEU/PRO	934,2792		124,686,1053	76.0	69.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5960	4.8	1.0	5	dbSNP_111	71	2712,5502		455,1802,1850	yes	missense	GPR98	NM_032119.3	98	579,2488,2903	TT,TC,CC		33.0168,25.0671,30.536	probably-damaging	1987/6307	89979698	3646,8294	1863	4107	5970	SO:0001583	missense	84059	exon28			ACAGACCTGTTAA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5960C>T	5.37:g.89979698C>T	ENSP00000384582:p.Pro1987Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	796	0.36446886446886445	135	0.27439024390243905	175	0.48342541436464087	245	0.42832167832167833	241	0.3179419525065963	C	16.25	3.070043	0.55539	0.250671	0.330168	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.29397	1.57	5.71	4.84	0.62591	Na-Ca exchanger/integrin-beta4 (2);	0.102433	0.64402	D	0.000002	T	0.00012	0.0000	M	0.75447	2.3	0.09310	P	1.0	D	0.76494	0.999	D	0.81914	0.995	T	0.32903	-0.9889	9	0.02654	T	1	.	14.7907	0.69841	0.0:0.9306:0.0:0.0694	rs4916685;rs57833806;rs4916685	1987	Q8WXG9	GPR98_HUMAN	L	1987	ENSP00000384582:P1987L	ENSP00000296619:P1987L	P	+	2	0	GPR98	90015454	1.000000	0.71417	0.990000	0.47175	0.778000	0.44026	3.803000	0.55560	1.419000	0.47118	0.591000	0.81541	CCT	C|0.655;T|0.345	0.345	strong		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
USP26	83844	hgsc.bcm.edu	37	X	132161159	132161159	+	Missense_Mutation	SNP	G	G	A	rs35397110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:132161159G>A	ENST00000511190.1	-	6	1559	c.1090C>T	c.(1090-1092)Ctt>Ttt	p.L364F	USP26_ENST00000406273.1_Missense_Mutation_p.L364F|USP26_ENST00000370832.1_Missense_Mutation_p.L364F	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	364	USP.		L -> F (in dbSNP:rs35397110). {ECO:0000269|PubMed:15970005, ECO:0000269|PubMed:18377898, ECO:0000269|PubMed:18927127}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					GCCTTTTTAAGATTCAAGAGT	0.373													g|||	61	0.0161589	0.0038	0.0101	3775	,	,		13219	0.0		0.0457	False		,,,				2504	0.0031				p.L364F	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.C1090T	GRCh37	CM056721	USP26	M	rs35397110	PASS	.		PHE/LEU	34,3801		0,29,5,1603,566	64.0	63.0	63.0		1090	-4.0	0.0	X	dbSNP_126	63	421,6305		8,297,108,2122,1764	yes	missense	USP26	NM_031907.1	22	8,326,113,3725,2330	AA,AG,A,GG,G		6.2593,0.8866,4.3083	benign	364/914	132161159	455,10106	2203	4299	6502	SO:0001583	missense	83844	exon1			TTTTAAGATTCAA	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"""Ubiquitin-specific peptidases"""	13485	protein-coding gene	gene with protein product		300309	"""ubiquitin specific protease 26"""			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.1090C>T	X.37:g.132161159G>A	ENSP00000423390:p.Leu364Phe	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	136	133	0.977941	NM_031907	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	37	CCDS14635.1	47	0.028330319469559977	1	0.0020325203252032522	4	0.0111731843575419	0	0.0	28	0.03814713896457766	g	9.121	1.009071	0.19199	0.008866	0.062593	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.74526	-0.85;-0.85;-0.85	3.78	-4.02	0.04034	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.458295	0.16597	N	0.207518	T	0.05914	0.0154	N	0.05124	-0.11	0.80722	P	0.0	B	0.10296	0.003	B	0.12156	0.007	T	0.15122	-1.0448	9	0.11794	T	0.64	-4.0857	2.0978	0.03672	0.1422:0.1889:0.4345:0.2344	rs35397110;rs61751330	364	Q9BXU7	UBP26_HUMAN	F	364	ENSP00000359869:L364F;ENSP00000423390:L364F;ENSP00000384360:L364F	ENSP00000359869:L364F	L	-	1	0	USP26	131988825	0.086000	0.21541	0.001000	0.08648	0.015000	0.08874	0.254000	0.18314	-0.932000	0.03742	-0.432000	0.05891	CTT	G|0.963;A|0.037	0.037	strong		0.373	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907	
ENPP4	22875	hgsc.bcm.edu	37	6	46107752	46107752	+	Missense_Mutation	SNP	C	C	G	rs7451713	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46107752C>G	ENST00000321037.4	+	2	662	c.432C>G	c.(430-432)caC>caG	p.H144Q		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	144			H -> Q (in dbSNP:rs7451713). {ECO:0000269|PubMed:14702039}.		blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						TACCCATTCACGATACCATCT	0.413													C|||	2262	0.451677	0.2186	0.4467	5008	,	,		20687	0.4444		0.5348	False		,,,				2504	0.6922				p.H144Q		Atlas-SNP	.											.	ENPP4	44	.	0			c.C432G						PASS	.	C	GLN/HIS	1130,3276	402.4+/-332.3	149,832,1222	184.0	171.0	176.0		432	2.1	0.9	6	dbSNP_116	176	4587,4013	597.7+/-393.8	1220,2147,933	yes	missense	ENPP4	NM_014936.4	24	1369,2979,2155	GG,GC,CC		46.6628,25.6468,43.9566	benign	144/454	46107752	5717,7289	2203	4300	6503	SO:0001583	missense	22875	exon2			CATTCACGATACC	AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.432C>G	6.37:g.46107752C>G	ENSP00000318066:p.His144Gln	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	182	74	0.406593	NM_014936	A8K5G1|Q7L2N1	Missense_Mutation	SNP	ENST00000321037.4	37	CCDS34468.1	927	0.42445054945054944	106	0.21544715447154472	178	0.49171270718232046	235	0.41083916083916083	408	0.5382585751978892	C	9.135	1.012363	0.19277	0.256468	0.533372	ENSG00000001561	ENST00000321037;ENST00000371401	T	0.71698	-0.59	5.97	2.08	0.27032	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.351086	0.36665	N	0.002465	T	0.28101	0.0693	N	0.16201	0.385	0.28757	P	0.9011321999999999	B	0.22909	0.077	B	0.28709	0.093	T	0.06716	-1.0811	9	0.09084	T	0.74	-13.6269	10.5855	0.45280	0.0:0.7418:0.0:0.2582	rs7451713;rs7451713	144	Q9Y6X5	ENPP4_HUMAN	Q	144	ENSP00000318066:H144Q	ENSP00000318066:H144Q	H	+	3	2	ENPP4	46215711	0.994000	0.37717	0.929000	0.37066	0.507000	0.33981	0.713000	0.25794	0.088000	0.17205	-0.345000	0.07892	CAC	C|0.562;G|0.438	0.438	strong		0.413	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2		
MYH11	4629	hgsc.bcm.edu	37	16	15870032	15870032	+	Splice_Site	SNP	A	A	G	rs587781079|rs34341838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15870032A>G	ENST00000300036.5	-	8	901	c.792T>C	c.(790-792)taT>taC	p.Y264Y	MYH11_ENST00000396324.3_Splice_Site_p.Y271Y|MYH11_ENST00000576790.2_Splice_Site_p.Y264Y|MYH11_ENST00000452625.2_Splice_Site_p.Y271Y	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	264	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TTTCTAGCAGATCTGGTTTGG	0.493			T	CBFB	AML								A|||	59	0.0117812	0.0023	0.0173	5008	,	,		21647	0.0		0.0417	False		,,,				2504	0.002				p.Y271Y		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.T813C						PASS	.	A	,,,	40,4354	43.1+/-76.7	0,40,2157	242.0	228.0	233.0		813,813,792,792	-0.4	1.0	16	dbSNP_126	233	364,8236	120.8+/-180.0	5,354,3941	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	5,394,6098	GG,GA,AA		4.2326,0.9103,3.1091	,,,	271/1946,271/1980,264/1973,264/1939	15870032	404,12590	2197	4300	6497	SO:0001630	splice_region_variant	4629	exon9			TAGCAGATCTGGT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.791-1T>C	16.37:g.15870032A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	184	94	0.51087	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			A|0.972;G|0.028	0.028	strong		0.493	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	Silent
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921209	12921209	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12921209C>T	ENST00000240189.2	+	4	1087	c.1000C>T	c.(1000-1002)Cgc>Tgc	p.R334C		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	334					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGCTGTTCCGCATCAGTCT	0.507																																					p.R334C		Atlas-SNP	.											PRAMEF2,NS,chondrosarcoma,0,1	PRAMEF2	85	1	0			c.C1000T						scavenged	.						181.0	181.0	181.0					1																	12921209		2202	4294	6496	SO:0001583	missense	65122	exon4			CTGTTCCGCATCA		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.1000C>T	1.37:g.12921209C>T	ENSP00000240189:p.Arg334Cys	Somatic	363	0	0		WXS	Illumina HiSeq	Phase_I	285	6	0.0210526	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	.	.	.	.	.	.	.	.	.	.	C	3.798	-0.042233	0.07452	.	.	ENSG00000120952	ENST00000240189	T	0.00958	5.5	0.766	-1.53	0.08611	.	4.154090	0.00851	N	0.001827	T	0.00875	0.0029	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.09377	0.004	T	0.47661	-0.9100	10	0.40728	T	0.16	.	4.5404	0.12054	0.0:0.4155:0.5845:0.0	.	334	O60811	PRAM2_HUMAN	C	334	ENSP00000240189:R334C	ENSP00000240189:R334C	R	+	1	0	PRAMEF2	12843796	0.000000	0.05858	0.001000	0.08648	0.165000	0.22458	-3.787000	0.00366	-0.202000	0.10268	0.089000	0.15464	CGC	.	.	none		0.507	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
FSIP1	161835	hgsc.bcm.edu	37	15	39910167	39910167	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:39910167C>T	ENST00000350221.3	-	11	1677	c.1468G>A	c.(1468-1470)Gga>Aga	p.G490R		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	490										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		ATGTTATGTCCAGTCAAGGCT	0.373																																					p.G490R		Atlas-SNP	.											FSIP1,extremity,malignant_melanoma,+1,1	FSIP1	53	1	0			c.G1468A						scavenged	.						144.0	136.0	139.0					15																	39910167		2200	4297	6497	SO:0001583	missense	161835	exon11			TATGTCCAGTCAA	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1468G>A	15.37:g.39910167C>T	ENSP00000280236:p.Gly490Arg	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	278	3	0.0107914	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.654068	0.29425	.	.	ENSG00000150667	ENST00000350221	T	0.13901	2.55	4.94	4.02	0.46733	.	0.200938	0.30979	N	0.008495	T	0.21427	0.0516	L	0.29908	0.895	0.09310	N	1	D	0.63046	0.992	D	0.67382	0.951	T	0.03695	-1.1012	9	.	.	.	-3.3792	10.8356	0.46685	0.0:0.9127:0.0:0.0873	.	490	Q8NA03	FSIP1_HUMAN	R	490	ENSP00000280236:G490R	.	G	-	1	0	FSIP1	37697459	0.806000	0.28996	0.106000	0.21319	0.014000	0.08584	1.966000	0.40481	1.444000	0.47605	0.655000	0.94253	GGA	.	.	none		0.373	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
NADSYN1	55191	hgsc.bcm.edu	37	11	71192439	71192439	+	Silent	SNP	C	C	A	rs59379414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71192439C>A	ENST00000319023.2	+	12	1224	c.1036C>A	c.(1036-1038)Cga>Aga	p.R346R	NADSYN1_ENST00000539574.1_Silent_p.R86R|NADSYN1_ENST00000530055.1_5'UTR|NADSYN1_ENST00000526039.2_3'UTR	NM_018161.4	NP_060631.2	Q6IA69	NADE_HUMAN	NAD synthetase 1	346	Ligase. {ECO:0000250}.				NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|NAD+ synthase (glutamine-hydrolyzing) activity (GO:0003952)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	25					L-Glutamine(DB00130)	TTTTTTAAGACGAAGTCAACA	0.527													C|||	522	0.104233	0.1762	0.0346	5008	,	,		17314	0.0863		0.0646	False		,,,				2504	0.1155				p.R346R	Ovarian(79;763 1781 6490 50276)	Atlas-SNP	.											NADSYN1,NS,carcinoma,-1,2	NADSYN1	48	2	0			c.C1036A						PASS	.	C		601,3799	261.6+/-264.4	45,511,1644	90.0	100.0	97.0		1036	5.1	0.3	11	dbSNP_129	97	441,8147	134.3+/-191.7	10,421,3863	no	coding-synonymous	NADSYN1	NM_018161.4		55,932,5507	AA,AC,CC		5.1351,13.6591,8.0228		346/707	71192439	1042,11946	2200	4294	6494	SO:0001819	synonymous_variant	55191	exon12			TTAAGACGAAGTC	AB091316	CCDS8201.1	11q13.4	2008-02-05				ENSG00000172890			29832	protein-coding gene	gene with protein product		608285				12547821	Standard	NM_018161		Approved	FLJ10631	uc001oqn.3	Q6IA69		ENST00000319023.2:c.1036C>A	11.37:g.71192439C>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_018161	B3KUU4|Q86SN2|Q9HA25|Q9NVM8	Silent	SNP	ENST00000319023.2	37	CCDS8201.1																																																																																			C|0.918;A|0.082	0.082	strong		0.527	NADSYN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394356.1	NM_018161	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969085	49969085	+	Silent	SNP	C	C	T	rs10853810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49969085C>T	ENST00000293350.4	+	13	1822	c.1659C>T	c.(1657-1659)aaC>aaT	p.N553N	CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Silent_p.N388N|ALDH16A1_ENST00000540132.1_Silent_p.N390N|ALDH16A1_ENST00000455361.2_Silent_p.N502N	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	553						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CGTCTGGCAACCTCCATGGCT	0.657													C|||	1048	0.209265	0.3427	0.2277	5008	,	,		15702	0.005		0.335	False		,,,				2504	0.0971				p.N553N		Atlas-SNP	.											ALDH16A1,colon,carcinoma,0,1	ALDH16A1	54	1	0			c.C1659T						PASS	.	C	,	1393,3013	451.2+/-349.6	220,953,1030	40.0	42.0	41.0		1506,1659	-4.2	0.3	19	dbSNP_120	41	3014,5586	460.2+/-365.1	526,1962,1812	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	746,2915,2842	TT,TC,CC		35.0465,31.616,33.8844	,	502/752,553/803	49969085	4407,8599	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon13			TGGCAACCTCCAT	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1659C>T	19.37:g.49969085C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			C|0.695;T|0.305	0.305	strong		0.657	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
CACNA2D2	9254	hgsc.bcm.edu	37	3	50513613	50513613	+	Missense_Mutation	SNP	C	C	T	rs41291734	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50513613C>T	ENST00000479441.1	-	2	223	c.224G>A	c.(223-225)cGg>cAg	p.R75Q	CACNA2D2_ENST00000424201.2_Missense_Mutation_p.R75Q|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.R75Q|CACNA2D2_ENST00000487413.1_5'UTR|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.R75Q|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.R6Q|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.R75Q|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.R75Q|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.R75Q			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	75					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CTCCAGACGCCGGGCCCAGTG	0.662													C|||	41	0.0081869	0.003	0.0115	5008	,	,		17463	0.0		0.0258	False		,,,				2504	0.0031				p.R75Q		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.G224A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	31,4371		0,31,2170	40.0	37.0	38.0		224,224,224	5.0	1.0	3	dbSNP_127	38	270,8326		6,258,4034	yes	missense,missense,missense	CACNA2D2	NM_001005505.1,NM_001174051.1,NM_006030.2	43,43,43	6,289,6204	TT,TC,CC		3.141,0.7042,2.3157	possibly-damaging,possibly-damaging,possibly-damaging	75/1146,75/1151,75/1144	50513613	301,12697	2201	4298	6499	SO:0001583	missense	9254	exon2			AGACGCCGGGCCC	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"""Calcium channel subunits"""	1400	protein-coding gene	gene with protein product	"""gene 26"""	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.224G>A	3.37:g.50513613C>T	ENSP00000418081:p.Arg75Gln	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	37	24	0.648649	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	37	CCDS54588.1	29	0.013278388278388278	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	22	0.029023746701846966	C	25.9	4.684093	0.88639	0.007042	0.03141	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	T;T;T;T;T;T;T;T	0.05925	3.37;3.37;3.37;3.4;3.37;3.37;3.37;3.37	5.01	5.01	0.66863	.	0.191369	0.34178	N	0.004184	T	0.02610	0.0079	L	0.46157	1.445	0.33882	D	0.636216	D;D	0.56521	0.962;0.976	B;B	0.44108	0.32;0.441	T	0.13656	-1.0501	10	0.45353	T	0.12	-20.2567	13.6709	0.62424	0.0:1.0:0.0:0.0	rs41291734;rs62260818	75;75	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	Q	75;75;75;6;75;75;75;75	ENSP00000407393:R75Q;ENSP00000404631:R75Q;ENSP00000266039:R75Q;ENSP00000354228:R6Q;ENSP00000390526:R75Q;ENSP00000378519:R75Q;ENSP00000390329:R75Q;ENSP00000418081:R75Q	ENSP00000266039:R75Q	R	-	2	0	CACNA2D2	50488617	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.985000	0.56930	2.591000	0.87537	0.561000	0.74099	CGG	C|0.981;T|0.019	0.019	strong		0.662	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030	
N4BP2	55728	hgsc.bcm.edu	37	4	40119501	40119501	+	Silent	SNP	T	T	C	rs1128372	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:40119501T>C	ENST00000261435.6	+	8	2093	c.1677T>C	c.(1675-1677)caT>caC	p.H559H		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	559					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						GTAACATTCATGGGGTAAGCA	0.313													T|||	569	0.113618	0.0106	0.255	5008	,	,		15891	0.0208		0.2207	False		,,,				2504	0.138				p.H559H		Atlas-SNP	.											.	N4BP2	166	.	0			c.T1677C						PASS	.	T		214,4192	129.4+/-166.1	10,194,1999	79.0	74.0	76.0		1677	4.1	1.0	4	dbSNP_86	76	1982,6618	345.4+/-325.7	235,1512,2553	no	coding-synonymous	N4BP2	NM_018177.4		245,1706,4552	CC,CT,TT		23.0465,4.857,16.8845		559/1771	40119501	2196,10810	2203	4300	6503	SO:0001819	synonymous_variant	55728	exon8			CATTCATGGGGTA	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.1677T>C	4.37:g.40119501T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Silent	SNP	ENST00000261435.6	37	CCDS3457.1	286	0.13095238095238096	6	0.012195121951219513	97	0.26795580110497236	10	0.017482517482517484	173	0.22823218997361477	T	5.040	0.193016	0.09599	0.04857	0.230465	ENSG00000078177	ENST00000513269	.	.	.	5.3	4.11	0.48088	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999999	.	.	.	.	.	.	T	0.02081	-1.1217	3	.	.	.	-15.8173	12.6937	0.56990	0.0:0.0716:0.0:0.9284	rs1128372;rs16995561;rs17439970;rs1128372	.	.	.	R	206	.	.	W	+	1	0	N4BP2	39795896	1.000000	0.71417	0.998000	0.56505	0.740000	0.42216	2.177000	0.42509	0.322000	0.23283	-1.139000	0.01908	TGG	T|0.851;C|0.149	0.149	strong		0.313	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989365	60989365	+	Missense_Mutation	SNP	C	C	T	rs3810553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60989365C>T	ENST00000252998.1	-	10	1198	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	348			D -> N (in dbSNP:rs3810553). {ECO:0000269|PubMed:15489334}.			extracellular space (GO:0005615)											AGGCGAAGGTCCTGCATGCCC	0.711													C|||	1395	0.278554	0.1006	0.3487	5008	,	,		12631	0.4266		0.3211	False		,,,				2504	0.273				p.D348N		Atlas-SNP	.											.	.	.	.	0			c.G1042A						PASS	.	C	ASN/ASP	468,3542		31,406,1568	5.0	5.0	5.0		1042	0.9	0.1	20	dbSNP_107	5	1966,5974		282,1402,2286	yes	missense	C20orf151	NM_080833.2	23	313,1808,3854	TT,TC,CC		24.7607,11.6708,20.3682	benign	348/665	60989365	2434,9516	2005	3970	5975	SO:0001583	missense	140893	exon10			GAAGGTCCTGCAT	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1042G>A	20.37:g.60989365C>T	ENSP00000252998:p.Asp348Asn	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	698	0.31959706959706957	68	0.13821138211382114	110	0.30386740331491713	264	0.46153846153846156	256	0.33773087071240104	C	12.04	1.817865	0.32145	0.116708	0.247607	ENSG00000130701	ENST00000252998	T	0.48201	0.82	5.05	0.895	0.19247	.	0.389162	0.26183	N	0.025844	T	0.00012	0.0000	L	0.46157	1.445	0.39568	P	0.030768000000000018	B	0.30033	0.266	B	0.31290	0.127	T	0.45731	-0.9241	9	0.35671	T	0.21	-13.9181	5.4657	0.16642	0.0:0.6147:0.144:0.2414	rs3810553;rs17846035;rs17859021;rs3810553	348	Q8NC74	CT151_HUMAN	N	348	ENSP00000252998:D348N	ENSP00000252998:D348N	D	-	1	0	C20orf151	60422760	0.075000	0.21258	0.123000	0.21794	0.227000	0.25037	0.339000	0.19875	-0.059000	0.13154	0.491000	0.48974	GAC	C|0.684;T|0.316	0.316	strong		0.711	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
IL17RC	84818	hgsc.bcm.edu	37	3	9974809	9974809	+	Silent	SNP	G	G	A	rs76999397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:9974809G>A	ENST00000295981.3	+	19	2126	c.1908G>A	c.(1906-1908)gcG>gcA	p.A636A	IL17RC_ENST00000498214.1_3'UTR|CRELD1_ENST00000326434.5_5'Flank|IL17RC_ENST00000413608.1_Silent_p.A552A|IL17RC_ENST00000403601.3_Silent_p.A565A|IL17RC_ENST00000416074.2_Silent_p.A391A|IL17RC_ENST00000455057.1_Silent_p.A533A|CRELD1_ENST00000397170.3_5'Flank|CRELD1_ENST00000452070.1_5'Flank|CRELD1_ENST00000383811.3_5'Flank|IL17RC_ENST00000383812.4_Silent_p.A550A|RP11-1020A11.1_ENST00000602411.1_RNA	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	636	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGTTTCACGCGCAGCGGCGCC	0.711											OREG0015383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	154	0.0307508	0.0	0.0216	5008	,	,		12731	0.0417		0.0378	False		,,,				2504	0.0603				p.A636A		Atlas-SNP	.											IL17RC,NS,carcinoma,0,1	IL17RC	55	1	0			c.G1908A						PASS	.	G	,,,,,	51,4341		1,49,2146	17.0	17.0	17.0		1656,1605,1599,1650,1695,1908	-7.9	0.8	3	dbSNP_132	17	417,8165		9,399,3883	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	,,,,,	10,448,6029	AA,AG,GG		4.859,1.1612,3.6072	,,,,,	552/708,535/691,533/689,550/706,565/721,636/792	9974809	468,12506	2196	4291	6487	SO:0001819	synonymous_variant	84818	exon19			TCACGCGCAGCGG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1908G>A	3.37:g.9974809G>A		Somatic	77	0	0	661	WXS	Illumina HiSeq	Phase_I	54	33	0.611111	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			G|0.968;A|0.032	0.032	strong		0.711	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
LY6G6D	58530	hgsc.bcm.edu	37	6	31683157	31683157	+	Missense_Mutation	SNP	T	T	G	rs3749952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31683157T>G	ENST00000375825.3	+	1	25	c.25T>G	c.(25-27)Ttg>Gtg	p.L9V	LY6G6E_ENST00000383418.4_5'Flank|LY6G6E_ENST00000409239.1_5'Flank|LY6G6F_ENST00000556581.1_Intron|XXbac-BPG32J3.20_ENST00000461287.1_5'Flank|MEGT1_ENST00000503322.1_Intron	NM_021246.2	NP_067069.2	O95868	LY66D_HUMAN	lymphocyte antigen 6 complex, locus G6D	9			L -> V (in dbSNP:rs3749952).			anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|plasma membrane (GO:0005886)				central_nervous_system(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						TGTTGGGATCTTGCTCAGCTC	0.647													T|||	514	0.102636	0.1649	0.0836	5008	,	,		14632	0.1438		0.0298	False		,,,				2504	0.0644				p.L9V		Atlas-SNP	.											.	LY6G6D	11	.	0			c.T25G						PASS	.	T	VAL/LEU	454,2566		42,370,1098	86.0	70.0	76.0		25	2.2	0.5	6	dbSNP_107	76	143,5275		1,141,2567	yes	missense	LY6G6D	NM_021246.2	32	43,511,3665	GG,GT,TT		2.6394,15.0331,7.0751		9/134	31683157	597,7841	1510	2709	4219	SO:0001583	missense	58530	exon1			GGGATCTTGCTCA		CCDS34404.1	6p21.3	2008-08-29	2002-07-29	2002-08-01	ENSG00000244355	ENSG00000244355			13935	protein-coding gene	gene with protein product		606038	"""chromosome 6 open reading frame 23"""	C6orf23		12079290	Standard	NM_021246		Approved	MEGT1, Ly6-D, G6D, LY6-D, NG25		O95868	OTTHUMG00000137370	ENST00000375825.3:c.25T>G	6.37:g.31683157T>G	ENSP00000364985:p.Leu9Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_021246	A2BEY8|B0UXC1|B0V019|B0V1Y6|Q4VX50	Missense_Mutation	SNP	ENST00000375825.3	37	CCDS34404.1	187	0.08562271062271062	81	0.16463414634146342	23	0.06353591160220995	64	0.11188811188811189	19	0.025065963060686015	T	14.39	2.521463	0.44866	0.150331	0.026394	ENSG00000244355	ENST00000375825;ENST00000375824	T;T	0.47528	1.14;0.84	5.17	2.22	0.28083	.	.	.	.	.	T	0.25121	0.0610	L	0.48362	1.52	0.53688	P	2.999999999997449E-5	P	0.46142	0.873	P	0.45681	0.49	T	0.09640	-1.0665	8	0.66056	D	0.02	-7.8172	4.2901	0.10874	0.0:0.599:0.1896:0.2114	rs3749952;rs17207384;rs52790927;rs57830593;rs3749952	9	O95868	LY66D_HUMAN	V	9	ENSP00000364985:L9V;ENSP00000364984:L9V	ENSP00000364984:L9V	L	+	1	2	LY6G6D	31791136	0.985000	0.35326	0.499000	0.27577	0.816000	0.46133	0.649000	0.24843	0.541000	0.28827	-0.242000	0.12053	TTG	T|0.920;G|0.080	0.080	strong		0.647	LY6G6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144875.2		
CAPN15	6650	hgsc.bcm.edu	37	16	602430	602430	+	Silent	SNP	C	C	T	rs148358614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:602430C>T	ENST00000219611.2	+	11	3000	c.2637C>T	c.(2635-2637)ttC>ttT	p.F879F	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	879					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCAAGAAGTTCGTCAGCTGCG	0.701													t|||	29	0.00579073	0.0008	0.0014	5008	,	,		12936	0.005		0.002	False		,,,				2504	0.0204				p.F879F		Atlas-SNP	.											SOLH,NS,carcinoma,0,1	SOLH	47	1	0			c.C2637T						PASS	.	T		5,4343		0,5,2169	21.0	26.0	24.0		2637	-8.4	0.4	16	dbSNP_134	24	68,8490		0,68,4211	no	coding-synonymous	SOLH	NM_005632.2		0,73,6380	TT,TC,CC		0.7946,0.115,0.5656		879/1087	602430	73,12833	2174	4279	6453	SO:0001819	synonymous_variant	6650	exon11			GAAGTTCGTCAGC	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2637C>T	16.37:g.602430C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent	SNP	ENST00000219611.2	37	CCDS10410.1																																																																																			C|0.995;T|0.005	0.005	strong		0.701	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	
POP4	10775	hgsc.bcm.edu	37	19	30104871	30104871	+	Missense_Mutation	SNP	G	G	T	rs61731483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:30104871G>T	ENST00000585603.1	+	6	2820	c.518G>T	c.(517-519)cGc>cTc	p.R173L	POP4_ENST00000221770.3_Missense_Mutation_p.R49L|POP4_ENST00000591824.1_3'UTR|POP4_ENST00000392279.3_Missense_Mutation_p.R92L			O95707	RPP29_HUMAN	processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae)	173					mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)|ribonuclease P complex (GO:0030677)	ribonuclease P activity (GO:0004526)|ribonuclease P RNA binding (GO:0033204)|RNA binding (GO:0003723)	p.R173H(1)		breast(1)|endometrium(1)|lung(4)	6	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)			AAAGAAGACCGCCTGAAAGGT	0.448													G|||	27	0.00539137	0.0	0.0115	5008	,	,		20151	0.0		0.0179	False		,,,				2504	0.001				p.R173L	Melanoma(89;1165 1449 14085 34436 43672)	Atlas-SNP	.											POP4,NS,carcinoma,0,1	POP4	20	1	1	Substitution - Missense(1)	lung(1)	c.G518T						PASS	.	G	LEU/ARG	22,4384	30.8+/-60.4	0,22,2181	79.0	73.0	75.0		518	1.5	1.0	19	dbSNP_129	75	200,8400	87.4+/-149.7	2,196,4102	yes	missense	POP4	NM_006627.2	102	2,218,6283	TT,TG,GG		2.3256,0.4993,1.7069	possibly-damaging	173/221	30104871	222,12784	2203	4300	6503	SO:0001583	missense	10775	exon6			AAGACCGCCTGAA	BC006098	CCDS12416.1	19q13.11	2012-05-21				ENSG00000105171			30081	protein-coding gene	gene with protein product		606114				10352175, 10024167	Standard	NM_006627		Approved	RPP29	uc002nsf.2	O95707		ENST00000585603.1:c.518G>T	19.37:g.30104871G>T	ENSP00000465213:p.Arg173Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_006627	Q5XKL7|Q6FHW9|Q9UQQ3	Missense_Mutation	SNP	ENST00000585603.1	37	CCDS12416.1	18	0.008241758241758242	0	0.0	7	0.019337016574585635	0	0.0	11	0.014511873350923483	G	11.62	1.694051	0.30052	0.004993	0.023256	ENSG00000105171	ENST00000221770;ENST00000392279	.	.	.	5.62	1.48	0.22813	Rof/RNase P-like (1);Ribonuclease P/MRP, subunit p29 (3);	0.394694	0.28214	N	0.016165	T	0.37348	0.1000	M	0.71036	2.16	0.35875	D	0.828512	B;B	0.30851	0.221;0.297	B;B	0.35607	0.109;0.206	T	0.54146	-0.8337	9	0.54805	T	0.06	-5.9765	6.2705	0.20951	0.6485:0.0:0.3515:0.0	rs61731483	92;173	A8MYC1;O95707	.;RPP29_HUMAN	L	173;92	.	ENSP00000221770:R173L	R	+	2	0	POP4	34796711	0.980000	0.34600	0.996000	0.52242	0.463000	0.32649	1.323000	0.33701	0.472000	0.27344	0.591000	0.81541	CGC	G|0.985;T|0.015	0.015	strong		0.448	POP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458710.1	NM_006627	
ITGA11	22801	hgsc.bcm.edu	37	15	68628143	68628143	+	Silent	SNP	C	C	T	rs2306023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:68628143C>T	ENST00000315757.7	-	12	1403	c.1317G>A	c.(1315-1317)cgG>cgA	p.R439R	ITGA11_ENST00000423218.2_Silent_p.R439R	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	439					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CCACGTACACCCGCCCCTGCC	0.627													C|||	3235	0.645966	0.2322	0.817	5008	,	,		18488	0.7956		0.7913	False		,,,				2504	0.7802				p.R439R		Atlas-SNP	.											.	ITGA11	110	.	0			c.G1317A						PASS	.	C		1444,2752		279,886,933	27.0	35.0	32.0		1317	2.6	1.0	15	dbSNP_100	32	6645,1773		2632,1381,196	no	coding-synonymous	ITGA11	NM_001004439.1		2911,2267,1129	TT,TC,CC		21.062,34.4137,35.8728		439/1189	68628143	8089,4525	2098	4209	6307	SO:0001819	synonymous_variant	22801	exon12			GTACACCCGCCCC	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1317G>A	15.37:g.68628143C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	143	141	0.986014	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			C|0.354;T|0.646	0.646	strong		0.627	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
DEFB108B	245911	hgsc.bcm.edu	37	11	71548465	71548465	+	Missense_Mutation	SNP	A	A	G	rs12285436	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71548465A>G	ENST00000328698.1	+	2	79	c.79A>G	c.(79-81)Atc>Gtc	p.I27V	DEFB108B_ENST00000529157.1_3'UTR	NM_001002035.1	NP_001002035.1	Q8NET1	D108B_HUMAN	defensin, beta 108B	27			I -> V (in dbSNP:rs12285436).		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|kidney(1)|lung(2)|skin(1)	5						ATTCAAGGAGATCTGTGAACG	0.463													.|||	2238	0.446885	0.329	0.3732	5008	,	,		17462	0.3631		0.5984	False		,,,				2504	0.589				p.I27V		Atlas-SNP	.											.	DEFB108B	6	.	0			c.A79G						PASS	.	A	VAL/ILE	1649,2751		304,1041,855	115.0	118.0	117.0		79	-3.0	0.5	11	dbSNP_120	117	5217,3369		1583,2051,659	no	missense	DEFB108B	NM_001002035.1	29	1887,3092,1514	GG,GA,AA		39.2383,37.4773,47.1277	benign	27/74	71548465	6866,6120	2200	4293	6493	SO:0001583	missense	245911	exon2			AAGGAGATCTGTG	AF529416	CCDS31631.1	11q13.4	2011-03-29			ENSG00000184276	ENSG00000184276		"""Defensins, beta"""	29966	protein-coding gene	gene with protein product							Standard	NM_001002035		Approved		uc010rqr.2	Q8NET1	OTTHUMG00000167533	ENST00000328698.1:c.79A>G	11.37:g.71548465A>G	ENSP00000333234:p.Ile27Val	Somatic	632	1	0.00158228		WXS	Illumina HiSeq	Phase_I	581	578	0.994837	NM_001002035		Missense_Mutation	SNP	ENST00000328698.1	37	CCDS31631.1	1013	0.46382783882783885	183	0.3719512195121951	153	0.42265193370165743	213	0.3723776223776224	464	0.6121372031662269	.	11.02	1.515361	0.27123	0.374773	0.607617	ENSG00000184276	ENST00000328698	T	0.12147	2.71	1.49	-2.97	0.05530	.	0.819276	0.09943	N	0.735666	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	B	0.16396	0.017	B	0.12156	0.007	T	0.38457	-0.9660	8	0.38643	T	0.18	.	3.0295	0.06102	0.3642:0.2566:0.3792:0.0	rs12285436;rs60334126	27	Q8NET1	D108B_HUMAN	V	27	ENSP00000333234:I27V	ENSP00000333234:I27V	I	+	1	0	DEFB108B	71226113	0.438000	0.25602	0.511000	0.27724	0.640000	0.38277	-1.707000	0.01893	-0.962000	0.03604	0.317000	0.21355	ATC	A|0.488;G|0.512	0.512	strong		0.463	DEFB108B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394945.1	NM_001002035	
WWC2	80014	hgsc.bcm.edu	37	4	184203886	184203886	+	Missense_Mutation	SNP	G	G	C	rs3814422	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:184203886G>C	ENST00000403733.3	+	18	2909	c.2710G>C	c.(2710-2712)Gat>Cat	p.D904H	WWC2_ENST00000504005.1_Missense_Mutation_p.D586H|WWC2_ENST00000508747.1_Missense_Mutation_p.D32H|WWC2_ENST00000513834.1_Missense_Mutation_p.D855H|WWC2_ENST00000448232.2_Missense_Mutation_p.D928H	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	904			D -> H (in dbSNP:rs3814422). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		AGAGGCCTCTGATGAAATTGT	0.428													G|||	1271	0.253794	0.1959	0.4063	5008	,	,		21674	0.2391		0.2634	False		,,,				2504	0.229				p.D904H		Atlas-SNP	.											WWC2,colon,carcinoma,0,1	WWC2	78	1	0			c.G2710C						PASS	.	G	HIS/ASP	956,3442		106,744,1349	49.0	46.0	47.0		2710	2.6	0.0	4	dbSNP_107	47	2477,6121		377,1723,2199	yes	missense	WWC2	NM_024949.5	81	483,2467,3548	CC,CG,GG		28.809,21.7372,26.4158	probably-damaging	904/1193	184203886	3433,9563	2199	4299	6498	SO:0001583	missense	80014	exon18			GCCTCTGATGAAA	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2710G>C	4.37:g.184203886G>C	ENSP00000384222:p.Asp904His	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	538	0.24633699633699635	96	0.1951219512195122	129	0.356353591160221	130	0.22727272727272727	183	0.24142480211081793	G	13.46	2.244444	0.39697	0.217372	0.28809	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	T;T;T;T;T	0.26373	3.46;3.46;3.26;3.3;1.74	5.27	2.62	0.31277	.	0.627510	0.16122	N	0.228617	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;B;D;P	0.53151	0.773;0.429;0.958;0.915	P;B;P;P	0.51170	0.487;0.372;0.661;0.621	T	0.42207	-0.9465	9	0.46703	T	0.11	-2.9709	10.708	0.45966	0.2825:0.0:0.7175:0.0	rs3814422;rs17855701;rs52831700;rs3814422	928;904;32;855	Q6AWC2-6;Q6AWC2;Q6AWC2-7;Q6AWC2-4	.;WWC2_HUMAN;.;.	H	904;855;928;586;32	ENSP00000384222:D904H;ENSP00000425054:D855H;ENSP00000398577:D928H;ENSP00000427569:D586H;ENSP00000420835:D32H	ENSP00000384222:D904H	D	+	1	0	WWC2	184440880	0.002000	0.14202	0.000000	0.03702	0.697000	0.40408	0.703000	0.25646	0.105000	0.17753	-0.797000	0.03246	GAT	G|0.747;C|0.253	0.253	strong		0.428	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
BSG	682	hgsc.bcm.edu	37	19	580665	580665	+	Silent	SNP	T	T	C	rs4682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:580665T>C	ENST00000333511.3	+	5	745	c.675T>C	c.(673-675)gcT>gcC	p.A225A	BSG_ENST00000545507.2_Silent_p.A16A|BSG_ENST00000353555.4_Silent_p.A109A|BSG_ENST00000346916.4_Silent_p.A45A	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	225	Ig-like V-type.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGTGAAGGCTGTGAAGTCGT	0.637													T|||	1635	0.326478	0.3275	0.2853	5008	,	,		16585	0.4563		0.1899	False		,,,				2504	0.3609				p.A225A		Atlas-SNP	.											BSG_ENST00000346916,NS,carcinoma,0,4	BSG	48	4	0			c.T675C						PASS	.	T	,,	1289,3113	431.0+/-342.8	202,885,1114	60.0	60.0	60.0		675,327,135	-8.2	0.0	19	dbSNP_52	60	1845,6755	328.2+/-318.2	199,1447,2654	no	coding-synonymous,coding-synonymous,coding-synonymous	BSG	NM_001728.2,NM_198589.1,NM_198591.1	,,	401,2332,3768	CC,CT,TT		21.4535,29.2821,24.104	,,	225/386,109/270,45/206	580665	3134,9868	2201	4300	6501	SO:0001819	synonymous_variant	682	exon5			GAAGGCTGTGAAG	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1116	protein-coding gene	gene with protein product	"""Ok blood group"""	109480	"""basigin"""	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.675T>C	19.37:g.580665T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	100	38	0.38	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Silent	SNP	ENST00000333511.3	37	CCDS12033.1																																																																																			T|0.744;C|0.256	0.256	strong		0.637	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728	
IDUA	3425	hgsc.bcm.edu	37	4	994414	994414	+	Missense_Mutation	SNP	G	G	A	rs3755955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:994414G>A	ENST00000247933.4	+	3	402	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	IDUA_ENST00000453894.1_Missense_Mutation_p.R58Q|IDUA_ENST00000514224.1_5'UTR	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	105			R -> Q (in dbSNP:rs3755955). {ECO:0000269|PubMed:15300847, ECO:0000269|PubMed:21394825}.		carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TCCACTGGACGGGGCCTGAGC	0.647													G|||	845	0.16873	0.1271	0.0908	5008	,	,		16643	0.2073		0.167	False		,,,				2504	0.2423				p.R105Q		Atlas-SNP	.											.	IDUA	33	.	0			c.G314A						PASS	.	G	GLN/ARG	473,3931	221.7+/-238.7	27,419,1756	72.0	66.0	68.0		314	1.5	0.0	4	dbSNP_107	68	1376,7222	266.8+/-286.9	113,1150,3036	yes	missense	IDUA	NM_000203.3	43	140,1569,4792	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	16.0037,10.7402,14.2209	benign	105/654	994414	1849,11153	2202	4299	6501	SO:0001583	missense	3425	exon3			CTGGACGGGGCCT	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.314G>A	4.37:g.994414G>A	ENSP00000247933:p.Arg105Gln	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	219	106	0.484018	NM_000203	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	328|328	0.15018315018315018|0.15018315018315018	56|56	0.11382113821138211|0.11382113821138211	33|33	0.09116022099447514|0.09116022099447514	114|114	0.1993006993006993|0.1993006993006993	125|125	0.16490765171503957|0.16490765171503957	G|G	4.542|4.542	0.100603|0.100603	0.08731|0.08731	0.107402|0.107402	0.160037|0.160037	ENSG00000127415|ENSG00000127415	ENST00000504568|ENST00000247933;ENST00000453894;ENST00000502910;ENST00000514192;ENST00000509948	.|D;D;D;D;D	.|0.92299	.|-3.01;-3.01;-3.01;-3.01;-3.01	4.97|4.97	1.53|1.53	0.23141|0.23141	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.|0.771606	.|0.12090	.|N	.|0.500501	T|T	0.00210|0.00210	0.0006|0.0006	N|N	0.01482|0.01482	-0.84|-0.84	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.10296	.|0.002;0.003	.|B;B	.|0.06405	.|0.001;0.002	T|T	0.14783|0.14783	-1.0460|-1.0460	4|9	.|0.08599	.|T	.|0.76	-26.7134|-26.7134	3.6885|3.6885	0.08338|0.08338	0.3914:0.0:0.4299:0.1786|0.3914:0.0:0.4299:0.1786	rs3755955;rs57374078;rs3755955|rs3755955;rs57374078;rs3755955	.|58;105	.|B3KWK6;P35475	.|.;IDUA_HUMAN	R|Q	92|105;58;58;44;36	.|ENSP00000247933:R105Q;ENSP00000396458:R58Q;ENSP00000422952:R58Q;ENSP00000423685:R44Q;ENSP00000424227:R36Q	.|ENSP00000247933:R105Q	G|R	+|+	1|2	0|0	IDUA|IDUA	984414|984414	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	0.012000|0.012000	0.13287|0.13287	-0.017000|-0.017000	0.14103|0.14103	-1.326000|-1.326000	0.01283|0.01283	GGG|CGG	G|0.859;A|0.141	0.141	strong		0.647	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
DPH3	285381	hgsc.bcm.edu	37	3	16305674	16305674	+	Silent	SNP	C	C	G	rs14080	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:16305674C>G	ENST00000488423.1	-	2	266	c.171G>C	c.(169-171)gtG>gtC	p.V57V	DPH3_ENST00000383775.4_Intron|OXNAD1_ENST00000606098.1_5'Flank|OXNAD1_ENST00000435829.2_5'Flank|DPH3_ENST00000285082.4_5'UTR|OXNAD1_ENST00000605932.1_5'Flank|OXNAD1_ENST00000285083.5_5'Flank	NM_206831.2	NP_996662.1	Q96FX2	DPH3_HUMAN	diphthamide biosynthesis 3	57					negative regulation of protein secretion (GO:0050709)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of binding (GO:0051099)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			large_intestine(2)	2						TGTCATAAATCACTTTTATAA	0.418													C|||	2172	0.433706	0.3079	0.4712	5008	,	,		17298	0.4762		0.4324	False		,,,				2504	0.5348				p.V57V		Atlas-SNP	.											DPH3,NS,adenoma,0,1	DPH3	7	1	0			c.G171C						scavenged	.	C	,	1546,2860	483.5+/-359.7	274,998,931	107.0	99.0	102.0		,171	3.8	1.0	3	dbSNP_52	102	3648,4952	520.9+/-379.8	782,2084,1434	no	intron,coding-synonymous	DPH3	NM_001047434.2,NM_206831.2	,	1056,3082,2365	GG,GC,CC		42.4186,35.0885,39.9354	,	,57/83	16305674	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	285381	exon2			ATAAATCACTTTT	BC010181	CCDS2629.1, CCDS43058.1	3p25.1	2013-06-19	2013-06-19	2006-10-25	ENSG00000154813	ENSG00000154813			27717	protein-coding gene	gene with protein product	"""DPH3A, KTI11 homolog A (S. cerevisiae)"""	608959	"""zinc finger, CSL-type containing 2"", ""DPH3 homolog (KTI11, S. cerevisiae)"", ""DPH3, KTI11 homolog (S. cerevisiae)"""	ZCSL2		14527407, 14980502, 15485916, 16648478	Standard	NM_001047434		Approved	DESR1, DELGIP1, MGC20197, KTI11, DELGIP, DPH3A	uc003cau.3	Q96FX2	OTTHUMG00000129866	ENST00000488423.1:c.171G>C	3.37:g.16305674C>G		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	128	42	0.328125	NM_206831		Silent	SNP	ENST00000488423.1	37	CCDS2629.1																																																																																			C|0.590;G|0.410	0.410	strong		0.418	DPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252108.2	NM_206831	
PAPPA	5069	hgsc.bcm.edu	37	9	119158814	119158814	+	Silent	SNP	T	T	C	rs8456	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:119158814T>C	ENST00000328252.3	+	22	5172	c.4803T>C	c.(4801-4803)gaT>gaC	p.D1601D	AL137024.1_ENST00000401363.1_RNA|PAPPA_ENST00000534838.1_Silent_p.D639D|PAPPA_ENST00000483254.1_3'UTR	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1601					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						TGTCCTGTGATCTACAAGGTG	0.527													C|||	3367	0.672324	0.5703	0.7349	5008	,	,		19633	0.6438		0.6938	False		,,,				2504	0.773				p.D1601D		Atlas-SNP	.											.	PAPPA	243	.	0			c.T4803C						PASS	.	C		2559,1847	537.8+/-374.8	732,1095,376	202.0	176.0	185.0		4803	4.7	1.0	9	dbSNP_120	185	6106,2494	410.2+/-350.1	2157,1792,351	no	coding-synonymous	PAPPA	NM_002581.3		2889,2887,727	CC,CT,TT		29.0,41.9201,33.3769		1601/1628	119158814	8665,4341	2203	4300	6503	SO:0001819	synonymous_variant	5069	exon22			CTGTGATCTACAA		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.4803T>C	9.37:g.119158814T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																			C|0.669;N|0.001	0.669	strong		0.527	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
ENDOD1	23052	hgsc.bcm.edu	37	11	94862577	94862577	+	Missense_Mutation	SNP	G	G	T	rs3740861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:94862577G>T	ENST00000278505.4	+	2	1455	c.1337G>T	c.(1336-1338)gGc>gTc	p.G446V		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	446			G -> V (in dbSNP:rs3740861).			extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				TACACCATGGGCGCTATTCCA	0.532													G|||	1002	0.20008	0.087	0.196	5008	,	,		19140	0.122		0.2684	False		,,,				2504	0.3661				p.G446V		Atlas-SNP	.											ENDOD1,NS,carcinoma,-1,1	ENDOD1	26	1	0			c.G1337T						PASS	.	G	VAL/GLY	488,3592		31,426,1583	189.0	180.0	183.0		1337	6.0	0.1	11	dbSNP_107	183	2329,6089		319,1691,2199	yes	missense	ENDOD1	NM_015036.2	109	350,2117,3782	TT,TG,GG		27.6669,11.9608,22.5396	probably-damaging	446/501	94862577	2817,9681	2040	4209	6249	SO:0001583	missense	23052	exon2			CCATGGGCGCTAT	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.1337G>T	11.37:g.94862577G>T	ENSP00000278505:p.Gly446Val	Somatic	404	1	0.00247525		WXS	Illumina HiSeq	Phase_I	460	221	0.480435	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	392	0.1794871794871795	53	0.10772357723577236	68	0.1878453038674033	66	0.11538461538461539	205	0.2704485488126649	G	13.52	2.261585	0.39995	0.119608	0.276669	ENSG00000149218	ENST00000278505	T	0.36699	1.24	5.97	5.97	0.96955	.	0.532850	0.21869	N	0.067907	T	0.00012	0.0000	M	0.65975	2.015	0.36868	P	0.11124599999999996	D	0.65815	0.995	P	0.58172	0.834	T	0.00163	-1.1969	9	0.46703	T	0.11	-10.5144	20.4301	0.99081	0.0:0.0:1.0:0.0	rs3740861;rs17693261;rs52803898;rs58207096;rs3740861	446	O94919	ENDD1_HUMAN	V	446	ENSP00000278505:G446V	ENSP00000278505:G446V	G	+	2	0	ENDOD1	94502225	0.981000	0.34729	0.067000	0.19924	0.018000	0.09664	6.268000	0.72552	2.834000	0.97654	0.557000	0.71058	GGC	G|0.794;T|0.206	0.206	strong		0.532	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036	
ZNF716	441234	hgsc.bcm.edu	37	7	57529392	57529392	+	Missense_Mutation	SNP	A	A	C	rs13235676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:57529392A>C	ENST00000420713.1	+	4	1337	c.1225A>C	c.(1225-1227)Aaa>Caa	p.K409Q		NM_001159279.1	NP_001152751.1	A6NP11	ZN716_HUMAN	zinc finger protein 716	409					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|lung(20)|ovary(2)	24						GAAACCCTACAAATGTGAAGA	0.403													a|||	2109	0.421126	0.3215	0.4798	5008	,	,		20228	0.5397		0.3797	False		,,,				2504	0.4346				p.K409Q		Atlas-SNP	.											.	ZNF716	207	.	0			c.A1225C						PASS	.	A	GLN/LYS	479,905		82,315,295	27.0	27.0	27.0		1225	0.2	0.2	7	dbSNP_121	27	1251,1931		247,757,587	no	missense	ZNF716	NM_001159279.1	53	329,1072,882	CC,CA,AA		39.3149,34.6098,37.8887	benign	409/496	57529392	1730,2836	692	1591	2283	SO:0001583	missense	441234	exon4			CCCTACAAATGTG	AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111		"""Zinc fingers, C2H2-type"", ""-"""	32458	protein-coding gene	gene with protein product							Standard	NM_001159279		Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	ENST00000420713.1:c.1225A>C	7.37:g.57529392A>C	ENSP00000394248:p.Lys409Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_001159279		Missense_Mutation	SNP	ENST00000420713.1	37	CCDS55112.1	906	0.41483516483516486	162	0.32926829268292684	158	0.43646408839779005	307	0.5367132867132867	279	0.36807387862796836	A	7.864	0.726705	0.15439	0.346098	0.393149	ENSG00000182111	ENST00000420713;ENST00000418732	T	0.18810	2.19	0.195	0.195	0.15151	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.55743	1.74	0.52501	P	4.4000000000044004E-5	B	0.33299	0.407	B	0.30716	0.119	T	0.43750	-0.9372	8	0.49607	T	0.09	.	4.8229	0.13400	0.9998:0.0:2.0E-4:0.0	rs13235676	397	A6NP11	ZN716_HUMAN	Q	409;397	ENSP00000394248:K409Q	ENSP00000387687:K397Q	K	+	1	0	ZNF716	57533334	0.000000	0.05858	0.190000	0.23270	0.191000	0.23601	-2.138000	0.01303	0.257000	0.21650	0.254000	0.18369	AAA	A|0.591;C|0.409	0.409	strong		0.403	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345309.1	NM_001159279	
SLC6A17	388662	hgsc.bcm.edu	37	1	110738296	110738296	+	Silent	SNP	G	G	A	rs2784140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110738296G>A	ENST00000331565.4	+	10	2066	c.1581G>A	c.(1579-1581)tcG>tcA	p.S527S		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	527					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)	p.S527S(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		ATGACTACTCGGCCACCCTGC	0.532													G|||	1451	0.289736	0.0439	0.3847	5008	,	,		20344	0.3016		0.4543	False		,,,				2504	0.3732				p.S527S		Atlas-SNP	.											SLC6A17,NS,carcinoma,0,1	SLC6A17	86	1	1	Substitution - coding silent(1)	stomach(1)	c.G1581A						PASS	.	G		505,3901	234.2+/-247.1	28,449,1726	104.0	86.0	92.0		1581	-1.0	1.0	1	dbSNP_100	92	4276,4324	575.3+/-390.2	1098,2080,1122	no	coding-synonymous	SLC6A17	NM_001010898.2		1126,2529,2848	AA,AG,GG		49.7209,11.4616,36.76		527/728	110738296	4781,8225	2203	4300	6503	SO:0001819	synonymous_variant	388662	exon10			CTACTCGGCCACC		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1581G>A	1.37:g.110738296G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	CCDS30799.1																																																																																			G|0.658;A|0.342	0.342	strong		0.532	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
UBXN6	80700	hgsc.bcm.edu	37	19	4457650	4457650	+	Silent	SNP	C	C	T	rs1044510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4457650C>T	ENST00000301281.6	-	1	169	c.45G>A	c.(43-45)aaG>aaA	p.K15K	CTB-50L17.16_ENST00000591414.1_lincRNA|CTB-50L17.9_ENST00000592034.1_RNA|UBXN6_ENST00000394765.3_5'Flank	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	15						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						GTCCCGCGCTCTTGAACTTGA	0.697													C|||	2034	0.40615	0.3374	0.4294	5008	,	,		3297	0.6171		0.2763	False		,,,				2504	0.3988				p.K15K		Atlas-SNP	.											.	UBXN6	27	.	0			c.G45A						PASS	.	C		1456,2946	448.5+/-348.7	253,950,998	34.0	31.0	32.0		45	3.1	1.0	19	dbSNP_86	32	2433,6161	385.4+/-341.5	334,1765,2198	no	coding-synonymous	UBXN6	NM_025241.2		587,2715,3196	TT,TC,CC		28.3104,33.0759,29.9246		15/442	4457650	3889,9107	2201	4297	6498	SO:0001819	synonymous_variant	80700	exon1			CGCGCTCTTGAAC	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.45G>A	19.37:g.4457650C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	46	17	0.369565	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Silent	SNP	ENST00000301281.6	37	CCDS12129.1																																																																																			C|0.660;T|0.340	0.340	strong		0.697	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
ZBTB3	79842	hgsc.bcm.edu	37	11	62519806	62519806	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62519806T>C	ENST00000394807.3	-	2	1606	c.1481A>G	c.(1480-1482)cAc>cGc	p.H494R		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	494					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						CTCACGTGTGTGCACCGTGGC	0.572																																					p.H494R		Atlas-SNP	.											.	ZBTB3	47	.	0			c.A1481G						PASS	.						92.0	81.0	85.0					11																	62519806		2202	4299	6501	SO:0001583	missense	79842	exon2			CGTGTGTGCACCG	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.1481A>G	11.37:g.62519806T>C	ENSP00000378286:p.His494Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	37	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.654116	0.67472	.	.	ENSG00000185670	ENST00000394807	T	0.67523	-0.27	4.61	4.61	0.57282	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.83138	0.5189	M	0.89095	3.005	0.43777	D	0.996307	D	0.89917	1.0	D	0.91635	0.999	D	0.86175	0.1602	10	0.87932	D	0	.	11.9849	0.53142	0.0:0.0:0.0:1.0	.	494	Q9H5J0	ZBTB3_HUMAN	R	494	ENSP00000378286:H494R	ENSP00000378286:H494R	H	-	2	0	ZBTB3	62276382	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.698000	0.84413	1.724000	0.51502	0.459000	0.35465	CAC	.	.	none		0.572	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
GUCY1A2	2977	hgsc.bcm.edu	37	11	106647224	106647224	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:106647224C>T	ENST00000526355.2	-	6	2245	c.1777G>A	c.(1777-1779)Gcc>Acc	p.A593T	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.A614T|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.A593T	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	593	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	ATCTTCAAGGCCATCAGAGCA	0.483																																					p.A593T		Atlas-SNP	.											GUCY1A2,NS,carcinoma,+1,2	GUCY1A2	180	2	0			c.G1777A						scavenged	.						112.0	95.0	101.0					11																	106647224		2201	4298	6499	SO:0001583	missense	2977	exon6			TCAAGGCCATCAG	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.1777G>A	11.37:g.106647224C>T	ENSP00000431245:p.Ala593Thr	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	185	2	0.0108108	NM_000855	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772333	0.90108	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.91686	-2.89;-1.92;-2.89	5.85	4.93	0.64822	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.152300	0.29715	U	0.011394	D	0.96679	0.8916	H	0.95328	3.655	0.80722	D	1	P;P;D	0.54964	0.946;0.917;0.969	P;P;P	0.56960	0.671;0.81;0.674	D	0.97688	1.0177	10	0.87932	D	0	.	16.0397	0.80654	0.0:0.8655:0.1345:0.0	.	614;593;593	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	T	593;593;614	ENSP00000431245:A593T;ENSP00000282249:A593T;ENSP00000344874:A614T	ENSP00000282249:A593T	A	-	1	0	GUCY1A2	106152434	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.772000	0.68889	1.459000	0.47892	0.650000	0.86243	GCC	.	.	none		0.483	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2		
GP6	51206	hgsc.bcm.edu	37	19	55527081	55527081	+	Missense_Mutation	SNP	C	C	T	rs2304167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55527081C>T	ENST00000417454.1	-	7	772	c.745G>A	c.(745-747)Gcc>Acc	p.A249T	GP6_ENST00000310373.3_Missense_Mutation_p.A249T|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Missense_Mutation_p.A231T|CTC-550B14.7_ENST00000586845.1_RNA	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	249			A -> T (in dbSNP:rs2304167). {ECO:0000269|PubMed:11027634, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		TTTGGACTGGCGGTGATACTC	0.517													C|||	3573	0.713458	0.4856	0.8228	5008	,	,		18160	0.8105		0.8459	False		,,,				2504	0.7076				p.A249T		Atlas-SNP	.											.	GP6	55	.	0			c.G745A						PASS	.	C	THR/ALA,THR/ALA	2097,1907		558,981,463	60.0	68.0	66.0		745,745	-6.3	0.0	19	dbSNP_100	66	6939,1419		2892,1155,132	yes	missense,missense	GP6	NM_001083899.1,NM_016363.4	58,58	3450,2136,595	TT,TC,CC		16.9777,47.6274,26.905	benign,benign	249/621,249/340	55527081	9036,3326	2002	4179	6181	SO:0001583	missense	51206	exon7			GACTGGCGGTGAT	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.745G>A	19.37:g.55527081C>T	ENSP00000394922:p.Ala249Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_016363	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	37	CCDS46184.1	1664	0.7619047619047619	256	0.5203252032520326	305	0.8425414364640884	469	0.8199300699300699	634	0.8364116094986808	C	5.479	0.273365	0.10403	0.523726	0.830223	ENSG00000088053	ENST00000417454;ENST00000310373;ENST00000333884	T;T;T	0.00529	7.04;6.78;7.02	3.15	-6.29	0.02013	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.33494	0.004;0.414;0.001	B;B;B	0.24006	0.009;0.05;0.0	T	0.49670	-0.8915	8	0.02654	T	1	.	4.4842	0.11781	0.2882:0.1969:0.0:0.5149	rs2304167;rs16960269;rs52815231;rs2304167	231;249;249	Q9HCN6-2;Q9HCN6-3;Q9HCN6	.;.;GPVI_HUMAN	T	249;249;231	ENSP00000394922:A249T;ENSP00000308782:A249T;ENSP00000334552:A231T	ENSP00000308782:A249T	A	-	1	0	GP6	60218893	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.923000	0.00692	-1.765000	0.01303	-1.268000	0.01426	GCC	C|0.236;N|0.000	.	strong		0.517	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
SEMA4B	10509	hgsc.bcm.edu	37	15	90764219	90764219	+	Missense_Mutation	SNP	G	G	A	rs4932305	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90764219G>A	ENST00000411539.2	+	5	749	c.489G>A	c.(487-489)atG>atA	p.M163I	SEMA4B_ENST00000379122.3_Missense_Mutation_p.M158I|SEMA4B_ENST00000332496.6_Missense_Mutation_p.M163I	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	158	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)			NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			TGCAGAACATGGAGAACTTCA	0.582													G|||	1387	0.276957	0.0613	0.2291	5008	,	,		21391	0.6081		0.1491	False		,,,				2504	0.3926				p.M163I		Atlas-SNP	.											.	SEMA4B	51	.	0			c.G489A						PASS	.	G	ILE/MET,ILE/MET	352,3776		20,312,1732	50.0	51.0	51.0		489,489	2.5	0.2	15	dbSNP_111	51	1175,7251		90,995,3128	yes	missense,missense	SEMA4B	NM_020210.3,NM_198925.2	10,10	110,1307,4860	AA,AG,GG		13.9449,8.5271,12.1635	benign,benign	163/838,163/838	90764219	1527,11027	2064	4213	6277	SO:0001583	missense	10509	exon6			GAACATGGAGAAC	AB051532	CCDS45347.1	15q25	2008-07-18						"""Semaphorins"""	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.489G>A	15.37:g.90764219G>A	ENSP00000394720:p.Met163Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Missense_Mutation	SNP	ENST00000411539.2	37	CCDS45347.1	546	0.25	31	0.06300813008130081	56	0.15469613259668508	348	0.6083916083916084	111	0.14643799472295516	G	16.69	3.192268	0.58017	0.085271	0.139449	ENSG00000185033	ENST00000332496;ENST00000379122;ENST00000411539	T;T;T	0.09445	2.98;2.98;2.98	5.58	2.5	0.30297	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.935120	0.09097	N	0.849095	T	0.00012	0.0000	N	0.01686	-0.76	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33803	-0.9854	9	0.18710	T	0.47	.	3.6283	0.08121	0.1476:0.1317:0.586:0.1348	rs4932305;rs52807404;rs58528304;rs4932305	163;158	Q2NL81;Q9NPR2	.;SEM4B_HUMAN	I	163;158;163	ENSP00000332204:M163I;ENSP00000368417:M158I;ENSP00000394720:M163I	ENSP00000332204:M163I	M	+	3	0	SEMA4B	88565223	0.000000	0.05858	0.245000	0.24217	0.330000	0.28571	0.077000	0.14738	0.809000	0.34255	0.655000	0.94253	ATG	G|0.755;A|0.245	0.245	strong		0.582	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
MUC16	94025	hgsc.bcm.edu	37	19	9083124	9083124	+	Silent	SNP	G	G	A	rs12608495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9083124G>A	ENST00000397910.4	-	1	8894	c.8691C>T	c.(8689-8691)gtC>gtT	p.V2897V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2898	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.V2897V(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCAAACTTGGGACCTCAGAAA	0.512													G|||	696	0.138978	0.0174	0.1527	5008	,	,		21125	0.0496		0.3042	False		,,,				2504	0.2157				p.V2897V		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - coding silent(2)	stomach(2)	c.C8691T						PASS	.	G		270,3522		12,246,1638	77.0	70.0	72.0		8691	-0.9	0.0	19	dbSNP_120	72	2507,5739		381,1745,1997	no	coding-synonymous	MUC16	NM_024690.2		393,1991,3635	AA,AG,GG		30.4026,7.1203,23.0686		2897/14508	9083124	2777,9261	1896	4123	6019	SO:0001819	synonymous_variant	94025	exon1			ACTTGGGACCTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8691C>T	19.37:g.9083124G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	193	79	0.409326	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.840;A|0.160	0.160	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CNTNAP3	79937	hgsc.bcm.edu	37	9	39103743	39103743	+	Missense_Mutation	SNP	C	C	T	rs7852039	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:39103743C>T	ENST00000297668.6	-	16	2607	c.2534G>A	c.(2533-2535)cGt>cAt	p.R845H	CNTNAP3_ENST00000377656.2_Missense_Mutation_p.R844H|CNTNAP3_ENST00000358144.2_Missense_Mutation_p.R757H	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	845	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		R -> H (in dbSNP:rs7852039). {ECO:0000269|PubMed:11214970}.		cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GAGCTTACCACGCAGCTCAAT	0.418													C|||	934	0.186502	0.062	0.1354	5008	,	,		15532	0.3036		0.2376	False		,,,				2504	0.2178				p.R845H		Atlas-SNP	.											.	CNTNAP3	82	.	0			c.G2534A						PASS	.	C	HIS/ARG	392,4014	190.5+/-216.4	24,344,1835	39.0	43.0	42.0		2534	-1.3	0.0	9	dbSNP_116	42	1860,6740	331.0+/-319.4	208,1444,2648	yes	missense	CNTNAP3	NM_033655.3	29	232,1788,4483	TT,TC,CC		21.6279,8.897,17.3151	benign	845/1289	39103743	2252,10754	2203	4300	6503	SO:0001583	missense	79937	exon16			TTACCACGCAGCT	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.2534G>A	9.37:g.39103743C>T	ENSP00000297668:p.Arg845His	Somatic	539	1	0.00185529		WXS	Illumina HiSeq	Phase_I	532	529	0.994361	NM_033655	B1AMA0|Q9C0E9	Missense_Mutation	SNP	ENST00000297668.6	37	CCDS6616.1	439	0.20100732600732601	26	0.052845528455284556	58	0.16022099447513813	164	0.2867132867132867	191	0.2519788918205805	C	11.25	1.582659	0.28180	0.08897	0.216279	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144	T;T;T	0.42513	0.97;0.97;0.97	3.23	-1.29	0.09288	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.00012	0.0000	L	0.42487	1.325	0.50813	P	1.0299999999996423E-4	B;B;B	0.27286	0.174;0.076;0.032	B;B;B	0.30179	0.048;0.112;0.032	T	0.37596	-0.9699	8	0.16896	T	0.51	.	3.4899	0.07634	0.195:0.2478:0.0:0.5572	rs7852039;rs7852039	845;844;845	Q9BZ76-2;A6NC89;Q9BZ76	.;.;CNTP3_HUMAN	H	845;844;757	ENSP00000297668:R845H;ENSP00000366884:R844H;ENSP00000350863:R757H	ENSP00000297668:R845H	R	-	2	0	CNTNAP3	39093743	0.000000	0.05858	0.008000	0.14137	0.241000	0.25554	-0.236000	0.09003	-0.130000	0.11599	0.485000	0.47835	CGT	C|0.824;T|0.176	0.176	strong		0.418	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
TACR2	6865	hgsc.bcm.edu	37	10	71176012	71176012	+	Missense_Mutation	SNP	A	A	G	rs5030920	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71176012A>G	ENST00000373306.4	-	1	611	c.68T>C	c.(67-69)aTc>aCc	p.I23T		NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	23			I -> T (in dbSNP:rs5030920). {ECO:0000269|PubMed:1659297, ECO:0000269|PubMed:1710456}.		excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						GAAGGCTGTGATGCCCGTGGT	0.597													G|||	1220	0.24361	0.4002	0.1758	5008	,	,		20717	0.0546		0.2356	False		,,,				2504	0.2832				p.I23T		Atlas-SNP	.											TACR2,colon,carcinoma,0,1	TACR2	37	1	0			c.T68C						PASS	.	G	THR/ILE	1649,2757	659.5+/-400.6	320,1009,874	71.0	69.0	70.0		68	2.8	0.4	10	dbSNP_113	70	1930,6670	725.9+/-406.6	220,1490,2590	yes	missense	TACR2	NM_001057.2	89	540,2499,3464	GG,GA,AA		22.4419,37.4262,27.5181	benign	23/399	71176012	3579,9427	2203	4300	6503	SO:0001583	missense	6865	exon1			GCTGTGATGCCCG		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"""GPCR / Class A : Tachykinin receptors"""	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.68T>C	10.37:g.71176012A>G	ENSP00000362403:p.Ile23Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	156	74	0.474359	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	37	CCDS7293.1	475	0.2174908424908425	196	0.3983739837398374	69	0.19060773480662985	27	0.0472027972027972	183	0.24142480211081793	G	1.368	-0.586835	0.03827	0.374262	0.224419	ENSG00000075073	ENST00000373306	T	0.36878	1.23	5.31	2.83	0.33086	.	0.651620	0.14923	N	0.290532	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47182	-0.9137	9	0.17832	T	0.49	.	7.3299	0.26575	0.6881:0.1194:0.1924:0.0	rs5030920;rs59892825;rs5030920	23	P21452	NK2R_HUMAN	T	23	ENSP00000362403:I23T	ENSP00000362403:I23T	I	-	2	0	TACR2	70846018	0.000000	0.05858	0.369000	0.25952	0.119000	0.20118	0.208000	0.17415	0.431000	0.26258	-1.073000	0.02249	ATC	A|0.748;G|0.252	0.252	strong		0.597	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1		
OC90	729330	hgsc.bcm.edu	37	8	133047071	133047071	+	Silent	SNP	G	G	A	rs11779306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:133047071G>A	ENST00000443356.2	-	11	824	c.738C>T	c.(736-738)caC>caT	p.H246H	OC90_ENST00000262283.5_Silent_p.H442H|OC90_ENST00000603859.1_Silent_p.H230H|OC90_ENST00000254627.3_Silent_p.H230H			Q02509	OC90_HUMAN	otoconin 90	246					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			CTTCCTGATCGTGGCCTGCTT	0.567													T|||	1309	0.261382	0.1717	0.2522	5008	,	,		18407	0.2629		0.3101	False		,,,				2504	0.3374				p.H230H		Atlas-SNP	.											.	OC90	163	.	0			c.C690T						PASS	.	T		729,3397		73,583,1407	117.0	127.0	123.0		690	-0.7	0.0	8	dbSNP_120	123	2788,5616		483,1822,1897	no	coding-synonymous	OC90	NM_001080399.2		556,2405,3304	AA,AG,GG		33.1747,17.6684,28.0686		230/478	133047071	3517,9013	2063	4202	6265	SO:0001819	synonymous_variant	729330	exon10			CTGATCGTGGCCT	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.738C>T	8.37:g.133047071G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	48	0.55814	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				G|0.717;A|0.283	0.283	strong		0.567	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
PNPLA1	285848	hgsc.bcm.edu	37	6	36260858	36260858	+	Silent	SNP	C	C	T	rs2239795	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:36260858C>T	ENST00000394571.2	+	3	459	c.459C>T	c.(457-459)ttC>ttT	p.F153F	PNPLA1_ENST00000388715.3_Silent_p.F58F|PNPLA1_ENST00000312917.5_Silent_p.F58F	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	153	Patatin.				lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						GCAGCTGCTTCGTCCCGGTGT	0.662													C|||	2095	0.418331	0.5703	0.3213	5008	,	,		17655	0.3472		0.4155	False		,,,				2504	0.3579				p.F153F		Atlas-SNP	.											PNPLA1_ENST00000394571,NS,carcinoma,+2,2	PNPLA1	92	2	0			c.C459T						PASS	.	C	,,	2278,2128	598.9+/-389.2	596,1086,521	116.0	96.0	103.0		174,459,174	-5.1	0.9	6	dbSNP_98	103	3346,5254	497.8+/-374.6	654,2038,1608	no	coding-synonymous,coding-synonymous,coding-synonymous	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	,,	1250,3124,2129	TT,TC,CC		38.907,48.2978,43.2416	,,	58/447,153/533,58/438	36260858	5624,7382	2203	4300	6503	SO:0001819	synonymous_variant	285848	exon3			CTGCTTCGTCCCG		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.459C>T	6.37:g.36260858C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	113	72	0.637168	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Silent	SNP	ENST00000394571.2	37	CCDS54997.1																																																																																			C|0.568;T|0.432	0.432	strong		0.662	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
OR51A2	401667	hgsc.bcm.edu	37	11	4976291	4976291	+	Missense_Mutation	SNP	G	G	A	rs55889636	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4976291G>A	ENST00000380371.1	-	1	652	c.653C>T	c.(652-654)tCt>tTt	p.S218F	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGGGTGTAAGACACAGCAAT	0.428													.|||	1878	0.375	0.3722	0.3905	5008	,	,		14851	0.379		0.4841	False		,,,				2504	0.2515				p.S218F		Atlas-SNP	.											OR51A2,NS,carcinoma,0,1	OR51A2	40	1	0			c.C653T						PASS	.		PHE/SER	1533,2741		432,669,1036	80.0	62.0	68.0		653	3.1	0.1	11	dbSNP_129	68	3770,4262		1350,1070,1596	yes	missense	OR51A2	NM_001004748.1	155	1782,1739,2632	AA,AG,GG		46.9373,35.868,43.0928	probably-damaging	218/314	4976291	5303,7003	2137	4016	6153	SO:0001583	missense	401667	exon1			GTGTAAGACACAG	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.653C>T	11.37:g.4976291G>A	ENSP00000369729:p.Ser218Phe	Somatic	605	0	0		WXS	Illumina HiSeq	Phase_I	371	355	0.956873	NM_001004748		Missense_Mutation	SNP	ENST00000380371.1	37	CCDS31368.1	802	0.36721611721611724	148	0.3008130081300813	117	0.32320441988950277	194	0.33916083916083917	343	0.4525065963060686	-	16.73	3.204617	0.58234	0.35868	0.469373	ENSG00000205496	ENST00000380371	T	0.42513	0.97	3.13	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	H	0.96208	3.785	0.32076	P	0.5937319999999999	D	0.89917	1.0	D	0.97110	1.0	T	0.42224	-0.9464	8	0.87932	D	0	.	13.3431	0.60555	0.0:0.0:1.0:0.0	rs55889636	218	Q8NGJ7	O51A2_HUMAN	F	218	ENSP00000369729:S218F	ENSP00000369729:S218F	S	-	2	0	OR51A2	4932867	0.998000	0.40836	0.057000	0.19452	0.032000	0.12392	5.391000	0.66266	1.757000	0.51966	0.395000	0.25975	TCT	G|0.661;A|0.339	0.339	strong		0.428	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
MUC4	4585	hgsc.bcm.edu	37	3	195508902	195508902	+	Silent	SNP	C	C	G	rs144571919		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508902C>G	ENST00000463781.3	-	2	10008	c.9549G>C	c.(9547-9549)acG>acC	p.T3183T	MUC4_ENST00000475231.1_Silent_p.T3183T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CAGGAAGAGGCGTGGTGTCAC	0.597																																					p.T3183T		Atlas-SNP	.											MUC4_ENST00000463781,NS,malignant_melanoma,-1,2	MUC4	1505	2	0			c.G9549C						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			AAGAGGCGTGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9549G>C	3.37:g.195508902C>G		Somatic	226	2	0.00884956		WXS	Illumina HiSeq	Phase_I	229	14	0.0611354	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			C|0.500;G|0.500	0.500	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TECRL	253017	hgsc.bcm.edu	37	4	65274937	65274937	+	Missense_Mutation	SNP	G	G	A	rs61744866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:65274937G>A	ENST00000381210.3	-	1	243	c.133C>T	c.(133-135)Cct>Tct	p.P45S	TECRL_ENST00000507440.1_Missense_Mutation_p.P45S	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	45					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						GGTCTTAGAGGGCCCGCTGAG	0.383													G|||	282	0.0563099	0.1694	0.0259	5008	,	,		16402	0.002		0.0129	False		,,,				2504	0.0256				p.P45S		Atlas-SNP	.											TECRL,NS,carcinoma,+1,1	TECRL	106	1	0			c.C133T						PASS	.	G	SER/PRO	649,3757	277.8+/-273.9	51,547,1605	81.0	81.0	81.0		133	4.1	1.0	4	dbSNP_129	81	121,8479	61.7+/-123.6	1,119,4180	yes	missense	TECRL	NM_001010874.4	74	52,666,5785	AA,AG,GG		1.407,14.7299,5.9203	benign	45/364	65274937	770,12236	2203	4300	6503	SO:0001583	missense	253017	exon1			TTAGAGGGCCCGC	AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678			27365	protein-coding gene	gene with protein product	"""glycoprotein, synaptic 2-like"""					12477932	Standard	NM_001010874		Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.133C>T	4.37:g.65274937G>A	ENSP00000370607:p.Pro45Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	151	78	0.516556	NM_001010874		Missense_Mutation	SNP	ENST00000381210.3	37	CCDS33990.1	105	0.04807692307692308	93	0.18902439024390244	6	0.016574585635359115	0	0.0	6	0.0079155672823219	G	8.680	0.904937	0.17760	0.147299	0.01407	ENSG00000205678	ENST00000507440;ENST00000381210;ENST00000509536	T;T;T	0.41758	0.99;0.99;0.99	4.99	4.09	0.47781	.	0.260412	0.32273	N	0.006335	T	0.00073	0.0002	L	0.48362	1.52	0.39087	P	0.038980000000000015	P;B	0.40180	0.705;0.427	B;B	0.41036	0.346;0.188	T	0.08146	-1.0736	9	0.49607	T	0.09	-5.5054	13.1	0.59214	0.0:0.1606:0.8394:0.0	.	45;45	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	S	45	ENSP00000426043:P45S;ENSP00000370607:P45S;ENSP00000422497:P45S	ENSP00000370607:P45S	P	-	1	0	TECRL	64957532	1.000000	0.71417	0.994000	0.49952	0.012000	0.07955	1.989000	0.40707	2.471000	0.83476	0.655000	0.94253	CCT	G|0.942;A|0.058	0.058	strong		0.383	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874	
PKD1	5310	hgsc.bcm.edu	37	16	2162839	2162839	+	Silent	SNP	T	T	C	rs2099534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2162839T>C	ENST00000262304.4	-	13	3319	c.3111A>G	c.(3109-3111)ctA>ctG	p.L1037L	PKD1_ENST00000423118.1_Silent_p.L1037L|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1037	PKD 5. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CCGTCAGTGCTAGCGTGGCAT	0.652													c|||	100	0.0199681	0.003	0.036	5008	,	,		10955	0.002		0.0676	False		,,,				2504	0.001				p.L1037L		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	1	0			c.A3111G						PASS	.	C	,	38,4356	813.1+/-416.1	1,36,2160	89.0	84.0	86.0		3111,3111	4.0	0.0	16	dbSNP_96	86	499,8101	791.7+/-407.5	14,471,3815	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	15,507,5975	CC,CT,TT		5.8023,0.8648,4.1327	,	1037/4303,1037/4304	2162839	537,12457	2197	4300	6497	SO:0001819	synonymous_variant	5310	exon13			CAGTGCTAGCGTG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.3111A>G	16.37:g.2162839T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			T|0.971;C|0.029	0.029	strong		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
MSH6	2956	hgsc.bcm.edu	37	2	48023115	48023115	+	Silent	SNP	T	T	C	rs1800935	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:48023115T>C	ENST00000234420.5	+	3	692	c.540T>C	c.(538-540)gaT>gaC	p.D180D	MSH6_ENST00000540021.1_Intron|MSH6_ENST00000538136.1_5'UTR|FBXO11_ENST00000405808.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	180					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AACGTGCAGATGAAGCCTTAA	0.433			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				t|||	677	0.135184	0.149	0.1772	5008	,	,		17166	0.0		0.2873	False		,,,				2504	0.0695				p.D180D		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T540C						PASS	.	C		795,3611	320.7+/-296.8	74,647,1482	78.0	72.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	540	1.2	1.0	2	dbSNP_89	74	2465,6135	406.1+/-348.7	358,1749,2193	no	coding-synonymous	MSH6	NM_000179.2		432,2396,3675	CC,CT,TT		28.6628,18.0436,25.0654		180/1361	48023115	3260,9746	2203	4300	6503	SO:0001819	synonymous_variant	2956	exon3	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TGCAGATGAAGCC	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.540T>C	2.37:g.48023115T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	157	66	0.420382	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	37	CCDS1836.1																																																																																			T|0.789;C|0.211	0.211	strong		0.433	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
STK36	27148	hgsc.bcm.edu	37	2	219544388	219544388	+	Missense_Mutation	SNP	A	A	G	rs1863703	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219544388A>G	ENST00000295709.3	+	8	1163	c.884A>G	c.(883-885)aAg>aGg	p.K295R	STK36_ENST00000440309.1_Missense_Mutation_p.K295R|STK36_ENST00000392105.3_Missense_Mutation_p.K295R|STK36_ENST00000392106.2_Missense_Mutation_p.K295R	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		TTGGCCCCCAAGGGTAATCAG	0.562													A|||	802	0.160144	0.4228	0.0663	5008	,	,		19147	0.0883		0.0487	False		,,,				2504	0.0603				p.K295R		Atlas-SNP	.											.	STK36	111	.	0			c.A884G						PASS	.	A	ARG/LYS	1548,2858	475.0+/-357.2	274,1000,929	47.0	51.0	49.0		884	3.0	1.0	2	dbSNP_92	49	486,8114	138.9+/-195.6	14,458,3828	yes	missense	STK36	NM_015690.4	26	288,1458,4757	GG,GA,AA		5.6512,35.1339,15.6389	benign	295/1316	219544388	2034,10972	2203	4300	6503	SO:0001583	missense	27148	exon8			CCCCCAAGGGTAA	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.884A>G	2.37:g.219544388A>G	ENSP00000295709:p.Lys295Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	318	0.14560439560439561	204	0.4146341463414634	28	0.07734806629834254	54	0.0944055944055944	32	0.04221635883905013	A	10.53	1.376618	0.24857	0.351339	0.056512	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	5.38	2.96	0.34315	.	0.000000	0.47852	D	0.000217	T	0.00012	0.0000	N	0.17082	0.46	0.41541	P	0.011480999999999963	B;B	0.29188	0.236;0.056	B;B	0.23716	0.048;0.013	T	0.40232	-0.9574	9	0.25106	T	0.35	-9.6	4.3692	0.11239	0.4844:0.3386:0.177:0.0	rs1863703;rs52801029;rs60396809;rs1863703	295;295	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	R	295	ENSP00000295709:K295R;ENSP00000375955:K295R;ENSP00000375954:K295R;ENSP00000394095:K295R	ENSP00000295709:K295R	K	+	2	0	STK36	219252632	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.858000	0.39408	0.465000	0.27167	0.533000	0.62120	AAG	A|0.834;G|0.166	0.166	strong		0.562	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
BIN2	51411	hgsc.bcm.edu	37	12	51685831	51685831	+	Silent	SNP	T	T	C	rs3210837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51685831T>C	ENST00000267012.4	-	10	1120	c.1059A>G	c.(1057-1059)gaA>gaG	p.E353E	BIN2_ENST00000604560.1_Silent_p.E326E|BIN2_ENST00000452142.2_Silent_p.E321E|BIN2_ENST00000544402.1_Silent_p.E327E	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	353					cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)			NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						ACTTGGCCCTTTCAGTGGTAG	0.587													C|||	3912	0.78115	0.5643	0.8631	5008	,	,		17238	0.8433		0.8598	False		,,,				2504	0.8712				p.E353E		Atlas-SNP	.											.	BIN2	58	.	0			c.A1059G						PASS	.	C		2607,1799	528.9+/-372.5	783,1041,379	47.0	46.0	46.0		1059	2.0	0.0	12	dbSNP_105	46	7417,1183	239.9+/-270.8	3197,1023,80	no	coding-synonymous	BIN2	NM_016293.2		3980,2064,459	CC,CT,TT		13.7558,40.8307,22.9279		353/566	51685831	10024,2982	2203	4300	6503	SO:0001819	synonymous_variant	51411	exon10			GGCCCTTTCAGTG	AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.1059A>G	12.37:g.51685831T>C		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	216	106	0.490741	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Silent	SNP	ENST00000267012.4	37	CCDS8811.1																																																																																			T|0.232;C|0.768	0.768	strong		0.587	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1		
SRP14	6727	hgsc.bcm.edu	37	15	40328665	40328665	+	Silent	SNP	G	G	A	rs8208	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40328665G>A	ENST00000267884.6	-	5	351	c.280C>T	c.(280-282)Ctg>Ttg	p.L94L	SRP14_ENST00000558720.1_Silent_p.L14L|SRP14_ENST00000558527.1_5'UTR|SRP14-AS1_ENST00000504245.1_lincRNA|SRP14_ENST00000560773.1_Silent_p.L14L	NM_003134.4	NP_003125.3	P37108	SRP14_HUMAN	signal recognition particle 14kDa (homologous Alu RNA binding protein)	94					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercellular bridge (GO:0045171)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|skin(1)|upper_aerodigestive_tract(1)	3		all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505)		CTCTTCTTCAGCCCATCCATG	0.488													G|||	2293	0.457867	0.2973	0.4741	5008	,	,		18223	0.2728		0.7058	False		,,,				2504	0.5992				p.L94L		Atlas-SNP	.											SRP14,pharynx,carcinoma,+2,1	SRP14	11	1	0			c.C280T						PASS	.	G		1670,2702		355,960,871	146.0	133.0	137.0		280	5.7	1.0	15	dbSNP_52	137	6188,2402		2249,1690,356	no	coding-synonymous	SRP14	NM_003134.4		2604,2650,1227	AA,AG,GG		27.9627,38.1976,39.3766		94/137	40328665	7858,5104	2186	4295	6481	SO:0001819	synonymous_variant	6727	exon5			TCTTCAGCCCATC		CCDS42017.1	15q22	2008-08-15	2002-08-29		ENSG00000140319	ENSG00000140319			11299	protein-coding gene	gene with protein product		600708	"""signal recognition particle 14kD (homologous Alu RNA-binding protein)"""			8196634	Standard	NM_003134		Approved	ALURBP, MGC14326	uc001zkq.2	P37108		ENST00000267884.6:c.280C>T	15.37:g.40328665G>A		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	166	165	0.993976	NM_003134	B5BUF5|Q6B0K5|Q96Q14	Silent	SNP	ENST00000267884.6	37	CCDS42017.1																																																																																			G|0.439;A|0.561	0.561	strong		0.488	SRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418262.2	NM_003134	
LRP2BP	55805	hgsc.bcm.edu	37	4	186299260	186299260	+	Silent	SNP	A	A	G	rs2030802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:186299260A>G	ENST00000328559.7	-	1	892	c.81T>C	c.(79-81)ttT>ttC	p.F27F	LRP2BP_ENST00000362004.3_Silent_p.F27F|RP11-714G18.1_ENST00000514884.1_RNA|LRP2BP_ENST00000505916.1_Silent_p.F27F|LRP2BP_ENST00000510776.1_5'UTR	NM_018409.3	NP_060879.2	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	27						cytoplasm (GO:0005737)		p.F27F(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(3)|prostate(1)|skin(2)	15		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)		TCCACTGGAAAAATTTTTGGT	0.378													G|||	1855	0.370407	0.612	0.3199	5008	,	,		19885	0.247		0.2624	False		,,,				2504	0.318				p.F27F		Atlas-SNP	.											LRP2BP,NS,carcinoma,0,1	LRP2BP	34	1	1	Substitution - coding silent(1)	prostate(1)	c.T81C						PASS	.	G		2369,2037	565.8+/-381.8	633,1103,467	135.0	137.0	137.0		81	2.9	0.3	4	dbSNP_94	137	2197,6403	712.0+/-405.9	273,1651,2376	no	coding-synonymous	LRP2BP	NM_018409.3		906,2754,2843	GG,GA,AA		25.5465,46.2324,35.1069		27/348	186299260	4566,8440	2203	4300	6503	SO:0001819	synonymous_variant	55805	exon1			CTGGAAAAATTTT	AB037746	CCDS3840.1	4q35.1	2011-05-03			ENSG00000109771	ENSG00000109771			25434	protein-coding gene	gene with protein product						10718198, 12508107	Standard	NM_018409		Approved	DKFZp761O0113	uc003ixj.2	Q9P2M1	OTTHUMG00000160460	ENST00000328559.7:c.81T>C	4.37:g.186299260A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	203	120	0.591133	NM_018409	A6NJR7|A7E219|B3KX83|Q9NSN6	Silent	SNP	ENST00000328559.7	37	CCDS3840.1																																																																																			A|0.641;G|0.359	0.359	strong		0.378	LRP2BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360679.2	NM_018409	
KIF27	55582	hgsc.bcm.edu	37	9	86518796	86518796	+	Missense_Mutation	SNP	T	T	C	rs12001918	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:86518796T>C	ENST00000297814.2	-	4	780	c.637A>G	c.(637-639)Atc>Gtc	p.I213V	KIF27_ENST00000334204.2_Missense_Mutation_p.I213V|KIF27_ENST00000413982.1_Missense_Mutation_p.I213V	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	213	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.		I -> V (in dbSNP:rs12001918).		ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						CAAATGCTGATTGTAAAAATT	0.428													T|||	605	0.120807	0.146	0.0937	5008	,	,		19236	0.1071		0.1312	False		,,,				2504	0.1094				p.I213V		Atlas-SNP	.											.	KIF27	103	.	0			c.A637G						PASS	.	T	VAL/ILE	644,3762	276.6+/-273.2	51,542,1610	184.0	181.0	182.0		637	4.4	1.0	9	dbSNP_120	182	1181,7419	241.0+/-271.5	83,1015,3202	yes	missense	KIF27	NM_017576.1	29	134,1557,4812	CC,CT,TT		13.7326,14.6164,14.032	benign	213/1402	86518796	1825,11181	2203	4300	6503	SO:0001583	missense	55582	exon4			TGCTGATTGTAAA	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.637A>G	9.37:g.86518796T>C	ENSP00000297814:p.Ile213Val	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	196	98	0.5	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	251	0.11492673992673992	70	0.14227642276422764	33	0.09116022099447514	47	0.08216783216783216	101	0.13324538258575197	T	8.680	0.904801	0.17760	0.146164	0.137326	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.76968	-1.06;-1.06;-1.06	5.57	4.44	0.53790	Kinesin, motor domain (5);	0.000000	0.64402	D	0.000016	T	0.01061	0.0035	N	0.25647	0.755	0.29845	P	0.82895	B;P;P	0.42692	0.394;0.763;0.787	B;B;P	0.54499	0.224;0.355;0.754	T	0.36601	-0.9741	9	0.28530	T	0.3	.	10.9173	0.47144	0.0:0.0732:0.0:0.9268	rs12001918;rs52810520;rs60740451;rs12001918	213;213;213	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	V	213	ENSP00000297814:I213V;ENSP00000401688:I213V;ENSP00000333928:I213V	ENSP00000297814:I213V	I	-	1	0	KIF27	85708616	0.971000	0.33674	0.999000	0.59377	0.997000	0.91878	1.695000	0.37763	2.109000	0.64355	0.482000	0.46254	ATC	T|0.869;C|0.131	0.131	strong		0.428	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
PLXDC2	84898	hgsc.bcm.edu	37	10	20506418	20506418	+	Missense_Mutation	SNP	G	G	A	rs3817405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:20506418G>A	ENST00000377252.4	+	11	2027	c.1186G>A	c.(1186-1188)Gta>Ata	p.V396I	PLXDC2_ENST00000377242.3_Missense_Mutation_p.V347I|PLXDC2_ENST00000377238.2_3'UTR	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	396	Thr-rich.		V -> I (in dbSNP:rs3817405). {ECO:0000269|PubMed:11559528, ECO:0000269|PubMed:14702039}.		multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						CACCACAACCGTAGGAGCGAC	0.463													G|||	2836	0.566294	0.7095	0.4481	5008	,	,		14771	0.3085		0.7048	False		,,,				2504	0.5798				p.V396I		Atlas-SNP	.											.	PLXDC2	108	.	0			c.G1186A						PASS	.	G	ILE/VAL	3050,1356	692.4+/-405.5	1061,928,214	105.0	93.0	98.0		1186	-11.1	0.0	10	dbSNP_107	98	5903,2697	683.3+/-403.9	2020,1863,417	yes	missense	PLXDC2	NM_032812.7	29	3081,2791,631	AA,AG,GG		31.3605,30.7762,31.1625	benign	396/530	20506418	8953,4053	2203	4300	6503	SO:0001583	missense	84898	exon11			ACAACCGTAGGAG	AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"""tumor endothelial marker 7-related precursor"""	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.1186G>A	10.37:g.20506418G>A	ENSP00000366460:p.Val396Ile	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_032812	Q96E59|Q96PD9|Q96SU9	Missense_Mutation	SNP	ENST00000377252.4	37	CCDS7132.1	1218	0.5576923076923077	328	0.6666666666666666	171	0.4723756906077348	189	0.3304195804195804	530	0.6992084432717678	G	2.036	-0.421120	0.04734	0.692238	0.686395	ENSG00000120594	ENST00000377252;ENST00000377242;ENST00000377238;ENST00000536022	T;T	0.76186	-1.0;-1.0	5.55	-11.1	0.00147	.	1.592360	0.03333	N	0.193686	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.06405	0.002;0.001	T	0.26155	-1.0111	9	0.20046	T	0.44	.	4.8745	0.13650	0.3482:0.1657:0.4043:0.0818	rs3817405;rs17701255;rs52810029;rs58107023;rs3817405	347;396	Q6UX71-2;Q6UX71	.;PXDC2_HUMAN	I	396;347;259;382	ENSP00000366460:V396I;ENSP00000366450:V347I	ENSP00000366446:V259I	V	+	1	0	PLXDC2	20546424	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-2.181000	0.01257	-2.080000	0.00870	-0.993000	0.02533	GTA	G|0.364;N|0.000	.	strong		0.463	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812	
FAM26D	221301	hgsc.bcm.edu	37	6	116875427	116875427	+	Silent	SNP	G	G	A	rs7762318	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116875427G>A	ENST00000368596.3	+	1	515	c.471G>A	c.(469-471)ctG>ctA	p.L157L	FAM26D_ENST00000416171.2_Intron|FAM26D_ENST00000405399.1_Silent_p.L14L|FAM26D_ENST00000368597.2_Intron			Q5JW98	FA26D_HUMAN	family with sequence similarity 26, member D	157					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				endometrium(1)|lung(5)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0458)|OV - Ovarian serous cystadenocarcinoma(136;0.0694)|Epithelial(106;0.222)		AAGAGATCCTGGCTGGGTTTC	0.438													A|||	3218	0.642572	0.4198	0.7349	5008	,	,		21800	0.8978		0.6123	False		,,,				2504	0.6462				p.L14L		Atlas-SNP	.											.	FAM26D	29	.	0			c.G42A						PASS	.																																			SO:0001819	synonymous_variant	221301	exon3			GATCCTGGCTGGG	AK056801	CCDS5109.1, CCDS59032.1	6q22.31	2008-02-05	2007-03-19	2007-03-19	ENSG00000164451	ENSG00000164451			21094	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 78"""	C6orf78			Standard	NM_153036		Approved	FLJ32239	uc010ked.4	Q5JW98	OTTHUMG00000015443	ENST00000368596.3:c.471G>A	6.37:g.116875427G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	93	62	0.666667	NM_001256887	B0QZ25|B0QZ27|B4DTQ0|Q96MK0	Silent	SNP	ENST00000368596.3	37																																																																																				G|0.359;A|0.641	0.641	strong		0.438	FAM26D-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000041958.1	NM_153036	
SLC38A10	124565	hgsc.bcm.edu	37	17	79255998	79255998	+	Silent	SNP	G	G	A	rs10871494	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79255998G>A	ENST00000374759.3	-	5	875	c.492C>T	c.(490-492)ttC>ttT	p.F164F	SLC38A10_ENST00000546352.1_5'UTR|SLC38A10_ENST00000288439.5_Silent_p.F164F	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	164					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCACGAACATGAACACGGTGT	0.632													G|||	567	0.113219	0.1157	0.1931	5008	,	,		19566	0.003		0.2207	False		,,,				2504	0.0562				p.F164F		Atlas-SNP	.											SLC38A10_ENST00000374759,NS,carcinoma,0,2	SLC38A10	133	2	0			c.C492T						PASS	.	G	,	567,3839	253.7+/-259.5	35,497,1671	117.0	97.0	104.0		492,492	4.4	1.0	17	dbSNP_120	104	1787,6813	322.2+/-315.5	210,1367,2723	no	coding-synonymous,coding-synonymous	SLC38A10	NM_001037984.1,NM_138570.2	,	245,1864,4394	AA,AG,GG		20.7791,12.8688,18.0993	,	164/1120,164/781	79255998	2354,10652	2203	4300	6503	SO:0001819	synonymous_variant	124565	exon5			GAACATGAACACG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.492C>T	17.37:g.79255998G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1	293	0.13415750915750915	53	0.10772357723577236	73	0.20165745856353592	1	0.0017482517482517483	166	0.21899736147757257	G	11.20	1.569041	0.28003	0.128688	0.207791	ENSG00000157637	ENST00000543204	.	.	.	5.34	4.36	0.52297	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.05115	-1.0905	3	.	.	.	-25.819	11.612	0.51066	0.1424:0.0:0.8576:0.0	rs10871494;rs10871494	.	.	.	Y	23	.	.	H	-	1	0	SLC38A10	76870593	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.645000	0.54389	2.485000	0.83878	0.655000	0.94253	CAT	G|0.845;A|0.155	0.155	strong		0.632	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
LAMA5	3911	hgsc.bcm.edu	37	20	60909060	60909060	+	Silent	SNP	A	A	G	rs13038331|rs112350373	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60909060A>G	ENST00000252999.3	-	23	2841	c.2775T>C	c.(2773-2775)ccT>ccC	p.P925P	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	925	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGAAAAGGTCAGGGGAGGTCA	0.667													a|||	3789	0.756589	0.4486	0.8069	5008	,	,		12822	0.9365		0.9165	False		,,,				2504	0.7873				p.P925P		Atlas-SNP	.											.	LAMA5	268	.	0			c.T2775C						PASS	.			2391,2009		654,1083,463	36.0	30.0	33.0		2775	-9.1	0.8	20	dbSNP_121	33	7961,629		3695,571,29	no	coding-synonymous	LAMA5	NM_005560.3		4349,1654,492	GG,GA,AA		7.3225,45.6591,20.3079		925/3696	60909060	10352,2638	2200	4295	6495	SO:0001819	synonymous_variant	3911	exon23			AAGGTCAGGGGAG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.2775T>C	20.37:g.60909060A>G		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	219	218	0.995434	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			A|0.201;G|0.799	0.799	strong		0.667	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
ZDHHC7	55625	hgsc.bcm.edu	37	16	85015541	85015541	+	Silent	SNP	G	G	A	rs16975086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:85015541G>A	ENST00000313732.4	-	4	727	c.375C>T	c.(373-375)ccC>ccT	p.P125P	ZDHHC7_ENST00000564466.1_Silent_p.P162P|ZDHHC7_ENST00000569488.1_Intron	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	125					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(4)	10						TGACTTCCCCGGGCTTCAGCT	0.517													G|||	668	0.133387	0.0083	0.304	5008	,	,		16621	0.1508		0.1571	False		,,,				2504	0.1391				p.P162P		Atlas-SNP	.											.	ZDHHC7	55	.	0			c.C486T						PASS	.	G	,	166,4232	110.8+/-149.0	2,162,2035	145.0	154.0	151.0		486,375	-10.7	0.0	16	dbSNP_123	151	1470,7130	281.8+/-295.3	126,1218,2956	no	coding-synonymous,coding-synonymous	ZDHHC7	NM_001145548.1,NM_017740.2	,	128,1380,4991	AA,AG,GG		17.093,3.7744,12.5866	,	162/346,125/309	85015541	1636,11362	2199	4300	6499	SO:0001819	synonymous_variant	55625	exon5			TTCCCCGGGCTTC	AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"""Zinc fingers, DHHC-type"""	18459	protein-coding gene	gene with protein product	"""Sertoli cell gene with zinc finger domain-&#946;"""	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.375C>T	16.37:g.85015541G>A		Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	218	100	0.458716	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Silent	SNP	ENST00000313732.4	37	CCDS10950.1																																																																																			G|0.870;A|0.129	0.129	strong		0.517	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740	
AGBL1	123624	hgsc.bcm.edu	37	15	86807884	86807884	+	Silent	SNP	A	A	C	rs11856833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:86807884A>C	ENST00000441037.2	+	10	1439	c.1344A>C	c.(1342-1344)gtA>gtC	p.V448V	AGBL1_ENST00000421325.2_Silent_p.V448V|AGBL1_ENST00000389298.3_Silent_p.V179V	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	448					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TTGTCAAAGTAATAGATAAGC	0.468													A|||	670	0.133786	0.1029	0.1988	5008	,	,		20122	0.0278		0.1809	False		,,,				2504	0.1902				p.V448V		Atlas-SNP	.											.	AGBL1	151	.	0			c.A1344C						PASS	.	A		453,3299		26,401,1449	129.0	127.0	127.0		1344	-2.8	0.0	15	dbSNP_120	127	1633,6603		162,1309,2647	no	coding-synonymous	AGBL1	NM_152336.2		188,1710,4096	CC,CA,AA		19.8276,12.0736,17.4007		448/1067	86807884	2086,9902	1876	4118	5994	SO:0001819	synonymous_variant	123624	exon10			CAAAGTAATAGAT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.1344A>C	15.37:g.86807884A>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			A|0.876;C|0.124	0.124	strong		0.468	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
LRP2	4036	hgsc.bcm.edu	37	2	170175334	170175334	+	Missense_Mutation	SNP	T	T	C	rs2229263	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170175334T>C	ENST00000263816.3	-	3	533	c.248A>G	c.(247-249)aAc>aGc	p.N83S	LRP2_ENST00000443831.1_Missense_Mutation_p.N83S	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	83	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.		N -> S (in dbSNP:rs2229263). {ECO:0000269|PubMed:8706697}.		cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CACCCAGGAGTTGGGGATGCA	0.473													T|||	1534	0.30631	0.4818	0.2118	5008	,	,		21257	0.2758		0.2783	False		,,,				2504	0.1963				p.N83S		Atlas-SNP	.											.	LRP2	751	.	0			c.A248G						PASS	.	T	SER/ASN	1915,2491	547.0+/-377.2	431,1053,719	144.0	122.0	129.0		248	-6.3	0.0	2	dbSNP_98	129	2524,6076	414.1+/-351.3	363,1798,2139	yes	missense	LRP2	NM_004525.2	46	794,2851,2858	CC,CT,TT		29.3488,43.4635,34.1304	benign	83/4656	170175334	4439,8567	2203	4300	6503	SO:0001583	missense	4036	exon3			CAGGAGTTGGGGA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.248A>G	2.37:g.170175334T>C	ENSP00000263816:p.Asn83Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	673	0.30815018315018317	240	0.4878048780487805	83	0.2292817679558011	142	0.24825174825174826	208	0.27440633245382584	T	5.794	0.330732	0.10956	0.434635	0.293488	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.95307	-3.67;-3.67	6.02	-6.27	0.02026	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	2.042490	0.01599	N	0.021945	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B;B	0.10296	0.0;0.003	B;B	0.10450	0.001;0.005	T	0.33497	-0.9866	8	.	.	.	.	2.1449	0.03784	0.1361:0.3669:0.1931:0.3039	rs2229263;rs2302916;rs6716834;rs17848145;rs52789446;rs58366843;rs6716834	83;83	E9PC35;P98164	.;LRP2_HUMAN	S	83	ENSP00000263816:N83S;ENSP00000409813:N83S	.	N	-	2	0	LRP2	169883580	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.760000	0.04756	-1.027000	0.03325	0.533000	0.62120	AAC	T|0.548;G|0.057	.	strong		0.473	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
MYPN	84665	hgsc.bcm.edu	37	10	69933969	69933969	+	Missense_Mutation	SNP	G	G	A	rs7916821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:69933969G>A	ENST00000358913.5	+	11	2608	c.2120G>A	c.(2119-2121)aGt>aAt	p.S707N	MYPN_ENST00000354393.2_Missense_Mutation_p.S432N|MYPN_ENST00000540630.1_Missense_Mutation_p.S707N	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	707			S -> N (in dbSNP:rs7916821). {ECO:0000269|PubMed:11309420, ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						ACAACATCCAGTAAGCAGGTG	0.532													G|||	1628	0.32508	0.1762	0.4035	5008	,	,		18267	0.2163		0.4851	False		,,,				2504	0.4182				p.S707N		Atlas-SNP	.											.	MYPN	189	.	0			c.G2120A						PASS	.	G	ASN/SER	977,3429	367.3+/-318.2	109,759,1335	126.0	122.0	123.0		2120	4.7	1.0	10	dbSNP_116	123	4126,4474	564.6+/-388.3	1042,2042,1216	yes	missense	MYPN	NM_032578.2	46	1151,2801,2551	AA,AG,GG		47.9767,22.1743,39.2357	benign	707/1321	69933969	5103,7903	2203	4300	6503	SO:0001583	missense	84665	exon11			CATCCAGTAAGCA	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2120G>A	10.37:g.69933969G>A	ENSP00000351790:p.Ser707Asn	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	247	121	0.489879	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	752	0.3443223443223443	103	0.20934959349593496	152	0.4198895027624309	129	0.22552447552447552	368	0.48548812664907653	G	11.58	1.680407	0.29872	0.221743	0.479767	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.58210	0.35;0.44;0.42	5.64	4.68	0.58851	.	0.566496	0.20639	N	0.088436	T	0.00012	0.0000	L	0.36672	1.1	0.40218	P	0.022298999999999958	B;B;B	0.23806	0.045;0.091;0.026	B;B;B	0.26310	0.068;0.032;0.031	T	0.44360	-0.9333	8	.	.	.	.	8.7519	0.34620	0.1116:0.0:0.7493:0.1391	rs7916821;rs17536754;rs52812363;rs56567864;rs57392128;rs7916821	707;432;707	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	N	432;432;707;707	ENSP00000346369:S432N;ENSP00000351790:S707N;ENSP00000441668:S707N	.	S	+	2	0	MYPN	69603975	0.513000	0.26194	1.000000	0.80357	0.719000	0.41307	0.501000	0.22578	2.832000	0.97577	0.655000	0.94253	AGT	G|0.638;A|0.362	0.362	strong		0.532	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
GCNT2	2651	hgsc.bcm.edu	37	6	10556872	10556872	+	Intron	SNP	C	C	T	rs2230906	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:10556872C>T	ENST00000379597.3	+	1	1481				GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000316170.3_Silent_p.C72C			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		AGTCTTCTTGCAAGGAATACT	0.413													C|||	270	0.0539137	0.0318	0.0533	5008	,	,		20722	0.0089		0.1322	False		,,,				2504	0.0501				p.C72C		Atlas-SNP	.											.	GCNT2	123	.	0			c.C216T						PASS	.	C	,	222,4184	134.5+/-170.7	11,200,1992	131.0	124.0	126.0		216,	4.2	0.5	6	dbSNP_98	126	1130,7470	233.6+/-266.8	90,950,3260	no	coding-synonymous,intron	GCNT2	NM_001491.2,NM_145649.4	,	101,1150,5252	TT,TC,CC		13.1395,5.0386,10.3952	,	72/401,	10556872	1352,11654	2203	4300	6503	SO:0001627	intron_variant	2651	exon1			TTCTTGCAAGGAA	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.925+26803C>T	6.37:g.10556872C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	178	97	0.544944	NM_001491		Silent	SNP	ENST00000379597.3	37	CCDS34338.1																																																																																			C|0.905;T|0.095	0.095	strong		0.413	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
MUC16	94025	hgsc.bcm.edu	37	19	9077803	9077803	+	Missense_Mutation	SNP	T	T	C	rs2591597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9077803T>C	ENST00000397910.4	-	3	9846	c.9643A>G	c.(9643-9645)Agc>Ggc	p.S3215G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3216	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGCTGATGCTGGGTTCCTTG	0.478													C|||	1244	0.248403	0.2005	0.2118	5008	,	,		19215	0.249		0.3121	False		,,,				2504	0.273				p.S3215G		Atlas-SNP	.											.	MUC16	4315	.	0			c.A9643G						PASS	.	C	GLY/SER	813,3071		96,621,1225	143.0	139.0	140.0		9643	0.8	0.0	19	dbSNP_100	140	2385,5895		346,1693,2101	yes	missense	MUC16	NM_024690.2	56	442,2314,3326	CC,CT,TT		28.8043,20.932,26.2907	benign	3215/14508	9077803	3198,8966	1942	4140	6082	SO:0001583	missense	94025	exon3			TGATGCTGGGTTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.9643A>G	19.37:g.9077803T>C	ENSP00000381008:p.Ser3215Gly	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	278	134	0.482014	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	553	0.2532051282051282	109	0.22154471544715448	88	0.2430939226519337	124	0.21678321678321677	232	0.30606860158311344	c	2.692	-0.272980	0.05716	0.20932	0.288043	ENSG00000181143	ENST00000397910	T	0.02606	4.23	1.86	0.813	0.18749	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.06786	0.001	B	0.09377	0.004	T	0.47071	-0.9145	8	0.87932	D	0	.	5.6327	0.17520	0.0:0.1705:0.0:0.8295	rs2591597;rs52795507;rs59466788;rs2591597	3215	B5ME49	.	G	3215	ENSP00000381008:S3215G	ENSP00000381008:S3215G	S	-	1	0	MUC16	8938803	0.003000	0.15002	0.002000	0.10522	0.012000	0.07955	-0.572000	0.05881	-0.165000	0.10908	-2.028000	0.00425	AGC	T|0.751;C|0.249	0.249	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
RNASE3	6037	hgsc.bcm.edu	37	14	21360216	21360216	+	Missense_Mutation	SNP	C	C	G	rs2073342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21360216C>G	ENST00000304639.3	+	2	429	c.371C>G	c.(370-372)aCg>aGg	p.T124R		NM_002935.2	NP_002926.2	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3	124			T -> R (in dbSNP:rs2073342). {ECO:0000269|PubMed:11102386, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2387583, ECO:0000269|PubMed:2473157, ECO:0000269|PubMed:2745977, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.		antibacterial humoral response (GO:0019731)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)	9	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	TCAAACTGCACGTATGCAGAC	0.468													N|||	3208	0.640575	0.3722	0.8199	5008	,	,		20428	0.7361		0.7197	False		,,,				2504	0.6963				p.T124R		Atlas-SNP	.											.	RNASE3	24	.	0			c.C371G	GRCh37	CM025442	RNASE3	M	rs2073342	PASS	.	G	ARG/THR	1936,2442		506,924,759	90.0	91.0	91.0		371	-3.4	0.0	14	dbSNP_96	91	6170,2430		2198,1774,328	yes	missense	RNASE3	NM_002935.2	71	2704,2698,1087	GG,GC,CC		28.2558,44.2211,37.5405	benign	124/161	21360216	8106,4872	2189	4300	6489	SO:0001583	missense	6037	exon2			ACTGCACGTATGC	X55990	CCDS9560.1	14q11.2	2014-03-13	2010-05-07		ENSG00000169397	ENSG00000169397	3.1.27.-	"""Ribonucleases, RNase A"""	10046	protein-coding gene	gene with protein product	"""eosinophil cationic protein"""	131398		RNS3		1577491	Standard	NM_002935		Approved	ECP	uc001vyj.3	P12724	OTTHUMG00000029604	ENST00000304639.3:c.371C>G	14.37:g.21360216C>G	ENSP00000302324:p.Thr124Arg	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	163	93	0.570552	NM_002935	Q4VBC1|Q8WTP7|Q8WZ62|Q9GZN9	Missense_Mutation	SNP	ENST00000304639.3	37	CCDS9560.1	1446	0.6620879120879121	192	0.3902439024390244	291	0.8038674033149171	418	0.7307692307692307	545	0.7189973614775725	N	0	-2.645508	0.00111	0.442211	0.717442	ENSG00000169397	ENST00000304639	T	0.70869	-0.52	2.38	-3.36	0.04913	Ribonuclease A, domain (4);	1.880480	0.03311	N	0.190493	T	0.00012	0.0000	N	0.00050	-2.405	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41998	-0.9477	9	0.02654	T	1	.	1.3073	0.02091	0.4407:0.1483:0.2609:0.1501	rs2073342;rs17097802;rs52830406;rs58295636;rs2073342	124	P12724	ECP_HUMAN	R	124	ENSP00000302324:T124R	ENSP00000302324:T124R	T	+	2	0	RNASE3	20430056	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.009000	0.00648	-1.709000	0.01399	-3.638000	0.00026	ACG	C|0.360;G|0.639	0.639	strong		0.468	RNASE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073795.2	NM_002935	
NFASC	23114	hgsc.bcm.edu	37	1	204970302	204970302	+	Silent	SNP	T	T	C	rs4951151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204970302T>C	ENST00000401399.1	+	25	3223	c.3024T>C	c.(3022-3024)ccT>ccC	p.P1008P	NFASC_ENST00000338515.6_Intron|NFASC_ENST00000404076.1_Intron|NFASC_ENST00000360049.4_Intron|NFASC_ENST00000367169.4_Intron|NFASC_ENST00000367172.4_Silent_p.P1115P|NFASC_ENST00000404907.1_Intron|NFASC_ENST00000338586.6_Intron|NFASC_ENST00000513543.1_Intron|NFASC_ENST00000367170.4_Silent_p.P1036P|NFASC_ENST00000367171.4_Silent_p.P1100P|NFASC_ENST00000495396.1_Intron|NFASC_ENST00000339876.6_Silent_p.P1008P|NFASC_ENST00000539706.1_Intron			O94856	NFASC_HUMAN	neurofascin	1115	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CACCAGCCCCTGATGAGCAGT	0.537													t|||	1155	0.230631	0.1573	0.1787	5008	,	,		19216	0.2401		0.2575	False		,,,				2504	0.3292				p.P1008P		Atlas-SNP	.											NFASC_ENST00000339876,NS,carcinoma,0,1	NFASC	396	1	0			c.T3024C						PASS	.	T	,,,	570,2562		54,462,1050	64.0	57.0	59.0		3024,,,	-0.9	1.0	1	dbSNP_111	59	1759,5405		206,1347,2029	no	coding-synonymous,intron,intron,intron	NFASC	NM_001005388.2,NM_001160331.1,NM_001160332.1,NM_015090.3	,,,	260,1809,3079	CC,CT,TT		24.5533,18.1992,22.6204	,,,	1008/1241,,,	204970302	2329,7967	1566	3582	5148	SO:0001819	synonymous_variant	23114	exon26			AGCCCCTGATGAG	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.3024T>C	1.37:g.204970302T>C		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	462	0.21153846153846154	64	0.13008130081300814	80	0.22099447513812154	124	0.21678321678321677	194	0.2559366754617414	t	9.682	1.149614	0.21288	0.181992	0.245533	ENSG00000163531	ENST00000413225	.	.	.	5.39	-0.904	0.10530	.	.	.	.	.	.	.	.	.	.	.	0.25184	P	0.99018937	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.876	0.24147	0.0:0.4903:0.1123:0.3974	rs4951151;rs4951151	.	.	.	R	55	.	.	X	+	1	0	NFASC	203236925	0.016000	0.18221	0.984000	0.44739	0.994000	0.84299	-1.014000	0.03641	-0.204000	0.10235	-0.140000	0.14226	TGA	T|0.790;C|0.210	0.210	strong		0.537	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
RAD21L1	642636	hgsc.bcm.edu	37	20	1221038	1221038	+	Silent	SNP	T	T	C	rs16992733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1221038T>C	ENST00000409241.1	+	8	909	c.816T>C	c.(814-816)acT>acC	p.T272T	RAD21L1_ENST00000381882.2_Silent_p.T272T|RAD21L1_ENST00000402452.1_Silent_p.T272T	NM_001136566.2	NP_001130038.2	Q9H4I0	RD21L_HUMAN	RAD21-like 1 (S. pombe)	272					attachment of telomeric heterochromatin to nuclear envelope (GO:0070197)|chromosome segregation (GO:0007059)|double-strand break repair via homologous recombination (GO:0000724)|fertilization (GO:0009566)|linear element assembly (GO:0030999)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleus (GO:0005634)				NS(1)|breast(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	7						TATTATCAACTGAAGAGGAAG	0.289													T|||	351	0.0700879	0.0219	0.0605	5008	,	,		18169	0.1726		0.0895	False		,,,				2504	0.0164				p.T272T		Atlas-SNP	.											.	RAD21L1	51	.	0			c.T816C						PASS	.	T		31,1353		0,31,661	74.0	66.0	69.0		816	1.9	1.0	20	dbSNP_123	69	285,2889		18,249,1320	no	coding-synonymous	RAD21L1	NM_001136566.2		18,280,1981	CC,CT,TT		8.9792,2.2399,6.9329		272/557	1221038	316,4242	692	1587	2279	SO:0001819	synonymous_variant	642636	exon8			ATCAACTGAAGAG	AL031665	CCDS46568.1	20p13	2011-08-12			ENSG00000244588	ENSG00000244588			16271	protein-coding gene	gene with protein product							Standard	NM_001136566		Approved	dJ545L17.2, RAD21L	uc010gab.1	Q9H4I0	OTTHUMG00000031664	ENST00000409241.1:c.816T>C	20.37:g.1221038T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_001136566	B2RXL0|B7ZBB1|B7ZW76|Q5W0X5	Silent	SNP	ENST00000409241.1	37	CCDS46568.1																																																																																			T|0.914;C|0.086	0.086	strong		0.289	RAD21L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334022.1		
UGT2B28	54490	hgsc.bcm.edu	37	4	70146230	70146230	+	Silent	SNP	G	G	A	rs13139691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70146230G>A	ENST00000335568.5	+	1	14	c.12G>A	c.(10-12)aaG>aaA	p.K4K	UGT2B28_ENST00000511240.1_Silent_p.K4K	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	4					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						TGGCTCTGAAGTGGACTTCAG	0.408													-|||	3206	0.640176	0.5877	0.67	5008	,	,		15999	0.5952		0.7654	False		,,,				2504	0.6074				p.K4K		Atlas-SNP	.											UGT2B28,colon,carcinoma,0,1	UGT2B28	101	1	0			c.G12A						PASS	.	A	,	2684,1408		1095,494,457	153.0	170.0	164.0		12,12	-0.6	0.0	4	dbSNP_121	164	6606,1872		2759,1088,392	no	coding-synonymous,coding-synonymous	UGT2B28	NM_001207004.1,NM_053039.1	,	3854,1582,849	AA,AG,GG		22.0807,34.4086,26.0939	,	4/336,4/530	70146230	9290,3280	2046	4239	6285	SO:0001819	synonymous_variant	54490	exon1			TCTGAAGTGGACT	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.12G>A	4.37:g.70146230G>A		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_053039	B5BUM0|Q9BY62|Q9BY63	Silent	SNP	ENST00000335568.5	37	CCDS3528.1																																																																																			G|0.337;A|0.663	0.663	strong		0.408	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
WDFY3	23001	hgsc.bcm.edu	37	4	85708792	85708792	+	Silent	SNP	G	G	A	rs34548715	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:85708792G>A	ENST00000295888.4	-	23	4151	c.3744C>T	c.(3742-3744)taC>taT	p.Y1248Y	WDFY3_ENST00000322366.6_Silent_p.Y1248Y	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1248					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GAGTACCAATGTAGGCATAGA	0.473													G|||	171	0.0341454	0.0454	0.0159	5008	,	,		18471	0.001		0.0358	False		,,,				2504	0.0644				p.Y1248Y		Atlas-SNP	.											.	WDFY3	314	.	0			c.C3744T						PASS	.	G		181,4225	117.1+/-155.0	4,173,2026	92.0	80.0	84.0		3744	4.2	0.8	4	dbSNP_126	84	308,8292	110.2+/-170.6	9,290,4001	no	coding-synonymous	WDFY3	NM_014991.4		13,463,6027	AA,AG,GG		3.5814,4.108,3.7598		1248/3527	85708792	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	23001	exon23			ACCAATGTAGGCA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.3744C>T	4.37:g.85708792G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	37	CCDS3609.1																																																																																			G|0.962;A|0.038	0.038	strong		0.473	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
MUC4	4585	hgsc.bcm.edu	37	3	195506147	195506147	+	Missense_Mutation	SNP	G	G	A	rs200473856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506147G>A	ENST00000463781.3	-	2	12763	c.12304C>T	c.(12304-12306)Ctt>Ttt	p.L4102F	MUC4_ENST00000475231.1_Missense_Mutation_p.L4102F|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAAGGCTGGTGAGA	0.592																																					p.L4102F		Atlas-SNP	.											MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	0			c.C12304T						scavenged	.						18.0	10.0	12.0					3																	195506147		567	1388	1955	SO:0001583	missense	4585	exon2			AGGAAAGGCTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12304C>T	3.37:g.195506147G>A	ENSP00000417498:p.Leu4102Phe	Somatic	216	2	0.00925926		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	12.07	1.828712	0.32329	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.49	.	.	.	.	.	.	.	.	T	0.22244	0.0536	N	0.19112	0.55	0.09310	N	0.999998	P	0.44006	0.824	P	0.48704	0.587	T	0.17107	-1.0380	6	.	.	.	.	.	.	.	.	3974	E7ESK3	.	F	4102	ENSP00000417498:L4102F;ENSP00000420243:L4102F	.	L	-	1	0	MUC4	196990926	0.002000	0.14202	0.004000	0.12327	0.022000	0.10575	0.632000	0.24583	-0.417000	0.07461	0.064000	0.15345	CTT	G|0.981;A|0.019	0.019	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DNAH5	1767	hgsc.bcm.edu	37	5	13894894	13894894	+	Missense_Mutation	SNP	T	T	A	rs4701997	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13894894T>A	ENST00000265104.4	-	16	2400	c.2296A>T	c.(2296-2298)Ata>Tta	p.I766L	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	766	Stem. {ECO:0000250}.		I -> L (in dbSNP:rs4701997).		cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I766L(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GCAGCAGGTATTTTTGACTTC	0.408									Kartagener syndrome				T|||	2443	0.487819	0.5681	0.4654	5008	,	,		18015	0.249		0.5	False		,,,				2504	0.6288				p.I766L		Atlas-SNP	.											DNAH5,NS,carcinoma,0,1	DNAH5	868	1	1	Substitution - Missense(1)	stomach(1)	c.A2296T						PASS	.	T	LEU/ILE	2349,2057	609.7+/-391.4	615,1119,469	175.0	164.0	168.0		2296	4.4	1.0	5	dbSNP_111	168	4368,4232	582.7+/-391.4	1127,2114,1059	yes	missense	DNAH5	NM_001369.2	5	1742,3233,1528	AA,AT,TT		49.2093,46.6863,48.3546	benign	766/4625	13894894	6717,6289	2203	4300	6503	SO:0001583	missense	1767	exon16	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAGGTATTTTTGA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.2296A>T	5.37:g.13894894T>A	ENSP00000265104:p.Ile766Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	965	0.44184981684981683	281	0.5711382113821138	175	0.48342541436464087	140	0.24475524475524477	369	0.4868073878627968	T	11.42	1.634972	0.29068	0.533137	0.507907	ENSG00000039139	ENST00000265104	T	0.47869	0.83	5.53	4.37	0.52481	Dynein heavy chain, domain-1 (1);	0.227351	0.51477	D	0.000098	T	0.00012	0.0000	M	0.64404	1.975	0.30184	P	0.800164	B	0.06786	0.001	B	0.20955	0.032	T	0.44967	-0.9293	9	0.13470	T	0.59	.	8.5314	0.33337	0.0:0.1491:0.0:0.8509	rs4701997;rs17210254;rs52819664;rs4701997	766	Q8TE73	DYH5_HUMAN	L	766	ENSP00000265104:I766L	ENSP00000265104:I766L	I	-	1	0	DNAH5	13947894	1.000000	0.71417	1.000000	0.80357	0.421000	0.31385	3.012000	0.49575	0.935000	0.37341	0.459000	0.35465	ATA	T|0.517;A|0.483	0.483	strong		0.408	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
SEMA3E	9723	hgsc.bcm.edu	37	7	82996931	82996931	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82996931G>A	ENST00000307792.3	-	17	2766	c.2299C>T	c.(2299-2301)Cgc>Tgc	p.R767C	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R707C	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	767	Arg/Lys-rich (basic).				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				CTGGGCAGGCGGTAATGCTCA	0.418																																					p.R767C		Atlas-SNP	.											.	SEMA3E	125	.	0			c.C2299T						PASS	.						172.0	172.0	172.0					7																	82996931		2203	4300	6503	SO:0001583	missense	9723	exon17			GCAGGCGGTAATG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.2299C>T	7.37:g.82996931G>A	ENSP00000303212:p.Arg767Cys	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	233	112	0.480687	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281561	0.80692	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.36157	1.31;1.27	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.65396	0.2687	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68727	-0.5332	10	0.87932	D	0	.	19.7061	0.96072	0.0:0.0:1.0:0.0	.	767	O15041	SEM3E_HUMAN	C	767;707;758	ENSP00000303212:R767C;ENSP00000405052:R707C	ENSP00000303212:R767C	R	-	1	0	SEMA3E	82834867	1.000000	0.71417	0.986000	0.45419	0.664000	0.39144	4.641000	0.61375	2.660000	0.90430	0.585000	0.79938	CGC	.	.	none		0.418	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
CAPN15	6650	hgsc.bcm.edu	37	16	602647	602647	+	Missense_Mutation	SNP	C	C	T	rs200960455	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:602647C>T	ENST00000219611.2	+	12	3143	c.2780C>T	c.(2779-2781)cCg>cTg	p.P927L	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	927					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCCCCAGAGCCGCCGGGCCAC	0.711													c|||	4	0.000798722	0.0008	0.0	5008	,	,		10136	0.001		0.002	False		,,,				2504	0.0				p.P927L		Atlas-SNP	.											.	SOLH	47	.	0			c.C2780T						PASS	.	C	LEU/PRO	2,3806		0,2,1902	4.0	6.0	5.0		2780	4.7	0.6	16		5	19,7667		0,19,3824	yes	missense	SOLH	NM_005632.2	98	0,21,5726	TT,TC,CC		0.2472,0.0525,0.1827	benign	927/1087	602647	21,11473	1904	3843	5747	SO:0001583	missense	6650	exon12			CAGAGCCGCCGGG	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2780C>T	16.37:g.602647C>T	ENSP00000219611:p.Pro927Leu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	37	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	c	3.563	-0.089241	0.07097	5.25E-4	0.002472	ENSG00000103326	ENST00000219611	D	0.87887	-2.31	4.71	4.71	0.59529	.	0.247201	0.41938	D	0.000781	T	0.76800	0.4038	N	0.22421	0.69	0.44012	D	0.99672	B	0.30179	0.271	B	0.15870	0.014	T	0.73672	-0.3909	10	0.14656	T	0.56	.	16.7447	0.85469	0.0:1.0:0.0:0.0	.	927	O75808	CAN15_HUMAN	L	927	ENSP00000219611:P927L	ENSP00000219611:P927L	P	+	2	0	SOLH	542648	0.953000	0.32496	0.593000	0.28771	0.069000	0.16628	1.901000	0.39838	2.607000	0.88179	0.556000	0.70494	CCG	.	.	weak		0.711	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	
CACNA1H	8912	hgsc.bcm.edu	37	16	1258033	1258033	+	Missense_Mutation	SNP	G	G	T	rs41292285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1258033G>T	ENST00000348261.5	+	16	3423	c.3175G>T	c.(3175-3177)Gcc>Tcc	p.A1059S	RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000358590.4_Missense_Mutation_p.A1059S|CACNA1H_ENST00000565831.1_Missense_Mutation_p.A1059S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1059					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GTGTTCCCTGGCCGTGACCCC	0.647													G|||	17	0.00339457	0.0008	0.0086	5008	,	,		15928	0.0		0.007	False		,,,				2504	0.0031				p.A1059S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G3175T	GRCh37	CM076048	CACNA1H	M	rs41292285	PASS	.	G	SER/ALA,SER/ALA	10,4036		0,10,2013	24.0	31.0	29.0		3175,3175	3.0	0.7	16	dbSNP_127	29	83,8211		0,83,4064	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	99,99	0,93,6077	TT,TG,GG		1.0007,0.2472,0.7536	probably-damaging,probably-damaging	1059/2348,1059/2354	1258033	93,12247	2023	4147	6170	SO:0001583	missense	8912	exon16			TCCCTGGCCGTGA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.3175G>T	16.37:g.1258033G>T	ENSP00000334198:p.Ala1059Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	14	0.00641025641025641	0	0.0	7	0.019337016574585635	0	0.0	7	0.009234828496042216	G	4.225	0.040710	0.08196	0.002472	0.010007	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96491	-4.03;-3.98	4.01	3.02	0.34903	.	1.003600	0.08028	N	0.992969	D	0.88865	0.6553	L	0.44542	1.39	0.29001	N	0.887463	P;P	0.48089	0.675;0.905	B;B	0.40825	0.311;0.341	T	0.82293	-0.0529	10	0.20046	T	0.44	.	11.9499	0.52948	0.0:0.0:0.8251:0.1749	rs41292285;rs61406959	1059;1059	O95180-2;O95180	.;CAC1H_HUMAN	S	1059	ENSP00000334198:A1059S;ENSP00000351401:A1059S	ENSP00000334198:A1059S	A	+	1	0	CACNA1H	1198034	1.000000	0.71417	0.742000	0.31022	0.188000	0.23474	5.661000	0.68025	0.876000	0.35872	0.650000	0.86243	GCC	G|0.992;T|0.008	0.008	strong		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
C8orf34	116328	hgsc.bcm.edu	37	8	69434195	69434195	+	Silent	SNP	T	T	C	rs2289831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:69434195T>C	ENST00000539993.1	+	6	1218	c.669T>C	c.(667-669)agT>agC	p.S223S	C8orf34_ENST00000348340.2_Silent_p.S223S|C8orf34_ENST00000337103.4_Silent_p.S198S|C8orf34_ENST00000518698.1_Silent_p.S309S			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	223										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			GTGGCTCTAGTCCTGCAGGAA	0.403													C|||	1038	0.207268	0.4077	0.1455	5008	,	,		16810	0.1121		0.1392	False		,,,				2504	0.1483				p.S309S		Atlas-SNP	.											.	C8orf34	170	.	0			c.T927C						PASS	.	C	,	1597,2809	664.7+/-401.4	286,1025,892	94.0	91.0	92.0		927,927	-0.8	0.9	8	dbSNP_100	92	1171,7429	765.0+/-407.6	79,1013,3208	no	coding-synonymous,coding-synonymous	C8orf34	NM_001195639.1,NM_052958.2	,	365,2038,4100	CC,CT,TT		13.6163,36.246,21.2825	,	309/374,309/539	69434195	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	116328	exon6			CTCTAGTCCTGCA	AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"""vestibule 1"""						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.669T>C	8.37:g.69434195T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Silent	SNP	ENST00000539993.1	37																																																																																				T|0.788;C|0.212	0.212	strong		0.403	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958	
KAT7	11143	hgsc.bcm.edu	37	17	47903381	47903381	+	Silent	SNP	C	C	T	rs61749929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:47903381C>T	ENST00000259021.4	+	13	1780	c.1500C>T	c.(1498-1500)gtC>gtT	p.V500V	KAT7_ENST00000513980.1_3'UTR|KAT7_ENST00000424009.2_Silent_p.V470V|KAT7_ENST00000454930.2_Silent_p.V361V|KAT7_ENST00000503935.2_Silent_p.V344V|KAT7_ENST00000509773.1_Silent_p.V390V|KAT7_ENST00000510819.1_Silent_p.V331V|KAT7_ENST00000435742.2_Silent_p.V314V	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	500	MYST-type HAT.				chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TTTCCAAAGTCGAAGAAAAAG	0.428													C|||	1015	0.202676	0.0113	0.1571	5008	,	,		19951	0.4792		0.1014	False		,,,				2504	0.3129				p.V500V		Atlas-SNP	.											.	.	.	.	0			c.C1500T						PASS	.	C	,,,,	163,4243	109.5+/-147.8	1,161,2041	89.0	86.0	87.0		1410,1083,1170,993,1500	-1.4	1.0	17	dbSNP_129	87	1013,7587	217.0+/-255.8	53,907,3340	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KAT7	NM_001199155.1,NM_001199156.1,NM_001199157.1,NM_001199158.1,NM_007067.4	,,,,	54,1068,5381	TT,TC,CC		11.7791,3.6995,9.042	,,,,	470/582,361/473,390/502,331/443,500/612	47903381	1176,11830	2203	4300	6503	SO:0001819	synonymous_variant	11143	exon13			CAAAGTCGAAGAA	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"""	17016	protein-coding gene	gene with protein product	"""histone acetyltransferase binding to ORC1"""	609880	"""MYST histone acetyltransferase 2"""	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.1500C>T	17.37:g.47903381C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	205	92	0.44878	NM_007067	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Silent	SNP	ENST00000259021.4	37	CCDS11554.1																																																																																			C|0.879;T|0.121	0.121	strong		0.428	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067	
MUC16	94025	hgsc.bcm.edu	37	19	9087758	9087758	+	Missense_Mutation	SNP	G	G	A	rs12611293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9087758G>A	ENST00000397910.4	-	1	4260	c.4057C>T	c.(4057-4059)Cat>Tat	p.H1353Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1353	Thr-rich.		H -> Y (in dbSNP:rs12611293).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCTTTGGATGGTTTTCTGTG	0.517													G|||	951	0.189896	0.0711	0.2709	5008	,	,		21703	0.3036		0.172	False		,,,				2504	0.1943				p.H1353Y		Atlas-SNP	.											.	MUC16	4315	.	0			c.C4057T						PASS	.	G	TYR/HIS	330,4064	156.6+/-189.7	6,318,1873	184.0	184.0	184.0		4057	0.6	0.0	19	dbSNP_120	184	1533,7063	282.0+/-295.3	132,1269,2897	yes	missense	MUC16	NM_024690.2	83	138,1587,4770	AA,AG,GG		17.8339,7.5102,14.3418	benign	1353/14508	9087758	1863,11127	2197	4298	6495	SO:0001583	missense	94025	exon1			TTGGATGGTTTTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4057C>T	19.37:g.9087758G>A	ENSP00000381008:p.His1353Tyr	Somatic	479	0	0		WXS	Illumina HiSeq	Phase_I	463	229	0.4946	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	g	2.142	-0.396620	0.04899	0.075102	0.178339	ENSG00000181143	ENST00000397910	T	0.02525	4.26	1.62	0.548	0.17208	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.12630	0.006	B	0.06405	0.002	T	0.48103	-0.9064	8	0.87932	D	0	.	3.1685	0.06544	0.7238:0.0:0.2762:0.0	rs12611293;rs52827539;rs61560919;rs12611293	1353	B5ME49	.	Y	1353	ENSP00000381008:H1353Y	ENSP00000381008:H1353Y	H	-	1	0	MUC16	8948758	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.884000	0.01622	0.107000	0.17824	0.305000	0.20034	CAT	G|0.812;A|0.188	0.188	strong		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NEURL4	84461	hgsc.bcm.edu	37	17	7230845	7230845	+	Missense_Mutation	SNP	G	G	T	rs11655578	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7230845G>T	ENST00000399464.2	-	2	656	c.641C>A	c.(640-642)cCt>cAt	p.P214H	NEURL4_ENST00000315614.7_Missense_Mutation_p.P214H|NEURL4_ENST00000570460.1_Missense_Mutation_p.P214H	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	214						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GATGGGAGTAGGGGGGCTGAA	0.637													G|||	675	0.134784	0.0038	0.1902	5008	,	,		14769	0.1081		0.1928	False		,,,				2504	0.2403				p.P214H		Atlas-SNP	.											.	NEURL4	192	.	0			c.C641A						PASS	.	G	HIS/PRO,HIS/PRO	168,3732		4,160,1786	40.0	47.0	45.0		641,641	5.5	1.0	17	dbSNP_120	45	1753,6513		198,1357,2578	yes	missense,missense	NEURL4	NM_001005408.1,NM_032442.2	77,77	202,1517,4364	TT,TG,GG		21.2074,4.3077,15.7899	probably-damaging,probably-damaging	214/1561,214/1563	7230845	1921,10245	1950	4133	6083	SO:0001583	missense	84461	exon2			GGAGTAGGGGGGC		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.641C>A	17.37:g.7230845G>T	ENSP00000382390:p.Pro214His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001005408	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	37	CCDS42251.1	288	0.13186813186813187	4	0.008130081300813009	71	0.19613259668508287	69	0.12062937062937062	144	0.18997361477572558	G	17.94	3.510410	0.64522	0.043077	0.212074	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.32988	1.43;1.43	5.49	5.49	0.81192	Concanavalin A-like lectin/glucanase (1);	0.292228	0.32918	N	0.005487	T	0.00039	0.0001	L	0.38175	1.15	0.26924	P	0.9666059	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.99	T	0.01030	-1.1475	9	0.46703	T	0.11	-6.967	15.22	0.73303	0.0:0.0:1.0:0.0	rs11655578	214;214	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	H	214	ENSP00000319826:P214H;ENSP00000382390:P214H	ENSP00000319826:P214H	P	-	2	0	NEURL4	7171569	0.998000	0.40836	0.985000	0.45067	0.797000	0.45037	3.356000	0.52269	2.735000	0.93741	0.655000	0.94253	CCT	G|0.844;T|0.156	0.156	strong		0.637	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
ABTB1	80325	hgsc.bcm.edu	37	3	127394820	127394820	+	Silent	SNP	C	C	T	rs35703629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:127394820C>T	ENST00000232744.8	+	4	269	c.183C>T	c.(181-183)cgC>cgT	p.R61R	ABTB1_ENST00000393363.3_5'UTR|ABTB1_ENST00000468137.1_5'UTR|ABTB1_ENST00000453791.2_5'UTR					ankyrin repeat and BTB (POZ) domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						CAGGAGCCCGCTGCGAGGCCA	0.637													c|||	577	0.115216	0.1089	0.121	5008	,	,		17290	0.0109		0.2227	False		,,,				2504	0.1166				p.R61R		Atlas-SNP	.											.	ABTB1	36	.	0			c.C183T						PASS	.		,	501,3899		26,449,1725	15.0	17.0	16.0		,183	1.8	1.0	3	dbSNP_126	16	1684,6908		148,1388,2760	no	utr-5,coding-synonymous	ABTB1	NM_032548.3,NM_172027.2	,	174,1837,4485	TT,TC,CC		19.5996,11.3864,16.818	,	,61/479	127394820	2185,10807	2200	4296	6496	SO:0001819	synonymous_variant	80325	exon4			AGCCCGCTGCGAG	AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.183C>T	3.37:g.127394820C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	101	42	0.415842	NM_172027		Silent	SNP	ENST00000232744.8	37	CCDS3045.1																																																																																			C|0.848;T|0.152	0.152	strong		0.637	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1	NM_172027	
OTUD7A	161725	hgsc.bcm.edu	37	15	31776837	31776837	+	Missense_Mutation	SNP	C	C	G	rs76704217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:31776837C>G	ENST00000307050.4	-	11	1533	c.1441G>C	c.(1441-1443)Gtg>Ctg	p.V481L	OTUD7A_ENST00000382902.1_Missense_Mutation_p.V488L	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	481					protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		TTGCTGCACACCGAATCGCGG	0.642													C|||	57	0.0113818	0.0015	0.0173	5008	,	,		19876	0.001		0.0378	False		,,,				2504	0.0041				p.V481L		Atlas-SNP	.											.	OTUD7A	89	.	0			c.G1441C						PASS	.	C	LEU/VAL	30,4354		0,30,2162	80.0	57.0	64.0		1441	2.4	1.0	15	dbSNP_131	64	415,8183		14,387,3898	yes	missense	OTUD7A	NM_130901.1	32	14,417,6060	GG,GC,CC		4.8267,0.6843,3.4278	benign	481/927	31776837	445,12537	2192	4299	6491	SO:0001583	missense	161725	exon11			TGCACACCGAATC	AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"""OTU domain containing"""	20718	protein-coding gene	gene with protein product		612024	"""chromosome 15 open reading frame 16"", ""OTU domain containing 7"", ""OTU domain containing 7A"""	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.1441G>C	15.37:g.31776837C>G	ENSP00000305926:p.Val481Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_130901	Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	37	CCDS10026.1	45	0.020604395604395604	2	0.0040650406504065045	7	0.019337016574585635	1	0.0017482517482517483	35	0.04617414248021108	C	14.83	2.652700	0.47362	0.006843	0.048267	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.34472	1.37;1.36	4.35	2.4	0.29515	.	0.175056	0.50627	D	0.000102	T	0.06005	0.0156	M	0.69823	2.125	0.28750	N	0.90147	B;B	0.12013	0.005;0.003	B;B	0.13407	0.009;0.004	T	0.12656	-1.0539	10	0.51188	T	0.08	-32.5726	3.9645	0.09424	0.0:0.5203:0.2199:0.2599	.	488;481	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	L	481;488	ENSP00000305926:V481L;ENSP00000372358:V488L	ENSP00000305926:V481L	V	-	1	0	OTUD7A	29564129	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	2.060000	0.41394	0.936000	0.37367	0.655000	0.94253	GTG	C|0.970;G|0.030	0.030	strong		0.642	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901	
MUC4	4585	hgsc.bcm.edu	37	3	195507379	195507379	+	Missense_Mutation	SNP	G	G	C	rs371423143		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507379G>C	ENST00000463781.3	-	2	11531	c.11072C>G	c.(11071-11073)aCa>aGa	p.T3691R	MUC4_ENST00000475231.1_Missense_Mutation_p.T3691R|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3691R(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGCCTGACCTGTGGATGCTGA	0.577																																					p.T3691R		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	stomach(2)	c.C11072G						scavenged	.						21.0	20.0	20.0					3																	195507379		635	1577	2212	SO:0001583	missense	4585	exon2			TGACCTGTGGATG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11072C>G	3.37:g.195507379G>C	ENSP00000417498:p.Thr3691Arg	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	132	30	0.227273	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	5.701	0.313839	0.10789	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34859	1.34;1.43	0.743	0.743	0.18347	.	.	.	.	.	T	0.20170	0.0485	N	0.08118	0	0.09310	N	1	P	0.44006	0.824	P	0.46208	0.507	T	0.10706	-1.0618	8	.	.	.	.	4.7007	0.12825	0.0:0.0:1.0:0.0	.	3563	E7ESK3	.	R	3691	ENSP00000417498:T3691R;ENSP00000420243:T3691R	.	T	-	2	0	MUC4	196992158	0.103000	0.21917	0.015000	0.15790	0.015000	0.08874	0.305000	0.19254	0.088000	0.17205	0.089000	0.15464	ACA	.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DOK7	285489	hgsc.bcm.edu	37	4	3494847	3494847	+	Silent	SNP	G	G	A	rs6831659	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:3494847G>A	ENST00000340083.5	+	7	1199	c.1134G>A	c.(1132-1134)gcG>gcA	p.A378A	DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR|DOK7_ENST00000389653.2_Silent_p.A378A	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	378					neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TGCCAGCAGCGGGGGCCCCCG	0.677													.|||	1076	0.214856	0.0272	0.1354	5008	,	,		13435	0.505		0.2207	False		,,,				2504	0.2198				p.A378A		Atlas-SNP	.											.	DOK7	44	.	0			c.G1134A						PASS	.	G	,	206,4112		9,188,1962	8.0	10.0	9.0		,1134	-7.5	0.0	4	dbSNP_116	9	1445,7043		122,1201,2921	no	utr-3,coding-synonymous	DOK7	NM_001164673.1,NM_173660.4	,	131,1389,4883	AA,AG,GG		17.024,4.7707,12.8924	,	,378/505	3494847	1651,11155	2159	4244	6403	SO:0001819	synonymous_variant	285489	exon7			AGCAGCGGGGGCC	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.1134G>A	4.37:g.3494847G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	22	15	0.681818	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Silent	SNP	ENST00000340083.5	37	CCDS3370.2																																																																																			G|0.740;A|0.260	0.260	strong		0.677	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
LZTS1	11178	hgsc.bcm.edu	37	8	20110641	20110641	+	Silent	SNP	C	C	T	rs2645386	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:20110641C>T	ENST00000381569.1	-	3	1158	c.801G>A	c.(799-801)gaG>gaA	p.E267E	LZTS1_ENST00000265801.6_Silent_p.E267E|LZTS1_ENST00000522290.1_Silent_p.E267E			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	267					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		ACAGCTTCTGCTCCAGCTCCT	0.657													C|||	1796	0.358626	0.3843	0.2205	5008	,	,		17260	0.4623		0.3231	False		,,,				2504	0.3517				p.E267E		Atlas-SNP	.											.	LZTS1	72	.	0			c.G801A						PASS	.	C		1774,2626		384,1006,810	49.0	45.0	46.0		801	5.6	1.0	8	dbSNP_100	46	2966,5612		546,1874,1869	no	coding-synonymous	LZTS1	NM_021020.2		930,2880,2679	TT,TC,CC		34.5768,40.3182,36.5233		267/597	20110641	4740,8238	2200	4289	6489	SO:0001819	synonymous_variant	11178	exon2			CTTCTGCTCCAGC	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"""F37/Esophageal cancer-related gene-coding leucine-zipper motif"""			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.801G>A	8.37:g.20110641C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	37	CCDS6015.1																																																																																			C|0.631;T|0.369	0.369	strong		0.657	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383134	41383134	+	Silent	SNP	A	A	G	rs147847954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41383134A>G	ENST00000301146.4	-	7	1663	c.1122T>C	c.(1120-1122)gtT>gtC	p.V374V	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Silent_p.V323V	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	374						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGTCCTTTTTAACCCTGCGGG	0.537													.|||	60	0.0119808	0.0	0.0144	5008	,	,		18790	0.002		0.0457	False		,,,				2504	0.002				p.V374V		Atlas-SNP	.											.	CYP2A7	71	.	0			c.T1122C						PASS	.	A	,	24,4382	27.2+/-55.0	0,24,2179	102.0	90.0	94.0		1122,969	-2.4	0.0	19	dbSNP_134	94	294,8304	99.5+/-161.0	15,264,4020	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	15,288,6199	GG,GA,AA		3.4194,0.5447,2.4454	,	374/495,323/444	41383134	318,12686	2203	4299	6502	SO:0001819	synonymous_variant	1549	exon7			CTTTTTAACCCTG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1122T>C	19.37:g.41383134A>G		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	254	112	0.440945	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			A|0.978;G|0.022	0.022	strong		0.537	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
SUOX	6821	hgsc.bcm.edu	37	12	56397802	56397802	+	Missense_Mutation	SNP	C	C	T	rs141735896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56397802C>T	ENST00000394109.3	+	3	1353	c.629C>T	c.(628-630)cCc>cTc	p.P210L	SUOX_ENST00000551841.2_Intron|SUOX_ENST00000266971.3_Missense_Mutation_p.P210L|SUOX_ENST00000548274.1_Missense_Mutation_p.P210L|SUOX_ENST00000394115.2_Missense_Mutation_p.P210L|SUOX_ENST00000356124.4_Missense_Mutation_p.P210L			P51687	SUOX_HUMAN	sulfite oxidase	210	Moco domain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|sulfite oxidase activity (GO:0008482)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)	15			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			TACATCACACCCAACCCTATC	0.552													C|||	9	0.00179712	0.0	0.0101	5008	,	,		20235	0.0		0.002	False		,,,				2504	0.0				p.P210L		Atlas-SNP	.											.	SUOX	33	.	0			c.C629T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	5,4401	9.9+/-24.2	0,5,2198	114.0	106.0	109.0		629,629,629	5.1	1.0	12	dbSNP_134	109	31,8569	21.6+/-65.8	0,31,4269	yes	missense,missense,missense	SUOX	NM_000456.2,NM_001032386.1,NM_001032387.1	98,98,98	0,36,6467	TT,TC,CC		0.3605,0.1135,0.2768	probably-damaging,probably-damaging,probably-damaging	210/546,210/546,210/546	56397802	36,12970	2203	4300	6503	SO:0001583	missense	6821	exon6			TCACACCCAACCC	BC065193	CCDS8901.2	12q13.13	2011-02-10			ENSG00000139531	ENSG00000139531	1.8.3.1		11460	protein-coding gene	gene with protein product		606887				7599189	Standard	XM_005269112		Approved		uc001siz.3	P51687	OTTHUMG00000128503	ENST00000394109.3:c.629C>T	12.37:g.56397802C>T	ENSP00000377668:p.Pro210Leu	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	270	131	0.485185	NM_000456		Missense_Mutation	SNP	ENST00000394109.3	37	CCDS8901.2	9	0.004120879120879121	0	0.0	6	0.016574585635359115	0	0.0	3	0.00395778364116095	C	23.2	4.384135	0.82792	0.001135	0.003605	ENSG00000139531	ENST00000356124;ENST00000266971;ENST00000394115;ENST00000548274;ENST00000394109	D;D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89;-3.89	5.12	5.12	0.69794	Oxidoreductase, molybdopterin-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.96185	0.8756	M	0.92317	3.295	0.80722	D	1	D	0.63880	0.993	P	0.60117	0.869	D	0.94083	0.7346	10	0.72032	D	0.01	-26.2213	17.8714	0.88812	0.0:1.0:0.0:0.0	.	210	P51687	SUOX_HUMAN	L	210	ENSP00000348440:P210L;ENSP00000266971:P210L;ENSP00000377674:P210L;ENSP00000450245:P210L;ENSP00000377668:P210L	ENSP00000266971:P210L	P	+	2	0	SUOX	54684069	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	6.994000	0.76251	2.837000	0.97791	0.591000	0.81541	CCC	C|0.997;T|0.003	0.003	strong		0.552	SUOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250309.1	NM_000456	
IFT140	9742	hgsc.bcm.edu	37	16	1634385	1634385	+	Missense_Mutation	SNP	C	C	T	rs34762152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1634385C>T	ENST00000426508.2	-	11	1555	c.1192G>A	c.(1192-1194)Gtc>Atc	p.V398I	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	398			V -> I (in dbSNP:rs34762152).		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				ACGGAGATGACGCTGTTCACT	0.562													C|||	429	0.0856629	0.1309	0.036	5008	,	,		18569	0.0913		0.0626	False		,,,				2504	0.0777				p.V398I		Atlas-SNP	.											.	IFT140	128	.	0			c.G1192A						PASS	.	C	ILE/VAL	576,3822	247.2+/-255.5	41,494,1664	46.0	36.0	40.0		1192	-8.8	0.0	16	dbSNP_126	40	564,8036	149.4+/-204.5	25,514,3761	yes	missense	IFT140	NM_014714.3	29	66,1008,5425	TT,TC,CC		6.5581,13.0969,8.7706	benign	398/1463	1634385	1140,11858	2199	4300	6499	SO:0001583	missense	9742	exon11			AGATGACGCTGTT	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1192G>A	16.37:g.1634385C>T	ENSP00000406012:p.Val398Ile	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	169	0.07738095238095238	65	0.13211382113821138	13	0.03591160220994475	51	0.08916083916083917	40	0.052770448548812667	C	14.15	2.448262	0.43429	0.130969	0.065581	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.59364	0.27	5.81	-8.77	0.00827	WD40/YVTN repeat-like-containing domain (1);	1.619900	0.02827	N	0.126242	T	0.00210	0.0006	N	0.01505	-0.83	0.80722	P	0.0	B;B	0.16166	0.001;0.016	B;B	0.08055	0.001;0.003	T	0.02581	-1.1138	9	0.15499	T	0.54	.	2.2341	0.04003	0.1662:0.1126:0.1661:0.555	rs34762152	398;123	Q96RY7;B4DR58	IF140_HUMAN;.	I	398	ENSP00000406012:V398I	ENSP00000380562:V398I	V	-	1	0	IFT140	1574386	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.219000	0.02973	-1.317000	0.02292	0.655000	0.94253	GTC	T|0.088;G|0.000;C|0.912;A|0.000	0.088	strong		0.562	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
CST4	1472	hgsc.bcm.edu	37	20	23666588	23666588	+	Silent	SNP	G	G	A	rs143990199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23666588G>A	ENST00000217423.3	-	3	439	c.369C>T	c.(367-369)taC>taT	p.Y123Y		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	123					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					AGGGAACTTCGTAGATCTCGA	0.537													N|||	24	0.00479233	0.0008	0.0101	5008	,	,		17400	0.0		0.0149	False		,,,				2504	0.001				p.Y123Y		Atlas-SNP	.											.	CST4	37	.	0			c.C369T						PASS	.	G		22,4384	28.1+/-56.4	0,22,2181	99.0	91.0	94.0		369	-3.9	0.0	20	dbSNP_134	94	129,8471	66.3+/-128.7	1,127,4172	no	coding-synonymous	CST4	NM_001899.2		1,149,6353	AA,AG,GG		1.5,0.4993,1.161		123/142	23666588	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	1472	exon3			AACTTCGTAGATC		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.369C>T	20.37:g.23666588G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	235	114	0.485106	NM_001899	Q9UBI5|Q9UCS9	Silent	SNP	ENST00000217423.3	37	CCDS13159.1																																																																																			G|0.992;A|0.008	0.008	strong		0.537	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
PTPN1	5770	hgsc.bcm.edu	37	20	49195749	49195749	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:49195749G>A	ENST00000371621.3	+	7	921	c.747G>A	c.(745-747)gtG>gtA	p.V249V	PTPN1_ENST00000541713.1_Silent_p.V176V|RP4-530I15.9_ENST00000431019.1_RNA	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	249	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	TCAAGAAAGTGCTGTTAGAAA	0.493																																					p.V249V		Atlas-SNP	.											.	PTPN1	36	.	0			c.G747A						PASS	.						148.0	149.0	148.0					20																	49195749		2203	4300	6503	SO:0001819	synonymous_variant	5770	exon7			GAAAGTGCTGTTA		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.747G>A	20.37:g.49195749G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			.	.	none		0.493	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2		
AATK	9625	hgsc.bcm.edu	37	17	79093822	79093822	+	Missense_Mutation	SNP	A	A	G	rs36000545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79093822A>G	ENST00000326724.4	-	12	3821	c.3797T>C	c.(3796-3798)tTc>tCc	p.F1266S	AATK_ENST00000417379.1_Missense_Mutation_p.F1163S	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1266			F -> S (in dbSNP:rs36000545). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CCCCCTAAGGAACGTAGGGGG	0.701													A|||	1802	0.359824	0.1982	0.3069	5008	,	,		12662	0.5437		0.3807	False		,,,				2504	0.4049				p.F1266S		Atlas-SNP	.											.	AATK	102	.	0			c.T3797C						PASS	.	A	SER/PHE,SER/PHE	499,2413		38,423,995	4.0	6.0	5.0		3797,3488	1.3	0.0	17	dbSNP_126	5	2232,4648		352,1528,1560	no	missense,missense	AATK	NM_001080395.2,NM_004920.2	155,155	390,1951,2555	GG,GA,AA		32.4419,17.136,27.8901	probably-damaging,probably-damaging	1266/1375,1163/1272	79093822	2731,7061	1456	3440	4896	SO:0001583	missense	9625	exon12			CTAAGGAACGTAG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3797T>C	17.37:g.79093822A>G	ENSP00000324196:p.Phe1266Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	804|804	0.36813186813186816|0.36813186813186816	106|106	0.21544715447154472|0.21544715447154472	124|124	0.3425414364640884|0.3425414364640884	288|288	0.5034965034965035|0.5034965034965035	286|286	0.37730870712401055|0.37730870712401055	A|A	4.293|4.293	0.053559|0.053559	0.08291|0.08291	0.17136|0.17136	0.324419|0.324419	ENSG00000181409|ENSG00000181409	ENST00000326724|ENST00000417379	T|.	0.09723|.	2.95|.	3.73|3.73	1.32|1.32	0.21799|0.21799	.|.	0.748873|.	0.11969|.	N|.	0.511923|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	P|P	0.0|0.0	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|T	0.46331|0.46331	-0.9199|-0.9199	9|4	0.15066|.	T|.	0.55|.	.|.	2.543|2.543	0.04730|0.04730	0.5197:0.0:0.2789:0.2015|0.5197:0.0:0.2789:0.2015	rs36000545;rs62073019|rs36000545;rs62073019	1266|.	Q6ZMQ8|.	LMTK1_HUMAN|.	S|P	1266|1219	ENSP00000324196:F1266S|.	ENSP00000324196:F1266S|.	F|S	-|-	2|1	0|0	AATK|AATK	76708417|76708417	0.130000|0.130000	0.22417|0.22417	0.005000|0.005000	0.12908|0.12908	0.021000|0.021000	0.10359|0.10359	0.846000|0.846000	0.27682|0.27682	0.108000|0.108000	0.17862|0.17862	0.260000|0.260000	0.18958|0.18958	TTC|TCC	A|0.631;G|0.369	0.369	strong		0.701	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
MED13L	23389	hgsc.bcm.edu	37	12	116408538	116408538	+	Silent	SNP	A	A	G	rs2304460	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:116408538A>G	ENST00000281928.3	-	27	6134	c.5928T>C	c.(5926-5928)acT>acC	p.T1976T		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1976						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.T1976T(1)		NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TGTTCAGTGCAGTACTTCGGC	0.428													A|||	765	0.152756	0.0696	0.1311	5008	,	,		20349	0.1696		0.1899	False		,,,				2504	0.2249				p.T1976T		Atlas-SNP	.											MED13L,NS,carcinoma,0,1	MED13L	193	1	1	Substitution - coding silent(1)	stomach(1)	c.T5928C						PASS	.	A		412,3994	203.1+/-225.7	13,386,1804	142.0	116.0	125.0		5928	3.2	1.0	12	dbSNP_100	125	1552,7048	292.0+/-300.6	122,1308,2870	no	coding-synonymous	MED13L	NM_015335.4		135,1694,4674	GG,GA,AA		18.0465,9.3509,15.1007		1976/2211	116408538	1964,11042	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon27			CAGTGCAGTACTT	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.5928T>C	12.37:g.116408538A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	137	61	0.445255	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1	332	0.152014652014652	61	0.12398373983739837	50	0.13812154696132597	91	0.1590909090909091	130	0.17150395778364116	A	9.767	1.171638	0.21704	0.093509	0.180465	ENSG00000123066	ENST00000552447	.	.	.	5.55	3.21	0.36854	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16247	-1.0409	3	.	.	.	-16.2838	1.7372	0.02944	0.5402:0.1283:0.208:0.1235	rs2304460;rs17426149;rs58700742;rs2304460	.	.	.	R	181	.	.	C	-	1	0	MED13L	114892921	0.994000	0.37717	1.000000	0.80357	0.998000	0.95712	0.413000	0.21148	0.534000	0.28695	0.533000	0.62120	TGC	A|0.842;G|0.158	0.158	strong		0.428	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
VRK1	7443	hgsc.bcm.edu	37	14	97321689	97321689	+	Silent	SNP	C	C	T	rs2230532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:97321689C>T	ENST00000216639.3	+	8	854	c.705C>T	c.(703-705)ggC>ggT	p.G235G		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	235	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		CACACAATGGCGTGGGTATGT	0.393													C|||	2087	0.416733	0.1649	0.4928	5008	,	,		19633	0.8442		0.3698	False		,,,				2504	0.3108				p.G235G		Atlas-SNP	.											.	VRK1	34	.	0			c.C705T						PASS	.	C		753,3653	309.1+/-290.9	67,619,1517	116.0	103.0	108.0		705	-6.1	0.6	14	dbSNP_98	108	3022,5578	465.1+/-366.4	560,1902,1838	yes	coding-synonymous	VRK1	NM_003384.2		627,2521,3355	TT,TC,CC		35.1395,17.0903,29.0251		235/397	97321689	3775,9231	2203	4300	6503	SO:0001819	synonymous_variant	7443	exon8			CAATGGCGTGGGT	AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.705C>T	14.37:g.97321689C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_003384	Q3SYL2	Silent	SNP	ENST00000216639.3	37	CCDS9947.1	1001	0.4583333333333333	81	0.16463414634146342	159	0.43922651933701656	486	0.8496503496503497	275	0.3627968337730871	C	9.288	1.049864	0.19827	0.170903	0.351395	ENSG00000100749	ENST00000557222;ENST00000557352	.	.	.	6.05	-6.05	0.02172	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11084	-1.0602	3	.	.	.	-22.2293	9.1188	0.36775	0.1465:0.5561:0.0:0.2974	rs2230532;rs11160370;rs11557224;rs57291592;rs2230532	.	.	.	C	92;17	.	.	R	+	1	0	VRK1	96391442	0.127000	0.22367	0.628000	0.29241	0.800000	0.45204	-0.690000	0.05138	-1.420000	0.02009	-0.813000	0.03139	CGT	C|0.650;T|0.350	0.350	strong		0.393	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384	
FXYD3	5349	hgsc.bcm.edu	37	19	35612159	35612159	+	Intron	SNP	C	C	G	rs2290649	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35612159C>G	ENST00000344013.6	+	5	293				FXYD3_ENST00000605550.1_Intron|FXYD3_ENST00000604804.1_Intron|FXYD3_ENST00000604621.1_Intron|FXYD3_ENST00000435734.2_Intron|FXYD3_ENST00000406242.3_Intron|FXYD3_ENST00000603181.1_Intron|FXYD3_ENST00000604255.1_Intron|FXYD3_ENST00000605552.1_Missense_Mutation_p.P36R|FXYD3_ENST00000604404.1_Intron|FXYD3_ENST00000346446.5_Intron|FXYD3_ENST00000605677.1_Intron|FXYD3_ENST00000406988.1_Intron|FXYD3_ENST00000454903.2_Missense_Mutation_p.P36R|FXYD3_ENST00000603524.1_Intron|FXYD3_ENST00000603449.1_Missense_Mutation_p.P36R|FXYD3_ENST00000535103.1_Intron			Q14802	FXYD3_HUMAN	FXYD domain containing ion transport regulator 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of catalytic activity (GO:0050790)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			endometrium(1)|lung(2)|prostate(1)	4	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			GGTGAGAGCCCGTGCCCCCTT	0.532													C|||	1186	0.236821	0.1815	0.415	5008	,	,		16551	0.2798		0.2455	False		,,,				2504	0.1319				p.P36R		Atlas-SNP	.											.	FXYD3	15	.	0			c.C107G						PASS	.	C	,,ARG/PRO,ARG/PRO,,,,	875,3531	336.5+/-304.4	90,695,1418	78.0	81.0	80.0		,,107,107,,,,	-8.3	0.0	19	dbSNP_100	80	2177,6423	370.0+/-335.7	295,1587,2418	yes	intron,intron,missense,missense,intron,intron,intron,intron	FXYD3	NM_001136007.1,NM_001136008.1,NM_001136009.1,NM_001136010.1,NM_001136011.1,NM_001136012.1,NM_005971.3,NM_021910.2	,,103,103,,,,	385,2282,3836	GG,GC,CC		25.314,19.8593,23.4661	,,,,,,,	,,36/62,36/62,,,,	35612159	3052,9954	2203	4300	6503	SO:0001627	intron_variant	5349	exon5			AGAGCCCGTGCCC	X93036	CCDS12442.1, CCDS12443.1, CCDS46048.1, CCDS46049.1, CCDS46050.1	19q13.11-q13.12	2008-05-14	2002-01-14			ENSG00000089356			4027	protein-coding gene	gene with protein product		604996	"""FXYD domain-containing ion transport regulator 3"""	PLML		7836447, 10950925	Standard	NM_005971		Approved	MAT-8	uc010xsm.2	Q14802		ENST00000344013.6:c.97+10C>G	19.37:g.35612159C>G		Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	244	134	0.54918	NM_001136010	A6NDE0|C9JDU2|F5H174|F8WB34|Q13211|Q6IB59	Missense_Mutation	SNP	ENST00000344013.6	37	CCDS12442.1	615	0.2815934065934066	103	0.20934959349593496	138	0.3812154696132597	187	0.3269230769230769	187	0.24670184696569922	C	1.879	-0.458439	0.04508	0.198593	0.25314	ENSG00000089356	ENST00000454903	.	.	.	4.16	-8.32	0.00996	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35226	-0.9797	5	.	.	.	.	4.2527	0.10702	0.0743:0.1728:0.2715:0.4814	rs2290649	36	C9JDU2	.	R	36	.	.	P	+	2	0	FXYD3	40303999	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.795000	0.01752	-2.597000	0.00453	-1.729000	0.00701	CCG	C|0.741;G|0.259	0.259	strong		0.532	FXYD3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000468985.1	NM_021910	
SPTBN2	6712	hgsc.bcm.edu	37	11	66481633	66481633	+	Silent	SNP	G	G	A	rs34775878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66481633G>A	ENST00000533211.1	-	7	916	c.585C>T	c.(583-585)aaC>aaT	p.N195N	SPTBN2_ENST00000529997.1_Silent_p.N195N|RN7SL12P_ENST00000473849.2_RNA|SPTBN2_ENST00000309996.2_Silent_p.N195N			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	195	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GTACATTGACGTTGGGATAAC	0.498													G|||	204	0.0407348	0.0076	0.0749	5008	,	,		24697	0.001		0.1163	False		,,,				2504	0.0245				p.N195N		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C585T						PASS	.	G		101,4299	80.4+/-118.8	0,101,2099	145.0	122.0	130.0		585	-0.4	1.0	11	dbSNP_126	130	1023,7567	218.7+/-257.0	54,915,3326	no	coding-synonymous	SPTBN2	NM_006946.2		54,1016,5425	AA,AG,GG		11.9092,2.2955,8.6528		195/2391	66481633	1124,11866	2200	4295	6495	SO:0001819	synonymous_variant	6712	exon6			ATTGACGTTGGGA	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.585C>T	11.37:g.66481633G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			G|0.922;A|0.078	0.078	strong		0.498	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
FAT1	2195	hgsc.bcm.edu	37	4	187534375	187534375	+	Silent	SNP	A	A	G	rs2249917	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187534375A>G	ENST00000441802.2	-	13	9560	c.9351T>C	c.(9349-9351)gaT>gaC	p.D3117D		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3117	Cadherin 28. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TATCGTTCACATCTTCTAGCG	0.527										HNSCC(5;0.00058)			G|||	2093	0.417931	0.5446	0.4683	5008	,	,		18291	0.2808		0.4702	False		,,,				2504	0.2986				p.D3117D	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T9351C						PASS	.	G		2142,1938		580,982,478	98.0	105.0	102.0		9351	-7.3	0.7	4	dbSNP_100	102	3759,4629		846,2067,1281	no	coding-synonymous	FAT1	NM_005245.3		1426,3049,1759	GG,GA,AA		44.814,47.5,47.3292		3117/4589	187534375	5901,6567	2040	4194	6234	SO:0001819	synonymous_variant	2195	exon13			GTTCACATCTTCT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.9351T>C	4.37:g.187534375A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			T|0.006;G|0.430	0.430	strong		0.527	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ASCL3	56676	hgsc.bcm.edu	37	11	8959511	8959511	+	Silent	SNP	T	T	G	rs4910179	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8959511T>G	ENST00000531618.1	-	1	247	c.198A>C	c.(196-198)ggA>ggC	p.G66G	ASCL3_ENST00000325884.1_Silent_p.G66G			Q9NQ33	ASCL3_HUMAN	achaete-scute family bHLH transcription factor 3	65					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(5)|stomach(1)	9				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)		CACTGTAATTTCCCAGGATAA	0.562													T|||	3309	0.660743	0.3215	0.7176	5008	,	,		17842	0.9306		0.6819	False		,,,				2504	0.7791				p.G66G		Atlas-SNP	.											.	ASCL3	19	.	0			c.A198C						PASS	.	T		1683,2719	510.4+/-367.5	327,1029,845	64.0	67.0	66.0		198	-4.9	0.1	11	dbSNP_111	66	6071,2519	692.8+/-404.6	2146,1779,370	no	coding-synonymous	ASCL3	NM_020646.1		2473,2808,1215	GG,GT,TT		29.3248,38.2326,40.3171		66/182	8959511	7754,5238	2201	4295	6496	SO:0001819	synonymous_variant	56676	exon2			GTAATTTCCCAGG	AJ400877	CCDS7795.1	11p15.3	2013-10-17	2013-10-17			ENSG00000176009		"""Basic helix-loop-helix proteins"""	740	protein-coding gene	gene with protein product		609154	"""achaete-scute complex (Drosophila) homolog-like 3"", ""achaete-scute complex homolog 3 (Drosophila)"""			11528127	Standard	NM_020646		Approved	bHLHa42, HASH3, Sgn1	uc001mhd.1	Q9NQ33	OTTHUMG00000165679	ENST00000531618.1:c.198A>C	11.37:g.8959511T>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_020646	Q8WYQ6	Silent	SNP	ENST00000531618.1	37	CCDS7795.1																																																																																			T|0.395;G|0.605	0.605	strong		0.562	ASCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385773.1		
AFAP1L2	84632	hgsc.bcm.edu	37	10	116060387	116060387	+	Silent	SNP	T	T	C	rs2286396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:116060387T>C	ENST00000304129.4	-	14	1634	c.1605A>G	c.(1603-1605)cgA>cgG	p.R535R	AFAP1L2_ENST00000491814.1_5'UTR|AFAP1L2_ENST00000369271.3_Silent_p.R535R|AFAP1L2_ENST00000545353.1_Silent_p.R588R			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	535					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		CCAGGTACACTCGGTCAGATT	0.577													T|||	3213	0.641573	0.3003	0.8372	5008	,	,		19091	0.7054		0.831	False		,,,				2504	0.7035				p.R535R		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.A1605G						PASS	.	T	,	1679,2727	509.8+/-367.3	326,1027,850	115.0	102.0	107.0		1605,1605	-9.2	0.0	10	dbSNP_100	107	7184,1416	753.3+/-407.4	3007,1170,123	no	coding-synonymous,coding-synonymous	AFAP1L2	NM_001001936.1,NM_032550.2	,	3333,2197,973	CC,CT,TT		16.4651,38.1071,31.8545	,	535/819,535/815	116060387	8863,4143	2203	4300	6503	SO:0001819	synonymous_variant	84632	exon14			GTACACTCGGTCA	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.1605A>G	10.37:g.116060387T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			A|0.000;C|0.679;G|0.000;T|0.320	0.679	strong		0.577	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
CPXCR1	53336	hgsc.bcm.edu	37	X	88008807	88008807	+	Missense_Mutation	SNP	G	G	A	rs5984611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:88008807G>A	ENST00000276127.4	+	3	651	c.392G>A	c.(391-393)cGt>cAt	p.R131H	CPXCR1_ENST00000373111.1_Missense_Mutation_p.R131H	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	131			R -> H (in dbSNP:rs5984611). {ECO:0000269|PubMed:11499681}.				metal ion binding (GO:0046872)			NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						CACAAAACTCGTTTTCGACTT	0.373													G|||	870	0.230464	0.1392	0.2017	3775	,	,		14154	0.0298		0.2684	False		,,,				2504	0.2515				p.R131H		Atlas-SNP	.											.	CPXCR1	83	.	0			c.G392A						PASS	.	G	HIS/ARG,HIS/ARG	696,3139		50,473,123,1109,448	53.0	47.0	49.0		392,392	0.1	0.0	X	dbSNP_114	49	2782,3946		410,1184,778,834,1094	yes	missense,missense	CPXCR1	NM_001184771.1,NM_033048.5	29,29	460,1657,901,1943,1542	AA,AG,A,GG,G		41.3496,18.1486,32.9263	probably-damaging,probably-damaging	131/302,131/302	88008807	3478,7085	2203	4300	6503	SO:0001583	missense	53336	exon3			AAACTCGTTTTCG	AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"""cancer/testis antigen 77"""					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.392G>A	X.37:g.88008807G>A	ENSP00000276127:p.Arg131His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001184771	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	37	CCDS14458.1	386	0.2326702833031947	58	0.13063063063063063	52	0.16455696202531644	13	0.023297491039426525	140	0.22580645161290322	G	10.91	1.483747	0.26598	0.181486	0.413496	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.46819	0.86;0.86	3.06	0.0957	0.14486	.	1.106060	0.07158	N	0.850257	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.65815	0.995	P	0.45881	0.496	T	0.33085	-0.9882	8	.	.	.	0.0	4.5942	0.12322	0.0:0.3717:0.4741:0.1542	rs5984611;rs17253963;rs52813984;rs57073371;rs5984611	131	Q8N123	CPXCR_HUMAN	H	131	ENSP00000276127:R131H;ENSP00000362203:R131H	.	R	+	2	0	CPXCR1	87895463	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.426000	0.07008	-0.091000	0.12440	-0.223000	0.12442	CGT	0|0.003;A|0.269	0.269	strong		0.373	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048	
MAST2	23139	hgsc.bcm.edu	37	1	46500613	46500613	+	Silent	SNP	T	T	C	rs17855317	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46500613T>C	ENST00000361297.2	+	29	4555	c.4272T>C	c.(4270-4272)acT>acC	p.T1424T	MAST2_ENST00000372009.2_Silent_p.T1234T	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					AGCTAGCCACTTCTCGCAAGC	0.592													t|||	588	0.117412	0.0469	0.1311	5008	,	,		17772	0.0149		0.2823	False		,,,				2504	0.1391				p.T1424T		Atlas-SNP	.											MAST2_ENST00000361297,NS,carcinoma,0,1	MAST2	136	1	0			c.T4272C						PASS	.			333,3749		18,297,1726	52.0	57.0	56.0		4272	0.8	0.2	1	dbSNP_123	56	2182,6200		293,1596,2302	no	coding-synonymous	MAST2	NM_015112.2		311,1893,4028	CC,CT,TT		26.032,8.1578,20.1781		1424/1799	46500613	2515,9949	2041	4191	6232	SO:0001819	synonymous_variant	23139	exon29			AGCCACTTCTCGC	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.4272T>C	1.37:g.46500613T>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	172	101	0.587209	NM_015112		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																			A|0.000;C|0.179;T|0.821	0.179	strong		0.592	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
TMTC2	160335	hgsc.bcm.edu	37	12	83290083	83290083	+	Missense_Mutation	SNP	G	G	A	rs35725509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:83290083G>A	ENST00000321196.3	+	3	1848	c.1141G>A	c.(1141-1143)Gta>Ata	p.V381I	TMTC2_ENST00000549919.1_Missense_Mutation_p.V375I|TMTC2_ENST00000548305.1_Missense_Mutation_p.V381I	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	381					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						TAAAAACGATGTATCACAGAG	0.408													G|||	58	0.0115815	0.0	0.0072	5008	,	,		20195	0.0		0.0089	False		,,,				2504	0.045				p.V381I		Atlas-SNP	.											.	TMTC2	100	.	0			c.G1141A						PASS	.	G	ILE/VAL	5,4401	11.4+/-27.6	0,5,2198	172.0	167.0	169.0		1141	5.0	0.0	12	dbSNP_126	169	66,8534	40.3+/-97.0	0,66,4234	yes	missense	TMTC2	NM_152588.1	29	0,71,6432	AA,AG,GG		0.7674,0.1135,0.5459	benign	381/837	83290083	71,12935	2203	4300	6503	SO:0001583	missense	160335	exon3			AACGATGTATCAC	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"""Tetratricopeptide (TTC) repeat domain containing"""	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.1141G>A	12.37:g.83290083G>A	ENSP00000322300:p.Val381Ile	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	37	CCDS9025.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	0.548	-0.850759	0.02651	0.001135	0.007674	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919;ENST00000546590	T;T;T	0.61274	0.77;0.12;0.67	5.86	4.98	0.66077	.	1.043000	0.07418	N	0.893502	T	0.27419	0.0673	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.26538	-1.0100	10	0.12766	T	0.61	-0.0418	6.9111	0.24335	0.1418:0.0:0.7159:0.1423	rs35725509	381;136;381	Q8N394;F8VRQ2;F8VSH2	TMTC2_HUMAN;.;.	I	381;381;375;136	ENSP00000322300:V381I;ENSP00000448292:V381I;ENSP00000447609:V375I	ENSP00000322300:V381I	V	+	1	0	TMTC2	81814214	0.028000	0.19301	0.014000	0.15608	0.171000	0.22731	1.832000	0.39151	1.494000	0.48533	-0.142000	0.14014	GTA	G|0.994;A|0.006	0.006	strong		0.408	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588	
CAPN5	726	hgsc.bcm.edu	37	11	76796082	76796082	+	Silent	SNP	G	G	A	rs368891933		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76796082G>A	ENST00000278559.3	+	2	339	c.150G>A	c.(148-150)agG>agA	p.R50R	CAPN5_ENST00000529629.1_Silent_p.R50R|CAPN5_ENST00000456580.2_Silent_p.R50R|CAPN5_ENST00000531028.1_Splice_Site	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	50	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						CCGCCGTCAGGTGGAAGCGAC	0.692																																					p.R50R		Atlas-SNP	.											.	CAPN5	67	.	0			c.G150A						PASS	.	G		0,4396		0,0,2198	21.0	24.0	23.0		150	3.0	0.9	11		23	1,8583		0,1,4291	no	coding-synonymous	CAPN5	NM_004055.4		0,1,6489	AA,AG,GG		0.0116,0.0,0.0077		50/641	76796082	1,12979	2198	4292	6490	SO:0001819	synonymous_variant	726	exon2			CGTCAGGTGGAAG		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"""vitreoretinopathy, neovascular inflammatory"""	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.150G>A	11.37:g.76796082G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	40	0.634921	NM_004055	O00263	Silent	SNP	ENST00000278559.3	37	CCDS8248.1																																																																																			.	.	weak		0.692	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055	
HLA-B	3106	hgsc.bcm.edu	37	6	31324921	31324921	+	Silent	SNP	C	C	T	rs1050459	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31324921C>T	ENST00000412585.2	-	1	43	c.15G>A	c.(13-15)gcG>gcA	p.A5A		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	5					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGGTTCGGGGCGCCATGACCA	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	796	0.158946	0.1513	0.1153	5008	,	,		9261	0.1895		0.1799	False		,,,				2504	0.1472				p.A5A		Atlas-SNP	.											.	HLA-B	54	.	0			c.G15A						PASS	.	C		512,3686		51,410,1638	14.0	12.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	15	-4.8	0.0	6	dbSNP_86	13	948,7200		67,814,3193	no	coding-synonymous	HLA-B	NM_005514.6		118,1224,4831	TT,TC,CC		11.6348,12.1963,11.8257		5/363	31324921	1460,10886	2099	4074	6173	SO:0001819	synonymous_variant	3106	exon1	Familial Cancer Database	;Lichen Sclerosis, Familial	TCGGGGCGCCATG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.15G>A	6.37:g.31324921C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	188	84	0.446809	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			C|0.873;T|0.127	0.127	strong		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
PER1	5187	hgsc.bcm.edu	37	17	8048283	8048283	+	Silent	SNP	G	G	A	rs2735611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8048283G>A	ENST00000317276.4	-	18	2484	c.2247C>T	c.(2245-2247)ggC>ggT	p.G749G	PER1_ENST00000581082.1_Silent_p.G729G|PER1_ENST00000354903.5_Silent_p.G733G|PER1_ENST00000578089.1_Intron	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	749	Required for phosphorylation by CSNK1E. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ctggggctaggCCAGGCAGGT	0.637			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					G|||	2857	0.570487	0.5076	0.5029	5008	,	,		11299	0.2837		0.8241	False		,,,				2504	0.7382				p.G749G		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.C2247T	GRCh37	CM066166	PER1	M	rs2735611	PASS	.	G		2444,1950		692,1060,445	18.0	21.0	20.0		2247	3.3	1.0	17	dbSNP_100	20	7195,1397		3042,1111,143	no	coding-synonymous	PER1	NM_002616.2		3734,2171,588	AA,AG,GG		16.2593,44.3787,25.7739		749/1291	8048283	9639,3347	2197	4296	6493	SO:0001819	synonymous_variant	5187	exon18			GGCTAGGCCAGGC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2247C>T	17.37:g.8048283G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_002616	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	37	CCDS11131.1																																																																																			G|0.356;A|0.644	0.644	strong		0.637	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
GSDMA	284110	hgsc.bcm.edu	37	17	38121993	38121993	+	Missense_Mutation	SNP	G	G	A	rs3894194	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38121993G>A	ENST00000301659.4	+	2	171	c.53G>A	c.(52-54)cGa>cAa	p.R18Q		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	18			R -> Q (in dbSNP:rs3894194).		apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CTAAACCCTCGAGGGGACCTG	0.582													G|||	2158	0.430911	0.2587	0.5043	5008	,	,		18378	0.5397		0.4463	False		,,,				2504	0.4836				p.R18Q		Atlas-SNP	.											.	GSDMA	26	.	0			c.G53A	GRCh37	CM073116	GSDMA	M	rs3894194	PASS	.	G	GLN/ARG	1170,2796		170,830,983	54.0	59.0	58.0	http://www.ncbi.nlm.nih.gov/pubmed?term	53	3.3	1.0	17	dbSNP_108	58	3796,4528		879,2038,1245	yes	missense	GSDMA	NM_178171.4	43	1049,2868,2228	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	45.6031,29.5008,40.4068	benign	18/446	38121993	4966,7324	1983	4162	6145	SO:0001583	missense	284110	exon2			ACCCTCGAGGGGA	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.53G>A	17.37:g.38121993G>A	ENSP00000301659:p.Arg18Gln	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	123	51	0.414634	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	930	0.4258241758241758	130	0.26422764227642276	181	0.5	284	0.4965034965034965	335	0.4419525065963061	G	13.55	2.270656	0.40194	0.295008	0.456031	ENSG00000167914	ENST00000301659	T	0.22743	1.94	5.36	3.34	0.38264	.	0.710982	0.12216	N	0.488832	T	0.00012	0.0000	L	0.49455	1.56	0.38224	P	0.05916500000000002	B	0.16166	0.016	B	0.14023	0.01	T	0.43393	-0.9394	9	0.20046	T	0.44	-4.2602	7.6027	0.28085	0.1926:0.0:0.8074:0.0	rs3894194;rs12948522;rs52814263;rs61411446;rs3894194	18	Q96QA5	GSDMA_HUMAN	Q	18	ENSP00000301659:R18Q	ENSP00000301659:R18Q	R	+	2	0	GSDMA	35375519	0.267000	0.24122	1.000000	0.80357	0.934000	0.57294	0.886000	0.28241	1.245000	0.43885	0.462000	0.41574	CGA	G|0.576;T|0.004	.	strong		0.582	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
ZNF224	7767	hgsc.bcm.edu	37	19	44611420	44611420	+	Silent	SNP	A	A	G	rs4508518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44611420A>G	ENST00000336976.6	+	6	1361	c.1107A>G	c.(1105-1107)gaA>gaG	p.E369E	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	369					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				ACACGGGAGAAAAGCCATATA	0.433													G|||	3226	0.644169	0.6195	0.5504	5008	,	,		21102	0.5308		0.8091	False		,,,				2504	0.6912				p.E369E		Atlas-SNP	.											.	ZNF224	70	.	0			c.A1107G						PASS	.	G		2888,1518		972,944,287	83.0	82.0	82.0		1107	-0.4	0.0	19	dbSNP_111	82	7053,1547		2913,1227,160	no	coding-synonymous	ZNF224	NM_013398.2		3885,2171,447	GG,GA,AA		17.9884,34.453,23.566		369/708	44611420	9941,3065	2203	4300	6503	SO:0001819	synonymous_variant	7767	exon6			GGGAGAAAAGCCA	AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"""Zinc fingers, C2H2-type"", ""-"""	13017	protein-coding gene	gene with protein product		194555	"""zinc finger protein 255"", ""zinc finger protein 27"""	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1107A>G	19.37:g.44611420A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Silent	SNP	ENST00000336976.6	37	CCDS33046.1																																																																																			A|0.277;G|0.723	0.723	strong		0.433	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398	
C16orf71	146562	hgsc.bcm.edu	37	16	4797457	4797457	+	Missense_Mutation	SNP	C	C	T	rs17853375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4797457C>T	ENST00000299320.5	+	9	1872	c.1394C>T	c.(1393-1395)cCt>cTt	p.P465L	C16orf71_ENST00000590191.1_Missense_Mutation_p.P482L|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	465			P -> L (in dbSNP:rs17853375). {ECO:0000269|PubMed:15489334}.							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GCTCAGGCCCCTGAAGACACA	0.647													C|||	2143	0.427915	0.0582	0.5086	5008	,	,		17368	0.6528		0.5994	False		,,,				2504	0.4622				p.P465L		Atlas-SNP	.											.	C16orf71	46	.	0			c.C1394T						PASS	.	C	LEU/PRO	621,3769		53,515,1627	30.0	35.0	33.0		1394	0.6	0.0	16	dbSNP_123	33	5119,3475		1552,2015,730	yes	missense	C16orf71	NM_139170.2	98	1605,2530,2357	TT,TC,CC		40.4352,14.1458,44.2083	probably-damaging	465/521	4797457	5740,7244	2195	4297	6492	SO:0001583	missense	146562	exon9			AGGCCCCTGAAGA	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.1394C>T	16.37:g.4797457C>T	ENSP00000299320:p.Pro465Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	1068	0.489010989010989	36	0.07317073170731707	187	0.5165745856353591	393	0.6870629370629371	452	0.5963060686015831	C	12.94	2.087887	0.36855	0.141458	0.595648	ENSG00000166246	ENST00000299320;ENST00000411541	T	0.33654	1.4	4.89	0.549	0.17213	.	1.628840	0.03628	N	0.237451	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.14805	0.011	B	0.11329	0.006	T	0.48328	-0.9045	9	0.51188	T	0.08	0.0573	4.3323	0.11069	0.3111:0.5144:0.0:0.1745	rs17853375	465	Q8IYS4	CP071_HUMAN	L	465;220	ENSP00000299320:P465L	ENSP00000299320:P465L	P	+	2	0	C16orf71	4737458	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.107000	0.10873	-0.045000	0.13468	-0.521000	0.04368	CCT	C|0.555;G|0.000;T|0.445	0.445	strong		0.647	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
WFIKKN2	124857	hgsc.bcm.edu	37	17	48913478	48913478	+	Silent	SNP	C	C	T	rs77632597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48913478C>T	ENST00000311378.4	+	1	708	c.180C>T	c.(178-180)agC>agT	p.S60S	WFIKKN2_ENST00000426127.1_Intron	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	60	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			ACGCACAGAGCACCTGCAGGC	0.677													C|||	100	0.0199681	0.0045	0.0375	5008	,	,		18568	0.0		0.0656	False		,,,				2504	0.002				p.S60S		Atlas-SNP	.											WFIKKN2,NS,carcinoma,0,1	WFIKKN2	69	1	0			c.C180T						PASS	.	C		57,4349	50.9+/-86.3	1,55,2147	31.0	25.0	27.0		180	5.4	1.0	17	dbSNP_132	27	493,8107	134.4+/-191.8	11,471,3818	no	coding-synonymous	WFIKKN2	NM_175575.5		12,526,5965	TT,TC,CC		5.7326,1.2937,4.2288		60/577	48913478	550,12456	2203	4300	6503	SO:0001819	synonymous_variant	124857	exon1			ACAGAGCACCTGC	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.180C>T	17.37:g.48913478C>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	231	102	0.441558	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			C|0.964;T|0.036	0.036	strong		0.677	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
WBSCR28	135886	hgsc.bcm.edu	37	7	73275565	73275565	+	Missense_Mutation	SNP	T	T	A	rs11770052	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73275565T>A	ENST00000320531.2	+	1	77	c.41T>A	c.(40-42)aTc>aAc	p.I14N		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	14			I -> N (in dbSNP:rs11770052). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18398435}.			integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				CTTTTGGGGATCCTGTTGCAG	0.622													T|||	2728	0.544728	0.2852	0.6037	5008	,	,		13720	0.63		0.7256	False		,,,				2504	0.5798				p.I14N		Atlas-SNP	.											.	WBSCR28	24	.	0			c.T41A						PASS	.	T	ASN/ILE	1476,2316		291,894,711	55.0	52.0	53.0		41	3.1	0.0	7	dbSNP_120	53	6148,2076		2304,1540,268	yes	missense	WBSCR28	NM_182504.3	149	2595,2434,979	AA,AT,TT		25.2432,38.9241,36.5513	benign	14/266	73275565	7624,4392	1896	4112	6008	SO:0001583	missense	135886	exon1			TGGGGATCCTGTT	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.41T>A	7.37:g.73275565T>A	ENSP00000316775:p.Ile14Asn	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_182504	Q6UE04|Q8NHP4	Missense_Mutation	SNP	ENST00000320531.2	37	CCDS43597.1	1264	0.5787545787545788	145	0.29471544715447157	213	0.5883977900552486	352	0.6153846153846154	554	0.7308707124010554	T	0.735	-0.778461	0.02929	0.389241	0.747568	ENSG00000175877	ENST00000320531	T	0.22134	1.97	4.21	3.07	0.35406	.	0.468250	0.16327	N	0.219284	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P	0.44429	0.835	P	0.48400	0.576	T	0.04153	-1.0973	9	0.54805	T	0.06	-1.7877	5.6334	0.17524	0.0:0.1295:0.0:0.8705	rs11770052;rs17845923;rs17858902;rs11770052	14	Q6UE05	WBS28_HUMAN	N	14	ENSP00000316775:I14N	ENSP00000316775:I14N	I	+	2	0	WBSCR28	72913501	0.030000	0.19436	0.002000	0.10522	0.019000	0.09904	2.013000	0.40942	0.805000	0.34159	0.529000	0.55759	ATC	T|0.385;A|0.615	0.615	strong		0.622	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
TLN2	83660	hgsc.bcm.edu	37	15	63047793	63047793	+	Silent	SNP	C	C	T	rs4775538	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63047793C>T	ENST00000561311.1	+	36	4769	c.4539C>T	c.(4537-4539)atC>atT	p.I1513I	TLN2_ENST00000472902.1_5'Flank|TLN2_ENST00000306829.6_Silent_p.I1513I			Q9Y4G6	TLN2_HUMAN	talin 2	1513					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CCTGCCGCATCGCCTCATCCA	0.577													C|||	1160	0.231629	0.2466	0.1297	5008	,	,		19253	0.3442		0.1988	False		,,,				2504	0.2014				p.I1513I		Atlas-SNP	.											.	TLN2	253	.	0			c.C4539T						PASS	.	C		889,3517	343.1+/-307.5	83,723,1397	97.0	73.0	81.0		4539	-6.1	0.7	15	dbSNP_111	81	1897,6703	337.4+/-322.3	211,1475,2614	no	coding-synonymous	TLN2	NM_015059.2		294,2198,4011	TT,TC,CC		22.0581,20.177,21.4209		1513/2543	63047793	2786,10220	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon34			CCGCATCGCCTCA	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.4539C>T	15.37:g.63047793C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	64	0.503937	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			C|0.774;T|0.226	0.226	strong		0.577	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
MUC4	4585	hgsc.bcm.edu	37	3	195509497	195509497	+	Missense_Mutation	SNP	G	G	A	rs201925754		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509497G>A	ENST00000463781.3	-	2	9413	c.8954C>T	c.(8953-8955)gCa>gTa	p.A2985V	MUC4_ENST00000475231.1_Missense_Mutation_p.A2985V|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A2985V(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.572																																					p.A2985V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	1	Substitution - Missense(1)	endometrium(1)	c.C8954T						scavenged	.						18.0	10.0	12.0					3																	195509497		655	1551	2206	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8954C>T	3.37:g.195509497G>A	ENSP00000417498:p.Ala2985Val	Somatic	106	10	0.0943396		WXS	Illumina HiSeq	Phase_I	210	26	0.12381	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	3.895	-0.023177	0.07634	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.55	.	.	.	.	.	.	.	.	T	0.14141	0.0342	N	0.14661	0.345	0.09310	N	0.999999	B	0.11235	0.004	B	0.01281	0.0	T	0.28332	-1.0047	7	.	.	.	.	3.5027	0.07679	0.3048:0.0:0.6952:0.0	.	2857	E7ESK3	.	V	2985	ENSP00000417498:A2985V;ENSP00000420243:A2985V	.	A	-	2	0	MUC4	196994276	.	.	0.011000	0.14972	0.000000	0.00434	.	.	0.482000	0.27582	0.000000	0.15137	GCA	G|0.998;A|0.002	0.002	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR1L8	138881	hgsc.bcm.edu	37	9	125330678	125330678	+	Missense_Mutation	SNP	T	T	G	rs10985704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:125330678T>G	ENST00000304865.2	-	1	160	c.79A>C	c.(79-81)Aca>Cca	p.T27P		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	27			T -> P (in dbSNP:rs10985704).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						ACAAAGAGTGTCTTTTGGTCC	0.507													G|||	3331	0.665136	0.5991	0.6225	5008	,	,		19581	0.9792		0.5477	False		,,,				2504	0.5818				p.T27P		Atlas-SNP	.											.	OR1L8	90	.	0			c.A79C						PASS	.	G	PRO/THR	2592,1814	532.3+/-373.4	758,1076,369	121.0	139.0	133.0		79	3.5	0.7	9	dbSNP_120	133	4819,3781	535.8+/-382.9	1317,2185,798	yes	missense	OR1L8	NM_001004454.1	38	2075,3261,1167	GG,GT,TT		43.9651,41.1711,43.0186	benign	27/310	125330678	7411,5595	2203	4300	6503	SO:0001583	missense	138881	exon1			AGAGTGTCTTTTG		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"""GPCR / Class A : Olfactory receptors"""	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.79A>C	9.37:g.125330678T>G	ENSP00000306607:p.Thr27Pro	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001004454	A3KFM3|B9EIR6|Q6IF15|Q96R79	Missense_Mutation	SNP	ENST00000304865.2	37	CCDS35124.1	1485	0.679945054945055	294	0.5975609756097561	227	0.6270718232044199	564	0.986013986013986	400	0.5277044854881267	G	9.033	0.987675	0.18966	0.588289	0.560349	ENSG00000171496	ENST00000304865	T	0.00438	7.42	4.39	3.48	0.39840	.	0.327705	0.22065	N	0.065106	T	0.00012	0.0000	N	0.00517	-1.405	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.50898	-0.8773	9	0.29301	T	0.29	-8.0918	12.5128	0.56015	0.0:0.0:0.6956:0.3044	rs10985704;rs17278713;rs52816957;rs60721400;rs10985704	27	Q8NGR8	OR1L8_HUMAN	P	27	ENSP00000306607:T27P	ENSP00000306607:T27P	T	-	1	0	OR1L8	124370499	0.000000	0.05858	0.733000	0.30861	0.806000	0.45545	-0.663000	0.05299	0.618000	0.30179	-0.386000	0.06593	ACA	T|0.381;G|0.619	0.619	strong		0.507	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1		
PTPRZ1	5803	hgsc.bcm.edu	37	7	121698871	121698871	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:121698871A>C	ENST00000393386.2	+	28	6957	c.6546A>C	c.(6544-6546)gaA>gaC	p.E2182D	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E1315D	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2182	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ATGTACTTGAAGTGAGGCACT	0.358																																					p.E2182D		Atlas-SNP	.											PTPRZ1_ENST00000393386,NS,carcinoma,0,2	PTPRZ1	605	2	0			c.A6546C						PASS	.						104.0	103.0	103.0					7																	121698871		2203	4300	6503	SO:0001583	missense	5803	exon28			ACTTGAAGTGAGG	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.6546A>C	7.37:g.121698871A>C	ENSP00000377047:p.Glu2182Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	87	8	0.091954	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.758217	0.69763	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	D;D	0.84146	-1.81;-1.81	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.90960	0.7158	M	0.76938	2.355	0.52501	D	0.999957	B;B;P	0.47191	0.38;0.236;0.891	B;B;P	0.55667	0.229;0.173;0.781	D	0.91729	0.5395	10	0.72032	D	0.01	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	1321;1315;2182	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	D	2182;1315	ENSP00000377047:E2182D;ENSP00000410000:E1315D	ENSP00000377047:E2182D	E	+	3	2	PTPRZ1	121486107	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.621000	0.54210	2.326000	0.78906	0.533000	0.62120	GAA	.	.	none		0.358	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
SIRPB2	284759	hgsc.bcm.edu	37	20	1459246	1459246	+	Missense_Mutation	SNP	C	C	T	rs6033876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1459246C>T	ENST00000359801.3	-	3	494	c.458G>A	c.(457-459)gGg>gAg	p.G153E	SIRPB2_ENST00000608747.1_5'UTR|SIRPB2_ENST00000444444.2_Missense_Mutation_p.G55E|SIRPB2_ENST00000537284.1_Missense_Mutation_p.G15E	NM_001122962.1	NP_001116434.1	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein beta 2	145	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TTCAGGGTCCCCAGCTCCTGA	0.532													C|||	268	0.0535144	0.1649	0.0317	5008	,	,		18513	0.0		0.0179	False		,,,				2504	0.0102				p.G153E		Atlas-SNP	.											.	SIRPB2	50	.	0			c.G458A						PASS	.	C	GLU/GLY,GLU/GLY	449,2687		30,389,1149	41.0	37.0	38.0		458,164	0.1	0.0	20	dbSNP_114	38	92,7072		1,90,3491	yes	missense,missense	SIRPB2	NM_001122962.1,NM_001134836.1	98,98	31,479,4640	TT,TC,CC		1.2842,14.3176,5.2524	possibly-damaging,possibly-damaging	153/343,55/245	1459246	541,9759	1568	3582	5150	SO:0001583	missense	284759	exon3			GGGTCCCCAGCTC	AL109658	CCDS42849.1, CCDS46570.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000196209	ENSG00000196209		"""Signal-regulatory proteins"", ""Immunoglobulin superfamily / V-set domain containing"""	16247	protein-coding gene	gene with protein product			"""protein tyrosine phosphatase, non-receptor type 1-like"", ""protein tyrosine phosphatase, non-receptor type substrate 1-like 3"""	PTPN1L, PTPNS1L3		16339511	Standard	NM_001122962		Approved	dJ776F14.2	uc002wfg.2	Q5JXA9	OTTHUMG00000031670	ENST00000359801.3:c.458G>A	20.37:g.1459246C>T	ENSP00000352849:p.Gly153Glu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	63	21	0.333333	NM_001122962	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000359801.3	37	CCDS42849.1	119	0.05448717948717949	85	0.17276422764227642	16	0.04419889502762431	1	0.0017482517482517483	17	0.022427440633245383	C	5.996	0.367638	0.11352	0.143176	0.012842	ENSG00000196209	ENST00000359801;ENST00000444444;ENST00000537284;ENST00000381630;ENST00000381628	T;T;T;T	0.49720	0.77;4.28;4.39;4.23	4.29	0.0999	0.14510	Immunoglobulin-like fold (1);	0.697148	0.12516	N	0.462051	T	0.00109	0.0003	L	0.60455	1.87	0.80722	P	0.0	B;B;B	0.31459	0.324;0.218;0.076	B;B;B	0.27262	0.078;0.035;0.028	T	0.10109	-1.0644	9	0.18276	T	0.48	-13.8878	6.3738	0.21495	0.0:0.5656:0.0:0.4344	rs6033876;rs52835417;rs58866006;rs6033876	15;55;153	F5H204;E9PCW6;Q5JXA9	.;.;SIRB2_HUMAN	E	153;55;15;55;55	ENSP00000352849:G153E;ENSP00000402438:G55E;ENSP00000445632:G15E;ENSP00000371043:G55E	ENSP00000352849:G153E	G	-	2	0	SIRPB2	1407246	0.000000	0.05858	0.000000	0.03702	0.292000	0.27327	-0.189000	0.09629	0.188000	0.20168	-0.258000	0.10820	GGG	C|0.957;T|0.043	0.043	strong		0.532	SIRPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077544.1	NM_178459	
SMC6	79677	hgsc.bcm.edu	37	2	17897488	17897488	+	Missense_Mutation	SNP	T	T	C	rs35195207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:17897488T>C	ENST00000448223.2	-	15	1659	c.1390A>G	c.(1390-1392)Agg>Ggg	p.R464G	SMC6_ENST00000351948.4_Missense_Mutation_p.R464G|SMC6_ENST00000381272.4_Missense_Mutation_p.R490G|SMC6_ENST00000402989.1_Missense_Mutation_p.R464G	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	464	Flexible hinge.		R -> G (in dbSNP:rs35195207). {ECO:0000269|PubMed:11408570, ECO:0000269|PubMed:15489334}.		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTCAGTTGCCTCTGATTGTAG	0.348													T|||	507	0.101238	0.0567	0.1671	5008	,	,		16462	0.0139		0.2416	False		,,,				2504	0.0603				p.R464G		Atlas-SNP	.											.	SMC6	102	.	0			c.A1390G						PASS	.	T	GLY/ARG,GLY/ARG	362,4044	182.9+/-210.6	14,334,1855	152.0	153.0	152.0		1390,1390	4.4	1.0	2	dbSNP_126	152	2272,6328	385.1+/-341.3	310,1652,2338	yes	missense,missense	SMC6	NM_001142286.1,NM_024624.5	125,125	324,1986,4193	CC,CT,TT		26.4186,8.2161,20.2522	benign,benign	464/1092,464/1092	17897488	2634,10372	2203	4300	6503	SO:0001583	missense	79677	exon15			GTTGCCTCTGATT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1390A>G	2.37:g.17897488T>C	ENSP00000404092:p.Arg464Gly	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	191	191	1	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	286	0.13095238095238096	32	0.06504065040650407	69	0.19060773480662985	13	0.022727272727272728	172	0.22691292875989447	T	12.70	2.016854	0.35606	0.082161	0.264186	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.34275	1.56;1.56;1.56;1.56;1.37	5.62	4.42	0.53409	RecF/RecN/SMC (1);	0.184484	0.53938	D	0.000043	T	0.00012	0.0000	L	0.43923	1.385	0.51233	P	8.900000000000574E-5	B;B;B	0.29508	0.246;0.001;0.083	B;B;B	0.33254	0.134;0.006;0.16	T	0.30822	-0.9965	9	0.21540	T	0.41	.	12.249	0.54587	0.0:0.0:0.2626:0.7374	rs35195207;rs61754181	490;490;464	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	G	464;464;490;464;490	ENSP00000404092:R464G;ENSP00000323439:R464G;ENSP00000370672:R490G;ENSP00000384539:R464G;ENSP00000408644:R490G	ENSP00000323439:R464G	R	-	1	2	SMC6	17760969	1.000000	0.71417	0.996000	0.52242	0.612000	0.37316	3.853000	0.55941	2.141000	0.66446	0.454000	0.30748	AGG	T|0.825;C|0.175	0.175	strong		0.348	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	
DNAH8	1769	hgsc.bcm.edu	37	6	38903421	38903421	+	Silent	SNP	G	G	A	rs61748646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38903421G>A	ENST00000359357.3	+	75	11114	c.10860G>A	c.(10858-10860)cgG>cgA	p.R3620R	DNAH8_ENST00000441566.1_Silent_p.R3584R|RP1-207H1.3_ENST00000453417.1_RNA|RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000449981.2_Silent_p.R3837R			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3620	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTAATAAGCGGAAGATGAAAG	0.308													G|||	59	0.0117812	0.003	0.0144	5008	,	,		17584	0.006		0.0328	False		,,,				2504	0.0061				p.R3837R		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G11511A						PASS	.	G		23,4383	29.9+/-59.1	0,23,2180	159.0	178.0	172.0		11511	5.1	1.0	6	dbSNP_129	172	286,8310	104.6+/-165.6	4,278,4016	no	coding-synonymous	DNAH8	NM_001206927.1		4,301,6196	AA,AG,GG		3.3271,0.522,2.3766		3837/4708	38903421	309,12693	2203	4298	6501	SO:0001819	synonymous_variant	1769	exon77			TAAGCGGAAGATG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.10860G>A	6.37:g.38903421G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				G|0.980;A|0.020	0.020	strong		0.308	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
TET1	80312	hgsc.bcm.edu	37	10	70332580	70332580	+	Missense_Mutation	SNP	A	A	G	rs10823229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:70332580A>G	ENST00000373644.4	+	2	694	c.485A>G	c.(484-486)gAc>gGc	p.D162G		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	162			D -> G (in dbSNP:rs10823229).		chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CCAATGCAAGACACCCAAGTC	0.398													A|||	1295	0.258586	0.0227	0.2622	5008	,	,		21591	0.3919		0.3877	False		,,,				2504	0.3047				p.D162G		Atlas-SNP	.											.	TET1	255	.	0			c.A485G						PASS	.	A	GLY/ASP	332,4074	174.8+/-204.3	18,296,1889	71.0	69.0	70.0		485	4.1	0.1	10	dbSNP_120	70	3390,5210	501.0+/-375.3	678,2034,1588	yes	missense	TET1	NM_030625.2	94	696,2330,3477	GG,GA,AA		39.4186,7.5352,28.6176	benign	162/2137	70332580	3722,9284	2203	4300	6503	SO:0001583	missense	80312	exon2			TGCAAGACACCCA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.485A>G	10.37:g.70332580A>G	ENSP00000362748:p.Asp162Gly	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	614	0.28113553113553114	16	0.032520325203252036	105	0.2900552486187845	205	0.3583916083916084	288	0.37994722955145116	A	5.268	0.234823	0.09969	0.075352	0.394186	ENSG00000138336	ENST00000373644	T	0.08546	3.08	5.24	4.08	0.47627	.	2.351840	0.02435	N	0.083983	T	0.00012	0.0000	N	0.19112	0.55	0.47905	P	4.6000000000001595E-4	B	0.30793	0.295	B	0.27608	0.081	T	0.46978	-0.9152	9	0.51188	T	0.08	.	9.424	0.38567	0.8415:0.0:0.0:0.1585	rs10823229;rs52809930;rs61239936;rs10823229	162	Q8NFU7	TET1_HUMAN	G	162	ENSP00000362748:D162G	ENSP00000362748:D162G	D	+	2	0	TET1	70002586	0.457000	0.25752	0.072000	0.20136	0.112000	0.19704	0.745000	0.26259	0.803000	0.34113	0.460000	0.39030	GAC	A|0.718;G|0.282	0.282	strong		0.398	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
D2HGDH	728294	hgsc.bcm.edu	37	2	242690770	242690770	+	Silent	SNP	T	T	C	rs141343442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242690770T>C	ENST00000321264.4	+	8	1316	c.1107T>C	c.(1105-1107)gaT>gaC	p.D369D	D2HGDH_ENST00000486953.1_Intron|D2HGDH_ENST00000403782.1_Silent_p.D235D	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	369					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TGGTGACCGATGGGACCATGG	0.627													T|||	156	0.0311502	0.0	0.0288	5008	,	,		18957	0.0079		0.0497	False		,,,				2504	0.0798				p.D369D		Atlas-SNP	.											.	D2HGDH	39	.	0			c.T1107C						PASS	.	T		27,4379	33.5+/-64.1	0,27,2176	46.0	43.0	44.0		1107	-10.2	0.0	2	dbSNP_134	44	414,8178	129.0+/-187.1	8,398,3890	no	coding-synonymous	D2HGDH	NM_152783.3		8,425,6066	CC,CT,TT		4.8184,0.6128,3.3928		369/522	242690770	441,12557	2203	4296	6499	SO:0001819	synonymous_variant	728294	exon8			GACCGATGGGACC	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.1107T>C	2.37:g.242690770T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Silent	SNP	ENST00000321264.4	37	CCDS33426.1	60	0.027472527472527472	0	0.0	12	0.03314917127071823	5	0.008741258741258742	43	0.05672823218997362	T	1.488	-0.555485	0.03967	0.006128	0.048184	ENSG00000180902	ENST00000432449	.	.	.	5.1	-10.2	0.00374	.	.	.	.	.	T	0.09468	0.0233	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59182	-0.7502	4	.	.	.	1.0142	11.2638	0.49099	0.0737:0.0822:0.0736:0.7705	.	.	.	.	R	123	.	.	W	+	1	0	D2HGDH	242339443	0.001000	0.12720	0.040000	0.18447	0.141000	0.21300	-2.318000	0.01121	-2.441000	0.00550	-1.017000	0.02453	TGG	T|0.973;C|0.027	0.027	strong		0.627	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
IRF2BP2	359948	hgsc.bcm.edu	37	1	234743237	234743237	+	Silent	SNP	G	G	A	rs7543281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:234743237G>A	ENST00000366609.3	-	2	1440	c.1410C>T	c.(1408-1410)ggC>ggT	p.G470G	IRF2BP2_ENST00000491430.1_5'UTR|IRF2BP2_ENST00000366610.3_Silent_p.G454G|RP4-781K5.2_ENST00000436039.1_RNA	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	470					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			CCTCTCTGGGGCCCAGCCTTC	0.622													G|||	427	0.0852636	0.0832	0.0764	5008	,	,		17412	0.0377		0.1531	False		,,,				2504	0.0736				p.G470G		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.C1410T						PASS	.	G	,	428,3978	207.8+/-229.1	14,400,1789	92.0	100.0	97.0		1362,1410	1.2	1.0	1	dbSNP_116	97	1187,7413	240.1+/-271.0	91,1005,3204	no	coding-synonymous,coding-synonymous	IRF2BP2	NM_001077397.1,NM_182972.2	,	105,1405,4993	AA,AG,GG		13.8023,9.714,12.4173	,	454/572,470/588	234743237	1615,11391	2203	4300	6503	SO:0001819	synonymous_variant	359948	exon2			TCTGGGGCCCAGC	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.1410C>T	1.37:g.234743237G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	137	72	0.525547	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	37	CCDS1602.1																																																																																			G|0.884;A|0.116	0.116	strong		0.622	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972	
EXOC6	54536	hgsc.bcm.edu	37	10	94608319	94608319	+	Missense_Mutation	SNP	C	C	T	rs139196824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:94608319C>T	ENST00000260762.6	+	1	43	c.29C>T	c.(28-30)aCc>aTc	p.T10I	EXOC6_ENST00000443748.2_Missense_Mutation_p.T10I|EXOC6_ENST00000371552.4_Intron|EXOC6_ENST00000371543.1_Missense_Mutation_p.T10I|EXOC6_ENST00000371547.4_Intron	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	10					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				AGTCTGGGCACCGTCCCCGAG	0.677													C|||	44	0.00878594	0.0008	0.0115	5008	,	,		5881	0.0		0.0298	False		,,,				2504	0.0051				p.T10I		Atlas-SNP	.											.	EXOC6	147	.	0			c.C29T						PASS	.	C	,ILE/THR	17,4369		0,17,2176	35.0	26.0	29.0		,29	3.9	1.0	10	dbSNP_134	29	179,8415		2,175,4120	yes	intron,missense	EXOC6	NM_001013848.2,NM_019053.4	,89	2,192,6296	TT,TC,CC		2.0828,0.3876,1.51	,benign	,10/805	94608319	196,12784	2193	4297	6490	SO:0001583	missense	54536	exon1			TGGGCACCGTCCC	BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"""SEC15-like 1 (S. cerevisiae)"""	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.29C>T	10.37:g.94608319C>T	ENSP00000260762:p.Thr10Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_019053	E9PHI3|Q5VXH8|Q9NZ24	Missense_Mutation	SNP	ENST00000260762.6	37	CCDS7424.2	34	0.015567765567765568	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	26	0.03430079155672823	C	15.09	2.728972	0.48833	0.003876	0.020828	ENSG00000138190	ENST00000371543;ENST00000443748;ENST00000260762	T;T	0.32515	1.45;1.87	3.94	3.94	0.45596	.	0.512406	0.19907	N	0.103362	T	0.08223	0.0205	L	0.29908	0.895	0.21527	N	0.99965	B;B;B	0.23058	0.013;0.079;0.037	B;B;B	0.25759	0.01;0.063;0.063	T	0.07770	-1.0755	10	0.19590	T	0.45	-0.4795	13.8059	0.63230	0.0:1.0:0.0:0.0	.	10;10;10	E7EW84;B4DEZ1;Q8TAG9	.;.;EXOC6_HUMAN	I	10	ENSP00000396206:T10I;ENSP00000260762:T10I	ENSP00000260762:T10I	T	+	2	0	EXOC6	94598299	0.430000	0.25538	1.000000	0.80357	0.968000	0.65278	1.209000	0.32357	1.903000	0.55091	0.313000	0.20887	ACC	C|0.984;T|0.016	0.016	strong		0.677	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053	
SLC4A9	83697	hgsc.bcm.edu	37	5	139745154	139745154	+	Silent	SNP	T	T	C	rs6860077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139745154T>C	ENST00000230993.6	+	12	1808	c.1773T>C	c.(1771-1773)atT>atC	p.I591I	SLC4A9_ENST00000506545.1_Silent_p.I567I|SLC4A9_ENST00000432095.2_Splice_Site_p.I556I|SLC4A9_ENST00000506757.2_Silent_p.I567I|SLC4A9_ENST00000507527.1_Silent_p.I591I	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	591	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGACGACATTGTAAGCATGG	0.507													C|||	3553	0.709465	0.5651	0.7493	5008	,	,		22618	0.8353		0.7177	False		,,,				2504	0.7382				p.I591I		Atlas-SNP	.											.	SLC4A9	125	.	0			c.T1773C						PASS	.	C		2435,1519		741,953,283	81.0	88.0	86.0		1701	1.5	0.0	5	dbSNP_116	86	5872,2448		2077,1718,365	no	coding-synonymous	SLC4A9	NM_031467.2		2818,2671,648	CC,CT,TT		29.4231,38.4168,32.3204		567/960	139745154	8307,3967	1977	4160	6137	SO:0001819	synonymous_variant	83697	exon12			CGACATTGTAAGC	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"""Solute carriers"""	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.1773T>C	5.37:g.139745154T>C		Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	328	103	0.314024	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Silent	SNP	ENST00000230993.6	37	CCDS58973.1																																																																																			T|0.282;C|0.718	0.718	strong		0.507	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467	
SLC35G6	643664	hgsc.bcm.edu	37	17	7386030	7386030	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7386030C>T	ENST00000412468.2	+	2	842	c.727C>T	c.(727-729)Ccc>Tcc	p.P243S	ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	243						integral component of membrane (GO:0016021)		p.P243S(1)									TGTGCTGCAGCCCCCCGTGTT	0.602																																					p.P243S		Atlas-SNP	.											POLR2A_ENST00000412468,caecum,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	large_intestine(1)	c.C727T						scavenged	.						62.0	59.0	60.0					17																	7386030		2203	4300	6503	SO:0001583	missense	643664	exon2			CTGCAGCCCCCCG		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.727C>T	17.37:g.7386030C>T	ENSP00000396523:p.Pro243Ser	Somatic	263	9	0.0342205		WXS	Illumina HiSeq	Phase_I	293	10	0.0341297	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	A	0.130	-1.114361	0.01799	.	.	ENSG00000181222	ENST00000412468	T	0.69561	-0.41	3.92	3.92	0.45320	.	.	.	.	.	T	0.38772	0.1053	N	0.08118	0	0.20638	N	0.999873	B	0.02656	0.0	B	0.01281	0.0	T	0.25745	-1.0123	9	0.11485	T	0.65	-1.3593	3.5858	0.07970	0.6037:0.2022:0.1941:0.0	.	243	P0C7Q6	S35G6_HUMAN	S	243	ENSP00000396523:P243S	ENSP00000396523:P243S	P	+	1	0	SLC35G6	7326754	1.000000	0.71417	0.961000	0.40146	0.138000	0.21146	3.276000	0.51646	0.504000	0.28082	-0.520000	0.04383	CCC	A|1.000;|0.000	.	alt		0.602	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
RPTOR	57521	hgsc.bcm.edu	37	17	78599562	78599562	+	Silent	SNP	C	C	G	rs17848685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:78599562C>G	ENST00000306801.3	+	2	596	c.234C>G	c.(232-234)acC>acG	p.T78T	RPTOR_ENST00000544334.2_Silent_p.T78T|RPTOR_ENST00000570891.1_Silent_p.T78T|RPTOR_ENST00000537330.1_5'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	78					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						TGGTGAAGACCACGCCCTGTG	0.552													C|||	579	0.115615	0.0431	0.1239	5008	,	,		13519	0.0565		0.2137	False		,,,				2504	0.1677				p.T78T		Atlas-SNP	.											RPTOR,right_lower_lobe,carcinoma,+1,1	RPTOR	122	1	0			c.C234G						PASS	.	C	,	304,4102	165.1+/-196.6	10,284,1909	212.0	162.0	178.0		234,234	1.7	1.0	17	dbSNP_123	178	1895,6705	336.0+/-321.7	209,1477,2614	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	219,1761,4523	GG,GC,CC		22.0349,6.8997,16.9076	,	78/1178,78/1336	78599562	2199,10807	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon2			GAAGACCACGCCC		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.234C>G	17.37:g.78599562C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	65	0.560345	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			C|0.836;G|0.164	0.164	strong		0.552	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
CLCA2	9635	hgsc.bcm.edu	37	1	86891073	86891073	+	Missense_Mutation	SNP	G	G	A	rs11580625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86891073G>A	ENST00000370565.4	+	2	400	c.238G>A	c.(238-240)Gta>Ata	p.V80I		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	80	Metalloprotease domain. {ECO:0000250|UniProtKB:A8K7I4}.		V -> I (in dbSNP:rs11580625).		cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CAAGAGAAGAGTATTTTTCAG	0.303													G|||	82	0.0163738	0.0045	0.0216	5008	,	,		15704	0.0		0.0517	False		,,,				2504	0.0092				p.V80I	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.G238A						PASS	.	G	ILE/VAL	37,4367	37.6+/-69.7	1,35,2166	45.0	49.0	48.0		238	3.1	1.0	1	dbSNP_120	48	361,8207	116.3+/-176.0	12,337,3935	yes	missense	CLCA2	NM_006536.5	29	13,372,6101	AA,AG,GG		4.2134,0.8401,3.0681	possibly-damaging	80/944	86891073	398,12574	2202	4284	6486	SO:0001583	missense	9635	exon2			AGAAGAGTATTTT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.238G>A	1.37:g.86891073G>A	ENSP00000359596:p.Val80Ile	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	161	49	0.304348	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	48	0.02197802197802198	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	39	0.051451187335092345	G	16.97	3.268510	0.59540	0.008401	0.042134	ENSG00000137975	ENST00000370565;ENST00000439777	T	0.12255	2.7	5.93	3.08	0.35506	Chloride channel calcium-activated (1);	0.438333	0.23265	N	0.050093	T	0.04318	0.0119	M	0.66939	2.045	0.31514	N	0.663187	B	0.13594	0.008	B	0.16289	0.015	T	0.37033	-0.9723	10	0.19147	T	0.46	-4.1577	4.4784	0.11755	0.2942:0.0:0.5286:0.1772	rs11580625;rs11580625	80	Q9UQC9	CLCA2_HUMAN	I	80	ENSP00000359596:V80I	ENSP00000359596:V80I	V	+	1	0	CLCA2	86663661	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	0.651000	0.24873	0.429000	0.26202	-0.136000	0.14681	GTA	G|0.969;A|0.031	0.031	strong		0.303	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
MLF2	8079	hgsc.bcm.edu	37	12	6858126	6858126	+	Silent	SNP	G	G	A	rs2302371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6858126G>A	ENST00000203630.5	-	8	1226	c.582C>T	c.(580-582)gaC>gaT	p.D194D	MLF2_ENST00000542154.1_Silent_p.D194D|MLF2_ENST00000435120.1_Silent_p.D194D|MLF2_ENST00000564181.1_5'Flank|MLF2_ENST00000539187.1_Silent_p.D194D			Q15773	MLF2_HUMAN	myeloid leukemia factor 2	194					defense response (GO:0006952)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				kidney(2)|large_intestine(3)|lung(4)	9						GCCGCCACTCGTCATCAAACG	0.677													G|||	426	0.0850639	0.0393	0.1427	5008	,	,		16981	0.119		0.1044	False		,,,				2504	0.0511				p.D194D		Atlas-SNP	.											MLF2,NS,carcinoma,0,3	MLF2	26	3	0			c.C582T						PASS	.	G		239,4151		6,227,1962	15.0	14.0	14.0		582	-1.6	0.8	12	dbSNP_100	14	1069,7493		62,945,3274	no	coding-synonymous	MLF2	NM_005439.2		68,1172,5236	AA,AG,GG		12.4854,5.4442,10.0988		194/249	6858126	1308,11644	2195	4281	6476	SO:0001819	synonymous_variant	8079	exon8			CCACTCGTCATCA	U57342	CCDS8559.1	12p13.31	2014-09-11			ENSG00000089693	ENSG00000089693			7126	protein-coding gene	gene with protein product		601401				8661158	Standard	NM_005439		Approved	NTN4	uc010sfi.2	Q15773	OTTHUMG00000168717	ENST00000203630.5:c.582C>T	12.37:g.6858126G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_005439		Silent	SNP	ENST00000203630.5	37	CCDS8559.1	223	0.1021062271062271	41	0.08333333333333333	42	0.11602209944751381	56	0.0979020979020979	84	0.11081794195250659	G	4.382	0.070542	0.08436	0.054442	0.124854	ENSG00000089693	ENST00000537126	.	.	.	5.21	-1.62	0.08372	.	.	.	.	.	T	0.00845	0.0028	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.36040	-0.9764	4	0.87932	D	0	.	8.2231	0.31554	0.3036:0.0:0.5745:0.1219	rs2302371;rs11538002;rs17630206;rs58054620;rs2302371	.	.	.	M	205	.	ENSP00000439789:T205M	T	-	2	0	MLF2	6728387	0.941000	0.31946	0.775000	0.31657	0.006000	0.05464	0.009000	0.13219	-0.249000	0.09569	-0.218000	0.12543	ACG	G|0.910;A|0.090	0.090	strong		0.677	MLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400733.2		
SH2B1	25970	hgsc.bcm.edu	37	16	28883241	28883241	+	Missense_Mutation	SNP	A	A	G	rs7498665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28883241A>G	ENST00000322610.8	+	8	1889	c.1450A>G	c.(1450-1452)Aca>Gca	p.T484A	SH2B1_ENST00000395532.4_Missense_Mutation_p.T484A|SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000337120.5_Missense_Mutation_p.T484A|SH2B1_ENST00000545570.1_Missense_Mutation_p.T174A|SH2B1_ENST00000538342.1_Missense_Mutation_p.T148A|SH2B1_ENST00000359285.5_Missense_Mutation_p.T484A			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	484	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.		T -> A (in dbSNP:rs7498665). {ECO:0000269|PubMed:15767667, ECO:0000269|PubMed:17974005}.		blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.T484A(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						GGGACCCCCAACAGGGACAGT	0.622													G|||	1309	0.261382	0.2277	0.4856	5008	,	,		14129	0.126		0.329	False		,,,				2504	0.2178				p.T484A		Atlas-SNP	.											SH2B1,NS,carcinoma,0,1	SH2B1	160	1	1	Substitution - Missense(1)	stomach(1)	c.A1450G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	1188,3206	708.1+/-407.6	147,894,1156	54.0	54.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1450,1450,1450,1450,1450	3.1	1.0	16	dbSNP_116	54	3280,5320	644.9+/-400.1	645,1990,1665	yes	missense,missense,missense,missense,missense	SH2B1	NM_001145795.1,NM_001145796.1,NM_001145797.1,NM_001145812.1,NM_015503.2	58,58,58,58,58	792,2884,2821	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	38.1395,27.0369,34.3851	benign,benign,benign,benign,benign	484/757,484/672,484/684,484/672,484/672	28883241	4468,8526	2197	4300	6497	SO:0001583	missense	25970	exon6			CCCCCAACAGGGA	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	30417	protein-coding gene	gene with protein product	"""SH2-B homolog"""	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1450A>G	16.37:g.28883241A>G	ENSP00000321221:p.Thr484Ala	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	232	87	0.375	NM_001145796	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	37	CCDS53996.1	582	0.2664835164835165	101	0.20528455284552846	146	0.40331491712707185	77	0.1346153846153846	258	0.3403693931398417	G	4.100	0.016531	0.07959	0.270369	0.381395	ENSG00000178188	ENST00000322610;ENST00000545570;ENST00000359285;ENST00000538342;ENST00000395532;ENST00000337120	T;T;T;T;T;T	0.42513	0.98;1.66;0.97;1.56;0.98;0.98	5.14	3.08	0.35506	.	0.786081	0.11222	N	0.586567	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.44682	-0.9312	9	0.06494	T	0.89	-34.7926	4.2204	0.10554	0.0868:0.3268:0.4473:0.1391	rs7498665;rs17856339;rs60209196;rs7498665	148;174;484;484;484	B4DLN5;F5GXU7;Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;.;.;SH2B1_HUMAN	A	484;174;484;148;484;484	ENSP00000321221:T484A;ENSP00000440354:T174A;ENSP00000352232:T484A;ENSP00000438784:T148A;ENSP00000378903:T484A;ENSP00000337163:T484A	ENSP00000321221:T484A	T	+	1	0	SH2B1	28790742	0.001000	0.12720	0.999000	0.59377	0.987000	0.75469	0.782000	0.26788	0.567000	0.29293	-0.186000	0.12905	ACA	A|0.711;G|0.289	0.289	strong		0.622	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503	
WDR18	57418	hgsc.bcm.edu	37	19	984537	984537	+	Missense_Mutation	SNP	A	A	G	rs61732720	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:984537A>G	ENST00000251289.5	+	1	207	c.184A>G	c.(184-186)Atc>Gtc	p.I62V	WDR18_ENST00000587001.2_Missense_Mutation_p.I62V|WDR18_ENST00000591997.1_Intron	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	62					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAAGAATTACATCAGCGCCTG	0.711													.|||	488	0.0974441	0.0061	0.0764	5008	,	,		11329	0.0853		0.1252	False		,,,				2504	0.2198				p.I62V		Atlas-SNP	.											.	WDR18	20	.	0			c.A184G						PASS	.	A	VAL/ILE	100,4082		1,98,1992	7.0	9.0	8.0		184	3.3	1.0	19	dbSNP_129	8	848,7344		40,768,3288	no	missense	WDR18	NM_024100.3	29	41,866,5280	GG,GA,AA		10.3516,2.3912,7.6612	possibly-damaging	62/433	984537	948,11426	2091	4096	6187	SO:0001583	missense	57418	exon1			AATTACATCAGCG		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.184A>G	19.37:g.984537A>G	ENSP00000251289:p.Ile62Val	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_024100	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	37	CCDS12051.1	176	0.08058608058608059	3	0.006097560975609756	31	0.0856353591160221	40	0.06993006993006994	102	0.1345646437994723	A	20.6	4.011325	0.75046	0.023912	0.103516	ENSG00000065268	ENST00000251289	T	0.16597	2.33	4.3	3.26	0.37387	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.056832	0.64402	D	0.000002	T	0.00271	0.0008	M	0.73962	2.25	0.22693	P	0.99884067	P	0.51351	0.944	P	0.52109	0.69	T	0.14448	-1.0472	9	0.12766	T	0.61	.	8.2707	0.31842	0.8224:0.0:0.0:0.1776	rs61732720	62	Q9BV38	WDR18_HUMAN	V	62	ENSP00000251289:I62V	ENSP00000251289:I62V	I	+	1	0	WDR18	935537	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	7.804000	0.85993	0.662000	0.31006	0.533000	0.62120	ATC	A|0.920;G|0.080	0.080	strong		0.711	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
ZNF579	163033	hgsc.bcm.edu	37	19	56089353	56089353	+	Silent	SNP	C	C	T	rs2292812	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56089353C>T	ENST00000325421.4	-	2	1681	c.1653G>A	c.(1651-1653)aaG>aaA	p.K551K	CTD-2537I9.5_ENST00000589396.1_lincRNA	NM_152600.2	NP_689813.2	Q8NAF0	ZN579_HUMAN	zinc finger protein 579	551					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.106)		GCAGGTGAGCCTTGCTGTCTA	0.677													C|||	2326	0.464457	0.4418	0.5216	5008	,	,		9135	0.2639		0.504	False		,,,				2504	0.6207				p.K551K		Atlas-SNP	.											.	ZNF579	21	.	0			c.G1653A						PASS	.	C		1941,2445		449,1043,701	26.0	24.0	25.0		1653	-0.0	1.0	19	dbSNP_100	25	4444,4142		1191,2062,1040	no	coding-synonymous	ZNF579	NM_152600.2		1640,3105,1741	TT,TC,CC		48.2413,44.2544,49.2214		551/563	56089353	6385,6587	2193	4293	6486	SO:0001819	synonymous_variant	163033	exon2			GTGAGCCTTGCTG	AK092772	CCDS12927.1	19q13.42	2013-09-20			ENSG00000218891	ENSG00000218891		"""Zinc fingers, C2H2-type"""	26646	protein-coding gene	gene with protein product							Standard	NM_152600		Approved	FLJ35453	uc002qlh.3	Q8NAF0	OTTHUMG00000180857	ENST00000325421.4:c.1653G>A	19.37:g.56089353C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_152600		Silent	SNP	ENST00000325421.4	37	CCDS12927.1																																																																																			C|0.562;T|0.438	0.438	strong		0.677	ZNF579-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453348.1	NM_152600	
GPD1	2819	hgsc.bcm.edu	37	12	50503269	50503269	+	Silent	SNP	C	C	T	rs836180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50503269C>T	ENST00000301149.3	+	8	1249	c.1017C>T	c.(1015-1017)atC>atT	p.I339I	COX14_ENST00000317943.2_5'Flank|COX14_ENST00000550487.1_5'Flank|RP4-605O3.4_ENST00000552815.1_RNA|COX14_ENST00000550654.1_5'Flank|COX14_ENST00000548985.1_5'Flank|GPD1_ENST00000548814.1_Silent_p.I316I	NM_001257199.1|NM_005276.3	NP_001244128.1|NP_005267.2	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	339					cellular lipid metabolic process (GO:0044255)|cellular response to cAMP (GO:0071320)|cellular response to tumor necrosis factor (GO:0071356)|gluconeogenesis (GO:0006094)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophosphate shuttle (GO:0006127)|glycerophospholipid biosynthetic process (GO:0046474)|NADH oxidation (GO:0006116)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrion (GO:0005739)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|NAD binding (GO:0051287)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GTGAATTCATCCACTGCCTGC	0.567													C|||	1030	0.205671	0.0983	0.2968	5008	,	,		19272	0.0962		0.3956	False		,,,				2504	0.2035				p.I339I	NSCLC(141;1402 1905 9497 13391 44868)	Atlas-SNP	.											.	GPD1	23	.	0			c.C1017T						PASS	.	C		616,3790	267.4+/-267.8	44,528,1631	118.0	98.0	105.0		1017	2.1	0.4	12	dbSNP_86	105	3237,5363	487.5+/-372.1	633,1971,1696	no	coding-synonymous	GPD1	NM_005276.2		677,2499,3327	TT,TC,CC		37.6395,13.9809,29.6248		339/350	50503269	3853,9153	2203	4300	6503	SO:0001819	synonymous_variant	2819	exon8			ATTCATCCACTGC		CCDS8799.1, CCDS58229.1	12q13.12	2013-09-20			ENSG00000167588	ENSG00000167588	1.1.1.8		4455	protein-coding gene	gene with protein product		138420					Standard	NM_005276		Approved		uc001rvz.4	P21695	OTTHUMG00000169813	ENST00000301149.3:c.1017C>T	12.37:g.50503269C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	54	0.6	NM_005276	F8W1L5|Q8N1B0	Silent	SNP	ENST00000301149.3	37	CCDS8799.1																																																																																			C|0.726;T|0.274	0.274	strong		0.567	GPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406018.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29912345	29912345	+	Missense_Mutation	SNP	A	A	T	rs3180278	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29912345A>T	ENST00000396634.1	+	7	1305	c.964A>T	c.(964-966)Atc>Ttc	p.I322F	HLA-A_ENST00000376806.5_Missense_Mutation_p.I322F|HLA-A_ENST00000376809.5_Missense_Mutation_p.I322F|HLA-A_ENST00000376802.2_Intron			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	322					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TGGAGCTGTGATCACTGGAGC	0.587									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	307	0.0613019	0.0787	0.072	5008	,	,		18946	0.0159		0.0785	False		,,,				2504	0.0593				p.I322F		Atlas-SNP	.											.	HLA-A	89	.	0			c.A964T						PASS	.						112.0	106.0	108.0					6																	29912345		1511	2708	4219	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCTGTGATCACTG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.964A>T	6.37:g.29912345A>T	ENSP00000379873:p.Ile322Phe	Somatic	492	0	0		WXS	Illumina HiSeq	Phase_I	501	77	0.153693	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	263	0.12042124542124542	76	0.15447154471544716	50	0.13812154696132597	68	0.11888111888111888	69	0.09102902374670185	.	4.417	0.077034	0.08485	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00717	5.79;5.82;5.79	3.09	-4.5	0.03493	.	1.170570	0.06908	U	0.807074	T	0.00241	0.0007	L	0.35414	1.06	0.80722	P	0.0	B;B;B;B;B	0.27932	0.0;0.0;0.194;0.001;0.0	B;B;B;B;B	0.28991	0.0;0.002;0.097;0.002;0.002	T	0.41840	-0.9486	9	0.87932	D	0	.	1.172	0.01827	0.2182:0.2979:0.3261:0.1578	rs3180278;rs3208431;rs41555221	201;322;322;322;322	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	F	322	ENSP00000379873:I322F;ENSP00000366002:I322F;ENSP00000366005:I322F	ENSP00000366002:I322F	I	+	1	0	HLA-A	30020324	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.536000	0.06135	-1.069000	0.03153	-2.032000	0.00423	ATC	A|0.898;T|0.102	0.102	strong		0.587	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
TRPT1	83707	hgsc.bcm.edu	37	11	63991801	63991801	+	Missense_Mutation	SNP	T	T	C	rs1059440	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:63991801T>C	ENST00000317459.6	-	6	683	c.515A>G	c.(514-516)cAt>cGt	p.H172R	TRPT1_ENST00000394547.3_Missense_Mutation_p.H123R|TRPT1_ENST00000541278.1_Missense_Mutation_p.H172R|NUDT22_ENST00000279206.3_5'Flank|TRPT1_ENST00000546133.1_Missense_Mutation_p.H46R|TRPT1_ENST00000546089.1_Missense_Mutation_p.H123R|NUDT22_ENST00000441250.2_5'Flank|TRPT1_ENST00000540472.1_5'Flank|TRPT1_ENST00000394546.2_Missense_Mutation_p.H174R			Q86TN4	TRPT1_HUMAN	tRNA phosphotransferase 1	172			H -> R (in dbSNP:rs1059440). {ECO:0000269|PubMed:14504659, ECO:0000269|PubMed:15489334}.		regulation of protein kinase activity (GO:0045859)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)		tRNA 2'-phosphotransferase activity (GO:0000215)			lung(2)|skin(1)	3						TATTTCACAATGGGACCGCAT	0.612													T|||	768	0.153355	0.0915	0.3242	5008	,	,		20657	0.1766		0.171	False		,,,				2504	0.0736				p.H174R		Atlas-SNP	.											.	TRPT1	14	.	0			c.A521G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	464,3938	221.3+/-238.5	18,428,1755	73.0	68.0	70.0	http://www.ncbi.nlm.nih.gov/pubmed?term	368,515,515,515,521,515	2.6	0.0	11	dbSNP_86	70	1483,7111	281.7+/-295.2	134,1215,2948	yes	missense,missense,missense,missense,missense,missense	TRPT1	NM_031472.3,NM_001160393.1,NM_001160392.1,NM_001160390.1,NM_001160389.1,NM_001033678.3	29,29,29,29,29,29	152,1643,4703	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	17.2562,10.5407,14.9815	benign,benign,benign,benign,benign,benign	123/205,172/255,172/217,172/254,174/256,172/254	63991801	1947,11049	2201	4297	6498	SO:0001583	missense	83707	exon6			TCACAATGGGACC		CCDS31595.1, CCDS44639.1, CCDS53652.1, CCDS53653.1	11q13	2012-05-03			ENSG00000149743	ENSG00000149743			20316	protein-coding gene	gene with protein product	"""tRNA splicing 2' phosphotransferase 1"""	610470				14504659	Standard	NM_001160389		Approved	MGC11134	uc010rnc.2	Q86TN4	OTTHUMG00000167844	ENST00000317459.6:c.515A>G	11.37:g.63991801T>C	ENSP00000314073:p.His172Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001160389	A8MU17|A8MYC9|F5H2B2|Q9BSB9	Missense_Mutation	SNP	ENST00000317459.6	37	CCDS31595.1	370	0.16941391941391942	38	0.07723577235772358	105	0.2900552486187845	99	0.17307692307692307	128	0.16886543535620052	T	11.87	1.766573	0.31228	0.105407	0.172562	ENSG00000149743	ENST00000394547;ENST00000394546;ENST00000541278;ENST00000546133;ENST00000317459;ENST00000546089;ENST00000545812	T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06	5.1	2.59	0.31030	.	0.304258	0.37178	N	0.002202	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.699999999997374E-5	B;B;B;B	0.24426	0.007;0.008;0.103;0.018	B;B;B;B	0.23574	0.004;0.002;0.047;0.004	T	0.32824	-0.9892	9	0.42905	T	0.14	-5.3674	6.1092	0.20092	0.1443:0.082:0.0:0.7737	rs1059440;rs3179178;rs56524851;rs61088741;rs1059440	172;174;123;172	F5H2B2;A8MU17;Q86TN4-2;Q86TN4	.;.;.;TRPT1_HUMAN	R	123;174;172;46;172;123;174	ENSP00000378051:H123R;ENSP00000378050:H174R;ENSP00000438683:H172R;ENSP00000439586:H46R;ENSP00000314073:H172R;ENSP00000437741:H123R;ENSP00000442066:H174R	ENSP00000314073:H172R	H	-	2	0	TRPT1	63748377	0.995000	0.38212	0.035000	0.18076	0.643000	0.38383	3.865000	0.56033	0.906000	0.36621	0.454000	0.30748	CAT	T|0.849;C|0.151	0.151	strong		0.612	TRPT1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396579.1	NM_031472	
SPAG17	200162	hgsc.bcm.edu	37	1	118693217	118693217	+	Silent	SNP	T	T	C	rs1935992	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:118693217T>C	ENST00000336338.5	-	3	329	c.264A>G	c.(262-264)tcA>tcG	p.S88S		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	88						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CCTTTTTAGATGAAGCAGATC	0.259													T|||	1137	0.227037	0.0129	0.3458	5008	,	,		15639	0.4048		0.2356	False		,,,				2504	0.2403				p.S88S		Atlas-SNP	.											SPAG17,NS,carcinoma,0,1	SPAG17	263	1	0			c.A264G						PASS	.	T		213,4183	122.5+/-159.9	7,199,1992	69.0	71.0	70.0		264	0.9	0.0	1	dbSNP_92	70	1868,6702	326.4+/-317.4	206,1456,2623	no	coding-synonymous	SPAG17	NM_206996.2		213,1655,4615	CC,CT,TT		21.797,4.8453,16.0497		88/2224	118693217	2081,10885	2198	4285	6483	SO:0001819	synonymous_variant	200162	exon3			TTTAGATGAAGCA		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.264A>G	1.37:g.118693217T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	182	60	0.32967	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			C|0.210;N|0.000	0.210	strong		0.259	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
CDC6	990	hgsc.bcm.edu	37	17	38450248	38450248	+	Missense_Mutation	SNP	G	G	A	rs4135012	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38450248G>A	ENST00000209728.4	+	6	1354	c.883G>A	c.(883-885)Gat>Aat	p.D295N		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	295			D -> N (in dbSNP:rs4135012). {ECO:0000269|Ref.3}.		DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						CAAAGGCCAGGATGTATTGTA	0.398													G|||	28	0.00559105	0.0008	0.0086	5008	,	,		19688	0.0		0.0159	False		,,,				2504	0.0051				p.D295N		Atlas-SNP	.											.	CDC6	53	.	0			c.G883A						PASS	.	G	ASN/ASP	21,4385	30.8+/-60.4	0,21,2182	323.0	284.0	297.0		883	5.9	1.0	17	dbSNP_108	297	182,8418	82.3+/-144.9	2,178,4120	yes	missense	CDC6	NM_001254.3	23	2,199,6302	AA,AG,GG		2.1163,0.4766,1.5608	possibly-damaging	295/561	38450248	203,12803	2203	4300	6503	SO:0001583	missense	990	exon6			GGCCAGGATGTAT	U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"""CDC6 (cell division cycle 6, S. cerevisiae) homolog"", ""CDC6 cell division cycle 6 homolog (S. cerevisiae)"", ""cell division cycle 6 homolog (S. cerevisiae)"""	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.883G>A	17.37:g.38450248G>A	ENSP00000209728:p.Asp295Asn	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	201	88	0.437811	NM_001254	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	17	0.007783882783882784	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	12	0.0158311345646438	G	31	5.059101	0.93846	0.004766	0.021163	ENSG00000094804	ENST00000209728	T	0.59638	0.25	5.95	5.95	0.96441	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.046090	0.85682	D	0.000000	T	0.55705	0.1937	L	0.52905	1.665	0.58432	D	0.999993	P	0.47191	0.891	P	0.58013	0.831	T	0.62320	-0.6879	10	0.48119	T	0.1	-6.0538	19.1646	0.93551	0.0:0.0:1.0:0.0	rs4135012;rs17617390;rs52797967;rs4135012	295	Q99741	CDC6_HUMAN	N	295	ENSP00000209728:D295N	ENSP00000209728:D295N	D	+	1	0	CDC6	35703774	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.109000	0.89561	2.824000	0.97209	0.655000	0.94253	GAT	G|0.986;A|0.014	0.014	strong		0.398	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1		
EFEMP2	30008	hgsc.bcm.edu	37	11	65638719	65638719	+	Silent	SNP	G	G	A	rs633800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65638719G>A	ENST00000307998.6	-	4	506	c.276C>T	c.(274-276)caC>caT	p.H92H	EFEMP2_ENST00000528176.1_Silent_p.H92H	NM_016938.4	NP_058634.4	O95967	FBLN4_HUMAN	EGF containing fibulin-like extracellular matrix protein 2	92					blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21				READ - Rectum adenocarcinoma(159;0.169)		GTCCCTCGCCGTGTAGGTCGT	0.647													G|||	1608	0.321086	0.0953	0.3127	5008	,	,		17334	0.2262		0.503	False		,,,				2504	0.5429				p.H92H		Atlas-SNP	.											.	EFEMP2	42	.	0			c.C276T						PASS	.	G		703,3699	293.0+/-282.3	52,599,1550	95.0	105.0	102.0		276	-2.5	0.7	11	dbSNP_83	102	4451,4141	588.0+/-392.3	1139,2173,984	no	coding-synonymous	EFEMP2	NM_016938.4		1191,2772,2534	AA,AG,GG		48.196,15.97,39.6645		92/444	65638719	5154,7840	2201	4296	6497	SO:0001819	synonymous_variant	30008	exon4			CTCGCCGTGTAGG	AF109121	CCDS8116.1	11q13	2011-06-17	2011-01-25		ENSG00000172638	ENSG00000172638		"""Fibulins"""	3219	protein-coding gene	gene with protein product	"""fibulin 4"""	604633	"""EGF-containing fibulin-like extracellular matrix protein 2"""			10601734, 10982184	Standard	NR_037718		Approved	FBLN4, UPH1	uc001ofy.4	O95967	OTTHUMG00000166664	ENST00000307998.6:c.276C>T	11.37:g.65638719G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_016938	A8K7R4|B3KM31|B3KQT1|O75967	Silent	SNP	ENST00000307998.6	37	CCDS8116.1																																																																																			G|0.642;A|0.358	0.358	strong		0.647	EFEMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391047.4	NM_016938	
OPA1	4976	hgsc.bcm.edu	37	3	193374964	193374964	+	Silent	SNP	T	T	C	rs9851685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:193374964T>C	ENST00000392438.3	+	21	2343	c.2109T>C	c.(2107-2109)gcT>gcC	p.A703A	OPA1_ENST00000361510.2_Silent_p.A758A|OPA1_ENST00000361715.2_Silent_p.A722A|OPA1_ENST00000361908.3_Silent_p.A740A|OPA1_ENST00000361150.2_Silent_p.A704A|OPA1_ENST00000361828.2_Silent_p.A721A	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	703					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		TTAAAGAGGCTGTTAAGGAAG	0.388													C|||	2336	0.466454	0.5862	0.4697	5008	,	,		16355	0.3571		0.4563	False		,,,				2504	0.4254				p.A758A		Atlas-SNP	.											.	OPA1	79	.	0			c.T2274C						PASS	.	C	,,,,,,,	2475,1931	547.6+/-377.3	693,1089,421	100.0	104.0	102.0		2109,2001,2055,2112,2163,2166,2220,2274	0.1	1.0	3	dbSNP_119	102	3991,4609	599.5+/-394.1	907,2177,1216	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OPA1	NM_015560.2,NM_130831.2,NM_130832.2,NM_130833.2,NM_130834.2,NM_130835.2,NM_130836.2,NM_130837.2	,,,,,,,	1600,3266,1637	CC,CT,TT		46.407,43.8266,49.7155	,,,,,,,	703/961,667/925,685/943,704/962,721/979,722/980,740/998,758/1016	193374964	6466,6540	2203	4300	6503	SO:0001819	synonymous_variant	4976	exon23			AGAGGCTGTTAAG	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"""mitochondrial dynamin-like GTPase"", ""dynamin-like guanosine triphosphatase"", ""Dynamin-like 120 kDa protein, mitochondrial"""	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.2109T>C	3.37:g.193374964T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_130837	D3DNW4	Silent	SNP	ENST00000392438.3	37	CCDS43186.1																																																																																			T|0.517;C|0.483	0.483	strong		0.388	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
TENM3	55714	hgsc.bcm.edu	37	4	183674697	183674697	+	Silent	SNP	C	C	T	rs17263582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:183674697C>T	ENST00000511685.1	+	21	4080	c.3957C>T	c.(3955-3957)ggC>ggT	p.G1319G	TENM3_ENST00000406950.2_Silent_p.G1319G|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1319					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G1319G(1)									CTCTTCTGGGCTCTAACGATT	0.393													C|||	825	0.164736	0.0628	0.1931	5008	,	,		17204	0.1587		0.2505	False		,,,				2504	0.2004				p.G1319G		Atlas-SNP	.											ODZ3,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	prostate(1)	c.C3957T						PASS	.	C		304,3592		7,290,1651	101.0	101.0	101.0		3957	3.0	1.0	4	dbSNP_123	101	1792,6530		194,1404,2563	no	coding-synonymous	ODZ3	NM_001080477.1		201,1694,4214	TT,TC,CC		21.5333,7.8029,17.155		1319/2700	183674697	2096,10122	1948	4161	6109	SO:0001819	synonymous_variant	55714	exon20			TCTGGGCTCTAAC	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.3957C>T	4.37:g.183674697C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	130	51	0.392308	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																			C|0.827;T|0.173	0.173	strong		0.393	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
AGAP1	116987	hgsc.bcm.edu	37	2	236761396	236761396	+	Intron	SNP	C	C	T	rs13006916	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:236761396C>T	ENST00000304032.8	+	10	1630				AGAP1_ENST00000409538.1_Intron|AGAP1_ENST00000336665.5_Intron|AGAP1_ENST00000409457.1_Missense_Mutation_p.R373C|AGAP1_ENST00000428334.2_Intron	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1						protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AGCCCGTGCCCGTCAGTCCTC	0.587													C|||	2402	0.479633	0.0968	0.6499	5008	,	,		15278	0.7688		0.5179	False		,,,				2504	0.5389				p.R373C		Atlas-SNP	.											.	AGAP1	95	.	0			c.C1117T						PASS	.																																			SO:0001627	intron_variant	116987	exon10			CGTGCCCGTCAGT	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1051-30593C>T	2.37:g.236761396C>T		Somatic	461	2	0.00433839		WXS	Illumina HiSeq	Phase_I	465	462	0.993548	NM_001244888	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	1127	0.5160256410256411	65	0.13211382113821138	217	0.5994475138121547	445	0.777972027972028	400	0.5277044854881267	C	10.78	1.447041	0.25987	.	.	ENSG00000157985	ENST00000409457	D	0.87491	-2.26	5.28	3.43	0.39272	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999999	.	.	.	.	.	.	T	0.46119	-0.9214	5	0.87932	D	0	.	10.554	0.45105	0.1506:0.7048:0.1446:0.0	rs13006916;rs13006916	.	.	.	C	373	ENSP00000387174:R373C	ENSP00000387174:R373C	R	+	1	0	AGAP1	236426135	0.462000	0.25791	0.379000	0.26080	0.855000	0.48748	0.726000	0.25984	0.587000	0.29643	0.655000	0.94253	CGT	C|0.485;T|0.515	0.515	strong		0.587	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	
KLHL38	340359	hgsc.bcm.edu	37	8	124664873	124664873	+	Silent	SNP	A	A	G	rs7387792|rs71505429	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:124664873A>G	ENST00000325995.7	-	1	317	c.294T>C	c.(292-294)caT>caC	p.H98H	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	98	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.			H -> R (in Ref. 3; EAW92045 and 4; AAI27887). {ECO:0000305}.						breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CAGTGGCAATATGTGCCTCCC	0.577													G|||	3644	0.727636	0.6694	0.7118	5008	,	,		20198	0.7113		0.8579	False		,,,				2504	0.7004				p.H98H		Atlas-SNP	.											.	KLHL38	81	.	0			c.T294C						PASS	.	G		2923,1171		1074,775,198	69.0	76.0	73.0		294	2.5	0.0	8	dbSNP_116	73	7033,1355		3030,973,191	no	coding-synonymous	KLHL38	NM_001081675.2		4104,1748,389	GG,GA,AA		16.154,28.6028,20.2371		98/582	124664873	9956,2526	2047	4194	6241	SO:0001819	synonymous_variant	340359	exon1			GGCAATATGTGCC		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.294T>C	8.37:g.124664873A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	37	CCDS43766.1																																																																																			A|0.287;G|0.713	0.713	strong		0.577	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
SLC25A23	79085	hgsc.bcm.edu	37	19	6454367	6454367	+	Silent	SNP	G	G	A	rs10402833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6454367G>A	ENST00000301454.4	-	6	868	c.762C>T	c.(760-762)ccC>ccT	p.P254P	SLC25A23_ENST00000334510.5_Silent_p.P254P|SLC25A23_ENST00000414491.2_Silent_p.P71P	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	254					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						TAGCTGACTCGGGGGCAATCT	0.537													g|||	92	0.0183706	0.0318	0.0043	5008	,	,		20678	0.0		0.0099	False		,,,				2504	0.0378				p.P254P		Atlas-SNP	.											.	SLC25A23	43	.	0			c.C762T						PASS	.	A		129,4277	94.8+/-133.5	2,125,2076	122.0	121.0	121.0		762	-11.6	0.0	19	dbSNP_119	121	156,8444	75.1+/-137.7	0,156,4144	no	coding-synonymous	SLC25A23	NM_024103.2		2,281,6220	AA,AG,GG		1.814,2.9278,2.1913		254/469	6454367	285,12721	2203	4300	6503	SO:0001819	synonymous_variant	79085	exon6			TGACTCGGGGGCA	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.762C>T	19.37:g.6454367G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Silent	SNP	ENST00000301454.4	37	CCDS32882.1																																																																																			G|0.982;A|0.018	0.018	strong		0.537	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
COL16A1	1307	hgsc.bcm.edu	37	1	32165495	32165495	+	Missense_Mutation	SNP	G	G	T	rs2228552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:32165495G>T	ENST00000373672.3	-	4	701	c.185C>A	c.(184-186)aCg>aAg	p.T62K	COL16A1_ENST00000271069.6_Missense_Mutation_p.T62K|COL16A1_ENST00000373668.3_Missense_Mutation_p.T62K	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	62	Laminin G-like.		T -> K (in dbSNP:rs2228552). {ECO:0000269|PubMed:1631157}.		cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GATGGCAGACGTCTTCATGAG	0.607													g|||	2140	0.427316	0.261	0.4553	5008	,	,		18858	0.2708		0.6481	False		,,,				2504	0.5665				p.T62K	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											COL16A1,colon,carcinoma,0,1	COL16A1	137	1	0			c.C185A						PASS	.		LYS/THR	1393,2625		248,897,864	103.0	102.0	103.0		185	-2.4	0.1	1	dbSNP_98	103	5284,3044		1698,1888,578	yes	missense	COL16A1	NM_001856.3	78	1946,2785,1442	TT,TG,GG		36.5514,34.669,45.9177	benign	62/1605	32165495	6677,5669	2009	4164	6173	SO:0001583	missense	1307	exon4			GCAGACGTCTTCA	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.185C>A	1.37:g.32165495G>T	ENSP00000362776:p.Thr62Lys	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	37	CCDS41297.1	936	0.42857142857142855	125	0.2540650406504065	183	0.505524861878453	135	0.23601398601398602	493	0.6503957783641161	g	11.33	1.607805	0.28623	0.34669	0.634486	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000373668	T;T;T	0.24538	1.85;1.85;1.85	4.63	-2.4	0.06583	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.848291	0.10321	N	0.688765	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	D;B	0.54964	0.969;0.047	P;B	0.45195	0.473;0.045	T	0.37888	-0.9686	9	0.38643	T	0.18	.	8.0524	0.30585	0.4022:0.1013:0.4966:0.0	rs2228552;rs2297673;rs10798885;rs17498623;rs52810622;rs56583694;rs58033914;rs2228552	62;62	A6NCT7;Q07092	.;COGA1_HUMAN	K	62	ENSP00000362776:T62K;ENSP00000271069:T62K;ENSP00000362772:T62K	ENSP00000271069:T62K	T	-	2	0	COL16A1	31938082	0.000000	0.05858	0.076000	0.20297	0.704000	0.40688	-0.788000	0.04614	-1.129000	0.02918	-2.101000	0.00361	ACG	G|0.551;T|0.449	0.449	strong		0.607	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
SERPINI2	5276	hgsc.bcm.edu	37	3	167189607	167189607	+	Missense_Mutation	SNP	A	A	C	rs17246389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167189607A>C	ENST00000476257.1	-	3	314	c.16T>G	c.(16-18)Ttg>Gtg	p.L6V	SERPINI2_ENST00000264677.4_Missense_Mutation_p.L6V|SERPINI2_ENST00000471111.1_Missense_Mutation_p.L6V|SERPINI2_ENST00000461846.1_Missense_Mutation_p.L6V|SERPINI2_ENST00000465031.1_5'UTR			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	6			L -> V (in dbSNP:rs17246389).		cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						AGACTCCACAAGAAGATTGTG	0.338													A|||	840	0.167732	0.056	0.134	5008	,	,		16707	0.0972		0.2624	False		,,,				2504	0.318				p.L16V		Atlas-SNP	.											.	SERPINI2	85	.	0			c.T46G	GRCh37	CM067714	SERPINI2	M	rs17246389	PASS	.	A	VAL/LEU	391,4015	191.2+/-216.9	14,363,1826	108.0	120.0	116.0		16	-1.4	0.0	3	dbSNP_123	116	2220,6378	375.5+/-337.8	304,1612,2383	yes	missense	SERPINI2	NM_006217.3	32	318,1975,4209	CC,CA,AA		25.82,8.8743,20.0784	possibly-damaging	6/406	167189607	2611,10393	2203	4299	6502	SO:0001583	missense	5276	exon3			TCCACAAGAAGAT	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"""Serine (or cysteine) peptidase inhibitors"""	8945	protein-coding gene	gene with protein product		605587	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2"", ""serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"""	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.16T>G	3.37:g.167189607A>C	ENSP00000420621:p.Leu6Val	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	338	0.15476190476190477	31	0.06300813008130081	56	0.15469613259668508	52	0.09090909090909091	199	0.262532981530343	A	10.34	1.322455	0.23994	0.088743	0.2582	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111;ENST00000466903;ENST00000467583	T;T;T;T;T;T	0.81247	-0.94;-0.94;-0.94;-0.94;-0.94;-1.47	5.41	-1.41	0.08941	Serpin domain (1);	0.649667	0.14912	N	0.291166	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;P	0.37781	0.608;0.608	B;B	0.32090	0.14;0.14	T	0.01972	-1.1237	9	0.72032	D	0.01	.	9.7473	0.40455	0.5821:0.0:0.4179:0.0	rs17246389;rs52822774;rs59746421;rs17246389	6;6	B4DDY9;O75830	.;SPI2_HUMAN	V	6	ENSP00000420621:L6V;ENSP00000417692:L6V;ENSP00000264677:L6V;ENSP00000419407:L6V;ENSP00000417752:L6V;ENSP00000419255:L6V	ENSP00000264677:L6V	L	-	1	2	SERPINI2	168672301	0.030000	0.19436	0.010000	0.14722	0.015000	0.08874	0.115000	0.15540	-0.484000	0.06763	-0.417000	0.06048	TTG	A|0.830;C|0.170	0.170	strong		0.338	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119213	38119213	+	Missense_Mutation	SNP	G	G	A	rs12628603	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38119213G>A	ENST00000406386.3	+	7	905	c.650G>A	c.(649-651)aGc>aAc	p.S217N		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	217			S -> N (in dbSNP:rs12628603).		actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GGGGGCCGGAGCGCAGGACAG	0.612													G|||	2637	0.526558	0.3752	0.611	5008	,	,		16088	0.7073		0.5696	False		,,,				2504	0.4407				p.S217N		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G650A						PASS	.	G	ASN/SER	1614,2338		348,918,710	18.0	21.0	20.0		650	3.2	0.7	22	dbSNP_120	20	5038,3244		1516,2006,619	yes	missense	TRIOBP	NM_001039141.2	46	1864,2924,1329	AA,AG,GG		39.1693,40.8401,45.6269	probably-damaging	217/2366	38119213	6652,5582	1976	4141	6117	SO:0001583	missense	11078	exon7			GCCGGAGCGCAGG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.650G>A	22.37:g.38119213G>A	ENSP00000384312:p.Ser217Asn	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	1212	0.554945054945055	192	0.3902439024390244	216	0.5966850828729282	378	0.6608391608391608	426	0.5620052770448549	G	13.36	2.213080	0.39102	0.408401	0.608307	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.26810	1.71	4.18	3.16	0.36331	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	0.99999081851	B	0.32781	0.384	B	0.30105	0.111	T	0.34775	-0.9815	8	0.66056	D	0.02	.	6.9728	0.24658	0.126:0.0:0.874:0.0	rs12628603	217	Q9H2D6	TARA_HUMAN	N	217	ENSP00000384312:S217N	ENSP00000384312:S217N	S	+	2	0	TRIOBP	36449159	0.985000	0.35326	0.709000	0.30452	0.656000	0.38851	3.006000	0.49529	1.910000	0.55303	0.456000	0.33151	AGC	G|0.436;A|0.564	0.564	strong		0.612	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
TIMM44	10469	hgsc.bcm.edu	37	19	7998386	7998386	+	Missense_Mutation	SNP	G	G	C	rs118048213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7998386G>C	ENST00000270538.3	-	7	1021	c.753C>G	c.(751-753)aaC>aaG	p.N251K	TIMM44_ENST00000598968.1_5'Flank	NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)	251					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						ACACCACGTTGTTCTCCTTGA	0.612													G|||	54	0.0107827	0.0015	0.0202	5008	,	,		18753	0.0		0.0338	False		,,,				2504	0.0041				p.N251K		Atlas-SNP	.											.	TIMM44	47	.	0			c.C753G						PASS	.	G	LYS/ASN	35,4371	40.8+/-73.8	1,33,2169	315.0	272.0	286.0		753	3.9	1.0	19	dbSNP_132	286	349,8251	117.6+/-177.1	10,329,3961	yes	missense	TIMM44	NM_006351.3	94	11,362,6130	CC,CG,GG		4.0581,0.7944,2.9525	possibly-damaging	251/453	7998386	384,12622	2203	4300	6503	SO:0001583	missense	10469	exon7			CACGTTGTTCTCC	AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.753C>G	19.37:g.7998386G>C	ENSP00000270538:p.Asn251Lys	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	174	93	0.534483	NM_006351	A8K0R9|D6W664|Q8N193	Missense_Mutation	SNP	ENST00000270538.3	37	CCDS12192.1	31	0.014194139194139194	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	23	0.030343007915567283	G	13.18	2.161023	0.38119	0.007944	0.040581	ENSG00000104980	ENST00000270538	T	0.77098	-1.07	5.0	3.89	0.44902	.	0.000000	0.85682	D	0.000000	T	0.35970	0.0950	L	0.53617	1.68	0.80722	D	1	B	0.17667	0.023	B	0.25759	0.063	T	0.48352	-0.9043	10	0.08381	T	0.77	-43.3753	8.053	0.30589	0.1539:0.0:0.8461:0.0	.	251	O43615	TIM44_HUMAN	K	251	ENSP00000270538:N251K	ENSP00000270538:N251K	N	-	3	2	TIMM44	7904386	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.138000	0.42140	2.335000	0.79485	0.561000	0.74099	AAC	G|0.972;C|0.028	0.028	strong		0.612	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3		
R3HCC1L	27291	hgsc.bcm.edu	37	10	99969475	99969475	+	Missense_Mutation	SNP	A	A	C	rs34494334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:99969475A>C	ENST00000298999.3	+	5	1907	c.1604A>C	c.(1603-1605)gAc>gCc	p.D535A	R3HCC1L_ENST00000370586.2_Intron|R3HCC1L_ENST00000370584.3_Missense_Mutation_p.D535A|R3HCC1L_ENST00000314594.5_5'UTR	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	535			D -> A (in dbSNP:rs34494334).				nucleotide binding (GO:0000166)										GAGCAAGATGACTCAGGGAGT	0.438													A|||	680	0.135783	0.1664	0.1499	5008	,	,		20094	0.0298		0.2217	False		,,,				2504	0.1053				p.D535A		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A1604C						PASS	.	A	ALA/ASP	806,3600	320.4+/-296.6	84,638,1481	133.0	124.0	127.0		1604	-0.5	1.0	10	dbSNP_126	127	1857,6743	332.1+/-320.0	195,1467,2638	yes	missense	C10orf28	NM_014472.4	126	279,2105,4119	CC,CA,AA		21.593,18.2932,20.4752	benign	535/779	99969475	2663,10343	2203	4300	6503	SO:0001583	missense	27291	exon4			AAGATGACTCAGG	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1604A>C	10.37:g.99969475A>C	ENSP00000298999:p.Asp535Ala	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	85	48	0.564706	NM_001256620	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	353	0.16163003663003664	104	0.21138211382113822	63	0.17403314917127072	19	0.033216783216783216	167	0.22031662269129287	A	5.598	0.295168	0.10622	0.182932	0.21593	ENSG00000166024	ENST00000370584;ENST00000298999	T;T	0.07216	3.21;3.21	5.15	-0.501	0.12008	.	0.693696	0.13424	N	0.388881	T	0.00012	0.0000	L	0.38838	1.175	0.09310	P	0.999999999439986	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.003	T	0.45338	-0.9268	8	.	.	.	0.4892	4.5381	0.12043	0.4801:0.0:0.0844:0.4355	rs34494334	535;535	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	A	535	ENSP00000359616:D535A;ENSP00000298999:D535A	.	D	+	2	0	C10orf28	99959465	0.992000	0.36948	0.987000	0.45799	0.581000	0.36288	0.319000	0.19522	-0.020000	0.14032	-0.501000	0.04562	GAC	A|0.813;C|0.187	0.187	strong		0.438	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136290672	136290672	+	Silent	SNP	G	G	A	rs28571612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136290672G>A	ENST00000371929.3	+	4	798	c.354G>A	c.(352-354)ccG>ccA	p.P118P	ADAMTS13_ENST00000371911.3_Silent_p.P118P|ADAMTS13_ENST00000356589.2_Silent_p.P118P|ADAMTS13_ENST00000355699.2_Silent_p.P118P|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000371916.1_Silent_p.P118P	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	118	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TTCGGGACCCGTCCCTGGGGG	0.627													G|||	130	0.0259585	0.0045	0.0403	5008	,	,		17635	0.001		0.0726	False		,,,				2504	0.0225				p.P118P		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.G354A						PASS	.	G	,,	75,4331	66.4+/-103.9	1,73,2129	50.0	43.0	46.0		354,354,354	-9.1	0.4	9	dbSNP_125	46	708,7892	173.9+/-224.3	36,636,3628	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	37,709,5757	AA,AG,GG		8.2326,1.7022,6.0203	,,	118/1428,118/1341,118/1372	136290672	783,12223	2203	4300	6503	SO:0001819	synonymous_variant	11093	exon4			GGACCCGTCCCTG	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.354G>A	9.37:g.136290672G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	44	0.611111	NM_139026	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			G|0.945;A|0.055	0.055	strong		0.627	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
ZNF469	84627	hgsc.bcm.edu	37	16	88497446	88497446	+	Missense_Mutation	SNP	A	A	G	rs7197071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88497446A>G	ENST00000437464.1	+	2	3484	c.3484A>G	c.(3484-3486)Aag>Gag	p.K1162E	ZNF469_ENST00000565624.1_Missense_Mutation_p.K1190E	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	1162			K -> E (in dbSNP:rs7197071).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GGGAGGCCCCAAGTGTGCTGA	0.726													A|||	4101	0.81889	0.4932	0.9207	5008	,	,		11067	0.9444		0.9344	False		,,,				2504	0.9387				p.K1162E		Atlas-SNP	.											.	ZNF469	121	.	0			c.A3484G						PASS	.	A	GLU/LYS	768,602		206,356,123	7.0	10.0	9.0		3484	-3.0	0.0	16	dbSNP_116	9	2908,238		1350,208,15	yes	missense	ZNF469	NM_001127464.1	56	1556,564,138	GG,GA,AA		7.5652,43.9416,18.6005	benign	1162/3926	88497446	3676,840	685	1573	2258	SO:0001583	missense	84627	exon2			GGCCCCAAGTGTG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.3484A>G	16.37:g.88497446A>G	ENSP00000402343:p.Lys1162Glu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	1811	0.8292124542124543	239	0.48577235772357724	329	0.9088397790055248	539	0.9423076923076923	704	0.9287598944591029	A	15.01	2.705532	0.48412	0.560584	0.924348	ENSG00000225614	ENST00000437464	T	0.08193	3.12	4.0	-2.95	0.05564	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.17667	0.023	B	0.15052	0.012	T	0.36744	-0.9735	8	0.02654	T	1	.	7.3727	0.26810	0.1903:0.6424:0.1674:0.0	rs7197071;rs59452256	1162	Q96JG9	ZN469_HUMAN	E	1162	ENSP00000402343:K1162E	ENSP00000402343:K1162E	K	+	1	0	ZNF469	87024947	0.000000	0.05858	0.002000	0.10522	0.370000	0.29829	-0.304000	0.08199	-0.425000	0.07371	0.260000	0.18958	AAG	A|0.170;G|0.830	0.830	strong		0.726	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
SPRY3	10251	hgsc.bcm.edu	37	X	155004280	155004280	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:155004280A>G	ENST00000302805.2	+	2	1178	c.747A>G	c.(745-747)caA>caG	p.Q249Q		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	249	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATCTGTGCCAACAGGGCTATG	0.592													A|||	970	0.19369	0.2489	0.1744	5008	,	,		20237	0.0179		0.2992	False		,,,				2504	0.2055				p.Q249Q		Atlas-SNP	.											.	SPRY3	52	.	0			c.A747G						PASS	.	A		1040,3366		132,776,1295	207.0	192.0	197.0		747	2.0	1.0	X	dbSNP_134	197	2390,6202		328,1734,2234	no	coding-synonymous	SPRY3	NM_005840.1		460,2510,3529	GG,GA,AA		27.8166,23.6042,26.3887		249/289	155004280	3430,9568	2203	4296	6499	SO:0001819	synonymous_variant	10251	exon2			GTGCCAACAGGGC	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"""Pseudoautosomal regions / PAR2"""	11271	protein-coding gene	gene with protein product	"""antagonist of FGF signaling"""	300531	"""sprouty (Drosophila) homolog 2"""			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.747A>G	X.37:g.155004280A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_005840	A8K0H8	Silent	SNP	ENST00000302805.2	37	CCDS14769.4																																																																																			A|0.771;G|0.229	0.229	strong		0.592	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840	
WDR83OS	51398	hgsc.bcm.edu	37	19	12780204	12780204	+	Missense_Mutation	SNP	T	T	C	rs117131055	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12780204T>C	ENST00000596731.1	-	1	1966	c.14A>G	c.(13-15)aAt>aGt	p.N5S	MAN2B1_ENST00000221363.4_5'Flank|MAN2B1_ENST00000456935.2_5'Flank|WDR83_ENST00000418543.3_Intron|WDR83_ENST00000242796.4_5'Flank|CTD-2192J16.24_ENST00000597961.1_Missense_Mutation_p.N3S|WDR83OS_ENST00000600694.1_5'Flank|WDR83OS_ENST00000222190.5_Missense_Mutation_p.N5S	NM_016145.3	NP_057229.1	Q9Y284	ASTER_HUMAN	WD repeat domain 83 opposite strand	5						integral component of membrane (GO:0016021)											GTCCGACATATTGTTAGTGGA	0.607													T|||	49	0.00978435	0.0023	0.0101	5008	,	,		16854	0.0		0.0268	False		,,,				2504	0.0123				p.N5S		Atlas-SNP	.											.	.	.	.	0			c.A14G						PASS	.	T	,SER/ASN	25,4381		1,23,2179	65.0	53.0	57.0		,14	-2.7	0.1	19	dbSNP_132	57	208,8392		2,204,4094	yes	intron,missense	C19orf56,WDR83	NM_001099737.2,NM_016145.3	,46	3,227,6273	CC,CT,TT		2.4186,0.5674,1.7915	,benign	,5/107	12780204	233,12773	2203	4300	6503	SO:0001583	missense	51398	exon1			GACATATTGTTAG	AF151898	CCDS12274.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000105583	ENSG00000105583			30203	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 56"""	C19orf56		10810093	Standard	NM_016145		Approved	PTD008	uc002mud.2	Q9Y284		ENST00000596731.1:c.14A>G	19.37:g.12780204T>C	ENSP00000468969:p.Asn5Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	NM_016145	B2R4T8|Q9BVI3	Missense_Mutation	SNP	ENST00000596731.1	37	CCDS12274.1	21	0.009615384615384616	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	15	0.01978891820580475	T	5.088	0.201877	0.09652	0.005674	0.024186	ENSG00000105583	ENST00000222190	T	0.40225	1.04	5.7	-2.74	0.05932	.	0.335387	0.34879	N	0.003605	T	0.07324	0.0185	N	0.03253	-0.375	0.25340	N	0.988951	B	0.02656	0.0	B	0.04013	0.001	T	0.24012	-1.0172	10	0.02654	T	1	-0.1585	14.0355	0.64642	0.0:0.5594:0.0:0.4406	.	5	Q9Y284	CS056_HUMAN	S	5	ENSP00000222190:N5S	ENSP00000222190:N5S	N	-	2	0	C19orf56	12641204	0.000000	0.05858	0.070000	0.20053	0.422000	0.31414	-0.489000	0.06490	-0.742000	0.04790	-0.256000	0.11100	AAT	T|0.986;C|0.014	0.014	strong		0.607	WDR83OS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462702.1	NM_016145	
HIPK4	147746	hgsc.bcm.edu	37	19	40886987	40886987	+	Missense_Mutation	SNP	G	G	T	rs79330270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40886987G>T	ENST00000291823.2	-	3	1195	c.911C>A	c.(910-912)aCc>aAc	p.T304N		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	304	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GTCAGGGAAGGTTAGCCGACT	0.612													G|||	10	0.00199681	0.0	0.0043	5008	,	,		19961	0.0		0.006	False		,,,				2504	0.001				p.T304N		Atlas-SNP	.											.	HIPK4	100	.	0			c.C911A						PASS	.	G	ASN/THR	13,4391		0,13,2189	44.0	40.0	41.0		911	-2.1	1.0	19	dbSNP_131	41	76,8522		0,76,4223	yes	missense	HIPK4	NM_144685.3	65	0,89,6412	TT,TG,GG		0.8839,0.2952,0.6845	benign	304/617	40886987	89,12913	2202	4299	6501	SO:0001583	missense	147746	exon3			GGGAAGGTTAGCC	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.911C>A	19.37:g.40886987G>T	ENSP00000291823:p.Thr304Asn	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	.	.	.	.	.	.	.	.	.	.	G	2.504	-0.314455	0.05422	0.002952	0.008839	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.20200	2.09	5.67	-2.14	0.07123	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.892967	0.09630	N	0.776416	T	0.03564	0.0102	N	0.01140	-0.99	0.25057	N	0.9911	B	0.06786	0.001	B	0.09377	0.004	T	0.41770	-0.9490	10	0.10902	T	0.67	.	5.9158	0.19053	0.0701:0.4725:0.2585:0.1989	.	304	Q8NE63	HIPK4_HUMAN	N	304;269	ENSP00000291823:T304N	ENSP00000291823:T304N	T	-	2	0	HIPK4	45578827	0.005000	0.15991	0.958000	0.39756	0.028000	0.11728	0.266000	0.18534	-0.454000	0.07066	-1.140000	0.01884	ACC	A|0.001;G|0.993;T|0.006	0.006	strong		0.612	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
KRT82	3888	hgsc.bcm.edu	37	12	52788928	52788928	+	Missense_Mutation	SNP	G	G	A	rs2658658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52788928G>A	ENST00000257974.2	-	9	1450	c.1373C>T	c.(1372-1374)aCg>aTg	p.T458M	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	458	Tail.		T -> M (in dbSNP:rs2658658).			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GAGGACAGGCGTGCTGACCCC	0.642													G|||	1696	0.338658	0.3374	0.3746	5008	,	,		20091	0.0645		0.4702	False		,,,				2504	0.4622				p.T458M		Atlas-SNP	.											.	KRT82	45	.	0			c.C1373T						PASS	.	G	MET/THR	1604,2802	494.1+/-362.9	305,994,904	52.0	45.0	47.0		1373	3.8	0.7	12	dbSNP_100	47	4105,4495	557.3+/-387.0	979,2147,1174	yes	missense	KRT82	NM_033033.3	81	1284,3141,2078	AA,AG,GG		47.7326,36.4049,43.8951	probably-damaging	458/514	52788928	5709,7297	2203	4300	6503	SO:0001583	missense	3888	exon9			ACAGGCGTGCTGA	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.1373C>T	12.37:g.52788928G>A	ENSP00000257974:p.Thr458Met	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	697	0.3191391941391941	170	0.34552845528455284	142	0.39226519337016574	32	0.055944055944055944	353	0.4656992084432718	G	10.42	1.344757	0.24426	0.364049	0.477326	ENSG00000161850	ENST00000257974	D	0.82711	-1.64	4.73	3.84	0.44239	.	0.181657	0.26967	N	0.021583	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	D	0.76494	0.999	P	0.59221	0.854	T	0.36962	-0.9726	9	0.72032	D	0.01	.	7.9321	0.29907	0.191:0.0:0.809:0.0	rs2658658;rs3741733;rs17715642;rs52836177;rs57500516;rs2658658	458	Q9NSB4	KRT82_HUMAN	M	458	ENSP00000257974:T458M	ENSP00000257974:T458M	T	-	2	0	KRT82	51075195	0.030000	0.19436	0.696000	0.30242	0.028000	0.11728	2.017000	0.40981	1.137000	0.42214	-0.215000	0.12644	ACG	G|0.611;A|0.389	0.389	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
VSTM1	284415	hgsc.bcm.edu	37	19	54545531	54545531	+	Splice_Site	SNP	T	T	C	rs2433724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54545531T>C	ENST00000338372.2	-	5	662	c.487A>G	c.(487-489)Agt>Ggt	p.S163G	VSTM1_ENST00000366170.2_Splice_Site_p.S75G|VSTM1_ENST00000425006.2_3'UTR|VSTM1_ENST00000376626.1_Intron	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	163			S -> G (in dbSNP:rs2433724). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:22960280, ECO:0000269|Ref.3}.		immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		CTGAGCTCACTGTGCTGGCTG	0.493													C|||	1623	0.324081	0.388	0.4352	5008	,	,		18838	0.1597		0.4344	False		,,,				2504	0.2147				p.S163G		Atlas-SNP	.											.	VSTM1	30	.	0			c.A487G						PASS	.	C	GLY/SER	1729,2677	648.5+/-398.7	322,1085,796	98.0	89.0	92.0		487	2.5	0.6	19	dbSNP_100	92	3746,4854	616.7+/-396.6	808,2130,1362	yes	missense-near-splice	VSTM1	NM_198481.3	56	1130,3215,2158	CC,CT,TT		43.5581,39.2419,42.096	benign	163/237	54545531	5475,7531	2203	4300	6503	SO:0001630	splice_region_variant	284415	exon5			GCTCACTGTGCTG	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.487+1A>G	19.37:g.54545531T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	142	140	0.985915	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Missense_Mutation	SNP	ENST00000338372.2	37	CCDS12872.1	765	0.35027472527472525	178	0.3617886178861789	158	0.43646408839779005	95	0.1660839160839161	334	0.44063324538258575	C	0.004	-2.287139	0.00248	0.392419	0.435581	ENSG00000189068	ENST00000338372;ENST00000366170	T;T	0.40225	6.9;1.04	3.58	2.55	0.30701	.	0.810448	0.10070	N	0.719777	T	0.00012	0.0000	N	0.01352	-0.895	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47898	-0.9081	9	0.22109	T	0.4	1.349	6.0866	0.19970	0.0:0.7659:0.0:0.2341	rs2433724;rs52834474;rs61465085;rs2433724	163	Q6UX27	VSTM1_HUMAN	G	163;75	ENSP00000343366:S163G;ENSP00000444153:S75G	ENSP00000343366:S163G	S	-	1	0	VSTM1	59237343	0.183000	0.23186	0.552000	0.28243	0.004000	0.04260	0.186000	0.16978	0.538000	0.28769	-0.136000	0.14681	AGT	T|0.619;C|0.381	0.381	strong		0.493	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481	Missense_Mutation
BRCA1	672	hgsc.bcm.edu	37	17	41223094	41223094	+	Missense_Mutation	SNP	T	T	C	rs397509199|rs397509198|rs1799966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41223094T>C	ENST00000357654.3	-	15	4955	c.4837A>G	c.(4837-4839)Agt>Ggt	p.S1613G	BRCA1_ENST00000354071.3_Intron|BRCA1_ENST00000351666.3_Missense_Mutation_p.S430G|BRCA1_ENST00000309486.4_Missense_Mutation_p.S1317G|BRCA1_ENST00000352993.3_Missense_Mutation_p.S471G|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.S1566G|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Missense_Mutation_p.S509G|BRCA1_ENST00000346315.3_Intron|BRCA1_ENST00000591534.1_Missense_Mutation_p.S104G|BRCA1_ENST00000471181.2_Missense_Mutation_p.S1634G|BRCA1_ENST00000468300.1_Missense_Mutation_p.S509G	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1613			S -> G (common polymorphism; dbSNP:rs1799966). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:12442274, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7894493, ECO:0000269|PubMed:9010228, ECO:0000269|Ref.6}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GCAGCTGGACTCTGGGCAGAT	0.473			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			T|||	1782	0.355831	0.2254	0.3746	5008	,	,		19602	0.372		0.3598	False		,,,				2504	0.498				p.S1634G		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.A4900G	GRCh37	CI045256|CM053798	BRCA1	I|M	rs1799966	PASS	.	T	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	1069,3337	389.1+/-327.2	124,821,1258	147.0	137.0	140.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4900,1525,1525,4696,4837	1.5	0.0	17	dbSNP_89	140	2809,5791	444.9+/-360.8	446,1917,1937	yes	missense,missense,missense,missense,missense	BRCA1	NM_007300.3,NM_007299.3,NM_007298.3,NM_007297.3,NM_007294.3	56,56,56,56,56	570,2738,3195	CC,CT,TT		32.6628,24.2624,29.817	benign,benign,benign,benign,benign	1634/1885,509/700,509/760,1566/1817,1613/1864	41223094	3878,9128	2203	4300	6503	SO:0001583	missense	672	exon16	Familial Cancer Database		CTGGACTCTGGGC	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.4837A>G	17.37:g.41223094T>C	ENSP00000350283:p.Ser1613Gly	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	715	0.3273809523809524	108	0.21951219512195122	143	0.39502762430939226	190	0.3321678321678322	274	0.36147757255936674	T	11.48	1.651916	0.29336	0.242624	0.326628	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000352993;ENST00000351666;ENST00000309486;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000484087;ENST00000493919	D;D;D;D;D;D;D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93	4.92	1.5	0.22942	BRCT (1);	0.699804	0.13653	N	0.372123	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B;B;P;B;B;B;B	0.34615	0.002;0.451;0.002;0.459;0.002;0.002;0.255;0.004	B;B;B;B;B;B;B;B	0.30401	0.003;0.079;0.002;0.115;0.003;0.003;0.038;0.006	T	0.06991	-1.0796	9	0.56958	D	0.05	.	6.8942	0.24247	0.0:0.248:0.0:0.752	rs1799966;rs52820998;rs58517211;rs1799966	509;462;508;510;509;1635;1613;1613	E7EUM2;B4DES0;E7ETR2;P38398-3;Q6IN79;E9PFC7;P38398;P38398-2	.;.;.;.;.;.;BRCA1_HUMAN;.	G	1613;1634;471;430;1317;509;462;1635;1566;508;509;384;463	ENSP00000350283:S1613G;ENSP00000312236:S471G;ENSP00000338007:S430G;ENSP00000310938:S1317G;ENSP00000417148:S509G;ENSP00000377294:S462G;ENSP00000418775:S1566G;ENSP00000420412:S509G;ENSP00000419481:S384G;ENSP00000418819:S463G	ENSP00000310938:S1317G	S	-	1	0	BRCA1	38476620	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.112000	0.10791	0.128000	0.18479	0.533000	0.62120	AGT	T|0.694;C|0.306	0.306	strong		0.473	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
AZU1	566	hgsc.bcm.edu	37	19	830820	830820	+	Missense_Mutation	SNP	G	G	A	rs28626600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:830820G>A	ENST00000233997.2	+	4	494	c.473G>A	c.(472-474)cGc>cAc	p.R158H		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	158	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGAGCCAGCGCAGTGGGGGG	0.657													G|||	285	0.0569089	0.0045	0.0576	5008	,	,		15019	0.0079		0.1223	False		,,,				2504	0.1104				p.R158H		Atlas-SNP	.											AZU1,rectum,carcinoma,0,2	AZU1	31	2	0			c.G473A						PASS	.	G	HIS/ARG	73,4331	58.7+/-95.3	1,71,2130	29.0	28.0	29.0		473	-0.8	0.0	19	dbSNP_125	29	869,7731	189.1+/-236.0	48,773,3479	yes	missense	AZU1	NM_001700.3	29	49,844,5609	AA,AG,GG		10.1047,1.6576,7.2439	probably-damaging	158/252	830820	942,12062	2202	4300	6502	SO:0001583	missense	566	exon4			GCCAGCGCAGTGG	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.473G>A	19.37:g.830820G>A	ENSP00000233997:p.Arg158His	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Missense_Mutation	SNP	ENST00000233997.2	37	CCDS12044.1	124	0.056776556776556776	2	0.0040650406504065045	26	0.0718232044198895	3	0.005244755244755245	93	0.12269129287598944	G	10.53	1.374773	0.24857	0.016576	0.101047	ENSG00000172232	ENST00000334630;ENST00000233997	D	0.88896	-2.44	1.51	-0.763	0.11030	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.04048	0.0113	N	0.16307	0.4	0.09310	N	1	D	0.65815	0.995	B	0.43950	0.437	T	0.40850	-0.9541	9	0.42905	T	0.14	.	3.9576	0.09396	0.4496:0.0:0.5504:0.0	rs28626600	158	P20160	CAP7_HUMAN	H	172;158	ENSP00000233997:R158H	ENSP00000233997:R158H	R	+	2	0	AZU1	781820	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.143000	0.16115	-0.178000	0.10672	-0.258000	0.10820	CGC	G|0.933;A|0.067	0.067	strong		0.657	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197485	39197485	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39197485A>G	ENST00000306271.4	-	1	228	c.165T>C	c.(163-165)tgT>tgC	p.C55C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	55			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TAGGAAATCCACAGAAGCTGG	0.602																																					p.C55C		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.T165C						PASS	.						83.0	92.0	89.0					17																	39197485		2026	4210	6236	SO:0001819	synonymous_variant	81851	exon1			AAATCCACAGAAG	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.165T>C	17.37:g.39197485A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	196	24	0.122449	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			.	.	none		0.602	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
ZNF554	115196	hgsc.bcm.edu	37	19	2833864	2833864	+	Missense_Mutation	SNP	G	G	A	rs867169	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:2833864G>A	ENST00000317243.5	+	5	829	c.631G>A	c.(631-633)Gtt>Att	p.V211I	ZNF554_ENST00000591265.1_3'UTR	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	211			V -> I (in dbSNP:rs867169).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGTAGTGGCCGTTCCTCAGGA	0.507													G|||	1278	0.255192	0.1165	0.4193	5008	,	,		19289	0.4415		0.2127	False		,,,				2504	0.1779				p.V211I		Atlas-SNP	.											.	ZNF554	47	.	0			c.G631A						PASS	.	G	ILE/VAL	428,3364		19,390,1487	99.0	101.0	100.0		631	-2.9	0.0	19	dbSNP_86	100	1456,6776		120,1216,2780	yes	missense	ZNF554	NM_001102651.1	29	139,1606,4267	AA,AG,GG		17.6871,11.2869,15.6687	benign	211/539	2833864	1884,10140	1896	4116	6012	SO:0001583	missense	115196	exon5			GTGGCCGTTCCTC	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.631G>A	19.37:g.2833864G>A	ENSP00000321132:p.Val211Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	133	77	0.578947	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	631	0.2889194139194139	71	0.1443089430894309	141	0.38950276243093923	249	0.4353146853146853	170	0.22427440633245382	G	0.551	-0.849394	0.02651	0.112869	0.176871	ENSG00000172006	ENST00000317243	T	0.06608	3.28	2.71	-2.92	0.05615	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44952	-0.9294	8	0.22706	T	0.39	.	3.0196	0.06071	0.1963:0.1042:0.5028:0.1968	rs867169;rs17685329;rs52800819;rs57600764;rs867169	211	Q86TJ5	ZN554_HUMAN	I	211	ENSP00000321132:V211I	ENSP00000321132:V211I	V	+	1	0	ZNF554	2784864	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.752000	0.04797	-1.490000	0.01842	-2.913000	0.00091	GTT	G|0.741;A|0.259	0.259	strong		0.507	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
LRRK1	79705	hgsc.bcm.edu	37	15	101567547	101567547	+	Silent	SNP	G	G	C	rs41319544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:101567547G>C	ENST00000388948.3	+	18	2846	c.2487G>C	c.(2485-2487)gtG>gtC	p.V829V	LRRK1_ENST00000284395.5_Silent_p.V826V	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGAAGGACGTGGGCAGCACCA	0.587													G|||	440	0.0878594	0.0938	0.0749	5008	,	,		20181	0.0278		0.1322	False		,,,				2504	0.1053				p.V829V		Atlas-SNP	.											.	LRRK1	310	.	0			c.G2487C						PASS	.	G		368,3670		14,340,1665	42.0	48.0	46.0		2487	-0.8	1.0	15	dbSNP_127	46	1236,7124		93,1050,3037	no	coding-synonymous	LRRK1	NM_024652.3		107,1390,4702	CC,CG,GG		14.7847,9.1134,12.9376		829/2016	101567547	1604,10794	2019	4180	6199	SO:0001819	synonymous_variant	79705	exon18			GGACGTGGGCAGC	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.2487G>C	15.37:g.101567547G>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			G|0.892;C|0.108	0.108	strong		0.587	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
ASPG	374569	hgsc.bcm.edu	37	14	104571054	104571054	+	Missense_Mutation	SNP	C	C	G	rs8012505	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:104571054C>G	ENST00000551177.1	+	9	1124	c.1032C>G	c.(1030-1032)agC>agG	p.S344R	ASPG_ENST00000546892.2_Missense_Mutation_p.S344R|ASPG_ENST00000455920.2_Missense_Mutation_p.S344R	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	344	Asparaginase.|Asparaginase/glutaminase. {ECO:0000255|PROSITE-ProRule:PRU01068}.		S -> R (in dbSNP:rs8012505). {ECO:0000269|PubMed:15489334}.		asparagine metabolic process (GO:0006528)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)		1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|asparaginase activity (GO:0004067)|lysophospholipase activity (GO:0004622)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	11						CAGGGCTGAGCCTGGATGTCA	0.657													C|||	523	0.104433	0.0915	0.0807	5008	,	,		17757	0.126		0.1402	False		,,,				2504	0.0798				p.S344R		Atlas-SNP	.											.	ASPG	34	.	0			c.C1032G						PASS	.	C	ARG/SER	378,3704		14,350,1677	27.0	32.0	30.0		1032	3.3	1.0	14	dbSNP_116	30	1075,7317		75,925,3196	yes	missense	ASPG	NM_001080464.2	110	89,1275,4873	GG,GC,CC		12.8098,9.2602,11.6482	probably-damaging	344/574	104571054	1453,11021	2041	4196	6237	SO:0001583	missense	374569	exon9			GCTGAGCCTGGAT		CCDS45170.1, CCDS45170.2	14q32.33	2014-03-14	2014-03-14	2008-11-06	ENSG00000166183	ENSG00000166183	3.1.1.5, 3.5.1.1	"""Ankyrin repeat domain containing"""	20123	protein-coding gene	gene with protein product	"""60-kDa-lysophospholipase"""		"""chromosome 14 open reading frame 76"", ""asparaginase homolog (S. cerevisiae)"""	C14orf76			Standard	NM_001080464		Approved		uc001yoq.2	Q86U10		ENST00000551177.1:c.1032C>G	14.37:g.104571054C>G	ENSP00000450040:p.Ser344Arg	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	NM_001080464	B9EGQ2|Q8IV80	Missense_Mutation	SNP	ENST00000551177.1	37	CCDS45170.2	262	0.11996336996336997	48	0.0975609756097561	39	0.10773480662983426	74	0.12937062937062938	101	0.13324538258575197	C	15.87	2.962014	0.53400	0.092602	0.128098	ENSG00000166183	ENST00000551177;ENST00000299234;ENST00000546892;ENST00000455920	T;T;T	0.24538	1.85;1.85;1.85	4.21	3.29	0.37713	.	0.239032	0.48286	N	0.000200	T	0.00496	0.0016	M	0.67517	2.055	0.27583	P	0.9495224	B;D;D;D	0.63046	0.321;0.988;0.985;0.992	B;D;P;P	0.63703	0.281;0.917;0.865;0.889	T	0.06935	-1.0799	9	0.62326	D	0.03	-33.7589	9.0743	0.36511	0.2196:0.7803:0.0:0.0	rs8012505;rs8012505	344;344;344;372	G3V1Y8;Q86U10;Q86U10-3;E5RFC2	.;LPP60_HUMAN;.;.	R	344;372;344;344	ENSP00000450040:S344R;ENSP00000448911:S344R;ENSP00000389003:S344R	ENSP00000299234:S372R	S	+	3	2	ASPG	103640807	0.077000	0.21312	0.997000	0.53966	0.684000	0.39900	1.149000	0.31626	0.702000	0.31825	0.462000	0.41574	AGC	C|0.778;G|0.222	0.222	strong		0.657	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464	
MUC16	94025	hgsc.bcm.edu	37	19	9072742	9072742	+	Missense_Mutation	SNP	T	T	C	rs2591590	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9072742T>C	ENST00000397910.4	-	3	14907	c.14704A>G	c.(14704-14706)Atc>Gtc	p.I4902V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4904	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.I4902V(2)|p.I535V(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCCTGGGAGATGCTGGTCTCC	0.488													T|||	1054	0.210463	0.0628	0.2046	5008	,	,		23106	0.249		0.3101	False		,,,				2504	0.272				p.I4902V		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+2,6	MUC16	4315	6	3	Substitution - Missense(3)	stomach(3)	c.A14704G						PASS	.	T	VAL/ILE	426,3770		24,378,1696	232.0	219.0	223.0		14704	2.2	0.0	19	dbSNP_100	223	2412,6032		344,1724,2154	yes	missense	MUC16	NM_024690.2	29	368,2102,3850	CC,CT,TT		28.5647,10.1525,22.4525	benign	4902/14508	9072742	2838,9802	2098	4222	6320	SO:0001583	missense	94025	exon3			GGGAGATGCTGGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14704A>G	19.37:g.9072742T>C	ENSP00000381008:p.Ile4902Val	Somatic	502	1	0.00199203		WXS	Illumina HiSeq	Phase_I	509	243	0.477407	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	488	0.22344322344322345	47	0.09552845528455285	87	0.24033149171270718	122	0.21328671328671328	232	0.30606860158311344	t	10.67	1.416022	0.25552	0.101525	0.285647	ENSG00000181143	ENST00000397910	T	0.02236	4.38	2.18	2.18	0.27775	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.22983	0.078	B	0.31946	0.138	T	0.47355	-0.9124	8	0.87932	D	0	.	6.3469	0.21355	0.0:0.0:0.0:1.0	rs2591590;rs52802082;rs58556174;rs2591590	4902	B5ME49	.	V	4902	ENSP00000381008:I4902V	ENSP00000381008:I4902V	I	-	1	0	MUC16	8933742	0.000000	0.05858	0.017000	0.16124	0.787000	0.44495	0.373000	0.20484	1.268000	0.44264	0.248000	0.18094	ATC	T|0.787;C|0.213	0.213	strong		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
C15orf27	123591	hgsc.bcm.edu	37	15	76494569	76494569	+	Missense_Mutation	SNP	A	A	G	rs62030189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:76494569A>G	ENST00000388942.3	+	10	1261	c.985A>G	c.(985-987)Agc>Ggc	p.S329G		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	329					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						CGACATGAACAGCTACATCAG	0.522													A|||	3	0.000599042	0.0	0.0	5008	,	,		21160	0.0		0.003	False		,,,				2504	0.0				p.S329G		Atlas-SNP	.											.	C15orf27	32	.	0			c.A985G						PASS	.	A	GLY/SER	4,4390	9.9+/-24.2	0,4,2193	191.0	141.0	158.0		985	3.3	1.0	15	dbSNP_129	158	47,8541	30.1+/-81.4	0,47,4247	yes	missense	C15orf27	NM_152335.2	56	0,51,6440	GG,GA,AA		0.5473,0.091,0.3929	benign	329/532	76494569	51,12931	2197	4294	6491	SO:0001583	missense	123591	exon10			ATGAACAGCTACA	AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.985A>G	15.37:g.76494569A>G	ENSP00000373594:p.Ser329Gly	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	80	0.529801	NM_152335	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	37	CCDS10289.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	14.79	2.640347	0.47153	9.1E-4	0.005473	ENSG00000169758	ENST00000388942	T	0.33865	1.39	4.48	3.31	0.37934	.	0.148543	0.64402	D	0.000016	T	0.19846	0.0477	L	0.40543	1.245	0.32431	N	0.548089	B;B	0.33171	0.4;0.03	B;B	0.30855	0.121;0.037	T	0.26087	-1.0113	10	0.44086	T	0.13	-11.903	9.2607	0.37610	0.8177:0.1823:0.0:0.0	rs62030189	293;329	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	G	329	ENSP00000373594:S329G	ENSP00000373594:S329G	S	+	1	0	C15orf27	74281624	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	6.533000	0.73829	0.630000	0.30394	0.379000	0.24179	AGC	A|0.996;G|0.004	0.004	strong		0.522	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335	
MUC4	4585	hgsc.bcm.edu	37	3	195509180	195509180	+	Missense_Mutation	SNP	C	C	G	rs62282477		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509180C>G	ENST00000463781.3	-	2	9730	c.9271G>C	c.(9271-9273)Gtc>Ctc	p.V3091L	MUC4_ENST00000475231.1_Missense_Mutation_p.V3091L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3091L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGCTGGTGACAGGAAGAGGG	0.597																																					p.V3091L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.G9271C						scavenged	.						14.0	11.0	12.0					3																	195509180		667	1551	2218	SO:0001583	missense	4585	exon2			TGGTGACAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9271G>C	3.37:g.195509180C>G	ENSP00000417498:p.Val3091Leu	Somatic	262	6	0.0229008		WXS	Illumina HiSeq	Phase_I	369	21	0.0569106	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	3.811	-0.039731	0.07497	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.58;1.53	.	.	.	.	.	.	.	.	T	0.16642	0.0400	N	0.19112	0.55	0.19945	N	0.999946	B	0.14805	0.011	B	0.08055	0.003	T	0.27673	-1.0067	7	.	.	.	.	6.7489	0.23475	0.0:0.9997:0.0:3.0E-4	.	2963	E7ESK3	.	L	3091	ENSP00000417498:V3091L;ENSP00000420243:V3091L	.	V	-	1	0	MUC4	196993959	0.152000	0.22762	0.008000	0.14137	0.000000	0.00434	0.189000	0.17037	0.497000	0.27926	0.000000	0.15137	GTC	C|0.895;G|0.105	0.105	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
IQSEC3	440073	hgsc.bcm.edu	37	12	274647	274647	+	Silent	SNP	T	T	C	rs4980859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:274647T>C	ENST00000538872.1	+	10	2875	c.2757T>C	c.(2755-2757)ttT>ttC	p.F919F	IQSEC3_ENST00000326261.4_Silent_p.F919F|RP11-598F7.6_ENST00000537295.1_lincRNA|RP11-598F7.5_ENST00000540136.1_RNA|IQSEC3_ENST00000382841.2_Silent_p.F616F			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	919	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		CGTACACCTTTTGCAAGTCAG	0.488													C|||	1306	0.260783	0.087	0.3199	5008	,	,		23066	0.3393		0.326	False		,,,				2504	0.3057				p.F919F		Atlas-SNP	.											.	IQSEC3	154	.	0			c.T2757C						PASS	.	C	,	593,3813	771.3+/-413.8	37,519,1647	189.0	176.0	180.0		2757,1848	4.9	1.0	12	dbSNP_111	180	2729,5871	680.5+/-403.6	434,1861,2005	yes	coding-synonymous,coding-synonymous	IQSEC3	NM_001170738.1,NM_015232.1	,	471,2380,3652	CC,CT,TT		31.7326,13.4589,25.5421	,	919/1183,616/760	274647	3322,9684	2203	4300	6503	SO:0001819	synonymous_variant	440073	exon10			CACCTTTTGCAAG	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2757T>C	12.37:g.274647T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	37	CCDS53728.1																																																																																			T|0.740;C|0.260	0.260	strong		0.488	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106799997	106799997	+	Silent	SNP	G	G	A	rs257376	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:106799997G>A	ENST00000265717.4	+	11	1486	c.1227G>A	c.(1225-1227)acG>acA	p.T409T		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	409					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TGTTTGGAACGAACATGGATA	0.418													A|||	2352	0.469649	0.5083	0.4597	5008	,	,		16877	0.4514		0.5408	False		,,,				2504	0.3701				p.T409T		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G1227A						PASS	.	A		2197,2209	590.7+/-387.4	544,1109,550	146.0	127.0	133.0		1227	-0.9	1.0	7	dbSNP_79	133	4627,3973	553.1+/-386.2	1253,2121,926	yes	coding-synonymous	PRKAR2B	NM_002736.2		1797,3230,1476	AA,AG,GG		46.1977,49.8638,47.5319		409/419	106799997	6824,6182	2203	4300	6503	SO:0001819	synonymous_variant	5577	exon11			TGGAACGAACATG		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.1227G>A	7.37:g.106799997G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.497;A|0.503	0.503	strong		0.418	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
CEBPZ	10153	hgsc.bcm.edu	37	2	37455232	37455232	+	Silent	SNP	C	C	A	rs35414551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:37455232C>A	ENST00000234170.5	-	2	1249	c.1104G>T	c.(1102-1104)gtG>gtT	p.V368V		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	368					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				GCTCATGAGCCACGGTAAGGG	0.423													C|||	19	0.00379393	0.0023	0.0029	5008	,	,		20686	0.0		0.0139	False		,,,				2504	0.0				p.V368V		Atlas-SNP	.											.	CEBPZ	68	.	0			c.G1104T						PASS	.	C		23,4383	29.9+/-59.1	0,23,2180	91.0	98.0	95.0		1104	-1.6	0.1	2	dbSNP_126	95	164,8436	77.5+/-140.1	1,162,4137	no	coding-synonymous	CEBPZ	NM_005760.2		1,185,6317	AA,AC,CC		1.907,0.522,1.4378		368/1055	37455232	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	10153	exon2			ATGAGCCACGGTA	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1104G>T	2.37:g.37455232C>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	158	78	0.493671	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	37	CCDS1787.1																																																																																			C|0.989;A|0.011	0.011	strong		0.423	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
RNASEL	6041	hgsc.bcm.edu	37	1	182554557	182554557	+	Missense_Mutation	SNP	C	C	T	rs486907	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:182554557C>T	ENST00000367559.3	-	2	1638	c.1385G>A	c.(1384-1386)cGa>cAa	p.R462Q	RNASEL_ENST00000444138.1_Missense_Mutation_p.R462Q|RNASEL_ENST00000539397.1_Missense_Mutation_p.R462Q	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	462	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (risk factor for prostate cancer; reduced enzymatic activity; dbSNP:rs486907). {ECO:0000269|PubMed:11799394, ECO:0000269|PubMed:11941539, ECO:0000269|PubMed:17344846}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						CAGGACATTTCGGGCAAATTC	0.453													C|||	1155	0.230631	0.0666	0.2233	5008	,	,		20473	0.2421		0.3708	False		,,,				2504	0.3016				p.R462Q		Atlas-SNP	.											.	RNASEL	83	.	0			c.G1385A	GRCh37	CM020962	RNASEL	M	rs486907	PASS	.	C	GLN/ARG	587,3819	257.7+/-262.0	42,503,1658	129.0	127.0	128.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1385	0.1	0.0	1	dbSNP_83	128	3065,5535	471.5+/-368.1	516,2033,1751	yes	missense	RNASEL	NM_021133.3	43	558,2536,3409	TT,TC,CC		35.6395,13.3227,28.0793	probably-damaging	462/742	182554557	3652,9354	2203	4300	6503	SO:0001583	missense	6041	exon2			ACATTTCGGGCAA	L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"""Ankyrin repeat domain containing"""	10050	protein-coding gene	gene with protein product		180435	"""prostate cancer 1"""	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.1385G>A	1.37:g.182554557C>T	ENSP00000356530:p.Arg462Gln	Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	333	183	0.54955	NM_021133	Q5W0L2|Q6AI46	Missense_Mutation	SNP	ENST00000367559.3	37	CCDS1347.1	533	0.24404761904761904	26	0.052845528455284556	93	0.2569060773480663	135	0.23601398601398602	279	0.36807387862796836	C	22.0	4.225120	0.79576	0.133227	0.356395	ENSG00000135828	ENST00000367559;ENST00000444138;ENST00000543858;ENST00000539397	T;T;T	0.20463	2.07;2.07;2.07	5.95	0.0561	0.14318	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.497265	0.17966	N	0.156039	T	0.00012	0.0000	M	0.76574	2.34	0.80722	P	0.0	D;D;D	0.71674	0.998;0.998;0.998	P;P;P	0.59825	0.864;0.864;0.864	T	0.36138	-0.9760	9	0.18276	T	0.48	-4.1493	0.4865	0.00557	0.1814:0.2702:0.1788:0.3696	rs486907;rs3738580;rs52825450;rs60634396;rs486907	462;462;462	Q5W0L2;Q6AI46;Q05823	.;.;RN5A_HUMAN	Q	462;462;106;462	ENSP00000356530:R462Q;ENSP00000411147:R462Q;ENSP00000440844:R462Q	ENSP00000356530:R462Q	R	-	2	0	RNASEL	180821180	0.001000	0.12720	0.001000	0.08648	0.188000	0.23474	0.217000	0.17603	0.102000	0.17638	0.650000	0.86243	CGA	C|0.737;T|0.263	0.263	strong		0.453	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1	NM_021133	
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206905040	206905040	+	Silent	SNP	C	C	T	rs34526867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206905040C>T	ENST00000367103.3	+	8	1141	c.948C>T	c.(946-948)atC>atT	p.I316I	MAPKAPK2_ENST00000294981.4_Silent_p.I316I|MAPKAPK2_ENST00000479009.1_3'UTR	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	316	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			GAATGACCATCACCGAGTTTA	0.562													C|||	204	0.0407348	0.1248	0.0288	5008	,	,		18568	0.0		0.0149	False		,,,				2504	0.0041				p.I316I		Atlas-SNP	.											.	MAPKAPK2	45	.	0			c.C948T						PASS	.	C	,	516,3890	237.7+/-249.4	28,460,1715	135.0	133.0	134.0		948,948	5.1	1.0	1	dbSNP_126	134	111,8489	59.1+/-120.7	0,111,4189	no	coding-synonymous,coding-synonymous	MAPKAPK2	NM_004759.4,NM_032960.3	,	28,571,5904	TT,TC,CC		1.2907,11.7113,4.8209	,	316/371,316/401	206905040	627,12379	2203	4300	6503	SO:0001819	synonymous_variant	9261	exon8			GACCATCACCGAG	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.948C>T	1.37:g.206905040C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	212	107	0.504717	NM_004759	Q5SY30|Q5SY41|Q8IYD6	Silent	SNP	ENST00000367103.3	37	CCDS31001.1																																																																																			C|0.956;T|0.044	0.044	strong		0.562	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759	
STK36	27148	hgsc.bcm.edu	37	2	219563602	219563602	+	Missense_Mutation	SNP	G	G	A	rs12993599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219563602G>A	ENST00000295709.3	+	26	3614	c.3335G>A	c.(3334-3336)cGg>cAg	p.R1112Q	STK36_ENST00000440309.1_Missense_Mutation_p.R1112Q|STK36_ENST00000392105.3_Missense_Mutation_p.R1091Q|STK36_ENST00000392106.2_Missense_Mutation_p.R1091Q	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		GAATCCTATCGGCCCCTGCGC	0.597													g|||	384	0.0766773	0.1278	0.0375	5008	,	,		19154	0.0873		0.0447	False		,,,				2504	0.0573				p.R1112Q		Atlas-SNP	.											.	STK36	111	.	0			c.G3335A						PASS	.	G	GLN/ARG	452,3954	216.4+/-235.1	26,400,1777	44.0	46.0	46.0		3335	5.2	1.0	2	dbSNP_121	46	441,8159	133.8+/-191.2	12,417,3871	yes	missense	STK36	NM_015690.4	43	38,817,5648	AA,AG,GG		5.1279,10.2587,6.8661	benign	1112/1316	219563602	893,12113	2203	4300	6503	SO:0001583	missense	27148	exon26			CCTATCGGCCCCT	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3335G>A	2.37:g.219563602G>A	ENSP00000295709:p.Arg1112Gln	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	206	94	0.456311	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	157|157	0.07188644688644688|0.07188644688644688	56|56	0.11382113821138211|0.11382113821138211	15|15	0.04143646408839779|0.04143646408839779	54|54	0.0944055944055944|0.0944055944055944	32|32	0.04221635883905013|0.04221635883905013	G|G	1.986|1.986	-0.433031|-0.433031	0.04669|0.04669	0.102587|0.102587	0.051279|0.051279	ENSG00000163482|ENSG00000163482	ENST00000431040|ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	.|T;T;T;T	.|0.62941	.|0.8;0.8;-0.01;0.8	6.06|6.06	5.19|5.19	0.71726|0.71726	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.356329	.|0.20537	.|N	.|0.090395	T|T	0.00754|0.00754	0.0025|0.0025	N|N	0.16478|0.16478	0.41|0.41	0.37979|0.37979	P|P	0.06647999999999998|0.06647999999999998	.|B;B;B	.|0.25048	.|0.028;0.117;0.071	.|B;B;B	.|0.13407	.|0.009;0.009;0.003	T|T	0.10567|0.10567	-1.0624|-1.0624	4|9	.|0.02654	.|T	.|1	-15.9808|-15.9808	8.2481|8.2481	0.31702|0.31702	0.2057:0.0:0.7943:0.0|0.2057:0.0:0.7943:0.0	rs12993599;rs12993599|rs12993599;rs12993599	.|1091;1091;1112	.|A8MU99;Q9NRP7-2;Q9NRP7	.|.;.;STK36_HUMAN	S|Q	305|1112;1091;1091;1112	.|ENSP00000295709:R1112Q;ENSP00000375955:R1091Q;ENSP00000375954:R1091Q;ENSP00000394095:R1112Q	.|ENSP00000295709:R1112Q	G|R	+|+	1|2	0|0	STK36|STK36	219271846|219271846	0.979000|0.979000	0.34478|0.34478	0.992000|0.992000	0.48379|0.48379	0.341000|0.341000	0.28922|0.28922	1.807000|1.807000	0.38902|0.38902	1.589000|1.589000	0.49982|0.49982	-0.126000|-0.126000	0.14955|0.14955	GGC|CGG	G|0.926;A|0.074	0.074	strong		0.597	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
LRRIQ3	127255	hgsc.bcm.edu	37	1	74648329	74648329	+	Missense_Mutation	SNP	G	G	A	rs17591320	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:74648329G>A	ENST00000395089.1	-	2	465	c.466C>T	c.(466-468)Cat>Tat	p.H156Y	LRRIQ3_ENST00000370909.2_Intron|LRRIQ3_ENST00000354431.4_Missense_Mutation_p.H156Y|LRRIQ3_ENST00000370911.3_Missense_Mutation_p.H156Y			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	156	LRRCT.		H -> Y (in dbSNP:rs17591320).							NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						ATCACATGATGATCCAGCGCT	0.378													G|||	76	0.0151757	0.0	0.0317	5008	,	,		13286	0.0		0.0417	False		,,,				2504	0.0123				p.H156Y		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.C466T						PASS	.	G	TYR/HIS	57,4347	54.9+/-90.9	0,57,2145	108.0	106.0	107.0		466	1.2	1.0	1	dbSNP_123	107	437,8163	132.0+/-189.7	12,413,3875	yes	missense	LRRIQ3	NM_001105659.1	83	12,470,6020	AA,AG,GG		5.0814,1.2943,3.7988	benign	156/625	74648329	494,12510	2202	4300	6502	SO:0001583	missense	127255	exon3			CATGATGATCCAG	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.466C>T	1.37:g.74648329G>A	ENSP00000378524:p.His156Tyr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	24	0.27907	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	CCDS41350.1	40	0.018315018315018316	0	0.0	10	0.027624309392265192	0	0.0	30	0.0395778364116095	G	3.432	-0.115833	0.06881	0.012943	0.050814	ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000388972;ENST00000370911	T;T;T	0.23348	1.91;1.91;1.91	5.52	1.17	0.20885	.	0.479111	0.21018	N	0.081562	T	0.06142	0.0159	L	0.50333	1.59	0.23381	N	0.997798	B	0.13145	0.007	B	0.06405	0.002	T	0.41963	-0.9479	10	0.16896	T	0.51	.	5.3457	0.16008	0.4466:0.1406:0.4127:0.0	rs17591320;rs52823690;rs17591320	156	A6PVS8	LRIQ3_HUMAN	Y	156	ENSP00000378524:H156Y;ENSP00000346414:H156Y;ENSP00000359948:H156Y	ENSP00000346414:H156Y	H	-	1	0	LRRIQ3	74420917	0.837000	0.29446	0.986000	0.45419	0.153000	0.21895	-0.302000	0.08221	-0.048000	0.13401	-0.262000	0.10625	CAT	G|0.970;A|0.030	0.030	strong		0.378	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	
LARP6	55323	hgsc.bcm.edu	37	15	71125339	71125339	+	Silent	SNP	G	G	A	rs28676469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:71125339G>A	ENST00000299213.8	-	3	598	c.528C>T	c.(526-528)ttC>ttT	p.F176F	RP11-138H8.7_ENST00000592096.1_lincRNA	NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	176	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						TCTCGTTGGGGAACAGTGGGA	0.562													G|||	283	0.0565096	0.1293	0.036	5008	,	,		18525	0.0		0.0477	False		,,,				2504	0.0399				p.F176F		Atlas-SNP	.											.	LARP6	43	.	0			c.C528T						PASS	.	G		499,3899	227.5+/-242.7	23,453,1723	70.0	71.0	71.0		528	4.2	1.0	15	dbSNP_125	71	448,8146	133.3+/-190.8	15,418,3864	no	coding-synonymous	LARP6	NM_018357.2		38,871,5587	AA,AG,GG		5.2129,11.3461,7.2891		176/492	71125339	947,12045	2199	4297	6496	SO:0001819	synonymous_variant	55323	exon3			GTTGGGGAACAGT	BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"""La ribonucleoprotein domain containing"""	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.528C>T	15.37:g.71125339G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																			G|0.929;A|0.071	0.071	strong		0.562	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357	
KRT6C	286887	hgsc.bcm.edu	37	12	52863038	52863038	+	Silent	SNP	G	G	A	rs410562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52863038G>A	ENST00000252250.6	-	9	1550	c.1503C>T	c.(1501-1503)agC>agT	p.S501S		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	501	Tail.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		TGCCGACACCGCTGGCACCGC	0.612													G|||	1253	0.2502	0.0242	0.2651	5008	,	,		19993	0.4812		0.3628	False		,,,				2504	0.1912				p.S501S		Atlas-SNP	.											.	KRT6C	55	.	0			c.C1503T						PASS	.	G		314,4092	166.2+/-197.5	15,284,1904	42.0	40.0	41.0		1503	-6.3	0.0	12	dbSNP_80	41	3150,5450	457.5+/-364.3	579,1992,1729	no	coding-synonymous	KRT6C	NM_173086.4		594,2276,3633	AA,AG,GG		36.6279,7.1266,26.6339		501/565	52863038	3464,9542	2203	4300	6503	SO:0001819	synonymous_variant	286887	exon9			GACACCGCTGGCA	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.1503C>T	12.37:g.52863038G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	165	64	0.387879	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			G|0.731;A|0.269	0.269	strong		0.612	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
FAT1	2195	hgsc.bcm.edu	37	4	187629538	187629538	+	Missense_Mutation	SNP	C	C	T	rs3733413	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187629538C>T	ENST00000441802.2	-	2	1653	c.1444G>A	c.(1444-1446)Gtc>Atc	p.V482I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	482	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.			V -> I (in Ref. 1; CAA60685). {ECO:0000305}.	actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AGGCTCATGACAGTAGTACCA	0.468										HNSCC(5;0.00058)			C|||	1697	0.338858	0.1581	0.4798	5008	,	,		21218	0.1399		0.5765	False		,,,				2504	0.4438				p.V482I	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G1444A						PASS	.	C	ILE/VAL	907,3177		110,687,1245	153.0	147.0	149.0		1444	2.8	0.3	4	dbSNP_107	149	4828,3536		1392,2044,746	yes	missense	FAT1	NM_005245.3	29	1502,2731,1991	TT,TC,CC		42.2764,22.2086,46.0717	probably-damaging	482/4589	187629538	5735,6713	2042	4182	6224	SO:0001583	missense	2195	exon2			TCATGACAGTAGT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1444G>A	4.37:g.187629538C>T	ENSP00000406229:p.Val482Ile	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	793	0.3630952380952381	93	0.18902439024390244	193	0.5331491712707183	75	0.13111888111888112	432	0.5699208443271768	C	12.18	1.860644	0.32884	0.222086	0.577236	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	T;T	0.60797	0.44;0.16	5.45	2.77	0.32553	Cadherin (4);Cadherin-like (1);	0.114202	0.64402	N	0.000016	T	0.00012	0.0000	L	0.58583	1.82	0.09310	P	0.999999538415	B	0.21688	0.059	B	0.28465	0.09	T	0.46748	-0.9169	9	0.27082	T	0.32	.	11.1193	0.48279	0.0:0.7968:0.0:0.2032	rs3733413;rs59353175;rs3733413	482	Q14517	FAT1_HUMAN	I	482	ENSP00000406229:V482I;ENSP00000423736:V482I	ENSP00000260147:V482I	V	-	1	0	FAT1	187866532	0.998000	0.40836	0.329000	0.25429	0.320000	0.28249	3.947000	0.56652	0.872000	0.35775	-0.258000	0.10820	GTC	C|0.650;T|0.350	0.350	strong		0.468	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ARGFX	503582	hgsc.bcm.edu	37	3	121304933	121304933	+	Missense_Mutation	SNP	G	G	A	rs9813391	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121304933G>A	ENST00000334384.3	+	4	444	c.434G>A	c.(433-435)cGa>cAa	p.R145Q		NM_001012659.1	NP_001012677.1	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	145			R -> Q (in dbSNP:rs9813391).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(114;0.152)		GCAAAGCAACGAAACCAGATC	0.502													G|||	857	0.171126	0.1127	0.4438	5008	,	,		19879	0.0506		0.2545	False		,,,				2504	0.0951				p.R145Q		Atlas-SNP	.											.	ARGFX	36	.	0			c.G434A						PASS	.	G	GLN/ARG	613,3793	263.1+/-265.3	38,537,1628	123.0	113.0	116.0		434	-0.9	0.0	3	dbSNP_119	116	2371,6229	390.0+/-343.1	324,1723,2253	yes	missense	ARGFX	NM_001012659.1	43	362,2260,3881	AA,AG,GG		27.5698,13.9128,22.9433	benign	145/316	121304933	2984,10022	2203	4300	6503	SO:0001583	missense	503582	exon5			AGCAACGAAACCA		CCDS33834.1	3q13.33	2011-06-20			ENSG00000186103	ENSG00000186103		"""Homeoboxes / PRD class"""	30146	protein-coding gene	gene with protein product		611164					Standard	XM_005247505		Approved		uc003eef.3	A6NJG6	OTTHUMG00000159395	ENST00000334384.3:c.434G>A	3.37:g.121304933G>A	ENSP00000335578:p.Arg145Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_001012659		Missense_Mutation	SNP	ENST00000334384.3	37	CCDS33834.1	440	0.20146520146520147	64	0.13008130081300814	142	0.39226519337016574	30	0.05244755244755245	204	0.2691292875989446	G	0.150	-1.091973	0.01858	0.139128	0.275698	ENSG00000186103	ENST00000334384	D	0.88354	-2.37	3.32	-0.937	0.10415	.	1.246050	0.06010	N	0.649304	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.16396	0.017	B	0.04013	0.001	T	0.04165	-1.0972	9	0.10111	T	0.7	-0.0198	2.7093	0.05170	0.1684:0.3796:0.344:0.108	rs9813391;rs17741793;rs52830852;rs9813391	145	A6NJG6	ARGFX_HUMAN	Q	145	ENSP00000335578:R145Q	ENSP00000335578:R145Q	R	+	2	0	ARGFX	122787623	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.293000	0.08320	-0.190000	0.10465	-0.270000	0.10280	CGA	G|0.786;A|0.214	0.214	strong		0.502	ARGFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355096.2	NM_001012659	
IGSF3	3321	hgsc.bcm.edu	37	1	117158899	117158899	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:117158899A>G	ENST00000369486.3	-	3	989	c.224T>C	c.(223-225)aTg>aCg	p.M75T	IGSF3_ENST00000369483.1_Missense_Mutation_p.M75T|IGSF3_ENST00000318837.6_Missense_Mutation_p.M75T	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	75	Ig-like C2-type 1.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.M75T(3)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GGAAGAGTCCATGGTGCTGAC	0.542																																					p.M75T		Atlas-SNP	.											IGSF3_ENST00000369483,right_upper_lobe,carcinoma,0,5	IGSF3	294	5	3	Substitution - Missense(3)	skin(2)|NS(1)	c.T224C						scavenged	.						9.0	9.0	9.0					1																	117158899		2172	4230	6402	SO:0001583	missense	3321	exon3			GAGTCCATGGTGC	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.224T>C	1.37:g.117158899A>G	ENSP00000358498:p.Met75Thr	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	264	25	0.094697	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	3.341	-0.134508	0.06711	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.64260	-0.09;-0.09;-0.09	4.79	2.35	0.29111	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.238710	0.05491	N	0.556554	T	0.18676	0.0448	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.11916	-1.0568	10	0.22109	T	0.4	-0.6305	3.687	0.08332	0.5706:0.0:0.0933:0.3361	.	75;75	O75054;A6NJZ6	IGSF3_HUMAN;.	T	75	ENSP00000358498:M75T;ENSP00000358495:M75T;ENSP00000321184:M75T	ENSP00000321184:M75T	M	-	2	0	IGSF3	116960422	0.001000	0.12720	0.632000	0.29296	0.982000	0.71751	0.222000	0.17699	0.282000	0.22254	0.454000	0.30748	ATG	.	.	none		0.542	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
GC	2638	hgsc.bcm.edu	37	4	72618323	72618323	+	Missense_Mutation	SNP	G	G	T	rs4588	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:72618323G>T	ENST00000273951.8	-	11	1650	c.1307C>A	c.(1306-1308)aCg>aAg	p.T436K	GC_ENST00000503472.1_5'UTR|GC_ENST00000513476.1_Missense_Mutation_p.T436K|GC_ENST00000504199.1_Missense_Mutation_p.T455K	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	436	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.		K -> T (in allele GC*1F, allele GC*1A1 and allele GC*1S; dbSNP:rs4588). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15815621, ECO:0000269|PubMed:2416779, ECO:0000269|PubMed:7505619, ECO:0000269|PubMed:7725672, ECO:0000269|PubMed:8325650, ECO:0000269|Ref.6, ECO:0000269|Ref.8}.		small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	actin binding (GO:0003779)|calcidiol binding (GO:1902118)|vitamin D binding (GO:0005499)|vitamin transporter activity (GO:0051183)			endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Alfacalcidol(DB01436)|Cholecalciferol(DB00169)	TGCCAGTTCCGTGGGTGTGGC	0.398													G|||	1041	0.207867	0.0673	0.2075	5008	,	,		18730	0.2609		0.2475	False		,,,				2504	0.3027				p.T455K		Atlas-SNP	.											.	GC	132	.	0			c.C1364A	GRCh37	CM931252	GC	M	rs4588	PASS	.	G	LYS/THR,LYS/THR,LYS/THR	467,3939	222.0+/-238.9	33,401,1769	182.0	154.0	164.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1307,1307,1364	-2.7	0.0	4	dbSNP_52	164	2489,6111	409.7+/-349.9	368,1753,2179	yes	missense,missense,missense	GC	NM_000583.3,NM_001204306.1,NM_001204307.1	78,78,78	401,2154,3948	TT,TG,GG		28.9419,10.5992,22.728	benign,benign,benign	436/475,436/475,455/494	72618323	2956,10050	2203	4300	6503	SO:0001583	missense	2638	exon12			AGTTCCGTGGGTG	L10641	CCDS3550.1, CCDS56332.1	4q12-q13	2008-08-29			ENSG00000145321	ENSG00000145321			4187	protein-coding gene	gene with protein product		139200				558959	Standard	NM_000583		Approved	DBP, VDBP, hDBP	uc010iif.3	P02774	OTTHUMG00000129915	ENST00000273951.8:c.1307C>A	4.37:g.72618323G>T	ENSP00000273951:p.Thr436Lys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	152	80	0.526316	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Missense_Mutation	SNP	ENST00000273951.8	37	CCDS3550.1	471	0.21565934065934067	32	0.06504065040650407	87	0.24033149171270718	162	0.28321678321678323	190	0.25065963060686014	G	2.250	-0.371885	0.05034	0.105992	0.289419	ENSG00000145321	ENST00000273951;ENST00000504199;ENST00000513476	T;T;T	0.16597	2.33;2.33;2.33	5.33	-2.73	0.05950	.	1.469460	0.03557	N	0.226483	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.14012	0.009;0.009	B;B	0.14578	0.011;0.011	T	0.43507	-0.9387	8	0.15499	T	0.54	.	5.7633	0.18213	0.2104:0.0:0.3152:0.4744	rs4588;rs1047220;rs3172681;rs3737552;rs4987170;rs16846941;rs4588	455;436	D6RAK8;D6RF35	.;.	K	436;455;436	ENSP00000273951:T436K;ENSP00000421725:T455K;ENSP00000426683:T436K	ENSP00000273951:T436K	T	-	2	0	GC	72837187	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.484000	0.06528	-0.461000	0.06993	-0.238000	0.12139	ACG	G|0.785;T|0.215	0.215	strong		0.398	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2		
KATNA1	11104	hgsc.bcm.edu	37	6	149953981	149953981	+	Silent	SNP	C	C	T	rs9800580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:149953981C>T	ENST00000335647.5	-	2	278	c.234G>A	c.(232-234)ctG>ctA	p.L78L	KATNA1_ENST00000367411.2_Silent_p.L78L|Y_RNA_ENST00000384562.1_RNA|KATNA1_ENST00000335643.8_Silent_p.L78L					katanin p60 (ATPase containing) subunit A 1											endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		GAGTGCTGTCCAGTTTAAAGC	0.428													T|||	2812	0.561502	0.6074	0.6398	5008	,	,		17029	0.8224		0.3579	False		,,,				2504	0.3845				p.L78L		Atlas-SNP	.											.	KATNA1	34	.	0			c.G234A						PASS	.	T	,	2526,1880	543.4+/-376.3	722,1082,399	123.0	109.0	114.0		234,234	-1.6	1.0	6	dbSNP_119	114	3117,5483	658.0+/-401.5	547,2023,1730	no	coding-synonymous,coding-synonymous	KATNA1	NM_001204076.1,NM_007044.3	,	1269,3105,2129	TT,TC,CC		36.2442,42.6691,43.3877	,	78/312,78/492	149953981	5643,7363	2203	4300	6503	SO:0001819	synonymous_variant	11104	exon3			GCTGTCCAGTTTA	AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"""ATPases / AAA-type"""	6216	protein-coding gene	gene with protein product		606696	"""katanin p60 (ATPase-containing) subunit A 1"""			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.234G>A	6.37:g.149953981C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	202	104	0.514852	NM_007044		Silent	SNP	ENST00000335647.5	37	CCDS5217.1																																																																																			C|0.522;T|0.478	0.478	strong		0.428	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044	
C12orf71	728858	hgsc.bcm.edu	37	12	27234999	27234999	+	Missense_Mutation	SNP	T	T	C	rs708167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:27234999T>C	ENST00000429849.2	-	1	448	c.418A>G	c.(418-420)Ata>Gta	p.I140V		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	140			I -> V (in dbSNP:rs708167).							endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						TCTAGAAATATCTGAAACTCT	0.418													T|||	894	0.178514	0.053	0.2118	5008	,	,		22542	0.0357		0.4423	False		,,,				2504	0.2004				p.I140V		Atlas-SNP	.											.	C12orf71	20	.	0			c.A418G						PASS	.	T	VAL/ILE	421,3263		26,369,1447	60.0	56.0	58.0		418	2.0	0.0	12	dbSNP_86	58	3670,4514		817,2036,1239	yes	missense	C12orf71	NM_001080406.1	29	843,2405,2686	CC,CT,TT		44.8436,11.4278,34.4708	benign	140/270	27234999	4091,7777	1842	4092	5934	SO:0001583	missense	728858	exon1			GAAATATCTGAAA		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.418A>G	12.37:g.27234999T>C	ENSP00000413728:p.Ile140Val	Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	287	286	0.996516	NM_001080406		Missense_Mutation	SNP	ENST00000429849.2	37	CCDS44851.1	473	0.21657509157509158	28	0.056910569105691054	84	0.23204419889502761	22	0.038461538461538464	339	0.4472295514511873	T	6.227	0.409973	0.11812	0.114278	0.448436	ENSG00000214700	ENST00000398815;ENST00000429849	T	0.40756	1.02	3.22	2.05	0.26809	.	0.260386	0.19682	U	0.108493	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46233	-0.9206	9	0.39692	T	0.17	-0.5574	5.1545	0.15027	0.0:0.1429:0.0:0.8571	rs708167;rs61061734;rs708167	140	A8MTZ7	CL071_HUMAN	V	140	ENSP00000413728:I140V	ENSP00000381796:I140V	I	-	1	0	C12orf71	27126266	0.001000	0.12720	0.030000	0.17652	0.021000	0.10359	-0.196000	0.09532	0.443000	0.26582	0.418000	0.28097	ATA	T|0.788;C|0.212	0.212	strong		0.418	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
YEATS2	55689	hgsc.bcm.edu	37	3	183476685	183476685	+	Missense_Mutation	SNP	G	G	A	rs262993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183476685G>A	ENST00000305135.5	+	13	1783	c.1588G>A	c.(1588-1590)Gtc>Atc	p.V530I		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	530			V -> I (in dbSNP:rs262993).		chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GGCTTCTCAGGTCTCCCAAGG	0.363													G|||	2132	0.425719	0.261	0.4467	5008	,	,		18474	0.5188		0.4533	False		,,,				2504	0.5092				p.V530I		Atlas-SNP	.											YEATS2,NS,carcinoma,-1,1	YEATS2	111	1	0			c.G1588A						PASS	.	G	ILE/VAL	1039,2615		149,741,937	129.0	118.0	121.0		1588	4.2	1.0	3	dbSNP_79	121	3602,4572		784,2034,1269	yes	missense	YEATS2	NM_018023.4	29	933,2775,2206	AA,AG,GG		44.0666,28.4346,39.2374	benign	530/1423	183476685	4641,7187	1827	4087	5914	SO:0001583	missense	55689	exon13			TCTCAGGTCTCCC	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.1588G>A	3.37:g.183476685G>A	ENSP00000306983:p.Val530Ile	Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	412	162	0.393204	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	37	CCDS43175.1	927	0.42445054945054944	117	0.23780487804878048	164	0.4530386740331492	309	0.5402097902097902	337	0.4445910290237467	G	16.01	3.001348	0.54254	0.284346	0.440666	ENSG00000163872	ENST00000421660;ENST00000305135	T	0.28895	1.59	5.22	4.15	0.48705	.	0.448888	0.20667	N	0.087912	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.100000000000325E-5	B	0.23937	0.094	B	0.14023	0.01	T	0.40308	-0.9570	9	0.72032	D	0.01	-1.2302	14.6752	0.68975	0.082:0.0:0.918:0.0	rs262993;rs58123380;rs262993	530	Q9ULM3	YETS2_HUMAN	I	530	ENSP00000306983:V530I	ENSP00000306983:V530I	V	+	1	0	YEATS2	184959379	1.000000	0.71417	0.990000	0.47175	0.979000	0.70002	5.373000	0.66162	2.449000	0.82847	0.585000	0.79938	GTC	G|0.576;A|0.424	0.424	strong		0.363	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
CA14	23632	hgsc.bcm.edu	37	1	150234657	150234657	+	Silent	SNP	G	G	T	rs34714364	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:150234657G>T	ENST00000369111.4	+	4	1327	c.357G>T	c.(355-357)ggG>ggT	p.G119G	snoU13_ENST00000458929.1_RNA	NM_012113.1	NP_036245.1	Q9ULX7	CAH14_HUMAN	carbonic anhydrase XIV	119					bicarbonate transport (GO:0015701)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	18	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)		Acetazolamide(DB00819)|Zonisamide(DB00909)	GATCCCCAGGGGGGTCAGAAC	0.552													G|||	270	0.0539137	0.0045	0.0764	5008	,	,		19443	0.0		0.1561	False		,,,				2504	0.0552				p.G119G		Atlas-SNP	.											.	CA14	37	.	0			c.G357T						PASS	.	G		150,4256	103.0+/-141.5	5,140,2058	88.0	89.0	89.0		357	2.1	0.5	1	dbSNP_126	89	1443,7157	275.3+/-291.7	130,1183,2987	no	coding-synonymous	CA14	NM_012113.1		135,1323,5045	TT,TG,GG		16.7791,3.4044,12.2482		119/338	150234657	1593,11413	2203	4300	6503	SO:0001819	synonymous_variant	23632	exon4			CCCAGGGGGGTCA	AB025904	CCDS947.1	1q21	2008-02-05			ENSG00000118298	ENSG00000118298		"""Carbonic anhydrases"""	1372	protein-coding gene	gene with protein product		604832				10512682	Standard	XM_005245059		Approved		uc001etx.3	Q9ULX7	OTTHUMG00000012549	ENST00000369111.4:c.357G>T	1.37:g.150234657G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	167	69	0.413174	NM_012113	Q5TB24|Q8NCF4	Silent	SNP	ENST00000369111.4	37	CCDS947.1																																																																																			G|0.897;T|0.103	0.103	strong		0.552	CA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035064.2	NM_012113	
CCIN	881	hgsc.bcm.edu	37	9	36169723	36169723	+	Missense_Mutation	SNP	G	G	A	rs34789048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:36169723G>A	ENST00000335119.2	+	1	335	c.224G>A	c.(223-225)aGt>aAt	p.S75N		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	75	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.		S -> N (in dbSNP:rs34789048).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			ATTGACACCAGTTACCTGAGC	0.547													G|||	278	0.0555112	0.0779	0.0375	5008	,	,		21854	0.0		0.0934	False		,,,				2504	0.0562				p.S75N		Atlas-SNP	.											.	CCIN	56	.	0			c.G224A						PASS	.	G	ASN/SER	396,4010	196.4+/-220.7	23,350,1830	84.0	78.0	80.0		224	3.3	1.0	9	dbSNP_126	80	811,7789	188.9+/-235.7	43,725,3532	yes	missense	CCIN	NM_005893.2	46	66,1075,5362	AA,AG,GG		9.4302,8.9877,9.2803	benign	75/589	36169723	1207,11799	2203	4300	6503	SO:0001583	missense	881	exon1			ACACCAGTTACCT	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"""BTB/POZ domain containing"""	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.224G>A	9.37:g.36169723G>A	ENSP00000334996:p.Ser75Asn	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	118	69	0.584746	NM_005893	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	37	CCDS6599.1	128	0.05860805860805861	47	0.09552845528455285	13	0.03591160220994475	0	0.0	68	0.08970976253298153	G	0.051	-1.248935	0.01469	0.089877	0.094302	ENSG00000185972	ENST00000335119	T	0.67345	-0.26	5.56	3.26	0.37387	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.312045	0.27710	N	0.018163	T	0.01254	0.0041	N	0.13140	0.3	0.22968	N	0.998498	B	0.02656	0.0	B	0.01281	0.0	T	0.02064	-1.1220	10	0.09084	T	0.74	.	6.0562	0.19812	0.796:0.0:0.204:0.0	rs34789048	75	Q13939	CALI_HUMAN	N	75	ENSP00000334996:S75N	ENSP00000334996:S75N	S	+	2	0	CCIN	36159723	1.000000	0.71417	1.000000	0.80357	0.400000	0.30750	2.016000	0.40971	0.957000	0.37930	-0.379000	0.06801	AGT	G|0.924;A|0.076	0.076	strong		0.547	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893	
TECPR2	9895	hgsc.bcm.edu	37	14	102901201	102901201	+	Missense_Mutation	SNP	A	A	G	rs10149146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:102901201A>G	ENST00000359520.7	+	9	2273	c.2047A>G	c.(2047-2049)Atc>Gtc	p.I683V	TECPR2_ENST00000558678.1_Missense_Mutation_p.I683V	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	683			I -> V (in dbSNP:rs10149146).		autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						AGAGCAGGACATCCTAACCAG	0.572													G|||	1076	0.214856	0.1286	0.1902	5008	,	,		21537	0.1478		0.2982	False		,,,				2504	0.3323				p.I683V		Atlas-SNP	.											.	TECPR2	114	.	0			c.A2047G						PASS	.	G	VAL/ILE,VAL/ILE	660,3746	763.6+/-413.2	58,544,1601	43.0	44.0	44.0		2047,2047	-6.8	0.0	14	dbSNP_119	44	2906,5694	669.8+/-402.7	470,1966,1864	yes	missense,missense	TECPR2	NM_001172631.1,NM_014844.3	29,29	528,2510,3465	GG,GA,AA		33.7907,14.9796,27.4181	benign,benign	683/1268,683/1412	102901201	3566,9440	2203	4300	6503	SO:0001583	missense	9895	exon9			CAGGACATCCTAA	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"""KIAA0329"""	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.2047A>G	14.37:g.102901201A>G	ENSP00000352510:p.Ile683Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	37	CCDS32162.1	456	0.2087912087912088	63	0.12804878048780488	74	0.20441988950276244	91	0.1590909090909091	228	0.3007915567282322	G	0.760	-0.769554	0.02974	0.149796	0.337907	ENSG00000196663	ENST00000359520	T	0.13778	2.56	4.97	-6.78	0.01721	.	2.517140	0.01012	N	0.003842	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43637	-0.9379	8	.	.	.	.	0.9405	0.01355	0.2882:0.2126:0.3267:0.1726	rs10149146;rs10149146	683;683	A5PKY3;O15040	.;TCPR2_HUMAN	V	683	ENSP00000352510:I683V	.	I	+	1	0	TECPR2	101970954	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.836000	0.04382	-1.132000	0.02907	-0.993000	0.02533	ATC	A|0.744;G|0.256	0.256	strong		0.572	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
FGFR4	2264	hgsc.bcm.edu	37	5	176517461	176517461	+	Silent	SNP	T	T	G	rs446382|rs200071427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176517461T>G	ENST00000292408.4	+	3	407	c.162T>G	c.(160-162)cgT>cgG	p.R54R	FGFR4_ENST00000393648.2_Silent_p.R54R|FGFR4_ENST00000507708.1_3'UTR|FGFR4_ENST00000393637.1_Silent_p.R54R|FGFR4_ENST00000502906.1_Silent_p.R54R|FGFR4_ENST00000292410.3_Silent_p.R54R	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	54	Ig-like C2-type 1.				alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	AGCCTGTGCGTCTGTGCTGTG	0.682										TSP Lung(9;0.080)			G|||	3886	0.775958	0.5756	0.8084	5008	,	,		18243	0.9772		0.6899	False		,,,				2504	0.9049				p.R54R		Atlas-SNP	.											.	FGFR4	174	.	0			c.T162G						PASS	.	G	,,	2708,1698		820,1068,315	32.0	34.0	33.0		162,162,162	-1.4	0.1	5	dbSNP_80	33	6174,2420		2248,1678,371	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	,,	3068,2746,686	GG,GT,TT		28.1592,38.5384,31.6769	,,	54/803,54/763,54/803	176517461	8882,4118	2203	4297	6500	SO:0001819	synonymous_variant	2264	exon2			TGTGCGTCTGTGC	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.162T>G	5.37:g.176517461T>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	17	0.265625	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Silent	SNP	ENST00000292408.4	37	CCDS4410.1																																																																																			T|0.294;G|0.706	0.706	strong		0.682	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507242	195507242	+	Missense_Mutation	SNP	C	C	A	rs567957149|rs74187968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507242C>A	ENST00000463781.3	-	2	11668	c.11209G>T	c.(11209-11211)Gca>Tca	p.A3737S	MUC4_ENST00000475231.1_Missense_Mutation_p.A3737S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGGG	0.572													.|||	53	0.0105831	0.0136	0.0086	5008	,	,		10241	0.0069		0.0139	False		,,,				2504	0.0082				p.A3737S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G11209T						scavenged	.						35.0	34.0	34.0					3																	195507242		619	1580	2199	SO:0001583	missense	4585	exon2			TGGATGCTGAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11209G>T	3.37:g.195507242C>A	ENSP00000417498:p.Ala3737Ser	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	289	53	0.183391	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	2.940	-0.219185	0.06101	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.56;1.45	.	.	.	.	0.435754	0.11199	U	0.589055	T	0.12561	0.0305	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.26155	-1.0111	8	.	.	.	.	2.155	0.03810	0.0:0.332:0.3413:0.3266	.	3609	E7ESK3	.	S	3737	ENSP00000417498:A3737S;ENSP00000420243:A3737S	.	A	-	1	0	MUC4	196992021	0.000000	0.05858	0.005000	0.12908	0.022000	0.10575	-0.526000	0.06207	-0.927000	0.03766	0.064000	0.15345	GCA	A|1.000;|0.000	1.000	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
C19orf35	374872	hgsc.bcm.edu	37	19	2278841	2278841	+	Silent	SNP	G	G	A	rs78560055	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:2278841G>A	ENST00000342063.3	-	3	447	c.354C>T	c.(352-354)gaC>gaT	p.D118D		NM_198532.2	NP_940934.1	Q6ZS72	CS035_HUMAN	chromosome 19 open reading frame 35	118										large_intestine(1)|lung(5)|pancreas(1)|prostate(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGTGGGGCGTCAGCCGGGC	0.677													G|||	14	0.00279553	0.0	0.0014	5008	,	,		13422	0.0		0.0109	False		,,,				2504	0.002				p.D118D		Atlas-SNP	.											.	C19orf35	18	.	0			c.C354T						PASS	.	G		6,4358		0,6,2176	9.0	10.0	10.0		354	-3.6	0.0	19	dbSNP_132	10	121,8435		0,121,4157	no	coding-synonymous	C19orf35	NM_198532.2		0,127,6333	AA,AG,GG		1.4142,0.1375,0.983		118/474	2278841	127,12793	2182	4278	6460	SO:0001819	synonymous_variant	374872	exon3			TGGGGCGTCAGCC	AK127680	CCDS12087.1	19p13.3	2012-10-26			ENSG00000188305	ENSG00000188305			24793	protein-coding gene	gene with protein product							Standard	NM_198532		Approved	FLJ45778	uc002lvn.2	Q6ZS72	OTTHUMG00000178460	ENST00000342063.3:c.354C>T	19.37:g.2278841G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_198532		Silent	SNP	ENST00000342063.3	37	CCDS12087.1																																																																																			G|0.993;A|0.007	0.007	strong		0.677	C19orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442080.1	NM_198532	
IBSP	3381	hgsc.bcm.edu	37	4	88732692	88732692	+	Missense_Mutation	SNP	G	G	A	rs1054627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88732692G>A	ENST00000226284.5	+	7	651	c.584G>A	c.(583-585)gGa>gAa	p.G195E		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	195			G -> E (in dbSNP:rs1054627). {ECO:0000269|PubMed:8061918, ECO:0000269|PubMed:8406493}.		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		AGCAGCGGAGGAGACAATGGA	0.527													G|||	954	0.190495	0.0189	0.2781	5008	,	,		17144	0.1062		0.328	False		,,,				2504	0.3057				p.G195E		Atlas-SNP	.											.	IBSP	53	.	0			c.G584A						PASS	.	G	GLU/GLY	287,4119	157.0+/-190.0	13,261,1929	151.0	137.0	142.0	http://www.ncbi.nlm.nih.gov/pubmed?term	584	2.2	0.1	4	dbSNP_86	142	2756,5844	437.0+/-358.5	438,1880,1982	yes	missense	IBSP	NM_004967.3	98	451,2141,3911	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	32.0465,6.5138,23.3969	probably-damaging	195/318	88732692	3043,9963	2203	4300	6503	SO:0001583	missense	3381	exon7			GCGGAGGAGACAA		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"""bone sialoprotein"", ""bone sialoprotein II"""	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.584G>A	4.37:g.88732692G>A	ENSP00000226284:p.Gly195Glu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_004967		Missense_Mutation	SNP	ENST00000226284.5	37	CCDS3624.1	405	0.18543956043956045	8	0.016260162601626018	96	0.26519337016574585	60	0.1048951048951049	241	0.3179419525065963	G	4.520	0.096488	0.08681	0.065138	0.320465	ENSG00000029559	ENST00000226284	T	0.15017	2.46	5.11	2.19	0.27852	.	0.308306	0.27696	N	0.018240	T	0.00012	0.0000	M	0.76574	2.34	0.80722	P	0.0	B	0.29085	0.232	B	0.35607	0.206	T	0.36383	-0.9750	9	0.10902	T	0.67	.	6.2398	0.20785	0.1417:0.3291:0.5291:0.0	rs1054627;rs17762603;rs52829278;rs57196651;rs1054627	195	P21815	SIAL_HUMAN	E	195	ENSP00000226284:G195E	ENSP00000226284:G195E	G	+	2	0	IBSP	88951716	0.038000	0.19896	0.054000	0.19295	0.155000	0.21991	0.539000	0.23175	1.105000	0.41606	0.491000	0.48974	GGA	G|0.781;A|0.219	0.219	strong		0.527	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2		
PIH1D1	55011	hgsc.bcm.edu	37	19	49954807	49954807	+	Missense_Mutation	SNP	T	T	G	rs2293012	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49954807T>G	ENST00000262265.5	-	1	260	c.25A>C	c.(25-27)Atg>Ctg	p.M9L	ALDH16A1_ENST00000293350.4_5'Flank|ALDH16A1_ENST00000433981.2_5'Flank|ALDH16A1_ENST00000540132.1_5'Flank|ALDH16A1_ENST00000455361.2_5'Flank|PIH1D1_ENST00000596049.1_Missense_Mutation_p.M9L	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	9			M -> L (in dbSNP:rs2293012). {ECO:0000269|PubMed:14702039}.	MG -> LE (in Ref. 2; AAH01108). {ECO:0000305}.	box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		CTTAGCCCCATTCCCAGCAGC	0.612													g|||	3049	0.608826	0.6475	0.6124	5008	,	,		16024	0.4117		0.7535	False		,,,				2504	0.6084				p.M9L		Atlas-SNP	.											.	PIH1D1	23	.	0			c.A25C						PASS	.		LEU/MET	2720,1686	511.7+/-367.9	855,1010,338	83.0	71.0	75.0		25	1.3	0.1	19	dbSNP_100	75	6586,2014	350.8+/-328.0	2511,1564,225	yes	missense	PIH1D1	NM_017916.2	15	3366,2574,563	GG,GT,TT		23.4186,38.266,28.4484	benign	9/291	49954807	9306,3700	2203	4300	6503	SO:0001583	missense	55011	exon1			GCCCCATTCCCAG	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.25A>C	19.37:g.49954807T>G	ENSP00000262265:p.Met9Leu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Missense_Mutation	SNP	ENST00000262265.5	37	CCDS12765.1	1326	0.6071428571428571	316	0.6422764227642277	229	0.6325966850828729	223	0.38986013986013984	558	0.7361477572559367	g	0.032	-1.325226	0.01309	0.61734	0.765814	ENSG00000104872	ENST00000262265	T	0.10477	2.87	4.87	1.33	0.21861	.	1.175780	0.06182	N	0.679642	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20706	-1.0267	9	0.17369	T	0.5	-8.6146	2.806	0.05427	0.0901:0.1603:0.4192:0.3304	rs2293012;rs17855354;rs2293012	9	Q9NWS0	PIHD1_HUMAN	L	9	ENSP00000262265:M9L	ENSP00000262265:M9L	M	-	1	0	PIH1D1	54646619	0.013000	0.17824	0.144000	0.22314	0.071000	0.16799	0.400000	0.20932	0.353000	0.24079	-0.225000	0.12378	ATG	T|0.332;G|0.668	0.668	strong		0.612	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916	
GCNT2	2651	hgsc.bcm.edu	37	6	10587056	10587056	+	Intron	SNP	A	A	G	rs71548508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:10587056A>G	ENST00000379597.3	+	2	1481				GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000265012.4_Silent_p.L278L|GCNT2_ENST00000316170.3_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.L278L(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		ACTTTGTTCTACGTGACCAAA	0.418													A|||	256	0.0511182	0.0121	0.062	5008	,	,		19022	0.0079		0.1471	False		,,,				2504	0.0419				p.L278L		Atlas-SNP	.											GCNT2_ENST00000265012,NS,carcinoma,0,1	GCNT2	123	1	1	Substitution - coding silent(1)	stomach(1)	c.A834G						PASS	.	A	,,	152,4254	105.6+/-144.1	5,142,2056	90.0	84.0	86.0		,,834	-1.1	0.0	6	dbSNP_130	86	1270,7330	253.0+/-278.9	105,1060,3135	no	intron,intron,coding-synonymous	GCNT2	NM_001491.2,NM_145649.4,NM_145655.3	,,	110,1202,5191	GG,GA,AA		14.7674,3.4498,10.9334	,,	,,278/403	10587056	1422,11584	2203	4300	6503	SO:0001627	intron_variant	2651	exon1			TGTTCTACGTGAC	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-34528A>G	6.37:g.10587056A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	241	134	0.556017	NM_145655		Silent	SNP	ENST00000379597.3	37	CCDS34338.1																																																																																			A|0.899;G|0.101	0.101	strong		0.418	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
ZPBP2	124626	hgsc.bcm.edu	37	17	38024626	38024626	+	Silent	SNP	C	C	T	rs11557466	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38024626C>T	ENST00000348931.4	+	1	210	c.19C>T	c.(19-21)Cta>Tta	p.L7L	ZPBP2_ENST00000377940.3_Silent_p.L7L|ZPBP2_ENST00000584588.1_Silent_p.L7L	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	7					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			AACGTGCGTCCTACTCTCCGC	0.692													C|||	1455	0.290535	0.115	0.3415	5008	,	,		14820	0.2827		0.4722	False		,,,				2504	0.3129				p.L7L		Atlas-SNP	.											.	ZPBP2	33	.	0			c.C19T						PASS	.	C	,	673,3733	285.7+/-278.4	49,575,1579	85.0	77.0	80.0		19,19	2.0	0.7	17	dbSNP_120	80	3867,4733	542.3+/-384.2	856,2155,1289	no	coding-synonymous,coding-synonymous	ZPBP2	NM_198844.2,NM_199321.2	,	905,2730,2868	TT,TC,CC		44.9651,15.2746,34.907	,	7/317,7/339	38024626	4540,8466	2203	4300	6503	SO:0001819	synonymous_variant	124626	exon1			TGCGTCCTACTCT	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.19C>T	17.37:g.38024626C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_199321	A8K8L8|Q6X783|Q86XL5	Silent	SNP	ENST00000348931.4	37	CCDS11352.1																																																																																			C|0.658;T|0.342	0.342	strong		0.692	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844	
DNAH8	1769	hgsc.bcm.edu	37	6	38805753	38805753	+	Silent	SNP	G	G	A	rs45622336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38805753G>A	ENST00000359357.3	+	31	4004	c.3750G>A	c.(3748-3750)acG>acA	p.T1250T	DNAH8_ENST00000441566.1_Silent_p.T1250T|DNAH8_ENST00000449981.2_Silent_p.T1467T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1250					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AATTTGTTACGTATTCATCTG	0.313													A|||	11	0.00219649	0.0023	0.0	5008	,	,		17985	0.0		0.007	False		,,,				2504	0.001				p.T1467T		Atlas-SNP	.											DNAH8_ENST00000359357,head_neck,malignant_melanoma,+1,2	DNAH8	1239	2	0			c.G4401A						PASS	.	A		10,4396	824.8+/-416.5	0,10,2193	169.0	154.0	159.0		4401	-9.2	0.6	6	dbSNP_127	159	76,8524	815.6+/-407.0	1,74,4225	no	coding-synonymous	DNAH8	NM_001206927.1		1,84,6418	AA,AG,GG		0.8837,0.227,0.6612		1467/4708	38805753	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon33			TGTTACGTATTCA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.3750G>A	6.37:g.38805753G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	173	95	0.549133	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				G|0.995;A|0.005	0.005	strong		0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
TBC1D8	11138	hgsc.bcm.edu	37	2	101656726	101656726	+	Missense_Mutation	SNP	T	T	C	rs2289953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:101656726T>C	ENST00000376840.4	-	6	948	c.949A>G	c.(949-951)Acg>Gcg	p.T317A	TBC1D8_ENST00000409318.1_Missense_Mutation_p.T332A			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	317	GRAM 2.		T -> A (in dbSNP:rs2289953). {ECO:0000269|PubMed:10373574, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:19077034}.		blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						ATCCGCCCCGTGGTGTGACAG	0.567													C|||	2432	0.485623	0.3502	0.5648	5008	,	,		17328	0.3075		0.6819	False		,,,				2504	0.5941				p.T317A		Atlas-SNP	.											.	TBC1D8	169	.	0			c.A949G						PASS	.	C	ALA/THR	1753,2329		379,995,667	63.0	67.0	65.0		949	4.0	0.0	2	dbSNP_100	65	5549,2813		1860,1829,492	yes	missense	TBC1D8	NM_001102426.1	58	2239,2824,1159	CC,CT,TT		33.6403,42.9446,41.3211	benign	317/1141	101656726	7302,5142	2041	4181	6222	SO:0001583	missense	11138	exon6			GCCCCGTGGTGTG	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.949A>G	2.37:g.101656726T>C	ENSP00000366036:p.Thr317Ala	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	115	62	0.53913	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation	SNP	ENST00000376840.4	37	CCDS46375.1	1122	0.5137362637362637	167	0.3394308943089431	230	0.6353591160220995	208	0.36363636363636365	517	0.6820580474934037	C	5.573	0.290495	0.10567	0.429446	0.663597	ENSG00000204634	ENST00000376840;ENST00000409318	D;D	0.86432	-2.12;-2.12	5.86	4.0	0.46444	GRAM (2);	0.957727	0.08663	N	0.912143	T	0.00012	0.0000	N	0.00413	-1.525	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48031	-0.9070	9	0.14656	T	0.56	-3.8362	11.3848	0.49778	0.0:0.6991:0.237:0.0639	rs2289953;rs52803932;rs59227734;rs2289953	317	O95759	TBCD8_HUMAN	A	317;332	ENSP00000366036:T317A;ENSP00000386856:T332A	ENSP00000366036:T317A	T	-	1	0	TBC1D8	101023158	0.000000	0.05858	0.000000	0.03702	0.367000	0.29736	1.185000	0.32065	0.360000	0.24265	-0.119000	0.15052	ACG	A|0.006;C|0.500	0.500	strong		0.567	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
NID1	4811	hgsc.bcm.edu	37	1	236212038	236212038	+	Silent	SNP	G	G	A	rs6665008	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:236212038G>A	ENST00000264187.6	-	2	559	c.477C>T	c.(475-477)tcC>tcT	p.S159S	NID1_ENST00000366595.3_Silent_p.S159S	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	159	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	AGGGGGCCACGGATTCCCAAG	0.577													G|||	293	0.0585064	0.0295	0.0749	5008	,	,		17208	0.001		0.1123	False		,,,				2504	0.09				p.S159S		Atlas-SNP	.											NID1,NS,carcinoma,0,1	NID1	196	1	0			c.C477T						PASS	.	G		205,4201	127.0+/-164.0	5,195,2003	72.0	64.0	67.0		477	-7.9	0.7	1	dbSNP_116	67	903,7697	202.4+/-245.7	37,829,3434	yes	coding-synonymous	NID1	NM_002508.2		42,1024,5437	AA,AG,GG		10.5,4.6527,8.5191		159/1248	236212038	1108,11898	2203	4300	6503	SO:0001819	synonymous_variant	4811	exon2			GGCCACGGATTCC	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.477C>T	1.37:g.236212038G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	34	0.971429	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																			G|0.912;A|0.088	0.088	strong		0.577	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
TLR2	7097	hgsc.bcm.edu	37	4	154625682	154625682	+	Silent	SNP	C	C	T	rs5743700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:154625682C>T	ENST00000260010.6	+	1	3031	c.1623C>T	c.(1621-1623)ttC>ttT	p.F541F		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	541	LRRCT.				apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	CCTGTGAATTCCTCTCCTTCA	0.473													C|||	81	0.0161741	0.0015	0.0259	5008	,	,		21594	0.0		0.0427	False		,,,				2504	0.0184				p.F541F		Atlas-SNP	.											.	TLR2	84	.	0			c.C1623T						PASS	.	C		45,4361	43.8+/-77.6	0,45,2158	53.0	54.0	54.0		1623	4.2	0.8	4	dbSNP_114	54	480,8118	128.0+/-186.3	14,452,3833	no	coding-synonymous	TLR2	NM_003264.3		14,497,5991	TT,TC,CC		5.5827,1.0213,4.0372		541/785	154625682	525,12479	2203	4299	6502	SO:0001819	synonymous_variant	7097	exon3			TGAATTCCTCTCC	U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"""CD molecules"""	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.1623C>T	4.37:g.154625682C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	195	112	0.574359	NM_003264	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Silent	SNP	ENST00000260010.6	37	CCDS3784.1																																																																																			C|0.962;T|0.038	0.038	strong		0.473	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1		
USP3	9960	hgsc.bcm.edu	37	15	63866278	63866278	+	Silent	SNP	C	C	T	rs61751107	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63866278C>T	ENST00000380324.3	+	10	1071	c.942C>T	c.(940-942)ttC>ttT	p.F314F	USP3_ENST00000536001.1_3'UTR|USP3-AS1_ENST00000559861.1_RNA|USP3_ENST00000268049.7_Silent_p.F292F|USP3_ENST00000559711.1_Silent_p.F225F|USP3_ENST00000558285.1_Silent_p.F297F|USP3_ENST00000540797.1_Silent_p.F270F|USP3-AS1_ENST00000560350.1_RNA|USP3_ENST00000539772.1_Silent_p.F65F|USP3-AS1_ENST00000559357.1_RNA	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	314	USP.				DNA repair (GO:0006281)|histone deubiquitination (GO:0016578)|mitotic cell cycle (GO:0000278)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear chromatin (GO:0000790)	histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(7)|lung(4)	14				GBM - Glioblastoma multiforme(80;0.0187)		CGGCTATATTCGGAGGCATTC	0.373													C|||	61	0.0121805	0.0	0.0187	5008	,	,		13706	0.0		0.0209	False		,,,				2504	0.0276				p.F314F		Atlas-SNP	.											.	USP3	37	.	0			c.C942T						PASS	.	C		16,4390	23.3+/-48.9	0,16,2187	105.0	103.0	104.0		942	-6.2	0.8	15	dbSNP_129	104	153,8447	74.5+/-137.1	2,149,4149	no	coding-synonymous	USP3	NM_006537.2		2,165,6336	TT,TC,CC		1.7791,0.3631,1.2994		314/521	63866278	169,12837	2203	4300	6503	SO:0001819	synonymous_variant	9960	exon10			TATATTCGGAGGC	AF073344	CCDS32265.1, CCDS58370.1	15q22.3	2008-04-11	2005-08-08			ENSG00000140455		"""Ubiquitin-specific peptidases"""	12626	protein-coding gene	gene with protein product		604728	"""ubiquitin specific protease 3"""			12838346	Standard	NM_006537		Approved		uc002amf.4	Q9Y6I4		ENST00000380324.3:c.942C>T	15.37:g.63866278C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	191	88	0.460733	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Silent	SNP	ENST00000380324.3	37	CCDS32265.1																																																																																			C|0.988;T|0.012	0.012	strong		0.373	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1		
TMEM245	23731	hgsc.bcm.edu	37	9	111868885	111868885	+	Silent	SNP	G	G	A	rs2271878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:111868885G>A	ENST00000374586.3	-	3	733	c.702C>T	c.(700-702)tcC>tcT	p.S234S		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	234						integral component of membrane (GO:0016021)											AGCCAGCCAGGGATGCTGCAA	0.353													G|||	990	0.197684	0.0166	0.3256	5008	,	,		13020	0.2937		0.2803	False		,,,				2504	0.1677				p.S234S		Atlas-SNP	.											.	.	.	.	0			c.C702T						PASS	.	G		192,3446		9,174,1636	47.0	42.0	43.0		702	0.9	1.0	9	dbSNP_100	43	2273,5879		299,1675,2102	no	coding-synonymous	C9orf5	NM_032012.3		308,1849,3738	AA,AG,GG		27.8827,5.2776,20.9075		234/880	111868885	2465,9325	1819	4076	5895	SO:0001819	synonymous_variant	23731	exon3			AGCCAGGGATGCT	AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 5"""	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.702C>T	9.37:g.111868885G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	130	57	0.438462	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Silent	SNP	ENST00000374586.3	37	CCDS43858.1																																																																																			G|0.789;A|0.211	0.211	strong		0.353	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012	
NARS2	79731	hgsc.bcm.edu	37	11	78189653	78189653	+	Missense_Mutation	SNP	T	T	C	rs116930926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:78189653T>C	ENST00000281038.5	-	8	1274	c.899A>G	c.(898-900)aAa>aGa	p.K300R	NARS2_ENST00000528850.1_Missense_Mutation_p.K73R	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	300					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	TGCTATGAATTTGTGACAGAG	0.313													T|||	29	0.00579073	0.0038	0.0043	5008	,	,		15374	0.0		0.0199	False		,,,				2504	0.001				p.K300R		Atlas-SNP	.											.	NARS2	62	.	0			c.A899G						PASS	.	T	ARG/LYS	26,4374	31.7+/-61.6	0,26,2174	118.0	112.0	114.0		899	0.6	0.8	11	dbSNP_132	114	240,8344	96.1+/-157.9	2,236,4054	yes	missense	NARS2	NM_024678.5	26	2,262,6228	CC,CT,TT		2.7959,0.5909,2.0487	benign	300/478	78189653	266,12718	2200	4292	6492	SO:0001583	missense	79731	exon8			ATGAATTTGTGAC	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"""Aminoacyl tRNA synthetases / Class II"""	26274	protein-coding gene	gene with protein product	"""asparagine tRNA ligase 2, mitochondrial (putative)"""	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.899A>G	11.37:g.78189653T>C	ENSP00000281038:p.Lys300Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	166	71	0.427711	NM_024678	G3V178	Missense_Mutation	SNP	ENST00000281038.5	37	CCDS8261.1	20	0.009157509157509158	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	15	0.01978891820580475	T	13.75	2.329174	0.41197	0.005909	0.027959	ENSG00000137513	ENST00000281038;ENST00000528850	T;T	0.77489	-1.1;0.92	5.38	0.559	0.17272	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.174888	0.64402	N	0.000011	T	0.41166	0.1147	L	0.37630	1.12	0.38330	D	0.943783	B	0.20459	0.045	B	0.23716	0.048	T	0.50996	-0.8761	10	0.62326	D	0.03	-6.9707	7.4242	0.27090	0.0:0.3544:0.0:0.6456	.	300	Q96I59	SYNM_HUMAN	R	300;73	ENSP00000281038:K300R;ENSP00000432635:K73R	ENSP00000281038:K300R	K	-	2	0	NARS2	77867301	0.997000	0.39634	0.798000	0.32154	0.997000	0.91878	1.180000	0.32005	-0.058000	0.13177	0.528000	0.53228	AAA	T|0.984;C|0.016	0.016	strong		0.313	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678	
AATK	9625	hgsc.bcm.edu	37	17	79102330	79102330	+	Silent	SNP	T	T	C	rs11871062	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79102330T>C	ENST00000326724.4	-	4	378	c.354A>G	c.(352-354)acA>acG	p.T118T	MIR338_ENST00000390137.2_RNA|AATK_ENST00000572339.1_5'UTR|AATK_ENST00000417379.1_Silent_p.T15T	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	118			T -> M (in dbSNP:rs8082016).		brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GGCCCACGTCTGTGGACTTGA	0.677													C|||	436	0.0870607	0.1445	0.0403	5008	,	,		16890	0.0446		0.0616	False		,,,				2504	0.1125				p.T118T		Atlas-SNP	.											.	AATK	102	.	0			c.A354G						PASS	.	C	,	393,3045		25,343,1351	32.0	39.0	37.0		354,45	-0.8	0.9	17	dbSNP_120	37	401,6555		8,385,3085	no	coding-synonymous,coding-synonymous	AATK	NM_001080395.2,NM_004920.2	,	33,728,4436	CC,CT,TT		5.7648,11.4311,7.639	,	118/1375,15/1272	79102330	794,9600	1719	3478	5197	SO:0001819	synonymous_variant	9625	exon4			CACGTCTGTGGAC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.354A>G	17.37:g.79102330T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	144	0.06593406593406594	61	0.12398373983739837	17	0.04696132596685083	23	0.04020979020979021	43	0.05672823218997362	C	10.10	1.257180	0.22965	0.114311	0.057648	ENSG00000181409	ENST00000417379	.	.	.	4.09	-0.844	0.10741	.	.	.	.	.	T	0.00524	0.0017	.	.	.	0.09310	P	0.9999999999770882	.	.	.	.	.	.	T	0.16305	-1.0407	3	.	.	.	.	6.0567	0.19815	0.1196:0.273:0.0:0.6074	rs11871062;rs11871062	.	.	.	R	71	.	.	Q	-	2	0	AATK	76716925	0.002000	0.14202	0.942000	0.38095	0.886000	0.51366	-1.636000	0.02016	-0.997000	0.03450	-1.201000	0.01664	CAG	T|0.922;C|0.078	0.078	strong		0.677	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
PARS2	25973	hgsc.bcm.edu	37	1	55224131	55224131	+	Missense_Mutation	SNP	T	T	C	rs2270004	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55224131T>C	ENST00000371279.3	-	2	786	c.704A>G	c.(703-705)aAc>aGc	p.N235S		NM_152268.3	NP_689481.2	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase 2, mitochondrial (putative)	235			N -> S (in dbSNP:rs2270004).		gene expression (GO:0010467)|prolyl-tRNA aminoacylation (GO:0006433)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|proline-tRNA ligase activity (GO:0004827)			breast(1)|endometrium(3)|kidney(2)|lung(4)|ovary(2)|prostate(2)|skin(1)	15					L-Proline(DB00172)	CCCTAGCTTGTTGAACAGGCT	0.552													T|||	798	0.159345	0.1596	0.1398	5008	,	,		19571	0.1756		0.1471	False		,,,				2504	0.1687				p.N235S		Atlas-SNP	.											.	PARS2	29	.	0			c.A704G						PASS	.	T	SER/ASN	622,3784	267.7+/-268.0	50,522,1631	45.0	43.0	44.0		704	-2.1	0.0	1	dbSNP_100	44	1241,7359	248.5+/-276.1	99,1043,3158	yes	missense	PARS2	NM_152268.3	46	149,1565,4789	CC,CT,TT		14.4302,14.1171,14.3242	benign	235/476	55224131	1863,11143	2203	4300	6503	SO:0001583	missense	25973	exon2			AGCTTGTTGAACA	AK025585	CCDS597.1	1p32.2	2011-07-01	2007-02-23		ENSG00000162396	ENSG00000162396	6.1.1.15	"""Aminoacyl tRNA synthetases / Class II"""	30563	protein-coding gene	gene with protein product	"""proline tRNA ligase 2, mitochondrial (putative)"""	612036				15779907	Standard	NM_152268		Approved	DKFZp727A071	uc001cxy.3	Q7L3T8	OTTHUMG00000009915	ENST00000371279.3:c.704A>G	1.37:g.55224131T>C	ENSP00000360327:p.Asn235Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_152268	A8K0W4|Q9H6S5|Q9UFT1	Missense_Mutation	SNP	ENST00000371279.3	37	CCDS597.1	330	0.1510989010989011	86	0.17479674796747968	45	0.12430939226519337	93	0.16258741258741258	106	0.13984168865435356	T	0.017	-1.504196	0.00992	0.141171	0.144302	ENSG00000162396	ENST00000371279	T	0.66995	-0.24	5.34	-2.1	0.07210	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	1.437100	0.03888	N	0.278172	T	0.00144	0.0004	N	0.12527	0.23	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.03231	-1.1058	9	0.06625	T	0.88	-0.019	6.5773	0.22573	0.0:0.303:0.2151:0.4819	rs2270004;rs2270004	235	Q7L3T8	SYPM_HUMAN	S	235	ENSP00000360327:N235S	ENSP00000360327:N235S	N	-	2	0	PARS2	54996719	0.022000	0.18835	0.011000	0.14972	0.006000	0.05464	0.203000	0.17315	-0.521000	0.06426	0.533000	0.62120	AAC	T|0.852;C|0.148	0.148	strong		0.552	PARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027436.1	NM_152268	
SSPO	23145	hgsc.bcm.edu	37	7	149483237	149483237	+	RNA	SNP	G	G	A	rs77510079	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149483237G>A	ENST00000378016.2	+	0	3305							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ACAGGCCCTGGGCTGAGCCTG	0.652													G|||	318	0.0634984	0.0076	0.0764	5008	,	,		15471	0.0933		0.0954	False		,,,				2504	0.0665				p.G1102E		Atlas-SNP	.											.	.	.	.	0			c.G3305A						PASS	.	G		79,4153		1,77,2038	36.0	43.0	41.0		3309	4.9	1.0	7	dbSNP_131	41	799,7663		46,707,3478	yes	coding-notMod3	SSPO	NM_198455.2		47,784,5516	AA,AG,GG		9.4422,1.8667,6.9167			149483237	878,11816	2116	4231	6347			23145	exon23			GCCCTGGGCTGAG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149483237G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.917;A|0.083	0.083	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
PTCHD3	374308	hgsc.bcm.edu	37	10	27687994	27687994	+	Silent	SNP	A	A	G	rs2484173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:27687994A>G	ENST00000438700.3	-	4	1650	c.1533T>C	c.(1531-1533)tcT>tcC	p.S511S		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	511	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						AACATTGTACAGACCTAAAAG	0.383													G|||	2755	0.55012	0.5257	0.5202	5008	,	,		17506	0.37		0.6829	False		,,,				2504	0.6534				p.S511S		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T1533C						PASS	.	G		2357,2049	565.7+/-381.7	623,1111,469	95.0	88.0	90.0		1533	-3.4	0.0	10	dbSNP_100	90	5857,2743	430.2+/-356.4	2005,1847,448	no	coding-synonymous	PTCHD3	NM_001034842.3		2628,2958,917	GG,GA,AA		31.8953,46.5048,36.8445		511/768	27687994	8214,4792	2203	4300	6503	SO:0001819	synonymous_variant	374308	exon4			TTGTACAGACCTA	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1533T>C	10.37:g.27687994A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	148	69	0.466216	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			A|0.406;G|0.594	0.594	strong		0.383	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
PARS2	25973	hgsc.bcm.edu	37	1	55224751	55224751	+	Missense_Mutation	SNP	C	C	A	rs11577368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55224751C>A	ENST00000371279.3	-	2	166	c.84G>T	c.(82-84)agG>agT	p.R28S		NM_152268.3	NP_689481.2	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase 2, mitochondrial (putative)	28			R -> S (in dbSNP:rs11577368).		gene expression (GO:0010467)|prolyl-tRNA aminoacylation (GO:0006433)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|proline-tRNA ligase activity (GO:0004827)			breast(1)|endometrium(3)|kidney(2)|lung(4)|ovary(2)|prostate(2)|skin(1)	15					L-Proline(DB00172)	AGTGGTGAAACCTGCAAGGAA	0.632													C|||	652	0.130192	0.0552	0.1297	5008	,	,		16827	0.1756		0.1471	False		,,,				2504	0.1677				p.R28S		Atlas-SNP	.											.	PARS2	29	.	0			c.G84T						PASS	.	C	SER/ARG	286,4120	146.9+/-181.5	12,262,1929	30.0	29.0	30.0		84	1.7	0.4	1	dbSNP_120	30	1229,7371	234.2+/-267.2	96,1037,3167	yes	missense	PARS2	NM_152268.3	110	108,1299,5096	AA,AC,CC		14.2907,6.4911,11.6485	benign	28/476	55224751	1515,11491	2203	4300	6503	SO:0001583	missense	25973	exon2			GTGAAACCTGCAA	AK025585	CCDS597.1	1p32.2	2011-07-01	2007-02-23		ENSG00000162396	ENSG00000162396	6.1.1.15	"""Aminoacyl tRNA synthetases / Class II"""	30563	protein-coding gene	gene with protein product	"""proline tRNA ligase 2, mitochondrial (putative)"""	612036				15779907	Standard	NM_152268		Approved	DKFZp727A071	uc001cxy.3	Q7L3T8	OTTHUMG00000009915	ENST00000371279.3:c.84G>T	1.37:g.55224751C>A	ENSP00000360327:p.Arg28Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_152268	A8K0W4|Q9H6S5|Q9UFT1	Missense_Mutation	SNP	ENST00000371279.3	37	CCDS597.1	274	0.12545787545787546	32	0.06504065040650407	43	0.11878453038674033	93	0.16258741258741258	106	0.13984168865435356	C	5.210	0.224267	0.09863	0.064911	0.142907	ENSG00000162396	ENST00000371279	T	0.43294	0.95	4.73	1.67	0.24075	.	0.459205	0.23293	N	0.049765	T	0.00109	0.0003	L	0.48362	1.52	0.80722	P	0.0	B	0.30482	0.281	B	0.25405	0.06	T	0.05971	-1.0853	9	0.66056	D	0.02	-15.8921	5.7474	0.18128	0.0:0.6119:0.1368:0.2514	rs11577368;rs52832291;rs11577368	28	Q7L3T8	SYPM_HUMAN	S	28	ENSP00000360327:R28S	ENSP00000360327:R28S	R	-	3	2	PARS2	54997339	0.000000	0.05858	0.366000	0.25914	0.172000	0.22775	-0.280000	0.08468	0.563000	0.29222	0.579000	0.79373	AGG	C|0.879;A|0.121	0.121	strong		0.632	PARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027436.1	NM_152268	
FAM120A	23196	hgsc.bcm.edu	37	9	96238578	96238578	+	Silent	SNP	C	C	T	rs10821135	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:96238578C>T	ENST00000277165.6	+	3	956	c.762C>T	c.(760-762)caC>caT	p.H254H	FAM120A_ENST00000340893.4_Silent_p.H254H|FAM120A_ENST00000333936.5_Silent_p.H254H|FAM120A_ENST00000375389.3_Silent_p.H254H	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	254						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.H254H(1)		endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CTTCCTTTCACTGGAGTTTAC	0.348													T|||	2627	0.524561	0.6838	0.5591	5008	,	,		19963	0.5972		0.498	False		,,,				2504	0.2372				p.H254H		Atlas-SNP	.											FAM120A,NS,carcinoma,+2,2	FAM120A	105	2	1	Substitution - coding silent(1)	stomach(1)	c.C762T						PASS	.	T		2905,1501	478.8+/-358.3	955,995,253	138.0	125.0	129.0		762	-1.4	1.0	9	dbSNP_120	129	4248,4352	581.2+/-391.2	1041,2166,1093	no	coding-synonymous	FAM120A	NM_014612.3		1996,3161,1346	TT,TC,CC		49.3953,34.0672,45.0023		254/1119	96238578	7153,5853	2203	4300	6503	SO:0001819	synonymous_variant	23196	exon3			CTTTCACTGGAGT	AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"""DNA polymerase-transactivated protein 1"", ""oxidative stess-associated Src activator"""	612265	"""chromosome 9 open reading frame 10"""	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.762C>T	9.37:g.96238578C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Silent	SNP	ENST00000277165.6	37	CCDS6706.1	1279	0.5856227106227107	330	0.6707317073170732	212	0.585635359116022	357	0.6241258741258742	380	0.5013192612137203	T	9.458	1.092407	0.20471	0.659328	0.493953	ENSG00000048828	ENST00000446420	.	.	.	5.52	-1.38	0.09027	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39881	-0.9592	3	.	.	.	-15.061	11.9011	0.52685	0.0:0.4902:0.0:0.5098	rs10821135;rs57788214;rs10821135	.	.	.	I	97	.	.	T	+	2	0	FAM120A	95278399	1.000000	0.71417	0.968000	0.41197	0.993000	0.82548	1.012000	0.29924	-0.707000	0.05022	-0.360000	0.07572	ACT	C|0.447;T|0.553	0.553	strong		0.348	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612	
MIPEP	4285	hgsc.bcm.edu	37	13	24436475	24436475	+	Missense_Mutation	SNP	C	C	T	rs11551114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:24436475C>T	ENST00000382172.3	-	9	1117	c.1019G>A	c.(1018-1020)cGa>cAa	p.R340Q		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	340			R -> Q (in dbSNP:rs11551114).		protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		TTTCATCCCTCGTATCATCTC	0.279													C|||	328	0.0654952	0.0582	0.072	5008	,	,		18310	0.001		0.1312	False		,,,				2504	0.0695				p.R340Q		Atlas-SNP	.											MIPEP,colon,carcinoma,-1,1	MIPEP	53	1	0			c.G1019A						PASS	.	C	GLN/ARG	272,4120		10,252,1934	50.0	47.0	48.0		1019	1.5	0.0	13	dbSNP_120	48	1126,7454		73,980,3237	yes	missense	MIPEP	NM_005932.3	43	83,1232,5171	TT,TC,CC		13.1235,6.1931,10.7771	benign	340/714	24436475	1398,11574	2196	4290	6486	SO:0001583	missense	4285	exon9			ATCCCTCGTATCA		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1019G>A	13.37:g.24436475C>T	ENSP00000371607:p.Arg340Gln	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	154	56	0.363636	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	147	0.0673076923076923	32	0.06504065040650407	19	0.052486187845303865	1	0.0017482517482517483	95	0.12532981530343007	C	6.085	0.383896	0.11524	0.061931	0.131235	ENSG00000027001	ENST00000382172	T	0.07114	3.22	4.79	1.51	0.23008	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.374324	0.28583	N	0.014834	T	0.00073	0.0002	L	0.31664	0.95	0.80722	P	0.0	B	0.19200	0.034	B	0.13407	0.009	T	0.38045	-0.9679	9	0.27785	T	0.31	.	4.5291	0.11995	0.0:0.3188:0.2723:0.4089	rs11551114;rs17424158;rs56587494;rs11551114	340	Q99797	MIPEP_HUMAN	Q	340	ENSP00000371607:R340Q	ENSP00000371607:R340Q	R	-	2	0	MIPEP	23334475	0.010000	0.17322	0.028000	0.17463	0.696000	0.40369	0.276000	0.18716	0.473000	0.27368	-0.150000	0.13652	CGA	C|0.909;T|0.091	0.091	strong		0.279	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
EFCAB7	84455	hgsc.bcm.edu	37	1	63999868	63999868	+	Missense_Mutation	SNP	T	T	C	rs6657480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:63999868T>C	ENST00000371088.4	+	6	1031	c.785T>C	c.(784-786)aTg>aCg	p.M262T	RNU7-123P_ENST00000515911.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	262			M -> T (in dbSNP:rs6657480). {ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						TCAAAGTTAATGGAGCCAAAT	0.343													C|||	1440	0.28754	0.5825	0.196	5008	,	,		15429	0.1925		0.1491	False		,,,				2504	0.1943				p.M262T		Atlas-SNP	.											.	EFCAB7	45	.	0			c.T785C						PASS	.	C	THR/MET	2103,2303	597.0+/-388.8	514,1075,614	64.0	65.0	65.0		785	2.3	1.0	1	dbSNP_116	65	1344,7256	754.1+/-407.5	94,1156,3050	yes	missense	EFCAB7	NM_032437.2	81	608,2231,3664	CC,CT,TT		15.6279,47.7304,26.5032	benign	262/630	63999868	3447,9559	2203	4300	6503	SO:0001583	missense	84455	exon6			AGTTAATGGAGCC	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.785T>C	1.37:g.63999868T>C	ENSP00000360129:p.Met262Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	561	0.25686813186813184	267	0.5426829268292683	74	0.20441988950276244	110	0.19230769230769232	110	0.14511873350923482	C	0.003	-2.489623	0.00161	0.477304	0.156279	ENSG00000203965	ENST00000371088	T	0.55588	0.51	5.65	2.32	0.28847	.	0.671131	0.16090	N	0.230086	T	0.04363	0.0120	N	0.00538	-1.39	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35276	-0.9795	9	0.08381	T	0.77	-6.203	4.47	0.11708	0.1582:0.5267:0.0:0.3151	rs6657480;rs17845480;rs17858360;rs52835496;rs60937630;rs6657480	262	A8K855	EFCB7_HUMAN	T	262	ENSP00000360129:M262T	ENSP00000360129:M262T	M	+	2	0	EFCAB7	63772456	0.083000	0.21467	0.980000	0.43619	0.037000	0.13140	0.268000	0.18571	0.346000	0.23899	-0.767000	0.03436	ATG	T|0.741;C|0.259	0.259	strong		0.343	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
DISP2	85455	hgsc.bcm.edu	37	15	40660043	40660043	+	Missense_Mutation	SNP	G	G	T	rs76331864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40660043G>T	ENST00000267889.3	+	8	1817	c.1730G>T	c.(1729-1731)gGg>gTg	p.G577V	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	577	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		CCGTCGGGGGGGCTGGCGCAG	0.667													G|||	93	0.0185703	0.0469	0.0144	5008	,	,		13554	0.002		0.0159	False		,,,				2504	0.0031				p.G577V		Atlas-SNP	.											.	DISP2	86	.	0			c.G1730T						PASS	.	G	VAL/GLY	178,4228	105.2+/-143.6	4,170,2029	23.0	23.0	23.0		1730	4.7	1.0	15	dbSNP_131	23	113,8487	52.7+/-113.3	1,111,4188	yes	missense	DISP2	NM_033510.1	109	5,281,6217	TT,TG,GG		1.314,4.0399,2.2374	benign	577/1402	40660043	291,12715	2203	4300	6503	SO:0001583	missense	85455	exon8			CGGGGGGGCTGGC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.1730G>T	15.37:g.40660043G>T	ENSP00000267889:p.Gly577Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	46	0.021062271062271064	27	0.054878048780487805	10	0.027624309392265192	0	0.0	9	0.011873350923482849	G	13.16	2.155343	0.38021	0.040399	0.01314	ENSG00000140323	ENST00000267889	D	0.95377	-3.69	5.58	4.66	0.58398	Sterol-sensing domain (1);	0.166012	0.53938	D	0.000060	T	0.75882	0.3910	L	0.48362	1.52	0.80722	D	1	P	0.45715	0.865	B	0.42555	0.391	T	0.81671	-0.0827	10	0.31617	T	0.26	-15.0114	14.6339	0.68676	0.0703:0.0:0.9297:0.0	.	577	A7MBM2	DISP2_HUMAN	V	577	ENSP00000267889:G577V	ENSP00000267889:G577V	G	+	2	0	DISP2	38447335	1.000000	0.71417	0.998000	0.56505	0.741000	0.42261	5.783000	0.68982	1.357000	0.45904	0.561000	0.74099	GGG	G|0.977;T|0.023	0.023	strong		0.667	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
VNN2	8875	hgsc.bcm.edu	37	6	133072650	133072650	+	Silent	SNP	A	A	G	rs1883617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:133072650A>G	ENST00000326499.6	-	5	958	c.834T>C	c.(832-834)ggT>ggC	p.G278G	VNN2_ENST00000525289.1_Intron|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000526192.1_5'Flank|VNN2_ENST00000525270.1_Silent_p.G225G	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	278	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		GTGCATAAATACCACTTCCTG	0.418													A|||	1578	0.315096	0.2632	0.4366	5008	,	,		18906	0.2272		0.34	False		,,,				2504	0.364				p.G278G		Atlas-SNP	.											.	VNN2	83	.	0			c.T834C						PASS	.	A	,,	1209,3113		163,883,1115	50.0	52.0	51.0		,834,675	-4.5	1.0	6	dbSNP_92	51	2718,5570		433,1852,1859	no	intron,coding-synonymous,coding-synonymous	VNN2	NM_001242350.1,NM_004665.2,NM_078488.1	,,	596,2735,2974	GG,GA,AA		32.7944,27.9732,31.142	,,	,278/521,225/468	133072650	3927,8683	2161	4144	6305	SO:0001819	synonymous_variant	8875	exon5			ATAAATACCACTT	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"""Vanins"""	12706	protein-coding gene	gene with protein product	"""pantetheinase"""	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.834T>C	6.37:g.133072650A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																			A|0.682;G|0.318	0.318	strong		0.418	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2		
C4orf33	132321	hgsc.bcm.edu	37	4	130032843	130032843	+	Missense_Mutation	SNP	A	A	G	rs17351999	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:130032843A>G	ENST00000281146.5	+	6	1218	c.497A>G	c.(496-498)cAt>cGt	p.H166R	C4orf33_ENST00000425929.1_Missense_Mutation_p.H166R	NM_173487.2	NP_775758.2	Q8N1A6	CD033_HUMAN	chromosome 4 open reading frame 33	166			H -> R (in dbSNP:rs17351999). {ECO:0000269|PubMed:14702039}.							endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	10						GCTTTTAGCCATTGCCTAGAA	0.353													A|||	483	0.0964457	0.0083	0.1311	5008	,	,		16238	0.0655		0.161	False		,,,				2504	0.1564				p.H166R		Atlas-SNP	.											C4orf33,NS,carcinoma,+1,1	C4orf33	15	1	0			c.A497G						PASS	.	A	ARG/HIS,ARG/HIS	152,4254	105.6+/-144.1	6,140,2057	111.0	105.0	107.0		497,497	5.8	1.0	4	dbSNP_123	107	1299,7301	254.3+/-279.6	120,1059,3121	yes	missense,missense	C4orf33	NM_001099783.1,NM_173487.2	29,29	126,1199,5178	GG,GA,AA		15.1047,3.4498,11.1564	probably-damaging,probably-damaging	166/200,166/200	130032843	1451,11555	2203	4300	6503	SO:0001583	missense	132321	exon6			TTAGCCATTGCCT	AK091022	CCDS3741.1	4q28.2	2008-02-05			ENSG00000151470	ENSG00000151470			27025	protein-coding gene	gene with protein product						12477932	Standard	NM_001099783		Approved	FLJ33703	uc010iod.3	Q8N1A6	OTTHUMG00000133347	ENST00000281146.5:c.497A>G	4.37:g.130032843A>G	ENSP00000281146:p.His166Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	132	75	0.568182	NM_001099783	D3DNY2|Q6PJF3|Q8NBC5	Missense_Mutation	SNP	ENST00000281146.5	37	CCDS3741.1	222	0.10164835164835165	6	0.012195121951219513	54	0.14917127071823205	46	0.08041958041958042	116	0.15303430079155672	A	20.2	3.955322	0.73902	0.034498	0.151047	ENSG00000151470	ENST00000281146;ENST00000425929	T;T	0.47528	0.84;0.84	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.00936	0.0031	M	0.86651	2.83	0.09310	P	0.99999999004049	D	0.89917	1.0	D	0.85130	0.997	T	0.30119	-0.9989	9	0.66056	D	0.02	-20.028	15.0534	0.71894	1.0:0.0:0.0:0.0	rs17351999;rs52811016;rs17351999	166	Q8N1A6	CD033_HUMAN	R	166	ENSP00000281146:H166R;ENSP00000401090:H166R	ENSP00000281146:H166R	H	+	2	0	C4orf33	130252293	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	8.045000	0.89436	2.198000	0.70561	0.528000	0.53228	CAT	A|0.892;G|0.108	0.108	strong		0.353	C4orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257177.2	NM_173487	
KRT5	3852	hgsc.bcm.edu	37	12	52912870	52912870	+	Silent	SNP	A	A	G	rs17852231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52912870A>G	ENST00000252242.4	-	2	1020	c.630T>C	c.(628-630)acT>acC	p.T210T		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	210	Linker 1.|Rod.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTGCCTCACAGTCTTGGTGC	0.602													G|||	641	0.127995	0.177	0.1859	5008	,	,		19370	0.0377		0.1481	False		,,,				2504	0.093				p.T210T		Atlas-SNP	.											.	KRT5	88	.	0			c.T630C						PASS	.	G		764,3642	749.7+/-412.0	59,646,1498	78.0	73.0	74.0		630	-3.6	0.1	12	dbSNP_123	74	1208,7382	761.6+/-407.6	86,1036,3173	no	coding-synonymous	KRT5	NM_000424.3		145,1682,4671	GG,GA,AA		14.0629,17.34,15.1739		210/591	52912870	1972,11024	2203	4295	6498	SO:0001819	synonymous_variant	3852	exon2			CCTCACAGTCTTG		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.630T>C	12.37:g.52912870A>G		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	223	97	0.434978	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	37	CCDS8830.1	284	0.13003663003663005	98	0.1991869918699187	59	0.16298342541436464	19	0.033216783216783216	108	0.1424802110817942	G	7.552	0.662992	0.14710	0.1734	0.140629	ENSG00000186081	ENST00000551188	.	.	.	5.31	-3.61	0.04556	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.23607	P	0.9973097	.	.	.	.	.	.	T	0.21586	-1.0241	3	.	.	.	.	5.9526	0.19255	0.4788:0.0:0.236:0.2852	rs17852231;rs17854192	.	.	.	P	11	.	.	L	-	2	0	KRT5	51199137	0.000000	0.05858	0.085000	0.20634	0.872000	0.50106	-1.619000	0.02048	-1.464000	0.01902	-1.617000	0.00794	CTG	A|0.861;G|0.139	0.139	strong		0.602	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
FERMT1	55612	hgsc.bcm.edu	37	20	6065729	6065729	+	Missense_Mutation	SNP	C	C	T	rs386812146|rs2232074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:6065729C>T	ENST00000217289.4	-	12	2365	c.1577G>A	c.(1576-1578)aGa>aAa	p.R526K	FERMT1_ENST00000536936.1_Missense_Mutation_p.R269K|FERMT1_ENST00000478194.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	526	FERM.		R -> K (in dbSNP:rs2232074). {ECO:0000269|PubMed:12697302, ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						GGATTTGTGTCTTTTTGCACA	0.418													t|||	2289	0.457069	0.4554	0.4784	5008	,	,		25132	0.6409		0.3797	False		,,,				2504	0.3344				p.R526K		Atlas-SNP	.											.	FERMT1	106	.	0			c.G1577A						PASS	.		LYS/ARG	371,4035		119,133,1951	120.0	108.0	112.0		1577	5.2	0.9	20	dbSNP_98	112	444,8156		135,174,3991	yes	missense	FERMT1	NM_017671.4	26	254,307,5942	TT,TC,CC		5.1628,8.4203,6.2663	benign	526/678	6065729	815,12191	2203	4300	6503	SO:0001583	missense	55612	exon12			TTGTGTCTTTTTG	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1577G>A	20.37:g.6065729C>T	ENSP00000217289:p.Arg526Lys	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	254	118	0.464567	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	37	CCDS13098.1	1038	0.47527472527472525	209	0.4247967479674797	169	0.46685082872928174	384	0.6713286713286714	276	0.3641160949868074	t	6.035	0.374774	0.11409	0.084203	0.051628	ENSG00000101311	ENST00000217289;ENST00000536936;ENST00000339538	T;T	0.74106	-0.81;-0.81	5.17	5.17	0.71159	Band 4.1 domain (1);FERM central domain (2);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00026	-2.67	0.34421	P	0.302492	B	0.02656	0.0	B	0.01281	0.0	T	0.47058	-0.9146	9	0.02654	T	1	-18.718	11.2802	0.49190	0.0:0.072:0.0:0.928	rs2232074;rs3818185;rs13036394	526	Q9BQL6	FERM1_HUMAN	K	526;269;526	ENSP00000217289:R526K;ENSP00000441063:R269K	ENSP00000217289:R526K	R	-	2	0	FERMT1	6013729	1.000000	0.71417	0.946000	0.38457	0.516000	0.34256	6.256000	0.72473	0.905000	0.36596	-0.376000	0.06991	AGA	C|0.581;T|0.419	0.419	strong		0.418	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
APOB	338	hgsc.bcm.edu	37	2	21232804	21232804	+	Silent	SNP	G	G	A	rs386643884|rs1041968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:21232804G>A	ENST00000233242.1	-	26	7063	c.6936C>T	c.(6934-6936)gaC>gaT	p.D2312D		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2312					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTCAAGAATGTCATTTATTC	0.348													G|||	1248	0.249201	0.2095	0.3775	5008	,	,		20035	0.0615		0.4423	False		,,,				2504	0.2065				p.D2312D		Atlas-SNP	.											APOB,NS,malignant_melanoma,-2,1	APOB	761	1	0			c.C6936T						PASS	.	G		1032,3374		139,754,1310	116.0	119.0	118.0		6936	-2.2	0.0	2	dbSNP_86	118	4118,4482		1092,1934,1274	no	coding-synonymous	APOB	NM_000384.2		1231,2688,2584	AA,AG,GG		47.8837,23.4226,39.5971		2312/4564	21232804	5150,7856	2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			AAGAATGTCATTT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.6936C>T	2.37:g.21232804G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	179	83	0.463687	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			G|0.640;A|0.360	0.360	strong		0.348	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
AKR7A2	8574	hgsc.bcm.edu	37	1	19635011	19635011	+	Missense_Mutation	SNP	C	C	T	rs1043657	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19635011C>T	ENST00000235835.3	-	2	445	c.424G>A	c.(424-426)Gca>Aca	p.A142T		NM_003689.3	NP_003680.2	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	142			A -> T (in dbSNP:rs1043657). {ECO:0000269|PubMed:18752886, ECO:0000269|PubMed:9576847}.		carbohydrate metabolic process (GO:0005975)|cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|phenanthrene-9,10-epoxide hydrolase activity (GO:0019119)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTCAGGTGCGTGTAGGTAG	0.617													C|||	188	0.0375399	0.0257	0.0605	5008	,	,		18086	0.003		0.0974	False		,,,				2504	0.0112				p.A142T		Atlas-SNP	.											.	AKR7A2	19	.	0			c.G424A						PASS	.	C	THR/ALA	136,4270	97.6+/-136.3	4,128,2071	78.0	77.0	77.0		424	0.9	0.0	1	dbSNP_86	77	806,7794	188.3+/-235.3	41,724,3535	yes	missense	AKR7A2	NM_003689.2	58	45,852,5606	TT,TC,CC		9.3721,3.0867,7.2428	possibly-damaging	142/360	19635011	942,12064	2203	4300	6503	SO:0001583	missense	8574	exon2			CAGGTGCGTGTAG	AF026947	CCDS194.1	1p36.13	2010-09-30			ENSG00000053371	ENSG00000053371		"""Aldo-keto reductases"""	389	protein-coding gene	gene with protein product		603418				9576847	Standard	NM_003689		Approved	AFAR	uc001bbw.3	O43488	OTTHUMG00000002522	ENST00000235835.3:c.424G>A	1.37:g.19635011C>T	ENSP00000235835:p.Ala142Thr	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	190	187	0.984211	NM_003689	O75749|Q5TG63	Missense_Mutation	SNP	ENST00000235835.3	37	CCDS194.1	108	0.04945054945054945	9	0.018292682926829267	26	0.0718232044198895	0	0.0	73	0.09630606860158311	C	10.15	1.272395	0.23221	0.030867	0.093721	ENSG00000053371	ENST00000235835;ENST00000330072	T;T	0.04275	3.66;3.66	4.09	0.911	0.19343	NADP-dependent oxidoreductase domain (3);	0.220555	0.46442	D	0.000292	T	0.00356	0.0011	M	0.66297	2.02	0.58432	P	5.000000000032756E-6	D;D;D	0.76494	0.998;0.999;0.998	D;D;P	0.67548	0.936;0.952;0.907	T	0.04115	-1.0976	9	0.66056	D	0.02	.	5.664	0.17684	0.1571:0.6414:0.0:0.2014	rs1043657;rs1043657	113;113;142	C9JSL3;B4DZX4;O43488	.;.;ARK72_HUMAN	T	142;132	ENSP00000235835:A142T;ENSP00000339084:A132T	ENSP00000235835:A142T	A	-	1	0	AKR7A2	19507598	0.850000	0.29656	0.001000	0.08648	0.040000	0.13550	2.267000	0.43329	0.384000	0.24942	-0.367000	0.07326	GCA	C|0.938;T|0.062	0.062	strong		0.617	AKR7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007165.2	NM_003689	
IFT57	55081	hgsc.bcm.edu	37	3	107937408	107937408	+	Silent	SNP	C	C	T	rs1135897	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:107937408C>T	ENST00000264538.3	-	3	715	c.468G>A	c.(466-468)ttG>ttA	p.L156L		NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	156					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			CAATATATTTCAATGCTTCTT	0.378													C|||	445	0.0888578	0.0658	0.0821	5008	,	,		16775	0.1052		0.1064	False		,,,				2504	0.09				p.L156L		Atlas-SNP	.											.	IFT57	44	.	0			c.G468A						PASS	.	C		291,4115	155.5+/-188.7	9,273,1921	83.0	84.0	84.0		468	2.5	1.0	3	dbSNP_86	84	905,7693	198.3+/-242.7	59,787,3453	no	coding-synonymous	IFT57	NM_018010.3		68,1060,5374	TT,TC,CC		10.5257,6.6046,9.1972		156/430	107937408	1196,11808	2203	4299	6502	SO:0001819	synonymous_variant	55081	exon3			ATATTTCAATGCT	AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"""Intraflagellar transport homologs"""	17367	protein-coding gene	gene with protein product		606621	"""estrogen-related receptor beta like 1"", ""intraflagellar transport 57 homolog (Chlamydomonas)"""	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.468G>A	3.37:g.107937408C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_018010	Q96DA9	Silent	SNP	ENST00000264538.3	37	CCDS2951.1																																																																																			C|0.914;T|0.086	0.086	strong		0.378	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010	
MYH9	4627	hgsc.bcm.edu	37	22	36684354	36684354	+	Missense_Mutation	SNP	T	T	C	rs2269529	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:36684354T>C	ENST00000216181.5	-	34	5106	c.4876A>G	c.(4876-4878)Atc>Gtc	p.I1626V	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1626			I -> V (in dbSNP:rs2269529). {ECO:0000269|PubMed:11776386}.		actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GCCGAGTCGATGTGCGCCTCC	0.652			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				.|||	1473	0.294129	0.0431	0.2118	5008	,	,		16121	0.5952		0.2078	False		,,,				2504	0.4703				p.I1626V		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.A4876G						PASS	.	T	VAL/ILE	319,4087	168.0+/-198.9	12,295,1896	125.0	101.0	109.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4876	4.5	0.9	22	dbSNP_100	109	1704,6896	311.4+/-310.3	194,1316,2790	yes	missense	MYH9	NM_002473.4	29	206,1611,4686	CC,CT,TT		19.814,7.2401,15.5544	benign	1626/1961	36684354	2023,10983	2203	4300	6503	SO:0001583	missense	4627	exon34	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	AGTCGATGTGCGC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4876A>G	22.37:g.36684354T>C	ENSP00000216181:p.Ile1626Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	621	0.28434065934065933	42	0.08536585365853659	78	0.2154696132596685	354	0.6188811188811189	147	0.19393139841688653	T	5.367	0.252980	0.10185	0.072401	0.19814	ENSG00000100345	ENST00000337818;ENST00000397231;ENST00000216181	T	0.76839	-1.05	5.5	4.47	0.54385	Myosin tail (1);	0.051153	0.85682	N	0.000000	T	0.00012	0.0000	N	0.21240	0.645	0.09310	P	1.0	B	0.20164	0.042	B	0.22753	0.041	T	0.47497	-0.9113	9	0.59425	D	0.04	.	11.6753	0.51425	0.0:0.0696:0.0:0.9304	rs2269529;rs56717084;rs2269529	1626	P35579	MYH9_HUMAN	V	1048;228;1626	ENSP00000216181:I1626V	ENSP00000216181:I1626V	I	-	1	0	MYH9	35014300	1.000000	0.71417	0.914000	0.36105	0.254000	0.26022	4.186000	0.58337	1.013000	0.39391	0.533000	0.62120	ATC	T|0.784;C|0.216	0.216	strong		0.652	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
COBLL1	22837	hgsc.bcm.edu	37	2	165578602	165578602	+	Missense_Mutation	SNP	C	C	T	rs74459242	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:165578602C>T	ENST00000392717.2	-	7	1097	c.1093G>A	c.(1093-1095)Gtg>Atg	p.V365M	COBLL1_ENST00000375458.2_Missense_Mutation_p.V327M|COBLL1_ENST00000342193.4_Missense_Mutation_p.V327M|COBLL1_ENST00000194871.6_Missense_Mutation_p.V393M|COBLL1_ENST00000491126.2_Intron|COBLL1_ENST00000409184.3_Missense_Mutation_p.V365M			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	365						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						GTCTCATCCACGCTCATGGAT	0.458													C|||	63	0.0125799	0.0023	0.0202	5008	,	,		16844	0.0		0.0368	False		,,,				2504	0.0092				p.V327M		Atlas-SNP	.											.	COBLL1	122	.	0			c.G979A						PASS	.	C	MET/VAL	34,4372	40.0+/-72.8	0,34,2169	77.0	83.0	81.0		979	1.4	0.5	2	dbSNP_132	81	421,8179	130.5+/-188.4	13,395,3892	yes	missense	COBLL1	NM_014900.3	21	13,429,6061	TT,TC,CC		4.8953,0.7717,3.4984	probably-damaging	327/1167	165578602	455,12551	2203	4300	6503	SO:0001583	missense	22837	exon6			CATCCACGCTCAT	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1093G>A	2.37:g.165578602C>T	ENSP00000376478:p.Val365Met	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		41	0.018772893772893772	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	29	0.03825857519788918	C	12.89	2.073757	0.36566	0.007717	0.048953	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	D	0.93076	-3.16	6.17	1.37	0.22104	Cordon-bleu domain (1);	0.602245	0.17823	N	0.160815	T	0.75428	0.3848	L	0.47716	1.5	0.21553	N	0.999649	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.982;0.982;0.968	T	0.76080	-0.3090	10	0.52906	T	0.07	-0.5122	2.5206	0.04679	0.1029:0.3543:0.2961:0.2466	.	365;393;365	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	M	327;327;365;365;393	ENSP00000194871:V393M	ENSP00000194871:V393M	V	-	1	0	COBLL1	165286848	0.099000	0.21834	0.503000	0.27626	0.406000	0.30931	0.134000	0.15932	0.180000	0.19960	0.655000	0.94253	GTG	C|0.971;T|0.029	0.029	strong		0.458	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
CD200R1L	344807	hgsc.bcm.edu	37	3	112546473	112546473	+	Silent	SNP	G	G	A	rs1997281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:112546473G>A	ENST00000398214.1	-	3	396	c.171C>T	c.(169-171)atC>atT	p.I57I	CD200R1L_ENST00000488794.1_Silent_p.I36I|CD200R1L_ENST00000448932.1_Silent_p.I36I	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	57	Ig-like V-type.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						TTCTTAATGCGATAGGAGGGC	0.388													G|||	1467	0.292931	0.093	0.3703	5008	,	,		19509	0.376		0.4026	False		,,,				2504	0.3098				p.I57I		Atlas-SNP	.											CD200R1L,colon,carcinoma,-2,1	CD200R1L	47	1	0			c.C171T						PASS	.	G	,	624,3782	267.1+/-267.6	36,552,1615	125.0	117.0	120.0		171,108	-2.2	0.0	3	dbSNP_92	120	3433,5167	503.2+/-375.9	695,2043,1562	no	coding-synonymous,coding-synonymous	CD200R1L	NM_001008784.2,NM_001199215.1	,	731,2595,3177	AA,AG,GG		39.9186,14.1625,31.1933	,	57/272,36/251	112546473	4057,8949	2203	4300	6503	SO:0001819	synonymous_variant	344807	exon3			TAATGCGATAGGA	AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"""Immunoglobulin superfamily / C2-set domain containing"""	24665	protein-coding gene	gene with protein product	"""CD200 receptor 2"""						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.171C>T	3.37:g.112546473G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	167	94	0.562874	NM_001008784	Q6WHB7	Silent	SNP	ENST00000398214.1	37	CCDS43131.1																																																																																			.	.	weak		0.388	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784	
CGN	57530	hgsc.bcm.edu	37	1	151502427	151502427	+	Missense_Mutation	SNP	C	C	T	rs34834099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151502427C>T	ENST00000271636.7	+	12	2282	c.2149C>T	c.(2149-2151)Cgg>Tgg	p.R717W	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	711	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCTGGGGCAGCGGCGGGCCGC	0.652													C|||	78	0.0155751	0.0008	0.0231	5008	,	,		18157	0.0		0.0537	False		,,,				2504	0.0072				p.R717W		Atlas-SNP	.											CGN,rectum,carcinoma,0,1	CGN	106	1	0			c.C2149T						PASS	.	C	TRP/ARG	51,4353		0,51,2151	28.0	35.0	32.0		2149	3.2	1.0	1	dbSNP_126	32	536,8062		19,498,3782	yes	missense	CGN	NM_020770.2	101	19,549,5933	TT,TC,CC		6.234,1.158,4.5147	probably-damaging	717/1204	151502427	587,12415	2202	4299	6501	SO:0001583	missense	57530	exon12			GGGCAGCGGCGGG	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.2149C>T	1.37:g.151502427C>T	ENSP00000271636:p.Arg717Trp	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	191	82	0.429319	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	54	0.024725274725274724	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	46	0.06068601583113457	C	15.44	2.834621	0.50951	0.01158	0.06234	ENSG00000143375	ENST00000271636	T	0.66280	-0.2	5.27	3.25	0.37280	.	0.472495	0.21879	N	0.067773	T	0.59810	0.2221	M	0.63428	1.95	0.33704	P	0.385058	D	0.89917	1.0	D	0.70016	0.967	T	0.64002	-0.6509	9	0.87932	D	0	-10.0013	3.549	0.07839	0.1774:0.561:0.1711:0.0904	rs34834099	711	Q9P2M7	CING_HUMAN	W	717	ENSP00000271636:R717W	ENSP00000271636:R717W	R	+	1	2	CGN	149769051	0.893000	0.30496	0.984000	0.44739	0.362000	0.29581	0.142000	0.16096	1.184000	0.42957	-0.309000	0.09137	CGG	C|0.964;T|0.036	0.036	strong		0.652	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
MYLK2	85366	hgsc.bcm.edu	37	20	30409452	30409452	+	Silent	SNP	T	T	C	rs6058469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:30409452T>C	ENST00000375994.2	+	3	957	c.684T>C	c.(682-684)atT>atC	p.I228I	MYLK2_ENST00000375985.4_Silent_p.I228I			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	228					cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CGAGGGGGATTGAGTTCCAGG	0.592													C|||	361	0.0720847	0.149	0.0836	5008	,	,		14415	0.001		0.0815	False		,,,				2504	0.0235				p.I228I		Atlas-SNP	.											.	MYLK2	76	.	0			c.T684C						PASS	.	C		622,3784	767.3+/-413.5	37,548,1618	96.0	105.0	102.0		684	0.4	0.7	20	dbSNP_114	102	690,7910	786.9+/-407.6	32,626,3642	no	coding-synonymous	MYLK2	NM_033118.3		69,1174,5260	CC,CT,TT		8.0233,14.1171,10.0877		228/597	30409452	1312,11694	2203	4300	6503	SO:0001819	synonymous_variant	85366	exon4			GGGGATTGAGTTC	AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"""skeletal muscle myosin light chain kinase"""	606566	"""myosin light chain kinase 2, skeletal muscle"""				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	ENST00000375994.2:c.684T>C	20.37:g.30409452T>C		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	181	72	0.39779	NM_033118	Q569L1|Q96I84	Silent	SNP	ENST00000375994.2	37	CCDS13191.1																																																																																			T|0.904;C|0.096	0.096	strong		0.592	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118	
OR13C5	138799	hgsc.bcm.edu	37	9	107360851	107360851	+	Missense_Mutation	SNP	T	T	C	rs1523678	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107360851T>C	ENST00000374779.2	-	1	937	c.844A>G	c.(844-846)Ata>Gta	p.I282V		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	282			I -> V (in dbSNP:rs1523678).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTGTAGAATATGAATATAAGT	0.393													T|||	2184	0.436102	0.6475	0.2277	5008	,	,		19814	0.5754		0.1789	False		,,,				2504	0.4192				p.I282V		Atlas-SNP	.											.	OR13C5	60	.	0			c.A844G						PASS	.	T	VAL/ILE	2577,1829	638.3+/-396.9	762,1053,388	123.0	118.0	120.0		844	-7.7	0.0	9	dbSNP_88	120	1669,6931	308.1+/-308.7	183,1303,2814	yes	missense	OR13C5	NM_001004482.1	29	945,2356,3202	CC,CT,TT		19.407,41.5116,32.6465	benign	282/319	107360851	4246,8760	2203	4300	6503	SO:0001583	missense	138799	exon1			AGAATATGAATAT		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.844A>G	9.37:g.107360851T>C	ENSP00000363911:p.Ile282Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	205	101	0.492683	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	839	0.3841575091575092	297	0.6036585365853658	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	T	6.399	0.441735	0.12164	0.584884	0.19407	ENSG00000255800	ENST00000374779	T	0.00019	9.06	3.85	-7.7	0.01259	GPCR, rhodopsin-like superfamily (1);	0.893919	0.09140	N	0.843087	T	0.00012	0.0000	N	0.00879	-1.12	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40421	-0.9564	9	0.51188	T	0.08	.	3.554	0.07857	0.3832:0.0767:0.4015:0.1386	rs1523678;rs52800382;rs58776918;rs1523678	282	Q8NGS8	O13C5_HUMAN	V	282	ENSP00000363911:I282V	ENSP00000363911:I282V	I	-	1	0	OR13C5	106400672	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-6.926000	0.00049	-2.857000	0.00329	0.347000	0.21830	ATA	T|0.634;C|0.366	0.366	strong		0.393	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
INMT	11185	hgsc.bcm.edu	37	7	30795436	30795436	+	Missense_Mutation	SNP	T	T	G	rs4720015	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:30795436T>G	ENST00000013222.5	+	3	777	c.761T>G	c.(760-762)tTc>tGc	p.F254C	INMT_ENST00000484180.1_3'UTR|INMT-FAM188B_ENST00000458257.1_Intron|INMT_ENST00000409539.1_Missense_Mutation_p.F253C	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	254			F -> C (in dbSNP:rs4720015). {ECO:0000269|PubMed:14702039}.		amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)			kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						GGGGTCTGCTTCATTGTGGCT	0.587													T|||	3872	0.773163	0.5514	0.8963	5008	,	,		20091	0.8423		0.8986	False		,,,				2504	0.7853				p.F254C		Atlas-SNP	.											.	INMT	38	.	0			c.T761G						PASS	.	T	CYS/PHE,CYS/PHE	2614,1792	640.4+/-397.3	772,1070,361	82.0	80.0	81.0		758,761	2.2	0.2	7	dbSNP_111	81	7608,992	773.2+/-407.7	3381,846,73	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	205,205	4153,1916,434	GG,GT,TT		11.5349,40.6718,21.4055	probably-damaging,probably-damaging	253/263,254/264	30795436	10222,2784	2203	4300	6503	SO:0001583	missense	11185	exon3			TCTGCTTCATTGT		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.761T>G	7.37:g.30795436T>G	ENSP00000013222:p.Phe254Cys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	1761	0.8063186813186813	288	0.5853658536585366	320	0.8839779005524862	471	0.8234265734265734	682	0.899736147757256	T	16.97	3.268417	0.59540	0.593282	0.884651	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.03951	3.75;3.75	3.41	2.22	0.28083	.	0.168140	0.38272	N	0.001743	T	0.00012	0.0000	M	0.82517	2.595	0.46096	P	0.0011330000000000506	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.11494	-1.0585	9	0.49607	T	0.09	-12.6164	5.9656	0.19322	0.2308:0.0:0.0:0.7692	rs4720015;rs10351225;rs61245095;rs4720015	253;254	B8ZZ69;O95050	.;INMT_HUMAN	C	254;253	ENSP00000013222:F254C;ENSP00000386961:F253C	ENSP00000013222:F254C	F	+	2	0	INMT	30761961	0.006000	0.16342	0.217000	0.23759	0.639000	0.38242	0.717000	0.25851	0.633000	0.30452	0.459000	0.35465	TTC	T|0.209;G|0.791	0.791	strong		0.587	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
EDNRA	1909	hgsc.bcm.edu	37	4	148461071	148461071	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:148461071G>A	ENST00000324300.5	+	6	1518	c.1003G>A	c.(1003-1005)Gag>Aag	p.E335K	EDNRA_ENST00000506066.1_Missense_Mutation_p.E226K|EDNRA_ENST00000358556.4_Missense_Mutation_p.E226K|EDNRA_ENST00000511804.1_Missense_Mutation_p.E110K|EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000503721.1_3'UTR	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	335					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGTGTATAACGAGATGGACAA	0.348																																					p.E335K		Atlas-SNP	.											EDNRA,NS,carcinoma,-1,2	EDNRA	48	2	0			c.G1003A						PASS	.						183.0	182.0	182.0					4																	148461071		2203	4300	6503	SO:0001583	missense	1909	exon6			TATAACGAGATGG	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"""GPCR / Class A : Endothelin receptors"""	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.1003G>A	4.37:g.148461071G>A	ENSP00000315011:p.Glu335Lys	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	174	30	0.172414	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Missense_Mutation	SNP	ENST00000324300.5	37	CCDS3769.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333880	0.81801	.	.	ENSG00000151617	ENST00000358556;ENST00000324300;ENST00000511804;ENST00000506066	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.44	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.197416	0.53938	D	0.000053	T	0.78246	0.4253	M	0.74258	2.255	0.80722	D	1	P;D	0.57899	0.951;0.981	B;P	0.51055	0.24;0.657	T	0.81680	-0.0823	10	0.59425	D	0.04	-18.8044	16.5127	0.84290	0.0:0.131:0.869:0.0	.	226;335	P25101-4;P25101	.;EDNRA_HUMAN	K	226;335;110;226	ENSP00000351359:E226K;ENSP00000315011:E335K;ENSP00000425354:E110K;ENSP00000425281:E226K	ENSP00000315011:E335K	E	+	1	0	EDNRA	148680521	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.186000	0.50942	1.409000	0.46915	0.650000	0.86243	GAG	.	.	none		0.348	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1		
PDGFRL	5157	hgsc.bcm.edu	37	8	17500223	17500223	+	Silent	SNP	T	T	C	rs4705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17500223T>C	ENST00000541323.1	+	7	1486	c.1041T>C	c.(1039-1041)ttT>ttC	p.F347F	PDGFRL_ENST00000398074.3_Silent_p.F347F|PDGFRL_ENST00000251630.6_Silent_p.F347F|PDGFRL_ENST00000523248.1_Intron	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	347	Ig-like C2-type 2.				G-protein coupled receptor signaling pathway (GO:0007186)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)	extracellular region (GO:0005576)	platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	9				Colorectal(111;0.0752)		TGGAAGACTTTGAGACGATTG	0.463													T|||	2038	0.406949	0.2012	0.4135	5008	,	,		20472	0.4593		0.5825	False		,,,				2504	0.4458				p.F347F		Atlas-SNP	.											.	PDGFRL	27	.	0			c.T1041C						PASS	.	T		1206,3200	418.5+/-338.3	161,884,1158	121.0	103.0	109.0		1041	-3.7	1.0	8	dbSNP_52	109	4890,3710	619.5+/-396.9	1384,2122,794	no	coding-synonymous	PDGFRL	NM_006207.2		1545,3006,1952	CC,CT,TT		43.1395,27.3718,46.8707		347/376	17500223	6096,6910	2203	4300	6503	SO:0001819	synonymous_variant	5157	exon7			AGACTTTGAGACG	D37965	CCDS6003.1	8p22-p21.3	2013-01-29			ENSG00000104213	ENSG00000104213		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8805	protein-coding gene	gene with protein product		604584					Standard	NM_006207		Approved	PRLTS	uc003wxr.3	Q15198	OTTHUMG00000130818	ENST00000541323.1:c.1041T>C	8.37:g.17500223T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_006207	A8K085|Q6FH04	Silent	SNP	ENST00000541323.1	37	CCDS6003.1																																																																																			T|0.548;C|0.452	0.452	strong		0.463	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253366.3	NM_006207	
TEX26	122046	hgsc.bcm.edu	37	13	31531009	31531009	+	Splice_Site	SNP	G	G	A	rs12857479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:31531009G>A	ENST00000380473.3	+	4	325		c.e4-1			NM_152325.1	NP_689538.1	Q8N6G2	TEX26_HUMAN	testis expressed 26																		TGCTTTGATAGGACATTTTCC	0.403													G|||	1276	0.254792	0.0469	0.3141	5008	,	,		19264	0.2946		0.3628	False		,,,				2504	0.3415				.		Atlas-SNP	.											.	.	.	.	0			c.313-1G>A						PASS	.	G		438,3968	209.5+/-230.2	35,368,1800	90.0	82.0	85.0			4.7	0.1	13	dbSNP_121	85	3185,5415	480.1+/-370.3	608,1969,1723	yes	splice-3	C13orf26	NM_152325.1		643,2337,3523	AA,AG,GG		37.0349,9.941,27.8564			31531009	3623,9383	2203	4300	6503	SO:0001630	splice_region_variant	122046	exon4			TTGATAGGACATT	BC030277	CCDS9339.1	13q12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000175664	ENSG00000175664			28622	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 26"""	C13orf26		12477932	Standard	NM_152325		Approved	MGC40178	uc001uti.3	Q8N6G2	OTTHUMG00000016682	ENST00000380473.3:c.313-1G>A	13.37:g.31531009G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	68	23	0.338235	NM_152325		Splice_Site	SNP	ENST00000380473.3	37	CCDS9339.1	571	0.26144688644688646	20	0.04065040650406504	116	0.32044198895027626	156	0.2727272727272727	279	0.36807387862796836	G	9.869	1.198433	0.22037	0.09941	0.370349	ENSG00000175664	ENST00000380473	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999998197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1627	0.59552	0.0:0.0:1.0:0.0	rs12857479;rs17535176;rs12857479	.	.	.	.	-1	.	.	.	+	.	.	C13orf26	30429009	0.910000	0.30920	0.073000	0.20177	0.014000	0.08584	2.665000	0.46791	2.145000	0.66743	0.591000	0.81541	.	G|0.732;A|0.268	0.268	strong		0.403	TEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044380.2	NM_152325	Intron
OR2B2	81697	hgsc.bcm.edu	37	6	27879982	27879982	+	Missense_Mutation	SNP	A	A	G	rs61742093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27879982A>G	ENST00000303324.2	-	1	192	c.116T>C	c.(115-117)aTc>aCc	p.I39T		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						ATTGCCAAAGATTGTCAAGAT	0.403													A|||	109	0.0217652	0.0106	0.0303	5008	,	,		18381	0.0		0.0736	False		,,,				2504	0.0				p.I39T		Atlas-SNP	.											.	OR2B2	54	.	0			c.T116C						PASS	.	A	THR/ILE	159,4247	106.0+/-144.5	4,151,2048	103.0	102.0	102.0		116	4.4	1.0	6	dbSNP_129	102	753,7847	180.3+/-229.3	35,683,3582	yes	missense	OR2B2	NM_033057.2	89	39,834,5630	GG,GA,AA		8.7558,3.6087,7.0121	possibly-damaging	39/358	27879982	912,12094	2203	4300	6503	SO:0001583	missense	81697	exon1			CCAAAGATTGTCA	Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"""GPCR / Class A : Olfactory receptors"""	13966	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 9"""	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.116T>C	6.37:g.27879982A>G	ENSP00000304419:p.Ile39Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	74	0.03388278388278388	6	0.012195121951219513	10	0.027624309392265192	0	0.0	58	0.07651715039577836	A	10.95	1.496750	0.26861	0.036087	0.087558	ENSG00000168131	ENST00000303324	T	0.00635	6.06	4.37	4.37	0.52481	.	0.000000	0.39909	U	0.001233	T	0.01061	0.0035	M	0.84433	2.695	0.51012	P	9.599999999998499E-5	P	0.48911	0.917	P	0.49301	0.606	T	0.42531	-0.9446	9	0.87932	D	0	.	12.1623	0.54110	1.0:0.0:0.0:0.0	rs61742093	39	Q9GZK3	OR2B2_HUMAN	T	39	ENSP00000304419:I39T	ENSP00000304419:I39T	I	-	2	0	OR2B2	27987961	0.732000	0.28121	0.994000	0.49952	0.124000	0.20399	5.072000	0.64389	1.901000	0.55032	0.460000	0.39030	ATC	A|0.943;G|0.057	0.057	strong		0.403	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
NARFL	64428	hgsc.bcm.edu	37	16	781633	781633	+	Silent	SNP	G	G	A	rs3829492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:781633G>A	ENST00000251588.2	-	9	982	c.966C>T	c.(964-966)caC>caT	p.H322H	NARFL_ENST00000301694.5_3'UTR|NARFL_ENST00000568545.1_Silent_p.H220H|NARFL_ENST00000540986.1_Silent_p.H220H|NARFL_ENST00000562862.1_5'UTR	NM_022493.1	NP_071938.1	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	322					hematopoietic progenitor cell differentiation (GO:0002244)|iron-sulfur cluster assembly (GO:0016226)|oxygen homeostasis (GO:0032364)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|large_intestine(1)|lung(7)	9		Hepatocellular(780;0.0218)				GCCGGAACACGTGCTCCAGGT	0.657													G|||	1908	0.38099	0.1271	0.4539	5008	,	,		18429	0.7599		0.2147	False		,,,				2504	0.453				p.H322H		Atlas-SNP	.											NARFL,NS,adenoma,0,1	NARFL	31	1	0			c.C966T						PASS	.	G		476,3844		18,440,1702	32.0	27.0	29.0		966	-4.5	0.9	16	dbSNP_107	29	1536,7010		136,1264,2873	no	coding-synonymous	NARFL	NM_022493.1		154,1704,4575	AA,AG,GG		17.9733,11.0185,15.6381		322/477	781633	2012,10854	2160	4273	6433	SO:0001819	synonymous_variant	64428	exon9			GAACACGTGCTCC	AY129231	CCDS10425.1	16p13.3	2009-12-17			ENSG00000103245	ENSG00000103245			14179	protein-coding gene	gene with protein product	"""iron-only hydrogenase-like protein 1"""	611118				16956324	Standard	NM_022493		Approved	FLJ21988, PRN, HPRN, IOP1	uc002cjr.3	Q9H6Q4	OTTHUMG00000122093	ENST00000251588.2:c.966C>T	16.37:g.781633G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_022493	A1L385|B3KTJ3|Q53GC6|Q96S10|Q9H6J8	Silent	SNP	ENST00000251588.2	37	CCDS10425.1																																																																																			G|0.714;A|0.286	0.286	strong		0.657	NARFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242855.1	NM_022493	
ICAM5	7087	hgsc.bcm.edu	37	19	10403368	10403368	+	Missense_Mutation	SNP	G	G	A	rs2228615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10403368G>A	ENST00000221980.4	+	5	1105	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	348	Ig-like C2-type 4.		A -> T (in dbSNP:rs2228615). {ECO:0000269|PubMed:8995416}.		phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CGCAGCTGGGGCCCAAGCTCT	0.657													G|||	1449	0.289337	0.0439	0.5202	5008	,	,		15041	0.2371		0.4066	False		,,,				2504	0.3906				p.A348T		Atlas-SNP	.											.	ICAM5	53	.	0			c.G1042A	GRCh37	CM065278	ICAM5	M	rs2228615	PASS	.	G	THR/ALA	437,3969	208.2+/-229.3	19,399,1785	40.0	39.0	39.0		1042	-0.8	0.0	19	dbSNP_98	39	3346,5254	493.3+/-373.5	664,2018,1618	yes	missense	ICAM5	NM_003259.3	58	683,2417,3403	AA,AG,GG		38.907,9.9183,29.0866	benign	348/925	10403368	3783,9223	2203	4300	6503	SO:0001583	missense	7087	exon5			GCTGGGGCCCAAG	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1042G>A	19.37:g.10403368G>A	ENSP00000221980:p.Ala348Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	127	125	0.984252	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	643	0.2944139194139194	11	0.022357723577235773	175	0.48342541436464087	145	0.2534965034965035	312	0.41160949868073876	G	12.92	2.082357	0.36758	0.099183	0.38907	ENSG00000105376	ENST00000221980	T	0.12672	2.66	5.61	-0.808	0.10868	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.562319	0.17184	N	0.183799	T	0.00012	0.0000	L	0.55743	1.74	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.43410	-0.9393	9	0.49607	T	0.09	-7.5346	5.0792	0.14647	0.2826:0.3719:0.3454:0.0	rs2228615;rs17856760;rs56676893;rs2228615	348	Q9UMF0	ICAM5_HUMAN	T	348	ENSP00000221980:A348T	ENSP00000221980:A348T	A	+	1	0	ICAM5	10264368	0.000000	0.05858	0.001000	0.08648	0.579000	0.36224	-1.124000	0.03260	0.041000	0.15688	0.561000	0.74099	GCC	G|0.713;A|0.287	0.287	strong		0.657	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
ZNF234	10780	hgsc.bcm.edu	37	19	44652954	44652954	+	Missense_Mutation	SNP	G	G	A	rs2293587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44652954G>A	ENST00000426739.2	+	4	304	c.46G>A	c.(46-48)Gtc>Atc	p.V16I	ZNF234_ENST00000592437.1_Missense_Mutation_p.V16I|ZNF234_ENST00000590748.1_3'UTR	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	16	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> I (in dbSNP:rs2293587).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				TGTGGCTGTGGTCTTCACTGA	0.483													G|||	1614	0.322284	0.2988	0.2767	5008	,	,		18565	0.4008		0.3121	False		,,,				2504	0.316				p.V16I		Atlas-SNP	.											.	ZNF234	132	.	0			c.G46A						PASS	.	G	ILE/VAL,ILE/VAL	1228,3178	424.5+/-340.5	176,876,1151	209.0	210.0	210.0		46,46	-1.1	0.9	19	dbSNP_100	210	3029,5571	467.2+/-367.0	563,1903,1834	yes	missense,missense	ZNF234	NM_001144824.1,NM_006630.2	29,29	739,2779,2985	AA,AG,GG		35.2209,27.8711,32.731	benign,benign	16/701,16/701	44652954	4257,8749	2203	4300	6503	SO:0001583	missense	10780	exon4			GCTGTGGTCTTCA	X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"""Zinc fingers, C2H2-type"", ""-"""	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.46G>A	19.37:g.44652954G>A	ENSP00000400878:p.Val16Ile	Somatic	309	1	0.00323625		WXS	Illumina HiSeq	Phase_I	299	144	0.481605	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Missense_Mutation	SNP	ENST00000426739.2	37	CCDS46101.1	720	0.32967032967032966	146	0.2967479674796748	113	0.31215469613259667	228	0.3986013986013986	233	0.3073878627968338	G	11.40	1.628303	0.28978	0.278711	0.352209	ENSG00000167380	ENST00000426739	T	0.01725	4.67	3.85	-1.13	0.09775	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.48696	P	3.0799999999997496E-4	B	0.27625	0.183	B	0.28916	0.096	T	0.36744	-0.9735	8	0.35671	T	0.21	.	5.0799	0.14651	0.2585:0.0:0.6053:0.1362	rs2293587;rs2293587	16	Q14588	ZN234_HUMAN	I	16	ENSP00000400878:V16I	ENSP00000400878:V16I	V	+	1	0	ZNF226	49344794	0.772000	0.28567	0.895000	0.35142	0.967000	0.64934	0.782000	0.26788	-0.212000	0.10109	0.561000	0.74099	GTC	G|0.660;A|0.340	0.340	strong		0.483	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2		
DEPDC7	91614	hgsc.bcm.edu	37	11	33053005	33053005	+	Silent	SNP	T	T	C	rs36077875	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:33053005T>C	ENST00000241051.3	+	5	956	c.864T>C	c.(862-864)ttT>ttC	p.F288F	DEPDC7_ENST00000311388.3_Silent_p.F279F	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	288					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						GCAGAAGCTTTCCTGAGCAAC	0.448													T|||	56	0.0111821	0.0	0.0231	5008	,	,		19058	0.0		0.0378	False		,,,				2504	0.002				p.F288F		Atlas-SNP	.											.	DEPDC7	94	.	0			c.T864C						PASS	.	T	,	23,3729		0,23,1853	110.0	106.0	107.0		864,837	-4.7	1.0	11	dbSNP_126	107	287,7909		7,273,3818	no	coding-synonymous,coding-synonymous	DEPDC7	NM_001077242.1,NM_139160.2	,	7,296,5671	CC,CT,TT		3.5017,0.613,2.5946	,	288/512,279/503	33053005	310,11638	1876	4098	5974	SO:0001819	synonymous_variant	91614	exon5			AAGCTTTCCTGAG		CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.864T>C	11.37:g.33053005T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_001077242	G5E941|Q8N602|Q8NCU9|Q9UGK5	Silent	SNP	ENST00000241051.3	37	CCDS41632.1																																																																																			T|0.977;C|0.023	0.023	strong		0.448	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160	
NPAS1	4861	hgsc.bcm.edu	37	19	47548678	47548678	+	Silent	SNP	G	G	A	rs889169	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47548678G>A	ENST00000602212.1	+	12	1762	c.1542G>A	c.(1540-1542)gcG>gcA	p.A514A	NPAS1_ENST00000449844.2_Silent_p.A514A|NPAS1_ENST00000602189.1_Silent_p.A339A|NPAS1_ENST00000439365.2_3'UTR			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	514					central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		GGGGCCTGGCGCCTCCCGGGG	0.751													G|||	2277	0.454673	0.1581	0.5346	5008	,	,		11084	0.6925		0.6093	False		,,,				2504	0.3947				p.A514A		Atlas-SNP	.											NPAS1,NS,carcinoma,+1,1	NPAS1	32	1	0			c.G1542A						PASS	.	G		1018,3372		134,750,1311	11.0	14.0	13.0		1542	-2.7	0.0	19	dbSNP_86	13	5152,3420		1570,2012,704	no	coding-synonymous	NPAS1	NM_002517.2		1704,2762,2015	AA,AG,GG		39.8973,23.1891,47.6007		514/591	47548678	6170,6792	2195	4286	6481	SO:0001819	synonymous_variant	4861	exon11			CCTGGCGCCTCCC	U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"""Basic helix-loop-helix proteins"""	7894	protein-coding gene	gene with protein product	"""neuronal PAS1"", ""member of PAS superfamily 5"""	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.1542G>A	19.37:g.47548678G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_002517	B4DR69|Q99632|Q9BY83	Silent	SNP	ENST00000602212.1	37	CCDS12694.1																																																																																			G|0.493;A|0.507	0.507	strong		0.751	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1	NM_002517	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605295	32605295	+	Silent	SNP	C	C	T	rs1129735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32605295C>T	ENST00000343139.5	+	1	162	c.60C>T	c.(58-60)ccC>ccT	p.P20P	HLA-DQA1_ENST00000374949.2_Silent_p.P20P|HLA-DQA1_ENST00000395363.1_Silent_p.P20P	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	20					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TGATGAGCCCCTGTGGAGGTG	0.512													.|||	1659	0.33127	0.2057	0.3963	5008	,	,		15856	0.4087		0.337	False		,,,				2504	0.3691				p.P20P		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C60T						PASS	.	T		980,3426		113,754,1336	76.0	68.0	71.0		60	-0.0	0.0	6	dbSNP_118	71	2968,5632		519,1930,1851	no	coding-synonymous	HLA-DQA1	NM_002122.3		632,2684,3187	TT,TC,CC		34.5116,22.2424,30.3552		20/256	32605295	3948,9058	2203	4300	6503	SO:0001819	synonymous_variant	3117	exon1			GAGCCCCTGTGGA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.60C>T	6.37:g.32605295C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	139	81	0.582734	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1																																																																																			C|0.693;T|0.307	0.307	strong		0.512	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
RYR1	6261	hgsc.bcm.edu	37	19	38983180	38983180	+	Missense_Mutation	SNP	G	G	T	rs35364374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38983180G>T	ENST00000359596.3	+	38	6178	c.6178G>T	c.(6178-6180)Ggc>Tgc	p.G2060C	RYR1_ENST00000355481.4_Missense_Mutation_p.G2060C|RYR1_ENST00000360985.3_Missense_Mutation_p.G2060C			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2060	6 X approximate repeats.		G -> C (in MHS1; dbSNP:rs35364374). {ECO:0000269|PubMed:1354642, ECO:0000269|PubMed:16380615, ECO:0000269|PubMed:19191329, ECO:0000269|PubMed:20681998, ECO:0000269|PubMed:21674524, ECO:0000269|PubMed:23558838}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GACCACCCTGGGCAGCCGCCT	0.532													G|||	275	0.0549121	0.0015	0.049	5008	,	,		15920	0.0079		0.0646	False		,,,				2504	0.1697				p.G2060C		Atlas-SNP	.											.	RYR1	708	.	0			c.G6178T						PASS	.	G	CYS/GLY,CYS/GLY	56,4350	55.5+/-91.7	0,56,2147	62.0	61.0	61.0		6178,6178	1.7	1.0	19	dbSNP_126	61	613,7987	160.7+/-213.8	27,559,3714	yes	missense,missense	RYR1	NM_000540.2,NM_001042723.1	159,159	27,615,5861	TT,TG,GG		7.1279,1.271,5.1438	benign,benign	2060/5039,2060/5034	38983180	669,12337	2203	4300	6503	SO:0001583	missense	6261	exon38			ACCCTGGGCAGCC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6178G>T	19.37:g.38983180G>T	ENSP00000352608:p.Gly2060Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	71	0.03250915750915751	1	0.0020325203252032522	16	0.04419889502762431	4	0.006993006993006993	50	0.06596306068601583	g	13.64	2.296940	0.40594	0.01271	0.071279	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.72725	-0.68;-0.68;-0.68	5.05	1.7	0.24286	.	0.320739	0.24039	U	0.042118	T	0.14141	0.0342	L	0.55481	1.735	0.18873	N	0.999989	D;P	0.55800	0.973;0.953	P;B	0.50378	0.639;0.436	T	0.28808	-1.0032	10	0.54805	T	0.06	.	4.1836	0.10387	0.339:0.1653:0.4957:0.0	rs35364374	2060;2060	P21817-2;P21817	.;RYR1_HUMAN	C	2060	ENSP00000352608:G2060C;ENSP00000347667:G2060C;ENSP00000354254:G2060C	ENSP00000347667:G2060C	G	+	1	0	RYR1	43675020	0.999000	0.42202	1.000000	0.80357	0.957000	0.61999	0.615000	0.24329	0.522000	0.28464	0.539000	0.68188	GGC	G|0.953;T|0.047	0.047	strong		0.532	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
ARHGEF19	128272	hgsc.bcm.edu	37	1	16534255	16534255	+	Missense_Mutation	SNP	C	C	G	rs221057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16534255C>G	ENST00000270747.3	-	4	848	c.712G>C	c.(712-714)Gag>Cag	p.E238Q	ARHGEF19_ENST00000478117.1_5'Flank	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	238			E -> Q (in dbSNP:rs221057). {ECO:0000269|PubMed:14702039}.		regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		CTTCGAGCCTCCATTCCAGAT	0.682													C|||	1337	0.266973	0.1664	0.4063	5008	,	,		14901	0.1528		0.2654	False		,,,				2504	0.4233				p.E238Q		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.G712C						PASS	.	C	GLN/GLU	778,3628	305.5+/-289.0	79,620,1504	46.0	49.0	48.0		712	4.9	0.5	1	dbSNP_79	48	2240,6356	367.8+/-334.9	298,1644,2356	yes	missense	ARHGEF19	NM_153213.3	29	377,2264,3860	GG,GC,CC		26.0586,17.6577,23.2118	benign	238/803	16534255	3018,9984	2203	4298	6501	SO:0001583	missense	128272	exon4			GAGCCTCCATTCC	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.712G>C	1.37:g.16534255C>G	ENSP00000270747:p.Glu238Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	480	0.21978021978021978	73	0.1483739837398374	123	0.3397790055248619	74	0.12937062937062938	210	0.2770448548812665	C	19.69	3.874660	0.72180	0.176577	0.260586	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.71579	-0.58;1.81	4.94	4.94	0.65067	.	4.578340	0.00702	N	0.000785	T	0.00012	0.0000	L	0.50333	1.59	0.40022	P	0.024572999999999956	B	0.20052	0.041	B	0.17433	0.018	T	0.04153	-1.0973	9	0.17369	T	0.5	.	13.8258	0.63351	0.0:1.0:0.0:0.0	rs221057;rs221057	238	Q8IW93	ARHGJ_HUMAN	Q	238	ENSP00000270747:E238Q;ENSP00000396001:E238Q	ENSP00000270747:E238Q	E	-	1	0	ARHGEF19	16406842	0.961000	0.32948	0.474000	0.27266	0.043000	0.13939	3.812000	0.55628	2.316000	0.78162	0.549000	0.68633	GAG	C|0.778;G|0.222	0.222	strong		0.682	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
REST	5978	hgsc.bcm.edu	37	4	57796900	57796900	+	Missense_Mutation	SNP	G	G	A	rs2228991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57796900G>A	ENST00000309042.7	+	4	2190	c.1876G>A	c.(1876-1878)Gtt>Att	p.V626I		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	626	Pro-rich.		V -> I (in dbSNP:rs2228991). {ECO:0000269|PubMed:15489334}.		cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					GAAGGGGCCCGTTCAGGTGGA	0.607													G|||	597	0.119209	0.1263	0.2522	5008	,	,		15051	0.2024		0.0328	False		,,,				2504	0.0184				p.V626I		Atlas-SNP	.											.	REST	104	.	0			c.G1876A						PASS	.	G	ILE/VAL,ILE/VAL	527,3873		28,471,1701	22.0	25.0	24.0		1876,1876	-5.2	0.0	4	dbSNP_98	24	348,8236		10,328,3954	yes	missense,missense	REST	NM_001193508.1,NM_005612.4	29,29	38,799,5655	AA,AG,GG		4.0541,11.9773,6.7391	benign,benign	626/1098,626/1098	57796900	875,12109	2200	4292	6492	SO:0001583	missense	5978	exon4			GGGCCCGTTCAGG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.1876G>A	4.37:g.57796900G>A	ENSP00000311816:p.Val626Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	142	78	0.549296	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	291	0.13324175824175824	53	0.10772357723577236	84	0.23204419889502761	133	0.23251748251748253	21	0.027704485488126648	G	9.343	1.063647	0.20067	0.119773	0.040541	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.07327	3.2	4.0	-5.2	0.02823	.	1.058360	0.07544	N	0.914444	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.24675	0.109;0.017	B;B	0.12156	0.007;0.003	T	0.48768	-0.9006	9	0.25751	T	0.34	.	2.1845	0.03883	0.2238:0.3785:0.2704:0.1273	rs2228991;rs3733302;rs58607248;rs2228991	603;626	F8WAN5;Q13127	.;REST_HUMAN	I	626;603	ENSP00000311816:V626I	ENSP00000311816:V626I	V	+	1	0	REST	57491657	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.254000	0.08781	-0.804000	0.04410	-0.315000	0.08773	GTT	G|0.906;A|0.094	0.094	strong		0.607	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
ATP4B	496	hgsc.bcm.edu	37	13	114303764	114303764	+	Silent	SNP	C	C	T	rs17852631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:114303764C>T	ENST00000335288.4	-	7	842	c.801G>A	c.(799-801)gcG>gcA	p.A267A		NM_000705.3	NP_000696.1	P51164	ATP4B_HUMAN	ATPase, H+/K+ exchanging, beta polypeptide	267	immunoglobulin-like.				cell adhesion (GO:0007155)|hydrogen ion transmembrane transport (GO:1902600)|ion transmembrane transport (GO:0034220)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	hydrogen:potassium-exchanging ATPase activity (GO:0008900)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.171)			TCACGTGCTCCGCCATGACCT	0.577													C|||	1025	0.204673	0.1263	0.3156	5008	,	,		20434	0.2024		0.1759	False		,,,				2504	0.2638				p.A267A		Atlas-SNP	.											.	ATP4B	35	.	0			c.G801A						PASS	.	C		599,3807		39,521,1643	113.0	79.0	91.0		801	-8.9	0.0	13	dbSNP_123	91	1627,6973		146,1335,2819	no	coding-synonymous	ATP4B	NM_000705.3		185,1856,4462	TT,TC,CC		18.9186,13.5951,17.1152		267/292	114303764	2226,10780	2203	4300	6503	SO:0001819	synonymous_variant	496	exon7			GTGCTCCGCCATG		CCDS9539.1	13q34	2011-08-01			ENSG00000186009	ENSG00000186009	3.6.3.10	"""ATPases / P-type"""	820	protein-coding gene	gene with protein product		137217				1330887, 15057823	Standard	NM_000705		Approved	ATP6B	uc001vtz.3	P51164	OTTHUMG00000140234	ENST00000335288.4:c.801G>A	13.37:g.114303764C>T		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	269	129	0.479554	NM_000705	B1B0N8	Silent	SNP	ENST00000335288.4	37	CCDS9539.1																																																																																			C|0.826;T|0.174	0.174	strong		0.577	ATP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276703.2	NM_000705	
C17orf102	400591	hgsc.bcm.edu	37	17	32906008	32906008	+	Missense_Mutation	SNP	C	C	G	rs58529418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:32906008C>G	ENST00000357754.1	-	1	380	c.292G>C	c.(292-294)Ggg>Cgg	p.G98R	TMEM132E_ENST00000321639.5_5'Flank	NM_207454.2	NP_997337.2	A2RUQ5	CQ102_HUMAN	chromosome 17 open reading frame 102	98			G -> R (in dbSNP:rs58529418). {ECO:0000269|PubMed:14702039}.							central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(3)|ovary(1)	9						CCAGAGCCCCCGCGGCCCGAG	0.672													C|||	752	0.15016	0.1074	0.0994	5008	,	,		14420	0.2361		0.0895	False		,,,				2504	0.2178				p.G98R		Atlas-SNP	.											.	C17orf102	24	.	0			c.G292C						PASS	.	C	ARG/GLY	337,3381		14,309,1536	44.0	51.0	49.0		292	-1.7	0.0	17	dbSNP_129	49	600,7576		27,546,3515	yes	missense	C17orf102	NM_207454.2	125	41,855,5051	GG,GC,CC		7.3386,9.064,7.8779	possibly-damaging	98/168	32906008	937,10957	1859	4088	5947	SO:0001583	missense	400591	exon1			AGCCCCCGCGGCC		CCDS42297.1	17q12	2009-02-11			ENSG00000197322	ENSG00000197322			34412	protein-coding gene	gene with protein product							Standard	NM_207454		Approved	FLJ44815	uc002hie.1	A2RUQ5	OTTHUMG00000156883	ENST00000357754.1:c.292G>C	17.37:g.32906008C>G	ENSP00000350392:p.Gly98Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_207454	A5PKX0|Q6ZTB3	Missense_Mutation	SNP	ENST00000357754.1	37	CCDS42297.1	301	0.13782051282051283	53	0.10772357723577236	34	0.09392265193370165	147	0.256993006993007	67	0.08839050131926121	C	11.00	1.511180	0.27036	0.09064	0.073386	ENSG00000197322	ENST00000357754	T	0.46819	0.86	3.59	-1.73	0.08081	.	1.147840	0.06879	N	0.802091	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.36125	0.538	B	0.40199	0.322	T	0.18524	-1.0334	9	0.87932	D	0	.	6.4711	0.22009	0.5276:0.31:0.1624:0.0	rs58529418	98	A2RUQ5	CQ102_HUMAN	R	98	ENSP00000350392:G98R	ENSP00000350392:G98R	G	-	1	0	C17orf102	29930121	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.000000	0.03693	-0.401000	0.07644	-0.165000	0.13383	GGG	C|0.876;G|0.124	0.124	strong		0.672	C17orf102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346435.1	NM_207454	
MDM1	56890	hgsc.bcm.edu	37	12	68707287	68707287	+	Missense_Mutation	SNP	G	G	A	rs2306392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:68707287G>A	ENST00000303145.7	-	11	1741	c.1655C>T	c.(1654-1656)cCa>cTa	p.P552L	MDM1_ENST00000411698.2_Missense_Mutation_p.P517L|MDM1_ENST00000540418.1_Missense_Mutation_p.P272L	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	552			P -> L (in dbSNP:rs2306392). {ECO:0000269|PubMed:15489334}.		retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		CCTCTGTTCTGGGGCTGGAGG	0.363													G|||	1059	0.211462	0.0726	0.2161	5008	,	,		19059	0.1736		0.3052	False		,,,				2504	0.3384				p.P552L		Atlas-SNP	.											.	MDM1	74	.	0			c.C1655T						PASS	.	G	LEU/PRO,LEU/PRO	557,3849	249.0+/-256.6	33,491,1679	84.0	89.0	88.0		1550,1655	2.2	0.0	12	dbSNP_100	88	2693,5907	432.3+/-357.1	398,1897,2005	yes	missense,missense	MDM1	NM_001205028.1,NM_017440.4	98,98	431,2388,3684	AA,AG,GG		31.314,12.6419,24.9885	benign,benign	517/680,552/715	68707287	3250,9756	2203	4300	6503	SO:0001583	missense	56890	exon11			TGTTCTGGGGCTG	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"""Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"""			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.1655C>T	12.37:g.68707287G>A	ENSP00000302537:p.Pro552Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	475	0.2174908424908425	51	0.10365853658536585	95	0.26243093922651933	95	0.1660839160839161	234	0.3087071240105541	G	1.012	-0.687468	0.03328	0.126419	0.31314	ENSG00000111554	ENST00000540418;ENST00000303145;ENST00000411698	T;T;T	0.22945	1.93;2.25;2.25	5.08	2.23	0.28157	.	0.415012	0.27986	N	0.017058	T	0.00012	0.0000	N	0.14661	0.345	0.49483	P	2.0399999999998197E-4	B;B	0.10296	0.001;0.003	B;B	0.09377	0.002;0.004	T	0.47548	-0.9109	8	.	.	.	1.4607	9.8312	0.40944	0.2266:0.0:0.7734:0.0	rs2306392;rs17350216;rs17845852;rs17858825;rs52796173;rs60355924;rs2306392	517;552	E7EPQ3;Q8TC05	.;MDM1_HUMAN	L	272;552;517	ENSP00000443815:P272L;ENSP00000302537:P552L;ENSP00000391006:P517L	.	P	-	2	0	MDM1	66993554	0.925000	0.31364	0.010000	0.14722	0.973000	0.67179	3.017000	0.49615	0.258000	0.21686	0.555000	0.69702	CCA	G|0.764;A|0.236	0.236	strong		0.363	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497986	32497986	+	Missense_Mutation	SNP	G	G	A	rs200744795		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32497986G>A	ENST00000374975.3	-	1	78	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CCTCCAGGGAGCTTCAGACAC	0.577																																					p.L6F		Atlas-SNP	.											HLA-DRB5,rectum,carcinoma,0,1	HLA-DRB5	31	1	0			c.C16T						scavenged	.						55.0	61.0	59.0					6																	32497986		2203	4296	6499	SO:0001583	missense	3127	exon1			CAGGGAGCTTCAG		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.16C>T	6.37:g.32497986G>A	ENSP00000364114:p.Leu6Phe	Somatic	62	2	0.0322581		WXS	Illumina HiSeq	Phase_I	209	13	0.062201	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	4.629	0.117010	0.08881	.	.	ENSG00000198502	ENST00000374975	T	0.00281	8.32	4.42	-2.83	0.05769	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.27975	0.815	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.28808	-1.0032	9	0.06891	T	0.86	.	5.2478	0.15506	0.2872:0.0:0.5657:0.1472	rs1059548;rs2308658;rs3200252;rs16822997	6	Q30154	DRB5_HUMAN	F	6	ENSP00000364114:L6F	ENSP00000364114:L6F	L	-	1	0	HLA-DRB5	32605964	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.163000	0.09997	-0.229000	0.09854	-0.350000	0.07774	CTC	.	.	weak		0.577	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
MBD3L3	653657	hgsc.bcm.edu	37	19	7056571	7056571	+	Missense_Mutation	SNP	G	G	T	rs111605618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7056571G>T	ENST00000333843.4	-	2	423	c.389C>A	c.(388-390)gCt>gAt	p.A130D		NM_001164425.1	NP_001157897.1	A6NE82	MB3L3_HUMAN	methyl-CpG binding domain protein 3-like 3	130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.A130D(1)		central_nervous_system(1)|lung(5)|stomach(1)	7						CTCAGCACCAGCCCTGTCCAG	0.637													-|||	838	0.167332	0.118	0.2522	5008	,	,		41704	0.0417		0.2962	False		,,,				2504	0.1708				p.A130D		Atlas-SNP	.											MBD3L3,NS,haematopoietic_neoplasm,0,3	MBD3L3	12	3	1	Substitution - Missense(1)	stomach(1)	c.C389A						scavenged	.						52.0	62.0	59.0					19																	7056571		692	1591	2283	SO:0001583	missense	653657	exon2			GCACCAGCCCTGT		CCDS45944.1	19p13.2	2014-04-01			ENSG00000182315	ENSG00000182315			37205	protein-coding gene	gene with protein product							Standard	NM_001164425		Approved		uc021uns.1	A6NE82	OTTHUMG00000181976	ENST00000333843.4:c.389C>A	19.37:g.7056571G>T	ENSP00000333183:p.Ala130Asp	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	390	70	0.179487	NM_001164425		Missense_Mutation	SNP	ENST00000333843.4	37	CCDS45944.1	.	.	.	.	.	.	.	.	.	.	.	3.926	-0.017102	0.07681	.	.	ENSG00000182315	ENST00000333843	.	.	.	0.742	-1.48	0.08745	.	.	.	.	.	T	0.32615	0.0835	L	0.43923	1.385	0.80722	P	0.0	.	.	.	.	.	.	T	0.33752	-0.9856	5	0.42905	T	0.14	-12.4801	2.5805	0.04817	0.2531:0.3037:0.4432:0.0	.	.	.	.	D	130	.	ENSP00000333183:A130D	A	-	2	0	MBD3L3	7007571	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.980000	0.03770	-1.270000	0.02433	-1.511000	0.00944	GCT	G|0.747;T|0.253	0.253	strong		0.637	MBD3L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458500.1	NM_001164425	
RASD2	23551	hgsc.bcm.edu	37	22	35947585	35947585	+	Silent	SNP	C	C	A	rs41279993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:35947585C>A	ENST00000216127.4	+	3	949	c.307C>A	c.(307-309)Cgg>Agg	p.R103R		NM_014310.3	NP_055125.2	Q96D21	RHES_HUMAN	RASD family, member 2	103					locomotory behavior (GO:0007626)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein sumoylation (GO:0033235)|regulation of cAMP-mediated signaling (GO:0043949)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission, dopaminergic (GO:0001963)	plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	13						CCTGGATAACCGGGAGTCCTT	0.602													C|||	233	0.0465256	0.0499	0.0749	5008	,	,		19226	0.0		0.1054	False		,,,				2504	0.0092				p.R103R		Atlas-SNP	.											.	RASD2	34	.	0			c.C307A						PASS	.	C		247,4159	143.5+/-178.5	4,239,1960	110.0	108.0	108.0		307	4.4	1.0	22	dbSNP_127	108	953,7647	208.6+/-250.0	65,823,3412	no	coding-synonymous	RASD2	NM_014310.3		69,1062,5372	AA,AC,CC		11.0814,5.606,9.2265		103/267	35947585	1200,11806	2203	4300	6503	SO:0001819	synonymous_variant	23551	exon3			GATAACCGGGAGT	AF279143	CCDS13916.1	22q13.1	2014-05-09			ENSG00000100302	ENSG00000100302			18229	protein-coding gene	gene with protein product	"""tumor endothelial marker 2"", ""Ras homolog enriched in striatum"""	612842				10947988, 10467249, 14724584	Standard	NM_014310		Approved	TEM2, Rhes, MGC:4834	uc003anx.3	Q96D21	OTTHUMG00000150607	ENST00000216127.4:c.307C>A	22.37:g.35947585C>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	164	81	0.493902	NM_014310	O95520|Q5THY8	Silent	SNP	ENST00000216127.4	37	CCDS13916.1																																																																																			C|0.924;A|0.076	0.076	strong		0.602	RASD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319063.1	NM_014310	
BDH2	56898	hgsc.bcm.edu	37	4	104004064	104004064	+	Silent	SNP	T	T	C	rs79460377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:104004064T>C	ENST00000296424.4	-	8	675	c.555A>G	c.(553-555)ctA>ctG	p.L185L		NM_020139.3	NP_064524.3	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2	185					epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|heme metabolic process (GO:0042168)|iron ion homeostasis (GO:0055072)|siderophore biosynthetic process (GO:0019290)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		TTCTTTCTTGTAGAGATGGCG	0.348													T|||	113	0.0225639	0.0045	0.0375	5008	,	,		19482	0.0		0.0755	False		,,,				2504	0.0051				p.L185L		Atlas-SNP	.											.	BDH2	18	.	0			c.A555G						PASS	.	T		60,4346	58.1+/-94.6	3,54,2146	179.0	182.0	181.0		555	3.0	1.0	4	dbSNP_132	181	623,7977	162.7+/-215.4	24,575,3701	no	coding-synonymous	BDH2	NM_020139.3		27,629,5847	CC,CT,TT		7.2442,1.3618,5.2514		185/246	104004064	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	56898	exon8			TTCTTGTAGAGAT	AF164790	CCDS3663.1	4q24	2011-09-14			ENSG00000164039	ENSG00000164039	1.1.1.30	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	32389	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 15C, member 1"""		"""dehydrogenase/reductase (SDR family) member 6"""	DHRS6		16380372, 19027726	Standard	XM_005263140		Approved	UCPA-OR, FLJ13261, UNQ6308, PRO20933, SDR15C1	uc003hwz.3	Q9BUT1	OTTHUMG00000074039	ENST00000296424.4:c.555A>G	4.37:g.104004064T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_020139	A8K295|B4DUF6|Q503A0|Q6IA46|Q6UWD3|Q9H8S8|Q9NRX8	Silent	SNP	ENST00000296424.4	37	CCDS3663.1																																																																																			T|0.955;C|0.045	0.045	strong		0.348	BDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157159.2	NM_020139	
FAM179A	165186	hgsc.bcm.edu	37	2	29221040	29221040	+	Silent	SNP	C	C	T	rs72786173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29221040C>T	ENST00000379558.4	+	3	411	c.60C>T	c.(58-60)tgC>tgT	p.C20C	FAM179A_ENST00000403861.2_Silent_p.C20C	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	20										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCGTGTACTGCGGGAGCATCC	0.622													C|||	62	0.0123802	0.0015	0.0231	5008	,	,		15479	0.0		0.0408	False		,,,				2504	0.0031				p.C20C		Atlas-SNP	.											.	FAM179A	106	.	0			c.C60T						PASS	.	C		27,3951		0,27,1962	19.0	21.0	20.0		60	1.1	0.1	2	dbSNP_130	20	275,8023		2,271,3876	no	coding-synonymous	FAM179A	NM_199280.2		2,298,5838	TT,TC,CC		3.3141,0.6787,2.4601		20/1020	29221040	302,11974	1989	4149	6138	SO:0001819	synonymous_variant	165186	exon3			GTACTGCGGGAGC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.60C>T	2.37:g.29221040C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	276	140	0.507246	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			C|0.978;T|0.022	0.022	strong		0.622	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
TDRD10	126668	hgsc.bcm.edu	37	1	154516571	154516571	+	Silent	SNP	T	T	C	rs6678164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154516571T>C	ENST00000368480.3	+	9	721	c.636T>C	c.(634-636)gcT>gcC	p.A212A	TDRD10_ENST00000368482.4_Silent_p.A212A|TDRD10_ENST00000479937.1_3'UTR			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	212	Tudor.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTTTCTGGGCTATGCACGTCA	0.642													C|||	4509	0.900359	0.6362	0.9784	5008	,	,		19201	1.0		0.997	False		,,,				2504	1.0				p.A212A		Atlas-SNP	.											.	TDRD10	48	.	0			c.T636C						PASS	.	C	,	3175,1231	428.5+/-341.9	1143,889,171	134.0	99.0	111.0		636,636	3.0	0.2	1	dbSNP_116	111	8593,7	4.3+/-15.6	4293,7,0	no	coding-synonymous,coding-synonymous	TDRD10	NM_001098475.1,NM_182499.3	,	5436,896,171	CC,CT,TT		0.0814,27.9392,9.5187	,	212/367,212/352	154516571	11768,1238	2203	4300	6503	SO:0001819	synonymous_variant	126668	exon9			CTGGGCTATGCAC	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"""Tudor domain containing"", ""RNA binding motif (RRM) containing"""	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.636T>C	1.37:g.154516571T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	215	214	0.995349	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Silent	SNP	ENST00000368480.3	37	CCDS41406.1																																																																																			T|0.094;C|0.906	0.906	strong		0.642	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499	
VAV2	7410	hgsc.bcm.edu	37	9	136640116	136640116	+	Silent	SNP	G	G	A	rs56006146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136640116G>A	ENST00000371850.3	-	25	2107	c.2076C>T	c.(2074-2076)agC>agT	p.S692S	VAV2_ENST00000371851.1_Silent_p.S682S|VAV2_ENST00000406606.3_Silent_p.S682S	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	692	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		GGTAGGTCCCGCTGGCGTGGG	0.617													g|||	238	0.047524	0.1324	0.0231	5008	,	,		18620	0.0119		0.0129	False		,,,				2504	0.0225				p.S692S		Atlas-SNP	.											.	VAV2	165	.	0			c.C2076T						PASS	.	A	,	499,3905	225.6+/-241.4	19,461,1722	70.0	64.0	66.0		2076,2046	-1.8	1.0	9	dbSNP_129	66	122,8476	62.8+/-124.8	1,120,4178	no	coding-synonymous,coding-synonymous	VAV2	NM_001134398.1,NM_003371.3	,	20,581,5900	AA,AG,GG		1.4189,11.3306,4.7762	,	692/879,682/840	136640116	621,12381	2202	4299	6501	SO:0001819	synonymous_variant	7410	exon25			GGTCCCGCTGGCG		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2076C>T	9.37:g.136640116G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Silent	SNP	ENST00000371850.3	37	CCDS48053.1																																																																																			G|0.958;A|0.042	0.042	strong		0.617	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
UGT2B17	7367	hgsc.bcm.edu	37	4	69417570	69417570	+	Silent	SNP	A	A	G	rs28374627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69417570A>G	ENST00000317746.2	-	4	1107	c.1065T>C	c.(1063-1065)taT>taC	p.Y355Y		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	355					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	GTAACCACTTATACAGTCGAG	0.348													G|||	2992	0.597444	0.3563	0.5274	5008	,	,		7632	0.7897		0.7296	False		,,,				2504	0.6391				p.Y355Y	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.T1065C						PASS	.	G		1633,2543		532,569,987	96.0	84.0	88.0		1065	-1.2	0.0	4	dbSNP_125	88	5142,2692		2121,900,896	no	coding-synonymous	UGT2B17	NM_001077.3		2653,1469,1883	GG,GA,AA		34.363,39.1044,43.5887		355/531	69417570	6775,5235	2088	3917	6005	SO:0001819	synonymous_variant	7367	exon4			CCACTTATACAGT	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.1065T>C	4.37:g.69417570A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	360	153	0.425	NM_001077		Silent	SNP	ENST00000317746.2	37	CCDS3523.1																																																																																			.	.	weak		0.348	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	
PIGR	5284	hgsc.bcm.edu	37	1	207109116	207109116	+	Missense_Mutation	SNP	C	C	T	rs2275531	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207109116C>T	ENST00000356495.4	-	5	1276	c.1093G>A	c.(1093-1095)Ggc>Agc	p.G365S		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	365	Ig-like V-type 4.		G -> S (in dbSNP:rs2275531). {ECO:0000269|PubMed:1355431, ECO:0000269|PubMed:1682231, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:1859628, ECO:0000269|PubMed:2920039, ECO:0000269|PubMed:6526384}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCCACAGAGCCTCCTGCCACC	0.612											OREG0014186	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1484	0.296326	0.1944	0.3271	5008	,	,		19680	0.3284		0.4563	False		,,,				2504	0.2147				p.G365S		Atlas-SNP	.											PIGR,NS,carcinoma,0,1	PIGR	98	1	0			c.G1093A						PASS	.	C	SER/GLY	963,3441		114,735,1353	31.0	34.0	33.0		1093	4.6	1.0	1	dbSNP_100	33	3938,4662		920,2098,1282	yes	missense	PIGR	NM_002644.3	56	1034,2833,2635	TT,TC,CC		45.7907,21.8665,37.6884	probably-damaging	365/765	207109116	4901,8103	2202	4300	6502	SO:0001583	missense	5284	exon5			CAGAGCCTCCTGC		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"""Immunoglobulin superfamily / V-set domain containing"""	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1093G>A	1.37:g.207109116C>T	ENSP00000348888:p.Gly365Ser	Somatic	102	0	0	2165	WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_002644	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	764	0.3498168498168498	111	0.22560975609756098	134	0.3701657458563536	179	0.3129370629370629	340	0.44854881266490765	C	15.25	2.777910	0.49786	0.218665	0.457907	ENSG00000162896	ENST00000356495	T	0.04275	3.66	5.55	4.64	0.57946	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.169823	0.42172	N	0.000742	T	0.00012	0.0000	M	0.75615	2.305	0.31681	P	0.643169	D	0.89917	1.0	D	0.97110	1.0	T	0.47509	-0.9112	9	0.44086	T	0.13	-22.293	8.6869	0.34243	0.0:0.8266:0.0:0.1734	rs2275531;rs2275531	365	P01833	PIGR_HUMAN	S	365	ENSP00000348888:G365S	ENSP00000348888:G365S	G	-	1	0	PIGR	205175739	0.755000	0.28372	1.000000	0.80357	0.242000	0.25591	0.601000	0.24119	1.352000	0.45808	-0.140000	0.14226	GGC	C|0.639;T|0.361	0.361	strong		0.612	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777422	18777422	+	Silent	SNP	G	G	A	rs45579937	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:18777422G>A	ENST00000380548.4	+	19	3534	c.3195G>A	c.(3193-3195)ctG>ctA	p.L1065L		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1065						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		AAGTGCTCCTGCACCTGCCCT	0.682													G|||	501	0.10004	0.0136	0.0807	5008	,	,		16632	0.123		0.171	False		,,,				2504	0.1339				p.L1065L		Atlas-SNP	.											ADAMTSL1_ENST00000380548,NS,carcinoma,0,1	ADAMTSL1	306	1	0			c.G3195A						PASS	.	G		186,3920		4,178,1871	12.0	16.0	14.0		3195	2.8	0.7	9	dbSNP_127	14	1652,6722		169,1314,2704	no	coding-synonymous	ADAMTSL1	NM_001040272.5		173,1492,4575	AA,AG,GG		19.7277,4.53,14.7276		1065/1763	18777422	1838,10642	2053	4187	6240	SO:0001819	synonymous_variant	92949	exon19			GCTCCTGCACCTG	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.3195G>A	9.37:g.18777422G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	66	41	0.621212	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																			G|0.884;A|0.116	0.116	strong		0.682	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
MFN2	9927	hgsc.bcm.edu	37	1	12061598	12061598	+	Silent	SNP	C	C	T	rs41278632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12061598C>T	ENST00000235329.5	+	9	1279	c.957C>T	c.(955-957)ggC>ggT	p.G319G	MFN2_ENST00000444836.1_Silent_p.G319G	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	319	Dynamin-type G.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AAGCCCAGGGCATGCCTGAAG	0.517											OREG0013107	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	22	0.00439297	0.0015	0.0072	5008	,	,		19027	0.0		0.0099	False		,,,				2504	0.0051				p.G319G		Atlas-SNP	.											.	MFN2	83	.	0			c.C957T						PASS	.	C	,	11,4395	19.1+/-41.9	0,11,2192	80.0	75.0	77.0		957,957	3.3	1.0	1	dbSNP_127	77	95,8505	53.6+/-114.3	0,95,4205	no	coding-synonymous,coding-synonymous	MFN2	NM_001127660.1,NM_014874.3	,	0,106,6397	TT,TC,CC		1.1047,0.2497,0.815	,	319/758,319/758	12061598	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	9927	exon9			CCAGGGCATGCCT	AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.957C>T	1.37:g.12061598C>T		Somatic	107	0	0	677	WXS	Illumina HiSeq	Phase_I	135	79	0.585185	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Silent	SNP	ENST00000235329.5	37	CCDS30587.1																																																																																			C|0.991;T|0.009	0.009	strong		0.517	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874	
OAF	220323	hgsc.bcm.edu	37	11	120099679	120099679	+	Missense_Mutation	SNP	G	G	A	rs2508490	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:120099679G>A	ENST00000328965.4	+	4	1163	c.650G>A	c.(649-651)cGc>cAc	p.R217H	OAF_ENST00000531220.1_Missense_Mutation_p.R101H	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	217			R -> H (in dbSNP:rs2508490).			extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		TGCGTCTGCCGCTATGGCCTG	0.667													G|||	2450	0.489217	0.4879	0.5951	5008	,	,		14499	0.1359		0.7922	False		,,,				2504	0.4683				p.R217H		Atlas-SNP	.											.	OAF	12	.	0			c.G650A						PASS	.	G	HIS/ARG	2360,2046	582.3+/-385.5	629,1102,472	39.0	36.0	37.0		650	-2.5	0.8	11	dbSNP_100	37	6817,1781	700.1+/-405.1	2704,1409,186	yes	missense	OAF	NM_178507.2	29	3333,2511,658	AA,AG,GG		20.7141,46.4367,29.4294	benign	217/274	120099679	9177,3827	2203	4299	6502	SO:0001583	missense	220323	exon4			TCTGCCGCTATGG	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.650G>A	11.37:g.120099679G>A	ENSP00000332613:p.Arg217His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_178507		Missense_Mutation	SNP	ENST00000328965.4	37	CCDS8430.1	1165	0.5334249084249084	251	0.5101626016260162	230	0.6353591160220995	75	0.13111888111888112	609	0.8034300791556728	G	6.417	0.445110	0.12164	0.535633	0.792859	ENSG00000184232	ENST00000328965;ENST00000531220	T;T	0.30981	1.51;1.51	4.72	-2.51	0.06365	.	0.542996	0.20057	N	0.100165	T	0.00012	0.0000	N	0.01874	-0.695	0.46011	P	0.0011870000000000491	B	0.12630	0.006	B	0.04013	0.001	T	0.17561	-1.0365	9	0.25106	T	0.35	-9.0545	7.3895	0.26901	0.4743:0.1132:0.4125:0.0	rs2508490;rs3740738;rs58492389;rs2508490	217	Q86UD1	OAF_HUMAN	H	217;101	ENSP00000332613:R217H;ENSP00000431865:R101H	ENSP00000332613:R217H	R	+	2	0	OAF	119604889	1.000000	0.71417	0.786000	0.31890	0.211000	0.24417	0.775000	0.26689	-0.376000	0.07943	-0.145000	0.13849	CGC	G|0.379;A|0.621	0.621	strong		0.667	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507	
ANKS1B	56899	hgsc.bcm.edu	37	12	99139559	99139559	+	Intron	SNP	G	G	T	rs61932058	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:99139559G>T	ENST00000547776.2	-	25	3672				ANKS1B_ENST00000549493.2_Silent_p.A497A|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000549025.2_Silent_p.A344A|ANKS1B_ENST00000549558.2_Intron|ANKS1B_ENST00000341752.7_Intron|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000546568.1_Silent_p.A413A|ANKS1B_ENST00000332712.7_Silent_p.A437A|ANKS1B_ENST00000547446.1_Silent_p.A381A|ANKS1B_ENST00000333732.7_Silent_p.A276A|ANKS1B_ENST00000550693.2_Silent_p.A437A	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B							cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGCCCCTCTTGGCTTCTTGGC	0.537													G|||	57	0.0113818	0.0113	0.0101	5008	,	,		16338	0.001		0.0189	False		,,,				2504	0.0153				p.A497A		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1491A						PASS	.	G	,,,,,,,,,,,	63,3759		1,61,1849	104.0	108.0	107.0		831,1032,1143,,1311,1239,831,759,,,,1491	2.7	1.0	12	dbSNP_129	107	181,8087		1,179,3954	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,intron,coding-synonymous	ANKS1B	NM_001204065.1,NM_001204066.1,NM_001204067.1,NM_001204068.1,NM_001204069.1,NM_001204070.1,NM_001204079.1,NM_001204080.1,NM_001204081.1,NM_020140.3,NM_152788.4,NM_181670.3	,,,,,,,,,,,	2,240,5803	TT,TG,GG		2.1892,1.6484,2.0182	,,,,,,,,,,,	277/291,344/358,381/395,,437/451,413/427,277/291,253/267,,,,497/511	99139559	244,11846	1911	4134	6045	SO:0001627	intron_variant	56899	exon13			CCTCTTGGCTTCT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3672+5573C>A	12.37:g.99139559G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_181670	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	37	CCDS55872.1	32	0.014652014652014652	10	0.02032520325203252	4	0.011049723756906077	0	0.0	18	0.023746701846965697	G	5.366	0.252738	0.10185	0.016484	0.021892	ENSG00000185046	ENST00000550778	.	.	.	4.66	2.65	0.31530	.	.	.	.	.	T	0.42585	0.1209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47761	-0.9092	4	.	.	.	.	9.5531	0.39321	0.0:0.1547:0.685:0.1604	rs61932058	.	.	.	Q	519	.	.	P	-	2	0	ANKS1B	97663690	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.200000	0.42724	1.048000	0.40298	-0.326000	0.08463	CCA	G|0.984;T|0.016	0.016	strong		0.537	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
ZFP64	55734	hgsc.bcm.edu	37	20	50769549	50769549	+	Silent	SNP	A	A	G	rs3746413	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:50769549A>G	ENST00000216923.4	-	6	1531	c.1182T>C	c.(1180-1182)caT>caC	p.H394H	ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000371515.4_Silent_p.H392H|ZFP64_ENST00000346617.4_Silent_p.H340H|ZFP64_ENST00000477786.1_Intron	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CCATGTCCCCATGGAACTTCT	0.567													A|||	840	0.167732	0.1445	0.2767	5008	,	,		20214	0.0843		0.2137	False		,,,				2504	0.1605				p.H394H		Atlas-SNP	.											.	ZFP64	240	.	0			c.T1182C						PASS	.	A	,,,	659,3747	281.6+/-276.1	52,555,1596	116.0	96.0	103.0		1182,1020,1176,	-0.1	0.4	20	dbSNP_107	103	1867,6733	332.4+/-320.1	193,1481,2626	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	,,,	245,2036,4222	GG,GA,AA		21.7093,14.9569,19.4218	,,,	394/682,340/628,392/680,	50769549	2526,10480	2203	4300	6503	SO:0001819	synonymous_variant	55734	exon6			GTCCCCATGGAAC	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1182T>C	20.37:g.50769549A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			A|0.821;G|0.179	0.179	strong		0.567	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
HSP90AB1	3326	hgsc.bcm.edu	37	6	44221293	44221293	+	Silent	SNP	C	C	T	rs147025760	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44221293C>T	ENST00000371554.1	+	12	2347	c.2133C>T	c.(2131-2133)ctC>ctT	p.L711L	SLC35B2_ENST00000495706.1_5'Flank|HSP90AB1_ENST00000353801.3_Silent_p.L711L|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000371646.5_Silent_p.L711L			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	711					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCCCCCCTCTCGAGGGCGATG	0.493											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L711L		Atlas-SNP	.											.	HSP90AB1	83	.	0			c.C2133T						PASS	.						78.0	80.0	79.0					6																	44221293		2203	4300	6503	SO:0001819	synonymous_variant	3326	exon12			CCCTCTCGAGGGC	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2133C>T	6.37:g.44221293C>T		Somatic	142	0	0	922	WXS	Illumina HiSeq	Phase_I	233	39	0.167382	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Silent	SNP	ENST00000371554.1	37	CCDS4909.1																																																																																			C|0.868;T|0.132	0.132	strong		0.493	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
ACSM2A	123876	hgsc.bcm.edu	37	16	20471450	20471450	+	Missense_Mutation	SNP	G	G	A	rs59292608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20471450G>A	ENST00000573854.1	+	2	128	c.14G>A	c.(13-15)cGa>cAa	p.R5Q	ACSM2A_ENST00000417235.2_Intron|ACSM2A_ENST00000424070.1_Missense_Mutation_p.R5Q|ACSM2A_ENST00000396104.2_Missense_Mutation_p.R5Q|ACSM2A_ENST00000219054.6_Missense_Mutation_p.R5Q|ACSM2A_ENST00000575690.1_Missense_Mutation_p.R5Q|ACSM2A_ENST00000575558.1_Intron|ACSM2A_ENST00000536134.1_5'UTR	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	5					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)	p.R5Q(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						CATTGGCTGCGAAAAGTTCAG	0.493													G|||	849	0.169529	0.0121	0.0706	5008	,	,		18579	0.4018		0.172	False		,,,				2504	0.2106				p.R5Q		Atlas-SNP	.											ACSM2A,colon,carcinoma,+1,2	ACSM2A	120	2	1	Substitution - Missense(1)	stomach(1)	c.G14A						PASS	.	G	GLN/ARG	138,4268	97.6+/-136.3	0,138,2065	65.0	65.0	65.0		14	-4.7	0.0	16	dbSNP_129	65	1271,7329	251.1+/-277.7	100,1071,3129	yes	missense	ACSM2A	NM_001010845.2	43	100,1209,5194	AA,AG,GG		14.7791,3.1321,10.8335	benign	5/578	20471450	1409,11597	2203	4300	6503	SO:0001583	missense	123876	exon3			GGCTGCGAAAAGT	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"""Acyl-CoA synthetase family"""	32017	protein-coding gene	gene with protein product		614358	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.14G>A	16.37:g.20471450G>A	ENSP00000459451:p.Arg5Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	406	0.1858974358974359	7	0.014227642276422764	30	0.08287292817679558	226	0.3951048951048951	143	0.18865435356200527	G	8.575	0.880844	0.17467	0.031321	0.147791	ENSG00000183747	ENST00000219054;ENST00000424070;ENST00000396104	T;T;T	0.42900	0.96;2.28;0.96	3.28	-4.66	0.03329	.	2.661960	0.01665	N	0.025335	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.41784	0.762	B	0.32149	0.141	T	0.31081	-0.9956	9	0.26408	T	0.33	1.0797	0.439	0.00483	0.2256:0.2934:0.228:0.253	rs59292608	5	Q08AH3	ACS2A_HUMAN	Q	5	ENSP00000219054:R5Q;ENSP00000394904:R5Q;ENSP00000379411:R5Q	ENSP00000219054:R5Q	R	+	2	0	ACSM2A	20378951	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-1.073000	0.03430	-0.830000	0.04262	0.454000	0.30748	CGA	G|0.870;A|0.130	0.130	strong		0.493	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
CHST5	23563	hgsc.bcm.edu	37	16	75563330	75563330	+	Missense_Mutation	SNP	G	G	A	rs3826107	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:75563330G>A	ENST00000336257.3	-	3	2347	c.953C>T	c.(952-954)aCg>aTg	p.T318M	CHST5_ENST00000541075.1_Missense_Mutation_p.T324M|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	318			T -> M (in dbSNP:rs3826107).		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						GAGCTGTGGCGTGAGGGTCAG	0.662													G|||	716	0.142971	0.1104	0.1398	5008	,	,		15049	0.2073		0.2048	False		,,,				2504	0.0593				p.T318M		Atlas-SNP	.											CHST5,NS,carcinoma,+1,4	CHST5	47	4	0			c.C953T						PASS	.	G	MET/THR	537,3859	230.7+/-244.8	39,459,1700	75.0	73.0	74.0		953	2.8	1.0	16	dbSNP_107	74	1701,6899	290.7+/-299.9	184,1333,2783	yes	missense	CHST5	NM_024533.4	81	223,1792,4483	AA,AG,GG		19.7791,12.2157,17.2207	probably-damaging	318/412	75563330	2238,10758	2198	4300	6498	SO:0001583	missense	23563	exon3			TGTGGCGTGAGGG	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"""Sulfotransferases, membrane-bound"""	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.953C>T	16.37:g.75563330G>A	ENSP00000338783:p.Thr318Met	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Missense_Mutation	SNP	ENST00000336257.3	37	CCDS10919.1	358	0.16391941391941392	49	0.09959349593495935	64	0.17679558011049723	98	0.17132867132867133	147	0.19393139841688653	G	13.45	2.242109	0.39598	0.122157	0.197791	ENSG00000135702	ENST00000336257;ENST00000541075	T;T	0.25579	1.79;1.79	2.84	2.84	0.33178	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	M	0.82823	2.61	0.09310	P	0.99999403796	D;D	0.76494	0.999;0.999	D;D	0.75484	0.975;0.986	T	0.06006	-1.0851	9	0.48119	T	0.1	.	12.6629	0.56824	0.0:0.0:1.0:0.0	rs3826107;rs61212449;rs3826107	324;318	Q9GZS9-2;Q9GZS9	.;CHST5_HUMAN	M	318;324	ENSP00000338783:T318M;ENSP00000441220:T324M	ENSP00000338783:T318M	T	-	2	0	CHST5	74120831	1.000000	0.71417	0.994000	0.49952	0.011000	0.07611	6.063000	0.71162	1.583000	0.49898	0.313000	0.20887	ACG	G|0.842;A|0.158	0.158	strong		0.662	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126	
REPIN1	29803	hgsc.bcm.edu	37	7	150068933	150068933	+	Silent	SNP	T	T	C	rs6722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150068933T>C	ENST00000425389.2	+	1	681	c.603T>C	c.(601-603)gcT>gcC	p.A201A	RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000444957.1_Silent_p.A201A|REPIN1_ENST00000489432.2_Silent_p.A258A|REPIN1_ENST00000540729.1_Silent_p.A201A|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000397281.2_Silent_p.A201A|REPIN1_ENST00000479668.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	201					DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			TGCACGTAGCTGAGGCCCTGG	0.746													C|||	2082	0.415735	0.4894	0.2176	5008	,	,		11294	0.4673		0.3181	False		,,,				2504	0.5041				p.A258A		Atlas-SNP	.											REPIN1_ENST00000489432,NS,carcinoma,0,2	REPIN1	74	2	0			c.T774C						PASS	.	C	,,,	1586,2058		384,818,620	8.0	10.0	10.0		774,603,603,603	-2.6	0.8	7	dbSNP_52	10	2511,5575		452,1607,1984	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	,,,	836,2425,2604	CC,CT,TT		31.0537,43.5236,34.9275	,,,	258/625,201/568,201/568,201/568	150068933	4097,7633	1822	4043	5865	SO:0001819	synonymous_variant	29803	exon3			CGTAGCTGAGGCC	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.603T>C	7.37:g.150068933T>C		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Silent	SNP	ENST00000425389.2	37	CCDS43677.1																																																																																			T|0.574;C|0.426	0.426	strong		0.746	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
TECTA	7007	hgsc.bcm.edu	37	11	121028666	121028666	+	Silent	SNP	C	C	T	rs33981325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:121028666C>T	ENST00000392793.1	+	14	4693	c.4422C>T	c.(4420-4422)aaC>aaT	p.N1474N	TECTA_ENST00000264037.2_Silent_p.N1474N			O75443	TECTA_HUMAN	tectorin alpha	1474					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CGCTGCGCAACGGGGTGCGCG	0.682													C|||	58	0.0115815	0.0015	0.0187	5008	,	,		10842	0.0		0.0348	False		,,,				2504	0.0082				p.N1474N		Atlas-SNP	.											TECTA,NS,carcinoma,+1,1	TECTA	329	1	0			c.C4422T						PASS	.	C		26,4380	32.6+/-62.9	1,24,2178	41.0	39.0	39.0		4422	-1.3	0.8	11	dbSNP_126	39	288,8308	105.2+/-166.2	4,280,4014	no	coding-synonymous	TECTA	NM_005422.2		5,304,6192	TT,TC,CC		3.3504,0.5901,2.415		1474/2156	121028666	314,12688	2203	4298	6501	SO:0001819	synonymous_variant	7007	exon13			GCGCAACGGGGTG	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.4422C>T	11.37:g.121028666C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	35	0.660377	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																			C|0.978;T|0.022	0.022	strong		0.682	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
SLC28A1	9154	hgsc.bcm.edu	37	15	85478729	85478729	+	Missense_Mutation	SNP	G	G	A	rs2242046	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85478729G>A	ENST00000286749.3	+	14	1651	c.1561G>A	c.(1561-1563)Gac>Aac	p.D521N	SLC28A1_ENST00000537624.1_Missense_Mutation_p.D521N|SLC28A1_ENST00000537216.1_Missense_Mutation_p.D521N|SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000394573.1_Missense_Mutation_p.D521N|RNU6-339P_ENST00000384310.1_RNA			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	521			D -> N (in B and C; dbSNP:rs2242046). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GTGGGTCGGCGACAGGAAGCA	0.627													G|||	1042	0.208067	0.0325	0.2622	5008	,	,		21265	0.0605		0.503	False		,,,				2504	0.2556				p.D521N		Atlas-SNP	.											.	SLC28A1	118	.	0			c.G1561A						PASS	.	G	ASN/ASP	456,3950	217.4+/-235.8	39,378,1786	98.0	95.0	96.0		1561	-0.1	0.0	15	dbSNP_98	96	4278,4320	576.3+/-390.4	1066,2146,1087	yes	missense	SLC28A1	NM_004213.3	23	1105,2524,2873	AA,AG,GG		49.7558,10.3495,36.4042	benign	521/650	85478729	4734,8270	2203	4299	6502	SO:0001583	missense	9154	exon15			GTCGGCGACAGGA	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1561G>A	15.37:g.85478729G>A	ENSP00000286749:p.Asp521Asn	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	561	0.25686813186813184	25	0.0508130081300813	105	0.2900552486187845	42	0.07342657342657342	389	0.5131926121372031	G	8.616	0.890211	0.17613	0.103495	0.497558	ENSG00000156222	ENST00000537216;ENST00000537624;ENST00000286749;ENST00000394573	T;T;T;T	0.02015	4.5;4.67;4.68;4.68	5.19	-0.144	0.13440	Na dependent nucleoside transporter, C-terminal (1);	0.994708	0.08157	N	0.989064	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	1.999999999946489E-6	B;B;B	0.21821	0.061;0.005;0.025	B;B;B	0.13407	0.009;0.002;0.009	T	0.32428	-0.9907	9	0.48119	T	0.1	-20.7634	2.0739	0.03619	0.1564:0.1197:0.4171:0.3067	rs2242046;rs17216003;rs17609392;rs57854627;rs2242046	521;521;521	B7Z533;F5H560;O00337	.;.;S28A1_HUMAN	N	521	ENSP00000440546:D521N;ENSP00000444700:D521N;ENSP00000286749:D521N;ENSP00000378074:D521N	ENSP00000286749:D521N	D	+	1	0	SLC28A1	83279733	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.816000	0.27267	-0.177000	0.10690	-0.391000	0.06502	GAC	G|0.690;A|0.310	0.310	strong		0.627	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
TLDC1	57707	hgsc.bcm.edu	37	16	84516309	84516309	+	Silent	SNP	G	G	A	rs433293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84516309G>A	ENST00000343629.6	-	6	1148	c.966C>T	c.(964-966)aaC>aaT	p.N322N	TLDC1_ENST00000535580.1_Silent_p.N295N	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	322	TLD.					lysosomal membrane (GO:0005765)											GGAAGCATCTGTTGTCCCCTG	0.547													G|||	2201	0.439497	0.1959	0.5187	5008	,	,		21112	0.5575		0.4205	False		,,,				2504	0.6104				p.N322N		Atlas-SNP	.											KIAA1609,NS,carcinoma,0,1	KIAA1609	39	1	0			c.C966T						PASS	.	G		1090,3310	392.6+/-328.5	145,800,1255	120.0	91.0	101.0		966	2.1	0.0	16	dbSNP_80	101	3644,4956	523.9+/-380.4	767,2110,1423	no	coding-synonymous	KIAA1609	NM_020947.3		912,2910,2678	AA,AG,GG		42.3721,24.7727,36.4154		322/457	84516309	4734,8266	2200	4300	6500	SO:0001819	synonymous_variant	57707	exon6			GCATCTGTTGTCC	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.966C>T	16.37:g.84516309G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	220	105	0.477273	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Silent	SNP	ENST00000343629.6	37	CCDS32498.1																																																																																			G|0.625;A|0.375	0.375	strong		0.547	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
LILRA6	79168	hgsc.bcm.edu	37	19	54745978	54745978	+	Silent	SNP	T	T	C	rs1052964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54745978T>C	ENST00000396365.2	-	3	318	c.279A>G	c.(277-279)gcA>gcG	p.A93A	LILRA6_ENST00000270464.5_Silent_p.A93A|LILRB3_ENST00000407860.2_Silent_p.A93A|LILRA6_ENST00000391735.3_Silent_p.A93A|LILRA6_ENST00000245621.5_Silent_p.A93A|LILRA6_ENST00000419410.2_Silent_p.A93A|LILRA6_ENST00000440558.2_Silent_p.A93A	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	93					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGTATCTCCCTGCATGGTGCT	0.567																																					p.A93A		Atlas-SNP	.											A2RRG4_HUMAN,NS,carcinoma,-1,1	LILRA6	75	1	0			c.A279G						PASS	.						284.0	253.0	264.0					19																	54745978		2198	4299	6497	SO:0001819	synonymous_variant	79168	exon3			TCTCCCTGCATGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.279A>G	19.37:g.54745978T>C		Somatic	1282	3	0.00234009		WXS	Illumina HiSeq	Phase_I	674	335	0.497033	NM_024318		Silent	SNP	ENST00000396365.2	37	CCDS42610.1																																																																																			T|0.500;C|0.500	0.500	strong		0.567	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
NUP98	4928	hgsc.bcm.edu	37	11	3723781	3723781	+	Missense_Mutation	SNP	G	G	C	rs35404087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:3723781G>C	ENST00000324932.7	-	23	3844	c.3424C>G	c.(3424-3426)Cag>Gag	p.Q1142E	NUP98_ENST00000355260.3_Missense_Mutation_p.Q1142E|NUP98_ENST00000359171.4_Missense_Mutation_p.Q1142E	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1159					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		CCATTCAGCTGTTCTCCACTA	0.473			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML								G|||	209	0.0417332	0.003	0.0735	5008	,	,		17865	0.001		0.1282	False		,,,				2504	0.0245				p.Q1142E		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.C3424G						PASS	.	G	GLU/GLN,GLU/GLN	110,4292	83.4+/-121.9	2,106,2093	120.0	112.0	115.0		3424,3424	4.4	1.0	11	dbSNP_126	115	1041,7555	220.5+/-258.2	75,891,3332	yes	missense,missense	NUP98	NM_016320.4,NM_139132.3	29,29	77,997,5425	CC,CG,GG		12.1103,2.4989,8.8552	possibly-damaging,possibly-damaging	1142/1801,1142/1727	3723781	1151,11847	2201	4298	6499	SO:0001583	missense	4928	exon23			TCAGCTGTTCTCC	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.3424C>G	11.37:g.3723781G>C	ENSP00000316032:p.Gln1142Glu	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	172	86	0.5	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	136	0.06227106227106227	0	0.0	34	0.09392265193370165	1	0.0017482517482517483	101	0.13324538258575197	G	12.65	2.001051	0.35320	0.024989	0.121103	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260	.	.	.	5.35	4.43	0.53597	.	0.327142	0.33235	N	0.005121	T	0.00440	0.0014	L	0.50333	1.59	0.32191	P	0.579048	B;B	0.32188	0.359;0.359	B;B	0.29862	0.108;0.108	T	0.11717	-1.0576	8	0.02654	T	1	0.0175	10.209	0.43131	0.0:0.1483:0.6977:0.154	rs35404087;rs61756124	1142;1142	P52948-2;P52948-5	.;.	E	1142	.	ENSP00000316032:Q1142E	Q	-	1	0	NUP98	3680357	1.000000	0.71417	0.997000	0.53966	0.908000	0.53690	3.251000	0.51453	1.218000	0.43458	0.462000	0.41574	CAG	G|0.917;C|0.083	0.083	strong		0.473	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
HDGFL1	154150	hgsc.bcm.edu	37	6	22570189	22570189	+	Silent	SNP	T	T	C	rs6922960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:22570189T>C	ENST00000230012.3	+	1	512	c.385T>C	c.(385-387)Ttg>Ctg	p.L129L	HDGFL1_ENST00000510882.2_Silent_p.L129L	NM_138574.2	NP_612641.2	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	129										kidney(1)|large_intestine(3)|lung(7)	11	Ovarian(93;0.163)					CGGCGACGAATTGGGGAAGCC	0.711													T|||	1190	0.23762	0.2587	0.2752	5008	,	,		11580	0.1706		0.2753	False		,,,				2504	0.2127				p.L129L		Atlas-SNP	.											.	HDGFL1	33	.	0			c.T385C						PASS	.	T		920,3106		121,678,1214	7.0	6.0	6.0		385	-5.4	0.0	6	dbSNP_116	6	1986,6022		265,1456,2283	no	coding-synonymous	HDGFL1	NM_138574.2		386,2134,3497	CC,CT,TT		24.8002,22.8515,24.1482		129/252	22570189	2906,9128	2013	4004	6017	SO:0001819	synonymous_variant	154150	exon1			GACGAATTGGGGA	AK056824	CCDS34347.1	6p22.2	2008-02-05	2005-04-07	2005-04-07	ENSG00000112273	ENSG00000112273			21095	protein-coding gene	gene with protein product			"""PWWP domain containing 1"""	PWWP1			Standard	NM_138574		Approved	dJ309H15.1	uc003nds.3	Q5TGJ6	OTTHUMG00000016206	ENST00000230012.3:c.385T>C	6.37:g.22570189T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_138574	Q96MJ6	Silent	SNP	ENST00000230012.3	37	CCDS34347.1																																																																																			T|0.751;C|0.249	0.249	strong		0.711	HDGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043500.1	NM_138574	
INPP5B	3633	hgsc.bcm.edu	37	1	38348506	38348506	+	Silent	SNP	G	G	A	rs41307896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:38348506G>A	ENST00000373026.1	-	13	1644	c.1644C>T	c.(1642-1644)gaC>gaT	p.D548D	INPP5B_ENST00000373024.3_Silent_p.D468D|INPP5B_ENST00000467066.1_5'Flank|RNU6-584P_ENST00000410350.1_RNA|INPP5B_ENST00000373023.2_Silent_p.D548D|SNORA63_ENST00000516639.1_RNA|INPP5B_ENST00000373027.1_Silent_p.D304D|INPP5B_ENST00000458109.2_Missense_Mutation_p.L169F			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	548	5-phosphatase. {ECO:0000250}.				in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GCATTTGAAAGTCCTTCTCTT	0.502													G|||	390	0.0778754	0.0166	0.0893	5008	,	,		20591	0.003		0.164	False		,,,				2504	0.1411				p.D468D		Atlas-SNP	.											.	INPP5B	76	.	0			c.C1404T						PASS	.	G		131,3793		2,127,1833	169.0	158.0	161.0		1404	4.6	1.0	1	dbSNP_127	161	1188,7134		77,1034,3050	no	coding-synonymous	INPP5B	NM_005540.2		79,1161,4883	AA,AG,GG		14.2754,3.3384,10.7709		468/914	38348506	1319,10927	1962	4161	6123	SO:0001819	synonymous_variant	3633	exon14			TTGAAAGTCCTTC	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.1644C>T	1.37:g.38348506G>A		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	241	140	0.580913	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	37		160	0.07326007326007326	11	0.022357723577235773	39	0.10773480662983426	0	0.0	110	0.14511873350923482	G	14.37	2.516326	0.44763	0.033384	0.142754	ENSG00000204084	ENST00000458109	D	0.97161	-4.27	5.58	4.6	0.57074	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.43745	P	0.003758999999999957	.	.	.	.	.	.	T	0.69446	-0.5143	5	0.02654	T	1	.	8.4959	0.33127	0.0869:0.0:0.703:0.2101	rs41307896;rs61742717	.	.	.	F	169	ENSP00000397748:L169F	ENSP00000397748:L169F	L	-	1	0	INPP5B	38121093	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.545000	0.23268	2.645000	0.89757	0.655000	0.94253	CTT	G|0.897;A|0.103	0.103	strong		0.502	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
ASS1	445	hgsc.bcm.edu	37	9	133364757	133364757	+	Silent	SNP	T	T	C	rs1057484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133364757T>C	ENST00000372394.1	+	13	1357	c.876T>C	c.(874-876)caT>caC	p.H292H	ASS1_ENST00000372393.3_Silent_p.H292H|ASS1_ENST00000352480.5_Silent_p.H292H|ASS1_ENST00000493984.2_3'UTR			P00966	ASSY_HUMAN	argininosuccinate synthase 1	292					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	TCCTTTACCATGCTCATTTAG	0.498													T|||	384	0.0766773	0.1188	0.0504	5008	,	,		15776	0.001		0.1262	False		,,,				2504	0.0654				p.H292H		Atlas-SNP	.											.	ASS1	37	.	0			c.T876C						PASS	.	T	,	491,3915	228.8+/-243.5	26,439,1738	113.0	122.0	119.0		876,876	2.6	1.0	9	dbSNP_86	119	847,7753	193.9+/-239.5	43,761,3496	no	coding-synonymous,coding-synonymous	ASS1	NM_000050.4,NM_054012.3	,	69,1200,5234	CC,CT,TT		9.8488,11.1439,10.2876	,	292/413,292/413	133364757	1338,11668	2203	4300	6503	SO:0001819	synonymous_variant	445	exon12			TTACCATGCTCAT	X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"""argininosuccinate synthetase"""	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.876T>C	9.37:g.133364757T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_054012	Q6LDL2|Q86UZ0|Q96GT4	Silent	SNP	ENST00000372394.1	37	CCDS6933.1																																																																																			T|0.900;C|0.100	0.100	strong		0.498	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050	
ZNF224	7767	hgsc.bcm.edu	37	19	44610843	44610843	+	Missense_Mutation	SNP	C	C	T	rs72480796	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44610843C>T	ENST00000336976.6	+	6	784	c.530C>T	c.(529-531)aCg>aTg	p.T177M	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	177					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				AAATCTCATACGTGTGATGAG	0.418													C|||	314	0.0626997	0.0061	0.0519	5008	,	,		23004	0.0992		0.1143	False		,,,				2504	0.0562				p.T177M		Atlas-SNP	.											.	ZNF224	70	.	0			c.C530T						PASS	.	C	MET/THR	103,4303	80.4+/-118.8	2,99,2102	115.0	115.0	115.0		530	-6.5	0.0	19	dbSNP_130	115	1040,7560	220.1+/-257.9	58,924,3318	yes	missense	ZNF224	NM_013398.2	81	60,1023,5420	TT,TC,CC		12.093,2.3377,8.7883	probably-damaging	177/708	44610843	1143,11863	2203	4300	6503	SO:0001583	missense	7767	exon6			CTCATACGTGTGA	AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"""Zinc fingers, C2H2-type"", ""-"""	13017	protein-coding gene	gene with protein product		194555	"""zinc finger protein 255"", ""zinc finger protein 27"""	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.530C>T	19.37:g.44610843C>T	ENSP00000337368:p.Thr177Met	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	143	89	0.622378	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Missense_Mutation	SNP	ENST00000336976.6	37	CCDS33046.1	187	0.08562271062271062	6	0.012195121951219513	27	0.07458563535911603	64	0.11188811188811189	90	0.11873350923482849	c	16.56	3.158551	0.57368	0.023377	0.12093	ENSG00000186019	ENST00000336976	T	0.15603	2.41	3.44	-6.48	0.01896	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00300	0.0009	L	0.41236	1.265	0.80722	P	0.0	D	0.76494	0.999	D	0.71870	0.975	T	0.06588	-1.0818	8	0.56958	D	0.05	.	2.5784	0.04812	0.4254:0.3053:0.1712:0.0981	.	177	Q9NZL3	ZN224_HUMAN	M	177	ENSP00000337368:T177M	ENSP00000337368:T177M	T	+	2	0	ZNF224	49302683	0.000000	0.05858	0.000000	0.03702	0.419000	0.31324	-4.625000	0.00207	-0.663000	0.05331	0.591000	0.81541	ACG	C|0.908;T|0.092	0.092	strong		0.418	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398	
TOPBP1	11073	hgsc.bcm.edu	37	3	133341988	133341988	+	Missense_Mutation	SNP	T	T	C	rs10935070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:133341988T>C	ENST00000260810.5	-	19	3256	c.3125A>G	c.(3124-3126)aAt>aGt	p.N1042S		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1042			N -> S (in dbSNP:rs10935070).		cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						CTCTTTATTATTGGTGGCCAT	0.289								Other conserved DNA damage response genes					T|||	941	0.187899	0.0106	0.2997	5008	,	,		17163	0.0258		0.3588	False		,,,				2504	0.3395				p.N1042S	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.A3125G						PASS	.	T	SER/ASN	212,3394		4,204,1595	40.0	37.0	38.0		3125	-9.4	0.0	3	dbSNP_120	38	2657,5461		434,1789,1836	yes	missense	TOPBP1	NM_007027.3	46	438,1993,3431	CC,CT,TT		32.7297,5.8791,24.4712	benign	1042/1523	133341988	2869,8855	1803	4059	5862	SO:0001583	missense	11073	exon19			TTATTATTGGTGG	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.3125A>G	3.37:g.133341988T>C	ENSP00000260810:p.Asn1042Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	87	34	0.390805	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	389	0.17811355311355312	6	0.012195121951219513	94	0.2596685082872928	18	0.03146853146853147	271	0.3575197889182058	T	2.223	-0.377961	0.05000	0.058791	0.327297	ENSG00000163781	ENST00000260810	T	0.11385	2.78	5.82	-9.36	0.00629	.	1.012260	0.07897	N	0.972048	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46652	-0.9176	9	0.07813	T	0.8	.	20.6666	0.99681	0.0:0.0977:0.0:0.9023	rs10935070;rs17301444;rs52791815;rs61344352;rs10935070	955;1042	A0AV47;Q92547	.;TOPB1_HUMAN	S	1042	ENSP00000260810:N1042S	ENSP00000260810:N1042S	N	-	2	0	TOPBP1	134824678	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.948000	0.00679	-2.029000	0.00930	-0.250000	0.11733	AAT	T|0.819;C|0.181	0.181	strong		0.289	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
PARP10	84875	hgsc.bcm.edu	37	8	145060112	145060112	+	Silent	SNP	G	G	A	rs11136345	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145060112G>A	ENST00000313028.7	-	3	307	c.213C>T	c.(211-213)caC>caT	p.H71H	PARP10_ENST00000533665.1_5'UTR|PARP10_ENST00000524918.1_Silent_p.H71H|PARP10_ENST00000525773.1_Silent_p.H83H	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	71					negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CATGTAGTTCGTGATCTGCCT	0.667													G|||	1959	0.391174	0.6165	0.2795	5008	,	,		15706	0.1458		0.4314	False		,,,				2504	0.3773				p.H71H		Atlas-SNP	.											.	PARP10	57	.	0			c.C213T						PASS	.			2616,1788		782,1052,368	18.0	20.0	19.0		213	-2.5	0.0	8	dbSNP_120	19	3620,4976		794,2032,1472	no	coding-synonymous	PARP10	NM_032789.3		1576,3084,1840	AA,AG,GG		42.1126,40.5995,47.9692		71/1026	145060112	6236,6764	2202	4298	6500	SO:0001819	synonymous_variant	84875	exon3			TAGTTCGTGATCT	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.213C>T	8.37:g.145060112G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Silent	SNP	ENST00000313028.7	37	CCDS34960.1																																																																																			G|0.551;A|0.449	0.449	strong		0.667	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
KIAA1755	85449	hgsc.bcm.edu	37	20	36841914	36841914	+	Missense_Mutation	SNP	G	G	A	rs3746471	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:36841914G>A	ENST00000279024.4	-	14	3404	c.3133C>T	c.(3133-3135)Cgg>Tgg	p.R1045W		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1045			R -> W (in dbSNP:rs3746471). {ECO:0000269|PubMed:11214970}.							breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AGGAGCATCCGGATCTCCTCA	0.672													G|||	1652	0.329872	0.1225	0.4121	5008	,	,		17757	0.4524		0.4235	False		,,,				2504	0.3292				p.R1045W		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C3133T						PASS	.	G	TRP/ARG	753,3653		83,587,1533	36.0	33.0	34.0		3133	3.3	0.9	20	dbSNP_107	34	3852,4748		872,2108,1320	yes	missense	KIAA1755	NM_001029864.1	101	955,2695,2853	AA,AG,GG		44.7907,17.0903,35.4067	probably-damaging	1045/1201	36841914	4605,8401	2203	4300	6503	SO:0001583	missense	85449	exon14			GCATCCGGATCTC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.3133C>T	20.37:g.36841914G>A	ENSP00000279024:p.Arg1045Trp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	797	0.3649267399267399	74	0.15040650406504066	147	0.40607734806629836	241	0.42132867132867136	335	0.4419525065963061	G	8.990	0.977444	0.18812	0.170903	0.447907	ENSG00000149633	ENST00000279024	T	0.06933	3.24	5.29	3.3	0.37823	.	0.630757	0.14110	N	0.340794	T	0.00012	0.0000	L	0.29908	0.895	0.41204	P	0.013606000000000007	B	0.10296	0.003	B	0.04013	0.001	T	0.43669	-0.9377	9	0.39692	T	0.17	.	8.5627	0.33520	0.1796:0.0:0.8204:0.0	rs3746471;rs17787894;rs52829066;rs56875311;rs3746471	1045	Q5JYT7	K1755_HUMAN	W	1045	ENSP00000279024:R1045W	ENSP00000279024:R1045W	R	-	1	2	KIAA1755	36275328	0.976000	0.34144	0.866000	0.34008	0.208000	0.24298	1.844000	0.39269	1.468000	0.48064	0.561000	0.74099	CGG	G|0.644;A|0.356	0.356	strong		0.672	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
DPYD	1806	hgsc.bcm.edu	37	1	98165091	98165091	+	Missense_Mutation	SNP	T	T	C	rs2297595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:98165091T>C	ENST00000370192.3	-	6	596	c.496A>G	c.(496-498)Atg>Gtg	p.M166V	DPYD_ENST00000423006.2_3'UTR|DPYD_ENST00000474241.1_5'UTR	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	166			M -> V (in dbSNP:rs2297595).		beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	GGGATACTCATTGCTTTGAAT	0.388													T|||	283	0.0565096	0.031	0.0634	5008	,	,		18189	0.0179		0.1193	False		,,,				2504	0.0613				p.M166V		Atlas-SNP	.											DPYD,NS,carcinoma,+1,3	DPYD	219	3	0			c.A496G	GRCh37	CM003589	DPYD	M	rs2297595	PASS	.	T	VAL/MET	180,4226	117.5+/-155.4	7,166,2030	123.0	125.0	124.0		496	5.3	1.0	1	dbSNP_100	124	852,7748	194.4+/-239.8	44,764,3492	yes	missense	DPYD	NM_000110.3	21	51,930,5522	CC,CT,TT		9.907,4.0853,7.9348	probably-damaging	166/1026	98165091	1032,11974	2203	4300	6503	SO:0001583	missense	1806	exon6			TACTCATTGCTTT	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.496A>G	1.37:g.98165091T>C	ENSP00000359211:p.Met166Val	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	153	85	0.555556	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	145	0.06639194139194139	24	0.04878048780487805	28	0.07734806629834254	2	0.0034965034965034965	91	0.12005277044854881	T	18.97	3.736404	0.69189	0.040853	0.09907	ENSG00000188641	ENST00000370192	T	0.71579	-0.58	5.26	5.26	0.73747	Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1);	0.000000	0.85682	D	0.000000	D	0.82426	0.5034	M	0.85299	2.745	0.09310	P	1.0	D	0.89917	1.0	D	0.85130	0.997	D	0.85494	0.1187	9	0.56958	D	0.05	-23.1633	15.1667	0.72833	0.0:0.0:0.0:1.0	rs2297595;rs52827192;rs61243782;rs2297595	166	Q12882	DPYD_HUMAN	V	166	ENSP00000359211:M166V	ENSP00000359211:M166V	M	-	1	0	DPYD	97937679	1.000000	0.71417	0.999000	0.59377	0.862000	0.49288	7.664000	0.83830	2.002000	0.58637	0.477000	0.44152	ATG	T|0.934;C|0.066	0.066	strong		0.388	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
GPNMB	10457	hgsc.bcm.edu	37	7	23313745	23313745	+	Silent	SNP	C	C	T	rs78340800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:23313745C>T	ENST00000381990.2	+	11	1782	c.1621C>T	c.(1621-1623)Ctg>Ttg	p.L541L	GPNMB_ENST00000478451.1_3'UTR|GPNMB_ENST00000258733.4_Silent_p.L529L|GPNMB_ENST00000539136.1_Silent_p.L430L|GPNMB_ENST00000453162.2_Silent_p.L483L	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	541					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			AAGCAAAGGCCTGAGTGTCTT	0.388													C|||	10	0.00199681	0.0	0.0	5008	,	,		17461	0.0		0.0099	False		,,,				2504	0.0				p.L541L		Atlas-SNP	.											.	GPNMB	88	.	0			c.C1621T						PASS	.	C	,	7,4399	12.9+/-30.5	0,7,2196	84.0	85.0	85.0		1621,1585	4.2	0.2	7	dbSNP_132	85	59,8541	35.9+/-90.5	0,59,4241	no	coding-synonymous,coding-synonymous	GPNMB	NM_001005340.1,NM_002510.2	,	0,66,6437	TT,TC,CC		0.686,0.1589,0.5075	,	541/573,529/561	23313745	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	10457	exon11			AAAGGCCTGAGTG	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1621C>T	7.37:g.23313745C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																			C|0.995;T|0.005	0.005	strong		0.388	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552048	32552048	+	Missense_Mutation	SNP	C	C	T	rs56158521		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32552048C>T	ENST00000360004.5	-	2	313	c.208G>A	c.(208-210)Gac>Aac	p.D70N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	70	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						ACGTCGCTGTCGAAGCGCACG	0.632										Multiple Myeloma(14;0.17)																											p.D70N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G208A						PASS	.						37.0	36.0	36.0					6																	32552048		2194	4292	6486	SO:0001583	missense	3123	exon2			CGCTGTCGAAGCG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.208G>A	6.37:g.32552048C>T	ENSP00000353099:p.Asp70Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	119	21	0.176471	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	364	0.16666666666666666	38	0.07723577235772358	73	0.20165745856353592	112	0.1958041958041958	141	0.18601583113456466	.	11.18	1.563454	0.27915	.	.	ENSG00000196126	ENST00000360004	T	0.00358	7.88	3.52	2.61	0.31194	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	0.431350	0.28119	N	0.016536	T	0.00524	0.0017	M	0.93328	3.405	0.33541	D	0.594893	D	0.89917	1.0	D	0.91635	0.999	T	0.26292	-1.0107	10	0.66056	D	0.02	.	10.5792	0.45246	0.0:0.8015:0.1985:0.0	rs56158521	70	P01911	2B1F_HUMAN	N	70	ENSP00000353099:D70N	ENSP00000353099:D70N	D	-	1	0	HLA-DRB1	32660026	1.000000	0.71417	1.000000	0.80357	0.040000	0.13550	4.293000	0.59037	0.781000	0.33589	0.453000	0.30009	GAC	C|0.833;T|0.167	0.167	strong		0.632	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
CYP3A5	1577	hgsc.bcm.edu	37	7	99261643	99261643	+	Nonsense_Mutation	SNP	A	A	T	rs201260783		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99261643A>T	ENST00000222982.4	-	8	845	c.746T>A	c.(745-747)tTa>tAa	p.L249*	CYP3A5_ENST00000480723.1_5'Flank|CYP3A5_ENST00000343703.5_Nonsense_Mutation_p.L239*|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	249					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	AGATTTACTTAAAAAATTTAT	0.318													A|||	1	0.000199681	0.0	0.0	5008	,	,		18056	0.001		0.0	False		,,,				2504	0.0				p.L249X		Atlas-SNP	.											.	CYP3A5	46	.	0			c.T746A						PASS	.						101.0	97.0	99.0					7																	99261643		2203	4300	6503	SO:0001587	stop_gained	1577	exon8			TTACTTAAAAAAT	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.746T>A	7.37:g.99261643A>T	ENSP00000222982:p.Leu249*	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	166	78	0.46988	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Nonsense_Mutation	SNP	ENST00000222982.4	37	CCDS5672.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.424707	0.83667	.	.	ENSG00000106258	ENST00000222982;ENST00000343703	.	.	.	4.61	4.61	0.57282	.	0.204155	0.50627	D	0.000105	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	11.9716	0.53067	1.0:0.0:0.0:0.0	.	.	.	.	X	249;239	.	ENSP00000222982:L249X	L	-	2	0	CYP3A5	99099579	1.000000	0.71417	0.708000	0.30435	0.010000	0.07245	6.921000	0.75805	1.708000	0.51301	0.533000	0.62120	TTA	.	.	weak		0.318	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
SUV39H2	79723	hgsc.bcm.edu	37	10	14939485	14939485	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:14939485G>A	ENST00000354919.6	+	3	818	c.818G>A	c.(817-819)aGa>aAa	p.R273K	SUV39H2_ENST00000378325.3_Intron|DCLRE1C_ENST00000378289.4_3'UTR|SUV39H2_ENST00000313519.5_Missense_Mutation_p.R213K	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	273	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.R213I(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						AAGATTAAAAGAATGAGTTTT	0.383																																					p.R273K		Atlas-SNP	.											SUV39H2,colon,carcinoma,0,1	SUV39H2	72	1	1	Substitution - Missense(1)	large_intestine(1)	c.G818A						PASS	.						73.0	69.0	71.0					10																	14939485		2203	4300	6503	SO:0001583	missense	79723	exon3			TTAAAAGAATGAG	AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"""Chromatin-modifying enzymes / K-methyltransferases"""	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	ENST00000354919.6:c.818G>A	10.37:g.14939485G>A	ENSP00000346997:p.Arg273Lys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_001193424	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Missense_Mutation	SNP	ENST00000354919.6	37	CCDS53494.1	.	.	.	.	.	.	.	.	.	.	G	4.956	0.177547	0.09443	.	.	ENSG00000152455	ENST00000354919;ENST00000313519;ENST00000420416	T;T;D	0.87103	-1.19;-1.19;-2.21	5.86	4.96	0.65561	SET domain (3);	0.200646	0.44688	N	0.000427	T	0.52885	0.1762	N	0.00226	-1.805	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60682	-0.7215	10	0.02654	T	1	.	6.9776	0.24686	0.1531:0.1541:0.6928:0.0	.	273	Q9H5I1	SUV92_HUMAN	K	273;213;213	ENSP00000346997:R273K;ENSP00000319208:R213K;ENSP00000392201:R213K	ENSP00000319208:R213K	R	+	2	0	SUV39H2	14979491	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.691000	0.47010	1.631000	0.50456	0.650000	0.86243	AGA	.	.	none		0.383	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859983	144859983	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859983G>A	ENST00000369354.3	-	38	6290	c.6101C>T	c.(6100-6102)gCc>gTc	p.A2034V	PDE4DIP_ENST00000313382.9_Missense_Mutation_p.A1928V|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.A2034V|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.A2119V|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.A2170V|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2034					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTGGTGACAGGCATCCAGGCT	0.517			T	PDGFRB	MPD																																p.A2034V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP,caecum,carcinoma,+1,1	PDE4DIP	817	1	0			c.C6101T						scavenged	.						116.0	110.0	112.0					1																	144859983		2203	4296	6499	SO:0001583	missense	9659	exon38			TGACAGGCATCCA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6101C>T	1.37:g.144859983G>A	ENSP00000358360:p.Ala2034Val	Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	251	7	0.0278884	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	6.315	0.426225	0.11987	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01787	4.64;4.72;4.74;4.74;4.73	5.1	0.914	0.19360	.	.	.	.	.	T	0.00724	0.0024	M	0.61703	1.905	0.09310	N	0.999996	B;B	0.16166	0.0;0.016	B;B	0.11329	0.001;0.006	T	0.44544	-0.9321	9	0.20046	T	0.44	.	5.7568	0.18178	0.2572:0.1457:0.597:0.0	.	1928;2034	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	V	1928;2034;2034;2119;2170	ENSP00000327209:A1928V;ENSP00000358360:A2034V;ENSP00000358363:A2034V;ENSP00000435654:A2119V;ENSP00000358366:A2170V	ENSP00000327209:A1928V	A	-	2	0	PDE4DIP	143571340	0.010000	0.17322	0.992000	0.48379	0.004000	0.04260	0.910000	0.28571	0.680000	0.31366	-0.759000	0.03464	GCC	.	.	none		0.517	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
UNC79	57578	hgsc.bcm.edu	37	14	94088369	94088369	+	Missense_Mutation	SNP	T	T	C	rs28670114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94088369T>C	ENST00000393151.2	+	30	4790	c.4790T>C	c.(4789-4791)gTa>gCa	p.V1597A	UNC79_ENST00000555664.1_Missense_Mutation_p.V1597A|UNC79_ENST00000256339.4_Missense_Mutation_p.V1420A|UNC79_ENST00000553484.1_Missense_Mutation_p.V1619A			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1597			V -> A (in dbSNP:rs28670114).		behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						GACTCGCCGGTAAAGCCTGCT	0.478													T|||	594	0.11861	0.1634	0.134	5008	,	,		19307	0.004		0.2038	False		,,,				2504	0.0777				p.V1420A		Atlas-SNP	.											.	UNC79	366	.	0			c.T4259C						PASS	.	T	ALA/VAL	675,3731	284.6+/-277.7	54,567,1582	69.0	73.0	72.0		4259	-10.5	0.0	14	dbSNP_125	72	1535,7065	288.0+/-298.5	140,1255,2905	yes	missense	UNC79	NM_020818.3	64	194,1822,4487	CC,CT,TT		17.8488,15.32,16.9922	benign	1420/2459	94088369	2210,10796	2203	4300	6503	SO:0001583	missense	57578	exon30			CGCCGGTAAAGCC	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4790T>C	14.37:g.94088369T>C	ENSP00000376858:p.Val1597Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		296	0.13553113553113552	77	0.1565040650406504	55	0.15193370165745856	1	0.0017482517482517483	163	0.21503957783641162	T	1.765	-0.485748	0.04352	0.1532	0.178488	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.17054	2.3;2.31;2.3;2.3	5.85	-10.5	0.00291	.	1.244990	0.05238	N	0.511633	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36311	-0.9753	9	0.07990	T	0.79	1.8056	7.1867	0.25803	0.0888:0.115:0.523:0.2731	rs28670114	1619	C9JQL1	.	A	1420;1597;1619;1597;1619	ENSP00000256339:V1420A;ENSP00000450868:V1597A;ENSP00000451360:V1619A;ENSP00000376858:V1597A	ENSP00000256339:V1420A	V	+	2	0	KIAA1409	93158122	0.000000	0.05858	0.000000	0.03702	0.230000	0.25150	-0.415000	0.07106	-1.287000	0.02381	-0.680000	0.03767	GTA	T|0.833;C|0.167	0.167	strong		0.478	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
C2orf16	84226	hgsc.bcm.edu	37	2	27802805	27802805	+	Silent	SNP	A	A	G	rs3811644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:27802805A>G	ENST00000408964.2	+	1	3417	c.3366A>G	c.(3364-3366)ctA>ctG	p.L1122L	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1122						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTATCTGCCTACAGTGTGGCC	0.463													A|||	1025	0.204673	0.0499	0.111	5008	,	,		20009	0.3383		0.2137	False		,,,				2504	0.3333				p.L1122L		Atlas-SNP	.											.	C2orf16	357	.	0			c.A3366G						PASS	.	A		293,3591		6,281,1655	108.0	109.0	109.0		3366	2.5	1.0	2	dbSNP_107	109	1677,6613		169,1339,2637	no	coding-synonymous	C2orf16	NM_032266.3		175,1620,4292	GG,GA,AA		20.2292,7.5438,16.182		1122/1985	27802805	1970,10204	1942	4145	6087	SO:0001819	synonymous_variant	84226	exon1			CTGCCTACAGTGT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3366A>G	2.37:g.27802805A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	171	73	0.426901	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			A|0.811;G|0.189	0.189	strong		0.463	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
LAD1	3898	hgsc.bcm.edu	37	1	201355653	201355653	+	Missense_Mutation	SNP	G	G	T	rs11805972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201355653G>T	ENST00000391967.2	-	3	1137	c.836C>A	c.(835-837)cCg>cAg	p.P279Q	LAD1_ENST00000367313.3_Missense_Mutation_p.P293Q|LAD1_ENST00000488842.1_5'Flank	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	279			P -> Q (in dbSNP:rs11805972).			basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						CTTTGGGGCCGGCTTAGCATC	0.637													G|||	435	0.086861	0.2466	0.0389	5008	,	,		12124	0.0377		0.0288	False		,,,				2504	0.0153				p.P279Q		Atlas-SNP	.											.	LAD1	42	.	0			c.C836A						PASS	.	G	GLN/PRO	965,3441	342.0+/-307.0	110,745,1348	55.0	62.0	60.0		836	-10.8	0.0	1	dbSNP_120	60	249,8351	96.8+/-158.5	4,241,4055	yes	missense	LAD1	NM_005558.3	76	114,986,5403	TT,TG,GG		2.8953,21.902,9.3342	possibly-damaging	279/518	201355653	1214,11792	2203	4300	6503	SO:0001583	missense	3898	exon3			GGGGCCGGCTTAG	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.836C>A	1.37:g.201355653G>T	ENSP00000375829:p.Pro279Gln	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	216	128	0.592593	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	37	CCDS1410.1	186	0.08516483516483517	129	0.2621951219512195	14	0.03867403314917127	20	0.03496503496503497	23	0.030343007915567283	G	11.58	1.681792	0.29872	0.21902	0.028953	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.12879	2.65;2.64	5.41	-10.8	0.00216	.	1.796930	0.02754	N	0.117796	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	B;B	0.23735	0.052;0.09	B;B	0.30572	0.027;0.117	T	0.14531	-1.0469	9	0.15952	T	0.53	0.1479	10.4961	0.44778	0.1594:0.1019:0.6387:0.1001	rs11805972;rs11805972	293;279	E9PDI4;O00515	.;LAD1_HUMAN	Q	279;293	ENSP00000375829:P279Q;ENSP00000356282:P293Q	ENSP00000356282:P293Q	P	-	2	0	LAD1	199622276	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.890000	0.01613	-3.296000	0.00193	-0.768000	0.03414	CCG	G|0.909;T|0.091	0.091	strong		0.637	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
PARP1	142	hgsc.bcm.edu	37	1	226589958	226589958	+	Silent	SNP	G	G	A	rs1805404	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:226589958G>A	ENST00000366794.5	-	2	386	c.243C>T	c.(241-243)gaC>gaT	p.D81D	PARP1_ENST00000366791.5_Silent_p.D81D|PARP1_ENST00000366790.3_Silent_p.D81D|PARP1_ENST00000366792.1_Silent_p.D81D	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	81					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CTTTCTGCTGGTCATCCCACC	0.587								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					G|||	1093	0.218251	0.115	0.3573	5008	,	,		18540	0.4365		0.1541	False		,,,				2504	0.1002				p.D81D		Atlas-SNP	.											PARP1,colon,carcinoma,-1,1	PARP1	100	1	0			c.C243T						PASS	.	G		553,3853	250.3+/-257.4	37,479,1687	102.0	88.0	93.0		243	3.3	1.0	1	dbSNP_92	93	1368,7232	267.2+/-287.2	124,1120,3056	no	coding-synonymous	PARP1	NM_001618.3		161,1599,4743	AA,AG,GG		15.907,12.5511,14.7701		81/1015	226589958	1921,11085	2203	4300	6503	SO:0001819	synonymous_variant	142	exon2			CTGCTGGTCATCC	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.243C>T	1.37:g.226589958G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_001618	B1ANJ4|Q8IUZ9	Silent	SNP	ENST00000366794.5	37	CCDS1554.1																																																																																			G|0.811;A|0.189	0.189	strong		0.587	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
ROM1	6094	hgsc.bcm.edu	37	11	62381106	62381106	+	Missense_Mutation	SNP	G	G	C	rs1799959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62381106G>C	ENST00000278833.3	+	1	894	c.353G>C	c.(352-354)gGc>gCc	p.G118A	EML3_ENST00000278845.4_5'Flank|EML3_ENST00000531557.1_5'Flank|EML3_ENST00000394773.2_5'Flank|EML3_ENST00000494176.2_5'Flank|ROM1_ENST00000534093.1_Intron|EML3_ENST00000529309.1_5'Flank	NM_000327.3	NP_000318	Q03395	ROM1_HUMAN	retinal outer segment membrane protein 1	118			G -> A (in dbSNP:rs1799959). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1610568, ECO:0000269|PubMed:7904211, ECO:0000269|PubMed:8504299}.		camera-type eye photoreceptor cell differentiation (GO:0060219)|cell adhesion (GO:0007155)|regulation of gene expression (GO:0010468)|retina vasculature development in camera-type eye (GO:0061298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	8						CTGGTCGTCGGCCTCGGGCTA	0.682													C|||	4684	0.935304	0.7723	0.9755	5008	,	,		13418	1.0		0.995	False		,,,				2504	0.999				p.G118A		Atlas-SNP	.											.	ROM1	32	.	0			c.G353C						PASS	.	C	ALA/GLY	3622,782	296.1+/-284.1	1480,662,60	23.0	25.0	24.0		353	3.7	0.6	11	dbSNP_89	24	8580,18	11.2+/-40.8	4281,18,0	yes	missense	ROM1	NM_000327.3	60	5761,680,60	CC,CG,GG		0.2094,17.7566,6.1529	benign	118/352	62381106	12202,800	2202	4299	6501	SO:0001583	missense	6094	exon1			TCGTCGGCCTCGG	L07894	CCDS8024.1	11q13	2013-02-14				ENSG00000149489		"""Tetraspanins"""	10254	protein-coding gene	gene with protein product		180721				8504299	Standard	NM_000327		Approved	TSPAN23, ROM	uc001ntv.3	Q03395		ENST00000278833.3:c.353G>C	11.37:g.62381106G>C	ENSP00000278833:p.Gly118Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	33	32	0.969697	NM_000327	B2R978	Missense_Mutation	SNP	ENST00000278833.3	37	CCDS8024.1	2040	0.9340659340659341	363	0.7378048780487805	351	0.9696132596685083	572	1.0	754	0.9947229551451188	C	0.004	-2.342039	0.00222	0.822434	0.997906	ENSG00000149489	ENST00000278833	T	0.76709	-1.04	4.64	3.72	0.42706	.	0.292336	0.33938	N	0.004414	T	0.00012	0.0000	N	0.00633	-1.31	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.44574	-0.9319	9	0.02654	T	1	-25.3964	11.3329	0.49487	0.0:0.6467:0.3533:0.0	rs1799959;rs4403810;rs17845150;rs17857954;rs61694018;rs1799959	118	Q03395	ROM1_HUMAN	A	118	ENSP00000278833:G118A	ENSP00000278833:G118A	G	+	2	0	ROM1	62137682	0.000000	0.05858	0.569000	0.28460	0.015000	0.08874	0.103000	0.15292	0.564000	0.29238	-0.647000	0.03941	GGC	G|0.071;C|0.929	0.929	strong		0.682	ROM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394929.1	NM_000327	
POLN	353497	hgsc.bcm.edu	37	4	2195024	2195024	+	Missense_Mutation	SNP	T	T	G	rs10018786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2195024T>G	ENST00000511885.2	-	7	1281	c.928A>C	c.(928-930)Atg>Ctg	p.M310L	POLN_ENST00000382865.1_Missense_Mutation_p.M310L|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	310			M -> L (in dbSNP:rs10018786). {ECO:0000269|Ref.3}.		double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			TTACATTTCATTGTTTGAAAT	0.318								DNA polymerases (catalytic subunits)					G|||	1656	0.330671	0.6029	0.2464	5008	,	,		19994	0.372		0.1243	False		,,,				2504	0.1922				p.M310L		Atlas-SNP	.											.	POLN	82	.	0			c.A928C						PASS	.	G	LEU/MET	2357,2049	564.7+/-381.5	662,1033,508	68.0	70.0	69.0		928	4.6	0.0	4	dbSNP_119	69	991,7609	772.3+/-407.7	59,873,3368	yes	missense	POLN	NM_181808.2	15	721,1906,3876	GG,GT,TT		11.5233,46.5048,25.742	benign	310/901	2195024	3348,9658	2203	4300	6503	SO:0001583	missense	353497	exon5			ATTTCATTGTTTG	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.928A>C	4.37:g.2195024T>G	ENSP00000435506:p.Met310Leu	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	170	77	0.452941	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	37	CCDS3360.1	694	0.31776556776556775	299	0.6077235772357723	91	0.2513812154696133	209	0.36538461538461536	95	0.12532981530343007	G	0.006	-2.116122	0.00349	0.534952	0.115233	ENSG00000130997	ENST00000511885;ENST00000382865;ENST00000253313	T;T	0.13196	2.61;2.61	5.48	4.64	0.57946	.	0.000000	0.64402	N	0.000016	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42716	-0.9435	9	0.02654	T	1	-6.3637	7.3201	0.26523	0.0855:0.0:0.748:0.1665	rs10018786;rs52806224;rs59046783;rs10018786	310;310	E7ERY2;Q7Z5Q5	.;DPOLN_HUMAN	L	310;310;1	ENSP00000435506:M310L;ENSP00000372316:M310L	ENSP00000253313:M1L	M	-	1	0	POLN	2164822	0.990000	0.36364	0.034000	0.17996	0.109000	0.19521	2.467000	0.45093	0.701000	0.31803	-0.770000	0.03390	ATG	T|0.710;G|0.290	0.290	strong		0.318	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
PDE5A	8654	hgsc.bcm.edu	37	4	120474859	120474859	+	Silent	SNP	A	A	G	rs11947234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:120474859A>G	ENST00000354960.3	-	8	1561	c.1242T>C	c.(1240-1242)taT>taC	p.Y414Y	PDE5A_ENST00000394439.1_Silent_p.Y362Y|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000264805.5_Silent_p.Y372Y	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	414	GAF 2.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TATTTTTGACATACTGAGCAT	0.358													A|||	1331	0.265775	0.2118	0.2867	5008	,	,		18474	0.3929		0.2863	False		,,,				2504	0.1718				p.Y414Y		Atlas-SNP	.											.	PDE5A	83	.	0			c.T1242C						PASS	.	A	,,	917,3489	351.8+/-311.4	104,709,1390	233.0	226.0	228.0		1242,1116,1086	3.3	1.0	4	dbSNP_120	228	2462,6138	404.9+/-348.3	347,1768,2185	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE5A	NM_001083.3,NM_033430.2,NM_033437.3	,,	451,2477,3575	GG,GA,AA		28.6279,20.8125,25.9803	,,	414/876,372/834,362/824	120474859	3379,9627	2203	4300	6503	SO:0001819	synonymous_variant	8654	exon8			TTTGACATACTGA	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"""Phosphodiesterases"""	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1242T>C	4.37:g.120474859A>G		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	180	179	0.994444	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Silent	SNP	ENST00000354960.3	37	CCDS3713.1																																																																																			A|0.732;G|0.268	0.268	strong		0.358	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	
GP2	2813	hgsc.bcm.edu	37	16	20335325	20335325	+	Silent	SNP	G	G	A	rs12930599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20335325G>A	ENST00000381362.4	-	3	424	c.348C>T	c.(346-348)gaC>gaT	p.D116D	GP2_ENST00000381360.5_Intron|GP2_ENST00000341642.5_Intron|GP2_ENST00000302555.5_Silent_p.D116D|GP2_ENST00000573897.1_5'Flank	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	116					antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						ACATGGGAGCGTCTGTCTGGC	0.572													G|||	414	0.0826677	0.0068	0.1772	5008	,	,		18878	0.0089		0.2256	False		,,,				2504	0.047				p.D116D		Atlas-SNP	.											.	GP2	122	.	0			c.C348T						PASS	.	G	,,,	205,4201	124.5+/-161.8	3,199,2001	98.0	77.0	84.0		348,,,348	-10.0	0.0	16	dbSNP_121	84	1890,6710	335.5+/-321.5	201,1488,2611	no	coding-synonymous,intron,intron,coding-synonymous	GP2	NM_001007240.1,NM_001007241.1,NM_001007242.1,NM_001502.2	,,,	204,1687,4612	AA,AG,GG		21.9767,4.6527,16.108	,,,	116/538,,,116/535	20335325	2095,10911	2203	4300	6503	SO:0001819	synonymous_variant	2813	exon3			GGGAGCGTCTGTC	U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.348C>T	16.37:g.20335325G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_001007240	A6NFM9|A6NJA8|Q13338|Q9UIF1	Silent	SNP	ENST00000381362.4	37	CCDS42128.1																																																																																			G|0.865;A|0.135	0.135	strong		0.572	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295	
CNGB1	1258	hgsc.bcm.edu	37	16	57950057	57950057	+	Silent	SNP	G	G	A	rs376270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:57950057G>A	ENST00000251102.8	-	22	2253	c.2193C>T	c.(2191-2193)aaC>aaT	p.N731N	CNGB1_ENST00000564448.1_Silent_p.N725N	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	731			N -> K (in dbSNP:rs376270).		cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						ACTTCAGGTAGTTATTTCGCA	0.522													G|||	1813	0.362021	0.1808	0.3372	5008	,	,		19169	0.5486		0.3191	False		,,,				2504	0.4765				p.N731N	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.C2193T						PASS	.	G		722,3178		56,610,1284	135.0	133.0	134.0		2193	-0.2	0.7	16	dbSNP_80	134	2856,5418		495,1866,1776	no	coding-synonymous	CNGB1	NM_001297.4		551,2476,3060	AA,AG,GG		34.5178,18.5128,29.3905		731/1252	57950057	3578,8596	1950	4137	6087	SO:0001819	synonymous_variant	1258	exon22			CAGGTAGTTATTT	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2193C>T	16.37:g.57950057G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	168	77	0.458333	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																			A|0.342;C|0.004;G|0.647;N|0.000;T|0.007	0.342	strong		0.522	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
PCDHB6	56130	hgsc.bcm.edu	37	5	140530529	140530529	+	Missense_Mutation	SNP	G	G	A	rs3776096	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140530529G>A	ENST00000231136.1	+	1	691	c.691G>A	c.(691-693)Gtt>Att	p.V231I	PCDHB6_ENST00000543635.1_Missense_Mutation_p.V95I	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	231	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> I (in dbSNP:rs3776096).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCAGATCCAGGTTTTGGACAT	0.587													G|||	1341	0.267772	0.0129	0.3141	5008	,	,		17417	0.5298		0.2416	False		,,,				2504	0.3364				p.V231I		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G691A						PASS	.	G	ILE/VAL	189,4217	119.2+/-156.9	3,183,2017	44.0	48.0	46.0		691	3.1	0.1	5	dbSNP_107	46	1988,6612	343.6+/-325.0	232,1524,2544	yes	missense	PCDHB6	NM_018939.2	29	235,1707,4561	AA,AG,GG		23.1163,4.2896,16.7384	benign	231/795	140530529	2177,10829	2203	4300	6503	SO:0001583	missense	56130	exon1			ATCCAGGTTTTGG	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.691G>A	5.37:g.140530529G>A	ENSP00000231136:p.Val231Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	130	72	0.553846	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	575	0.2632783882783883	7	0.014227642276422764	92	0.2541436464088398	301	0.5262237762237763	175	0.23087071240105542	G	13.78	2.339532	0.41398	0.042896	0.231163	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.61510	0.1;0.1	4.85	3.06	0.35304	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.45698	1.435	0.33384	P	0.424759	B	0.27316	0.175	B	0.33339	0.162	T	0.46775	-0.9167	8	0.44086	T	0.13	.	10.3152	0.43732	0.2167:0.0:0.7833:0.0	rs3776096;rs17844430;rs52836452;rs58825835;rs3776096	231	Q9Y5E3	PCDB6_HUMAN	I	95;231;16	ENSP00000438466:V95I;ENSP00000231136:V231I	ENSP00000231136:V231I	V	+	1	0	PCDHB6	140510713	1.000000	0.71417	0.079000	0.20413	0.849000	0.48306	4.095000	0.57728	0.566000	0.29273	0.561000	0.74099	GTT	G|0.783;A|0.217	0.217	strong		0.587	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
SLC25A47	283600	hgsc.bcm.edu	37	14	100795139	100795139	+	Missense_Mutation	SNP	G	G	T	rs35007880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:100795139G>T	ENST00000361529.3	+	5	482	c.404G>T	c.(403-405)cGg>cTg	p.R135L	SLC25A47_ENST00000557052.1_5'UTR	NM_207117.2	NP_997000.2	Q6Q0C1	S2547_HUMAN	solute carrier family 25, member 47	135					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	13						CAGCAGCGGCGGCTTTCGGCC	0.682													G|||	1639	0.327276	0.0424	0.3127	5008	,	,		17253	0.2262		0.492	False		,,,				2504	0.6575				p.R135L	GBM(11;1289 1351)	Atlas-SNP	.											SLC25A47,NS,carcinoma,0,1	SLC25A47	36	1	0			c.G404T						PASS	.	G	LEU/ARG	440,3886		47,346,1770	21.0	23.0	22.0		404	3.9	0.9	14	dbSNP_126	22	4022,4358		1006,2010,1174	yes	missense	SLC25A47	NM_207117.2	102	1053,2356,2944	TT,TG,GG		47.9952,10.1711,35.1173	probably-damaging	135/309	100795139	4462,8244	2163	4190	6353	SO:0001583	missense	283600	exon5			AGCGGCGGCTTTC		CCDS9959.1	14q32.2	2013-05-22	2010-07-19	2010-07-19	ENSG00000140107	ENSG00000140107		"""Solute carriers"""	20115	protein-coding gene	gene with protein product		609911	"""chromosome 14 open reading frame 68"""	C14orf68			Standard	NM_207117		Approved		uc001yhc.3	Q6Q0C1	OTTHUMG00000171571	ENST00000361529.3:c.404G>T	14.37:g.100795139G>T	ENSP00000354886:p.Arg135Leu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_207117	B2RP39|Q68CL2|Q6PZD8|Q86U14	Missense_Mutation	SNP	ENST00000361529.3	37	CCDS9959.1	604	0.2765567765567766	24	0.04878048780487805	118	0.3259668508287293	101	0.17657342657342656	361	0.4762532981530343	G	8.690	0.907281	0.17833	0.101711	0.479952	ENSG00000140107	ENST00000361529	D	0.81659	-1.52	4.89	3.93	0.45458	Mitochondrial carrier domain (2);	2.605420	0.01942	N	0.042002	T	0.00012	0.0000	L	0.33485	1.01	0.18873	P	0.9999839802	P	0.50528	0.936	P	0.47206	0.541	T	0.42649	-0.9439	9	0.10636	T	0.68	-0.5229	3.1999	0.06646	0.0966:0.3091:0.4294:0.1649	rs35007880	135	Q6Q0C1	S2547_HUMAN	L	135	ENSP00000354886:R135L	ENSP00000354886:R135L	R	+	2	0	SLC25A47	99864892	0.942000	0.31987	0.930000	0.37139	0.463000	0.32649	1.603000	0.36794	2.262000	0.75019	0.491000	0.48974	CGG	G|0.667;T|0.333	0.333	strong		0.682	SLC25A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414231.1		
HERPUD1	9709	hgsc.bcm.edu	37	16	56974077	56974077	+	Silent	SNP	T	T	C	rs147630132	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:56974077T>C	ENST00000439977.2	+	6	1022	c.825T>C	c.(823-825)tcT>tcC	p.S275S	RP11-325K4.3_ENST00000565861.1_RNA|HERPUD1_ENST00000570273.1_Intron|HERPUD1_ENST00000379792.2_Silent_p.S250S|HERPUD1_ENST00000344114.4_Intron|RP11-325K4.2_ENST00000570210.1_RNA|HERPUD1_ENST00000300302.5_Silent_p.S274S	NM_001010989.1|NM_014685.2	NP_001010989.1|NP_055500.1	Q15011	HERP1_HUMAN	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	275					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of protein binding (GO:0032092)|regulation of protein ubiquitination (GO:0031396)|response to unfolded protein (GO:0006986)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|stomach(1)	11						CTACATTTTCTGTTTTTCTCA	0.433			T	ERG	prostate								T|||	25	0.00499201	0.0015	0.0072	5008	,	,		20452	0.0		0.0149	False		,,,				2504	0.0031				p.S275S		Atlas-SNP	.		Dom	yes		16	16q12.2-q13	9709	"""homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1"""		E	.	HERPUD1	28	.	0			c.T825C						PASS	.	T	,,	24,4372	30.8+/-60.4	0,24,2174	237.0	220.0	226.0		822,750,825	-9.3	0.7	16	dbSNP_134	226	207,8393	89.2+/-151.4	3,201,4096	no	coding-synonymous,coding-synonymous,coding-synonymous	HERPUD1	NM_001010989.1,NM_001010990.1,NM_014685.2	,,	3,225,6270	CC,CT,TT		2.407,0.546,1.7775	,,	274/391,250/367,275/392	56974077	231,12765	2198	4300	6498	SO:0001819	synonymous_variant	9709	exon6			ATTTTCTGTTTTT	AB034989	CCDS10771.1, CCDS45492.1	16q13	2008-05-14			ENSG00000051108	ENSG00000051108			13744	protein-coding gene	gene with protein product		608070				10922362, 10708769	Standard	NM_001010989		Approved	KIAA0025, Mif1, HERP, SUP	uc002eke.2	Q15011	OTTHUMG00000133276	ENST00000439977.2:c.825T>C	16.37:g.56974077T>C		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	326	164	0.503067	NM_014685	E9PGD1|O60644|Q6IAN8|Q96D92	Silent	SNP	ENST00000439977.2	37	CCDS10771.1																																																																																			T|0.985;C|0.015	0.015	strong		0.433	HERPUD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257056.5		
ZNF469	84627	hgsc.bcm.edu	37	16	88494976	88494976	+	Missense_Mutation	SNP	A	A	C	rs11640794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88494976A>C	ENST00000437464.1	+	1	1098	c.1098A>C	c.(1096-1098)agA>agC	p.R366S	ZNF469_ENST00000565624.1_Missense_Mutation_p.R366S	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	366	Pro-rich.		R -> S (in dbSNP:rs11640794).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CGGCCCCGAGACCCTTCTCTG	0.637													A|||	4282	0.855032	0.5991	0.9424	5008	,	,		14149	0.9147		0.9453	False		,,,				2504	0.9847				p.R366S		Atlas-SNP	.											.	ZNF469	121	.	0			c.A1098C						PASS	.						5.0	6.0	6.0					16																	88494976		667	1544	2211	SO:0001583	missense	84627	exon1			CCCGAGACCCTTC	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.1098A>C	16.37:g.88494976A>C	ENSP00000402343:p.Arg366Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	1869	0.8557692307692307	293	0.5955284552845529	342	0.9447513812154696	520	0.9090909090909091	714	0.941952506596306	A	3.854	-0.031218	0.07543	.	.	ENSG00000225614	ENST00000437464	T	0.04502	3.61	4.6	0.792	0.18625	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.10296	0.003	B	0.01281	0.0	T	0.31641	-0.9936	8	0.02654	T	1	.	4.2752	0.10806	0.163:0.5853:0.1471:0.1046	rs11640794;rs52802024;rs57771670;rs11640794	366	Q96JG9	ZN469_HUMAN	S	366	ENSP00000402343:R366S	ENSP00000402343:R366S	R	+	3	2	ZNF469	87022477	0.925000	0.31364	0.657000	0.29651	0.285000	0.27093	0.562000	0.23531	0.325000	0.23359	-0.648000	0.03929	AGA	A|0.169;C|0.831	0.831	strong		0.637	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
OR8D1	283159	hgsc.bcm.edu	37	11	124180282	124180282	+	Missense_Mutation	SNP	A	A	C	rs7107539	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124180282A>C	ENST00000357821.2	-	1	451	c.381T>G	c.(379-381)tgT>tgG	p.C127W		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	127			C -> W (in dbSNP:rs7107539).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GCAGTGGGCTACAGATGGCAA	0.498													A|||	1340	0.267572	0.0893	0.3372	5008	,	,		20356	0.4177		0.4066	False		,,,				2504	0.1616				p.C127W		Atlas-SNP	.											.	OR8D1	53	.	0			c.T381G						PASS	.	A	TRP/CYS	619,3783	268.6+/-268.5	39,541,1621	84.0	74.0	78.0		381	-3.2	0.0	11	dbSNP_116	78	3381,5217	499.8+/-375.1	672,2037,1590	yes	missense	OR8D1	NM_001002917.1	215	711,2578,3211	CC,CA,AA		39.3231,14.0618,30.7692	probably-damaging	127/309	124180282	4000,9000	2201	4299	6500	SO:0001583	missense	283159	exon1			TGGGCTACAGATG	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"""GPCR / Class A : Olfactory receptors"""	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.381T>G	11.37:g.124180282A>C	ENSP00000350474:p.Cys127Trp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	37	CCDS31706.1	708	0.3241758241758242	35	0.07113821138211382	132	0.36464088397790057	243	0.42482517482517484	298	0.39313984168865435	a	14.89	2.670230	0.47677	0.140618	0.393231	ENSG00000196341	ENST00000357821	T	0.07327	3.2	4.29	-3.22	0.05125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40302	U	0.001137	T	0.00012	0.0000	H	0.96518	3.835	0.33753	P	0.37909400000000004	D	0.89917	1.0	D	0.97110	1.0	T	0.30446	-0.9978	9	0.72032	D	0.01	.	14.3721	0.66846	0.2778:0.0:0.7222:0.0	rs7107539;rs7107539	127	Q8WZ84	OR8D1_HUMAN	W	127	ENSP00000350474:C127W	ENSP00000350474:C127W	C	-	3	2	OR8D1	123685492	0.000000	0.05858	0.009000	0.14445	0.097000	0.18754	-1.117000	0.03283	-0.868000	0.04058	0.416000	0.27883	TGT	A|0.693;C|0.307	0.307	strong		0.498	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917	
C1QTNF9B	387911	hgsc.bcm.edu	37	13	24471048	24471048	+	Silent	SNP	C	C	T	rs35159134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:24471048C>T	ENST00000382140.2	-	3	138	c.78G>A	c.(76-78)ggG>ggA	p.G26G	C1QTNF9B-AS1_ENST00000417034.1_RNA|C1QTNF9B_ENST00000382145.1_Silent_p.G26G|C1QTNF9B_ENST00000382137.3_Silent_p.G26G|C1QTNF9B_ENST00000556521.1_5'UTR|C1QTNF9B_ENST00000382057.3_Silent_p.G26G			B2RNN3	C1T9B_HUMAN	C1q and tumor necrosis factor related protein 9B	26	Collagen-like 1.					collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(1)	6						TTCCAGGGTGCCCTTGCCTGC	0.547													C|||	1054	0.210463	0.025	0.2637	5008	,	,		22510	0.4752		0.2495	False		,,,				2504	0.1104				p.G26G		Atlas-SNP	.											.	C1QTNF9B	27	.	0			c.G78A						PASS	.						107.0	103.0	105.0					13																	24471048		2202	4281	6483	SO:0001819	synonymous_variant	387911	exon1			AGGGTGCCCTTGC	BC110413	CCDS31947.1	13q12.12	2011-05-08			ENSG00000205863	ENSG00000205863			34072	protein-coding gene	gene with protein product		614148				17544811	Standard	NM_001007537		Approved	CTRP9B	uc010tcv.1	B2RNN3	OTTHUMG00000016570	ENST00000382140.2:c.78G>A	13.37:g.24471048C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	223	125	0.560538	NM_001007537	A2A3T6|B9EH31|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	Silent	SNP	ENST00000382140.2	37	CCDS31947.1																																																																																			.	.	weak		0.547	C1QTNF9B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044162.3	NM_001007537	
OR10Q1	219960	hgsc.bcm.edu	37	11	57995777	57995777	+	Missense_Mutation	SNP	G	G	A	rs11229301	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57995777G>A	ENST00000316770.2	-	1	613	c.571C>T	c.(571-573)Cgc>Tgc	p.R191C		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	191			R -> C (in dbSNP:rs11229301).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				CAGGCCAGGCGCAGGACGGGA	0.612													G|||	776	0.154952	0.1513	0.1873	5008	,	,		21565	0.123		0.163	False		,,,				2504	0.1616				p.R191C		Atlas-SNP	.											OR10Q1,NS,carcinoma,+1,2	OR10Q1	79	2	0			c.C571T						PASS	.	G	CYS/ARG	624,3778	271.9+/-270.5	53,518,1630	73.0	63.0	67.0		571	1.4	1.0	11	dbSNP_120	67	1199,7391	241.9+/-272.1	91,1017,3187	yes	missense	OR10Q1	NM_001004471.2	180	144,1535,4817	AA,AG,GG		13.9581,14.1754,14.0317	benign	191/320	57995777	1823,11169	2201	4295	6496	SO:0001583	missense	219960	exon1			CCAGGCGCAGGAC	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"""GPCR / Class A : Olfactory receptors"""	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.571C>T	11.37:g.57995777G>A	ENSP00000314324:p.Arg191Cys	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	158	84	0.531646	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	37	CCDS31547.1	325	0.1488095238095238	56	0.11382113821138211	71	0.19613259668508287	78	0.13636363636363635	120	0.158311345646438	G	5.949	0.359011	0.11239	0.141754	0.139581	ENSG00000180475	ENST00000316770	T	0.00158	8.65	4.47	1.43	0.22495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000943	T	0.00012	0.0000	M	0.80847	2.515	0.80722	P	0.0	B	0.29301	0.241	B	0.28784	0.094	T	0.36335	-0.9752	9	0.72032	D	0.01	.	6.7485	0.23474	0.0889:0.0:0.3361:0.575	rs11229301;rs56678494;rs11229301	191	Q8NGQ4	O10Q1_HUMAN	C	191	ENSP00000314324:R191C	ENSP00000314324:R191C	R	-	1	0	OR10Q1	57752353	0.000000	0.05858	0.986000	0.45419	0.101000	0.19017	-1.080000	0.03407	0.113000	0.18004	0.585000	0.79938	CGC	G|0.865;A|0.135	0.135	strong		0.612	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471	
CTAGE1	64693	hgsc.bcm.edu	37	18	19996805	19996805	+	5'Flank	SNP	T	T	C	rs12961009	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:19996805T>C	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.I324V			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					AGATTTTTAATATGCTCTGTA	0.313													T|||	78	0.0155751	0.0015	0.0245	5008	,	,		18989	0.001		0.0497	False		,,,				2504	0.0082				p.I324V		Atlas-SNP	.											.	CTAGE1	146	.	0			c.A970G						PASS	.	T	VAL/ILE	43,4211		0,43,2084	34.0	38.0	37.0		970	0.7	0.0	18	dbSNP_121	37	371,8155		6,359,3898	no	missense	CTAGE1	NM_172241.2	29	6,402,5982	CC,CT,TT		4.3514,1.0108,3.2394	benign	324/746	19996805	414,12366	2127	4263	6390	SO:0001631	upstream_gene_variant	64693	exon1			TTTTAATATGCTC	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 1"", ""cutaneous T-cell lymphoma-associated antigen 2"", ""cancer/testis antigen family 21, member 1"", ""cancer/testis antigen family 21, member 2"""	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19996805T>C	Exception_encountered	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_172241	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	37		45	0.020604395604395604	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	34	0.044854881266490766	T	6.941	0.543343	0.13250	0.010108	0.043514	ENSG00000212710	ENST00000391403	T	0.37584	1.19	0.741	0.741	0.18336	.	.	.	.	.	T	0.10252	0.0251	M	0.77486	2.375	0.09310	N	1	B	0.33940	0.433	B	0.35470	0.203	T	0.15838	-1.0423	8	.	.	.	.	3.7843	0.08694	0.0:0.0:0.0:1.0	rs12961009	324	Q96RT6	CTGE2_HUMAN	V	324	ENSP00000375220:I324V	.	I	-	1	0	CTAGE1	18250803	1.000000	0.71417	0.034000	0.17996	0.294000	0.27393	2.665000	0.46791	0.560000	0.29169	0.369000	0.22263	ATT	T|0.976;C|0.024	0.024	strong		0.313	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241	
CSHL1	1444	hgsc.bcm.edu	37	17	61987570	61987570	+	Missense_Mutation	SNP	G	G	T	rs2727307	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:61987570G>T	ENST00000309894.5	-	4	422	c.423C>A	c.(421-423)gaC>gaA	p.D141E	CSHL1_ENST00000392824.4_3'UTR|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000259003.10_Missense_Mutation_p.D79E|CSHL1_ENST00000438387.2_Missense_Mutation_p.D58E|CSHL1_ENST00000346606.6_Missense_Mutation_p.D47E|CSHL1_ENST00000450719.3_Missense_Mutation_p.D47E|CSHL1_ENST00000561003.1_Missense_Mutation_p.D58E	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	141			D -> E (in dbSNP:rs2727307). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						GGAGGTGATAGTCATCGCTGT	0.592													G|||	1392	0.277955	0.059	0.3256	5008	,	,		19686	0.4196		0.4185	False		,,,				2504	0.2495				p.D141E		Atlas-SNP	.											CSHL1_ENST00000561003,bladder,carcinoma,-2,4	CSHL1	42	4	0			c.C423A						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	555,3851	249.3+/-256.8	32,491,1680	90.0	78.0	82.0		141,423,174,354	3.1	0.2	17	dbSNP_100	82	3562,5038	516.7+/-378.9	747,2068,1485	no	missense,missense,missense,missense	CSHL1	NM_001318.2,NM_022579.1,NM_022580.1,NM_022581.1	45,45,45,45	779,2559,3165	TT,TG,GG		41.4186,12.5965,31.6546	benign,benign,benign,benign	47/129,141/223,58/140,118/200	61987570	4117,8889	2203	4300	6503	SO:0001583	missense	1444	exon4			GTGATAGTCATCG	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"""chorionic somatomammotropin CS-5"""	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.423C>A	17.37:g.61987570G>T	ENSP00000309524:p.Asp141Glu	Somatic	488	0	0		WXS	Illumina HiSeq	Phase_I	404	400	0.990099	NM_022579	D3DU26|D3DU27|Q0VDB2	Missense_Mutation	SNP	ENST00000309894.5	37	CCDS11652.1	708	0.3241758241758242	38	0.07723577235772358	135	0.3729281767955801	217	0.3793706293706294	318	0.41952506596306066	g	8.404	0.842563	0.16963	0.125965	0.414186	ENSG00000204414	ENST00000309894;ENST00000438387;ENST00000259003;ENST00000346606;ENST00000450719	D;D;D	0.90261	-2.64;-2.64;-2.64	3.07	3.07	0.35406	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.304551	0.31145	N	0.008174	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.99999999455923	B;B;B;B	0.32893	0.007;0.337;0.389;0.337	B;B;B;B	0.38156	0.007;0.173;0.266;0.253	T	0.08411	-1.0723	9	0.87932	D	0	.	8.2735	0.31857	0.0:0.2465:0.7534:0.0	rs2727307;rs57082825	47;58;141;118	Q14406-4;Q14406-3;Q14406;Q14406-2	.;.;CSHL_HUMAN;.	E	141;58;136;47;136	ENSP00000309524:D141E;ENSP00000402632:D58E;ENSP00000316360:D47E	ENSP00000259003:D136E	D	-	3	2	GH1	59341302	1.000000	0.71417	0.247000	0.24249	0.002000	0.02628	1.431000	0.34925	1.730000	0.51580	0.305000	0.20034	GAC	G|0.670;T|0.330	0.330	strong		0.592	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579	
FZD3	7976	hgsc.bcm.edu	37	8	28384712	28384712	+	Silent	SNP	A	A	G	rs2241802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:28384712A>G	ENST00000240093.3	+	5	913	c.435A>G	c.(433-435)ttA>ttG	p.L145L	FZD3_ENST00000537916.1_Silent_p.L145L	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	145					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		ATCTGAATTTAGCTGGAGAAC	0.413													A|||	2716	0.542332	0.3949	0.598	5008	,	,		18780	0.5675		0.5944	False		,,,				2504	0.6227				p.L145L		Atlas-SNP	.											.	FZD3	65	.	0			c.A435G						PASS	.	A	,	1875,2531	541.3+/-375.7	377,1121,705	168.0	175.0	173.0		435,435	2.4	1.0	8	dbSNP_98	173	4882,3718	618.6+/-396.8	1391,2100,809	no	coding-synonymous,coding-synonymous	FZD3	NM_017412.3,NM_145866.1	,	1768,3221,1514	GG,GA,AA		43.2326,42.5556,48.0471	,	145/667,145/667	28384712	6757,6249	2203	4300	6503	SO:0001819	synonymous_variant	7976	exon5			GAATTTAGCTGGA	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"""GPCR / Class F : Frizzled receptors"""	4041	protein-coding gene	gene with protein product		606143	"""frizzled (Drosophila) homolog 3"", ""frizzled homolog 3 (Drosophila)"", ""frizzled 3, seven transmembrane spanning receptor"", ""frizzled family receptor 3"""			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.435A>G	8.37:g.28384712A>G		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	290	147	0.506897	NM_017412	A8K615	Silent	SNP	ENST00000240093.3	37	CCDS6069.1																																																																																			A|0.459;G|0.541	0.541	strong		0.413	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866	
ZNF572	137209	hgsc.bcm.edu	37	8	125989698	125989698	+	Silent	SNP	C	C	T	rs16900167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:125989698C>T	ENST00000319286.5	+	3	1342	c.1188C>T	c.(1186-1188)agC>agT	p.S396S		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	396					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	31	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TTGGCCTTAGCTCCCATCTCA	0.418										HNSCC(60;0.17)			C|||	829	0.165535	0.1369	0.2752	5008	,	,		20258	0.2113		0.0845	False		,,,				2504	0.1626				p.S396S		Atlas-SNP	.											.	ZNF572	82	.	0			c.C1188T						PASS	.	C		633,3773	274.9+/-272.2	54,525,1624	91.0	87.0	88.0		1188	3.1	1.0	8	dbSNP_123	88	823,7777	190.8+/-237.2	36,751,3513	no	coding-synonymous	ZNF572	NM_152412.2		90,1276,5137	TT,TC,CC		9.5698,14.3668,11.1948		396/530	125989698	1456,11550	2203	4300	6503	SO:0001819	synonymous_variant	137209	exon3			CCTTAGCTCCCAT	BX537876	CCDS6354.1	8q24.13	2013-09-20			ENSG00000180938	ENSG00000180938		"""Zinc fingers, C2H2-type"""	26758	protein-coding gene	gene with protein product							Standard	NM_152412		Approved	FLJ38002	uc003yrr.3	Q7Z3I7	OTTHUMG00000164988	ENST00000319286.5:c.1188C>T	8.37:g.125989698C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_152412	A1L4F1|Q8N1Q0	Silent	SNP	ENST00000319286.5	37	CCDS6354.1																																																																																			C|0.867;T|0.133	0.133	strong		0.418	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412	
CNDP1	84735	hgsc.bcm.edu	37	18	72234635	72234635	+	Silent	SNP	C	C	T	rs12960862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72234635C>T	ENST00000358821.3	+	6	951	c.723C>T	c.(721-723)taC>taT	p.Y241Y	CNDP1_ENST00000582365.1_Silent_p.Y198Y	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	241						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		CAATCACTTACGGAACCCGGG	0.493													C|||	2276	0.454473	0.2852	0.4856	5008	,	,		17870	0.4008		0.671	False		,,,				2504	0.4939				p.Y241Y	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											.	CNDP1	98	.	0			c.C723T						PASS	.	C		1625,2781	499.3+/-364.4	307,1011,885	95.0	93.0	94.0		723	-5.6	0.0	18	dbSNP_121	94	5730,2870	672.9+/-403.0	1907,1916,477	no	coding-synonymous	CNDP1	NM_032649.5		2214,2927,1362	TT,TC,CC		33.3721,36.8815,43.4492		241/508	72234635	7355,5651	2203	4300	6503	SO:0001819	synonymous_variant	84735	exon6			CACTTACGGAACC		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.723C>T	18.37:g.72234635C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Silent	SNP	ENST00000358821.3	37	CCDS12007.1																																																																																			C|0.481;T|0.519	0.519	strong		0.493	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167592571G>A	ENST00000366832.2	+	6	861	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	244										endometrium(1)|kidney(2)|lung(3)	6						TTCCCAGGCCGCCACGCTGCA	0.592																																					p.A244T		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G730A						PASS	.						23.0	28.0	27.0					6																	167592571		692	1591	2283	SO:0001583	missense	401285	exon6			CAGGCCGCCACGC		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.730G>A	6.37:g.167592571G>A	ENSP00000355797:p.Ala244Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	135	16	0.118519	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	87	0.03983516483516483	17	0.034552845528455285	12	0.03314917127071823	14	0.024475524475524476	44	0.05804749340369393	c	8.486	0.860926	0.17178	.	.	ENSG00000166984	ENST00000366832	T	0.13901	2.55	1.87	-1.19	0.09585	.	.	.	.	.	T	0.00906	0.0030	N	0.11560	0.145	0.09310	N	1	B	0.32968	0.392	B	0.17433	0.018	T	0.43718	-0.9374	9	0.02654	T	1	.	2.6095	0.04887	0.3443:0.2689:0.3868:0.0	rs28690444	244	B9ZVM9	TCP2L_HUMAN	T	244	ENSP00000355797:A244T	ENSP00000283507:A244T	A	+	1	0	TCP10L2	167512561	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.863000	0.04259	-0.321000	0.08627	-1.962000	0.00476	GCC	G|0.965;A|0.035	0.035	strong		0.592	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
ZNF831	128611	hgsc.bcm.edu	37	20	57768399	57768399	+	Silent	SNP	T	T	C	rs442091	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57768399T>C	ENST00000371030.2	+	1	2325	c.2325T>C	c.(2323-2325)gcT>gcC	p.A775A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	775							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					ATGTAGAGGCTCCCAGGCCAG	0.652													.|||	1808	0.361022	0.5643	0.3141	5008	,	,		16119	0.372		0.2356	False		,,,				2504	0.2372				p.A775A		Atlas-SNP	.											ZNF831,NS,carcinoma,+2,1	ZNF831	287	1	0			c.T2325C						PASS	.	C		1847,1895		445,957,469	22.0	29.0	27.0		2325	-1.1	0.0	20	dbSNP_80	27	1835,6361		198,1439,2461	yes	coding-synonymous	ZNF831	NM_178457.1		643,2396,2930	CC,CT,TT		22.389,49.3586,30.8427		775/1678	57768399	3682,8256	1871	4098	5969	SO:0001819	synonymous_variant	128611	exon1			AGAGGCTCCCAGG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2325T>C	20.37:g.57768399T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																			T|0.666;C|0.334	0.334	strong		0.652	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
SLC22A24	283238	hgsc.bcm.edu	37	11	62850775	62850775	+	Nonsense_Mutation	SNP	G	G	A	rs77002186	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62850775G>A	ENST00000417740.1	-	7	1666	c.1225C>T	c.(1225-1227)Cag>Tag	p.Q409*		NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	0					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						AACAATATCTGGCTTATTCGA	0.468													G|||	157	0.0313498	0.0	0.0274	5008	,	,		20608	0.0903		0.0229	False		,,,				2504	0.0245				p.Q409X		Atlas-SNP	.											.	SLC22A24	31	.	0			c.C1225T						PASS	.	G	stop/GLN	6,1378		0,6,686	150.0	120.0	129.0		1225	1.8	0.0	11	dbSNP_132	129	66,3116		2,62,1527	yes	stop-gained	SLC22A24	NM_001136506.2		2,68,2213	AA,AG,GG		2.0742,0.4335,1.5769		409/553	62850775	72,4494	692	1591	2283	SO:0001587	stop_gained	283238	exon7			ATATCTGGCTTAT		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.1225C>T	11.37:g.62850775G>A	ENSP00000396586:p.Gln409*	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_001136506		Nonsense_Mutation	SNP	ENST00000417740.1	37		86	0.039377289377289376	0	0.0	10	0.027624309392265192	60	0.1048951048951049	16	0.021108179419525065	G	36	5.757227	0.96898	0.004335	0.020742	ENSG00000197658	ENST00000417740	.	.	.	3.8	1.78	0.24846	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	6.0117	0.19580	0.1108:0.0:0.6977:0.1915	.	.	.	.	X	409	.	ENSP00000396586:Q409X	Q	-	1	0	SLC22A24	62607351	0.746000	0.28272	0.011000	0.14972	0.056000	0.15407	2.902000	0.48703	1.975000	0.57531	0.596000	0.82720	CAG	G|0.958;A|0.042	0.042	strong		0.468	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
OTOF	9381	hgsc.bcm.edu	37	2	26696374	26696374	+	Missense_Mutation	SNP	C	C	T	rs56054534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:26696374C>T	ENST00000272371.2	-	28	3596	c.3470G>A	c.(3469-3471)cGg>cAg	p.R1157Q	OTOF_ENST00000338581.6_Missense_Mutation_p.R410Q|OTOF_ENST00000339598.3_Missense_Mutation_p.R410Q|OTOF_ENST00000402415.3_Missense_Mutation_p.R467Q|OTOF_ENST00000403946.3_Missense_Mutation_p.R1157Q	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1157			R -> Q (in dbSNP:rs56054534). {ECO:0000269|PubMed:16371502}.		membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGTCCACCCGTGGCCGGTC	0.592													C|||	23	0.00459265	0.0	0.013	5008	,	,		16468	0.0		0.0139	False		,,,				2504	0.0				p.R1157Q	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G3470A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	14,4392	20.2+/-43.8	0,14,2189	63.0	63.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1229,3470,1400,1229	5.2	1.0	2	dbSNP_129	63	129,8471	66.0+/-128.3	1,127,4172	yes	missense,missense,missense,missense	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	43,43,43,43	1,141,6361	TT,TC,CC		1.5,0.3177,1.0995	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	410/1231,1157/1998,467/1308,410/1231	26696374	143,12863	2203	4300	6503	SO:0001583	missense	9381	exon28			TCCACCCGTGGCC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3470G>A	2.37:g.26696374C>T	ENSP00000272371:p.Arg1157Gln	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	15.19	2.761009	0.49468	0.003177	0.015	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	D;D;D;T;T	0.84516	-1.86;-1.86;-1.86;-0.22;-0.22	5.21	5.21	0.72293	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.76807	0.4039	N	0.03281	-0.365	0.80722	D	1	D;P;D;B	0.89917	1.0;0.477;0.99;0.304	D;B;P;B	0.87578	0.998;0.08;0.596;0.08	T	0.76650	-0.2881	10	0.07813	T	0.8	-22.4695	18.3421	0.90309	0.0:1.0:0.0:0.0	rs56054534	1157;410;467;410	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	Q	410;410;467;1157;1157	ENSP00000345137:R410Q;ENSP00000344521:R410Q;ENSP00000383906:R467Q;ENSP00000272371:R1157Q;ENSP00000385255:R1157Q	ENSP00000272371:R1157Q	R	-	2	0	OTOF	26549878	0.995000	0.38212	0.997000	0.53966	0.870000	0.49936	3.321000	0.51999	2.436000	0.82500	0.484000	0.47621	CGG	C|0.991;T|0.009	0.009	strong		0.592	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
FERMT1	55612	hgsc.bcm.edu	37	20	6065731	6065731	+	Silent	SNP	T	T	C	rs386812146|rs2232073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:6065731T>C	ENST00000217289.4	-	12	2363	c.1575A>G	c.(1573-1575)aaA>aaG	p.K525K	FERMT1_ENST00000536936.1_Silent_p.K268K|FERMT1_ENST00000478194.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	525	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						ATTTGTGTCTTTTTGCACACC	0.413													t|||	2289	0.457069	0.4554	0.4784	5008	,	,		25176	0.6409		0.3797	False		,,,				2504	0.3344				p.K525K		Atlas-SNP	.											.	FERMT1	106	.	0			c.A1575G						PASS	.			393,4013		135,123,1945	121.0	109.0	113.0		1575	2.8	1.0	20	dbSNP_98	113	464,8136		150,164,3986	no	coding-synonymous	FERMT1	NM_017671.4		285,287,5931	CC,CT,TT		5.3953,8.9197,6.5893		525/678	6065731	857,12149	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon12			GTGTCTTTTTGCA	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1575A>G	20.37:g.6065731T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	255	120	0.470588	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			T|0.572;C|0.428	0.428	strong		0.413	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
MYOM3	127294	hgsc.bcm.edu	37	1	24417415	24417415	+	Missense_Mutation	SNP	T	T	C	rs6700245	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:24417415T>C	ENST00000374434.3	-	12	1466	c.1304A>G	c.(1303-1305)cAa>cGa	p.Q435R	MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000329601.7_Missense_Mutation_p.Q435R|MYOM3_ENST00000330966.7_Missense_Mutation_p.Q436R	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	435	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> R (in dbSNP:rs6700245). {ECO:0000269|PubMed:14702039}.			M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GACGAGGCCTTGGATTGGGCA	0.637													T|||	849	0.169529	0.239	0.1311	5008	,	,		17130	0.003		0.1759	False		,,,				2504	0.2679				p.Q435R		Atlas-SNP	.											.	MYOM3	131	.	0			c.A1304G						PASS	.	T	ARG/GLN	818,3318		89,640,1339	96.0	106.0	102.0		1304	3.0	1.0	1	dbSNP_116	102	1344,7032		106,1132,2950	yes	missense	MYOM3	NM_152372.3	43	195,1772,4289	CC,CT,TT		16.0458,19.7776,17.2794	possibly-damaging	435/1438	24417415	2162,10350	2068	4188	6256	SO:0001583	missense	127294	exon12			AGGCCTTGGATTG	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.1304A>G	1.37:g.24417415T>C	ENSP00000363557:p.Gln435Arg	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	260	0.11904761904761904	90	0.18292682926829268	57	0.1574585635359116	2	0.0034965034965034965	111	0.14643799472295516	T	11.82	1.751658	0.31046	0.197776	0.160458	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.56776	0.44;0.44;0.44	5.3	3.03	0.35002	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.531566	0.21490	N	0.073699	T	0.00039	0.0001	N	0.12887	0.27	0.09310	P	0.9999999873397	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.18263	0.021;0.007;0.009	T	0.13045	-1.0524	9	0.12766	T	0.61	.	3.636	0.08148	0.2217:0.1547:0.0:0.6236	rs6700245;rs61179261;rs6700245	92;435;435	Q6ZU56;Q5VTT5-2;Q5VTT5	.;.;MYOM3_HUMAN	R	435;436;435	ENSP00000363557:Q435R;ENSP00000332670:Q436R;ENSP00000328415:Q435R	ENSP00000328415:Q435R	Q	-	2	0	MYOM3	24290002	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	1.310000	0.33551	2.007000	0.58848	0.460000	0.39030	CAA	T|0.841;C|0.159	0.159	strong		0.637	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
SNED1	25992	hgsc.bcm.edu	37	2	241991198	241991198	+	Silent	SNP	C	C	T	rs138612536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:241991198C>T	ENST00000310397.8	+	13	1773	c.1773C>T	c.(1771-1773)aaC>aaT	p.N591N	SNED1_ENST00000469006.1_3'UTR|SNED1_ENST00000401884.1_Silent_p.N591N|SNED1_ENST00000405547.3_Silent_p.N591N|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.N591N	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	591	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		CCTGCCGGAACGGGGGCACGT	0.692													C|||	10	0.00199681	0.0	0.0043	5008	,	,		16266	0.0		0.006	False		,,,				2504	0.001				p.N591N		Atlas-SNP	.											.	SNED1	76	.	0			c.C1773T						PASS	.	C		4,4012		0,4,2004	8.0	11.0	10.0		1773	0.3	1.0	2	dbSNP_134	10	44,8186		0,44,4071	no	coding-synonymous	SNED1	NM_001080437.1		0,48,6075	TT,TC,CC		0.5346,0.0996,0.392		591/1414	241991198	48,12198	2008	4115	6123	SO:0001819	synonymous_variant	25992	exon13			CCGGAACGGGGGC	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1773C>T	2.37:g.241991198C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	7.019	0.558409	0.13436	9.96E-4	0.005346	ENSG00000162804	ENST00000401644	.	.	.	3.9	0.258	0.15578	.	.	.	.	.	T	0.47116	0.1428	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41592	-0.9500	4	.	.	.	.	8.4102	0.32638	0.0:0.4713:0.0:0.5287	.	.	.	.	W	288	.	.	R	+	1	2	SNED1	241639871	0.002000	0.14202	0.998000	0.56505	0.767000	0.43475	-1.458000	0.02372	-0.014000	0.14175	-0.463000	0.05309	CGG	C|0.999;T|0.001	0.001	strong		0.692	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
ACSM1	116285	hgsc.bcm.edu	37	16	20636814	20636814	+	Silent	SNP	G	G	A	rs2301672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20636814G>A	ENST00000307493.4	-	11	1525	c.1458C>T	c.(1456-1458)agC>agT	p.S486S	ACSM1_ENST00000520010.1_Silent_p.S486S|ACSM1_ENST00000219151.4_Silent_p.S137S	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	486					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						CCACCAAAGCGCTTTCAACCT	0.602													G|||	903	0.180312	0.0166	0.1297	5008	,	,		20014	0.499		0.1461	False		,,,				2504	0.1442				p.S486S		Atlas-SNP	.											.	ACSM1	118	.	0			c.C1458T						PASS	.	G		166,4236	111.2+/-149.4	6,154,2041	62.0	54.0	57.0		1458	-8.9	0.2	16	dbSNP_100	57	1065,7535	223.7+/-260.4	72,921,3307	no	coding-synonymous	ACSM1	NM_052956.2		78,1075,5348	AA,AG,GG		12.3837,3.771,9.4678		486/578	20636814	1231,11771	2201	4300	6501	SO:0001819	synonymous_variant	116285	exon11			CAAAGCGCTTTCA	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1458C>T	16.37:g.20636814G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_052956	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	37	CCDS10587.1	474	0.21703296703296704	13	0.026422764227642278	52	0.143646408839779	305	0.5332167832167832	104	0.13720316622691292	g	0.277	-0.989211	0.02162	0.03771	0.123837	ENSG00000166743	ENST00000524149	.	.	.	4.47	-8.94	0.00768	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999910392	.	.	.	.	.	.	T	0.01356	-1.1376	3	.	.	.	.	17.369	0.87371	0.7921:0.0:0.2079:0.0	rs2301672;rs58546411;rs2301672	.	.	.	V	158	.	.	A	-	2	0	ACSM1	20544315	0.022000	0.18835	0.202000	0.23494	0.001000	0.01503	-0.608000	0.05641	-2.250000	0.00701	-0.794000	0.03295	GCG	G|0.849;A|0.151	0.151	strong		0.602	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	
SPINK5	11005	hgsc.bcm.edu	37	5	147477551	147477551	+	Missense_Mutation	SNP	C	C	T	rs34482796	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147477551C>T	ENST00000256084.7	+	11	1046	c.1004C>T	c.(1003-1005)gCc>gTc	p.A335V	SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000398454.1_Missense_Mutation_p.A335V|SPINK5_ENST00000359874.3_Missense_Mutation_p.A335V	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	335	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.		A -> V (in dbSNP:rs34482796). {ECO:0000269|PubMed:10419450, ECO:0000269|PubMed:16374478}.		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGTGTCAAGCCTACTTGTGA	0.403													C|||	2236	0.446486	0.2534	0.6282	5008	,	,		17872	0.4802		0.4831	False		,,,				2504	0.5061				p.A335V		Atlas-SNP	.											SPINK5_ENST00000359874,colon,carcinoma,+1,2	SPINK5	245	2	0			c.C1004T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	1107,2613		166,775,919	106.0	94.0	98.0		1004,1004,1004	2.7	1.0	5	dbSNP_126	98	4153,4055		1037,2079,988	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	64,64,64	1203,2854,1907	TT,TC,CC		49.403,29.7581,44.0979	benign,benign,benign	335/1095,335/917,335/1065	147477551	5260,6668	1860	4104	5964	SO:0001583	missense	11005	exon11			GTCAAGCCTACTT	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1004C>T	5.37:g.147477551C>T	ENSP00000256084:p.Ala335Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	965	0.44184981684981683	139	0.28252032520325204	218	0.6022099447513812	262	0.458041958041958	346	0.45646437994722955	C	10.64	1.408263	0.25378	0.297581	0.50597	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.05025	3.51;3.51;3.51;3.51	5.4	2.65	0.31530	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.283230	0.25386	N	0.031058	T	0.00012	0.0000	L	0.52126	1.63	0.45777	P	0.0013400000000000079	B;B;B	0.16396	0.009;0.003;0.017	B;B;B	0.23419	0.019;0.032;0.046	T	0.23261	-1.0193	9	0.33141	T	0.24	-0.5071	7.8004	0.29170	0.1326:0.7134:0.0:0.154	rs34482796;rs56847883	335;335;335	Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;ISK5_HUMAN;.	V	335;335;316;335	ENSP00000381472:A335V;ENSP00000352936:A335V;ENSP00000421519:A316V;ENSP00000256084:A335V	ENSP00000256084:A335V	A	+	2	0	SPINK5	147457744	0.931000	0.31567	0.998000	0.56505	0.757000	0.42996	0.065000	0.14466	0.095000	0.17434	-1.094000	0.02160	GCC	C|0.530;T|0.470	0.470	strong		0.403	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
DZIP1L	199221	hgsc.bcm.edu	37	3	137787192	137787192	+	Missense_Mutation	SNP	T	T	C	rs446644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:137787192T>C	ENST00000327532.2	-	13	1995	c.1633A>G	c.(1633-1635)Aca>Gca	p.T545A	DZIP1L_ENST00000488595.1_5'UTR	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	545			T -> A (in dbSNP:rs446644). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						GTGACCAGTGTGCTCTGCTGG	0.562											OREG0015830	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	3149	0.628794	0.3094	0.7767	5008	,	,		17065	0.626		0.8608	False		,,,				2504	0.7198				p.T545A		Atlas-SNP	.											.	DZIP1L	88	.	0			c.A1633G						PASS	.	T	ALA/THR	1933,2473	530.0+/-372.8	419,1095,689	59.0	65.0	63.0		1633	-0.9	0.0	3	dbSNP_80	63	7485,1115	758.9+/-407.5	3260,965,75	yes	missense	DZIP1L	NM_173543.2	58	3679,2060,764	CC,CT,TT		12.9651,43.872,27.5873	benign	545/768	137787192	9418,3588	2203	4300	6503	SO:0001583	missense	199221	exon13			CCAGTGTGCTCTG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1633A>G	3.37:g.137787192T>C	ENSP00000332148:p.Thr545Ala	Somatic	156	0	0	1636	WXS	Illumina HiSeq	Phase_I	170	170	1	NM_173543	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	1465	0.6707875457875457	179	0.3638211382113821	271	0.7486187845303868	365	0.6381118881118881	650	0.8575197889182058	T	8.398	0.841212	0.16891	0.43872	0.870349	ENSG00000158163	ENST00000327532	T	0.40225	1.04	4.91	-0.849	0.10723	.	0.662439	0.14924	N	0.290463	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.19817	0.039	B	0.14578	0.011	T	0.31392	-0.9945	9	0.10111	T	0.7	1.2072	3.4686	0.07558	0.099:0.1022:0.4251:0.3737	rs446644;rs17856976;rs52835251;rs57326700;rs446644	545	Q8IYY4	DZI1L_HUMAN	A	545	ENSP00000332148:T545A	ENSP00000332148:T545A	T	-	1	0	DZIP1L	139269882	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.127000	0.03251	-0.383000	0.07858	0.528000	0.53228	ACA	T|0.303;C|0.697	0.697	strong		0.562	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
MUC4	4585	hgsc.bcm.edu	37	3	195508010	195508010	+	Missense_Mutation	SNP	C	C	A	rs61388923		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508010C>A	ENST00000463781.3	-	2	10900	c.10441G>T	c.(10441-10443)Gca>Tca	p.A3481S	MUC4_ENST00000475231.1_Missense_Mutation_p.A3481S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTAGATGCTGAGGAAGGG	0.577																																					p.A3481S		Atlas-SNP	.											MUC4_ENST00000463781,colon,carcinoma,0,1	MUC4	1505	1	0			c.G10441T						scavenged	.						28.0	24.0	25.0					3																	195508010		678	1580	2258	SO:0001583	missense	4585	exon2			TAGATGCTGAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10441G>T	3.37:g.195508010C>A	ENSP00000417498:p.Ala3481Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	289	75	0.259516	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	C	6.749	0.506940	0.12883	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.36;1.3	0.743	-0.725	0.11174	.	.	.	.	.	T	0.31734	0.0806	N	0.14661	0.345	0.09310	N	1	D	0.60575	0.988	D	0.66196	0.942	T	0.16837	-1.0389	8	.	.	.	.	3.4262	0.07412	0.0:0.343:0.0:0.657	.	3353	E7ESK3	.	S	3481	ENSP00000417498:A3481S;ENSP00000420243:A3481S	.	A	-	1	0	MUC4	196992789	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-0.865000	0.04250	0.088000	0.17205	0.089000	0.15464	GCA	.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NID1	4811	hgsc.bcm.edu	37	1	236144951	236144951	+	Silent	SNP	A	A	G	rs3738525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:236144951A>G	ENST00000264187.6	-	16	3269	c.3187T>C	c.(3187-3189)Ttg>Ctg	p.L1063L	NID1_ENST00000366595.3_Silent_p.L930L	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1063					basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GGATTCACCAAGTCAGTCTCA	0.493													G|||	1675	0.334465	0.3555	0.2579	5008	,	,		19135	0.6151		0.1402	False		,,,				2504	0.271				p.L1063L		Atlas-SNP	.											.	NID1	196	.	0			c.T3187C						PASS	.	G		1481,2925	678.6+/-403.6	235,1011,957	92.0	91.0	91.0		3187	-3.7	0.0	1	dbSNP_107	91	1478,7122	749.6+/-407.4	118,1242,2940	no	coding-synonymous	NID1	NM_002508.2		353,2253,3897	GG,GA,AA		17.186,33.6133,22.751		1063/1248	236144951	2959,10047	2203	4300	6503	SO:0001819	synonymous_variant	4811	exon16			TCACCAAGTCAGT	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.3187T>C	1.37:g.236144951A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																			A|0.729;G|0.271	0.271	strong		0.493	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
KIAA0556	23247	hgsc.bcm.edu	37	16	27720201	27720201	+	Missense_Mutation	SNP	C	C	T	rs12930355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:27720201C>T	ENST00000261588.4	+	13	1584	c.1565C>T	c.(1564-1566)aCg>aTg	p.T522M	CTD-2049O4.1_ENST00000563052.1_RNA|KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000568831.1_RNA|CTD-2049O4.1_ENST00000564893.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	522			T -> M (in dbSNP:rs12930355).			extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T522M(1)		breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						AACACAGCCACGCCTGGGGAG	0.537													C|||	342	0.0682907	0.0189	0.1715	5008	,	,		19377	0.001		0.1551	False		,,,				2504	0.0419				p.T522M		Atlas-SNP	.											KIAA0556_ENST00000261588,caecum,carcinoma,-1,3	KIAA0556	348	3	1	Substitution - Missense(1)	large_intestine(1)	c.C1565T						PASS	.	C	MET/THR	222,4172	132.9+/-169.3	4,214,1979	69.0	63.0	65.0		1565	-4.6	0.0	16	dbSNP_121	65	1284,7316	255.1+/-280.1	87,1110,3103	yes	missense	KIAA0556	NM_015202.2	81	91,1324,5082	TT,TC,CC		14.9302,5.0523,11.59	benign	522/1619	27720201	1506,11488	2197	4300	6497	SO:0001583	missense	23247	exon13			CAGCCACGCCTGG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.1565C>T	16.37:g.27720201C>T	ENSP00000261588:p.Thr522Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	190	0.08699633699633699	11	0.022357723577235773	56	0.15469613259668508	0	0.0	123	0.16226912928759896	C	3.230	-0.157586	0.06544	0.050523	0.149302	ENSG00000047578	ENST00000261588;ENST00000327217	T	0.13901	2.55	5.49	-4.56	0.03431	.	1.266200	0.04883	N	0.448051	T	0.00039	0.0001	N	0.16478	0.41	0.80722	P	0.0	B;B	0.16166	0.016;0.007	B;B	0.12837	0.008;0.006	T	0.42155	-0.9468	9	0.33940	T	0.23	-5.3447	4.9772	0.14146	0.3099:0.3468:0.0:0.3433	rs12930355;rs12930355	430;522	Q8N803;O60303	.;K0556_HUMAN	M	522;429	ENSP00000261588:T522M	ENSP00000261588:T522M	T	+	2	0	KIAA0556	27627702	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-1.350000	0.02624	-0.536000	0.06298	-0.448000	0.05591	ACG	C|0.898;T|0.102	0.102	strong		0.537	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
SOX30	11063	hgsc.bcm.edu	37	5	157065306	157065306	+	Silent	SNP	G	G	A	rs35793864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:157065306G>A	ENST00000265007.6	-	4	2153	c.1812C>T	c.(1810-1812)ttC>ttT	p.F604F	SOX30_ENST00000519442.1_Silent_p.F299F|SOX30_ENST00000311371.5_Intron	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	604	Pro-rich.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTGGTGTCCCGAACAGTGTGG	0.498													G|||	485	0.096845	0.0053	0.0778	5008	,	,		17909	0.123		0.1362	False		,,,				2504	0.1667				p.F604F	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.C1812T						PASS	.	G	,	115,4291	86.3+/-125.0	0,115,2088	70.0	70.0	70.0		,1812	1.8	1.0	5	dbSNP_126	70	1236,7364	247.8+/-275.7	101,1034,3165	no	intron,coding-synonymous	SOX30	NM_007017.2,NM_178424.1	,	101,1149,5253	AA,AG,GG		14.3721,2.6101,10.3875	,	,604/754	157065306	1351,11655	2203	4300	6503	SO:0001819	synonymous_variant	11063	exon4			TGTCCCGAACAGT	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.1812C>T	5.37:g.157065306G>A		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	256	172	0.671875	NM_178424	O94995|Q8IYX6	Silent	SNP	ENST00000265007.6	37	CCDS4339.1																																																																																			G|0.902;A|0.098	0.098	strong		0.498	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
ZNF516	9658	hgsc.bcm.edu	37	18	74090864	74090864	+	Missense_Mutation	SNP	A	A	G	rs140499406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:74090864A>G	ENST00000443185.2	-	5	3522	c.3205T>C	c.(3205-3207)Ttt>Ctt	p.F1069L	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1069					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		AGGGTCGCAAAGTCCTTTGGA	0.602													A|||	14	0.00279553	0.0015	0.0043	5008	,	,		17438	0.0		0.008	False		,,,				2504	0.001				p.F1069L		Atlas-SNP	.											.	ZNF516	102	.	0			c.T3205C						PASS	.	A	LEU/PHE	5,4081		0,5,2038	41.0	48.0	46.0		3206	-0.6	1.0	18	dbSNP_134	46	77,8287		2,73,4107	yes	missense	ZNF516	NM_014643.3	22	2,78,6145	GG,GA,AA		0.9206,0.1224,0.6586	benign	1069/1164	74090864	82,12368	2043	4182	6225	SO:0001583	missense	9658	exon5			TCGCAAAGTCCTT	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.3205T>C	18.37:g.74090864A>G	ENSP00000394757:p.Phe1069Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	77	26	0.337662	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	a|a	3.367|3.367	-0.129188|-0.129188	0.06753|0.06753	0.001224|0.001224	0.009206|0.009206	ENSG00000101493|ENSG00000101493	ENST00000443185|ENST00000542818	T|.	0.05786|.	3.39|.	3.8|3.8	-0.563|-0.563	0.11778|0.11778	.|.	0.482470|.	0.19919|.	N|.	0.103134|.	T|T	0.14614|0.14614	0.0353|0.0353	N|N	0.08118|0.08118	0|0	0.31674|0.31674	N|N	0.643972|0.643972	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.34750|0.34750	-0.9816|-0.9816	10|5	0.02654|.	T|.	1|.	-0.2046|-0.2046	7.7942|7.7942	0.29138|0.29138	0.34:0.0:0.66:0.0|0.34:0.0:0.66:0.0	.|.	1069|.	Q92618|.	ZN516_HUMAN|.	L|P	1069|2	ENSP00000394757:F1069L|.	ENSP00000394757:F1069L|.	F|L	-|-	1|2	0|0	ZNF516|ZNF516	72219852|72219852	1.000000|1.000000	0.71417|0.71417	0.961000|0.961000	0.40146|0.40146	0.841000|0.841000	0.47740|0.47740	3.490000|3.490000	0.53245|0.53245	-0.197000|-0.197000	0.10350|0.10350	0.478000|0.478000	0.44815|0.44815	TTT|CTT	A|0.994;G|0.006	0.006	strong		0.602	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
FCGBP	8857	hgsc.bcm.edu	37	19	40383905	40383905	+	Silent	SNP	G	G	A	rs145218790		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40383905G>A	ENST00000221347.6	-	21	9712	c.9705C>T	c.(9703-9705)tgC>tgT	p.C3235C		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3235						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCCCAGGCCCGCAGCGACACC	0.677																																					p.C3235C		Atlas-SNP	.											FCGBP,NS,carcinoma,0,6	FCGBP	416	6	0			c.C9705T						scavenged	.						1.0	1.0	1.0					19																	40383905		234	700	934	SO:0001819	synonymous_variant	8857	exon21			AGGCCCGCAGCGA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.9705C>T	19.37:g.40383905G>A		Somatic	405	1	0.00246914		WXS	Illumina HiSeq	Phase_I	476	86	0.180672	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.667;A|0.333	0.333	strong		0.677	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PRRC1	133619	hgsc.bcm.edu	37	5	126887569	126887569	+	Silent	SNP	G	G	A	rs7522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:126887569G>A	ENST00000296666.8	+	9	1487	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	PRRC1_ENST00000512635.2_Splice_Site_p.A433A|PRRC1_ENST00000513427.1_3'UTR|PRRC1_ENST00000442138.2_3'UTR	NM_130809.3	NP_570721.1	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	433						Golgi apparatus (GO:0005794)				endometrium(1)|large_intestine(1)|lung(4)	6		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		GAGCGATAGCGGGCATGTATA	0.512													A|||	1942	0.38778	0.3185	0.4524	5008	,	,		17375	0.5506		0.2893	False		,,,				2504	0.3691				p.A433A		Atlas-SNP	.											.	PRRC1	22	.	0			c.G1299A						PASS	.	A		1346,3060	693.9+/-405.7	214,918,1071	84.0	85.0	85.0		1299	-10.7	0.0	5	dbSNP_52	85	2637,5963	686.7+/-404.1	419,1799,2082	no	coding-synonymous	PRRC1	NM_130809.3		633,2717,3153	AA,AG,GG		30.6628,30.5493,30.6243		433/446	126887569	3983,9023	2203	4300	6503	SO:0001819	synonymous_variant	133619	exon9			GATAGCGGGCATG	AJ515429	CCDS4143.1, CCDS68943.1	5q23.2	2008-02-05			ENSG00000164244	ENSG00000164244			28164	protein-coding gene	gene with protein product						15541471	Standard	NM_130809		Approved	FLJ32875	uc003kuk.3	Q96M27	OTTHUMG00000128982	ENST00000296666.8:c.1299G>A	5.37:g.126887569G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_130809	Q69YM8|Q7L2U7|Q86Y42|Q8IVJ4|Q8IVL4|Q8NEZ7|Q96AJ3	Silent	SNP	ENST00000296666.8	37	CCDS4143.1																																																																																			G|0.650;A|0.350	0.350	strong		0.512	PRRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250971.3	NM_130809	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128842873	128842873	+	Silent	SNP	T	T	C	rs581258	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:128842873T>C	ENST00000310343.9	-	21	3485	c.3486A>G	c.(3484-3486)gaA>gaG	p.E1162E	ARHGAP32_ENST00000392657.3_Silent_p.E813E|ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000527272.1_Silent_p.E813E	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1162					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TTCTGGCCTTTTCTGGGTCCC	0.448													T|||	999	0.199481	0.2625	0.2219	5008	,	,		20466	0.1746		0.1332	False		,,,				2504	0.1922				p.E1162E		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.A3486G						PASS	.	T	,	1165,3237	411.5+/-335.8	156,853,1192	165.0	158.0	160.0		3486,2439	-2.8	0.9	11	dbSNP_83	160	1266,7328	253.3+/-279.0	110,1046,3141	no	coding-synonymous,coding-synonymous	ARHGAP32	NM_001142685.1,NM_014715.3	,	266,1899,4333	CC,CT,TT		14.7312,26.4652,18.7058	,	1162/2088,813/1739	128842873	2431,10565	2201	4297	6498	SO:0001819	synonymous_variant	9743	exon21			GGCCTTTTCTGGG	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.3486A>G	11.37:g.128842873T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	163	68	0.417178	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			T|0.809;G|0.002	.	strong		0.448	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370659	26370659	+	Silent	SNP	C	C	T	rs71544290|rs9393711	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26370659C>T	ENST00000356386.2	+	5	731	c.543C>T	c.(541-543)aaC>aaT	p.N181N	BTN3A2_ENST00000527422.1_Silent_p.N181N|BTN3A2_ENST00000377708.2_Silent_p.N181N|BTN3A2_ENST00000508906.2_Silent_p.N139N|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000396948.1_Silent_p.N181N|BTN3A2_ENST00000396934.3_Silent_p.N158N	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	181			N -> D (in dbSNP:rs9358936). {ECO:0000269|PubMed:14702039}.		interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						AGTGGAGCAACGCCAAGGGAG	0.552													C|||	410	0.081869	0.0287	0.0418	5008	,	,		18398	0.0992		0.1123	False		,,,				2504	0.1329				p.N181N		Atlas-SNP	.											.	BTN3A2	44	.	0			c.C543T						PASS	.	C	,,,,	168,4238	111.2+/-149.4	2,164,2037	131.0	117.0	122.0		543,543,474,417,543	-4.6	0.0	6	dbSNP_119	122	944,7656	206.8+/-248.7	51,842,3407	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	53,1006,5444	TT,TC,CC		10.9767,3.813,8.5499	,,,,	181/335,181/335,158/312,139/293,181/335	26370659	1112,11894	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			GAGCAACGCCAAG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.543C>T	6.37:g.26370659C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	271	128	0.472325	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			C|0.923;T|0.077	0.077	strong		0.552	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
FAM205A	259308	hgsc.bcm.edu	37	9	34726821	34726821	+	Missense_Mutation	SNP	A	A	C	rs117956208	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:34726821A>C	ENST00000378788.3	-	4	455	c.416T>G	c.(415-417)cTa>cGa	p.L139R		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	139						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						CAGCATCTCTAGGCAAGAGGA	0.493													A|||	61	0.0121805	0.0	0.0245	5008	,	,		19454	0.0109		0.0109	False		,,,				2504	0.0225				p.L139R		Atlas-SNP	.											.	FAM205A	45	.	0			c.T416G						PASS	.	A	ARG/LEU	7,1377		0,7,685	60.0	54.0	56.0		416	1.7	0.0	9	dbSNP_132	56	53,3129		0,53,1538	yes	missense	FAM205A	NM_001141917.1	102	0,60,2223	CC,CA,AA		1.6656,0.5058,1.3141	probably-damaging	139/1336	34726821	60,4506	692	1591	2283	SO:0001583	missense	259308	exon4			ATCTCTAGGCAAG		CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.416T>G	9.37:g.34726821A>C	ENSP00000417711:p.Leu139Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	22	0.010073260073260074	0	0.0	7	0.019337016574585635	8	0.013986013986013986	7	0.009234828496042216	A	13.77	2.335402	0.41398	0.005058	0.016656	ENSG00000205108	ENST00000378788	T	0.30981	1.51	4.17	1.73	0.24493	.	21.267300	0.00357	U	0.000026	T	0.33206	0.0855	M	0.67397	2.05	0.09310	N	1	D	0.67145	0.996	P	0.62740	0.906	T	0.03077	-1.1075	10	0.59425	D	0.04	.	3.1708	0.06551	0.6786:0.0:0.1141:0.2073	.	139	Q6ZU69	F205A_HUMAN	R	139	ENSP00000417711:L139R	ENSP00000417711:L139R	L	-	2	0	RP11-195F19.10	34716821	0.003000	0.15002	0.004000	0.12327	0.013000	0.08279	0.550000	0.23345	0.236000	0.21180	0.528000	0.53228	CTA	A|0.987;C|0.013	0.013	strong		0.493	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
FAM179A	165186	hgsc.bcm.edu	37	2	29240686	29240686	+	Silent	SNP	A	A	C	rs34261417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29240686A>C	ENST00000379558.4	+	10	1575	c.1224A>C	c.(1222-1224)acA>acC	p.T408T	FAM179A_ENST00000465300.1_Intron|FAM179A_ENST00000403861.2_Intron	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	408										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GCAGCGGGACACTGTCTGTGC	0.607													C|||	1049	0.209465	0.2549	0.1859	5008	,	,		20001	0.1567		0.2485	False		,,,				2504	0.1789				p.T408T		Atlas-SNP	.											.	FAM179A	106	.	0			c.A1224C						PASS	.	C		906,3182		100,706,1238	29.0	33.0	32.0		1224	-1.3	0.0	2	dbSNP_126	32	1961,6383		240,1481,2451	no	coding-synonymous	FAM179A	NM_199280.2		340,2187,3689	CC,CA,AA		23.5019,22.1624,23.0615		408/1020	29240686	2867,9565	2044	4172	6216	SO:0001819	synonymous_variant	165186	exon10			CGGGACACTGTCT	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.1224A>C	2.37:g.29240686A>C		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	244	122	0.5	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			A|0.776;C|0.224	0.224	strong		0.607	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
CEACAM3	1084	hgsc.bcm.edu	37	19	42312933	42312933	+	Silent	SNP	G	G	A	rs3752172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:42312933G>A	ENST00000357396.3	+	3	748	c.507G>A	c.(505-507)gcG>gcA	p.A169A	CEACAM3_ENST00000221999.4_Silent_p.A169A|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000344550.4_Silent_p.A169A	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	169						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						TGGTGGCCGCGCTGGTGTGTT	0.602													N|||	948	0.189297	0.0318	0.2161	5008	,	,		16901	0.1964		0.1938	False		,,,				2504	0.3712				p.A169A		Atlas-SNP	.											.	CEACAM3	37	.	0			c.G507A						PASS	.	C		294,4112		11,272,1920	147.0	142.0	144.0		507	-1.2	0.0	19	dbSNP_107	144	1736,6864		184,1368,2748	no	coding-synonymous	CEACAM3	NM_001815.2		195,1640,4668	AA,AG,GG		20.186,6.6727,15.6082		169/253	42312933	2030,10976	2203	4300	6503	SO:0001819	synonymous_variant	1084	exon3			GGCCGCGCTGGTG	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.507G>A	19.37:g.42312933G>A		Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	280	142	0.507143	NM_001815	G5E978|Q3KPH9	Silent	SNP	ENST00000357396.3	37	CCDS12586.2																																																																																			G|0.840;A|0.160	0.160	strong		0.602	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815	
MT-ND5	4540	hgsc.bcm.edu	37	M	13759	13759	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrM:13759G>A	ENST00000361567.2	+	1	1423	c.1423G>A	c.(1423-1425)Gca>Aca	p.A475T	MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	475			A -> T. {ECO:0000269|PubMed:9461455}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACATTTCCCCCGCATCCCCCT	0.478																																					p.A475T		Atlas-SNP	.											.	.	.	.	0			c.G1423A						PASS	.																																			SO:0001583	missense	0	exon1			TCCCCCGCATCCC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1423G>A	M.37:g.13759G>A	ENSP00000354813:p.Ala475Thr	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	9	8	0.888889	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.478	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
APH1B	83464	hgsc.bcm.edu	37	15	63569902	63569902	+	Missense_Mutation	SNP	C	C	T	rs117618017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63569902C>T	ENST00000261879.5	+	1	150	c.80C>T	c.(79-81)aCc>aTc	p.T27I	APH1B_ENST00000380343.4_Missense_Mutation_p.T27I	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	27				T -> I (in Ref. 4; AAQ89061). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)	p.T27I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						ACCATCGCCACCGAGCCGTTG	0.682													C|||	222	0.0443291	0.0045	0.0879	5008	,	,		8198	0.0		0.1352	False		,,,				2504	0.0194				p.T27I		Atlas-SNP	.											APH1B,NS,lymphoid_neoplasm,0,3	APH1B	27	3	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C80T						PASS	.	C	ILE/THR,ILE/THR	129,4277	93.0+/-131.7	4,121,2078	49.0	49.0	49.0		80,80	1.0	0.0	15	dbSNP_132	49	1099,7501	226.9+/-262.5	68,963,3269	yes	missense,missense	APH1B	NM_001145646.1,NM_031301.3	89,89	72,1084,5347	TT,TC,CC		12.7791,2.9278,9.4418	probably-damaging,probably-damaging	27/217,27/258	63569902	1228,11778	2203	4300	6503	SO:0001583	missense	83464	exon1			TCGCCACCGAGCC	AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"""anterior pharynx defective 1 homolog B (C. elegans)"""			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.80C>T	15.37:g.63569902C>T	ENSP00000261879:p.Thr27Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_001145646	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Missense_Mutation	SNP	ENST00000261879.5	37	CCDS10184.1	138	0.06318681318681318	5	0.01016260162601626	35	0.09668508287292818	0	0.0	98	0.12928759894459102	C	7.955	0.745633	0.15710	0.029278	0.127791	ENSG00000138613	ENST00000380343;ENST00000261879;ENST00000380340	T;T;T	0.43688	0.94;0.94;0.94	4.11	0.961	0.19638	.	0.534132	0.18319	N	0.144870	T	0.00328	0.0010	M	0.62723	1.935	0.80722	P	0.0	P;P	0.38677	0.642;0.521	B;B	0.37650	0.193;0.255	T	0.04029	-1.0983	9	0.37606	T	0.19	-2.1163	1.1628	0.01809	0.1834:0.4361:0.1783:0.2022	.	27;27	Q564N3;Q8WW43	.;APH1B_HUMAN	I	27	ENSP00000369700:T27I;ENSP00000261879:T27I;ENSP00000369697:T27I	ENSP00000261879:T27I	T	+	2	0	APH1B	61356955	0.013000	0.17824	0.005000	0.12908	0.350000	0.29205	1.171000	0.31896	0.098000	0.17522	-0.719000	0.03609	ACC	C|0.915;T|0.085	0.085	strong		0.682	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301	
CEMIP	57214	hgsc.bcm.edu	37	15	81172104	81172104	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:81172104C>T	ENST00000394685.3	+	5	708	c.289C>T	c.(289-291)Cgg>Tgg	p.R97W	KIAA1199_ENST00000220244.3_Missense_Mutation_p.R97W|KIAA1199_ENST00000356249.5_Missense_Mutation_p.R97W			Q8WUJ3	CEMIP_HUMAN		97	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TTTGCGAACCCGGCACATCCT	0.507																																					p.R97W		Atlas-SNP	.											KIAA1199,caecum,carcinoma,-1,1	KIAA1199	118	1	0			c.C289T						scavenged	.						89.0	75.0	80.0					15																	81172104		2203	4300	6503	SO:0001583	missense	57214	exon4			CGAACCCGGCACA																												ENST00000394685.3:c.289C>T	15.37:g.81172104C>T	ENSP00000378177:p.Arg97Trp	Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	128	2	0.015625	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.371731	0.42003	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	D;D;D	0.89485	-2.52;-2.52;-2.52	6.03	1.78	0.24846	G8 domain (2);	0.067014	0.56097	D	0.000027	D	0.94450	0.8214	M	0.85373	2.75	0.39115	D	0.961546	D	0.89917	1.0	D	0.79108	0.992	D	0.95353	0.8448	10	0.66056	D	0.02	-38.3943	16.4731	0.84124	0.6052:0.3948:0.0:0.0	.	97	Q8WUJ3	K1199_HUMAN	W	97	ENSP00000220244:R97W;ENSP00000378177:R97W;ENSP00000348583:R97W	ENSP00000220244:R97W	R	+	1	2	KIAA1199	78959159	0.986000	0.35501	0.706000	0.30403	0.087000	0.18053	1.624000	0.37018	0.404000	0.25506	-0.953000	0.02652	CGG	.	.	none		0.507	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
C7	730	hgsc.bcm.edu	37	5	40964885	40964885	+	Missense_Mutation	SNP	A	A	T	rs60714178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:40964885A>T	ENST00000313164.9	+	14	2151	c.1792A>T	c.(1792-1794)Act>Tct	p.T598S		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	598	CCP 1.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				TGTAGTGTACACTTGCAATGA	0.403													A|||	331	0.0660942	0.0272	0.1081	5008	,	,		18463	0.001		0.1481	False		,,,				2504	0.0716				p.T598S		Atlas-SNP	.											.	C7	136	.	0			c.A1792T						PASS	.	A	SER/THR	180,3684		6,168,1758	163.0	161.0	162.0		1792	-0.2	0.6	5	dbSNP_129	162	1278,6984		83,1112,2936	yes	missense	C7	NM_000587.2	58	89,1280,4694	TT,TA,AA		15.4684,4.6584,12.0238	benign	598/844	40964885	1458,10668	1932	4131	6063	SO:0001583	missense	730	exon14			GTGTACACTTGCA	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.1792A>T	5.37:g.40964885A>T	ENSP00000322061:p.Thr598Ser	Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	233	139	0.596566	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	177	0.08104395604395605	15	0.03048780487804878	37	0.10220994475138122	1	0.0017482517482517483	124	0.16358839050131926	A	11.28	1.591300	0.28357	0.046584	0.154684	ENSG00000112936	ENST00000313164;ENST00000440677	T	0.63744	-0.06	6.04	-0.173	0.13322	Complement control module (2);Sushi/SCR/CCP (3);	0.363303	0.29100	N	0.013144	T	0.00144	0.0004	N	0.20304	0.555	0.45118	P	0.0018700000000000383	B	0.20550	0.046	B	0.23574	0.047	T	0.04178	-1.0971	9	0.16420	T	0.52	-8.1559	4.3042	0.10938	0.3711:0.0:0.1734:0.4555	rs60714178;rs61741887	598	P10643	CO7_HUMAN	S	598;438	ENSP00000322061:T598S	ENSP00000322061:T598S	T	+	1	0	C7	41000642	0.340000	0.24792	0.595000	0.28798	0.893000	0.52053	0.756000	0.26419	0.035000	0.15519	0.460000	0.39030	ACT	A|0.902;T|0.098	0.098	strong		0.403	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
IPO11	51194	hgsc.bcm.edu	37	5	61772535	61772535	+	Silent	SNP	G	G	T	rs26635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:61772535G>T	ENST00000325324.6	+	9	952	c.783G>T	c.(781-783)gtG>gtT	p.V261V	IPO11_ENST00000409296.3_Silent_p.V301V|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	261					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.V261V(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		CAGATAATGTGTGTAGAGATA	0.254													G|||	2216	0.442492	0.413	0.4942	5008	,	,		14958	0.3155		0.4881	False		,,,				2504	0.5297				p.V301V		Atlas-SNP	.											IPO11,NS,carcinoma,0,1	IPO11	76	1	1	Substitution - coding silent(1)	stomach(1)	c.G903T						PASS	.	G	,	1804,2576	497.6+/-363.9	361,1082,747	68.0	76.0	73.0		903,783	-2.3	1.0	5	dbSNP_76	73	4158,4386	554.4+/-386.5	1034,2090,1148	no	coding-synonymous,coding-synonymous	IPO11	NM_001134779.1,NM_016338.4	,	1395,3172,1895	TT,TG,GG		48.6657,41.1872,46.1312	,	301/1016,261/976	61772535	5962,6962	2190	4272	6462	SO:0001819	synonymous_variant	51194	exon9			TAATGTGTGTAGA	AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"""Importins"""	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.783G>T	5.37:g.61772535G>T		Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	320	320	1	NM_001134779	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Silent	SNP	ENST00000325324.6	37	CCDS34167.1																																																																																			G|0.567;T|0.433	0.433	strong		0.254	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338	
ADNP	23394	hgsc.bcm.edu	37	20	49509184	49509184	+	Silent	SNP	G	G	A	rs17790938	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:49509184G>A	ENST00000396029.3	-	5	2634	c.2067C>T	c.(2065-2067)ggC>ggT	p.G689G	ADNP_ENST00000371602.4_Silent_p.G689G|ADNP_ENST00000396032.3_Silent_p.G689G|ADNP_ENST00000349014.3_Silent_p.G689G	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	689					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						TCTTTCCAACGCCCCTGCAGT	0.483													A|||	523	0.104433	0.171	0.0648	5008	,	,		20035	0.0992		0.0656	False		,,,				2504	0.0879				p.G689G		Atlas-SNP	.											.	ADNP	106	.	0			c.C2067T						PASS	.	A	,	557,3849	775.1+/-414.1	34,489,1680	133.0	118.0	123.0		2067,2067	-2.4	0.9	20	dbSNP_123	123	677,7923	788.8+/-407.6	26,625,3649	no	coding-synonymous,coding-synonymous	ADNP	NM_015339.2,NM_181442.1	,	60,1114,5329	AA,AG,GG		7.8721,12.6419,9.4879	,	689/1103,689/1103	49509184	1234,11772	2203	4300	6503	SO:0001819	synonymous_variant	23394	exon5			TCCAACGCCCCTG	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"""Homeoboxes / ZF class"""	15766	protein-coding gene	gene with protein product	"""ADNP homeobox 1"""	611386	"""activity-dependent neuroprotector"""			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.2067C>T	20.37:g.49509184G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	159	74	0.465409	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Silent	SNP	ENST00000396029.3	37	CCDS13433.1																																																																																			G|0.899;A|0.100	0.100	strong		0.483	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442	
AQP1	358	hgsc.bcm.edu	37	7	30961790	30961790	+	Missense_Mutation	SNP	G	G	A	rs28362731	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:30961790G>A	ENST00000311813.4	+	2	549	c.494G>A	c.(493-495)gGt>gAt	p.G165D	AQP1_ENST00000409899.1_Missense_Mutation_p.G50D|AQP1_ENST00000441328.2_Missense_Mutation_p.G82D|AQP1_ENST00000482461.1_3'UTR|AQP1_ENST00000509504.1_Missense_Mutation_p.G342D|AQP1_ENST00000409611.1_Missense_Mutation_p.G114D|AQP1_ENST00000434909.2_Missense_Mutation_p.G225D	NM_198098.2	NP_932766.1	P29972	AQP1_HUMAN	aquaporin 1 (Colton blood group)	165			G -> D (in dbSNP:rs28362731). {ECO:0000269|Ref.6}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|camera-type eye morphogenesis (GO:0048593)|carbon dioxide transmembrane transport (GO:0035378)|carbon dioxide transport (GO:0015670)|cation transmembrane transport (GO:0098655)|cell volume homeostasis (GO:0006884)|cellular homeostasis (GO:0019725)|cellular hyperosmotic response (GO:0071474)|cellular response to cAMP (GO:0071320)|cellular response to copper ion (GO:0071280)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to inorganic substance (GO:0071241)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mercury ion (GO:0071288)|cellular response to nitric oxide (GO:0071732)|cellular response to retinoic acid (GO:0071300)|cellular response to salt stress (GO:0071472)|cellular response to stress (GO:0033554)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|cGMP biosynthetic process (GO:0006182)|corticotropin secretion (GO:0051458)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|glomerular filtration (GO:0003094)|glycerol transport (GO:0015793)|hyperosmotic salinity response (GO:0042538)|lateral ventricle development (GO:0021670)|lipid digestion (GO:0044241)|maintenance of symbiont-containing vacuole by host (GO:0085018)|metanephric descending thin limb development (GO:0072220)|metanephric glomerulus vasculature development (GO:0072239)|metanephric proximal convoluted tubule segment 2 development (GO:0072232)|metanephric proximal straight tubule development (GO:0072230)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|nitric oxide transport (GO:0030185)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|positive regulation of angiogenesis (GO:0045766)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of saliva secretion (GO:0046878)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|renal water absorption (GO:0070295)|renal water transport (GO:0003097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|secretory granule organization (GO:0033363)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)|transepithelial water transport (GO:0035377)|transmembrane transport (GO:0055085)|water transport (GO:0006833)|wound healing (GO:0042060)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|symbiont-containing vacuole (GO:0020003)	ammonium transmembrane transporter activity (GO:0008519)|carbon dioxide transmembrane transporter activity (GO:0035379)|glycerol transmembrane transporter activity (GO:0015168)|intracellular cGMP activated cation channel activity (GO:0005223)|nitric oxide transmembrane transporter activity (GO:0030184)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)|transmembrane transporter activity (GO:0022857)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(1)|large_intestine(2)|lung(9)	12		Melanoma(862;0.16)			Acetazolamide(DB00819)	CGTGACCTTGGTGGCTCAGCC	0.672													G|||	108	0.0215655	0.0015	0.0389	5008	,	,		14449	0.0		0.0437	False		,,,				2504	0.0358				p.G165D		Atlas-SNP	.											.	AQP1	38	.	0			c.G494A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	42,4364	44.6+/-78.6	1,40,2162	64.0	57.0	60.0		245,341,149,494	4.5	0.7	7	dbSNP_125	60	362,8238	120.6+/-179.8	7,348,3945	yes	missense,missense,missense,missense	AQP1	NM_001185060.1,NM_001185061.1,NM_001185062.1,NM_198098.2	94,94,94,94	8,388,6107	AA,AG,GG		4.2093,0.9532,3.1063	,,,	82/187,114/219,50/155,165/270	30961790	404,12602	2203	4300	6503	SO:0001583	missense	358	exon2			ACCTTGGTGGCTC	M77829	CCDS5431.1, CCDS55096.1, CCDS55097.1, CCDS55098.1	7p14	2014-07-19	2014-01-02		ENSG00000240583	ENSG00000240583		"""Ion channels / Aquaporins"", ""Blood group antigens"""	633	protein-coding gene	gene with protein product		107776	"""Colton blood group"", ""aquaporin 1 (channel-forming integral protein, 28kDa)"", ""aquaporin 1 (channel-forming integral protein, 28kDa, CO blood group)"", ""aquaporin 1"""	CO		1722319, 3166547	Standard	NM_198098		Approved	CHIP28		P29972	OTTHUMG00000023944	ENST00000311813.4:c.494G>A	7.37:g.30961790G>A	ENSP00000311165:p.Gly165Asp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	104	62	0.596154	NM_198098	B5BU39|E7EM69|E9PC21|F5GY19|Q8TBI5|Q8TDC1	Missense_Mutation	SNP	ENST00000311813.4	37	CCDS5431.1	39	0.017857142857142856	0	0.0	13	0.03591160220994475	0	0.0	26	0.03430079155672823	G	10.56	1.385791	0.25031	0.009532	0.042093	ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000250424	ENST00000434909;ENST00000265298;ENST00000311813;ENST00000413400;ENST00000441328;ENST00000409899;ENST00000409611;ENST00000509504	D;D;D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88;-1.88;-1.88	5.45	4.52	0.55395	Aquaporin-like (2);	0.449907	0.24970	N	0.034158	T	0.56352	0.1979	L	0.35341	1.055	0.09310	N	1	P;P;P;P	0.51057	0.926;0.941;0.627;0.511	P;P;P;B	0.51742	0.678;0.603;0.453;0.155	T	0.63233	-0.6683	10	0.12103	T	0.63	2.6832	13.4995	0.61445	0.0:0.2415:0.7585:0.0	rs28362731;rs28362731	225;114;50;165	B4E220;E7EM69;E9PC21;P29972	.;.;.;AQP1_HUMAN	D	225;70;165;150;82;50;114;342	ENSP00000395059:G225D;ENSP00000311165:G165D;ENSP00000405698:G82D;ENSP00000386712:G50D;ENSP00000387178:G114D;ENSP00000421315:G342D	ENSP00000265298:G70D	G	+	2	0	RP5-877J2.1;AQP1	30928315	0.000000	0.05858	0.659000	0.29680	0.609000	0.37215	0.719000	0.25881	2.569000	0.86673	0.561000	0.74099	GGT	G|0.972;A|0.028	0.028	strong		0.672	AQP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215002.3	NM_000385	
ZNF75A	7627	hgsc.bcm.edu	37	16	3367229	3367229	+	Missense_Mutation	SNP	T	T	C	rs17611866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3367229T>C	ENST00000574298.1	+	6	724	c.251T>C	c.(250-252)gTg>gCg	p.V84A	ZNF75A_ENST00000498240.2_3'UTR	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	84			V -> A (in dbSNP:rs17611866).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|lung(7)|prostate(1)	12						CATCAGCCTGTGTCTCTTTCT	0.373													T|||	648	0.129393	0.0219	0.3055	5008	,	,		19754	0.0327		0.2704	False		,,,				2504	0.1043				p.V84A		Atlas-SNP	.											.	ZNF75A	34	.	0			c.T251C						PASS	.	T	ALA/VAL	245,4149	135.3+/-171.4	4,237,1956	67.0	67.0	67.0		251	0.9	0.0	16	dbSNP_123	67	2159,6441	358.9+/-331.3	267,1625,2408	yes	missense	ZNF75A	NM_153028.2	64	271,1862,4364	CC,CT,TT		25.1047,5.5758,18.5008	benign	84/297	3367229	2404,10590	2197	4300	6497	SO:0001583	missense	7627	exon6			AGCCTGTGTCTCT	X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"""Zinc fingers, C2H2-type"", ""-"""	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.251T>C	16.37:g.3367229T>C	ENSP00000459566:p.Val84Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_153028	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	37	CCDS10501.1	342	0.1565934065934066	14	0.028455284552845527	109	0.3011049723756906	19	0.033216783216783216	200	0.2638522427440633	T	0.497	-0.872896	0.02570	0.055758	0.251047	ENSG00000162086	ENST00000293995	.	.	.	4.57	0.954	0.19595	.	1.904780	0.02871	N	0.131634	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.25398	-1.0133	8	0.16420	T	0.52	.	7.8956	0.29704	0.0:0.2533:0.0:0.7467	rs17611866;rs52814213;rs17611866	84	Q96N20	ZN75A_HUMAN	A	84	.	ENSP00000293995:V84A	V	+	2	0	ZNF75A	3307230	0.000000	0.05858	0.001000	0.08648	0.236000	0.25371	0.004000	0.13106	0.033000	0.15463	0.455000	0.32223	GTG	T|0.835;C|0.165	0.165	strong		0.373	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028	
KIF19	124602	hgsc.bcm.edu	37	17	72346918	72346918	+	Silent	SNP	C	C	T	rs73995260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72346918C>T	ENST00000389916.4	+	12	1599	c.1461C>T	c.(1459-1461)gaC>gaT	p.D487D	AC103809.2_ENST00000599136.1_Silent_p.S131S	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	487					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						ACGCTAAGGACGACAGCGAGA	0.642													c|||	364	0.0726837	0.1952	0.0447	5008	,	,		17763	0.001		0.0586	False		,,,				2504	0.0153				p.D487D		Atlas-SNP	.											.	KIF19	102	.	0			c.C1461T						PASS	.			807,3599	320.4+/-296.6	83,641,1479	124.0	112.0	116.0		1461	-10.7	0.0	17	dbSNP_130	116	444,8156	134.9+/-192.2	15,414,3871	no	coding-synonymous	KIF19	NM_153209.3		98,1055,5350	TT,TC,CC		5.1628,18.3159,9.6186		487/999	72346918	1251,11755	2203	4300	6503	SO:0001819	synonymous_variant	124602	exon12			TAAGGACGACAGC	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.1461C>T	17.37:g.72346918C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	161	89	0.552795	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			C|0.906;T|0.094	0.094	strong		0.642	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
RGS22	26166	hgsc.bcm.edu	37	8	100977644	100977644	+	Silent	SNP	T	T	C	rs147697097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:100977644T>C	ENST00000360863.6	-	24	3728	c.3534A>G	c.(3532-3534)caA>caG	p.Q1178Q	RGS22_ENST00000523287.1_Silent_p.Q997Q|RGS22_ENST00000523437.1_Silent_p.Q1166Q	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	1178					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TATTTGCATATTGTTTGATTC	0.343													T|||	27	0.00539137	0.0	0.0029	5008	,	,		15653	0.0		0.0139	False		,,,				2504	0.0112				p.Q1178Q		Atlas-SNP	.											.	RGS22	319	.	0			c.A3534G						PASS	.	T		27,3661		0,27,1817	121.0	113.0	116.0		3534	-1.0	0.2	8	dbSNP_134	116	220,7964		1,218,3873	no	coding-synonymous	RGS22	NM_015668.3		1,245,5690	CC,CT,TT		2.6882,0.7321,2.0805		1178/1265	100977644	247,11625	1844	4092	5936	SO:0001819	synonymous_variant	26166	exon24			TGCATATTGTTTG	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"""Regulators of G-protein signaling"""	24499	protein-coding gene	gene with protein product		615650	"""regulator of G-protein signalling 22"""				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.3534A>G	8.37:g.100977644T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	45	14	0.311111	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	37	CCDS43758.1																																																																																			T|0.987;C|0.013	0.013	strong		0.343	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668	
LIPI	149998	hgsc.bcm.edu	37	21	15481365	15481365	+	Missense_Mutation	SNP	G	G	T	rs7278737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:15481365G>T	ENST00000536861.1	-	10	1331	c.1332C>A	c.(1330-1332)gaC>gaA	p.D444E	AP001347.6_ENST00000428809.1_RNA|LIPI_ENST00000344577.2_Missense_Mutation_p.D465E|AP001347.6_ENST00000432621.1_RNA			Q6XZB0	LIPI_HUMAN	lipase, member I	444			D -> E (in dbSNP:rs7278737). {ECO:0000269|PubMed:12719377}.		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		CTTCCTCTCTGTCTTTAAGTA	0.338													T|||	2599	0.51897	0.503	0.5403	5008	,	,		16535	0.5099		0.502	False		,,,				2504	0.5521				p.D465E		Atlas-SNP	.											LIPI,caecum,carcinoma,-2,1	LIPI	95	1	0			c.C1395A	GRCh37	CM035699	LIPI	M	rs7278737	PASS	.	T	GLU/ASP	2238,2168	584.2+/-386.0	562,1114,527	160.0	168.0	165.0		1395	0.1	0.1	21	dbSNP_116	165	4250,4348	578.6+/-390.7	1064,2122,1113	yes	missense	LIPI	NM_198996.2	45	1626,3236,1640	TT,TG,GG		49.4301,49.2056,49.8923	benign	465/482	15481365	6488,6516	2203	4299	6502	SO:0001583	missense	149998	exon10			CTCTCTGTCTTTA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.1332C>A	21.37:g.15481365G>T	ENSP00000440381:p.Asp444Glu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	37		1085	0.4967948717948718	252	0.5121951219512195	199	0.5497237569060773	265	0.4632867132867133	369	0.4868073878627968	t	0	-2.714912	0.00093	0.507944	0.494301	ENSG00000188992	ENST00000344577;ENST00000536861	D;D	0.86097	-2.07;-2.02	3.7	0.125	0.14718	.	0.058071	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35599	-0.9782	9	0.02654	T	1	.	3.8141	0.08808	0.0:0.3319:0.2:0.4681	rs7278737;rs52812022;rs57390284;rs7278737	465	Q6XZB0-2	.	E	465;444	ENSP00000343331:D465E;ENSP00000440381:D444E	ENSP00000343331:D465E	D	-	3	2	LIPI	14403236	0.186000	0.23225	0.055000	0.19348	0.092000	0.18411	0.194000	0.17135	-0.228000	0.09869	-0.976000	0.02587	GAC	G|0.501;T|0.499	0.499	strong		0.338	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
OR10H5	284433	hgsc.bcm.edu	37	19	15905002	15905002	+	Silent	SNP	T	T	C	rs4808379	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15905002T>C	ENST00000308940.8	+	1	242	c.144T>C	c.(142-144)acT>acC	p.T48T		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						TCATGGCCACTGTCTGGAGCG	0.597													.|||	2431	0.485423	0.4433	0.4841	5008	,	,		19819	0.7907		0.3052	False		,,,				2504	0.4141				p.T48T		Atlas-SNP	.											.	OR10H5	49	.	0			c.T144C						PASS	.	C		1909,2497		406,1097,700	205.0	166.0	179.0		144	-6.8	0.0	19	dbSNP_111	179	2918,5682		510,1898,1892	no	coding-synonymous	OR10H5	NM_001004466.1		916,2995,2592	CC,CT,TT		33.9302,43.3273,37.1136		48/316	15905002	4827,8179	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			GGCCACTGTCTGG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.144T>C	19.37:g.15905002T>C		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	252	252	1	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			.	.	weak		0.597	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
OR1A2	26189	hgsc.bcm.edu	37	17	3101691	3101691	+	Missense_Mutation	SNP	G	G	T	rs12150427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3101691G>T	ENST00000381951.1	+	1	879	c.879G>T	c.(877-879)tgG>tgT	p.W293C		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	293			W -> C (in dbSNP:rs12150427). {ECO:0000269|PubMed:15489334}.		positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W293C(1)		breast(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						TGAGAAATTGGGATATGAAGG	0.463													G|||	1447	0.288938	0.0598	0.2853	5008	,	,		18238	0.5595		0.3509	False		,,,				2504	0.2587				p.W293C		Atlas-SNP	.											OR1A2,NS,carcinoma,0,1	OR1A2	52	1	1	Substitution - Missense(1)	stomach(1)	c.G879T						PASS	.	G	CYS/TRP	506,3900	232.3+/-245.9	33,440,1730	102.0	102.0	102.0		879	-3.0	0.0	17	dbSNP_120	102	3181,5419	476.1+/-369.3	595,1991,1714	yes	missense	OR1A2	NM_012352.1	215	628,2431,3444	TT,TG,GG		36.9884,11.4843,28.3485	benign	293/310	3101691	3687,9319	2203	4300	6503	SO:0001583	missense	26189	exon1			AAATTGGGATATG	AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"""GPCR / Class A : Olfactory receptors"""	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.879G>T	17.37:g.3101691G>T	ENSP00000371377:p.Trp293Cys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	143	61	0.426573	NM_012352	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Missense_Mutation	SNP	ENST00000381951.1	37	CCDS11021.1	731	0.3347069597069597	35	0.07113821138211382	119	0.3287292817679558	313	0.5472027972027972	264	0.3482849604221636	G	0.906	-0.720596	0.03182	0.114843	0.369884	ENSG00000172150	ENST00000381951	T	0.37058	1.22	4.0	-3.05	0.05396	.	0.337248	0.21566	N	0.072494	T	0.00012	0.0000	N	0.14661	0.345	0.41321	P	0.012827000000000033	B	0.13145	0.007	B	0.06405	0.002	T	0.45775	-0.9238	9	0.87932	D	0	.	5.0262	0.14385	0.5003:0.0:0.3583:0.1413	rs12150427;rs17822470;rs52823271;rs60260068;rs12150427	293	Q9Y585	OR1A2_HUMAN	C	293	ENSP00000371377:W293C	ENSP00000371377:W293C	W	+	3	0	OR1A2	3048441	0.000000	0.05858	0.020000	0.16555	0.009000	0.06853	-0.330000	0.07925	-0.665000	0.05317	0.543000	0.68304	TGG	G|0.697;N|0.000	.	strong		0.463	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352	
DHRS7C	201140	hgsc.bcm.edu	37	17	9676134	9676134	+	Missense_Mutation	SNP	G	G	A	rs2280490	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:9676134G>A	ENST00000330255.5	-	5	692	c.680C>T	c.(679-681)tCg>tTg	p.S227L	DHRS7C_ENST00000571134.1_Missense_Mutation_p.S226L	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	227			S -> L (in dbSNP:rs2280490).		regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						CACGTGGTACGACCGGATGAA	0.582													G|||	447	0.0892572	0.0741	0.062	5008	,	,		18957	0.0992		0.1054	False		,,,				2504	0.1022				p.S227L		Atlas-SNP	.											.	DHRS7C	34	.	0			c.C680T						PASS	.	G	LEU/SER,LEU/SER	399,3997	174.1+/-203.8	24,351,1823	73.0	81.0	78.0		680,677	4.7	0.3	17	dbSNP_100	78	909,7683	196.8+/-241.6	49,811,3436	yes	missense,missense	DHRS7C	NM_001220493.1,NM_001105571.2	145,145	73,1162,5259	AA,AG,GG		10.5796,9.0764,10.0708	benign,benign	227/313,226/312	9676134	1308,11680	2198	4296	6494	SO:0001583	missense	201140	exon5			TGGTACGACCGGA		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	32423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 32C, member 2"""					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.680C>T	17.37:g.9676134G>A	ENSP00000327975:p.Ser227Leu	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_001220493	B7ZW74|B9EJH3	Missense_Mutation	SNP	ENST00000330255.5	37	CCDS56020.1	212	0.09706959706959707	50	0.1016260162601626	19	0.052486187845303865	60	0.1048951048951049	83	0.10949868073878628	G	10.84	1.462937	0.26248	0.090764	0.105796	ENSG00000184544	ENST00000330255	T	0.54866	0.55	4.68	4.68	0.58851	NAD(P)-binding domain (1);	0.490245	0.21837	N	0.068386	T	0.00875	0.0029	L	0.40543	1.245	0.27351	P	0.956257	B;P	0.38110	0.226;0.618	B;B	0.20184	0.028;0.023	T	0.35400	-0.9790	9	0.87932	D	0	.	16.5323	0.84364	0.0:0.0:1.0:0.0	rs2280490;rs17207682;rs56923642;rs2280490	227;223	A6NNS2;B9EJH3	DRS7C_HUMAN;.	L	227	ENSP00000327975:S227L	ENSP00000327975:S227L	S	-	2	0	DHRS7C	9616859	1.000000	0.71417	0.317000	0.25265	0.045000	0.14185	7.355000	0.79434	2.429000	0.82318	0.655000	0.94253	TCG	G|0.907;A|0.093	0.093	strong		0.582	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912	
ALG1	56052	hgsc.bcm.edu	37	16	5128817	5128817	+	Missense_Mutation	SNP	G	G	A	rs17849848	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:5128817G>A	ENST00000262374.5	+	7	831	c.800G>A	c.(799-801)aGc>aAc	p.S267N	ALG1_ENST00000544428.1_Missense_Mutation_p.S156N|ALG1_ENST00000588623.1_Missense_Mutation_p.S156N	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	267			S -> N (in dbSNP:rs17849848). {ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				GATGCTGGGAGCGGGCTGGTG	0.642													G|||	364	0.0726837	0.0061	0.1571	5008	,	,		16094	0.128		0.0815	False		,,,				2504	0.0368				p.S267N		Atlas-SNP	.											ALG1,NS,haematopoietic_neoplasm,-1,1	ALG1	35	1	0			c.G800A						PASS	.	G	ASN/SER	60,4334		1,58,2138	29.0	31.0	30.0		800	3.3	0.0	16	dbSNP_123	30	733,7863		38,657,3603	no	missense	ALG1	NM_019109.4	46	39,715,5741	AA,AG,GG		8.5272,1.3655,6.1047	benign	267/465	5128817	793,12197	2197	4298	6495	SO:0001583	missense	56052	exon7			CTGGGAGCGGGCT	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.800G>A	16.37:g.5128817G>A	ENSP00000262374:p.Ser267Asn	Somatic	549	1	0.00182149		WXS	Illumina HiSeq	Phase_I	459	247	0.538126	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	210	0.09615384615384616	6	0.012195121951219513	52	0.143646408839779	79	0.1381118881118881	73	0.09630606860158311	G	8.409	0.843640	0.16963	0.013655	0.085272	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.77229	-1.08;-1.07	5.32	3.29	0.37713	.	0.411911	0.31554	N	0.007450	T	0.00845	0.0028	L	0.45051	1.395	0.80722	P	0.0	B;B	0.10296	0.003;0.002	B;B	0.12156	0.002;0.007	T	0.14980	-1.0453	9	0.09338	T	0.73	-15.871	7.5941	0.28037	0.0858:0.3124:0.6018:0.0	rs17849848;rs60659731	156;267	B4DP08;Q9BT22	.;ALG1_HUMAN	N	267;156	ENSP00000262374:S267N;ENSP00000440019:S156N	ENSP00000262374:S267N	S	+	2	0	ALG1	5068818	0.041000	0.20044	0.006000	0.13384	0.004000	0.04260	0.415000	0.21181	0.585000	0.29608	0.555000	0.69702	AGC	G|0.925;A|0.075	0.075	strong		0.642	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
ZSCAN30	100101467	hgsc.bcm.edu	37	18	32844056	32844056	+	Silent	SNP	G	G	T	rs75902053	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:32844056G>T	ENST00000420878.3	-	3	716	c.261C>A	c.(259-261)atC>atA	p.I87I	ZNF397_ENST00000589420.1_Intron|ZSCAN30_ENST00000333206.5_Silent_p.I87I|ZSCAN30_ENST00000589178.1_Silent_p.I87I|ZSCAN30_ENST00000601405.1_Intron|ZSCAN30_ENST00000592278.1_Silent_p.I87I|ZSCAN30_ENST00000383091.2_Silent_p.I87I	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	87	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(3)|urinary_tract(1)	9						GCAGCTCCAGGATCTGCTCCT	0.592													G|||	123	0.0245607	0.003	0.0274	5008	,	,		17331	0.0		0.0845	False		,,,				2504	0.0153				p.I87I		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.C261A						PASS	.	G	,	53,3083		1,51,1516	57.0	56.0	56.0		261,261	0.5	1.0	18	dbSNP_132	56	557,6607		25,507,3050	no	coding-synonymous,coding-synonymous	ZSCAN30	NM_001112734.2,NM_001166012.1	,	26,558,4566	TT,TG,GG		7.775,1.6901,5.9223	,	87/495,87/495	32844056	610,9690	1568	3582	5150	SO:0001819	synonymous_variant	100101467	exon3			CTCCAGGATCTGC	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"""-"", ""Zinc fingers, C2H2-type"""	33517	protein-coding gene	gene with protein product			"""zinc finger protein 397 opposite strand"", ""ZNF397 opposite strand"""	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.261C>A	18.37:g.32844056G>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	130	55	0.423077	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Silent	SNP	ENST00000420878.3	37	CCDS42427.1																																																																																			G|0.958;T|0.042	0.042	strong		0.592	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734	
COL18A1	80781	hgsc.bcm.edu	37	21	46931109	46931109	+	Missense_Mutation	SNP	G	G	A	rs12483377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46931109G>A	ENST00000359759.4	+	40	5044	c.5023G>A	c.(5023-5025)Gac>Aac	p.D1675N	COL18A1_ENST00000355480.5_Missense_Mutation_p.D1440N|SLC19A1_ENST00000468508.1_5'Flank|SLC19A1_ENST00000567670.1_Intron|COL18A1_ENST00000400337.2_Missense_Mutation_p.D1260N			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1675	Nonhelical region 11 (NC11).		D -> N (decreased activity for binding laminin; increased risk of developing prostate cancer; in compound heterozygotes may cause Knobloch syndrome when in combination with a frameshift/ truncating mutation; dbSNP:rs12483377). {ECO:0000269|PubMed:11606364, ECO:0000269|PubMed:14614989, ECO:0000269|Ref.7}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTTCTCCTTTGACGGCAAGGA	0.647													G|||	222	0.0443291	0.025	0.0519	5008	,	,		11305	0.0268		0.0835	False		,,,				2504	0.0429				p.D1437N		Atlas-SNP	.											COL18A1,lymph_node,lymphoid_neoplasm,0,1	COL18A1	129	1	0			c.G4309A						PASS	.	G	ASN/ASP,ASN/ASP	142,3830		3,136,1847	38.0	40.0	39.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4318,3778	5.0	0.6	21	dbSNP_120	39	732,7602		35,662,3470	yes	missense,missense	COL18A1	NM_030582.3,NM_130445.2	23,23	38,798,5317	AA,AG,GG		8.7833,3.575,7.1022	probably-damaging,probably-damaging	1440/1520,1260/1340	46931109	874,11432	1986	4167	6153	SO:0001583	missense	80781	exon41			TCCTTTGACGGCA		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.5023G>A	21.37:g.46931109G>A	ENSP00000352798:p.Asp1675Asn	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		120	0.054945054945054944	10	0.02032520325203252	26	0.0718232044198895	19	0.033216783216783216	65	0.08575197889182058	G	21.5	4.162404	0.78226	0.03575	0.087833	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	5.04	5.04	0.67666	Collagenase NC10/endostatin (1);C-type lectin fold (1);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.07188	0.0182	L	0.52266	1.64	0.09310	P	1.0	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.998;0.995	T	0.44034	-0.9354	9	0.54805	T	0.06	.	16.2451	0.82437	0.0:0.0:1.0:0.0	rs12483377;rs58372598;rs12483377	1675;1257;1440;1260	P39060;D3DSM4;P39060-1;P39060-2	COIA1_HUMAN;.;.;.	N	1260;1260;1440;1675;1675;608	ENSP00000383191:D1260N;ENSP00000347665:D1440N;ENSP00000352798:D1675N;ENSP00000339118:D608N	ENSP00000339118:D608N	D	+	1	0	COL18A1	45755537	1.000000	0.71417	0.644000	0.29465	0.393000	0.30537	5.798000	0.69095	2.516000	0.84829	0.655000	0.94253	GAC	G|0.953;A|0.047	0.047	strong		0.647	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
OBP2A	29991	hgsc.bcm.edu	37	9	138439806	138439806	+	Missense_Mutation	SNP	C	C	T	rs72766543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:138439806C>T	ENST00000539850.1	+	4	393	c.367C>T	c.(367-369)Cgc>Tgc	p.R123C	OBP2A_ENST00000342114.4_Missense_Mutation_p.A78V|OBP2A_ENST00000371776.1_Missense_Mutation_p.R123C|OBP2A_ENST00000340780.3_Missense_Mutation_p.R123C			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	123					response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		TGGGGGCCTGCGCTACATGGG	0.617													.|||	734	0.146565	0.0303	0.1326	5008	,	,		16953	0.1567		0.2515	False		,,,				2504	0.1953				p.R123C		Atlas-SNP	.											OBP2A,NS,carcinoma,-1,1	OBP2A	21	1	0			c.C367T						PASS	.	C	CYS/ARG	288,4118	155.5+/-188.7	18,252,1933	43.0	39.0	40.0		367	-2.1	0.0	9	dbSNP_130	40	2254,6346	376.8+/-338.3	302,1650,2348	yes	missense	OBP2A	NM_014582.2	180	320,1902,4281	TT,TC,CC		26.2093,6.5365,19.5448	benign	123/171	138439806	2542,10464	2203	4300	6503	SO:0001583	missense	29991	exon4			GGCCTGCGCTACA	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.367C>T	9.37:g.138439806C>T	ENSP00000441028:p.Arg123Cys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	352|352	0.16117216117216118|0.16117216117216118	17|17	0.034552845528455285|0.034552845528455285	60|60	0.16574585635359115|0.16574585635359115	82|82	0.14335664335664336|0.14335664335664336	193|193	0.2546174142480211|0.2546174142480211	c|c	6.857|6.857	0.527344|0.527344	0.13066|0.13066	0.065365|0.065365	0.262093|0.262093	ENSG00000122136|ENSG00000122136	ENST00000342114|ENST00000340780;ENST00000371776;ENST00000539850	T|T;T;T	0.09073|0.11821	3.02|2.74;2.97;2.97	2.25|2.25	-2.08|-2.08	0.07254|0.07254	.|Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.|1.620130	.|0.03800	.|N	.|0.264331	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|P;P	0.02656|0.48911	0.0|0.832;0.917	B|B;B	0.01281|0.39738	0.0|0.308;0.109	T|T	0.21793|0.21793	-1.0235|-1.0235	8|9	0.45353|0.30854	T|T	0.12|0.27	-12.4885|-12.4885	2.1381|2.1381	0.03768|0.03768	0.2454:0.3235:0.0:0.4311|0.2454:0.3235:0.0:0.4311	.|.	78|123;123	Q5T8A4|Q5T8A5;Q9NY56	.|.;OBP2A_HUMAN	V|C	78|123	ENSP00000340950:A78V|ENSP00000342097:R123C;ENSP00000360841:R123C;ENSP00000441028:R123C	ENSP00000340950:A78V|ENSP00000342097:R123C	A|R	+|+	2|1	0|0	OBP2A|OBP2A	137579627|137579627	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-3.799000|-3.799000	0.00363|0.00363	-0.438000|-0.438000	0.07232|0.07232	-0.537000|-0.537000	0.04273|0.04273	GCG|CGC	C|0.813;T|0.187	0.187	strong		0.617	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	
KDM6B	23135	hgsc.bcm.edu	37	17	7750232	7750232	+	Silent	SNP	T	T	C	rs11078709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7750232T>C	ENST00000448097.2	+	9	1138	c.807T>C	c.(805-807)gcT>gcC	p.A269A	KDM6B_ENST00000254846.5_Silent_p.A269A			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	269	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						CTGGCCTGGCTACCAGCCCCC	0.662													C|||	2149	0.429113	0.3949	0.3646	5008	,	,		6510	0.7917		0.173	False		,,,				2504	0.411				p.A269A		Atlas-SNP	.											.	KDM6B	95	.	0			c.T807C						PASS	.	C		1540,2862		276,988,937	17.0	19.0	18.0		807	0.6	1.0	17	dbSNP_120	18	1670,6926		170,1330,2798	no	coding-synonymous	KDM6B	NM_001080424.1		446,2318,3735	CC,CT,TT		19.4276,34.9841,24.6961		269/1683	7750232	3210,9788	2201	4298	6499	SO:0001819	synonymous_variant	23135	exon9			CCTGGCTACCAGC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.807T>C	17.37:g.7750232T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_001080424	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																				T|0.682;C|0.318	0.318	strong		0.662	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
RTP5	285093	hgsc.bcm.edu	37	2	242814535	242814535	+	Silent	SNP	C	C	G	rs146481716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242814535C>G	ENST00000343216.3	+	2	856	c.828C>G	c.(826-828)ctC>ctG	p.L276L		NM_173821.2	NP_776182.2																					CCGGCCTCCTCGGCAGCAGCA	0.672													C|||	5	0.000998403	0.0008	0.0	5008	,	,		17583	0.0		0.004	False		,,,				2504	0.0				p.L276L		Atlas-SNP	.											.	.	.	.	0			c.C828G						PASS	.			2,3846		0,2,1922	40.0	46.0	44.0		828	-5.7	0.0	2	dbSNP_134	44	32,8220		0,32,4094	no	coding-synonymous	C2orf85	NM_173821.2		0,34,6016	GG,GC,CC		0.3878,0.052,0.281		276/573	242814535	34,12066	1924	4126	6050	SO:0001819	synonymous_variant	285093	exon2			CCTCCTCGGCAGC																												ENST00000343216.3:c.828C>G	2.37:g.242814535C>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_173821		Silent	SNP	ENST00000343216.3	37	CCDS42843.1																																																																																			C|0.997;G|0.003	0.003	strong		0.672	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10467571	10467571	+	Missense_Mutation	SNP	C	C	T	rs200175359		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:10467571C>T	ENST00000382483.3	-	4	4260	c.4037G>A	c.(4036-4038)gGa>gAa	p.G1346E		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1362	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		Missing (in allele RP1L1-1).|Missing (in allele RP1L1-2).		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ctgtccttctccttctgtttc	0.478																																					p.G1346E		Atlas-SNP	.											RP1L1,NS,carcinoma,-1,1	RP1L1	453	1	0			c.G4037A						scavenged	.						87.0	83.0	84.0					8																	10467571		1931	4120	6051	SO:0001583	missense	94137	exon4			CCTTCTCCTTCTG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.4037G>A	8.37:g.10467571C>T	ENSP00000371923:p.Gly1346Glu	Somatic	203	7	0.0344828		WXS	Illumina HiSeq	Phase_I	264	31	0.117424	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.799182	0.00617	.	.	ENSG00000183638	ENST00000382483	T	0.06068	3.35	1.72	-3.41	0.04839	.	.	.	.	.	T	0.02418	0.0074	N	0.08118	0	0.09310	N	1	B	0.28324	0.207	B	0.18561	0.022	T	0.44787	-0.9305	9	0.31617	T	0.26	.	4.437	0.11555	0.0:0.4052:0.3013:0.2935	.	1346	A6NKC6	.	E	1346	ENSP00000371923:G1346E	ENSP00000371923:G1346E	G	-	2	0	RP1L1	10504981	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.353000	0.07691	-0.392000	0.07751	0.109000	0.15622	GGA	.	.	weak		0.478	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
UQCRC2	7385	hgsc.bcm.edu	37	16	21994411	21994411	+	Silent	SNP	G	G	A	rs7282	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:21994411G>A	ENST00000268379.4	+	14	2045	c.1281G>A	c.(1279-1281)gcG>gcA	p.A427A	UQCRC2_ENST00000561553.1_Missense_Mutation_p.R376Q	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II	427					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(48;0.0264)		CTTTAAAGGCGGCAAAGAAGT	0.333													T|||	545	0.108826	0.0121	0.049	5008	,	,		17922	0.124		0.0994	False		,,,				2504	0.2761				p.A427A	Colon(123;450 1645 12841 25393 45623)	Atlas-SNP	.											UQCRC2,NS,carcinoma,+1,1	UQCRC2	46	1	0			c.G1281A						PASS	.	T		137,4259		2,133,2063	89.0	81.0	84.0		1281	1.0	1.0	16	dbSNP_52	84	909,7691		40,829,3431	no	coding-synonymous	UQCRC2	NM_003366.2		42,962,5494	AA,AG,GG		10.5698,3.1165,8.0486		427/454	21994411	1046,11950	2198	4300	6498	SO:0001819	synonymous_variant	7385	exon14			AAAGGCGGCAAAG	J04973	CCDS10601.1	16p12	2011-07-04			ENSG00000140740	ENSG00000140740	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12586	protein-coding gene	gene with protein product		191329				8288258, 2547763	Standard	NM_003366		Approved	QCR2, UQCR2	uc002djx.3	P22695	OTTHUMG00000131585	ENST00000268379.4:c.1281G>A	16.37:g.21994411G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_003366	B3KSN4|Q9BQ05	Silent	SNP	ENST00000268379.4	37	CCDS10601.1																																																																																			A|0.089;C|0.000;G|0.911	0.089	strong		0.333	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	NM_003366	
IL12RB1	3594	hgsc.bcm.edu	37	19	18186618	18186618	+	Missense_Mutation	SNP	T	T	C	rs11575934	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18186618T>C	ENST00000600835.2	-	8	939	c.641A>G	c.(640-642)cAg>cGg	p.Q214R	IL12RB1_ENST00000322153.7_Missense_Mutation_p.Q214R|IL12RB1_ENST00000593993.2_Missense_Mutation_p.Q214R			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	214	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> R (in dbSNP:rs11575934). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GCTCCCCAGCTGCCGTCGTCG	0.587													C|||	1149	0.229433	0.0991	0.1628	5008	,	,		15532	0.373		0.3111	False		,,,				2504	0.2209				p.Q214R		Atlas-SNP	.											.	IL12RB1	92	.	0			c.A641G	GRCh37	CM984025	IL12RB1	M	rs11575934	PASS	.	C	ARG/GLN,ARG/GLN	578,3828	762.4+/-413.1	33,512,1658	54.0	58.0	56.0		641,641	1.7	0.0	19	dbSNP_120	56	2715,5885	671.8+/-402.9	425,1865,2010	yes	missense,missense	IL12RB1	NM_005535.1,NM_153701.1	43,43	458,2377,3668	CC,CT,TT		31.5698,13.1185,25.3191	benign,benign	214/663,214/382	18186618	3293,9713	2203	4300	6503	SO:0001583	missense	3594	exon7			CCCAGCTGCCGTC	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.641A>G	19.37:g.18186618T>C	ENSP00000470788:p.Gln214Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	563	0.25778388278388276	52	0.10569105691056911	72	0.19889502762430938	204	0.35664335664335667	235	0.3100263852242744	C	0.046	-1.267102	0.01433	0.131185	0.315698	ENSG00000096996	ENST00000430026;ENST00000322153	T;D	0.85258	0.42;-1.96	3.96	1.68	0.24146	Immunoglobulin-like fold (1);	0.862795	0.09320	N	0.818308	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.17258	-1.0375	9	0.02654	T	1	-13.2546	5.3217	0.15885	0.0:0.5943:0.0:0.4057	rs11575934;rs17845872;rs17858847;rs17884858	214;214;214	P42701-2;P42701-3;P42701	.;.;I12R1_HUMAN	R	214	ENSP00000403103:Q214R;ENSP00000314425:Q214R	ENSP00000314425:Q214R	Q	-	2	0	IL12RB1	18047618	0.000000	0.05858	0.004000	0.12327	0.057000	0.15508	-0.209000	0.09358	0.360000	0.24265	-1.145000	0.01858	CAG	T|0.736;C|0.264	0.264	strong		0.587	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
UROC1	131669	hgsc.bcm.edu	37	3	126202257	126202257	+	Silent	SNP	G	G	A	rs1687477	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126202257G>A	ENST00000290868.2	-	19	1898	c.1845C>T	c.(1843-1845)gcC>gcT	p.A615A	UROC1_ENST00000383579.3_Silent_p.A675A	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	615					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		CTCTCCCCTCGGCCTCCGGGG	0.622													g|||	2049	0.409145	0.1853	0.4697	5008	,	,		20269	0.4901		0.5239	False		,,,				2504	0.4673				p.A675A		Atlas-SNP	.											UROC1_ENST00000383579,NS,carcinoma,0,4	UROC1	150	4	0			c.C2025T						PASS	.		,	1025,3381	375.1+/-321.5	124,777,1302	67.0	61.0	63.0		2025,1845	-10.3	0.5	3	dbSNP_89	63	4524,4076	592.7+/-393.0	1177,2170,953	no	coding-synonymous,coding-synonymous	UROC1	NM_001165974.1,NM_144639.2	,	1301,2947,2255	AA,AG,GG		47.3953,23.2637,42.6649	,	675/737,615/677	126202257	5549,7457	2203	4300	6503	SO:0001819	synonymous_variant	131669	exon20			CCCCTCGGCCTCC	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1845C>T	3.37:g.126202257G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_001165974	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	37	CCDS3038.1																																																																																			G|0.576;A|0.424	0.424	strong		0.622	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639	
ADCYAP1	116	hgsc.bcm.edu	37	18	909561	909561	+	Silent	SNP	A	A	G	rs2231187	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:909561A>G	ENST00000579794.1	+	4	734	c.456A>G	c.(454-456)aaA>aaG	p.K152K	RP11-672L10.3_ENST00000582554.1_RNA|ADCYAP1_ENST00000450565.3_Silent_p.K152K|RP11-672L10.2_ENST00000581719.2_RNA	NM_001117.3	NP_001108.2	P18509	PACA_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary)	152	Important for receptor binding.				activation of adenylate cyclase activity (GO:0007190)|ATP metabolic process (GO:0046034)|behavioral fear response (GO:0001662)|cAMP-mediated signaling (GO:0019933)|cell-cell signaling (GO:0007267)|cellular response to glucocorticoid stimulus (GO:0071385)|female pregnancy (GO:0007565)|histamine secretion (GO:0001821)|negative regulation of acute inflammatory response to antigenic stimulus (GO:0002865)|negative regulation of acute inflammatory response to non-antigenic stimulus (GO:0002878)|negative regulation of cell cycle (GO:0045786)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of Rho GTPase activity (GO:0034259)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|pituitary gland development (GO:0021983)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of somatostatin secretion (GO:0090274)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)|regulation of postsynaptic membrane potential (GO:0060078)|regulation of protein localization (GO:0032880)|response to ethanol (GO:0045471)|response to starvation (GO:0042594)|sensory perception of pain (GO:0019233)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|terminal bouton (GO:0043195)	neuropeptide hormone activity (GO:0005184)|peptide hormone receptor binding (GO:0051428)|pituitary adenylate cyclase activating polypeptide activity (GO:0016521)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						CTGTCAAGAAATACTTGGCGG	0.557													A|||	1014	0.202476	0.0802	0.2709	5008	,	,		11583	0.2411		0.3191	False		,,,				2504	0.1595				p.C152W		Atlas-SNP	.											ADCYAP1,NS,carcinoma,0,1	ADCYAP1	24	1	0			c.T456G						PASS	.	A	,	548,3858	241.8+/-252.1	36,476,1691	99.0	118.0	111.0		456,456	5.2	1.0	18	dbSNP_98	111	2798,5802	435.4+/-358.0	454,1890,1956	no	coding-synonymous,coding-synonymous	ADCYAP1	NM_001099733.1,NM_001117.3	,	490,2366,3647	GG,GA,AA		32.5349,12.4376,25.7266	,	152/177,152/177	909561	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	116	exon4			CAAGAAATACTTG	S83513	CCDS11825.1	18p11	2013-02-28			ENSG00000141433	ENSG00000141433		"""Endogenous ligands"""	241	protein-coding gene	gene with protein product	"""prepro-PACAP"""	102980				1730060	Standard	NM_001099733		Approved	PACAP	uc010dkh.4	P18509	OTTHUMG00000131479	ENST00000579794.1:c.456A>G	18.37:g.909561A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	98	72	0.734694	NM_001117	B2R7N4|Q52LQ0	Missense_Mutation	SNP	ENST00000579794.1	37	CCDS11825.1																																																																																			A|0.757;C|0.001	.	strong		0.557	ADCYAP1-003	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440765.3	NM_001117	
TMEM106C	79022	hgsc.bcm.edu	37	12	48359984	48359984	+	Missense_Mutation	SNP	C	C	T	rs2286025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48359984C>T	ENST00000429772.2	+	5	637	c.524C>T	c.(523-525)tCc>tTc	p.S175F	TMEM106C_ENST00000552561.1_Missense_Mutation_p.S175F|TMEM106C_ENST00000256686.6_Intron|TMEM106C_ENST00000552546.1_Missense_Mutation_p.S104F|TMEM106C_ENST00000549288.1_Intron|TMEM106C_ENST00000550552.1_Intron|TMEM106C_ENST00000449758.2_Intron	NM_001143842.1	NP_001137314.1	Q9BVX2	T106C_HUMAN	transmembrane protein 106C	175			S -> F (in dbSNP:rs2286025).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	14		Acute lymphoblastic leukemia(13;0.11)		GBM - Glioblastoma multiforme(48;0.241)		ACTAACGTCTCCCTTATTCCA	0.498													C|||	843	0.168331	0.0038	0.3372	5008	,	,		21604	0.376		0.1014	False		,,,				2504	0.1258				p.S175F		Atlas-SNP	.											.	TMEM106C	24	.	0			c.C524T						PASS	.	C	,PHE/SER,,PHE/SER	105,4301	82.9+/-121.4	4,97,2102	126.0	102.0	110.0		,524,,524	3.5	1.0	12	dbSNP_100	110	857,7743	194.7+/-240.0	46,765,3489	yes	intron,missense,intron,missense	TMEM106C	NM_001143841.1,NM_001143842.1,NM_001143843.1,NM_024056.3	,155,,155	50,862,5591	TT,TC,CC		9.9651,2.3831,7.3966	,probably-damaging,,probably-damaging	,175/251,,175/251	48359984	962,12044	2203	4300	6503	SO:0001583	missense	79022	exon5			ACGTCTCCCTTAT	BC000854	CCDS8758.1, CCDS44867.1	12q13.1	2005-12-19				ENSG00000134291			28775	protein-coding gene	gene with protein product							Standard	NM_024056		Approved	MGC5576	uc001rqr.3	Q9BVX2	OTTHUMG00000169892	ENST00000429772.2:c.524C>T	12.37:g.48359984C>T	ENSP00000400471:p.Ser175Phe	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	141	138	0.978723	NM_024056	B2R998|B7Z5M4|Q3B761	Missense_Mutation	SNP	ENST00000429772.2	37	CCDS8758.1	424	0.19413919413919414	5	0.01016260162601626	110	0.30386740331491713	223	0.38986013986013984	86	0.11345646437994723	C	17.08	3.298020	0.60086	0.023831	0.099651	ENSG00000134291	ENST00000552561;ENST00000546749;ENST00000552546;ENST00000429772	T;T;T;T	0.22945	2.03;1.93;2.03;2.03	4.39	3.47	0.39725	.	0.131177	0.49916	D	0.000139	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	1.0	D	0.59357	0.985	P	0.58013	0.831	T	0.48479	-0.9032	8	.	.	.	10.7131	13.808	0.63246	0.0:0.8443:0.1557:0.0	rs2286025;rs52797566;rs58751191;rs2286025	175	Q9BVX2	T106C_HUMAN	F	175;39;104;175	ENSP00000446657:S175F;ENSP00000446622:S39F;ENSP00000448268:S104F;ENSP00000400471:S175F	.	S	+	2	0	TMEM106C	46646251	0.980000	0.34600	1.000000	0.80357	0.967000	0.64934	3.082000	0.50128	1.409000	0.46915	0.655000	0.94253	TCC	C|0.874;T|0.126	0.126	strong		0.498	TMEM106C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406452.1	NM_024056	
PRAME	23532	hgsc.bcm.edu	37	22	22890792	22890792	+	Silent	SNP	T	T	C	rs17497547	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22890792T>C	ENST00000398741.1	-	6	1533	c.1227A>G	c.(1225-1227)acA>acG	p.T409T	PRAME_ENST00000539862.1_Silent_p.T393T|PRAME_ENST00000398743.2_Silent_p.T409T|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000543184.1_Silent_p.T409T|PRAME_ENST00000424204.2_Silent_p.T393T|PRAME_ENST00000405655.3_Silent_p.T409T|PRAME_ENST00000402697.1_Silent_p.T409T	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	409					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		AGCTTAAGGTTGTAAGCTGGG	0.562													C|||	353	0.0704872	0.031	0.1354	5008	,	,		19699	0.0308		0.1402	False		,,,				2504	0.047				p.T409T	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.A1227G						PASS	.	C	,,,,	241,4165	804.3+/-415.8	7,227,1969	83.0	82.0	82.0		1227,1227,1227,1227,1227	-7.4	0.0	22	dbSNP_123	82	1304,7296	758.3+/-407.5	103,1098,3099	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRAME	NM_006115.3,NM_206953.1,NM_206954.1,NM_206955.1,NM_206956.1	,,,,	110,1325,5068	CC,CT,TT		15.1628,5.4698,11.8791	,,,,	409/510,409/510,409/510,409/510,409/510	22890792	1545,11461	2203	4300	6503	SO:0001819	synonymous_variant	23532	exon6			TAAGGTTGTAAGC	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.1227A>G	22.37:g.22890792T>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_206954	B2R6Y7|O43481|Q8IXN8	Silent	SNP	ENST00000398741.1	37	CCDS13801.1																																																																																			T|0.894;C|0.106	0.106	strong		0.562	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
C5orf22	55322	hgsc.bcm.edu	37	5	31538692	31538692	+	Missense_Mutation	SNP	A	A	C	rs17410000	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:31538692A>C	ENST00000325366.9	+	4	830	c.703A>C	c.(703-705)Act>Cct	p.T235P	C5orf22_ENST00000355907.3_5'UTR	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	235			T -> P (in dbSNP:rs17410000).							kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						TGCTGCCAGCACTGGGGAAAT	0.403													A|||	983	0.196286	0.0711	0.1816	5008	,	,		19851	0.131		0.3141	False		,,,				2504	0.3221				p.T235P		Atlas-SNP	.											.	C5orf22	48	.	0			c.A703C						PASS	.	A	PRO/THR	551,3855	239.3+/-250.5	30,491,1682	50.0	49.0	49.0		703	-6.8	0.0	5	dbSNP_123	49	2835,5765	442.1+/-360.0	445,1945,1910	yes	missense	C5orf22	NM_018356.2	38	475,2436,3592	CC,CA,AA		32.9651,12.5057,26.0341	benign	235/443	31538692	3386,9620	2203	4300	6503	SO:0001583	missense	55322	exon4			GCCAGCACTGGGG	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.703A>C	5.37:g.31538692A>C	ENSP00000326879:p.Thr235Pro	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	143	64	0.447552	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Missense_Mutation	SNP	ENST00000325366.9	37	CCDS3895.1	411	0.18818681318681318	24	0.04878048780487805	72	0.19889502762430938	84	0.14685314685314685	231	0.30474934036939316	A	10.64	1.406699	0.25378	0.125057	0.329651	ENSG00000082213	ENST00000325366	T	0.31769	1.48	5.99	-6.83	0.01693	.	0.662711	0.16506	N	0.211437	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	2.9999999999752447E-6	P	0.42584	0.784	P	0.45377	0.478	T	0.08889	-1.0700	9	0.42905	T	0.14	-1.5846	5.4152	0.16370	0.1444:0.2375:0.5003:0.1178	rs17410000;rs52792560;rs17410000	235	Q49AR2	CE022_HUMAN	P	235	ENSP00000326879:T235P	ENSP00000326879:T235P	T	+	1	0	C5orf22	31574449	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.792000	0.26929	-1.130000	0.02914	-0.313000	0.08912	ACT	A|0.767;C|0.233	0.233	strong		0.403	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356	
HELZ2	85441	hgsc.bcm.edu	37	20	62193019	62193019	+	Silent	SNP	C	C	T	rs11551684	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62193019C>T	ENST00000467148.1	-	12	6840	c.6771G>A	c.(6769-6771)ccG>ccA	p.P2257P	HELZ2_ENST00000427522.2_Silent_p.P1688P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2257	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P2257P(1)									TGCCCACACGCGGCACTGGGA	0.652													C|||	1096	0.21885	0.0068	0.085	5008	,	,		15633	0.5734		0.166	False		,,,				2504	0.2894				p.P2257P		Atlas-SNP	.											PRIC285,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	prostate(1)	c.G6771A						PASS	.	C	,	169,4237	106.5+/-144.9	2,165,2036	40.0	45.0	43.0		6771,5064	-9.0	0.0	20	dbSNP_120	43	1371,7229	253.3+/-279.0	110,1151,3039	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	112,1316,5075	TT,TC,CC		15.9419,3.8357,11.8407	,	2257/2650,1688/2081	62193019	1540,11466	2203	4300	6503	SO:0001819	synonymous_variant	85441	exon13			CACACGCGGCACT	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6771G>A	20.37:g.62193019C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			C|0.849;T|0.151	0.151	strong		0.652	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
SDPR	8436	hgsc.bcm.edu	37	2	192701393	192701393	+	Silent	SNP	A	A	G	rs10167187	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:192701393A>G	ENST00000304141.4	-	2	863	c.534T>C	c.(532-534)ggT>ggC	p.G178G		NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			CTTCCACGGCACCGGAAACGG	0.488													G|||	3174	0.633786	0.5121	0.6686	5008	,	,		17761	0.7609		0.5795	False		,,,				2504	0.6984				p.G178G		Atlas-SNP	.											.	SDPR	67	.	0			c.T534C						PASS	.	G		2229,2177	527.3+/-372.1	578,1073,552	42.0	48.0	46.0		534	2.3	0.0	2	dbSNP_119	46	4996,3602	502.7+/-375.8	1481,2034,784	no	coding-synonymous	SDPR	NM_004657.5		2059,3107,1336	GG,GA,AA		41.8935,49.4099,44.4402		178/426	192701393	7225,5779	2203	4299	6502	SO:0001819	synonymous_variant	8436	exon2			CACGGCACCGGAA	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"""phosphatidylserine binding protein"""	606728	"""serum deprivation response (phosphatidylserine-binding protein)"", ""serum deprivation response (phosphatidylserine binding protein)"""			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.534T>C	2.37:g.192701393A>G		Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_004657		Silent	SNP	ENST00000304141.4	37	CCDS2313.1																																																																																			A|0.407;G|0.593	0.593	strong		0.488	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657	
C4orf36	132989	hgsc.bcm.edu	37	4	87809025	87809025	+	Missense_Mutation	SNP	T	T	C	rs28664715	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:87809025T>C	ENST00000473559.1	-	7	905	c.242A>G	c.(241-243)tAt>tGt	p.Y81C	C4orf36_ENST00000295898.3_Missense_Mutation_p.Y81C|C4orf36_ENST00000503001.1_5'Flank			Q96KX1	CD036_HUMAN	chromosome 4 open reading frame 36	81										breast(1)|kidney(1)|lung(1)|prostate(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)		CTTCACTTCATACTCCCTTTC	0.373													T|||	188	0.0375399	0.0083	0.0519	5008	,	,		22453	0.0		0.1004	False		,,,				2504	0.0409				p.Y81C		Atlas-SNP	.											.	C4orf36	10	.	0			c.A242G						PASS	.	T	CYS/TYR	80,4326	69.2+/-107.0	1,78,2124	79.0	74.0	76.0		242	1.1	1.0	4	dbSNP_125	76	775,7825	183.3+/-231.6	36,703,3561	yes	missense	C4orf36	NM_144645.3	194	37,781,5685	CC,CT,TT		9.0116,1.8157,6.5739	possibly-damaging	81/118	87809025	855,12151	2203	4300	6503	SO:0001583	missense	132989	exon4			ACTTCATACTCCC	BC016746	CCDS3615.1	4q21.3	2008-02-05			ENSG00000163633	ENSG00000163633			28386	protein-coding gene	gene with protein product						12477932	Standard	NM_144645		Approved	MGC26744	uc003hqe.4	Q96KX1	OTTHUMG00000130597	ENST00000473559.1:c.242A>G	4.37:g.87809025T>C	ENSP00000420949:p.Tyr81Cys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	131	68	0.519084	NM_144645		Missense_Mutation	SNP	ENST00000473559.1	37	CCDS3615.1	105	0.04807692307692308	6	0.012195121951219513	20	0.055248618784530384	0	0.0	79	0.10422163588390501	T	14.49	2.549723	0.45383	0.018157	0.090116	ENSG00000163633	ENST00000295898;ENST00000473559;ENST00000506308;ENST00000504008	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.23	1.14	0.20703	.	0.707713	0.12912	N	0.428898	T	0.00695	0.0023	L	0.29908	0.895	0.32622	P	0.5232479999999999	B	0.20261	0.043	B	0.23018	0.043	T	0.10132	-1.0643	9	0.87932	D	0	-2.0824	4.1319	0.10152	0.3133:0.0873:0.0:0.5994	rs28664715	81	Q96KX1	CD036_HUMAN	C	81	ENSP00000295898:Y81C;ENSP00000420949:Y81C;ENSP00000421141:Y81C;ENSP00000422720:Y81C	ENSP00000295898:Y81C	Y	-	2	0	C4orf36	88028049	0.533000	0.26354	0.997000	0.53966	0.473000	0.32948	0.163000	0.16520	0.424000	0.26061	-0.441000	0.05720	TAT	T|0.938;C|0.062	0.062	strong		0.373	C4orf36-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253045.2	NM_144645	
NDUFAF1	51103	hgsc.bcm.edu	37	15	41689232	41689232	+	Missense_Mutation	SNP	C	C	T	rs1899	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41689232C>T	ENST00000260361.4	-	2	407	c.26G>A	c.(25-27)cGt>cAt	p.R9H		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	9			R -> H (in dbSNP:rs1899). {ECO:0000269|PubMed:11935339}.		mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		ATAAGTACCACGCAGCAATTT	0.408													C|||	763	0.152356	0.1392	0.1744	5008	,	,		17465	0.0079		0.2724	False		,,,				2504	0.18				p.R9H		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.G26A						PASS	.	C	HIS/ARG	721,3681		61,599,1541	33.0	34.0	33.0		26	-4.7	0.0	15	dbSNP_36	33	2232,6364		279,1674,2345	yes	missense	NDUFAF1	NM_016013.2	29	340,2273,3886	TT,TC,CC		25.9656,16.3789,22.7189	benign	9/328	41689232	2953,10045	2201	4298	6499	SO:0001583	missense	51103	exon2			GTACCACGCAGCA	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"""Mitochondrial respiratory chain complex assembly factors"""	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.26G>A	15.37:g.41689232C>T	ENSP00000260361:p.Arg9His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	125	43	0.344	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	37	CCDS10075.1	346	0.15842490842490842	69	0.1402439024390244	73	0.20165745856353592	3	0.005244755244755245	201	0.26517150395778366	C	6.822	0.520728	0.13005	0.163789	0.259656	ENSG00000137806	ENST00000260361	T	0.59502	0.26	4.7	-4.67	0.03319	.	1.281150	0.04961	N	0.462130	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.21452	0.056	B	0.14578	0.011	T	0.08534	-1.0717	9	0.28530	T	0.3	-5.8832	1.2213	0.01924	0.1242:0.221:0.257:0.3977	rs1899;rs3193542;rs59161962;rs1899	9	Q9Y375	CIA30_HUMAN	H	9	ENSP00000260361:R9H	ENSP00000260361:R9H	R	-	2	0	NDUFAF1	39476524	0.000000	0.05858	0.001000	0.08648	0.051000	0.14879	-0.810000	0.04505	-0.867000	0.04063	-0.458000	0.05436	CGT	C|0.825;T|0.175	0.175	strong		0.408	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
CERS4	79603	hgsc.bcm.edu	37	19	8326672	8326672	+	Missense_Mutation	SNP	G	G	A	rs141592194		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8326672G>A	ENST00000251363.5	+	11	1249	c.949G>A	c.(949-951)Gtg>Atg	p.V317M	CERS4_ENST00000558331.1_Missense_Mutation_p.V266M|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559336.1_Intron|CERS4_ENST00000559450.1_Missense_Mutation_p.V317M	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	317	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GCTGCTGCACGTGTTCTGGTC	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		16989	0.0		0.0	False		,,,				2504	0.001				p.V317M		Atlas-SNP	.											.	.	.	.	0			c.G949A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	105.0	88.0	94.0		949	0.6	0.7	19	dbSNP_134	94	6,8594	5.0+/-18.6	0,6,4294	yes	missense	CERS4	NM_024552.2	21	0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538	probably-damaging	317/395	8326672	7,12999	2203	4300	6503	SO:0001583	missense	79603	exon11			CTGCACGTGTTCT		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.949G>A	19.37:g.8326672G>A	ENSP00000251363:p.Val317Met	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	269	110	0.408922	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	37	CCDS12197.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454447	0.63290	2.27E-4	6.98E-4	ENSG00000090661	ENST00000251363	D	0.86164	-2.08	5.13	0.644	0.17776	TRAM/LAG1/CLN8 homology domain (3);	0.257428	0.39985	N	0.001212	D	0.90363	0.6984	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.87521	0.2446	10	0.62326	D	0.03	-22.7678	6.9208	0.24387	0.4709:0.0:0.5291:0.0	.	317	Q9HA82	CERS4_HUMAN	M	317	ENSP00000251363:V317M	ENSP00000251363:V317M	V	+	1	0	CERS4	8232672	0.711000	0.27906	0.672000	0.29872	0.694000	0.40290	1.129000	0.31381	0.194000	0.20326	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.567	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
SLC5A12	159963	hgsc.bcm.edu	37	11	26694979	26694979	+	Silent	SNP	A	A	G	rs4369354	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:26694979A>G	ENST00000396005.3	-	14	1986	c.1677T>C	c.(1675-1677)tgT>tgC	p.C559C		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	559					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						GCTGAACTCCACACCAGCATA	0.408													G|||	2118	0.422923	0.4448	0.3127	5008	,	,		19336	0.3502		0.4881	False		,,,				2504	0.4796				p.C559C		Atlas-SNP	.											SLC5A12,colon,carcinoma,-2,1	SLC5A12	134	1	0			c.T1677C						PASS	.	G		1797,2329		404,989,670	142.0	145.0	144.0		1677	1.9	1.0	11	dbSNP_111	144	4258,4184		1086,2086,1049	no	coding-synonymous	SLC5A12	NM_178498.3		1490,3075,1719	GG,GA,AA		49.5617,43.5531,48.1779		559/619	26694979	6055,6513	2063	4221	6284	SO:0001819	synonymous_variant	159963	exon14			AACTCCACACCAG	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"""Solute carriers"""	28750	protein-coding gene	gene with protein product		612455	"""solute carrier family 5 (sodium/glucose cotransporter), member 12"""			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1677T>C	11.37:g.26694979A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			A|0.555;G|0.445	0.445	strong		0.408	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
OR4K15	81127	hgsc.bcm.edu	37	14	20444490	20444490	+	Silent	SNP	C	C	T	rs11158071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20444490C>T	ENST00000305051.5	+	1	888	c.813C>T	c.(811-813)gtC>gtT	p.V271V		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCACTGTGGTCACTTTATTCT	0.458													C|||	2837	0.566494	0.1604	0.755	5008	,	,		21137	0.8323		0.6938	False		,,,				2504	0.5767				p.V271V		Atlas-SNP	.											.	OR4K15	82	.	0			c.C813T						PASS	.	C		1012,3394		113,786,1304	146.0	120.0	129.0		813	3.1	1.0	14	dbSNP_120	129	5640,2958		1832,1976,491	no	coding-synonymous	OR4K15	NM_001005486.1		1945,2762,1795	TT,TC,CC		34.4033,22.9687,48.8465		271/349	20444490	6652,6352	2203	4299	6502	SO:0001819	synonymous_variant	81127	exon1			TGTGGTCACTTTA		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.813C>T	14.37:g.20444490C>T		Somatic	290	2	0.00689655		WXS	Illumina HiSeq	Phase_I	269	267	0.992565	NM_001005486	B9EIL3|Q6IEZ4	Silent	SNP	ENST00000305051.5	37	CCDS32026.1																																																																																			C|0.443;T|0.557	0.557	strong		0.458	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
FANCM	57697	hgsc.bcm.edu	37	14	45606387	45606387	+	Missense_Mutation	SNP	A	A	G	rs45547534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:45606387A>G	ENST00000267430.5	+	2	709	c.624A>G	c.(622-624)atA>atG	p.I208M	FANCM_ENST00000556036.1_Missense_Mutation_p.I208M|FKBP3_ENST00000216330.3_5'Flank|FKBP3_ENST00000396062.3_5'Flank|FANCM_ENST00000542564.2_Missense_Mutation_p.I208M	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	208	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		I -> M (in dbSNP:rs45547534).		DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						CTGCTGAAATAAAGTGTTTAG	0.388								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				A|||	27	0.00539137	0.0015	0.0202	5008	,	,		18558	0.0		0.0089	False		,,,				2504	0.002				p.I208M		Atlas-SNP	.											.	FANCM	225	.	0			c.A624G						PASS	.	A	MET/ILE	18,4388	25.3+/-52.1	0,18,2185	88.0	84.0	85.0		624	0.0	1.0	14	dbSNP_127	85	130,8470	64.9+/-127.2	1,128,4171	yes	missense	FANCM	NM_020937.2	10	1,146,6356	GG,GA,AA		1.5116,0.4085,1.1379	probably-damaging	208/2049	45606387	148,12858	2203	4300	6503	SO:0001583	missense	57697	exon2	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGAAATAAAGTGT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.624A>G	14.37:g.45606387A>G	ENSP00000267430:p.Ile208Met	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	19	0.0086996336996337	0	0.0	12	0.03314917127071823	0	0.0	7	0.009234828496042216	A	18.20	3.570941	0.65765	0.004085	0.015116	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	T;T;T	0.15952	2.38;2.38;2.38	5.39	0.00779	0.14072	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.208574	0.49916	N	0.000138	T	0.13243	0.0321	M	0.83118	2.625	0.29632	N	0.845403	D;D;P	0.63046	0.992;0.992;0.904	D;D;P	0.71184	0.972;0.944;0.784	T	0.08493	-1.0719	10	0.72032	D	0.01	.	1.4329	0.02337	0.4625:0.2436:0.1626:0.1313	rs45547534	208;208;208	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	M	208	ENSP00000450596:I208M;ENSP00000267430:I208M;ENSP00000442493:I208M	ENSP00000267430:I208M	I	+	3	3	FANCM	44676137	0.940000	0.31905	1.000000	0.80357	0.953000	0.61014	0.125000	0.15749	0.338000	0.23692	0.528000	0.53228	ATA	A|0.990;G|0.010	0.010	strong		0.388	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
SAGE1	55511	hgsc.bcm.edu	37	X	134994005	134994005	+	Missense_Mutation	SNP	T	T	C	rs4829799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:134994005T>C	ENST00000370709.3	+	17	2414	c.2414T>C	c.(2413-2415)tTg>tCg	p.L805S	SAGE1_ENST00000535938.1_Missense_Mutation_p.L805S|SAGE1_ENST00000324447.3_Missense_Mutation_p.L805S|SAGE1_ENST00000537770.1_Missense_Mutation_p.L429S			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	805			L -> S (in dbSNP:rs4829799). {ECO:0000269|PubMed:10919659}.			nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GTAATGTCTTTGGTGGAAACT	0.373													N|||	611	0.161854	0.0681	0.1585	3775	,	,		15825	0.1012		0.2058	False		,,,				2504	0.1043				p.L805S		Atlas-SNP	.											.	SAGE1	160	.	0			c.T2414C						PASS	.	C	SER/LEU	557,3278		30,426,71,1176,500	95.0	86.0	89.0		2414	2.7	0.0	X	dbSNP_111	89	1753,4975		188,922,455,1318,1417	yes	missense	SAGE1	NM_018666.2	145	218,1348,526,2494,1917	CC,CT,C,TT,T		26.0553,14.5241,21.8688	benign	805/905	134994005	2310,8253	2203	4300	6503	SO:0001583	missense	55511	exon18			TGTCTTTGGTGGA	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.2414T>C	X.37:g.134994005T>C	ENSP00000359743:p.Leu805Ser	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	37	CCDS14652.1	310	0.18685955394816153	24	0.05	41	0.12732919254658384	38	0.07196969696969698	105	0.16153846153846155	C	0.014	-1.605379	0.00842	0.145241	0.260553	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709	T;T;T;T	0.29397	1.57;1.57;1.62;1.57	2.67	2.67	0.31697	.	0.944741	0.08754	N	0.898686	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.42155	-0.9468	9	0.07482	T	0.82	.	8.6217	0.33864	0.0:0.8737:0.0:0.1263	rs4829799;rs17221796;rs52801822;rs61577447;rs4829799	429;805	F5H2Z8;Q9NXZ1	.;SAGE1_HUMAN	S	805;805;429;805	ENSP00000323191:L805S;ENSP00000445959:L805S;ENSP00000438276:L429S;ENSP00000359743:L805S	ENSP00000323191:L805S	L	+	2	0	SAGE1	134821671	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	0.100000	0.15231	0.146000	0.19002	-1.150000	0.01838	TTG	0|0.015;C|0.189	0.189	strong		0.373	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
GALNT11	63917	hgsc.bcm.edu	37	7	151791435	151791435	+	Silent	SNP	C	C	T	rs138436495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151791435C>T	ENST00000434507.1	+	4	560	c.123C>T	c.(121-123)ccC>ccT	p.P41P	GALNT11_ENST00000320311.2_Silent_p.P41P|GALNT11_ENST00000452146.2_Intron|GALNT11_ENST00000415421.1_Silent_p.P41P|GALNT11_ENST00000430044.2_Silent_p.P41P|GALNT11_ENST00000422997.2_Silent_p.P41P|GALNT11_ENST00000482812.1_3'UTR			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	41					cellular protein metabolic process (GO:0044267)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via threonine (GO:0018243)|regulation of Notch signaling pathway (GO:0008593)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|Notch binding (GO:0005112)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		AGAATGTGCCCGTCAAGGGGT	0.473													C|||	4	0.000798722	0.0	0.0029	5008	,	,		16967	0.0		0.002	False		,,,				2504	0.0				p.P41P		Atlas-SNP	.											GALNT11,NS,carcinoma,+1,1	GALNT11	59	1	0			c.C123T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	138.0	141.0	140.0		123	5.7	1.0	7	dbSNP_134	140	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous	GALNT11	NM_022087.2		0,27,6476	TT,TC,CC		0.2674,0.0908,0.2076		41/609	151791435	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	63917	exon2			TGTGCCCGTCAAG	AC006017	CCDS5930.1	7q36.1	2014-05-09	2014-05-09		ENSG00000178234	ENSG00000178234	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19875	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 11"""	615130	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)"""			11925450	Standard	NM_022087		Approved	GalNAc-T11	uc010lqg.1	Q8NCW6	OTTHUMG00000157251	ENST00000434507.1:c.123C>T	7.37:g.151791435C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	122	72	0.590164	NM_022087	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Silent	SNP	ENST00000434507.1	37	CCDS5930.1																																																																																			C|0.998;T|0.002	0.002	strong		0.473	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087	
CROCC	9696	hgsc.bcm.edu	37	1	17273443	17273443	+	Missense_Mutation	SNP	C	C	T	rs74657070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17273443C>T	ENST00000375541.5	+	17	2540	c.2471C>T	c.(2470-2472)aCg>aTg	p.T824M	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGCTCCCCACGCTGCGCCAT	0.701													c|||	151	0.0301518	0.0469	0.0375	5008	,	,		20767	0.0		0.0537	False		,,,				2504	0.0092				p.T824M		Atlas-SNP	.											CROCC,NS,carcinoma,-1,1	CROCC	185	1	0			c.C2471T						PASS	.	C	MET/THR	171,4089		0,171,1959	9.0	9.0	9.0		2471	1.2	0.0	1	dbSNP_131	9	329,7969		0,329,3820	no	missense	CROCC	NM_014675.3	81	0,500,5779	TT,TC,CC		3.9648,4.0141,3.9815	possibly-damaging	824/2018	17273443	500,12058	2130	4149	6279	SO:0001583	missense	9696	exon17			TCCCCACGCTGCG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2471C>T	1.37:g.17273443C>T	ENSP00000364691:p.Thr824Met	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	90	55	0.611111	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	56	0.02564102564102564	10	0.02032520325203252	9	0.024861878453038673	0	0.0	37	0.048812664907651716	C	1.643	-0.515945	0.04200	0.040141	0.039648	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09911	2.93	3.18	1.2	0.21068	.	.	.	.	.	T	0.00815	0.0027	N	0.14661	0.345	0.09310	N	1	B;P;P	0.46020	0.053;0.769;0.871	B;B;B	0.39876	0.01;0.216;0.312	T	0.36648	-0.9739	9	0.46703	T	0.11	.	4.9245	0.13887	0.2224:0.6507:0.0:0.1269	.	687;127;824	A1L0S8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	M	824;705	ENSP00000364691:T824M	ENSP00000364691:T824M	T	+	2	0	CROCC	17146030	0.000000	0.05858	0.006000	0.13384	0.035000	0.12851	-0.679000	0.05203	0.322000	0.23283	0.462000	0.41574	ACG	C|0.974;T|0.026	0.026	strong		0.701	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179852074	179852074	+	Missense_Mutation	SNP	T	T	C	rs1281378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:179852074T>C	ENST00000606911.2	+	1	628	c.437T>C	c.(436-438)aTg>aCg	p.M146T	TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.M25T|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.M146T|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.M146T|RP11-533E19.7_ENST00000610272.1_lincRNA			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	146			M -> T (in dbSNP:rs1281378). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:21406692}.		positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						TCTCCTGTTATGACCAGGAGA	0.657													T|||	3049	0.608826	0.3812	0.6758	5008	,	,		15312	0.7778		0.6133	False		,,,				2504	0.6902				p.M146T		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.T437C						PASS	.	T	THR/MET	1953,2443		455,1043,700	16.0	19.0	18.0		437	-1.5	0.0	1	dbSNP_87	18	5433,3147		1737,1959,594	yes	missense	TOR1AIP1	NM_015602.2	81	2192,3002,1294	CC,CT,TT		36.6783,44.4268,43.0795	benign	146/584	179852074	7386,5590	2198	4290	6488	SO:0001583	missense	26092	exon1			CTGTTATGACCAG		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.437T>C	1.37:g.179852074T>C	ENSP00000476687:p.Met146Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	37	CCDS1335.1	1338	0.6126373626373627	189	0.38414634146341464	234	0.6464088397790055	451	0.7884615384615384	464	0.6121372031662269	T	0.020	-1.444634	0.01089	0.444268	0.633217	ENSG00000143337	ENST00000528443;ENST00000325993;ENST00000271583;ENST00000435319	T;T;T	0.20738	2.05;2.05;2.05	4.2	-1.54	0.08584	.	0.677608	0.12768	N	0.440772	T	0.00012	0.0000	N	0.00182	-1.905	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29181	-1.0020	9	0.02654	T	1	0.019	3.6348	0.08145	0.1718:0.3958:0.0:0.4323	rs1281378;rs1758150;rs3889647;rs17370693;rs17845719;rs17858667;rs57247449;rs1281378	146;146	Q5JTV8;E9PKD1	TOIP1_HUMAN;.	T	146	ENSP00000435365:M146T;ENSP00000271583:M146T;ENSP00000393292:M146T	ENSP00000271583:M146T	M	+	2	0	TOR1AIP1	178118697	0.014000	0.17966	0.000000	0.03702	0.010000	0.07245	0.473000	0.22132	-0.363000	0.08101	-0.230000	0.12252	ATG	T|0.410;C|0.590	0.590	strong		0.657	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602	
SENP7	57337	hgsc.bcm.edu	37	3	101066717	101066717	+	Splice_Site	SNP	T	T	A	rs2433031	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:101066717T>A	ENST00000394095.2	-	13	1889	c.1836A>T	c.(1834-1836)caA>caT	p.Q612H	SENP7_ENST00000348610.3_Splice_Site_p.Q579H|SENP7_ENST00000394091.1_Splice_Site_p.Q448H|SENP7_ENST00000358203.3_Splice_Site_p.Q448H|SENP7_ENST00000394094.2_Splice_Site_p.Q547H|SENP7_ENST00000314261.7_Splice_Site_p.Q546H	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	612			Q -> H (in dbSNP:rs2433031). {ECO:0000269|PubMed:11214970}.			intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.Q546H(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TATACTCACATTGCTGGCTTA	0.294													T|||	1508	0.301118	0.177	0.2767	5008	,	,		13620	0.3403		0.3827	False		,,,				2504	0.362				p.Q612H		Atlas-SNP	.											SENP7,NS,carcinoma,0,1	SENP7	170	1	1	Substitution - Missense(1)	prostate(1)	c.A1836T						PASS	.	T	HIS/GLN,HIS/GLN	989,3417	356.4+/-313.5	98,793,1312	66.0	67.0	67.0		1641,1836	1.1	1.0	3	dbSNP_100	67	3167,5431	468.5+/-367.3	596,1975,1728	yes	missense-near-splice,missense-near-splice	SENP7	NM_001077203.1,NM_020654.3	24,24	694,2768,3040	AA,AT,TT		36.8341,22.4467,31.9594	possibly-damaging,possibly-damaging	547/986,612/1051	101066717	4156,8848	2203	4299	6502	SO:0001630	splice_region_variant	57337	exon13			CTCACATTGCTGG		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.1837+1A>T	3.37:g.101066717T>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	678|678	0.31043956043956045|0.31043956043956045	81|81	0.16463414634146342|0.16463414634146342	103|103	0.2845303867403315|0.2845303867403315	192|192	0.3356643356643357|0.3356643356643357	302|302	0.39841688654353563|0.39841688654353563	T|T	13.81|13.81	2.347976|2.347976	0.41599|0.41599	0.224467|0.224467	0.368341|0.368341	ENSG00000138468|ENSG00000138468	ENST00000366089|ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	.|T;T;T;T;T;T	.|0.19532	.|2.14;2.16;2.16;2.16;2.16;2.14	5.69|5.69	1.12|1.12	0.20585|0.20585	.|.	.|0.239918	.|0.33938	.|N	.|0.004414	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.43271|0.43271	P|P	0.0047719999999999985|0.0047719999999999985	.|D;D;D;D	.|0.67145	.|0.995;0.996;0.991;0.993	.|P;P;D;P	.|0.63192	.|0.871;0.878;0.912;0.753	T|T	0.38243|0.38243	-0.9670|-0.9670	4|9	.|0.15066	.|T	.|0.55	-2.9468|-2.9468	5.1706|5.1706	0.15108|0.15108	0.0:0.2965:0.1434:0.5601|0.0:0.2965:0.1434:0.5601	rs2433031;rs52806065;rs2433031|rs2433031;rs52806065;rs2433031	.|448;546;579;612	.|Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.|.;.;.;SENP7_HUMAN	I|H	14|612;547;546;448;448;579	.|ENSP00000377655:Q612H;ENSP00000377654:Q547H;ENSP00000313624:Q546H;ENSP00000377651:Q448H;ENSP00000350936:Q448H;ENSP00000342159:Q579H	.|ENSP00000313624:Q546H	N|Q	-|-	2|3	0|2	SENP7|SENP7	102549407|102549407	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.862000|0.862000	0.49288|0.49288	0.454000|0.454000	0.21827|0.21827	-0.055000|-0.055000	0.13244|0.13244	-0.417000|-0.417000	0.06048|0.06048	AAT|CAA	T|0.679;A|0.321	0.321	strong		0.294	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	Missense_Mutation
SLC28A2	9153	hgsc.bcm.edu	37	15	45545478	45545478	+	Missense_Mutation	SNP	C	C	T	rs11854484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45545478C>T	ENST00000347644.3	+	2	130	c.65C>T	c.(64-66)cCg>cTg	p.P22L	CTD-2651B20.3_ENST00000559003.1_RNA|CTD-2651B20.3_ENST00000561404.1_RNA|CTD-2651B20.3_ENST00000560344.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	22			P -> L (in dbSNP:rs11854484). {ECO:0000269|PubMed:15861032, ECO:0000269|PubMed:17700367}.		nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Mercaptopurine(DB01033)	ACAGTGAACCCGGGGCTGGAG	0.522													C|||	1517	0.302915	0.1059	0.3775	5008	,	,		16452	0.1052		0.6123	False		,,,				2504	0.4018				p.P22L	NSCLC(92;493 1501 26361 28917 47116)	Atlas-SNP	.											.	SLC28A2	64	.	0			c.C65T						PASS	.	C	LEU/PRO	840,3556	330.4+/-301.5	88,664,1446	79.0	74.0	76.0		65	-0.8	0.0	15	dbSNP_120	76	5402,3194	650.0+/-400.7	1684,2034,580	yes	missense	SLC28A2	NM_004212.3	98	1772,2698,2026	TT,TC,CC		37.1568,19.1083,48.045	benign	22/659	45545478	6242,6750	2198	4298	6496	SO:0001583	missense	9153	exon2			TGAACCCGGGGCT	U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"""Solute carriers"""	11002	protein-coding gene	gene with protein product		606208	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"""			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.65C>T	15.37:g.45545478C>T	ENSP00000315006:p.Pro22Leu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	153	68	0.444444	NM_004212	A8K7F9|O43239|Q52LZ0	Missense_Mutation	SNP	ENST00000347644.3	37	CCDS10121.1	723	0.33104395604395603	62	0.12601626016260162	149	0.4116022099447514	34	0.05944055944055944	478	0.6306068601583114	C	10.61	1.399257	0.25291	0.191083	0.628432	ENSG00000137860	ENST00000347644	T	0.01505	4.82	5.04	-0.812	0.10853	.	0.483231	0.18996	N	0.125488	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.16660	-1.0395	9	0.27785	T	0.31	0.7301	1.5014	0.02477	0.1643:0.3793:0.2735:0.183	rs61637002	22	O43868	S28A2_HUMAN	L	22	ENSP00000315006:P22L	ENSP00000315006:P22L	P	+	2	0	SLC28A2	43332770	0.000000	0.05858	0.007000	0.13788	0.220000	0.24768	-1.438000	0.02416	0.028000	0.15324	0.655000	0.94253	CCG	C|0.580;N|0.000	.	strong		0.522	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212	
DNAH10	196385	hgsc.bcm.edu	37	12	124335521	124335521	+	Silent	SNP	C	C	T	rs201453347		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124335521C>T	ENST00000409039.3	+	34	5860	c.5835C>T	c.(5833-5835)ccC>ccT	p.P1945P		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1945	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CGGAGCTGCCCGAGTCGGTGA	0.607																																					p.P1945P		Atlas-SNP	.											.	DNAH10	888	.	0			c.C5835T						PASS	.	C		0,4298		0,0,2149	40.0	45.0	43.0		5835	-8.6	0.6	12		43	1,8571		0,1,4285	no	coding-synonymous	DNAH10	NM_207437.3		0,1,6434	TT,TC,CC		0.0117,0.0,0.0078		1945/4472	124335521	1,12869	2149	4286	6435	SO:0001819	synonymous_variant	196385	exon34			GCTGCCCGAGTCG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.5835C>T	12.37:g.124335521C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	144	6	0.0416667	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|1.000;G|0.000	.	strong		0.607	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
ALS2	57679	hgsc.bcm.edu	37	2	202598113	202598113	+	Silent	SNP	C	C	T	rs2276615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:202598113C>T	ENST00000264276.6	-	13	2838	c.2466G>A	c.(2464-2466)gtG>gtA	p.V822V	ALS2_ENST00000457679.2_Silent_p.V134V	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	822	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.V822V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TTTCGTCATTCACTTCTGACA	0.323													C|||	1865	0.372404	0.1006	0.6542	5008	,	,		18412	0.3502		0.5875	False		,,,				2504	0.3415				p.V822V		Atlas-SNP	.											ALS2,NS,carcinoma,0,2	ALS2	172	2	1	Substitution - coding silent(1)	stomach(1)	c.G2466A						PASS	.	C		592,3032		53,486,1273	91.0	78.0	82.0		2466	3.1	1.0	2	dbSNP_100	82	4922,3236		1489,1944,646	no	coding-synonymous	ALS2	NM_020919.3		1542,2430,1919	TT,TC,CC		39.6666,16.3355,46.8002		822/1658	202598113	5514,6268	1812	4079	5891	SO:0001819	synonymous_variant	57679	exon13			GTCATTCACTTCT	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.2466G>A	2.37:g.202598113C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Silent	SNP	ENST00000264276.6	37	CCDS42800.1																																																																																			C|0.552;T|0.448	0.448	strong		0.323	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
VCL	7414	hgsc.bcm.edu	37	10	75865065	75865065	+	Silent	SNP	G	G	A	rs767809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:75865065G>A	ENST00000211998.4	+	16	2482	c.2388G>A	c.(2386-2388)ccG>ccA	p.P796P	VCL_ENST00000417648.2_Intron|VCL_ENST00000372755.3_Silent_p.P796P	NM_014000.2	NP_054706.1	P18206	VINC_HUMAN	vinculin	796	N-terminal globular head.				adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					CCATCTCCCCGATGGTGATGG	0.512													G|||	1626	0.324681	0.0598	0.4568	5008	,	,		19604	0.254		0.5915	False		,,,				2504	0.3875				p.P796P		Atlas-SNP	.											.	VCL	77	.	0			c.G2388A						PASS	.	G	,	636,3770	273.1+/-271.2	51,534,1618	90.0	67.0	75.0		2388,2388	-8.4	0.9	10	dbSNP_86	75	5070,3530	632.4+/-398.6	1505,2060,735	no	coding-synonymous,coding-synonymous	VCL	NM_003373.3,NM_014000.2	,	1556,2594,2353	AA,AG,GG		41.0465,14.4349,43.8721	,	796/1067,796/1135	75865065	5706,7300	2203	4300	6503	SO:0001819	synonymous_variant	7414	exon16			CTCCCCGATGGTG	M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403			12665	protein-coding gene	gene with protein product	"""metavinculin"""	193065				1339348	Standard	NM_014000		Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000211998.4:c.2388G>A	10.37:g.75865065G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_003373	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	Silent	SNP	ENST00000211998.4	37	CCDS7341.1																																																																																			G|0.604;A|0.396	0.396	strong		0.512	VCL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003373, NM_014000	
CSF1	1435	hgsc.bcm.edu	37	1	110466466	110466466	+	Missense_Mutation	SNP	T	T	C	rs1058885	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110466466T>C	ENST00000329608.6	+	6	1614	c.1223T>C	c.(1222-1224)cTg>cCg	p.L408P	CSF1_ENST00000369802.3_Missense_Mutation_p.L408P|CSF1_ENST00000369801.1_Intron|CSF1_ENST00000420111.2_Intron|CSF1_ENST00000344188.5_Intron	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	408	O-glycosylated at one site.		L -> P (in dbSNP:rs1058885). {ECO:0000269|PubMed:2660794}.		branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		ATCTCATCACTGCGCCCCCAG	0.657													C|||	2111	0.421526	0.4554	0.3271	5008	,	,		15689	0.5972		0.336	False		,,,				2504	0.3497				p.L408P		Atlas-SNP	.											.	CSF1	40	.	0			c.T1223C	GRCh37	CM066774	CSF1	M	rs1058885	PASS	.	C	PRO/LEU,,,PRO/LEU	1940,2466	604.3+/-390.3	432,1076,695	42.0	52.0	48.0		1223,,,1223	-9.1	0.0	1	dbSNP_86	48	3204,5396	633.4+/-398.7	603,1998,1699	yes	missense,intron,intron,missense	CSF1	NM_000757.5,NM_172210.2,NM_172211.2,NM_172212.2	98,,,98	1035,3074,2394	CC,CT,TT		37.2558,44.0309,39.551	benign,,,benign	408/555,,,408/555	110466466	5144,7862	2203	4300	6503	SO:0001583	missense	1435	exon6			CATCACTGCGCCC	BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.1223T>C	1.37:g.110466466T>C	ENSP00000327513:p.Leu408Pro	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_000757	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Missense_Mutation	SNP	ENST00000329608.6	37	CCDS816.1	930	0.4258241758241758	201	0.40853658536585363	127	0.35082872928176795	347	0.6066433566433567	255	0.33641160949868076	C	8.471	0.857555	0.17106	0.440309	0.372558	ENSG00000184371	ENST00000329608;ENST00000369802	T;T	0.15139	2.45;2.45	4.98	-9.14	0.00701	.	1.321200	0.05647	N	0.584474	T	0.01353	0.0044	N	0.04508	-0.205	0.58432	P	1.999999999946489E-6	B	0.09022	0.002	B	0.12156	0.007	T	0.36720	-0.9736	9	0.26408	T	0.33	.	3.9327	0.09293	0.0867:0.3667:0.1863:0.3603	rs1058885;rs3093042;rs3738762;rs60942435;rs1058885	408	P09603	CSF1_HUMAN	P	408	ENSP00000327513:L408P;ENSP00000358817:L408P	ENSP00000327513:L408P	L	+	2	0	CSF1	110267989	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.105000	0.03323	-2.705000	0.00396	-2.386000	0.00229	CTG	T|0.587;C|0.413	0.413	strong		0.657	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757	
ZDHHC19	131540	hgsc.bcm.edu	37	3	195936382	195936382	+	Silent	SNP	G	G	A	rs11719281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195936382G>A	ENST00000296326.3	-	3	352	c.273C>T	c.(271-273)tcC>tcT	p.S91S	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	91						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		CCTGCTCAGCGGAGCCTGGCG	0.692													G|||	712	0.142173	0.2254	0.098	5008	,	,		18877	0.1637		0.1362	False		,,,				2504	0.045				p.S91S		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.C273T						PASS	.	G		789,3303		76,637,1333	29.0	37.0	34.0		273	1.0	0.3	3	dbSNP_120	34	1035,7321		76,883,3219	no	coding-synonymous	ZDHHC19	NM_001039617.1		152,1520,4552	AA,AG,GG		12.3863,19.2815,14.653		91/310	195936382	1824,10624	2046	4178	6224	SO:0001819	synonymous_variant	131540	exon3			CTCAGCGGAGCCT	BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958		"""Zinc fingers, DHHC-type"""	20713	protein-coding gene	gene with protein product							Standard	XR_246038		Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.273C>T	3.37:g.195936382G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_001039617	A8MSY6|B3KVI1	Silent	SNP	ENST00000296326.3	37	CCDS43190.1																																																																																			G|0.851;A|0.149	0.149	strong		0.692	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637	
MANSC1	54682	hgsc.bcm.edu	37	12	12483713	12483713	+	Silent	SNP	A	A	G	rs4763282	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:12483713A>G	ENST00000535902.1	-	4	1107	c.544T>C	c.(544-546)Ttg>Ctg	p.L182L	MANSC1_ENST00000396349.3_Silent_p.L148L|MANSC1_ENST00000545735.1_Silent_p.L101L			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	182						integral component of membrane (GO:0016021)		p.L182L(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		AGTTTCTCCAAGTGATCTGAG	0.428													A|||	2914	0.581869	0.4894	0.6614	5008	,	,		21284	0.375		0.7306	False		,,,				2504	0.7106				p.L182L		Atlas-SNP	.											MANSC1,NS,carcinoma,0,1	MANSC1	38	1	1	Substitution - coding silent(1)	stomach(1)	c.T544C						PASS	.	A		2313,2093	603.1+/-390.1	595,1123,485	74.0	75.0	75.0		544	2.4	0.6	12	dbSNP_111	75	6493,2107	716.5+/-406.1	2467,1559,274	no	coding-synonymous	MANSC1	NM_018050.2		3062,2682,759	GG,GA,AA		24.5,47.5034,32.2928		182/432	12483713	8806,4200	2203	4300	6503	SO:0001819	synonymous_variant	54682	exon4			TCTCCAAGTGATC	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.544T>C	12.37:g.12483713A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	184	93	0.505435	NM_018050	Q8NEC1|Q9NW60	Silent	SNP	ENST00000535902.1	37	CCDS8648.1																																																																																			A|0.380;G|0.620	0.620	strong		0.428	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
ANKS1B	56899	hgsc.bcm.edu	37	12	100048924	100048924	+	Missense_Mutation	SNP	G	G	A	rs377459874		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:100048924G>A	ENST00000547776.2	-	9	1192	c.1193C>T	c.(1192-1194)aCg>aTg	p.T398M	ANKS1B_ENST00000329257.7_Missense_Mutation_p.T398M|ANKS1B_ENST00000547010.1_De_novo_Start_InFrame	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	398						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGGCCCACACGTATTTTCATC	0.378													G|||	1	0.000199681	0.0	0.0	5008	,	,		16060	0.0		0.001	False		,,,				2504	0.0				p.T398M		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1193T						PASS	.	G	MET/THR	1,3821		0,1,1910	119.0	117.0	118.0		1193	3.5	0.2	12		118	1,8241		0,1,4120	no	missense	ANKS1B	NM_152788.4	81	0,2,6030	AA,AG,GG		0.0121,0.0262,0.0166	possibly-damaging	398/1249	100048924	2,12062	1911	4121	6032	SO:0001583	missense	56899	exon9			CCACACGTATTTT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1193C>T	12.37:g.100048924G>A	ENSP00000449629:p.Thr398Met	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	250	114	0.456	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	9.507	1.104632	0.20632	2.62E-4	1.21E-4	ENSG00000185046	ENST00000547776;ENST00000329257;ENST00000549866	T;T;T	0.51071	0.85;0.85;0.72	5.47	3.51	0.40186	.	0.251827	0.30959	N	0.008522	T	0.31104	0.0786	N	0.22421	0.69	0.46078	D	0.998858	P;P	0.51791	0.948;0.913	B;B	0.39876	0.312;0.165	T	0.05971	-1.0853	9	.	.	.	-4.2304	12.7356	0.57222	0.0:0.4365:0.5635:0.0	.	364;398	F8VVQ4;Q7Z6G8	.;ANS1B_HUMAN	M	398;398;364	ENSP00000449629:T398M;ENSP00000331381:T398M;ENSP00000449894:T364M	.	T	-	2	0	ANKS1B	98573055	1.000000	0.71417	0.180000	0.23079	0.246000	0.25737	2.677000	0.46892	1.292000	0.44672	-0.283000	0.09986	ACG	.	.	weak		0.378	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
CSMD2	114784	hgsc.bcm.edu	37	1	34052137	34052137	+	Silent	SNP	G	G	A	rs371199413		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:34052137G>A	ENST00000373381.4	-	46	7194	c.7018C>T	c.(7018-7020)Ctg>Ttg	p.L2340L		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2342	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCAAACTGCAGGTAGGTTCCA	0.483																																					p.L2342L		Atlas-SNP	.											.	CSMD2	946	.	0			c.C7024T						PASS	.	G		0,4406		0,0,2203	109.0	99.0	102.0		7024	4.0	1.0	1		102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CSMD2	NM_052896.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		2342/3488	34052137	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	114784	exon47			ACTGCAGGTAGGT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.7018C>T	1.37:g.34052137G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	37																																																																																				.	.	none		0.483	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
MAP2K2	5605	hgsc.bcm.edu	37	19	4101062	4101062	+	Silent	SNP	G	G	T	rs10250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4101062G>T	ENST00000262948.5	-	6	913	c.660C>A	c.(658-660)atC>atA	p.I220I	MAP2K2_ENST00000599345.1_5'Flank|MAP2K2_ENST00000394867.4_Silent_p.I123I	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	CCATGGAGTCGATGAGCTGGC	0.637													.|||	2170	0.433307	0.2443	0.5562	5008	,	,		13338	0.625		0.4761	False		,,,				2504	0.3599				p.I220I		Atlas-SNP	.											MAP2K2_ENST00000262948,NS,carcinoma,0,2	MAP2K2	72	2	0			c.C660A						PASS	.	G		1264,3138		189,886,1126	62.0	46.0	51.0		660	0.8	1.0	19	dbSNP_52	51	4165,4423		1014,2137,1143	no	coding-synonymous	MAP2K2	NM_030662.3		1203,3023,2269	TT,TG,GG		48.4979,28.7142,41.7937		220/401	4101062	5429,7561	2201	4294	6495	SO:0001819	synonymous_variant	5605	exon6			GGAGTCGATGAGC	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.660C>A	19.37:g.4101062G>T		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	227	96	0.422908	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			.	.	weak		0.637	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
KDM6B	23135	hgsc.bcm.edu	37	17	7751050	7751050	+	Missense_Mutation	SNP	C	C	T	rs62059713	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7751050C>T	ENST00000448097.2	+	11	1775	c.1444C>T	c.(1444-1446)Ccc>Tcc	p.P482S	KDM6B_ENST00000254846.5_Missense_Mutation_p.P482S			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	482	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						ccccccaccaccccctgccTG	0.682													C|||	839	0.167532	0.0083	0.2853	5008	,	,		2939	0.2748		0.1402	False		,,,				2504	0.2168				p.P482S		Atlas-SNP	.											.	KDM6B	95	.	0			c.C1444T						PASS	.	C	SER/PRO	108,2522		7,94,1214	2.0	2.0	2.0		1444	2.9	0.4	17	dbSNP_129	2	851,5139		53,745,2197	no	missense	KDM6B	NM_001080424.1	74	60,839,3411	TT,TC,CC		14.207,4.1065,11.1253	possibly-damaging	482/1683	7751050	959,7661	1315	2995	4310	SO:0001583	missense	23135	exon11			CCACCACCCCCTG	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.1444C>T	17.37:g.7751050C>T	ENSP00000412513:p.Pro482Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		330	0.1510989010989011	15	0.03048780487804878	78	0.2154696132596685	133	0.23251748251748253	104	0.13720316622691292	C	9.633	1.136940	0.21123	0.041065	0.14207	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.14391	2.51;2.51	3.91	2.91	0.33838	.	0.319879	0.22680	N	0.056942	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.36909	0.573	B	0.35278	0.199	T	0.49041	-0.8980	9	0.17832	T	0.49	-4.818	8.8132	0.34981	0.2247:0.7753:0.0:0.0	rs62059713	482	O15054-1	.	S	482	ENSP00000254846:P482S;ENSP00000412513:P482S	ENSP00000254846:P482S	P	+	1	0	KDM6B	7691775	0.284000	0.24287	0.360000	0.25837	0.956000	0.61745	1.486000	0.35530	0.974000	0.38366	0.555000	0.69702	CCC	C|0.848;T|0.152	0.152	strong		0.682	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
SLC19A1	6573	hgsc.bcm.edu	37	21	46951556	46951556	+	Silent	SNP	A	A	G	rs12659	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46951556A>G	ENST00000311124.4	-	3	848	c.696T>C	c.(694-696)ccT>ccC	p.P232P	SLC19A1_ENST00000567670.1_Silent_p.P232P|SLC19A1_ENST00000380010.4_Silent_p.P232P|SLC19A1_ENST00000485649.2_Silent_p.P192P	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	232					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	CGCCTGGGCCAGGATTCATGC	0.711													G|||	2770	0.553115	0.5189	0.5908	5008	,	,		12778	0.4752		0.5557	False		,,,				2504	0.6503				p.P232P		Atlas-SNP	.											.	SLC19A1	53	.	0			c.T696C						PASS	.	G	,,	2461,1943		713,1035,454	31.0	37.0	35.0		696,576,696	-6.6	0.0	21	dbSNP_52	35	4985,3615		1473,2039,788	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC19A1	NM_001205206.1,NM_001205207.1,NM_194255.2	,,	2186,3074,1242	GG,GA,AA		42.0349,44.119,42.7407	,,	232/490,192/552,232/592	46951556	7446,5558	2202	4300	6502	SO:0001819	synonymous_variant	6573	exon3			TGGGCCAGGATTC	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"""Solute carriers"""	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.696T>C	21.37:g.46951556A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_001205206	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Silent	SNP	ENST00000311124.4	37	CCDS13725.1																																																																																			A|0.440;G|0.560	0.560	strong		0.711	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152694184	152694184	+	Silent	SNP	T	T	C	rs6913579	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152694184T>C	ENST00000367255.5	-	59	10096	c.9495A>G	c.(9493-9495)gaA>gaG	p.E3165E	SYNE1_ENST00000265368.4_Silent_p.E3165E|SYNE1_ENST00000341594.5_Silent_p.E3204E|SYNE1_ENST00000448038.1_Silent_p.E3172E|SYNE1_ENST00000423061.1_Silent_p.E3172E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3165					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTAGAGCAGATTCTTTTTGGT	0.378										HNSCC(10;0.0054)			T|||	2345	0.468251	0.4365	0.536	5008	,	,		17998	0.4613		0.5308	False		,,,				2504	0.4059				p.E3172E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A9516G						PASS	.	T	,	2184,2222	585.1+/-386.2	541,1102,560	187.0	198.0	194.0		9516,9495	3.0	1.0	6	dbSNP_116	194	4694,3906	605.6+/-395.0	1320,2054,926	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	1861,3156,1486	CC,CT,TT		45.4186,49.5688,47.1167	,	3172/8750,3165/8798	152694184	6878,6128	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon59			AGCAGATTCTTTT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.9495A>G	6.37:g.152694184T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2	1021|1021	0.4674908424908425|0.4674908424908425	203|203	0.41260162601626016|0.41260162601626016	184|184	0.5082872928176796|0.5082872928176796	237|237	0.4143356643356643|0.4143356643356643	397|397	0.5237467018469657|0.5237467018469657	T|T	4.796|4.796	0.148083|0.148083	0.09134|0.09134	0.495688|0.495688	0.545814|0.545814	ENSG00000131018|ENSG00000131018	ENST00000469439|ENST00000454018	.|.	.|.	.|.	5.74|5.74	3.04|3.04	0.35103|0.35103	.|.	.|.	.|.	.|.	.|.	T|T	0.38957|0.38957	0.1060|0.1060	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999984213|0.9999999999984213	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.25537|0.25537	-1.0129|-1.0129	3|3	.|.	.|.	.|.	.|.	10.8986|10.8986	0.47038|0.47038	0.0:0.1482:0.0:0.8518|0.0:0.1482:0.0:0.8518	rs6913579;rs6913579|rs6913579;rs6913579	.|.	.|.	.|.	V|S	30|282	.|.	.|.	I|N	-|-	1|2	0|0	SYNE1|SYNE1	152735877|152735877	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.639000|0.639000	0.38242|0.38242	0.825000|0.825000	0.27393|0.27393	1.007000|1.007000	0.39238|0.39238	0.533000|0.533000	0.62120|0.62120	ATC|AAT	T|0.507;C|0.493	0.493	strong		0.378	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
FREM1	158326	hgsc.bcm.edu	37	9	14801710	14801710	+	Missense_Mutation	SNP	C	C	A	rs35870000	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:14801710C>A	ENST00000380880.3	-	20	4417	c.3634G>T	c.(3634-3636)Gcc>Tcc	p.A1212S	FREM1_ENST00000422223.2_Missense_Mutation_p.A1212S|FREM1_ENST00000380881.4_Missense_Mutation_p.A1213S			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1212					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TGAGGGTTGGCTGGCTGCTTA	0.488													C|||	1302	0.259984	0.0681	0.3991	5008	,	,		18978	0.2321		0.3579	False		,,,				2504	0.3487				p.A1212S		Atlas-SNP	.											.	FREM1	261	.	0			c.G3634T						PASS	.	C	SER/ALA	472,3482		41,390,1546	146.0	143.0	144.0		3634	1.8	0.0	9	dbSNP_126	144	2824,5528		465,1894,1817	yes	missense	FREM1	NM_144966.5	99	506,2284,3363	AA,AC,CC		33.8123,11.9373,26.7837	benign	1212/2180	14801710	3296,9010	1977	4176	6153	SO:0001583	missense	158326	exon21			GGTTGGCTGGCTG	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.3634G>T	9.37:g.14801710C>A	ENSP00000370262:p.Ala1212Ser	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	261	167	0.639847	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	591	0.2706043956043956	43	0.08739837398373984	158	0.43646408839779005	127	0.22202797202797203	263	0.3469656992084433	C	9.841	1.191048	0.21954	0.119373	0.338123	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.10860	2.83;2.83;2.83	5.12	1.79	0.24919	.	1.028690	0.07657	N	0.932920	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.10296	0.003	B	0.14578	0.011	T	0.47086	-0.9144	9	0.09338	T	0.73	-0.03	2.6233	0.04922	0.0:0.376:0.2601:0.3638	rs35870000;rs61737620	1212	Q5H8C1	FREM1_HUMAN	S	1213;1212;1212	ENSP00000370263:A1213S;ENSP00000412940:A1212S;ENSP00000370262:A1212S	ENSP00000370257:A1215S	A	-	1	0	FREM1	14791710	0.003000	0.15002	0.001000	0.08648	0.084000	0.17831	0.988000	0.29616	0.542000	0.28846	0.591000	0.81541	GCC	C|0.719;A|0.281	0.281	strong		0.488	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
SPAG17	200162	hgsc.bcm.edu	37	1	118583408	118583408	+	Silent	SNP	G	G	A	rs10923477	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:118583408G>A	ENST00000336338.5	-	22	3176	c.3111C>T	c.(3109-3111)taC>taT	p.Y1037Y		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1037						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		AAGGATACAGGTAGTAATTTG	0.358													G|||	1445	0.288538	0.1573	0.4135	5008	,	,		19632	0.1567		0.4324	False		,,,				2504	0.365				p.Y1037Y		Atlas-SNP	.											.	SPAG17	263	.	0			c.C3111T						PASS	.	G		894,3512	347.7+/-309.6	87,720,1396	137.0	118.0	125.0		3111	-2.6	0.9	1	dbSNP_120	125	3923,4677	546.5+/-385.0	910,2103,1287	no	coding-synonymous	SPAG17	NM_206996.2		997,2823,2683	AA,AG,GG		45.6163,20.2905,37.0368		1037/2224	118583408	4817,8189	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon22			ATACAGGTAGTAA		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.3111C>T	1.37:g.118583408G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	158	95	0.601266	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			G|0.677;A|0.323	0.323	strong		0.358	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
GRIN2B	2904	hgsc.bcm.edu	37	12	13715954	13715954	+	Silent	SNP	G	G	A	rs1805246	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:13715954G>A	ENST00000609686.1	-	13	4427	c.4218C>T	c.(4216-4218)ttC>ttT	p.F1406F		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1406					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGGGCTGCCTGAAGAAGTAGG	0.627													G|||	184	0.0367412	0.0023	0.0115	5008	,	,		16300	0.0754		0.0278	False		,,,				2504	0.0706				p.F1406F		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C4218T						PASS	.	G		32,4374	37.6+/-69.7	0,32,2171	38.0	38.0	38.0		4218	5.2	1.0	12	dbSNP_92	38	330,8270	114.0+/-174.0	5,320,3975	no	coding-synonymous	GRIN2B	NM_000834.3		5,352,6146	AA,AG,GG		3.8372,0.7263,2.7833		1406/1485	13715954	362,12644	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon13			CTGCCTGAAGAAG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.4218C>T	12.37:g.13715954G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.969;A|0.031	0.031	strong		0.627	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
C1orf112	55732	hgsc.bcm.edu	37	1	169822088	169822088	+	Missense_Mutation	SNP	G	G	C	rs41308405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169822088G>C	ENST00000286031.6	+	24	3222	c.2522G>C	c.(2521-2523)aGg>aCg	p.R841T	SCYL3_ENST00000367771.6_3'UTR|SCYL3_ENST00000367772.4_3'UTR|C1orf112_ENST00000359326.4_Missense_Mutation_p.R841T|C1orf112_ENST00000498289.1_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	841										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CTCCAAGAAAGGATGGATAAG	0.443													G|||	6	0.00119808	0.0	0.0	5008	,	,		17208	0.0		0.006	False		,,,				2504	0.0				p.R841T		Atlas-SNP	.											.	C1orf112	74	.	0			c.G2522C						PASS	.	G	THR/ARG,,	4,4402	8.1+/-20.4	0,4,2199	105.0	107.0	107.0		2522,,	3.1	0.3	1	dbSNP_127	107	33,8567	22.2+/-67.0	0,33,4267	yes	missense,utr-3,utr-3	C1orf112,SCYL3	NM_018186.2,NM_020423.5,NM_181093.2	71,,	0,37,6466	CC,CG,GG		0.3837,0.0908,0.2845	benign,,	841/854,,	169822088	37,12969	2203	4300	6503	SO:0001583	missense	55732	exon24			AAGAAAGGATGGA	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.2522G>C	1.37:g.169822088G>C	ENSP00000286031:p.Arg841Thr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	212	81	0.382075	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	9.340	1.062674	0.19987	9.08E-4	0.003837	ENSG00000000460	ENST00000359326;ENST00000286031	T;T	0.43688	0.94;0.94	5.33	3.1	0.35709	.	0.413038	0.27759	N	0.017969	T	0.17874	0.0429	M	0.68317	2.08	0.58432	D	0.999997	B	0.16166	0.016	B	0.12837	0.008	T	0.08006	-1.0743	10	0.09843	T	0.71	-9.1287	8.3298	0.32180	0.2116:0.0:0.7884:0.0	rs41308405	841	Q9NSG2	CA112_HUMAN	T	841	ENSP00000352276:R841T;ENSP00000286031:R841T	ENSP00000286031:R841T	R	+	2	0	C1orf112	168088712	0.379000	0.25123	0.315000	0.25238	0.110000	0.19582	-0.004000	0.12878	1.240000	0.43803	0.467000	0.42956	AGG	G|0.996;C|0.004	0.004	strong		0.443	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
DCHS2	54798	hgsc.bcm.edu	37	4	155158284	155158284	+	Nonsense_Mutation	SNP	A	A	C	rs146298768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155158284A>C	ENST00000357232.4	-	25	6154	c.6155T>G	c.(6154-6156)tTa>tGa	p.L2052*		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2052	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ATCCAGAAGTAATACGGGACT	0.378																																					p.L2052X		Atlas-SNP	.											.	DCHS2	594	.	0			c.T6155G						PASS	.	A	stop/LEU	2,4402	4.2+/-10.8	0,2,2200	69.0	71.0	70.0		6155	2.0	0.0	4	dbSNP_134	70	34,8566	22.2+/-67.0	0,34,4266	yes	stop-gained	DCHS2	NM_017639.3		0,36,6466	CC,CA,AA		0.3953,0.0454,0.2768		2052/2917	155158284	36,12968	2202	4300	6502	SO:0001587	stop_gained	54798	exon25			AGAAGTAATACGG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6155T>G	4.37:g.155158284A>C	ENSP00000349768:p.Leu2052*	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Nonsense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	42	9.636087	0.99226	4.54E-4	0.003953	ENSG00000197410	ENST00000357232	.	.	.	5.67	2.04	0.26737	.	1.456590	0.04346	N	0.354832	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	5.7442	0.18110	0.5901:0.1313:0.2786:0.0	.	.	.	.	X	2052	.	ENSP00000349768:L2052X	L	-	2	0	DCHS2	155377734	0.000000	0.05858	0.007000	0.13788	0.558000	0.35554	0.244000	0.18124	0.130000	0.18549	0.455000	0.32223	TTA	A|0.998;C|0.002	0.002	strong		0.378	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
POTEF	728378	hgsc.bcm.edu	37	2	130832364	130832364	+	Missense_Mutation	SNP	G	G	A	rs185469611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130832364G>A	ENST00000409914.2	-	17	3080	c.2681C>T	c.(2680-2682)aCc>aTc	p.T894I	POTEF_ENST00000357462.5_Missense_Mutation_p.T894I	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	894	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GCCATGCTCGGTGAGGATCTT	0.582													.|||	89	0.0177716	0.0424	0.013	5008	,	,		11371	0.0		0.0229	False		,,,				2504	0.001				p.T894I		Atlas-SNP	.											.	POTEF	140	.	0			c.C2681T						PASS	.	G	ILE/THR	58,3640		3,52,1794	20.0	28.0	25.0		2681		0.1	2		25	120,7650		23,74,3788	no	missense	POTEF	NM_001099771.2	89	26,126,5582	AA,AG,GG		1.5444,1.5684,1.5521	probably-damaging	894/1076	130832364	178,11290	1849	3885	5734	SO:0001583	missense	728378	exon17			TGCTCGGTGAGGA	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2681C>T	2.37:g.130832364G>A	ENSP00000386786:p.Thr894Ile	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	409	362	0.885086	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	25	0.011446886446886446	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	.	14.01	2.406630	0.42715	0.015684	0.015444	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.94613	-3.47;-3.47	.	.	.	.	.	.	.	.	D	0.89371	0.6696	M	0.90650	3.135	0.80722	D	1	B	0.18863	0.031	B	0.22152	0.038	D	0.86999	0.2115	8	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	894	A5A3E0	POTEF_HUMAN	I	894	ENSP00000350052:T894I;ENSP00000386786:T894I	ENSP00000350052:T894I	T	-	2	0	POTEF	130548834	1.000000	0.71417	0.105000	0.21289	0.105000	0.19272	4.869000	0.63028	0.119000	0.18210	0.121000	0.15741	ACC	G|0.988;A|0.012	0.012	strong		0.582	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
LRRTM3	347731	hgsc.bcm.edu	37	10	68687942	68687942	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:68687942G>C	ENST00000361320.4	+	2	1846	c.1268G>C	c.(1267-1269)gGc>gCc	p.G423A	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	423					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						ATCATCGCGGGCAGCGTGGCG	0.612																																					p.G423A		Atlas-SNP	.											.	LRRTM3	241	.	0			c.G1268C						PASS	.						70.0	68.0	69.0					10																	68687942		2203	4300	6503	SO:0001583	missense	347731	exon2			TCGCGGGCAGCGT	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.1268G>C	10.37:g.68687942G>C	ENSP00000355187:p.Gly423Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	37	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692071	0.68271	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.75367	-0.93	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000001	D	0.87525	0.6199	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87653	0.2529	10	0.62326	D	0.03	.	19.1373	0.93433	0.0:0.0:1.0:0.0	.	423;423	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	A	423	ENSP00000355187:G423A	ENSP00000355187:G423A	G	+	2	0	LRRTM3	68357948	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.869000	0.99810	2.820000	0.97059	0.650000	0.86243	GGC	.	.	none		0.612	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011	
C5orf49	134121	hgsc.bcm.edu	37	5	7835555	7835555	+	Missense_Mutation	SNP	C	C	G	rs6883562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:7835555C>G	ENST00000399810.2	-	2	672	c.204G>C	c.(202-204)caG>caC	p.Q68H	C5orf49_ENST00000509627.1_Missense_Mutation_p.Q68H	NM_001089584.2	NP_001083053.1	A4QMS7	CE049_HUMAN	chromosome 5 open reading frame 49	68			Q -> H (in dbSNP:rs6883562).							large_intestine(3)|lung(5)|skin(1)	9						GGTGCAACTTCTGATCATAAT	0.363													C|||	888	0.177316	0.1762	0.1715	5008	,	,		19617	0.0972		0.2217	False		,,,				2504	0.2198				p.Q68H		Atlas-SNP	.											.	C5orf49	27	.	0			c.G204C						PASS	.	C	HIS/GLN	739,2905		76,587,1159	128.0	123.0	124.0		204	1.7	0.7	5	dbSNP_116	124	1991,6177		224,1543,2317	yes	missense	C5orf49	NM_001089584.1	24	300,2130,3476	GG,GC,CC		24.3756,20.2799,23.1121	probably-damaging	68/148	7835555	2730,9082	1822	4084	5906	SO:0001583	missense	134121	exon2			CAACTTCTGATCA		CCDS43300.1	5p15.31	2008-07-16			ENSG00000215217	ENSG00000215217			27028	protein-coding gene	gene with protein product						12477932	Standard	NM_001089584		Approved	LOC134121	uc003jea.5	A4QMS7	OTTHUMG00000161897	ENST00000399810.2:c.204G>C	5.37:g.7835555C>G	ENSP00000382708:p.Gln68His	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001089584		Missense_Mutation	SNP	ENST00000399810.2	37	CCDS43300.1	377	0.17261904761904762	89	0.18089430894308944	67	0.1850828729281768	51	0.08916083916083917	170	0.22427440633245382	C	16.02	3.005516	0.54254	0.202799	0.243756	ENSG00000215217	ENST00000399810;ENST00000509627	T;T	0.32023	1.47;1.47	4.95	1.68	0.24146	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.36009	P	0.162049	D	0.54207	0.965	P	0.45138	0.471	T	0.17992	-1.0351	8	0.51188	T	0.08	-31.5049	5.3712	0.16140	0.0:0.5471:0.0:0.4529	rs6883562;rs17183443;rs6883562	68	A4QMS7	CE049_HUMAN	H	68	ENSP00000382708:Q68H;ENSP00000426019:Q68H	ENSP00000382708:Q68H	Q	-	3	2	C5orf49	7888555	0.989000	0.36119	0.714000	0.30535	0.969000	0.65631	0.512000	0.22755	0.625000	0.30304	0.561000	0.74099	CAG	C|0.808;G|0.192	0.192	strong		0.363	C5orf49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366322.1	NM_001089584	
HAX1	10456	hgsc.bcm.edu	37	1	154245917	154245917	+	Silent	SNP	T	T	C	rs13796	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154245917T>C	ENST00000328703.7	+	2	372	c.159T>C	c.(157-159)agT>agC	p.S53S	HAX1_ENST00000532105.1_Intron|HAX1_ENST00000457918.2_Intron|HAX1_ENST00000483970.2_Silent_p.S53S	NM_006118.3	NP_006109.2	O00165	HAX1_HUMAN	HCLS1 associated protein X-1	53					cellular response to cytokine stimulus (GO:0071345)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin filament polymerization (GO:0030833)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein targeting to mitochondrion (GO:1903214)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|lamellipodium (GO:0030027)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|sarcoplasmic reticulum (GO:0016529)|transcription factor complex (GO:0005667)	interleukin-1 binding (GO:0019966)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	15	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GGTTCCATAGTCCTCAGCACC	0.527									Kostmann syndrome				T|||	377	0.0752796	0.0136	0.0922	5008	,	,		17207	0.0496		0.1193	False		,,,				2504	0.1278				p.S53S		Atlas-SNP	.											.	HAX1	25	.	0			c.T159C						PASS	.	T	,	158,4248	106.0+/-144.5	2,154,2047	71.0	67.0	69.0		,159	-1.1	0.9	1	dbSNP_52	69	1132,7468	232.6+/-266.2	73,986,3241	no	intron,coding-synonymous	HAX1	NM_001018837.1,NM_006118.3	,	75,1140,5288	CC,CT,TT		13.1628,3.586,9.9185	,	,53/280	154245917	1290,11716	2203	4300	6503	SO:0001819	synonymous_variant	10456	exon2	Familial Cancer Database	Kostmann Infantile Agranulocytosis, Severe Congenital Neutropenia, Congenital Agranulocytosis	CCATAGTCCTCAG	U68566	CCDS1064.1, CCDS44230.1	1q21.3	2014-09-17			ENSG00000143575	ENSG00000143575			16915	protein-coding gene	gene with protein product	"""HCLS1 (and PKD2) associated protein"""	605998				9058808, 10760273	Standard	NM_006118		Approved	HS1BP1, HCLSBP1	uc001fes.3	O00165	OTTHUMG00000035978	ENST00000328703.7:c.159T>C	1.37:g.154245917T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	154	77	0.5	NM_006118	A8W4W9|A8W4X0|B4DUJ7|Q5VYD5|Q5VYD7|Q96AU4|Q9BS80	Silent	SNP	ENST00000328703.7	37	CCDS1064.1																																																																																			T|0.915;C|0.085	0.085	strong		0.527	HAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087650.1	NM_006118	
ADAM21	8747	hgsc.bcm.edu	37	14	70924736	70924736	+	Missense_Mutation	SNP	G	G	A	rs148146367		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70924736G>A	ENST00000603540.1	+	2	778	c.520G>A	c.(520-522)Ggc>Agc	p.G174S	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.G174S	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	174					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TATGAGATGTGGCTTAACAGA	0.448																																					p.G174S		Atlas-SNP	.											.	ADAM21	181	.	0			c.G520A						PASS	.						55.0	60.0	58.0					14																	70924736		2203	4300	6503	SO:0001583	missense	8747	exon2			AGATGTGGCTTAA	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.520G>A	14.37:g.70924736G>A	ENSP00000474385:p.Gly174Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	211	37	0.175355	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.599483	0.28534	.	.	ENSG00000139985	ENST00000267499	T	0.01246	5.11	3.86	1.96	0.26148	.	0.306760	0.22801	N	0.055472	T	0.02649	0.0080	M	0.63843	1.955	0.26522	N	0.974403	P	0.40553	0.721	B	0.43478	0.421	T	0.28138	-1.0053	10	0.52906	T	0.07	.	9.6627	0.39965	0.1897:0.0:0.8103:0.0	.	174	Q9UKJ8	ADA21_HUMAN	S	174	ENSP00000267499:G174S	ENSP00000267499:G174S	G	+	1	0	ADAM21	69994489	0.998000	0.40836	0.988000	0.46212	0.557000	0.35523	1.445000	0.35079	0.932000	0.37266	0.557000	0.71058	GGC	G|0.999;A|0.001	0.001	weak		0.448	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
ATRN	8455	hgsc.bcm.edu	37	20	3624830	3624830	+	Silent	SNP	G	G	A	rs2246808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:3624830G>A	ENST00000262919.5	+	28	4148	c.4080G>A	c.(4078-4080)ccG>ccA	p.P1360P		NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	1360					cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						CACTGGAGCCGTGTTTTGGCA	0.502													g|||	1916	0.382588	0.5855	0.3718	5008	,	,		20619	0.1964		0.3917	False		,,,				2504	0.2986				p.P1360P		Atlas-SNP	.											.	ATRN	118	.	0			c.G4080A						PASS	.	A		2357,2049	609.6+/-391.4	643,1071,489	136.0	116.0	123.0		4080	-10.2	0.4	20	dbSNP_100	123	3494,5106	511.4+/-377.7	735,2024,1541	no	coding-synonymous	ATRN	NM_139321.2		1378,3095,2030	AA,AG,GG		40.6279,46.5048,44.9869		1360/1430	3624830	5851,7155	2203	4300	6503	SO:0001819	synonymous_variant	8455	exon28			GGAGCCGTGTTTT	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.4080G>A	20.37:g.3624830G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	177	177	1	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Silent	SNP	ENST00000262919.5	37	CCDS13053.1																																																																																			G|0.577;A|0.423	0.423	strong		0.502	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
NCOR2	9612	hgsc.bcm.edu	37	12	124831388	124831388	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124831388G>A	ENST00000405201.1	-	31	4081	c.4081C>T	c.(4081-4083)Cgg>Tgg	p.R1361W	NCOR2_ENST00000397355.1_Missense_Mutation_p.R1352W|NCOR2_ENST00000429285.2_Missense_Mutation_p.R1351W|NCOR2_ENST00000404621.1_Missense_Mutation_p.R1351W|NCOR2_ENST00000356219.3_Missense_Mutation_p.R1368W|NCOR2_ENST00000404121.2_Missense_Mutation_p.R922W			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1369					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		ACGTAGGACCGAGGGATCCCT	0.687																																					p.R1361W		Atlas-SNP	.											.	NCOR2	475	.	0			c.C4081T						PASS	.						7.0	10.0	9.0					12																	124831388		2025	4146	6171	SO:0001583	missense	9612	exon33			AGGACCGAGGGAT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.4081C>T	12.37:g.124831388G>A	ENSP00000384018:p.Arg1361Trp	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846645	0.32606	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15	5.2	2.19	0.27852	.	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	M	0.71036	2.16	0.54753	D	0.999988	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.993;0.997	T	0.74544	-0.3630	10	0.87932	D	0	-29.7811	13.8264	0.63352	0.0:0.0:0.5877:0.4123	.	1351;1352;1361	C9J0Q5;C9J239;C9JFD3	.;.;.	W	1361;1351;1368;1352;1360;922;1351;1369	ENSP00000384018:R1361W;ENSP00000384202:R1351W;ENSP00000348551:R1368W;ENSP00000380513:R1352W;ENSP00000385618:R922W;ENSP00000400281:R1351W;ENSP00000402808:R1369W	ENSP00000348551:R1368W	R	-	1	2	NCOR2	123397341	1.000000	0.71417	0.020000	0.16555	0.346000	0.29079	3.614000	0.54160	0.144000	0.18951	-0.448000	0.05591	CGG	.	.	none		0.687	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
SOGA1	140710	hgsc.bcm.edu	37	20	35467713	35467713	+	Silent	SNP	G	G	A	rs1146250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:35467713G>A	ENST00000357779.3	-	2	431	c.105C>T	c.(103-105)taC>taT	p.Y35Y	SOGA1_ENST00000237536.4_Silent_p.Y273Y|SOGA1_ENST00000279034.6_Silent_p.Y35Y			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	35					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						TGCGCAGCCGGTACTGCAGGA	0.647													G|||	1154	0.230431	0.2368	0.2983	5008	,	,		17673	0.0109		0.3926	False		,,,				2504	0.2331				p.Y273Y		Atlas-SNP	.											.	SOGA1	136	.	0			c.C819T						PASS	.	G	,	1010,3026		129,752,1137	43.0	47.0	46.0		819,105	4.9	1.0	20	dbSNP_87	46	3113,5245		571,1971,1637	no	coding-synonymous,coding-synonymous	KIAA0889	NM_080627.2,NM_199181.2	,	700,2723,2774	AA,AG,GG		37.2458,25.0248,33.2661	,	273/1662,35/1017	35467713	4123,8271	2018	4179	6197	SO:0001819	synonymous_variant	140710	exon2			CAGCCGGTACTGC	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.105C>T	20.37:g.35467713G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	66	43	0.651515	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Silent	SNP	ENST00000357779.3	37																																																																																				G|0.733;A|0.267	0.267	strong		0.647	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181	
KRT25	147183	hgsc.bcm.edu	37	17	38911212	38911212	+	Silent	SNP	G	G	A	rs12951078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38911212G>A	ENST00000312150.4	-	1	372	c.312C>T	c.(310-312)aaC>aaT	p.N104N		NM_181534.3	NP_853512.1			keratin 25											endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(4)	16		Breast(137;0.00526)				CCAGGTCAGCGTTGGCCTCCT	0.527													G|||	2341	0.467452	0.1641	0.5735	5008	,	,		17042	0.8224		0.506	False		,,,				2504	0.3967				p.N104N		Atlas-SNP	.											.	KRT25	63	.	0			c.C312T						PASS	.	G		996,3410	372.2+/-320.3	121,754,1328	142.0	133.0	136.0		312	-4.9	0.1	17	dbSNP_121	136	4582,4018	598.3+/-393.9	1233,2116,951	no	coding-synonymous	KRT25	NM_181534.3		1354,2870,2279	AA,AG,GG		46.7209,22.6055,42.8879		104/451	38911212	5578,7428	2203	4300	6503	SO:0001819	synonymous_variant	147183	exon1			GTCAGCGTTGGCC	AK129503	CCDS11373.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000204897	ENSG00000204897		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30839	protein-coding gene	gene with protein product			"""keratin 25A"""	KRT25A		16831889	Standard	NM_181534		Approved		uc002hve.3	Q7Z3Z0	OTTHUMG00000133373	ENST00000312150.4:c.312C>T	17.37:g.38911212G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_181534		Silent	SNP	ENST00000312150.4	37	CCDS11373.1																																																																																			G|0.543;A|0.457	0.457	strong		0.527	KRT25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257218.1	NM_181534	
CASZ1	54897	hgsc.bcm.edu	37	1	10725469	10725469	+	Missense_Mutation	SNP	G	G	A	rs149479567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:10725469G>A	ENST00000377022.3	-	5	493	c.176C>T	c.(175-177)tCg>tTg	p.S59L	CASZ1_ENST00000344008.5_Missense_Mutation_p.S59L|CASZ1_ENST00000478728.2_5'UTR	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	59					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CCGGGGCTGCGATGGGCTGCC	0.687													G|||	24	0.00479233	0.0008	0.0086	5008	,	,		15263	0.001		0.0149	False		,,,				2504	0.001				p.S59L		Atlas-SNP	.											.	CASZ1	150	.	0			c.C176T						PASS	.	G	LEU/SER,LEU/SER	7,4247		0,7,2120	28.0	34.0	32.0		176,176	2.1	0.0	1	dbSNP_134	32	95,8333		1,93,4120	yes	missense,missense	CASZ1	NM_001079843.1,NM_017766.3	145,145	1,100,6240	AA,AG,GG		1.1272,0.1646,0.8043	benign,benign	59/1760,59/1167	10725469	102,12580	2127	4214	6341	SO:0001583	missense	54897	exon5			GGCTGCGATGGGC	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.176C>T	1.37:g.10725469G>A	ENSP00000366221:p.Ser59Leu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	32	24	0.75	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	11	0.014511873350923483	G	3.148	-0.174917	0.06421	0.001646	0.011272	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.42	2.11	0.27256	.	0.674203	0.13380	N	0.392225	T	0.08670	0.0215	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.31641	-0.9936	9	0.06891	T	0.86	-2.4618	4.9221	0.13874	0.6052:0.0:0.3948:0.0	.	83;59;59	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	L	59	.	ENSP00000339445:S59L	S	-	2	0	CASZ1	10648056	0.004000	0.15560	0.008000	0.14137	0.008000	0.06430	1.763000	0.38461	0.692000	0.31613	-0.424000	0.05967	TCG	G|0.993;A|0.007	0.007	strong		0.687	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
ATM	472	hgsc.bcm.edu	37	11	108124761	108124761	+	Missense_Mutation	SNP	T	T	C	rs4986761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108124761T>C	ENST00000452508.2	+	14	2308	c.2119T>C	c.(2119-2121)Tct>Cct	p.S707P	ATM_ENST00000278616.4_Missense_Mutation_p.S707P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	707			S -> P (in dbSNP:rs4986761). {ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846}.|YSS -> FIP (in AT; might be associated with susceptibility to cancer).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.S707P(2)|p.S707fs*29(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TAATTACTCATCTGAGGTGAG	0.393			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			T|||	22	0.00439297	0.0	0.0101	5008	,	,		16199	0.0		0.0129	False		,,,				2504	0.002				p.S707P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM,NS,carcinoma,0,2	ATM	1657	2	3	Substitution - Missense(2)|Deletion - Frameshift(1)	breast(2)|haematopoietic_and_lymphoid_tissue(1)	c.T2119C	GRCh37	CM013692	ATM	M	rs4986761	PASS	.	T	PRO/SER	17,4383	21.2+/-45.6	0,17,2183	55.0	55.0	55.0		2119	3.8	1.0	11	dbSNP_111	55	94,8502	50.6+/-110.7	1,92,4205	yes	missense	ATM	NM_000051.3	74	1,109,6388	CC,CT,TT		1.0935,0.3864,0.8541	benign	707/3057	108124761	111,12885	2200	4298	6498	SO:0001583	missense	472	exon13	Familial Cancer Database	AT, Louis-Bar syndrome	TACTCATCTGAGG	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2119T>C	11.37:g.108124761T>C	ENSP00000388058:p.Ser707Pro	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	11.63	1.694897	0.30052	0.003864	0.010935	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.78364	-1.17;-1.17;-1.17	6.11	3.81	0.43845	Armadillo-type fold (1);	0.179298	0.50627	N	0.000119	T	0.52141	0.1716	N	0.17872	0.535	0.23076	N	0.998335	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	10	0.31617	T	0.26	.	7.5463	0.27768	0.0:0.2362:0.0:0.7638	rs4986761;rs52832782;rs4986761	707	Q13315	ATM_HUMAN	P	707	ENSP00000435747:S707P;ENSP00000278616:S707P;ENSP00000388058:S707P	ENSP00000278616:S707P	S	+	1	0	ATM	107629971	0.015000	0.18098	0.999000	0.59377	0.911000	0.54048	-0.127000	0.10547	0.553000	0.29044	0.533000	0.62120	TCT	T|0.993;C|0.007	0.007	strong		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
PDE1C	5137	hgsc.bcm.edu	37	7	31848706	31848706	+	Silent	SNP	A	A	G	rs3213709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:31848706A>G	ENST00000396191.1	-	16	2285	c.1830T>C	c.(1828-1830)ggT>ggC	p.G610G	PDE1C_ENST00000396182.2_Silent_p.G610G|PDE1C_ENST00000321453.7_Silent_p.G610G|PDE1C_ENST00000396193.1_Silent_p.G670G|PDE1C_ENST00000396184.3_Silent_p.G610G|PDE1C_ENST00000479980.1_5'UTR	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	610					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.G610G(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TCTTATTTTTACCATCTTTGA	0.323													A|||	951	0.189896	0.2209	0.1542	5008	,	,		18715	0.124		0.2167	False		,,,				2504	0.2137				p.G670G		Atlas-SNP	.											PDE1C_ENST00000396193,NS,carcinoma,-2,8	PDE1C	465	8	2	Substitution - coding silent(2)	stomach(2)	c.T2010C						PASS	.	A	,,,,	938,3466	352.6+/-311.8	93,752,1357	140.0	125.0	130.0		1830,1830,2010,1830,1830	1.6	1.0	7	dbSNP_106	130	1750,6848	317.4+/-313.2	164,1422,2713	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE1C	NM_001191056.1,NM_001191057.1,NM_001191058.1,NM_001191059.1,NM_005020.2	,,,,	257,2174,4070	GG,GA,AA		20.3536,21.2988,20.6737	,,,,	610/635,610/710,670/770,610/710,610/635	31848706	2688,10314	2202	4299	6501	SO:0001819	synonymous_variant	5137	exon17			ATTTTTACCATCT	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1830T>C	7.37:g.31848706A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396191.1	37	CCDS55099.1																																																																																			A|0.792;G|0.208	0.208	strong		0.323	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
LIMCH1	22998	hgsc.bcm.edu	37	4	41691601	41691601	+	Silent	SNP	T	T	C	rs1061597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:41691601T>C	ENST00000313860.7	+	25	3126	c.3072T>C	c.(3070-3072)gcT>gcC	p.A1024A	LIMCH1_ENST00000512820.1_Silent_p.A1010A|LIMCH1_ENST00000511496.1_Silent_p.A838A|LIMCH1_ENST00000508501.1_Silent_p.A997A|LIMCH1_ENST00000396595.3_Silent_p.A843A|LIMCH1_ENST00000512632.1_Silent_p.A921A|LIMCH1_ENST00000513024.1_Silent_p.A851A|RP11-227F19.5_ENST00000506475.1_RNA|LIMCH1_ENST00000514096.1_Silent_p.A838A|LIMCH1_ENST00000381753.4_Silent_p.A831A|LIMCH1_ENST00000509277.1_Silent_p.A857A|LIMCH1_ENST00000503057.1_Silent_p.A1408A|LIMCH1_ENST00000512946.1_Silent_p.A998A	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	1024	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						GTAAAGGAGCTGCAATGATCA	0.393													T|||	340	0.0678914	0.0219	0.1282	5008	,	,		19439	0.002		0.174	False		,,,				2504	0.046				p.A1024A		Atlas-SNP	.											.	LIMCH1	233	.	0			c.T3072C						PASS	.	T	,,,,	181,4225	115.4+/-153.4	5,171,2027	167.0	159.0	161.0		2994,2991,2529,2493,3072	-6.9	0.8	4	dbSNP_86	161	1451,7149	278.4+/-293.4	132,1187,2981	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LIMCH1	NM_001112717.1,NM_001112718.1,NM_001112719.1,NM_001112720.1,NM_014988.2	,,,,	137,1358,5008	CC,CT,TT		16.8721,4.108,12.5481	,,,,	998/1058,997/1057,843/903,831/891,1024/1084	41691601	1632,11374	2203	4300	6503	SO:0001819	synonymous_variant	22998	exon25			AGGAGCTGCAATG	AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.3072T>C	4.37:g.41691601T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	217	102	0.470046	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Silent	SNP	ENST00000313860.7	37	CCDS33977.1	198	0.09065934065934066	9	0.018292682926829267	60	0.16574585635359115	0	0.0	129	0.17018469656992086	T	10.98	1.504574	0.26949	0.04108	0.168721	ENSG00000064042	ENST00000508466	.	.	.	5.03	-6.91	0.01649	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.24799	-1.0150	3	.	.	.	-17.7799	2.6009	0.04866	0.126:0.3246:0.1032:0.4462	rs1061597;rs3202689;rs17444675;rs1061597	.	.	.	P	858	.	.	L	+	2	0	LIMCH1	41386358	0.006000	0.16342	0.783000	0.31826	0.988000	0.76386	-1.357000	0.02607	-1.048000	0.03238	0.456000	0.33151	CTG	T|0.885;C|0.115	0.115	strong		0.393	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988	
CR2	1380	hgsc.bcm.edu	37	1	207646462	207646462	+	Missense_Mutation	SNP	G	G	A	rs17615	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207646462G>A	ENST00000367058.3	+	10	2105	c.1916G>A	c.(1915-1917)aGt>aAt	p.S639N	CR2_ENST00000367057.3_Missense_Mutation_p.S639N|CR2_ENST00000367059.3_Missense_Mutation_p.S639N|CR2_ENST00000458541.2_Missense_Mutation_p.S612N	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	639	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.		S -> N (in dbSNP:rs17615). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17360460}.		B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TTGAAGGGCAGTAGTCAGATT	0.388													G|||	1294	0.258387	0.4251	0.2017	5008	,	,		20652	0.1071		0.2913	False		,,,				2504	0.1953				p.S639N		Atlas-SNP	.											.	CR2	164	.	0			c.G1916A						PASS	.	G	ASN/SER,ASN/SER	1674,2732	508.8+/-367.0	334,1006,863	93.0	92.0	92.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1916,1916	4.8	1.0	1	dbSNP_63	92	2714,5886	433.7+/-357.5	422,1870,2008	yes	missense,missense	CR2	NM_001006658.2,NM_001877.4	46,46	756,2876,2871	AA,AG,GG		31.5581,37.9936,33.7383	probably-damaging,probably-damaging	639/1093,639/1034	207646462	4388,8618	2203	4300	6503	SO:0001583	missense	1380	exon10			AGGGCAGTAGTCA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1916G>A	1.37:g.207646462G>A	ENSP00000356025:p.Ser639Asn	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	586	0.2683150183150183	206	0.4186991869918699	90	0.24861878453038674	65	0.11363636363636363	225	0.29683377308707126	G	19.15	3.772477	0.69992	0.379936	0.315581	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.77	4.8	0.61643	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.52823	1.66	0.30327	P	0.786987	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.83275	0.995;0.982;0.996;0.986	T	0.38415	-0.9662	8	0.41790	T	0.15	.	11.2876	0.49230	0.0:0.0:0.8184:0.1816	rs17615;rs2274565;rs17045200;rs57858208;rs17615	639;639;639;639	C9JHD2;Q5SR47;P20023;P20023-3	.;.;CR2_HUMAN;.	N	639;639;639;612	ENSP00000356025:S639N;ENSP00000356024:S639N;ENSP00000356026:S639N;ENSP00000404222:S612N	ENSP00000356024:S639N	S	+	2	0	CR2	205713085	0.056000	0.20664	0.971000	0.41717	0.994000	0.84299	0.504000	0.22626	2.723000	0.93209	0.655000	0.94253	AGT	G|0.702;A|0.298	0.298	strong		0.388	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
KCNA1	3736	hgsc.bcm.edu	37	12	5021228	5021228	+	Silent	SNP	T	T	C	rs1048500	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:5021228T>C	ENST00000382545.3	+	2	1791	c.684T>C	c.(682-684)tgT>tgC	p.C228C	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	228					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	AAACGCTGTGTATCATCTGGT	0.512													T|||	2449	0.489018	0.4183	0.5072	5008	,	,		20287	0.631		0.498	False		,,,				2504	0.4162				p.C228C		Atlas-SNP	.											KCNA1,colon,carcinoma,0,1	KCNA1	112	1	0			c.T684C						PASS	.	T		1794,2612	528.7+/-372.5	342,1110,751	114.0	87.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	684	-0.1	1.0	12	dbSNP_86	96	4306,4294	577.7+/-390.6	1078,2150,1072	no	coding-synonymous	KCNA1	NM_000217.2		1420,3260,1823	CC,CT,TT		49.9302,40.7172,46.9014		228/496	5021228	6100,6906	2203	4300	6503	SO:0001819	synonymous_variant	3736	exon2			GCTGTGTATCATC	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.684T>C	12.37:g.5021228T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_000217	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	37	CCDS8535.1																																																																																			T|0.498;C|0.502	0.502	strong		0.512	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
OSBPL7	114881	hgsc.bcm.edu	37	17	45890707	45890707	+	Silent	SNP	C	C	T	rs2301690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45890707C>T	ENST00000007414.3	-	16	1853	c.1662G>A	c.(1660-1662)aaG>aaA	p.K554K	OSBPL7_ENST00000392507.3_Silent_p.K554K	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	554					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GGTTGAAGGGCTTGCAGCCGG	0.622													c|||	795	0.158746	0.0643	0.2233	5008	,	,		19047	0.0139		0.3569	False		,,,				2504	0.1861				p.K554K		Atlas-SNP	.											.	OSBPL7	65	.	0			c.G1662A						PASS	.			480,3926	224.6+/-240.7	22,436,1745	65.0	64.0	64.0		1662	1.4	1.0	17	dbSNP_100	64	3302,5298	494.0+/-373.7	653,1996,1651	no	coding-synonymous	OSBPL7	NM_145798.2		675,2432,3396	TT,TC,CC		38.3953,10.8942,29.0789		554/843	45890707	3782,9224	2203	4300	6503	SO:0001819	synonymous_variant	114881	exon16			GAAGGGCTTGCAG	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1662G>A	17.37:g.45890707C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																			C|0.759;T|0.241	0.241	strong		0.622	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
GBP7	388646	hgsc.bcm.edu	37	1	89599084	89599084	+	Missense_Mutation	SNP	G	G	C	rs79037912		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89599084G>C	ENST00000294671.2	-	10	1657	c.1519C>G	c.(1519-1521)Caa>Gaa	p.Q507E		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	507						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.Q507E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TTCTGTTTTTGTCTTAGCAGC	0.458																																					p.Q507E		Atlas-SNP	.											GBP7,extremity,malignant_melanoma,0,1	GBP7	57	1	1	Substitution - Missense(1)	skin(1)	c.C1519G						PASS	.						204.0	189.0	194.0					1																	89599084		2202	4300	6502	SO:0001583	missense	388646	exon10			GTTTTTGTCTTAG	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1519C>G	1.37:g.89599084G>C	ENSP00000294671:p.Gln507Glu	Somatic	498	0	0		WXS	Illumina HiSeq	Phase_I	524	80	0.152672	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	G	1.816	-0.473563	0.04445	.	.	ENSG00000213512	ENST00000294671	T	0.01725	4.67	3.6	2.66	0.31614	Guanylate-binding protein, C-terminal (3);	0.212783	0.40554	N	0.001075	T	0.00384	0.0012	N	0.17800	0.525	0.09310	N	1	B	0.20052	0.041	B	0.25405	0.06	T	0.47018	-0.9149	10	0.02654	T	1	.	9.0852	0.36577	0.0:0.2488:0.7512:0.0	.	507	Q8N8V2	GBP7_HUMAN	E	507	ENSP00000294671:Q507E	ENSP00000294671:Q507E	Q	-	1	0	GBP7	89371672	0.436000	0.25586	0.084000	0.20598	0.621000	0.37620	0.585000	0.23879	0.812000	0.34326	0.591000	0.81541	CAA	.	.	weak		0.458	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
PITRM1	10531	hgsc.bcm.edu	37	10	3207632	3207632	+	Missense_Mutation	SNP	A	A	G	rs3814596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:3207632A>G	ENST00000224949.4	-	5	540	c.506T>C	c.(505-507)tTc>tCc	p.F169S	PITRM1_ENST00000380989.2_Missense_Mutation_p.F169S|PITRM1_ENST00000451104.2_Missense_Mutation_p.F137S|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	169			F -> S (in dbSNP:rs3814596). {ECO:0000269|PubMed:10360838}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TAAACATGGGAAAAAGGTGGC	0.383													A|||	667	0.133187	0.1407	0.1066	5008	,	,		18416	0.0526		0.1869	False		,,,				2504	0.1697				p.F169S		Atlas-SNP	.											PITRM1,colon,carcinoma,0,1	PITRM1	109	1	0			c.T506C						PASS	.	A	SER/PHE,SER/PHE,SER/PHE	523,3215		49,425,1395	98.0	99.0	99.0		506,410,506	5.4	0.8	10	dbSNP_107	99	1599,6625		159,1281,2672	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	155,155,155	208,1706,4067	GG,GA,AA		19.4431,13.9914,17.7395	possibly-damaging,possibly-damaging,possibly-damaging	169/1039,137/940,169/1038	3207632	2122,9840	1869	4112	5981	SO:0001583	missense	10531	exon5			CATGGGAAAAAGG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.506T>C	10.37:g.3207632A>G	ENSP00000224949:p.Phe169Ser	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	150	85	0.566667	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	274	0.12545787545787546	60	0.12195121951219512	42	0.11602209944751381	29	0.050699300699300696	143	0.18865435356200527	a	17.90	3.501492	0.64298	0.139914	0.194431	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.27104	1.69;1.69;1.69	5.37	5.37	0.77165	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	M	0.79693	2.465	0.09310	P	0.99999623526	B;B;P;P;P	0.41498	0.377;0.11;0.708;0.752;0.752	B;B;P;P;P	0.53760	0.146;0.215;0.615;0.734;0.734	T	0.01105	-1.1450	9	0.33141	T	0.24	.	15.4166	0.74974	1.0:0.0:0.0:0.0	rs3814596;rs52789691;rs57308152;rs3814596	162;137;169;169;169	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3	.;.;.;.;PREP_HUMAN	S	169;162;169;137	ENSP00000224949:F169S;ENSP00000370377:F169S;ENSP00000401201:F137S	ENSP00000224949:F169S	F	-	2	0	PITRM1	3197632	1.000000	0.71417	0.829000	0.32907	0.889000	0.51656	8.663000	0.91134	2.037000	0.60232	0.477000	0.44152	TTC	A|0.857;G|0.143	0.143	strong		0.383	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
SCN8A	6334	hgsc.bcm.edu	37	12	52200742	52200742	+	Silent	SNP	C	C	A	rs60637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52200742C>A	ENST00000354534.6	+	27	5650	c.5472C>A	c.(5470-5472)ccC>ccA	p.P1824P	SCN8A_ENST00000545061.1_Silent_p.P1783P|RP11-923I11.3_ENST00000565518.1_lincRNA	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1824					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	TGCCCAAGCCCAATACCATTG	0.552													C|||	2449	0.489018	0.2526	0.7464	5008	,	,		21281	0.5665		0.7276	False		,,,				2504	0.3006				p.P1824P		Atlas-SNP	.											.	SCN8A	331	.	0			c.C5472A						PASS	.	C	,	1391,2853		236,919,967	73.0	74.0	73.0		5349,5472	2.2	1.0	12	dbSNP_79	73	6345,2165		2360,1625,270	no	coding-synonymous,coding-synonymous	SCN8A	NM_001177984.1,NM_014191.2	,	2596,2544,1237	AA,AC,CC		25.4407,32.7757,39.3445	,	1783/1940,1824/1981	52200742	7736,5018	2122	4255	6377	SO:0001819	synonymous_variant	6334	exon27			CAAGCCCAATACC	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.5472C>A	12.37:g.52200742C>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	37	CCDS44891.1																																																																																			C|0.455;A|0.545	0.545	strong		0.552	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
LTBP1	4052	hgsc.bcm.edu	37	2	33488419	33488419	+	Silent	SNP	G	G	A	rs12468099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33488419G>A	ENST00000404816.2	+	15	2930	c.2577G>A	c.(2575-2577)acG>acA	p.T859T	LTBP1_ENST00000407925.1_Silent_p.T533T|LTBP1_ENST00000418533.2_Silent_p.T533T|LTBP1_ENST00000390003.4_Silent_p.T534T|LTBP1_ENST00000402934.1_Silent_p.T480T|LTBP1_ENST00000354476.3_Silent_p.T860T|LTBP1_ENST00000404525.1_Silent_p.T480T			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	859					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AAGCTTCTACGTCTAGTGCCA	0.428													G|||	839	0.167532	0.0166	0.1844	5008	,	,		17578	0.2371		0.2863	False		,,,				2504	0.1656				p.T859T		Atlas-SNP	.											.	LTBP1	317	.	0			c.G2577A						PASS	.	G	,,,,	277,4129	153.7+/-187.2	8,261,1934	143.0	138.0	139.0		1599,1599,1440,1440,2577	-4.5	0.9	2	dbSNP_120	139	2489,6111	409.6+/-349.9	373,1743,2184	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	381,2004,4118	AA,AG,GG		28.9419,6.2869,21.2671	,,,,	533/1396,533/1354,480/1343,480/1301,859/1722	33488419	2766,10240	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon15			TTCTACGTCTAGT		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.2577G>A	2.37:g.33488419G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			G|0.797;A|0.203	0.203	strong		0.428	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
UBE2Z	65264	hgsc.bcm.edu	37	17	47000251	47000251	+	Silent	SNP	C	C	T	rs1058018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:47000251C>T	ENST00000360943.5	+	6	981	c.846C>T	c.(844-846)taC>taT	p.Y282Y		NM_023079.4	NP_075567.2	Q9H832	UBE2Z_HUMAN	ubiquitin-conjugating enzyme E2Z	282					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)										ACGACTTCTACGAGGTGGCCT	0.502													T|||	3179	0.634784	0.5575	0.5187	5008	,	,		18844	0.747		0.6044	False		,,,				2504	0.7372				p.Y282Y		Atlas-SNP	.											.	.	.	.	0			c.C846T						PASS	.	T		2399,2007	561.6+/-380.8	654,1091,458	97.0	82.0	87.0		846	3.1	1.0	17	dbSNP_86	87	4949,3651	524.4+/-380.5	1398,2153,749	no	coding-synonymous	UBE2Z	NM_023079.4		2052,3244,1207	TT,TC,CC		42.4535,45.5515,43.503		282/355	47000251	7348,5658	2203	4300	6503	SO:0001819	synonymous_variant	65264	exon6			CTTCTACGAGGTG	BC015890	CCDS11540.2	17q21.32	2010-01-14	2007-07-18		ENSG00000159202	ENSG00000159202		"""Ubiquitin-conjugating enzymes E2"""	25847	protein-coding gene	gene with protein product	"""UBA6-specific enzyme E2"""	611362				17597759	Standard	NM_023079		Approved	FLJ13855, USE1	uc002ioi.3	Q9H832	OTTHUMG00000150521	ENST00000360943.5:c.846C>T	17.37:g.47000251C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	181	83	0.458564	NM_023079	A6N8M6|A6NC60|Q7L354|Q8TCM4|Q9H893	Silent	SNP	ENST00000360943.5	37	CCDS11540.2																																																																																			C|0.408;T|0.592	0.592	strong		0.502	UBE2Z-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318724.2	NM_023079	
KLF3	51274	hgsc.bcm.edu	37	4	38690515	38690515	+	Missense_Mutation	SNP	A	A	G	rs199559194		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38690515A>G	ENST00000261438.5	+	3	672	c.367A>G	c.(367-369)Atg>Gtg	p.M123V	KLF3_ENST00000514033.1_Missense_Mutation_p.M123V	NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	123	Pro-rich.				cellular response to peptide (GO:1901653)|multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18						GCCGCTGTCCATGCCACCAGT	0.632																																					p.M123V		Atlas-SNP	.											.	KLF3	40	.	0			c.A367G						PASS	.	A	VAL/MET	0,4406		0,0,2203	51.0	54.0	53.0		367	5.5	1.0	4		53	1,8599	1.2+/-3.3	0,1,4299	no	missense	KLF3	NM_016531.5	21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	123/346	38690515	1,13005	2203	4300	6503	SO:0001583	missense	51274	exon3			CTGTCCATGCCAC	AF285837	CCDS3444.1	4p16.1-p15.2	2013-01-08			ENSG00000109787	ENSG00000109787		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	16516	protein-coding gene	gene with protein product	"""basic Kruppel-like factor"""	609392				18391014	Standard	NM_016531		Approved	BKLF	uc003gth.4	P57682	OTTHUMG00000097821	ENST00000261438.5:c.367A>G	4.37:g.38690515A>G	ENSP00000261438:p.Met123Val	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Missense_Mutation	SNP	ENST00000261438.5	37	CCDS3444.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.607253	0.46527	0.0	1.16E-4	ENSG00000109787	ENST00000261438;ENST00000514033	T;T	0.42900	0.96;0.96	5.53	5.53	0.82687	.	0.059640	0.64402	D	0.000002	T	0.24160	0.0585	N	0.08118	0	0.28589	N	0.909727	B	0.02656	0.0	B	0.01281	0.0	T	0.06917	-1.0800	10	0.14656	T	0.56	.	15.827	0.78718	1.0:0.0:0.0:0.0	.	123	P57682	KLF3_HUMAN	V	123	ENSP00000261438:M123V;ENSP00000421252:M123V	ENSP00000261438:M123V	M	+	1	0	KLF3	38366910	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.350000	0.59392	2.324000	0.78689	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	weak		0.632	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2		
NCAPH2	29781	hgsc.bcm.edu	37	22	50960682	50960682	+	Splice_Site	SNP	C	C	T	rs140524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50960682C>T	ENST00000420993.2	+	14	1355		c.e14+2		NCAPH2_ENST00000395701.3_Splice_Site|CTA-384D8.36_ENST00000608319.1_RNA|NCAPH2_ENST00000520297.1_Splice_Site|NCAPH2_ENST00000299821.11_Splice_Site	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2						chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)		p.?(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		AGGAGGGAGGCAAGTCCCAGC	0.592													C|||	1153	0.230232	0.2315	0.2378	5008	,	,		17582	0.2986		0.1551	False		,,,				2504	0.2301				.		Atlas-SNP	.											NCAPH2,NS,carcinoma,0,1	NCAPH2	69	1	1	Unknown(1)	stomach(1)	c.1233+2C>T						PASS	.	C	,	1026,3380	380.9+/-323.9	115,796,1292	76.0	79.0	78.0		,	-1.7	0.9	22	dbSNP_78	78	1408,7192	271.7+/-289.7	119,1170,3011	yes	splice-5,splice-5	NCAPH2	NM_001185011.1,NM_152299.3	,	234,1966,4303	TT,TC,CC		16.3721,23.2864,18.7144	,	,	50960682	2434,10572	2203	4300	6503	SO:0001630	splice_region_variant	29781	exon14			GGGAGGCAAGTCC	BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"""kleisin beta"", ""CAP-H2 subunit of the condensin II complex"""	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.1233+2C>T	22.37:g.50960682C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_001185011	B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Splice_Site	SNP	ENST00000420993.2	37	CCDS14094.2	457	0.20924908424908426	108	0.21951219512195122	87	0.24033149171270718	145	0.2534965034965035	117	0.15435356200527706	C	11.97	1.798696	0.31777	0.232864	0.163721	ENSG00000025770	ENST00000420993;ENST00000395701;ENST00000299821	.	.	.	4.93	-1.73	0.08081	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3457	0.11131	0.1726:0.2524:0.0:0.575	rs140524;rs57584715;rs140524	.	.	.	.	-1	.	.	.	+	.	.	NCAPH2	49307548	0.036000	0.19791	0.853000	0.33588	0.792000	0.44763	-0.585000	0.05794	0.110000	0.17919	0.591000	0.81541	.	C|0.810;T|0.190	0.190	strong		0.592	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317012.1	NM_152299	Intron
C7orf31	136895	hgsc.bcm.edu	37	7	25194753	25194753	+	Missense_Mutation	SNP	C	C	T	rs12535348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:25194753C>T	ENST00000409280.1	-	6	780	c.472G>A	c.(472-474)Gcc>Acc	p.A158T	C7orf31_ENST00000283905.3_Missense_Mutation_p.A158T			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	158			A -> T (in dbSNP:rs12535348). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.					p.A158T(1)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						GGGAACATGGCGCCGCGACAG	0.502													C|||	1409	0.28135	0.0484	0.3919	5008	,	,		16730	0.1567		0.4891	False		,,,				2504	0.4325				p.A158T		Atlas-SNP	.											C7orf31,caecum,carcinoma,0,2	C7orf31	53	2	1	Substitution - Missense(1)	stomach(1)	c.G472A						PASS	.	C	THR/ALA	507,3899	234.6+/-247.4	33,441,1729	124.0	129.0	127.0		472	4.6	0.9	7	dbSNP_120	127	4293,4307	576.9+/-390.5	1042,2209,1049	yes	missense	C7orf31	NM_138811.3	58	1075,2650,2778	TT,TC,CC		49.9186,11.507,36.906	benign	158/591	25194753	4800,8206	2203	4300	6503	SO:0001583	missense	136895	exon6			ACATGGCGCCGCG	AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790			21722	protein-coding gene	gene with protein product							Standard	NM_138811		Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.472G>A	7.37:g.25194753C>T	ENSP00000386604:p.Ala158Thr	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	244	121	0.495902	NM_138811	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	Missense_Mutation	SNP	ENST00000409280.1	37	CCDS5394.1	615	0.2815934065934066	27	0.054878048780487805	150	0.4143646408839779	80	0.13986013986013987	358	0.47229551451187335	c	15.50	2.850917	0.51270	0.11507	0.499186	ENSG00000153790	ENST00000409280;ENST00000283905	T;T	0.09445	2.98;2.98	5.47	4.58	0.56647	.	0.102433	0.42964	D	0.000621	T	0.00012	0.0000	M	0.68952	2.095	0.31562	P	0.65745	D	0.63046	0.992	P	0.54431	0.752	T	0.49153	-0.8969	9	0.51188	T	0.08	-37.4962	11.8433	0.52368	0.1741:0.8259:0.0:0.0	rs12535348;rs17301740;rs52832524;rs59627706;rs12535348	158	Q8N865	CG031_HUMAN	T	158	ENSP00000386604:A158T;ENSP00000283905:A158T	ENSP00000283905:A158T	A	-	1	0	C7orf31	25161278	0.918000	0.31147	0.857000	0.33713	0.038000	0.13279	1.734000	0.38166	1.293000	0.44690	0.563000	0.77884	GCC	C|0.675;N|0.000	.	strong		0.502	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326929.1	NM_138811	
EML5	161436	hgsc.bcm.edu	37	14	89220874	89220874	+	Silent	SNP	C	C	T	rs201072176		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:89220874C>T	ENST00000380664.5	-	2	338	c.339G>A	c.(337-339)gcG>gcA	p.A113A	EML5_ENST00000352093.5_Silent_p.A113A|EML5_ENST00000554922.1_Silent_p.A113A			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	113						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CTAAGTCAAACGCCAAGCAAG	0.299													C|||	1	0.000199681	0.0	0.0	5008	,	,		15572	0.0		0.0	False		,,,				2504	0.001				p.A113A		Atlas-SNP	.											.	EML5	141	.	0			c.G339A						PASS	.	C		1,3729		0,1,1864	105.0	92.0	96.0		339	1.0	1.0	14		96	8,8200		0,8,4096	no	coding-synonymous	EML5	NM_183387.2		0,9,5960	TT,TC,CC		0.0975,0.0268,0.0754		113/1978	89220874	9,11929	1865	4104	5969	SO:0001819	synonymous_variant	161436	exon2			GTCAAACGCCAAG	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.339G>A	14.37:g.89220874C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Silent	SNP	ENST00000380664.5	37	CCDS45148.1																																																																																			C|0.999;T|0.001	0.001	weak		0.299	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
FSD1	79187	hgsc.bcm.edu	37	19	4306311	4306311	+	Silent	SNP	T	T	C	rs4807578	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4306311T>C	ENST00000221856.6	+	3	375	c.228T>C	c.(226-228)cgT>cgC	p.R76R	FSD1_ENST00000597590.1_Silent_p.R76R	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	76					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGCCAGCCGTACCTACGAGC	0.572													c|||	2921	0.583267	0.553	0.6412	5008	,	,		16805	0.4107		0.663	False		,,,				2504	0.6789				p.R76R		Atlas-SNP	.											.	FSD1	51	.	0			c.T228C						PASS	.			2595,1811	528.1+/-372.3	763,1069,371	58.0	57.0	58.0		228	-4.5	1.0	19	dbSNP_111	58	5479,3121	472.5+/-368.4	1718,2043,539	no	coding-synonymous	FSD1	NM_024333.2		2481,3112,910	CC,CT,TT		36.2907,41.103,37.921		76/497	4306311	8074,4932	2203	4300	6503	SO:0001819	synonymous_variant	79187	exon3			CAGCCGTACCTAC	AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"""Fibronectin type III domain containing"""	13745	protein-coding gene	gene with protein product		609828	"""fibronectin type 3 and SPRY domain containing 1"""			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.228T>C	19.37:g.4306311T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_024333	B2RDT0|Q9BXN0|Q9HAG4	Silent	SNP	ENST00000221856.6	37	CCDS12127.1																																																																																			T|0.402;C|0.598	0.598	strong		0.572	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333	
POTEE	445582	hgsc.bcm.edu	37	2	132021766	132021766	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:132021766A>C	ENST00000356920.5	+	15	2832	c.2738A>C	c.(2737-2739)aAa>aCa	p.K913T	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	913	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K913T(1)									CGTGACATCAAAGAGAAGCTG	0.602																																					p.K913T		Atlas-SNP	.											ENSG00000188219,rectum,NS,0,1	.	.	1	1	Substitution - Missense(1)	large_intestine(1)	c.A2738C						scavenged	.						73.0	77.0	75.0					2																	132021766		1926	3862	5788	SO:0001583	missense	445582	exon15			ACATCAAAGAGAA	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2738A>C	2.37:g.132021766A>C	ENSP00000439189:p.Lys913Thr	Somatic	309	2	0.00647249		WXS	Illumina HiSeq	Phase_I	371	8	0.0215633	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	15.85	2.956333	0.53293	.	.	ENSG00000188219	ENST00000356920	D	0.97850	-4.57	.	.	.	.	.	.	.	.	D	0.99177	0.9715	H	0.99884	4.89	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96111	0.9077	8	0.87932	D	0	.	4.5487	0.12098	0.9994:0.0:6.0E-4:0.0	.	913	Q6S8J3	POTEE_HUMAN	T	913	ENSP00000439189:K913T	ENSP00000439189:K913T	K	+	2	0	AC131180.1	131738236	1.000000	0.71417	0.327000	0.25402	0.329000	0.28539	6.177000	0.71961	0.103000	0.17682	0.102000	0.15555	AAA	.	.	none		0.602	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
LMTK2	22853	hgsc.bcm.edu	37	7	97822115	97822115	+	Missense_Mutation	SNP	T	T	A	rs11765552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:97822115T>A	ENST00000297293.5	+	11	2631	c.2338T>A	c.(2338-2340)Ttg>Atg	p.L780M		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	780			L -> M (in dbSNP:rs11765552). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:17344846}.		early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					TAAGCCAGGCTTGTCTTTGTT	0.428													T|||	1121	0.223842	0.0356	0.3156	5008	,	,		19913	0.1528		0.5119	False		,,,				2504	0.1902				p.L780M		Atlas-SNP	.											.	LMTK2	228	.	0			c.T2338A						PASS	.	T	MET/LEU	551,3855	247.2+/-255.5	34,483,1686	119.0	124.0	122.0		2338	-0.9	0.0	7	dbSNP_120	122	4710,3890	607.9+/-395.3	1300,2110,890	yes	missense	LMTK2	NM_014916.3	15	1334,2593,2576	AA,AT,TT		45.2326,12.5057,40.4506	benign	780/1504	97822115	5261,7745	2203	4300	6503	SO:0001583	missense	22853	exon11			CCAGGCTTGTCTT	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.2338T>A	7.37:g.97822115T>A	ENSP00000297293:p.Leu780Met	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_014916	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	613	0.2806776556776557	21	0.042682926829268296	120	0.3314917127071823	81	0.14160839160839161	391	0.5158311345646438	T	12.80	2.047819	0.36085	0.125057	0.547674	ENSG00000164715	ENST00000297293	T	0.78126	-1.15	5.66	-0.876	0.10624	.	1.102820	0.06652	N	0.762926	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.41748	0.761	B	0.35413	0.202	T	0.31052	-0.9957	9	0.33940	T	0.23	.	6.0057	0.19544	0.0:0.2644:0.1255:0.6101	rs11765552;rs17527184;rs11765552	780	Q8IWU2	LMTK2_HUMAN	M	780	ENSP00000297293:L780M	ENSP00000297293:L780M	L	+	1	2	LMTK2	97660051	0.002000	0.14202	0.000000	0.03702	0.033000	0.12548	1.132000	0.31418	-0.292000	0.08999	0.533000	0.62120	TTG	T|0.639;A|0.361	0.361	strong		0.428	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720851	135720851	+	Missense_Mutation	SNP	G	G	T	rs6779903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:135720851G>T	ENST00000264977.3	+	2	1128	c.511G>T	c.(511-513)Gcc>Tcc	p.A171S	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	171			A -> S (in dbSNP:rs6779903).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CGATGGGAACGCCCCATCCTT	0.423													G|||	1731	0.345647	0.5537	0.281	5008	,	,		17100	0.1964		0.2823	False		,,,				2504	0.3292				p.A171S		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.G511T						PASS	.	G	,SER/ALA	2231,2175	591.1+/-387.5	570,1091,542	74.0	79.0	77.0		,511	0.1	0.5	3	dbSNP_116	77	2364,6236	394.2+/-344.6	313,1738,2249	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,99	883,2829,2791	TT,TG,GG		27.4884,49.3645,35.3298	,benign	,171/1151	135720851	4595,8411	2203	4300	6503	SO:0001583	missense	5523	exon2			GGGAACGCCCCAT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.511G>T	3.37:g.135720851G>T	ENSP00000264977:p.Ala171Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	58	0.591837	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	748	0.3424908424908425	278	0.5650406504065041	111	0.30662983425414364	133	0.23251748251748253	226	0.29815303430079154	G	0.001	-2.910977	0.00056	0.506355	0.274884	ENSG00000073711	ENST00000264977	T	0.05258	3.47	5.55	0.0664	0.14361	.	0.420852	0.26000	N	0.026941	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22626	-1.0211	9	0.09590	T	0.72	.	8.5274	0.33313	0.1218:0.0:0.3925:0.4856	rs6779903;rs52800757;rs61128780;rs6779903	171	Q06190	P2R3A_HUMAN	S	171	ENSP00000264977:A171S	ENSP00000264977:A171S	A	+	1	0	PPP2R3A	137203541	0.567000	0.26626	0.471000	0.27229	0.086000	0.17979	1.057000	0.30492	0.060000	0.16281	-1.072000	0.02254	GCC	G|0.660;T|0.340	0.340	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
PHC3	80012	hgsc.bcm.edu	37	3	169846937	169846937	+	Silent	SNP	A	A	G	rs373112767		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:169846937A>G	ENST00000494943.1	-	8	1355	c.1287T>C	c.(1285-1287)gcT>gcC	p.A429A	PHC3_ENST00000467570.1_Silent_p.A388A|PHC3_ENST00000495893.2_Silent_p.A441A			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	429	Gln-rich.|Pro-rich.				multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			CTGGCTGGAGAGCTGATGACA	0.493													A|||	1	0.000199681	0.0	0.0	5008	,	,		22525	0.0		0.001	False		,,,				2504	0.0				p.A441A		Atlas-SNP	.											.	PHC3	113	.	0			c.T1323C						PASS	.	A		0,4170		0,0,2085	61.0	64.0	63.0		1323	2.4	1.0	3		63	1,8431		0,1,4215	no	coding-synonymous	PHC3	NM_024947.3		0,1,6300	GG,GA,AA		0.0119,0.0,0.0079		441/996	169846937	1,12601	2085	4216	6301	SO:0001819	synonymous_variant	80012	exon8			CTGGAGAGCTGAT		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"""Sterile alpha motif (SAM) domain containing"""	15682	protein-coding gene	gene with protein product	"""early development regulator 3"", ""polyhomeotic like 3"""		"""polyhomeotic like 3 (Drosophila)"""			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.1287T>C	3.37:g.169846937A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	131	58	0.442748	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Silent	SNP	ENST00000494943.1	37																																																																																				.	.	weak		0.493	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947	
DHRS1	115817	hgsc.bcm.edu	37	14	24760808	24760808	+	Silent	SNP	C	C	T	rs1131941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24760808C>T	ENST00000288111.7	-	7	954	c.678G>A	c.(676-678)gcG>gcA	p.A226A	DHRS1_ENST00000559088.1_5'UTR|DHRS1_ENST00000396813.1_Silent_p.A226A	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	226						endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6				GBM - Glioblastoma multiforme(265;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(311;0.0442)		CTGTGGTTTCCGCAGATGAGA	0.498													C|||	746	0.148962	0.1513	0.3473	5008	,	,		22102	0.004		0.1869	False		,,,				2504	0.1155				p.A226A		Atlas-SNP	.											.	DHRS1	21	.	0			c.G678A						PASS	.	C	,	728,3678	301.0+/-286.6	62,604,1537	196.0	192.0	193.0		678,678	-7.2	0.0	14	dbSNP_86	193	1783,6817	322.1+/-315.4	189,1405,2706	no	coding-synonymous,coding-synonymous	DHRS1	NM_001136050.2,NM_138452.2	,	251,2009,4243	TT,TC,CC		20.7326,16.5229,19.3065	,	226/314,226/314	24760808	2511,10495	2203	4300	6503	SO:0001819	synonymous_variant	115817	exon7			GGTTTCCGCAGAT	AK058159	CCDS9623.1	14q11.2	2011-09-14			ENSG00000157379	ENSG00000157379	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16445	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 19C, member 1"""	610410				12153138, 19027726	Standard	NM_138452		Approved	FLJ25430, MGC20204, SDR19C1	uc001wok.3	Q96LJ7	OTTHUMG00000029333	ENST00000288111.7:c.678G>A	14.37:g.24760808C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	55	0.426357	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Silent	SNP	ENST00000288111.7	37	CCDS9623.1																																																																																			C|0.827;T|0.173	0.173	strong		0.498	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452	
PLEC	5339	hgsc.bcm.edu	37	8	144996408	144996408	+	Silent	SNP	T	T	G	rs11778026	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144996408T>G	ENST00000322810.4	-	32	8161	c.7992A>C	c.(7990-7992)gcA>gcC	p.A2664A	PLEC_ENST00000354589.3_Silent_p.A2527A|PLEC_ENST00000357649.2_Silent_p.A2531A|PLEC_ENST00000356346.3_Silent_p.A2513A|PLEC_ENST00000398774.2_Silent_p.A2495A|PLEC_ENST00000345136.3_Silent_p.A2527A|PLEC_ENST00000527096.1_Silent_p.A2550A|PLEC_ENST00000436759.2_Silent_p.A2554A|PLEC_ENST00000354958.2_Silent_p.A2505A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2664	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCAGCTGCTGTGCCTTGGCCA	0.657													T|||	1157	0.23103	0.028	0.2968	5008	,	,		16590	0.1429		0.4284	False		,,,				2504	0.3466				p.A2664A		Atlas-SNP	.											.	PLEC	1144	.	0			c.A7992C						PASS	.	T	,,,,,,,	382,4000		24,334,1833	12.0	13.0	13.0		7662,7539,7515,7992,7485,7581,7593,7581	-5.4	0.9	8	dbSNP_120	13	3440,5132		731,1978,1577	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	755,2312,3410	GG,GT,TT		40.1307,8.7175,29.5044	,,,,,,,	2554/4575,2513/4534,2505/4526,2664/4685,2495/4516,2527/4548,2531/4552,2527/4548	144996408	3822,9132	2191	4286	6477	SO:0001819	synonymous_variant	5339	exon32			CTGCTGTGCCTTG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.7992A>C	8.37:g.144996408T>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	17	0.369565	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1	538	0.24633699633699635	15	0.03048780487804878	108	0.2983425414364641	94	0.16433566433566432	321	0.4234828496042216	t	9.155	1.017286	0.19355	0.087175	0.401307	ENSG00000178209	ENST00000527303	.	.	.	4.38	-5.41	0.02648	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999983	.	.	.	.	.	.	T	0.47509	-0.9112	3	.	.	.	.	1.205	0.01893	0.195:0.1813:0.155:0.4687	rs11778026	.	.	.	P	97	.	.	H	-	2	0	PLEC	145068396	0.000000	0.05858	0.870000	0.34147	0.990000	0.78478	-2.721000	0.00811	-0.830000	0.04262	0.364000	0.22116	CAC	A|0.000;G|0.248;T|0.752	0.248	strong		0.657	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
AK2	204	hgsc.bcm.edu	37	1	33502376	33502376	+	Silent	SNP	G	G	A	rs76061645	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33502376G>A	ENST00000487289.1	-	1	69	c.54C>T	c.(52-54)gcC>gcT	p.A18A	AK2_ENST00000548033.1_Silent_p.A18A|AK2_ENST00000467905.1_Silent_p.A18A|AK2_ENST00000373449.2_Silent_p.A18A|AK2_ENST00000354858.6_Silent_p.A18A|AK2_ENST00000480134.1_Silent_p.A18A					adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CCAGCAGCACGGCCCGGATGC	0.682																																					p.A18A		Atlas-SNP	.											.	AK2	27	.	0			c.C54T						PASS	.						14.0	13.0	14.0					1																	33502376		2202	4296	6498	SO:0001819	synonymous_variant	204	exon1			CAGCACGGCCCGG	U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"""Adenylate kinases"""	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000487289.1:c.54C>T	1.37:g.33502376G>A		Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	244	26	0.106557	NM_001199199		Silent	SNP	ENST00000487289.1	37																																																																																				G|0.955;A|0.045	0.045	strong		0.682	AK2-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000011889.4	NM_001625	
VPS13A	23230	hgsc.bcm.edu	37	9	79986057	79986057	+	Silent	SNP	A	A	G	rs3737289	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79986057A>G	ENST00000360280.3	+	67	9329	c.9069A>G	c.(9067-9069)ggA>ggG	p.G3023G	VPS13A_ENST00000376634.4_Silent_p.G3023G|VPS13A_ENST00000357409.5_Silent_p.G3023G|VPS13A_ENST00000376636.3_Silent_p.G2984G	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	3023					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CATTTCAGGGAATAAAAAGGT	0.408													A|||	2079	0.415136	0.2958	0.5159	5008	,	,		17902	0.3542		0.4394	False		,,,				2504	0.5429				p.G3023G		Atlas-SNP	.											.	VPS13A	735	.	0			c.A9069G						PASS	.	A	,,,	1432,2974	461.1+/-352.8	239,954,1010	83.0	75.0	78.0		8952,9069,9069,9069	3.3	1.0	9	dbSNP_107	78	3740,4860	527.3+/-381.1	796,2148,1356	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	1035,3102,2366	GG,GA,AA		43.4884,32.5011,39.7663	,,,	2984/3136,3023/3070,3023/3096,3023/3175	79986057	5172,7834	2203	4300	6503	SO:0001819	synonymous_variant	23230	exon67			TCAGGGAATAAAA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.9069A>G	9.37:g.79986057A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			A|0.606;G|0.394	0.394	strong		0.408	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
TYSND1	219743	hgsc.bcm.edu	37	10	71905569	71905569	+	Silent	SNP	C	C	A	rs3750774	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71905569C>A	ENST00000287078.6	-	1	773	c.774G>T	c.(772-774)ctG>ctT	p.L258L	TYSND1_ENST00000494143.1_5'Flank|TYSND1_ENST00000335494.5_Silent_p.L258L	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	258					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CGGTGCCGGGCAGGCAGCGTG	0.721													C|||	1936	0.386581	0.1679	0.513	5008	,	,		13548	0.5327		0.4115	False		,,,				2504	0.4162				p.L258L		Atlas-SNP	.											.	TYSND1	20	.	0			c.G774T						PASS	.	C	,	604,2414		129,346,1034	2.0	3.0	3.0		774,774	1.5	1.0	10	dbSNP_107	3	2435,3707		602,1231,1238	no	coding-synonymous,coding-synonymous	TYSND1	NM_001040273.1,NM_173555.2	,	731,1577,2272	AA,AC,CC		39.6451,20.0133,33.1769	,	258/399,258/567	71905569	3039,6121	1509	3071	4580	SO:0001819	synonymous_variant	219743	exon1			GCCGGGCAGGCAG	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.774G>T	10.37:g.71905569C>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_173555	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Silent	SNP	ENST00000287078.6	37	CCDS31213.1																																																																																			C|0.608;A|0.392	0.392	strong		0.721	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555	
ANKFN1	162282	hgsc.bcm.edu	37	17	54450038	54450038	+	Silent	SNP	C	C	A	rs957724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:54450038C>A	ENST00000318698.2	+	6	677	c.642C>A	c.(640-642)ctC>ctA	p.L214L	ANKFN1_ENST00000566473.2_Silent_p.L214L	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	214										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						CAATGCACCTCAACACACTGG	0.483													C|||	3083	0.615615	0.2005	0.755	5008	,	,		18502	0.9573		0.7038	False		,,,				2504	0.635				p.L214L		Atlas-SNP	.											.	ANKFN1	115	.	0			c.C642A						PASS	.	C		1197,3209	417.6+/-338.0	146,905,1152	125.0	121.0	122.0		642	1.3	0.8	17	dbSNP_86	122	5770,2830	675.7+/-403.2	1935,1900,465	no	coding-synonymous	ANKFN1	NM_153228.2		2081,2805,1617	AA,AC,CC		32.907,27.1675,46.4324		214/764	54450038	6967,6039	2203	4300	6503	SO:0001819	synonymous_variant	162282	exon6			GCACCTCAACACA	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.642C>A	17.37:g.54450038C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	67	27	0.402985	NM_153228		Silent	SNP	ENST00000318698.2	37	CCDS32686.1																																																																																			C|0.416;A|0.584	0.584	strong		0.483	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	
FBXL16	146330	hgsc.bcm.edu	37	16	746884	746884	+	Silent	SNP	A	A	C	rs4984683	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:746884A>C	ENST00000397621.1	-	2	853	c.522T>G	c.(520-522)gtT>gtG	p.V174V	FBXL16_ENST00000562563.1_5'Flank|FBXL16_ENST00000324361.5_Silent_p.V174V|FBXL16_ENST00000562585.1_5'Flank	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	174										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				CGGAGACGCCAACCAGGCAGA	0.577													A|||	1924	0.384185	0.2095	0.3833	5008	,	,		8611	0.7123		0.2565	False		,,,				2504	0.4141				p.V174V		Atlas-SNP	.											.	FBXL16	25	.	0			c.T522G						PASS	.	A		842,3558	328.5+/-300.6	87,668,1445	88.0	77.0	80.0		522	-7.7	0.2	16	dbSNP_111	80	1907,6691	337.1+/-322.1	205,1497,2597	no	coding-synonymous	FBXL16	NM_153350.3		292,2165,4042	CC,CA,AA		22.1796,19.1364,21.1494		174/480	746884	2749,10249	2200	4299	6499	SO:0001819	synonymous_variant	146330	exon2			GACGCCAACCAGG	BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"""F-boxes / Leucine-rich repeats"""	14150	protein-coding gene	gene with protein product		609082	"""chromosome 16 open reading frame 22"""	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.522T>G	16.37:g.746884A>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_153350	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Silent	SNP	ENST00000397621.1	37	CCDS10421.1																																																																																			A|0.718;C|0.282	0.282	strong		0.577	FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350	
PKP3	11187	hgsc.bcm.edu	37	11	404317	404317	+	Silent	SNP	C	C	T	rs1134578	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:404317C>T	ENST00000331563.2	+	12	2428	c.2352C>T	c.(2350-2352)ttC>ttT	p.F784F		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	784					desmosome assembly (GO:0002159)|establishment of protein localization to plasma membrane (GO:0090002)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|desmosome (GO:0030057)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)			breast(1)|central_nervous_system(1)|endometrium(3)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ACCGTGACTTCCGGGCGGTAC	0.667													c|||	2261	0.451478	0.3147	0.5893	5008	,	,		17904	0.3542		0.5586	False		,,,				2504	0.5286				p.F784F		Atlas-SNP	.											.	PKP3	36	.	0			c.C2352T						PASS	.	C		1609,2781	490.6+/-361.9	294,1021,880	64.0	60.0	61.0		2352	3.4	1.0	11	dbSNP_86	61	4798,3776	611.5+/-395.8	1350,2098,839	no	coding-synonymous	PKP3	NM_007183.2		1644,3119,1719	TT,TC,CC		44.0401,36.6515,49.4215		784/798	404317	6407,6557	2195	4287	6482	SO:0001819	synonymous_variant	11187	exon12			TGACTTCCGGGCG	Z98265	CCDS7695.1	11p15	2013-02-14			ENSG00000184363	ENSG00000184363		"""Armadillo repeat containing"""	9025	protein-coding gene	gene with protein product		605561				10374265	Standard	XM_005252760		Approved		uc001lpc.3	Q9Y446	OTTHUMG00000119068	ENST00000331563.2:c.2352C>T	11.37:g.404317C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	37	CCDS7695.1	956	0.43772893772893773	139	0.28252032520325204	201	0.5552486187845304	200	0.34965034965034963	416	0.5488126649076517	c	8.024	0.760279	0.15914	0.366515	0.559599	ENSG00000184363	ENST00000525642	.	.	.	4.28	3.36	0.38483	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.50056	-0.8872	3	.	.	.	-26.8957	9.5666	0.39402	0.0:0.827:0.0:0.173	rs1134578;rs3088021;rs3196808;rs11545916;rs12420261;rs17348549;rs17844819;rs17857527;rs56710170;rs1134578	.	.	.	F	44	.	.	S	+	2	0	PKP3	394317	1.000000	0.71417	1.000000	0.80357	0.535000	0.34838	2.547000	0.45786	0.931000	0.37242	0.313000	0.20887	TCC	C|0.528;T|0.472	0.472	strong		0.667	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183	
AKNAD1	254268	hgsc.bcm.edu	37	1	109394978	109394978	+	Silent	SNP	G	G	A	rs17563390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109394978G>A	ENST00000370001.3	-	2	577	c.309C>T	c.(307-309)gaC>gaT	p.D103D	AKNAD1_ENST00000369995.3_Silent_p.D103D|AKNAD1_ENST00000357393.4_Intron|AKNAD1_ENST00000369994.1_Silent_p.D103D	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	103						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						ACTTAGAAGCGTCTCCTTCAT	0.403													G|||	626	0.125	0.1528	0.1095	5008	,	,		18682	0.1369		0.1402	False		,,,				2504	0.0706				p.D103D		Atlas-SNP	.											.	AKNAD1	83	.	0			c.C309T						PASS	.	G		677,3729	288.1+/-279.7	50,577,1576	105.0	104.0	104.0		309	-7.9	0.0	1	dbSNP_123	104	1225,7375	246.7+/-275.0	72,1081,3147	no	coding-synonymous	AKNAD1	NM_152763.3		122,1658,4723	AA,AG,GG		14.2442,15.3654,14.624		103/837	109394978	1902,11104	2203	4300	6503	SO:0001819	synonymous_variant	254268	exon2			AGAAGCGTCTCCT	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.309C>T	1.37:g.109394978G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Silent	SNP	ENST00000370001.3	37	CCDS791.2																																																																																			G|0.858;A|0.142	0.142	strong		0.403	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
HDAC4	9759	hgsc.bcm.edu	37	2	240036959	240036959	+	Silent	SNP	C	C	T	rs79199572	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:240036959C>T	ENST00000345617.3	-	13	2357	c.1566G>A	c.(1564-1566)ccG>ccA	p.P522P	HDAC4_ENST00000543185.1_Silent_p.P106P|HDAC4_ENST00000541256.1_Silent_p.P496P	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	522					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CCGTCTCCTCCGGGTGGCTCT	0.677													C|||	92	0.0183706	0.0015	0.0216	5008	,	,		16923	0.0		0.0547	False		,,,				2504	0.0204				p.P522P		Atlas-SNP	.											.	HDAC4	127	.	0			c.G1566A						PASS	.	C		39,4367	39.2+/-71.8	0,39,2164	40.0	48.0	45.0		1566	-6.5	0.6	2	dbSNP_132	45	495,8105	135.1+/-192.4	13,469,3818	no	coding-synonymous	HDAC4	NM_006037.3		13,508,5982	TT,TC,CC		5.7558,0.8852,4.1058		522/1085	240036959	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon13			CTCCTCCGGGTGG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1566G>A	2.37:g.240036959C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	67	42	0.626866	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			C|0.968;T|0.032	0.032	strong		0.677	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
C10orf11	83938	hgsc.bcm.edu	37	10	77807027	77807027	+	Silent	SNP	T	T	C	rs1898071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:77807027T>C	ENST00000372499.1	+	3	495	c.280T>C	c.(280-282)Ttg>Ctg	p.L94L	C10orf11_ENST00000593699.1_3'UTR	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	94					melanocyte differentiation (GO:0030318)					endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					GCTGGTCAGCTTGGAAAAGGA	0.502													T|||	1488	0.297125	0.4266	0.3055	5008	,	,		21008	0.0119		0.4384	False		,,,				2504	0.2648				p.L94L		Atlas-SNP	.											.	C10orf11	19	.	0			c.T280C						PASS	.	T		1905,2501	545.5+/-376.8	409,1087,707	88.0	81.0	83.0		280	2.6	1.0	10	dbSNP_92	83	3950,4650	547.6+/-385.2	907,2136,1257	no	coding-synonymous	C10orf11	NM_032024.3		1316,3223,1964	CC,CT,TT		45.9302,43.2365,45.0177		94/199	77807027	5855,7151	2203	4300	6503	SO:0001819	synonymous_variant	83938	exon3			GTCAGCTTGGAAA	AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655			23405	protein-coding gene	gene with protein product	"""oculocutaneous albinism 7, autosomal recessive"""	614537				23395477	Standard	NM_032024		Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.280T>C	10.37:g.77807027T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_032024	B1AVW6	Silent	SNP	ENST00000372499.1	37	CCDS7351.1																																																																																			T|0.608;C|0.392	0.392	strong		0.502	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048839.1	NM_032024	
XPC	7508	hgsc.bcm.edu	37	3	14193889	14193889	+	Silent	SNP	C	C	T	rs2227998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14193889C>T	ENST00000285021.7	-	11	2275	c.2061G>A	c.(2059-2061)agG>agA	p.R687R	XPC_ENST00000449060.2_Silent_p.R650R	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	687	DNA-binding; preference for heteroduplex DNA.|Interaction with RAD23B.|Minimal sensor domain involved in damage recognition.				DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GCCACGTGTCCCTGGAATGCA	0.572			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	1179	0.235423	0.3343	0.2637	5008	,	,		20346	0.0327		0.2396	False		,,,				2504	0.2863				p.R687R		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	.	XPC	60	.	0			c.G2061A						PASS	.	C	,	1164,2980		169,826,1077	102.0	108.0	106.0		1950,2061	5.1	1.0	3	dbSNP_98	106	2178,6250		292,1594,2328	no	coding-synonymous,coding-synonymous	XPC	NM_001145769.1,NM_004628.4	,	461,2420,3405	TT,TC,CC		25.8424,28.0888,26.5829	,	650/904,687/941	14193889	3342,9230	2072	4214	6286	SO:0001819	synonymous_variant	7508	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CGTGTCCCTGGAA		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.2061G>A	3.37:g.14193889C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	121	67	0.553719	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Silent	SNP	ENST00000285021.7	37	CCDS46763.1	470	0.21520146520146521	176	0.35772357723577236	97	0.26795580110497236	17	0.02972027972027972	180	0.23746701846965698	C	3.544	-0.093045	0.07053	0.280888	0.258424	ENSG00000154767	ENST00000538683	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.28459	-1.0043	3	.	.	.	-14.0125	13.3993	0.60872	0.1573:0.8427:0.0:0.0	rs2227998;rs3731151;rs17562799;rs17851403	.	.	.	R	130	.	.	G	-	1	0	XPC	14168890	0.996000	0.38824	1.000000	0.80357	0.388000	0.30384	2.326000	0.43849	2.342000	0.79632	0.563000	0.77884	GGA	T|0.221;G|0.000;C|0.778	0.221	strong		0.572	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
LARP1B	55132	hgsc.bcm.edu	37	4	129100643	129100643	+	Missense_Mutation	SNP	G	G	A	rs12645577	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:129100643G>A	ENST00000326639.6	+	15	2190	c.1979G>A	c.(1978-1980)cGt>cAt	p.R660H	LARP1B_ENST00000354456.3_Missense_Mutation_p.R79H|LARP1B_ENST00000506199.1_3'UTR|LARP1B_ENST00000441387.1_Missense_Mutation_p.R660H|LARP1B_ENST00000264584.5_Missense_Mutation_p.R601H	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	660			R -> H (in dbSNP:rs12645577). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TCCAGAGACCGTGGGCCAGGA	0.373													A|||	2852	0.569489	0.3306	0.6758	5008	,	,		16772	0.5218		0.6769	False		,,,				2504	0.7556				p.R660H		Atlas-SNP	.											.	LARP1B	120	.	0			c.G1979A						PASS	.	A	HIS/ARG	1787,2619	641.3+/-397.4	361,1065,777	143.0	150.0	148.0		1979	4.2	0.8	4	dbSNP_120	148	5718,2882	453.3+/-363.2	1918,1882,500	yes	missense	LARP1B	NM_018078.2	29	2279,2947,1277	AA,AG,GG		33.5116,40.5583,42.2959	benign	660/915	129100643	7505,5501	2203	4300	6503	SO:0001583	missense	55132	exon15			GAGACCGTGGGCC		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"""La ribonucleoprotein domain containing"""	24704	protein-coding gene	gene with protein product			"""La ribonucleoprotein domain family, member 2"""	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.1979G>A	4.37:g.129100643G>A	ENSP00000321997:p.Arg660His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_018078	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	37	CCDS3738.1	1186	0.543040293040293	171	0.3475609756097561	244	0.6740331491712708	257	0.4493006993006993	514	0.6781002638522428	A	0.154	-1.087992	0.01873	0.405583	0.664884	ENSG00000138709	ENST00000326639;ENST00000264584;ENST00000441387;ENST00000354456	T;T;T;T	0.39787	2.21;2.18;2.21;1.06	4.16	4.16	0.48862	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00015	-2.89	0.40696	P	0.017550999999999983	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46624	-0.9178	9	0.02654	T	1	.	9.6091	0.39652	0.9165:0.0:0.0835:0.0	rs12645577;rs17846606;rs17859689;rs52828591;rs57853702;rs12645577	79;660	Q659C4-5;Q659C4	.;LAR1B_HUMAN	H	660;601;660;79	ENSP00000321997:R660H;ENSP00000264584:R601H;ENSP00000396521:R660H;ENSP00000346444:R79H	ENSP00000264584:R601H	R	+	2	0	LARP1B	129320093	1.000000	0.71417	0.838000	0.33150	0.023000	0.10783	5.071000	0.64382	0.645000	0.30675	-0.516000	0.04426	CGT	G|0.447;A|0.553	0.553	strong		0.373	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078	
BTBD6	90135	hgsc.bcm.edu	37	14	105716377	105716377	+	Silent	SNP	C	C	T	rs45452103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105716377C>T	ENST00000392554.3	+	4	1123	c.826C>T	c.(826-828)Ctg>Ttg	p.L276L	BTBD6_ENST00000463376.2_Silent_p.L201L|BRF1_ENST00000392557.4_5'Flank|BTBD6_ENST00000327471.3_Silent_p.L201L|BRF1_ENST00000446501.2_5'Flank|BRF1_ENST00000440513.3_Intron|BTBD6_ENST00000536364.1_Silent_p.L276L|BRF1_ENST00000379932.4_5'Flank|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000551787.1_5'Flank|BRF1_ENST00000546474.1_Intron|BRF1_ENST00000379937.2_Intron			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	276						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		GAGGCATGTTCTGGGGCGAGC	0.607													C|||	43	0.00858626	0.0008	0.0159	5008	,	,		18651	0.0		0.0229	False		,,,				2504	0.0082				p.L276L		Atlas-SNP	.											.	BTBD6	24	.	0			c.C826T						PASS	.	C	,,,,	16,4386		0,16,2185	49.0	48.0	48.0		,,,,826	-6.2	0.0	14	dbSNP_127	48	217,8371		3,211,4080	no	intron,intron,intron,intron,coding-synonymous	BRF1,BTBD6	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001519.3,NM_033271.2	,,,,	3,227,6265	TT,TC,CC		2.5268,0.3635,1.7937	,,,,	,,,,276/486	105716377	233,12757	2201	4294	6495	SO:0001819	synonymous_variant	90135	exon5			CATGTTCTGGGGC	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"""BTB/POZ domain containing"""	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.826C>T	14.37:g.105716377C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_033271	Q8IVQ7|Q9BR94	Silent	SNP	ENST00000392554.3	37	CCDS10002.2																																																																																			C|0.983;T|0.017	0.017	strong		0.607	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4		
FGF9	2254	hgsc.bcm.edu	37	13	22275394	22275394	+	Silent	SNP	A	A	G	rs9509841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:22275394A>G	ENST00000382353.5	+	3	977	c.447A>G	c.(445-447)tcA>tcG	p.S149S	FGF9_ENST00000478546.1_3'UTR	NM_002010.2	NP_002001.1	P31371	FGF9_HUMAN	fibroblast growth factor 9	149					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic digestive tract development (GO:0048566)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein import into nucleus (GO:0006606)|regulation of timing of cell differentiation (GO:0048505)|signal transduction (GO:0007165)|substantia nigra development (GO:0021762)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|skin(2)	9		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)		ATACGTACTCATCAAACCTAT	0.408													A|||	4169	0.832468	0.6339	0.8847	5008	,	,		17524	0.9603		0.8449	False		,,,				2504	0.9192				p.S149S	Melanoma(195;1939 2127 12623 13963 52730)	Atlas-SNP	.											.	FGF9	25	.	0			c.A447G						PASS	.	A		2928,1478	678.7+/-403.6	972,984,247	98.0	87.0	91.0		447	-1.5	0.9	13	dbSNP_119	91	7139,1461	750.8+/-407.4	2966,1207,127	no	coding-synonymous	FGF9	NM_002010.2		3938,2191,374	GG,GA,AA		16.9884,33.5452,22.5973		149/209	22275394	10067,2939	2203	4300	6503	SO:0001819	synonymous_variant	2254	exon3			GTACTCATCAAAC	D14838	CCDS9298.1	13q11-q12	2014-01-30	2013-06-18		ENSG00000102678	ENSG00000102678		"""Endogenous ligands"""	3687	protein-coding gene	gene with protein product	"""glia-activating factor"""	600921	"""fibroblast growth factor 9 (glia-activating factor)"""			8321227	Standard	NM_002010		Approved		uc001uog.2	P31371	OTTHUMG00000017412	ENST00000382353.5:c.447A>G	13.37:g.22275394A>G		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	241	241	1	NM_002010	A8K427|Q3SY32	Silent	SNP	ENST00000382353.5	37	CCDS9298.1																																																																																			A|0.203;G|0.797	0.797	strong		0.408	FGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046002.2		
ELF5	2001	hgsc.bcm.edu	37	11	34502345	34502345	+	Silent	SNP	T	T	C	rs2231828	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34502345T>C	ENST00000312319.2	-	6	904	c.675A>G	c.(673-675)acA>acG	p.T225T	ELF5_ENST00000429939.2_Silent_p.T120T|ELF5_ENST00000528709.1_5'Flank|ELF5_ENST00000257832.2_Silent_p.T215T	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	225					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				ACTTTTCATATGTCATTCTGT	0.398													C|||	961	0.191893	0.0333	0.2334	5008	,	,		15592	0.0288		0.4076	False		,,,				2504	0.3231				p.T225T	Melanoma(61;202 1660 4348 21594)	Atlas-SNP	.											.	ELF5	21	.	0			c.A675G						PASS	.	C	,	381,4023	791.1+/-415.1	26,329,1847	174.0	169.0	170.0		645,675	-11.4	0.0	11	dbSNP_98	170	3489,5107	633.6+/-398.7	718,2053,1527	no	coding-synonymous,coding-synonymous	ELF5	NM_001422.3,NM_198381.1	,	744,2382,3374	CC,CT,TT		40.5886,8.6512,29.7692	,	215/256,225/266	34502345	3870,9130	2202	4298	6500	SO:0001819	synonymous_variant	2001	exon6			TTCATATGTCATT	AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.675A>G	11.37:g.34502345T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	233	99	0.424893	NM_198381	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Silent	SNP	ENST00000312319.2	37	CCDS7892.1																																																																																			T|0.745;C|0.255	0.255	strong		0.398	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381	
MRPS11	64963	hgsc.bcm.edu	37	15	89011232	89011232	+	Silent	SNP	G	G	T	rs61741121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89011232G>T	ENST00000325844.4	+	2	424	c.159G>T	c.(157-159)gcG>gcT	p.A53A	MRPS11_ENST00000557974.1_3'UTR|MRPL46_ENST00000312475.4_5'Flank|MRPS11_ENST00000353598.6_Silent_p.A53A	NM_022839.3	NP_073750.2	P82912	RT11_HUMAN	mitochondrial ribosomal protein S11	53					DNA damage response, detection of DNA damage (GO:0042769)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(3)	3	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			AACAGAACGCGGCTCCCAGCC	0.637													G|||	32	0.00638978	0.0	0.0086	5008	,	,		16062	0.0		0.0209	False		,,,				2504	0.0051				p.A53A		Atlas-SNP	.											.	MRPS11	14	.	0			c.G159T						PASS	.	G	,	16,4378		0,16,2181	25.0	24.0	24.0		159,159	-6.4	0.0	15	dbSNP_129	24	184,8408		4,176,4116	no	coding-synonymous,coding-synonymous	MRPS11	NM_022839.3,NM_176805.2	,	4,192,6297	TT,TG,GG		2.1415,0.3641,1.5401	,	53/195,53/162	89011232	200,12786	2197	4296	6493	SO:0001819	synonymous_variant	64963	exon2			GAACGCGGCTCCC	AB051349	CCDS10342.1, CCDS10343.1	15q25	2012-09-13			ENSG00000181991	ENSG00000181991		"""Mitochondrial ribosomal proteins / small subunits"""	14050	protein-coding gene	gene with protein product	"""cervical cancer proto-oncogene 2"""	611977				11402041	Standard	NM_022839		Approved	FLJ23406, HCC-2, FLJ22512	uc002bml.3	P82912	OTTHUMG00000148678	ENST00000325844.4:c.159G>T	15.37:g.89011232G>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	192	100	0.520833	NM_176805	B2RD52|Q969D7|Q96GI3|Q9BYC3	Silent	SNP	ENST00000325844.4	37	CCDS10342.1																																																																																			G|0.990;T|0.010	0.010	strong		0.637	MRPS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309067.2	NM_022839	
HAGH	3029	hgsc.bcm.edu	37	16	1869147	1869147	+	Silent	SNP	G	G	A	rs56316151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1869147G>A	ENST00000397356.3	-	5	916	c.510C>T	c.(508-510)ccC>ccT	p.P170P	HAGH_ENST00000566709.1_Silent_p.P122P|HAGH_ENST00000455446.2_Intron|HAGH_ENST00000397353.2_Silent_p.P122P	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	170					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	CCGAGCCTCCGGGCTTGCTCA	0.627													G|||	53	0.0105831	0.0023	0.0173	5008	,	,		14613	0.0		0.0278	False		,,,				2504	0.0102				p.P170P	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.C510T						PASS	.	G	,	40,4356	42.3+/-75.8	0,40,2158	44.0	44.0	44.0		366,510	-6.6	0.0	16	dbSNP_129	44	332,8268	112.9+/-173.0	6,320,3974	no	coding-synonymous,coding-synonymous	HAGH	NM_001040427.1,NM_005326.4	,	6,360,6132	AA,AG,GG		3.8605,0.9099,2.8624	,	122/261,170/309	1869147	372,12624	2198	4300	6498	SO:0001819	synonymous_variant	3029	exon5			GCCTCCGGGCTTG	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"""hydroxyacyl glutathione hydrolase"""			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.510C>T	16.37:g.1869147G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			G|0.975;A|0.025	0.025	strong		0.627	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326	
HMGXB3	22993	hgsc.bcm.edu	37	5	149390148	149390148	+	Missense_Mutation	SNP	G	G	A	rs2241698	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:149390148G>A	ENST00000502717.1	+	4	1251	c.787G>A	c.(787-789)Gta>Ata	p.V263I	HMGXB3_ENST00000503427.1_Missense_Mutation_p.V263I	NM_014983.2	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	509					phosphorylation (GO:0016310)	nucleus (GO:0005634)	DNA binding (GO:0003677)|kinase activity (GO:0016301)			central_nervous_system(1)|endometrium(3)|kidney(3)|skin(2)	9						TGGGGAGAGTGTATCAGTGGT	0.512													G|||	572	0.114217	0.09	0.2579	5008	,	,		21250	0.1002		0.1292	False		,,,				2504	0.044				p.V263I		Atlas-SNP	.											.	HMGXB3	31	.	0			c.G787A						PASS	.	G	ILE/VAL	117,1267		4,109,579	10.0	11.0	11.0		787	1.7	0.9	5	dbSNP_98	11	360,2820		18,324,1248	yes	missense	HMGXB3	NM_014983.2	29	22,433,1827	AA,AG,GG		11.3208,8.4538,10.4514	benign	263/1293	149390148	477,4087	692	1590	2282	SO:0001583	missense	22993	exon4			GAGAGTGTATCAG	D83778	CCDS54935.1	5q33.1	2011-07-01		2009-01-05	ENSG00000113716	ENSG00000113716		"""High mobility group / Non-canonical"""	28982	protein-coding gene	gene with protein product				HMGX3		8724849	Standard	NM_014983		Approved	SMF, KIAA0194	uc003lrk.4	Q12766	OTTHUMG00000163493	ENST00000502717.1:c.787G>A	5.37:g.149390148G>A	ENSP00000421917:p.Val263Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	70	44	0.628571	NM_014983	G5E9Y4|Q86UG3|Q9UMF4	Missense_Mutation	SNP	ENST00000502717.1	37	CCDS54935.1	295	0.13507326007326007	52	0.10569105691056911	80	0.22099447513812154	69	0.12062937062937062	94	0.12401055408970976	G	11.69	1.714490	0.30413	0.084538	0.113208	ENSG00000113716	ENST00000503427;ENST00000502717	.	.	.	5.91	1.74	0.24563	.	0.581569	0.19816	N	0.105425	T	0.00012	0.0000	L	0.44542	1.39	0.50467	P	1.2500000000004174E-4	B	0.13594	0.008	B	0.08055	0.003	T	0.13683	-1.0500	8	0.87932	D	0	-4.5868	1.4062	0.02281	0.1925:0.1287:0.403:0.2759	rs2241698;rs61145259;rs2241698	509	Q12766	HMGX3_HUMAN	I	263	.	ENSP00000421917:V263I	V	+	1	0	HMGXB3	149370341	0.352000	0.24895	0.888000	0.34837	0.974000	0.67602	0.359000	0.20233	0.017000	0.15025	0.655000	0.94253	GTA	G|0.869;A|0.131	0.131	strong		0.512	HMGXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373771.1	XM_001717202	
PTPRH	5794	hgsc.bcm.edu	37	19	55708573	55708573	+	Silent	SNP	G	G	A	rs2288520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55708573G>A	ENST00000376350.3	-	9	1924	c.1902C>T	c.(1900-1902)gcC>gcT	p.A634A	PTPRH_ENST00000263434.5_Silent_p.A456A|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	634	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CGGGTTCCAGGGCCTCCACTT	0.587													G|||	346	0.0690895	0.0151	0.0706	5008	,	,		18796	0.0536		0.1262	False		,,,				2504	0.0982				p.A634A		Atlas-SNP	.											.	PTPRH	139	.	0			c.C1902T						PASS	.	G	,	121,4285	91.6+/-130.3	2,117,2084	122.0	104.0	110.0		1368,1902	0.5	0.0	19	dbSNP_100	110	980,7620	212.5+/-252.8	53,874,3373	no	coding-synonymous,coding-synonymous	PTPRH	NM_001161440.1,NM_002842.3	,	55,991,5457	AA,AG,GG		11.3953,2.7463,8.4653	,	456/938,634/1116	55708573	1101,11905	2203	4300	6503	SO:0001819	synonymous_variant	5794	exon9			TTCCAGGGCCTCC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.1902C>T	19.37:g.55708573G>A		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	278	157	0.564748	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	37	CCDS33110.1																																																																																			G|0.925;A|0.075	0.075	strong		0.587	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
CR1L	1379	hgsc.bcm.edu	37	1	207850879	207850879	+	Silent	SNP	C	C	T	rs34509370	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207850879C>T	ENST00000508064.2	+	2	303	c.243C>T	c.(241-243)aaC>aaT	p.N81N	CR1L_ENST00000530905.1_3'UTR	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	81	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GCCTAAAAAACTCAGTCTGGA	0.423													N|||	535	0.106829	0.034	0.1441	5008	,	,		18366	0.0327		0.2525	False		,,,				2504	0.1053				p.N81N		Atlas-SNP	.											.	CR1L	97	.	0			c.C243T						PASS	.	C		256,3420		14,228,1596	186.0	167.0	173.0		243	-0.5	0.0	1	dbSNP_126	173	2160,6006		280,1600,2203	no	coding-synonymous	CR1L	NM_175710.1		294,1828,3799	TT,TC,CC		26.4511,6.9641,20.402		81/570	207850879	2416,9426	1838	4083	5921	SO:0001819	synonymous_variant	1379	exon2			AAAAAACTCAGTC	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.243C>T	1.37:g.207850879C>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	226	108	0.477876	NM_175710	Q32MC9|Q8NEU7	Silent	SNP	ENST00000508064.2	37	CCDS44310.1																																																																																			C|0.836;T|0.164	0.164	strong		0.423	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
NCR1	9437	hgsc.bcm.edu	37	19	55418054	55418054	+	Missense_Mutation	SNP	A	A	C	rs2278428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55418054A>C	ENST00000291890.4	+	3	282	c.244A>C	c.(244-246)Aaa>Caa	p.K82Q	NCR1_ENST00000598576.1_Missense_Mutation_p.K70Q|NCR1_ENST00000338835.5_Missense_Mutation_p.K82Q|NCR1_ENST00000350790.5_Intron|NCR1_ENST00000447255.1_Missense_Mutation_p.K82Q|NCR1_ENST00000594765.1_Missense_Mutation_p.K82Q|NCR1_ENST00000357397.5_Intron	NM_004829.5	NP_004820.2	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	82	Ig-like 1.		K -> Q (in dbSNP:rs2278428).		cellular defense response (GO:0006968)|intracellular signal transduction (GO:0035556)|natural killer cell activation (GO:0030101)|regulation of natural killer cell mediated cytotoxicity (GO:0042269)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|SWI/SNF complex (GO:0016514)	receptor signaling protein activity (GO:0005057)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		TAACAAAGTCAAATTCTACAT	0.517													.|||	885	0.176717	0.0212	0.1902	5008	,	,		19990	0.37		0.0825	False		,,,				2504	0.2751				p.K82Q		Atlas-SNP	.											.	NCR1	60	.	0			c.A244C						PASS	.	A	GLN/LYS,GLN/LYS,,,GLN/LYS	140,4266	100.3+/-138.9	3,134,2066	71.0	75.0	73.0		244,244,,,244	-1.0	0.0	19	dbSNP_100	73	714,7886	174.8+/-225.0	35,644,3621	yes	missense,missense,intron,intron,missense	NCR1	NM_001145457.1,NM_001145458.1,NM_001242356.1,NM_001242357.1,NM_004829.5	53,53,,,53	38,778,5687	CC,CA,AA		8.3023,3.1775,6.5662	benign,benign,,,benign	82/304,82/288,,,82/305	55418054	854,12152	2203	4300	6503	SO:0001583	missense	9437	exon3			AAAGTCAAATTCT	AJ001383	CCDS12911.1, CCDS46181.1, CCDS46182.1, CCDS56103.1	19q13.42	2013-09-20	2002-11-13	2002-11-15	ENSG00000189430	ENSG00000189430		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6731	protein-coding gene	gene with protein product		604530	"""lymphocyte antigen 94 (mouse) homolog (activating NK-receptor; NK-p46)"""	LY94		9730896	Standard	NM_001145457		Approved	NK-p46, NKP46, CD335	uc002qib.2	O76036	OTTHUMG00000183212	ENST00000291890.4:c.244A>C	19.37:g.55418054A>C	ENSP00000291890:p.Lys82Gln	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_001145458	B0V3L2|B0V3L3|B0V3L4|B0V3L5|B8JL03|O76016|O76017|O76018	Missense_Mutation	SNP	ENST00000291890.4	37	CCDS12911.1	351	0.16071428571428573	20	0.04065040650406504	50	0.13812154696132597	219	0.38286713286713286	62	0.08179419525065963	A	5.939	0.357282	0.11239	0.031775	0.083023	ENSG00000189430	ENST00000291890;ENST00000447255;ENST00000338835	T;T;T	0.09630	2.96;2.96;2.96	3.74	-1.05	0.10036	Immunoglobulin-like fold (1);	2.117220	0.01876	N	0.037536	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.28439	0.059;0.003;0.212	B;B;B	0.29440	0.031;0.002;0.102	T	0.45862	-0.9232	9	0.16896	T	0.51	.	1.5695	0.02612	0.384:0.3464:0.1016:0.168	rs2278428;rs17814584;rs60743772;rs2278428	82;82;82	B0V3L5;O76036-6;O76036	.;.;NCTR1_HUMAN	Q	82	ENSP00000291890:K82Q;ENSP00000404434:K82Q;ENSP00000339515:K82Q	ENSP00000291890:K82Q	K	+	1	0	NCR1	60109866	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.952000	0.03881	-0.318000	0.08665	-0.421000	0.06004	AAA	A|0.889;C|0.111	0.111	strong		0.517	NCR1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465680.1		
DNAH3	55567	hgsc.bcm.edu	37	16	21008690	21008690	+	Silent	SNP	T	T	C	rs3115446	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:21008690T>C	ENST00000261383.3	-	44	6515	c.6516A>G	c.(6514-6516)aaA>aaG	p.K2172K	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2172	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TTGTGTCTTTTTTGTCAAACC	0.562													C|||	2705	0.540136	0.5976	0.5259	5008	,	,		20850	0.4851		0.4543	False		,,,				2504	0.6176				p.K2172K		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A6516G						PASS	.	C		2605,1797	528.4+/-372.4	773,1059,369	128.0	118.0	122.0		6516	2.2	1.0	16	dbSNP_103	122	3841,4759	609.9+/-395.6	857,2127,1316	no	coding-synonymous	DNAH3	NM_017539.1		1630,3186,1685	CC,CT,TT		44.6628,40.8224,49.577		2172/4117	21008690	6446,6556	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon44			GTCTTTTTTGTCA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.6516A>G	16.37:g.21008690T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	212	106	0.5	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			C|0.498;N|0.000	0.498	strong		0.562	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
MERTK	10461	hgsc.bcm.edu	37	2	112765973	112765973	+	Silent	SNP	A	A	G	rs1131244	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:112765973A>G	ENST00000295408.4	+	14	2138	c.1881A>G	c.(1879-1881)tcA>tcG	p.S627S	MERTK_ENST00000409780.1_Silent_p.S451S|MERTK_ENST00000421804.2_Silent_p.S627S			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	627	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						ACAACTCTTCACAGCGGGAGA	0.448													G|||	2580	0.515176	0.4992	0.5951	5008	,	,		19421	0.2738		0.6243	False		,,,				2504	0.6166				p.S627S		Atlas-SNP	.											.	MERTK	112	.	0			c.A1881G						PASS	.	G		2277,2129	579.1+/-384.8	581,1115,507	95.0	88.0	90.0		1881	-11.9	0.0	2	dbSNP_86	90	5368,3232	486.5+/-371.9	1694,1980,626	no	coding-synonymous	MERTK	NM_006343.2		2275,3095,1133	GG,GA,AA		37.5814,48.3205,41.2194		627/1000	112765973	7645,5361	2203	4300	6503	SO:0001819	synonymous_variant	10461	exon14			CTCTTCACAGCGG	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1881A>G	2.37:g.112765973A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																			A|0.458;G|0.542	0.542	strong		0.448	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
MUC4	4585	hgsc.bcm.edu	37	3	195507927	195507927	+	Silent	SNP	G	G	A	rs201230361	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507927G>A	ENST00000463781.3	-	2	10983	c.10524C>T	c.(10522-10524)acC>acT	p.T3508T	MUC4_ENST00000475231.1_Silent_p.T3508T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGCGCCGGTGACAGGAA	0.602																																					p.T3508T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C10524T						PASS	.						40.0	35.0	37.0					3																	195507927		644	1582	2226	SO:0001819	synonymous_variant	4585	exon2			AGCGCCGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10524C>T	3.37:g.195507927G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	557	149	0.267504	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.941;T|0.059	.	alt		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs200267449		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41351321C>T	ENST00000301141.5	-	7	1059	c.1039G>A	c.(1039-1041)Gcc>Acc	p.A347T	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	347					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GGCATCTTGGCCCGGTCCTCA	0.537																																					p.A347T		Atlas-SNP	.											.	CYP2A6	69	.	0			c.G1039A						PASS	.						115.0	104.0	108.0					19																	41351321		2203	4300	6503	SO:0001583	missense	1548	exon7			TCTTGGCCCGGTC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1039G>A	19.37:g.41351321C>T	ENSP00000301141:p.Ala347Thr	Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	368	44	0.119565	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	4.025	0.002161	0.07819	.	.	ENSG00000255974	ENST00000301141	T	0.69306	-0.39	2.76	-2.87	0.05700	.	0.614141	0.16066	U	0.231229	T	0.43853	0.1266	L	0.31120	0.905	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.17319	-1.0373	10	0.22706	T	0.39	.	4.9051	0.13795	0.0:0.2915:0.1649:0.5436	.	347;347	Q13120;P11509	.;CP2A6_HUMAN	T	347	ENSP00000301141:A347T	ENSP00000301141:A347T	A	-	1	0	CYP2A6	46043161	0.000000	0.05858	0.011000	0.14972	0.659000	0.38960	-1.191000	0.03055	-0.603000	0.05767	-0.912000	0.02778	GCC	C|0.500;T|0.500	0.500	strong		0.537	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
FBP1	2203	hgsc.bcm.edu	37	9	97369151	97369151	+	Silent	SNP	G	G	A	rs1042144|rs386736436	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:97369151G>A	ENST00000375326.4	-	5	847	c.651C>T	c.(649-651)gcC>gcT	p.A217A	FBP1_ENST00000415431.1_Silent_p.A217A	NM_000507.3	NP_000498.2	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	217					carbohydrate metabolic process (GO:0005975)|cellular response to drug (GO:0035690)|cellular response to magnesium ion (GO:0071286)|dephosphorylation (GO:0016311)|fructose 6-phosphate metabolic process (GO:0006002)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|negative regulation of cell growth (GO:0030308)|negative regulation of glycolytic process (GO:0045820)|negative regulation of Ras protein signal transduction (GO:0046580)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	AMP binding (GO:0016208)|fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|monosaccharide binding (GO:0048029)			kidney(1)|liver(1)|lung(1)	3		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	CAAAGTCCCTGGCGTAGCCCT	0.522													G|||	1765	0.352436	0.2716	0.2046	5008	,	,		20345	0.5496		0.3499	False		,,,				2504	0.3661				p.A217A	Ovarian(142;590 2466 25593 44496)	Atlas-SNP	.											.	FBP1	13	.	0			c.C651T						PASS	.	G	,	1229,3177	426.4+/-341.1	164,901,1138	120.0	109.0	113.0		651,651	3.6	1.0	9	dbSNP_86	113	2822,5778	445.1+/-360.9	456,1910,1934	no	coding-synonymous,coding-synonymous	FBP1	NM_000507.3,NM_001127628.1	,	620,2811,3072	AA,AG,GG		32.814,27.8938,31.1472	,	217/339,217/339	97369151	4051,8955	2203	4300	6503	SO:0001819	synonymous_variant	2203	exon5			GTCCCTGGCGTAG	M19922	CCDS6712.1	9q22.3	2012-08-13			ENSG00000165140	ENSG00000165140	3.1.3.11		3606	protein-coding gene	gene with protein product		611570		FBP		8387495	Standard	NM_000507		Approved		uc004auw.4	P09467	OTTHUMG00000020268	ENST00000375326.4:c.651C>T	9.37:g.97369151G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	182	85	0.467033	NM_000507	O75571|Q53F94|Q96E46	Silent	SNP	ENST00000375326.4	37	CCDS6712.1																																																																																			T|0.000;G|0.682;A|0.318	0.318	strong		0.522	FBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053187.1	NM_000507	
RBMXL3	139804	hgsc.bcm.edu	37	X	114424597	114424597	+	Missense_Mutation	SNP	G	G	A	rs12009026		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:114424597G>A	ENST00000424776.3	+	1	635	c.593G>A	c.(592-594)cGc>cAc	p.R198H	LRCH2_ENST00000317135.8_Intron|LRCH2_ENST00000538422.1_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	198							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						CAGCCACGGCGCTGGGCCGGC	0.697													g|||	452	0.119735	0.0862	0.1095	3775	,	,		10243	0.0694		0.0567	False		,,,				2504	0.138				p.R198H		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G593A						PASS	.						6.0	11.0	9.0					X																	114424597		649	1530	2179	SO:0001583	missense	139804	exon1			CACGGCGCTGGGC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.593G>A	X.37:g.114424597G>A	ENSP00000417451:p.Arg198His	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	37	CCDS55478.1	178	0.10729355033152502	54	0.1111111111111111	22	0.06470588235294118	34	0.061371841155234655	46	0.0625	g	11.20	1.567540	0.28003	.	.	ENSG00000175718	ENST00000424776	T	0.04234	3.67	0.776	-0.407	0.12385	.	.	.	.	.	T	0.00073	0.0002	L	0.43923	1.385	0.80722	P	0.0	P	0.43287	0.802	B	0.20955	0.032	T	0.45205	-0.9277	8	0.87932	D	0	.	2.47	0.04562	0.269:0.315:0.416:0.0	rs12009026	198	Q8N7X1	RMXL3_HUMAN	H	198	ENSP00000417451:R198H	ENSP00000417451:R198H	R	+	2	0	RBMXL3	114330853	0.118000	0.22208	0.000000	0.03702	0.006000	0.05464	0.046000	0.14035	-0.246000	0.09611	0.183000	0.17082	CGC	G|0.891;A|0.109	0.109	strong		0.697	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
SPTAN1	6709	hgsc.bcm.edu	37	9	131379967	131379967	+	Silent	SNP	C	C	T	rs2227862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131379967C>T	ENST00000372731.4	+	41	5501	c.5391C>T	c.(5389-5391)acC>acT	p.T1797T	SPTAN1_ENST00000372739.3_Silent_p.T1802T|SPTAN1_ENST00000358161.5_Silent_p.T1802T	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1797					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GGGACCTAACCGGCGTGCAGA	0.592													C|||	3090	0.617013	0.3321	0.781	5008	,	,		17313	0.5139		0.8827	False		,,,				2504	0.7188				p.T1802T	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.C5406T						PASS	.	C	,,	1760,2646	523.1+/-371.0	348,1064,791	58.0	61.0	60.0		5406,5331,5391	-11.5	0.1	9	dbSNP_98	60	7771,829	781.1+/-407.6	3519,733,48	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	3867,1797,839	TT,TC,CC		9.6395,39.9455,26.7184	,,	1802/2478,1777/2453,1797/2473	131379967	9531,3475	2203	4300	6503	SO:0001819	synonymous_variant	6709	exon42			CCTAACCGGCGTG	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.5391C>T	9.37:g.131379967C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			A|0.099;C|0.234;G|0.085;N|0.000;T|0.582	0.582	strong		0.592	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
ZNF248	57209	hgsc.bcm.edu	37	10	38120720	38120720	+	Silent	SNP	C	C	T	rs1779132	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:38120720C>T	ENST00000395867.3	-	6	2113	c.1563G>A	c.(1561-1563)aaG>aaA	p.K521K	ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000357328.4_Silent_p.K521K|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000494133.1_Intron	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						ATTCATTACACTTATATGGTT	0.413													C|||	158	0.0315495	0.0015	0.0648	5008	,	,		20360	0.0		0.1024	False		,,,				2504	0.0082				p.K521K		Atlas-SNP	.											.	ZNF248	61	.	0			c.G1563A						PASS	.	C		79,4327	69.2+/-107.0	1,77,2125	115.0	107.0	110.0		1563	-0.5	1.0	10	dbSNP_89	110	756,7842	181.0+/-229.8	32,692,3575	no	coding-synonymous	ZNF248	NM_021045.1		33,769,5700	TT,TC,CC		8.7927,1.793,6.4211		521/580	38120720	835,12169	2203	4299	6502	SO:0001819	synonymous_variant	57209	exon6			ATTACACTTATAT	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1563G>A	10.37:g.38120720C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_001267597	Q8NDV8|Q9UMP3	Silent	SNP	ENST00000395867.3	37	CCDS7194.1																																																																																			C|0.937;T|0.063	0.063	strong		0.413	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
NOB1	28987	hgsc.bcm.edu	37	16	69782855	69782855	+	Missense_Mutation	SNP	C	C	T	rs3811348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:69782855C>T	ENST00000268802.5	-	6	721	c.692G>A	c.(691-693)cGg>cAg	p.R231Q		NM_014062.1	NP_054781.1	Q9ULX3	NOB1_HUMAN	NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)	231			R -> Q (in dbSNP:rs3811348). {ECO:0000269|PubMed:1791827}.		visual perception (GO:0007601)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GCAGCCAACCCGCACGTCCTC	0.612													C|||	1722	0.34385	0.0983	0.4899	5008	,	,		18913	0.2341		0.5736	False		,,,				2504	0.4489				p.R231Q		Atlas-SNP	.											.	NOB1	24	.	0			c.G692A						PASS	.	C	GLN/ARG	792,3604	316.6+/-294.7	77,638,1483	79.0	51.0	60.0		692	1.1	1.0	16	dbSNP_107	60	4906,3694	613.8+/-396.2	1406,2094,800	yes	missense	NOB1	NM_014062.1	43	1483,2732,2283	TT,TC,CC		42.9535,18.0164,43.8443	benign	231/413	69782855	5698,7298	2198	4300	6498	SO:0001583	missense	28987	exon6			CCAACCCGCACGT	AB026125	CCDS10884.1	16q22.1	2008-02-05	2006-04-20	2006-04-20	ENSG00000141101	ENSG00000141101			29540	protein-coding gene	gene with protein product	"""nin one binding protein"""	613586	"""PSMD8 binding protein 1"""	PSMD8BP1		16172919	Standard	NM_014062		Approved	NOB1P, ART-4, MST158	uc002exs.4	Q9ULX3	OTTHUMG00000137576	ENST00000268802.5:c.692G>A	16.37:g.69782855C>T	ENSP00000268802:p.Arg231Gln	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	193	190	0.984456	NM_014062	Q7L6B7|Q7M4M4|Q7Z4B5|Q9NWB0	Missense_Mutation	SNP	ENST00000268802.5	37	CCDS10884.1	818	0.37454212454212454	60	0.12195121951219512	173	0.47790055248618785	132	0.23076923076923078	453	0.5976253298153035	C	5.737	0.320468	0.10845	0.180164	0.570465	ENSG00000141101	ENST00000268802	T	0.27104	1.69	5.33	1.11	0.20524	.	0.688293	0.15053	N	0.283193	T	0.00012	0.0000	N	0.00566	-1.37	0.49915	P	1.6199999999999548E-4	B	0.10296	0.003	B	0.06405	0.002	T	0.38090	-0.9677	8	.	.	.	.	4.6223	0.12461	0.1481:0.4192:0.0:0.4327	rs3811348;rs11541646;rs61596743;rs3811348	231	Q9ULX3	NOB1_HUMAN	Q	231	ENSP00000268802:R231Q	.	R	-	2	0	NOB1	68340356	0.006000	0.16342	0.990000	0.47175	0.285000	0.27093	-0.419000	0.07071	0.315000	0.23110	0.585000	0.79938	CGG	C|0.585;T|0.415	0.415	strong		0.612	NOB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268958.2	NM_014062	
TG	7038	hgsc.bcm.edu	37	8	133920518	133920518	+	Missense_Mutation	SNP	A	A	G	rs2069556	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:133920518A>G	ENST00000220616.4	+	18	3975	c.3935A>G	c.(3934-3936)gAt>gGt	p.D1312G	TG_ENST00000377869.1_Missense_Mutation_p.D1312G	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1312			D -> G (in dbSNP:rs2069556). {ECO:0000269|PubMed:11124863, ECO:0000269|PubMed:3595599, ECO:0000269|PubMed:9186272}.		hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GACTACGCGGATTTGCTGCAG	0.597													G|||	1997	0.398762	0.0734	0.5836	5008	,	,		17705	0.3571		0.6093	False		,,,				2504	0.5337				p.D1312G		Atlas-SNP	.											TG,caecum,carcinoma,0,1	TG	416	1	0			c.A3935G						PASS	.	G	GLY/ASP	714,3692	759.9+/-412.9	61,592,1550	79.0	71.0	74.0		3935	5.5	0.1	8	dbSNP_96	74	5290,3310	493.3+/-373.5	1650,1990,660	yes	missense	TG	NM_003235.4	94	1711,2582,2210	GG,GA,AA		38.4884,16.2052,46.1633	benign	1312/2769	133920518	6004,7002	2203	4300	6503	SO:0001583	missense	7038	exon18			ACGCGGATTTGCT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3935A>G	8.37:g.133920518A>G	ENSP00000220616:p.Asp1312Gly	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	920	0.42124542124542125	44	0.08943089430894309	208	0.574585635359116	198	0.34615384615384615	470	0.6200527704485488	G	0.017	-1.490680	0.01018	0.162052	0.615116	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.60424	0.21;0.19	5.47	5.47	0.80525	.	0.089084	0.49305	N	0.000155	T	0.00012	0.0000	N	0.00237	-1.79	0.24819	P	0.99259603	B	0.02656	0.0	B	0.01281	0.0	T	0.43147	-0.9409	9	0.02654	T	1	.	10.5261	0.44950	0.0885:0.0:0.9115:0.0	rs2069556;rs13268183;rs17684997;rs34148413;rs52793422;rs60073338;rs2069556	1312	P01266	THYG_HUMAN	G	1312;118;1312	ENSP00000367100:D1312G;ENSP00000220616:D1312G	ENSP00000220616:D1312G	D	+	2	0	TG	133989700	1.000000	0.71417	0.072000	0.20136	0.001000	0.01503	4.289000	0.59013	1.325000	0.45301	-0.128000	0.14901	GAT	A|0.577;G|0.423	0.423	strong		0.597	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
MXD1	4084	hgsc.bcm.edu	37	2	70162534	70162534	+	Silent	SNP	T	T	G	rs2228183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:70162534T>G	ENST00000264444.2	+	4	515	c.255T>G	c.(253-255)ctT>ctG	p.L85L	MXD1_ENST00000540449.1_Silent_p.L75L	NM_001202513.1|NM_001202514.1|NM_002357.3	NP_001189442.1|NP_001189443.1|NP_002348.1	Q05195	MAD1_HUMAN	MAX dimerization protein 1	85	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						TGGTGCCACTTGGACCCGAAT	0.453													T|||	2924	0.583866	0.8502	0.4035	5008	,	,		20786	0.5407		0.4443	False		,,,				2504	0.5399				p.L85L		Atlas-SNP	.											.	MXD1	23	.	0			c.T255G						PASS	.	T	,,	3451,955	735.3+/-410.7	1350,751,102	115.0	100.0	105.0		255,225,255	-2.1	1.0	2	dbSNP_120	105	3669,4931	525.4+/-380.7	803,2063,1434	no	coding-synonymous,coding-synonymous,coding-synonymous	MXD1	NM_001202513.1,NM_001202514.1,NM_002357.3	,,	2153,2814,1536	GG,GT,TT		42.6628,21.675,45.256	,,	85/221,75/212,85/222	70162534	7120,5886	2203	4300	6503	SO:0001819	synonymous_variant	4084	exon4			GCCACTTGGACCC		CCDS1896.1, CCDS56123.1	2p13-p12	2010-07-07		2005-02-11	ENSG00000059728	ENSG00000059728		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	6761	protein-coding gene	gene with protein product		600021		MAD		7829091	Standard	NM_002357		Approved	MAD1, bHLHc58	uc002sfy.3	Q05195	OTTHUMG00000129646	ENST00000264444.2:c.255T>G	2.37:g.70162534T>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	165	58	0.351515	NM_001202513	B2R6V8|B7ZLI6|D6W5G2|Q6FI41	Silent	SNP	ENST00000264444.2	37	CCDS1896.1																																																																																			T|0.439;G|0.561	0.561	strong		0.453	MXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251845.3	NM_002357	
MAEA	10296	hgsc.bcm.edu	37	4	1305802	1305802	+	Silent	SNP	C	C	T	rs34402978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1305802C>T	ENST00000303400.4	+	2	168	c.105C>T	c.(103-105)gcC>gcT	p.A35A	MAEA_ENST00000505177.2_Silent_p.A35A|MAEA_ENST00000452175.2_Silent_p.A24A|MAEA_ENST00000264750.6_Silent_p.A35A|MAEA_ENST00000505839.1_5'UTR|MAEA_ENST00000510794.1_Silent_p.A34A|MAEA_ENST00000514708.1_Silent_p.A35A	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	35	Extracellular and involved in cell to cell contact.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cytoskeleton organization (GO:0007010)|enucleate erythrocyte development (GO:0048822)|erythrocyte maturation (GO:0043249)|negative regulation of myeloid cell apoptotic process (GO:0033033)|regulation of mitotic cell cycle (GO:0007346)	actomyosin contractile ring (GO:0005826)|cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(23;0.0201)		WF10(DB05389)	GCTTTCGCGCCGCTCAGAAGA	0.642													C|||	67	0.0133786	0.0008	0.0159	5008	,	,		18940	0.001		0.0388	False		,,,				2504	0.0153				p.A35A		Atlas-SNP	.											.	MAEA	39	.	0			c.C105T						PASS	.	C	,	34,4372	39.2+/-71.8	0,34,2169	72.0	57.0	62.0		105,105	-4.3	0.9	4	dbSNP_126	62	415,8185	129.2+/-187.3	11,393,3896	yes	coding-synonymous,coding-synonymous	MAEA	NM_001017405.1,NM_005882.3	,	11,427,6065	TT,TC,CC		4.8256,0.7717,3.4523	,	35/397,35/356	1305802	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	10296	exon2			TCGCGCCGCTCAG	AF084928	CCDS33936.1, CCDS33937.1, CCDS75090.1	4p16.3	2012-07-20			ENSG00000090316	ENSG00000090316			13731	protein-coding gene	gene with protein product	"""GID complex subunit 9, FYV10 homolog (S. cerevisiae)"""	606801				9763581	Standard	XM_005272243		Approved	EMP, GID9	uc003gda.3	Q7L5Y9	OTTHUMG00000160169	ENST00000303400.4:c.105C>T	4.37:g.1305802C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	223	103	0.461883	NM_005882	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Silent	SNP	ENST00000303400.4	37	CCDS33936.1																																																																																			C|0.972;T|0.028	0.028	strong		0.642	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882	
TBX1	6899	hgsc.bcm.edu	37	22	19766782	19766782	+	Missense_Mutation	SNP	C	C	T	rs4819522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:19766782C>T	ENST00000329705.7	+	9	1178	c.1049C>T	c.(1048-1050)aCg>aTg	p.T350M	TBX1_ENST00000359500.3_Intron	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	350			T -> M (in dbSNP:rs4819522).		angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				AAAGCTGAGACGTCTAGGAAC	0.547													C|||	1048	0.209265	0.1551	0.255	5008	,	,		19033	0.119		0.169	False		,,,				2504	0.3845				p.T350M		Atlas-SNP	.											TBX1_ENST00000329705,colon,carcinoma,0,1	TBX1	62	1	0			c.C1049T						PASS	.	C	,MET/THR	666,3740	284.0+/-277.4	61,544,1598	93.0	78.0	83.0		,1049	-3.4	0.0	22	dbSNP_111	83	1577,7023	295.1+/-302.2	155,1267,2878	yes	intron,missense	TBX1	NM_005992.1,NM_080646.1	,81	216,1811,4476	TT,TC,CC		18.3372,15.1158,17.2459	,	,350/399	19766782	2243,10763	2203	4300	6503	SO:0001583	missense	6899	exon9			CTGAGACGTCTAG	AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"""T-boxes"""	11592	protein-coding gene	gene with protein product		602054	"""velocardiofacial syndrome"""	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.1049C>T	22.37:g.19766782C>T	ENSP00000331176:p.Thr350Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_080646	C6G493|C6G494|O43436|Q96RJ2	Missense_Mutation	SNP	ENST00000329705.7	37	CCDS13766.1	368	0.1684981684981685	90	0.18292682926829268	83	0.2292817679558011	68	0.11888111888111888	127	0.16754617414248021	C	12.48	1.950373	0.34377	0.151158	0.183372	ENSG00000184058	ENST00000329705	D	0.86956	-2.19	1.69	-3.37	0.04898	.	.	.	.	.	T	0.00109	0.0003	N	0.19112	0.55	0.80722	P	0.0	D	0.69078	0.997	P	0.53861	0.736	T	0.17410	-1.0370	8	0.44086	T	0.13	.	3.5111	0.07708	0.0:0.2533:0.4805:0.2661	rs4819522;rs59530459;rs4819522	350	O43435	TBX1_HUMAN	M	350	ENSP00000331176:T350M	ENSP00000331176:T350M	T	+	2	0	TBX1	18146782	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.716000	0.04991	-0.727000	0.04888	0.555000	0.69702	ACG	C|0.829;T|0.171	0.171	strong		0.547	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647	
SLC38A7	55238	hgsc.bcm.edu	37	16	58713798	58713798	+	Missense_Mutation	SNP	G	G	A	rs7191331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:58713798G>A	ENST00000570101.1	-	2	1116	c.233C>T	c.(232-234)aCt>aTt	p.T78I	SLC38A7_ENST00000566953.1_Intron|SLC38A7_ENST00000564010.1_Intron|SLC38A7_ENST00000219320.4_Missense_Mutation_p.T78I|SLC38A7_ENST00000564391.1_Missense_Mutation_p.T78I|SLC38A7_ENST00000564100.1_Missense_Mutation_p.T78I			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	78			T -> I (in dbSNP:rs7191331).		sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						GCCCCCCGCAGTGCTGAAGGC	0.622													G|||	564	0.11262	0.0998	0.0778	5008	,	,		19815	0.0228		0.1948	False		,,,				2504	0.1626				p.T78I		Atlas-SNP	.											SLC38A7,NS,carcinoma,0,1	SLC38A7	26	1	0			c.C233T						PASS	.	G	ILE/THR	510,3886	234.6+/-247.4	40,430,1728	47.0	44.0	45.0		233	5.9	0.9	16	dbSNP_116	45	1671,6929	304.9+/-307.2	165,1341,2794	yes	missense	SLC38A7	NM_018231.1	89	205,1771,4522	AA,AG,GG		19.4302,11.6015,16.7821	benign	78/463	58713798	2181,10815	2198	4300	6498	SO:0001583	missense	55238	exon3			CCCGCAGTGCTGA	BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"""Solute carriers"""	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.233C>T	16.37:g.58713798G>A	ENSP00000454646:p.Thr78Ile	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	76	46	0.605263	NM_018231	Q53GJ9|Q9H9I5	Missense_Mutation	SNP	ENST00000570101.1	37	CCDS10800.1	253	0.11584249084249085	56	0.11382113821138211	32	0.08839779005524862	13	0.022727272727272728	152	0.20052770448548812	G	10.74	1.434544	0.25813	0.116015	0.194302	ENSG00000103042	ENST00000219320	T	0.02301	4.35	5.91	5.91	0.95273	.	0.257812	0.49916	D	0.000130	T	0.00012	0.0000	N	0.08118	0	0.31568	P	0.656709	B;B	0.12630	0.005;0.006	B;B	0.15870	0.013;0.014	T	0.58137	-0.7689	8	.	.	.	.	12.4954	0.55925	0.0836:0.0:0.9164:0.0	rs7191331;rs17419846;rs57824527;rs7191331	78;78	Q9NVC3;Q9NVC3-2	S38A7_HUMAN;.	I	78	ENSP00000219320:T78I	.	T	-	2	0	SLC38A7	57271299	0.991000	0.36638	0.916000	0.36221	0.010000	0.07245	2.320000	0.43797	2.813000	0.96785	0.655000	0.94253	ACT	G|0.855;A|0.145	0.145	strong		0.622	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231	
UNC5C	8633	hgsc.bcm.edu	37	4	96166270	96166270	+	Silent	SNP	C	C	T	rs35120448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:96166270C>T	ENST00000453304.1	-	6	1149	c.801G>A	c.(799-801)acG>acA	p.T267T	UNC5C_ENST00000506749.1_Silent_p.T267T	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	267	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CAGACCACTCCGTCCAGGTGG	0.512													C|||	116	0.0231629	0.0159	0.0346	5008	,	,		17093	0.0		0.0537	False		,,,				2504	0.0174				p.T267T		Atlas-SNP	.											UNC5C,NS,carcinoma,-1,1	UNC5C	141	1	0			c.G801A						scavenged	.	C		97,4309	78.3+/-116.7	3,91,2109	64.0	55.0	58.0		801	-5.9	1.0	4	dbSNP_126	58	444,8156	133.1+/-190.7	8,428,3864	no	coding-synonymous	UNC5C	NM_003728.3		11,519,5973	TT,TC,CC		5.1628,2.2015,4.1596		267/932	96166270	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon6			CCACTCCGTCCAG	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.801G>A	4.37:g.96166270C>T		Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.961;T|0.039	0.039	strong		0.512	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
NEB	4703	hgsc.bcm.edu	37	2	152422087	152422087	+	Silent	SNP	A	A	G	rs2288211	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:152422087A>G	ENST00000172853.10	-	88	13338	c.13191T>C	c.(13189-13191)taT>taC	p.Y4397Y	NEB_ENST00000409198.1_Silent_p.Y4397Y|NEB_ENST00000397345.3_Silent_p.Y6098Y|NEB_ENST00000604864.1_Silent_p.Y6098Y|NEB_ENST00000603639.1_Silent_p.Y6098Y|NEB_ENST00000427231.2_Silent_p.Y6098Y			P20929	NEBU_HUMAN	nebulin	4397					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.Y4397Y(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TAAAGTTAGGATAGTTTTCAA	0.388													A|||	1121	0.223842	0.0363	0.3761	5008	,	,		19432	0.3036		0.328	False		,,,				2504	0.18				p.Y6098Y		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	1	Substitution - coding silent(1)	stomach(1)	c.T18294C						PASS	.	A	,,	314,3372		8,298,1537	70.0	63.0	65.0		18294,18294,13191	1.2	1.0	2	dbSNP_100	65	2380,5802		349,1682,2060	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	357,1980,3597	GG,GA,AA		29.0882,8.5187,22.6997	,,	6098/8526,6098/8526,4397/6670	152422087	2694,9174	1843	4091	5934	SO:0001819	synonymous_variant	4703	exon116			GTTAGGATAGTTT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.13191T>C	2.37:g.152422087A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				A|0.732;G|0.268	0.268	strong		0.388	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
MUC4	4585	hgsc.bcm.edu	37	3	195507193	195507193	+	Missense_Mutation	SNP	G	G	A	rs201474621	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507193G>A	ENST00000463781.3	-	2	11717	c.11258C>T	c.(11257-11259)gCa>gTa	p.A3753V	MUC4_ENST00000475231.1_Missense_Mutation_p.A3753V|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.587																																					p.A3753V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C11258T						scavenged	.						31.0	26.0	27.0					3																	195507193		683	1583	2266	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11258C>T	3.37:g.195507193G>A	ENSP00000417498:p.Ala3753Val	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	244	66	0.270492	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	4.279	0.050873	0.08243	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.5	0.885	-1.56	0.08532	.	0.000000	0.24912	U	0.034619	T	0.14184	0.0343	N	0.19112	0.55	0.09310	N	1	B	0.19200	0.034	B	0.14023	0.01	T	0.20706	-1.0267	9	.	.	.	.	5.5971	0.17333	0.2308:0.0:0.7692:0.0	rs9755674	3625	E7ESK3	.	V	3753	ENSP00000417498:A3753V;ENSP00000420243:A3753V	.	A	-	2	0	MUC4	196991972	0.009000	0.17119	0.041000	0.18516	0.025000	0.11179	0.313000	0.19415	-1.696000	0.01421	-2.092000	0.00371	GCA	G|0.993;T|0.007	.	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DNAH9	1770	hgsc.bcm.edu	37	17	11511480	11511480	+	Missense_Mutation	SNP	G	G	A	rs17599639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11511480G>A	ENST00000262442.4	+	2	520	c.452G>A	c.(451-453)cGc>cAc	p.R151H	DNAH9_ENST00000454412.2_Missense_Mutation_p.R151H|DNAH9_ENST00000579828.1_Missense_Mutation_p.R151H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	151	Stem. {ECO:0000250}.		R -> H (in dbSNP:rs17599639).		cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAGAAGAATCGCCTAAACTGG	0.488													G|||	117	0.0233626	0.0159	0.0216	5008	,	,		19075	0.0		0.0417	False		,,,				2504	0.0399				p.R151H		Atlas-SNP	.											DNAH9,NS,malignant_melanoma,+1,1	DNAH9	695	1	0			c.G452A						PASS	.	G	HIS/ARG	82,4324	69.8+/-107.6	0,82,2121	150.0	146.0	147.0		452	0.9	0.0	17	dbSNP_123	147	353,8247	119.9+/-179.2	8,337,3955	yes	missense	DNAH9	NM_001372.3	29	8,419,6076	AA,AG,GG		4.1047,1.8611,3.3446	benign	151/4487	11511480	435,12571	2203	4300	6503	SO:0001583	missense	1770	exon2			AGAATCGCCTAAA	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.452G>A	17.37:g.11511480G>A	ENSP00000262442:p.Arg151His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	54	0.024725274725274724	11	0.022357723577235773	9	0.024861878453038673	0	0.0	34	0.044854881266490766	G	0.021	-1.427313	0.01117	0.018611	0.041047	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.25749	1.82;1.78	5.7	0.937	0.19494	.	0.633514	0.15787	N	0.244627	T	0.01124	0.0037	N	0.00321	-1.65	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.45366	-0.9266	10	0.02654	T	1	.	11.4204	0.49978	0.8892:0.0:0.1108:0.0	rs17599639;rs52801139;rs17599639	151;151	Q9NYC9;E7EP17	DYH9_HUMAN;.	H	151	ENSP00000262442:R151H;ENSP00000414874:R151H	ENSP00000262442:R151H	R	+	2	0	DNAH9	11452205	0.998000	0.40836	0.000000	0.03702	0.104000	0.19210	4.213000	0.58520	-0.114000	0.11936	-0.812000	0.03155	CGC	G|0.971;A|0.029	0.029	strong		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
CFAP46	54777	hgsc.bcm.edu	37	10	134736026	134736026	+	Silent	SNP	G	G	A	rs4880286	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134736026G>A	ENST00000368586.5	-	12	1543	c.1443C>T	c.(1441-1443)gcC>gcT	p.A481A	TTC40_ENST00000368582.2_Silent_p.A481A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CGCGCTCAGGGGCCTGGTATA	0.701													G|||	1798	0.359026	0.2821	0.4986	5008	,	,		15308	0.3264		0.3459	False		,,,				2504	0.411				p.A481A		Atlas-SNP	.											.	TTC40	100	.	0			c.C1443T						PASS	.																																			SO:0001819	synonymous_variant	54777	exon12			CTCAGGGGCCTGG																												ENST00000368586.5:c.1443C>T	10.37:g.134736026G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			G|0.640;A|0.360	0.360	strong		0.701	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
PLCG2	5336	hgsc.bcm.edu	37	16	81971403	81971403	+	Silent	SNP	T	T	C	rs1071644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81971403T>C	ENST00000359376.3	+	28	3307	c.3093T>C	c.(3091-3093)aaT>aaC	p.N1031N		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1031	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						TTTCTCTCAATGGGCGCACGG	0.547													T|||	1572	0.313898	0.0764	0.3199	5008	,	,		20866	0.3442		0.504	False		,,,				2504	0.4039				p.N1031N		Atlas-SNP	.											.	PLCG2	276	.	0			c.T3093C						PASS	.	T		636,3558		55,526,1516	102.0	99.0	100.0		3093	-5.8	0.9	16	dbSNP_86	100	4490,3954		1225,2040,957	no	coding-synonymous	PLCG2	NM_002661.3		1280,2566,2473	CC,CT,TT		46.8261,15.1645,40.5602		1031/1266	81971403	5126,7512	2097	4222	6319	SO:0001819	synonymous_variant	5336	exon28			TCTCAATGGGCGC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3093T>C	16.37:g.81971403T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			C|0.387;N|0.000	0.387	strong		0.547	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
FAM186A	121006	hgsc.bcm.edu	37	12	50744171	50744171	+	Silent	SNP	T	T	C	rs7312252	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50744171T>C	ENST00000327337.5	-	4	6443	c.6444A>G	c.(6442-6444)acA>acG	p.T2148T	FAM186A_ENST00000543096.1_Silent_p.T159T|FAM186A_ENST00000543111.1_Silent_p.T2148T	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2148								p.T2148T(1)									CCAACTGAACTGTGTCCATAT	0.388													C|||	3002	0.599441	0.4766	0.732	5008	,	,		20513	0.7431		0.659	False		,,,				2504	0.4622				p.T2148T	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - coding silent(1)	stomach(1)	c.A6444G						PASS	.	C		686,698		165,356,171	184.0	149.0	160.0		6444	-0.1	0.2	12	dbSNP_116	160	2067,1115		704,659,228	no	coding-synonymous	FAM186A	NM_001145475.1		869,1015,399	CC,CT,TT		35.0409,49.5665,39.7065		2148/2352	50744171	2753,1813	692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			CTGAACTGTGTCC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6444A>G	12.37:g.50744171T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			T|0.378;C|0.622	0.622	strong		0.388	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049941	69049941	+	Missense_Mutation	SNP	T	T	C	rs10177248	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:69049941T>C	ENST00000295381.3	+	10	2086	c.1667T>C	c.(1666-1668)aTg>aCg	p.M556T	ARHGAP25_ENST00000479844.1_Missense_Mutation_p.M250T|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.M549T|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.M557T|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.M517T|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.M550T	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	556			M -> T (in dbSNP:rs10177248). {ECO:0000269|PubMed:14702039}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						TTGCAGAGGATGGTCCAAGAG	0.453													t|||	1603	0.320088	0.3525	0.3213	5008	,	,		20565	0.4097		0.335	False		,,,				2504	0.1677				p.M557T		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.T1670C						PASS	.	T	THR/MET,THR/MET,THR/MET,THR/MET	1578,2826	454.7+/-350.8	286,1006,910	69.0	77.0	75.0		1670,1649,1550,1646	-1.1	0.7	2	dbSNP_119	75	2743,5857	409.6+/-349.9	454,1835,2011	yes	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	81,81,81,81	740,2841,2921	CC,CT,TT		31.8953,35.8311,33.2282	benign,benign,benign,benign	557/647,550/640,517/607,549/639	69049941	4321,8683	2202	4300	6502	SO:0001583	missense	9938	exon10			AGAGGATGGTCCA	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1667T>C	2.37:g.69049941T>C	ENSP00000295381:p.Met556Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		809|809	0.37042124542124544|0.37042124542124544	194|194	0.3943089430894309|0.3943089430894309	99|99	0.27348066298342544|0.27348066298342544	279|279	0.48776223776223776|0.48776223776223776	237|237	0.31266490765171506|0.31266490765171506	t|t	0.793|0.793	-0.758089|-0.758089	0.03019|0.03019	0.358311|0.358311	0.318953|0.318953	ENSG00000163219|ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844|ENST00000497259	T;T;T;T;T;T|.	0.44083|.	2.89;2.89;2.63;0.93;0.93;0.93|.	5.42|5.42	-1.08|-1.08	0.09936|0.09936	.|.	1.099060|.	0.06758|.	N|.	0.781298|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	P|P	0.99999229651|0.99999229651	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0|.	T|T	0.47699|0.47699	-0.9097|-0.9097	9|4	0.21014|.	T|.	0.42|.	.|.	9.614|9.614	0.39681|0.39681	0.0:0.3108:0.0:0.6892|0.0:0.3108:0.0:0.6892	rs10177248|rs10177248	517;557;550;549;556|.	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331|.	.;.;.;.;RHG25_HUMAN|.	T|R	556;557;517;549;550;550;541;250|416	ENSP00000295381:M556T;ENSP00000386911:M557T;ENSP00000420583:M517T;ENSP00000386863:M549T;ENSP00000386241:M550T;ENSP00000417467:M250T|.	ENSP00000295381:M556T|.	M|W	+|+	2|1	0|0	ARHGAP25|ARHGAP25	68903445|68903445	0.003000|0.003000	0.15002|0.15002	0.678000|0.678000	0.29963|0.29963	0.441000|0.441000	0.31987|0.31987	-0.142000|-0.142000	0.10311|0.10311	-0.347000|-0.347000	0.08299|0.08299	-1.438000|-1.438000	0.01074|0.01074	ATG|TGG	T|0.655;C|0.345	0.345	strong		0.453	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766776	27766776	+	Silent	SNP	G	G	A	rs45553337	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:27766776G>A	ENST00000451261.2	+	5	2163	c.1764G>A	c.(1762-1764)acG>acA	p.T588T		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	588								p.T555T(1)		central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						GTCACGTGACGCAGAGAGGTC	0.507													A|||	620	0.164238	0.1324	0.1167	3775	,	,		15143	0.0546		0.2078	False		,,,				2504	0.1022				p.T588T		Atlas-SNP	.											.	DCAF8L2	79	.	1	Substitution - coding silent(1)	kidney(1)	c.G1764A						PASS	.	A		250,959		19,183,29,315,146	83.0	59.0	67.0		1764	2.5	0.0	X	dbSNP_127	67	671,1720		61,306,243,433,548	no	coding-synonymous	DCAF8L2	NM_001136533.1		80,489,272,748,694	AA,AG,A,GG,G		28.0636,20.6782,25.5833		588/632	27766776	921,2679	692	1591	2283	SO:0001819	synonymous_variant	347442	exon1			CGTGACGCAGAGA		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1764G>A	X.37:g.27766776G>A		Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	159	157	0.987421	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			G|0.816;A|0.184	0.184	strong		0.507	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
ADRA2C	152	hgsc.bcm.edu	37	4	3769500	3769500	+	Silent	SNP	C	C	T	rs7434630	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:3769500C>T	ENST00000330055.5	+	1	1376	c.1167C>T	c.(1165-1167)ggC>ggT	p.G389G	ADRA2C_ENST00000509482.1_Intron	NM_000683.3	NP_000674.2	P18825	ADA2C_HUMAN	adrenoceptor alpha 2C	389					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|platelet activation (GO:0030168)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of vasoconstriction (GO:0045907)|regulation of insulin secretion (GO:0050796)|regulation of sensory perception of pain (GO:0051930)|small molecule metabolic process (GO:0044281)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Fenoldopam(DB00800)|Iloperidone(DB04946)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TGGTCATGGGCGTGTTCGTGC	0.672													C|||	950	0.189696	0.4349	0.0879	5008	,	,		9975	0.1389		0.0507	False		,,,				2504	0.1258				p.G389G	Esophageal Squamous(12;454 628 4517 14479)	Atlas-SNP	.											.	ADRA2C	24	.	0			c.C1167T						PASS	.	C		1643,2751	457.3+/-351.6	316,1011,870	47.0	52.0	50.0		1167	2.7	1.0	4	dbSNP_132	50	474,8126	133.9+/-191.4	13,448,3839	no	coding-synonymous	ADRA2C	NM_000683.3		329,1459,4709	TT,TC,CC		5.5116,37.3919,16.2921		389/463	3769500	2117,10877	2197	4300	6497	SO:0001819	synonymous_variant	152	exon1			CATGGGCGTGTTC	AY455666	CCDS47004.1	4p16.3	2013-10-22	2012-05-09		ENSG00000184160	ENSG00000184160		"""GPCR / Class A : Adrenoceptors : alpha"""	283	protein-coding gene	gene with protein product		104250	"""adrenergic, alpha-2C-, receptor"""	ADRA2L2, ADRA2RL2		1849485	Standard	NM_000683		Approved	ADRARL2	uc003ghm.3	P18825	OTTHUMG00000159830	ENST00000330055.5:c.1167C>T	4.37:g.3769500C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	97	35	0.360825	NM_000683	P35369|Q9HB49	Silent	SNP	ENST00000330055.5	37	CCDS47004.1																																																																																			C|0.858;T|0.142	0.142	strong		0.672	ADRA2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357607.1	NM_000683	
PNPLA5	150379	hgsc.bcm.edu	37	22	44286950	44286950	+	Missense_Mutation	SNP	G	G	A	rs2071883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:44286950G>A	ENST00000597664.1	-	2	547	c.418C>T	c.(418-420)Ctc>Ttc	p.L140F	PNPLA5_ENST00000593866.1_Intron|PNPLA5_ENST00000381198.2_Intron|PNPLA5_ENST00000216177.4_Missense_Mutation_p.L140F			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	140	Patatin.		L -> F (in dbSNP:rs2071883).		lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				ACCTGGATGAGCTCATCGCAG	0.652													G|||	1202	0.240016	0.1944	0.2478	5008	,	,		15120	0.4851		0.1004	False		,,,				2504	0.1871				p.L140F		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C418T						PASS	.	G	,PHE/LEU	741,3659		79,583,1538	25.0	24.0	24.0		,418	-0.5	0.9	22	dbSNP_96	24	848,7750		43,762,3494	yes	intron,missense	PNPLA5	NM_001177675.1,NM_138814.3	,22	122,1345,5032	AA,AG,GG		9.8628,16.8409,12.225	,benign	,140/430	44286950	1589,11409	2200	4299	6499	SO:0001583	missense	150379	exon2			GGATGAGCTCATC	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.418C>T	22.37:g.44286950G>A	ENSP00000471069:p.Leu140Phe	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	118	45	0.381356	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	37		532	0.24358974358974358	91	0.18495934959349594	71	0.19613259668508287	283	0.49475524475524474	87	0.11477572559366754	G	11.59	1.682580	0.29872	0.168409	0.098628	ENSG00000100341	ENST00000216177;ENST00000438734	D;D	0.83673	-1.75;-1.58	4.37	-0.542	0.11854	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.311492	0.25132	N	0.032883	T	0.00012	0.0000	M	0.68593	2.085	0.09310	P	0.9999999999986664	B	0.25390	0.125	B	0.28011	0.085	T	0.29941	-0.9995	9	0.59425	D	0.04	-26.5497	4.3342	0.11078	0.0951:0.3321:0.4475:0.1252	rs2071883;rs59156036;rs2071883	140	Q7Z6Z6	PLPL5_HUMAN	F	140	ENSP00000216177:L140F;ENSP00000405732:L140F	ENSP00000216177:L140F	L	-	1	0	PNPLA5	42618283	1.000000	0.71417	0.908000	0.35775	0.055000	0.15305	1.909000	0.39917	-0.076000	0.12775	0.561000	0.74099	CTC	G|0.807;A|0.193	0.193	strong		0.652	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
DNAH9	1770	hgsc.bcm.edu	37	17	11651057	11651057	+	Missense_Mutation	SNP	A	A	G	rs3744581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11651057A>G	ENST00000262442.4	+	32	6652	c.6584A>G	c.(6583-6585)aAt>aGt	p.N2195S	DNAH9_ENST00000454412.2_Missense_Mutation_p.N2195S	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2195	AAA 2. {ECO:0000250}.		N -> S (in dbSNP:rs3744581).		cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GGCATCATCAATCCAGCCACA	0.527													A|||	1125	0.224641	0.1543	0.2349	5008	,	,		17290	0.3294		0.2356	False		,,,				2504	0.1933				p.N2195S		Atlas-SNP	.											DNAH9,colon,carcinoma,0,1	DNAH9	695	1	0			c.A6584G	GRCh37	CM065137	DNAH9	M	rs3744581	PASS	.	A	SER/ASN	712,3694	296.4+/-284.2	58,596,1549	58.0	55.0	56.0		6584	3.3	1.0	17	dbSNP_107	56	2099,6501	360.3+/-331.9	250,1599,2451	yes	missense	DNAH9	NM_001372.3	46	308,2195,4000	GG,GA,AA		24.407,16.1598,21.6131	possibly-damaging	2195/4487	11651057	2811,10195	2203	4300	6503	SO:0001583	missense	1770	exon32			TCATCAATCCAGC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6584A>G	17.37:g.11651057A>G	ENSP00000262442:p.Asn2195Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	512	0.23443223443223443	73	0.1483739837398374	71	0.19613259668508287	193	0.3374125874125874	175	0.23087071240105542	A	19.41	3.822547	0.71028	0.161598	0.24407	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	D;D	0.87650	-2.28;-2.28	4.36	3.29	0.37713	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.194965	0.42682	D	0.000662	T	0.00012	0.0000	M	0.82056	2.57	0.09310	P	1.0	P	0.46220	0.874	P	0.53760	0.734	T	0.00000	-1.2947	9	0.51188	T	0.08	.	9.7558	0.40502	0.918:0.0:0.082:0.0	rs3744581;rs58949980;rs3744581	2195	Q9NYC9	DYH9_HUMAN	S	2195;2195;777	ENSP00000262442:N2195S;ENSP00000414874:N2195S	ENSP00000262442:N2195S	N	+	2	0	DNAH9	11591782	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.249000	0.78278	0.722000	0.32252	0.455000	0.32223	AAT	A|0.779;G|0.221	0.221	strong		0.527	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
PUM1	9698	hgsc.bcm.edu	37	1	31441316	31441316	+	Silent	SNP	T	T	C	rs202191174	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:31441316T>C	ENST00000257075.5	-	11	1623	c.1530A>G	c.(1528-1530)caA>caG	p.Q510Q	PUM1_ENST00000373742.2_Silent_p.Q451Q|PUM1_ENST00000426105.2_Silent_p.Q510Q|PUM1_ENST00000440538.2_Silent_p.Q511Q|SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000373747.3_Silent_p.Q511Q|PUM1_ENST00000423018.2_Silent_p.Q414Q|PUM1_ENST00000490546.1_5'UTR|PUM1_ENST00000424085.2_Silent_p.Q268Q|PUM1_ENST00000373741.4_Silent_p.Q546Q	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	510	Ala-rich.|Gln-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TCAAAGGACGTTGGCTGGCTC	0.522													T|||	2	0.000399361	0.0	0.0014	5008	,	,		18651	0.0		0.0	False		,,,				2504	0.001				p.Q510Q		Atlas-SNP	.											.	PUM1	107	.	0			c.A1530G						PASS	.	T	,	0,4406		0,0,2203	105.0	96.0	99.0		1530,1530	0.6	1.0	1		99	7,8593	5.7+/-21.5	0,7,4293	yes	coding-synonymous,coding-synonymous	PUM1	NM_001020658.1,NM_014676.2	,	0,7,6496	CC,CT,TT		0.0814,0.0,0.0538	,	510/1189,510/1187	31441316	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	9698	exon11			AGGACGTTGGCTG	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.1530A>G	1.37:g.31441316T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	100	29	0.29	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Silent	SNP	ENST00000257075.5	37	CCDS338.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	9.593	1.126645	0.20959	0.0	8.14E-4	ENSG00000134644	ENST00000525843;ENST00000498419;ENST00000532678	.	.	.	5.77	0.558	0.17266	.	.	.	.	.	T	0.58836	0.2150	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53940	-0.8367	4	.	.	.	-4.9988	11.0358	0.47799	0.0:0.6746:0.0:0.3254	.	.	.	.	A	528;222;198	.	.	T	-	1	0	PUM1	31213903	1.000000	0.71417	0.999000	0.59377	0.955000	0.61496	0.888000	0.28268	0.136000	0.18733	-0.912000	0.02778	ACG	T|1.000;C|0.000	0.000	strong		0.522	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
MIA3	375056	hgsc.bcm.edu	37	1	222833538	222833538	+	Silent	SNP	C	C	G	rs2291835	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:222833538C>G	ENST00000344922.5	+	24	5020	c.4995C>G	c.(4993-4995)ggC>ggG	p.G1665G	MIA3_ENST00000344507.1_Intron|RP11-378J18.8_ENST00000608771.1_RNA|MIA3_ENST00000344441.6_Silent_p.G1665G|MIA3_ENST00000340535.7_Silent_p.G543G	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1665	Pro-rich.				chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.G1665G(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GCCAGAATGGCTCTTTTGGCC	0.468													C|||	635	0.126797	0.087	0.1311	5008	,	,		17069	0.1607		0.1988	False		,,,				2504	0.0685				p.G1665G		Atlas-SNP	.											MIA3,NS,carcinoma,0,1	MIA3	167	1	1	Substitution - coding silent(1)	stomach(1)	c.C4995G						PASS	.	C		330,3474		14,302,1586	92.0	95.0	94.0		4995	4.1	1.0	1	dbSNP_100	94	1579,6659		147,1285,2687	no	coding-synonymous	MIA3	NM_198551.2		161,1587,4273	GG,GC,CC		19.1673,8.6751,15.8528		1665/1908	222833538	1909,10133	1902	4119	6021	SO:0001819	synonymous_variant	375056	exon24			GAATGGCTCTTTT		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.4995C>G	1.37:g.222833538C>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	180	89	0.494444	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Silent	SNP	ENST00000344922.5	37	CCDS41470.1																																																																																			C|0.832;G|0.168	0.168	strong		0.468	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
QRSL1	55278	hgsc.bcm.edu	37	6	107113715	107113715	+	Silent	SNP	G	G	A	rs2015205	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:107113715G>A	ENST00000369046.4	+	11	1529	c.1425G>A	c.(1423-1425)ctG>ctA	p.L475L		NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1											endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		CAATAGGACTGCAGTTTATTG	0.438													G|||	1671	0.333666	0.3109	0.402	5008	,	,		18184	0.1617		0.4642	False		,,,				2504	0.3589				p.L475L	NSCLC(192;2127 2142 11668 26277 49545)	Atlas-SNP	.											.	QRSL1	30	.	0			c.G1425A						PASS	.	G		1583,2823	493.8+/-362.8	275,1033,895	79.0	73.0	75.0		1425	0.8	1.0	6	dbSNP_92	75	4274,4326	574.0+/-390.0	1113,2048,1139	no	coding-synonymous	QRSL1	NM_018292.4		1388,3081,2034	AA,AG,GG		49.6977,35.9283,45.0331		475/529	107113715	5857,7149	2203	4300	6503	SO:0001819	synonymous_variant	55278	exon11			AGGACTGCAGTTT	AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348			21020	protein-coding gene	gene with protein product	"""glutamyl-tRNA(Gln) amidotransferase, subunit A"""					11230166, 19805282	Standard	NM_018292		Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.1425G>A	6.37:g.107113715G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	122	70	0.57377	NM_018292		Silent	SNP	ENST00000369046.4	37	CCDS5057.1																																																																																			G|0.595;A|0.405	0.405	strong		0.438	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041667.1	NM_018292	
CLSTN2	64084	hgsc.bcm.edu	37	3	140178485	140178485	+	Missense_Mutation	SNP	G	G	A	rs7632885	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:140178485G>A	ENST00000458420.3	+	7	1286	c.1096G>A	c.(1096-1098)Gtc>Atc	p.V366I	RP11-68L1.2_ENST00000503357.1_RNA|RP11-68L1.1_ENST00000483759.2_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	366			V -> I (in dbSNP:rs7632885). {ECO:0000269|PubMed:12498782, ECO:0000269|PubMed:12972431, ECO:0000269|Ref.5}.		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GGGTGCCAAAGTCCCCGATGG	0.577										HNSCC(16;0.037)			A|||	2666	0.532348	0.6112	0.4265	5008	,	,		19051	0.502		0.5944	False		,,,				2504	0.4683				p.V366I	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G1096A						PASS	.	A	ILE/VAL	2582,1824	533.3+/-373.7	744,1094,365	82.0	70.0	74.0		1096	4.2	1.0	3	dbSNP_116	74	5209,3391	501.9+/-375.6	1606,1997,697	yes	missense	CLSTN2	NM_022131.2	29	2350,3091,1062	AA,AG,GG		39.4302,41.3981,40.0969	benign	366/956	140178485	7791,5215	2203	4300	6503	SO:0001583	missense	64084	exon7			GCCAAAGTCCCCG	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1096G>A	3.37:g.140178485G>A	ENSP00000402460:p.Val366Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	1202	0.5503663003663004	295	0.5995934959349594	162	0.44751381215469616	293	0.5122377622377622	452	0.5963060686015831	A	2.739	-0.262611	0.05754	0.586019	0.605698	ENSG00000158258	ENST00000458420	T	0.74209	-0.82	5.4	4.25	0.50352	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.178921	0.47852	N	0.000210	T	0.00012	0.0000	N	0.03917	-0.325	0.48040	P	4.210000000000047E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.47018	-0.9149	9	0.10902	T	0.67	-15.312	8.393	0.32540	0.8373:0.0:0.1627:0.0	rs7632885;rs13090511;rs16850312;rs52798163;rs60628243;rs7632885	366	Q9H4D0	CSTN2_HUMAN	I	366	ENSP00000402460:V366I	ENSP00000402460:V366I	V	+	1	0	CLSTN2	141661175	1.000000	0.71417	0.999000	0.59377	0.739000	0.42172	2.225000	0.42954	0.369000	0.24510	-0.269000	0.10298	GTC	G|0.425;A|0.574	0.574	strong		0.577	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
CYP4F11	57834	hgsc.bcm.edu	37	19	16040292	16040292	+	Silent	SNP	A	A	G	rs3765070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:16040292A>G	ENST00000402119.4	-	2	744	c.318T>C	c.(316-318)atT>atC	p.I106I	CYP4F11_ENST00000248041.8_Silent_p.I106I|CYP4F11_ENST00000326742.8_Silent_p.I106I|CYP4F11_ENST00000591841.1_5'Flank	NM_021187.3	NP_067010.3			cytochrome P450, family 4, subfamily F, polypeptide 11											NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						TAGGCCGGATAATGTCAGGGT	0.557													.|||	2465	0.492212	0.447	0.5216	5008	,	,		17391	0.379		0.5865	False		,,,				2504	0.5521				p.I106I		Atlas-SNP	.											.	CYP4F11	83	.	0			c.T318C						PASS	.	G	,	1967,2439		438,1091,674	150.0	151.0	151.0		318,318	-0.1	0.0	19	dbSNP_107	151	5137,3463		1541,2055,704	no	coding-synonymous,coding-synonymous	CYP4F11	NM_001128932.1,NM_021187.3	,	1979,3146,1378	GG,GA,AA		40.2674,44.6437,45.3791	,	106/525,106/525	16040292	7104,5902	2203	4300	6503	SO:0001819	synonymous_variant	57834	exon3			CCGGATAATGTCA	AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"""Cytochrome P450s"""	13265	protein-coding gene	gene with protein product		611517	"""cytochrome P450, subfamily IVF, polypeptide 11"""			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000402119.4:c.318T>C	19.37:g.16040292A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	144	80	0.555556	NM_001128932		Silent	SNP	ENST00000402119.4	37	CCDS12337.1																																																																																			A|0.476;G|0.524	0.524	strong		0.557	CYP4F11-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460385.2	NM_021187	
VWF	7450	hgsc.bcm.edu	37	12	6172202	6172202	+	Missense_Mutation	SNP	T	T	C	rs1800378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6172202T>C	ENST00000261405.5	-	13	1705	c.1451A>G	c.(1450-1452)cAt>cGt	p.H484R		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	484	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.		H -> R (in dbSNP:rs1800378). {ECO:0000269|PubMed:3019665}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CGTCACTGTATGCTGGATGCG	0.642											OREG0021618	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2598	0.51877	0.1437	0.5101	5008	,	,		17764	0.6667		0.6541	False		,,,				2504	0.7403				p.H484R		Atlas-SNP	.											VWF,NS,carcinoma,0,1	VWF	338	1	0			c.A1451G						PASS	.	T	ARG/HIS	966,3440	358.6+/-314.5	111,744,1348	58.0	46.0	50.0		1451	1.2	0.9	12	dbSNP_89	50	5649,2951	664.9+/-402.2	1837,1975,488	yes	missense	VWF	NM_000552.3	29	1948,2719,1836	CC,CT,TT		34.314,21.9246,49.1389	possibly-damaging	484/2814	6172202	6615,6391	2203	4300	6503	SO:0001583	missense	7450	exon13			ACTGTATGCTGGA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1451A>G	12.37:g.6172202T>C	ENSP00000261405:p.His484Arg	Somatic	73	0	0	632	WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	1141	0.5224358974358975	93	0.18902439024390244	185	0.511049723756906	374	0.6538461538461539	489	0.6451187335092349	T	0.006	-2.078172	0.00375	0.219246	0.65686	ENSG00000110799	ENST00000261405	T	0.57436	0.4	4.88	1.25	0.21368	von Willebrand factor, type D domain (3);	0.519257	0.16288	N	0.221055	T	0.00012	0.0000	N	0.01631	-0.79	0.09310	P	0.999999862247	B	0.16396	0.017	B	0.19391	0.025	T	0.43491	-0.9388	9	0.02654	T	1	.	1.2808	0.02040	0.1393:0.1801:0.349:0.3316	rs1800378;rs12816761;rs16932399;rs59176412;rs1800378	484	P04275	VWF_HUMAN	R	484	ENSP00000261405:H484R	ENSP00000261405:H484R	H	-	2	0	VWF	6042463	0.129000	0.22400	0.905000	0.35620	0.004000	0.04260	0.272000	0.18644	0.120000	0.18254	-0.333000	0.08304	CAT	T|0.486;C|0.514	0.514	strong		0.642	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
OLIG2	10215	hgsc.bcm.edu	37	21	34399401	34399401	+	Silent	SNP	A	A	G	rs762178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:34399401A>G	ENST00000333337.3	+	1	1159	c.231A>G	c.(229-231)tcA>tcG	p.S77S	AP000282.2_ENST00000420356.1_RNA|OLIG2_ENST00000382357.3_Silent_p.S77S|AP000282.2_ENST00000454622.1_RNA			Q13516	OLIG2_HUMAN	oligodendrocyte lineage transcription factor 2	77	Poly-Ser.				myelination (GO:0042552)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate commitment (GO:0048663)|positive regulation of oligodendrocyte differentiation (GO:0048714)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|thalamus development (GO:0021794)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|central_nervous_system(2)	3						GCTTCAAGTCATCCTCGTCCA	0.657			T	TRA@	T-ALL								A|||	2202	0.439696	0.4939	0.5245	5008	,	,		14973	0.1845		0.5726	False		,,,				2504	0.4325				p.S77S		Atlas-SNP	.		Dom	yes		21	21q22.11	10215	oligodendrocyte lineage transcription factor 2 (BHLHB1)		L	.	OLIG2	22	.	0			c.A231G						PASS	.	A		2279,2123		617,1045,539	25.0	29.0	27.0	http://www.ncbi.nlm.nih.gov/omim/181500,606386|http://omim.org/entry/606386|http://omim.org/entry/181500	231	-5.1	1.0	21	dbSNP_86	27	4949,3651		1437,2075,788	no	coding-synonymous	OLIG2	NM_005806.3		2054,3120,1327	GG,GA,AA		42.4535,48.2281,44.4086		77/324	34399401	7228,5774	2201	4300	6501	SO:0001819	synonymous_variant	10215	exon2			CAAGTCATCCTCG	U48250	CCDS13620.1	21q22.11	2013-05-21	2001-12-04	2001-12-07	ENSG00000205927	ENSG00000205927		"""Basic helix-loop-helix proteins"""	9398	protein-coding gene	gene with protein product	"""oligodendrocyte-specific bHLH transcription factor 2"", ""protein kinase C binding protein 2"", ""human protein kinase C-binding protein RACK17"", ""basic domain, helix-loop-helix protein, class B, 1"""	606386	"""protein kinase C binding protein 2"""	PRKCBP2, BHLHB1		11526205	Standard	NM_005806		Approved	RACK17, OLIGO2, bHLHe19	uc002yqx.2	Q13516	OTTHUMG00000065032	ENST00000333337.3:c.231A>G	21.37:g.34399401A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_005806	B3KRF3|Q05BP9|Q49AL3|Q86X04|Q9NZ14	Silent	SNP	ENST00000333337.3	37	CCDS13620.1																																																																																			A|0.498;G|0.502	0.502	strong		0.657	OLIG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139663.1	NM_005806	
PCDHGA3	56112	hgsc.bcm.edu	37	5	140723835	140723835	+	Missense_Mutation	SNP	C	C	T	rs11575947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140723835C>T	ENST00000253812.6	+	1	235	c.235C>T	c.(235-237)Ccg>Tcg	p.P79S	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	79	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> S (in dbSNP:rs11575947).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTCTGAATCCGCAAAGCGG	0.597											OREG0016855	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	215	0.0429313	0.0068	0.0793	5008	,	,		15088	0.0		0.1272	False		,,,				2504	0.0235				p.P79S		Atlas-SNP	.											PCDHGA3_ENST00000253812,NS,carcinoma,-2,3	PCDHGA3	246	3	0			c.C235T						PASS	.	C	,,SER/PRO,SER/PRO	106,4236		0,106,2065	57.0	67.0	64.0		,,235,235	1.5	0.1	5	dbSNP_120	64	1087,7497		61,965,3266	no	intron,intron,missense,missense	PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_032011.1	,,74,74	61,1071,5331	TT,TC,CC		12.6631,2.4413,9.2295	,,,	,,79/933,79/830	140723835	1193,11733	2171	4292	6463	SO:0001583	missense	56112	exon1			CTGAATCCGCAAA	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.235C>T	5.37:g.140723835C>T	ENSP00000253812:p.Pro79Ser	Somatic	139	0	0	1658	WXS	Illumina HiSeq	Phase_I	136	78	0.573529	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	118	0.05402930402930403	4	0.008130081300813009	27	0.07458563535911603	0	0.0	87	0.11477572559366754	.	0.040	-1.289463	0.01387	0.024413	0.126631	ENSG00000254245	ENST00000253812	T	0.38077	1.16	5.65	1.48	0.22813	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	1.414840	0.06193	U	0.681803	T	0.00300	0.0009	L	0.59912	1.85	0.80722	P	0.0	B;B	0.14012	0.009;0.001	B;B	0.19666	0.013;0.026	T	0.19811	-1.0294	9	0.16420	T	0.52	.	1.9256	0.03316	0.2429:0.2403:0.3708:0.1459	rs11575947;rs11575947	79;79	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	S	79	ENSP00000253812:P79S	ENSP00000253812:P79S	P	+	1	0	PCDHGA3	140704019	0.000000	0.05858	0.053000	0.19242	0.032000	0.12392	-1.107000	0.03316	0.773000	0.33404	0.655000	0.94253	CCG	C|0.935;T|0.065	0.065	strong		0.597	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
RYR2	6262	hgsc.bcm.edu	37	1	237617757	237617757	+	Silent	SNP	C	C	T	rs3765097	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:237617757C>T	ENST00000366574.2	+	15	1676	c.1359C>T	c.(1357-1359)agC>agT	p.S453S	RYR2_ENST00000360064.6_Silent_p.S451S|RYR2_ENST00000542537.1_Silent_p.S437S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	453					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGTCCGTAAGCCTAAGTCTGC	0.458													T|||	2683	0.535743	0.2769	0.5447	5008	,	,		17132	0.7391		0.5994	False		,,,				2504	0.6043				p.S453S		Atlas-SNP	.											RYR2,lower_third,carcinoma,+1,1	RYR2	1273	1	0			c.C1359T						scavenged	.	T		1231,2599		190,851,874	90.0	86.0	87.0		1359	-1.8	0.8	1	dbSNP_107	87	4947,3291		1477,1993,649	no	coding-synonymous	RYR2	NM_001035.2		1667,2844,1523	TT,TC,CC		39.949,32.141,48.8068		453/4968	237617757	6178,5890	1915	4119	6034	SO:0001819	synonymous_variant	6262	exon15			CGTAAGCCTAAGT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1359C>T	1.37:g.237617757C>T		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			C|0.454;T|0.546	0.546	strong		0.458	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
NRG1	3084	hgsc.bcm.edu	37	8	32613983	32613983	+	Missense_Mutation	SNP	T	T	C	rs10503929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:32613983T>C	ENST00000405005.3	+	9	866	c.866T>C	c.(865-867)aTg>aCg	p.M289T	NRG1_ENST00000519301.1_Missense_Mutation_p.M239T|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000287842.3_Missense_Mutation_p.M286T|NRG1_ENST00000521670.1_Missense_Mutation_p.M289T|NRG1_ENST00000338921.4_Missense_Mutation_p.M297T|NRG1_ENST00000356819.4_Missense_Mutation_p.M294T|NRG1_ENST00000539990.1_Missense_Mutation_p.M132T|NRG1_ENST00000523079.1_Missense_Mutation_p.M286T|NRG1_ENST00000287845.5_Missense_Mutation_p.M260T			Q02297	NRG1_HUMAN	neuregulin 1	289			M -> T (in dbSNP:rs10503929). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17565985}.		activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CGAAACAATATGATGAACATT	0.473													T|||	337	0.0672923	0.0061	0.111	5008	,	,		17966	0.0		0.1928	False		,,,				2504	0.0593				p.M294T		Atlas-SNP	.											.	NRG1	260	.	0			c.T881C						PASS	.	T	THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET	138,4268	99.4+/-138.0	1,136,2066	146.0	140.0	142.0		767,404,818,716,857,857,881,857,866,866	6.0	1.0	8	dbSNP_119	142	1553,7047	293.2+/-301.3	123,1307,2870	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	NRG1	NM_001159995.1,NM_001159996.1,NM_001159999.1,NM_001160001.1,NM_001160004.1,NM_001160008.1,NM_013956.3,NM_013957.3,NM_013960.3,NM_013964.3	81,81,81,81,81,81,81,81,81,81	124,1443,4936	CC,CT,TT		18.0581,3.1321,13.0017	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	256/608,135/309,273/625,239/591,286/460,286/421,294/646,286/638,289/463,289/641	32613983	1691,11315	2203	4300	6503	SO:0001583	missense	3084	exon10			ACAATATGATGAA	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.866T>C	8.37:g.32613983T>C	ENSP00000384620:p.Met289Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	200	0.09157509157509157	1	0.0020325203252032522	45	0.12430939226519337	0	0.0	154	0.20316622691292877	T	11.77	1.738097	0.30774	0.031321	0.180581	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000519240;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	5.96	5.96	0.96718	Neuregulin 1-related, C-terminal (1);	0.287528	0.42964	D	0.000626	T	0.00073	0.0002	L	0.36672	1.1	0.26533	P	0.9742284	B;B;B;B;B;B;B;B;B;B	0.20671	0.042;0.001;0.034;0.015;0.047;0.002;0.015;0.0;0.015;0.0	B;B;B;B;B;B;B;B;B;B	0.27380	0.079;0.004;0.069;0.039;0.069;0.002;0.054;0.004;0.054;0.002	T	0.08493	-1.0719	9	0.26408	T	0.33	-2.8858	12.9023	0.58133	0.0:0.0:0.1353:0.8647	rs10503929;rs17732660;rs52791118;rs58325568;rs10503929	132;135;286;260;285;297;286;289;294;289	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;NRG1_HUMAN;.;.	T	256;239;362;286;297;294;289;260;286;289;289;132;132	ENSP00000430053:M256T;ENSP00000429582:M239T;ENSP00000429067:M362T;ENSP00000430120:M286T;ENSP00000343395:M297T;ENSP00000349275:M294T;ENSP00000287840:M289T;ENSP00000287845:M260T;ENSP00000287842:M286T;ENSP00000384620:M289T;ENSP00000428828:M289T;ENSP00000428411:M132T;ENSP00000439276:M132T	ENSP00000287840:M289T	M	+	2	0	NRG1	32733525	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.815000	0.38981	2.285000	0.76669	0.533000	0.62120	ATG	T|0.891;C|0.109	0.109	strong		0.473	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
SBNO1	55206	hgsc.bcm.edu	37	12	123806219	123806219	+	Missense_Mutation	SNP	C	C	T	rs1060105	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123806219C>T	ENST00000602398.1	-	17	2313	c.2186G>A	c.(2185-2187)aGt>aAt	p.S729N	SBNO1_ENST00000602750.1_Missense_Mutation_p.S728N|SBNO1_ENST00000420886.2_Missense_Mutation_p.S729N|SBNO1_ENST00000267176.4_Missense_Mutation_p.S728N			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	729			S -> N (in dbSNP:rs1060105).		regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GTCGTCAGAACTGCTACCAGT	0.433													C|||	624	0.124601	0.0514	0.1888	5008	,	,		19285	0.002		0.2227	False		,,,				2504	0.2035				p.S729N		Atlas-SNP	.											.	SBNO1	138	.	0			c.G2186A						PASS	.	C	ASN/SER,ASN/SER	363,4043	186.7+/-213.5	13,337,1853	225.0	202.0	209.0		2186,2183	5.5	1.0	12	dbSNP_86	209	1698,6902	311.3+/-310.3	154,1390,2756	yes	missense,missense	SBNO1	NM_001167856.1,NM_018183.3	46,46	167,1727,4609	TT,TC,CC		19.7442,8.2388,15.8465	probably-damaging,probably-damaging	729/1394,728/1393	123806219	2061,10945	2203	4300	6503	SO:0001583	missense	55206	exon16			TCAGAACTGCTAC	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2186G>A	12.37:g.123806219C>T	ENSP00000473665:p.Ser729Asn	Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	325	160	0.492308	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	278	0.12728937728937728	31	0.06300813008130081	70	0.19337016574585636	0	0.0	177	0.23350923482849603	C	20.9	4.064827	0.76187	0.082388	0.197442	ENSG00000139697	ENST00000420886;ENST00000267176	T;T	0.32515	1.45;1.45	5.48	5.48	0.80851	.	0.043447	0.85682	D	0.000000	T	0.00039	0.0001	L	0.44542	1.39	0.09310	P	0.99999865456	B;B;D	0.57899	0.085;0.138;0.981	B;B;D	0.66351	0.017;0.037;0.943	T	0.02202	-1.1196	9	0.18276	T	0.48	-13.2537	19.3611	0.94438	0.0:1.0:0.0:0.0	rs1060105;rs3200951;rs17568382;rs17880539;rs52804765;rs56434819;rs60926174;rs1060105	729;728;727	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	N	729;728	ENSP00000387361:S729N;ENSP00000267176:S728N	ENSP00000267176:S728N	S	-	2	0	SBNO1	122372172	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.921000	0.75805	2.551000	0.86045	0.563000	0.77884	AGT	C|0.855;T|0.145	0.145	strong		0.433	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
FMO3	2328	hgsc.bcm.edu	37	1	171076966	171076966	+	Missense_Mutation	SNP	G	G	A	rs2266782	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:171076966G>A	ENST00000367755.4	+	4	583	c.472G>A	c.(472-474)Gag>Aag	p.E158K	FMO3_ENST00000392085.2_Missense_Mutation_p.E158K|FMO3_ENST00000542847.1_Missense_Mutation_p.E138K|FMO3_ENST00000538429.1_Missense_Mutation_p.E95K	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	158			E -> K (35%, 45% and 71% increase in catalytic efficiency toward trimethylamine, benzydamine and methyl p- tolyl sulfide, respectively; dbSNP:rs2266782). {ECO:0000269|PubMed:10479479, ECO:0000269|PubMed:12527699, ECO:0000269|PubMed:17050781, ECO:0000269|PubMed:9536088, ECO:0000269|Ref.4}.		drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CCTACCAAAAGAGTCCTTTCC	0.388													G|||	1742	0.347843	0.4955	0.3199	5008	,	,		16474	0.1905		0.3668	False		,,,				2504	0.3108				p.E158K		Atlas-SNP	.											.	FMO3	73	.	0			c.G472A	GRCh37	CM992884	FMO3	M	rs2266782	PASS	.	G	LYS/GLU,LYS/GLU	2050,2356	565.4+/-381.7	471,1108,624	125.0	128.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	472,472	3.8	1.0	1	dbSNP_100	127	3530,5070	510.4+/-377.5	692,2146,1462	yes	missense,missense	FMO3	NM_001002294.2,NM_006894.5	56,56	1163,3254,2086	AA,AG,GG		41.0465,46.5275,42.9033	benign,benign	158/533,158/533	171076966	5580,7426	2203	4300	6503	SO:0001583	missense	2328	exon4			CCAAAAGAGTCCT	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.472G>A	1.37:g.171076966G>A	ENSP00000356729:p.Glu158Lys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	170	97	0.570588	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	772	0.3534798534798535	258	0.524390243902439	108	0.2983425414364641	118	0.2062937062937063	288	0.37994722955145116	G	10.12	1.262427	0.23051	0.465275	0.410465	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	4.7	3.78	0.43462	.	0.529823	0.21657	N	0.071087	T	0.21674	0.0522	L	0.43923	1.385	0.42291	P	0.007869000000000015	P;B;B	0.35033	0.481;0.014;0.006	B;B;B	0.33454	0.164;0.025;0.023	T	0.04153	-1.0973	9	0.09338	T	0.73	-7.4879	10.54	0.45026	0.1587:0.0:0.8413:0.0	rs2266782;rs3738810;rs52795018;rs60462518;rs2266782	95;138;158	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	K	158;158;138;95	ENSP00000356729:E158K;ENSP00000375935:E158K;ENSP00000444073:E138K;ENSP00000439500:E95K	ENSP00000356729:E158K	E	+	1	0	FMO3	169343590	0.000000	0.05858	1.000000	0.80357	0.664000	0.39144	0.182000	0.16900	2.130000	0.65690	0.491000	0.48974	GAG	G|0.622;A|0.378	0.378	strong		0.388	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
CYP2F1	1572	hgsc.bcm.edu	37	19	41633980	41633980	+	Missense_Mutation	SNP	C	C	T	rs7246981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41633980C>T	ENST00000331105.2	+	10	1541	c.1469C>T	c.(1468-1470)cCg>cTg	p.P490L		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	490			P -> L (in allele CYP2F1*3; dbSNP:rs7246981).		naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						TGCCTGCGCCCGCGCTAACGC	0.657													c|||	279	0.0557109	0.0015	0.2161	5008	,	,		16107	0.001		0.0875	False		,,,				2504	0.0389				p.P490L		Atlas-SNP	.											.	CYP2F1	60	.	0			c.C1469T						PASS	.	C	LEU/PRO	59,4313		7,45,2134	21.0	25.0	24.0		1469	-0.2	0.0	19	dbSNP_116	24	607,7989		30,547,3721	no	missense	CYP2F1	NM_000774.3	98	37,592,5855	TT,TC,CC		7.0614,1.3495,5.1357	benign	490/492	41633980	666,12302	2186	4298	6484	SO:0001583	missense	1572	exon10			TGCGCCCGCGCTA	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.1469C>T	19.37:g.41633980C>T	ENSP00000333534:p.Pro490Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	162	80	0.493827	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	127	0.05815018315018315	1	0.0020325203252032522	55	0.15193370165745856	1	0.0017482517482517483	70	0.09234828496042216	c	10.37	1.332271	0.24167	0.013495	0.070614	ENSG00000197446	ENST00000331105	T	0.15372	2.43	2.75	-0.195	0.13236	.	0.389555	0.25261	U	0.031959	T	0.00073	0.0002	L	0.52573	1.65	0.58432	P	1.0000000000287557E-6	B	0.11235	0.004	B	0.04013	0.001	T	0.15435	-1.0437	9	0.72032	D	0.01	.	2.8731	0.05623	0.0:0.4753:0.2636:0.2611	rs7246981;rs7246981	490	P24903	CP2F1_HUMAN	L	490	ENSP00000333534:P490L	ENSP00000333534:P490L	P	+	2	0	CYP2F1	46325820	0.000000	0.05858	0.010000	0.14722	0.098000	0.18820	-0.276000	0.08514	-0.211000	0.10124	-1.902000	0.00527	CCG	C|0.948;T|0.052	0.052	strong		0.657	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
SLIT1	6585	hgsc.bcm.edu	37	10	98820528	98820528	+	Silent	SNP	C	C	G	rs33970910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:98820528C>G	ENST00000266058.4	-	9	1055	c.810G>C	c.(808-810)ggG>ggC	p.G270G	SLIT1_ENST00000371070.4_Silent_p.G270G|SLIT1_ENST00000371041.3_Silent_p.G270G|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	270					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TGGGCACGCGCCCCGCTTCTC	0.637													C|||	485	0.096845	0.1271	0.0994	5008	,	,		19661	0.002		0.175	False		,,,				2504	0.0716				p.G270G		Atlas-SNP	.											.	SLIT1	154	.	0			c.G810C						PASS	.	C		525,3881		39,447,1717	33.0	27.0	29.0		810	-0.3	0.0	10	dbSNP_126	29	1244,7356		81,1082,3137	no	coding-synonymous	SLIT1	NM_003061.2		120,1529,4854	GG,GC,CC		14.4651,11.9156,13.6014		270/1535	98820528	1769,11237	2203	4300	6503	SO:0001819	synonymous_variant	6585	exon9			CACGCGCCCCGCT	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.810G>C	10.37:g.98820528C>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	37	CCDS7453.1																																																																																			C|0.870;G|0.130	0.130	strong		0.637	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
F13B	2165	hgsc.bcm.edu	37	1	197029592	197029592	+	Missense_Mutation	SNP	C	C	T	rs145637157		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197029592C>T	ENST00000367412.1	-	5	752	c.709G>A	c.(709-711)Gtt>Att	p.V237I		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	237	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						AAAAACTGAACGACATCTCCT	0.313																																					p.V237I		Atlas-SNP	.											.	F13B	137	.	0			c.G709A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	66.0	73.0	71.0		709	3.9	0.8	1	dbSNP_134	71	6,8588	5.0+/-18.6	0,6,4291	yes	missense	F13B	NM_001994.2	29	0,7,6493	TT,TC,CC		0.0698,0.0227,0.0538	probably-damaging	237/662	197029592	7,12993	2203	4297	6500	SO:0001583	missense	2165	exon5			ACTGAACGACATC	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.709G>A	1.37:g.197029592C>T	ENSP00000356382:p.Val237Ile	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	203	105	0.517241	NM_001994	A8K3E5|Q5VYL5	Missense_Mutation	SNP	ENST00000367412.1	37	CCDS1388.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.908059	0.52333	2.27E-4	6.98E-4	ENSG00000143278	ENST00000367412	T	0.68331	-0.32	5.76	3.86	0.44501	Complement control module (2);Sushi/SCR/CCP (3);	0.296520	0.18406	N	0.142199	T	0.68220	0.2977	L	0.50847	1.595	0.34229	D	0.676347	D	0.54772	0.968	P	0.49085	0.6	T	0.73707	-0.3898	10	0.35671	T	0.21	.	15.9628	0.79945	0.0:0.8763:0.0:0.1237	.	237	P05160	F13B_HUMAN	I	237	ENSP00000356382:V237I	ENSP00000356382:V237I	V	-	1	0	F13B	195296215	0.828000	0.29307	0.781000	0.31783	0.963000	0.63663	1.393000	0.34497	0.448000	0.26722	-0.813000	0.03139	GTT	C|1.000;T|0.000	0.000	weak		0.313	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994	
NAV2	89797	hgsc.bcm.edu	37	11	20065673	20065673	+	Missense_Mutation	SNP	G	G	T	rs3802799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:20065673G>T	ENST00000396087.3	+	14	3222	c.3123G>T	c.(3121-3123)gaG>gaT	p.E1041D	NAV2_ENST00000533917.1_Missense_Mutation_p.E104D|NAV2_ENST00000360655.4_Missense_Mutation_p.E954D|NAV2_ENST00000540292.1_Missense_Mutation_p.E972D|NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000349880.4_Missense_Mutation_p.E1018D|NAV2_ENST00000396085.1_Missense_Mutation_p.E1018D|NAV2_ENST00000527559.2_Missense_Mutation_p.E970D|NAV2_ENST00000311043.8_Missense_Mutation_p.E104D	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1041			E -> D (in dbSNP:rs3802799). {ECO:0000269|PubMed:14702039}.		glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TGTCTGACGAGTCCGACAAAA	0.547													G|||	1354	0.270367	0.0242	0.2709	5008	,	,		17876	0.4504		0.2227	False		,,,				2504	0.4663				p.E1041D		Atlas-SNP	.											.	NAV2	255	.	0			c.G3123T						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	238,4168	140.8+/-176.2	9,220,1974	98.0	87.0	91.0		2862,312,3054,3054	4.5	1.0	11	dbSNP_107	91	1683,6917	309.6+/-309.4	172,1339,2789	yes	missense,missense,missense,missense	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	45,45,45,45	181,1559,4763	TT,TG,GG		19.5698,5.4017,14.7701	probably-damaging,probably-damaging,probably-damaging,probably-damaging	954/2366,104/1494,1018/2430,1018/2433	20065673	1921,11085	2203	4300	6503	SO:0001583	missense	89797	exon14			TGACGAGTCCGAC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.3123G>T	11.37:g.20065673G>T	ENSP00000379396:p.Glu1041Asp	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	569	0.26053113553113555	11	0.022357723577235773	103	0.2845303867403315	280	0.48951048951048953	175	0.23087071240105542	G	14.05	2.420641	0.42918	0.054017	0.195698	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000525322;ENST00000530408;ENST00000311043;ENST00000536595	T;T;T;T;T;T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68	5.51	4.5	0.54988	.	0.000000	0.64402	D	0.000015	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.99999173364	D;D;D;B;D	0.76494	0.999;0.996;0.997;0.13;0.999	D;D;D;B;D	0.79784	0.99;0.987;0.99;0.185;0.993	T	0.46233	-0.9206	8	.	.	.	.	10.7967	0.46464	0.2137:0.0:0.7863:0.0	rs3802799;rs52837716;rs57731346;rs3802799	1041;104;104;1018;954	Q8IVL1;Q8IVL1-5;E9PNV5;Q8IVL1-3;Q8IVL1-4	NAV2_HUMAN;.;.;.;.	D	954;1018;1018;1041;970;972;104;104;104;104;104	ENSP00000353871:E954D;ENSP00000379394:E1018D;ENSP00000309577:E1018D;ENSP00000379396:E1041D;ENSP00000435395:E970D;ENSP00000443489:E972D;ENSP00000437316:E104D;ENSP00000437136:E104D;ENSP00000431276:E104D;ENSP00000312169:E104D	.	E	+	3	2	NAV2	20022249	1.000000	0.71417	0.994000	0.49952	0.672000	0.39443	2.664000	0.46783	1.169000	0.42739	0.655000	0.94253	GAG	G|0.806;T|0.194	0.194	strong		0.547	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
SLC44A5	204962	hgsc.bcm.edu	37	1	75699771	75699771	+	Silent	SNP	A	A	G	rs10493565	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:75699771A>G	ENST00000370855.5	-	12	866	c.753T>C	c.(751-753)atT>atC	p.I251I	SLC44A5_ENST00000535611.1_Silent_p.I121I|SLC44A5_ENST00000370859.3_Silent_p.I251I	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	251					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I251I(1)		kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						GGACCATGGCAATCGTCAGGC	0.383													G|||	1170	0.233626	0.3654	0.2291	5008	,	,		15755	0.0486		0.2694	False		,,,				2504	0.2127				p.I251I		Atlas-SNP	.											SLC44A5,NS,carcinoma,0,1	SLC44A5	231	1	1	Substitution - coding silent(1)	stomach(1)	c.T753C						PASS	.	G	,	1558,2848	667.0+/-401.8	290,978,935	99.0	98.0	98.0		753,753	-2.6	0.0	1	dbSNP_119	98	2301,6299	704.1+/-405.4	315,1671,2314	no	coding-synonymous,coding-synonymous	SLC44A5	NM_001130058.1,NM_152697.4	,	605,2649,3249	GG,GA,AA		26.7558,35.3609,29.6709	,	251/718,251/720	75699771	3859,9147	2203	4300	6503	SO:0001819	synonymous_variant	204962	exon12			CATGGCAATCGTC	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.753T>C	1.37:g.75699771A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	126	66	0.52381	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	37	CCDS667.1																																																																																			A|0.766;G|0.234	0.234	strong		0.383	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697	
UGT2B11	10720	hgsc.bcm.edu	37	4	70079838	70079838	+	Silent	SNP	T	T	C	rs4694697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70079838T>C	ENST00000446444.1	-	1	611	c.603A>G	c.(601-603)ttA>ttG	p.L201L	RP11-704M14.1_ENST00000504301.1_RNA|RP11-704M14.1_ENST00000505646.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	201					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.L201L(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						TTTGATCACTTAATTTTGACA	0.378													.|||	1520	0.303514	0.177	0.3804	5008	,	,		19110	0.2946		0.4155	False		,,,				2504	0.3139				p.L201L		Atlas-SNP	.											UGT2B11,NS,carcinoma,0,1	UGT2B11	92	1	1	Substitution - coding silent(1)	stomach(1)	c.A603G						PASS	.	T		1035,3371		124,787,1292	60.0	59.0	60.0		603	0.8	0.3	4	dbSNP_111	60	3861,4725		855,2151,1287	no	coding-synonymous	UGT2B11	NM_001073.1		979,2938,2579	CC,CT,TT		44.9686,23.4907,37.6847		201/530	70079838	4896,8096	2203	4293	6496	SO:0001819	synonymous_variant	10720	exon1			ATCACTTAATTTT	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.603A>G	4.37:g.70079838T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	261	123	0.471264	NM_001073	Q3KNV9	Silent	SNP	ENST00000446444.1	37	CCDS3527.1																																																																																			.	.	weak		0.378	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
MAGED2	10916	hgsc.bcm.edu	37	X	54841737	54841737	+	Silent	SNP	G	G	A	rs11555927	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:54841737G>A	ENST00000375068.1	+	12	1676	c.1443G>A	c.(1441-1443)gcG>gcA	p.A481A	MAGED2_ENST00000375062.4_Silent_p.A396A|MAGED2_ENST00000347546.4_Silent_p.A463A|MAGED2_ENST00000218439.4_Silent_p.A481A|MAGED2_ENST00000396224.1_Silent_p.A481A|MAGED2_ENST00000375060.1_Silent_p.A396A|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000375053.2_Silent_p.A481A|MAGED2_ENST00000375058.1_Silent_p.A481A			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	481						membrane (GO:0016020)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						CGATGGAAGCGGATTTGAagg	0.542													G|||	218	0.0577483	0.0061	0.0706	3775	,	,		13412	0.0		0.1441	False		,,,				2504	0.0164				p.A481A		Atlas-SNP	.											.	MAGED2	74	.	0			c.G1443A						PASS	.	G	,,	83,3752		0,76,7,1556,564	34.0	35.0	34.0		1443,1443,1443	1.6	1.0	X	dbSNP_120	34	970,5754		47,593,283,1788,1585	no	coding-synonymous,coding-synonymous,coding-synonymous	MAGED2	NM_014599.4,NM_177433.1,NM_201222.1	,,	47,669,290,3344,2149	AA,AG,A,GG,G		14.4259,2.1643,9.9725	,,	481/607,481/607,481/607	54841737	1053,9506	2203	4296	6499	SO:0001819	synonymous_variant	10916	exon12			GGAAGCGGATTTG	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated protein"", ""breast cancer associated gene 1"", ""melanoma-associated antigen D2"", ""hepatocellular carcinoma-associated protein HCA10"""	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.1443G>A	X.37:g.54841737G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Silent	SNP	ENST00000375068.1	37	CCDS14362.1																																																																																			G|0.906;0|0.003	.	strong		0.542	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599	
FAT1	2195	hgsc.bcm.edu	37	4	187629497	187629497	+	Silent	SNP	G	G	A	rs458021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187629497G>A	ENST00000441802.2	-	2	1694	c.1485C>T	c.(1483-1485)aaC>aaT	p.N495N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	495	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TCACGTACCCGTTCTCACCCT	0.478										HNSCC(5;0.00058)			A|||	2113	0.421925	0.2859	0.5692	5008	,	,		21177	0.2242		0.6461	False		,,,				2504	0.4744				p.N495N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C1485T						PASS	.	A		1529,2559		292,945,807	142.0	136.0	138.0		1485	-6.7	0.2	4	dbSNP_80	138	5456,2890		1792,1872,509	no	coding-synonymous	FAT1	NM_005245.3		2084,2817,1316	AA,AG,GG		34.6274,37.4022,43.8234		495/4589	187629497	6985,5449	2044	4173	6217	SO:0001819	synonymous_variant	2195	exon2			GTACCCGTTCTCA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1485C>T	4.37:g.187629497G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.554;A|0.446	0.446	strong		0.478	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
IGSF10	285313	hgsc.bcm.edu	37	3	151161112	151161112	+	Missense_Mutation	SNP	A	A	G	rs12487205	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:151161112A>G	ENST00000282466.3	-	5	5622	c.5623T>C	c.(5623-5625)Tac>Cac	p.Y1875H	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1875	Ig-like C2-type 5.		Y -> H (in dbSNP:rs12487205).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGGACCCAGTAAACGCTGGGC	0.423													A|||	131	0.0261581	0.0076	0.0504	5008	,	,		21296	0.0238		0.0358	False		,,,				2504	0.0266				p.Y1875H		Atlas-SNP	.											.	IGSF10	279	.	0			c.T5623C						PASS	.	A	HIS/TYR	63,4343	56.8+/-93.2	0,63,2140	72.0	74.0	73.0		5623	3.2	0.7	3	dbSNP_120	73	315,8285	112.5+/-172.7	4,307,3989	yes	missense	IGSF10	NM_178822.4	83	4,370,6129	GG,GA,AA		3.6628,1.4299,2.9064	benign	1875/2624	151161112	378,12628	2203	4300	6503	SO:0001583	missense	285313	exon5			CCCAGTAAACGCT	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5623T>C	3.37:g.151161112A>G	ENSP00000282466:p.Tyr1875His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	121	48	0.396694	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	57	0.0260989010989011	5	0.01016260162601626	19	0.052486187845303865	13	0.022727272727272728	20	0.026385224274406333	A	1.558	-0.537371	0.04082	0.014299	0.036628	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.66460	-0.21	5.26	3.24	0.37175	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.128097	0.35151	N	0.003416	T	0.06554	0.0168	N	0.01679	-0.765	0.27030	N	0.964264	B	0.06786	0.001	B	0.06405	0.002	T	0.06881	-1.0802	9	.	.	.	.	9.0014	0.36083	0.2633:0.0:0.7367:0.0	rs12487205;rs61027607;rs12487205	1875	Q6WRI0	IGS10_HUMAN	H	1875;502	ENSP00000282466:Y1875H	.	Y	-	1	0	IGSF10	152643802	1.000000	0.71417	0.719000	0.30619	0.927000	0.56198	4.877000	0.63086	0.452000	0.26830	-0.326000	0.08463	TAC	A|0.969;G|0.031	0.031	strong		0.423	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
MUC16	94025	hgsc.bcm.edu	37	19	9056982	9056982	+	Missense_Mutation	SNP	G	G	A	rs11670318	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9056982G>A	ENST00000397910.4	-	3	30667	c.30464C>T	c.(30463-30465)aCa>aTa	p.T10155I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10157	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCAAATCCTGTGGTCTCAAA	0.468													G|||	1241	0.247804	0.1543	0.2161	5008	,	,		22860	0.2391		0.336	False		,,,				2504	0.3149				p.T10155I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C30464T						PASS	.	G	ILE/THR	691,3181		64,563,1309	81.0	78.0	79.0		30464	0.5	0.0	19	dbSNP_120	79	2676,5598		418,1840,1879	yes	missense	MUC16	NM_024690.2	89	482,2403,3188	AA,AG,GG		32.3423,17.8461,27.7211	probably-damaging	10155/14508	9056982	3367,8779	1936	4137	6073	SO:0001583	missense	94025	exon3			AATCCTGTGGTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30464C>T	19.37:g.9056982G>A	ENSP00000381008:p.Thr10155Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	549	0.25137362637362637	89	0.18089430894308944	90	0.24861878453038674	119	0.20804195804195805	251	0.3311345646437995	g	4.903	0.167900	0.09339	0.178461	0.323423	ENSG00000181143	ENST00000397910	T	0.28666	1.6	2.78	0.467	0.16721	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	D	0.69078	0.997	D	0.63793	0.918	T	0.36625	-0.9740	8	0.87932	D	0	.	5.0713	0.14608	0.0:0.2366:0.5203:0.2431	rs11670318;rs60325742	10155	B5ME49	.	I	10155	ENSP00000381008:T10155I	ENSP00000381008:T10155I	T	-	2	0	MUC16	8917982	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.151000	0.10175	0.193000	0.20303	0.563000	0.77884	ACA	G|0.740;A|0.260	0.260	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KIAA1217	56243	hgsc.bcm.edu	37	10	24834980	24834980	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:24834980C>T	ENST00000376454.3	+	21	5589	c.5559C>T	c.(5557-5559)ctC>ctT	p.L1853L	KIAA1217_ENST00000458595.1_Silent_p.L1259L|KIAA1217_ENST00000376462.1_Silent_p.L1174L|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000376452.3_Silent_p.L1284L|KIAA1217_ENST00000376451.2_3'UTR	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1853	Ser-rich. {ECO:0000255}.				embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.L1853L(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CTGCCTCCCTCATCCCTTCTG	0.502																																					p.L1853L		Atlas-SNP	.											KIAA1217,NS,carcinoma,0,1	KIAA1217	235	1	1	Substitution - coding silent(1)	kidney(1)	c.C5559T						PASS	.						173.0	177.0	176.0					10																	24834980		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon21			CTCCCTCATCCCT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5559C>T	10.37:g.24834980C>T		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	271	129	0.476015	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			.	.	none		0.502	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
GFRA4	64096	hgsc.bcm.edu	37	20	3640823	3640823	+	Silent	SNP	C	C	T	rs2853208	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:3640823C>T	ENST00000319242.3	-	4	800	c.801G>A	c.(799-801)ccG>ccA	p.P267P	GFRA4_ENST00000290417.2_Silent_p.P237P			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	267					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						GGCTGTGCTCCGGGTCTCCCT	0.677													C|||	1900	0.379393	0.0499	0.5303	5008	,	,		14648	0.4117		0.5258	False		,,,				2504	0.5337				p.P267P		Atlas-SNP	.											GFRA4,NS,carcinoma,0,1	GFRA4	10	1	0			c.G801A						PASS	.	C	,	611,3773		62,487,1643	12.0	13.0	13.0		711,801	-6.0	0.0	20	dbSNP_100	13	4376,4176		1164,2048,1064	no	coding-synonymous,coding-synonymous	GFRA4	NM_022139.3,NM_145762.2	,	1226,2535,2707	TT,TC,CC		48.8307,13.937,38.5513	,	237/270,267/300	3640823	4987,7949	2192	4276	6468	SO:0001819	synonymous_variant	64096	exon4			GTGCTCCGGGTCT	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"""persephin receptor"""					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.801G>A	20.37:g.3640823C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_145762	Q5JT74|Q9H191|Q9H192	Silent	SNP	ENST00000319242.3	37	CCDS13056.1																																																																																			C|0.641;T|0.359	0.359	strong		0.677	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762	
ATN1	1822	hgsc.bcm.edu	37	12	7047143	7047143	+	Silent	SNP	C	C	A	rs7969685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7047143C>A	ENST00000356654.4	+	6	2667	c.2430C>A	c.(2428-2430)cgC>cgA	p.R810R	ATN1_ENST00000396684.2_Silent_p.R810R	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	810	Ala/Arg-rich.				cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						CCGAGCAGCGCGCGCGCGAAG	0.692											OREG0021641	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	814	0.16254	0.1059	0.2046	5008	,	,		-128	0.0109		0.3787	False		,,,				2504	0.1431				p.R810R		Atlas-SNP	.											.	ATN1	95	.	0			c.C2430A						PASS	.	C	,	560,3648		48,464,1592	8.0	9.0	9.0		2430,2430	3.0	1.0	12	dbSNP_116	9	2744,5534		492,1760,1887	no	coding-synonymous,coding-synonymous	ATN1	NM_001007026.1,NM_001940.3	,	540,2224,3479	AA,AC,CC		33.1481,13.308,26.4616	,	810/1191,810/1191	7047143	3304,9182	2104	4139	6243	SO:0001819	synonymous_variant	1822	exon6			GCAGCGCGCGCGC	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"""dentatorubral-pallidoluysian atrophy (atrophin-1)"""	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.2430C>A	12.37:g.7047143C>A		Somatic	47	0	0	638	WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	37	CCDS31734.1																																																																																			C|0.802;A|0.198	0.198	strong		0.692	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	
MLPH	79083	hgsc.bcm.edu	37	2	238449023	238449023	+	Silent	SNP	T	T	C	rs3817363	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238449023T>C	ENST00000264605.3	+	10	1431	c.1137T>C	c.(1135-1137)gaT>gaC	p.D379D	MLPH_ENST00000338530.4_Silent_p.D351D|MLPH_ENST00000445024.2_Silent_p.D379D|MLPH_ENST00000410032.1_Silent_p.D236D|MLPH_ENST00000409373.1_Silent_p.D311D|MLPH_ENST00000468178.1_3'UTR	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	379					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)	p.D379D(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		CGGAGGCCGATGTAGAGGAGG	0.612													T|||	955	0.190695	0.1309	0.2161	5008	,	,		19640	0.3165		0.0805	False		,,,				2504	0.2372				p.D379D		Atlas-SNP	.											MLPH,NS,carcinoma,0,2	MLPH	41	2	1	Substitution - coding silent(1)	stomach(1)	c.T1137C						PASS	.	T	,	663,3741	277.8+/-273.9	35,593,1574	81.0	74.0	76.0		1053,1137	4.2	0.0	2	dbSNP_107	76	807,7791	187.9+/-235.0	27,753,3519	no	coding-synonymous,coding-synonymous	MLPH	NM_001042467.1,NM_024101.5	,	62,1346,5093	CC,CT,TT		9.3859,15.0545,11.306	,	351/573,379/601	238449023	1470,11532	2202	4299	6501	SO:0001819	synonymous_variant	79083	exon10			GGCCGATGTAGAG	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1137T>C	2.37:g.238449023T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	148	54	0.364865	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Silent	SNP	ENST00000264605.3	37	CCDS2518.1	366|366	0.16758241758241757|0.16758241758241757	68|68	0.13821138211382114|0.13821138211382114	64|64	0.17679558011049723|0.17679558011049723	174|174	0.3041958041958042|0.3041958041958042	60|60	0.079155672823219|0.079155672823219	T|T	5.179|5.179	0.218543|0.218543	0.09810|0.09810	0.150545|0.150545	0.093859|0.093859	ENSG00000115648|ENSG00000115648	ENST00000415753|ENST00000436965	.|.	.|.	.|.	5.1|5.1	4.22|4.22	0.49857|0.49857	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.32244|0.32244	P|P	0.572326|0.572326	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.19289|0.19289	-1.0310|-1.0310	3|3	.|.	.|.	.|.	-21.6645|-21.6645	10.659|10.659	0.45692|0.45692	0.0:0.9038:0.0:0.0962|0.0:0.9038:0.0:0.0962	rs3817363|rs3817363	.|.	.|.	.|.	R|T	67|100	.|.	.|.	C|M	+|+	1|2	0|0	MLPH|MLPH	238113762|238113762	0.210000|0.210000	0.23517|0.23517	0.008000|0.008000	0.14137|0.14137	0.000000|0.000000	0.00434|0.00434	0.402000|0.402000	0.20965|0.20965	1.121000|1.121000	0.41925|0.41925	-0.248000|-0.248000	0.11899|0.11899	TGT|ATG	T|0.874;C|0.126	0.126	strong		0.612	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
UHRF2	115426	hgsc.bcm.edu	37	9	6506038	6506038	+	Silent	SNP	C	C	T	rs33962342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:6506038C>T	ENST00000276893.5	+	16	2436	c.2268C>T	c.(2266-2268)tgC>tgT	p.C756C	UHRF2_ENST00000485617.2_3'UTR	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	756					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		CATAGGATTGCCTACAGCGCT	0.413													C|||	652	0.130192	0.0053	0.1801	5008	,	,		22069	0.2371		0.1342	False		,,,				2504	0.1493				p.C756C		Atlas-SNP	.											UHRF2,right_upper_lobe,carcinoma,+1,1	UHRF2	50	1	0			c.C2268T						PASS	.	C		126,4280	93.4+/-132.2	2,122,2079	128.0	117.0	121.0		2268	3.1	1.0	9	dbSNP_126	121	975,7625	212.4+/-252.7	58,859,3383	no	coding-synonymous	UHRF2	NM_152896.2		60,981,5462	TT,TC,CC		11.3372,2.8597,8.4653		756/803	6506038	1101,11905	2203	4300	6503	SO:0001819	synonymous_variant	115426	exon16			GGATTGCCTACAG	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.2268C>T	9.37:g.6506038C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	37	CCDS6469.1																																																																																			C|0.886;T|0.114	0.114	strong		0.413	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	
CACNA1G	8913	hgsc.bcm.edu	37	17	48653354	48653354	+	Silent	SNP	C	C	A	rs12449998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48653354C>A	ENST00000359106.5	+	8	1591	c.1591C>A	c.(1591-1593)Cgg>Agg	p.R531R	CACNA1G_ENST00000514717.1_Silent_p.R531R|CACNA1G_ENST00000354983.4_Silent_p.R531R|CACNA1G_ENST00000512389.1_Silent_p.R531R|CACNA1G_ENST00000513689.2_Silent_p.R531R|CACNA1G_ENST00000416767.4_Silent_p.R531R|CACNA1G_ENST00000513964.1_Silent_p.R531R|CACNA1G_ENST00000507609.1_Silent_p.R531R|CACNA1G_ENST00000507896.1_Silent_p.R531R|CACNA1G_ENST00000507336.1_Silent_p.R531R|CACNA1G_ENST00000503485.1_Silent_p.R531R|CACNA1G_ENST00000515411.1_Silent_p.R531R|CACNA1G_ENST00000514079.1_Silent_p.R531R|CACNA1G_ENST00000502264.1_Silent_p.R531R|CACNA1G_ENST00000429973.2_Silent_p.R531R|CACNA1G_ENST00000360761.4_Silent_p.R531R|CACNA1G_ENST00000515165.1_Silent_p.R531R|CACNA1G_ENST00000358244.5_Silent_p.R531R|CACNA1G_ENST00000507510.2_Silent_p.R531R|CACNA1G_ENST00000515765.1_Silent_p.R531R|CACNA1G_ENST00000352832.5_Silent_p.R531R|CACNA1G_ENST00000514181.1_Silent_p.R531R|CACNA1G_ENST00000505165.1_Silent_p.R531R|CACNA1G_ENST00000442258.2_Silent_p.R531R|CACNA1G_ENST00000510115.1_Silent_p.R531R|CACNA1G_ENST00000510366.1_Silent_p.R531R	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	531					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TGGGTCCCGCCGGCTCATGCT	0.682													C|||	2624	0.523962	0.143	0.5562	5008	,	,		14607	0.9177		0.4642	False		,,,				2504	0.6718				p.R531R		Atlas-SNP	.											CACNA1G_ENST00000416767,caecum,carcinoma,0,8	CACNA1G	659	8	0			c.C1591A						PASS	.	C	,,,,,,,,,,,,,,	769,3071		99,571,1250	10.0	18.0	15.0		1591,1591,1591,1591,1591,1591,1591,1591,1591,1591,1591,1591,1591,1591,1591	3.4	1.0	17	dbSNP_120	15	3739,4467		927,1885,1291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1,NM_198397.1	,,,,,,,,,,,,,,	1026,2456,2541	AA,AC,CC		45.5642,20.026,37.4232	,,,,,,,,,,,,,,	531/2378,531/2172,531/2355,531/2274,531/2299,531/2322,531/2262,531/2307,531/2285,531/2333,531/2267,531/2251,531/2244,531/2344,531/1556	48653354	4508,7538	1920	4103	6023	SO:0001819	synonymous_variant	8913	exon8			TCCCGCCGGCTCA	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1591C>A	17.37:g.48653354C>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																			C|0.469;A|0.531	0.531	strong		0.682	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
FCRL5	83416	hgsc.bcm.edu	37	1	157508882	157508882	+	Missense_Mutation	SNP	C	C	T	rs6427384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:157508882C>T	ENST00000361835.3	-	7	1553	c.1396G>A	c.(1396-1398)Gtc>Atc	p.V466I	FCRL5_ENST00000368189.3_Missense_Mutation_p.V466I|FCRL5_ENST00000356953.4_Missense_Mutation_p.V466I|FCRL5_ENST00000368191.3_Missense_Mutation_p.V381I|FCRL5_ENST00000368190.3_Missense_Mutation_p.V466I	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	466			V -> I (in dbSNP:rs6427384). {ECO:0000269|PubMed:11290337, ECO:0000269|PubMed:11453668, ECO:0000269|PubMed:11493702, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				TTACCAGTGACGGAGAGGCTC	0.567													C|||	3472	0.693291	0.3222	0.8098	5008	,	,		19274	0.7887		0.8539	False		,,,				2504	0.8487				p.V466I		Atlas-SNP	.											.	FCRL5	177	.	0			c.G1396A						PASS	.	C	ILE/VAL,ILE/VAL	1796,2610	523.1+/-371.0	384,1028,791	47.0	42.0	44.0		1396,1396	-1.7	0.0	1	dbSNP_116	44	7298,1302	753.8+/-407.5	3085,1128,87	yes	missense,missense	FCRL5	NM_001195388.1,NM_031281.2	29,29	3469,2156,878	TT,TC,CC		15.1395,40.7626,30.0784	benign,benign	466/999,466/978	157508882	9094,3912	2203	4300	6503	SO:0001583	missense	83416	exon7			CAGTGACGGAGAG	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1396G>A	1.37:g.157508882C>T	ENSP00000354691:p.Val466Ile	Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	1549	0.7092490842490843	166	0.33739837398373984	290	0.8011049723756906	438	0.7657342657342657	655	0.8641160949868074	C	10.39	1.335903	0.24253	0.407626	0.848605	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.11821	2.74;2.74;2.74;2.74;2.74	3.0	-1.74	0.08056	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02494	0.0076	L	0.39020	1.185	0.58432	P	1.999999999946489E-6	B;B;B;P;B	0.40476	0.056;0.055;0.019;0.718;0.132	B;B;B;B;B	0.37144	0.027;0.027;0.019;0.242;0.027	T	0.38650	-0.9651	8	0.30078	T	0.28	.	3.0118	0.06046	0.1926:0.4366:0.0:0.3708	rs6427384;rs52813953;rs61191274;rs6427384	381;466;466;466;466	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;FCRL5_HUMAN	I	466;466;466;381;466	ENSP00000354691:V466I;ENSP00000349434:V466I;ENSP00000357173:V466I;ENSP00000357174:V381I;ENSP00000357172:V466I	ENSP00000349434:V466I	V	-	1	0	FCRL5	155775506	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-2.010000	0.01454	-0.541000	0.06257	-0.448000	0.05591	GTC	C|0.305;T|0.695	0.695	strong		0.567	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
FAM46D	169966	hgsc.bcm.edu	37	X	79698593	79698593	+	Missense_Mutation	SNP	C	C	G	rs1113265	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:79698593C>G	ENST00000308293.5	+	3	794	c.555C>G	c.(553-555)gaC>gaG	p.D185E	FAM46D_ENST00000538312.1_Missense_Mutation_p.D185E	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	185			D -> E (in dbSNP:rs1113265). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.							kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						CCATGTTAGACTTCTACAGTG	0.388													C|||	1406	0.37245	0.2685	0.4207	3775	,	,		15522	0.0615		0.5199	False		,,,				2504	0.1779				p.D185E		Atlas-SNP	.											.	FAM46D	69	.	0			c.C555G						PASS	.	C	GLU/ASP,GLU/ASP	1500,2332		247,778,228,606,342	67.0	64.0	65.0		555,555	-8.8	0.1	X	dbSNP_86	65	4774,1951		1219,991,1345,217,526	yes	missense,missense	FAM46D	NM_001170574.1,NM_152630.4	45,45	1466,1769,1573,823,868	GG,GC,G,CC,C		29.0112,39.1441,40.5702	benign,benign	185/390,185/390	79698593	6274,4283	2201	4298	6499	SO:0001583	missense	169966	exon5			GTTAGACTTCTAC	BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"""cancer/testis antigen 112"""					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.555C>G	X.37:g.79698593C>G	ENSP00000308575:p.Asp185Glu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_001170574	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	37	CCDS14446.1	709	0.4273658830620856	85	0.20238095238095238	107	0.41796875	23	0.04151624548736462	278	0.5325670498084292	C	0.008	-1.924635	0.00493	0.391441	0.709888	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.21031	2.03;2.03	4.8	-8.75	0.00834	Domain of unknown function DUF1693 (1);	2.784390	0.01166	N	0.006750	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.45131	-0.9282	9	0.02654	T	1	-0.0151	3.1878	0.06607	0.2954:0.0963:0.0925:0.5158	rs1113265;rs1113265	185	Q8NEK8	FA46D_HUMAN	E	185	ENSP00000443410:D185E;ENSP00000308575:D185E	ENSP00000308575:D185E	D	+	3	2	FAM46D	79585249	0.482000	0.25948	0.050000	0.19076	0.702000	0.40608	-0.369000	0.07533	-2.291000	0.00666	-0.996000	0.02517	GAC	C|0.503;0|0.028	.	strong		0.388	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630	
TEKT4	150483	hgsc.bcm.edu	37	2	95537568	95537568	+	Missense_Mutation	SNP	C	C	T	rs80243548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:95537568C>T	ENST00000295201.4	+	1	381	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	TEKT4_ENST00000427593.2_Missense_Mutation_p.R82C|AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	82					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCTGGCGCAGCGCACGCAGCA	0.692													.|||	53	0.0105831	0.0	0.0072	5008	,	,		16615	0.001		0.0169	False		,,,				2504	0.0307				p.R82C		Atlas-SNP	.											TEKT4,bladder,carcinoma,-2,2	TEKT4	72	2	0			c.C244T						PASS	.	C	CYS/ARG	12,4370		0,12,2179	16.0	17.0	17.0		244	2.0	0.7	2	dbSNP_131	17	182,8356		2,178,4089	no	missense	TEKT4	NM_144705.2	180	2,190,6268	TT,TC,CC		2.1316,0.2738,1.5015	benign	82/436	95537568	194,12726	2191	4269	6460	SO:0001583	missense	150483	exon1			GCGCAGCGCACGC	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.244C>T	2.37:g.95537568C>T	ENSP00000295201:p.Arg82Cys	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	14	0.00641025641025641	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	12	0.0158311345646438	.	13.71	2.317321	0.40996	0.002738	0.021316	ENSG00000163060	ENST00000295201;ENST00000427593	T;T	0.02863	4.13;4.13	1.97	1.97	0.26223	.	0.121716	0.56097	N	0.000027	T	0.01592	0.0051	L	0.55990	1.75	0.80722	D	1	B	0.27997	0.197	B	0.25405	0.06	T	0.49808	-0.8900	10	0.37606	T	0.19	-10.6904	9.5816	0.39490	0.0:1.0:0.0:0.0	.	82	Q8WW24	TEKT4_HUMAN	C	82	ENSP00000295201:R82C;ENSP00000407596:R82C	ENSP00000295201:R82C	R	+	1	0	TEKT4	94901295	0.174000	0.23070	0.741000	0.31004	0.479000	0.33129	-0.002000	0.12924	1.094000	0.41399	0.558000	0.71614	CGC	C|0.978;G|0.007;T|0.015	0.015	strong		0.692	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
NDUFA6	4700	hgsc.bcm.edu	37	22	42486723	42486723	+	Missense_Mutation	SNP	G	G	A	rs1801311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:42486723G>A	ENST00000498737.2	-	1	236	c.104C>T	c.(103-105)gCt>gTt	p.A35V	NDUFA6-AS1_ENST00000595777.1_RNA|RP1-257I20.14_ENST00000602718.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000608974.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6_ENST00000602404.1_Missense_Mutation_p.A9V|NDUFA6-AS1_ENST00000417327.1_RNA	NM_002490.3	NP_002481.2	P56556	NDUA6_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa	35			A -> V (in dbSNP:rs1801311). {ECO:0000269|PubMed:14702039}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			kidney(1)|lung(3)|upper_aerodigestive_tract(1)	5						GGTAGAAGTAGCTTGGCGGAC	0.632													G|||	1772	0.353834	0.5371	0.3271	5008	,	,		15164	0.1508		0.335	False		,,,				2504	0.3538				p.A35V		Atlas-SNP	.											.	NDUFA6	13	.	0			c.C104T						PASS	.	G	VAL/ALA	2174,2232	583.2+/-385.8	537,1100,566	88.0	90.0	90.0		104	2.4	0.1	22	dbSNP_89	90	2889,5711	453.3+/-363.2	506,1877,1917	yes	missense	NDUFA6	NM_002490.3	64	1043,2977,2483	AA,AG,GG		33.593,49.3418,38.9282	benign	35/155	42486723	5063,7943	2203	4300	6503	SO:0001583	missense	4700	exon1			GAAGTAGCTTGGC	AF047182	CCDS33656.1	22q13.2	2010-05-07	2002-08-29		ENSG00000184983	ENSG00000184983		"""LYR motif containing"", ""Mitochondrial respiratory chain complex / Complex I"""	7690	protein-coding gene	gene with protein product	"""complex I B14 subunit"""	602138	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (14kD, B14)"""			9763676, 9425316	Standard	NM_002490		Approved	B14, LYRM6, CI-B14, NADHB14	uc003bcb.3	P56556	OTTHUMG00000151287	ENST00000498737.2:c.104C>T	22.37:g.42486723G>A	ENSP00000418842:p.Ala35Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	121	71	0.586777	NM_002490	B2RE54|O43675|Q6FGW0|Q6IBT8|Q6IC39	Missense_Mutation	SNP	ENST00000498737.2	37	CCDS33656.1	731	0.3347069597069597	270	0.5487804878048781	115	0.31767955801104975	95	0.1660839160839161	251	0.3311345646437995	G	16.70	3.196846	0.58126	0.493418	0.33593	ENSG00000184983	ENST00000498737	T	0.69685	-0.42	5.64	2.39	0.29439	.	0.213179	0.49916	D	0.000138	T	0.00012	0.0000	N	0.12569	0.235	0.25870	P	0.9837283	B	0.17852	0.024	B	0.10450	0.005	T	0.44967	-0.9293	9	0.48119	T	0.1	-3.0867	5.8599	0.18740	0.2233:0.1494:0.6273:0.0	rs1801311;rs57054953;rs1801311	35	P56556	NDUA6_HUMAN	V	35	ENSP00000418842:A35V	ENSP00000418842:A35V	A	-	2	0	NDUFA6	40816669	0.974000	0.33945	0.066000	0.19879	0.009000	0.06853	1.568000	0.36418	0.720000	0.32209	0.655000	0.94253	GCT	G|0.625;A|0.375	0.375	strong		0.632	NDUFA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322089.4	NM_002490	
FRMPD2	143162	hgsc.bcm.edu	37	10	49400730	49400730	+	Missense_Mutation	SNP	C	C	T	rs116034788	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:49400730C>T	ENST00000374201.3	-	16	2464	c.2162G>A	c.(2161-2163)cGc>cAc	p.R721H	FRMPD2_ENST00000305531.3_Missense_Mutation_p.R696H|FRMPD2_ENST00000407470.4_Missense_Mutation_p.R689H	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	721					tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CACCCACCTGCGCCCGATGCC	0.493													C|||	14	0.00279553	0.0	0.0029	5008	,	,		20123	0.0089		0.003	False		,,,				2504	0.0				p.R721H		Atlas-SNP	.											FRMPD2,NS,carcinoma,-1,1	FRMPD2	157	1	0			c.G2162A						PASS	.	C	HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	75.0	54.0	61.0		2162	0.9	0.7	10	dbSNP_132	61	19,8581	14.0+/-48.4	0,19,4281	yes	missense	FRMPD2	NM_001018071.3	29	0,25,6478	TT,TC,CC		0.2209,0.1362,0.1922	possibly-damaging	721/1310	49400730	25,12981	2203	4300	6503	SO:0001583	missense	143162	exon16			CACCTGCGCCCGA	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.2162G>A	10.37:g.49400730C>T	ENSP00000363317:p.Arg721His	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	131	60	0.458015	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	4	0.006993006993006993	1	0.0013192612137203166	C	9.151	1.016217	0.19355	0.001362	0.002209	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.64803	-0.08;-0.12;-0.11	5.01	0.934	0.19477	.	.	.	.	.	T	0.29882	0.0747	N	0.14661	0.345	0.21184	N	0.999768	B;D;B	0.54207	0.024;0.965;0.024	B;B;B	0.38156	0.003;0.266;0.003	T	0.13818	-1.0495	9	0.45353	T	0.12	.	6.935	0.24461	0.0:0.5514:0.2905:0.1581	.	696;721;689	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	H	721;696;689	ENSP00000363317:R721H;ENSP00000307079:R696H;ENSP00000384339:R689H	ENSP00000307079:R696H	R	-	2	0	FRMPD2	49070736	0.170000	0.23016	0.681000	0.30009	0.090000	0.18270	0.379000	0.20585	0.234000	0.21139	-0.211000	0.12701	CGC	C|0.998;T|0.002	0.002	strong		0.493	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
DNHD1	144132	hgsc.bcm.edu	37	11	6532519	6532519	+	Missense_Mutation	SNP	C	C	T	rs4758423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6532519C>T	ENST00000527990.2	+	5	1252	c.1252C>T	c.(1252-1254)Cac>Tac	p.H418Y	DNHD1_ENST00000254579.6_Missense_Mutation_p.H418Y|DNHD1_ENST00000354685.3_Missense_Mutation_p.H418Y			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	418			H -> Y (in dbSNP:rs4758423).		microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GCAGGAGCTACACTCTGTGTC	0.547													C|||	1104	0.220447	0.1377	0.3199	5008	,	,		19977	0.128		0.3549	False		,,,				2504	0.2188				p.H418Y		Atlas-SNP	.											DNHD1,NS,adenoma,0,2	DNHD1	198	2	0			c.C1252T						PASS	.	C	TYR/HIS,TYR/HIS	734,3668	300.1+/-286.2	59,616,1526	118.0	102.0	108.0		1252,1252	4.4	0.4	11	dbSNP_111	108	2831,5761	447.9+/-361.7	464,1903,1929	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	83,83	523,2519,3455	TT,TC,CC		32.9493,16.6742,27.4357	possibly-damaging,possibly-damaging	418/4754,418/598	6532519	3565,9429	2201	4296	6497	SO:0001583	missense	144132	exon6			GAGCTACACTCTG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.1252C>T	11.37:g.6532519C>T	ENSP00000436180:p.His418Tyr	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	201	94	0.467662	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	533	0.24404761904761904	66	0.13414634146341464	120	0.3314917127071823	86	0.15034965034965034	261	0.34432717678100266	C	10.10	1.257615	0.22965	0.166742	0.329493	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.26957	1.7;2.7;1.7	5.32	4.41	0.53225	.	1.602800	0.03315	N	0.190977	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P;B	0.44521	0.837;0.168	B;B	0.34991	0.193;0.086	T	0.32640	-0.9899	9	0.31617	T	0.26	.	8.1675	0.31235	0.0:0.8193:0.0:0.1807	rs4758423;rs17244249;rs61213507;rs4758423	418;418	Q96M86;Q96M86-4	DNHD1_HUMAN;.	Y	418	ENSP00000254579:H418Y;ENSP00000346716:H418Y;ENSP00000436180:H418Y	ENSP00000254579:H418Y	H	+	1	0	DNHD1	6489095	0.000000	0.05858	0.406000	0.26421	0.327000	0.28475	0.136000	0.15974	1.372000	0.46190	0.655000	0.94253	CAC	C|0.748;T|0.252	0.252	strong		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
GIF	2694	hgsc.bcm.edu	37	11	59611362	59611362	+	Silent	SNP	G	G	A	rs35792306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59611362G>A	ENST00000257248.2	-	2	293	c.246C>T	c.(244-246)agC>agT	p.S82S	GIF_ENST00000541311.1_Silent_p.S57S	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	82					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)			large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	CGTTGTTGTCGCTGGACATGA	0.547													G|||	269	0.0537141	0.003	0.0259	5008	,	,		19218	0.0952		0.0785	False		,,,				2504	0.0736				p.S82S	NSCLC(53;1139 1245 16872 38474 42853)	Atlas-SNP	.											.	GIF	43	.	0			c.C246T						PASS	.	G		84,4318	72.0+/-110.0	1,82,2118	100.0	87.0	91.0		246	-0.0	0.8	11	dbSNP_126	91	680,7910	169.7+/-221.0	24,632,3639	no	coding-synonymous	GIF	NM_005142.2		25,714,5757	AA,AG,GG		7.9162,1.9082,5.8805		82/418	59611362	764,12228	2201	4295	6496	SO:0001819	synonymous_variant	2694	exon2			GTTGTCGCTGGAC	X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.246C>T	11.37:g.59611362G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	209	98	0.4689	NM_005142	B2RAN8|B4DVZ1	Silent	SNP	ENST00000257248.2	37	CCDS7977.1																																																																																			G|0.937;A|0.063	0.063	strong		0.547	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142	
RTCB	51493	hgsc.bcm.edu	37	22	32795641	32795641	+	Silent	SNP	C	C	T	rs5749426	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:32795641C>T	ENST00000216038.5	-	6	701	c.603G>A	c.(601-603)caG>caA	p.Q201Q	RTCB_ENST00000476619.1_5'UTR|RTCB_ENST00000451746.2_Intron	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		TGGGGTCAGCCTGCAGCATCC	0.498													T|||	2232	0.445687	0.6392	0.3487	5008	,	,		16455	0.5179		0.3032	False		,,,				2504	0.3252				p.Q201Q		Atlas-SNP	.											.	C22orf28	43	.	0			c.G603A						PASS	.	T		2691,1715	516.5+/-369.2	800,1091,312	204.0	194.0	197.0		603	1.1	1.0	22	dbSNP_114	197	2998,5602	665.3+/-402.3	523,1952,1825	no	coding-synonymous	C22orf28	NM_014306.4		1323,3043,2137	TT,TC,CC		34.8605,38.9242,43.7414		201/506	32795641	5689,7317	2203	4300	6503	SO:0001819	synonymous_variant	51493	exon6			GTCAGCCTGCAGC	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"""focal adhesion-associated protein"""	613901	"""chromosome 22 open reading frame 28"""	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.603G>A	22.37:g.32795641C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_014306		Silent	SNP	ENST00000216038.5	37	CCDS13905.1																																																																																			C|0.552;T|0.448	0.448	strong		0.498	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	
CROCC	9696	hgsc.bcm.edu	37	1	17272037	17272037	+	Missense_Mutation	SNP	G	G	A	rs142404824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17272037G>A	ENST00000375541.5	+	15	2141	c.2072G>A	c.(2071-2073)cGc>cAc	p.R691H	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCGCTGAGCCGCGCCACACTG	0.637																																					p.R691H		Atlas-SNP	.											CROCC,colon,carcinoma,-1,1	CROCC	185	1	0			c.G2072A						PASS	.						18.0	15.0	16.0					1																	17272037		2196	4279	6475	SO:0001583	missense	9696	exon15			TGAGCCGCGCCAC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2072G>A	1.37:g.17272037G>A	ENSP00000364691:p.Arg691His	Somatic	344	0	0		WXS	Illumina HiSeq	Phase_I	413	197	0.476998	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	52	0.023809523809523808	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	35	0.04617414248021108	G	9.043	0.990268	0.18966	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.11063	2.81	5.01	0.883	0.19177	.	.	.	.	.	T	0.00784	0.0026	N	0.14661	0.345	0.09310	N	1	P;B	0.43578	0.811;0.002	B;B	0.36504	0.226;0.001	T	0.37079	-0.9721	9	0.62326	D	0.03	.	4.9211	0.13871	0.3313:0.1887:0.48:0.0	.	554;691	A1L0S8;Q5TZA2	.;CROCC_HUMAN	H	691;572	ENSP00000364691:R691H	ENSP00000364691:R691H	R	+	2	0	CROCC	17144624	0.000000	0.05858	0.061000	0.19648	0.207000	0.24258	-0.033000	0.12246	0.298000	0.22638	-0.224000	0.12420	CGC	G|0.972;A|0.028	0.028	strong		0.637	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
LILRA6	79168	hgsc.bcm.edu	37	19	54746051	54746051	+	Missense_Mutation	SNP	A	A	C	rs620207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54746051A>C	ENST00000396365.2	-	3	245	c.206T>G	c.(205-207)tTg>tGg	p.L69W	LILRA6_ENST00000270464.5_Missense_Mutation_p.L69W|LILRB3_ENST00000407860.2_Missense_Mutation_p.L69W|LILRA6_ENST00000391735.3_Missense_Mutation_p.L69W|LILRA6_ENST00000245621.5_Missense_Mutation_p.L69W|LILRA6_ENST00000419410.2_Missense_Mutation_p.L69W|LILRA6_ENST00000440558.2_Missense_Mutation_p.L69W	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	69			L -> W (in dbSNP:rs620207).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ATTTCTGTCCAAGGGCTCTGG	0.572																																					p.L69W		Atlas-SNP	.											.	LILRA6	75	.	0			c.T206G						PASS	.						289.0	279.0	282.0					19																	54746051		2203	4300	6503	SO:0001583	missense	79168	exon3			CTGTCCAAGGGCT	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.206T>G	19.37:g.54746051A>C	ENSP00000379651:p.Leu69Trp	Somatic	1616	1	0.000618812		WXS	Illumina HiSeq	Phase_I	1104	563	0.509964	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	1062	0.48626373626373626	225	0.4573170731707317	158	0.43646408839779005	322	0.5629370629370629	357	0.470976253298153	a	0.012	-1.690115	0.00738	.	.	ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88;2.88;2.88	2.87	-3.51	0.04696	Immunoglobulin-like fold (1);	1.026710	0.07786	N	0.954165	T	0.00012	0.0000	N	0.01086	-1.025	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B	0.27117	0.001;0.0;0.0;0.0;0.168;0.0;0.0;0.001;0.0;0.002	B;B;B;B;B;B;B;B;B;B	0.33339	0.003;0.001;0.002;0.004;0.162;0.001;0.002;0.002;0.001;0.003	T	0.42085	-0.9472	9	0.02654	T	1	.	2.6283	0.04936	0.5375:0.2118:0.1436:0.1071	rs620207;rs3193439;rs7258570;rs61515109	69;69;69;69;69;69;69;69;69;69	C9JFH3;Q6PI73-2;B5MCX0;B5ME96;Q6PI73;F8WCY4;F8WD89;D3YTC4;F8W6G6;O75022-2	.;.;.;.;LIRA6_HUMAN;.;.;.;.;.	W	69	ENSP00000384274:L69W;ENSP00000390120:L69W;ENSP00000270464:L69W;ENSP00000411227:L69W;ENSP00000375615:L69W;ENSP00000379651:L69W;ENSP00000245621:L69W	ENSP00000245621:L69W	L	-	2	0	LILRB3;LILRA6	59437863	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.410000	0.02480	-1.020000	0.03354	-1.124000	0.02001	TTG	A|0.514;C|0.486	0.486	strong		0.572	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
TMEM2	23670	hgsc.bcm.edu	37	9	74354983	74354983	+	Silent	SNP	A	A	G	rs25691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:74354983A>G	ENST00000377044.4	-	5	1739	c.1200T>C	c.(1198-1200)atT>atC	p.I400I	TMEM2_ENST00000377066.5_Silent_p.I400I	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	400					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GCCTACCTTCAATCCATTCAC	0.368													G|||	407	0.08127	0.0393	0.0476	5008	,	,		17161	0.0198		0.0815	False		,,,				2504	0.2249				p.I400I		Atlas-SNP	.											.	TMEM2	112	.	0			c.T1200C						PASS	.	G	,	173,4233	810.4+/-416.0	6,161,2036	100.0	98.0	99.0		1200,1200	-1.6	0.9	9	dbSNP_72	99	722,7878	786.7+/-407.6	31,660,3609	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	37,821,5645	GG,GA,AA		8.3953,3.9265,6.8814	,	400/1321,400/1384	74354983	895,12111	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon5			ACCTTCAATCCAT		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1200T>C	9.37:g.74354983A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			A|0.937;G|0.063	0.063	strong		0.368	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
Unknown	0	hgsc.bcm.edu	37	Y	21154426	21154426	+	IGR	SNP	G	G	A	rs52812045		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrY:21154426G>A								TTTY14 (114312 upstream) : RNU6-255P (26442 downstream)																							ACCACCAGCCGCCTTGGTGGT	0.493																																					p.A57V		Atlas-SNP	.											.	.	.	.	0			c.C170T						PASS	.						41.0	51.0	48.0					Y																	21154426		692	1591	2283	SO:0001628	intergenic_variant	100133941	exon1			CCAGCCGCCTTGG																													Y.37:g.21154426G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	122	25	0.204918	NM_013230		Missense_Mutation	SNP		37																																																																																				G|0.500;A|0.500	0.500	weak	0	0.493								
SH3RF1	57630	hgsc.bcm.edu	37	4	170037572	170037572	+	Missense_Mutation	SNP	G	G	A	rs3811813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:170037572G>A	ENST00000284637.9	-	10	2328	c.1987C>T	c.(1987-1989)Cca>Tca	p.P663S	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	663			P -> S (in dbSNP:rs3811813).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		GAAGTCAGTGGAGCAGCTGCT	0.622													G|||	462	0.0922524	0.0083	0.062	5008	,	,		19880	0.0813		0.1362	False		,,,				2504	0.1933				p.P663S		Atlas-SNP	.											SH3RF1,NS,carcinoma,+2,1	SH3RF1	60	1	0			c.C1987T						PASS	.	G	SER/PRO	166,4240	109.1+/-147.4	3,160,2040	61.0	52.0	55.0		1987	1.4	0.0	4	dbSNP_107	55	1098,7502	228.7+/-263.7	80,938,3282	yes	missense	SH3RF1	NM_020870.3	74	83,1098,5322	AA,AG,GG		12.7674,3.7676,9.7186	benign	663/889	170037572	1264,11742	2203	4300	6503	SO:0001583	missense	57630	exon10			TCAGTGGAGCAGC	BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"""RING-type (C3HC4) zinc fingers"""	17650	protein-coding gene	gene with protein product	"""plenty of SH3 domains"""		"""SH3 multiple domains 2"""	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.1987C>T	4.37:g.170037572G>A	ENSP00000284637:p.Pro663Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	139	74	0.532374	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Missense_Mutation	SNP	ENST00000284637.9	37	CCDS34099.1	177	0.08104395604395605	5	0.01016260162601626	28	0.07734806629834254	39	0.06818181818181818	105	0.13852242744063326	G	0.259	-1.000945	0.02128	0.037676	0.127674	ENSG00000154447	ENST00000284637	T	0.10960	2.82	5.24	1.38	0.22167	.	0.261100	0.27563	N	0.018810	T	0.00039	0.0001	N	0.00926	-1.1	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43572	-0.9383	9	0.02654	T	1	-1.1484	5.8399	0.18627	0.7065:0.1407:0.1528:0.0	rs3811813;rs60713833;rs3811813	663	Q7Z6J0	SH3R1_HUMAN	S	663	ENSP00000284637:P663S	ENSP00000284637:P663S	P	-	1	0	SH3RF1	170274147	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	3.648000	0.54410	0.009000	0.14813	-0.378000	0.06908	CCA	G|0.906;A|0.094	0.094	strong		0.622	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870	
ZNF317	57693	hgsc.bcm.edu	37	19	9267319	9267319	+	Missense_Mutation	SNP	G	G	T	rs3752199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9267319G>T	ENST00000247956.6	+	3	362	c.57G>T	c.(55-57)caG>caT	p.Q19H	ZNF317_ENST00000360385.3_Missense_Mutation_p.Q19H	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	19			Q -> H (in dbSNP:rs3752199).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q19H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						CCTGTCTCCAGGACTCAGAAT	0.498													G|||	646	0.128994	0.0408	0.1657	5008	,	,		19806	0.1488		0.1998	False		,,,				2504	0.1288				p.Q19H		Atlas-SNP	.											ZNF317,NS,carcinoma,0,1	ZNF317	61	1	1	Substitution - Missense(1)	stomach(1)	c.G57T						PASS	.	G	HIS/GLN,HIS/GLN	321,4085	169.8+/-200.3	8,305,1890	163.0	164.0	163.0		57,57	-3.5	0.0	19	dbSNP_107	163	1593,7007	297.8+/-303.6	164,1265,2871	yes	missense,missense	ZNF317	NM_001190791.1,NM_020933.4	24,24	172,1570,4761	TT,TG,GG		18.5233,7.2855,14.7163	benign,benign	19/564,19/596	9267319	1914,11092	2203	4300	6503	SO:0001583	missense	57693	exon3			TCTCCAGGACTCA	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"""Zinc fingers, C2H2-type"", ""-"""	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.57G>T	19.37:g.9267319G>T	ENSP00000247956:p.Gln19His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	37	CCDS12210.1	312	0.14285714285714285	23	0.046747967479674794	57	0.1574585635359116	76	0.13286713286713286	156	0.20580474934036938	G	2.367	-0.345291	0.05208	0.072855	0.185233	ENSG00000130803	ENST00000247956;ENST00000360385;ENST00000419608	T;T	0.07908	3.42;3.15	3.04	-3.55	0.04639	.	0.424674	0.17436	N	0.174304	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44143	-0.9347	9	0.34782	T	0.22	-9.111	2.7311	0.05227	0.3513:0.0:0.2805:0.3682	rs3752199;rs17205997;rs59177470;rs3752199	19;19	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	H	19;19;33	ENSP00000247956:Q19H;ENSP00000353554:Q19H	ENSP00000247956:Q19H	Q	+	3	2	ZNF317	9128319	0.001000	0.12720	0.021000	0.16686	0.279000	0.26890	-0.351000	0.07711	-0.647000	0.05444	-0.225000	0.12378	CAG	G|0.865;T|0.135	0.135	strong		0.498	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933	
KIAA1683	80726	hgsc.bcm.edu	37	19	18376517	18376517	+	Silent	SNP	C	C	T	rs61740752	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18376517C>T	ENST00000600328.3	-	3	2026	c.1833G>A	c.(1831-1833)caG>caA	p.Q611Q	KIAA1683_ENST00000600359.3_Silent_p.Q565Q|KIAA1683_ENST00000392413.4_Silent_p.Q611Q			Q9H0B3	K1683_HUMAN	KIAA1683	611						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TCGCCTGTTTCTGGGTGCCAG	0.557													C|||	761	0.151957	0.0257	0.1196	5008	,	,		20306	0.3036		0.1292	False		,,,				2504	0.2127				p.Q611Q		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G1833A						PASS	.	C	,,	177,4229	115.4+/-153.4	1,175,2027	53.0	59.0	57.0		1833,1695,1833	0.8	0.0	19	dbSNP_129	57	1171,7429	236.1+/-268.4	79,1013,3208	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	80,1188,5235	TT,TC,CC		13.6163,4.0172,10.3644	,,	611/1368,565/1135,611/1181	18376517	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	80726	exon3			CTGTTTCTGGGTG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1833G>A	19.37:g.18376517C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	175	79	0.451429	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			C|0.886;T|0.114	0.114	strong		0.557	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
AMICA1	120425	hgsc.bcm.edu	37	11	118081345	118081345	+	Missense_Mutation	SNP	A	A	T	rs17121881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118081345A>T	ENST00000356289.5	-	4	454	c.281T>A	c.(280-282)aTc>aAc	p.I94N	AMICA1_ENST00000533261.1_Missense_Mutation_p.I94N|AMICA1_ENST00000526620.1_Missense_Mutation_p.I55N|AMICA1_ENST00000292067.7_Missense_Mutation_p.I84N	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	94	Ig-like V-type 1.		I -> N (in dbSNP:rs17121881). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.		blood coagulation (GO:0007596)|gamma-delta T cell activation (GO:0046629)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte migration (GO:0050900)|monocyte extravasation (GO:0035696)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)	p.I84N(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|stomach(2)	20	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		ATTGCATAAGATGTCCCCCAT	0.502													A|||	2341	0.467452	0.1346	0.487	5008	,	,		18947	0.5387		0.5298	False		,,,				2504	0.7658				p.I94N		Atlas-SNP	.											AMICA1,caecum,carcinoma,0,2	AMICA1	49	2	1	Substitution - Missense(1)	stomach(1)	c.T281A						PASS	.	A	ASN/ILE,ASN/ILE	902,3498	347.5+/-309.5	92,718,1390	143.0	127.0	132.0		281,251	4.0	0.1	11	dbSNP_123	132	4910,3682	621.3+/-397.2	1406,2098,792	yes	missense,missense	AMICA1	NM_001098526.1,NM_153206.2	149,149	1498,2816,2182	TT,TA,AA		42.8538,20.5,44.7352	possibly-damaging,possibly-damaging	94/395,84/385	118081345	5812,7180	2200	4296	6496	SO:0001583	missense	120425	exon4			CATAAGATGTCCC	AY138965, AY358362	CCDS8391.1, CCDS41723.1, CCDS66240.1	11q23.3	2013-01-11				ENSG00000160593		"""Immunoglobulin superfamily / V-set domain containing"""	19084	protein-coding gene	gene with protein product		609770				12975309	Standard	NM_001098526		Approved	Gm638, AMICA	uc001psk.2	Q86YT9		ENST00000356289.5:c.281T>A	11.37:g.118081345A>T	ENSP00000348635:p.Ile94Asn	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	185	112	0.605405	NM_001098526	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Missense_Mutation	SNP	ENST00000356289.5	37	CCDS41723.1	985	0.451007326007326	74	0.15040650406504066	173	0.47790055248618785	325	0.5681818181818182	413	0.5448548812664907	A	9.598	1.127979	0.20959	0.205	0.571462	ENSG00000160593	ENST00000356289;ENST00000292067;ENST00000533261;ENST00000526620;ENST00000537867;ENST00000524477;ENST00000525565	T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.14	3.98	0.46160	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.691620	0.13216	N	0.404776	T	0.00012	0.0000	M	0.63843	1.955	0.80722	P	0.0	B;P;P;D	0.63880	0.237;0.952;0.952;0.993	B;P;P;P	0.54238	0.1;0.695;0.695;0.746	T	0.49476	-0.8936	9	0.33141	T	0.24	-8.4456	7.8888	0.29665	0.9063:0.0:0.0937:0.0	rs17121881;rs17121881	55;94;94;84	E9PKK2;Q86YT9;E9PR26;Q86YT9-2	.;JAML1_HUMAN;.;.	N	94;84;94;55;55;55;94	ENSP00000348635:I94N;ENSP00000292067:I84N;ENSP00000436117:I94N;ENSP00000431218:I55N;ENSP00000432769:I55N;ENSP00000431791:I94N	ENSP00000292067:I84N	I	-	2	0	AMICA1	117586555	0.008000	0.16893	0.073000	0.20177	0.011000	0.07611	1.514000	0.35834	0.925000	0.37094	0.533000	0.62120	ATC	A|0.546;N|0.000	.	strong		0.502	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206	
FAM205A	259308	hgsc.bcm.edu	37	9	34726155	34726155	+	Missense_Mutation	SNP	C	C	T	rs76045500	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:34726155C>T	ENST00000378788.3	-	4	1121	c.1082G>A	c.(1081-1083)tGt>tAt	p.C361Y		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	361						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						CACACATGAACACCAGGTCTG	0.478													c|||	596	0.11901	0.2965	0.0735	5008	,	,		14160	0.0367		0.0328	False		,,,				2504	0.0849				p.C361Y		Atlas-SNP	.											.	FAM205A	45	.	0			c.G1082A						PASS	.						27.0	22.0	24.0					9																	34726155		681	1369	2050	SO:0001583	missense	259308	exon4			CATGAACACCAGG		CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.1082G>A	9.37:g.34726155C>T	ENSP00000417711:p.Cys361Tyr	Somatic	540	0	0		WXS	Illumina HiSeq	Phase_I	525	212	0.40381	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	147	0.0673076923076923	81	0.16463414634146342	24	0.06629834254143646	20	0.03496503496503497	22	0.029023746701846966	c	14.81	2.646414	0.47258	.	.	ENSG00000205108	ENST00000378788	T	0.21361	2.01	4.11	-0.233	0.13078	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	P	0.45176	0.852	B	0.38378	0.272	T	0.10706	-1.0618	8	0.02654	T	1	.	4.4897	0.11808	0.0:0.4317:0.3575:0.2108	.	361	Q6ZU69	F205A_HUMAN	Y	361	ENSP00000417711:C361Y	ENSP00000417711:C361Y	C	-	2	0	RP11-195F19.10	34716155	0.000000	0.05858	0.000000	0.03702	0.641000	0.38312	-0.146000	0.10250	0.143000	0.18926	-0.226000	0.12346	TGT	C|0.937;T|0.063	0.063	strong		0.478	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
LAMC3	10319	hgsc.bcm.edu	37	9	133963008	133963008	+	Splice_Site	SNP	G	G	A	rs4740412	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133963008G>A	ENST00000361069.4	+	26	4509	c.4376G>A	c.(4375-4377)cGg>cAg	p.R1459Q	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1459	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GAAGCTGAGCGGGTACGTTTG	0.657													G|||	818	0.163339	0.0635	0.2435	5008	,	,		18447	0.0833		0.2714	False		,,,				2504	0.2127				p.R1459Q		Atlas-SNP	.											LAMC3,NS,carcinoma,-1,1	LAMC3	167	1	0			c.G4376A						scavenged	.	G	GLN/ARG	359,4047	184.0+/-211.4	15,329,1859	66.0	72.0	70.0		4376	-4.3	0.1	9	dbSNP_111	70	2287,6313	383.0+/-340.6	301,1685,2314	yes	missense-near-splice	LAMC3	NM_006059.3	43	316,2014,4173	AA,AG,GG		26.593,8.148,20.3445	benign	1459/1576	133963008	2646,10360	2203	4300	6503	SO:0001630	splice_region_variant	10319	exon26			CTGAGCGGGTACG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.4377+1G>A	9.37:g.133963008G>A		Somatic	77	2	0.025974		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	374|374	0.17124542124542125|0.17124542124542125	39|39	0.07926829268292683|0.07926829268292683	94|94	0.2596685082872928|0.2596685082872928	41|41	0.07167832167832168|0.07167832167832168	200|200	0.2638522427440633|0.2638522427440633	G|G	0.779|0.779	-0.763118|-0.763118	0.02996|0.02996	0.08148|0.08148	0.26593|0.26593	ENSG00000050555|ENSG00000050555	ENST00000355452|ENST00000361069;ENST00000355048	.|T	.|0.26518	.|1.73	4.62|4.62	-4.34|-4.34	0.03666|0.03666	.|.	.|1.674320	.|0.03126	.|N	.|0.164480	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00823|0.00823	-1.155|-1.155	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.34403|0.34403	-0.9830|-0.9830	4|9	.|0.14656	.|T	.|0.56	.|.	8.3932|8.3932	0.32542|0.32542	0.2491:0.0:0.6052:0.1457|0.2491:0.0:0.6052:0.1457	rs4740412;rs17453122;rs52815542;rs4740412|rs4740412;rs17453122;rs52815542;rs4740412	.|140;1459	.|Q9UF61;Q9Y6N6	.|.;LAMC3_HUMAN	R|Q	141|1459;1471	.|ENSP00000354360:R1459Q	.|ENSP00000347156:R1471Q	G|R	+|+	1|2	0|0	LAMC3|LAMC3	132952829|132952829	0.001000|0.001000	0.12720|0.12720	0.080000|0.080000	0.20451|0.20451	0.126000|0.126000	0.20510|0.20510	-0.404000|-0.404000	0.07205|0.07205	-0.993000|-0.993000	0.03467|0.03467	-1.595000|-1.595000	0.00837|0.00837	GGG|CGG	G|0.817;A|0.183	0.183	strong		0.657	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	Missense_Mutation
PADI4	23569	hgsc.bcm.edu	37	1	17674537	17674537	+	Silent	SNP	C	C	A	rs2240335	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17674537C>A	ENST00000375448.4	+	10	1175	c.1149C>A	c.(1147-1149)cgC>cgA	p.R383R	PADI4_ENST00000487048.1_3'UTR|AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	383					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	CCATCAAACGCGTGATGGTAC	0.582													c|||	2110	0.421326	0.3517	0.4121	5008	,	,		16071	0.5635		0.3469	False		,,,				2504	0.4519				p.R383R		Atlas-SNP	.											.	PADI4	70	.	0			c.C1149A						PASS	.			1635,2771		297,1041,865	79.0	71.0	74.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1149	-2.2	0.0	1	dbSNP_98	74	3026,5574		524,1978,1798	yes	coding-synonymous	PADI4	NM_012387.2		821,3019,2663	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	35.186,37.1085,35.8373		383/664	17674537	4661,8345	2203	4300	6503	SO:0001819	synonymous_variant	23569	exon10			CAAACGCGTGATG	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.1149C>A	1.37:g.17674537C>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Silent	SNP	ENST00000375448.4	37	CCDS180.1																																																																																			C|0.608;A|0.392	0.392	strong		0.582	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
IL32	9235	hgsc.bcm.edu	37	16	3119304	3119304	+	Missense_Mutation	SNP	A	A	G	rs398100042|rs2981599		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3119304A>G	ENST00000534507.1	+	6	864	c.653A>G	c.(652-654)gAc>gGc	p.D218G	IL32_ENST00000551513.1_Missense_Mutation_p.D209G|IL32_ENST00000008180.9_Missense_Mutation_p.D152G|IL32_ENST00000552356.1_Missense_Mutation_p.D152G|IL32_ENST00000551122.1_Missense_Mutation_p.D115G|IL32_ENST00000529699.1_Missense_Mutation_p.D152G|IL32_ENST00000548652.1_Missense_Mutation_p.D163G|IL32_ENST00000530890.1_Missense_Mutation_p.D152G|IL32_ENST00000526464.2_Missense_Mutation_p.D172G|IL32_ENST00000529550.1_Missense_Mutation_p.D172G|IL32_ENST00000528163.2_Missense_Mutation_p.D172G|IL32_ENST00000530538.2_Missense_Mutation_p.D172G|IL32_ENST00000548476.1_Missense_Mutation_p.D218G|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000444393.3_Missense_Mutation_p.D172G|IL32_ENST00000525643.2_Missense_Mutation_p.D172G|IL32_ENST00000325568.5_Missense_Mutation_p.D172G|IL32_ENST00000382213.3_Missense_Mutation_p.D163G|IL32_ENST00000552936.1_Missense_Mutation_p.D196G|IL32_ENST00000552664.1_Missense_Mutation_p.D172G|IL32_ENST00000548246.1_Missense_Mutation_p.D132G|IL32_ENST00000396890.2_Missense_Mutation_p.D218G|IL32_ENST00000533097.2_Missense_Mutation_p.D172G|IL32_ENST00000440815.3_Missense_Mutation_p.D172G|IL32_ENST00000549213.1_Missense_Mutation_p.D115G|IL32_ENST00000396887.3_Missense_Mutation_p.D115G|IL32_ENST00000531965.1_Missense_Mutation_p.D162G			P24001	IL32_HUMAN	interleukin 32	218					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CCACGGGGGGACAAGGAGGAG	0.577																																					p.D172G		Atlas-SNP	.											IL32,NS,carcinoma,+1,2	IL32	32	2	0			c.A515G						PASS	.						91.0	117.0	108.0					16																	3119304		2197	4300	6497	SO:0001583	missense	9235	exon7			GGGGGGACAAGGA	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.653A>G	16.37:g.3119304A>G	ENSP00000431775:p.Asp218Gly	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	197	66	0.335025	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Missense_Mutation	SNP	ENST00000534507.1	37		.	.	.	.	.	.	.	.	.	.	G	0.809	-0.752764	0.03041	.	.	ENSG00000008517	ENST00000325568;ENST00000534507;ENST00000531965;ENST00000396887;ENST00000529699;ENST00000526464;ENST00000440815;ENST00000529550;ENST00000551122;ENST00000525643;ENST00000548807;ENST00000528163;ENST00000530890;ENST00000444393;ENST00000533097;ENST00000008180;ENST00000396890;ENST00000548652;ENST00000530538;ENST00000549213;ENST00000552936;ENST00000548476;ENST00000552664;ENST00000552356;ENST00000551513;ENST00000382213;ENST00000548246	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56776	0.45;0.46;0.45;0.44;0.45;0.45;0.45;0.45;0.44;0.45;0.46;0.45;0.45;0.45;0.45;0.45;0.46;0.45;0.45;0.44;0.46;0.46;0.45;0.45;0.46;0.45;0.45	1.26	-2.53	0.06326	.	.	.	.	.	T	0.24736	0.0600	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.0;0.0	T	0.14839	-1.0458	9	0.15952	T	0.53	.	0.7126	0.00926	0.1695:0.1865:0.3513:0.2928	rs2981599	132;152;163;152;218;172;115	B8Q191;C6GKH1;A6NNM0;A8MPX0;P24001;P24001-2;P24001-4	.;.;.;.;IL32_HUMAN;.;.	G	172;218;162;115;152;172;172;172;115;172;218;172;152;172;172;152;218;163;172;115;196;218;172;152;209;163;132	ENSP00000324742:D172G;ENSP00000431775:D218G;ENSP00000433177:D162G;ENSP00000380096:D115G;ENSP00000436937:D152G;ENSP00000450364:D172G;ENSP00000405063:D172G;ENSP00000437020:D172G;ENSP00000447496:D115G;ENSP00000432218:D172G;ENSP00000448354:D218G;ENSP00000432850:D172G;ENSP00000433747:D152G;ENSP00000411958:D172G;ENSP00000432917:D172G;ENSP00000008180:D152G;ENSP00000380099:D218G;ENSP00000446624:D163G;ENSP00000436929:D172G;ENSP00000447812:D115G;ENSP00000447033:D196G;ENSP00000449483:D218G;ENSP00000448683:D172G;ENSP00000446978:D152G;ENSP00000449147:D209G;ENSP00000371648:D163G;ENSP00000447979:D132G	ENSP00000008180:D152G	D	+	2	0	IL32	3059305	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.447000	0.02396	-1.773000	0.01290	-0.245000	0.11935	GAC	.	.	weak		0.577	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
SDC4	6385	hgsc.bcm.edu	37	20	43956017	43956017	+	Missense_Mutation	SNP	C	C	T	rs202142981		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43956017C>T	ENST00000372733.3	-	5	523	c.484G>A	c.(484-486)Gtc>Atc	p.V162I	SDC4_ENST00000537976.1_Missense_Mutation_p.V90I	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	162					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				ATCAGGAAGACGGCAAAGAGG	0.532			T	ROS1	NSCLC								C|||	1	0.000199681	0.0	0.0	5008	,	,		17406	0.0		0.001	False		,,,				2504	0.0				p.V162I		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.G484A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	95.0	85.0	89.0		484	-3.4	0.0	20		89	0,8600		0,0,4300	yes	missense	SDC4	NM_002999.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	162/199	43956017	1,13005	2203	4300	6503	SO:0001583	missense	6385	exon5			GGAAGACGGCAAA	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"""Proteoglycans / Cell Surface : Syndecans"""	10661	protein-coding gene	gene with protein product	"""syndecan proteoglycan 4"""	600017	"""syndecan 4 (amphiglycan, ryudocan)"""			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.484G>A	20.37:g.43956017C>T	ENSP00000361818:p.Val162Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.725885	0.00694	2.27E-4	0.0	ENSG00000124145	ENST00000372733;ENST00000537976	T	0.24350	1.86	5.24	-3.38	0.04883	.	0.925625	0.09152	N	0.841349	T	0.13372	0.0324	N	0.21194	0.64	0.19300	N	0.999978	B	0.29766	0.256	B	0.23150	0.044	T	0.31888	-0.9927	10	0.07482	T	0.82	-1.8487	13.6197	0.62130	0.0:0.4611:0.0:0.5389	.	162	P31431	SDC4_HUMAN	I	162;90	ENSP00000361818:V162I	ENSP00000361818:V162I	V	-	1	0	SDC4	43389431	0.000000	0.05858	0.004000	0.12327	0.064000	0.16182	-0.645000	0.05409	-0.505000	0.06568	-0.253000	0.11424	GTC	.	.	weak		0.532	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999	
GABRR1	2569	hgsc.bcm.edu	37	6	89926966	89926966	+	Missense_Mutation	SNP	T	T	C	rs12200969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:89926966T>C	ENST00000454853.2	-	1	186	c.76A>G	c.(76-78)Atg>Gtg	p.M26V	GABRR1_ENST00000435811.1_Missense_Mutation_p.M26V|GABRR1_ENST00000369451.3_Intron|GABRR1_ENST00000481493.1_5'UTR	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	26			M -> V (in dbSNP:rs12200969). {ECO:0000269|PubMed:14702039}.		gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	GGCCAGTGCATTCTGCTTTCA	0.463													C|||	1533	0.30611	0.5272	0.2118	5008	,	,		18075	0.0942		0.3529	False		,,,				2504	0.2444				p.M26V		Atlas-SNP	.											.	GABRR1	63	.	0			c.A76G						PASS	.	C	VAL/MET	2072,2334	606.9+/-390.8	483,1106,614	95.0	80.0	85.0		76	2.9	1.0	6	dbSNP_120	85	3000,5600	665.5+/-402.3	550,1900,1850	yes	missense	GABRR1	NM_002042.3	21	1033,3006,2464	CC,CT,TT		34.8837,47.0268,38.9974	benign	26/480	89926966	5072,7934	2203	4300	6503	SO:0001583	missense	2569	exon1			AGTGCATTCTGCT		CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4090	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 1"""	137161	"""gamma-aminobutyric acid (GABA) receptor, rho 1"""			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.76A>G	6.37:g.89926966T>C	ENSP00000412673:p.Met26Val	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	157	84	0.535032	NM_001256703	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Missense_Mutation	SNP	ENST00000454853.2	37	CCDS5019.2	641	0.2934981684981685	243	0.49390243902439024	76	0.20994475138121546	56	0.0979020979020979	266	0.35092348284960423	C	9.759	1.169648	0.21621	0.470268	0.348837	ENSG00000146276	ENST00000454853;ENST00000435811	T;T	0.23754	1.89;1.89	5.75	2.91	0.33838	.	0.428050	0.21492	N	0.073662	T	0.02571	0.0078	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46442	-0.9191	8	.	.	.	-4.2998	5.3971	0.16275	0.0:0.4594:0.246:0.2946	rs12200969;rs61289123;rs12200969	26;26	P24046-2;P24046	.;GBRR1_HUMAN	V	26	ENSP00000412673:M26V;ENSP00000394687:M26V	.	M	-	1	0	GABRR1	89983685	0.989000	0.36119	0.992000	0.48379	0.995000	0.86356	0.261000	0.18442	0.051000	0.15978	-0.128000	0.14901	ATG	T|0.651;C|0.349	0.349	strong		0.463	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2		
CPN1	1369	hgsc.bcm.edu	37	10	101802262	101802262	+	Silent	SNP	G	G	A	rs61733667	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:101802262G>A	ENST00000370418.3	-	9	1550	c.1299C>T	c.(1297-1299)caC>caT	p.H433H		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	433					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		CTCTGACTCCGTGCCTTCTGC	0.542													G|||	113	0.0225639	0.0023	0.0663	5008	,	,		16811	0.0238		0.0338	False		,,,				2504	0.0061				p.H433H		Atlas-SNP	.											.	CPN1	62	.	0			c.C1299T						PASS	.			34,4372	39.2+/-71.8	0,34,2169	99.0	85.0	90.0		1299	-9.1	0.0	10	dbSNP_129	90	327,8273	114.2+/-174.2	5,317,3978	no	coding-synonymous	CPN1	NM_001308.2		5,351,6147	AA,AG,GG		3.8023,0.7717,2.7756		433/459	101802262	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	1369	exon9			GACTCCGTGCCTT	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1299C>T	10.37:g.101802262G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	112	65	0.580357	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	37	CCDS7486.1																																																																																			G|0.971;A|0.029	0.029	strong		0.542	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
STXBP4	252983	hgsc.bcm.edu	37	17	53158492	53158492	+	Silent	SNP	G	G	A	rs8069999	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:53158492G>A	ENST00000376352.2	+	16	1644	c.1437G>A	c.(1435-1437)gcG>gcA	p.A479A	STXBP4_ENST00000434978.2_Silent_p.A457A	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	479					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						CAACGCTGGCGCTTGAATCTA	0.378													g|||	947	0.189097	0.0613	0.1484	5008	,	,		17488	0.2431		0.2455	False		,,,				2504	0.2771				p.A479A		Atlas-SNP	.											.	STXBP4	41	.	0			c.G1437A						PASS	.	A		337,4069	176.2+/-205.4	17,303,1883	125.0	113.0	117.0		1437	-11.0	0.0	17	dbSNP_116	117	1976,6624	346.4+/-326.2	214,1548,2538	no	coding-synonymous	STXBP4	NM_178509.5		231,1851,4421	AA,AG,GG		22.9767,7.6487,17.7841		479/554	53158492	2313,10693	2203	4300	6503	SO:0001819	synonymous_variant	252983	exon16			GCTGGCGCTTGAA	BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.1437G>A	17.37:g.53158492G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	197	82	0.416244	NM_178509	Q8IVZ5	Silent	SNP	ENST00000376352.2	37	CCDS11584.2																																																																																			G|0.813;A|0.187	0.187	strong		0.378	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509	
NOL10	79954	hgsc.bcm.edu	37	2	10717806	10717806	+	Missense_Mutation	SNP	C	C	T	rs2287059	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:10717806C>T	ENST00000381685.5	-	20	2008	c.1903G>A	c.(1903-1905)Gac>Aac	p.D635N	NOL10_ENST00000538384.1_Missense_Mutation_p.D609N|NOL10_ENST00000345985.3_Missense_Mutation_p.D585N|NOL10_ENST00000542668.1_Missense_Mutation_p.D585N	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	635			D -> N (in dbSNP:rs2287059).			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		ACGGTGGTGTCGGATACACTC	0.333													C|||	668	0.133387	0.0113	0.1844	5008	,	,		20026	0.128		0.2744	False		,,,				2504	0.1227				p.D635N		Atlas-SNP	.											.	NOL10	22	.	0			c.G1903A						PASS	.	C	ASN/ASP	261,4145	148.4+/-182.8	13,235,1955	155.0	131.0	139.0		1903	6.0	1.0	2	dbSNP_100	139	2613,5987	418.0+/-352.6	397,1819,2084	yes	missense	NOL10	NM_024894.2	23	410,2054,4039	TT,TC,CC		30.3837,5.9237,22.0975	benign	635/689	10717806	2874,10132	2203	4300	6503	SO:0001583	missense	79954	exon20			TGGTGTCGGATAC	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1903G>A	2.37:g.10717806C>T	ENSP00000371101:p.Asp635Asn	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	189	188	0.994709	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	362	0.16575091575091574	10	0.02032520325203252	75	0.20718232044198895	73	0.12762237762237763	204	0.2691292875989446	C	15.24	2.773842	0.49786	0.059237	0.303837	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384	T;T;T;T	0.43294	0.95;2.28;1.56;2.28	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.67953	2.075	0.09310	P	0.999999821855	B;B;P	0.35411	0.003;0.003;0.5	B;B;B	0.34038	0.004;0.004;0.174	T	0.26538	-1.0100	9	0.16896	T	0.51	-1.9775	20.4777	0.99188	0.0:1.0:0.0:0.0	rs2287059;rs52834264;rs56708754;rs2287059	609;635;585	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	N	585;635;585;609	ENSP00000263837:D585N;ENSP00000371101:D635N;ENSP00000437625:D585N;ENSP00000439663:D609N	ENSP00000263837:D585N	D	-	1	0	NOL10	10635257	0.997000	0.39634	0.961000	0.40146	0.711000	0.40976	4.025000	0.57225	2.840000	0.97914	0.655000	0.94253	GAC	C|0.810;T|0.190	0.190	strong		0.333	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
VARS2	57176	hgsc.bcm.edu	37	6	30887988	30887988	+	Silent	SNP	C	C	T	rs2249459	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30887988C>T	ENST00000321897.5	+	12	1920	c.1288C>T	c.(1288-1290)Ctg>Ttg	p.L430L	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Silent_p.L290L|VARS2_ENST00000416670.2_Silent_p.L430L|VARS2_ENST00000541562.1_Silent_p.L460L			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	430					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CGGGGACTGGCTGCAGGTGGT	0.562													C|||	1112	0.222045	0.0983	0.2075	5008	,	,		16319	0.247		0.3559	False		,,,				2504	0.2362				p.L460L		Atlas-SNP	.											.	VARS2	60	.	0			c.C1378T						PASS	.	C	,,	443,2579		34,375,1102	49.0	46.0	47.0		868,1378,1288	3.7	1.0	6	dbSNP_100	47	2042,3376		364,1314,1031	no	coding-synonymous,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	398,1689,2133	TT,TC,CC		37.6892,14.6592,29.4431	,,	290/924,460/1094,430/1064	30887988	2485,5955	1511	2709	4220	SO:0001819	synonymous_variant	57176	exon13			GACTGGCTGCAGG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1288C>T	6.37:g.30887988C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	152	91	0.598684	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			C|0.730;T|0.270	0.270	strong		0.562	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
MYOM1	8736	hgsc.bcm.edu	37	18	3141939	3141939	+	Missense_Mutation	SNP	T	T	C	rs200179081	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:3141939T>C	ENST00000356443.4	-	14	2356	c.2023A>G	c.(2023-2025)Aag>Gag	p.K675E	MYOM1_ENST00000400569.3_Missense_Mutation_p.K675E|MYOM1_ENST00000261606.7_Missense_Mutation_p.K675E	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	675	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGTCTTACCTTTTCCACAAAG	0.507													T|||	2	0.000399361	0.0	0.0	5008	,	,		19010	0.0		0.002	False		,,,				2504	0.0				p.K675E		Atlas-SNP	.											.	MYOM1	192	.	0			c.A2023G						PASS	.	T	GLU/LYS,GLU/LYS	0,3942		0,0,1971	91.0	93.0	93.0		2023,2023	5.8	1.0	18		93	4,8312		0,4,4154	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	56,56	0,4,6125	CC,CT,TT		0.0481,0.0,0.0326	probably-damaging,probably-damaging	675/1686,675/1590	3141939	4,12254	1971	4158	6129	SO:0001583	missense	8736	exon14			TTACCTTTTCCAC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2023A>G	18.37:g.3141939T>C	ENSP00000348821:p.Lys675Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	29	0.325843	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336470	0.81801	0.0	4.81E-4	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.57752	0.38;0.38;0.38	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75824	0.3902	M	0.87758	2.905	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.76942	-0.2772	10	0.34782	T	0.22	.	16.1611	0.81712	0.0:0.0:0.0:1.0	.	675;675	P52179-2;P52179	.;MYOM1_HUMAN	E	675	ENSP00000348821:K675E;ENSP00000383413:K675E;ENSP00000261606:K675E	ENSP00000261606:K675E	K	-	1	0	MYOM1	3131939	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.040000	0.89188	2.213000	0.71641	0.477000	0.44152	AAG	.	.	weak		0.507	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ZNF415	55786	hgsc.bcm.edu	37	19	53612989	53612989	+	Silent	SNP	A	A	G	rs1054484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53612989A>G	ENST00000500065.4	-	4	642	c.309T>C	c.(307-309)gaT>gaC	p.D103D	ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000601215.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000243643.4_Silent_p.D103D|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000421033.1_Silent_p.D115D|ZNF415_ENST00000440291.1_Silent_p.D90D|ZNF415_ENST00000455735.2_Silent_p.D151D|ZNF415_ENST00000448501.1_Silent_p.D151D	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D103D(1)		breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		AATTTCTTTCATCATCTCTCC	0.378													A|||	819	0.163538	0.0219	0.2896	5008	,	,		19563	0.3224		0.1769	False		,,,				2504	0.0879				p.D103D		Atlas-SNP	.											ZNF415,NS,carcinoma,0,1	ZNF415	68	1	1	Substitution - coding silent(1)	stomach(1)	c.T309C						PASS	.	A	,,	208,4198	128.6+/-165.4	5,198,2000	139.0	126.0	130.0		309,309,309	0.5	0.0	19	dbSNP_86	130	1386,7214	267.2+/-287.2	115,1156,3029	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	,,	120,1354,5029	GG,GA,AA		16.1163,4.7208,12.2559	,,	103/556,103/556,103/556	53612989	1594,11412	2203	4300	6503	SO:0001819	synonymous_variant	55786	exon4			TCTTTCATCATCT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.309T>C	19.37:g.53612989A>G		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	311	159	0.511254	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	37	CCDS54313.1																																																																																			A|0.848;G|0.152	0.152	strong		0.378	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
PPL	5493	hgsc.bcm.edu	37	16	4935146	4935146	+	Silent	SNP	C	C	T	rs1049206	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4935146C>T	ENST00000345988.2	-	22	3599	c.3510G>A	c.(3508-3510)gtG>gtA	p.V1170V	PPL_ENST00000590782.2_Silent_p.V1168V	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1170					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.V1170V(1)		breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CCTTCTCCTGCACCACCACTT	0.622													C|||	1841	0.367612	0.3359	0.4135	5008	,	,		18711	0.2907		0.3241	False		,,,				2504	0.502				p.V1170V		Atlas-SNP	.											PPL,NS,carcinoma,0,1	PPL	168	1	1	Substitution - coding silent(1)	stomach(1)	c.G3510A						PASS	.	C		1539,2855	487.3+/-360.9	274,991,932	120.0	110.0	113.0		3510	2.1	1.0	16	dbSNP_86	113	2550,6050	414.9+/-351.6	376,1798,2126	no	coding-synonymous	PPL	NM_002705.4		650,2789,3058	TT,TC,CC		29.6512,35.025,31.4684		1170/1757	4935146	4089,8905	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			CTCCTGCACCACC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3510G>A	16.37:g.4935146C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			C|0.673;T|0.327	0.327	strong		0.622	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
FCRL1	115350	hgsc.bcm.edu	37	1	157771880	157771880	+	Silent	SNP	C	C	T	rs4971154	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:157771880C>T	ENST00000368176.3	-	5	778	c.711G>A	c.(709-711)ccG>ccA	p.P237P	FCRL1_ENST00000358292.3_Silent_p.P237P|FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000491942.1_Silent_p.P237P	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	237	Ig-like C2-type 3.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGTACAGGATCGGAGGAGAGC	0.597													C|||	1951	0.389577	0.0643	0.5072	5008	,	,		19272	0.5238		0.493	False		,,,				2504	0.501				p.P237P	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											FCRL1,NS,carcinoma,-1,1	FCRL1	164	1	0			c.G711A						PASS	.	C	,,	595,3811	261.3+/-264.2	42,511,1650	43.0	44.0	44.0		711,711,711	-9.9	0.0	1	dbSNP_111	44	4426,4174	585.6+/-391.9	1118,2190,992	no	coding-synonymous,coding-synonymous,coding-synonymous	FCRL1	NM_001159397.1,NM_001159398.1,NM_052938.4	,,	1160,2701,2642	TT,TC,CC		48.5349,13.5043,38.6053	,,	237/367,237/429,237/430	157771880	5021,7985	2203	4300	6503	SO:0001819	synonymous_variant	115350	exon5			CAGGATCGGAGGA	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.711G>A	1.37:g.157771880C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	303	167	0.551155	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			C|0.596;T|0.404	0.404	strong		0.597	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	
TCEB3B	51224	hgsc.bcm.edu	37	18	44559844	44559844	+	Missense_Mutation	SNP	G	G	A	rs61743415	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44559844G>A	ENST00000332567.4	-	1	2144	c.1792C>T	c.(1792-1794)Cca>Tca	p.P598S	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	598	Activation domain. {ECO:0000250}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TTTTCCTGTGGCTTTTCTTCC	0.502													G|||	38	0.00758786	0.0008	0.0101	5008	,	,		18649	0.006		0.0209	False		,,,				2504	0.0031				p.P598S		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C1792T						PASS	.	G	SER/PRO,	18,4388	25.3+/-52.1	0,18,2185	68.0	69.0	69.0		1792,	1.4	0.0	18	dbSNP_129	69	123,8477	63.5+/-125.6	0,123,4177	yes	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	74,	0,141,6362	AA,AG,GG		1.4302,0.4085,1.0841	probably-damaging,	598/754,	44559844	141,12865	2203	4300	6503	SO:0001583	missense	51224	exon1			CCTGTGGCTTTTC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1792C>T	18.37:g.44559844G>A	ENSP00000331302:p.Pro598Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	25	0.011446886446886446	1	0.0020325203252032522	4	0.011049723756906077	5	0.008741258741258742	15	0.01978891820580475	G	14.38	2.518739	0.44763	0.004085	0.014302	ENSG00000206181	ENST00000332567	T	0.32272	1.46	1.4	1.4	0.22301	.	0.128321	0.35320	N	0.003294	T	0.35248	0.0925	M	0.85299	2.745	0.25538	N	0.987207	D	0.61697	0.99	D	0.64776	0.929	T	0.18304	-1.0341	10	0.72032	D	0.01	-17.4889	8.7644	0.34694	0.0:0.0:1.0:0.0	.	598	Q8IYF1	ELOA2_HUMAN	S	598	ENSP00000331302:P598S	ENSP00000331302:P598S	P	-	1	0	TCEB3B	42813842	0.998000	0.40836	0.001000	0.08648	0.002000	0.02628	5.083000	0.64456	1.090000	0.41315	0.609000	0.83330	CCA	G|0.988;A|0.012	0.012	strong		0.502	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
PHRF1	57661	hgsc.bcm.edu	37	11	582056	582056	+	Silent	SNP	G	G	A	rs117660271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:582056G>A	ENST00000264555.5	+	3	317	c.189G>A	c.(187-189)gaG>gaA	p.E63E	PHRF1_ENST00000533464.1_Silent_p.E59E|PHRF1_ENST00000413872.2_Silent_p.E62E|PHRF1_ENST00000416188.2_Silent_p.E63E	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	63					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GGGCGTCTGAGGAGGAAGACC	0.572													G|||	7	0.00139776	0.0	0.0014	5008	,	,		17686	0.0		0.005	False		,,,				2504	0.001				p.E63E		Atlas-SNP	.											.	PHRF1	188	.	0			c.G189A						PASS	.	G		4,4256		0,4,2126	50.0	67.0	62.0		189	-5.6	0.0	11	dbSNP_132	62	35,8479		0,35,4222	no	coding-synonymous	PHRF1	NM_020901.2		0,39,6348	AA,AG,GG		0.4111,0.0939,0.3053		63/1649	582056	39,12735	2130	4257	6387	SO:0001819	synonymous_variant	57661	exon3			GTCTGAGGAGGAA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.189G>A	11.37:g.582056G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																				G|0.997;A|0.003	0.003	strong		0.572	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
E2F2	1870	hgsc.bcm.edu	37	1	23847464	23847464	+	Missense_Mutation	SNP	C	C	A	rs2075995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:23847464C>A	ENST00000361729.2	-	4	1104	c.678G>T	c.(676-678)caG>caT	p.Q226H	E2F2_ENST00000487237.1_5'Flank	NM_004091.3	NP_004082.1	Q14209	E2F2_HUMAN	E2F transcription factor 2	226	Dimerization. {ECO:0000255}.		Q -> H (in dbSNP:rs2075995). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(2)|lung(1)|ovary(3)|skin(2)|urinary_tract(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)		TCTGGATGAGCTGGTCCAAGG	0.577													C|||	1779	0.355232	0.062	0.4092	5008	,	,		15948	0.5992		0.5089	False		,,,				2504	0.3037				p.Q226H		Atlas-SNP	.											E2F2,colon,carcinoma,-2,1	E2F2	31	1	0			c.G678T						PASS	.	C	HIS/GLN	564,3842	250.0+/-257.2	40,484,1679	112.0	101.0	105.0		678	5.1	1.0	1	dbSNP_96	105	4324,4276	579.2+/-390.8	1079,2166,1055	yes	missense	E2F2	NM_004091.3	24	1119,2650,2734	AA,AC,CC		49.7209,12.8007,37.5827	probably-damaging	226/438	23847464	4888,8118	2203	4300	6503	SO:0001583	missense	1870	exon4			GATGAGCTGGTCC	L22846	CCDS236.1	1p36	2008-02-05			ENSG00000007968	ENSG00000007968			3114	protein-coding gene	gene with protein product		600426				8246995, 8246996	Standard	NM_004091		Approved	E2F-2	uc001bhe.2	Q14209	OTTHUMG00000003223	ENST00000361729.2:c.678G>T	1.37:g.23847464C>A	ENSP00000355249:p.Gln226His	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_004091	B2R9W1|Q7Z6H1	Missense_Mutation	SNP	ENST00000361729.2	37	CCDS236.1	926	0.423992673992674	32	0.06504065040650407	136	0.3756906077348066	367	0.6416083916083916	391	0.5158311345646438	C	14.92	2.679578	0.47886	0.128007	0.502791	ENSG00000007968	ENST00000361729	D	0.85556	-2.0	5.97	5.06	0.68205	.	0.171574	0.45867	D	0.000332	T	0.00012	0.0000	L	0.54323	1.7	0.26452	P	0.9755961	D	0.59357	0.985	P	0.51415	0.669	T	0.50988	-0.8762	9	0.24483	T	0.36	-21.0358	14.1362	0.65289	0.0:0.9271:0.0:0.0729	rs2075995;rs2228221;rs3218171;rs17846515;rs17859587;rs57250008;rs2075995	226	Q14209	E2F2_HUMAN	H	226	ENSP00000355249:Q226H	ENSP00000355249:Q226H	Q	-	3	2	E2F2	23720051	0.943000	0.32029	1.000000	0.80357	0.981000	0.71138	0.027000	0.13621	1.521000	0.48983	0.655000	0.94253	CAG	C|0.614;A|0.386	0.386	strong		0.577	E2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008885.1	NM_004091	
GLIS1	148979	hgsc.bcm.edu	37	1	54060248	54060248	+	Missense_Mutation	SNP	T	T	C	rs4307514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:54060248T>C	ENST00000312233.2	-	3	894	c.328A>G	c.(328-330)Acg>Gcg	p.T110A		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						AGATCTCCCGTCAGAGGGGGG	0.657													C|||	1076	0.214856	0.1074	0.1599	5008	,	,		16057	0.1885		0.2962	False		,,,				2504	0.3425				p.T110A		Atlas-SNP	.											GLIS1,NS,carcinoma,0,1	GLIS1	52	1	0			c.A328G						PASS	.	C	ALA/THR	469,3885		39,391,1747	20.0	25.0	24.0		328	1.8	0.7	1	dbSNP_111	24	2634,5870		442,1750,2060	yes	missense	GLIS1	NM_147193.2	58	481,2141,3807	CC,CT,TT		30.9737,10.7717,24.1328	benign	110/621	54060248	3103,9755	2177	4252	6429	SO:0001583	missense	148979	exon3			CTCCCGTCAGAGG	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"""Zinc fingers, C2H2-type"""	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.328A>G	1.37:g.54060248T>C	ENSP00000309653:p.Thr110Ala	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	469	0.21474358974358973	59	0.11991869918699187	66	0.18232044198895028	114	0.1993006993006993	230	0.3034300791556728	C	4.520	0.096571	0.08681	0.107717	0.309737	ENSG00000174332	ENST00000312233	T	0.09163	3.01	4.8	1.81	0.25067	.	0.384219	0.22553	N	0.058568	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47649	-0.9101	9	0.05436	T	0.98	.	5.5009	0.16829	0.0701:0.1254:0.5527:0.2518	rs4307514	110	Q8NBF1	GLIS1_HUMAN	A	110	ENSP00000309653:T110A	ENSP00000309653:T110A	T	-	1	0	GLIS1	53832836	0.999000	0.42202	0.685000	0.30070	0.006000	0.05464	0.857000	0.27831	0.041000	0.15688	-1.109000	0.02080	ACG	T|0.751;C|0.249	0.249	strong		0.657	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
FAM86A	196483	hgsc.bcm.edu	37	16	5140541	5140541	+	Missense_Mutation	SNP	G	G	C	rs9673733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:5140541G>C	ENST00000427587.4	-	5	436	c.368C>G	c.(367-369)tCc>tGc	p.S123C	FAM86A_ENST00000458008.4_Missense_Mutation_p.S89C|FAM86A_ENST00000587133.1_Missense_Mutation_p.S62C	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	123			S -> C (in dbSNP:rs9673733).			cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						CGTGCTCTCGGAGAGTGTGAC	0.602													g|||	502	0.10024	0.0779	0.147	5008	,	,		20466	0.1339		0.0736	False		,,,				2504	0.09				p.S123C		Atlas-SNP	.											.	FAM86A	32	.	0			c.C368G						PASS	.	G	CYS/SER,CYS/SER	341,4053	176.9+/-206.0	17,307,1873	74.0	74.0	74.0		368,266	1.8	0.1	16	dbSNP_119	74	622,7978	161.7+/-214.6	19,584,3697	no	missense,missense	FAM86A	NM_201400.2,NM_201598.2	112,112	36,891,5570	CC,CG,GG		7.2326,7.7606,7.4111	benign,benign	123/331,89/297	5140541	963,12031	2197	4300	6497	SO:0001583	missense	196483	exon5			CTCTCGGAGAGTG	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.368C>G	16.37:g.5140541G>C	ENSP00000398502:p.Ser123Cys	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	241	113	0.46888	NM_201400	D3DUF0|Q96S85	Missense_Mutation	SNP	ENST00000427587.4	37	CCDS10529.1	229	0.10485347985347986	31	0.06300813008130081	50	0.13812154696132597	83	0.1451048951048951	65	0.08575197889182058	g	4.769	0.142952	0.09083	0.077606	0.072326	ENSG00000118894	ENST00000458008;ENST00000427587	T;T	0.06218	3.33;4.0	5.02	1.83	0.25207	.	0.991024	0.08210	N	0.980832	T	0.00039	0.0001	L	0.45422	1.42	0.53688	P	2.1000000000048757E-5	B;B	0.15473	0.009;0.013	B;B	0.21151	0.019;0.033	T	0.30149	-0.9988	9	0.48119	T	0.1	.	15.0818	0.72119	0.0:0.6183:0.3817:0.0	rs9673733;rs9673733	89;123	Q96G04-2;Q96G04	.;FA86A_HUMAN	C	89;123	ENSP00000389710:S89C;ENSP00000398502:S123C	ENSP00000398502:S123C	S	-	2	0	FAM86A	5080542	0.000000	0.05858	0.099000	0.21106	0.061000	0.15899	0.342000	0.19926	0.258000	0.21686	0.450000	0.29827	TCC	G|0.920;C|0.080	0.080	strong		0.602	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400	
PTPRB	5787	hgsc.bcm.edu	37	12	70989977	70989977	+	Silent	SNP	T	T	C	rs11178317	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:70989977T>C	ENST00000261266.5	-	3	485	c.456A>G	c.(454-456)caA>caG	p.Q152Q	PTPRB_ENST00000451516.2_Silent_p.Q152Q|PTPRB_ENST00000550358.1_Silent_p.Q370Q|PTPRB_ENST00000334414.6_Silent_p.Q370Q|PTPRB_ENST00000551525.1_Silent_p.Q369Q|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000538708.1_Silent_p.Q152Q|PTPRB_ENST00000550857.1_Silent_p.Q152Q	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	152	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CCTGTATCTTTTGGTTATTTT	0.383													T|||	853	0.170327	0.1566	0.2464	5008	,	,		16133	0.2103		0.1272	False		,,,				2504	0.138				p.Q370Q		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1110G						PASS	.	T	,,,	564,3102		47,470,1316	100.0	97.0	98.0		1110,456,456,456	0.6	0.5	12	dbSNP_120	98	894,7278		53,788,3245	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	,,,	100,1258,4561	CC,CT,TT		10.9398,15.3846,12.3163	,,,	370/2216,152/1908,152/1908,152/1998	70989977	1458,10380	1833	4086	5919	SO:0001819	synonymous_variant	5787	exon5			TATCTTTTGGTTA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.456A>G	12.37:g.70989977T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	150	76	0.506667	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1																																																																																			C|0.170;N|0.000	0.170	strong		0.383	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
CCDC50	152137	hgsc.bcm.edu	37	3	191100561	191100561	+	Silent	SNP	C	C	A	rs364519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:191100561C>A	ENST00000392455.3	+	9	1339	c.741C>A	c.(739-741)tcC>tcA	p.S247S	CCDC50_ENST00000392456.3_Silent_p.S423S	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	247	Lys-rich.					cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		CAGCAAATTCCAAGTCAAAAG	0.378													A|||	3230	0.644968	0.8548	0.5778	5008	,	,		18207	0.6865		0.495	False		,,,				2504	0.5204				p.S423S		Atlas-SNP	.											.	CCDC50	39	.	0			c.C1269A						PASS	.	A	,	3481,925	354.4+/-312.6	1370,741,92	74.0	81.0	79.0		741,1269	0.8	0.6	3	dbSNP_80	79	3963,4637	601.7+/-394.4	921,2121,1258	no	coding-synonymous,coding-synonymous	CCDC50	NM_174908.3,NM_178335.2	,	2291,2862,1350	AA,AC,CC		46.0814,20.9941,42.7649	,	247/307,423/483	191100561	7444,5562	2203	4300	6503	SO:0001819	synonymous_variant	152137	exon10			AAATTCCAAGTCA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.741C>A	3.37:g.191100561C>A		Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	265	264	0.996226	NM_178335	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																			A|0.606;C|0.394;G|0.000;T|0.000	0.606	strong		0.378	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
CCT6B	10693	hgsc.bcm.edu	37	17	33269648	33269648	+	Missense_Mutation	SNP	C	C	G	rs2230553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:33269648C>G	ENST00000314144.5	-	7	855	c.740G>C	c.(739-741)gGt>gCt	p.G247A	CCT6B_ENST00000421975.3_Missense_Mutation_p.G210A|CCT6B_ENST00000436961.3_Missense_Mutation_p.G202A	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	247			G -> A (in dbSNP:rs2230553). {ECO:0000269|PubMed:8812458}.		chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				ATAAAAGAAACCAGAGTTCAC	0.328													C|||	1218	0.243211	0.149	0.1859	5008	,	,		14931	0.2639		0.3728	False		,,,				2504	0.2566				p.G247A		Atlas-SNP	.											.	CCT6B	63	.	0			c.G740C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	765,3635	276.0+/-272.9	73,619,1508	48.0	47.0	48.0		629,605,740	4.1	1.0	17	dbSNP_98	48	3152,5434	452.4+/-362.9	585,1982,1726	yes	missense,missense,missense	CCT6B	NM_001193529.1,NM_001193530.1,NM_006584.3	60,60,60	658,2601,3234	GG,GC,CC		36.7109,17.3864,30.1633	possibly-damaging,possibly-damaging,possibly-damaging	210/494,202/486,247/531	33269648	3917,9069	2200	4293	6493	SO:0001583	missense	10693	exon7			AAGAAACCAGAGT	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.740G>C	17.37:g.33269648C>G	ENSP00000327191:p.Gly247Ala	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_006584	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	582	0.2664835164835165	87	0.17682926829268292	75	0.20718232044198895	131	0.229020979020979	289	0.3812664907651715	C	16.88	3.244978	0.59103	0.173864	0.367109	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.67523	-0.27;-0.27;-0.27	4.06	4.06	0.47325	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.91920	3.255	0.09310	P	0.9999999860995	B;B;P	0.37233	0.155;0.248;0.588	B;B;P	0.44696	0.276;0.303;0.458	T	0.08006	-1.0743	9	0.62326	D	0.03	-9.8571	14.0935	0.65006	0.0:1.0:0.0:0.0	rs2230553;rs16970466;rs52825862;rs2230553	202;210;247	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	A	210;247;202	ENSP00000398044:G210A;ENSP00000327191:G247A;ENSP00000400917:G202A	ENSP00000327191:G247A	G	-	2	0	CCT6B	30293761	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	7.019000	0.76412	2.220000	0.72140	0.591000	0.81541	GGT	C|0.717;G|0.283	0.283	strong		0.328	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584	
SH2D4B	387694	hgsc.bcm.edu	37	10	82369219	82369219	+	Missense_Mutation	SNP	T	T	A	rs17107368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:82369219T>A	ENST00000470604.2	+	6	894	c.894T>A	c.(892-894)gaT>gaA	p.D298E	SH2D4B_ENST00000313455.4_Missense_Mutation_p.D251E|SH2D4B_ENST00000339284.2_Missense_Mutation_p.D299E|SH2D4B_ENST00000372150.3_3'UTR			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	298										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			TCTCCAGAGATGTCATCGTCC	0.597													T|||	751	0.14996	0.0242	0.1239	5008	,	,		14881	0.3442		0.171	False		,,,				2504	0.1166				p.D299E		Atlas-SNP	.											SH2D4B,colon,carcinoma,+2,1	SH2D4B	44	1	0			c.T897A						PASS	.	T	GLU/ASP,GLU/ASP	235,4171	137.7+/-173.5	7,221,1975	76.0	73.0	74.0		753,897	-6.9	0.9	10	dbSNP_123	74	1463,7137	278.7+/-293.6	142,1179,2979	yes	missense,missense	SH2D4B	NM_001145719.1,NM_207372.2	45,45	149,1400,4954	AA,AT,TT		17.0116,5.3336,13.0555	benign,benign	251/310,299/358	82369219	1698,11308	2203	4300	6503	SO:0001583	missense	387694	exon6			CAGAGATGTCATC		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"""SH2 domain containing"""	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.894T>A	10.37:g.82369219T>A	ENSP00000417953:p.Asp298Glu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Missense_Mutation	SNP	ENST00000470604.2	37		413	0.1891025641025641	18	0.036585365853658534	43	0.11878453038674033	219	0.38286713286713286	133	0.17546174142480211	T	4.624	0.116020	0.08831	0.053336	0.170116	ENSG00000178217	ENST00000339284;ENST00000470604;ENST00000313455	T;T;T	0.08193	3.12;3.12;3.12	5.32	-6.92	0.01644	.	0.496191	0.21175	N	0.078911	T	0.00012	0.0000	N	0.00666	-1.275	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.002;0.001	T	0.28996	-1.0026	9	0.02654	T	1	-5.2867	1.4482	0.02369	0.1492:0.1968:0.3315:0.3224	rs17107368;rs52818132;rs17107368	298;251;299	Q5SQS7;Q5SQS7-3;Q5SQS7-2	SH24B_HUMAN;.;.	E	299;298;251	ENSP00000345295:D299E;ENSP00000417953:D298E;ENSP00000314242:D251E	ENSP00000314242:D251E	D	+	3	2	SH2D4B	82359199	0.007000	0.16637	0.901000	0.35422	0.780000	0.44128	-0.914000	0.04038	-0.527000	0.06374	-0.400000	0.06385	GAT	T|0.847;A|0.153	0.153	strong		0.597	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
WDR90	197335	hgsc.bcm.edu	37	16	706534	706534	+	Silent	SNP	G	G	A	rs28485323	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:706534G>A	ENST00000293879.4	+	18	2199	c.2199G>A	c.(2197-2199)caG>caA	p.Q733Q	LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Silent_p.Q733Q			Q96KV7	WDR90_HUMAN	WD repeat domain 90	733										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCACCCTGCAGCAGGTGGGGT	0.701													G|||	1949	0.389177	0.2708	0.3948	5008	,	,		14412	0.6756		0.2584	False		,,,				2504	0.3845				p.Q733Q		Atlas-SNP	.											.	WDR90	107	.	0			c.G2199A						PASS	.	G		857,2909		112,633,1138	6.0	8.0	8.0		2199	2.7	1.0	16	dbSNP_125	8	1762,6382		204,1354,2514	no	coding-synonymous	WDR90	NM_145294.4		316,1987,3652	AA,AG,GG		21.6356,22.7562,21.9899		733/1749	706534	2619,9291	1883	4072	5955	SO:0001819	synonymous_variant	197335	exon18			CCTGCAGCAGGTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2199G>A	16.37:g.706534G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			G|0.606;A|0.394	0.394	strong		0.701	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
VEZT	55591	hgsc.bcm.edu	37	12	95693943	95693943	+	Missense_Mutation	SNP	G	G	A	rs17344738	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:95693943G>A	ENST00000436874.1	+	12	1939	c.1834G>A	c.(1834-1836)Gtg>Atg	p.V612M	VEZT_ENST00000261219.6_Missense_Mutation_p.V564M|VEZT_ENST00000356859.4_3'UTR	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	612			V -> M (in dbSNP:rs17344738). {ECO:0000269|PubMed:17974005}.		chordate embryonic development (GO:0043009)|single organismal cell-cell adhesion (GO:0016337)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stereocilia ankle link complex (GO:0002142)				endometrium(2)|kidney(3)|large_intestine(1)|lung(14)|ovary(2)|upper_aerodigestive_tract(1)	23						atttGAAGCCGTGTTGAAATC	0.299													G|||	352	0.0702875	0.0174	0.1297	5008	,	,		15706	0.0417		0.0696	False		,,,				2504	0.1299				p.V612M		Atlas-SNP	.											.	VEZT	106	.	0			c.G1834A						PASS	.	G	MET/VAL	66,3394		0,66,1664	13.0	11.0	12.0		1834	4.4	1.0	12	dbSNP_123	12	454,7410		10,434,3488	no	missense	VEZT	NM_017599.3	21	10,500,5152	AA,AG,GG		5.7731,1.9075,4.592	possibly-damaging	612/780	95693943	520,10804	1730	3932	5662	SO:0001583	missense	55591	exon12			GAAGCCGTGTTGA	AF216644	CCDS44954.1	12q22	2011-02-15			ENSG00000028203	ENSG00000028203			18258	protein-coding gene	gene with protein product						11080149, 16199027, 21156161	Standard	NM_017599		Approved	DKFZP761C241	uc001tdz.2	Q9HBM0	OTTHUMG00000170182	ENST00000436874.1:c.1834G>A	12.37:g.95693943G>A	ENSP00000410083:p.Val612Met	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_017599	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Missense_Mutation	SNP	ENST00000436874.1	37	CCDS44954.1	136	0.06227106227106227	9	0.018292682926829267	42	0.11602209944751381	27	0.0472027972027972	58	0.07651715039577836	G	14.51	2.556863	0.45590	0.019075	0.057731	ENSG00000028203	ENST00000436874;ENST00000261219;ENST00000397792;ENST00000397796	T;T;T	0.18016	2.25;2.24;2.26	6.16	4.37	0.52481	.	0.194341	0.47852	D	0.000209	T	0.00210	0.0006	L	0.50333	1.59	0.38142	D	0.938482	P	0.43938	0.822	B	0.26864	0.074	T	0.11916	-1.0568	10	0.62326	D	0.03	-31.7729	13.7008	0.62608	0.1121:0.0:0.8879:0.0	rs17344738;rs52799363;rs17344738	612	Q9HBM0	VEZA_HUMAN	M	612;564;568;612	ENSP00000410083:V612M;ENSP00000261219:V564M;ENSP00000380894:V568M	ENSP00000261219:V564M	V	+	1	0	VEZT	94218074	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	4.425000	0.59875	0.952000	0.37798	-0.808000	0.03180	GTG	G|0.947;A|0.053	0.053	strong		0.299	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599	
IREB2	3658	hgsc.bcm.edu	37	15	78789534	78789534	+	Missense_Mutation	SNP	A	A	G	rs140959198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78789534A>G	ENST00000258886.8	+	21	2811	c.2662A>G	c.(2662-2664)Ata>Gta	p.I888V		NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	888					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		TGGAATTGGCATAGCTCCACT	0.393													A|||	8	0.00159744	0.0	0.0058	5008	,	,		16922	0.0		0.004	False		,,,				2504	0.0				p.I888V	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.A2662G						PASS	.	A	VAL/ILE	2,4390	4.2+/-10.8	0,2,2194	114.0	106.0	109.0		2662	4.8	1.0	15	dbSNP_134	109	41,8545	27.4+/-76.7	0,41,4252	yes	missense	IREB2	NM_004136.2	29	0,43,6446	GG,GA,AA		0.4775,0.0455,0.3313	benign	888/964	78789534	43,12935	2196	4293	6489	SO:0001583	missense	3658	exon21			ATTGGCATAGCTC	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.2662A>G	15.37:g.78789534A>G	ENSP00000258886:p.Ile888Val	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	170	83	0.488235	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	37	CCDS10302.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	12.03	1.814651	0.32053	4.55E-4	0.004775	ENSG00000136381	ENST00000258886	T	0.13657	2.57	5.87	4.75	0.60458	Aconitase/3-isopropylmalate dehydratase, swivel (2);Aconitase A/isopropylmalate dehydratase small subunit, swivel (1);	0.084546	0.85682	D	0.000000	T	0.06962	0.0177	L	0.28458	0.855	0.80722	D	1	B	0.12630	0.006	B	0.20184	0.028	T	0.10636	-1.0621	10	0.09843	T	0.71	.	12.1948	0.54290	0.9334:0.0:0.0666:0.0	.	888	P48200	IREB2_HUMAN	V	888	ENSP00000258886:I888V	ENSP00000258886:I888V	I	+	1	0	IREB2	76576589	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	6.693000	0.74582	1.148000	0.42385	0.533000	0.62120	ATA	A|0.998;G|0.002	0.002	strong		0.393	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136	
NBPF10	100132406	hgsc.bcm.edu	37	1	145299838	145299838	+	Missense_Mutation	SNP	G	G	A	rs200473325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145299838G>A	ENST00000369338.1	+	2	264	c.74G>A	c.(73-75)cGc>cAc	p.R25H	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000342960.5_Missense_Mutation_p.R296H|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	296						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.R296H(3)|p.R25H(3)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAGAAATTGCGCCCCCAGCTG	0.488																																					p.R296H		Atlas-SNP	.											NBPF10_ENST00000369338,NS,carcinoma,0,10	NBPF10	221	10	6	Substitution - Missense(6)	endometrium(4)|urinary_tract(2)	c.G887A						scavenged	.						15.0	13.0	13.0					1																	145299838		690	1577	2267	SO:0001583	missense	100132406	exon6			AATTGCGCCCCCA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.74G>A	1.37:g.145299838G>A	ENSP00000358344:p.Arg25His	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	98	7	0.0714286	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369338.1	37		.	.	.	.	.	.	.	.	.	.	.	2.633	-0.285860	0.05605	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.03301	4.04;3.98	1.05	-2.1	0.07210	.	.	.	.	.	T	0.01905	0.0060	.	.	.	0.09310	N	1	D	0.59767	0.986	P	0.53006	0.715	T	0.27088	-1.0084	8	0.31617	T	0.26	.	5.8606	0.18745	0.445:0.0:0.555:0.0	.	25	Q86T75-2	.	H	221;25;25;296	ENSP00000358344:R25H;ENSP00000345684:R296H	ENSP00000345684:R296H	R	+	2	0	NBPF10	144011195	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.156000	0.03160	-1.371000	0.02141	-1.477000	0.00996	CGC	G|0.733;A|0.266	0.266	strong		0.488	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1	NM_001039703	
MUC16	94025	hgsc.bcm.edu	37	19	9076929	9076929	+	Missense_Mutation	SNP	T	T	G	rs2547075	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9076929T>G	ENST00000397910.4	-	3	10720	c.10517A>C	c.(10516-10518)aAa>aCa	p.K3506T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3507	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATGTCACTTTTCACTGCACT	0.512													G|||	1243	0.248203	0.2005	0.2118	5008	,	,		24537	0.249		0.3121	False		,,,				2504	0.272				p.K3506T		Atlas-SNP	.											.	MUC16	4315	.	0			c.A10517C						PASS	.	G	THR/LYS	895,3329		104,687,1321	147.0	140.0	142.0		10517	0.6	0.0	19	dbSNP_100	142	2436,6014		352,1732,2141	yes	missense	MUC16	NM_024690.2	78	456,2419,3462	GG,GT,TT		28.8284,21.1884,26.2822	benign	3506/14508	9076929	3331,9343	2112	4225	6337	SO:0001583	missense	94025	exon3			TCACTTTTCACTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10517A>C	19.37:g.9076929T>G	ENSP00000381008:p.Lys3506Thr	Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	286	152	0.531469	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	g	3.061	-0.193142	0.06259	0.211884	0.288284	ENSG00000181143	ENST00000397910	T	0.02763	4.17	1.66	0.596	0.17496	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.49011	-0.8983	8	0.87932	D	0	.	2.3389	0.04254	0.1874:0.0:0.5152:0.2974	rs2547075;rs17516118;rs60765070	3506	B5ME49	.	T	3506	ENSP00000381008:K3506T	ENSP00000381008:K3506T	K	-	2	0	MUC16	8937929	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.092000	0.11129	-0.065000	0.13021	-0.750000	0.03501	AAA	T|0.743;G|0.257	0.257	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744127	31744127	+	Nonsense_Mutation	SNP	A	A	T	rs877346	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:31744127A>T	ENST00000399889.2	-	1	430	c.405T>A	c.(403-405)tgT>tgA	p.C135*		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	135						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						AAGGGAAGCCACAGCTTCCAT	0.572													A|||	1593	0.318091	0.1679	0.3473	5008	,	,		17991	0.2688		0.4483	False		,,,				2504	0.4172				p.C135X		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.T405A						PASS	.	A	stop/CYS	948,3458	360.4+/-315.2	101,746,1356	67.0	63.0	64.0		405	2.3	0.1	21	dbSNP_86	64	4176,4424	568.4+/-389.0	1014,2148,1138	yes	stop-gained	KRTAP13-2	NM_181621.3		1115,2894,2494	TT,TA,AA		48.5581,21.5161,39.3972		135/176	31744127	5124,7882	2203	4300	6503	SO:0001587	stop_gained	337959	exon1			GAAGCCACAGCTT	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"""Keratin associated proteins"""	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.405T>A	21.37:g.31744127A>T	ENSP00000382777:p.Cys135*	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	173	91	0.526012	NM_181621		Nonsense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	676	0.30952380952380953	79	0.16056910569105692	127	0.35082872928176795	131	0.229020979020979	339	0.4472295514511873	A	10.96	1.499213	0.26861	0.215161	0.485581	ENSG00000182816	ENST00000399889	.	.	.	4.63	2.31	0.28768	.	1.593970	0.04788	U	0.431189	.	.	.	.	.	.	0.41237	P	0.013387999999999955	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	5.6289	0.17499	0.7863:0.0:0.2137:0.0	rs877346;rs3804009;rs52833590;rs877346	.	.	.	X	135	.	ENSP00000382777:C135X	C	-	3	2	KRTAP13-2	30665998	0.001000	0.12720	0.081000	0.20488	0.063000	0.16089	0.246000	0.18160	0.865000	0.35603	-0.274000	0.10170	TGT	A|0.636;T|0.364	0.364	strong		0.572	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
TEP1	7011	hgsc.bcm.edu	37	14	20841707	20841707	+	Missense_Mutation	SNP	C	C	T	rs1713449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20841707C>T	ENST00000262715.5	-	46	6680	c.6640G>A	c.(6640-6642)Gtc>Atc	p.V2214I	TEP1_ENST00000545983.1_Missense_Mutation_p.V552I|TEP1_ENST00000556935.1_Missense_Mutation_p.V2106I	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2214			V -> I (in dbSNP:rs1713449).		RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TCTAGCCCGACGGTTACCACC	0.552													T|||	1623	0.324081	0.4675	0.3646	5008	,	,		21201	0.3056		0.2187	False		,,,				2504	0.229				p.V2214I		Atlas-SNP	.											TEP1,NS,carcinoma,0,1	TEP1	224	1	0			c.G6640A						PASS	.	T	ILE/VAL	1806,2600	640.4+/-397.3	363,1080,760	74.0	67.0	69.0		6640	4.3	0.4	14	dbSNP_89	69	1767,6833	734.4+/-406.9	176,1415,2709	yes	missense	TEP1	NM_007110.4	29	539,2495,3469	TT,TC,CC		20.5465,40.9896,27.4719	benign	2214/2628	20841707	3573,9433	2203	4300	6503	SO:0001583	missense	7011	exon46			GCCCGACGGTTAC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.6640G>A	14.37:g.20841707C>T	ENSP00000262715:p.Val2214Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	682	0.31227106227106227	226	0.45934959349593496	115	0.31767955801104975	169	0.29545454545454547	172	0.22691292875989447	T	4.632	0.117390	0.08881	0.409896	0.205465	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.56103	2.19;2.19;0.48	5.25	4.35	0.52113	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.575156	0.17401	N	0.175537	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.31209	0.002;0.002;0.313;0.001	B;B;B;B	0.27380	0.001;0.004;0.079;0.002	T	0.46638	-0.9177	9	0.23302	T	0.38	-0.1231	12.057	0.53540	0.0:0.9059:0.0:0.0941	rs1713449;rs2228024;rs59335611;rs1713449	552;2106;1557;2214	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	I	2214;2214;2106;552	ENSP00000262715:V2214I;ENSP00000452574:V2106I;ENSP00000438849:V552I	ENSP00000262715:V2214I	V	-	1	0	TEP1	19911547	0.047000	0.20315	0.434000	0.26772	0.140000	0.21249	1.561000	0.36342	0.601000	0.29879	-0.977000	0.02584	GTC	C|0.712;T|0.288	0.288	strong		0.552	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
UTRN	7402	hgsc.bcm.edu	37	6	144843252	144843252	+	Missense_Mutation	SNP	C	C	T	rs148691257	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:144843252C>T	ENST00000367545.3	+	39	5678	c.5678C>T	c.(5677-5679)cCa>cTa	p.P1893L		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1893					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CTTAATGTTCCAGAGCTCAAC	0.383																																					p.P1893L		Atlas-SNP	.											.	UTRN	327	.	0			c.C5678T						PASS	.	C	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	148.0	142.0	144.0		5678	5.6	0.9	6	dbSNP_134	144	1,8599	1.2+/-3.3	0,1,4299	no	missense	UTRN	NM_007124.2	98	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	1893/3434	144843252	2,13004	2203	4300	6503	SO:0001583	missense	7402	exon39			ATGTTCCAGAGCT	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.5678C>T	6.37:g.144843252C>T	ENSP00000356515:p.Pro1893Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	126	40	0.31746	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566695	0.86439	2.27E-4	1.16E-4	ENSG00000152818	ENST00000367545	T	0.62105	0.05	5.6	5.6	0.85130	.	0.000000	0.53938	D	0.000052	T	0.60971	0.2310	M	0.73598	2.24	0.80722	D	1	D	0.54207	0.965	P	0.46758	0.526	T	0.60311	-0.7288	10	0.27082	T	0.32	.	19.6143	0.95626	0.0:1.0:0.0:0.0	.	1893	P46939	UTRO_HUMAN	L	1893	ENSP00000356515:P1893L	ENSP00000356515:P1893L	P	+	2	0	UTRN	144884945	1.000000	0.71417	0.946000	0.38457	0.692000	0.40212	7.288000	0.78691	2.640000	0.89533	0.561000	0.74099	CCA	C|1.000;T|0.000	0.000	strong		0.383	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
UQCC3	790955	hgsc.bcm.edu	37	11	62439569	62439569	+	Missense_Mutation	SNP	G	G	A	rs13941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62439569G>A	ENST00000531323.1	+	3	808	c.265G>A	c.(265-267)Ggc>Agc	p.G89S	C11orf48_ENST00000354588.3_5'Flank|C11orf83_ENST00000377953.3_Missense_Mutation_p.G89S|C11orf48_ENST00000431002.2_5'Flank|C11orf48_ENST00000532208.1_5'Flank			Q6UW78	CK083_HUMAN		89				G -> S (in Ref. 1; AAQ89294 and 3; AAH90057). {ECO:0000305}.		extracellular region (GO:0005576)		p.G89S(1)		cervix(1)|lung(1)|prostate(1)	3						AGGCGGCGCCGGCGGGAGGTC	0.682													G|||	3753	0.749401	0.584	0.7522	5008	,	,		15513	0.9385		0.7296	False		,,,				2504	0.7965				p.G89S		Atlas-SNP	.											C11orf83,NS,carcinoma,0,2	C11orf83	13	2	1	Substitution - Missense(1)	prostate(1)	c.G265A						PASS	.	G	SER/GLY	2713,1609		851,1011,299	16.0	26.0	23.0		265	-3.4	0.0	11	dbSNP_52	23	5998,2498		2155,1688,405	yes	missense	C11orf83	NM_001085372.2	56	3006,2699,704	AA,AG,GG		29.4021,37.2281,32.0409	possibly-damaging	89/94	62439569	8711,4107	2161	4248	6409	SO:0001583	missense	790955	exon2			GGCGCCGGCGGGA																												ENST00000531323.1:c.265G>A	11.37:g.62439569G>A	ENSP00000432692:p.Gly89Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_001085372	Q5FVD5	Missense_Mutation	SNP	ENST00000531323.1	37	CCDS41658.1	1601	0.733058608058608	265	0.5386178861788617	252	0.6961325966850829	532	0.9300699300699301	552	0.7282321899736148	G	9.952	1.220343	0.22457	0.627719	0.705979	ENSG00000204922	ENST00000531323;ENST00000377953	.	.	.	3.14	-3.42	0.04825	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.22983	0.078	B	0.15484	0.013	T	0.20806	-1.0264	6	0.34782	T	0.22	-11.1992	8.551	0.33451	0.642:0.0:0.358:0.0	rs13941;rs3195442;rs13941	89	Q6UW78	CK083_HUMAN	S	89	.	ENSP00000367189:G89S	G	+	1	0	C11orf83	62196145	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.297000	0.19101	-0.828000	0.04273	-0.367000	0.07326	GGC	G|0.263;A|0.737	0.737	strong		0.682	C11orf83-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394992.2		
OR1I1	126370	hgsc.bcm.edu	37	19	15198024	15198024	+	Missense_Mutation	SNP	A	A	T	rs59166286	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198024A>T	ENST00000209540.2	+	1	234	c.148A>T	c.(148-150)Atc>Ttc	p.I50F		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	50			I -> F (in dbSNP:rs59166286).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						CCTGGCCATCATCACGGACTC	0.502													A|||	911	0.181909	0.0242	0.219	5008	,	,		22818	0.2371		0.17	False		,,,				2504	0.3241				p.I50F		Atlas-SNP	.											OR1I1,NS,meningioma,0,1	OR1I1	58	1	0			c.A148T						PASS	.	A	PHE/ILE	203,4203	126.1+/-163.2	3,197,2003	323.0	242.0	270.0		148	-7.6	0.0	19	dbSNP_129	270	1454,7146	278.0+/-293.2	108,1238,2954	yes	missense	OR1I1	NM_001004713.1	21	111,1435,4957	TT,TA,AA		16.907,4.6074,12.7403	possibly-damaging	50/356	15198024	1657,11349	2203	4300	6503	SO:0001583	missense	126370	exon1			GCCATCATCACGG	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.148A>T	19.37:g.15198024A>T	ENSP00000209540:p.Ile50Phe	Somatic	430	0	0		WXS	Illumina HiSeq	Phase_I	382	205	0.536649	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	351	0.16071428571428573	17	0.034552845528455285	76	0.20994475138121546	119	0.20804195804195805	139	0.18337730870712401	a	0.012	-1.676069	0.00751	0.046074	0.16907	ENSG00000094661	ENST00000209540	T	0.01043	5.41	4.84	-7.59	0.01308	GPCR, rhodopsin-like superfamily (1);	0.632727	0.11973	U	0.511519	T	0.00012	0.0000	L	0.28400	0.85	0.80722	P	0.0	P	0.36027	0.533	B	0.34489	0.184	T	0.44847	-0.9301	9	0.10111	T	0.7	.	2.2359	0.04008	0.3173:0.2959:0.2811:0.1057	rs59166286	50	O60431	OR1I1_HUMAN	F	50	ENSP00000209540:I50F	ENSP00000209540:I50F	I	+	1	0	OR1I1	15059024	0.000000	0.05858	0.026000	0.17262	0.012000	0.07955	-1.373000	0.02568	-1.432000	0.01979	-1.508000	0.00951	ATC	A|0.866;T|0.134	0.134	strong		0.502	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
VPRBP	9730	hgsc.bcm.edu	37	3	51475454	51475454	+	Intron	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:51475454T>C	ENST00000335891.5	-	6	682							Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein						B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CGCTGCTCGATAGCAGGAGTC	0.433																																					p.I325V		Atlas-SNP	.											.	VPRBP	107	.	0			c.A973G						PASS	.						68.0	60.0	63.0					3																	51475454		1873	4112	5985	SO:0001627	intron_variant	9730	exon8			GCTCGATAGCAGG	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"""DDB1 and CUL4 associated factors"""	30911	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 1"""					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.672+300A>G	3.37:g.51475454T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	T	9.759	1.169677	0.21621	.	.	ENSG00000145041	ENST00000504652	D	0.98684	-5.07	5.5	4.27	0.50696	Armadillo-type fold (1);	0.050174	0.85682	D	0.000000	D	0.97185	0.9080	N	0.19112	0.55	0.80722	D	1	P	0.38863	0.65	P	0.54140	0.743	D	0.95430	0.8515	10	0.19147	T	0.46	-17.7053	12.3368	0.55071	0.1262:0.0:0.0:0.8738	.	325	Q9Y4B6	VPRBP_HUMAN	V	325	ENSP00000421724:I325V	ENSP00000421724:I325V	I	-	1	0	VPRBP	51450494	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.890000	0.69774	2.209000	0.71365	0.533000	0.62120	ATC	.	.	none		0.433	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703	
TPTE	7179	hgsc.bcm.edu	37	21	10943003	10943003	+	Missense_Mutation	SNP	C	C	T	rs1810856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:10943003C>T	ENST00000361285.4	-	12	913	c.584G>A	c.(583-585)cGa>cAa	p.R195Q	TPTE_ENST00000298232.7_Missense_Mutation_p.R177Q|TPTE_ENST00000342420.5_Missense_Mutation_p.R157Q|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	195			R -> Q (in dbSNP:rs1810856).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCGTAGAAGTCGAAGTAAATG	0.313																																					p.R195Q		Atlas-SNP	.											TPTE_ENST00000361285,lower_third,carcinoma,-1,8	TPTE	513	8	0			c.G584A						PASS	.						72.0	67.0	69.0					21																	10943003		2203	4299	6502	SO:0001583	missense	7179	exon12			AGAAGTCGAAGTA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.584G>A	21.37:g.10943003C>T	ENSP00000355208:p.Arg195Gln	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	498	138	0.277108	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	10.95	1.494560	0.26774	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.98028	-4.67;-4.67;-4.67	2.07	1.16	0.20824	Ion transport (1);	0.072998	0.56097	U	0.000040	D	0.97368	0.9139	M	0.75615	2.305	0.45733	D	0.998638	D;D;D	0.65815	0.995;0.995;0.994	P;P;P	0.56788	0.795;0.795;0.806	D	0.95693	0.8742	10	0.72032	D	0.01	-5.7066	6.6713	0.23070	0.0:0.836:0.0:0.164	rs1810856;rs59194479	157;177;195	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	Q	177;195;157	ENSP00000298232:R177Q;ENSP00000355208:R195Q;ENSP00000344441:R157Q	ENSP00000298232:R177Q	R	-	2	0	TPTE	9964874	0.005000	0.15991	0.035000	0.18076	0.042000	0.13812	0.889000	0.28282	0.423000	0.26033	0.194000	0.17425	CGA	C|0.923;T|0.077	0.077	strong		0.313	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
SLC4A2	6522	hgsc.bcm.edu	37	7	150763655	150763655	+	Silent	SNP	T	T	A	rs2229549	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150763655T>A	ENST00000485713.1	+	6	1670	c.630T>A	c.(628-630)acT>acA	p.T210T	SLC4A2_ENST00000413384.2_Silent_p.T210T|SLC4A2_ENST00000310317.5_Silent_p.T128T|SLC4A2_ENST00000392826.2_Silent_p.T201T|SLC4A2_ENST00000461735.1_Silent_p.T196T	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	210	Pro-rich.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCAGTGGCACTGCAGGGGGTG	0.706													T|||	2682	0.535543	0.2935	0.6945	5008	,	,		13256	0.7034		0.6163	False		,,,				2504	0.4939				p.T210T		Atlas-SNP	.											.	SLC4A2	98	.	0			c.T630A						PASS	.	T	,,,	1267,2645		259,749,948	7.0	8.0	7.0		630,603,588,630	-10.0	0.5	7	dbSNP_98	7	3900,3724		1106,1688,1018	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	,,,	1365,2437,1966	AA,AT,TT		48.8458,32.3875,44.7902	,,,	210/1242,201/1233,196/1228,210/1242	150763655	5167,6369	1956	3812	5768	SO:0001819	synonymous_variant	6522	exon6			TGGCACTGCAGGG		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.630T>A	7.37:g.150763655T>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	37	CCDS5917.1																																																																																			T|0.406;A|0.594	0.594	strong		0.706	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
SPHKAP	80309	hgsc.bcm.edu	37	2	228882970	228882970	+	Missense_Mutation	SNP	T	T	C	rs3828161	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228882970T>C	ENST00000392056.3	-	7	2646	c.2600A>G	c.(2599-2601)cAg>cGg	p.Q867R	SPHKAP_ENST00000344657.5_Missense_Mutation_p.Q867R	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	867			Q -> R (in dbSNP:rs3828161).			extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		ACTTCTGGACTGGCTGACCGT	0.493													T|||	1235	0.246605	0.2874	0.2795	5008	,	,		20550	0.3998		0.1581	False		,,,				2504	0.1012				p.Q867R		Atlas-SNP	.											SPHKAP_ENST00000392056,colon,carcinoma,0,2	SPHKAP	750	2	0			c.A2600G						PASS	.	T	ARG/GLN,ARG/GLN	1280,3126	435.9+/-344.5	195,890,1118	584.0	558.0	567.0		2600,2600	-0.8	0.0	2	dbSNP_107	567	1370,7230	267.6+/-287.4	110,1150,3040	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	43,43	305,2040,4158	CC,CT,TT		15.9302,29.0513,20.3752	benign,benign	867/1701,867/1672	228882970	2650,10356	2203	4300	6503	SO:0001583	missense	80309	exon7			CTGGACTGGCTGA		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2600A>G	2.37:g.228882970T>C	ENSP00000375909:p.Gln867Arg	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	314	160	0.509554	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	548	0.2509157509157509	138	0.2804878048780488	77	0.212707182320442	218	0.3811188811188811	115	0.1517150395778364	T	0.527	-0.859464	0.02610	0.290513	0.159302	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11169	2.8;2.8	6.17	-0.751	0.11076	.	0.584522	0.18502	N	0.139308	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.48547	-0.9026	9	0.22706	T	0.39	.	11.3332	0.49487	0.0:0.3465:0.0:0.6535	rs3828161;rs56528711;rs57833139;rs3828161	867;867	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	R	867	ENSP00000375909:Q867R;ENSP00000339886:Q867R	ENSP00000339886:Q867R	Q	-	2	0	SPHKAP	228591214	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	1.086000	0.30853	-0.029000	0.13827	0.533000	0.62120	CAG	T|0.776;C|0.224	0.224	strong		0.493	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
MYH3	4621	hgsc.bcm.edu	37	17	10542886	10542886	+	Silent	SNP	T	T	C	rs2285472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10542886T>C	ENST00000583535.1	-	23	3003	c.2916A>G	c.(2914-2916)acA>acG	p.T972T	MYH3_ENST00000226209.7_Silent_p.T972T	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	972					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CCTTGTTCTCTGTGGCATGCT	0.403													t|||	2335	0.466254	0.2398	0.5346	5008	,	,		20062	0.3839		0.7575	False		,,,				2504	0.5092				p.T972T		Atlas-SNP	.											.	MYH3	227	.	0			c.A2916G						PASS	.	C		1302,3104	440.8+/-346.1	198,906,1099	255.0	239.0	244.0		2916	-3.2	1.0	17	dbSNP_100	244	6268,2332	704.6+/-405.4	2261,1746,293	no	coding-synonymous	MYH3	NM_002470.3		2459,2652,1392	CC,CT,TT		27.1163,29.5506,41.7961		972/1941	10542886	7570,5436	2203	4300	6503	SO:0001819	synonymous_variant	4621	exon23			GTTCTCTGTGGCA		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2916A>G	17.37:g.10542886T>C		Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	262	259	0.98855	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	37	CCDS11157.1																																																																																			T|0.431;C|0.569	0.569	strong		0.403	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
CLPTM1	1209	hgsc.bcm.edu	37	19	45490636	45490636	+	Silent	SNP	T	T	C	rs204468	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45490636T>C	ENST00000337392.5	+	8	1143	c.993T>C	c.(991-993)ggT>ggC	p.G331G	CLPTM1_ENST00000541297.2_Silent_p.G317G|CLPTM1_ENST00000589158.1_3'UTR|CLPTM1_ENST00000546079.1_Silent_p.G229G	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	331					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		ACTTCCTGGGTGATGAGTTGT	0.647													C|||	2334	0.466054	0.2988	0.4452	5008	,	,		19712	0.3998		0.6262	False		,,,				2504	0.6104				p.G331G		Atlas-SNP	.											.	CLPTM1	109	.	0			c.T993C						PASS	.	C		1458,2948	680.1+/-403.8	257,944,1002	62.0	59.0	60.0		993	-8.8	0.2	19	dbSNP_79	60	5455,3145	477.9+/-369.8	1744,1967,589	no	coding-synonymous	CLPTM1	NM_001294.2		2001,2911,1591	CC,CT,TT		36.5698,33.0912,46.8476		331/670	45490636	6913,6093	2203	4300	6503	SO:0001819	synonymous_variant	1209	exon8			CCTGGGTGATGAG	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.993T>C	19.37:g.45490636T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Silent	SNP	ENST00000337392.5	37	CCDS12651.1																																																																																			T|0.502;C|0.498	0.498	strong		0.647	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294	
PNMAL1	55228	hgsc.bcm.edu	37	19	46974003	46974003	+	Missense_Mutation	SNP	C	C	T	rs7248888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46974003C>T	ENST00000313683.10	-	2	595	c.290G>A	c.(289-291)tGt>tAt	p.C97Y	PNMAL1_ENST00000438932.2_Missense_Mutation_p.C97Y|PNMAL1_ENST00000602246.1_Intron	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	97			C -> Y (in dbSNP:rs7248888).							cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		agggtctctacagaccactct	0.542													C|||	337	0.0672923	0.1649	0.0418	5008	,	,		19029	0.0129		0.0586	False		,,,				2504	0.0184				p.C97Y		Atlas-SNP	.											.	PNMAL1	87	.	0			c.G290A						PASS	.	C	TYR/CYS,TYR/CYS	597,3809	262.8+/-265.1	33,531,1639	49.0	46.0	47.0		290,290	2.4	1.0	19	dbSNP_116	47	503,8097	144.2+/-200.1	7,489,3804	yes	missense,missense	PNMAL1	NM_001103149.1,NM_018215.3	194,194	40,1020,5443	TT,TC,CC		5.8488,13.5497,8.4576	benign,benign	97/379,97/440	46974003	1100,11906	2203	4300	6503	SO:0001583	missense	55228	exon2			TCTCTACAGACCA	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.290G>A	19.37:g.46974003C>T	ENSP00000318131:p.Cys97Tyr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	25	0.337838	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Missense_Mutation	SNP	ENST00000313683.10	37	CCDS33059.1	138	0.06318681318681318	81	0.16463414634146342	12	0.03314917127071823	7	0.012237762237762238	38	0.05013192612137203	C	7.921	0.738653	0.15642	0.135497	0.058488	ENSG00000182013	ENST00000438932;ENST00000313683;ENST00000417103	T;T	0.10099	2.91;2.91	3.46	2.39	0.29439	.	0.187510	0.26474	N	0.024161	T	0.00039	0.0001	L	0.36672	1.1	0.31986	P	0.605256	B;B	0.32800	0.385;0.063	B;B	0.30251	0.113;0.04	T	0.40021	-0.9585	9	0.13470	T	0.59	-17.1361	7.161	0.25664	0.0:0.8754:0.0:0.1246	rs7248888;rs52809978;rs7248888	97;97	Q86V59-2;Q86V59	.;PNML1_HUMAN	Y	97	ENSP00000410273:C97Y;ENSP00000318131:C97Y	ENSP00000318131:C97Y	C	-	2	0	PNMAL1	51665843	0.005000	0.15991	0.991000	0.47740	0.979000	0.70002	0.623000	0.24447	1.011000	0.39340	0.655000	0.94253	TGT	C|0.924;T|0.076	0.076	strong		0.542	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
SLC29A3	55315	hgsc.bcm.edu	37	10	73111408	73111408	+	Missense_Mutation	SNP	C	C	T	rs780668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:73111408C>T	ENST00000373189.5	+	4	525	c.473C>T	c.(472-474)tCc>tTc	p.S158F		NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	158			S -> F (in dbSNP:rs780668). {ECO:0000269|PubMed:11396612, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		transmembrane transport (GO:0055085)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	15						GTGGACACTTCCTCCTGGACC	0.587													C|||	2403	0.479832	0.2943	0.4957	5008	,	,		20447	0.4325		0.7644	False		,,,				2504	0.4755				p.S158F	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											.	SLC29A3	51	.	0			c.C473T						PASS	.	C	PHE/SER,PHE/SER	1615,2791	499.1+/-364.3	277,1061,865	218.0	159.0	179.0		473,473	4.6	1.0	10	dbSNP_86	179	6426,2174	713.2+/-405.9	2394,1638,268	yes	missense,missense	SLC29A3	NM_001174098.1,NM_018344.5	155,155	2671,2699,1133	TT,TC,CC		25.2791,36.6546,38.1747	probably-damaging,probably-damaging	158/259,158/476	73111408	8041,4965	2203	4300	6503	SO:0001583	missense	55315	exon4			ACACTTCCTCCTG	AF326987	CCDS7310.1	10q22.2	2013-07-17	2013-07-17		ENSG00000198246	ENSG00000198246		"""Solute carriers"""	23096	protein-coding gene	gene with protein product		612373	"""solute carrier family 29 (nucleoside transporters), member 3"""			11396612	Standard	NM_018344		Approved	ENT3, FLJ11160	uc001jrr.4	Q9BZD2	OTTHUMG00000018424	ENST00000373189.5:c.473C>T	10.37:g.73111408C>T	ENSP00000362285:p.Ser158Phe	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	155	90	0.580645	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Missense_Mutation	SNP	ENST00000373189.5	37	CCDS7310.1	1155	0.5288461538461539	147	0.29878048780487804	210	0.580110497237569	227	0.3968531468531469	571	0.7532981530343008	C	21.0	4.085709	0.76642	0.366546	0.747209	ENSG00000198246	ENST00000373189	T	0.58506	0.33	5.53	4.62	0.57501	.	0.113216	0.64402	N	0.000007	T	0.00012	0.0000	M	0.89785	3.06	0.48901	P	2.790000000000292E-4	P	0.39044	0.656	B	0.41466	0.358	T	0.37709	-0.9694	9	0.56958	D	0.05	-52.0588	12.7363	0.57225	0.0:0.9239:0.0:0.0761	rs780668;rs946975;rs3740455;rs52798647;rs58614882;rs780668	158	Q9BZD2	S29A3_HUMAN	F	158	ENSP00000362285:S158F	ENSP00000362285:S158F	S	+	2	0	SLC29A3	72781414	1.000000	0.71417	0.988000	0.46212	0.753000	0.42808	7.464000	0.80887	1.478000	0.48253	0.555000	0.69702	TCC	T|0.565;G|0.003	0.565	strong		0.587	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344	
HEATR5A	25938	hgsc.bcm.edu	37	14	31782394	31782394	+	Silent	SNP	G	G	A	rs61754286	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:31782394G>A	ENST00000389961.3	-	27	4202	c.4203C>T	c.(4201-4203)gtC>gtT	p.V1401V	HEATR5A_ENST00000439727.1_Silent_p.V1114V|HEATR5A_ENST00000543095.2_Silent_p.V1407V|AL136418.1_ENST00000582500.1_RNA|HEATR5A_ENST00000439348.1_Silent_p.V1401V			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1401										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		CAATTATGTAGACCTGTTAAA	0.348													G|||	20	0.00399361	0.0008	0.0086	5008	,	,		20010	0.001		0.0119	False		,,,				2504	0.0				p.V1407V		Atlas-SNP	.											.	HEATR5A	181	.	0			c.C4221T						PASS	.	G		11,3657		0,11,1823	186.0	169.0	174.0		4221	2.5	1.0	14	dbSNP_129	174	100,8076		1,98,3989	no	coding-synonymous	HEATR5A	NM_015473.3		1,109,5812	AA,AG,GG		1.2231,0.2999,0.9372		1407/2047	31782394	111,11733	1834	4088	5922	SO:0001819	synonymous_variant	25938	exon28			TATGTAGACCTGT	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.4203C>T	14.37:g.31782394G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	230	111	0.482609	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Silent	SNP	ENST00000389961.3	37		13	0.005952380952380952	0	0.0	6	0.016574585635359115	0	0.0	7	0.009234828496042216	G	0.797	-0.756913	0.03019	0.002999	0.012231	ENSG00000129493	ENST00000538864	.	.	.	4.81	2.49	0.30216	.	.	.	.	.	T	0.28466	0.0704	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21724	-1.0237	4	.	.	.	.	2.7975	0.05405	0.1769:0.0:0.3385:0.4846	rs61754286	.	.	.	F	1035	.	.	S	-	2	0	HEATR5A	30852145	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	1.306000	0.33505	1.116000	0.41820	0.655000	0.94253	TCT	G|0.993;A|0.007	0.007	strong		0.348	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473	
COL4A2	1284	hgsc.bcm.edu	37	13	111102126	111102126	+	Silent	SNP	C	C	T	rs74941798	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:111102126C>T	ENST00000360467.5	+	19	1485	c.1179C>T	c.(1177-1179)atC>atT	p.I393I		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	393	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GCCTCTCCATCGGAGATGGAG	0.612													C|||	1236	0.246805	0.0862	0.2118	5008	,	,		17174	0.2679		0.3847	False		,,,				2504	0.3252				p.I393I		Atlas-SNP	.											.	COL4A2	178	.	0			c.C1179T						PASS	.	C		357,2425		17,323,1051	12.0	14.0	14.0		1179	-1.2	0.0	13	dbSNP_131	14	2125,3809		385,1355,1227	no	coding-synonymous	COL4A2	NM_001846.2		402,1678,2278	TT,TC,CC		35.8106,12.8325,28.4764		393/1713	111102126	2482,6234	1391	2967	4358	SO:0001819	synonymous_variant	1284	exon19			CTCCATCGGAGAT	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1179C>T	13.37:g.111102126C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			A|0.000;C|0.724;T|0.276	0.276	strong		0.612	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
AFF3	3899	hgsc.bcm.edu	37	2	100218080	100218080	+	Silent	SNP	G	G	A	rs4851214	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:100218080G>A	ENST00000409236.2	-	12	1300	c.1188C>T	c.(1186-1188)gcC>gcT	p.A396A	AFF3_ENST00000317233.4_Silent_p.A396A|AFF3_ENST00000409579.1_Silent_p.A421A|AFF3_ENST00000356421.2_Silent_p.A421A			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	396					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GCTGGACCACGGCGCTGCCAG	0.632													G|||	1201	0.239816	0.0129	0.2291	5008	,	,		16538	0.4038		0.2932	False		,,,				2504	0.3303				p.A421A		Atlas-SNP	.											.	AFF3	164	.	0			c.C1263T						PASS	.	G	,	247,4131		8,231,1950	11.0	13.0	13.0		1263,1188	-0.9	0.3	2	dbSNP_111	13	2318,6252		328,1662,2295	no	coding-synonymous,coding-synonymous	AFF3	NM_001025108.1,NM_002285.2	,	336,1893,4245	AA,AG,GG		27.0478,5.6418,19.81	,	421/1252,396/1227	100218080	2565,10383	2189	4285	6474	SO:0001819	synonymous_variant	3899	exon13			GACCACGGCGCTG	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1188C>T	2.37:g.100218080G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	13	8	0.615385	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	37	CCDS42723.1																																																																																			G|0.776;A|0.224	0.224	strong		0.632	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
JPH3	57338	hgsc.bcm.edu	37	16	87678165	87678165	+	Silent	SNP	G	G	A	rs3751725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:87678165G>A	ENST00000284262.2	+	2	926	c.684G>A	c.(682-684)tcG>tcA	p.S228S		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	228					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		TGCGCAAGTCGGAGTCCAAGA	0.632													G|||	931	0.185903	0.0454	0.2291	5008	,	,		13766	0.3204		0.2028	False		,,,				2504	0.1892				p.S228S		Atlas-SNP	.											.	JPH3	95	.	0			c.G684A						PASS	.	G		319,4077	161.4+/-193.6	12,295,1891	51.0	53.0	52.0		684	-10.3	0.7	16	dbSNP_107	52	1973,6627	333.2+/-320.4	223,1527,2550	no	coding-synonymous	JPH3	NM_020655.2		235,1822,4441	AA,AG,GG		22.9419,7.2566,17.6362		228/749	87678165	2292,10704	2198	4300	6498	SO:0001819	synonymous_variant	57338	exon2			CAAGTCGGAGTCC	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.684G>A	16.37:g.87678165G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Silent	SNP	ENST00000284262.2	37	CCDS10962.1																																																																																			G|0.816;A|0.184	0.184	strong		0.632	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
SH3GL3	6457	hgsc.bcm.edu	37	15	84255758	84255758	+	Silent	SNP	T	T	C	rs17158793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:84255758T>C	ENST00000427482.2	+	7	954	c.648T>C	c.(646-648)gcT>gcC	p.A216A	SH3GL3_ENST00000434347.1_Silent_p.A224A|SH3GL3_ENST00000535412.1_Silent_p.A216A|SH3GL3_ENST00000324537.5_Silent_p.A224A	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	216	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						GCCAGTTGGCTGTGTTCATAG	0.507													T|||	387	0.0772764	0.0227	0.1715	5008	,	,		18263	0.1359		0.0616	False		,,,				2504	0.0399				p.A216A		Atlas-SNP	.											.	SH3GL3	91	.	0			c.T648C						PASS	.	T		171,4235	113.3+/-151.4	5,161,2037	65.0	55.0	59.0		648	-7.8	0.9	15	dbSNP_123	59	510,8090	144.3+/-200.2	12,486,3802	no	coding-synonymous	SH3GL3	NM_003027.3		17,647,5839	CC,CT,TT		5.9302,3.8811,5.236		216/348	84255758	681,12325	2203	4300	6503	SO:0001819	synonymous_variant	6457	exon7			GTTGGCTGTGTTC	AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.648T>C	15.37:g.84255758T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	229	125	0.545852	NM_003027	O43553|O43554	Silent	SNP	ENST00000427482.2	37	CCDS10325.2																																																																																			T|0.936;C|0.064	0.064	strong		0.507	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027	
RBM15	64783	hgsc.bcm.edu	37	1	110883569	110883569	+	Silent	SNP	A	A	T	rs3738752	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110883569A>T	ENST00000369784.3	+	1	2442	c.1542A>T	c.(1540-1542)ccA>ccT	p.P514P	RBM15_ENST00000487146.2_Silent_p.P514P|RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Silent_p.P514P	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	514	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P514P(1)		ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGGGCTTCCCACTTGGTGGCC	0.532			T	MKL1	acute megakaryocytic leukemia								A|||	882	0.176118	0.0318	0.1614	5008	,	,		19788	0.2609		0.1889	False		,,,				2504	0.2812				p.P514P		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	RBM15_ENST00000369784,NS,carcinoma,0,1	RBM15	93	1	1	Substitution - coding silent(1)	stomach(1)	c.A1542T						PASS	.	A	,	246,4160	142.7+/-177.9	7,232,1964	69.0	72.0	71.0		1542,1542	-2.4	1.0	1	dbSNP_107	71	1595,7005	294.2+/-301.7	138,1319,2843	no	coding-synonymous,coding-synonymous	RBM15	NM_001201545.1,NM_022768.4	,	145,1551,4807	TT,TA,AA		18.5465,5.5833,14.155	,	514/970,514/978	110883569	1841,11165	2203	4300	6503	SO:0001819	synonymous_variant	64783	exon1			CTTCCCACTTGGT	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"""RNA binding motif (RRM) containing"""	14959	protein-coding gene	gene with protein product	"""one twenty-two"""	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.1542A>T	1.37:g.110883569A>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Silent	SNP	ENST00000369784.3	37	CCDS822.1																																																																																			A|0.840;T|0.160	0.160	strong		0.532	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768	
CD163	9332	hgsc.bcm.edu	37	12	7649484	7649484	+	Missense_Mutation	SNP	T	T	C	rs4883263	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7649484T>C	ENST00000359156.4	-	5	1226	c.1024A>G	c.(1024-1026)Atc>Gtc	p.I342V	CD163_ENST00000541972.1_Missense_Mutation_p.I330V|CD163_ENST00000396620.3_Missense_Mutation_p.I342V|CD163_ENST00000432237.2_Missense_Mutation_p.I342V	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	342	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.		I -> V (in dbSNP:rs4883263). {ECO:0000269|PubMed:10403791, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8370408, ECO:0000269|Ref.3}.		acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	CATTGCCAGATAGCAGGTTCA	0.458													C|||	3819	0.76258	0.5628	0.8487	5008	,	,		-128	0.6905		0.9662	False		,,,				2504	0.8364				p.I342V		Atlas-SNP	.											.	CD163	221	.	0			c.A1024G						PASS	.	C	VAL/ILE,VAL/ILE	2759,1647	505.6+/-366.2	866,1027,310	132.0	95.0	108.0		1024,1024	-1.5	0.0	12	dbSNP_111	108	8324,276	104.0+/-165.0	4027,270,3	yes	missense,missense	CD163	NM_004244.5,NM_203416.3	29,29	4893,1297,313	CC,CT,TT		3.2093,37.3808,14.7855	benign,benign	342/1157,342/1122	7649484	11083,1923	2203	4300	6503	SO:0001583	missense	9332	exon5			GCCAGATAGCAGG	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.1024A>G	12.37:g.7649484T>C	ENSP00000352071:p.Ile342Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	37	CCDS8578.1	1736	0.7948717948717948	293	0.5955284552845529	307	0.8480662983425414	402	0.7027972027972028	734	0.9683377308707124	C	5.366	0.252828	0.10185	0.626192	0.967907	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.35421	1.31;1.31;1.31;1.31	5.03	-1.5	0.08691	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.380288	0.25106	N	0.033085	T	0.00012	0.0000	L	0.31804	0.96	0.80722	P	0.0	B;B;B	0.11235	0.0;0.0;0.004	B;B;B	0.12156	0.002;0.001;0.007	T	0.22977	-1.0201	9	0.49607	T	0.09	.	11.1117	0.48237	0.0:0.4561:0.243:0.3009	rs4883263;rs12814313;rs16916991;rs17846471;rs17859529;rs52798051;rs61044999;rs4883263	342;342;342	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	V	342;330;342;342	ENSP00000352071:I342V;ENSP00000444071:I330V;ENSP00000379863:I342V;ENSP00000403885:I342V	ENSP00000352071:I342V	I	-	1	0	CD163	7540751	0.001000	0.12720	0.003000	0.11579	0.289000	0.27227	-0.207000	0.09384	-0.925000	0.03775	-0.994000	0.02522	ATC	T|0.180;C|0.820	0.820	strong		0.458	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416	
EVC	2121	hgsc.bcm.edu	37	4	5806512	5806512	+	Silent	SNP	G	G	A	rs115976359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:5806512G>A	ENST00000264956.6	+	17	2689	c.2505G>A	c.(2503-2505)tcG>tcA	p.S835S	EVC_ENST00000382674.2_Silent_p.S835S	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	835					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				GCAACCCTTCGTCGGGCAGCA	0.552													G|||	66	0.0131789	0.0008	0.0043	5008	,	,		20795	0.0		0.0109	False		,,,				2504	0.0521				p.S835S		Atlas-SNP	.											EVC,colon,carcinoma,0,3	EVC	90	3	0			c.G2505A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	113.0	110.0	111.0		2505	-5.0	0.0	4	dbSNP_132	111	123,8477	64.2+/-126.4	1,121,4178	no	coding-synonymous	EVC	NM_153717.2		1,131,6371	AA,AG,GG		1.4302,0.227,1.0226		835/993	5806512	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon17			CCCTTCGTCGGGC	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.2505G>A	4.37:g.5806512G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			G|0.991;A|0.009	0.009	strong		0.552	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
BTBD7	55727	hgsc.bcm.edu	37	14	93712290	93712290	+	Missense_Mutation	SNP	C	C	A	rs61991737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:93712290C>A	ENST00000334746.5	-	10	2771	c.2464G>T	c.(2464-2466)Gct>Tct	p.A822S	BTBD7_ENST00000554565.1_Missense_Mutation_p.A471S|BTBD7_ENST00000393170.2_Missense_Mutation_p.A396S	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	822	Pro-rich.				multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		GGCGGTGCAGCTTTCACACTC	0.572													C|||	3	0.000599042	0.0	0.0	5008	,	,		17134	0.0		0.001	False		,,,				2504	0.002				p.A822S		Atlas-SNP	.											.	BTBD7	112	.	0			c.G2464T						PASS	.	C	SER/ALA	2,4404	4.2+/-10.8	0,2,2201	55.0	56.0	55.0		2464	5.9	0.3	14	dbSNP_129	55	10,8590	7.7+/-29.5	0,10,4290	yes	missense	BTBD7	NM_001002860.2	99	0,12,6491	AA,AC,CC		0.1163,0.0454,0.0923	possibly-damaging	822/1133	93712290	12,12994	2203	4300	6503	SO:0001583	missense	55727	exon10			GTGCAGCTTTCAC	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"""BTB/POZ domain containing"""	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2464G>T	14.37:g.93712290C>A	ENSP00000335615:p.Ala822Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	37	CCDS32146.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.21	2.766791	0.49574	4.54E-4	0.001163	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	T;T	0.49139	1.14;0.79	5.94	5.94	0.96194	.	0.141339	0.64402	D	0.000004	T	0.41627	0.1167	N	0.19112	0.55	0.37849	D	0.929331	P;B;B	0.39480	0.675;0.449;0.058	B;B;B	0.41813	0.367;0.26;0.042	T	0.32241	-0.9914	10	0.34782	T	0.22	.	20.3517	0.98814	0.0:1.0:0.0:0.0	rs61991737	396;471;822	E7ERI4;Q9P203-5;Q9P203	.;.;BTBD7_HUMAN	S	822;471;437;396	ENSP00000335615:A822S;ENSP00000451010:A471S	ENSP00000335615:A822S	A	-	1	0	BTBD7	92782043	1.000000	0.71417	0.295000	0.24960	0.026000	0.11368	3.688000	0.54699	2.818000	0.97014	0.650000	0.86243	GCT	C|0.999;A|0.001	0.001	strong		0.572	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860	
HMGCS2	3158	hgsc.bcm.edu	37	1	120293454	120293454	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120293454G>A	ENST00000369406.3	-	9	1547	c.1498C>T	c.(1498-1500)Cgc>Tgc	p.R500C	HMGCS2_ENST00000544913.2_Missense_Mutation_p.R458C	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	500			R -> H (in HMGCS deficiency). {ECO:0000269|PubMed:11479731}.		cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		TACTTTCGGCGATGCTGCTCG	0.517																																					p.R500C		Atlas-SNP	.											.	HMGCS2	58	.	0			c.C1498T						PASS	.						78.0	68.0	72.0					1																	120293454		2203	4300	6503	SO:0001583	missense	3158	exon9			TTCGGCGATGCTG	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"""			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.1498C>T	1.37:g.120293454G>A	ENSP00000358414:p.Arg500Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Missense_Mutation	SNP	ENST00000369406.3	37	CCDS905.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499155	0.64298	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	D;D	0.90324	-2.65;-2.65	5.3	5.3	0.74995	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like (1);	0.000000	0.64402	D	0.000002	D	0.95928	0.8674	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96419	0.9310	10	0.87932	D	0	-2.0E-4	12.9248	0.58254	0.0:0.0:0.8377:0.1623	.	458;500	B7Z8R3;P54868	.;HMCS2_HUMAN	C	500;458	ENSP00000358414:R500C;ENSP00000439495:R458C	ENSP00000358414:R500C	R	-	1	0	HMGCS2	120094977	1.000000	0.71417	0.511000	0.27724	0.425000	0.31504	5.604000	0.67626	2.633000	0.89246	0.561000	0.74099	CGC	.	.	none		0.517	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518	
UNC13A	23025	hgsc.bcm.edu	37	19	17740115	17740115	+	Silent	SNP	G	G	A	rs61753902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17740115G>A	ENST00000519716.2	-	31	3686	c.3687C>T	c.(3685-3687)ctC>ctT	p.L1229L	UNC13A_ENST00000252773.7_Silent_p.L1229L|UNC13A_ENST00000550896.1_Silent_p.L1227L|UNC13A_ENST00000551649.1_Silent_p.L1229L|UNC13A_ENST00000552293.1_Silent_p.L1229L|UNC13A_ENST00000428389.2_Silent_p.L1317L	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1229	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CATACTGGAGGAGCACATTAC	0.572													G|||	96	0.0191693	0.0144	0.0274	5008	,	,		21764	0.001		0.0527	False		,,,				2504	0.0041				p.L1229L		Atlas-SNP	.											.	UNC13A	299	.	0			c.C3687T						PASS	.			78,4094		0,78,2008	86.0	83.0	84.0		3687	-5.7	1.0	19	dbSNP_129	84	514,7916		15,484,3716	no	coding-synonymous	UNC13A	NM_001080421.2		15,562,5724	AA,AG,GG		6.0973,1.8696,4.6977		1229/1704	17740115	592,12010	2086	4215	6301	SO:0001819	synonymous_variant	23025	exon30			CTGGAGGAGCACA	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3687C>T	19.37:g.17740115G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			G|0.968;A|0.032	0.032	strong		0.572	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
POLR2A	5430	hgsc.bcm.edu	37	17	7412403	7412403	+	Silent	SNP	T	T	C	rs2228133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7412403T>C	ENST00000322644.6	+	21	4005	c.3606T>C	c.(3604-3606)ttT>ttC	p.F1202F		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1202					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				TGCCTGACTTTGATGTGGCCC	0.542													T|||	553	0.110423	0.0431	0.1859	5008	,	,		18045	0.2183		0.0805	False		,,,				2504	0.0675				p.F1202F		Atlas-SNP	.											.	POLR2A	157	.	0			c.T3606C						PASS	.	T		273,4133	153.3+/-186.9	11,251,1941	137.0	92.0	107.0		3606	-0.4	1.0	17	dbSNP_98	107	605,7995	159.2+/-212.6	23,559,3718	no	coding-synonymous	POLR2A	NM_000937.4		34,810,5659	CC,CT,TT		7.0349,6.1961,6.7507		1202/1971	7412403	878,12128	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon21			TGACTTTGATGTG			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.3606T>C	17.37:g.7412403T>C		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	272	117	0.430147	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			T|0.909;C|0.091	0.091	strong		0.542	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
ATF7IP	55729	hgsc.bcm.edu	37	12	14587301	14587301	+	Missense_Mutation	SNP	A	A	G	rs3213764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:14587301A>G	ENST00000540793.1	+	2	1744	c.1589A>G	c.(1588-1590)aAa>aGa	p.K530R	ATF7IP_ENST00000543189.1_Missense_Mutation_p.K529R|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000261168.4_Missense_Mutation_p.K530R|ATF7IP_ENST00000536444.1_Missense_Mutation_p.K529R|ATF7IP_ENST00000544627.1_Missense_Mutation_p.K538R			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	530	Glu-rich.		K -> R (in dbSNP:rs3213764). {ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.K530R(1)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						AAGGACAACAAACCTGAGGAA	0.294													A|||	2201	0.439497	0.2852	0.3674	5008	,	,		16181	0.6181		0.496	False		,,,				2504	0.4571				p.K530R		Atlas-SNP	.											ATF7IP,NS,carcinoma,0,1	ATF7IP	136	1	1	Substitution - Missense(1)	prostate(1)	c.A1589G						PASS	.	A	ARG/LYS	1310,3096	439.2+/-345.6	202,906,1095	108.0	110.0	109.0		1589	4.4	1.0	12	dbSNP_106	109	4184,4416	566.8+/-388.7	1021,2142,1137	yes	missense	ATF7IP	NM_018179.3	26	1223,3048,2232	GG,GA,AA		48.6512,29.7322,42.242	probably-damaging	530/1271	14587301	5494,7512	2203	4300	6503	SO:0001583	missense	55729	exon3			ACAACAAACCTGA	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.1589A>G	12.37:g.14587301A>G	ENSP00000444589:p.Lys530Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	143	61	0.426573	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	1027	0.47023809523809523	151	0.30691056910569103	147	0.40607734806629836	352	0.6153846153846154	377	0.4973614775725594	A	19.46	3.832458	0.71258	0.297322	0.486512	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000540793	T;T;T;T;T	0.22539	1.95;1.96;2.03;1.95;1.95	4.43	4.43	0.53597	.	0.345516	0.23883	N	0.043632	T	0.00012	0.0000	L	0.54323	1.7	0.31248	P	0.694437	D;D;D	0.60575	0.988;0.974;0.982	P;P;P	0.58013	0.794;0.736;0.831	T	0.38950	-0.9637	9	0.56958	D	0.05	-7.4338	10.6344	0.45556	1.0:0.0:0.0:0.0	rs3213764;rs17403385;rs17855886;rs3213764	529;530;529	G3V1U0;Q6VMQ6;Q6VMQ6-2	.;MCAF1_HUMAN;.	R	530;529;529;538;530	ENSP00000261168:K530R;ENSP00000443179:K529R;ENSP00000445955:K529R;ENSP00000440440:K538R;ENSP00000444589:K530R	ENSP00000261168:K530R	K	+	2	0	ATF7IP	14478568	0.993000	0.37304	1.000000	0.80357	0.861000	0.49209	2.126000	0.42026	1.935000	0.56089	0.383000	0.25322	AAA	A|0.556;G|0.444	0.444	strong		0.294	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
FOLH1	2346	hgsc.bcm.edu	37	11	49196490	49196490	+	Silent	SNP	T	T	C	rs202716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49196490T>C	ENST00000256999.2	-	9	1319	c.1059A>G	c.(1057-1059)acA>acG	p.T353T	FOLH1_ENST00000343844.4_Silent_p.T45T|FOLH1_ENST00000340334.7_Silent_p.T338T|FOLH1_ENST00000356696.3_Silent_p.T353T|FOLH1_ENST00000533034.1_Silent_p.T338T|FOLH1_ENST00000525629.1_5'UTR	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	353	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGTAAATTCTTGTCACTTCAT	0.338													C|||	2095	0.418331	0.6483	0.3156	5008	,	,		17405	0.3175		0.2744	False		,,,				2504	0.4325				p.T353T		Atlas-SNP	.											.	FOLH1	141	.	0			c.A1059G						PASS	.						90.0	110.0	103.0					11																	49196490		2201	4297	6498	SO:0001819	synonymous_variant	2346	exon9			AATTCTTGTCACT	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.1059A>G	11.37:g.49196490T>C		Somatic	411	0	0		WXS	Illumina HiSeq	Phase_I	417	136	0.326139	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Silent	SNP	ENST00000256999.2	37	CCDS7946.1																																																																																			C|1.000;|0.000	1.000	weak		0.338	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
CUTC	51076	hgsc.bcm.edu	37	10	101502968	101502968	+	Silent	SNP	A	A	G	rs3740076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:101502968A>G	ENST00000370476.5	+	4	381	c.252A>G	c.(250-252)ccA>ccG	p.P84P	CUTC_ENST00000493385.1_3'UTR	NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	84					copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		TGATTCGGCCACGGGGAGGTG	0.418													A|||	320	0.0638978	0.0053	0.1499	5008	,	,		19471	0.0228		0.1083	False		,,,				2504	0.0787				p.P84P		Atlas-SNP	.											.	CUTC	32	.	0			c.A252G						PASS	.	A		81,4325	69.2+/-107.0	1,79,2123	215.0	198.0	204.0		252	0.7	1.0	10	dbSNP_107	204	928,7672	204.0+/-246.8	49,830,3421	no	coding-synonymous	CUTC	NM_015960.2		50,909,5544	GG,GA,AA		10.7907,1.8384,7.758		84/274	101502968	1009,11997	2203	4300	6503	SO:0001819	synonymous_variant	51076	exon4			TCGGCCACGGGGA	AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"""cutC copper transporter homolog (E. coli)"""			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.252A>G	10.37:g.101502968A>G		Somatic	383	0	0		WXS	Illumina HiSeq	Phase_I	338	188	0.556213	NM_015960	Q5TCZ8|Q9Y321	Silent	SNP	ENST00000370476.5	37	CCDS7483.1																																																																																			A|0.931;G|0.069	0.069	strong		0.418	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960	
FAM46C	54855	hgsc.bcm.edu	37	1	118166096	118166096	+	Silent	SNP	C	C	T	rs2884587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:118166096C>T	ENST00000369448.3	+	2	853	c.606C>T	c.(604-606)atC>atT	p.I202I		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	202										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		ATAATCCCATCTCTGAGCACT	0.483			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			C|||	673	0.134385	0.0159	0.2233	5008	,	,		21188	0.1141		0.164	False		,,,				2504	0.2219				p.I202I		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C606T						PASS	.	C		211,4195	129.0+/-165.8	10,191,2002	137.0	132.0	134.0		606	1.5	0.9	1	dbSNP_101	134	1423,7177	273.5+/-290.7	121,1181,2998	no	coding-synonymous	FAM46C	NM_017709.3		131,1372,5000	TT,TC,CC		16.5465,4.7889,12.5634		202/392	118166096	1634,11372	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			TCCCATCTCTGAG	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.606C>T	1.37:g.118166096C>T		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	216	76	0.351852	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.874;T|0.126	0.126	strong		0.483	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
ERCC6	2074	hgsc.bcm.edu	37	10	50681033	50681033	+	Silent	SNP	G	G	A	rs2229760	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50681033G>A	ENST00000355832.5	-	15	2829	c.2751C>T	c.(2749-2751)ggC>ggT	p.G917G	ERCC6_ENST00000542458.1_Silent_p.G287G|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000465653.1_5'Flank	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	917	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.G917G(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CACCTAAGCCGCCCACCCGCG	0.473								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	1273	0.254193	0.0893	0.2968	5008	,	,		14918	0.3155		0.3926	False		,,,				2504	0.2413				p.R917R		Atlas-SNP	.											ERCC6,NS,carcinoma,0,1	ERCC6	162	1	1	Substitution - coding silent(1)	stomach(1)	c.G2751T						PASS	.	G		659,3747	281.4+/-275.9	47,565,1591	67.0	62.0	64.0		2751	-8.2	0.5	10	dbSNP_98	64	3552,5048	516.8+/-378.9	720,2112,1468	no	coding-synonymous	ERCC6	NM_000124.2		767,2677,3059	AA,AG,GG		41.3023,14.9569,32.3774		917/1494	50681033	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	2074	exon15			TAAGCCGCCCACC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.2751C>T	10.37:g.50681033G>A		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			G|0.702;A|0.298	0.298	strong		0.473	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057422	46057422	+	Missense_Mutation	SNP	T	T	A	rs112205018|rs386819192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46057422T>A	ENST00000380095.1	+	1	150	c.88T>A	c.(88-90)Tgc>Agc	p.C30S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	30	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CTGCGAGCCCTGCTGCTGTGC	0.677													T|||	1453	0.290136	0.2337	0.2075	5008	,	,		16831	0.253		0.3101	False		,,,				2504	0.4427				p.C30S		Atlas-SNP	.											KRTAP10-10,caecum,carcinoma,0,1	KRTAP10-10	37	1	0			c.T88A						PASS	.						64.0	70.0	68.0					21																	46057422		2203	4299	6502	SO:0001583	missense	353333	exon1			GAGCCCTGCTGCT	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.88T>A	21.37:g.46057422T>A	ENSP00000369438:p.Cys30Ser	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	149	79	0.530201	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	540	0.24725274725274726	93	0.18902439024390244	74	0.20441988950276244	138	0.24125874125874125	235	0.3100263852242744	t	0.004	-2.351941	0.00217	.	.	ENSG00000221859	ENST00000380095	T	0.09911	2.93	3.09	0.455	0.16649	.	.	.	.	.	T	0.00012	0.0000	N	0.01686	-0.76	0.50313	P	1.3399999999996748E-4	B	0.16166	0.016	B	0.10450	0.005	T	0.45948	-0.9226	8	0.06365	T	0.9	.	5.6129	0.17416	0.0:0.6006:0.0:0.3994	.	30	P60014	KR10A_HUMAN	S	30	ENSP00000369438:C30S	ENSP00000369438:C30S	C	+	1	0	KRTAP10-10	44881850	.	.	0.910000	0.35882	0.005000	0.04900	.	.	-0.062000	0.13088	-0.407000	0.06327	TGC	T|0.742;A|0.258	0.258	strong		0.677	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
ATG2B	55102	hgsc.bcm.edu	37	14	96829290	96829290	+	Silent	SNP	G	G	A	rs12434329	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:96829290G>A	ENST00000359933.4	-	1	917	c.24C>T	c.(22-24)tcC>tcT	p.S8S	GSKIP_ENST00000555181.1_5'Flank|GSKIP_ENST00000554182.1_5'Flank|GSKIP_ENST00000556095.1_5'Flank	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	8					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TCTTCTTGATGGACTCCGAAA	0.642													A|||	2401	0.479433	0.2595	0.6873	5008	,	,		15336	0.4276		0.6839	False		,,,				2504	0.4724				p.S8S		Atlas-SNP	.											.	ATG2B	169	.	0			c.C24T						PASS	.	A		1580,2618		307,966,826	52.0	55.0	54.0		24	0.2	1.0	14	dbSNP_120	54	6047,2423		2174,1699,362	no	coding-synonymous	ATG2B	NM_018036.5		2481,2665,1188	AA,AG,GG		28.6068,37.637,39.7932		8/2079	96829290	7627,5041	2099	4235	6334	SO:0001819	synonymous_variant	55102	exon1			CTTGATGGACTCC	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.24C>T	14.37:g.96829290G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	37	CCDS9944.2																																																																																			G|0.482;A|0.518	0.518	strong		0.642	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
COL6A5	256076	hgsc.bcm.edu	37	3	130116696	130116696	+	Missense_Mutation	SNP	A	A	C	rs12488457	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130116696A>C	ENST00000432398.2	+	9	4332	c.3838A>C	c.(3838-3840)Act>Cct	p.T1280P	COL6A5_ENST00000265379.6_Missense_Mutation_p.T1280P	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1280	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.		T -> P (in dbSNP:rs12488457). {ECO:0000269|PubMed:18276594}.		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						CAGTGGGCCAACTCATCTGAA	0.473													A|||	1699	0.339257	0.0492	0.4294	5008	,	,		19613	0.1726		0.7247	False		,,,				2504	0.4427				p.T1280P		Atlas-SNP	.											.	COL6A5	205	.	0			c.A3838C	GRCh37	CM076119	COL6A5	M	rs12488457	PASS	.	A	PRO/THR	226,1158		20,186,486	174.0	148.0	156.0		3838	4.0	1.0	3	dbSNP_120	156	2263,919		808,647,136	yes	missense	COL6A5	NM_153264.5	38	828,833,622	CC,CA,AA		28.8812,16.3295,45.4884	possibly-damaging	1280/2527	130116696	2489,2077	692	1591	2283	SO:0001583	missense	256076	exon9			GGGCCAACTCATC	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.3838A>C	3.37:g.130116696A>C	ENSP00000390895:p.Thr1280Pro	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		868	0.3974358974358974	36	0.07317073170731707	172	0.47513812154696133	95	0.1660839160839161	565	0.7453825857519789	A	13.49	2.254022	0.39896	0.163295	0.711188	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.38077	1.16;1.16	5.26	3.97	0.46021	.	.	.	.	.	T	0.00012	0.0000	L	0.56769	1.78	0.42892	P	0.005793000000000048	D	0.65815	0.995	D	0.71184	0.972	T	0.18178	-1.0345	8	0.29301	T	0.29	.	10.2233	0.43209	0.7739:0.0:0.0:0.2261	rs12488457;rs17687135;rs52789955;rs12488457	1280	A8TX70-2	.	P	1280	ENSP00000390895:T1280P;ENSP00000265379:T1280P	ENSP00000265379:T1280P	T	+	1	0	COL6A5	131599386	0.878000	0.30173	0.997000	0.53966	0.927000	0.56198	1.267000	0.33050	1.985000	0.57927	0.459000	0.35465	ACT	A|0.620;C|0.380	0.380	strong		0.473	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
SLC3A1	6519	hgsc.bcm.edu	37	2	44547574	44547574	+	Missense_Mutation	SNP	G	G	A	rs698761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:44547574G>A	ENST00000260649.6	+	10	1930	c.1854G>A	c.(1852-1854)atG>atA	p.M618I	PREPL_ENST00000409957.1_3'UTR|PREPL_ENST00000409411.1_3'UTR|PREPL_ENST00000409936.1_3'UTR|SLC3A1_ENST00000409380.1_Missense_Mutation_p.M340I|PREPL_ENST00000541738.1_3'UTR|SLC3A1_ENST00000409740.3_Missense_Mutation_p.M249I	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	618			M -> I (in dbSNP:rs698761). {ECO:0000269|PubMed:11318953, ECO:0000269|PubMed:11748844, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15913950, ECO:0000269|PubMed:7573036, ECO:0000269|PubMed:8486766, ECO:0000269|PubMed:8663184, ECO:0000269|PubMed:9186880}.		amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	CCGCTAAAATGAGAATAAGGT	0.403													G|||	2308	0.460863	0.2126	0.5447	5008	,	,		20446	0.3214		0.661	False		,,,				2504	0.6748				p.M618I		Atlas-SNP	.											.	SLC3A1	62	.	0			c.G1854A						PASS	.	G	ILE/MET,,,,,,,	1270,3136	431.8+/-343.0	188,894,1121	98.0	89.0	92.0		1854,,,,,,,	-1.4	0.0	2	dbSNP_86	92	5817,2783	677.8+/-403.4	1960,1897,443	yes	missense,utr-3,utr-3,utr-3,utr-3,utr-3,utr-3,utr-3	SLC3A1,PREPL	NM_000341.3,NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	10,,,,,,,	2148,2791,1564	AA,AG,GG		32.3605,28.8243,45.5098	benign,,,,,,,	618/686,,,,,,,	44547574	7087,5919	2203	4300	6503	SO:0001583	missense	6519	exon10			TAAAATGAGAATA		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"""Solute carriers"""	11025	protein-coding gene	gene with protein product		104614	"""solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"""			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.1854G>A	2.37:g.44547574G>A	ENSP00000260649:p.Met618Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Missense_Mutation	SNP	ENST00000260649.6	37	CCDS1819.1	1000	0.45787545787545786	100	0.2032520325203252	206	0.569060773480663	198	0.34615384615384615	496	0.6543535620052771	G	7.667	0.686183	0.14973	0.288243	0.676395	ENSG00000138079	ENST00000260649;ENST00000540334;ENST00000409380;ENST00000409740	D;D;D	0.99014	-5.33;-4.75;-4.41	5.99	-1.37	0.09056	.	0.561087	0.19190	N	0.120443	T	0.00012	0.0000	L	0.35854	1.095	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.48525	-0.9028	9	0.08179	T;T	0.78;0.78	-1.1288	2.1005	0.03678	0.3431:0.3168:0.233:0.1071	rs698761;rs3172075;rs17580044;rs17845690;rs17858631;rs58800787;rs698761	618	Q07837	SLC31_HUMAN	I	618;554;340;249	ENSP00000260649:M618I;ENSP00000386709:M340I;ENSP00000386677:M249I	ENSP00000260649:M618I;ENSP00000260649:M618I	M	+	3	0	SLC3A1	44401078	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.163000	0.09997	0.140000	0.18849	-0.165000	0.13383	ATG	G|0.505;A|0.495	0.495	strong		0.403	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	
FLT1	2321	hgsc.bcm.edu	37	13	28883061	28883061	+	Silent	SNP	G	G	A	rs7993418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:28883061G>A	ENST00000282397.4	-	28	3890	c.3639C>T	c.(3637-3639)taC>taT	p.Y1213Y	FLT1_ENST00000540678.1_Silent_p.Y431Y|FLT1_ENST00000543394.1_Silent_p.Y236Y	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	1213					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAGCATTTACGTATCTAATGA	0.408													A|||	3660	0.730831	0.2769	0.8285	5008	,	,		22236	1.0		0.7952	False		,,,				2504	0.9315				p.Y1213Y		Atlas-SNP	.											.	FLT1	393	.	0			c.C3639T						PASS	.	A		1619,2787	661.8+/-401.0	295,1029,879	83.0	70.0	74.0		3639	-7.0	0.7	13	dbSNP_116	74	6790,1810	323.4+/-316.0	2676,1438,186	no	coding-synonymous	FLT1	NM_002019.4		2971,2467,1065	AA,AG,GG		21.0465,36.7453,35.3452		1213/1339	28883061	8409,4597	2203	4300	6503	SO:0001819	synonymous_variant	2321	exon28			ATTTACGTATCTA	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.3639C>T	13.37:g.28883061G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																			G|0.320;A|0.680	0.680	strong		0.408	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
FRG1	2483	hgsc.bcm.edu	37	4	190876277	190876277	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:190876277A>T	ENST00000226798.4	+	5	625	c.403A>T	c.(403-405)Aga>Tga	p.R135*	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	135					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.R135*(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		AATTGGACCAAGAGAACAATG	0.358																																					p.R135X		Atlas-SNP	.											FRG1,trunk,malignant_melanoma,0,1	FRG1	76	1	1	Substitution - Nonsense(1)	skin(1)	c.A403T						PASS	.						89.0	89.0	89.0					4																	190876277		2203	4300	6503	SO:0001587	stop_gained	2483	exon5			GGACCAAGAGAAC	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.403A>T	4.37:g.190876277A>T	ENSP00000226798:p.Arg135*	Somatic	401	0	0		WXS	Illumina HiSeq	Phase_I	543	43	0.0791897	NM_004477	A8K775	Nonsense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	37	6.057581	0.97241	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	.	.	.	4.04	2.81	0.32909	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-5.2304	8.7138	0.34399	0.7565:0.2435:0.0:0.0	.	.	.	.	X	135;72	.	ENSP00000226798:R135X	R	+	1	2	FRG1	191113271	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.691000	0.54720	1.599000	0.50093	0.462000	0.41574	AGA	.	.	none		0.358	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
AMPD3	272	hgsc.bcm.edu	37	11	10521764	10521764	+	Silent	SNP	T	T	C	rs3741041	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:10521764T>C	ENST00000396554.3	+	11	2057	c.1716T>C	c.(1714-1716)taT>taC	p.Y572Y	AMPD3_ENST00000444303.2_Silent_p.Y404Y|AMPD3_ENST00000530864.1_3'UTR	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	563					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		ACTACATGTATGCCAACATCA	0.547													T|||	1840	0.367412	0.0545	0.3991	5008	,	,		27067	0.6944		0.4145	False		,,,				2504	0.3824				p.Y572Y		Atlas-SNP	.											.	AMPD3	68	.	0			c.T1716C						PASS	.	T	,,,,	540,3862	244.0+/-253.5	31,478,1692	324.0	208.0	247.0		1716,1689,1710,1689,1212	-2.7	1.0	11	dbSNP_107	247	3545,5043	516.6+/-378.9	727,2091,1476	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	,,,,	758,2569,3168	CC,CT,TT		41.2785,12.2672,31.4473	,,,,	572/777,563/768,570/775,563/768,404/609	10521764	4085,8905	2201	4294	6495	SO:0001819	synonymous_variant	272	exon11			CATGTATGCCAAC	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.1716T>C	11.37:g.10521764T>C		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																			T|0.653;C|0.347	0.347	strong		0.547	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
CELSR3	1951	hgsc.bcm.edu	37	3	48681053	48681053	+	Silent	SNP	C	C	T	rs9868809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:48681053C>T	ENST00000164024.4	-	28	8503	c.8223G>A	c.(8221-8223)ggG>ggA	p.G2741G	MIR4793_ENST00000577502.1_RNA|CELSR3_ENST00000544264.1_Silent_p.G2746G	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2741					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.G2741G(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTGCCAGGAGCCCAAAGAGCC	0.612													C|||	563	0.11242	0.1687	0.0821	5008	,	,		18351	0.128		0.1133	False		,,,				2504	0.0409				p.G2741G		Atlas-SNP	.											CELSR3,NS,carcinoma,0,1	CELSR3	237	1	1	Substitution - coding silent(1)	stomach(1)	c.G8223A						PASS	.	C		599,3687		36,527,1580	81.0	65.0	71.0		8223	-2.0	1.0	3	dbSNP_119	71	845,7497		51,743,3377	no	coding-synonymous	CELSR3	NM_001407.2		87,1270,4957	TT,TC,CC		10.1295,13.9757,11.4349		2741/3313	48681053	1444,11184	2143	4171	6314	SO:0001819	synonymous_variant	1951	exon28			CAGGAGCCCAAAG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.8223G>A	3.37:g.48681053C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	54	0.613636	NM_001407	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																			C|0.880;T|0.120	0.120	strong		0.612	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
C10orf71	118461	hgsc.bcm.edu	37	10	50533841	50533841	+	Missense_Mutation	SNP	G	G	C	rs11101094	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50533841G>C	ENST00000374144.3	+	3	3539	c.3251G>C	c.(3250-3252)gGa>gCa	p.G1084A	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1084			G -> A (in dbSNP:rs11101094).							endometrium(1)	1						CAGGCCCCTGGAGGACCAGAG	0.677													G|||	479	0.095647	0.053	0.0663	5008	,	,		14063	0.122		0.1203	False		,,,				2504	0.1217				p.G1084A		Atlas-SNP	.											.	C10orf71	179	.	0			c.G3251C						PASS	.						9.0	13.0	12.0					10																	50533841		689	1588	2277	SO:0001583	missense	118461	exon3			CCCCTGGAGGACC	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.3251G>C	10.37:g.50533841G>C	ENSP00000363259:p.Gly1084Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	211	0.09661172161172162	32	0.06504065040650407	30	0.08287292817679558	60	0.1048951048951049	89	0.11741424802110818	G	0.004	-2.326711	0.00229	.	.	ENSG00000177354	ENST00000374144	T	0.04317	3.65	5.22	0.808	0.18719	.	0.766268	0.10833	N	0.629157	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	.	.	.	.	.	.	T	0.43032	-0.9416	7	0.07175	T	0.84	.	3.9484	0.09358	0.1554:0.122:0.5817:0.1409	rs11101094;rs11101094	.	.	.	A	1084	ENSP00000363259:G1084A	ENSP00000363259:G1084A	G	+	2	0	C10orf71	50203847	0.000000	0.05858	0.007000	0.13788	0.009000	0.06853	0.581000	0.23819	0.593000	0.29745	0.313000	0.20887	GGA	G|0.907;C|0.093	0.093	strong		0.677	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
CEP78	84131	hgsc.bcm.edu	37	9	80851350	80851350	+	Silent	SNP	G	G	C	rs10867166	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:80851350G>C	ENST00000424347.2	+	1	373	c.84G>C	c.(82-84)tcG>tcC	p.S28S	CEP78_ENST00000376597.4_Silent_p.S28S|CEP78_ENST00000277082.5_Silent_p.S28S|CEP78_ENST00000376598.2_Silent_p.S28S|CEP78_ENST00000415759.2_Silent_p.S28S			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	28					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						TGCAGAACTCGGTGCCGCTGC	0.711													g|||	1421	0.283746	0.1558	0.3199	5008	,	,		13470	0.2738		0.3559	False		,,,				2504	0.3671				p.S28S		Atlas-SNP	.											.	CEP78	79	.	0			c.G84C						PASS	.		,	627,3331		52,523,1404	10.0	12.0	12.0		84,84	0.9	1.0	9	dbSNP_120	12	3058,5216		572,1914,1651	no	coding-synonymous,coding-synonymous	CEP78	NM_001098802.1,NM_032171.1	,	624,2437,3055	CC,CG,GG		36.9591,15.8413,30.1259	,	28/723,28/707	80851350	3685,8547	1979	4137	6116	SO:0001819	synonymous_variant	84131	exon1			GAACTCGGTGCCG	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 81"""	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.84G>C	9.37:g.80851350G>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	37	23	0.621622	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Silent	SNP	ENST00000424347.2	37																																																																																				G|0.732;C|0.268	0.268	strong		0.711	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991	
ADAM29	11086	hgsc.bcm.edu	37	4	175899088	175899088	+	Missense_Mutation	SNP	G	G	T	rs146933346	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175899088G>T	ENST00000359240.3	+	5	3082	c.2412G>T	c.(2410-2412)agG>agT	p.R804S	ADAM29_ENST00000445694.1_Missense_Mutation_p.R804S|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.R804S|ADAM29_ENST00000404450.4_Missense_Mutation_p.R804S	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	804	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCTCCCAGAGGCAACCTCAGT	0.572													T|||	28	0.00559105	0.0	0.0014	5008	,	,		19556	0.0099		0.0109	False		,,,				2504	0.0061				p.R804S	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,NS,lymphoid_neoplasm,0,1	ADAM29	262	1	0			c.G2412T						scavenged	.						133.0	124.0	127.0					4																	175899088		2203	4300	6503	SO:0001583	missense	11086	exon4			CCAGAGGCAACCT	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2412G>T	4.37:g.175899088G>T	ENSP00000352177:p.Arg804Ser	Somatic	130	2	0.0153846		WXS	Illumina HiSeq	Phase_I	190	56	0.294737	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.909135	0.00056	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01871	4.59;4.59;4.59;4.59	0.439	-0.878	0.10617	.	.	.	.	.	T	0.01124	0.0037	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47947	-0.9077	8	.	.	.	.	2.6605	0.05025	0.2447:0.0:0.4895:0.2658	.	804	Q9UKF5	ADA29_HUMAN	S	804	ENSP00000352177:R804S;ENSP00000414544:R804S;ENSP00000384229:R804S;ENSP00000423517:R804S	.	R	+	3	2	ADAM29	176135663	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-3.656000	0.00401	-1.571000	0.01663	-1.187000	0.01702	AGG	C|0.001;G|0.998;T|0.001	0.001	weak		0.572	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
UBR4	23352	hgsc.bcm.edu	37	1	19499560	19499560	+	Missense_Mutation	SNP	T	T	C	rs16862578	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19499560T>C	ENST00000375254.3	-	25	3346	c.3319A>G	c.(3319-3321)Acc>Gcc	p.T1107A	UBR4_ENST00000375267.2_Missense_Mutation_p.T1107A|UBR4_ENST00000375217.2_Missense_Mutation_p.T1107A|UBR4_ENST00000375226.2_Missense_Mutation_p.T1107A	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1107			T -> A (in dbSNP:rs16862578).		protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T1107A(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AAGATGGTGGTACAGTCGATA	0.418													T|||	694	0.138578	0.2814	0.1671	5008	,	,		21057	0.0109		0.164	False		,,,				2504	0.0307				p.T1107A		Atlas-SNP	.											UBR4,NS,carcinoma,0,1	UBR4	415	1	1	Substitution - Missense(1)	stomach(1)	c.A3319G						PASS	.	T	ALA/THR	1102,3304	397.4+/-330.4	127,848,1228	90.0	85.0	87.0		3319	4.8	1.0	1	dbSNP_123	87	1407,7193	272.4+/-290.1	116,1175,3009	yes	missense	UBR4	NM_020765.2	58	243,2023,4237	CC,CT,TT		16.3605,25.0113,19.2911	benign	1107/5184	19499560	2509,10497	2203	4300	6503	SO:0001583	missense	23352	exon25			TGGTGGTACAGTC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.3319A>G	1.37:g.19499560T>C	ENSP00000364403:p.Thr1107Ala	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	330	0.1510989010989011	132	0.2682926829268293	70	0.19337016574585636	7	0.012237762237762238	121	0.15963060686015831	T	15.15	2.747935	0.49257	0.250113	0.163605	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.95	4.82	0.62117	.	0.165648	0.52532	N	0.000069	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21280	-1.0250	9	0.45353	T	0.12	.	6.8415	0.23965	0.134:0.0711:0.0:0.7948	rs16862578;rs52813973;rs16862578	1107	Q5T4S7	UBR4_HUMAN	A	1107;1107;1107;1107;323	ENSP00000364403:T1107A;ENSP00000364416:T1107A;ENSP00000364365:T1107A;ENSP00000364374:T1107A	ENSP00000364365:T1107A	T	-	1	0	UBR4	19372147	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.726000	0.61986	1.075000	0.40932	0.533000	0.62120	ACC	T|0.826;C|0.174	0.174	strong		0.418	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
SCN2A	6326	hgsc.bcm.edu	37	2	166152389	166152389	+	Missense_Mutation	SNP	G	G	A	rs17183814	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:166152389G>A	ENST00000375437.2	+	2	346	c.56G>A	c.(55-57)aGg>aAg	p.R19K	SCN2A_ENST00000375427.2_Missense_Mutation_p.R19K|SCN2A_ENST00000283256.6_Missense_Mutation_p.R19K|SCN2A_ENST00000357398.3_Missense_Mutation_p.R19K	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	19			R -> K (in dbSNP:rs17183814). {ECO:0000269|PubMed:11371648, ECO:0000269|PubMed:12610651, ECO:0000269|PubMed:19786696}.		intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCTTTACCAGGGAATCCCTT	0.483													G|||	420	0.0838658	0.0212	0.0821	5008	,	,		20245	0.1379		0.0567	False		,,,				2504	0.1421				p.R19K		Atlas-SNP	.											.	SCN2A	589	.	0			c.G56A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	148,4258	103.4+/-141.9	2,144,2057	84.0	75.0	78.0		56,56,56	5.6	1.0	2	dbSNP_123	78	616,7984	160.4+/-213.5	21,574,3705	yes	missense,missense,missense	SCN2A	NM_001040142.1,NM_001040143.1,NM_021007.2	26,26,26	23,718,5762	AA,AG,GG		7.1628,3.3591,5.8742	probably-damaging,probably-damaging,probably-damaging	19/2006,19/2006,19/2006	166152389	764,12242	2203	4300	6503	SO:0001583	missense	6326	exon1			TTACCAGGGAATC	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.56G>A	2.37:g.166152389G>A	ENSP00000364586:p.Arg19Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	113	44	0.389381	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	159	0.07280219780219781	9	0.018292682926829267	30	0.08287292817679558	74	0.12937062937062938	46	0.06068601583113457	G	11.85	1.760255	0.31137	0.033591	0.071628	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D;D	0.96459	-4.02;-4.0;-4.0;-4.0;-4.0	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.22820	0.0551	M	0.65975	2.015	0.36123	P	0.15438799999999997	B;B	0.09022	0.002;0.001	B;B	0.16289	0.015;0.007	T	0.71477	-0.4581	9	0.44086	T	0.13	.	13.7552	0.62933	0.0732:0.0:0.9268:0.0	rs17183814;rs52803852;rs17183814	19;19	Q99250-2;Q99250	.;SCN2A_HUMAN	K	19	ENSP00000406454:R19K;ENSP00000364586:R19K;ENSP00000349973:R19K;ENSP00000283256:R19K;ENSP00000364576:R19K	ENSP00000283256:R19K	R	+	2	0	SCN2A	165860635	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.409000	0.44583	2.619000	0.88677	0.655000	0.94253	AGG	G|0.933;A|0.067	0.067	strong		0.483	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
NAV2	89797	hgsc.bcm.edu	37	11	20089944	20089944	+	Splice_Site	SNP	T	T	C	rs1442710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:20089944T>C	ENST00000396087.3	+	24	5250	c.5151T>C	c.(5149-5151)aaT>aaC	p.N1717N	NAV2_ENST00000533917.1_Splice_Site_p.N725N|NAV2_ENST00000360655.4_Splice_Site_p.N1597N|NAV2_ENST00000540292.1_Splice_Site_p.N1648N|NAV2_ENST00000349880.4_Splice_Site_p.N1661N|NAV2_ENST00000396085.1_Splice_Site_p.N1661N|NAV2_ENST00000527559.2_Splice_Site_p.N1646N|NAV2_ENST00000311043.8_Splice_Site_p.N725N	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1717					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TGACAGCAAATGTAAGTACAG	0.512													T|||	1573	0.314097	0.348	0.2853	5008	,	,		18294	0.5526		0.1928	False		,,,				2504	0.1677				p.N1717N		Atlas-SNP	.											.	NAV2	255	.	0			c.T5151C						PASS	.	T	,,,	1394,3012	459.6+/-352.3	218,958,1027	89.0	84.0	86.0		4791,2175,4983,4983	3.1	1.0	11	dbSNP_88	86	1589,7011	295.8+/-302.6	147,1295,2858	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	365,2253,3885	CC,CT,TT		18.4767,31.6387,22.9356	,,,	1597/2366,725/1494,1661/2430,1661/2433	20089944	2983,10023	2203	4300	6503	SO:0001630	splice_region_variant	89797	exon24			AGCAAATGTAAGT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.5151+1T>C	11.37:g.20089944T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			T|0.724;C|0.276	0.276	strong		0.512	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	Silent
PRPH	5630	hgsc.bcm.edu	37	12	49691250	49691250	+	Silent	SNP	A	A	G	rs73112143	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49691250A>G	ENST00000257860.4	+	6	2606	c.1107A>G	c.(1105-1107)aaA>aaG	p.K369K	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						GACAGCTAAAAGAGGAGATGG	0.657											OREG0021790	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1028	0.205272	0.3979	0.1484	5008	,	,		11296	0.0367		0.2048	False		,,,				2504	0.1595				p.K369K		Atlas-SNP	.											.	PRPH	26	.	0			c.A1107G						PASS	.	G		1549,2857		284,981,938	23.0	25.0	24.0		1107	3.7	1.0	12	dbSNP_130	24	1722,6876		201,1320,2778	no	coding-synonymous	PRPH	NM_006262.3		485,2301,3716	GG,GA,AA		20.0279,35.1566,25.1538		369/471	49691250	3271,9733	2203	4299	6502	SO:0001819	synonymous_variant	5630	exon6			GCTAAAAGAGGAG		CCDS8783.1	12q12-q13	2013-01-16						"""Intermediate filaments type III"""	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.1107A>G	12.37:g.49691250A>G		Somatic	60	0	0	964	WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_006262	Q5TFH5|Q6DK65	Silent	SNP	ENST00000257860.4	37	CCDS8783.1	437	0.2000915750915751	189	0.38414634146341464	62	0.1712707182320442	27	0.0472027972027972	159	0.20976253298153033	G	18.31	3.596407	0.66332	0.351566	0.200279	ENSG00000135406	ENST00000532332	.	.	.	5.48	3.65	0.41850	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38950	-0.9637	3	.	.	.	.	9.7563	0.40504	0.2302:0.0:0.7698:0.0	.	.	.	.	G	98	.	.	R	+	1	2	PRPH	47977517	1.000000	0.71417	0.993000	0.49108	0.968000	0.65278	4.851000	0.62896	0.690000	0.31570	-0.119000	0.15052	AGA	A|0.778;G|0.222	0.222	strong		0.657	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262	
GUCA1B	2979	hgsc.bcm.edu	37	6	42152583	42152583	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:42152583A>G	ENST00000230361.3	-	4	668	c.573T>C	c.(571-573)gcT>gcC	p.A191A		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	191					body fluid secretion (GO:0007589)|cell-cell signaling (GO:0007267)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			large_intestine(3)|lung(3)|skin(2)	8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)			GTCTCTGCTGAGCGAGCCAGC	0.587																																					p.A191A		Atlas-SNP	.											.	GUCA1B	19	.	0			c.T573C						PASS	.						117.0	99.0	105.0					6																	42152583		2203	4300	6503	SO:0001819	synonymous_variant	2979	exon4			CTGCTGAGCGAGC	AF173227	CCDS4865.1	6p21.1	2013-02-14			ENSG00000112599	ENSG00000112599		"""EF-hand domain containing"""	4679	protein-coding gene	gene with protein product		602275				9119368	Standard	NM_002098		Approved	GCAP2, RP48	uc003orz.3	Q9UMX6	OTTHUMG00000014697	ENST00000230361.3:c.573T>C	6.37:g.42152583A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_002098	Q9NU15	Silent	SNP	ENST00000230361.3	37	CCDS4865.1																																																																																			.	.	none		0.587	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098	
SLC5A8	160728	hgsc.bcm.edu	37	12	101560328	101560328	+	Missense_Mutation	SNP	C	C	A	rs164365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:101560328C>A	ENST00000536262.2	-	12	2028	c.1470G>T	c.(1468-1470)atG>atT	p.M490I		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTGTGGTTGTCATCAAATTTG	0.328													C|||	1304	0.260383	0.149	0.1268	5008	,	,		18912	0.5437		0.2485	False		,,,				2504	0.226				p.M490I	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.G1470T						PASS	.	C	ILE/MET	597,3809	262.8+/-265.1	40,517,1646	122.0	112.0	115.0		1470	3.0	0.8	12	dbSNP_79	115	1932,6668	340.0+/-323.4	207,1518,2575	yes	missense	SLC5A8	NM_145913.3	10	247,2035,4221	AA,AC,CC		22.4651,13.5497,19.4449	benign	490/611	101560328	2529,10477	2203	4300	6503	SO:0001583	missense	160728	exon12			GGTTGTCATCAAA	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"""Solute carriers"""	19119	protein-coding gene	gene with protein product		608044	"""solute carrier family 5 (iodide transporter), member 8"""			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1470G>T	12.37:g.101560328C>A	ENSP00000445340:p.Met490Ile	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_145913		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	600	0.27472527472527475	66	0.13414634146341464	55	0.15193370165745856	301	0.5262237762237763	178	0.23482849604221637	C	0.514	-0.865250	0.02590	0.135497	0.224651	ENSG00000256870	ENST00000536262	T	0.62498	0.02	4.86	2.95	0.34219	.	0.878925	0.10389	N	0.680659	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.49133	-0.8971	9	0.17832	T	0.49	.	3.7188	0.08448	0.3282:0.4963:0.0:0.1755	rs164365;rs1681107;rs2128633;rs52791556;rs59386786;rs164365	490	Q8N695	SC5A8_HUMAN	I	490	ENSP00000445340:M490I	ENSP00000445340:M490I	M	-	3	0	SLC5A8	100084459	0.003000	0.15002	0.751000	0.31187	0.092000	0.18411	0.204000	0.17335	2.530000	0.85305	0.655000	0.94253	ATG	C|0.767;A|0.233	0.233	strong		0.328	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913	
ULK4	54986	hgsc.bcm.edu	37	3	41960006	41960006	+	Missense_Mutation	SNP	T	T	C	rs1716975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:41960006T>C	ENST00000301831.4	-	7	1132	c.670A>G	c.(670-672)Att>Gtt	p.I224V	ULK4_ENST00000420927.1_Missense_Mutation_p.I224V	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	224	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> V (in dbSNP:rs1716975).		cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		AATTCTGAAATACTTTCTGAG	0.284													T|||	3405	0.679912	0.2821	0.7997	5008	,	,		17328	0.8522		0.8042	False		,,,				2504	0.8272				p.I224V		Atlas-SNP	.											.	ULK4	150	.	0			c.A670G						PASS	.	T	VAL/ILE	1249,2381		229,791,795	65.0	65.0	65.0		670	-5.9	0.0	3	dbSNP_89	65	6702,1452		2756,1190,131	yes	missense	ULK4	NM_017886.2	29	2985,1981,926	CC,CT,TT		17.8072,34.4077,32.5272	benign	224/1276	41960006	7951,3833	1815	4077	5892	SO:0001583	missense	54986	exon7			CTGAAATACTTTC	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.670A>G	3.37:g.41960006T>C	ENSP00000301831:p.Ile224Val	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	1513	0.6927655677655677	140	0.2845528455284553	287	0.7928176795580111	482	0.8426573426573427	604	0.7968337730870713	T	1.381	-0.583388	0.03827	0.344077	0.821928	ENSG00000168038	ENST00000301831;ENST00000420927	T;T	0.64438	-0.1;-0.1	5.4	-5.89	0.02282	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.303810	0.04720	N	0.419091	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.28618	-1.0038	9	0.11182	T	0.66	.	4.2228	0.10567	0.1888:0.48:0.0685:0.2627	rs1716975;rs52830123;rs58036033;rs1716975	224;224	B4E2M4;Q96C45	.;ULK4_HUMAN	V	224	ENSP00000301831:I224V;ENSP00000412187:I224V	ENSP00000301831:I224V	I	-	1	0	ULK4	41935010	0.190000	0.23276	0.000000	0.03702	0.603000	0.37013	0.078000	0.14761	-1.466000	0.01897	-1.201000	0.01664	ATT	T|0.321;C|0.679	0.679	strong		0.284	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
ESRP1	54845	hgsc.bcm.edu	37	8	95680229	95680229	+	Silent	SNP	C	C	T	rs1549466	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95680229C>T	ENST00000433389.2	+	10	1174	c.984C>T	c.(982-984)gtC>gtT	p.V328V	ESRP1_ENST00000454170.2_Silent_p.V328V|ESRP1_ENST00000423620.2_Silent_p.V328V|ESRP1_ENST00000358397.5_Silent_p.V328V	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	328	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						AAGTCATTGTCCGCATGCGGG	0.483													C|||	1765	0.352436	0.0514	0.3804	5008	,	,		19140	0.5387		0.3897	False		,,,				2504	0.5092				p.V328V		Atlas-SNP	.											ESRP1_ENST00000433389,NS,carcinoma,+2,2	ESRP1	148	2	0			c.C984T						PASS	.	C	,,,,	393,3341		21,351,1495	61.0	60.0	60.0		984,984,984,984,984	-0.6	1.0	8	dbSNP_88	60	3101,5085		579,1943,1571	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	600,2294,3066	TT,TC,CC		37.8817,10.5249,29.3121	,,,,	328/678,328/609,328/660,328/605,328/682	95680229	3494,8426	1867	4093	5960	SO:0001819	synonymous_variant	54845	exon10			CATTGTCCGCATG	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.984C>T	8.37:g.95680229C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	165	84	0.509091	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1	780	0.35714285714285715	28	0.056910569105691054	135	0.3729281767955801	307	0.5367132867132867	310	0.40897097625329815	C	9.611	1.131193	0.21041	0.105249	0.378817	ENSG00000104413	ENST00000519505	.	.	.	5.78	-0.637	0.11504	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47761	-0.9092	3	.	.	.	-9.6706	9.8714	0.41177	0.0:0.28:0.5332:0.1868	rs1549466;rs17717111;rs1549466	.	.	.	S	194	.	.	P	+	1	0	ESRP1	95749405	0.112000	0.22096	0.981000	0.43875	0.994000	0.84299	-0.523000	0.06230	-0.440000	0.07211	-0.302000	0.09304	CCG	C|0.648;T|0.352	0.352	strong		0.483	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
FANCD2	2177	hgsc.bcm.edu	37	3	10138069	10138069	+	Silent	SNP	T	T	G	rs2272125	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:10138069T>G	ENST00000419585.1	+	42	4259	c.4098T>G	c.(4096-4098)ctT>ctG	p.L1366L	FANCD2OS_ENST00000436517.1_5'Flank|FANCD2_ENST00000383806.1_3'UTR|FANCD2OS_ENST00000524279.1_Intron|FANCD2_ENST00000287647.3_Silent_p.L1366L|FANCD2_ENST00000383807.1_Silent_p.L1366L			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	1366					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CCCTGGAACTTTTAGTTTGCA	0.433			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	1213	0.242212	0.5174	0.196	5008	,	,		20261	0.0675		0.1412	False		,,,				2504	0.1871				p.L1366L		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	FANCD2	253	.	0			c.T4098G	GRCh37	CM066071	FANCD2	M	rs2272125	PASS	.	G	,,	2077,2329	604.9+/-390.4	491,1095,617	125.0	119.0	121.0		4098,4098,	3.9	0.9	3	dbSNP_100	121	1416,7184	752.7+/-407.4	119,1178,3003	no	coding-synonymous,coding-synonymous,intron	FANCD2,C3orf24	NM_001018115.1,NM_033084.3,NM_173472.1	,,	610,2273,3620	GG,GT,TT		16.4651,47.1403,26.8568	,,	1366/1452,1366/1472,	10138069	3493,9513	2203	4300	6503	SO:0001819	synonymous_variant	2177	exon42	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGAACTTTTAGTT	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.4098T>G	3.37:g.10138069T>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																			T|0.743;G|0.257	0.257	strong		0.433	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
GUF1	60558	hgsc.bcm.edu	37	4	44680660	44680660	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:44680660G>A	ENST00000281543.5	+	1	215	c.21G>A	c.(19-21)cgG>cgA	p.R7R	GUF1_ENST00000506793.1_Intron	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						TCGTGGGTCGGGGCTGGGGGT	0.721																																					p.R7R		Atlas-SNP	.											.	GUF1	72	.	0			c.G21A						PASS	.						5.0	6.0	5.0					4																	44680660		1813	3768	5581	SO:0001819	synonymous_variant	60558	exon1			GGGTCGGGGCTGG		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.21G>A	4.37:g.44680660G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_021927		Silent	SNP	ENST00000281543.5	37	CCDS3468.1																																																																																			.	.	none		0.721	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927	
ARSD	414	hgsc.bcm.edu	37	X	2833638	2833638	+	Missense_Mutation	SNP	C	C	T	rs370769167		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2833638C>T	ENST00000381154.1	-	6	1034	c.959G>A	c.(958-960)gGc>gAc	p.G320D	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	320					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCATATAAGCCATGCTGACT	0.507																																					p.G320D		Atlas-SNP	.											.	ARSD	47	.	0			c.G959A						PASS	.						231.0	156.0	181.0					X																	2833638		2203	4300	6503	SO:0001583	missense	414	exon6			TATAAGCCATGCT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.959G>A	X.37:g.2833638C>T	ENSP00000370546:p.Gly320Asp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	91	22	0.241758	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.767977	0.69878	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.93859	-3.3	3.68	3.68	0.42216	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.062472	0.64402	U	0.000005	D	0.96390	0.8822	M	0.81497	2.545	0.19775	P	0.9999576602	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.986	D	0.97757	1.0218	9	0.87932	D	0	.	14.8467	0.70264	0.0:1.0:0.0:0.0	.	320;320	E9PAW5;P51689	.;ARSD_HUMAN	D	320	ENSP00000370546:G320D	ENSP00000217890:G320D	G	-	2	0	ARSD	2843638	1.000000	0.71417	0.011000	0.14972	0.003000	0.03518	6.334000	0.72944	1.478000	0.48253	0.508000	0.49915	GGC	.	.	weak		0.507	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
PRICKLE1	144165	hgsc.bcm.edu	37	12	42854208	42854208	+	Silent	SNP	A	A	G	rs3747563|rs111643910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:42854208A>G	ENST00000455697.1	-	8	2184	c.1899T>C	c.(1897-1899)ttT>ttC	p.F633F	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000445766.2_Silent_p.F633F|PRICKLE1_ENST00000345127.3_Silent_p.F633F|PRICKLE1_ENST00000552240.1_Silent_p.F633F|PRICKLE1_ENST00000548696.1_Silent_p.F633F	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	633					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		CATCATCAGAAAACTTGACCT	0.488													A|||	1355	0.270567	0.1634	0.3847	5008	,	,		18152	0.256		0.3678	False		,,,				2504	0.2495				p.F633F		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.T1899C						PASS	.	A	,,,	887,3519		115,657,1431	99.0	94.0	96.0		1899,1899,1899,1899	-4.5	0.5	12	dbSNP_107	96	3013,5587		588,1837,1875	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRICKLE1	NM_001144881.1,NM_001144882.1,NM_001144883.1,NM_153026.2	,,,	703,2494,3306	GG,GA,AA		35.0349,20.1316,29.9862	,,,	633/832,633/832,633/832,633/832	42854208	3900,9106	2203	4300	6503	SO:0001819	synonymous_variant	144165	exon8			ATCAGAAAACTTG	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1899T>C	12.37:g.42854208A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	184	184	1	NM_001144882	Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	37	CCDS8742.1																																																																																			A|0.686;G|0.314	0.314	strong		0.488	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
OR8D1	283159	hgsc.bcm.edu	37	11	124179835	124179835	+	Silent	SNP	C	C	T	rs4936918	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124179835C>T	ENST00000357821.2	-	1	898	c.828G>A	c.(826-828)gtG>gtA	p.V276V		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	276						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		TGGTGTAGAACACAGAGGACA	0.453													T|||	1440	0.28754	0.1626	0.3429	5008	,	,		18422	0.4167		0.4066	False		,,,				2504	0.1616				p.V276V		Atlas-SNP	.											.	OR8D1	53	.	0			c.G828A						PASS	.	T		941,3461	736.0+/-410.7	101,739,1361	111.0	107.0	108.0		828	-3.0	0.2	11	dbSNP_111	108	3384,5214	640.3+/-399.6	673,2038,1588	no	coding-synonymous	OR8D1	NM_001002917.1		774,2777,2949	TT,TC,CC		39.358,21.3766,33.2692		276/309	124179835	4325,8675	2201	4299	6500	SO:0001819	synonymous_variant	283159	exon1			GTAGAACACAGAG	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"""GPCR / Class A : Olfactory receptors"""	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.828G>A	11.37:g.124179835C>T		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	196	100	0.510204	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Silent	SNP	ENST00000357821.2	37	CCDS31706.1																																																																																			C|0.669;T|0.331	0.331	strong		0.453	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917	
BTN3A2	11118	hgsc.bcm.edu	37	6	26373507	26373507	+	Missense_Mutation	SNP	G	G	A	rs13216828	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26373507G>A	ENST00000356386.2	+	7	1108	c.920G>A	c.(919-921)aGc>aAc	p.S307N	BTN3A2_ENST00000527422.1_Missense_Mutation_p.S307N|BTN3A2_ENST00000377708.2_Missense_Mutation_p.S307N|BTN3A2_ENST00000508906.2_Missense_Mutation_p.S265N|BTN3A2_ENST00000396948.1_Missense_Mutation_p.S307N|BTN3A2_ENST00000396934.3_Missense_Mutation_p.S284N	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	307			S -> N (in dbSNP:rs13216828). {ECO:0000269|PubMed:14702039}.		interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						TTTCCAGAGAGCCTCCAGGAG	0.403													G|||	406	0.0810703	0.0287	0.0389	5008	,	,		10942	0.0992		0.1103	False		,,,				2504	0.1329				p.S307N		Atlas-SNP	.											.	BTN3A2	44	.	0			c.G920A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	166,4240	110.4+/-148.6	2,162,2039	120.0	112.0	115.0		920,920,851,794,920	-4.6	0.0	6	dbSNP_121	115	929,7671	204.7+/-247.3	50,829,3421	yes	missense,missense,missense,missense,missense	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	46,46,46,46,46	52,991,5460	AA,AG,GG		10.8023,3.7676,8.4192	benign,benign,benign,benign,benign	307/335,307/335,284/312,265/293,307/335	26373507	1095,11911	2203	4300	6503	SO:0001583	missense	11118	exon5			CAGAGAGCCTCCA	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.920G>A	6.37:g.26373507G>A	ENSP00000348751:p.Ser307Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	157	0.07188644688644688	22	0.044715447154471545	13	0.03591160220994475	40	0.06993006993006994	82	0.10817941952506596	g	11.08	1.534478	0.27475	0.037676	0.108023	ENSG00000186470	ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T	0.03413	4.09;4.09;3.94;4.09;4.09;4.5	2.55	-4.61	0.03380	.	.	.	.	.	T	0.00695	0.0023	N	0.22421	0.69	0.80722	P	0.0	B;B	0.22211	0.066;0.039	B;B	0.24006	0.05;0.01	T	0.48559	-0.9025	8	0.56958	D	0.05	.	0.4235	0.00460	0.3467:0.1904:0.2757:0.1872	rs13216828;rs52811297;rs13216828	284;307	F8W6E0;P78410	.;BT3A2_HUMAN	N	307;307;307;284;307;307;265	ENSP00000432138:S307N;ENSP00000348751:S307N;ENSP00000380140:S284N;ENSP00000366937:S307N;ENSP00000380152:S307N;ENSP00000442687:S265N	ENSP00000348751:S307N	S	+	2	0	BTN3A2	26481486	0.025000	0.19082	0.008000	0.14137	0.627000	0.37826	0.231000	0.17872	-1.164000	0.02790	-0.474000	0.04947	AGC	G|0.922;A|0.078	0.078	strong		0.403	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
PCLO	27445	hgsc.bcm.edu	37	7	82764425	82764425	+	Missense_Mutation	SNP	C	C	G	rs2877	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82764425C>G	ENST00000333891.9	-	3	2778	c.2441G>C	c.(2440-2442)aGc>aCc	p.S814T	PCLO_ENST00000423517.2_Missense_Mutation_p.S814T	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATCAAATGGGCTGACTTTTTC	0.433													G|||	4048	0.808307	0.6936	0.781	5008	,	,		17834	0.9931		0.6839	False		,,,				2504	0.9202				p.S814T		Atlas-SNP	.											.	PCLO	1506	.	0			c.G2441C						PASS	.	G	THR/SER,THR/SER	2632,1080		944,744,168	186.0	172.0	176.0		2441,2441	3.9	0.7	7	dbSNP_36	176	5576,2616		1917,1742,437	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	58,58	2861,2486,605	GG,GC,CC		31.9336,29.0948,31.0484	benign,benign	814/5143,814/4936	82764425	8208,3696	1856	4096	5952	SO:0001583	missense	27445	exon3			AATGGGCTGACTT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2441G>C	7.37:g.82764425C>G	ENSP00000334319:p.Ser814Thr	Somatic	383	0	0		WXS	Illumina HiSeq	Phase_I	387	197	0.509044	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	1705	0.7806776556776557	331	0.6727642276422764	278	0.7679558011049724	570	0.9965034965034965	526	0.6939313984168866	G	0.079	-1.186532	0.01620	0.709052	0.680664	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16196	2.36;2.36	5.91	3.89	0.44902	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38090	-0.9677	8	0.87932	D	0	.	1.0805	0.01641	0.21:0.1786:0.4266:0.1848	rs2877;rs57270789;rs2877	814;814	Q9Y6V0-5;Q9Y6V0-6	.;.	T	760;814;814	ENSP00000334319:S814T;ENSP00000388393:S814T	ENSP00000334319:S814T	S	-	2	0	PCLO	82602361	0.935000	0.31712	0.723000	0.30687	0.010000	0.07245	1.287000	0.33284	0.863000	0.35553	-0.744000	0.03518	AGC	C|0.246;G|0.754	0.754	strong		0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
PADI4	23569	hgsc.bcm.edu	37	1	17668609	17668609	+	Missense_Mutation	SNP	C	C	T	rs1748020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17668609C>T	ENST00000375448.4	+	7	850	c.824C>T	c.(823-825)tCc>tTc	p.S275F	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	275			S -> F (in dbSNP:rs1748020). {ECO:0000269|PubMed:15087120}.		cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	CTGGACACGTCCAACCTGGTA	0.647													C|||	256	0.0511182	0.1135	0.0274	5008	,	,		16929	0.001		0.0577	False		,,,				2504	0.0286				p.S275F		Atlas-SNP	.											.	PADI4	70	.	0			c.C824T						PASS	.	C	PHE/SER	456,3950	217.1+/-235.6	26,404,1773	64.0	63.0	63.0		824	4.6	0.5	1	dbSNP_89	63	456,8144	134.9+/-192.2	16,424,3860	yes	missense	PADI4	NM_012387.2	155	42,828,5633	TT,TC,CC		5.3023,10.3495,7.0121	benign	275/664	17668609	912,12094	2203	4300	6503	SO:0001583	missense	23569	exon7			ACACGTCCAACCT	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.824C>T	1.37:g.17668609C>T	ENSP00000364597:p.Ser275Phe	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	124	78	0.629032	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	37	CCDS180.1	120	0.054945054945054944	63	0.12804878048780488	12	0.03314917127071823	0	0.0	45	0.059366754617414245	c	12.60	1.985170	0.35036	0.103495	0.053023	ENSG00000159339	ENST00000375448	T	0.14640	2.49	4.63	4.63	0.57726	Protein-arginine deiminase (PAD), central domain (1);	0.600161	0.18074	N	0.152512	T	0.00271	0.0008	M	0.73962	2.25	0.80722	P	0.0	P;P	0.48911	0.917;0.917	P;P	0.49226	0.603;0.603	T	0.04153	-1.0973	9	0.59425	D	0.04	-28.0689	13.4078	0.60924	0.0:1.0:0.0:0.0	rs1748020;rs52822621;rs61531826;rs1748020	275;275	A8K392;Q9UM07	.;PADI4_HUMAN	F	275	ENSP00000364597:S275F	ENSP00000364597:S275F	S	+	2	0	PADI4	17541196	0.000000	0.05858	0.496000	0.27539	0.137000	0.21094	0.358000	0.20216	2.290000	0.77057	0.555000	0.69702	TCC	C|0.939;T|0.061	0.061	strong		0.647	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
LRRC43	254050	hgsc.bcm.edu	37	12	122674758	122674758	+	Silent	SNP	G	G	A	rs4758651	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:122674758G>A	ENST00000339777.4	+	5	772	c.744G>A	c.(742-744)cgG>cgA	p.R248R	LRRC43_ENST00000425921.1_Silent_p.R63R	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	248										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		GGACCCTCCGGCACCTGCGAC	0.657													G|||	3251	0.649161	0.3404	0.6383	5008	,	,		19152	0.9008		0.7326	False		,,,				2504	0.729				p.R248R		Atlas-SNP	.											.	LRRC43	105	.	0			c.G744A						PASS	.	G	,	1780,2540		374,1032,754	89.0	101.0	97.0		744,189	-1.9	0.0	12	dbSNP_111	97	6169,2345		2247,1675,335	no	coding-synonymous,coding-synonymous	LRRC43	NM_001098519.1,NM_152759.4	,	2621,2707,1089	AA,AG,GG		27.5429,41.2037,38.063	,	248/657,63/472	122674758	7949,4885	2160	4257	6417	SO:0001819	synonymous_variant	254050	exon5			CCTCCGGCACCTG	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.744G>A	12.37:g.122674758G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_001098519	Q6ZVT9	Silent	SNP	ENST00000339777.4	37	CCDS45001.1																																																																																			G|0.305;N|0.003	.	strong		0.657	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
HIST1H2AA	221613	hgsc.bcm.edu	37	6	25726621	25726621	+	Silent	SNP	C	C	T	rs9467583	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:25726621C>T	ENST00000297012.3	-	1	169	c.135G>A	c.(133-135)ggG>ggA	p.G45G	HIST1H2BA_ENST00000274764.2_5'Flank	NM_170745.3	NP_734466.1	Q96QV6	H2A1A_HUMAN	histone cluster 1, H2aa	45						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)	13						GTGCGCCTGCCCCTATCCGCT	0.532													C|||	1124	0.224441	0.3222	0.196	5008	,	,		18740	0.1062		0.2505	False		,,,				2504	0.2076				p.G45G		Atlas-SNP	.											HIST1H2AA,NS,malignant_melanoma,0,3	HIST1H2AA	34	3	0			c.G135A						PASS	.	C		1346,3060	448.7+/-348.8	202,942,1059	302.0	226.0	252.0		135	-1.5	0.0	6	dbSNP_119	252	2250,6350	380.1+/-339.5	313,1624,2363	no	coding-synonymous	HIST1H2AA	NM_170745.3		515,2566,3422	TT,TC,CC		26.1628,30.5493,27.6488		45/132	25726621	3596,9410	2203	4300	6503	SO:0001819	synonymous_variant	221613	exon1			GCCTGCCCCTATC	AY131982	CCDS4562.1	6p22.2	2011-01-27	2006-10-11		ENSG00000164508	ENSG00000164508		"""Histones / Replication-dependent"""	18729	protein-coding gene	gene with protein product		613499	"""H2A histone family, member R"", ""histone 1, H2aa"""			12408966	Standard	NM_170745		Approved	bA317E16.2, H2AFR	uc003nfc.3	Q96QV6	OTTHUMG00000014407	ENST00000297012.3:c.135G>A	6.37:g.25726621C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_170745		Silent	SNP	ENST00000297012.3	37	CCDS4562.1																																																																																			C|0.749;T|0.251	0.251	strong		0.532	HIST1H2AA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040065.1	NM_170745	
PXDNL	137902	hgsc.bcm.edu	37	8	52325796	52325796	+	Silent	SNP	G	G	A	rs10504119	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:52325796G>A	ENST00000356297.4	-	15	1918	c.1818C>T	c.(1816-1818)ggC>ggT	p.G606G	PXDNL_ENST00000543296.1_Silent_p.G606G	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	606					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CAAAGTCATCGCCAGCTTGTC	0.343													G|||	355	0.0708866	0.0008	0.0187	5008	,	,		20133	0.2212		0.0358	False		,,,				2504	0.0838				p.G606G		Atlas-SNP	.											.	PXDNL	414	.	0			c.C1818T						PASS	.	G		35,3731		0,35,1848	113.0	110.0	111.0		1818	-8.7	0.0	8	dbSNP_119	111	260,7964		4,252,3856	no	coding-synonymous	PXDNL	NM_144651.4		4,287,5704	AA,AG,GG		3.1615,0.9294,2.4604		606/1464	52325796	295,11695	1883	4112	5995	SO:0001819	synonymous_variant	137902	exon15			GTCATCGCCAGCT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1818C>T	8.37:g.52325796G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	37	CCDS47855.1																																																																																			G|0.837;A|0.163	0.163	strong		0.343	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
TEP1	7011	hgsc.bcm.edu	37	14	20837701	20837701	+	Missense_Mutation	SNP	G	G	C	rs938886	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20837701G>C	ENST00000262715.5	-	53	7498	c.7458C>G	c.(7456-7458)atC>atG	p.I2486M	TEP1_ENST00000556935.1_Missense_Mutation_p.I2378M	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2486			I -> M (in dbSNP:rs938886).		RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GGTTCCATAGGATCCCATCAG	0.507													C|||	1699	0.339257	0.5129	0.3718	5008	,	,		18936	0.3065		0.2237	False		,,,				2504	0.2342				p.I2486M		Atlas-SNP	.											.	TEP1	224	.	0			c.C7458G						PASS	.	C	MET/ILE	1925,2481	624.5+/-394.3	436,1053,714	140.0	133.0	135.0		7458	2.8	0.9	14	dbSNP_86	135	1780,6820	733.8+/-406.9	176,1428,2696	yes	missense	TEP1	NM_007110.4	10	612,2481,3410	CC,CG,GG		20.6977,43.6904,28.4869	benign	2486/2628	20837701	3705,9301	2203	4300	6503	SO:0001583	missense	7011	exon53			CCATAGGATCCCA		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.7458C>G	14.37:g.20837701G>C	ENSP00000262715:p.Ile2486Met	Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	358	187	0.522346	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	710|710|710	0.3250915750915751|0.3250915750915751|0.3250915750915751	246|246|246	0.5|0.5|0.5	118|118|118	0.3259668508287293|0.3259668508287293|0.3259668508287293	169|169|169	0.29545454545454547|0.29545454545454547|0.29545454545454547	177|177|177	0.23350923482849603|0.23350923482849603|0.23350923482849603	C|C|C	1.075|1.075|1.075	-0.668871|-0.668871|-0.668871	0.03403|0.03403|0.03403	0.436904|0.436904|0.436904	0.206977|0.206977|0.206977	ENSG00000129566|ENSG00000129566|ENSG00000129566	ENST00000262715;ENST00000556935|ENST00000553984|ENST00000359243	T;T|.|.	0.36340|.|.	1.26;1.26|.|.	5.82|5.82|5.82	2.82|2.82|2.82	0.32997|0.32997|0.32997	.|.|.	0.474590|.|.	0.23096|.|.	N|.|.	0.051971|.|.	T|T|T	0.00012|0.00012|0.00012	0.0000|0.0000|0.0000	N|N|N	0.01048|0.01048|0.01048	-1.04|-1.04|-1.04	0.09310|0.09310|0.09310	P|P|P	0.99999074952|0.99999074952|0.99999074952	B;B;B|.|.	0.02656|.|.	0.0;0.0;0.0|.|.	B;B;B|.|.	0.06405|.|.	0.0;0.002;0.0|.|.	T|T|T	0.37478|0.37478|0.37478	-0.9704|-0.9704|-0.9704	9|4|5	0.18276|.|0.44086	T|.|T	0.48|.|0.13	-4.4158|-4.4158|-4.4158	9.0619|9.0619|9.0619	0.36440|0.36440|0.36440	0.2591:0.4878:0.2531:0.0|0.2591:0.4878:0.2531:0.0|0.2591:0.4878:0.2531:0.0	rs938886;rs1713445;rs2228025;rs17110682;rs52804129;rs58609794;rs938886|rs938886;rs1713445;rs2228025;rs17110682;rs52804129;rs58609794;rs938886|rs938886;rs1713445;rs2228025;rs17110682;rs52804129;rs58609794;rs938886	2378;1829;2486|.|.	G3V5X7;G3V2A4;Q99973|.|.	.;.;TEP1_HUMAN|.|.	M|A|C	2486;2378|143|2479	ENSP00000262715:I2486M;ENSP00000452574:I2378M|.|.	ENSP00000262715:I2486M|.|ENSP00000352180:S2479C	I|P|S	-|-|-	3|1|2	3|0|0	TEP1|TEP1|TEP1	19907541|19907541|19907541	0.561000|0.561000|0.561000	0.26578|0.26578|0.26578	0.937000|0.937000|0.937000	0.37676|0.37676|0.37676	0.953000|0.953000|0.953000	0.61014|0.61014|0.61014	0.569000|0.569000|0.569000	0.23638|0.23638|0.23638	0.788000|0.788000|0.788000	0.33755|0.33755|0.33755	-0.187000|-0.187000|-0.187000	0.12897|0.12897|0.12897	ATC|CCT|TCC	G|0.702;C|0.297	0.297	strong		0.507	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
CAPN13	92291	hgsc.bcm.edu	37	2	30975961	30975961	+	Missense_Mutation	SNP	G	G	T	rs62142192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:30975961G>T	ENST00000295055.8	-	10	1221	c.1045C>A	c.(1045-1047)Caa>Aaa	p.Q349K	CAPN13_ENST00000534090.2_Missense_Mutation_p.Q349K	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	349					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					AACATTATTTGGGACCATCCT	0.478													G|||	283	0.0565096	0.0091	0.0836	5008	,	,		22793	0.0		0.1779	False		,,,				2504	0.0348				p.Q349K		Atlas-SNP	.											.	CAPN13	70	.	0			c.C1045A						PASS	.	G	LYS/GLN	133,3773		1,131,1821	316.0	291.0	299.0		1045	3.4	0.2	2	dbSNP_129	299	1551,6727		146,1259,2734	yes	missense	CAPN13	NM_144575.2	53	147,1390,4555	TT,TG,GG		18.7364,3.405,13.8214	benign	349/670	30975961	1684,10500	1953	4139	6092	SO:0001583	missense	92291	exon10			TTATTTGGGACCA		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1045C>A	2.37:g.30975961G>T	ENSP00000295055:p.Gln349Lys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	163	79	0.484663	NM_144575	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	37	CCDS46252.1	193	0.08836996336996338	12	0.024390243902439025	38	0.10497237569060773	0	0.0	143	0.18865435356200527	G	0.369	-0.935101	0.02340	0.03405	0.187364	ENSG00000162949	ENST00000295055;ENST00000534090	D;D	0.87029	-2.2;-2.2	5.27	3.44	0.39384	Peptidase C2, calpain, large subunit, domain III (2);	5.742170	0.00166	N	0.000002	T	0.00580	0.0019	L	0.54323	1.7	0.80722	P	0.0	B	0.31256	0.316	B	0.27608	0.081	T	0.35301	-0.9794	9	0.56958	D	0.05	.	7.1577	0.25647	0.0944:0.2003:0.7053:0.0	rs62142192	349	Q6MZZ7	CAN13_HUMAN	K	349	ENSP00000295055:Q349K;ENSP00000431298:Q349K	ENSP00000295055:Q349K	Q	-	1	0	CAPN13	30829465	0.406000	0.25344	0.237000	0.24090	0.016000	0.09150	1.400000	0.34577	0.573000	0.29400	-0.258000	0.10820	CAA	G|0.896;T|0.104	0.104	strong		0.478	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575	
MST1L	11223	hgsc.bcm.edu	37	1	17085447	17085447	+	RNA	SNP	G	G	A	rs202225848		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17085447G>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GGCGGGAGCGGGAGCAAAATC	0.617																																					p.P415L		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,+1,3	.	.	3	0			c.C1244T						PASS	.																																					11223	exon10			GGAGCGGGAGCAA	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17085447G>A		Somatic	443	0	0		WXS	Illumina HiSeq	Phase_I	391	77	0.196931	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	6.869	0.529727	0.13127	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.761459	0.11178	N	0.591248	T	0.23766	0.0575	.	.	.	.	.	.	B	0.16166	0.016	B	0.16289	0.015	T	0.29852	-0.9998	5	.	.	.	.	5.8178	0.18506	0.001:0.0:0.999:0.0	.	415	Q2TV78-2	.	L	415	.	.	P	-	2	0	MST1P9	16958034	0.995000	0.38212	0.000000	0.03702	0.000000	0.00434	1.307000	0.33516	-0.000000	0.14550	0.000000	0.15137	CCC	G|0.996;A|0.004	0.004	weak		0.617	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
TTC39A	22996	hgsc.bcm.edu	37	1	51767352	51767352	+	Silent	SNP	G	G	A	rs41287290	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:51767352G>A	ENST00000447632.2	-	12	1101	c.1053C>T	c.(1051-1053)ttC>ttT	p.F351F	TTC39A_ENST00000371747.3_Silent_p.F350F|TTC39A_ENST00000262675.7_Silent_p.F288F|TTC39A_ENST00000262676.5_3'UTR|TTC39A_ENST00000413473.2_Silent_p.F319F|TTC39A_ENST00000371750.5_Silent_p.F316F|TTC39A_ENST00000451380.1_Silent_p.F315F			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	351								p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						ACATGTGGTGGAACTGCTTCC	0.602													G|||	267	0.0533147	0.0106	0.0836	5008	,	,		20364	0.0		0.1441	False		,,,				2504	0.0511				p.F319F		Atlas-SNP	.											TTC39A,colon,carcinoma,0,2	TTC39A	40	2	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.C957T						PASS	.	G	,	99,4159		1,97,2031	67.0	70.0	69.0		948,957	0.7	1.0	1	dbSNP_127	69	1047,7399		70,907,3246	no	coding-synonymous,coding-synonymous	TTC39A	NM_001080494.2,NM_001144832.1	,	71,1004,5277	AA,AG,GG		12.3964,2.325,9.0208	,	316/579,319/582	51767352	1146,11558	2129	4223	6352	SO:0001819	synonymous_variant	22996	exon12			GTGGTGGAACTGC	AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"""Tetratricopeptide (TTC) repeat domain containing"""	18657	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 34"""	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.1053C>T	1.37:g.51767352G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Silent	SNP	ENST00000447632.2	37																																																																																				A|0.083;C|0.000;G|0.917	0.083	strong		0.602	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2		
XRN1	54464	hgsc.bcm.edu	37	3	142078759	142078759	+	Missense_Mutation	SNP	C	C	T	rs73238159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:142078759C>T	ENST00000264951.4	-	30	3526	c.3409G>A	c.(3409-3411)Gat>Aat	p.D1137N	XRN1_ENST00000392981.2_Missense_Mutation_p.D1137N	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1137					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						AATAGTACATCGGCTTCTCTA	0.318													C|||	417	0.0832668	0.0303	0.0821	5008	,	,		16090	0.0952		0.1451	False		,,,				2504	0.0798				p.D1137N		Atlas-SNP	.											.	XRN1	138	.	0			c.G3409A						PASS	.	C	ASN/ASP,ASN/ASP	206,4200	126.6+/-163.6	4,198,2001	69.0	71.0	70.0		3409,3409	5.5	1.0	3	dbSNP_130	70	1151,7447	233.7+/-266.9	75,1001,3223	yes	missense,missense	XRN1	NM_001042604.1,NM_019001.3	23,23	79,1199,5224	TT,TC,CC		13.3868,4.6754,10.4353	benign,benign	1137/1694,1137/1707	142078759	1357,11647	2203	4299	6502	SO:0001583	missense	54464	exon30			GTACATCGGCTTC	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.3409G>A	3.37:g.142078759C>T	ENSP00000264951:p.Asp1137Asn	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	219	0.10027472527472528	14	0.028455284552845527	30	0.08287292817679558	64	0.11188811188811189	111	0.14643799472295516	C	28.2	4.902564	0.92035	0.046754	0.133868	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.33216	1.42;1.42	5.51	5.51	0.81932	.	0.056674	0.64402	D	0.000001	T	0.00271	0.0008	L	0.61036	1.89	0.09310	P	1.0	P;P	0.52170	0.951;0.919	P;B	0.46940	0.532;0.332	T	0.00185	-1.1943	9	0.42905	T	0.14	-17.9298	19.427	0.94746	0.0:1.0:0.0:0.0	.	1137;1137	Q8IZH2-2;Q8IZH2	.;XRN1_HUMAN	N	1137	ENSP00000264951:D1137N;ENSP00000376707:D1137N	ENSP00000264951:D1137N	D	-	1	0	XRN1	143561449	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.656000	0.74396	2.573000	0.86826	0.655000	0.94253	GAT	C|0.901;T|0.099	0.099	strong		0.318	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
TMCC2	9911	hgsc.bcm.edu	37	1	205238530	205238530	+	Silent	SNP	C	C	T	rs1779411	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205238530C>T	ENST00000358024.3	+	3	1589	c.1200C>T	c.(1198-1200)ggC>ggT	p.G400G	TMCC2_ENST00000330675.7_Silent_p.G175G|TMCC2_ENST00000545499.1_Silent_p.G322G|TMCC2_ENST00000329800.7_Silent_p.G160G|TMCC2_ENST00000495538.1_3'UTR	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	400						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GCTTTGGGGGCGGCGTGGTGG	0.706													C|||	630	0.125799	0.0287	0.1816	5008	,	,		14780	0.0377		0.3549	False		,,,				2504	0.0726				p.G400G		Atlas-SNP	.											.	TMCC2	89	.	0			c.C1200T						PASS	.	C	,	329,4069		20,289,1890	27.0	30.0	29.0		966,1200	-4.8	0.9	1	dbSNP_89	29	3031,5563		539,1953,1805	no	coding-synonymous,coding-synonymous	TMCC2	NM_001242925.1,NM_014858.3	,	559,2242,3695	TT,TC,CC		35.2688,7.4807,25.8621	,	322/632,400/710	205238530	3360,9632	2199	4297	6496	SO:0001819	synonymous_variant	9911	exon3			TGGGGGCGGCGTG	AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"""Transmembrane and coiled-coil domain containing"""	24239	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 2"""			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.1200C>T	1.37:g.205238530C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Silent	SNP	ENST00000358024.3	37	CCDS30984.1																																																																																			C|0.784;T|0.216	0.216	strong		0.706	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858	
IQCJ-SCHIP1	100505385	hgsc.bcm.edu	37	3	159605510	159605510	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:159605510C>T	ENST00000460298.1	+	5	1131	c.890C>T	c.(889-891)tCt>tTt	p.S297F	IQCJ-SCHIP1_ENST00000476809.1_Missense_Mutation_p.S386F|IQCJ-SCHIP1_ENST00000485419.1_Missense_Mutation_p.S413F|SCHIP1_ENST00000482804.1_Missense_Mutation_p.S110F|IQCJ-SCHIP1_ENST00000527095.1_Missense_Mutation_p.S105F|IQCJ-SCHIP1_ENST00000337808.6_Missense_Mutation_p.S337F|SCHIP1_ENST00000445224.2_Missense_Mutation_p.S94F|IQCJ-SCHIP1_ENST00000412423.2_Missense_Mutation_p.S324F					IQCJ-SCHIP1 readthrough											central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(7)	12						AAACAGAGTTCTTCCTATTCT	0.458																																					p.S413F		Atlas-SNP	.											SCHIP1,NS,carcinoma,0,2	IQCJ-SCHIP1	40	2	0			c.C1238T						scavenged	.						178.0	188.0	185.0					3																	159605510		2203	4300	6503	SO:0001583	missense	100505385	exon8			AGAGTTCTTCCTA		CCDS56289.1, CCDS56291.1	3q25.33	2011-03-24			ENSG00000250588	ENSG00000250588			38842	other	readthrough							Standard	NM_001197113		Approved		uc003fcq.2		OTTHUMG00000162426	ENST00000460298.1:c.890C>T	3.37:g.159605510C>T	ENSP00000417305:p.Ser297Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	130	3	0.0230769	NM_001197113		Missense_Mutation	SNP	ENST00000460298.1	37		.	.	.	.	.	.	.	.	.	.	C	24.6	4.553010	0.86127	.	.	ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000151967;ENSG00000151967	ENST00000476809;ENST00000485419;ENST00000337808;ENST00000412423;ENST00000527095;ENST00000460298;ENST00000445224;ENST00000482804	T;T;T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47;0.47;0.47	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.66567	0.2802	L	0.40543	1.245	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;0.996;0.994;0.999;0.999;0.999	D;D;D;D;D;D	0.91635	0.999;0.993;0.983;0.997;0.998;0.997	T	0.68127	-0.5491	10	0.59425	D	0.04	.	18.9961	0.92813	0.0:1.0:0.0:0.0	.	297;110;94;324;337;413	C9J366;C9JWG6;Q9P0W5-4;Q9P0W5-2;Q9P0W5;Q9P0W5-5	.;.;.;.;SCHI1_HUMAN;.	F	386;413;337;324;105;297;94;110	ENSP00000418692:S386F;ENSP00000420182:S413F;ENSP00000337239:S337F;ENSP00000400942:S324F;ENSP00000436076:S105F;ENSP00000417305:S297F;ENSP00000404860:S94F;ENSP00000419230:S110F	ENSP00000337239:S337F	S	+	2	0	SCHIP1;IQCJ-SCHIP1	161088204	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.338000	0.79269	2.544000	0.85801	0.650000	0.86243	TCT	.	.	none		0.458	IQCJ-SCHIP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000352558.2	NM_001197113	
ANKRD34C	390616	hgsc.bcm.edu	37	15	79586361	79586361	+	Silent	SNP	T	T	C	rs8038778	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79586361T>C	ENST00000558647.2	+	1	735	c.735T>C	c.(733-735)ccT>ccC	p.P245P	ANKRD34C_ENST00000421388.2_Silent_p.P245P			P0C6C1	AN34C_HUMAN	ankyrin repeat domain 34C	245										endometrium(3)|kidney(1)|skin(1)	5						CCCGTTTGCCTCAACTGAAGA	0.572													C|||	3424	0.683706	0.677	0.7233	5008	,	,		18774	0.7649		0.6531	False		,,,				2504	0.6125				p.P245P		Atlas-SNP	.											.	ANKRD34C	29	.	0			c.T735C						PASS	.						15.0	15.0	15.0					15																	79586361		685	1584	2269	SO:0001819	synonymous_variant	390616	exon2			TTTGCCTCAACTG		CCDS53965.1	15q25.1	2013-01-10			ENSG00000235711	ENSG00000235711		"""Ankyrin repeat domain containing"""	33888	protein-coding gene	gene with protein product							Standard	NM_001146341		Approved		uc002bet.3	P0C6C1		ENST00000558647.2:c.735T>C	15.37:g.79586361T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001146341	H3BNM1	Silent	SNP	ENST00000558647.2	37	CCDS53965.1																																																																																			T|0.315;C|0.685	0.685	strong		0.572	ANKRD34C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416713.2	NM_001146341	
LAMA5	3911	hgsc.bcm.edu	37	20	60907446	60907446	+	Silent	SNP	T	T	C	rs2151513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60907446T>C	ENST00000252999.3	-	28	3600	c.3534A>G	c.(3532-3534)gaA>gaG	p.E1178E	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1178	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGCGTGCCTGTTCGGCTGTGA	0.622													C|||	3664	0.731629	0.3427	0.804	5008	,	,		17224	0.9375		0.9225	False		,,,				2504	0.7975				p.E1178E		Atlas-SNP	.											LAMA5,caecum,carcinoma,0,1	LAMA5	268	1	0			c.A3534G						PASS	.	C		1989,2417	593.7+/-388.1	460,1069,674	53.0	56.0	55.0		3534	-0.1	0.4	20	dbSNP_96	55	8012,588	152.5+/-207.1	3732,548,20	no	coding-synonymous	LAMA5	NM_005560.3		4192,1617,694	CC,CT,TT		6.8372,45.143,23.1047		1178/3696	60907446	10001,3005	2203	4300	6503	SO:0001819	synonymous_variant	3911	exon28			TGCCTGTTCGGCT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.3534A>G	20.37:g.60907446T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			T|0.223;G|0.000;C|0.777;A|0.000	0.777	strong		0.622	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
DNAH14	127602	hgsc.bcm.edu	37	1	225452983	225452983	+	Missense_Mutation	SNP	A	A	G	rs76767146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:225452983A>G	ENST00000445597.2	+	32	5684	c.5684A>G	c.(5683-5685)aAt>aGt	p.N1895S	DNAH14_ENST00000439375.2_Missense_Mutation_p.N2435S|DNAH14_ENST00000430092.1_Missense_Mutation_p.N2435S			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1895					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TTTAGCACCAATGTAACAGCT	0.328													A|||	163	0.0325479	0.0038	0.0375	5008	,	,		15142	0.0129		0.0686	False		,,,				2504	0.0511				p.N2435S		Atlas-SNP	.											.	DNAH14	300	.	0			c.A7304G						PASS	.	A	SER/ASN	18,1366		0,18,674	96.0	80.0	85.0		7304	-4.4	0.0	1	dbSNP_131	85	199,2981		4,191,1395	yes	missense	DNAH14	NM_001373.1	46	4,209,2069	GG,GA,AA		6.2579,1.3006,4.7546	benign	2435/4516	225452983	217,4347	692	1590	2282	SO:0001583	missense	127602	exon48			GCACCAATGTAAC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.5684A>G	1.37:g.225452983A>G	ENSP00000409472:p.Asn1895Ser	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	166	78	0.46988	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		84|84	0.038461538461538464|0.038461538461538464	3|3	0.006097560975609756|0.006097560975609756	16|16	0.04419889502762431|0.04419889502762431	9|9	0.015734265734265736|0.015734265734265736	56|56	0.07387862796833773|0.07387862796833773	A|A	8.743|8.743	0.919471|0.919471	0.17982|0.17982	0.013006|0.013006	0.062579|0.062579	ENSG00000185842|ENSG00000185842	ENST00000450490|ENST00000445597;ENST00000430092;ENST00000439375	.|T;T;T	.|0.34859	.|2.57;1.34;1.34	5.42|5.42	-4.42|-4.42	0.03579|0.03579	.|.	.|.	.|.	.|.	.|.	T|T	0.01189|0.01189	0.0039|0.0039	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.13145	.|0.007	.|B	.|0.08055	.|0.003	T|T	0.27502|0.27502	-1.0072|-1.0072	5|9	.|0.07990	.|T	.|0.79	.|.	7.3639|7.3639	0.26762|0.26762	0.4497:0.1284:0.4218:0.0|0.4497:0.1284:0.4218:0.0	.|.	.|2435	.|Q0VDD8-4	.|.	V|S	207|1895;2435;2435	.|ENSP00000409472:N1895S;ENSP00000414402:N2435S;ENSP00000392061:N2435S	.|ENSP00000414402:N2435S	M|N	+|+	1|2	0|0	DNAH14|DNAH14	223519606|223519606	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.773000|0.773000	0.43773|0.43773	-0.001000|-0.001000	0.12947|0.12947	-1.190000|-1.190000	0.02698|0.02698	-0.419000|-0.419000	0.06015|0.06015	ATG|AAT	A|0.953;G|0.047	0.047	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
SCARA5	286133	hgsc.bcm.edu	37	8	27729532	27729532	+	Silent	SNP	G	G	A	rs61737291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27729532G>A	ENST00000354914.3	-	9	1892	c.1407C>T	c.(1405-1407)atC>atT	p.I469I	SCARA5_ENST00000380385.2_Silent_p.I244I	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	469	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		TGCAGCGGAAGATGGTTTCCT	0.552													G|||	762	0.152157	0.1074	0.0908	5008	,	,		22281	0.245		0.1243	False		,,,				2504	0.1892				p.I469I		Atlas-SNP	.											.	SCARA5	53	.	0			c.C1407T						PASS	.	G		498,3908	230.4+/-244.6	25,448,1730	149.0	102.0	118.0		1407	4.3	1.0	8	dbSNP_129	118	1053,7547	222.3+/-259.4	71,911,3318	no	coding-synonymous	SCARA5	NM_173833.5		96,1359,5048	AA,AG,GG		12.2442,11.3028,11.9253		469/496	27729532	1551,11455	2203	4300	6503	SO:0001819	synonymous_variant	286133	exon9			GCGGAAGATGGTT	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"""scavenger receptor class A, member 5 (putative)"""			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.1407C>T	8.37:g.27729532G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	163	68	0.417178	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Silent	SNP	ENST00000354914.3	37	CCDS6064.1																																																																																			G|0.870;A|0.130	0.130	strong		0.552	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136319600	136319600	+	Silent	SNP	G	G	A	rs34934621	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136319600G>A	ENST00000371929.3	+	24	3552	c.3108G>A	c.(3106-3108)tcG>tcA	p.S1036S	ADAMTS13_ENST00000356589.2_Silent_p.S1005S|ADAMTS13_ENST00000371910.1_5'Flank|ADAMTS13_ENST00000355699.2_Silent_p.S1036S|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000371916.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	1036	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CTAGACGCTCGGTGGCCTGTG	0.647													G|||	88	0.0175719	0.0045	0.0331	5008	,	,		16824	0.001		0.0437	False		,,,				2504	0.0143				p.S1036S		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.G3108A						PASS	.	G	,,	48,4358	48.9+/-83.8	1,46,2156	89.0	74.0	79.0		3108,3015,3108	-10.8	0.0	9	dbSNP_126	79	427,8173	132.2+/-189.8	13,401,3886	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	14,447,6042	AA,AG,GG		4.9651,1.0894,3.6522	,,	1036/1428,1005/1341,1036/1372	136319600	475,12531	2203	4300	6503	SO:0001819	synonymous_variant	11093	exon24			ACGCTCGGTGGCC	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.3108G>A	9.37:g.136319600G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	47	0.566265	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			G|0.963;A|0.037	0.037	strong		0.647	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
NEU4	129807	hgsc.bcm.edu	37	2	242758179	242758179	+	Silent	SNP	C	C	T	rs2293764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242758179C>T	ENST00000391969.2	+	5	1971	c.1260C>T	c.(1258-1260)tcC>tcT	p.S420S	NEU4_ENST00000325935.6_Silent_p.S433S|NEU4_ENST00000405370.1_Silent_p.S420S|NEU4_ENST00000407683.1_Silent_p.S420S|NEU4_ENST00000404257.1_Silent_p.S432S	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	420					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		GCGGCTACTCCGACCTGGCGT	0.652													C|||	1081	0.215855	0.3306	0.1715	5008	,	,		12562	0.1994		0.161	False		,,,				2504	0.1656				p.S433S		Atlas-SNP	.											.	NEU4	39	.	0			c.C1299T						PASS	.		,,,,	1025,3263		106,813,1225	10.0	13.0	12.0		1299,1260,1260,1260,1296	-8.5	0.7	2	dbSNP_100	12	987,7445		66,855,3295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	172,1668,4520	TT,TC,CC		11.7054,23.9039,15.8176	,,,,	433/498,420/485,420/485,420/485,432/497	242758179	2012,10708	2144	4216	6360	SO:0001819	synonymous_variant	129807	exon4			CTACTCCGACCTG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.1260C>T	2.37:g.242758179C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1																																																																																			C|0.819;T|0.181	0.181	strong		0.652	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971081	45971081	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45971081C>T	ENST00000391621.1	-	1	307	c.261G>A	c.(259-261)ccG>ccA	p.P87P	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	87	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						TGCAGCAAGCCGGCTGGCAGC	0.687																																					p.P87P		Atlas-SNP	.											KRTAP10-2,trunk,malignant_melanoma,-1,1	KRTAP10-2	21	1	0			c.G261A						scavenged	.						57.0	61.0	60.0					21																	45971081		2202	4292	6494	SO:0001819	synonymous_variant	386679	exon1			GCAAGCCGGCTGG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.261G>A	21.37:g.45971081C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	162	19	0.117284	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			.	.	weak		0.687	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
SSC5D	284297	hgsc.bcm.edu	37	19	56011460	56011460	+	Silent	SNP	C	C	T	rs4801713	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56011460C>T	ENST00000389623.6	+	10	2006	c.1983C>T	c.(1981-1983)acC>acT	p.T661T	SSC5D_ENST00000587166.1_Silent_p.T661T	NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	661	Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						CAGACCTAACCTCACAGACCA	0.572													C|||	1933	0.385982	0.1929	0.3847	5008	,	,		16876	0.2302		0.5606	False		,,,				2504	0.6288				p.T661T		Atlas-SNP	.											.	SSC5D	65	.	0			c.C1983T						PASS	.	C	,	330,1054		27,276,389	132.0	144.0	140.0		1983,1983	3.2	0.1	19	dbSNP_111	140	1832,1350		526,780,285	no	coding-synonymous,coding-synonymous	SSC5D	NM_001144950.1,NM_001195267.1	,	553,1056,674	TT,TC,CC		42.4261,23.8439,47.35	,	661/1574,661/952	56011460	2162,2404	692	1591	2283	SO:0001819	synonymous_variant	284297	exon10			CCTAACCTCACAG		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.1983C>T	19.37:g.56011460C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_001195267	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Silent	SNP	ENST00000389623.6	37	CCDS46196.1																																																																																			A|0.000;C|0.582;G|0.000;T|0.417	0.417	strong		0.572	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
SLC25A24	29957	hgsc.bcm.edu	37	1	108728484	108728484	+	Silent	SNP	T	T	C	rs862493	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:108728484T>C	ENST00000565488.1	-	2	495	c.276A>G	c.(274-276)aaA>aaG	p.K92K	SLC25A24_ENST00000370041.4_Silent_p.K73K	NM_013386.4	NP_037518.3	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24	92	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				ATP transport (GO:0015867)|cellular response to calcium ion (GO:0071277)|cellular response to oxidative stress (GO:0034599)|mitochondrial transport (GO:0006839)|regulation of cell death (GO:0010941)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP transmembrane transporter activity (GO:0005347)|calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)		TAAATGCCAATTTCATTTTCT	0.303													T|||	825	0.164736	0.1815	0.1657	5008	,	,		14544	0.0794		0.2157	False		,,,				2504	0.1769				p.K92K		Atlas-SNP	.											.	SLC25A24	65	.	0			c.A276G						PASS	.	T	,	815,3581	315.2+/-294.0	86,643,1469	96.0	91.0	93.0		276,219	0.8	0.9	1	dbSNP_86	93	1794,6794	310.8+/-310.0	193,1408,2693	no	coding-synonymous,coding-synonymous	SLC25A24	NM_013386.3,NM_213651.1	,	279,2051,4162	CC,CT,TT		20.8896,18.5396,20.094	,	92/478,73/459	108728484	2609,10375	2198	4294	6492	SO:0001819	synonymous_variant	29957	exon2			TGCCAATTTCATT	AJ619961	CCDS786.1, CCDS41361.1	1p13.2	2013-05-22			ENSG00000085491	ENSG00000085491		"""Solute carriers"", ""EF-hand domain containing"""	20662	protein-coding gene	gene with protein product		608744				15123600	Standard	NM_013386		Approved	DKFZp586G0123, APC1	uc001dvn.5	Q6NUK1	OTTHUMG00000011013	ENST00000565488.1:c.276A>G	1.37:g.108728484T>C		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_013386	B7ZAI9|Q5T331|Q5T485|Q6PJJ9|Q705K4|Q9P129	Silent	SNP	ENST00000565488.1	37	CCDS41361.1																																																																																			C|0.183;N|0.000	0.183	strong		0.303	SLC25A24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030280.2	NM_013386	
SIPA1L1	26037	hgsc.bcm.edu	37	14	72090809	72090809	+	Silent	SNP	G	G	A	rs113082664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:72090809G>A	ENST00000555818.1	+	4	2022	c.1674G>A	c.(1672-1674)tcG>tcA	p.S558S	SIPA1L1_ENST00000358550.2_Silent_p.S558S|SIPA1L1_ENST00000537413.1_Silent_p.S33S|SIPA1L1_ENST00000381232.3_Silent_p.S558S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	558					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CCATTCCGTCGACAGCCAAGC	0.577													G|||	26	0.00519169	0.0151	0.0029	5008	,	,		19331	0.0		0.004	False		,,,				2504	0.0				p.S558S		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G1674A						PASS	.	G		78,4328	69.2+/-107.0	1,76,2126	170.0	154.0	159.0		1674	-4.7	0.9	14	dbSNP_132	159	14,8586	11.2+/-40.8	0,14,4286	no	coding-synonymous	SIPA1L1	NM_015556.1		1,90,6412	AA,AG,GG		0.1628,1.7703,0.7074		558/1805	72090809	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	26037	exon4			TCCGTCGACAGCC	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1674G>A	14.37:g.72090809G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																			G|0.994;A|0.006	0.006	strong		0.577	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
FBXL13	222235	hgsc.bcm.edu	37	7	102462636	102462636	+	Silent	SNP	T	T	C	rs10279449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:102462636T>C	ENST00000313221.4	-	19	2295	c.1869A>G	c.(1867-1869)gcA>gcG	p.A623A	FBXL13_ENST00000393772.2_Silent_p.A595A|FBXL13_ENST00000379308.3_Silent_p.A578A|FBXL13_ENST00000436908.1_Silent_p.A623A|FBXL13_ENST00000379306.3_Silent_p.A341A|FBXL13_ENST00000379305.3_Silent_p.A595A|FBXL13_ENST00000455112.2_Silent_p.A578A|FBXL13_ENST00000456695.1_Silent_p.A341A	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	623										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						ACATCTCCATTGCTGAGTCAG	0.418													C|||	2621	0.523363	0.7451	0.3602	5008	,	,		21922	0.5744		0.3181	False		,,,				2504	0.498				p.A623A		Atlas-SNP	.											.	FBXL13	65	.	0			c.A1869G						PASS	.	C	,	3005,1401	461.1+/-352.8	1018,969,216	142.0	126.0	132.0		1734,1869	-7.6	0.0	7	dbSNP_119	132	3058,5542	661.9+/-401.9	542,1974,1784	no	coding-synonymous,coding-synonymous	FBXL13	NM_001111038.1,NM_145032.3	,	1560,2943,2000	CC,CT,TT		35.5581,31.7975,46.6169	,	578/691,623/736	102462636	6063,6943	2203	4300	6503	SO:0001819	synonymous_variant	222235	exon19			CTCCATTGCTGAG	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"""F-boxes / Leucine-rich repeats"""	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.1869A>G	7.37:g.102462636T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_145032	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Silent	SNP	ENST00000313221.4	37	CCDS5726.1																																																																																			T|0.517;C|0.483	0.483	strong		0.418	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032	
SLIT2	9353	hgsc.bcm.edu	37	4	20533613	20533613	+	Silent	SNP	C	C	G	rs150677598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:20533613C>G	ENST00000504154.1	+	17	1872	c.1620C>G	c.(1618-1620)ctC>ctG	p.L540L	SLIT2_ENST00000503837.1_Silent_p.L536L|SLIT2_ENST00000503823.1_Silent_p.L532L|SLIT2_ENST00000273739.5_Silent_p.L544L	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	540					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						TCAGGCGTCTCAATAATAATG	0.279													C|||	8	0.00159744	0.0015	0.0029	5008	,	,		15813	0.0		0.002	False		,,,				2504	0.002				p.L540L		Atlas-SNP	.											SLIT2,NS,carcinoma,+2,1	SLIT2	290	1	0			c.C1620G						PASS	.	C		3,4403	4.2+/-10.8	0,3,2200	45.0	44.0	45.0		1620	3.0	1.0	4	dbSNP_134	45	30,8560	21.0+/-64.5	0,30,4265	no	coding-synonymous	SLIT2	NM_004787.1		0,33,6465	GG,GC,CC		0.3492,0.0681,0.2539		540/1530	20533613	33,12963	2203	4295	6498	SO:0001819	synonymous_variant	9353	exon17			GCGTCTCAATAAT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1620C>G	4.37:g.20533613C>G		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	265	128	0.483019	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			C|0.998;G|0.002	0.002	strong		0.279	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
ZNF280A	129025	hgsc.bcm.edu	37	22	22869218	22869218	+	Missense_Mutation	SNP	T	T	C	rs362132	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22869218T>C	ENST00000302097.3	-	2	989	c.737A>G	c.(736-738)aAt>aGt	p.N246S	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	246			N -> S (in dbSNP:rs362132). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9074928}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		GCCAGACTCATTTGCTCTCTC	0.408													T|||	2371	0.473442	0.2383	0.732	5008	,	,		18900	0.4147		0.7038	False		,,,				2504	0.4315				p.N246S		Atlas-SNP	.											.	ZNF280A	67	.	0			c.A737G						PASS	.	T	SER/ASN	1358,3048	445.5+/-347.7	220,918,1065	128.0	117.0	121.0		737	0.0	0.0	22	dbSNP_79	121	5856,2744	678.6+/-403.5	2009,1838,453	yes	missense	ZNF280A	NM_080740.3	46	2229,2756,1518	CC,CT,TT		31.907,30.8216,44.5333	benign	246/543	22869218	7214,5792	2203	4300	6503	SO:0001583	missense	129025	exon2			GACTCATTTGCTC	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.737A>G	22.37:g.22869218T>C	ENSP00000302855:p.Asn246Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	1156	0.5293040293040293	127	0.258130081300813	254	0.7016574585635359	244	0.42657342657342656	531	0.7005277044854882	T	8.469	0.857162	0.17106	0.308216	0.68093	ENSG00000169548	ENST00000302097	T	0.01209	5.17	3.56	0.0271	0.14153	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.32245	0.361	B	0.23419	0.046	T	0.03423	-1.1038	8	0.11182	T	0.66	-0.1742	2.4867	0.04601	0.2032:0.2418:0.0:0.555	rs362132;rs695356;rs17857438;rs61161512	246	P59817	Z280A_HUMAN	S	246	ENSP00000302855:N246S	ENSP00000302855:N246S	N	-	2	0	ZNF280A	21199218	0.264000	0.24093	0.000000	0.03702	0.042000	0.13812	1.136000	0.31467	-0.070000	0.12908	0.533000	0.62120	AAT	T|0.469;C|0.531	0.531	strong		0.408	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
LRWD1	222229	hgsc.bcm.edu	37	7	102106306	102106306	+	Silent	SNP	A	A	G	rs11538919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:102106306A>G	ENST00000292616.5	+	2	275	c.123A>G	c.(121-123)aaA>aaG	p.K41K	MIR5090_ENST00000582533.1_RNA|ALKBH4_ENST00000292566.3_5'Flank	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	41					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						TGGACCCCAAACTCCTGTGCC	0.627													G|||	204	0.0407348	0.0605	0.0461	5008	,	,		16442	0.0		0.0706	False		,,,				2504	0.0215				p.K41K		Atlas-SNP	.											.	LRWD1	41	.	0			c.A123G						PASS	.	G		230,4176	787.4+/-414.9	5,220,1978	40.0	41.0	41.0		123	0.4	1.0	7	dbSNP_120	41	581,8019	776.4+/-407.7	22,537,3741	no	coding-synonymous	LRWD1	NM_152892.1		27,757,5719	GG,GA,AA		6.7558,5.2202,6.2356		41/648	102106306	811,12195	2203	4300	6503	SO:0001819	synonymous_variant	222229	exon2			CCCCAAACTCCTG	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"""WD repeat domain containing"""	21769	protein-coding gene	gene with protein product	"""origin recognition complex associated"", ""centromere protein 33"""	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.123A>G	7.37:g.102106306A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1																																																																																			A|0.942;G|0.058	0.058	strong		0.627	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
CFAP46	54777	hgsc.bcm.edu	37	10	134646988	134646988	+	Missense_Mutation	SNP	C	C	T	rs4880433	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134646988C>T	ENST00000368586.5	-	50	7091	c.6991G>A	c.(6991-6993)Gca>Aca	p.A2331T	TTC40_ENST00000263170.5_Missense_Mutation_p.A492T	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TGTCTGTCTGCGACCAGGACT	0.547													C|||	1602	0.319888	0.1399	0.513	5008	,	,		15265	0.2788		0.3986	False		,,,				2504	0.3875				p.A2331T		Atlas-SNP	.											.	TTC40	100	.	0			c.G6991A						PASS	.	C	THR/ALA	771,3635	309.7+/-291.2	66,639,1498	117.0	117.0	117.0		1927	1.4	0.0	10	dbSNP_111	117	3461,5139	507.9+/-376.9	715,2031,1554	yes	missense	C10orf92	NM_001200049.1	58	781,2670,3052	TT,TC,CC		40.2442,17.4989,32.5388	benign	643/1028	134646988	4232,8774	2203	4300	6503	SO:0001583	missense	54777	exon50			TGTCTGCGACCAG																												ENST00000368586.5:c.6991G>A	10.37:g.134646988C>T	ENSP00000357575:p.Ala2331Thr	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	693	0.3173076923076923	68	0.13821138211382114	172	0.47513812154696133	155	0.270979020979021	298	0.39313984168865435	C	9.644	1.139755	0.21205	0.174989	0.402442	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.32023	1.47;1.47	4.32	1.39	0.22231	.	1.053680	0.07597	N	0.922951	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.23490	0.086	B	0.12837	0.008	T	0.46898	-0.9158	9	0.62326	D	0.03	.	7.7247	0.28753	0.0:0.7151:0.0:0.2849	rs4880433;rs17853281;rs52791356;rs56954370;rs4880433	492	Q8IYW2	CJ092_HUMAN	T	2331;492	ENSP00000357575:A2331T;ENSP00000263170:A492T	ENSP00000263170:A492T	A	-	1	0	C10orf93	134496978	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.199000	0.17237	0.305000	0.22832	-0.143000	0.13931	GCA	C|0.686;T|0.314	0.314	strong		0.547	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
NTNG2	84628	hgsc.bcm.edu	37	9	135102254	135102254	+	Silent	SNP	C	C	T	rs2149171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135102254C>T	ENST00000393229.3	+	4	1652	c.876C>T	c.(874-876)caC>caT	p.H292H	NTNG2_ENST00000393228.4_Silent_p.H292H|NTNG2_ENST00000372179.3_Silent_p.H292H|NTNG2_ENST00000360670.3_Silent_p.H292H	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	292	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		GCAACCTGCACGCCAACCTGT	0.647													C|||	2879	0.57488	0.5779	0.5879	5008	,	,		19224	0.4306		0.6243	False		,,,				2504	0.6595				p.H292H		Atlas-SNP	.											.	NTNG2	66	.	0			c.C876T						PASS	.	C		2510,1896	600.5+/-389.5	715,1080,408	39.0	33.0	35.0		876	-0.8	1.0	9	dbSNP_96	35	5334,3266	617.8+/-396.7	1648,2038,614	no	coding-synonymous	NTNG2	NM_032536.2		2363,3118,1022	TT,TC,CC		37.9767,43.0322,39.6894		292/531	135102254	7844,5162	2203	4300	6503	SO:0001819	synonymous_variant	84628	exon4			CCTGCACGCCAAC	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"""Netrins"""	14288	protein-coding gene	gene with protein product	"""Netrin-G2"""		"""netrin G1"""	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.876C>T	9.37:g.135102254C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Silent	SNP	ENST00000393229.3	37	CCDS6946.1																																																																																			C|0.408;T|0.592	0.592	strong		0.647	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536	
DST	667	hgsc.bcm.edu	37	6	56489412	56489412	+	Silent	SNP	C	C	T	rs41271870	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:56489412C>T	ENST00000361203.3	-	32	4219	c.4212G>A	c.(4210-4212)agG>agA	p.R1404R	DST_ENST00000244364.6_Silent_p.R1078R|DST_ENST00000446842.2_Silent_p.R1078R|DST_ENST00000370769.4_Silent_p.R1404R|DST_ENST00000370765.6_Silent_p.R1078R|DST_ENST00000312431.6_Silent_p.R1404R|DST_ENST00000421834.2_Silent_p.R1404R|DST_ENST00000370754.5_Silent_p.R1582R|DST_ENST00000518935.1_Silent_p.R1078R|DST_ENST00000370788.2_Silent_p.R1404R			Q03001	DYST_HUMAN	dystonin	1404					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TATATCGAGTCCTTAGGTCCA	0.348													C|||	22	0.00439297	0.0	0.0086	5008	,	,		16810	0.0		0.0139	False		,,,				2504	0.002				p.R1078R		Atlas-SNP	.											.	DST	1427	.	0			c.G3234A						PASS	.	C	,	18,4388	25.3+/-52.1	0,18,2185	70.0	66.0	67.0		3234,3234	1.2	0.3	6	dbSNP_127	67	161,8439	74.8+/-137.4	0,161,4139	no	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	0,179,6324	TT,TC,CC		1.8721,0.4085,1.3763	,	1078/2650,1078/5172	56489412	179,12827	2203	4300	6503	SO:0001819	synonymous_variant	667	exon22			TCGAGTCCTTAGG	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.4212G>A	6.37:g.56489412C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	48	15	0.3125	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37		18	0.008241758241758242	0	0.0	7	0.019337016574585635	0	0.0	11	0.014511873350923483	C	7.897	0.733504	0.15574	0.004085	0.018721	ENSG00000151914	ENST00000522360	.	.	.	5.1	1.23	0.21249	.	.	.	.	.	T	0.19927	0.0479	.	.	.	.	.	.	.	.	.	.	.	.	T	0.10359	-1.0633	3	.	.	.	.	5.8012	0.18414	0.1333:0.5775:0.0:0.2892	rs41271870	.	.	.	E	76	.	.	G	-	2	0	DST	56597371	0.872000	0.30054	0.255000	0.24374	0.928000	0.56348	-0.019000	0.12546	0.355000	0.24131	0.650000	0.86243	GGA	C|0.988;T|0.012	0.012	strong		0.348	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
CCDC36	339834	hgsc.bcm.edu	37	3	49294250	49294250	+	Missense_Mutation	SNP	C	C	A	rs13068038	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49294250C>A	ENST00000438782.1	+	8	1556	c.1320C>A	c.(1318-1320)gaC>gaA	p.D440E	CCDC36_ENST00000452691.2_Missense_Mutation_p.D440E|CCDC36_ENST00000296449.5_Missense_Mutation_p.D440E			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	440			D -> E (in dbSNP:rs13068038).							endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		GGGGGAAAGACAAGAAGCAGC	0.473													C|||	328	0.0654952	0.059	0.0706	5008	,	,		19749	0.0437		0.1133	False		,,,				2504	0.044				p.D440E		Atlas-SNP	.											.	CCDC36	77	.	0			c.C1320A						PASS	.	C	GLU/ASP,GLU/ASP	384,4022	192.3+/-217.7	12,360,1831	89.0	95.0	93.0		1320,1320	-0.4	0.0	3	dbSNP_121	93	930,7670	205.2+/-247.7	51,828,3421	yes	missense,missense	CCDC36	NM_001135197.1,NM_178173.3	45,45	63,1188,5252	AA,AC,CC		10.814,8.7154,10.103	benign,benign	440/595,440/595	49294250	1314,11692	2203	4300	6503	SO:0001583	missense	339834	exon8			GAAAGACAAGAAG	AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421			27945	protein-coding gene	gene with protein product	"""cancer/testis antigen 74"""						Standard	NM_178173		Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.1320C>A	3.37:g.49294250C>A	ENSP00000391788:p.Asp440Glu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	92	34	0.369565	NM_001135197	C9JJL0|Q05DG9|Q96LP7	Missense_Mutation	SNP	ENST00000438782.1	37	CCDS33755.2	188	0.08608058608058608	33	0.06707317073170732	33	0.09116022099447514	36	0.06293706293706294	86	0.11345646437994723	C	7.810	0.715551	0.15306	0.087154	0.10814	ENSG00000173421	ENST00000296449;ENST00000438782;ENST00000452691;ENST00000309062	T;T;T	0.40756	1.02;1.02;1.02	5.0	-0.445	0.12242	.	0.449187	0.21073	N	0.080638	T	0.00300	0.0009	N	0.08118	0	0.80722	P	0.0	B	0.21225	0.053	B	0.23574	0.047	T	0.10776	-1.0615	9	0.13470	T	0.59	-0.8952	0.9242	0.01321	0.3178:0.3455:0.155:0.1818	rs13068038;rs57851143;rs13068038	440	Q8IYA8	CCD36_HUMAN	E	440;440;440;420	ENSP00000296449:D440E;ENSP00000391788:D440E;ENSP00000407837:D440E	ENSP00000296449:D440E	D	+	3	2	CCDC36	49269254	0.012000	0.17670	0.004000	0.12327	0.770000	0.43624	0.082000	0.14847	0.070000	0.16634	0.561000	0.74099	GAC	C|0.906;A|0.094	0.094	strong		0.473	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342332.1	NM_178173	
ARHGEF3	50650	hgsc.bcm.edu	37	3	56763525	56763525	+	Silent	SNP	A	A	G	rs1009118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:56763525A>G	ENST00000296315.3	-	10	1522	c.1354T>C	c.(1354-1356)Ttg>Ctg	p.L452L	ARHGEF3_ENST00000497267.1_Silent_p.L423L|ARHGEF3_ENST00000338458.4_Silent_p.L484L|ARHGEF3_ENST00000496106.1_Silent_p.L458L|ARHGEF3_ENST00000413728.2_Silent_p.L458L	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	452					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		GCAGCACACAAAACTGTTTCT	0.498													A|||	1337	0.266973	0.2458	0.1124	5008	,	,		20882	0.3442		0.165	False		,,,				2504	0.4305				p.L484L		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.T1450C						PASS	.	A	,,	1083,3323	392.8+/-328.6	115,853,1235	135.0	136.0	136.0		1450,1372,1354	0.4	0.2	3	dbSNP_86	136	1321,7279	259.7+/-282.8	98,1125,3077	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF3	NM_001128615.1,NM_001128616.1,NM_019555.2	,,	213,1978,4312	GG,GA,AA		15.3605,24.5801,18.4838	,,	484/559,458/533,452/527	56763525	2404,10602	2203	4300	6503	SO:0001819	synonymous_variant	50650	exon13			CACACAAAACTGT	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"""Rho guanine nucleotide exchange factors"""	683	protein-coding gene	gene with protein product	"""exchange factor found in platelets and leukemic and neuronal tissues, XPLN"", ""RhoGEF protein"""	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.1354T>C	3.37:g.56763525A>G		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	254	254	1	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			A|0.788;G|0.212	0.212	strong		0.498	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
CLASP1	23332	hgsc.bcm.edu	37	2	122104692	122104692	+	Silent	SNP	G	G	A	rs374603441		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:122104692G>A	ENST00000263710.4	-	39	4841	c.4452C>T	c.(4450-4452)agC>agT	p.S1484S	CLASP1_ENST00000545861.1_Silent_p.S1191S|CLASP1_ENST00000541377.1_Silent_p.S1423S|CLASP1_ENST00000409078.3_Silent_p.S1417S|CLASP1_ENST00000397587.3_Silent_p.S1424S|CLASP1_ENST00000541859.1_Silent_p.S1201S|CLASP1_ENST00000455322.2_Silent_p.S1440S	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1484	Interaction with CLIP2. {ECO:0000250}.|Interaction with PHLDB2 and RSN.|Localization to kinetochores.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					AGCAAAACACGCTGGCCTTAC	0.468																																					p.S1484S		Atlas-SNP	.											.	CLASP1	135	.	0			c.C4452T						PASS	.	G	,,,	0,4100		0,0,2050	93.0	89.0	90.0		4275,4251,4269,4452	-5.2	0.9	2		90	1,8377		0,1,4188	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLASP1	NM_001142273.1,NM_001142274.1,NM_001207051.1,NM_015282.2	,,,	0,1,6238	AA,AG,GG		0.0119,0.0,0.0080	,,,	1425/1480,1417/1472,1423/1478,1484/1539	122104692	1,12477	2050	4189	6239	SO:0001819	synonymous_variant	23332	exon38			AAACACGCTGGCC	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.4452C>T	2.37:g.122104692G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Silent	SNP	ENST00000263710.4	37																																																																																				.	.	weak		0.468	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	
GCSH	2653	hgsc.bcm.edu	37	16	81124275	81124275	+	Silent	SNP	G	G	A	rs8177876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81124275G>A	ENST00000315467.3	-	2	283	c.159C>T	c.(157-159)ttC>ttT	p.F53F	GCSH_ENST00000566566.1_Silent_p.F53F	NM_004483.4	NP_004474.2	P23434	GCSH_HUMAN	glycine cleavage system protein H (aminomethyl carrier)	53					glycine catabolic process (GO:0006546)|glycine decarboxylation via glycine cleavage system (GO:0019464)|methylation (GO:0032259)	glycine cleavage complex (GO:0005960)|mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|skin(2)	5					Glycine(DB00145)	GTTTCTCTGTGAATTTACGCA	0.363													G|||	177	0.0353435	0.0393	0.036	5008	,	,		22015	0.001		0.0845	False		,,,				2504	0.0143				p.F53F		Atlas-SNP	.											.	GCSH	14	.	0			c.C159T						PASS	.	G		175,4225	115.0+/-153.0	5,165,2030	161.0	141.0	148.0		159	4.7	1.0	16	dbSNP_117	148	570,8030	154.9+/-209.1	20,530,3750	no	coding-synonymous	GCSH	NM_004483.4		25,695,5780	AA,AG,GG		6.6279,3.9773,5.7308		53/174	81124275	745,12255	2200	4300	6500	SO:0001819	synonymous_variant	2653	exon2			CTCTGTGAATTTA	M69175	CCDS10933.1	16q23.2	2014-09-17			ENSG00000140905	ENSG00000140905			4208	protein-coding gene	gene with protein product	"""lipoic acid-containing protein"""	238330				1671321, 2025283	Standard	NM_004483		Approved		uc002fgd.3	P23434	OTTHUMG00000137626	ENST00000315467.3:c.159C>T	16.37:g.81124275G>A		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	296	138	0.466216	NM_004483	Q9H1E9	Silent	SNP	ENST00000315467.3	37	CCDS10933.1																																																																																			G|0.947;A|0.053	0.053	strong		0.363	GCSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269049.1	NM_004483	
TM4SF5	9032	hgsc.bcm.edu	37	17	4684095	4684095	+	Silent	SNP	G	G	A	rs13520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4684095G>A	ENST00000270560.3	+	2	220	c.189G>A	c.(187-189)ccG>ccA	p.P63P		NM_003963.2	NP_003954.2	O14894	T4S5_HUMAN	transmembrane 4 L six family member 5	63						integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(3)|ovary(1)	6						TACTGTGTCCGGGGATTGCAG	0.582													G|||	1636	0.326677	0.1717	0.4337	5008	,	,		18244	0.1865		0.5089	False		,,,				2504	0.4172				p.P63P		Atlas-SNP	.											.	TM4SF5	26	.	0			c.G189A						PASS	.	G		1067,3339	384.7+/-325.4	137,793,1273	67.0	62.0	64.0		189	-9.6	0.0	17	dbSNP_123	64	4445,4155	583.6+/-391.6	1143,2159,998	no	coding-synonymous	TM4SF5	NM_003963.2		1280,2952,2271	AA,AG,GG		48.314,24.217,42.3804		63/198	4684095	5512,7494	2203	4300	6503	SO:0001819	synonymous_variant	9032	exon2			GTGTCCGGGGATT	AF027204	CCDS11054.1	17p13.3	2007-01-06	2005-03-21		ENSG00000142484	ENSG00000142484			11857	protein-coding gene	gene with protein product		604657	"""transmembrane 4 superfamily member 5"""			9479038	Standard	NM_003963		Approved		uc002fyw.1	O14894	OTTHUMG00000090776	ENST00000270560.3:c.189G>A	17.37:g.4684095G>A		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	124	121	0.975806	NM_003963	Q17RW9|Q6IB79	Silent	SNP	ENST00000270560.3	37	CCDS11054.1																																																																																			G|0.612;A|0.388	0.388	strong		0.582	TM4SF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207558.2		
SEMA6B	10501	hgsc.bcm.edu	37	19	4558431	4558431	+	Silent	SNP	C	C	G	rs2304213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4558431C>G	ENST00000586582.1	-	2	349	c.39G>C	c.(37-39)ctG>ctC	p.L13L	SEMA6B_ENST00000301293.3_Silent_p.L13L|SEMA6B_ENST00000586965.1_Silent_p.L13L	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	13					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGAAGCAGCAGGGCCGGGC	0.736											OREG0025169	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2336	0.466454	0.3707	0.4841	5008	,	,		9439	0.5952		0.4543	False		,,,				2504	0.4632				p.L13L		Atlas-SNP	.											SEMA6B,NS,carcinoma,0,2	SEMA6B	51	2	0			c.G39C						PASS	.	C		1228,2490		275,678,906	3.0	5.0	4.0		39	-1.8	0.5	19	dbSNP_100	4	2974,4598		716,1542,1528	no	coding-synonymous	SEMA6B	NM_032108.3		991,2220,2434	GG,GC,CC		39.2763,33.0285,37.2188		13/889	4558431	4202,7088	1859	3786	5645	SO:0001819	synonymous_variant	10501	exon2			AAGCAGCAGGGCC	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.39G>C	19.37:g.4558431C>G		Somatic	21	0	0	619	WXS	Illumina HiSeq	Phase_I	20	20	1	NM_032108	A5PKU4|F6IB19|Q9NRK9	Silent	SNP	ENST00000586582.1	37	CCDS12131.1																																																																																			C|0.510;G|0.490	0.490	strong		0.736	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
IKZF3	22806	hgsc.bcm.edu	37	17	37922259	37922259	+	Silent	SNP	G	G	A	rs907092	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:37922259G>A	ENST00000346872.3	-	8	1375	c.1314C>T	c.(1312-1314)tcC>tcT	p.S438S	IKZF3_ENST00000377944.3_Silent_p.S295S|IKZF3_ENST00000346243.3_Silent_p.S360S|IKZF3_ENST00000439016.2_Silent_p.S343S|IKZF3_ENST00000439167.2_Silent_p.S365S|IKZF3_ENST00000377945.3_Silent_p.S304S|IKZF3_ENST00000351680.3_Silent_p.S399S|IKZF3_ENST00000467757.1_Silent_p.S382S|RP11-94L15.2_ENST00000488188.2_lincRNA|IKZF3_ENST00000377958.2_Silent_p.S351S|IKZF3_ENST00000377952.2_Silent_p.S217S|IKZF3_ENST00000394189.2_Silent_p.S256S|IKZF3_ENST00000583368.1_Silent_p.S191S|IKZF3_ENST00000350532.3_Silent_p.S399S|IKZF3_ENST00000535189.1_Silent_p.S404S	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	438					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S438S(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TCACTTTGACGGAGTCTCTTG	0.562													G|||	1496	0.298722	0.1384	0.3401	5008	,	,		20021	0.2937		0.4732	False		,,,				2504	0.3119				p.S438S		Atlas-SNP	.											IKZF3,NS,carcinoma,0,1	IKZF3	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C1314T						PASS	.	G	,,,,,	736,3670	303.0+/-287.7	70,596,1537	133.0	134.0	133.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1314,1146,1197,1197,1029,1080	4.7	1.0	17	dbSNP_86	133	3899,4701	545.6+/-384.8	869,2161,1270	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IKZF3	NM_012481.3,NM_183228.1,NM_183229.1,NM_183230.1,NM_183231.1,NM_183232.1	,,,,,	939,2757,2807	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	45.3372,16.7045,35.6374	,,,,,	438/510,382/454,399/471,399/471,343/415,360/432	37922259	4635,8371	2203	4300	6503	SO:0001819	synonymous_variant	22806	exon8			TTTGACGGAGTCT	AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13178	protein-coding gene	gene with protein product		606221	"""zinc finger protein, subfamily 1A, 3 (Aiolos)"""	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.1314C>T	17.37:g.37922259G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Silent	SNP	ENST00000346872.3	37	CCDS11346.1	757	0.3466117216117216	64	0.13008130081300814	131	0.36187845303867405	198	0.34615384615384615	364	0.48021108179419525	G	8.414	0.844787	0.16963	0.167045	0.453372	ENSG00000161405	ENST00000439167;ENST00000439016	.	.	.	5.72	4.73	0.59995	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999982	.	.	.	.	.	.	T	0.51236	-0.8731	3	.	.	.	-8.8222	9.9806	0.41811	0.0716:0.1395:0.7888:0.0	rs907092;rs3751904;rs17607446;rs56570169;rs58485549;rs907092	.	.	.	L	353;392	.	.	P	-	2	0	IKZF3	35175785	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.032000	0.41127	1.382000	0.46385	0.655000	0.94253	CCG	G|0.660;A|0.340	0.340	strong		0.562	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388728	1388728	+	Silent	SNP	C	C	T	rs9760383	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388728C>T	ENST00000324803.4	+	1	3389	c.429C>T	c.(427-429)tgC>tgT	p.C143C		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	143					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCCATGCGGAGTGCCCG	0.701													N|||	654	0.130591	0.1558	0.1585	5008	,	,		13677	0.2073		0.0676	False		,,,				2504	0.0624				p.C143C		Atlas-SNP	.											CRIPAK,colon,carcinoma,+2,4	CRIPAK	185	4	0			c.C429T						scavenged	.						38.0	38.0	38.0					4																	1388728		1909	3682	5591	SO:0001819	synonymous_variant	285464	exon1			CCCATGCGGAGTG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.429C>T	4.37:g.1388728C>T		Somatic	87	5	0.0574713		WXS	Illumina HiSeq	Phase_I	24	6	0.25	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.654	0.305317	0.10678	.	.	ENSG00000179979	ENST00000382944	.	.	.	0.948	-1.08	0.09936	.	.	.	.	.	T	0.24736	0.0600	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.19943	-1.0290	5	0.37606	T	0.19	.	2.3505	0.04282	0.2615:0.4143:0.0:0.3242	rs9760383	.	.	.	W	127	.	ENSP00000372402:R127W	R	+	1	2	CRIPAK	1378728	0.000000	0.05858	0.003000	0.11579	0.009000	0.06853	-1.656000	0.01980	-1.804000	0.01241	-1.950000	0.00486	CGG	C|0.500;T|0.500	0.500	weak		0.701	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
SLC22A12	116085	hgsc.bcm.edu	37	11	64359286	64359286	+	Silent	SNP	C	C	T	rs3825016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64359286C>T	ENST00000377574.1	+	1	1005	c.258C>T	c.(256-258)caC>caT	p.H86H	SLC22A12_ENST00000377572.1_Silent_p.H86H|SLC22A12_ENST00000473690.1_5'UTR|SLC22A12_ENST00000377567.2_Silent_p.H86H|SLC22A12_ENST00000336464.7_Silent_p.H86H	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	86					cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	AGAGGCCCCACCAGTGCCGCC	0.672													C|||	1939	0.387181	0.1014	0.4323	5008	,	,		12614	0.2192		0.7058	False		,,,				2504	0.5869				p.H86H		Atlas-SNP	.											.	SLC22A12	68	.	0			c.C258T	GRCh37	CM063146	SLC22A12	M	rs3825016	PASS	.	C	,	909,3489		99,711,1389	24.0	28.0	27.0		258,	1.3	0.0	11	dbSNP_107	27	6085,2509		2167,1751,379	no	coding-synonymous,utr-5	SLC22A12	NM_144585.2,NM_153378.1	,	2266,2462,1768	TT,TC,CC		29.1948,20.6685,46.1669	,	86/554,	64359286	6994,5998	2199	4297	6496	SO:0001819	synonymous_variant	116085	exon1			GCCCCACCAGTGC	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"""Solute carriers"""	17989	protein-coding gene	gene with protein product		607096	"""solute carrier family 22 (organic anion/cation transporter), member 12"""			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.258C>T	11.37:g.64359286C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Silent	SNP	ENST00000377574.1	37	CCDS8075.1																																																																																			C|0.512;T|0.488	0.488	strong		0.672	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585	
COL6A5	256076	hgsc.bcm.edu	37	3	130134492	130134492	+	Missense_Mutation	SNP	T	T	C	rs16827497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130134492T>C	ENST00000432398.2	+	23	5259	c.4765T>C	c.(4765-4767)Tca>Cca	p.S1589P	COL6A5_ENST00000265379.6_Missense_Mutation_p.S1589P	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1589	Triple-helical region.		S -> P (in dbSNP:rs16827497).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ACTAAAGGGGTCACAGGGAAA	0.443													T|||	2260	0.451278	0.3321	0.4914	5008	,	,		16996	0.1875		0.7674	False		,,,				2504	0.5307				p.S1589P		Atlas-SNP	.											.	COL6A5	205	.	0			c.T4765C						PASS	.	T	PRO/SER	584,800		125,334,233	67.0	63.0	64.0		4765	-5.3	0.0	3	dbSNP_123	64	2417,765		931,555,105	yes	missense	COL6A5	NM_153264.5	74	1056,889,338	CC,CT,TT		24.0415,42.1965,34.2751	benign	1589/2527	130134492	3001,1565	692	1591	2283	SO:0001583	missense	256076	exon23			AAGGGGTCACAGG	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.4765T>C	3.37:g.130134492T>C	ENSP00000390895:p.Ser1589Pro	Somatic	370	1	0.0027027		WXS	Illumina HiSeq	Phase_I	347	346	0.997118	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		1078	0.4935897435897436	183	0.3719512195121951	197	0.5441988950276243	97	0.16958041958041958	601	0.7928759894459103	T	7.235	0.600083	0.13939	0.421965	0.759585	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.94280	-3.39;-3.39	3.81	-5.28	0.02755	.	.	.	.	.	T	0.00012	0.0000	N	0.00504	-1.425	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.37549	-0.9701	8	0.25106	T	0.35	.	5.9244	0.19101	0.0:0.3035:0.4473:0.2492	rs16827497;rs16827497	1589	A8TX70-2	.	P	1589	ENSP00000390895:S1589P;ENSP00000265379:S1589P	ENSP00000265379:S1589P	S	+	1	0	COL6A5	131617182	0.000000	0.05858	0.000000	0.03702	0.141000	0.21300	-2.755000	0.00789	-1.043000	0.03258	0.454000	0.30748	TCA	T|0.539;C|0.461	0.461	strong		0.443	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16532803	16532803	+	Silent	SNP	G	G	A	rs221050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16532803G>A	ENST00000270747.3	-	7	1306	c.1170C>T	c.(1168-1170)tcC>tcT	p.S390S	ARHGEF19_ENST00000478117.1_5'UTR	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	390	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		TGTGGATGTAGGAGGCCTCGG	0.622													G|||	1346	0.26877	0.1747	0.4049	5008	,	,		13256	0.1518		0.2654	False		,,,				2504	0.4233				p.S390S		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.C1170T						PASS	.	G		786,3618		80,626,1496	32.0	29.0	30.0		1170	-9.7	0.6	1	dbSNP_79	30	2186,6404		297,1592,2406	no	coding-synonymous	ARHGEF19	NM_153213.3		377,2218,3902	AA,AG,GG		25.4482,17.8474,22.8721		390/803	16532803	2972,10022	2202	4295	6497	SO:0001819	synonymous_variant	128272	exon7			GATGTAGGAGGCC	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.1170C>T	1.37:g.16532803G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	96	34	0.354167	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Silent	SNP	ENST00000270747.3	37	CCDS170.1	485	0.22206959706959706	79	0.16056910569105692	123	0.3397790055248619	73	0.12762237762237763	210	0.2770448548812665	G	11.21	1.571221	0.28003	0.178474	0.254482	ENSG00000142632	ENST00000449495	.	.	.	4.85	-9.7	0.00521	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999926941	.	.	.	.	.	.	T	0.06197	-1.0840	3	.	.	.	.	12.7933	0.57547	0.0:0.2802:0.5479:0.1719	rs221050;rs3738623	.	.	.	L	79	.	.	P	-	2	0	ARHGEF19	16405390	0.005000	0.15991	0.630000	0.29268	0.995000	0.86356	-1.891000	0.01611	-2.358000	0.00611	0.555000	0.69702	CCT	G|0.786;A|0.214	0.214	strong		0.622	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
RNF20	56254	hgsc.bcm.edu	37	9	104309445	104309445	+	Silent	SNP	T	T	C	rs2273976	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:104309445T>C	ENST00000389120.3	+	8	1011	c.921T>C	c.(919-921)taT>taC	p.Y307Y	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	307					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		ATAAGGTGTATGGAGCGGGGA	0.413													T|||	551	0.110024	0.0847	0.1513	5008	,	,		20243	0.1111		0.1461	False		,,,				2504	0.0767				p.Y307Y		Atlas-SNP	.											.	RNF20	110	.	0			c.T921C						PASS	.	T		437,3969	209.8+/-230.5	17,403,1783	128.0	122.0	124.0		921	0.6	1.0	9	dbSNP_100	124	1389,7211	269.8+/-288.6	118,1153,3029	no	coding-synonymous	RNF20	NM_019592.5		135,1556,4812	CC,CT,TT		16.1512,9.9183,14.0397		307/976	104309445	1826,11180	2203	4300	6503	SO:0001819	synonymous_variant	56254	exon8			GGTGTATGGAGCG	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"""RING-type (C3HC4) zinc fingers"""	10062	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"""	607699	"""ring finger protein 20"""			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.921T>C	9.37:g.104309445T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	205	104	0.507317	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Silent	SNP	ENST00000389120.3	37	CCDS35084.1																																																																																			T|0.867;C|0.133	0.133	strong		0.413	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592	
ANO2	57101	hgsc.bcm.edu	37	12	6030405	6030405	+	Missense_Mutation	SNP	A	A	G	rs3741903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6030405A>G	ENST00000356134.5	-	3	394	c.323T>C	c.(322-324)gTg>gCg	p.V108A	ANO2_ENST00000327087.8_Missense_Mutation_p.V108A|ANO2_ENST00000546188.1_Missense_Mutation_p.V108A	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	112					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						GGCCAGGTGCACCCCGCGTTT	0.607													G|||	784	0.15655	0.0386	0.1441	5008	,	,		18430	0.1915		0.2167	False		,,,				2504	0.227				p.V108A		Atlas-SNP	.											.	ANO2	309	.	0			c.T323C						PASS	.	G	ALA/VAL	292,3824		6,280,1772	56.0	57.0	57.0		323	1.4	0.0	12	dbSNP_107	57	1711,6679		180,1351,2664	yes	missense	ANO2	NM_020373.2	64	186,1631,4436	GG,GA,AA		20.3933,7.0943,16.0163	benign	108/999	6030405	2003,10503	2058	4195	6253	SO:0001583	missense	57101	exon3			AGGTGCACCCCGC	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.323T>C	12.37:g.6030405A>G	ENSP00000348453:p.Val108Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_020373	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		344	0.1575091575091575	17	0.034552845528455285	62	0.1712707182320442	102	0.17832167832167833	163	0.21503957783641162	G	0	-2.586289	0.00128	0.070943	0.203933	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277	T;T;T	0.66638	-0.22;-0.22;-0.22	4.52	1.37	0.22104	.	0.669254	0.14551	N	0.312671	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10543	-1.0625	9	0.02654	T	1	.	7.1216	0.25448	0.2452:0.1241:0.6307:0.0	rs3741903;rs17786472;rs58403475;rs3741903	108	Q9NQ90-3	.	A	108;108;108;112	ENSP00000314048:V108A;ENSP00000348453:V108A;ENSP00000440981:V108A	ENSP00000314048:V108A	V	-	2	0	ANO2	5900666	0.000000	0.05858	0.002000	0.10522	0.030000	0.12068	0.524000	0.22940	-0.076000	0.12775	-2.318000	0.00253	GTG	A|0.834;G|0.166	0.166	strong		0.607	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
FRMD8	83786	hgsc.bcm.edu	37	11	65161129	65161129	+	Silent	SNP	C	C	T	rs2073800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65161129C>T	ENST00000317568.5	+	4	502	c.339C>T	c.(337-339)gaC>gaT	p.D113D	FRMD8_ENST00000355991.5_Silent_p.D57D|FRMD8_ENST00000416776.2_Intron	NM_031904.3	NP_114110.1	Q9BZ67	FRMD8_HUMAN	FERM domain containing 8	113	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|urinary_tract(1)	17						GTGCCCCAGACGATGACGTGG	0.652													C|||	1442	0.287939	0.028	0.2911	5008	,	,		19252	0.2698		0.5467	False		,,,				2504	0.3896				p.D113D		Atlas-SNP	.											.	FRMD8	28	.	0			c.C339T						PASS	.	C		508,3894	228.8+/-243.5	40,428,1733	74.0	55.0	61.0		339	-6.7	0.1	11	dbSNP_96	61	4803,3789	601.3+/-394.3	1363,2077,856	no	coding-synonymous	FRMD8	NM_031904.3		1403,2505,2589	TT,TC,CC		44.0992,11.5402,40.8727		113/465	65161129	5311,7683	2201	4296	6497	SO:0001819	synonymous_variant	83786	exon4			CCCAGACGATGAC	AK074850	CCDS8102.1, CCDS73320.1	11q13.1	2007-08-14			ENSG00000126391	ENSG00000126391			25462	protein-coding gene	gene with protein product						12477932	Standard	NM_031904		Approved	FLJ90369, FKSG44	uc001odu.4	Q9BZ67	OTTHUMG00000166275	ENST00000317568.5:c.339C>T	11.37:g.65161129C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	16	0.313726	NM_031904	B4E2P1|Q86V56|Q8NCB5	Silent	SNP	ENST00000317568.5	37	CCDS8102.1																																																																																			C|0.651;T|0.349	0.349	strong		0.652	FRMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388833.1	NM_031904	
SEMA3F	6405	hgsc.bcm.edu	37	3	50222926	50222926	+	Missense_Mutation	SNP	T	T	A	rs1046956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50222926T>A	ENST00000002829.3	+	14	1991	c.1507T>A	c.(1507-1509)Ttg>Atg	p.L503M	SEMA3F_ENST00000434342.1_Missense_Mutation_p.L472M|SEMA3F_ENST00000413852.1_Missense_Mutation_p.L404M	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	503	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		L -> M (in dbSNP:rs1046956). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8786119}.		axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		TGACCAGGAGTTGGAGGAGCT	0.647													A|||	3836	0.765974	0.587	0.7478	5008	,	,		19661	0.9871		0.671	False		,,,				2504	0.8906				p.L503M		Atlas-SNP	.											.	SEMA3F	62	.	0			c.T1507A						PASS	.	A	MET/LEU	2645,1761	521.2+/-370.5	809,1027,367	127.0	105.0	112.0		1507	0.3	1.0	3	dbSNP_86	112	5598,3002	463.5+/-366.0	1798,2002,500	yes	missense	SEMA3F	NM_004186.3	15	2607,3029,867	AA,AT,TT		34.907,39.9682,36.6216	benign	503/786	50222926	8243,4763	2203	4300	6503	SO:0001583	missense	6405	exon14			CAGGAGTTGGAGG	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10728	protein-coding gene	gene with protein product	"""sema IV"""	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.1507T>A	3.37:g.50222926T>A	ENSP00000002829:p.Leu503Met	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	311	168	0.540193	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Missense_Mutation	SNP	ENST00000002829.3	37	CCDS2811.1	1667	0.7632783882783882	309	0.6280487804878049	267	0.7375690607734806	571	0.9982517482517482	520	0.6860158311345647	A	1.585	-0.530459	0.04112	0.600318	0.65093	ENSG00000001617	ENST00000413852;ENST00000002829;ENST00000434342	T;T;T	0.11169	2.8;2.8;2.8	5.16	0.291	0.15732	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.429595	0.29028	N	0.013364	T	0.00012	0.0000	N	0.10685	0.025	0.58432	P	1.999999999946489E-6	B;B	0.15473	0.002;0.013	B;B	0.15052	0.004;0.012	T	0.38134	-0.9675	9	0.02654	T	1	.	3.5309	0.07777	0.3261:0.0:0.28:0.394	rs1046956;rs2229865;rs3186953;rs13327092;rs17411869;rs52800496;rs57341472;rs1046956	472;503	C9JQ85;Q13275	.;SEM3F_HUMAN	M	404;503;472	ENSP00000388931:L404M;ENSP00000002829:L503M;ENSP00000409859:L472M	ENSP00000002829:L503M	L	+	1	2	SEMA3F	50197930	0.904000	0.30761	0.987000	0.45799	0.708000	0.40852	1.139000	0.31504	-0.356000	0.08187	-2.372000	0.00235	TTG	T|0.322;A|0.678	0.678	strong		0.647	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186	
ATRNL1	26033	hgsc.bcm.edu	37	10	117228794	117228794	+	Silent	SNP	A	A	G	rs10885721	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:117228794A>G	ENST00000355044.3	+	24	3735	c.3609A>G	c.(3607-3609)acA>acG	p.T1203T	ATRNL1_ENST00000423111.2_Silent_p.T254T|ATRNL1_ENST00000303745.7_Intron	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1203					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CTAACATTACATTCTATGTGT	0.303													A|||	1725	0.344449	0.2935	0.4654	5008	,	,		13018	0.1677		0.4911	False		,,,				2504	0.3589				p.T1203T		Atlas-SNP	.											.	ATRNL1	219	.	0			c.A3609G						PASS	.	A		1525,2869	443.9+/-347.2	262,1001,934	56.0	61.0	59.0		3609	0.7	1.0	10	dbSNP_120	59	4374,4182	568.5+/-389.0	1115,2144,1019	no	coding-synonymous	ATRNL1	NM_207303.2		1377,3145,1953	GG,GA,AA		48.878,34.7064,45.5521		1203/1380	117228794	5899,7051	2197	4278	6475	SO:0001819	synonymous_variant	26033	exon24			CATTACATTCTAT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3609A>G	10.37:g.117228794A>G		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1																																																																																			A|0.586;G|0.414	0.414	strong		0.303	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
IMP4	92856	hgsc.bcm.edu	37	2	131100734	131100734	+	Missense_Mutation	SNP	G	G	A	rs11542411	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:131100734G>A	ENST00000259239.3	+	2	787	c.79G>A	c.(79-81)Gag>Aag	p.E27K	CCDC115_ENST00000437688.2_5'Flank|IMP4_ENST00000409935.1_Missense_Mutation_p.E27K|CCDC115_ENST00000259229.2_5'Flank|CCDC115_ENST00000409127.1_5'Flank	NM_033416.1	NP_219484.1	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein	27	Arg-rich.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)|ribonucleoprotein complex (GO:0030529)				central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	18	Colorectal(110;0.1)					CTCAGCCCAGGAGAGGAAGGA	0.697													G|||	395	0.0788738	0.0151	0.0807	5008	,	,		14012	0.002		0.2177	False		,,,				2504	0.1002				p.E27K		Atlas-SNP	.											.	IMP4	35	.	0			c.G79A						PASS	.	G	LYS/GLU	110,3678		3,104,1787	3.0	5.0	4.0		79	4.9	1.0	2	dbSNP_120	4	1178,6408		90,998,2705	no	missense	IMP4	NM_033416.1	56	93,1102,4492	AA,AG,GG		15.5286,2.9039,11.3241	possibly-damaging	27/292	131100734	1288,10086	1894	3793	5687	SO:0001583	missense	92856	exon2			GCCCAGGAGAGGA	BC010042	CCDS2160.1	2q21.1	2014-02-19	2014-02-19		ENSG00000136718	ENSG00000136718			30856	protein-coding gene	gene with protein product		612981	"""IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			8619474, 9110174, 12655004	Standard	NM_033416		Approved	MGC19606, BXDC4	uc002tra.1	Q96G21	OTTHUMG00000131627	ENST00000259239.3:c.79G>A	2.37:g.131100734G>A	ENSP00000259239:p.Glu27Lys	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_033416	Q3ZTT3	Missense_Mutation	SNP	ENST00000259239.3	37	CCDS2160.1	213	0.09752747252747253	9	0.018292682926829267	32	0.08839779005524862	0	0.0	172	0.22691292875989447	G	17.57	3.422106	0.62622	0.029039	0.155286	ENSG00000136718	ENST00000259239;ENST00000409935	T;T	0.46819	0.86;0.87	4.86	4.86	0.63082	.	0.364058	0.30538	N	0.009414	T	0.00039	0.0001	M	0.72576	2.205	0.09310	P	0.9999999129378	P	0.40970	0.734	B	0.34652	0.187	T	0.09357	-1.0678	9	0.44086	T	0.13	-16.6431	15.8506	0.78927	0.0:0.0:1.0:0.0	rs11542411;rs58820695;rs11542411	27	Q96G21	IMP4_HUMAN	K	27	ENSP00000259239:E27K;ENSP00000386411:E27K	ENSP00000259239:E27K	E	+	1	0	IMP4	130817204	1.000000	0.71417	0.999000	0.59377	0.066000	0.16364	7.891000	0.87319	2.431000	0.82371	0.436000	0.28706	GAG	G|0.895;A|0.105	0.105	strong		0.697	IMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254520.2	NM_033416	
KIF13A	63971	hgsc.bcm.edu	37	6	17834213	17834213	+	Silent	SNP	T	T	C	rs4716190	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:17834213T>C	ENST00000259711.6	-	12	1350	c.1245A>G	c.(1243-1245)agA>agG	p.R415R	KIF13A_ENST00000378843.2_Silent_p.R415R|KIF13A_ENST00000378826.2_Silent_p.R415R|KIF13A_ENST00000378814.5_Silent_p.R415R|KIF13A_ENST00000378816.5_Silent_p.R415R	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	415					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			CTTCTGTTTTTCTCAGCTTCT	0.388													C|||	2349	0.46905	0.3797	0.536	5008	,	,		16523	0.4018		0.5308	False		,,,				2504	0.5481				p.R415R		Atlas-SNP	.											.	KIF13A	276	.	0			c.A1245G						PASS	.	C	,,,	1554,2130		344,866,632	154.0	142.0	145.0		1245,1245,1245,1245	3.8	1.0	6	dbSNP_111	145	4239,3941		1095,2049,946	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	1439,2915,1578	CC,CT,TT		48.1785,42.1824,48.8284	,,,	415/1771,415/1758,415/1750,415/1806	17834213	5793,6071	1842	4090	5932	SO:0001819	synonymous_variant	63971	exon12			TGTTTTTCTCAGC	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1245A>G	6.37:g.17834213T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	152	71	0.467105	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			T|0.528;C|0.472	0.472	strong		0.388	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
OR2T34	127068	hgsc.bcm.edu	37	1	248737167	248737167	+	Missense_Mutation	SNP	G	G	A	rs148590921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248737167G>A	ENST00000328782.2	-	1	913	c.892C>T	c.(892-894)Cgc>Tgc	p.R298C		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCTTTGTTGCGGAGACTGTAA	0.483																																					p.R298C		Atlas-SNP	.											OR2T34,NS,carcinoma,+2,1	OR2T34	72	1	0			c.C892T						scavenged	.						13.0	13.0	13.0					1																	248737167		1841	3755	5596	SO:0001583	missense	127068	exon1			TGTTGCGGAGACT	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.892C>T	1.37:g.248737167G>A	ENSP00000330904:p.Arg298Cys	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	243	48	0.197531	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	418	0.19139194139194138	111	0.22560975609756098	65	0.17955801104972377	145	0.2534965034965035	97	0.1279683377308707	.	8.250	0.808823	0.16467	.	.	ENSG00000183310	ENST00000328782	T	0.40476	1.03	2.37	-4.74	0.03249	.	.	.	.	.	T	0.00012	0.0000	M	0.77820	2.39	0.80722	P	0.0	D	0.89917	1.0	D	0.74348	0.983	T	0.06588	-1.0818	8	0.72032	D	0.01	.	5.5241	0.16949	0.1475:0.0:0.2286:0.624	.	298	Q8NGX1	O2T34_HUMAN	C	298	ENSP00000330904:R298C	ENSP00000330904:R298C	R	-	1	0	OR2T34	246803790	0.000000	0.05858	0.003000	0.11579	0.341000	0.28922	-0.784000	0.04633	-1.176000	0.02747	0.123000	0.15791	CGC	G|0.500;A|0.500	0.500	strong		0.483	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
RECK	8434	hgsc.bcm.edu	37	9	36110063	36110063	+	Silent	SNP	T	T	A	rs10972727	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:36110063T>A	ENST00000377966.3	+	15	2441	c.1875T>A	c.(1873-1875)cgT>cgA	p.R625R		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	625					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			AAGATGACCGTCGTACCTTCA	0.483													T|||	1232	0.246006	0.0469	0.2378	5008	,	,		18159	0.3056		0.3638	False		,,,				2504	0.3384				p.R625R		Atlas-SNP	.											.	RECK	73	.	0			c.T1875A						PASS	.	T		426,3980	207.2+/-228.6	26,374,1803	195.0	151.0	166.0		1875	-5.2	0.9	9	dbSNP_120	166	3241,5359	487.6+/-372.2	645,1951,1704	no	coding-synonymous	RECK	NM_021111.2		671,2325,3507	AA,AT,TT		37.686,9.6686,28.1947		625/972	36110063	3667,9339	2203	4300	6503	SO:0001819	synonymous_variant	8434	exon15			TGACCGTCGTACC	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.1875T>A	9.37:g.36110063T>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	181	72	0.39779	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Silent	SNP	ENST00000377966.3	37	CCDS6597.1																																																																																			T|0.719;A|0.281	0.281	strong		0.483	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
MUC1	4582	hgsc.bcm.edu	37	1	155160747	155160747	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:155160747G>A	ENST00000368395.1	-	3	851	c.780C>T	c.(778-780)gtC>gtT	p.V260V	MUC1_ENST00000368390.3_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000368393.3_Silent_p.V58V|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000368389.2_Silent_p.V58V|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000462215.1_Intron|MUC1_ENST00000337604.5_Silent_p.V58V|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000368398.3_Intron|MUC1_ENST00000438413.1_Intron|MUC1_ENST00000343256.5_Intron|MUC1_ENST00000342482.4_Intron	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	1040	42 X 20 AA approximate tandem repeats of P-A-P-G-S-T-A-P-P-A-H-G-V-T-S-A-P-D-T-R.				cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AAAAGAAAGAGACCCCAGTAG	0.488			T	IGH@	B-NHL																																p.V269V		Atlas-SNP	.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	MUC1_ENST00000368395,NS,neuroblastoma,0,2	MUC1	94	2	0			c.C807T						scavenged	.						59.0	68.0	65.0					1																	155160747		2198	4297	6495	SO:0001819	synonymous_variant	4582	exon4			GAAAGAGACCCCA	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.780C>T	1.37:g.155160747G>A		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	286	5	0.0174825	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Silent	SNP	ENST00000368395.1	37	CCDS55640.1																																																																																			.	.	none		0.488	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
POU4F2	5458	hgsc.bcm.edu	37	4	147561147	147561147	+	Missense_Mutation	SNP	C	C	A	rs147517729	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:147561147C>A	ENST00000281321.3	+	2	665	c.417C>A	c.(415-417)gaC>gaA	p.D139E	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	139					axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					TCAAACCGGACGCCACCTACC	0.657													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		13029	0.0		0.007	False		,,,				2504	0.001				p.D139E		Atlas-SNP	.											.	POU4F2	83	.	0			c.C417A						PASS	.	C	GLU/ASP	16,4390	23.3+/-48.9	0,16,2187	118.0	143.0	135.0		417	5.8	1.0	4	dbSNP_134	135	111,8489	59.8+/-121.6	2,107,4191	yes	missense	POU4F2	NM_004575.2	45	2,123,6378	AA,AC,CC		1.2907,0.3631,0.9765	probably-damaging	139/410	147561147	127,12879	2203	4300	6503	SO:0001583	missense	5458	exon2			ACCGGACGCCACC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.417C>A	4.37:g.147561147C>A	ENSP00000281321:p.Asp139Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Missense_Mutation	SNP	ENST00000281321.3	37	CCDS34074.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	19.43	3.826606	0.71143	0.003631	0.012907	ENSG00000151615	ENST00000281321	T	0.25912	1.77	5.77	5.77	0.91146	.	0.000000	0.43110	D	0.000613	T	0.39064	0.1064	L	0.58510	1.815	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	T	0.04976	-1.0914	10	0.23891	T	0.37	.	18.7641	0.91865	0.0:1.0:0.0:0.0	.	139	Q12837	PO4F2_HUMAN	E	139	ENSP00000281321:D139E	ENSP00000281321:D139E	D	+	3	2	POU4F2	147780597	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.140000	0.50585	2.729000	0.93468	0.467000	0.42956	GAC	C|0.992;A|0.008	0.008	strong		0.657	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575	
ARHGAP12	94134	hgsc.bcm.edu	37	10	32128611	32128611	+	Missense_Mutation	SNP	A	A	G	rs2808096	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:32128611A>G	ENST00000344936.2	-	8	1559	c.1325T>C	c.(1324-1326)tTt>tCt	p.F442S	ARHGAP12_ENST00000311380.4_Missense_Mutation_p.F395S|ARHGAP12_ENST00000375250.5_Intron|ARHGAP12_ENST00000375245.4_Missense_Mutation_p.F395S|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.F442S	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	442			F -> S (in dbSNP:rs2808096).		morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				ATTTTCAGGAAAGCAGGGTTT	0.343													A|||	1161	0.231829	0.0545	0.2954	5008	,	,		13632	0.4127		0.2048	False		,,,				2504	0.2679				p.F442S		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.T1325C						PASS	.	A	SER/PHE	371,4035	186.4+/-213.3	16,339,1848	109.0	110.0	110.0		1325	3.2	1.0	10	dbSNP_100	110	1824,6776	326.4+/-317.4	190,1444,2666	yes	missense	ARHGAP12	NM_018287.5	155	206,1783,4514	GG,GA,AA		21.2093,8.4203,16.8768	benign	442/847	32128611	2195,10811	2203	4300	6503	SO:0001583	missense	94134	exon8			TCAGGAAAGCAGG	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1325T>C	10.37:g.32128611A>G	ENSP00000345808:p.Phe442Ser	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_001270695	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	505	0.23122710622710624	28	0.056910569105691054	89	0.24585635359116023	219	0.38286713286713286	169	0.22295514511873352	A	11.71	1.718440	0.30503	0.084203	0.212093	ENSG00000165322	ENST00000311380;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.51	3.15	0.36227	.	0.228703	0.38548	N	0.001653	T	0.00012	0.0000	N	0.08118	0	0.36264	P	0.145235	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.48091	-0.9065	9	0.20046	T	0.44	.	6.4215	0.21746	0.7804:0.0:0.0739:0.1457	rs2808096;rs17582209;rs52793660;rs2808096	442;442;395	Q504X1;Q8IWW6;Q8IWW6-3	.;RHG12_HUMAN;.	S	395;442;442;395	ENSP00000310984:F395S;ENSP00000345808:F442S;ENSP00000379448:F442S;ENSP00000364394:F395S	ENSP00000310984:F395S	F	-	2	0	ARHGAP12	32168617	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.817000	0.39002	0.443000	0.26582	0.533000	0.62120	TTT	G|0.199;N|0.000	0.199	strong		0.343	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
COL15A1	1306	hgsc.bcm.edu	37	9	101797679	101797679	+	Silent	SNP	C	C	G	rs35494947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:101797679C>G	ENST00000375001.3	+	19	2691	c.2268C>G	c.(2266-2268)ctC>ctG	p.L756L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	756	Nonhelical region 3 (NC3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				AACCCAAACTCTCCAGACCAA	0.512													C|||	21	0.00419329	0.0	0.0058	5008	,	,		19093	0.001		0.0129	False		,,,				2504	0.0031				p.L756L		Atlas-SNP	.											.	COL15A1	211	.	0			c.C2268G						PASS	.	C		13,4393	20.2+/-43.8	0,13,2190	100.0	95.0	97.0		2268	4.2	0.1	9	dbSNP_126	97	107,8493	58.3+/-119.8	0,107,4193	no	coding-synonymous	COL15A1	NM_001855.3		0,120,6383	GG,GC,CC		1.2442,0.2951,0.9227		756/1389	101797679	120,12886	2203	4300	6503	SO:0001819	synonymous_variant	1306	exon19			CAAACTCTCCAGA	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2268C>G	9.37:g.101797679C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																			C|0.992;G|0.008	0.008	strong		0.512	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
ECHS1	1892	hgsc.bcm.edu	37	10	135184126	135184126	+	Missense_Mutation	SNP	G	G	A	rs1049951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:135184126G>A	ENST00000368547.3	-	2	579	c.224C>T	c.(223-225)aCc>aTc	p.T75I	MIR3944_ENST00000581277.1_RNA	NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	75			T -> I (in dbSNP:rs1049951). {ECO:0000269|PubMed:11271497, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8012501, ECO:0000269|PubMed:9073515, ECO:0000269|Ref.3}.		cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		CTCCTCGAAGGTCTTCAGGGC	0.612													g|||	4113	0.821286	0.4697	0.9135	5008	,	,		18768	0.9851		0.9453	False		,,,				2504	0.9346				p.T75I	GBM(132;1720 1771 5373 10277 21402)	Atlas-SNP	.											.	ECHS1	31	.	0			c.C224T						PASS	.	G	ILE/THR	2335,2069	598.3+/-389.1	620,1095,487	75.0	63.0	67.0		224	3.8	0.4	10	dbSNP_86	67	8084,514	791.8+/-407.5	3798,488,13	yes	missense	ECHS1	NM_004092.3	89	4418,1583,500	AA,AG,GG		5.9781,46.98,19.8662	benign	75/291	135184126	10419,2583	2202	4299	6501	SO:0001583	missense	1892	exon2			TCGAAGGTCTTCA		CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"""enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"""			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.224C>T	10.37:g.135184126G>A	ENSP00000357535:p.Thr75Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_004092	O00739|Q5VWY1|Q96H54	Missense_Mutation	SNP	ENST00000368547.3	37	CCDS7681.1	1846	0.8452380952380952	243	0.49390243902439024	323	0.8922651933701657	559	0.9772727272727273	721	0.9511873350923483	g	7.698	0.692430	0.15039	0.5302	0.940219	ENSG00000127884	ENST00000368547	T	0.68181	-0.31	5.76	3.82	0.43975	Crotonase, core (1);	0.789708	0.12303	N	0.480913	T	0.00012	0.0000	N	0.21583	0.68	0.80722	P	0.0	B	0.19935	0.04	B	0.24269	0.052	T	0.36744	-0.9735	9	0.44086	T	0.13	.	8.7834	0.34804	0.0789:0.0:0.7718:0.1493	rs1049951;rs2070199;rs2230259;rs3190160;rs7901604;rs17845190;rs17858001;rs56845656;rs1049951	75	P30084	ECHM_HUMAN	I	75	ENSP00000357535:T75I	ENSP00000357535:T75I	T	-	2	0	ECHS1	135034116	0.756000	0.28383	0.410000	0.26471	0.007000	0.05969	1.007000	0.29860	1.460000	0.47911	-0.131000	0.14894	ACC	G|0.189;A|0.811	0.811	strong		0.612	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1		
MIA3	375056	hgsc.bcm.edu	37	1	222802926	222802926	+	Silent	SNP	C	C	T	rs3008620	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:222802926C>T	ENST00000344922.5	+	4	2389	c.2364C>T	c.(2362-2364)agC>agT	p.S788S	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Silent_p.S788S|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	788					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		TTTTGGATAGCGAAAAAACAA	0.438													T|||	4009	0.800519	0.5711	0.9035	5008	,	,		18862	0.8899		0.8976	False		,,,				2504	0.8456				p.S788S		Atlas-SNP	.											.	MIA3	167	.	0			c.C2364T						PASS	.	T		2294,1442		698,898,272	64.0	59.0	61.0		2364	-1.4	0.0	1	dbSNP_101	61	7267,949		3221,825,62	no	coding-synonymous	MIA3	NM_198551.2		3919,1723,334	TT,TC,CC		11.5506,38.5974,20.005		788/1908	222802926	9561,2391	1868	4108	5976	SO:0001819	synonymous_variant	375056	exon4			GGATAGCGAAAAA		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.2364C>T	1.37:g.222802926C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Silent	SNP	ENST00000344922.5	37	CCDS41470.1	1813	0.8301282051282052	297	0.6036585365853658	323	0.8922651933701657	515	0.9003496503496503	678	0.8944591029023746	T	3.223	-0.159105	0.06544	0.614026	0.884494	ENSG00000154305	ENST00000354906	.	.	.	4.39	-1.42	0.08913	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5866	0.00721	0.3511:0.2136:0.11:0.3253	rs3008620;rs3748627;rs9441839;rs17163328	.	.	.	X	371	.	.	R	+	1	2	MIA3	220869549	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.003000	0.03682	-0.919000	0.03803	-0.521000	0.04368	CGA	C|0.150;T|0.850	0.850	strong		0.438	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
GATA3	2625	hgsc.bcm.edu	37	10	8100647	8100647	+	Silent	SNP	C	C	T	rs1778076|rs2229359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:8100647C>T	ENST00000346208.3	+	3	1076	c.621C>T	c.(619-621)gcC>gcT	p.A207A	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Silent_p.A207A			P23771	GATA3_HUMAN	GATA binding protein 3	207					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						GCATGACCGCCCTGGGTGGAG	0.677			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""						C|||	102	0.0203674	0.0015	0.0288	5008	,	,		14000	0.0		0.0716	False		,,,				2504	0.0082				p.A207A		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.C621T						PASS	.	C	,	66,4340	59.9+/-96.7	1,64,2138	81.0	73.0	76.0		621,621	0.3	1.0	10	dbSNP_98	76	649,7951	164.2+/-216.6	28,593,3679	no	coding-synonymous,coding-synonymous	GATA3	NM_001002295.1,NM_002051.2	,	29,657,5817	TT,TC,CC		7.5465,1.498,5.4975	,	207/445,207/444	8100647	715,12291	2203	4300	6503	SO:0001819	synonymous_variant	2625	exon3			GACCGCCCTGGGT	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.621C>T	10.37:g.8100647C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	37	CCDS7083.1																																																																																			C|0.956;T|0.044	0.044	strong		0.677	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295	
COA7	65260	hgsc.bcm.edu	37	1	53153432	53153432	+	Missense_Mutation	SNP	T	T	C	rs443751	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:53153432T>C	ENST00000371538.3	-	3	695	c.656A>G	c.(655-657)aAa>aGa	p.K219R	SELRC1_ENST00000486918.1_5'UTR	NM_023077.2	NP_075565.2												p.K219R(1)		breast(1)|lung(3)|prostate(1)|urinary_tract(1)	6						CTGCTGTTCTTTGTGTAGCTG	0.532													T|||	1056	0.210863	0.1611	0.2205	5008	,	,		19949	0.0139		0.3658	False		,,,				2504	0.3149				p.K219R		Atlas-SNP	.											SELRC1,NS,carcinoma,0,1	SELRC1	11	1	1	Substitution - Missense(1)	prostate(1)	c.A656G						PASS	.	T	ARG/LYS	879,3527	341.8+/-306.9	80,719,1404	165.0	144.0	152.0		656	5.6	1.0	1	dbSNP_80	152	3053,5547	468.3+/-367.3	539,1975,1786	yes	missense	SELRC1	NM_023077.2	26	619,2694,3190	CC,CT,TT		35.5,19.9501,30.2322	benign	219/232	53153432	3932,9074	2203	4300	6503	SO:0001583	missense	65260	exon3			TGTTCTTTGTGTA																												ENST00000371538.3:c.656A>G	1.37:g.53153432T>C	ENSP00000360593:p.Lys219Arg	Somatic	319	1	0.0031348		WXS	Illumina HiSeq	Phase_I	260	91	0.35	NM_023077		Missense_Mutation	SNP	ENST00000371538.3	37	CCDS570.1	447	0.20467032967032966	68	0.13821138211382114	94	0.2596685082872928	7	0.012237762237762238	278	0.36675461741424803	T	10.92	1.485729	0.26686	0.199501	0.355	ENSG00000162377	ENST00000371538	T	0.44482	0.92	5.55	5.55	0.83447	.	0.269500	0.43260	N	0.000598	T	0.00012	0.0000	L	0.29908	0.895	0.28440	P	0.9168529	B	0.12630	0.006	B	0.08055	0.003	T	0.40646	-0.9552	9	0.18276	T	0.48	-22.7937	8.2315	0.31601	0.0:0.1487:0.0:0.8513	rs443751;rs3174551;rs17845459;rs17858336;rs52795029;rs60837595;rs443751	219	Q96BR5	SELR1_HUMAN	R	219	ENSP00000360593:K219R	ENSP00000360593:K219R	K	-	2	0	SELRC1	52926020	.	.	1.000000	0.80357	0.608000	0.37181	.	.	2.123000	0.65237	0.449000	0.29647	AAA	T|0.745;C|0.255	0.255	strong		0.532	SELRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023462.1		
SH3TC2	79628	hgsc.bcm.edu	37	5	148407893	148407893	+	Missense_Mutation	SNP	C	C	A	rs6875902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:148407893C>A	ENST00000515425.1	-	11	1503	c.1402G>T	c.(1402-1404)Gcc>Tcc	p.A468S	SH3TC2_ENST00000512049.1_Missense_Mutation_p.A461S|SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000538184.1_Missense_Mutation_p.A15S|SH3TC2_ENST00000394358.2_Missense_Mutation_p.A353S	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	468			A -> S (in dbSNP:rs6875902). {ECO:0000269|PubMed:11853319, ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATATGGGGGCGAAGTTCTCA	0.502													C|||	983	0.196286	0.3351	0.1326	5008	,	,		21682	0.0198		0.2207	False		,,,				2504	0.2106				p.A468S		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G1402T						PASS	.	C	SER/ALA	1347,3059	446.5+/-348.0	212,923,1068	86.0	90.0	89.0		1402	0.8	0.0	5	dbSNP_116	89	1752,6848	317.0+/-313.0	170,1412,2718	yes	missense	SH3TC2	NM_024577.3	99	382,2335,3786	AA,AC,CC		20.3721,30.5719,23.8275	benign	468/1289	148407893	3099,9907	2203	4300	6503	SO:0001583	missense	79628	exon11			TGGGGGCGAAGTT	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"""Tetratricopeptide (TTC) repeat domain containing"""	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.1402G>T	5.37:g.148407893C>A	ENSP00000423660:p.Ala468Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	47	13	0.276596	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	37	CCDS4293.1	403	0.18452380952380953	154	0.3130081300813008	64	0.17679558011049723	16	0.027972027972027972	169	0.22295514511873352	C	4.539	0.100081	0.08731	0.305719	0.203721	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049;ENST00000394358	T;T;T;T	0.80304	-1.36;-0.93;-0.92;-0.56	6.03	0.802	0.18686	.	0.446910	0.23591	N	0.046555	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B;P;P;P	0.46395	0.129;0.877;0.877;0.877	B;B;B;B	0.40982	0.065;0.345;0.345;0.345	T	0.09796	-1.0658	9	0.18276	T	0.48	.	11.5415	0.50669	0.0:0.6777:0.0927:0.2296	rs6875902;rs52794538;rs58221348;rs6875902	353;461;468;468	C9JLC3;Q14CC0;E9PDF1;Q8TF17	.;.;.;S3TC2_HUMAN	S	15;468;461;353	ENSP00000441427:A15S;ENSP00000423660:A468S;ENSP00000421860:A461S;ENSP00000377886:A353S	ENSP00000377886:A353S	A	-	1	0	SH3TC2	148388086	0.808000	0.29022	0.006000	0.13384	0.123000	0.20343	0.945000	0.29056	-0.042000	0.13535	-0.797000	0.03246	GCC	C|0.784;A|0.216	0.216	strong		0.502	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
RPL7A	6130	hgsc.bcm.edu	37	9	136216882	136216882	+	Silent	SNP	G	G	A	rs7700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136216882G>A	ENST00000323345.6	+	4	420	c.390G>A	c.(388-390)acG>acA	p.T130T	SNORD36A_ENST00000362874.1_RNA|SNORD24_ENST00000383884.1_RNA|RPL7A_ENST00000463740.1_3'UTR|SNORD36B_ENST00000363961.1_RNA|RPL7A_ENST00000315731.4_Silent_p.T15T|MED22_ENST00000343730.5_5'Flank|MED22_ENST00000471524.1_5'Flank|SNORD36C_ENST00000516733.1_RNA|SURF1_ENST00000495952.1_5'Flank|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000476080.1_5'Flank|MED22_ENST00000344469.5_5'Flank|MED22_ENST00000371999.1_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	130					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		ACGTCCCAACGAAGAGACCAC	0.557													G|||	153	0.0305511	0.003	0.0389	5008	,	,		19124	0.0198		0.0795	False		,,,				2504	0.0225				p.T130T		Atlas-SNP	.											.	RPL7A	9	.	0			c.G390A						PASS	.	G		75,4331	66.4+/-103.9	1,73,2129	58.0	63.0	61.0		390	-8.4	0.8	9	dbSNP_52	61	706,7894	171.4+/-222.4	32,642,3626	no	coding-synonymous	RPL7A	NM_000972.2		33,715,5755	AA,AG,GG		8.2093,1.7022,6.0049		130/267	136216882	781,12225	2203	4300	6503	SO:0001819	synonymous_variant	6130	exon4			CCCAACGAAGAGA	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"""L ribosomal proteins"""	10364	protein-coding gene	gene with protein product	"""surfeit 3"", ""PLA-X polypeptide"", ""surfeit locus protein 3"", ""60S ribosomal protein L7a"", "";"", ""thyroid hormone receptor uncoupling protein"""	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.390G>A	9.37:g.136216882G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_000972	P11518|Q5T8U4	Silent	SNP	ENST00000323345.6	37	CCDS6965.1																																																																																			G|0.942;A|0.058	0.058	strong		0.557	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887433	9887433	+	Silent	SNP	A	A	G	rs2240907	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:9887433A>G	ENST00000306084.6	+	2	1156	c.957A>G	c.(955-957)gaA>gaG	p.E319E	TXNDC2_ENST00000536353.2_3'UTR|TXNDC2_ENST00000357775.5_Silent_p.E252E	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	319	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						AGTCCCCAGAAGAAGCCATCC	0.592													A|||	1247	0.249002	0.3472	0.1787	5008	,	,		20422	0.1508		0.2952	False		,,,				2504	0.2198				p.E319E		Atlas-SNP	.											.	TXNDC2	168	.	0			c.A957G						PASS	.	A	,	863,3541		192,479,1531	116.0	114.0	115.0		957,756	-1.1	0.0	18	dbSNP_98	115	1637,6961		282,1073,2944	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	474,1552,4475	GG,GA,AA		19.0393,19.5958,19.2278	,	319/554,252/487	9887433	2500,10502	2202	4299	6501	SO:0001819	synonymous_variant	84203	exon2			CCCAGAAGAAGCC	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.957A>G	18.37:g.9887433A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	98	33	0.336735	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			A|0.791;G|0.209	0.209	strong		0.592	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
LAMA5	3911	hgsc.bcm.edu	37	20	60908969	60908969	+	Missense_Mutation	SNP	T	T	C	rs13042941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60908969T>C	ENST00000252999.3	-	23	2932	c.2866A>G	c.(2866-2868)Acc>Gcc	p.T956A	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	956	Domain IV 1 (domain IV B).			T -> A (in Ref. 1; AAM12527). {ECO:0000305}.	angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TTGGCGCAGGTGGCCGACCTG	0.692													c|||	3612	0.721246	0.3109	0.7983	5008	,	,		8279	0.9355		0.9155	False		,,,				2504	0.8006				p.T956A		Atlas-SNP	.											.	LAMA5	268	.	0			c.A2866G						PASS	.		ALA/THR	1812,2576		428,956,810	24.0	17.0	19.0		2866	-2.0	0.0	20	dbSNP_121	19	7857,683		3656,545,69	yes	missense	LAMA5	NM_005560.3	58	4084,1501,879	CC,CT,TT		7.9977,41.2944,25.2088	benign	956/3696	60908969	9669,3259	2194	4270	6464	SO:0001583	missense	3911	exon23			CGCAGGTGGCCGA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.2866A>G	20.37:g.60908969T>C	ENSP00000252999:p.Thr956Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	1678	0.7683150183150184	167	0.3394308943089431	291	0.8038674033149171	537	0.9388111888111889	683	0.9010554089709762	c	0.139	-1.104490	0.01828	0.412944	0.920023	ENSG00000130702	ENST00000252999	T	0.18657	2.2	4.83	-1.97	0.07503	.	0.650169	0.15381	N	0.265331	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40831	-0.9542	9	0.06494	T	0.89	.	14.6204	0.68579	0.0:0.4929:0.0:0.5071	rs13042941	956	O15230	LAMA5_HUMAN	A	956	ENSP00000252999:T956A	ENSP00000252999:T956A	T	-	1	0	LAMA5	60342364	0.074000	0.21230	0.004000	0.12327	0.052000	0.14988	-0.029000	0.12329	-0.784000	0.04528	-1.085000	0.02201	ACC	T|0.272;C|0.728	0.728	strong		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43636484	43636484	+	Silent	SNP	C	C	G	rs1049276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43636484C>G	ENST00000236051.2	-	4	531	c.390G>C	c.(388-390)acG>acC	p.T130T	EBNA1BP2_ENST00000431635.2_Silent_p.T185T|WDR65_ENST00000372492.4_5'Flank|WDR65_ENST00000528956.1_5'Flank|EBNA1BP2_ENST00000472982.1_5'Flank	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	130					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGGGTCGCTTCGTAGGGACTT	0.473													G|||	705	0.140775	0.1278	0.1513	5008	,	,		20277	0.0		0.2883	False		,,,				2504	0.1442				p.T185T		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.G555C						PASS	.	G	,	526,3880	778.0+/-414.3	31,464,1708	168.0	164.0	166.0		555,390	-1.3	0.9	1	dbSNP_86	166	2216,6384	710.4+/-405.8	292,1632,2376	no	coding-synonymous,coding-synonymous	EBNA1BP2	NM_001159936.1,NM_006824.2	,	323,2096,4084	GG,GC,CC		25.7674,11.9383,21.0826	,	185/362,130/307	43636484	2742,10264	2203	4300	6503	SO:0001819	synonymous_variant	10969	exon5			TCGCTTCGTAGGG	U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"""EBNA1-binding protein 2"""			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.390G>C	1.37:g.43636484C>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	37	CCDS478.1																																																																																			C|0.799;G|0.201	0.201	strong		0.473	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1		
ECE2	9718	hgsc.bcm.edu	37	3	183994447	183994447	+	Intron	SNP	C	C	T	rs13063766	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183994447C>T	ENST00000402825.3	+	3	480				EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000357474.5_Missense_Mutation_p.T73I|ECE2_ENST00000404464.3_Intron|ECE2_ENST00000359140.4_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2						brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGGAGGGTCACCTGCCCCCAC	0.622													C|||	106	0.0211661	0.0023	0.0346	5008	,	,		16846	0.0		0.0408	False		,,,				2504	0.0389				p.T73I		Atlas-SNP	.											.	ECE2	303	.	0			c.C218T						PASS	.	C	,ILE/THR,,	23,4177		1,21,2078	19.0	21.0	20.0		,218,,	1.4	0.0	3	dbSNP_121	20	238,8178		6,226,3976	yes	intron,missense,intron,intron	ECE2	NM_001037324.2,NM_001100120.1,NM_001100121.1,NM_014693.3	,89,,	7,247,6054	TT,TC,CC		2.8279,0.5476,2.0688	,,,	,73/812,,	183994447	261,12355	2100	4208	6308	SO:0001627	intron_variant	9718	exon2			GGGTCACCTGCCC	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.481-233C>T	3.37:g.183994447C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	91	53	0.582418	NM_001100120	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	48	0.02197802197802198	1	0.0020325203252032522	15	0.04143646408839779	0	0.0	32	0.04221635883905013	C	16.14	3.039338	0.55003	0.005476	0.028279	ENSG00000145194	ENST00000357474;ENST00000430587	D;T	0.81908	-1.55;-1.26	3.22	1.36	0.22044	.	3.528980	0.02380	U	0.078724	T	0.38026	0.1025	N	0.08118	0	0.19300	N	0.999975	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.50882	-0.8775	10	0.33940	T	0.23	.	8.484	0.33061	0.0:0.7903:0.0:0.2097	rs13063766	73;73	B7Z1P1;O60344-5	.;.	I	73;19	ENSP00000350066:T73I;ENSP00000398444:T19I	ENSP00000350066:T73I	T	+	2	0	ECE2	185477141	0.912000	0.30974	0.046000	0.18839	0.943000	0.58893	0.900000	0.28431	0.344000	0.23847	0.462000	0.41574	ACC	C|0.977;T|0.023	0.023	strong		0.622	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
METTL2A	339175	hgsc.bcm.edu	37	17	60525113	60525113	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:60525113A>C	ENST00000311506.5	+	8	1004	c.968A>C	c.(967-969)tAc>tCc	p.Y323S		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	323					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(2)|central_nervous_system(1)|endometrium(1)|upper_aerodigestive_tract(2)	6			BRCA - Breast invasive adenocarcinoma(2;1.08e-10)			ACCAGAGTTTACTTCTTCACA	0.408																																					p.Y323S		Atlas-SNP	.											.	METTL2A	31	.	0			c.A968C						PASS	.						268.0	272.0	271.0					17																	60525113		2203	4300	6503	SO:0001583	missense	339175	exon8			GAGTTTACTTCTT	AK000991	CCDS45752.1	17q23.3	2012-12-20		2006-02-10	ENSG00000087995	ENSG00000087995			25755	protein-coding gene	gene with protein product						12477932	Standard	NM_181725		Approved	FLJ12760, METTL2	uc002izv.2	Q96IZ6	OTTHUMG00000164527	ENST00000311506.5:c.968A>C	17.37:g.60525113A>C	ENSP00000309610:p.Tyr323Ser	Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	274	134	0.489051	NM_181725	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Missense_Mutation	SNP	ENST00000311506.5	37	CCDS45752.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.102365	0.76983	.	.	ENSG00000087995	ENST00000311506	T	0.11821	2.74	4.26	4.26	0.50523	.	0.056321	0.64402	D	0.000001	T	0.50137	0.1598	H	0.97415	4	0.80722	D	1	D	0.69078	0.997	D	0.74348	0.983	T	0.66590	-0.5885	10	0.87932	D	0	-0.4554	11.69	0.51510	1.0:0.0:0.0:0.0	.	323	Q96IZ6	MTL2A_HUMAN	S	323	ENSP00000309610:Y323S	ENSP00000309610:Y323S	Y	+	2	0	METTL2A	57878845	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.901000	0.92560	1.712000	0.51347	0.397000	0.26171	TAC	.	.	none		0.408	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445130.1	NM_181725	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847050	100847050	+	Silent	SNP	A	A	G	rs569270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100847050A>G	ENST00000298815.8	+	20	2121	c.2118A>G	c.(2116-2118)tcA>tcG	p.S706S	ARHGAP42_ENST00000524892.2_Silent_p.S672S	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	706	Ser-rich.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						GTGTTGCTTCAGTCACTAGCC	0.478													G|||	2805	0.560104	0.2027	0.6009	5008	,	,		21556	0.997		0.4344	False		,,,				2504	0.6933				p.S706S		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A2118G						PASS	.	G		423,961		64,295,333	73.0	55.0	61.0		2118	-11.4	0.0	11	dbSNP_83	61	1402,1780		313,776,502	no	coding-synonymous	ARHGAP42	NM_152432.2		377,1071,835	GG,GA,AA		44.0603,30.5636,39.9693		706/875	100847050	1825,2741	692	1591	2283	SO:0001819	synonymous_variant	143872	exon20			TGCTTCAGTCACT			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2118A>G	11.37:g.100847050A>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	175	74	0.422857	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.479;G|0.521	0.521	strong		0.478	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
CASQ1	844	hgsc.bcm.edu	37	1	160162591	160162591	+	Splice_Site	SNP	G	G	C	rs145486953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:160162591G>C	ENST00000368078.3	+	2	475		c.e2-1		CASQ1_ENST00000368079.3_Splice_Site			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)						endoplasmic reticulum organization (GO:0007029)|ion transmembrane transport (GO:0034220)|protein polymerization (GO:0051258)|regulation of sequestering of calcium ion (GO:0051282)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to heat (GO:0009408)|response to organic substance (GO:0010033)|sarcomere organization (GO:0045214)|skeletal muscle tissue development (GO:0007519)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna lumen (GO:0014804)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTTCCCTCCAGTTAGCAGCCC	0.488											OREG0013927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3	0.000599042	0.0	0.0	5008	,	,		16886	0.0		0.003	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CASQ1	55	.	0			c.280-1G>C						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	115.0	123.0	121.0			4.5	1.0	1	dbSNP_134	121	19,8581	14.0+/-48.4	0,19,4281	yes	splice-3	CASQ1	NM_001231.4		0,20,6483	CC,CG,GG		0.2209,0.0227,0.1538			160162591	20,12986	2203	4300	6503	SO:0001630	splice_region_variant	844	exon2			CCTCCAGTTAGCA	S73775	CCDS1198.1, CCDS1198.2	1q21	2011-10-19			ENSG00000143318	ENSG00000143318		"""Protein disulfide isomerases"""	1512	protein-coding gene	gene with protein product	"""calsequestrin 1, fast-twitch, skeletal muscle"", ""calmitine"""	114250		CASQ		8406504, 2321095	Standard	NM_001231		Approved	PDIB1	uc010pja.2	P31415	OTTHUMG00000031607	ENST00000368078.3:c.280-1G>C	1.37:g.160162591G>C		Somatic	117	0	0	1806	WXS	Illumina HiSeq	Phase_I	144	51	0.354167	NM_001231	B1AKZ2|B2R863|Q8TBW7	Splice_Site	SNP	ENST00000368078.3	37	CCDS1198.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.18	3.566858	0.65651	2.27E-4	0.002209	ENSG00000143318	ENST00000368079;ENST00000368078	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2739	0.82634	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CASQ1	158429215	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.990000	0.93510	2.358000	0.79984	0.449000	0.29647	.	G|0.998;C|0.002	0.002	strong		0.488	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231	Intron
CRISPLD2	83716	hgsc.bcm.edu	37	16	84883102	84883102	+	Silent	SNP	C	C	T	rs8061351	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84883102C>T	ENST00000262424.5	+	4	695	c.471C>T	c.(469-471)ccC>ccT	p.P157P	CRISPLD2_ENST00000566431.1_3'UTR|CRISPLD2_ENST00000567845.1_Silent_p.P157P|CRISPLD2_ENST00000564567.1_Silent_p.P157P	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	157	SCP.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						GCTCGGGGCCCATGTGCACGC	0.622													C|||	2974	0.59385	0.2882	0.6484	5008	,	,		16035	0.6786		0.7326	False		,,,				2504	0.7382				p.P157P		Atlas-SNP	.											.	CRISPLD2	36	.	0			c.C471T						PASS	.	C		1502,2896	478.3+/-358.2	243,1016,940	121.0	99.0	106.0		471	4.7	1.0	16	dbSNP_116	106	6352,2248	708.1+/-405.6	2355,1642,303	no	coding-synonymous	CRISPLD2	NM_031476.3		2598,2658,1243	TT,TC,CC		26.1395,34.1519,39.5753		157/498	84883102	7854,5144	2199	4300	6499	SO:0001819	synonymous_variant	83716	exon4			GGGGCCCATGTGC	AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"""LCCL domain containing cysteine-rich secretory protein 2"""	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.471C>T	16.37:g.84883102C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Silent	SNP	ENST00000262424.5	37	CCDS10949.1																																																																																			C|0.398;T|0.602	0.602	strong		0.622	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206905043	206905043	+	Silent	SNP	C	C	T	rs4073250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206905043C>T	ENST00000367103.3	+	8	1144	c.951C>T	c.(949-951)acC>acT	p.T317T	MAPKAPK2_ENST00000294981.4_Silent_p.T317T|MAPKAPK2_ENST00000479009.1_3'UTR	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	317	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			TGACCATCACCGAGTTTATGA	0.562													C|||	979	0.195487	0.1838	0.1729	5008	,	,		18715	0.0526		0.2137	False		,,,				2504	0.3558				p.T317T		Atlas-SNP	.											.	MAPKAPK2	45	.	0			c.C951T						PASS	.	C	,	847,3559	334.9+/-303.7	95,657,1451	132.0	131.0	131.0		951,951	-10.2	0.0	1	dbSNP_108	131	1652,6948	305.2+/-307.3	168,1316,2816	no	coding-synonymous,coding-synonymous	MAPKAPK2	NM_004759.4,NM_032960.3	,	263,1973,4267	TT,TC,CC		19.2093,19.2238,19.2142	,	317/371,317/401	206905043	2499,10507	2203	4300	6503	SO:0001819	synonymous_variant	9261	exon8			CATCACCGAGTTT	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.951C>T	1.37:g.206905043C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	209	105	0.502392	NM_004759	Q5SY30|Q5SY41|Q8IYD6	Silent	SNP	ENST00000367103.3	37	CCDS31001.1																																																																																			C|0.820;T|0.180	0.180	strong		0.562	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759	
C16orf89	146556	hgsc.bcm.edu	37	16	5106184	5106184	+	Silent	SNP	C	C	T	rs741164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:5106184C>T	ENST00000315997.5	-	5	834	c.633G>A	c.(631-633)ggG>ggA	p.G211G	C16orf89_ENST00000474471.3_Silent_p.G211G|C16orf89_ENST00000350219.4_Silent_p.G249G|C16orf89_ENST00000422873.1_Silent_p.G249G|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000472572.3_Silent_p.G211G	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	211						cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	12						CCTGTGTGCACCCCCTCTGGG	0.547													T|||	2619	0.522963	0.3971	0.6398	5008	,	,		15812	0.5665		0.6292	False		,,,				2504	0.456				p.G211G		Atlas-SNP	.											.	C16orf89	64	.	0			c.G633A						PASS	.	T	,	1976,2308		475,1026,641	99.0	103.0	102.0		633,633	-11.4	0.0	16	dbSNP_86	102	5301,3219		1655,1991,614	no	coding-synonymous,coding-synonymous	C16orf89	NM_001098514.2,NM_152459.4	,	2130,3017,1255	TT,TC,CC		37.7817,46.1251,43.1662	,	211/362,211/403	5106184	7277,5527	2142	4260	6402	SO:0001819	synonymous_variant	146556	exon5			TGTGCACCCCCTC		CCDS42116.1, CCDS45404.1, CCDS42116.2, CCDS45404.2	16p13.3	2011-12-12			ENSG00000153446	ENSG00000153446			28687	protein-coding gene	gene with protein product						12975309, 20578903	Standard	NM_001098514		Approved	MGC45438	uc010bud.3	Q6UX73	OTTHUMG00000159314	ENST00000315997.5:c.633G>A	16.37:g.5106184C>T		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Silent	SNP	ENST00000315997.5	37	CCDS42116.2																																																																																			C|0.432;T|0.568	0.568	strong		0.547	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459	
SGCG	6445	hgsc.bcm.edu	37	13	23824818	23824818	+	Missense_Mutation	SNP	G	G	A	rs17314986	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:23824818G>A	ENST00000218867.3	+	4	471	c.347G>A	c.(346-348)cGc>cAc	p.R116H	SGCG_ENST00000545013.1_Missense_Mutation_p.R116H|SGCG_ENST00000537476.1_Missense_Mutation_p.R116H	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	116			R -> H (in dbSNP:rs17314986). {ECO:0000269|PubMed:8900232}.		muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		GTAAATGCGCGCAACTCAGAA	0.403													G|||	388	0.077476	0.0098	0.0951	5008	,	,		15833	0.0159		0.1481	False		,,,				2504	0.1472				p.R116H		Atlas-SNP	.											SGCG,colon,carcinoma,+1,1	SGCG	64	1	0			c.G347A						PASS	.	G	HIS/ARG	134,4272	97.6+/-136.3	2,130,2071	113.0	95.0	101.0		347	3.5	0.1	13	dbSNP_123	101	1198,7402	242.9+/-272.7	73,1052,3175	yes	missense	SGCG	NM_000231.2	29	75,1182,5246	AA,AG,GG		13.9302,3.0413,10.2414	probably-damaging	116/292	23824818	1332,11674	2203	4300	6503	SO:0001583	missense	6445	exon4			ATGCGCGCAACTC	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.347G>A	13.37:g.23824818G>A	ENSP00000218867:p.Arg116His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_000231	Q32M32|Q5T9J6	Missense_Mutation	SNP	ENST00000218867.3	37	CCDS9299.1	172	0.07875457875457875	6	0.012195121951219513	45	0.12430939226519337	10	0.017482517482517484	111	0.14643799472295516	G	12.50	1.955947	0.34471	0.030413	0.139302	ENSG00000102683	ENST00000218867;ENST00000537476;ENST00000545013	D;D;D	0.95853	-3.83;-3.83;-3.83	5.22	3.49	0.39957	.	0.048036	0.85682	D	0.000000	T	0.19366	0.0465	M	0.87682	2.9	0.35155	P	0.22989000000000004	D	0.63880	0.993	P	0.59012	0.85	T	0.59547	-0.7434	9	0.40728	T	0.16	-3.0208	8.023	0.30421	0.1885:0.0:0.8115:0.0	rs17314986;rs17314986	116	Q13326	SGCG_HUMAN	H	116	ENSP00000218867:R116H;ENSP00000444100:R116H;ENSP00000442232:R116H	ENSP00000218867:R116H	R	+	2	0	SGCG	22722818	0.877000	0.30153	0.149000	0.22428	0.002000	0.02628	2.679000	0.46909	0.603000	0.29913	-0.136000	0.14681	CGC	G|0.910;A|0.090	0.090	strong		0.403	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
NRROS	375387	hgsc.bcm.edu	37	3	196388099	196388099	+	Missense_Mutation	SNP	G	G	C	rs62623661	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:196388099G>C	ENST00000328557.4	+	3	1788	c.1585G>C	c.(1585-1587)Gcg>Ccg	p.A529P		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	529					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CAGCTTTATGGCGTTGGACTT	0.582													G|||	242	0.0483227	0.0083	0.0836	5008	,	,		18830	0.0		0.1392	False		,,,				2504	0.0337				p.A529P		Atlas-SNP	.											LRRC33,colon,carcinoma,-1,2	LRRC33	91	2	0			c.G1585C						PASS	.	G	PRO/ALA	117,4289	87.3+/-125.9	4,109,2090	127.0	125.0	126.0		1585	3.2	0.0	3	dbSNP_129	126	1093,7507	229.3+/-264.0	64,965,3271	yes	missense	LRRC33	NM_198565.1	27	68,1074,5361	CC,CG,GG		12.7093,2.6555,9.3034	benign	529/693	196388099	1210,11796	2203	4300	6503	SO:0001583	missense	375387	exon3			TTTATGGCGTTGG	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"""leucine rich repeat containing 33"""	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1585G>C	3.37:g.196388099G>C	ENSP00000328625:p.Ala529Pro	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	208	129	0.620192	NM_198565		Missense_Mutation	SNP	ENST00000328557.4	37	CCDS3319.1	126	0.057692307692307696	7	0.014227642276422764	28	0.07734806629834254	0	0.0	91	0.12005277044854881	G	2.087	-0.409399	0.04799	0.026555	0.127093	ENSG00000174004	ENST00000328557	T	0.52057	0.68	5.97	3.23	0.37069	.	0.288824	0.37095	N	0.002260	T	0.00241	0.0007	N	0.08118	0	0.18873	N	0.999988	B	0.20550	0.046	B	0.17722	0.019	T	0.05632	-1.0873	10	0.31617	T	0.26	.	6.9554	0.24568	0.2497:0.0:0.6374:0.1128	rs62623661	529	Q86YC3	LRC33_HUMAN	P	529	ENSP00000328625:A529P	ENSP00000328625:A529P	A	+	1	0	LRRC33	197872496	0.783000	0.28701	0.009000	0.14445	0.012000	0.07955	1.444000	0.35068	0.877000	0.35895	-0.137000	0.14449	GCG	G|0.915;C|0.085	0.085	strong		0.582	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565	
KIAA1614	57710	hgsc.bcm.edu	37	1	180897569	180897569	+	Silent	SNP	C	C	T	rs3747958	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180897569C>T	ENST00000367588.4	+	4	1120	c.1065C>T	c.(1063-1065)acC>acT	p.T355T	KIAA1614_ENST00000367587.1_5'UTR	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	355										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						GCTGCAGGACCGTTGGTCCCA	0.637													C|||	1953	0.389976	0.2731	0.4063	5008	,	,		16840	0.5516		0.4135	False		,,,				2504	0.3456				p.T355T		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C1065T						PASS	.	C		1136,2920		167,802,1059	111.0	116.0	114.0		1065	5.4	1.0	1	dbSNP_107	114	3433,4953		709,2015,1469	no	coding-synonymous	KIAA1614	NM_020950.1		876,2817,2528	TT,TC,CC		40.9373,28.0079,36.7224		355/1191	180897569	4569,7873	2028	4193	6221	SO:0001819	synonymous_variant	57710	exon4			CAGGACCGTTGGT	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.1065C>T	1.37:g.180897569C>T		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	242	242	1	NM_020950	Q5VZ45|Q9HCF8	Silent	SNP	ENST00000367588.4	37	CCDS41442.1																																																																																			C|0.600;T|0.400	0.400	strong		0.637	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
ABCA7	10347	hgsc.bcm.edu	37	19	1056065	1056065	+	Splice_Site	SNP	A	A	G	rs881768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1056065A>G	ENST00000263094.6	+	32	4470	c.4239A>G	c.(4237-4239)agA>agG	p.R1413R	ABCA7_ENST00000435683.2_Splice_Site_p.R1275R|ABCA7_ENST00000433129.1_Splice_Site_p.R1413R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1413					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCCCCACAGATACGGAGGCT	0.716													G|||	2214	0.442093	0.5393	0.4265	5008	,	,		12724	0.3552		0.4195	False		,,,				2504	0.4346				p.R1413R		Atlas-SNP	.											.	ABCA7	174	.	0			c.A4239G						PASS	.	G		2320,2082		606,1108,487	26.0	30.0	29.0		4239	0.5	0.4	19	dbSNP_86	29	3650,4944		777,2096,1424	no	coding-synonymous-near-splice	ABCA7	NM_019112.3		1383,3204,1911	GG,GA,AA		42.4715,47.2967,45.9372		1413/2147	1056065	5970,7026	2201	4297	6498	SO:0001630	splice_region_variant	10347	exon32			CCACAGATACGGA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.4239-1A>G	19.37:g.1056065A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			A|0.536;G|0.464	0.464	strong		0.716	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	Silent
AQP12A	375318	hgsc.bcm.edu	37	2	241631413	241631413	+	Missense_Mutation	SNP	T	T	G	rs71428454	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:241631413T>G	ENST00000337801.4	+	1	152	c.83T>G	c.(82-84)cTg>cGg	p.L28R	AQP12A_ENST00000429564.1_Missense_Mutation_p.L28R|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	28						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		TCCAAGGCCCTGCTCCCAGTG	0.692													t|||	1001	0.19988	0.1989	0.3242	5008	,	,		17103	0.0357		0.3519	False		,,,				2504	0.1258				p.L28R		Atlas-SNP	.											AQP12A,caecum,carcinoma,0,1	AQP12A	32	1	0			c.T83G						PASS	.						40.0	47.0	45.0					2																	241631413		2180	4285	6465	SO:0001583	missense	375318	exon1			AGGCCCTGCTCCC	AB040748		2q37.3	2013-06-03	2005-05-26	2005-05-26	ENSG00000184945	ENSG00000184945		"""Ion channels / Aquaporins"""	19941	protein-coding gene	gene with protein product		609789	"""aquaporin 12"""	AQP12			Standard	NM_198998		Approved		uc002vzu.3	Q8IXF9	OTTHUMG00000183906	ENST00000337801.4:c.83T>G	2.37:g.241631413T>G	ENSP00000337144:p.Leu28Arg	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	110	36	0.327273	NM_198998		Missense_Mutation	SNP	ENST00000337801.4	37		457|457	0.20924908424908426|0.20924908424908426	95|95	0.19308943089430894|0.19308943089430894	110|110	0.30386740331491713|0.30386740331491713	18|18	0.03146853146853147|0.03146853146853147	234|234	0.3087071240105541|0.3087071240105541	.|.	3.061|3.061	-0.193201|-0.193201	0.06259|0.06259	.|.	.|.	ENSG00000184945|ENSG00000184945	ENST00000420599|ENST00000337801;ENST00000429564	.|T;T	.|0.11385	.|2.78;2.78	2.43|2.43	2.43|2.43	0.29744|0.29744	.|.	.|0.166965	.|0.42682	.|D	.|0.000664	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.62723|0.62723	1.935|1.935	0.25432|0.25432	P|P	0.9881739|0.9881739	.|D	.|0.67145	.|0.996	.|P	.|0.57548	.|0.823	T|T	0.38457|0.38457	-0.9660|-0.9660	5|9	0.87932|0.66056	D|D	0|0.02	-20.1652|-20.1652	8.4076|8.4076	0.32625|0.32625	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|28	.|Q8IXF9	.|AQ12A_HUMAN	G|R	1|28	.|ENSP00000337144:L28R;ENSP00000405899:L28R	ENSP00000399666:C1G|ENSP00000337144:L28R	C|L	+|+	1|2	0|0	AQP12A|AQP12A	241280086|241280086	0.134000|0.134000	0.22483|0.22483	0.878000|0.878000	0.34440|0.34440	0.334000|0.334000	0.28698|0.28698	1.538000|1.538000	0.36094|0.36094	1.134000|1.134000	0.42165|0.42165	0.156000|0.156000	0.16432|0.16432	TGC|CTG	T|0.790;G|0.210	0.210	strong		0.692	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
EPHA5	2044	hgsc.bcm.edu	37	4	66197804	66197804	+	Silent	SNP	C	C	T	rs7349683	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:66197804C>T	ENST00000273854.3	-	17	3495	c.2895G>A	c.(2893-2895)ggG>ggA	p.G965G	EPHA5_ENST00000432638.2_Silent_p.G802G|EPHA5_ENST00000511294.1_Silent_p.G966G|EPHA5_ENST00000354839.4_Silent_p.G943G	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	965	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						ATCTGTAGGCCCCAGATCCTA	0.368										TSP Lung(17;0.13)			C|||	1636	0.326677	0.0893	0.3098	5008	,	,		15856	0.4613		0.3748	False		,,,				2504	0.4714				p.G965G		Atlas-SNP	.											.	EPHA5	315	.	0			c.G2895A						PASS	.	C	,	607,3799	264.1+/-265.8	44,519,1640	75.0	69.0	71.0		2895,2829	3.7	1.0	4	dbSNP_116	71	3073,5527	471.0+/-368.0	550,1973,1777	no	coding-synonymous,coding-synonymous	EPHA5	NM_004439.5,NM_182472.2	,	594,2492,3417	TT,TC,CC		35.7326,13.7767,28.2946	,	965/1038,943/1016	66197804	3680,9326	2203	4300	6503	SO:0001819	synonymous_variant	2044	exon17			GTAGGCCCCAGAT	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2895G>A	4.37:g.66197804C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_004439	Q7Z3F2	Silent	SNP	ENST00000273854.3	37	CCDS3513.1																																																																																			C|0.704;T|0.296	0.296	strong		0.368	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
ANKMY1	51281	hgsc.bcm.edu	37	2	241496770	241496770	+	Splice_Site	SNP	C	C	A	rs62621191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:241496770C>A	ENST00000391987.1	-	2	83		c.e2-1		ANKMY1_ENST00000403283.1_Splice_Site|ANKMY1_ENST00000272972.3_Intron|ANKMY1_ENST00000401804.1_Splice_Site|ANKMY1_ENST00000373320.4_Splice_Site|ANKMY1_ENST00000361678.4_Splice_Site|ANKMY1_ENST00000373318.2_Splice_Site|DUSP28_ENST00000343217.2_5'Flank|ANKMY1_ENST00000406958.1_Splice_Site|ANKMY1_ENST00000405523.3_Splice_Site|DUSP28_ENST00000405954.1_5'Flank|ANKMY1_ENST00000462004.1_Intron|ANKMY1_ENST00000405002.1_Intron|ANKMY1_ENST00000536462.1_Intron	NM_001282771.1	NP_001269700.1	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1								metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		GTCTTCCAACCTGCAAGCGAC	0.687													C|||	388	0.077476	0.062	0.1095	5008	,	,		12495	0.0099		0.1511	False		,,,				2504	0.0695				.		Atlas-SNP	.											.	ANKMY1	112	.	0			.						PASS	.	C	,	332,4074	175.9+/-205.1	15,302,1886	65.0	61.0	62.0		,	2.5	0.1	2	dbSNP_129	62	1297,7303	257.0+/-281.3	97,1103,3100	yes	intron,splice-3	ANKMY1	NM_016552.2,NM_017844.2	,	112,1405,4986	AA,AC,CC		15.0814,7.5352,12.525	,	,	241496770	1629,11377	2203	4300	6503	SO:0001630	splice_region_variant	51281	.			TCCAACCTGCAAG	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000391987.1:c.284-1G>T	2.37:g.241496770C>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	56	36	0.642857	.	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Splice_Site	SNP	ENST00000391987.1	37	CCDS2536.1	192	0.08791208791208792	31	0.06300813008130081	44	0.12154696132596685	6	0.01048951048951049	111	0.14643799472295516	C	7.819	0.717388	0.15372	0.075352	0.150814	ENSG00000144504	ENST00000403283	.	.	.	2.5	2.5	0.30297	.	.	.	.	.	.	.	.	.	.	.	0.34875	P	0.25601700000000005	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.5999	0.33738	0.0:1.0:0.0:0.0	rs62621191	.	.	.	.	-1	.	.	.	-	.	.	ANKMY1	241145443	0.928000	0.31464	0.128000	0.21923	0.006000	0.05464	1.406000	0.34646	1.704000	0.51252	0.467000	0.42956	.	C|0.883;A|0.117	0.117	strong		0.687	ANKMY1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017844	Intron
TFAP2C	7022	hgsc.bcm.edu	37	20	55206401	55206401	+	Silent	SNP	C	C	G	rs140675668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55206401C>G	ENST00000201031.2	+	2	432	c.189C>G	c.(187-189)ccC>ccG	p.P63P	TFAP2C_ENST00000544508.1_5'UTR	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	63	Gln/Pro-rich (transactivation domain).				cell-cell signaling (GO:0007267)|cerebral cortex development (GO:0021987)|dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis (GO:0060598)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|forebrain neuron fate commitment (GO:0021877)|germ-line stem cell maintenance (GO:0030718)|hair follicle development (GO:0001942)|keratinocyte development (GO:0003334)|male gonad development (GO:0008584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sebaceous gland development (GO:0048733)|somatic stem cell maintenance (GO:0035019)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			TTCCCCCTCCCTACCAGCAGC	0.697													C|||	29	0.00579073	0.0	0.0187	5008	,	,		11402	0.0		0.0139	False		,,,				2504	0.002				p.P63P		Atlas-SNP	.											.	TFAP2C	51	.	0			c.C189G						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	33.0	33.0	33.0		189	-1.6	0.5	20	dbSNP_134	33	93,8507	48.5+/-108.0	1,91,4208	no	coding-synonymous	TFAP2C	NM_003222.3		1,96,6406	GG,GC,CC		1.0814,0.1135,0.7535		63/451	55206401	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	7022	exon2			CCCTCCCTACCAG		CCDS13454.1	20q13.2	2008-07-17	2001-11-28		ENSG00000087510	ENSG00000087510			11744	protein-coding gene	gene with protein product	"""estrogen receptor factor 1"""	601602	"""transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma)"""			8661133	Standard	NM_003222		Approved	AP2-GAMMA, ERF1, TFAP2G, hAP-2g	uc002xya.3	Q92754	OTTHUMG00000032805	ENST00000201031.2:c.189C>G	20.37:g.55206401C>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	175	89	0.508571	NM_003222	B4DWK3|O00685|O00730|Q86V30|Q8IVB6|Q9P1X2	Silent	SNP	ENST00000201031.2	37	CCDS13454.1																																																																																			C|0.994;G|0.006	0.006	strong		0.697	TFAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079823.2	NM_003222	
CHIA	27159	hgsc.bcm.edu	37	1	111857951	111857951	+	Missense_Mutation	SNP	A	A	G	rs61756687	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111857951A>G	ENST00000369740.1	+	6	477	c.374A>G	c.(373-375)aAa>aGa	p.K125R	RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.K125R|CHIA_ENST00000451398.2_5'UTR|CHIA_ENST00000430615.1_Missense_Mutation_p.K17R|CHIA_ENST00000353665.6_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	125			K -> R (in dbSNP:rs61756687). {ECO:0000269|PubMed:19435888}.		apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TCAGTCATCAAATTCCTGCGC	0.542													A|||	331	0.0660942	0.0234	0.0677	5008	,	,		18683	0.0228		0.1382	False		,,,				2504	0.093				p.K125R		Atlas-SNP	.											.	CHIA	115	.	0			c.A374G						PASS	.	A	ARG/LYS,ARG/LYS	200,4206	124.9+/-162.1	3,194,2006	118.0	114.0	115.0		50,374	-0.8	1.0	1	dbSNP_129	115	1262,7338	251.4+/-277.9	82,1098,3120	yes	missense,missense	CHIA	NM_021797.2,NM_201653.2	26,26	85,1292,5126	GG,GA,AA		14.6744,4.5393,11.241	benign,benign	17/369,125/477	111857951	1462,11544	2203	4300	6503	SO:0001583	missense	27159	exon6			TCATCAAATTCCT	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.374A>G	1.37:g.111857951A>G	ENSP00000358755:p.Lys125Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	149	0.06822344322344322	13	0.026422764227642278	25	0.06906077348066299	3	0.005244755244755245	108	0.1424802110817942	A	11.51	1.659340	0.29515	0.045393	0.146744	ENSG00000134216	ENST00000422815;ENST00000369740;ENST00000343320;ENST00000430615	T;T;T;T	0.05717	3.4;3.4;3.4;3.4	4.72	-0.796	0.10912	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.144833	0.43579	N	0.000544	T	0.01489	0.0048	L	0.42529	1.33	0.09310	P	0.99999999764018	B	0.09022	0.002	B	0.15484	0.013	T	0.45425	-0.9262	9	0.29301	T	0.29	-10.7027	4.8	0.13292	0.5206:0.3028:0.1766:0.0	rs61756687	125	Q9BZP6	CHIA_HUMAN	R	69;125;125;17	ENSP00000387671:K69R;ENSP00000358755:K125R;ENSP00000341828:K125R;ENSP00000391132:K17R	ENSP00000341828:K125R	K	+	2	0	CHIA	111659474	0.921000	0.31238	0.991000	0.47740	0.748000	0.42578	0.251000	0.18257	-0.016000	0.14127	0.533000	0.62120	AAA	A|0.900;G|0.100	0.100	strong		0.542	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
BPIFC	254240	hgsc.bcm.edu	37	22	32810378	32810378	+	Missense_Mutation	SNP	T	T	G	rs35856742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:32810378T>G	ENST00000397452.1	-	16	1546	c.1436A>C	c.(1435-1437)gAa>gCa	p.E479A	BPIFC_ENST00000432451.2_Missense_Mutation_p.E236A|RTCB_ENST00000216038.5_5'Flank|BPIFC_ENST00000534972.1_Missense_Mutation_p.E203A|RTCB_ENST00000451746.2_5'Flank|BPIFC_ENST00000300399.3_Missense_Mutation_p.E479A			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	479			E -> A (in dbSNP:rs35856742).			extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										TGAGGATGTTTCATACTTCAG	0.493													T|||	296	0.0591054	0.1233	0.0303	5008	,	,		18467	0.0139		0.0527	False		,,,				2504	0.046				p.E479A		Atlas-SNP	.											.	.	.	.	0			c.A1436C						PASS	.	T	ALA/GLU	496,3910	230.4+/-244.6	35,426,1742	144.0	123.0	130.0		1436	4.3	0.8	22	dbSNP_126	130	372,8228	122.2+/-181.2	15,342,3943	yes	missense	BPIFC	NM_174932.2	107	50,768,5685	GG,GT,TT		4.3256,11.2574,6.6738	benign	479/508	32810378	868,12138	2203	4300	6503	SO:0001583	missense	254240	exon15			GATGTTTCATACT	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.1436A>C	22.37:g.32810378T>G	ENSP00000380594:p.Glu479Ala	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	37	CCDS13906.1	129	0.059065934065934064	68	0.13821138211382114	12	0.03314917127071823	4	0.006993006993006993	45	0.059366754617414245	T	14.93	2.681075	0.47886	0.112574	0.043256	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972;ENST00000432451	T;T;T;T	0.04917	3.53;3.53;4.28;3.97	5.39	4.29	0.51040	.	0.550764	0.20116	N	0.098913	T	0.00039	0.0001	M	0.68317	2.08	0.80722	P	0.0	B;P	0.35745	0.047;0.518	B;B	0.30401	0.014;0.115	T	0.18967	-1.0320	9	0.10111	T	0.7	-2.8015	9.7286	0.40348	0.0:0.0:0.1729:0.8271	rs35856742	236;479	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	A	479;479;203;236	ENSP00000380594:E479A;ENSP00000300399:E479A;ENSP00000439123:E203A;ENSP00000408920:E236A	ENSP00000300399:E479A	E	-	2	0	BPIFC	31140378	0.939000	0.31865	0.819000	0.32651	0.995000	0.86356	1.613000	0.36900	2.167000	0.68274	0.460000	0.39030	GAA	T|0.936;G|0.064	0.064	strong		0.493	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
ZHX2	22882	hgsc.bcm.edu	37	8	123964431	123964431	+	Silent	SNP	G	G	A	rs3204141	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:123964431G>A	ENST00000314393.4	+	3	1516	c.681G>A	c.(679-681)tcG>tcA	p.S227S		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	227	Required for homodimerization.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S227S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			AGATCCTCTCGAGACTCGGCG	0.597													G|||	1162	0.232029	0.0174	0.3256	5008	,	,		17175	0.1319		0.3549	False		,,,				2504	0.4325				p.S227S	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											ZHX2,NS,carcinoma,0,1	ZHX2	106	1	1	Substitution - coding silent(1)	stomach(1)	c.G681A						PASS	.	G		323,4083	170.5+/-200.9	11,301,1891	112.0	120.0	117.0		681	-6.4	0.5	8	dbSNP_105	117	2984,5616	462.5+/-365.7	510,1964,1826	no	coding-synonymous	ZHX2	NM_014943.3		521,2265,3717	AA,AG,GG		34.6977,7.3309,25.4267		227/838	123964431	3307,9699	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CCTCTCGAGACTC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.681G>A	8.37:g.123964431G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			G|0.767;A|0.233	0.233	strong		0.597	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204399061	204399061	+	Silent	SNP	A	A	G	rs2271419	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204399061A>G	ENST00000367187.3	-	30	4942	c.4386T>C	c.(4384-4386)ccT>ccC	p.P1462P	RP11-739N20.2_ENST00000443515.1_RNA|PIK3C2B_ENST00000424712.2_Silent_p.P1434P	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1462	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CGGCCACCTCAGGGGGTGCGT	0.667													G|||	690	0.13778	0.2784	0.1037	5008	,	,		17000	0.0774		0.1113	False		,,,				2504	0.0613				p.P1462P		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.T4386C						PASS	.	G		130,4276		55,20,2128	83.0	75.0	78.0		4386	-10.9	0.0	1	dbSNP_100	78	34,8566		11,12,4277	no	coding-synonymous	PIK3C2B	NM_002646.3		66,32,6405	GG,GA,AA		0.3953,2.9505,1.261		1462/1635	204399061	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon30			CACCTCAGGGGGT	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4386T>C	1.37:g.204399061A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	51	14	0.27451	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			A|0.866;G|0.134	0.134	strong		0.667	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
TOP1MT	116447	hgsc.bcm.edu	37	8	144392368	144392368	+	Missense_Mutation	SNP	G	G	A	rs2293925	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144392368G>A	ENST00000329245.4	-	13	1607	c.1573C>T	c.(1573-1575)Cgg>Tgg	p.R525W	TOP1MT_ENST00000523676.1_Missense_Mutation_p.R427W|TOP1MT_ENST00000521193.1_Missense_Mutation_p.R427W|TOP1MT_ENST00000519148.1_Missense_Mutation_p.R427W	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	525			R -> W (in dbSNP:rs2293925). {ECO:0000269|PubMed:14702039}.		DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	TCCAGGAGCCGCCTCTTCTTC	0.652													G|||	2288	0.456869	0.0393	0.6326	5008	,	,		17622	0.6716		0.4592	False		,,,				2504	0.6728				p.R525W		Atlas-SNP	.											.	TOP1MT	63	.	0			c.C1573T	GRCh37	CM066250	TOP1MT	M	rs2293925	PASS	.	G	TRP/ARG	434,3964		32,370,1797	28.0	29.0	29.0		1573	-3.1	0.0	8	dbSNP_100	29	3794,4806		845,2104,1351	yes	missense	TOP1MT	NM_052963.1	101	877,2474,3148	AA,AG,GG		44.1163,9.8681,32.5281	probably-damaging	525/602	144392368	4228,8770	2199	4300	6499	SO:0001583	missense	116447	exon13			GGAGCCGCCTCTT	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1573C>T	8.37:g.144392368G>A	ENSP00000328835:p.Arg525Trp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	37	CCDS6400.1	990|990	0.4532967032967033|0.4532967032967033	27|27	0.054878048780487805|0.054878048780487805	211|211	0.5828729281767956|0.5828729281767956	397|397	0.6940559440559441|0.6940559440559441	355|355	0.4683377308707124|0.4683377308707124	G|G	23.0|23.0	4.365437|4.365437	0.82463|0.82463	0.098681|0.098681	0.441163|0.441163	ENSG00000184428|ENSG00000184428	ENST00000519977|ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676	.|T;T;T;T	.|0.50813	.|0.73;0.73;0.73;0.73	4.14|4.14	-3.14|-3.14	0.05250|0.05250	.|DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (1);DNA topoisomerases I, dispensable insert, eukaryotic-type (1);	.|0.179425	.|0.24889	.|U	.|0.034784	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.68952|0.68952	2.095|2.095	0.53688|0.53688	P|P	2.2999999999995246E-5|2.2999999999995246E-5	.|D;D	.|0.71674	.|0.998;0.991	.|P;P	.|0.57468	.|0.821;0.586	T|T	0.43750|0.43750	-0.9372|-0.9372	4|9	.|0.66056	.|D	.|0.02	.|.	6.8892|6.8892	0.24220|0.24220	0.0:0.1693:0.3022:0.5285|0.0:0.1693:0.3022:0.5285	rs2293925;rs11544481;rs2293925|rs2293925;rs11544481;rs2293925	.|320;525	.|E7ESI1;Q969P6	.|.;TOP1M_HUMAN	V|W	34|525;427;427;427	.|ENSP00000328835:R525W;ENSP00000428369:R427W;ENSP00000429169:R427W;ENSP00000429181:R427W	.|ENSP00000328835:R525W	A|R	-|-	2|1	0|2	TOP1MT|TOP1MT	144463743|144463743	0.634000|0.634000	0.27190|0.27190	0.000000|0.000000	0.03702|0.03702	0.865000|0.865000	0.49528|0.49528	0.360000|0.360000	0.20250|0.20250	-1.133000|-1.133000	0.02903|0.02903	0.508000|0.508000	0.49915|0.49915	GCG|CGG	G|0.617;A|0.383	0.383	strong		0.652	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
TSHZ1	10194	hgsc.bcm.edu	37	18	72997677	72997677	+	Silent	SNP	C	C	T	rs3826609	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72997677C>T	ENST00000580243.1	+	2	663	c.315C>T	c.(313-315)agC>agT	p.S105S	TSHZ1_ENST00000322038.5_Silent_p.S60S			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	105	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GTCCCGACAGCGTCTCGTACC	0.557													C|||	926	0.184904	0.0295	0.2997	5008	,	,		13935	0.1498		0.329	False		,,,				2504	0.2014				p.S60S		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C180T						PASS	.	C		374,4032	191.6+/-217.2	16,342,1845	97.0	80.0	86.0		180	-1.2	0.0	18	dbSNP_107	86	2667,5933	429.2+/-356.1	418,1831,2051	yes	coding-synonymous	TSHZ1	NM_005786.4		434,2173,3896	TT,TC,CC		31.0116,8.4884,23.3815		60/1033	72997677	3041,9965	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			CGACAGCGTCTCG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.315C>T	18.37:g.72997677C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	36	28	0.777778	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				C|0.779;T|0.221	0.221	strong		0.557	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
QRICH2	84074	hgsc.bcm.edu	37	17	74275160	74275160	+	Silent	SNP	C	C	T	rs347675	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74275160C>T	ENST00000262765.5	-	14	4559	c.4380G>A	c.(4378-4380)acG>acA	p.T1460T		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1460								p.T1460T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						GTTCAAACACCGTGTAGGGGC	0.642													C|||	753	0.150359	0.1021	0.1023	5008	,	,		17993	0.2113		0.0755	False		,,,				2504	0.2638				p.T1460T		Atlas-SNP	.											QRICH2,NS,carcinoma,0,1	QRICH2	143	1	1	Substitution - coding silent(1)	stomach(1)	c.G4380A						PASS	.	C		470,3936	221.0+/-238.3	26,418,1759	50.0	49.0	50.0		4380	-8.6	0.0	17	dbSNP_79	50	755,7845	178.8+/-228.1	27,701,3572	no	coding-synonymous	QRICH2	NM_032134.1		53,1119,5331	TT,TC,CC		8.7791,10.6673,9.4187		1460/1664	74275160	1225,11781	2203	4300	6503	SO:0001819	synonymous_variant	84074	exon14			AAACACCGTGTAG	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.4380G>A	17.37:g.74275160C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	60	13	0.216667	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1	248	0.11355311355311355	46	0.09349593495934959	33	0.09116022099447514	118	0.2062937062937063	51	0.06728232189973615	C	7.924	0.739161	0.15642	0.106673	0.087791	ENSG00000129646	ENST00000532549	.	.	.	5.44	-8.58	0.00897	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.34707	P	0.272664	.	.	.	.	.	.	T	0.18745	-1.0327	3	.	.	.	-12.4882	3.0647	0.06211	0.1983:0.5084:0.1582:0.1351	rs347675;rs58169828;rs347675	.	.	.	Q	108	.	.	R	-	2	0	QRICH2	71786755	0.000000	0.05858	0.005000	0.12908	0.765000	0.43378	-0.797000	0.04570	-1.919000	0.01071	-0.812000	0.03155	CGG	C|0.892;T|0.108	0.108	strong		0.642	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
MADCAM1	8174	hgsc.bcm.edu	37	19	501701	501701	+	Missense_Mutation	SNP	G	G	A	rs71171990|rs72970252	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:501701G>A	ENST00000215637.3	+	4	746	c.700G>A	c.(700-702)Gac>Aac	p.D234N	MADCAM1_ENST00000587541.1_Missense_Mutation_p.D15N|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	234	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGCCTCCCGACACCACCTC	0.652																																					p.D234N		Atlas-SNP	.											MADCAM1,NS,lymphoid_neoplasm,0,2	MADCAM1	29	2	0			c.G700A						PASS	.						31.0	45.0	40.0					19																	501701		2203	4299	6502	SO:0001583	missense	8174	exon4			CCTCCCGACACCA	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.700G>A	19.37:g.501701G>A	ENSP00000215637:p.Asp234Asn	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	246	38	0.154472	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	308	0.14102564102564102	38	0.07723577235772358	55	0.15193370165745856	90	0.15734265734265734	125	0.16490765171503957	g	8.795	0.931415	0.18131	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10382	2.88	4.28	-4.55	0.03441	.	3.221950	0.01471	N	0.016293	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.37641	-0.9697	9	0.13853	T	0.58	.	12.1068	0.53818	0.7972:0.0:0.2028:0.0	.	234	Q13477	MADCA_HUMAN	N	258;250;242;234	ENSP00000215637:D234N	ENSP00000215637:D234N	D	+	1	0	MADCAM1	452701	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.470000	0.06639	-0.806000	0.04398	-0.199000	0.12753	GAC	G|0.865;A|0.135	0.135	strong		0.652	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
PER3	8863	hgsc.bcm.edu	37	1	7880683	7880683	+	Missense_Mutation	SNP	T	T	G	rs10462020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7880683T>G	ENST00000361923.2	+	15	2091	c.1916T>G	c.(1915-1917)gTc>gGc	p.V639G	PER3_ENST00000377532.3_Missense_Mutation_p.V647G|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	639	CSNK1E binding domain. {ECO:0000250}.		V -> G (associated with delayed sleep phase syndrome (DSPS); dbSNP:rs10462020). {ECO:0000269|PubMed:11306557, ECO:0000269|PubMed:12655319}.		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		ATTGTCCATGTCCCACCCCCA	0.483													T|||	604	0.120607	0.0696	0.2133	5008	,	,		18504	0.0079		0.1968	False		,,,				2504	0.1616				p.V639G		Atlas-SNP	.											.	PER3	95	.	0			c.T1916G	GRCh37	CM035907	PER3	M	rs10462020	PASS	.	T	GLY/VAL	424,3982	206.5+/-228.1	19,386,1798	80.0	66.0	71.0		1916	-6.9	0.0	1	dbSNP_119	71	1643,6957	302.9+/-306.2	162,1319,2819	yes	missense	PER3	NM_016831.1	109	181,1705,4617	GG,GT,TT		19.1047,9.6232,15.8927	possibly-damaging	639/1202	7880683	2067,10939	2203	4300	6503	SO:0001583	missense	8863	exon15			TCCATGTCCCACC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.1916T>G	1.37:g.7880683T>G	ENSP00000355031:p.Val639Gly	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	258	0.11813186813186813	48	0.0975609756097561	62	0.1712707182320442	8	0.013986013986013986	140	0.18469656992084432	T	15.17	2.752957	0.49362	0.096232	0.191047	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.28069	1.7;1.63	4.43	-6.91	0.01649	.	0.368047	0.27056	N	0.021160	T	0.00073	0.0002	M	0.72118	2.19	0.52099	P	5.3999999999998494E-5	B;P;P;B	0.51791	0.22;0.913;0.948;0.22	B;P;P;B	0.53861	0.115;0.548;0.736;0.115	T	0.04178	-1.0971	9	0.87932	D	0	.	8.5405	0.33390	0.0:0.4789:0.1186:0.4024	rs10462020;rs60667815;rs10462020	639;647;647;639	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	G	647;639	ENSP00000366755:V647G;ENSP00000355031:V639G	ENSP00000355031:V639G	V	+	2	0	PER3	7803270	0.260000	0.24053	0.000000	0.03702	0.010000	0.07245	0.680000	0.25306	-1.725000	0.01371	0.459000	0.35465	GTC	T|0.862;G|0.138	0.138	strong		0.483	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
ZFYVE28	57732	hgsc.bcm.edu	37	4	2275835	2275835	+	Silent	SNP	G	G	A	rs2051561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2275835G>A	ENST00000290974.2	-	9	2499	c.2160C>T	c.(2158-2160)ttC>ttT	p.F720F	ZFYVE28_ENST00000515312.1_Silent_p.F650F|ZFYVE28_ENST00000508471.1_Silent_p.F25F|ZFYVE28_ENST00000511071.1_Silent_p.F690F	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	720					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						GGCTGCCGTGGAACCTGGACC	0.642													G|||	1784	0.35623	0.3623	0.513	5008	,	,		14371	0.12		0.5427	False		,,,				2504	0.2883				p.F720F		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.C2160T						PASS	.	G	,,	1557,2849	487.6+/-361.0	256,1045,902	136.0	119.0	125.0		2070,1950,2160	2.8	1.0	4	dbSNP_94	125	4616,3984	599.4+/-394.1	1260,2096,944	no	coding-synonymous,coding-synonymous,coding-synonymous	ZFYVE28	NM_001172656.1,NM_001172659.1,NM_020972.2	,,	1516,3141,1846	AA,AG,GG		46.3256,35.3382,47.4627	,,	690/858,650/818,720/888	2275835	6173,6833	2203	4300	6503	SO:0001819	synonymous_variant	57732	exon9			GCCGTGGAACCTG	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"""Zinc fingers, FYVE domain containing"""	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.2160C>T	4.37:g.2275835G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Silent	SNP	ENST00000290974.2	37	CCDS33942.1																																																																																			G|0.575;A|0.425	0.425	strong		0.642	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
CEACAM20	125931	hgsc.bcm.edu	37	19	45024581	45024581	+	RNA	SNP	C	C	G	rs12982449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45024581C>G	ENST00000454753.1	-	0	1235							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				CATAGGGCCCCGTGTCATTCC	0.627													c|||	1870	0.373403	0.1392	0.4265	5008	,	,		19458	0.2698		0.6392	False		,,,				2504	0.4857				p.T319T		Atlas-SNP	.											.	CEACAM20	31	.	0			c.G957C						PASS	.		,,,	884,3018		114,656,1181	58.0	57.0	57.0		957,957,957,957	-7.5	0.0	19	dbSNP_121	57	5113,3187		1597,1919,634	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	,,,	1711,2575,1815	GG,GC,CC		38.3976,22.655,49.1477	,,,	319/597,319/492,319/504,319/585	45024581	5997,6205	1951	4150	6101			125931	exon5			GGGCCCCGTGTCA	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45024581C>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001102600		Silent	SNP	ENST00000454753.1	37																																																																																				C|0.617;G|0.383	0.383	strong		0.627	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
REEP4	80346	hgsc.bcm.edu	37	8	21997738	21997738	+	Silent	SNP	A	A	T	rs35574275	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:21997738A>T	ENST00000306306.3	-	3	597	c.129T>A	c.(127-129)atT>atA	p.I43I	REEP4_ENST00000523293.1_Silent_p.I43I|REEP4_ENST00000334530.5_Silent_p.I43I	NM_025232.2	NP_079508.2	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	43					mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|nuclear envelope organization (GO:0006998)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)	microtubule binding (GO:0008017)			kidney(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	7				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		GTGCAAAAACAATCCAGTACA	0.592													A|||	220	0.0439297	0.0076	0.0346	5008	,	,		18355	0.0437		0.1133	False		,,,				2504	0.0286				p.I43I		Atlas-SNP	.											REEP4,NS,carcinoma,0,1	REEP4	13	1	0			c.T129A						PASS	.	A		103,4303	80.9+/-119.3	1,101,2101	74.0	66.0	69.0		129	-4.9	1.0	8	dbSNP_126	69	973,7627	213.4+/-253.3	60,853,3387	no	coding-synonymous	REEP4	NM_025232.2		61,954,5488	TT,TA,AA		11.314,2.3377,8.2731		43/258	21997738	1076,11930	2203	4300	6503	SO:0001819	synonymous_variant	80346	exon3			AAAAACAATCCAG	BC013048	CCDS6024.1	8p21.3	2008-05-02	2006-02-07	2006-02-07	ENSG00000168476	ENSG00000168476		"""Receptor accessory proteins"""	26176	protein-coding gene	gene with protein product		609349	"""chromosome 8 open reading frame 20"""	C8orf20		16271481, 15550249	Standard	NM_025232		Approved	FLJ22246, FLJ22277, PP432	uc003xau.1	Q9H6H4	OTTHUMG00000131491	ENST00000306306.3:c.129T>A	8.37:g.21997738A>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_025232	D3DSQ9|Q86VL1|Q9H6I5|Q9HBP4	Silent	SNP	ENST00000306306.3	37	CCDS6024.1																																																																																			A|0.923;T|0.077	0.077	strong		0.592	REEP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254337.2	NM_025232	
LGALS9	3965	hgsc.bcm.edu	37	17	25958304	25958304	+	Missense_Mutation	SNP	G	G	A	rs3751093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:25958304G>A	ENST00000395473.2	+	1	1481	c.13G>A	c.(13-15)Ggt>Agt	p.G5S	AC015688.3_ENST00000584605.1_Intron|LGALS9_ENST00000413914.2_5'UTR|LGALS9_ENST00000313648.6_Missense_Mutation_p.G5S|LGALS9_ENST00000310394.5_Missense_Mutation_p.G5S|LGALS9_ENST00000302228.5_Missense_Mutation_p.G5S|LGALS9_ENST00000448970.2_3'UTR	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	5			G -> S (in dbSNP:rs3751093). {ECO:0000269|PubMed:9642261, ECO:0000269|Ref.7}.		positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		GGCCTTCAGCGGTTCCCAGGC	0.577													G|||	1014	0.202476	0.1014	0.2767	5008	,	,		14825	0.2331		0.2008	False		,,,				2504	0.2566				p.G5S	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.G13A						PASS	.	G	SER/GLY,SER/GLY	568,3838	252.1+/-258.6	45,478,1680	68.0	67.0	67.0		13,13	-5.4	0.0	17	dbSNP_107	67	1808,6792	325.0+/-316.7	220,1368,2712	yes	missense,missense	LGALS9	NM_002308.3,NM_009587.2	56,56	265,1846,4392	AA,AG,GG		21.0233,12.8915,18.2685	benign,benign	5/324,5/356	25958304	2376,10630	2203	4300	6503	SO:0001583	missense	3965	exon1			TTCAGCGGTTCCC	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"""Lectins, galactoside-binding"""	6570	protein-coding gene	gene with protein product	"""galectin 9"""	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.13G>A	17.37:g.25958304G>A	ENSP00000378856:p.Gly5Ser	Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	344	149	0.43314	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	431	0.19734432234432234	45	0.09146341463414634	97	0.26795580110497236	143	0.25	146	0.19261213720316622	G	8.369	0.834917	0.16820	0.128915	0.210233	ENSG00000168961	ENST00000395473;ENST00000302228;ENST00000310394;ENST00000313648;ENST00000448970	T;T;T;T	0.03801	4.02;3.99;3.97;3.8	2.8	-5.36	0.02689	.	1.415160	0.04312	N	0.349115	T	0.00012	0.0000	N	0.11064	0.09	0.51482	P	7.100000000004325E-5	B;B;B	0.14012	0.009;0.003;0.0	B;B;B	0.15052	0.012;0.001;0.001	T	0.46569	-0.9182	9	0.08381	T	0.77	.	1.5284	0.02530	0.2392:0.1671:0.4281:0.1657	rs3751093;rs3751093	5;5;5	F8W9W4;Q3B8N1;O00182	.;.;LEG9_HUMAN	S	5	ENSP00000378856:G5S;ENSP00000306228:G5S;ENSP00000312259:G5S;ENSP00000318214:G5S	ENSP00000306228:G5S	G	+	1	0	LGALS9	22982431	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.980000	0.00663	-1.287000	0.02381	-0.217000	0.12591	GGT	G|0.811;A|0.189	0.189	strong		0.577	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587	
LRRC4C	57689	hgsc.bcm.edu	37	11	40136049	40136049	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:40136049A>G	ENST00000278198.2	-	2	3757	c.1794T>C	c.(1792-1794)taT>taC	p.Y598Y	LRRC4C_ENST00000530763.1_Silent_p.Y598Y|LRRC4C_ENST00000527150.1_Silent_p.Y598Y|LRRC4C_ENST00000528697.1_Silent_p.Y598Y			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	598					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TGTATGAGTTATAGTGATTTA	0.408																																					p.Y598Y		Atlas-SNP	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	0			c.T1794C						PASS	.						230.0	222.0	225.0					11																	40136049		2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			TGAGTTATAGTGA	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1794T>C	11.37:g.40136049A>G		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	295	133	0.450847	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																			.	.	none		0.408	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
PDZRN3	23024	hgsc.bcm.edu	37	3	73433369	73433369	+	Missense_Mutation	SNP	G	G	A	rs3205537	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:73433369G>A	ENST00000263666.4	-	10	2462	c.2348C>T	c.(2347-2349)gCg>gTg	p.A783V	PDZRN3_ENST00000462146.2_Missense_Mutation_p.A440V|PDZRN3_ENST00000535920.1_Missense_Mutation_p.A505V|PDZRN3_ENST00000479530.1_Missense_Mutation_p.A500V|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000466780.1_Missense_Mutation_p.A440V	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	783			A -> V (in dbSNP:rs3205537). {ECO:0000269|PubMed:17974005}.		neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GATGCCCTCCGCCGCTCTCCT	0.647													G|||	1364	0.272364	0.0635	0.3415	5008	,	,		16006	0.4435		0.3549	False		,,,				2504	0.2444				p.A783V		Atlas-SNP	.											.	PDZRN3	196	.	0			c.C2348T						PASS	.	G	VAL/ALA	468,3938	217.8+/-236.0	30,408,1765	35.0	38.0	37.0		2348	4.1	0.2	3	dbSNP_105	37	2851,5749	440.9+/-359.6	471,1909,1920	yes	missense	PDZRN3	NM_015009.1	64	501,2317,3685	AA,AG,GG		33.1512,10.6219,25.519	possibly-damaging	783/1067	73433369	3319,9687	2203	4300	6503	SO:0001583	missense	23024	exon10			CCCTCCGCCGCTC	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2348C>T	3.37:g.73433369G>A	ENSP00000263666:p.Ala783Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	709	0.32463369963369965	41	0.08333333333333333	119	0.3287292817679558	267	0.46678321678321677	282	0.3720316622691293	G	1.520	-0.547126	0.04024	0.106219	0.331512	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000492909	T;T;T;T;T;T	0.10099	2.91;3.61;3.5;3.5;3.62;3.58	4.93	4.05	0.47172	.	1.618580	0.02891	N	0.134123	T	0.00012	0.0000	L	0.57536	1.79	0.58432	P	5.000000000032756E-6	B;B;B;B	0.27286	0.005;0.011;0.003;0.174	B;B;B;B	0.14578	0.005;0.004;0.003;0.011	T	0.48536	-0.9027	9	0.23891	T	0.37	.	13.1789	0.59642	0.0793:0.0:0.9207:0.0	rs3205537;rs3732435;rs52810062;rs57871998;rs3205537	505;500;500;783	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	V	783;505;440;440;500;481	ENSP00000263666:A783V;ENSP00000442026:A505V;ENSP00000418168:A440V;ENSP00000418484:A440V;ENSP00000418624:A500V;ENSP00000419250:A481V	ENSP00000263666:A783V	A	-	2	0	PDZRN3	73516059	0.713000	0.27926	0.216000	0.23742	0.081000	0.17604	2.975000	0.49281	1.030000	0.39839	0.655000	0.94253	GCG	G|0.729;A|0.271	0.271	strong		0.647	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
TMEM259	91304	hgsc.bcm.edu	37	19	1010406	1010406	+	Silent	SNP	G	G	A	rs62131162	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1010406G>A	ENST00000356663.3	-	11	1927	c.1806C>T	c.(1804-1806)ggC>ggT	p.G602G	TMEM259_ENST00000333175.5_3'UTR	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	602						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GGCTAGGCCCGCCTACCGCAG	0.741													N|||	505	0.100839	0.1278	0.098	5008	,	,		11980	0.001		0.1322	False		,,,				2504	0.137				p.G602G		Atlas-SNP	.											.	.	.	.	0			c.C1806T						PASS	.		,	328,3510		20,288,1611	3.0	4.0	4.0		1806,	-2.6	0.0	19	dbSNP_129	4	874,6922		40,794,3064	no	coding-synonymous,utr-3	C19orf6	NM_001033026.1,NM_033420.3	,	60,1082,4675	AA,AG,GG		11.2109,8.5461,10.3318	,	602/621,	1010406	1202,10432	1919	3898	5817	SO:0001819	synonymous_variant	91304	exon11			AGGCCCGCCTACC	BC008957	CCDS12052.1, CCDS32862.1	19p13.3	2013-02-06	2013-02-06	2013-02-06	ENSG00000182087	ENSG00000182087			17039	protein-coding gene	gene with protein product	"""membralin"", ""aspecific BCL2 ARE-binding protein 1"""	611011	"""chromosome 19 open reading frame 6"""	C19orf6		12638133, 16084606	Standard	XM_005259675		Approved	MGC4022, ASBABP1, MBRL	uc002lqr.1	Q4ZIN3		ENST00000356663.3:c.1806C>T	19.37:g.1010406G>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	12	6	0.5	NM_001033026	O60392|Q8NF79|Q96H30	Silent	SNP	ENST00000356663.3	37	CCDS32862.1																																																																																			G|0.903;A|0.097	0.097	strong		0.741	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420	
FBXO25	26260	hgsc.bcm.edu	37	8	381344	381344	+	Missense_Mutation	SNP	C	C	G	rs28438773	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:381344C>G	ENST00000276326.5	+	3	257	c.138C>G	c.(136-138)atC>atG	p.I46M	FBXO25_ENST00000350302.3_Missense_Mutation_p.I46M|FBXO25_ENST00000382824.1_5'UTR|FBXO25_ENST00000352684.2_5'UTR	NM_183421.1	NP_904357.1	Q8TCJ0	FBX25_HUMAN	F-box protein 25	46	Interaction with beta-actin.				protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		ATTTCAGTATCTTAAATAGTG	0.279													C|||	854	0.170527	0.1044	0.1412	5008	,	,		16678	0.2927		0.1392	False		,,,				2504	0.1871				p.I46M		Atlas-SNP	.											.	FBXO25	25	.	0			c.C138G						PASS	.	C	,MET/ILE,MET/ILE	484,3890		25,434,1728	31.0	36.0	34.0		,138,138	2.3	1.0	8	dbSNP_125	34	1289,7225		97,1095,3065	no	utr-5,missense,missense	FBXO25	NM_012173.3,NM_183420.1,NM_183421.1	,10,10	122,1529,4793	GG,GC,CC		15.1398,11.0654,13.757	,benign,benign	,46/359,46/368	381344	1773,11115	2187	4257	6444	SO:0001583	missense	26260	exon3			CAGTATCTTAAAT	AF174605	CCDS5952.1, CCDS5953.1, CCDS5954.1	8p23.3	2007-03-30	2004-06-15		ENSG00000147364	ENSG00000147364		"""F-boxes /  ""other"""""	13596	protein-coding gene	gene with protein product		609098	"""F-box only protein 25"""			10531035, 10531037	Standard	NM_012173		Approved	FBX25	uc003wox.3	Q8TCJ0	OTTHUMG00000090341	ENST00000276326.5:c.138C>G	8.37:g.381344C>G	ENSP00000276326:p.Ile46Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_183420	Q6PJ83|Q7Z4V4|Q9UKB8	Missense_Mutation	SNP	ENST00000276326.5	37	CCDS5953.1	334	0.15293040293040294	52	0.10569105691056911	44	0.12154696132596685	134	0.23426573426573427	104	0.13720316622691292	.	9.568	1.120164	0.20877	0.110654	0.151398	ENSG00000147364	ENST00000518240;ENST00000350302;ENST00000276326;ENST00000447233	T;T;T	0.27890	1.64;1.64;1.64	4.22	2.29	0.28610	.	0.503034	0.22867	N	0.054666	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.9999999981248	B;B	0.17268	0.021;0.021	B;B	0.17722	0.019;0.019	T	0.28396	-1.0045	9	0.36615	T	0.2	-39.8882	3.344	0.07128	0.1757:0.5496:0.1714:0.1034	rs28438773;rs59135522	46;46	Q8TCJ0-2;Q8TCJ0	.;FBX25_HUMAN	M	46	ENSP00000428872:I46M;ENSP00000342077:I46M;ENSP00000276326:I46M	ENSP00000276326:I46M	I	+	3	3	FBXO25	371344	0.988000	0.35896	1.000000	0.80357	0.898000	0.52572	0.269000	0.18589	0.863000	0.35553	0.449000	0.29647	ATC	C|0.860;G|0.140	0.140	strong		0.279	FBXO25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206710.2	NM_012173	
ARHGAP19	84986	hgsc.bcm.edu	37	10	99006083	99006083	+	Silent	SNP	G	G	A	rs13439	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:99006083G>A	ENST00000358531.4	-	7	967	c.939C>T	c.(937-939)taC>taT	p.Y313Y	ARHGAP19_ENST00000355366.5_Silent_p.Y304Y|ARHGAP19-SLIT1_ENST00000316676.8_Silent_p.Y313Y|ARHGAP19_ENST00000371027.1_Silent_p.Y304Y|ARHGAP19_ENST00000487035.1_5'UTR|ARHGAP19-SLIT1_ENST00000453547.2_Silent_p.Y313Y|ARHGAP19-SLIT1_ENST00000358308.3_Silent_p.Y284Y	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	313					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.Y313Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		ACTCCCGAATGTAAGCAGGAG	0.433													G|||	1263	0.252196	0.3321	0.2651	5008	,	,		17612	0.0992		0.2674	False		,,,				2504	0.2771				p.Y313Y		Atlas-SNP	.											ARHGAP19_ENST00000358531,caecum,carcinoma,-2,3	ARHGAP19	72	3	1	Substitution - coding silent(1)	stomach(1)	c.C939T						PASS	.	G	,	1426,2980	462.8+/-353.4	233,960,1010	66.0	65.0	65.0		852,939	-10.1	0.6	10	dbSNP_52	65	2719,5881	434.0+/-357.6	422,1875,2003	no	coding-synonymous,coding-synonymous	ARHGAP19	NM_001204300.1,NM_032900.5	,	655,2835,3013	AA,AG,GG		31.6163,32.365,31.8699	,	284/466,313/495	99006083	4145,8861	2203	4300	6503	SO:0001819	synonymous_variant	84986	exon7			CCGAATGTAAGCA	AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"""Rho GTPase activating proteins"""	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.939C>T	10.37:g.99006083G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	40	39	0.975	NM_032900	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	Silent	SNP	ENST00000358531.4	37	CCDS7454.2																																																																																			G|0.724;A|0.276	0.276	strong		0.433	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900	
AARS2	57505	hgsc.bcm.edu	37	6	44269193	44269193	+	Silent	SNP	C	C	T	rs498512	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44269193C>T	ENST00000244571.4	-	20	2609	c.2607G>A	c.(2605-2607)aaG>aaA	p.K869K	TMEM151B_ENST00000438774.2_Intron|AARS2_ENST00000491573.1_5'Flank|RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCTGAGTTTTCTTTGCAGCCT	0.572													C|||	2918	0.582668	0.4622	0.7666	5008	,	,		15062	0.4256		0.7266	False		,,,				2504	0.6288				p.K869K		Atlas-SNP	.											.	AARS2	77	.	0			c.G2607A						PASS	.	C		2260,2146	590.3+/-387.3	589,1082,532	65.0	71.0	69.0		2607	4.3	0.9	6	dbSNP_83	69	6571,2029	714.2+/-406.0	2522,1527,251	no	coding-synonymous	AARS2	NM_020745.2		3111,2609,783	TT,TC,CC		23.593,48.7063,32.1006		869/986	44269193	8831,4175	2203	4300	6503	SO:0001819	synonymous_variant	57505	exon20			AGTTTTCTTTGCA	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.2607G>A	6.37:g.44269193C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_020745		Silent	SNP	ENST00000244571.4	37	CCDS34464.1																																																																																			C|0.343;T|0.657	0.657	strong		0.572	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
FUS	2521	hgsc.bcm.edu	37	16	31195279	31195279	+	Silent	SNP	C	C	T	rs1052352	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31195279C>T	ENST00000254108.7	+	4	396	c.291C>T	c.(289-291)taC>taT	p.Y97Y	FUS_ENST00000568685.1_Silent_p.Y97Y|FUS_ENST00000380244.3_Silent_p.Y96Y|RP11-388M20.6_ENST00000564743.1_RNA	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	97	Gln/Gly/Ser/Tyr-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		AGTCCTCCTACCCTGGCTATG	0.582			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""								C|||	2373	0.473842	0.2315	0.5173	5008	,	,		14060	0.7431		0.5517	False		,,,				2504	0.4131				p.Y97Y		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	FUS	52	.	0			c.C291T						PASS	.	C	,,	1184,3210	408.9+/-334.8	169,846,1182	90.0	90.0	90.0		288,291,291	-3.3	1.0	16	dbSNP_86	90	4772,3828	601.9+/-394.4	1334,2104,862	no	coding-synonymous,coding-synonymous,coding-synonymous	FUS	NM_001170634.1,NM_001170937.1,NM_004960.3	,,	1503,2950,2044	TT,TC,CC		44.5116,26.9458,45.8365	,,	96/526,97/523,97/527	31195279	5956,7038	2197	4300	6497	SO:0001819	synonymous_variant	2521	exon4			CTCCTACCCTGGC	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.291C>T	16.37:g.31195279C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_004960	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																			C|0.517;T|0.483	0.483	strong		0.582	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
RNF144B	255488	hgsc.bcm.edu	37	6	18457574	18457574	+	Silent	SNP	C	C	T	rs75403847		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:18457574C>T	ENST00000259939.3	+	5	837	c.520C>T	c.(520-522)Ctg>Ttg	p.L174L	RNF144B_ENST00000429054.2_Silent_p.L85L	NM_182757.3	NP_877434.2	Q7Z419	R144B_HUMAN	ring finger protein 144B	174					apoptotic process (GO:0006915)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)	11	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			GCCTATTGTCCTGCCAACAGA	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		20281	0.0		0.001	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	RNF144B	18	.	0			c.C520T						PASS	.	C		0,4406		0,0,2203	184.0	170.0	175.0		520	3.3	1.0	6	dbSNP_132	175	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	RNF144B	NM_182757.3		0,11,6492	TT,TC,CC		0.1279,0.0,0.0846		174/304	18457574	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	255488	exon5			ATTGTCCTGCCAA	AK096832	CCDS34345.1	6p22.3	2011-05-23	2009-01-05	2007-08-20	ENSG00000137393	ENSG00000137393		"""RING-type (C3HC4) zinc fingers"""	21578	protein-coding gene	gene with protein product			"""IBR domain containing 2"""	IBRDC2			Standard	NM_182757		Approved	bA528A10.3	uc003ncs.3	Q7Z419	OTTHUMG00000014322	ENST00000259939.3:c.520C>T	6.37:g.18457574C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_182757	B3KUA8|B4DZI2|Q5TB85|Q6P4Q0|Q8N3R7|Q9BX38	Silent	SNP	ENST00000259939.3	37	CCDS34345.1																																																																																			C|0.999;T|0.001	0.001	strong		0.453	RNF144B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039965.2	XM_172581	
MEPE	56955	hgsc.bcm.edu	37	4	88766969	88766969	+	Missense_Mutation	SNP	A	A	G	rs61731014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88766969A>G	ENST00000424957.3	+	4	1022	c.949A>G	c.(949-951)Att>Gtt	p.I317V	MEPE_ENST00000560249.1_Missense_Mutation_p.I204V|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000497649.2_Missense_Mutation_p.I293V|MEPE_ENST00000361056.3_Missense_Mutation_p.I317V|MEPE_ENST00000395102.4_Missense_Mutation_p.I348V|MEPE_ENST00000540395.1_Missense_Mutation_p.I204V	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	317					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		TGGAAATACCATTGGAACTAG	0.448													A|||	53	0.0105831	0.0	0.0187	5008	,	,		20945	0.001		0.0268	False		,,,				2504	0.0123				p.I317V		Atlas-SNP	.											.	MEPE	86	.	0			c.A949G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	23,4383	30.8+/-60.4	0,23,2180	65.0	66.0	65.0		949,610,610,610,949	-4.5	0.0	4	dbSNP_129	65	203,8397	87.4+/-149.7	5,193,4102	yes	missense,missense,missense,missense,missense	MEPE	NM_001184694.1,NM_001184695.1,NM_001184696.1,NM_001184697.1,NM_020203.3	29,29,29,29,29	5,216,6282	GG,GA,AA		2.3605,0.522,1.7377	benign,benign,benign,benign,benign	317/526,204/413,204/413,204/413,317/526	88766969	226,12780	2203	4300	6503	SO:0001583	missense	56955	exon4			AATACCATTGGAA	AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"""matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"""			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.949A>G	4.37:g.88766969A>G	ENSP00000416984:p.Ile317Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	31	0.014194139194139194	0	0.0	9	0.024861878453038673	1	0.0017482517482517483	21	0.027704485488126648	A	6.730	0.503419	0.12822	0.00522	0.023605	ENSG00000152595	ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.96;0.94	4.99	-4.51	0.03483	.	1.439880	0.04269	N	0.341765	T	0.08313	0.0207	L	0.28274	0.84	0.09310	N	1	B	0.18863	0.031	B	0.14578	0.011	T	0.06481	-1.0824	10	0.28530	T	0.3	-0.3564	0.3973	0.00420	0.2932:0.1333:0.2641:0.3095	rs61731014	317	Q9NQ76	MEPE_HUMAN	V	317;348;293;204;317	ENSP00000416984:I317V;ENSP00000378534:I348V;ENSP00000422747:I293V;ENSP00000443491:I204V;ENSP00000354341:I317V	ENSP00000354341:I317V	I	+	1	0	MEPE	88985993	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.044000	0.12023	-0.960000	0.03613	-0.290000	0.09829	ATT	A|0.983;G|0.017	0.017	strong		0.448	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1		
OR13G1	441933	hgsc.bcm.edu	37	1	247835674	247835674	+	Missense_Mutation	SNP	G	G	A	rs28446289	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247835674G>A	ENST00000359688.2	-	1	691	c.670C>T	c.(670-672)Cgt>Tgt	p.R224C	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	224			R -> C (in dbSNP:rs28446289).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			GTGCGGATACGGAGAATAGCA	0.428													G|||	1657	0.330871	0.2958	0.2392	5008	,	,		24096	0.3839		0.3519	False		,,,				2504	0.3671				p.R224C		Atlas-SNP	.											.	OR13G1	78	.	0			c.C670T						PASS	.	G	CYS/ARG	1312,3094	441.4+/-346.4	188,936,1079	119.0	106.0	111.0		670	1.1	0.0	1	dbSNP_125	111	3098,5502	474.1+/-368.8	562,1974,1764	yes	missense	OR13G1	NM_001005487.1	180	750,2910,2843	AA,AG,GG		36.0233,29.7776,33.9074	possibly-damaging	224/308	247835674	4410,8596	2203	4300	6503	SO:0001583	missense	441933	exon1			GGATACGGAGAAT	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.670C>T	1.37:g.247835674G>A	ENSP00000352717:p.Arg224Cys	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	CCDS31094.1	682	0.31227106227106227	138	0.2804878048780488	88	0.2430939226519337	191	0.3339160839160839	265	0.3496042216358839	G	7.576	0.667780	0.14710	0.297776	0.360233	ENSG00000197437	ENST00000359688	T	0.00267	8.38	4.2	1.11	0.20524	GPCR, rhodopsin-like superfamily (1);	0.317710	0.22947	N	0.053716	T	0.00012	0.0000	M	0.87180	2.865	0.80722	P	0.0	B	0.24823	0.112	B	0.24269	0.052	T	0.43734	-0.9373	9	0.72032	D	0.01	-8.4764	6.3931	0.21597	0.0908:0.0:0.5911:0.3181	rs28446289;rs58765113;rs28446289	224	Q8NGZ3	O13G1_HUMAN	C	224	ENSP00000352717:R224C	ENSP00000352717:R224C	R	-	1	0	OR13G1	245902297	0.000000	0.05858	0.001000	0.08648	0.335000	0.28730	0.339000	0.19875	0.122000	0.18314	0.563000	0.77884	CGT	G|0.665;A|0.335	0.335	strong		0.428	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487	
C5orf22	55322	hgsc.bcm.edu	37	5	31534460	31534460	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:31534460C>T	ENST00000325366.9	+	2	290	c.163C>T	c.(163-165)Cca>Tca	p.P55S	C5orf22_ENST00000355907.3_5'UTR|DROSHA_ENST00000511367.2_5'Flank|DROSHA_ENST00000513349.1_5'Flank|DROSHA_ENST00000504361.1_5'Flank	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	55										kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						CGACTCACATCCAGACCTCCT	0.403																																					p.P55S		Atlas-SNP	.											C5orf22,NS,malignant_melanoma,0,2	C5orf22	48	2	0			c.C163T						scavenged	.						173.0	161.0	165.0					5																	31534460		2203	4300	6503	SO:0001583	missense	55322	exon2			TCACATCCAGACC	AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.163C>T	5.37:g.31534460C>T	ENSP00000326879:p.Pro55Ser	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	271	4	0.0147601	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Missense_Mutation	SNP	ENST00000325366.9	37	CCDS3895.1	.	.	.	.	.	.	.	.	.	.	C	34	5.301546	0.95601	.	.	ENSG00000082213	ENST00000325366;ENST00000507818	T;T	0.50001	0.76;0.76	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.67163	0.2864	M	0.72479	2.2	0.80722	D	1	D	0.60575	0.988	P	0.60473	0.875	T	0.70392	-0.4884	10	0.87932	D	0	-8.0573	19.3533	0.94401	0.0:1.0:0.0:0.0	.	55	Q49AR2	CE022_HUMAN	S	55	ENSP00000326879:P55S;ENSP00000430860:P55S	ENSP00000326879:P55S	P	+	1	0	C5orf22	31570217	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.961000	0.76042	2.559000	0.86315	0.655000	0.94253	CCA	.	.	none		0.403	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356	
FAM214A	56204	hgsc.bcm.edu	37	15	52901977	52901977	+	Silent	SNP	G	G	A	rs2414166	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:52901977G>A	ENST00000261844.7	-	6	1286	c.1134C>T	c.(1132-1134)gcC>gcT	p.A378A	FAM214A_ENST00000546305.2_Silent_p.A385A	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	378								p.A378A(1)									TCAAATGTTGGGCAATTCTTG	0.418													G|||	2089	0.417133	0.202	0.6095	5008	,	,		19527	0.1081		0.7445	False		,,,				2504	0.5532				p.A378A		Atlas-SNP	.											KIAA1370,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C1134T						scavenged	.	G		1126,2538		154,818,860	85.0	78.0	80.0		1134	-1.7	1.0	15	dbSNP_100	80	5986,2198		2198,1590,304	no	coding-synonymous	KIAA1370	NM_019600.2		2352,2408,1164	AA,AG,GG		26.8573,30.7314,39.973		378/1077	52901977	7112,4736	1832	4092	5924	SO:0001819	synonymous_variant	56204	exon6			ATGTTGGGCAATT	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.1134C>T	15.37:g.52901977G>A		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			G|0.561;A|0.439	0.439	strong		0.418	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
NLRP8	126205	hgsc.bcm.edu	37	19	56459458	56459458	+	Missense_Mutation	SNP	C	C	T	rs61195059	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56459458C>T	ENST00000291971.3	+	1	261	c.190C>T	c.(190-192)Ctc>Ttc	p.L64F	NLRP8_ENST00000590542.1_Missense_Mutation_p.L64F	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	64	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		ACTGACTGAGCTCAGTACTGG	0.562													C|||	329	0.0656949	0.1014	0.0648	5008	,	,		17703	0.005		0.0696	False		,,,				2504	0.0767				p.L64F		Atlas-SNP	.											.	NLRP8	225	.	0			c.C190T						PASS	.	C	PHE/LEU	511,3895	236.1+/-248.4	31,449,1723	112.0	88.0	96.0		190	-0.6	0.0	19	dbSNP_129	96	515,8085	145.1+/-200.9	16,483,3801	yes	missense	NLRP8	NM_176811.2	22	47,932,5524	TT,TC,CC		5.9884,11.5978,7.8887	possibly-damaging	64/1049	56459458	1026,11980	2203	4300	6503	SO:0001583	missense	126205	exon1			ACTGAGCTCAGTA	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.190C>T	19.37:g.56459458C>T	ENSP00000291971:p.Leu64Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	141	0.06456043956043957	57	0.11585365853658537	28	0.07734806629834254	1	0.0017482517482517483	55	0.07255936675461741	C	0.017	-1.488451	0.01018	0.115978	0.059884	ENSG00000179709	ENST00000291971	T	0.61274	0.12	1.75	-0.573	0.11742	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.00608	0.0020	L	0.38175	1.15	0.80722	P	0.0	B;B	0.13594	0.005;0.008	B;B	0.18263	0.007;0.021	T	0.08330	-1.0727	8	0.42905	T	0.14	.	2.2831	0.04119	0.299:0.5096:0.0:0.1914	rs61195059;rs61738700	64;64	Q86W28-2;Q86W28	.;NALP8_HUMAN	F	64	ENSP00000291971:L64F	ENSP00000291971:L64F	L	+	1	0	NLRP8	61151270	0.022000	0.18835	0.000000	0.03702	0.002000	0.02628	0.195000	0.17155	-0.067000	0.12976	-1.322000	0.01289	CTC	C|0.925;T|0.075	0.075	strong		0.562	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
SNX18	112574	hgsc.bcm.edu	37	5	53815066	53815066	+	Silent	SNP	C	C	A	rs2548613	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:53815066C>A	ENST00000326277.3	+	1	1474	c.1284C>A	c.(1282-1284)atC>atA	p.I428I	SNX18_ENST00000381410.4_Silent_p.I428I|SNX18_ENST00000343017.6_Silent_p.I428I	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	428	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				AGAGCAAGATCGACGGCTTCA	0.617													c|||	1740	0.347444	0.3979	0.3674	5008	,	,		20413	0.2897		0.4056	False		,,,				2504	0.2648				p.I428I		Atlas-SNP	.											.	SNX18	102	.	0			c.C1284A						PASS	.	C	,,	1854,2552	528.2+/-372.3	412,1030,761	52.0	58.0	56.0		1284,1284,1284	2.3	1.0	5	dbSNP_100	56	3227,5373	482.7+/-370.9	610,2007,1683	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX18	NM_001102575.1,NM_001145427.1,NM_052870.2	,,	1022,3037,2444	AA,AC,CC		37.5233,42.079,39.0666	,,	428/625,428/592,428/629	53815066	5081,7925	2203	4300	6503	SO:0001819	synonymous_variant	112574	exon1			CAAGATCGACGGC	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1284C>A	5.37:g.53815066C>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Silent	SNP	ENST00000326277.3	37	CCDS3962.1																																																																																			C|0.625;A|0.375	0.375	strong		0.617	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
LMX1B	4010	hgsc.bcm.edu	37	9	129455587	129455587	+	Silent	SNP	G	G	C	rs13295990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:129455587G>C	ENST00000373474.4	+	4	733	c.726G>C	c.(724-726)tcG>tcC	p.S242S	LMX1B_ENST00000561065.1_Silent_p.S219S|LMX1B_ENST00000355497.5_Silent_p.S242S|LMX1B_ENST00000526117.1_Silent_p.S242S|LMX1B_ENST00000425646.2_Silent_p.S219S			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	242					cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						AGGTCTCGTCGAAGCCTTGCC	0.697									Nail-Patella Syndrome				C|||	2200	0.439297	0.4009	0.3948	5008	,	,		16241	0.5575		0.4364	False		,,,				2504	0.4039				p.S242S	Pancreas(110;1796 2278 18357 20466)	Atlas-SNP	.											LMX1B_ENST00000355497,NS,carcinoma,+1,2	LMX1B	86	2	0			c.G726C						PASS	.	C	,,	1731,2659		383,965,847	24.0	26.0	26.0		726,726,726	3.1	1.0	9	dbSNP_121	26	3691,4903		818,2055,1424	no	coding-synonymous,coding-synonymous,coding-synonymous	LMX1B	NM_001174146.1,NM_001174147.1,NM_002316.3	,,	1201,3020,2271	CC,CG,GG		42.9486,39.4305,41.7591	,,	242/407,242/403,242/396	129455587	5422,7562	2195	4297	6492	SO:0001819	synonymous_variant	4010	exon4	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	CTCGTCGAAGCCT	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"""Homeoboxes / LIM class"""	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.726G>C	9.37:g.129455587G>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_001174146	F8W7W6|O75463|Q5JU95|Q6ISC9	Silent	SNP	ENST00000373474.4	37	CCDS55342.1																																																																																			G|0.573;C|0.427	0.427	strong		0.697	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2		
SLCO1B3	28234	hgsc.bcm.edu	37	12	21054369	21054369	+	Silent	SNP	G	G	A	rs3764006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:21054369G>A	ENST00000381545.3	+	15	2052	c.1833G>A	c.(1831-1833)ggG>ggA	p.G611G	SLCO1B3_ENST00000553473.1_Silent_p.G611G|SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000381541.3_Intron|SLCO1B3_ENST00000261196.2_Silent_p.G611G|LST3_ENST00000540229.1_Silent_p.G611G	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	611					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	GAGCACAAGGGGCTTGTAGGA	0.358													G|||	3399	0.678714	0.2375	0.7882	5008	,	,		17480	0.7312		0.8757	False		,,,				2504	0.9407				p.G611G		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.G1833A						PASS	.	G		1599,2807		297,1005,901	182.0	175.0	177.0		1833	-9.1	0.0	12	dbSNP_107	177	7666,934		3417,832,51	no	coding-synonymous	SLCO1B3	NM_019844.2		3714,1837,952	AA,AG,GG		10.8605,36.2914,28.7636		611/703	21054369	9265,3741	2203	4300	6503	SO:0001819	synonymous_variant	28234	exon15			ACAAGGGGCTTGT		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1833G>A	12.37:g.21054369G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_019844	E7EMT8|Q5JAR4	Silent	SNP	ENST00000381545.3	37	CCDS8684.1																																																																																			G|0.312;A|0.688	0.688	strong		0.358	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
SLC26A8	116369	hgsc.bcm.edu	37	6	35980121	35980121	+	Missense_Mutation	SNP	C	C	T	rs743923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:35980121C>T	ENST00000490799.1	-	3	570	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	SLC26A8_ENST00000355574.2_Missense_Mutation_p.V73M|SLC26A8_ENST00000394602.2_Missense_Mutation_p.V73M	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						ATTGTAAGCACGCATCGTAGG	0.458													T|||	1307	0.260982	0.4652	0.2277	5008	,	,		21601	0.1151		0.2366	False		,,,				2504	0.184				p.V73M		Atlas-SNP	.											.	SLC26A8	95	.	0			c.G217A						PASS	.	T	MET/VAL,MET/VAL,MET/VAL	1815,2591	638.7+/-397.0	369,1077,757	163.0	148.0	153.0		217,217,217	-2.6	0.1	6	dbSNP_86	153	2119,6481	716.1+/-406.1	273,1573,2454	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	21,21,21	642,2650,3211	TT,TC,CC		24.6395,41.1938,30.2476	benign,benign,benign	73/971,73/971,73/866	35980121	3934,9072	2203	4300	6503	SO:0001583	missense	116369	exon3			TAAGCACGCATCG	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.217G>A	6.37:g.35980121C>T	ENSP00000417638:p.Val73Met	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	80	49	0.6125	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	555	0.2541208791208791	208	0.42276422764227645	93	0.2569060773480663	73	0.12762237762237763	181	0.23878627968337732	T	4.919	0.170748	0.09391	0.411938	0.246395	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574;ENST00000480663	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.81	-2.58	0.06228	.	0.746757	0.13261	N	0.401271	T	0.03178	0.0093	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.001	T	0.36915	-0.9728	9	0.23891	T	0.37	.	1.9852	0.03435	0.1208:0.1984:0.3719:0.3089	rs743923;rs16883644;rs17845762;rs17858719;rs52822911;rs61568225;rs743923	73;73	Q96RN1;Q96RN1-2	S26A8_HUMAN;.	M	73;73;73;159	ENSP00000417638:V73M;ENSP00000378100:V73M;ENSP00000347778:V73M;ENSP00000420488:V159M	ENSP00000347778:V73M	V	-	1	0	SLC26A8	36088099	0.614000	0.27017	0.066000	0.19879	0.692000	0.40212	0.027000	0.13621	-0.450000	0.07107	-0.269000	0.10298	GTG	C|0.714;T|0.286	0.286	strong		0.458	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
RGL3	57139	hgsc.bcm.edu	37	19	11526765	11526765	+	Missense_Mutation	SNP	G	G	T	rs167479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11526765G>T	ENST00000380456.3	-	5	548	c.485C>A	c.(484-486)cCc>cAc	p.P162H	RGL3_ENST00000393423.3_Missense_Mutation_p.P162H	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	162	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.		P -> H (in dbSNP:rs167479). {ECO:0000269|PubMed:15489334}.		small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						ATGGGCAGGGGGGTCTCGGAA	0.622													G|||	2232	0.445687	0.1861	0.5476	5008	,	,		14345	0.4782		0.4602	False		,,,				2504	0.6759				p.P162H	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.C485A						PASS	.	G	HIS/PRO,HIS/PRO	1036,3370		122,792,1289	26.0	31.0	30.0		485,485	3.8	1.0	19	dbSNP_79	30	4171,4429		1031,2109,1160	yes	missense,missense	RGL3	NM_001035223.2,NM_001161616.1	77,77	1153,2901,2449	TT,TG,GG		48.5,23.5134,40.0354	benign,benign	162/711,162/717	11526765	5207,7799	2203	4300	6503	SO:0001583	missense	57139	exon5			GCAGGGGGGTCTC	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.485C>A	19.37:g.11526765G>T	ENSP00000369823:p.Pro162His	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	37	CCDS32910.1	880	0.40293040293040294	86	0.17479674796747968	188	0.5193370165745856	265	0.4632867132867133	341	0.449868073878628	G	19.51	3.841900	0.71488	0.235134	0.485	ENSG00000205517	ENST00000393423;ENST00000380456	T;T	0.30182	1.54;1.54	4.88	3.81	0.43845	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.126603	0.52532	D	0.000062	T	0.00012	0.0000	M	0.72894	2.215	0.27426	P	0.9541637	D;D	0.89917	0.992;1.0	D;D	0.79784	0.943;0.993	T	0.48758	-0.9007	9	0.87932	D	0	.	13.1993	0.59758	0.0:0.0:0.839:0.161	rs167479;rs167515;rs1687569;rs61292330;rs167479	162;162	Q3MIN7;B5ME84	RGL3_HUMAN;.	H	162	ENSP00000377075:P162H;ENSP00000369823:P162H	ENSP00000369823:P162H	P	-	2	0	RGL3	11387765	1.000000	0.71417	0.951000	0.38953	0.871000	0.50021	3.633000	0.54295	0.990000	0.38787	0.511000	0.50034	CCC	G|0.596;T|0.404	0.404	strong		0.622	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123291036	123291036	+	Missense_Mutation	SNP	C	C	G	rs4836822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:123291036C>G	ENST00000349780.4	-	9	1044	c.865G>C	c.(865-867)Gaa>Caa	p.E289Q	CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.E289Q|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.E289Q|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.E289Q	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	289			E -> Q (in dbSNP:rs4836822). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:17974005}.		brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						ATCCTCTCTTCAAAGCTGTTT	0.393													C|||	4012	0.801118	0.6808	0.866	5008	,	,		21742	0.7123		0.9374	False		,,,				2504	0.8691				p.E289Q		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.G865C						PASS	.	C	GLN/GLU,GLN/GLU	3053,1353	692.5+/-405.5	1063,927,213	122.0	113.0	116.0		865,865	4.0	1.0	9	dbSNP_111	116	7981,619	791.2+/-407.6	3700,581,19	yes	missense,missense	CDK5RAP2	NM_001011649.1,NM_018249.4	29,29	4763,1508,232	GG,GC,CC		7.1977,30.7081,15.1622	probably-damaging,probably-damaging	289/1815,289/1894	123291036	11034,1972	2203	4300	6503	SO:0001583	missense	55755	exon9			TCTCTTCAAAGCT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.865G>C	9.37:g.123291036C>G	ENSP00000343818:p.Glu289Gln	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	37	CCDS6823.1	1794	0.8214285714285714	349	0.709349593495935	324	0.8950276243093923	411	0.7185314685314685	710	0.9366754617414248	C	11.62	1.694259	0.30052	0.692919	0.928023	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000345313;ENST00000482047	T;T;T;T;T	0.46451	3.78;3.64;3.74;3.64;0.87	4.91	3.97	0.46021	.	0.000000	0.52532	D	0.000067	T	0.00012	0.0000	M	0.67953	2.075	0.24200	P	0.99551274	P;B;P	0.47841	0.873;0.003;0.901	P;B;P	0.51297	0.619;0.015;0.665	T	0.04128	-1.0975	9	0.41790	T	0.15	.	12.2205	0.54431	0.0:0.8277:0.1723:0.0	rs4836822;rs56428300;rs59989067;rs4836822	289;289;289	Q96SN8-2;Q96SN8-4;Q96SN8	.;.;CK5P2_HUMAN	Q	289;289;289;289;291;43	ENSP00000354065:E289Q;ENSP00000352258:E289Q;ENSP00000343818:E289Q;ENSP00000353317:E289Q;ENSP00000419640:E43Q	ENSP00000341695:E291Q	E	-	1	0	CDK5RAP2	122330857	1.000000	0.71417	0.961000	0.40146	0.485000	0.33311	2.527000	0.45615	1.121000	0.41925	0.557000	0.71058	GAA	C|0.168;G|0.832	0.832	strong		0.393	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
AKAP3	10566	hgsc.bcm.edu	37	12	4737042	4737042	+	Silent	SNP	G	G	A	rs7972737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:4737042G>A	ENST00000545990.2	-	5	1550	c.1026C>T	c.(1024-1026)caC>caT	p.H342H	AKAP3_ENST00000228850.1_Silent_p.H342H|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	342					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						CTGTGACGCTGTGGAGATTCC	0.488													G|||	1425	0.284545	0.0371	0.4625	5008	,	,		23282	0.2073		0.5258	False		,,,				2504	0.3241				p.H342H		Atlas-SNP	.											AKAP3_ENST00000545990,colon,carcinoma,0,2	AKAP3	212	2	0			c.C1026T						PASS	.	G		482,3924	224.3+/-240.5	40,402,1761	157.0	149.0	152.0		1026	3.8	1.0	12	dbSNP_116	152	4404,4196	585.5+/-391.9	1154,2096,1050	no	coding-synonymous	AKAP3	NM_006422.2		1194,2498,2811	AA,AG,GG		48.7907,10.9396,37.5673		342/854	4737042	4886,8120	2203	4300	6503	SO:0001819	synonymous_variant	10566	exon4			GACGCTGTGGAGA	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1026C>T	12.37:g.4737042G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	229	229	1	NM_006422	O75945|Q86X01|Q9UM61	Silent	SNP	ENST00000545990.2	37	CCDS8531.1																																																																																			G|0.653;A|0.347	0.347	strong		0.488	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
ZBED4	9889	hgsc.bcm.edu	37	22	50280136	50280136	+	Silent	SNP	T	T	C	rs5770755	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50280136T>C	ENST00000216268.5	+	2	3303	c.2826T>C	c.(2824-2826)gcT>gcC	p.A942A		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	942						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CCTTCGAGGCTGCGAGCCGGG	0.582													T|||	2955	0.590056	0.174	0.8199	5008	,	,		20444	0.8264		0.7932	False		,,,				2504	0.5368				p.A942A		Atlas-SNP	.											.	ZBED4	102	.	0			c.T2826C						PASS	.	T		1268,3138	431.8+/-343.0	191,886,1126	93.0	66.0	75.0		2826	-11.9	0.0	22	dbSNP_114	75	6766,1834	731.2+/-406.8	2662,1442,196	no	coding-synonymous	ZBED4	NM_014838.2		2853,2328,1322	CC,CT,TT		21.3256,28.7789,38.2285		942/1172	50280136	8034,4972	2203	4300	6503	SO:0001819	synonymous_variant	9889	exon2			CGAGGCTGCGAGC	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.2826T>C	22.37:g.50280136T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			T|0.382;C|0.618	0.618	strong		0.582	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
SPATA3	130560	hgsc.bcm.edu	37	2	231865144	231865144	+	Missense_Mutation	SNP	G	G	C	rs12105962	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231865144G>C	ENST00000452881.1	+	2	473	c.365G>C	c.(364-366)tGc>tCc	p.C122S	SPATA3_ENST00000433428.2_Missense_Mutation_p.C122S|SPATA3_ENST00000455816.1_Missense_Mutation_p.C122S|SPATA3_ENST00000409956.1_Intron|SPATA3_ENST00000424440.1_Missense_Mutation_p.C122S			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	122										endometrium(2)|lung(1)	3						AGCTCCGCTTGCTGGCGTCGT	0.652													G|||	1085	0.216653	0.1876	0.3256	5008	,	,		17115	0.1736		0.2565	False		,,,				2504	0.182				p.C122S		Atlas-SNP	.											.	SPATA3	52	.	0			c.G365C						PASS	.	G	SER/CYS	251,1133		19,213,460	37.0	35.0	36.0		365	4.2	1.0	2	dbSNP_120	36	817,2365		99,619,873	yes	missense	SPATA3	NM_139073.3	112	118,832,1333	CC,CG,GG		25.6757,18.1358,23.3903	probably-damaging	122/193	231865144	1068,3498	692	1591	2283	SO:0001583	missense	130560	exon2			CCGCTTGCTGGCG	AY032925	CCDS2481.1	2q37.1	2008-02-05			ENSG00000173699	ENSG00000173699			17884	protein-coding gene	gene with protein product							Standard	NM_139073		Approved	TSARG1	uc010zmd.2	Q8NHX4	OTTHUMG00000133221	ENST00000452881.1:c.365G>C	2.37:g.231865144G>C	ENSP00000388895:p.Cys122Ser	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	273	150	0.549451	NM_139073	Q86WX5|Q8N9Y6	Missense_Mutation	SNP	ENST00000452881.1	37	CCDS2481.1	513	0.2348901098901099	94	0.1910569105691057	119	0.3287292817679558	106	0.1853146853146853	194	0.2559366754617414	G	10.64	1.405615	0.25378	0.181358	0.256757	ENSG00000173699	ENST00000424440;ENST00000452881;ENST00000433428;ENST00000455816;ENST00000355662	.	.	.	4.25	4.25	0.50352	.	0.000000	0.49916	D	0.000135	T	0.00012	0.0000	L	0.34521	1.04	0.26558	P	0.9737856	D	0.89917	1.0	D	0.87578	0.998	T	0.16335	-1.0406	8	0.66056	D	0.02	-27.4861	12.4701	0.55781	0.0:0.0:1.0:0.0	rs12105962;rs59056322	113	Q8NHX4	SPTA3_HUMAN	S	122;122;122;122;113	.	ENSP00000347884:C113S	C	+	2	0	SPATA3	231573388	1.000000	0.71417	1.000000	0.80357	0.527000	0.34593	3.817000	0.55668	2.657000	0.90304	0.655000	0.94253	TGC	G|0.771;C|0.229	0.229	strong		0.652	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
LRRC48	83450	hgsc.bcm.edu	37	17	17896205	17896205	+	Missense_Mutation	SNP	C	C	T	rs4584886	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17896205C>T	ENST00000399187.1	+	6	789	c.571C>T	c.(571-573)Cgg>Tgg	p.R191W	LRRC48_ENST00000399182.1_Missense_Mutation_p.R191W|LRRC48_ENST00000584166.1_Missense_Mutation_p.R191W|LRRC48_ENST00000313838.8_Missense_Mutation_p.R191W|LRRC48_ENST00000411504.2_Missense_Mutation_p.R191W	NM_031294.3	NP_112584.3	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48	191	LRRCT.		R -> W (in dbSNP:rs4584886). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)				breast(1)|large_intestine(2)|lung(2)|pancreas(1)|urinary_tract(1)	7	all_neural(463;0.228)					CCTGGACTACCGGCGCATTGA	0.542													C|||	2915	0.582069	0.4153	0.5187	5008	,	,		20965	0.8641		0.3748	False		,,,				2504	0.7751				p.R191W		Atlas-SNP	.											.	LRRC48	49	.	0			c.C571T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1688,2530		355,978,776	93.0	93.0	93.0		571,571,571,571	3.0	1.0	17	dbSNP_111	93	2759,5693		452,1855,1919	yes	missense,missense,missense,missense	LRRC48	NM_001130090.1,NM_001130091.1,NM_001130092.1,NM_031294.3	101,101,101,101	807,2833,2695	TT,TC,CC		32.6432,40.019,35.0987	probably-damaging,probably-damaging,probably-damaging,probably-damaging	191/524,191/458,191/458,191/524	17896205	4447,8223	2109	4226	6335	SO:0001583	missense	83450	exon6			GACTACCGGCGCA	AK093317	CCDS45622.1, CCDS45623.1	17p11.2	2014-07-18			ENSG00000171962	ENSG00000171962			25384	protein-coding gene	gene with protein product						11997338, 23354437	Standard	NM_001130090		Approved	DKFZP586M1120	uc021trk.1	Q9H069	OTTHUMG00000059355	ENST00000399187.1:c.571C>T	17.37:g.17896205C>T	ENSP00000382140:p.Arg191Trp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	147	62	0.421769	NM_031294	A8KAE6|Q86SF9|Q86W73|Q8IWG0	Missense_Mutation	SNP	ENST00000399187.1	37	CCDS45622.1	1170	0.5357142857142857	220	0.44715447154471544	167	0.4613259668508287	503	0.8793706293706294	280	0.36939313984168864	C	18.50	3.637604	0.67130	0.40019	0.326432	ENSG00000171962	ENST00000313838;ENST00000448396;ENST00000411504;ENST00000399184;ENST00000399187;ENST00000399182;ENST00000399185	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	5.22	3.04	0.35103	.	0.200569	0.51477	D	0.000091	T	0.00012	0.0000	M	0.86740	2.835	0.09310	P	0.999999999725949	D;D	0.89917	1.0;1.0	D;D	0.74674	0.964;0.984	T	0.11916	-1.0568	9	0.72032	D	0.01	-17.5	12.1487	0.54038	0.4277:0.5723:0.0:0.0	rs4584886;rs17854522;rs17859520;rs59823215;rs4584886	191;191	Q9H069;Q9H069-2	LRC48_HUMAN;.	W	191	ENSP00000326870:R191W;ENSP00000394020:R191W;ENSP00000382140:R191W;ENSP00000382136:R191W	ENSP00000326870:R191W	R	+	1	2	LRRC48	17836930	1.000000	0.71417	0.986000	0.45419	0.690000	0.40134	3.333000	0.52090	1.156000	0.42514	0.655000	0.94253	CGG	C|0.472;T|0.528	0.528	strong		0.542	LRRC48-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131945.3	NM_031294	
LRRN2	10446	hgsc.bcm.edu	37	1	204587240	204587240	+	Silent	SNP	G	G	A	rs3747632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204587240G>A	ENST00000367175.1	-	1	4093	c.1881C>T	c.(1879-1881)gaC>gaT	p.D627D	LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367176.3_Silent_p.D627D|LRRN2_ENST00000367177.3_Silent_p.D627D|RP11-430C7.4_ENST00000453895.1_RNA			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	627					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GCCCAGGACGGTCCCCTAAGG	0.632													G|||	1473	0.294129	0.0318	0.5014	5008	,	,		20223	0.3383		0.4294	False		,,,				2504	0.317				p.D627D		Atlas-SNP	.											.	LRRN2	81	.	0			c.C1881T						PASS	.	G	,	424,3982	204.5+/-226.7	29,366,1808	45.0	47.0	46.0		1881,1881	3.7	1.0	1	dbSNP_107	46	3886,4714	540.4+/-383.8	881,2124,1295	no	coding-synonymous,coding-synonymous	LRRN2	NM_006338.2,NM_201630.1	,	910,2490,3103	AA,AG,GG		45.186,9.6232,33.1386	,	627/714,627/714	204587240	4310,8696	2203	4300	6503	SO:0001819	synonymous_variant	10446	exon3			AGGACGGTCCCCT	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1881C>T	1.37:g.204587240G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Silent	SNP	ENST00000367175.1	37	CCDS1448.1																																																																																			G|0.690;A|0.310	0.310	strong		0.632	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
KMT2C	58508	hgsc.bcm.edu	37	7	151970951	151970951	+	Splice_Site	SNP	C	C	T	rs201009236		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151970951C>T	ENST00000262189.6	-	7	1069	c.851G>A	c.(850-852)cGa>cAa	p.R284Q	KMT2C_ENST00000355193.2_Splice_Site_p.R284Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	284					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AAATGCACATCGCTGAAAGGG	0.393																																					p.R284Q		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,12	MLL3	1564	12	0			c.G851A						scavenged	.						54.0	51.0	52.0					7																	151970951		2202	4299	6501	SO:0001630	splice_region_variant	58508	exon7			GCACATCGCTGAA	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.850-1G>A	7.37:g.151970951C>T		Somatic	411	0	0		WXS	Illumina HiSeq	Phase_I	338	10	0.0295858	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	14.49	2.551821	0.45487	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.70631	-0.5;-0.5	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.258206	0.20689	N	0.087494	T	0.78381	0.4274	M	0.69463	2.115	0.80722	D	1	D	0.58970	0.984	P	0.52159	0.691	T	0.81093	-0.1089	10	0.59425	D	0.04	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	284	Q8NEZ4	MLL3_HUMAN	Q	284	ENSP00000262189:R284Q;ENSP00000347325:R284Q	ENSP00000262189:R284Q	R	-	2	0	MLL3	151601884	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.773000	0.55333	2.423000	0.82170	0.650000	0.86243	CGA	C|0.750;T|0.250	0.250	strong		0.393	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		Missense_Mutation
MEDAG	84935	hgsc.bcm.edu	37	13	31495733	31495733	+	Silent	SNP	C	C	T	rs6563571	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:31495733C>T	ENST00000380482.4	+	4	862	c.537C>T	c.(535-537)ccC>ccT	p.P179P	TEX26-AS1_ENST00000590344.1_RNA|TEX26-AS1_ENST00000590721.1_RNA|TEX26-AS1_ENST00000451495.2_RNA|TEX26-AS1_ENST00000588726.1_RNA|TEX26-AS1_ENST00000586464.1_RNA|TEX26-AS1_ENST00000588425.1_RNA|TEX26-AS1_ENST00000592950.1_RNA|TEX26-AS1_ENST00000593246.1_RNA|TEX26-AS1_ENST00000586973.1_RNA|TEX26-AS1_ENST00000585870.1_RNA	NM_032849.3	NP_116238	Q5VYS4	MEDAG_HUMAN	mesenteric estrogen-dependent adipogenesis	179					positive regulation of fat cell differentiation (GO:0045600)	cytoplasm (GO:0005737)											ATTTCTTCCCCCCAGGAAATG	0.353													C|||	437	0.0872604	0.1324	0.1239	5008	,	,		18226	0.0139		0.0994	False		,,,				2504	0.0634				p.P179P		Atlas-SNP	.											.	.	.	.	0			c.C537T						PASS	.	C		548,3858	240.9+/-251.5	36,476,1691	88.0	88.0	88.0		537	1.6	1.0	13	dbSNP_116	88	686,7914	171.2+/-222.1	24,638,3638	no	coding-synonymous	C13orf33	NM_032849.3		60,1114,5329	TT,TC,CC		7.9767,12.4376,9.4879		179/304	31495733	1234,11772	2203	4300	6503	SO:0001819	synonymous_variant	84935	exon4			CTTCCCCCCAGGA	AB055407	CCDS9338.1	13q12.3	2013-10-11	2012-09-26	2012-09-26	ENSG00000102802	ENSG00000102802			25926	protein-coding gene	gene with protein product	"""mesenteric estrogen-dependent adipose 4"", ""activated in W/Wv mouse stomach 3 homolog"""		"""chromosome 13 open reading frame 33"""	C13orf33		22510272	Standard	NM_032849		Approved	FLJ14834, AWMS3, MEDA-4	uc001uth.4	Q5VYS4	OTTHUMG00000016679	ENST00000380482.4:c.537C>T	13.37:g.31495733C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	122	51	0.418033	NM_032849	Q8IXF1|Q96K26|Q96NC8	Silent	SNP	ENST00000380482.4	37	CCDS9338.1																																																																																			C|0.908;T|0.092	0.092	strong		0.353	MEDAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044375.1	NM_032849	
FAM21A	387680	hgsc.bcm.edu	37	10	47909792	47909792	+	Missense_Mutation	SNP	C	C	T	rs201373575	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:47909792C>T	ENST00000358474.5	+	11	889	c.889C>T	c.(889-891)Cgg>Tgg	p.R297W		NM_018232.1	NP_060702.1	Q5SNT6	FA21B_HUMAN		297					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.R297W(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						CCCCCAGGATCGGCAAGCTGG	0.498													C|||	1254	0.250399	0.1861	0.1513	5008	,	,		7006	0.4306		0.2028	False		,,,				2504	0.271				p.R297W		Atlas-SNP	.											FAM21B_ENST00000358474,NS,carcinoma,0,2	FAM21B	31	2	2	Substitution - Missense(2)	prostate(2)	c.C889T						scavenged	.						17.0	21.0	20.0					10																	47909792		589	2506	3095	SO:0001583	missense	55747	exon11			CAGGATCGGCAAG																												ENST00000358474.5:c.889C>T	10.37:g.47909792C>T	ENSP00000351259:p.Arg297Trp	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	147	8	0.0544218	NM_018232		Missense_Mutation	SNP	ENST00000358474.5	37	CCDS44379.1	.	.	.	.	.	.	.	.	.	.	.	12.06	1.824831	0.32237	.	.	ENSG00000152726	ENST00000358474;ENST00000535219;ENST00000355876	.	.	.	2.3	1.19	0.21007	.	1.629960	0.03041	N	0.153324	T	0.31295	0.0792	M	0.68317	2.08	0.09310	N	1	P;B	0.39352	0.669;0.41	B;B	0.20577	0.03;0.021	T	0.44922	-0.9296	9	0.72032	D	0.01	0.1363	5.4742	0.16686	0.3296:0.6704:0.0:0.0	.	297;385	Q5SNT6;B7ZME8	FA21B_HUMAN;.	W	297;134;288	.	ENSP00000348138:R288W	R	+	1	2	FAM21B	47429798	0.000000	0.05858	0.005000	0.12908	0.138000	0.21146	0.358000	0.20216	1.299000	0.44798	0.152000	0.16155	CGG	C|0.949;T|0.051	0.051	strong		0.498	FAM21B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047871.2		
SLC4A7	9497	hgsc.bcm.edu	37	3	27478899	27478899	+	Silent	SNP	A	A	G	rs2029618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:27478899A>G	ENST00000295736.5	-	4	451	c.381T>C	c.(379-381)taT>taC	p.Y127Y	SLC4A7_ENST00000425128.2_Silent_p.Y132Y|SLC4A7_ENST00000428386.1_Silent_p.Y127Y|SLC4A7_ENST00000446700.1_Silent_p.Y132Y|SLC4A7_ENST00000454389.1_Silent_p.Y136Y|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000435667.2_Silent_p.Y136Y|SLC4A7_ENST00000440156.1_Silent_p.Y136Y|SLC4A7_ENST00000445684.1_Silent_p.Y136Y|SLC4A7_ENST00000437179.1_Silent_p.Y132Y|SLC4A7_ENST00000455077.1_Silent_p.Y132Y	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	127					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CTTTCCATTCATATTCTTCTC	0.398													A|||	520	0.103834	0.1543	0.1081	5008	,	,		16933	0.0446		0.1531	False		,,,				2504	0.0429				p.Y132Y		Atlas-SNP	.											.	SLC4A7	119	.	0			c.T396C						PASS	.	A		664,3742	280.2+/-275.2	44,576,1583	164.0	163.0	163.0		381	-2.6	0.9	3	dbSNP_94	163	1241,7359	249.3+/-276.6	93,1055,3152	no	coding-synonymous	SLC4A7	NM_003615.3		137,1631,4735	GG,GA,AA		14.4302,15.0704,14.6471		127/1215	27478899	1905,11101	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon4			CCATTCATATTCT	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.381T>C	3.37:g.27478899A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	70	42	0.6	NM_001258379	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			A|0.867;G|0.133	0.133	strong		0.398	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
DNAH12	201625	hgsc.bcm.edu	37	3	57475351	57475351	+	Missense_Mutation	SNP	T	T	G	rs6806444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:57475351T>G	ENST00000351747.2	-	12	1579	c.1399A>C	c.(1399-1401)Act>Cct	p.T467P	DNAH12_ENST00000389536.4_Missense_Mutation_p.T467P	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	467	Stem. {ECO:0000250}.		T -> P (in dbSNP:rs6806444).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						CGCACCATAGTGTAATGAATC	0.308													G|||	3173	0.633586	0.6074	0.6138	5008	,	,		15638	0.5		0.7087	False		,,,				2504	0.7434				p.T467P		Atlas-SNP	.											DNAH12,colon,carcinoma,0,1	DNAH12	182	1	0			c.A1399C						PASS	.	G	PRO/THR	871,513		284,303,105	83.0	65.0	71.0		1399	5.4	1.0	3	dbSNP_116	71	2182,1000		752,678,161	yes	missense	DNAH12	NM_178504.4	38	1036,981,266	GG,GT,TT		31.4268,37.0665,33.1362	benign	467/3093	57475351	3053,1513	692	1591	2283	SO:0001583	missense	201625	exon12			CCATAGTGTAATG	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.1399A>C	3.37:g.57475351T>G	ENSP00000295937:p.Thr467Pro	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	247	247	1	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		1360	0.6227106227106227	310	0.6300813008130082	221	0.6104972375690608	279	0.48776223776223776	550	0.7255936675461742	G	11.68	1.709438	0.30322	0.629335	0.685732	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536	T;T;T	0.21734	2.14;1.99;3.7	5.42	5.42	0.78866	.	0.077297	0.51477	N	0.000087	T	0.00012	0.0000	N	0.00413	-1.525	0.09310	P	0.9999999999993405	B	0.02656	0.0	B	0.01281	0.0	T	0.20306	-1.0279	9	0.17369	T	0.5	.	13.1521	0.59494	0.0:0.0:0.7088:0.2912	rs6806444;rs57940008;rs6806444	467	Q6ZR08	DYH12_HUMAN	P	467	ENSP00000295937:T467P;ENSP00000418137:T467P;ENSP00000374187:T467P	ENSP00000295937:T467P	T	-	1	0	DNAH12	57450391	1.000000	0.71417	0.963000	0.40424	0.982000	0.71751	2.310000	0.43708	1.305000	0.44909	-0.121000	0.15023	ACT	T|0.370;G|0.630	0.630	strong		0.308	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
KIAA1522	57648	hgsc.bcm.edu	37	1	33235626	33235626	+	Silent	SNP	G	G	A	rs3737995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33235626G>A	ENST00000373480.1	+	6	772	c.669G>A	c.(667-669)gcG>gcA	p.A223A	KIAA1522_ENST00000373481.3_Silent_p.A234A|KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Silent_p.A282A	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	223										breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				AGGCGGAGGCGGAGGCTGGCG	0.706													G|||	1542	0.307907	0.0333	0.438	5008	,	,		14338	0.4484		0.3648	False		,,,				2504	0.3834				p.A282A		Atlas-SNP	.											.	KIAA1522	68	.	0			c.G846A						PASS	.	G	,,	408,3616		29,350,1633	15.0	21.0	19.0		669,,846	-8.9	0.0	1	dbSNP_107	19	2943,5379		531,1881,1749	no	coding-synonymous,intron,coding-synonymous	KIAA1522	NM_001198972.1,NM_001198973.1,NM_020888.2	,,	560,2231,3382	AA,AG,GG		35.3641,10.1392,27.1424	,,	223/1036,,282/1095	33235626	3351,8995	2012	4161	6173	SO:0001819	synonymous_variant	57648	exon6			GGAGGCGGAGGCT	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.669G>A	1.37:g.33235626G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Silent	SNP	ENST00000373480.1	37	CCDS55588.1																																																																																			A|0.328;C|0.000;G|0.672	0.328	strong		0.706	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
ANKRD27	84079	hgsc.bcm.edu	37	19	33096816	33096816	+	Silent	SNP	C	C	T	rs7248273	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33096816C>T	ENST00000306065.4	-	24	2576	c.2418G>A	c.(2416-2418)aaG>aaA	p.K806K	SNORA68_ENST00000364518.1_RNA	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	806					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.K806K(1)		breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CACTGAGGTCCTTCTTATTGG	0.507													C|||	909	0.18151	0.2572	0.1297	5008	,	,		12726	0.2262		0.1113	False		,,,				2504	0.1421				p.K806K		Atlas-SNP	.											ANKRD27,NS,NS,0,1	ANKRD27	86	1	1	Substitution - coding silent(1)	pancreas(1)	c.G2418A						PASS	.	C		980,3426	359.9+/-315.0	113,754,1336	161.0	152.0	155.0		2418	5.8	1.0	19	dbSNP_116	155	1026,7574	215.0+/-254.5	62,902,3336	no	coding-synonymous	ANKRD27	NM_032139.2		175,1656,4672	TT,TC,CC		11.9302,22.2424,15.4237		806/1051	33096816	2006,11000	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon24			GAGGTCCTTCTTA	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2418G>A	19.37:g.33096816C>T		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	209	92	0.440191	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			C|0.838;N|0.000	.	strong		0.507	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
CIITA	4261	hgsc.bcm.edu	37	16	11001914	11001914	+	Silent	SNP	G	G	A	rs2229321	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11001914G>A	ENST00000324288.8	+	11	2698	c.2565G>A	c.(2563-2565)gcG>gcA	p.A855A	CIITA_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	855					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						TGGAGGCGGCGGGCCAAGACT	0.652			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								G|||	199	0.0397364	0.0348	0.0375	5008	,	,		15561	0.0		0.0944	False		,,,				2504	0.0327				p.A855A		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.G2565A						PASS	.	G		168,4222		2,164,2029	15.0	17.0	16.0		2565	-9.7	0.0	16	dbSNP_98	16	752,7832		39,674,3579	no	coding-synonymous	CIITA	NM_000246.3		41,838,5608	AA,AG,GG		8.7605,3.8269,7.0911		855/1131	11001914	920,12054	2195	4292	6487	SO:0001819	synonymous_variant	4261	exon11			GGCGGCGGGCCAA	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2565G>A	16.37:g.11001914G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			G|0.932;A|0.068	0.068	strong		0.652	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
DOCK6	57572	hgsc.bcm.edu	37	19	11358799	11358799	+	Missense_Mutation	SNP	G	G	A	rs12978266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11358799G>A	ENST00000294618.7	-	7	760	c.749C>T	c.(748-750)cCa>cTa	p.P250L		NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	250			P -> L (in dbSNP:rs12978266).		blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GGGTGGCTCTGGGCGGCTACA	0.577													G|||	2602	0.519569	0.118	0.634	5008	,	,		16734	0.5367		0.7316	False		,,,				2504	0.7454				p.P250L		Atlas-SNP	.											.	DOCK6	104	.	0			c.C749T						PASS	.	G	LEU/PRO	916,2964		122,672,1146	35.0	39.0	38.0		749	5.1	0.1	19	dbSNP_121	38	5789,2469		2043,1703,383	yes	missense	DOCK6	NM_020812.2	98	2165,2375,1529	AA,AG,GG		29.8983,23.6082,44.7603	possibly-damaging	250/2048	11358799	6705,5433	1940	4129	6069	SO:0001583	missense	57572	exon7			GGCTCTGGGCGGC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.749C>T	19.37:g.11358799G>A	ENSP00000294618:p.Pro250Leu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	1176	0.5384615384615384	64	0.13008130081300814	237	0.6546961325966851	314	0.548951048951049	561	0.7401055408970977	G	17.80	3.479027	0.63849	0.236082	0.701017	ENSG00000130158	ENST00000294618	T	0.16324	2.35	5.05	5.05	0.67936	.	0.127369	0.52532	D	0.000069	T	0.00012	0.0000	M	0.71581	2.175	0.09310	P	1.0	D	0.58268	0.982	P	0.58454	0.839	T	0.13124	-1.0521	9	0.72032	D	0.01	-31.0597	15.9008	0.79373	0.0:0.0:1.0:0.0	rs12978266;rs60245977;rs12978266	250	Q96HP0	DOCK6_HUMAN	L	250	ENSP00000294618:P250L	ENSP00000294618:P250L	P	-	2	0	DOCK6	11219799	1.000000	0.71417	0.070000	0.20053	0.409000	0.31022	7.197000	0.77814	2.343000	0.79666	0.462000	0.41574	CCA	G|0.480;A|0.520	0.520	strong		0.577	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
CEP152	22995	hgsc.bcm.edu	37	15	49048705	49048705	+	Missense_Mutation	SNP	G	G	C	rs16961560	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:49048705G>C	ENST00000380950.2	-	20	2927	c.2740C>G	c.(2740-2742)Ctt>Gtt	p.L914V	CEP152_ENST00000399334.3_Missense_Mutation_p.L914V|CEP152_ENST00000325747.5_Missense_Mutation_p.L821V	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	914			L -> V (in dbSNP:rs16961560).		cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		ATATTTTCAAGCTCACTCTTC	0.353													G|||	253	0.0505192	0.0053	0.0476	5008	,	,		17356	0.0724		0.0815	False		,,,				2504	0.0593				p.L914V		Atlas-SNP	.											.	CEP152	145	.	0			c.C2740G						PASS	.	G	VAL/LEU,VAL/LEU	50,3578		0,50,1764	42.0	40.0	41.0		2740,2740	0.3	0.9	15	dbSNP_123	41	603,7539		16,571,3484	yes	missense,missense	CEP152	NM_001194998.1,NM_014985.3	32,32	16,621,5248	CC,CG,GG		7.406,1.3782,5.548	benign,benign	914/1711,914/1655	49048705	653,11117	1814	4071	5885	SO:0001583	missense	22995	exon20			TTTCAAGCTCACT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.2740C>G	15.37:g.49048705G>C	ENSP00000370337:p.Leu914Val	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_014985	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	130	0.05952380952380952	3	0.006097560975609756	12	0.03314917127071823	47	0.08216783216783216	68	0.08970976253298153	G	7.966	0.748128	0.15710	0.013782	0.07406	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	T;T;T	0.54866	0.55;0.58;0.57	5.68	0.317	0.15861	.	0.691841	0.14451	N	0.318785	T	0.01287	0.0042	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.12013	0.001;0.005;0.005	B;B;B	0.12156	0.003;0.007;0.004	T	0.08513	-1.0718	9	0.17369	T	0.5	-0.3226	1.1175	0.01718	0.1777:0.1994:0.2942:0.3287	rs16961560;rs16961560	821;914;914	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	V	914;821;914	ENSP00000370337:L914V;ENSP00000321000:L821V;ENSP00000382271:L914V	ENSP00000321000:L821V	L	-	1	0	CEP152	46835997	0.606000	0.26949	0.894000	0.35097	0.974000	0.67602	0.785000	0.26830	-0.108000	0.12066	-0.229000	0.12294	CTT	G|0.933;C|0.067	0.067	strong		0.353	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	
ALOX12	239	hgsc.bcm.edu	37	17	6902760	6902760	+	Missense_Mutation	SNP	A	A	G	rs1126667	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6902760A>G	ENST00000251535.6	+	6	835	c.782A>G	c.(781-783)cAg>cGg	p.Q261R	RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000574377.1_3'UTR|AC027763.2_ENST00000575727.1_3'UTR	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	261	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		Q -> R (in dbSNP:rs1126667). {ECO:0000269|PubMed:15308583, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17151091, ECO:0000269|PubMed:17460548, ECO:0000269|PubMed:2217179, ECO:0000269|Ref.4}.		aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						GAAGAGCTTCAGGCTCAACTG	0.547													G|||	3025	0.604034	0.6861	0.67	5008	,	,		18708	0.5218		0.5984	False		,,,				2504	0.5368				p.Q261R		Atlas-SNP	.											ALOX12,colon,carcinoma,+1,1	ALOX12	49	1	0			c.A782G	GRCh37	CM062424	ALOX12	M	rs1126667	PASS	.	G	ARG/GLN	2939,1467	473.0+/-356.5	975,989,239	122.0	103.0	110.0		782	-6.1	0.0	17	dbSNP_86	110	4970,3630	523.2+/-380.3	1438,2094,768	yes	missense	ALOX12	NM_000697.2	43	2413,3083,1007	GG,GA,AA		42.2093,33.2955,39.1896	benign	261/664	6902760	7909,5097	2203	4300	6503	SO:0001583	missense	239	exon6			AGCTTCAGGCTCA	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.782A>G	17.37:g.6902760A>G	ENSP00000251535:p.Gln261Arg	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_000697	O95569|Q6ISF8|Q9UQM4	Missense_Mutation	SNP	ENST00000251535.6	37	CCDS11084.1	1337	0.6121794871794872	335	0.6808943089430894	238	0.6574585635359116	307	0.5367132867132867	457	0.6029023746701847	G	6.765	0.509948	0.12883	0.667045	0.577907	ENSG00000108839	ENST00000251535	T	0.77750	-1.12	5.13	-6.14	0.02111	Lipoxygenase, C-terminal (3);	0.641083	0.16074	N	0.230826	T	0.00012	0.0000	L	0.52266	1.64	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.30357	-0.9981	9	0.26408	T	0.33	-9.7598	11.8644	0.52484	0.7277:0.0911:0.1812:0.0	rs1126667;rs2251194;rs17202973;rs52806289;rs59219931;rs1126667	261	P18054	LOX12_HUMAN	R	261	ENSP00000251535:Q261R	ENSP00000251535:Q261R	Q	+	2	0	ALOX12	6843484	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.555000	0.02170	-1.676000	0.01457	-0.131000	0.14894	CAG	A|0.400;G|0.600	0.600	strong		0.547	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
GLTSCR2	29997	hgsc.bcm.edu	37	19	48255804	48255804	+	Silent	SNP	A	A	G	rs1042558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48255804A>G	ENST00000246802.5	+	6	743	c.705A>G	c.(703-705)gcA>gcG	p.A235A	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	235				A -> S (in Ref. 2; AAH04229). {ECO:0000305}.		intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CGTCCCAGGCACCCGCCGTGG	0.667																																					p.A235A	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.A705G						PASS	.	A		826,3580	323.4+/-298.1	89,648,1466	61.0	54.0	56.0		705	-8.1	0.0	19	dbSNP_86	56	4769,3831	607.4+/-395.2	1297,2175,828	no	coding-synonymous	GLTSCR2	NM_015710.4		1386,2823,2294	GG,GA,AA		44.5465,18.7472,43.0186		235/479	48255804	5595,7411	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon6			CCAGGCACCCGCC	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.705A>G	19.37:g.48255804A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			A|0.570;G|0.430	0.430	strong		0.667	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
FLT1	2321	hgsc.bcm.edu	37	13	28964198	28964198	+	Silent	SNP	C	C	T	rs17537350	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:28964198C>T	ENST00000282397.4	-	13	1955	c.1704G>A	c.(1702-1704)acG>acA	p.T568T	FLT1_ENST00000541932.1_Silent_p.T568T	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	568	Ig-like C2-type 6.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCTCTCCTTCCGTCGGCATTT	0.363													C|||	301	0.0601038	0.003	0.2248	5008	,	,		21422	0.0139		0.0626	False		,,,				2504	0.0654				p.T568T		Atlas-SNP	.											FLT1_ENST00000541932,colon,carcinoma,-1,2	FLT1	393	2	0			c.G1704A						PASS	.	C	,,	65,4341	58.1+/-94.6	2,61,2140	125.0	117.0	120.0		1704,1704,1704	-6.8	0.1	13	dbSNP_123	120	564,8036	153.3+/-207.7	22,520,3758	no	coding-synonymous,coding-synonymous,coding-synonymous	FLT1	NM_001159920.1,NM_001160030.1,NM_002019.4	,,	24,581,5898	TT,TC,CC		6.5581,1.4753,4.8362	,,	568/688,568/734,568/1339	28964198	629,12377	2203	4300	6503	SO:0001819	synonymous_variant	2321	exon13			TCCTTCCGTCGGC	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1704G>A	13.37:g.28964198C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																			C|0.951;T|0.049	0.049	strong		0.363	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
STRBP	55342	hgsc.bcm.edu	37	9	125920376	125920376	+	Silent	SNP	G	G	A	rs803736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:125920376G>A	ENST00000348403.5	-	11	1389	c.960C>T	c.(958-960)ggC>ggT	p.G320G	STRBP_ENST00000447404.2_Silent_p.G320G|STRBP_ENST00000360998.3_Silent_p.G306G	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	320	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						TGTAAATCTGGCCAAAGGCTG	0.383													G|||	2419	0.483027	0.0688	0.5461	5008	,	,		19694	0.2798		0.8529	False		,,,				2504	0.8272				p.G320G		Atlas-SNP	.											.	STRBP	73	.	0			c.C960T						PASS	.	G	,	780,3626	313.6+/-293.2	81,618,1504	109.0	108.0	108.0		918,960	2.0	1.0	9	dbSNP_86	108	7387,1213	760.4+/-407.6	3176,1035,89	no	coding-synonymous,coding-synonymous	STRBP	NM_001171137.1,NM_018387.4	,	3257,1653,1593	AA,AG,GG		14.1047,17.7031,37.2059	,	306/659,320/673	125920376	8167,4839	2203	4300	6503	SO:0001819	synonymous_variant	55342	exon11			AATCTGGCCAAAG	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.960C>T	9.37:g.125920376G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_018387	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Silent	SNP	ENST00000348403.5	37	CCDS6851.1																																																																																			G|0.441;A|0.559	0.559	strong		0.383	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1		
HRNR	388697	hgsc.bcm.edu	37	1	152188847	152188847	+	Missense_Mutation	SNP	A	A	G	rs145667921		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152188847A>G	ENST00000368801.2	-	3	5333	c.5258T>C	c.(5257-5259)gTc>gCc	p.V1753A	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1753					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGACCAAAGACAGAAGAGTG	0.562																																					p.V1753A		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.T5258C						scavenged	.						1.0	1.0	1.0					1																	152188847		388	960	1348	SO:0001583	missense	388697	exon3			CCAAAGACAGAAG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5258T>C	1.37:g.152188847A>G	ENSP00000357791:p.Val1753Ala	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	1455	164	0.112715	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.191978	0.38707	.	.	ENSG00000197915	ENST00000368801	T	0.01548	4.78	3.15	2.19	0.27852	.	.	.	.	.	T	0.00412	0.0013	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48103	-0.9064	9	0.07482	T	0.82	.	1.9459	0.03356	0.2121:0.4632:0.2061:0.1186	.	1753	Q86YZ3	HORN_HUMAN	A	1753	ENSP00000357791:V1753A	ENSP00000357791:V1753A	V	-	2	0	HRNR	150455471	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.214000	0.09292	0.170000	0.19704	-0.294000	0.09567	GTC	.	.	weak		0.562	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
PYGO1	26108	hgsc.bcm.edu	37	15	55838976	55838976	+	Missense_Mutation	SNP	C	C	G	rs144876912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:55838976C>G	ENST00000302000.6	-	3	599	c.505G>C	c.(505-507)Gtc>Ctc	p.V169L	PYGO1_ENST00000563719.1_Missense_Mutation_p.V169L	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	169	Asn-rich.				hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		GGCATGTTGACATTCTGACTT	0.383																																					p.V169L		Atlas-SNP	.											PYGO1,NS,carcinoma,+2,1	PYGO1	56	1	0			c.G505C						PASS	.	C	LEU/VAL	2,4384	4.2+/-10.8	0,2,2191	114.0	116.0	115.0		505	3.3	1.0	15	dbSNP_134	115	16,8568	11.9+/-42.8	0,16,4276	yes	missense	PYGO1	NM_015617.1	32	0,18,6467	GG,GC,CC		0.1864,0.0456,0.1388	benign	169/420	55838976	18,12952	2193	4292	6485	SO:0001583	missense	26108	exon3			TGTTGACATTCTG	AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016		"""Zinc fingers, PHD-type"""	30256	protein-coding gene	gene with protein product		606902	"""pygopus homolog 1 (Drosophila)"""			11988739	Standard	NM_015617		Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.505G>C	15.37:g.55838976C>G	ENSP00000302327:p.Val169Leu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	187	99	0.529412	NM_015617	A7Y2D6	Missense_Mutation	SNP	ENST00000302000.6	37	CCDS10155.1	.	.	.	.	.	.	.	.	.	.	C	9.561	1.118537	0.20877	4.56E-4	0.001864	ENSG00000171016	ENST00000302000;ENST00000401688	T	0.45668	0.89	5.23	3.33	0.38152	.	0.395337	0.23849	N	0.043976	T	0.23532	0.0569	N	0.19112	0.55	0.27105	N	0.962529	B;B	0.15473	0.013;0.013	B;B	0.17979	0.011;0.02	T	0.21484	-1.0244	10	0.11794	T	0.64	-7.226	8.1499	0.31134	0.0:0.7585:0.0:0.2415	.	169;169	A7Y2D6;Q9Y3Y4	.;PYGO1_HUMAN	L	169	ENSP00000302327:V169L	ENSP00000302327:V169L	V	-	1	0	PYGO1	53626268	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.943000	0.29030	0.685000	0.31468	0.585000	0.79938	GTC	C|0.998;G|0.002	0.002	strong		0.383	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617	
BTN2A1	11120	hgsc.bcm.edu	37	6	26468326	26468326	+	Missense_Mutation	SNP	G	G	A	rs3734542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26468326G>A	ENST00000312541.5	+	8	1381	c.1133G>A	c.(1132-1134)cGg>cAg	p.R378Q	BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000541522.1_Missense_Mutation_p.R317Q|BTN2A1_ENST00000429381.1_3'UTR	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	378	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		R -> Q (in dbSNP:rs3734542).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						GTCCTAGGCCGGGAGAGCTTC	0.567													G|||	190	0.0379393	0.0333	0.0346	5008	,	,		22106	0.0099		0.0825	False		,,,				2504	0.0297				p.R378Q		Atlas-SNP	.											BTN2A1_ENST00000265424,NS,carcinoma,-1,2	BTN2A1	118	2	0			c.G1133A						PASS	.	G	GLN/ARG,,GLN/ARG,	189,4217	119.2+/-156.9	4,181,2018	163.0	156.0	158.0		950,,1133,	-3.4	0.0	6	dbSNP_107	158	796,7804	186.2+/-233.7	39,718,3543	yes	missense,intron,missense,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	43,,43,	43,899,5561	AA,AG,GG		9.2558,4.2896,7.5734	benign,,benign,	317/467,,378/528,	26468326	985,12021	2203	4300	6503	SO:0001583	missense	11120	exon8			TAGGCCGGGAGAG	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1133G>A	6.37:g.26468326G>A	ENSP00000312158:p.Arg378Gln	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	213	101	0.474178	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	100	0.045787545787545784	16	0.032520325203252036	11	0.03038674033149171	8	0.013986013986013986	65	0.08575197889182058	G	1.077	-0.668091	0.03428	0.042896	0.092558	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000265424	T;T	0.11063	2.81;2.81	2.67	-3.36	0.04913	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	1.455890	0.04492	N	0.379807	T	0.01661	0.0053	L	0.29908	0.895	0.80722	P	0.0	B;B	0.24368	0.102;0.025	B;B	0.19391	0.025;0.015	T	0.43410	-0.9393	9	0.27082	T	0.32	.	1.0184	0.01513	0.3381:0.1348:0.3589:0.1681	rs3734542;rs52798417;rs3734542	317;378	B4DLP9;Q7KYR7	.;BT2A1_HUMAN	Q	378;317;364	ENSP00000312158:R378Q;ENSP00000443909:R317Q	ENSP00000265424:R364Q	R	+	2	0	BTN2A1	26576305	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-5.767000	0.00099	-0.907000	0.03862	0.491000	0.48974	CGG	G|0.937;A|0.063	0.063	strong		0.567	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
ZNF831	128611	hgsc.bcm.edu	37	20	57766113	57766113	+	Silent	SNP	G	G	A	rs148289392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57766113G>A	ENST00000371030.2	+	1	39	c.39G>A	c.(37-39)gcG>gcA	p.A13A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	13	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CCCCTCCTGCGAGGGACCAGC	0.637													.|||	3	0.000599042	0.0	0.0014	5008	,	,		17085	0.0		0.002	False		,,,				2504	0.0				p.A13A		Atlas-SNP	.											.	ZNF831	287	.	0			c.G39A						PASS	.	G		0,3912		0,0,1956	27.0	32.0	30.0		39	2.5	1.0	20	dbSNP_134	30	6,8286		0,6,4140	no	coding-synonymous	ZNF831	NM_178457.1		0,6,6096	AA,AG,GG		0.0724,0.0,0.0492		13/1678	57766113	6,12198	1956	4146	6102	SO:0001819	synonymous_variant	128611	exon1			TCCTGCGAGGGAC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.39G>A	20.37:g.57766113G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																			G|0.999;A|0.001	0.001	strong		0.637	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956196	18956196	+	Missense_Mutation	SNP	C	C	T	rs78179510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18956196C>T	ENST00000302797.3	-	1	360	c.136G>A	c.(136-138)Gca>Aca	p.A46T	MRGPRX1_ENST00000526914.1_5'UTR|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	46					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A46T(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						AGCACAACTGCGTTTCCTGTC	0.582																																					p.A46T		Atlas-SNP	.											MRGPRX1,caecum,carcinoma,0,3	MRGPRX1	84	3	1	Substitution - Missense(1)	stomach(1)	c.G136A						PASS	.	C	THR/ALA	708,3680		4,700,1490	170.0	161.0	164.0		136	-0.9	0.0	11	dbSNP_131	164	1289,7285		4,1281,3002	no	missense	MRGPRX1	NM_147199.3	58	8,1981,4492	TT,TC,CC		15.0338,16.1349,15.4066	possibly-damaging	46/323	18956196	1997,10965	2194	4287	6481	SO:0001583	missense	259249	exon1			CAACTGCGTTTCC		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.136G>A	11.37:g.18956196C>T	ENSP00000305766:p.Ala46Thr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	254	80	0.314961	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	380	0.17399267399267399	86	0.17479674796747968	73	0.20165745856353592	104	0.18181818181818182	117	0.15435356200527706	.	14.50	2.554820	0.45487	0.161349	0.150338	ENSG00000170255	ENST00000302797	T	0.09350	2.99	2.43	-0.872	0.10638	GPCR, rhodopsin-like superfamily (1);	0.959312	0.08638	N	0.915990	T	0.00012	0.0000	L	0.55213	1.73	0.80722	P	0.0	D	0.60575	0.988	P	0.54238	0.746	T	0.34104	-0.9842	9	0.31617	T	0.26	.	7.0239	0.24930	0.0:0.6214:0.0:0.3786	.	46	Q96LB2	MRGX1_HUMAN	T	46	ENSP00000305766:A46T	ENSP00000305766:A46T	A	-	1	0	MRGPRX1	18912772	0.000000	0.05858	0.004000	0.12327	0.047000	0.14425	-0.160000	0.10041	-0.190000	0.10465	0.491000	0.48974	GCA	C|0.842;T|0.158	0.158	strong		0.582	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
AGGF1	55109	hgsc.bcm.edu	37	5	76359024	76359024	+	Missense_Mutation	SNP	C	C	A	rs34400049	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:76359024C>A	ENST00000312916.7	+	14	2474	c.2092C>A	c.(2092-2094)Cct>Act	p.P698T		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	698			P -> T (in dbSNP:rs34400049). {ECO:0000269|PubMed:14961121}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		AGAAACTAAGCCTCAAAAAGA	0.378													C|||	1027	0.205072	0.0802	0.3199	5008	,	,		16784	0.2728		0.2952	False		,,,				2504	0.1299				p.P698T		Atlas-SNP	.											.	AGGF1	71	.	0			c.C2092A						PASS	.	C	THR/PRO	440,3966	210.8+/-231.2	31,378,1794	83.0	88.0	86.0		2092	1.6	0.9	5	dbSNP_126	86	2499,6101	409.6+/-349.9	366,1767,2167	yes	missense	AGGF1	NM_018046.4	38	397,2145,3961	AA,AC,CC		29.0581,9.9864,22.5973	benign	698/715	76359024	2939,10067	2203	4300	6503	SO:0001583	missense	55109	exon14			ACTAAGCCTCAAA	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.2092C>A	5.37:g.76359024C>A	ENSP00000316109:p.Pro698Thr	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	192	189	0.984375	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	514	0.23534798534798534	47	0.09552845528455285	107	0.2955801104972376	143	0.25	217	0.2862796833773087	C	0.081	-1.184419	0.01620	0.099864	0.290581	ENSG00000164252	ENST00000312916	T	0.35421	1.31	5.47	1.61	0.23674	.	0.795454	0.12324	N	0.478965	T	0.00012	0.0000	L	0.29908	0.895	0.29291	P	0.869337	B	0.28713	0.22	B	0.19148	0.024	T	0.33497	-0.9866	9	0.02654	T	1	-18.1993	1.31	0.02096	0.1414:0.3459:0.1383:0.3744	rs34400049	698	Q8N302	AGGF1_HUMAN	T	698	ENSP00000316109:P698T	ENSP00000316109:P698T	P	+	1	0	AGGF1	76394780	0.008000	0.16893	0.924000	0.36721	0.903000	0.53119	-0.210000	0.09345	0.003000	0.14656	-0.145000	0.13849	CCT	A|0.225;C|0.775	0.225	strong		0.378	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
IPPK	64768	hgsc.bcm.edu	37	9	95396712	95396712	+	Missense_Mutation	SNP	G	G	A	rs2277170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:95396712G>A	ENST00000287996.3	-	11	1402	c.1126C>T	c.(1126-1128)Ctt>Ttt	p.L376F	IPPK_ENST00000375522.1_Missense_Mutation_p.L48F	NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	376			L -> F (in dbSNP:rs2277170).		inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						TCAGTGGAAAGGTCAAGCAGC	0.453											OREG0019315	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	234	0.0467252	0.0015	0.0288	5008	,	,		18801	0.0476		0.0348	False		,,,				2504	0.1319				p.L376F		Atlas-SNP	.											.	IPPK	34	.	0			c.C1126T						PASS	.	G	PHE/LEU	32,4374	36.0+/-67.5	0,32,2171	106.0	88.0	94.0		1126	4.8	0.7	9	dbSNP_100	94	465,8135	138.1+/-194.9	18,429,3853	yes	missense	IPPK	NM_022755.5	22	18,461,6024	AA,AG,GG		5.407,0.7263,3.8213	probably-damaging	376/492	95396712	497,12509	2203	4300	6503	SO:0001583	missense	64768	exon11			TGGAAAGGTCAAG	AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 12"""	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.1126C>T	9.37:g.95396712G>A	ENSP00000287996:p.Leu376Phe	Somatic	67	0	0	1312	WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_022755	Q5T9F7|Q9H7V8	Missense_Mutation	SNP	ENST00000287996.3	37	CCDS6699.1	56	0.02564102564102564	0	0.0	12	0.03314917127071823	19	0.033216783216783216	25	0.032981530343007916	G	18.19	3.568436	0.65651	0.007263	0.05407	ENSG00000127080	ENST00000287996;ENST00000375522	T;T	0.32515	1.45;1.45	5.71	4.8	0.61643	.	0.240288	0.43416	D	0.000566	T	0.13756	0.0333	M	0.64997	1.995	0.41718	D	0.989496	D;D	0.76494	0.999;0.983	D;P	0.72338	0.977;0.876	T	0.18493	-1.0335	10	0.14656	T	0.56	-5.6458	16.8525	0.85998	0.0:0.1285:0.8714:0.0	rs2277170;rs2277170	376;75	Q9H8X2;B3KVX7	IPPK_HUMAN;.	F	376;48	ENSP00000287996:L376F;ENSP00000364672:L48F	ENSP00000287996:L376F	L	-	1	0	IPPK	94436533	1.000000	0.71417	0.720000	0.30636	0.974000	0.67602	4.656000	0.61483	1.527000	0.49086	0.561000	0.74099	CTT	G|0.961;A|0.039	0.039	strong		0.453	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755	
TSTD2	158427	hgsc.bcm.edu	37	9	100364900	100364900	+	Missense_Mutation	SNP	A	A	C	rs145024955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100364900A>C	ENST00000341170.4	-	10	1784	c.1402T>G	c.(1402-1404)Tca>Gca	p.S468A		NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	468										large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						ATAGGGCCTGAAACTTTCCTG	0.557													A|||	2	0.000399361	0.0	0.0	5008	,	,		20972	0.0		0.002	False		,,,				2504	0.0				p.S468A		Atlas-SNP	.											.	TSTD2	42	.	0			c.T1402G						PASS	.	A	ALA/SER	1,4405	2.1+/-5.4	0,1,2202	264.0	222.0	236.0		1402	1.8	0.2	9	dbSNP_134	236	14,8586	10.5+/-38.8	0,14,4286	yes	missense	TSTD2	NM_139246.4	99	0,15,6488	CC,CA,AA		0.1628,0.0227,0.1153	benign	468/517	100364900	15,12991	2203	4300	6503	SO:0001583	missense	158427	exon10			GGCCTGAAACTTT	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 97"""	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.1402T>G	9.37:g.100364900A>C	ENSP00000342499:p.Ser468Ala	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	228	111	0.486842	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	37	CCDS6727.2	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	5.124	0.208479	0.09757	2.27E-4	0.001628	ENSG00000136925	ENST00000375173;ENST00000341170	T;T	0.28895	1.59;1.59	5.5	1.77	0.24775	.	0.830019	0.10733	N	0.640447	T	0.15478	0.0373	N	0.17872	0.535	0.26488	N	0.974986	B	0.06786	0.001	B	0.04013	0.001	T	0.29912	-0.9996	10	0.25106	T	0.35	-2.0967	1.4504	0.02373	0.4114:0.2983:0.1611:0.1292	.	468	Q5T7W7	TSTD2_HUMAN	A	64;468	ENSP00000364316:S64A;ENSP00000342499:S468A	ENSP00000342499:S468A	S	-	1	0	TSTD2	99404721	0.016000	0.18221	0.206000	0.23566	0.267000	0.26476	0.794000	0.26958	0.117000	0.18138	0.460000	0.39030	TCA	A|0.999;C|0.001	0.001	strong		0.557	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246	
UTP20	27340	hgsc.bcm.edu	37	12	101732670	101732670	+	Silent	SNP	C	C	T	rs11110755	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:101732670C>T	ENST00000261637.4	+	31	4122	c.3948C>T	c.(3946-3948)agC>agT	p.S1316S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1316					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CCACAATAAGCGCAGAAAAGG	0.333													C|||	842	0.168131	0.1513	0.134	5008	,	,		17041	0.4613		0.0179	False		,,,				2504	0.0675				p.S1316S		Atlas-SNP	.											.	UTP20	222	.	0			c.C3948T						PASS	.	C		543,3863	245.0+/-254.1	33,477,1693	86.0	86.0	86.0		3948	1.6	1.0	12	dbSNP_120	86	78,8518	44.9+/-103.4	0,78,4220	no	coding-synonymous	UTP20	NM_014503.2		33,555,5913	TT,TC,CC		0.9074,12.3241,4.7762		1316/2786	101732670	621,12381	2203	4298	6501	SO:0001819	synonymous_variant	27340	exon31			AATAAGCGCAGAA	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.3948C>T	12.37:g.101732670C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	186	184	0.989247	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			C|0.917;T|0.083	0.083	strong		0.333	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
ANPEP	290	hgsc.bcm.edu	37	15	90347814	90347814	+	Missense_Mutation	SNP	G	G	A	rs17240268	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90347814G>A	ENST00000300060.6	-	5	1245	c.932C>T	c.(931-933)gCg>gTg	p.A311V	ANPEP_ENST00000558177.1_5'Flank	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	311	Interaction with HCoV-229E.|Metalloprotease.		A -> V (in dbSNP:rs17240268).		angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.A311E(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GCCGTGGCCCGCCGCAATGGC	0.602													g|||	360	0.071885	0.1362	0.0576	5008	,	,		17208	0.002		0.0924	False		,,,				2504	0.046				p.A311V	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											ANPEP,NS,carcinoma,0,1	ANPEP	124	1	1	Substitution - Missense(1)	lung(1)	c.C932T						PASS	.	A	VAL/ALA	602,3798	257.7+/-262.0	37,528,1635	64.0	70.0	68.0		932	-2.8	0.0	15	dbSNP_123	68	697,7901	171.0+/-222.0	31,635,3633	yes	missense	ANPEP	NM_001150.2	64	68,1163,5268	AA,AG,GG		8.1065,13.6818,9.9938	benign	311/968	90347814	1299,11699	2200	4299	6499	SO:0001583	missense	290	exon5			TGGCCCGCCGCAA	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.932C>T	15.37:g.90347814G>A	ENSP00000300060:p.Ala311Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	170	0.07783882783882784	78	0.15853658536585366	20	0.055248618784530384	2	0.0034965034965034965	70	0.09234828496042216	g	15.25	2.776990	0.49786	0.136818	0.081065	ENSG00000166825	ENST00000300060	T	0.02944	4.1	4.87	-2.78	0.05859	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.464602	0.22775	N	0.055785	T	0.00039	0.0001	M	0.82716	2.605	0.80722	P	0.0	P	0.48230	0.907	P	0.46253	0.509	T	0.32587	-0.9901	9	0.30854	T	0.27	.	8.8366	0.35115	0.1182:0.0:0.5073:0.3745	rs17240268;rs17240268	311	P15144	AMPN_HUMAN	V	311	ENSP00000300060:A311V	ENSP00000300060:A311V	A	-	2	0	ANPEP	88148818	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.465000	0.06680	-0.056000	0.13221	-0.642000	0.03964	GCG	G|0.909;A|0.091	0.091	strong		0.602	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
DENND4C	55667	hgsc.bcm.edu	37	9	19341045	19341045	+	Silent	SNP	A	A	G	rs928128	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:19341045A>G	ENST00000380432.2	+	16	2115	c.2082A>G	c.(2080-2082)gcA>gcG	p.A694A	DENND4C_ENST00000434457.2_Silent_p.A979A|DENND4C_ENST00000602925.1_Silent_p.A930A			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	694					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						AGGATGATGCAGAAATTCATG	0.343													A|||	1071	0.213858	0.354	0.2046	5008	,	,		14125	0.0159		0.2535	False		,,,				2504	0.1943				p.A930A		Atlas-SNP	.											DENND4C,colon,carcinoma,0,1	DENND4C	120	1	0			c.A2790G						PASS	.	A		1405,3001	459.6+/-352.3	221,963,1019	86.0	86.0	86.0		2082	4.6	1.0	9	dbSNP_86	86	2030,6570	354.2+/-329.4	240,1550,2510	no	coding-synonymous	DENND4C	NM_017925.4		461,2513,3529	GG,GA,AA		23.6047,31.8883,26.4109		694/1674	19341045	3435,9571	2203	4300	6503	SO:0001819	synonymous_variant	55667	exon20			TGATGCAGAAATT	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.2082A>G	9.37:g.19341045A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	144	142	0.986111	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Silent	SNP	ENST00000380432.2	37																																																																																				A|0.760;G|0.240	0.240	strong		0.343	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
RAET1E	135250	hgsc.bcm.edu	37	6	150210685	150210685	+	Missense_Mutation	SNP	C	C	T	rs9383921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:150210685C>T	ENST00000357183.4	-	3	553	c.421G>A	c.(421-423)Gcc>Acc	p.A141T	RP11-244K5.8_ENST00000606915.1_RNA|RAET1E_ENST00000367363.3_Missense_Mutation_p.A105T|RAET1E_ENST00000529948.1_Missense_Mutation_p.A141T|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000532335.1_Missense_Mutation_p.A141T|RAET1E-AS1_ENST00000605899.1_RNA	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	141	MHC class I alpha-2 like.		A -> T (in dbSNP:rs9383921).	AT -> TI (in Ref. 8; AAL76417). {ECO:0000305}.	antigen processing and presentation (GO:0019882)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			cervix(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		CCATTGGTGGCGAACTGCCAG	0.463													N|||	2350	0.469249	0.1747	0.487	5008	,	,		21589	0.8859		0.4175	False		,,,				2504	0.4785				p.A141T		Atlas-SNP	.											.	RAET1E	20	.	0			c.G421A						PASS	.	C	THR/ALA	905,3501	349.3+/-310.3	101,703,1399	151.0	123.0	133.0		421	-2.1	0.0	6	dbSNP_119	133	3445,5155	506.7+/-376.6	694,2057,1549	yes	missense	RAET1E	NM_139165.2	58	795,2760,2948	TT,TC,CC		40.0581,20.5402,33.4461	benign	141/264	150210685	4350,8656	2203	4300	6503	SO:0001583	missense	135250	exon3			TGGTGGCGAACTG	AF359243	CCDS5221.1, CCDS59042.1, CCDS59043.1, CCDS59044.1	6q24.3	2011-02-09			ENSG00000164520	ENSG00000164520			16793	protein-coding gene	gene with protein product		609243				11827464	Standard	NM_139165		Approved	LETAL, bA350J20.7, ULBP4	uc003qnl.1	Q8TD07	OTTHUMG00000015796	ENST00000357183.4:c.421G>A	6.37:g.150210685C>T	ENSP00000349709:p.Ala141Thr	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	258	123	0.476744	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	37	CCDS5221.1	1086	0.49725274725274726	100	0.2032520325203252	179	0.494475138121547	500	0.8741258741258742	307	0.4050131926121372	C	4.036	0.004177	0.07866	0.205402	0.400581	ENSG00000164520	ENST00000532335;ENST00000357183;ENST00000367363;ENST00000529948	T;T;T;T	0.61742	2.55;2.55;0.08;2.55	3.68	-2.12	0.07165	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.800400	0.11223	N	0.586490	T	0.12135	0.0295	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.22080	0.019;0.009;0.064	B;B;B	0.12837	0.008;0.003;0.005	T	0.10800	-1.0614	9	0.35671	T	0.21	-7.3577	3.5695	0.07912	0.1956:0.4216:0.0:0.3828	rs9383921;rs52819953;rs9383921	141;105;141	Q8TD07;Q8TD07-2;Q8TD07-3	N2DL4_HUMAN;.;.	T	141;141;105;141	ENSP00000437067:A141T;ENSP00000349709:A141T;ENSP00000356332:A105T;ENSP00000432366:A141T	ENSP00000349709:A141T	A	-	1	0	RAET1E	150252378	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.522000	0.06237	-0.380000	0.07894	0.485000	0.47835	GCC	C|0.608;T|0.392	0.392	strong		0.463	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
TMEM61	199964	hgsc.bcm.edu	37	1	55451850	55451850	+	Silent	SNP	G	G	A	rs148773188		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55451850G>A	ENST00000371268.3	+	2	370	c.96G>A	c.(94-96)acG>acA	p.T32T	RP11-12C17.2_ENST00000436960.1_RNA	NM_182532.1	NP_872338.1	Q8N0U2	TMM61_HUMAN	transmembrane protein 61	32						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	4						TGGCCGGGACGCTCTGCTTCG	0.667																																					p.T32T		Atlas-SNP	.											.	TMEM61	22	.	0			c.G96A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	51.0	52.0	51.0		96	-7.4	0.2	1	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	TMEM61	NM_182532.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		32/211	55451850	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	199964	exon2			CGGGACGCTCTGC	BC029775	CCDS601.1	1p32.3	2008-02-05			ENSG00000143001	ENSG00000143001			27296	protein-coding gene	gene with protein product						12477932	Standard	NM_182532		Approved		uc001cyd.3	Q8N0U2	OTTHUMG00000009991	ENST00000371268.3:c.96G>A	1.37:g.55451850G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_182532		Silent	SNP	ENST00000371268.3	37	CCDS601.1																																																																																			G|1.000;A|0.000	0.000	weak		0.667	TMEM61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027683.1	NM_182532	
SMPD1	6609	hgsc.bcm.edu	37	11	6412931	6412931	+	Silent	SNP	T	T	C	rs7951904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6412931T>C	ENST00000342245.4	+	2	804	c.636T>C	c.(634-636)gaT>gaC	p.D212D	SMPD1_ENST00000527275.1_Silent_p.D211D|SMPD1_ENST00000299397.3_Silent_p.D212D|SMPD1_ENST00000356761.2_Silent_p.D212D|SMPD1_ENST00000533196.1_Intron	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	210					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	TGCACTGGGATCATGACTACC	0.677													T|||	642	0.128195	0.2118	0.0994	5008	,	,		7721	0.004		0.1243	False		,,,				2504	0.1677				p.D212D		Atlas-SNP	.											SMPD1_ENST00000342245,NS,carcinoma,+1,2	SMPD1	108	2	0			c.T636C						PASS	.	T	,	809,3591		70,669,1461	27.0	27.0	27.0		636,633	1.7	1.0	11	dbSNP_116	27	1156,7432		97,962,3235	yes	coding-synonymous,coding-synonymous	SMPD1	NM_000543.4,NM_001007593.2	,	167,1631,4696	CC,CT,TT		13.4606,18.3864,15.1294	,	212/632,211/631	6412931	1965,11023	2200	4294	6494	SO:0001819	synonymous_variant	6609	exon2			CTGGGATCATGAC	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"""acid sphingomyelinase"""	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.636T>C	11.37:g.6412931T>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	37	CCDS44531.1																																																																																			T|0.864;C|0.136	0.136	strong		0.677	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543	
PTPRF	5792	hgsc.bcm.edu	37	1	44072018	44072018	+	Silent	SNP	C	C	T	rs1065772	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:44072018C>T	ENST00000359947.4	+	20	3931	c.3591C>T	c.(3589-3591)acC>acT	p.T1197T	PTPRF_ENST00000372413.3_Silent_p.T1188T|PTPRF_ENST00000372414.3_Silent_p.T1197T|PTPRF_ENST00000422171.2_Silent_p.T545T|PTPRF_ENST00000438120.1_Silent_p.T1188T|PTPRF_ENST00000496447.1_3'UTR	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1197					cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TCCCGGAGACCTTTACCTTGG	0.602													C|||	1393	0.278155	0.0371	0.268	5008	,	,		15577	0.4702		0.3569	False		,,,				2504	0.3323				p.T1197T		Atlas-SNP	.											.	PTPRF	172	.	0			c.C3591T						PASS	.	C	,	418,3988	203.8+/-226.2	21,376,1806	118.0	129.0	125.0		3591,3564	1.1	1.0	1	dbSNP_86	125	3000,5600	462.2+/-365.6	525,1950,1825	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	546,2326,3631	TT,TC,CC		34.8837,9.4871,26.2802	,	1197/1908,1188/1899	44072018	3418,9588	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon20			GGAGACCTTTACC	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3591C>T	1.37:g.44072018C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	67	0.632075	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	629|629	0.288003663003663|0.288003663003663	24|24	0.04878048780487805|0.04878048780487805	109|109	0.3011049723756906|0.3011049723756906	228|228	0.3986013986013986|0.3986013986013986	268|268	0.35356200527704484|0.35356200527704484	C|C	0.778|0.778	-0.763508|-0.763508	0.02996|0.02996	0.094871|0.094871	0.348837|0.348837	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.2|5.2	1.07|1.07	0.20283|0.20283	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44937|0.44937	-0.9295|-0.9295	3|3	.|.	.|.	.|.	.|.	5.306|5.306	0.15803|0.15803	0.2361:0.4699:0.2289:0.0652|0.2361:0.4699:0.2289:0.0652	rs1065772;rs17849110;rs1065772|rs1065772;rs17849110;rs1065772	.|.	.|.	.|.	F|L	570;611|843	.|.	.|.	L|P	+|+	1|2	0|0	PTPRF|PTPRF	43844605|43844605	0.268000|0.268000	0.24133|0.24133	0.996000|0.996000	0.52242|0.52242	0.030000|0.030000	0.12068|0.12068	0.196000|0.196000	0.17176|0.17176	0.023000|0.023000	0.15187|0.15187	-1.083000|-1.083000	0.02208|0.02208	CTT|CCT	C|0.732;T|0.268	0.268	strong		0.602	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
CEP350	9857	hgsc.bcm.edu	37	1	179989742	179989742	+	Missense_Mutation	SNP	G	G	C	rs2477120	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:179989742G>C	ENST00000367607.3	+	12	3251	c.2833G>C	c.(2833-2835)Gaa>Caa	p.E945Q		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	945			E -> Q (in dbSNP:rs2477120). {ECO:0000269|Ref.1}.		microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TCCCAAACCAGAAGGGCTACT	0.438													G|||	2826	0.564297	0.2436	0.7349	5008	,	,		20768	0.7044		0.6461	False		,,,				2504	0.6483				p.E945Q		Atlas-SNP	.											.	CEP350	418	.	0			c.G2833C						PASS	.	G	GLN/GLU	1467,2939	472.6+/-356.4	240,987,976	86.0	86.0	86.0		2833	6.0	1.0	1	dbSNP_100	86	5532,3068	660.8+/-401.8	1795,1942,563	yes	missense	CEP350	NM_014810.4	29	2035,2929,1539	CC,CG,GG		35.6744,33.2955,46.1864	benign	945/3118	179989742	6999,6007	2203	4300	6503	SO:0001583	missense	9857	exon12			AAACCAGAAGGGC	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.2833G>C	1.37:g.179989742G>C	ENSP00000356579:p.Glu945Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	190	102	0.536842	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	1286	0.5888278388278388	128	0.2601626016260163	255	0.7044198895027625	414	0.7237762237762237	489	0.6451187335092349	G	9.910	1.209166	0.22205	0.332955	0.643256	ENSG00000135837	ENST00000367607	T	0.08546	3.08	6.02	6.02	0.97574	.	0.136062	0.33235	N	0.005124	T	0.00012	0.0000	L	0.29908	0.895	0.34091	P	0.33927300000000005	D;B	0.53885	0.963;0.038	P;B	0.47299	0.543;0.029	T	0.09335	-1.0679	8	.	.	.	.	20.1358	0.98028	0.0:0.0:1.0:0.0	rs2477120;rs12737315;rs17371220;rs52804523;rs56997988;rs2477120	945;945	E7EU22;Q5VT06	.;CE350_HUMAN	Q	945	ENSP00000356579:E945Q	.	E	+	1	0	CEP350	178256365	1.000000	0.71417	1.000000	0.80357	0.701000	0.40568	4.603000	0.61105	2.865000	0.98341	0.655000	0.94253	GAA	G|0.450;C|0.550	0.550	strong		0.438	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
UGT1A7	54577	hgsc.bcm.edu	37	2	234590974	234590974	+	Silent	SNP	C	C	A	rs17863778|rs397726009|rs66534818|rs386656364|rs71405712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234590974C>A	ENST00000373426.3	+	1	391	c.391C>A	c.(391-393)Cga>Aga	p.R131R	UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A9_ENST00000354728.4_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	131			R -> K (in allele UGT1A7*2 and allele UGT1A7*3). {ECO:0000269|PubMed:11037804, ECO:0000269|PubMed:11434514, ECO:0000269|PubMed:19204906, ECO:0000269|Ref.3}.|R -> Q (in dbSNP:rs17868324).		cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	GTTTAATGACCGAAAATTAGT	0.368													A|||	2886	0.576278	0.6097	0.5072	5008	,	,		18899	0.4385		0.6034	False		,,,				2504	0.6943				p.R131R		Atlas-SNP	.											.	UGT1A7	74	.	0			c.C391A	GRCh37	CP005325	UGT1A7	X	rs17863778	PASS	.						69.0	76.0	74.0					2																	234590974		2200	4297	6497	SO:0001819	synonymous_variant	54577	exon1			AATGACCGAAAAT	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.391C>A	2.37:g.234590974C>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	129	46	0.356589	NM_019077	B8K293|O00473	Silent	SNP	ENST00000373426.3	37	CCDS2506.1																																																																																			C|0.567;A|0.433	0.433	strong		0.368	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
TEX40	25858	hgsc.bcm.edu	37	11	64071272	64071272	+	Missense_Mutation	SNP	G	G	C	rs117629442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64071272G>C	ENST00000328404.6	+	4	480	c.460G>C	c.(460-462)Gag>Cag	p.E154Q	TEX40_ENST00000539943.1_Missense_Mutation_p.E112Q|ESRRA_ENST00000405666.1_5'Flank|RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000406310.1_5'Flank|ESRRA_ENST00000000442.6_5'Flank	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	154					cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											GGAACTCATGGAGAATGAAGC	0.567													G|||	27	0.00539137	0.0008	0.0101	5008	,	,		13275	0.0		0.0169	False		,,,				2504	0.002				p.E154Q		Atlas-SNP	.											.	.	.	.	0			c.G460C						PASS	.	G	GLN/GLU	13,3981		0,13,1984	33.0	36.0	35.0		460	2.3	1.0	11	dbSNP_132	35	123,8191		0,123,4034	yes	missense	C11orf20	NM_001039496.1	29	0,136,6018	CC,CG,GG		1.4794,0.3255,1.105	possibly-damaging	154/201	64071272	136,12172	1997	4157	6154	SO:0001583	missense	25858	exon4			CTCATGGAGAATG			11q13.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000219435	ENSG00000219435			19231	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 20"""	C11orf20			Standard	NM_001039496		Approved	DKFZP566E164	uc009ypm.3	Q9NTU4	OTTHUMG00000167820	ENST00000328404.6:c.460G>C	11.37:g.64071272G>C	ENSP00000330877:p.Glu154Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	126	66	0.52381	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	37		18	0.008241758241758242	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	13	0.017150395778364115	G	13.31	2.198647	0.38806	0.003255	0.014794	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.58210	0.35;0.37	4.22	2.3	0.28687	.	.	.	.	.	T	0.39572	0.1083	L	0.32530	0.975	0.25789	N	0.984643	D	0.76494	0.999	D	0.70487	0.969	T	0.28870	-1.0030	9	0.62326	D	0.03	-18.7303	5.3022	0.15783	0.1056:0.0:0.6949:0.1995	.	154	Q9NTU4	CK020_HUMAN	Q	154;112	ENSP00000330877:E154Q;ENSP00000443917:E112Q	ENSP00000330877:E154Q	E	+	1	0	C11orf20	63827848	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	2.823000	0.48081	0.528000	0.28580	-0.300000	0.09419	GAG	G|0.991;C|0.009	0.009	strong		0.567	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496	
MUC16	94025	hgsc.bcm.edu	37	19	9088330	9088330	+	Missense_Mutation	SNP	G	G	A	rs17000947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9088330G>A	ENST00000397910.4	-	1	3688	c.3485C>T	c.(3484-3486)aCt>aTt	p.T1162I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1162	Thr-rich.		T -> I (in dbSNP:rs17000947).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GACTTTGGGAGTAGGAGAAGA	0.483													G|||	951	0.189896	0.0711	0.2709	5008	,	,		22315	0.3036		0.172	False		,,,				2504	0.1943				p.T1162I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C3485T						PASS	.	G	ILE/THR	299,3929		5,289,1820	148.0	142.0	144.0		3485	-0.7	0.0	19	dbSNP_123	144	1504,6954		128,1248,2853	yes	missense	MUC16	NM_024690.2	89	133,1537,4673	AA,AG,GG		17.782,7.0719,14.2125	benign	1162/14508	9088330	1803,10883	2114	4229	6343	SO:0001583	missense	94025	exon1			TTGGGAGTAGGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.3485C>T	19.37:g.9088330G>A	ENSP00000381008:p.Thr1162Ile	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	207	108	0.521739	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	g	2.677	-0.276221	0.05679	0.070719	0.17782	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.09	-0.731	0.11151	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.19817	0.039	B	0.11329	0.006	T	0.47058	-0.9146	8	0.87932	D	0	.	3.4331	0.07436	0.4447:0.0:0.5553:0.0	rs17000947;rs17000947	1162	B5ME49	.	I	1162	ENSP00000381008:T1162I	ENSP00000381008:T1162I	T	-	2	0	MUC16	8949330	0.000000	0.05858	0.000000	0.03702	0.250000	0.25880	-0.783000	0.04638	-0.176000	0.10707	0.305000	0.20034	ACT	G|0.811;A|0.189	0.189	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
RASGRF2	5924	hgsc.bcm.edu	37	5	80409526	80409526	+	Missense_Mutation	SNP	T	T	C	rs34193571	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:80409526T>C	ENST00000265080.4	+	15	2324	c.2257T>C	c.(2257-2259)Tca>Cca	p.S753P	CTD-2193P3.2_ENST00000508993.1_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	753	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		TCCCTTGAACTCAAAGATAGG	0.552													T|||	257	0.0513179	0.0098	0.0663	5008	,	,		17597	0.0109		0.0726	False		,,,				2504	0.1166				p.S753P		Atlas-SNP	.											.	RASGRF2	165	.	0			c.T2257C						PASS	.	T	PRO/SER	85,4321	72.0+/-110.0	0,85,2118	95.0	94.0	94.0		2257	4.2	1.0	5	dbSNP_126	94	699,7901	172.7+/-223.4	33,633,3634	yes	missense	RASGRF2	NM_006909.1	74	33,718,5752	CC,CT,TT		8.1279,1.9292,6.028	benign	753/1238	80409526	784,12222	2203	4300	6503	SO:0001583	missense	5924	exon15			TTGAACTCAAAGA	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.2257T>C	5.37:g.80409526T>C	ENSP00000265080:p.Ser753Pro	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_006909	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	37	CCDS4052.1	84	0.038461538461538464	10	0.02032520325203252	21	0.058011049723756904	7	0.012237762237762238	46	0.06068601583113457	T	14.84	2.656523	0.47467	0.019292	0.081279	ENSG00000113319	ENST00000265080	T	0.74947	-0.89	5.31	4.15	0.48705	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	0.199450	0.33553	U	0.004786	T	0.08358	0.0208	L	0.40543	1.245	0.44485	D	0.997426	B	0.09022	0.002	B	0.09377	0.004	T	0.14254	-1.0479	10	0.23302	T	0.38	.	10.7549	0.46230	0.0:0.075:0.0:0.925	rs34193571	753	O14827	RGRF2_HUMAN	P	753	ENSP00000265080:S753P	ENSP00000265080:S753P	S	+	1	0	RASGRF2	80445282	0.968000	0.33430	1.000000	0.80357	0.961000	0.63080	1.984000	0.40658	0.878000	0.35920	-0.256000	0.11100	TCA	T|0.947;C|0.053	0.053	strong		0.552	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
POLE2	5427	hgsc.bcm.edu	37	14	50131846	50131846	+	Silent	SNP	G	G	T	rs3218791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50131846G>T	ENST00000216367.5	-	8	711	c.612C>A	c.(610-612)gtC>gtA	p.V204V	POLE2_ENST00000556584.1_5'UTR|POLE2_ENST00000539565.2_Silent_p.V178V|POLE2_ENST00000554396.1_Silent_p.V204V	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	204					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	GGTCTAGTTGGACTGTTCCAG	0.279													T|||	1039	0.207468	0.4939	0.1657	5008	,	,		17661	0.0268		0.2127	False		,,,				2504	0.0307				p.V204V		Atlas-SNP	.											.	POLE2	36	.	0			c.C612A						PASS	.	T	,,	1928,2472	601.4+/-389.7	419,1090,691	46.0	46.0	46.0		534,612,612	2.9	1.0	14	dbSNP_106	46	1683,6905	723.2+/-406.4	170,1343,2781	no	coding-synonymous,coding-synonymous,coding-synonymous	POLE2	NM_001197330.1,NM_001197331.1,NM_002692.3	,,	589,2433,3472	TT,TG,GG		19.5971,43.8182,27.8026	,,	178/502,204/503,204/528	50131846	3611,9377	2200	4294	6494	SO:0001819	synonymous_variant	5427	exon8			TAGTTGGACTGTT	AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"""DNA polymerases"""	9178	protein-coding gene	gene with protein product	"""DNA polymerase epsilon subunit B"""	602670	"""polymerase (DNA directed), epsilon 2 (p59 subunit)"""			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.612C>A	14.37:g.50131846G>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_001197331	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Silent	SNP	ENST00000216367.5	37	CCDS32073.1																																																																																			G|0.766;T|0.234	0.234	strong		0.279	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692	
KNSTRN	90417	hgsc.bcm.edu	37	15	40685406	40685406	+	Missense_Mutation	SNP	A	A	T	rs8036457	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40685406A>T	ENST00000416151.2	+	9	950	c.835A>T	c.(835-837)Aat>Tat	p.N279Y	KNSTRN_ENST00000448395.2_Intron|KNSTRN_ENST00000249776.8_Intron|KNSTRN_ENST00000608100.1_Intron	NM_001142761.1	NP_001136233.1			kinetochore-localized astrin/SPAG5 binding protein																		TGCTTGGATGAATCATGGGAT	0.393													A|||	578	0.115415	0.1929	0.0922	5008	,	,		19439	0.0129		0.1431	False		,,,				2504	0.1043				p.N279Y		Atlas-SNP	.											.	.	.	.	0			c.A835T						PASS	.	A	TYR/ASN,,	548,2588		57,434,1077	204.0	179.0	187.0		835,,	0.0	0.0	15	dbSNP_116	187	1050,6114		84,882,2616	yes	missense,intron,intron	C15orf23	NM_001142761.1,NM_001142762.1,NM_033286.3	143,,	141,1316,3693	TT,TA,AA		14.6566,17.4745,15.5146	,,	279/287,,	40685406	1598,8702	1568	3582	5150	SO:0001583	missense	90417	exon9			TGGATGAATCATG	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"""small kinetochore-associated protein"", ""kinetochore-localized astrin-binding protein"", ""TRAF4 associated factor 1"""	614718	"""chromosome 15 open reading frame 23"""	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000416151.2:c.835A>T	15.37:g.40685406A>T	ENSP00000391233:p.Asn279Tyr	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	272	137	0.503676	NM_001142761		Missense_Mutation	SNP	ENST00000416151.2	37	CCDS45226.1	270	0.12362637362637363	101	0.20528455284552846	35	0.09668508287292818	5	0.008741258741258742	129	0.17018469656992086	A	14.50	2.553931	0.45487	0.174745	0.146566	ENSG00000128944	ENST00000416151	T	0.24908	1.83	3.55	0.0151	0.14103	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	1.0000000000287557E-6	D	0.54207	0.965	P	0.51229	0.663	T	0.11131	-1.0600	7	0.87932	D	0	.	5.6657	0.17695	0.6196:0.0:0.3804:0.0	rs8036457;rs8036457	279	Q9Y448-2	.	Y	279	ENSP00000391233:N279Y	ENSP00000391233:N279Y	N	+	1	0	C15orf23	38472698	0.000000	0.05858	0.001000	0.08648	0.104000	0.19210	0.611000	0.24268	-0.014000	0.14175	0.482000	0.46254	AAT	A|0.876;T|0.124	0.124	strong		0.393	KNSTRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418634.1	NM_001142761	
GALR1	2587	hgsc.bcm.edu	37	18	74980553	74980553	+	Missense_Mutation	SNP	G	G	A	rs142216832	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:74980553G>A	ENST00000299727.3	+	3	745	c.745G>A	c.(745-747)Gtt>Att	p.V249I		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	249					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		TGCACAGACAGTTCTGGTGGT	0.517													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		13369	0.0		0.0	False		,,,				2504	0.0				p.V249I		Atlas-SNP	.											.	GALR1	53	.	0			c.G745A						PASS	.	G	ILE/VAL	89,4317	74.7+/-112.8	0,89,2114	100.0	107.0	104.0		745	3.0	0.1	18	dbSNP_134	104	0,8600		0,0,4300	yes	missense	GALR1	NM_001480.3	29	0,89,6414	AA,AG,GG		0.0,2.02,0.6843	probably-damaging	249/350	74980553	89,12917	2203	4300	6503	SO:0001583	missense	2587	exon3			CAGACAGTTCTGG	U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"""GPCR / Class A : Galanin receptors"""	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.745G>A	18.37:g.74980553G>A	ENSP00000299727:p.Val249Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_001480	Q4VBL7	Missense_Mutation	SNP	ENST00000299727.3	37	CCDS12012.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	7.358	0.624331	0.14193	0.0202	0.0	ENSG00000166573	ENST00000299727	T	0.36878	1.23	4.74	2.96	0.34315	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.32704	0.0838	L	0.58101	1.795	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.21415	-1.0246	10	0.17369	T	0.5	.	10.7925	0.46440	0.152:0.0:0.848:0.0	.	249	P47211	GALR1_HUMAN	I	249	ENSP00000299727:V249I	ENSP00000299727:V249I	V	+	1	0	GALR1	73109541	1.000000	0.71417	0.071000	0.20095	0.026000	0.11368	4.647000	0.61418	0.446000	0.26666	-1.012000	0.02466	GTT	G|0.993;A|0.007	0.007	strong		0.517	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1		
COL16A1	1307	hgsc.bcm.edu	37	1	32127953	32127953	+	Silent	SNP	G	G	A	rs2271928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:32127953G>A	ENST00000373672.3	-	58	4179	c.3663C>T	c.(3661-3663)gaC>gaT	p.D1221D	RP11-73M7.6_ENST00000609549.1_RNA|RP11-73M7.6_ENST00000607926.1_RNA|RP11-73M7.6_ENST00000588288.1_RNA|COL16A1_ENST00000271069.6_Silent_p.D1221D|RP11-73M7.6_ENST00000608246.1_RNA|RP11-73M7.6_ENST00000609338.1_RNA|RP11-73M7.6_ENST00000610216.1_RNA|RP11-73M7.6_ENST00000609373.1_RNA|RP11-73M7.6_ENST00000587445.1_RNA|RP11-73M7.6_ENST00000589462.1_RNA|RP11-73M7.6_ENST00000591592.1_RNA|RP11-73M7.6_ENST00000593188.1_RNA|RP11-73M7.6_ENST00000591929.1_RNA|RP11-73M7.6_ENST00000610043.1_RNA|RP11-73M7.6_ENST00000609033.1_RNA|RP11-73M7.6_ENST00000585413.1_RNA|RP11-73M7.6_ENST00000445166.1_RNA|RP11-73M7.6_ENST00000585660.1_RNA|RP11-73M7.6_ENST00000608888.1_RNA|RP11-73M7.6_ENST00000608332.1_RNA|RP11-73M7.6_ENST00000609625.1_RNA	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1221	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CAGGCTTGCCGTCCTTCCCAT	0.612													G|||	2363	0.471845	0.5174	0.4741	5008	,	,		14434	0.6369		0.4016	False		,,,				2504	0.3108				p.D1221D	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.C3663T						PASS	.	G		1855,2017		441,973,522	40.0	43.0	42.0		3663	-2.8	1.0	1	dbSNP_100	42	3290,4958		658,1974,1492	no	coding-synonymous	COL16A1	NM_001856.3		1099,2947,2014	AA,AG,GG		39.8885,47.9081,42.4505		1221/1605	32127953	5145,6975	1936	4124	6060	SO:0001819	synonymous_variant	1307	exon58			CTTGCCGTCCTTC	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3663C>T	1.37:g.32127953G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																			G|0.511;A|0.489	0.489	strong		0.612	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
GUCA1B	2979	hgsc.bcm.edu	37	6	42162388	42162388	+	Silent	SNP	A	A	G	rs3749921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:42162388A>G	ENST00000230361.3	-	1	266	c.171T>C	c.(169-171)taT>taC	p.Y57Y		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	57	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				body fluid secretion (GO:0007589)|cell-cell signaling (GO:0007267)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			large_intestine(3)|lung(3)|skin(2)	8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)			TGCCCTCTACATACTGGGAGG	0.552													A|||	2929	0.584864	0.2035	0.6354	5008	,	,		19260	0.8204		0.6372	False		,,,				2504	0.7679				p.Y57Y		Atlas-SNP	.											.	GUCA1B	19	.	0			c.T171C						PASS	.	A		1380,3026	455.9+/-351.1	216,948,1039	116.0	96.0	103.0		171	-7.9	0.1	6	dbSNP_107	103	5303,3297	646.2+/-400.2	1613,2077,610	no	coding-synonymous	GUCA1B	NM_002098.5		1829,3025,1649	GG,GA,AA		38.3372,31.3209,48.616		57/201	42162388	6683,6323	2203	4300	6503	SO:0001819	synonymous_variant	2979	exon1			CTCTACATACTGG	AF173227	CCDS4865.1	6p21.1	2013-02-14			ENSG00000112599	ENSG00000112599		"""EF-hand domain containing"""	4679	protein-coding gene	gene with protein product		602275				9119368	Standard	NM_002098		Approved	GCAP2, RP48	uc003orz.3	Q9UMX6	OTTHUMG00000014697	ENST00000230361.3:c.171T>C	6.37:g.42162388A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	207	77	0.371981	NM_002098	Q9NU15	Silent	SNP	ENST00000230361.3	37	CCDS4865.1																																																																																			A|0.459;G|0.541	0.541	strong		0.552	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098	
TMEM63B	55362	hgsc.bcm.edu	37	6	44119676	44119676	+	Silent	SNP	A	A	G	rs3734697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44119676A>G	ENST00000259746.9	+	19	1950	c.1767A>G	c.(1765-1767)ccA>ccG	p.P589P	TMEM63B_ENST00000323267.6_Silent_p.P589P			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	589					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.P589P(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			TGCGCATCCCAGGCCTGCTCA	0.667											OREG0017465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	525	0.104832	0.0068	0.0965	5008	,	,		15711	0.2262		0.0994	False		,,,				2504	0.1237				p.P589P		Atlas-SNP	.											TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	1	Substitution - coding silent(1)	stomach(1)	c.A1767G						PASS	.	A		107,4299	84.8+/-123.5	2,103,2098	79.0	55.0	63.0		1767	-9.3	0.5	6	dbSNP_107	63	917,7683	200.6+/-244.3	52,813,3435	no	coding-synonymous	TMEM63B	NM_018426.1		54,916,5533	GG,GA,AA		10.6628,2.4285,7.8733		589/833	44119676	1024,11982	2203	4300	6503	SO:0001819	synonymous_variant	55362	exon19			CATCCCAGGCCTG	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1767A>G	6.37:g.44119676A>G		Somatic	135	0	0	921	WXS	Illumina HiSeq	Phase_I	152	67	0.440789	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	255	0.11675824175824176	3	0.006097560975609756	38	0.10497237569060773	143	0.25	71	0.09366754617414248	A	11.02	1.514920	0.27123	0.024285	0.106628	ENSG00000137216	ENST00000371893	.	.	.	5.14	-9.26	0.00662	.	.	.	.	.	T	0.10165	0.0249	.	.	.	0.09310	P	0.9999999999999982	.	.	.	.	.	.	T	0.10451	-1.0629	3	.	.	.	.	8.3418	0.32247	0.1371:0.0914:0.5774:0.194	rs3734697	.	.	.	R	518	.	.	Q	+	2	0	TMEM63B	44227654	0.000000	0.05858	0.513000	0.27749	0.994000	0.84299	-3.661000	0.00400	-2.162000	0.00784	-0.385000	0.06624	CAG	A|0.910;G|0.090	0.090	strong		0.667	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
PCP2	126006	hgsc.bcm.edu	37	19	7698320	7698320	+	Silent	SNP	C	C	T	rs1862514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7698320C>T	ENST00000311069.5	-	1	314	c.24G>A	c.(22-24)acG>acA	p.T8T	CTD-3214H19.6_ENST00000601797.1_RNA|PCP2_ENST00000598935.1_5'Flank|CTD-3214H19.4_ENST00000595866.1_Intron	NM_174895.1	NP_777555.1	Q8IVA1	PCP2_HUMAN	Purkinje cell protein 2	8					rhodopsin mediated signaling pathway (GO:0016056)	neuronal cell body (GO:0043025)	GTPase regulator activity (GO:0030695)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|urinary_tract(1)	2						AGCCTTCCTCCGTCTTCTCCT	0.602													C|||	1241	0.247804	0.1483	0.2161	5008	,	,		15740	0.2113		0.3827	False		,,,				2504	0.3037				p.T8T		Atlas-SNP	.											.	PCP2	6	.	0			c.G24A						PASS	.	C		719,3679		60,599,1540	95.0	62.0	73.0		24	-3.1	0.0	19	dbSNP_92	73	3163,5425		577,2009,1708	no	coding-synonymous	PCP2	NM_174895.1		637,2608,3248	TT,TC,CC		36.8305,16.3483,29.8937		8/137	7698320	3882,9104	2199	4294	6493	SO:0001819	synonymous_variant	126006	exon1			TTCCTCCGTCTTC	BC025387	CCDS32893.1, CCDS62521.1	19p13.3	2008-02-05				ENSG00000174788			30209	protein-coding gene	gene with protein product						12477932	Standard	NM_174895		Approved	MGC41903, GPSM4	uc031rjd.1	Q8IVA1		ENST00000311069.5:c.24G>A	19.37:g.7698320C>T		Somatic	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	262	130	0.496183	NM_174895	M0R2R7|Q3KRG7	Silent	SNP	ENST00000311069.5	37	CCDS32893.1																																																																																			C|0.738;T|0.262	0.262	strong		0.602	PCP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461026.2	XM_058956	
TTN	7273	hgsc.bcm.edu	37	2	179579025	179579025	+	Missense_Mutation	SNP	C	C	T	rs200116046		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179579025C>T	ENST00000591111.1	-	89	25749	c.25525G>A	c.(25525-25527)Gtt>Att	p.V8509I	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V7582I|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V8826I			Q8WZ42	TITIN_HUMAN	titin	12673					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V7582I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAACCGAGAACGGATAGCGTG	0.393																																					p.V8826I		Atlas-SNP	.											TTN_ENST00000356127,caecum,carcinoma,0,1	TTN	18412	1	1	Substitution - Missense(1)	large_intestine(1)	c.G26476A						scavenged	.	C	,,,ILE/VAL	0,3838		0,0,1919	131.0	127.0	128.0		,,,22744	-1.8	0.0	2		128	1,8259		0,1,4129	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,29	0,1,6048	TT,TC,CC		0.0121,0.0,0.0083	,,,benign	,,,7582/33424	179579025	1,12097	1919	4130	6049	SO:0001583	missense	7273	exon91			CGAGAACGGATAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25525G>A	2.37:g.179579025C>T	ENSP00000465570:p.Val8509Ile	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	224	3	0.0133929	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	6.224	0.409421	0.11812	0.0	1.21E-4	ENSG00000155657	ENST00000342992	T	0.74209	-0.82	5.96	-1.8	0.07907	Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.70996	0.3288	M	0.72479	2.2	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.64927	-0.6292	9	0.87932	D	0	.	13.7985	0.63186	0.0:0.6647:0.0:0.3353	.	8509	Q8WZ42	TITIN_HUMAN	I	7582	ENSP00000343764:V7582I	ENSP00000343764:V7582I	V	-	1	0	TTN	179287270	0.540000	0.26410	0.000000	0.03702	0.012000	0.07955	1.228000	0.32588	-0.429000	0.07329	-1.004000	0.02495	GTT	.	.	weak		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DCHS2	54798	hgsc.bcm.edu	37	4	155244462	155244462	+	Intron	SNP	C	C	T	rs74430037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155244462C>T	ENST00000357232.4	-	13	2653				DCHS2_ENST00000339452.1_Silent_p.K1346K	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CTGTTTTTCCCTTCAGAGGCA	0.428													C|||	98	0.0195687	0.0023	0.0288	5008	,	,		14541	0.0		0.0706	False		,,,				2504	0.0041				p.K1346K		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4038A						PASS	.						58.0	43.0	48.0					4																	155244462		692	1591	2283	SO:0001627	intron_variant	54798	exon8			TTTTCCCTTCAGA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.2654-822G>A	4.37:g.155244462C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			C|0.966;T|0.034	0.034	strong		0.428	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
ZNF582	147948	hgsc.bcm.edu	37	19	56895496	56895496	+	Silent	SNP	C	C	T	rs12978696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56895496C>T	ENST00000301310.4	-	5	1448	c.1290G>A	c.(1288-1290)aaG>aaA	p.K430K	ZNF582_ENST00000586929.1_Silent_p.K430K	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		GACTAAAAGCCTTCCCACATT	0.388													C|||	794	0.158546	0.1029	0.0965	5008	,	,		20972	0.3095		0.1382	False		,,,				2504	0.1431				p.K430K	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G1290A						PASS	.	C		466,3940	219.7+/-237.4	23,420,1760	124.0	119.0	121.0		1290	-5.4	0.0	19	dbSNP_121	121	1094,7506	228.9+/-263.8	76,942,3282	no	coding-synonymous	ZNF582	NM_144690.1		99,1362,5042	TT,TC,CC		12.7209,10.5765,11.9945		430/518	56895496	1560,11446	2203	4300	6503	SO:0001819	synonymous_variant	147948	exon5			AAAAGCCTTCCCA	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"""Zinc fingers, C2H2-type"", ""-"""	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.1290G>A	19.37:g.56895496C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Silent	SNP	ENST00000301310.4	37	CCDS33121.1																																																																																			C|0.865;T|0.135	0.135	strong		0.388	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690	
FAH	2184	hgsc.bcm.edu	37	15	80454615	80454615	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:80454615G>A	ENST00000407106.1	+	6	547	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	FAH_ENST00000539156.1_Missense_Mutation_p.R61Q|FAH_ENST00000558627.1_3'UTR|FAH_ENST00000561421.1_Missense_Mutation_p.R131Q|FAH_ENST00000261755.5_Missense_Mutation_p.R131Q			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	131					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TATTCCTCTCGGCAGCATGCT	0.483									Tyrosinemia, type 1																												p.R131Q		Atlas-SNP	.											FAH,NS,carcinoma,+1,2	FAH	36	2	0			c.G392A						scavenged	.						170.0	154.0	160.0					15																	80454615		2203	4300	6503	SO:0001583	missense	2184	exon5	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	CCTCTCGGCAGCA	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.392G>A	15.37:g.80454615G>A	ENSP00000385080:p.Arg131Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	91	3	0.032967	NM_000137	B2R9X1|D3DW95|Q53XA7	Missense_Mutation	SNP	ENST00000407106.1	37	CCDS10314.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.352972	0.41700	.	.	ENSG00000103876	ENST00000407106;ENST00000261755;ENST00000539156	D;D;D	0.95137	-3.62;-3.62;-3.62	4.81	3.88	0.44766	Fumarylacetoacetase, C-terminal-related (2);Fumarylacetoacetase, C-terminal (1);	0.198730	0.41823	D	0.000820	D	0.93314	0.7869	M	0.75085	2.285	0.43025	D	0.994589	P;P	0.49961	0.682;0.93	B;B	0.41764	0.023;0.366	D	0.92334	0.5876	10	0.42905	T	0.14	-15.5724	13.7515	0.62910	0.0:0.0:0.8452:0.1548	.	61;131	Q53XA7;P16930	.;FAAA_HUMAN	Q	131;131;61	ENSP00000385080:R131Q;ENSP00000261755:R131Q;ENSP00000454271:R61Q	ENSP00000261755:R131Q	R	+	2	0	FAH	78241670	0.882000	0.30256	0.751000	0.31187	0.525000	0.34531	2.155000	0.42301	1.118000	0.41863	0.650000	0.86243	CGG	.	.	none		0.483	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2		
PGS1	9489	hgsc.bcm.edu	37	17	76421443	76421443	+	IGR	SNP	G	G	A	rs1134541	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76421443G>A	ENST00000262764.6	+	0	2201				DNAH17_ENST00000389840.5_Silent_p.Y4398Y|AC061992.1_ENST00000600087.1_5'Flank|DNAH17_ENST00000585328.1_Silent_p.Y4370Y|DNAH17_ENST00000586052.1_5'UTR	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TGAAGAGTCCGTACACGTAGG	0.532													G|||	536	0.107029	0.1997	0.072	5008	,	,		20979	0.0288		0.0905	False		,,,				2504	0.1043				p.Y4375Y	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.C13125T						PASS	.	G		726,3680	301.3+/-286.8	57,612,1534	101.0	101.0	101.0		13125	0.4	1.0	17	dbSNP_86	101	800,7800	187.3+/-234.6	47,706,3547	no	coding-synonymous	DNAH17	NM_173628.3		104,1318,5081	AA,AG,GG		9.3023,16.4775,11.733		4375/4463	76421443	1526,11480	2203	4300	6503	SO:0001628	intergenic_variant	8632	exon80			GAGTCCGTACACG		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76421443G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	37	CCDS42391.1																																																																																			G|0.885;A|0.115	0.115	strong		0.532	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
POC5	134359	hgsc.bcm.edu	37	5	75001582	75001582	+	Missense_Mutation	SNP	A	A	G	rs17672542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:75001582A>G	ENST00000428202.2	-	4	443	c.254T>C	c.(253-255)aTa>aCa	p.I85T	POC5_ENST00000504862.1_5'UTR|POC5_ENST00000514838.2_Intron|POC5_ENST00000446329.2_Missense_Mutation_p.I60T|POC5_ENST00000510798.1_5'UTR|POC5_ENST00000380475.2_5'UTR	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	85			I -> T (in dbSNP:rs17672542). {ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TCCAACTTCTATTGCAGTTTC	0.279													A|||	932	0.186102	0.1475	0.1542	5008	,	,		16356	0.3234		0.0944	False		,,,				2504	0.2137				p.I85T		Atlas-SNP	.											.	POC5	82	.	0			c.T254C						PASS	.	A	THR/ILE,THR/ILE	517,3061		38,441,1310	83.0	74.0	77.0		254,179	-0.6	0.1	5	dbSNP_123	77	631,7459		33,565,3447	yes	missense,missense	POC5	NM_001099271.1,NM_152408.2	89,89	71,1006,4757	GG,GA,AA		7.7998,14.4494,9.8389	benign,benign	85/576,60/551	75001582	1148,10520	1789	4045	5834	SO:0001583	missense	134359	exon4			ACTTCTATTGCAG	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.254T>C	5.37:g.75001582A>G	ENSP00000410216:p.Ile85Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	407	0.18635531135531136	83	0.16869918699186992	44	0.12154696132596685	202	0.3531468531468531	78	0.10290237467018469	A	1.576	-0.532826	0.04112	0.144494	0.077998	ENSG00000152359	ENST00000428202;ENST00000446329	T;T	0.22539	1.95;1.95	4.91	-0.613	0.11594	.	1.098280	0.06625	N	0.758152	T	0.00012	0.0000	L	0.39898	1.24	0.54753	P	1.2000000000012001E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.47195	-0.9136	9	0.27785	T	0.31	-1.6696	3.2629	0.06855	0.4837:0.0:0.335:0.1813	rs17672542;rs56922302;rs17672542	85;60	Q8NA72;Q8NA72-3	POC5_HUMAN;.	T	85;60	ENSP00000410216:I85T;ENSP00000399481:I60T	ENSP00000410216:I85T	I	-	2	0	POC5	75037338	0.365000	0.25006	0.123000	0.21794	0.190000	0.23558	0.942000	0.29017	0.099000	0.17552	0.528000	0.53228	ATA	A|0.814;G|0.186	0.186	strong		0.279	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
POLR1E	64425	hgsc.bcm.edu	37	9	37492679	37492679	+	Silent	SNP	G	G	T	rs3739576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37492679G>T	ENST00000377798.4	+	5	482	c.369G>T	c.(367-369)gcG>gcT	p.A123A	POLR1E_ENST00000442009.2_Silent_p.A53A|POLR1E_ENST00000377792.3_Silent_p.A185A	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		GTGAACTGGCGCTAGAGAGTC	0.388													G|||	1078	0.215256	0.1694	0.3112	5008	,	,		19655	0.244		0.2018	False		,,,				2504	0.1933				p.A123A	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.G369T						PASS	.	G		806,3600	319.9+/-296.3	71,664,1468	148.0	131.0	137.0		369	-4.0	0.0	9	dbSNP_107	137	1870,6730	333.7+/-320.7	199,1472,2629	no	coding-synonymous	POLR1E	NM_022490.1		270,2136,4097	TT,TG,GG		21.7442,18.2932,20.5751		123/420	37492679	2676,10330	2203	4300	6503	SO:0001819	synonymous_variant	64425	exon5			ACTGGCGCTAGAG	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.369G>T	9.37:g.37492679G>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	210	101	0.480952	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000377798.4	37	CCDS6611.1																																																																																			G|0.796;T|0.204	0.204	strong		0.388	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
NPBWR1	2831	hgsc.bcm.edu	37	8	53852871	53852871	+	Missense_Mutation	SNP	A	A	T	rs33977775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:53852871A>T	ENST00000331251.3	+	1	1881	c.404A>T	c.(403-405)tAc>tTc	p.Y135F		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	135			Y -> F (in dbSNP:rs33977775).		G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GCCGACCGCTACCTGGTGGTG	0.667													A|||	436	0.0870607	0.0038	0.085	5008	,	,		16505	0.12		0.1302	False		,,,				2504	0.1227				p.Y135F		Atlas-SNP	.											.	NPBWR1	38	.	0			c.A404T						PASS	.	A	PHE/TYR	131,4271		3,125,2073	28.0	29.0	29.0		404	5.1	1.0	8	dbSNP_126	29	1016,7574		60,896,3339	yes	missense	NPBWR1	NM_005285.3	22	63,1021,5412	TT,TA,AA		11.8277,2.9759,8.8285	probably-damaging	135/329	53852871	1147,11845	2201	4295	6496	SO:0001583	missense	2831	exon1			ACCGCTACCTGGT	BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4522	protein-coding gene	gene with protein product		600730	"""G protein-coupled receptor 7"""	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.404A>T	8.37:g.53852871A>T	ENSP00000330284:p.Tyr135Phe	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_005285	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	205	0.09386446886446886	5	0.01016260162601626	34	0.09392265193370165	70	0.12237762237762238	96	0.1266490765171504	A	27.3	4.816662	0.90790	0.029759	0.118277	ENSG00000183729	ENST00000331251	D	0.87029	-2.2	5.06	5.06	0.68205	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000144	T	0.16385	0.0394	M	0.78801	2.425	0.21416	P	0.999690328	D	0.89917	1.0	D	0.91635	0.999	T	0.61232	-0.7104	9	0.87932	D	0	.	14.9709	0.71232	1.0:0.0:0.0:0.0	rs33977775	135	P48145	NPBW1_HUMAN	F	135	ENSP00000330284:Y135F	ENSP00000330284:Y135F	Y	+	2	0	NPBWR1	54015424	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.875000	0.75551	2.120000	0.65058	0.533000	0.62120	TAC	A|0.907;T|0.093	0.093	strong		0.667	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167463	140167463	+	Silent	SNP	C	C	T	rs3733710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140167463C>T	ENST00000504120.2	+	1	1588	c.1588C>T	c.(1588-1590)Ctg>Ttg	p.L530L	PCDHA1_ENST00000378133.3_Silent_p.L530L|PCDHA1_ENST00000394633.3_Silent_p.L530L	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	530	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCTGGAGCTGCTGCAGTT	0.687													.|||	2612	0.521565	0.4796	0.5865	5008	,	,		16751	0.5149		0.5368	False		,,,				2504	0.5235				p.L530L		Atlas-SNP	.											PCDHA1_ENST00000504120,NS,carcinoma,0,2	PCDHA1	387	2	0			c.C1588T						PASS	.	C	,,	2186,2220	568.1+/-382.3	529,1128,546	70.0	74.0	73.0		1588,1588,1588	1.7	1.0	5	dbSNP_107	73	4543,4057	573.5+/-389.9	1196,2151,953	no	coding-synonymous,coding-synonymous,coding-synonymous	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	,,	1725,3279,1499	TT,TC,CC		47.1744,49.6142,48.2623	,,	530/951,530/808,530/687	140167463	6729,6277	2203	4300	6503	SO:0001819	synonymous_variant	56147	exon1			CTGGAGCTGCTGC	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1588C>T	5.37:g.140167463C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_031411	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	CCDS54913.1																																																																																			C|0.485;T|0.515	0.515	strong		0.687	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
EPHA3	2042	hgsc.bcm.edu	37	3	89448610	89448610	+	Missense_Mutation	SNP	A	A	T	rs150469112		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:89448610A>T	ENST00000336596.2	+	7	1799	c.1574A>T	c.(1573-1575)gAg>gTg	p.E525V	EPHA3_ENST00000494014.1_Missense_Mutation_p.E525V|EPHA3_ENST00000452448.2_Missense_Mutation_p.E525V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	525	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CGCAAGTTTGAGTTTGAAACT	0.448										TSP Lung(6;0.00050)																											p.E525V		Atlas-SNP	.											.	EPHA3	501	.	0			c.A1574T						PASS	.	A	VAL/GLU,VAL/GLU	0,4406		0,0,2203	106.0	98.0	101.0		1574,1574	5.5	1.0	3	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EPHA3	NM_005233.5,NM_182644.2	121,121	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	525/984,525/540	89448610	1,13005	2203	4300	6503	SO:0001583	missense	2042	exon7			AGTTTGAGTTTGA	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1574A>T	3.37:g.89448610A>T	ENSP00000337451:p.Glu525Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.578556	0.86645	0.0	1.16E-4	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.53423	0.62;0.62;0.62	5.53	5.53	0.82687	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.051723	0.85682	D	0.000000	T	0.61502	0.2352	M	0.67700	2.07	0.80722	D	1	B;D	0.53312	0.181;0.959	B;P	0.56088	0.134;0.791	T	0.62191	-0.6906	9	.	.	.	.	15.6643	0.77213	1.0:0.0:0.0:0.0	.	525;525	P29320;P29320-2	EPHA3_HUMAN;.	V	525	ENSP00000337451:E525V;ENSP00000399926:E525V;ENSP00000419190:E525V	.	E	+	2	0	EPHA3	89531300	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	9.339000	0.96797	2.107000	0.64212	0.460000	0.39030	GAG	A|1.000;T|0.000	0.000	weak		0.448	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
ANKUB1	389161	hgsc.bcm.edu	37	3	149485293	149485293	+	Missense_Mutation	SNP	T	T	C	rs7610425	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:149485293T>C	ENST00000383050.3	-	5	1612	c.1156A>G	c.(1156-1158)Agc>Ggc	p.S386G	ANKUB1_ENST00000446160.1_Missense_Mutation_p.S386G|ANKUB1_ENST00000462519.2_Missense_Mutation_p.S386G			A6NFN9	ANKUB_HUMAN	ankyrin repeat and ubiquitin domain containing 1	386			S -> G (in dbSNP:rs7610425).							breast(1)|kidney(1)|lung(1)|skin(1)	4						GGTTTGCTGCTTGCAGTTTGT	0.458													T|||	1326	0.264776	0.1717	0.2579	5008	,	,		19084	0.247		0.3907	False		,,,				2504	0.2843				p.S386G		Atlas-SNP	.											.	ANKUB1	27	.	0			c.A1156G						PASS	.	T	GLY/SER	285,1099		25,235,432	187.0	133.0	149.0		1156	-1.1	0.0	3	dbSNP_116	149	1266,1916		249,768,574	yes	missense	ANKUB1	NM_001144960.1	56	274,1003,1006	CC,CT,TT		39.7863,20.5925,33.9685	benign	386/545	149485293	1551,3015	692	1591	2283	SO:0001583	missense	389161	exon5			TGCTGCTTGCAGT	AK027233		3q25.1	2013-01-11	2011-05-10	2011-05-10	ENSG00000206199	ENSG00000206199		"""Ankyrin repeat domain containing"""	29642	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 16"""	C3orf16			Standard	NM_001144960		Approved		uc003exl.3	A6NFN9	OTTHUMG00000159615	ENST00000383050.3:c.1156A>G	3.37:g.149485293T>C	ENSP00000372522:p.Ser386Gly	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	242	123	0.508264	NM_001144960	B4E2N8	Missense_Mutation	SNP	ENST00000383050.3	37		614	0.28113553113553114	88	0.17886178861788618	92	0.2541436464088398	123	0.21503496503496503	311	0.4102902374670185	T	11.33	1.607832	0.28623	0.205925	0.397863	ENSG00000206199	ENST00000446160;ENST00000383050;ENST00000462519	T;T;T	0.24908	1.86;1.83;1.86	5.6	-1.11	0.09840	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.49113	-0.8973	8	0.22706	T	0.39	.	6.0018	0.19525	0.0:0.2809:0.126:0.593	rs7610425;rs17788044;rs52792421;rs57468189;rs7610425	386;386	A6NFN9;E9PHT4	ANKUB_HUMAN;.	G	386	ENSP00000387907:S386G;ENSP00000372522:S386G;ENSP00000417635:S386G	ENSP00000372522:S386G	S	-	1	0	ANKUB1	150967983	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.012000	0.29924	-0.423000	0.07394	-0.353000	0.07706	AGC	C|0.286;N|0.000	0.286	strong		0.458	ANKUB1-201	KNOWN	basic	protein_coding	protein_coding		NM_001144960	
BTN2A2	10385	hgsc.bcm.edu	37	6	26392515	26392515	+	Intron	SNP	G	G	C	rs2072803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26392515G>C	ENST00000356709.4	+	8	1090				BTN2A2_ENST00000469230.1_Intron|BTN2A2_ENST00000432533.2_Missense_Mutation_p.A255P|BTN2A2_ENST00000416795.2_Intron|BTN2A2_ENST00000352867.2_Intron|BTN2A2_ENST00000482536.1_Intron	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2						negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cellular metabolic process (GO:0031324)|negative regulation of cytokine secretion (GO:0050710)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						ACCCCCTTCAGCTTTCTGAGA	0.547													G|||	433	0.0864617	0.0257	0.0403	5008	,	,		17206	0.12		0.1173	False		,,,				2504	0.135				p.A255P		Atlas-SNP	.											.	BTN2A2	87	.	0			c.G763C						PASS	.																																			SO:0001627	intron_variant	10385	exon7			CCTTCAGCTTTCT	U90550	CCDS4606.1, CCDS4607.1, CCDS56401.1, CCDS56402.1, CCDS56403.1	6p22.1	2014-01-14			ENSG00000124508	ENSG00000124508		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1137	protein-coding gene	gene with protein product		613591				10354554, 9149941	Standard	NM_006995		Approved	BTF2, BT2.2, BTN2.2	uc003nhq.3	Q8WVV5	OTTHUMG00000014452	ENST00000356709.4:c.980-88G>C	6.37:g.26392515G>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_001197240	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Missense_Mutation	SNP	ENST00000356709.4	37	CCDS4606.1	186	0.08516483516483517	18	0.036585365853658534	12	0.03314917127071823	69	0.12062937062937062	87	0.11477572559366754	.	4.349	0.064166	0.08388	.	.	ENSG00000124508	ENST00000432533	D	0.90676	-2.71	2.38	-2.77	0.05877	.	.	.	.	.	T	0.67646	0.2915	.	.	.	0.80722	P	0.0	B	0.15141	0.012	B	0.04013	0.001	T	0.54234	-0.8324	7	0.87932	D	0	.	0.3045	0.00278	0.3006:0.219:0.2858:0.1946	rs2072803;rs17609688;rs2072803	255	B4DQ01	.	P	255	ENSP00000394241:A255P	ENSP00000394241:A255P	A	+	1	0	BTN2A2	26500494	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-0.140000	0.10342	-0.529000	0.06358	-0.396000	0.06452	GCT	G|0.911;C|0.089	0.089	strong		0.547	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1		
PKD1L2	114780	hgsc.bcm.edu	37	16	81208515	81208515	+	RNA	SNP	G	G	A	rs12596941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81208515G>A	ENST00000527937.1	-	0	469				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GTCTCCGAGTGCCACCTGTTA	0.557													G|||	1013	0.202276	0.0068	0.2104	5008	,	,		20376	0.3046		0.2247	False		,,,				2504	0.3323				p.A863V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2588T						PASS	.	G	VAL/ALA,VAL/ALA	202,3868		5,192,1838	50.0	47.0	48.0		2588,2588	0.4	0.0	16	dbSNP_120	48	1882,6504		214,1454,2525	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	64,64	219,1646,4363	AA,AG,GG		22.4422,4.9631,16.7309	benign,benign	863/992,863/2460	81208515	2084,10372	2035	4193	6228			114780	exon16			CCGAGTGCCACCT	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81208515G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		445	0.20375457875457875	7	0.014227642276422764	77	0.212707182320442	181	0.31643356643356646	180	0.23746701846965698	G	9.620	1.133700	0.21123	0.049631	0.224422	ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937	T;T;T	0.29655	1.56;1.56;1.56	4.7	0.362	0.16113	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	2.898440	0.00953	N	0.002980	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.28933	0.078;0.228;0.216	B;B;B	0.27796	0.025;0.083;0.074	T	0.33240	-0.9876	8	0.42905	T	0.14	-0.0057	6.5899	0.22642	0.0:0.5186:0.3065:0.1748	rs12596941;rs52800976;rs12596941	119;863;863	Q7Z442-6;Q7Z442-3;Q7Z442	.;.;PK1L2_HUMAN	V	178;863;119	ENSP00000436309:A178V;ENSP00000337397:A863V;ENSP00000432818:A119V	ENSP00000337397:A863V	A	-	2	0	PKD1L2	79766016	0.000000	0.05858	0.029000	0.17559	0.022000	0.10575	0.054000	0.14205	0.151000	0.19162	-0.321000	0.08615	GCA	G|0.789;A|0.211	0.211	strong		0.557	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
OR4M1	441670	hgsc.bcm.edu	37	14	20249176	20249176	+	Missense_Mutation	SNP	G	G	A	rs2815960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20249176G>A	ENST00000315957.4	+	1	776	c.695G>A	c.(694-696)gGt>gAt	p.G232D		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	232			G -> D (in dbSNP:rs2815960).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCAGGCTCAGGTGAGAATACC	0.463																																					p.G232D		Atlas-SNP	.											.	OR4M1	104	.	0			c.G695A						PASS	.		ASP/GLY	584,3822		18,548,1637	353.0	300.0	318.0		695	3.5	1.0	14	dbSNP_100	318	2769,5831		267,2235,1798	yes	missense	OR4M1	NM_001005500.1	94	285,2783,3435	AA,AG,GG		32.1977,13.2547,25.7804	benign	232/314	20249176	3353,9653	2203	4300	6503	SO:0001583	missense	441670	exon1			GCTCAGGTGAGAA		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"""GPCR / Class A : Olfactory receptors"""	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.695G>A	14.37:g.20249176G>A	ENSP00000319654:p.Gly232Asp	Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	498	237	0.475904	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	CCDS32021.1	595	0.2724358974358974	42	0.08536585365853659	120	0.3314917127071823	163	0.28496503496503495	270	0.3562005277044855	.	10.89	1.478364	0.26511	0.132547	0.321977	ENSG00000176299	ENST00000315957	T	0.00293	8.26	4.42	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.392518	0.21951	N	0.066723	T	0.00012	0.0000	N	0.08118	0	0.37415	P	0.08660699999999999	B	0.02656	0.0	B	0.08055	0.003	T	0.16571	-1.0398	9	0.72032	D	0.01	-1.8975	7.0717	0.25181	0.2025:0.0:0.7975:0.0	rs2815960;rs52830018	232	Q8NGD0	OR4M1_HUMAN	D	232	ENSP00000319654:G232D	ENSP00000319654:G232D	G	+	2	0	OR4M1	19319016	0.000000	0.05858	1.000000	0.80357	0.744000	0.42396	0.118000	0.15605	1.225000	0.43566	0.506000	0.49869	GGT	G|0.739;A|0.261	0.261	strong		0.463	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1		
OR5A2	219981	hgsc.bcm.edu	37	11	59189912	59189912	+	Missense_Mutation	SNP	G	G	A	rs1453547	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59189912G>A	ENST00000302040.4	-	1	537	c.515C>T	c.(514-516)cCc>cTc	p.P172L		NM_001001954.1	NP_001001954.1	Q8NGI9	OR5A2_HUMAN	olfactory receptor, family 5, subfamily A, member 2	172			P -> L (in dbSNP:rs1453547).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	21						GATCATATAGGGCCCACAGAA	0.463													G|||	631	0.125998	0.0242	0.1311	5008	,	,		22596	0.1121		0.2515	False		,,,				2504	0.1452				p.P172L		Atlas-SNP	.											.	OR5A2	35	.	0			c.C515T						PASS	.	G	LEU/PRO	256,4146	148.8+/-183.1	10,236,1955	95.0	88.0	91.0		515	4.6	0.3	11	dbSNP_88	91	2258,6332	382.8+/-340.5	282,1694,2319	yes	missense	OR5A2	NM_001001954.1	98	292,1930,4274	AA,AG,GG		26.2864,5.8155,19.3504	probably-damaging	172/325	59189912	2514,10478	2201	4295	6496	SO:0001583	missense	219981	exon1			ATATAGGGCCCAC	AB065805	CCDS31560.1	11q12.1	2012-08-09			ENSG00000172324	ENSG00000172324		"""GPCR / Class A : Olfactory receptors"""	15249	protein-coding gene	gene with protein product							Standard	NM_001001954		Approved		uc010rkt.2	Q8NGI9	OTTHUMG00000167419	ENST00000302040.4:c.515C>T	11.37:g.59189912G>A	ENSP00000303834:p.Pro172Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_001001954	B9EH21|Q6IFF4|Q96RB0	Missense_Mutation	SNP	ENST00000302040.4	37	CCDS31560.1	349	0.15979853479853479	19	0.03861788617886179	59	0.16298342541436464	71	0.12412587412587413	200	0.2638522427440633	G	19.64	3.865680	0.71949	0.058155	0.262864	ENSG00000172324	ENST00000302040	T	0.00076	8.76	5.47	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34932	U	0.003564	T	0.00012	0.0000	M	0.79343	2.45	0.30789	P	0.741141	D	0.69078	0.997	D	0.79784	0.993	T	0.68070	-0.5506	9	0.72032	D	0.01	.	13.8893	0.63729	0.0:0.0:0.8469:0.1531	rs1453547;rs17499129;rs57323320;rs1453547	172	Q8NGI9	OR5A2_HUMAN	L	172	ENSP00000303834:P172L	ENSP00000303834:P172L	P	-	2	0	OR5A2	58946488	0.328000	0.24687	0.276000	0.24689	0.826000	0.46750	3.157000	0.50716	1.428000	0.47296	0.585000	0.79938	CCC	G|0.820;A|0.180	0.180	strong		0.463	OR5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394552.1	NM_001001954	
DNAH14	127602	hgsc.bcm.edu	37	1	225211422	225211422	+	Missense_Mutation	SNP	T	T	C	rs75568712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:225211422T>C	ENST00000445597.2	+	9	1270	c.1270T>C	c.(1270-1272)Ttc>Ctc	p.F424L	DNAH14_ENST00000439375.2_Missense_Mutation_p.F405L|DNAH14_ENST00000430092.1_Missense_Mutation_p.F405L|DNAH14_ENST00000366849.1_Missense_Mutation_p.F382L|DNAH14_ENST00000400952.3_Missense_Mutation_p.F405L			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	424				F -> L (in Ref. 3; AAI19718). {ECO:0000305}.	microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AGAAACATTTTTCAAGTTTGT	0.328													T|||	169	0.033746	0.0045	0.036	5008	,	,		16444	0.0129		0.0736	False		,,,				2504	0.0521				p.F405L		Atlas-SNP	.											.	DNAH14	300	.	0			c.T1213C						PASS	.						158.0	138.0	144.0					1																	225211422		692	1589	2281	SO:0001583	missense	127602	exon11			ACATTTTTCAAGT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.1270T>C	1.37:g.225211422T>C	ENSP00000409472:p.Phe424Leu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	248	115	0.46371	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		85	0.03891941391941392	4	0.008130081300813009	15	0.04143646408839779	9	0.015734265734265736	57	0.07519788918205805	T	0.742	-0.776128	0.02951	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000400952;ENST00000366849;ENST00000439375	T;T;T;T;T	0.28895	2.65;1.65;1.6;1.59;1.65	5.37	-0.367	0.12541	.	0.811230	0.10693	N	0.644943	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.26677	-1.0096	10	0.08837	T	0.75	.	1.0652	0.01609	0.1512:0.1812:0.1566:0.511	.	405;405;424	Q0VDD8-4;Q0VDD8-2;Q0VDD8	.;.;DYH14_HUMAN	L	424;405;405;382;405	ENSP00000409472:F424L;ENSP00000414402:F405L;ENSP00000383737:F405L;ENSP00000355814:F382L;ENSP00000392061:F405L	ENSP00000355814:F382L	F	+	1	0	DNAH14	223278045	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	-0.636000	0.05465	-0.234000	0.09782	0.421000	0.28195	TTC	T|0.955;C|0.045	0.045	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
TBP	6908	hgsc.bcm.edu	37	6	170871103	170871103	+	Silent	SNP	G	G	A	rs149441883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:170871103G>A	ENST00000392092.2	+	3	558	c.279G>A	c.(277-279)caG>caA	p.Q93Q	TBP_ENST00000540980.1_Silent_p.Q73Q|TBP_ENST00000230354.6_Silent_p.Q93Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	93	Poly-Gln.		Missing. {ECO:0000269|PubMed:2374612}.		cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcaacaggcag	0.612													G|||	7	0.00139776	0.0015	0.0029	5008	,	,		13775	0.0		0.002	False		,,,				2504	0.001				p.Q93Q		Atlas-SNP	.											TBP,NS,carcinoma,0,2	TBP	58	2	0			c.G279A						scavenged	.						28.0	33.0	31.0					6																	170871103		1986	3826	5812	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAG	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.279G>A	6.37:g.170871103G>A		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	113	6	0.0530973	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			G|0.998;A|0.002	0.002	strong		0.612	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
ST6GAL1	6480	hgsc.bcm.edu	37	3	186760520	186760520	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760520T>G	ENST00000169298.3	+	4	703	c.29T>G	c.(28-30)tTc>tGc	p.F10C	ST6GAL1_ENST00000448044.1_Missense_Mutation_p.F10C|ST6GAL1_ENST00000457772.2_Intron	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	10					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		AAGAAAAAGTTCAGCTGCTGC	0.403																																					p.F10C		Atlas-SNP	.											ST6GAL1,NS,carcinoma,+1,1	ST6GAL1	36	1	0			c.T29G						PASS	.						165.0	161.0	163.0					3																	186760520		2203	4300	6503	SO:0001583	missense	6480	exon3			AAAAGTTCAGCTG	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.29T>G	3.37:g.186760520T>G	ENSP00000169298:p.Phe10Cys	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	196	23	0.117347	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	37	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	T	18.32	3.599029	0.66332	.	.	ENSG00000073849	ENST00000169298;ENST00000458216;ENST00000430309;ENST00000417392;ENST00000438590;ENST00000448408;ENST00000440338;ENST00000448044;ENST00000416235;ENST00000423451;ENST00000446170	T;T	0.23950	1.88;1.88	5.44	5.44	0.79542	.	0.415059	0.26804	N	0.022416	T	0.24586	0.0596	L	0.52364	1.645	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.03103	-1.1072	10	0.33940	T	0.23	-27.897	12.2097	0.54373	0.0:0.0:0.0:1.0	.	10	P15907	SIAT1_HUMAN	C	10	ENSP00000169298:F10C;ENSP00000389337:F10C	ENSP00000169298:F10C	F	+	2	0	ST6GAL1	188243214	0.614000	0.27017	0.996000	0.52242	0.933000	0.57130	1.719000	0.38011	2.200000	0.70718	0.459000	0.35465	TTC	.	.	none		0.403	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	
ZHX3	23051	hgsc.bcm.edu	37	20	39832628	39832628	+	Missense_Mutation	SNP	T	T	C	rs17265513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:39832628T>C	ENST00000309060.3	-	4	1344	c.929A>G	c.(928-930)aAt>aGt	p.N310S	ZHX3_ENST00000544979.2_Missense_Mutation_p.N310S|ZHX3_ENST00000559234.1_Missense_Mutation_p.N310S|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000560361.1_Missense_Mutation_p.N310S|ZHX3_ENST00000432768.2_Missense_Mutation_p.N310S|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000540170.1_Missense_Mutation_p.N310S			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	310	Required for homodimerization and interaction with NFYA.|Required for repressor activity.		N -> S (in dbSNP:rs17265513).		cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CATGGCTGCATTGTACGTTGG	0.557													T|||	295	0.0589058	0.0113	0.0706	5008	,	,		20230	0.001		0.1948	False		,,,				2504	0.0348				p.N310S		Atlas-SNP	.											.	ZHX3	78	.	0			c.A929G						PASS	.	T	SER/ASN	175,4231	114.6+/-152.6	8,159,2036	104.0	95.0	98.0		929	4.8	0.8	20	dbSNP_123	98	1612,6988	299.4+/-304.4	162,1288,2850	yes	missense	ZHX3	NM_015035.3	46	170,1447,4886	CC,CT,TT		18.7442,3.9719,13.7398	probably-damaging	310/957	39832628	1787,11219	2203	4300	6503	SO:0001583	missense	23051	exon3			GCTGCATTGTACG	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.929A>G	20.37:g.39832628T>C	ENSP00000312222:p.Asn310Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	147	63	0.428571	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	194	0.08882783882783883	4	0.008130081300813009	34	0.09392265193370165	1	0.0017482517482517483	155	0.20448548812664907	T	15.34	2.803175	0.50315	0.039719	0.187442	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262;ENST00000432768	T;T;T;T;T	0.41758	0.99;2.4;2.4;2.16;0.99	5.88	4.79	0.61399	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.044464	0.85682	D	0.000000	T	0.00109	0.0003	M	0.79926	2.475	0.22500	P	0.999041207	D;D;D	0.58268	0.974;0.974;0.982	P;P;P	0.58970	0.829;0.78;0.849	T	0.04165	-1.0972	9	0.36615	T	0.2	-25.1632	11.8515	0.52413	0.0:0.068:0.0:0.932	rs17265513;rs17265513	310;310;310	A8K8Q0;Q9H4I2;F5H820	.;ZHX3_HUMAN;.	S	310;310;310;310;88;310	ENSP00000312222:N310S;ENSP00000362360:N310S;ENSP00000442290:N310S;ENSP00000443783:N310S;ENSP00000415498:N310S	ENSP00000312222:N310S	N	-	2	0	ZHX3	39266042	1.000000	0.71417	0.817000	0.32601	0.778000	0.44026	4.110000	0.57831	1.055000	0.40461	0.533000	0.62120	AAT	T|0.891;C|0.109	0.109	strong		0.557	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
OR10G7	390265	hgsc.bcm.edu	37	11	123909342	123909342	+	Silent	SNP	G	G	A	rs470242	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123909342G>A	ENST00000330487.5	-	1	375	c.367C>T	c.(367-369)Ctg>Ttg	p.L123L		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CTGATGGCCAGGTAGCGATCA	0.567													A|||	1188	0.23722	0.0363	0.2983	5008	,	,		20086	0.3264		0.2853	False		,,,				2504	0.3241				p.L123L		Atlas-SNP	.											.	OR10G7	103	.	0			c.C367T						PASS	.	A		362,4038	174.4+/-204.0	23,316,1861	174.0	151.0	159.0		367	1.4	1.0	11	dbSNP_83	159	2475,6123	390.5+/-343.3	402,1671,2226	no	coding-synonymous	OR10G7	NM_001004463.1		425,1987,4087	AA,AG,GG		28.7858,8.2273,21.8264		123/312	123909342	2837,10161	2200	4299	6499	SO:0001819	synonymous_variant	390265	exon1			TGGCCAGGTAGCG	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.367C>T	11.37:g.123909342G>A		Somatic	776	1	0.00128866		WXS	Illumina HiSeq	Phase_I	786	342	0.435115	NM_001004463	Q6IFE8	Silent	SNP	ENST00000330487.5	37	CCDS31705.1																																																																																			G|0.759;A|0.241	0.241	strong		0.567	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
MYH6	4624	hgsc.bcm.edu	37	14	23859610	23859610	+	Missense_Mutation	SNP	C	C	T	rs28730771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:23859610C>T	ENST00000356287.3	-	25	3417	c.3388G>A	c.(3388-3390)Gcc>Acc	p.A1130T	MYH6_ENST00000405093.3_Missense_Mutation_p.A1130T|MIR208A_ENST00000362287.1_RNA			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1130			A -> T (in dbSNP:rs28730771). {ECO:0000269|PubMed:15998695}.		adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TTAGCCCTGGCGGTGCGCTCG	0.672													C|||	365	0.0728834	0.0098	0.121	5008	,	,		17242	0.0605		0.1352	False		,,,				2504	0.0726				p.A1130T		Atlas-SNP	.											.	MYH6	274	.	0			c.G3388A						PASS	.						11.0	12.0	12.0					14																	23859610		2165	4260	6425	SO:0001583	missense	4624	exon26			CCCTGGCGGTGCG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3388G>A	14.37:g.23859610C>T	ENSP00000348634:p.Ala1130Thr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	46	0.345865	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	195	0.08928571428571429	5	0.01016260162601626	52	0.143646408839779	40	0.06993006993006994	98	0.12928759894459102	c	18.48	3.634015	0.67130	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.82893	-1.66;-1.66	4.25	3.35	0.38373	Myosin tail (1);	.	.	.	.	T	0.03390	0.0098	L	0.61387	1.9	0.24006	P	0.99619363	P	0.47191	0.891	P	0.52909	0.713	T	0.50898	-0.8773	8	0.33141	T	0.24	.	9.869	0.41162	0.2343:0.6364:0.1294:0.0	rs28730771	1130	P13533	MYH6_HUMAN	T	1130	ENSP00000386041:A1130T;ENSP00000348634:A1130T	ENSP00000348634:A1130T	A	-	1	0	MYH6	22929450	0.478000	0.25917	0.861000	0.33841	0.989000	0.77384	1.165000	0.31822	0.888000	0.36160	0.561000	0.74099	GCC	C|0.931;T|0.069	0.069	strong		0.672	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
SIPA1L2	57568	hgsc.bcm.edu	37	1	232650163	232650163	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:232650163G>A	ENST00000366630.1	-	2	1281	c.923C>T	c.(922-924)aCg>aTg	p.T308M	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.T308M			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	308					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CAGCTCAGACGTGAACTTGAA	0.458																																					p.T308M		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C923T						PASS	.						57.0	59.0	58.0					1																	232650163		1921	4141	6062	SO:0001583	missense	57568	exon1			TCAGACGTGAACT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.923C>T	1.37:g.232650163G>A	ENSP00000355589:p.Thr308Met	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.974684	0.34848	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.78924	-1.22;-1.22	5.39	4.48	0.54585	.	0.295098	0.33144	N	0.005238	T	0.58452	0.2123	N	0.08118	0	0.34703	D	0.726925	P	0.35493	0.505	B	0.32465	0.146	T	0.68123	-0.5492	10	0.33141	T	0.24	-5.5177	14.1111	0.65121	0.0719:0.0:0.9281:0.0	.	308	Q9P2F8	SI1L2_HUMAN	M	308	ENSP00000355589:T308M;ENSP00000262861:T308M	ENSP00000262861:T308M	T	-	2	0	SIPA1L2	230716786	1.000000	0.71417	0.818000	0.32626	0.930000	0.56654	4.769000	0.62300	1.503000	0.48686	0.650000	0.86243	ACG	.	.	none		0.458	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
SLC16A13	201232	hgsc.bcm.edu	37	17	6942108	6942108	+	Silent	SNP	C	C	T	rs11078663	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6942108C>T	ENST00000308027.6	+	3	1289	c.981C>T	c.(979-981)tcC>tcT	p.S327S		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	327						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						TGGCCTTCTCCGTGCTGCCTG	0.607													C|||	1763	0.352037	0.0469	0.4035	5008	,	,		18080	0.5149		0.6044	False		,,,				2504	0.3006				p.S327S		Atlas-SNP	.											.	SLC16A13	28	.	0			c.C981T						PASS	.	C		571,3835	247.5+/-255.7	51,469,1683	72.0	79.0	76.0		981	-0.4	1.0	17	dbSNP_120	76	5171,3429	621.5+/-397.2	1612,1947,741	no	coding-synonymous	SLC16A13	NM_201566.2		1663,2416,2424	TT,TC,CC		39.8721,12.9596,44.1489		327/427	6942108	5742,7264	2203	4300	6503	SO:0001819	synonymous_variant	201232	exon3			CTTCTCCGTGCTG	BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"""Solute carriers"""	31037	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 13"""		"""solute carrier family 16 (monocarboxylic acid transporters), member 13"""				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.981C>T	17.37:g.6942108C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_201566	A3KMG3|A5PKU5|Q2VP92	Silent	SNP	ENST00000308027.6	37	CCDS11085.1																																																																																			C|0.571;T|0.429	0.429	strong		0.607	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2		
BUD13	84811	hgsc.bcm.edu	37	11	116633825	116633825	+	Silent	SNP	C	C	T	rs918144	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:116633825C>T	ENST00000260210.4	-	4	503	c.480G>A	c.(478-480)ccG>ccA	p.P160P	BUD13_ENST00000375445.3_Silent_p.P160P	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	160	Arg-rich.				mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		GAGAAGGATCCGGGGTGTCAT	0.607													T|||	2730	0.545128	0.6785	0.6023	5008	,	,		16203	0.381		0.4821	False		,,,				2504	0.5583				p.P160P		Atlas-SNP	.											.	BUD13	41	.	0			c.G480A						PASS	.	T	,	2736,1666	507.1+/-366.6	830,1076,295	98.0	106.0	103.0		480,480	-5.0	0.0	11	dbSNP_86	103	4094,4498	588.7+/-392.4	960,2174,1162	no	coding-synonymous,coding-synonymous	BUD13	NM_001159736.1,NM_032725.3	,	1790,3250,1457	TT,TC,CC		47.649,37.8464,47.4373	,	160/486,160/620	116633825	6830,6164	2201	4296	6497	SO:0001819	synonymous_variant	84811	exon4			AGGATCCGGGGTG	BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 71"""		"""BUD13 homolog (yeast)"""			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.480G>A	11.37:g.116633825C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_001159736	A8K0S0|Q96LS7	Silent	SNP	ENST00000260210.4	37	CCDS8374.1																																																																																			C|0.470;T|0.530	0.530	strong		0.607	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000104864.1	NM_032725	
FSHR	2492	hgsc.bcm.edu	37	2	49191041	49191041	+	Missense_Mutation	SNP	C	C	T	rs6165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:49191041C>T	ENST00000406846.2	-	10	1038	c.919G>A	c.(919-921)Gct>Act	p.A307T	FSHR_ENST00000304421.4_Missense_Mutation_p.A281T|FSHR_ENST00000346173.3_Missense_Mutation_p.A245T|FSHR_ENST00000541117.1_Missense_Mutation_p.A43T	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	307			A -> T (in dbSNP:rs6165). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12059813, ECO:0000269|PubMed:1301382, ECO:0000269|PubMed:1322283, ECO:0000269|PubMed:1359889, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7916967, ECO:0000269|Ref.5}.		female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	TGACCCCTAGCCTGAGTCATA	0.388									Gonadal Dysgenesis, 46 XX				C|||	2465	0.492212	0.2375	0.5793	5008	,	,		21707	0.6597		0.5487	False		,,,				2504	0.544				p.A307T		Atlas-SNP	.											.	FSHR	164	.	0			c.G919A	GRCh37	CM062747	FSHR	M	rs6165	PASS	.	C	THR/ALA,THR/ALA	1256,3150	431.2+/-342.8	188,880,1135	188.0	174.0	179.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	919,841	1.8	1.0	2	dbSNP_52	179	4657,3943	603.7+/-394.7	1247,2163,890	yes	missense,missense	FSHR	NM_000145.3,NM_181446.2	58,58	1435,3043,2025	TT,TC,CC		45.8488,28.5066,45.4636	benign,benign	307/696,281/670	49191041	5913,7093	2203	4300	6503	SO:0001583	missense	2492	exon10	Familial Cancer Database		CCCTAGCCTGAGT		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"""GPCR / Class A : Gonadotropin and TSH receptors"""	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.919G>A	2.37:g.49191041C>T	ENSP00000384708:p.Ala307Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	146	66	0.452055	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	37	CCDS1843.1	1123	0.5141941391941391	120	0.24390243902439024	209	0.5773480662983426	382	0.6678321678321678	412	0.5435356200527705	C	5.128	0.209238	0.09757	0.285066	0.541512	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000541117;ENST00000454032	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06	5.53	1.76	0.24704	Gonadotropin hormone receptor, transmembrane domain (1);	1.030830	0.07635	N	0.929398	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.11329	0.006;0.004;0.006	T	0.45396	-0.9264	8	.	.	.	.	4.4676	0.11696	0.0:0.4356:0.1575:0.4068	rs6165;rs17434419;rs52810983;rs60724827;rs6165	281;245;307	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	T	307;245;281;43;245	ENSP00000384708:A307T;ENSP00000333908:A245T;ENSP00000306780:A281T;ENSP00000444172:A43T;ENSP00000415504:A245T	.	A	-	1	0	FSHR	49044545	0.000000	0.05858	0.989000	0.46669	0.977000	0.68977	-0.110000	0.10824	0.150000	0.19136	-0.136000	0.14681	GCT	C|0.525;T|0.475	0.475	strong		0.388	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2		
MANSC1	54682	hgsc.bcm.edu	37	12	12483275	12483275	+	Silent	SNP	G	G	A	rs1861676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:12483275G>A	ENST00000535902.1	-	4	1545	c.982C>T	c.(982-984)Cta>Tta	p.L328L	MANSC1_ENST00000396349.3_Silent_p.L294L|MANSC1_ENST00000545735.1_Silent_p.L247L			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	328	Thr-rich.					integral component of membrane (GO:0016021)		p.L328L(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		TTCAAAGTTAGGTTGGAGATT	0.448													G|||	2991	0.597244	0.5454	0.6628	5008	,	,		22631	0.38		0.7266	False		,,,				2504	0.7117				p.L328L		Atlas-SNP	.											MANSC1,NS,carcinoma,0,1	MANSC1	38	1	1	Substitution - coding silent(1)	stomach(1)	c.C982T						PASS	.	G		2560,1846	634.7+/-396.3	725,1110,368	139.0	131.0	134.0		982	1.9	0.0	12	dbSNP_92	134	6486,2114	716.2+/-406.1	2461,1564,275	no	coding-synonymous	MANSC1	NM_018050.2		3186,2674,643	AA,AG,GG		24.5814,41.8974,30.4475		328/432	12483275	9046,3960	2203	4300	6503	SO:0001819	synonymous_variant	54682	exon4			AAGTTAGGTTGGA	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.982C>T	12.37:g.12483275G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	173	82	0.473988	NM_018050	Q8NEC1|Q9NW60	Silent	SNP	ENST00000535902.1	37	CCDS8648.1																																																																																			G|0.358;A|0.642	0.642	strong		0.448	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
ALX4	60529	hgsc.bcm.edu	37	11	44296946	44296946	+	Silent	SNP	C	C	T	rs11037928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:44296946C>T	ENST00000329255.3	-	2	832	c.729G>A	c.(727-729)gcG>gcA	p.A243A		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	243					anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						GCTGTTCCCGCGCATACACGT	0.622													C|||	294	0.0587061	0.0703	0.0836	5008	,	,		18659	0.003		0.1193	False		,,,				2504	0.0204				p.A243A		Atlas-SNP	.											ALX4,NS,carcinoma,-1,1	ALX4	58	1	0			c.G729A						PASS	.	C		340,4066	180.1+/-208.5	12,316,1875	96.0	95.0	95.0		729	-7.5	0.5	11	dbSNP_120	95	982,7616	212.2+/-252.6	47,888,3364	no	coding-synonymous	ALX4	NM_021926.3		59,1204,5239	TT,TC,CC		11.4213,7.7167,10.1661		243/412	44296946	1322,11682	2203	4299	6502	SO:0001819	synonymous_variant	60529	exon2			TTCCCGCGCATAC	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.729G>A	11.37:g.44296946C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	189	87	0.460317	NM_021926	Q96JN7|Q9H198|Q9HAY9	Silent	SNP	ENST00000329255.3	37	CCDS31468.1																																																																																			C|0.915;T|0.085	0.085	strong		0.622	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
SLC16A9	220963	hgsc.bcm.edu	37	10	61414176	61414176	+	Missense_Mutation	SNP	G	G	A	rs56370926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:61414176G>A	ENST00000395348.3	-	5	1244	c.608C>T	c.(607-609)gCt>gTt	p.A203V	SLC16A9_ENST00000395347.1_Missense_Mutation_p.A203V	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	203			A -> V (in dbSNP:rs56370926).		urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						ATCTTCTGGAGCTATTTTTTT	0.378													G|||	159	0.0317492	0.0023	0.0173	5008	,	,		18499	0.0		0.0616	False		,,,				2504	0.0838				p.A203V		Atlas-SNP	.											.	SLC16A9	58	.	0			c.C608T						PASS	.	G	VAL/ALA	46,4360	50.2+/-85.5	0,46,2157	106.0	112.0	110.0		608	1.9	0.7	10	dbSNP_129	110	461,8139	136.7+/-193.7	14,433,3853	yes	missense	SLC16A9	NM_194298.2	64	14,479,6010	AA,AG,GG		5.3605,1.044,3.8982	benign	203/510	61414176	507,12499	2203	4300	6503	SO:0001583	missense	220963	exon5			TCTGGAGCTATTT	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"""Solute carriers"""	23520	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 9"""	614242	"""chromosome 10 open reading frame 36"", ""solute carrier family 16 (monocarboxylic acid transporters), member 9"", ""solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"""	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.608C>T	10.37:g.61414176G>A	ENSP00000378757:p.Ala203Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	CCDS7256.1	55	0.025183150183150184	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	48	0.0633245382585752	G	1.699	-0.502086	0.04261	0.01044	0.053605	ENSG00000165449	ENST00000395348;ENST00000395347	D;D	0.81579	-1.51;-1.51	5.12	1.94	0.25998	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.526148	0.17511	N	0.171612	T	0.17704	0.0425	N	0.20986	0.625	0.09310	N	1	B	0.28128	0.201	B	0.28232	0.087	T	0.17198	-1.0377	10	0.30854	T	0.27	.	6.5243	0.22293	0.2549:0.2418:0.5033:0.0	rs56370926	203	Q7RTY1	MOT9_HUMAN	V	203	ENSP00000378757:A203V;ENSP00000378756:A203V	ENSP00000378756:A203V	A	-	2	0	SLC16A9	61084182	0.004000	0.15560	0.673000	0.29887	0.020000	0.10135	0.456000	0.21859	1.147000	0.42369	-0.216000	0.12614	GCT	G|0.965;A|0.035	0.035	strong		0.378	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298	
KIF14	9928	hgsc.bcm.edu	37	1	200522566	200522566	+	Missense_Mutation	SNP	G	G	C	rs12120084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:200522566G>C	ENST00000367350.4	-	30	5335	c.4897C>G	c.(4897-4899)Cca>Gca	p.P1633A		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1633	Required for CIT-binding.		P -> A (in dbSNP:rs12120084). {ECO:0000269|PubMed:15489334}.		ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						CTCACTGCTGGGGATGAGCCA	0.448													G|||	1100	0.219649	0.0424	0.2017	5008	,	,		17288	0.2302		0.3917	False		,,,				2504	0.2843				p.P1633A		Atlas-SNP	.											.	KIF14	156	.	0			c.C4897G						PASS	.	G	ALA/PRO	454,3952	217.8+/-236.0	20,414,1769	187.0	160.0	169.0		4897	0.6	0.0	1	dbSNP_120	169	3523,5077	513.6+/-378.2	722,2079,1499	yes	missense	KIF14	NM_014875.2	27	742,2493,3268	CC,CG,GG		40.9651,10.3041,30.5782	benign	1633/1649	200522566	3977,9029	2203	4300	6503	SO:0001583	missense	9928	exon30			CTGCTGGGGATGA	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"""Kinesins"""	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.4897C>G	1.37:g.200522566G>C	ENSP00000356319:p.Pro1633Ala	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	241	239	0.991701	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	561	0.25686813186813184	32	0.06504065040650407	90	0.24861878453038674	139	0.243006993006993	300	0.39577836411609496	G	11.55	1.670804	0.29693	0.103041	0.409651	ENSG00000118193	ENST00000367350	T	0.73681	-0.77	5.37	0.605	0.17553	.	0.796636	0.11311	N	0.577155	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.31077	0.307	B	0.27380	0.079	T	0.23154	-1.0196	9	0.44086	T	0.13	.	7.3427	0.26646	0.1681:0.2592:0.5727:0.0	rs12120084;rs17448854;rs12120084	1633	Q15058	KIF14_HUMAN	A	1633	ENSP00000356319:P1633A	ENSP00000356319:P1633A	P	-	1	0	KIF14	198789189	0.002000	0.14202	0.001000	0.08648	0.046000	0.14306	-0.107000	0.10873	0.214000	0.20742	-0.176000	0.13171	CCA	G|0.707;C|0.293	0.293	strong		0.448	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875	
TERT	7015	hgsc.bcm.edu	37	5	1294086	1294086	+	Silent	SNP	C	C	T	rs2736098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:1294086C>T	ENST00000310581.5	-	2	972	c.915G>A	c.(913-915)gcG>gcA	p.A305A	TERT_ENST00000296820.5_Silent_p.A305A|TERT_ENST00000334602.6_Silent_p.A305A|TERT_ENST00000522877.1_5'Flank|TERT_ENST00000508104.2_Silent_p.A305A	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	305	Linker.|Required for oligomerization.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	ATGGGGGGCCCGCGTGGTGCT	0.682									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis				C|||	1330	0.265575	0.0658	0.2032	5008	,	,		15213	0.371		0.2346	False		,,,				2504	0.5031				p.A305A		Atlas-SNP	.											.	TERT	2594	.	0			c.G915A						PASS	.	C	,	454,3864		27,400,1732	16.0	16.0	16.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	915,915	-4.8	0.0	5	dbSNP_100	16	2202,6278		319,1564,2357	no	coding-synonymous,coding-synonymous	TERT	NM_001193376.1,NM_198253.2	,	346,1964,4089	TT,TC,CC		25.967,10.5141,20.7532	,	305/1070,305/1133	1294086	2656,10142	2159	4240	6399	SO:0001819	synonymous_variant	7015	exon2	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GGGGCCCGCGTGG	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.915G>A	5.37:g.1294086C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_001193376	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	37	CCDS3861.2																																																																																			C|0.792;T|0.208	0.208	strong		0.682	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2		
RHOBTB3	22836	hgsc.bcm.edu	37	5	95091194	95091194	+	Silent	SNP	C	C	T	rs34898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:95091194C>T	ENST00000379982.3	+	6	1285	c.777C>T	c.(775-777)taC>taT	p.Y259Y	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	259	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		TGGTATTTTACAACCCCAATT	0.418													C|||	2272	0.453674	0.2806	0.3329	5008	,	,		16305	0.6895		0.4324	False		,,,				2504	0.5521				p.Y259Y		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.C777T						PASS	.	C		1359,3047	451.2+/-349.6	206,947,1050	173.0	167.0	169.0		777	4.0	0.9	5	dbSNP_76	169	3572,5028	518.5+/-379.3	729,2114,1457	no	coding-synonymous	RHOBTB3	NM_014899.3		935,3061,2507	TT,TC,CC		41.5349,30.8443,37.9133		259/612	95091194	4931,8075	2203	4300	6503	SO:0001819	synonymous_variant	22836	exon6			ATTTTACAACCCC	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"""BTB/POZ domain containing"""	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.777C>T	5.37:g.95091194C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	279	134	0.480287	NM_014899	A0PJA4|A8K1W9|Q8IW06	Silent	SNP	ENST00000379982.3	37	CCDS4077.1																																																																																			C|0.586;T|0.414	0.414	strong		0.418	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
SCN1A	6323	hgsc.bcm.edu	37	2	166850872	166850872	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:166850872T>G	ENST00000303395.4	-	25	4635	c.4636A>C	c.(4636-4638)Agc>Cgc	p.S1546R	AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.S1535R|SCN1A_ENST00000409050.1_Missense_Mutation_p.S1518R|SCN1A_ENST00000423058.2_Missense_Mutation_p.S1546R|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1546					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATCATGATGCTTATGTCAAAA	0.363																																					p.S1546R		Atlas-SNP	.											.	SCN1A	641	.	0			c.A4636C						PASS	.						129.0	113.0	118.0					2																	166850872		2203	4300	6503	SO:0001583	missense	6323	exon25			TGATGCTTATGTC	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4636A>C	2.37:g.166850872T>G	ENSP00000303540:p.Ser1546Arg	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	160	21	0.13125	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.657766	0.67586	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37	5.9	5.9	0.94986	.	0.118890	0.64402	D	0.000011	D	0.97278	0.9110	M	0.61703	1.905	0.32543	N	0.533434	D	0.59357	0.985	P	0.59012	0.85	D	0.99104	1.0844	10	0.62326	D	0.03	.	10.6319	0.45541	0.0:0.0709:0.0:0.9291	.	1535	P35498-2	.	R	1546;1546;1535;1518	ENSP00000407030:S1546R;ENSP00000303540:S1546R;ENSP00000364554:S1535R;ENSP00000386312:S1518R	ENSP00000303540:S1546R	S	-	1	0	SCN1A	166559118	0.452000	0.25713	0.998000	0.56505	0.995000	0.86356	0.724000	0.25954	2.251000	0.74343	0.528000	0.53228	AGC	.	.	none		0.363	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
CPT1B	1375	hgsc.bcm.edu	37	22	51011348	51011348	+	Silent	SNP	G	G	A	rs34744246	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:51011348G>A	ENST00000360719.2	-	11	1445	c.1308C>T	c.(1306-1308)ctC>ctT	p.L436L	CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000312108.7_Silent_p.L436L|CPT1B_ENST00000457250.1_Silent_p.L402L|CPT1B_ENST00000440709.1_Silent_p.L355L|CPT1B_ENST00000405237.3_Silent_p.L436L|CPT1B_ENST00000395650.2_Silent_p.L436L|CPT1B_ENST00000434492.2_Silent_p.L233L	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	436					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		CATAGAGGCTGAGGCTGGCCT	0.552													G|||	169	0.033746	0.0348	0.0101	5008	,	,		19238	0.0079		0.0298	False		,,,				2504	0.0798				p.L436L	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.C1308T						PASS	.	G	,,,,,,	145,4261	101.6+/-140.2	2,141,2060	132.0	126.0	128.0		1206,1308,1065,1308,1308,1308,1308	2.8	1.0	22	dbSNP_126	128	251,8349	99.7+/-161.2	1,249,4050	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPT1B	NM_001145134.1,NM_001145135.1,NM_001145136.1,NM_001145137.1,NM_004377.3,NM_152245.2,NM_152246.2	,,,,,,	3,390,6110	AA,AG,GG		2.9186,3.291,3.0447	,,,,,,	402/739,436/773,355/692,436/773,436/773,436/773,436/773	51011348	396,12610	2203	4300	6503	SO:0001819	synonymous_variant	1375	exon11			GAGGCTGAGGCTG	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.1308C>T	22.37:g.51011348G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	235	147	0.625532	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Silent	SNP	ENST00000360719.2	37	CCDS14098.1																																																																																			G|0.973;A|0.027	0.027	strong		0.552	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49379167	49379167	+	Silent	SNP	C	C	T	rs386810065|rs524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49379167C>T	ENST00000200453.5	+	3	2231	c.1962C>T	c.(1960-1962)gcC>gcT	p.A654A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	654					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		AAGCTGTGGCCACACCTTCCC	0.587													C|||	1786	0.356629	0.5764	0.2896	5008	,	,		15979	0.1984		0.2803	False		,,,				2504	0.3487				p.A654A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.C1962T						PASS	.	C		2270,2136	590.6+/-387.4	567,1136,500	85.0	83.0	83.0		1962	2.1	0.0	19	dbSNP_36	83	2469,6131	402.4+/-347.5	352,1765,2183	no	coding-synonymous	PPP1R15A	NM_014330.3		919,2901,2683	TT,TC,CC		28.7093,48.4793,36.437		654/675	49379167	4739,8267	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon3			TGTGGCCACACCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1962C>T	19.37:g.49379167C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	172	80	0.465116	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			C|0.647;T|0.353	0.353	strong		0.587	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
OR2J2	26707	hgsc.bcm.edu	37	6	29142064	29142064	+	Missense_Mutation	SNP	A	A	G	rs3130743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29142064A>G	ENST00000377167.2	+	1	754	c.652A>G	c.(652-654)Acc>Gcc	p.T218A		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	218			A -> T (in allele 6M1-6*02 and allele 6M1-6*03; dbSNP:rs3130743). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						CATTCTCACTACCTATGGTGC	0.463													T|||	1585	0.316494	0.0408	0.4035	5008	,	,		21023	0.3512		0.5149	False		,,,				2504	0.3875				p.T218A		Atlas-SNP	.											.	OR2J2	51	.	0			c.A652G						PASS	.	T	ALA/THR	449,3439		38,373,1533	156.0	130.0	138.0		652	2.0	0.7	6	dbSNP_103	138	4079,4209		1007,2065,1072	no	missense	OR2J2	NM_030905.2	58	1045,2438,2605	GG,GA,AA		49.2157,11.5484,37.1879	benign	218/313	29142064	4528,7648	1944	4144	6088	SO:0001583	missense	26707	exon1			CTCACTACCTATG		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.652A>G	6.37:g.29142064A>G	ENSP00000366372:p.Thr218Ala	Somatic	413	1	0.00242131		WXS	Illumina HiSeq	Phase_I	516	305	0.591085	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	37	CCDS43434.1	779	0.3566849816849817	22	0.044715447154471545	150	0.4143646408839779	198	0.34615384615384615	409	0.5395778364116095	T	12.40	1.926755	0.34002	0.115484	0.492157	ENSG00000204700	ENST00000377167	T	0.37058	1.22	2.0	2.0	0.26442	.	.	.	.	.	T	0.51415	0.1673	H	0.97077	3.935	0.80722	P	0.0	.	.	.	.	.	.	T	0.54754	-0.8246	6	0.72032	D	0.01	.	6.1521	0.20318	0.227:0.0:0.0:0.773	rs3130743;rs3130743	.	.	.	A	218	ENSP00000366372:T218A	ENSP00000366372:T218A	T	+	1	0	OR2J2	29250043	0.089000	0.21612	0.730000	0.30809	0.147000	0.21601	1.946000	0.40283	0.045000	0.15804	-1.155000	0.01812	ACC	A|0.601;G|0.399	0.399	strong		0.463	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2		
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:116397572A>G	ENST00000318493.6	+	7	2131	c.1944A>G	c.(1942-1944)caA>caG	p.Q648Q	MET_ENST00000436117.2_Silent_p.Q648Q|MET_ENST00000397752.3_Silent_p.Q648Q			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GGACAACACAATACAGTACAT	0.318			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	941	0.187899	0.1089	0.1254	5008	,	,		17860	0.2728		0.2048	False		,,,				2504	0.2342				p.Q648Q		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1944G						PASS	.	A	,	486,3224		27,432,1396	93.0	92.0	92.0		1944,1944	-6.5	0.0	7	dbSNP_121	92	1521,6665		129,1263,2701	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	156,1695,4097	GG,GA,AA		18.5805,13.0997,16.8712	,	648/1391,648/1409	116397572	2007,9889	1855	4093	5948	SO:0001819	synonymous_variant	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AACACAATACAGT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1944A>G	7.37:g.116397572A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	71	25	0.352113	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			A|0.817;G|0.183	0.183	strong		0.318	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
PELP1	27043	hgsc.bcm.edu	37	17	4576203	4576203	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576203C>T	ENST00000574876.1	-	16	2100	c.2083G>A	c.(2083-2085)Gtg>Atg	p.V695M	PELP1_ENST00000301396.4_Missense_Mutation_p.V839M|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Missense_Mutation_p.V605M|PELP1_ENST00000572293.1_Missense_Mutation_p.V745M|PELP1_ENST00000436683.2_Missense_Mutation_p.V548M			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	695	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GCCGAGGGCACAGGGCCTGCT	0.687																																					p.V695M		Atlas-SNP	.											.	PELP1	102	.	0			c.G2083A						PASS	.						33.0	39.0	37.0					17																	4576203		1990	4145	6135	SO:0001583	missense	27043	exon16			AGGGCACAGGGCC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2083G>A	17.37:g.4576203C>T	ENSP00000461625:p.Val695Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	136	26	0.191176	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	37	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	1.457	-0.563579	0.03939	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.48201	0.82;0.88;1.48	4.54	-7.16	0.01516	.	0.654618	0.14932	N	0.290033	T	0.21468	0.0517	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.06303	-1.0834	10	0.37606	T	0.19	-2.13	6.9569	0.24576	0.0:0.2953:0.3218:0.3829	.	548;695	E7EV54;Q8IZL8	.;PELP1_HUMAN	M	839;605;548	ENSP00000301396:V839M;ENSP00000269230:V605M;ENSP00000416231:V548M	ENSP00000269230:V605M	V	-	1	0	AC091153.1	4522952	0.000000	0.05858	0.001000	0.08648	0.155000	0.21991	-1.525000	0.02231	-1.363000	0.02164	-0.136000	0.14681	GTG	.	.	none		0.687	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
WDR34	89891	hgsc.bcm.edu	37	9	131397479	131397479	+	Silent	SNP	G	G	A	rs4837291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131397479G>A	ENST00000372715.2	-	6	933	c.873C>T	c.(871-873)acC>acT	p.T291T	WDR34_ENST00000483181.1_5'UTR	NM_052844.3	NP_443076.2	Q96EX3	WDR34_HUMAN	WD repeat domain 34	291						axoneme (GO:0005930)|centriole (GO:0005814)|ciliary basal body (GO:0036064)				central_nervous_system(2)|lung(5)|skin(1)|urinary_tract(1)	9						CCTTCCCGTCGGTGGCCACAC	0.652											OREG0019522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3112	0.621406	0.3699	0.7853	5008	,	,		17063	0.4921		0.8698	False		,,,				2504	0.7229				p.T291T		Atlas-SNP	.											.	WDR34	29	.	0			c.C873T						PASS	.	G		1869,2537	525.5+/-371.6	398,1073,732	30.0	32.0	31.0		873	-9.9	0.4	9	dbSNP_111	31	7659,941	760.9+/-407.6	3420,819,61	no	coding-synonymous	WDR34	NM_052844.3		3818,1892,793	AA,AG,GG		10.9419,42.4194,26.7415		291/537	131397479	9528,3478	2203	4300	6503	SO:0001819	synonymous_variant	89891	exon6			CCCGTCGGTGGCC	BC011874	CCDS6906.2	9q34.11	2013-11-15	2013-02-19	2013-02-19	ENSG00000119333	ENSG00000119333		"""WD repeat domain containing"""	28296	protein-coding gene	gene with protein product		613363				19521662, 21953912, 24183451	Standard	NM_052844		Approved	DIC5, MGC20486, bA216B9.3, FAP133	uc004bvq.1	Q96EX3	OTTHUMG00000020750	ENST00000372715.2:c.873C>T	9.37:g.131397479G>A		Somatic	143	0	0	1587	WXS	Illumina HiSeq	Phase_I	121	121	1	NM_052844	Q5VXV4|Q9BV46	Silent	SNP	ENST00000372715.2	37	CCDS6906.2																																																																																			G|0.322;A|0.678	0.678	strong		0.652	WDR34-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054463.1	NM_052844	
SEMA6B	10501	hgsc.bcm.edu	37	19	4555079	4555079	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4555079G>A	ENST00000586582.1	-	8	901	c.591C>T	c.(589-591)acC>acT	p.T197T	SEMA6B_ENST00000301293.3_Silent_p.T197T|SEMA6B_ENST00000586965.1_Silent_p.T197T	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	197	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CTAGGAAGTCGGTAACAGTAG	0.592																																					p.T197T		Atlas-SNP	.											.	SEMA6B	51	.	0			c.C591T						PASS	.						111.0	89.0	96.0					19																	4555079		2202	4300	6502	SO:0001819	synonymous_variant	10501	exon8			GAAGTCGGTAACA	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.591C>T	19.37:g.4555079G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	75	9	0.12	NM_032108	A5PKU4|F6IB19|Q9NRK9	Silent	SNP	ENST00000586582.1	37	CCDS12131.1																																																																																			.	.	none		0.592	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
SVIL	6840	hgsc.bcm.edu	37	10	29812602	29812602	+	Silent	SNP	G	G	T	rs7070678	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29812602G>T	ENST00000355867.4	-	15	3693	c.2941C>A	c.(2941-2943)Cga>Aga	p.R981R	SVIL_ENST00000375398.2_Silent_p.R981R|SVIL_ENST00000375400.3_Silent_p.R555R|SVIL_ENST00000535393.1_5'Flank	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	981					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TCCCTGGCTCGGTTCAGGATG	0.537													T|||	1915	0.382388	0.562	0.438	5008	,	,		18611	0.0804		0.4284	False		,,,				2504	0.364				p.R981R		Atlas-SNP	.											SVIL,colon,carcinoma,0,1	SVIL	226	1	0			c.C2941A						PASS	.	T	,	2409,1997	560.6+/-380.5	663,1083,457	155.0	136.0	143.0		1663,2941	-1.8	0.0	10	dbSNP_116	143	3521,5079	632.1+/-398.6	738,2045,1517	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	1401,3128,1974	TT,TG,GG		40.9419,45.3246,45.5943	,	555/1789,981/2215	29812602	5930,7076	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon15			TGGCTCGGTTCAG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2941C>A	10.37:g.29812602G>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	189	90	0.47619	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			G|0.584;T|0.416	0.416	strong		0.537	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
GPR155	151556	hgsc.bcm.edu	37	2	175300997	175300997	+	Silent	SNP	G	G	A	rs6757461	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:175300997G>A	ENST00000392552.2	-	16	2698	c.2460C>T	c.(2458-2460)aaC>aaT	p.N820N	GPR155_ENST00000295500.4_Silent_p.N820N|GPR155_ENST00000459996.1_5'Flank|GPR155_ENST00000392551.2_Silent_p.N820N	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	820	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						ATTCATACTCGTTGGTAATAT	0.463													G|||	1070	0.213658	0.0825	0.1974	5008	,	,		20403	0.2143		0.3827	False		,,,				2504	0.228				p.N820N		Atlas-SNP	.											GPR155,NS,carcinoma,-1,1	GPR155	76	1	0			c.C2460T						PASS	.	G	,	544,3862	247.2+/-255.5	37,470,1696	162.0	160.0	161.0		2460,2460	-2.2	0.9	2	dbSNP_116	161	2944,5656	459.0+/-364.8	521,1902,1877	no	coding-synonymous,coding-synonymous	GPR155	NM_001033045.2,NM_152529.5	,	558,2372,3573	AA,AG,GG		34.2326,12.3468,26.8184	,	820/871,820/871	175300997	3488,9518	2203	4300	6503	SO:0001819	synonymous_variant	151556	exon17			ATACTCGTTGGTA	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.2460C>T	2.37:g.175300997G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	181	85	0.469613	NM_001033045	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Silent	SNP	ENST00000392552.2	37	CCDS2259.1																																																																																			G|0.734;A|0.266	0.266	strong		0.463	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529	
PEX14	5195	hgsc.bcm.edu	37	1	10596341	10596341	+	Silent	SNP	C	C	T	rs12375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:10596341C>T	ENST00000356607.4	+	3	236	c.156C>T	c.(154-156)ttC>ttT	p.F52F	PEX14_ENST00000538836.1_Intron|PEX14_ENST00000492696.1_3'UTR	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	52					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		GGAGAGCATTCCTAAAGAAGA	0.562													C|||	1142	0.228035	0.0658	0.4265	5008	,	,		16571	0.2004		0.3141	False		,,,				2504	0.2464				p.F52F		Atlas-SNP	.											.	PEX14	40	.	0			c.C156T						PASS	.	C		472,3934	220.7+/-238.1	30,412,1761	52.0	50.0	51.0		156	3.4	1.0	1	dbSNP_52	51	2770,5830	432.8+/-357.2	469,1832,1999	no	coding-synonymous	PEX14	NM_004565.2		499,2244,3760	TT,TC,CC		32.2093,10.7127,24.927		52/378	10596341	3242,9764	2203	4300	6503	SO:0001819	synonymous_variant	5195	exon3			AGCATTCCTAAAG	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.156C>T	1.37:g.10596341C>T		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	201	117	0.58209	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			C|0.770;T|0.230	0.230	strong		0.562	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
PSPN	5623	hgsc.bcm.edu	37	19	6375831	6375831	+	Silent	SNP	G	G	A	rs2304198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6375831G>A	ENST00000245810.1	-	1	29	c.30C>T	c.(28-30)tcC>tcT	p.S10S	PSPN_ENST00000597721.1_Silent_p.S10S	NM_004158.2	NP_004149.1	O60542	PSPN_HUMAN	persephin	10					axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|central nervous system development (GO:0007417)|nervous system development (GO:0007399)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			lung(1)|ovary(1)|skin(1)	3						GGAGCAGCAGGGAGCCCAGCA	0.642													A|||	2204	0.440096	0.8744	0.2032	5008	,	,		14171	0.3889		0.1789	False		,,,				2504	0.3425				p.S10S		Atlas-SNP	.											PSPN,colon,carcinoma,0,1	PSPN	5	1	0			c.C30T						PASS	.	A		3333,1073	382.3+/-324.4	1267,799,137	41.0	44.0	43.0		30	-0.4	0.0	19	dbSNP_100	43	1395,7205	749.3+/-407.4	109,1177,3014	no	coding-synonymous	PSPN	NM_004158.2		1376,1976,3151	AA,AG,GG		16.2209,24.3532,36.3525		10/157	6375831	4728,8278	2203	4300	6503	SO:0001819	synonymous_variant	5623	exon1			CAGCAGGGAGCCC	AF040962	CCDS12164.1	19p13.3	2014-01-30				ENSG00000125650		"""Endogenous ligands"""	9579	protein-coding gene	gene with protein product		602921				10072588	Standard	NM_004158		Approved	PSP	uc010xja.2	O60542		ENST00000245810.1:c.30C>T	19.37:g.6375831G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_004158		Silent	SNP	ENST00000245810.1	37	CCDS12164.1																																																																																			G|0.609;A|0.391	0.391	strong		0.642	PSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398032.1	NM_004158	
MUC16	94025	hgsc.bcm.edu	37	19	9086318	9086318	+	Missense_Mutation	SNP	G	G	A	rs4520945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9086318G>A	ENST00000397910.4	-	1	5700	c.5497C>T	c.(5497-5499)Ctc>Ttc	p.L1833F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1833	Ser-rich.|Thr-rich.		L -> F (in dbSNP:rs4520945).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGAGAGTGAGAGAAATCCAT	0.478													G|||	952	0.190096	0.0711	0.2709	5008	,	,		22597	0.3036		0.172	False		,,,				2504	0.1953				p.L1833F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C5497T						PASS	.	G	PHE/LEU	280,3662		5,270,1696	146.0	141.0	142.0		5497	0.7	0.0	19	dbSNP_111	142	1489,6845		126,1237,2804	yes	missense	MUC16	NM_024690.2	22	131,1507,4500	AA,AG,GG		17.8666,7.103,14.4102	probably-damaging	1833/14508	9086318	1769,10507	1971	4167	6138	SO:0001583	missense	94025	exon1			GAGTGAGAGAAAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5497C>T	19.37:g.9086318G>A	ENSP00000381008:p.Leu1833Phe	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	167	83	0.497006	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	g	2.939	-0.219341	0.06061	0.07103	0.178666	ENSG00000181143	ENST00000397910	T	0.03124	4.04	0.732	0.732	0.18283	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.62365	0.991	D	0.65323	0.934	T	0.55159	-0.8184	7	0.87932	D	0	.	.	.	.	rs4520945;rs52791576;rs60060127;rs4520945	1833	B5ME49	.	F	1833	ENSP00000381008:L1833F	ENSP00000381008:L1833F	L	-	1	0	MUC16	8947318	0.000000	0.05858	0.002000	0.10522	0.158000	0.22134	0.004000	0.13106	0.648000	0.30732	0.305000	0.20034	CTC	G|0.812;A|0.188	0.188	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SLC5A7	60482	hgsc.bcm.edu	37	2	108608648	108608648	+	Missense_Mutation	SNP	A	A	G	rs1013940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:108608648A>G	ENST00000264047.2	+	3	541	c.265A>G	c.(265-267)Att>Gtt	p.I89V	SLC5A7_ENST00000409059.1_Missense_Mutation_p.I89V|SLC5A7_ENST00000540517.1_5'UTR	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	89			I -> V (40% reduction in choline uptake rate; found in 0.06 of Ashkenazi Jews; dbSNP:rs1013940). {ECO:0000269|PubMed:12237312}.		acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	TCAGGCACCAATTGGATATTC	0.418													A|||	381	0.0760783	0.0151	0.1643	5008	,	,		19777	0.1379		0.0805	False		,,,				2504	0.0276				p.I89V		Atlas-SNP	.											.	SLC5A7	109	.	0			c.A265G	GRCh37	CM025890	SLC5A7	M	rs1013940	PASS	.	A	VAL/ILE	126,4280	93.0+/-131.7	0,126,2077	142.0	123.0	130.0		265	3.8	1.0	2	dbSNP_86	130	700,7900	173.5+/-223.9	36,628,3636	yes	missense	SLC5A7	NM_021815.2	29	36,754,5713	GG,GA,AA		8.1395,2.8597,6.3509	benign	89/581	108608648	826,12180	2203	4300	6503	SO:0001583	missense	60482	exon3			GCACCAATTGGAT	AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"""Solute carriers"""	14025	protein-coding gene	gene with protein product		608761	"""solute carrier family 5 (choline transporter), member 7"""			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.265A>G	2.37:g.108608648A>G	ENSP00000264047:p.Ile89Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	188	81	0.430851	NM_021815	Q53TF2	Missense_Mutation	SNP	ENST00000264047.2	37	CCDS2074.1	206	0.09432234432234432	4	0.008130081300813009	49	0.13535911602209943	85	0.1486013986013986	68	0.08970976253298153	A	6.354	0.433392	0.12045	0.028597	0.081395	ENSG00000115665	ENST00000409059;ENST00000264047	D;D	0.88818	-2.43;-2.43	6.16	3.78	0.43462	.	0.046926	0.85682	D	0.000000	T	0.00998	0.0033	N	0.03224	-0.385	0.09310	P	1.0	B	0.15930	0.015	B	0.20184	0.028	T	0.23476	-1.0187	9	0.18710	T	0.47	-1.1064	10.9259	0.47191	0.8734:0.0:0.1266:0.0	rs1013940;rs52811555;rs57220582;rs1013940	89	Q9GZV3	SC5A7_HUMAN	V	89	ENSP00000387346:I89V;ENSP00000264047:I89V	ENSP00000264047:I89V	I	+	1	0	SLC5A7	107975080	1.000000	0.71417	0.980000	0.43619	0.936000	0.57629	5.251000	0.65438	0.550000	0.28991	0.528000	0.53228	ATT	A|0.923;G|0.077	0.077	strong		0.418	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1		
CLRN2	645104	hgsc.bcm.edu	37	4	17528463	17528463	+	Missense_Mutation	SNP	G	G	A	rs2597791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:17528463G>A	ENST00000511148.2	+	3	559	c.457G>A	c.(457-459)Gcc>Acc	p.A153T	snoU13_ENST00000459186.1_RNA	NM_001079827.2	NP_001073296.1	A0PK11	CLRN2_HUMAN	clarin 2	153			A -> T (in dbSNP:rs2597791).			integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|upper_aerodigestive_tract(1)	15						GTTAGCCATCGCCAGCTTCGT	0.522													G|||	273	0.0545128	0.1203	0.0331	5008	,	,		18056	0.0		0.0338	False		,,,				2504	0.0583				p.A153T		Atlas-SNP	.											.	CLRN2	40	.	0			c.G457A						PASS	.	G	THR/ALA	468,3570		24,420,1575	75.0	78.0	77.0		457	-2.9	0.0	4	dbSNP_100	77	327,8023		6,315,3854	yes	missense	CLRN2	NM_001079827.2	58	30,735,5429	AA,AG,GG		3.9162,11.5899,6.4175	benign	153/233	17528463	795,11593	2019	4175	6194	SO:0001583	missense	645104	exon3			GCCATCGCCAGCT		CCDS47032.1	4p15.32	2008-01-17			ENSG00000249581	ENSG00000249581			33939	protein-coding gene	gene with protein product						12080385	Standard	NM_001079827		Approved		uc003gpg.1	A0PK11	OTTHUMG00000160273	ENST00000511148.2:c.457G>A	4.37:g.17528463G>A	ENSP00000424711:p.Ala153Thr	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	154	69	0.448052	NM_001079827		Missense_Mutation	SNP	ENST00000511148.2	37	CCDS47032.1	94	0.04304029304029304	60	0.12195121951219512	11	0.03038674033149171	0	0.0	23	0.030343007915567283	G	3.859	-0.030181	0.07543	0.115899	0.039162	ENSG00000249581	ENST00000511148	T	0.76316	-1.01	5.75	-2.93	0.05598	.	1.233240	0.05279	N	0.518963	T	0.01254	0.0041	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04178	-1.0971	10	0.44086	T	0.13	-1.0E-4	7.1179	0.25427	0.5886:0.0:0.201:0.2104	rs2597791;rs2597791	153	A0PK11	CLRN2_HUMAN	T	153	ENSP00000424711:A153T	ENSP00000424711:A153T	A	+	1	0	CLRN2	17137561	0.002000	0.14202	0.024000	0.17045	0.223000	0.24884	0.121000	0.15667	-0.747000	0.04759	0.650000	0.86243	GCC	G|0.948;A|0.052	0.052	strong		0.522	CLRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359990.2	NM_001079827	
MYH3	4621	hgsc.bcm.edu	37	17	10536018	10536018	+	Silent	SNP	G	G	A	rs2285479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10536018G>A	ENST00000583535.1	-	34	4818	c.4731C>T	c.(4729-4731)atC>atT	p.I1577I	MYH3_ENST00000226209.7_Silent_p.I1577I	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1577					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CCTTCTCGGCGATCTTTCTAT	0.488													G|||	2352	0.469649	0.2504	0.5346	5008	,	,		18822	0.3849		0.7584	False		,,,				2504	0.5102				p.I1577I		Atlas-SNP	.											.	MYH3	227	.	0			c.C4731T						PASS	.	G		1326,3080	445.9+/-347.8	206,914,1083	223.0	215.0	218.0		4731	-11.5	0.0	17	dbSNP_100	218	6267,2333	704.6+/-405.4	2259,1749,292	no	coding-synonymous	MYH3	NM_002470.3		2465,2663,1375	AA,AG,GG		27.1279,30.0953,41.6193		1577/1941	10536018	7593,5413	2203	4300	6503	SO:0001819	synonymous_variant	4621	exon34			CTCGGCGATCTTT		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4731C>T	17.37:g.10536018G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	221	220	0.995475	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	37	CCDS11157.1																																																																																			G|0.468;A|0.532	0.532	strong		0.488	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
HIST1H3C	8352	hgsc.bcm.edu	37	6	26045905	26045905	+	Silent	SNP	G	G	C	rs3752417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26045905G>C	ENST00000540144.1	+	1	267	c.267G>C	c.(265-267)gcG>gcC	p.A89A	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	89					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|skin(1)	8						AGAGCTCTGCGGTGATGGCGC	0.587													G|||	334	0.0666933	0.1203	0.0634	5008	,	,		19784	0.0149		0.0835	False		,,,				2504	0.0327				p.A89A		Atlas-SNP	.											.	HIST1H3C	34	.	0			c.G267C						PASS	.	G		487,3919	224.6+/-240.7	32,423,1748	59.0	57.0	58.0		267	-4.6	0.7	6	dbSNP_107	58	840,7760	190.8+/-237.2	39,762,3499	no	coding-synonymous	HIST1H3C	NM_003531.2		71,1185,5247	CC,CG,GG		9.7674,11.0531,10.203		89/137	26045905	1327,11679	2203	4300	6503	SO:0001819	synonymous_variant	8352	exon1			CTCTGCGGTGATG	X57128	CCDS4576.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196532	ENSG00000278272		"""Histones / Replication-dependent"""	4768	protein-coding gene	gene with protein product		602812	"""H3 histone family, member C"", ""histone 1, H3c"""	H3FC		8227173, 9119399, 12408966	Standard	NM_003531		Approved	H3/c, H3.1	uc003nfv.3	P68431	OTTHUMG00000014416	ENST00000540144.1:c.267G>C	6.37:g.26045905G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	182	182	1	NM_003531	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000540144.1	37	CCDS4576.1																																																																																			G|0.908;C|0.092	0.092	strong		0.587	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040078.1	NM_003531	
TLN2	83660	hgsc.bcm.edu	37	15	62990971	62990971	+	Silent	SNP	C	C	T	rs12905981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:62990971C>T	ENST00000561311.1	+	15	1722	c.1492C>T	c.(1492-1494)Ctg>Ttg	p.L498L	TLN2_ENST00000306829.6_Silent_p.L498L			Q9Y4G6	TLN2_HUMAN	talin 2	498					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.L498L(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CCAGCAGGCCCTGATGGGGAC	0.552													C|||	1755	0.350439	0.1899	0.3718	5008	,	,		19202	0.6855		0.2942	False		,,,				2504	0.2648				p.L498L		Atlas-SNP	.											TLN2,rectum,carcinoma,0,1	TLN2	253	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1492T						PASS	.	C		929,3477	353.3+/-312.1	94,741,1368	73.0	63.0	67.0		1492	5.0	1.0	15	dbSNP_121	67	2729,5871	432.8+/-357.2	420,1889,1991	no	coding-synonymous	TLN2	NM_015059.2		514,2630,3359	TT,TC,CC		31.7326,21.0849,28.1255		498/2543	62990971	3658,9348	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon13			CAGGCCCTGATGG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.1492C>T	15.37:g.62990971C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			C|0.701;T|0.299	0.299	strong		0.552	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
EMC1	23065	hgsc.bcm.edu	37	1	19566881	19566881	+	Silent	SNP	C	C	T	rs12084825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19566881C>T	ENST00000477853.1	-	7	738	c.696G>A	c.(694-696)gaG>gaA	p.E232E	EMC1_ENST00000375199.3_Silent_p.E232E|RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375208.3_Silent_p.E210E	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	232						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											CCAGGACAGCCTCATCCACCA	0.542													C|||	430	0.0858626	0.1051	0.1455	5008	,	,		17569	0.001		0.166	False		,,,				2504	0.0225				p.E232E		Atlas-SNP	.											.	.	.	.	0			c.G696A						PASS	.	C		477,3929	223.9+/-240.3	18,441,1744	109.0	98.0	102.0		696	-1.4	1.0	1	dbSNP_120	102	1399,7201	271.1+/-289.3	115,1169,3016	no	coding-synonymous	KIAA0090	NM_015047.1		133,1610,4760	TT,TC,CC		16.2674,10.8261,14.4241		232/994	19566881	1876,11130	2203	4300	6503	SO:0001819	synonymous_variant	23065	exon7			GACAGCCTCATCC		CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"""KIAA0090"""	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.696G>A	1.37:g.19566881C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_001271427	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Silent	SNP	ENST00000477853.1	37	CCDS190.1																																																																																			C|0.864;T|0.136	0.136	strong		0.542	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
UBE2U	148581	hgsc.bcm.edu	37	1	64672478	64672478	+	Silent	SNP	A	A	G	rs35112334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:64672478A>G	ENST00000371076.3	+	3	424	c.180A>G	c.(178-180)acA>acG	p.T60T		NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	60					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			large_intestine(3)|lung(2)|skin(1)	6						TACATTTTACATCGGAGTACA	0.299													A|||	51	0.0101837	0.0	0.0159	5008	,	,		16516	0.004		0.0288	False		,,,				2504	0.0072				p.T60T		Atlas-SNP	.											.	UBE2U	16	.	0			c.A180G						PASS	.	A		22,4380	29.9+/-59.1	0,22,2179	56.0	58.0	57.0		180	-2.9	0.0	1	dbSNP_126	57	265,8319	99.5+/-161.0	7,251,4034	no	coding-synonymous	UBE2U	NM_152489.1		7,273,6213	GG,GA,AA		3.0871,0.4998,2.2101		60/227	64672478	287,12699	2201	4292	6493	SO:0001819	synonymous_variant	148581	exon3			TTTTACATCGGAG	BC029895	CCDS627.1	1p31.3	2008-02-05			ENSG00000177414	ENSG00000177414		"""Ubiquitin-conjugating enzymes E2"""	28559	protein-coding gene	gene with protein product						12477932	Standard	NM_152489		Approved	MGC35130	uc001dbn.1	Q5VVX9	OTTHUMG00000009023	ENST00000371076.3:c.180A>G	1.37:g.64672478A>G		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	225	87	0.386667	NM_152489	Q8N1D4	Silent	SNP	ENST00000371076.3	37	CCDS627.1																																																																																			A|0.982;G|0.018	0.018	strong		0.299	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489	
PTK2B	2185	hgsc.bcm.edu	37	8	27255263	27255263	+	Silent	SNP	A	A	G	rs1045512	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27255263A>G	ENST00000397501.1	+	7	970	c.162A>G	c.(160-162)aaA>aaG	p.K54K	PTK2B_ENST00000346049.5_Silent_p.K54K|PTK2B_ENST00000338238.4_Silent_p.K54K|PTK2B_ENST00000544172.1_Silent_p.K54K|PTK2B_ENST00000420218.2_Silent_p.K54K|PTK2B_ENST00000517339.1_Silent_p.K54K	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	54	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)	p.K54K(1)		breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	ATCCTGGGAAAAACTTCAAAC	0.522													G|||	1591	0.317692	0.2057	0.3818	5008	,	,		21011	0.2748		0.4304	False		,,,				2504	0.3517				p.K54K		Atlas-SNP	.											PTK2B_ENST00000544172,NS,carcinoma,0,1	PTK2B	304	1	1	Substitution - coding silent(1)	stomach(1)	c.A162G						PASS	.	G	,,,	1024,3382	727.9+/-409.9	128,768,1307	155.0	142.0	146.0		162,162,162,162	3.9	1.0	8	dbSNP_86	146	3840,4760	610.7+/-395.7	868,2104,1328	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	996,2872,2635	GG,GA,AA		44.6512,23.241,37.3981	,,,	54/1010,54/1010,54/968,54/1010	27255263	4864,8142	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon7			TGGGAAAAACTTC	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.162A>G	8.37:g.27255263A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	159	79	0.496855	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			A|0.641;G|0.359	0.359	strong		0.522	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
ITPKB	3707	hgsc.bcm.edu	37	1	226924642	226924642	+	Missense_Mutation	SNP	C	C	T	rs3754415	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:226924642C>T	ENST00000272117.3	-	1	517	c.518G>A	c.(517-519)cGc>cAc	p.R173H	ITPKB_ENST00000366784.1_Missense_Mutation_p.R173H|ITPKB_ENST00000429204.1_Missense_Mutation_p.R173H			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	173				R -> H (in Ref. 2; CAC40650 and 4; AAH15009). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				GGAGGGCGAGCGAGCCCTGCC	0.672													C|||	1137	0.227037	0.1694	0.2032	5008	,	,		15203	0.3393		0.2127	False		,,,				2504	0.2209				p.R173H	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	0			c.G518A						PASS	.	C	HIS/ARG	773,3615		65,643,1486	48.0	54.0	52.0		518	4.6	1.0	1	dbSNP_107	52	1557,7003		156,1245,2879	yes	missense	ITPKB	NM_002221.3	29	221,1888,4365	TT,TC,CC		18.1893,17.6162,17.9951	probably-damaging	173/947	226924642	2330,10618	2194	4280	6474	SO:0001583	missense	3707	exon2			GGCGAGCGAGCCC	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.518G>A	1.37:g.226924642C>T	ENSP00000272117:p.Arg173His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	32	0.666667	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	521	0.23855311355311357	88	0.17886178861788618	80	0.22099447513812154	186	0.32517482517482516	167	0.22031662269129287	C	20.6	4.025053	0.75390	0.176162	0.181893	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.37752	1.24;1.24;1.18	4.6	4.6	0.57074	.	0.000000	0.53938	D	0.000055	T	0.00012	0.0000	L	0.27053	0.805	0.32169	P	0.581978	P	0.51537	0.946	B	0.36418	0.224	T	0.40040	-0.9584	9	0.54805	T	0.06	.	9.1902	0.37195	0.0:0.8609:0.0:0.1391	rs3754415;rs17851263	173	P27987	IP3KB_HUMAN	H	173	ENSP00000272117:R173H;ENSP00000411152:R173H;ENSP00000355748:R173H	ENSP00000272117:R173H	R	-	2	0	ITPKB	224991265	0.985000	0.35326	0.998000	0.56505	0.888000	0.51559	2.942000	0.49018	2.374000	0.81015	0.561000	0.74099	CGC	C|0.795;T|0.205	0.205	strong		0.672	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
CTNNA2	1496	hgsc.bcm.edu	37	2	80136811	80136811	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:80136811C>T	ENST00000402739.4	+	6	949	c.944C>T	c.(943-945)gCg>gTg	p.A315V	CTNNA2_ENST00000496558.1_Missense_Mutation_p.A315V|CTNNA2_ENST00000541047.1_Missense_Mutation_p.A315V|CTNNA2_ENST00000361291.4_Missense_Mutation_p.A349V|CTNNA2_ENST00000540488.1_Missense_Mutation_p.A315V|CTNNA2_ENST00000466387.1_Missense_Mutation_p.A315V	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	315					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						AGCGGCGCAGCGCTGATGGCC	0.647																																					p.A315V		Atlas-SNP	.											CTNNA2_ENST00000466387,colon,carcinoma,+1,4	CTNNA2	462	4	0			c.C944T						scavenged	.						46.0	54.0	51.0					2																	80136811		2040	4199	6239	SO:0001583	missense	1496	exon7			GCGCAGCGCTGAT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.944C>T	2.37:g.80136811C>T	ENSP00000384638:p.Ala315Val	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	164	4	0.0243902	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	C	36	5.676764	0.96764	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9	5.6	5.6	0.85130	.	0.066990	0.64402	D	0.000014	T	0.71273	0.3320	M	0.88842	2.985	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.992;0.992	T	0.73110	-0.4086	10	0.41790	T	0.15	.	19.6081	0.95588	0.0:1.0:0.0:0.0	.	315;315;315	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	V	315;315;349;315;315;315	ENSP00000418191:A315V;ENSP00000419295:A315V;ENSP00000355398:A349V;ENSP00000384638:A315V;ENSP00000444675:A315V;ENSP00000441705:A315V	ENSP00000355398:A349V	A	+	2	0	CTNNA2	79990322	1.000000	0.71417	0.849000	0.33467	0.937000	0.57800	7.811000	0.86092	2.652000	0.90054	0.591000	0.81541	GCG	.	.	none		0.647	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
SPTB	6710	hgsc.bcm.edu	37	14	65271780	65271780	+	Silent	SNP	G	G	A	rs2277503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:65271780G>A	ENST00000389721.5	-	2	209	c.177C>T	c.(175-177)acC>acT	p.T59T	SPTB_ENST00000556626.1_Silent_p.T59T|SPTB_ENST00000542895.1_Silent_p.T59T|SPTB_ENST00000389720.3_Silent_p.T59T|SPTB_ENST00000389722.3_Silent_p.T59T	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	59	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		ATTTCGTGAAGGTCTTTTTCT	0.567													G|||	341	0.0680911	0.028	0.0303	5008	,	,		18063	0.1815		0.0358	False		,,,				2504	0.0654				p.T59T		Atlas-SNP	.											.	SPTB	378	.	0			c.C177T						PASS	.	G	,	174,4232	112.5+/-150.6	5,164,2034	106.0	95.0	99.0		177,177	2.8	1.0	14	dbSNP_100	99	395,8205	126.3+/-184.8	6,383,3911	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	11,547,5945	AA,AG,GG		4.593,3.9492,4.3749	,	59/2138,59/2329	65271780	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon2			CGTGAAGGTCTTT		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.177C>T	14.37:g.65271780G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			G|0.945;A|0.055	0.055	strong		0.567	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
FAM64A	54478	hgsc.bcm.edu	37	17	6348642	6348642	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6348642G>A	ENST00000250056.8	+	2	295	c.212G>A	c.(211-213)cGc>cAc	p.R71H	FAM64A_ENST00000570337.2_Missense_Mutation_p.R71H|FAM64A_ENST00000571373.1_Missense_Mutation_p.R71H|FAM64A_ENST00000572595.2_Missense_Mutation_p.R71H|FAM64A_ENST00000576056.1_Missense_Mutation_p.R71H|FAM64A_ENST00000572447.1_Missense_Mutation_p.R71H	NM_001195228.1	NP_001182157.1	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A	71					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				COAD - Colon adenocarcinoma(228;0.141)		TCCTGGAAACGCCTGGAAACC	0.622																																					p.R71H		Atlas-SNP	.											FAM64A,NS,carcinoma,0,1	FAM64A	20	1	0			c.G212A						scavenged	.						46.0	51.0	49.0					17																	6348642		2203	4300	6503	SO:0001583	missense	54478	exon2			GGAAACGCCTGGA		CCDS32541.1, CCDS56016.1	17p13.2	2013-10-11			ENSG00000129195	ENSG00000129195			25483	protein-coding gene	gene with protein product	"""CALM interacting protein expressed in thymus and spleen"""					19383357, 16491119	Standard	NM_019013		Approved	FLJ10156, FLJ10491, CATS	uc002gcw.2	Q9BSJ6	OTTHUMG00000177832	ENST00000250056.8:c.212G>A	17.37:g.6348642G>A	ENSP00000250056:p.Arg71His	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	124	3	0.0241935	NM_019013	Q96CT4|Q9NVV1|Q9NWB5	Missense_Mutation	SNP	ENST00000250056.8	37	CCDS56016.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.864343	0.71949	.	.	ENSG00000129195	ENST00000250056;ENST00000308855	T	0.58060	0.36	5.08	1.74	0.24563	.	0.418318	0.23779	N	0.044649	T	0.63462	0.2513	M	0.72118	2.19	0.30743	N	0.745993	D;D	0.76494	0.999;0.999	D;P	0.63033	0.91;0.855	T	0.63265	-0.6676	10	0.56958	D	0.05	-13.0342	7.9329	0.29912	0.0:0.3598:0.4744:0.1658	.	71;71	Q9BSJ6;Q9BSJ6-2	FA64A_HUMAN;.	H	71	ENSP00000250056:R71H	ENSP00000250056:R71H	R	+	2	0	FAM64A	6289366	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.458000	0.35223	0.698000	0.31739	0.655000	0.94253	CGC	.	.	none		0.622	FAM64A-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439156.1	NM_019013	
VARS2	57176	hgsc.bcm.edu	37	6	30888169	30888169	+	Silent	SNP	G	G	A	rs2517468	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30888169G>A	ENST00000321897.5	+	13	1985	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Silent_p.L311L|VARS2_ENST00000416670.2_Silent_p.L451L|VARS2_ENST00000541562.1_Silent_p.L481L			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	451					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						AATGGGGCCTGTTCCGGGGCC	0.522													G|||	1113	0.222244	0.0983	0.2075	5008	,	,		16403	0.247		0.3559	False		,,,				2504	0.2372				p.L481L		Atlas-SNP	.											VARS2,NS,carcinoma,0,1	VARS2	60	1	0			c.G1443A						PASS	.	G	,,	615,3791	266.5+/-267.3	40,535,1628	47.0	50.0	49.0		933,1443,1353	2.3	1.0	6	dbSNP_100	49	3196,5404	483.9+/-371.3	581,2034,1685	no	coding-synonymous,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	621,2569,3313	AA,AG,GG		37.1628,13.9582,29.3019	,,	311/924,481/1094,451/1064	30888169	3811,9195	2203	4300	6503	SO:0001819	synonymous_variant	57176	exon14			GGGCCTGTTCCGG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1353G>A	6.37:g.30888169G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			G|0.731;A|0.269	0.269	strong		0.522	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
EML4	27436	hgsc.bcm.edu	37	2	42515437	42515437	+	Missense_Mutation	SNP	A	A	G	rs28651764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:42515437A>G	ENST00000318522.5	+	11	1455	c.1193A>G	c.(1192-1194)aAg>aGg	p.K398R	EML4_ENST00000401738.3_Missense_Mutation_p.K409R|EML4_ENST00000402711.2_Missense_Mutation_p.K340R	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	398			K -> R (in dbSNP:rs28651764). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						GACTGGCAGAAGAAAGCAAAA	0.333			T	ALK	NSCLC								A|||	1365	0.272564	0.1679	0.1657	5008	,	,		17440	0.5784		0.3131	False		,,,				2504	0.1329				p.K398R		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	EML4_ENST00000318522,NS,carcinoma,-1,2	EML4	92	2	0			c.A1193G						PASS	.	A	ARG/LYS,ARG/LYS	765,3641	306.6+/-289.6	80,605,1518	128.0	133.0	131.0		1019,1193	1.8	1.0	2	dbSNP_125	131	2649,5951	425.5+/-355.0	406,1837,2057	yes	missense,missense	EML4	NM_001145076.1,NM_019063.3	26,26	486,2442,3575	GG,GA,AA		30.8023,17.3627,26.2494	benign,benign	340/924,398/982	42515437	3414,9592	2203	4300	6503	SO:0001583	missense	27436	exon11			GGCAGAAGAAAGC	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"""WD repeat domain containing"""	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.1193A>G	2.37:g.42515437A>G	ENSP00000320663:p.Lys398Arg	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Missense_Mutation	SNP	ENST00000318522.5	37	CCDS1807.1	716	0.32783882783882784	83	0.16869918699186992	74	0.20441988950276244	310	0.541958041958042	249	0.32849604221635886	A	13.48	2.249720	0.39797	0.173627	0.308023	ENSG00000143924	ENST00000318522;ENST00000402711;ENST00000401738	T;T;T	0.56941	0.43;0.43;0.43	5.43	1.76	0.24704	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.100460	0.64402	N	0.000003	T	0.00012	0.0000	N	0.13168	0.305	0.09310	P	0.9999999999936345	B;B;B	0.10296	0.003;0.003;0.002	B;B;B	0.13407	0.005;0.009;0.006	T	0.48502	-0.9030	9	0.20519	T	0.43	-9.7437	9.4373	0.38646	0.7214:0.0:0.2786:0.0	rs28651764	340;409;398	B5MCW9;B5MBZ0;Q9HC35	.;.;EMAL4_HUMAN	R	398;340;409	ENSP00000320663:K398R;ENSP00000385059:K340R;ENSP00000384939:K409R	ENSP00000320663:K398R	K	+	2	0	EML4	42368941	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	3.107000	0.50329	0.352000	0.24053	0.482000	0.46254	AAG	A|0.717;G|0.283	0.283	strong		0.333	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063	
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107533175	107533175	+	Missense_Mutation	SNP	C	C	G	rs3739741	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107533175C>G	ENST00000374762.3	+	4	547	c.476C>G	c.(475-477)gCt>gGt	p.A159G	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	159			A -> G (in dbSNP:rs3739741). {ECO:0000269|PubMed:14702039}.					p.A159G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						GGTGGGCCAGCTCTGTGGGGT	0.383													C|||	882	0.176118	0.0257	0.1427	5008	,	,		17296	0.2847		0.1769	False		,,,				2504	0.2904				p.A159G		Atlas-SNP	.											NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	1	Substitution - Missense(1)	stomach(1)	c.C476G						PASS	.	C	GLY/ALA	199,4207	126.1+/-163.2	6,187,2010	136.0	129.0	131.0		476	2.4	1.0	9	dbSNP_107	131	1631,6969	302.9+/-306.2	172,1287,2841	yes	missense	NIPSNAP3B	NM_018376.2	60	178,1474,4851	GG,GC,CC		18.9651,4.5166,14.0704	benign	159/248	107533175	1830,11176	2203	4300	6503	SO:0001583	missense	55335	exon4			GGCCAGCTCTGTG	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.476C>G	9.37:g.107533175C>G	ENSP00000363894:p.Ala159Gly	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_018376	Q5VX30|Q9NUM2	Missense_Mutation	SNP	ENST00000374762.3	37	CCDS6761.1	356	0.163003663003663	15	0.03048780487804878	59	0.16298342541436464	146	0.25524475524475526	136	0.17941952506596306	C	19.13	3.767716	0.69878	0.045166	0.189651	ENSG00000165028	ENST00000374762	T	0.70986	-0.53	4.3	2.44	0.29823	Dimeric alpha-beta barrel (1);	0.177687	0.47852	D	0.000203	T	0.00039	0.0001	M	0.67625	2.065	0.24750	P	0.99298667	D	0.76494	0.999	D	0.74023	0.982	T	0.07271	-1.0781	9	0.22706	T	0.39	-9.1353	10.6947	0.45892	0.0:0.8331:0.0:0.1669	rs3739741;rs3739741	159	Q9BS92	NPS3B_HUMAN	G	159	ENSP00000363894:A159G	ENSP00000363894:A159G	A	+	2	0	NIPSNAP3B	106572996	0.974000	0.33945	1.000000	0.80357	0.980000	0.70556	1.528000	0.35985	1.148000	0.42385	0.655000	0.94253	GCT	C|0.851;G|0.149	0.149	strong		0.383	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376	
IMPA2	3613	hgsc.bcm.edu	37	18	11999115	11999115	+	Silent	SNP	T	T	C	rs11545506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:11999115T>C	ENST00000269159.3	+	2	401	c.159T>C	c.(157-159)ctT>ctC	p.L53L	IMPA2_ENST00000588927.1_5'UTR|IMPA2_ENST00000589238.1_5'UTR|IMPA2_ENST00000588752.1_3'UTR	NM_014214.2	NP_055029.1	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	53					inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)	p.L53L(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)|stomach(2)|urinary_tract(1)	12					Lithium(DB01356)	CTGCAGATCTTGTGACAGAAA	0.418													T|||	934	0.186502	0.2368	0.1643	5008	,	,		14151	0.3194		0.0596	False		,,,				2504	0.1278				p.L53L		Atlas-SNP	.											IMPA2,NS,carcinoma,0,1	IMPA2	27	1	1	Substitution - coding silent(1)	stomach(1)	c.T159C						PASS	.	T		926,3480	354.1+/-312.5	86,754,1363	136.0	137.0	136.0		159	-3.9	1.0	18	dbSNP_120	136	585,8015	156.3+/-210.2	25,535,3740	no	coding-synonymous	IMPA2	NM_014214.2		111,1289,5103	CC,CT,TT		6.8023,21.0168,11.6177		53/289	11999115	1511,11495	2203	4300	6503	SO:0001819	synonymous_variant	3613	exon2			AGATCTTGTGACA	AF014398	CCDS11855.1	18p11.2	2008-03-18			ENSG00000141401	ENSG00000141401	3.1.3.25		6051	protein-coding gene	gene with protein product		605922				9322233	Standard	NM_014214		Approved		uc002kqp.2	O14732	OTTHUMG00000131693	ENST00000269159.3:c.159T>C	18.37:g.11999115T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	183	47	0.256831	NM_014214	B0YJ29|Q9UJT3	Silent	SNP	ENST00000269159.3	37	CCDS11855.1																																																																																			T|0.854;C|0.146	0.146	strong		0.418	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254601.1		
SLC12A8	84561	hgsc.bcm.edu	37	3	124896668	124896668	+	Missense_Mutation	SNP	G	G	A	rs2993631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:124896668G>A	ENST00000393469.4	-	4	590	c.541C>T	c.(541-543)Cgc>Tgc	p.R181C	SLC12A8_ENST00000423114.2_Missense_Mutation_p.R210C|SLC12A8_ENST00000469902.1_Missense_Mutation_p.R181C|SLC12A8_ENST00000314584.7_5'UTR	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	181			R -> C (in dbSNP:rs2993631). {ECO:0000269|PubMed:11863360}.		potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						AGCTGGAGGCGGATTATCCAT	0.557													G|||	168	0.0335463	0.0008	0.0807	5008	,	,		14908	0.0099		0.0447	False		,,,				2504	0.0573				p.R181C		Atlas-SNP	.											.	SLC12A8	81	.	0			c.C541T						PASS	.	G	CYS/ARG,CYS/ARG	46,4110		0,46,2032	71.0	83.0	79.0		541,541	5.5	1.0	3	dbSNP_101	79	403,8051		11,381,3835	yes	missense,missense	SLC12A8	NM_001195483.1,NM_024628.5	180,180	11,427,5867	AA,AG,GG		4.767,1.1068,3.5607	probably-damaging,probably-damaging	181/715,181/715	124896668	449,12161	2078	4227	6305	SO:0001583	missense	84561	exon5			GGAGGCGGATTAT		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.541C>T	3.37:g.124896668G>A	ENSP00000377112:p.Arg181Cys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	37	CCDS43143.1	67	0.030677655677655676	3	0.006097560975609756	25	0.06906077348066299	5	0.008741258741258742	34	0.044854881266490766	g	21.0	4.077054	0.76415	0.011068	0.04767	ENSG00000221955	ENST00000393469;ENST00000423114;ENST00000469902	D;D;D	0.98807	-5.15;-5.15;-5.15	5.5	5.5	0.81552	Amino acid permease domain (1);	.	.	.	.	D	0.92277	0.7550	M	0.88181	2.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.81339	-0.0977	9	0.66056	D	0.02	.	14.1094	0.65113	0.0:0.0:0.8505:0.1495	rs2993631;rs60764229;rs2993631	73;210;181	B5MDT1;A0AV02-2;A0AV02	.;.;S12A8_HUMAN	C	181;210;181	ENSP00000377112:R181C;ENSP00000404243:R210C;ENSP00000418783:R181C	ENSP00000377112:R181C	R	-	1	0	SLC12A8	126379358	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.895000	0.63214	2.599000	0.87857	0.448000	0.29417	CGC	G|0.964;A|0.036	0.036	strong		0.557	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
NWD2	57495	hgsc.bcm.edu	37	4	37445885	37445885	+	Silent	SNP	T	T	C	rs11724784	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:37445885T>C	ENST00000309447.5	+	7	3123	c.2275T>C	c.(2275-2277)Tta>Cta	p.L759L		NM_001144990.1	NP_001138462.1	Q9ULI1	NWD2_HUMAN		759										breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(2)|skin(2)	16						GCACACCATCTTAGCAGATTA	0.507													C|||	943	0.188299	0.1142	0.219	5008	,	,		21120	0.1577		0.2207	False		,,,				2504	0.2648				p.L759L		Atlas-SNP	.											.	KIAA1239	79	.	0			c.T2275C						PASS	.	C		162,1222		9,144,539	46.0	43.0	44.0		2275	4.3	1.0	4	dbSNP_120	44	650,2532		74,502,1015	no	coding-synonymous	KIAA1239	NM_001144990.1		83,646,1554	CC,CT,TT		20.4274,11.7052,17.7836		759/1743	37445885	812,3754	692	1591	2283	SO:0001819	synonymous_variant	57495	exon7			ACCATCTTAGCAG																												ENST00000309447.5:c.2275T>C	4.37:g.37445885T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_001144990	A8MRU1	Silent	SNP	ENST00000309447.5	37	CCDS47040.1																																																																																			T|0.812;C|0.188	0.188	strong		0.507	KIAA1239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347551.2		
ADAM7	8756	hgsc.bcm.edu	37	8	24359068	24359068	+	Silent	SNP	G	G	A	rs13277171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:24359068G>A	ENST00000175238.6	+	20	2270	c.2187G>A	c.(2185-2187)ctG>ctA	p.L729L	ADAM7_ENST00000520720.1_Silent_p.L501L|RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000380789.1_Silent_p.L729L	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	729						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		AGCCAATCCTGCCAGAAATTC	0.378													G|||	1326	0.264776	0.1006	0.428	5008	,	,		15229	0.1885		0.3042	False		,,,				2504	0.409				p.L729L		Atlas-SNP	.											ADAM7,colon,carcinoma,0,1	ADAM7	165	1	0			c.G2187A						PASS	.	G		558,3848	250.3+/-257.4	38,482,1683	77.0	78.0	78.0		2187	-2.7	0.0	8	dbSNP_121	78	2858,5742	449.2+/-362.0	482,1894,1924	no	coding-synonymous	ADAM7	NM_003817.2		520,2376,3607	AA,AG,GG		33.2326,12.6645,26.2648		729/755	24359068	3416,9590	2203	4300	6503	SO:0001819	synonymous_variant	8756	exon20			AATCCTGCCAGAA	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.2187G>A	8.37:g.24359068G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_003817	A8K8X7|O75959|Q6PEJ6	Silent	SNP	ENST00000175238.6	37	CCDS6045.1																																																																																			G|0.743;A|0.257	0.257	strong		0.378	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
IDUA	3425	hgsc.bcm.edu	37	4	995305	995305	+	Silent	SNP	T	T	C	rs6815946	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:995305T>C	ENST00000247933.4	+	5	631	c.543T>C	c.(541-543)aaT>aaC	p.N181N	IDUA_ENST00000453894.1_Silent_p.N134N|IDUA_ENST00000514224.1_Silent_p.N49N	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	181					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			AGACGTGGAATGAGCCAGACC	0.597													C|||	1101	0.219848	0.2526	0.111	5008	,	,		17046	0.2133		0.17	False		,,,				2504	0.3108				p.N181N		Atlas-SNP	.											.	IDUA	33	.	0			c.T543C						PASS	.	C		894,3512	739.9+/-411.1	103,688,1412	210.0	156.0	174.0		543	-5.4	0.7	4	dbSNP_116	174	1386,7214	753.2+/-407.4	115,1156,3029	no	coding-synonymous	IDUA	NM_000203.3		218,1844,4441	CC,CT,TT		16.1163,20.2905,17.5304		181/654	995305	2280,10726	2203	4300	6503	SO:0001819	synonymous_variant	3425	exon5			GTGGAATGAGCCA	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.543T>C	4.37:g.995305T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_000203	B3KWK6	Silent	SNP	ENST00000247933.4	37	CCDS3343.1	409	0.18727106227106227	121	0.2459349593495935	43	0.11878453038674033	119	0.20804195804195805	126	0.1662269129287599	C	7.991	0.753384	0.15778	0.202905	0.161163	ENSG00000127415	ENST00000504568	.	.	.	4.58	-5.41	0.02648	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11470	-1.0586	3	.	.	.	0.1224	12.6687	0.56855	0.0:0.3344:0.0:0.6656	rs6815946;rs6815946	.	.	.	T	168	.	.	M	+	2	0	IDUA	985305	0.010000	0.17322	0.724000	0.30704	0.493000	0.33554	-1.159000	0.03150	-1.688000	0.01435	-1.163000	0.01768	ATG	T|0.821;C|0.179	0.179	strong		0.597	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
TTL	150465	hgsc.bcm.edu	37	2	113277949	113277949	+	Silent	SNP	T	T	C	rs62157538	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113277949T>C	ENST00000233336.6	+	6	1157	c.966T>C	c.(964-966)gaT>gaC	p.D322D		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	322	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		TCATGGTCGATGAGGAGCTGA	0.537			T	ETV6	ALL								T|||	923	0.184305	0.1188	0.0937	5008	,	,		19479	0.2758		0.2068	False		,,,				2504	0.2198				p.D322D		Atlas-SNP	.		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	TTL_ENST00000233336,colon,carcinoma,0,1	TTL	27	1	0			c.T966C						PASS	.	T		564,3842	252.1+/-258.6	40,484,1679	132.0	112.0	119.0		966	-9.1	0.5	2	dbSNP_129	119	1346,7254	263.8+/-285.2	115,1116,3069	no	coding-synonymous	TTL	NM_153712.4		155,1600,4748	CC,CT,TT		15.6512,12.8007,14.6855		322/378	113277949	1910,11096	2203	4300	6503	SO:0001819	synonymous_variant	150465	exon6			GGTCGATGAGGAG		CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.966T>C	2.37:g.113277949T>C		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	233	122	0.523605	NM_153712	Q585T3|Q7Z302|Q8N426	Silent	SNP	ENST00000233336.6	37	CCDS2096.1																																																																																			T|0.838;C|0.162	0.162	strong		0.537	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712	
MAGEA1	4100	hgsc.bcm.edu	37	X	152482796	152482796	+	Missense_Mutation	SNP	C	C	T	rs2008144	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:152482796C>T	ENST00000356661.5	-	3	433	c.215G>A	c.(214-216)cGa>cAa	p.R72Q		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	72			R -> Q (in dbSNP:rs2008144).		negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TTGCCTCTGTCGAGTGAAGTT	0.587													c|||	707	0.187285	0.1044	0.2032	3775	,	,		13088	0.3403		0.0378	False		,,,				2504	0.0481				p.R72Q		Atlas-SNP	.											.	MAGEA1	57	.	0			c.G215A						PASS	.	C	GLN/ARG	571,3264		34,414,89,1184,482	85.0	87.0	86.0		215	-2.4	0.0	X	dbSNP_92	86	327,6401		7,217,96,2204,1776	yes	missense	MAGEA1	NM_004988.4	43	41,631,185,3388,2258	TT,TC,T,CC,C		4.8603,14.8892,8.5014	possibly-damaging	72/310	152482796	898,9665	2203	4300	6503	SO:0001583	missense	4100	exon3			CTCTGTCGAGTGA		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"""melanoma-associated antigen 1"", ""melanoma-associated antigen MZ2-E"", ""melanoma antigen MAGE-1"", ""melanoma antigen family A 1"", ""cancer/testis antigen family 1, member 1"""	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.215G>A	X.37:g.152482796C>T	ENSP00000349085:p.Arg72Gln	Somatic	333	2	0.00600601		WXS	Illumina HiSeq	Phase_I	181	181	1	NM_004988	B2RC81|O00346	Missense_Mutation	SNP	ENST00000356661.5	37	CCDS14720.1	346	0.20855937311633513	45	0.09955752212389381	50	0.16025641025641027	120	0.26905829596412556	19	0.025333333333333333	C	4.922	0.171293	0.09391	0.148892	0.048603	ENSG00000198681	ENST00000356661	T	0.04194	3.68	1.19	-2.38	0.06622	Melanoma associated antigen, MAGE, N-terminal (1);	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.47910	0.902	B	0.42738	0.396	T	0.33752	-0.9856	9	0.30078	T	0.28	.	0.4318	0.00472	0.1978:0.2504:0.3123:0.2396	rs2008144;rs2008144	72	P43355	MAGA1_HUMAN	Q	72	ENSP00000349085:R72Q	ENSP00000349085:R72Q	R	-	2	0	MAGEA1	152135990	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.253000	0.01184	-1.902000	0.01094	-2.856000	0.00102	CGA	0|0.027;T|0.150	0.150	strong		0.587	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242102	81242102	+	RNA	SNP	G	G	A	rs6420424	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81242102G>A	ENST00000525539.1	-	0	753				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TCACCTTCCCGGCACTGGTAC	0.552													G|||	2832	0.565495	0.4629	0.5086	5008	,	,		21299	0.881		0.4632	False		,,,				2504	0.5245				p.R252W		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C754T						PASS	.	G	TRP/ARG,TRP/ARG	1858,2332		449,960,686	80.0	77.0	78.0	http://omim.org/entry/115300	754,754	2.0	0.6	16	dbSNP_116	78	3958,4490		918,2122,1184	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	101,101	1367,3082,1870	AA,AG,GG		46.8513,44.3437,46.0199	benign,benign	252/992,252/2460	81242102	5816,6822	2095	4224	6319			114780	exon4			CTTCCCGGCACTG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242102G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1278	0.5851648351648352	235	0.47764227642276424	180	0.4972375690607735	493	0.8618881118881119	370	0.48812664907651715	G	2.983	-0.209849	0.06140	0.443437	0.468513	ENSG00000166473	ENST00000337114	T	0.01397	4.94	4.11	2.0	0.26442	D-galactoside/L-rhamnose binding SUEL lectin domain (1);	2.014490	0.02501	N	0.090491	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.15930	0.015;0.013	B;B	0.08055	0.003;0.002	T	0.26916	-1.0089	8	0.48119	T	0.1	-0.1764	2.9711	0.05923	0.1018:0.1597:0.4865:0.252	rs6420424;rs61420732;rs6420424	252;252	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	W	252	ENSP00000337397:R252W	ENSP00000337397:R252W	R	-	1	2	PKD1L2	79799603	0.965000	0.33210	0.580000	0.28601	0.086000	0.17979	1.700000	0.37815	0.223000	0.20920	-1.598000	0.00824	CGG	G|0.437;A|0.563	0.563	strong		0.552	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
MFHAS1	9258	hgsc.bcm.edu	37	8	8654898	8654898	+	Silent	SNP	C	C	T	rs3827812	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:8654898C>T	ENST00000276282.6	-	2	3688	c.3102G>A	c.(3100-3102)ccG>ccA	p.P1034P	MFHAS1_ENST00000520091.1_5'UTR	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	1034								p.P1034P(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TGATCACAGTCGGCGTGGGTG	0.557													C|||	470	0.0938498	0.0348	0.1023	5008	,	,		16278	0.0466		0.1958	False		,,,				2504	0.1115				p.P1034P	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											MFHAS1,NS,carcinoma,0,1	MFHAS1	58	1	1	Substitution - coding silent(1)	stomach(1)	c.G3102A						PASS	.	C		260,4146	148.0+/-182.4	6,248,1949	118.0	91.0	100.0		3102	-5.8	0.8	8	dbSNP_107	100	1648,6952	304.0+/-306.7	156,1336,2808	no	coding-synonymous	MFHAS1	NM_004225.2		162,1584,4757	TT,TC,CC		19.1628,5.901,14.6702		1034/1053	8654898	1908,11098	2203	4300	6503	SO:0001819	synonymous_variant	9258	exon2			CACAGTCGGCGTG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.3102G>A	8.37:g.8654898C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	164	75	0.457317	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			C|0.876;T|0.124	0.124	strong		0.557	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
SPATA5	166378	hgsc.bcm.edu	37	4	123855513	123855513	+	Missense_Mutation	SNP	T	T	C	rs55643281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:123855513T>C	ENST00000274008.4	+	5	836	c.767T>C	c.(766-768)aTt>aCt	p.I256T	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	256					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						TATAAACCAATTGATGACAGA	0.438													T|||	28	0.00559105	0.0023	0.0101	5008	,	,		19039	0.0		0.0169	False		,,,				2504	0.001				p.I256T		Atlas-SNP	.											.	SPATA5	62	.	0			c.T767C						PASS	.	T	THR/ILE	19,4387	27.2+/-55.0	0,19,2184	76.0	75.0	76.0		767	-5.6	0.0	4	dbSNP_129	76	137,8463	69.4+/-131.9	1,135,4164	yes	missense	SPATA5	NM_145207.2	89	1,154,6348	CC,CT,TT		1.593,0.4312,1.1994	benign	256/894	123855513	156,12850	2203	4300	6503	SO:0001583	missense	166378	exon5			AACCAATTGATGA	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"""ATPases / AAA-type"""	18119	protein-coding gene	gene with protein product	"""ATPase family gene 2 homolog (S. cerevisiae)"""	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.767T>C	4.37:g.123855513T>C	ENSP00000274008:p.Ile256Thr	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	205	100	0.487805	NM_145207	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Missense_Mutation	SNP	ENST00000274008.4	37	CCDS3730.1	24	0.01098901098901099	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	16	0.021108179419525065	T	0.044	-1.271777	0.01421	0.004312	0.01593	ENSG00000145375	ENST00000274008	D	0.93953	-3.32	4.58	-5.56	0.02529	.	1.021630	0.07765	N	0.950718	T	0.63486	0.2515	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.63651	-0.6589	10	0.31617	T	0.26	-22.3238	3.8171	0.08819	0.0931:0.3613:0.307:0.2386	rs55643281	256;256	Q8NB90;Q8NB90-3	SPAT5_HUMAN;.	T	256	ENSP00000274008:I256T	ENSP00000274008:I256T	I	+	2	0	SPATA5	124074963	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.362000	0.02595	-0.653000	0.05401	0.533000	0.62120	ATT	T|0.987;C|0.013	0.013	strong		0.438	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207	
ZNF708	7562	hgsc.bcm.edu	37	19	21477379	21477379	+	Missense_Mutation	SNP	C	C	T	rs504280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:21477379C>T	ENST00000356929.3	-	4	586	c.389G>A	c.(388-390)cGg>cAg	p.R130Q		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	66					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						TGTCACACACCGGTTAAGTCC	0.378													C|||	929	0.185503	0.1755	0.1816	5008	,	,		18026	0.1091		0.2624	False		,,,				2504	0.2014				p.R130Q		Atlas-SNP	.											.	ZNF708	66	.	0			c.G389A						PASS	.	C	GLN/ARG	791,3615		67,657,1479	176.0	158.0	164.0		389	-0.9	0.0	19	dbSNP_83	164	2114,6486		258,1598,2444	yes	missense	ZNF708	NM_021269.2	43	325,2255,3923	TT,TC,CC		24.5814,17.9528,22.3358	benign	130/564	21477379	2905,10101	2203	4300	6503	SO:0001583	missense	7562	exon4			ACACACCGGTTAA	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"""Zinc fingers, C2H2-type"", ""-"""	12945	protein-coding gene	gene with protein product			"""zinc finger protein 15-like 1 (KOX 8)"", ""zinc finger protein 708"", ""zinc finger protein 708 (KOX8)"""	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.389G>A	19.37:g.21477379C>T	ENSP00000349401:p.Arg130Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	157	83	0.528662	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	422	0.19322344322344323	85	0.17276422764227642	72	0.19889502762430938	56	0.0979020979020979	209	0.2757255936675462	.	0.005	-2.169809	0.00315	0.179528	0.245814	ENSG00000182141	ENST00000356929	T	0.32988	1.43	0.449	-0.883	0.10600	.	.	.	.	.	T	0.00012	0.0000	N	0.00043	-2.465	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28396	-1.0045	7	0.02654	T	1	.	.	.	.	rs504280;rs17618630;rs52789772;rs504280	130	P17019	ZN708_HUMAN	Q	130	ENSP00000349401:R130Q	ENSP00000349401:R130Q	R	-	2	0	ZNF708	21269219	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.722000	0.04958	-0.737000	0.04824	-0.811000	0.03165	CGG	C|0.780;T|0.220	0.220	strong		0.378	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269	
DDIT4L	115265	hgsc.bcm.edu	37	4	101109161	101109161	+	Silent	SNP	G	G	C	rs3749604	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:101109161G>C	ENST00000273990.2	-	3	469	c.255C>G	c.(253-255)acC>acG	p.T85T	RP11-15B17.1_ENST00000515026.1_RNA|RP11-588P8.1_ENST00000515782.1_RNA	NM_145244.3	NP_660287.1	Q96D03	DDT4L_HUMAN	DNA-damage-inducible transcript 4-like	85					negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(2)	12				OV - Ovarian serous cystadenocarcinoma(123;5.75e-09)		CAATTCTCTGGGTCAGTTTCT	0.453													G|||	631	0.125998	0.1626	0.1254	5008	,	,		19326	0.006		0.2316	False		,,,				2504	0.092				p.T85T		Atlas-SNP	.											DDIT4L,NS,carcinoma,-1,1	DDIT4L	33	1	0			c.C255G						PASS	.	G		785,3621	316.1+/-294.4	60,665,1478	139.0	133.0	135.0		255	2.9	1.0	4	dbSNP_107	135	1940,6660	342.1+/-324.3	215,1510,2575	no	coding-synonymous	DDIT4L	NM_145244.3		275,2175,4053	CC,CG,GG		22.5581,17.8166,20.9519		85/194	101109161	2725,10281	2203	4300	6503	SO:0001819	synonymous_variant	115265	exon3			TCTCTGGGTCAGT	BC013592	CCDS34036.1	4q23	2008-02-05				ENSG00000145358			30555	protein-coding gene	gene with protein product	"""regulated in development and DNA damage response 2"", "" similar to Smhs1 protein"""	607730				12477932	Standard	NM_145244		Approved	REDD2, Rtp801L	uc003hvq.3	Q96D03		ENST00000273990.2:c.255C>G	4.37:g.101109161G>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_145244	B2R7C3	Silent	SNP	ENST00000273990.2	37	CCDS34036.1																																																																																			G|0.813;C|0.187	0.187	strong		0.453	DDIT4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363423.1	NM_145244	
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179876988	179876988	+	Missense_Mutation	SNP	C	C	G	rs609521	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:179876988C>G	ENST00000606911.2	+	7	1018	c.827C>G	c.(826-828)cCt>cGt	p.P276R	TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.P155R|TOR1AIP1_ENST00000474875.1_3'UTR|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.P277R|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.P277R			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	276			P -> R (in dbSNP:rs609521). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						GATAAGCAACCTTCAGTGCTA	0.338													C|||	2925	0.584065	0.3041	0.6715	5008	,	,		11847	0.7778		0.6093	False		,,,				2504	0.6748				p.P277R		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.C830G						PASS	.	C	ARG/PRO	1613,2793	495.5+/-363.3	292,1029,882	130.0	118.0	122.0		827	3.8	0.0	1	dbSNP_83	122	5413,3187	652.5+/-400.9	1700,2013,587	yes	missense	TOR1AIP1	NM_015602.2	103	1992,3042,1469	GG,GC,CC		37.0581,36.6092,45.9788	benign	276/584	179876988	7026,5980	2203	4300	6503	SO:0001583	missense	26092	exon7			AGCAACCTTCAGT		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.827C>G	1.37:g.179876988C>G	ENSP00000476687:p.Pro276Arg	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	164	162	0.987805	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	37	CCDS1335.1	1296|1296	0.5934065934065934|0.5934065934065934	150|150	0.3048780487804878|0.3048780487804878	234|234	0.6464088397790055|0.6464088397790055	451|451	0.7884615384615384|0.7884615384615384	461|461	0.6081794195250659|0.6081794195250659	c|c	10.85|10.85	1.466776|1.466776	0.26335|0.26335	0.366092|0.366092	0.629419|0.629419	ENSG00000143337|ENSG00000143337	ENST00000447964|ENST00000528443;ENST00000325993;ENST00000271583;ENST00000435319	.|T;T;T	.|0.42900	.|0.96;0.96;0.96	4.74|4.74	3.81|3.81	0.43845|0.43845	.|.	.|1.063160	.|0.07290	.|N	.|0.872300	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	P|P	0.0|0.0	.|B;P	.|0.43542	.|0.175;0.81	.|B;B	.|0.40375	.|0.104;0.327	T|T	0.34950|0.34950	-0.9808|-0.9808	4|8	.|.	.|.	.|.	-1.1775|-1.1775	10.0678|10.0678	0.42315|0.42315	0.2007:0.7993:0.0:0.0|0.2007:0.7993:0.0:0.0	rs609521;rs1281381;rs2482472;rs11551052;rs16854942;rs17852134;rs52832171;rs609521|rs609521;rs1281381;rs2482472;rs11551052;rs16854942;rs17852134;rs52832171;rs609521	.|276;277	.|Q5JTV8;E9PKD1	.|TOIP1_HUMAN;.	V|R	30|277;276;277;276	.|ENSP00000435365:P277R;ENSP00000271583:P277R;ENSP00000393292:P276R	.|.	L|P	+|+	1|2	0|0	TOR1AIP1|TOR1AIP1	178143611|178143611	0.003000|0.003000	0.15002|0.15002	0.002000|0.002000	0.10522|0.10522	0.042000|0.042000	0.13812|0.13812	1.705000|1.705000	0.37867|0.37867	1.187000|1.187000	0.43000|0.43000	0.650000|0.650000	0.86243|0.86243	CTT|CCT	C|0.442;G|0.557	0.557	strong		0.338	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602	
CCDC86	79080	hgsc.bcm.edu	37	11	60610056	60610056	+	Missense_Mutation	SNP	G	G	C	rs2074421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60610056G>C	ENST00000227520.5	+	1	513	c.459G>C	c.(457-459)caG>caC	p.Q153H	RP11-804A23.2_ENST00000539897.1_RNA|RP11-804A23.4_ENST00000538705.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	153	Pro-rich.		Q -> H (in dbSNP:rs2074421).		viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						CCCAGCATCAGCTACCGCCGG	0.647													G|||	403	0.0804712	0.0461	0.196	5008	,	,		13962	0.0496		0.1024	False		,,,				2504	0.0542				p.Q153H		Atlas-SNP	.											.	CCDC86	24	.	0			c.G459C						PASS	.	G	HIS/GLN	244,4148		7,230,1959	24.0	30.0	28.0		459	2.5	0.1	11	dbSNP_96	28	882,7686		54,774,3456	yes	missense	CCDC86	NM_024098.3	24	61,1004,5415	CC,CG,GG		10.2941,5.5556,8.6883	probably-damaging	153/361	60610056	1126,11834	2196	4284	6480	SO:0001583	missense	79080	exon1			GCATCAGCTACCG	AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.459G>C	11.37:g.60610056G>C	ENSP00000227520:p.Gln153His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_024098	B4DY99	Missense_Mutation	SNP	ENST00000227520.5	37	CCDS7993.1	198	0.09065934065934066	24	0.04878048780487805	59	0.16298342541436464	33	0.057692307692307696	82	0.10817941952506596	G	11.56	1.673993	0.29693	0.055556	0.102941	ENSG00000110104	ENST00000227520;ENST00000339492	T	0.47528	0.84	2.46	2.46	0.29980	.	0.303860	0.26635	N	0.023285	T	0.00384	0.0012	L	0.60455	1.87	0.09310	P	0.999999999980983	D	0.69078	0.997	D	0.68353	0.957	T	0.13818	-1.0495	9	0.52906	T	0.07	.	11.0471	0.47865	0.0:0.0:1.0:0.0	rs2074421	153	Q9H6F5	CCD86_HUMAN	H	153;117	ENSP00000227520:Q153H	ENSP00000227520:Q153H	Q	+	3	2	CCDC86	60366632	0.001000	0.12720	0.113000	0.21522	0.081000	0.17604	-0.240000	0.08952	1.686000	0.51046	0.561000	0.74099	CAG	G|0.909;C|0.091	0.091	strong		0.647	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098	
MYLK	4638	hgsc.bcm.edu	37	3	123411589	123411589	+	Silent	SNP	G	G	A	rs40305	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:123411589G>A	ENST00000475616.1	-	16	3557	c.3558C>T	c.(3556-3558)acC>acT	p.T1186T	MYLK-AS2_ENST00000515464.1_RNA|MYLK_ENST00000510775.1_5'UTR|MYLK_ENST00000346322.5_Silent_p.T1117T|MYLK_ENST00000360304.3_Silent_p.T1186T|MYLK_ENST00000359169.1_Silent_p.T1186T|MYLK_ENST00000354792.5_5'Flank|MYLK-AS2_ENST00000510827.1_RNA|MYLK_ENST00000360772.3_Silent_p.T1186T			Q15746	MYLK_HUMAN	myosin light chain kinase	1186	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.|Ig-like C2-type 7.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TACCATCCACGGTGACTTGGC	0.587													G|||	1666	0.332668	0.0643	0.4856	5008	,	,		17004	0.0685		0.7594	False		,,,				2504	0.4202				p.T1186T		Atlas-SNP	.											.	MYLK	224	.	0			c.C3558T						PASS	.	G	,,,	769,3637	311.6+/-292.2	55,659,1489	97.0	73.0	81.0		3558,3351,3558,3351	-5.4	0.9	3	dbSNP_76	81	6558,2042	718.3+/-406.2	2522,1514,264	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	2577,2173,1753	AA,AG,GG		23.7442,17.4535,43.6645	,,,	1186/1915,1117/1846,1186/1864,1117/1795	123411589	7327,5679	2203	4300	6503	SO:0001819	synonymous_variant	4638	exon19			ATCCACGGTGACT	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.3558C>T	3.37:g.123411589G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	35	0.346535	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	37	CCDS46896.1																																																																																			G|0.525;A|0.475	0.475	strong		0.587	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
LHX2	9355	hgsc.bcm.edu	37	9	126783433	126783433	+	Silent	SNP	G	G	C	rs1042486	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126783433G>C	ENST00000373615.4	+	4	1522	c.783G>C	c.(781-783)ccG>ccC	p.P261P		NM_004789.3	NP_004780.3	P50458	LHX2_HUMAN	LIM homeobox 2	261					axon extension (GO:0048675)|axon guidance (GO:0007411)|cerebral cortex development (GO:0021987)|dorsal/ventral pattern formation (GO:0009953)|mesoderm development (GO:0007498)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural tube closure (GO:0001843)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|retina development in camera-type eye (GO:0060041)|telencephalon regionalization (GO:0021978)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)	10						AGCCATACCCGAGCAGCCAGA	0.592													G|||	1798	0.359026	0.1846	0.4712	5008	,	,		18263	0.4286		0.4433	False		,,,				2504	0.3569				p.P261P		Atlas-SNP	.											.	LHX2	30	.	0			c.G783C						PASS	.	G		1050,3356	384.0+/-325.1	133,784,1286	106.0	90.0	95.0		783	-3.8	0.9	9	dbSNP_86	95	3902,4698	544.9+/-384.7	919,2064,1317	no	coding-synonymous	LHX2	NM_004789.3		1052,2848,2603	CC,CG,GG		45.3721,23.8311,38.0747		261/407	126783433	4952,8054	2203	4300	6503	SO:0001819	synonymous_variant	9355	exon4			ATACCCGAGCAGC	U11701	CCDS6853.1	9q33.3	2011-06-20			ENSG00000106689	ENSG00000106689		"""Homeoboxes / LIM class"""	6594	protein-coding gene	gene with protein product		603759				8649822, 10051612	Standard	NM_004789		Approved	LH-2, hLhx2	uc004boe.1	P50458	OTTHUMG00000020647	ENST00000373615.4:c.783G>C	9.37:g.126783433G>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	75	29	0.386667	NM_004789	O95860|Q52M57|Q8N1Z3	Silent	SNP	ENST00000373615.4	37	CCDS6853.1	841	0.3850732600732601	101	0.20528455284552846	160	0.4419889502762431	237	0.4143356643356643	343	0.4525065963060686	G	10.14	1.268589	0.23136	0.238311	0.453721	ENSG00000106689	ENST00000446480	.	.	.	5.39	-3.77	0.04346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999775296	.	.	.	.	.	.	T	0.30208	-0.9986	3	.	.	.	.	12.2133	0.54391	0.071:0.6581:0.2034:0.0674	rs1042486;rs3181970;rs1042486	.	.	.	Q	267	.	.	E	+	1	0	LHX2	125823254	0.881000	0.30235	0.880000	0.34516	0.955000	0.61496	0.039000	0.13884	-1.288000	0.02378	0.561000	0.74099	GAG	G|0.625;C|0.375	0.375	strong		0.592	LHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054010.2		
NCAN	1463	hgsc.bcm.edu	37	19	19351431	19351431	+	Silent	SNP	G	G	A	rs2229851	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19351431G>A	ENST00000252575.6	+	12	3528	c.3429G>A	c.(3427-3429)acG>acA	p.T1143T	NCAN_ENST00000538881.1_Silent_p.T594T	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1143	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	ATGAAAACACGTGGATCGGCC	0.642													G|||	320	0.0638978	0.0023	0.1037	5008	,	,		19510	0.1319		0.0358	False		,,,				2504	0.0777				p.T1143T		Atlas-SNP	.											.	NCAN	277	.	0			c.G3429A						PASS	.	G		49,4357	50.9+/-86.3	0,49,2154	142.0	103.0	116.0		3429	-8.0	1.0	19	dbSNP_132	116	397,8203	126.8+/-185.2	10,377,3913	no	coding-synonymous	NCAN	NM_004386.2		10,426,6067	AA,AG,GG		4.6163,1.1121,3.4292		1143/1322	19351431	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	1463	exon12			AAACACGTGGATC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3429G>A	19.37:g.19351431G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	27	0.3375	NM_004386	Q9UPK6	Silent	SNP	ENST00000252575.6	37	CCDS12397.1																																																																																			G|0.956;A|0.044	0.044	strong		0.642	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
AGO4	192670	hgsc.bcm.edu	37	1	36316571	36316571	+	Silent	SNP	A	A	C	rs4652895	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36316571A>C	ENST00000373210.3	+	17	2639	c.2394A>C	c.(2392-2394)tcA>tcC	p.S798S	AGO4_ENST00000488778.1_3'UTR	NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	798	Piwi. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										GCACTCGCTCAGTCTCTATTC	0.488													A|||	2459	0.491014	0.1407	0.5375	5008	,	,		14750	0.253		0.8539	False		,,,				2504	0.8037				p.S798S		Atlas-SNP	.											.	.	.	.	0			c.A2394C						PASS	.	A		1161,3245	410.0+/-335.2	174,813,1216	112.0	96.0	101.0		2394	-6.8	1.0	1	dbSNP_111	101	7390,1210	762.7+/-407.6	3190,1010,100	no	coding-synonymous	EIF2C4	NM_017629.3		3364,1823,1316	CC,CA,AA		14.0698,26.3504,34.2534		798/862	36316571	8551,4455	2203	4300	6503	SO:0001819	synonymous_variant	192670	exon17			TCGCTCAGTCTCT	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"""Argonaute/PIWI family"""	18424	protein-coding gene	gene with protein product	"""argonaute 4"""	607356	"""eukaryotic translation initiation factor 2C, 4"""	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.2394A>C	1.37:g.36316571A>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_017629	A7MD27	Silent	SNP	ENST00000373210.3	37	CCDS397.1																																																																																			A|0.436;C|0.564	0.564	strong		0.488	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629	
ZNF354A	6940	hgsc.bcm.edu	37	5	178139355	178139355	+	Silent	SNP	T	T	C	rs113805764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178139355T>C	ENST00000335815.2	-	5	1721	c.1524A>G	c.(1522-1524)tcA>tcG	p.S508S		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	508					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		GATTACTAAGTGATGAGTTAC	0.403													C|||	49	0.00978435	0.0083	0.013	5008	,	,		19708	0.0		0.0249	False		,,,				2504	0.0041				p.S508S		Atlas-SNP	.											.	ZNF354A	74	.	0			c.A1524G						PASS	.	C		30,4376	823.4+/-416.5	0,30,2173	118.0	116.0	117.0		1524	-1.5	1.0	5	dbSNP_132	117	134,8466	810.1+/-407.1	0,134,4166	no	coding-synonymous	ZNF354A	NM_005649.2		0,164,6339	CC,CT,TT		1.5581,0.6809,1.261		508/606	178139355	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			ACTAAGTGATGAG	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.1524A>G	5.37:g.178139355T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	143	26	0.181818	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			T|0.988;C|0.012	0.012	strong		0.403	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
SRRM5	100170229	hgsc.bcm.edu	37	19	44118353	44118353	+	Missense_Mutation	SNP	G	G	A	rs2302421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44118353G>A	ENST00000607544.1	+	3	2402	c.2080G>A	c.(2080-2082)Gac>Aac	p.D694N	ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000417606.1_Missense_Mutation_p.D694N|SRRM5_ENST00000526798.1_Missense_Mutation_p.D709N			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	694	Ser-rich.			D -> N (in Ref. 1; BAG60212). {ECO:0000305}.						endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						CAGTCAAGCCGACGCCACCAC	0.562													A|||	825	0.164736	0.1293	0.2478	5008	,	,		16647	0.2569		0.1461	False		,,,				2504	0.0777				p.D694N		Atlas-SNP	.											.	SRRM5	38	.	0			c.G2080A						PASS	.	A	ASN/ASP,	566,3840	773.8+/-414.0	39,488,1676	98.0	77.0	84.0		2080,	1.0	0.0	19	dbSNP_100	84	1354,7246	755.9+/-407.5	95,1164,3041	yes	missense,intron	ZNF428,SRRM5	NM_001145641.1,NM_182498.3	23,	134,1652,4717	AA,AG,GG		15.7442,12.8461,14.7624	benign,	694/716,	44118353	1920,11086	2203	4300	6503	SO:0001583	missense	100170229	exon1			CAAGCCGACGCCA	AK297891	CCDS46095.1	19q13.31	2013-09-20			ENSG00000226763	ENSG00000226763			37248	protein-coding gene	gene with protein product							Standard	NM_001145641		Approved		uc010xwr.2	B3KS81	OTTHUMG00000165480	ENST00000607544.1:c.2080G>A	19.37:g.44118353G>A	ENSP00000476253:p.Asp694Asn	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	NM_001145641	B4DNF0	Missense_Mutation	SNP	ENST00000607544.1	37	CCDS46095.1	406	0.1858974358974359	66	0.13414634146341464	78	0.2154696132596685	143	0.25	119	0.15699208443271767	A	0.902	-0.721898	0.03182	0.128461	0.157442	ENSG00000226763	ENST00000526798;ENST00000417606	.	.	.	4.28	1.0	0.19881	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35301	-0.9794	7	0.02654	T	1	.	4.0233	0.09675	0.5239:0.1807:0.2954:0.0	rs2302421;rs61130640;rs2302421	694	B3KS81	SRRM5_HUMAN	N	709;694	.	ENSP00000414512:D694N	D	+	1	0	SRRM5	48810193	0.000000	0.05858	0.000000	0.03702	0.140000	0.21249	-0.131000	0.10482	-0.131000	0.11578	-0.361000	0.07541	GAC	G|0.833;A|0.167	0.167	strong		0.562	SRRM5-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000384398.2	NM_001145641	
USP42	84132	hgsc.bcm.edu	37	7	6175526	6175526	+	Missense_Mutation	SNP	C	C	T	rs61757573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6175526C>T	ENST00000306177.5	+	4	655	c.497C>T	c.(496-498)gCa>gTa	p.A166V		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	166	USP.				cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		ATTACCCAGGCACTCAGTAAT	0.348													C|||	8	0.00159744	0.0	0.0058	5008	,	,		16238	0.0		0.001	False		,,,				2504	0.0031				p.A166V		Atlas-SNP	.											.	USP42	138	.	0			c.C497T						PASS	.	C	VAL/ALA	2,3760		0,2,1879	119.0	110.0	113.0		497	5.2	1.0	7	dbSNP_129	113	42,8208		0,42,4083	yes	missense	USP42	NM_032172.2	64	0,44,5962	TT,TC,CC		0.5091,0.0532,0.3663	benign	166/1317	6175526	44,11968	1881	4125	6006	SO:0001583	missense	84132	exon4			CCCAGGCACTCAG	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.497C>T	7.37:g.6175526C>T	ENSP00000301962:p.Ala166Val	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	170	69	0.405882	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	37	CCDS47535.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	19.15	3.771386	0.69992	5.32E-4	0.005091	ENSG00000106346	ENST00000306177;ENST00000465073;ENST00000426246	T;T;T	0.02709	4.19;4.19;4.19	5.19	5.19	0.71726	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.091899	0.47455	D	0.000230	T	0.03178	0.0093	N	0.21373	0.66	0.35910	D	0.831063	P;P;P	0.41597	0.712;0.756;0.756	P;P;P	0.49953	0.493;0.627;0.627	T	0.54330	-0.8310	10	0.40728	T	0.16	.	13.4431	0.61125	0.0:0.9214:0.0:0.0786	rs61757573	166;166;166	Q9H9J4-2;Q9H9J4;A4D2N6	.;UBP42_HUMAN;.	V	166;99;12	ENSP00000301962:A166V;ENSP00000430568:A99V;ENSP00000408217:A12V	ENSP00000301962:A166V	A	+	2	0	USP42	6142052	0.755000	0.28372	1.000000	0.80357	0.997000	0.91878	1.296000	0.33389	2.578000	0.87016	0.467000	0.42956	GCA	C|0.999;T|0.001	0.001	strong		0.348	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
WBSCR28	135886	hgsc.bcm.edu	37	7	73280020	73280020	+	Silent	SNP	C	C	T	rs1136647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73280020C>T	ENST00000320531.2	+	3	651	c.615C>T	c.(613-615)acC>acT	p.T205T		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	205						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				ATCTCATCACCTGGACCACCT	0.617													C|||	2117	0.422724	0.2625	0.4928	5008	,	,		18551	0.4335		0.5726	False		,,,				2504	0.4243				p.T205T		Atlas-SNP	.											WBSCR28,NS,carcinoma,+1,1	WBSCR28	24	1	0			c.C615T						PASS	.	C		1402,2984	414.6+/-336.9	227,948,1018	151.0	160.0	157.0		615	0.0	1.0	7	dbSNP_86	157	4981,3577	610.4+/-395.7	1456,2069,754	no	coding-synonymous	WBSCR28	NM_182504.3		1683,3017,1772	TT,TC,CC		41.7971,31.9653,49.3124		205/266	73280020	6383,6561	2193	4279	6472	SO:0001819	synonymous_variant	135886	exon3			CATCACCTGGACC	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.615C>T	7.37:g.73280020C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	241	101	0.419087	NM_182504	Q6UE04|Q8NHP4	Silent	SNP	ENST00000320531.2	37	CCDS43597.1																																																																																			C|0.529;T|0.471	0.471	strong		0.617	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
DECR2	26063	hgsc.bcm.edu	37	16	461443	461443	+	Silent	SNP	C	C	T	rs138044046	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:461443C>T	ENST00000219481.5	+	8	882	c.744C>T	c.(742-744)agC>agT	p.S248S	DECR2_ENST00000424398.2_Silent_p.S236S|DECR2_ENST00000461947.1_Intron	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	248					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				TCGCCCACAGCGTGCTCTACC	0.667													C|||	4	0.000798722	0.0	0.0	5008	,	,		17246	0.0		0.004	False		,,,				2504	0.0				p.S248S		Atlas-SNP	.											.	DECR2	47	.	0			c.C744T						PASS	.	C		4,4400	8.1+/-20.4	0,4,2198	80.0	75.0	77.0		744	-5.8	0.0	16	dbSNP_134	77	51,8549	32.3+/-84.9	0,51,4249	no	coding-synonymous	DECR2	NM_020664.3		0,55,6447	TT,TC,CC		0.593,0.0908,0.4229		248/293	461443	55,12949	2202	4300	6502	SO:0001819	synonymous_variant	26063	exon8			CCACAGCGTGCTC	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	2754	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 17C, member 1"""	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.744C>T	16.37:g.461443C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_020664	Q6ZRS7|Q96ET0	Silent	SNP	ENST00000219481.5	37	CCDS10409.1																																																																																			C|0.997;T|0.003	0.003	strong		0.667	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664	
RIC1	57589	hgsc.bcm.edu	37	9	5762600	5762600	+	Silent	SNP	G	G	A	rs3739646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:5762600G>A	ENST00000414202.2	+	18	2243	c.2052G>A	c.(2050-2052)agG>agA	p.R684R	KIAA1432_ENST00000251879.6_Silent_p.R684R|KIAA1432_ENST00000418622.3_Silent_p.R605R|KIAA1432_ENST00000381532.2_Silent_p.R605R|KIAA1432_ENST00000449720.2_Silent_p.R568R	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		TGATGCAGAGGGACAGGTCAG	0.413													G|||	375	0.0748802	0.0136	0.0288	5008	,	,		20596	0.0714		0.0398	False		,,,				2504	0.2301				p.R684R		Atlas-SNP	.											.	KIAA1432	97	.	0			c.G2052A						PASS	.	G	,,	71,4335	65.3+/-102.7	0,71,2132	113.0	99.0	104.0		2052,1941,2052	3.1	1.0	9	dbSNP_107	104	335,8265	115.9+/-175.7	6,323,3971	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1432	NM_001135920.2,NM_001206557.1,NM_020829.3	,,	6,394,6103	AA,AG,GG		3.8953,1.6114,3.1216	,,	684/1166,647/1387,684/1424	5762600	406,12600	2203	4300	6503	SO:0001819	synonymous_variant	57589	exon18			GCAGAGGGACAGG																												ENST00000414202.2:c.2052G>A	9.37:g.5762600G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	99	59	0.59596	NM_001135920		Silent	SNP	ENST00000414202.2	37	CCDS34982.2	87	0.03983516483516483	8	0.016260162601626018	10	0.027624309392265192	38	0.06643356643356643	31	0.040897097625329816	G	8.262	0.811395	0.16537	0.016114	0.038953	ENSG00000107036	ENST00000545641	.	.	.	5.92	3.13	0.36017	.	.	.	.	.	T	0.06735	0.0172	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39981	-0.9587	3	.	.	.	-17.3179	8.9245	0.35632	0.2772:0.0:0.7228:0.0	rs3739646;rs3739646	.	.	.	R	576	.	.	G	+	1	0	KIAA1432	5752600	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.503000	0.45407	0.861000	0.35504	0.561000	0.74099	GGA	G|0.960;A|0.040	0.040	strong		0.413	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3		
AAGAB	79719	hgsc.bcm.edu	37	15	67528374	67528374	+	Missense_Mutation	SNP	T	T	G	rs7173826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:67528374T>G	ENST00000261880.5	-	4	498	c.394A>C	c.(394-396)Atc>Ctc	p.I132L	AAGAB_ENST00000542650.1_Missense_Mutation_p.I23L|AAGAB_ENST00000561452.1_Missense_Mutation_p.I23L	NM_001271885.1|NM_001271886.1|NM_024666.3	NP_001258814.1|NP_001258815.1|NP_078942.3	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin binding protein	132			I -> L (in dbSNP:rs7173826). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9						CCATGTTTGATGCACCATTCT	0.338													T|||	1820	0.363419	0.0613	0.4179	5008	,	,		18244	0.6478		0.331	False		,,,				2504	0.4734				p.I132L		Atlas-SNP	.											.	AAGAB	24	.	0			c.A394C						PASS	.	T	LEU/ILE	392,3332		25,342,1495	194.0	166.0	175.0		394	5.5	1.0	15	dbSNP_116	175	2639,5575		415,1809,1883	yes	missense	AAGAB	NM_024666.3	5	440,2151,3378	GG,GT,TT		32.1281,10.5263,25.3895	benign	132/316	67528374	3031,8907	1862	4107	5969	SO:0001583	missense	79719	exon4			GTTTGATGCACCA	AL136715	CCDS42050.1, CCDS61679.1	15q22.33-q23	2014-02-12	2009-07-20		ENSG00000103591	ENSG00000103591			25662	protein-coding gene	gene with protein product		614888				11230166, 10477754	Standard	NM_024666		Approved	FLJ11506, p34	uc002aqk.5	Q6PD74	OTTHUMG00000172246	ENST00000261880.5:c.394A>C	15.37:g.67528374T>G	ENSP00000261880:p.Ile132Leu	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	170	83	0.488235	NM_024666	B4DG44|Q6FI86|Q7Z5X9|Q9H0P1|Q9HAK0	Missense_Mutation	SNP	ENST00000261880.5	37	CCDS42050.1	775	0.35485347985347987	23	0.046747967479674794	136	0.3756906077348066	360	0.6293706293706294	256	0.33773087071240104	T	13.11	2.139046	0.37728	0.105263	0.321281	ENSG00000103591	ENST00000261880;ENST00000542650	T;T	0.79352	-1.26;0.82	5.48	5.48	0.80851	.	0.061993	0.64402	D	0.000001	T	0.00012	0.0000	N	0.16201	0.385	0.22911	P	0.99857885	B	0.16802	0.019	B	0.17722	0.019	T	0.30149	-0.9988	9	0.07813	T	0.8	-18.0746	15.8531	0.78952	0.0:0.0:0.0:1.0	rs7173826;rs17295480;rs52837722;rs57918939;rs7173826	132	Q6PD74	AAGAB_HUMAN	L	132;23	ENSP00000261880:I132L;ENSP00000440735:I23L	ENSP00000261880:I132L	I	-	1	0	AAGAB	65315428	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.056000	0.49923	2.210000	0.71456	0.482000	0.46254	ATC	T|0.662;G|0.338	0.338	strong		0.338	AAGAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417472.1	NM_024666	
LRRC56	115399	hgsc.bcm.edu	37	11	551708	551708	+	Missense_Mutation	SNP	C	C	T	rs113929032	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:551708C>T	ENST00000270115.7	+	10	1354	c.854C>T	c.(853-855)aCg>aTg	p.T285M		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	285										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGCCTGAGACGCAGTCCCGG	0.672													C|||	13	0.00259585	0.0	0.0029	5008	,	,		14883	0.0079		0.002	False		,,,				2504	0.001				p.T285M		Atlas-SNP	.											.	LRRC56	23	.	0			c.C854T						PASS	.	C	MET/THR	5,4395	11.4+/-27.6	0,5,2195	29.0	35.0	33.0		854	0.8	0.0	11	dbSNP_132	33	48,8552	30.7+/-82.3	0,48,4252	yes	missense	LRRC56	NM_198075.3	81	0,53,6447	TT,TC,CC		0.5581,0.1136,0.4077	probably-damaging	285/543	551708	53,12947	2200	4300	6500	SO:0001583	missense	115399	exon10			CTGAGACGCAGTC		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.854C>T	11.37:g.551708C>T	ENSP00000270115:p.Thr285Met	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	37	CCDS7700.1	5	0.0022893772893772895	0	0.0	0	0.0	4	0.006993006993006993	1	0.0013192612137203166	C	5.429	0.264315	0.10294	0.001136	0.005581	ENSG00000161328	ENST00000270115	T	0.09445	2.98	3.82	0.823	0.18812	.	1.130080	0.06470	N	0.730906	T	0.07052	0.0179	L	0.29908	0.895	0.09310	N	1	D	0.61697	0.99	P	0.46299	0.511	T	0.33803	-0.9854	10	0.33940	T	0.23	-5.4819	6.4449	0.21871	0.0:0.6697:0.0:0.3303	.	285	Q8IYG6	LRC56_HUMAN	M	285	ENSP00000270115:T285M	ENSP00000270115:T285M	T	+	2	0	LRRC56	541708	0.000000	0.05858	0.019000	0.16419	0.082000	0.17680	-0.531000	0.06171	0.076000	0.16826	-0.224000	0.12420	ACG	C|0.996;T|0.004	0.004	strong		0.672	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
LRIT3	345193	hgsc.bcm.edu	37	4	110791361	110791361	+	Missense_Mutation	SNP	G	G	A	rs2347131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110791361G>A	ENST00000594814.1	+	4	1456	c.1456G>A	c.(1456-1458)Gca>Aca	p.A486T	LRIT3_ENST00000327908.3_Missense_Mutation_p.A303T|LRIT3_ENST00000379920.3_Missense_Mutation_p.A441T|LRIT3_ENST00000409621.2_Missense_Mutation_p.A303T	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	486	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> T (in dbSNP:rs2347131). {ECO:0000269|PubMed:15489334}.		regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		GACAAATGCCGCAATAGAAAA	0.443													A|||	1245	0.248602	0.2693	0.3804	5008	,	,		23075	0.2728		0.1481	False		,,,				2504	0.2055				p.A486T		Atlas-SNP	.											LRIT3_ENST00000379920,colon,carcinoma,0,2	LRIT3	107	2	0			c.G1456A						PASS	.	A	THR/ALA	1072,3334	723.1+/-409.4	133,806,1264	101.0	96.0	97.0		1321	3.9	0.4	4	dbSNP_100	97	1186,7414	764.2+/-407.6	100,986,3214	yes	missense	LRIT3	NM_198506.2	58	233,1792,4478	AA,AG,GG		13.7907,24.3305,17.3612	benign	441/635	110791361	2258,10748	2203	4300	6503	SO:0001583	missense	345193	exon4			AATGCCGCAATAG	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1456G>A	4.37:g.110791361G>A	ENSP00000469759:p.Ala486Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	520	0.23809523809523808	129	0.2621951219512195	117	0.32320441988950277	163	0.28496503496503495	111	0.14643799472295516	A	0.008	-1.888198	0.00527	0.243305	0.137907	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.56103	0.48;0.65;0.48	5.06	3.9	0.45041	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.447137	0.26840	N	0.022224	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34229	-0.9837	9	0.10111	T	0.7	.	4.6429	0.12558	0.6104:0.1553:0.2343:0.0	rs2347131;rs61705605;rs2347131	441;303	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	T	303;441;303	ENSP00000328222:A303T;ENSP00000369252:A441T;ENSP00000386734:A303T	ENSP00000328222:A303T	A	+	1	0	LRIT3	111010810	0.016000	0.18221	0.428000	0.26697	0.168000	0.22595	1.201000	0.32259	0.772000	0.33382	-0.254000	0.11334	GCA	G|0.794;A|0.206	0.206	strong		0.443	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
PKHD1	5314	hgsc.bcm.edu	37	6	51613177	51613177	+	Silent	SNP	C	C	T	rs765525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:51613177C>T	ENST00000371117.3	-	58	9512	c.9237G>A	c.(9235-9237)gcG>gcA	p.A3079A	PKHD1_ENST00000340994.4_Silent_p.A3079A	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3079					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CTTTGATTCCCGCCACCCAAA	0.517													T|||	1933	0.385982	0.0318	0.4769	5008	,	,		21619	0.6548		0.3926	False		,,,				2504	0.5164				p.A3079A		Atlas-SNP	.											.	PKHD1	927	.	0			c.G9237A						PASS	.	T	,	452,3954	784.9+/-414.7	16,420,1767	190.0	166.0	174.0		9237,9237	3.3	1.0	6	dbSNP_86	174	3112,5488	658.0+/-401.5	567,1978,1755	yes	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	583,2398,3522	TT,TC,CC		36.186,10.2587,27.4027	,	3079/4075,3079/3397	51613177	3564,9442	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon58			GATTCCCGCCACC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.9237G>A	6.37:g.51613177C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	159	90	0.566038	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			T|0.317;G|0.011	0.317	strong		0.517	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PIGQ	9091	hgsc.bcm.edu	37	16	624101	624101	+	Silent	SNP	G	G	A	rs61753370	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:624101G>A	ENST00000026218.5	+	2	115	c.27G>A	c.(25-27)acG>acA	p.T9T	PIGQ_ENST00000409527.2_Silent_p.T9T|PIGQ_ENST00000321878.5_Silent_p.T9T|PIGQ_ENST00000470411.2_Silent_p.T9T	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	9					C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				TCTTCCCCACGTGCTGCGTCT	0.682													G|||	45	0.00898562	0.003	0.0173	5008	,	,		17267	0.0		0.0239	False		,,,				2504	0.0051				p.T9T		Atlas-SNP	.											PIGQ,NS,carcinoma,0,1	PIGQ	43	1	0			c.G27A						PASS	.	G	,	23,4379	29.9+/-59.1	0,23,2178	54.0	48.0	50.0		27,27	-7.0	1.0	16	dbSNP_129	50	304,8296	110.0+/-170.5	2,300,3998	no	coding-synonymous,coding-synonymous	PIGQ	NM_004204.3,NM_148920.1	,	2,323,6176	AA,AG,GG		3.5349,0.5225,2.515	,	9/582,9/761	624101	327,12675	2201	4300	6501	SO:0001819	synonymous_variant	9091	exon2			CCCCACGTGCTGC	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.27G>A	16.37:g.624101G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	57	34	0.596491	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Silent	SNP	ENST00000026218.5	37	CCDS10411.1																																																																																			G|0.978;A|0.022	0.022	strong		0.682	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
CYP17A1	1586	hgsc.bcm.edu	37	10	104596981	104596981	+	Silent	SNP	G	G	A	rs6162	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:104596981G>A	ENST00000369887.3	-	1	309	c.138C>T	c.(136-138)caC>caT	p.H46H	CYP17A1_ENST00000489268.1_5'UTR|CYP17A1-AS1_ENST00000369884.4_RNA	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	46					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	GCATATGGCCGTGTCTGGGGA	0.542													A|||	2216	0.442492	0.323	0.4236	5008	,	,		19226	0.5913		0.4115	False		,,,				2504	0.4959				p.H46H		Atlas-SNP	.											.	CYP17A1	48	.	0			c.C138T						PASS	.	A		1606,2800	664.8+/-401.4	297,1012,894	106.0	107.0	107.0		138	-3.2	0.0	10	dbSNP_52	107	3530,5070	631.6+/-398.5	721,2088,1491	no	coding-synonymous	CYP17A1	NM_000102.3		1018,3100,2385	AA,AG,GG		41.0465,36.4503,39.4895		46/509	104596981	5136,7870	2203	4300	6503	SO:0001819	synonymous_variant	1586	exon1			ATGGCCGTGTCTG	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"""Cytochrome P450s"""	2593	protein-coding gene	gene with protein product	"""Steroid 17-alpha-monooxygenase"""	609300	"""cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"""	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.138C>T	10.37:g.104596981G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_000102	Q5TZV7	Silent	SNP	ENST00000369887.3	37	CCDS7541.1																																																																																			G|0.600;A|0.400	0.400	strong		0.542	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102	
ZNF189	7743	hgsc.bcm.edu	37	9	104171523	104171523	+	Silent	SNP	A	A	G	rs45455902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:104171523A>G	ENST00000339664.2	+	3	1602	c.1473A>G	c.(1471-1473)aaA>aaG	p.K491K	ZNF189_ENST00000259395.4_Silent_p.K449K|ZNF189_ENST00000374861.3_Silent_p.K477K	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	491					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				TCTGTGGGAAAAGCTTCAGCC	0.423													A|||	198	0.0395367	0.0023	0.0634	5008	,	,		19868	0.002		0.0785	False		,,,				2504	0.0716				p.K491K		Atlas-SNP	.											.	ZNF189	79	.	0			c.A1473G						PASS	.	A	,	63,4343	57.4+/-93.9	1,61,2141	88.0	94.0	92.0		1473,1347	4.5	1.0	9	dbSNP_127	92	691,7909	172.3+/-223.0	28,635,3637	yes	coding-synonymous,coding-synonymous	ZNF189	NM_003452.2,NM_197977.1	,	29,696,5778	GG,GA,AA		8.0349,1.4299,5.7973	,	491/627,449/585	104171523	754,12252	2203	4300	6503	SO:0001819	synonymous_variant	7743	exon3			TGGGAAAAGCTTC	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1473A>G	9.37:g.104171523A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	37	CCDS6754.1																																																																																			A|0.952;G|0.048	0.048	strong		0.423	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
HAO2	51179	hgsc.bcm.edu	37	1	119923724	119923724	+	Silent	SNP	T	T	C	rs2275607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:119923724T>C	ENST00000325945.3	+	2	89	c.16T>C	c.(16-18)Ttg>Ctg	p.L6L	HAO2_ENST00000361035.4_Silent_p.L19L	NM_001005783.1|NM_016527.2	NP_001005783.1|NP_057611.1	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2 (long chain)	6	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				fatty acid oxidation (GO:0019395)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		CTTGGTGTGTTTGACAGACTT	0.473													T|||	1794	0.358227	0.0817	0.5216	5008	,	,		20465	0.4504		0.5298	False		,,,				2504	0.3446				p.L6L		Atlas-SNP	.											.	HAO2	62	.	0			c.T16C						PASS	.	T	,	816,3590		129,558,1516	189.0	179.0	183.0		16,16	-9.5	0.6	1	dbSNP_100	183	4447,4153		1166,2115,1019	no	coding-synonymous,coding-synonymous	HAO2	NM_001005783.1,NM_016527.2	,	1295,2673,2535	CC,CT,TT		48.2907,18.5202,40.4659	,	6/352,6/352	119923724	5263,7743	2203	4300	6503	SO:0001819	synonymous_variant	51179	exon3			GTGTGTTTGACAG	AF231917	CCDS901.1	1p13.3-p13.1	2008-07-18			ENSG00000116882	ENSG00000116882	1.1.3.15		4810	protein-coding gene	gene with protein product	"""(S)-2-hydroxy-acid oxidase"", ""glycolate oxidase"", ""long-chain L-2-hydroxy acid oxidase"", ""growth-inhibiting protein 16"""	605176				10777549	Standard	XM_005270913		Approved	HAOX2, GIG16	uc001ehr.1	Q9NYQ3	OTTHUMG00000012410	ENST00000325945.3:c.16T>C	1.37:g.119923724T>C		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001005783	Q2TU86|Q5QP00|Q9UJS6	Silent	SNP	ENST00000325945.3	37	CCDS901.1																																																																																			C|0.420;G|0.000;T|0.579	0.420	strong		0.473	HAO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034984.1	NM_001005783	
EEA1	8411	hgsc.bcm.edu	37	12	93172994	93172994	+	Missense_Mutation	SNP	G	G	A	rs138526188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:93172994G>A	ENST00000322349.8	-	25	3815	c.3551C>T	c.(3550-3552)gCa>gTa	p.A1184V		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1184	Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TTCAACAGCTGCCTTCAGGGA	0.388																																					p.A1184V		Atlas-SNP	.											.	EEA1	104	.	0			c.C3551T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	132.0	128.0	129.0		3551	3.7	0.0	12	dbSNP_134	129	3,8597	3.0+/-9.4	0,3,4297	yes	missense	EEA1	NM_003566.3	64	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	1184/1412	93172994	3,13003	2203	4300	6503	SO:0001583	missense	8411	exon25			ACAGCTGCCTTCA	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.3551C>T	12.37:g.93172994G>A	ENSP00000317955:p.Ala1184Val	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	258	139	0.53876	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	G	7.333	0.619287	0.14129	0.0	3.49E-4	ENSG00000102189	ENST00000322349	T	0.65549	-0.16	5.63	3.74	0.42951	.	0.607873	0.14539	N	0.313361	T	0.46171	0.1379	N	0.19112	0.55	0.09310	N	1	B	0.24258	0.1	B	0.19148	0.024	T	0.24657	-1.0154	10	0.30078	T	0.28	.	12.553	0.56238	0.0:0.1276:0.7395:0.1329	.	1184	Q15075	EEA1_HUMAN	V	1184	ENSP00000317955:A1184V	ENSP00000317955:A1184V	A	-	2	0	EEA1	91697125	0.159000	0.22864	0.032000	0.17829	0.164000	0.22412	1.860000	0.39428	0.672000	0.31204	0.557000	0.71058	GCA	G|1.000;A|0.000	0.000	strong		0.388	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
ARMC3	219681	hgsc.bcm.edu	37	10	23295903	23295903	+	Missense_Mutation	SNP	T	T	C	rs11013233	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:23295903T>C	ENST00000298032.5	+	14	1906	c.1822T>C	c.(1822-1824)Tct>Cct	p.S608P	ARMC3_ENST00000409049.3_Missense_Mutation_p.S608P|ARMC3_ENST00000409983.3_Missense_Mutation_p.S608P|ARMC3_ENST00000376528.4_Missense_Mutation_p.S345P	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	608			S -> P (in dbSNP:rs11013233).			extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CAACAGTAAATCTTACGTGTG	0.458													T|||	108	0.0215655	0.003	0.0058	5008	,	,		18472	0.0		0.0467	False		,,,				2504	0.0542				p.S608P		Atlas-SNP	.											.	ARMC3	102	.	0			c.T1822C						PASS	.	T	PRO/SER	21,4385	29.0+/-57.7	0,21,2182	102.0	95.0	98.0		1822	3.5	1.0	10	dbSNP_120	98	347,8253	117.9+/-177.5	6,335,3959	yes	missense	ARMC3	NM_173081.3	74	6,356,6141	CC,CT,TT		4.0349,0.4766,2.8295	benign	608/873	23295903	368,12638	2203	4300	6503	SO:0001583	missense	219681	exon14			AGTAAATCTTACG	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1822T>C	10.37:g.23295903T>C	ENSP00000298032:p.Ser608Pro	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	37	CCDS7142.1	41	0.018772893772893772	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	36	0.047493403693931395	T	11.20	1.569678	0.28003	0.004766	0.040349	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376523;ENST00000409049;ENST00000376528	T;T;T;T	0.38722	1.12;1.12;1.12;2.35	4.66	3.5	0.40072	.	2.474190	0.00883	N	0.002159	T	0.06416	0.0165	N	0.19112	0.55	0.25558	N	0.98701	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.002	T	0.11012	-1.0605	10	0.45353	T	0.12	-18.3618	8.4211	0.32700	0.0:0.0:0.1984:0.8016	rs11013233;rs52800294;rs11013233	608;608	Q5W041-4;Q5W041	.;ARMC3_HUMAN	P	608;608;544;608;345	ENSP00000298032:S608P;ENSP00000386943:S608P;ENSP00000387288:S608P;ENSP00000365711:S345P	ENSP00000298032:S608P	S	+	1	0	ARMC3	23335909	0.494000	0.26043	0.972000	0.41901	0.674000	0.39518	1.337000	0.33862	0.905000	0.36596	0.533000	0.62120	TCT	T|0.970;C|0.030	0.030	strong		0.458	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081	
CCDC88B	283234	hgsc.bcm.edu	37	11	64110668	64110668	+	Silent	SNP	G	G	A	rs574835	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64110668G>A	ENST00000356786.5	+	11	1124	c.1080G>A	c.(1078-1080)tcG>tcA	p.S360S	CCDC88B_ENST00000301897.4_5'Flank|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	360						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGGTGCTCTCGGGGGTGCTGG	0.697													A|||	1126	0.22484	0.0855	0.3703	5008	,	,		10601	0.1657		0.3658	False		,,,				2504	0.226				p.S360S		Atlas-SNP	.											.	CCDC88B	89	.	0			c.G1080A						PASS	.	A		471,3691		29,413,1639	9.0	8.0	8.0		1080	-8.7	0.0	11	dbSNP_83	8	2492,5608		402,1688,1960	no	coding-synonymous	CCDC88B	NM_032251.5		431,2101,3599	AA,AG,GG		30.7654,11.3167,24.1641		360/1477	64110668	2963,9299	2081	4050	6131	SO:0001819	synonymous_variant	283234	exon11			GCTCTCGGGGGTG	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1080G>A	11.37:g.64110668G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.738;A|0.262	0.262	strong		0.697	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
TNXB	7148	hgsc.bcm.edu	37	6	32064726	32064726	+	Missense_Mutation	SNP	T	T	C	rs1150752	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32064726T>C	ENST00000479795.1	-	3	1044	c.904A>G	c.(904-906)Act>Gct	p.T302A	TNXB_ENST00000375244.3_Missense_Mutation_p.T302A|TNXB_ENST00000375247.2_Missense_Mutation_p.T302A			P22105	TENX_HUMAN	tenascin XB	302	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> A (in dbSNP:rs1150752). {ECO:0000269|PubMed:14574404}.		actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TCCTCGCCAGTGTAGCCGGGG	0.677													T|||	94	0.01877	0.0023	0.0216	5008	,	,		16586	0.0		0.0755	False		,,,				2504	0.0				p.T302A		Atlas-SNP	.											.	TNXB	553	.	0			c.A904G						PASS	.	T	ALA/THR	94,4262		2,90,2086	32.0	38.0	36.0		904	-2.2	0.4	6	dbSNP_87	36	900,7614		48,804,3405	yes	missense	TNXB	NM_019105.6	58	50,894,5491	CC,CT,TT		10.5708,2.1579,7.7234	benign	302/4243	32064726	994,11876	2178	4257	6435	SO:0001583	missense	7148	exon3			CGCCAGTGTAGCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.904A>G	6.37:g.32064726T>C	ENSP00000418248:p.Thr302Ala	Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	316	117	0.370253	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000479795.1	37		67	0.030677655677655676	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	57	0.07519788918205805	T	5.247	0.230987	0.09969	0.021579	0.105708	ENSG00000168477	ENST00000375244;ENST00000375247;ENST00000479795	T;T;T	0.62788	0.0;0.0;0.0	4.13	-2.19	0.07015	.	0.846146	0.10066	N	0.720316	T	0.26048	0.0635	L	0.53671	1.685	0.20703	N	0.999867	B	0.16603	0.018	B	0.16722	0.016	T	0.17198	-1.0377	10	0.23302	T	0.38	.	3.0831	0.06269	0.3851:0.1996:0.0:0.4153	rs1150752;rs57909093;rs1150752	302	P22105-3	.	A	302	ENSP00000364393:T302A;ENSP00000364396:T302A;ENSP00000418248:T302A	ENSP00000364393:T302A	T	-	1	0	TNXB	32172704	0.000000	0.05858	0.376000	0.26042	0.237000	0.25408	-0.203000	0.09438	-0.427000	0.07350	-0.468000	0.05107	ACT	T|0.967;C|0.033	0.033	strong		0.677	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105	
BRAT1	221927	hgsc.bcm.edu	37	7	2583328	2583328	+	Silent	SNP	C	C	T	rs61753095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2583328C>T	ENST00000340611.4	-	5	955	c.699G>A	c.(697-699)acG>acA	p.T233T	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	233					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						ACAGGGCTTCCGTCCAGGGGC	0.662													C|||	482	0.096246	0.0106	0.1859	5008	,	,		13569	0.0079		0.1819	False		,,,				2504	0.1513				p.T233T		Atlas-SNP	.											BRAT1,NS,carcinoma,0,1	BRAT1	57	1	0			c.G699A						PASS	.	C		207,4199	122.1+/-159.5	7,193,2003	35.0	42.0	40.0		699	-11.4	0.0	7	dbSNP_129	40	1761,6837	307.3+/-308.3	179,1403,2717	no	coding-synonymous	BRAT1	NM_152743.3		186,1596,4720	TT,TC,CC		20.4815,4.6981,15.1338		233/822	2583328	1968,11036	2203	4299	6502	SO:0001819	synonymous_variant	221927	exon5			GGCTTCCGTCCAG	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.699G>A	7.37:g.2583328C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Silent	SNP	ENST00000340611.4	37	CCDS5334.1																																																																																			C|0.871;T|0.129	0.129	strong		0.662	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
AMOTL1	154810	hgsc.bcm.edu	37	11	94602414	94602414	+	Missense_Mutation	SNP	C	C	T	rs11020968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:94602414C>T	ENST00000433060.2	+	12	2681	c.2540C>T	c.(2539-2541)cCa>cTa	p.P847L	AMOTL1_ENST00000317829.8_Missense_Mutation_p.P797L|AMOTL1_ENST00000317837.9_Missense_Mutation_p.P434L	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	847			P -> L (in dbSNP:rs11020968).		establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				CCACTGCTGCCACCCCCACCC	0.552													C|||	462	0.0922524	0.0023	0.0533	5008	,	,		15974	0.1548		0.1272	False		,,,				2504	0.1411				p.P847L		Atlas-SNP	.											.	AMOTL1	95	.	0			c.C2540T						PASS	.	C	LEU/PRO	82,4216		0,82,2067	27.0	35.0	32.0		2540	5.0	0.4	11	dbSNP_120	32	930,7582		44,842,3370	yes	missense	AMOTL1	NM_130847.2	98	44,924,5437	TT,TC,CC		10.9258,1.9079,7.9001	benign	847/957	94602414	1012,11798	2149	4256	6405	SO:0001583	missense	154810	exon12			TGCTGCCACCCCC	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2540C>T	11.37:g.94602414C>T	ENSP00000387739:p.Pro847Leu	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	204	0.09340659340659341	3	0.006097560975609756	19	0.052486187845303865	79	0.1381118881118881	103	0.1358839050131926	C	5.147	0.212776	0.09757	0.019079	0.109258	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.50813	2.23;0.73;2.23	5.02	5.02	0.67125	.	0.252596	0.34750	N	0.003701	T	0.00524	0.0017	L	0.37507	1.11	0.31810	P	0.627264	D;B	0.71674	0.998;0.014	D;B	0.63703	0.917;0.007	T	0.05257	-1.0896	9	0.19147	T	0.46	-7.4421	11.7978	0.52110	0.0:0.9192:0.0:0.0808	rs11020968;rs11020968	797;847	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	L	797;434;847	ENSP00000320968:P797L;ENSP00000323474:P434L;ENSP00000387739:P847L	ENSP00000320968:P797L	P	+	2	0	AMOTL1	94242062	0.928000	0.31464	0.391000	0.26233	0.007000	0.05969	2.380000	0.44327	2.340000	0.79590	0.561000	0.74099	CCA	C|0.899;T|0.101	0.101	strong		0.552	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
FBXO18	84893	hgsc.bcm.edu	37	10	5948352	5948352	+	Silent	SNP	G	G	A	rs138692839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:5948352G>A	ENST00000362091.4	+	3	625	c.510G>A	c.(508-510)acG>acA	p.T170T	FBXO18_ENST00000470089.1_3'UTR|FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000379999.5_Silent_p.T221T	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	170	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						AGGACAGTACGTCTCGGCTCT	0.572													G|||	6	0.00119808	0.0	0.0	5008	,	,		22855	0.0		0.006	False		,,,				2504	0.0				p.T221T		Atlas-SNP	.											.	FBXO18	108	.	0			c.G663A						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	60.0	52.0	55.0		663,510	0.3	0.0	10	dbSNP_134	55	42,8558	27.4+/-76.7	0,42,4258	no	coding-synonymous,coding-synonymous	FBXO18	NM_032807.3,NM_178150.1	,	0,46,6457	AA,AG,GG		0.4884,0.0908,0.3537	,	221/1095,170/1044	5948352	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	84893	exon4			CAGTACGTCTCGG	AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"""F-boxes /  ""other"""""	13620	protein-coding gene	gene with protein product		607222	"""F-box only protein 18"""			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.510G>A	10.37:g.5948352G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	140	78	0.557143	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Silent	SNP	ENST00000362091.4	37	CCDS7072.1																																																																																			G|0.998;A|0.002	0.002	strong		0.572	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807	
DDN	23109	hgsc.bcm.edu	37	12	49391682	49391682	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49391682T>C	ENST00000421952.2	-	2	998	c.977A>G	c.(976-978)aAc>aGc	p.N326S	RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	326						cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						GCTACCACTGTTCAGGTCAGC	0.662																																					p.N326S		Atlas-SNP	.											.	DDN	54	.	0			c.A977G						PASS	.						45.0	53.0	50.0					12																	49391682		2203	4298	6501	SO:0001583	missense	23109	exon2			CCACTGTTCAGGT	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.977A>G	12.37:g.49391682T>C	ENSP00000390590:p.Asn326Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	37	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	T	9.110	1.006312	0.19199	.	.	ENSG00000181418	ENST00000421952	T	0.47528	0.84	3.88	0.238	0.15480	.	0.712920	0.12723	N	0.444514	T	0.24044	0.0582	N	0.12182	0.205	0.09310	N	1	B	0.16396	0.017	B	0.10450	0.005	T	0.21415	-1.0246	10	0.18710	T	0.47	-24.1145	6.6688	0.23056	0.0:0.3358:0.0:0.6642	.	326	O94850	DEND_HUMAN	S	326	ENSP00000390590:N326S	ENSP00000390590:N326S	N	-	2	0	DDN	47677949	0.000000	0.05858	0.001000	0.08648	0.629000	0.37895	0.452000	0.21795	0.039000	0.15632	0.459000	0.35465	AAC	.	.	none		0.662	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1		
PCDHB16	57717	hgsc.bcm.edu	37	5	140563579	140563579	+	Missense_Mutation	SNP	C	C	T	rs17844646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140563579C>T	ENST00000361016.2	+	1	2600	c.1445C>T	c.(1444-1446)aCc>aTc	p.T482I		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	482	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.			T -> I (in Ref. 3; BAB13447). {ECO:0000305}.	calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GACTCAGGCACCAACGCCCAG	0.657													C|||	1318	0.263179	0.0129	0.3069	5008	,	,		11803	0.5308		0.2376	False		,,,				2504	0.3211				p.T482I		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C1445T						PASS	.						56.0	52.0	54.0					5																	140563579		2203	4279	6482	SO:0001583	missense	57717	exon1			CAGGCACCAACGC	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1445C>T	5.37:g.140563579C>T	ENSP00000354293:p.Thr482Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	117	97	0.82906	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	569	0.26053113553113555	7	0.014227642276422764	87	0.24033149171270718	303	0.5297202797202797	172	0.22691292875989447	c	13.55	2.269951	0.40095	.	.	ENSG00000196963	ENST00000361016	T	0.52983	0.64	4.26	2.24	0.28232	Cadherin (4);Cadherin-like (1);	1.787010	0.03514	N	0.220040	T	0.00012	0.0000	N	0.20328	0.56	0.54753	P	1.4999999999987246E-5	P	0.45986	0.87	P	0.48524	0.58	T	0.39820	-0.9595	9	0.42905	T	0.14	.	7.8603	0.29506	0.3851:0.4774:0.1376:0.0	rs17844646	482	Q9NRJ7	PCDBG_HUMAN	I	482	ENSP00000354293:T482I	ENSP00000354293:T482I	T	+	2	0	PCDHB16	140543763	0.000000	0.05858	0.841000	0.33234	0.574000	0.36063	-0.036000	0.12185	0.747000	0.32809	0.580000	0.79431	ACC	C|0.878;T|0.122	0.122	strong		0.657	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
DGKQ	1609	hgsc.bcm.edu	37	4	954885	954885	+	Silent	SNP	G	G	T	rs77382558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:954885G>T	ENST00000273814.3	-	22	2752	c.2679C>A	c.(2677-2679)ccC>ccA	p.P893P	DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	893					blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCTGGACCCAGGGCTCCCCGT	0.692													g|||	198	0.0395367	0.0113	0.013	5008	,	,		13953	0.1161		0.0398	False		,,,				2504	0.0174				p.P893P	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											.	DGKQ	29	.	0			c.C2679A						PASS	.			67,4339	60.5+/-97.4	2,63,2138	33.0	40.0	38.0		2679	2.3	1.0	4	dbSNP_131	38	351,8247	117.2+/-176.8	8,335,3956	no	coding-synonymous	DGKQ	NM_001347.2		10,398,6094	TT,TG,GG		4.0823,1.5207,3.2144		893/943	954885	418,12586	2203	4299	6502	SO:0001819	synonymous_variant	1609	exon22			GACCCAGGGCTCC	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"""diacylglycerol kinase, theta (110kD)"""	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.2679C>A	4.37:g.954885G>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	149	82	0.550336	NM_001347	Q6P3W4	Silent	SNP	ENST00000273814.3	37	CCDS3342.1	100	0.045787545787545784	7	0.014227642276422764	5	0.013812154696132596	59	0.10314685314685315	29	0.03825857519788918	G	10.86	1.470491	0.26423	0.015207	0.040823	ENSG00000145214	ENST00000509465	T	0.46819	0.86	5.3	2.32	0.28847	.	0.049655	0.85682	D	0.000000	T	0.02047	0.0064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01566	-1.1323	7	0.87932	D	0	.	5.6211	0.17457	0.1872:0.0:0.6415:0.1713	.	.	.	.	H	827	ENSP00000425862:P827H	ENSP00000425862:P827H	P	-	2	0	DGKQ	944885	0.855000	0.29742	1.000000	0.80357	0.983000	0.72400	-0.073000	0.11468	1.229000	0.43630	0.556000	0.70494	CCT	G|0.965;T|0.035	0.035	strong		0.692	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		
WRNIP1	56897	hgsc.bcm.edu	37	6	2784571	2784571	+	Silent	SNP	G	G	A	rs160703	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:2784571G>A	ENST00000380773.4	+	6	1865	c.1656G>A	c.(1654-1656)ccG>ccA	p.P552P	WRNIP1_ENST00000380769.4_Silent_p.P332P|WRNIP1_ENST00000380764.1_Silent_p.P168P|WRNIP1_ENST00000380771.4_Silent_p.P527P	NM_020135.2	NP_064520.2			Werner helicase interacting protein 1											breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				TGGCAGACCCGTCTGCGTTAA	0.502													G|||	1052	0.210064	0.0968	0.2147	5008	,	,		20281	0.256		0.1968	False		,,,				2504	0.3262				p.P552P		Atlas-SNP	.											.	WRNIP1	39	.	0			c.G1656A						PASS	.	G	,	464,3942	219.1+/-236.9	32,400,1771	113.0	88.0	96.0		1656,1581	-11.1	0.1	6	dbSNP_79	96	1689,6911	308.8+/-309.1	169,1351,2780	no	coding-synonymous,coding-synonymous	WRNIP1	NM_020135.2,NM_130395.1	,	201,1751,4551	AA,AG,GG		19.6395,10.5311,16.5539	,	552/666,527/641	2784571	2153,10853	2203	4300	6503	SO:0001819	synonymous_variant	56897	exon6			AGACCCGTCTGCG	AB056152	CCDS4475.1, CCDS4476.1	6p25.2	2010-04-21			ENSG00000124535	ENSG00000124535		"""ATPases / AAA-type"""	20876	protein-coding gene	gene with protein product		608196				11301316	Standard	NM_020135		Approved	WHIP, FLJ22526, bA420G6.2	uc003mtz.3	Q96S55	OTTHUMG00000014126	ENST00000380773.4:c.1656G>A	6.37:g.2784571G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	188	103	0.547872	NM_020135		Silent	SNP	ENST00000380773.4	37	CCDS4475.1																																																																																			G|0.824;A|0.176	0.176	strong		0.502	WRNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039641.1	NM_130395	
GLOD4	51031	hgsc.bcm.edu	37	17	663468	663468	+	Missense_Mutation	SNP	G	G	T	rs75027378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:663468G>T	ENST00000301328.5	-	10	910	c.887C>A	c.(886-888)gCa>gAa	p.A296E	GLOD4_ENST00000575800.1_5'Flank|GLOD4_ENST00000301329.6_Missense_Mutation_p.A281E|GLOD4_ENST00000536578.1_Missense_Mutation_p.A272E			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4	296						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		ACTTTTATCTGCTGCCATTGC	0.418													G|||	94	0.01877	0.0008	0.0086	5008	,	,		16392	0.0456		0.0179	False		,,,				2504	0.0235				p.A281E		Atlas-SNP	.											.	GLOD4	12	.	0			c.C842A						PASS	.						178.0	148.0	158.0					17																	663468		2203	4300	6503	SO:0001583	missense	51031	exon9			TTATCTGCTGCCA	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38		ENST00000301328.5:c.887C>A	17.37:g.663468G>T	ENSP00000301328:p.Ala296Glu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_016080	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	37		40	0.018315018315018316	1	0.0020325203252032522	3	0.008287292817679558	22	0.038461538461538464	14	0.018469656992084433	G	10.13	1.266498	0.23136	.	.	ENSG00000167699	ENST00000301329;ENST00000397393;ENST00000301328;ENST00000536578	T;T;T	0.41400	1.0;1.01;1.0	6.02	4.02	0.46733	.	0.097095	0.64402	D	0.000001	T	0.07548	0.0190	N	0.25890	0.77	0.44702	D	0.997699	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.10450	0.005;0.005;0.005	T	0.02477	-1.1153	10	0.16896	T	0.51	-3.299	12.3462	0.55122	0.0:0.1236:0.7342:0.1423	.	272;296;281	B7Z403;Q9HC38;Q9HC38-2	.;GLOD4_HUMAN;.	E	281;484;296;272	ENSP00000301329:A281E;ENSP00000301328:A296E;ENSP00000444315:A272E	ENSP00000301328:A296E	A	-	2	0	GLOD4	610218	1.000000	0.71417	0.988000	0.46212	0.991000	0.79684	3.342000	0.52159	0.856000	0.35383	0.655000	0.94253	GCA	G|0.978;T|0.022	0.022	strong		0.418	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
APOBR	55911	hgsc.bcm.edu	37	16	28506872	28506872	+	Silent	SNP	A	A	G	rs149271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28506872A>G	ENST00000431282.1	+	2	520	c.510A>G	c.(508-510)gaA>gaG	p.E170E	CLN3_ENST00000567160.1_5'Flank|CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000564831.1_Silent_p.E170E|APOBR_ENST00000328423.5_Silent_p.E170E			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	170	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						TGAACAGAGAAGAGAGGCTGA	0.607													G|||	1476	0.294728	0.3888	0.4294	5008	,	,		16994	0.1042		0.3479	False		,,,				2504	0.2137				p.E170E		Atlas-SNP	.											.	APOBR	89	.	0			c.A510G						PASS	.	G		1634,2640		361,912,864	11.0	13.0	12.0		510	2.1	0.9	16	dbSNP_79	12	3311,5217		694,1923,1647	no	coding-synonymous	APOBR	NM_018690.3		1055,2835,2511	GG,GA,AA		38.825,38.2312,38.6268		170/1089	28506872	4945,7857	2137	4264	6401	SO:0001819	synonymous_variant	55911	exon2			CAGAGAAGAGAGG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.510A>G	16.37:g.28506872A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	118	66	0.559322	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				A|0.711;G|0.289	0.289	strong		0.607	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
SPTY2D1	144108	hgsc.bcm.edu	37	11	18633897	18633897	+	Missense_Mutation	SNP	T	T	C	rs35411689	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18633897T>C	ENST00000336349.5	-	4	2085	c.1850A>G	c.(1849-1851)aAg>aGg	p.K617R	SPTY2D1-AS1_ENST00000501599.2_RNA	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	617			K -> R (in dbSNP:rs35411689). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.					p.K617R(1)		breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						TCTAATGTGCTTGGATATTTC	0.333													T|||	514	0.102636	0.0091	0.0605	5008	,	,		16987	0.2232		0.0974	False		,,,				2504	0.1401				p.K617R		Atlas-SNP	.											SPTY2D1,NS,carcinoma,0,1	SPTY2D1	72	1	1	Substitution - Missense(1)	stomach(1)	c.A1850G						PASS	.	T	ARG/LYS	94,4304	76.8+/-115.0	0,94,2105	133.0	131.0	132.0		1850	3.7	1.0	11	dbSNP_126	132	714,7872	174.2+/-224.5	27,660,3606	yes	missense	SPTY2D1	NM_194285.2	26	27,754,5711	CC,CT,TT		8.3159,2.1373,6.223	possibly-damaging	617/686	18633897	808,12176	2199	4293	6492	SO:0001583	missense	144108	exon4			ATGTGCTTGGATA	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1850A>G	11.37:g.18633897T>C	ENSP00000337991:p.Lys617Arg	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	182	90	0.494505	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	37	CCDS31441.1	249	0.11401098901098901	9	0.018292682926829267	22	0.06077348066298342	136	0.23776223776223776	82	0.10817941952506596	T	15.32	2.797273	0.50208	0.021373	0.083159	ENSG00000179119	ENST00000336349	T	0.47528	0.84	5.99	3.67	0.42095	.	0.092812	0.64402	N	0.000001	T	0.00012	0.0000	L	0.43757	1.38	0.21933	P	0.99946053	P	0.34724	0.465	B	0.33568	0.166	T	0.15925	-1.0420	9	0.27785	T	0.31	-6.5418	10.2959	0.43625	0.0:0.1332:0.0:0.8668	rs35411689	617	Q68D10	SPT2_HUMAN	R	617	ENSP00000337991:K617R	ENSP00000337991:K617R	K	-	2	0	SPTY2D1	18590473	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.257000	0.43240	0.514000	0.28300	0.533000	0.62120	AAG	T|0.921;C|0.079	0.079	strong		0.333	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285	
USP17L10	100287144	hgsc.bcm.edu	37	4	9212676	9212676	+	Silent	SNP	G	G	A	rs528291442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:9212676G>A	ENST00000417945.1	+	1	294	c.294G>A	c.(292-294)ctG>ctA	p.L98L	USP17L13_ENST00000421288.2_Intron	NM_001256852.1	NP_001243781.1	C9JJH3	U17LA_HUMAN	ubiquitin specific peptidase 17-like family member 10	98	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)										TGCAGTGCCTGACATACAAAC	0.557													g|||	4	0.000798722	0.0	0.0	5008	,	,		2145	0.0		0.0	False		,,,				2504	0.0041				p.L98L		Atlas-SNP	.											.	.	.	.	0			c.G294A						PASS	.																																			SO:0001819	synonymous_variant	100287144	exon1			GTGCCTGACATAC		CCDS59454.1	4p16.1	2014-02-12	2012-10-09		ENSG00000231396	ENSG00000231396			44438	protein-coding gene	gene with protein product							Standard	NM_001256852		Approved		uc031sdg.1	C9JJH3	OTTHUMG00000160160	ENST00000417945.1:c.294G>A	4.37:g.9212676G>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_001256852		Silent	SNP	ENST00000417945.1	37	CCDS59454.1																																																																																			.	.	none		0.557	USP17L10-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359428.1	NM_001256852	
SPNS3	201305	hgsc.bcm.edu	37	17	4391132	4391132	+	Silent	SNP	C	C	T	rs2291743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4391132C>T	ENST00000355530.2	+	12	1762	c.1482C>T	c.(1480-1482)aaC>aaT	p.N494N	SPNS3_ENST00000333476.2_Silent_p.N367N|RP13-580F15.2_ENST00000576086.1_RNA	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	494					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.N494N(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						TGGACAGCAACGACCTGGAGA	0.622													C|||	775	0.154752	0.0567	0.1715	5008	,	,		18930	0.0437		0.3171	False		,,,				2504	0.2229				p.N494N		Atlas-SNP	.											SPNS3,NS,carcinoma,0,1	SPNS3	52	1	1	Substitution - coding silent(1)	stomach(1)	c.C1482T						PASS	.	C		402,4004	200.4+/-223.7	21,360,1822	130.0	119.0	123.0		1482	-3.1	0.0	17	dbSNP_100	123	2582,6018	419.5+/-353.1	371,1840,2089	no	coding-synonymous	SPNS3	NM_182538.4		392,2200,3911	TT,TC,CC		30.0233,9.1239,22.9433		494/513	4391132	2984,10022	2203	4300	6503	SO:0001819	synonymous_variant	201305	exon12			CAGCAACGACCTG		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.1482C>T	17.37:g.4391132C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	158	71	0.449367	NM_182538	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																			C|0.793;T|0.207	0.207	strong		0.622	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
OR10H1	26539	hgsc.bcm.edu	37	19	15918654	15918654	+	Missense_Mutation	SNP	G	G	A	rs4808382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15918654G>A	ENST00000334920.2	-	1	282	c.194C>T	c.(193-195)gCc>gTc	p.A65V		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	65			A -> V (in dbSNP:rs4808382).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						GACGGAGAGGGCGCACAGGAA	0.647													.|||	767	0.153155	0.1369	0.1153	5008	,	,		20012	0.119		0.1769	False		,,,				2504	0.2127				p.A65V		Atlas-SNP	.											OR10H1,colon,carcinoma,-1,2	OR10H1	59	2	0			c.C194T						scavenged	.						114.0	99.0	104.0					19																	15918654		2203	4297	6500	SO:0001583	missense	26539	exon1			GAGAGGGCGCACA	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.194C>T	19.37:g.15918654G>A	ENSP00000335596:p.Ala65Val	Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	220	37	0.168182	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	271	0.12408424908424909	53	0.10772357723577236	34	0.09392265193370165	62	0.10839160839160839	122	0.16094986807387862	g	2.686	-0.274334	0.05679	.	.	ENSG00000186723	ENST00000334920	T	0.03065	4.06	4.71	4.71	0.59529	GPCR, rhodopsin-like superfamily (1);	0.271882	0.26200	N	0.025747	T	0.00012	0.0000	N	0.01771	-0.73	0.39146	P	0.037856	B	0.11235	0.004	B	0.15052	0.012	T	0.39881	-0.9592	9	0.02654	T	1	.	15.1534	0.72720	0.0:0.0:1.0:0.0	rs4808382	65	Q9Y4A9	O10H1_HUMAN	V	65	ENSP00000335596:A65V	ENSP00000335596:A65V	A	-	2	0	OR10H1	15779654	0.589000	0.26807	0.964000	0.40570	0.471000	0.32888	1.685000	0.37659	2.169000	0.68431	0.643000	0.83706	GCC	A|1.000;|0.000	1.000	weak		0.647	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
NLRP2	55655	hgsc.bcm.edu	37	19	55494740	55494740	+	Silent	SNP	T	T	C	rs10412915	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55494740T>C	ENST00000543010.1	+	6	1817	c.1674T>C	c.(1672-1674)ttT>ttC	p.F558F	NLRP2_ENST00000537859.1_Silent_p.F536F|NLRP2_ENST00000263437.6_Silent_p.F555F|NLRP2_ENST00000391721.4_Silent_p.F534F|NLRP2_ENST00000448584.2_Silent_p.F558F|NLRP2_ENST00000427260.2_Silent_p.F535F|NLRP2_ENST00000339757.7_Silent_p.F536F|NLRP2_ENST00000538819.1_Silent_p.F534F	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	558					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		ACTACTCCTTTGGCCTCGCTA	0.552													C|||	1428	0.285144	0.2655	0.3141	5008	,	,		19437	0.3085		0.3211	False		,,,				2504	0.2301				p.F558F		Atlas-SNP	.											.	NLRP2	161	.	0			c.T1674C						PASS	.	C	,,,	1118,3288	399.2+/-331.1	137,844,1222	78.0	72.0	74.0		1674,1608,1605,1674	-3.6	0.0	19	dbSNP_119	74	2520,6080	413.3+/-351.1	371,1778,2151	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	508,2622,3373	CC,CT,TT		29.3023,25.3745,27.9717	,,,	558/1063,536/1041,535/1040,558/1063	55494740	3638,9368	2203	4300	6503	SO:0001819	synonymous_variant	55655	exon6			CTCCTTTGGCCTC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.1674T>C	19.37:g.55494740T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			T|0.710;C|0.290	0.290	strong		0.552	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
VARS2	57176	hgsc.bcm.edu	37	6	30882781	30882781	+	Silent	SNP	G	G	T	rs1264301	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30882781G>T	ENST00000321897.5	+	1	800	c.168G>T	c.(166-168)gcG>gcT	p.A56A	VARS2_ENST00000542001.1_Intron|VARS2_ENST00000416670.2_Silent_p.A56A|VARS2_ENST00000541562.1_Silent_p.A86A			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	56					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						AGAAGCAGGCGACTCTGGAGG	0.582													G|||	1112	0.222045	0.0983	0.2075	5008	,	,		17920	0.247		0.3559	False		,,,				2504	0.2362				p.A86A		Atlas-SNP	.											.	VARS2	60	.	0			c.G258T						PASS	.	G	,,	442,2578		35,372,1103	50.0	61.0	57.0		,258,168	-1.4	0.2	6	dbSNP_87	57	2042,3376		366,1310,1033	no	intron,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	401,1682,2136	TT,TG,GG		37.6892,14.6358,29.4383	,,	,86/1094,56/1064	30882781	2484,5954	1510	2709	4219	SO:0001819	synonymous_variant	57176	exon2			GCAGGCGACTCTG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.168G>T	6.37:g.30882781G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	44	0.666667	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			G|0.731;T|0.269	0.269	strong		0.582	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
L3MBTL3	84456	hgsc.bcm.edu	37	6	130374102	130374102	+	Missense_Mutation	SNP	C	C	A	rs9388768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:130374102C>A	ENST00000529410.1	+	9	1027	c.548C>A	c.(547-549)aCc>aAc	p.T183N	L3MBTL3_ENST00000368136.2_Missense_Mutation_p.T183N|L3MBTL3_ENST00000533560.1_Missense_Mutation_p.T158N|L3MBTL3_ENST00000368139.2_Missense_Mutation_p.T158N|L3MBTL3_ENST00000361794.2_Missense_Mutation_p.T183N|L3MBTL3_ENST00000526019.1_Missense_Mutation_p.T158N			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	183			T -> N (in dbSNP:rs9388768). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:15489334}.		chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		AAAGCTGACACCAAGGAGGAT	0.453													C|||	2524	0.503994	0.1142	0.6124	5008	,	,		21524	0.7599		0.6461	False		,,,				2504	0.544				p.T183N		Atlas-SNP	.											.	L3MBTL3	99	.	0			c.C548A						PASS	.	C	ASN/THR,ASN/THR	934,3472	354.6+/-312.7	124,686,1393	84.0	71.0	76.0		473,548	5.0	0.9	6	dbSNP_119	76	5856,2744	679.9+/-403.6	1983,1890,427	yes	missense,missense	L3MBTL3	NM_001007102.2,NM_032438.2	65,65	2107,2576,1820	AA,AC,CC		31.907,21.1984,47.7933	benign,benign	158/756,183/781	130374102	6790,6216	2203	4300	6503	SO:0001583	missense	84456	exon7			CTGACACCAAGGA	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"""Sterile alpha motif (SAM) domain containing"""	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.548C>A	6.37:g.130374102C>A	ENSP00000431962:p.Thr183Asn	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Missense_Mutation	SNP	ENST00000529410.1	37	CCDS34537.1	1190	0.5448717948717948	55	0.11178861788617886	220	0.6077348066298343	418	0.7307692307692307	497	0.6556728232189973	C	9.113	1.007105	0.19199	0.211984	0.68093	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000528385;ENST00000368139;ENST00000526019;ENST00000368136	T;T;T;T;T;T;T	0.42131	2.57;2.58;2.57;0.98;2.58;2.58;2.57	5.03	5.03	0.67393	.	0.471044	0.24165	N	0.040947	T	0.11495	0.0280	N	0.08118	0	0.54753	P	1.2000000000012001E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.06935	-1.0799	9	0.28530	T	0.3	.	13.1795	0.59647	0.0:0.8398:0.1602:0.0	rs9388768;rs17758829;rs17855060;rs52831490;rs9388768	158;183	Q96JM7-2;Q96JM7	.;LMBL3_HUMAN	N	183;158;183;183;158;158;183	ENSP00000431962:T183N;ENSP00000437185:T158N;ENSP00000354526:T183N;ENSP00000433257:T183N;ENSP00000357121:T158N;ENSP00000436706:T158N;ENSP00000357118:T183N	ENSP00000354526:T183N	T	+	2	0	L3MBTL3	130415795	0.754000	0.28360	0.948000	0.38648	0.370000	0.29829	1.151000	0.31651	2.498000	0.84270	0.563000	0.77884	ACC	C|0.478;A|0.522	0.522	strong		0.453	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074	
CARD11	84433	hgsc.bcm.edu	37	7	2976767	2976767	+	Silent	SNP	G	G	A	rs6945582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2976767G>A	ENST00000396946.4	-	9	1648	c.1245C>T	c.(1243-1245)gaC>gaT	p.D415D		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	415					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TCCTCATCTCGTCGTTCTTCT	0.577			Mis		DLBCL								G|||	454	0.090655	0.0424	0.1556	5008	,	,		22008	0.0109		0.2078	False		,,,				2504	0.0716				p.D415D		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.C1245T						PASS	.	G		309,4097	166.5+/-197.7	10,289,1904	179.0	145.0	156.0		1245	-0.6	1.0	7	dbSNP_116	156	1622,6978	301.8+/-305.6	159,1304,2837	no	coding-synonymous	CARD11	NM_032415.4		169,1593,4741	AA,AG,GG		18.8605,7.0132,14.847		415/1155	2976767	1931,11075	2203	4300	6503	SO:0001819	synonymous_variant	84433	exon9			CATCTCGTCGTTC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1245C>T	7.37:g.2976767G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	219	98	0.447489	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			G|0.868;A|0.132	0.132	strong		0.577	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
B3GNT1	11041	hgsc.bcm.edu	37	11	66113995	66113995	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66113995C>T	ENST00000311181.4	-	1	1168	c.1022G>A	c.(1021-1023)cGc>cAc	p.R341H	BRMS1_ENST00000425825.2_5'Flank|RP11-867G23.8_ENST00000531602.1_5'Flank|BRMS1_ENST00000359957.3_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	341					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			breast(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	12						CTGCCGAAAGCGCTCGTCGAA	0.627																																					p.R341H		Atlas-SNP	.											.	B3GNT1	28	.	0			c.G1022A						PASS	.						77.0	82.0	80.0					11																	66113995		2200	4291	6491	SO:0001583	missense	11041	exon1			CGAAAGCGCTCGT	AF029893	CCDS8136.1	11q13.2	2014-07-08	2006-04-12	2006-04-12	ENSG00000174684	ENSG00000174684	2.4.1.149	"""Beta 3-glycosyltransferases"""	15685	protein-coding gene	gene with protein product	"""N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase"""	605517	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6"""	B3GNT6		9405606	Standard	NM_006876		Approved	iGNT, iGAT, iGnT, BETA3GNTI, B3GN-T1	uc001ohr.3	O43505	OTTHUMG00000167082	ENST00000311181.4:c.1022G>A	11.37:g.66113995C>T	ENSP00000309096:p.Arg341His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_006876	Q4TTN0	Missense_Mutation	SNP	ENST00000311181.4	37	CCDS8136.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640477	0.67244	.	.	ENSG00000174684	ENST00000311181;ENST00000538757	T	0.32272	1.46	5.83	5.83	0.93111	.	0.165306	0.51477	D	0.000098	T	0.61627	0.2362	M	0.84846	2.72	0.46203	D	0.998928	D	0.89917	1.0	D	0.79784	0.993	T	0.65450	-0.6165	10	0.66056	D	0.02	-24.2929	17.6063	0.88039	0.0:1.0:0.0:0.0	.	341	O43505	B3GN1_HUMAN	H	341;112	ENSP00000309096:R341H	ENSP00000309096:R341H	R	-	2	0	B3GNT1	65870571	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.911000	0.48774	2.761000	0.94854	0.563000	0.77884	CGC	.	.	none		0.627	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394003	103394003	+	RNA	SNP	G	G	A	rs1449707	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103394003G>A	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		CTCCTGGCAAGTCTTCTGTTG	0.403													G|||	3476	0.694089	0.5408	0.7493	5008	,	,		19700	0.5913		0.826	False		,,,				2504	0.8323				p.T3015I		Atlas-SNP	.											.	.	.	.	0			c.C9044T						PASS	.	G	ILE/THR	773,611		217,339,136	63.0	52.0	55.0		9044	-2.2	0.0	13	dbSNP_88	55	2543,637		1023,497,70	yes	missense	CCDC168	NM_001146197.1	89	1240,836,206	AA,AG,GG		20.0314,44.1474,27.3444		3015/7082	103394003	3316,1248	692	1590	2282			643677	exon4			TGGCAAGTCTTCT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103394003G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				G|0.336;A|0.664	0.664	strong		0.403	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
SH3PXD2B	285590	hgsc.bcm.edu	37	5	171849471	171849471	+	Silent	SNP	G	G	A	rs17074773	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:171849471G>A	ENST00000311601.5	-	2	275	c.105C>T	c.(103-105)agC>agT	p.S35S	SH3PXD2B_ENST00000519643.1_Silent_p.S35S	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	35	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGGTGGAGCCGCTGGACCACG	0.552													G|||	1876	0.374601	0.2171	0.4179	5008	,	,		18002	0.6617		0.2783	False		,,,				2504	0.3599				p.S35S		Atlas-SNP	.											.	SH3PXD2B	91	.	0			c.C105T						PASS	.	G		1042,3364	376.3+/-322.0	129,784,1290	45.0	44.0	44.0		105	-8.7	0.6	5	dbSNP_123	44	2354,6246	386.0+/-341.7	332,1690,2278	no	coding-synonymous	SH3PXD2B	NM_001017995.2		461,2474,3568	AA,AG,GG		27.3721,23.6496,26.111		35/912	171849471	3396,9610	2203	4300	6503	SO:0001819	synonymous_variant	285590	exon2			GGAGCCGCTGGAC	AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"""KIAA1295"""	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.105C>T	5.37:g.171849471G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	34	26	0.764706	NM_001017995	B6F0V2|Q9P2Q1	Silent	SNP	ENST00000311601.5	37	CCDS34291.1																																																																																			G|0.692;A|0.308	0.308	strong		0.552	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963	
MROH6	642475	hgsc.bcm.edu	37	8	144654730	144654730	+	Missense_Mutation	SNP	G	G	T	rs185255597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144654730G>T	ENST00000398882.3	-	1	411	c.155C>A	c.(154-156)cCt>cAt	p.P52H	MROH6_ENST00000533679.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000460623.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	52																	CTCAGCCTCAGGTTTGACCTC	0.682													g|||	4	0.000798722	0.0	0.0	5008	,	,		13956	0.0		0.004	False		,,,				2504	0.0				p.P52H		Atlas-SNP	.											.	.	.	.	0			c.C155A						PASS	.		HIS/PRO	6,3902		0,6,1948	16.0	20.0	19.0		155	0.3	0.0	8		19	28,8238		0,28,4105	yes	missense	C8orf73	NM_001100878.1	77	0,34,6053	TT,TG,GG		0.3387,0.1535,0.2793	probably-damaging	52/720	144654730	34,12140	1954	4133	6087	SO:0001583	missense	642475	exon1			GCCTCAGGTTTGA	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.155C>A	8.37:g.144654730G>T	ENSP00000381857:p.Pro52His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	67	42	0.626866	NM_001100878	A8MWB1	Missense_Mutation	SNP	ENST00000398882.3	37	CCDS47928.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	16.46	3.129400	0.56721	0.001535	0.003387	ENSG00000204839	ENST00000398882;ENST00000529971	T;T	0.30981	3.71;1.51	4.54	0.342	0.15996	.	.	.	.	.	T	0.15262	0.0368	N	0.14661	0.345	0.09310	N	0.999998	D;P	0.54207	0.965;0.681	P;B	0.50378	0.639;0.371	T	0.09796	-1.0658	9	0.87932	D	0	-1.6263	2.8407	0.05528	0.1024:0.334:0.3925:0.1711	.	52;52	E9PPP7;A6NGR9	.;CH073_HUMAN	H	52	ENSP00000381857:P52H;ENSP00000436959:P52H	ENSP00000381857:P52H	P	-	2	0	C8orf73	144725873	0.000000	0.05858	0.000000	0.03702	0.131000	0.20780	0.024000	0.13555	0.449000	0.26747	0.461000	0.40582	CCT	G|0.998;T|0.002	0.002	strong		0.682	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878	
ATG2B	55102	hgsc.bcm.edu	37	14	96777468	96777468	+	Missense_Mutation	SNP	G	G	C	rs3759601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:96777468G>C	ENST00000359933.4	-	28	5040	c.4147C>G	c.(4147-4149)Caa>Gaa	p.Q1383E	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1383			Q -> E (in dbSNP:rs3759601). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		GACCTTCTTTGAAAGGCTCCA	0.443													G|||	1251	0.2498	0.1142	0.4568	5008	,	,		18272	0.1776		0.4066	False		,,,				2504	0.1994				p.Q1383E		Atlas-SNP	.											.	ATG2B	169	.	0			c.C4147G						PASS	.	G	GLU/GLN	755,3651	306.3+/-289.4	46,663,1494	183.0	172.0	176.0		4147	2.5	0.0	14	dbSNP_107	176	3634,4966	523.4+/-380.3	771,2092,1437	yes	missense	ATG2B	NM_018036.5	29	817,2755,2931	CC,CG,GG		42.2558,17.1357,33.746	benign	1383/2079	96777468	4389,8617	2203	4300	6503	SO:0001583	missense	55102	exon28			TTCTTTGAAAGGC	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.4147C>G	14.37:g.96777468G>C	ENSP00000353010:p.Gln1383Glu	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	205	111	0.541463	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	645	0.29532967032967034	49	0.09959349593495935	160	0.4419889502762431	118	0.2062937062937063	318	0.41952506596306066	G	5.230	0.228002	0.09916	0.171357	0.422558	ENSG00000066739	ENST00000359933	T	0.44083	0.93	5.48	2.55	0.30701	.	0.681226	0.14654	N	0.306432	T	0.00012	0.0000	L	0.41236	1.265	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.42616	-0.9441	9	0.02654	T	1	.	8.8268	0.35061	0.0:0.2187:0.3659:0.4154	rs3759601;rs52803484;rs3759601	1383	Q96BY7	ATG2B_HUMAN	E	1383	ENSP00000353010:Q1383E	ENSP00000261834:Q27E	Q	-	1	0	ATG2B	95847221	0.016000	0.18221	0.000000	0.03702	0.840000	0.47671	1.403000	0.34612	0.241000	0.21283	0.655000	0.94253	CAA	G|0.686;C|0.314	0.314	strong		0.443	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
TBCD	6904	hgsc.bcm.edu	37	17	80899281	80899281	+	Silent	SNP	G	G	A	rs9390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80899281G>A	ENST00000355528.4	+	38	3616	c.3486G>A	c.(3484-3486)gcG>gcA	p.A1162A	TBCD_ENST00000539345.2_Silent_p.A1200A|TBCD_ENST00000576691.1_3'UTR	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1162					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			ACAGGGACGCGGAGCTTGCAG	0.647													G|||	2153	0.429912	0.1997	0.4798	5008	,	,		18481	0.5486		0.5507	False		,,,				2504	0.4591				p.A1162A		Atlas-SNP	.											.	TBCD	94	.	0			c.G3486A						PASS	.	G		964,3292		125,714,1289	37.0	48.0	44.0		3486	-9.6	0.0	17	dbSNP_52	44	4091,4383		988,2115,1134	no	coding-synonymous	TBCD	NM_005993.4		1113,2829,2423	AA,AG,GG		48.2771,22.6504,39.7093		1162/1193	80899281	5055,7675	2128	4237	6365	SO:0001819	synonymous_variant	6904	exon38			GGACGCGGAGCTT	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.3486G>A	17.37:g.80899281G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	37	CCDS45818.1																																																																																			A|0.453;C|0.000;G|0.546;T|0.000	0.453	strong		0.647	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
AP3D1	8943	hgsc.bcm.edu	37	19	2109157	2109157	+	Missense_Mutation	SNP	T	T	C	rs25673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:2109157T>C	ENST00000345016.5	-	28	3445	c.3214A>G	c.(3214-3216)Atc>Gtc	p.I1072V	AP3D1_ENST00000350812.6_Missense_Mutation_p.I903V|AP3D1_ENST00000355272.6_Missense_Mutation_p.I1134V|AP3D1_ENST00000356926.4_Missense_Mutation_p.I1031V	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	1072			I -> V (in dbSNP:rs25673).		anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGACTTTGATTGAGCTCATG	0.552													T|||	390	0.0778754	0.0779	0.0677	5008	,	,		19994	0.0		0.1153	False		,,,				2504	0.1268				p.I1134V		Atlas-SNP	.											.	AP3D1	81	.	0			c.A3400G						PASS	.	T	VAL/ILE,VAL/ILE	391,3769		13,365,1702	91.0	96.0	94.0		3214,3091	-5.9	0.0	19	dbSNP_72	94	1327,7133		105,1117,3008	yes	missense,missense	AP3D1	NM_003938.5,NM_001077523.1	29,29	118,1482,4710	CC,CT,TT		15.6856,9.399,13.6133	benign,benign	1072/1154,1031/1113	2109157	1718,10902	2080	4230	6310	SO:0001583	missense	8943	exon30			CTTTGATTGAGCT	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.3214A>G	19.37:g.2109157T>C	ENSP00000344055:p.Ile1072Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	37	CCDS42459.1	156	0.07142857142857142	43	0.08739837398373984	31	0.0856353591160221	0	0.0	82	0.10817941952506596	T	0.014	-1.603914	0.00849	0.09399	0.156856	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	4.4	-5.88	0.02290	.	0.279925	0.34314	N	0.004080	T	0.00109	0.0003	L	0.50919	1.6	0.47476	P	5.669999999999842E-4	B;B;B;B	0.11235	0.0;0.004;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.19516	-1.0303	9	0.17369	T	0.5	-16.7795	7.6107	0.28129	0.0:0.3668:0.1132:0.52	rs25673;rs3189383;rs17403023;rs17604917;rs58724636;rs25673	903;1134;1072;1031	E7EMM2;O14617-5;O14617;G5E988	.;.;AP3D1_HUMAN;.	V	1031;1072;1134;940;903	ENSP00000349398:I1031V;ENSP00000344055:I1072V;ENSP00000347416:I1134V;ENSP00000342321:I903V	ENSP00000341579:I940V	I	-	1	0	AP3D1	2060157	0.000000	0.05858	0.003000	0.11579	0.233000	0.25261	-0.827000	0.04424	-1.861000	0.01153	-2.245000	0.00285	ATC	T|0.907;C|0.093	0.093	strong		0.552	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
AASDH	132949	hgsc.bcm.edu	37	4	57215677	57215677	+	Missense_Mutation	SNP	G	G	A	rs3796544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57215677G>A	ENST00000205214.6	-	11	2420	c.2240C>T	c.(2239-2241)gCg>gTg	p.A747V	AASDH_ENST00000451613.1_Missense_Mutation_p.A747V|AASDH_ENST00000502617.1_Missense_Mutation_p.A747V|AASDH_ENST00000434343.2_Missense_Mutation_p.A262V|AASDH_ENST00000602986.1_Missense_Mutation_p.A594V|AASDH_ENST00000513376.1_Missense_Mutation_p.A647V	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	747			A -> V (in dbSNP:rs3796544). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.A747V(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				AGTCCCTATCGCAGGTTTCCC	0.418													G|||	1392	0.277955	0.2829	0.2939	5008	,	,		19646	0.0724		0.4155	False		,,,				2504	0.3303				p.A747V		Atlas-SNP	.											AASDH,NS,carcinoma,0,3	AASDH	101	3	1	Substitution - Missense(1)	prostate(1)	c.C2240T						scavenged	.	G	VAL/ALA	1285,3121	437.2+/-344.9	170,945,1088	123.0	119.0	121.0		2240	-10.5	0.0	4	dbSNP_107	121	3665,4935	526.7+/-381.0	760,2145,1395	yes	missense	AASDH	NM_181806.2	64	930,3090,2483	AA,AG,GG		42.6163,29.1648,38.0594	benign	747/1099	57215677	4950,8056	2203	4300	6503	SO:0001583	missense	132949	exon11			CCTATCGCAGGTT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.2240C>T	4.37:g.57215677G>A	ENSP00000205214:p.Ala747Val	Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	204	94	0.460784	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	608	0.2783882783882784	139	0.28252032520325204	112	0.30939226519337015	36	0.06293706293706294	321	0.4234828496042216	G	0.022	-1.407769	0.01155	0.291648	0.426163	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T;T	0.63255	-0.03;0.1;2.3;0.51;0.52	5.26	-10.5	0.00291	Quinonprotein alcohol dehydrogenase-like (1);	1.244260	0.05327	N	0.527586	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B;B;B;B	0.10296	0.003;0.001;0.0;0.0	B;B;B;B	0.08055	0.003;0.001;0.001;0.0	T	0.13072	-1.0523	9	0.14656	T	0.56	0.0183	1.9415	0.03348	0.2842:0.2376:0.3226:0.1556	rs3796544;rs17490588;rs52809767;rs59885880;rs3796544	594;747;747;747	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	V	747;647;262;747;594;747	ENSP00000205214:A747V;ENSP00000423760:A647V;ENSP00000392158:A262V;ENSP00000409656:A747V;ENSP00000421171:A747V	ENSP00000205214:A747V	A	-	2	0	AASDH	56910434	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.527000	0.06200	-2.299000	0.00659	-2.178000	0.00318	GCG	G|0.679;A|0.321	0.321	strong		0.418	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
PTH1R	5745	hgsc.bcm.edu	37	3	46944274	46944274	+	Silent	SNP	T	T	C	rs1138518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46944274T>C	ENST00000313049.5	+	13	1592	c.1389T>C	c.(1387-1389)aaT>aaC	p.N463N	PTH1R_ENST00000449590.1_Silent_p.N463N|PTH1R_ENST00000418619.1_Silent_p.N463N|PTH1R_ENST00000430002.2_Silent_p.N463N			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	463					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)	p.N463N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	GTTTCTGCAATGGCGAGGTAA	0.557													C|||	3222	0.643371	0.8215	0.6513	5008	,	,		17106	0.4425		0.6431	False		,,,				2504	0.6043				p.N463N		Atlas-SNP	.											PTH1R,NS,carcinoma,0,1	PTH1R	49	1	1	Substitution - coding silent(1)	stomach(1)	c.T1389C						PASS	.	C	,	3520,886	344.6+/-308.2	1407,706,90	102.0	112.0	109.0		1389,1389	-8.4	0.6	3	dbSNP_86	109	5320,3280	491.4+/-373.1	1652,2016,632	no	coding-synonymous,coding-synonymous	PTH1R	NM_000316.2,NM_001184744.1	,	3059,2722,722	CC,CT,TT		38.1395,20.1089,32.0314	,	463/594,463/594	46944274	8840,4166	2203	4300	6503	SO:0001819	synonymous_variant	5745	exon14			CTGCAATGGCGAG		CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"""GPCR / Class B : Parathyroid hormone receptors"""	9608	protein-coding gene	gene with protein product		168468	"""parathyroid hormone receptor 1"""	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.1389T>C	3.37:g.46944274T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_001184744	Q2M1U3	Silent	SNP	ENST00000313049.5	37	CCDS2747.1																																																																																			T|0.343;C|0.657	0.657	strong		0.557	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	
BTN3A2	11118	hgsc.bcm.edu	37	6	26373150	26373150	+	Silent	SNP	C	C	T	rs12174631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26373150C>T	ENST00000356386.2	+	6	929	c.741C>T	c.(739-741)ccC>ccT	p.P247P	BTN3A2_ENST00000527422.1_Silent_p.P247P|BTN3A2_ENST00000377708.2_Silent_p.P247P|BTN3A2_ENST00000508906.2_Silent_p.P205P|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000396948.1_Silent_p.P247P|BTN3A2_ENST00000396934.3_Silent_p.P224P	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	247					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						GCGCCCAGCCCTGGATCGCAG	0.607													C|||	406	0.0810703	0.0287	0.0389	5008	,	,		16332	0.0992		0.1103	False		,,,				2504	0.1329				p.P247P		Atlas-SNP	.											.	BTN3A2	44	.	0			c.C741T						PASS	.	C	,,,,	165,4241	108.2+/-146.6	2,161,2040	61.0	62.0	62.0		741,741,672,615,741	0.6	0.0	6	dbSNP_120	62	929,7671	200.9+/-244.5	50,829,3421	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	52,990,5461	TT,TC,CC		10.8023,3.7449,8.4115	,,,,	247/335,247/335,224/312,205/293,247/335	26373150	1094,11912	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon4			CCAGCCCTGGATC	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.741C>T	6.37:g.26373150C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	180	96	0.533333	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			C|0.924;T|0.076	0.076	strong		0.607	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
PLA2G4D	283748	hgsc.bcm.edu	37	15	42371752	42371752	+	Missense_Mutation	SNP	A	A	T	rs4924618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42371752A>T	ENST00000290472.3	-	13	1394	c.1300T>A	c.(1300-1302)Tcc>Acc	p.S434T		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	434	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		S -> T (in dbSNP:rs4924618).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		TGCAGCATGGACTCCAGCACT	0.711													A|||	1502	0.29992	0.1634	0.4726	5008	,	,		15047	0.3958		0.3429	False		,,,				2504	0.2188				p.S434T		Atlas-SNP	.											PLA2G4D,NS,carcinoma,0,1	PLA2G4D	72	1	0			c.T1300A						PASS	.	A	THR/SER	864,3540		81,702,1419	22.0	24.0	23.0		1300	1.3	0.2	15	dbSNP_111	23	2980,5614		521,1938,1838	yes	missense	PLA2G4D	NM_178034.3	58	602,2640,3257	TT,TA,AA		34.6754,19.6185,29.5738	benign	434/819	42371752	3844,9154	2202	4297	6499	SO:0001583	missense	283748	exon13			GCATGGACTCCAG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1300T>A	15.37:g.42371752A>T	ENSP00000290472:p.Ser434Thr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	710	0.3250915750915751	67	0.13617886178861788	160	0.4419889502762431	215	0.3758741258741259	268	0.35356200527704484	A	13.24	2.179065	0.38511	0.196185	0.346754	ENSG00000159337	ENST00000290472	T	0.04502	3.61	5.0	1.28	0.21552	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.813383	0.11149	N	0.594335	T	0.00012	0.0000	L	0.33485	1.01	0.40941	P	0.015539999999999998	B	0.27264	0.173	B	0.21151	0.033	T	0.41413	-0.9510	9	0.23891	T	0.37	-1.1751	3.7273	0.08480	0.6594:0.1369:0.0728:0.1309	rs4924618	434	Q86XP0	PA24D_HUMAN	T	434	ENSP00000290472:S434T	ENSP00000290472:S434T	S	-	1	0	PLA2G4D	40159044	0.086000	0.21541	0.183000	0.23137	0.987000	0.75469	0.628000	0.24522	-0.029000	0.13827	0.459000	0.35465	TCC	A|0.716;T|0.284	0.284	strong		0.711	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
PARP4	143	hgsc.bcm.edu	37	13	25021211	25021211	+	Silent	SNP	C	C	T	rs7333856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25021211C>T	ENST00000381989.3	-	26	3333	c.3228G>A	c.(3226-3228)ccG>ccA	p.P1076P		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1076					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GAAACAAGGACGGCACCTGGG	0.512													c|||	3941	0.786941	0.469	0.8588	5008	,	,		13697	0.9177		0.8777	False		,,,				2504	0.9376				p.P1076P		Atlas-SNP	.											.	PARP4	142	.	0			c.G3228A						PASS	.						64.0	50.0	55.0					13																	25021211		2203	4300	6503	SO:0001819	synonymous_variant	143	exon26			CAAGGACGGCACC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3228G>A	13.37:g.25021211C>T		Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	158	136	0.860759	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.274;T|0.726	0.726	strong		0.512	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
PLP1	5354	hgsc.bcm.edu	37	X	103042882	103042882	+	Silent	SNP	T	T	C	rs1126707	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:103042882T>C	ENST00000303958.2	+	4	755	c.609T>C	c.(607-609)gaT>gaC	p.D203D	PLP1_ENST00000361621.2_Silent_p.D168D|PLP1_ENST00000418604.1_Silent_p.D203D|PLP1_ENST00000466486.1_3'UTR	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	203			D -> E (in HLD1). {ECO:0000269|PubMed:10417279, ECO:0000269|PubMed:11093273}.|D -> G (in HLD1). {ECO:0000269|PubMed:10417279}.|D -> H (in HLD1). {ECO:0000269|PubMed:1376966}.|D -> N (in HLD1). {ECO:0000269|PubMed:10417279}.|D -> V (in HLD1). {ECO:0000269|PubMed:9747038}.		astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						TCTGTGCTGATGCCAGAATGT	0.488													T|||	780	0.206623	0.0628	0.2738	3775	,	,		15438	0.1736		0.2107	False		,,,				2504	0.1227				p.D203D		Atlas-SNP	.											.	PLP1	37	.	0			c.T609C	GRCh37	CM002830	PLP1	M	rs1126707	PASS	.	T	,,	489,3346		41,348,59,1243,512	159.0	116.0	130.0		609,609,504	4.4	1.0	X	dbSNP_86	130	2100,4628		212,1073,603,1143,1269	no	coding-synonymous,coding-synonymous,coding-synonymous	PLP1	NM_000533.3,NM_001128834.1,NM_199478.1	,,	253,1421,662,2386,1781	CC,CT,C,TT,T		31.2128,12.751,24.5101	,,	203/278,203/278,168/243	103042882	2589,7974	2203	4300	6503	SO:0001819	synonymous_variant	5354	exon5			TGCTGATGCCAGA	M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"""Pelizaeus-Merzbacher disease"""	300401	"""spastic paraplegia 2, uncomplicated"""	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.609T>C	X.37:g.103042882T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001128834	P04400|P06905|Q502Y1|Q6FHZ6	Silent	SNP	ENST00000303958.2	37	CCDS14513.1																																																																																			T|0.774;C|0.226	0.226	strong		0.488	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2		
CEP170	9859	hgsc.bcm.edu	37	1	243328887	243328887	+	Nonsense_Mutation	SNP	G	G	T	rs2728433		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:243328887G>T	ENST00000366542.1	-	13	2426	c.2375C>A	c.(2374-2376)tCa>tAa	p.S792*	CEP170_ENST00000490813.1_5'Flank|CEP170_ENST00000366543.1_Nonsense_Mutation_p.S694*|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Nonsense_Mutation_p.S694*|RP11-261C10.4_ENST00000422938.1_RNA	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	792						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.S792*(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			AGAATGTCCTGAATTTTTTTC	0.398																																					p.S792X		Atlas-SNP	.											CEP170,extremity,malignant_melanoma,0,1	CEP170	153	1	1	Substitution - Nonsense(1)	skin(1)	c.C2375A						scavenged	.						85.0	80.0	81.0					1																	243328887		1846	4111	5957	SO:0001587	stop_gained	9859	exon13			TGTCCTGAATTTT	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2375C>A	1.37:g.243328887G>T	ENSP00000355500:p.Ser792*	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	151	11	0.0728477	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Nonsense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.986185|3.986185	0.74589|0.74589	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000336415|ENST00000366542;ENST00000366544;ENST00000366543	.|.	.|.	.|.	5.34|5.34	0.747|0.747	0.18371|0.18371	.|.	.|0.921055	.|0.09339	.|N	.|0.815762	T|.	0.31263|.	0.0791|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.31779|.	-0.9931|.	4|.	.|.	.|.	.|.	1.7324|1.7324	6.9628|6.9628	0.24608|0.24608	0.2357:0.0:0.6372:0.1271|0.2357:0.0:0.6372:0.1271	.|.	.|.	.|.	.|.	K|X	756|792;694;694	.|.	.|.	Q|S	-|-	1|2	0|0	CEP170|CEP170	241395510|241395510	0.785000|0.785000	0.28726|0.28726	0.030000|0.030000	0.17652|0.17652	0.547000|0.547000	0.35210|0.35210	1.683000|1.683000	0.37638|0.37638	0.240000|0.240000	0.21263|0.21263	0.555000|0.555000	0.69702|0.69702	CAG|TCA	T|0.500;G|0.500	0.500	weak		0.398	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
TIMELESS	8914	hgsc.bcm.edu	37	12	56815922	56815922	+	Missense_Mutation	SNP	C	C	T	rs774047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56815922C>T	ENST00000553532.1	-	20	2642	c.2492G>A	c.(2491-2493)cGg>cAg	p.R831Q	TIMELESS_ENST00000229201.4_Missense_Mutation_p.R830Q|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GTACAGCTCCCGAAGATGAGC	0.532													C|||	2498	0.498802	0.2262	0.6772	5008	,	,		21940	0.7371		0.4503	False		,,,				2504	0.545				p.R831Q		Atlas-SNP	.											TIMELESS,NS,carcinoma,+1,1	TIMELESS	107	1	0			c.G2492A						PASS	.	C	GLN/ARG	1078,3328	388.6+/-327.0	123,832,1248	104.0	97.0	99.0		2492	-1.1	1.0	12	dbSNP_86	99	3895,4705	546.2+/-384.9	867,2161,1272	yes	missense	TIMELESS	NM_003920.3	43	990,2993,2520	TT,TC,CC		45.2907,24.4666,38.2362	benign	831/1209	56815922	4973,8033	2203	4300	6503	SO:0001583	missense	8914	exon20			AGCTCCCGAAGAT	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2492G>A	12.37:g.56815922C>T	ENSP00000450607:p.Arg831Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	119	69	0.579832	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	1059	0.4848901098901099	103	0.20934959349593496	217	0.5994475138121547	401	0.701048951048951	338	0.44591029023746703	C	12.08	1.829831	0.32329	0.244666	0.452907	ENSG00000111602	ENST00000229201;ENST00000553532	T;T	0.12255	2.7;2.7	4.55	-1.07	0.09968	Timeless C-terminal (1);	0.467638	0.22929	N	0.053924	T	0.00012	0.0000	N	0.03967	-0.31	0.09310	P	0.999999999999715	B	0.12013	0.005	B	0.09377	0.004	T	0.20773	-1.0265	9	0.10902	T	0.67	-2.5193	9.4952	0.38984	0.0:0.5777:0.0:0.4223	rs774047;rs1063962;rs3204992;rs3816941;rs17441717;rs52816475;rs58232886;rs774047	831	Q9UNS1	TIM_HUMAN	Q	830;831	ENSP00000229201:R830Q;ENSP00000450607:R831Q	ENSP00000229201:R831Q	R	-	2	0	TIMELESS	55102189	0.759000	0.28416	0.997000	0.53966	0.731000	0.41821	-0.241000	0.08940	-0.079000	0.12707	0.555000	0.69702	CGG	C|0.576;T|0.424	0.424	strong		0.532	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
CCDC74A	90557	hgsc.bcm.edu	37	2	132289293	132289293	+	Missense_Mutation	SNP	T	T	C	rs149647165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:132289293T>C	ENST00000295171.6	+	4	739	c.601T>C	c.(601-603)Tcc>Ccc	p.S201P	CCDC74A_ENST00000467992.2_Missense_Mutation_p.S303P|CCDC74A_ENST00000409856.3_Missense_Mutation_p.S135P	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	201										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						AGCTGACGTCTCCCAGAAGGC	0.582													N|||	1396	0.278754	0.553	0.1787	5008	,	,		12784	0.3452		0.0875	False		,,,				2504	0.1074				p.S243P		Atlas-SNP	.											CCDC74A,NS,carcinoma,-2,1	CCDC74A	44	1	0			c.T727C						scavenged	.						60.0	102.0	89.0					2																	132289293		1843	4191	6034	SO:0001583	missense	90557	exon4			GACGTCTCCCAGA		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.601T>C	2.37:g.132289293T>C	ENSP00000295171:p.Ser201Pro	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	114	32	0.280702	NM_001258304	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	635	0.2907509157509158	166	0.33739837398373984	105	0.2900552486187845	255	0.4458041958041958	109	0.1437994722955145	.	0.001	-3.126559	0.00031	.	.	ENSG00000163040	ENST00000295171;ENST00000409856;ENST00000434330;ENST00000467992	T;T;T;T	0.45668	2.03;2.05;0.89;0.9	1.57	0.658	0.17855	.	0.634264	0.12332	N	0.478305	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42965	-0.9420	9	0.02654	T	1	-0.2433	4.0985	0.10002	0.0:0.5799:0.0:0.4201	.	135;201	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	P	201;135;130;303	ENSP00000295171:S201P;ENSP00000387009:S135P;ENSP00000406839:S130P;ENSP00000444610:S303P	ENSP00000295171:S201P	S	+	1	0	CCDC74A	132005763	0.000000	0.05858	0.037000	0.18230	0.168000	0.22595	-0.493000	0.06459	-0.120000	0.11809	-1.033000	0.02402	TCC	T|0.300;C|0.700	0.700	strong		0.582	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
WDR59	79726	hgsc.bcm.edu	37	16	74920191	74920191	+	Silent	SNP	G	G	A	rs14308	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:74920191G>A	ENST00000262144.6	-	24	2653	c.2523C>T	c.(2521-2523)cgC>cgT	p.R841R		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	841										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CATGCTGGTCGCGTTCTCGCT	0.537													G|||	493	0.0984425	0.143	0.111	5008	,	,		17683	0.001		0.167	False		,,,				2504	0.0593				p.R841R		Atlas-SNP	.											.	WDR59	66	.	0			c.C2523T						PASS	.	G		655,3741	279.9+/-275.1	50,555,1593	131.0	124.0	126.0		2523	-10.6	0.2	16	dbSNP_52	126	1412,7188	273.1+/-290.5	118,1176,3006	no	coding-synonymous	WDR59	NM_030581.3		168,1731,4599	AA,AG,GG		16.4186,14.8999,15.9049		841/975	74920191	2067,10929	2198	4300	6498	SO:0001819	synonymous_variant	79726	exon24			CTGGTCGCGTTCT	AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"""WD repeat domain containing"""	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.2523C>T	16.37:g.74920191G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Silent	SNP	ENST00000262144.6	37	CCDS32488.1																																																																																			G|0.853;A|0.147	0.147	strong		0.537	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581	
CHD5	26038	hgsc.bcm.edu	37	1	6196869	6196869	+	Silent	SNP	A	A	G	rs2250358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:6196869A>G	ENST00000262450.3	-	16	2592	c.2493T>C	c.(2491-2493)atT>atC	p.I831I	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TGGCCTGGTCAATGGTGATGA	0.587													G|||	2593	0.517772	0.3366	0.4697	5008	,	,		18356	0.7996		0.3946	False		,,,				2504	0.6329				p.I831I		Atlas-SNP	.											.	CHD5	267	.	0			c.T2493C						PASS	.	G		1509,2897	675.5+/-403.1	249,1011,943	72.0	71.0	72.0		2493	1.1	1.0	1	dbSNP_100	72	3563,5037	628.8+/-398.2	733,2097,1470	no	coding-synonymous	CHD5	NM_015557.2		982,3108,2413	GG,GA,AA		41.4302,34.2488,38.9974		831/1955	6196869	5072,7934	2203	4300	6503	SO:0001819	synonymous_variant	26038	exon16			CTGGTCAATGGTG	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2493T>C	1.37:g.6196869A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			A|0.550;G|0.450	0.450	strong		0.587	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
TLR1	7096	hgsc.bcm.edu	37	4	38799493	38799493	+	Silent	SNP	A	A	G	rs200631178		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38799493A>G	ENST00000502213.2	-	3	1189	c.960T>C	c.(958-960)taT>taC	p.Y320Y	TLR1_ENST00000308979.2_Silent_p.Y320Y			Q15399	TLR1_HUMAN	toll-like receptor 1	320					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						AAAAGATTTCATAGATATAAC	0.413																																					p.Y320Y	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.T960C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	58.0	61.0	60.0		960	-4.8	0.0	4		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TLR1	NM_003263.3		0,2,6501	GG,GA,AA		0.0116,0.0227,0.0154		320/787	38799493	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			GATTTCATAGATA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.960T>C	4.37:g.38799493A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	37	CCDS33973.1																																																																																			A|0.999;G|0.001	0.001	weak		0.413	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
CACNA1A	773	hgsc.bcm.edu	37	19	13387904	13387904	+	Silent	SNP	A	A	G	rs16030	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:13387904A>G	ENST00000360228.5	-	23	3860	c.3861T>C	c.(3859-3861)ttT>ttC	p.F1287F	CACNA1A_ENST00000573710.2_Silent_p.F1288F	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1288					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TCTCAAAGGTAAAGACGCCTG	0.463											OREG0025295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	835	0.166733	0.0938	0.2147	5008	,	,		19438	0.0923		0.2475	False		,,,				2504	0.2249				p.F1288F		Atlas-SNP	.											.	CACNA1A	715	.	0			c.T3864C						PASS	.	A	,,,,	329,3505		9,311,1597	107.0	97.0	100.0		3873,3864,3861,3864,3873	1.1	1.0	19	dbSNP_54	100	1792,6458		188,1416,2521	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	197,1727,4118	GG,GA,AA		21.7212,8.5811,17.5521	,,,,	1291/2267,1288/2262,1287/2507,1288/2264,1291/2513	13387904	2121,9963	1917	4125	6042	SO:0001819	synonymous_variant	773	exon23			AAAGGTAAAGACG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3861T>C	19.37:g.13387904A>G		Somatic	58	0	0	687	WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			A|0.841;G|0.159	0.159	strong		0.463	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
GPANK1	7918	hgsc.bcm.edu	37	6	31632134	31632134	+	Missense_Mutation	SNP	C	C	A	rs3130618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31632134C>A	ENST00000375906.1	-	3	806	c.122G>T	c.(121-123)cGa>cTa	p.R41L	GPANK1_ENST00000375900.4_Missense_Mutation_p.R41L|GPANK1_ENST00000375893.2_Missense_Mutation_p.R41L|CSNK2B_ENST00000375865.2_5'Flank|Y_RNA_ENST00000364337.1_RNA|GPANK1_ENST00000375896.4_Missense_Mutation_p.R41L|CSNK2B_ENST00000375885.4_5'Flank|GPANK1_ENST00000375895.2_Missense_Mutation_p.R41L|CSNK2B_ENST00000375866.2_5'Flank|CSNK2B-LY6G5B-1181_ENST00000375880.2_5'Flank|CSNK2B_ENST00000375882.2_5'Flank	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	41			R -> L (in dbSNP:rs3130618). {ECO:0000269|PubMed:14574404}.				nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						ATAGAAAGCTCGGGCTGCAGC	0.582													C|||	668	0.133387	0.2126	0.0793	5008	,	,		16816	0.0714		0.1461	False		,,,				2504	0.1155				p.R41L		Atlas-SNP	.											GPANK1,colon,carcinoma,0,1	GPANK1	19	1	0			c.G122T	GRCh37	CM062443	GPANK1	M	rs3130618	PASS	.	C	LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG	881,3525	341.5+/-306.7	85,711,1407	45.0	50.0	48.0		122,122,122,122,122	5.2	1.0	6	dbSNP_103	48	1541,7059	288.9+/-299.0	146,1249,2905	yes	missense,missense,missense,missense,missense	GPANK1	NM_001199237.1,NM_001199238.1,NM_001199239.1,NM_001199240.1,NM_033177.3	102,102,102,102,102	231,1960,4312	AA,AC,CC		17.9186,19.9955,18.6222	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	41/357,41/357,41/357,41/357,41/357	31632134	2422,10584	2203	4300	6503	SO:0001583	missense	7918	exon3			AAAGCTCGGGCTG		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.122G>T	6.37:g.31632134C>A	ENSP00000365071:p.Arg41Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	137	54	0.394161	NM_001199238	A6NG25|B0UXA2|Q5SQ49	Missense_Mutation	SNP	ENST00000375906.1	37	CCDS4711.1	285	0.1304945054945055	112	0.22764227642276422	30	0.08287292817679558	33	0.057692307692307696	110	0.14511873350923482	C	16.43	3.121880	0.56613	0.199955	0.179186	ENSG00000204438	ENST00000375906;ENST00000375896;ENST00000375893;ENST00000375895;ENST00000375900;ENST00000440842;ENST00000458083;ENST00000445768;ENST00000432291;ENST00000456540	T;T;T;T;T;T;T;T	0.61392	2.66;2.66;2.66;2.66;2.66;0.79;0.82;0.11	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.59609	0.2206	L	0.34521	1.04	0.09310	P	0.999999151211	D	0.89917	1.0	D	0.85130	0.997	T	0.63225	-0.6685	9	0.51188	T	0.08	-0.4689	16.1888	0.81972	0.0:1.0:0.0:0.0	rs3130618;rs34603477;rs59584303;rs3130618	41	O95872	GPAN1_HUMAN	L	41	ENSP00000365071:R41L;ENSP00000365060:R41L;ENSP00000365057:R41L;ENSP00000365059:R41L;ENSP00000365065:R41L;ENSP00000395307:R41L;ENSP00000409349:R41L;ENSP00000395484:R41L	ENSP00000365057:R41L	R	-	2	0	GPANK1	31740113	0.989000	0.36119	0.996000	0.52242	0.994000	0.84299	3.194000	0.51005	2.415000	0.81967	0.561000	0.74099	CGA	C|0.839;A|0.161	0.161	strong		0.582	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177	
HIVEP3	59269	hgsc.bcm.edu	37	1	42045747	42045747	+	Silent	SNP	T	T	C	rs35730380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:42045747T>C	ENST00000372583.1	-	4	5607	c.4722A>G	c.(4720-4722)tcA>tcG	p.S1574S	HIVEP3_ENST00000372584.1_Silent_p.S1574S|HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000247584.5_Silent_p.S1574S|HIVEP3_ENST00000429157.2_Silent_p.S1574S	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1574					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				AGGACGTTTCTGACAGAGGCA	0.537													T|||	229	0.0457268	0.0083	0.1124	5008	,	,		20084	0.003		0.0398	False		,,,				2504	0.0992				p.S1574S		Atlas-SNP	.											.	HIVEP3	235	.	0			c.A4722G						PASS	.	T	,	85,4321	72.5+/-110.5	0,85,2118	131.0	119.0	123.0		4722,4722	4.3	1.0	1	dbSNP_126	123	471,8129	138.4+/-195.2	11,449,3840	no	coding-synonymous,coding-synonymous	HIVEP3	NM_001127714.2,NM_024503.4	,	11,534,5958	CC,CT,TT		5.4767,1.9292,4.275	,	1574/2406,1574/2407	42045747	556,12450	2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			CGTTTCTGACAGA	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.4722A>G	1.37:g.42045747T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																			T|0.958;C|0.042	0.042	strong		0.537	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
COL11A1	1301	hgsc.bcm.edu	37	1	103354428	103354428	+	Silent	SNP	A	A	G	rs1763347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:103354428A>G	ENST00000370096.3	-	60	4824	c.4512T>C	c.(4510-4512)ggT>ggC	p.G1504G	COL11A1_ENST00000358392.2_Silent_p.G1516G|COL11A1_ENST00000353414.4_Silent_p.G1465G|COL11A1_ENST00000512756.1_Silent_p.G1388G	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1504	Collagen-like 8.|Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTACTGGTAAACCTGGAGGAC	0.393													G|||	3118	0.622604	0.2587	0.8401	5008	,	,		17143	0.746		0.8042	False		,,,				2504	0.6462				p.G1516G		Atlas-SNP	.											COL11A1_ENST00000370096,NS,carcinoma,0,2	COL11A1	972	2	0			c.T4548C						PASS	.	G	,,,	1409,2997	680.0+/-403.8	237,935,1031	91.0	99.0	96.0		4395,4512,4548,4164	0.3	1.0	1	dbSNP_89	96	6693,1907	337.8+/-322.5	2608,1477,215	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL11A1	NM_001190709.1,NM_001854.3,NM_080629.2,NM_080630.3	,,,	2845,2412,1246	GG,GA,AA		22.1744,31.9791,37.7057	,,,	1465/1768,1504/1807,1516/1819,1388/1691	103354428	8102,4904	2203	4300	6503	SO:0001819	synonymous_variant	1301	exon60			TGGTAAACCTGGA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.4512T>C	1.37:g.103354428A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	37	CCDS778.1																																																																																			A|0.365;G|0.635	0.635	strong		0.393	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557487	32557487	+	Silent	SNP	G	G	A	rs34396110		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32557487G>A	ENST00000360004.5	-	1	138	c.33C>T	c.(31-33)tgC>tgT	p.C11C		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	11					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCGCTGTCATGCAGGAGCCTC	0.577										Multiple Myeloma(14;0.17)																											p.C11C		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,-2,1	HLA-DRB1	41	1	0			c.C33T						scavenged	.						86.0	104.0	97.0					6																	32557487		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon1			TGTCATGCAGGAG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.33C>T	6.37:g.32557487G>A		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	413	4	0.00968523	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.993;A|0.007	0.007	weak		0.577	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
FBXL16	146330	hgsc.bcm.edu	37	16	746914	746914	+	Silent	SNP	G	G	A	rs4984915	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:746914G>A	ENST00000397621.1	-	2	823	c.492C>T	c.(490-492)gcC>gcT	p.A164A	FBXL16_ENST00000562563.1_5'Flank|FBXL16_ENST00000324361.5_Silent_p.A164A|FBXL16_ENST00000562585.1_5'Flank	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	164										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				AGCCTCTGGCGGCAAAACCCT	0.587													G|||	1919	0.383187	0.208	0.3833	5008	,	,		8377	0.7123		0.2535	False		,,,				2504	0.4141				p.A164A		Atlas-SNP	.											FBXL16,NS,carcinoma,0,1	FBXL16	25	1	0			c.C492T						PASS	.	G		837,3563	328.0+/-300.3	86,665,1449	80.0	71.0	74.0		492	-8.3	0.0	16	dbSNP_111	74	1906,6692	337.4+/-322.3	205,1496,2598	no	coding-synonymous	FBXL16	NM_153350.3		291,2161,4047	AA,AG,GG		22.1679,19.0227,21.1032		164/480	746914	2743,10255	2200	4299	6499	SO:0001819	synonymous_variant	146330	exon2			TCTGGCGGCAAAA	BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"""F-boxes / Leucine-rich repeats"""	14150	protein-coding gene	gene with protein product		609082	"""chromosome 16 open reading frame 22"""	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.492C>T	16.37:g.746914G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_153350	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Silent	SNP	ENST00000397621.1	37	CCDS10421.1																																																																																			G|0.718;A|0.282	0.282	strong		0.587	FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350	
SLIT3	6586	hgsc.bcm.edu	37	5	168175324	168175324	+	Silent	SNP	G	G	T	rs17634681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:168175324G>T	ENST00000519560.1	-	20	2672	c.2253C>A	c.(2251-2253)ccC>ccA	p.P751P	SLIT3_ENST00000404867.3_Silent_p.P751P|SLIT3_ENST00000332966.8_Silent_p.P751P	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	751	LRRNT 4.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCACATCCTTGGGCATGCCTC	0.617													G|||	124	0.0247604	0.0038	0.0403	5008	,	,		18810	0.001		0.0706	False		,,,				2504	0.0194				p.P751P	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C2253A						PASS	.			62,4344	58.7+/-95.3	0,62,2141	109.0	110.0	110.0		2253	4.4	1.0	5	dbSNP_123	110	602,7998	156.6+/-210.4	19,564,3717	no	coding-synonymous	SLIT3	NM_003062.2		19,626,5858	TT,TG,GG		7.0,1.4072,5.1053		751/1524	168175324	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	6586	exon20			ATCCTTGGGCATG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2253C>A	5.37:g.168175324G>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	102	64	0.627451	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			G|0.957;T|0.043	0.043	strong		0.617	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
EMILIN2	84034	hgsc.bcm.edu	37	18	2891847	2891847	+	Silent	SNP	C	C	T	rs3826638	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:2891847C>T	ENST00000254528.3	+	4	1881	c.1722C>T	c.(1720-1722)cgC>cgT	p.R574R		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	574					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GGGAAGACCGCGCAGTACGCG	0.483													C|||	734	0.146565	0.0817	0.3012	5008	,	,		20747	0.2103		0.1382	False		,,,				2504	0.0675				p.R574R		Atlas-SNP	.											.	EMILIN2	97	.	0			c.C1722T						PASS	.	C		410,3996	200.4+/-223.7	20,370,1813	68.0	63.0	65.0		1722	-0.7	0.0	18	dbSNP_107	65	1254,7346	250.1+/-277.1	104,1046,3150	no	coding-synonymous	EMILIN2	NM_032048.2		124,1416,4963	TT,TC,CC		14.5814,9.3055,12.7941		574/1054	2891847	1664,11342	2203	4300	6503	SO:0001819	synonymous_variant	84034	exon4			AGACCGCGCAGTA	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"""EMI domain containing"""	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1722C>T	18.37:g.2891847C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	37	CCDS11828.1																																																																																			C|0.860;T|0.140	0.140	strong		0.483	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048	
CUBN	8029	hgsc.bcm.edu	37	10	17113563	17113563	+	Silent	SNP	C	C	T	rs1801225	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:17113563C>T	ENST00000377833.4	-	19	2552	c.2487G>A	c.(2485-2487)tcG>tcA	p.S829S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	829	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAAAAAAAGGCGAGCGAATGA	0.408													c|||	1783	0.35603	0.0552	0.4827	5008	,	,		13947	0.5407		0.3966	False		,,,				2504	0.4407				p.S829S		Atlas-SNP	.											.	CUBN	515	.	0			c.G2487A						PASS	.	T		477,3929	223.9+/-240.3	24,429,1750	70.0	72.0	72.0		2487	-10.9	0.0	10	dbSNP_89	72	3889,4711	543.6+/-384.4	871,2147,1282	no	coding-synonymous	CUBN	NM_001081.3		895,2576,3032	TT,TC,CC		45.2209,10.8261,33.5691		829/3624	17113563	4366,8640	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon19			AAAAGGCGAGCGA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2487G>A	10.37:g.17113563C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	31	10	0.322581	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			C|0.657;T|0.343	0.343	strong		0.408	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
CTDSP1	58190	hgsc.bcm.edu	37	2	219266423	219266423	+	Silent	SNP	C	C	A	rs2227251	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219266423C>A	ENST00000273062.2	+	2	540	c.204C>A	c.(202-204)ggC>ggA	p.G68G	CTDSP1_ENST00000443891.1_Silent_p.G68G|MIR26B_ENST00000362251.2_RNA|CTDSP1_ENST00000488627.1_3'UTR|RP11-378A13.2_ENST00000608367.1_RNA	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	68					negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|protein dephosphorylation (GO:0006470)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGAGAATGGCGCCATCCCTA	0.662													C|||	844	0.16853	0.0734	0.232	5008	,	,		15186	0.0714		0.2753	False		,,,				2504	0.2423				p.G68G		Atlas-SNP	.											.	CTDSP1	19	.	0			c.C204A						PASS	.	C	,,,	412,3994	194.0+/-219.0	27,358,1818	23.0	22.0	22.0		204,,204,204	-10.2	0.0	2	dbSNP_96	22	2335,6265	362.5+/-332.8	312,1711,2277	no	coding-synonymous,utr-5,coding-synonymous,coding-synonymous	CTDSP1	NM_001206878.1,NM_001206879.1,NM_021198.2,NM_182642.2	,,,	339,2069,4095	AA,AC,CC		27.1512,9.3509,21.121	,,,	68/261,,68/262,68/261	219266423	2747,10259	2203	4300	6503	SO:0001819	synonymous_variant	58190	exon2			GAATGGCGCCATC	AF229162	CCDS2416.1, CCDS56166.1	2q35	2010-06-21			ENSG00000144579	ENSG00000144579		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	21614	protein-coding gene	gene with protein product	"""nuclear LIM interactor-interacting factor"", ""small CTD phosphatase 1"""	605323				11950066, 12721286	Standard	NM_021198		Approved	NLIIF, SCP1	uc021vwv.1	Q9GZU7	OTTHUMG00000133109	ENST00000273062.2:c.204C>A	2.37:g.219266423C>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	148	70	0.472973	NM_001206878	C9IYG0|Q7Z5Q3|Q7Z5Q4	Silent	SNP	ENST00000273062.2	37	CCDS2416.1	372	0.17032967032967034	40	0.08130081300813008	84	0.23204419889502761	53	0.09265734265734266	195	0.25725593667546176	C	7.987	0.752419	0.15778	0.093509	0.271512	ENSG00000144579	ENST00000452977;ENST00000428361;ENST00000431127	.	.	.	5.08	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.05386	-1.0888	3	.	.	.	-29.3308	6.4941	0.22132	0.0692:0.2202:0.1145:0.5961	rs2227251;rs17850988;rs2227251	.	.	.	E	54;70;138	.	.	A	+	2	0	CTDSP1	218974667	0.000000	0.05858	0.006000	0.13384	0.840000	0.47671	-1.017000	0.03630	-3.228000	0.00210	-1.910000	0.00522	GCG	C|0.811;A|0.189	0.189	strong		0.662	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	NM_182642, NM_021198	
PSMA7	5688	hgsc.bcm.edu	37	20	60713311	60713311	+	Silent	SNP	G	G	A	rs7076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60713311G>A	ENST00000370873.4	-	5	633	c.507C>T	c.(505-507)cgC>cgT	p.R169R	PSMA7_ENST00000484488.1_5'UTR|PSMA7_ENST00000370861.1_Silent_p.R99R	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	169					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			CCAGGAACTCGCGCACTGACT	0.507													G|||	2996	0.598243	0.143	0.7392	5008	,	,		23907	0.7738		0.8032	False		,,,				2504	0.7219				p.R169R		Atlas-SNP	.											.	PSMA7	13	.	0			c.C507T						PASS	.	G		1121,3285		162,797,1244	178.0	123.0	142.0		507	-1.7	0.9	20	dbSNP_52	142	6854,1746		2747,1360,193	no	coding-synonymous	PSMA7	NM_002792.2		2909,2157,1437	AA,AG,GG		20.3023,25.4426,38.6821		169/249	60713311	7975,5031	2203	4300	6503	SO:0001819	synonymous_variant	5688	exon5			GAACTCGCGCACT	AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"""Proteasome (prosome, macropain) subunits"""	9536	protein-coding gene	gene with protein product	"""proteasome subunit XAPC7"", ""proteasome subunit RC6-1"""	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.507C>T	20.37:g.60713311G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	140	138	0.985714	NM_002792	B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Silent	SNP	ENST00000370873.4	37	CCDS13489.1	1429	0.6543040293040293	81	0.16463414634146342	276	0.7624309392265194	455	0.7954545454545454	617	0.8139841688654353	.	1.999	-0.429897	0.04701	0.254426	0.796977	ENSG00000101182	ENST00000442551	.	.	.	5.12	-1.69	0.08186	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25502	-1.0130	3	.	.	.	.	6.494	0.22132	0.5381:0.1241:0.3378:0.0	rs7076;rs1058341;rs3171398;rs6089329;rs17849854	.	.	.	V	95	.	.	A	-	2	0	PSMA7	60146706	0.112000	0.22096	0.946000	0.38457	0.151000	0.21798	-0.355000	0.07671	-0.567000	0.06046	-1.008000	0.02478	GCG	G|0.369;A|0.631	0.631	strong		0.507	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792	
MAGED2	10916	hgsc.bcm.edu	37	X	54836361	54836361	+	Silent	SNP	A	A	G	rs1043031	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:54836361A>G	ENST00000375068.1	+	3	485	c.252A>G	c.(250-252)tcA>tcG	p.S84S	MAGED2_ENST00000497484.1_3'UTR|MAGED2_ENST00000375062.4_Silent_p.S46S|MAGED2_ENST00000347546.4_Silent_p.S66S|MAGED2_ENST00000218439.4_Silent_p.S84S|MAGED2_ENST00000396224.1_Silent_p.S84S|MAGED2_ENST00000375060.1_Silent_p.S46S|MAGED2_ENST00000375053.2_Silent_p.S84S|MAGED2_ENST00000375058.1_Silent_p.S84S			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	84						membrane (GO:0016020)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						CCCAGGCCTCATCTACTACTC	0.547													A|||	1548	0.410066	0.2398	0.2911	3775	,	,		13239	0.4534		0.2992	False		,,,				2504	0.2771				p.S84S		Atlas-SNP	.											.	MAGED2	74	.	0			c.A252G						PASS	.	A	,,	1090,2745		119,687,165,826,406	21.0	19.0	19.0		252,252,252	0.5	0.0	X	dbSNP_86	19	2267,4457		252,1097,666,1078,1204	no	coding-synonymous,coding-synonymous,coding-synonymous	MAGED2	NM_014599.4,NM_177433.1,NM_201222.1	,,	371,1784,831,1904,1610	GG,GA,G,AA,A		33.7151,28.4224,31.7928	,,	84/607,84/607,84/607	54836361	3357,7202	2203	4297	6500	SO:0001819	synonymous_variant	10916	exon3			GGCCTCATCTACT	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated protein"", ""breast cancer associated gene 1"", ""melanoma-associated antigen D2"", ""hepatocellular carcinoma-associated protein HCA10"""	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.252A>G	X.37:g.54836361A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Silent	SNP	ENST00000375068.1	37	CCDS14362.1																																																																																			A|0.630;0|0.003	.	strong		0.547	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599	
APEH	327	hgsc.bcm.edu	37	3	49723167	49723167	+	IGR	SNP	T	T	G	rs9714011		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49723167T>G	ENST00000296456.5	+	0	3220				MST1_ENST00000449682.2_Splice_Site|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_Splice_Site|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		AACGTGAACCTAGGCGGAAGC	0.602																																					.		Atlas-SNP	.											MST1,NS,neuroblastoma,0,1	MST1	84	1	0			c.1251-2A>C						scavenged	.						42.0	42.0	42.0					3																	49723167		2202	4300	6502	SO:0001628	intergenic_variant	4485	exon12			TGAACCTAGGCGG	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723167T>G		Somatic	179	7	0.0391061		WXS	Illumina HiSeq	Phase_I	202	16	0.0792079	NM_020998	Q9BQ33|Q9P0Y2	Splice_Site	SNP	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	t	13.18	2.160635	0.38119	.	.	ENSG00000173531	ENST00000449682	.	.	.	5.22	4.06	0.47325	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6902	0.17825	0.1492:0.0819:0.0:0.7689	rs9714011	.	.	.	.	-1	.	.	.	-	.	.	MST1	49698171	0.995000	0.38212	0.977000	0.42913	0.071000	0.16799	2.394000	0.44450	0.825000	0.34637	-0.253000	0.11424	.	.	.	weak		0.602	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
ACACA	31	hgsc.bcm.edu	37	17	35696804	35696804	+	5'UTR	SNP	G	G	A	rs58654829	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:35696804G>A	ENST00000394406.2	-	0	124				ACACA_ENST00000353139.5_Silent_p.F15F|ACACA_ENST00000416895.1_5'UTR	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha						acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TCCACTTCCAGAAAGACCTAG	0.289													A|||	2932	0.585463	0.2625	0.5245	5008	,	,		16114	0.6915		0.8101	False		,,,				2504	0.7249				p.F15F	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.C45T						PASS	.	A	,,	1165,2397		199,767,815	85.0	71.0	75.0		45,,	4.4	1.0	17	dbSNP_129	75	6444,1660		2579,1286,187	no	coding-synonymous,utr-5,utr-5	ACACA	NM_198834.1,NM_198836.1,NM_198839.1	,,	2778,2053,1002	AA,AG,GG		20.4837,32.7063,34.7763	,,	15/2384,,	35696804	7609,4057	1781	4052	5833	SO:0001623	5_prime_UTR_variant	31	exon2			CTTCCAGAAAGAC	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.-67C>T	17.37:g.35696804G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																			A|0.687;G|0.313	0.687	strong		0.289	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
ZNF106	64397	hgsc.bcm.edu	37	15	42742435	42742435	+	Missense_Mutation	SNP	T	T	C	rs34792942	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42742435T>C	ENST00000263805.4	-	2	2292	c.1966A>G	c.(1966-1968)Atg>Gtg	p.M656V	ZNF106_ENST00000565611.1_Intron|ZNF106_ENST00000565380.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	656			M -> V (in dbSNP:rs34792942).		insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GCAGATGTCATTTGTAATTCA	0.428													T|||	290	0.0579073	0.0363	0.0533	5008	,	,		20394	0.002		0.0746	False		,,,				2504	0.1309				p.M656V		Atlas-SNP	.											.	ZFP106	117	.	0			c.A1966G						PASS	.	T	VAL/MET	176,4230	113.3+/-151.4	4,168,2031	155.0	162.0	159.0		1966	-1.5	0.3	15	dbSNP_126	159	643,7955	165.4+/-217.5	28,587,3684	yes	missense	ZFP106	NM_022473.1	21	32,755,5715	CC,CT,TT		7.4785,3.9946,6.2981	benign	656/1884	42742435	819,12185	2203	4299	6502	SO:0001583	missense	64397	exon2			ATGTCATTTGTAA	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.1966A>G	15.37:g.42742435T>C	ENSP00000263805:p.Met656Val	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	190	105	0.552632	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	92	0.04212454212454213	13	0.026422764227642278	21	0.058011049723756904	2	0.0034965034965034965	56	0.07387862796833773	T	1.828	-0.470613	0.04445	0.039946	0.074785	ENSG00000103994	ENST00000263805	T	0.30182	1.54	5.14	-1.54	0.08584	.	0.736294	0.13897	N	0.355220	T	0.00998	0.0033	N	0.17474	0.49	0.22940	N	0.998538	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.001	T	0.26677	-1.0096	10	0.12766	T	0.61	-0.6967	9.503	0.39028	0.0:0.3702:0.0:0.6298	rs34792942	439;656	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	V	656	ENSP00000263805:M656V	ENSP00000263805:M656V	M	-	1	0	ZFP106	40529727	0.263000	0.24083	0.284000	0.24805	0.414000	0.31173	0.654000	0.24918	-0.341000	0.08376	0.528000	0.53228	ATG	T|0.944;C|0.056	0.056	strong		0.428	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
SRD5A1	6715	hgsc.bcm.edu	37	5	6651970	6651970	+	Silent	SNP	A	A	G	rs3822430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:6651970A>G	ENST00000274192.5	+	2	543	c.309A>G	c.(307-309)ccA>ccG	p.P103P	SRD5A1_ENST00000537411.1_3'UTR|SRD5A1_ENST00000538824.1_Intron|SRD5A1_ENST00000504286.1_3'UTR	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	103					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)	p.P103P(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TAATTTACCCATTTCTGATGC	0.368													A|||	1451	0.289736	0.3321	0.3919	5008	,	,		13397	0.1587		0.3897	False		,,,				2504	0.1922				p.P103P		Atlas-SNP	.											SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	1	Substitution - coding silent(1)	stomach(1)	c.A309G						PASS	.	A		1441,2965	467.7+/-354.9	242,957,1004	126.0	113.0	118.0		309	-11.4	0.0	5	dbSNP_107	118	3219,5381	486.1+/-371.8	610,1999,1691	no	coding-synonymous	SRD5A1	NM_001047.2		852,2956,2695	GG,GA,AA		37.4302,32.7054,35.8296		103/260	6651970	4660,8346	2203	4300	6503	SO:0001819	synonymous_variant	6715	exon2			TTACCCATTTCTG	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.309A>G	5.37:g.6651970A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	200	79	0.395	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Silent	SNP	ENST00000274192.5	37	CCDS3870.1																																																																																			A|0.667;G|0.333	0.333	strong		0.368	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
GSAP	54103	hgsc.bcm.edu	37	7	76950699	76950699	+	Missense_Mutation	SNP	C	C	T	rs17151692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76950699C>T	ENST00000257626.7	-	25	2023	c.1945G>A	c.(1945-1947)Gta>Ata	p.V649I	GSAP_ENST00000440473.1_5'UTR|GSAP_ENST00000441833.2_Intron	NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	649			V -> I (in dbSNP:rs17151692).		positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										TTGGTTTCTACGATGTGGCAA	0.463													C|||	403	0.0804712	0.1611	0.0447	5008	,	,		21096	0.0089		0.0845	False		,,,				2504	0.0665				p.V649I		Atlas-SNP	.											.	PION	74	.	0			c.G1945A						PASS	.	C	ILE/VAL	555,3389		36,483,1453	119.0	117.0	117.0		1945	-0.9	0.1	7	dbSNP_123	117	755,7579		28,699,3440	yes	missense	PION	NM_017439.3	29	64,1182,4893	TT,TC,CC		9.0593,14.072,10.6695	benign	649/855	76950699	1310,10968	1972	4167	6139	SO:0001583	missense	54103	exon25			TTTCTACGATGTG		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.1945G>A	7.37:g.76950699C>T	ENSP00000257626:p.Val649Ile	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	175	81	0.462857	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	37	CCDS34672.2	185	0.08470695970695971	88	0.17886178861788618	23	0.06353591160220995	6	0.01048951048951049	68	0.08970976253298153	C	7.281	0.609096	0.14066	0.14072	0.090593	ENSG00000186088	ENST00000257626;ENST00000415112	T;T	0.30182	1.54;1.54	5.56	-0.929	0.10444	.	0.537583	0.18979	N	0.125926	T	0.00039	0.0001	N	0.14661	0.345	0.21897	P	0.999484972	B	0.19445	0.036	B	0.09377	0.004	T	0.20009	-1.0288	9	0.54805	T	0.06	.	4.3285	0.11051	0.07:0.3403:0.2441:0.3456	rs17151692;rs56813531;rs17151692	649	A4D1B5	GSAP_HUMAN	I	649;102	ENSP00000257626:V649I;ENSP00000396230:V102I	ENSP00000257626:V649I	V	-	1	0	PION	76788635	0.208000	0.23494	0.059000	0.19551	0.047000	0.14425	-0.038000	0.12144	-0.084000	0.12595	-0.891000	0.02926	GTA	C|0.907;T|0.093	0.093	strong		0.463	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
LMTK2	22853	hgsc.bcm.edu	37	7	97822210	97822210	+	Silent	SNP	G	G	A	rs3801294	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:97822210G>A	ENST00000297293.5	+	11	2726	c.2433G>A	c.(2431-2433)ccG>ccA	p.P811P		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	811					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					AGTCTTCCCCGGAAGTGCAGG	0.537													G|||	1121	0.223842	0.0356	0.3156	5008	,	,		19064	0.1528		0.5119	False		,,,				2504	0.1902				p.P811P		Atlas-SNP	.											.	LMTK2	228	.	0			c.G2433A						PASS	.	G		551,3855	247.2+/-255.5	34,483,1686	94.0	99.0	97.0		2433	-10.8	0.0	7	dbSNP_107	97	4709,3891	607.7+/-395.3	1299,2111,890	no	coding-synonymous	LMTK2	NM_014916.3		1333,2594,2576	AA,AG,GG		45.2442,12.5057,40.4429		811/1504	97822210	5260,7746	2203	4300	6503	SO:0001819	synonymous_variant	22853	exon11			TTCCCCGGAAGTG	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.2433G>A	7.37:g.97822210G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_014916	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	37	CCDS5654.1																																																																																			G|0.650;A|0.350	0.350	strong		0.537	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
FAM129C	199786	hgsc.bcm.edu	37	19	17641667	17641667	+	Silent	SNP	G	G	A	rs74336438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17641667G>A	ENST00000335393.4	+	3	390	c.252G>A	c.(250-252)ccG>ccA	p.P84P	FAM129C_ENST00000600871.1_Intron|FAM129C_ENST00000300971.2_Silent_p.P84P|FAM129C_ENST00000599124.1_Silent_p.P53P|FAM129C_ENST00000597887.1_Intron|FAM129C_ENST00000332386.5_Silent_p.P84P|FAM129C_ENST00000601861.1_Silent_p.P53P|FAM129C_ENST00000599164.1_Silent_p.P53P|FAM129C_ENST00000449408.2_Intron|FAM129C_ENST00000595684.1_Silent_p.P84P|FAM129C_ENST00000352727.3_Silent_p.P84P	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	84										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						CTCAGGAGCCGACCGGAAGCC	0.632													G|||	292	0.0583067	0.0787	0.0403	5008	,	,		15633	0.0298		0.0378	False		,,,				2504	0.0941				p.P84P		Atlas-SNP	.											.	FAM129C	110	.	0			c.G252A						PASS	.	G	,	326,4080	173.4+/-203.2	9,308,1886	60.0	57.0	58.0		252,252	-9.2	0.0	19	dbSNP_132	58	424,8176	131.7+/-189.4	8,408,3884	no	coding-synonymous,coding-synonymous	FAM129C	NM_001098524.1,NM_173544.4	,	17,716,5770	AA,AG,GG		4.9302,7.399,5.7666	,	84/652,84/698	17641667	750,12256	2203	4300	6503	SO:0001819	synonymous_variant	199786	exon3			GGAGCCGACCGGA	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.252G>A	19.37:g.17641667G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																			G|0.948;A|0.052	0.052	strong		0.632	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
FAT2	2196	hgsc.bcm.edu	37	5	150945699	150945699	+	Silent	SNP	G	G	A	rs10085060	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150945699G>A	ENST00000261800.5	-	1	2806	c.2794C>T	c.(2794-2796)Ctg>Ttg	p.L932L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	932	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGAACCTTCAGCCTGTTGTGT	0.547													G|||	2102	0.419728	0.441	0.4539	5008	,	,		20695	0.3571		0.4901	False		,,,				2504	0.3589				p.L932L		Atlas-SNP	.											.	FAT2	465	.	0			c.C2794T						PASS	.	G		1959,2447	553.0+/-378.7	422,1115,666	60.0	52.0	55.0		2794	3.6	1.0	5	dbSNP_119	55	4499,4101	591.6+/-392.9	1184,2131,985	no	coding-synonymous	FAT2	NM_001447.2		1606,3246,1651	AA,AG,GG		47.686,44.4621,49.654		932/4350	150945699	6458,6548	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			CCTTCAGCCTGTT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2794C>T	5.37:g.150945699G>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	267	70	0.262172	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.529;A|0.471	0.471	strong		0.547	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
KDSR	2531	hgsc.bcm.edu	37	18	61022791	61022791	+	Silent	SNP	C	C	T	rs2003149	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:61022791C>T	ENST00000406396.3	-	4	652	c.261G>A	c.(259-261)gtG>gtA	p.V87V	KDSR_ENST00000326575.5_Silent_p.V87V	NM_002035.2	NP_002026.1	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase	87					3-keto-sphinganine metabolic process (GO:0006666)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-dehydrosphinganine reductase activity (GO:0047560)	p.V87V(1)		endometrium(2)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	9						ATATGCAAAGCACCACCTGTT	0.318													C|||	2789	0.556909	0.438	0.6628	5008	,	,		18665	0.4335		0.6481	False		,,,				2504	0.6759				p.V87V		Atlas-SNP	.											KDSR,NS,carcinoma,0,1	KDSR	17	1	1	Substitution - coding silent(1)	stomach(1)	c.G261A						PASS	.	C		2176,2230	582.9+/-385.7	535,1106,562	108.0	101.0	104.0		261	2.7	1.0	18	dbSNP_92	104	5652,2948	667.0+/-402.4	1840,1972,488	no	coding-synonymous	KDSR	NM_002035.2		2375,3078,1050	TT,TC,CC		34.2791,49.3872,39.8124		87/333	61022791	7828,5178	2203	4300	6503	SO:0001819	synonymous_variant	2531	exon4			GCAAAGCACCACC		CCDS11982.1	18q21	2011-09-20	2008-02-20	2008-02-20	ENSG00000119537	ENSG00000119537	1.1.1.102	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	4021	protein-coding gene	gene with protein product	"""3-dehydrosphinganine reductase"", ""short chain dehydrogenase/reductase family 35C, member 1"""	136440	"""follicular lymphoma variant translocation 1"""	FVT1		8417785, 15328338, 17420465, 19027726	Standard	NM_002035		Approved	DHSR, SDR35C1	uc010dpw.3	Q06136	OTTHUMG00000132792	ENST00000406396.3:c.261G>A	18.37:g.61022791C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_002035	B2R5Y1|B4DMX0	Silent	SNP	ENST00000406396.3	37	CCDS11982.1																																																																																			C|0.423;T|0.577	0.577	strong		0.318	KDSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256200.2		
FFAR3	2865	hgsc.bcm.edu	37	19	35849926	35849926	+	Missense_Mutation	SNP	G	G	A	rs62109581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35849926G>A	ENST00000327809.4	+	2	335	c.134G>A	c.(133-135)cGc>cAc	p.R45H	FFAR3_ENST00000594310.1_Missense_Mutation_p.R45H	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	45			R -> C (in dbSNP:rs423385). {ECO:0000269|PubMed:19630535}.		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.R45H(1)		endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			AAGCTGCAGCGCCGCCCGGTG	0.647																																					p.R45H	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											FFAR3,NS,carcinoma,0,1	FFAR3	40	1	1	Substitution - Missense(1)	stomach(1)	c.G134A						PASS	.	G	HIS/ARG	631,3767		14,603,1582	188.0	172.0	178.0		134	0.4	0.6	19	dbSNP_131	178	1976,6614		53,1870,2372	no	missense	FFAR3	NM_005304.3	29	67,2473,3954	AA,AG,GG		23.0035,14.3474,20.0724	probably-damaging	45/347	35849926	2607,10381	2199	4295	6494	SO:0001583	missense	2865	exon2			TGCAGCGCCGCCC	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"""GPCR / Class A : Fatty acid receptors"""	4499	protein-coding gene	gene with protein product		603821	"""G protein-coupled receptor 41"""	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.134G>A	19.37:g.35849926G>A	ENSP00000328230:p.Arg45His	Somatic	535	0	0		WXS	Illumina HiSeq	Phase_I	827	293	0.354293	NM_005304	B2RWM8|Q14CM7	Missense_Mutation	SNP	ENST00000327809.4	37	CCDS12459.1	404	0.184981684981685	58	0.11788617886178862	62	0.1712707182320442	119	0.20804195804195805	165	0.21767810026385223	G	11.81	1.750715	0.31046	0.143474	0.230035	ENSG00000185897	ENST00000327809	T	0.39406	1.08	4.99	0.408	0.16377	GPCR, rhodopsin-like superfamily (1);	0.283555	0.33610	U	0.004728	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.6000000000016E-5	B	0.32425	0.371	B	0.28553	0.091	T	0.28902	-1.0029	9	0.45353	T	0.12	-13.598	4.4639	0.11680	0.3446:0.1552:0.5002:0.0	.	45	O14843	FFAR3_HUMAN	H	45	ENSP00000328230:R45H	ENSP00000328230:R45H	R	+	2	0	FFAR3	40541766	0.000000	0.05858	0.608000	0.28969	0.840000	0.47671	-0.177000	0.09796	0.033000	0.15463	0.455000	0.32223	CGC	G|0.800;A|0.200	0.200	strong		0.647	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304	
NACA	4666	hgsc.bcm.edu	37	12	57109931	57109931	+	Missense_Mutation	SNP	A	A	T	rs2926747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57109931A>T	ENST00000454682.1	-	3	5664	c.5383T>A	c.(5383-5385)Tcc>Acc	p.S1795T	NACA_ENST00000552540.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.S642T|NACA_ENST00000548563.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000551793.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1795	Pro-rich.		S -> T (in dbSNP:rs2926747). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						ACTGGTGGGGAGGGTGCTGCA	0.567			T	BCL6	NHL								T|||	3248	0.648562	0.4826	0.6744	5008	,	,		18231	0.7421		0.6262	False		,,,				2504	0.7812				p.S642T		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.T1924A						PASS	.	T	,,THR/SER,	1633,1503		429,775,364	43.0	41.0	41.0		,,1924,	2.5	0.0	12	dbSNP_101	41	4453,2711		1392,1669,521	yes	intron,intron,missense,intron	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,58,	1821,2444,885	TT,TA,AA		37.842,47.9273,40.9126	,,benign,	,,642/926,	57109931	6086,4214	1568	3582	5150	SO:0001583	missense	4666	exon5			GTGGGGAGGGTGC	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.5383T>A	12.37:g.57109931A>T	ENSP00000403817:p.Ser1795Thr	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	193	182	0.943005	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		1392	0.6373626373626373	248	0.5040650406504065	252	0.6961325966850829	426	0.7447552447552448	466	0.6147757255936676	T	0.563	-0.844356	0.02671	0.520727	0.62158	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.41400	1.0;1.02	3.77	2.55	0.30701	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27806	-1.0063	8	0.26408	T	0.33	.	4.1621	0.10289	0.1778:0.1045:0.0:0.7177	rs2926747;rs3782231;rs59687646	1795;642	E9PAV3;F8VU71	.;.	T	1795;642	ENSP00000403817:S1795T;ENSP00000448035:S642T	ENSP00000403817:S1795T	S	-	1	0	NACA	55396198	0.000000	0.05858	0.043000	0.18650	0.174000	0.22865	-0.595000	0.05727	0.051000	0.15978	-0.514000	0.04452	TCC	A|0.363;T|0.637	0.637	strong		0.567	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
TMX4	56255	hgsc.bcm.edu	37	20	7967980	7967980	+	Silent	SNP	G	G	C	rs17425725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:7967980G>C	ENST00000246024.2	-	6	785	c.570C>G	c.(568-570)gtC>gtG	p.V190V	TMX4_ENST00000530935.1_5'UTR	NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	190					cell redox homeostasis (GO:0045454)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(2)|lung(11)|skin(1)	17						TGACGAAAAAGACATAAGAAC	0.328													G|||	348	0.0694888	0.0023	0.0706	5008	,	,		16113	0.0437		0.1461	False		,,,				2504	0.1074				p.V190V		Atlas-SNP	.											.	TMX4	39	.	0			c.C570G						PASS	.	G		149,4257	100.7+/-139.4	5,139,2059	77.0	76.0	76.0		570	3.1	0.7	20	dbSNP_123	76	1319,7281	257.5+/-281.5	103,1113,3084	no	coding-synonymous	TMX4	NM_021156.2		108,1252,5143	CC,CG,GG		15.3372,3.3818,11.2871		190/350	7967980	1468,11538	2203	4300	6503	SO:0001819	synonymous_variant	56255	exon6			GAAAAAGACATAA		CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827		"""Protein disulfide isomerases"""	25237	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 14"""		"""thioredoxin domain containing 13"""	TXNDC13			Standard	NM_021156		Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.570C>G	20.37:g.7967980G>C		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Silent	SNP	ENST00000246024.2	37	CCDS13101.1																																																																																			G|0.895;C|0.105	0.105	strong		0.328	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156	
NRAP	4892	hgsc.bcm.edu	37	10	115370274	115370274	+	Missense_Mutation	SNP	T	T	C	rs10749138	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115370274T>C	ENST00000359988.3	-	31	3791	c.3547A>G	c.(3547-3549)Att>Gtt	p.I1183V	NRAP_ENST00000369360.3_Missense_Mutation_p.I1156V|NRAP_ENST00000360478.3_Missense_Mutation_p.I1148V|NRAP_ENST00000369358.4_Missense_Mutation_p.I1191V	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GTGCCTGGAATGACACATGCA	0.433													T|||	2318	0.462859	0.3321	0.4669	5008	,	,		17368	0.5992		0.4652	False		,,,				2504	0.4939				p.I1183V		Atlas-SNP	.											NRAP,head_neck,carcinoma,0,1	NRAP	208	1	0			c.A3547G						PASS	.	T	VAL/ILE,VAL/ILE	1472,2934	475.2+/-357.2	261,950,992	178.0	151.0	160.0		3442,3547	0.6	1.0	10	dbSNP_120	160	4163,4437	567.5+/-388.9	1002,2159,1139	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	29,29	1263,3109,2131	CC,CT,TT		48.407,33.409,43.3262	benign,benign	1148/1696,1183/1731	115370274	5635,7371	2203	4300	6503	SO:0001583	missense	4892	exon31			CTGGAATGACACA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3547A>G	10.37:g.115370274T>C	ENSP00000353078:p.Ile1183Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	981	0.4491758241758242	149	0.30284552845528456	173	0.47790055248618785	325	0.5681818181818182	334	0.44063324538258575	T	7.807	0.714817	0.15306	0.33409	0.48407	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.15256	2.64;2.66;2.52;2.44	5.85	0.626	0.17670	.	0.409872	0.29438	N	0.012143	T	0.00012	0.0000	N	0.16790	0.44	0.48395	P	3.6000000000002697E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45745	-0.9240	9	0.02654	T	1	.	9.7306	0.40359	0.0:0.335:0.0:0.665	rs10749138;rs52826105;rs57988639;rs10749138	1148;1183	Q86VF7-4;Q86VF7	.;NRAP_HUMAN	V	1191;1156;1183;1148	ENSP00000358365:I1191V;ENSP00000358367:I1156V;ENSP00000353078:I1183V;ENSP00000353666:I1148V	ENSP00000353078:I1183V	I	-	1	0	NRAP	115360264	0.993000	0.37304	0.996000	0.52242	0.264000	0.26372	0.173000	0.16724	-0.123000	0.11745	0.528000	0.53228	ATT	T|0.556;C|0.444	0.444	strong		0.433	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
FYCO1	79443	hgsc.bcm.edu	37	3	46008087	46008087	+	Silent	SNP	G	G	A	rs13079869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46008087G>A	ENST00000296137.2	-	8	2944	c.2739C>T	c.(2737-2739)tgC>tgT	p.C913C	FYCO1_ENST00000535325.1_Silent_p.C913C	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	913					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CGGTCAGTGCGCAAACCTGGA	0.632													G|||	529	0.105631	0.0076	0.0605	5008	,	,		20768	0.004		0.1223	False		,,,				2504	0.3579				p.C913C		Atlas-SNP	.											.	FYCO1	115	.	0			c.C2739T						PASS	.	G		109,4297	83.9+/-122.4	0,109,2094	50.0	47.0	48.0		2739	-5.3	0.0	3	dbSNP_121	48	947,7653	205.8+/-248.1	48,851,3401	no	coding-synonymous	FYCO1	NM_024513.2		48,960,5495	AA,AG,GG		11.0116,2.4739,8.1193		913/1479	46008087	1056,11950	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			CAGTGCGCAAACC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.2739C>T	3.37:g.46008087G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	226	122	0.539823	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			G|0.920;A|0.080	0.080	strong		0.632	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
CHRNA2	1135	hgsc.bcm.edu	37	8	27328511	27328511	+	Missense_Mutation	SNP	G	G	A	rs2472553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27328511G>A	ENST00000520933.2	-	1	218	c.65C>T	c.(64-66)aCc>aTc	p.T22I	CHRNA2_ENST00000240132.2_Missense_Mutation_p.T22I|CHRNA2_ENST00000407991.1_Missense_Mutation_p.T22I			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	22			T -> I (in dbSNP:rs2472553).		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	ACCTGCTGGGGTCAGAAGGAG	0.542													G|||	1107	0.221046	0.1921	0.1945	5008	,	,		20986	0.4325		0.1372	False		,,,				2504	0.1472				p.T22I		Atlas-SNP	.											.	CHRNA2	48	.	0			c.C65T						PASS	.	G	ILE/THR	810,3596	322.9+/-297.8	75,660,1468	78.0	69.0	72.0		65	-2.5	0.0	8	dbSNP_100	72	1125,7475	232.1+/-265.8	78,969,3253	yes	missense	CHRNA2	NM_000742.3	89	153,1629,4721	AA,AG,GG		13.0814,18.384,14.8777	benign	22/530	27328511	1935,11071	2203	4300	6503	SO:0001583	missense	1135	exon2			GCTGGGGTCAGAA	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.65C>T	8.37:g.27328511G>A	ENSP00000429616:p.Thr22Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	155	73	0.470968	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	550	0.2518315018315018	93	0.18902439024390244	69	0.19060773480662985	291	0.5087412587412588	97	0.1279683377308707	G	0	-2.672280	0.00104	0.18384	0.130814	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132;ENST00000524096;ENST00000518712;ENST00000521921	T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51	4.42	-2.5	0.06384	.	3.327300	0.00649	N	0.000552	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36744	-0.9735	9	0.02654	T	1	.	5.1178	0.14845	0.4675:0.1607:0.3719:0.0	rs2472553;rs57302661;rs2472553	22;22	B4DK19;Q15822	.;ACHA2_HUMAN	I	22	ENSP00000385026:T22I;ENSP00000429616:T22I;ENSP00000240132:T22I;ENSP00000430422:T22I;ENSP00000430856:T22I;ENSP00000429953:T22I	ENSP00000240132:T22I	T	-	2	0	CHRNA2	27384428	0.793000	0.28825	0.004000	0.12327	0.072000	0.16883	0.305000	0.19254	-0.388000	0.07797	-0.794000	0.03295	ACC	G|0.819;A|0.181	0.181	strong		0.542	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
MYO3A	53904	hgsc.bcm.edu	37	10	26357748	26357748	+	Missense_Mutation	SNP	G	G	A	rs3817420|rs386742102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:26357748G>A	ENST00000265944.5	+	12	1271	c.1105G>A	c.(1105-1107)Gtc>Atc	p.V369I	MYO3A_ENST00000543632.1_Missense_Mutation_p.V369I	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	369	Myosin motor.		V -> I (in dbSNP:rs3817420). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TCAGATCTACGTCTATGTGGG	0.373													A|||	3350	0.66893	0.7133	0.6369	5008	,	,		17383	0.6181		0.7227	False		,,,				2504	0.6288				p.V369I		Atlas-SNP	.											.	MYO3A	371	.	0			c.G1105A						PASS	.	A	ILE/VAL	3004,1402		1075,854,274	140.0	122.0	128.0		1105	3.2	0.6	10	dbSNP_107	128	5668,2932		2035,1598,667	yes	missense	MYO3A	NM_017433.4	29	3110,2452,941	AA,AG,GG		34.093,31.8202,33.3231	benign	369/1617	26357748	8672,4334	2203	4300	6503	SO:0001583	missense	53904	exon12			ATCTACGTCTATG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1105G>A	10.37:g.26357748G>A	ENSP00000265944:p.Val369Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	30	0.340909	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	1353	0.6195054945054945	319	0.6483739837398373	217	0.5994475138121547	338	0.5909090909090909	479	0.6319261213720316	A	12.64	1.999339	0.35226	0.681798	0.65907	ENSG00000095777	ENST00000265944;ENST00000543632	T;D	0.87179	-0.59;-2.22	5.55	3.19	0.36642	Myosin head, motor domain (3);	0.148197	0.64402	N	0.000014	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.48547	-0.9026	9	0.35671	T	0.21	.	6.1439	0.20275	0.7469:0.0:0.1329:0.1202	rs3817420;rs61242953	369;369	F5H0U9;Q8NEV4	.;MYO3A_HUMAN	I	369	ENSP00000265944:V369I;ENSP00000445909:V369I	ENSP00000265944:V369I	V	+	1	0	MYO3A	26397754	1.000000	0.71417	0.616000	0.29078	0.921000	0.55340	4.224000	0.58593	0.068000	0.16574	-0.254000	0.11334	GTC	G|0.322;A|0.678	0.678	strong		0.373	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
REV3L	5980	hgsc.bcm.edu	37	6	111696852	111696852	+	Silent	SNP	T	T	C	rs458486	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:111696852T>C	ENST00000358835.3	-	14	3160	c.2706A>G	c.(2704-2706)ggA>ggG	p.G902G	REV3L_ENST00000368805.1_Silent_p.G902G|REV3L_ENST00000368802.3_Silent_p.G902G|REV3L_ENST00000435970.1_Silent_p.G824G			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	902					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TTTCTAACGTTCCATCTCCAA	0.378								DNA polymerases (catalytic subunits)					T|||	1774	0.354233	0.0461	0.4337	5008	,	,		16140	0.4187		0.497	False		,,,				2504	0.501				p.G902G		Atlas-SNP	.											.	REV3L	386	.	0			c.A2706G						PASS	.	T		563,3843	242.5+/-252.5	58,447,1698	97.0	98.0	98.0		2706	3.2	0.8	6	dbSNP_80	98	4567,4031	594.5+/-393.3	1216,2135,948	no	coding-synonymous	REV3L	NM_002912.3		1274,2582,2646	CC,CT,TT		46.883,12.778,39.4494		902/3131	111696852	5130,7874	2203	4299	6502	SO:0001819	synonymous_variant	5980	exon13			TAACGTTCCATCT	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.2706A>G	6.37:g.111696852T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			T|0.619;C|0.381	0.381	strong		0.378	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
SKOR1	390598	hgsc.bcm.edu	37	15	68124665	68124665	+	Silent	SNP	C	C	A	rs72751453	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:68124665C>A	ENST00000380035.2	+	6	2699	c.2641C>A	c.(2641-2643)Cgg>Agg	p.R881R	RP11-34F13.3_ENST00000558889.1_RNA|SKOR1_ENST00000554240.1_Silent_p.R842R|SKOR1_ENST00000554054.1_Silent_p.R853R|RP11-34F13.2_ENST00000502156.1_lincRNA|SKOR1_ENST00000389002.1_Silent_p.R837R|SKOR1_ENST00000341418.5_Silent_p.R784R			P84550	SKOR1_HUMAN	SKI family transcriptional corepressor 1	881					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(7)|urinary_tract(1)	23						GAAGCTGGAACGGGAATTTCA	0.552											OREG0023215	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	874	0.174521	0.1157	0.2291	5008	,	,		14590	0.003		0.3986	False		,,,				2504	0.1616				p.R784R		Atlas-SNP	.											.	SKOR1	144	.	0			c.C2350A						PASS	.	C		660,3740	280.5+/-275.4	51,558,1591	122.0	120.0	121.0		2509	4.4	1.0	15	dbSNP_130	121	3757,4839	534.5+/-382.6	828,2101,1369	no	coding-synonymous	SKOR1	NM_001031807.1		879,2659,2960	AA,AC,CC		43.7064,15.0,33.9874		837/922	68124665	4417,8579	2200	4298	6498	SO:0001819	synonymous_variant	390598	exon12			CTGGAACGGGAAT		CCDS58374.1	15q23	2011-08-04	2010-06-23	2010-06-23	ENSG00000188779	ENSG00000188779		"""SKI transcriptional corepressors"""	21326	protein-coding gene	gene with protein product	"""transcriptional corepressor CORL1"", ""functional smad suppressing element 15"", ""corepressor for LBX1"""	611273	"""Lbxcor1 homolog (mouse)"""	LBXCOR1		15528197	Standard	NM_001258024		Approved	CORL1, FUSSEL15	uc031qsn.1	P84550		ENST00000380035.2:c.2641C>A	15.37:g.68124665C>A		Somatic	121	0	0	1104	WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_001258024	A6NIP4|A6NJY0|Q2VWA5	Silent	SNP	ENST00000380035.2	37																																																																																				C|0.702;A|0.298	0.298	strong		0.552	SKOR1-003	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000410832.1	NM_001031807	
ZNF496	84838	hgsc.bcm.edu	37	1	247473018	247473018	+	Missense_Mutation	SNP	G	G	A	rs149858668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247473018G>A	ENST00000294753.4	-	7	1339	c.875C>T	c.(874-876)cCc>cTc	p.P292L	ZNF496_ENST00000366498.2_Missense_Mutation_p.P328L|ZNF496_ENST00000462139.1_5'UTR	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	292					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			GGAGACCTGGGGCACTTCTTT	0.572													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		17285	0.0		0.0	False		,,,				2504	0.0				p.P292L		Atlas-SNP	.											.	ZNF496	80	.	0			c.C875T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	86.0	76.0	80.0		875	4.7	0.9	1	dbSNP_134	80	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZNF496	NM_032752.1	98	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	benign	292/588	247473018	6,13000	2203	4300	6503	SO:0001583	missense	84838	exon7			ACCTGGGGCACTT	BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.875C>T	1.37:g.247473018G>A	ENSP00000294753:p.Pro292Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_032752	Q8TBS2	Missense_Mutation	SNP	ENST00000294753.4	37	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184918	0.38609	0.0	6.98E-4	ENSG00000162714	ENST00000294753;ENST00000366498	T;T	0.07800	3.18;3.16	4.7	4.7	0.59300	.	0.508746	0.16561	N	0.209034	T	0.07098	0.0180	N	0.24115	0.695	0.46260	D	0.998956	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.30707	-0.9969	10	0.33940	T	0.23	-9.6614	13.5458	0.61702	0.0:0.0:1.0:0.0	.	328;292	Q96IT1-2;Q96IT1	.;ZN496_HUMAN	L	292;328	ENSP00000294753:P292L;ENSP00000355454:P328L	ENSP00000294753:P292L	P	-	2	0	ZNF496	245539641	0.976000	0.34144	0.911000	0.35937	0.925000	0.55904	1.892000	0.39748	2.341000	0.79615	0.561000	0.74099	CCC	G|0.999;A|0.001	0.001	strong		0.572	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752	
THSD7A	221981	hgsc.bcm.edu	37	7	11509561	11509561	+	Missense_Mutation	SNP	G	G	C	rs2285744	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:11509561G>C	ENST00000423059.4	-	9	2564	c.2313C>G	c.(2311-2313)gaC>gaG	p.D771E	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	771	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.		D -> E (in dbSNP:rs2285744).		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TCACAATACAGTCCTTCTTAC	0.448										HNSCC(18;0.044)			G|||	1396	0.278754	0.1195	0.2435	5008	,	,		17089	0.2252		0.4125	False		,,,				2504	0.4366				p.D771E		Atlas-SNP	.											.	THSD7A	219	.	0			c.C2313G						PASS	.	G	GLU/ASP	604,3212		60,484,1364	64.0	56.0	59.0		2313	3.7	1.0	7	dbSNP_100	59	3576,4686		762,2052,1317	yes	missense	THSD7A	NM_015204.2	45	822,2536,2681	CC,CG,GG		43.2825,15.8281,34.6084	probably-damaging	771/1658	11509561	4180,7898	1908	4131	6039	SO:0001583	missense	221981	exon9			AATACAGTCCTTC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2313C>G	7.37:g.11509561G>C	ENSP00000406482:p.Asp771Glu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	600	0.27472527472527475	71	0.1443089430894309	102	0.281767955801105	123	0.21503496503496503	304	0.40105540897097625	G	21.5	4.156823	0.78114	0.158281	0.432825	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.20332	2.08	5.56	3.74	0.42951	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.90595	3.13	0.19775	P	0.9999597667	D	0.89917	1.0	D	0.91635	0.999	T	0.45234	-0.9275	9	0.23302	T	0.38	.	8.8978	0.35476	0.2856:0.0:0.7144:0.0	rs2285744;rs17631276;rs52802345;rs2285744	771	Q9UPZ6	THS7A_HUMAN	E	771	ENSP00000406482:D771E	ENSP00000262042:D771E	D	-	3	2	THSD7A	11476086	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.051000	0.41307	0.801000	0.34066	0.650000	0.86243	GAC	G|0.719;C|0.281	0.281	strong		0.448	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
STRA6	64220	hgsc.bcm.edu	37	15	74472525	74472525	+	Missense_Mutation	SNP	G	G	A	rs200178616		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:74472525G>A	ENST00000323940.5	-	19	2145	c.1900C>T	c.(1900-1902)Cgc>Tgc	p.R634C	STRA6_ENST00000395105.4_Missense_Mutation_p.R634C|STRA6_ENST00000574439.1_5'UTR|STRA6_ENST00000416286.3_Missense_Mutation_p.R626C|STRA6_ENST00000449139.2_Missense_Mutation_p.R634C|STRA6_ENST00000423167.2_Missense_Mutation_p.R625C|RP11-665J16.1_ENST00000561647.1_RNA|STRA6_ENST00000535552.1_Missense_Mutation_p.R671C|STRA6_ENST00000563965.1_Missense_Mutation_p.R673C|STRA6_ENST00000574278.1_Missense_Mutation_p.R649C	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	634					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						GCCCTGCCGCGGCTGGCCCCG	0.637													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.R673C		Atlas-SNP	.											STRA6,NS,carcinoma,+1,1	STRA6	66	1	0			c.C2017T						scavenged	.						91.0	104.0	100.0					15																	74472525		2198	4297	6495	SO:0001583	missense	64220	exon19			TGCCGCGGCTGGC	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"""retinol binding protein 4 receptor"""	610745	"""stimulated by retinoic acid gene 6 homolog (mouse)"", ""stimulated by retinoic acid 6 homolog (mouse)"""			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.1900C>T	15.37:g.74472525G>A	ENSP00000326085:p.Arg634Cys	Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	37	CCDS10261.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666348	0.29604	.	.	ENSG00000137868	ENST00000395105;ENST00000323940;ENST00000416286;ENST00000545137;ENST00000449139;ENST00000423167;ENST00000535552;ENST00000536129	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	4.5	2.61	0.31194	.	0.757532	0.12544	N	0.459624	D	0.86205	0.5877	L	0.48642	1.525	0.21473	N	0.999671	D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999;0.999	P;P;P;P;P;P	0.56916	0.804;0.804;0.736;0.736;0.804;0.809	T	0.75286	-0.3371	10	0.66056	D	0.02	-2.8476	8.8353	0.35109	0.1759:0.0:0.8241:0.0	.	671;672;625;634;673;443	F5GYI8;B7Z5G7;Q9BX79-3;Q9BX79;Q9BX79-4;B3KRT6	.;.;.;STRA6_HUMAN;.;.	C	634;634;566;443;673;625;671;524	ENSP00000378537:R634C;ENSP00000326085:R634C;ENSP00000413012:R625C;ENSP00000440238:R671C	ENSP00000326085:R634C	R	-	1	0	STRA6	72259578	0.075000	0.21258	0.004000	0.12327	0.013000	0.08279	2.732000	0.47352	0.351000	0.24027	-0.379000	0.06801	CGC	G|0.999;A|0.001	0.001	weak		0.637	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1		
IL6R	3570	hgsc.bcm.edu	37	1	154426970	154426970	+	Missense_Mutation	SNP	A	A	C	rs2228145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154426970A>C	ENST00000368485.3	+	9	1510	c.1073A>C	c.(1072-1074)gAt>gCt	p.D358A	IL6R_ENST00000344086.4_Intron|IL6R_ENST00000507256.1_3'UTR	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	358			D -> A (significantly associated with circulating levels of IL6 and soluble IL6R; dbSNP:rs2228145). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17357077}.		acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	CTAGTGCAAGATTCTTCTTCA	0.473													A|||	1468	0.293131	0.087	0.536	5008	,	,		19463	0.3234		0.3598	False		,,,				2504	0.2996				p.D358A		Atlas-SNP	.											.	IL6R	47	.	0			c.A1073C	GRCh37	CM034737	IL6R	M	rs2228145	PASS	.	A	ALA/ASP,	641,3765	274.0+/-271.7	46,549,1608	74.0	65.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1073,	2.8	0.7	1	dbSNP_98	68	3480,5120	508.5+/-377.1	706,2068,1526	yes	missense,intron	IL6R	NM_000565.3,NM_181359.2	126,	752,2617,3134	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	40.4651,14.5483,31.6854	benign,	358/469,	154426970	4121,8885	2203	4300	6503	SO:0001583	missense	3570	exon9			TGCAAGATTCTTC	X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.1073A>C	1.37:g.154426970A>C	ENSP00000357470:p.Asp358Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_000565	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Missense_Mutation	SNP	ENST00000368485.3	37	CCDS1067.1	698|698	0.31959706959706957|0.31959706959706957	43|43	0.08739837398373984|0.08739837398373984	175|175	0.48342541436464087|0.48342541436464087	207|207	0.3618881118881119|0.3618881118881119	273|273	0.36015831134564646|0.36015831134564646	A|A	10.96|10.96	1.499781|1.499781	0.26861|0.26861	0.145483|0.145483	0.404651|0.404651	ENSG00000160712|ENSG00000160712	ENST00000368485|ENST00000515190	T|.	0.16457|.	2.34|.	4.03|4.03	2.85|2.85	0.33270|0.33270	.|.	7.394690|.	0.00166|.	N|.	0.000000|.	T|T	0.41743|0.41743	0.1172|0.1172	M|M	0.70595|0.70595	2.14|2.14	0.21822|0.21822	P|P	0.999521233|0.999521233	B|.	0.25312|.	0.123|.	B|.	0.17979|.	0.02|.	T|T	0.35992|0.35992	-0.9766|-0.9766	9|4	0.25106|.	T|.	0.35|.	-2.254|-2.254	6.5|6.5	0.22164|0.22164	0.8858:0.0:0.1142:0.0|0.8858:0.0:0.1142:0.0	rs2228145;rs8192284;rs52837205;rs58037860;rs8192284|rs2228145;rs8192284;rs52837205;rs58037860;rs8192284	358|.	P08887|.	IL6RA_HUMAN|.	A|L	358|161	ENSP00000357470:D358A|.	ENSP00000357470:D358A|.	D|I	+|+	2|1	0|0	IL6R|IL6R	152693594|152693594	0.167000|0.167000	0.22975|0.22975	0.672000|0.672000	0.29872|0.29872	0.291000|0.291000	0.27294|0.27294	0.915000|0.915000	0.28638|0.28638	0.662000|0.662000	0.31006|0.31006	0.454000|0.454000	0.30748|0.30748	GAT|ATT	A|0.687;C|0.313;T|0.000	0.313	strong		0.473	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565	
ZC3H7A	29066	hgsc.bcm.edu	37	16	11876203	11876203	+	Missense_Mutation	SNP	T	T	C	rs1429077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11876203T>C	ENST00000396516.2	-	1	205	c.8A>G	c.(7-9)aAt>aGt	p.N3S	ZC3H7A_ENST00000575170.1_5'UTR|ZC3H7A_ENST00000355758.4_Missense_Mutation_p.N3S			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	3			N -> S (in dbSNP:rs1429077).			nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						CTCGGACACATTGGACATGTT	0.438													C|||	291	0.058107	0.0953	0.0634	5008	,	,		19921	0.0		0.0845	False		,,,				2504	0.0368				p.N3S		Atlas-SNP	.											.	ZC3H7A	72	.	0			c.A8G						PASS	.	C	SER/ASN	459,3935	782.2+/-414.5	32,395,1770	228.0	196.0	207.0		8	4.3	1.0	16	dbSNP_88	207	579,8021	792.8+/-407.5	15,549,3736	yes	missense	ZC3H7A	NM_014153.3	46	47,944,5506	CC,CT,TT		6.7326,10.4461,7.9883	benign	3/972	11876203	1038,11956	2197	4300	6497	SO:0001583	missense	29066	exon2			GACACATTGGACA	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30959	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 7"", ""zinc finger CCCH-type containing 7"""	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.8A>G	16.37:g.11876203T>C	ENSP00000379773:p.Asn3Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	37	CCDS10550.1	127	0.05815018315018315	41	0.08333333333333333	24	0.06629834254143646	0	0.0	62	0.08179419525065963	C	2.940	-0.219000	0.06101	0.104461	0.067326	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.09538	2.97;2.97	5.28	4.31	0.51392	.	0.322769	0.42294	N	0.000728	T	0.00109	0.0003	N	0.03115	-0.41	0.09310	P	0.999999999800655	B	0.02656	0.0	B	0.01281	0.0	T	0.33854	-0.9852	9	0.02654	T	1	.	7.1432	0.25568	0.0:0.6799:0.0:0.3201	rs1429077;rs52833537;rs1429077	3	Q8IWR0	Z3H7A_HUMAN	S	3	ENSP00000347999:N3S;ENSP00000379773:N3S	ENSP00000347999:N3S	N	-	2	0	ZC3H7A	11783704	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	0.430000	0.21428	1.377000	0.46286	-0.320000	0.08662	AAT	T|0.926;C|0.074	0.074	strong		0.438	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	A	G	rs537300122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38119902A>G	ENST00000406386.3	+	7	1594	c.1339A>G	c.(1339-1341)Aca>Gca	p.T447A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	447					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T447A(3)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGTAGAGCTACACGAGACAA	0.587													A|||	50	0.00998403	0.0	0.0029	5008	,	,		19561	0.0337		0.0119	False		,,,				2504	0.002				p.T447A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,4	TRIOBP	262	4	3	Substitution - Missense(3)	prostate(2)|skin(1)	c.A1339G						scavenged	.						60.0	64.0	63.0					22																	38119902		1870	4095	5965	SO:0001583	missense	11078	exon7			AGAGCTACACGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1339A>G	22.37:g.38119902A>G	ENSP00000384312:p.Thr447Ala	Somatic	333	2	0.00600601		WXS	Illumina HiSeq	Phase_I	386	20	0.0518135	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	5.040	0.193024	0.09599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19806	2.12	2.54	2.54	0.30619	.	.	.	.	.	T	0.23727	0.0574	L	0.36672	1.1	0.19945	N	0.999945	P	0.52463	0.953	P	0.53988	0.739	T	0.07558	-1.0766	9	0.30854	T	0.27	.	6.7436	0.23449	1.0:0.0:0.0:0.0	.	447	Q9H2D6	TARA_HUMAN	A	447	ENSP00000384312:T447A	ENSP00000384312:T447A	T	+	1	0	TRIOBP	36449848	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-0.062000	0.11674	1.059000	0.40554	0.113000	0.15668	ACA	.	.	none		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
DMRT2	10655	hgsc.bcm.edu	37	9	1056728	1056728	+	Missense_Mutation	SNP	G	G	C	rs3824419	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:1056728G>C	ENST00000358146.2	+	3	1141	c.1141G>C	c.(1141-1143)Gca>Cca	p.A381P	DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382251.3_Missense_Mutation_p.A381P|DMRT2_ENST00000302441.6_Missense_Mutation_p.A381P			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	381			A -> P (in dbSNP:rs3824419). {ECO:0000269|PubMed:15489334}.		embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		CTTGAAGGGAGCACGAGTCCA	0.577													G|||	1736	0.346645	0.1528	0.4222	5008	,	,		19498	0.4762		0.3489	False		,,,				2504	0.4192				p.A381P		Atlas-SNP	.											DMRT2_ENST00000302441,NS,carcinoma,0,2	DMRT2	70	2	0			c.G1141C						scavenged	.	G	,,PRO/ALA	823,3583	328.0+/-300.3	83,657,1463	90.0	86.0	88.0		,,1141	-1.6	0.0	9	dbSNP_107	88	2956,5644	459.2+/-364.8	521,1914,1865	yes	utr-3,utr-3,missense	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,27	604,2571,3328	CC,CG,GG		34.3721,18.6791,29.0558	,,benign	,,381/562	1056728	3779,9227	2203	4300	6503	SO:0001583	missense	10655	exon4			AAGGGAGCACGAG	AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"""terra-like protein"""	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.1141G>C	9.37:g.1056728G>C	ENSP00000350865:p.Ala381Pro	Somatic	52	1	0.0192308		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	751	0.34386446886446886	60	0.12195121951219512	139	0.3839779005524862	284	0.4965034965034965	268	0.35356200527704484	G	6.760	0.509175	0.12883	0.186791	0.343721	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.23754	1.89;1.89;1.89	5.78	-1.62	0.08372	.	0.746171	0.13395	N	0.391098	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.31730	0.337	B	0.25759	0.063	T	0.46176	-0.9210	9	0.33141	T	0.24	0.1605	1.5529	0.02578	0.4335:0.1001:0.275:0.1914	rs3824419;rs17722173;rs60311434;rs3824419	381	Q9Y5R5	DMRT2_HUMAN	P	381	ENSP00000371686:A381P;ENSP00000305785:A381P;ENSP00000350865:A381P	ENSP00000305785:A381P	A	+	1	0	DMRT2	1046728	0.004000	0.15560	0.003000	0.11579	0.472000	0.32918	0.457000	0.21875	-0.150000	0.11195	-0.156000	0.13503	GCA	G|0.685;C|0.315	0.315	strong		0.577	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
CNDP2	55748	hgsc.bcm.edu	37	18	72176083	72176083	+	Missense_Mutation	SNP	T	T	C	rs2278161	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72176083T>C	ENST00000324262.4	+	5	692	c.376T>C	c.(376-378)Tat>Cat	p.Y126H	CNDP2_ENST00000324301.8_Intron|CNDP2_ENST00000579847.1_Missense_Mutation_p.Y126H	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	126			Y -> H (in dbSNP:rs2278161). {ECO:0000269|Ref.2}.		cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.Y126H(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		AGGCAAGCTGTATGGGAGAGG	0.522													T|||	1081	0.215855	0.0802	0.3156	5008	,	,		18577	0.3006		0.1899	False		,,,				2504	0.2679				p.Y126H		Atlas-SNP	.											CNDP2,NS,carcinoma,0,1	CNDP2	55	1	1	Substitution - Missense(1)	stomach(1)	c.T376C						PASS	.	T	,HIS/TYR	521,3885	239.0+/-250.2	41,439,1723	83.0	76.0	78.0		,376	5.6	0.9	18	dbSNP_100	78	1919,6681	340.5+/-323.6	190,1539,2571	yes	intron,missense	CNDP2	NM_001168499.1,NM_018235.2	,83	231,1978,4294	CC,CT,TT		22.314,11.8248,18.7606	,probably-damaging	,126/476	72176083	2440,10566	2203	4300	6503	SO:0001583	missense	55748	exon5			AAGCTGTATGGGA	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.376T>C	18.37:g.72176083T>C	ENSP00000325548:p.Tyr126His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	37	CCDS12006.1	435	0.19917582417582416	37	0.07520325203252033	95	0.26243093922651933	170	0.2972027972027972	133	0.17546174142480211	T	13.04	2.119143	0.37436	0.118248	0.22314	ENSG00000133313	ENST00000324262	T	0.53640	0.61	5.57	5.57	0.84162	.	0.055379	0.85682	D	0.000000	T	0.00012	0.0000	H	0.97516	4.02	0.09310	P	1.0	P;P	0.36065	0.535;0.535	P;P	0.55545	0.778;0.778	T	0.01420	-1.1359	9	0.72032	D	0.01	-29.6742	15.7428	0.77914	0.0:0.0:0.0:1.0	rs2278161;rs11539408;rs17816172;rs52835248;rs60808093;rs2278161	114;126	B4DV28;Q96KP4	.;CNDP2_HUMAN	H	126	ENSP00000325548:Y126H	ENSP00000325548:Y126H	Y	+	1	0	CNDP2	70327063	1.000000	0.71417	0.950000	0.38849	0.459000	0.32528	7.629000	0.83207	2.114000	0.64651	0.533000	0.62120	TAT	T|0.801;C|0.198	0.198	strong		0.522	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
IGFN1	91156	hgsc.bcm.edu	37	1	201184275	201184275	+	Silent	SNP	C	C	T	rs2275673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201184275C>T	ENST00000335211.4	+	14	9118	c.8988C>T	c.(8986-8988)acC>acT	p.T2996T	IGFN1_ENST00000451870.2_Silent_p.T539T|IGFN1_ENST00000295591.8_Silent_p.T156T	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	539						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CCACCCTGACCGTCCAGGGTA	0.582													T|||	1652	0.329872	0.2383	0.3314	5008	,	,		19691	0.3452		0.3509	False		,,,				2504	0.4151				p.T2996T		Atlas-SNP	.											.	IGFN1	220	.	0			c.C8988T						PASS	.	T		1176,3230	710.0+/-407.8	148,880,1175	56.0	45.0	49.0		8988	-6.3	0.0	1	dbSNP_100	49	2885,5715	670.8+/-402.8	495,1895,1910	no	coding-synonymous	IGFN1	NM_001164586.1		643,2775,3085	TT,TC,CC		33.5465,26.6909,31.2241		2996/3709	201184275	4061,8945	2203	4300	6503	SO:0001819	synonymous_variant	91156	exon14			CCTGACCGTCCAG	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.8988C>T	1.37:g.201184275C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	255	253	0.992157	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	728	0.3333333333333333	129	0.2621951219512195	116	0.32044198895027626	216	0.3776223776223776	267	0.35224274406332456	T	6.988	0.552422	0.13374	0.266909	0.335465	ENSG00000163395	ENST00000412892	.	.	.	4.65	-6.29	0.02013	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.12502	-1.0545	3	.	.	.	.	10.8458	0.46743	0.0948:0.2532:0.0:0.652	rs2275673;rs59363565;rs2275673	.	.	.	C	414	.	.	R	+	1	0	IGFN1	199450898	0.000000	0.05858	0.001000	0.08648	0.201000	0.24016	-1.251000	0.02882	-2.397000	0.00581	-3.288000	0.00047	CGT	C|0.683;T|0.317	0.317	strong		0.582	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
C6orf15	29113	hgsc.bcm.edu	37	6	31079310	31079310	+	Missense_Mutation	SNP	T	T	G	rs560168888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31079310T>G	ENST00000259870.3	-	2	829	c.826A>C	c.(826-828)Aat>Cat	p.N276H		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	276	Gly-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GGATACCGATTAATATTCCCC	0.502													T|||	2	0.000399361	0.0008	0.0	5008	,	,		16631	0.0		0.0	False		,,,				2504	0.001				p.N276H		Atlas-SNP	.											.	C6orf15	29	.	0			c.A826C						PASS	.						67.0	76.0	73.0					6																	31079310		1743	3414	5157	SO:0001583	missense	29113	exon2			ACCGATTAATATT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.826A>C	6.37:g.31079310T>G	ENSP00000259870:p.Asn276His	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	137	9	0.0656934	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.378711	0.42207	.	.	ENSG00000204542	ENST00000259870	T	0.06687	3.27	4.19	1.66	0.24008	.	0.372474	0.19119	U	0.122222	T	0.07143	0.0181	L	0.54323	1.7	0.09310	N	1	D	0.76494	0.999	D	0.65684	0.937	T	0.15954	-1.0419	10	0.45353	T	0.12	-12.0482	3.1014	0.06327	0.3753:0.1067:0.0:0.518	.	276	Q6UXA7	CF015_HUMAN	H	276	ENSP00000259870:N276H	ENSP00000259870:N276H	N	-	1	0	C6orf15	31187289	0.000000	0.05858	0.012000	0.15200	0.265000	0.26407	-0.001000	0.12947	0.149000	0.19098	0.372000	0.22366	AAT	.	.	none		0.502	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
DTX3L	151636	hgsc.bcm.edu	37	3	122290579	122290579	+	Silent	SNP	C	C	T	rs2036342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122290579C>T	ENST00000296161.4	+	5	2397	c.2208C>T	c.(2206-2208)gcC>gcT	p.A736A	DTX3L_ENST00000383661.3_Silent_p.A224A	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	736					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		AGCTGAAAGCCAAAGGAATTG	0.368													C|||	1720	0.34345	0.2731	0.2622	5008	,	,		19773	0.4355		0.3211	False		,,,				2504	0.4243				p.A736A		Atlas-SNP	.											.	DTX3L	59	.	0			c.C2208T						PASS	.	C		1296,3110	437.6+/-345.0	181,934,1088	103.0	97.0	99.0		2208	-10.5	0.0	3	dbSNP_94	99	2699,5901	430.0+/-356.4	439,1821,2040	no	coding-synonymous	DTX3L	NM_138287.3		620,2755,3128	TT,TC,CC		31.3837,29.4144,30.7166		736/741	122290579	3995,9011	2203	4300	6503	SO:0001819	synonymous_variant	151636	exon5			GAAAGCCAAAGGA		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"""RING-type (C3HC4) zinc fingers"""	30323	protein-coding gene	gene with protein product	"""rhysin 2"""	613143	"""deltex 3-like (Drosophila)"""			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.2208C>T	3.37:g.122290579C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Silent	SNP	ENST00000296161.4	37	CCDS3015.1																																																																																			C|0.681;T|0.319	0.319	strong		0.368	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287	
MUC16	94025	hgsc.bcm.edu	37	19	9063678	9063678	+	Missense_Mutation	SNP	T	T	G	rs2547064	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9063678T>G	ENST00000397910.4	-	3	23971	c.23768A>C	c.(23767-23769)gAc>gCc	p.D7923A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7925	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.D7923A(2)|p.D3556A(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCTTGACGTGTCCAAAGTACT	0.458													T|||	1052	0.210064	0.0628	0.2003	5008	,	,		22937	0.249		0.3101	False		,,,				2504	0.273				p.D7923A		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,3	MUC16	4315	3	3	Substitution - Missense(3)	stomach(3)	c.A23768C						PASS	.		ALA/ASP	422,3676		23,376,1650	256.0	235.0	242.0		23768	0.1	0.0	19	dbSNP_100	242	2422,5990		344,1734,2128	yes	missense	MUC16	NM_024690.2	126	367,2110,3778	GG,GT,TT		28.7922,10.2977,22.7338	benign	7923/14508	9063678	2844,9666	2049	4206	6255	SO:0001583	missense	94025	exon3			GACGTGTCCAAAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.23768A>C	19.37:g.9063678T>G	ENSP00000381008:p.Asp7923Ala	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	286	123	0.43007	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	486	0.22252747252747251	47	0.09552845528455285	85	0.23480662983425415	122	0.21328671328671328	232	0.30606860158311344	t	2.485	-0.318782	0.05386	0.102977	0.287922	ENSG00000181143	ENST00000397910	T	0.21191	2.02	2.34	0.103	0.14526	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B	0.27997	0.197	B	0.23574	0.047	T	0.42275	-0.9461	7	0.87932	D	0	.	4.6397	0.12543	0.0:0.3267:0.0:0.6733	rs2547064;rs60568941;rs2547064	7923	B5ME49	.	A	7923	ENSP00000381008:D7923A	ENSP00000381008:D7923A	D	-	2	0	MUC16	8924678	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.154000	0.01285	-0.045000	0.13468	-1.750000	0.00680	GAC	T|0.788;G|0.212	0.212	strong		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
RSPH4A	345895	hgsc.bcm.edu	37	6	116950734	116950734	+	Missense_Mutation	SNP	G	G	A	rs6927567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116950734G>A	ENST00000229554.5	+	4	1804	c.1667G>A	c.(1666-1668)cGc>cAc	p.R556H	RSPH4A_ENST00000368581.4_Intron|RSPH4A_ENST00000368580.4_Missense_Mutation_p.R309H	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	556	Glu-rich.		R -> H (in dbSNP:rs6927567).		axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TCCCAGGGTCGCTGTAATTGG	0.378									Kartagener syndrome				G|||	1026	0.204872	0.1089	0.2089	5008	,	,		17994	0.2857		0.2157	False		,,,				2504	0.2372				p.R556H		Atlas-SNP	.											.	RSPH4A	54	.	0			c.G1667A						PASS	.	G	HIS/ARG,	529,3877	240.3+/-251.1	30,469,1704	80.0	80.0	80.0		1667,	5.2	1.0	6	dbSNP_116	80	1679,6921	309.7+/-309.5	167,1345,2788	yes	missense,intron	RSPH4A	NM_001010892.2,NM_001161664.1	29,	197,1814,4492	AA,AG,GG		19.5233,12.0064,16.9768	probably-damaging,	556/717,	116950734	2208,10798	2203	4300	6503	SO:0001583	missense	345895	exon4	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGGTCGCTGTAA		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"""radial spokehead-like 3"""	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.1667G>A	6.37:g.116950734G>A	ENSP00000229554:p.Arg556His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_001010892	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	464	0.21245421245421245	56	0.11382113821138211	72	0.19889502762430938	166	0.2902097902097902	170	0.22427440633245382	G	20.7	4.027171	0.75390	0.120064	0.195233	ENSG00000111834	ENST00000229554;ENST00000447842;ENST00000368580	T;T	0.38077	1.16;1.16	6.06	5.2	0.72013	.	0.146244	0.64402	N	0.000005	T	0.33030	0.0849	M	0.91768	3.24	0.09310	P	1.0	P	0.43024	0.798	B	0.36608	0.229	T	0.53781	-0.8390	9	0.56958	D	0.05	-4.1885	13.1277	0.59364	0.0768:0.0:0.9232:0.0	rs6927567;rs61322119;rs6927567	556	Q5TD94	RSH4A_HUMAN	H	556;351;309	ENSP00000229554:R556H;ENSP00000357569:R309H	ENSP00000229554:R556H	R	+	2	0	RSPH4A	117057427	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	5.660000	0.68018	1.582000	0.49881	0.650000	0.86243	CGC	G|0.812;A|0.188	0.188	strong		0.378	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	
THBS2	7058	hgsc.bcm.edu	37	6	169632219	169632219	+	Silent	SNP	G	G	A	rs35935937	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:169632219G>A	ENST00000366787.3	-	14	2256	c.2007C>T	c.(2005-2007)ggC>ggT	p.G669G	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	669	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.G669G(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGCTGAAGTGGCCCAGGTAGA	0.632													G|||	960	0.191693	0.1218	0.2161	5008	,	,		16580	0.2679		0.17	False		,,,				2504	0.2127				p.G669G	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	1	1	Substitution - coding silent(1)	stomach(1)	c.C2007T						PASS	.	G		538,3868	241.2+/-251.7	41,456,1706	205.0	177.0	187.0		2007	-0.2	1.0	6	dbSNP_126	187	1347,7253	263.1+/-284.8	124,1099,3077	no	coding-synonymous	THBS2	NM_003247.2		165,1555,4783	AA,AG,GG		15.6628,12.2106,14.4933		669/1173	169632219	1885,11121	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon14			GAAGTGGCCCAGG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2007C>T	6.37:g.169632219G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|0.839;C|0.000;A|0.161	0.161	strong		0.632	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
RET	5979	hgsc.bcm.edu	37	10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	rs1799939	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43610119G>A	ENST00000355710.3	+	11	2303	c.2071G>A	c.(2071-2073)Ggt>Agt	p.G691S	RET_ENST00000340058.5_Missense_Mutation_p.G691S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	691			G -> S (in dbSNP:rs1799939). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9223675, ECO:0000269|PubMed:9497256}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTCCTCTTCCGGTGCCCGCCG	0.647		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				G|||	847	0.169129	0.0923	0.2565	5008	,	,		18422	0.121		0.1889	False		,,,				2504	0.2403				p.G691S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	RET_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	0			c.G2071A	GRCh37	CM023821	RET	M	rs1799939	PASS	.	G	SER/GLY,SER/GLY	455,3951	216.4+/-235.1	19,417,1767	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2071,2071	-1.1	0.0	10	dbSNP_89	57	1587,7013	295.7+/-302.5	155,1277,2868	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	174,1694,4635	AA,AG,GG		18.4535,10.3268,15.7004	possibly-damaging,possibly-damaging	691/1073,691/1115	43610119	2042,10964	2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TCTTCCGGTGCCC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2071G>A	10.37:g.43610119G>A	ENSP00000347942:p.Gly691Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	338	0.15476190476190477	45	0.09146341463414634	82	0.2265193370165746	60	0.1048951048951049	151	0.19920844327176782	G	8.525	0.869582	0.17322	0.103268	0.184535	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.78246	-1.05;-1.16	4.75	-1.08	0.09936	.	0.349618	0.34603	N	0.003826	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.24426	0.062;0.062;0.103	B;B;B	0.16722	0.004;0.007;0.016	T	0.04128	-1.0975	9	0.07990	T	0.79	.	9.2584	0.37597	0.7374:0.0:0.2626:0.0	rs1799939;rs3781260;rs17362555;rs17845010;rs17857772;rs1799939	437;691;691	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	691	ENSP00000347942:G691S;ENSP00000344798:G691S	ENSP00000344798:G691S	G	+	1	0	RET	42930125	1.000000	0.71417	0.000000	0.03702	0.411000	0.31082	4.395000	0.59678	-0.060000	0.13132	0.462000	0.41574	GGT	G|0.839;A|0.161	0.161	strong		0.647	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
CRB2	286204	hgsc.bcm.edu	37	9	126125327	126125327	+	Missense_Mutation	SNP	G	G	A	rs138381817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126125327G>A	ENST00000373631.3	+	2	279	c.278G>A	c.(277-279)cGc>cAc	p.R93H	CRB2_ENST00000359999.3_Missense_Mutation_p.R93H	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	93	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						ACCGGCTTCCGCTGCTACTGC	0.692													G|||	15	0.00299521	0.0	0.0101	5008	,	,		14806	0.0		0.008	False		,,,				2504	0.0				p.R93H		Atlas-SNP	.											.	CRB2	86	.	0			c.G278A						PASS	.	G	HIS/ARG	8,4398		0,8,2195	40.0	39.0	39.0		278	2.7	1.0	9	dbSNP_134	39	102,8494		2,98,4198	yes	missense	CRB2	NM_173689.5	29	2,106,6393	AA,AG,GG		1.1866,0.1816,0.846	probably-damaging	93/1286	126125327	110,12892	2203	4298	6501	SO:0001583	missense	286204	exon2			GCTTCCGCTGCTA	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.278G>A	9.37:g.126125327G>A	ENSP00000362734:p.Arg93His	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	37	CCDS6852.2	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	14.66	2.601296	0.46423	0.001816	0.011866	ENSG00000148204	ENST00000359999;ENST00000373631	T;T	0.61274	0.12;0.12	4.7	2.69	0.31865	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.172979	0.27841	N	0.017634	T	0.28366	0.0701	L	0.31664	0.95	0.80722	D	1	B;B	0.28971	0.013;0.229	B;B	0.21360	0.004;0.034	T	0.24440	-1.0160	10	0.51188	T	0.08	.	2.6651	0.05041	0.104:0.1689:0.5289:0.1981	.	93;93	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	H	93	ENSP00000353092:R93H;ENSP00000362734:R93H	ENSP00000353092:R93H	R	+	2	0	CRB2	125165148	0.035000	0.19736	1.000000	0.80357	0.834000	0.47266	0.452000	0.21795	1.214000	0.43395	0.448000	0.29417	CGC	G|0.993;A|0.007	0.007	strong		0.692	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
PARP4	143	hgsc.bcm.edu	37	13	25075864	25075864	+	Missense_Mutation	SNP	T	T	C	rs35200240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25075864T>C	ENST00000381989.3	-	3	346	c.241A>G	c.(241-243)Atc>Gtc	p.I81V		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	81	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.		I -> V (in dbSNP:rs35200240).		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TTTTCCCTGATAGATTTCCAT	0.393													.|||	62	0.0123802	0.0023	0.0115	5008	,	,		16444	0.0		0.0467	False		,,,				2504	0.0041				p.I81V		Atlas-SNP	.											.	PARP4	142	.	0			c.A241G						PASS	.	T	VAL/ILE	41,4365	46.0+/-80.4	0,41,2162	121.0	126.0	124.0		241	-4.1	0.3	13	dbSNP_126	124	379,8221	124.1+/-182.9	7,365,3928	yes	missense	PARP4	NM_006437.3	29	7,406,6090	CC,CT,TT		4.407,0.9305,3.2293	benign	81/1725	25075864	420,12586	2203	4300	6503	SO:0001583	missense	143	exon3			CCCTGATAGATTT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.241A>G	13.37:g.25075864T>C	ENSP00000371419:p.Ile81Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	117	43	0.367521	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	44	0.020146520146520148	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	38	0.05013192612137203	T	0.013	-1.644060	0.00792	0.009305	0.04407	ENSG00000102699	ENST00000381989	D	0.82081	-1.57	5.25	-4.06	0.03986	BRCT (4);	0.514144	0.18310	N	0.145128	T	0.18257	0.0438	N	0.11023	0.085	0.09310	N	1	B	0.14805	0.011	B	0.22152	0.038	T	0.45469	-0.9259	10	0.02654	T	1	-9.3495	8.1442	0.31102	0.0:0.4962:0.2873:0.2165	rs35200240	81	Q9UKK3	PARP4_HUMAN	V	81	ENSP00000371419:I81V	ENSP00000371419:I81V	I	-	1	0	PARP4	23973864	0.014000	0.17966	0.329000	0.25429	0.399000	0.30720	-1.441000	0.02409	-0.469000	0.06911	-0.290000	0.09829	ATC	T|0.972;C|0.028	0.028	strong		0.393	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
C16orf46	123775	hgsc.bcm.edu	37	16	81094951	81094951	+	Missense_Mutation	SNP	A	A	G	rs10459872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81094951A>G	ENST00000299578.5	-	4	1238	c.1003T>C	c.(1003-1005)Tac>Cac	p.Y335H	C16orf46_ENST00000378611.4_Missense_Mutation_p.Y335H|C16orf46_ENST00000444657.3_5'Flank|RP11-303E16.8_ENST00000564536.1_RNA	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	335			Y -> H (in dbSNP:rs10459872).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						TTGGATTTGTAGCTTTGCACT	0.537													A|||	524	0.104633	0.0393	0.1052	5008	,	,		18310	0.1944		0.0934	False		,,,				2504	0.1115				p.Y335H		Atlas-SNP	.											.	C16orf46	57	.	0			c.T1003C						PASS	.	A	HIS/TYR,HIS/TYR	181,4223	117.1+/-155.0	6,169,2027	135.0	130.0	132.0		1003,1003	0.3	0.4	16	dbSNP_119	132	670,7930	169.6+/-220.9	26,618,3656	yes	missense,missense	C16orf46	NM_001100873.1,NM_152337.2	83,83	32,787,5683	GG,GA,AA		7.7907,4.1099,6.5441	benign,benign	335/389,335/396	81094951	851,12153	2202	4300	6502	SO:0001583	missense	123775	exon3			ATTTGTAGCTTTG	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.1003T>C	16.37:g.81094951A>G	ENSP00000299578:p.Tyr335His	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	272	129	0.474265	NM_001100873	Q96MA7	Missense_Mutation	SNP	ENST00000299578.5	37	CCDS10932.1	243	0.11126373626373626	20	0.04065040650406504	38	0.10497237569060773	111	0.19405594405594406	74	0.09762532981530343	A	0.219	-1.029958	0.02045	0.041099	0.077907	ENSG00000166455	ENST00000378611;ENST00000444657;ENST00000299578	T;T	0.17213	2.29;2.29	5.23	0.334	0.15948	.	0.903604	0.09492	N	0.794752	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B;B	0.12013	0.005;0.005	B;B	0.14578	0.011;0.011	T	0.46062	-0.9218	9	0.15499	T	0.54	.	0.931	0.01335	0.4241:0.1573:0.267:0.1515	rs10459872;rs56607219;rs59323807;rs10459872	335;335	Q6P387-2;Q6P387	.;CP046_HUMAN	H	335;62;335	ENSP00000367874:Y335H;ENSP00000299578:Y335H	ENSP00000299578:Y335H	Y	-	1	0	C16orf46	79652452	0.013000	0.17824	0.415000	0.26534	0.010000	0.07245	0.090000	0.15025	0.393000	0.25203	-0.400000	0.06385	TAC	A|0.912;G|0.088	0.088	strong		0.537	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337	
PARP1	142	hgsc.bcm.edu	37	1	226555302	226555302	+	Missense_Mutation	SNP	A	A	G	rs1136410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:226555302A>G	ENST00000366794.5	-	17	2428	c.2285T>C	c.(2284-2286)gTg>gCg	p.V762A	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	762	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.		V -> A (in dbSNP:rs1136410). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		AAGCATTTCCACCTTGGCCTG	0.522								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					A|||	986	0.196885	0.0371	0.3516	5008	,	,		22171	0.4365		0.1541	False		,,,				2504	0.1002				p.V762A		Atlas-SNP	.											.	PARP1	100	.	0			c.T2285C	GRCh37	CM042761	PARP1	M	rs1136410	PASS	.	A	ALA/VAL	233,4173	138.8+/-174.5	10,213,1980	106.0	93.0	98.0		2285	5.6	1.0	1	dbSNP_86	98	1371,7229	267.6+/-287.4	125,1121,3054	yes	missense	PARP1	NM_001618.3	64	135,1334,5034	GG,GA,AA		15.9419,5.2882,12.3328	possibly-damaging	762/1015	226555302	1604,11402	2203	4300	6503	SO:0001583	missense	142	exon17			ATTTCCACCTTGG	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2285T>C	1.37:g.226555302A>G	ENSP00000355759:p.Val762Ala	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	37	CCDS1554.1	533	0.24404761904761904	27	0.054878048780487805	119	0.3287292817679558	261	0.4562937062937063	126	0.1662269129287599	A	20.9	4.059621	0.76074	0.052882	0.159419	ENSG00000143799	ENST00000366794	T	0.12361	2.69	5.56	5.56	0.83823	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.69358	2.11	0.09310	P	1.0	P	0.40731	0.728	P	0.53649	0.731	T	0.53995	-0.8359	9	0.33141	T	0.24	.	15.7086	0.77606	1.0:0.0:0.0:0.0	rs1136410;rs1805412;rs3199701;rs11541665;rs16845751;rs17853760;rs59953823;rs1136410	762	P09874	PARP1_HUMAN	A	762	ENSP00000355759:V762A	ENSP00000355759:V762A	V	-	2	0	PARP1	224621925	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.957000	0.93082	2.122000	0.65172	0.533000	0.62120	GTG	A|0.827;G|0.173	0.173	strong		0.522	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
MBD1	4152	hgsc.bcm.edu	37	18	47801800	47801800	+	Intron	SNP	G	G	A	rs140690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:47801800G>A	ENST00000591416.1	-	8	1224				MBD1_ENST00000269468.5_Intron|MBD1_ENST00000436910.1_Intron|MBD1_ENST00000339998.6_Intron|MBD1_ENST00000398495.2_Silent_p.R269R|MBD1_ENST00000398493.1_Intron|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000457839.2_Silent_p.R269R|MBD1_ENST00000353909.3_Intron|MBD1_ENST00000585595.1_Silent_p.R269R|MBD1_ENST00000591535.1_Intron|MBD1_ENST00000590208.1_Intron|MBD1_ENST00000347968.3_Intron|MBD1_ENST00000349085.2_Intron|MBD1_ENST00000588937.1_Intron|MBD1_ENST00000424334.2_Silent_p.R295R|MBD1_ENST00000382948.5_Intron|MBD1_ENST00000398488.1_Intron|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000269471.5_Intron			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1						negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						GGCGACGCAGGCGGTGAGCAA	0.622													G|||	1019	0.203474	0.1051	0.1873	5008	,	,		17450	0.123		0.3956	False		,,,				2504	0.2331				p.R269R		Atlas-SNP	.											MBD1_ENST00000457839,NS,carcinoma,0,1	MBD1	228	1	0			c.C807T						PASS	.	G	,,,,,,,,,,,,,	286,1460		21,244,608	14.0	14.0	14.0		,807,807,,807,,,,,,,,,	-1.5	0.9	18	dbSNP_78	14	1479,2495		281,917,789	no	intron,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron	MBD1	NM_001204136.1,NM_001204137.1,NM_001204138.1,NM_001204139.1,NM_001204140.1,NM_001204141.1,NM_001204142.1,NM_001204143.1,NM_001204151.1,NM_002384.2,NM_015844.2,NM_015845.3,NM_015846.3,NM_015847.3	,,,,,,,,,,,,,	302,1161,1397	AA,AG,GG		37.2169,16.3803,30.8566	,,,,,,,,,,,,,	,269/631,269/630,,269/575,,,,,,,,,	47801800	1765,3955	873	1987	2860	SO:0001627	intron_variant	4152	exon9			ACGCAGGCGGTGA	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.792+169C>T	18.37:g.47801800G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	ENST00000591416.1	37	CCDS11943.1																																																																																			G|0.782;A|0.218	0.218	strong		0.622	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
TOPAZ1	375337	hgsc.bcm.edu	37	3	44329245	44329245	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:44329245C>T	ENST00000309765.4	+	11	3763	c.3595C>T	c.(3595-3597)Ctg>Ttg	p.L1199L		NM_001145030.1	NP_001138502.1	Q8N9V7	TOPZ1_HUMAN	testis and ovary specific PAZ domain containing 1	1199						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)										CCAGCCTTCTCTGAAAATATT	0.284																																					p.L1199L		Atlas-SNP	.											.	.	.	.	0			c.C3595T						PASS	.						190.0	167.0	174.0					3																	44329245		692	1591	2283	SO:0001819	synonymous_variant	375337	exon11			CCTTCTCTGAAAA	AK093476	CCDS46809.1	3p21.33	2012-10-08	2012-10-08	2012-10-08	ENSG00000173769	ENSG00000173769			24746	protein-coding gene	gene with protein product		614412	"""chromosome 3 open reading frame 77"""	C3orf77		22069478	Standard	NM_001145030		Approved	FLJ36157	uc003cna.4	Q8N9V7	OTTHUMG00000156172	ENST00000309765.4:c.3595C>T	3.37:g.44329245C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	59	14	0.237288	NM_001145030		Silent	SNP	ENST00000309765.4	37	CCDS46809.1																																																																																			.	.	none		0.284	TOPAZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343247.1	NM_001145030	
ITPA	3704	hgsc.bcm.edu	37	20	3193978	3193978	+	Silent	SNP	G	G	A	rs8362	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:3193978G>A	ENST00000380113.3	+	3	330	c.138G>A	c.(136-138)caG>caA	p.Q46Q	ITPA_ENST00000399838.3_Intron|ITPA_ENST00000455664.2_Silent_p.Q29Q|ITPA_ENST00000483354.1_Intron	NM_033453.3|NM_181493.2	NP_258412.1|NP_852470.1			inosine triphosphatase (nucleoside triphosphate pyrophosphatase)											autonomic_ganglia(1)|large_intestine(3)|ovary(1)|stomach(1)	6						CGGAGTACCAGGGGGAGCCGG	0.483													G|||	2356	0.470447	0.4705	0.3055	5008	,	,		18388	0.6131		0.3022	False		,,,				2504	0.6135				p.Q46Q		Atlas-SNP	.											.	ITPA	16	.	0			c.G138A						PASS	.	G	,	2017,2389	561.6+/-380.8	466,1085,652	116.0	112.0	113.0		138,87	2.0	1.0	20	dbSNP_52	113	2404,6196	399.2+/-346.4	364,1676,2260	no	coding-synonymous,coding-synonymous	ITPA	NM_033453.2,NM_181493.1	,	830,2761,2912	AA,AG,GG		27.9535,45.7785,33.992	,	46/195,29/178	3193978	4421,8585	2203	4300	6503	SO:0001819	synonymous_variant	3704	exon3			GTACCAGGGGGAG	AF026816	CCDS13051.1, CCDS46576.1, CCDS58762.1	20p	2002-02-01			ENSG00000125877	ENSG00000125877	3.6.1.19		6176	protein-coding gene	gene with protein product		147520		C20orf37		11278832	Standard	NM_033453		Approved	HLC14-06-P, dJ794I6.3	uc002wid.4	Q9BY32	OTTHUMG00000031738	ENST00000380113.3:c.138G>A	20.37:g.3193978G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	167	167	1	NM_033453		Silent	SNP	ENST00000380113.3	37	CCDS13051.1																																																																																			G|0.607;A|0.393	0.393	strong		0.483	ITPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077719.2		
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23058220	23058220	+	Missense_Mutation	SNP	T	T	G	rs20576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:23058220T>G	ENST00000221132.3	-	5	747	c.683A>C	c.(682-684)gAg>gCg	p.E228A		NM_003844.3	NP_003835.3	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily, member 10a	228			E -> A (in dbSNP:rs20576).		activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|signal transduction (GO:0007165)|TRAIL-activated apoptotic signaling pathway (GO:0036462)	integral component of membrane (GO:0016021)	death receptor activity (GO:0005035)|protease binding (GO:0002020)|receptor activity (GO:0004872)|TRAIL binding (GO:0045569)|transcription factor binding (GO:0008134)			NS(2)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|skin(1)	16		Prostate(55;0.0421)|Breast(100;0.14)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)		GTGGACACACTCGATGTCACT	0.577													T|||	409	0.0816693	0.0053	0.1441	5008	,	,		14956	0.0119		0.2157	False		,,,				2504	0.0746				p.E228A		Atlas-SNP	.											TNFRSF10A,NS,malignant_melanoma,-1,1	TNFRSF10A	40	1	0			c.A683C						PASS	.	T	ALA/GLU	207,4199	129.4+/-166.1	11,185,2007	116.0	110.0	112.0		683	0.6	0.0	8	dbSNP_67	112	1720,6880	313.9+/-311.6	182,1356,2762	yes	missense	TNFRSF10A	NM_003844.3	107	193,1541,4769	GG,GT,TT		20.0,4.6981,14.8162	possibly-damaging	228/469	23058220	1927,11079	2203	4300	6503	SO:0001583	missense	8797	exon5			ACACACTCGATGT	U90875	CCDS6039.1	8p21	2006-02-22			ENSG00000104689	ENSG00000104689		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11904	protein-coding gene	gene with protein product		603611				9311998, 9082980	Standard	NM_003844		Approved	DR4, Apo2, TRAILR-1, CD261	uc003xda.3	O00220	OTTHUMG00000097843	ENST00000221132.3:c.683A>C	8.37:g.23058220T>G	ENSP00000221132:p.Glu228Ala	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	212	99	0.466981	NM_003844	A8K5I4|Q53Y72|Q96E62	Missense_Mutation	SNP	ENST00000221132.3	37	CCDS6039.1	235	0.10760073260073261	6	0.012195121951219513	66	0.18232044198895028	5	0.008741258741258742	158	0.20844327176781002	T	9.872	1.199087	0.22121	0.046981	0.2	ENSG00000104689	ENST00000221132;ENST00000524158	D;T	0.91686	-2.89;1.49	3.18	0.625	0.17665	TNFR/CD27/30/40/95 cysteine-rich region (4);	1.136660	0.06841	N	0.795710	T	0.00356	0.0011	L	0.34521	1.04	0.80722	P	0.0	B	0.31100	0.308	B	0.34991	0.193	T	0.29610	-1.0006	9	0.51188	T	0.08	.	5.2334	0.15434	0.0:0.2674:0.0:0.7326	rs20576;rs11550538;rs17088993;rs17759912;rs52836024;rs20576	228	O00220	TR10A_HUMAN	A	228;26	ENSP00000221132:E228A;ENSP00000428884:E26A	ENSP00000221132:E228A	E	-	2	0	TNFRSF10A	23114165	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.872000	0.28037	0.010000	0.14839	-1.151000	0.01829	GAG	T|0.873;G|0.127	0.127	strong		0.577	TNFRSF10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215133.2	NM_003844	
SLC9C1	285335	hgsc.bcm.edu	37	3	111983157	111983157	+	Silent	SNP	G	G	A	rs62276974	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:111983157G>A	ENST00000305815.5	-	9	1164	c.912C>T	c.(910-912)ctC>ctT	p.L304L	SLC9C1_ENST00000487372.1_Intron	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	304					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TAAACACCATGAGAAAAGCAA	0.244													G|||	609	0.121605	0.1346	0.1354	5008	,	,		13446	0.0109		0.2604	False		,,,				2504	0.0654				p.L304L		Atlas-SNP	.											.	.	.	.	0			c.C912T						PASS	.	G		638,3710		46,546,1582	35.0	37.0	36.0		912	-2.9	1.0	3	dbSNP_129	36	2040,6468		240,1560,2454	no	coding-synonymous	SLC9A10	NM_183061.1		286,2106,4036	AA,AG,GG		23.9774,14.6734,20.8307		304/1178	111983157	2678,10178	2174	4254	6428	SO:0001819	synonymous_variant	285335	exon9			CACCATGAGAAAA	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.912C>T	3.37:g.111983157G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_183061	Q6ZRP4|Q7RTP2	Silent	SNP	ENST00000305815.5	37	CCDS33817.1																																																																																			G|0.803;A|0.197	0.197	strong		0.244	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
OR5M3	219482	hgsc.bcm.edu	37	11	56237410	56237410	+	Silent	SNP	A	A	G	rs617315	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56237410A>G	ENST00000312240.2	-	1	604	c.564T>C	c.(562-564)gcT>gcC	p.A188A		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	188						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					CAAAGGTCCCAGCACAGGCCA	0.393													a|||	750	0.14976	0.1112	0.1268	5008	,	,		19469	0.129		0.2237	False		,,,				2504	0.1636				p.A188A		Atlas-SNP	.											OR5M3,NS,carcinoma,-1,1	OR5M3	103	1	0			c.T564C						PASS	.	A		516,3886	221.7+/-238.7	24,468,1709	131.0	121.0	124.0		564	-10.2	0.2	11	dbSNP_83	124	1911,6681	321.1+/-314.9	261,1389,2646	no	coding-synonymous	OR5M3	NM_001004742.2		285,1857,4355	GG,GA,AA		22.2416,11.7219,18.6779		188/308	56237410	2427,10567	2201	4296	6497	SO:0001819	synonymous_variant	219482	exon1			GGTCCCAGCACAG	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"""GPCR / Class A : Olfactory receptors"""	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.564T>C	11.37:g.56237410A>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	227	119	0.524229	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Silent	SNP	ENST00000312240.2	37	CCDS31532.1																																																																																			A|0.822;G|0.178	0.178	strong		0.393	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742	
LSR	51599	hgsc.bcm.edu	37	19	35741456	35741456	+	Silent	SNP	T	T	C	rs2073900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35741456T>C	ENST00000361790.3	+	2	651	c.492T>C	c.(490-492)gtT>gtC	p.V164V	LSR_ENST00000360798.3_Silent_p.V164V|LSR_ENST00000354900.3_Silent_p.V164V|AC002128.5_ENST00000604161.1_RNA|LSR_ENST00000347609.4_Silent_p.V127V|LSR_ENST00000597933.1_3'UTR|LSR_ENST00000427250.1_Silent_p.V116V|LSR_ENST00000602122.1_Silent_p.V164V	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	164	Ig-like V-type.				embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ACCCCTACGTTGAGTGCCAGG	0.647													C|||	2824	0.563898	0.3888	0.6844	5008	,	,		18673	0.4683		0.7445	False		,,,				2504	0.6278				p.V164V		Atlas-SNP	.											.	LSR	60	.	0			c.T492C						PASS	.	C	,,	2000,2406	616.3+/-392.7	455,1090,658	61.0	58.0	59.0		492,492,492	3.7	1.0	19	dbSNP_96	59	6395,2205	374.4+/-337.4	2388,1619,293	no	coding-synonymous,coding-synonymous,coding-synonymous	LSR	NM_015925.5,NM_205834.2,NM_205835.2	,,	2843,2709,951	CC,CT,TT		25.6395,45.3926,35.4529	,,	164/631,164/650,164/582	35741456	8395,4611	2203	4300	6503	SO:0001819	synonymous_variant	51599	exon2			CTACGTTGAGTGC	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29572	protein-coding gene	gene with protein product	"""lipolysis-stimulated remnant"", ""immunoglobulin-like domain containing receptor 3"""					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.492T>C	19.37:g.35741456T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Silent	SNP	ENST00000361790.3	37	CCDS12450.1																																																																																			T|0.384;C|0.616	0.616	strong		0.647	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	
MUC4	4585	hgsc.bcm.edu	37	3	195507323	195507323	+	Missense_Mutation	SNP	T	T	C	rs201618076		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507323T>C	ENST00000463781.3	-	2	11587	c.11128A>G	c.(11128-11130)Acc>Gcc	p.T3710A	MUC4_ENST00000475231.1_Missense_Mutation_p.T3710A|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGTGTGACCTGAG	0.572																																					p.T3710A		Atlas-SNP	.											MUC4_ENST00000463781,uveal_tract,malignant_melanoma,0,1	MUC4	1505	1	0			c.A11128G						scavenged	.						67.0	57.0	60.0					3																	195507323		660	1591	2251	SO:0001583	missense	4585	exon2			GGGTGGTGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11128A>G	3.37:g.195507323T>C	ENSP00000417498:p.Thr3710Ala	Somatic	24	8	0.333333		WXS	Illumina HiSeq	Phase_I	382	50	0.13089	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	t	5.476	0.272841	0.10349	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.51;1.49	0.885	-1.77	0.07982	.	.	.	.	.	T	0.11067	0.0270	N	0.14661	0.345	0.09310	N	1	P	0.37985	0.613	B	0.25140	0.058	T	0.14062	-1.0486	8	.	.	.	.	3.5153	0.07722	0.0:0.2995:0.0:0.7005	.	3582	E7ESK3	.	A	3710	ENSP00000417498:T3710A;ENSP00000420243:T3710A	.	T	-	1	0	MUC4	196992102	0.927000	0.31430	0.003000	0.11579	0.039000	0.13416	0.650000	0.24858	-1.812000	0.01227	-2.075000	0.00382	ACC	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ATP10D	57205	hgsc.bcm.edu	37	4	47525054	47525054	+	Missense_Mutation	SNP	T	T	C	rs7683838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:47525054T>C	ENST00000273859.3	+	4	780	c.511T>C	c.(511-513)Tgc>Cgc	p.C171R	ATP10D_ENST00000504445.1_Missense_Mutation_p.C171R	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	171			C -> R (in dbSNP:rs7683838).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						CATTGACCGATGCTGGAAAGA	0.333													T|||	465	0.0928514	0.1551	0.1138	5008	,	,		15375	0.004		0.1322	False		,,,				2504	0.045				p.C171R		Atlas-SNP	.											.	ATP10D	168	.	0			c.T511C						PASS	.	T	ARG/CYS	705,3701	295.0+/-283.4	56,593,1554	83.0	76.0	78.0		511	2.2	0.5	4	dbSNP_116	78	1114,7486	231.5+/-265.5	76,962,3262	yes	missense	ATP10D	NM_020453.3	180	132,1555,4816	CC,CT,TT		12.9535,16.0009,13.9859	benign	171/1427	47525054	1819,11187	2203	4300	6503	SO:0001583	missense	57205	exon4			GACCGATGCTGGA	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.511T>C	4.37:g.47525054T>C	ENSP00000273859:p.Cys171Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	231	0.10576923076923077	79	0.16056910569105692	51	0.1408839779005525	4	0.006993006993006993	97	0.1279683377308707	T	3.952	-0.012021	0.07727	0.160009	0.129535	ENSG00000145246	ENST00000273859;ENST00000504445	T;T	0.74526	-0.85;-0.85	5.94	2.25	0.28309	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.173510	0.52532	N	0.000077	T	0.00210	0.0006	N	0.01219	-0.95	0.28006	P	0.9350931	B;B	0.18741	0.03;0.0	B;B	0.18263	0.021;0.002	T	0.03662	-1.1015	9	0.25106	T	0.35	-9.2528	9.2908	0.37786	0.0:0.2759:0.0:0.7241	rs7683838;rs52836286;rs61027912;rs7683838	171;171	Q9P241;Q6PEW3	AT10D_HUMAN;.	R	171	ENSP00000273859:C171R;ENSP00000420909:C171R	ENSP00000273859:C171R	C	+	1	0	ATP10D	47219811	0.658000	0.27402	0.517000	0.27799	0.453000	0.32348	0.973000	0.29422	0.498000	0.27948	0.397000	0.26171	TGC	T|0.869;C|0.131	0.131	strong		0.333	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
SLC22A3	6581	hgsc.bcm.edu	37	6	160858188	160858188	+	Silent	SNP	G	G	A	rs2292334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:160858188G>A	ENST00000275300.2	+	7	1385	c.1233G>A	c.(1231-1233)gcG>gcA	p.A411A	SLC22A3_ENST00000392145.1_Silent_p.A411A	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	411					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	TCCCCTTTGCGGCAAGCAATA	0.507													G|||	1557	0.310903	0.1006	0.4625	5008	,	,		15509	0.4603		0.3529	False		,,,				2504	0.2904				p.A411A		Atlas-SNP	.											.	SLC22A3	58	.	0			c.G1233A						PASS	.	G		601,3805	263.4+/-265.5	50,501,1652	138.0	142.0	141.0		1233	-11.7	0.0	6	dbSNP_100	141	3126,5474	476.2+/-369.3	570,1986,1744	no	coding-synonymous	SLC22A3	NM_021977.2		620,2487,3396	AA,AG,GG		36.3488,13.6405,28.656		411/557	160858188	3727,9279	2203	4300	6503	SO:0001819	synonymous_variant	6581	exon7			CTTTGCGGCAAGC	AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"""Solute carriers"""	10967	protein-coding gene	gene with protein product		604842	"""solute carrier family 22 (extraneuronal monoamine transporter), member 3"""			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.1233G>A	6.37:g.160858188G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_021977	Q5SYN6|Q9UP02	Silent	SNP	ENST00000275300.2	37	CCDS5277.1																																																																																			G|0.697;A|0.303	0.303	strong		0.507	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977	
ADORA2A	135	hgsc.bcm.edu	37	22	24837301	24837301	+	Silent	SNP	T	T	C	rs5751876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:24837301T>C	ENST00000337539.7	+	3	1542	c.1083T>C	c.(1081-1083)taT>taC	p.Y361Y	SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000326341.4_RNA|ADORA2A-AS1_ENST00000427813.2_RNA|ADORA2A-AS1_ENST00000543438.1_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	361					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	CCAATGGCTATGCCCTGGGGC	0.667													C|||	2215	0.442292	0.3185	0.5418	5008	,	,		18502	0.4722		0.6093	False		,,,				2504	0.3364				p.Y361Y		Atlas-SNP	.											.	ADORA2A	44	.	0			c.T1083C						PASS	.	C		1575,2831		291,993,919	22.0	20.0	21.0		1083	-7.2	0.0	22	dbSNP_114	21	5162,3436		1579,2004,716	no	coding-synonymous	ADORA2A	NM_000675.4		1870,2997,1635	CC,CT,TT		39.9628,35.7467,48.1929		361/413	24837301	6737,6267	2203	4299	6502	SO:0001819	synonymous_variant	135	exon3			TGGCTATGCCCTG	X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"""GPCR / Class A : Adenosine receptors"""	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.1083T>C	22.37:g.24837301T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_000675	B2R7E0	Silent	SNP	ENST00000337539.7	37	CCDS13826.1																																																																																			T|0.492;C|0.508	0.508	strong		0.667	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675	
CCDC61	729440	hgsc.bcm.edu	37	19	46520506	46520506	+	Splice_Site	SNP	G	G	C	rs61742389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46520506G>C	ENST00000595358.1	+	12	1361	c.1312G>C	c.(1312-1314)Ggt>Cgt	p.G438R	CCDC61_ENST00000263284.2_Splice_Site_p.G457R|CCDC61_ENST00000536603.1_Splice_Site_p.G258R|CCDC61_ENST00000594087.1_Splice_Site_p.G258R|MIR769_ENST00000390225.1_RNA	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	438						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		TTTTCTCAGGGGTCACCGCCG	0.607											OREG0025565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	40	0.00798722	0.0015	0.0101	5008	,	,		10932	0.0		0.0219	False		,,,				2504	0.0092				p.G438R		Atlas-SNP	.											.	CCDC61	32	.	0			c.G1312C						PASS	.		ARG/GLY	20,3958		0,20,1969	21.0	26.0	25.0		1369	-1.7	0.0	19	dbSNP_129	25	131,8161		0,131,4015	yes	missense-near-splice	CCDC61	NM_001080402.1	125	0,151,5984	CC,CG,GG		1.5798,0.5028,1.2306	benign	457/532	46520506	151,12119	1989	4146	6135	SO:0001630	splice_region_variant	729440	exon12			CTCAGGGGTCACC		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.1311-1G>C	19.37:g.46520506G>C		Somatic	53	0	0	939	WXS	Illumina HiSeq	Phase_I	39	14	0.358974	NM_001267723	C8CAP4|Q9HDB6	Missense_Mutation	SNP	ENST00000595358.1	37	CCDS46120.2	24	0.01098901098901099	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	8.859	0.946358	0.18356	0.005028	0.015798	ENSG00000104983	ENST00000263284;ENST00000536603	.	.	.	3.77	-1.73	0.08081	.	1.284800	0.05551	N	0.567480	T	0.04227	0.0117	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24048	-1.0171	9	0.10636	T	0.68	5.2453	2.635	0.04955	0.1288:0.4667:0.2536:0.1509	rs61742389	400	Q9Y6R9	CCD61_HUMAN	R	457;258	.	ENSP00000263284:G457R	G	+	1	0	CCDC61	51212346	0.000000	0.05858	0.002000	0.10522	0.022000	0.10575	-0.122000	0.10627	-0.025000	0.13918	0.450000	0.29827	GGT	A|0.000;C|0.012;G|0.987	0.012	strong		0.607	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	Missense_Mutation
EPSTI1	94240	hgsc.bcm.edu	37	13	43462422	43462422	+	IGR	SNP	A	A	T	rs1044856	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:43462422A>T	ENST00000398762.3	-	0	957				EPSTI1_ENST00000313624.7_3'UTR|EPSTI1_ENST00000313640.7_Missense_Mutation_p.N399K			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)											endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		GGCAGTAGAGATTAAATATGA	0.423													A|||	788	0.157348	0.0182	0.2003	5008	,	,		17038	0.126		0.3419	False		,,,				2504	0.1575				p.N399K		Atlas-SNP	.											.	EPSTI1	47	.	0			c.T1197A						PASS	.	A	LYS/ASN,	290,4116	159.2+/-191.8	15,260,1928	87.0	87.0	87.0		1197,	-0.1	0.0	13	dbSNP_86	87	2934,5666	456.7+/-364.1	503,1928,1869	yes	missense,utr-3	EPSTI1	NM_001002264.1,NM_033255.2	94,	518,2188,3797	TT,TA,AA		34.1163,6.5819,24.7886	probably-damaging,	399/411,	43462422	3224,9782	2203	4300	6503	SO:0001628	intergenic_variant	94240	exon13			GTAGAGATTAAAT	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"""epithelial stromal interaction protein 1"""	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814		13.37:g.43462422A>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	187	107	0.572192	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	37	CCDS9387.1	407	0.18635531135531136	12	0.024390243902439025	82	0.2265193370165746	62	0.10839160839160839	251	0.3311345646437995	A	16.66	3.184624	0.57909	0.065819	0.341163	ENSG00000133106	ENST00000313640	.	.	.	5.2	-0.0576	0.13800	.	0.505521	0.16647	N	0.205374	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999421063	D	0.63046	0.992	P	0.60541	0.876	T	0.15780	-1.0425	7	0.87932	D	0	-3.571	7.6816	0.28518	0.621:0.0:0.379:0.0	rs1044856;rs3184675;rs56461472;rs1044856	399	Q96J88-3	.	K	399	.	ENSP00000318982:N399K	N	-	3	2	EPSTI1	42360422	1.000000	0.71417	0.028000	0.17463	0.596000	0.36781	1.479000	0.35453	-0.144000	0.11314	0.533000	0.62120	AAT	A|0.789;T|0.211	0.211	strong		0.423	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264	
THUMPD3	25917	hgsc.bcm.edu	37	3	9425944	9425944	+	Silent	SNP	G	G	C	rs1046788	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:9425944G>C	ENST00000345094.3	+	9	1618	c.1284G>C	c.(1282-1284)cgG>cgC	p.R428R	SETD5-AS1_ENST00000523354.1_RNA|SETD5-AS1_ENST00000519043.1_RNA|SETD5-AS1_ENST00000520629.1_RNA|THUMPD3_ENST00000452837.2_Silent_p.R428R|SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000515662.2_Silent_p.R428R|SETD5-AS1_ENST00000521609.1_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	428						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		CTTGCCTACGGGAGATGAGCC	0.428													g|||	531	0.10603	0.0348	0.2248	5008	,	,		17980	0.0615		0.1879	False		,,,				2504	0.0798				p.R428R		Atlas-SNP	.											.	THUMPD3	46	.	0			c.G1284C						PASS	.		,	268,4138	150.3+/-184.3	5,258,1940	202.0	209.0	207.0		1284,1284	-3.0	0.1	3	dbSNP_86	207	1276,7324	254.7+/-279.9	85,1106,3109	no	coding-synonymous,coding-synonymous	THUMPD3	NM_001114092.1,NM_015453.2	,	90,1364,5049	CC,CG,GG		14.8372,6.0826,11.8714	,	428/508,428/508	9425944	1544,11462	2203	4300	6503	SO:0001819	synonymous_variant	25917	exon9			CCTACGGGAGATG	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.1284G>C	3.37:g.9425944G>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Silent	SNP	ENST00000345094.3	37	CCDS2573.1	290	0.13278388278388278	23	0.046747967479674794	82	0.2265193370165746	43	0.07517482517482517	142	0.18733509234828497	G	7.498	0.652120	0.14580	0.060826	0.148372	ENSG00000134077	ENST00000416603	.	.	.	5.66	-3.01	0.05463	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999956	.	.	.	.	.	.	T	0.31641	-0.9936	3	.	.	.	-8.8946	5.1373	0.14941	0.3653:0.0:0.4284:0.2063	rs1046788;rs3172463;rs1046788	.	.	.	R	199	.	.	G	+	1	0	THUMPD3	9400944	0.156000	0.22821	0.056000	0.19401	0.937000	0.57800	0.545000	0.23268	-0.398000	0.07679	-0.188000	0.12872	GGA	G|0.878;C|0.122	0.122	strong		0.428	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453	
VWA5B2	90113	hgsc.bcm.edu	37	3	183955109	183955109	+	Silent	SNP	C	C	T	rs843334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183955109C>T	ENST00000426955.2	+	11	1729	c.1629C>T	c.(1627-1629)ccC>ccT	p.P543P	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Silent_p.P324P	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	554										breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						TGCTGACCCCCCGGGAGATCC	0.622													C|||	996	0.198882	0.1377	0.1844	5008	,	,		16035	0.2351		0.2256	False		,,,				2504	0.227				p.P543P		Atlas-SNP	.											.	VWA5B2	47	.	0			c.C1629T						PASS	.	C		207,1177		17,173,502	42.0	43.0	43.0		1629	1.4	1.0	3	dbSNP_86	43	660,2522		69,522,1000	no	coding-synonymous	VWA5B2	NM_138345.1		86,695,1502	TT,TC,CC		20.7417,14.9566,18.9882		543/1243	183955109	867,3699	692	1591	2283	SO:0001819	synonymous_variant	90113	exon11			GACCCCCCGGGAG		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.1629C>T	3.37:g.183955109C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	143	55	0.384615	NM_138345	B9EGN7	Silent	SNP	ENST00000426955.2	37	CCDS54686.1																																																																																			C|0.817;T|0.183	0.183	strong		0.622	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
HERC2	8924	hgsc.bcm.edu	37	15	28419619	28419619	+	Missense_Mutation	SNP	C	C	T	rs141441362	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28419619C>T	ENST00000261609.7	-	65	10087	c.9979G>A	c.(9979-9981)Gtg>Atg	p.V3327M		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GCCACATCCACAGTTGTCCAC	0.547																																					p.V3327M		Atlas-SNP	.											.	HERC2	501	.	0			c.G9979A						PASS	.						54.0	37.0	43.0					15																	28419619		2203	4300	6503	SO:0001583	missense	8924	exon65			CATCCACAGTTGT	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9979G>A	15.37:g.28419619C>T	ENSP00000261609:p.Val3327Met	Somatic	551	0	0		WXS	Illumina HiSeq	Phase_I	515	129	0.250485	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	127	0.05815018315018315	30	0.06097560975609756	24	0.06629834254143646	0	0.0	73	0.09630606860158311	C	10.06	1.246296	0.22796	.	.	ENSG00000128731	ENST00000261609	T	0.39787	1.06	5.72	4.81	0.61882	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (1);	0.063541	0.64402	D	0.000009	T	0.01156	0.0038	L	0.59436	1.845	0.54753	D	0.999986	B	0.15719	0.014	B	0.15052	0.012	T	0.01294	-1.1393	10	0.30078	T	0.28	.	11.8976	0.52665	0.0:0.8593:0.0:0.1407	.	3327	O95714	HERC2_HUMAN	M	3327	ENSP00000261609:V3327M	ENSP00000261609:V3327M	V	-	1	0	HERC2	26093214	1.000000	0.71417	0.016000	0.15963	0.067000	0.16453	4.974000	0.63771	1.420000	0.47138	0.591000	0.81541	GTG	C|0.947;T|0.053	0.053	strong		0.547	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1812972	1812972	+	Silent	SNP	G	G	C	rs2294616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1812972G>C	ENST00000250894.4	+	16	2017	c.1860G>C	c.(1858-1860)tcG>tcC	p.S620S	MAPK8IP3_ENST00000356010.5_Silent_p.S614S	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	620					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						GCCCGATCTCGGCAGGCAGCC	0.657													G|||	754	0.150559	0.0371	0.0965	5008	,	,		16664	0.2698		0.1441	False		,,,				2504	0.226				p.S620S		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.G1860C						PASS	.	G	,	172,3746		1,170,1788	53.0	62.0	59.0		1842,1860	-9.4	0.1	16	dbSNP_100	59	1053,7275		65,923,3176	no	coding-synonymous,coding-synonymous	MAPK8IP3	NM_001040439.1,NM_015133.3	,	66,1093,4964	CC,CG,GG		12.6441,4.39,10.0033	,	614/1331,620/1337	1812972	1225,11021	1959	4164	6123	SO:0001819	synonymous_variant	23162	exon16			GATCTCGGCAGGC	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.1860G>C	16.37:g.1812972G>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	183	98	0.535519	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	37	CCDS10442.2																																																																																			G|0.835;C|0.165	0.165	strong		0.657	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
PDXDC1	23042	hgsc.bcm.edu	37	16	15098047	15098047	+	Missense_Mutation	SNP	C	C	G	rs11549900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15098047C>G	ENST00000396410.4	+	5	343	c.246C>G	c.(244-246)atC>atG	p.I82M	PDXDC1_ENST00000447912.2_Intron|PDXDC1_ENST00000569715.1_Missense_Mutation_p.I55M|PDXDC1_ENST00000455313.2_Missense_Mutation_p.I82M|PDXDC1_ENST00000535621.2_Missense_Mutation_p.I82M|PDXDC1_ENST00000450288.2_Missense_Mutation_p.I54M|PDXDC1_ENST00000563679.1_Missense_Mutation_p.I100M|PDXDC1_ENST00000325823.7_Missense_Mutation_p.I67M	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	82				I -> M (in Ref. 2; BAG61167 and 5; AAZ14099). {ECO:0000305}.	carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTAACAGAATCCAAAATATTG	0.348																																					p.I82M		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C246G						PASS	.						107.0	119.0	115.0					16																	15098047		2197	4300	6497	SO:0001583	missense	23042	exon5			CAGAATCCAAAAT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.246C>G	16.37:g.15098047C>G	ENSP00000379691:p.Ile82Met	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	237	70	0.295359	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	653	0.298992673992674	66	0.13414634146341464	138	0.3812154696132597	251	0.4388111888111888	198	0.2612137203166227	C	6.258	0.415784	0.11870	.	.	ENSG00000179889	ENST00000325823;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000455313	T;T;T;T;T	0.37915	1.17;1.17;1.17;2.07;1.17	5.72	2.76	0.32466	Pyridoxal phosphate-dependent transferase, major domain (1);	0.318283	0.36555	N	0.002527	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	B;B;B;B	0.20780	0.048;0.005;0.048;0.005	B;B;B;B	0.19391	0.02;0.005;0.012;0.025	T	0.47142	-0.9140	9	0.40728	T	0.16	.	9.1032	0.36681	0.0:0.6898:0.0:0.3102	rs11549900	54;82;82;82	E7EPL4;Q86XE2;Q6P996;Q6P996-2	.;.;PDXD1_HUMAN;.	M	67;82;82;54;82	ENSP00000322807:I67M;ENSP00000437835:I82M;ENSP00000379691:I82M;ENSP00000391147:I54M;ENSP00000406703:I82M	ENSP00000322807:I67M	I	+	3	3	PDXDC1	15005548	1.000000	0.71417	1.000000	0.80357	0.351000	0.29236	1.821000	0.39041	0.455000	0.26910	-0.142000	0.14014	ATC	C|0.742;G|0.258	0.258	strong		0.348	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
GGA2	23062	hgsc.bcm.edu	37	16	23480294	23480294	+	Silent	SNP	C	C	T	rs35347972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23480294C>T	ENST00000309859.4	-	16	1726	c.1644G>A	c.(1642-1644)ccG>ccA	p.P548P	GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	548	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		AGCTGGATGCCGGCTGCAGCT	0.493													C|||	48	0.00958466	0.0023	0.0144	5008	,	,		22151	0.0		0.0338	False		,,,				2504	0.001				p.P548P		Atlas-SNP	.											.	GGA2	49	.	0			c.G1644A						PASS	.			29,4365	36.0+/-67.5	0,29,2168	86.0	81.0	83.0		1644	-9.6	0.3	16	dbSNP_126	83	295,8305	108.2+/-168.9	6,283,4011	no	coding-synonymous	GGA2	NM_015044.4		6,312,6179	TT,TC,CC		3.4302,0.66,2.4935		548/614	23480294	324,12670	2197	4300	6497	SO:0001819	synonymous_variant	23062	exon16			GGATGCCGGCTGC	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1644G>A	16.37:g.23480294C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Silent	SNP	ENST00000309859.4	37	CCDS10611.1																																																																																			C|0.977;T|0.023	0.023	strong		0.493	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		
ACOT9	23597	hgsc.bcm.edu	37	X	23722835	23722835	+	Silent	SNP	A	A	G	rs11175	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:23722835A>G	ENST00000336430.7	-	14	1338	c.1207T>C	c.(1207-1209)Ttg>Ctg	p.L403L	ACOT9_ENST00000379295.1_Silent_p.L343L|ACOT9_ENST00000379303.5_Silent_p.L412L	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	403					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)			breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						GGGAAAACCAATGGCACTTCT	0.418													A|||	351	0.0929801	0.0817	0.0663	3775	,	,		15047	0.0		0.165	False		,,,				2504	0.0317				p.L412L		Atlas-SNP	.											.	ACOT9	33	.	0			c.T1234C						PASS	.	A	,	396,3439		17,304,58,1311,513	169.0	162.0	165.0		1207,1234	2.9	1.0	X	dbSNP_52	165	1265,5463		94,727,350,1607,1522	no	coding-synonymous,coding-synonymous	ACOT9	NM_001033583.2,NM_001037171.1	,	111,1031,408,2918,2035	GG,GA,G,AA,A		18.802,10.3259,15.7247	,	403/440,412/449	23722835	1661,8902	2203	4300	6503	SO:0001819	synonymous_variant	23597	exon15			AAACCAATGGCAC	AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"""Acyl CoA thioesterases"""	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.1207T>C	X.37:g.23722835A>G		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_001037171	B3KNC9|B7ZM94	Silent	SNP	ENST00000336430.7	37	CCDS35216.1																																																																																			A|0.840;0|0.026	.	strong		0.418	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1	NM_012332	
NXPE2	120406	hgsc.bcm.edu	37	11	114576626	114576626	+	Missense_Mutation	SNP	A	A	T	rs1356428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:114576626A>T	ENST00000389586.4	+	5	1242	c.1052A>T	c.(1051-1053)aAt>aTt	p.N351I	NXPE2_ENST00000375475.5_Intron	NM_182495.5	NP_872301.2	Q96DL1	NXPE2_HUMAN	neurexophilin and PC-esterase domain family, member 2	351						integral component of membrane (GO:0016021)		p.N351I(1)									GAAACAAAAAATATAAATGAC	0.328													A|||	1527	0.304912	0.1067	0.3343	5008	,	,		11387	0.378		0.3956	False		,,,				2504	0.3834				p.N351I		Atlas-SNP	.											FAM55B_ENST00000389586,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A1052T						PASS	.	A	ILE/ASN	196,1188		18,160,514	60.0	57.0	58.0		1052	-4.2	0.0	11	dbSNP_88	58	1139,2037		219,701,668	yes	missense	FAM55B	NM_182495.5	149	237,861,1182	TT,TA,AA		35.8627,14.1618,29.2763	benign	351/560	114576626	1335,3225	692	1588	2280	SO:0001583	missense	120406	exon5			CAAAAAATATAAA	AK057953	CCDS44738.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000204361	ENSG00000204361			26331	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member B"""	FAM55B			Standard	NM_182495		Approved	FLJ25224	uc009yyy.2	Q96DL1	OTTHUMG00000168293	ENST00000389586.4:c.1052A>T	11.37:g.114576626A>T	ENSP00000374237:p.Asn351Ile	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	169	84	0.497041	NM_182495	Q2NKI8	Missense_Mutation	SNP	ENST00000389586.4	37	CCDS44738.1	663	0.30357142857142855	60	0.12195121951219512	118	0.3259668508287293	184	0.32167832167832167	301	0.3970976253298153	A	7.433	0.639102	0.14386	0.141618	0.358627	ENSG00000204361	ENST00000389586	T	0.12255	2.7	5.24	-4.15	0.03881	.	1.854680	0.02760	N	0.118463	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.13594	0.008	B	0.08055	0.003	T	0.48456	-0.9034	9	0.44086	T	0.13	.	0.8123	0.01096	0.3654:0.1138:0.1562:0.3647	rs1356428;rs17117289;rs58365752	351	Q96DL1	FA55B_HUMAN	I	351	ENSP00000374237:N351I	ENSP00000374237:N351I	N	+	2	0	FAM55B	114081836	0.000000	0.05858	0.000000	0.03702	0.481000	0.33189	-0.551000	0.06027	-0.279000	0.09167	0.460000	0.39030	AAT	A|0.682;T|0.318	0.318	strong		0.328	NXPE2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399181.1	NM_182495	
DDX58	23586	hgsc.bcm.edu	37	9	32526146	32526146	+	Missense_Mutation	SNP	G	G	A	rs10813831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:32526146G>A	ENST00000379883.2	-	1	176	c.19C>T	c.(19-21)Cgc>Tgc	p.R7C	DDX58_ENST00000379868.1_De_novo_Start_InFrame|DDX58_ENST00000379882.1_Missense_Mutation_p.R7C|DDX58_ENST00000545044.1_De_novo_Start_InFrame	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	7	CARD 1.		R -> C (in dbSNP:rs10813831). {ECO:0000269|PubMed:17974005}.		cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TGCAGGCTGCGTCGCTGCTCG	0.607													G|||	922	0.184105	0.2073	0.1628	5008	,	,		14229	0.1052		0.2773	False		,,,				2504	0.1534				p.R7C		Atlas-SNP	.											.	DDX58	82	.	0			c.C19T						PASS	.	G	CYS/ARG	1018,3388	377.1+/-322.3	122,774,1307	64.0	56.0	59.0		19	-2.1	0.0	9	dbSNP_120	59	2213,6387	375.4+/-337.8	288,1637,2375	yes	missense	DDX58	NM_014314.3	180	410,2411,3682	AA,AG,GG		25.7326,23.1049,24.8424	probably-damaging	7/926	32526146	3231,9775	2203	4300	6503	SO:0001583	missense	23586	exon1			GGCTGCGTCGCTG	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.19C>T	9.37:g.32526146G>A	ENSP00000369213:p.Arg7Cys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	416	0.19047619047619047	99	0.20121951219512196	70	0.19337016574585636	41	0.07167832167832168	206	0.2717678100263852	G	15.14	2.743956	0.49151	0.231049	0.257326	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000542960	T;T	0.06371	3.4;3.31	4.02	-2.08	0.07254	.	1.305430	0.05512	N	0.560359	T	0.00012	0.0000	L	0.56769	1.78	0.49915	P	1.6099999999996673E-4	D;D	0.71674	0.997;0.998	P;P	0.53861	0.736;0.65	T	0.35773	-0.9775	9	0.87932	D	0	0.1979	8.0968	0.30833	0.0:0.2914:0.1955:0.513	rs10813831;rs17553642;rs52815553;rs59478737;rs10813831	7;7	O95786-2;O95786	.;DDX58_HUMAN	C	7	ENSP00000369212:R7C;ENSP00000369213:R7C	ENSP00000369212:R7C	R	-	1	0	DDX58	32516146	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.144000	0.10280	-0.381000	0.07882	-0.261000	0.10672	CGC	G|0.788;A|0.212	0.212	strong		0.607	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
C4orf17	84103	hgsc.bcm.edu	37	4	100443800	100443800	+	Missense_Mutation	SNP	G	G	A	rs17029087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100443800G>A	ENST00000326581.4	+	3	633	c.271G>A	c.(271-273)Gag>Aag	p.E91K	C4orf17_ENST00000514652.1_Missense_Mutation_p.E91K|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	91			E -> K (in dbSNP:rs17029087). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		TGCAGTCCAGGAGAGCCCTGT	0.498													G|||	1032	0.20607	0.1838	0.1873	5008	,	,		16608	0.1161		0.2744	False		,,,				2504	0.272				p.E91K		Atlas-SNP	.											.	C4orf17	42	.	0			c.G271A						PASS	.	G	LYS/GLU	885,3521	342.0+/-307.0	101,683,1419	92.0	88.0	89.0		271	0.5	0.0	4	dbSNP_123	89	2356,6244	392.0+/-343.8	328,1700,2272	yes	missense	C4orf17	NM_032149.2	56	429,2383,3691	AA,AG,GG		27.3953,20.0862,24.9193	benign	91/360	100443800	3241,9765	2203	4300	6503	SO:0001583	missense	84103	exon3			GTCCAGGAGAGCC	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.271G>A	4.37:g.100443800G>A	ENSP00000322582:p.Glu91Lys	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	399	0.18269230769230768	64	0.13008130081300814	70	0.19337016574585636	66	0.11538461538461539	199	0.262532981530343	G	11.57	1.677464	0.29783	0.200862	0.273953	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.17854	2.25;2.25	4.41	0.478	0.16789	.	2.099710	0.01389	N	0.013186	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B	0.20164	0.042	B	0.26310	0.068	T	0.37888	-0.9686	9	0.27785	T	0.31	0.2327	7.6519	0.28352	0.0955:0.4981:0.4064:0.0	rs17029087;rs52812387;rs17029087	91	Q53FE4	CD017_HUMAN	K	91	ENSP00000322582:E91K;ENSP00000427663:E91K	ENSP00000322582:E91K	E	+	1	0	C4orf17	100662823	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.370000	0.20433	0.048000	0.15891	-0.894000	0.02916	GAG	G|0.780;A|0.220	0.220	strong		0.498	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
MYH15	22989	hgsc.bcm.edu	37	3	108147510	108147510	+	Silent	SNP	A	A	G	rs201473403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108147510A>G	ENST00000273353.3	-	28	3647	c.3591T>C	c.(3589-3591)ttT>ttC	p.F1197F		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1197						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						AAGTTGTCTCAAAGTGCAGAG	0.483													A|||	5	0.000998403	0.0	0.0014	5008	,	,		19235	0.0		0.004	False		,,,				2504	0.0				p.F1197F		Atlas-SNP	.											.	MYH15	223	.	0			c.T3591C						PASS	.	A		2,3922		0,2,1960	130.0	125.0	126.0		3591	-3.7	0.3	3		126	19,8307		0,19,4144	no	coding-synonymous	MYH15	NM_014981.1		0,21,6104	GG,GA,AA		0.2282,0.051,0.1714		1197/1947	108147510	21,12229	1962	4163	6125	SO:0001819	synonymous_variant	22989	exon28			TGTCTCAAAGTGC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3591T>C	3.37:g.108147510A>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	261	139	0.532567	NM_014981		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			A|0.999;G|0.001	0.001	strong		0.483	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
LIG1	3978	hgsc.bcm.edu	37	19	48654553	48654553	+	Silent	SNP	G	G	T	rs20580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48654553G>T	ENST00000263274.7	-	7	929	c.510C>A	c.(508-510)gcC>gcA	p.A170A	LIG1_ENST00000599165.1_5'UTR|LIG1_ENST00000536218.1_Intron|LIG1_ENST00000427526.2_Silent_p.A139A	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	170					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	CCTTCTCTGTGGCCACTTCAG	0.567								Nucleotide excision repair (NER)					T|||	2669	0.532947	0.5613	0.4726	5008	,	,		13171	0.6885		0.4901	False		,,,				2504	0.4213				p.A170A		Atlas-SNP	.											LIG1,NS,carcinoma,-2,1	LIG1	151	1	0			c.C510A						PASS	.	T		2454,1952	552.7+/-378.6	681,1092,430	138.0	128.0	131.0		510	1.3	0.0	19	dbSNP_67	131	4135,4465	590.2+/-392.6	1003,2129,1168	no	coding-synonymous	LIG1	NM_000234.1		1684,3221,1598	TT,TG,GG		48.0814,44.3032,49.3388		170/920	48654553	6589,6417	2203	4300	6503	SO:0001819	synonymous_variant	3978	exon7			CTCTGTGGCCACT		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.510C>A	19.37:g.48654553G>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_000234	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	37	CCDS12711.1																																																																																			G|0.479;T|0.521	0.521	strong		0.567	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
SCN3A	6328	hgsc.bcm.edu	37	2	166003479	166003479	+	Silent	SNP	G	G	A	rs16850131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:166003479G>A	ENST00000360093.3	-	12	1932	c.1441C>T	c.(1441-1443)Ctg>Ttg	p.L481L	SCN3A_ENST00000283254.7_Silent_p.L481L|RN7SL455P_ENST00000580629.1_RNA|SCN3A_ENST00000409101.3_Silent_p.L481L	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	481					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTTTCCAACAGCTCTCCTAAC	0.448													A|||	1289	0.257388	0.267	0.2032	5008	,	,		15691	0.3065		0.2008	False		,,,				2504	0.2904				p.L481L		Atlas-SNP	.											.	SCN3A	544	.	0			c.C1441T						PASS	.	A	,,	1089,3317	722.2+/-409.3	138,813,1252	125.0	125.0	125.0		1441,1441,1441	3.7	0.9	2	dbSNP_123	125	1841,6759	730.9+/-406.8	211,1419,2670	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN3A	NM_001081676.1,NM_001081677.1,NM_006922.3	,,	349,2232,3922	AA,AG,GG		21.407,24.7163,22.5281	,,	481/1952,481/1952,481/2001	166003479	2930,10076	2203	4300	6503	SO:0001819	synonymous_variant	6328	exon12			CCAACAGCTCTCC	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.1441C>T	2.37:g.166003479G>A		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	234	106	0.452991	NM_001081676	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																				G|0.756;A|0.244	0.244	strong		0.448	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
HIBCH	26275	hgsc.bcm.edu	37	2	191161622	191161622	+	Missense_Mutation	SNP	T	T	C	rs1058180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:191161622T>C	ENST00000359678.5	-	3	430	c.136A>G	c.(136-138)Acg>Gcg	p.T46A	HIBCH_ENST00000392332.3_Missense_Mutation_p.T46A	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	46			T -> A (in dbSNP:rs1058180). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			ATGACTCCCGTGCAACCTTTT	0.353													C|||	3427	0.684305	0.6331	0.7493	5008	,	,		18031	0.5724		0.7555	False		,,,				2504	0.7495				p.T46A		Atlas-SNP	.											.	HIBCH	28	.	0			c.A136G						PASS	.	C	ALA/THR,ALA/THR	2889,1517	482.1+/-359.3	968,953,282	126.0	114.0	118.0		136,136	5.3	1.0	2	dbSNP_86	118	6530,2070	357.3+/-330.7	2473,1584,243	yes	missense,missense	HIBCH	NM_014362.3,NM_198047.2	58,58	3441,2537,525	CC,CT,TT		24.0698,34.4303,27.5796	benign,benign	46/387,46/339	191161622	9419,3587	2203	4300	6503	SO:0001583	missense	26275	exon3			CTCCCGTGCAACC	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"""3-hydroxyisobutyryl-Coenzyme A hydrolase"""			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.136A>G	2.37:g.191161622T>C	ENSP00000352706:p.Thr46Ala	Somatic	360	1	0.00277778		WXS	Illumina HiSeq	Phase_I	355	157	0.442254	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	37	CCDS2304.1	1458	0.6675824175824175	308	0.6260162601626016	272	0.7513812154696132	306	0.534965034965035	572	0.7546174142480211	C	5.514	0.279732	0.10458	0.655697	0.759302	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000409934	T;T;T	0.71579	-0.58;-0.58;1.01	5.33	5.33	0.75918	.	0.096235	0.64402	N	0.000001	T	0.00012	0.0000	N	0.01109	-1.01	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38415	-0.9662	9	0.06625	T	0.88	-12.7013	12.0375	0.53433	0.0:0.9158:0.0:0.0842	rs1058180;rs3198778;rs3749019;rs17845047;rs17857824;rs52790607;rs56722526;rs1058180	46;46	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	A	46;46;100	ENSP00000376144:T46A;ENSP00000352706:T46A;ENSP00000387247:T100A	ENSP00000352706:T46A	T	-	1	0	HIBCH	190869867	1.000000	0.71417	0.997000	0.53966	0.611000	0.37282	2.982000	0.49337	1.274000	0.44362	-0.119000	0.15052	ACG	T|0.309;C|0.691	0.691	strong		0.353	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1		
PLIN4	729359	hgsc.bcm.edu	37	19	4511181	4511181	+	Missense_Mutation	SNP	C	C	T	rs115537722	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4511181C>T	ENST00000301286.3	-	3	2748	c.2749G>A	c.(2749-2751)Gtc>Atc	p.V917I		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	917	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CCACTGCAGACGGTGTCCTTG	0.602													C|||	138	0.0275559	0.053	0.0115	5008	,	,		22431	0.0		0.0119	False		,,,				2504	0.0491				p.V917I		Atlas-SNP	.											.	PLIN4	191	.	0			c.G2749A						PASS	.	C	ILE/VAL	156,4088		2,152,1968	87.0	89.0	88.0		2749	-0.3	0.0	19	dbSNP_132	88	125,8331		1,123,4104	yes	missense	PLIN4	NM_001080400.1	29	3,275,6072	TT,TC,CC		1.4782,3.6758,2.2126	probably-damaging	917/1358	4511181	281,12419	2122	4228	6350	SO:0001583	missense	729359	exon3			TGCAGACGGTGTC	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2749G>A	19.37:g.4511181C>T	ENSP00000301286:p.Val917Ile	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	171	101	0.590643	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	34	0.015567765567765568	23	0.046747967479674794	4	0.011049723756906077	0	0.0	7	0.009234828496042216	C	11.24	1.579143	0.28180	0.036758	0.014782	ENSG00000167676	ENST00000301286	T	0.07444	3.19	4.78	-0.273	0.12915	.	0.188403	0.25280	N	0.031810	T	0.00998	0.0033	M	0.77820	2.39	0.09310	N	1	P	0.38978	0.652	B	0.32149	0.141	T	0.27020	-1.0086	10	0.22109	T	0.4	-11.5486	2.3485	0.04278	0.1381:0.4268:0.2697:0.1654	.	917	Q96Q06	PLIN4_HUMAN	I	917	ENSP00000301286:V917I	ENSP00000301286:V917I	V	-	1	0	PLIN4	4462181	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-5.203000	0.00142	0.093000	0.17368	-0.448000	0.05591	GTC	C|0.985;T|0.015	0.015	strong		0.602	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
ZGRF1	55345	hgsc.bcm.edu	37	4	113524723	113524723	+	Missense_Mutation	SNP	G	G	A	rs17669218	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:113524723G>A	ENST00000505019.1	-	10	3058	c.2933C>T	c.(2932-2934)aCa>aTa	p.T978I	C4orf21_ENST00000309071.5_Missense_Mutation_p.T978I	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		978			T -> I (in dbSNP:rs17669218).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		TAACTCTGGTGTCTCTGTCAT	0.388													G|||	184	0.0367412	0.0068	0.0648	5008	,	,		17252	0.0		0.1183	False		,,,				2504	0.0112				p.T978I		Atlas-SNP	.											.	C4orf21	223	.	0			c.C2933T						PASS	.	G	ILE/THR	76,4330	67.0+/-104.6	1,74,2128	216.0	176.0	190.0		2933	1.6	0.0	4	dbSNP_123	190	866,7734	195.9+/-241.0	46,774,3480	yes	missense	C4orf21	NM_018392.4	89	47,848,5608	AA,AG,GG		10.0698,1.7249,7.2428	probably-damaging	978/2105	113524723	942,12064	2203	4300	6503	SO:0001583	missense	55345	exon10			TCTGGTGTCTCTG																												ENST00000505019.1:c.2933C>T	4.37:g.113524723G>A	ENSP00000424737:p.Thr978Ile	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	122	45	0.368852	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	37		117	0.05357142857142857	2	0.0040650406504065045	22	0.06077348066298342	0	0.0	93	0.12269129287598944	G	11.10	1.539541	0.27563	0.017249	0.100698	ENSG00000138658	ENST00000505019;ENST00000309071	D;T	0.81821	-1.54;1.88	5.38	1.63	0.23807	.	0.602886	0.15072	N	0.282141	T	0.03095	0.0091	L	0.60455	1.87	0.80722	P	0.0	B;B	0.24186	0.099;0.069	B;B	0.24701	0.034;0.055	T	0.47861	-0.9084	9	0.87932	D	0	0.4098	4.8825	0.13686	0.1598:0.0:0.5436:0.2966	rs17669218;rs52823729;rs57738409;rs17669218	978;978	Q86YA3;G5EA02	CD021_HUMAN;.	I	978	ENSP00000424737:T978I;ENSP00000309095:T978I	ENSP00000309095:T978I	T	-	2	0	C4orf21	113744172	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.313000	0.19415	-0.012000	0.14223	-0.266000	0.10368	ACA	G|0.937;A|0.063	0.063	strong		0.388	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
COL2A1	1280	hgsc.bcm.edu	37	12	48367976	48367976	+	Missense_Mutation	SNP	C	C	T	rs2070739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48367976C>T	ENST00000380518.3	-	53	4377	c.4213G>A	c.(4213-4215)Ggc>Agc	p.G1405S	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Missense_Mutation_p.G1336S	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	1405	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.		G -> S (in dbSNP:rs2070739). {ECO:0000269|PubMed:18272325}.		axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TTGAGGTTGCCAGCTGCTTCG	0.572													C|||	856	0.170927	0.0038	0.2896	5008	,	,		22912	0.4286		0.0964	False		,,,				2504	0.1237				p.G1405S		Atlas-SNP	.											.	COL2A1	368	.	0			c.G4213A						PASS	.	C	SER/GLY,SER/GLY	98,4308	79.9+/-118.3	3,92,2108	133.0	105.0	115.0		4213,4006	5.1	1.0	12	dbSNP_96	115	810,7790	188.9+/-235.7	42,726,3532	yes	missense,missense	COL2A1	NM_001844.4,NM_033150.2	56,56	45,818,5640	TT,TC,CC		9.4186,2.2242,6.9814	probably-damaging,probably-damaging	1405/1488,1336/1419	48367976	908,12098	2203	4300	6503	SO:0001583	missense	1280	exon53			GGTTGCCAGCTGC	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.4213G>A	12.37:g.48367976C>T	ENSP00000369889:p.Gly1405Ser	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	345	167	0.484058	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	37	CCDS41778.1	428	0.19597069597069597	5	0.01016260162601626	97	0.26795580110497236	244	0.42657342657342656	82	0.10817941952506596	C	24.2	4.509832	0.85282	0.022242	0.094186	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	T;T	0.74002	-0.8;-0.8	5.06	5.06	0.68205	Fibrillar collagen, C-terminal (4);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.86740	2.835	0.09310	P	0.999999999953964	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.02484	-1.1152	9	0.39692	T	0.17	.	18.3795	0.90445	0.0:1.0:0.0:0.0	rs2070739;rs2229808;rs57134744;rs2070739	1336;1405	P02458-1;P02458	.;CO2A1_HUMAN	S	1405;1336;1336	ENSP00000369889:G1405S;ENSP00000338213:G1336S	ENSP00000338213:G1336S	G	-	1	0	COL2A1	46654243	0.999000	0.42202	0.969000	0.41365	0.997000	0.91878	4.064000	0.57506	2.500000	0.84329	0.655000	0.94253	GGC	T|0.125;G|0.000	0.125	strong		0.572	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
NFKBIA	4792	hgsc.bcm.edu	37	14	35873770	35873770	+	Silent	SNP	G	G	A	rs1957106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:35873770G>A	ENST00000216797.5	-	1	182	c.81C>T	c.(79-81)gaC>gaT	p.D27D	NFKBIA_ENST00000557100.1_5'UTR|NFKBIA_ENST00000557140.1_Silent_p.D27D|NFKBIA_ENST00000557389.1_5'Flank	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	27					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	CGTGGCGGTCGTCCAGTAGCC	0.697													G|||	1224	0.244409	0.1354	0.1988	5008	,	,		7649	0.2649		0.2962	False		,,,				2504	0.3497				p.D27D		Atlas-SNP	.											.	NFKBIA	28	.	0			c.C81T						PASS	.	G		582,3696		63,456,1620	12.0	12.0	12.0		81	1.9	1.0	14	dbSNP_92	12	2316,6078		352,1612,2233	no	coding-synonymous	NFKBIA	NM_020529.2		415,2068,3853	AA,AG,GG		27.5911,13.6045,22.8693		27/318	35873770	2898,9774	2139	4197	6336	SO:0001819	synonymous_variant	4792	exon1			GCGGTCGTCCAGT		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"""Ankyrin repeat domain containing"""	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.81C>T	14.37:g.35873770G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_020529	B2R8L6	Silent	SNP	ENST00000216797.5	37	CCDS9656.1																																																																																			G|0.770;A|0.230	0.230	strong		0.697	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529	
ALPK2	115701	hgsc.bcm.edu	37	18	56205262	56205262	+	Missense_Mutation	SNP	A	A	C	rs12103986	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56205262A>C	ENST00000361673.3	-	5	2370	c.2157T>G	c.(2155-2157)caT>caG	p.H719Q	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	719			H -> Q (in dbSNP:rs12103986). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GTTTTTCTTCATGCTGTGGAC	0.448													C|||	2025	0.404353	0.4312	0.4294	5008	,	,		23677	0.2361		0.5736	False		,,,				2504	0.3497				p.H719Q		Atlas-SNP	.											.	ALPK2	487	.	0			c.T2157G						PASS	.	C	GLN/HIS	1987,2419	616.7+/-392.8	446,1095,662	169.0	145.0	153.0		2157	-5.1	0.0	18	dbSNP_120	153	4593,4007	555.2+/-386.6	1237,2119,944	yes	missense	ALPK2	NM_052947.3	24	1683,3214,1606	CC,CA,AA		46.593,45.0976,49.408	benign	719/2171	56205262	6580,6426	2203	4300	6503	SO:0001583	missense	115701	exon5			TTCTTCATGCTGT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2157T>G	18.37:g.56205262A>C	ENSP00000354991:p.His719Gln	Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	303	105	0.346535	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	955	0.43727106227106227	189	0.38414634146341464	184	0.5082872928176796	137	0.2395104895104895	445	0.5870712401055409	C	0.376	-0.931153	0.02359	0.450976	0.53407	ENSG00000198796	ENST00000361673	T	0.39592	1.07	5.64	-5.12	0.02893	.	0.972088	0.08477	N	0.940021	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39800	-0.9596	9	0.02654	T	1	0.6961	10.1225	0.42630	0.3517:0.2202:0.4281:0.0	rs12103986;rs52837847;rs58231351;rs12103986	719;719	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	Q	719	ENSP00000354991:H719Q	ENSP00000354991:H719Q	H	-	3	2	ALPK2	54356242	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.093000	0.03362	-1.351000	0.02197	-2.084000	0.00378	CAT	A|0.529;C|0.471	0.471	strong		0.448	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
SLX4	84464	hgsc.bcm.edu	37	16	3656482	3656482	+	Silent	SNP	C	C	T	rs8061528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3656482C>T	ENST00000294008.3	-	3	1393	c.753G>A	c.(751-753)gcG>gcA	p.A251A		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	251	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TACCATTCCCCGCCATCATCT	0.507								Direct reversal of damage					C|||	1156	0.230831	0.2466	0.1902	5008	,	,		19972	0.2808		0.1978	False		,,,				2504	0.2209				p.A251A		Atlas-SNP	.											.	SLX4	173	.	0			c.G753A						PASS	.	C		1099,3295	395.4+/-329.6	135,829,1233	237.0	230.0	233.0		753	-8.8	0.0	16	dbSNP_116	233	1746,6854	318.3+/-313.6	183,1380,2737	no	coding-synonymous	SLX4	NM_032444.2		318,2209,3970	TT,TC,CC		20.3023,25.0114,21.8947		251/1835	3656482	2845,10149	2197	4300	6497	SO:0001819	synonymous_variant	84464	exon3			ATTCCCCGCCATC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.753G>A	16.37:g.3656482C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	202	91	0.450495	NM_032444	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	37	CCDS10506.2																																																																																			C|0.767;T|0.233	0.233	strong		0.507	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
MED13L	23389	hgsc.bcm.edu	37	12	116446445	116446445	+	Silent	SNP	C	C	T	rs3741768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:116446445C>T	ENST00000281928.3	-	10	1979	c.1773G>A	c.(1771-1773)caG>caA	p.Q591Q		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	591						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		GAGTAGACAACTGCTGGAGTT	0.532													C|||	718	0.143371	0.0461	0.1268	5008	,	,		20760	0.1637		0.1869	False		,,,				2504	0.2209				p.Q591Q		Atlas-SNP	.											.	MED13L	193	.	0			c.G1773A						PASS	.	C		319,4087	171.2+/-201.5	4,311,1888	66.0	58.0	60.0		1773	-2.3	1.0	12	dbSNP_107	60	1530,7070	287.8+/-298.4	121,1288,2891	no	coding-synonymous	MED13L	NM_015335.4		125,1599,4779	TT,TC,CC		17.7907,7.2401,14.2165		591/2211	116446445	1849,11157	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon10			AGACAACTGCTGG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.1773G>A	12.37:g.116446445C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	215	110	0.511628	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																			C|0.855;T|0.145	0.145	strong		0.532	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
P2RY11	5032	hgsc.bcm.edu	37	19	10226686	10226686	+	IGR	SNP	G	G	A	rs200490441	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10226686G>A	ENST00000321826.4	+	0	1943				EIF3G_ENST00000587168.1_5'Flank|EIF3G_ENST00000253108.4_Silent_p.D220D	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11						activation of adenylate cyclase activity (GO:0007190)|adenosine receptor signaling pathway (GO:0001973)|calcium-mediated signaling (GO:0019722)|cellular response to ATP (GO:0071318)|defense response (GO:0006952)|G-protein coupled receptor signaling pathway (GO:0007186)|neuronal signal transduction (GO:0023041)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|neurotransmitter receptor activity (GO:0030594)|receptor activity (GO:0004872)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)	16			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			GGCTGGCCCCGTCGCGCAGGC	0.662													G|||	2	0.000399361	0.0	0.0	5008	,	,		15153	0.002		0.0	False		,,,				2504	0.0				p.D220D		Atlas-SNP	.											.	EIF3G	16	.	0			c.C660T						PASS	.	G		0,4402		0,0,2201	26.0	27.0	27.0		660	-5.3	0.9	19		27	1,8593		0,1,4296	no	coding-synonymous	EIF3G	NM_003755.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		220/321	10226686	1,12995	2201	4297	6498	SO:0001628	intergenic_variant	8666	exon8			GGCCCCGTCGCGC	AF030335	CCDS12226.1	19p13.2	2012-08-08			ENSG00000244165	ENSG00000244165		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8540	protein-coding gene	gene with protein product		602697				9405388	Standard	NM_002566		Approved	P2Y11		Q96G91	OTTHUMG00000150166		19.37:g.10226686G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	NM_003755	B2R8X9|O43190|Q9BYU4|Q9H170	Silent	SNP	ENST00000321826.4	37	CCDS12226.1																																																																																			G|0.999;A|0.001	0.001	strong		0.662	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
FAT1	2195	hgsc.bcm.edu	37	4	187534363	187534363	+	Silent	SNP	G	G	A	rs2249916	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187534363G>A	ENST00000441802.2	-	13	9572	c.9363C>T	c.(9361-9363)aaC>aaT	p.N3121N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3121	Cadherin 28. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATTCGGGGGCGTTATCGTTCA	0.532										HNSCC(5;0.00058)			g|||	3062	0.611422	0.7398	0.6571	5008	,	,		17924	0.6657		0.5805	False		,,,				2504	0.3814				p.N3121N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C9363T						PASS	.	A		2897,1185		1046,805,190	95.0	101.0	99.0		9363	-10.4	0.0	4	dbSNP_100	99	4862,3526		1409,2044,741	no	coding-synonymous	FAT1	NM_005245.3		2455,2849,931	AA,AG,GG		42.0362,29.0299,37.7787		3121/4589	187534363	7759,4711	2041	4194	6235	SO:0001819	synonymous_variant	2195	exon13			GGGGGCGTTATCG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.9363C>T	4.37:g.187534363G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.346;T|0.010	.	strong		0.532	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
EPPK1	83481	hgsc.bcm.edu	37	8	144941419	144941419	+	Silent	SNP	C	C	T	rs12681478	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144941419C>T	ENST00000525985.1	-	2	6074	c.6003G>A	c.(6001-6003)gcG>gcA	p.A2001A				P58107	EPIPL_HUMAN	epiplakin 1	2001						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCAGTGCCTCCGCCTTCTCGA	0.642													C|||	1066	0.212859	0.0113	0.33	5008	,	,		18060	0.1399		0.3708	False		,,,				2504	0.3149				p.A2001A		Atlas-SNP	.											EPPK1,NS,carcinoma,0,1	EPPK1	199	1	0			c.G6003A						PASS	.	C		369,3945		22,325,1810	35.0	39.0	37.0		6003	-3.7	0.0	8	dbSNP_120	37	3411,5111		676,2059,1526	no	coding-synonymous	EPPK1	NM_031308.1		698,2384,3336	TT,TC,CC		40.0258,8.5535,29.4484		2001/2420	144941419	3780,9056	2157	4261	6418	SO:0001819	synonymous_variant	83481	exon1			TGCCTCCGCCTTC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6003G>A	8.37:g.144941419C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.740;T|0.260	0.260	strong		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
USP8	9101	hgsc.bcm.edu	37	15	50785016	50785016	+	Missense_Mutation	SNP	A	A	G	rs148783236	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:50785016A>G	ENST00000396444.3	+	15	2691	c.2353A>G	c.(2353-2355)Act>Gct	p.T785A	RP11-562A8.5_ENST00000560159.1_lincRNA|USP8_ENST00000433963.1_Missense_Mutation_p.T785A|USP8_ENST00000425032.3_Missense_Mutation_p.T679A|USP8_ENST00000307179.4_Missense_Mutation_p.T785A	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	785	USP.				cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.T785A(2)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		CTTAGGAAATACTTGTTATAT	0.398																																					p.T785A		Atlas-SNP	.											USP8,NS,carcinoma,0,3	USP8	90	3	2	Substitution - Missense(2)	prostate(2)	c.A2353G						scavenged	.						118.0	105.0	110.0					15																	50785016		2196	4294	6490	SO:0001583	missense	9101	exon15			GGAAATACTTGTT	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2353A>G	15.37:g.50785016A>G	ENSP00000379721:p.Thr785Ala	Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	170	15	0.0882353	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	37	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.653902	0.88056	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032;ENST00000419830;ENST00000396440	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.74496	0.3724	H	0.95712	3.71	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.79108	0.964;0.992	T	0.83303	-0.0027	10	0.87932	D	0	-18.2981	15.3993	0.74827	1.0:0.0:0.0:0.0	.	679;785	B4DKA8;P40818	.;UBP8_HUMAN	A	785;785;785;679;10;10	ENSP00000379721:T785A;ENSP00000405537:T785A;ENSP00000302239:T785A;ENSP00000412682:T679A	ENSP00000302239:T785A	T	+	1	0	USP8	48572308	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.648000	0.91062	2.096000	0.63516	0.528000	0.53228	ACT	G|1.000;|0.000	1.000	weak		0.398	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154	
PLXNA3	55558	hgsc.bcm.edu	37	X	153696247	153696247	+	Silent	SNP	G	G	C	rs5987266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153696247G>C	ENST00000369682.3	+	21	3898	c.3723G>C	c.(3721-3723)gcG>gcC	p.A1241A		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1241					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGCTGGTGGCGTACAAGCGCA	0.667													C|||	1443	0.382252	0.6422	0.1037	3775	,	,		9172	0.131		0.0994	False		,,,				2504	0.2965				p.A1241A		Atlas-SNP	.											.	PLXNA3	156	.	0			c.G3723C						PASS	.	C		2874,960		918,603,435,111,135	46.0	46.0	46.0		3723	3.0	1.0	X	dbSNP_114	46	947,5781		52,559,284,1817,1588	no	coding-synonymous	PLXNA3	NM_017514.3		970,1162,719,1928,1723	CC,CG,C,GG,G		14.0755,25.0391,36.1769		1241/1872	153696247	3821,6741	2202	4300	6502	SO:0001819	synonymous_variant	55558	exon21			GGTGGCGTACAAG	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.3723G>C	X.37:g.153696247G>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_017514	Q5HY36	Silent	SNP	ENST00000369682.3	37	CCDS14752.1																																																																																			G|0.642;C|0.358	0.358	strong		0.667	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
CLMN	79789	hgsc.bcm.edu	37	14	95660242	95660242	+	Silent	SNP	A	A	G	rs1128468	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:95660242A>G	ENST00000298912.4	-	12	2897	c.2784T>C	c.(2782-2784)taT>taC	p.Y928Y	CLMN_ENST00000556441.1_5'UTR|CLMN_ENST00000557215.1_5'UTR	NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	928					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		TCAACTGAACATAGCTAAAAT	0.373													A|||	757	0.151158	0.0915	0.0648	5008	,	,		16060	0.3333		0.0706	False		,,,				2504	0.1881				p.Y928Y		Atlas-SNP	.											.	CLMN	103	.	0			c.T2784C						PASS	.	A		454,3952	218.1+/-236.3	22,410,1771	110.0	104.0	106.0		2784	4.9	1.0	14	dbSNP_86	106	684,7916	171.0+/-222.0	26,632,3642	no	coding-synonymous	CLMN	NM_024734.3		48,1042,5413	GG,GA,AA		7.9535,10.3041,8.7498		928/1003	95660242	1138,11868	2203	4300	6503	SO:0001819	synonymous_variant	79789	exon12			CTGAACATAGCTA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2784T>C	14.37:g.95660242A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Silent	SNP	ENST00000298912.4	37	CCDS9933.1																																																																																			A|0.884;G|0.116	0.116	strong		0.373	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
ZNF221	7638	hgsc.bcm.edu	37	19	44471252	44471252	+	Missense_Mutation	SNP	T	T	C	rs61734609	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44471252T>C	ENST00000251269.5	+	6	1926	c.1598T>C	c.(1597-1599)cTa>cCa	p.L533P	ZNF221_ENST00000587682.1_Missense_Mutation_p.L533P|ZNF221_ENST00000592350.1_Missense_Mutation_p.L533P	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	533					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				GGAGAAAAGCTATACAAATGT	0.433													T|||	479	0.095647	0.0151	0.0893	5008	,	,		22087	0.1389		0.1163	False		,,,				2504	0.1431				p.L533P		Atlas-SNP	.											.	ZNF221	59	.	0			c.T1598C						PASS	.	T	PRO/LEU	128,4278	93.0+/-131.7	1,126,2076	94.0	87.0	90.0		1598	1.7	0.0	19	dbSNP_129	90	942,7658	207.2+/-249.0	44,854,3402	yes	missense	ZNF221	NM_013359.2	98	45,980,5478	CC,CT,TT		10.9535,2.9051,8.227	benign	533/618	44471252	1070,11936	2203	4300	6503	SO:0001583	missense	7638	exon6			AAAAGCTATACAA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"""Zinc fingers, C2H2-type"", ""-"""	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1598T>C	19.37:g.44471252T>C	ENSP00000251269:p.Leu533Pro	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	37	CCDS12633.1	223	0.1021062271062271	12	0.024390243902439025	36	0.09944751381215469	83	0.1451048951048951	92	0.12137203166226913	t	0.015	-1.548005	0.00926	0.029051	0.109535	ENSG00000159905	ENST00000251269	T	0.09911	2.93	2.9	1.74	0.24563	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.01405	-0.89	0.29025	P	0.886041	B	0.02656	0.0	B	0.04013	0.001	T	0.44590	-0.9318	8	0.02654	T	1	.	7.5568	0.27829	0.0:0.8416:0.0:0.1584	rs61734609	533	Q9UK13	ZN221_HUMAN	P	533	ENSP00000251269:L533P	ENSP00000251269:L533P	L	+	2	0	ZNF221	49163092	0.085000	0.21516	0.001000	0.08648	0.183000	0.23260	0.945000	0.29056	0.403000	0.25479	0.379000	0.24179	CTA	T|0.910;C|0.090	0.090	strong		0.433	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1		
ANO1	55107	hgsc.bcm.edu	37	11	70007311	70007311	+	Silent	SNP	A	A	G	rs2276066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:70007311A>G	ENST00000355303.5	+	17	1928	c.1623A>G	c.(1621-1623)agA>agG	p.R541R	ANO1_ENST00000316296.5_Silent_p.R483R|ANO1_ENST00000538023.1_Silent_p.R541R|ANO1_ENST00000530676.1_Silent_p.R395R|ANO1_ENST00000531349.1_Silent_p.R250R|ANO1_ENST00000398543.2_Silent_p.R395R	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	541					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	TCATCTACAGAATCTCCATGG	0.617													A|||	3021	0.603235	0.3986	0.5807	5008	,	,		20089	0.7798		0.6501	False		,,,				2504	0.6656				p.R541R		Atlas-SNP	.											.	ANO1	156	.	0			c.A1623G						PASS	.	A		1872,2378		415,1042,668	69.0	73.0	71.0		1623	-2.7	1.0	11	dbSNP_100	71	5568,2866		1856,1856,505	no	coding-synonymous	ANO1	NM_018043.5		2271,2898,1173	GG,GA,AA		33.9815,44.0471,41.3434		541/987	70007311	7440,5244	2125	4217	6342	SO:0001819	synonymous_variant	55107	exon17			CTACAGAATCTCC	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.1623A>G	11.37:g.70007311A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	55	0.433071	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Silent	SNP	ENST00000355303.5	37	CCDS44663.1																																																																																			A|0.393;G|0.607	0.607	strong		0.617	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
ATP6V0A2	23545	hgsc.bcm.edu	37	12	124241506	124241506	+	Missense_Mutation	SNP	C	C	T	rs17883456	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124241506C>T	ENST00000330342.3	+	19	2686	c.2438C>T	c.(2437-2439)gCg>gTg	p.A813V	ATP6V0A2_ENST00000543687.1_3'UTR|ATP6V0A2_ENST00000544833.1_Missense_Mutation_p.A95V	NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	813			A -> V (in dbSNP:rs17883456).		ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		GGGCTTTCTGCGTTTCTTCAC	0.522													C|||	74	0.0147764	0.0023	0.0187	5008	,	,		15236	0.0		0.0398	False		,,,				2504	0.0184				p.A813V		Atlas-SNP	.											.	ATP6V0A2	68	.	0			c.C2438T						PASS	.	C	VAL/ALA	33,4373	38.4+/-70.7	0,33,2170	158.0	124.0	136.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2438	5.7	0.8	12	dbSNP_124	136	303,8297	110.2+/-170.6	5,293,4002	yes	missense	ATP6V0A2	NM_012463.3	64	5,326,6172	TT,TC,CC		3.5233,0.749,2.5834	probably-damaging	813/857	124241506	336,12670	2203	4300	6503	SO:0001583	missense	23545	exon19			TTTCTGCGTTTCT	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"""ATPases / V-type"""	18481	protein-coding gene	gene with protein product	"""infantile malignant osteopetrosis"""	611716	"""infantile malignant osteopetrosis"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 2"", ""ATPase, H+ transporting, lysosomal V0 subunit A2"""			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.2438C>T	12.37:g.124241506C>T	ENSP00000332247:p.Ala813Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_012463	A8K026|Q6NUM0	Missense_Mutation	SNP	ENST00000330342.3	37	CCDS9254.1	37	0.01694139194139194	3	0.006097560975609756	7	0.019337016574585635	0	0.0	27	0.03562005277044855	C	36	5.742703	0.96873	0.00749	0.035233	ENSG00000185344	ENST00000330342;ENST00000534943;ENST00000544833	D;D;D	0.91843	-2.92;-2.92;-2.92	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.90745	0.7095	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.90091	0.4177	10	0.72032	D	0.01	-23.8071	19.8579	0.96771	0.0:1.0:0.0:0.0	rs17883456	813	Q9Y487	VPP2_HUMAN	V	813;93;95	ENSP00000332247:A813V;ENSP00000443726:A93V;ENSP00000441143:A95V	ENSP00000332247:A813V	A	+	2	0	ATP6V0A2	122807459	1.000000	0.71417	0.791000	0.31998	0.964000	0.63967	7.743000	0.85020	2.687000	0.91594	0.655000	0.94253	GCG	C|0.976;T|0.024	0.024	strong		0.522	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463	
PLXNA2	5362	hgsc.bcm.edu	37	1	208227814	208227814	+	Silent	SNP	C	C	T	rs2274447	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:208227814C>T	ENST00000367033.3	-	14	3565	c.2808G>A	c.(2806-2808)gaG>gaA	p.E936E		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	936	IPT/TIG 1.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CTGGCTTACACTCGCCAATAC	0.582													C|||	52	0.0103834	0.0	0.0029	5008	,	,		21260	0.0129		0.004	False		,,,				2504	0.0337				p.E936E		Atlas-SNP	.											PLXNA2,caecum,carcinoma,-2,1	PLXNA2	178	1	0			c.G2808A						scavenged	.	C		6,4400	11.4+/-27.6	0,6,2197	105.0	83.0	90.0		2808	3.5	1.0	1	dbSNP_100	90	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	PLXNA2	NM_025179.3		0,41,6462	TT,TC,CC		0.407,0.1362,0.3152		936/1895	208227814	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon14			CTTACACTCGCCA	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2808G>A	1.37:g.208227814C>T		Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	127	52	0.409449	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			C|0.995;T|0.005	0.005	strong		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
AKAP5	9495	hgsc.bcm.edu	37	14	64935726	64935726	+	Missense_Mutation	SNP	C	C	T	rs2230492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:64935726C>T	ENST00000394718.4	+	2	992	c.614C>T	c.(613-615)tCt>tTt	p.S205F	ZBTB25_ENST00000555220.1_Intron|AKAP5_ENST00000320636.5_Missense_Mutation_p.S205F|ZBTB25_ENST00000555424.1_Intron	NM_004857.3	NP_004848.3	P24588	AKAP5_HUMAN	A kinase (PRKA) anchor protein 5	205					energy reserve metabolic process (GO:0006112)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|stomach(1)	13				all cancers(60;0.00749)|OV - Ovarian serous cystadenocarcinoma(108;0.0095)|BRCA - Breast invasive adenocarcinoma(234;0.0449)		AGCACAACTTCTGGAGAGAAA	0.413													C|||	7	0.00139776	0.0	0.0	5008	,	,		21422	0.0		0.006	False		,,,				2504	0.001				p.S205F		Atlas-SNP	.											.	AKAP5	23	.	0			c.C614T						PASS	.	C	PHE/SER	7,4399	12.9+/-30.5	0,7,2196	97.0	101.0	100.0		614	6.0	1.0	14	dbSNP_98	100	56,8544	35.9+/-90.5	0,56,4244	yes	missense	AKAP5	NM_004857.3	155	0,63,6440	TT,TC,CC		0.6512,0.1589,0.4844	benign	205/428	64935726	63,12943	2203	4300	6503	SO:0001583	missense	9495	exon2			CAACTTCTGGAGA	M90359	CCDS9764.1	14q23.3	2012-05-16			ENSG00000179841	ENSG00000179841		"""A-kinase anchor proteins"""	375	protein-coding gene	gene with protein product		604688				1512224, 1618839	Standard	NM_004857		Approved	AKAP75, AKAP79	uc001xhd.4	P24588	OTTHUMG00000029634	ENST00000394718.4:c.614C>T	14.37:g.64935726C>T	ENSP00000378207:p.Ser205Phe	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_004857	A2RRB8	Missense_Mutation	SNP	ENST00000394718.4	37	CCDS9764.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	15.66	2.899719	0.52227	0.001589	0.006512	ENSG00000179841	ENST00000394718;ENST00000320636	T;T	0.32272	1.46;1.46	6.02	6.02	0.97574	.	0.341615	0.25383	N	0.031074	T	0.39860	0.1094	L	0.55481	1.735	0.37227	D	0.905491	D	0.65815	0.995	P	0.57371	0.819	T	0.46652	-0.9176	10	0.87932	D	0	-9.0253	17.454	0.87602	0.0:1.0:0.0:0.0	rs2230492;rs2230492	205	P24588	AKAP5_HUMAN	F	205	ENSP00000378207:S205F;ENSP00000315615:S205F	ENSP00000315615:S205F	S	+	2	0	AKAP5	64005479	0.035000	0.19736	0.957000	0.39632	0.717000	0.41224	1.428000	0.34892	2.857000	0.98124	0.650000	0.86243	TCT	C|0.996;T|0.004	0.004	strong		0.413	AKAP5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268070.3		
GOLGB1	2804	hgsc.bcm.edu	37	3	121416623	121416623	+	Missense_Mutation	SNP	G	G	C	rs3732407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121416623G>C	ENST00000340645.5	-	13	2857	c.2732C>G	c.(2731-2733)aCt>aGt	p.T911S	GOLGB1_ENST00000393667.3_Missense_Mutation_p.T916S	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	911			T -> S (in dbSNP:rs3732407). {ECO:0000269|PubMed:18487259}.		Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CATTTTCTCAGTCATACTAAA	0.383													G|||	528	0.105431	0.0121	0.147	5008	,	,		20713	0.0476		0.2435	False		,,,				2504	0.1196				p.T916S		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C2747G						PASS	.	G	SER/THR	181,4225	116.7+/-154.6	3,175,2025	143.0	148.0	146.0		2732	4.5	1.0	3	dbSNP_107	146	2073,6525	359.6+/-331.6	263,1547,2489	yes	missense	GOLGB1	NM_004487.3	58	266,1722,4514	CC,CG,GG		24.1103,4.108,17.3331	benign	911/3260	121416623	2254,10750	2203	4299	6502	SO:0001583	missense	2804	exon13			TTCTCAGTCATAC	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.2732C>G	3.37:g.121416623G>C	ENSP00000341848:p.Thr911Ser	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	212	101	0.476415	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	303|303	0.13873626373626374|0.13873626373626374	10|10	0.02032520325203252|0.02032520325203252	70|70	0.19337016574585636|0.19337016574585636	34|34	0.05944055944055944|0.05944055944055944	189|189	0.24934036939313983|0.24934036939313983	G|G	7.435|7.435	0.639547|0.639547	0.14386|0.14386	0.04108|0.04108	0.241103|0.241103	ENSG00000173230|ENSG00000173230	ENST00000489400|ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	.|T;T;T	.|0.13089	.|3.16;3.16;2.62	5.35|5.35	4.48|4.48	0.54585|0.54585	.|.	.|0.198851	.|0.35495	.|N	.|0.003174	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.13043|0.13043	0.29|0.29	0.43545|0.43545	P|P	0.004153999999999991|0.004153999999999991	.|B;B;B;B	.|0.15141	.|0.012;0.005;0.012;0.002	.|B;B;B;B	.|0.19946	.|0.027;0.013;0.027;0.012	T|T	0.42481|0.42481	-0.9449|-0.9449	4|9	.|0.09843	.|T	.|0.71	.|.	12.0937|12.0937	0.53742|0.53742	0.0827:0.0:0.9173:0.0|0.0827:0.0:0.9173:0.0	rs3732407;rs17549959;rs52791658;rs3732407|rs3732407;rs17549959;rs52791658;rs3732407	.|836;875;916;911	.|F1T0J2;E7EU81;E7EP74;Q14789	.|.;.;.;GOGB1_HUMAN	V|S	782|911;916;875;723	.|ENSP00000341848:T911S;ENSP00000377275:T916S;ENSP00000418231:T875S	.|ENSP00000341848:T911S	L|T	-|-	1|2	2|0	GOLGB1|GOLGB1	122899313|122899313	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.999000|0.999000	0.98932|0.98932	3.941000|3.941000	0.56607|0.56607	1.493000|1.493000	0.48517|0.48517	0.655000|0.655000	0.94253|0.94253	CTG|ACT	G|0.843;C|0.157	0.157	strong		0.383	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
TRPA1	8989	hgsc.bcm.edu	37	8	72948588	72948588	+	Silent	SNP	C	C	T	rs13280644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:72948588C>T	ENST00000262209.4	-	21	2697	c.2490G>A	c.(2488-2490)ctG>ctA	p.L830L	RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron|TRPA1_ENST00000519720.1_5'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	830					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ATTGCCACTGCAGATGAGCTG	0.353													C|||	251	0.0501198	0.0045	0.0634	5008	,	,		17025	0.003		0.0924	False		,,,				2504	0.1074				p.L830L		Atlas-SNP	.											.	TRPA1	256	.	0			c.G2490A						PASS	.	C		78,4328	69.8+/-107.6	0,78,2125	67.0	66.0	67.0		2490	0.2	0.6	8	dbSNP_121	67	841,7759	193.7+/-239.3	46,749,3505	no	coding-synonymous	TRPA1	NM_007332.2		46,827,5630	TT,TC,CC		9.7791,1.7703,7.066		830/1120	72948588	919,12087	2203	4300	6503	SO:0001819	synonymous_variant	8989	exon21			CCACTGCAGATGA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2490G>A	8.37:g.72948588C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	254	119	0.468504	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			C|0.934;T|0.066	0.066	strong		0.353	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
MYO15A	51168	hgsc.bcm.edu	37	17	18058468	18058468	+	Missense_Mutation	SNP	G	G	A	rs140140417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18058468G>A	ENST00000205890.5	+	46	8607	c.8269G>A	c.(8269-8271)Gtg>Atg	p.V2757M	MYO15A_ENST00000418233.3_Missense_Mutation_p.V21M|MYO15A_ENST00000585180.1_Missense_Mutation_p.V21M	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2757	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					AACGGAAAGCGTGAAGCGGGC	0.642													G|||	11	0.00219649	0.0015	0.0058	5008	,	,		18941	0.0		0.002	False		,,,				2504	0.0031				p.V2757M		Atlas-SNP	.											.	MYO15A	268	.	0			c.G8269A						PASS	.	G	MET/VAL	0,4188		0,0,2094	41.0	51.0	47.0		8269	-0.2	0.3	17	dbSNP_134	47	18,8416		0,18,4199	yes	missense	MYO15A	NM_016239.3	21	0,18,6293	AA,AG,GG		0.2134,0.0,0.1426	probably-damaging	2757/3531	18058468	18,12604	2094	4217	6311	SO:0001583	missense	51168	exon45			GAAAGCGTGAAGC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8269G>A	17.37:g.18058468G>A	ENSP00000205890:p.Val2757Met	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	6	0.0027472527472527475	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	4.445	0.082431	0.08533	0.0	0.002134	ENSG00000091536	ENST00000205890	D	0.90788	-2.73	5.2	-0.241	0.13043	.	.	.	.	.	D	0.83709	0.5313	M	0.71206	2.165	0.39248	D	0.963971	B;B	0.29341	0.242;0.149	B;B	0.29663	0.105;0.01	T	0.80765	-0.1236	9	0.87932	D	0	.	6.7414	0.23439	0.2809:0.0:0.5946:0.1245	.	21;2757	B4DFC7;Q9UKN7	.;MYO15_HUMAN	M	2757	ENSP00000205890:V2757M	ENSP00000205890:V2757M	V	+	1	0	MYO15A	17999193	0.906000	0.30813	0.279000	0.24732	0.136000	0.21042	1.276000	0.33156	0.104000	0.17725	0.561000	0.74099	GTG	G|0.998;A|0.002	0.002	strong		0.642	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
PER3	8863	hgsc.bcm.edu	37	1	7890053	7890053	+	Missense_Mutation	SNP	G	G	A	rs1776342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7890053G>A	ENST00000361923.2	+	18	3194	c.3019G>A	c.(3019-3021)Gct>Act	p.A1007T	PER3_ENST00000377532.3_Missense_Mutation_p.A1016T|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1007	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.		A -> T (in dbSNP:rs1776342).|Missing (associated with eveningness and better cognitive performance during sleep deprivation exepriments; dbSNP:rs57875989).		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.A1007T(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TACTGCCAGCGCTCTGTCCAC	0.587																																					p.A1007T		Atlas-SNP	.											PER3,NS,carcinoma,0,1	PER3	95	1	1	Substitution - Missense(1)	kidney(1)	c.G3019A						PASS	.						87.0	69.0	75.0					1																	7890053		1995	3902	5897	SO:0001583	missense	8863	exon18			GCCAGCGCTCTGT	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3019G>A	1.37:g.7890053G>A	ENSP00000355031:p.Ala1007Thr	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	98	28	0.285714	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	g	0.668	-0.803078	0.02841	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.14391	2.51;2.51	0.119	0.119	0.14685	Period circadian-like, C-terminal (1);	9.368370	0.00166	N	0.000019	T	0.09158	0.0226	N	0.20685	0.6	0.09310	N	1	B;B;B;B;B	0.25048	0.025;0.007;0.066;0.117;0.007	B;B;B;B;B	0.23018	0.002;0.004;0.004;0.043;0.004	T	0.25676	-1.0125	9	0.18710	T	0.47	.	.	.	.	rs1776342	56;1007;1016;1016;1007	B4DR65;A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;.;PER3_HUMAN	T	1016;1007	ENSP00000366755:A1016T;ENSP00000355031:A1007T	ENSP00000355031:A1007T	A	+	1	0	PER3	7812640	0.000000	0.05858	0.068000	0.19968	0.074000	0.17049	-0.849000	0.04322	0.275000	0.22094	0.280000	0.19369	GCT	G|0.990;A|0.010	0.010	strong		0.587	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
KIAA1755	85449	hgsc.bcm.edu	37	20	36845738	36845738	+	Missense_Mutation	SNP	C	C	T	rs760998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:36845738C>T	ENST00000279024.4	-	13	3089	c.2818G>A	c.(2818-2820)Gag>Aag	p.E940K		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	940			E -> K (in dbSNP:rs760998). {ECO:0000269|PubMed:11214970}.							breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				TGGGTCAGCTCAGCCTGGAAG	0.667													T|||	1685	0.336462	0.2504	0.3429	5008	,	,		14156	0.5188		0.2982	False		,,,				2504	0.2996				p.E940K		Atlas-SNP	.											KIAA1755,NS,carcinoma,0,1	KIAA1755	145	1	0			c.G2818A						scavenged	.	T	LYS/GLU	1119,3285	703.8+/-407.0	143,833,1226	41.0	36.0	37.0		2818	3.5	0.2	20	dbSNP_86	37	2711,5889	666.8+/-402.4	415,1881,2004	yes	missense	KIAA1755	NM_001029864.1	56	558,2714,3230	TT,TC,CC		31.5233,25.4087,29.4525	benign	940/1201	36845738	3830,9174	2202	4300	6502	SO:0001583	missense	85449	exon13			TCAGCTCAGCCTG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2818G>A	20.37:g.36845738C>T	ENSP00000279024:p.Glu940Lys	Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	171	93	0.54386	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	765	0.35027472527472525	125	0.2540650406504065	121	0.3342541436464088	283	0.49475524475524474	236	0.3113456464379947	T	1.353	-0.590772	0.03799	0.254087	0.315233	ENSG00000149633	ENST00000279024;ENST00000373398;ENST00000435901	T;T	0.21031	3.53;2.03	4.59	3.46	0.39613	.	0.419614	0.20255	N	0.095994	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46569	-0.9182	9	0.02654	T	1	.	5.9032	0.18978	0.0:0.0899:0.1666:0.7435	rs760998;rs57283281;rs760998	940;448	Q5JYT7;E9PFS1	K1755_HUMAN;.	K	940;448;239	ENSP00000279024:E940K;ENSP00000393503:E239K	ENSP00000279024:E940K	E	-	1	0	KIAA1755	36279152	0.981000	0.34729	0.171000	0.22900	0.605000	0.37080	2.366000	0.44204	0.271000	0.22005	-0.361000	0.07541	GAG	C|0.680;T|0.320	0.320	strong		0.667	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
PER3	8863	hgsc.bcm.edu	37	1	7897133	7897133	+	Missense_Mutation	SNP	A	A	G	rs10462021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7897133A>G	ENST00000361923.2	+	20	3621	c.3446A>G	c.(3445-3447)cAt>cGt	p.H1149R	PER3_ENST00000377532.3_Missense_Mutation_p.H1158R	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1149	CRY binding domain. {ECO:0000250}.		H -> R (in dbSNP:rs10462021). {ECO:0000269|PubMed:11306557}.		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CAGTTTTCTCATGGGCAAAAG	0.408													A|||	606	0.121006	0.0711	0.2133	5008	,	,		9049	0.0079		0.1968	False		,,,				2504	0.1616				p.H1149R		Atlas-SNP	.											.	PER3	95	.	0			c.A3446G						PASS	.	A	ARG/HIS	423,3983	206.8+/-228.3	19,385,1799	66.0	63.0	64.0		3446	-8.5	0.0	1	dbSNP_119	64	1644,6956	303.4+/-306.4	162,1320,2818	yes	missense	PER3	NM_016831.1	29	181,1705,4617	GG,GA,AA		19.1163,9.6005,15.8927	benign	1149/1202	7897133	2067,10939	2203	4300	6503	SO:0001583	missense	8863	exon20			TTTCTCATGGGCA	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3446A>G	1.37:g.7897133A>G	ENSP00000355031:p.His1149Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	87	57	0.655172	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	258	0.11813186813186813	48	0.0975609756097561	62	0.1712707182320442	8	0.013986013986013986	140	0.18469656992084432	A	9.503	1.103720	0.20632	0.096005	0.191163	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.13657	2.57;2.57	4.26	-8.51	0.00923	Period circadian-like, C-terminal (1);	1.810430	0.02765	N	0.119042	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.002	T	0.32693	-0.9897	9	0.20046	T	0.44	.	1.3889	0.02246	0.2056:0.3554:0.2425:0.1965	rs10462021;rs52823932;rs57558236;rs10462021	198;1158;1149	B4DR65;P56645-2;P56645	.;.;PER3_HUMAN	R	1158;1149;342	ENSP00000366755:H1158R;ENSP00000355031:H1149R	ENSP00000355031:H1149R	H	+	2	0	PER3	7819720	0.000000	0.05858	0.000000	0.03702	0.772000	0.43724	0.007000	0.13174	-2.475000	0.00527	0.377000	0.23210	CAT	A|0.865;G|0.135	0.135	strong		0.408	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
TRIM5	85363	hgsc.bcm.edu	37	11	5701001	5701001	+	Missense_Mutation	SNP	C	C	T	rs10838525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5701001C>T	ENST00000380034.3	-	2	663	c.407G>A	c.(406-408)cGg>cAg	p.R136Q	TRIM5_ENST00000396853.4_Missense_Mutation_p.R136Q|TRIM5_ENST00000396847.3_Missense_Mutation_p.R136Q|TRIM5_ENST00000396855.3_Missense_Mutation_p.R136Q|TRIM5_ENST00000380027.1_Missense_Mutation_p.R136Q|TRIM5_ENST00000483835.1_5'UTR|TRIM5_ENST00000305836.5_Missense_Mutation_p.R136Q	NM_033034.2|NM_033092.2	NP_149023.2|NP_149083.2	Q9C035	TRIM5_HUMAN	tripartite motif containing 5	136			R -> Q (in dbSNP:rs10838525). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18312418, ECO:0000269|Ref.9}.		activation of innate immune response (GO:0002218)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|signaling pattern recognition receptor activity (GO:0008329)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R136Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		TTGGTACTCCCGGGCAACCTC	0.512													T|||	926	0.184904	0.1029	0.2349	5008	,	,		18833	0.0784		0.3847	False		,,,				2504	0.1646				p.R136Q		Atlas-SNP	.											TRIM5_ENST00000380034,NS,carcinoma,0,1	TRIM5	111	1	1	Substitution - Missense(1)	stomach(1)	c.G407A	GRCh37	CM068300	TRIM5	M	rs10838525	PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	633,3769	271.0+/-269.9	49,535,1617	105.0	92.0	97.0		407,407,407	0.2	0.0	11	dbSNP_120	97	3012,5582	465.6+/-366.6	554,1904,1839	yes	missense,missense,missense	TRIM5	NM_033034.2,NM_033092.2,NM_033093.2	43,43,43	603,2439,3456	TT,TC,CC		35.0477,14.3798,28.0471	benign,benign,benign	136/494,136/348,136/327	5701001	3645,9351	2201	4297	6498	SO:0001583	missense	85363	exon2			TACTCCCGGGCAA	AF220025	CCDS31392.1, CCDS31393.1, CCDS31394.1	11p15	2014-06-03	2011-01-25		ENSG00000132256	ENSG00000132256		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16276	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM5"", ""tripartite motif protein TRIM"""	608487	"""tripartite motif-containing 5"""			11331580	Standard	NM_033034		Approved	RNF88, TRIM5alpha	uc001mbm.2	Q9C035	OTTHUMG00000066893	ENST00000380034.3:c.407G>A	11.37:g.5701001C>T	ENSP00000369373:p.Arg136Gln	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_033093	A6NGQ1|A8WFA8|D3DQS8|D3DQS9|G3GJY1|Q2MLV4|Q2MLV8|Q2MLV9|Q2MLW1|Q2MLW3|Q2MLW4|Q2MLW6|Q2MLW7|Q2MLX1|Q2MLX2|Q2MLX3|Q2MLX5|Q2MLY3|Q2MLY4|Q2V6Q6|Q6GX26|Q8WU46|Q96SR5|Q9C031|Q9C032|Q9C033|Q9C034	Missense_Mutation	SNP	ENST00000380034.3	37	CCDS31393.1	462|462	0.21153846153846154|0.21153846153846154	49|49	0.09959349593495935|0.09959349593495935	91|91	0.2513812154696133|0.2513812154696133	30|30	0.05244755244755245|0.05244755244755245	292|292	0.38522427440633245|0.38522427440633245	c|c	0.006|0.006	-2.061954|-2.061954	0.00386|0.00386	0.143798|0.143798	0.350477|0.350477	ENSG00000132256|ENSG00000132256	ENST00000438025|ENST00000396855;ENST00000305836;ENST00000380034;ENST00000380027;ENST00000396847;ENST00000396853;ENST00000412903	.|T;T;T;T;T;T;T	.|0.55413	.|0.52;0.52;0.52;0.52;0.52;0.52;0.52	4.07|4.07	0.203|0.203	0.15195|0.15195	.|.	.|0.418264	.|0.20632	.|N	.|0.088573	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00252|0.00252	-1.77|-1.77	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.13145	.|0.007;0.0;0.0	.|B;B;B	.|0.06405	.|0.002;0.002;0.0	T|T	0.36841|0.36841	-0.9731|-0.9731	4|9	.|0.02654	.|T	.|1	.|.	4.1195|4.1195	0.10099|0.10099	0.0:0.2902:0.1754:0.5344|0.0:0.2902:0.1754:0.5344	rs10838525;rs52810416;rs57044514;rs10838525|rs10838525;rs52810416;rs57044514;rs10838525	.|136;136;136	.|Q9C035-3;Q9C035-4;Q9C035	.|.;.;TRIM5_HUMAN	R|Q	13|136	.|ENSP00000380064:R136Q;ENSP00000307031:R136Q;ENSP00000369373:R136Q;ENSP00000369366:R136Q;ENSP00000380058:R136Q;ENSP00000380062:R136Q;ENSP00000388031:R136Q	.|ENSP00000307031:R136Q	G|R	-|-	1|2	0|0	TRIM5|TRIM5	5657577|5657577	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.761000|0.761000	0.26489|0.26489	0.015000|0.015000	0.14971|0.14971	-0.295000|-0.295000	0.09555|0.09555	GGG|CGG	C|0.763;T|0.237	0.237	strong		0.512	TRIM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143360.3	NM_033034	
WDFY2	115825	hgsc.bcm.edu	37	13	52313253	52313253	+	Missense_Mutation	SNP	G	G	A	rs77486739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:52313253G>A	ENST00000298125.5	+	7	847	c.667G>A	c.(667-669)Gtc>Atc	p.V223I		NM_052950.3	NP_443182.1	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2	223							metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)		AGATCACTCTGTCATCATGTG	0.512													G|||	18	0.00359425	0.0106	0.0058	5008	,	,		18017	0.0		0.0	False		,,,				2504	0.0				p.V223I		Atlas-SNP	.											.	WDFY2	36	.	0			c.G667A						PASS	.	G	ILE/VAL	63,4343	59.3+/-96.0	0,63,2140	160.0	140.0	147.0		667	5.3	1.0	13	dbSNP_131	147	4,8596	3.7+/-12.6	0,4,4296	yes	missense	WDFY2	NM_052950.3	29	0,67,6436	AA,AG,GG		0.0465,1.4299,0.5151	benign	223/401	52313253	67,12939	2203	4300	6503	SO:0001583	missense	115825	exon7			CACTCTGTCATCA	AF411978	CCDS9429.1	13q14.12	2013-01-09	2003-03-13		ENSG00000139668	ENSG00000139668		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20482	protein-coding gene	gene with protein product		610418	"""WD40 and FYVE domain containing 2"""				Standard	NM_052950		Approved	ZFYVE22	uc001vfp.3	Q96P53	OTTHUMG00000017407	ENST00000298125.5:c.667G>A	13.37:g.52313253G>A	ENSP00000298125:p.Val223Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_052950	B1AL86|Q96CS1	Missense_Mutation	SNP	ENST00000298125.5	37	CCDS9429.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	9.675	1.147653	0.21288	0.014299	4.65E-4	ENSG00000139668	ENST00000298125	T	0.57107	0.42	6.17	5.32	0.75619	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.049499	0.85682	D	0.000000	T	0.25680	0.0625	L	0.35542	1.07	0.49798	D	0.999829	B;B	0.14805	0.011;0.001	B;B	0.14023	0.01;0.003	T	0.16482	-1.0401	10	0.02654	T	1	-25.4701	7.2469	0.26127	0.2059:0.0:0.7941:0.0	.	120;223	Q96LK4;Q96P53	.;WDFY2_HUMAN	I	223	ENSP00000298125:V223I	ENSP00000298125:V223I	V	+	1	0	WDFY2	51211254	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.740000	0.68629	2.941000	0.99782	0.655000	0.94253	GTC	G|0.996;A|0.004	0.004	strong		0.512	WDFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045985.3	NM_052950	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178770981	178770981	+	Silent	SNP	A	A	G	rs2271212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178770981A>G	ENST00000251582.7	-	2	422	c.321T>C	c.(319-321)agT>agC	p.S107S	ADAMTS2_ENST00000274609.5_Silent_p.S107S	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	107					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		AGAAGAGGTGACTGCCAGGCT	0.701																																					p.S107S		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.T321C						PASS	.	G	,	986,3412		117,752,1330	21.0	25.0	24.0		321,321	-0.6	0.0	5	dbSNP_100	24	3026,5562		541,1944,1809	no	coding-synonymous,coding-synonymous	ADAMTS2	NM_014244.4,NM_021599.2	,	658,2696,3139	GG,GA,AA		35.2352,22.4193,30.8948	,	107/1212,107/567	178770981	4012,8974	2199	4294	6493	SO:0001819	synonymous_variant	9509	exon2			GAGGTGACTGCCA	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.321T>C	5.37:g.178770981A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	95	27	0.284211	NM_021599		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			A|0.677;G|0.323	0.323	strong		0.701	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
ZNF224	7767	hgsc.bcm.edu	37	19	44612231	44612231	+	Missense_Mutation	SNP	A	A	G	rs3746319	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44612231A>G	ENST00000336976.6	+	6	2172	c.1918A>G	c.(1918-1920)Aaa>Gaa	p.K640E	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	640			K -> E (in dbSNP:rs3746319). {ECO:0000269|PubMed:10585455, ECO:0000269|PubMed:12239212}.		negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				TTCATTCTCTAAAGTGCAAGA	0.458													A|||	3011	0.601238	0.4675	0.5259	5008	,	,		22451	0.5357		0.8091	False		,,,				2504	0.6892				p.K640E		Atlas-SNP	.											.	ZNF224	70	.	0			c.A1918G						PASS	.	A	GLU/LYS	2243,2163	594.5+/-388.2	590,1063,550	84.0	80.0	81.0		1918	-4.3	0.0	19	dbSNP_107	81	7041,1559	745.5+/-407.3	2907,1227,166	yes	missense	ZNF224	NM_013398.2	56	3497,2290,716	GG,GA,AA		18.1279,49.0921,28.6176	benign	640/708	44612231	9284,3722	2203	4300	6503	SO:0001583	missense	7767	exon6			TTCTCTAAAGTGC	AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"""Zinc fingers, C2H2-type"", ""-"""	13017	protein-coding gene	gene with protein product		194555	"""zinc finger protein 255"", ""zinc finger protein 27"""	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1918A>G	19.37:g.44612231A>G	ENSP00000337368:p.Lys640Glu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	70	0.514706	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Missense_Mutation	SNP	ENST00000336976.6	37	CCDS33046.1	1384	0.6336996336996337	254	0.516260162601626	217	0.5994475138121547	309	0.5402097902097902	604	0.7968337730870713	a	8.797	0.931901	0.18131	0.509079	0.818721	ENSG00000186019	ENST00000336976	T	0.05855	3.38	2.16	-4.31	0.03698	.	.	.	.	.	T	0.00012	0.0000	L	0.50919	1.6	0.80722	P	0.0	B	0.18741	0.03	B	0.18263	0.021	T	0.16988	-1.0384	8	0.23302	T	0.38	.	9.9081	0.41388	0.3279:0.6721:0.0:0.0	rs3746319;rs52833696;rs57910446;rs3746319	640	Q9NZL3	ZN224_HUMAN	E	640	ENSP00000337368:K640E	ENSP00000337368:K640E	K	+	1	0	ZNF224	49304071	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-2.663000	0.00849	-0.847000	0.04168	0.482000	0.46254	AAA	A|0.330;G|0.670	0.670	strong		0.458	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398	
GRIN3A	116443	hgsc.bcm.edu	37	9	104433347	104433347	+	Silent	SNP	G	G	A	rs13284303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:104433347G>A	ENST00000361820.3	-	3	1947	c.1347C>T	c.(1345-1347)atC>atT	p.I449I		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	449					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	CTTTTACTCTGATGGAACCAC	0.468													G|||	615	0.122804	0.0068	0.1931	5008	,	,		18256	0.1716		0.167	False		,,,				2504	0.1339				p.I449I		Atlas-SNP	.											.	GRIN3A	186	.	0			c.C1347T						PASS	.	G		153,4253	103.4+/-141.9	6,141,2056	117.0	119.0	118.0		1347	5.8	1.0	9	dbSNP_121	118	1454,7146	276.9+/-292.6	124,1206,2970	no	coding-synonymous	GRIN3A	NM_133445.2		130,1347,5026	AA,AG,GG		16.907,3.4725,12.3558		449/1116	104433347	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			TACTCTGATGGAA		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.1347C>T	9.37:g.104433347G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			G|0.871;A|0.129	0.129	strong		0.468	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
OR4C15	81309	hgsc.bcm.edu	37	11	55322539	55322539	+	Missense_Mutation	SNP	G	G	A	rs12790125	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55322539G>A	ENST00000314644.2	+	1	757	c.757G>A	c.(757-759)Gtc>Atc	p.V253I		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						CCTCATGGTGGTCATCAACAG	0.468										HNSCC(20;0.049)			g|||	867	0.173123	0.118	0.2378	5008	,	,		18208	0.1528		0.2107	False		,,,				2504	0.184				p.V253I		Atlas-SNP	.											OR4C15,arm,malignant_melanoma,-2,1	OR4C15	145	1	0			c.G757A						PASS	.	G	ILE/VAL	591,3811	261.0+/-264.0	39,513,1649	172.0	114.0	134.0		757	2.0	0.1	11	dbSNP_121	134	1897,6695	338.2+/-322.6	225,1447,2624	yes	missense	OR4C15	NM_001001920.1	29	264,1960,4273	AA,AG,GG		22.0787,13.4257,19.1473	benign	253/371	55322539	2488,10506	2201	4296	6497	SO:0001583	missense	81309	exon1			ATGGTGGTCATCA	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"""GPCR / Class A : Olfactory receptors"""	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.757G>A	11.37:g.55322539G>A	ENSP00000324958:p.Val253Ile	Somatic	376	1	0.00265957		WXS	Illumina HiSeq	Phase_I	355	137	0.385915	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	379	0.17353479853479853	35	0.07113821138211382	84	0.23204419889502761	94	0.16433566433566432	166	0.21899736147757257	G	2.293	-0.362064	0.05103	0.134257	0.220787	ENSG00000181939	ENST00000314644	T	0.00076	8.76	5.02	1.98	0.26296	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B	0.17038	0.02	B	0.24269	0.052	T	0.01078	-1.1459	8	0.27785	T	0.31	.	3.4223	0.07398	0.2944:0.0:0.5283:0.1773	rs12790125;rs17496779;rs52792703;rs58731558;rs12790125	199	Q8NGM1	OR4CF_HUMAN	I	253	ENSP00000324958:V253I	ENSP00000324958:V253I	V	+	1	0	OR4C15	55079115	0.000000	0.05858	0.064000	0.19789	0.012000	0.07955	-0.121000	0.10643	0.244000	0.21351	0.385000	0.25706	GTC	G|0.819;A|0.181	0.181	strong		0.468	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
SLC44A3	126969	hgsc.bcm.edu	37	1	95294089	95294089	+	Silent	SNP	T	T	C	rs2640065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:95294089T>C	ENST00000271227.6	+	5	558	c.456T>C	c.(454-456)taT>taC	p.Y152Y	SLC44A3_ENST00000527077.1_Silent_p.Y84Y|SLC44A3_ENST00000532427.1_Silent_p.Y72Y|SLC44A3_ENST00000529450.1_Silent_p.Y120Y|SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000467909.1_Silent_p.Y104Y|SLC44A3_ENST00000446120.2_Silent_p.Y116Y	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	152					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Y104Y(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	CCTTCAACTATACCCACAGTC	0.428													C|||	1012	0.202077	0.2466	0.1398	5008	,	,		18783	0.1012		0.2117	False		,,,				2504	0.2802				p.Y152Y		Atlas-SNP	.											SLC44A3,NS,carcinoma,0,1	SLC44A3	109	1	1	Substitution - coding silent(1)	stomach(1)	c.T456C						PASS	.	C	,	1101,3305	720.1+/-409.0	151,799,1253	162.0	151.0	155.0		456,312	-1.5	0.3	1	dbSNP_100	155	1758,6842	734.9+/-406.9	179,1400,2721	no	coding-synonymous,coding-synonymous	SLC44A3	NM_001114106.1,NM_152369.3	,	330,2199,3974	CC,CT,TT		20.4419,24.9887,21.9822	,	152/654,104/606	95294089	2859,10147	2203	4300	6503	SO:0001819	synonymous_variant	126969	exon5			CAACTATACCCAC	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"""Solute carriers"""	28689	protein-coding gene	gene with protein product			"""solute carrier family, member 3"""			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.456T>C	1.37:g.95294089T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	37	CCDS44176.1																																																																																			T|0.790;C|0.210	0.210	strong		0.428	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369	
ADCK3	56997	hgsc.bcm.edu	37	1	227172290	227172290	+	Silent	SNP	C	C	T	rs12593	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:227172290C>T	ENST00000366779.1	+	17	4211	c.1440C>T	c.(1438-1440)ttC>ttT	p.F480F	ADCK3_ENST00000366778.1_Silent_p.F428F|ADCK3_ENST00000433743.2_Silent_p.F154F|ADCK3_ENST00000458507.2_Silent_p.F201F|ADCK3_ENST00000478406.1_3'UTR|ADCK3_ENST00000366777.3_Silent_p.F480F			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	480	Protein kinase.				cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.F480F(1)|p.F201F(1)		endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						GGGAGCTGTTCGAGTTCCACT	0.607													C|||	1195	0.238618	0.1649	0.2695	5008	,	,		18538	0.1716		0.4274	False		,,,				2504	0.1912				p.F480F		Atlas-SNP	.											ADCK3_ENST00000366779,caecum,carcinoma,0,4	ADCK3	77	4	2	Substitution - coding silent(2)	stomach(2)	c.C1440T						scavenged	.	C		921,3485	353.8+/-312.3	101,719,1383	128.0	105.0	113.0		1440	-3.9	1.0	1	dbSNP_52	113	3939,4661	549.1+/-385.5	898,2143,1259	no	coding-synonymous	ADCK3	NM_020247.4		999,2862,2642	TT,TC,CC		45.8023,20.9033,37.3674		480/648	227172290	4860,8146	2203	4300	6503	SO:0001819	synonymous_variant	56997	exon12			GCTGTTCGAGTTC	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"""coenzyme Q8 homolog (yeast)"""	606980	"""chaperone-ABC1 (activity of bc1 complex, S.pombe)-like"", ""chaperone, ABC1 activity of bc1 complex like (S. pombe)"", ""chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"""	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.1440C>T	1.37:g.227172290C>T		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	140	57	0.407143	NM_020247	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Silent	SNP	ENST00000366779.1	37	CCDS1557.1																																																																																			C|0.672;T|0.328	0.328	strong		0.607	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247	
RBMX	27316	hgsc.bcm.edu	37	X	135956411	135956411	+	Missense_Mutation	SNP	C	C	A	rs35085326		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:135956411C>A	ENST00000320676.7	-	9	1220	c.1066G>T	c.(1066-1068)Ggg>Tgg	p.G356W	RBMX_ENST00000570135.1_Missense_Mutation_p.G221W|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000496459.2_5'Flank|RBMX_ENST00000565438.1_Missense_Mutation_p.G228W|RBMX_ENST00000562646.1_3'UTR	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	356	Necessary for RNA-binding.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GGAGGGTACCCCCTTTCCATA	0.562																																					p.G356W		Atlas-SNP	.											.	RBMX	149	.	0			c.G1066T						PASS	.						81.0	78.0	79.0					X																	135956411		2203	4299	6502	SO:0001583	missense	27316	exon9			GGTACCCCCTTTC		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.1066G>T	X.37:g.135956411C>A	ENSP00000359645:p.Gly356Trp	Somatic	774	2	0.00258398		WXS	Illumina HiSeq	Phase_I	700	234	0.334286	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	18	0.0108499095840868	0	0.0	5	0.013812154696132596	0	0.0	14	0.018469656992084433	.	13.49	2.252860	0.39797	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.78364	-1.17	5.66	5.66	0.87406	.	0.000000	0.85682	U	0.000000	T	0.79335	0.4428	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.84437	0.0580	10	0.66056	D	0.02	.	18.7648	0.91868	0.0:1.0:0.0:0.0	rs35085326	356	P38159	HNRPG_HUMAN	W	356;343	ENSP00000359645:G356W	ENSP00000359645:G356W	G	-	1	0	RBMX	135784077	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.845000	0.62853	2.377000	0.81083	0.596000	0.82720	GGG	C|0.989;A|0.011	0.011	strong		0.562	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
DDX18	8886	hgsc.bcm.edu	37	2	118583940	118583940	+	Silent	SNP	C	C	T	rs2303348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:118583940C>T	ENST00000263239.2	+	11	1745	c.1617C>T	c.(1615-1617)cgC>cgT	p.R539R		NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	539	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GTTTTCTTCGCTACTTGAAAC	0.438													C|||	1521	0.303714	0.0378	0.3242	5008	,	,		19496	0.5298		0.3767	False		,,,				2504	0.3405				p.R539R		Atlas-SNP	.											DDX18,colon,carcinoma,+1,1	DDX18	79	1	0			c.C1617T						PASS	.	C		489,3917	225.9+/-241.6	29,431,1743	76.0	68.0	71.0		1617	-0.6	1.0	2	dbSNP_100	71	3361,5239	496.5+/-374.3	653,2055,1592	no	coding-synonymous	DDX18	NM_006773.3		682,2486,3335	TT,TC,CC		39.0814,11.0985,29.6017		539/671	118583940	3850,9156	2203	4300	6503	SO:0001819	synonymous_variant	8886	exon11			TCTTCGCTACTTG	X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"""DEAD-boxes"""	2741	protein-coding gene	gene with protein product		606355	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"""			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.1617C>T	2.37:g.118583940C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_006773	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Silent	SNP	ENST00000263239.2	37	CCDS2120.1																																																																																			C|0.689;T|0.311	0.311	strong		0.438	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773	
CD101	9398	hgsc.bcm.edu	37	1	117560818	117560818	+	Silent	SNP	A	A	G	rs3736908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:117560818A>G	ENST00000256652.4	+	6	1711	c.1653A>G	c.(1651-1653)caA>caG	p.Q551Q	CD101_ENST00000369470.1_Silent_p.Q551Q	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	551	Ig-like C2-type 5.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GTCAGCCGCAAGTGATGTTAA	0.438													A|||	1725	0.344449	0.0408	0.4438	5008	,	,		19499	0.6181		0.2813	False		,,,				2504	0.4673				p.Q551Q		Atlas-SNP	.											.	CD101	95	.	0			c.A1653G						PASS	.	A		367,4039	185.3+/-212.5	18,331,1854	106.0	82.0	90.0		1653	1.6	1.0	1	dbSNP_107	90	2365,6235	390.0+/-343.1	324,1717,2259	no	coding-synonymous	CD101	NM_004258.3		342,2048,4113	GG,GA,AA		27.5,8.3296,21.0057		551/1022	117560818	2732,10274	2203	4300	6503	SO:0001819	synonymous_variant	9398	exon6			GCCGCAAGTGATG	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1653A>G	1.37:g.117560818A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001256109	Q15856	Silent	SNP	ENST00000256652.4	37	CCDS891.1																																																																																			A|0.738;G|0.262	0.262	strong		0.438	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
PPFIA4	8497	hgsc.bcm.edu	37	1	203024767	203024767	+	Silent	SNP	C	C	T	rs3736314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:203024767C>T	ENST00000447715.2	+	21	2412	c.1971C>T	c.(1969-1971)gcC>gcT	p.A657A	PPFIA4_ENST00000272198.6_Silent_p.A173A|PPFIA4_ENST00000295706.4_Silent_p.A173A|PPFIA4_ENST00000367240.2_Silent_p.A658A|PPFIA4_ENST00000414050.2_Silent_p.A386A|PPFIA4_ENST00000599966.1_Silent_p.A173A			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	657					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						GCAGTGCTGCCCAGGACCTGG	0.662													c|||	774	0.154553	0.2216	0.1138	5008	,	,		18276	0.128		0.1541	False		,,,				2504	0.1207				p.A173A		Atlas-SNP	.											.	PPFIA4	139	.	0			c.C519T						PASS	.			951,3315		102,747,1284	46.0	53.0	50.0		519	2.7	1.0	1	dbSNP_107	50	1333,7131		98,1137,2997	no	coding-synonymous	PPFIA4	NM_015053.1		200,1884,4281	TT,TC,CC		15.7491,22.2925,17.9419		173/702	203024767	2284,10446	2133	4232	6365	SO:0001819	synonymous_variant	8497	exon3			TGCTGCCCAGGAC	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.1971C>T	1.37:g.203024767C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	278	105	0.377698	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	37																																																																																				C|0.848;T|0.152	0.152	strong		0.662	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
KIAA1244	57221	hgsc.bcm.edu	37	6	138608212	138608212	+	Splice_Site	SNP	C	C	T	rs17568867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138608212C>T	ENST00000251691.4	+	17	2953	c.2787C>T	c.(2785-2787)ggC>ggT	p.G929G		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CCTCTGAAGGCGTTGCTGCTA	0.547													G|||	51	0.0101837	0.0023	0.013	5008	,	,		22261	0.0		0.0258	False		,,,				2504	0.0133				p.G929G		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C2787T						PASS	.	G		29,4377		0,29,2174	66.0	55.0	59.0		2787	-1.5	1.0	6	dbSNP_123	59	343,8253		3,337,3958	yes	coding-synonymous-near-splice	KIAA1244	NM_020340.4		3,366,6132	TT,TC,CC		3.9902,0.6582,2.8611		929/2178	138608212	372,12630	2203	4298	6501	SO:0001630	splice_region_variant	57221	exon17			TGAAGGCGTTGCT	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.2786-1C>T	6.37:g.138608212C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																			C|0.977;T|0.023	0.023	strong		0.547	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	Silent
NAA38	84316	hgsc.bcm.edu	37	17	7760397	7760397	+	Silent	SNP	G	G	A	rs4724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7760397G>A	ENST00000335155.5	-	2	200	c.201C>T	c.(199-201)ttC>ttT	p.F67F	CYB5D1_ENST00000570446.1_5'Flank|CYB5D1_ENST00000571846.1_5'Flank|LSMD1_ENST00000576861.1_Silent_p.F41F|LSMD1_ENST00000575208.1_Silent_p.F15F|CYB5D1_ENST00000332439.4_5'Flank|LSMD1_ENST00000570555.1_5'Flank|LSMD1_ENST00000576384.1_Silent_p.F15F|LSMD1_ENST00000575771.1_Silent_p.F15F|LSMD1_ENST00000333775.5_Silent_p.F115F|LSMD1_ENST00000575071.1_Silent_p.F15F			Q9BRA0	LSMD1_HUMAN		67					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|lung(2)|ovary(1)	4		all_cancers(10;0.11)|Prostate(122;0.219)				CAGTGCAGAGGAAGCAGCCGA	0.627											OREG0024146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1267	0.252995	0.3336	0.2882	5008	,	,		16927	0.2748		0.0924	False		,,,				2504	0.2618				p.F115F	GBM(66;626 1401 29924 42527)	Atlas-SNP	.											LSMD1,NS,carcinoma,0,2	LSMD1	8	2	0			c.C345T						PASS	.	G		1287,3119	431.0+/-342.8	187,913,1103	110.0	108.0	109.0		345	4.4	1.0	17	dbSNP_52	109	956,7644	208.9+/-250.2	46,864,3390	no	coding-synonymous	LSMD1	NM_032356.3		233,1777,4493	AA,AG,GG		11.1163,29.2102,17.2459		115/174	7760397	2243,10763	2203	4300	6503	SO:0001819	synonymous_variant	84316	exon1			GCAGAGGAAGCAG																												ENST00000335155.5:c.201C>T	17.37:g.7760397G>A		Somatic	88	0	0	644	WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_032356	Q8N4M0	Silent	SNP	ENST00000335155.5	37																																																																																				G|0.831;A|0.169	0.169	strong		0.627	LSMD1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
MUS81	80198	hgsc.bcm.edu	37	11	65631973	65631973	+	Silent	SNP	G	G	A	rs630303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65631973G>A	ENST00000308110.4	+	11	1414	c.1065G>A	c.(1063-1065)cgG>cgA	p.R355R	MUS81_ENST00000533035.1_Silent_p.R280R|EFEMP2_ENST00000532648.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	355	ERCC4.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		CCTAGTTCCGGCTGAAGCGCT	0.587								Homologous recombination					G|||	2153	0.429912	0.208	0.4063	5008	,	,		19654	0.3323		0.668	False		,,,				2504	0.6022				p.R355R		Atlas-SNP	.											MUS81_ENST00000308110,NS,adenoma,0,3	MUS81	68	3	0			c.G1065A						PASS	.	G		1158,3244	409.5+/-335.0	156,846,1199	87.0	71.0	76.0		1065	-0.6	0.7	11	dbSNP_83	76	5739,2853	673.0+/-403.0	1894,1951,451	no	coding-synonymous	MUS81	NM_025128.4		2050,2797,1650	AA,AG,GG		33.2053,26.3062,46.9217		355/552	65631973	6897,6097	2201	4296	6497	SO:0001819	synonymous_variant	80198	exon11			GTTCCGGCTGAAG		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.1065G>A	11.37:g.65631973G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_025128	Q9H7D9	Silent	SNP	ENST00000308110.4	37	CCDS8115.1	984	0.45054945054945056	125	0.2540650406504065	176	0.4861878453038674	174	0.3041958041958042	509	0.6715039577836411	G	2.473	-0.321494	0.05386	0.263062	0.667947	ENSG00000172732	ENST00000529374	.	.	.	5.91	-0.587	0.11690	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999971704	.	.	.	.	.	.	T	0.42849	-0.9427	3	.	.	.	-23.5175	9.8829	0.41245	0.1842:0.4923:0.3234:0.0	rs630303;rs17147165;rs17850600;rs56552962;rs59962116;rs630303	.	.	.	T	281	.	.	A	+	1	0	MUS81	65388549	0.706000	0.27856	0.720000	0.30636	0.375000	0.29983	-0.241000	0.08940	-0.290000	0.09025	-2.590000	0.00165	GCT	A|0.474;C|0.004	0.474	strong		0.587	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
CASKIN2	57513	hgsc.bcm.edu	37	17	73498623	73498623	+	Silent	SNP	A	A	G	rs7502835	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73498623A>G	ENST00000321617.3	-	18	3118	c.2532T>C	c.(2530-2532)agT>agC	p.S844S	CASKIN2_ENST00000433559.2_Silent_p.S762S	NM_020753.3	NP_065804.2	Q8WXE0	CSKI2_HUMAN	CASK interacting protein 2	844	Pro-rich.					cytoplasm (GO:0005737)				endometrium(1)|kidney(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTGGGGTCACACTAGGACTGG	0.711													A|||	2268	0.452875	0.0825	0.5994	5008	,	,		10463	0.4415		0.7207	False		,,,				2504	0.5859				p.A844A		Atlas-SNP	.											CASKIN2,NS,carcinoma,0,1	CASKIN2	66	1	0			c.C2532C						PASS	.	A	,	854,3520		92,670,1425	18.0	20.0	19.0		2286,2532	-0.5	0.0	17	dbSNP_116	19	6504,2072		2505,1494,289	no	coding-synonymous,coding-synonymous	CASKIN2	NM_001142643.1,NM_020753.3	,	2597,2164,1714	GG,GA,AA		24.1604,19.5245,43.1815	,	762/1121,844/1203	73498623	7358,5592	2187	4288	6475	SO:0001819	synonymous_variant	57513	exon18			GGTCACACTAGGA	AB032965	CCDS11723.1, CCDS45775.1	17q25.1	2014-09-04			ENSG00000177303	ENSG00000177303		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	18200	protein-coding gene	gene with protein product		612185				12040031	Standard	NM_020753		Approved	KIAA1139, FLJ21609, ANKS5B	uc002joc.4	Q8WXE0	OTTHUMG00000179683	ENST00000321617.3:c.2532T>C	17.37:g.73498623A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_020753	B4DTT3|B7Z9H1|Q7LG69|Q9ULT1	Silent	SNP	ENST00000321617.3	37	CCDS11723.1																																																																																			A|0.557;G|0.443	0.443	strong		0.711	CASKIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447609.1	NM_020753	
PTK2B	2185	hgsc.bcm.edu	37	8	27255128	27255128	+	Silent	SNP	T	T	C	rs1045510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27255128T>C	ENST00000397501.1	+	7	835	c.27T>C	c.(25-27)agT>agC	p.S9S	PTK2B_ENST00000346049.5_Silent_p.S9S|PTK2B_ENST00000338238.4_Silent_p.S9S|PTK2B_ENST00000544172.1_Silent_p.S9S|PTK2B_ENST00000420218.2_Silent_p.S9S|PTK2B_ENST00000517339.1_Silent_p.S9S	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	9					activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	AGCCCCTGAGTCGAGTAAAGT	0.592													C|||	1593	0.318091	0.2057	0.3818	5008	,	,		18715	0.2748		0.4324	False		,,,				2504	0.3517				p.S9S		Atlas-SNP	.											.	PTK2B	304	.	0			c.T27C						PASS	.	C	,,,	1024,3382	728.0+/-409.9	128,768,1307	121.0	104.0	110.0		27,27,27,27	2.9	1.0	8	dbSNP_86	110	3841,4759	610.6+/-395.7	868,2105,1327	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	996,2873,2634	CC,CT,TT		44.6628,23.241,37.4058	,,,	9/1010,9/1010,9/968,9/1010	27255128	4865,8141	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon7			CCTGAGTCGAGTA	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.27T>C	8.37:g.27255128T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			T|0.642;C|0.358	0.358	strong		0.592	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
OR8J3	81168	hgsc.bcm.edu	37	11	55905078	55905078	+	Missense_Mutation	SNP	C	C	T	rs61742348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55905078C>T	ENST00000301529.1	-	1	116	c.117G>A	c.(115-117)atG>atA	p.M39I		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M39I(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					GGTTCCCTGCCATGGTCAGCA	0.498													C|||	517	0.103235	0.0499	0.098	5008	,	,		18332	0.1429		0.1213	False		,,,				2504	0.1196				p.M39I		Atlas-SNP	.											OR8J3,NS,carcinoma,0,2	OR8J3	112	2	2	Substitution - Missense(2)	stomach(1)|pancreas(1)	c.G117A						scavenged	.	C	ILE/MET	239,4163	140.4+/-175.9	7,225,1969	136.0	132.0	134.0		117	1.3	0.0	11	dbSNP_129	134	1007,7585	216.6+/-255.6	54,899,3343	no	missense	OR8J3	NM_001004064.1	10	61,1124,5312	TT,TC,CC		11.7202,5.4294,9.589	benign	39/316	55905078	1246,11748	2201	4296	6497	SO:0001583	missense	81168	exon1			CCCTGCCATGGTC		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.117G>A	11.37:g.55905078C>T	ENSP00000301529:p.Met39Ile	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	186	93	0.5	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	253	0.11584249084249085	32	0.06504065040650407	33	0.09116022099447514	88	0.15384615384615385	100	0.13192612137203166	C	10.71	1.426952	0.25726	0.054294	0.117202	ENSG00000167822	ENST00000301529	T	0.00524	6.82	3.26	1.31	0.21738	.	1.026030	0.07741	N	0.946937	T	0.00012	0.0000	N	0.05467	-0.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39231	-0.9624	9	0.59425	D	0.04	.	4.5064	0.11891	0.0:0.5487:0.162:0.2893	.	39	Q8NGG0	OR8J3_HUMAN	I	39	ENSP00000301529:M39I	ENSP00000301529:M39I	M	-	3	0	OR8J3	55661654	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-0.509000	0.06336	0.065000	0.16485	0.289000	0.19496	ATG	C|0.901;T|0.099	0.099	strong		0.498	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331599	21331599	+	Silent	SNP	T	T	C	rs4149057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:21331599T>C	ENST00000256958.2	+	6	667	c.571T>C	c.(571-573)Ttg>Ctg	p.L191L		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	191					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	CATAGTACCATTGGGGCTTTC	0.353													T|||	1840	0.367412	0.1445	0.5043	5008	,	,		15151	0.2431		0.6074	False		,,,				2504	0.453				p.L191L		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.T571C						PASS	.	T		974,3432	366.1+/-317.7	112,750,1341	136.0	126.0	130.0		571	-1.5	0.0	12	dbSNP_110	130	5374,3226	650.3+/-400.7	1704,1966,630	no	coding-synonymous	SLCO1B1	NM_006446.4		1816,2716,1971	CC,CT,TT		37.5116,22.1062,48.8082		191/692	21331599	6348,6658	2203	4300	6503	SO:0001819	synonymous_variant	10599	exon6			GTACCATTGGGGC		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.571T>C	12.37:g.21331599T>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	238	135	0.567227	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																			T|0.566;C|0.434	0.434	strong		0.353	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
ANKRD44	91526	hgsc.bcm.edu	37	2	197863698	197863698	+	Silent	SNP	G	G	A	rs17385301	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:197863698G>A	ENST00000328737.2	-	24	2599	c.2523C>T	c.(2521-2523)aaC>aaT	p.N841N	ANKRD44_ENST00000337207.5_Silent_p.N841N|ANKRD44_ENST00000450567.1_Silent_p.N841N|ANKRD44_ENST00000282272.8_Silent_p.N858N			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	866										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TATCTACTGCGTTCACTGGAG	0.483													G|||	112	0.0223642	0.0008	0.0187	5008	,	,		19781	0.001		0.0447	False		,,,				2504	0.0532				p.N866N		Atlas-SNP	.											ANKRD44_ENST00000424317,caecum,carcinoma,0,2	ANKRD44	281	2	0			c.C2598T						PASS	.	G		47,4359	47.5+/-82.1	0,47,2156	122.0	106.0	112.0		2598	-4.2	0.7	2	dbSNP_123	112	413,8187	130.0+/-188.0	10,393,3897	no	coding-synonymous	ANKRD44	NM_001195144.1		10,440,6053	AA,AG,GG		4.8023,1.0667,3.5368		866/994	197863698	460,12546	2203	4300	6503	SO:0001819	synonymous_variant	91526	exon24			TACTGCGTTCACT	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.2523C>T	2.37:g.197863698G>A		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	313	153	0.488818	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37		51	0.023351648351648352	2	0.0040650406504065045	9	0.024861878453038673	1	0.0017482517482517483	39	0.051451187335092345	G	0.078	-1.188825	0.01607	0.010667	0.048023	ENSG00000065413	ENST00000448801	.	.	.	4.97	-4.22	0.03800	.	.	.	.	.	T	0.23926	0.0579	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57230	-0.7847	4	.	.	.	.	15.0927	0.72207	0.6876:0.0:0.3124:0.0	rs17385301;rs52808385;rs17385301	.	.	.	C	55	.	.	R	-	1	0	ANKRD44	197571943	0.001000	0.12720	0.738000	0.30950	0.031000	0.12232	-1.071000	0.03437	-0.747000	0.04759	-0.237000	0.12165	CGC	G|0.972;A|0.028	0.028	strong		0.483	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
CACNA2D1	781	hgsc.bcm.edu	37	7	81593541	81593541	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:81593541T>C	ENST00000356253.5	-	33	3000	c.2745A>G	c.(2743-2745)ggA>ggG	p.G915G	CACNA2D1_ENST00000356860.3_Silent_p.G903G|CACNA2D1_ENST00000535308.1_Silent_p.G115G			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	915					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CTGAGCGATGTCCTGCTCCTT	0.408																																					p.G903G		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A2709G						PASS	.						128.0	128.0	128.0					7																	81593541		2203	4300	6503	SO:0001819	synonymous_variant	781	exon33			GCGATGTCCTGCT	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2745A>G	7.37:g.81593541T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	121	8	0.0661157	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	37																																																																																				.	.	none		0.408	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
PGAM5	192111	hgsc.bcm.edu	37	12	133294371	133294371	+	Missense_Mutation	SNP	A	A	G	rs117147264	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133294371A>G	ENST00000498926.2	+	4	630	c.572A>G	c.(571-573)aAg>aGg	p.K191R	PXMP2_ENST00000545677.1_3'UTR|PGAM5_ENST00000317555.2_Missense_Mutation_p.K191R|PGAM5_ENST00000543955.1_Missense_Mutation_p.K42R|PGAM5_ENST00000454808.2_Missense_Mutation_p.K42R	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	191					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		TCTCATTGGAAGCCGGAAGCT	0.652													A|||	163	0.0325479	0.003	0.1671	5008	,	,		12769	0.0		0.0358	False		,,,				2504	0.0072				p.K191R		Atlas-SNP	.											PGAM5,NS,carcinoma,0,1	PGAM5	18	1	0			c.A572G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	38,4320		0,38,2141	22.0	28.0	26.0		572,572,572	5.5	1.0	12	dbSNP_132	26	321,8239		3,315,3962	yes	missense,missense,missense	PGAM5	NM_001170543.1,NM_001170544.1,NM_138575.3	26,26,26	3,353,6103	GG,GA,AA		3.75,0.872,2.7791	benign,benign,benign	191/290,191/289,191/256	133294371	359,12559	2179	4280	6459	SO:0001583	missense	192111	exon4			ATTGGAAGCCGGA	BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.572A>G	12.37:g.133294371A>G	ENSP00000438465:p.Lys191Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	52	15	0.288462	NM_138575	A9LN06|C9IZY7|Q96JB0	Missense_Mutation	SNP	ENST00000498926.2	37	CCDS53845.1	74	0.03388278388278388	2	0.0040650406504065045	48	0.13259668508287292	0	0.0	24	0.0316622691292876	A	11.76	1.734893	0.30774	0.00872	0.0375	ENSG00000247077	ENST00000317555;ENST00000498926;ENST00000543955;ENST00000454808	T;T	0.71817	-0.6;-0.6	5.5	5.5	0.81552	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	T	0.00724	0.0024	N	0.10760	0.04	0.09310	P	0.99999969864	B;B	0.22683	0.035;0.073	B;B	0.19148	0.024;0.019	T	0.10245	-1.0638	9	0.34782	T	0.22	-20.1292	15.6131	0.76744	1.0:0.0:0.0:0.0	.	191;191	Q96HS1;Q96HS1-2	PGAM5_HUMAN;.	R	191;191;42;42	ENSP00000321503:K191R;ENSP00000438465:K191R	ENSP00000321503:K191R	K	+	2	0	PGAM5	131804444	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	8.497000	0.90488	2.084000	0.62774	0.533000	0.62120	AAG	A|0.971;G|0.029	0.029	strong		0.652	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575	
LMO7	4008	hgsc.bcm.edu	37	13	76395464	76395464	+	Missense_Mutation	SNP	C	C	T	rs41286126	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:76395464C>T	ENST00000321797.8	+	12	2381	c.1660C>T	c.(1660-1662)Cct>Tct	p.P554S	LMO7_ENST00000465261.2_Missense_Mutation_p.P554S|LMO7_ENST00000377534.3_Missense_Mutation_p.P839S|LMO7_ENST00000526202.1_Missense_Mutation_p.P404S|LMO7_ENST00000341547.4_Missense_Mutation_p.P505S|LMO7_ENST00000357063.3_Missense_Mutation_p.P839S			Q8WWI1	LMO7_HUMAN	LIM domain 7	839					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AGCAACTTATCCTTCAGAAAT	0.433													C|||	357	0.0712859	0.0764	0.0562	5008	,	,		20219	0.0407		0.0755	False		,,,				2504	0.1022				p.P554S		Atlas-SNP	.											.	LMO7	334	.	0			c.C1660T						PASS	.	C	SER/PRO,SER/PRO	271,4135	153.3+/-186.9	11,249,1943	89.0	87.0	87.0		1513,1660	2.0	0.0	13	dbSNP_127	87	597,8003	158.0+/-211.6	25,547,3728	yes	missense,missense	LMO7	NM_005358.5,NM_015842.2	74,74	36,796,5671	TT,TC,CC		6.9419,6.1507,6.6738	benign,benign	505/1350,554/1386	76395464	868,12138	2203	4300	6503	SO:0001583	missense	4008	exon11			ACTTATCCTTCAG	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.1660C>T	13.37:g.76395464C>T	ENSP00000317802:p.Pro554Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		145|145	0.06639194139194139|0.06639194139194139	45|45	0.09146341463414634|0.09146341463414634	22|22	0.06077348066298342|0.06077348066298342	28|28	0.04895104895104895|0.04895104895104895	50|50	0.06596306068601583|0.06596306068601583	C|C	2.415|2.415	-0.334386|-0.334386	0.05278|0.05278	0.061507|0.061507	0.069419|0.069419	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261|ENST00000447038	T;T;T;T;T;T;T|.	0.41758|.	1.58;1.58;1.58;1.0;1.0;0.99;0.99|.	6.05|6.05	2.02|2.02	0.26589|0.26589	.|.	1.124490|.	0.06385|.	N|.	0.716019|.	T|T	0.01454|0.01454	0.0047|0.0047	N|N	0.25890|0.25890	0.77|0.77	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B|.	0.17667|.	0.008;0.023;0.005;0.008;0.012|.	B;B;B;B;B|.	0.14023|.	0.003;0.007;0.001;0.003;0.01|.	T|T	0.15206|0.15206	-1.0445|-1.0445	9|4	0.14252|.	T|.	0.57|.	-2.2781|-2.2781	8.1716|8.1716	0.31258|0.31258	0.0:0.4949:0.3371:0.168|0.0:0.4949:0.3371:0.168	rs41286126|rs41286126	404;505;839;554;787|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	S|F	505;839;839;453;554;404;554|462	ENSP00000342112:P505S;ENSP00000349571:P839S;ENSP00000366757:P839S;ENSP00000366719:P453S;ENSP00000317802:P554S;ENSP00000431129:P404S;ENSP00000433352:P554S|.	ENSP00000317802:P554S|.	P|S	+|+	1|2	0|0	LMO7|LMO7	75293465|75293465	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.048000|0.048000	0.14542|0.14542	0.059000|0.059000	0.14322|0.14322	0.403000|0.403000	0.25479|0.25479	-0.182000|-0.182000	0.12963|0.12963	CCT|TCC	C|0.935;T|0.065	0.065	strong		0.433	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
ALPK2	115701	hgsc.bcm.edu	37	18	56204991	56204991	+	Missense_Mutation	SNP	C	C	T	rs3809970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56204991C>T	ENST00000361673.3	-	5	2641	c.2428G>A	c.(2428-2430)Ggt>Agt	p.G810S	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	810			G -> S (in dbSNP:rs3809970). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCTTGGTCACCAGCCTCAAAA	0.473													C|||	2021	0.403554	0.4312	0.4265	5008	,	,		22527	0.2361		0.5716	False		,,,				2504	0.3497				p.G810S		Atlas-SNP	.											.	ALPK2	487	.	0			c.G2428A						PASS	.	C	SER/GLY	1983,2423	557.1+/-379.7	445,1093,665	134.0	122.0	126.0		2428	1.6	0.0	18	dbSNP_107	126	4590,4010	598.1+/-393.9	1236,2118,946	yes	missense	ALPK2	NM_052947.3	56	1681,3211,1611	TT,TC,CC		46.6279,45.0068,49.4618	probably-damaging	810/2171	56204991	6573,6433	2203	4300	6503	SO:0001583	missense	115701	exon5			GGTCACCAGCCTC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2428G>A	18.37:g.56204991C>T	ENSP00000354991:p.Gly810Ser	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	211	76	0.36019	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	955	0.43727106227106227	189	0.38414634146341464	184	0.5082872928176796	137	0.2395104895104895	445	0.5870712401055409	C	12.69	2.012911	0.35511	0.450068	0.533721	ENSG00000198796	ENST00000361673	T	0.52983	0.64	5.39	1.65	0.23941	.	1.545420	0.03173	N	0.171067	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P;B	0.50943	0.94;0.197	P;B	0.47015	0.534;0.092	T	0.41787	-0.9489	9	0.41790	T	0.15	-2.7978	2.4506	0.04517	0.1531:0.5408:0.1483:0.1578	rs3809970;rs17309830;rs52812207;rs57583190;rs3809970	810;810	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	S	810	ENSP00000354991:G810S	ENSP00000354991:G810S	G	-	1	0	ALPK2	54355971	0.000000	0.05858	0.040000	0.18447	0.017000	0.09413	0.230000	0.17852	0.021000	0.15133	0.591000	0.81541	GGT	C|0.532;T|0.468	0.468	strong		0.473	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
RAB3IL1	5866	hgsc.bcm.edu	37	11	61674118	61674118	+	Silent	SNP	C	C	T	rs174476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:61674118C>T	ENST00000394836.2	-	5	634	c.477G>A	c.(475-477)acG>acA	p.T159T	RAB3IL1_ENST00000301773.5_Intron	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	159					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						TGATGACCAGCGTCTTCAAGG	0.642													C|||	804	0.160543	0.025	0.2291	5008	,	,		17022	0.0308		0.4016	False		,,,				2504	0.181				p.T159T		Atlas-SNP	.											.	RAB3IL1	39	.	0			c.G477A						PASS	.	C		378,4026	180.1+/-208.5	20,338,1844	67.0	49.0	55.0		477	-9.2	0.6	11	dbSNP_79	55	3530,5068	486.4+/-371.9	744,2042,1513	no	coding-synonymous	RAB3IL1	NM_013401.2		764,2380,3357	TT,TC,CC		41.0561,8.5831,30.0569		159/383	61674118	3908,9094	2202	4299	6501	SO:0001819	synonymous_variant	5866	exon5			GACCAGCGTCTTC	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.477G>A	11.37:g.61674118C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	48	0.564706	NM_013401	Q86V32|Q9P1Q8	Silent	SNP	ENST00000394836.2	37	CCDS8014.1																																																																																			C|0.743;T|0.257	0.257	strong		0.642	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
Unknown	0	hgsc.bcm.edu	37	14	20181502	20181502	+	IGR	SNP	C	C	T	rs201024081		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20181502C>T								RP11-597A11.2 (28604 upstream) : OR4Q3 (34084 downstream)																							TCACACACAACATGGTCAATA	0.443																																					p.V192I		Atlas-SNP	.											.	.	.	.	0			c.G574A						PASS	.																																			SO:0001628	intergenic_variant	79334	exon2			ACACAACATGGTC																													14.37:g.20181502C>T		Somatic	725	2	0.00275862		WXS	Illumina HiSeq	Phase_I	792	289	0.364899	NM_001197287		Missense_Mutation	SNP		37																																																																																				.	.	weak	0	0.443								
KIF17	57576	hgsc.bcm.edu	37	1	21031042	21031042	+	Missense_Mutation	SNP	T	T	C	rs2296225	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:21031042T>C	ENST00000247986.2	-	5	1331	c.1021A>G	c.(1021-1023)Atc>Gtc	p.I341V	KIF17_ENST00000400463.3_Missense_Mutation_p.I341V|KIF17_ENST00000375044.1_Missense_Mutation_p.I241V			Q9P2E2	KIF17_HUMAN	kinesin family member 17	341			I -> V (in dbSNP:rs2296225).		ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TCCTCATTGATGCGCGGCTTG	0.597													T|||	820	0.163738	0.1021	0.062	5008	,	,		17209	0.2927		0.0915	False		,,,				2504	0.2607				p.I341V		Atlas-SNP	.											.	KIF17	130	.	0			c.A1021G						PASS	.	T	VAL/ILE,VAL/ILE	428,3978	207.5+/-228.8	17,394,1792	158.0	119.0	132.0		1021,1021	5.3	1.0	1	dbSNP_100	132	720,7880	176.2+/-226.1	33,654,3613	yes	missense,missense	KIF17	NM_001122819.1,NM_020816.2	29,29	50,1048,5405	CC,CT,TT		8.3721,9.714,8.8267	benign,benign	341/1029,341/1030	21031042	1148,11858	2203	4300	6503	SO:0001583	missense	57576	exon5			CATTGATGCGCGG	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1021A>G	1.37:g.21031042T>C	ENSP00000247986:p.Ile341Val	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	240	100	0.416667	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	306	0.1401098901098901	56	0.11382113821138211	28	0.07734806629834254	155	0.270979020979021	67	0.08839050131926121	T	12.43	1.936368	0.34189	0.09714	0.083721	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.71579	-0.58;-0.58;-0.58	5.26	5.26	0.73747	Kinesin, motor domain (2);	0.000000	0.33057	U	0.005340	T	0.00012	0.0000	N	0.13168	0.305	0.23221	P	0.99809292	B;B	0.23377	0.084;0.05	B;B	0.28784	0.094;0.039	T	0.05852	-1.0860	9	0.56958	D	0.05	.	9.2176	0.37358	0.0:0.0811:0.0:0.9189	rs2296225;rs52834908;rs2296225	341;341	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	V	241;341;341	ENSP00000364184:I241V;ENSP00000383311:I341V;ENSP00000247986:I341V	ENSP00000247986:I341V	I	-	1	0	KIF17	20903629	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	1.483000	0.35497	2.127000	0.65507	0.379000	0.24179	ATC	T|0.885;C|0.115	0.115	strong		0.597	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
LRRCC1	85444	hgsc.bcm.edu	37	8	86021994	86021994	+	Missense_Mutation	SNP	G	G	A	rs62525422	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:86021994G>A	ENST00000360375.3	+	2	418	c.269G>A	c.(268-270)tGc>tAc	p.C90Y	LRRCC1_ENST00000414626.2_Missense_Mutation_p.C70Y	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	90				C -> Y (in Ref. 1; BAB21855 and 2; BAG63888). {ECO:0000305}.	mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ACAAAACTGTGCACATTAAAT	0.308													G|||	283	0.0565096	0.0083	0.0389	5008	,	,		14924	0.0149		0.0905	False		,,,				2504	0.1421				p.C90Y		Atlas-SNP	.											.	LRRCC1	212	.	0			c.G269A						PASS	.	G	TYR/CYS	73,3603		0,73,1765	60.0	55.0	57.0		269	5.5	1.0	8	dbSNP_129	57	898,7258		42,814,3222	yes	missense	LRRCC1	NM_033402.4	194	42,887,4987	AA,AG,GG		11.0103,1.9859,8.2066	probably-damaging	90/1033	86021994	971,10861	1838	4078	5916	SO:0001583	missense	85444	exon2			AACTGTGCACATT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.269G>A	8.37:g.86021994G>A	ENSP00000353538:p.Cys90Tyr	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	174	73	0.41954	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	99	0.04532967032967033	4	0.008130081300813009	16	0.04419889502762431	7	0.012237762237762238	72	0.09498680738786279	G	14.18	2.457495	0.43634	0.019859	0.110103	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.09163	3.01;3.01	5.52	5.52	0.82312	.	0.185354	0.26871	N	0.022066	T	0.00210	0.0006	N	0.08118	0	0.33173	P	0.45148299999999997	D;P	0.54964	0.969;0.91	P;P	0.51135	0.66;0.544	T	0.31280	-0.9949	9	0.54805	T	0.06	-0.1137	12.7415	0.57255	0.075:0.0:0.925:0.0	rs62525422	70;90	Q9C099-2;Q9C099	.;LRCC1_HUMAN	Y	90;70	ENSP00000353538:C90Y;ENSP00000394695:C70Y	ENSP00000353538:C90Y	C	+	2	0	LRRCC1	86209246	1.000000	0.71417	0.997000	0.53966	0.186000	0.23388	5.294000	0.65687	2.582000	0.87167	0.591000	0.81541	TGC	G|0.925;A|0.075	0.075	strong		0.308	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
IGSF3	3321	hgsc.bcm.edu	37	1	117158745	117158745	+	Missense_Mutation	SNP	A	A	C	rs373093989		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:117158745A>C	ENST00000369486.3	-	3	1143	c.378T>G	c.(376-378)gaT>gaG	p.D126E	IGSF3_ENST00000369483.1_Missense_Mutation_p.D126E|IGSF3_ENST00000318837.6_Missense_Mutation_p.D126E	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	126	Ig-like C2-type 1.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.D126E(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		AGTATTGCTTATCAGTGCTGG	0.498																																					p.D126E		Atlas-SNP	.											IGSF3,extremity,malignant_melanoma,0,1	IGSF3	294	1	1	Substitution - Missense(1)	skin(1)	c.T378G						scavenged	.						61.0	55.0	57.0					1																	117158745		2203	4300	6503	SO:0001583	missense	3321	exon3			TTGCTTATCAGTG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.378T>G	1.37:g.117158745A>C	ENSP00000358498:p.Asp126Glu	Somatic	445	0	0		WXS	Illumina HiSeq	Phase_I	470	26	0.0553191	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	8.319	0.823848	0.16678	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.65364	-0.15;-0.15;-0.15	4.63	-8.69	0.00855	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.109427	0.64402	N	0.000011	T	0.34250	0.0891	M	0.69523	2.12	0.30895	N	0.729963	B;B	0.10296	0.003;0.002	B;B	0.20384	0.015;0.029	T	0.06481	-1.0824	10	0.66056	D	0.02	-9.8434	10.4193	0.44341	0.1981:0.2275:0.5744:0.0	.	126;126	O75054;A6NJZ6	IGSF3_HUMAN;.	E	126	ENSP00000358498:D126E;ENSP00000358495:D126E;ENSP00000321184:D126E	ENSP00000321184:D126E	D	-	3	2	IGSF3	116960268	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-2.110000	0.01334	-1.801000	0.01245	0.454000	0.30748	GAT	.	.	none		0.498	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
TOR1B	27348	hgsc.bcm.edu	37	9	132569532	132569532	+	Silent	SNP	C	C	T	rs16936946	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:132569532C>T	ENST00000259339.2	+	3	591	c.531C>T	c.(529-531)gaC>gaT	p.D177D		NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	177					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				TCATATTTGACGAGATGGATA	0.473													C|||	40	0.00798722	0.0008	0.0187	5008	,	,		19278	0.001		0.0239	False		,,,				2504	0.001				p.D177D		Atlas-SNP	.											.	TOR1B	20	.	0			c.C531T						PASS	.	C		16,4390	23.3+/-48.9	0,16,2187	208.0	188.0	195.0		531	-6.1	0.9	9	dbSNP_123	195	173,8427	78.9+/-141.6	0,173,4127	no	coding-synonymous	TOR1B	NM_014506.1		0,189,6314	TT,TC,CC		2.0116,0.3631,1.4532		177/337	132569532	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	27348	exon3			ATTTGACGAGATG	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.531C>T	9.37:g.132569532C>T		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	202	91	0.450495	NM_014506		Silent	SNP	ENST00000259339.2	37	CCDS6929.1																																																																																			C|0.987;T|0.013	0.013	strong		0.473	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506	
FAM181B	220382	hgsc.bcm.edu	37	11	82443817	82443817	+	Silent	SNP	G	G	A	rs2291793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:82443817G>A	ENST00000329203.3	-	1	1089	c.955C>T	c.(955-957)Ctg>Ttg	p.L319L		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	319	Pro-rich.									large_intestine(1)|lung(2)|prostate(1)	4						TCGGGGTACAGTAGGTTTCCC	0.711													G|||	1146	0.228834	0.0658	0.2262	5008	,	,		10575	0.497		0.172	False		,,,				2504	0.2331				p.L319L		Atlas-SNP	.											.	FAM181B	14	.	0			c.C955T						PASS	.	G		83,2091		1,81,1005	1.0	1.0	1.0		955	2.3	0.1	11	dbSNP_100	1	480,4156		6,468,1844	no	coding-synonymous	FAM181B	NM_175885.3		7,549,2849	AA,AG,GG		10.3538,3.8178,8.2673		319/427	82443817	563,6247	1087	2318	3405	SO:0001819	synonymous_variant	220382	exon1			GGTACAGTAGGTT	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.955C>T	11.37:g.82443817G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_175885	B2RWP1	Silent	SNP	ENST00000329203.3	37	CCDS31648.1																																																																																			G|0.745;A|0.255	0.255	strong		0.711	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885	
SUSD5	26032	hgsc.bcm.edu	37	3	33194990	33194990	+	Missense_Mutation	SNP	C	C	A	rs6810039	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:33194990C>A	ENST00000309558.3	-	5	1551	c.1134G>T	c.(1132-1134)gaG>gaT	p.E378D		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	378			E -> D (in dbSNP:rs6810039). {ECO:0000269|PubMed:9628581}.		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						TCCAAGCCCCCTCTGTCACAG	0.557													A|||	3305	0.659944	0.7307	0.6441	5008	,	,		21284	0.8542		0.3936	False		,,,				2504	0.6493				p.E378D		Atlas-SNP	.											.	SUSD5	53	.	0			c.G1134T						PASS	.	A	ASP/GLU	2899,1285		1014,871,207	99.0	107.0	105.0		1134	-9.8	0.0	3	dbSNP_116	105	3273,5189		644,1985,1602	yes	missense	SUSD5	NM_015551.1	45	1658,2856,1809	AA,AC,CC		38.6788,30.7122,48.8059	benign	378/630	33194990	6172,6474	2092	4231	6323	SO:0001583	missense	26032	exon5			AGCCCCCTCTGTC	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.1134G>T	3.37:g.33194990C>A	ENSP00000308727:p.Glu378Asp	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	271	117	0.431734	NM_015551		Missense_Mutation	SNP	ENST00000309558.3	37	CCDS46787.1	1384	0.6336996336996337	362	0.7357723577235772	205	0.5662983425414365	510	0.8916083916083916	307	0.4050131926121372	A	2.099	-0.406519	0.04832	0.692878	0.386788	ENSG00000173705	ENST00000309558	T	0.05996	3.36	5.84	-9.81	0.00487	.	0.218834	0.37955	N	0.001879	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41270	-0.9518	9	0.08381	T	0.77	-19.8019	8.3556	0.32329	0.1666:0.1655:0.5626:0.1052	rs6810039;rs52836781;rs56655667;rs6810039	378	O60279	SUSD5_HUMAN	D	378	ENSP00000308727:E378D	ENSP00000308727:E378D	E	-	3	2	SUSD5	33169994	0.057000	0.20700	0.005000	0.12908	0.820000	0.46376	-0.950000	0.03889	-2.418000	0.00566	-0.996000	0.02517	GAG	C|0.374;A|0.626	0.626	strong		0.557	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054	
Unknown	0	hgsc.bcm.edu	37	13	103410782	103410782	+	IGR	SNP	T	T	C	rs1375719	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103410782T>C								LINC00283 (13208 upstream) : TEX30 (7557 downstream)																							GATGAATTAATAACTGACCAA	0.294													T|||	1911	0.381589	0.1044	0.5043	5008	,	,		17536	0.4097		0.5089	False		,,,				2504	0.5092				p.I96V		Atlas-SNP	.											.	.	.	.	0			c.A286G						PASS	.	T	VAL/ILE	262,1122		28,206,458	81.0	69.0	73.0		286	2.1	0.0	13	dbSNP_88	73	1591,1581		410,771,405	yes	missense	CCDC168	NM_001146197.1	29	438,977,863	CC,CT,TT		49.8424,18.9306,40.6716		96/7082	103410782	1853,2703	692	1586	2278	SO:0001628	intergenic_variant	643677	exon3			AATTAATAACTGA																													13.37:g.103410782T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_001146197		Missense_Mutation	SNP		37																																																																																				A|0.014;C|0.352	0.352	strong	0	0.294								
KIAA1024	23251	hgsc.bcm.edu	37	15	79750127	79750127	+	Silent	SNP	A	A	G	rs2902954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79750127A>G	ENST00000305428.3	+	2	1713	c.1638A>G	c.(1636-1638)ggA>ggG	p.G546G		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	546						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						ACAGCACAGGATCCTTGTCTC	0.507													G|||	1576	0.314696	0.0976	0.304	5008	,	,		22339	0.5704		0.3698	False		,,,				2504	0.2955				p.G546G		Atlas-SNP	.											KIAA1024,NS,carcinoma,0,1	KIAA1024	146	1	0			c.A1638G						PASS	.	G		589,3803	770.6+/-413.7	42,505,1649	84.0	68.0	73.0		1638	-0.9	0.9	15	dbSNP_101	73	2852,5734	673.3+/-403.0	475,1902,1916	no	coding-synonymous	KIAA1024	NM_015206.2		517,2407,3565	GG,GA,AA		33.2169,13.4107,26.5141		546/917	79750127	3441,9537	2196	4293	6489	SO:0001819	synonymous_variant	23251	exon2			CACAGGATCCTTG	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.1638A>G	15.37:g.79750127A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_015206	A7MD43	Silent	SNP	ENST00000305428.3	37	CCDS32306.1																																																																																			A|0.701;G|0.299	0.299	strong		0.507	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
THRAP3	9967	hgsc.bcm.edu	37	1	36752152	36752152	+	Silent	SNP	C	C	T	rs2242428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36752152C>T	ENST00000354618.5	+	4	545	c.321C>T	c.(319-321)taC>taT	p.Y107Y	THRAP3_ENST00000469141.2_Silent_p.Y107Y	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	107	Arg-rich.|Required for mRNA splicing activation.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.Y107Y(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ATGGAAACTACCGCTCAAATT	0.522			T	USP6	aneurysmal bone cysts								C|||	1240	0.247604	0.1036	0.2219	5008	,	,		17948	0.0754		0.4205	False		,,,				2504	0.4601				p.Y107Y	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	THRAP3,NS,carcinoma,+1,2	THRAP3	93	2	1	Substitution - coding silent(1)	stomach(1)	c.C321T						PASS	.	C		615,3791	268.3+/-268.4	54,507,1642	116.0	117.0	116.0		321	3.9	1.0	1	dbSNP_98	116	3300,5300	493.9+/-373.7	624,2052,1624	no	coding-synonymous	THRAP3	NM_005119.3		678,2559,3266	TT,TC,CC		38.3721,13.9582,30.1015		107/956	36752152	3915,9091	2203	4300	6503	SO:0001819	synonymous_variant	9967	exon4			AAACTACCGCTCA	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.321C>T	1.37:g.36752152C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	123	72	0.585366	NM_005119	D3DPS5|Q5VTK6	Silent	SNP	ENST00000354618.5	37	CCDS405.1																																																																																			C|0.710;T|0.290	0.290	strong		0.522	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119	
LBX2	85474	hgsc.bcm.edu	37	2	74725178	74725178	+	Missense_Mutation	SNP	G	G	A	rs17009998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74725178G>A	ENST00000377566.4	-	2	651	c.473C>T	c.(472-474)tCc>tTc	p.S158F	LBX2_ENST00000460508.3_Missense_Mutation_p.S154F|LBX2_ENST00000341396.2_3'UTR|LBX2_ENST00000550249.1_5'UTR|AC005041.17_ENST00000479098.1_RNA	NM_001282430.1	NP_001269359.1	Q6XYB7	LBX2_HUMAN	ladybird homeobox 2	158			S -> F (in dbSNP:rs17009998).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(1)	4						GACTTCCGGGGACAACGCGCG	0.687													G|||	1668	0.333067	0.1399	0.2579	5008	,	,		15440	0.8204		0.1551	False		,,,				2504	0.3282				p.S154F		Atlas-SNP	.											.	LBX2	13	.	0			c.C461T						PASS	.	G	PHE/SER	662,3744	276.3+/-273.0	54,554,1595	49.0	48.0	48.0		461	3.0	0.2	2	dbSNP_123	48	1139,7459	227.9+/-263.1	77,985,3237	yes	missense	LBX2	NM_001009812.1	155	131,1539,4832	AA,AG,GG		13.2473,15.025,13.8496	probably-damaging	154/195	74725178	1801,11203	2203	4299	6502	SO:0001583	missense	85474	exon2			TCCGGGGACAACG	AC005041	CCDS33228.1, CCDS62938.1	2p13.1	2014-05-06	2007-02-15		ENSG00000179528	ENSG00000179528		"""Homeoboxes / ANTP class : NKL subclass"""	15525	protein-coding gene	gene with protein product		607164	"""ladybird homeobox homolog 2 (Drosophila)"""			11386758	Standard	NM_001282430		Approved		uc002slw.3	Q6XYB7	OTTHUMG00000170595	ENST00000377566.4:c.473C>T	2.37:g.74725178G>A	ENSP00000366789:p.Ser158Phe	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_001009812	Q7Z5Y8	Missense_Mutation	SNP	ENST00000377566.4	37		718	0.32875457875457875	63	0.12804878048780488	72	0.19889502762430938	471	0.8234265734265734	112	0.14775725593667546	G	15.19	2.759678	0.49468	0.15025	0.132473	ENSG00000179528	ENST00000377566;ENST00000460508	D;D	0.91945	-2.82;-2.94	4.76	2.95	0.34219	.	0.647217	0.13712	N	0.367991	T	0.00012	0.0000	L	0.29908	0.895	0.20563	P	0.999885927	B;B	0.12630	0.006;0.002	B;B	0.19148	0.024;0.002	T	0.44174	-0.9345	9	0.66056	D	0.02	.	7.3598	0.26739	0.0893:0.0:0.7431:0.1677	rs17009998;rs60339187;rs17009998	154;158	Q6XYB7-2;Q6XYB7	.;LBX2_HUMAN	F	158;154	ENSP00000366789:S158F;ENSP00000417116:S154F	ENSP00000366789:S158F	S	-	2	0	LBX2	74578686	0.000000	0.05858	0.178000	0.23040	0.034000	0.12701	0.297000	0.19101	0.605000	0.29947	0.561000	0.74099	TCC	G|0.774;A|0.226	0.226	strong		0.687	LBX2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328490.1	NM_001009812	
NPHS1	4868	hgsc.bcm.edu	37	19	36339247	36339247	+	Missense_Mutation	SNP	C	C	T	rs33950747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36339247C>T	ENST00000378910.5	-	10	1222	c.1223G>A	c.(1222-1224)cGg>cAg	p.R408Q	NPHS1_ENST00000353632.6_Missense_Mutation_p.R408Q	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	408	Ig-like C2-type 4.		R -> Q (in NPHS1; uncertain pathological significance; does not affect protein expression on the cell surface; dbSNP:rs33950747). {ECO:0000269|PubMed:11317351, ECO:0000269|PubMed:20172850, ECO:0000269|PubMed:9915943}.		cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTTGTCCTCCCGCCGCGCCAG	0.577													C|||	103	0.0205671	0.0023	0.0403	5008	,	,		17854	0.0		0.0557	False		,,,				2504	0.0164				p.R408Q		Atlas-SNP	.											.	NPHS1	165	.	0			c.G1223A	GRCh37	CM990958	NPHS1	M	rs33950747	PASS	.	C	GLN/ARG	56,4350	53.6+/-89.4	0,56,2147	99.0	87.0	91.0		1223	5.5	0.9	19	dbSNP_126	91	545,8055	151.0+/-205.8	27,491,3782	yes	missense	NPHS1	NM_004646.3	43	27,547,5929	TT,TC,CC		6.3372,1.271,4.6209	probably-damaging	408/1242	36339247	601,12405	2203	4300	6503	SO:0001583	missense	4868	exon10			TCCTCCCGCCGCG		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.1223G>A	19.37:g.36339247C>T	ENSP00000368190:p.Arg408Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	64	0.029304029304029304	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	47	0.06200527704485488	C	20.4	3.982368	0.74474	0.01271	0.063372	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.78003	-1.14;-1.14	5.53	5.53	0.82687	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.135150	0.49305	D	0.000144	T	0.51024	0.1650	M	0.72894	2.215	0.48901	D	0.999722	D	0.89917	1.0	D	0.85130	0.997	T	0.72297	-0.4335	10	0.35671	T	0.21	-25.372	16.9674	0.86290	0.0:1.0:0.0:0.0	rs33950747	408	O60500	NPHN_HUMAN	Q	408	ENSP00000368190:R408Q;ENSP00000343634:R408Q	ENSP00000343634:R408Q	R	-	2	0	NPHS1	41031087	0.795000	0.28851	0.933000	0.37362	0.485000	0.33311	5.506000	0.66993	2.596000	0.87737	0.591000	0.81541	CGG	C|0.958;T|0.042	0.042	strong		0.577	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
TTN	7273	hgsc.bcm.edu	37	2	179462494	179462494	+	Silent	SNP	A	A	G	rs35833641	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179462494A>G	ENST00000591111.1	-	244	52616	c.52392T>C	c.(52390-52392)caT>caC	p.H17464H	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.H10232H|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.H10040H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Silent_p.H16537H|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.H10165H|TTN_ENST00000589042.1_Silent_p.H19105H			Q8WZ42	TITIN_HUMAN	titin	17464	Ig-like 103.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCCCTCCAGCATGGACAACAA	0.448													A|||	636	0.126997	0.0053	0.1124	5008	,	,		20014	0.0387		0.3072	False		,,,				2504	0.2076				p.H19105H		Atlas-SNP	.											.	TTN	18412	.	0			c.T57315C						PASS	.	A	,,,	210,3788		5,200,1794	113.0	102.0	106.0		30120,49611,30495,30696	0.1	1.0	2	dbSNP_126	106	2508,5848		366,1776,2036	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	371,1976,3830	GG,GA,AA		30.0144,5.2526,22.001	,,,	10040/26927,16537/33424,10165/27052,10232/27119	179462494	2718,9636	1999	4178	6177	SO:0001819	synonymous_variant	7273	exon294			TCCAGCATGGACA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.52392T>C	2.37:g.179462494A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	208	106	0.509615	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.821;G|0.179	0.179	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ARHGEF26	26084	hgsc.bcm.edu	37	3	153943770	153943770	+	Missense_Mutation	SNP	C	C	G	rs74965475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:153943770C>G	ENST00000356448.4	+	11	2345	c.2061C>G	c.(2059-2061)aaC>aaG	p.N687K	ARHGEF26_ENST00000465093.1_Missense_Mutation_p.N687K|ARHGEF26_ENST00000483068.1_3'UTR|ARHGEF26_ENST00000465817.1_Intron	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	687	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.			N -> K (in Ref. 6; AAH16628). {ECO:0000305}.	endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						TTCTCTTTAACGATGTGCTCA	0.398													C|||	37	0.00738818	0.003	0.0101	5008	,	,		18598	0.0		0.0189	False		,,,				2504	0.0072				p.N687K	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.C2061G						PASS	.	C	LYS/ASN	15,3767		0,15,1876	104.0	91.0	95.0		2061	-6.0	0.7	3	dbSNP_131	95	158,8064		1,156,3954	yes	missense	ARHGEF26	NM_015595.3	94	1,171,5830	GG,GC,CC		1.9217,0.3966,1.4412	probably-damaging	687/872	153943770	173,11831	1891	4111	6002	SO:0001583	missense	26084	exon11			CTTTAACGATGTG	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24490	protein-coding gene	gene with protein product	"""Src homology 3 domain-containing guanine nucleotide exchange factor"""					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.2061C>G	3.37:g.153943770C>G	ENSP00000348828:p.Asn687Lys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	221	105	0.475113	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	37	CCDS46938.1	17	0.007783882783882784	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	C	17.13	3.310099	0.60414	0.003966	0.019217	ENSG00000114790	ENST00000356448;ENST00000465093	T;T	0.68331	-0.32;-0.32	5.65	-5.96	0.02234	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	M	0.84219	2.685	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.991;0.995	T	0.80441	-0.1381	10	0.87932	D	0	-33.6174	16.1896	0.81977	0.0:0.3521:0.0:0.6479	.	687;687	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	K	687	ENSP00000348828:N687K;ENSP00000423418:N687K	ENSP00000348828:N687K	N	+	3	2	ARHGEF26	155426460	0.000000	0.05858	0.726000	0.30738	0.884000	0.51177	-3.244000	0.00542	-0.995000	0.03459	-1.193000	0.01689	AAC	C|0.990;G|0.010	0.010	strong		0.398	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	
ZMYND8	23613	hgsc.bcm.edu	37	20	45878118	45878118	+	Missense_Mutation	SNP	C	C	G	rs77137073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:45878118C>G	ENST00000311275.7	-	13	1880	c.1627G>C	c.(1627-1629)Gtt>Ctt	p.V543L	ZMYND8_ENST00000372023.3_Missense_Mutation_p.V538L|ZMYND8_ENST00000461685.1_Missense_Mutation_p.V563L|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000355972.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000262975.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000540497.1_Missense_Mutation_p.V491L|ZMYND8_ENST00000352431.2_Missense_Mutation_p.V563L|ZMYND8_ENST00000471951.2_Missense_Mutation_p.V563L|ZMYND8_ENST00000446994.2_Missense_Mutation_p.V480L|ZMYND8_ENST00000536340.1_Missense_Mutation_p.V570L|ZMYND8_ENST00000458360.2_Missense_Mutation_p.V538L|ZMYND8_ENST00000396281.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000360911.3_Missense_Mutation_p.V538L	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	543					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)	p.V563L(1)		NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			ATGAGAGGAACAGGGGTGGAC	0.493													C|||	19	0.00379393	0.0	0.0043	5008	,	,		21570	0.0		0.0149	False		,,,				2504	0.001				p.V563L		Atlas-SNP	.											ZMYND8,NS,lymphoid_neoplasm,0,1	ZMYND8	166	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1687C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	15,4391	22.3+/-47.3	0,15,2188	148.0	129.0	136.0		1687,1687,1612	5.7	0.1	20	dbSNP_132	136	114,8486	61.0+/-122.8	3,108,4189	yes	missense,missense,missense	ZMYND8	NM_012408.3,NM_183047.1,NM_183048.1	32,32,32	3,123,6377	GG,GC,CC		1.3256,0.3404,0.9918	benign,benign,benign	563/1161,563/1189,538/1136	45878118	129,12877	2203	4300	6503	SO:0001583	missense	23613	exon13			GAGGAACAGGGGT	U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"""Zinc fingers, MYND-type"", ""Zinc fingers, PHD-type"""	9397	protein-coding gene	gene with protein product		615713	"""protein kinase C binding protein 1"""	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.1627G>C	20.37:g.45878118C>G	ENSP00000312237:p.Val543Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	135	62	0.459259	NM_183047	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	37		14|14	0.00641025641025641|0.00641025641025641	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	8.782|8.782	0.928382|0.928382	0.18131|0.18131	0.003404|0.003404	0.013256|0.013256	ENSG00000101040|ENSG00000101040	ENST00000467200|ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	.|D;D;D;D;D;D;D;D;D;D;D	.|0.90563	.|-1.84;-1.74;-1.87;-1.74;-1.85;-1.75;-1.74;-2.69;-1.73;-1.84;-1.8	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.203494	.|0.42294	.|D	.|0.000725	D|D	0.82953|0.82953	0.5149|0.5149	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	0.999992|0.999992	.|P;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	.|0.46621	.|0.881;0.243;0.078;0.078;0.0;0.277;0.112;0.0;0.0;0.0;0.0;0.078;0.0;0.0;0.078;0.073;0.0;0.078	.|B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	.|0.40702	.|0.338;0.138;0.217;0.217;0.009;0.314;0.138;0.005;0.005;0.005;0.005;0.217;0.012;0.012;0.217;0.053;0.006;0.217	T|T	0.79969|0.79969	-0.1579|-0.1579	5|10	.|0.42905	.|T	.|0.14	-17.669|-17.669	13.0828|13.0828	0.59123|0.59123	0.0:0.927:0.0:0.073|0.0:0.927:0.0:0.073	.|.	.|538;570;538;538;518;537;563;543;538;563;563;543;480;538;491;563;491;543	.|B7ZM62;F5H0X3;Q2HXV7;Q2HXV3;Q5TH11;Q5JV90;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q9ULU4-8;Q2HXV4;B7Z2A8	.|.;.;.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.;.	S|L	470|538;543;538;544;564;563;543;570;543;480;563;538;491	.|ENSP00000354166:V538L;ENSP00000312237:V543L;ENSP00000392964:V538L;ENSP00000335537:V563L;ENSP00000379577:V543L;ENSP00000439800:V570L;ENSP00000348246:V543L;ENSP00000396725:V480L;ENSP00000418210:V563L;ENSP00000361093:V538L;ENSP00000443086:V491L	.|ENSP00000262975:V544L	C|V	-|-	2|1	0|0	ZMYND8|ZMYND8	45311525|45311525	0.952000|0.952000	0.32445|0.32445	0.053000|0.053000	0.19242|0.19242	0.055000|0.055000	0.15305|0.15305	3.209000|3.209000	0.51122|0.51122	2.683000|2.683000	0.91414|0.91414	0.650000|0.650000	0.86243|0.86243	TGT|GTT	C|0.991;G|0.009	0.009	strong		0.493	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047	
GPR111	222611	hgsc.bcm.edu	37	6	47654742	47654742	+	Silent	SNP	A	A	T	rs9296573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:47654742A>T	ENST00000398742.2	+	6	1927	c.1878A>T	c.(1876-1878)ctA>ctT	p.L626L	GPR115_ENST00000371220.1_Intron			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	0					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TCTTCATCCTAGTGTTTGGAA	0.368													A|||	2590	0.517173	0.4637	0.4337	5008	,	,		18601	0.3085		0.6262	False		,,,				2504	0.7515				p.L626L		Atlas-SNP	.											.	GPR111	123	.	0			c.A1878T						PASS	.	A		1711,1961		390,931,515	233.0	210.0	217.0		1878	3.1	1.0	6	dbSNP_119	217	5276,2888		1714,1848,520	no	coding-synonymous	GPR111	NM_153839.6		2104,2779,1035	TT,TA,AA		35.3748,46.5959,40.9682		626/643	47654742	6987,4849	1836	4082	5918	SO:0001819	synonymous_variant	222611	exon8			CATCCTAGTGTTT	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000398742.2:c.1878A>T	6.37:g.47654742A>T		Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	388	222	0.572165	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Silent	SNP	ENST00000398742.2	37																																																																																				A|0.464;T|0.536	0.536	strong		0.368	GPR111-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153839	
WDR88	126248	hgsc.bcm.edu	37	19	33635761	33635761	+	Silent	SNP	C	C	T	rs3848596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33635761C>T	ENST00000355868.3	+	3	475	c.399C>T	c.(397-399)gaC>gaT	p.D133D	WDR88_ENST00000361680.2_Silent_p.D133D|WDR88_ENST00000592765.1_Silent_p.D133D	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	133										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					ATCCGGTGGACGGTTCTGTGG	0.532													T|||	2560	0.511182	0.4932	0.5692	5008	,	,		18215	0.5258		0.3241	False		,,,				2504	0.6718				p.D133D		Atlas-SNP	.											.	WDR88	50	.	0			c.C399T						PASS	.	T		2109,2297	600.6+/-389.5	503,1103,597	123.0	92.0	103.0		399	-2.0	0.0	19	dbSNP_108	103	2903,5697	669.9+/-402.7	472,1959,1869	yes	coding-synonymous	WDR88	NM_173479.3		975,3062,2466	TT,TC,CC		33.7558,47.8665,38.5361		133/473	33635761	5012,7994	2203	4300	6503	SO:0001819	synonymous_variant	126248	exon3			GGTGGACGGTTCT	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.399C>T	19.37:g.33635761C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	212	94	0.443396	NM_173479	Q8NEF8	Silent	SNP	ENST00000355868.3	37	CCDS12429.1																																																																																			C|0.574;N|0.000	.	strong		0.532	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
TPO	7173	hgsc.bcm.edu	37	2	1497803	1497803	+	Silent	SNP	C	C	T	rs1126797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:1497803C>T	ENST00000345913.4	+	11	2089	c.1998C>T	c.(1996-1998)gaC>gaT	p.D666D	TPO_ENST00000337415.3_Silent_p.D666D|TPO_ENST00000382198.1_Silent_p.D493D|TPO_ENST00000349624.3_Silent_p.D493D|TPO_ENST00000346956.3_Silent_p.D666D|TPO_ENST00000329066.4_Silent_p.D666D|TPO_ENST00000382201.3_Silent_p.D609D|TPO_ENST00000497517.2_3'UTR	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	666					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CTCTGCGGGACGGTGACTGGT	0.572													C|||	1798	0.359026	0.3147	0.3689	5008	,	,		17099	0.4067		0.3688	False		,,,				2504	0.3528				p.D666D		Atlas-SNP	.											.	TPO	224	.	0			c.C1998T						PASS	.	C	,,,,,	1419,2987	464.2+/-353.8	227,965,1011	89.0	86.0	87.0		1998,1998,1827,1827,1998,1479	-9.6	0.1	2	dbSNP_86	87	3140,5460	477.6+/-369.7	555,2030,1715	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	782,2995,2726	TT,TC,CC		36.5116,32.2061,35.0531	,,,,,	666/934,666/934,609/877,609/877,666/890,493/761	1497803	4559,8447	2203	4300	6503	SO:0001819	synonymous_variant	7173	exon11			GCGGGACGGTGAC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1998C>T	2.37:g.1497803C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1	823	0.3768315018315018	166	0.33739837398373984	137	0.3784530386740331	248	0.43356643356643354	272	0.35883905013192613	C	0.096	-1.159934	0.01686	0.322061	0.365116	ENSG00000115705	ENST00000446278	.	.	.	4.84	-9.63	0.00544	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999956	.	.	.	.	.	.	T	0.17531	-1.0366	3	.	.	.	-31.7375	9.8612	0.41116	0.2006:0.1257:0.0:0.6737	rs1126797;rs3182052;rs17415659;rs17731853;rs59472239;rs17415659	.	.	.	M	141	.	.	T	+	2	0	TPO	1476810	0.000000	0.05858	0.103000	0.21229	0.038000	0.13279	-4.038000	0.00308	-1.948000	0.01033	-0.995000	0.02519	ACG	A|0.000;C|0.646;G|0.000;T|0.354	0.354	strong		0.572	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
ZNF880	400713	hgsc.bcm.edu	37	19	52887904	52887904	+	Silent	SNP	T	T	C	rs2042913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52887904T>C	ENST00000422689.2	+	4	1086	c.1071T>C	c.(1069-1071)tgT>tgC	p.C357C		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	357					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GTAATAAATGTGGCAAGGTCT	0.403																																					p.C357C		Atlas-SNP	.											ZNF880,colon,carcinoma,0,1	ZNF880	45	1	0			c.T1071C						PASS	.						41.0	38.0	39.0					19																	52887904		1568	3582	5150	SO:0001819	synonymous_variant	400713	exon4			TAAATGTGGCAAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1071T>C	19.37:g.52887904T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_001145434	B4DNA6	Silent	SNP	ENST00000422689.2	37	CCDS46164.1																																																																																			T|0.637;C|0.363	0.363	strong		0.403	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
PRAME	23532	hgsc.bcm.edu	37	22	22890492	22890492	+	Silent	SNP	G	G	A	rs13604	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22890492G>A	ENST00000398741.1	-	6	1833	c.1527C>T	c.(1525-1527)aaC>aaT	p.N509N	PRAME_ENST00000539862.1_Silent_p.N493N|PRAME_ENST00000398743.2_Silent_p.N509N|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000543184.1_Silent_p.N509N|PRAME_ENST00000424204.2_Silent_p.N493N|PRAME_ENST00000405655.3_Silent_p.N509N|PRAME_ENST00000402697.1_Silent_p.N509N	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	509	Mediates interaction with RARA.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CACCCAGCTAGTTAGGCATGA	0.522													G|||	264	0.0527157	0.0234	0.085	5008	,	,		19469	0.0		0.1402	False		,,,				2504	0.0337				p.N509N	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.C1527T						PASS	.	G	,,,,	203,4203	127.0+/-164.0	5,193,2005	161.0	155.0	157.0		1527,1527,1527,1527,1527	1.2	0.0	22	dbSNP_52	157	1301,7299	256.5+/-280.9	101,1099,3100	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRAME	NM_006115.3,NM_206953.1,NM_206954.1,NM_206955.1,NM_206956.1	,,,,	106,1292,5105	AA,AG,GG		15.1279,4.6074,11.5639	,,,,	509/510,509/510,509/510,509/510,509/510	22890492	1504,11502	2203	4300	6503	SO:0001819	synonymous_variant	23532	exon6			CAGCTAGTTAGGC	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.1527C>T	22.37:g.22890492G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_206954	B2R6Y7|O43481|Q8IXN8	Silent	SNP	ENST00000398741.1	37	CCDS13801.1																																																																																			G|0.903;A|0.097	0.097	strong		0.522	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
C3orf18	51161	hgsc.bcm.edu	37	3	50598396	50598396	+	Silent	SNP	G	G	A	rs41291736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50598396G>A	ENST00000357203.3	-	5	899	c.360C>T	c.(358-360)gaC>gaT	p.D120D	C3orf18_ENST00000422619.1_Silent_p.D68D|C3orf18_ENST00000486175.1_5'UTR|C3orf18_ENST00000441239.1_Silent_p.D100D|C3orf18_ENST00000449241.1_Silent_p.D120D|C3orf18_ENST00000426034.1_Silent_p.D120D	NM_016210.4	NP_057294.2	Q9UK00	CC018_HUMAN	chromosome 3 open reading frame 18	120						integral component of membrane (GO:0016021)				lung(1)|pancreas(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)		CAGAGGCGGCGTCCCGCCCAT	0.632													G|||	280	0.0559105	0.0242	0.0937	5008	,	,		18530	0.0		0.1243	False		,,,				2504	0.0593				p.D120D		Atlas-SNP	.											.	C3orf18	12	.	0			c.C360T						PASS	.	G	,,,	179,4227	115.9+/-153.8	2,175,2026	95.0	83.0	87.0		360,360,300,360	-4.8	0.1	3	dbSNP_127	87	1140,7460	234.9+/-267.6	68,1004,3228	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C3orf18	NM_001171740.2,NM_001171741.2,NM_001171743.2,NM_016210.4	,,,	70,1179,5254	AA,AG,GG		13.2558,4.0626,10.1415	,,,	120/163,120/163,100/143,120/163	50598396	1319,11687	2203	4300	6503	SO:0001819	synonymous_variant	51161	exon5			GGCGGCGTCCCGC	AF188706	CCDS2829.1, CCDS54589.1	3p21.3	2006-01-11			ENSG00000088543	ENSG00000088543			24837	protein-coding gene	gene with protein product						12477932	Standard	NM_016210		Approved	G20	uc010hlp.3	Q9UK00	OTTHUMG00000156854	ENST00000357203.3:c.360C>T	3.37:g.50598396G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	147	66	0.44898	NM_016210	C9JNP0	Silent	SNP	ENST00000357203.3	37	CCDS2829.1																																																																																			G|0.908;A|0.092	0.092	strong		0.632	C3orf18-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346260.2	NM_016210	
STEAP1B	256227	hgsc.bcm.edu	37	7	22478207	22478207	+	Intron	SNP	G	G	T	rs2528843	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:22478207G>T	ENST00000406890.2	-	5	800				STEAP1B_ENST00000404369.4_Silent_p.A310A	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B							integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						ttgaagggctggctgctgata	0.398													T|||	2614	0.521965	0.5832	0.4135	5008	,	,		20390	0.6071		0.4702	False		,,,				2504	0.4816				p.A310A		Atlas-SNP	.											.	STEAP1B	22	.	0			c.C930A						PASS	.	T	,	764,620		218,328,146	155.0	139.0	144.0		930,	0.6	0.0	7	dbSNP_100	144	1397,1785		302,793,496	no	coding-synonymous,intron	STEAP1B	NM_001164460.1,NM_207342.2	,	520,1121,642	TT,TG,GG		43.9032,44.7977,47.3281	,	310/343,	22478207	2161,2405	692	1591	2283	SO:0001627	intron_variant	256227	exon5			AGGGCTGGCTGCT		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.706-18752C>A	7.37:g.22478207G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_001164460	B5MCI2	Silent	SNP	ENST00000406890.2	37	CCDS55094.1																																																																																			G|0.488;T|0.512	0.512	strong		0.398	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
QSOX1	5768	hgsc.bcm.edu	37	1	180163390	180163390	+	Missense_Mutation	SNP	A	A	G	rs12371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180163390A>G	ENST00000367602.3	+	11	1405	c.1331A>G	c.(1330-1332)cAc>cGc	p.H444R	QSOX1_ENST00000367600.5_Missense_Mutation_p.H444R			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	444	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.		H -> R (in dbSNP:rs12371). {ECO:0000269|PubMed:16806532}.		cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						GGCTACGTGCACTACTTCTTC	0.657													A|||	136	0.0271565	0.003	0.0461	5008	,	,		15673	0.0		0.0775	False		,,,				2504	0.0225				p.H444R		Atlas-SNP	.											.	QSOX1	79	.	0			c.A1331G						PASS	.	A	ARG/HIS,ARG/HIS	86,4320	68.1+/-105.8	2,82,2119	45.0	39.0	41.0		1331,1331	1.0	0.0	1	dbSNP_52	41	791,7809	178.6+/-228.0	35,721,3544	yes	missense,missense	QSOX1	NM_001004128.2,NM_002826.4	29,29	37,803,5663	GG,GA,AA		9.1977,1.9519,6.743	benign,benign	444/605,444/748	180163390	877,12129	2203	4300	6503	SO:0001583	missense	5768	exon11			ACGTGCACTACTT	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1331A>G	1.37:g.180163390A>G	ENSP00000356574:p.His444Arg	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	174	86	0.494253	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Missense_Mutation	SNP	ENST00000367602.3	37	CCDS1337.1	88	0.040293040293040296	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	67	0.08839050131926121	A	0.009	-1.838203	0.00573	0.019519	0.091977	ENSG00000116260	ENST00000367602;ENST00000367600	T;T	0.51325	0.71;2.6	4.75	1.02	0.19986	Erv1/Alr (3);ERV/ALR sulphydryl oxidase (1);	1.093820	0.06782	N	0.785533	T	0.00552	0.0018	N	0.00637	-1.305	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.20338	-1.0278	9	0.11794	T	0.64	-6.7752	7.2178	0.25969	0.5075:0.0:0.4925:0.0	rs12371;rs1050155;rs3190456;rs11541658;rs17354773;rs58201785	444;444	O00391;O00391-2	QSOX1_HUMAN;.	R	444	ENSP00000356574:H444R;ENSP00000356572:H444R	ENSP00000356572:H444R	H	+	2	0	QSOX1	178430013	0.000000	0.05858	0.018000	0.16275	0.125000	0.20455	-0.150000	0.10189	0.406000	0.25560	-0.624000	0.04008	CAC	A|0.940;G|0.060	0.060	strong		0.657	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
RORA	6095	hgsc.bcm.edu	37	15	60789798	60789798	+	Silent	SNP	G	G	T	rs11071539	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:60789798G>T	ENST00000335670.6	-	11	1528	c.1428C>A	c.(1426-1428)acC>acA	p.T476T	RP11-219B17.1_ENST00000501579.2_RNA|RP11-219B17.1_ENST00000558235.1_RNA|RORA_ENST00000449337.2_Silent_p.T421T|RORA_ENST00000261523.5_Silent_p.T509T|RP11-219B17.1_ENST00000558140.1_RNA|RP11-219B17.1_ENST00000559824.1_RNA|RORA_ENST00000309157.4_Silent_p.T501T	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	476	Ligand-binding.				angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						AGGCTCTTAAGGTAGACACCT	0.398													T|||	4709	0.940296	0.7965	0.9755	5008	,	,		20185	1.0		0.999	False		,,,				2504	0.9877				p.T509T		Atlas-SNP	.											.	RORA	114	.	0			c.C1527A						PASS	.	T	,,,	3670,736	304.4+/-288.4	1523,624,56	149.0	127.0	134.0		1503,1527,1428,1263	-0.1	1.0	15	dbSNP_120	134	8589,11	7.1+/-27.0	4289,11,0	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RORA	NM_002943.3,NM_134260.2,NM_134261.2,NM_134262.2	,,,	5812,635,56	TT,TG,GG		0.1279,16.7045,5.7435	,,,	501/549,509/557,476/524,421/469	60789798	12259,747	2203	4300	6503	SO:0001819	synonymous_variant	6095	exon12			TCTTAAGGTAGAC	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"""Nuclear hormone receptors"""	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.1428C>A	15.37:g.60789798G>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	176	174	0.988636	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Silent	SNP	ENST00000335670.6	37	CCDS10177.1																																																																																			G|0.056;T|0.944	0.944	strong		0.398	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2		
AGAP6	414189	hgsc.bcm.edu	37	10	51769799	51769799	+	Silent	SNP	C	C	T	rs61848275	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:51769799C>T	ENST00000374056.4	+	7	2243	c.1845C>T	c.(1843-1845)gtC>gtT	p.V615V	AGAP6_ENST00000412531.3_Silent_p.V638V			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	615					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						GGAATGTGGTCCTGGCGCAGC	0.667													.|||	597	0.119209	0.0461	0.1542	5008	,	,		18357	0.0317		0.2654	False		,,,				2504	0.1329				p.V638V		Atlas-SNP	.											AGAP6,NS,carcinoma,0,1	AGAP6	53	1	0			c.C1914T						scavenged	.																																			SO:0001819	synonymous_variant	414189	exon8			TGTGGTCCTGGCG		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.1845C>T	10.37:g.51769799C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	244	68	0.278689	NM_001077665		Silent	SNP	ENST00000374056.4	37																																																																																				C|0.500;T|0.500	0.500	weak		0.667	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
FAM205A	259308	hgsc.bcm.edu	37	9	34725112	34725112	+	Missense_Mutation	SNP	C	C	T	rs200209883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:34725112C>T	ENST00000378788.3	-	4	2164	c.2125G>A	c.(2125-2127)Gca>Aca	p.A709T		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	709						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						GGAGCCACTGCCAGGACCCCA	0.552																																					p.A709T		Atlas-SNP	.											FAM205A_ENST00000378788,NS,haematopoietic_neoplasm,0,2	FAM205A	45	2	0			c.G2125A						PASS	.						22.0	16.0	18.0					9																	34725112		692	1591	2283	SO:0001583	missense	259308	exon4			CCACTGCCAGGAC		CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.2125G>A	9.37:g.34725112C>T	ENSP00000417711:p.Ala709Thr	Somatic	475	0	0		WXS	Illumina HiSeq	Phase_I	436	176	0.40367	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730297	0.48939	.	.	ENSG00000205108	ENST00000378788	T	0.54279	0.58	4.43	-2.72	0.05968	.	.	.	.	.	T	0.42268	0.1195	L	0.29908	0.895	0.09310	N	1	D	0.54207	0.965	P	0.50659	0.647	T	0.34900	-0.9810	9	0.35671	T	0.21	.	5.4131	0.16358	0.0:0.2766:0.4419:0.2815	.	709	Q6ZU69	F205A_HUMAN	T	709	ENSP00000417711:A709T	ENSP00000417711:A709T	A	-	1	0	RP11-195F19.10	34715112	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.932000	0.03963	-0.528000	0.06366	-0.300000	0.09419	GCA	C|0.978;T|0.022	0.022	strong		0.552	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
NBPF10	100132406	hgsc.bcm.edu	37	1	145293515	145293515	+	Missense_Mutation	SNP	A	A	G	rs12565078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145293515A>G	ENST00000369339.3	+	3	363	c.110A>G	c.(109-111)aAc>aGc	p.N37S	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000342960.5_Missense_Mutation_p.N37S|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	308						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CAGTTCAGAAACCTCAAAGAG	0.478																																					p.N37S		Atlas-SNP	.											.	NBPF10	221	.	0			c.A110G						PASS	.																																			SO:0001583	missense	100132406	exon1			TCAGAAACCTCAA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.110A>G	1.37:g.145293515A>G	ENSP00000358345:p.Asn37Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	172	61	0.354651	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	0.712	-0.786747	0.02907	.	.	ENSG00000163386	ENST00000369339;ENST00000342960	T	0.03094	4.05	1.06	-0.231	0.13086	.	.	.	.	.	T	0.00875	0.0029	L	0.46157	1.445	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.48456	-0.9034	9	0.11794	T	0.64	.	3.1661	0.06536	0.7225:0.0:0.2775:0.0	rs12565078;rs57282873	37	A8MQ30	.	S	37	ENSP00000345684:N37S	ENSP00000345684:N37S	N	+	2	0	NBPF10	144004872	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	0.914000	0.28624	-0.082000	0.12640	-1.412000	0.01120	AAC	A|0.731;G|0.269	0.269	strong		0.478	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
MS4A15	219995	hgsc.bcm.edu	37	11	60531346	60531346	+	Missense_Mutation	SNP	T	T	G	rs1032939	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60531346T>G	ENST00000405633.3	+	2	219	c.140T>G	c.(139-141)cTg>cGg	p.L47R	MS4A15_ENST00000337911.4_Intron|MS4A15_ENST00000528170.1_Missense_Mutation_p.L47R	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	47			L -> R (in dbSNP:rs1032939). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(3)	6						GAGCCACCGCTGGGGGCACAG	0.602													T|||	2033	0.40595	0.0628	0.4769	5008	,	,		18434	0.628		0.4841	False		,,,				2504	0.5102				p.L47R		Atlas-SNP	.											.	MS4A15	37	.	0			c.T140G						PASS	.	T	ARG/LEU,	577,3469		54,469,1500	48.0	50.0	50.0		140,	4.1	0.2	11	dbSNP_86	50	3807,4499		874,2059,1220	yes	missense,intron	MS4A15	NM_001098835.1,NM_152717.2	102,	928,2528,2720	GG,GT,TT		45.8343,14.261,35.4922	benign,	47/241,	60531346	4384,7968	2023	4153	6176	SO:0001583	missense	219995	exon2			CACCGCTGGGGGC	AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.140T>G	11.37:g.60531346T>G	ENSP00000386022:p.Leu47Arg	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_001098835	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	37	CCDS44617.1	947	0.4336080586080586	38	0.07723577235772358	168	0.46408839779005523	373	0.6520979020979021	368	0.48548812664907653	T	8.610	0.888974	0.17540	0.14261	0.458343	ENSG00000166961	ENST00000528170;ENST00000405633	T;T	0.30981	1.51;2.77	5.21	4.08	0.47627	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.45284	P	0.0017179999999999973	D;B	0.76494	0.999;0.027	D;B	0.83275	0.996;0.012	T	0.23084	-1.0198	8	0.15952	T	0.53	-8.9953	7.9879	0.30222	0.0:0.0942:0.0:0.9058	rs1032939;rs61387995;rs1032939	47;47	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	R	47	ENSP00000434165:L47R;ENSP00000386022:L47R	ENSP00000386022:L47R	L	+	2	0	MS4A15	60287922	0.980000	0.34600	0.154000	0.22540	0.421000	0.31385	1.528000	0.35985	0.806000	0.34183	-0.566000	0.04163	CTG	T|0.597;G|0.403	0.403	strong		0.602	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1		
ACSBG2	81616	hgsc.bcm.edu	37	19	6156510	6156510	+	Missense_Mutation	SNP	A	A	G	rs33937754	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6156510A>G	ENST00000586696.1	+	5	731	c.455A>G	c.(454-456)aAa>aGa	p.K152R	ACSBG2_ENST00000591403.1_Missense_Mutation_p.K152R|ACSBG2_ENST00000252669.5_Missense_Mutation_p.K152R|ACSBG2_ENST00000588485.1_Intron|ACSBG2_ENST00000588304.1_Missense_Mutation_p.K102R			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	152			K -> R (in dbSNP:rs33937754).		cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACTCATGCCAAAGTGAACATC	0.463													A|||	248	0.0495208	0.0068	0.0677	5008	,	,		19458	0.0		0.1332	False		,,,				2504	0.0593				p.K152R		Atlas-SNP	.											.	ACSBG2	83	.	0			c.A455G						PASS	.	A	ARG/LYS	115,4291	86.3+/-125.0	4,107,2092	168.0	156.0	160.0		455	5.9	1.0	19	dbSNP_126	160	1319,7281	260.1+/-283.0	80,1159,3061	yes	missense	ACSBG2	NM_030924.3	26	84,1266,5153	GG,GA,AA		15.3372,2.6101,11.0257	benign	152/667	6156510	1434,11572	2203	4300	6503	SO:0001583	missense	81616	exon5			ATGCCAAAGTGAA		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.455A>G	19.37:g.6156510A>G	ENSP00000465589:p.Lys152Arg	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	209	100	0.478469	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	127	0.05815018315018315	2	0.0040650406504065045	26	0.0718232044198895	0	0.0	99	0.13060686015831136	A	6.947	0.544588	0.13312	0.026101	0.153372	ENSG00000130377	ENST00000252669	T	0.10763	2.84	5.9	5.9	0.94986	AMP-dependent synthetase/ligase (1);	0.174718	0.27500	N	0.019096	T	0.00039	0.0001	L	0.28608	0.87	0.43267	P	0.004782999999999982	B;B	0.11235	0.002;0.004	B;B	0.20384	0.02;0.029	T	0.22977	-1.0201	9	0.05959	T	0.93	-29.5263	14.2842	0.66235	1.0:0.0:0.0:0.0	rs33937754	152;152	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	R	152	ENSP00000252669:K152R	ENSP00000252669:K152R	K	+	2	0	ACSBG2	6107510	1.000000	0.71417	0.972000	0.41901	0.904000	0.53231	4.329000	0.59260	2.251000	0.74343	0.528000	0.53228	AAA	A|0.908;G|0.092	0.092	strong		0.463	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
MAML1	9794	hgsc.bcm.edu	37	5	179193598	179193598	+	Silent	SNP	C	C	T	rs3797776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:179193598C>T	ENST00000292599.3	+	2	1850	c.1587C>T	c.(1585-1587)agC>agT	p.S529S	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCAAGGCAGCCCGGGGTCTG	0.532													C|||	831	0.165935	0.0257	0.2161	5008	,	,		18528	0.1488		0.3231	False		,,,				2504	0.1759				p.S529S		Atlas-SNP	.											.	MAML1	118	.	0			c.C1587T						PASS	.	C		314,4092	168.7+/-199.5	17,280,1906	62.0	61.0	62.0		1587	1.2	0.4	5	dbSNP_107	62	2556,6044	416.9+/-352.3	391,1774,2135	no	coding-synonymous	MAML1	NM_014757.4		408,2054,4041	TT,TC,CC		29.7209,7.1266,22.0667		529/1017	179193598	2870,10136	2203	4300	6503	SO:0001819	synonymous_variant	9794	exon2			AGGCAGCCCGGGG	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1587C>T	5.37:g.179193598C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	128	36	0.28125	NM_014757		Silent	SNP	ENST00000292599.3	37	CCDS34315.1																																																																																			C|0.800;T|0.200	0.200	strong		0.532	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
WDR66	144406	hgsc.bcm.edu	37	12	122372183	122372183	+	Missense_Mutation	SNP	G	G	A	rs77540055	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:122372183G>A	ENST00000288912.4	+	5	1773	c.919G>A	c.(919-921)Gtc>Atc	p.V307I	WDR66_ENST00000397454.2_Missense_Mutation_p.V307I	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	307							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		CTGCCTCTGCGTCAGTGAAGA	0.527													G|||	172	0.034345	0.003	0.0375	5008	,	,		19010	0.0496		0.0457	False		,,,				2504	0.047				p.V307I	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,caecum,carcinoma,0,1	WDR66	143	1	0			c.G919A						PASS	.	G	ILE/VAL,ILE/VAL	40,4036		2,36,2000	74.0	78.0	77.0		919,919	-5.8	0.0	12	dbSNP_131	77	380,7974		14,352,3811	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	29,29	16,388,5811	AA,AG,GG		4.5487,0.9814,3.3789	benign,benign	307/942,307/1150	122372183	420,12010	2038	4177	6215	SO:0001583	missense	144406	exon5			CTCTGCGTCAGTG	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.919G>A	12.37:g.122372183G>A	ENSP00000288912:p.Val307Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	53	17	0.320755	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	69	0.03159340659340659	3	0.006097560975609756	15	0.04143646408839779	20	0.03496503496503497	31	0.040897097625329816	G	9.960	1.222419	0.22457	0.009814	0.045487	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.59083	0.29;0.29	5.05	-5.79	0.02354	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.636624	0.15986	N	0.235056	T	0.07954	0.0199	N	0.21097	0.63	0.22066	N	0.999387	B	0.15473	0.013	B	0.17979	0.02	T	0.03761	-1.1006	10	0.18710	T	0.47	.	16.0506	0.80760	0.0984:0.0956:0.806:0.0	.	307	Q8TBY9	WDR66_HUMAN	I	307	ENSP00000288912:V307I;ENSP00000380595:V307I	ENSP00000288912:V307I	V	+	1	0	WDR66	120856566	0.548000	0.26473	0.034000	0.17996	0.288000	0.27193	-0.029000	0.12329	-1.655000	0.01497	-0.672000	0.03802	GTC	G|0.960;A|0.040	0.040	strong		0.527	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
RHD	6007	hgsc.bcm.edu	37	1	25629896	25629896	+	Missense_Mutation	SNP	G	G	T	rs371803235		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:25629896G>T	ENST00000328664.4	+	6	1040	c.885G>T	c.(883-885)atG>atT	p.M295I	RHD_ENST00000454452.2_Missense_Mutation_p.M295I|RHD_ENST00000342055.5_Missense_Mutation_p.M295I|RHD_ENST00000357542.4_Missense_Mutation_p.M295I|RHD_ENST00000423253.1_3'UTR|RHD_ENST00000417538.2_Missense_Mutation_p.M295I|RHD_ENST00000568195.1_Missense_Mutation_p.M295I|RHD_ENST00000423810.2_Missense_Mutation_p.M295I	NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	295						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGCTTGCCATGGTGCTGGGTC	0.572																																					p.M295I		Atlas-SNP	.											.	RHD	38	.	0			c.G885T	GRCh37	CM994723	RHD	M		PASS	.	G	ILE/MET,ILE/MET	0,4226		0,0,2113	85.0	59.0	68.0		885,885	3.2	1.0	1		68	1,7421		0,1,3710	no	missense,missense	RHD	NM_001127691.1,NM_016124.3	10,10	0,1,5823	TT,TG,GG		0.0135,0.0,0.0086	probably-damaging,probably-damaging	295/322,295/418	25629896	1,11647	2113	3711	5824	SO:0001583	missense	6007	exon6			TGCCATGGTGCTG	AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010		"""CD molecules"", ""Blood group antigens"""	10009	protein-coding gene	gene with protein product		111680	"""Rhesus blood group, D antigen"", ""Rh blood group, D antigen"""	RH		8220426	Standard	NM_016124		Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.885G>T	1.37:g.25629896G>T	ENSP00000331871:p.Met295Ile	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	247	101	0.408907	NM_001127691	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	Missense_Mutation	SNP	ENST00000328664.4	37	CCDS262.1	.	.	.	.	.	.	.	.	.	.	.	7.093	0.572463	0.13623	0.0	1.35E-4	ENSG00000187010	ENST00000328664;ENST00000419831;ENST00000454452;ENST00000342055;ENST00000357542;ENST00000417538;ENST00000423810	T;T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05;2.05	3.19	3.19	0.36642	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	T	0.38852	0.1056	M	0.61703	1.905	0.58432	D	0.999998	D;D;P;D;D;P;D;D	0.89917	1.0;1.0;0.86;1.0;1.0;0.947;1.0;1.0	D;D;P;D;D;D;D;D	0.97110	1.0;0.999;0.844;1.0;1.0;0.932;0.999;1.0	T	0.11131	-1.0600	10	0.42905	T	0.14	-40.782	9.7501	0.40470	0.0:0.0:1.0:0.0	.	295;295;295;295;295;295;295;295	B4DLT8;Q5XLT1;Q5XLS9;Q5XLT2;Q5XLT3;E7EVW1;Q5XLT0;Q02161	.;.;.;.;.;.;.;RHD_HUMAN	I	295	ENSP00000331871:M295I;ENSP00000413849:M295I;ENSP00000339577:M295I;ENSP00000350150:M295I;ENSP00000396420:M295I;ENSP00000399640:M295I	ENSP00000331871:M295I	M	+	3	0	RHD	25502483	1.000000	0.71417	0.994000	0.49952	0.027000	0.11550	5.868000	0.69605	1.623000	0.50342	0.393000	0.25936	ATG	.	.	none		0.572	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009660.5	NM_016124	
SMG1	23049	hgsc.bcm.edu	37	16	18847416	18847416	+	Silent	SNP	G	G	A	rs3816919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:18847416G>A	ENST00000446231.2	-	48	8308	c.7896C>T	c.(7894-7896)tcC>tcT	p.S2632S	SMG1_ENST00000389467.3_Silent_p.S2632S			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2632					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CACGGAGCACGGAGCGCCTCT	0.562													G|||	539	0.107628	0.0794	0.1657	5008	,	,		19236	0.1151		0.0765	False		,,,				2504	0.1288				p.S2632S		Atlas-SNP	.											.	SMG1	401	.	0			c.C7896T						PASS	.	G		345,3851		13,319,1766	43.0	42.0	42.0		7896	-11.6	0.0	16	dbSNP_107	42	771,7675		35,701,3487	no	coding-synonymous	SMG1	NM_015092.4		48,1020,5253	AA,AG,GG		9.1286,8.2221,8.8277		2632/3662	18847416	1116,11526	2098	4223	6321	SO:0001819	synonymous_variant	23049	exon48			GAGCACGGAGCGC	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.7896C>T	16.37:g.18847416G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			G|0.899;A|0.101	0.101	strong		0.562	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
DZIP1L	199221	hgsc.bcm.edu	37	3	137807259	137807259	+	Missense_Mutation	SNP	G	G	A	rs2724693	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:137807259G>A	ENST00000327532.2	-	6	1323	c.961C>T	c.(961-963)Cgg>Tgg	p.R321W	DZIP1L_ENST00000469243.1_Missense_Mutation_p.R321W|DZIP1L_ENST00000488595.1_5'UTR	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	321			R -> W (in dbSNP:rs2724693). {ECO:0000269|PubMed:14702039}.		cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						TGAAGCTCCCGTGCCTGCCGA	0.547													G|||	2689	0.536941	0.1884	0.6859	5008	,	,		17069	0.6131		0.6869	False		,,,				2504	0.6697				p.R321W		Atlas-SNP	.											.	DZIP1L	88	.	0			c.C961T						PASS	.	G	TRP/ARG,TRP/ARG	1291,3115	437.2+/-344.9	180,931,1092	65.0	54.0	58.0		961,961	3.3	0.1	3	dbSNP_100	58	6110,2490	694.8+/-404.8	2164,1782,354	yes	missense,missense	DZIP1L	NM_001170538.1,NM_173543.2	101,101	2344,2713,1446	AA,AG,GG		28.9535,29.301,43.0955	probably-damaging,probably-damaging	321/540,321/768	137807259	7401,5605	2203	4300	6503	SO:0001583	missense	199221	exon7			GCTCCCGTGCCTG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.961C>T	3.37:g.137807259G>A	ENSP00000332148:p.Arg321Trp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_001170538	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	1229	0.5627289377289377	118	0.23983739837398374	234	0.6464088397790055	360	0.6293706293706294	517	0.6820580474934037	G	12.10	1.835476	0.32421	0.29301	0.710465	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.47869	0.83;0.83	5.33	3.29	0.37713	.	0.680747	0.12775	N	0.440182	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D;D	0.65815	0.995;0.995	P;B	0.46975	0.533;0.446	T	0.17561	-1.0365	9	0.66056	D	0.02	-5.9845	6.8846	0.24193	0.0:0.1434:0.5549:0.3017	rs2724693;rs13060733;rs16847842;rs52833476;rs59499377;rs2724693	321;321	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	W	321	ENSP00000332148:R321W;ENSP00000419486:R321W	ENSP00000332148:R321W	R	-	1	2	DZIP1L	139289949	0.574000	0.26684	0.113000	0.21522	0.002000	0.02628	0.994000	0.29693	1.206000	0.43276	0.655000	0.94253	CGG	G|0.448;A|0.552	0.552	strong		0.547	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
OGFOD1	55239	hgsc.bcm.edu	37	16	56500176	56500176	+	Silent	SNP	T	T	A	rs11544885	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:56500176T>A	ENST00000566157.1	+	5	684	c.561T>A	c.(559-561)atT>atA	p.I187I	OGFOD1_ENST00000568397.1_Silent_p.I187I	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	187	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	TGTACAGCATTGATGGTAAGA	0.483													T|||	303	0.0605032	0.0174	0.0403	5008	,	,		20494	0.1409		0.0268	False		,,,				2504	0.0849				p.I187I		Atlas-SNP	.											.	OGFOD1	31	.	0			c.T561A						PASS	.	T		117,4279	88.2+/-126.9	0,117,2081	135.0	100.0	112.0		561	-2.9	0.1	16	dbSNP_120	112	334,8266	115.2+/-175.0	7,320,3973	no	coding-synonymous	OGFOD1	NM_018233.3		7,437,6054	AA,AT,TT		3.8837,2.6615,3.4703		187/543	56500176	451,12545	2198	4300	6498	SO:0001819	synonymous_variant	55239	exon5			CAGCATTGATGGT	BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"""TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"""	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.561T>A	16.37:g.56500176T>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Silent	SNP	ENST00000566157.1	37	CCDS10761.2																																																																																			T|0.961;A|0.039	0.039	strong		0.483	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	
ZNF302	55900	hgsc.bcm.edu	37	19	35175592	35175592	+	Missense_Mutation	SNP	G	G	A	rs10425561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35175592G>A	ENST00000446502.2	+	6	990	c.782G>A	c.(781-783)aGt>aAt	p.S261N	ZNF302_ENST00000457781.2_Missense_Mutation_p.S217N|ZNF302_ENST00000505242.1_Missense_Mutation_p.S217N|ZNF302_ENST00000505365.2_3'UTR|ZNF302_ENST00000423823.2_Missense_Mutation_p.S217N			Q9NR11	ZN302_HUMAN	zinc finger protein 302	296					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TCAATCCTCAGTCGCCACTGG	0.443													A|||	595	0.11881	0.0666	0.0951	5008	,	,		18354	0.0694		0.1233	False		,,,				2504	0.2526				p.S217N		Atlas-SNP	.											ZNF302,right_upper_lobe,carcinoma,+1,1	ZNF302	27	1	0			c.G650A						PASS	.	A	ASN/SER,ASN/SER	312,4080	726.3+/-409.7	8,296,1892	93.0	100.0	98.0		650,650	-0.1	0.8	19	dbSNP_119	98	1116,7476	746.8+/-407.3	72,972,3252	no	missense,missense	ZNF302	NM_001012320.1,NM_018443.2	46,46	80,1268,5144	AA,AG,GG		12.9888,7.1038,10.9982	benign,benign	217/400,217/400	35175592	1428,11556	2196	4296	6492	SO:0001583	missense	55900	exon5			TCCTCAGTCGCCA	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.782G>A	19.37:g.35175592G>A	ENSP00000396379:p.Ser261Asn	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	37		168	0.07692307692307693	31	0.06300813008130081	37	0.10220994475138122	19	0.033216783216783216	81	0.10686015831134564	A	0.014	-1.600804	0.00849	0.071038	0.129888	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000423823;ENST00000446502	T;T;T;T	0.18338	3.18;3.18;3.18;2.22	0.967	-0.1	0.13621	.	.	.	.	.	T	0.00073	0.0002	N	0.04880	-0.145	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41052	-0.9530	8	0.29301	T	0.29	.	6.1893	0.20516	0.3779:0.0:0.6221:0.0	rs10425561	261;217	E7EVR1;Q9NR11-2	.;.	N	217;217;217;261	ENSP00000391067:S217N;ENSP00000421028:S217N;ENSP00000405219:S217N;ENSP00000396379:S261N	ENSP00000405219:S217N	S	+	2	0	ZNF302	39867432	0.000000	0.05858	0.751000	0.31187	0.272000	0.26649	-0.848000	0.04326	-0.698000	0.05085	-1.673000	0.00743	AGT	G|0.500;A|0.500	0.500	weak		0.443	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
WNK2	65268	hgsc.bcm.edu	37	9	95993215	95993215	+	Silent	SNP	C	C	T	rs34976687	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:95993215C>T	ENST00000297954.4	+	3	900	c.900C>T	c.(898-900)agC>agT	p.S300S	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_5'UTR|WNK2_ENST00000395475.2_Silent_p.S286S|WNK2_ENST00000395477.2_Silent_p.S300S|WNK2_ENST00000349097.3_5'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	300	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TTCTCCGCAGCTGGTGCCGGC	0.592													C|||	142	0.0283546	0.0015	0.1081	5008	,	,		18339	0.0		0.0586	False		,,,				2504	0.0061				p.S300S		Atlas-SNP	.											.	WNK2	277	.	0			c.C900T						PASS	.	C		71,4335	64.1+/-101.4	0,71,2132	86.0	75.0	79.0		900	4.6	1.0	9	dbSNP_126	79	609,7991	159.5+/-212.8	31,547,3722	no	coding-synonymous	WNK2	NM_006648.3		31,618,5854	TT,TC,CC		7.0814,1.6114,5.2284		300/2218	95993215	680,12326	2203	4300	6503	SO:0001819	synonymous_variant	65268	exon3			CCGCAGCTGGTGC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.900C>T	9.37:g.95993215C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		81	0.03708791208791209	1	0.0020325203252032522	36	0.09944751381215469	0	0.0	44	0.05804749340369393	C	10.61	1.397401	0.25205	0.016114	0.070814	ENSG00000165238	ENST00000432730	.	.	.	5.52	4.62	0.57501	.	.	.	.	.	T	0.03053	0.0090	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01643	-1.1305	4	.	.	.	.	8.8405	0.35140	0.0:0.7609:0.0:0.2391	rs34976687;rs62618691	.	.	.	V	296	.	.	A	+	2	0	WNK2	95033036	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.847000	0.27696	1.333000	0.45449	0.655000	0.94253	GCT	C|0.953;T|0.047	0.047	strong		0.592	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
LAMB3	3914	hgsc.bcm.edu	37	1	209795909	209795909	+	Silent	SNP	T	T	C	rs3179860	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:209795909T>C	ENST00000356082.4	-	18	2807	c.2673A>G	c.(2671-2673)ctA>ctG	p.L891L	LAMB3_ENST00000391911.1_Silent_p.L891L|LAMB3_ENST00000367030.3_Silent_p.L891L|MIR4260_ENST00000583107.1_RNA	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	891	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		CCTGCTGGATTAGGAGCCGTG	0.597													T|||	515	0.102835	0.0446	0.0865	5008	,	,		18362	0.001		0.16	False		,,,				2504	0.2393				p.L891L		Atlas-SNP	.											.	LAMB3	136	.	0			c.A2673G						PASS	.	T	,,	241,4165	141.1+/-176.5	5,231,1967	178.0	163.0	168.0		2673,2673,2673	3.5	1.0	1	dbSNP_105	168	1331,7269	261.4+/-283.8	105,1121,3074	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	110,1352,5041	CC,CT,TT		15.4767,5.4698,12.0867	,,	891/1173,891/1173,891/1173	209795909	1572,11434	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon18			CTGGATTAGGAGC	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.2673A>G	1.37:g.209795909T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			T|0.896;C|0.104	0.104	strong		0.597	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
DNAH9	1770	hgsc.bcm.edu	37	17	11786951	11786951	+	Silent	SNP	T	T	C	rs8070256	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11786951T>C	ENST00000262442.4	+	56	10923	c.10855T>C	c.(10855-10857)Ttg>Ctg	p.L3619L	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Silent_p.L3619L|DNAH9_ENST00000608377.1_5'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3619	AAA 5. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.L3619L(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CCTGAAAACGTTGGAAGACAG	0.512													T|||	1933	0.385982	0.1256	0.3674	5008	,	,		19406	0.4643		0.5278	False		,,,				2504	0.5245				p.L3619L		Atlas-SNP	.											DNAH9,NS,carcinoma,0,1	DNAH9	695	1	1	Substitution - coding silent(1)	stomach(1)	c.T10855C						PASS	.	T	,	880,3526	342.5+/-307.2	94,692,1417	139.0	118.0	125.0		10855,	-3.6	0.0	17	dbSNP_116	125	4401,4199	584.7+/-391.8	1121,2159,1020	no	coding-synonymous,utr-5	DNAH9	NM_001372.3,NM_004662.2	,	1215,2851,2437	CC,CT,TT		48.8256,19.9728,40.6043	,	3619/4487,	11786951	5281,7725	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon56			AAAACGTTGGAAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10855T>C	17.37:g.11786951T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			T|0.612;C|0.388	0.388	strong		0.512	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
RBMS1	5937	hgsc.bcm.edu	37	2	161174693	161174693	+	Silent	SNP	C	C	T	rs1430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:161174693C>T	ENST00000348849.3	-	3	727	c.297G>A	c.(295-297)acG>acA	p.T99T	RBMS1_ENST00000392753.3_Silent_p.T99T|RBMS1_ENST00000409289.2_Silent_p.T66T|RBMS1_ENST00000409075.1_Silent_p.T66T|RBMS1_ENST00000474820.1_5'UTR|RBMS1_ENST00000409972.1_Silent_p.T66T	NM_002897.4|NM_016836.3	NP_002888.1|NP_058520.1	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting protein 1	99	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA replication (GO:0006260)|RNA processing (GO:0006396)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)		PLA2R1/RBMS1(2)								TGCATTTGTTCGTTGTCTTAT	0.284													c|||	1308	0.261182	0.1195	0.2104	5008	,	,		14319	0.5308		0.3032	False		,,,				2504	0.1677				p.T99T		Atlas-SNP	.											RBMS1_ENST00000348849,caecum,carcinoma,0,1	RBMS1	34	1	0			c.G297A						PASS	.	T	,	663,3743	277.2+/-273.6	48,567,1588	118.0	112.0	114.0		297,297	-12.1	0.1	2	dbSNP_36	114	2494,6104	408.8+/-349.6	380,1734,2185	no	coding-synonymous,coding-synonymous	RBMS1	NM_002897.4,NM_016836.3	,	428,2301,3773	TT,TC,CC		29.0067,15.0477,24.2771	,	99/404,99/407	161174693	3157,9847	2203	4299	6502	SO:0001819	synonymous_variant	5937	exon3			TTTGTTCGTTGTC	D28482	CCDS2213.1	2q24.2	2013-02-12			ENSG00000153250	ENSG00000153250		"""RNA binding motif (RRM) containing"""	9907	protein-coding gene	gene with protein product	"""suppressor of cdc 2 (cdc13) with RNA binding motif 2"", ""c-myc gene single strand binding protein 2"""	602310	"""chromosome 2 open reading frame 12"""	C2orf12		8041632, 8134115, 7838710	Standard	NM_016836		Approved	SCR2, MSSP-1, MSSP-2, MSSP-3, YC1, HCC-4, DKFZp564H0764	uc002ubo.3	P29558	OTTHUMG00000132031	ENST00000348849.3:c.297G>A	2.37:g.161174693C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_016836	Q14869|Q15433|Q53P46|Q53QX8|Q53RG6|Q8WV20	Silent	SNP	ENST00000348849.3	37	CCDS2213.1																																																																																			C|0.733;T|0.267	0.267	strong		0.284	RBMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255043.4	NM_016836	
VIPR1	7433	hgsc.bcm.edu	37	3	42568935	42568935	+	Silent	SNP	C	C	T	rs201579976		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:42568935C>T	ENST00000325123.4	+	5	563	c.450C>T	c.(448-450)taC>taT	p.Y150Y	VIPR1-AS1_ENST00000593611.1_RNA|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1_ENST00000433647.1_Silent_p.Y109Y|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1_ENST00000543411.1_Silent_p.Y102Y|VIPR1_ENST00000438259.2_Intron|VIPR1_ENST00000473575.1_3'UTR	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	150					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		CCATTGGCTACGGCCTGTCCC	0.602																																					p.Y150Y		Atlas-SNP	.											VIPR1,NS,carcinoma,0,1	VIPR1	45	1	0			c.C450T						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	118.0	105.0	110.0		450	4.1	1.0	3		110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	VIPR1	NM_004624.3		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		150/458	42568935	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	7433	exon5			TGGCTACGGCCTG	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12694	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 1"""	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.450C>T	3.37:g.42568935C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	53	35	0.660377	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	37	CCDS2698.1																																																																																			C|0.999;T|0.001	0.001	strong		0.602	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624	
TANC1	85461	hgsc.bcm.edu	37	2	160074132	160074132	+	Silent	SNP	G	G	T	rs373000954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160074132G>T	ENST00000263635.6	+	20	3606	c.3369G>T	c.(3367-3369)ggG>ggT	p.G1123G	TANC1_ENST00000454300.1_Silent_p.G1017G	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1123					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						CACGCCAGGGGCATTGGCAGG	0.592													G|||	3	0.000599042	0.0	0.0	5008	,	,		20076	0.0		0.003	False		,,,				2504	0.0				p.G1123G		Atlas-SNP	.											TANC1,NS,NS,+2,1	TANC1	157	1	0			c.G3369T						PASS	.	G	,	0,3934		0,0,1967	61.0	68.0	66.0		3345,3369	-5.3	1.0	2		66	7,8347		0,7,4170	no	coding-synonymous,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	0,7,6137	TT,TG,GG		0.0838,0.0,0.057	,	1115/1391,1123/1862	160074132	7,12281	1967	4177	6144	SO:0001819	synonymous_variant	85461	exon20			CCAGGGGCATTGG	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.3369G>T	2.37:g.160074132G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	150	82	0.546667	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			.	.	weak		0.592	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
CYP8B1	1582	hgsc.bcm.edu	37	3	42915878	42915878	+	Silent	SNP	C	C	T	rs735320	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:42915878C>T	ENST00000316161.4	-	1	1755	c.1431G>A	c.(1429-1431)ccG>ccA	p.P477P	KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	477					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		CCCAGCGCTGCGGGTCAACAT	0.557													C|||	577	0.115216	0.1747	0.1196	5008	,	,		17878	0.002		0.168	False		,,,				2504	0.0941				p.P477P		Atlas-SNP	.											.	CYP8B1	59	.	0			c.G1431A						PASS	.	C		744,3662	305.2+/-288.9	58,628,1517	75.0	69.0	71.0		1431	-9.1	0.0	3	dbSNP_86	71	1479,7121	280.3+/-294.4	120,1239,2941	no	coding-synonymous	CYP8B1	NM_004391.2		178,1867,4458	TT,TC,CC		17.1977,16.8861,17.0921		477/502	42915878	2223,10783	2203	4300	6503	SO:0001819	synonymous_variant	1582	exon1			GCGCTGCGGGTCA	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"""Cytochrome P450s"""	2653	protein-coding gene	gene with protein product		602172	"""cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"""			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.1431G>A	3.37:g.42915878C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Silent	SNP	ENST00000316161.4	37	CCDS2707.1																																																																																			C|0.861;T|0.139	0.139	strong		0.557	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391	
MICB	4277	hgsc.bcm.edu	37	6	31474000	31474000	+	Missense_Mutation	SNP	G	G	A	rs1051788	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31474000G>A	ENST00000252229.6	+	3	485	c.406G>A	c.(406-408)Gat>Aat	p.D136N	MICB_ENST00000538442.1_Missense_Mutation_p.D104N|MICB_ENST00000399150.3_Intron	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						TTTCTACTACGATGGGGAGCT	0.552													g|||	1415	0.282548	0.3835	0.1902	5008	,	,		17992	0.2738		0.2624	False		,,,				2504	0.2413				p.D136N		Atlas-SNP	.											.	MICB	26	.	0			c.G406A						PASS	.	T	ASN/ASP	1409,2419		251,907,756	50.0	52.0	51.0		406	-0.6	0.0	6	dbSNP_86	51	2523,5701		418,1687,2007	no	missense	MICB	NM_005931.3	23	669,2594,2763	AA,AG,GG		30.6785,36.8077,32.6253	possibly-damaging	136/384	31474000	3932,8120	1914	4112	6026	SO:0001583	missense	4277	exon3			TACTACGATGGGG		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"""Immunoglobulin superfamily / C1-set domain containing"""	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.406G>A	6.37:g.31474000G>A	ENSP00000252229:p.Asp136Asn	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	246	72	0.292683	NM_005931		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	613	0.2806776556776557	199	0.40447154471544716	77	0.212707182320442	127	0.22202797202797203	210	0.2770448548812665	N	6.301	0.423715	0.11928	0.368077	0.306785	ENSG00000204516	ENST00000538442;ENST00000252229	T;T	0.02301	4.35;4.35	2.34	-0.599	0.11645	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.419890	0.17289	N	0.179739	T	0.00998	0.0033	M	0.79343	2.45	0.80722	P	0.0	B;P	0.39964	0.077;0.697	B;B	0.33521	0.019;0.165	T	0.43956	-0.9359	9	0.56958	D	0.05	.	3.6257	0.08112	0.2537:0.0:0.5513:0.1951	rs1051788;rs3176028	104;136	F5H7Q8;Q29980	.;MICB_HUMAN	N	104;136	ENSP00000442345:D104N;ENSP00000252229:D136N	ENSP00000252229:D136N	D	+	1	0	MICB	31581979	0.039000	0.19947	0.004000	0.12327	0.001000	0.01503	0.640000	0.24705	-0.172000	0.10779	-0.677000	0.03784	GAT	A|0.285;G|0.715	0.285	strong		0.552	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931	
COL19A1	1310	hgsc.bcm.edu	37	6	70866609	70866609	+	Silent	SNP	C	C	T	rs2229799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:70866609C>T	ENST00000322773.4	+	34	2388	c.2286C>T	c.(2284-2286)ggC>ggT	p.G762G	COL19A1_ENST00000393344.1_Silent_p.G384G	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	762	Collagen-like 7.|Triple-helical region 4 (COL4).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GGGAGAAAGGCGATGAGGTAA	0.383													C|||	2578	0.514776	0.6914	0.5101	5008	,	,		14917	0.3145		0.4742	False		,,,				2504	0.5276				p.G762G		Atlas-SNP	.											.	COL19A1	232	.	0			c.C2286T						PASS	.	C		2912,1494	669.0+/-402.1	948,1016,239	81.0	84.0	83.0		2286	-6.8	0.5	6	dbSNP_98	83	4042,4558	553.2+/-386.3	941,2160,1199	no	coding-synonymous	COL19A1	NM_001858.4		1889,3176,1438	TT,TC,CC		47.0,33.9083,46.5324		762/1143	70866609	6954,6052	2203	4300	6503	SO:0001819	synonymous_variant	1310	exon34			GAAAGGCGATGAG		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2286C>T	6.37:g.70866609C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	37	CCDS4970.1																																																																																			C|0.481;T|0.519	0.519	strong		0.383	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
PTPRN2	5799	hgsc.bcm.edu	37	7	157959636	157959636	+	Silent	SNP	G	G	A	rs1130498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:157959636G>A	ENST00000389418.4	-	6	906	c.897C>T	c.(895-897)tcC>tcT	p.S299S	PTPRN2_ENST00000389413.3_Silent_p.S299S|PTPRN2_ENST00000389416.4_Silent_p.S282S|PTPRN2_ENST00000409483.1_Silent_p.S261S|PTPRN2_ENST00000404321.2_Silent_p.S322S	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	299					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CGCCTGTGCTGGAGGGGTCTT	0.612													G|||	3130	0.625	0.3971	0.7392	5008	,	,		17471	0.751		0.7256	False		,,,				2504	0.6186				p.S299S		Atlas-SNP	.											PTPRN2,NS,carcinoma,0,1	PTPRN2	243	1	0			c.C897T						PASS	.	G	,,	1813,2343		443,927,708	15.0	13.0	14.0		897,846,897	-4.2	0.0	7	dbSNP_119	14	5578,2562		2003,1572,495	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	2446,2499,1203	AA,AG,GG		31.4742,43.6237,39.891	,,	299/1016,282/999,299/987	157959636	7391,4905	2078	4070	6148	SO:0001819	synonymous_variant	5799	exon6			TGTGCTGGAGGGG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.897C>T	7.37:g.157959636G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.341;A|0.659	0.659	strong		0.612	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
ISG20	3669	hgsc.bcm.edu	37	15	89182702	89182702	+	Silent	SNP	T	T	C	rs35008759	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89182702T>C	ENST00000306072.5	+	2	463	c.105T>C	c.(103-105)ggT>ggC	p.G35G	ISG20_ENST00000560741.1_Silent_p.G35G|ISG20_ENST00000379224.5_Silent_p.G35G	NM_002201.4	NP_002192.2	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease gene 20kDa	35					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA catabolic process, exonucleolytic (GO:0000738)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	3'-5'-exoribonuclease activity (GO:0000175)|exonuclease activity (GO:0004527)|exoribonuclease II activity (GO:0008859)|metal ion binding (GO:0046872)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|U1 snRNA binding (GO:0030619)|U2 snRNA binding (GO:0030620)|U3 snoRNA binding (GO:0034511)			large_intestine(1)|lung(3)|prostate(1)	5	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			ACGTCCACGGTGCTGTGCTGT	0.657											OREG0023441	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	48	0.00958466	0.0015	0.0144	5008	,	,		15628	0.0		0.0318	False		,,,				2504	0.0041				p.G35G		Atlas-SNP	.											.	ISG20	17	.	0			c.T105C						PASS	.	T		22,4378	29.0+/-57.7	0,22,2178	63.0	62.0	62.0		105	-0.5	0.0	15	dbSNP_126	62	250,8348	99.3+/-160.8	6,238,4055	no	coding-synonymous	ISG20	NM_002201.4		6,260,6233	CC,CT,TT		2.9077,0.5,2.0926		35/182	89182702	272,12726	2200	4299	6499	SO:0001819	synonymous_variant	3669	exon2			CCACGGTGCTGTG	X89773	CCDS10345.1	15q26	2006-02-22	2002-08-29		ENSG00000172183	ENSG00000172183			6130	protein-coding gene	gene with protein product		604533	"""interferon stimulated gene (20kD)"""			9235947, 9605874	Standard	NM_002201		Approved	HEM45, CD25	uc002bmv.1	Q96AZ6	OTTHUMG00000148679	ENST00000306072.5:c.105T>C	15.37:g.89182702T>C		Somatic	54	0	0	1265	WXS	Illumina HiSeq	Phase_I	91	52	0.571429	NM_002201	O00441|O00586	Silent	SNP	ENST00000306072.5	37	CCDS10345.1																																																																																			A|0.000;C|0.017;T|0.983	0.017	strong		0.657	ISG20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309069.2	NM_002201	
ACSM2B	348158	hgsc.bcm.edu	37	16	20554294	20554294	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20554294T>C	ENST00000329697.6	-	12	1619	c.1451A>G	c.(1450-1452)aAg>aGg	p.K484R	ACSM2B_ENST00000567001.1_Missense_Mutation_p.K484R|ACSM2B_ENST00000565322.1_Missense_Mutation_p.K405R|ACSM2B_ENST00000567288.1_5'Flank|ACSM2B_ENST00000565232.1_Missense_Mutation_p.K484R	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	484					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						AGCAGGGTGCTTCATCAGTGC	0.567																																					p.K484R		Atlas-SNP	.											ACSM2B,NS,carcinoma,+1,1	ACSM2B	121	1	0			c.A1451G						scavenged	.						137.0	130.0	132.0					16																	20554294		2201	4299	6500	SO:0001583	missense	348158	exon13			GGGTGCTTCATCA	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"""Acyl-CoA synthetase family"""	30931	protein-coding gene	gene with protein product	"""xenobiotic/medium chain fatty acid:CoA ligase"""	614359	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.1451A>G	16.37:g.20554294T>C	ENSP00000327453:p.Lys484Arg	Somatic	363	1	0.00275482		WXS	Illumina HiSeq	Phase_I	378	5	0.0132275	NM_182617	Q86YT1	Missense_Mutation	SNP	ENST00000329697.6	37	CCDS10586.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.295439	0.40594	.	.	ENSG00000066813	ENST00000329697	T	0.56776	0.44	3.1	3.1	0.35709	AMP-dependent synthetase/ligase (1);	0.629441	0.13724	N	0.367151	T	0.37348	0.1000	N	0.12443	0.215	0.80722	D	1	B;B	0.20459	0.025;0.045	B;B	0.28784	0.094;0.094	T	0.34625	-0.9821	10	0.87932	D	0	-7.1571	11.459	0.50199	0.0:0.0:0.0:1.0	.	484;484	A8K051;Q68CK6	.;ACS2B_HUMAN	R	484	ENSP00000327453:K484R	ENSP00000327453:K484R	K	-	2	0	ACSM2B	20461795	1.000000	0.71417	0.997000	0.53966	0.564000	0.35744	6.095000	0.71439	1.423000	0.47198	0.416000	0.27883	AAG	.	.	none		0.567	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2	NM_182617	
CNTN4	152330	hgsc.bcm.edu	37	3	3076351	3076351	+	Missense_Mutation	SNP	G	G	A	rs374090181		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:3076351G>A	ENST00000397461.1	+	16	2203	c.1819G>A	c.(1819-1821)Gaa>Aaa	p.E607K	CNTN4_ENST00000418658.1_Missense_Mutation_p.E607K|CNTN4_ENST00000448906.2_Missense_Mutation_p.E279K|CNTN4_ENST00000427331.1_Missense_Mutation_p.E607K|CNTN4_ENST00000397459.2_Missense_Mutation_p.E279K|CNTN4_ENST00000358480.3_Missense_Mutation_p.E388K	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	607	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GACAATAGACGAAATCACAGA	0.537																																					p.E607K		Atlas-SNP	.											CNTN4_ENST00000418658,NS,malignant_melanoma,0,4	CNTN4	335	4	0			c.G1819A						scavenged	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	85.0	72.0	76.0		1819,832,1819,835	4.3	1.0	3		76	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	CNTN4	NM_001206955.1,NM_001206956.1,NM_175607.2,NM_175613.2	56,56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign	607/1027,278/698,607/1027,279/699	3076351	1,13005	2203	4300	6503	SO:0001583	missense	152330	exon17			ATAGACGAAATCA	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.1819G>A	3.37:g.3076351G>A	ENSP00000380602:p.Glu607Lys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	2	0.0151515	NM_175607	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	37	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444907	0.83993	0.0	1.16E-4	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31	4.27	4.27	0.50696	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.60830	0.2299	M	0.70108	2.13	0.80722	D	1	P;P;P	0.44946	0.678;0.725;0.846	B;B;B	0.42188	0.22;0.379;0.327	T	0.69672	-0.5082	10	0.59425	D	0.04	.	17.0894	0.86618	0.0:0.0:1.0:0.0	.	606;607;607	Q8IWV2-3;B3KTK4;Q8IWV2	.;.;CNTN4_HUMAN	K	607;607;607;388;279;279	ENSP00000396010:E607K;ENSP00000380602:E607K;ENSP00000413642:E607K;ENSP00000351267:E388K;ENSP00000380600:E279K;ENSP00000392077:E279K	ENSP00000351267:E388K	E	+	1	0	CNTN4	3051351	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	7.609000	0.82925	2.086000	0.62901	0.563000	0.77884	GAA	.	.	weak		0.537	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
KRTAP6-3	337968	hgsc.bcm.edu	37	21	31964916	31964916	+	Missense_Mutation	SNP	A	A	C	rs9305426	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:31964916A>C	ENST00000391624.1	+	1	158	c.131A>C	c.(130-132)tAt>tCt	p.Y44S	KRTAP22-2_ENST00000382830.2_5'Flank	NM_181605.3	NP_853636.3	Q3LI67	KRA63_HUMAN	keratin associated protein 6-3	44			Y -> S (in dbSNP:rs9305426).			intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(7)	10						ggctttggctatggaggcctg	0.627													A|||	2840	0.567093	0.6112	0.6715	5008	,	,		12721	0.2937		0.5915	False		,,,				2504	0.6902				p.Y51S		Atlas-SNP	.											.	KRTAP6-3	30	.	0			c.A152C						PASS	.	A	SER/TYR	2634,1772	641.9+/-397.6	784,1066,353	84.0	94.0	91.0		152	2.3	1.0	21	dbSNP_119	91	5285,3315	643.7+/-400.0	1622,2041,637	no	missense	KRTAP6-3	NM_181605.3	144	2406,3107,990	CC,CA,AA		38.5465,40.2179,39.1127	possibly-damaging	51/111	31964916	7919,5087	2203	4300	6503	SO:0001583	missense	337968	exon1			TTGGCTATGGAGG	AP001708		21q22.1	2012-04-19			ENSG00000212938	ENSG00000212938		"""Keratin associated proteins"""	18933	protein-coding gene	gene with protein product						12359730	Standard	NM_181605		Approved	KAP6.3	uc002yom.3	Q3LI67	OTTHUMG00000057791	ENST00000391624.1:c.131A>C	21.37:g.31964916A>C	ENSP00000375482:p.Tyr44Ser	Somatic	273	2	0.00732601		WXS	Illumina HiSeq	Phase_I	227	217	0.955947	NM_181605	A4IF26	Missense_Mutation	SNP	ENST00000391624.1	37		1151	0.527014652014652	304	0.6178861788617886	243	0.6712707182320442	172	0.3006993006993007	432	0.5699208443271768	A	1.138	-0.650370	0.03506	0.597821	0.614535	ENSG00000212938	ENST00000391624	T	0.41400	1.0	2.33	2.33	0.28932	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.40155	P	0.02300100000000005	P	0.50710	0.938	P	0.61800	0.894	T	0.35871	-0.9771	8	0.87932	D	0	.	6.5963	0.22674	1.0:0.0:0.0:0.0	rs9305426	44	Q3LI67	KRA63_HUMAN	S	44	ENSP00000375482:Y44S	ENSP00000375482:Y44S	Y	+	2	0	KRTAP6-3	30886787	0.813000	0.29090	0.998000	0.56505	0.083000	0.17756	0.056000	0.14256	1.313000	0.45069	0.449000	0.29647	TAT	A|0.451;C|0.549	0.549	strong		0.627	KRTAP6-3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128243.2	NM_181605	
SDR42E1	93517	hgsc.bcm.edu	37	16	82033810	82033810	+	Nonsense_Mutation	SNP	G	G	A	rs11542462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:82033810G>A	ENST00000328945.5	-	3	215	c.88C>T	c.(88-90)Caa>Taa	p.Q30*	SDR42E1_ENST00000534209.1_5'UTR	NM_145168.2	NP_660151.2	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E, member 1	30					steroid biosynthetic process (GO:0006694)	integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)			NS(2)|endometrium(1)|lung(4)|skin(3)	10						ACTCCATTTTGGTTCAGGGCA	0.438													G|||	365	0.0728834	0.0053	0.0663	5008	,	,		22000	0.003		0.1511	False		,,,				2504	0.1605				p.Q30X		Atlas-SNP	.											SDR42E1,colon,carcinoma,0,1	SDR42E1	26	1	0			c.C88T						scavenged	.	G	stop/GLN	86,3730		1,84,1823	146.0	139.0	141.0		88	3.9	1.0	16	dbSNP_120	141	1023,7217		72,879,3169	yes	stop-gained	SDR42E1	NM_145168.2		73,963,4992	AA,AG,GG		12.415,2.2537,9.1987		30/394	82033810	1109,10947	1908	4120	6028	SO:0001587	stop_gained	93517	exon3			CATTTTGGTTCAG	AF161368	CCDS42205.1	16q23.3	2011-09-14				ENSG00000184860	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	29834	protein-coding gene	gene with protein product						19027726	Standard	NM_145168		Approved	HSPC105	uc002fgu.3	Q8WUS8		ENST00000328945.5:c.88C>T	16.37:g.82033810G>A	ENSP00000332407:p.Gln30*	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_145168	B2RDS1|Q9P0D1	Nonsense_Mutation	SNP	ENST00000328945.5	37	CCDS42205.1	155	0.07097069597069597	4	0.008130081300813009	29	0.08011049723756906	1	0.0017482517482517483	121	0.15963060686015831	G	34	5.300565	0.95601	0.022537	0.12415	ENSG00000184860	ENST00000328945;ENST00000532128	.	.	.	6.03	3.91	0.45181	.	0.539402	0.20588	N	0.089406	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-8.7241	12.3949	0.55378	0.0:0.1016:0.7237:0.1747	rs11542462;rs52836378;rs11542462	.	.	.	X	30;27	.	ENSP00000332407:Q30X	Q	-	1	0	SDR42E1	80591311	0.847000	0.29606	0.974000	0.42286	0.849000	0.48306	0.919000	0.28692	1.517000	0.48917	0.655000	0.94253	CAA	G|0.916;A|0.084	0.084	strong		0.438	SDR42E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388081.2	NM_145168	
FHAD1	114827	hgsc.bcm.edu	37	1	15653563	15653563	+	Silent	SNP	C	C	T	rs3765357	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:15653563C>T	ENST00000375998.4	+	11	1482	c.1482C>T	c.(1480-1482)caC>caT	p.H494H	RP3-467K16.2_ENST00000428747.1_RNA|FHAD1_ENST00000417793.1_Silent_p.H494H|FHAD1_ENST00000375995.3_Silent_p.H99H|FHAD1_ENST00000401090.2_Silent_p.H164H|FHAD1_ENST00000375999.3_Silent_p.H494H|FHAD1_ENST00000358897.4_Silent_p.H494H			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	494										skin(1)|stomach(1)	2						AGCTGGAGCACTTCAGAAGTC	0.632													C|||	1107	0.221046	0.1293	0.3228	5008	,	,		15223	0.0486		0.329	False		,,,				2504	0.3395				p.H494H		Atlas-SNP	.											.	FHAD1	78	.	0			c.C1482T						PASS	.	C		219,1165		18,183,491	41.0	43.0	42.0		1482	-4.2	1.0	1	dbSNP_107	42	944,2238		142,660,789	no	coding-synonymous	FHAD1	NM_052929.1		160,843,1280	TT,TC,CC		29.6669,15.8237,25.4709		494/1413	15653563	1163,3403	692	1591	2283	SO:0001819	synonymous_variant	114827	exon12			GGAGCACTTCAGA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.1482C>T	1.37:g.15653563C>T		Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	257	127	0.494163	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37		456	0.2087912087912088	60	0.12195121951219512	111	0.30662983425414364	26	0.045454545454545456	259	0.341688654353562	C	11.36	1.616153	0.28801	0.158237	0.296669	ENSG00000142621	ENST00000375997	.	.	.	5.38	-4.2	0.03823	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999804148	.	.	.	.	.	.	T	0.43669	-0.9377	3	.	.	.	-5.6922	2.1205	0.03724	0.1237:0.3211:0.1261:0.4291	rs3765357;rs60818774;rs3765357	.	.	.	F	173	.	.	L	+	1	0	FHAD1	15526150	0.688000	0.27680	0.969000	0.41365	0.717000	0.41224	-0.664000	0.05292	-0.649000	0.05430	-0.258000	0.10820	CTT	C|0.799;T|0.201	0.201	strong		0.632	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
BMP8A	353500	hgsc.bcm.edu	37	1	39988708	39988708	+	Silent	SNP	A	A	G	rs2889739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39988708A>G	ENST00000331593.5	+	6	1324	c.978A>G	c.(976-978)tcA>tcG	p.S326S	RP11-69E11.4_ENST00000440190.1_RNA|RP11-69E11.4_ENST00000458207.1_RNA|RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000441741.1_RNA|RP11-69E11.4_ENST00000450157.1_RNA|RP11-69E11.4_ENST00000331856.2_RNA|RP11-69E11.4_ENST00000417869.1_RNA	NM_181809.3	NP_861525.2	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8a	326					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|diet induced thermogenesis (GO:0002024)|growth (GO:0040007)|negative regulation of insulin secretion (GO:0046676)|ossification (GO:0001503)|regulation of energy homeostasis (GO:2000505)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(1)|skin(1)	5	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AAGGCTACTCAGCCTATTACT	0.627													A|||	130	0.0259585	0.0045	0.0303	5008	,	,		17612	0.0		0.0905	False		,,,				2504	0.0123				p.S326S		Atlas-SNP	.											.	BMP8A	24	.	0			c.A978G						PASS	.	A		70,4336	64.1+/-101.4	1,68,2134	184.0	161.0	169.0		978	-8.4	0.3	1	dbSNP_101	169	664,7936	167.8+/-219.5	21,622,3657	no	coding-synonymous	BMP8A	NM_181809.3		22,690,5791	GG,GA,AA		7.7209,1.5887,5.6435		326/403	39988708	734,12272	2203	4300	6503	SO:0001819	synonymous_variant	353500	exon6			CTACTCAGCCTAT	AY303954	CCDS437.1	1p35-p32	2014-01-30			ENSG00000183682	ENSG00000183682		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	21650	protein-coding gene	gene with protein product							Standard	NM_181809		Approved		uc001cdi.3	Q7Z5Y6	OTTHUMG00000008394	ENST00000331593.5:c.978A>G	1.37:g.39988708A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	150	59	0.393333	NM_181809	Q5T3A5	Silent	SNP	ENST00000331593.5	37	CCDS437.1																																																																																			A|0.945;G|0.055	0.055	strong		0.627	BMP8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023079.1	NM_181809	
MYO18B	84700	hgsc.bcm.edu	37	22	26194045	26194045	+	Silent	SNP	T	T	C	rs738643	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26194045T>C	ENST00000407587.2	+	12	2671	c.2502T>C	c.(2500-2502)ggT>ggC	p.G834G	MYO18B_ENST00000335473.7_Silent_p.G834G|MYO18B_ENST00000536101.1_Silent_p.G834G			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	834	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ACCACCTGGGTGCGGCGGGGG	0.662													C|||	2849	0.56889	0.2655	0.6282	5008	,	,		15977	0.6647		0.6978	False		,,,				2504	0.7055				p.G834G		Atlas-SNP	.											.	MYO18B	322	.	0			c.T2502C						PASS	.	C		1375,2513		242,891,811	24.0	27.0	26.0		2502	-5.1	0.0	22	dbSNP_86	26	5829,2419		2057,1715,352	no	coding-synonymous	MYO18B	NM_032608.5		2299,2606,1163	CC,CT,TT		29.3283,35.3652,40.6394		834/2568	26194045	7204,4932	1944	4124	6068	SO:0001819	synonymous_variant	84700	exon12			CCTGGGTGCGGCG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2502T>C	22.37:g.26194045T>C		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	141	139	0.985816	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				T|0.410;C|0.590	0.590	strong		0.662	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
VSX1	30813	hgsc.bcm.edu	37	20	25059381	25059381	+	Intron	SNP	A	A	T	rs56157240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:25059381A>T	ENST00000376709.4	-	3	891				VSX1_ENST00000429762.3_Intron|VSX1_ENST00000451258.1_Intron|VSX1_ENST00000424574.1_Intron|VSX1_ENST00000376707.3_Silent_p.P237P|VSX1_ENST00000444511.2_Intron	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1						neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(3)|lung(2)	6						GCTATAGAGAAGGGACTGCTG	0.512													A|||	1455	0.290535	0.4992	0.3516	5008	,	,		18538	0.0268		0.2207	False		,,,				2504	0.3088				p.P237P		Atlas-SNP	.											.	VSX1	20	.	0			c.T711A						PASS	.	A	,	1132,1522		244,644,439	164.0	153.0	157.0		,711	0.9	0.0	20	dbSNP_129	157	1061,3557		130,801,1378	no	intron,coding-synonymous	VSX1	NM_014588.4,NM_199425.1	,	374,1445,1817	TT,TA,AA		22.9753,42.6526,30.1568	,	,237/240	25059381	2193,5079	1327	2309	3636	SO:0001627	intron_variant	30813	exon3			TAGAGAAGGGACT	AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"""Homeoboxes / PRD class"""	12723	protein-coding gene	gene with protein product		605020	"""posterior polymorphous corneal dystrophy"", ""visual system homeobox 1 homolog, CHX10-like (zebrafish)"""	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.627+83T>A	20.37:g.25059381A>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_199425	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Silent	SNP	ENST00000376709.4	37	CCDS13168.1																																																																																			A|0.749;T|0.251	0.251	strong		0.512	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3		
SEMA5A	9037	hgsc.bcm.edu	37	5	9190404	9190404	+	Silent	SNP	G	G	A	rs1806095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:9190404G>A	ENST00000382496.5	-	11	1913	c.1248C>T	c.(1246-1248)ctC>ctT	p.L416L		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	416	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						TGATGTGGACGAGCGCTTCTC	0.512													G|||	1416	0.282748	0.3116	0.2305	5008	,	,		17846	0.4395		0.1372	False		,,,				2504	0.2689				p.L416L		Atlas-SNP	.											.	SEMA5A	236	.	0			c.C1248T						PASS	.	G		1281,3125	434.9+/-344.1	188,905,1110	76.0	66.0	70.0		1248	-10.6	0.0	5	dbSNP_92	70	1017,7583	217.3+/-256.0	56,905,3339	no	coding-synonymous	SEMA5A	NM_003966.2		244,1810,4449	AA,AG,GG		11.8256,29.074,17.6688		416/1075	9190404	2298,10708	2203	4300	6503	SO:0001819	synonymous_variant	9037	exon11			GTGGACGAGCGCT	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1248C>T	5.37:g.9190404G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			G|0.771;A|0.229	0.229	strong		0.512	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
MSL1	339287	hgsc.bcm.edu	37	17	38282624	38282624	+	Silent	SNP	C	C	T	rs28526298	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38282624C>T	ENST00000398532.4	+	2	1272	c.957C>T	c.(955-957)ccC>ccT	p.P319P	MSL1_ENST00000577454.1_Silent_p.P319P|MSL1_ENST00000578648.1_Silent_p.P319P|MSL1_ENST00000579565.1_Silent_p.P56P	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	319					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	7						CTCCCAAGCCCTTCTCATGTG	0.478													T|||	410	0.081869	0.27	0.0403	5008	,	,		17773	0.0		0.0219	False		,,,				2504	0.0031				p.P56P		Atlas-SNP	.											.	MSL1	21	.	0			c.C168T						PASS	.	T		876,3026		83,710,1158	67.0	69.0	69.0		168	3.7	1.0	17	dbSNP_125	69	205,8073		3,199,3937	no	coding-synonymous	MSL1	NM_001012241.1		86,909,5095	TT,TC,CC		2.4764,22.45,8.8752		56/352	38282624	1081,11099	1951	4139	6090	SO:0001819	synonymous_variant	339287	exon3			CAAGCCCTTCTCA		CCDS45670.1	17q21.1	2011-03-21			ENSG00000188895	ENSG00000188895			27905	protein-coding gene	gene with protein product		614801				16227571, 16543150	Standard	NM_001012241		Approved	hMSL1, MSL-1, DKFZp686P24239	uc002hua.4	Q68DK7		ENST00000398532.4:c.957C>T	17.37:g.38282624C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_001012241	Q0VF46|Q69Z03	Silent	SNP	ENST00000398532.4	37																																																																																				C|0.938;T|0.062	0.062	strong		0.478	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241	
SEC61A2	55176	hgsc.bcm.edu	37	10	12191933	12191933	+	Silent	SNP	C	C	T	rs10466280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:12191933C>T	ENST00000298428.9	+	6	524	c.435C>T	c.(433-435)gcC>gcT	p.A145A	SEC61A2_ENST00000379017.3_Silent_p.A145A|SEC61A2_ENST00000304267.8_Silent_p.A145A|SEC61A2_ENST00000379051.1_Silent_p.A145A|SEC61A2_ENST00000379020.4_Silent_p.A145A|SEC61A2_ENST00000379033.3_Silent_p.A123A|SEC61A2_ENST00000495368.1_3'UTR	NM_018144.3	NP_060614.2	Q9H9S3	S61A2_HUMAN	Sec61 alpha 2 subunit (S. cerevisiae)	145					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ribosome binding (GO:0043022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Renal(717;0.228)				AAATGGGTGCCGGAATCTGTC	0.418													C|||	2125	0.424321	0.41	0.4986	5008	,	,		19774	0.5258		0.4056	False		,,,				2504	0.3057				p.A145A		Atlas-SNP	.											.	SEC61A2	48	.	0			c.C435T						PASS	.	C	,,	1844,2562	538.7+/-375.1	401,1042,760	142.0	137.0	139.0		435,369,435	-3.7	0.9	10	dbSNP_119	139	3583,5017	519.1+/-379.4	736,2111,1453	no	coding-synonymous,coding-synonymous,coding-synonymous	SEC61A2	NM_001142627.1,NM_001142628.1,NM_018144.3	,,	1137,3153,2213	TT,TC,CC		41.6628,41.852,41.7269	,,	145/438,123/455,145/477	12191933	5427,7579	2203	4300	6503	SO:0001819	synonymous_variant	55176	exon6			GGGTGCCGGAATC	AF346603	CCDS7088.1, CCDS44358.1, CCDS44359.1	10p14	2004-01-06			ENSG00000065665	ENSG00000065665			17702	protein-coding gene	gene with protein product							Standard	NM_018144		Approved	FLJ10578	uc001ile.2	Q9H9S3	OTTHUMG00000017679	ENST00000298428.9:c.435C>T	10.37:g.12191933C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	90	36	0.4	NM_001142627	A8K8D0|B4DX72|F8W773	Silent	SNP	ENST00000298428.9	37	CCDS7088.1	963	0.4409340659340659	184	0.37398373983739835	165	0.4558011049723757	295	0.5157342657342657	319	0.420844327176781	C	5.271	0.235421	0.10023	0.41852	0.416628	ENSG00000065665	ENST00000418772;ENST00000419021	.	.	.	5.07	-3.7	0.04437	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44636	-0.9315	3	.	.	.	-10.1484	6.6785	0.23108	0.1062:0.2462:0.0:0.6476	rs10466280;rs17558441;rs17845804;rs17858766;rs61561401;rs10466280	.	.	.	W	91;27	.	.	R	+	1	2	SEC61A2	12231939	0.942000	0.31987	0.874000	0.34290	0.562000	0.35680	-0.009000	0.12765	-1.051000	0.03226	-1.402000	0.01139	CGG	C|0.580;T|0.420	0.420	strong		0.418	SEC61A2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046795.1	NM_018144	
PRPSAP2	5636	hgsc.bcm.edu	37	17	18775900	18775900	+	Silent	SNP	A	A	G	rs4393623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18775900A>G	ENST00000268835.2	+	5	460	c.177A>G	c.(175-177)acA>acG	p.T59T	PRPSAP2_ENST00000536323.1_5'UTR|PRPSAP2_ENST00000542013.1_Silent_p.T59T|PRPSAP2_ENST00000419071.2_Intron	NM_002767.3	NP_002758.1	O60256	KPRB_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 2	59					bone development (GO:0060348)|negative regulation of catalytic activity (GO:0043086)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11						TGCCAGAAACAAGAGTACAAA	0.348													G|||	2316	0.46246	0.562	0.5101	5008	,	,		17222	0.3294		0.5577	False		,,,				2504	0.3333				p.T59T		Atlas-SNP	.											PRPSAP2,NS,carcinoma,0,1	PRPSAP2	23	1	0			c.A177G						PASS	.	G		2451,1955	553.6+/-378.8	666,1119,418	165.0	174.0	171.0		177	-2.3	1.0	17	dbSNP_111	171	4809,3791	537.4+/-383.2	1341,2127,832	yes	coding-synonymous	PRPSAP2	NM_002767.3		2007,3246,1250	GG,GA,AA		44.0814,44.3713,44.1796		59/370	18775900	7260,5746	2203	4300	6503	SO:0001819	synonymous_variant	5636	exon4			AGAAACAAGAGTA	AB007851	CCDS11200.1, CCDS58525.1, CCDS58526.1, CCDS58527.1	17p12-p11.2	2008-05-14			ENSG00000141127	ENSG00000141127			9467	protein-coding gene	gene with protein product		603762				9806849	Standard	NM_002767		Approved	PAP41	uc002gup.2	O60256	OTTHUMG00000059406	ENST00000268835.2:c.177A>G	17.37:g.18775900A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	122	74	0.606557	NM_001243940	B4E1M8|B4E329|B7ZKZ1|E7EMY2|Q6IAS2	Silent	SNP	ENST00000268835.2	37	CCDS11200.1																																																																																			A|0.478;G|0.522	0.522	strong		0.348	PRPSAP2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132112.3	NM_002767	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31088145	31088145	+	Intron	SNP	T	T	A	rs546626089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31088145T>A	ENST00000259881.9	+	2	61				CDSN_ENST00000376288.2_Missense_Mutation_p.M18L	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGCAGTGCCATCATCCCGTGC	0.687													T|||	510	0.101837	0.1172	0.0778	5008	,	,		15043	0.0625		0.1819	False		,,,				2504	0.0562				p.M18L		Atlas-SNP	.											CDSN,NS,carcinoma,0,1	CDSN	48	1	0			c.A52T						PASS	.	T	LEU/MET,	615,3769		33,549,1610	36.0	30.0	32.0		52,	0.5	0.0	6	dbSNP_103	32	1831,6765		210,1411,2677	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	15,	243,1960,4287	AA,AT,TT		21.3006,14.0283,18.8444	benign,	18/530,	31088145	2446,10534	2192	4298	6490	SO:0001627	intron_variant	1041	exon1			GTGCCATCATCCC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-228-5308T>A	6.37:g.31088145T>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	299	119	0.397993	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	256	0.11721611721611722	55	0.11178861788617886	29	0.08011049723756906	29	0.050699300699300696	143	0.18865435356200527	T	4.791	0.147084	0.09134	0.140283	0.213006	ENSG00000204539	ENST00000376288	T	0.05855	3.38	4.35	0.505	0.16953	.	0.370723	0.19751	N	0.106888	T	0.00695	0.0023	N	0.25201	0.72	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45920	-0.9228	9	0.02654	T	1	0.1892	0.8311	0.01130	0.1927:0.1215:0.1999:0.4859	rs3095318;rs9263680;rs17855560	18	Q15517	CDSN_HUMAN	L	18	ENSP00000365465:M18L	ENSP00000365465:M18L	M	-	1	0	CDSN	31196124	0.005000	0.15991	0.002000	0.10522	0.557000	0.35523	-0.033000	0.12246	-0.059000	0.13154	0.519000	0.50382	ATG	T|0.831;A|0.169	0.169	strong		0.687	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
MUC2	4583	hgsc.bcm.edu	37	11	1092954	1092954	+	Splice_Site	SNP	G	G	A	rs56352686		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1092954G>A	ENST00000359061.5	+	30	4776	c.4776G>A	c.(4774-4776)acG>acA	p.T1592T	MUC2_ENST00000441003.2_Silent_p.T1591T|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron			Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccactacggtgaccccaa	0.627																																					p.T1591T		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,0,4	MUC2	614	4	0			c.G4773A						PASS	.						52.0	85.0	74.0					11																	1092954		1812	3296	5108	SO:0001630	splice_region_variant	4583	exon30			CACTACGGTGACC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000359061.5:c.4776+1G>A	11.37:g.1092954G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	136	7	0.0514706	NM_002457	Q14878	Silent	SNP	ENST00000359061.5	37																																																																																				.	.	none		0.627	MUC2-202	KNOWN	basic	protein_coding	protein_coding		NM_002457	Silent
KIAA0100	9703	hgsc.bcm.edu	37	17	26938651	26938651	+	IGR	SNP	C	C	T	rs34026109	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:26938651C>T	ENST00000528896.2	-	0	7407				RP11-192H23.4_ENST00000577790.1_Intron|SPAG5-AS1_ENST00000414744.1_RNA|RP11-192H23.4_ENST00000534850.1_3'UTR|SGK494_ENST00000301037.5_Missense_Mutation_p.G249S|SPAG5-AS1_ENST00000424210.1_RNA|SPAG5-AS1_ENST00000554154.1_RNA|SGK494_ENST00000469832.3_5'Flank|RP11-192H23.6_ENST00000579019.2_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100							extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					CGGGACAGACCAAAGTCTGTC	0.498													C|||	47	0.00938498	0.0008	0.0187	5008	,	,		17084	0.001		0.0278	False		,,,				2504	0.0041				p.G249S		Atlas-SNP	.											.	.	.	.	0			c.G745A						PASS	.	C	SER/GLY	20,4386	28.1+/-56.4	0,20,2183	146.0	126.0	133.0		745	5.4	1.0	17	dbSNP_126	133	271,8329	102.9+/-164.1	4,263,4033	yes	missense	SGK494	NM_001174103.1	56	4,283,6216	TT,TC,CC		3.1512,0.4539,2.2374		249/411	26938651	291,12715	2203	4300	6503	SO:0001628	intergenic_variant	0	exon9			ACAGACCAAAGTC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587		17.37:g.26938651C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_001174103	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	33	0.01510989010989011	0	0.0	8	0.022099447513812154	0	0.0	25	0.032981530343007916	C	26.0	4.694340	0.88830	0.004539	0.031512	ENSG00000167524	ENST00000301037	T	0.61392	0.11	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65749	0.2721	M	0.93808	3.46	0.58432	D	0.999993	D	0.76494	0.999	D	0.83275	0.996	T	0.82218	-0.0566	10	0.87932	D	0	-7.9003	18.2718	0.90070	0.0:1.0:0.0:0.0	rs34026109;rs34026109	249	Q96LW2	SG494_HUMAN	S	249	ENSP00000301037:G249S	ENSP00000301037:G249S	G	-	1	0	AC005726.6	23962778	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.156000	0.64905	2.566000	0.86566	0.467000	0.42956	GGT	C|0.980;T|0.020	0.020	strong		0.498	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
MNS1	55329	hgsc.bcm.edu	37	15	56756285	56756285	+	Missense_Mutation	SNP	T	T	G	rs1715919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:56756285T>G	ENST00000260453.3	-	2	328	c.164A>C	c.(163-165)cAa>cCa	p.Q55P		NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	55			Q -> P (in dbSNP:rs1715919).		cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		TCTGAGAAATTGCTTGCGCTG	0.318													T|||	268	0.0535144	0.0083	0.0677	5008	,	,		19084	0.0694		0.0905	False		,,,				2504	0.0501				p.Q55P		Atlas-SNP	.											.	MNS1	39	.	0			c.A164C						PASS	.	T	PRO/GLN	130,4250	95.7+/-134.4	3,124,2063	146.0	147.0	147.0		164	3.5	0.3	15	dbSNP_89	147	922,7662	204.4+/-247.1	51,820,3421	yes	missense	MNS1	NM_018365.2	76	54,944,5484	GG,GT,TT		10.7409,2.968,8.1148	benign	55/496	56756285	1052,11912	2190	4292	6482	SO:0001583	missense	55329	exon2			AGAAATTGCTTGC	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"""spermatogenesis associated 40"""	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.164A>C	15.37:g.56756285T>G	ENSP00000260453:p.Gln55Pro	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	146	79	0.541096	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	37	CCDS10158.1	137	0.06272893772893773	7	0.014227642276422764	22	0.06077348066298342	36	0.06293706293706294	72	0.09498680738786279	T	11.78	1.740455	0.30865	0.02968	0.107409	ENSG00000138587	ENST00000260453	T	0.14893	2.47	5.42	3.5	0.40072	.	0.111317	0.56097	D	0.000023	T	0.00210	0.0006	N	0.14661	0.345	0.80722	P	0.0	B	0.24533	0.105	B	0.19666	0.026	T	0.09975	-1.0650	9	0.66056	D	0.02	-12.8365	9.0354	0.36284	0.0:0.8152:0.0:0.1848	rs1715919;rs3736530;rs17819479;rs61224656;rs1715919	55	Q8NEH6	MNS1_HUMAN	P	55	ENSP00000260453:Q55P	ENSP00000260453:Q55P	Q	-	2	0	MNS1	54543577	0.014000	0.17966	0.258000	0.24420	0.034000	0.12701	1.225000	0.32551	1.391000	0.46566	-0.462000	0.05337	CAA	G|0.074;N|0.000	0.074	strong		0.318	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365	
KIF24	347240	hgsc.bcm.edu	37	9	34310927	34310927	+	Missense_Mutation	SNP	T	T	C	rs10972048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:34310927T>C	ENST00000402558.2	-	1	442	c.418A>G	c.(418-420)Atg>Gtg	p.M140V	KIF24_ENST00000379174.3_Missense_Mutation_p.M140V|KIF24_ENST00000379166.2_Missense_Mutation_p.M140V|KIF24_ENST00000345050.2_Missense_Mutation_p.M140V			Q5T7B8	KIF24_HUMAN	kinesin family member 24	140			M -> V (in dbSNP:rs10972048).		ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			TCTGGTAGCATGTGTTCTAGC	0.398													T|||	2058	0.410942	0.1059	0.5	5008	,	,		20677	0.3353		0.6223	False		,,,				2504	0.6207				p.M140V		Atlas-SNP	.											.	KIF24	64	.	0			c.A418G						PASS	.	T	VAL/MET	691,3101		66,559,1271	179.0	170.0	173.0		418	1.9	0.9	9	dbSNP_120	173	5160,3120		1604,1952,584	yes	missense	KIF24	NM_194313.2	21	1670,2511,1855	CC,CT,TT		37.6812,18.2226,48.4675	benign	140/1369	34310927	5851,6221	1896	4140	6036	SO:0001583	missense	347240	exon2			GTAGCATGTGTTC	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.418A>G	9.37:g.34310927T>C	ENSP00000384433:p.Met140Val	Somatic	370	2	0.00540541		WXS	Illumina HiSeq	Phase_I	294	294	1	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	37	CCDS6551.2	913	0.41804029304029305	51	0.10365853658536585	200	0.5524861878453039	185	0.32342657342657344	477	0.6292875989445911	T	0.005	-2.128481	0.00342	0.182226	0.623188	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.70045	-0.28;-0.45;-0.28;-0.45	5.48	1.9	0.25705	.	0.406548	0.21334	N	0.076241	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.44050	-0.9353	9	0.28530	T	0.3	.	4.2329	0.10611	0.1386:0.2167:0.0:0.6446	rs10972048;rs17259557;rs52797474;rs56911205;rs10972048	140;140	Q5T7B8-4;Q5T7B8	.;KIF24_HUMAN	V	140	ENSP00000384433:M140V;ENSP00000368472:M140V;ENSP00000368464:M140V;ENSP00000340179:M140V	ENSP00000340179:M140V	M	-	1	0	KIF24	34300927	0.420000	0.25457	0.874000	0.34290	0.231000	0.25187	0.035000	0.13797	0.383000	0.24910	0.528000	0.53228	ATG	T|0.590;C|0.410	0.410	strong		0.398	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
FGFBP2	83888	hgsc.bcm.edu	37	4	15964670	15964670	+	Missense_Mutation	SNP	C	C	T	rs35496730	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:15964670C>T	ENST00000259989.6	-	1	189	c.83G>A	c.(82-84)aGc>aAc	p.S28N	FGFBP2_ENST00000509331.1_Intron	NM_031950.3	NP_114156.1	Q9BYJ0	FGFP2_HUMAN	fibroblast growth factor binding protein 2	28			S -> N (in dbSNP:rs35496730).			extracellular region (GO:0005576)				central_nervous_system(1)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	9						CTCCCCAGTGCTTCCTTGCTT	0.577													C|||	606	0.121006	0.0794	0.1297	5008	,	,		20896	0.0853		0.1541	False		,,,				2504	0.1738				p.S28N		Atlas-SNP	.											.	FGFBP2	22	.	0			c.G83A						PASS	.	C	ASN/SER	425,3981	206.5+/-228.1	21,383,1799	71.0	62.0	65.0		83	-2.1	0.0	4	dbSNP_126	65	1325,7275	259.8+/-282.9	112,1101,3087	yes	missense	FGFBP2	NM_031950.3	46	133,1484,4886	TT,TC,CC		15.407,9.6459,13.4553	benign	28/224	15964670	1750,11256	2203	4300	6503	SO:0001583	missense	83888	exon1			CCAGTGCTTCCTT	AB021123	CCDS3419.1	4p15.32	2008-07-16			ENSG00000137441	ENSG00000137441			29451	protein-coding gene	gene with protein product	"""killer-specific secretory protein of 37 kDa"""	607713				11342666, 12322897	Standard	NM_031950		Approved	KSP37	uc003gon.3	Q9BYJ0	OTTHUMG00000128513	ENST00000259989.6:c.83G>A	4.37:g.15964670C>T	ENSP00000259989:p.Ser28Asn	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	79	0.975309	NM_031950		Missense_Mutation	SNP	ENST00000259989.6	37	CCDS3419.1	255	0.11675824175824176	39	0.07926829268292683	52	0.143646408839779	47	0.08216783216783216	117	0.15435356200527706	C	3.733	-0.055220	0.07362	0.096459	0.15407	ENSG00000137441	ENST00000259989	T	0.16073	2.37	2.98	-2.08	0.07254	.	1.294600	0.05643	U	0.583857	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.39542	-0.9609	9	0.18276	T	0.48	0.8044	3.5788	0.07945	0.1651:0.4992:0.0:0.3357	rs35496730	28	Q9BYJ0	FGFP2_HUMAN	N	28	ENSP00000259989:S28N	ENSP00000259989:S28N	S	-	2	0	FGFBP2	15573768	0.044000	0.20184	0.000000	0.03702	0.002000	0.02628	-0.015000	0.12634	-0.762000	0.04664	-0.896000	0.02909	AGC	C|0.872;T|0.128	0.128	strong		0.577	FGFBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250324.1	NM_031950	
PCED1B	91523	hgsc.bcm.edu	37	12	47471439	47471439	+	5'Flank	SNP	G	G	A	rs2269828	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:47471439G>A	ENST00000546455.1	+	0	0				AMIGO2_ENST00000429635.1_Silent_p.P449P|AMIGO2_ENST00000550413.1_Silent_p.P449P|AMIGO2_ENST00000266581.4_Silent_p.P449P|AMIGO2_ENST00000321382.3_Silent_p.P449P			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										CATCACTAGCGGGGCCAGGAC	0.507													G|||	1110	0.221645	0.1346	0.2882	5008	,	,		21472	0.124		0.3211	False		,,,				2504	0.2904				p.P449P		Atlas-SNP	.											.	AMIGO2	50	.	0			c.C1347T						PASS	.	G	,	756,3650	310.5+/-291.6	61,634,1508	153.0	156.0	155.0		1347,1347	-9.6	0.0	12	dbSNP_100	155	2788,5812	443.1+/-360.3	444,1900,1956	no	coding-synonymous,coding-synonymous	AMIGO2	NM_001143668.1,NM_181847.4	,	505,2534,3464	AA,AG,GG		32.4186,17.1584,27.249	,	449/523,449/523	47471439	3544,9462	2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			ACTAGCGGGGCCA	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		12.37:g.47471439G>A	Exception_encountered	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	341	337	0.98827	NM_181847	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																			G|0.750;A|0.250	0.250	strong		0.507	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
FLRT3	23767	hgsc.bcm.edu	37	20	14306953	14306953	+	Missense_Mutation	SNP	G	G	T	rs6079391	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:14306953G>T	ENST00000378053.3	-	2	1456	c.1200C>A	c.(1198-1200)caC>caA	p.H400Q	MACROD2_ENST00000217246.4_Intron|MACROD2_ENST00000310348.4_Intron|FLRT3_ENST00000341420.4_Missense_Mutation_p.H400Q|FLRT3_ENST00000462077.1_5'Flank	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	400			H -> Q (in dbSNP:rs6079391). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.7}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		CTGTGGTTTGGTGATCCTTAG	0.458													G|||	1306	0.260783	0.1543	0.4107	5008	,	,		20429	0.1597		0.4652	False		,,,				2504	0.1922				p.H400Q		Atlas-SNP	.											FLRT3,colon,carcinoma,0,1	FLRT3	67	1	0			c.C1200A						scavenged	.	G	GLN/HIS,,GLN/HIS	932,3474	355.6+/-313.1	109,714,1380	188.0	183.0	184.0		1200,,1200	1.6	1.0	20	dbSNP_114	184	4141,4459	564.3+/-388.3	993,2155,1152	yes	missense,intron,missense	FLRT3,MACROD2	NM_013281.3,NM_080676.5,NM_198391.2	24,,24	1102,2869,2532	TT,TG,GG		48.1512,21.153,39.0051	benign,,benign	400/650,,400/650	14306953	5073,7933	2203	4300	6503	SO:0001583	missense	23767	exon2			GGTTTGGTGATCC	AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"""Fibronectin type III domain containing"""	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.1200C>A	20.37:g.14306953G>T	ENSP00000367292:p.His400Gln	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	184	74	0.402174	NM_013281	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Missense_Mutation	SNP	ENST00000378053.3	37	CCDS13121.1	668	0.3058608058608059	77	0.1565040650406504	147	0.40607734806629836	79	0.1381118881118881	365	0.4815303430079156	G	3.751	-0.051493	0.07407	0.21153	0.481512	ENSG00000125848	ENST00000378053;ENST00000341420;ENST00000541882	T;T	0.57907	0.37;0.37	6.06	1.58	0.23477	.	0.381456	0.27294	N	0.020027	T	0.00012	0.0000	N	0.08118	0	0.38381	P	0.05487299999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.47328	-0.9126	9	0.28530	T	0.3	-1.925	4.3331	0.11073	0.2037:0.3164:0.4025:0.0774	rs6079391;rs6514511;rs59910157;rs6079391	400	Q9NZU0	FLRT3_HUMAN	Q	400	ENSP00000367292:H400Q;ENSP00000339912:H400Q	ENSP00000339912:H400Q	H	-	3	2	FLRT3	14254953	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.833000	0.39161	0.899000	0.36444	-0.153000	0.13522	CAC	G|0.667;T|0.333	0.333	strong		0.458	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281	
DRAXIN	374946	hgsc.bcm.edu	37	1	11771988	11771988	+	Silent	SNP	A	A	G	rs17037327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11771988A>G	ENST00000294485.5	+	4	858	c.723A>G	c.(721-723)ttA>ttG	p.L241L		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		ATGAAGACTTAAAACCTGATG	0.582													A|||	484	0.0966454	0.0938	0.0821	5008	,	,		20678	0.0655		0.1262	False		,,,				2504	0.1125				p.L241L		Atlas-SNP	.											.	.	.	.	0			c.A723G						PASS	.	A		423,3983	204.1+/-226.4	19,385,1799	90.0	61.0	71.0		723	-1.9	0.8	1	dbSNP_123	71	1134,7466	232.1+/-265.8	55,1024,3221	no	coding-synonymous	C1orf187	NM_198545.3		74,1409,5020	GG,GA,AA		13.186,9.6005,11.9714		241/350	11771988	1557,11449	2203	4300	6503	SO:0001819	synonymous_variant	374946	exon4			AGACTTAAAACCT	AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"""dorsal repulsive axon guidance protein"", ""neural tissue-specific cysteine-rich protein"""	612682	"""chromosome 1 open reading frame 187"""	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.723A>G	1.37:g.11771988A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_198545		Silent	SNP	ENST00000294485.5	37	CCDS135.1																																																																																			A|0.885;G|0.115	0.115	strong		0.582	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545	
GALNT7	51809	hgsc.bcm.edu	37	4	174090004	174090004	+	Silent	SNP	G	G	A	rs3733477	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:174090004G>A	ENST00000265000.4	+	1	101	c.18G>A	c.(16-18)ggG>ggA	p.G6G	GALNT7_ENST00000512285.1_Silent_p.G6G|RP11-10K16.1_ENST00000500914.2_RNA|RP11-10K16.1_ENST00000510523.1_RNA|RP11-10K16.1_ENST00000499322.2_RNA	NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	6					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TGAAGATTGGGTTCATCTTAC	0.667													G|||	3213	0.641573	0.5825	0.5231	5008	,	,		7096	0.7183		0.7018	False		,,,				2504	0.6646				p.G6G		Atlas-SNP	.											.	GALNT7	61	.	0			c.G18A						PASS	.	G		2679,1727	646.0+/-398.3	831,1017,355	150.0	132.0	138.0		18	2.2	1.0	4	dbSNP_107	138	5837,2763	677.0+/-403.3	1997,1843,460	no	coding-synonymous	GALNT7	NM_017423.2		2828,2860,815	AA,AG,GG		32.1279,39.1966,34.5225		6/658	174090004	8516,4490	2203	4300	6503	SO:0001819	synonymous_variant	51809	exon1			GATTGGGTTCATC	AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"""Glycosyltransferase family 2 domain containing"""	4129	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 7"""	605005	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"""			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.18G>A	4.37:g.174090004G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	80	78	0.975	NM_017423	B3KQU3|Q7Z5W7|Q9UJ28	Silent	SNP	ENST00000265000.4	37	CCDS3815.1																																																																																			T|0.000;G|0.353;A|0.647	0.647	strong		0.667	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423	
CPA1	1357	hgsc.bcm.edu	37	7	130023561	130023561	+	Missense_Mutation	SNP	G	G	A	rs34474469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:130023561G>A	ENST00000011292.3	+	6	772	c.622G>A	c.(622-624)Gcc>Acc	p.A208T	CPA1_ENST00000484324.1_Missense_Mutation_p.A120T	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	208			A -> T (in dbSNP:rs34474469).		proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					AGCTTTCACCGCCATTCTCGA	0.602													G|||	77	0.0153754	0.0008	0.0187	5008	,	,		20659	0.0		0.0298	False		,,,				2504	0.0337				p.A208T		Atlas-SNP	.											.	CPA1	73	.	0			c.G622A						PASS	.	G	THR/ALA	23,4383	31.7+/-61.6	0,23,2180	181.0	153.0	163.0		622	-2.1	0.0	7	dbSNP_126	163	292,8308	108.2+/-168.9	5,282,4013	yes	missense	CPA1	NM_001868.2	58	5,305,6193	AA,AG,GG		3.3953,0.522,2.422	benign	208/420	130023561	315,12691	2203	4300	6503	SO:0001583	missense	1357	exon6			TTCACCGCCATTC		CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"""pancreatic carboxypeptidase A"""	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.622G>A	7.37:g.130023561G>A	ENSP00000011292:p.Ala208Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	143	67	0.468531	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Missense_Mutation	SNP	ENST00000011292.3	37	CCDS5820.1	30	0.013736263736263736	0	0.0	8	0.022099447513812154	0	0.0	22	0.029023746701846966	G	13.32	2.201184	0.38905	0.00522	0.033953	ENSG00000091704	ENST00000011292;ENST00000476062;ENST00000484324	T;T;T	0.10860	2.83;2.83;2.83	5.27	-2.08	0.07254	Peptidase M14, carboxypeptidase A (2);	1.042680	0.07449	N	0.898735	T	0.02571	0.0078	L	0.46819	1.47	0.09310	N	1	P;P	0.42941	0.731;0.794	B;B	0.36464	0.157;0.225	T	0.25641	-1.0126	10	0.41790	T	0.15	.	6.0182	0.19615	0.2234:0.0:0.201:0.5756	rs34474469	120;208	B4DDW9;P15085	.;CBPA1_HUMAN	T	208;120;120	ENSP00000011292:A208T;ENSP00000419408:A120T;ENSP00000419497:A120T	ENSP00000011292:A208T	A	+	1	0	CPA1	129810797	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	0.104000	0.15313	-0.660000	0.05352	-0.367000	0.07326	GCC	G|0.979;A|0.021	0.021	strong		0.602	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868	
LRP1B	53353	hgsc.bcm.edu	37	2	142567910	142567910	+	Missense_Mutation	SNP	T	T	C	rs12990449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:142567910T>C	ENST00000389484.3	-	2	1114	c.143A>G	c.(142-144)cAg>cGg	p.Q48R	LRP1B_ENST00000486364.1_5'UTR	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	48	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.		Q -> R (in dbSNP:rs12990449).		protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CAGCCAGCTCTGGGAGACACA	0.433										TSP Lung(27;0.18)			T|||	1089	0.217452	0.0658	0.1787	5008	,	,		17310	0.3532		0.2296	False		,,,				2504	0.2975				p.Q48R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A143G						PASS	.	T	ARG/GLN	427,3979	205.5+/-227.4	19,389,1795	61.0	57.0	59.0		143	4.4	1.0	2	dbSNP_121	59	1852,6748	331.2+/-319.6	211,1430,2659	yes	missense	LRP1B	NM_018557.2	43	230,1819,4454	CC,CT,TT		21.5349,9.6913,17.5227	benign	48/4600	142567910	2279,10727	2203	4300	6503	SO:0001583	missense	53353	exon2			CAGCTCTGGGAGA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.143A>G	2.37:g.142567910T>C	ENSP00000374135:p.Gln48Arg	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	277	158	0.570397	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	471	0.21565934065934067	29	0.05894308943089431	59	0.16298342541436464	213	0.3723776223776224	170	0.22427440633245382	T	13.77	2.335108	0.41398	0.096913	0.215349	ENSG00000168702	ENST00000389484;ENST00000434794	D;D	0.95342	-3.68;-3.68	5.62	4.45	0.53987	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.173808	0.37906	N	0.001897	T	0.00012	0.0000	N	0.13235	0.315	0.35468	P	0.20288899999999999	B;B	0.06786	0.001;0.001	B;B	0.10450	0.003;0.005	T	0.08554	-1.0716	9	0.15499	T	0.54	.	7.8759	0.29592	0.0:0.072:0.1396:0.7884	rs12990449;rs52808262;rs12990449	86;48	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	R	48	ENSP00000374135:Q48R;ENSP00000413239:Q48R	ENSP00000374135:Q48R	Q	-	2	0	LRP1B	142284380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.525000	0.53502	0.946000	0.37632	0.528000	0.53228	CAG	C|0.208;N|0.000	0.208	strong		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
SLC16A4	9122	hgsc.bcm.edu	37	1	110924353	110924353	+	Silent	SNP	G	G	A	rs3738750	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110924353G>A	ENST00000369779.4	-	4	534	c.285C>T	c.(283-285)ttC>ttT	p.F95F	SLC16A4_ENST00000541986.1_Silent_p.F33F|SLC16A4_ENST00000472422.2_Intron|LAMTOR5-AS1_ENST00000590413.1_RNA|SLC16A4_ENST00000369781.4_Silent_p.F95F|SLC16A4_ENST00000497687.1_Intron|SLC16A4_ENST00000437429.2_Intron	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	95					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)	p.F95F(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CAGTAACAACGAAAGCCCCAA	0.418													G|||	881	0.175919	0.0318	0.1614	5008	,	,		20217	0.2609		0.1889	False		,,,				2504	0.2802				p.F95F		Atlas-SNP	.											SLC16A4,NS,carcinoma,0,2	SLC16A4	47	2	1	Substitution - coding silent(1)	stomach(1)	c.C285T						PASS	.	G	,,,,	245,4161	145.0+/-179.8	6,233,1964	111.0	102.0	105.0		,99,,285,285	0.8	0.0	1	dbSNP_107	105	1593,7007	297.9+/-303.7	135,1323,2842	no	intron,coding-synonymous,intron,coding-synonymous,coding-synonymous	SLC16A4	NM_001201546.1,NM_001201547.1,NM_001201548.1,NM_001201549.1,NM_004696.2	,,,,	141,1556,4806	AA,AG,GG		18.5233,5.5606,14.1319	,,,,	,33/426,,95/320,95/488	110924353	1838,11168	2203	4300	6503	SO:0001819	synonymous_variant	9122	exon4			AACAACGAAAGCC	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.285C>T	1.37:g.110924353G>A		Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	299	121	0.404682	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Silent	SNP	ENST00000369779.4	37	CCDS823.1																																																																																			G|0.839;A|0.161	0.161	strong		0.418	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696	
ZNF443	10224	hgsc.bcm.edu	37	19	12541547	12541547	+	Missense_Mutation	SNP	T	T	G	rs10402252|rs74181783	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12541547T>G	ENST00000301547.5	-	4	1636	c.1439A>C	c.(1438-1440)aAa>aCa	p.K480T	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	480				K -> T (in Ref. 1; BAA75543 and 3; AAH32753). {ECO:0000305}.	apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						TTTCCCAAGTTTGCATTTATA	0.398													.|||	1308	0.261182	0.171	0.4207	5008	,	,		21103	0.1071		0.496	False		,,,				2504	0.1871				p.K480T		Atlas-SNP	.											.	ZNF443	63	.	0			c.A1439C						PASS	.	T	THR/LYS	949,3453	350.0+/-310.6	110,729,1362	68.0	72.0	71.0		1439	1.3	0.0	19	dbSNP_119	71	4323,4277	570.1+/-389.3	1098,2127,1075	no	missense	ZNF443	NM_005815.4	78	1208,2856,2437	GG,GT,TT		49.7326,21.5584,40.5476	possibly-damaging	480/672	12541547	5272,7730	2201	4300	6501	SO:0001583	missense	10224	exon4			CCAAGTTTGCATT	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1439A>C	19.37:g.12541547T>G	ENSP00000301547:p.Lys480Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	711	0.32554945054945056	97	0.19715447154471544	161	0.4447513812154696	60	0.1048951048951049	393	0.5184696569920845	T	11.17	1.558917	0.27827	0.215584	0.502674	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.19250	2.16	1.26	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12920	0.275	0.80722	P	0.0	D	0.60575	0.988	D	0.64877	0.93	T	0.44967	-0.9293	8	0.66056	D	0.02	.	4.2601	0.10737	0.0:0.1986:0.0:0.8014	rs10402252;rs17846014;rs17858998;rs60951533	480	Q9Y2A4	ZN443_HUMAN	T	480	ENSP00000301547:K480T	ENSP00000301547:K480T	K	-	2	0	ZNF443	12402547	0.000000	0.05858	0.004000	0.12327	0.031000	0.12232	-1.386000	0.02537	0.841000	0.35020	0.378000	0.23410	AAA	T|0.615;G|0.385	0.385	strong		0.398	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
COL6A3	1293	hgsc.bcm.edu	37	2	238244781	238244781	+	Missense_Mutation	SNP	T	T	C	rs11690358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238244781T>C	ENST00000295550.4	-	40	9414	c.8962A>G	c.(8962-8964)Atg>Gtg	p.M2988V	COL6A3_ENST00000409809.1_Missense_Mutation_p.M2782V|COL6A3_ENST00000346358.4_Missense_Mutation_p.M2788V|COL6A3_ENST00000347401.3_Missense_Mutation_p.M2787V|COL6A3_ENST00000353578.4_Missense_Mutation_p.M2782V|COL6A3_ENST00000472056.1_Missense_Mutation_p.M2381V	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2988	Nonhelical region.		M -> V (in dbSNP:rs11690358). {ECO:0000269|PubMed:1689238, ECO:0000269|PubMed:17886299}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTCTTACCCATGGGCTTAGTG	0.572													C|||	237	0.0473243	0.0151	0.0461	5008	,	,		21536	0.0109		0.1123	False		,,,				2504	0.0624				p.M2988V		Atlas-SNP	.											.	COL6A3	608	.	0			c.A8962G						PASS	.	C	VAL/MET,VAL/MET,VAL/MET	100,3998		1,98,1950	49.0	42.0	44.0		8344,7141,8962	-4.8	0.0	2	dbSNP_120	44	749,7497		30,689,3404	yes	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	21,21,21	31,787,5354	CC,CT,TT		9.0832,2.4402,6.8778	benign,benign,benign	2782/2972,2381/2571,2988/3178	238244781	849,11495	2049	4123	6172	SO:0001583	missense	1293	exon40			TACCCATGGGCTT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8962A>G	2.37:g.238244781T>C	ENSP00000295550:p.Met2988Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	110	0.05036630036630037	7	0.014227642276422764	16	0.04419889502762431	6	0.01048951048951049	81	0.10686015831134564	C	7.541	0.660628	0.14645	0.024402	0.090832	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.87491	-2.26;-2.24;-2.22;-2.22;-2.22;-2.21	5.56	-4.78	0.03209	Fibronectin, type III (1);	1.728000	0.03320	N	0.191771	T	0.01905	0.0060	N	0.00926	-1.1	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.51803	-0.8659	10	0.02654	T	1	.	2.5857	0.04829	0.1063:0.2207:0.2092:0.4637	rs11690358;rs61396974;rs11690358	2381;2782;2988	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	V	2988;2787;2782;2381;2782;2788	ENSP00000295550:M2988V;ENSP00000315609:M2787V;ENSP00000315873:M2782V;ENSP00000418285:M2381V;ENSP00000386844:M2782V;ENSP00000295546:M2788V	ENSP00000295550:M2988V	M	-	1	0	COL6A3	237909520	0.000000	0.05858	0.000000	0.03702	0.722000	0.41435	-1.242000	0.02908	-1.635000	0.01535	-0.213000	0.12676	ATG	T|0.934;C|0.066	0.066	strong		0.572	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
STARD3	10948	hgsc.bcm.edu	37	17	37814080	37814080	+	Missense_Mutation	SNP	G	G	A	rs1877031	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:37814080G>A	ENST00000336308.5	+	4	568	c.350G>A	c.(349-351)cGg>cAg	p.R117Q	STARD3_ENST00000580611.1_Missense_Mutation_p.R91Q|STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000544210.2_Missense_Mutation_p.R117Q|STARD3_ENST00000394250.4_Missense_Mutation_p.R117Q	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	117	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.		R -> Q (in dbSNP:rs1877031). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7490069, ECO:0000269|PubMed:9270027, ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)	p.R117Q(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			GCCGTGCTGCGGCTCCGGCAC	0.637													G|||	2349	0.46905	0.1853	0.5043	5008	,	,		19160	0.4157		0.673	False		,,,				2504	0.6728				p.R117Q		Atlas-SNP	.											STARD3,colon,carcinoma,0,2	STARD3	33	2	1	Substitution - Missense(1)	stomach(1)	c.G350A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	1043,3363	381.8+/-324.2	121,801,1281	97.0	101.0	99.0		350,350,350	4.4	1.0	17	dbSNP_92	99	5613,2987	664.1+/-402.1	1830,1953,517	yes	missense,missense,missense	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	43,43,43	1951,2754,1798	AA,AG,GG		34.7326,23.6723,48.8236	benign,benign,benign	117/446,117/428,117/446	37814080	6656,6350	2203	4300	6503	SO:0001583	missense	10948	exon4			TGCTGCGGCTCCG		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"""StAR-related lipid transfer (START) domain containing"""	17579	protein-coding gene	gene with protein product		607048	"""START domain containing 3"""				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.350G>A	17.37:g.37814080G>A	ENSP00000337446:p.Arg117Gln	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	241	241	1	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Missense_Mutation	SNP	ENST00000336308.5	37	CCDS11341.1	1072	0.4908424908424908	91	0.18495934959349594	192	0.5303867403314917	277	0.48426573426573427	512	0.6754617414248021	G	16.60	3.168811	0.57584	0.236723	0.652674	ENSG00000131748	ENST00000336308;ENST00000544210;ENST00000394250;ENST00000443521	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	4.38	4.38	0.52667	MENTAL domain (2);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.999999127011	D;B;B	0.55172	0.97;0.127;0.132	P;B;B	0.50314	0.637;0.183;0.109	T	0.35549	-0.9784	9	0.27785	T	0.31	.	17.3051	0.87192	0.0:0.0:1.0:0.0	rs1877031;rs3817159;rs17850374;rs59894565;rs1877031	117;117;117	F5H0G2;A8MXA4;Q14849	.;.;STAR3_HUMAN	Q	117	ENSP00000337446:R117Q;ENSP00000439869:R117Q;ENSP00000377794:R117Q;ENSP00000411710:R117Q	ENSP00000337446:R117Q	R	+	2	0	STARD3	35067606	0.991000	0.36638	1.000000	0.80357	0.665000	0.39181	3.666000	0.54540	2.125000	0.65367	0.561000	0.74099	CGG	G|0.499;T|0.004	.	strong		0.637	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		
MAPT	4137	hgsc.bcm.edu	37	17	44067382	44067382	+	Missense_Mutation	SNP	T	T	C	rs2258689	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:44067382T>C	ENST00000571987.1	+	7	1321	c.1321T>C	c.(1321-1323)Tac>Cac	p.Y441H	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.Y441H|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.Y441H|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.Y441H			P10636	TAU_HUMAN	microtubule-associated protein tau	441			Y -> H (in dbSNP:rs2258689). {ECO:0000269|PubMed:1420178, ECO:0000269|PubMed:15365985, ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.H441Y(1)|p.Y441H(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	CTCTCCTAAATACGTCTCTTC	0.542													T|||	1567	0.312899	0.146	0.2867	5008	,	,		17087	0.628		0.2117	False		,,,				2504	0.3364				p.Y441H		Atlas-SNP	.											MAPT_ENST00000344290,NS,adenoma,-2,3	MAPT	135	3	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.T1321C						PASS	.	T	HIS/TYR,,,,,,HIS/TYR,	651,3755	278.7+/-274.4	39,573,1591	160.0	161.0	161.0		1321,,,,,,1321,	1.8	1.0	17	dbSNP_100	161	1707,6893	312.9+/-311.0	174,1359,2767	no	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	83,,,,,,83,	213,1932,4358	CC,CT,TT		19.8488,14.7753,18.1301	benign,,,,,,benign,	441/777,,,,,,441/759,	44067382	2358,10648	2203	4300	6503	SO:0001583	missense	4137	exon8			CCTAAATACGTCT	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1321T>C	17.37:g.44067382T>C	ENSP00000458742:p.Tyr441His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	707	0.32371794871794873	66	0.13414634146341464	112	0.30939226519337015	359	0.6276223776223776	170	0.22427440633245382	T	4.814	0.151267	0.09185	0.147753	0.198488	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.28069	1.63;1.63;1.63	4.96	1.82	0.25136	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999784324	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.35574	-0.9783	8	0.31617	T	0.26	-2.8969	6.8926	0.24238	0.0:0.7086:0.0:0.2914	rs2258689;rs17572963;rs52834697;rs59032677;rs2258689	441;441	P10636-9;P10636	.;TAU_HUMAN	H	441	ENSP00000340820:Y441H;ENSP00000262410:Y441H;ENSP00000410838:Y441H	ENSP00000262410:Y441H	Y	+	1	0	MAPT	41423219	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	1.139000	0.31504	0.254000	0.21573	-0.415000	0.06103	TAC	A|0.134;C|0.198	0.198	strong		0.542	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
USP18	11274	hgsc.bcm.edu	37	22	18650682	18650682	+	Missense_Mutation	SNP	C	C	T	rs3180408	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:18650682C>T	ENST00000215794.7	+	6	936	c.506C>T	c.(505-507)aCg>aTg	p.T169M		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	169	USP.		T -> M (in dbSNP:rs3180408). {ECO:0000269|Ref.7}.		cytokine-mediated signaling pathway (GO:0019221)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.T169M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GCCCTGTATACGATCCGGGTG	0.547													c|||	1489	0.297324	0.3979	0.2997	5008	,	,		16115	0.1637		0.3072	False		,,,				2504	0.2873				p.T169M		Atlas-SNP	.											USP18,NS,carcinoma,0,1	USP18	22	1	1	Substitution - Missense(1)	stomach(1)	c.C506T						PASS	.	C	MET/THR	1709,2697		320,1069,814	121.0	94.0	103.0		506	-3.1	0.0	22	dbSNP_105	103	2965,5635		496,1973,1831	no	missense	USP18	NM_017414.3	81	816,3042,2645	TT,TC,CC		34.4767,38.788,35.9373	benign	169/373	18650682	4674,8332	2203	4300	6503	SO:0001583	missense	11274	exon6			TGTATACGATCCG	AJ243526	CCDS13752.1	22q11.2	2008-04-11	2005-08-08		ENSG00000184979	ENSG00000184979		"""Ubiquitin-specific peptidases"""	12616	protein-coding gene	gene with protein product		607057	"""ubiquitin specific protease 18"""			12838346	Standard	NM_017414		Approved		uc002zny.3	Q9UMW8	OTTHUMG00000150104	ENST00000215794.7:c.506C>T	22.37:g.18650682C>T	ENSP00000215794:p.Thr169Met	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	268	268	1	NM_017414	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	614	0.28113553113553114	173	0.3516260162601626	107	0.2955801104972376	92	0.16083916083916083	242	0.31926121372031663	.	2.520	-0.311064	0.05458	0.38788	0.344767	ENSG00000184979	ENST00000215794;ENST00000441683	T	0.31769	1.48	5.62	-3.07	0.05363	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.540147	0.20380	N	0.093467	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P	0.36789	0.57	B	0.33521	0.165	T	0.40270	-0.9572	9	0.46703	T	0.11	.	7.1474	0.25591	0.0:0.5396:0.1135:0.347	rs3180408;rs3210451;rs3180408	169	Q9UMW8	UBP18_HUMAN	M	169;1	ENSP00000215794:T169M	ENSP00000215794:T169M	T	+	2	0	USP18	17030682	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.076000	0.11412	-0.757000	0.04697	-1.789000	0.00628	ACG	C|0.674;N|0.000	.	strong		0.547	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1		
FASTKD1	79675	hgsc.bcm.edu	37	2	170411698	170411698	+	Missense_Mutation	SNP	C	C	G	rs12618227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170411698C>G	ENST00000453153.2	-	7	1496	c.1150G>C	c.(1150-1152)Gaa>Caa	p.E384Q	FASTKD1_ENST00000453929.2_Missense_Mutation_p.E384Q	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	384			E -> Q (in dbSNP:rs12618227).		cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.E384*(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						AAAGTTAATTCTTGAGTTATC	0.299													C|||	175	0.0349441	0.0008	0.0086	5008	,	,		20027	0.1111		0.0288	False		,,,				2504	0.0276				p.E384Q		Atlas-SNP	.											FASTKD1,colon,carcinoma,0,1	FASTKD1	86	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1150C						PASS	.	C	GLN/GLU	31,4371	37.6+/-69.7	0,31,2170	73.0	78.0	76.0		1150	3.0	0.6	2	dbSNP_120	76	302,8298	108.8+/-169.4	4,294,4002	yes	missense	FASTKD1	NM_024622.3	29	4,325,6172	GG,GC,CC		3.5116,0.7042,2.5611	benign	384/848	170411698	333,12669	2201	4300	6501	SO:0001583	missense	79675	exon7			TTAATTCTTGAGT	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1150G>C	2.37:g.170411698C>G	ENSP00000400513:p.Glu384Gln	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	37	CCDS33318.1	85	0.03891941391941392	1	0.0020325203252032522	5	0.013812154696132596	58	0.10139860139860139	21	0.027704485488126648	C	9.994	1.231609	0.22626	0.007042	0.035116	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.17370	2.28;2.28	4.84	3.04	0.35103	.	0.408805	0.27946	N	0.017214	T	0.00241	0.0007	N	0.08118	0	0.80722	P	0.0	B;B	0.24132	0.098;0.059	B;B	0.28305	0.088;0.04	T	0.19095	-1.0316	9	0.42905	T	0.14	-9.8948	4.3534	0.11167	0.1921:0.6197:0.0:0.1882	rs12618227	384;384	Q53R41-2;Q53R41	.;FAKD1_HUMAN	Q	384	ENSP00000400513:E384Q;ENSP00000403229:E384Q	ENSP00000400513:E384Q	E	-	1	0	FASTKD1	170119944	0.321000	0.24625	0.556000	0.28293	0.504000	0.33889	0.243000	0.18106	0.629000	0.30376	0.650000	0.86243	GAA	C|0.969;G|0.031	0.031	strong		0.299	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
CARD11	84433	hgsc.bcm.edu	37	7	2969680	2969680	+	Silent	SNP	G	G	A	rs1621509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2969680G>A	ENST00000396946.4	-	12	2002	c.1599C>T	c.(1597-1599)gaC>gaT	p.D533D		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	533					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TAGGGCTGGCGTCCGTGCCTT	0.617			Mis		DLBCL								G|||	511	0.102037	0.0378	0.1787	5008	,	,		16347	0.0129		0.2366	False		,,,				2504	0.0879				p.D533D		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.C1599T						PASS	.	G		332,4074	174.4+/-204.0	12,308,1883	124.0	85.0	98.0		1599	-3.3	0.0	7	dbSNP_89	98	1898,6702	337.8+/-322.5	216,1466,2618	no	coding-synonymous	CARD11	NM_032415.4		228,1774,4501	AA,AG,GG		22.0698,7.5352,17.1459		533/1155	2969680	2230,10776	2203	4300	6503	SO:0001819	synonymous_variant	84433	exon12			GCTGGCGTCCGTG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1599C>T	7.37:g.2969680G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			G|0.852;A|0.148	0.148	strong		0.617	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
ACSF3	197322	hgsc.bcm.edu	37	16	89199651	89199651	+	Silent	SNP	G	G	A	rs12447947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:89199651G>A	ENST00000317447.4	+	8	1724	c.1347G>A	c.(1345-1347)ctG>ctA	p.L449L	ACSF3_ENST00000378345.4_Silent_p.L184L|ACSF3_ENST00000406948.3_Silent_p.L449L	NM_001127214.2|NM_001243279.1|NM_001284316.1|NM_174917.3	NP_001120686.1|NP_001230208.1|NP_001271245.1|NP_777577.2	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3	449					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|malonate catabolic process (GO:0090410)	mitochondrion (GO:0005739)	acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)|malonyl-CoA synthetase activity (GO:0090409)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(9)|prostate(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(80;0.0281)		CATTCACCCTGGATGGCTGGT	0.557													G|||	728	0.145367	0.0295	0.2608	5008	,	,		18812	0.0109		0.3608	False		,,,				2504	0.137				p.L449L		Atlas-SNP	.											.	ACSF3	40	.	0			c.G1347A						PASS	.	G	,	320,4076	170.9+/-201.2	16,288,1894	61.0	61.0	61.0		1347,1347	-9.6	0.0	16	dbSNP_120	61	3095,5505	472.3+/-368.3	573,1949,1778	no	coding-synonymous,coding-synonymous	ACSF3	NM_001127214.2,NM_174917.3	,	589,2237,3672	AA,AG,GG		35.9884,7.2793,26.2773	,	449/577,449/577	89199651	3415,9581	2198	4300	6498	SO:0001819	synonymous_variant	197322	exon8			CACCCTGGATGGC	AK075499	CCDS10974.1, CCDS73926.1	16q24.3	2013-01-15			ENSG00000176715	ENSG00000176715		"""Acyl-CoA synthetase family"""	27288	protein-coding gene	gene with protein product	"""malonyl-CoA synthetase"""	614245				17762044, 21846720	Standard	XM_005256293		Approved		uc010cig.2	Q4G176	OTTHUMG00000138044	ENST00000317447.4:c.1347G>A	16.37:g.89199651G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	70	23	0.328571	NM_174917	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	Silent	SNP	ENST00000317447.4	37	CCDS10974.1																																																																																			G|0.746;A|0.254	0.254	strong		0.557	ACSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269919.1	NM_174917	
HID1	283987	hgsc.bcm.edu	37	17	72949146	72949146	+	Silent	SNP	C	C	T	rs2307010	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72949146C>T	ENST00000425042.2	-	16	2084	c.2007G>A	c.(2005-2007)ccG>ccA	p.P669P		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	669					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											ATGAGGTGGACGGTCGCCGCT	0.692													C|||	984	0.196486	0.0734	0.1859	5008	,	,		13990	0.2698		0.2396	False		,,,				2504	0.2505				p.P669P		Atlas-SNP	.											C17orf28,colon,carcinoma,0,1	.	.	1	0			c.G2007A						PASS	.	C		440,3966		25,390,1788	23.0	20.0	21.0		2007	-1.3	0.8	17	dbSNP_100	21	2060,6536		256,1548,2494	no	coding-synonymous	C17orf28	NM_030630.2		281,1938,4282	TT,TC,CC		23.9646,9.9864,19.2278		669/789	72949146	2500,10502	2203	4298	6501	SO:0001819	synonymous_variant	283987	exon16			GGTGGACGGTCGC		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"""downregulated in multiple cancer 1"""	605752	"""chromosome 17 open reading frame 28"""	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.2007G>A	17.37:g.72949146C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	216	103	0.476852	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Silent	SNP	ENST00000425042.2	37	CCDS32726.1																																																																																			C|0.809;T|0.191	0.191	strong		0.692	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630	
NOS1	4842	hgsc.bcm.edu	37	12	117693817	117693817	+	Missense_Mutation	SNP	G	G	A	rs11068428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:117693817G>A	ENST00000338101.4	-	16	2561	c.2557C>T	c.(2557-2559)Ccc>Tcc	p.P853S	NOS1_ENST00000344089.3_Intron|NOS1_ENST00000317775.6_Intron			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCTTTACGGGGAAAGAAACGC	0.592													G|||	1740	0.347444	0.2012	0.5231	5008	,	,		18489	0.502		0.3161	False		,,,				2504	0.2935				p.P853S	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C2557T						PASS	.	G	,,,SER/PRO	332,1420		40,252,584	152.0	137.0	142.0		,,,2557	5.1	1.0	12	dbSNP_120	142	1251,2731		204,843,944	yes	intron,intron,intron,missense	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,74	244,1095,1528	AA,AG,GG		31.4164,18.9498,27.6073	,,,	,,,853/1469	117693817	1583,4151	876	1991	2867	SO:0001583	missense	4842	exon17			TACGGGGAAAGAA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2557C>T	12.37:g.117693817G>A	ENSP00000337459:p.Pro853Ser	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	790	0.3617216117216117	95	0.19308943089430894	181	0.5	265	0.4632867132867133	249	0.32849604221635886	G	10.24	1.296247	0.23650	0.189498	0.314164	ENSG00000089250	ENST00000338101;ENST00000544320	T	0.01265	5.08	5.93	5.05	0.67936	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	.	.	.	.	.	.	T	0.05750	-1.0866	6	0.27082	T	0.32	-22.5766	11.0829	0.48070	0.0844:0.0:0.9156:0.0	rs11068428;rs11068428	.	.	.	S	853;19	ENSP00000337459:P853S	ENSP00000337459:P853S	P	-	1	0	NOS1	116178200	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.955000	0.49121	1.529000	0.49120	0.655000	0.94253	CCC	G|0.651;A|0.349	0.349	strong		0.592	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
LILRA6	79168	hgsc.bcm.edu	37	19	54744919	54744919	+	Missense_Mutation	SNP	T	T	A	rs61734504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54744919T>A	ENST00000396365.2	-	5	782	c.743A>T	c.(742-744)gAt>gTt	p.D248V	LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000245621.5_Missense_Mutation_p.D248V|LILRA6_ENST00000419410.2_Missense_Mutation_p.D248V|LILRA6_ENST00000440558.2_Missense_Mutation_p.D248V	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	248	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTAGCCGACATCAGAGCCACA	0.637																																					p.D248V		Atlas-SNP	.											LILRA6,NS,carcinoma,-1,1	LILRA6	75	1	0			c.A743T						PASS	.	T	VAL/ASP	22,4384	23.3+/-48.9	0,22,2181	98.0	107.0	104.0		743	1.3	0.0	19	dbSNP_129	104	253,8347	85.0+/-147.5	0,253,4047	no	missense	LILRA6	NM_024318.2	152	0,275,6228	AA,AT,TT		2.9419,0.4993,2.1144		248/482	54744919	275,12731	2203	4300	6503	SO:0001583	missense	79168	exon5			CCGACATCAGAGC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.743A>T	19.37:g.54744919T>A	ENSP00000379651:p.Asp248Val	Somatic	655	1	0.00152672		WXS	Illumina HiSeq	Phase_I	666	171	0.256757	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	31	0.014194139194139194	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	28	0.036939313984168866	T	12.50	1.957220	0.34565	0.004993	0.029419	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	2.39	1.27	0.21489	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.862360	0.09874	N	0.744562	T	0.11367	0.0277	M	0.87547	2.89	0.09310	N	1	D;D;D;D	0.89917	0.999;0.999;0.994;1.0	D;D;D;D	0.87578	0.992;0.989;0.925;0.998	T	0.02821	-1.1106	10	0.87932	D	0	.	5.2029	0.15275	0.0:0.0:0.3054:0.6946	rs61734504	248;248;248;248	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	V	248	ENSP00000390120:D248V;ENSP00000411227:D248V;ENSP00000379651:D248V;ENSP00000245621:D248V	ENSP00000245621:D248V	D	-	2	0	LILRA6	59436731	0.003000	0.15002	0.006000	0.13384	0.043000	0.13939	0.447000	0.21710	0.312000	0.23038	0.155000	0.16302	GAT	T|0.968;A|0.032	0.032	strong		0.637	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
LRRC16A	55604	hgsc.bcm.edu	37	6	25600602	25600602	+	Silent	SNP	A	A	G	rs9885888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:25600602A>G	ENST00000329474.6	+	33	3548	c.3180A>G	c.(3178-3180)aaA>aaG	p.K1060K		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1060	Inhibits capping activity of CAPZA2. {ECO:0000250}.				actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						ATGAAAAGAAAAAGCGAGATT	0.433													A|||	247	0.0493211	0.0643	0.0173	5008	,	,		18378	0.0238		0.0239	False		,,,				2504	0.1043				p.K1060K		Atlas-SNP	.											.	LRRC16A	168	.	0			c.A3180G						PASS	.	A	,	264,3442		11,242,1600	75.0	73.0	73.0		3180,3180	-1.3	1.0	6	dbSNP_119	73	206,7996		1,204,3896	no	coding-synonymous,coding-synonymous	LRRC16A	NM_001173977.1,NM_017640.5	,	12,446,5496	GG,GA,AA		2.5116,7.1236,3.9469	,	1060/1366,1060/1372	25600602	470,11438	1853	4101	5954	SO:0001819	synonymous_variant	55604	exon33			AAAGAAAAAGCGA	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.3180A>G	6.37:g.25600602A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	212	109	0.514151	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Silent	SNP	ENST00000329474.6	37	CCDS54973.1																																																																																			A|0.948;G|0.052	0.052	strong		0.433	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
SLC12A6	9990	hgsc.bcm.edu	37	15	34542872	34542872	+	Silent	SNP	C	C	G	rs17236798	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:34542872C>G	ENST00000354181.3	-	12	2043	c.1551G>C	c.(1549-1551)ccG>ccC	p.P517P	SLC12A6_ENST00000451844.2_Silent_p.P329P|SLC12A6_ENST00000290209.5_Silent_p.P466P|SLC12A6_ENST00000558667.1_Silent_p.P517P|SLC12A6_ENST00000397707.2_Silent_p.P502P|SLC12A6_ENST00000560164.1_Silent_p.P329P|SLC12A6_ENST00000397702.2_Silent_p.P458P|SLC12A6_ENST00000560611.1_Silent_p.P517P|SLC12A6_ENST00000458406.2_Silent_p.P458P|SLC12A6_ENST00000558589.1_Silent_p.P508P			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	517					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TAGTACCAATCGGAATAGACT	0.418													G|||	1038	0.207268	0.1263	0.2017	5008	,	,		19869	0.2827		0.2068	False		,,,				2504	0.2434				p.P517P		Atlas-SNP	.											.	SLC12A6	205	.	0			c.G1551C						PASS	.	G	,,,,,	563,3839	773.7+/-414.0	36,491,1674	124.0	116.0	119.0		1374,1374,1524,1506,1398,1551	3.0	1.0	15	dbSNP_123	119	1465,7131	749.9+/-407.4	123,1219,2956	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A6	NM_001042494.1,NM_001042495.1,NM_001042496.1,NM_001042497.1,NM_005135.2,NM_133647.1	,,,,,	159,1710,4630	GG,GC,CC		17.0428,12.7896,15.6024	,,,,,	458/1092,458/1092,508/1142,502/1136,466/1100,517/1151	34542872	2028,10970	2201	4298	6499	SO:0001819	synonymous_variant	9990	exon11			ACCAATCGGAATA	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.1551G>C	15.37:g.34542872C>G		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	267	129	0.483146	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Silent	SNP	ENST00000354181.3	37	CCDS58352.1																																																																																			C|0.822;G|0.178	0.178	strong		0.418	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
CYP2C8	1558	hgsc.bcm.edu	37	10	96827030	96827030	+	Missense_Mutation	SNP	C	C	T	rs11572080	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96827030C>T	ENST00000371270.3	-	3	510	c.416G>A	c.(415-417)aGg>aAg	p.R139K	CYP2C8_ENST00000539050.1_Missense_Mutation_p.R53K|CYP2C8_ENST00000535898.1_Missense_Mutation_p.R37K	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	139			R -> K (in allele CYP2C8*3; dbSNP:rs11572080). {ECO:0000269|PubMed:11668219, ECO:0000269|PubMed:12429347, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:2729895, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	CTCAATGCTCCTCTTCCCCAT	0.483													C|||	229	0.0457268	0.0083	0.0994	5008	,	,		20114	0.001		0.1183	False		,,,				2504	0.0297				p.R139K		Atlas-SNP	.											.	CYP2C8	73	.	0			c.G416A	GRCh37	CM014700	CYP2C8	M	rs11572080	PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	108,4298	83.9+/-122.4	2,104,2097	209.0	188.0	195.0		416,206,110,206	2.8	1.0	10	dbSNP_120	195	1002,7598	215.5+/-254.8	67,868,3365	yes	missense,missense,missense,missense	CYP2C8	NM_000770.3,NM_001198853.1,NM_001198854.1,NM_001198855.1	26,26,26,26	69,972,5462	TT,TC,CC		11.6512,2.4512,8.5345	benign,benign,benign,benign	139/491,69/421,37/389,69/421	96827030	1110,11896	2203	4300	6503	SO:0001583	missense	1558	exon3			ATGCTCCTCTTCC	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"""Cytochrome P450s"""	2622	protein-coding gene	gene with protein product		601129	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"""			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.416G>A	10.37:g.96827030C>T	ENSP00000360317:p.Arg139Lys	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	251	120	0.478088	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	141	0.06456043956043957	6	0.012195121951219513	46	0.1270718232044199	2	0.0034965034965034965	87	0.11477572559366754	C	15.48	2.845990	0.51164	0.024512	0.116512	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.11712	2.75;2.75;2.75	4.64	2.8	0.32819	.	0.133357	0.49305	U	0.000147	T	0.00109	0.0003	L	0.42529	1.33	0.31880	P	0.618617	B;B;B;B	0.22080	0.052;0.015;0.064;0.015	B;B;B;B	0.33295	0.027;0.15;0.161;0.15	T	0.25117	-1.0141	9	0.30078	T	0.28	.	9.4607	0.38783	0.0:0.8256:0.0:0.1744	rs11572080;rs60090616	53;37;107;139	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	K	139;106;37;53	ENSP00000360317:R139K;ENSP00000445062:R37K;ENSP00000442343:R53K	ENSP00000360317:R139K	R	-	2	0	CYP2C8	96817020	0.078000	0.21339	0.992000	0.48379	0.983000	0.72400	0.356000	0.20181	0.594000	0.29761	0.561000	0.74099	AGG	C|0.931;T|0.069	0.069	strong		0.483	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
C15orf57	90416	hgsc.bcm.edu	37	15	40855210	40855210	+	Missense_Mutation	SNP	T	T	A	rs10152546	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40855210T>A	ENST00000358005.3	-	2	278	c.5A>T	c.(4-6)aAa>aTa	p.K2I	C15orf57_ENST00000416810.2_Missense_Mutation_p.K2I|C15orf57_ENST00000559911.1_Missense_Mutation_p.K2I|C15orf57_ENST00000561011.1_Missense_Mutation_p.K2I|C15orf57_ENST00000558871.1_Missense_Mutation_p.K2I|C15orf57_ENST00000560305.1_Missense_Mutation_p.K2I|C15orf57_ENST00000558113.1_Missense_Mutation_p.K2I|C15orf57_ENST00000560109.1_5'UTR|C15orf57_ENST00000558750.1_Missense_Mutation_p.K11I	NM_001080791.1|NM_052849.2	NP_001074260.1|NP_443081.1	Q9BV29	CO057_HUMAN	chromosome 15 open reading frame 57	2			K -> I (in dbSNP:rs10152546). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.					p.K2I(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	9						CTCAAACATTTTCATTTGGAA	0.448													T|||	1294	0.258387	0.2027	0.2925	5008	,	,		21813	0.0923		0.4742	False		,,,				2504	0.2587				p.K11I		Atlas-SNP	.											C15orf57,NS,carcinoma,0,1	C15orf57	20	1	1	Substitution - Missense(1)	stomach(1)	c.A32T						PASS	.	T	ILE/LYS,ILE/LYS,ILE/LYS	1108,3298	396.3+/-330.0	151,806,1246	115.0	122.0	119.0		32,5,5	4.1	1.0	15	dbSNP_119	119	3846,4754	540.9+/-383.9	839,2168,1293	yes	missense,missense,missense	C15orf57	NM_001080791.1,NM_001080792.1,NM_052849.2	102,102,102	990,2974,2539	AA,AT,TT		44.7209,25.1475,38.0901	probably-damaging,probably-damaging,probably-damaging	11/195,2/186,2/186	40855210	4954,8052	2203	4300	6503	SO:0001583	missense	90416	exon2			AACATTTTCATTT	BC012189	CCDS10060.1, CCDS42022.1, CCDS73706.1	15q15.1	2008-05-30	2008-05-30	2008-05-30	ENSG00000128891	ENSG00000128891			28295	protein-coding gene	gene with protein product			"""coiled-coil domain containing 32"""	CCDC32		12477932	Standard	NM_001080791		Approved	MGC20481	uc001zma.1	Q9BV29	OTTHUMG00000129993	ENST00000358005.3:c.5A>T	15.37:g.40855210T>A	ENSP00000350695:p.Lys2Ile	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_001080791	A8KAL4|Q86TC4|Q8N788|Q8NAR7	Missense_Mutation	SNP	ENST00000358005.3	37	CCDS10060.1	597	0.2733516483516483	98	0.1991869918699187	122	0.3370165745856354	38	0.06643356643356643	339	0.4472295514511873	T	8.192	0.796261	0.16327	0.251475	0.447209	ENSG00000128891	ENST00000358005;ENST00000416810	T	0.50277	0.75	5.22	4.08	0.47627	.	0.215176	0.39834	N	0.001251	T	0.00012	0.0000	L	0.48642	1.525	0.26379	P	0.9767653	B;B	0.28783	0.091;0.222	B;B	0.26202	0.039;0.067	T	0.45644	-0.9247	9	0.45353	T	0.12	-15.767	2.9313	0.05800	0.1436:0.0822:0.1497:0.6245	rs10152546;rs16970825;rs52833420;rs10152546	2;11	Q9BV29;Q9BV29-2	CO057_HUMAN;.	I	2;11	ENSP00000350695:K2I	ENSP00000350695:K2I	K	-	2	0	C15orf57	38642502	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	1.454000	0.35178	0.805000	0.34159	-0.478000	0.04885	AAA	T|0.660;A|0.340	0.340	strong		0.448	C15orf57-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252259.2	NM_052849	
ZNF211	10520	hgsc.bcm.edu	37	19	58153009	58153009	+	Silent	SNP	C	C	T	rs3746217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58153009C>T	ENST00000347302.3	+	3	1334	c.1155C>T	c.(1153-1155)atC>atT	p.I385I	ZNF211_ENST00000420680.1_Silent_p.I389I|ZNF211_ENST00000240731.4_Silent_p.I398I|ZNF211_ENST00000544273.1_Silent_p.I397I|ZNF211_ENST00000391703.3_Silent_p.I324I|ZNF211_ENST00000541801.1_Silent_p.I376I|ZNF211_ENST00000299871.5_Silent_p.I450I|ZNF211_ENST00000254182.7_Silent_p.I376I	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTAGCCTGATCTACCACCAGA	0.473													T|||	1072	0.214058	0.2352	0.1297	5008	,	,		22138	0.3214		0.159	False		,,,				2504	0.1912				p.I450I		Atlas-SNP	.											.	ZNF211	78	.	0			c.C1350T						PASS	.	T	,	979,3427	731.6+/-410.3	117,745,1341	70.0	76.0	74.0		1194,1155	-1.4	0.0	19	dbSNP_107	74	1346,7254	756.1+/-407.5	97,1152,3051	no	coding-synonymous,coding-synonymous	ZNF211	NM_006385.3,NM_198855.2	,	214,1897,4392	TT,TC,CC		15.6512,22.2197,17.8764	,	398/578,385/565	58153009	2325,10681	2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			CCTGATCTACCAC	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1155C>T	19.37:g.58153009C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	59	34	0.576271	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	37	CCDS12957.1																																																																																			C|0.789;T|0.211	0.211	strong		0.473	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
WBP4	11193	hgsc.bcm.edu	37	13	41646958	41646958	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:41646958A>G	ENST00000379487.3	+	7	927	c.527A>G	c.(526-528)gAt>gGt	p.D176G	WBP4_ENST00000542082.1_Missense_Mutation_p.D155G	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	176	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		TTAAGTGAAGATGGTTTTACC	0.343																																					p.D176G		Atlas-SNP	.											.	WBP4	40	.	0			c.A527G						PASS	.						136.0	137.0	137.0					13																	41646958		2203	4300	6503	SO:0001583	missense	11193	exon7			GTGAAGATGGTTT	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.527A>G	13.37:g.41646958A>G	ENSP00000368801:p.Asp176Gly	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_007187	B7Z4M2|Q32P29	Missense_Mutation	SNP	ENST00000379487.3	37	CCDS9375.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704428	0.88924	.	.	ENSG00000120688	ENST00000379487;ENST00000542082	D;D	0.84223	-1.82;-1.82	5.6	5.6	0.85130	WW/Rsp5/WWP (6);	0.156971	0.56097	D	0.000034	D	0.90741	0.7094	M	0.72624	2.21	0.58432	D	0.999994	P;D	0.64830	0.865;0.994	P;D	0.64595	0.57;0.927	D	0.89758	0.3945	10	0.33940	T	0.23	-16.308	15.7909	0.78364	1.0:0.0:0.0:0.0	.	155;176	B7Z4M2;O75554	.;WBP4_HUMAN	G	176;155	ENSP00000368801:D176G;ENSP00000439301:D155G	ENSP00000368801:D176G	D	+	2	0	WBP4	40544958	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.627000	0.83176	2.121000	0.65114	0.460000	0.39030	GAT	.	.	none		0.343	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187	
VAV3	10451	hgsc.bcm.edu	37	1	108185301	108185301	+	Missense_Mutation	SNP	C	C	G	rs12403266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:108185301C>G	ENST00000370056.4	-	20	2128	c.1854G>C	c.(1852-1854)caG>caC	p.Q618H	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000544443.1_Missense_Mutation_p.Q22H|VAV3_ENST00000415432.2_Missense_Mutation_p.Q58H|VAV3_ENST00000527011.1_Missense_Mutation_p.Q618H	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	618	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.|Sufficient for interaction with ROS1.		Q -> H (in dbSNP:rs12403266).		angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.Q618H(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		CGGCCTGGAGCTGTAAAGGGG	0.493													G|||	762	0.152157	0.0469	0.1671	5008	,	,		17062	0.2262		0.1302	False		,,,				2504	0.2301				p.Q618H		Atlas-SNP	.											VAV3_ENST00000415432,colon,carcinoma,-1,6	VAV3	176	6	1	Substitution - Missense(1)	stomach(1)	c.G1854C						PASS	.	G	HIS/GLN,HIS/GLN	344,4062	795.1+/-415.3	20,304,1879	113.0	111.0	112.0		174,1854	-0.4	0.7	1	dbSNP_120	112	1288,7312	758.9+/-407.5	91,1106,3103	yes	missense,missense	VAV3	NM_001079874.1,NM_006113.4	24,24	111,1410,4982	GG,GC,CC		14.9767,7.8075,12.5481	benign,benign	58/288,618/848	108185301	1632,11374	2203	4300	6503	SO:0001583	missense	10451	exon20			CTGGAGCTGTAAA	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1854G>C	1.37:g.108185301C>G	ENSP00000359073:p.Gln618His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	301|301	0.13782051282051283|0.13782051282051283	20|20	0.04065040650406504|0.04065040650406504	53|53	0.1464088397790055|0.1464088397790055	135|135	0.23601398601398602|0.23601398601398602	93|93	0.12269129287598944|0.12269129287598944	G|G	0.031|0.031	-1.336155|-1.336155	0.01287|0.01287	0.078075|0.078075	0.149767|0.149767	ENSG00000134215|ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000544443;ENST00000415432|ENST00000529809	T;T;T;T|.	0.29397|.	1.57;2.56;2.56;1.57|.	5.67|5.67	-0.382|-0.382	0.12481|0.12481	Src homology-3 domain (3);Variant SH3 (1);|.	0.485345|.	0.25294|.	N|.	0.031703|.	T|T	0.07007|0.07007	0.0178|0.0178	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	P|P	0.999999668219|0.999999668219	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.001;0.0;0.001|.	T|T	0.22277|0.22277	-1.0221|-1.0221	9|5	0.39692|0.87932	T|D	0.17|0	.|.	6.4299|6.4299	0.21790|0.21790	0.5352:0.2413:0.2235:0.0|0.5352:0.2413:0.2235:0.0	rs12403266;rs17229682;rs12403266|rs12403266;rs17229682;rs12403266	618;22;618;58|.	E9PQ97;B7Z3Z5;Q9UKW4;Q9UKW4-3|.	.;.;VAV3_HUMAN;.|.	H|T	618;618;22;58|146	ENSP00000359073:Q618H;ENSP00000432540:Q618H;ENSP00000446404:Q22H;ENSP00000394897:Q58H|.	ENSP00000359073:Q618H|ENSP00000434944:S43T	Q|S	-|-	3|2	2|0	VAV3|VAV3	107986824|107986824	0.923000|0.923000	0.31300|0.31300	0.694000|0.694000	0.30210|0.30210	0.049000|0.049000	0.14656|0.14656	-0.104000|-0.104000	0.10923|0.10923	-0.270000|-0.270000	0.09285|0.09285	-0.225000|-0.225000	0.12378|0.12378	CAG|AGC	C|0.866;G|0.134	0.134	strong		0.493	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
TRIM41	90933	hgsc.bcm.edu	37	5	180661468	180661468	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:180661468G>A	ENST00000315073.5	+	6	2296	c.1586G>A	c.(1585-1587)cGc>cAc	p.R529H	TRIM41_ENST00000351937.5_Intron|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	529	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCTCCTCGCGCCATCACCAT	0.692																																					p.R529H		Atlas-SNP	.											.	TRIM41	96	.	0			c.G1586A						PASS	.						21.0	23.0	22.0					5																	180661468		2200	4296	6496	SO:0001583	missense	90933	exon6			CCTCGCGCCATCA	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19013	protein-coding gene	gene with protein product	"""RING-finger protein that interacts with C kinase"""	610530	"""tripartite motif-containing 41"""			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1586G>A	5.37:g.180661468G>A	ENSP00000320869:p.Arg529His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_033549	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.989186	0.35131	.	.	ENSG00000146063	ENST00000315073;ENST00000438174	T	0.55413	0.52	5.32	4.45	0.53987	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.52532	D	0.000063	T	0.33731	0.0873	N	0.14661	0.345	0.27302	N	0.957547	B	0.15141	0.012	B	0.10450	0.005	T	0.19128	-1.0315	10	0.37606	T	0.19	.	9.9313	0.41523	0.0946:0.0:0.9054:0.0	.	529	Q8WV44	TRI41_HUMAN	H	529;214	ENSP00000320869:R529H	ENSP00000320869:R529H	R	+	2	0	TRIM41	180594074	0.998000	0.40836	0.955000	0.39395	0.211000	0.24417	4.196000	0.58407	1.255000	0.44051	0.449000	0.29647	CGC	.	.	none		0.692	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627	
COL13A1	1305	hgsc.bcm.edu	37	10	71678058	71678058	+	Silent	SNP	C	C	G	rs2274181	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71678058C>G	ENST00000398978.3	+	19	1506	c.1014C>G	c.(1012-1014)gcC>gcG	p.A338A	COL13A1_ENST00000356340.3_Silent_p.A338A|COL13A1_ENST00000398969.3_Silent_p.A281A|COL13A1_ENST00000398968.3_Silent_p.A319A|COL13A1_ENST00000354547.3_Silent_p.A316A|COL13A1_ENST00000517713.1_Silent_p.A316A|COL13A1_ENST00000398971.3_Silent_p.A338A|COL13A1_ENST00000398966.3_Silent_p.A316A|COL13A1_ENST00000520133.1_Silent_p.A287A|COL13A1_ENST00000398964.3_Silent_p.A309A|COL13A1_ENST00000398973.3_Silent_p.A338A|COL13A1_ENST00000520267.1_Silent_p.A281A|COL13A1_ENST00000357811.3_Silent_p.A316A|COL13A1_ENST00000398974.3_Silent_p.A326A|COL13A1_ENST00000522165.1_Silent_p.A319A|COL13A1_ENST00000398972.3_Silent_p.A338A	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						CCGGAATTGCCGTGGCTGGGA	0.597													C|||	1072	0.214058	0.0083	0.2752	5008	,	,		16449	0.2946		0.2217	False		,,,				2504	0.3579				p.A338A		Atlas-SNP	.											COL13A1_ENST00000398978,NS,carcinoma,+2,2	COL13A1	133	2	0			c.C1014G						PASS	.	C	,,,,,	169,3591		8,153,1719	47.0	50.0	49.0		1014,843,957,948,948,861	-8.5	0.0	10	dbSNP_100	49	1913,6315		216,1481,2417	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL13A1	NM_001130103.1,NM_080798.3,NM_080800.3,NM_080801.3,NM_080802.3,NM_080805.3	,,,,,	224,1634,4136	GG,GC,CC		23.2499,4.4947,17.3674	,,,,,	338/718,281/646,319/687,316/696,316/669,287/611	71678058	2082,9906	1880	4114	5994	SO:0001819	synonymous_variant	1305	exon19			AATTGCCGTGGCT	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"""Collagens"""	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.1014C>G	10.37:g.71678058C>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_001130103		Silent	SNP	ENST00000398978.3	37	CCDS44419.1																																																																																			C|0.804;G|0.196	0.196	strong		0.597	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203	
SPNS3	201305	hgsc.bcm.edu	37	17	4391153	4391153	+	Silent	SNP	A	A	G	rs333122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4391153A>G	ENST00000355530.2	+	12	1783	c.1503A>G	c.(1501-1503)ctA>ctG	p.L501L	SPNS3_ENST00000333476.2_Silent_p.L374L|RP13-580F15.2_ENST00000576086.1_RNA	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	501					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.L501L(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						GACAAGGCCTACTTTCGGGCG	0.622													G|||	869	0.173522	0.1256	0.1729	5008	,	,		18292	0.0446		0.3171	False		,,,				2504	0.2239				p.L501L		Atlas-SNP	.											SPNS3,NS,carcinoma,0,1	SPNS3	52	1	1	Substitution - coding silent(1)	stomach(1)	c.A1503G						PASS	.	G		626,3780	767.8+/-413.5	50,526,1627	114.0	104.0	107.0		1503	1.2	0.0	17	dbSNP_79	107	2537,6063	692.6+/-404.6	364,1809,2127	no	coding-synonymous	SPNS3	NM_182538.4		414,2335,3754	GG,GA,AA		29.5,14.2079,24.3195		501/513	4391153	3163,9843	2203	4300	6503	SO:0001819	synonymous_variant	201305	exon12			AGGCCTACTTTCG		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.1503A>G	17.37:g.4391153A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	151	69	0.456954	NM_182538	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																			A|0.784;G|0.216	0.216	strong		0.622	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
BRDT	676	hgsc.bcm.edu	37	1	92445257	92445257	+	Missense_Mutation	SNP	C	C	G	rs3088232	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:92445257C>G	ENST00000362005.3	+	9	1648	c.1230C>G	c.(1228-1230)aaC>aaG	p.N410K	BRDT_ENST00000370389.2_Missense_Mutation_p.N337K|BRDT_ENST00000394530.3_Missense_Mutation_p.N364K|BRDT_ENST00000399546.2_Missense_Mutation_p.N410K|BRDT_ENST00000402388.1_Missense_Mutation_p.N410K	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	410			N -> K (in dbSNP:rs3088232). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		CTGAAGGGAACTCTTCTGATG	0.398													C|||	653	0.130391	0.0242	0.2392	5008	,	,		15081	0.0278		0.2167	False		,,,				2504	0.2137				p.N414K		Atlas-SNP	.											.	BRDT	133	.	0			c.C1242G						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN	260,4146	149.9+/-184.0	7,246,1950	110.0	108.0	109.0		1230,1242,1092,1092,1011,1230,1230	3.8	0.9	1	dbSNP_102	109	2137,6463	368.2+/-335.0	259,1619,2422	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	94,94,94,94,94,94,94	266,1865,4372	GG,GC,CC		24.8488,5.901,18.43	benign,benign,benign,benign,benign,benign,benign	410/948,414/952,364/902,364/902,337/875,410/948,410/948	92445257	2397,10609	2203	4300	6503	SO:0001583	missense	676	exon8			AGGGAACTCTTCT	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.1230C>G	1.37:g.92445257C>G	ENSP00000354568:p.Asn410Lys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	176	63	0.357955	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	293	0.13415750915750915	20	0.04065040650406504	78	0.2154696132596685	18	0.03146853146853147	177	0.23350923482849603	C	8.787	0.929564	0.18131	0.05901	0.248488	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.09255	3.31;3.31;3.31;3.36;3.0;3.31	5.65	3.76	0.43208	.	0.950790	0.08804	N	0.891225	T	0.02304	0.0071	L	0.27053	0.805	0.37695	P	0.07602399999999998	B;B;B;B	0.15473	0.003;0.003;0.013;0.003	B;B;B;B	0.12156	0.002;0.002;0.007;0.002	T	0.44065	-0.9352	9	0.51188	T	0.08	-0.8136	2.5253	0.04689	0.1655:0.5348:0.1407:0.159	rs3088232;rs52821661;rs3088232	364;364;414;410	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	K	410;337;410;410;364;410;410	ENSP00000354568:N410K;ENSP00000359416:N337K;ENSP00000387822:N410K;ENSP00000378038:N364K;ENSP00000404969:N410K;ENSP00000384051:N410K	ENSP00000354568:N410K	N	+	3	2	BRDT	92217845	0.022000	0.18835	0.889000	0.34880	0.201000	0.24016	0.236000	0.17967	0.728000	0.32382	0.655000	0.94253	AAC	C|0.838;G|0.162	0.162	strong		0.398	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
FAM20A	54757	hgsc.bcm.edu	37	17	66596463	66596463	+	Silent	SNP	C	C	T	rs986099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:66596463C>T	ENST00000592554.1	-	1	1067	c.345G>A	c.(343-345)tcG>tcA	p.S115S		NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	115					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					TGGCCAGGAGCGAGTCCTCGG	0.716													c|||	849	0.169529	0.0961	0.2522	5008	,	,		12777	0.2748		0.163	False		,,,				2504	0.1084				p.S115S		Atlas-SNP	.											.	FAM20A	35	.	0			c.G345A						PASS	.			375,3867		18,339,1764	5.0	8.0	7.0		345	1.2	1.0	17	dbSNP_86	7	1255,7133		85,1085,3024	no	coding-synonymous	FAM20A	NM_017565.3		103,1424,4788	TT,TC,CC		14.9619,8.8402,12.9058		115/542	66596463	1630,11000	2121	4194	6315	SO:0001819	synonymous_variant	54757	exon1			CAGGAGCGAGTCC	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.345G>A	17.37:g.66596463C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_017565	B2RN47|B2RN49|Q9UF95	Silent	SNP	ENST00000592554.1	37	CCDS11679.1																																																																																			C|0.816;T|0.184	0.184	strong		0.716	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
ZIM3	114026	hgsc.bcm.edu	37	19	57646570	57646570	+	Missense_Mutation	SNP	T	T	C	rs4801433	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57646570T>C	ENST00000269834.1	-	5	1520	c.1135A>G	c.(1135-1137)Att>Gtt	p.I379V	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	379			I -> V (in dbSNP:rs4801433).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTATGTTGAATGAGGTTTTTC	0.378													T|||	2116	0.422524	0.2678	0.4741	5008	,	,		18716	0.3621		0.5149	False		,,,				2504	0.5624				p.I379V		Atlas-SNP	.											.	ZIM3	107	.	0			c.A1135G						PASS	.	T	VAL/ILE	1368,3038	451.6+/-349.7	220,928,1055	117.0	120.0	119.0		1135	1.7	0.3	19	dbSNP_111	119	4577,4023	596.9+/-393.7	1244,2089,967	yes	missense	ZIM3	NM_052882.1	29	1464,3017,2022	CC,CT,TT		46.7791,31.0486,45.7097	probably-damaging	379/473	57646570	5945,7061	2203	4300	6503	SO:0001583	missense	114026	exon5			GTTGAATGAGGTT	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"""Zinc fingers, C2H2-type"", ""-"""	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.1135A>G	19.37:g.57646570T>C	ENSP00000269834:p.Ile379Val	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	175	78	0.445714	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	884	0.40476190476190477	118	0.23983739837398374	182	0.5027624309392266	208	0.36363636363636365	376	0.49604221635883905	T	0.071	-1.202238	0.01581	0.310486	0.532209	ENSG00000141946	ENST00000269834	T	0.07216	3.21	2.71	1.68	0.24146	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.11154	0.105	0.80722	P	0.0	D	0.56968	0.978	D	0.67548	0.952	T	0.37776	-0.9691	8	0.40728	T	0.16	.	5.6843	0.17794	0.0:0.1502:0.0:0.8498	rs4801433;rs17207642;rs52814763;rs61115896;rs4801433	379	Q96PE6	ZIM3_HUMAN	V	379	ENSP00000269834:I379V	ENSP00000269834:I379V	I	-	1	0	ZIM3	62338382	0.000000	0.05858	0.326000	0.25389	0.471000	0.32888	-0.574000	0.05868	1.237000	0.43756	0.260000	0.18958	ATT	C|0.425;N|0.000	0.425	strong		0.378	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
RARS	5917	hgsc.bcm.edu	37	5	167919726	167919726	+	Silent	SNP	A	A	G	rs2305727	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:167919726A>G	ENST00000231572.3	+	3	297	c.243A>G	c.(241-243)caA>caG	p.Q81Q	RARS_ENST00000538719.1_5'UTR	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	81					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		GCCGCCTACAAGAGGTCTTTG	0.408													A|||	372	0.0742812	0.0091	0.0908	5008	,	,		18589	0.0645		0.1799	False		,,,				2504	0.0521				p.Q81Q		Atlas-SNP	.											RARS,NS,carcinoma,+1,1	RARS	58	1	0			c.A243G						PASS	.	A		160,4246	108.2+/-146.6	2,156,2045	117.0	117.0	117.0		243	-4.8	0.0	5	dbSNP_100	117	1627,6973	300.5+/-305.0	162,1303,2835	no	coding-synonymous	RARS	NM_002887.3		164,1459,4880	GG,GA,AA		18.9186,3.6314,13.7398		81/661	167919726	1787,11219	2203	4300	6503	SO:0001819	synonymous_variant	5917	exon3			CCTACAAGAGGTC	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.243A>G	5.37:g.167919726A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	37	CCDS4367.1																																																																																			A|0.881;G|0.119	0.119	strong		0.408	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
AGTR2	186	hgsc.bcm.edu	37	X	115303837	115303837	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:115303837A>C	ENST00000371906.4	+	3	494	c.304A>C	c.(304-306)Acc>Ccc	p.T102P		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	102					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	TCTATGGGCAACCTATTATTC	0.378																																					p.T102P		Atlas-SNP	.											.	AGTR2	62	.	0			c.A304C						PASS	.						177.0	172.0	174.0					X																	115303837		2203	4300	6503	SO:0001583	missense	186	exon3			TGGGCAACCTATT	AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"""GPCR / Class A : Angiotensin receptors"""	338	protein-coding gene	gene with protein product		300034	"""angiotensin receptor 2"""			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.304A>C	X.37:g.115303837A>C	ENSP00000360973:p.Thr102Pro	Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	181	52	0.287293	NM_000686	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.235143	0.39498	.	.	ENSG00000180772	ENST00000371906	T	0.37584	1.19	4.48	2.01	0.26516	GPCR, rhodopsin-like superfamily (1);	0.327695	0.32459	N	0.006071	T	0.47838	0.1467	M	0.82630	2.6	0.29718	N	0.8389	B	0.33777	0.425	P	0.48227	0.571	T	0.48525	-0.9028	10	0.37606	T	0.19	-0.9265	4.2699	0.10782	0.7194:0.0:0.1019:0.1787	.	102	P50052	AGTR2_HUMAN	P	102	ENSP00000360973:T102P	ENSP00000360973:T102P	T	+	1	0	AGTR2	115217865	0.000000	0.05858	0.995000	0.50966	0.995000	0.86356	0.792000	0.26929	0.122000	0.18314	0.412000	0.27726	ACC	.	.	none		0.378	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686	
KIAA2018	205717	hgsc.bcm.edu	37	3	113379865	113379865	+	Missense_Mutation	SNP	G	G	C	rs9866806	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:113379865G>C	ENST00000478658.1	-	5	681	c.664C>G	c.(664-666)Cct>Gct	p.P222A	KIAA2018_ENST00000316407.4_Missense_Mutation_p.P222A|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	222			P -> A (in dbSNP:rs9866806). {ECO:0000269|PubMed:17974005}.			membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						AGAGGAACAGGCTGGTTGGTA	0.483													G|||	1035	0.206669	0.1536	0.1758	5008	,	,		18612	0.2004		0.3519	False		,,,				2504	0.1575				p.P222A		Atlas-SNP	.											KIAA2018,NS,carcinoma,+1,1	KIAA2018	180	1	0			c.C664G						PASS	.	G	ALA/PRO	577,3327		48,481,1423	65.0	70.0	68.0		664	3.0	1.0	3	dbSNP_119	68	2765,5539		483,1799,1870	yes	missense	KIAA2018	NM_001009899.2	27	531,2280,3293	CC,CG,GG		33.2972,14.7797,27.3755	benign	222/2246	113379865	3342,8866	1952	4152	6104	SO:0001583	missense	205717	exon7			GAACAGGCTGGTT	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.664C>G	3.37:g.113379865G>C	ENSP00000420721:p.Pro222Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	564	0.25824175824175827	78	0.15853658536585366	76	0.20994475138121546	120	0.2097902097902098	290	0.38258575197889183	G	7.481	0.648761	0.14516	0.147797	0.332972	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.13307	2.6;2.6	5.43	3.04	0.35103	.	0.486738	0.19311	N	0.117389	T	0.00012	0.0000	N	0.08118	0	0.37600	P	0.07947800000000005	B	0.24483	0.104	B	0.18871	0.023	T	0.48768	-0.9006	9	0.40728	T	0.16	-7.8482	1.794	0.03057	0.2708:0.1415:0.4432:0.1445	rs9866806;rs17326610;rs52791201;rs56479814;rs9866806	222	Q68DE3	K2018_HUMAN	A	222	ENSP00000320794:P222A;ENSP00000420721:P222A	ENSP00000320794:P222A	P	-	1	0	KIAA2018	114862555	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.716000	0.25836	1.179000	0.42884	0.655000	0.94253	CCT	G|0.747;C|0.253	0.253	strong		0.483	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
OR5W2	390148	hgsc.bcm.edu	37	11	55681336	55681336	+	Silent	SNP	G	G	A	rs11231529	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55681336G>A	ENST00000344514.1	-	1	722	c.723C>T	c.(721-723)tgC>tgT	p.C241C		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGTGGGAAGTGCATGTAGAGA	0.408													G|||	1320	0.263578	0.3434	0.3112	5008	,	,		17093	0.1438		0.329	False		,,,				2504	0.1779				p.C241C	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.C723T						PASS	.	G		1620,2782	497.1+/-363.7	300,1020,881	82.0	93.0	89.0		723	-3.8	0.1	11	dbSNP_120	89	3007,5585	464.8+/-366.3	545,1917,1834	no	coding-synonymous	OR5W2	NM_001001960.1		845,2937,2715	AA,AG,GG		34.9977,36.8015,35.6087		241/311	55681336	4627,8367	2201	4296	6497	SO:0001819	synonymous_variant	390148	exon1			GGAAGTGCATGTA	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.723C>T	11.37:g.55681336G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	155	81	0.522581	NM_001001960		Silent	SNP	ENST00000344514.1	37	CCDS31513.1																																																																																			G|0.677;A|0.323	0.323	strong		0.408	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
NUDT7	283927	hgsc.bcm.edu	37	16	77769834	77769834	+	Missense_Mutation	SNP	G	G	A	rs308925	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:77769834G>A	ENST00000268533.5	+	3	368	c.299G>A	c.(298-300)cGt>cAt	p.R100H	NUDT7_ENST00000564085.1_Missense_Mutation_p.R100H|NUDT7_ENST00000568787.1_Missense_Mutation_p.R100H|NUDT7_ENST00000563839.1_Intron|NUDT7_ENST00000437314.3_Intron	NM_001105663.2	NP_001099133.1	P0C024	NUDT7_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 7	100	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.		R -> H (in dbSNP:rs308925).		acetyl-CoA catabolic process (GO:0046356)|brown fat cell differentiation (GO:0050873)|coenzyme A catabolic process (GO:0015938)|nucleoside diphosphate metabolic process (GO:0009132)	peroxisome (GO:0005777)	acetyl-CoA hydrolase activity (GO:0003986)|hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides (GO:0016818)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|receptor binding (GO:0005102)|snoRNA binding (GO:0030515)			breast(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|skin(1)	18						GTGGGTCTCCGTCCTCACCAA	0.572													G|||	1164	0.232428	0.1157	0.2075	5008	,	,		15914	0.2778		0.2336	False		,,,				2504	0.3599				p.R100H		Atlas-SNP	.											.	NUDT7	47	.	0			c.G299A						PASS	.	G	HIS/ARG	473,3621		30,413,1604	113.0	120.0	118.0		299	-3.4	0.0	16	dbSNP_79	118	1410,6976		117,1176,2900	yes	missense	NUDT7	NM_001105663.2	29	147,1589,4504	AA,AG,GG		16.8137,11.5535,15.0881	benign	100/239	77769834	1883,10597	2047	4193	6240	SO:0001583	missense	283927	exon3			GTCTCCGTCCTCA	AA227330	CCDS42195.1, CCDS58480.1, CCDS58479.1, CCDS73916.1	16q23.1	2007-06-15				ENSG00000140876		"""Nudix motif containing"""	8054	protein-coding gene	gene with protein product		609231				11415433	Standard	NM_001105663		Approved		uc010chd.3	P0C024		ENST00000268533.5:c.299G>A	16.37:g.77769834G>A	ENSP00000268533:p.Arg100His	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	174	82	0.471264	NM_001243657	B4DLE5|H3BUB8	Missense_Mutation	SNP	ENST00000268533.5	37	CCDS42195.1	481	0.22023809523809523	62	0.12601626016260162	70	0.19337016574585636	167	0.291958041958042	182	0.24010554089709762	G	6.335	0.429953	0.11987	0.115535	0.168137	ENSG00000140876	ENST00000268533	T	0.08807	3.05	5.72	-3.44	0.04796	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	1.158930	0.06024	N	0.651727	T	0.00012	0.0000	N	0.05078	-0.115	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.48490	-0.9031	9	0.23302	T	0.38	0.1902	13.0348	0.58864	0.4973:0.0:0.5027:0.0	rs308925;rs17773575;rs52819583;rs59180982;rs308925	100	P0C024	NUDT7_HUMAN	H	100	ENSP00000268533:R100H	ENSP00000268533:R100H	R	+	2	0	NUDT7	76327335	0.000000	0.05858	0.021000	0.16686	0.161000	0.22273	-2.239000	0.01198	-1.072000	0.03141	-0.133000	0.14855	CGT	G|0.801;N|0.001	.	strong		0.572	NUDT7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433873.1		
ARHGAP8	23779	hgsc.bcm.edu	37	22	45255688	45255688	+	Missense_Mutation	SNP	C	C	T	rs73176189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45255688C>T	ENST00000389774.2	+	12	1189	c.1048C>T	c.(1048-1050)Cgc>Tgc	p.R350C	ARHGAP8_ENST00000517296.3_Missense_Mutation_p.R529C|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.R450C|ARHGAP8_ENST00000336963.4_Intron|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.R529C|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.R441C|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.R319C	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	350	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CGTCGTCCTCCGCTACCTCAT	0.652													c|||	16	0.00319489	0.0008	0.0014	5008	,	,		19710	0.001		0.0099	False		,,,				2504	0.0031				p.R441C		Atlas-SNP	.											PRR5-ARHGAP8,caecum,carcinoma,0,2	PRR5-ARHGAP8	53	2	0			c.C1321T						PASS	.	T	CYS/ARG,,CYS/ARG,CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	80.0	67.0	71.0		1048,,1321,955	-5.2	0.5	22	dbSNP_130	71	18,8582	11.9+/-42.8	0,18,4282	yes	missense,intron,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	180,,180,180	0,23,6480	TT,TC,CC		0.2093,0.1135,0.1768	benign,,benign,benign	350/465,,441/556,319/434	45255688	23,12983	2203	4300	6503	SO:0001583	missense	553158	exon14			GTCCTCCGCTACC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1048C>T	22.37:g.45255688C>T	ENSP00000374424:p.Arg350Cys	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	c	5.988	0.366197	0.11352	0.001135	0.002093	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000356099	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01	4.14	-5.19	0.02832	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	1.659120	0.04129	N	0.317650	T	0.13200	0.0320	L	0.28014	0.82	0.29807	N	0.831972	B;D;B;D;P	0.76494	0.03;0.999;0.033;0.989;0.56	B;P;B;B;B	0.50617	0.008;0.646;0.013;0.337;0.032	T	0.27088	-1.0084	10	0.52906	T	0.07	.	5.1071	0.14790	0.4424:0.3917:0.0766:0.0893	.	372;355;350;529;450	B7ZMA4;A2RU51;P85298;B1AHC4;B1AHC3	.;.;RHG08_HUMAN;.;.	C	450;529;529;441;350;319	ENSP00000354732:R450C;ENSP00000262731:R529C;ENSP00000429240:R529C;ENSP00000374423:R441C;ENSP00000374424:R350C;ENSP00000348407:R319C	ENSP00000348407:R319C	R	+	1	0	PRR5-ARHGAP8;ARHGAP8	43634352	0.427000	0.25514	0.455000	0.27031	0.005000	0.04900	0.560000	0.23500	-1.150000	0.02840	-1.499000	0.00960	CGC	C|0.998;T|0.002	0.002	strong		0.652	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
NEK1	4750	hgsc.bcm.edu	37	4	170477125	170477125	+	Missense_Mutation	SNP	G	G	A	rs34540355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:170477125G>A	ENST00000439128.2	-	16	2028	c.1388C>T	c.(1387-1389)gCt>gTt	p.A463V	NEK1_ENST00000507142.1_Missense_Mutation_p.A463V|NEK1_ENST00000510533.1_Missense_Mutation_p.A463V|NEK1_ENST00000511633.1_Missense_Mutation_p.A463V|NEK1_ENST00000512193.1_Missense_Mutation_p.A438V	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	463			A -> V (in dbSNP:rs34540355). {ECO:0000269|PubMed:17344846}.		cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TTTCCATTTAGCTTCATTATC	0.388													G|||	81	0.0161741	0.0008	0.0317	5008	,	,		19501	0.0		0.0497	False		,,,				2504	0.0082				p.A463V		Atlas-SNP	.											.	NEK1	203	.	0			c.C1388T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	38,3678		1,36,1821	158.0	142.0	147.0		1388,1388,1313,1388,1388	4.0	0.2	4	dbSNP_126	147	470,7746		11,448,3649	yes	missense,missense,missense,missense,missense	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	64,64,64,64,64	12,484,5470	AA,AG,GG		5.7205,1.0226,4.2575	benign,benign,benign,benign,benign	463/1287,463/1243,438/1190,463/1215,463/1259	170477125	508,11424	1858	4108	5966	SO:0001583	missense	4750	exon16			CATTTAGCTTCAT	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.1388C>T	4.37:g.170477125G>A	ENSP00000408020:p.Ala463Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_012224	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	47	0.02152014652014652	0	0.0	14	0.03867403314917127	0	0.0	33	0.04353562005277045	G	12.30	1.896204	0.33442	0.010226	0.057205	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.69561	-0.38;-0.32;-0.34;-0.41;-0.36	5.66	3.95	0.45737	.	0.279103	0.30949	N	0.008542	T	0.14141	0.0342	L	0.53249	1.67	0.26899	N	0.967153	B;B;B;B;B;B	0.15473	0.002;0.004;0.013;0.01;0.013;0.01	B;B;B;B;B;B	0.21546	0.005;0.011;0.035;0.011;0.035;0.006	T	0.19745	-1.0296	10	0.31617	T	0.26	.	9.2614	0.37614	0.2176:0.0:0.7824:0.0	rs34540355	463;438;463;463;463;463	Q96PY6-5;Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;.;NEK1_HUMAN	V	463;463;463;463;438	ENSP00000408020:A463V;ENSP00000423332:A463V;ENSP00000427653:A463V;ENSP00000424757:A463V;ENSP00000424938:A438V	ENSP00000408020:A463V	A	-	2	0	NEK1	170713700	0.731000	0.28111	0.249000	0.24280	0.796000	0.44982	1.494000	0.35616	0.767000	0.33267	0.585000	0.79938	GCT	G|0.975;A|0.025	0.025	strong		0.388	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
SLX4	84464	hgsc.bcm.edu	37	16	3639827	3639827	+	Missense_Mutation	SNP	G	G	A	rs3810813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3639827G>A	ENST00000294008.3	-	12	4452	c.3812C>T	c.(3811-3813)tCc>tTc	p.S1271F		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1271	Interaction with PLK1 and TERF2-TERF2IP.		S -> F (in dbSNP:rs3810813). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TTGGGTCTGGGAAGAACAGTC	0.652								Direct reversal of damage					G|||	315	0.0628994	0.0	0.0663	5008	,	,		15111	0.1429		0.0537	False		,,,				2504	0.0726				p.S1271F		Atlas-SNP	.											SLX4,colon,carcinoma,0,1	SLX4	173	1	0			c.C3812T						PASS	.	G	PHE/SER	58,4336	46.7+/-81.2	0,58,2139	75.0	75.0	75.0		3812	5.1	0.9	16	dbSNP_107	75	469,8131	129.2+/-187.3	12,445,3843	yes	missense	SLX4	NM_032444.2	155	12,503,5982	AA,AG,GG		5.4535,1.32,4.0557	probably-damaging	1271/1835	3639827	527,12467	2197	4300	6497	SO:0001583	missense	84464	exon12			GTCTGGGAAGAAC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.3812C>T	16.37:g.3639827G>A	ENSP00000294008:p.Ser1271Phe	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	163	0.07463369963369963	0	0.0	27	0.07458563535911603	90	0.15734265734265734	46	0.06068601583113457	G	19.87	3.907943	0.72868	0.0132	0.054535	ENSG00000188827	ENST00000294008	T	0.36340	1.26	6.07	5.11	0.69529	.	0.284216	0.30649	N	0.009179	T	0.00300	0.0009	L	0.59436	1.845	0.34090	P	0.33942399999999995	D	0.76494	0.999	D	0.68765	0.96	T	0.02975	-1.1087	9	0.87932	D	0	.	12.1585	0.54091	0.0775:0.0:0.9225:0.0	rs3810813;rs17183645;rs52833846;rs3810813	1271	Q8IY92	SLX4_HUMAN	F	1271	ENSP00000294008:S1271F	ENSP00000294008:S1271F	S	-	2	0	SLX4	3579828	0.909000	0.30893	0.866000	0.34008	0.792000	0.44763	3.057000	0.49931	2.884000	0.98904	0.655000	0.94253	TCC	G|0.943;A|0.057	0.057	strong		0.652	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
CHI3L1	1116	hgsc.bcm.edu	37	1	203152801	203152801	+	Missense_Mutation	SNP	T	T	C	rs880633	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:203152801T>C	ENST00000255409.3	-	5	558	c.433A>G	c.(433-435)Aga>Gga	p.R145G		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	145			R -> G (in dbSNP:rs880633). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						TGTTTGTCTCTCCGTCCAGGG	0.582													T|||	1868	0.373003	0.1747	0.3343	5008	,	,		22710	0.3839		0.5417	False		,,,				2504	0.4836				p.R145G		Atlas-SNP	.											.	CHI3L1	51	.	0			c.A433G						PASS	.	T	GLY/ARG	968,3438	366.6+/-317.9	92,784,1327	134.0	106.0	116.0		433	5.7	0.5	1	dbSNP_86	116	4422,4178	586.2+/-392.0	1144,2134,1022	yes	missense	CHI3L1	NM_001276.2	125	1236,2918,2349	CC,CT,TT		48.5814,21.97,41.4424	benign	145/384	203152801	5390,7616	2203	4300	6503	SO:0001583	missense	1116	exon5			TGTCTCTCCGTCC	BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.433A>G	1.37:g.203152801T>C	ENSP00000255409:p.Arg145Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_001276	B2R7B0|P30923|Q8IVA4|Q96HI7	Missense_Mutation	SNP	ENST00000255409.3	37	CCDS1435.1	817	0.3740842490842491	82	0.16666666666666666	130	0.35911602209944754	204	0.35664335664335667	401	0.5290237467018469	T	12.34	1.907189	0.33628	0.2197	0.514186	ENSG00000133048	ENST00000255409	T	0.05447	3.44	5.69	5.69	0.88448	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.093728	0.47093	D	0.000247	T	0.00012	0.0000	M	0.73430	2.235	0.29869	P	0.826959	P	0.45044	0.849	B	0.36186	0.219	T	0.40098	-0.9581	9	0.87932	D	0	-17.9582	13.9002	0.63799	0.0:0.0:0.0:1.0	rs880633;rs17531391;rs17853825;rs17853876;rs52821800;rs58661966;rs880633	145	P36222	CH3L1_HUMAN	G	145	ENSP00000255409:R145G	ENSP00000255409:R145G	R	-	1	2	CHI3L1	201419424	0.970000	0.33590	0.457000	0.27056	0.358000	0.29455	1.716000	0.37981	2.153000	0.67306	0.533000	0.62120	AGA	C|0.391;N|0.001	0.391	strong		0.582	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276	
OR5D13	390142	hgsc.bcm.edu	37	11	55541284	55541284	+	Missense_Mutation	SNP	G	G	A	rs11230983	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55541284G>A	ENST00000361760.1	+	1	371	c.371G>A	c.(370-372)cGt>cAt	p.R124H		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	124			R -> H (in dbSNP:rs11230983).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R124H(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				GCTTATGACCGTTTTGTGGCA	0.438													A|||	514	0.102636	0.0514	0.0994	5008	,	,		20064	0.1448		0.1223	False		,,,				2504	0.1104				p.R124H		Atlas-SNP	.											OR5D13,caecum,carcinoma,0,2	OR5D13	96	2	1	Substitution - Missense(1)	stomach(1)	c.G371A						PASS	.	A	HIS/ARG	241,4159	804.0+/-415.7	10,221,1969	238.0	231.0	234.0		371	2.4	0.1	11	dbSNP_120	234	1021,7571	771.9+/-407.7	56,909,3331	yes	missense	OR5D13	NM_001001967.1	29	66,1130,5300	AA,AG,GG		11.8831,5.4773,9.7137	benign	124/315	55541284	1262,11730	2200	4296	6496	SO:0001583	missense	390142	exon1			ATGACCGTTTTGT	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"""GPCR / Class A : Olfactory receptors"""	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.371G>A	11.37:g.55541284G>A	ENSP00000354800:p.Arg124His	Somatic	389	1	0.00257069		WXS	Illumina HiSeq	Phase_I	362	181	0.5	NM_001001967	Q6IF68|Q6IFC9	Missense_Mutation	SNP	ENST00000361760.1	37	CCDS31507.1	250	0.11446886446886446	30	0.06097560975609756	33	0.09116022099447514	87	0.1520979020979021	100	0.13192612137203166	A	9.062	0.994853	0.19043	0.054773	0.118831	ENSG00000198877	ENST00000361760	T	0.77489	-1.1	3.3	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.339612	0.16661	N	0.204770	T	0.01320	0.0043	M	0.83384	2.64	0.49299	P	2.2500000000003073E-4	B	0.16166	0.016	B	0.17098	0.017	T	0.51505	-0.8697	9	0.62326	D	0.03	-0.0508	11.9762	0.53094	0.1038:0.0:0.8962:0.0	rs11230983;rs52789774;rs58654024;rs11230983	124	Q8NGL4	OR5DD_HUMAN	H	124	ENSP00000354800:R124H	ENSP00000354800:R124H	R	+	2	0	OR5D13	55297860	0.199000	0.23386	0.079000	0.20413	0.000000	0.00434	2.879000	0.48522	0.251000	0.21505	-1.682000	0.00735	CGT	G|0.898;A|0.102	0.102	strong		0.438	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967	
OR13C5	138799	hgsc.bcm.edu	37	9	107361460	107361460	+	Missense_Mutation	SNP	G	G	A	rs116283639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107361460G>A	ENST00000374779.2	-	1	328	c.235C>T	c.(235-237)Ccc>Tcc	p.P79S		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AGCGTGGAGGGAATAGAGGTG	0.498																																					p.P79S		Atlas-SNP	.											.	OR13C5	60	.	0			c.C235T						PASS	.						13.0	23.0	19.0					9																	107361460		2094	4253	6347	SO:0001583	missense	138799	exon1			TGGAGGGAATAGA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.235C>T	9.37:g.107361460G>A	ENSP00000363911:p.Pro79Ser	Somatic	719	1	0.00139082		WXS	Illumina HiSeq	Phase_I	588	92	0.156463	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	1360	0.6227106227106227	323	0.6565040650406504	203	0.5607734806629834	514	0.8986013986013986	320	0.42216358839050133	A	17.41	3.383650	0.61845	.	.	ENSG00000255800	ENST00000374779	T	0.01854	4.6	4.03	-7.31	0.01441	GPCR, rhodopsin-like superfamily (1);	0.212137	0.23448	N	0.048080	T	0.00012	0.0000	H	0.96365	3.81	0.80722	P	0.0	D	0.60160	0.987	D	0.65010	0.931	T	0.51140	-0.8743	9	0.72032	D	0.01	.	5.005	0.14284	0.0793:0.0989:0.3269:0.4948	.	79	Q8NGS8	O13C5_HUMAN	S	79	ENSP00000363911:P79S	ENSP00000363911:P79S	P	-	1	0	OR13C5	106401281	0.413000	0.25400	0.000000	0.03702	0.241000	0.25554	0.659000	0.24994	-2.424000	0.00561	-1.535000	0.00915	CCC	G|0.417;A|0.583	0.583	strong		0.498	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
NARFL	64428	hgsc.bcm.edu	37	16	784765	784765	+	Silent	SNP	C	C	T	rs9928077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:784765C>T	ENST00000251588.2	-	5	562	c.546G>A	c.(544-546)gcG>gcA	p.A182A	NARFL_ENST00000301694.5_Missense_Mutation_p.R138H|NARFL_ENST00000568545.1_Silent_p.A80A|NARFL_ENST00000540986.1_Silent_p.A80A|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000569604.1_3'UTR	NM_022493.1	NP_071938.1	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	182					hematopoietic progenitor cell differentiation (GO:0002244)|iron-sulfur cluster assembly (GO:0016226)|oxygen homeostasis (GO:0032364)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|large_intestine(1)|lung(7)	9		Hepatocellular(780;0.0218)				GCAGGGGCAGCGCCTGTCTGC	0.597													C|||	1886	0.376597	0.149	0.464	5008	,	,		17362	0.6736		0.2406	False		,,,				2504	0.456				p.A182A		Atlas-SNP	.											NARFL,NS,carcinoma,0,1	NARFL	31	1	0			c.G546A						PASS	.	C		560,3840	246.8+/-255.3	31,498,1671	73.0	82.0	79.0		546	3.8	1.0	16	dbSNP_119	79	1831,6769	329.0+/-318.6	201,1429,2670	no	coding-synonymous	NARFL	NM_022493.1		232,1927,4341	TT,TC,CC		21.2907,12.7273,18.3923		182/477	784765	2391,10609	2200	4300	6500	SO:0001819	synonymous_variant	64428	exon5			GGGCAGCGCCTGT	AY129231	CCDS10425.1	16p13.3	2009-12-17			ENSG00000103245	ENSG00000103245			14179	protein-coding gene	gene with protein product	"""iron-only hydrogenase-like protein 1"""	611118				16956324	Standard	NM_022493		Approved	FLJ21988, PRN, HPRN, IOP1	uc002cjr.3	Q9H6Q4	OTTHUMG00000122093	ENST00000251588.2:c.546G>A	16.37:g.784765C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	187	95	0.508021	NM_022493	A1L385|B3KTJ3|Q53GC6|Q96S10|Q9H6J8	Silent	SNP	ENST00000251588.2	37	CCDS10425.1	820	0.37545787545787546	71	0.1443089430894309	149	0.4116022099447514	398	0.6958041958041958	202	0.26649076517150394	C	10.53	1.375962	0.24857	0.127273	0.212907	ENSG00000103245	ENST00000301694	T	0.30448	1.53	4.79	3.84	0.44239	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46927	P	7.420000000000204E-4	P	0.42078	0.77	B	0.33750	0.169	T	0.14420	-1.0473	7	0.46703	T	0.11	-20.9669	9.771	0.40589	0.0801:0.1424:0.7775:0.0	rs9928077;rs9928077	138	B4DEE7	.	H	138	ENSP00000301694:R138H	ENSP00000301694:R138H	R	-	2	0	NARFL	724766	0.999000	0.42202	0.983000	0.44433	0.135000	0.20990	1.588000	0.36633	1.020000	0.39573	-0.299000	0.09455	CGC	C|0.740;T|0.260	0.260	strong		0.597	NARFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242855.1	NM_022493	
PCDHA5	56143	hgsc.bcm.edu	37	5	140203432	140203432	+	Missense_Mutation	SNP	C	C	T	rs4141841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140203432C>T	ENST00000529859.1	+	1	2072	c.2072C>T	c.(2071-2073)gCc>gTc	p.A691V	PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.A691V|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.A691V|PCDHA1_ENST00000504120.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	691			A -> V (in dbSNP:rs4141841).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCGAGGCTGCCCTGGTGGAT	0.677													.|||	2675	0.534145	0.5106	0.5922	5008	,	,		16194	0.5317		0.5378	False		,,,				2504	0.5235				p.A691V		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C2072T						PASS	.	C	,,,,VAL/ALA,,VAL/ALA	2306,2100	588.0+/-386.8	597,1112,494	54.0	57.0	56.0		,,,,2072,,2072	3.9	0.2	5	dbSNP_110	56	4540,4058	580.4+/-391.1	1195,2150,954	no	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,64,,64	1792,3262,1448	TT,TC,CC		47.197,47.6623,47.3547	,,,,,,	,,,,691/937,,691/817	140203432	6846,6158	2203	4299	6502	SO:0001583	missense	56143	exon1			AGGCTGCCCTGGT	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2072C>T	5.37:g.140203432C>T	ENSP00000436557:p.Ala691Val	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	132	48	0.363636	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	1174	0.5375457875457875	262	0.532520325203252	196	0.5414364640883977	311	0.5437062937062938	405	0.5343007915567283	C	13.21	2.168726	0.38315	0.523377	0.52803	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.51574	0.75;0.7;0.72	3.9	3.9	0.45041	.	.	.	.	.	T	0.00012	0.0000	L	0.58428	1.81	0.80722	P	0.0	B;B;B	0.13145	0.005;0.007;0.007	B;B;B	0.12837	0.004;0.008;0.005	T	0.45011	-0.9290	8	0.45353	T	0.12	.	14.4262	0.67218	0.0:1.0:0.0:0.0	rs4141841;rs17661626;rs17844299;rs58318977;rs4141841	691;691;691	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	V	691	ENSP00000433416:A691V;ENSP00000436557:A691V;ENSP00000367366:A691V	ENSP00000367366:A691V	A	+	2	0	PCDHA5	140183616	0.000000	0.05858	0.173000	0.22940	0.517000	0.34286	-0.140000	0.10342	1.899000	0.54978	0.313000	0.20887	GCC	C|0.471;T|0.529	0.529	strong		0.677	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51920196	51920196	+	Missense_Mutation	SNP	G	G	T	rs73049612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51920196G>T	ENST00000339313.5	-	3	546	c.430C>A	c.(430-432)Cag>Aag	p.Q144K	SIGLEC10_ENST00000436984.2_Intron|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000439889.2_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.Q144K|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.Q144K|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.Q144K|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.Q144K			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	144					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		TCAGGCTTCTGAGTCAGGGCT	0.617																																					p.Q144K		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C430A						PASS	.						70.0	81.0	77.0					19																	51920196		2203	4300	6503	SO:0001583	missense	89790	exon3			GCTTCTGAGTCAG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.430C>A	19.37:g.51920196G>T	ENSP00000345243:p.Gln144Lys	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	198	30	0.151515	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	11.57	1.677583	0.29783	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000525998;ENST00000339313;ENST00000530476	T;T;T;T;T;T	0.18810	3.96;2.19;3.96;3.96;3.96;3.96	4.85	2.57	0.30868	Immunoglobulin-like fold (1);	0.404011	0.21813	N	0.068733	T	0.21468	0.0517	M	0.79343	2.45	0.20638	N	0.999877	P;B;B	0.41929	0.765;0.095;0.243	B;B;B	0.35899	0.213;0.094;0.032	T	0.16837	-1.0389	10	0.18710	T	0.47	.	11.5078	0.50476	0.0:0.3473:0.6527:0.0	.	144;144;144	E9PL79;Q96LC7-2;Q96LC7	.;.;SIG10_HUMAN	K	144;144;144;144;144;111	ENSP00000342389:Q144K;ENSP00000396742:Q144K;ENSP00000348646:Q144K;ENSP00000431444:Q144K;ENSP00000345243:Q144K;ENSP00000433838:Q111K	ENSP00000345243:Q144K	Q	-	1	0	SIGLEC10	56612008	0.002000	0.14202	0.320000	0.25306	0.554000	0.35429	0.861000	0.27885	1.019000	0.39547	0.313000	0.20887	CAG	.	.	weak		0.617	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ADAM29	11086	hgsc.bcm.edu	37	4	175899091	175899091	+	Missense_Mutation	SNP	A	A	T	rs199709256	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175899091A>T	ENST00000359240.3	+	5	3085	c.2415A>T	c.(2413-2415)caA>caT	p.Q805H	ADAM29_ENST00000445694.1_Missense_Mutation_p.Q805H|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.Q805H|ADAM29_ENST00000404450.4_Missense_Mutation_p.Q805H	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	805	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCCAGAGGCAACCTCAGTTGA	0.572													A|||	28	0.00559105	0.0	0.0014	5008	,	,		18703	0.0099		0.0109	False		,,,				2504	0.0061				p.Q805H	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,NS,lymphoid_neoplasm,0,1	ADAM29	262	1	0			c.A2415T						scavenged	.						132.0	124.0	127.0					4																	175899091		2203	4300	6503	SO:0001583	missense	11086	exon4			GAGGCAACCTCAG	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2415A>T	4.37:g.175899091A>T	ENSP00000352177:p.Gln805His	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	184	48	0.26087	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	A	6.375	0.437341	0.12104	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01963	4.53;4.53;4.53;4.53	0.439	-0.878	0.10617	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48614	-0.9020	8	.	.	.	.	2.1049	0.03688	0.3501:0.3447:0.3051:0.0	.	805	Q9UKF5	ADA29_HUMAN	H	805	ENSP00000352177:Q805H;ENSP00000414544:Q805H;ENSP00000384229:Q805H;ENSP00000423517:Q805H	.	Q	+	3	2	ADAM29	176135666	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.040000	0.13905	-0.595000	0.05828	0.232000	0.17820	CAA	A|0.999;T|0.001	0.001	weak		0.572	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
OR4N4	283694	hgsc.bcm.edu	37	15	22383249	22383249	+	Missense_Mutation	SNP	G	G	A	rs112081824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:22383249G>A	ENST00000328795.4	+	1	868	c.777G>A	c.(775-777)atG>atA	p.M259I	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TCATCTACATGTGCCCTTTCA	0.453													g|||	41	0.0081869	0.0	0.013	5008	,	,		29574	0.0		0.0229	False		,,,				2504	0.0092				p.M259I		Atlas-SNP	.											.	OR4N4	108	.	0			c.G777A						PASS	.	G	ILE/MET	33,4347		2,29,2159	228.0	202.0	211.0		777	-6.4	0.0	15	dbSNP_132	211	274,8250		18,238,4006	yes	missense	OR4N4	NM_001005241.2	10	20,267,6165	AA,AG,GG		3.2145,0.7534,2.3791	benign	259/317	22383249	307,12597	2190	4262	6452	SO:0001583	missense	283694	exon1			CTACATGTGCCCT	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"""GPCR / Class A : Olfactory receptors"""	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.777G>A	15.37:g.22383249G>A	ENSP00000332500:p.Met259Ile	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	266	87	0.327068	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	22	0.010073260073260074	0	0.0	5	0.013812154696132596	0	0.0	17	0.022427440633245383	.	0.019	-1.461475	0.01062	0.007534	0.032145	ENSG00000183706	ENST00000328795	T	0.34859	1.34	3.2	-6.41	0.01938	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000178	T	0.03520	0.0101	N	0.13327	0.33	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27806	-1.0063	10	0.07644	T	0.81	-1.7405	2.6751	0.05079	0.3035:0.1655:0.4088:0.1222	.	259	Q8N0Y3	OR4N4_HUMAN	I	259	ENSP00000332500:M259I	ENSP00000332500:M259I	M	+	3	0	OR4N4	19884613	0.000000	0.05858	0.049000	0.19019	0.010000	0.07245	-5.448000	0.00121	-2.894000	0.00314	-2.355000	0.00241	ATG	G|0.983;A|0.017	0.017	strong		0.453	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
AGBL2	79841	hgsc.bcm.edu	37	11	47712213	47712213	+	Missense_Mutation	SNP	C	C	T	rs7941404	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:47712213C>T	ENST00000525123.1	-	10	1331	c.1046G>A	c.(1045-1047)cGc>cAc	p.R349H	AGBL2_ENST00000357610.3_Missense_Mutation_p.R349H|AGBL2_ENST00000298861.4_Missense_Mutation_p.R349H|AGBL2_ENST00000528244.1_Missense_Mutation_p.R311H|AGBL2_ENST00000529712.1_5'UTR	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	349			R -> H (in dbSNP:rs7941404).			cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						GCCAATATTGCGGGTGTTGGC	0.468													C|||	195	0.0389377	0.0061	0.0648	5008	,	,		20653	0.0		0.1252	False		,,,				2504	0.0164				p.R349H		Atlas-SNP	.											AGBL2,caecum,carcinoma,-1,1	AGBL2	73	1	0			c.G1046A						PASS	.	C	HIS/ARG	126,4276	92.5+/-131.2	1,124,2076	137.0	130.0	132.0		1046	-0.4	0.0	11	dbSNP_116	132	1191,7405	243.2+/-272.9	80,1031,3187	yes	missense	AGBL2	NM_024783.3	29	81,1155,5263	TT,TC,CC		13.8553,2.8623,10.1323	benign	349/903	47712213	1317,11681	2201	4298	6499	SO:0001583	missense	79841	exon10			ATATTGCGGGTGT		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"""cytoplasmic carboxypeptidase 2"""					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.1046G>A	11.37:g.47712213C>T	ENSP00000435582:p.Arg349His	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Missense_Mutation	SNP	ENST00000525123.1	37	CCDS7944.1	121	0.0554029304029304	2	0.0040650406504065045	26	0.0718232044198895	0	0.0	93	0.12269129287598944	C	0.040	-1.287887	0.01387	0.028623	0.138553	ENSG00000165923	ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244;ENST00000532595	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.72	-0.361	0.12564	.	1.009670	0.07907	N	0.973673	T	0.00109	0.0003	N	0.05383	-0.06	0.80722	P	0.0	B;B	0.11235	0.001;0.004	B;B	0.06405	0.002;0.002	T	0.34079	-0.9843	9	0.02654	T	1	-4.9958	10.9986	0.47591	0.0:0.4528:0.0:0.5472	rs7941404;rs52838057;rs56962476;rs7941404	311;349	F6U0I4;Q5U5Z8	.;CBPC2_HUMAN	H	349;349;349;311;293	ENSP00000435582:R349H;ENSP00000350228:R349H;ENSP00000298861:R349H;ENSP00000436630:R311H;ENSP00000436063:R293H	ENSP00000298861:R349H	R	-	2	0	AGBL2	47668789	0.000000	0.05858	0.001000	0.08648	0.432000	0.31715	-0.368000	0.07543	-0.086000	0.12550	-0.302000	0.09304	CGC	C|0.916;T|0.084	0.084	strong		0.468	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783	
TRPA1	8989	hgsc.bcm.edu	37	8	72977703	72977703	+	Missense_Mutation	SNP	C	C	T	rs920829	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:72977703C>T	ENST00000262209.4	-	4	742	c.535G>A	c.(535-537)Gaa>Aaa	p.E179K		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	179			E -> K (in dbSNP:rs920829).		calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TGCAATGCTTCGCTATTATTT	0.318													C|||	1001	0.19988	0.295	0.0793	5008	,	,		17410	0.2847		0.1272	False		,,,				2504	0.1442				p.E179K		Atlas-SNP	.											.	TRPA1	256	.	0			c.G535A						PASS	.	C	LYS/GLU	1223,3181	423.2+/-340.0	157,909,1136	117.0	99.0	105.0		535	5.4	1.0	8	dbSNP_86	105	937,7659	206.1+/-248.3	62,813,3423	yes	missense	TRPA1	NM_007332.2	56	219,1722,4559	TT,TC,CC		10.9004,27.7702,16.6154	probably-damaging	179/1120	72977703	2160,10840	2202	4298	6500	SO:0001583	missense	8989	exon4			ATGCTTCGCTATT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.535G>A	8.37:g.72977703C>T	ENSP00000262209:p.Glu179Lys	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	263	124	0.471483	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	457	0.20924908424908426	157	0.31910569105691056	38	0.10497237569060773	166	0.2902097902097902	96	0.1266490765171504	C	27.9	4.869104	0.91587	0.277702	0.109004	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.68903	-0.36;-0.33	5.39	5.39	0.77823	Ankyrin repeat-containing domain (3);	0.093119	0.64402	D	0.000001	T	0.00012	0.0000	L	0.52266	1.64	0.09310	P	0.9999999301687	D	0.64830	0.994	P	0.53988	0.739	T	0.00749	-1.1582	9	0.30854	T	0.27	-29.6026	19.5245	0.95199	0.0:1.0:0.0:0.0	rs920829;rs52810580;rs920829	179	O75762	TRPA1_HUMAN	K	31;179	ENSP00000428151:E31K;ENSP00000262209:E179K	ENSP00000262209:E179K	E	-	1	0	TRPA1	73140257	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	6.718000	0.74713	2.689000	0.91719	0.650000	0.86243	GAA	C|0.798;T|0.202	0.202	strong		0.318	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
NT5C3A	51251	hgsc.bcm.edu	37	7	33075573	33075573	+	Intron	SNP	A	A	G	rs17170223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:33075573A>G	ENST00000242210.7	-	2	230				NT5C3A_ENST00000610140.1_Intron|NT5C3A_ENST00000381626.2_5'UTR|AVL9_ENST00000404479.1_Intron|NT5C3A_ENST00000405342.1_Silent_p.N3N|NT5C3A_ENST00000409787.1_Silent_p.N3N|NT5C3A_ENST00000409467.1_5'UTR|NT5C3A_ENST00000396152.2_Silent_p.N3N	NM_001002009.2|NM_001002010.2	NP_001002009.1|NP_001002010.1	Q9H0P0	5NT3A_HUMAN	5'-nucleotidase, cytosolic IIIA						dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside metabolic process (GO:0006213)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	2'-phosphotransferase activity (GO:0008665)|5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)										CAGACTCTTGATTAGTCATTT	0.363													A|||	241	0.048123	0.0545	0.0187	5008	,	,		17000	0.0149		0.0288	False		,,,				2504	0.1145				p.N3N		Atlas-SNP	.											.	.	.	.	0			c.T9C						PASS	.	A	,,	237,4169	141.1+/-176.5	10,217,1976	190.0	186.0	187.0		,,9	0.4	1.0	7	dbSNP_123	187	187,8413	83.7+/-146.2	0,187,4113	no	intron,utr-5,coding-synonymous	NT5C3	NM_001002010.1,NM_001166118.1,NM_016489.11	,,	10,404,6089	GG,GA,AA		2.1744,5.379,3.26	,,	,,3/298	33075573	424,12582	2203	4300	6503	SO:0001627	intron_variant	0	exon2			CTCTTGATTAGTC	AF312735	CCDS34616.1, CCDS34617.1, CCDS55101.1	7p14.3	2013-03-06	2013-03-06	2013-03-06	ENSG00000122643	ENSG00000122643	3.1.3.5		17820	protein-coding gene	gene with protein product	"""lupin"""	606224	"""5'-nucleotidase, cytosolic III"""	NT5C3		11042152, 10942414	Standard	NM_001002010		Approved	UMPH1, PSN1, PN-I, UMPH, P5'N-1, cN-III, p36, POMP, hUMP1	uc003tdk.4	Q9H0P0	OTTHUMG00000152983	ENST00000242210.7:c.154-9046T>C	7.37:g.33075573A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_001002009	A8K253|B2RAA5|B8ZZC4|Q6IPZ1|Q6NXS6|Q7L3G6|Q9P0P5|Q9UC42|Q9UC43|Q9UC44|Q9UC45	Silent	SNP	ENST00000242210.7	37	CCDS34616.1																																																																																			A|0.971;G|0.029	0.029	strong		0.363	NT5C3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328880.1	NM_016489	
SHE	126669	hgsc.bcm.edu	37	1	154474131	154474131	+	Silent	SNP	C	C	G	rs4845635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154474131C>G	ENST00000304760.2	-	1	458	c.372G>C	c.(370-372)cgG>cgC	p.R124R	TDRD10_ENST00000368482.4_5'Flank|TDRD10_ENST00000368480.3_5'Flank	NM_001010846.2	NP_001010846.1	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	124										breast(4)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	14	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			CCTCCGTGGCCCGGGAGTTTT	0.682													c|||	3891	0.776957	0.5635	0.879	5008	,	,		13162	0.9117		0.8241	False		,,,				2504	0.8057				p.R124R		Atlas-SNP	.											SHE,colon,carcinoma,-2,3	SHE	41	3	0			c.G372C						PASS	.			2736,1668	637.7+/-396.8	845,1046,311	40.0	38.0	39.0		372	3.8	0.6	1	dbSNP_111	39	7153,1447	738.8+/-407.1	2990,1173,137	no	coding-synonymous	SHE	NM_001010846.2		3835,2219,448	GG,GC,CC		16.8256,37.8747,23.9542		124/496	154474131	9889,3115	2202	4300	6502	SO:0001819	synonymous_variant	126669	exon1			CGTGGCCCGGGAG	AK074067	CCDS30877.1	1q21.3	2013-02-14			ENSG00000169291	ENSG00000169291		"""SH2 domain containing"""	27004	protein-coding gene	gene with protein product		610482				9315092	Standard	NM_001010846		Approved		uc001ffb.3	Q5VZ18	OTTHUMG00000036072	ENST00000304760.2:c.372G>C	1.37:g.154474131C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001010846	Q8TEQ5	Silent	SNP	ENST00000304760.2	37	CCDS30877.1																																																																																			C|0.222;G|0.778	0.778	strong		0.682	SHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087910.2	NM_001010846	
NPAS2	4862	hgsc.bcm.edu	37	2	101587455	101587455	+	Silent	SNP	C	C	T	rs1562313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:101587455C>T	ENST00000335681.5	+	12	1344	c.1059C>T	c.(1057-1059)taC>taT	p.Y353Y	AC016738.3_ENST00000439150.1_RNA|AC016738.3_ENST00000446644.1_RNA|NPAS2_ENST00000542504.1_Silent_p.Y418Y	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	353	PAC.				cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGTACAGTTACGCAGATGTCC	0.567													C|||	1185	0.236621	0.3033	0.1095	5008	,	,		16076	0.2808		0.2256	False		,,,				2504	0.2025				p.Y353Y		Atlas-SNP	.											.	NPAS2	88	.	0			c.C1059T						PASS	.	C		1190,3216	417.6+/-338.0	152,886,1165	90.0	88.0	89.0		1059	-8.2	0.1	2	dbSNP_88	89	1787,6813	321.3+/-315.0	184,1419,2697	no	coding-synonymous	NPAS2	NM_002518.3		336,2305,3862	TT,TC,CC		20.7791,27.0086,22.8894		353/825	101587455	2977,10029	2203	4300	6503	SO:0001819	synonymous_variant	4862	exon12			CAGTTACGCAGAT	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1059C>T	2.37:g.101587455C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	144	61	0.423611	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Silent	SNP	ENST00000335681.5	37	CCDS2048.1	518	0.23717948717948717	152	0.3089430894308943	43	0.11878453038674033	144	0.2517482517482518	179	0.23614775725593667	C	0.085	-1.177368	0.01633	0.270086	0.207791	ENSG00000170485	ENST00000448812	.	.	.	6.06	-8.22	0.01037	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999888017	.	.	.	.	.	.	T	0.25082	-1.0142	3	.	.	.	.	20.7068	0.99706	0.0:0.2374:0.0:0.7626	rs1562313;rs3739007;rs58016169;rs1562313	.	.	.	C	240	.	.	R	+	1	0	NPAS2	100953887	0.018000	0.18449	0.083000	0.20561	0.032000	0.12392	-1.204000	0.03017	-2.172000	0.00774	-2.084000	0.00378	CGC	C|0.766;T|0.234	0.234	strong		0.567	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
CCDC96	257236	hgsc.bcm.edu	37	4	7044600	7044600	+	Silent	SNP	G	G	A	rs2359010	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:7044600G>A	ENST00000310085.4	-	1	128	c.66C>T	c.(64-66)gcC>gcT	p.A22A	RP11-367J11.2_ENST00000500031.1_RNA|TADA2B_ENST00000512388.1_5'Flank|TADA2B_ENST00000310074.7_5'Flank	NM_153376.2	NP_699207.1	Q2M329	CCD96_HUMAN	coiled-coil domain containing 96	22										endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11						ACGGCCGCGCGGCCAGGCTTT	0.716													G|||	978	0.195288	0.0121	0.1427	5008	,	,		11772	0.3849		0.1859	False		,,,				2504	0.2945				p.A22A		Atlas-SNP	.											CCDC96,NS,carcinoma,0,1	CCDC96	34	1	0			c.C66T						PASS	.	G		160,4184		4,152,2016	11.0	14.0	13.0		66	0.5	0.0	4	dbSNP_100	13	1554,7016		143,1268,2874	yes	coding-synonymous	CCDC96	NM_153376.2		147,1420,4890	AA,AG,GG		18.133,3.6832,13.2724		22/556	7044600	1714,11200	2172	4285	6457	SO:0001819	synonymous_variant	257236	exon1			CCGCGCGGCCAGG	AK075056	CCDS3395.1	4p16.1	2008-02-05			ENSG00000173013	ENSG00000173013			26900	protein-coding gene	gene with protein product							Standard	NM_153376		Approved	FLJ90575	uc003gjv.2	Q2M329	OTTHUMG00000125511	ENST00000310085.4:c.66C>T	4.37:g.7044600G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	22	0.814815	NM_153376	Q8N2I7	Silent	SNP	ENST00000310085.4	37	CCDS3395.1																																																																																			G|0.816;A|0.184	0.184	strong		0.716	CCDC96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246838.1	NM_153376	
TOMM40	10452	hgsc.bcm.edu	37	19	45396144	45396144	+	Silent	SNP	C	C	T	rs11556505	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45396144C>T	ENST00000426677.2	+	3	573	c.393C>T	c.(391-393)ttC>ttT	p.F131F	CTB-129P6.4_ENST00000585408.1_RNA|TOMM40_ENST00000252487.5_Silent_p.F131F|TOMM40_ENST00000592434.1_Silent_p.F131F|TOMM40_ENST00000405636.2_Silent_p.F131F	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	131					cellular protein metabolic process (GO:0044267)|ion transport (GO:0006811)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane translocase complex (GO:0005742)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein transmembrane transporter activity (GO:0008320)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		ACTACCACTTCGGGGTCACAT	0.488													C|||	571	0.114018	0.1112	0.1052	5008	,	,		22184	0.0962		0.1312	False		,,,				2504	0.1247				p.F131F		Atlas-SNP	.											.	TOMM40	13	.	0			c.C393T						PASS	.	C	,,	516,3890	238.0+/-249.6	46,424,1733	90.0	75.0	80.0		393,393,393	-3.0	1.0	19	dbSNP_120	80	1134,7466	234.6+/-267.5	81,972,3247	no	coding-synonymous,coding-synonymous,coding-synonymous	TOMM40	NM_001128916.1,NM_001128917.1,NM_006114.2	,,	127,1396,4980	TT,TC,CC		13.186,11.7113,12.6865	,,	131/362,131/362,131/362	45396144	1650,11356	2203	4300	6503	SO:0001819	synonymous_variant	10452	exon3			CCACTTCGGGGTC	AF043250	CCDS12646.1	19q13	2008-07-04				ENSG00000130204			18001	protein-coding gene	gene with protein product		608061				10980201, 15644312	Standard	NM_006114		Approved	PEREC1, D19S1177E, C19orf1, TOM40, PER-EC1	uc002paa.4	O96008		ENST00000426677.2:c.393C>T	19.37:g.45396144C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	238	125	0.52521	NM_001128917	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Silent	SNP	ENST00000426677.2	37	CCDS12646.1																																																																																			C|0.866;T|0.134	0.134	strong		0.488	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1		
ZNF862	643641	hgsc.bcm.edu	37	7	149559273	149559273	+	Silent	SNP	C	C	T	rs2074700	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149559273C>T	ENST00000223210.4	+	7	3269	c.3024C>T	c.(3022-3024)ctC>ctT	p.L1008L	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	1008					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						TCTCCATGCTCTGCAAAAACG	0.602													C|||	1859	0.371206	0.2368	0.4625	5008	,	,		18854	0.3264		0.5676	False		,,,				2504	0.3323				p.L1008L		Atlas-SNP	.											.	ZNF862	97	.	0			c.C3024T						PASS	.	C		1213,2967		182,849,1059	45.0	51.0	49.0		3024	-0.2	0.9	7	dbSNP_96	49	4856,3566		1430,1996,785	no	coding-synonymous	ZNF862	NM_001099220.1		1612,2845,1844	TT,TC,CC		42.3415,29.0191,48.159		1008/1170	149559273	6069,6533	2090	4211	6301	SO:0001819	synonymous_variant	643641	exon7			CATGCTCTGCAAA	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.3024C>T	7.37:g.149559273C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																			C|0.546;T|0.454	0.454	strong		0.602	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
PCDHA7	56141	hgsc.bcm.edu	37	5	140214381	140214381	+	Missense_Mutation	SNP	G	G	A	rs10067182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140214381G>A	ENST00000525929.1	+	1	413	c.413G>A	c.(412-414)aGg>aAg	p.R138K	PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.R138K|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	138	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> K (in dbSNP:rs10067182).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGACACAAAGGAATCTGTTC	0.567																																					p.R138K	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											PCDHA7_ENST00000525929,NS,carcinoma,-1,2	PCDHA7	367	2	0			c.G413A						PASS	.						89.0	83.0	85.0					5																	140214381		2203	4292	6495	SO:0001583	missense	56141	exon1			CACAAAGGAATCT	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.413G>A	5.37:g.140214381G>A	ENSP00000436426:p.Arg138Lys	Somatic	536	0	0		WXS	Illumina HiSeq	Phase_I	494	125	0.253036	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	37	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	A	0.329	-0.957217	0.02267	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.19806	2.12;2.12	4.17	1.71	0.24356	Cadherin (2);Cadherin-like (1);	0.611706	0.11874	N	0.521196	T	0.03608	0.0103	N	0.00092	-2.175	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.39165	-0.9627	9	0.09590	T	0.72	.	8.3686	0.32402	0.7623:0.0:0.2377:0.0	rs10067182;rs17844308	138;138	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	K	138	ENSP00000436426:R138K;ENSP00000367365:R138K	ENSP00000367365:R138K	R	+	2	0	PCDHA7	140194565	0.000000	0.05858	0.008000	0.14137	0.059000	0.15707	-0.655000	0.05348	-0.134000	0.11516	-0.556000	0.04195	AGG	G|0.399;A|0.601	0.601	strong		0.567	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
AK2	204	hgsc.bcm.edu	37	1	33502357	33502357	+	Missense_Mutation	SNP	C	C	T	rs199641857		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33502357C>T	ENST00000487289.1	-	1	88	c.73G>A	c.(73-75)Ggg>Agg	p.G25R	AK2_ENST00000548033.1_Missense_Mutation_p.G25R|AK2_ENST00000467905.1_Missense_Mutation_p.G25R|AK2_ENST00000373449.2_Missense_Mutation_p.G25R|AK2_ENST00000354858.6_Missense_Mutation_p.G25R|AK2_ENST00000480134.1_Missense_Mutation_p.G25R					adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				TTACCGGCCCCGGGAGGCCCC	0.672																																					p.G25R		Atlas-SNP	.											.	AK2	27	.	0			c.G73A						PASS	.						10.0	11.0	11.0					1																	33502357		2201	4289	6490	SO:0001583	missense	204	exon1			CGGCCCCGGGAGG	U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"""Adenylate kinases"""	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000487289.1:c.73G>A	1.37:g.33502357C>T	ENSP00000446849:p.Gly25Arg	Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	229	14	0.0611354	NM_001199199		Missense_Mutation	SNP	ENST00000487289.1	37		.	.	.	.	.	.	.	.	.	.	C	27.9	4.874354	0.91664	.	.	ENSG00000004455	ENST00000373449;ENST00000548033;ENST00000467905;ENST00000480134;ENST00000354858;ENST00000398192;ENST00000487289	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89;-2.89;-2.89	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.97470	0.9172	H	0.99958	5.055	0.80722	D	1	P;P;D;P	0.54207	0.895;0.826;0.965;0.895	P;B;P;P	0.52710	0.459;0.142;0.707;0.459	D	0.98100	1.0414	10	0.72032	D	0.01	-23.3449	13.8506	0.63494	0.0:1.0:0.0:0.0	.	25;25;25;25	P54819-5;F8VY04;P54819;P54819-2	.;.;KAD2_HUMAN;.	R	25	ENSP00000362548:G25R;ENSP00000449003:G25R;ENSP00000447082:G25R;ENSP00000450109:G25R;ENSP00000346921:G25R;ENSP00000446849:G25R	ENSP00000346921:G25R	G	-	1	0	AK2	33274944	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.868000	0.56055	2.724000	0.93272	0.563000	0.77884	GGG	.	.	weak		0.672	AK2-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000011889.4	NM_001625	
DENND1A	57706	hgsc.bcm.edu	37	9	126144390	126144390	+	Missense_Mutation	SNP	G	G	T	rs189947178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126144390G>T	ENST00000373624.2	-	22	2552	c.2351C>A	c.(2350-2352)gCc>gAc	p.A784D	DENND1A_ENST00000394219.3_Missense_Mutation_p.A795D|DENND1A_ENST00000542603.1_Missense_Mutation_p.A569D|DENND1A_ENST00000473039.1_5'UTR	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	784	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						GTCCAGGAGGGCGAGCAGGGC	0.697													G|||	16	0.00319489	0.0	0.0101	5008	,	,		10971	0.0		0.0089	False		,,,				2504	0.0				p.A784D		Atlas-SNP	.											.	DENND1A	112	.	0			c.C2351A						PASS	.	G	ASP/ALA	8,4368		0,8,2180	10.0	14.0	13.0		2351	3.5	1.0	9		13	81,8467		1,79,4194	no	missense	DENND1A	NM_020946.1	126	1,87,6374	TT,TG,GG		0.9476,0.1828,0.6886	possibly-damaging	784/1010	126144390	89,12835	2188	4274	6462	SO:0001583	missense	57706	exon22			AGGAGGGCGAGCA	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.2351C>A	9.37:g.126144390G>T	ENSP00000362727:p.Ala784Asp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	30	0.652174	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	15	0.006868131868131868	5	0.01016260162601626	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	11.10	1.538370	0.27475	0.001828	0.009476	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219	T;T;T	0.23754	3.34;1.89;3.21	4.47	3.5	0.40072	.	0.251626	0.36101	N	0.002785	T	0.20210	0.0486	L	0.27053	0.805	0.80722	D	1	D;D;P;P	0.58970	0.984;0.984;0.926;0.483	P;P;P;B	0.55161	0.77;0.77;0.454;0.084	T	0.01405	-1.1363	10	0.56958	D	0.05	-15.6303	9.6391	0.39828	0.0:0.3391:0.5308:0.1301	.	795;785;784;647	Q8TEH3-6;Q8TEH3-7;Q8TEH3;Q9HCG4	.;.;DEN1A_HUMAN;.	D	784;569;795	ENSP00000362727:A784D;ENSP00000437457:A569D;ENSP00000377766:A795D	ENSP00000362727:A784D	A	-	2	0	DENND1A	125184211	1.000000	0.71417	0.982000	0.44146	0.008000	0.06430	2.369000	0.44231	2.029000	0.59856	0.557000	0.71058	GCC	G|0.993;T|0.007	0.007	strong		0.697	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
PLS3	5358	hgsc.bcm.edu	37	X	114863593	114863593	+	Silent	SNP	T	T	A	rs140121121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:114863593T>A	ENST00000420625.2	+	4	455	c.321T>A	c.(319-321)ggT>ggA	p.G107G	PLS3_ENST00000539310.1_Silent_p.G62G|PLS3_ENST00000289290.3_Silent_p.G62G|PLS3_ENST00000537301.1_Silent_p.G85G|PLS3_ENST00000355899.3_Silent_p.G107G	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	107					bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						GTGCTCTGGGTGGAACTTCAG	0.378													T|||	23	0.00609272	0.0	0.0029	3775	,	,		12691	0.0		0.0169	False		,,,				2504	0.0041				p.G107G	Colon(160;1047 1864 8490 12969 29601)	Atlas-SNP	.											.	PLS3	60	.	0			c.T321A						PASS	.	T	,,	10,3825		0,9,1,1623,570	130.0	115.0	120.0		321,240,321	-0.8	1.0	X	dbSNP_134	120	99,6629		2,75,20,2351,1852	no	coding-synonymous,coding-synonymous,coding-synonymous	PLS3	NM_001136025.3,NM_001172335.1,NM_005032.5	,,	2,84,21,3974,2422	AA,AT,A,TT,T		1.4715,0.2608,1.0319	,,	107/631,80/604,107/631	114863593	109,10454	2203	4300	6503	SO:0001819	synonymous_variant	5358	exon4			TCTGGGTGGAACT	L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"""EF-hand domain containing"""	9091	protein-coding gene	gene with protein product		300131	"""plastin 3 (T isoform)"""			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.321T>A	X.37:g.114863593T>A		Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_005032	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Silent	SNP	ENST00000420625.2	37	CCDS14568.1																																																																																			T|0.990;A|0.010	0.010	strong		0.378	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2		
HERC1	8925	hgsc.bcm.edu	37	15	63954029	63954029	+	Silent	SNP	C	C	T	rs2228511	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63954029C>T	ENST00000443617.2	-	45	9180	c.9093G>A	c.(9091-9093)ccG>ccA	p.P3031P		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3031					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ACAGGTAGTACGGATTTCCAC	0.493													T|||	3182	0.635383	0.8752	0.647	5008	,	,		18830	0.0962		0.8966	False		,,,				2504	0.59				p.P3031P		Atlas-SNP	.											.	HERC1	624	.	0			c.G9093A						PASS	.	T		3571,603		1532,507,48	210.0	207.0	208.0		9093	0.6	1.0	15	dbSNP_98	208	7433,1019		3259,915,52	no	coding-synonymous	HERC1	NM_003922.3		4791,1422,100	TT,TC,CC		12.0563,14.4466,12.8465		3031/4862	63954029	11004,1622	2087	4226	6313	SO:0001819	synonymous_variant	8925	exon45			GTAGTACGGATTT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.9093G>A	15.37:g.63954029C>T		Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	184	183	0.994565	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																			C|0.332;T|0.668	0.668	strong		0.493	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
SCEL	8796	hgsc.bcm.edu	37	13	78188078	78188078	+	Missense_Mutation	SNP	A	A	G	rs8002725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:78188078A>G	ENST00000349847.3	+	24	1523	c.1439A>G	c.(1438-1440)aAa>aGa	p.K480R	SCEL_ENST00000469982.1_3'UTR|SCEL_ENST00000377246.3_Missense_Mutation_p.K460R|SCEL_ENST00000535157.1_Missense_Mutation_p.K438R	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	480	16 X approximate tandem repeats.		K -> R (in dbSNP:rs8002725).		embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AAAGCTGTCAAAAACACTGAT	0.328													A|||	1081	0.215855	0.3903	0.1729	5008	,	,		17587	0.1409		0.1183	False		,,,				2504	0.1881				p.K480R		Atlas-SNP	.											.	SCEL	85	.	0			c.A1439G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	1565,2841	489.0+/-361.4	284,997,922	182.0	174.0	177.0		1313,1379,1439	3.9	1.0	13	dbSNP_116	177	1284,7316	254.1+/-279.5	110,1064,3126	yes	missense,missense,missense	SCEL	NM_001160706.1,NM_003843.3,NM_144777.2	26,26,26	394,2061,4048	GG,GA,AA		14.9302,35.5197,21.9053	possibly-damaging,possibly-damaging,possibly-damaging	438/647,460/669,480/689	78188078	2849,10157	2203	4300	6503	SO:0001583	missense	8796	exon24			CTGTCAAAAACAC	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.1439A>G	13.37:g.78188078A>G	ENSP00000302579:p.Lys480Arg	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	187	94	0.502674	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	37	CCDS9459.1	413	0.1891025641025641	176	0.35772357723577236	68	0.1878453038674033	82	0.14335664335664336	87	0.11477572559366754	A	8.124	0.781687	0.16120	0.355197	0.149302	ENSG00000136155	ENST00000535157;ENST00000377246;ENST00000349847	D;T;D	0.81579	-1.51;1.84;-1.51	5.14	3.93	0.45458	.	0.112463	0.40144	N	0.001165	T	0.00012	0.0000	L	0.55103	1.725	0.42313	P	0.007777999999999952	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.14578	0.01;0.011;0.01	T	0.16512	-1.0400	9	0.15952	T	0.53	-18.9715	8.1757	0.31281	0.9068:0.0:0.0932:0.0	rs8002725;rs52813774;rs61017956;rs8002725	438;460;480	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	R	438;460;480	ENSP00000437895:K438R;ENSP00000366454:K460R;ENSP00000302579:K480R	ENSP00000302579:K480R	K	+	2	0	SCEL	77086079	0.958000	0.32768	0.980000	0.43619	0.070000	0.16714	1.211000	0.32382	0.883000	0.36040	0.454000	0.30748	AAA	A|0.790;G|0.209	0.209	strong		0.328	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79059040	79059040	+	Silent	SNP	A	A	G	rs199919711		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79059040A>G	ENST00000388820.4	-	19	3423	c.3213T>C	c.(3211-3213)aaT>aaC	p.N1071N	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1071					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.N1071N(2)|p.N1071S(2)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CCTCGTGGAAATTGATGAAAT	0.617																																					p.N1071N		Atlas-SNP	.											ADAMTS7,NS,carcinoma,-1,5	ADAMTS7	142	5	4	Substitution - Missense(2)|Substitution - coding silent(2)	lung(2)|kidney(2)	c.T3213C						scavenged	.																																			SO:0001819	synonymous_variant	11173	exon19			GTGGAAATTGATG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3213T>C	15.37:g.79059040A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	137	8	0.0583942	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			A|0.999;G|0.001	0.001	weak		0.617	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
SPATA5	166378	hgsc.bcm.edu	37	4	123868456	123868456	+	Silent	SNP	C	C	T	rs6534369	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:123868456C>T	ENST00000274008.4	+	9	1596	c.1527C>T	c.(1525-1527)ctC>ctT	p.L509L	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	509					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						ATGCTGCTCTCCGAAGACCTG	0.433													C|||	265	0.0529153	0.1747	0.0216	5008	,	,		14286	0.0		0.0189	False		,,,				2504	0.0				p.L509L		Atlas-SNP	.											.	SPATA5	62	.	0			c.C1527T						PASS	.	C		697,3709	290.4+/-280.9	61,575,1567	50.0	47.0	48.0		1527	-1.2	1.0	4	dbSNP_116	48	151,8449	73.2+/-135.9	1,149,4150	no	coding-synonymous	SPATA5	NM_145207.2		62,724,5717	TT,TC,CC		1.7558,15.8193,6.5201		509/894	123868456	848,12158	2203	4300	6503	SO:0001819	synonymous_variant	166378	exon9			TGCTCTCCGAAGA	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"""ATPases / AAA-type"""	18119	protein-coding gene	gene with protein product	"""ATPase family gene 2 homolog (S. cerevisiae)"""	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.1527C>T	4.37:g.123868456C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_145207	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Silent	SNP	ENST00000274008.4	37	CCDS3730.1																																																																																			C|0.934;T|0.066	0.066	strong		0.433	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207	
BMP1	649	hgsc.bcm.edu	37	8	22021517	22021517	+	5'Flank	SNP	G	G	A	rs1124	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:22021517G>A	ENST00000306385.5	+	0	0				BMP1_ENST00000354870.5_5'Flank|BMP1_ENST00000397816.3_5'Flank|BMP1_ENST00000397814.3_5'Flank|SFTPC_ENST00000522109.1_3'UTR|SFTPC_ENST00000520605.1_Intron|SFTPC_ENST00000521315.1_Missense_Mutation_p.S180N|SFTPC_ENST00000318561.3_Missense_Mutation_p.S186N|BMP1_ENST00000306349.8_5'Flank|SFTPC_ENST00000524255.1_Missense_Mutation_p.S133N|SFTPC_ENST00000437090.2_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1						cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		ATGGCCGTGAGCACCCTGTGT	0.682													G|||	1182	0.236022	0.0832	0.2695	5008	,	,		16924	0.3006		0.3211	False		,,,				2504	0.2648				p.S186N		Atlas-SNP	.											.	SFTPC	19	.	0			c.G557A	GRCh37	CM040800	SFTPC	M	rs1124	PASS	.	G	ASN/SER,ASN/SER,ASN/SER	432,3668		30,372,1648	44.0	53.0	50.0		539,557,557	2.3	1.0	8	dbSNP_36	50	2800,5560		470,1860,1850	yes	missense,missense,missense	SFTPC	NM_001172357.1,NM_001172410.1,NM_003018.3	46,46,46	500,2232,3498	AA,AG,GG		33.4928,10.5366,25.939	benign,benign,benign	180/192,186/198,186/198	22021517	3232,9228	2050	4180	6230	SO:0001631	upstream_gene_variant	6440	exon5			CCGTGAGCACCCT		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761		8.37:g.22021517G>A	Exception_encountered	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	188	91	0.484043	NM_003018	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	37	CCDS6026.1	570	0.260989010989011	47	0.09552845528455285	100	0.27624309392265195	172	0.3006993006993007	251	0.3311345646437995	G	15.20	2.762010	0.49468	0.105366	0.334928	ENSG00000168484	ENST00000318561;ENST00000521315;ENST00000524255	T;T;T	0.79141	-1.24;-1.24;-1.24	5.5	2.33	0.28932	.	0.630262	0.15776	N	0.245165	T	0.00012	0.0000	.	.	.	0.37419	P	0.08645499999999995	B	0.11235	0.004	B	0.09377	0.004	T	0.11203	-1.0597	8	0.23302	T	0.38	-30.2415	5.3591	0.16077	0.3956:0.0:0.6043:0.0	rs1124;rs1126834;rs2239663;rs3182311;rs17845062;rs17857843;rs1124	180	E9PGX3	.	N	186;180;133	ENSP00000316152:S186N;ENSP00000430410:S180N;ENSP00000429552:S133N	ENSP00000316152:S186N	S	+	2	0	SFTPC	22077462	0.398000	0.25279	0.980000	0.43619	0.927000	0.56198	0.610000	0.24253	0.695000	0.31675	-0.145000	0.13849	AGC	G|0.748;A|0.252	0.252	strong		0.682	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
EHMT1	79813	hgsc.bcm.edu	37	9	140638416	140638416	+	Silent	SNP	G	G	A	rs1129767	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140638416G>A	ENST00000460843.1	+	6	1071	c.1044G>A	c.(1042-1044)tcG>tcA	p.S348S	EHMT1_ENST00000462484.1_Silent_p.S348S|EHMT1_ENST00000334856.6_Silent_p.S317S|EHMT1_ENST00000371394.2_3'UTR	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	348					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		AGATGGACTCGGATGAGGACG	0.632													G|||	763	0.152356	0.0068	0.3862	5008	,	,		18222	0.1012		0.167	False		,,,				2504	0.2209				p.S348S		Atlas-SNP	.											EHMT1_ENST00000460843,colon,carcinoma,+1,2	EHMT1	196	2	0			c.G1044A						PASS	.	G	,	169,4237	109.9+/-148.2	2,165,2036	56.0	50.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1044,1044	-10.8	0.0	9	dbSNP_86	52	1537,7063	288.9+/-299.0	144,1249,2907	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	146,1414,4943	AA,AG,GG		17.8721,3.8357,13.117	,	348/809,348/1299	140638416	1706,11300	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon6			GGACTCGGATGAG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1044G>A	9.37:g.140638416G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			G|0.862;A|0.138	0.138	strong		0.632	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
HS1BP3	64342	hgsc.bcm.edu	37	2	20824498	20824498	+	Missense_Mutation	SNP	C	C	T	rs2305458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:20824498C>T	ENST00000304031.3	-	5	803	c.778G>A	c.(778-780)Gtg>Atg	p.V260M		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	260			V -> M (in dbSNP:rs2305458). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTACGGTCCACGGATGACACG	0.642													T|||	1913	0.381989	0.3139	0.4063	5008	,	,		17685	0.2748		0.5726	False		,,,				2504	0.3712				p.V260M		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G778A						PASS	.	T	MET/VAL	1447,2959	681.3+/-404.0	240,967,996	75.0	79.0	77.0		778	-8.8	0.0	2	dbSNP_100	77	4995,3605	520.9+/-379.8	1450,2095,755	yes	missense	HS1BP3	NM_022460.3	21	1690,3062,1751	TT,TC,CC		41.9186,32.8416,49.531	benign	260/393	20824498	6442,6564	2203	4300	6503	SO:0001583	missense	64342	exon5			GGTCCACGGATGA		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.778G>A	2.37:g.20824498C>T	ENSP00000305193:p.Val260Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Missense_Mutation	SNP	ENST00000304031.3	37	CCDS1700.1	893|893	0.4088827838827839|0.4088827838827839	154|154	0.3130081300813008|0.3130081300813008	159|159	0.43922651933701656|0.43922651933701656	146|146	0.25524475524475526|0.25524475524475526	434|434	0.5725593667546174|0.5725593667546174	T|T	8.686|8.686	0.906356|0.906356	0.17833|0.17833	0.328416|0.328416	0.580814|0.580814	ENSG00000118960|ENSG00000118960	ENST00000445102|ENST00000304031;ENST00000458740	.|T;T	.|0.30714	.|2.28;1.52	4.38|4.38	-8.76|-8.76	0.00830|0.00830	.|.	.|4.463180	.|0.00678	.|N	.|0.000666	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02011|0.02011	-0.69|-0.69	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.11235	.|0.004	.|B	.|0.06405	.|0.002	T|T	0.35992|0.35992	-0.9766|-0.9766	4|9	.|0.44086	.|T	.|0.13	9.7378|9.7378	5.9354|5.9354	0.19163|0.19163	0.0925:0.2869:0.4934:0.1273|0.0925:0.2869:0.4934:0.1273	rs2305458;rs11544151;rs17857390;rs61096584;rs2305458|rs2305458;rs11544151;rs17857390;rs61096584;rs2305458	.|260	.|Q53T59	.|H1BP3_HUMAN	H|M	52|260;79	.|ENSP00000305193:V260M;ENSP00000392203:V79M	.|ENSP00000305193:V260M	R|V	-|-	2|1	0|0	HS1BP3|HS1BP3	20687979|20687979	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.273000|-2.273000	0.01164|0.01164	-2.766000|-2.766000	0.00367|0.00367	-2.777000|-2.777000	0.00118|0.00118	CGT|GTG	C|0.551;T|0.449	0.449	strong		0.642	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
KLHL14	57565	hgsc.bcm.edu	37	18	30350165	30350165	+	Silent	SNP	G	G	A	rs61737324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:30350165G>A	ENST00000359358.4	-	2	828	c.390C>T	c.(388-390)tgC>tgT	p.C130C	AC012123.1_ENST00000426194.1_Intron|KLHL14_ENST00000358095.4_Silent_p.C130C	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	130	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						CGATGGACGAGCAGCCCTGCA	0.672													G|||	287	0.0573083	0.1188	0.0418	5008	,	,		16238	0.0079		0.0447	False		,,,				2504	0.0491				p.C130C		Atlas-SNP	.											.	KLHL14	92	.	0			c.C390T						PASS	.	G		531,3875	239.6+/-250.7	34,463,1706	87.0	91.0	90.0		390	1.3	1.0	18	dbSNP_129	90	426,8174	131.3+/-189.1	11,404,3885	no	coding-synonymous	KLHL14	NM_020805.1		45,867,5591	AA,AG,GG		4.9535,12.0517,7.3581		130/629	30350165	957,12049	2203	4300	6503	SO:0001819	synonymous_variant	57565	exon2			GGACGAGCAGCCC	AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"""Kelch-like"", ""BTB/POZ domain containing"""	29266	protein-coding gene	gene with protein product	"""printor"""	613772	"""kelch-like 14 (Drosophila)"""			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.390C>T	18.37:g.30350165G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	142	51	0.359155	NM_020805	A6NNW1|B4DHA0|Q8WU41	Silent	SNP	ENST00000359358.4	37	CCDS32813.1																																																																																			G|0.934;A|0.066	0.066	strong		0.672	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1		
BTRC	8945	hgsc.bcm.edu	37	10	103285900	103285900	+	Silent	SNP	C	C	T	rs17767748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:103285900C>T	ENST00000370187.3	+	6	805	c.687C>T	c.(685-687)atC>atT	p.I229I	BTRC_ENST00000408038.2_Silent_p.I193I|BTRC_ENST00000393441.4_Silent_p.I188I	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	229					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		AGAAGCTTATCGAGAGAATGG	0.483													C|||	228	0.0455272	0.0613	0.0403	5008	,	,		19674	0.003		0.0755	False		,,,				2504	0.0409				p.I229I		Atlas-SNP	.											.	BTRC	64	.	0			c.C687T						PASS	.	C	,	304,4102	165.1+/-196.6	10,284,1909	179.0	156.0	163.0		579,687	-1.0	1.0	10	dbSNP_123	163	642,7958	164.5+/-216.8	21,600,3679	no	coding-synonymous,coding-synonymous	BTRC	NM_003939.3,NM_033637.2	,	31,884,5588	TT,TC,CC		7.4651,6.8997,7.2736	,	193/570,229/606	103285900	946,12060	2203	4300	6503	SO:0001819	synonymous_variant	8945	exon6			GCTTATCGAGAGA	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1144	protein-coding gene	gene with protein product		603482	"""beta-transducin repeat containing"""			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.687C>T	10.37:g.103285900C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	251	250	0.996016	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Silent	SNP	ENST00000370187.3	37	CCDS7512.1																																																																																			C|0.934;T|0.066	0.066	strong		0.483	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637	
AGAP1	116987	hgsc.bcm.edu	37	2	236708166	236708166	+	Splice_Site	SNP	C	C	T	rs2292708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:236708166C>T	ENST00000304032.8	+	8	1537	c.957C>T	c.(955-957)acC>acT	p.T319T	AGAP1_ENST00000409538.1_Splice_Site_p.T584T|AGAP1_ENST00000336665.5_Splice_Site_p.T319T|AGAP1_ENST00000428334.2_Splice_Site_p.T158T|AGAP1_ENST00000409457.1_Splice_Site_p.T319T	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	319					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)	p.T319T(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ACCTGTTCACCGTGAGTGTCA	0.542													C|||	960	0.191693	0.0295	0.4063	5008	,	,		18911	0.2708		0.2624	False		,,,				2504	0.1043				p.T319T		Atlas-SNP	.											AGAP1,NS,carcinoma,0,1	AGAP1	95	1	1	Substitution - coding silent(1)	prostate(1)	c.C957T						PASS	.	C	,	293,4113	159.6+/-192.1	14,265,1924	94.0	79.0	84.0		957,957	-2.0	1.0	2	dbSNP_100	84	2504,6096	412.1+/-350.7	374,1756,2170	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	AGAP1	NM_001037131.2,NM_014914.4	,	388,2021,4094	TT,TC,CC		29.1163,6.65,21.5055	,	319/858,319/805	236708166	2797,10209	2203	4300	6503	SO:0001630	splice_region_variant	116987	exon8			GTTCACCGTGAGT	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.957+1C>T	2.37:g.236708166C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Silent	SNP	ENST00000304032.8	37	CCDS33408.1																																																																																			C|0.787;T|0.213	0.213	strong		0.542	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	Silent
TGFBI	7045	hgsc.bcm.edu	37	5	135382989	135382989	+	Silent	SNP	G	G	C	rs1442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:135382989G>C	ENST00000442011.2	+	6	812	c.651G>C	c.(649-651)ctG>ctC	p.L217L	TGFBI_ENST00000305126.8_Silent_p.L217L	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	217	FAS1 1. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTGCCCGGCTGCTGAAAGCCG	0.537													G|||	1591	0.317692	0.0272	0.4481	5008	,	,		20502	0.369		0.4732	False		,,,				2504	0.4049				p.L217L		Atlas-SNP	.											.	TGFBI	76	.	0			c.G651C						PASS	.	G		394,3758		22,350,1704	123.0	118.0	119.0		651	3.2	1.0	5	dbSNP_36	119	3927,4501		950,2027,1237	no	coding-synonymous	TGFBI	NM_000358.2		972,2377,2941	CC,CG,GG		46.5947,9.4894,34.3482		217/684	135382989	4321,8259	2076	4214	6290	SO:0001819	synonymous_variant	7045	exon6			CCGGCTGCTGAAA	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.651G>C	5.37:g.135382989G>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	149	93	0.624161	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1																																																																																			G|0.651;C|0.349	0.349	strong		0.537	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
ALKBH3	221120	hgsc.bcm.edu	37	11	43940644	43940644	+	Silent	SNP	G	G	T	rs1048928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:43940644G>T	ENST00000302708.4	+	9	1137	c.726G>T	c.(724-726)ggG>ggT	p.G242G	ALKBH3-AS1_ENST00000528285.1_RNA|ALKBH3_ENST00000532410.1_3'UTR|ALKBH3-AS1_ENST00000499194.1_RNA|ALKBH3-AS1_ENST00000534287.1_RNA|ALKBH3-AS1_ENST00000527960.1_RNA|RP11-613D13.4_ENST00000526408.1_RNA	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	242	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	TGGATCATGGGACCTTGTTAA	0.423								Direct reversal of damage					G|||	3086	0.616214	0.2958	0.6542	5008	,	,		23097	0.8373		0.6243	False		,,,				2504	0.7863				p.G242G		Atlas-SNP	.											.	ALKBH3	33	.	0			c.G726T						PASS	.	G		1596,2810	497.6+/-363.9	288,1020,895	202.0	167.0	179.0		726	2.8	1.0	11	dbSNP_86	179	5368,3232	651.2+/-400.8	1671,2026,603	no	coding-synonymous	ALKBH3	NM_139178.3		1959,3046,1498	TT,TG,GG		37.5814,36.2233,46.4555		242/287	43940644	6964,6042	2203	4300	6503	SO:0001819	synonymous_variant	221120	exon9			TCATGGGACCTTG	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"""Alkylation repair homologs"""	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.726G>T	11.37:g.43940644G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Silent	SNP	ENST00000302708.4	37	CCDS7906.1	1346	0.6163003663003663	144	0.2926829268292683	236	0.6519337016574586	487	0.8513986013986014	479	0.6319261213720316	G	9.945	1.218599	0.22373	0.362233	0.624186	ENSG00000166199	ENST00000532129	.	.	.	5.91	2.83	0.33086	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999711	.	.	.	.	.	.	T	0.13926	-1.0491	3	.	.	.	-24.6034	7.4352	0.27152	0.167:0.1501:0.6829:0.0	rs1048928;rs3188976;rs3740987;rs17499464;rs58267847;rs1048928	.	.	.	Y	112	.	.	D	+	1	0	ALKBH3	43897220	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	0.148000	0.16224	0.837000	0.34925	0.655000	0.94253	GAC	G|0.420;T|0.580	0.580	strong		0.423	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178	
USP17L2	377630	hgsc.bcm.edu	37	8	11995062	11995062	+	Missense_Mutation	SNP	G	G	A	rs75807755	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11995062G>A	ENST00000333796.3	-	1	1524	c.1208C>T	c.(1207-1209)gCa>gTa	p.A403V	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	403	Mediates interaction with SUDS3.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A403V(1)		central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						TCCTTGCGTTGCTCGCCTGTC	0.562													G|||	1249	0.249401	0.0605	0.2233	5008	,	,		19556	0.5407		0.2316	False		,,,				2504	0.2413				p.A403V		Atlas-SNP	.											USP17L2,NS,carcinoma,0,1	USP17L2	47	1	1	Substitution - Missense(1)	stomach(1)	c.C1208T						PASS	.	G	VAL/ALA	281,3181		27,227,1477	40.0	44.0	43.0		1208	0.7	0.0	8	dbSNP_131	43	1722,6022		160,1402,2310	no	missense	USP17L2	NM_201402.2	64	187,1629,3787	AA,AG,GG		22.2366,8.1167,17.8744	probably-damaging	403/531	11995062	2003,9203	1731	3872	5603	SO:0001583	missense	377630	exon1			TGCGTTGCTCGCC	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.1208C>T	8.37:g.11995062G>A	ENSP00000333329:p.Ala403Val	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.790914	0.31685	0.081167	0.222366	ENSG00000223443	ENST00000333796	T	0.42513	0.97	0.745	0.745	0.18359	Hyaluronan/mRNA-binding protein (1);	27.040100	0.00616	N	0.000438	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.34241	0.444	B	0.42062	0.374	T	0.11036	-1.0604	9	0.27082	T	0.32	.	4.9133	0.13833	0.0:0.0:1.0:0.0	.	403	Q6R6M4	U17L2_HUMAN	V	403	ENSP00000333329:A403V	ENSP00000333329:A403V	A	-	2	0	USP17L2	12032471	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.587000	0.05780	0.733000	0.32492	0.472000	0.43445	GCA	G|0.841;A|0.159	0.159	strong		0.562	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
WDR93	56964	hgsc.bcm.edu	37	15	90248819	90248819	+	Silent	SNP	A	A	T	rs17238056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90248819A>T	ENST00000268130.7	+	4	632	c.531A>T	c.(529-531)ggA>ggT	p.G177G	RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000560294.1_Silent_p.G177G	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	177					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			ATAAGGAAGGACTTTACCTAG	0.328													T|||	2684	0.535942	0.6815	0.5058	5008	,	,		18671	0.2073		0.6183	False		,,,				2504	0.6145				p.G177G		Atlas-SNP	.											.	WDR93	63	.	0			c.A531T						PASS	.	T		2997,1403	459.6+/-352.3	1022,953,225	95.0	95.0	95.0		531	1.3	0.0	15	dbSNP_123	95	5711,2887	452.4+/-362.9	1888,1935,476	no	coding-synonymous	WDR93	NM_020212.1		2910,2888,701	TT,TA,AA		33.5776,31.8864,33.0051		177/687	90248819	8708,4290	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon4			GGAAGGACTTTAC		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.531A>T	15.37:g.90248819A>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	196	195	0.994898	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			A|0.382;T|0.618	0.618	strong		0.328	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
SH2D4B	387694	hgsc.bcm.edu	37	10	82363404	82363404	+	Missense_Mutation	SNP	A	A	G	rs7075840	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:82363404A>G	ENST00000470604.2	+	5	710	c.710A>G	c.(709-711)cAc>cGc	p.H237R	SH2D4B_ENST00000313455.4_Missense_Mutation_p.H189R|SH2D4B_ENST00000339284.2_Missense_Mutation_p.H238R			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	237			H -> R (in dbSNP:rs7075840).							endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			GAGTACCGACACCACTCGCTC	0.652													G|||	1806	0.360623	0.4592	0.255	5008	,	,		16244	0.5188		0.2386	False		,,,				2504	0.2648				p.H238R		Atlas-SNP	.											SH2D4B,NS,carcinoma,0,1	SH2D4B	44	1	0			c.A713G						scavenged	.	G	ARG/HIS,ARG/HIS	1903,2493		428,1047,723	23.0	25.0	24.0		566,713	6.0	1.0	10	dbSNP_116	24	2206,6388		278,1650,2369	no	missense,missense	SH2D4B	NM_001145719.1,NM_207372.2	29,29	706,2697,3092	GG,GA,AA		25.6691,43.2894,31.632	benign,benign	189/310,238/358	82363404	4109,8881	2198	4297	6495	SO:0001583	missense	387694	exon5			ACCGACACCACTC		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"""SH2 domain containing"""	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.710A>G	10.37:g.82363404A>G	ENSP00000417953:p.His237Arg	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Missense_Mutation	SNP	ENST00000470604.2	37		799	0.3658424908424908	208	0.42276422764227645	102	0.281767955801105	305	0.5332167832167832	184	0.24274406332453827	G	9.692	1.152045	0.21371	0.432894	0.256691	ENSG00000178217	ENST00000339284;ENST00000470604;ENST00000313455	T;T;T	0.04454	3.62;3.62;3.62	6.02	6.02	0.97574	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00030	-2.605	0.54753	P	1.4999999999987246E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40720	-0.9548	9	0.02654	T	1	-16.2888	13.3408	0.60542	0.0757:0.0:0.9243:0.0	rs7075840;rs7075840	189;238	Q5SQS7-3;Q5SQS7-2	.;.	R	238;237;189	ENSP00000345295:H238R;ENSP00000417953:H237R;ENSP00000314242:H189R	ENSP00000314242:H189R	H	+	2	0	SH2D4B	82353384	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.429000	0.59901	1.579000	0.49836	-0.119000	0.15052	CAC	A|0.661;G|0.339	0.339	strong		0.652	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
ASPM	259266	hgsc.bcm.edu	37	1	197094030	197094030	+	Silent	SNP	C	C	T	rs6676084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197094030C>T	ENST00000367409.4	-	12	3394	c.3138G>A	c.(3136-3138)agG>agA	p.R1046R	ASPM_ENST00000367408.1_Silent_p.R296R|ASPM_ENST00000294732.7_Silent_p.R1046R	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1046	CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TCCAAAGCAACCTGAGAGTTT	0.294													C|||	1085	0.216653	0.1324	0.2147	5008	,	,		15024	0.1488		0.328	False		,,,				2504	0.2873				p.R1046R		Atlas-SNP	.											.	ASPM	444	.	0			c.G3138A						PASS	.	C	,	692,3714	285.7+/-278.4	70,552,1581	146.0	156.0	153.0		3138,3138	-5.4	0.0	1	dbSNP_116	153	2735,5863	433.6+/-357.5	421,1893,1985	no	coding-synonymous,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	491,2445,3566	TT,TC,CC		31.8097,15.7059,26.3534	,	1046/1893,1046/3478	197094030	3427,9577	2203	4299	6502	SO:0001819	synonymous_variant	259266	exon12			AAGCAACCTGAGA	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3138G>A	1.37:g.197094030C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			C|0.754;N|0.000	.	strong		0.294	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
CD44	960	hgsc.bcm.edu	37	11	35222681	35222681	+	Silent	SNP	C	C	T	rs35356320	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:35222681C>T	ENST00000428726.2	+	8	1098	c.975C>T	c.(973-975)acC>acT	p.T325T	CD44_ENST00000415148.2_Silent_p.T282T|CD44_ENST00000360158.4_Intron|CD44_ENST00000437706.2_Silent_p.T325T|CD44_ENST00000433892.2_Intron|CD44_ENST00000433354.2_Silent_p.T325T|CD44_ENST00000278386.6_Intron|CD44_ENST00000263398.6_Intron|CD44_ENST00000526669.2_Intron|CD44_ENST00000449691.2_Silent_p.T325T|CD44_ENST00000352818.4_Intron|CD44_ENST00000434472.2_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	325	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	AGGACTGGACCCAGTGGAACC	0.418													C|||	137	0.0273562	0.0166	0.049	5008	,	,		19029	0.0		0.0686	False		,,,				2504	0.0123				p.T325T		Atlas-SNP	.											.	CD44	48	.	0			c.C975T						PASS	.	C	,,,,,,,	99,4305	80.9+/-119.3	1,97,2104	148.0	151.0	150.0		975,846,,,,,,	-6.0	0.0	11	dbSNP_126	150	504,8092	144.7+/-200.5	16,472,3810	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,intron	CD44	NM_000610.3,NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1,NM_001202555.1,NM_001202556.1,NM_001202557.1	,,,,,,,	17,569,5914	TT,TC,CC		5.8632,2.248,4.6385	,,,,,,,	325/743,282/700,,,,,,	35222681	603,12397	2202	4298	6500	SO:0001819	synonymous_variant	960	exon8			CTGGACCCAGTGG	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.975C>T	11.37:g.35222681C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	45	0.56962	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	37	CCDS7897.1	89	0.04075091575091575	10	0.02032520325203252	19	0.052486187845303865	0	0.0	60	0.079155672823219	C	3.793	-0.043357	0.07452	0.02248	0.058632	ENSG00000026508	ENST00000528455;ENST00000524922;ENST00000526553	.	.	.	5.49	-5.96	0.02234	.	.	.	.	.	T	0.00936	0.0031	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.22173	-1.0224	4	.	.	.	2.0058	4.4764	0.11746	0.3631:0.1692:0.3913:0.0764	rs35356320;rs61752931	.	.	.	S	177;70;18	.	.	P	+	1	0	CD44	35179257	0.000000	0.05858	0.000000	0.03702	0.569000	0.35902	-2.207000	0.01230	-0.939000	0.03709	0.655000	0.94253	CCA	C|0.956;T|0.044	0.044	strong		0.418	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
ZBTB21	49854	hgsc.bcm.edu	37	21	43413158	43413158	+	Silent	SNP	C	C	T	rs147318145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43413158C>T	ENST00000310826.5	-	3	1230	c.1047G>A	c.(1045-1047)caG>caA	p.Q349Q	ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398505.3_Silent_p.Q349Q|ZBTB21_ENST00000398499.1_Silent_p.Q349Q|ZBTB21_ENST00000398511.3_Silent_p.Q349Q	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	349					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										AGACAGGAACCTGGCTATCCA	0.478													C|||	38	0.00758786	0.0008	0.0144	5008	,	,		19466	0.0		0.0229	False		,,,				2504	0.0041				p.Q349Q		Atlas-SNP	.											.	.	.	.	0			c.G1047A						PASS	.	C	,,	27,4379	33.5+/-64.1	0,27,2176	99.0	98.0	99.0		1047,1047,1047	5.1	1.0	21	dbSNP_134	99	232,8368	94.2+/-156.2	3,226,4071	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF295	NM_001098402.1,NM_001098403.1,NM_020727.4	,,	3,253,6247	TT,TC,CC		2.6977,0.6128,1.9914	,,	349/1067,349/866,349/1067	43413158	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	49854	exon3			AGGAACCTGGCTA	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.1047G>A	21.37:g.43413158C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Silent	SNP	ENST00000310826.5	37	CCDS13678.1																																																																																			C|0.983;T|0.017	0.017	strong		0.478	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610401	32610401	+	Missense_Mutation	SNP	G	G	A	rs9272785|rs386699558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32610401G>A	ENST00000343139.5	+	4	730	c.628G>A	c.(628-630)Gcc>Acc	p.A210T	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.A210T|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.A210T	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	209	Connecting peptide.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TGAGATTCCAGCCCCTATGTC	0.552													.|||	859	0.171526	0.0968	0.2738	5008	,	,		16922	0.2738		0.168	False		,,,				2504	0.0982				p.A210T		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.G628A						PASS	.	G	THR/ALA	325,2695		20,285,1205	142.0	125.0	131.0		628	-3.5	0.0	6	dbSNP_118	131	965,4453		86,793,1830	yes	missense	HLA-DQA1	NM_002122.3	58	106,1078,3035	AA,AG,GG		17.811,10.7616,15.288	benign	210/256	32610401	1290,7148	1510	2709	4219	SO:0001583	missense	3117	exon4			ATTCCAGCCCCTA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.628G>A	6.37:g.32610401G>A	ENSP00000339398:p.Ala210Thr	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	266	94	0.353383	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	427	0.1955128205128205	35	0.07113821138211382	84	0.23204419889502761	173	0.30244755244755245	135	0.17810026385224276	.	0.208	-1.038663	0.02013	0.107616	0.17811	ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000374949	T;T;T	0.01745	4.66;4.66;4.66	4.08	-3.47	0.04753	.	1.218800	0.05995	N	0.646663	T	0.00241	0.0007	N	0.03224	-0.385	0.53688	P	2.5000000000052758E-5	B	0.06786	0.001	B	0.14578	0.011	T	0.45234	-0.9275	9	0.10111	T	0.7	.	2.2792	0.04110	0.3309:0.1297:0.4092:0.1302	rs9272785;rs12722091	210	G4XQK2	.	T	210	ENSP00000339398:A210T;ENSP00000378767:A210T;ENSP00000364087:A210T	ENSP00000339398:A210T	A	+	1	0	HLA-DQA1	32718379	0.000000	0.05858	0.046000	0.18839	0.001000	0.01503	-1.255000	0.02872	-0.445000	0.07159	-0.162000	0.13425	GCC	G|0.834;A|0.166	0.166	strong		0.552	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
PASD1	139135	hgsc.bcm.edu	37	X	150840742	150840742	+	Missense_Mutation	SNP	G	G	A	rs41312626		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:150840742G>A	ENST00000370357.4	+	14	1770	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	509	Lys-rich.					nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					GCAAAGGAAGGTGCagaagca	0.537													G|||	54	0.0143046	0.0023	0.0115	3775	,	,		13895	0.0		0.0219	False		,,,				2504	0.0215				p.V509M		Atlas-SNP	.											.	PASD1	286	.	0			c.G1525A						PASS	.	G	MET/VAL	14,3589		0,12,2,1559,459	29.0	28.0	28.0		1525	-0.6	0.0	X	dbSNP_127	28	141,6183		0,92,49,2258,1575	yes	missense	PASD1	NM_173493.2	21	0,104,51,3817,2034	AA,AG,A,GG,G		2.2296,0.3886,1.5614	probably-damaging	509/774	150840742	155,9772	2032	3974	6006	SO:0001583	missense	139135	exon14			AGGAAGGTGCAGA	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1525G>A	X.37:g.150840742G>A	ENSP00000359382:p.Val509Met	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	26	0.01567209162145871	3	0.006097560975609756	2	0.005555555555555556	0	0.0	14	0.01876675603217158	G	3.288	-0.145490	0.06627	0.003886	0.022296	ENSG00000166049	ENST00000370357	T	0.19394	2.15	0.681	-0.58	0.11717	.	.	.	.	.	T	0.07279	0.0184	N	0.08118	0	0.80722	P	0.0	D	0.62365	0.991	P	0.53224	0.721	T	0.22765	-1.0207	7	0.66056	D	0.02	.	.	.	.	rs41312626	509	Q8IV76	PASD1_HUMAN	M	509	ENSP00000359382:V509M	ENSP00000359382:V509M	V	+	1	0	PASD1	150591398	0.012000	0.17670	0.007000	0.13788	0.217000	0.24651	-0.070000	0.11523	-0.274000	0.09232	0.462000	0.41574	GTG	G|0.984;A|0.016	0.016	strong		0.537	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
MDN1	23195	hgsc.bcm.edu	37	6	90408589	90408589	+	Silent	SNP	A	A	G	rs3736984	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90408589A>G	ENST00000369393.3	-	59	9278	c.9163T>C	c.(9163-9165)Ttg>Ctg	p.L3055L	MDN1_ENST00000428876.1_Silent_p.L3055L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3055					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CAAACCTTCAATGTGGAGTCC	0.408													A|||	770	0.153754	0.0779	0.1225	5008	,	,		16357	0.0813		0.1869	False		,,,				2504	0.319				p.L3055L		Atlas-SNP	.											.	MDN1	478	.	0			c.T9163C						PASS	.	A		384,4022	191.6+/-217.2	22,340,1841	100.0	105.0	103.0		9163	-4.8	0.0	6	dbSNP_107	103	1547,7053	290.7+/-299.9	156,1235,2909	no	coding-synonymous	MDN1	NM_014611.1		178,1575,4750	GG,GA,AA		17.9884,8.7154,14.847		3055/5597	90408589	1931,11075	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon59			CCTTCAATGTGGA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.9163T>C	6.37:g.90408589A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	55	18	0.327273	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			A|0.865;G|0.135	0.135	strong		0.408	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
DNAH7	56171	hgsc.bcm.edu	37	2	196837129	196837129	+	Missense_Mutation	SNP	G	G	C	rs73042525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:196837129G>C	ENST00000312428.6	-	16	1995	c.1895C>G	c.(1894-1896)tCc>tGc	p.S632C		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	632	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GCAGTTTTTGGAATCCACTAA	0.398													G|||	284	0.0567093	0.149	0.036	5008	,	,		18315	0.0		0.0527	False		,,,				2504	0.0092				p.S632C		Atlas-SNP	.											.	DNAH7	512	.	0			c.C1895G						PASS	.	G	CYS/SER	450,3296		26,398,1449	172.0	158.0	163.0		1895	4.8	1.0	2	dbSNP_130	163	406,7816		7,392,3712	yes	missense	DNAH7	NM_018897.2	112	33,790,5161	CC,CG,GG		4.938,12.0128,7.1524	benign	632/4025	196837129	856,11112	1873	4111	5984	SO:0001583	missense	56171	exon16			TTTTTGGAATCCA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.1895C>G	2.37:g.196837129G>C	ENSP00000311273:p.Ser632Cys	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	256	121	0.472656	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	125	0.05723443223443223	71	0.1443089430894309	12	0.03314917127071823	0	0.0	42	0.055408970976253295	G	12.47	1.946662	0.34377	0.120128	0.04938	ENSG00000118997	ENST00000312428	T	0.22945	1.93	4.75	4.75	0.60458	.	0.073027	0.56097	D	0.000033	T	0.00210	0.0006	L	0.55103	1.725	0.09310	P	1.0	B	0.14012	0.009	B	0.11329	0.006	T	0.06144	-1.0843	9	0.31617	T	0.26	.	17.7101	0.88319	0.0:0.0:1.0:0.0	.	632	Q8WXX0	DYH7_HUMAN	C	632	ENSP00000311273:S632C	ENSP00000311273:S632C	S	-	2	0	DNAH7	196545374	1.000000	0.71417	0.997000	0.53966	0.443000	0.32047	8.374000	0.90133	2.350000	0.79820	0.557000	0.71058	TCC	G|0.943;C|0.057	0.057	strong		0.398	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
LRRC61	65999	hgsc.bcm.edu	37	7	150034184	150034184	+	Silent	SNP	T	T	C	rs3735170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150034184T>C	ENST00000359623.4	+	3	822	c.234T>C	c.(232-234)gcT>gcC	p.A78A	LRRC61_ENST00000323078.7_Silent_p.A78A|LRRC61_ENST00000493307.1_Silent_p.A78A	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	78										endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			GCCAGCTAGCTGTGCTCAATG	0.647													C|||	1295	0.258586	0.2625	0.1571	5008	,	,		17325	0.2907		0.2455	False		,,,				2504	0.3057				p.A78A		Atlas-SNP	.											LRRC61,rectum,carcinoma,0,1	LRRC61	17	1	0			c.T234C						PASS	.	C	,	1062,3342	697.3+/-406.2	129,804,1269	49.0	46.0	47.0		234,234	-7.1	0.0	7	dbSNP_107	47	2188,6412	681.9+/-403.8	286,1616,2398	no	coding-synonymous,coding-synonymous	LRRC61	NM_001142928.1,NM_023942.2	,	415,2420,3667	CC,CT,TT		25.4419,24.1144,24.9923	,	78/260,78/260	150034184	3250,9754	2202	4300	6502	SO:0001819	synonymous_variant	65999	exon2			GCTAGCTGTGCTC	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.234T>C	7.37:g.150034184T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_023942	B3KUW0|D3DWY8	Silent	SNP	ENST00000359623.4	37	CCDS5901.1																																																																																			T|0.745;C|0.255	0.255	strong		0.647	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942	
ABHD15	116236	hgsc.bcm.edu	37	17	27889963	27889963	+	Silent	SNP	C	C	G	rs721479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:27889963C>G	ENST00000307201.4	-	2	1193	c.1023G>C	c.(1021-1023)ccG>ccC	p.P341P	RP11-68I3.2_ENST00000581474.1_RNA	NM_198147.2	NP_937790.2	Q6UXT9	ABH15_HUMAN	abhydrolase domain containing 15	341						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	10						CATCCCGGAGCGGGTCGTTGC	0.587													G|||	1116	0.222843	0.3631	0.1354	5008	,	,		18592	0.2044		0.1759	False		,,,				2504	0.1626				p.P341P		Atlas-SNP	.											.	ABHD15	18	.	0			c.G1023C						PASS	.	G		1479,2927	676.1+/-403.2	269,941,993	69.0	64.0	66.0		1023	1.5	1.0	17	dbSNP_86	66	1425,7175	750.0+/-407.4	115,1195,2990	no	coding-synonymous	ABHD15	NM_198147.2		384,2136,3983	GG,GC,CC		16.5698,33.5679,22.3282		341/469	27889963	2904,10102	2203	4300	6503	SO:0001819	synonymous_variant	116236	exon2			CCGGAGCGGGTCG	AK056717	CCDS32602.1	17q11.2	2009-11-20			ENSG00000168792	ENSG00000168792		"""Abhydrolase domain containing"""	26971	protein-coding gene	gene with protein product						12975309	Standard	NM_198147		Approved		uc002hed.2	Q6UXT9		ENST00000307201.4:c.1023G>C	17.37:g.27889963C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_198147	Q96EC5	Silent	SNP	ENST00000307201.4	37	CCDS32602.1																																																																																			C|0.776;G|0.224	0.224	strong		0.587	ABHD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447796.2	NM_198147	
CHRND	1144	hgsc.bcm.edu	37	2	233390937	233390937	+	Silent	SNP	A	A	G	rs2245601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:233390937A>G	ENST00000258385.3	+	1	44	c.12A>G	c.(10-12)ccA>ccG	p.P4P	CHRND_ENST00000543200.1_Silent_p.P4P|CHRND_ENST00000457943.2_5'UTR|CHRND_ENST00000536614.1_Silent_p.P4P	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	4					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)	p.P4P(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	TGGAGGGGCCAGTGCTGACAC	0.667													A|||	2421	0.483427	0.3502	0.5461	5008	,	,		11714	0.6518		0.4483	False		,,,				2504	0.4816				p.P4P		Atlas-SNP	.											CHRND,NS,carcinoma,0,1	CHRND	67	1	1	Substitution - coding silent(1)	stomach(1)	c.A12G						PASS	.	A		1676,2730	501.5+/-365.0	313,1050,840	60.0	61.0	61.0		12	-4.7	0.1	2	dbSNP_100	61	4159,4439	564.2+/-388.3	1024,2111,1164	no	coding-synonymous	CHRND	NM_000751.1		1337,3161,2004	GG,GA,AA		48.3717,38.039,44.8708		4/518	233390937	5835,7169	2203	4299	6502	SO:0001819	synonymous_variant	1144	exon1			GGGGCCAGTGCTG	X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1965	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, delta (muscle)"""	100720	"""cholinergic receptor, nicotinic, delta"""	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.12A>G	2.37:g.233390937A>G		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	230	107	0.465217	NM_000751	A8K661|B4DT92|Q52LH4	Silent	SNP	ENST00000258385.3	37	CCDS2494.1																																																																																			A|0.542;G|0.458	0.458	strong		0.667	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2		
GNPTAB	79158	hgsc.bcm.edu	37	12	102158763	102158763	+	Silent	SNP	T	T	C	rs386765812|rs10778148	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:102158763T>C	ENST00000299314.7	-	13	2194	c.1932A>G	c.(1930-1932)acA>acG	p.T644T	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	644					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)	p.T644T(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						CCTTCTGGGCTGTAGAATTCA	0.403													C|||	3262	0.651358	0.6241	0.5346	5008	,	,		20492	0.8978		0.5318	False		,,,				2504	0.6401				p.T644T		Atlas-SNP	.											GNPTAB,NS,carcinoma,0,1	GNPTAB	120	1	1	Substitution - coding silent(1)	prostate(1)	c.A1932G						PASS	.	C		2824,1582	491.7+/-362.2	921,982,300	188.0	179.0	182.0		1932	-11.9	0.0	12	dbSNP_120	182	4492,4108	561.2+/-387.7	1173,2146,981	no	coding-synonymous	GNPTAB	NM_024312.4		2094,3128,1281	CC,CT,TT		47.7674,35.9056,43.749		644/1257	102158763	7316,5690	2203	4300	6503	SO:0001819	synonymous_variant	79158	exon13			CTGGGCTGTAGAA	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"""EF-hand domain containing"""	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.1932A>G	12.37:g.102158763T>C		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	278	278	1	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Silent	SNP	ENST00000299314.7	37	CCDS9088.1																																																																																			T|0.398;C|0.602	0.602	strong		0.403	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1		
DPP10	57628	hgsc.bcm.edu	37	2	116510817	116510817	+	Missense_Mutation	SNP	G	G	C	rs2053724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:116510817G>C	ENST00000410059.1	+	11	1498	c.1018G>C	c.(1018-1020)Gct>Cct	p.A340P	DPP10_ENST00000409163.1_Missense_Mutation_p.A290P|DPP10_ENST00000393147.2_Missense_Mutation_p.A344P|DPP10_ENST00000310323.8_Missense_Mutation_p.A333P	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	340			A -> P (in dbSNP:rs2053724). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:12675227}.			integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						GTTAAACCGAGCTCAGAACAT	0.343													C|||	2651	0.529353	0.1589	0.732	5008	,	,		14616	0.7321		0.6252	False		,,,				2504	0.5787				p.A344P		Atlas-SNP	.											DPP10_ENST00000410059,NS,carcinoma,0,2	DPP10	415	2	0			c.G1030C						PASS	.	C	PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA	1001,3405	729.7+/-410.1	114,773,1316	124.0	110.0	115.0		997,1030,868,1006,1018	3.2	1.0	2	dbSNP_94	115	5216,3384	499.2+/-374.9	1581,2054,665	yes	missense,missense,missense,missense,missense	DPP10	NM_001004360.3,NM_001178034.1,NM_001178036.1,NM_001178037.1,NM_020868.3	27,27,27,27,27	1695,2827,1981	CC,CG,GG		39.3488,22.719,47.801	benign,benign,benign,benign,benign	333/790,344/801,290/747,336/793,340/797	116510817	6217,6789	2203	4300	6503	SO:0001583	missense	57628	exon11			AACCGAGCTCAGA	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1018G>C	2.37:g.116510817G>C	ENSP00000386565:p.Ala340Pro	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	157	81	0.515924	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	1249	0.5718864468864469	92	0.18699186991869918	254	0.7016574585635359	429	0.75	474	0.6253298153034301	C	10.02	1.237402	0.22711	0.22719	0.606512	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.1	3.2	0.36748	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.270402	0.36893	N	0.002354	T	0.00012	0.0000	L	0.42744	1.35	0.50467	P	1.24000000000013E-4	B;B;B;B	0.18310	0.01;0.0;0.027;0.013	B;B;B;B	0.10450	0.002;0.0;0.005;0.004	T	0.17289	-1.0374	9	0.19147	T	0.46	-19.192	17.1445	0.86763	0.0:0.5308:0.4691:0.0	rs2053724;rs52799400;rs60675889;rs2053724	333;344;336;340	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	P	340;290;344;333;290	ENSP00000386565:A340P;ENSP00000387038:A290P;ENSP00000376855:A344P;ENSP00000309066:A333P	ENSP00000309066:A333P	A	+	1	0	DPP10	116227287	1.000000	0.71417	0.991000	0.47740	0.927000	0.56198	1.938000	0.40203	0.734000	0.32515	-0.127000	0.14921	GCT	G|0.483;C|0.517	0.517	strong		0.343	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
SOS2	6655	hgsc.bcm.edu	37	14	50585248	50585248	+	Silent	SNP	C	C	T	rs2227276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50585248C>T	ENST00000216373.5	-	23	4087	c.3813G>A	c.(3811-3813)ccG>ccA	p.P1271P	VCPKMT_ENST00000395859.2_5'Flank|VCPKMT_ENST00000395860.2_5'Flank|SOS2_ENST00000543680.1_Silent_p.P1238P	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	1271					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					AGCATCGACGCGGTACCCTTG	0.517													C|||	1218	0.243211	0.2201	0.2435	5008	,	,		17245	0.4315		0.1461	False		,,,				2504	0.18				p.P1271P		Atlas-SNP	.											.	SOS2	195	.	0			c.G3813A						PASS	.	C		883,3523	342.8+/-307.3	89,705,1409	145.0	120.0	128.0		3813	-3.7	1.0	14	dbSNP_98	128	1355,7245	264.9+/-285.8	113,1129,3058	no	coding-synonymous	SOS2	NM_006939.2		202,1834,4467	TT,TC,CC		15.7558,20.0409,17.2074		1271/1333	50585248	2238,10768	2203	4300	6503	SO:0001819	synonymous_variant	6655	exon23			TCGACGCGGTACC	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.3813G>A	14.37:g.50585248C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	166	72	0.433735	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Silent	SNP	ENST00000216373.5	37	CCDS9697.1																																																																																			T|0.202;C|0.798	0.202	strong		0.517	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
CDNF	441549	hgsc.bcm.edu	37	10	14862082	14862082	+	Missense_Mutation	SNP	C	C	G	rs61738953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:14862082C>G	ENST00000378442.1	-	6	658	c.155G>C	c.(154-156)tGg>tCg	p.W52S	CDNF_ENST00000378441.2_5'UTR			Q49AH0	CDNF_HUMAN	cerebral dopamine neurotrophic factor	154						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(1)	5						CTCCTCCCCCCAGCTATGCAG	0.502													C|||	68	0.0135783	0.0008	0.0259	5008	,	,		17873	0.0		0.0408	False		,,,				2504	0.0082				p.W154S		Atlas-SNP	.											.	CDNF	19	.	0			c.G461C						PASS	.	C	SER/TRP	39,4367	43.1+/-76.7	0,39,2164	138.0	138.0	138.0		461	5.9	1.0	10	dbSNP_129	138	350,8250	118.3+/-177.8	4,342,3954	yes	missense	CDNF	NM_001029954.2	177	4,381,6118	GG,GC,CC		4.0698,0.8852,2.9909	probably-damaging	154/188	14862082	389,12617	2203	4300	6503	SO:0001583	missense	441549	exon4			TCCCCCCAGCTAT	BC037872	CCDS31148.1	10p13	2009-06-04	2009-06-04	2009-06-04	ENSG00000185267	ENSG00000185267			24913	protein-coding gene	gene with protein product	"""conserved dopamine neurotrophic factor"""	611233	"""arginine-rich, mutated in early stage tumors-like 1"""	ARMETL1		17611540	Standard	NM_001029954		Approved		uc001inb.1	Q49AH0	OTTHUMG00000017713	ENST00000378442.1:c.155G>C	10.37:g.14862082C>G	ENSP00000367703:p.Trp52Ser	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	199	98	0.492462	NM_001029954	A2RUU0|B4DVW3	Missense_Mutation	SNP	ENST00000378442.1	37		45	0.020604395604395604	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	32	0.04221635883905013	C	26.0	4.693187	0.88735	0.008852	0.040698	ENSG00000185267	ENST00000378442;ENST00000465530	.	.	.	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.62551	0.2437	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78999	-0.1982	9	0.72032	D	0.01	-19.457	19.0536	0.93054	0.0:1.0:0.0:0.0	rs61738953	154	Q49AH0	CDNF_HUMAN	S	52;154	.	ENSP00000367703:W52S	W	-	2	0	CDNF	14902088	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	6.699000	0.74613	2.806000	0.96561	0.655000	0.94253	TGG	C|0.964;G|0.036	0.036	strong		0.502	CDNF-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000046919.1	NM_001029954	
CEP63	80254	hgsc.bcm.edu	37	3	134278270	134278270	+	Splice_Site	SNP	C	C	T	rs1127826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:134278270C>T	ENST00000337090.3	+	14	2125	c.1952C>T	c.(1951-1953)tCg>tTg	p.S651L	CEP63_ENST00000354446.3_Intron|CEP63_ENST00000513612.2_Splice_Site_p.S651L|CEP63_ENST00000606977.1_Splice_Site_p.S651L|CEP63_ENST00000383229.3_Intron|CEP63_ENST00000332047.5_Intron			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	651			S -> L (in dbSNP:rs1127826).		centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TTTATATCTTCGGTATGGAAA	0.313													C|||	1638	0.327077	0.0219	0.5288	5008	,	,		19506	0.6002		0.3668	False		,,,				2504	0.274				p.S651L		Atlas-SNP	.											.	CEP63	56	.	0			c.C1952T						PASS	.	C	,,,LEU/SER	402,4004	187.4+/-214.1	17,368,1818	47.0	46.0	47.0		,,,1952	-2.9	0.8	3	dbSNP_86	47	3075,5525	463.1+/-365.9	531,2013,1756	yes	intron,intron,intron,missense-near-splice	CEP63	NM_001042383.1,NM_001042384.1,NM_001042400.1,NM_025180.3	,,,145	548,2381,3574	TT,TC,CC		35.7558,9.1239,26.7338	,,,possibly-damaging	,,,651/704	134278270	3477,9529	2203	4300	6503	SO:0001630	splice_region_variant	80254	exon15			TATCTTCGGTATG	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1953+1C>T	3.37:g.134278270C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	796	0.36446886446886445	20	0.04065040650406504	166	0.4585635359116022	341	0.5961538461538461	269	0.3548812664907652	C	12.56	1.975602	0.34848	0.091239	0.357558	ENSG00000182923	ENST00000337090;ENST00000513612	T;T	0.18016	2.24;2.24	5.35	-2.93	0.05598	.	0.948307	0.08789	N	0.893552	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	0.9999999403245	B	0.06786	0.001	B	0.06405	0.002	T	0.42616	-0.9441	9	0.26408	T	0.33	1.3872	6.7487	0.23475	0.1413:0.1855:0.0:0.6732	rs1127826;rs9868985;rs17352684;rs52808223;rs57512520;rs9868985	651	Q96MT8	CEP63_HUMAN	L	651	ENSP00000336524:S651L;ENSP00000426129:S651L	ENSP00000336524:S651L	S	+	2	0	CEP63	135760960	0.998000	0.40836	0.840000	0.33206	0.950000	0.60333	0.235000	0.17948	-0.737000	0.04824	-0.142000	0.14014	TCG	C|0.695;T|0.305	0.305	strong		0.313	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	Missense_Mutation
CCDC6	8030	hgsc.bcm.edu	37	10	61552692	61552692	+	Missense_Mutation	SNP	G	G	T	rs1053266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:61552692G>T	ENST00000263102.6	-	9	1639	c.1408C>A	c.(1408-1410)Ccc>Acc	p.P470T		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	470			P -> T (in dbSNP:rs1053266). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8058316, ECO:0000269|Ref.4}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)	p.P470T(1)	CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		TGGGAGGAGGGGTGCGCCGAA	0.597			T	RET	NSCLC								G|||	2180	0.435304	0.1989	0.598	5008	,	,		16944	0.6121		0.4503	False		,,,				2504	0.4417				p.P470T		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	CCDC6,NS,carcinoma,0,1	CCDC6	44	1	1	Substitution - Missense(1)	stomach(1)	c.C1408A						scavenged	.	G	THR/PRO	1164,3242	411.7+/-335.8	177,810,1216	146.0	139.0	142.0		1408	5.6	1.0	10	dbSNP_86	142	4329,4271	579.5+/-390.9	1098,2133,1069	yes	missense	CCDC6	NM_005436.4	38	1275,2943,2285	TT,TG,GG		49.6628,26.4185,42.2344	probably-damaging	470/475	61552692	5493,7513	2203	4300	6503	SO:0001583	missense	8030	exon9			AGGAGGGGTGCGC	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.1408C>A	10.37:g.61552692G>T	ENSP00000263102:p.Pro470Thr	Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	201	97	0.482587	NM_005436	Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	37	CCDS7257.1	1001	0.4583333333333333	109	0.22154471544715448	211	0.5828729281767956	328	0.5734265734265734	353	0.4656992084432718	G	17.13	3.311702	0.60414	0.264185	0.503372	ENSG00000108091	ENST00000263102	T	0.55052	0.54	5.6	5.6	0.85130	.	0.410909	0.25467	N	0.030472	T	0.00012	0.0000	L	0.44542	1.39	0.09310	P	0.999999823558	D	0.71674	0.998	D	0.76071	0.987	T	0.51482	-0.8700	9	0.66056	D	0.02	1.6527	19.9854	0.97342	0.0:0.0:1.0:0.0	rs1053266;rs3193780;rs3750802;rs57560743;rs1053266	470	Q16204	CCDC6_HUMAN	T	470	ENSP00000263102:P470T	ENSP00000263102:P470T	P	-	1	0	CCDC6	61222698	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.852000	0.92215	2.786000	0.95864	0.563000	0.77884	CCC	G|0.577;T|0.423	0.423	strong		0.597	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
AK9	221264	hgsc.bcm.edu	37	6	109954518	109954518	+	Silent	SNP	T	T	C	rs9374111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:109954518T>C	ENST00000424296.2	-	11	1018	c.942A>G	c.(940-942)ctA>ctG	p.L314L	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000368948.2_Silent_p.L314L|AK9_ENST00000285397.5_Silent_p.L314L	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	314					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)	p.L314L(2)									GAGTACGAAATAGCTCATCCT	0.313													T|||	1224	0.244409	0.1097	0.2839	5008	,	,		16419	0.3433		0.2197	False		,,,				2504	0.3221				p.L314L		Atlas-SNP	.											AKD1_ENST00000424296,NS,carcinoma,0,2	AKD1	223	2	2	Substitution - coding silent(2)	stomach(2)	c.A942G						PASS	.	T	,	557,3849	237.7+/-249.4	40,477,1686	77.0	75.0	76.0		942,942	-4.4	0.0	6	dbSNP_119	76	1977,6615	342.4+/-324.5	215,1547,2534	no	coding-synonymous,coding-synonymous	AKD1	NM_001145128.2,NM_145025.4	,	255,2024,4220	CC,CT,TT		23.0098,12.6419,19.4953	,	314/1912,314/422	109954518	2534,10464	2203	4296	6499	SO:0001819	synonymous_variant	221264	exon11			ACGAAATAGCTCA	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.942A>G	6.37:g.109954518T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	30	9	0.3	NM_145025	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	37	CCDS55048.1	477	0.2184065934065934	52	0.10569105691056911	94	0.2596685082872928	163	0.28496503496503495	168	0.22163588390501318	T	3.665	-0.068715	0.07228	0.126419	0.230098	ENSG00000155085	ENST00000524674	.	.	.	5.76	-4.37	0.03633	.	.	.	.	.	T	0.06600	0.0169	.	.	.	0.19300	P	0.999979151	.	.	.	.	.	.	T	0.34179	-0.9839	3	.	.	.	-2.1874	2.143	0.03779	0.1254:0.1704:0.2628:0.4414	rs9374111;rs56417458;rs9374111	.	.	.	C	169	.	.	Y	-	2	0	AKD1	110061211	0.003000	0.15002	0.001000	0.08648	0.003000	0.03518	-0.982000	0.03762	-0.398000	0.07679	-1.064000	0.02280	TAT	C|0.211;N|0.000	0.211	strong		0.313	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
GDPD5	81544	hgsc.bcm.edu	37	11	75160575	75160575	+	Silent	SNP	G	G	A	rs518611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:75160575G>A	ENST00000336898.3	-	8	1392	c.555C>T	c.(553-555)cgC>cgT	p.R185R	GDPD5_ENST00000529721.1_Silent_p.R185R|GDPD5_ENST00000533784.1_Silent_p.R66R|GDPD5_ENST00000376282.3_Silent_p.R66R|GDPD5_ENST00000533805.1_5'UTR|GDPD5_ENST00000526177.1_Silent_p.R47R|GDPD5_ENST00000443276.2_3'UTR	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	185					cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						TCCGCTCTGCGCGGGCGAACT	0.642													g|||	2679	0.534944	0.2073	0.6282	5008	,	,		15737	0.8095		0.6203	False		,,,				2504	0.5409				p.R185R		Atlas-SNP	.											.	GDPD5	49	.	0			c.C555T						PASS	.	A		1241,3153		194,853,1150	35.0	32.0	33.0		555	-9.9	0.1	11	dbSNP_83	33	5459,3099		1772,1915,592	no	coding-synonymous	GDPD5	NM_030792.6		1966,2768,1742	AA,AG,GG		36.2117,28.2431,48.2705		185/606	75160575	6700,6252	2197	4279	6476	SO:0001819	synonymous_variant	81544	exon8			CTCTGCGCGGGCG	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.555C>T	11.37:g.75160575G>A		Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	364	362	0.994505	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Silent	SNP	ENST00000336898.3	37	CCDS8238.1																																																																																			G|0.479;A|0.521	0.521	strong		0.642	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792	
DNAH9	1770	hgsc.bcm.edu	37	17	11833287	11833287	+	Silent	SNP	A	A	G	rs2286303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11833287A>G	ENST00000262442.4	+	63	12050	c.11982A>G	c.(11980-11982)ccA>ccG	p.P3994P	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Intron|DNAH9_ENST00000608377.1_Silent_p.P306P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3994	AAA 6. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GTGCAGAGCCAGCACCCTCCC	0.592													G|||	1114	0.222444	0.0787	0.2651	5008	,	,		17640	0.1815		0.341	False		,,,				2504	0.3067				p.P3994P		Atlas-SNP	.											.	DNAH9	695	.	0			c.A11982G						PASS	.	G	,	491,3915	779.8+/-414.4	32,427,1744	84.0	63.0	70.0		11982,918	-4.5	0.3	17	dbSNP_100	70	2858,5742	673.2+/-403.0	483,1892,1925	no	coding-synonymous,coding-synonymous	DNAH9	NM_001372.3,NM_004662.2	,	515,2319,3669	GG,GA,AA		33.2326,11.1439,25.7497	,	3994/4487,306/799	11833287	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon63			AGAGCCAGCACCC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.11982A>G	17.37:g.11833287A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			A|0.755;G|0.245	0.245	strong		0.592	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
MUC4	4585	hgsc.bcm.edu	37	3	195513680	195513680	+	Missense_Mutation	SNP	A	A	T	rs7372250		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513680A>T	ENST00000463781.3	-	2	5230	c.4771T>A	c.(4771-4773)Tcc>Acc	p.S1591T	MUC4_ENST00000475231.1_Missense_Mutation_p.S1591T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GATGCTGAGGAAGTGTCGGTG	0.577																																					p.S1591T		Atlas-SNP	.											.	MUC4	1505	.	0			c.T4771A						PASS	.						29.0	23.0	25.0					3																	195513680		672	1580	2252	SO:0001583	missense	4585	exon2			CTGAGGAAGTGTC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4771T>A	3.37:g.195513680A>T	ENSP00000417498:p.Ser1591Thr	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	389	111	0.285347	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	0.021	-1.419052	0.01136	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.48;1.48	0.312	-0.624	0.11552	.	.	.	.	.	T	0.15869	0.0382	N	0.19112	0.55	0.09310	N	1	P	0.42584	0.784	B	0.39419	0.299	T	0.12400	-1.0549	8	.	.	.	.	4.0022	0.09585	0.7133:0.0:0.2867:0.0	.	1591	E7ESK3	.	T	1591	ENSP00000417498:S1591T;ENSP00000420243:S1591T	.	S	-	1	0	MUC4	196998075	0.676000	0.27567	0.005000	0.12908	0.002000	0.02628	1.188000	0.32102	-1.513000	0.01789	-2.001000	0.00444	TCC	A|1.000;|0.000	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LEPROTL1	23484	hgsc.bcm.edu	37	8	29961951	29961951	+	Silent	SNP	C	C	T	rs11557703	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:29961951C>T	ENST00000321250.8	+	3	343	c.228C>T	c.(226-228)ggC>ggT	p.G76G	LEPROTL1_ENST00000523116.1_Silent_p.G76G|LEPROTL1_ENST00000518001.1_Silent_p.G15G|LEPROTL1_ENST00000442880.2_Silent_p.G76G|LEPROTL1_ENST00000518192.1_Silent_p.G99G	NM_015344.2	NP_056159.2	O95214	LERL1_HUMAN	leptin receptor overlapping transcript-like 1	76						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)	5				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		TTACAACGGGCATTGTCGTGT	0.378													C|||	601	0.120008	0.0809	0.0692	5008	,	,		18534	0.2312		0.0944	False		,,,				2504	0.1207				p.G76G		Atlas-SNP	.											LEPROTL1_ENST00000523116,NS,carcinoma,+1,2	LEPROTL1	16	2	0			c.C228T						PASS	.	C	,	410,3996	200.4+/-223.7	17,376,1810	204.0	187.0	193.0		228,228	4.0	1.0	8	dbSNP_120	193	692,7908	172.2+/-222.9	22,648,3630	no	coding-synonymous,coding-synonymous	LEPROTL1	NM_001128208.1,NM_015344.2	,	39,1024,5440	TT,TC,CC		8.0465,9.3055,8.473	,	76/170,76/132	29961951	1102,11904	2203	4300	6503	SO:0001819	synonymous_variant	23484	exon3			AACGGGCATTGTC	AF063605	CCDS6075.1, CCDS47834.1	8p12	2014-09-11			ENSG00000104660	ENSG00000104660			6555	protein-coding gene	gene with protein product		607338				11342119	Standard	NM_015344		Approved	my047, Vps55	uc003xhx.2	O95214	OTTHUMG00000163820	ENST00000321250.8:c.228C>T	8.37:g.29961951C>T		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	262	125	0.477099	NM_001128208	E9PHP8|Q9BW48	Silent	SNP	ENST00000321250.8	37	CCDS6075.1	275	0.1259157509157509	48	0.0975609756097561	27	0.07458563535911603	135	0.23601398601398602	65	0.08575197889182058	C	9.414	1.081188	0.20309	0.093055	0.080465	ENSG00000104660	ENST00000519466	.	.	.	5.89	4.04	0.47022	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.08722	-1.0708	3	.	.	.	.	9.4609	0.38785	0.1427:0.7814:0.0:0.0758	rs11557703;rs11557703	.	.	.	V	57	.	.	A	+	2	0	LEPROTL1	30081493	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	2.359000	0.44142	0.772000	0.33382	0.585000	0.79938	GCA	C|0.898;T|0.102	0.102	strong		0.378	LEPROTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375771.2		
PLXNA3	55558	hgsc.bcm.edu	37	X	153694334	153694334	+	Missense_Mutation	SNP	C	C	G	rs5945430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153694334C>G	ENST00000369682.3	+	14	2764	c.2589C>G	c.(2587-2589)gaC>gaG	p.D863E		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	863	IPT/TIG 1.		D -> E (in dbSNP:rs5945430). {ECO:0000269|PubMed:8570614}.		axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCGTGGGTGACAACCTGGGCC	0.642													g|||	1453	0.384901	0.6725	0.0994	3775	,	,		12442	0.128		0.0875	False		,,,				2504	0.2843				p.D863E		Atlas-SNP	.											.	PLXNA3	156	.	0			c.C2589G						PASS	.		GLU/ASP	3042,793		1031,515,465,86,106	64.0	57.0	59.0		2589	4.4	1.0	X	dbSNP_114	59	895,5833		46,535,268,1847,1604	no	missense	PLXNA3	NM_017514.3	45	1077,1050,733,1933,1710	GG,GC,G,CC,C		13.3026,20.678,37.2716	benign	863/1872	153694334	3937,6626	2203	4300	6503	SO:0001583	missense	55558	exon14			GGGTGACAACCTG	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.2589C>G	X.37:g.153694334C>G	ENSP00000358696:p.Asp863Glu	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	482	0.29053646775165765	225	0.7867132867132867	24	0.06857142857142857	38	0.07063197026022305	44	0.062146892655367235	G	0.144	-1.099405	0.01843	0.79322	0.133026	ENSG00000130827	ENST00000369682	T	0.75821	-0.97	5.32	4.45	0.53987	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.129129	0.52532	N	0.000076	T	0.00012	0.0000	N	0.00041	-2.485	0.46499	P	9.219999999999784E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42865	-0.9426	9	0.06365	T	0.9	.	7.6459	0.28321	0.0881:0.3108:0.6011:0.0	rs5945430;rs58038932	863	P51805	PLXA3_HUMAN	E	863	ENSP00000358696:D863E	ENSP00000358696:D863E	D	+	3	2	PLXNA3	153347528	1.000000	0.71417	0.998000	0.56505	0.197000	0.23852	2.837000	0.48191	1.024000	0.39682	-0.176000	0.13171	GAC	C|0.625;G|0.375	0.375	strong		0.642	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
AKAP2	11217	hgsc.bcm.edu	37	9	112900199	112900199	+	Missense_Mutation	SNP	T	T	C	rs914358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:112900199T>C	ENST00000259318.7	+	2	1889	c.1682T>C	c.(1681-1683)tTg>tCg	p.L561S	AKAP2_ENST00000555236.1_Missense_Mutation_p.L792S|AKAP2_ENST00000374525.1_Missense_Mutation_p.L650S|AKAP2_ENST00000510514.5_Missense_Mutation_p.L792S|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.L792S|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.L792S|AKAP2_ENST00000434623.2_Missense_Mutation_p.L650S	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	561			L -> S (in dbSNP:rs914358). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						GACTCTCCGTTGGTTGATGAC	0.542													C|||	2282	0.455671	0.5877	0.3588	5008	,	,		18697	0.3135		0.4493	False		,,,				2504	0.499				p.L792S		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.T2375C						PASS	.	C	SER/LEU,SER/LEU,SER/LEU,SER/LEU,SER/LEU	2533,1873	538.1+/-374.9	737,1059,407	45.0	44.0	44.0		1949,1682,1949,2375,2375	5.0	0.0	9	dbSNP_86	44	3976,4624	598.5+/-393.9	913,2150,1237	yes	missense,missense,missense,missense,missense	AKAP2,PALM2-AKAP2	NM_001004065.4,NM_001136562.2,NM_001198656.1,NM_007203.4,NM_147150.2	145,145,145,145,145	1650,3209,1644	CC,CT,TT		46.2326,42.5102,49.9539	benign,benign,benign,benign,benign	650/949,561/860,650/962,792/1104,792/1091	112900199	6509,6497	2203	4300	6503	SO:0001583	missense	445815	exon8			CTCCGTTGGTTGA	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.1682T>C	9.37:g.112900199T>C	ENSP00000259318:p.Leu561Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	37	CCDS48003.1	948	0.4340659340659341	290	0.5894308943089431	132	0.36464088397790057	172	0.3006993006993007	354	0.46701846965699206	C	0.542	-0.853209	0.02630	0.574898	0.462326	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.44083	2.26;2.26;2.26;2.26;1.51;0.93;0.94;1.53	5.95	4.96	0.65561	.	0.537430	0.19317	N	0.117222	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.19200	0.0;0.003;0.0;0.034;0.02;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.18263	0.001;0.004;0.001;0.021;0.009;0.001;0.001;0.0	T	0.43940	-0.9360	9	0.09843	T	0.71	-4.3473	5.127	0.14890	0.0:0.6987:0.0:0.3013	rs914358;rs56524515;rs61095828;rs914358	561;650;644;650;651;792;792;610	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	S	792;792;792;792;650;650;610;561	ENSP00000363654:L792S;ENSP00000305861:L792S;ENSP00000451476:L792S;ENSP00000421522:L792S;ENSP00000404782:L650S;ENSP00000363649:L650S;ENSP00000419268:L610S;ENSP00000259318:L561S	ENSP00000259318:L561S	L	+	2	0	PALM2-AKAP2;AKAP2	111940020	0.000000	0.05858	0.031000	0.17742	0.218000	0.24690	0.734000	0.26101	1.529000	0.49120	-0.128000	0.14901	TTG	T|0.526;C|0.474	0.474	strong		0.542	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548628	32548628	+	Missense_Mutation	SNP	G	G	A	rs34624872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32548628G>A	ENST00000360004.5	-	4	763	c.658C>T	c.(658-660)Cgg>Tgg	p.R220W		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	220	Beta-2.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GATTCAGACCGTGCTCCTGAG	0.483										Multiple Myeloma(14;0.17)																											p.R220W		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C658T						PASS	.						77.0	86.0	83.0					6																	32548628		1511	2709	4220	SO:0001583	missense	3123	exon4			CAGACCGTGCTCC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.658C>T	6.37:g.32548628G>A	ENSP00000353099:p.Arg220Trp	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	565	113	0.2	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	12.70	2.016010	0.35606	.	.	ENSG00000196126	ENST00000360004	T	0.00635	6.06	3.98	3.98	0.46160	Immunoglobulin-like fold (3);	0.849923	0.10912	N	0.620484	T	0.00580	0.0019	L	0.56769	1.78	0.24665	N	0.993446	B;B;D	0.71674	0.007;0.007;0.998	B;B;P	0.47430	0.0;0.001;0.547	T	0.53995	-0.8359	10	0.66056	D	0.02	.	10.0825	0.42399	0.0:0.2056:0.7944:0.0	rs34624872	220;220;220	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	W	220	ENSP00000353099:R220W	ENSP00000353099:R220W	R	-	1	2	HLA-DRB1	32656606	0.013000	0.17824	0.747000	0.31113	0.149000	0.21700	1.804000	0.38873	1.943000	0.56356	0.453000	0.30009	CGG	G|0.814;A|0.185	0.185	strong		0.483	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ITGAM	3684	hgsc.bcm.edu	37	16	31336719	31336719	+	Silent	SNP	G	G	A	rs1143682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31336719G>A	ENST00000287497.8	+	20	2574	c.2499G>A	c.(2497-2499)acG>acA	p.T833T	ITGAM_ENST00000544665.3_Silent_p.T834T			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	833					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)	p.T833T(1)		endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						AGGTGTCCACGCTCCAGGTAG	0.562													G|||	1475	0.294529	0.0832	0.3329	5008	,	,		18561	0.6558		0.3519	False		,,,				2504	0.1217				p.T834T		Atlas-SNP	.											ITGAM,NS,carcinoma,0,3	ITGAM	137	3	1	Substitution - coding silent(1)	prostate(1)	c.G2502A						PASS	.	G	,	576,3644		46,484,1580	68.0	72.0	71.0		2499,2502	-8.9	0.0	16	dbSNP_86	71	3164,5294		609,1946,1674	no	coding-synonymous,coding-synonymous	ITGAM	NM_000632.3,NM_001145808.1	,	655,2430,3254	AA,AG,GG		37.4084,13.6493,29.4999	,	833/1153,834/1154	31336719	3740,8938	2110	4229	6339	SO:0001819	synonymous_variant	3684	exon20			GTCCACGCTCCAG	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2499G>A	16.37:g.31336719G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Silent	SNP	ENST00000287497.8	37	CCDS45470.1																																																																																			G|0.631;A|0.369	0.369	strong		0.562	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
CCDC91	55297	hgsc.bcm.edu	37	12	28605426	28605426	+	Missense_Mutation	SNP	G	G	A	rs10771427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:28605426G>A	ENST00000545336.1	+	14	1359	c.940G>A	c.(940-942)Gtg>Atg	p.V314M	CCDC91_ENST00000381259.1_Missense_Mutation_p.V314M|CCDC91_ENST00000539107.1_Missense_Mutation_p.V278M|CCDC91_ENST00000381256.1_Missense_Mutation_p.V278M|CCDC91_ENST00000540401.1_3'UTR|CCDC91_ENST00000306172.5_Missense_Mutation_p.V284M			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	314	Homodimerization.		V -> M (in dbSNP:rs10771427). {ECO:0000269|PubMed:12808037, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6, ECO:0000269|Ref.7}.		protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					AAAAGAAGCAGTGAAGGATGC	0.313													A|||	3351	0.669129	0.8268	0.6398	5008	,	,		13616	0.4702		0.7475	False		,,,				2504	0.6012				p.V314M		Atlas-SNP	.											.	CCDC91	63	.	0			c.G940A						PASS	.	A	MET/VAL	3626,768	282.8+/-276.7	1495,636,66	56.0	69.0	64.0		940	-5.7	0.2	12	dbSNP_120	64	6544,2038	339.8+/-323.3	2510,1524,257	yes	missense	CCDC91	NM_018318.3	21	4005,2160,323	AA,AG,GG		23.7474,17.4784,21.6245	benign	314/442	28605426	10170,2806	2197	4291	6488	SO:0001583	missense	55297	exon10			GAAGCAGTGAAGG	AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"""GGA binding partner"""					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.940G>A	12.37:g.28605426G>A	ENSP00000438040:p.Val314Met	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	88	31	0.352273	NM_018318	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	37	CCDS8716.1	1462	0.6694139194139194	407	0.8272357723577236	235	0.649171270718232	252	0.4405594405594406	568	0.7493403693931399	A	2.110	-0.403863	0.04832	0.825216	0.762526	ENSG00000123106	ENST00000540794;ENST00000536154;ENST00000539107;ENST00000536442;ENST00000545336;ENST00000545737;ENST00000381259;ENST00000381256;ENST00000306172;ENST00000535212	T;T;T;T;T;T;T;T;T;T	0.46063	1.45;1.48;0.97;1.5;1.49;1.5;1.49;0.97;1.49;0.88	5.43	-5.71	0.02413	.	0.735756	0.13394	N	0.391196	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.14578	0.002;0.011;0.002	T	0.43988	-0.9357	9	0.42905	T	0.14	-0.5073	19.6535	0.95827	0.2682:0.0:0.7318:0.0	rs10771427;rs52823249;rs59885605;rs10771427	278;314;284	Q7Z6B0-3;Q7Z6B0;Q7Z6B0-2	.;CCD91_HUMAN;.	M	110;54;278;314;314;314;314;278;284;13	ENSP00000441714:V110M;ENSP00000444440:V54M;ENSP00000440513:V278M;ENSP00000445660:V314M;ENSP00000438040:V314M;ENSP00000442544:V314M;ENSP00000370658:V314M;ENSP00000370655:V278M;ENSP00000305075:V284M;ENSP00000445999:V13M	ENSP00000305075:V284M	V	+	1	0	CCDC91	28496693	0.013000	0.17824	0.203000	0.23512	0.968000	0.65278	-0.271000	0.08572	-1.887000	0.01115	-0.352000	0.07741	GTG	G|0.275;A|0.725	0.725	strong		0.313	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318	
UGT2B28	54490	hgsc.bcm.edu	37	4	70146704	70146704	+	Silent	SNP	G	G	A	rs7689398	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70146704G>A	ENST00000335568.5	+	1	488	c.486G>A	c.(484-486)gcG>gcA	p.A162A	UGT2B28_ENST00000511240.1_Silent_p.A162A	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	162					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						TGCTGGCTGCGCTACTTAACA	0.408													-|||	1842	0.367812	0.2345	0.4496	5008	,	,		14454	0.3829		0.4771	False		,,,				2504	0.362				p.A162A		Atlas-SNP	.											.	UGT2B28	101	.	0			c.G486A						PASS	.	G	,	1284,2778		402,480,1149	116.0	124.0	121.0		486,486	1.3	0.1	4	dbSNP_116	121	4326,4140		1358,1610,1265	no	coding-synonymous,coding-synonymous	UGT2B28	NM_001207004.1,NM_053039.1	,	1760,2090,2414	AA,AG,GG		48.9015,31.61,44.7797	,	162/336,162/530	70146704	5610,6918	2031	4233	6264	SO:0001819	synonymous_variant	54490	exon1			GGCTGCGCTACTT	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.486G>A	4.37:g.70146704G>A		Somatic	553	0	0		WXS	Illumina HiSeq	Phase_I	261	257	0.984674	NM_053039	B5BUM0|Q9BY62|Q9BY63	Silent	SNP	ENST00000335568.5	37	CCDS3528.1																																																																																			G|0.593;A|0.407	0.407	strong		0.408	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
KRT1	3848	hgsc.bcm.edu	37	12	53070174	53070174	+	Missense_Mutation	SNP	C	C	A	rs17678945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53070174C>A	ENST00000252244.3	-	7	1418	c.1360G>T	c.(1360-1362)Gcc>Tcc	p.A454S		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	454	Coil 2.|Rod.		A -> S (in dbSNP:rs17678945).		complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						TCTTCCTTGGCCTGCTGCAGG	0.587													c|||	27	0.00539137	0.0	0.0101	5008	,	,		19137	0.0		0.0169	False		,,,				2504	0.0031				p.A454S		Atlas-SNP	.											.	KRT1	110	.	0			c.G1360T						PASS	.	C	SER/ALA	26,4380	31.7+/-61.6	0,26,2177	80.0	71.0	74.0		1360	3.2	1.0	12	dbSNP_123	74	231,8369	94.5+/-156.4	3,225,4072	no	missense	KRT1	NM_006121.3	99	3,251,6249	AA,AC,CC		2.686,0.5901,1.976	benign	454/645	53070174	257,12749	2203	4300	6503	SO:0001583	missense	3848	exon7			CCTTGGCCTGCTG	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1360G>T	12.37:g.53070174C>A	ENSP00000252244:p.Ala454Ser	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	238	121	0.508403	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	c	17.21	3.332241	0.60853	0.005901	0.02686	ENSG00000167768	ENST00000252244	T	0.75589	-0.95	5.03	3.15	0.36227	Prefoldin (1);Filament (1);	.	.	.	.	T	0.62085	0.2399	M	0.73217	2.22	0.25099	N	0.990795	P	0.47350	0.894	D	0.63033	0.91	T	0.62895	-0.6757	9	0.59425	D	0.04	.	3.3536	0.07162	0.1474:0.5686:0.143:0.141	rs17678945;rs17678945	454	P04264	K2C1_HUMAN	S	454	ENSP00000252244:A454S	ENSP00000252244:A454S	A	-	1	0	KRT1	51356441	0.595000	0.26857	0.965000	0.40720	0.684000	0.39900	1.225000	0.32551	1.226000	0.43582	0.462000	0.41574	GCC	C|0.981;A|0.019	0.019	strong		0.587	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
ITGA6	3655	hgsc.bcm.edu	37	2	173362720	173362720	+	Silent	SNP	T	T	C	rs139596061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:173362720T>C	ENST00000264106.6	+	25	3326	c.3123T>C	c.(3121-3123)ttT>ttC	p.F1041F	AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Silent_p.F883F|ITGA6_ENST00000264107.7_Silent_p.F1002F|ITGA6_ENST00000409080.1_Silent_p.F1002F|ITGA6_ENST00000343713.4_Silent_p.F997F|ITGA6_ENST00000375221.2_Silent_p.F1041F			P23229	ITA6_HUMAN	integrin, alpha 6	1041					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TGACTGTGTTTCCCTCAAAGA	0.438													T|||	4	0.000798722	0.0008	0.0	5008	,	,		18824	0.0		0.003	False		,,,				2504	0.0				p.F1002F		Atlas-SNP	.											.	ITGA6	171	.	0			c.T3006C						PASS	.	T	,	2,4404	4.2+/-10.8	0,2,2201	248.0	214.0	225.0		3006,3006	3.8	1.0	2	dbSNP_134	225	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	ITGA6	NM_000210.2,NM_001079818.1	,	0,14,6489	CC,CT,TT		0.1395,0.0454,0.1076	,	1002/1074,1002/1092	173362720	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	3655	exon24			TGTGTTTCCCTCA		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.3123T>C	2.37:g.173362720T>C		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	252	107	0.424603	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	37																																																																																				T|0.999;C|0.001	0.001	strong		0.438	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
PLK3	1263	hgsc.bcm.edu	37	1	45270024	45270024	+	Silent	SNP	G	G	C	rs11211036	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45270024G>C	ENST00000372201.4	+	12	1595	c.1356G>C	c.(1354-1356)ccG>ccC	p.P452P	PLK3_ENST00000465443.1_3'UTR	NM_004073.2	NP_004064.2	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	452					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic microtubule organization (GO:0031122)|endomitotic cell cycle (GO:0007113)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi disassembly (GO:0090166)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G1/S transition checkpoint (GO:0044819)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell division (GO:0051302)|regulation of cytokinesis (GO:0032465)|response to osmotic stress (GO:0006970)|response to radiation (GO:0009314)|response to reactive oxygen species (GO:0000302)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi stack (GO:0005795)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					AACAGAACCCGGCCCCCCTGG	0.622													G|||	961	0.191893	0.1445	0.245	5008	,	,		16124	0.2857		0.1402	False		,,,				2504	0.1748				p.P452P		Atlas-SNP	.											.	PLK3	41	.	0			c.G1356C						PASS	.	G		628,3778	257.4+/-261.8	46,536,1621	65.0	75.0	72.0		1356	-10.9	0.1	1	dbSNP_120	72	1445,7155	268.9+/-288.1	131,1183,2986	no	coding-synonymous	PLK3	NM_004073.2		177,1719,4607	CC,CG,GG		16.8023,14.2533,15.9388		452/647	45270024	2073,10933	2203	4300	6503	SO:0001819	synonymous_variant	1263	exon12			GAACCCGGCCCCC	AJ293866	CCDS515.1	1p34.1	2013-01-18	2010-06-24	2004-01-28	ENSG00000173846	ENSG00000173846			2154	protein-coding gene	gene with protein product		602913	"""cytokine-inducible kinase"", ""polo-like kinase 3 (Drosophila)"""	CNK		8702627	Standard	NM_004073		Approved	FNK, PRK	uc001cmn.3	Q9H4B4	OTTHUMG00000008491	ENST00000372201.4:c.1356G>C	1.37:g.45270024G>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	104	61	0.586538	NM_004073	Q15767|Q5JR99|Q96CV1	Silent	SNP	ENST00000372201.4	37	CCDS515.1																																																																																			G|0.828;C|0.172	0.172	strong		0.622	PLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023429.1	NM_004073	
Unknown	0	hgsc.bcm.edu	37	7	63680099	63680099	+	IGR	SNP	C	C	A	rs35920205|rs4320434	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:63680099C>A								GUSBP6 (69000 upstream) : ZNF679 (8752 downstream)																							ATCCTTTAACCACTCCTCAAG	0.398													.|||	1119	0.223442	0.1551	0.2205	5008	,	,		19877	0.2679		0.2565	False		,,,				2504	0.2382				p.H224N		Atlas-SNP	.											.	.	.	.	0			c.C670A						PASS	.						42.0	39.0	40.0					7																	63680099		692	1591	2283	SO:0001628	intergenic_variant	730291	exon4			TTTAACCACTCCT																													7.37:g.63680099C>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_001159524		Missense_Mutation	SNP		37																																																																																				C|0.813;A|0.187	0.187	strong	0	0.398								
MOV10L1	54456	hgsc.bcm.edu	37	22	50584201	50584201	+	Silent	SNP	A	A	C	rs2272838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50584201A>C	ENST00000262794.5	+	19	2672	c.2589A>C	c.(2587-2589)acA>acC	p.T863T	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395852.1_5'Flank|MOV10L1_ENST00000395858.3_Silent_p.T863T|MOV10L1_ENST00000545383.1_Silent_p.T863T|MOV10L1_ENST00000540615.1_Silent_p.T843T	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	863					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.T863T(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TCATCACCACATGCAGCAGCT	0.582													a|||	1252	0.25	0.1233	0.3934	5008	,	,		17468	0.252		0.2376	False		,,,				2504	0.3303				p.T863T		Atlas-SNP	.											MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	1	Substitution - coding silent(1)	stomach(1)	c.A2589C						PASS	.		,,	676,3730	287.2+/-279.2	56,564,1583	123.0	120.0	121.0		2589,2529,2589	-11.4	0.0	22	dbSNP_100	121	2081,6519	362.5+/-332.8	254,1573,2473	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	310,2137,4056	CC,CA,AA		24.1977,15.3427,21.1979	,,	863/1166,843/1166,863/1212	50584201	2757,10249	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon19			CACCACATGCAGC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2589A>C	22.37:g.50584201A>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	43	0.614286	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			A|0.774;C|0.226	0.226	strong		0.582	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
FAM174A	345757	hgsc.bcm.edu	37	5	99897866	99897866	+	Silent	SNP	G	G	A	rs6874840	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:99897866G>A	ENST00000312637.4	+	2	769	c.543G>A	c.(541-543)acG>acA	p.T181T	FAM174A_ENST00000505792.1_3'UTR	NM_198507.1	NP_940909.1	Q8TBP5	F174A_HUMAN	family with sequence similarity 174, member A	181						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						ATGACAACACGTTGTTTGATG	0.383													A|||	933	0.186302	0.2292	0.3732	5008	,	,		14098	0.0179		0.2694	False		,,,				2504	0.0838				p.T181T		Atlas-SNP	.											.	FAM174A	13	.	0			c.G543A						PASS	.	A		1013,3393	728.5+/-409.9	122,769,1312	153.0	140.0	145.0		543	-1.2	0.9	5	dbSNP_116	145	2091,6509	717.0+/-406.1	231,1629,2440	no	coding-synonymous	FAM174A	NM_198507.1		353,2398,3752	AA,AG,GG		24.314,22.9914,23.8659		181/191	99897866	3104,9902	2203	4300	6503	SO:0001819	synonymous_variant	345757	exon2			CAACACGTTGTTT	AY359108	CCDS4090.1	5q21.1	2008-06-19	2008-06-19	2008-06-19	ENSG00000174132	ENSG00000174132			24943	protein-coding gene	gene with protein product			"""transmembrane protein 157"""	TMEM157		12975309	Standard	NM_198507		Approved	UNQ1912	uc003knj.1	Q8TBP5	OTTHUMG00000128726	ENST00000312637.4:c.543G>A	5.37:g.99897866G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	263	133	0.505703	NM_198507	A8K0H4	Silent	SNP	ENST00000312637.4	37	CCDS4090.1																																																																																			G|0.774;A|0.226	0.226	strong		0.383	FAM174A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250631.2	NM_198507	
SLC52A3	113278	hgsc.bcm.edu	37	20	745963	745963	+	Silent	SNP	G	G	A	rs3746807	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:745963G>A	ENST00000217254.7	-	2	697	c.456C>T	c.(454-456)ccC>ccT	p.P152P	SLC52A3_ENST00000473664.1_5'UTR|SLC52A3_ENST00000381944.3_Silent_p.P152P	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	152					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										CCACCAGGGCGGGCAAGAGGC	0.597													A|||	491	0.0980431	0.0968	0.0663	5008	,	,		17870	0.1637		0.0924	False		,,,				2504	0.0603				p.P152P		Atlas-SNP	.											.	.	.	.	0			c.C456T						PASS	.	A		494,3912	780.3+/-414.4	22,450,1731	68.0	65.0	66.0		456	0.1	1.0	20	dbSNP_107	66	888,7712	778.5+/-407.7	60,768,3472	no	coding-synonymous	C20orf54	NM_033409.3		82,1218,5203	AA,AG,GG		10.3256,11.212,10.6259		152/470	745963	1382,11624	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon2			CAGGGCGGGCAAG	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.456C>T	20.37:g.745963G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.885;A|0.115	0.115	strong		0.597	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
OR13C9	286362	hgsc.bcm.edu	37	9	107380177	107380177	+	Silent	SNP	A	A	G	rs1813819	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107380177A>G	ENST00000259362.1	-	1	308	c.309T>C	c.(307-309)ctT>ctC	p.L103L		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						TGGCCAAGCCAAGGAACATCT	0.498													a|||	2155	0.430312	0.6271	0.2262	5008	,	,		20857	0.5754		0.1779	False		,,,				2504	0.4192				p.L103L		Atlas-SNP	.											.	OR13C9	42	.	0			c.T309C						PASS	.	G		2358,2048	598.6+/-389.1	674,1010,519	116.0	135.0	129.0		309	-3.7	0.9	9	dbSNP_92	129	1591,7009	286.3+/-297.7	184,1223,2893	no	coding-synonymous	OR13C9	NM_001001956.1		858,2233,3412	GG,GA,AA		18.5,46.4821,30.3629		103/319	107380177	3949,9057	2203	4300	6503	SO:0001819	synonymous_variant	286362	exon1			CAAGCCAAGGAAC		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.309T>C	9.37:g.107380177A>G		Somatic	529	0	0		WXS	Illumina HiSeq	Phase_I	490	233	0.47551	NM_001001956	Q6IFL2	Silent	SNP	ENST00000259362.1	37	CCDS35093.1																																																																																			A|0.694;G|0.306	0.306	strong		0.498	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
ZNF227	7770	hgsc.bcm.edu	37	19	44739303	44739303	+	Silent	SNP	T	T	C	rs2279073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44739303T>C	ENST00000313040.7	+	6	925	c.720T>C	c.(718-720)aaT>aaC	p.N240N	ZNF227_ENST00000391961.2_Silent_p.N189N|ZNF227_ENST00000589005.1_Silent_p.N189N	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				ATGGCTCCAATCAGAAATTAC	0.423													T|||	2095	0.418331	0.115	0.4841	5008	,	,		18758	0.4286		0.5417	False		,,,				2504	0.6442				p.N240N		Atlas-SNP	.											.	ZNF227	62	.	0			c.T720C						PASS	.	T		887,3519	339.4+/-305.8	108,671,1424	55.0	56.0	56.0		720	-0.8	0.0	19	dbSNP_100	56	4712,3888	603.4+/-394.7	1309,2094,897	no	coding-synonymous	ZNF227	NM_182490.1		1417,2765,2321	CC,CT,TT		45.2093,20.1316,43.0494		240/800	44739303	5599,7407	2203	4300	6503	SO:0001819	synonymous_variant	7770	exon6			CTCCAATCAGAAA	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.720T>C	19.37:g.44739303T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	37	CCDS12636.1																																																																																			T|0.587;C|0.413	0.413	strong		0.423	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
PCLO	27445	hgsc.bcm.edu	37	7	82453708	82453708	+	Missense_Mutation	SNP	A	A	C	rs2522833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82453708A>C	ENST00000333891.9	-	19	14777	c.14440T>G	c.(14440-14442)Tct>Gct	p.S4814A	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.S4814A	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCGAGGTGAGATGTGCTAGAT	0.368													A|||	2016	0.402556	0.0424	0.4164	5008	,	,		16504	0.6865		0.4324	False		,,,				2504	0.5562				p.S4814A		Atlas-SNP	.											.	PCLO	1506	.	0			c.T14440G						PASS	.	A	ALA/SER,ALA/SER	394,3448		29,336,1556	102.0	93.0	96.0		14440,14440	5.7	1.0	7	dbSNP_100	96	3466,4802		745,1976,1413	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	99,99	774,2312,2969	CC,CA,AA		41.9207,10.2551,31.8745	benign,benign	4814/5143,4814/4936	82453708	3860,8250	1921	4134	6055	SO:0001583	missense	27445	exon19			GGTGAGATGTGCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14440T>G	7.37:g.82453708A>C	ENSP00000334319:p.Ser4814Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	925	0.42353479853479853	35	0.07113821138211382	150	0.4143646408839779	402	0.7027972027972028	338	0.44591029023746703	A	13.22	2.173542	0.38413	0.102551	0.419207	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.41065	1.01;1.01	5.72	5.72	0.89469	.	.	.	.	.	T	0.00012	0.0000	N	0.04880	-0.145	0.09310	P	1.0	B;B;B	0.15473	0.013;0.013;0.0	B;B;B	0.30646	0.118;0.118;0.002	T	0.37361	-0.9709	8	0.87932	D	0	.	15.9926	0.80217	1.0:0.0:0.0:0.0	rs2522833;rs17285459;rs57906002;rs2522833	4814;4814;235	Q9Y6V0-5;Q9Y6V0-6;Q9Y6V0-3	.;.;.	A	4814;4814;301	ENSP00000334319:S4814A;ENSP00000388393:S4814A	ENSP00000334319:S4814A	S	-	1	0	PCLO	82291644	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.108000	0.64609	2.179000	0.69175	0.482000	0.46254	TCT	A|0.586;C|0.414	0.414	strong		0.368	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
GAL3ST4	79690	hgsc.bcm.edu	37	7	99757612	99757612	+	Missense_Mutation	SNP	G	G	A	rs3823646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99757612G>A	ENST00000360039.4	-	4	1792	c.1400C>T	c.(1399-1401)gCc>gTc	p.A467V	GAL3ST4_ENST00000411994.1_3'UTR|C7orf43_ENST00000316937.3_5'Flank|C7orf43_ENST00000498638.1_5'Flank|GAL3ST4_ENST00000413800.1_Missense_Mutation_p.A467V|GAL3ST4_ENST00000426974.2_Missense_Mutation_p.A405V|C7orf43_ENST00000457641.1_5'Flank|C7orf43_ENST00000419841.1_5'Flank|GAL3ST4_ENST00000423751.1_3'UTR	NM_024637.4	NP_078913.3	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	467			A -> V (in dbSNP:rs3823646). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874}.		cell-cell signaling (GO:0007267)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(5)|prostate(1)|upper_aerodigestive_tract(1)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAACTGCTTGGCATCCAGCTT	0.527													G|||	2537	0.506589	0.3328	0.4222	5008	,	,		18142	0.6438		0.5586	False		,,,				2504	0.6063				p.A467V		Atlas-SNP	.											.	GAL3ST4	59	.	0			c.C1400T						PASS	.	G	VAL/ALA	1699,2707	514.2+/-368.6	321,1057,825	107.0	89.0	95.0		1400	5.0	1.0	7	dbSNP_107	95	4887,3713	619.4+/-396.9	1400,2087,813	yes	missense	GAL3ST4	NM_024637.4	64	1721,3144,1638	AA,AG,GG		43.1744,38.5611,49.3618	possibly-damaging	467/487	99757612	6586,6420	2203	4300	6503	SO:0001583	missense	79690	exon4			TGCTTGGCATCCA	AF316113	CCDS5688.1	7q22.1	2007-04-02			ENSG00000197093	ENSG00000197093		"""Sulfotransferases, membrane-bound"""	24145	protein-coding gene	gene with protein product		608235				11333265	Standard	NM_024637		Approved	FLJ12116	uc003utu.3	Q96RP7	OTTHUMG00000154885	ENST00000360039.4:c.1400C>T	7.37:g.99757612G>A	ENSP00000353142:p.Ala467Val	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	163	162	0.993865	NM_024637	A4D2A8|B4DWL8|D6W5U5|Q8N3P7|Q8WZ17|Q96E33|Q9HA78	Missense_Mutation	SNP	ENST00000360039.4	37	CCDS5688.1	1080	0.4945054945054945	159	0.3231707317073171	150	0.4143646408839779	343	0.5996503496503497	428	0.5646437994722955	G	20.2	3.949298	0.73787	0.385611	0.568256	ENSG00000197093	ENST00000413800;ENST00000360039;ENST00000426974	T;T;T	0.17054	2.3;2.3;2.3	5.92	5.04	0.67666	.	0.353495	0.24211	U	0.040522	T	0.00012	0.0000	L	0.32530	0.975	0.26429	P	0.9759661	B;B	0.21452	0.056;0.008	B;B	0.23419	0.046;0.019	T	0.36138	-0.9760	9	0.30078	T	0.28	-5.0108	7.9872	0.30218	0.0802:0.0:0.7619:0.1579	rs3823646;rs17845361;rs17858212;rs58496926;rs3823646	405;467	B4DWL8;Q96RP7	.;G3ST4_HUMAN	V	467;467;405	ENSP00000400451:A467V;ENSP00000353142:A467V;ENSP00000398304:A405V	ENSP00000353142:A467V	A	-	2	0	GAL3ST4	99595548	0.717000	0.27966	1.000000	0.80357	0.977000	0.68977	1.499000	0.35671	1.515000	0.48885	0.561000	0.74099	GCC	G|0.497;A|0.503	0.503	strong		0.527	GAL3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337495.2	NM_024637	
MSGN1	343930	hgsc.bcm.edu	37	2	17998095	17998095	+	Missense_Mutation	SNP	C	C	T	rs35858730	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:17998095C>T	ENST00000281047.3	+	1	333	c.310C>T	c.(310-312)Cac>Tac	p.H104Y		NM_001105569.1	NP_001099039.1	A6NI15	MSGN1_HUMAN	mesogenin 1	104			H -> Y (in dbSNP:rs35858730).		cell differentiation (GO:0030154)|segment specification (GO:0007379)|somitogenesis (GO:0001756)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CCAGCCCACCCACCTTCAGGG	0.642													T|||	1482	0.295927	0.1884	0.3429	5008	,	,		18652	0.0278		0.5398	False		,,,				2504	0.4335				p.H104Y	Melanoma(127;325 1712 14802 40657 49130)	Atlas-SNP	.											MSGN1,NS,carcinoma,0,1	MSGN1	39	1	0			c.C310T						PASS	.	T	TYR/HIS	1015,3067		125,765,1151	30.0	38.0	36.0		310	5.8	0.1	2	dbSNP_126	36	4794,3576		1393,2008,784	yes	missense	MSGN1	NM_001105569.1	83	1518,2773,1935	TT,TC,CC		42.724,24.8653,46.6511	benign	104/194	17998095	5809,6643	2041	4185	6226	SO:0001583	missense	343930	exon1			CCCACCCACCTTC		CCDS42657.1	2p24.2	2007-07-23			ENSG00000151379	ENSG00000151379			14907	protein-coding gene	gene with protein product	"""paraxial mesogenin"""	612209				10837126	Standard	NM_001105569		Approved	pMesogenin1	uc010yjt.2	A6NI15	OTTHUMG00000159089	ENST00000281047.3:c.310C>T	2.37:g.17998095C>T	ENSP00000281047:p.His104Tyr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_001105569		Missense_Mutation	SNP	ENST00000281047.3	37	CCDS42657.1	666	0.30494505494505497	96	0.1951219512195122	143	0.39502762430939226	17	0.02972027972027972	410	0.5408970976253298	T	0	-2.614259	0.00120	0.248653	0.57276	ENSG00000151379	ENST00000281047	T	0.16324	2.35	5.77	5.77	0.91146	.	0.301187	0.28901	N	0.013765	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37596	-0.9699	9	0.13470	T	0.59	-25.2315	8.8701	0.35311	0.0:0.2062:0.0:0.7938	rs35858730;rs62130917	104	A6NI15	MSGN1_HUMAN	Y	104	ENSP00000281047:H104Y	ENSP00000281047:H104Y	H	+	1	0	MSGN1	17861576	0.024000	0.19004	0.066000	0.19879	0.062000	0.15995	1.350000	0.34010	1.020000	0.39573	-0.254000	0.11334	CAC	C|0.602;T|0.398	0.398	strong		0.642	MSGN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353253.1	XM_292850	
C1orf68	100129271	hgsc.bcm.edu	37	1	152692472	152692472	+	Missense_Mutation	SNP	A	A	C	rs873775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152692472A>C	ENST00000368775.2	+	1	475	c.475A>C	c.(475-477)Act>Cct	p.T159P		NM_001024679.2	NP_001019850.1	Q5T750	XP32_HUMAN	chromosome 1 open reading frame 68	159	Cys-rich.		T -> P (in dbSNP:rs873775).		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)		p.T159P(1)		NS(1)|breast(1)|lung(2)|prostate(1)|stomach(3)	8						GTACTGTGTCACTGACCCATG	0.592													C|||	1749	0.349241	0.5461	0.3804	5008	,	,		19221	0.1716		0.3608	False		,,,				2504	0.2321				p.T159P		Atlas-SNP	.											C1orf68,NS,malignant_melanoma,-1,2	C1orf68	19	2	1	Substitution - Missense(1)	stomach(1)	c.A475C						PASS	.	C	PRO/THR	693,691		176,341,175	110.0	103.0	105.0		475	5.4	0.8	1	dbSNP_86	105	1114,2068		190,734,667	yes	missense	C1orf68	NM_001024679.2	38	366,1075,842	CC,CA,AA		35.0094,49.9277,39.5751	benign	159/251	152692472	1807,2759	692	1591	2283	SO:0001583	missense	100129271	exon1			TGTGTCACTGACC	AF005081	CCDS44226.1	1q21.3	2014-05-30			ENSG00000198854	ENSG00000198854			29468	protein-coding gene	gene with protein product						11698679	Standard	NM_001024679		Approved	LEP7	uc010pdu.2	Q5T750	OTTHUMG00000012401	ENST00000368775.2:c.475A>C	1.37:g.152692472A>C	ENSP00000357764:p.Thr159Pro	Somatic	223	2	0.00896861		WXS	Illumina HiSeq	Phase_I	264	264	1	NM_001024679	O14634	Missense_Mutation	SNP	ENST00000368775.2	37	CCDS44226.1	767	0.35119047619047616	259	0.5264227642276422	137	0.3784530386740331	103	0.18006993006993008	268	0.35356200527704484	C	0.348	-0.946669	0.02304	0.500723	0.350094	ENSG00000198854	ENST00000362017;ENST00000368775	T;T	0.18174	2.23;2.23	5.4	5.4	0.78164	.	0.000000	0.40302	N	0.001132	T	0.01523	0.0049	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42447	-0.9451	9	0.11485	T	0.65	-6.6677	12.041	0.53452	0.1727:0.8273:0.0:0.0	rs873775;rs3829884;rs56870105;rs873775	159	Q5T750	XP32_HUMAN	P	159	ENSP00000354769:T159P;ENSP00000357764:T159P	ENSP00000354769:T159P	T	+	1	0	C1orf68	150959096	0.607000	0.26958	0.769000	0.31535	0.287000	0.27160	2.046000	0.41260	1.452000	0.47756	-0.225000	0.12378	ACT	A|0.656;C|0.344	0.344	strong		0.592	C1orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034521.2	NM_001024679	
OR10K2	391107	hgsc.bcm.edu	37	1	158390501	158390501	+	Silent	SNP	G	G	A	rs34616883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158390501G>A	ENST00000314902.2	-	1	155	c.156C>T	c.(154-156)gaC>gaT	p.D52D		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					GAAGGGCCCTGTCCAGGACAA	0.512													G|||	1405	0.280551	0.2186	0.2695	5008	,	,		22238	0.1687		0.4592	False		,,,				2504	0.3037				p.D52D		Atlas-SNP	.											OR10K2,NS,carcinoma,0,1	OR10K2	69	1	0			c.C156T						PASS	.	G		1068,3338	389.1+/-327.2	134,800,1269	170.0	141.0	151.0		156	1.1	1.0	1	dbSNP_126	151	3769,4831	534.6+/-382.6	807,2155,1338	no	coding-synonymous	OR10K2	NM_001004476.1		941,2955,2607	AA,AG,GG		43.8256,24.2397,37.1905		52/313	158390501	4837,8169	2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			GGCCCTGTCCAGG	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"""GPCR / Class A : Olfactory receptors"""	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.156C>T	1.37:g.158390501G>A		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	388	386	0.994845	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			G|0.643;A|0.357	0.357	strong		0.512	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476	
DCTN5	84516	hgsc.bcm.edu	37	16	23677006	23677006	+	Silent	SNP	A	A	G	rs35586	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23677006A>G	ENST00000300087.2	+	5	559	c.408A>G	c.(406-408)ccA>ccG	p.P136P	DCTN5_ENST00000568589.1_Silent_p.P136P|DCTN5_ENST00000563998.1_Silent_p.P136P	NM_001199743.1|NM_032486.3	NP_001186672.1|NP_115875.1	Q9BTE1	DCTN5_HUMAN	dynactin 5 (p25)	136					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)				endometrium(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(48;0.0156)		TATTACCTCCAGAAACTGTGG	0.393													A|||	1170	0.233626	0.1021	0.1758	5008	,	,		18063	0.4355		0.2117	False		,,,				2504	0.2669				p.P136P		Atlas-SNP	.											.	DCTN5	21	.	0			c.A408G						PASS	.	A	,	516,3878	235.8+/-248.2	34,448,1715	94.0	87.0	89.0		408,408	-1.1	1.0	16	dbSNP_76	89	1738,6862	315.7+/-312.4	172,1394,2734	no	coding-synonymous,coding-synonymous	DCTN5	NM_001199743.1,NM_032486.3	,	206,1842,4449	GG,GA,AA		20.2093,11.7433,17.3465	,	136/153,136/183	23677006	2254,10740	2197	4300	6497	SO:0001819	synonymous_variant	84516	exon5			ACCTCCAGAAACT		CCDS10615.1, CCDS58435.1, CCDS58436.1	16p12.1	2008-02-05			ENSG00000166847	ENSG00000166847			24594	protein-coding gene	gene with protein product		612962				10525537, 15043994	Standard	NM_032486		Approved	MGC3248, p25	uc002dly.2	Q9BTE1	OTTHUMG00000131610	ENST00000300087.2:c.408A>G	16.37:g.23677006A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_032486	A8K9X8|H3BN51|H3BQA4	Silent	SNP	ENST00000300087.2	37	CCDS10615.1																																																																																			A|0.799;G|0.201	0.201	strong		0.393	DCTN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254497.1	NM_032486	
KIFC2	90990	hgsc.bcm.edu	37	8	145698758	145698758	+	Silent	SNP	G	G	A	rs201074786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145698758G>A	ENST00000301332.2	+	17	2819	c.2442G>A	c.(2440-2442)agG>agA	p.R814R	FOXH1_ENST00000525197.1_5'Flank|KIFC2_ENST00000301331.5_3'UTR	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	814	Pro-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GCCCGCAGAGGGCCTGCCCCT	0.706													G|||	11	0.00219649	0.0	0.0072	5008	,	,		9786	0.0		0.006	False		,,,				2504	0.0				p.R814R		Atlas-SNP	.											.	KIFC2	53	.	0			c.G2442A						PASS	.	G		2,3926		0,2,1962	7.0	6.0	6.0		2442	1.7	0.0	8		6	61,7875		0,61,3907	no	coding-synonymous	KIFC2	NM_145754.2		0,63,5869	AA,AG,GG		0.7686,0.0509,0.531		814/839	145698758	63,11801	1964	3968	5932	SO:0001819	synonymous_variant	90990	exon17			GCAGAGGGCCTGC	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"""Kinesins"""	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.2442G>A	8.37:g.145698758G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_145754	E9PHB2|Q96NN6	Silent	SNP	ENST00000301332.2	37	CCDS6427.1	6	0.0027472527472527475	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.900	0.956047	0.18507	5.09E-4	0.007686	ENSG00000167702	ENST00000528415	.	.	.	3.48	1.66	0.24008	.	.	.	.	.	T	0.26738	0.0654	.	.	.	0.28321	N	0.922249	.	.	.	.	.	.	T	0.22103	-1.0226	4	.	.	.	-4.4999	7.859	0.29499	0.2172:0.0:0.7828:0.0	.	.	.	.	E	539	.	.	G	+	2	0	KIFC2	145669566	0.001000	0.12720	0.037000	0.18230	0.019000	0.09904	0.281000	0.18810	0.474000	0.27392	0.484000	0.47621	GGG	G|0.997;A|0.003	0.003	strong		0.706	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754	
LRRC4	64101	hgsc.bcm.edu	37	7	127669584	127669584	+	Silent	SNP	T	T	C	rs73238074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:127669584T>C	ENST00000249363.3	-	2	1367	c.1110A>G	c.(1108-1110)gcA>gcG	p.A370A	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	370	Ig-like.				postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		ACTTAAGTTCTGCCATCCGAC	0.607													T|||	719	0.14357	0.0688	0.2608	5008	,	,		20904	0.0853		0.1382	False		,,,				2504	0.227				p.A370A		Atlas-SNP	.											.	LRRC4	72	.	0			c.A1110G						PASS	.	T	,	375,4031	190.2+/-216.2	13,349,1841	79.0	70.0	73.0		,1110	-4.1	0.9	7	dbSNP_130	73	1205,7395	244.0+/-273.4	91,1023,3186	no	intron,coding-synonymous	SND1,LRRC4	NM_014390.2,NM_022143.4	,	104,1372,5027	CC,CT,TT		14.0116,8.5111,12.1482	,	,370/654	127669584	1580,11426	2203	4300	6503	SO:0001819	synonymous_variant	64101	exon2			AAGTTCTGCCATC	AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"""Immunoglobulin superfamily / I-set domain containing"""	15586	protein-coding gene	gene with protein product		610486	"""leucine-rich repeat-containing 4"""			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.1110A>G	7.37:g.127669584T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_022143	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Silent	SNP	ENST00000249363.3	37	CCDS5799.1																																																																																			T|0.881;C|0.119	0.119	strong		0.607	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143	
TBC1D4	9882	hgsc.bcm.edu	37	13	75884216	75884216	+	Missense_Mutation	SNP	C	C	T	rs1062087|rs11537635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:75884216C>T	ENST00000377636.3	-	14	2801	c.2455G>A	c.(2455-2457)Gta>Ata	p.V819I	TBC1D4_ENST00000431480.2_Missense_Mutation_p.V811I|TBC1D4_ENST00000425511.1_Missense_Mutation_p.V36I|TBC1D4_ENST00000377625.2_Missense_Mutation_p.V756I	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	819			V -> I (in dbSNP:rs1062087). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:19077034, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:9628581}.		cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GACAGGAATACAACCAGCGGT	0.478													T|||	3565	0.711861	0.3979	0.6643	5008	,	,		17372	0.7956		0.8579	False		,,,				2504	0.9335				p.V819I		Atlas-SNP	.											.	TBC1D4	142	.	0			c.G2455A						PASS	.	T	ILE/VAL	1880,1848		458,964,442	85.0	76.0	79.0		2455	1.9	0.1	13	dbSNP_86	79	7236,952		3197,842,55	yes	missense	TBC1D4	NM_014832.2	29	3655,1806,497	TT,TC,CC		11.6268,49.5708,23.4978	benign	819/1299	75884216	9116,2800	1864	4094	5958	SO:0001583	missense	9882	exon14			GGAATACAACCAG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2455G>A	13.37:g.75884216C>T	ENSP00000366863:p.Val819Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	1570	0.7188644688644689	219	0.4451219512195122	248	0.6850828729281768	453	0.791958041958042	650	0.8575197889182058	T	8.270	0.813047	0.16537	0.504292	0.883732	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511;ENST00000413735	T;T;T;T;T	0.21031	4.09;4.09;4.08;3.83;2.03	5.93	1.89	0.25635	.	0.185024	0.37809	N	0.001940	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.001	T	0.20472	-1.0274	9	0.25751	T	0.34	-9.8159	0.1809	0.00123	0.2243:0.2433:0.2136:0.3188	rs1062087;rs3203202;rs61677219;rs1062087	36;756;811;819	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	I	819;811;756;36;268	ENSP00000366863:V819I;ENSP00000395986:V811I;ENSP00000366852:V756I;ENSP00000390654:V36I;ENSP00000396932:V268I	ENSP00000366852:V756I	V	-	1	0	TBC1D4	74782217	0.000000	0.05858	0.119000	0.21687	0.988000	0.76386	0.019000	0.13444	0.143000	0.18926	-0.254000	0.11334	GTA	C|0.263;T|0.737	0.737	strong		0.478	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
CCDC87	55231	hgsc.bcm.edu	37	11	66358126	66358126	+	Silent	SNP	C	C	T	rs486584	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66358126C>T	ENST00000333861.3	-	1	2428	c.2361G>A	c.(2359-2361)ctG>ctA	p.L787L	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	787					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CTATCTCCTCCAGGAGGGAAA	0.507													C|||	2131	0.425519	0.1089	0.6268	5008	,	,		17655	0.4484		0.5129	False		,,,				2504	0.5971				p.L787L		Atlas-SNP	.											.	CCDC87	83	.	0			c.G2361A						PASS	.	C		843,3557	331.0+/-301.8	95,653,1452	134.0	141.0	139.0		2361	-1.6	0.5	11	dbSNP_83	139	4541,4049	596.0+/-393.5	1169,2203,923	no	coding-synonymous	CCDC87	NM_018219.2		1264,2856,2375	TT,TC,CC		47.1362,19.1591,41.4473		787/850	66358126	5384,7606	2200	4295	6495	SO:0001819	synonymous_variant	55231	exon1			CTCCTCCAGGAGG	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.2361G>A	11.37:g.66358126C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_018219	Q8NE76	Silent	SNP	ENST00000333861.3	37	CCDS8145.1																																																																																			C|0.597;T|0.402	0.402	strong		0.507	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219	
SPATA18	132671	hgsc.bcm.edu	37	4	52938243	52938243	+	Missense_Mutation	SNP	T	T	C	rs199988934|rs3860707	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:52938243T>C	ENST00000295213.4	+	6	1053	c.679T>C	c.(679-681)Tcc>Ccc	p.S227P	SPATA18_ENST00000419395.2_Missense_Mutation_p.S195P|SPATA18_ENST00000506829.1_3'UTR	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	227			S -> P (in dbSNP:rs3860707). {ECO:0000269|PubMed:14702039}.		cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			AGAAGCCATGTCCGATTATAA	0.502													T|||	1920	0.383387	0.084	0.6182	5008	,	,		17975	0.3968		0.6441	False		,,,				2504	0.3395				p.S227P		Atlas-SNP	.											.	SPATA18	222	.	0			c.T679C						PASS	.	T	PRO/SER	756,3650	306.6+/-289.6	79,598,1526	98.0	87.0	91.0		679	-3.8	0.0	4	dbSNP_108	91	5532,3068	659.8+/-401.7	1848,1836,616	yes	missense	SPATA18	NM_145263.2	74	1927,2434,2142	CC,CT,TT		35.6744,17.1584,48.3469	possibly-damaging	227/539	52938243	6288,6718	2203	4300	6503	SO:0001583	missense	132671	exon6			GCCATGTCCGATT	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"""spermatogenesis associated 18 homolog (rat)"""			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.679T>C	4.37:g.52938243T>C	ENSP00000295213:p.Ser227Pro	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	1006	0.4606227106227106	38	0.07723577235772358	245	0.6767955801104972	223	0.38986013986013984	500	0.6596306068601583	T	12.64	1.999411	0.35226	0.171584	0.643256	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.31247	1.5;1.5	4.12	-3.84	0.04256	.	0.510211	0.22627	N	0.057626	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B	0.32620	0.378;0.378	B;B	0.34931	0.192;0.192	T	0.25916	-1.0118	9	0.29301	T	0.29	-1.304	16.5276	0.84335	0.0:0.0:0.7746:0.2254	rs3860707;rs17611875;rs57910332;rs3860707	195;227	Q8TC71-2;Q8TC71	.;MIEAP_HUMAN	P	227;195	ENSP00000295213:S227P;ENSP00000415309:S195P	ENSP00000295213:S227P	S	+	1	0	SPATA18	52633000	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.287000	0.18920	-0.593000	0.05844	-1.267000	0.01435	TCC	T|0.544;C|0.456	0.456	strong		0.502	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263	
ADPGK	83440	hgsc.bcm.edu	37	15	73052845	73052845	+	Silent	SNP	A	A	G	rs8023358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:73052845A>G	ENST00000311669.8	-	4	639	c.546T>C	c.(544-546)ggT>ggC	p.G182G	ADPGK_ENST00000567733.1_5'UTR	NM_031284.4	NP_112574.3	Q9BRR6	ADPGK_HUMAN	ADP-dependent glucokinase	182	ADPK. {ECO:0000255|PROSITE- ProRule:PRU00584}.				glycolytic process (GO:0006096)	extracellular region (GO:0005576)|membrane (GO:0016020)	ADP-specific glucokinase activity (GO:0043843)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	7						GTAGCTTTGGACCAACTGGAC	0.498													A|||	980	0.195687	0.3003	0.1657	5008	,	,		19483	0.2252		0.1441	False		,,,				2504	0.0982				p.G182G		Atlas-SNP	.											.	ADPGK	19	.	0			c.T546C						PASS	.	A		1027,2957		135,757,1100	123.0	125.0	124.0		546	-3.2	1.0	15	dbSNP_116	124	1113,7187		72,969,3109	no	coding-synonymous	ADPGK	NM_031284.4		207,1726,4209	GG,GA,AA		13.4096,25.7781,17.421		182/497	73052845	2140,10144	1992	4150	6142	SO:0001819	synonymous_variant	83440	exon4			CTTTGGACCAACT	AL136873	CCDS42057.1	15q24.1	2012-07-02			ENSG00000159322	ENSG00000159322			25250	protein-coding gene	gene with protein product		611861				11230166	Standard	NM_031284		Approved	DKFZp434B195, ADP-GK	uc002avf.4	Q9BRR6	OTTHUMG00000172777	ENST00000311669.8:c.546T>C	15.37:g.73052845A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_031284	Q49AU7|Q8NBI1|Q8WZ90|Q96NF8|Q9H0A7	Silent	SNP	ENST00000311669.8	37	CCDS42057.1																																																																																			A|0.822;G|0.178	0.178	strong		0.498	ADPGK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420434.1	NM_031284	
SLAMF8	56833	hgsc.bcm.edu	37	1	159799910	159799910	+	Missense_Mutation	SNP	G	G	A	rs34687326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:159799910G>A	ENST00000289707.5	+	2	444	c.295G>A	c.(295-297)Ggc>Agc	p.G99S	SLAMF8_ENST00000368104.4_Intron|SLAMF8_ENST00000471286.1_3'UTR	NM_020125.2	NP_064510.1	Q9P0V8	SLAF8_HUMAN	SLAM family member 8	99			G -> S (in dbSNP:rs34687326). {ECO:0000269|PubMed:11313408}.		cellular response to drug (GO:0035690)|defense response to bacterium (GO:0042742)|phagosome acidification (GO:0090383)|regulation of kinase activity (GO:0043549)|regulation of NAD(P)H oxidase activity (GO:0033860)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(4)|lung(6)	12	all_hematologic(112;0.0597)					TGGAGACAGCGGCAACTTCTC	0.632													G|||	154	0.0307508	0.003	0.0389	5008	,	,		19364	0.0		0.1054	False		,,,				2504	0.0174				p.G99S		Atlas-SNP	.											.	SLAMF8	30	.	0			c.G295A						PASS	.	G	SER/GLY	89,4317	73.6+/-111.7	1,87,2115	49.0	52.0	51.0		295	4.4	1.0	1	dbSNP_126	51	1055,7545	221.5+/-258.9	75,905,3320	yes	missense	SLAMF8	NM_020125.2	56	76,992,5435	AA,AG,GG		12.2674,2.02,8.7959	probably-damaging	99/286	159799910	1144,11862	2203	4300	6503	SO:0001583	missense	56833	exon2			GACAGCGGCAACT	AF146761	CCDS1188.1	1q23.1	2013-01-11			ENSG00000158714	ENSG00000158714		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21391	protein-coding gene	gene with protein product		606620				11313408	Standard	NM_020125		Approved	BLAME, SBBI42, CD353	uc001fue.4	Q9P0V8	OTTHUMG00000035433	ENST00000289707.5:c.295G>A	1.37:g.159799910G>A	ENSP00000289707:p.Gly99Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_020125	Q32MC6|Q5VU15	Missense_Mutation	SNP	ENST00000289707.5	37	CCDS1188.1	101	0.04624542124542125	1	0.0020325203252032522	17	0.04696132596685083	0	0.0	83	0.10949868073878628	G	23.0	4.365236	0.82463	0.0202	0.122674	ENSG00000158714	ENST00000289707	T	0.52754	0.65	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	L	0.34521	1.04	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.51474	-0.8701	9	0.54805	T	0.06	-21.1515	12.4262	0.55548	0.0:0.0:1.0:0.0	rs34687326	99	Q9P0V8	SLAF8_HUMAN	S	99	ENSP00000289707:G99S	ENSP00000289707:G99S	G	+	1	0	SLAMF8	158066534	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.543000	0.60684	2.296000	0.77279	0.313000	0.20887	GGC	G|0.926;A|0.074	0.074	strong		0.632	SLAMF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085983.1	NM_020125	
TMEM161A	54929	hgsc.bcm.edu	37	19	19230816	19230816	+	Missense_Mutation	SNP	T	T	C	rs45467802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19230816T>C	ENST00000162044.9	-	12	1427	c.1363A>G	c.(1363-1365)Atc>Gtc	p.I455V	TMEM161A_ENST00000450333.2_Missense_Mutation_p.I352V|TMEM161A_ENST00000587583.2_Missense_Mutation_p.I430V	NM_017814.2	NP_060284.1	Q9NX61	T161A_HUMAN	transmembrane protein 161A	455				I -> V (in Ref. 2; BAG53402). {ECO:0000305}.	cellular response to oxidative stress (GO:0034599)|cellular response to UV (GO:0034644)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of DNA repair (GO:0045739)|response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			GTCCACCAGATGAGGTAGGCC	0.662													T|||	243	0.0485224	0.0477	0.0331	5008	,	,		15175	0.0446		0.0437	False		,,,				2504	0.0695				p.I455V		Atlas-SNP	.											.	TMEM161A	37	.	0			c.A1363G						PASS	.	T	VAL/ILE	231,4151		4,223,1964	20.0	21.0	20.0		1363	3.5	1.0	19	dbSNP_127	20	406,8160		11,384,3888	yes	missense	TMEM161A	NM_017814.1	29	15,607,5852	CC,CT,TT		4.7397,5.2716,4.9197	benign	455/480	19230816	637,12311	2191	4283	6474	SO:0001583	missense	54929	exon12			ACCAGATGAGGTA	BC005210	CCDS12393.1, CCDS58656.1	19p13.11	2008-02-05				ENSG00000064545			26020	protein-coding gene	gene with protein product						12975309	Standard	NM_017814		Approved	FLJ39645, FLJ20422	uc002nlg.4	Q9NX61		ENST00000162044.9:c.1363A>G	19.37:g.19230816T>C	ENSP00000162044:p.Ile455Val	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_017814	B3KUE0|G5E9M6|Q7L2Y1	Missense_Mutation	SNP	ENST00000162044.9	37	CCDS12393.1	319	0.14606227106227107	104	0.21138211382113822	37	0.10220994475138122	65	0.11363636363636363	113	0.14907651715039577	T	11.76	1.735741	0.30774	0.052716	0.047397	ENSG00000064545	ENST00000450333;ENST00000162044	.	.	.	4.53	3.48	0.39840	.	0.051611	0.85682	D	0.000000	T	0.00039	0.0001	N	0.22421	0.69	0.33292	P	0.436354	B;B	0.14012	0.009;0.0	B;B	0.11329	0.006;0.002	T	0.10917	-1.0609	8	0.36615	T	0.2	-15.4835	7.5498	0.27790	0.0:0.1139:0.0:0.8861	rs45467802;rs61739370	352;455	G5E9M6;Q9NX61	.;T161A_HUMAN	V	352;455	.	ENSP00000162044:I455V	I	-	1	0	TMEM161A	19091816	1.000000	0.71417	0.998000	0.56505	0.343000	0.28985	1.729000	0.38115	0.602000	0.29896	0.260000	0.18958	ATC	T|0.911;C|0.089	0.089	strong		0.662	TMEM161A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460089.2	NM_017814	
HOXD12	3238	hgsc.bcm.edu	37	2	176964904	176964904	+	Silent	SNP	G	G	A	rs847151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:176964904G>A	ENST00000406506.2	+	1	447	c.375G>A	c.(373-375)ctG>ctA	p.L125L	HOXD12_ENST00000404162.2_Silent_p.L125L			P35452	HXD12_HUMAN	homeobox D12	125					embryonic digit morphogenesis (GO:0042733)|pattern specification process (GO:0007389)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		AGTCTAGCCTGGCTCCTGCAG	0.687													G|||	1516	0.302716	0.5076	0.4121	5008	,	,		14543	0.0585		0.3052	False		,,,				2504	0.1973				p.L125L		Atlas-SNP	.											.	HOXD12	25	.	0			c.G375A						PASS	.	G		1767,2087		421,925,581	17.0	20.0	19.0		375	5.4	0.9	2	dbSNP_86	19	2688,5598		454,1780,1909	no	coding-synonymous	HOXD12	NM_021193.3		875,2705,2490	AA,AG,GG		32.4403,45.8485,36.6969		125/271	176964904	4455,7685	1927	4143	6070	SO:0001819	synonymous_variant	3238	exon1			TAGCCTGGCTCCT		CCDS46456.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170178	ENSG00000170178		"""Homeoboxes / ANTP class : HOXL subclass"""	5135	protein-coding gene	gene with protein product		142988	"""homeo box D12"""	HOX4H		1675198, 1973146	Standard	NM_021193		Approved		uc010zev.1	P35452	OTTHUMG00000150358	ENST00000406506.2:c.375G>A	2.37:g.176964904G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_021193	B5MCP0|Q0VAD7|Q0VAD8|Q9NS03	Silent	SNP	ENST00000406506.2	37	CCDS46456.1																																																																																			G|0.702;A|0.298	0.298	strong		0.687	HOXD12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359253.2	NM_021193	
STRN3	29966	hgsc.bcm.edu	37	14	31425437	31425437	+	Silent	SNP	T	T	C	rs12886419	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:31425437T>C	ENST00000357479.5	-	2	490	c.294A>G	c.(292-294)gcA>gcG	p.A98A	STRN3_ENST00000355683.5_Silent_p.A98A	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	98					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		CTTGTAGAAATGCAATCCGGG	0.328													T|||	859	0.171526	0.2526	0.17	5008	,	,		19408	0.003		0.2704	False		,,,				2504	0.135				p.A98A		Atlas-SNP	.											.	STRN3	117	.	0			c.A294G						PASS	.	T	,	1093,3313	395.4+/-329.6	135,823,1245	125.0	113.0	117.0		294,294	2.8	1.0	14	dbSNP_121	117	2247,6351	379.4+/-339.3	260,1727,2312	no	coding-synonymous,coding-synonymous	STRN3	NM_001083893.1,NM_014574.3	,	395,2550,3557	CC,CT,TT		26.134,24.8071,25.6844	,	98/798,98/714	31425437	3340,9664	2203	4299	6502	SO:0001819	synonymous_variant	29966	exon2			TAGAAATGCAATC		CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.294A>G	14.37:g.31425437T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	101	58	0.574257	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Silent	SNP	ENST00000357479.5	37	CCDS41938.1																																																																																			T|0.773;C|0.227	0.227	strong		0.328	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
AXL	558	hgsc.bcm.edu	37	19	41754430	41754430	+	Missense_Mutation	SNP	G	G	A	rs35538872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41754430G>A	ENST00000301178.4	+	13	1739	c.1549G>A	c.(1549-1551)Ggc>Agc	p.G517S	AXL_ENST00000359092.3_Missense_Mutation_p.G508S|AXL_ENST00000593513.1_Missense_Mutation_p.G249S	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	517					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G508S(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						GAACAGCCTGGGCATCAGTGA	0.582													G|||	11	0.00219649	0.0	0.0014	5008	,	,		19187	0.0		0.006	False		,,,				2504	0.0041				p.G517S		Atlas-SNP	.											AXL,colon,carcinoma,-2,4	AXL	126	4	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G1549A						PASS	.	G	SER/GLY,SER/GLY	6,4400	12.9+/-30.5	0,6,2197	119.0	109.0	112.0		1522,1549	4.9	1.0	19	dbSNP_126	112	57,8543	35.9+/-90.5	0,57,4243	yes	missense,missense	AXL	NM_001699.4,NM_021913.3	56,56	0,63,6440	AA,AG,GG		0.6628,0.1362,0.4844	probably-damaging,probably-damaging	508/886,517/895	41754430	63,12943	2203	4300	6503	SO:0001583	missense	558	exon13			AGCCTGGGCATCA	M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.1549G>A	19.37:g.41754430G>A	ENSP00000301178:p.Gly517Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	156	81	0.519231	NM_021913	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	37	CCDS12575.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	34	5.357852	0.95854	0.001362	0.006628	ENSG00000167601	ENST00000301178;ENST00000359092	T;T	0.75477	-0.94;-0.89	4.88	4.88	0.63580	.	0.117673	0.56097	D	0.000028	T	0.80757	0.4684	M	0.67397	2.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74348	0.981;0.983	D	0.84540	0.0638	10	0.66056	D	0.02	-28.2531	17.1535	0.86783	0.0:0.0:1.0:0.0	rs35538872	508;517	P30530-2;P30530	.;UFO_HUMAN	S	517;508	ENSP00000301178:G517S;ENSP00000351995:G508S	ENSP00000301178:G517S	G	+	1	0	AXL	46446270	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.317000	0.96327	2.426000	0.82243	0.561000	0.74099	GGC	G|0.995;A|0.005	0.005	strong		0.582	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2		
KCNA4	3739	hgsc.bcm.edu	37	11	30033191	30033191	+	Silent	SNP	G	G	A	rs3802914	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:30033191G>A	ENST00000328224.6	-	2	2268	c.1035C>T	c.(1033-1035)ggC>ggT	p.G345G	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	345					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	CACCATGCCCGCCAGCACTCA	0.498													g|||	855	0.170727	0.3154	0.1801	5008	,	,		19509	0.0357		0.171	False		,,,				2504	0.1074				p.G345G		Atlas-SNP	.											.	KCNA4	158	.	0			c.C1035T						PASS	.	A		1191,2871		182,827,1022	84.0	77.0	79.0		1035	-10.9	0.1	11	dbSNP_107	79	1368,7020		118,1132,2944	no	coding-synonymous	KCNA4	NM_002233.3		300,1959,3966	AA,AG,GG		16.309,29.3205,20.5542		345/654	30033191	2559,9891	2031	4194	6225	SO:0001819	synonymous_variant	3739	exon2			ATGCCCGCCAGCA	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1035C>T	11.37:g.30033191G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_002233		Silent	SNP	ENST00000328224.6	37	CCDS41629.1																																																																																			G|0.833;A|0.167	0.167	strong		0.498	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233	
CA9	768	hgsc.bcm.edu	37	9	35674053	35674053	+	Missense_Mutation	SNP	G	G	A	rs2071676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35674053G>A	ENST00000378357.4	+	1	201	c.97G>A	c.(97-99)Gtg>Atg	p.V33M	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	33			V -> M (in dbSNP:rs2071676). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8084592}.		bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	GCTGCTTCTGGTGCCTGTCCA	0.657													G|||	1619	0.323283	0.0764	0.4078	5008	,	,		17771	0.4444		0.3569	False		,,,				2504	0.4376				p.V33M		Atlas-SNP	.											.	CA9	48	.	0			c.G97A						PASS	.	G	MET/VAL	507,3899	236.1+/-248.4	28,451,1724	62.0	56.0	58.0		97	3.1	1.0	9	dbSNP_96	58	2993,5607	462.1+/-365.6	527,1939,1834	yes	missense	CA9	NM_001216.2	21	555,2390,3558	AA,AG,GG		34.8023,11.507,26.9107	possibly-damaging	33/460	35674053	3500,9506	2203	4300	6503	SO:0001583	missense	768	exon1			CTTCTGGTGCCTG	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.97G>A	9.37:g.35674053G>A	ENSP00000367608:p.Val33Met	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	37	CCDS6585.1	705	0.3228021978021978	54	0.10975609756097561	133	0.3674033149171271	264	0.46153846153846156	254	0.33509234828496043	G	11.61	1.688594	0.29962	0.11507	0.348023	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.72505	-0.66	5.01	3.11	0.35812	.	1.392810	0.04640	N	0.405154	T	0.00012	0.0000	L	0.34521	1.04	0.39357	P	0.034143000000000034	P;P	0.43701	0.815;0.718	P;B	0.46389	0.515;0.316	T	0.22836	-1.0205	9	0.87932	D	0	.	8.0091	0.30342	0.0:0.1758:0.6418:0.1824	rs2071676;rs17855453;rs2071676	33;33	F5H404;Q16790	.;CAH9_HUMAN	M	33	ENSP00000367608:V33M	ENSP00000367608:V33M	V	+	1	0	CA9	35664053	0.004000	0.15560	0.989000	0.46669	0.478000	0.33099	0.359000	0.20233	0.654000	0.30846	0.655000	0.94253	GTG	G|0.707;A|0.293	0.293	strong		0.657	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
OLFM2	93145	hgsc.bcm.edu	37	19	9968434	9968434	+	Missense_Mutation	SNP	C	C	T	rs2303100	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9968434C>T	ENST00000264833.4	-	3	502	c.317G>A	c.(316-318)cGg>cAg	p.R106Q	OLFM2_ENST00000590841.1_Missense_Mutation_p.R28Q	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	106			R -> Q (in dbSNP:rs2303100). {ECO:0000269|Ref.1}.		protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						TGCCCGGAGCCGCGCATCCAG	0.597													C|||	1555	0.310503	0.0401	0.5403	5008	,	,		19097	0.3095		0.5427	False		,,,				2504	0.2751				p.R106Q		Atlas-SNP	.											.	OLFM2	42	.	0			c.G317A	GRCh37	CM066940	OLFM2	M	rs2303100	PASS	.	C	GLN/ARG	564,3842	250.6+/-257.6	43,478,1682	45.0	47.0	47.0		317	3.9	0.9	19	dbSNP_100	47	4718,3882	605.1+/-394.9	1298,2122,880	yes	missense	OLFM2	NM_058164.2	43	1341,2600,2562	TT,TC,CC		45.1395,12.8007,40.612	possibly-damaging	106/455	9968434	5282,7724	2203	4300	6503	SO:0001583	missense	93145	exon3			CGGAGCCGCGCAT	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"""noelin 2"""						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.317G>A	19.37:g.9968434C>T	ENSP00000264833:p.Arg106Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_058164	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	37	CCDS12221.1	816	0.37362637362637363	26	0.052845528455284556	195	0.5386740331491713	180	0.3146853146853147	415	0.5474934036939314	C	15.68	2.904240	0.52333	0.128007	0.548605	ENSG00000105088	ENST00000264833	T	0.46063	0.88	3.92	3.92	0.45320	.	0.063680	0.64402	D	0.000012	T	0.00012	0.0000	L	0.36672	1.1	0.37247	P	0.09359600000000001	P	0.51147	0.942	B	0.40444	0.329	T	0.48681	-0.9014	8	.	.	.	.	7.3267	0.26560	0.0:0.8818:0.0:0.1182	rs2303100;rs12983966;rs17795374;rs2303100	106	O95897	NOE2_HUMAN	Q	106	ENSP00000264833:R106Q	.	R	-	2	0	OLFM2	9829434	0.761000	0.28439	0.942000	0.38095	0.791000	0.44710	1.246000	0.32803	2.025000	0.59659	0.313000	0.20887	CGG	C|0.622;T|0.378	0.378	strong		0.597	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1		
PRODH	5625	hgsc.bcm.edu	37	22	18905964	18905964	+	Missense_Mutation	SNP	C	C	T	rs2904552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:18905964C>T	ENST00000357068.6	-	11	1557	c.1292G>A	c.(1291-1293)cGc>cAc	p.R431H	PRODH_ENST00000420436.1_Missense_Mutation_p.R323H|PRODH_ENST00000334029.2_Missense_Mutation_p.R323H	NM_016335.4	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase (oxidase) 1	431			R -> H (associated with HP-1 in a subset of schizophrenia patients; moderate reduction of enzymatic activity; dbSNP:rs2904552). {ECO:0000269|PubMed:12217952, ECO:0000269|PubMed:17135275}.		4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)	FAD binding (GO:0071949)|proline dehydrogenase activity (GO:0004657)			breast(1)|endometrium(3)|lung(4)|upper_aerodigestive_tract(1)	9					L-Proline(DB00172)	GCCCTCACGGCGAGCCAGCTC	0.642													.|||	215	0.0429313	0.0234	0.0576	5008	,	,		17166	0.001		0.1054	False		,,,				2504	0.0378				p.R431H		Atlas-SNP	.											.	PRODH	42	.	0			c.G1292A	GRCh37	CM057555	PRODH	M	rs2904552	PASS	.	C	HIS/ARG,HIS/ARG	161,4243	801.7+/-415.6	5,151,2046	58.0	51.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	968,1292	1.2	1.0	22	dbSNP_101	54	900,7700	773.2+/-407.7	43,814,3443	no	missense,missense	PRODH	NM_001195226.1,NM_016335.4	29,29	48,965,5489	TT,TC,CC		10.4651,3.6558,8.159	probably-damaging,probably-damaging	323/493,431/601	18905964	1061,11943	2202	4300	6502	SO:0001583	missense	5625	exon12			TCACGGCGAGCCA	AF010310	CCDS13754.1, CCDS56223.1	22q11.2	2014-07-10	2001-12-05		ENSG00000100033	ENSG00000100033	1.5.5.2		9453	protein-coding gene	gene with protein product		606810	"""proline dehydrogenase (proline oxidase )"""			9385373, 10192398	Standard	NM_001195226		Approved	HSPOX2, PRODH1, PIG6, PRODH2, TP53I6	uc002zok.4	O43272	OTTHUMG00000150163	ENST00000357068.6:c.1292G>A	22.37:g.18905964C>T	ENSP00000349577:p.Arg431His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	162	83	0.512346	NM_016335	A6NF53|O14680|Q0P507|Q147W8|Q504W1|Q59FI8|Q6NV86|Q9UF13	Missense_Mutation	SNP	ENST00000357068.6	37	CCDS13754.1	109	0.04990842490842491	12	0.024390243902439025	18	0.049723756906077346	0	0.0	79	0.10422163588390501	t	19.91	3.913871	0.72983	0.036558	0.104651	ENSG00000100033	ENST00000357068;ENST00000313755	T	0.35421	1.31	4.49	1.16	0.20824	Proline dehydrogenase (1);	0.229694	0.45606	N	0.000345	T	0.01870	0.0059	M	0.76574	2.34	0.47621	D	0.999478	P;D;P	0.67145	0.932;0.996;0.945	B;P;B	0.60173	0.286;0.87;0.408	T	0.00324	-1.1817	10	0.40728	T	0.16	-32.1286	8.7389	0.34545	0.0:0.7169:0.0:0.2831	rs2904552	347;431;323	O43272-1;O43272;E7EQL6	.;PROD_HUMAN;.	H	431;76	ENSP00000349577:R431H	ENSP00000318329:R76H	R	-	2	0	PRODH	17285964	0.994000	0.37717	1.000000	0.80357	0.977000	0.68977	1.178000	0.31981	0.474000	0.27392	-0.287000	0.09952	CGC	C|0.930;T|0.070	0.070	strong		0.642	PRODH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316637.2	NM_016335	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76587331	76587331	+	Silent	SNP	T	T	C	rs7184958	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:76587331T>C	ENST00000563764.1	+	1	18	c.18T>C	c.(16-18)acT>acC	p.T6T	CNTNAP4_ENST00000377504.4_Silent_p.T1149T|CNTNAP4_ENST00000307431.8_Silent_p.T1197T|CNTNAP4_ENST00000476707.1_Silent_p.T1201T|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Silent_p.T1125T																							GACACGTGACTGAGTCCAGCT	0.582													C|||	1506	0.300719	0.3449	0.1945	5008	,	,		17303	0.2867		0.2773	False		,,,				2504	0.3548				p.T1125T		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.T3375C						PASS	.	C	,	1424,2818		233,958,930	47.0	51.0	49.0		3593,3375	-8.7	0.2	16	dbSNP_116	49	2380,6088		331,1718,2185	yes	coding-synonymous,coding-synonymous	CNTNAP4	NM_033401.3,NM_138994.3	,	564,2676,3115	CC,CT,TT		28.1058,33.5691,29.9292	,	1198/1309,1125/1236	76587331	3804,8906	2121	4234	6355	SO:0001819	synonymous_variant	85445	exon21			CGTGACTGAGTCC																												ENST00000563764.1:c.18T>C	16.37:g.76587331T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	161	60	0.372671	NM_138994		Silent	SNP	ENST00000563764.1	37																																																																																				T|0.714;C|0.286	0.286	strong		0.582	RP11-58C22.1-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000421971.1		
CYSRT1	375791	hgsc.bcm.edu	37	9	140120396	140120396	+	Missense_Mutation	SNP	C	C	T	rs6606566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140120396C>T	ENST00000359069.2	+	2	373	c.323C>T	c.(322-324)gCg>gTg	p.A108V	C9orf169_ENST00000409414.1_Missense_Mutation_p.A148V|RNF224_ENST00000445101.2_5'Flank	NM_199001.2	NP_945352.2	A8MQ03	CRTP1_HUMAN		108				A -> V (in Ref. 2; AAH52297). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)	1						CCTCCGCCCGCGGGGCGCGGG	0.711													T|||	4216	0.841853	0.7988	0.8559	5008	,	,		14592	0.8968		0.7972	False		,,,				2504	0.8793				p.A108V		Atlas-SNP	.											.	C9orf169	6	.	0			c.C323T						PASS	.	T	VAL/ALA	1092,262		443,206,28	6.0	8.0	8.0		323	3.1	0.0	9	dbSNP_116	8	2581,563		1059,463,50	no	missense	C9orf169	NM_199001.2	64	1502,669,78	TT,TC,CC		17.9071,19.3501,18.3415	benign	108/145	140120396	3673,825	677	1572	2249	SO:0001583	missense	375791	exon2			CGCCCGCGGGGCG																												ENST00000359069.2:c.323C>T	9.37:g.140120396C>T	ENSP00000351967:p.Ala108Val	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_199001	Q86UY7	Missense_Mutation	SNP	ENST00000359069.2	37	CCDS48064.1	1834	0.8397435897435898	396	0.8048780487804879	308	0.850828729281768	519	0.9073426573426573	611	0.8060686015831134	T	0.011	-1.728644	0.00694	0.806499	0.820929	ENSG00000197191	ENST00000409414;ENST00000359069	.	.	.	4.28	3.11	0.35812	.	0.267760	0.19428	N	0.114508	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39354	-0.9618	8	0.02654	T	1	.	6.4109	0.21690	0.0:0.2184:0.0:0.7816	rs6606566;rs62587588	108	A8MQ03	CI169_HUMAN	V	148;108	.	ENSP00000351967:A108V	A	+	2	0	C9orf169	139240217	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.261000	0.18442	0.515000	0.28320	-0.521000	0.04368	GCG	C|0.160;T|0.840	0.840	strong		0.711	C9orf169-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
RIPK4	54101	hgsc.bcm.edu	37	21	43161022	43161022	+	Silent	SNP	C	C	T	rs7276592	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43161022C>T	ENST00000352483.2	-	9	2539	c.2475G>A	c.(2473-2475)acG>acA	p.T825T	RIPK4_ENST00000332512.3_Silent_p.T777T|RIPK4_ENST00000544709.1_Silent_p.T714T|RIPK4_ENST00000542057.1_Silent_p.T714T|AP001615.9_ENST00000423276.1_RNA			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	825					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GCCGCAGGAGCGTGGCGGCGG	0.672													c|||	2231	0.445487	0.2799	0.4654	5008	,	,		15770	0.5933		0.4851	False		,,,				2504	0.4622				p.T777T		Atlas-SNP	.											.	RIPK4	151	.	0			c.G2331A						PASS	.	A		1342,3028		210,922,1053	24.0	25.0	25.0		2331	-9.2	0.0	21	dbSNP_116	25	3644,4866		847,1950,1458	no	coding-synonymous	RIPK4	NM_020639.2		1057,2872,2511	TT,TC,CC		42.8202,30.7094,38.7112		777/785	43161022	4986,7894	2185	4255	6440	SO:0001819	synonymous_variant	54101	exon8			CAGGAGCGTGGCG	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.2475G>A	21.37:g.43161022C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				C|0.579;T|0.421	0.421	strong		0.672	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
DOCK2	1794	hgsc.bcm.edu	37	5	169174484	169174484	+	Silent	SNP	A	A	G	rs13155521	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:169174484A>G	ENST00000256935.8	+	23	2432	c.2352A>G	c.(2350-2352)caA>caG	p.Q784Q	DOCK2_ENST00000520908.1_Silent_p.Q276Q|DOCK2_ENST00000540750.1_5'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	784					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGAAAAGTCAATACAAAACTA	0.363													A|||	90	0.0179712	0.0038	0.0245	5008	,	,		19878	0.0		0.0616	False		,,,				2504	0.0061				p.Q784Q		Atlas-SNP	.											.	DOCK2	389	.	0			c.A2352G						PASS	.	A		65,4341	61.1+/-98.1	0,65,2138	92.0	86.0	88.0		2352	0.0	1.0	5	dbSNP_121	88	603,7997	159.1+/-212.4	25,553,3722	no	coding-synonymous	DOCK2	NM_004946.2		25,618,5860	GG,GA,AA		7.0116,1.4753,5.1361		784/1831	169174484	668,12338	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon23			AAGTCAATACAAA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2352A>G	5.37:g.169174484A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	29	0.337209	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			A|0.957;G|0.043	0.043	strong		0.363	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
PKD1L1	168507	hgsc.bcm.edu	37	7	47971626	47971626	+	Silent	SNP	G	G	A	rs885338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:47971626G>A	ENST00000289672.2	-	5	476	c.426C>T	c.(424-426)atC>atT	p.I142I		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	142					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AGGCCCTTGCGATTATAATGA	0.498													G|||	732	0.146166	0.1256	0.1383	5008	,	,		19276	0.251		0.0676	False		,,,				2504	0.1524				p.I142I		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C426T						PASS	.	G		603,3803	266.8+/-267.5	42,519,1642	86.0	99.0	94.0		426	0.4	0.0	7	dbSNP_86	94	832,7768	192.4+/-238.4	44,744,3512	no	coding-synonymous	PKD1L1	NM_138295.3		86,1263,5154	AA,AG,GG		9.6744,13.6859,11.0334		142/2850	47971626	1435,11571	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon5			CCTTGCGATTATA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.426C>T	7.37:g.47971626G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.878;A|0.122	0.122	strong		0.498	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
TMEM17	200728	hgsc.bcm.edu	37	2	62733189	62733189	+	Missense_Mutation	SNP	C	C	T	rs17854454	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:62733189C>T	ENST00000335390.5	-	1	287	c.76G>A	c.(76-78)Ggt>Agt	p.G26S		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	26			G -> S (in dbSNP:rs17854454). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GACTCTGGACCGGTCCGATTG	0.647													C|||	773	0.154353	0.0492	0.134	5008	,	,		12335	0.2302		0.1541	False		,,,				2504	0.2331				p.G26S		Atlas-SNP	.											.	TMEM17	19	.	0			c.G76A						PASS	.	C	SER/GLY	287,4119	151.4+/-185.3	11,265,1927	35.0	36.0	36.0		76	3.9	1.0	2	dbSNP_123	36	1491,7109	271.9+/-289.8	137,1217,2946	yes	missense	TMEM17	NM_198276.2	56	148,1482,4873	TT,TC,CC		17.3372,6.5138,13.6706	benign	26/199	62733189	1778,11228	2203	4300	6503	SO:0001583	missense	200728	exon1			CTGGACCGGTCCG		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.76G>A	2.37:g.62733189C>T	ENSP00000335094:p.Gly26Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	139	64	0.460432	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	37	CCDS1871.1	344	0.1575091575091575	29	0.05894308943089431	52	0.143646408839779	141	0.2465034965034965	122	0.16094986807387862	C	8.752	0.921567	0.17982	0.065138	0.173372	ENSG00000186889	ENST00000335390	T	0.42513	0.97	4.82	3.92	0.45320	.	0.476121	0.23926	N	0.043188	T	0.00012	0.0000	L	0.27053	0.805	0.30744	P	0.745851	B	0.24368	0.102	B	0.15052	0.012	T	0.13229	-1.0517	9	0.08599	T	0.76	-3.2417	10.6935	0.45886	0.0:0.9078:0.0:0.0922	rs17854454	26	Q86X19	TMM17_HUMAN	S	26	ENSP00000335094:G26S	ENSP00000335094:G26S	G	-	1	0	TMEM17	62586693	1.000000	0.71417	0.991000	0.47740	0.022000	0.10575	2.764000	0.47613	2.525000	0.85131	0.456000	0.33151	GGT	C|0.865;T|0.135	0.135	strong		0.647	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
EPSTI1	94240	hgsc.bcm.edu	37	13	43462607	43462607	+	IGR	SNP	G	G	A	rs11557739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:43462607G>A	ENST00000398762.3	-	0	957				EPSTI1_ENST00000313624.7_3'UTR|EPSTI1_ENST00000313640.7_Missense_Mutation_p.P338S			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)											endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		GTTGATGAAGGCCAGATAGGA	0.353													G|||	207	0.0413339	0.0053	0.0865	5008	,	,		20773	0.002		0.0716	False		,,,				2504	0.0675				p.P338S		Atlas-SNP	.											.	EPSTI1	47	.	0			c.C1012T						PASS	.	G	SER/PRO,	78,4328	69.8+/-107.6	0,78,2125	71.0	76.0	74.0		1012,	2.8	0.0	13	dbSNP_120	74	659,7941	166.1+/-218.1	25,609,3666	yes	missense,utr-3	EPSTI1	NM_001002264.1,NM_033255.2	74,	25,687,5791	AA,AG,GG		7.6628,1.7703,5.6666	benign,	338/411,	43462607	737,12269	2203	4300	6503	SO:0001628	intergenic_variant	94240	exon13			ATGAAGGCCAGAT	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"""epithelial stromal interaction protein 1"""	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814		13.37:g.43462607G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	37	CCDS9387.1	90	0.04120879120879121	6	0.012195121951219513	25	0.06906077348066299	1	0.0017482517482517483	58	0.07651715039577836	G	5.999	0.368270	0.11352	0.017703	0.076628	ENSG00000133106	ENST00000313640	.	.	.	5.53	2.78	0.32641	.	0.764642	0.11076	N	0.602392	T	0.02193	0.0068	.	.	.	0.58432	P	1.0000000000287557E-6	P	0.50443	0.935	P	0.45639	0.488	T	0.09058	-1.0692	7	0.42905	T	0.14	0.3441	5.1008	0.14759	0.1821:0.1742:0.6437:0.0	rs11557739;rs52821329;rs56461441;rs11557739	338	Q96J88-3	.	S	338	.	ENSP00000318982:P338S	P	-	1	0	EPSTI1	42360607	0.001000	0.12720	0.003000	0.11579	0.008000	0.06430	0.147000	0.16202	0.789000	0.33779	0.655000	0.94253	CCT	G|0.952;A|0.048	0.048	strong		0.353	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264	
GBP4	115361	hgsc.bcm.edu	37	1	89652072	89652072	+	Missense_Mutation	SNP	C	C	T	rs561037|rs386633303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89652072C>T	ENST00000355754.6	-	10	1748	c.1651G>A	c.(1651-1653)Gag>Aag	p.E551K	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	551			E -> G (in dbSNP:rs561042).|E -> K (in dbSNP:rs561037).	LEE -> MER (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TCCCTTTCCTCCTCCAACTTC	0.493													C|||	1797	0.358826	0.1445	0.3141	5008	,	,		19123	0.3978		0.4891	False		,,,				2504	0.5061				p.E551K		Atlas-SNP	.											GBP4,NS,carcinoma,+2,1	GBP4	89	1	0			c.G1651A						PASS	.	C	LYS/GLU	21,4385		1,19,2183	193.0	135.0	155.0		1651	-4.4	0.0	1	dbSNP_83	155	118,8482		8,102,4190	yes	missense	GBP4	NM_052941.4	56	9,121,6373	TT,TC,CC		1.3721,0.4766,1.0687	benign	551/641	89652072	139,12867	2203	4300	6503	SO:0001583	missense	115361	exon10			TTTCCTCCTCCAA	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1651G>A	1.37:g.89652072C>T	ENSP00000359490:p.Glu551Lys	Somatic	432	0	0		WXS	Illumina HiSeq	Phase_I	133	131	0.984962	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	.	.	.	.	.	.	.	.	.	.	C	5.059	0.196600	0.09599	0.004766	0.013721	ENSG00000162654	ENST00000355754	T	0.01981	4.52	4.29	-4.45	0.03546	Guanylate-binding protein, C-terminal (3);	1.061500	0.07205	N	0.858069	T	0.00384	0.0012	N	0.13098	0.295	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.47355	-0.9124	10	0.23891	T	0.37	.	1.5862	0.02644	0.141:0.322:0.2889:0.2481	rs561037;rs34980170;rs52804413;rs561037	551	Q96PP9	GBP4_HUMAN	K	551	ENSP00000359490:E551K	ENSP00000359490:E551K	E	-	1	0	GBP4	89424660	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.422000	0.07043	-0.652000	0.05408	-3.050000	0.00069	GAG	C|0.633;T|0.367	0.367	strong		0.493	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377433	138377433	+	Silent	SNP	G	G	A	rs3827827	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:138377433G>A	ENST00000356818.2	+	4	1626	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	PPP1R26_ENST00000605286.1_Silent_p.A359A|PPP1R26_ENST00000604351.1_Silent_p.A359A|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000401470.3_Silent_p.A359A|PPP1R26_ENST00000605660.1_Silent_p.A359A	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	359					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CGTCCGAGGCGTCCGACTCCA	0.622													G|||	1001	0.19988	0.1717	0.2839	5008	,	,		18482	0.1141		0.175	False		,,,				2504	0.2924				p.A359A		Atlas-SNP	.											KIAA0649,NS,carcinoma,0,1	.	.	1	0			c.G1077A						PASS	.	G		660,3746	267.4+/-267.8	44,572,1587	51.0	59.0	57.0		1077	-10.7	0.0	9	dbSNP_107	57	1507,7093	274.3+/-291.2	141,1225,2934	no	coding-synonymous	KIAA0649	NM_014811.3		185,1797,4521	AA,AG,GG		17.5233,14.9796,16.6615		359/1210	138377433	2167,10839	2203	4300	6503	SO:0001819	synonymous_variant	9858	exon4			CGAGGCGTCCGAC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1077G>A	9.37:g.138377433G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			G|0.824;A|0.176	0.176	strong		0.622	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
MYO3B	140469	hgsc.bcm.edu	37	2	171260787	171260787	+	Missense_Mutation	SNP	G	G	A	rs6736609	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:171260787G>A	ENST00000408978.4	+	20	2451	c.2308G>A	c.(2308-2310)Gta>Ata	p.V770I	MYO3B_ENST00000334231.6_Missense_Mutation_p.V779I|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.V770I	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	770	Myosin motor.		V -> I (in dbSNP:rs6736609). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						CATTGATGCTGTACCCGTGGA	0.498													A|||	3907	0.780152	0.6846	0.889	5008	,	,		18168	0.7292		0.8966	False		,,,				2504	0.7648				p.V770I		Atlas-SNP	.											.	MYO3B	320	.	0			c.G2308A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	2784,1054		1014,756,149	157.0	148.0	151.0		2308,2308,2308	-7.5	0.0	2	dbSNP_116	151	7435,827		3344,747,40	yes	missense,missense,missense	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	29,29,29	4358,1503,189	AA,AG,GG		10.0097,27.4622,15.5455	benign,benign,benign	770/1315,770/1276,770/1342	171260787	10219,1881	1919	4131	6050	SO:0001583	missense	140469	exon20			GATGCTGTACCCG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2308G>A	2.37:g.171260787G>A	ENSP00000386213:p.Val770Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	1726	0.7902930402930403	315	0.6402439024390244	321	0.8867403314917127	405	0.708041958041958	685	0.9036939313984169	A	5.434	0.265211	0.10294	0.725378	0.899903	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21	5.47	-7.46	0.01369	Myosin head, motor domain (3);	0.677771	0.16089	N	0.230141	T	0.00012	0.0000	N	0.25890	0.77	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.002;0.003	T	0.34775	-0.9815	9	0.36615	T	0.2	.	14.019	0.64543	0.1863:0.0:0.6397:0.174	rs6736609;rs61401130;rs6736609	770;770;770	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	I	770;770;769;779;779	ENSP00000386497:V770I;ENSP00000386213:V770I;ENSP00000446237:V779I;ENSP00000335100:V779I	ENSP00000314213:V769I	V	+	1	0	MYO3B	170969033	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.022000	0.12480	-1.626000	0.01552	-1.213000	0.01624	GTA	G|0.197;A|0.803	0.803	strong		0.498	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
RELN	5649	hgsc.bcm.edu	37	7	103180872	103180872	+	Silent	SNP	A	A	G	rs2075043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:103180872A>G	ENST00000428762.1	-	44	6861	c.6702T>C	c.(6700-6702)tgT>tgC	p.C2234C	RELN_ENST00000343529.5_Silent_p.C2234C|RELN_ENST00000424685.2_Silent_p.C2234C	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2234					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CGCCTTTACCACATCCCAGTC	0.463													A|||	548	0.109425	0.0582	0.0951	5008	,	,		20069	0.2798		0.0378	False		,,,				2504	0.0869				p.C2234C	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T6702C						PASS	.	A	,	231,4175	138.4+/-174.2	4,223,1976	103.0	98.0	100.0		6702,6702	4.2	1.0	7	dbSNP_96	100	377,8223	123.6+/-182.4	6,365,3929	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	10,588,5905	GG,GA,AA		4.3837,5.2429,4.6748	,	2234/3461,2234/3459	103180872	608,12398	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon44			TTTACCACATCCC		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.6702T>C	7.37:g.103180872A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			A|0.937;G|0.063	0.063	strong		0.463	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
TMEM176A	55365	hgsc.bcm.edu	37	7	150500520	150500520	+	Silent	SNP	C	C	T	rs741066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150500520C>T	ENST00000484928.1	+	4	899	c.318C>T	c.(316-318)taC>taT	p.Y106Y	TMEM176B_ENST00000434545.1_5'Flank|TMEM176B_ENST00000447204.2_5'Flank|TMEM176A_ENST00000461345.1_Silent_p.Y47Y|TMEM176A_ENST00000004103.3_Silent_p.Y106Y			Q96HP8	T176A_HUMAN	transmembrane protein 176A	106					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)		p.Y106Y(1)		breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCTTCATTTACGAGAAACGGG	0.582													C|||	984	0.196486	0.1271	0.2089	5008	,	,		17428	0.0377		0.3549	False		,,,				2504	0.2822				p.Y106Y		Atlas-SNP	.											TMEM176A,NS,carcinoma,0,1	TMEM176A	35	1	1	Substitution - coding silent(1)	stomach(1)	c.C318T						PASS	.	C		726,3680	299.8+/-286.0	62,602,1539	57.0	53.0	55.0		318	-8.8	0.0	7	dbSNP_86	55	2699,5901	431.6+/-356.9	415,1869,2016	no	coding-synonymous	TMEM176A	NM_018487.2		477,2471,3555	TT,TC,CC		31.3837,16.4775,26.334		106/236	150500520	3425,9581	2203	4300	6503	SO:0001819	synonymous_variant	55365	exon4			CATTTACGAGAAA	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.318C>T	7.37:g.150500520C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	140	58	0.414286	NM_018487	D3DX00|Q9NYC7	Silent	SNP	ENST00000484928.1	37	CCDS5909.1																																																																																			C|0.750;G|0.000;T|0.250	0.250	strong		0.582	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	
WNK2	65268	hgsc.bcm.edu	37	9	96021312	96021312	+	Missense_Mutation	SNP	G	G	A	rs10761203	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:96021312G>A	ENST00000297954.4	+	11	2482	c.2482G>A	c.(2482-2484)Gtg>Atg	p.V828M	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.V440M|WNK2_ENST00000395475.2_Missense_Mutation_p.V762M|WNK2_ENST00000395477.2_Missense_Mutation_p.V828M|WNK2_ENST00000349097.3_Missense_Mutation_p.V440M	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	828			V -> M (in dbSNP:rs10761203).		intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TGTGCCTCCCGTGCCACCACC	0.682													G|||	1570	0.313498	0.0681	0.5058	5008	,	,		11697	0.4345		0.4573	False		,,,				2504	0.2362				p.V828M		Atlas-SNP	.											WNK2_ENST00000297954,NS,carcinoma,0,2	WNK2	277	2	0			c.G2482A						PASS	.	G	MET/VAL	642,3764	263.4+/-265.5	47,548,1608	36.0	42.0	40.0		2482	2.9	0.7	9	dbSNP_120	40	4143,4455	555.8+/-386.7	991,2161,1147	yes	missense	WNK2	NM_006648.3	21	1038,2709,2755	AA,AG,GG		48.1856,14.571,36.7964	possibly-damaging	828/2218	96021312	4785,8219	2203	4299	6502	SO:0001583	missense	65268	exon11			CCTCCCGTGCCAC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.2482G>A	9.37:g.96021312G>A	ENSP00000297954:p.Val828Met	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	229	227	0.991266	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		829|829	0.37957875457875456|0.37957875457875456	42|42	0.08536585365853659|0.08536585365853659	182|182	0.5027624309392266|0.5027624309392266	253|253	0.4423076923076923|0.4423076923076923	352|352	0.46437994722955145|0.46437994722955145	G|G	10.12|10.12	1.262253|1.262253	0.23051|0.23051	0.14571|0.14571	0.481856|0.481856	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000448039;ENST00000297954;ENST00000395477;ENST00000395475;ENST00000349097;ENST00000427277	.|T;T;T;T;T;T	.|0.73152	.|-0.72;-0.47;-0.47;-0.72;0.16;0.12	5.11|5.11	2.9|2.9	0.33743|0.33743	.|.	.|0.659654	.|0.14927	.|N	.|0.290292	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.29908|0.29908	0.895|0.895	0.45284|0.45284	P|P	0.0017179999999999973|0.0017179999999999973	.|P;B;P;P;P	.|0.40970	.|0.675;0.421;0.491;0.675;0.734	.|B;B;B;B;B	.|0.29353	.|0.056;0.056;0.036;0.056;0.101	T|T	0.46952|0.46952	-0.9154|-0.9154	4|9	.|0.44086	.|T	.|0.13	.|.	3.5811|3.5811	0.07954|0.07954	0.2889:0.0:0.5135:0.1976|0.2889:0.0:0.5135:0.1976	rs10761203;rs59411385;rs10761203|rs10761203;rs59411385;rs10761203	.|828;828;431;828;828	.|Q9Y3S1-2;Q9Y3S1-4;A6PVR4;F8W9F9;Q9Y3S1	.|.;.;.;.;WNK2_HUMAN	H|M	431|776;828;828;762;440;440	.|ENSP00000412465:V776M;ENSP00000297954:V828M;ENSP00000378860:V828M;ENSP00000378858:V762M;ENSP00000297876:V440M;ENSP00000411181:V440M	.|ENSP00000297954:V828M	R|V	+|+	2|1	0|0	WNK2|WNK2	95061133|95061133	0.530000|0.530000	0.26330|0.26330	0.668000|0.668000	0.29813|0.29813	0.126000|0.126000	0.20510|0.20510	1.047000|1.047000	0.30367|0.30367	1.143000|1.143000	0.42306|0.42306	0.462000|0.462000	0.41574|0.41574	CGT|GTG	G|0.644;A|0.356	0.356	strong		0.682	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
DAXX	1616	hgsc.bcm.edu	37	6	33287810	33287810	+	Silent	SNP	G	G	A	rs370615019		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33287810G>A	ENST00000374542.5	-	5	1647	c.1443C>T	c.(1441-1443)gaC>gaT	p.D481D	DAXX_ENST00000266000.6_Silent_p.D481D|DAXX_ENST00000414083.2_Silent_p.D406D|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000477162.1_5'UTR|ZBTB22_ENST00000431845.2_5'Flank	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	481	Asp/Glu-rich (acidic).|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						cttcctcttcgtcctcctctt	0.502			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM								G|||	1	0.000199681	0.0	0.0	5008	,	,		20984	0.001		0.0	False		,,,				2504	0.0				p.D493D		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.C1479T						PASS	.	G	,,	0,4406		0,0,2203	238.0	162.0	188.0		1443,1479,1443	-2.5	0.2	6		188	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	DAXX	NM_001141969.1,NM_001141970.1,NM_001350.4	,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,	481/741,493/753,481/741	33287810	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1616	exon5			CTCTTCGTCCTCC	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1443C>T	6.37:g.33287810G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	303	170	0.561056	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	37	CCDS4776.1																																																																																			.	.	weak		0.502	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1		
CCR6	1235	hgsc.bcm.edu	37	6	167549775	167549775	+	Silent	SNP	T	T	C	rs3093007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167549775T>C	ENST00000341935.5	+	3	609	c.57T>C	c.(55-57)ttT>ttC	p.F19F	CCR6_ENST00000349984.4_Silent_p.F19F|CCR6_ENST00000400926.2_Silent_p.F19F|RP11-517H2.6_ENST00000609590.1_RNA	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	19					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		AAGATTATTTTGTGTCAGTCA	0.418													T|||	655	0.130791	0.1778	0.1167	5008	,	,		22549	0.0476		0.1759	False		,,,				2504	0.1166				p.F19F		Atlas-SNP	.											.	CCR6	36	.	0			c.T57C						PASS	.	T	,	777,3629	315.8+/-294.3	79,619,1505	149.0	147.0	148.0		57,57	-3.2	0.0	6	dbSNP_103	148	1594,7006	297.5+/-303.5	149,1296,2855	no	coding-synonymous,coding-synonymous	CCR6	NM_004367.5,NM_031409.3	,	228,1915,4360	CC,CT,TT		18.5349,17.635,18.23	,	19/375,19/375	167549775	2371,10635	2203	4300	6503	SO:0001819	synonymous_variant	1235	exon3			TTATTTTGTGTCA	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.57T>C	6.37:g.167549775T>C		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_004367	E1P5C6|P78553|Q92846	Silent	SNP	ENST00000341935.5	37	CCDS5298.1																																																																																			T|0.835;C|0.165	0.165	strong		0.418	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1		
IL12RB1	3594	hgsc.bcm.edu	37	19	18186575	18186575	+	Silent	SNP	G	G	A	rs17852635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18186575G>A	ENST00000600835.2	-	8	982	c.684C>T	c.(682-684)ccC>ccT	p.P228P	IL12RB1_ENST00000322153.7_Silent_p.P228P|IL12RB1_ENST00000593993.2_Silent_p.P228P			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	228	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GAACGCACACGGGGCTGCTCC	0.592													G|||	1151	0.229832	0.0998	0.1643	5008	,	,		17094	0.373		0.3111	False		,,,				2504	0.2209				p.P228P		Atlas-SNP	.											.	IL12RB1	92	.	0			c.C684T						PASS	.	G	,	589,3817	260.1+/-263.5	32,525,1646	65.0	64.0	64.0		684,684	-7.2	0.2	19	dbSNP_123	64	2715,5885	433.5+/-357.4	424,1867,2009	no	coding-synonymous,coding-synonymous	IL12RB1	NM_005535.1,NM_153701.1	,	456,2392,3655	AA,AG,GG		31.5698,13.3681,25.4037	,	228/663,228/382	18186575	3304,9702	2203	4300	6503	SO:0001819	synonymous_variant	3594	exon7			GCACACGGGGCTG	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.684C>T	19.37:g.18186575G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	37	CCDS54232.1																																																																																			G|0.748;A|0.252	0.252	strong		0.592	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
GRM8	2918	hgsc.bcm.edu	37	7	126542667	126542667	+	Missense_Mutation	SNP	A	A	T	rs78124913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:126542667A>T	ENST00000339582.2	-	6	1893	c.1085T>A	c.(1084-1086)tTc>tAc	p.F362Y	GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000405249.1_Missense_Mutation_p.F362Y|GRM8_ENST00000444921.2_Missense_Mutation_p.F362Y|GRM8_ENST00000358373.3_Missense_Mutation_p.F362Y			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	362			F -> Y. {ECO:0000269|Ref.6}.		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.F362Y(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				CTCCTCCCAGAATTCTGCAAA	0.378										HNSCC(24;0.065)			A|||	614	0.122604	0.0098	0.1369	5008	,	,		16946	0.2083		0.1481	False		,,,				2504	0.1503				p.F362Y		Atlas-SNP	.											GRM8,NS,carcinoma,0,1	GRM8	377	1	1	Substitution - Missense(1)	stomach(1)	c.T1085A						PASS	.	A	TYR/PHE,TYR/PHE	135,4271	96.7+/-135.4	5,125,2073	91.0	90.0	90.0		1085,1085	4.9	1.0	7	dbSNP_131	90	1068,7532	224.5+/-260.9	78,912,3310	no	missense,missense	GRM8	NM_000845.2,NM_001127323.1	22,22	83,1037,5383	TT,TA,AA		12.4186,3.064,9.2496	benign,benign	362/909,362/909	126542667	1203,11803	2203	4300	6503	SO:0001583	missense	2918	exon5			TCCCAGAATTCTG		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1085T>A	7.37:g.126542667A>T	ENSP00000344173:p.Phe362Tyr	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	197	92	0.467005	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	292	0.1336996336996337	5	0.01016260162601626	52	0.143646408839779	121	0.21153846153846154	114	0.1503957783641161	A	16.48	3.135052	0.56828	0.03064	0.124186	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	4.88	4.88	0.63580	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	L	0.36672	1.1	0.09310	P	0.999999464699	B;P;B	0.41450	0.077;0.75;0.035	B;P;B	0.45195	0.17;0.473;0.074	T	0.04242	-1.0966	9	0.23302	T	0.38	.	13.6821	0.62491	1.0:0.0:0.0:0.0	rs61755380	362;362;362	O00222-3;O00222-2;O00222	.;.;GRM8_HUMAN	Y	362	ENSP00000344173:F362Y;ENSP00000409790:F362Y;ENSP00000351142:F362Y;ENSP00000385731:F362Y	ENSP00000344173:F362Y	F	-	2	0	GRM8	126329903	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.283000	0.95860	1.827000	0.53221	0.418000	0.28097	TTC	A|0.896;T|0.104	0.104	strong		0.378	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
ICE1	23379	hgsc.bcm.edu	37	5	5461976	5461976	+	Silent	SNP	T	T	C	rs72646682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:5461976T>C	ENST00000296564.7	+	13	2751	c.2529T>C	c.(2527-2529)aaT>aaC	p.N843N		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		843					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AAAATAACAATCCTGTAGAAT	0.403													t|||	4	0.000798722	0.0	0.0029	5008	,	,		19727	0.0		0.002	False		,,,				2504	0.0				p.N843N		Atlas-SNP	.											.	KIAA0947	301	.	0			c.T2529C						PASS	.			2,3766		0,2,1882	86.0	80.0	82.0		2529	-5.2	0.0	5	dbSNP_130	82	21,8215		0,21,4097	no	coding-synonymous	KIAA0947	NM_015325.1		0,23,5979	CC,CT,TT		0.255,0.0531,0.1916		843/2267	5461976	23,11981	1884	4118	6002	SO:0001819	synonymous_variant	23379	exon13			TAACAATCCTGTA																												ENST00000296564.7:c.2529T>C	5.37:g.5461976T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	147	58	0.394558	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	CCDS47187.1																																																																																			T|0.998;C|0.002	0.002	strong		0.403	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
DCAF13	25879	hgsc.bcm.edu	37	8	104432631	104432631	+	Silent	SNP	T	T	C	rs3098238	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:104432631T>C	ENST00000297579.5	+	2	943	c.666T>C	c.(664-666)aaT>aaC	p.N222N	DCAF13_ENST00000521716.1_Silent_p.N66N|DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000519682.1_Silent_p.N66N|DCAF13_ENST00000521971.1_Silent_p.N66N	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	70					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ATGGAGTCAATTGCTTGGCAA	0.438													T|||	126	0.0251597	0.0151	0.0418	5008	,	,		19085	0.001		0.0626	False		,,,				2504	0.0133				p.N222N		Atlas-SNP	.											.	DCAF13	66	.	0			c.T666C						PASS	.	T		114,4292	86.3+/-125.0	4,106,2093	84.0	81.0	82.0		666	5.3	1.0	8	dbSNP_103	82	677,7923	169.6+/-220.9	31,615,3654	no	coding-synonymous	DCAF13	NM_015420.6		35,721,5747	CC,CT,TT		7.8721,2.5874,6.0818		222/598	104432631	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	25879	exon2			AGTCAATTGCTTG	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	24535	protein-coding gene	gene with protein product			"""WD repeats and SOF1 domain containing"""	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.666T>C	8.37:g.104432631T>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	198	112	0.565657	NM_015420	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Silent	SNP	ENST00000297579.5	37	CCDS34934.1																																																																																			T|0.945;C|0.055	0.055	strong		0.438	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420	
BTNL2	56244	hgsc.bcm.edu	37	6	32363955	32363955	+	Silent	SNP	T	T	C	rs2076529	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32363955T>C	ENST00000374993.1	-	5	938	c.939A>G	c.(937-939)gtA>gtG	p.V313V	BTNL2_ENST00000540315.1_Silent_p.V103V|BTNL2_ENST00000429232.2_Silent_p.V220V|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000414363.1_Silent_p.V103V|BTNL2_ENST00000454136.3_Silent_p.V313V|BTNL2_ENST00000374995.3_Silent_p.V219V|BTNL2_ENST00000544175.1_Silent_p.V36V	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	313	Ig-like V-type 3.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CACTCACCAGTACAGTCCTCC	0.562													c|||	1888	0.376997	0.3268	0.4784	5008	,	,		19952	0.2728		0.4364	False		,,,				2504	0.4192				p.V313V		Atlas-SNP	.											.	BTNL2	50	.	0			c.A939G						PASS	.			970,2052		155,660,696	159.0	106.0	125.0	http://www.ncbi.nlm.nih.gov/pubmed?term	939	-5.6	0.0	6	dbSNP_96	125	2334,3084		490,1354,865	no	coding-synonymous	BTNL2	NM_019602.1		645,2014,1561	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	43.0786,32.0979,39.1469		313/456	32363955	3304,5136	1511	2709	4220	SO:0001819	synonymous_variant	56244	exon5			CACCAGTACAGTC	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.939A>G	6.37:g.32363955T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	173	78	0.450867	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				T|0.636;C|0.364	0.364	strong		0.562	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
SLC5A6	8884	hgsc.bcm.edu	37	2	27424636	27424636	+	Missense_Mutation	SNP	G	G	A	rs1395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:27424636G>A	ENST00000310574.3	-	14	1915	c.1442C>T	c.(1441-1443)tCc>tTc	p.S481F	SLC5A6_ENST00000408041.1_Missense_Mutation_p.S481F|SLC5A6_ENST00000461319.1_5'UTR	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	481			S -> F (in dbSNP:rs1395). {ECO:0000269|PubMed:10329687, ECO:0000269|PubMed:10334869, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	TGGCATGCTGGAGCCCATGCT	0.602													G|||	2667	0.532548	0.1626	0.5245	5008	,	,		19434	0.8492		0.6928	False		,,,				2504	0.547				p.S481F		Atlas-SNP	.											.	SLC5A6	63	.	0			c.C1442T						PASS	.	G	PHE/SER	1108,3298	395.4+/-329.6	145,818,1240	120.0	101.0	107.0		1442	4.8	0.9	2	dbSNP_36	107	5933,2667	684.0+/-403.9	2048,1837,415	yes	missense	SLC5A6	NM_021095.2	155	2193,2655,1655	AA,AG,GG		31.0116,25.1475,45.8634	possibly-damaging	481/636	27424636	7041,5965	2203	4300	6503	SO:0001583	missense	8884	exon14			ATGCTGGAGCCCA	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"""Solute carriers"""	11041	protein-coding gene	gene with protein product		604024	"""solute carrier family 5 (sodium-dependent vitamin transporter), member 6"""			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.1442C>T	2.37:g.27424636G>A	ENSP00000310208:p.Ser481Phe	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	287	287	1	NM_021095	B2RB85|D6W549|Q969Y5	Missense_Mutation	SNP	ENST00000310574.3	37	CCDS1740.1	1345	0.6158424908424909	92	0.18699186991869918	208	0.574585635359116	507	0.8863636363636364	538	0.7097625329815304	G	13.43	2.234358	0.39498	0.251475	0.689884	ENSG00000138074	ENST00000310574;ENST00000408041	D;D	0.86366	-2.11;-2.11	5.66	4.78	0.61160	.	0.743599	0.13271	N	0.400532	T	0.00012	0.0000	L	0.59436	1.845	0.28175	P	0.9284319	B	0.15141	0.012	B	0.14578	0.011	T	0.46428	-0.9192	9	0.56958	D	0.05	.	12.5598	0.56275	0.081:0.0:0.919:0.0	rs1395;rs1006897;rs1064844;rs3171998;rs17005902;rs60533761;rs1395	481	Q9Y289	SC5A6_HUMAN	F	481	ENSP00000310208:S481F;ENSP00000384853:S481F	ENSP00000310208:S481F	S	-	2	0	SLC5A6	27278140	0.731000	0.28111	0.868000	0.34077	0.225000	0.24961	2.014000	0.40951	1.391000	0.46566	0.563000	0.77884	TCC	A|0.565;C|0.001	0.565	strong		0.602	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095	
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56704101	56704101	+	Silent	SNP	G	G	A	rs11084427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56704101G>A	ENST00000586855.2	-	2	634	c.321C>T	c.(319-321)aaC>aaT	p.N107N	ZSCAN5B_ENST00000358992.3_Silent_p.N107N			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	107	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TCTGCACACCGTTCACCTTGA	0.552													G|||	1060	0.211661	0.0681	0.1988	5008	,	,		18806	0.2798		0.2942	False		,,,				2504	0.2597				p.N107N		Atlas-SNP	.											.	ZSCAN5B	160	.	0			c.C321T						PASS	.	G		444,3946		27,390,1778	36.0	39.0	38.0		321	-1.0	0.0	19	dbSNP_120	38	2653,5865		421,1811,2027	no	coding-synonymous	ZSCAN5B	NM_001080456.2		448,2201,3805	AA,AG,GG		31.1458,10.1139,23.9929		107/496	56704101	3097,9811	2195	4259	6454	SO:0001819	synonymous_variant	342933	exon1			CACACCGTTCACC		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"""-"", ""Zinc fingers, C2H2-type"""	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.321C>T	19.37:g.56704101G>A		Somatic	772	2	0.00259067		WXS	Illumina HiSeq	Phase_I	843	350	0.415184	NM_001080456		Silent	SNP	ENST00000586855.2	37	CCDS46203.1																																																																																			G|0.869;A|0.131	0.131	strong		0.552	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456	
EVA1A	84141	hgsc.bcm.edu	37	2	75720664	75720664	+	Silent	SNP	G	G	A	rs6741778	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:75720664G>A	ENST00000233712.1	-	4	594	c.157C>T	c.(157-159)Ctg>Ttg	p.L53L	EVA1A_ENST00000490746.1_Intron|EVA1A_ENST00000393913.3_Silent_p.L53L|EVA1A_ENST00000410071.1_Silent_p.L53L|EVA1A_ENST00000410113.1_Silent_p.L53L|EVA1A_ENST00000410010.1_Silent_p.L41L	NM_032181.2	NP_115557.1	Q9H8M9	EVA1A_HUMAN	eva-1 homolog A (C. elegans)	53	Necessary for the localization and biological activity.				apoptotic process (GO:0006915)|autophagy (GO:0006914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|plasma membrane (GO:0005886)											CTTATCACCAGAGCAGCCAGG	0.572													A|||	1155	0.230631	0.4576	0.1599	5008	,	,		17088	0.0298		0.2078	False		,,,				2504	0.2045				p.L53L		Atlas-SNP	.											.	.	.	.	0			c.C157T						PASS	.	A	,	1810,2596	638.3+/-396.9	376,1058,769	41.0	39.0	40.0		157,157	-8.4	0.0	2	dbSNP_116	40	1801,6799	732.1+/-406.8	198,1405,2697	no	coding-synonymous,coding-synonymous	FAM176A	NM_001135032.1,NM_032181.2	,	574,2463,3466	AA,AG,GG		20.9419,41.0803,27.7641	,	53/153,53/153	75720664	3611,9395	2203	4300	6503	SO:0001819	synonymous_variant	84141	exon4			TCACCAGAGCAGC	BC016157	CCDS1959.1	2p12	2012-11-05	2012-11-05	2012-11-05	ENSG00000115363	ENSG00000115363			25816	protein-coding gene	gene with protein product			"""transmembrane protein 166"", ""family with sequence similarity 176, member A"""	TMEM166, FAM176A		12477932	Standard	NM_001135032		Approved	FLJ13391	uc002sni.2	Q9H8M9	OTTHUMG00000129991	ENST00000233712.1:c.157C>T	2.37:g.75720664G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_032181	D6W5J3|Q9HC41	Silent	SNP	ENST00000233712.1	37	CCDS1959.1																																																																																			G|0.745;A|0.255	0.255	strong		0.572	EVA1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328707.1	NM_032181	
DNAH2	146754	hgsc.bcm.edu	37	17	7680159	7680159	+	Silent	SNP	G	G	A	rs62059684	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7680159G>A	ENST00000572933.1	+	32	6470	c.5010G>A	c.(5008-5010)gcG>gcA	p.A1670A	DNAH2_ENST00000389173.2_Silent_p.A1670A			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1670	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGCTGACAGCGAAGGAGCGGG	0.572													G|||	603	0.120407	0.0113	0.2046	5008	,	,		18971	0.0		0.3579	False		,,,				2504	0.0879				p.A1670A		Atlas-SNP	.											.	DNAH2	498	.	0			c.G5010A						PASS	.	G		288,4118	158.1+/-190.9	11,266,1926	69.0	55.0	60.0		5010	-3.8	0.9	17	dbSNP_129	60	2942,5658	456.2+/-364.0	477,1988,1835	no	coding-synonymous	DNAH2	NM_020877.2		488,2254,3761	AA,AG,GG		34.2093,6.5365,24.8347		1670/4428	7680159	3230,9776	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon31			GACAGCGAAGGAG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.5010G>A	17.37:g.7680159G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			G|0.764;A|0.236	0.236	strong		0.572	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
TFCP2L1	29842	hgsc.bcm.edu	37	2	121989489	121989489	+	Silent	SNP	G	G	A	rs2304667	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:121989489G>A	ENST00000263707.5	-	13	1351	c.1254C>T	c.(1252-1254)atC>atT	p.I418I		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	418					cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					ACAGGTTGGCGATCTTCTCAA	0.597													G|||	1602	0.319888	0.0726	0.4135	5008	,	,		17834	0.3472		0.504	False		,,,				2504	0.3701				p.I418I		Atlas-SNP	.											.	TFCP2L1	54	.	0			c.C1254T						PASS	.	G		623,3783	269.8+/-269.2	47,529,1627	216.0	163.0	181.0		1254	-4.7	0.9	2	dbSNP_100	181	4587,4013	596.9+/-393.7	1235,2117,948	no	coding-synonymous	TFCP2L1	NM_014553.2		1282,2646,2575	AA,AG,GG		46.6628,14.1398,40.0584		418/480	121989489	5210,7796	2203	4300	6503	SO:0001819	synonymous_variant	29842	exon13			GTTGGCGATCTTC	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.1254C>T	2.37:g.121989489G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_014553	Q4ZG43	Silent	SNP	ENST00000263707.5	37	CCDS2134.1																																																																																			G|0.631;A|0.369	0.369	strong		0.597	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553	
KIAA2026	158358	hgsc.bcm.edu	37	9	5969249	5969249	+	Silent	SNP	A	A	G	rs10739080	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:5969249A>G	ENST00000399933.3	-	3	981	c.982T>C	c.(982-984)Ttg>Ctg	p.L328L	KIAA2026_ENST00000381461.2_Silent_p.L328L	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	328										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CAACGTTCCAATTCGTAAAAG	0.398													A|||	2552	0.509585	0.3238	0.5605	5008	,	,		19352	0.5427		0.6869	False		,,,				2504	0.5082				p.L328L		Atlas-SNP	.											.	KIAA2026	231	.	0			c.T982C						PASS	.	A		1465,2287		284,897,695	81.0	74.0	77.0		982	1.0	1.0	9	dbSNP_120	77	5897,2309		2103,1691,309	no	coding-synonymous	KIAA2026	NM_001017969.2		2387,2588,1004	GG,GA,AA		28.1379,39.0458,38.4345		328/2104	5969249	7362,4596	1876	4103	5979	SO:0001819	synonymous_variant	158358	exon3			GTTCCAATTCGTA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.982T>C	9.37:g.5969249A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	110	43	0.390909	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	37																																																																																				A|0.421;G|0.579	0.579	strong		0.398	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
HAUS6	54801	hgsc.bcm.edu	37	9	19058821	19058821	+	Silent	SNP	A	A	G	rs10511671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:19058821A>G	ENST00000380502.3	-	16	2411	c.1944T>C	c.(1942-1944)ttT>ttC	p.F648F	HAUS6_ENST00000380496.1_Silent_p.F512F	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	648					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GAGACTGGCCAAAATCTGATA	0.398													A|||	389	0.0776757	0.0673	0.0476	5008	,	,		19442	0.13		0.0865	False		,,,				2504	0.0501				p.F648F		Atlas-SNP	.											.	HAUS6	66	.	0			c.T1944C						PASS	.	A		289,4117	159.2+/-191.8	11,267,1925	96.0	92.0	93.0		1944	2.6	0.0	9	dbSNP_119	93	777,7823	184.0+/-232.1	46,685,3569	no	coding-synonymous	HAUS6	NM_017645.3		57,952,5494	GG,GA,AA		9.0349,6.5592,8.1962		648/956	19058821	1066,11940	2203	4300	6503	SO:0001819	synonymous_variant	54801	exon16			CTGGCCAAAATCT	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.1944T>C	9.37:g.19058821A>G		Somatic	411	0	0		WXS	Illumina HiSeq	Phase_I	335	159	0.474627	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																			A|0.910;G|0.090	0.090	strong		0.398	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
LOX	4015	hgsc.bcm.edu	37	5	121413208	121413208	+	Missense_Mutation	SNP	C	C	T	rs1800449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:121413208C>T	ENST00000231004.4	-	1	772	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	LOX_ENST00000513319.1_5'Flank	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	158			R -> Q (in dbSNP:rs1800449). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8100215}.		blood vessel development (GO:0001568)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|wound healing (GO:0042060)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)			endometrium(1)|lung(6)|prostate(1)	8		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)		GCTGGGCGGCCGCAGGTTACT	0.592													T|||	785	0.156749	0.1437	0.1599	5008	,	,		14108	0.1875		0.162	False		,,,				2504	0.135				p.R158Q		Atlas-SNP	.											LOX,NS,carcinoma,0,1	LOX	29	1	0			c.G473A						PASS	.	T	GLN/ARG	784,3610		81,622,1494	40.0	49.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	473	2.4	0.4	5	dbSNP_89	46	1494,7104		148,1198,2953	yes	missense	LOX	NM_002317.5	43	229,1820,4447	TT,TC,CC		17.3761,17.8425,17.5339	benign	158/418	121413208	2278,10714	2197	4299	6496	SO:0001583	missense	4015	exon1			GGCGGCCGCAGGT		CCDS4129.1	5q23.3-q31.2	2008-02-05			ENSG00000113083	ENSG00000113083	1.4.3.13		6664	protein-coding gene	gene with protein product		153455				1685472	Standard	NM_002317		Approved		uc003ksu.3	P28300	OTTHUMG00000128914	ENST00000231004.4:c.473G>A	5.37:g.121413208C>T	ENSP00000231004:p.Arg158Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_002317	B2R5Q3|Q5FWF0	Missense_Mutation	SNP	ENST00000231004.4	37	CCDS4129.1	363	0.1662087912087912	73	0.1483739837398374	62	0.1712707182320442	113	0.19755244755244755	115	0.1517150395778364	T	2.703	-0.270433	0.05716	0.178425	0.173761	ENSG00000113083	ENST00000231004;ENST00000543620	T	0.22134	1.97	4.3	2.41	0.29592	.	0.596299	0.16360	N	0.217810	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36187	-0.9758	9	0.09338	T	0.73	.	9.8413	0.40999	0.0:0.7856:0.0:0.2144	rs1800449;rs1800449	158	P28300	LYOX_HUMAN	Q	158;118	ENSP00000231004:R158Q	ENSP00000231004:R158Q	R	-	2	0	LOX	121441107	0.000000	0.05858	0.397000	0.26308	0.054000	0.15201	-0.034000	0.12225	-0.042000	0.13535	-0.893000	0.02921	CGG	C|0.827;T|0.173	0.173	strong		0.592	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2		
THSD7A	221981	hgsc.bcm.edu	37	7	11521428	11521428	+	Silent	SNP	A	A	G	rs61996277	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:11521428A>G	ENST00000423059.4	-	7	2255	c.2004T>C	c.(2002-2004)taT>taC	p.Y668Y	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	668	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CTTCACCCGCATAGGCCAGAA	0.493										HNSCC(18;0.044)			A|||	168	0.0335463	0.0068	0.0865	5008	,	,		18995	0.002		0.0636	False		,,,				2504	0.0337				p.Y668Y		Atlas-SNP	.											.	THSD7A	219	.	0			c.T2004C						PASS	.	A		78,4216		1,76,2070	122.0	118.0	119.0		2004	0.9	1.0	7	dbSNP_129	119	741,7753		34,673,3540	no	coding-synonymous	THSD7A	NM_015204.2		35,749,5610	GG,GA,AA		8.7238,1.8165,6.4044		668/1658	11521428	819,11969	2147	4247	6394	SO:0001819	synonymous_variant	221981	exon7			ACCCGCATAGGCC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2004T>C	7.37:g.11521428A>G		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	276	131	0.474638	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			A|0.946;G|0.054	0.054	strong		0.493	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
OR8H2	390151	hgsc.bcm.edu	37	11	55873334	55873334	+	Silent	SNP	A	A	G	rs11227212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55873334A>G	ENST00000313503.1	+	1	816	c.816A>G	c.(814-816)caA>caG	p.Q272Q		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q272Q(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					GAAGAGATCAAGTGGCTTCTG	0.373										HNSCC(53;0.14)			a|||	514	0.102636	0.0477	0.098	5008	,	,		17441	0.1429		0.1213	False		,,,				2504	0.1196				p.Q272Q		Atlas-SNP	.											OR8H2,NS,carcinoma,0,1	OR8H2	117	1	1	Substitution - coding silent(1)	stomach(1)	c.A816G						PASS	.	A		234,4168	127.4+/-164.3	7,220,1974	81.0	86.0	85.0		816	-0.3	0.3	11	dbSNP_120	85	1002,7588	212.1+/-252.5	54,894,3347	no	coding-synonymous	OR8H2	NM_001005200.1		61,1114,5321	GG,GA,AA		11.6647,5.3158,9.5135		272/313	55873334	1236,11756	2201	4295	6496	SO:0001819	synonymous_variant	390151	exon1			AGATCAAGTGGCT	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.816A>G	11.37:g.55873334A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	198	118	0.59596	NM_001005200	Q6IFC1	Silent	SNP	ENST00000313503.1	37	CCDS31518.1																																																																																			A|0.902;G|0.098	0.098	strong		0.373	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
DZIP1L	199221	hgsc.bcm.edu	37	3	137787047	137787047	+	Missense_Mutation	SNP	C	C	T	rs199606339|rs374045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:137787047C>T	ENST00000327532.2	-	13	2140	c.1778G>A	c.(1777-1779)cGc>cAc	p.R593H	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	593			R -> H (in dbSNP:rs374045). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CAGTCCGGGGCGTGGAGCGGG	0.697													C|||	3149	0.628794	0.3094	0.7767	5008	,	,		14534	0.626		0.8608	False		,,,				2504	0.7198				p.R593H		Atlas-SNP	.											DZIP1L,rectum,carcinoma,0,1	DZIP1L	88	1	0			c.G1778A						PASS	.	C	HIS/ARG	1930,2476	539.0+/-375.1	417,1096,690	43.0	47.0	46.0		1778	2.2	0.0	3	dbSNP_80	46	7483,1117	760.0+/-407.6	3260,963,77	no	missense	DZIP1L	NM_173543.2	29	3677,2059,767	TT,TC,CC		12.9884,43.8039,27.6257	benign	593/768	137787047	9413,3593	2203	4300	6503	SO:0001583	missense	199221	exon13			CCGGGGCGTGGAG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1778G>A	3.37:g.137787047C>T	ENSP00000332148:p.Arg593His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	150	147	0.98	NM_173543	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	1465	0.6707875457875457	179	0.3638211382113821	271	0.7486187845303868	365	0.6381118881118881	650	0.8575197889182058	C	11.55	1.673457	0.29693	0.438039	0.870116	ENSG00000158163	ENST00000327532	T	0.38722	1.12	4.91	2.16	0.27623	.	0.815396	0.11163	N	0.592824	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B	0.19073	0.033	B	0.12156	0.007	T	0.22138	-1.0225	9	0.28530	T	0.3	-0.6235	6.6861	0.23146	0.0:0.7076:0.0:0.2924	rs374045;rs17853174;rs58860132	593	Q8IYY4	DZI1L_HUMAN	H	593	ENSP00000332148:R593H	ENSP00000332148:R593H	R	-	2	0	DZIP1L	139269737	0.001000	0.12720	0.002000	0.10522	0.043000	0.13939	0.080000	0.14802	0.268000	0.21939	0.650000	0.86243	CGC	C|0.306;T|0.694	0.694	strong		0.697	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
LRRC8E	80131	hgsc.bcm.edu	37	19	7964727	7964727	+	Silent	SNP	G	G	A	rs3745382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7964727G>A	ENST00000306708.6	+	3	1421	c.1320G>A	c.(1318-1320)gaG>gaA	p.E440E	AC010336.1_ENST00000539278.1_Silent_p.D180D|RN7SL115P_ENST00000392196.5_RNA	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	440					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						GTGAGGTGGAGTCACTCAGGC	0.657													G|||	815	0.16274	0.1407	0.1671	5008	,	,		16202	0.1339		0.2445	False		,,,				2504	0.135				p.E440E		Atlas-SNP	.											.	LRRC8E	67	.	0			c.G1320A						PASS	.	G		756,3650		63,630,1510	37.0	30.0	32.0		1320	2.5	1.0	19	dbSNP_107	32	2116,6480		274,1568,2456	no	coding-synonymous	LRRC8E	NM_025061.3		337,2198,3966	AA,AG,GG		24.6161,17.1584,22.0889		440/797	7964727	2872,10130	2203	4298	6501	SO:0001819	synonymous_variant	80131	exon4			GGTGGAGTCACTC		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.1320G>A	19.37:g.7964727G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Silent	SNP	ENST00000306708.6	37	CCDS12189.1																																																																																			G|0.802;A|0.198	0.198	strong		0.657	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
CNTNAP3	79937	hgsc.bcm.edu	37	9	39103796	39103796	+	Silent	SNP	G	G	A	rs145100345	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:39103796G>A	ENST00000297668.6	-	16	2554	c.2481C>T	c.(2479-2481)tcC>tcT	p.S827S	CNTNAP3_ENST00000377656.2_Silent_p.S826S|CNTNAP3_ENST00000358144.2_Silent_p.S739S	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	827	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S827S(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TAAACACCCCGGAGGAAACTG	0.483													G|||	11	0.00219649	0.0015	0.0	5008	,	,		15781	0.002		0.002	False		,,,				2504	0.0051				p.S827S		Atlas-SNP	.											CNTNAP3,NS,carcinoma,0,1	CNTNAP3	82	1	1	Substitution - coding silent(1)	endometrium(1)	c.C2481T						PASS	.	G		4,4402	6.2+/-15.9	0,4,2199	34.0	39.0	38.0		2481	-5.6	0.8	9	dbSNP_134	38	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	CNTNAP3	NM_033655.3		0,10,6493	AA,AG,GG		0.0698,0.0908,0.0769		827/1289	39103796	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	79937	exon16			CACCCCGGAGGAA	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.2481C>T	9.37:g.39103796G>A		Somatic	597	0	0		WXS	Illumina HiSeq	Phase_I	633	256	0.404423	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			G|0.999;A|0.001	0.001	strong		0.483	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
SUPT6H	6830	hgsc.bcm.edu	37	17	27009749	27009749	+	Silent	SNP	C	C	T	rs12051648	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:27009749C>T	ENST00000314616.6	+	14	1885	c.1602C>T	c.(1600-1602)ggC>ggT	p.G534G	SUPT6H_ENST00000347486.4_Silent_p.G534G	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	534	Interaction with KDM6A. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CTTTAGATGGCCTGGCCAAAA	0.527													C|||	2018	0.402955	0.0318	0.4568	5008	,	,		20230	0.5962		0.5646	False		,,,				2504	0.501				p.G534G		Atlas-SNP	.											.	SUPT6H	165	.	0			c.C1602T						PASS	.	C		539,3867	242.8+/-252.7	32,475,1696	78.0	77.0	77.0		1602	-3.9	0.1	17	dbSNP_120	77	4963,3637	622.6+/-397.3	1451,2061,788	no	coding-synonymous	SUPT6H	NM_003170.3		1483,2536,2484	TT,TC,CC		42.2907,12.2333,42.3036		534/1727	27009749	5502,7504	2203	4300	6503	SO:0001819	synonymous_variant	6830	exon14			AGATGGCCTGGCC	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.1602C>T	17.37:g.27009749C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																			C|0.588;T|0.412	0.412	strong		0.527	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
SLC35E4	339665	hgsc.bcm.edu	37	22	31042606	31042606	+	Missense_Mutation	SNP	G	G	A	rs148304964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:31042606G>A	ENST00000343605.4	+	2	1440	c.641G>A	c.(640-642)aGg>aAg	p.R214K	SLC35E4_ENST00000300385.8_Intron|SLC35E4_ENST00000406566.1_Intron	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	214	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						CAGGAGGAGAGGCTGGACGCG	0.672													G|||	7	0.00139776	0.0	0.0029	5008	,	,		15892	0.0		0.005	False		,,,				2504	0.0				p.R214K		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G641A						PASS	.	C	LYS/ARG	4,4374		0,4,2185	47.0	44.0	45.0		641	0.6	0.9	22	dbSNP_134	45	44,8528		0,44,4242	yes	missense	SLC35E4	NM_001001479.2	26	0,48,6427	AA,AG,GG		0.5133,0.0914,0.3707	benign	214/351	31042606	48,12902	2189	4286	6475	SO:0001583	missense	339665	exon2			AGGAGAGGCTGGA		CCDS13882.1	22q12.2	2013-05-22			ENSG00000100036	ENSG00000100036		"""Solute carriers"""	17058	protein-coding gene	gene with protein product							Standard	NM_001001479		Approved		uc003ais.1	Q6ICL7	OTTHUMG00000151110	ENST00000343605.4:c.641G>A	22.37:g.31042606G>A	ENSP00000339626:p.Arg214Lys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_001001479	Q567P0	Missense_Mutation	SNP	ENST00000343605.4	37	CCDS13882.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	g	0.181	-1.061767	0.01950	9.14E-4	0.005133	ENSG00000100036	ENST00000343605	T	0.60672	0.17	5.02	0.588	0.17445	Domain of unknown function DUF250 (1);	0.168007	0.51477	D	0.000083	T	0.15089	0.0364	N	0.02357	-0.585	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.26121	-1.0112	10	0.02654	T	1	-15.9629	4.9658	0.14089	0.3219:0.148:0.53:0.0	.	214	Q6ICL7	S35E4_HUMAN	K	214	ENSP00000339626:R214K	ENSP00000339626:R214K	R	+	2	0	SLC35E4	29372606	0.994000	0.37717	0.915000	0.36163	0.067000	0.16453	0.739000	0.26173	0.267000	0.21916	-0.217000	0.12591	AGG	G|0.997;A|0.003	0.003	strong		0.672	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973	
CEP192	55125	hgsc.bcm.edu	37	18	13095591	13095591	+	Missense_Mutation	SNP	G	G	A	rs56913743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:13095591G>A	ENST00000325971.8	+	33	6149	c.4556G>A	c.(4555-4557)cGg>cAg	p.R1519Q	CEP192_ENST00000506447.1_Missense_Mutation_p.R2115Q|CEP192_ENST00000430049.2_Missense_Mutation_p.R1640Q|CEP192_ENST00000540847.2_3'UTR			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1519				R -> Q (in Ref. 3). {ECO:0000305}.	centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CTTCTCTCACGGGCGGCTCGC	0.537													A|||	951	0.189896	0.1452	0.1239	5008	,	,		14798	0.2986		0.1262	False		,,,				2504	0.2505				p.R2115Q		Atlas-SNP	.											.	CEP192	340	.	0			c.G6344A						PASS	.	A	GLN/ARG	527,3879	777.3+/-414.2	27,473,1703	81.0	80.0	81.0		6344	4.8	0.1	18	dbSNP_129	81	1096,7504	768.7+/-407.6	84,928,3288	yes	missense	CEP192	NM_032142.3	43	111,1401,4991	AA,AG,GG		12.7442,11.961,12.4789	benign	2115/2538	13095591	1623,11383	2203	4300	6503	SO:0001583	missense	55125	exon35			TCTCACGGGCGGC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.4556G>A	18.37:g.13095591G>A	ENSP00000317156:p.Arg1519Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	169	75	0.443787	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		373	0.1707875457875458	86	0.17479674796747968	46	0.1270718232044199	150	0.26223776223776224	91	0.12005277044854881	A	0.249	-1.008251	0.02112	0.11961	0.127442	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	T;T;T	0.27557	1.66;1.66;1.66	5.91	4.77	0.60923	.	0.449991	0.22993	N	0.053164	T	0.00012	0.0000	N	0.00182	-1.905	0.80722	P	0.0	B;B;B;B	0.10296	0.0;0.0;0.003;0.003	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.36672	-0.9738	9	0.02654	T	1	-5.5576	5.8633	0.18760	0.7177:0.1397:0.1426:0.0	rs56913743;rs61740541	1640;2115;119;717	C9JT09;E9PF99;F5GZ47;Q9HCK3	.;.;.;.	Q	2115;1519;1519;1640;119	ENSP00000427550:R2115Q;ENSP00000317156:R1519Q;ENSP00000389190:R1640Q	ENSP00000317156:R1519Q	R	+	2	0	CEP192	13085591	0.000000	0.05858	0.080000	0.20451	0.026000	0.11368	1.070000	0.30653	0.510000	0.28216	-0.254000	0.11334	CGG	G|0.861;A|0.139	0.139	strong		0.537	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
FAT4	79633	hgsc.bcm.edu	37	4	126370709	126370709	+	Silent	SNP	C	C	T	rs139132509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:126370709C>T	ENST00000394329.3	+	9	8551	c.8538C>T	c.(8536-8538)tcC>tcT	p.S2846S	FAT4_ENST00000335110.5_Silent_p.S1144S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2846	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S2846S(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TTCGAGTTTCCGCACATGATT	0.388													T|||	12	0.00239617	0.0	0.0043	5008	,	,		19459	0.0		0.0089	False		,,,				2504	0.0				p.S2846S		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	2	2	Substitution - coding silent(2)	prostate(2)	c.C8538T						PASS	.	T		12,4394	821.1+/-416.4	0,12,2191	78.0	77.0	77.0		8538	-11.2	0.6	4	dbSNP_134	77	100,8498	812.8+/-407.1	0,100,4199	no	coding-synonymous	FAT4	NM_024582.4		0,112,6390	TT,TC,CC		1.1631,0.2724,0.8613		2846/4982	126370709	112,12892	2203	4299	6502	SO:0001819	synonymous_variant	79633	exon9			AGTTTCCGCACAT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.8538C>T	4.37:g.126370709C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			C|0.994;T|0.006	0.006	strong		0.388	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
PRMT9	90826	hgsc.bcm.edu	37	4	148589711	148589711	+	Missense_Mutation	SNP	G	G	A	rs146854725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:148589711G>A	ENST00000322396.6	-	6	1174	c.932C>T	c.(931-933)gCa>gTa	p.A311V	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Missense_Mutation_p.A198V	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		311	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TCTTATCTCTGCACATTCTAC	0.348													G|||	4	0.000798722	0.0	0.0	5008	,	,		19299	0.0		0.004	False		,,,				2504	0.0				p.A311V		Atlas-SNP	.											.	PRMT10	68	.	0			c.C932T						PASS	.	G	VAL/ALA	5,4399	9.9+/-24.2	0,5,2197	133.0	123.0	126.0		932	4.2	1.0	4	dbSNP_134	126	50,8550	31.2+/-83.2	0,50,4250	yes	missense	PRMT10	NM_138364.2	64	0,55,6447	AA,AG,GG		0.5814,0.1135,0.4229	benign	311/846	148589711	55,12949	2202	4300	6502	SO:0001583	missense	90826	exon6			ATCTCTGCACATT																												ENST00000322396.6:c.932C>T	4.37:g.148589711G>A	ENSP00000314396:p.Ala311Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	13.63	2.295916	0.40594	0.001135	0.005814	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.43294	0.95;0.95	5.9	4.17	0.49024	.	0.605454	0.18477	N	0.140055	T	0.21022	0.0506	N	0.25647	0.755	0.29735	N	0.837584	B	0.02656	0.0	B	0.04013	0.001	T	0.13469	-1.0508	10	0.28530	T	0.3	-30.4136	9.1674	0.37060	0.0703:0.0:0.617:0.3127	.	311	Q6P2P2	ANM10_HUMAN	V	311;198	ENSP00000314396:A311V;ENSP00000439508:A198V	ENSP00000314396:A311V	A	-	2	0	PRMT10	148809161	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.665000	0.37449	0.836000	0.34901	0.453000	0.30009	GCA	G|0.996;A|0.004	0.004	strong		0.348	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
PKP2	5318	hgsc.bcm.edu	37	12	33021934	33021934	+	Missense_Mutation	SNP	A	A	G	rs1046116	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:33021934A>G	ENST00000070846.6	-	4	1121	c.1097T>C	c.(1096-1098)cTg>cCg	p.L366P	PKP2_ENST00000340811.4_Missense_Mutation_p.L366P	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	366			L -> P (in dbSNP:rs1046116). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:19955750, ECO:0000269|PubMed:20031617, ECO:0000269|PubMed:8922383}.		adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CCTGGATGGCAGCATGTGGTC	0.502													G|||	758	0.151358	0.2103	0.1614	5008	,	,		17069	0.0308		0.2157	False		,,,				2504	0.1227				p.L366P		Atlas-SNP	.											.	PKP2	110	.	0			c.T1097C						PASS	.	G	PRO/LEU,PRO/LEU	883,3523	742.6+/-411.4	79,725,1399	123.0	107.0	112.0		1097,1097	4.2	0.0	12	dbSNP_86	112	1979,6621	723.3+/-406.4	242,1495,2563	yes	missense,missense	PKP2	NM_001005242.2,NM_004572.3	98,98	321,2220,3962	GG,GA,AA		23.0116,20.0409,22.0052	benign,benign	366/838,366/882	33021934	2862,10144	2203	4300	6503	SO:0001583	missense	5318	exon4			GATGGCAGCATGT	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.1097T>C	12.37:g.33021934A>G	ENSP00000070846:p.Leu366Pro	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	312	0.14285714285714285	89	0.18089430894308944	50	0.13812154696132597	17	0.02972027972027972	156	0.20580474934036938	G	0.048	-1.258580	0.01445	0.200409	0.230116	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.47869	0.83;0.83	5.09	4.19	0.49359	Armadillo-like helical (1);Armadillo-type fold (1);	0.399870	0.18207	N	0.148319	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.20075	-1.0286	9	0.25106	T	0.35	-5.3062	4.8003	0.13294	0.242:0.0:0.6059:0.1521	rs1046116;rs3186092;rs52789256;rs58434362;rs1046116	366;366;366	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	P	366	ENSP00000342800:L366P;ENSP00000070846:L366P	ENSP00000070846:L366P	L	-	2	0	PKP2	32913201	0.086000	0.21541	0.002000	0.10522	0.000000	0.00434	1.844000	0.39269	1.144000	0.42321	-0.128000	0.14901	CTG	A|0.807;G|0.193	0.193	strong		0.502	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
LITAF	9516	hgsc.bcm.edu	37	16	11647492	11647492	+	Missense_Mutation	SNP	T	T	C	rs4280262	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11647492T>C	ENST00000571688.1	-	3	504	c.274A>G	c.(274-276)Atc>Gtc	p.I92V	LITAF_ENST00000572255.1_5'UTR|LITAF_ENST00000571459.1_Intron|LITAF_ENST00000571976.1_Missense_Mutation_p.I92V|LITAF_ENST00000413364.2_Missense_Mutation_p.I92V|LITAF_ENST00000381810.3_Missense_Mutation_p.I92V|LITAF_ENST00000576036.1_Missense_Mutation_p.I92V|LITAF_ENST00000574763.1_Missense_Mutation_p.I92V|LITAF_ENST00000339430.5_Missense_Mutation_p.I92V|LITAF_ENST00000570904.1_Missense_Mutation_p.I92V	NM_001136472.1	NP_001129944.1	Q99732	LITAF_HUMAN	lipopolysaccharide-induced TNF factor	92			I -> V (in dbSNP:rs4280262). {ECO:0000269|PubMed:15776429, ECO:0000269|PubMed:15786462}.		aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of cytokine production (GO:0001817)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			endometrium(1)|large_intestine(1)|liver(1)|lung(3)|skin(1)	7						CACATTTGGATAGGGCGGTCC	0.552													C|||	514	0.102636	0.0393	0.1513	5008	,	,		19842	0.0625		0.2058	False		,,,				2504	0.089				p.I92V		Atlas-SNP	.											.	LITAF	16	.	0			c.A274G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE	318,4076	796.0+/-415.3	10,298,1889	113.0	72.0	86.0		274,274,274	1.1	0.1	16	dbSNP_111	86	1831,6769	731.2+/-406.8	184,1463,2653	yes	missense,missense,missense	LITAF	NM_001136472.1,NM_001136473.1,NM_004862.3	29,29,29	194,1761,4542	CC,CT,TT		21.2907,7.2371,16.5384	benign,benign,benign	92/162,92/153,92/162	11647492	2149,10845	2197	4300	6497	SO:0001583	missense	9516	exon3			TTTGGATAGGGCG	AB034747	CCDS32386.1, CCDS45411.1	16p13.3-p12	2014-09-17							16841	protein-coding gene	gene with protein product		603795				9305847, 10200294	Standard	NM_004862		Approved	PIG7, SIMPLE, FLJ38636, TP53I7	uc002dbb.3	Q99732		ENST00000571688.1:c.274A>G	16.37:g.11647492T>C	ENSP00000459533:p.Ile92Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001136473	D3DUG1|G5E9K0|Q05DW0|Q9C0L6	Missense_Mutation	SNP	ENST00000571688.1	37	CCDS32386.1	281	0.12866300366300365	24	0.04878048780487805	56	0.15469613259668508	40	0.06993006993006994	161	0.21240105540897097	C	0.007	-2.004687	0.00431	0.072371	0.212907	ENSG00000189067	ENST00000339430;ENST00000413364;ENST00000381810	D;D;D	0.85702	-2.02;-2.02;-2.02	5.38	1.12	0.20585	LPS-induced tumor necrosis factor alpha factor (2);	0.145452	0.44902	N	0.000408	T	0.00039	0.0001	N	0.00327	-1.64	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.18053	-1.0349	9	0.02654	T	1	-9.3056	9.8475	0.41037	0.0:0.6357:0.0:0.3643	rs4280262;rs17605605;rs56421922;rs4280262	92;92	G5E9K0;Q99732	.;LITAF_HUMAN	V	92	ENSP00000340118:I92V;ENSP00000397958:I92V;ENSP00000371231:I92V	ENSP00000340118:I92V	I	-	1	0	LITAF	11554993	0.046000	0.20272	0.100000	0.21137	0.028000	0.11728	0.244000	0.18124	0.009000	0.14813	-0.119000	0.15052	ATC	T|0.859;C|0.141	0.141	strong		0.552	LITAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436794.2	NM_004862	
IQGAP3	128239	hgsc.bcm.edu	37	1	156508792	156508792	+	Silent	SNP	T	T	C	rs79402045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156508792T>C	ENST00000361170.2	-	26	3100	c.3090A>G	c.(3088-3090)acA>acG	p.T1030T	IQGAP3_ENST00000498755.1_5'UTR	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1030	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTGGGTTGCCTGTCACCACGT	0.542													T|||	21	0.00419329	0.0015	0.0	5008	,	,		21851	0.001		0.0139	False		,,,				2504	0.0041				p.T1030T		Atlas-SNP	.											.	IQGAP3	146	.	0			c.A3090G						PASS	.	T		13,4393	17.9+/-39.9	0,13,2190	72.0	64.0	67.0		3090	-2.6	1.0	1	dbSNP_132	67	117,8483	61.7+/-123.6	0,117,4183	no	coding-synonymous	IQGAP3	NM_178229.4		0,130,6373	CC,CT,TT		1.3605,0.2951,0.9995		1030/1632	156508792	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	128239	exon26			GTTGCCTGTCACC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.3090A>G	1.37:g.156508792T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	209	114	0.545455	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																			T|0.992;C|0.008	0.008	strong		0.542	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
BSG	682	hgsc.bcm.edu	37	19	580388	580388	+	Silent	SNP	C	C	G	rs2229664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:580388C>G	ENST00000333511.3	+	4	652	c.582C>G	c.(580-582)tcC>tcG	p.S194S	BSG_ENST00000353555.4_Silent_p.S78S|BSG_ENST00000545507.2_5'UTR|BSG_ENST00000346916.4_Silent_p.S14S	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	194	Ig-like C2-type.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGTGGACTCCGACGACCAGT	0.672													G|||	952	0.190096	0.2103	0.0908	5008	,	,		15828	0.2341		0.1113	False		,,,				2504	0.2689				p.S194S		Atlas-SNP	.											.	BSG	48	.	0			c.C582G						PASS	.	G	,,	746,3654	750.5+/-412.1	58,630,1512	75.0	64.0	68.0		582,234,42	-7.3	0.0	19	dbSNP_98	68	868,7724	777.4+/-407.7	52,764,3480	no	coding-synonymous,coding-synonymous,coding-synonymous	BSG	NM_001728.2,NM_198589.1,NM_198591.1	,,	110,1394,4992	GG,GC,CC		10.1024,16.9545,12.423	,,	194/386,78/270,14/206	580388	1614,11378	2200	4296	6496	SO:0001819	synonymous_variant	682	exon4			GGACTCCGACGAC	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1116	protein-coding gene	gene with protein product	"""Ok blood group"""	109480	"""basigin"""	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.582C>G	19.37:g.580388C>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Silent	SNP	ENST00000333511.3	37	CCDS12033.1																																																																																			C|0.869;G|0.131	0.131	strong		0.672	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728	
NKAIN4	128414	hgsc.bcm.edu	37	20	61878950	61878950	+	Missense_Mutation	SNP	A	A	C	rs872808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61878950A>C	ENST00000370316.3	-	4	540	c.451T>G	c.(451-453)Tgc>Ggc	p.C151G	NKAIN4_ENST00000370313.1_Missense_Mutation_p.C89G|NKAIN4_ENST00000370307.2_Missense_Mutation_p.C89G|NKAIN4_ENST00000466885.1_5'UTR	NM_152864.3	NP_690603.3	Q8IVV8	NKAI4_HUMAN	Na+/K+ transporting ATPase interacting 4	151			C -> G (in dbSNP:rs872808).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|lung(1)|ovary(1)	4	all_cancers(38;2.72e-09)					ATCTGCAGGCAACTGTGTAGG	0.692													C|||	2160	0.43131	0.4705	0.4352	5008	,	,		14312	0.5099		0.3588	False		,,,				2504	0.3691				p.C151G		Atlas-SNP	.											NKAIN4,NS,carcinoma,0,1	NKAIN4	23	1	0			c.T451G						PASS	.	C	GLY/CYS	1541,2281		345,851,715	20.0	18.0	19.0		451	-4.8	0.1	20	dbSNP_86	19	2390,4884		464,1462,1711	yes	missense	NKAIN4	NM_152864.3	159	809,2313,2426	CC,CA,AA		32.8568,40.3192,35.4272	benign	151/209	61878950	3931,7165	1911	3637	5548	SO:0001583	missense	128414	exon4			GCAGGCAACTGTG	BC041812	CCDS13514.1	20q13.33	2007-10-04	2007-10-04	2007-10-04	ENSG00000101198	ENSG00000101198		"""Na+/K+ transporting ATPase interacting"""	16191	protein-coding gene	gene with protein product		612873	"""chromosome 20 open reading frame 58"""	C20orf58		17606467	Standard	NM_152864		Approved	bA261N11.2, FAM77A	uc002yek.3	Q8IVV8	OTTHUMG00000032959	ENST00000370316.3:c.451T>G	20.37:g.61878950A>C	ENSP00000359340:p.Cys151Gly	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	188	82	0.43617	NM_152864	Q4VXQ6|Q9BQU8|Q9BQU9	Missense_Mutation	SNP	ENST00000370316.3	37	CCDS13514.1	980	0.44871794871794873	241	0.4898373983739837	149	0.4116022099447514	307	0.5367132867132867	283	0.3733509234828496	C	0	-2.659752	0.00108	0.403192	0.328568	ENSG00000101198	ENST00000370313;ENST00000370316;ENST00000370307;ENST00000370317	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	3.48	-4.78	0.03209	.	0.822085	0.10785	N	0.634470	T	0.00012	0.0000	N	0.00125	-2.05	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39502	-0.9611	9	0.12766	T	0.61	0.2307	5.5207	0.16931	0.2665:0.3829:0.0:0.3505	rs872808;rs61451727;rs872808	89;151	A6NNM2;Q8IVV8	.;NKAI4_HUMAN	G	89;151;89;81	ENSP00000359336:C89G;ENSP00000359340:C151G;ENSP00000359330:C89G;ENSP00000359341:C81G	ENSP00000359330:C89G	C	-	1	0	NKAIN4	61349395	0.000000	0.05858	0.115000	0.21578	0.002000	0.02628	-1.247000	0.02893	-1.184000	0.02720	-1.879000	0.00546	TGC	A|0.529;C|0.471	0.471	strong		0.692	NKAIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080117.3	NM_152864	
ZDHHC11	79844	hgsc.bcm.edu	37	5	837556	837556	+	Missense_Mutation	SNP	T	T	G	rs28449575	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:837556T>G	ENST00000283441.8	-	6	1207	c.824A>C	c.(823-825)aAc>aCc	p.N275T	ZDHHC11_ENST00000424784.2_Missense_Mutation_p.N275T|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	275						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			TTCTTTGCGGTTATTAATGAG	0.488													G|||	6	0.00119808	0.0	0.0029	5008	,	,		28152	0.0		0.002	False		,,,				2504	0.002				p.N275T		Atlas-SNP	.											ZDHHC11_ENST00000424784,NS,neuroblastoma,0,2	ZDHHC11	97	2	0			c.A824C						scavenged	.						189.0	218.0	208.0					5																	837556		2203	4300	6503	SO:0001583	missense	79844	exon6			TTGCGGTTATTAA	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.824A>C	5.37:g.837556T>G	ENSP00000283441:p.Asn275Thr	Somatic	370	4	0.0108108		WXS	Illumina HiSeq	Phase_I	505	60	0.118812	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	g	0.012	-1.689102	0.00738	.	.	ENSG00000188818	ENST00000424784;ENST00000283441;ENST00000511193	T;T;T	0.40225	1.67;1.67;1.04	1.39	-2.52	0.06346	.	.	.	.	.	T	0.19927	0.0479	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28522	-1.0041	8	0.14656	T	0.56	-13.2458	3.5805	0.07950	0.0:0.2923:0.214:0.4937	rs28449575;rs58716713	275	Q9H8X9	ZDH11_HUMAN	T	275;275;50	ENSP00000397719:N275T;ENSP00000283441:N275T;ENSP00000426873:N50T	ENSP00000283441:N275T	N	-	2	0	ZDHHC11	890556	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.297000	0.01141	-1.469000	0.01890	-2.058000	0.00401	AAC	T|0.617;G|0.383	0.383	strong		0.488	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
CACNA1C	775	hgsc.bcm.edu	37	12	2694638	2694638	+	Silent	SNP	C	C	T	rs215976	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:2694638C>T	ENST00000347598.4	+	17	2436	c.2436C>T	c.(2434-2436)gaC>gaT	p.D812D	CACNA1C_ENST00000399601.1_Silent_p.D812D|CACNA1C_ENST00000402845.3_Silent_p.D812D|CACNA1C_ENST00000406454.3_Silent_p.D812D|CACNA1C_ENST00000344100.3_Silent_p.D812D|CACNA1C_ENST00000399591.1_Silent_p.D812D|CACNA1C_ENST00000399637.1_Silent_p.D812D|CACNA1C_ENST00000399649.1_Silent_p.D812D|CACNA1C_ENST00000399595.1_Silent_p.D812D|CACNA1C_ENST00000399597.1_Silent_p.D812D|CACNA1C_ENST00000335762.5_Silent_p.D837D|CACNA1C_ENST00000480911.1_Silent_p.D812D|CACNA1C_ENST00000399629.1_Silent_p.D812D|CACNA1C_ENST00000399606.1_Silent_p.D812D|CACNA1C_ENST00000399638.1_Silent_p.D812D|CACNA1C_ENST00000399655.1_Silent_p.D812D|CACNA1C_ENST00000327702.7_Silent_p.D812D|CACNA1C_ENST00000399621.1_Silent_p.D812D|CACNA1C_ENST00000399603.1_Silent_p.D812D|CACNA1C_ENST00000399634.1_Silent_p.D812D|CACNA1C_ENST00000399641.1_Silent_p.D812D|CACNA1C_ENST00000399617.1_Silent_p.D812D|CACNA1C_ENST00000399644.1_Silent_p.D812D	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	812					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCACGGCTGACGGAGAGTCTC	0.612													C|||	729	0.145567	0.0877	0.0576	5008	,	,		14849	0.2966		0.0885	False		,,,				2504	0.1892				p.D812D		Atlas-SNP	.											Q6YL47_HUMAN,NS,carcinoma,0,5	CACNA1C	1023	5	0			c.C2436T						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,,	319,3661		15,289,1686	14.0	19.0	17.0		2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2436,2427,2436,2436,2436,2436,2436	-0.6	0.9	12	dbSNP_79	17	652,7638		26,600,3519	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1C	NM_000719.6,NM_001129827.1,NM_001129829.1,NM_001129830.1,NM_001129831.1,NM_001129832.1,NM_001129833.1,NM_001129834.1,NM_001129835.1,NM_001129836.1,NM_001129837.1,NM_001129838.1,NM_001129839.1,NM_001129840.1,NM_001129841.1,NM_001129842.1,NM_001129843.1,NM_001129844.1,NM_001129846.1,NM_001167623.1,NM_001167624.1,NM_001167625.1,NM_199460.2	,,,,,,,,,,,,,,,,,,,,,,	41,889,5205	TT,TC,CC		7.8649,8.0151,7.9136	,,,,,,,,,,,,,,,,,,,,,,	812/2139,812/2187,812/2180,812/2174,812/2167,812/2159,812/2158,812/2158,812/2158,812/2156,812/2147,812/2147,812/2145,812/2139,812/2139,812/2139,812/2139,809/2136,812/2128,812/2139,812/2174,812/2199,812/2222	2694638	971,11299	1990	4145	6135	SO:0001819	synonymous_variant	775	exon17			GGCTGACGGAGAG	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.2436C>T	12.37:g.2694638C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	82	30	0.365854	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																			C|0.836;T|0.164	0.164	strong		0.612	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
DHX57	90957	hgsc.bcm.edu	37	2	39050141	39050141	+	Silent	SNP	A	A	C	rs3770681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:39050141A>C	ENST00000295373.6	-	17	3411	c.3285T>G	c.(3283-3285)tcT>tcG	p.S1095S		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1095							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TTACAAACGGAGACTTAAAAG	0.473													A|||	3001	0.599241	0.3306	0.5836	5008	,	,		17536	0.8046		0.66	False		,,,				2504	0.6994				p.S1095S	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.T3285G						PASS	.	A		1652,2754	503.4+/-365.5	309,1034,860	70.0	59.0	63.0		3285	1.8	1.0	2	dbSNP_107	63	5586,3014	662.8+/-402.0	1824,1938,538	no	coding-synonymous	DHX57	NM_198963.1		2133,2972,1398	CC,CA,AA		35.0465,37.4943,44.3488		1095/1387	39050141	7238,5768	2203	4300	6503	SO:0001819	synonymous_variant	90957	exon17			AAACGGAGACTTA	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3285T>G	2.37:g.39050141A>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Silent	SNP	ENST00000295373.6	37	CCDS1800.1	1353	0.6195054945054945	164	0.3333333333333333	217	0.5994475138121547	464	0.8111888111888111	508	0.6701846965699209	A	9.500	1.102961	0.20632	0.374943	0.649535	ENSG00000163214	ENST00000452978	T	0.34472	1.36	5.51	1.79	0.24919	.	0.000000	0.51477	D	0.000095	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09707	-1.0662	6	0.66056	D	0.02	.	4.1767	0.10355	0.4934:0.0:0.3166:0.19	rs3770681;rs11557278;rs17494252;rs3770681	.	.	.	A	419	ENSP00000397841:S419A	ENSP00000397841:S419A	S	-	1	0	DHX57	38903645	0.975000	0.34042	1.000000	0.80357	0.987000	0.75469	0.123000	0.15708	0.381000	0.24851	0.528000	0.53228	TCC	A|0.422;C|0.578	0.578	strong		0.473	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
GPBP1L1	60313	hgsc.bcm.edu	37	1	46095272	46095272	+	Silent	SNP	T	T	C	rs1135812	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46095272T>C	ENST00000290795.3	-	11	2469	c.1248A>G	c.(1246-1248)aaA>aaG	p.K416K	GPBP1L1_ENST00000355105.3_Silent_p.K416K|GPBP1L1_ENST00000479235.1_5'UTR			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	416					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					TGTGGAACTCTTTGAGCTCAT	0.463													T|||	1598	0.319089	0.267	0.3473	5008	,	,		17762	0.3165		0.2833	False		,,,				2504	0.409				p.K416K		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.A1248G						PASS	.	T		1115,3291	400.8+/-331.7	145,825,1233	165.0	153.0	157.0		1248	3.9	1.0	1	dbSNP_86	157	2548,6052	414.0+/-351.3	386,1776,2138	no	coding-synonymous	GPBP1L1	NM_021639.4		531,2601,3371	CC,CT,TT		29.6279,25.3064,28.1639		416/475	46095272	3663,9343	2203	4300	6503	SO:0001819	synonymous_variant	60313	exon12			GAACTCTTTGAGC		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.1248A>G	1.37:g.46095272T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	37	CCDS528.1																																																																																			T|0.709;C|0.291;A|0.000	0.291	strong		0.463	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
COL6A2	1292	hgsc.bcm.edu	37	21	47545768	47545768	+	Missense_Mutation	SNP	G	G	A	rs1042917	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47545768G>A	ENST00000300527.4	+	26	2143	c.2039G>A	c.(2038-2040)cGt>cAt	p.R680H	COL6A2_ENST00000357838.4_Missense_Mutation_p.R680H|COL6A2_ENST00000397763.1_Missense_Mutation_p.R680H|COL6A2_ENST00000409416.1_Missense_Mutation_p.R680H|COL6A2_ENST00000310645.5_Missense_Mutation_p.R680H	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	680	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.		R -> H (in dbSNP:rs1042917). {ECO:0000269|PubMed:15563506, ECO:0000269|PubMed:15689448, ECO:0000269|PubMed:1690728, ECO:0000269|PubMed:17886299, ECO:0000269|Ref.1}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GACGACGAACGTATCGACTCC	0.632													G|||	1973	0.39397	0.208	0.6398	5008	,	,		15125	0.4306		0.5099	False		,,,				2504	0.3139				p.R680H		Atlas-SNP	.											.	COL6A2	351	.	0			c.G2039A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	1061,3345	385.6+/-325.8	148,765,1290	69.0	58.0	62.0		2039,2039,2039	4.4	1.0	21	dbSNP_86	62	4310,4290	576.3+/-390.4	1050,2210,1040	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	29,29,29	1198,2975,2330	AA,AG,GG		49.8837,24.0808,41.2963	probably-damaging,probably-damaging,probably-damaging	680/1020,680/919,680/829	47545768	5371,7635	2203	4300	6503	SO:0001583	missense	1292	exon26			ACGAACGTATCGA	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2039G>A	21.37:g.47545768G>A	ENSP00000300527:p.Arg680His	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	966	0.4423076923076923	111	0.22560975609756098	223	0.6160220994475138	233	0.40734265734265734	399	0.5263852242744064	G	14.70	2.613296	0.46631	0.240808	0.501163	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763;ENST00000413758	T;T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15;-1.15	4.4	4.4	0.53042	von Willebrand factor, type A (3);	0.119103	0.56097	D	0.000030	T	0.00012	0.0000	L	0.44542	1.39	0.20196	P	0.9999286073	D;D;D	0.89917	1.0;0.999;0.998	D;P;P	0.74023	0.982;0.871;0.784	T	0.52675	-0.8544	9	0.49607	T	0.09	-16.3153	16.9942	0.86362	0.0:0.0:1.0:0.0	rs1042917;rs3171502;rs17272877;rs59723476;rs1042917	680;680;680	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	H	680;680;680;680;680;237	ENSP00000300527:R680H;ENSP00000350497:R680H;ENSP00000312529:R680H;ENSP00000387115:R680H;ENSP00000380870:R680H;ENSP00000395751:R237H	ENSP00000300527:R680H	R	+	2	0	COL6A2	46370196	1.000000	0.71417	0.998000	0.56505	0.638000	0.38207	4.764000	0.62264	1.998000	0.58463	0.491000	0.48974	CGT	G|0.585;A|0.415	0.415	strong		0.632	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
ZNF33A	7581	hgsc.bcm.edu	37	10	38345465	38345465	+	Missense_Mutation	SNP	G	G	C	rs10508862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:38345465G>C	ENST00000458705.2	+	5	2568	c.2410G>C	c.(2410-2412)Gat>Cat	p.D804H	ZNF33A_ENST00000307441.9_Missense_Mutation_p.D804H|ZNF33A_ENST00000432900.2_Missense_Mutation_p.D811H|ZNF33A_ENST00000374618.3_Missense_Mutation_p.D805H|ZNF33A_ENST00000469037.2_Intron			Q06730	ZN33A_HUMAN	zinc finger protein 33A	804			D -> H (in dbSNP:rs10508862).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AGAAAGCCCTGATGACATCCT	0.383													G|||	159	0.0317492	0.0015	0.0648	5008	,	,		18726	0.0		0.1034	False		,,,				2504	0.0082				p.D805H		Atlas-SNP	.											.	ZNF33A	103	.	0			c.G2413C						PASS	.	G	HIS/ASP,HIS/ASP	78,4328	65.8+/-103.3	1,76,2126	58.0	56.0	57.0		2413,2410	-1.4	0.0	10	dbSNP_119	57	753,7845	176.3+/-226.2	31,691,3577	yes	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	81,81	32,767,5703	CC,CG,GG		8.7579,1.7703,6.3903	benign,benign	805/812,804/811	38345465	831,12173	2203	4299	6502	SO:0001583	missense	7581	exon5			AGCCCTGATGACA	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2410G>C	10.37:g.38345465G>C	ENSP00000387713:p.Asp804His	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	108	0.04945054945054945	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	75	0.09894459102902374	G	0.577	-0.838757	0.02692	0.017703	0.087579	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.06528	3.3;3.29;3.29;3.29	2.14	-1.36	0.09085	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.80722	P	0.0	B;B;B	0.28783	0.222;0.044;0.073	B;B;B	0.19391	0.025;0.011;0.025	T	0.44832	-0.9302	8	0.59425	D	0.04	.	2.3013	0.04162	0.4573:0.0:0.3056:0.2371	rs10508862;rs17663822;rs56465645;rs10508862	811;804;805	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	H	805;811;804;804	ENSP00000363747:D805H;ENSP00000402467:D811H;ENSP00000387713:D804H;ENSP00000304268:D804H	ENSP00000304268:D804H	D	+	1	0	ZNF33A	38385471	0.037000	0.19845	0.003000	0.11579	0.003000	0.03518	-0.229000	0.09098	-0.196000	0.10366	-0.657000	0.03884	GAT	G|0.940;C|0.060	0.060	strong		0.383	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
KCNH6	81033	hgsc.bcm.edu	37	17	61611423	61611423	+	Silent	SNP	T	T	C	rs7225568	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:61611423T>C	ENST00000583023.1	+	5	863	c.852T>C	c.(850-852)gaT>gaC	p.D284D	KCNH6_ENST00000580652.1_Silent_p.D284D|KCNH6_ENST00000314672.5_Silent_p.D284D|KCNH6_ENST00000581784.1_Silent_p.D284D|KCNH6_ENST00000456941.2_Silent_p.D284D	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	284					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TGCTCAGCGATCAGGACGAAT	0.587													C|||	2241	0.447484	0.5295	0.4251	5008	,	,		18615	0.2599		0.6064	False		,,,				2504	0.3824				p.D284D		Atlas-SNP	.											KCNH6,NS,malignant_melanoma,+2,1	KCNH6	122	1	0			c.T852C						PASS	.	C	,	2341,2065	570.5+/-382.9	637,1067,499	161.0	140.0	147.0		852,852	1.8	1.0	17	dbSNP_116	147	5115,3485	509.5+/-377.3	1559,1997,744	no	coding-synonymous,coding-synonymous	KCNH6	NM_030779.2,NM_173092.1	,	2196,3064,1243	CC,CT,TT		40.5233,46.8679,42.6726	,	284/995,284/906	61611423	7456,5550	2203	4300	6503	SO:0001819	synonymous_variant	81033	exon5			CAGCGATCAGGAC	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.852T>C	17.37:g.61611423T>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	197	88	0.446701	NM_030779	Q9BRD7	Silent	SNP	ENST00000583023.1	37	CCDS11638.1																																																																																			C|0.529;N|0.000	0.529	strong		0.587	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
OR13C3	138803	hgsc.bcm.edu	37	9	107299001	107299001	+	Missense_Mutation	SNP	C	C	A	rs41304943	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107299001C>A	ENST00000374781.2	-	1	136	c.94G>T	c.(94-96)Ggt>Tgt	p.G32C		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						TTAATCTCACCCATGTCATCT	0.343													C|||	518	0.103435	0.1596	0.0663	5008	,	,		21252	0.0665		0.0815	False		,,,				2504	0.1145				p.G32C	GBM(86;1248 1274 14222 15028 46219)	Atlas-SNP	.											.	OR13C3	45	.	0			c.G94T						PASS	.	C	CYS/GLY	638,3768	267.4+/-267.8	43,552,1608	67.0	67.0	67.0		94	1.4	0.1	9	dbSNP_127	67	780,7820	184.2+/-232.2	37,706,3557	yes	missense	OR13C3	NM_001001961.1	159	80,1258,5165	AA,AC,CC		9.0698,14.4803,10.9027	possibly-damaging	32/348	107299001	1418,11588	2203	4300	6503	SO:0001583	missense	138803	exon1			TCTCACCCATGTC		CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"""GPCR / Class A : Olfactory receptors"""	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.94G>T	9.37:g.107299001C>A	ENSP00000363913:p.Gly32Cys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	60	0.405405	NM_001001961	Q5VVG1|Q6IF52	Missense_Mutation	SNP	ENST00000374781.2	37	CCDS35089.1	195	0.08928571428571429	85	0.17276422764227642	25	0.06906077348066299	25	0.043706293706293704	60	0.079155672823219	C	12.31	1.900658	0.33535	0.144803	0.090698	ENSG00000204246	ENST00000374781	T	0.03094	4.05	4.25	1.41	0.22369	.	0.501437	0.16547	N	0.209662	T	0.00012	0.0000	L	0.41079	1.255	0.47994	P	4.3199999999998795E-4	P	0.35401	0.499	B	0.40285	0.325	T	0.43228	-0.9404	9	0.72032	D	0.01	.	8.2181	0.31526	0.0:0.7241:0.0:0.2759	rs41304943;rs61740139	32	Q8NGS6	O13C3_HUMAN	C	32	ENSP00000363913:G32C	ENSP00000363913:G32C	G	-	1	0	OR13C3	106338822	0.012000	0.17670	0.076000	0.20297	0.083000	0.17756	0.380000	0.20602	0.327000	0.23409	-0.150000	0.13652	GGT	C|0.896;A|0.104	0.104	strong		0.343	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2		
ZNF414	84330	hgsc.bcm.edu	37	19	8578035	8578035	+	Missense_Mutation	SNP	T	T	C	rs8100431	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8578035T>C	ENST00000255616.8	-	2	295	c.194A>G	c.(193-195)cAg>cGg	p.Q65R	ZNF414_ENST00000393927.4_Missense_Mutation_p.Q65R	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	65			Q -> R (in dbSNP:rs8100431). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(2)	2						GGAGCCCTGCTGCATCCCTCC	0.706													T|||	1544	0.308307	0.1415	0.2709	5008	,	,		15055	0.5357		0.3082	False		,,,				2504	0.3262				p.Q65R		Atlas-SNP	.											.	ZNF414	25	.	0			c.A194G						PASS	.	T	ARG/GLN,ARG/GLN	655,3647		61,533,1557	8.0	8.0	8.0		194,194	2.0	0.4	19	dbSNP_116	8	2293,6123		349,1595,2264	yes	missense,missense	ZNF414	NM_001146175.1,NM_032370.2	43,43	410,2128,3821	CC,CT,TT		27.2457,15.2255,23.1797	benign,benign	65/391,65/313	8578035	2948,9770	2151	4208	6359	SO:0001583	missense	84330	exon2			CCCTGCTGCATCC	AK074191	CCDS12205.1, CCDS54211.1	19p13.2	2008-02-05				ENSG00000133250		"""Zinc fingers, C2H2-type"""	20630	protein-coding gene	gene with protein product							Standard	NM_032370		Approved	MGC15716, Zfp414	uc002mke.4	Q96IQ9		ENST00000255616.8:c.194A>G	19.37:g.8578035T>C	ENSP00000255616:p.Gln65Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	48	46	0.958333	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	37	CCDS12205.1	713	0.32646520146520147	69	0.1402439024390244	113	0.31215469613259667	297	0.5192307692307693	234	0.3087071240105541	T	13.78	2.338251	0.41398	0.152255	0.272457	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.08546	3.08;3.08	4.13	1.95	0.26073	.	0.000000	0.33438	N	0.004910	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D;D	0.57899	0.981;0.981	D;D	0.70487	0.969;0.954	T	0.47459	-0.9116	9	0.66056	D	0.02	-9.8746	3.2547	0.06827	0.2039:0.1132:0.0:0.6829	rs8100431;rs17355273;rs17855387	65;65	Q96IQ9;A8MY94	ZN414_HUMAN;.	R	65	ENSP00000377504:Q65R;ENSP00000255616:Q65R	ENSP00000255616:Q65R	Q	-	2	0	ZNF414	8484035	0.982000	0.34865	0.422000	0.26621	0.367000	0.29736	0.944000	0.29043	0.223000	0.20920	0.533000	0.62120	CAG	T|0.673;C|0.327	0.327	strong		0.706	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370	
DLG1	1739	hgsc.bcm.edu	37	3	196771513	196771513	+	Missense_Mutation	SNP	G	G	A	rs34492126	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:196771513G>A	ENST00000419354.1	-	26	2982	c.2696C>T	c.(2695-2697)cCg>cTg	p.P899L	DLG1_ENST00000314062.3_Missense_Mutation_p.P848L|DLG1_ENST00000346964.2_Missense_Mutation_p.P921L|DLG1_ENST00000422288.1_Missense_Mutation_p.P848L|DLG1_ENST00000452595.1_Missense_Mutation_p.P783L|DLG1_ENST00000392382.2_Missense_Mutation_p.P866L|DLG1_ENST00000443183.1_Missense_Mutation_p.P795L|DLG1_ENST00000448528.2_Missense_Mutation_p.P899L|DLG1_ENST00000357674.4_Missense_Mutation_p.P888L|DLG1_ENST00000450955.1_Missense_Mutation_p.P888L			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	899			P -> L (in dbSNP:rs34492126).		actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TTCTTTTGCCGGAACCCAGAT	0.393													G|||	126	0.0251597	0.003	0.0303	5008	,	,		17679	0.0		0.0577	False		,,,				2504	0.044				p.P921L		Atlas-SNP	.											DLG1_ENST00000419354,NS,adenoma,0,3	DLG1	120	3	0			c.C2762T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	57,4349	56.2+/-92.4	0,57,2146	149.0	143.0	145.0		2696,2660,2384,2348,2762	5.5	1.0	3	dbSNP_126	145	405,8195	129.0+/-187.1	9,387,3904	yes	missense,missense,missense,missense,missense	DLG1	NM_001098424.1,NM_001204386.1,NM_001204387.1,NM_001204388.1,NM_004087.2	98,98,98,98,98	9,444,6050	AA,AG,GG		4.7093,1.2937,3.5522	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	899/905,887/893,795/801,783/789,921/927	196771513	462,12544	2203	4300	6503	SO:0001583	missense	1739	exon26			TTTGCCGGAACCC	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.2696C>T	3.37:g.196771513G>A	ENSP00000407531:p.Pro899Leu	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	118	75	0.635593	NM_004087	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	37	CCDS43194.1	58	0.026556776556776556	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	43	0.05672823218997362	G	20.6	4.022579	0.75275	0.012937	0.047093	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000452595;ENST00000422288;ENST00000448528;ENST00000443183;ENST00000392382;ENST00000450955	T;T;T;T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.48	5.48	0.80851	.	0.064498	0.64402	D	0.000007	T	0.22126	0.0533	M	0.87682	2.9	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.998;0.992;0.997;0.999	D;P;P;P;P	0.65010	0.931;0.854;0.684;0.806;0.899	T	0.60311	-0.7288	10	0.87932	D	0	.	18.3398	0.90302	0.0:0.0:1.0:0.0	rs34492126	888;783;795;899;921	Q12959-4;E9PG21;E7EWL7;Q12959;Q12959-2	.;.;.;DLG1_HUMAN;.	L	921;912;888;886;848;899;783;848;899;795;866;888	ENSP00000345731:P921L;ENSP00000350303:P888L;ENSP00000321087:P848L;ENSP00000407531:P899L;ENSP00000398939:P783L;ENSP00000413238:P848L;ENSP00000391732:P899L;ENSP00000396658:P795L;ENSP00000376187:P866L;ENSP00000411278:P888L	ENSP00000321087:P848L	P	-	2	0	DLG1	198255910	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.461000	0.60115	2.587000	0.87381	0.655000	0.94253	CCG	G|0.966;A|0.034	0.034	strong		0.393	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087	
ACER3	55331	hgsc.bcm.edu	37	11	76701606	76701606	+	Silent	SNP	G	G	A	rs3740767	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76701606G>A	ENST00000532485.1	+	6	530	c.426G>A	c.(424-426)ccG>ccA	p.P142P	ACER3_ENST00000533873.1_Silent_p.P105P|ACER3_ENST00000526597.1_Silent_p.P47P|ACER3_ENST00000538157.1_Silent_p.P100P|ACER3_ENST00000530182.1_3'UTR	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	142					ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						TAAAAGAGCCGATATTCCATC	0.333													G|||	2669	0.532947	0.1906	0.5072	5008	,	,		20718	0.6349		0.7366	False		,,,				2504	0.6994				p.P142P		Atlas-SNP	.											.	ACER3	19	.	0			c.G426A						PASS	.	G		1259,3141	428.9+/-342.0	201,857,1142	195.0	187.0	190.0		426	-0.8	0.6	11	dbSNP_107	190	6522,2062	717.8+/-406.2	2488,1546,258	yes	coding-synonymous	ACER3	NM_018367.5		2689,2403,1400	AA,AG,GG		24.0214,28.6136,40.0724		142/268	76701606	7781,5203	2200	4292	6492	SO:0001819	synonymous_variant	55331	exon6			AGAGCCGATATTC	AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	3.5.1.23	"""Alkaline ceramidase"""	16066	protein-coding gene	gene with protein product	"""alkaline phytoceramidase"""		"""phytoceramidase, alkaline"""	PHCA		11356846, 18619555	Standard	XM_005274090		Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.426G>A	11.37:g.76701606G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_018367	B2RC99	Silent	SNP	ENST00000532485.1	37	CCDS8247.1																																																																																			G|0.409;A|0.591	0.591	strong		0.333	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382770.2	NM_018367	
ZNF485	220992	hgsc.bcm.edu	37	10	44112245	44112245	+	Missense_Mutation	SNP	G	G	A	rs12354886	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:44112245G>A	ENST00000361807.3	+	5	948	c.754G>A	c.(754-756)Gct>Act	p.A252T	ZNF485_ENST00000374435.3_Missense_Mutation_p.A252T|ZNF485_ENST00000374437.2_Missense_Mutation_p.A161T	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	252			A -> T (in dbSNP:rs12354886).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GAAAGCCTTCGCTCAGAATGC	0.393													G|||	926	0.184904	0.2943	0.2133	5008	,	,		21170	0.003		0.2177	False		,,,				2504	0.1708				p.A252T		Atlas-SNP	.											.	ZNF485	102	.	0			c.G754A						PASS	.	G	THR/ALA	1183,3223	413.7+/-336.6	169,845,1189	70.0	74.0	73.0		754	0.5	0.0	10	dbSNP_120	73	1995,6605	348.3+/-327.0	222,1551,2527	yes	missense	ZNF485	NM_145312.3	58	391,2396,3716	AA,AG,GG		23.1977,26.8498,24.4349	benign	252/442	44112245	3178,9828	2203	4300	6503	SO:0001583	missense	220992	exon5			GCCTTCGCTCAGA	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.754G>A	10.37:g.44112245G>A	ENSP00000354694:p.Ala252Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	37	CCDS7205.2	366	0.16758241758241757	136	0.2764227642276423	77	0.212707182320442	0	0.0	153	0.20184696569920843	G	0.238	-1.015652	0.02078	0.268498	0.231977	ENSG00000198298	ENST00000361807;ENST00000374437;ENST00000374435	T;T;T	0.07567	3.18;3.18;3.18	2.46	0.496	0.16896	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04655	-0.195	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.47699	-0.9097	8	0.10902	T	0.67	.	2.3447	0.04269	0.2826:0.0:0.4752:0.2422	rs12354886;rs52806454;rs59867017;rs12354886	252	Q8NCK3	ZN485_HUMAN	T	252;161;252	ENSP00000354694:A252T;ENSP00000363560:A161T;ENSP00000363558:A252T	ENSP00000354694:A252T	A	+	1	0	ZNF485	43432251	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.058000	0.11750	0.119000	0.18210	-0.521000	0.04368	GCT	G|0.786;A|0.214	0.214	strong		0.393	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
SERPINB5	5268	hgsc.bcm.edu	37	18	61170721	61170721	+	Silent	SNP	T	T	C	rs1455556	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:61170721T>C	ENST00000382771.4	+	7	1186	c.894T>C	c.(892-894)agT>agC	p.S298S		NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	298					cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						ATATCTTCAGTGAAGACACAT	0.423													T|||	2633	0.525759	0.3396	0.6037	5008	,	,		20574	0.5972		0.6978	False		,,,				2504	0.4714				p.S298S		Atlas-SNP	.											.	SERPINB5	35	.	0			c.T894C						PASS	.	T		1712,2694	515.9+/-369.0	345,1022,836	99.0	88.0	92.0		894	-4.8	0.5	18	dbSNP_88	92	5921,2679	684.4+/-404.0	2044,1833,423	no	coding-synonymous	SERPINB5	NM_002639.4		2389,2855,1259	CC,CT,TT		31.1512,38.8561,41.3117		298/376	61170721	7633,5373	2203	4300	6503	SO:0001819	synonymous_variant	5268	exon7			CTTCAGTGAAGAC	U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"""Serine (or cysteine) peptidase inhibitors"""	8949	protein-coding gene	gene with protein product	"""protease inhibitor 5 (maspin)"""	154790	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"""	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.894T>C	18.37:g.61170721T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_002639	B2R6Y4|Q6N0B4|Q8WW89	Silent	SNP	ENST00000382771.4	37	CCDS32839.1																																																																																			T|0.435;C|0.565	0.565	strong		0.423	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639	
COL17A1	1308	hgsc.bcm.edu	37	10	105819956	105819956	+	Silent	SNP	G	G	A	rs805701	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:105819956G>A	ENST00000353479.5	-	14	1352	c.1062C>T	c.(1060-1062)gcC>gcT	p.A354A	COL17A1_ENST00000369733.3_Silent_p.A354A|COL17A1_ENST00000393211.3_Silent_p.A354A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	354	Nonhelical region (NC16).				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TCTCCTTCTTGGCAGGTGTGT	0.537													G|||	2767	0.552516	0.2519	0.6902	5008	,	,		22036	0.6875		0.6551	False		,,,				2504	0.6166				p.A354A		Atlas-SNP	.											.	COL17A1	149	.	0			c.C1062T						PASS	.	G		1425,2981	464.5+/-353.9	238,949,1016	218.0	149.0	172.0		1062	4.8	1.0	10	dbSNP_86	172	5796,2804	677.0+/-403.3	1960,1876,464	no	coding-synonymous	COL17A1	NM_000494.3		2198,2825,1480	AA,AG,GG		32.6047,32.3423,44.4795		354/1498	105819956	7221,5785	2203	4300	6503	SO:0001819	synonymous_variant	1308	exon14			CTTCTTGGCAGGT	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.1062C>T	10.37:g.105819956G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	227	226	0.995595	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																			G|0.437;A|0.563	0.563	strong		0.537	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
PLXNA1	5361	hgsc.bcm.edu	37	3	126735453	126735453	+	Silent	SNP	C	C	T	rs9858521	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126735453C>T	ENST00000393409.2	+	15	3108	c.3108C>T	c.(3106-3108)acC>acT	p.T1036T	PLXNA1_ENST00000251772.4_Silent_p.T1013T	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1036	IPT/TIG 2.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CCCAGCTCACCAACCCTGAGG	0.627													C|||	748	0.149361	0.0946	0.0548	5008	,	,		18241	0.2083		0.1203	False		,,,				2504	0.2597				p.T1036T		Atlas-SNP	.											.	PLXNA1	185	.	0			c.C3108T						PASS	.	C		403,4003	198.7+/-222.5	15,373,1815	117.0	118.0	118.0		3108	3.8	1.0	3	dbSNP_119	118	870,7730	197.3+/-242.0	51,768,3481	no	coding-synonymous	PLXNA1	NM_032242.3		66,1141,5296	TT,TC,CC		10.1163,9.1466,9.7878		1036/1897	126735453	1273,11733	2203	4300	6503	SO:0001819	synonymous_variant	5361	exon15			GCTCACCAACCCT	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.3108C>T	3.37:g.126735453C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	155	82	0.529032	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																			C|0.897;T|0.103	0.103	strong		0.627	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
CTC1	80169	hgsc.bcm.edu	37	17	8135444	8135444	+	Missense_Mutation	SNP	C	C	G	rs62620189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8135444C>G	ENST00000315684.8	-	13	2169	c.2162G>C	c.(2161-2163)gGc>gCc	p.G721A		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	721					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						TCCCTCTGGGCCGGTGGGATC	0.577													C|||	38	0.00758786	0.0015	0.0202	5008	,	,		17008	0.0		0.0189	False		,,,				2504	0.0031				p.G721A		Atlas-SNP	.											.	CTC1	75	.	0			c.G2162C						PASS	.	C	ALA/GLY	16,3888		1,14,1937	20.0	21.0	21.0		2162	-2.9	0.0	17	dbSNP_129	21	159,8113		2,155,3979	yes	missense	CTC1	NM_025099.5	60	3,169,5916	GG,GC,CC		1.9221,0.4098,1.4373	benign	721/1218	8135444	175,12001	1952	4136	6088	SO:0001583	missense	80169	exon13			TCTGGGCCGGTGG	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.2162G>C	17.37:g.8135444C>G	ENSP00000313759:p.Gly721Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	37	CCDS42259.1	23	0.010531135531135532	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	13	0.017150395778364115	C	3.137	-0.177232	0.06380	0.004098	0.019221	ENSG00000178971	ENST00000315684;ENST00000449476	D;D	0.81739	-1.53;-1.53	5.59	-2.87	0.05700	.	1.336170	0.04479	N	0.377577	T	0.44180	0.1281	N	0.22421	0.69	0.09310	N	1	B	0.16166	0.016	B	0.14023	0.01	T	0.37596	-0.9699	10	0.09590	T	0.72	3.2836	0.7639	0.01011	0.1604:0.3482:0.2124:0.279	rs62620189	721	Q2NKJ3	CTC1_HUMAN	A	721;686	ENSP00000313759:G721A;ENSP00000396018:G686A	ENSP00000313759:G721A	G	-	2	0	CTC1	8076169	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.771000	0.04699	-0.378000	0.07918	0.655000	0.94253	GGC	C|0.962;G|0.038	0.038	strong		0.577	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
RAB11FIP4	84440	hgsc.bcm.edu	37	17	29857460	29857460	+	Silent	SNP	G	G	A	rs61731602	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29857460G>A	ENST00000325874.8	+	14	1999	c.1770G>A	c.(1768-1770)gcG>gcA	p.A590A	RAB11FIP4_ENST00000394744.2_Silent_p.A488A	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	590	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.|Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				CTCTGGCTGCGGAGATAGACA	0.592													G|||	457	0.091254	0.0113	0.2003	5008	,	,		17485	0.0833		0.174	False		,,,				2504	0.045				p.A590A		Atlas-SNP	.											.	RAB11FIP4	65	.	0			c.G1770A						PASS	.	G		152,4254	104.3+/-142.8	6,140,2057	88.0	89.0	88.0		1770	-10.9	0.7	17	dbSNP_129	88	1406,7194	269.7+/-288.6	120,1166,3014	no	coding-synonymous	RAB11FIP4	NM_032932.3		126,1306,5071	AA,AG,GG		16.3488,3.4498,11.9791		590/638	29857460	1558,11448	2203	4300	6503	SO:0001819	synonymous_variant	84440	exon14			GGCTGCGGAGATA	AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"""EF-hand domain containing"""	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.1770G>A	17.37:g.29857460G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_032932	Q52LI1|Q8N829|Q8NDT7|Q969D8	Silent	SNP	ENST00000325874.8	37	CCDS11267.1																																																																																			G|0.878;A|0.122	0.122	strong		0.592	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932	
PRKAA2	5563	hgsc.bcm.edu	37	1	57158051	57158051	+	Silent	SNP	G	G	A	rs17848595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:57158051G>A	ENST00000371244.4	+	4	417	c.351G>A	c.(349-351)agG>agA	p.R117R		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	117	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	TGGAAGCCAGGCGGCTCTTTC	0.483													G|||	870	0.173722	0.2231	0.0677	5008	,	,		17103	0.2252		0.0437	False		,,,				2504	0.2628				p.R117R		Atlas-SNP	.											.	PRKAA2	177	.	0			c.G351A						PASS	.	G		801,3605	321.5+/-297.2	76,649,1478	173.0	167.0	169.0		351	-0.7	0.5	1	dbSNP_123	169	423,8177	131.5+/-189.3	12,399,3889	no	coding-synonymous	PRKAA2	NM_006252.3		88,1048,5367	AA,AG,GG		4.9186,18.1798,9.411		117/553	57158051	1224,11782	2203	4300	6503	SO:0001819	synonymous_variant	5563	exon4			AGCCAGGCGGCTC	BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.351G>A	1.37:g.57158051G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	151	53	0.350993	NM_006252	Q9H1E8|Q9UD43	Silent	SNP	ENST00000371244.4	37	CCDS605.1																																																																																			G|0.891;A|0.109	0.109	strong		0.483	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252	
NBAS	51594	hgsc.bcm.edu	37	2	15679410	15679410	+	Silent	SNP	G	G	A	rs147692911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:15679410G>A	ENST00000281513.5	-	7	475	c.450C>T	c.(448-450)gcC>gcT	p.A150A	NBAS_ENST00000441750.1_Silent_p.A150A	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	150					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CTGTGCTTTCGGCATAGGCCA	0.443													G|||	2	0.000399361	0.0	0.0	5008	,	,		18414	0.0		0.002	False		,,,				2504	0.0				p.A150A		Atlas-SNP	.											.	NBAS	246	.	0			c.C450T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	116.0	104.0	108.0		450	-11.6	0.0	2	dbSNP_134	108	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	NBAS	NM_015909.2		0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384		150/2372	15679410	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	51594	exon7			GCTTTCGGCATAG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.450C>T	2.37:g.15679410G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	186	77	0.413978	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			G|0.999;A|0.001	0.001	strong		0.443	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
FOXD4	2298	hgsc.bcm.edu	37	9	117506	117506	+	Missense_Mutation	SNP	G	G	A	rs2492215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:117506G>A	ENST00000382500.2	-	1	911	c.614C>T	c.(613-615)cCg>cTg	p.P205L		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	205	Pro-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		TCCCGGGGTCGGTTGGTGGCG	0.692																																					p.P205L		Atlas-SNP	.											FOXD4_ENST00000382500,NS,carcinoma,0,2	FOXD4	75	2	0			c.C614T						scavenged	.						68.0	97.0	87.0					9																	117506		2161	4225	6386	SO:0001583	missense	2298	exon1			GGGGTCGGTTGGT	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.614C>T	9.37:g.117506G>A	ENSP00000371940:p.Pro205Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	10	0.181818	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	0.044	-1.274072	0.01421	.	.	ENSG00000170122	ENST00000382500	D	0.95171	-3.63	1.69	-1.03	0.10102	.	0.440036	0.16375	U	0.217150	D	0.82751	0.5105	N	0.08118	0	0.29875	N	0.826511	B	0.06786	0.001	B	0.04013	0.001	T	0.70741	-0.4789	10	0.27785	T	0.31	.	3.973	0.09462	0.1519:0.0:0.492:0.356	rs2492215	205	Q12950	FOXD4_HUMAN	L	205	ENSP00000371940:P205L	ENSP00000371940:P205L	P	-	2	0	FOXD4	107506	0.908000	0.30866	0.046000	0.18839	0.053000	0.15095	1.199000	0.32235	-0.557000	0.06126	-2.183000	0.00315	CCG	.	.	weak		0.692	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
CUBN	8029	hgsc.bcm.edu	37	10	17147521	17147521	+	Missense_Mutation	SNP	G	G	T	rs1801224	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:17147521G>T	ENST00000377833.4	-	11	1230	c.1165C>A	c.(1165-1167)Cca>Aca	p.P389T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	389			P -> T (in dbSNP:rs1801224). {ECO:0000269|PubMed:10080186}.		cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CATCCATTTGGCCCATAACCA	0.448													G|||	2676	0.534345	0.3676	0.6009	5008	,	,		18892	0.6558		0.5875	False		,,,				2504	0.5327				p.P389T		Atlas-SNP	.											.	CUBN	515	.	0			c.C1165A						PASS	.	G	THR/PRO	1819,2587	533.3+/-373.7	371,1077,755	146.0	126.0	133.0		1165	1.4	0.5	10	dbSNP_89	133	5823,2777	678.5+/-403.5	1983,1857,460	yes	missense	CUBN	NM_001081.3	38	2354,2934,1215	TT,TG,GG		32.2907,41.2846,41.2425	possibly-damaging	389/3624	17147521	7642,5364	2203	4300	6503	SO:0001583	missense	8029	exon11			CATTTGGCCCATA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1165C>A	10.37:g.17147521G>T	ENSP00000367064:p.Pro389Thr	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	213	109	0.511737	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	1225	0.5608974358974359	205	0.4166666666666667	220	0.6077348066298343	365	0.6381118881118881	435	0.5738786279683378	G	14.04	2.415303	0.42817	0.412846	0.677093	ENSG00000107611	ENST00000377833	T	0.40756	1.02	5.65	1.37	0.22104	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.670270	0.13115	N	0.412718	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	0.999999999795783	P	0.39282	0.666	B	0.35859	0.212	T	0.37384	-0.9708	9	0.66056	D	0.02	.	5.4646	0.16635	0.0693:0.1251:0.5467:0.2588	rs1801224;rs2228052;rs10795446;rs41538725;rs41538899;rs41539425;rs52807320;rs61727981;rs10795446	389	O60494	CUBN_HUMAN	T	389	ENSP00000367064:P389T	ENSP00000367064:P389T	P	-	1	0	CUBN	17187527	0.991000	0.36638	0.490000	0.27465	0.703000	0.40648	3.034000	0.49751	0.296000	0.22592	-0.282000	0.10007	CCA	T|0.469;G|0.343;C|0.092;A|0.097	0.469	strong		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
ERCC2	2068	hgsc.bcm.edu	37	19	45855524	45855524	+	Silent	SNP	G	G	A	rs1052555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45855524G>A	ENST00000391945.4	-	22	2210	c.2133C>T	c.(2131-2133)gaC>gaT	p.D711D	ERCC2_ENST00000391944.3_Silent_p.D633D	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	711					7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		GGACACCCTCGTCCACGGTCA	0.672			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	913	0.182308	0.0726	0.1527	5008	,	,		18987	0.0625		0.337	False		,,,				2504	0.316				p.D711D		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	ERCC2_ENST00000391945,trunk,malignant_melanoma,-2,1	ERCC2	78	1	0			c.C2133T	GRCh37	CM052870	ERCC2	M	rs1052555	scavenged	.	G		500,3906	234.2+/-247.1	32,436,1735	96.0	72.0	80.0		2133	-10.0	0.3	19	dbSNP_86	80	2865,5735	451.6+/-362.7	512,1841,1947	no	coding-synonymous	ERCC2	NM_000400.3		544,2277,3682	AA,AG,GG		33.314,11.3482,25.8727		711/761	45855524	3365,9641	2203	4300	6503	SO:0001819	synonymous_variant	2068	exon22	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACCCTCGTCCACG		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.2133C>T	19.37:g.45855524G>A		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Silent	SNP	ENST00000391945.4	37	CCDS33049.1																																																																																			G|0.767;N|0.002	.	strong		0.672	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
LRRC75A	388341	hgsc.bcm.edu	37	17	16347325	16347325	+	Missense_Mutation	SNP	T	T	C	rs61745139	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:16347325T>C	ENST00000409083.3	-	3	658	c.496A>G	c.(496-498)Aga>Gga	p.R166G	C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000391079.1_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000582911.1_RNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000475953.1_RNA|FAM211A_ENST00000470794.1_Silent_p.V204V|C17orf76-AS1_ENST00000584141.1_RNA	NM_207387.3	NP_997270.2														lung(1)	1						CCACGCTGTCTACCTGCTCCC	0.647													T|||	241	0.048123	0.0083	0.0562	5008	,	,		18322	0.0		0.1203	False		,,,				2504	0.0716				p.R166G		Atlas-SNP	.											FAM211A_ENST00000470794,NS,carcinoma,0,3	FAM211A	21	3	0			c.A496G						PASS	.	T	,GLY/ARG	119,4287	87.3+/-125.9	3,113,2087	58.0	48.0	51.0		612,496	3.4	1.0	17	dbSNP_129	51	1153,7447	234.3+/-267.3	70,1013,3217	yes	coding-synonymous,missense	C17orf76	NM_001113567.1,NM_207387.2	,125	73,1126,5304	CC,CT,TT		13.407,2.7009,9.7801	,	204/345,166/213	16347325	1272,11734	2203	4300	6503	SO:0001583	missense	388341	exon3			GCTGTCTACCTGC																												ENST00000409083.3:c.496A>G	17.37:g.16347325T>C	ENSP00000386504:p.Arg166Gly	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_207387		Missense_Mutation	SNP	ENST00000409083.3	37	CCDS11178.2	130	0.05952380952380952	15	0.03048780487804878	22	0.06077348066298342	0	0.0	93	0.12269129287598944	T	14.35	2.510037	0.44660	0.027009	0.13407	ENSG00000181350	ENST00000409083	.	.	.	5.34	3.36	0.38483	.	1.464120	0.03657	N	0.242032	T	0.00496	0.0016	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10337	-1.0634	7	0.87932	D	0	.	10.0548	0.42239	0.0:0.8345:0.0:0.1655	.	166	Q8NAA5-2	.	G	166	.	ENSP00000386504:R166G	R	-	1	2	C17orf76	16288050	0.982000	0.34865	1.000000	0.80357	0.980000	0.70556	0.185000	0.16958	0.772000	0.33382	-0.232000	0.12228	AGA	T|0.918;C|0.082	0.082	strong		0.647	FAM211A-001	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130461.2		
MCF2L	23263	hgsc.bcm.edu	37	13	113720476	113720476	+	Silent	SNP	C	C	T	rs2297192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:113720476C>T	ENST00000375608.3	+	9	1021	c.963C>T	c.(961-963)acC>acT	p.T321T	MCF2L_ENST00000423482.2_Silent_p.T289T|MCF2L_ENST00000535094.2_Silent_p.T291T|MCF2L_ENST00000375601.3_Silent_p.T295T|MCF2L_ENST00000375604.2_Silent_p.T348T|MCF2L_ENST00000375597.4_Silent_p.T289T|MCF2L_ENST00000397030.1_Silent_p.T324T|MCF2L_ENST00000421756.1_Silent_p.T295T|MCF2L_ENST00000434480.2_Silent_p.T297T|MCF2L_ENST00000442652.2_Silent_p.T321T			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	321					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				ACCAGGCCACCGTGCAGAGGT	0.617													C|||	944	0.188498	0.025	0.2478	5008	,	,		18249	0.4573		0.1571	False		,,,				2504	0.1227				p.T291T		Atlas-SNP	.											.	MCF2L	182	.	0			c.C873T						PASS	.	C	,	235,4171	137.3+/-173.1	8,219,1976	86.0	72.0	77.0		873,867	-10.0	0.4	13	dbSNP_100	77	1400,7198	269.3+/-288.3	107,1186,3006	yes	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	115,1405,4982	TT,TC,CC		16.2829,5.3336,12.5731	,	291/1126,289/1124	113720476	1635,11369	2203	4299	6502	SO:0001819	synonymous_variant	23263	exon8			GGCCACCGTGCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.963C>T	13.37:g.113720476C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37																																																																																				C|0.846;T|0.154	0.154	strong		0.617	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
GPRIN2	9721	hgsc.bcm.edu	37	10	46999922	46999922	+	Missense_Mutation	SNP	G	G	T	rs4926046	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:46999922G>T	ENST00000374317.1	+	3	1315	c.1042G>T	c.(1042-1044)Gtg>Ttg	p.V348L	GPRIN2_ENST00000374314.4_Missense_Mutation_p.V348L	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	348										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CTGCAAGGCTGTGGCCACCAG	0.672																																					p.V348L		Atlas-SNP	.											GPRIN2,colon,carcinoma,0,1	GPRIN2	94	1	0			c.G1042T						PASS	.						51.0	53.0	52.0					10																	46999922		2203	4300	6503	SO:0001583	missense	9721	exon3			AAGGCTGTGGCCA	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.1042G>T	10.37:g.46999922G>T	ENSP00000363436:p.Val348Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	153	29	0.189542	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	799	0.3658424908424908	95	0.19308943089430894	136	0.3756906077348066	287	0.5017482517482518	281	0.370712401055409	G	20.7	4.034376	0.75617	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.30981	1.51;1.51	4.85	4.85	0.62838	.	0.000000	0.38111	N	0.001808	T	0.00012	0.0000	M	0.77103	2.36	0.53688	D	0.999976	D	0.76494	0.999	D	0.80764	0.994	T	0.49978	-0.8881	10	0.87932	D	0	-18.1542	15.8316	0.78757	0.0:0.0:1.0:0.0	rs4926046	348	O60269	GRIN2_HUMAN	L	348	ENSP00000363436:V348L;ENSP00000363433:V348L	ENSP00000363433:V348L	V	+	1	0	GPRIN2	46419928	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	4.918000	0.63376	2.415000	0.81967	0.313000	0.20887	GTG	G|0.634;T|0.366	0.366	strong		0.672	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
KIAA0922	23240	hgsc.bcm.edu	37	4	154514965	154514965	+	Missense_Mutation	SNP	T	T	C	rs17370297	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:154514965T>C	ENST00000409663.3	+	19	1986	c.1934T>C	c.(1933-1935)aTg>aCg	p.M645T	KIAA0922_ENST00000440693.1_Missense_Mutation_p.M562T|KIAA0922_ENST00000409959.3_Missense_Mutation_p.M646T	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	645			M -> T (in dbSNP:rs17370297). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)		p.M498T(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				GGCACTGATATGCAGATGATT	0.368													T|||	1133	0.226238	0.149	0.2161	5008	,	,		17835	0.2371		0.3072	False		,,,				2504	0.2434				p.M646T		Atlas-SNP	.											KIAA0922,NS,carcinoma,0,1	KIAA0922	214	1	1	Substitution - Missense(1)	stomach(1)	c.T1937C						PASS	.	T	THR/MET,THR/MET	794,3612	319.9+/-296.3	66,662,1475	118.0	108.0	111.0		1937,1934	2.9	0.8	4	dbSNP_123	111	2671,5929	430.0+/-356.4	427,1817,2056	yes	missense,missense	KIAA0922	NM_001131007.1,NM_015196.3	81,81	493,2479,3531	CC,CT,TT		31.0581,18.0209,26.6416	benign,benign	646/1611,645/1610	154514965	3465,9541	2203	4300	6503	SO:0001583	missense	23240	exon19			CTGATATGCAGAT	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.1934T>C	4.37:g.154514965T>C	ENSP00000386574:p.Met645Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	564	0.25824175824175827	67	0.13617886178861788	95	0.26243093922651933	157	0.2744755244755245	245	0.3232189973614776	T	1.584	-0.530847	0.04112	0.180209	0.310581	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.17213	2.57;2.29;2.57;2.29	5.36	2.94	0.34122	.	0.428043	0.29783	N	0.011205	T	0.00012	0.0000	L	0.33485	1.01	0.43014	P	0.005445000000000033	P;B;B	0.35908	0.527;0.141;0.007	B;B;B	0.37422	0.249;0.066;0.007	T	0.46091	-0.9216	9	0.13853	T	0.58	-2.7421	5.0096	0.14306	0.1342:0.1445:0.0:0.7213	rs17370297;rs52809861;rs58185156;rs17370297	562;646;645	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	T	645;562;646;423	ENSP00000386574:M645T;ENSP00000409663:M562T;ENSP00000386787:M646T;ENSP00000240487:M423T	ENSP00000240487:M423T	M	+	2	0	KIAA0922	154734415	0.807000	0.29009	0.821000	0.32701	0.718000	0.41266	0.795000	0.26972	0.442000	0.26555	0.528000	0.53228	ATG	T|0.744;C|0.256	0.256	strong		0.368	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
RPS15	6209	hgsc.bcm.edu	37	19	1440068	1440068	+	Missense_Mutation	SNP	G	G	C	rs201657403		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1440068G>C	ENST00000586686.2	+	3	179	c.140G>C	c.(139-141)cGg>cCg	p.R47P	RPS15_ENST00000585665.1_Missense_Mutation_p.R14P|RPS15_ENST00000586096.2_Missense_Mutation_p.R47P|RPS15_ENST00000233609.4_Missense_Mutation_p.R20P|RPS15_ENST00000593052.1_Missense_Mutation_p.R54P|RPS15_ENST00000591804.2_Missense_Mutation_p.R14P|RPS15_ENST00000589656.2_Missense_Mutation_p.R47P|RPS15_ENST00000591032.1_Missense_Mutation_p.R14P|AC027307.3_ENST00000594262.1_5'Flank			P62841	RS15_HUMAN	ribosomal protein S15	47					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|osteoblast differentiation (GO:0001649)|ribosomal small subunit biogenesis (GO:0042274)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.R47P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGCTGAACCGGGGCCTGCGG	0.687																																					p.R47P	Ovarian(170;79 2680 5719 44260)	Atlas-SNP	.											RPS15,extremity,malignant_melanoma,0,1	RPS15	11	1	1	Substitution - Missense(1)	skin(1)	c.G140C						scavenged	.						3.0	5.0	4.0					19																	1440068		2019	3993	6012	SO:0001583	missense	6209	exon3			TGAACCGGGGCCT		CCDS12067.1	19p13.3	2012-12-20			ENSG00000115268	ENSG00000115268		"""S ribosomal proteins"""	10388	protein-coding gene	gene with protein product	"""40S ribosomal protein S15"", ""homolog of rat insulinoma"", ""insulinoma protein"""	180535				2159154	Standard	NM_001018		Approved	RIG, MGC111130, S15	uc002lsp.1	P62841	OTTHUMG00000140099	ENST00000586686.2:c.140G>C	19.37:g.1440068G>C	ENSP00000467676:p.Arg47Pro	Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	25	6	0.24	NM_001018	A5D8V9|P11174|Q3KRA1|Q9UDC2	Missense_Mutation	SNP	ENST00000586686.2	37	CCDS12067.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.516509	0.27123	.	.	ENSG00000115268	ENST00000233609	.	.	.	4.26	3.21	0.36854	Ribosomal protein S19, superfamily (2);	0.000000	0.64402	U	0.000002	T	0.79452	0.4448	H	0.96489	3.83	0.80722	D	1	B	0.17465	0.022	B	0.26310	0.068	T	0.78595	-0.2143	9	0.51188	T	0.08	-26.4524	11.4241	0.50001	0.0902:0.0:0.9098:0.0	.	47	P62841	RS15_HUMAN	P	47	.	ENSP00000233609:R47P	R	+	2	0	RPS15	1391068	1.000000	0.71417	0.710000	0.30468	0.007000	0.05969	9.198000	0.94994	0.908000	0.36671	-0.192000	0.12808	CGG	G|0.442;C|0.558	0.558	strong		0.687	RPS15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449609.4	NM_001018	
WDR55	54853	hgsc.bcm.edu	37	5	140048707	140048707	+	Missense_Mutation	SNP	A	A	G	rs35983033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140048707A>G	ENST00000358337.5	+	6	941	c.704A>G	c.(703-705)tAc>tGc	p.Y235C	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	235			Y -> C (in dbSNP:rs35983033).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTACCATCTACCTCTTCAAT	0.527													A|||	237	0.0473243	0.0045	0.0692	5008	,	,		21419	0.0437		0.0726	False		,,,				2504	0.0675				p.Y235C		Atlas-SNP	.											.	WDR55	27	.	0			c.A704G						PASS	.	A	CYS/TYR	70,4336	64.1+/-101.4	0,70,2133	88.0	88.0	88.0		704	5.0	1.0	5	dbSNP_126	88	803,7797	186.9+/-234.3	40,723,3537	yes	missense	WDR55	NM_017706.4	194	40,793,5670	GG,GA,AA		9.3372,1.5887,6.7123	probably-damaging	235/384	140048707	873,12133	2203	4300	6503	SO:0001583	missense	54853	exon6			CCATCTACCTCTT	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"""WD repeat domain containing"""	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.704A>G	5.37:g.140048707A>G	ENSP00000351100:p.Tyr235Cys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	49	0.583333	NM_017706	Q9NXK4	Missense_Mutation	SNP	ENST00000358337.5	37	CCDS4235.1	115	0.052655677655677656	7	0.014227642276422764	28	0.07734806629834254	24	0.04195804195804196	56	0.07387862796833773	A	13.50	2.256320	0.39896	0.015887	0.093372	ENSG00000120314	ENST00000358337	T	0.41065	1.01	4.97	4.97	0.65823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000004	T	0.03434	0.0099	L	0.55213	1.73	0.80722	D	1	P;D	0.71674	0.869;0.998	P;P	0.57911	0.563;0.829	T	0.01099	-1.1452	10	0.51188	T	0.08	-2.0255	13.6399	0.62243	1.0:0.0:0.0:0.0	rs35983033	74;235	G3V1J0;Q9H6Y2	.;WDR55_HUMAN	C	235	ENSP00000351100:Y235C	ENSP00000351100:Y235C	Y	+	2	0	WDR55	140028891	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.279000	0.78599	1.853000	0.53794	0.383000	0.25322	TAC	A|0.936;G|0.064	0.064	strong		0.527	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706	
FAM221A	340277	hgsc.bcm.edu	37	7	23728916	23728916	+	Missense_Mutation	SNP	G	G	A	rs34518648	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:23728916G>A	ENST00000344962.4	+	3	357	c.268G>A	c.(268-270)Gcg>Acg	p.A90T	FAM221A_ENST00000409653.1_Missense_Mutation_p.A32T|FAM221A_ENST00000409994.3_Missense_Mutation_p.A32T|FAM221A_ENST00000409192.3_Missense_Mutation_p.A90T	NM_199136.3	NP_954587.2	A4D161	F221A_HUMAN	family with sequence similarity 221, member A	90			A -> T (in dbSNP:rs34518648).														TGACTTGGAAGCGATTCCTCA	0.408													A|||	418	0.0834665	0.0408	0.0706	5008	,	,		16228	0.1339		0.0746	False		,,,				2504	0.1074				p.A90T		Atlas-SNP	.											.	.	.	.	0			c.G268A						PASS	.	A	THR/ALA,THR/ALA,THR/ALA	196,4210	808.0+/-415.9	7,182,2014	80.0	78.0	79.0		268,94,268	1.4	0.2	7	dbSNP_126	79	612,7988	791.0+/-407.6	23,566,3711	yes	missense,missense,missense	C7orf46	NM_001127364.1,NM_001127365.1,NM_199136.3	58,58,58	30,748,5725	AA,AG,GG		7.1163,4.4485,6.2125	benign,benign,benign	90/263,32/205,90/299	23728916	808,12198	2203	4300	6503	SO:0001583	missense	340277	exon3			TTGGAAGCGATTC		CCDS5385.1, CCDS47561.1, CCDS47562.1, CCDS75570.1	7p15.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000188732	ENSG00000188732			27977	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 46"""	C7orf46		12477932	Standard	XR_242080		Approved	FLJ45875, MGC72075, DKFZp686F0810	uc003swo.4	A4D161	OTTHUMG00000128463	ENST00000344962.4:c.268G>A	7.37:g.23728916G>A	ENSP00000342576:p.Ala90Thr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_199136	Q05CG4|Q4G0Q7|Q6P519	Missense_Mutation	SNP	ENST00000344962.4	37	CCDS5385.1	190	0.08699633699633699	16	0.032520325203252036	20	0.055248618784530384	92	0.16083916083916083	62	0.08179419525065963	A	3.707	-0.060393	0.07317	0.044485	0.071163	ENSG00000188732	ENST00000409192;ENST00000344962;ENST00000409653;ENST00000409994	T;T;T;T	0.16897	2.31;2.31;2.31;2.31	5.41	1.36	0.22044	.	0.499012	0.22088	N	0.064788	T	0.00039	0.0001	N	0.05031	-0.125	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.43766	-0.9371	9	0.13470	T	0.59	0.0044	8.5544	0.33471	0.3972:0.0:0.6028:0.0	rs34518648	32;90;90	A4D161-3;A4D161-2;A4D161	.;.;CG046_HUMAN	T	90;90;32;32	ENSP00000386927:A90T;ENSP00000342576:A90T;ENSP00000386900:A32T;ENSP00000386631:A32T	ENSP00000342576:A90T	A	+	1	0	C7orf46	23695441	0.961000	0.32948	0.197000	0.23402	0.033000	0.12548	1.888000	0.39708	0.112000	0.17975	-1.177000	0.01723	GCG	G|0.927;A|0.073	0.073	strong		0.408	FAM221A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250261.1	NM_199136	
BCS1L	617	hgsc.bcm.edu	37	2	219527866	219527866	+	Silent	SNP	T	T	C	rs35843327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219527866T>C	ENST00000431802.1	+	8	1716	c.1017T>C	c.(1015-1017)ccT>ccC	p.P339P	BCS1L_ENST00000465706.1_3'UTR|BCS1L_ENST00000392109.1_Silent_p.P339P|BCS1L_ENST00000392111.2_Silent_p.P339P|BCS1L_ENST00000392110.2_Silent_p.P339P|BCS1L_ENST00000359273.3_Silent_p.P339P|BCS1L_ENST00000412366.1_Silent_p.P339P|BCS1L_ENST00000439945.1_Silent_p.P339P			Q9Y276	BCS1_HUMAN	BC1 (ubiquinol-cytochrome c reductase) synthesis-like	339					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex III assembly (GO:0034551)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|mitochondrion organization (GO:0007005)	mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	8		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGCTGGACCCTGCCCTGATAC	0.612													C|||	918	0.183307	0.5045	0.0605	5008	,	,		19537	0.124		0.0278	False		,,,				2504	0.0573				p.P339P		Atlas-SNP	.											.	BCS1L	22	.	0			c.T1017C						PASS	.	C	,	1830,2576	635.5+/-396.4	385,1060,758	74.0	76.0	76.0		1017,1017	2.5	1.0	2	dbSNP_126	76	326,8274	804.8+/-407.3	8,310,3982	no	coding-synonymous,coding-synonymous	BCS1L	NM_001079866.1,NM_004328.4	,	393,1370,4740	CC,CT,TT		3.7907,41.5343,16.577	,	339/420,339/420	219527866	2156,10850	2203	4300	6503	SO:0001819	synonymous_variant	617	exon9			GGACCCTGCCCTG	AF026849	CCDS2419.1	2q35	2014-09-17	2012-10-12		ENSG00000074582	ENSG00000074582		"""ATPases / AAA-type"", ""Mitochondrial respiratory chain complex assembly factors"""	1020	protein-coding gene	gene with protein product	"""GRACILE syndrome"", ""Bjornstad syndrome"""	603647	"""BCS1 (yeast homolog)-like"", ""BCS1-like (yeast)"", ""BCS1-like (S. cerevisiae)"""			9878253, 17314340	Standard	NM_001079866		Approved	Hs.6719, BCS, h-BCS, BJS	uc002viq.3	Q9Y276	OTTHUMG00000133114	ENST00000431802.1:c.1017T>C	2.37:g.219527866T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	218	101	0.463303	NM_001257343	B3KTW9|Q7Z2V7	Silent	SNP	ENST00000431802.1	37	CCDS2419.1	379	0.17353479853479853	252	0.5121951219512195	27	0.07458563535911603	83	0.1451048951048951	17	0.022427440633245383	C	3.297	-0.143731	0.06627	0.415343	0.037907	ENSG00000074582	ENST00000426649	.	.	.	5.12	2.49	0.30216	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46748	-0.9169	3	.	.	.	-18.7943	2.8528	0.05563	0.2157:0.0798:0.107:0.5976	rs35843327;rs58413417	.	.	.	R	121	.	.	C	+	1	0	BCS1L	219236110	0.985000	0.35326	1.000000	0.80357	0.360000	0.29518	0.138000	0.16016	0.066000	0.16515	-1.381000	0.01174	TGC	T|0.834;C|0.166	0.166	strong		0.612	BCS1L-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336756.1	NM_004328	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370572	26370572	+	Silent	SNP	C	C	T	rs34878490	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26370572C>T	ENST00000356386.2	+	5	644	c.456C>T	c.(454-456)gtC>gtT	p.V152V	BTN3A2_ENST00000396948.1_Silent_p.V152V|BTN3A2_ENST00000377708.2_Silent_p.V152V|BTN3A2_ENST00000527422.1_Silent_p.V152V|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000508906.2_Silent_p.V110V|BTN3A2_ENST00000396934.3_Silent_p.V129V	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	152					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						ATCTTCACGTCGAAGTGAAGG	0.512													C|||	422	0.0842652	0.0287	0.0403	5008	,	,		19875	0.1101		0.1123	False		,,,				2504	0.135				p.V152V		Atlas-SNP	.											.	BTN3A2	44	.	0			c.C456T						PASS	.	C	,,,,	168,4238	111.2+/-149.4	2,164,2037	94.0	85.0	88.0		456,456,387,330,456	-5.7	0.0	6	dbSNP_126	88	939,7661	205.9+/-248.2	50,839,3411	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	52,1003,5448	TT,TC,CC		10.9186,3.813,8.5115	,,,,	152/335,152/335,129/312,110/293,152/335	26370572	1107,11899	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			TCACGTCGAAGTG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.456C>T	6.37:g.26370572C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	198	99	0.5	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			C|0.923;T|0.077	0.077	strong		0.512	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
WHAMM	123720	hgsc.bcm.edu	37	15	83481859	83481859	+	Missense_Mutation	SNP	T	T	A	rs76374995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:83481859T>A	ENST00000286760.4	+	2	713	c.614T>A	c.(613-615)aTt>aAt	p.I205N		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	205	Mediates association with membranes. {ECO:0000269|PubMed:18614018}.				actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)			endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						TTCTAGGTTATTCAAGGACAC	0.378													T|||	93	0.0185703	0.0182	0.0014	5008	,	,		17109	0.0575		0.005	False		,,,				2504	0.0051				p.I205N		Atlas-SNP	.											.	WHAMM	63	.	0			c.T614A						PASS	.	T	ASN/ILE	48,3680		0,48,1816	75.0	63.0	67.0		614	4.4	0.2	15	dbSNP_131	67	73,8153		1,71,4041	yes	missense	WHAMM	NM_001080435.1	149	1,119,5857	AA,AT,TT		0.8874,1.2876,1.0122	possibly-damaging	205/810	83481859	121,11833	1864	4113	5977	SO:0001583	missense	123720	exon2			AGGTTATTCAAGG	AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"""WAS protein homology region 2 domain containing 1"""	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.614T>A	15.37:g.83481859T>A	ENSP00000286760:p.Ile205Asn	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	284	127	0.447183	NM_001080435	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	37	CCDS45333.1	48	0.02197802197802198	7	0.014227642276422764	0	0.0	36	0.06293706293706294	5	0.006596306068601583	T	15.46	2.841544	0.51057	0.012876	0.008874	ENSG00000156232	ENST00000286760;ENST00000234505	T	0.07021	3.23	4.42	4.42	0.53409	.	0.213738	0.40818	N	0.001014	T	0.00967	0.0032	N	0.22421	0.69	0.34133	D	0.665434	P	0.42649	0.786	P	0.47251	0.542	T	0.16719	-1.0393	10	0.87932	D	0	.	12.9808	0.58562	0.0:0.0:0.0:1.0	.	205	Q8TF30	WHAMM_HUMAN	N	205	ENSP00000286760:I205N	ENSP00000234505:I205N	I	+	2	0	WHAMM	81278913	1.000000	0.71417	0.186000	0.23195	0.341000	0.28922	5.129000	0.64739	1.855000	0.53841	0.533000	0.62120	ATT	T|0.982;A|0.018	0.018	strong		0.378	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
ATP13A1	57130	hgsc.bcm.edu	37	19	19758522	19758522	+	Silent	SNP	T	T	C	rs142259293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19758522T>C	ENST00000357324.6	-	20	2705	c.2679A>G	c.(2677-2679)cgA>cgG	p.R893R	ATP13A1_ENST00000291503.5_Silent_p.R775R	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	893	Poly-Arg.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.R893R(2)		central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GGGGCCGCCGTCGCCGCTCGA	0.701													T|||	39	0.00778754	0.0008	0.0187	5008	,	,		12844	0.0		0.0239	False		,,,				2504	0.001				p.R893R	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											ATP13A1,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,2	ATP13A1	82	2	2	Substitution - coding silent(2)	central_nervous_system(1)|skin(1)	c.A2679G						PASS	.	T		11,4393		0,11,2191	17.0	17.0	17.0		2679	-10.5	0.6	19	dbSNP_134	17	165,8431		2,161,4135	no	coding-synonymous	ATP13A1	NM_020410.2		2,172,6326	CC,CT,TT		1.9195,0.2498,1.3538		893/1205	19758522	176,12824	2202	4298	6500	SO:0001819	synonymous_variant	57130	exon20			CCGCCGTCGCCGC	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"""ATPases / P-type"""	24215	protein-coding gene	gene with protein product	"""cation transporting ATPase"""		"""ATPase type 13A"""	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.2679A>G	19.37:g.19758522T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Silent	SNP	ENST00000357324.6	37	CCDS32970.2																																																																																			T|0.989;C|0.011	0.011	strong		0.701	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410	
OR5H15	403274	hgsc.bcm.edu	37	3	97888337	97888337	+	Missense_Mutation	SNP	C	C	T	rs13082608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:97888337C>T	ENST00000356526.2	+	1	794	c.794C>T	c.(793-795)cCg>cTg	p.P265L		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						CCTGCATCTCCGCAAGCAGAT	0.438													C|||	1563	0.312101	0.2534	0.3444	5008	,	,		15123	0.4782		0.1819	False		,,,				2504	0.3313				p.P265L		Atlas-SNP	.											.	OR5H15	70	.	0			c.C794T						PASS	.	C	LEU/PRO	1035,3371		113,809,1281	86.0	90.0	88.0		794	0.3	0.0	3	dbSNP_121	88	1565,7035		140,1285,2875	yes	missense	OR5H15	NM_001005515.1	98	253,2094,4156	TT,TC,CC		18.1977,23.4907,19.9908	benign	265/314	97888337	2600,10406	2203	4300	6503	SO:0001583	missense	403274	exon1			CATCTCCGCAAGC		CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"""GPCR / Class A : Olfactory receptors"""	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.794C>T	3.37:g.97888337C>T	ENSP00000373195:p.Pro265Leu	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	244	120	0.491803	NM_001005515		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	675	0.3090659340659341	127	0.258130081300813	93	0.2569060773480663	309	0.5402097902097902	146	0.19261213720316622	-	3.880	-0.026185	0.07589	0.234907	0.181977	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.00069	8.77	2.48	0.278	0.15673	GPCR, rhodopsin-like superfamily (1);	1.334550	0.05193	N	0.503515	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.18166	0.026	B	0.13407	0.009	T	0.01675	-1.1298	9	0.42905	T	0.14	.	5.1938	0.15225	0.0:0.6419:0.2131:0.1451	rs13082608	265	A6NDH6	O5H15_HUMAN	L	265	ENSP00000373195:P265L	ENSP00000373195:P265L	P	+	2	0	OR5H15	99371027	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.925000	0.00691	0.370000	0.24538	0.184000	0.17185	CCG	C|0.771;T|0.229	0.229	strong		0.438	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1		
SIGLEC5	8778	hgsc.bcm.edu	37	19	52132668	52132668	+	Missense_Mutation	SNP	T	T	C	rs34553740		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52132668T>C	ENST00000534261.2	-	4	1042	c.643A>G	c.(643-645)Atg>Gtg	p.M215V	SIGLEC5_ENST00000570106.2_Missense_Mutation_p.M215V|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.M215V|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.M215V|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.M215V			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	215	Ig-like C2-type 1.		M -> V (in dbSNP:rs1807124).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.M215V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGGCGTTTCATCTGACAGGTG	0.637																																					p.M215V		Atlas-SNP	.											SIGLEC5,NS,carcinoma,0,1	SIGLEC5	67	1	1	Substitution - Missense(1)	prostate(1)	c.A643G						scavenged	.						122.0	109.0	113.0					19																	52132668		2203	4300	6503	SO:0001583	missense	8778	exon3			GTTTCATCTGACA	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.643A>G	19.37:g.52132668T>C	ENSP00000473238:p.Met215Val	Somatic	877	0	0		WXS	Illumina HiSeq	Phase_I	922	13	0.0140998	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.691237	0.00731	.	.	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.02050	4.48;4.48	3.69	2.65	0.31530	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.42682	N	0.000676	T	0.00412	0.0013	N	0.00023	-2.71	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44651	-0.9314	10	0.02654	T	1	.	6.1979	0.20559	0.0:0.7599:0.0:0.2401	rs34553740	215	O15389	SIGL5_HUMAN	V	215	ENSP00000222107:M215V;ENSP00000415200:M215V	ENSP00000222107:M215V	M	-	1	0	SIGLEC5	56824480	0.020000	0.18652	0.004000	0.12327	0.034000	0.12701	1.066000	0.30604	0.367000	0.24454	-0.320000	0.08662	ATG	.	.	weak		0.637	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
ZNF621	285268	hgsc.bcm.edu	37	3	40574395	40574395	+	Silent	SNP	C	C	T	rs151057224		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:40574395C>T	ENST00000339296.5	+	5	1586	c.1134C>T	c.(1132-1134)gcC>gcT	p.A378A	ZNF621_ENST00000431278.1_Silent_p.A267A|ZNF621_ENST00000490457.1_Intron|ZNF621_ENST00000403205.2_Silent_p.A378A|ZNF621_ENST00000310898.1_Intron	NM_198484.3	NP_940886.1	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		ctgcttcagccgtagctgtgc	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19238	0.0		0.0	False		,,,				2504	0.0				p.A378A		Atlas-SNP	.											.	ZNF621	42	.	0			c.C1134T						PASS	.	C	,	3,4397		0,3,2197	102.0	72.0	82.0		1134,1134	-6.8	0.0	3	dbSNP_134	82	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous	ZNF621	NM_001098414.1,NM_198484.3	,	0,4,6494	TT,TC,CC		0.0116,0.0682,0.0308	,	378/440,378/440	40574395	4,12992	2200	4298	6498	SO:0001819	synonymous_variant	285268	exon5			TTCAGCCGTAGCT	AK127181	CCDS2693.1, CCDS74920.1	3p21.33	2013-01-08			ENSG00000172888	ENSG00000172888		"""Zinc fingers, C2H2-type"", ""-"""	24787	protein-coding gene	gene with protein product							Standard	XM_005265079		Approved	FLJ45246	uc003ckm.2	Q6ZSS3	OTTHUMG00000131389	ENST00000339296.5:c.1134C>T	3.37:g.40574395C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	162	55	0.339506	NM_001098414	Q14DC7|Q8TE91	Silent	SNP	ENST00000339296.5	37	CCDS2693.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	ZNF621-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254178.2	NM_198484	
PFAS	5198	hgsc.bcm.edu	37	17	8161149	8161149	+	Missense_Mutation	SNP	C	C	T	rs4791641	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8161149C>T	ENST00000314666.6	+	10	1233	c.1100C>T	c.(1099-1101)cCa>cTa	p.P367L	PFAS_ENST00000545834.1_5'UTR	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	367			P -> L (in dbSNP:rs4791641). {ECO:0000269|PubMed:10548741, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9205841}.		'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	TGGGAGGATCCAAGCTTCCAG	0.537													C|||	1697	0.338858	0.2292	0.3184	5008	,	,		17331	0.2272		0.5288	False		,,,				2504	0.4213				p.P367L		Atlas-SNP	.											.	PFAS	91	.	0			c.C1100T	GRCh37	CM067707	PFAS	M	rs4791641	PASS	.	C	LEU/PRO	1230,3176	424.0+/-340.3	160,910,1133	62.0	61.0	61.0		1100	4.8	0.4	17	dbSNP_111	61	4203,4397	569.3+/-389.2	1039,2125,1136	yes	missense	PFAS	NM_012393.2	98	1199,3035,2269	TT,TC,CC		48.8721,27.9165,41.773	possibly-damaging	367/1339	8161149	5433,7573	2203	4300	6503	SO:0001583	missense	5198	exon10			AGGATCCAAGCTT	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.1100C>T	17.37:g.8161149C>T	ENSP00000313490:p.Pro367Leu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	134	69	0.514925	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	774	0.3543956043956044	107	0.21747967479674796	131	0.36187845303867405	124	0.21678321678321677	412	0.5435356200527705	C	14.18	2.458258	0.43634	0.279165	0.488721	ENSG00000178921	ENST00000314666	T	0.40225	1.04	5.79	4.82	0.62117	PurM, N-terminal-like (1);AIR synthase-related protein (1);	0.260679	0.39407	N	0.001378	T	0.00012	0.0000	L	0.49640	1.575	0.09310	P	0.999999651095	B	0.02656	0.0	B	0.09377	0.004	T	0.43393	-0.9394	9	0.87932	D	0	-4.4143	12.4284	0.55561	0.0:0.9191:0.0:0.0809	rs4791641;rs4791641	367	O15067	PUR4_HUMAN	L	367	ENSP00000313490:P367L	ENSP00000313490:P367L	P	+	2	0	PFAS	8101874	0.006000	0.16342	0.408000	0.26446	0.975000	0.68041	1.652000	0.37313	1.467000	0.48044	0.561000	0.74099	CCA	C|0.624;T|0.376	0.376	strong		0.537	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
TPCN2	219931	hgsc.bcm.edu	37	11	68840160	68840160	+	Missense_Mutation	SNP	A	A	G	rs3750965	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:68840160A>G	ENST00000294309.3	+	12	1228	c.1127A>G	c.(1126-1128)aAa>aGa	p.K376R	TPCN2_ENST00000542467.1_Missense_Mutation_p.K376R|TPCN2_ENST00000442692.2_Intron	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	376			K -> R (in dbSNP:rs3750965).		calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGCTCCCACAAACAGGCCATG	0.632													A|||	1456	0.290735	0.2322	0.1945	5008	,	,		15326	0.2063		0.3032	False		,,,				2504	0.5123				p.K376R		Atlas-SNP	.											TPCN2,colon,carcinoma,0,1	TPCN2	63	1	0			c.A1127G						PASS	.	A	ARG/LYS	1078,3322	387.7+/-326.6	133,812,1255	51.0	49.0	50.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1127	2.6	0.0	11	dbSNP_107	50	2710,5878	429.7+/-356.3	408,1894,1992	yes	missense	TPCN2	NM_139075.3	26	541,2706,3247	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	31.5557,24.5,29.1654	benign	376/753	68840160	3788,9200	2200	4294	6494	SO:0001583	missense	219931	exon12			CCCACAAACAGGC	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1127A>G	11.37:g.68840160A>G	ENSP00000294309:p.Lys376Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	138	136	0.985507	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	37	CCDS8189.1	558	0.2554945054945055	104	0.21138211382113822	83	0.2292817679558011	135	0.23601398601398602	236	0.3113456464379947	A	0.628	-0.818239	0.02776	0.245	0.315557	ENSG00000162341	ENST00000294309;ENST00000535009;ENST00000542467	D;D	0.96913	-4.16;-4.17	4.94	2.61	0.31194	.	0.188884	0.44688	N	0.000427	T	0.00039	0.0001	M	0.64997	1.995	0.33812	P	0.37205200000000005	B;B;B	0.33379	0.287;0.287;0.41	B;B;B	0.29524	0.048;0.048;0.103	T	0.00862	-1.1536	9	0.25106	T	0.35	-5.9663	6.5291	0.22316	0.8026:0.0:0.1974:0.0	rs3750965;rs57180849;rs3750965	376;376;291	E7ETX0;Q8NHX9;F5H1G5	.;TPC2_HUMAN;.	R	376;291;376	ENSP00000294309:K376R;ENSP00000445551:K376R	ENSP00000294309:K376R	K	+	2	0	TPCN2	68596736	0.057000	0.20700	0.030000	0.17652	0.117000	0.20001	0.272000	0.18644	0.327000	0.23409	0.459000	0.35465	AAA	A|0.718;G|0.282	0.282	strong		0.632	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
KLK3	354	hgsc.bcm.edu	37	19	51359503	51359503	+	Silent	SNP	A	A	G	rs1135766	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51359503A>G	ENST00000326003.2	+	2	95	c.54A>G	c.(52-54)gcA>gcG	p.A18A	KLK3_ENST00000593997.1_Silent_p.A18A|KLK3_ENST00000595952.1_Silent_p.A18A|KLK3_ENST00000597483.1_Silent_p.A18A|KLK3_ENST00000360617.3_Silent_p.A18A	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	18					cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		CAGGTGCTGCACCCCTCATCC	0.592													a|||	1702	0.339856	0.1921	0.4914	5008	,	,		19322	0.4851		0.4195	False		,,,				2504	0.2004				p.A18A	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											KLK3_ENST00000360617,colon,carcinoma,0,2	KLK3	76	2	0			c.A54G						PASS	.	G	,,,	1071,3335	391.4+/-328.1	140,791,1272	96.0	86.0	89.0		54,54,54,54	-4.2	0.0	19	dbSNP_86	89	3585,5015	518.6+/-379.3	765,2055,1480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLK3	NM_001030047.1,NM_001030048.1,NM_001030050.1,NM_001648.2	,,,	905,2846,2752	GG,GA,AA		41.686,24.3078,35.7989	,,,	18/239,18/219,18/70,18/262	51359503	4656,8350	2203	4300	6503	SO:0001819	synonymous_variant	354	exon2			TGCTGCACCCCTC	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.54A>G	19.37:g.51359503A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	142	75	0.528169	NM_001030050	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			A|0.599;C|0.019	.	strong		0.592	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
ITPR2	3709	hgsc.bcm.edu	37	12	26834858	26834858	+	Missense_Mutation	SNP	G	G	A	rs2230384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:26834858G>A	ENST00000381340.3	-	13	1774	c.1358C>T	c.(1357-1359)gCg>gTg	p.A453V		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	453			A -> V (in dbSNP:rs41453348).		activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	AACTGTGGTCGCTAGTACTTT	0.388													G|||	50	0.00998403	0.0023	0.0072	5008	,	,		19464	0.0		0.0408	False		,,,				2504	0.001				p.A453V		Atlas-SNP	.											.	ITPR2	270	.	0			c.C1358T						PASS	.	G	VAL/ALA	31,3647		0,31,1808	200.0	185.0	190.0		1358	4.2	0.9	12	dbSNP_127	190	379,7819		7,365,3727	yes	missense	ITPR2	NM_002223.2	64	7,396,5535	AA,AG,GG		4.6231,0.8428,3.4523	benign	453/2702	26834858	410,11466	1839	4099	5938	SO:0001583	missense	3709	exon13			GTGGTCGCTAGTA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1358C>T	12.37:g.26834858G>A	ENSP00000370744:p.Ala453Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	31	0.014194139194139194	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	29	0.03825857519788918	G	17.28	3.349134	0.61183	0.008428	0.046231	ENSG00000123104	ENST00000381340	D	0.89050	-2.46	5.09	4.16	0.48862	.	0.053073	0.85682	D	0.000000	T	0.59959	0.2232	L	0.46157	1.445	0.80722	D	1	P	0.52061	0.95	P	0.47075	0.536	T	0.74951	-0.3489	10	0.30854	T	0.27	.	15.7357	0.77842	0.0:0.1361:0.8639:0.0	rs61728395	453	Q14571	ITPR2_HUMAN	V	453	ENSP00000370744:A453V	ENSP00000370744:A453V	A	-	2	0	ITPR2	26726125	1.000000	0.71417	0.850000	0.33497	0.953000	0.61014	4.535000	0.60629	2.630000	0.89119	0.650000	0.86243	GCG	G|0.975;A|0.025	0.025	strong		0.388	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
SDCBP2	27111	hgsc.bcm.edu	37	20	1293046	1293046	+	Missense_Mutation	SNP	G	G	A	rs1048621	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1293046G>A	ENST00000360779.3	-	7	840	c.667C>T	c.(667-669)Cgc>Tgc	p.R223C	SDCBP2_ENST00000339987.3_Missense_Mutation_p.R223C|SDCBP2_ENST00000467129.1_5'Flank|SDCBP2_ENST00000381808.3_Missense_Mutation_p.R138C|SDCBP2_ENST00000381812.1_Missense_Mutation_p.R223C	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	223	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.		R -> C (in dbSNP:rs1048621).		intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						AGCCCGTTGCGGGCCGCAGAA	0.612													G|||	680	0.135783	0.149	0.1974	5008	,	,		19368	0.0208		0.2247	False		,,,				2504	0.1012				p.R223C		Atlas-SNP	.											.	SDCBP2	78	.	0			c.C667T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	737,3669	300.4+/-286.3	59,619,1525	77.0	62.0	67.0		667,412,667	2.8	1.0	20	dbSNP_86	67	2320,6280	380.0+/-339.5	312,1696,2292	yes	missense,missense,missense	SDCBP2	NM_001199784.1,NM_015685.5,NM_080489.4	180,180,180	371,2315,3817	AA,AG,GG		26.9767,16.7272,23.5045	probably-damaging,probably-damaging,probably-damaging	223/293,138/208,223/293	1293046	3057,9949	2203	4300	6503	SO:0001583	missense	27111	exon7			CGTTGCGGGCCGC	AF131809	CCDS13013.1, CCDS42848.1	20p13	2008-07-02			ENSG00000125775	ENSG00000125775			15756	protein-coding gene	gene with protein product						11152476	Standard	NM_080489		Approved	ST-2, SITAC18	uc021vzn.1	Q9H190	OTTHUMG00000031661	ENST00000360779.3:c.667C>T	20.37:g.1293046G>A	ENSP00000354013:p.Arg223Cys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	103	62	0.601942	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	37	CCDS42848.1	310	0.14194139194139194	61	0.12398373983739837	77	0.212707182320442	12	0.02097902097902098	160	0.21108179419525067	g	19.83	3.900364	0.72754	0.167272	0.269767	ENSG00000125775	ENST00000381812;ENST00000381808;ENST00000360779;ENST00000339987	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	4.7	2.75	0.32379	PDZ/DHR/GLGF (4);	0.133760	0.51477	N	0.000093	T	0.00012	0.0000	M	0.93197	3.39	0.09310	P	0.999999283908	D	0.62365	0.991	P	0.55508	0.777	T	0.05068	-1.0908	9	0.87932	D	0	-22.5959	5.8309	0.18581	0.163:0.0:0.6836:0.1534	rs1048621;rs3188641;rs17718154;rs52811665;rs59907914;rs1048621	223	Q9H190	SDCB2_HUMAN	C	223;138;223;223	ENSP00000371233:R223C;ENSP00000371229:R138C;ENSP00000354013:R223C;ENSP00000342935:R223C	ENSP00000342935:R223C	R	-	1	0	SDCBP2	1241046	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.735000	0.55044	0.582000	0.29556	-0.291000	0.09656	CGC	G|0.816;A|0.184	0.184	strong		0.612	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489	
POR	5447	hgsc.bcm.edu	37	7	75615287	75615287	+	Silent	SNP	G	G	A	rs1057870	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:75615287G>A	ENST00000461988.1	+	14	1821	c.1716G>A	c.(1714-1716)tcG>tcA	p.S572S	TMEM120A_ENST00000493111.2_RNA|POR_ENST00000545601.1_Silent_p.S380S|TMEM120A_ENST00000338761.4_RNA|POR_ENST00000394893.1_Silent_p.S572S|POR_ENST00000419840.1_Intron|POR_ENST00000439269.1_Silent_p.S310S|POR_ENST00000450476.1_Silent_p.S471S	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	569					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GCCGCCGCTCGGATGAGGACT	0.697													G|||	978	0.195288	0.1256	0.2133	5008	,	,		15903	0.0377		0.341	False		,,,				2504	0.2894				p.S572S		Atlas-SNP	.											.	POR	46	.	0			c.G1716A						PASS	.	G		610,3330		41,528,1401	10.0	16.0	14.0		1716	-7.2	0.0	7	dbSNP_86	14	2849,5335		524,1801,1767	no	coding-synonymous	POR	NM_000941.2		565,2329,3168	AA,AG,GG		34.8118,15.4822,28.5302		572/681	75615287	3459,8665	1970	4092	6062	SO:0001819	synonymous_variant	5447	exon14			CCGCTCGGATGAG	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1716G>A	7.37:g.75615287G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	37	CCDS5579.1	402	0.18406593406593408	53	0.10772357723577236	79	0.21823204419889503	20	0.03496503496503497	250	0.32981530343007914	G	4.067	0.010290	0.07912	0.154822	0.348118	ENSG00000127948	ENST00000447222	.	.	.	3.59	-7.18	0.01505	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.4999999999987246E-5	.	.	.	.	.	.	T	0.15752	-1.0426	3	.	.	.	-21.412	3.4043	0.07335	0.339:0.1397:0.4265:0.0949	rs1057870;rs2228105;rs3198404;rs10954733;rs11540676;rs17148959;rs56753821;rs1057870	.	.	.	R	623	.	.	G	+	1	0	POR	75453223	0.000000	0.05858	0.020000	0.16555	0.705000	0.40729	-2.390000	0.01057	-3.492000	0.00153	-2.868000	0.00100	GGA	G|0.826;A|0.174	0.174	strong		0.697	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
DNAJC1	64215	hgsc.bcm.edu	37	10	22048330	22048330	+	Silent	SNP	C	C	T	rs9045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:22048330C>T	ENST00000376980.3	-	11	1655	c.1365G>A	c.(1363-1365)gcG>gcA	p.A455A	DNAJC1_ENST00000483085.1_5'Flank	NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	455					negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				GCTCCGGCTTCGCTGTAGCCT	0.627													C|||	629	0.125599	0.0061	0.1427	5008	,	,		16995	0.2242		0.169	False		,,,				2504	0.1288				p.A455A		Atlas-SNP	.											DNAJC1,colon,carcinoma,0,2	DNAJC1	42	2	0			c.G1365A						PASS	.	C		168,4238	111.2+/-149.4	4,160,2039	60.0	61.0	61.0		1365	-10.0	0.0	10	dbSNP_52	61	1451,7149	277.5+/-292.9	126,1199,2975	no	coding-synonymous	DNAJC1	NM_022365.3		130,1359,5014	TT,TC,CC		16.8721,3.813,12.4481		455/555	22048330	1619,11387	2203	4300	6503	SO:0001819	synonymous_variant	64215	exon11			CGGCTTCGCTGTA	AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"""Heat shock proteins / DNAJ (HSP40)"""	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.1365G>A	10.37:g.22048330C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	172	86	0.5	NM_022365	B0YIZ8|Q5VX89|Q9H6B8	Silent	SNP	ENST00000376980.3	37	CCDS7136.1																																																																																			C|0.861;T|0.139	0.139	strong		0.627	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365	
POTEF	728378	hgsc.bcm.edu	37	2	130832762	130832762	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130832762T>C	ENST00000409914.2	-	17	2682	c.2283A>G	c.(2281-2283)aaA>aaG	p.K761K	POTEF_ENST00000357462.5_Silent_p.K761K	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	761	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K761K(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GGATGCCTCTTTTGCTCTGGG	0.582																																					p.K761K		Atlas-SNP	.											POTEF,NS,carcinoma,0,1	POTEF	140	1	1	Substitution - coding silent(1)	prostate(1)	c.A2283G						scavenged	.																																			SO:0001819	synonymous_variant	728378	exon17			GCCTCTTTTGCTC	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2283A>G	2.37:g.130832762T>C		Somatic	456	0	0		WXS	Illumina HiSeq	Phase_I	477	26	0.0545073	NM_001099771	A6NC34	Silent	SNP	ENST00000409914.2	37	CCDS46409.1																																																																																			.	.	weak		0.582	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
NLRP13	126204	hgsc.bcm.edu	37	19	56419263	56419263	+	Missense_Mutation	SNP	T	T	C	rs17711239	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56419263T>C	ENST00000342929.3	-	7	2341	c.2342A>G	c.(2341-2343)aAc>aGc	p.N781S	NLRP13_ENST00000588751.1_Missense_Mutation_p.N781S	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	781			N -> S (in dbSNP:rs17711239).				ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CAGCTTGCTGTTACCCTGAAG	0.493													T|||	600	0.119808	0.1384	0.0836	5008	,	,		17023	0.119		0.0974	False		,,,				2504	0.1442				p.N781S		Atlas-SNP	.											.	NLRP13	220	.	0			c.A2342G						PASS	.	T	SER/ASN	584,3822	258.9+/-262.7	37,510,1656	152.0	138.0	143.0		2342	1.1	0.0	19	dbSNP_123	143	880,7720	199.0+/-243.2	44,792,3464	yes	missense	NLRP13	NM_176810.2	46	81,1302,5120	CC,CT,TT		10.2326,13.2547,11.2563	possibly-damaging	781/1044	56419263	1464,11542	2203	4300	6503	SO:0001583	missense	126204	exon7			TTGCTGTTACCCT	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2342A>G	19.37:g.56419263T>C	ENSP00000343891:p.Asn781Ser	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_176810	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	227	0.10393772893772894	63	0.12804878048780488	32	0.08839779005524862	56	0.0979020979020979	76	0.10026385224274406	T	9.651	1.141650	0.21205	0.132547	0.102326	ENSG00000173572	ENST00000342929	T	0.53857	0.6	2.18	1.15	0.20763	.	.	.	.	.	T	0.00754	0.0025	L	0.48642	1.525	0.80722	P	0.0	P	0.41673	0.759	P	0.53490	0.727	T	0.14144	-1.0483	8	0.48119	T	0.1	.	3.8947	0.09135	0.0:0.1862:0.0:0.8138	rs17711239;rs52831891;rs61233957;rs17711239	781	Q86W25	NAL13_HUMAN	S	781	ENSP00000343891:N781S	ENSP00000343891:N781S	N	-	2	0	NLRP13	61111075	0.000000	0.05858	0.004000	0.12327	0.025000	0.11179	0.327000	0.19663	0.309000	0.22966	-0.334000	0.08254	AAC	C|0.112;N|0.000	0.112	strong		0.493	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
CENPU	79682	hgsc.bcm.edu	37	4	185650154	185650154	+	Silent	SNP	G	G	A	rs6818447	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:185650154G>A	ENST00000281453.5	-	3	202	c.132C>T	c.(130-132)ttC>ttT	p.F44F	MLF1IP_ENST00000541971.1_Silent_p.F44F	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		CAGGAAAGTCGAACACGTCAA	0.368													G|||	724	0.144569	0.295	0.1354	5008	,	,		19297	0.001		0.1481	False		,,,				2504	0.092				p.F44F		Atlas-SNP	.											.	MLF1IP	33	.	0			c.C132T						PASS	.	G		1187,3219	415.9+/-337.4	159,869,1175	95.0	96.0	95.0		132	-2.2	0.6	4	dbSNP_116	95	1406,7194	270.9+/-289.3	116,1174,3010	no	coding-synonymous	MLF1IP	NM_024629.3		275,2043,4185	AA,AG,GG		16.3488,26.9405,19.937		44/419	185650154	2593,10413	2203	4300	6503	SO:0001819	synonymous_variant	79682	exon3			AAAGTCGAACACG																												ENST00000281453.5:c.132C>T	4.37:g.185650154G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	NM_024629		Silent	SNP	ENST00000281453.5	37	CCDS3838.1																																																																																			G|0.823;A|0.177	0.177	strong		0.368	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		
LY75	4065	hgsc.bcm.edu	37	2	160746800	160746800	+	Silent	SNP	T	T	C	rs34592866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160746800T>C	ENST00000263636.4	-	4	753	c.726A>G	c.(724-726)gaA>gaG	p.E242E	LY75_ENST00000554112.1_Silent_p.E242E|LY75-CD302_ENST00000505052.1_Silent_p.E242E|LY75-CD302_ENST00000504764.1_Silent_p.E242E|LY75_ENST00000553424.1_Silent_p.E242E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	242	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AAACATAAGCTTCTTTCCAAG	0.368													T|||	94	0.01877	0.0023	0.0288	5008	,	,		20298	0.0		0.0517	False		,,,				2504	0.0194				p.E242E		Atlas-SNP	.											.	LY75	151	.	0			c.A726G						PASS	.	T	,,	49,4357	48.9+/-83.8	2,45,2156	100.0	104.0	103.0		726,726,726	3.2	1.0	2	dbSNP_126	103	571,8029	153.7+/-208.1	21,529,3750	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	23,574,5906	CC,CT,TT		6.6395,1.1121,4.767	,,	242/1874,242/1818,242/1723	160746800	620,12386	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon4			ATAAGCTTCTTTC	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.726A>G	2.37:g.160746800T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			T|0.962;C|0.038	0.038	strong		0.368	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
TFRC	7037	hgsc.bcm.edu	37	3	195800811	195800811	+	Missense_Mutation	SNP	C	C	T	rs3817672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195800811C>T	ENST00000360110.4	-	4	593	c.424G>A	c.(424-426)Ggc>Agc	p.G142S	TFRC_ENST00000420415.1_Missense_Mutation_p.G61S|TFRC_ENST00000540528.1_3'UTR|RNU7-18P_ENST00000516365.1_RNA|TFRC_ENST00000535031.1_Intron|TFRC_ENST00000392396.3_Missense_Mutation_p.G142S	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	142			G -> S (rare polymorphism; dbSNP:rs3817672). {ECO:0000269|PubMed:11702220, ECO:0000269|PubMed:6090955, ECO:0000269|PubMed:6094009}.		cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	TTGATGGTGCCGGTGAAGTCT	0.502			T	BCL6	NHL						OREG0016005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	1534	0.30631	0.1641	0.3617	5008	,	,		18870	0.1518		0.5427	False		,,,				2504	0.3753				p.G142S		Atlas-SNP	.		Dom	yes		3	3q29	7037	"""transferrin receptor (p90, CD71)"""		L	.	TFRC	54	.	0			c.G424A	GRCh37	CM991171	TFRC	M	rs3817672	PASS	.	C	SER/GLY,SER/GLY	1004,3402	373.7+/-320.9	112,780,1311	76.0	69.0	72.0		424,424	1.5	0.0	3	dbSNP_107	72	4692,3908	605.0+/-394.9	1281,2130,889	yes	missense,missense	TFRC	NM_001128148.1,NM_003234.2	56,56	1393,2910,2200	TT,TC,CC		45.4419,22.7871,43.7952	benign,benign	142/761,142/761	195800811	5696,7310	2203	4300	6503	SO:0001583	missense	7037	exon4			TGGTGCCGGTGAA	X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274		"""CD molecules"""	11763	protein-coding gene	gene with protein product		190010	"""transferrin receptor (p90, CD71)"""				Standard	NM_003234		Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.424G>A	3.37:g.195800811C>T	ENSP00000353224:p.Gly142Ser	Somatic	85	0	0	2078	WXS	Illumina HiSeq	Phase_I	82	48	0.585366	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Missense_Mutation	SNP	ENST00000360110.4	37	CCDS3312.1	718	0.32875457875457875	83	0.16869918699186992	138	0.3812154696132597	83	0.1451048951048951	414	0.5461741424802111	c	7.704	0.693807	0.15039	0.227871	0.545581	ENSG00000072274	ENST00000360110;ENST00000420415;ENST00000392396	T;T;T	0.38240	1.15;1.15;1.15	5.2	1.51	0.23008	.	1.393470	0.03757	N	0.257483	T	0.00012	0.0000	N	0.00729	-1.24	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.43196	-0.9406	9	0.12103	T	0.63	0.58	6.9135	0.24347	0.0:0.2856:0.0:0.7144	rs3817672;rs17196183;rs52799905;rs61158992;rs3817672	142	P02786	TFR1_HUMAN	S	142;61;142	ENSP00000353224:G142S;ENSP00000390133:G61S;ENSP00000376197:G142S	ENSP00000353224:G142S	G	-	1	0	TFRC	197285208	0.000000	0.05858	0.001000	0.08648	0.080000	0.17528	-0.262000	0.08682	0.076000	0.16826	-0.374000	0.07098	GGC	C|0.624;T|0.376	0.376	strong		0.502	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1		
TESK2	10420	hgsc.bcm.edu	37	1	45810865	45810865	+	Missense_Mutation	SNP	G	G	A	rs17853159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45810865G>A	ENST00000372086.3	-	11	1763	c.1363C>T	c.(1363-1365)Cgt>Tgt	p.R455C	TESK2_ENST00000341771.6_Missense_Mutation_p.R426C|TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Missense_Mutation_p.R426C|TESK2_ENST00000538496.1_Missense_Mutation_p.R372C	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	455				R -> C (in Ref. 6; AAH33085). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					GGCAAGGAACGCCACCGGCGA	0.597													G|||	114	0.0227636	0.0015	0.0274	5008	,	,		17513	0.001		0.0626	False		,,,				2504	0.0297				p.R455C		Atlas-SNP	.											.	TESK2	60	.	0			c.C1363T						PASS	.	G	CYS/ARG	52,3806		0,52,1877	57.0	63.0	61.0		1363	4.0	1.0	1	dbSNP_123	61	602,7636		32,538,3549	yes	missense	TESK2	NM_007170.2	180	32,590,5426	AA,AG,GG		7.3076,1.3478,5.4067	benign	455/572	45810865	654,11442	1929	4119	6048	SO:0001583	missense	10420	exon11			AGGAACGCCACCG	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.1363C>T	1.37:g.45810865G>A	ENSP00000361158:p.Arg455Cys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	45	29	0.644444	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Missense_Mutation	SNP	ENST00000372086.3	37	CCDS41323.1	64	0.029304029304029304	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	53	0.06992084432717678	G	6.108	0.388214	0.11581	0.013478	0.073076	ENSG00000070759	ENST00000372084;ENST00000372086;ENST00000372083;ENST00000341771;ENST00000538496	T;T;T;T	0.79352	-1.18;-1.0;-1.18;-1.26	5.89	3.99	0.46301	.	0.275088	0.30781	N	0.008900	T	0.13841	0.0335	L	0.34521	1.04	0.80722	D	1	B;B	0.18741	0.03;0.008	B;B	0.18871	0.023;0.009	T	0.40646	-0.9552	10	0.62326	D	0.03	-4.4219	8.5936	0.33701	0.0724:0.0:0.5295:0.3981	rs17853159	426;455	Q96S53-3;Q96S53	.;TESK2_HUMAN	C	426;455;439;426;372	ENSP00000361156:R426C;ENSP00000361158:R455C;ENSP00000343940:R426C;ENSP00000441746:R372C	ENSP00000343940:R426C	R	-	1	0	TESK2	45583452	1.000000	0.71417	0.998000	0.56505	0.026000	0.11368	4.339000	0.59322	0.800000	0.34041	-0.320000	0.08662	CGT	G|0.952;A|0.048	0.048	strong		0.597	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170	
GET4	51608	hgsc.bcm.edu	37	7	930608	930608	+	Silent	SNP	G	G	A	rs11543223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:930608G>A	ENST00000265857.3	+	5	604	c.510G>A	c.(508-510)gcG>gcA	p.A170A	GET4_ENST00000407192.1_Silent_p.A117A	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	170					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TGCACTCAGCGGACGGGGAGG	0.502													G|||	291	0.058107	0.1172	0.0346	5008	,	,		22241	0.0		0.0765	False		,,,				2504	0.0358				p.A170A		Atlas-SNP	.											.	GET4	17	.	0			c.G510A						PASS	.	G		569,3837	252.7+/-259.0	35,499,1669	136.0	124.0	128.0		510	-10.2	0.0	7	dbSNP_120	128	577,8023	155.5+/-209.5	21,535,3744	no	coding-synonymous	GET4	NM_015949.2		56,1034,5413	AA,AG,GG		6.7093,12.9142,8.8113		170/328	930608	1146,11860	2203	4300	6503	SO:0001819	synonymous_variant	51608	exon5			CTCAGCGGACGGG	AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"""CGI-20 protein"", ""conserved edge protein"", ""transmembrane domain recognition complex, 35kDa"""	612056	"""chromosome 7 open reading frame 20"""	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.510G>A	7.37:g.930608G>A		Somatic	288	1	0.00347222		WXS	Illumina HiSeq	Phase_I	318	147	0.462264	NM_015949	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Silent	SNP	ENST00000265857.3	37	CCDS5317.1																																																																																			G|0.921;A|0.079	0.079	strong		0.502	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949	
GBP3	2635	hgsc.bcm.edu	37	1	89478868	89478868	+	Splice_Site	SNP	G	G	A	rs113490655	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89478868G>A	ENST00000370481.4	-	6	1088	c.868C>T	c.(868-870)Cgt>Tgt	p.R290C	GBP3_ENST00000475853.2_5'Flank	NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	324	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.R290C(1)		breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		GGGGACTTACGAGGCCCATTG	0.463													.|||	676	0.134984	0.0098	0.1513	5008	,	,		19236	0.1677		0.1879	False		,,,				2504	0.2045				p.R290C		Atlas-SNP	.											GBP3,NS,carcinoma,0,1	GBP3	53	1	1	Substitution - Missense(1)	stomach(1)	c.C868T						PASS	.	G	CYS/ARG	185,4221	119.6+/-157.3	5,175,2023	112.0	102.0	106.0		868	3.8	0.8	1	dbSNP_132	106	1661,6939	308.0+/-308.7	156,1349,2795	yes	missense-near-splice	GBP3	NM_018284.2	180	161,1524,4818	AA,AG,GG		19.314,4.1988,14.1934	possibly-damaging	290/596	89478868	1846,11160	2203	4300	6503	SO:0001630	splice_region_variant	2635	exon6			ACTTACGAGGCCC	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.868+1C>T	1.37:g.89478868G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	162	97	0.598765	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	309	0.14148351648351648	5	0.01016260162601626	58	0.16022099447513813	92	0.16083916083916083	154	0.20316622691292877	G	18.70	3.680847	0.68042	0.041988	0.19314	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000235878	T	0.02323	4.34	3.85	3.85	0.44370	Guanylate-binding protein, C-terminal (3);	0.289745	0.31188	N	0.008088	T	0.06050	0.0157	M	0.85041	2.73	0.26906	P	0.9670115	D;D	0.58970	0.984;0.965	P;P	0.54210	0.745;0.673	T	0.02632	-1.1131	8	.	.	.	.	11.4749	0.50291	0.0:0.0:1.0:0.0	.	156;290	F6X827;Q9H0R5	.;GBP3_HUMAN	C	258;290;290	ENSP00000359512:R290C	.	R	-	1	0	GBP3	89251456	0.847000	0.29606	0.848000	0.33437	0.401000	0.30781	1.032000	0.30178	2.154000	0.67381	0.514000	0.50259	CGT	G|0.857;A|0.143	0.143	strong		0.463	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	Missense_Mutation
LCT	3938	hgsc.bcm.edu	37	2	136575199	136575199	+	Silent	SNP	G	G	T	rs6719488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:136575199G>T	ENST00000264162.2	-	6	1429	c.1419C>A	c.(1417-1419)ggC>ggA	p.G473G	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	473	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	AGTAGGCAACGCCTGGGAGGC	0.637													G|||	1783	0.35603	0.1195	0.4323	5008	,	,		18831	0.3998		0.5954	False		,,,				2504	0.3303				p.G473G		Atlas-SNP	.											.	LCT	309	.	0			c.C1419A						PASS	.	G		1040,3366		120,800,1283	55.0	49.0	51.0		1419	-11.5	0.0	2	dbSNP_116	51	5998,2602		2180,1638,482	no	coding-synonymous	LCT	NM_002299.2		2300,2438,1765	TT,TG,GG		30.2558,23.6042,45.8865		473/1928	136575199	7038,5968	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon6			GGCAACGCCTGGG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1419C>A	2.37:g.136575199G>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.592;T|0.408	0.408	strong		0.637	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
TMCO3	55002	hgsc.bcm.edu	37	13	114175038	114175038	+	Missense_Mutation	SNP	G	G	A	rs7319493	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:114175038G>A	ENST00000434316.2	+	8	1692	c.1333G>A	c.(1333-1335)Gca>Aca	p.A445T	TMCO3_ENST00000375391.1_Intron|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	445			A -> T (in dbSNP:rs7319493). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			GGGCGCCAGTGCATCTTCTAG	0.473													G|||	960	0.191693	0.205	0.3199	5008	,	,		16465	0.123		0.1302	False		,,,				2504	0.2168				p.A445T		Atlas-SNP	.											.	TMCO3	77	.	0			c.G1333A						PASS	.	G	THR/ALA	929,3477	354.9+/-312.8	100,729,1374	78.0	71.0	73.0		1333	-9.9	0.0	13	dbSNP_116	73	1256,7344	251.8+/-278.1	84,1088,3128	yes	missense	TMCO3	NM_017905.4	58	184,1817,4502	AA,AG,GG		14.6047,21.0849,16.7999	benign	445/678	114175038	2185,10821	2203	4300	6503	SO:0001583	missense	55002	exon8			GCCAGTGCATCTT	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1333G>A	13.37:g.114175038G>A	ENSP00000389399:p.Ala445Thr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	37	CCDS9537.1	349	0.15979853479853479	101	0.20528455284552846	95	0.26243093922651933	62	0.10839160839160839	91	0.12005277044854881	G	5.097	0.203455	0.09704	0.210849	0.146047	ENSG00000150403	ENST00000434316	T	0.15372	2.43	4.94	-9.87	0.00470	Cation/H+ exchanger (1);	0.637765	0.16438	N	0.214420	T	0.00012	0.0000	N	0.11818	0.18	0.46028	P	0.0011799999999999589	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.26430	-1.0103	9	0.13108	T	0.6	-11.3682	2.3263	0.04223	0.244:0.0853:0.3363:0.3343	rs7319493;rs60291985;rs7319493	445;445	Q6UWJ1;Q6UWJ1-2	TMCO3_HUMAN;.	T	445	ENSP00000389399:A445T	ENSP00000389399:A445T	A	+	1	0	TMCO3	113223039	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.505000	0.06367	-5.105000	0.00021	-2.375000	0.00234	GCA	G|0.835;A|0.165	0.165	strong		0.473	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
DES	1674	hgsc.bcm.edu	37	2	220285666	220285666	+	Silent	SNP	G	G	C	rs12920	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220285666G>C	ENST00000373960.3	+	5	1100	c.1014G>C	c.(1012-1014)ctG>ctC	p.L338L		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	338	Coil 2B.|Rod.		L -> R (in MFM1; results in the formation of a filamentous network disrupted by multiple breaks and clumps or large aggregates). {ECO:0000269|PubMed:16865695}.		cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		TTGACGCCCTGAAGGGCACTG	0.592													C|||	1691	0.33766	0.475	0.3444	5008	,	,		19718	0.1835		0.3648	False		,,,				2504	0.2781				p.L338L		Atlas-SNP	.											.	DES	53	.	0			c.G1014C						PASS	.	C		1974,2432	614.6+/-392.4	454,1066,683	77.0	66.0	70.0		1014	2.1	1.0	2	dbSNP_52	70	3054,5546	658.0+/-401.5	564,1926,1810	no	coding-synonymous	DES	NM_001927.3		1018,2992,2493	CC,CG,GG		35.5116,44.8025,38.6591		338/471	220285666	5028,7978	2203	4300	6503	SO:0001819	synonymous_variant	1674	exon5			CGCCCTGAAGGGC	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.1014G>C	2.37:g.220285666G>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Silent	SNP	ENST00000373960.3	37	CCDS33383.1																																																																																			G|0.635;C|0.365	0.365	strong		0.592	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
KRTAP9-4	85280	hgsc.bcm.edu	37	17	39406409	39406409	+	Missense_Mutation	SNP	C	C	A	rs2191379	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39406409C>A	ENST00000334109.2	+	1	471	c.437C>A	c.(436-438)tCc>tAc	p.S146Y		NM_033191.2	NP_149461.2	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4	146	15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].		S -> Y (in dbSNP:rs62065349). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				breast(1)|large_intestine(1)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			ACCTGTGTGTCCAGCTGCTGT	0.552													.|||	3385	0.675919	0.5053	0.8012	5008	,	,		21709	0.631		0.7336	False		,,,				2504	0.8047				p.S146Y		Atlas-SNP	.											.	KRTAP9-4	30	.	0			c.C437A						PASS	.	C	TYR/SER	2292,2114		611,1070,522	169.0	170.0	170.0		437	1.4	0.0	17	dbSNP_96	170	6228,2372		2222,1784,294	no	missense	KRTAP9-4	NM_033191.2	144	2833,2854,816	AA,AC,CC		27.5814,47.98,34.4918	benign	146/155	39406409	8520,4486	2203	4300	6503	SO:0001583	missense	85280	exon1			GTGTGTCCAGCTG	AJ406948	CCDS11386.1	17q21.2	2013-06-25			ENSG00000241595	ENSG00000241595		"""Keratin associated proteins"""	18902	protein-coding gene	gene with protein product						11279113	Standard	NM_033191		Approved	KAP9.4	uc002hwi.3	Q9BYQ2	OTTHUMG00000133438	ENST00000334109.2:c.437C>A	17.37:g.39406409C>A	ENSP00000334922:p.Ser146Tyr	Somatic	452	2	0.00442478		WXS	Illumina HiSeq	Phase_I	426	421	0.988263	NM_033191	Q0VAE3	Missense_Mutation	SNP	ENST00000334109.2	37	CCDS11386.1	1460	0.6684981684981685	257	0.5223577235772358	282	0.7790055248618785	368	0.6433566433566433	553	0.7295514511873351	.	10.72	1.429114	0.25726	0.5202	0.724186	ENSG00000241595	ENST00000334109	T	0.01126	5.3	2.38	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.31769	0.339	B	0.28709	0.093	T	0.01382	-1.1369	8	0.39692	T	0.17	.	4.3378	0.11095	0.0:0.7905:0.0:0.2095	rs62065349	146	Q9BYQ2	KRA94_HUMAN	Y	146	ENSP00000334922:S146Y	ENSP00000334922:S146Y	S	+	2	0	KRTAP9-4	36659935	0.947000	0.32204	0.008000	0.14137	0.507000	0.33981	-0.100000	0.10990	0.535000	0.28714	0.393000	0.25936	TCC	C|0.336;A|0.664	0.664	strong		0.552	KRTAP9-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257306.1		
NOX5	79400	hgsc.bcm.edu	37	15	69325581	69325581	+	Silent	SNP	C	C	T	rs311893	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:69325581C>T	ENST00000388866.3	+	5	860	c.819C>T	c.(817-819)tgC>tgT	p.C273C	NOX5_ENST00000448182.3_Silent_p.C227C|NOX5_ENST00000530406.2_Silent_p.C245C|NOX5_ENST00000455873.3_Silent_p.C238C|NOX5_ENST00000260364.5_Silent_p.C255C	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	273					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						CCAAGGGCTGCGGCCAGTGCC	0.647													C|||	4040	0.806709	0.6157	0.9395	5008	,	,		13939	0.7381		0.9573	False		,,,				2504	0.8865				p.C273C		Atlas-SNP	.											.	NOX5	60	.	0			c.C819T						PASS	.	C	,,	2954,1440		1006,942,249	26.0	26.0	26.0		735,714,819	-2.3	1.0	15	dbSNP_79	26	8236,360		3950,336,12	no	coding-synonymous,coding-synonymous,coding-synonymous	NOX5	NM_001184779.1,NM_001184780.1,NM_024505.3	,,	4956,1278,261	TT,TC,CC		4.188,32.772,13.8568	,,	245/738,238/731,273/766	69325581	11190,1800	2197	4298	6495	SO:0001819	synonymous_variant	79400	exon5			GGGCTGCGGCCAG	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"""EF-hand domain containing"""	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.819C>T	15.37:g.69325581C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Silent	SNP	ENST00000388866.3	37	CCDS32276.2																																																																																			C|0.166;T|0.834	0.834	strong		0.647	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505	
CALHM1	255022	hgsc.bcm.edu	37	10	105218254	105218254	+	Silent	SNP	C	C	T	rs4918016|rs386747134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:105218254C>T	ENST00000329905.5	-	1	391	c.255G>A	c.(253-255)ccG>ccA	p.P85P	RP11-225H22.4_ENST00000411906.1_RNA	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	85					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						GGCGGCCCAGCGGCCGCTTCC	0.672													C|||	1521	0.303714	0.1997	0.4063	5008	,	,		14923	0.4137		0.2992	False		,,,				2504	0.2628				p.P85P		Atlas-SNP	.											.	CALHM1	33	.	0			c.G255A						PASS	.	C		951,3449		112,727,1361	21.0	27.0	25.0		255	-10.8	0.0	10	dbSNP_111	25	2724,5866		440,1844,2011	no	coding-synonymous	CALHM1	NM_001001412.3		552,2571,3372	TT,TC,CC		31.7113,21.6136,28.291		85/347	105218254	3675,9315	2200	4295	6495	SO:0001819	synonymous_variant	255022	exon1			GCCCAGCGGCCGC	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"""family with sequence similarity 26, member C"""	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.255G>A	10.37:g.105218254C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_001001412	Q5W091	Silent	SNP	ENST00000329905.5	37	CCDS7550.1																																																																																			C|0.702;T|0.298	0.298	strong		0.672	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412	
PCDHB13	56123	hgsc.bcm.edu	37	5	140594466	140594466	+	Silent	SNP	G	G	A	rs17844608		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140594466G>A	ENST00000341948.4	+	1	958	c.771G>A	c.(769-771)ccG>ccA	p.P257P		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	257	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGACAGTCCGGTAGGCTTCC	0.493																																					p.P257P		Atlas-SNP	.											PCDHB13,rectum,carcinoma,+1,1	PCDHB13	142	1	0			c.G771A						scavenged	.						174.0	172.0	173.0					5																	140594466		2203	4300	6503	SO:0001819	synonymous_variant	56123	exon1			CAGTCCGGTAGGC	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.771G>A	5.37:g.140594466G>A		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	291	27	0.0927835	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			.	.	weak		0.493	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
NRAP	4892	hgsc.bcm.edu	37	10	115410234	115410234	+	Missense_Mutation	SNP	T	T	C	rs2185913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115410234T>C	ENST00000359988.3	-	8	990	c.746A>G	c.(745-747)tAt>tGt	p.Y249C	NRAP_ENST00000369360.3_Missense_Mutation_p.Y249C|NRAP_ENST00000360478.3_Missense_Mutation_p.Y249C|NRAP_ENST00000369358.4_Missense_Mutation_p.Y249C	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.Y249C(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GGCTATCTGATAGGCGGGTGT	0.458													T|||	1019	0.203474	0.0182	0.245	5008	,	,		22449	0.3343		0.3012	False		,,,				2504	0.1892				p.Y249C		Atlas-SNP	.											NRAP,NS,carcinoma,0,1	NRAP	208	1	1	Substitution - Missense(1)	stomach(1)	c.A746G						PASS	.	T	CYS/TYR,CYS/TYR	256,4150	148.0+/-182.4	12,232,1959	193.0	156.0	169.0		746,746	6.2	1.0	10	dbSNP_96	169	2512,6088	411.5+/-350.5	351,1810,2139	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	194,194	363,2042,4098	CC,CT,TT		29.2093,5.8103,21.2825	probably-damaging,probably-damaging	249/1696,249/1731	115410234	2768,10238	2203	4300	6503	SO:0001583	missense	4892	exon8			ATCTGATAGGCGG		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.746A>G	10.37:g.115410234T>C	ENSP00000353078:p.Tyr249Cys	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	216	113	0.523148	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	531	0.24313186813186813	14	0.028455284552845527	100	0.27624309392265195	199	0.3479020979020979	218	0.287598944591029	T	24.3	4.512888	0.85389	0.058103	0.292093	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.20463	2.32;2.25;2.18;2.07	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.79123	2.44	0.18873	P	0.9999877178	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.10683	-1.0619	9	0.66056	D	0.02	.	16.8222	0.85835	0.0:0.0:0.0:1.0	rs2185913;rs17773512;rs59388325;rs2185913	249;249	Q86VF7-4;Q86VF7	.;NRAP_HUMAN	C	249	ENSP00000358365:Y249C;ENSP00000358367:Y249C;ENSP00000353078:Y249C;ENSP00000353666:Y249C	ENSP00000353078:Y249C	Y	-	2	0	NRAP	115400224	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.283000	0.78640	2.371000	0.80710	0.533000	0.62120	TAT	T|0.781;C|0.219	0.219	strong		0.458	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246956	47246956	+	Missense_Mutation	SNP	C	C	T	rs61743617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:47246956C>T	ENST00000300404.2	+	11	1626	c.1567C>T	c.(1567-1569)Cgg>Tgg	p.R523W	B4GALNT2_ENST00000393354.2_Missense_Mutation_p.R463W|B4GALNT2_ENST00000504681.1_Missense_Mutation_p.R437W|RP11-708H21.4_ENST00000575159.1_lincRNA	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	523					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			TCACCAGTCTCGGTCTCCAGT	0.542													C|||	24	0.00479233	0.0008	0.0101	5008	,	,		20911	0.0		0.0129	False		,,,				2504	0.0031				p.R523W	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.C1567T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	12,4394	19.1+/-41.9	0,12,2191	96.0	93.0	94.0		1387,1309,1567	2.5	0.0	17	dbSNP_129	94	130,8470	67.3+/-129.8	0,130,4170	yes	missense,missense,missense	B4GALNT2	NM_001159387.1,NM_001159388.1,NM_153446.2	101,101,101	0,142,6361	TT,TC,CC		1.5116,0.2724,1.0918	probably-damaging,probably-damaging,probably-damaging	463/507,437/481,523/567	47246956	142,12864	2203	4300	6503	SO:0001583	missense	124872	exon11			CAGTCTCGGTCTC	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1567C>T	17.37:g.47246956C>T	ENSP00000300404:p.Arg523Trp	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	29	19	0.655172	NM_153446	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	17.61	3.432031	0.62844	0.002724	0.015116	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.22743	1.94;1.94;1.94	5.79	2.47	0.30058	.	0.829068	0.10702	N	0.643916	T	0.14141	0.0342	L	0.50333	1.59	0.09310	N	1	D;D	0.69078	0.996;0.997	P;P	0.50231	0.635;0.543	T	0.07481	-1.0770	10	0.66056	D	0.02	-1.4776	7.8032	0.29187	0.3935:0.5316:0.0:0.0749	rs61743617	463;523	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	W	437;463;523	ENSP00000425510:R437W;ENSP00000377022:R463W;ENSP00000300404:R523W	ENSP00000300404:R523W	R	+	1	2	B4GALNT2	44601955	0.000000	0.05858	0.000000	0.03702	0.178000	0.23041	0.599000	0.24089	0.757000	0.33036	0.561000	0.74099	CGG	C|0.989;T|0.011	0.011	strong		0.542	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446	
LTBP1	4052	hgsc.bcm.edu	37	2	33567990	33567990	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33567990T>C	ENST00000404816.2	+	25	4169	c.3816T>C	c.(3814-3816)taT>taC	p.Y1272Y	LTBP1_ENST00000272273.5_Intron|LTBP1_ENST00000407925.1_Silent_p.Y946Y|LTBP1_ENST00000402934.1_Silent_p.Y893Y|LTBP1_ENST00000390003.4_Silent_p.Y947Y|LTBP1_ENST00000354476.3_Silent_p.Y1273Y|LTBP1_ENST00000404525.1_Silent_p.Y893Y|LTBP1_ENST00000418533.2_Intron			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1272	EGF-like 13; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GCCTCTGTTATCAGGGCTTTC	0.448																																					p.Y1272Y		Atlas-SNP	.											.	LTBP1	317	.	0			c.T3816C						PASS	.						101.0	85.0	90.0					2																	33567990		2203	4300	6503	SO:0001819	synonymous_variant	4052	exon25			CTGTTATCAGGGC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3816T>C	2.37:g.33567990T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	138	83	0.601449	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	T	9.629	1.135806	0.21123	.	.	ENSG00000049323	ENST00000415140	.	.	.	5.91	3.39	0.38822	.	.	.	.	.	T	0.55924	0.1951	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50792	-0.8786	4	.	.	.	.	7.2434	0.26109	0.0:0.3609:0.0:0.6391	.	.	.	.	T	234	.	.	I	+	2	0	LTBP1	33421494	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.377000	0.44300	0.932000	0.37266	0.455000	0.32223	ATC	.	.	none		0.448	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79059041	79059041	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79059041T>C	ENST00000388820.4	-	19	3422	c.3212A>G	c.(3211-3213)aAt>aGt	p.N1071S	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1071					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.N1071S(4)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CTCGTGGAAATTGATGAAATT	0.617																																					p.N1071S		Atlas-SNP	.											ADAMTS7,NS,carcinoma,0,5	ADAMTS7	142	5	4	Substitution - Missense(4)	lung(2)|kidney(2)	c.A3212G						scavenged	.																																			SO:0001583	missense	11173	exon19			TGGAAATTGATGA	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3212A>G	15.37:g.79059041T>C	ENSP00000373472:p.Asn1071Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	136	8	0.0588235	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	t	16.38	3.107658	0.56291	.	.	ENSG00000136378	ENST00000388820	T	0.61742	0.08	4.66	2.13	0.27403	.	0.056036	0.64402	D	0.000002	T	0.59252	0.2180	M	0.76002	2.32	0.35198	D	0.774007	P	0.48503	0.911	P	0.46144	0.505	T	0.66571	-0.5890	10	0.41790	T	0.15	.	10.1871	0.43004	0.0:0.0:0.3202:0.6798	.	1071	Q9UKP4	ATS7_HUMAN	S	1071	ENSP00000373472:N1071S	ENSP00000373472:N1071S	N	-	2	0	ADAMTS7	76846096	1.000000	0.71417	0.986000	0.45419	0.484000	0.33280	3.143000	0.50608	0.107000	0.17824	0.367000	0.22151	AAT	.	.	none		0.617	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
TAS1R2	80834	hgsc.bcm.edu	37	1	19181082	19181082	+	Silent	SNP	A	A	C	rs28470550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19181082A>C	ENST00000375371.3	-	3	903	c.882T>G	c.(880-882)acT>acG	p.T294T	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	294					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ACACGGCGCCAGTGAAGTTCT	0.637													C|||	1196	0.238818	0.2602	0.2536	5008	,	,		18981	0.1032		0.3201	False		,,,				2504	0.2556				p.T294T		Atlas-SNP	.											TAS1R2,NS,carcinoma,0,2	TAS1R2	134	2	0			c.T882G						PASS	.	C		1096,3310	717.7+/-408.7	130,836,1237	56.0	54.0	55.0		882	-9.8	0.0	1	dbSNP_125	55	2810,5790	674.9+/-403.2	449,1912,1939	no	coding-synonymous	TAS1R2	NM_152232.2		579,2748,3176	CC,CA,AA		32.6744,24.8752,30.0323		294/840	19181082	3906,9100	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon3			GGCGCCAGTGAAG		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.882T>G	1.37:g.19181082A>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			A|0.717;C|0.283	0.283	strong		0.637	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152665261	152665261	+	Missense_Mutation	SNP	C	C	A	rs4645434	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152665261C>A	ENST00000367255.5	-	74	12781	c.12180G>T	c.(12178-12180)gaG>gaT	p.E4060D	SYNE1_ENST00000341594.5_Missense_Mutation_p.E3925D|SYNE1_ENST00000423061.1_Missense_Mutation_p.E3989D|SYNE1_ENST00000448038.1_Missense_Mutation_p.E3989D|SYNE1_ENST00000265368.4_Missense_Mutation_p.E4060D	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4060			E -> D (in dbSNP:rs4645434).		cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.E4060D(3)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAGGACTTGGCTCTAAATCCG	0.498										HNSCC(10;0.0054)			C|||	2732	0.545527	0.4138	0.6182	5008	,	,		18310	0.6488		0.6024	False		,,,				2504	0.5072				p.E4060D		Atlas-SNP	.											SYNE1_ENST00000423061,colon,carcinoma,-2,12	SYNE1	3227	12	3	Substitution - Missense(3)	skin(2)|central_nervous_system(1)	c.G12180T						scavenged	.	C	ASP/GLU,ASP/GLU	2065,2341	569.8+/-382.7	487,1091,625	106.0	102.0	103.0		11967,12180	-1.2	0.0	6	dbSNP_111	103	5313,3287	647.1+/-400.3	1664,1985,651	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	45,45	2151,3076,1276	AA,AC,CC		38.2209,46.8679,43.2723	benign,benign	3989/8750,4060/8798	152665261	7378,5628	2203	4300	6503	SO:0001583	missense	23345	exon74			ACTTGGCTCTAAA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.12180G>T	6.37:g.152665261C>A	ENSP00000356224:p.Glu4060Asp	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	1271	0.581959706959707	217	0.4410569105691057	222	0.6132596685082873	373	0.6520979020979021	459	0.6055408970976254	C	6.405	0.442830	0.12164	0.468679	0.617791	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33	5.76	-1.25	0.09405	.	0.176957	0.39341	N	0.001392	T	0.05914	0.0154	N	0.14661	0.345	0.22911	P	0.99857779	B;B;B;B	0.28208	0.203;0.203;0.203;0.082	B;B;B;B	0.24541	0.031;0.031;0.031;0.054	T	0.36187	-0.9758	9	0.11182	T	0.66	.	10.9634	0.47397	0.0:0.4861:0.0:0.5139	rs4645434;rs52832929;rs56482475;rs57199459;rs4645434	4060;4060;4060;3989	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	D	4060;3989;4060;3989;3925	ENSP00000356224:E4060D;ENSP00000396024:E3989D;ENSP00000265368:E4060D;ENSP00000390975:E3989D;ENSP00000341887:E3925D	ENSP00000265368:E4060D	E	-	3	2	SYNE1	152706954	0.996000	0.38824	0.016000	0.15963	0.190000	0.23558	0.426000	0.21363	-0.234000	0.09782	-0.749000	0.03505	GAG	C|0.427;A|0.573	0.573	strong		0.498	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SPG7	6687	hgsc.bcm.edu	37	16	89613123	89613123	+	Missense_Mutation	SNP	A	A	G	rs2292954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:89613123A>G	ENST00000268704.2	+	11	1522	c.1507A>G	c.(1507-1509)Acc>Gcc	p.T503A		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	503			T -> A (neutral polymorphism; dbSNP:rs2292954). {ECO:0000269|PubMed:16534102, ECO:0000269|PubMed:20186691}.		anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CCAGTCCAGCACCTTTTACTC	0.597													A|||	533	0.10643	0.0106	0.1124	5008	,	,		15594	0.131		0.168	False		,,,				2504	0.1431				p.T503A		Atlas-SNP	.											.	SPG7	75	.	0			c.A1507G						PASS	.	A	ALA/THR	168,4228	111.2+/-149.4	3,162,2033	103.0	101.0	102.0		1507	4.3	1.0	16	dbSNP_100	102	1666,6934	305.7+/-307.6	152,1362,2786	yes	missense	SPG7	NM_003119.2	58	155,1524,4819	GG,GA,AA		19.3721,3.8217,14.112	benign	503/796	89613123	1834,11162	2198	4300	6498	SO:0001583	missense	6687	exon11			TCCAGCACCTTTT	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1507A>G	16.37:g.89613123A>G	ENSP00000268704:p.Thr503Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	37	CCDS10977.1	259	0.11858974358974358	9	0.018292682926829267	43	0.11878453038674033	77	0.1346153846153846	130	0.17150395778364116	A	13.33	2.204196	0.38905	0.038217	0.193721	ENSG00000197912	ENST00000268704	D	0.94650	-3.48	5.42	4.33	0.51752	Peptidase M41, FtsH (2);	0.298369	0.46145	D	0.000305	T	0.00695	0.0023	N	0.11927	0.2	0.09310	P	0.9999999999866063	B	0.02656	0.0	B	0.06405	0.002	T	0.45131	-0.9282	9	0.30854	T	0.27	-1.1817	10.9407	0.47273	0.9266:0.0:0.0734:0.0	rs2292954;rs3205047;rs17404897;rs17775132;rs52815392;rs59421193;rs2292954	503	Q9UQ90	SPG7_HUMAN	A	503	ENSP00000268704:T503A	ENSP00000268704:T503A	T	+	1	0	SPG7	88140624	0.998000	0.40836	1.000000	0.80357	0.908000	0.53690	2.181000	0.42547	0.915000	0.36847	0.459000	0.35465	ACC	G|0.121;N|0.000	0.121	strong		0.597	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119	
MTPAP	55149	hgsc.bcm.edu	37	10	30629226	30629226	+	Missense_Mutation	SNP	G	G	A	rs1047991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:30629226G>A	ENST00000263063.4	-	3	527	c.484C>T	c.(484-486)Cgc>Tgc	p.R162C	MTPAP_ENST00000358107.4_Missense_Mutation_p.R292C|MTPAP_ENST00000488290.1_5'UTR	NM_018109.3	NP_060579.3	Q9NVV4	PAPD1_HUMAN	mitochondrial poly(A) polymerase	162			R -> C (in dbSNP:rs1047991).		cell death (GO:0008219)|histone mRNA catabolic process (GO:0071044)|mRNA polyadenylation (GO:0006378)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)|protein homodimerization activity (GO:0042803)|UTP binding (GO:0002134)			breast(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GACCGTACGCGTGACCGTTCA	0.413													G|||	1094	0.21845	0.1929	0.121	5008	,	,		19041	0.2103		0.2495	False		,,,				2504	0.2986				p.R162C		Atlas-SNP	.											.	MTPAP	113	.	0			c.C484T						PASS	.	G	CYS/ARG	935,3471	356.6+/-313.6	99,737,1367	126.0	113.0	117.0		484	-10.2	0.0	10	dbSNP_86	117	2476,6124	408.5+/-349.5	376,1724,2200	yes	missense	MTPAP	NM_018109.3	180	475,2461,3567	AA,AG,GG		28.7907,21.2211,26.2264	benign	162/583	30629226	3411,9595	2203	4300	6503	SO:0001583	missense	55149	exon3			GTACGCGTGACCG	AL122121	CCDS7165.1	10p12.1	2014-01-30	2009-01-12	2009-01-12	ENSG00000107951	ENSG00000107951			25532	protein-coding gene	gene with protein product	"""TUTase1"""	613669	"""PAP associated domain containing 1"""	PAPD1		12239557, 15769737, 15547249	Standard	NM_018109		Approved	FLJ10486, mtPAP, SPAX4	uc001iva.4	Q9NVV4	OTTHUMG00000017895	ENST00000263063.4:c.484C>T	10.37:g.30629226G>A	ENSP00000263063:p.Arg162Cys	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	167	165	0.988024	NM_018109	D3DRX0|Q659E3|Q6P7E5|Q9HA74	Missense_Mutation	SNP	ENST00000263063.4	37	CCDS7165.1	455	0.20833333333333334	71	0.1443089430894309	57	0.1574585635359116	137	0.2395104895104895	190	0.25065963060686014	G	7.660	0.684719	0.14973	0.212211	0.287907	ENSG00000107951	ENST00000358107;ENST00000263063;ENST00000417581;ENST00000421701	T;T;T;T	0.45276	2.02;2.02;2.02;0.9	5.08	-10.2	0.00374	.	3.461010	0.00794	N	0.001365	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.18013	0.001;0.025;0.001	B;B;B	0.09377	0.001;0.004;0.001	T	0.12502	-1.0545	9	0.52906	T	0.07	13.6516	5.5208	0.16931	0.2334:0.0678:0.4959:0.2028	rs1047991;rs3187968;rs17295129;rs17569747;rs61559846;rs1047991	124;292;162	Q5T851;Q9NVV4-2;Q9NVV4	.;.;PAPD1_HUMAN	C	292;162;97;124	ENSP00000350820:R292C;ENSP00000263063:R162C;ENSP00000404392:R97C;ENSP00000394118:R124C	ENSP00000263063:R162C	R	-	1	0	MTPAP	30669232	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.273000	0.00531	-4.256000	0.00061	-3.879000	0.00017	CGC	G|0.755;A|0.245	0.245	strong		0.413	MTPAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047426.2	NM_018109	
FAM186A	121006	hgsc.bcm.edu	37	12	50745863	50745863	+	Silent	SNP	C	C	G	rs12317337	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745863C>G	ENST00000327337.5	-	4	4751	c.4752G>C	c.(4750-4752)gcG>gcC	p.A1584A	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Silent_p.A1584A	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1584								p.A1584A(1)									CCAGTTCCTGCGCCTGCTGAG	0.667													c|||	1768	0.353035	0.2995	0.415	5008	,	,		22865	0.4008		0.3797	False		,,,				2504	0.3047				p.A1584A	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - coding silent(1)	stomach(1)	c.G4752C						scavenged	.						5.0	6.0	6.0					12																	50745863		675	1563	2238	SO:0001819	synonymous_variant	121006	exon4			TTCCTGCGCCTGC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4752G>C	12.37:g.50745863C>G		Somatic	233	2	0.00858369		WXS	Illumina HiSeq	Phase_I	255	81	0.317647	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			A|1.000	.	weak		0.667	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
GPBP1L1	60313	hgsc.bcm.edu	37	1	46094027	46094027	+	Silent	SNP	A	A	G	rs1250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46094027A>G	ENST00000290795.3	-	12	2547	c.1326T>C	c.(1324-1326)agT>agC	p.S442S	GPBP1L1_ENST00000355105.3_Silent_p.S442S|GPBP1L1_ENST00000479235.1_5'UTR			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	442					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S442S(1)	GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					GGGAGAACAGACTGGAACTGC	0.448													G|||	1615	0.322484	0.2648	0.3458	5008	,	,		17803	0.3472		0.2823	False		,,,				2504	0.3998				p.S442S		Atlas-SNP	.											GPBP1L1,NS,carcinoma,0,1	GPBP1L1	43	1	1	Substitution - coding silent(1)	stomach(1)	c.T1326C						PASS	.	G		1118,3288	718.0+/-408.8	148,822,1233	123.0	118.0	120.0		1326	6.0	1.0	1	dbSNP_36	120	2535,6065	692.7+/-404.6	387,1761,2152	no	coding-synonymous	GPBP1L1	NM_021639.4		535,2583,3385	GG,GA,AA		29.4767,25.3745,28.087		442/475	46094027	3653,9353	2203	4300	6503	SO:0001819	synonymous_variant	60313	exon13			GAACAGACTGGAA		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.1326T>C	1.37:g.46094027A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	37	CCDS528.1																																																																																			A|0.704;G|0.296	0.296	strong		0.448	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
ELFN1	392617	hgsc.bcm.edu	37	7	1785738	1785738	+	Silent	SNP	G	G	A	rs61236605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:1785738G>A	ENST00000424383.2	+	3	1993	c.1506G>A	c.(1504-1506)gcG>gcA	p.A502A	ELFN1_ENST00000561626.1_Silent_p.A502A|ELFN1_ENST00000541472.1_Silent_p.A502A			P0C7U0	ELFN1_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 1	502					negative regulation of phosphatase activity (GO:0010923)|synapse organization (GO:0050808)	dendrite (GO:0030425)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)	1						ACCTGCCTGCGGCCGGCGAGG	0.711													G|||	684	0.136581	0.0325	0.1138	5008	,	,		13818	0.1042		0.2018	False		,,,				2504	0.2597				p.A502A		Atlas-SNP	.											.	ELFN1	22	.	0			c.G1506A						PASS	.						32.0	37.0	35.0					7																	1785738		692	1591	2283	SO:0001819	synonymous_variant	392617	exon2			GCCTGCGGCCGGC		CCDS59046.1	7p22.3	2013-02-11	2011-10-27	2011-10-27	ENSG00000225968	ENSG00000225968		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	33154	protein-coding gene	gene with protein product		614964	"""extracellular leucine-rich repeat and fibronectin type III containing 1"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 1"", ""protein phosphatase 1, regulatory subunit 28"""	PPP1R28		17868438	Standard	NM_001128636		Approved		uc010ksg.2	P0C7U0	OTTHUMG00000151495	ENST00000424383.2:c.1506G>A	7.37:g.1785738G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	23	16	0.695652	NM_001128636	H3BS57	Silent	SNP	ENST00000424383.2	37	CCDS59046.1																																																																																			G|0.868;A|0.132	0.132	strong		0.711	ELFN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322893.2	NM_001128636	
WFIKKN2	124857	hgsc.bcm.edu	37	17	48917333	48917333	+	Silent	SNP	C	C	T	rs9675120	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48917333C>T	ENST00000311378.4	+	2	1212	c.684C>T	c.(682-684)agC>agT	p.S228S	RP11-506D12.5_ENST00000572491.2_RNA|WFIKKN2_ENST00000426127.1_Silent_p.S135S	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	228	Ig-like C2-type.				muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			AGACAGTGAGCTTCCTCTGTG	0.637													C|||	2113	0.421925	0.1838	0.4928	5008	,	,		18283	0.4187		0.66	False		,,,				2504	0.4519				p.S228S		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.C684T						PASS	.			1154,3252	408.0+/-334.4	157,840,1206	86.0	86.0	86.0		684	4.5	1.0	17	dbSNP_119	86	5890,2710	682.4+/-403.8	2012,1866,422	no	coding-synonymous	WFIKKN2	NM_175575.5		2169,2706,1628	TT,TC,CC		31.5116,26.1916,45.8404		228/577	48917333	7044,5962	2203	4300	6503	SO:0001819	synonymous_variant	124857	exon2			AGTGAGCTTCCTC	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.684C>T	17.37:g.48917333C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			C|0.501;T|0.499	0.499	strong		0.637	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
T	6862	hgsc.bcm.edu	37	6	166580188	166580188	+	Silent	SNP	G	G	A	rs1056048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:166580188G>A	ENST00000296946.2	-	3	831	c.363C>T	c.(361-363)agC>agT	p.S121S	T_ENST00000366871.3_Silent_p.S121S	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	121					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		TGTAGACGCAGCTGGGCGCCT	0.642									Chordoma, Familial Clustering of				G|||	1063	0.21226	0.3737	0.2176	5008	,	,		14789	0.0437		0.2137	False		,,,				2504	0.1626				p.S121S		Atlas-SNP	.											.	T	77	.	0			c.C363T						PASS	.	G		1535,2871	474.6+/-357.0	253,1029,921	49.0	54.0	52.0		363	3.8	1.0	6	dbSNP_86	52	1805,6795	318.6+/-313.7	192,1421,2687	no	coding-synonymous	T	NM_003181.2		445,2450,3608	AA,AG,GG		20.9884,34.8389,25.6805		121/436	166580188	3340,9666	2203	4300	6503	SO:0001819	synonymous_variant	6862	exon3	Familial Cancer Database		GACGCAGCTGGGC	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.363C>T	6.37:g.166580188G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_003181	E7ERD6|Q4KMP4	Silent	SNP	ENST00000296946.2	37	CCDS5290.1																																																																																			G|0.749;A|0.251	0.251	strong		0.642	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
NUB1	51667	hgsc.bcm.edu	37	7	151064064	151064064	+	Silent	SNP	C	C	T	rs386956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151064064C>T	ENST00000355851.4	+	9	917	c.840C>T	c.(838-840)taC>taT	p.Y280Y	NUB1_ENST00000568733.1_Silent_p.Y304Y|NUB1_ENST00000566856.1_Silent_p.Y280Y|NUB1_ENST00000413040.2_Silent_p.Y304Y	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	280					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TGGATAACTACGCCGTCCTCC	0.458													C|||	1925	0.384385	0.1634	0.4553	5008	,	,		19414	0.4603		0.6302	False		,,,				2504	0.3016				p.Y304Y		Atlas-SNP	.											NUB1,caecum,carcinoma,0,1	NUB1	31	1	0			c.C912T						PASS	.	C		867,3207		101,665,1271	75.0	74.0	74.0		840	-9.4	0.1	7	dbSNP_80	74	5179,3203		1574,2031,586	no	coding-synonymous	NUB1	NM_016118.4		1675,2696,1857	TT,TC,CC		38.2128,21.2813,48.5389		280/602	151064064	6046,6410	2037	4191	6228	SO:0001819	synonymous_variant	51667	exon9			TAACTACGCCGTC	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.840C>T	7.37:g.151064064C>T		Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	115	113	0.982609	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37																																																																																				C|0.538;T|0.462	0.462	strong		0.458	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
MTHFR	4524	hgsc.bcm.edu	37	1	11856378	11856378	+	Missense_Mutation	SNP	G	G	A	rs1801133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11856378G>A	ENST00000376592.1	-	4	793	c.665C>T	c.(664-666)gCc>gTc	p.A222V	MTHFR_ENST00000376583.3_Missense_Mutation_p.A263V|MTHFR_ENST00000376590.3_Missense_Mutation_p.A222V|MTHFR_ENST00000376585.1_Missense_Mutation_p.A263V			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	222			A -> V (common polymorphism; thermolabile; 50% reduced activity; at homozygosity reduces the risk for colorectal cancer in individuals with adequate folate status; decreased risk for adult acute leukemia; increased risk for FS-NTD; dbSNP:rs1801133). {ECO:0000269|PubMed:10536004, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7647779, ECO:0000269|PubMed:9545406, ECO:0000269|Ref.5}.		blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)	p.A222V(1)		NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	GATGAAATCGGCTCCCGCAGA	0.557													G|||	1229	0.245407	0.09	0.4741	5008	,	,		21284	0.2956		0.3648	False		,,,				2504	0.1186				p.A222V		Atlas-SNP	.											MTHFR,NS,carcinoma,0,1	MTHFR	65	1	1	Substitution - Missense(1)	stomach(1)	c.C665T	GRCh37	CM950819	MTHFR	M	rs1801133	PASS	.	G	VAL/ALA	536,3870	242.1+/-252.3	31,474,1698	237.0	215.0	223.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	665	5.1	1.0	1	dbSNP_89	223	2983,5617	461.7+/-365.5	519,1945,1836	yes	missense	MTHFR	NM_005957.4	64	550,2419,3534	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.686,12.1652,27.0567	possibly-damaging	222/657	11856378	3519,9487	2203	4300	6503	SO:0001583	missense	4524	exon5			AAATCGGCTCCCG	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.665C>T	1.37:g.11856378G>A	ENSP00000365777:p.Ala222Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	708	0.3241758241758242	55	0.11178861788617886	176	0.4861878453038674	210	0.36713286713286714	267	0.35224274406332456	G	21.9	4.210837	0.79240	0.121652	0.34686	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	D;D;D;D	0.96491	-4.03;-4.03;-4.03;-4.03	5.08	5.08	0.68730	.	0.047442	0.85682	D	0.000000	T	0.00012	0.0000	M	0.78801	2.425	0.09310	P	0.9999999135526	D;D	0.76494	0.998;0.999	D;D	0.76071	0.941;0.987	T	0.00000	-1.4547	9	0.56958	D	0.05	.	17.4321	0.87542	0.0:0.0:1.0:0.0	rs1801133;rs4134713;rs59514310;rs1801133	222;263	P42898;Q5SNW6	MTHR_HUMAN;.	V	222;263;222;263	ENSP00000365777:A222V;ENSP00000365767:A263V;ENSP00000365775:A222V;ENSP00000365770:A263V	ENSP00000365767:A263V	A	-	2	0	MTHFR	11778965	1.000000	0.71417	0.994000	0.49952	0.116000	0.19942	9.044000	0.93805	2.514000	0.84764	0.655000	0.94253	GCC	G|0.719;A|0.281	0.281	strong		0.557	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
MUC16	94025	hgsc.bcm.edu	37	19	9088772	9088772	+	Missense_Mutation	SNP	T	T	C	rs17000950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9088772T>C	ENST00000397910.4	-	1	3246	c.3043A>G	c.(3043-3045)Agg>Ggg	p.R1015G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1015	Thr-rich.		R -> G (in dbSNP:rs17000950).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GATGGTTCCCTGATAGAAGTT	0.468													T|||	952	0.190096	0.0711	0.2709	5008	,	,		23512	0.3046		0.172	False		,,,				2504	0.1943				p.R1015G		Atlas-SNP	.											.	MUC16	4315	.	0			c.A3043G						PASS	.	T	GLY/ARG	293,3673		7,279,1697	221.0	208.0	212.0		3043	1.4	0.0	19	dbSNP_123	212	1484,6842		126,1232,2805	yes	missense	MUC16	NM_024690.2	125	133,1511,4502	CC,CT,TT		17.8237,7.3878,14.4566	probably-damaging	1015/14508	9088772	1777,10515	1983	4163	6146	SO:0001583	missense	94025	exon1			GTTCCCTGATAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.3043A>G	19.37:g.9088772T>C	ENSP00000381008:p.Arg1015Gly	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	182	95	0.521978	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	451	0.2065018315018315	37	0.07520325203252033	89	0.24585635359116023	194	0.33916083916083917	131	0.17282321899736147	t	3.114	-0.181980	0.06340	0.073878	0.178237	ENSG00000181143	ENST00000397910	T	0.02890	4.12	1.36	1.36	0.22044	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.54772	0.968	P	0.61874	0.895	T	0.54417	-0.8297	8	0.87932	D	0	.	4.8612	0.13585	0.0:0.0:0.0:1.0	rs17000950;rs52824067;rs17000950	1015	B5ME49	.	G	1015	ENSP00000381008:R1015G	ENSP00000381008:R1015G	R	-	1	2	MUC16	8949772	0.000000	0.05858	0.021000	0.16686	0.046000	0.14306	-0.105000	0.10907	0.872000	0.35775	0.260000	0.18958	AGG	T|0.797;C|0.203	0.203	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ADCK3	56997	hgsc.bcm.edu	37	1	227149203	227149203	+	Silent	SNP	G	G	A	rs11549708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:227149203G>A	ENST00000366779.1	+	7	2888	c.117G>A	c.(115-117)gcG>gcA	p.A39A	ADCK3_ENST00000366777.3_Silent_p.A39A|ADCK3_ENST00000478406.1_Intron|ADCK3_ENST00000366778.1_Intron|ADCK3_ENST00000458507.2_Intron			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	39					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						TGATCATGGCGGCCAGGGCCC	0.632													G|||	404	0.0806709	0.031	0.111	5008	,	,		18320	0.001		0.2187	False		,,,				2504	0.0665				p.A39A		Atlas-SNP	.											.	ADCK3	77	.	0			c.G117A						PASS	.	G		245,4161	137.3+/-173.1	5,235,1963	39.0	40.0	40.0		117	-11.2	0.3	1	dbSNP_120	40	2055,6543	339.2+/-323.1	251,1553,2495	no	coding-synonymous	ADCK3	NM_020247.4		256,1788,4458	AA,AG,GG		23.9009,5.5606,17.6869		39/648	227149203	2300,10704	2203	4299	6502	SO:0001819	synonymous_variant	56997	exon2			CATGGCGGCCAGG	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"""coenzyme Q8 homolog (yeast)"""	606980	"""chaperone-ABC1 (activity of bc1 complex, S.pombe)-like"", ""chaperone, ABC1 activity of bc1 complex like (S. pombe)"", ""chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"""	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.117G>A	1.37:g.227149203G>A		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	291	141	0.484536	NM_020247	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Silent	SNP	ENST00000366779.1	37	CCDS1557.1																																																																																			G|0.849;A|0.151	0.151	strong		0.632	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247	
COL27A1	85301	hgsc.bcm.edu	37	9	117050998	117050998	+	Missense_Mutation	SNP	G	G	A	rs10982134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:117050998G>A	ENST00000356083.3	+	43	4452	c.4061G>A	c.(4060-4062)cGa>cAa	p.R1354Q		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1354	Collagen-like 12.|Pro-rich.|Triple-helical region.		R -> Q (in dbSNP:rs10982134).		extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GTGGGTGATCGAGGAGACCGC	0.622													G|||	2122	0.423722	0.2436	0.4467	5008	,	,		16464	0.629		0.2922	False		,,,				2504	0.5746				p.R1354Q		Atlas-SNP	.											COL27A1,NS,carcinoma,+1,1	COL27A1	200	1	0			c.G4061A						scavenged	.	G	GLN/ARG	1136,3270	403.5+/-332.8	151,834,1218	64.0	68.0	67.0		4061	1.8	1.0	9	dbSNP_120	67	2772,5828	439.0+/-359.1	449,1874,1977	yes	missense	COL27A1	NM_032888.2	43	600,2708,3195	AA,AG,GG		32.2326,25.783,30.0477	benign	1354/1861	117050998	3908,9098	2203	4300	6503	SO:0001583	missense	85301	exon43			GTGATCGAGGAGA	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4061G>A	9.37:g.117050998G>A	ENSP00000348385:p.Arg1354Gln	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	138	66	0.478261	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	843	0.385989010989011	116	0.23577235772357724	146	0.40331491712707185	357	0.6241258741258742	224	0.2955145118733509	G	13.36	2.214824	0.39102	0.25783	0.322326	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.90788	-2.73	4.77	1.84	0.25277	.	.	.	.	.	T	0.00012	0.0000	N	0.17474	0.49	0.27045	P	0.9639178	B	0.16166	0.016	B	0.09377	0.004	T	0.42103	-0.9471	8	0.10902	T	0.67	.	7.1776	0.25753	0.1735:0.1452:0.6813:0.0	rs10982134;rs56444233;rs59519437;rs10982134	1354	Q8IZC6	CORA1_HUMAN	Q	1354	ENSP00000348385:R1354Q	ENSP00000348385:R1354Q	R	+	2	0	COL27A1	116090819	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	1.987000	0.40687	0.544000	0.28883	0.491000	0.48974	CGA	G|0.655;A|0.345	0.345	strong		0.622	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
TTN	7273	hgsc.bcm.edu	37	2	179644855	179644855	+	Missense_Mutation	SNP	T	T	C	rs10497520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179644855T>C	ENST00000591111.1	-	22	3825	c.3601A>G	c.(3601-3603)Aaa>Gaa	p.K1201E	RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.K1201E|TTN_ENST00000342992.6_Missense_Mutation_p.K1201E|TTN_ENST00000342175.6_Missense_Mutation_p.K1155E|TTN_ENST00000589042.1_Missense_Mutation_p.K1201E|TTN_ENST00000359218.5_Missense_Mutation_p.K1155E|TTN_ENST00000460472.2_Missense_Mutation_p.K1155E			Q8WZ42	TITIN_HUMAN	titin	33414			K -> E (in dbSNP:rs10497520). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTCCAACTTTAGGTTCTTGA	0.358													T|||	2505	0.5002	0.4077	0.5086	5008	,	,		18494	0.2173		0.8569	False		,,,				2504	0.544				p.K1201E		Atlas-SNP	.											.	TTN	18412	.	0			c.A3601G						PASS	.	T	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	2074,2332	569.2+/-382.6	490,1094,619	136.0	128.0	131.0		3463,3463,3601,3601,3463	4.6	1.0	2	dbSNP_119	131	7484,1116	767.4+/-407.6	3260,964,76	yes	missense,missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133379.3,NM_133378.4,NM_003319.4	56,56,56,56,56	3750,2058,695	CC,CT,TT		12.9767,47.0722,26.5108	benign,benign,benign,benign,benign	1155/27119,1155/27052,1201/5605,1201/33424,1155/26927	179644855	9558,3448	2203	4300	6503	SO:0001583	missense	7273	exon22			CAACTTTAGGTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3601A>G	2.37:g.179644855T>C	ENSP00000465570:p.Lys1201Glu	Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	273	272	0.996337	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		1201	0.549908424908425	211	0.42886178861788615	218	0.6022099447513812	116	0.20279720279720279	656	0.8654353562005277	T	15.15	2.748077	0.49257	0.470722	0.870233	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.62788	0.0;0.21;0.19;0.18;0.37	5.78	4.56	0.56223	Ribonuclease H-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.44247	P	0.0029010000000000424	B;B;B;B;P	0.45531	0.044;0.044;0.044;0.044;0.86	B;B;B;B;P	0.44561	0.036;0.036;0.036;0.036;0.453	T	0.10382	-1.0632	8	0.87932	D	0	.	12.6469	0.56740	0.0:0.0:0.1378:0.8622	rs10497520;rs58913365;rs10497520	1155;1155;1155;1201;1201	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	E	1201;1155;1155;1155;1155;1201	ENSP00000343764:K1201E;ENSP00000434586:K1155E;ENSP00000340554:K1155E;ENSP00000352154:K1155E;ENSP00000354117:K1201E	ENSP00000340554:K1155E	K	-	1	0	TTN	179353100	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.116000	0.57871	2.204000	0.70986	0.528000	0.53228	AAA	T|0.445;C|0.555	0.555	strong		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CCDC7	79741	hgsc.bcm.edu	37	10	32856746	32856746	+	Missense_Mutation	SNP	A	A	C	rs12268559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:32856746A>C	ENST00000362006.5	+	16	1889	c.1346A>C	c.(1345-1347)aAa>aCa	p.K449T	C10orf68_ENST00000572165.1_3'UTR|C10orf68_ENST00000375030.2_5'Flank|CCDC7_ENST00000277657.6_Missense_Mutation_p.K449T|C10orf68_ENST00000375028.3_5'Flank	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	449			K -> T (in dbSNP:rs12268559).							NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				CCATTGGAGAAAGAAACAAGA	0.353													A|||	828	0.165335	0.0893	0.2421	5008	,	,		15555	0.1726		0.0875	False		,,,				2504	0.2863				p.K449T		Atlas-SNP	.											.	CCDC7	47	.	0			c.A1346C						PASS	.	A	THR/LYS,,THR/LYS	363,4043	184.7+/-212.0	12,339,1852	85.0	84.0	85.0		1346,,1346	1.4	0.0	10	dbSNP_120	85	726,7872	174.6+/-224.8	39,648,3612	yes	missense,utr-5,missense	C10orf68,CCDC7	NM_001026383.1,NM_024688.2,NM_145023.4	78,,78	51,987,5464	CC,CA,AA		8.4438,8.2388,8.3743	possibly-damaging,,possibly-damaging	449/487,,449/487	32856746	1089,11915	2203	4299	6502	SO:0001583	missense	221016	exon16			TGGAGAAAGAAAC	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 68"""	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.1346A>C	10.37:g.32856746A>C	ENSP00000355078:p.Lys449Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	110	34	0.309091	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	37	CCDS7173.1	275	0.1259157509157509	41	0.08333333333333333	68	0.1878453038674033	98	0.17132867132867133	68	0.08970976253298153	A	10.99	1.506391	0.26949	0.082388	0.084438	ENSG00000216937	ENST00000277657;ENST00000362006;ENST00000435402	T;T;T	0.58940	0.94;0.94;0.3	5.11	1.37	0.22104	.	.	.	.	.	T	0.00073	0.0002	L	0.27053	0.805	0.80722	P	0.0	B	0.32101	0.356	B	0.27715	0.082	T	0.05257	-1.0896	8	0.46703	T	0.11	-4.0852	4.3141	0.10984	0.6456:0.1715:0.1829:0.0	rs12268559;rs16905996;rs52821925;rs59554278;rs12268559	449	Q96M83	CCDC7_HUMAN	T	449;449;118	ENSP00000277657:K449T;ENSP00000355078:K449T;ENSP00000401923:K118T	ENSP00000277657:K449T	K	+	2	0	CCDC7	32896752	0.001000	0.12720	0.001000	0.08648	0.007000	0.05969	0.009000	0.13219	0.037000	0.15575	0.528000	0.53228	AAA	A|0.896;C|0.104	0.104	strong		0.353	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	
LCP1	3936	hgsc.bcm.edu	37	13	46705068	46705068	+	Silent	SNP	C	C	A	rs11558762	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:46705068C>A	ENST00000398576.2	-	18	2020	c.1632G>T	c.(1630-1632)ccG>ccT	p.P544P	LCP1_ENST00000323076.2_Silent_p.P544P|LCP1_ENST00000435666.2_Silent_p.P113P			P13796	PLSL_HUMAN	lymphocyte cytosolic protein 1 (L-plastin)	544	Actin-binding 2.|CH 4. {ECO:0000255|PROSITE- ProRule:PRU00044}.		P -> A (in dbSNP:rs17067725).		actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|organ regeneration (GO:0031100)|protein kinase A signaling (GO:0010737)|regulation of intracellular protein transport (GO:0033157)|T cell activation involved in immune response (GO:0002286)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			breast(2)|kidney(1)|large_intestine(6)|lung(18)|ovary(4)|prostate(2)|skin(1)	34		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		TACTAATCTTCGGGTCCTATG	0.443			T	BCL6	NHL								C|||	319	0.0636981	0.0098	0.0951	5008	,	,		18693	0.0268		0.173	False		,,,				2504	0.0399				p.P544P		Atlas-SNP	.		Dom	yes		13	13q14.1-q14.3	3936	lymphocyte cytosolic protein 1 (L-plastin)		L	.	LCP1	69	.	0			c.G1632T						PASS	.	C		194,4212	123.7+/-161.0	3,188,2012	164.0	151.0	155.0		1632	-10.7	0.1	13	dbSNP_120	155	1752,6848	318.4+/-313.7	186,1380,2734	no	coding-synonymous	LCP1	NM_002298.4		189,1568,4746	AA,AC,CC		20.3721,4.4031,14.9623		544/628	46705068	1946,11060	2203	4300	6503	SO:0001819	synonymous_variant	3936	exon15			AATCTTCGGGTCC	M22300	CCDS9403.1	13q14.3	2013-01-10			ENSG00000136167	ENSG00000136167		"""EF-hand domain containing"""	6528	protein-coding gene	gene with protein product	"""plastin 2"""	153430				2111166	Standard	NM_002298		Approved	PLS2, CP64, L-PLASTIN, LC64P	uc001vba.4	P13796	OTTHUMG00000016864	ENST00000398576.2:c.1632G>T	13.37:g.46705068C>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	155	65	0.419355	NM_002298	B2R613|B4DUA0|Q5TBN4	Silent	SNP	ENST00000398576.2	37	CCDS9403.1																																																																																			T|0.011;G|0.182	.	strong		0.443	LCP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044800.3	NM_002298	
TBCD	6904	hgsc.bcm.edu	37	17	80887244	80887244	+	Silent	SNP	T	T	C	rs1127986	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80887244T>C	ENST00000355528.4	+	32	2989	c.2859T>C	c.(2857-2859)gaT>gaC	p.D953D	TBCD_ENST00000539345.2_Silent_p.D953D	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	953					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GCAGGTCCGATGTGGCCTCCG	0.657													C|||	1207	0.241014	0.2496	0.2406	5008	,	,		16468	0.1796		0.2893	False		,,,				2504	0.2434				p.D953D		Atlas-SNP	.											.	TBCD	94	.	0			c.T2859C						PASS	.	C		969,3357		113,743,1307	56.0	64.0	61.0		2859	-4.5	0.0	17	dbSNP_86	61	2121,6365		268,1585,2390	no	coding-synonymous	TBCD	NM_005993.4		381,2328,3697	CC,CT,TT		24.9941,22.3994,24.118		953/1193	80887244	3090,9722	2163	4243	6406	SO:0001819	synonymous_variant	6904	exon32			GTCCGATGTGGCC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.2859T>C	17.37:g.80887244T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	37	CCDS45818.1																																																																																			T|0.751;C|0.249	0.249	strong		0.657	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
RSRP1	57035	hgsc.bcm.edu	37	1	25570081	25570081	+	Missense_Mutation	SNP	T	T	C	rs1043879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:25570081T>C	ENST00000243189.7	-	4	992	c.716A>G	c.(715-717)gAa>gGa	p.E239G	C1orf63_ENST00000417642.2_Missense_Mutation_p.E240G	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		239			E -> G (in dbSNP:rs1043879). {ECO:0000269|PubMed:15489334}.							breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGTAGGTTTTTCATTGGGATT	0.353													T|||	540	0.107827	0.0129	0.2089	5008	,	,		17228	0.0327		0.2724	False		,,,				2504	0.0726				p.E239G		Atlas-SNP	.											.	C1orf63	17	.	0			c.A716G						PASS	.	T	GLY/GLU	237,4169	138.8+/-174.5	11,215,1977	228.0	204.0	212.0	http://www.ncbi.nlm.nih.gov/pubmed?term	716	4.0	0.2	1	dbSNP_86	212	2306,6294	388.1+/-342.4	314,1678,2308	yes	missense	C1orf63	NM_020317.3	98	325,1893,4285	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	26.814,5.379,19.5525	probably-damaging	239/291	25570081	2543,10463	2203	4300	6503	SO:0001583	missense	57035	exon4			GGTTTTTCATTGG																												ENST00000243189.7:c.716A>G	1.37:g.25570081T>C	ENSP00000243189:p.Glu239Gly	Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	208	208	1	NM_020317	A8K917|Q49AA4|Q5TH71|Q9GZP6	Missense_Mutation	SNP	ENST00000243189.7	37	CCDS260.1	316	0.1446886446886447	10	0.02032520325203252	76	0.20994475138121546	13	0.022727272727272728	217	0.2862796833773087	T	8.815	0.936144	0.18206	0.05379	0.26814	ENSG00000117616	ENST00000243189;ENST00000417642	T;T	0.34472	1.36;1.41	5.1	3.97	0.46021	.	0.551981	0.14928	N	0.290259	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.999999853191	B	0.23540	0.087	B	0.25759	0.063	T	0.17653	-1.0362	9	0.59425	D	0.04	-3.633	8.5213	0.33277	0.0:0.0886:0.0:0.9114	rs1043879;rs17844932;rs17857662;rs17859787;rs57469912;rs1043879	239	Q9BUV0	CA063_HUMAN	G	239;240	ENSP00000243189:E239G;ENSP00000411631:E240G	ENSP00000243189:E239G	E	-	2	0	C1orf63	25442668	1.000000	0.71417	0.182000	0.23118	0.052000	0.14988	1.995000	0.40767	0.969000	0.38237	0.477000	0.44152	GAA	T|0.831;C|0.169	0.169	strong		0.353	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2		
RDH14	57665	hgsc.bcm.edu	37	2	18736613	18736613	+	Silent	SNP	A	A	G	rs72775091	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:18736613A>G	ENST00000381249.3	-	2	962	c.855T>C	c.(853-855)acT>acC	p.T285T	RDH14_ENST00000468071.1_5'UTR	NM_020905.3	NP_065956.1	Q9HBH5	RDH14_HUMAN	retinol dehydrogenase 14 (all-trans/9-cis/11-cis)	285					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)				Vitamin A(DB00162)	AATAAATGGAAGTCTGGGCAC	0.443													A|||	77	0.0153754	0.0015	0.0231	5008	,	,		18158	0.001		0.0457	False		,,,				2504	0.0123				p.T599T		Atlas-SNP	.											.	.	.	.	0			c.T1797C						PASS	.	A	,,	35,4371	40.0+/-72.8	0,35,2168	141.0	137.0	139.0		1797,,855	-8.6	0.2	2	dbSNP_130	139	335,8263	116.1+/-175.8	11,313,3975	no	coding-synonymous,utr-3,coding-synonymous	RDH14,NT5C1B-RDH14	NM_001199103.1,NM_001199104.1,NM_020905.3	,,	11,348,6143	GG,GA,AA		3.8963,0.7944,2.8453	,,	599/651,,285/337	18736613	370,12634	2203	4299	6502	SO:0001819	synonymous_variant	100526794	exon9			AATGGAAGTCTGG	AF237952	CCDS1693.1	2p24.2	2011-09-14	2006-05-09		ENSG00000240857	ENSG00000240857	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19979	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 4"""		"""retinol dehydrogenase 14 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_020905		Approved	PAN2, SDR7C4		Q9HBH5	OTTHUMG00000090705	ENST00000381249.3:c.855T>C	2.37:g.18736613A>G		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	197	106	0.538071	NM_001199103		Silent	SNP	ENST00000381249.3	37	CCDS1693.1																																																																																			A|0.974;G|0.026	0.026	strong		0.443	RDH14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207394.1		
GGTLC2	91227	hgsc.bcm.edu	37	22	22988864	22988864	+	Missense_Mutation	SNP	G	G	C	rs143048497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22988864G>C	ENST00000480559.1	+	1	49	c.49G>C	c.(49-51)Gac>Cac	p.D17H	POM121L1P_ENST00000402027.1_RNA|GGTLC2_ENST00000448514.1_Missense_Mutation_p.D17H	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	17					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)	gamma-glutamyltransferase activity (GO:0003840)	p.D17H(1)		endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		GATCTCTGACGACACCACTCA	0.627													.|||	77	0.0153754	0.0068	0.0288	5008	,	,		6462	0.0129		0.0278	False		,,,				2504	0.0072				p.D17H		Atlas-SNP	.											GGTLC2,NS,carcinoma,0,1	GGTLC2	20	1	1	Substitution - Missense(1)	prostate(1)	c.G49C						scavenged	.	G	HIS/ASP	25,4335		0,25,2155	24.0	18.0	20.0		49		0.0	22	dbSNP_134	20	200,8106		5,190,3958	no	missense	GGTLC2	NM_199127.2	81	5,215,6113	CC,CG,GG		2.4079,0.5734,1.7764	benign	17/219	22988864	225,12441	2180	4153	6333	SO:0001583	missense	91227	exon1			TCTGACGACACCA	X98922	CCDS13802.2	22q11.21	2008-03-25	2008-03-10	2008-03-10	ENSG00000100121	ENSG00000100121		"""Gamma-glutamyltransferases"""	18596	protein-coding gene	gene with protein product		612339	"""gamma-glutamyltransferase-like 4"""	GGTL4		9074928, 18357469	Standard	NM_199127		Approved		uc010gtt.2	Q14390	OTTHUMG00000151177	ENST00000480559.1:c.49G>C	22.37:g.22988864G>C	ENSP00000419751:p.Asp17His	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	424	17	0.0400943	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Missense_Mutation	SNP	ENST00000480559.1	37	CCDS13802.2	.	.	.	.	.	.	.	.	.	.	g	8.959	0.970048	0.18659	0.005734	0.024079	ENSG00000100121	ENST00000480559;ENST00000448514	T;T	0.07021	3.23;3.23	.	.	.	.	0.363223	0.30060	N	0.010509	T	0.05640	0.0148	M	0.76574	2.34	0.36339	D	0.859361	B;B	0.23185	0.034;0.081	B;B	0.34991	0.054;0.193	T	0.05699	-1.0869	9	0.42905	T	0.14	-4.1646	5.8178	0.18506	0.001:0.0:0.999:0.0	.	17;17	Q14390;B7WND7	GGTL2_HUMAN;.	H	17	ENSP00000419751:D17H;ENSP00000415676:D17H	ENSP00000415676:D17H	D	+	1	0	GGTLC2	21318864	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	1.021000	0.30040	-0.000000	0.14550	0.000000	0.15137	GAC	.	.	weak		0.627	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127	
PLA2G7	7941	hgsc.bcm.edu	37	6	46684222	46684222	+	Missense_Mutation	SNP	C	C	T	rs1805017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46684222C>T	ENST00000274793.7	-	4	471	c.275G>A	c.(274-276)cGc>cAc	p.R92H	PLA2G7_ENST00000541026.1_Intron|PLA2G7_ENST00000538237.1_Missense_Mutation_p.R47H|PLA2G7_ENST00000537365.1_Missense_Mutation_p.R92H	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	92			R -> H (common polymorphism; dbSNP:rs1805017). {ECO:0000269|PubMed:10733466, ECO:0000269|Ref.3}.		cellular protein metabolic process (GO:0044267)|lipid catabolic process (GO:0016042)|lipid oxidation (GO:0034440)|low-density lipoprotein particle remodeling (GO:0034374)|plasma lipoprotein particle oxidation (GO:0034441)|positive regulation of inflammatory response (GO:0050729)|positive regulation of monocyte chemotaxis (GO:0090026)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|low-density lipoprotein particle (GO:0034362)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|skin(1)|soft_tissue(1)	14			Lung(136;0.192)			GGTGTCAAGGCGATCATTATC	0.373													C|||	1590	0.317492	0.2572	0.3746	5008	,	,		18617	0.2192		0.2555	False		,,,				2504	0.5235				p.R92H		Atlas-SNP	.											PLA2G7,NS,carcinoma,0,1	PLA2G7	49	1	0			c.G275A	GRCh37	CM081751	PLA2G7	M	rs1805017	scavenged	.	C	HIS/ARG,HIS/ARG	1216,3190	421.3+/-339.3	159,898,1146	108.0	108.0	108.0	http://www.ncbi.nlm.nih.gov/pubmed?term	275,275	-10.0	0.0	6	dbSNP_89	108	2250,6350	380.3+/-339.6	322,1606,2372	yes	missense,missense	PLA2G7	NM_001168357.1,NM_005084.3	29,29	481,2504,3518	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	26.1628,27.5987,26.6492	benign,benign	92/442,92/442	46684222	3466,9540	2203	4300	6503	SO:0001583	missense	7941	exon4			TCAAGGCGATCAT	U20157	CCDS4917.1	6p21.2-p12	2008-09-19			ENSG00000146070	ENSG00000146070	3.1.1.4		9040	protein-coding gene	gene with protein product		601690				7700381, 8624782	Standard	NM_005084		Approved	PAFAH, LDL-PLA2	uc021zae.1	Q13093	OTTHUMG00000014789	ENST00000274793.7:c.275G>A	6.37:g.46684222C>T	ENSP00000274793:p.Arg92His	Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_005084	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Missense_Mutation	SNP	ENST00000274793.7	37	CCDS4917.1	552	0.25274725274725274	115	0.23373983739837398	127	0.35082872928176795	115	0.20104895104895104	195	0.25725593667546176	C	6.523	0.464769	0.12402	0.275987	0.261628	ENSG00000146070	ENST00000274793;ENST00000537365;ENST00000538237	T;T;T	0.54071	0.59;0.59;0.59	5.29	-10.0	0.00425	.	1.092260	0.06797	N	0.788055	T	0.08179	0.0204	N	0.04746	-0.17	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21314	-1.0249	9	0.37606	T	0.19	.	5.6226	0.17465	0.0969:0.4775:0.1969:0.2287	rs1805017;rs17288912;rs52794316;rs1805017	47;92	F5GYY6;Q13093	.;PAFA_HUMAN	H	92;92;47	ENSP00000274793:R92H;ENSP00000445666:R92H;ENSP00000441416:R47H	ENSP00000274793:R92H	R	-	2	0	PLA2G7	46792181	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	-2.392000	0.01056	-1.652000	0.01502	-0.251000	0.11542	CGC	C|0.737;T|0.263	0.263	strong		0.373	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1		
DHTKD1	55526	hgsc.bcm.edu	37	10	12131081	12131081	+	Missense_Mutation	SNP	T	T	G	rs3740015	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:12131081T>G	ENST00000263035.4	+	5	876	c.814T>G	c.(814-816)Tac>Gac	p.Y272D	DHTKD1_ENST00000465617.1_Intron	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	272			Y -> D (in dbSNP:rs3740015). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TGTGGACCTGTACTTTGGGGC	0.562													G|||	2426	0.484425	0.2073	0.4669	5008	,	,		18050	0.4812		0.5915	False		,,,				2504	0.7648				p.Y272D		Atlas-SNP	.											.	DHTKD1	104	.	0			c.T814G						PASS	.	G	ASP/TYR	1180,3226	712.0+/-408.1	144,892,1167	136.0	113.0	121.0		814	4.2	1.0	10	dbSNP_107	121	5064,3536	515.9+/-378.7	1474,2116,710	yes	missense	DHTKD1	NM_018706.5	160	1618,3008,1877	GG,GT,TT		41.1163,26.7817,48.0086	benign	272/920	12131081	6244,6762	2203	4300	6503	SO:0001583	missense	55526	exon5			GACCTGTACTTTG	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.814T>G	10.37:g.12131081T>G	ENSP00000263035:p.Tyr272Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	37	CCDS7087.1	1020	0.46703296703296704	119	0.241869918699187	181	0.5	274	0.479020979020979	446	0.5883905013192612	G	2.179	-0.388009	0.04932	0.267817	0.588837	ENSG00000181192	ENST00000263035;ENST00000437298	D;T	0.95853	-3.83;2.35	5.1	4.19	0.49359	Dehydrogenase, E1 component (1);	0.043855	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00265	-1.74	0.29948	P	0.8204819999999999	B	0.02656	0.0	B	0.01281	0.0	T	0.47761	-0.9092	9	0.21014	T	0.42	-5.2831	12.1561	0.54077	0.0:0.1304:0.7337:0.1359	rs3740015;rs17819995;rs17844945;rs17857684;rs52831881;rs61557928;rs3740015	272	Q96HY7	DHTK1_HUMAN	D	272;207	ENSP00000263035:Y272D;ENSP00000388163:Y207D	ENSP00000263035:Y272D	Y	+	1	0	DHTKD1	12171087	1.000000	0.71417	0.999000	0.59377	0.483000	0.33249	6.649000	0.74364	0.554000	0.29061	-0.215000	0.12644	TAC	T|0.518;G|0.482	0.482	strong		0.562	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706	
PLEKHH3	79990	hgsc.bcm.edu	37	17	40822678	40822678	+	Silent	SNP	C	C	T	rs2277618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:40822678C>T	ENST00000591022.1	-	10	1854	c.1467G>A	c.(1465-1467)ggG>ggA	p.G489G	PLEKHH3_ENST00000412503.1_Silent_p.G486G|PLEKHH3_ENST00000293349.6_Silent_p.G486G|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	489	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		ATAGTCTCCACCCGGAGTCGG	0.647													C|||	1066	0.212859	0.0098	0.2378	5008	,	,		11351	0.5347		0.1421	False		,,,				2504	0.2106				p.G489G		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.G1467A						PASS	.	C		140,4266	98.9+/-137.6	0,140,2063	48.0	47.0	47.0		1467	-1.6	0.9	17	dbSNP_100	47	1083,7517	224.1+/-260.6	59,965,3276	no	coding-synonymous	PLEKHH3	NM_024927.4		59,1105,5339	TT,TC,CC		12.593,3.1775,9.4034		489/794	40822678	1223,11783	2203	4300	6503	SO:0001819	synonymous_variant	79990	exon10			TCTCCACCCGGAG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1467G>A	17.37:g.40822678C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Silent	SNP	ENST00000591022.1	37	CCDS11434.1																																																																																			C|0.843;T|0.157	0.157	strong		0.647	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
HLA-C	3107	hgsc.bcm.edu	37	6	31238147	31238147	+	Silent	SNP	C	C	G	rs1050326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31238147C>G	ENST00000376228.5	-	4	749	c.735G>C	c.(733-735)ggG>ggC	p.G245G	HLA-C_ENST00000383329.3_Silent_p.G245G	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	245	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TCTGGTCCTCCCCATCCCGCT	0.637																																					p.G245G		Atlas-SNP	.											.	HLA-C	92	.	0			c.G735C						PASS	.						39.0	36.0	37.0					6																	31238147		2197	4283	6480	SO:0001819	synonymous_variant	3107	exon4			GTCCTCCCCATCC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.735G>C	6.37:g.31238147C>G		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	295	104	0.352542	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1																																																																																			G|0.330;C|0.670	0.330	strong		0.637	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
HBS1L	10767	hgsc.bcm.edu	37	6	135358916	135358916	+	Intron	SNP	G	G	A	rs9373121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:135358916G>A	ENST00000367837.5	-	4	637				HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367822.5_Silent_p.L227L|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000314674.3_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		TCATGAATTAGGTTAGCTAGT	0.353													G|||	975	0.194688	0.0976	0.2579	5008	,	,		20761	0.2897		0.1332	False		,,,				2504	0.2464				p.L227L		Atlas-SNP	.											.	HBS1L	75	.	0			c.C679T						PASS	.	G	,,	140,1244		5,130,557	205.0	158.0	172.0		,679,	4.1	1.0	6	dbSNP_119	172	376,2806		14,348,1229	no	intron,coding-synonymous,intron	HBS1L	NM_001145158.1,NM_001145207.1,NM_006620.3	,,	19,478,1786	AA,AG,GG		11.8165,10.1156,11.3009	,,	,227/633,	135358916	516,4050	692	1591	2283	SO:0001627	intron_variant	10767	exon5			GAATTAGGTTAGC	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+1794C>T	6.37:g.135358916G>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1																																																																																			G|0.831;A|0.169	0.169	strong		0.353	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
MUC4	4585	hgsc.bcm.edu	37	3	195508986	195508986	+	Silent	SNP	G	G	A	rs370883367|rs71291870		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508986G>A	ENST00000463781.3	-	2	9924	c.9465C>T	c.(9463-9465)gtC>gtT	p.V3155V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V3155V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3155V(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGTGTCGGTGACAGGAAGAG	0.582																																					p.V3155V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	stomach(2)	c.C9465T						PASS	.						5.0	4.0	4.0					3																	195508986		555	1304	1859	SO:0001819	synonymous_variant	4585	exon2			GTCGGTGACAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9465C>T	3.37:g.195508986G>A		Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	223	128	0.573991	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			AACAG|0.500;GACAT|0.500	.	alt		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZBED8	63920	hgsc.bcm.edu	37	5	159820931	159820931	+	Missense_Mutation	SNP	C	C	A	rs10515808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:159820931C>A	ENST00000408953.3	-	2	2074	c.1567G>T	c.(1567-1569)Gca>Tca	p.A523S	C5orf54_ENST00000523213.1_Missense_Mutation_p.A523S	NM_022090.3	NP_071373.2														breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	12						tttggaaatgctgtgaattgg	0.378													C|||	259	0.0517173	0.0242	0.0692	5008	,	,		18533	0.001		0.1143	False		,,,				2504	0.0644				p.A523S		Atlas-SNP	.											C5orf54,NS,carcinoma,+1,1	C5orf54	46	1	0			c.G1567T						PASS	.	C	SER/ALA	176,4230	112.9+/-151.0	1,174,2028	98.0	91.0	93.0		1567	1.0	1.0	5	dbSNP_119	93	881,7719	198.9+/-243.1	45,791,3464	yes	missense	C5orf54	NM_022090.3	99	46,965,5492	AA,AC,CC		10.2442,3.9946,8.127	benign	523/595	159820931	1057,11949	2203	4300	6503	SO:0001583	missense	63920	exon2			GAAATGCTGTGAA																												ENST00000408953.3:c.1567G>T	5.37:g.159820931C>A	ENSP00000386184:p.Ala523Ser	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	181	126	0.696133	NM_022090		Missense_Mutation	SNP	ENST00000408953.3	37	CCDS34283.1	123	0.05631868131868132	12	0.024390243902439025	25	0.06906077348066299	1	0.0017482517482517483	85	0.11213720316622691	C	0.955	-0.705164	0.03255	0.039946	0.102442	ENSG00000221886	ENST00000408953;ENST00000523213	T;T	0.20881	2.04;2.04	2.82	1.03	0.20045	.	.	.	.	.	T	0.00109	0.0003	N	0.01576	-0.805	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40384	-0.9566	8	0.02654	T	1	.	5.1216	0.14863	0.0:0.7156:0.0:0.2844	rs10515808;rs17475306;rs52822306;rs10515808	523	Q8IZ13	CE054_HUMAN	S	523	ENSP00000386184:A523S;ENSP00000428831:A523S	ENSP00000386184:A523S	A	-	1	0	C5orf54	159753509	0.924000	0.31332	0.959000	0.39883	0.725000	0.41563	0.468000	0.22051	0.261000	0.21753	-0.137000	0.14449	GCA	C|0.943;A|0.057	0.057	strong		0.378	C5orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374143.1		
PDZRN4	29951	hgsc.bcm.edu	37	12	41966771	41966771	+	Silent	SNP	G	G	A	rs113916113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:41966771G>A	ENST00000402685.2	+	10	2198	c.2190G>A	c.(2188-2190)aaG>aaA	p.K730K	PDZRN4_ENST00000539469.2_Silent_p.K472K|PDZRN4_ENST00000298919.7_Silent_p.K470K	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	730							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				ATCCAGAAAAGTCTGACAAGG	0.478													G|||	14	0.00279553	0.0008	0.0029	5008	,	,		22463	0.0		0.008	False		,,,				2504	0.0031				p.K730K		Atlas-SNP	.											.	PDZRN4	346	.	0			c.G2190A						PASS	.	G	,	11,4395	17.9+/-39.9	0,11,2192	114.0	116.0	115.0		2190,1416	3.1	1.0	12	dbSNP_132	115	98,8502	54.4+/-115.2	1,96,4203	no	coding-synonymous,coding-synonymous	PDZRN4	NM_001164595.1,NM_013377.3	,	1,107,6395	AA,AG,GG		1.1395,0.2497,0.8381	,	730/1037,472/779	41966771	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	29951	exon10			AGAAAAGTCTGAC	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2190G>A	12.37:g.41966771G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	41	0.602941	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																			G|0.992;A|0.008	0.008	strong		0.478	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
SLC17A4	10050	hgsc.bcm.edu	37	6	25776949	25776949	+	Missense_Mutation	SNP	G	G	A	rs11754288	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:25776949G>A	ENST00000377905.4	+	9	1233	c.1114G>A	c.(1114-1116)Gcc>Acc	p.A372T	SLC17A4_ENST00000397076.2_Missense_Mutation_p.A142T|SLC17A4_ENST00000439485.2_Missense_Mutation_p.A142T	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	372			A -> T (in dbSNP:rs11754288). {ECO:0000269|PubMed:15489334}.		phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						ACTCTTCACTGCCATTGGTAA	0.488													G|||	1302	0.259984	0.053	0.2781	5008	,	,		19704	0.1726		0.4205	False		,,,				2504	0.4519				p.A372T		Atlas-SNP	.											.	SLC17A4	79	.	0			c.G1114A						PASS	.	G	THR/ALA	490,3916	228.8+/-243.5	37,416,1750	151.0	133.0	139.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1114	-2.3	0.0	6	dbSNP_120	139	3781,4819	535.5+/-382.8	825,2131,1344	yes	missense	SLC17A4	NM_005495.2	58	862,2547,3094	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	43.9651,11.1212,32.8387	benign	372/498	25776949	4271,8735	2203	4300	6503	SO:0001583	missense	10050	exon9			TTCACTGCCATTG	AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"""Solute carriers"""	10932	protein-coding gene	gene with protein product		604216	"""solute carrier family 17 (sodium phosphate), member 4"""			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.1114G>A	6.37:g.25776949G>A	ENSP00000367137:p.Ala372Thr	Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	329	137	0.416413	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	37	CCDS4564.1	527	0.2413003663003663	19	0.03861788617886179	107	0.2955801104972376	86	0.15034965034965034	315	0.4155672823218997	G	18.40	3.615050	0.66672	0.111212	0.439651	ENSG00000146039	ENST00000377905;ENST00000439485;ENST00000397076	T;T;T	0.62364	0.31;0.03;0.05	5.63	-2.34	0.06704	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.404392	0.21229	N	0.078008	T	0.15739	0.0379	N	0.11255	0.115	0.80722	P	0.0	B;B;B	0.27416	0.103;0.178;0.003	B;B;B	0.32928	0.038;0.155;0.023	T	0.10291	-1.0636	9	0.24483	T	0.36	.	4.0818	0.09929	0.2924:0.0:0.3584:0.3493	rs11754288;rs52807624;rs60432554;rs11754288	142;142;372	E7EPE8;E7EU17;Q9Y2C5	.;.;S17A4_HUMAN	T	372;142;142	ENSP00000367137:A372T;ENSP00000391345:A142T;ENSP00000380266:A142T	ENSP00000367137:A372T	A	+	1	0	SLC17A4	25884928	0.000000	0.05858	0.001000	0.08648	0.998000	0.95712	0.261000	0.18442	-0.335000	0.08451	0.655000	0.94253	GCC	G|0.711;A|0.289	0.289	strong		0.488	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1		
AASDH	132949	hgsc.bcm.edu	37	4	57237683	57237683	+	Silent	SNP	G	G	A	rs6554354	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57237683G>A	ENST00000205214.6	-	5	975	c.795C>T	c.(793-795)tcC>tcT	p.S265S	AASDH_ENST00000510762.1_Intron|AASDH_ENST00000451613.1_Silent_p.S265S|AASDH_ENST00000513376.1_Silent_p.S165S|AASDH_ENST00000502617.1_Silent_p.S265S|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000602986.1_Silent_p.S112S	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	265					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.S265S(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				GCAACTTGACGGAAGTTGGTA	0.408													G|||	1392	0.277955	0.2829	0.2939	5008	,	,		18504	0.0724		0.4155	False		,,,				2504	0.3303				p.S265S		Atlas-SNP	.											AASDH,NS,carcinoma,0,1	AASDH	101	1	1	Substitution - coding silent(1)	prostate(1)	c.C795T						PASS	.	G		1284,3122	436.8+/-344.8	170,944,1089	104.0	92.0	96.0		795	-1.7	1.0	4	dbSNP_116	96	3664,4936	526.6+/-381.0	759,2146,1395	no	coding-synonymous	AASDH	NM_181806.2		929,3090,2484	AA,AG,GG		42.6047,29.1421,38.044		265/1099	57237683	4948,8058	2203	4300	6503	SO:0001819	synonymous_variant	132949	exon5			CTTGACGGAAGTT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.795C>T	4.37:g.57237683G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Silent	SNP	ENST00000205214.6	37	CCDS3504.1																																																																																			G|0.663;A|0.337	0.337	strong		0.408	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
NLRC3	197358	hgsc.bcm.edu	37	16	3613126	3613126	+	RNA	SNP	C	C	T	rs12445430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3613126C>T	ENST00000301749.7	-	0	2217				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGAGGTAGGCCAGGGCAGCGC	0.706													C|||	1118	0.223243	0.2224	0.1916	5008	,	,		14200	0.2708		0.1988	False		,,,				2504	0.2229				p.L604L		Atlas-SNP	.											.	NLRC3	103	.	0			c.G1812A						PASS	.	C		876,3152		102,672,1240	9.0	12.0	11.0		1812	4.1	1.0	16	dbSNP_120	11	1662,6652		192,1278,2687	no	coding-synonymous	NLRC3	NM_178844.2		294,1950,3927	TT,TC,CC		19.9904,21.7478,20.5639		604/1066	3613126	2538,9804	2014	4157	6171			197358	exon5			GTAGGCCAGGGCA	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613126C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				C|0.748;T|0.252	0.252	strong		0.706	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
TEX40	25858	hgsc.bcm.edu	37	11	64068310	64068310	+	Missense_Mutation	SNP	C	C	T	rs2286614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64068310C>T	ENST00000328404.6	+	2	223	c.203C>T	c.(202-204)cCg>cTg	p.P68L	TEX40_ENST00000539943.1_Missense_Mutation_p.P26L|RP11-783K16.10_ENST00000539086.1_RNA	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	68			P -> L (in dbSNP:rs2286614).		cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											TGGCACAGCCCGGGGCGGGGC	0.682											OREG0021050	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	442	0.0882588	0.025	0.1182	5008	,	,		13923	0.1071		0.16	False		,,,				2504	0.0593				p.P68L		Atlas-SNP	.											.	.	.	.	0			c.C203T						PASS	.	C	LEU/PRO	167,3713		6,155,1779	7.0	9.0	8.0		203	-6.6	0.0	11	dbSNP_100	8	1167,6977		94,979,2999	yes	missense	C11orf20	NM_001039496.1	98	100,1134,4778	TT,TC,CC		14.3296,4.3041,11.0945	possibly-damaging	68/201	64068310	1334,10690	1940	4072	6012	SO:0001583	missense	25858	exon2			ACAGCCCGGGGCG			11q13.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000219435	ENSG00000219435			19231	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 20"""	C11orf20			Standard	NM_001039496		Approved	DKFZP566E164	uc009ypm.3	Q9NTU4	OTTHUMG00000167820	ENST00000328404.6:c.203C>T	11.37:g.64068310C>T	ENSP00000330877:p.Pro68Leu	Somatic	99	0	0	1073	WXS	Illumina HiSeq	Phase_I	137	72	0.525547	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	37		237	0.10851648351648352	11	0.022357723577235773	44	0.12154696132596685	61	0.10664335664335664	121	0.15963060686015831	C	11.23	1.578537	0.28180	0.043041	0.143296	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.44083	0.93;0.94	3.28	-6.56	0.01848	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.16928	-1.0386	8	0.45353	T	0.12	-0.0108	2.1128	0.03707	0.26:0.2503:0.3698:0.1199	rs2286614;rs60336112;rs2286614	68	Q9NTU4	CK020_HUMAN	L	68;26	ENSP00000330877:P68L;ENSP00000443917:P26L	ENSP00000330877:P68L	P	+	2	0	C11orf20	63824886	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.403000	0.01046	-1.516000	0.01782	-0.410000	0.06199	CCG	C|0.899;T|0.101	0.101	strong		0.682	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496	
APOBEC3G	60489	hgsc.bcm.edu	37	22	39477123	39477123	+	Silent	SNP	T	T	C	rs5757465	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:39477123T>C	ENST00000407997.3	+	3	714	c.357T>C	c.(355-357)ttT>ttC	p.F119F	APOBEC3G_ENST00000461827.1_3'UTR|APOBEC3G_ENST00000452957.2_Silent_p.F119F	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	119					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.F119F(1)		central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					TGACCATCTTTGTTGCCCGCC	0.557													T|||	1425	0.284545	0.0287	0.3977	5008	,	,		16691	0.2242		0.4473	False		,,,				2504	0.4448				p.F119F		Atlas-SNP	.											APOBEC3G_ENST00000407997,NS,carcinoma,0,1	APOBEC3G	69	1	1	Substitution - coding silent(1)	stomach(1)	c.T357C						PASS	.	T		391,4015		18,355,1830	102.0	90.0	94.0		357	-4.9	0.0	22	dbSNP_114	94	3739,4861		831,2077,1392	no	coding-synonymous	APOBEC3G	NM_021822.3		849,2432,3222	CC,CT,TT		43.4767,8.8743,31.7546		119/385	39477123	4130,8876	2203	4300	6503	SO:0001819	synonymous_variant	60489	exon3			CATCTTTGTTGCC	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"""Apolipoprotein B mRNA editing enzymes"""	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.357T>C	22.37:g.39477123T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	170	168	0.988235	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Silent	SNP	ENST00000407997.3	37	CCDS13984.1																																																																																			T|0.692;C|0.308	0.308	strong		0.557	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822	
DMKN	93099	hgsc.bcm.edu	37	19	35998362	35998362	+	Intron	SNP	T	T	G	rs4254439	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35998362T>G	ENST00000339686.3	-	8	1215				DMKN_ENST00000392206.2_Intron|DMKN_ENST00000440396.1_Silent_p.R376R|DMKN_ENST00000602781.1_Intron|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_Intron|DMKN_ENST00000480502.1_Intron|DMKN_ENST00000402589.2_Intron|DMKN_ENST00000467637.1_Intron|DMKN_ENST00000436012.1_Intron|DMKN_ENST00000414866.2_Intron|DMKN_ENST00000488892.1_Intron|DMKN_ENST00000443640.1_Silent_p.R89R|DMKN_ENST00000492341.2_Intron|DMKN_ENST00000458071.1_Intron|DMKN_ENST00000462126.1_Intron|DMKN_ENST00000447113.2_Silent_p.R376R|DMKN_ENST00000472252.2_Intron|DMKN_ENST00000474928.1_Intron|DMKN_ENST00000418261.1_Intron|DMKN_ENST00000419602.1_Silent_p.R315R|DMKN_ENST00000451297.2_Intron|DMKN_ENST00000461300.1_Intron	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine							extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGGCTCACCCTATAATTGTCT	0.507													G|||	1927	0.384784	0.4455	0.3184	5008	,	,		18711	0.4425		0.3022	False		,,,				2504	0.3753				p.R376R		Atlas-SNP	.											.	DMKN	116	.	0			c.A1126C						PASS	.						94.0	84.0	87.0					19																	35998362		692	1591	2283	SO:0001627	intron_variant	93099	exon9			TCACCCTATAATT	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.1039-1474A>C	19.37:g.35998362T>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_001190348	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1	837	0.38324175824175827	224	0.45528455284552843	108	0.2983425414364641	269	0.47027972027972026	236	0.3113456464379947	G	8.948	0.967522	0.18659	.	.	ENSG00000161249	ENST00000434389	.	.	.	3.66	3.66	0.41972	.	.	.	.	.	.	.	.	.	.	.	0.20074	P	0.9999308811	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.7274	0.34478	0.0:0.0:0.7736:0.2264	rs4254439;rs59459723	.	.	.	S	56	.	.	X	-	2	0	DMKN	40690202	0.932000	0.31603	0.543000	0.28128	0.000000	0.00434	1.913000	0.39956	1.133000	0.42147	-0.121000	0.15023	TAG	G|0.367;N|0.002	0.367	strong		0.507	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
SERPINH1	871	hgsc.bcm.edu	37	11	75277992	75277992	+	Silent	SNP	C	C	T	rs651581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:75277992C>T	ENST00000524558.1	+	2	2033	c.598C>T	c.(598-600)Cta>Tta	p.L200L	SERPINH1_ENST00000533603.1_Silent_p.L200L|SERPINH1_ENST00000525876.1_5'Flank|SERPINH1_ENST00000358171.3_Silent_p.L200L|SERPINH1_ENST00000530284.1_Silent_p.L200L			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	200					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					CGGCGCCCTGCTAGTCAACGC	0.667													C|||	1499	0.299321	0.0847	0.3213	5008	,	,		17900	0.2976		0.5417	False		,,,				2504	0.3262				p.L200L		Atlas-SNP	.											.	SERPINH1	33	.	0			c.C598T						PASS	.	C	,	757,3633		68,621,1506	28.0	27.0	27.0		598,598	2.6	1.0	11	dbSNP_83	27	4755,3803		1324,2107,848	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	1392,2728,2354	TT,TC,CC		44.438,17.2437,42.5703	,	200/419,200/419	75277992	5512,7436	2195	4279	6474	SO:0001819	synonymous_variant	871	exon2			GCCCTGCTAGTCA	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.598C>T	11.37:g.75277992C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			C|0.626;T|0.374	0.374	strong		0.667	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
TPO	7173	hgsc.bcm.edu	37	2	1418192	1418192	+	Silent	SNP	C	C	G	rs9678281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:1418192C>G	ENST00000345913.4	+	2	103	c.12C>G	c.(10-12)ctC>ctG	p.L4L	TPO_ENST00000382198.1_Silent_p.L4L|TPO_ENST00000337415.3_Silent_p.L4L|TPO_ENST00000382269.3_Silent_p.L4L|TPO_ENST00000539820.1_Silent_p.L4L|TPO_ENST00000382201.3_Silent_p.L4L|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Silent_p.L4L|TPO_ENST00000329066.4_Silent_p.L4L|TPO_ENST00000346956.3_Silent_p.L4L	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	4					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGAGAGCGCTCGCTGTGCTGT	0.512													C|||	1561	0.311701	0.2769	0.3703	5008	,	,		16931	0.2361		0.3887	False		,,,				2504	0.316				p.L4L		Atlas-SNP	.											TPO,colon,carcinoma,0,1	TPO	224	1	0			c.C12G						scavenged	.	C	,,,,,	1280,3126	431.4+/-342.9	186,908,1109	76.0	73.0	74.0		12,12,12,12,12,12	-10.3	0.0	2	dbSNP_119	74	3341,5259	494.8+/-373.9	662,2017,1621	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	848,2925,2730	GG,GC,CC		38.8488,29.0513,35.5298	,,,,,	4/934,4/934,4/877,4/877,4/890,4/761	1418192	4621,8385	2203	4300	6503	SO:0001819	synonymous_variant	7173	exon2			AGCGCTCGCTGTG		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.12C>G	2.37:g.1418192C>G		Somatic	149	2	0.0134228		WXS	Illumina HiSeq	Phase_I	138	49	0.355072	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1																																																																																			C|0.654;G|0.346;T|0.000	0.346	strong		0.512	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
ZNF211	10520	hgsc.bcm.edu	37	19	58152361	58152361	+	Silent	SNP	T	T	A	rs3746219	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58152361T>A	ENST00000347302.3	+	3	686	c.507T>A	c.(505-507)acT>acA	p.T169T	ZNF211_ENST00000240731.4_Silent_p.T182T|ZNF211_ENST00000541801.1_Silent_p.T160T|ZNF211_ENST00000299871.5_Silent_p.T234T|ZNF211_ENST00000544273.1_Silent_p.T181T|ZNF211_ENST00000420680.1_Silent_p.T173T|ZNF211_ENST00000391703.3_Silent_p.T108T|ZNF211_ENST00000254182.7_Silent_p.T160T	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ATGTGGACACTGCCTCGTTTA	0.463													A|||	1072	0.214058	0.2352	0.1297	5008	,	,		22324	0.3214		0.159	False		,,,				2504	0.1912				p.T234T		Atlas-SNP	.											.	ZNF211	78	.	0			c.T702A						PASS	.	A	,	980,3426	732.6+/-410.4	117,746,1340	94.0	84.0	88.0		546,507	-3.0	0.0	19	dbSNP_107	88	1346,7254	756.5+/-407.5	97,1152,3051	no	coding-synonymous,coding-synonymous	ZNF211	NM_006385.3,NM_198855.2	,	214,1898,4391	AA,AT,TT		15.6512,22.2424,17.8841	,	182/578,169/565	58152361	2326,10680	2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			GGACACTGCCTCG	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.507T>A	19.37:g.58152361T>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	127	77	0.606299	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	37	CCDS12957.1	485	0.22206959706959706	135	0.27439024390243905	52	0.143646408839779	180	0.3146853146853147	118	0.15567282321899736	a	3.445	-0.113268	0.06881	0.222424	0.156512	ENSG00000121417	ENST00000407202	.	.	.	3.01	-3.05	0.05396	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.39333	-0.9619	3	.	.	.	.	1.5958	0.02663	0.21:0.1384:0.3799:0.2718	rs3746219;rs58797181;rs3746219	.	.	.	S	173	.	.	C	+	1	0	ZNF211	62844173	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.114000	0.01329	-1.426000	0.01994	-3.087000	0.00065	TGC	T|0.805;A|0.195	0.195	strong		0.463	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507324	195507324	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507324G>C	ENST00000463781.3	-	2	11586	c.11127C>G	c.(11125-11127)caC>caG	p.H3709Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3709Q	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H3709Q(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGTGTGACCTGAGG	0.572																																					p.H3709Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C11127G						PASS	.						66.0	57.0	59.0					3																	195507324		660	1591	2251	SO:0001583	missense	4585	exon2			GGTGGTGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11127C>G	3.37:g.195507324G>C	ENSP00000417498:p.His3709Gln	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	381	49	0.128609	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.440	0.081383	0.08533	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.52;1.44	0.885	-1.56	0.08532	.	.	.	.	.	T	0.22244	0.0536	N	0.19112	0.55	0.09310	N	1	P	0.44006	0.824	P	0.48770	0.589	T	0.18116	-1.0347	8	.	.	.	.	5.328	0.15917	0.2604:0.0:0.7396:0.0	.	3581	E7ESK3	.	Q	3709	ENSP00000417498:H3709Q;ENSP00000420243:H3709Q	.	H	-	3	2	MUC4	196992103	0.869000	0.29996	0.010000	0.14722	0.046000	0.14306	1.281000	0.33214	-0.535000	0.06307	0.064000	0.15345	CAC	.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC16A8	23539	hgsc.bcm.edu	37	22	38477275	38477275	+	Missense_Mutation	SNP	G	G	A	rs75640043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38477275G>A	ENST00000320521.5	-	4	878	c.770C>T	c.(769-771)gCc>gTc	p.A257V	SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8	257					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|lactate transmembrane transport (GO:0035873)|lactate transport (GO:0015727)|leukocyte migration (GO:0050900)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			kidney(1)|large_intestine(1)|prostate(1)	3	Melanoma(58;0.045)				Pyruvic acid(DB00119)	CTTGGTGACGGCGTACACGGC	0.721													G|||	140	0.0279553	0.0053	0.0533	5008	,	,		11403	0.003		0.0785	False		,,,				2504	0.0143				p.A257V		Atlas-SNP	.											SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	0			c.C770T						PASS	.	G	VAL/ALA	70,4292		2,66,2113	18.0	17.0	17.0		770	-0.7	0.9	22	dbSNP_131	17	783,7775		28,727,3524	yes	missense	SLC16A8	NM_013356.2	64	30,793,5637	AA,AG,GG		9.1493,1.6048,6.6022	benign	257/505	38477275	853,12067	2181	4279	6460	SO:0001583	missense	23539	exon4			GTGACGGCGTACA	AF132610	CCDS13966.1	22q12.3-q13.2	2013-07-18	2013-07-18		ENSG00000100156	ENSG00000100156		"""Solute carriers"""	16270	protein-coding gene	gene with protein product	"""monocarboxylate transporter 3"""	610409	"""solute carrier 16 (monocarboxylic acid transporters), member 8"""			10493836	Standard	NM_013356		Approved	MCT3, REMP	uc003auu.3	O95907	OTTHUMG00000151196	ENST00000320521.5:c.770C>T	22.37:g.38477275G>A	ENSP00000321735:p.Ala257Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	38	28	0.736842	NM_013356	Q9UBE2	Missense_Mutation	SNP	ENST00000320521.5	37	CCDS13966.1	82	0.037545787545787544	5	0.01016260162601626	13	0.03591160220994475	2	0.0034965034965034965	62	0.08179419525065963	G	13.23	2.173754	0.38413	0.016048	0.091493	ENSG00000100156	ENST00000320521	T	0.55930	0.49	3.34	-0.715	0.11215	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.106640	0.06977	N	0.819091	T	0.01870	0.0059	L	0.41124	1.26	0.22975	N	0.998482	B	0.19583	0.037	B	0.24974	0.057	T	0.10428	-1.0630	10	0.20046	T	0.44	.	7.5375	0.27719	0.4057:0.0:0.5943:0.0	.	257	O95907	MOT3_HUMAN	V	257	ENSP00000321735:A257V	ENSP00000321735:A257V	A	-	2	0	SLC16A8	36807221	0.995000	0.38212	0.948000	0.38648	0.931000	0.56810	2.753000	0.47524	-0.042000	0.13535	0.313000	0.20887	GCC	G|0.951;A|0.049	0.049	strong		0.721	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356	
FAM131B	9715	hgsc.bcm.edu	37	7	143053723	143053723	+	Missense_Mutation	SNP	C	C	T	rs17854363	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:143053723C>T	ENST00000409408.1	-	6	2627	c.919G>A	c.(919-921)Gct>Act	p.A307T	FAM131B_ENST00000409222.3_Missense_Mutation_p.A307T|FAM131B_ENST00000443739.2_Missense_Mutation_p.A335T|FAM131B_ENST00000409578.1_Missense_Mutation_p.A323T|FAM131B_ENST00000409346.1_Missense_Mutation_p.A307T			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	307			A -> T (in dbSNP:rs17854363). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					CGGCTGAGAGCGGTAGACATC	0.582													C|||	941	0.187899	0.112	0.2406	5008	,	,		19428	0.2679		0.2087	False		,,,				2504	0.1493				p.A335T		Atlas-SNP	.											.	FAM131B	104	.	0			c.G1003A						PASS	.	C	THR/ALA,THR/ALA	546,3860	244.0+/-253.5	36,474,1693	180.0	162.0	168.0		919,1003	5.8	1.0	7	dbSNP_123	168	1662,6938	308.1+/-308.7	168,1326,2806	yes	missense,missense	FAM131B	NM_014690.4,NM_001031690.2	58,58	204,1800,4499	TT,TC,CC		19.3256,12.3922,16.9768	benign,benign	307/333,335/361	143053723	2208,10798	2203	4300	6503	SO:0001583	missense	9715	exon7			TGAGAGCGGTAGA	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.919G>A	7.37:g.143053723C>T	ENSP00000387017:p.Ala307Thr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	123	43	0.349593	NM_001031690	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	37	CCDS5882.1	487	0.222985347985348	63	0.12804878048780488	86	0.23756906077348067	165	0.28846153846153844	173	0.22823218997361477	C	15.60	2.881674	0.51908	0.123922	0.193256	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88	5.81	5.81	0.92471	.	0.539404	0.18955	N	0.126564	T	0.00012	0.0000	L	0.40543	1.245	0.26047	P	0.9815394	B;P	0.38642	0.198;0.641	B;B	0.28305	0.088;0.08	T	0.48843	-0.8999	9	0.17832	T	0.49	-6.3713	15.5509	0.76152	0.0:0.8627:0.1373:0.0	rs17854363	323;307	Q86XD5-2;Q86XD5	.;F131B_HUMAN	T	335;323;307;311;307;307	ENSP00000410603:A335T;ENSP00000386568:A323T;ENSP00000386984:A307T;ENSP00000387017:A307T;ENSP00000387147:A307T	ENSP00000387147:A307T	A	-	1	0	FAM131B	142763845	0.962000	0.33011	0.959000	0.39883	0.790000	0.44656	3.776000	0.55356	2.746000	0.94184	0.655000	0.94253	GCT	C|0.809;T|0.191	0.191	strong		0.582	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690	
OR4C46	119749	hgsc.bcm.edu	37	11	51516000	51516000	+	Missense_Mutation	SNP	C	C	T	rs11246607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:51516000C>T	ENST00000328188.1	+	1	719	c.719C>T	c.(718-720)tCc>tTc	p.S240F		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	240			S -> F (in dbSNP:rs11246607).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						ACCTGTGTCTCCCACATCACG	0.463													.|||	2170	0.433307	0.202	0.5893	5008	,	,		20028	0.5427		0.5467	False		,,,				2504	0.4059				p.S240F		Atlas-SNP	.											.	OR4C46	96	.	0			c.C719T						PASS	.	C	PHE/SER	1149,3253		158,833,1210	134.0	113.0	120.0		719	2.3	0.4	11	dbSNP_120	120	4688,3904		1303,2082,911	no	missense	OR4C46	NM_001004703.1	155	1461,2915,2121	TT,TC,CC		45.4376,26.1018,44.9207	probably-damaging	240/310	51516000	5837,7157	2201	4296	6497	SO:0001583	missense	119749	exon1			GTGTCTCCCACAT		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.719C>T	11.37:g.51516000C>T	ENSP00000329056:p.Ser240Phe	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	292	136	0.465753	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	1023	0.4684065934065934	78	0.15853658536585366	218	0.6022099447513812	305	0.5332167832167832	422	0.5567282321899736	.	10.83	1.460606	0.26248	0.261018	0.545624	ENSG00000185926	ENST00000328188	T	0.39056	1.1	2.33	2.33	0.28932	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45361	D	0.000373	T	0.00012	0.0000	M	0.89601	3.045	0.37509	P	0.08294599999999996	P	0.46784	0.884	P	0.51806	0.68	T	0.48547	-0.9026	9	0.72032	D	0.01	.	10.4622	0.44585	0.0:1.0:0.0:0.0	rs11246607;rs58689069;rs11246607	240	A6NHA9	O4C46_HUMAN	F	240	ENSP00000329056:S240F	ENSP00000329056:S240F	S	+	2	0	OR4C46	51372576	0.379000	0.25123	0.439000	0.26833	0.110000	0.19582	5.273000	0.65564	1.345000	0.45676	0.121000	0.15741	TCC	C|0.541;T|0.459	0.459	strong		0.463	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
GARS	2617	hgsc.bcm.edu	37	7	30634548	30634548	+	Missense_Mutation	SNP	C	C	T	rs62636572	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:30634548C>T	ENST00000389266.3	+	1	252	c.11C>T	c.(10-12)cCg>cTg	p.P4L	AC005154.6_ENST00000579174.1_RNA|AC005154.6_ENST00000584372.1_RNA|AC005154.6_ENST00000583664.1_RNA|AC005154.6_ENST00000578994.1_RNA|AC005154.6_ENST00000581665.1_RNA|AC005154.6_ENST00000580440.1_RNA|AC005154.6_ENST00000582549.1_RNA|AC005154.6_ENST00000584199.1_RNA	NM_002047.2	NP_002038.2	P41250	SYG_HUMAN	glycyl-tRNA synthetase	4					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|glycyl-tRNA aminoacylation (GO:0006426)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|glycine-tRNA ligase activity (GO:0004820)|protein dimerization activity (GO:0046983)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	24					Glycine(DB00145)	ATGCCCTCTCCGCGTCCAGTG	0.711													C|||	42	0.00838658	0.0	0.0245	5008	,	,		14101	0.0		0.0239	False		,,,				2504	0.001				p.P4L		Atlas-SNP	.											.	GARS	52	.	0			c.C11T						PASS	.	C	LEU/PRO	10,3978		0,10,1984	7.0	8.0	8.0		11	-1.4	0.0	7	dbSNP_129	8	113,8037		0,113,3962	yes	missense	GARS	NM_002047.2	98	0,123,5946	TT,TC,CC		1.3865,0.2508,1.0133	benign	4/740	30634548	123,12015	1994	4075	6069	SO:0001583	missense	2617	exon1			CCTCTCCGCGTCC	AK074524	CCDS43564.1	7p15	2014-09-17	2004-02-13		ENSG00000106105	ENSG00000106105	6.1.1.14	"""Aminoacyl tRNA synthetases / Class II"""	4162	protein-coding gene	gene with protein product	"""glycine tRNA ligase"""	600287	"""Charcot-Marie-Tooth neuropathy 2D"""	CMT2D		8595897, 8872480	Standard	NM_002047		Approved	GlyRS, DSMAV, SMAD1	uc003tbm.3	P41250	OTTHUMG00000152769	ENST00000389266.3:c.11C>T	7.37:g.30634548C>T	ENSP00000373918:p.Pro4Leu	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_002047	B3KQA2|B4DIA0|Q969Y1	Missense_Mutation	SNP	ENST00000389266.3	37	CCDS43564.1	29	0.013278388278388278	0	0.0	11	0.03038674033149171	0	0.0	18	0.023746701846965697	C	0.026	-1.372300	0.01214	0.002508	0.013865	ENSG00000106105	ENST00000389266	T	0.80566	-1.39	3.33	-1.39	0.08997	.	0.647368	0.15500	N	0.259091	T	0.29817	0.0745	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25641	-1.0126	10	0.10377	T	0.69	0.9595	7.0049	0.24830	0.0:0.4002:0.0:0.5998	rs62636572	4	P41250	SYG_HUMAN	L	4	ENSP00000373918:P4L	ENSP00000373918:P4L	P	+	2	0	GARS	30601073	0.000000	0.05858	0.011000	0.14972	0.317000	0.28152	-0.624000	0.05540	-0.325000	0.08577	-0.133000	0.14855	CCG	C|0.986;T|0.014	0.014	strong		0.711	GARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327735.1	NM_002047	
FAT1	2195	hgsc.bcm.edu	37	4	187549443	187549443	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187549443C>T	ENST00000441802.2	-	9	4884	c.4675G>A	c.(4675-4677)Gcc>Acc	p.A1559T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1559	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AACCACGGGGCGTGGTCATTC	0.498										HNSCC(5;0.00058)																											p.A1559T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G4675A						PASS	.						56.0	58.0	57.0					4																	187549443		2103	4226	6329	SO:0001583	missense	2195	exon9			ACGGGGCGTGGTC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.4675G>A	4.37:g.187549443C>T	ENSP00000406229:p.Ala1559Thr	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.117363	0.56505	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.03181	4.02	5.36	4.52	0.55395	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.100704	0.64402	D	0.000002	T	0.06600	0.0169	M	0.72894	2.215	0.80722	D	1	B	0.24920	0.114	B	0.17722	0.019	T	0.20605	-1.0270	10	0.19590	T	0.45	.	15.7693	0.78152	0.1368:0.8631:0.0:0.0	.	1559	Q14517	FAT1_HUMAN	T	1559;1558	ENSP00000406229:A1559T	ENSP00000260147:A1558T	A	-	1	0	FAT1	187786437	0.945000	0.32115	0.915000	0.36163	0.916000	0.54674	2.092000	0.41700	1.477000	0.48234	0.563000	0.77884	GCC	.	.	none		0.498	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
PSG5	5673	hgsc.bcm.edu	37	19	43680037	43680037	+	Missense_Mutation	SNP	T	T	A	rs1135901	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:43680037T>A	ENST00000366175.3	-	3	824	c.694A>T	c.(694-696)Acc>Tcc	p.T232S	PSG5_ENST00000407356.1_Missense_Mutation_p.T232S|PSG5_ENST00000407568.1_Intron|PSG5_ENST00000342951.6_Missense_Mutation_p.T232S|PSG5_ENST00000599812.1_Missense_Mutation_p.T325S|PSG5_ENST00000404580.1_Missense_Mutation_p.T232S			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	232	Ig-like C2-type 1.			T -> S (in Ref. 2; AAA60205 and 3; AAA36514). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				ACATTCAGGGTGACTGGGTCA	0.493													T|||	621	0.124002	0.1687	0.1383	5008	,	,		19877	0.0		0.2614	False		,,,				2504	0.0399				p.T232S		Atlas-SNP	.											PSG5,colon,carcinoma,0,2	PSG5	58	2	0			c.A694T						PASS	.	T	SER/THR,SER/THR	850,3552	334.7+/-303.5	100,650,1451	142.0	139.0	140.0		694,694	-2.2	0.1	19	dbSNP_86	140	2225,6365	378.7+/-339.0	338,1549,2408	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	58,58	438,2199,3859	AA,AT,TT		25.9022,19.3094,23.6684	probably-damaging,probably-damaging	232/336,232/336	43680037	3075,9917	2201	4295	6496	SO:0001583	missense	5673	exon3			TCAGGGTGACTGG		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.694A>T	19.37:g.43680037T>A	ENSP00000382334:p.Thr232Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	331	0.15155677655677655	78	0.15853658536585366	51	0.1408839779005525	0	0.0	202	0.26649076517150394	t	11.12	1.544429	0.27563	0.193094	0.259022	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951;ENST00000404580	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	1.08	-2.17	0.07059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.79258	2.445	0.51012	P	9.700000000001374E-5	B;B	0.33739	0.272;0.422	B;P	0.45712	0.189;0.491	T	0.35500	-0.9786	8	0.45353	T	0.12	.	2.8794	0.05642	0.4002:0.0:0.0:0.5998	rs1135901;rs3179037;rs3198898	325;232	Q15228;Q15238	.;PSG5_HUMAN	S	232	ENSP00000382334:T232S;ENSP00000386008:T232S;ENSP00000344413:T232S;ENSP00000385250:T232S	ENSP00000344413:T232S	T	-	1	0	PSG5	48371877	0.004000	0.15560	0.075000	0.20258	0.024000	0.10985	-0.018000	0.12568	-0.711000	0.04995	0.155000	0.16302	ACC	T|0.792;A|0.208	0.208	strong		0.493	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
FAN1	22909	hgsc.bcm.edu	37	15	31197564	31197564	+	Missense_Mutation	SNP	G	G	A	rs4779794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:31197564G>A	ENST00000362065.4	+	2	989	c.698G>A	c.(697-699)gGa>gAa	p.G233E	FAN1_ENST00000565466.1_Missense_Mutation_p.G233E|FAN1_ENST00000561594.1_Missense_Mutation_p.G233E|FAN1_ENST00000561607.1_Missense_Mutation_p.G233E	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	233			G -> E (in dbSNP:rs4779794). {ECO:0000269|PubMed:15489334}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						ATGGTAAGAGGAAGTAAAATA	0.408								Direct reversal of damage					G|||	2116	0.422524	0.0401	0.4539	5008	,	,		21085	0.7679		0.4374	False		,,,				2504	0.546				p.G233E		Atlas-SNP	.											FAN1,NS,carcinoma,+1,1	FAN1	77	1	0			c.G698A						PASS	.	G	GLU/GLY,GLU/GLY,GLU/GLY,GLU/GLY	494,3910	225.6+/-241.4	34,426,1742	53.0	52.0	52.0		698,698,698,698	-2.2	0.0	15	dbSNP_111	52	3661,4939	522.8+/-380.2	760,2141,1399	yes	missense,missense,missense,missense	FAN1	NM_001146094.1,NM_001146095.1,NM_001146096.1,NM_014967.4	98,98,98,98	794,2567,3141	AA,AG,GG		42.5698,11.2171,31.9517	benign,benign,benign,benign	233/534,233/534,233/534,233/1018	31197564	4155,8849	2202	4300	6502	SO:0001583	missense	22909	exon2			TAAGAGGAAGTAA		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.698G>A	15.37:g.31197564G>A	ENSP00000354497:p.Gly233Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	32	0.4	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	37	CCDS32186.1	985	0.451007326007326	28	0.056910569105691054	157	0.43370165745856354	456	0.7972027972027972	344	0.45382585751978893	G	1.907	-0.451723	0.04572	0.112171	0.425698	ENSG00000198690	ENST00000362065	T	0.41065	1.01	5.18	-2.16	0.07080	.	1.092420	0.06802	N	0.788905	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.33583	0.146;0.418	B;B	0.30855	0.026;0.121	T	0.48547	-0.9026	9	0.02654	T	1	-2.2897	6.1061	0.20073	0.5001:0.0:0.3751:0.1248	rs4779794;rs17227870;rs57472252;rs4779794	233;233	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	E	233	ENSP00000354497:G233E	ENSP00000354497:G233E	G	+	2	0	FAN1	28984856	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.063000	0.11655	-0.319000	0.08652	-0.126000	0.14955	GGA	G|0.626;A|0.374	0.374	strong		0.408	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967	
Unknown	0	hgsc.bcm.edu	37	11	5989293	5989293	+	IGR	SNP	G	G	A	rs7113548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5989293G>A								OR56A3 (19702 upstream) : OR52L1 (17828 downstream)																							CAGCCCTAGCGACAAATTGAT	0.483													.|||	1143	0.228235	0.1989	0.2233	5008	,	,		22002	0.2133		0.2883	False		,,,				2504	0.2249				p.V144V		Atlas-SNP	.											.	.	.	.	0			c.C432T						PASS	.	G		297,1087		30,237,425	70.0	63.0	65.0		432	-3.5	0.0	11	dbSNP_116	65	887,2295		131,625,835	no	coding-synonymous	OR56A5	NM_001146033.1		161,862,1260	AA,AG,GG		27.8755,21.4595,25.9308		144/314	5989293	1184,3382	692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			CCTAGCGACAAAT																													11.37:g.5989293G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_001146033		Silent	SNP		37																																																																																				G|0.755;A|0.245	0.245	strong	0	0.483								
SLC39A13	91252	hgsc.bcm.edu	37	11	47434986	47434986	+	Silent	SNP	G	G	A	rs2293576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:47434986G>A	ENST00000362021.4	+	5	615	c.573G>A	c.(571-573)gcG>gcA	p.A191A	SLC39A13_ENST00000529740.1_3'UTR|SLC39A13_ENST00000524928.1_Silent_p.A191A|SLC39A13_ENST00000533076.1_Silent_p.A191A|SLC39A13_ENST00000354884.4_Silent_p.A191A	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	191	Poly-Ala.				cellular zinc ion homeostasis (GO:0006882)|connective tissue development (GO:0061448)|zinc ion transmembrane transport (GO:0071577)	Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|kidney(1)|lung(1)|prostate(1)	4				Lung(87;0.0936)		CTGCCGCCGCGCTCAATGGAG	0.667													G|||	1355	0.270567	0.0136	0.2147	5008	,	,		15354	0.3988		0.3111	False		,,,				2504	0.4836				p.A191A		Atlas-SNP	.											SLC39A13,NS,carcinoma,+2,1	SLC39A13	18	1	0			c.G573A						PASS	.	G	,	306,4096	159.2+/-191.8	12,282,1907	29.0	32.0	31.0		573,573	-1.7	0.0	11	dbSNP_100	31	2889,5707	430.6+/-356.6	464,1961,1873	no	coding-synonymous,coding-synonymous	SLC39A13	NM_001128225.2,NM_152264.4	,	476,2243,3780	AA,AG,GG		33.6087,6.9514,24.5807	,	191/372,191/365	47434986	3195,9803	2201	4298	6499	SO:0001819	synonymous_variant	91252	exon5			CGCCGCGCTCAAT		CCDS7934.1, CCDS44592.1	11p11.2	2013-05-22			ENSG00000165915	ENSG00000165915		"""Solute carriers"""	20859	protein-coding gene	gene with protein product		608735	"""solute carrier family 39 (metal ion transporter), member 13"""			12659941	Standard	NM_001128225		Approved	FLJ25785	uc009ylq.3	Q96H72	OTTHUMG00000166890	ENST00000362021.4:c.573G>A	11.37:g.47434986G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	96	54	0.5625	NM_152264	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Silent	SNP	ENST00000362021.4	37	CCDS44592.1																																																																																			G|0.756;A|0.244	0.244	strong		0.667	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264	
WDR43	23160	hgsc.bcm.edu	37	2	29135468	29135468	+	Silent	SNP	C	C	G	rs6715296	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29135468C>G	ENST00000407426.3	+	4	554	c.498C>G	c.(496-498)ggC>ggG	p.G166G	SNORD92_ENST00000585078.1_RNA	NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	166						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					AATGGAAAGGCGACAATAGCA	0.373													C|||	3502	0.699281	0.5166	0.7622	5008	,	,		18134	0.8591		0.7048	False		,,,				2504	0.7311				p.G166G		Atlas-SNP	.											.	WDR43	38	.	0			c.C498G						PASS	.	C		2125,1609		595,935,337	134.0	124.0	127.0		498	-2.6	1.0	2	dbSNP_116	127	5907,2289		2134,1639,325	no	coding-synonymous	WDR43	NM_015131.1		2729,2574,662	GG,GC,CC		27.9283,43.0905,32.6739		166/678	29135468	8032,3898	1867	4098	5965	SO:0001819	synonymous_variant	23160	exon4			GAAAGGCGACAAT	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"""WD repeat domain containing"""	28945	protein-coding gene	gene with protein product	"""UTP5, small subunit (SSU) processome component, homolog (yeast)"""					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.498C>G	2.37:g.29135468C>G		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	243	109	0.44856	NM_015131	Q15395|Q92577	Silent	SNP	ENST00000407426.3	37	CCDS46251.1																																																																																			C|0.293;G|0.707	0.707	strong		0.373	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089	
GANC	2595	hgsc.bcm.edu	37	15	42570718	42570718	+	Missense_Mutation	SNP	A	A	G	rs8024732	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42570718A>G	ENST00000318010.8	+	3	371	c.131A>G	c.(130-132)cAg>cGg	p.Q44R	GANC_ENST00000440615.2_Missense_Mutation_p.Q44R|GANC_ENST00000566442.1_Missense_Mutation_p.Q44R	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	44			Q -> R (in dbSNP:rs8024732). {ECO:0000269|PubMed:12370436, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	TCCACCTATCAGGCATTATTG	0.393													A|||	3227	0.644369	0.3396	0.6254	5008	,	,		18527	0.8423		0.8668	False		,,,				2504	0.637				p.Q44R		Atlas-SNP	.											.	GANC	57	.	0			c.A131G						PASS	.	A	ARG/GLN	1925,2481	549.3+/-377.7	448,1029,726	120.0	108.0	112.0		131	-2.8	0.5	15	dbSNP_116	112	7406,1192	763.4+/-407.6	3201,1004,94	yes	missense	GANC	NM_198141.2	43	3649,2033,820	GG,GA,AA		13.8637,43.6904,28.2452	benign	44/915	42570718	9331,3673	2203	4299	6502	SO:0001583	missense	2595	exon3			CCTATCAGGCATT	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.131A>G	15.37:g.42570718A>G	ENSP00000326227:p.Gln44Arg	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	285	153	0.536842	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	1601	0.733058608058608	189	0.38414634146341464	245	0.6767955801104972	499	0.8723776223776224	668	0.8812664907651715	A	0.012	-1.652020	0.00785	0.436904	0.861363	ENSG00000214013	ENST00000318010;ENST00000440615	T;T	0.16743	2.32;2.32	5.44	-2.85	0.05734	.	0.368234	0.26418	N	0.024488	T	0.00012	0.0000	N	0.02202	-0.64	0.37350	P	0.08925499999999997	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.35025	-0.9805	9	0.02654	T	1	-1.1648	10.9723	0.47446	0.545:0.0:0.455:0.0	rs8024732;rs17855008;rs59002636;rs8024732	44;44;44	E7EWB6;Q8TET4;Q2M2A3	.;GANC_HUMAN;.	R	44	ENSP00000326227:Q44R;ENSP00000399557:Q44R	ENSP00000326227:Q44R	Q	+	2	0	GANC	40358010	0.952000	0.32445	0.454000	0.27019	0.015000	0.08874	-0.262000	0.08682	-0.763000	0.04658	-0.353000	0.07706	CAG	A|0.276;G|0.724	0.724	strong		0.393	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
HIST3H3	8290	hgsc.bcm.edu	37	1	228612810	228612810	+	Missense_Mutation	SNP	G	G	A	rs148579172		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228612810G>A	ENST00000366696.1	-	1	216	c.217C>T	c.(217-219)Cgc>Tgc	p.R73C		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	73					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				GCGATCTCGCGCATCAGCCGC	0.642																																					p.R73C		Atlas-SNP	.											HIST3H3,colon,carcinoma,+1,1	HIST3H3	20	1	0			c.C217T						scavenged	.						83.0	84.0	84.0					1																	228612810		2203	4300	6503	SO:0001583	missense	8290	exon1			TCTCGCGCATCAG	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"""Histones / Replication-dependent"""	4778	protein-coding gene	gene with protein product		602820	"""H3 histone family, member T"", ""histone 3, H3"""	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.217C>T	1.37:g.228612810G>A	ENSP00000355657:p.Arg73Cys	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	178	5	0.0280899	NM_003493	B2R5K3|Q6FGU4	Missense_Mutation	SNP	ENST00000366696.1	37	CCDS1572.1	.	.	.	.	.	.	.	.	.	.	g	6.736	0.504537	0.12822	.	.	ENSG00000168148	ENST00000366696	T	0.77750	-1.12	3.72	1.82	0.25136	Histone-fold (2);Histone core (1);	0.000000	0.39834	N	0.001259	D	0.91116	0.7203	H	0.98996	4.395	0.38317	D	0.94342	D	0.89917	1.0	D	0.97110	1.0	D	0.89884	0.4032	10	0.87932	D	0	.	7.0988	0.25325	0.1018:0.1757:0.7225:0.0	.	73	Q16695	H31T_HUMAN	C	73	ENSP00000355657:R73C	ENSP00000355657:R73C	R	-	1	0	HIST3H3	226679433	0.236000	0.23804	0.328000	0.25416	0.005000	0.04900	1.814000	0.38972	0.522000	0.28464	-0.248000	0.11899	CGC	G|1.000;T|0.000	.	alt		0.642	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493	
RELN	5649	hgsc.bcm.edu	37	7	103251161	103251161	+	Missense_Mutation	SNP	G	G	C	rs362691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:103251161G>C	ENST00000428762.1	-	22	3148	c.2989C>G	c.(2989-2991)Ctt>Gtt	p.L997V	RELN_ENST00000343529.5_Missense_Mutation_p.L997V|RELN_ENST00000424685.2_Missense_Mutation_p.L997V	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	997			L -> V (in dbSNP:rs362691).		associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TGGGGAAGAAGCACTATGACT	0.398													G|||	606	0.121006	0.0658	0.121	5008	,	,		18694	0.1458		0.1054	False		,,,				2504	0.1861				p.L997V	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C2989G						PASS	.	G	VAL/LEU,VAL/LEU	367,4039	186.4+/-213.3	15,337,1851	175.0	140.0	152.0		2989,2989	4.4	0.1	7	dbSNP_79	152	893,7707	200.7+/-244.4	53,787,3460	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	32,32	68,1124,5311	CC,CG,GG		10.3837,8.3296,9.6878	benign,benign	997/3461,997/3459	103251161	1260,11746	2203	4300	6503	SO:0001583	missense	5649	exon22			GAAGAAGCACTAT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.2989C>G	7.37:g.103251161G>C	ENSP00000392423:p.Leu997Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	227	0.10393772893772894	33	0.06707317073170732	44	0.12154696132596685	67	0.11713286713286714	83	0.10949868073878628	G	8.848	0.943780	0.18281	0.083296	0.103837	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.22539	1.99;1.98;1.95	6.17	4.36	0.52297	.	0.314360	0.36034	N	0.002827	T	0.00178	0.0005	N	0.14661	0.345	0.43787	P	0.00367099999999998	B;B	0.27791	0.185;0.189	B;B	0.31101	0.124;0.073	T	0.29488	-1.0010	9	0.15066	T	0.55	.	12.0604	0.53559	0.0:0.1302:0.734:0.1358	rs362691;rs17310959;rs52796689;rs362691	997;997	P78509-2;P78509	.;RELN_HUMAN	V	997	ENSP00000392423:L997V;ENSP00000345694:L997V;ENSP00000388446:L997V	ENSP00000345694:L997V	L	-	1	0	RELN	103038397	1.000000	0.71417	0.062000	0.19696	0.993000	0.82548	4.021000	0.57196	0.916000	0.36871	0.655000	0.94253	CTT	C|0.101;G|0.899;N|0.000	0.101	strong		0.398	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
NOBOX	135935	hgsc.bcm.edu	37	7	144107279	144107279	+	Silent	SNP	A	A	G	rs1208179	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:144107279A>G	ENST00000467773.1	-	1	41	c.42T>C	c.(40-42)ggT>ggC	p.G14G	NOBOX_ENST00000483238.1_Silent_p.G14G	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	14					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					TGTCCCAGGTACCCTCCAGGT	0.502													A|||	526	0.105032	0.0431	0.0965	5008	,	,		20108	0.0238		0.1461	False		,,,				2504	0.2362				p.G14G		Atlas-SNP	.											NOBOX_ENST00000467773,NS,carcinoma,0,4	NOBOX	130	4	0			c.T42C						PASS	.	A		234,3704		6,222,1741	105.0	106.0	106.0		42	-7.0	0.0	7	dbSNP_87	106	1321,6997		103,1115,2941	no	coding-synonymous	NOBOX	NM_001080413.3		109,1337,4682	GG,GA,AA		15.8812,5.9421,12.6877		14/692	144107279	1555,10701	1969	4159	6128	SO:0001819	synonymous_variant	135935	exon1			CCAGGTACCCTCC			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.42T>C	7.37:g.144107279A>G		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	239	83	0.34728	NM_001080413	A6NCD3|A8MZN5	Silent	SNP	ENST00000467773.1	37																																																																																				A|0.900;G|0.100	0.100	strong		0.502	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
TEK	7010	hgsc.bcm.edu	37	9	27213580	27213580	+	Silent	SNP	T	T	C	rs3737188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:27213580T>C	ENST00000380036.4	+	18	3418	c.2976T>C	c.(2974-2976)taT>taC	p.Y992Y	TEK_ENST00000519097.1_Silent_p.Y844Y|TEK_ENST00000406359.4_Silent_p.Y949Y	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	992	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	AAGAGGTGTATGTGAAAAAGA	0.458													T|||	770	0.153754	0.0651	0.1787	5008	,	,		19621	0.1925		0.2008	False		,,,				2504	0.1677				p.Y992Y		Atlas-SNP	.											.	TEK	250	.	0			c.T2976C						PASS	.	T		453,3953	215.5+/-234.4	27,399,1777	125.0	121.0	122.0		2976	0.6	1.0	9	dbSNP_107	122	1873,6727	335.0+/-321.2	190,1493,2617	no	coding-synonymous	TEK	NM_000459.3		217,1892,4394	CC,CT,TT		21.7791,10.2814,17.8841		992/1125	27213580	2326,10680	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon18			GGTGTATGTGAAA	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2976T>C	9.37:g.27213580T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			T|0.835;C|0.165	0.165	strong		0.458	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
SART1	9092	hgsc.bcm.edu	37	11	65735174	65735174	+	Missense_Mutation	SNP	G	G	C	rs660118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65735174G>C	ENST00000312397.5	+	12	1546	c.1454G>C	c.(1453-1455)gGg>gCg	p.G485A		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	485			G -> A (in dbSNP:rs660118). {ECO:0000269|Ref.4}.		cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CCACCGCCGGGGTCCCCGCAG	0.677													G|||	1834	0.366214	0.0393	0.5793	5008	,	,		13594	0.5218		0.4404	False		,,,				2504	0.4202				p.G485A		Atlas-SNP	.											.	SART1	41	.	0			c.G1454C	GRCh37	CM024558	SART1	M	rs660118	PASS	.	G	ALA/GLY	442,3874		37,368,1753	11.0	12.0	12.0		1454	4.2	0.8	11	dbSNP_83	12	3506,4952		754,1998,1477	no	missense	SART1	NM_005146.4	60	791,2366,3230	CC,CG,GG		41.4519,10.241,30.9065	possibly-damaging	485/801	65735174	3948,8826	2158	4229	6387	SO:0001583	missense	9092	exon12			CGCCGGGGTCCCC	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"""small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"""	605941	"""squamous cell carcinoma antigen recognised by T cells"""			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.1454G>C	11.37:g.65735174G>C	ENSP00000310448:p.Gly485Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_005146	A6NDN1|Q53GB5	Missense_Mutation	SNP	ENST00000312397.5	37	CCDS31611.1	882	0.40384615384615385	30	0.06097560975609756	194	0.5359116022099447	323	0.5646853146853147	335	0.4419525065963061	G	6.367	0.435751	0.12104	0.10241	0.414519	ENSG00000175467	ENST00000312397;ENST00000542816	T	0.21543	2.0	5.12	4.17	0.49024	.	0.349123	0.25532	N	0.030034	T	0.00012	0.0000	L	0.46157	1.445	0.24437	P	0.99454935	B	0.30179	0.271	B	0.24541	0.054	T	0.39901	-0.9591	9	0.87932	D	0	-48.9249	11.2382	0.48953	0.0:0.1857:0.8143:0.0	rs660118;rs61398889;rs660118	485	O43290	SNUT1_HUMAN	A	485;327	ENSP00000310448:G485A	ENSP00000310448:G485A	G	+	2	0	SART1	65491750	0.633000	0.27181	0.837000	0.33122	0.452000	0.32318	-0.229000	0.09098	1.090000	0.41315	0.491000	0.48974	GGG	G|0.591;C|0.409	0.409	strong		0.677	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1		
MUC4	4585	hgsc.bcm.edu	37	3	195477791	195477791	+	Silent	SNP	G	G	A	rs2291652	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195477791G>A	ENST00000346145.4	-	22	3171	c.3132C>T	c.(3130-3132)atC>atT	p.I1044I	MUC4_ENST00000349607.4_Silent_p.I993I|MUC4_ENST00000463781.3_Silent_p.I5280I|MUC4_ENST00000475231.1_Silent_p.I5228I	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2037					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTTCCCCGGAGATGGGCTGGA	0.637													.|||	2034	0.40615	0.0787	0.4179	5008	,	,		11844	0.7679		0.4583	False		,,,				2504	0.4141				p.I5280I		Atlas-SNP	.											.	MUC4	1505	.	0			c.C15840T						PASS	.	G	,,	658,3748	276.6+/-273.2	54,550,1599	64.0	57.0	60.0		3132,15840,2979	3.0	0.9	3	dbSNP_100	60	3871,4729	540.4+/-383.8	868,2135,1297	no	coding-synonymous,coding-synonymous,coding-synonymous	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	922,2685,2896	AA,AG,GG		45.0116,14.9342,34.8224	,,	1044/1177,5280/5413,993/1126	195477791	4529,8477	2203	4300	6503	SO:0001819	synonymous_variant	4585	exon23			CCCGGAGATGGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.3132C>T	3.37:g.195477791G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																			G|0.628;A|0.372	0.372	strong		0.637	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
SERPINB10	5273	hgsc.bcm.edu	37	18	61584749	61584749	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:61584749G>A	ENST00000238508.3	+	3	287	c.228G>A	c.(226-228)agG>agA	p.R76R		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	76					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				AAAAAAAAAGGAAAATGGTAT	0.299																																					p.R76R		Atlas-SNP	.											SERPINB10,colon,carcinoma,+2,1	SERPINB10	53	1	0			c.G228A						scavenged	.						22.0	23.0	23.0					18																	61584749		2167	4251	6418	SO:0001819	synonymous_variant	5273	exon2			AAAAAGGAAAATG	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.228G>A	18.37:g.61584749G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	2	0.0363636	NM_005024	Q4VAX4|Q4VAX7	Silent	SNP	ENST00000238508.3	37	CCDS11990.1																																																																																			.	.	none		0.299	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
CD163L1	283316	hgsc.bcm.edu	37	12	7585971	7585971	+	Splice_Site	SNP	A	A	G	rs10845159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7585971A>G	ENST00000313599.3	-	3	501	c.444T>C	c.(442-444)taT>taC	p.Y148Y	CD163L1_ENST00000416109.2_Silent_p.Y148Y|CD163L1_ENST00000396630.1_Splice_Site_p.Y148Y			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	148	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						GACTCTTACCATAACAGTTCA	0.438													A|||	1437	0.286941	0.0242	0.3458	5008	,	,		-128	0.3413		0.5457	False		,,,				2504	0.2781				p.Y148Y		Atlas-SNP	.											.	CD163L1	238	.	0			c.T444C						PASS	.	A		502,3904	230.7+/-244.8	42,418,1743	102.0	94.0	97.0		444	-4.4	0.0	12	dbSNP_120	97	4725,3875	608.2+/-395.4	1311,2103,886	yes	coding-synonymous-near-splice	CD163L1	NM_174941.4		1353,2521,2629	GG,GA,AA		45.0581,11.3936,40.1891		148/1454	7585971	5227,7779	2203	4300	6503	SO:0001630	splice_region_variant	283316	exon3			CTTACCATAACAG	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.445+1T>C	12.37:g.7585971A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	183	83	0.453552	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																			A|0.625;G|0.375	0.375	strong		0.438	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	Silent
MARCH1	55016	hgsc.bcm.edu	37	4	164466824	164466824	+	Silent	SNP	C	C	T	rs13130399	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:164466824C>T	ENST00000503008.1	-	7	1471	c.495G>A	c.(493-495)gcG>gcA	p.A165A	MARCH1_ENST00000514618.1_Silent_p.A421A|MARCH1_ENST00000274056.7_Silent_p.A165A|MARCH1_ENST00000339875.5_Silent_p.A148A	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase	165					antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A148A(2)		endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CACAGGTGATCGCGATTACGT	0.428													C|||	1933	0.385982	0.2776	0.6037	5008	,	,		19890	0.3482		0.4583	False		,,,				2504	0.3425				p.A165A		Atlas-SNP	.											MARCH1,NS,carcinoma,0,2	MARCH1	83	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.G495A						PASS	.	C	,	1242,3164	428.5+/-341.9	173,896,1134	301.0	226.0	252.0		495,444	0.3	1.0	4	dbSNP_121	252	4042,4558	557.0+/-387.0	965,2112,1223	no	coding-synonymous,coding-synonymous	MARCH1	NM_001166373.1,NM_017923.3	,	1138,3008,2357	TT,TC,CC		47.0,28.1888,40.6274	,	165/290,148/273	164466824	5284,7722	2203	4300	6503	SO:0001819	synonymous_variant	55016	exon7			GGTGATCGCGATT	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26077	protein-coding gene	gene with protein product		613331	"""membrane-associated ring finger (C3HC4) 1"""			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.495G>A	4.37:g.164466824C>T		Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	215	109	0.506977	NM_001166373	D3DP29|Q9NWR0	Silent	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			C|0.612;T|0.388	0.388	strong		0.428	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
BTN2A1	11120	hgsc.bcm.edu	37	6	26463660	26463660	+	Missense_Mutation	SNP	G	G	A	rs13195509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26463660G>A	ENST00000312541.5	+	4	867	c.619G>A	c.(619-621)Gtg>Atg	p.V207M	BTN2A1_ENST00000469185.1_Missense_Mutation_p.V207M|BTN2A1_ENST00000541522.1_Missense_Mutation_p.V146M|BTN2A1_ENST00000429381.1_Missense_Mutation_p.V207M	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	207			V -> M (in dbSNP:rs13195509).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						CACCACGGCTGTGATCATCAG	0.537													G|||	187	0.0373403	0.034	0.0346	5008	,	,		20403	0.0089		0.0825	False		,,,				2504	0.0266				p.V207M		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G619A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL	188,4218	118.8+/-156.5	4,180,2019	142.0	128.0	132.0		436,619,619,619	2.0	0.5	6	dbSNP_121	132	795,7805	185.9+/-233.5	39,717,3544	yes	missense,missense,missense,missense	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	21,21,21,21	43,897,5563	AA,AG,GG		9.2442,4.2669,7.5581	benign,benign,benign,benign	146/467,207/331,207/528,207/335	26463660	983,12023	2203	4300	6503	SO:0001583	missense	11120	exon4			ACGGCTGTGATCA	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.619G>A	6.37:g.26463660G>A	ENSP00000312158:p.Val207Met	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	212	96	0.45283	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	101	0.04624542124542125	18	0.036585365853658534	11	0.03038674033149171	7	0.012237762237762238	65	0.08575197889182058	G	14.35	2.508995	0.44660	0.042669	0.092442	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95	2.88	2.0	0.26442	CD80-like, immunoglobulin C2-set (1);	0.341466	0.22162	N	0.063768	T	0.75451	0.3851	M	0.79475	2.455	0.46564	P	8.909999999999751E-4	D;D	0.71674	0.998;0.996	D;D	0.76071	0.987;0.97	T	0.72782	-0.4189	9	0.52906	T	0.07	.	4.7866	0.13227	0.2899:0.0:0.7101:0.0	rs13195509;rs52819217;rs57892055;rs13195509	207;207	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	M	207;146;207;207;207	ENSP00000312158:V207M;ENSP00000443909:V146M;ENSP00000416945:V207M;ENSP00000419043:V207M	ENSP00000265424:V207M	V	+	1	0	BTN2A1	26571639	0.012000	0.17670	0.513000	0.27749	0.926000	0.56050	0.225000	0.17757	0.756000	0.33013	0.561000	0.74099	GTG	G|0.939;A|0.061	0.061	strong		0.537	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
MDGA1	266727	hgsc.bcm.edu	37	6	37623626	37623626	+	Silent	SNP	C	C	T	rs13204070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:37623626C>T	ENST00000434837.3	-	4	1607	c.429G>A	c.(427-429)gtG>gtA	p.V143V	MDGA1_ENST00000297153.7_Silent_p.V143V|MDGA1_ENST00000505425.1_Silent_p.V143V	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	143	Ig-like 2.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						AGTTGCCTCGCACATCGCTCA	0.607													C|||	681	0.135982	0.0454	0.1499	5008	,	,		18497	0.1627		0.1988	False		,,,				2504	0.1564				p.V143V		Atlas-SNP	.											.	MDGA1	104	.	0			c.G429A						PASS	.	C		292,3960		12,268,1846	46.0	48.0	47.0		429	-7.2	0.3	6	dbSNP_121	47	1638,6808		162,1314,2747	no	coding-synonymous	MDGA1	NM_153487.3		174,1582,4593	TT,TC,CC		19.3938,6.8674,15.1992		143/956	37623626	1930,10768	2126	4223	6349	SO:0001819	synonymous_variant	266727	exon4			GCCTCGCACATCG	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.429G>A	6.37:g.37623626C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	154	96	0.623377	NM_153487	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	37	CCDS47417.1																																																																																			C|0.847;T|0.153	0.153	strong		0.607	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
IRAK2	3656	hgsc.bcm.edu	37	3	10264480	10264480	+	Missense_Mutation	SNP	C	C	G	rs3844283	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:10264480C>G	ENST00000256458.4	+	9	1264	c.1174C>G	c.(1174-1176)Ctg>Gtg	p.L392V		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	392	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> V (in dbSNP:rs3844283). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						GGTGGGGCAGCTGACAAAGCG	0.537													C|||	1443	0.288139	0.2126	0.464	5008	,	,		19517	0.1339		0.4185	False		,,,				2504	0.2904				p.L392V		Atlas-SNP	.											IRAK2_ENST00000256458,caecum,carcinoma,-1,2	IRAK2	113	2	0			c.C1174G						PASS	.	C	VAL/LEU	1026,3380	379.2+/-323.2	115,796,1292	108.0	106.0	107.0		1174	5.1	1.0	3	dbSNP_108	107	3605,4995	521.0+/-379.8	768,2069,1463	yes	missense	IRAK2	NM_001570.3	32	883,2865,2755	GG,GC,CC		41.9186,23.2864,35.6066	probably-damaging	392/626	10264480	4631,8375	2203	4300	6503	SO:0001583	missense	3656	exon9			GGGCAGCTGACAA	AF026273	CCDS33697.1	3p25.2	2008-08-18			ENSG00000134070	ENSG00000134070			6113	protein-coding gene	gene with protein product		603304				9374458	Standard	XR_245126		Approved		uc003bve.1	O43187	OTTHUMG00000155358	ENST00000256458.4:c.1174C>G	3.37:g.10264480C>G	ENSP00000256458:p.Leu392Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_001570	B4DQZ6|Q08AG6|Q5K546	Missense_Mutation	SNP	ENST00000256458.4	37	CCDS33697.1	663	0.30357142857142855	90	0.18292682926829268	158	0.43646408839779005	84	0.14685314685314685	331	0.4366754617414248	C	19.36	3.812335	0.70912	0.232864	0.419186	ENSG00000134070	ENST00000256458	T	0.34667	1.35	5.14	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38436	N	0.001683	T	0.00012	0.0000	L	0.56199	1.76	0.19300	P	0.9999795581	D	0.89917	1.0	D	0.87578	0.998	T	0.46610	-0.9179	9	0.62326	D	0.03	-15.6131	14.105	0.65083	0.0:1.0:0.0:0.0	rs3844283;rs52790097;rs57169457;rs3844283	392	O43187	IRAK2_HUMAN	V	392	ENSP00000256458:L392V	ENSP00000256458:L392V	L	+	1	2	IRAK2	10239480	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	1.933000	0.40153	2.369000	0.80426	0.655000	0.94253	CTG	C|0.667;G|0.333	0.333	strong		0.537	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		
HLA-E	3133	hgsc.bcm.edu	37	6	30458064	30458064	+	Missense_Mutation	SNP	G	G	A	rs1264457	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30458064G>A	ENST00000376630.4	+	3	447	c.382G>A	c.(382-384)Ggg>Agg	p.G128R		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	128	Alpha-2.		R -> G (in allele E*01:03 and allele E*01:04; dbSNP:rs1264457).		antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						GGGGCCCGACGGGCGCTTCCT	0.687													G|||	2576	0.514377	0.5726	0.5331	5008	,	,		12211	0.3433		0.5676	False		,,,				2504	0.544				p.G128R		Atlas-SNP	.											.	HLA-E	35	.	0			c.G382A	GRCh37	CM076230	HLA-E	M	rs1264457	PASS	.	G	ARG/GLY	1690,1328		478,734,297	56.0	63.0	61.0		382	0.8	0.9	6	dbSNP_87	61	3076,2342		903,1270,536	yes	missense	HLA-E	NM_005516.5	125	1381,2004,833	AA,AG,GG		43.2263,44.0027,43.504	benign	128/359	30458064	4766,3670	1509	2709	4218	SO:0001583	missense	3133	exon3			CCCGACGGGCGCT	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.382G>A	6.37:g.30458064G>A	ENSP00000365817:p.Gly128Arg	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	162	161	0.993827	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Missense_Mutation	SNP	ENST00000376630.4	37	CCDS34379.1	1110	0.5082417582417582	278	0.5650406504065041	184	0.5082872928176796	208	0.36363636363636365	440	0.5804749340369393	.	12.92	2.083505	0.36758	0.559973	0.567737	ENSG00000204592	ENST00000376630	T	0.00016	9.11	1.66	0.764	0.18465	.	0.432766	0.16257	N	0.222447	T	0.00039	0.0001	.	.	.	0.41565	P	0.011349000000000053	P;P	0.39940	0.696;0.552	B;B	0.26770	0.073;0.051	T	0.00001	-1.2710	8	0.72032	D	0.01	.	4.3	0.10920	0.2177:0.0:0.7823:0.0	rs1264457;rs7767992;rs17195355	169;128	E7ENN9;Q6DU44	.;.	R	128	ENSP00000365817:G128R	ENSP00000365817:G128R	G	+	1	0	HLA-E	30566043	0.021000	0.18746	0.857000	0.33713	0.239000	0.25481	0.815000	0.27253	0.265000	0.21872	-0.374000	0.07098	GGG	G|0.454;A|0.546	0.546	strong		0.687	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516	
BSND	7809	hgsc.bcm.edu	37	1	55474262	55474262	+	Silent	SNP	G	G	A	rs33938617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55474262G>A	ENST00000371265.4	+	4	1178	c.924G>A	c.(922-924)ccG>ccA	p.P308P		NM_057176.2	NP_476517.1	Q8WZ55	BSND_HUMAN	barttin CLCNK-type chloride channel accessory beta subunit	308					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride channel activity (GO:0005254)|chloride channel regulator activity (GO:0017081)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17						ACCTCCTCCCGGACAAGGAGC	0.577													g|||	581	0.116014	0.211	0.098	5008	,	,		18850	0.001		0.1859	False		,,,				2504	0.047				p.P308P	Ovarian(191;1657 2078 22894 42033 48899)	Atlas-SNP	.											.	BSND	36	.	0			c.G924A						PASS	.			829,3577	326.4+/-299.6	87,655,1461	86.0	84.0	85.0		924	-9.2	0.0	1	dbSNP_126	85	1768,6832	319.9+/-314.4	182,1404,2714	no	coding-synonymous	BSND	NM_057176.2		269,2059,4175	AA,AG,GG		20.5581,18.8153,19.9677		308/321	55474262	2597,10409	2203	4300	6503	SO:0001819	synonymous_variant	7809	exon4			CCTCCCGGACAAG	AY034632	CCDS602.1	1p32.3	2014-06-17	2014-06-17		ENSG00000162399	ENSG00000162399			16512	protein-coding gene	gene with protein product		606412	"""deafness, autosomal recessive 73"", ""Bartter syndrome, infantile, with sensorineural deafness (Barttin)"""	DFNB73		11687798, 11734858, 19646679	Standard	NM_057176		Approved	BART	uc001cye.3	Q8WZ55	OTTHUMG00000008112	ENST00000371265.4:c.924G>A	1.37:g.55474262G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	19	0.322034	NM_057176	Q6NT28	Silent	SNP	ENST00000371265.4	37	CCDS602.1																																																																																			G|0.824;A|0.176	0.176	strong		0.577	BSND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022213.4	NM_057176	
ZNF574	64763	hgsc.bcm.edu	37	19	42583743	42583743	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:42583743C>T	ENST00000600245.1	+	2	1640	c.985C>T	c.(985-987)Cgg>Tgg	p.R329W	ZNF574_ENST00000359044.4_Missense_Mutation_p.R329W|ZNF574_ENST00000222339.7_Missense_Mutation_p.R419W|CTB-59C6.3_ENST00000594531.1_RNA			Q6ZN55	ZN574_HUMAN	zinc finger protein 574	329					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20		Prostate(69;0.059)				GCAGCACCTGCGGAGTCACCG	0.607																																					p.R329W		Atlas-SNP	.											.	ZNF574	57	.	0			c.C985T						PASS	.						99.0	108.0	105.0					19																	42583743		2203	4300	6503	SO:0001583	missense	64763	exon2			CACCTGCGGAGTC	AK074788	CCDS12596.1	19q13.2	2013-09-20			ENSG00000105732	ENSG00000105732		"""Zinc fingers, C2H2-type"""	26166	protein-coding gene	gene with protein product						12477932	Standard	NM_022752		Approved	FLJ22059	uc002osm.4	Q6ZN55	OTTHUMG00000182751	ENST00000600245.1:c.985C>T	19.37:g.42583743C>T	ENSP00000469029:p.Arg329Trp	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	159	69	0.433962	NM_022752	Q6IPE0|Q6ZN10|Q7L5Z5|Q8NCE3|Q9H6N0	Missense_Mutation	SNP	ENST00000600245.1	37	CCDS12596.1	.	.	.	.	.	.	.	.	.	.	c	15.18	2.756649	0.49362	.	.	ENSG00000105732	ENST00000222339;ENST00000359044	T;T	0.26223	1.75;1.75	4.63	3.58	0.41010	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.141481	0.45361	D	0.000364	T	0.53190	0.1781	M	0.86502	2.82	0.26272	N	0.978409	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.992	T	0.50800	-0.8785	10	0.87932	D	0	-19.0607	11.469	0.50257	0.3259:0.6741:0.0:0.0	.	329;418	Q6ZN55;Q6ZN55-2	ZN574_HUMAN;.	W	419;329	ENSP00000222339:R419W;ENSP00000351939:R329W	ENSP00000222339:R419W	R	+	1	2	ZNF574	47275583	0.563000	0.26594	1.000000	0.80357	0.762000	0.43233	2.030000	0.41108	1.287000	0.44583	-0.174000	0.13273	CGG	.	.	none		0.607	ZNF574-002	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463458.1	NM_022752	
FAM131C	348487	hgsc.bcm.edu	37	1	16389026	16389026	+	Missense_Mutation	SNP	T	T	C	rs2863458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16389026T>C	ENST00000375662.4	-	3	325	c.142A>G	c.(142-144)Aaa>Gaa	p.K48E	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	48			K -> E (in dbSNP:rs2863458). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		TCCATCTGTTTGTCCTAAAAC	0.617													T|||	1494	0.298323	0.4213	0.4207	5008	,	,		16287	0.0188		0.3121	False		,,,				2504	0.319				p.K48E		Atlas-SNP	.											.	FAM131C	21	.	0			c.A142G						PASS	.	T	GLU/LYS	1416,2370		244,928,721	18.0	20.0	19.0		142	3.9	1.0	1	dbSNP_101	19	2327,5867		323,1681,2093	no	missense	FAM131C	NM_182623.2	56	567,2609,2814	CC,CT,TT		28.3988,37.401,31.2437	possibly-damaging	48/281	16389026	3743,8237	1893	4097	5990	SO:0001583	missense	348487	exon3			TCTGTTTGTCCTA		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.142A>G	1.37:g.16389026T>C	ENSP00000364814:p.Lys48Glu	Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	279	107	0.383513	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	575	0.2632783882783883	188	0.3821138211382114	146	0.40331491712707185	6	0.01048951048951049	235	0.3100263852242744	T	19.11	3.763043	0.69763	0.37401	0.283988	ENSG00000185519	ENST00000375662	T	0.16073	2.37	5.07	3.9	0.45041	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	L	0.56769	1.78	0.33293	P	0.43623900000000004	P	0.49559	0.925	P	0.47162	0.54	T	0.48490	-0.9031	9	0.48119	T	0.1	5.667	8.7891	0.34839	0.0:0.0:0.1907:0.8093	rs2863458;rs57426802;rs2863458	48	Q96AQ9	F131C_HUMAN	E	48	ENSP00000364814:K48E	ENSP00000364814:K48E	K	-	1	0	FAM131C	16261613	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.546000	0.45778	0.733000	0.32492	0.459000	0.35465	AAA	.	.	weak		0.617	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
AKAP6	9472	hgsc.bcm.edu	37	14	33293022	33293022	+	Silent	SNP	A	A	G	rs1051694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:33293022A>G	ENST00000280979.4	+	13	6173	c.6003A>G	c.(6001-6003)gcA>gcG	p.A2001A	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2001					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		ACTCTGATGCACTGAAATCAT	0.428													G|||	771	0.153954	0.1551	0.1297	5008	,	,		21204	0.0615		0.1372	False		,,,				2504	0.2822				p.A2001A	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A6003G						PASS	.	G		693,3713	761.1+/-413.0	47,599,1557	93.0	89.0	90.0		6003	-2.8	0.0	14	dbSNP_86	90	1174,7426	764.7+/-407.6	80,1014,3206	no	coding-synonymous	AKAP6	NM_004274.4		127,1613,4763	GG,GA,AA		13.6512,15.7286,14.3549		2001/2320	33293022	1867,11139	2203	4300	6503	SO:0001819	synonymous_variant	9472	exon13			TGATGCACTGAAA	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6003A>G	14.37:g.33293022A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	37	CCDS9644.1																																																																																			A|0.861;G|0.139	0.139	strong		0.428	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
SLC22A14	9389	hgsc.bcm.edu	37	3	38357817	38357817	+	Missense_Mutation	SNP	C	C	T	rs2070492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38357817C>T	ENST00000273173.4	+	9	1626	c.1535C>T	c.(1534-1536)gCg>gTg	p.A512V	SLC22A14_ENST00000448498.1_Missense_Mutation_p.A512V	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	512			A -> V (in dbSNP:rs2070492).		organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		ACTTTCAGGGCGACAGGTCTG	0.617													C|||	535	0.106829	0.0719	0.1499	5008	,	,		17650	0.1647		0.1143	False		,,,				2504	0.0562				p.A512V		Atlas-SNP	.											.	SLC22A14	64	.	0			c.C1535T						PASS	.	C	VAL/ALA	325,4081	171.6+/-201.8	16,293,1894	76.0	67.0	70.0		1535	3.3	0.0	3	dbSNP_96	70	863,7737	194.2+/-239.7	53,757,3490	yes	missense	SLC22A14	NM_004803.3	64	69,1050,5384	TT,TC,CC		10.0349,7.3763,9.1342	possibly-damaging	512/595	38357817	1188,11818	2203	4300	6503	SO:0001583	missense	9389	exon9			TCAGGGCGACAGG	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"""Solute carriers"""	8495	protein-coding gene	gene with protein product		604048	"""organic cationic transporter-like 4"", ""solute carrier family 22 (organic cation transporter), member 14"""	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.1535C>T	3.37:g.38357817C>T	ENSP00000273173:p.Ala512Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	60	39	0.65	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	264	0.12087912087912088	42	0.08536585365853659	47	0.1298342541436464	91	0.1590909090909091	84	0.11081794195250659	C	4.885	0.164525	0.09287	0.073763	0.100349	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.61980	0.06;0.06	4.2	3.32	0.38043	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.341437	0.30365	N	0.009781	T	0.00328	0.0010	L	0.54323	1.7	0.80722	P	0.0	P	0.51147	0.942	B	0.43445	0.42	T	0.12041	-1.0563	9	0.46703	T	0.11	.	9.6139	0.39679	0.2082:0.7918:0.0:0.0	rs2070492;rs61374957;rs2070492	512	Q9Y267	S22AE_HUMAN	V	512;497;512	ENSP00000396283:A512V;ENSP00000273173:A512V	ENSP00000273173:A512V	A	+	2	0	SLC22A14	38332821	0.006000	0.16342	0.035000	0.18076	0.003000	0.03518	0.679000	0.25291	1.340000	0.45581	-0.152000	0.13540	GCG	C|0.897;T|0.103	0.103	strong		0.617	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
AEBP1	165	hgsc.bcm.edu	37	7	44153780	44153780	+	Missense_Mutation	SNP	A	A	G	rs13928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:44153780A>G	ENST00000223357.3	+	21	3702	c.3397A>G	c.(3397-3399)Aaa>Gaa	p.K1133E	AEBP1_ENST00000450684.2_Missense_Mutation_p.K708E	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	1133	Glu-rich.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for transcriptional repression. {ECO:0000250}.		K -> E (in dbSNP:rs13928). {ECO:0000269|Ref.3}.		cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						ggaggaggagaaagaggagga	0.547													a|||	1846	0.36861	0.4062	0.4006	5008	,	,		15723	0.2629		0.4583	False		,,,				2504	0.3119				p.K1133E		Atlas-SNP	.											.	AEBP1	102	.	0			c.A3397G						PASS	.	G	GLU/LYS	1834,2572	635.8+/-396.5	389,1056,758	106.0	100.0	102.0		3397	3.7	0.0	7	dbSNP_52	102	4098,4502	590.8+/-392.7	948,2202,1150	yes	missense	AEBP1	NM_001129.3	56	1337,3258,1908	GG,GA,AA		47.6512,41.6251,45.6097	benign	1133/1159	44153780	5932,7074	2203	4300	6503	SO:0001583	missense	165	exon21			GAGGAGAAAGAGG	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.3397A>G	7.37:g.44153780A>G	ENSP00000223357:p.Lys1133Glu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	845	0.3869047619047619	191	0.3882113821138211	152	0.4198895027624309	155	0.270979020979021	347	0.4577836411609499	G	1.679	-0.506908	0.04231	0.416251	0.476512	ENSG00000106624	ENST00000223357;ENST00000450684	D;D	0.94138	-3.36;-2.79	3.7	3.7	0.42460	.	1818.460000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48581	-0.9023	9	0.02654	T	1	-0.0093	7.4085	0.27004	0.1234:0.0:0.8766:0.0	rs13928;rs3173775;rs11558047;rs56834340;rs13928	708;1133	Q8IUX7-2;Q8IUX7	.;AEBP1_HUMAN	E	1133;708	ENSP00000223357:K1133E;ENSP00000398878:K708E	ENSP00000223357:K1133E	K	+	1	0	AEBP1	44120305	0.689000	0.27690	0.003000	0.11579	0.002000	0.02628	1.342000	0.33919	0.921000	0.36994	-0.355000	0.07637	AAA	A|0.582;G|0.418	0.418	strong		0.547	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129	
MAML1	9794	hgsc.bcm.edu	37	5	179201847	179201847	+	Missense_Mutation	SNP	G	G	A	rs6895902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:179201847G>A	ENST00000292599.3	+	5	3283	c.3020G>A	c.(3019-3021)aGt>aAt	p.S1007N	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGTGGATGAGTGATTTGGAC	0.463													A|||	1146	0.228834	0.1967	0.2594	5008	,	,		19614	0.1518		0.3579	False		,,,				2504	0.1973				p.S1007N		Atlas-SNP	.											MAML1,brain,glioma,0,1	MAML1	118	1	0			c.G3020A						PASS	.	A	ASN/SER	977,3427	707.4+/-407.5	109,759,1334	123.0	114.0	117.0		3020	1.6	0.6	5	dbSNP_116	117	2925,5675	643.1+/-399.9	503,1919,1878	yes	missense	MAML1	NM_014757.4	46	612,2678,3212	AA,AG,GG		34.0116,22.1844,30.0062	benign	1007/1017	179201847	3902,9102	2202	4300	6502	SO:0001583	missense	9794	exon5			GGATGAGTGATTT	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.3020G>A	5.37:g.179201847G>A	ENSP00000292599:p.Ser1007Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	22	0.278481	NM_014757		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	551	0.2522893772893773	96	0.1951219512195122	97	0.26795580110497236	77	0.1346153846153846	281	0.370712401055409	A	0.840	-0.742301	0.03088	0.221844	0.340116	ENSG00000161021	ENST00000292599	T	0.21734	1.99	5.28	1.61	0.23674	.	0.198509	0.44285	N	0.000479	T	0.00012	0.0000	N	0.00392	-1.555	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48091	-0.9065	9	0.02654	T	1	-2.2874	9.1608	0.37021	0.7206:0.0:0.2794:0.0	rs6895902;rs57675371;rs6895902	1007	Q92585	MAML1_HUMAN	N	1007	ENSP00000292599:S1007N	ENSP00000292599:S1007N	S	+	2	0	MAML1	179134453	0.882000	0.30256	0.579000	0.28588	0.991000	0.79684	1.053000	0.30442	-0.182000	0.10602	-0.361000	0.07541	AGT	G|0.733;A|0.267	0.267	strong		0.463	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
TYW3	127253	hgsc.bcm.edu	37	1	75199023	75199023	+	Missense_Mutation	SNP	A	A	C	rs143670067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:75199023A>C	ENST00000370867.3	+	1	184	c.95A>C	c.(94-96)gAg>gCg	p.E32A	CRYZ_ENST00000417775.1_5'UTR|CRYZ_ENST00000370871.3_5'Flank|TYW3_ENST00000479111.1_5'UTR|CRYZ_ENST00000370872.3_5'Flank|CRYZ_ENST00000340866.5_5'Flank|TYW3_ENST00000421739.2_Missense_Mutation_p.E32A|TYW3_ENST00000457880.2_Missense_Mutation_p.E32A	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	32					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						GATGTGGTAGAGCTTGTGCAG	0.572													A|||	10	0.00199681	0.0	0.0029	5008	,	,		19178	0.0		0.008	False		,,,				2504	0.0				p.E32A		Atlas-SNP	.											.	TYW3	36	.	0			c.A95C						PASS	.	A	,,,ALA/GLU,,ALA/GLU	6,4400	11.4+/-27.6	0,6,2197	142.0	114.0	123.0		,,,95,,95	3.5	0.4	1	dbSNP_134	123	35,8565	24.6+/-71.5	0,35,4265	yes	utr-5,utr-5,utr-5,missense,utr-5,missense	CRYZ,TYW3	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001162916.1,NM_001889.3,NM_138467.2	,,,107,,107	0,41,6462	CC,CA,AA		0.407,0.1362,0.3152	,,,possibly-damaging,,possibly-damaging	,,,32/227,,32/260	75199023	41,12965	2203	4300	6503	SO:0001583	missense	127253	exon1			TGGTAGAGCTTGT	BX647591	CCDS666.1, CCDS53334.1	1p31.1	2008-02-05	2006-05-25	2006-05-25	ENSG00000162623	ENSG00000162623			24757	protein-coding gene	gene with protein product		611245	"""chromosome 1 open reading frame 171"""	C1orf171		17150819	Standard	NM_138467		Approved	FLJ40918	uc001dgn.3	Q6IPR3	OTTHUMG00000009641	ENST00000370867.3:c.95A>C	1.37:g.75199023A>C	ENSP00000359904:p.Glu32Ala	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	84	32	0.380952	NM_001162916	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Missense_Mutation	SNP	ENST00000370867.3	37	CCDS666.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	12.16	1.854352	0.32791	0.001362	0.00407	ENSG00000162623	ENST00000457880;ENST00000370867;ENST00000421739	T;T;T	0.31247	1.5;1.5;1.5	4.61	3.49	0.39957	tRNA wybutosine-synthesizing protein (2);	0.257365	0.39615	N	0.001304	T	0.10981	0.0268	M	0.66378	2.025	0.09310	N	1	B;P;B	0.40970	0.153;0.734;0.056	B;B;B	0.34452	0.076;0.183;0.053	T	0.12116	-1.0560	10	0.24483	T	0.36	-7.0777	7.3561	0.26719	0.8192:0.0:0.1808:0.0	.	32;32;32	B4DFU6;E9PGR7;Q6IPR3	.;.;TYW3_HUMAN	A	32	ENSP00000407025:E32A;ENSP00000359904:E32A;ENSP00000409336:E32A	ENSP00000359904:E32A	E	+	2	0	TYW3	74971611	0.089000	0.21612	0.445000	0.26908	0.987000	0.75469	1.673000	0.37534	0.797000	0.33971	0.459000	0.35465	GAG	A|0.997;C|0.003	0.003	strong		0.572	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467	
HSP90AA1	3320	hgsc.bcm.edu	37	14	102548703	102548703	+	Silent	SNP	T	T	G	rs34644998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:102548703T>G	ENST00000216281.8	-	10	2039	c.1834A>C	c.(1834-1836)Aga>Cga	p.R612R	HSP90AA1_ENST00000334701.7_Silent_p.R734R	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	612					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	TTCATGATTCTCTCCATGTTT	0.433													.|||	26	0.00519169	0.0015	0.0101	5008	,	,		19458	0.0		0.0149	False		,,,				2504	0.002				p.R734R		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.A2200C						PASS	.	T	,	14,4392	22.3+/-47.3	0,14,2189	86.0	85.0	86.0		2200,1834	2.0	0.5	14	dbSNP_126	86	193,8401	85.3+/-147.7	2,189,4106	no	coding-synonymous,coding-synonymous	HSP90AA1	NM_001017963.2,NM_005348.3	,	2,203,6295	GG,GT,TT		2.2458,0.3177,1.5923	,	734/855,612/733	102548703	207,12793	2203	4297	6500	SO:0001819	synonymous_variant	3320	exon11			TGATTCTCTCCAT	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"""Heat shock proteins / HSPC"""	5253	protein-coding gene	gene with protein product		140571	"""heat shock 90kD protein 1, alpha"", ""heat shock 90kDa protein 1, alpha"""	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.1834A>C	14.37:g.102548703T>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	144	75	0.520833	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Silent	SNP	ENST00000216281.8	37	CCDS9967.1																																																																																			T|0.986;G|0.014	0.014	strong		0.433	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348	
GRM6	2916	hgsc.bcm.edu	37	5	178415937	178415937	+	Splice_Site	SNP	A	A	G	rs2067011	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178415937A>G	ENST00000517717.1	-	7	1391	c.1353T>C	c.(1351-1353)aaT>aaC	p.N451N	GRM6_ENST00000231188.5_Splice_Site_p.N451N|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	451					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CCCACTCACCATTGAAGCGGA	0.637													A|||	2539	0.506989	0.388	0.5317	5008	,	,		13198	0.5913		0.5547	False		,,,				2504	0.5143				p.N451N		Atlas-SNP	.											.	GRM6	149	.	0			c.T1353C						PASS	.	A		1806,2600	523.5+/-371.1	382,1042,779	38.0	37.0	38.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1353	-4.4	1.0	5	dbSNP_96	38	4625,3975	592.2+/-392.9	1195,2235,870	yes	coding-synonymous-near-splice	GRM6	NM_000843.3		1577,3277,1649	GG,GA,AA		46.2209,40.9896,49.4464		451/878	178415937	6431,6575	2203	4300	6503	SO:0001630	splice_region_variant	2916	exon6			CTCACCATTGAAG	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1354+1T>C	5.37:g.178415937A>G		Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	203	203	1	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1	1153	0.5279304029304029	219	0.4451219512195122	180	0.4972375690607735	336	0.5874125874125874	418	0.5514511873350924	A	11.88	1.769401	0.31320	0.409896	0.537791	ENSG00000113262	ENST00000319065	.	.	.	5.29	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46020	-0.9221	4	0.87932	D	0	.	15.2442	0.73493	0.2527:0.0:0.7473:0.0	rs2067011;rs17839799;rs52803732;rs61390692;rs2067011	.	.	.	R	491	.	ENSP00000325675:W491R	W	-	1	0	GRM6	178348543	0.002000	0.14202	0.973000	0.42090	0.937000	0.57800	-1.561000	0.02158	-0.676000	0.05238	0.459000	0.35465	TGG	A|0.500;G|0.500	0.500	strong		0.637	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		Silent
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360055	71360055	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71360055C>T	ENST00000244230.2	+	2	469	c.117C>T	c.(115-117)ttC>ttT	p.F39F	MPHOSPH10_ENST00000498451.2_Silent_p.F39F|MPHOSPH10_ENST00000468427.1_3'UTR|MCEE_ENST00000244217.5_5'Flank	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	39					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						CATCAAAGTTCACTTCTTTAA	0.308																																					p.F39F		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.C117T						PASS	.						34.0	40.0	38.0					2																	71360055		2151	4271	6422	SO:0001819	synonymous_variant	10199	exon2			AAAGTTCACTTCT	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.117C>T	2.37:g.71360055C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_005791	A0AVJ8	Silent	SNP	ENST00000244230.2	37	CCDS1916.1																																																																																			.	.	none		0.308	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
KIAA1683	80726	hgsc.bcm.edu	37	19	18377761	18377761	+	Missense_Mutation	SNP	A	A	G	rs12609001	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18377761A>G	ENST00000600328.3	-	3	782	c.589T>C	c.(589-591)Tgt>Cgt	p.C197R	KIAA1683_ENST00000392413.4_Missense_Mutation_p.C197R|KIAA1683_ENST00000600359.3_Missense_Mutation_p.C151R			Q9H0B3	K1683_HUMAN	KIAA1683	197			C -> R (in dbSNP:rs12609001). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						AGATTGTCACAGGAAGGGAAC	0.627													A|||	763	0.152356	0.0257	0.1196	5008	,	,		18253	0.3036		0.1292	False		,,,				2504	0.2147				p.C197R		Atlas-SNP	.											.	KIAA1683	190	.	0			c.T589C						PASS	.	A	ARG/CYS,ARG/CYS,ARG/CYS	174,4226	102.5+/-141.1	1,172,2027	36.0	37.0	37.0		589,451,589	-2.6	0.0	19	dbSNP_120	37	1172,7422	228.6+/-263.6	81,1010,3206	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	180,180,180	82,1182,5233	GG,GA,AA		13.6374,3.9545,10.3586	benign,benign,benign	197/1368,151/1135,197/1181	18377761	1346,11648	2200	4297	6497	SO:0001583	missense	80726	exon3			TGTCACAGGAAGG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.589T>C	19.37:g.18377761A>G	ENSP00000470780:p.Cys197Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	311	0.1423992673992674	15	0.03048780487804878	35	0.09668508287292818	167	0.291958041958042	94	0.12401055408970976	A	4.784	0.145746	0.09134	0.039545	0.136374	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000358422;ENST00000411671	T;T;T	0.03496	3.97;3.98;3.91	3.23	-2.62	0.06152	.	2.005360	0.03107	N	0.162000	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P;B	0.39809	0.689;0.0	B;B	0.31337	0.128;0.001	T	0.46233	-0.9206	9	0.11182	T	0.66	2.0952	1.4637	0.02401	0.2975:0.4085:0.1226:0.1714	rs12609001;rs17797876;rs52806099;rs59053306;rs12609001	197;197	E9PDE0;Q9H0B3	.;K1683_HUMAN	R	197;197;151;196;197	ENSP00000376213:C197R;ENSP00000352774:C197R;ENSP00000404501:C151R	ENSP00000351198:C196R	C	-	1	0	KIAA1683	18238761	0.001000	0.12720	0.000000	0.03702	0.098000	0.18820	-0.505000	0.06367	-0.301000	0.08882	0.260000	0.18958	TGT	A|0.874;G|0.126	0.126	strong		0.627	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
WDR6	11180	hgsc.bcm.edu	37	3	49044932	49044932	+	Missense_Mutation	SNP	G	G	T	rs62262472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49044932G>T	ENST00000608424.1	+	1	107	c.68G>T	c.(67-69)gGt>gTt	p.G23V	WDR6_ENST00000415265.2_Missense_Mutation_p.G23V|WDR6_ENST00000448293.1_5'Flank|WDR6_ENST00000489684.1_3'UTR|WDR6_ENST00000395474.3_Missense_Mutation_p.G53V			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	23					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		CCAGTGACGGGTCTGGAGTGC	0.657													g|||	3	0.000599042	0.0	0.0	5008	,	,		15634	0.0		0.003	False		,,,				2504	0.0				p.G53V		Atlas-SNP	.											.	WDR6	79	.	0			c.G158T						PASS	.		VAL/GLY	9,4397	15.5+/-35.6	0,9,2194	48.0	43.0	45.0		158	4.1	1.0	3	dbSNP_129	45	42,8558	26.8+/-75.7	0,42,4258	yes	missense	WDR6	NM_018031.3	109	0,51,6452	TT,TG,GG		0.4884,0.2043,0.3921	probably-damaging	53/1152	49044932	51,12955	2203	4300	6503	SO:0001583	missense	11180	exon1			TGACGGGTCTGGA	AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"""WD repeat domain containing"""	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.68G>T	3.37:g.49044932G>T	ENSP00000477389:p.Gly23Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	162	80	0.493827	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Missense_Mutation	SNP	ENST00000608424.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	14.52	2.560336	0.45590	0.002043	0.004884	ENSG00000178252	ENST00000395474;ENST00000438660;ENST00000354294;ENST00000415265	T;T	0.69685	-0.34;-0.42	5.02	4.08	0.47627	.	0.245193	0.30930	N	0.008587	T	0.62889	0.2465	N	0.19112	0.55	0.80722	D	1	B;D	0.64830	0.002;0.994	B;P	0.56865	0.003;0.808	T	0.65619	-0.6124	10	0.59425	D	0.04	-10.7481	10.8606	0.46825	0.0:0.2887:0.7113:0.0	rs62262472	23;23	E9PBK6;B4DK45	.;.	V	53;23;23;23	ENSP00000378857:G53V;ENSP00000387692:G23V	ENSP00000346247:G23V	G	+	2	0	WDR6	49019936	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	1.989000	0.40707	2.505000	0.84491	0.645000	0.84053	GGT	G|0.997;T|0.003	0.003	strong		0.657	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1		
ATP12A	479	hgsc.bcm.edu	37	13	25255705	25255705	+	Silent	SNP	C	C	A	rs41288276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25255705C>A	ENST00000381946.3	+	2	182	c.15C>A	c.(13-15)acC>acA	p.T5T	ATP12A_ENST00000218548.6_Silent_p.T5T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	5					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TTCAGAAAACCCCAGAAATTT	0.542													C|||	256	0.0511182	0.1044	0.0303	5008	,	,		17355	0.001		0.0477	False		,,,				2504	0.0491				p.T5T	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C15A						PASS	.	C	,	401,4005	199.8+/-223.2	18,365,1820	51.0	54.0	53.0		15,15	-6.3	0.0	13	dbSNP_127	53	391,8209	125.5+/-184.1	5,381,3914	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	23,746,5734	AA,AC,CC		4.5465,9.1012,6.0895	,	5/1046,5/1040	25255705	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	479	exon2			GAAAACCCCAGAA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.15C>A	13.37:g.25255705C>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.942;A|0.058	0.058	strong		0.542	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
FDX1L	112812	hgsc.bcm.edu	37	19	10426628	10426628	+	Silent	SNP	T	T	C	rs395782	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10426628T>C	ENST00000393708.3	-	1	63	c.45A>G	c.(43-45)ctA>ctG	p.L15L	CTD-2369P2.12_ENST00000586529.1_Intron|FDX1L_ENST00000494368.1_Intron|FDX1L_ENST00000541276.1_Silent_p.L18L|FDX1L_ENST00000492239.1_5'Flank|CTD-2369P2.10_ENST00000452032.2_Silent_p.L15L	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	15					oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			NS(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(20;9.5e-10)|Epithelial(33;2.11e-06)|all cancers(31;5.06e-06)			CAGCCTGCAGTAGAACCCTGG	0.672													C|||	2468	0.492812	0.6089	0.5576	5008	,	,		12108	0.3403		0.4771	False		,,,				2504	0.4632				p.L15L		Atlas-SNP	.											FDX1L,NS,carcinoma,0,2	FDX1L	21	2	0			c.A45G						PASS	.	C		2633,1769		794,1045,362	20.0	22.0	21.0		45	-0.2	0.0	19	dbSNP_80	21	4043,4553		959,2125,1214	no	coding-synonymous	FDX1L	NM_001031734.2		1753,3170,1576	CC,CT,TT		47.0335,40.1863,48.6383		15/184	10426628	6676,6322	2201	4298	6499	SO:0001819	synonymous_variant	112812	exon1			CTGCAGTAGAACC	AK097022	CCDS32905.1	19p13.2	2012-10-09			ENSG00000267673	ENSG00000267673			30546	protein-coding gene	gene with protein product		614585				12477932	Standard	NM_001031734		Approved	MGC19604	uc002mny.1	Q6P4F2	OTTHUMG00000141299	ENST00000393708.3:c.45A>G	19.37:g.10426628T>C		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_001031734	Q8N8B8	Silent	SNP	ENST00000393708.3	37	CCDS32905.1																																																																																			T|0.511;C|0.489	0.489	strong		0.672	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2		
ALPK2	115701	hgsc.bcm.edu	37	18	56202982	56202982	+	Silent	SNP	A	A	T	rs3826594	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56202982A>T	ENST00000361673.3	-	5	4650	c.4437T>A	c.(4435-4437)gcT>gcA	p.A1479A	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1479						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GAATTTGTTCAGCCTCCTGCT	0.478													A|||	3370	0.672923	0.4728	0.6758	5008	,	,		21388	0.7966		0.7674	False		,,,				2504	0.7168				p.A1479A		Atlas-SNP	.											.	ALPK2	487	.	0			c.T4437A						PASS	.	A		2285,2121	595.9+/-388.5	600,1085,518	58.0	61.0	60.0		4437	-6.4	0.0	18	dbSNP_107	60	6607,1993	714.5+/-406.0	2550,1507,243	no	coding-synonymous	ALPK2	NM_052947.3		3150,2592,761	TT,TA,AA		23.1744,48.1389,31.6316		1479/2171	56202982	8892,4114	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			TTGTTCAGCCTCC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4437T>A	18.37:g.56202982A>T		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	227	227	1	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			A|0.304;T|0.696	0.696	strong		0.478	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ABCA7	10347	hgsc.bcm.edu	37	19	1053524	1053524	+	Silent	SNP	C	C	G	rs3752241	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1053524C>G	ENST00000263094.6	+	24	3648	c.3417C>G	c.(3415-3417)ctC>ctG	p.L1139L	ABCA7_ENST00000435683.2_Silent_p.L1001L|ABCA7_ENST00000433129.1_Silent_p.L1139L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1139					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACACCAGCCTCGAGGAGGTGT	0.627													C|||	915	0.182708	0.1876	0.0821	5008	,	,		17726	0.1915		0.173	False		,,,				2504	0.2485				p.L1139L		Atlas-SNP	.											.	ABCA7	174	.	0			c.C3417G						PASS	.	C		778,3578		65,648,1465	11.0	11.0	11.0		3417	-8.8	1.0	19	dbSNP_107	11	1338,7218		115,1108,3055	no	coding-synonymous	ABCA7	NM_019112.3		180,1756,4520	GG,GC,CC		15.6381,17.8604,16.3879		1139/2147	1053524	2116,10796	2178	4278	6456	SO:0001819	synonymous_variant	10347	exon24			CAGCCTCGAGGAG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3417C>G	19.37:g.1053524C>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			C|0.829;G|0.171	0.171	strong		0.627	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
ESR1	2099	hgsc.bcm.edu	37	6	152129308	152129308	+	Silent	SNP	G	G	C	rs746432	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152129308G>C	ENST00000206249.3	+	1	623	c.261G>C	c.(259-261)gcG>gcC	p.A87A	ESR1_ENST00000406599.1_Silent_p.A87A|ESR1_ENST00000440973.1_Silent_p.A87A|ESR1_ENST00000338799.5_Silent_p.A87A|ESR1_ENST00000456483.2_Silent_p.A87A|ESR1_ENST00000443427.1_Silent_p.A87A|ESR1_ENST00000427531.2_5'Flank	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	87	Interaction with DDX5; self-association.|Modulating (transactivation AF-1); mediates interaction with MACROD1.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	CTGAGGCTGCGGCGTTCGGCT	0.721													G|||	194	0.038738	0.0325	0.0403	5008	,	,		10099	0.0		0.0964	False		,,,				2504	0.0266				p.A87A		Atlas-SNP	.											.	ESR1	94	.	0			c.G261C						PASS	.	G	,,,	143,4171		2,139,2016	7.0	9.0	8.0		261,261,261,261	-0.2	0.9	6	dbSNP_86	8	624,7818		24,576,3621	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR1	NM_000125.3,NM_001122740.1,NM_001122741.1,NM_001122742.1	,,,	26,715,5637	CC,CG,GG		7.3916,3.3148,6.0129	,,,	87/596,87/596,87/596,87/596	152129308	767,11989	2157	4221	6378	SO:0001819	synonymous_variant	2099	exon1			GGCTGCGGCGTTC	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.261G>C	6.37:g.152129308G>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1																																																																																			G|0.959;C|0.041	0.041	strong		0.721	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
OR8S1	341568	hgsc.bcm.edu	37	12	48919659	48919659	+	Missense_Mutation	SNP	T	T	C	rs4075258|rs71439450	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48919659T>C	ENST00000310194.1	+	1	245	c.245T>C	c.(244-246)cTg>cCg	p.L82P	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	82			L -> P (in dbSNP:rs4075258).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						CCCAAGATGCTGGAGAACCTC	0.488													T|||	2896	0.578275	0.4849	0.6599	5008	,	,		21421	0.6905		0.5139	False		,,,				2504	0.5971				p.L82P		Atlas-SNP	.											.	OR8S1	47	.	0			c.T245C						PASS	.	T	PRO/LEU	2183,2223	585.8+/-386.3	519,1145,539	136.0	129.0	132.0		245	5.0	0.2	12	dbSNP_108	132	4566,4034	596.6+/-393.6	1210,2146,944	yes	missense	OR8S1	NM_001005203.2	98	1729,3291,1483	CC,CT,TT		46.907,49.5461,48.1086	probably-damaging	82/360	48919659	6749,6257	2203	4300	6503	SO:0001583	missense	341568	exon1			AGATGCTGGAGAA		CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"""GPCR / Class A : Olfactory receptors"""	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.245T>C	12.37:g.48919659T>C	ENSP00000310632:p.Leu82Pro	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	186	186	1	NM_001005203		Missense_Mutation	SNP	ENST00000310194.1	37	CCDS31789.1	1183	0.5416666666666666	224	0.45528455284552843	223	0.6160220994475138	405	0.708041958041958	331	0.4366754617414248	T	19.46	3.831371	0.71258	0.495461	0.53093	ENSG00000197376	ENST00000310194	T	0.00441	7.41	5.03	5.03	0.67393	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32503	N	0.006015	T	0.00012	0.0000	H	0.96805	3.885	0.18873	P	0.9999875511	D	0.89917	1.0	D	0.79108	0.992	T	0.04140	-1.0974	9	0.87932	D	0	-22.5349	12.7618	0.57370	0.0:0.0:0.0:1.0	rs4075258;rs4590919;rs59443622;rs4075258	82	Q8NH09	OR8S1_HUMAN	P	82	ENSP00000310632:L82P	ENSP00000310632:L82P	L	+	2	0	OR8S1	47205926	0.688000	0.27680	0.192000	0.23308	0.928000	0.56348	4.302000	0.59092	2.105000	0.64084	0.533000	0.62120	CTG	CA|0.500;TG|0.500	.	alt		0.488	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
TTLL2	83887	hgsc.bcm.edu	37	6	167754710	167754710	+	Missense_Mutation	SNP	A	A	C	rs41266331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167754710A>C	ENST00000239587.5	+	3	1410	c.1322A>C	c.(1321-1323)aAa>aCa	p.K441T		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	441			K -> T (in dbSNP:rs41266331).		cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)	p.K441T(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GACGCTGCAAAAAGTGACAGA	0.433													A|||	679	0.135583	0.2746	0.1729	5008	,	,		22985	0.0565		0.0855	False		,,,				2504	0.0542				p.K441T		Atlas-SNP	.											TTLL2,NS,carcinoma,0,1	TTLL2	82	1	1	Substitution - Missense(1)	stomach(1)	c.A1322C						PASS	.	A	THR/LYS	1077,3329	391.0+/-327.9	123,831,1249	103.0	94.0	97.0		1322	-5.2	0.0	6	dbSNP_127	97	820,7780	190.0+/-236.6	34,752,3514	yes	missense	TTLL2	NM_031949.4	78	157,1583,4763	CC,CA,AA		9.5349,24.4439,14.5856	benign	441/593	167754710	1897,11109	2203	4300	6503	SO:0001583	missense	83887	exon3			CTGCAAAAAGTGA	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1322A>C	6.37:g.167754710A>C	ENSP00000239587:p.Lys441Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	106	62	0.584906	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	308	0.14102564102564102	142	0.2886178861788618	64	0.17679558011049723	39	0.06818181818181818	63	0.08311345646437995	A	8.722	0.914665	0.17907	0.244439	0.095349	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.02498	4.27	3.61	-5.22	0.02806	.	1.455760	0.04343	N	0.354315	T	0.00552	0.0018	N	0.19112	0.55	0.80722	P	0.0	B	0.30326	0.276	B	0.24394	0.053	T	0.46624	-0.9178	9	0.21540	T	0.41	.	6.8002	0.23746	0.7308:0.1268:0.1423:0.0	rs41266331;rs61740797	441	Q9BWV7	TTLL2_HUMAN	T	441;368	ENSP00000239587:K441T	ENSP00000239587:K441T	K	+	2	0	TTLL2	167674700	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.140000	0.10342	-1.286000	0.02384	0.402000	0.26972	AAA	A|0.858;C|0.142	0.142	strong		0.433	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
C1orf68	100129271	hgsc.bcm.edu	37	1	152692588	152692588	+	Silent	SNP	A	A	G	rs944682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152692588A>G	ENST00000368775.2	+	1	591	c.591A>G	c.(589-591)tcA>tcG	p.S197S		NM_001024679.2	NP_001019850.1	Q5T750	XP32_HUMAN	chromosome 1 open reading frame 68	197	Cys-rich.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)		p.S197S(1)		NS(1)|breast(1)|lung(2)|prostate(1)|stomach(3)	8						ACACAGGATCATCTGGCTGCT	0.607													G|||	1749	0.349241	0.5461	0.3804	5008	,	,		17978	0.1716		0.3608	False		,,,				2504	0.2321				p.S197S		Atlas-SNP	.											C1orf68,NS,carcinoma,+1,2	C1orf68	19	2	1	Substitution - coding silent(1)	stomach(1)	c.A591G						PASS	.	G		693,691		176,341,175	51.0	49.0	50.0		591	-8.4	0.1	1	dbSNP_86	50	1113,2069		189,735,667	no	coding-synonymous	C1orf68	NM_001024679.2		365,1076,842	GG,GA,AA		34.978,49.9277,39.5532		197/251	152692588	1806,2760	692	1591	2283	SO:0001819	synonymous_variant	100129271	exon1			AGGATCATCTGGC	AF005081	CCDS44226.1	1q21.3	2014-05-30			ENSG00000198854	ENSG00000198854			29468	protein-coding gene	gene with protein product						11698679	Standard	NM_001024679		Approved	LEP7	uc010pdu.2	Q5T750	OTTHUMG00000012401	ENST00000368775.2:c.591A>G	1.37:g.152692588A>G		Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	288	287	0.996528	NM_001024679	O14634	Silent	SNP	ENST00000368775.2	37	CCDS44226.1																																																																																			A|0.651;G|0.349	0.349	strong		0.607	C1orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034521.2	NM_001024679	
ADAMTS19	171019	hgsc.bcm.edu	37	5	129040056	129040056	+	Missense_Mutation	SNP	A	A	T	rs11749126	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:129040056A>T	ENST00000274487.4	+	21	3411	c.3266A>T	c.(3265-3267)tAt>tTt	p.Y1089F	CTC-575N7.1_ENST00000503616.1_RNA|ADAMTS19_ENST00000509467.1_3'UTR	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	1089	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.		Y -> F (in dbSNP:rs11749126).			proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		TCAAAATGCTATGTGTGGCGA	0.448													A|||	355	0.0708866	0.0083	0.1009	5008	,	,		19397	0.002		0.163	False		,,,				2504	0.1104				p.Y1089F		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.A3266T						PASS	.	A	PHE/TYR	176,4230	113.8+/-151.8	6,164,2033	176.0	152.0	160.0		3266	4.3	1.0	5	dbSNP_120	160	1583,7017	296.2+/-302.8	131,1321,2848	yes	missense	ADAMTS19	NM_133638.3	22	137,1485,4881	TT,TA,AA		18.407,3.9946,13.5245	benign	1089/1208	129040056	1759,11247	2203	4300	6503	SO:0001583	missense	171019	exon21			AATGCTATGTGTG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.3266A>T	5.37:g.129040056A>T	ENSP00000274487:p.Tyr1089Phe	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	215	103	0.47907	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	178	0.0815018315018315	8	0.016260162601626018	45	0.12430939226519337	0	0.0	125	0.16490765171503957	A	13.84	2.356939	0.41801	0.039946	0.18407	ENSG00000145808	ENST00000274487	T	0.60424	0.19	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000008	T	0.00109	0.0003	L	0.33137	0.985	0.20975	P	0.999813509	B	0.21606	0.058	B	0.18561	0.022	T	0.05451	-1.0884	8	.	.	.	.	14.4892	0.67639	1.0:0.0:0.0:0.0	rs11749126;rs17681638;rs52806550;rs11749126	1089	Q8TE59	ATS19_HUMAN	F	1089	ENSP00000274487:Y1089F	.	Y	+	2	0	ADAMTS19	129067955	0.999000	0.42202	0.996000	0.52242	0.994000	0.84299	4.259000	0.58828	2.166000	0.68216	0.533000	0.62120	TAT	A|0.890;T|0.110	0.110	strong		0.448	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
DLGAP1	9229	hgsc.bcm.edu	37	18	3581966	3581966	+	Silent	SNP	G	G	A	rs56017170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:3581966G>A	ENST00000315677.3	-	8	2467	c.1872C>T	c.(1870-1872)acC>acT	p.T624T	DLGAP1_ENST00000584874.1_Silent_p.T624T|DLGAP1_ENST00000400155.1_Silent_p.T330T|DLGAP1_ENST00000400149.3_Silent_p.T314T|DLGAP1_ENST00000515196.2_Silent_p.T624T|DLGAP1_ENST00000400147.2_Silent_p.T322T|DLGAP1_ENST00000581527.1_Silent_p.T624T|DLGAP1_ENST00000581699.1_Silent_p.T330T|DLGAP1_ENST00000400150.3_Silent_p.T340T|DLGAP1_ENST00000539435.1_Silent_p.T332T|DLGAP1_ENST00000400145.2_Silent_p.T322T|DLGAP1_ENST00000534970.1_Silent_p.T308T	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	624	Poly-Thr.				synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				tggtggtgacggtggcagtgT	0.542													G|||	616	0.123003	0.0303	0.2291	5008	,	,		17443	0.005		0.3062	False		,,,				2504	0.1063				p.T624T		Atlas-SNP	.											.	DLGAP1	201	.	0			c.C1872T						PASS	.	G	,,,,,,,	283,4123	156.3+/-189.4	7,269,1927	135.0	104.0	114.0		966,1872,924,1038,990,966,996,1872	-10.8	0.0	18	dbSNP_129	114	2294,6306	386.4+/-341.8	309,1676,2315	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLGAP1	NM_001003809.2,NM_001242761.1,NM_001242762.1,NM_001242763.1,NM_001242764.1,NM_001242765.1,NM_001242766.1,NM_004746.3	,,,,,,,	316,1945,4242	AA,AG,GG		26.6744,6.4231,19.8139	,,,,,,,	322/676,624/930,308/662,346/700,330/684,322/628,332/686,624/978	3581966	2577,10429	2203	4300	6503	SO:0001819	synonymous_variant	9229	exon8			GGTGACGGTGGCA	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"""discs, large (Drosophila) homolog-associated protein 1"""			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.1872C>T	18.37:g.3581966G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Silent	SNP	ENST00000315677.3	37	CCDS11836.1																																																																																			G|0.822;A|0.178	0.178	strong		0.542	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4		
E4F1	1877	hgsc.bcm.edu	37	16	2285357	2285357	+	Silent	SNP	C	C	T	rs26840	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2285357C>T	ENST00000301727.4	+	14	2187	c.2139C>T	c.(2137-2139)atC>atT	p.I713I	DNASE1L2_ENST00000320700.5_5'Flank|DNASE1L2_ENST00000567494.1_5'Flank|E4F1_ENST00000564139.1_3'UTR|DNASE1L2_ENST00000382437.4_5'Flank|RP11-304L19.12_ENST00000564055.1_lincRNA|E4F1_ENST00000565090.1_Silent_p.I536I|DNASE1L2_ENST00000564065.1_5'Flank	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	713					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|mitotic cell cycle arrest (GO:0071850)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell cycle process (GO:0010564)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle, embryonic (GO:0009794)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			ovary(1)	1						CCATCACCATCGCCACCCCCG	0.687													C|||	1554	0.310304	0.0726	0.3184	5008	,	,		15288	0.4018		0.4046	False		,,,				2504	0.4346				p.I713I		Atlas-SNP	.											.	E4F1	53	.	0			c.C2139T						PASS	.	C		482,3904		31,420,1742	31.0	36.0	34.0		2139	-1.6	1.0	16	dbSNP_76	34	3478,5096		725,2028,1534	no	coding-synonymous	E4F1	NM_004424.3		756,2448,3276	TT,TC,CC		40.5645,10.9895,30.5556		713/785	2285357	3960,9000	2193	4287	6480	SO:0001819	synonymous_variant	1877	exon14			CACCATCGCCACC	U87269	CCDS32370.1, CCDS73809.1, CCDS73810.1	16p13.3	2013-01-08				ENSG00000167967		"""Zinc fingers, C2H2-type"""	3121	protein-coding gene	gene with protein product		603022				9763670, 8828041	Standard	XM_005255155		Approved	E4F	uc002cpm.3	Q66K89		ENST00000301727.4:c.2139C>T	16.37:g.2285357C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_004424	A8K2R4|O00146	Silent	SNP	ENST00000301727.4	37	CCDS32370.1																																																																																			C|0.702;T|0.298	0.298	strong		0.687	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424	
CPT1C	126129	hgsc.bcm.edu	37	19	50216050	50216050	+	Missense_Mutation	SNP	C	C	A	rs79488403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50216050C>A	ENST00000392518.4	+	18	2449	c.2077C>A	c.(2077-2079)Ctg>Atg	p.L693M	CPT1C_ENST00000405931.2_Missense_Mutation_p.L682M|CPT1C_ENST00000354199.5_Intron|CPT1C_ENST00000598293.1_Missense_Mutation_p.L693M|CPT1C_ENST00000323446.5_Missense_Mutation_p.L693M	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	693					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		GCAAATGCATCTGTTTGACGT	0.592													c|||	4	0.000798722	0.0	0.0	5008	,	,		15329	0.0		0.004	False		,,,				2504	0.0				p.L693M		Atlas-SNP	.											.	CPT1C	93	.	0			c.C2077A						PASS	.	C	MET/LEU,MET/LEU,MET/LEU,MET/LEU	4,4402	8.1+/-20.4	0,4,2199	103.0	80.0	88.0		2044,2077,2077,2077	3.5	1.0	19	dbSNP_131	88	63,8537	37.4+/-92.8	0,63,4237	yes	missense,missense,missense,missense	CPT1C	NM_001136052.2,NM_001199752.1,NM_001199753.1,NM_152359.2	15,15,15,15	0,67,6436	AA,AC,CC		0.7326,0.0908,0.5151	probably-damaging,probably-damaging,probably-damaging,probably-damaging	682/793,693/804,693/804,693/804	50216050	67,12939	2203	4300	6503	SO:0001583	missense	126129	exon18			ATGCATCTGTTTG	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.2077C>A	19.37:g.50216050C>A	ENSP00000376303:p.Leu693Met	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	218	90	0.412844	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Missense_Mutation	SNP	ENST00000392518.4	37	CCDS12779.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.60	3.167352	0.57476	9.08E-4	0.007326	ENSG00000169169	ENST00000392518;ENST00000405931;ENST00000323446	D;D;D	0.86366	-2.11;-2.09;-2.11	4.59	3.55	0.40652	.	0.000000	0.35207	N	0.003375	D	0.84804	0.5553	L	0.45698	1.435	0.80722	D	1	P;P	0.42649	0.746;0.786	P;P	0.55222	0.561;0.771	D	0.84213	0.0457	10	0.34782	T	0.22	-14.6614	11.8375	0.52333	0.0:0.9125:0.0:0.0875	.	682;693	Q8TCG5-2;Q8TCG5	.;CPT1C_HUMAN	M	693;682;693	ENSP00000376303:L693M;ENSP00000384465:L682M;ENSP00000319343:L693M	ENSP00000319343:L693M	L	+	1	2	CPT1C	54907862	0.882000	0.30256	0.987000	0.45799	0.996000	0.88848	0.767000	0.26575	1.305000	0.44909	0.650000	0.86243	CTG	C|0.996;A|0.004	0.004	strong		0.592	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359	
STAT2	6773	hgsc.bcm.edu	37	12	56740394	56740394	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56740394A>G	ENST00000314128.4	-	21	1899	c.1876T>C	c.(1876-1878)Tac>Cac	p.Y626H	STAT2_ENST00000556539.1_5'UTR|STAT2_ENST00000557235.1_Missense_Mutation_p.Y622H			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	626	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.Y626N(1)		NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						TGCACAGAGTAGATGAGCACC	0.552																																					p.Y626H		Atlas-SNP	.											STAT2,NS,carcinoma,0,1	STAT2	70	1	1	Substitution - Missense(1)	lung(1)	c.T1876C						scavenged	.						78.0	66.0	70.0					12																	56740394		2203	4300	6503	SO:0001583	missense	6773	exon21			CAGAGTAGATGAG	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"""SH2 domain containing"""	11363	protein-coding gene	gene with protein product		600556	"""signal transducer and activator of transcription 2, 113kD"""			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1876T>C	12.37:g.56740394A>G	ENSP00000315768:p.Tyr626His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	145	3	0.0206897	NM_005419	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Missense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	.	.	.	.	.	.	.	.	.	.	A	4.837	0.155531	0.09236	.	.	ENSG00000170581	ENST00000314128;ENST00000557235	D;D	0.96427	-4.01;-4.01	5.71	-4.7	0.03288	SH2 motif (4);	0.878227	0.10207	N	0.702525	D	0.84433	0.5471	N	0.03050	-0.425	0.44254	D	0.997107	B;B	0.09022	0.0;0.002	B;B	0.10450	0.001;0.005	T	0.68780	-0.5318	10	0.09590	T	0.72	0.1947	6.5379	0.22365	0.3145:0.0:0.4602:0.2253	.	622;626	G3V2M6;P52630	.;STAT2_HUMAN	H	626;622	ENSP00000315768:Y626H;ENSP00000450751:Y622H	ENSP00000315768:Y626H	Y	-	1	0	STAT2	55026661	0.919000	0.31177	0.796000	0.32109	0.122000	0.20287	0.412000	0.21131	-0.649000	0.05430	0.459000	0.35465	TAC	.	.	none		0.552	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	
SON	6651	hgsc.bcm.edu	37	21	34945721	34945721	+	Silent	SNP	T	T	C	rs3174808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:34945721T>C	ENST00000356577.4	+	9	7468	c.6993T>C	c.(6991-6993)aaT>aaC	p.N2331N	SON_ENST00000381692.2_Silent_p.N359N|SON_ENST00000470533.1_3'UTR|SON_ENST00000290239.6_3'UTR	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	2331	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						AAGAAGGCAATAAGGAACCCA	0.383													T|||	1450	0.289537	0.2474	0.3242	5008	,	,		18499	0.249		0.328	False		,,,				2504	0.3241				p.N2331N		Atlas-SNP	.											.	SON	343	.	0			c.T6993C						PASS	.	T		1129,3277	401.3+/-331.9	141,847,1215	113.0	110.0	111.0		6993	1.8	1.0	21	dbSNP_105	111	2805,5791	441.8+/-359.9	460,1885,1953	yes	coding-synonymous	SON	NM_138927.1		601,2732,3168	CC,CT,TT		32.6315,25.6241,30.2569		2331/2427	34945721	3934,9068	2203	4298	6501	SO:0001819	synonymous_variant	6651	exon9			AGGCAATAAGGAA	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.6993T>C	21.37:g.34945721T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	174	93	0.534483	NM_138927	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	37	CCDS13629.1	629	0.288003663003663	121	0.2459349593495935	102	0.281767955801105	150	0.26223776223776224	256	0.33773087071240104	T	5.834	0.338035	0.11013	0.256241	0.326315	ENSG00000159140	ENST00000436227	.	.	.	5.44	1.81	0.25067	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999137549	.	.	.	.	.	.	T	0.32640	-0.9899	3	.	.	.	.	9.5434	0.39266	0.0:0.2748:0.0:0.7252	rs3174808;rs16839001	.	.	.	T	1326	.	.	I	+	2	0	SON	33867591	0.956000	0.32656	1.000000	0.80357	0.976000	0.68499	0.026000	0.13599	0.447000	0.26695	0.477000	0.44152	ATA	T|0.696;C|0.304	0.304	strong		0.383	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
BRD2	6046	hgsc.bcm.edu	37	6	32944094	32944094	+	Silent	SNP	G	G	C	rs15912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32944094G>C	ENST00000374825.4	+	6	2379	c.678G>C	c.(676-678)ctG>ctC	p.L226L	BRD2_ENST00000395287.1_Silent_p.L226L|BRD2_ENST00000443797.2_Silent_p.L106L|BRD2_ENST00000374831.4_Silent_p.L226L|BRD2_ENST00000395289.2_Silent_p.L226L|BRD2_ENST00000449085.2_Silent_p.L179L	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	226					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						ACACAGCCCTGTATACTCCTC	0.512													G|||	239	0.0477236	0.0068	0.0548	5008	,	,		20224	0.0208		0.0805	False		,,,				2504	0.092				p.L226L		Atlas-SNP	.											.	BRD2	70	.	0			c.G678C						PASS	.	G	,,,	62,2960		1,60,1450	125.0	109.0	115.0		678,678,537,678	1.4	1.0	6	dbSNP_52	115	419,4999		12,395,2302	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	13,455,3752	CC,CG,GG		7.7335,2.0516,5.6991	,,,	226/802,226/837,179/755,226/802	32944094	481,7959	1511	2709	4220	SO:0001819	synonymous_variant	6046	exon6			AGCCCTGTATACT	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.678G>C	6.37:g.32944094G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	98	0.04487179487179487	3	0.006097560975609756	20	0.055248618784530384	14	0.024475524475524476	61	0.08047493403693931	G	7.849	0.723590	0.15439	0.020516	0.077335	ENSG00000204256	ENST00000456339;ENST00000449025	.	.	.	5.33	1.43	0.22495	.	.	.	.	.	T	0.35653	0.0939	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18178	-1.0345	4	.	.	.	-10.1803	5.1342	0.14926	0.2501:0.0:0.6055:0.1444	rs15912;rs17430759;rs52789941;rs15912	.	.	.	S	228;232	.	.	C	+	2	0	BRD2	33052072	0.539000	0.26402	0.999000	0.59377	0.998000	0.95712	-0.195000	0.09546	0.141000	0.18875	0.643000	0.83706	TGT	G|0.946;C|0.054	0.054	strong		0.512	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
C2orf71	388939	hgsc.bcm.edu	37	2	29296870	29296870	+	Silent	SNP	C	C	T	rs62132765	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29296870C>T	ENST00000331664.5	-	1	257	c.258G>A	c.(256-258)agG>agA	p.R86R		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	86					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CCATATCTTTCCTTTTGCCTG	0.512													C|||	557	0.111222	0.0129	0.1527	5008	,	,		20671	0.123		0.2137	False		,,,				2504	0.0971				p.R86R		Atlas-SNP	.											C2orf71,rectum,carcinoma,-1,1	C2orf71	146	1	0			c.G258A						PASS	.	C		189,3673		4,181,1746	213.0	196.0	202.0		258	1.3	0.0	2	dbSNP_129	202	1854,6434		192,1470,2482	no	coding-synonymous	C2orf71	NM_001029883.1		196,1651,4228	TT,TC,CC		22.3697,4.8938,16.8148		86/1289	29296870	2043,10107	1931	4144	6075	SO:0001819	synonymous_variant	388939	exon1			ATCTTTCCTTTTG		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.258G>A	2.37:g.29296870C>T		Somatic	502	0	0		WXS	Illumina HiSeq	Phase_I	562	263	0.467972	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			C|0.825;T|0.175	0.175	strong		0.512	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
NAGK	55577	hgsc.bcm.edu	37	2	71304726	71304726	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71304726C>T	ENST00000244204.6	+	9	866	c.804C>T	c.(802-804)tgC>tgT	p.C268C	NAGK_ENST00000418807.3_Silent_p.C217C|NAGK_ENST00000455662.2_Silent_p.C314C|NAGK_ENST00000443938.2_Silent_p.C264C|NAGK_ENST00000443872.2_Silent_p.C120C			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	268					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	CCATCCTGTGCGTGGGCTCTG	0.627																																					p.C314C		Atlas-SNP	.											NAGK,colon,carcinoma,0,2	NAGK	34	2	0			c.C942T						scavenged	.						60.0	50.0	53.0					2																	71304726		2203	4300	6503	SO:0001819	synonymous_variant	55577	exon9			CCTGTGCGTGGGC	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.804C>T	2.37:g.71304726C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	173	3	0.017341	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Silent	SNP	ENST00000244204.6	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.374|8.374	0.835991|0.835991	0.16891|0.16891	.|.	.|.	ENSG00000124357|ENSG00000124357	ENST00000443938|ENST00000524537	.|.	.|.	.|.	5.63|5.63	3.28|3.28	0.37604|0.37604	.|.	.|.	.|.	.|.	.|.	T|T	0.57740|0.57740	0.2074|0.2074	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.50541|0.50541	-0.8816|-0.8816	4|4	.|.	.|.	.|.	-30.2512|-30.2512	8.0305|8.0305	0.30461|0.30461	0.0:0.1719:0.0:0.8281|0.0:0.1719:0.0:0.8281	.|.	.|.	.|.	.|.	V|C	286|33	.|.	.|.	A|R	+|+	2|1	0|0	NAGK|NAGK	71158234|71158234	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.740000|0.740000	0.42216|0.42216	0.555000|0.555000	0.23422|0.23422	0.427000|0.427000	0.26145|0.26145	-0.302000|-0.302000	0.09304|0.09304	GCG|CGT	.	.	none		0.627	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1		
LAMA5	3911	hgsc.bcm.edu	37	20	60907675	60907675	+	Silent	SNP	G	G	A	rs6142734	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60907675G>A	ENST00000252999.3	-	27	3447	c.3381C>T	c.(3379-3381)gcC>gcT	p.A1127A	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1127	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGGTGTGCACGGCCACGCCCA	0.687													G|||	3512	0.701278	0.2844	0.7781	5008	,	,		15512	0.9355		0.8787	False		,,,				2504	0.7863				p.A1127A		Atlas-SNP	.											LAMA5,NS,carcinoma,0,1	LAMA5	268	1	0			c.C3381T						PASS	.	G		1814,2572		388,1038,767	16.0	18.0	17.0		3381	-8.5	0.2	20	dbSNP_114	17	7642,938		3411,820,59	no	coding-synonymous	LAMA5	NM_005560.3		3799,1858,826	AA,AG,GG		10.9324,41.3589,27.0708		1127/3696	60907675	9456,3510	2193	4290	6483	SO:0001819	synonymous_variant	3911	exon27			GTGCACGGCCACG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.3381C>T	20.37:g.60907675G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.242;A|0.758	0.758	strong		0.687	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
RADIL	55698	hgsc.bcm.edu	37	7	4841313	4841313	+	Missense_Mutation	SNP	A	A	G	rs6966329	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4841313A>G	ENST00000399583.3	-	12	3000	c.2813T>C	c.(2812-2814)cTc>cCc	p.L938P	RADIL_ENST00000538469.1_Missense_Mutation_p.L698P|RADIL_ENST00000536091.1_3'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	938			L -> P (in dbSNP:rs6966329). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GAGGCCGCTGAGTCCGTTCCT	0.706													G|||	1611	0.321685	0.6929	0.1816	5008	,	,		14142	0.0476		0.1988	False		,,,				2504	0.3282				p.L938P		Atlas-SNP	.											.	RADIL	110	.	0			c.T2813C						PASS	.	G	PRO/LEU	1981,1773		532,917,428	7.0	9.0	8.0		2813	-4.7	0.0	7	dbSNP_116	8	1467,6725		154,1159,2783	no	missense	RADIL	NM_018059.4	98	686,2076,3211	GG,GA,AA		17.9077,47.2296,28.8632	benign	938/1076	4841313	3448,8498	1877	4096	5973	SO:0001583	missense	55698	exon12			CCGCTGAGTCCGT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2813T>C	7.37:g.4841313A>G	ENSP00000382492:p.Leu938Pro	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	106	41	0.386792	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	562	0.2573260073260073	321	0.6524390243902439	68	0.1878453038674033	28	0.04895104895104895	145	0.19129287598944592	g	7.674	0.687678	0.14973	0.527704	0.179077	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000538469	T;T	0.08282	3.19;3.11	4.38	-4.71	0.03279	.	1.741870	0.03289	N	0.187370	T	0.00012	0.0000	N	0.03608	-0.345	0.54753	P	1.3000000000040757E-5	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.37150	-0.9718	9	0.33141	T	0.24	-0.2438	3.9384	0.09316	0.6381:0.1122:0.1292:0.1205	rs6966329;rs10365081;rs59937119	938;246	Q96JH8;Q75LH2	RADIL_HUMAN;.	P	938;909;698	ENSP00000382492:L938P;ENSP00000442966:L698P	ENSP00000320946:L909P	L	-	2	0	RADIL	4807839	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.097000	0.03349	-1.885000	0.01118	-2.333000	0.00248	CTC	A|0.744;G|0.256	0.256	strong		0.706	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
C3orf30	152405	hgsc.bcm.edu	37	3	118867047	118867047	+	Missense_Mutation	SNP	C	C	G	rs9289122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:118867047C>G	ENST00000295622.1	+	2	1459	c.1419C>G	c.(1417-1419)gaC>gaG	p.D473E	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_Intron|IGSF11_ENST00000441144.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	473			D -> E (in dbSNP:rs9289122).							NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		CAGAAATTGACCAAGGAAAGG	0.363													G|||	2352	0.469649	0.4818	0.4856	5008	,	,		18727	0.5119		0.4404	False		,,,				2504	0.4284				p.D473E		Atlas-SNP	.											.	C3orf30	64	.	0			c.C1419G						PASS	.	G	GLU/ASP	2098,2308	595.5+/-388.5	494,1110,599	81.0	88.0	86.0		1419	-2.6	0.0	3	dbSNP_119	86	4077,4523	590.5+/-392.7	984,2109,1207	yes	missense	C3orf30	NM_152539.2	45	1478,3219,1806	GG,GC,CC		47.407,47.6169,47.4781	benign	473/537	118867047	6175,6831	2203	4300	6503	SO:0001583	missense	152405	exon2			AATTGACCAAGGA	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1419C>G	3.37:g.118867047C>G	ENSP00000295622:p.Asp473Glu	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	280	149	0.532143	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	1084	0.49633699633699635	256	0.5203252032520326	176	0.4861878453038674	303	0.5297202797202797	349	0.4604221635883905	G	0.041	-1.283573	0.01398	0.476169	0.47407	ENSG00000163424	ENST00000295622;ENST00000470341	T	0.11495	2.77	4.74	-2.61	0.06171	.	1.523470	0.04778	N	0.429264	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45629	-0.9248	9	0.02654	T	1	3.0155	0.727	0.00950	0.41:0.1284:0.2103:0.2513	rs9289122;rs52829346;rs9289122	473;473	E9PFE5;Q96M34	.;CC030_HUMAN	E	473	ENSP00000295622:D473E	ENSP00000295622:D473E	D	+	3	2	C3orf30	120349737	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.870000	0.01641	-0.718000	0.04949	-0.120000	0.15030	GAC	C|0.521;G|0.479	0.479	strong		0.363	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
CCDC74A	90557	hgsc.bcm.edu	37	2	132288315	132288315	+	Silent	SNP	G	G	A	rs11547023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:132288315G>A	ENST00000295171.6	+	3	597	c.459G>A	c.(457-459)gcG>gcA	p.A153A	CCDC74A_ENST00000467992.2_Silent_p.A255A|CCDC74A_ENST00000409856.3_Intron	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	153										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						GGCGTCTTGCGGGCGGTAGCG	0.632																																					p.A195A		Atlas-SNP	.											.	CCDC74A	44	.	0			c.G585A						PASS	.						102.0	95.0	98.0					2																	132288315		2202	4300	6502	SO:0001819	synonymous_variant	90557	exon3			TCTTGCGGGCGGT		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.459G>A	2.37:g.132288315G>A		Somatic	482	0	0		WXS	Illumina HiSeq	Phase_I	514	113	0.219844	NM_001258304	Q6P4I5	Silent	SNP	ENST00000295171.6	37	CCDS2167.1																																																																																			G|0.949;A|0.051	0.051	strong		0.632	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
DAPL1	92196	hgsc.bcm.edu	37	2	159660870	159660870	+	Silent	SNP	C	C	T	rs17810398	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:159660870C>T	ENST00000309950.3	+	2	191	c.135C>T	c.(133-135)ttC>ttT	p.F45F	DAPL1_ENST00000409042.1_Silent_p.F45F	NM_001017920.2	NP_001017920.2	A0PJW8	DAPL1_HUMAN	death associated protein-like 1	45					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)					prostate(1)	1						AAACAGGATTCGAGAAAACAA	0.388													C|||	292	0.0583067	0.0159	0.1023	5008	,	,		15777	0.0		0.1561	False		,,,				2504	0.044				p.F45F		Atlas-SNP	.											.	DAPL1	11	.	0			c.C135T						PASS	.	C		139,4267	93.9+/-132.6	1,137,2065	55.0	54.0	54.0		135	-5.9	0.4	2	dbSNP_123	54	1155,7445	228.3+/-263.4	82,991,3227	no	coding-synonymous	DAPL1	NM_001017920.2		83,1128,5292	TT,TC,CC		13.4302,3.1548,9.9493		45/108	159660870	1294,11712	2203	4300	6503	SO:0001819	synonymous_variant	92196	exon2			AGGATTCGAGAAA		CCDS33307.1	2q24	2007-06-26			ENSG00000163331	ENSG00000163331			21490	protein-coding gene	gene with protein product							Standard	NM_001017920		Approved		uc002uaf.3	A0PJW8	OTTHUMG00000153970	ENST00000309950.3:c.135C>T	2.37:g.159660870C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_001017920	A0PJW9|B9EIK6	Silent	SNP	ENST00000309950.3	37	CCDS33307.1	166	0.076007326007326	12	0.024390243902439025	48	0.13259668508287292	0	0.0	106	0.13984168865435356	C	7.900	0.734156	0.15574	0.031548	0.134302	ENSG00000163331	ENST00000343761	.	.	.	5.83	-5.87	0.02297	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999990897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.6942	0.05129	0.2775:0.2467:0.3631:0.1127	rs17810398;rs17810398	.	.	.	X	21	.	.	R	+	1	2	DAPL1	159369116	0.515000	0.26210	0.405000	0.26409	0.821000	0.46438	-0.281000	0.08456	-1.474000	0.01879	-0.271000	0.10264	CGA	C|0.916;T|0.084	0.084	strong		0.388	DAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333265.1	NM_001017920	
NXNL1	115861	hgsc.bcm.edu	37	19	17566634	17566634	+	Missense_Mutation	SNP	T	T	A	rs56248314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17566634T>A	ENST00000301944.2	-	2	545	c.461A>T	c.(460-462)gAg>gTg	p.E154V	AC010319.1_ENST00000410873.1_RNA|CTD-2521M24.11_ENST00000598950.1_lincRNA|CTD-2521M24.10_ENST00000594663.1_Missense_Mutation_p.E61V	NM_138454.1	NP_612463.1	Q96CM4	NXNL1_HUMAN	nucleoredoxin-like 1	154	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				photoreceptor cell maintenance (GO:0045494)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	6						CTCGGCCGCCTCCTGCCAGTT	0.711													t|||	355	0.0708866	0.0068	0.0749	5008	,	,		9724	0.0734		0.1302	False		,,,				2504	0.091				p.E154V		Atlas-SNP	.											.	NXNL1	13	.	0			c.A461T						PASS	.		VAL/GLU	114,4066		2,110,1978	11.0	9.0	10.0		461	3.6	1.0	19	dbSNP_129	10	1071,7205		65,941,3132	yes	missense	NXNL1	NM_138454.1	121	67,1051,5110	AA,AT,TT		12.941,2.7273,9.5135	probably-damaging	154/213	17566634	1185,11271	2090	4138	6228	SO:0001583	missense	115861	exon2			GCCGCCTCCTGCC	BC014127	CCDS12360.1	19p13.11	2014-05-21	2007-08-16	2007-08-16	ENSG00000171773	ENSG00000171773			25179	protein-coding gene	gene with protein product		608791	"""thioredoxin-like 6"""	TXNL6		12477932	Standard	NM_138454		Approved	RDCVF	uc002ngs.3	Q96CM4	OTTHUMG00000182798	ENST00000301944.2:c.461A>T	19.37:g.17566634T>A	ENSP00000305631:p.Glu154Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_138454	Q0QD37	Missense_Mutation	SNP	ENST00000301944.2	37	CCDS12360.1	179	0.08195970695970696	5	0.01016260162601626	30	0.08287292817679558	47	0.08216783216783216	97	0.1279683377308707	t	19.56	3.850035	0.71603	0.027273	0.12941	ENSG00000171773	ENST00000301944	D	0.86297	-2.1	3.6	3.6	0.41247	Thioredoxin-like fold (1);	0.000000	0.85682	U	0.000000	T	0.12646	0.0307	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.55573	-0.8120	10	0.54805	T	0.06	.	10.221	0.43196	0.0:0.0:0.0:1.0	rs56248314	154	Q96CM4	NXNL1_HUMAN	V	154	ENSP00000305631:E154V	ENSP00000305631:E154V	E	-	2	0	NXNL1	17427634	1.000000	0.71417	0.981000	0.43875	0.555000	0.35460	7.395000	0.79876	1.519000	0.48950	0.235000	0.17854	GAG	T|0.913;A|0.087	0.087	strong		0.711	NXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463803.1	NM_138454	
AMPD1	270	hgsc.bcm.edu	37	1	115231254	115231254	+	Missense_Mutation	SNP	G	G	A	rs61752479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:115231254G>A	ENST00000520113.2	-	3	257	c.242C>T	c.(241-243)cCg>cTg	p.P81L	AMPD1_ENST00000353928.6_Missense_Mutation_p.P48L|AMPD1_ENST00000369538.3_Missense_Mutation_p.P77L			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	81			P -> L (polymorphism; activity comparable to wild-type; dbSNP:rs61752479). {ECO:0000269|PubMed:1631143}.		IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	ATGAGAAATCGGACAGATCTC	0.473													G|||	195	0.0389377	0.0045	0.0634	5008	,	,		20447	0.001		0.1233	False		,,,				2504	0.0204				p.P81L		Atlas-SNP	.											AMPD1_ENST00000520113,NS,carcinoma,0,2	AMPD1	223	2	0			c.C242T	GRCh37	CM920026	AMPD1	M	rs61752479	scavenged	.	G	LEU/PRO,LEU/PRO	103,4303	82.4+/-120.9	2,99,2102	147.0	140.0	142.0		242,230	5.6	1.0	1	dbSNP_129	142	1144,7456	236.7+/-268.8	90,964,3246	yes	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	98,98	92,1063,5348	AA,AG,GG		13.3023,2.3377,9.5879	probably-damaging,probably-damaging	81/781,77/777	115231254	1247,11759	2203	4300	6503	SO:0001583	missense	270	exon3			GAAATCGGACAGA	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.242C>T	1.37:g.115231254G>A	ENSP00000430075:p.Pro81Leu	Somatic	217	2	0.00921659		WXS	Illumina HiSeq	Phase_I	168	94	0.559524	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	119	0.05448717948717949	3	0.006097560975609756	31	0.0856353591160221	0	0.0	85	0.11213720316622691	G	19.67	3.871817	0.72180	0.023377	0.133023	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	T;T;T	0.63744	-0.06;-0.06;-0.06	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	L	0.43152	1.355	0.09310	P	0.9999999999943356	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.72354	-0.4319	9	0.87932	D	0	-11.3019	20.0247	0.97519	0.0:0.0:1.0:0.0	rs61752479	77;48	Q5TF02;P23109	.;AMPD1_HUMAN	L	81;77;48	ENSP00000430075:P81L;ENSP00000358551:P77L;ENSP00000316520:P48L	ENSP00000316520:P48L	P	-	2	0	AMPD1	115032777	1.000000	0.71417	1.000000	0.80357	0.172000	0.22775	9.232000	0.95325	2.804000	0.96469	0.655000	0.94253	CCG	G|0.913;A|0.087	0.087	strong		0.473	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058090	79058090	+	Missense_Mutation	SNP	A	A	G	rs2929158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79058090A>G	ENST00000388820.4	-	19	4373	c.4163T>C	c.(4162-4164)gTc>gCc	p.V1388A	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1388					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GGTCTCAGGGACTCTGTGGCT	0.687																																					p.V1388A		Atlas-SNP	.											ADAMTS7,rectum,carcinoma,0,1	ADAMTS7	142	1	0			c.T4163C						scavenged	.						22.0	29.0	26.0					15																	79058090		2166	4248	6414	SO:0001583	missense	11173	exon19			TCAGGGACTCTGT	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.4163T>C	15.37:g.79058090A>G	ENSP00000373472:p.Val1388Ala	Somatic	146	2	0.0136986		WXS	Illumina HiSeq	Phase_I	86	12	0.139535	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	249	0.11401098901098901	2	0.0040650406504065045	43	0.11878453038674033	198	0.34615384615384615	6	0.0079155672823219	a	0.637	-0.814774	0.02776	.	.	ENSG00000136378	ENST00000388820	T	0.58506	0.33	3.65	-3.31	0.04988	.	0.591257	0.16562	N	0.209003	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35724	-0.9777	9	0.15066	T	0.55	.	0.8256	0.01120	0.1904:0.2419:0.3106:0.2571	rs2929158	1388	Q9UKP4	ATS7_HUMAN	A	1388	ENSP00000373472:V1388A	ENSP00000373472:V1388A	V	-	2	0	ADAMTS7	76845145	0.000000	0.05858	0.052000	0.19188	0.008000	0.06430	-1.706000	0.01895	-0.534000	0.06315	-2.103000	0.00360	GTC	A|0.897;G|0.103	0.103	strong		0.687	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
RECK	8434	hgsc.bcm.edu	37	9	36105264	36105264	+	Silent	SNP	A	A	G	rs11788747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:36105264A>G	ENST00000377966.3	+	13	2126	c.1560A>G	c.(1558-1560)ccA>ccG	p.P520P		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	520					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			CCTGTCTTCCATACTTTTGTG	0.438													A|||	1279	0.255391	0.0469	0.2464	5008	,	,		18176	0.3075		0.3907	False		,,,				2504	0.3507				p.P520P		Atlas-SNP	.											.	RECK	73	.	0			c.A1560G						PASS	.	A		449,3957	214.8+/-234.0	27,395,1781	148.0	134.0	139.0		1560	-4.0	1.0	9	dbSNP_120	139	3450,5150	507.1+/-376.8	724,2002,1574	no	coding-synonymous	RECK	NM_021111.2		751,2397,3355	GG,GA,AA		40.1163,10.1906,29.9785		520/972	36105264	3899,9107	2203	4300	6503	SO:0001819	synonymous_variant	8434	exon13			TCTTCCATACTTT	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.1560A>G	9.37:g.36105264A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	177	85	0.480226	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Silent	SNP	ENST00000377966.3	37	CCDS6597.1																																																																																			A|0.721;G|0.279	0.279	strong		0.438	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
MUC16	94025	hgsc.bcm.edu	37	19	9076278	9076278	+	Missense_Mutation	SNP	G	G	A	rs953551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9076278G>A	ENST00000397910.4	-	3	11371	c.11168C>T	c.(11167-11169)aCg>aTg	p.T3723M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3724	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGACAGGGGCGTATTTGGGTC	0.473													A|||	1282	0.25599	0.2035	0.2161	5008	,	,		21497	0.254		0.335	False		,,,				2504	0.2761				p.T3723M		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	2	0			c.C11168T						PASS	.	A	MET/THR	853,3105		98,657,1224	129.0	127.0	128.0		11168	-1.1	0.0	19	dbSNP_86	128	2580,5764		389,1802,1981	yes	missense	MUC16	NM_024690.2	81	487,2459,3205	AA,AG,GG		30.9204,21.5513,27.906	benign	3723/14508	9076278	3433,8869	1979	4172	6151	SO:0001583	missense	94025	exon3			AGGGGCGTATTTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11168C>T	19.37:g.9076278G>A	ENSP00000381008:p.Thr3723Met	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	275	124	0.450909	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	573	0.2623626373626374	110	0.22357723577235772	88	0.2430939226519337	126	0.2202797202797203	249	0.32849604221635886	a	1.415	-0.574322	0.03882	0.215513	0.309204	ENSG00000181143	ENST00000397910	T	0.02579	4.24	1.65	-1.07	0.09968	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.06786	0.001	B	0.01281	0.0	T	0.47129	-0.9141	8	0.87932	D	0	.	2.4527	0.04522	0.3366:0.0:0.413:0.2504	rs953551;rs17516069;rs52791023;rs59907804;rs953551	3723	B5ME49	.	M	3723	ENSP00000381008:T3723M	ENSP00000381008:T3723M	T	-	2	0	MUC16	8937278	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.808000	0.01732	-0.903000	0.03881	-0.817000	0.03123	ACG	G|0.739;A|0.261	0.261	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ABCG5	64240	hgsc.bcm.edu	37	2	44040401	44040401	+	Missense_Mutation	SNP	G	G	C	rs6720173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:44040401G>C	ENST00000260645.1	-	13	1949	c.1810C>G	c.(1810-1812)Caa>Gaa	p.Q604E	ABCG5_ENST00000405322.1_Missense_Mutation_p.Q433E|ABCG5_ENST00000543989.1_Missense_Mutation_p.Q209E	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	604	ABC transmembrane type-2.		Q -> E (in dbSNP:rs6720173). {ECO:0000269|PubMed:11099417, ECO:0000269|PubMed:11138003, ECO:0000269|PubMed:11452359, ECO:0000269|PubMed:11668628}.		ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TGAATTCCTTGAGTGAAGGCA	0.383													G|||	1202	0.240016	0.3298	0.3012	5008	,	,		20767	0.121		0.164	False		,,,				2504	0.2761				p.Q604E		Atlas-SNP	.											.	ABCG5	72	.	0			c.C1810G	GRCh37	CM025438	ABCG5	M	rs6720173	PASS	.	G	GLU/GLN	1353,3053	448.3+/-348.6	210,933,1060	97.0	96.0	96.0		1810	3.9	1.0	2	dbSNP_116	96	1382,7218	267.2+/-287.2	123,1136,3041	yes	missense	ABCG5	NM_022436.2	29	333,2069,4101	CC,CG,GG		16.0698,30.7081,21.0288	possibly-damaging	604/652	44040401	2735,10271	2203	4300	6503	SO:0001583	missense	64240	exon13			TTCCTTGAGTGAA	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"""ATP binding cassette transporters / subfamily G"""	13886	protein-coding gene	gene with protein product	"""sterolin 1"""	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1810C>G	2.37:g.44040401G>C	ENSP00000260645:p.Gln604Glu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	37	CCDS1814.1	460	0.21062271062271062	171	0.3475609756097561	98	0.27071823204419887	65	0.11363636363636363	126	0.1662269129287599	G	7.416	0.635703	0.14322	0.307081	0.160698	ENSG00000138075	ENST00000260645;ENST00000405322;ENST00000543989	D;T;T	0.89552	-2.53;2.33;2.33	4.79	3.91	0.45181	.	0.835327	0.11000	N	0.610637	T	0.00012	0.0000	L	0.54323	1.7	0.32863	P	0.491858	B;B	0.23806	0.091;0.067	B;B	0.19391	0.025;0.012	T	0.10154	-1.0642	9	0.15066	T	0.55	.	14.8473	0.70270	0.0:0.1446:0.8554:0.0	rs6720173;rs17423788;rs52807957;rs6720173	433;604	E7EX35;Q9H222	.;ABCG5_HUMAN	E	604;433;209	ENSP00000260645:Q604E;ENSP00000384513:Q433E;ENSP00000445107:Q209E	ENSP00000260645:Q604E	Q	-	1	0	ABCG5	43893905	1.000000	0.71417	0.985000	0.45067	0.272000	0.26649	2.978000	0.49305	1.221000	0.43506	-0.165000	0.13383	CAA	G|0.792;C|0.208	0.208	strong		0.383	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436	
SPRED2	200734	hgsc.bcm.edu	37	2	65540905	65540905	+	Silent	SNP	C	C	G	rs8827	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:65540905C>G	ENST00000356388.4	-	6	1176	c.987G>C	c.(985-987)gcG>gcC	p.A329A	SPRED2_ENST00000443619.2_Silent_p.A326A|SPRED2_ENST00000474228.1_5'Flank	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	329	SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						CGGAGTCGGGCGCGTCCTGGC	0.647													C|||	1980	0.395367	0.112	0.4784	5008	,	,		17430	0.755		0.2505	False		,,,				2504	0.498				p.A329A		Atlas-SNP	.											SPRED2,colon,carcinoma,0,1	SPRED2	70	1	0			c.G987C						PASS	.	C	,	670,3736	273.1+/-271.2	53,564,1586	82.0	81.0	81.0		978,987	-6.7	0.9	2	dbSNP_52	81	2208,6390	354.6+/-329.6	291,1626,2382	no	coding-synonymous,coding-synonymous	SPRED2	NM_001128210.1,NM_181784.2	,	344,2190,3968	GG,GC,CC		25.6804,15.2065,22.1317	,	326/416,329/419	65540905	2878,10126	2203	4299	6502	SO:0001819	synonymous_variant	200734	exon6			GTCGGGCGCGTCC	AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.987G>C	2.37:g.65540905C>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_181784	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Silent	SNP	ENST00000356388.4	37	CCDS33211.1																																																																																			C|0.713;G|0.287	0.287	strong		0.647	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1		
PLEKHG4	25894	hgsc.bcm.edu	37	16	67322118	67322118	+	Missense_Mutation	SNP	G	G	C	rs17680862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:67322118G>C	ENST00000360461.5	+	19	5804	c.3269G>C	c.(3268-3270)aGc>aCc	p.S1090T	PLEKHG4_ENST00000427155.2_Missense_Mutation_p.S1090T|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.S1009T|PLEKHG4_ENST00000379344.3_Missense_Mutation_p.S1090T	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	1090			S -> T (in dbSNP:rs17680862).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		GACCATGACAGCCTCTACCTG	0.612													G|||	143	0.0285543	0.0212	0.0101	5008	,	,		19993	0.0		0.0268	False		,,,				2504	0.0828				p.S1090T		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.G3269C						PASS	.	G	THR/SER,THR/SER,THR/SER,THR/SER,THR/SER	102,4294	80.4+/-118.8	0,102,2096	118.0	117.0	117.0		3269,3269,3269,3026,3269	-1.0	0.3	16	dbSNP_123	117	237,8363	96.3+/-158.1	2,233,4065	yes	missense,missense,missense,missense,missense	PLEKHG4	NM_001129727.1,NM_001129728.1,NM_001129729.1,NM_001129731.1,NM_015432.3	58,58,58,58,58	2,335,6161	CC,CG,GG		2.7558,2.3203,2.6085	benign,benign,benign,benign,benign	1090/1192,1090/1192,1090/1192,1009/1111,1090/1192	67322118	339,12657	2198	4300	6498	SO:0001583	missense	25894	exon20			ATGACAGCCTCTA	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.3269G>C	16.37:g.67322118G>C	ENSP00000353646:p.Ser1090Thr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	43	0.019688644688644688	14	0.028455284552845527	6	0.016574585635359115	0	0.0	23	0.030343007915567283	G	8.357	0.832318	0.16820	0.023203	0.027558	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.1	-1.04	0.10068	.	0.419988	0.17644	N	0.166936	T	0.04770	0.0129	L	0.31065	0.9	0.19945	N	0.999947	P;P	0.38922	0.571;0.651	B;B	0.30855	0.121;0.084	T	0.28170	-1.0052	10	0.13470	T	0.59	.	9.5062	0.39048	0.6291:0.0:0.3709:0.0	rs17680862;rs17680862	1009;1090	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	T	1090;1090;1090;1009	ENSP00000353646:S1090T;ENSP00000401118:S1090T;ENSP00000368649:S1090T;ENSP00000398030:S1009T	ENSP00000353646:S1090T	S	+	2	0	PLEKHG4	65879619	0.928000	0.31464	0.296000	0.24974	0.376000	0.30014	1.977000	0.40589	-0.049000	0.13379	0.462000	0.41574	AGC	G|0.977;C|0.023	0.023	strong		0.612	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
DNHD1	144132	hgsc.bcm.edu	37	11	6530278	6530278	+	Silent	SNP	C	C	T	rs10839568	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6530278C>T	ENST00000527990.2	+	3	1089	c.1089C>T	c.(1087-1089)ttC>ttT	p.F363F	DNHD1_ENST00000254579.6_Silent_p.F363F|DNHD1_ENST00000354685.3_Silent_p.F363F			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	363					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TCATTCCATTCTTTAAGTATT	0.468													C|||	1098	0.219249	0.1377	0.3199	5008	,	,		19924	0.128		0.3519	False		,,,				2504	0.2157				p.F363F		Atlas-SNP	.											.	DNHD1	198	.	0			c.C1089T						PASS	.	C	,	733,3669	298.1+/-285.1	59,615,1527	207.0	186.0	193.0		1089,1089	4.6	1.0	11	dbSNP_120	193	2831,5761	447.3+/-361.5	465,1901,1930	no	coding-synonymous,coding-synonymous	DNHD1	NM_144666.2,NM_173589.3	,	524,2516,3457	TT,TC,CC		32.9493,16.6515,27.428	,	363/4754,363/598	6530278	3564,9430	2201	4296	6497	SO:0001819	synonymous_variant	144132	exon4			TCCATTCTTTAAG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.1089C>T	11.37:g.6530278C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	257	109	0.424125	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			C|0.744;T|0.256	0.256	strong		0.468	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
PDXDC1	23042	hgsc.bcm.edu	37	16	15100301	15100301	+	Missense_Mutation	SNP	C	C	T	rs141901522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15100301C>T	ENST00000396410.4	+	6	537	c.440C>T	c.(439-441)gCa>gTa	p.A147V	PDXDC1_ENST00000535621.2_Missense_Mutation_p.A147V|PDXDC1_ENST00000447912.2_Missense_Mutation_p.A56V|PDXDC1_ENST00000455313.2_Missense_Mutation_p.A147V|PDXDC1_ENST00000569715.1_Missense_Mutation_p.A120V|PDXDC1_ENST00000450288.2_Missense_Mutation_p.A119V|PDXDC1_ENST00000563679.1_Missense_Mutation_p.A165V|PDXDC1_ENST00000325823.7_Missense_Mutation_p.A132V	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	147					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAAGGACTTGCAAAGATATGT	0.353													.|||	3	0.000599042	0.0	0.0	5008	,	,		33956	0.0		0.003	False		,,,				2504	0.0				p.A147V		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C440T						PASS	.	C	VAL/ALA	2,4392	4.2+/-10.8	0,2,2195	149.0	150.0	150.0		440	4.8	1.0	16	dbSNP_134	150	21,8579	14.0+/-48.4	0,21,4279	no	missense	PDXDC1	NM_015027.2	64	0,23,6474	TT,TC,CC		0.2442,0.0455,0.177	benign	147/789	15100301	23,12971	2197	4300	6497	SO:0001583	missense	23042	exon6			GACTTGCAAAGAT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.440C>T	16.37:g.15100301C>T	ENSP00000379691:p.Ala147Val	Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	372	103	0.276882	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.813847	0.32053	4.55E-4	0.002442	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000455313	T;T;T;T;T;T	0.36157	1.27;2.41;1.27;1.27;1.27;1.27	5.82	4.79	0.61399	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.260219	0.37178	N	0.002204	T	0.11153	0.0272	N	0.02539	-0.55	0.33168	D	0.547894	B;B;B;B;B;B;B	0.13145	0.005;0.002;0.005;0.007;0.005;0.005;0.003	B;B;B;B;B;B;B	0.15052	0.008;0.004;0.008;0.007;0.012;0.008;0.006	T	0.32428	-0.9907	10	0.06891	T	0.86	-0.0283	4.3523	0.11162	0.0:0.7219:0.0:0.2781	.	119;56;132;147;119;147;147	E7EPL4;E7EMH5;B4DHL7;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;.;PDXD1_HUMAN;.	V	132;56;147;147;119;147	ENSP00000322807:A132V;ENSP00000400310:A56V;ENSP00000437835:A147V;ENSP00000379691:A147V;ENSP00000391147:A119V;ENSP00000406703:A147V	ENSP00000322807:A132V	A	+	2	0	PDXDC1	15007802	0.932000	0.31603	1.000000	0.80357	0.901000	0.52897	3.426000	0.52778	2.765000	0.95021	0.650000	0.86243	GCA	C|0.998;T|0.002	0.002	strong		0.353	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
MUC2	4583	hgsc.bcm.edu	37	11	1092973	1092973	+	Missense_Mutation	SNP	C	C	T	rs55847666		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1092973C>T	ENST00000441003.2	+	30	4819	c.4792C>T	c.(4792-4794)Ccc>Tcc	p.P1598S	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.P1598S(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aaccccaacacccaccggcac	0.637																																					p.P1598S		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	1	Substitution - Missense(1)	endometrium(1)	c.C4792T						PASS	.						47.0	83.0	70.0					11																	1092973		1782	3238	5020	SO:0001583	missense	4583	exon30			CCAACACCCACCG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4792C>T	11.37:g.1092973C>T	ENSP00000415183:p.Pro1598Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	121	8	0.0661157	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.622	-0.077443	0.07184	.	.	ENSG00000198788	ENST00000441003	T	0.13778	2.56	1.75	-2.88	0.05682	.	.	.	.	.	T	0.04363	0.0120	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.43686	-0.9376	8	0.07482	T	0.82	.	3.4241	0.07403	0.4105:0.429:0.0:0.1605	rs55847666	1598	E7EUV1	.	S	1598	ENSP00000415183:P1598S	ENSP00000415183:P1598S	P	+	1	0	MUC2	1082973	0.007000	0.16637	0.000000	0.03702	0.120000	0.20174	0.230000	0.17852	-0.314000	0.08716	0.121000	0.15741	CCC	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
NADK	65220	hgsc.bcm.edu	37	1	1684472	1684472	+	Silent	SNP	C	C	T	rs7407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1684472C>T	ENST00000341426.5	-	12	1433	c.1212G>A	c.(1210-1212)ccG>ccA	p.P404P	NADK_ENST00000342348.5_Silent_p.P372P|NADK_ENST00000341991.3_Silent_p.P404P|NADK_ENST00000344463.4_Silent_p.P549P|NADK_ENST00000378625.1_Silent_p.P549P	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	404					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		TGGAGGGGAGCGGGTAGCATG	0.637													C|||	1701	0.339657	0.0552	0.5634	5008	,	,		15082	0.3452		0.505	False		,,,				2504	0.3896				p.P549P		Atlas-SNP	.											NADK,NS,carcinoma,-2,1	NADK	79	1	0			c.G1647A						PASS	.	C	,,,	549,3849	232.6+/-246.1	43,463,1693	44.0	29.0	34.0		1212,1647,1116,1212	-6.1	0.7	1	dbSNP_52	34	4405,4193	553.0+/-386.2	1171,2063,1065	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NADK	NM_001198993.1,NM_001198994.1,NM_001198995.1,NM_023018.4	,,,	1214,2526,2758	TT,TC,CC		48.7672,12.4829,38.1194	,,,	404/447,549/592,372/415,404/447	1684472	4954,8042	2199	4299	6498	SO:0001819	synonymous_variant	65220	exon14			GGGGAGCGGGTAG	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.1212G>A	1.37:g.1684472C>T		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	186	63	0.33871	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Silent	SNP	ENST00000341426.5	37	CCDS30565.1																																																																																			C|0.648;T|0.352	0.352	strong		0.637	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
HRNR	388697	hgsc.bcm.edu	37	1	152189016	152189016	+	Missense_Mutation	SNP	G	G	A	rs200517377		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152189016G>A	ENST00000368801.2	-	3	5164	c.5089C>T	c.(5089-5091)Cgt>Tgt	p.R1697C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1697					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAGACTGACGGGAGCCAGAC	0.632																																					p.R1697C		Atlas-SNP	.											HRNR,NS,carcinoma,0,4	HRNR	403	4	0			c.C5089T						scavenged	.						57.0	73.0	68.0					1																	152189016		1629	3176	4805	SO:0001583	missense	388697	exon3			ACTGACGGGAGCC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5089C>T	1.37:g.152189016G>A	ENSP00000357791:p.Arg1697Cys	Somatic	205	2	0.0097561		WXS	Illumina HiSeq	Phase_I	804	32	0.039801	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	3.089	-0.187379	0.06299	.	.	ENSG00000197915	ENST00000368801	T	0.01647	4.71	3.82	-7.65	0.01281	.	.	.	.	.	T	0.00440	0.0014	L	0.38175	1.15	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.43988	-0.9357	9	0.56958	D	0.05	.	3.7438	0.08540	0.0806:0.2135:0.2435:0.4624	.	1697	Q86YZ3	HORN_HUMAN	C	1697	ENSP00000357791:R1697C	ENSP00000357791:R1697C	R	-	1	0	HRNR	150455640	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.680000	0.00395	-2.946000	0.00295	-1.447000	0.01057	CGT	.	.	weak		0.632	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
GPSM3	63940	hgsc.bcm.edu	37	6	32159956	32159956	+	Silent	SNP	T	T	C	rs3134605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32159956T>C	ENST00000375040.3	-	2	506	c.114A>G	c.(112-114)ccA>ccG	p.P38P	PBX2_ENST00000375050.4_5'Flank|GPSM3_ENST00000487761.1_Silent_p.P35P|GPSM3_ENST00000375043.3_Silent_p.P38P	NM_001276501.1	NP_001263430.1	Q9Y4H4	GPSM3_HUMAN	G-protein signaling modulator 3	38	Pro-rich.				regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cytoplasm (GO:0005737)	GDP-dissociation inhibitor activity (GO:0005092)			large_intestine(1)	1						GAGGAGGGGATGGAGGAGCAG	0.627													C|||	1144	0.228435	0.1974	0.1772	5008	,	,		11010	0.2688		0.1918	False		,,,				2504	0.3027				p.P38P		Atlas-SNP	.											GPSM3,colon,carcinoma,0,1	GPSM3	9	1	0			c.A114G						PASS	.	C		812,3594	739.1+/-411.0	76,660,1467	44.0	48.0	47.0		114	-7.0	0.9	6	dbSNP_103	47	1792,6806	727.0+/-406.6	188,1416,2695	yes	coding-synonymous	GPSM3	NM_022107.1		264,2076,4162	CC,CT,TT		20.8421,18.4294,20.0246		38/161	32159956	2604,10400	2203	4299	6502	SO:0001819	synonymous_variant	63940	exon6			AGGGGATGGAGGA	AF155657	CCDS34419.1	6p21.3	2010-06-24	2010-06-24	2004-02-04	ENSG00000213654	ENSG00000213654			13945	protein-coding gene	gene with protein product	"""activator of G-protein signaling 4"""		"""chromosome 6 open reading frame 9"", ""G-protein signalling modulator 3 (AGS3-like, C. elegans)"""	C6orf9		2259622, 15096500	Standard	NM_022107		Approved	NG1, G18, G18.1a, G18.1b, G18.2, AGS4	uc003oaz.3	Q9Y4H4	OTTHUMG00000031244	ENST00000375040.3:c.114A>G	6.37:g.32159956T>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	155	63	0.406452	NM_022107	A2BFJ3	Silent	SNP	ENST00000375040.3	37	CCDS34419.1																																																																																			T|0.814;C|0.186	0.186	strong		0.627	GPSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076509.1	NM_022107	
RING1	6015	hgsc.bcm.edu	37	6	33179689	33179689	+	Silent	SNP	C	C	T	rs2854028	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33179689C>T	ENST00000374656.4	+	6	1237	c.1029C>T	c.(1027-1029)gaC>gaT	p.D343D	RING1_ENST00000478431.1_3'UTR	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	343	Gly-rich.|Necessary for interaction with CBX2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						GAGGAGGTGACGGTCCTGAGG	0.667													C|||	876	0.17492	0.0272	0.2219	5008	,	,		11671	0.1488		0.2147	False		,,,				2504	0.3272				p.D343D		Atlas-SNP	.											.	RING1	40	.	0			c.C1029T						PASS	.	C		259,4137		11,237,1950	21.0	25.0	24.0		1029	-3.6	0.8	6	dbSNP_100	24	2034,6556		229,1576,2490	yes	coding-synonymous	RING1	NM_002931.3		240,1813,4440	TT,TC,CC		23.6787,5.8917,17.6575		343/407	33179689	2293,10693	2198	4295	6493	SO:0001819	synonymous_variant	6015	exon6			AGGTGACGGTCCT		CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"""RING-type (C3HC4) zinc fingers"""	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.1029C>T	6.37:g.33179689C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_002931	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Silent	SNP	ENST00000374656.4	37	CCDS34424.1																																																																																			C|0.842;T|0.158	0.158	strong		0.667	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2		
KLHL38	340359	hgsc.bcm.edu	37	8	124664792	124664792	+	Silent	SNP	C	C	T	rs7387544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:124664792C>T	ENST00000325995.7	-	1	398	c.375G>A	c.(373-375)tcG>tcA	p.S125S	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	125										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						TCTGCAAGTACGAGGAGCAGG	0.562													C|||	3548	0.708466	0.6657	0.6902	5008	,	,		20607	0.7113		0.8022	False		,,,				2504	0.68				p.S125S		Atlas-SNP	.											KLHL38,NS,carcinoma,-1,1	KLHL38	81	1	0			c.G375A						PASS	.	C		2820,1162		994,832,165	47.0	52.0	51.0		375	-10.9	0.3	8	dbSNP_116	51	6554,1758		2596,1362,198	no	coding-synonymous	KLHL38	NM_001081675.2		3590,2194,363	TT,TC,CC		21.1501,29.1813,23.7514		125/582	124664792	9374,2920	1991	4156	6147	SO:0001819	synonymous_variant	340359	exon1			CAAGTACGAGGAG		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.375G>A	8.37:g.124664792C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	37	CCDS43766.1																																																																																			C|0.264;T|0.736	0.736	strong		0.562	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
IRX4	50805	hgsc.bcm.edu	37	5	1880865	1880865	+	Silent	SNP	T	T	C	rs4975753	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:1880865T>C	ENST00000505790.1	-	4	837	c.381A>G	c.(379-381)ccA>ccG	p.P127P	IRX4_ENST00000505938.1_5'UTR|IRX4_ENST00000513692.1_Silent_p.P127P|IRX4_ENST00000231357.2_Silent_p.P127P	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	127					establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		GGCCCAGAGCTGGCTCGTAAG	0.627													C|||	1489	0.297324	0.3404	0.3184	5008	,	,		14238	0.3313		0.2276	False		,,,				2504	0.2607				p.P127P		Atlas-SNP	.											.	IRX4	45	.	0			c.A381G						PASS	.	C		1303,3103	695.1+/-405.9	183,937,1083	68.0	71.0	70.0		381	-2.3	0.2	5	dbSNP_111	70	1991,6609	720.5+/-406.3	236,1519,2545	no	coding-synonymous	IRX4	NM_016358.2		419,2456,3628	CC,CT,TT		23.1512,29.5733,25.3268		127/520	1880865	3294,9712	2203	4300	6503	SO:0001819	synonymous_variant	50805	exon3			CAGAGCTGGCTCG	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"""Homeoboxes / TALE class"""	6129	protein-coding gene	gene with protein product		606199	"""iroquois homeobox protein 4"""			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.381A>G	5.37:g.1880865T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	112	39	0.348214	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Silent	SNP	ENST00000505790.1	37	CCDS3867.1																																																																																			T|0.732;C|0.268	0.268	strong		0.627	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358	
PRG2	5553	hgsc.bcm.edu	37	11	57155001	57155001	+	Missense_Mutation	SNP	G	G	A	rs536455	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57155001G>A	ENST00000311862.5	-	6	689	c.616C>T	c.(616-618)Cac>Tac	p.H206Y	PRG2_ENST00000525955.1_Missense_Mutation_p.H206Y|PRG2_ENST00000533605.1_Missense_Mutation_p.H195Y	NM_001243245.1|NM_002728.4	NP_001230174.1|NP_002719.3	P13727	PRG2_HUMAN	proteoglycan 2, bone marrow (natural killer cell activator, eosinophil granule major basic protein)	206	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		H -> Y (in dbSNP:rs536455). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1565101, ECO:0000269|PubMed:2323577, ECO:0000269|PubMed:3171483, ECO:0000269|PubMed:3199069, ECO:0000269|PubMed:7531438, ECO:0000269|Ref.8}.		defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Sargramostim(DB00020)	CGACGCCAGTGGCCTCCTGTG	0.582													G|||	4432	0.884984	0.5908	0.9697	5008	,	,		18066	0.996		0.997	False		,,,				2504	0.9928				p.H206Y		Atlas-SNP	.											.	PRG2	65	.	0			c.C616T						PASS	.	G	TYR/HIS	2853,1549	669.2+/-402.1	902,1049,250	66.0	66.0	66.0		616	3.0	0.5	11	dbSNP_83	66	8574,18	818.1+/-406.9	4278,18,0	yes	missense	PRG2	NM_002728.4	83	5180,1067,250	AA,AG,GG		0.2095,35.1886,12.0594		206/223	57155001	11427,1567	2201	4296	6497	SO:0001583	missense	5553	exon6			GCCAGTGGCCTCC	BC005929	CCDS7955.1, CCDS58133.1	11q12	2005-11-25				ENSG00000186652			9362	protein-coding gene	gene with protein product		605601				1565101	Standard	NM_001243245		Approved	MBP, BMPG		P13727		ENST00000311862.5:c.616C>T	11.37:g.57155001G>A	ENSP00000312134:p.His206Tyr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_002728	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Missense_Mutation	SNP	ENST00000311862.5	37	CCDS7955.1	1972	0.9029304029304029	295	0.5995934959349594	349	0.9640883977900553	570	0.9965034965034965	758	1.0	G	11.27	1.587838	0.28268	0.648114	0.997905	ENSG00000186652	ENST00000311862;ENST00000533605;ENST00000525955	T;T;T	0.18502	2.21;2.21;2.21	4.92	3.03	0.35002	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.534882	0.15531	N	0.257502	T	0.00012	0.0000	L	0.33792	1.035	0.50171	P	1.4099999999994672E-4	B;P	0.35982	0.031;0.531	B;P	0.45406	0.078;0.479	T	0.36939	-0.9727	9	0.26408	T	0.33	.	6.8289	0.23898	0.0967:0.1777:0.7256:0.0	rs536455;rs2228383;rs17850013;rs536455	195;206	A6XMW0;P13727	.;PRG2_HUMAN	Y	206;195;206	ENSP00000312134:H206Y;ENSP00000433231:H195Y;ENSP00000433016:H206Y	ENSP00000312134:H206Y	H	-	1	0	PRG2	56911577	0.003000	0.15002	0.504000	0.27639	0.064000	0.16182	0.974000	0.29436	0.463000	0.27118	0.650000	0.86243	CAC	G|0.123;A|0.877	0.877	strong		0.582	PRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392468.1	NM_002728	
NXPE1	120400	hgsc.bcm.edu	37	11	114401283	114401283	+	Silent	SNP	C	C	T	rs7941923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:114401283C>T	ENST00000424269.1	-	2	446	c.447G>A	c.(445-447)acG>acA	p.T149T	NXPE1_ENST00000536312.1_Silent_p.T149T|NXPE1_ENST00000536271.1_5'Flank|NXPE1_ENST00000251921.2_Silent_p.T7T			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	149						extracellular region (GO:0005576)											AAGCACCTGCCGTCAGTGCTG	0.572													C|||	1204	0.240415	0.5061	0.2421	5008	,	,		19321	0.0		0.1332	False		,,,				2504	0.2382				p.T7T		Atlas-SNP	.											.	NXPE1	8	.	0			c.G21A						PASS	.	C		1901,2501	543.6+/-376.3	407,1087,707	77.0	80.0	79.0		21	2.6	0.7	11	dbSNP_116	79	1188,7404	240.6+/-271.2	97,994,3205	no	coding-synonymous	FAM55A	NM_152315.2		504,2081,3912	TT,TC,CC		13.8268,43.1849,23.7725		7/406	114401283	3089,9905	2201	4296	6497	SO:0001819	synonymous_variant	120400	exon3			ACCTGCCGTCAGT	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.447G>A	11.37:g.114401283C>T		Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	209	109	0.521531	NM_152315	B0YJ13	Silent	SNP	ENST00000424269.1	37																																																																																				C|0.779;T|0.221	0.221	strong		0.572	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
APBB2	323	hgsc.bcm.edu	37	4	41015823	41015823	+	Silent	SNP	G	G	T	rs2292234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:41015823G>T	ENST00000295974.8	-	6	1241	c.612C>A	c.(610-612)ggC>ggA	p.G204G	APBB2_ENST00000513140.1_Silent_p.G204G|APBB2_ENST00000508593.1_Silent_p.G204G|APBB2_ENST00000506352.1_Silent_p.G204G	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	204					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						GCAGCAAATCGCCATTCCCAA	0.562													G|||	664	0.132588	0.084	0.1124	5008	,	,		17107	0.1786		0.1869	False		,,,				2504	0.1094				p.G204G	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.C612A						PASS	.						285.0	273.0	277.0					4																	41015823		2000	4167	6167	SO:0001819	synonymous_variant	323	exon6			CAAATCGCCATTC	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.612C>A	4.37:g.41015823G>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	243	127	0.522634	NM_173075	B4DSL4|E9PG87|Q8IUI6	Silent	SNP	ENST00000295974.8	37	CCDS54761.1																																																																																			A|0.342;G|0.575;T|0.083	0.083	strong		0.562	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
CACNA1E	777	hgsc.bcm.edu	37	1	181759657	181759657	+	Missense_Mutation	SNP	G	G	A	rs704326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:181759657G>A	ENST00000367573.2	+	44	5863	c.5863G>A	c.(5863-5865)Gcc>Acc	p.A1955T	CACNA1E_ENST00000357570.5_Missense_Mutation_p.A1906T|CACNA1E_ENST00000360108.3_Missense_Mutation_p.A1936T|CACNA1E_ENST00000367570.1_Missense_Mutation_p.A1955T|CACNA1E_ENST00000526775.1_Missense_Mutation_p.A1936T|CACNA1E_ENST00000358338.5_Missense_Mutation_p.A1887T|CACNA1E_ENST00000367567.4_Missense_Mutation_p.A1562T	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1955			A -> T (in dbSNP:rs704326). {ECO:0000269|PubMed:7536609}.		calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TATGGACCCCGCCGATGACGG	0.483													G|||	1384	0.276358	0.1203	0.3242	5008	,	,		18450	0.3879		0.4314	False		,,,				2504	0.1789				p.A1955T		Atlas-SNP	.											.	CACNA1E	778	.	0			c.G5863A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	591,3217		55,481,1368	81.0	92.0	89.0		5863,5863,5806	-1.5	0.0	1	dbSNP_86	89	3736,4484		850,2036,1224	yes	missense,missense,missense	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	58,58,58	905,2517,2592	AA,AG,GG		45.4501,15.52,35.9744	benign,benign,benign	1955/2271,1955/2314,1936/2252	181759657	4327,7701	1904	4110	6014	SO:0001583	missense	777	exon44			GACCCCGCCGATG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5863G>A	1.37:g.181759657G>A	ENSP00000356545:p.Ala1955Thr	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	216	212	0.981481	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	784	0.358974358974359	58	0.11788617886178862	139	0.3839779005524862	254	0.44405594405594406	333	0.4393139841688654	G	1.618	-0.522134	0.04171	0.1552	0.454501	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96365	-3.92;-3.92;-3.83;-3.92;-3.99;-3.84;-3.83	5.54	-1.5	0.08691	.	1.620940	0.02678	N	0.109393	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.001	T	0.31336	-0.9947	9	0.14656	T	0.56	.	11.663	0.51358	0.5216:0.0:0.4784:0.0	rs704326;rs56466668;rs60254499;rs704326	1936;1955	Q15878-2;Q15878-3	.;.	T	1955;1936;1906;1887;1562;1936;1955	ENSP00000356542:A1955T;ENSP00000434814:A1936T;ENSP00000350183:A1906T;ENSP00000351101:A1887T;ENSP00000356539:A1562T;ENSP00000353222:A1936T;ENSP00000356545:A1955T	ENSP00000350183:A1906T	A	+	1	0	CACNA1E	180026280	0.000000	0.05858	0.002000	0.10522	0.463000	0.32649	0.331000	0.19733	-0.148000	0.11234	-0.768000	0.03414	GCC	G|0.652;T|0.008	.	strong		0.483	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
DCBLD2	131566	hgsc.bcm.edu	37	3	98541116	98541116	+	Silent	SNP	G	G	A	rs828616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:98541116G>A	ENST00000326840.6	-	6	1148	c.786C>T	c.(784-786)atC>atT	p.I262I	DCBLD2_ENST00000326857.9_Silent_p.I262I|DCBLD2_ENST00000469648.1_5'Flank	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	262	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						CATAATAGGGGATACCTTTAC	0.393													G|||	1933	0.385982	0.0772	0.5115	5008	,	,		18220	0.6806		0.3757	False		,,,				2504	0.4213				p.I262I		Atlas-SNP	.											.	DCBLD2	62	.	0			c.C786T						PASS	.	G		439,3373		30,379,1497	63.0	58.0	59.0		786	2.8	1.0	3	dbSNP_86	59	2903,5363		495,1913,1725	no	coding-synonymous	DCBLD2	NM_080927.3		525,2292,3222	AA,AG,GG		35.1198,11.5163,27.6701		262/776	98541116	3342,8736	1906	4133	6039	SO:0001819	synonymous_variant	131566	exon6			ATAGGGGATACCT		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.786C>T	3.37:g.98541116G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	140	79	0.564286	NM_080927	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Silent	SNP	ENST00000326840.6	37	CCDS46878.1																																																																																			G|0.593;A|0.407	0.407	strong		0.393	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927	
KLHL31	401265	hgsc.bcm.edu	37	6	53519857	53519857	+	Silent	SNP	G	G	A	rs12210809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:53519857G>A	ENST00000407079.1	-	1	213	c.214C>T	c.(214-216)Cta>Tta	p.L72L	KLHL31_ENST00000370905.3_Silent_p.L72L			Q9H511	KLH31_HUMAN	kelch-like family member 31	72					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					AAGTCACATAGGAAGTTCTCC	0.408													G|||	2456	0.490415	0.1694	0.6729	5008	,	,		18848	0.5982		0.5924	False		,,,				2504	0.5787				p.L72L		Atlas-SNP	.											.	KLHL31	48	.	0			c.C214T						PASS	.	G		1038,3368	379.9+/-323.5	113,812,1278	90.0	83.0	85.0		214	4.4	1.0	6	dbSNP_120	85	5214,3386	639.8+/-399.5	1559,2096,645	no	coding-synonymous	KLHL31	NM_001003760.4		1672,2908,1923	AA,AG,GG		39.3721,23.5588,48.0701		72/635	53519857	6252,6754	2203	4300	6503	SO:0001819	synonymous_variant	401265	exon2			CACATAGGAAGTT		CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"""Kelch-like"", ""BTB/POZ domain containing"""	21353	protein-coding gene	gene with protein product		610749	"""kelch repeat and BTB (POZ) domain containing 1"", ""kelch-like 31 (Drosophila)"""	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.214C>T	6.37:g.53519857G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	229	119	0.519651	NM_001003760	A6N9J2|B2RP49	Silent	SNP	ENST00000407079.1	37	CCDS34478.1																																																																																			G|0.516;A|0.484	0.484	strong		0.408	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760	
PRSS58	136541	hgsc.bcm.edu	37	7	141957504	141957504	+	Silent	SNP	A	A	G	rs7786497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:141957504A>G	ENST00000552471.1	-	1	343	c.24T>C	c.(22-24)gcT>gcC	p.A8A	PRSS58_ENST00000547058.2_Silent_p.A8A			Q8IYP2	PRS58_HUMAN	protease, serine, 58	8						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						GATTCAAGAGAGCCCAGAGGA	0.433													A|||	1399	0.279353	0.059	0.3329	5008	,	,		19561	0.5109		0.2485	False		,,,				2504	0.3323				p.A8A		Atlas-SNP	.											.	PRSS58	41	.	0			c.T24C						PASS	.	A		380,4026	193.6+/-218.7	13,354,1836	135.0	129.0	131.0		24	-0.1	0.0	7	dbSNP_116	131	2152,6448	369.5+/-335.5	269,1614,2417	no	coding-synonymous	PRSS58	NM_001001317.3		282,1968,4253	GG,GA,AA		25.0233,8.6246,19.4679		8/242	141957504	2532,10474	2203	4300	6503	SO:0001819	synonymous_variant	136541	exon2			CAAGAGAGCCCAG		CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"""Serine peptidases / Serine peptidases"""	39125	protein-coding gene	gene with protein product	"""trypsin X3"""						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.24T>C	7.37:g.141957504A>G		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_001001317	B3KVJ6|D3DXD2	Silent	SNP	ENST00000552471.1	37	CCDS5871.1																																																																																			A|0.764;G|0.236	0.236	strong		0.433	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317	
RASA2	5922	hgsc.bcm.edu	37	3	141295907	141295907	+	Missense_Mutation	SNP	G	G	A	rs201190266		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:141295907G>A	ENST00000452898.1	+	15	1584	c.1549G>A	c.(1549-1551)Gta>Ata	p.V517I	RASA2_ENST00000286364.3_Missense_Mutation_p.V517I	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	517	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.V517I(2)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TGCTGTAGCCGTAGTATCACC	0.353																																					p.V517I		Atlas-SNP	.											RASA2_ENST00000286364,NS,carcinoma,0,2	RASA2	169	2	2	Substitution - Missense(2)	kidney(2)	c.G1549A						PASS	.						228.0	215.0	219.0					3																	141295907		2203	4300	6503	SO:0001583	missense	5922	exon15			GTAGCCGTAGTAT	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.1549G>A	3.37:g.141295907G>A	ENSP00000391677:p.Val517Ile	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	170	98	0.576471	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	G	7.080	0.570046	0.13560	.	.	ENSG00000155903	ENST00000286364;ENST00000452898;ENST00000423660	T;T	0.71934	-0.61;-0.61	6.03	4.24	0.50183	Ras GTPase-activating protein, conserved site (1);Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.059991	0.64402	N	0.000004	T	0.35653	0.0939	N	0.00808	-1.17	0.49213	D	0.999769	B;B;B;B	0.21147	0.052;0.005;0.004;0.005	B;B;B;B	0.21917	0.037;0.012;0.007;0.012	T	0.43376	-0.9395	10	0.02654	T	1	.	12.1791	0.54202	0.1391:0.0:0.8609:0.0	.	109;517;517;517	E7EU60;A8K7K1;G3V0F9;Q15283	.;.;.;RASA2_HUMAN	I	517;517;109	ENSP00000286364:V517I;ENSP00000391677:V517I	ENSP00000286364:V517I	V	+	1	0	RASA2	142778597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.269000	0.72558	0.870000	0.35726	0.557000	0.71058	GTA	G|0.999;T|0.001	.	alt		0.353	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	
WDR43	23160	hgsc.bcm.edu	37	2	29164387	29164387	+	Missense_Mutation	SNP	A	A	G	rs200896154		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29164387A>G	ENST00000407426.3	+	15	1737	c.1681A>G	c.(1681-1683)Act>Gct	p.T561A		NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	561						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					CAGAGTCAAAACTTTTCAGAA	0.383																																					p.T561A		Atlas-SNP	.											.	WDR43	38	.	0			c.A1681G						PASS	.	A	ALA/THR	1,3707		0,1,1853	96.0	89.0	91.0		1681	5.5	1.0	2		91	6,8144		0,6,4069	yes	missense	WDR43	NM_015131.1	58	0,7,5922	GG,GA,AA		0.0736,0.027,0.059	possibly-damaging	561/678	29164387	7,11851	1854	4075	5929	SO:0001583	missense	23160	exon15			GTCAAAACTTTTC	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"""WD repeat domain containing"""	28945	protein-coding gene	gene with protein product	"""UTP5, small subunit (SSU) processome component, homolog (yeast)"""					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.1681A>G	2.37:g.29164387A>G	ENSP00000384302:p.Thr561Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_015131	Q15395|Q92577	Missense_Mutation	SNP	ENST00000407426.3	37	CCDS46251.1	.	.	.	.	.	.	.	.	.	.	A	16.06	3.016175	0.54468	2.7E-4	7.36E-4	ENSG00000163811	ENST00000407426	T	0.66460	-0.21	5.51	5.51	0.81932	.	0.171968	0.56097	D	0.000034	T	0.73094	0.3543	L	0.50333	1.59	0.34623	D	0.71884	D	0.63880	0.993	P	0.58928	0.848	T	0.76049	-0.3101	10	0.21014	T	0.42	-17.4972	15.9198	0.79552	1.0:0.0:0.0:0.0	.	561	Q15061	WDR43_HUMAN	A	561	ENSP00000384302:T561A	ENSP00000384302:T561A	T	+	1	0	WDR43	29017891	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.032000	0.57274	2.222000	0.72286	0.454000	0.30748	ACT	.	.	weak		0.383	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089	
MUC16	94025	hgsc.bcm.edu	37	19	9085004	9085004	+	Missense_Mutation	SNP	T	T	C	rs11085805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9085004T>C	ENST00000397910.4	-	1	7014	c.6811A>G	c.(6811-6813)Act>Gct	p.T2271A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2271	Ser-rich.|Thr-rich.		T -> A (in dbSNP:rs11085805).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATGAATGAGTTGTCTTTTCT	0.448													T|||	952	0.190096	0.0711	0.2709	5008	,	,		21748	0.3036		0.172	False		,,,				2504	0.1953				p.T2271A		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+1,2	MUC16	4315	2	0			c.A6811G						PASS	.	T	ALA/THR	277,3563		5,267,1648	66.0	63.0	64.0		6811	-0.4	0.0	19	dbSNP_120	64	1482,6780		126,1230,2775	yes	missense	MUC16	NM_024690.2	58	131,1497,4423	CC,CT,TT		17.9375,7.2135,14.5348	benign	2271/14508	9085004	1759,10343	1920	4131	6051	SO:0001583	missense	94025	exon1			AATGAGTTGTCTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6811A>G	19.37:g.9085004T>C	ENSP00000381008:p.Thr2271Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	t	0.055	-1.238975	0.01493	0.072135	0.179375	ENSG00000181143	ENST00000397910	T	0.02301	4.35	0.225	-0.451	0.12214	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.46247	-0.9205	7	0.87932	D	0	.	.	.	.	rs11085805;rs52821244;rs59875884;rs11085805	2271	B5ME49	.	A	2271	ENSP00000381008:T2271A	ENSP00000381008:T2271A	T	-	1	0	MUC16	8946004	0.003000	0.15002	0.016000	0.15963	0.016000	0.09150	-0.705000	0.05052	-0.874000	0.04027	-0.902000	0.02854	ACT	T|0.812;C|0.188	0.188	strong		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TOMM40	10452	hgsc.bcm.edu	37	19	45395714	45395714	+	Silent	SNP	T	T	C	rs157581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45395714T>C	ENST00000426677.2	+	2	519	c.339T>C	c.(337-339)ttT>ttC	p.F113F	TOMM40_ENST00000252487.5_Silent_p.F113F|CTB-129P6.4_ENST00000585408.1_RNA|TOMM40_ENST00000405636.2_Silent_p.F113F|TOMM40_ENST00000592434.1_Silent_p.F113F	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	113					cellular protein metabolic process (GO:0044267)|ion transport (GO:0006811)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane translocase complex (GO:0005742)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein transmembrane transporter activity (GO:0008320)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		GTAACCATTTTCAGGTGAGCC	0.547													.|||	1534	0.30631	0.5023	0.2507	5008	,	,		21063	0.246		0.2078	False		,,,				2504	0.2444				p.F113F		Atlas-SNP	.											.	TOMM40	13	.	0			c.T339C	GRCh37	CM073386	TOMM40	M	rs157581	PASS	.	C	,,	2058,2348	604.8+/-390.4	482,1094,627	174.0	146.0	155.0		339,339,339	3.3	1.0	19	dbSNP_79	155	1803,6797	729.3+/-406.7	180,1443,2677	no	coding-synonymous,coding-synonymous,coding-synonymous	TOMM40	NM_001128916.1,NM_001128917.1,NM_006114.2	,,	662,2537,3304	CC,CT,TT		20.9651,46.709,29.6863	,,	113/362,113/362,113/362	45395714	3861,9145	2203	4300	6503	SO:0001819	synonymous_variant	10452	exon2			CCATTTTCAGGTG	AF043250	CCDS12646.1	19q13	2008-07-04				ENSG00000130204			18001	protein-coding gene	gene with protein product		608061				10980201, 15644312	Standard	NM_006114		Approved	PEREC1, D19S1177E, C19orf1, TOM40, PER-EC1	uc002paa.4	O96008		ENST00000426677.2:c.339T>C	19.37:g.45395714T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_001128917	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Silent	SNP	ENST00000426677.2	37	CCDS12646.1																																																																																			T|0.698;C|0.302	0.302	strong		0.547	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1		
ATAD5	79915	hgsc.bcm.edu	37	17	29167653	29167653	+	Missense_Mutation	SNP	A	A	C	rs3764421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29167653A>C	ENST00000321990.4	+	4	2473	c.2095A>C	c.(2095-2097)Aac>Cac	p.N699H	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	699			N -> H (in dbSNP:rs3764421).		cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TACTTCAAAAAACATATCAAA	0.284													A|||	722	0.144169	0.0711	0.1859	5008	,	,		15768	0.1359		0.1074	False		,,,				2504	0.2597				p.N699H		Atlas-SNP	.											ATAD5,NS,carcinoma,0,1	ATAD5	150	1	0			c.A2095C						PASS	.	A	HIS/ASN	320,4086	147.6+/-182.1	15,290,1898	79.0	85.0	83.0		2095	5.9	1.0	17	dbSNP_107	83	890,7710	175.5+/-225.5	37,816,3447	yes	missense	ATAD5	NM_024857.3	68	52,1106,5345	CC,CA,AA		10.3488,7.2628,9.3034	possibly-damaging	699/1845	29167653	1210,11796	2203	4300	6503	SO:0001583	missense	79915	exon4			TCAAAAAACATAT		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.2095A>C	17.37:g.29167653A>C	ENSP00000313171:p.Asn699His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	106	104	0.981132	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	274	0.12545787545787546	45	0.09146341463414634	65	0.17955801104972377	92	0.16083916083916083	72	0.09498680738786279	A	12.78	2.039141	0.35989	0.072628	0.103488	ENSG00000176208	ENST00000321990	T	0.09817	2.94	5.9	5.9	0.94986	.	0.925252	0.09360	N	0.812877	T	0.00073	0.0002	M	0.61703	1.905	0.28364	P	0.9203312	D;D	0.71674	0.996;0.998	D;D	0.65874	0.939;0.915	T	0.01795	-1.1272	9	0.72032	D	0.01	.	16.3155	0.82918	1.0:0.0:0.0:0.0	rs3764421;rs52792999;rs59938755;rs3764421	699;699	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	H	699	ENSP00000313171:N699H	ENSP00000313171:N699H	N	+	1	0	ATAD5	26191779	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.491000	0.60326	2.260000	0.74910	0.528000	0.53228	AAC	A|0.885;C|0.115	0.115	strong		0.284	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
DNAH6	1768	hgsc.bcm.edu	37	2	84771567	84771567	+	Silent	SNP	C	C	T	rs1542477	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:84771567C>T	ENST00000237449.6	+	4	881	c.873C>T	c.(871-873)tcC>tcT	p.S291S	DNAH6_ENST00000398278.2_Silent_p.S291S|DNAH6_ENST00000389394.3_Silent_p.S291S			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	291	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ATGTCCGCTCCAAGAAAATCA	0.308													C|||	4090	0.816693	0.4871	0.9121	5008	,	,		14091	0.9861		0.9364	False		,,,				2504	0.8967				p.S291S		Atlas-SNP	.											.	DNAH6	194	.	0			c.C873T						PASS	.	C		732,652		175,382,135	35.0	27.0	29.0		873	2.5	1.0	2	dbSNP_88	29	2960,218		1379,202,8	no	coding-synonymous	DNAH6	NM_001370.1		1554,584,143	TT,TC,CC		6.8597,47.1098,19.0706		291/4159	84771567	3692,870	692	1589	2281	SO:0001819	synonymous_variant	1768	exon5			CCGCTCCAAGAAA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.873C>T	2.37:g.84771567C>T		Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	151	148	0.980132	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			C|0.159;T|0.841	0.841	strong		0.308	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
NPAT	4863	hgsc.bcm.edu	37	11	108043988	108043988	+	Missense_Mutation	SNP	C	C	T	rs2070661	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108043988C>T	ENST00000278612.8	-	13	1828	c.1723G>A	c.(1723-1725)Gtt>Att	p.V575I	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	575			V -> I (in dbSNP:rs2070661). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8743993, ECO:0000269|PubMed:8923007, ECO:0000269|PubMed:9205109}.		positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		CTCTTGTGAACTTCACTAGAA	0.294													T|||	3083	0.615615	0.652	0.6729	5008	,	,		19423	0.4554		0.6302	False		,,,				2504	0.6759				p.V575I		Atlas-SNP	.											.	NPAT	124	.	0			c.G1723A						PASS	.	T	ILE/VAL	2292,1324		716,860,232	79.0	76.0	77.0		1723	4.9	0.9	11	dbSNP_96	77	4676,3454		1378,1920,767	yes	missense	NPAT	NM_002519.2	29	2094,2780,999	TT,TC,CC		42.4846,36.615,40.6777	benign	575/1428	108043988	6968,4778	1808	4065	5873	SO:0001583	missense	4863	exon13			TGTGAACTTCACT	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.1723G>A	11.37:g.108043988C>T	ENSP00000278612:p.Val575Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	1287	0.5892857142857143	308	0.6260162601626016	240	0.6629834254143646	267	0.46678321678321677	472	0.6226912928759895	T	0.016	-1.529948	0.00951	0.63385	0.575154	ENSG00000149308	ENST00000278612	T	0.19806	2.12	6.08	4.93	0.64822	.	0.350905	0.30201	N	0.010179	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	9	0.05959	T	0.93	-5.3002	4.4367	0.11554	0.0:0.1957:0.1665:0.6378	rs2070661;rs52799779;rs2070661	575	Q14207	NPAT_HUMAN	I	575	ENSP00000278612:V575I	ENSP00000278612:V575I	V	-	1	0	NPAT	107549198	0.979000	0.34478	0.934000	0.37439	0.395000	0.30598	1.311000	0.33562	0.518000	0.28383	-0.254000	0.11334	GTT	T|0.575;G|0.005	0.575	strong		0.294	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519	
ME3	10873	hgsc.bcm.edu	37	11	86161388	86161388	+	Missense_Mutation	SNP	C	C	G	rs1042780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:86161388C>G	ENST00000393324.3	-	8	1225	c.972G>C	c.(970-972)aaG>aaC	p.K324N	ME3_ENST00000543262.1_Missense_Mutation_p.K324N|RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000359636.2_Missense_Mutation_p.K324N	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	324			K -> N (in dbSNP:rs1042780). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7818469}.		aerobic respiration (GO:0009060)|malate metabolic process (GO:0006108)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|pyruvate metabolic process (GO:0006090)	mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)	p.K324N(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|skin(3)|stomach(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)				AAAGCTTGTTCTTGGTGATTC	0.532													C|||	1494	0.298323	0.2201	0.3516	5008	,	,		19621	0.2728		0.327	False		,,,				2504	0.363				p.K324N		Atlas-SNP	.											ME3,NS,carcinoma,0,1	ME3	70	1	1	Substitution - Missense(1)	stomach(1)	c.G972C						PASS	.	C	ASN/LYS,ASN/LYS,ASN/LYS	1029,3375	381.6+/-324.1	116,797,1289	95.0	81.0	86.0		972,972,972	2.5	1.0	11	dbSNP_86	86	2887,5711	452.4+/-362.9	473,1941,1885	yes	missense,missense,missense	ME3	NM_001014811.1,NM_001161586.1,NM_006680.2	94,94,94	589,2738,3174	GG,GC,CC		33.5776,23.3651,30.1184	benign,benign,benign	324/605,324/605,324/605	86161388	3916,9086	2202	4299	6501	SO:0001583	missense	10873	exon9			CTTGTTCTTGGTG	X79440	CCDS8277.1	11q14.2	2012-09-20			ENSG00000151376	ENSG00000151376	1.1.1.40		6985	protein-coding gene	gene with protein product		604626				7818469	Standard	NM_001161586		Approved		uc001pbz.3	Q16798	OTTHUMG00000167217	ENST00000393324.3:c.972G>C	11.37:g.86161388C>G	ENSP00000376998:p.Lys324Asn	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_006680	B7Z6V0|Q8TBJ0	Missense_Mutation	SNP	ENST00000393324.3	37	CCDS8277.1	594	0.27197802197802196	109	0.22154471544715448	123	0.3397790055248619	130	0.22727272727272727	232	0.30606860158311344	C	13.79	2.343035	0.41498	0.233651	0.335776	ENSG00000151376	ENST00000359636;ENST00000543262;ENST00000393324;ENST00000524826	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.83	2.51	0.30379	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.421069	0.27375	N	0.019649	T	0.00012	0.0000	L	0.31420	0.93	0.09310	P	0.9999999999993138	B	0.13594	0.008	B	0.20184	0.028	T	0.41805	-0.9488	8	.	.	.	.	8.0009	0.30297	0.0:0.6642:0.1193:0.2165	rs1042780;rs1042834;rs3182272;rs17845699;rs17858641;rs52794182;rs59484229;rs1042780	324	Q16798	MAON_HUMAN	N	324	ENSP00000352657:K324N;ENSP00000440246:K324N;ENSP00000376998:K324N;ENSP00000431182:K324N	.	K	-	3	2	ME3	85839036	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	2.043000	0.41231	0.814000	0.34374	-0.150000	0.13652	AAG	C|0.715;G|0.285	0.285	strong		0.532	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
TIRAP	114609	hgsc.bcm.edu	37	11	126162843	126162843	+	Missense_Mutation	SNP	C	C	T	rs8177374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:126162843C>T	ENST00000392680.2	+	5	944	c.539C>T	c.(538-540)tCg>tTg	p.S180L	RP11-712L6.5_ENST00000528876.1_5'Flank|RP11-712L6.7_ENST00000533378.1_RNA|TIRAP_ENST00000392678.3_Missense_Mutation_p.S180L|TIRAP_ENST00000392679.1_Missense_Mutation_p.S180L	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	180	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.		S -> L (at heterozygosity it protects against invasive pneumococcal disease, malaria, bacteremia and tuberculosis; does not affect NF-kappa-B activation and TNF-alpha production; attenuates TLR2 signal transduction; dbSNP:rs8177374). {ECO:0000269|PubMed:17322885, ECO:0000269|PubMed:19602285, ECO:0000269|Ref.7}.		3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)			breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		CCCCTGCTGTCGGGCCTCAGC	0.627													C|||	430	0.0858626	0.0091	0.0836	5008	,	,		17938	0.0139		0.1859	False		,,,				2504	0.1626				p.S180L		Atlas-SNP	.											.	TIRAP	37	.	0			c.C539T	GRCh37	CM072081	TIRAP	M	rs8177374	PASS	.	C	LEU/SER,LEU/SER	134,4268	95.7+/-134.4	1,132,2068	37.0	40.0	39.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	539,539	4.7	0.0	11	dbSNP_117	39	1362,7234	261.6+/-283.9	119,1124,3055	yes	missense,missense	TIRAP	NM_001039661.1,NM_148910.2	145,145	120,1256,5123	TT,TC,CC		15.8446,3.0441,11.5095	benign,benign	180/222,180/236	126162843	1496,11502	2201	4298	6499	SO:0001583	missense	114609	exon5			TGCTGTCGGGCCT	AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.539C>T	11.37:g.126162843C>T	ENSP00000376447:p.Ser180Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Missense_Mutation	SNP	ENST00000392680.2	37	CCDS8472.1	183	0.08379120879120878	8	0.016260162601626018	39	0.10773480662983426	9	0.015734265734265736	127	0.16754617414248021	C	10.15	1.272220	0.23221	0.030441	0.158446	ENSG00000150455	ENST00000392679;ENST00000279992;ENST00000392678;ENST00000392680	T;T;T	0.01725	4.67;4.67;4.67	5.67	4.71	0.59529	Toll/interleukin-1 receptor homology (TIR) domain (1);	0.817778	0.11333	N	0.574848	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	P;P	0.39216	0.456;0.664	B;B	0.25987	0.026;0.065	T	0.48502	-0.9030	8	.	.	.	-6.7925	4.1225	0.10112	0.2057:0.5808:0.1309:0.0826	rs8177374;rs8177374	180;180	P58753;Q56UH9	TIRAP_HUMAN;.	L	180	ENSP00000376446:S180L;ENSP00000376445:S180L;ENSP00000376447:S180L	.	S	+	2	0	TIRAP	125668053	0.001000	0.12720	0.024000	0.17045	0.539000	0.34962	0.471000	0.22100	2.672000	0.90937	0.655000	0.94253	TCG	C|0.900;T|0.100	0.100	strong		0.627	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910	
ARHGEF3	50650	hgsc.bcm.edu	37	3	56766435	56766435	+	Silent	SNP	C	C	G	rs3732511	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:56766435C>G	ENST00000296315.3	-	9	1227	c.1059G>C	c.(1057-1059)ctG>ctC	p.L353L	ARHGEF3_ENST00000497267.1_Silent_p.L324L|ARHGEF3_ENST00000338458.4_Silent_p.L385L|ARHGEF3_ENST00000496106.1_Silent_p.L359L|ARHGEF3_ENST00000413728.2_Silent_p.L359L|ARHGEF3_ENST00000495373.1_Silent_p.L353L	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	353	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		CTTCTTGGAACAGGAAAACAT	0.458													C|||	1285	0.256589	0.239	0.1023	5008	,	,		20815	0.3442		0.1372	False		,,,				2504	0.4223				p.L385L		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.G1155C						PASS	.	C	,,	1020,3386	378.0+/-322.7	99,822,1282	102.0	104.0	103.0		1155,1077,1059	3.0	1.0	3	dbSNP_107	103	992,7608	212.8+/-253.0	65,862,3373	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF3	NM_001128615.1,NM_001128616.1,NM_019555.2	,,	164,1684,4655	GG,GC,CC		11.5349,23.1502,15.4698	,,	385/559,359/533,353/527	56766435	2012,10994	2203	4300	6503	SO:0001819	synonymous_variant	50650	exon12			TTGGAACAGGAAA	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"""Rho guanine nucleotide exchange factors"""	683	protein-coding gene	gene with protein product	"""exchange factor found in platelets and leukemic and neuronal tissues, XPLN"", ""RhoGEF protein"""	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.1059G>C	3.37:g.56766435C>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			C|0.827;G|0.173	0.173	strong		0.458	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
ZNF761	388561	hgsc.bcm.edu	37	19	53959568	53959568	+	RNA	SNP	G	G	C	rs2617726	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53959568G>C	ENST00000454407.1	+	0	2260							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TCATACTGAAGAGAATCCTTA	0.393													g|||	1936	0.386581	0.3964	0.5346	5008	,	,		24330	0.2401		0.3986	False		,,,				2504	0.407				p.E603Q		Atlas-SNP	.											ZNF761,rectum,carcinoma,0,1	ZNF761	104	1	0			c.G1807C						PASS	.	G	GLN/GLU	1775,2631	521.7+/-370.6	392,991,820	116.0	121.0	119.0		1808	1.1	0.2	19	dbSNP_100	119	3494,5102	510.5+/-377.5	706,2082,1510	no	missense	ZNF761	NM_001008401.3	29	1098,3073,2330	CC,CG,GG		40.6468,40.286,40.5245	benign	603/747	53959568	5269,7733	2203	4298	6501			388561	exon7			ACTGAAGAGAATC	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959568G>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																				.	.	weak		0.393	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
PCDHA4	56144	hgsc.bcm.edu	37	5	140187048	140187048	+	Silent	SNP	G	G	C	rs3822349	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140187048G>C	ENST00000530339.1	+	1	276	c.276G>C	c.(274-276)cgG>cgC	p.R92R	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.R92R|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_Silent_p.R92R|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	92	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R92R(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGATCGACCGGGAGGAGCTGT	0.617																																					p.R92R		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,4	PCDHA4	419	4	2	Substitution - coding silent(2)	stomach(2)	c.G276C						scavenged	.						71.0	82.0	78.0					5																	140187048		2201	4284	6485	SO:0001819	synonymous_variant	56144	exon1			CGACCGGGAGGAG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.276G>C	5.37:g.140187048G>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	107	33	0.308411	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			G|0.926;C|0.074	0.074	strong		0.617	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713784	32713784	+	Missense_Mutation	SNP	C	C	A	rs62619945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32713784C>A	ENST00000374940.3	+	3	650	c.548C>A	c.(547-549)gCt>gAt	p.A183D		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	183	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	CTCCCTTCTGCTGATGAGATT	0.493																																					p.A183D		Atlas-SNP	.											HLA-DQA2,NS,carcinoma,+1,1	HLA-DQA2	27	1	0			c.C548A						PASS	.						190.0	211.0	203.0					6																	32713784		1511	2707	4218	SO:0001583	missense	3118	exon3			CTTCTGCTGATGA		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.548C>A	6.37:g.32713784C>A	ENSP00000364076:p.Ala183Asp	Somatic	645	0	0		WXS	Illumina HiSeq	Phase_I	787	95	0.120712	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	3.489	-0.104314	0.06967	.	.	ENSG00000237541	ENST00000374940	T	0.02890	4.12	3.06	-0.376	0.12505	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.680175	0.13893	N	0.355519	T	0.00695	0.0023	N	0.21324	0.655	0.22112	N	0.999352	B	0.14805	0.011	B	0.20184	0.028	T	0.42258	-0.9462	10	0.19590	T	0.45	.	10.1342	0.42697	0.7082:0.2918:0.0:0.0	rs62619945	183	P01906	DQA2_HUMAN	D	183	ENSP00000364076:A183D	ENSP00000364076:A183D	A	+	2	0	HLA-DQA2	32821762	0.000000	0.05858	0.960000	0.40013	0.740000	0.42216	-1.389000	0.02530	-0.242000	0.09667	0.174000	0.16983	GCT	.	.	weak		0.493	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
PRG4	10216	hgsc.bcm.edu	37	1	186276307	186276307	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:186276307G>A	ENST00000445192.2	+	7	1501	c.1456G>A	c.(1456-1458)Gcc>Acc	p.A486T	PRG4_ENST00000367485.4_Missense_Mutation_p.A393T|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_Missense_Mutation_p.A445T|PRG4_ENST00000367486.3_Missense_Mutation_p.A443T	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	486	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.A486T(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TGCACCCACTGCCCCCAAGAA	0.652																																					p.A486T		Atlas-SNP	.											PRG4,trunk,malignant_melanoma,0,2	PRG4	259	2	2	Substitution - Missense(2)	skin(2)	c.G1456A						scavenged	.						99.0	106.0	104.0					1																	186276307		2203	4298	6501	SO:0001583	missense	10216	exon7			CCCACTGCCCCCA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1456G>A	1.37:g.186276307G>A	ENSP00000399679:p.Ala486Thr	Somatic	226	12	0.0530973		WXS	Illumina HiSeq	Phase_I	306	18	0.0588235	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	g	4.368	0.067762	0.08436	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05199	3.48;3.61;3.48;3.63	2.46	-4.92	0.03075	.	0.448390	0.15713	N	0.248334	T	0.00936	0.0031	N	0.00217	-1.83	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.27571	-1.0070	9	.	.	.	-0.2819	1.0766	0.01634	0.1724:0.3622:0.2099:0.2556	.	352;393;486;445	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	T	443;352;445;393;486	ENSP00000356456:A443T;ENSP00000356453:A445T;ENSP00000356455:A393T;ENSP00000399679:A486T	.	A	+	1	0	PRG4	184542930	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.012000	0.13287	-2.873000	0.00322	-3.452000	0.00036	GCC	.	.	none		0.652	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
ZNF280A	129025	hgsc.bcm.edu	37	22	22869123	22869123	+	Missense_Mutation	SNP	T	T	C	rs362003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22869123T>C	ENST00000302097.3	-	2	1084	c.832A>G	c.(832-834)Aac>Gac	p.N278D	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	278			N -> D (in dbSNP:rs362003). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9074928}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TAGTAAAAGTTGCTAAGTAAC	0.413													T|||	2372	0.473642	0.2398	0.7334	5008	,	,		19411	0.4137		0.7028	False		,,,				2504	0.4315				p.N278D		Atlas-SNP	.											.	ZNF280A	67	.	0			c.A832G						PASS	.	T	ASP/ASN	1357,3049	451.6+/-349.7	220,917,1066	122.0	110.0	114.0		832	2.5	0.4	22	dbSNP_79	114	5855,2745	680.2+/-403.6	2008,1839,453	yes	missense	ZNF280A	NM_080740.3	23	2228,2756,1519	CC,CT,TT		31.9186,30.7989,44.5487	benign	278/543	22869123	7212,5794	2203	4300	6503	SO:0001583	missense	129025	exon2			AAAAGTTGCTAAG	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.832A>G	22.37:g.22869123T>C	ENSP00000302855:p.Asn278Asp	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	120	52	0.433333	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	1156	0.5293040293040293	127	0.258130081300813	254	0.7016574585635359	244	0.42657342657342656	531	0.7005277044854882	t	0.022	-1.412170	0.01145	0.307989	0.680814	ENSG00000169548	ENST00000302097	T	0.00832	5.64	3.56	2.54	0.30619	.	.	.	.	.	T	0.00012	0.0000	N	0.00034	-2.56	0.48236	P	3.830000000000222E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.17258	-1.0375	8	0.02654	T	1	.	7.2962	0.26395	0.0:0.8779:0.0:0.1221	rs362003;rs17857434;rs61534286	278	P59817	Z280A_HUMAN	D	278	ENSP00000302855:N278D	ENSP00000302855:N278D	N	-	1	0	ZNF280A	21199123	0.995000	0.38212	0.370000	0.25965	0.180000	0.23129	3.227000	0.51262	1.063000	0.40649	-0.146000	0.13790	AAC	T|0.455;C|0.545	0.545	strong		0.413	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
UBR3	130507	hgsc.bcm.edu	37	2	170762566	170762566	+	Silent	SNP	A	A	T	rs10194785	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170762566A>T	ENST00000272793.5	+	10	1721	c.1671A>T	c.(1669-1671)ctA>ctT	p.L557L	UBR3_ENST00000418381.1_Silent_p.L557L			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	557					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						AGCGAGAACTAAACGAGCATG	0.408													A|||	1388	0.277157	0.2663	0.1945	5008	,	,		16538	0.376		0.1581	False		,,,				2504	0.3712				p.L557L		Atlas-SNP	.											.	UBR3	182	.	0			c.A1671T						PASS	.	A		383,1001		58,267,367	119.0	103.0	108.0		1671	1.6	1.0	2	dbSNP_119	108	545,2637		49,447,1095	no	coding-synonymous	UBR3	NM_172070.3		107,714,1462	TT,TA,AA		17.1276,27.6734,20.3241		557/1889	170762566	928,3638	692	1591	2283	SO:0001819	synonymous_variant	130507	exon10			AGAACTAAACGAG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.1671A>T	2.37:g.170762566A>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				A|0.748;T|0.252	0.252	strong		0.408	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
C1orf85	112770	hgsc.bcm.edu	37	1	156264648	156264648	+	Missense_Mutation	SNP	C	C	T	rs1570805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156264648C>T	ENST00000362007.1	-	2	306	c.280G>A	c.(280-282)Gtc>Atc	p.V94I	C1orf85_ENST00000482579.1_5'Flank	NM_001256604.1|NM_001256609.1|NM_144580.2	NP_001243533.1|NP_001243538.1|NP_653181.1	Q8WWB7	NCUG1_HUMAN	chromosome 1 open reading frame 85	94			V -> I (in dbSNP:rs1570805). {ECO:0000269|PubMed:12975309}.		intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(2)|skin(3)	14	Hepatocellular(266;0.158)					CTCCAGTTGACGCTCAGGGTG	0.592													C|||	291	0.058107	0.0113	0.1254	5008	,	,		17017	0.0466		0.1074	False		,,,				2504	0.0348				p.V94I		Atlas-SNP	.											.	C1orf85	41	.	0			c.G280A						PASS	.	C	ILE/VAL	103,4303	82.4+/-120.9	1,101,2101	92.0	100.0	97.0		280	3.2	0.8	1	dbSNP_88	97	908,7692	203.0+/-246.1	51,806,3443	yes	missense	C1orf85	NM_144580.1	29	52,907,5544	TT,TC,CC		10.5581,2.3377,7.7733	possibly-damaging	94/407	156264648	1011,11995	2203	4300	6503	SO:0001583	missense	112770	exon2			AGTTGACGCTCAG	BC011575	CCDS1139.1, CCDS72947.1, CCDS72948.1, CCDS72949.1	1q22	2014-08-07			ENSG00000198715	ENSG00000198715			29436	protein-coding gene	gene with protein product	"""kidney lysosomal membrane protein"""					12975309, 18021396, 19489740	Standard	NM_144580		Approved	MGC31963, NCU-G1	uc001foh.4	Q8WWB7	OTTHUMG00000019789	ENST00000362007.1:c.280G>A	1.37:g.156264648C>T	ENSP00000354553:p.Val94Ile	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_001256608	A6NH16|B4DJN4|Q5SZX4|Q6UX96|Q8IV07|Q96F65	Missense_Mutation	SNP	ENST00000362007.1	37	CCDS1139.1	144	0.06593406593406594	10	0.02032520325203252	29	0.08011049723756906	19	0.033216783216783216	86	0.11345646437994723	C	14.72	2.619989	0.46736	0.023377	0.105581	ENSG00000198715	ENST00000362007	T	0.22336	1.96	5.03	3.15	0.36227	.	0.072496	0.53938	N	0.000046	T	0.10594	0.0259	M	0.75264	2.295	0.09310	P	0.9999999999999845	B	0.27791	0.189	B	0.17722	0.019	T	0.05022	-1.0911	9	0.54805	T	0.06	1.2106	8.546	0.33421	0.0:0.812:0.0:0.188	rs1570805	94	Q8WWB7	NCUG1_HUMAN	I	94	ENSP00000354553:V94I	ENSP00000354553:V94I	V	-	1	0	C1orf85	154531272	0.372000	0.25064	0.810000	0.32431	0.979000	0.70002	0.861000	0.27885	1.118000	0.41863	0.561000	0.74099	GTC	C|0.930;T|0.070	0.070	strong		0.592	C1orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052108.1	NM_144580	
PRCC	5546	hgsc.bcm.edu	37	1	156737969	156737969	+	Missense_Mutation	SNP	C	C	T	rs11264542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156737969C>T	ENST00000271526.4	+	1	678	c.406C>T	c.(406-408)Ccc>Tcc	p.P136S	PRCC_ENST00000353233.3_Missense_Mutation_p.P136S|PRCC_ENST00000491853.1_Intron|HDGF_ENST00000465180.1_5'Flank	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	136			P -> S (in dbSNP:rs11264542). {ECO:0000269|PubMed:14702039}.		mitotic cell cycle checkpoint (GO:0007093)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)			PRCC/TFE3(25)	breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(5)|upper_aerodigestive_tract(1)	15	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCTGGGGCTTCCCAAGCCAAA	0.647			T	TFE3	papillary renal								C|||	636	0.126997	0.034	0.2277	5008	,	,		13402	0.0655		0.2177	False		,,,				2504	0.1513				p.P136S		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.C406T						PASS	.	C	SER/PRO	288,3996		13,262,1867	7.0	10.0	9.0		406	3.1	1.0	1	dbSNP_120	9	1500,6834		149,1202,2816	yes	missense	PRCC	NM_005973.4	74	162,1464,4683	TT,TC,CC		17.9986,6.7227,14.1702	benign	136/492	156737969	1788,10830	2142	4167	6309	SO:0001583	missense	5546	exon1			GGGCTTCCCAAGC	X99720	CCDS1157.1	1q21.1	2008-02-05			ENSG00000143294	ENSG00000143294			9343	protein-coding gene	gene with protein product		179755				8872474	Standard	NM_005973		Approved	RCCP1	uc001fqa.3	Q92733	OTTHUMG00000041294	ENST00000271526.4:c.406C>T	1.37:g.156737969C>T	ENSP00000271526:p.Pro136Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Missense_Mutation	SNP	ENST00000271526.4	37	CCDS1157.1	297	0.13598901098901098	18	0.036585365853658534	73	0.20165745856353592	43	0.07517482517482517	163	0.21503957783641162	C	13.76	2.334106	0.41297	0.067227	0.179986	ENSG00000143294	ENST00000271526;ENST00000353233;ENST00000368201	T;T	0.60040	0.22;0.41	4.95	3.08	0.35506	.	0.259771	0.39083	N	0.001473	T	0.31104	0.0786	L	0.55481	1.735	0.20307	P	0.9999113728	B;B	0.10296	0.0;0.003	B;B	0.06405	0.001;0.002	T	0.12477	-1.0546	9	0.45353	T	0.12	-10.2275	8.4913	0.33102	0.0:0.8195:0.0:0.1805	rs11264542;rs59423858;rs11264542	136;136	A6NG79;Q92733	.;PRCC_HUMAN	S	136;136;80	ENSP00000271526:P136S;ENSP00000339300:P136S	ENSP00000271526:P136S	P	+	1	0	PRCC	155004593	1.000000	0.71417	0.996000	0.52242	0.978000	0.69477	4.498000	0.60373	0.679000	0.31345	0.655000	0.94253	CCC	C|0.871;T|0.129	0.129	strong		0.647	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973	
MUC16	94025	hgsc.bcm.edu	37	19	9086984	9086984	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9086984T>C	ENST00000397910.4	-	1	5034	c.4831A>G	c.(4831-4833)Aca>Gca	p.T1611A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1611	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTGTGTCTGTAGATGGTTTC	0.512																																					p.T1611A		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	0			c.A4831G						scavenged	.						243.0	233.0	236.0					19																	9086984		2012	4174	6186	SO:0001583	missense	94025	exon1			TGTCTGTAGATGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4831A>G	19.37:g.9086984T>C	ENSP00000381008:p.Thr1611Ala	Somatic	462	0	0		WXS	Illumina HiSeq	Phase_I	494	5	0.0101215	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	4.059	0.008794	0.07912	.	.	ENSG00000181143	ENST00000397910	T	0.02301	4.35	1.33	-1.25	0.09405	.	.	.	.	.	T	0.01222	0.0040	N	0.08118	0	.	.	.	B	0.13145	0.007	B	0.04013	0.001	T	0.47736	-0.9094	8	0.87932	D	0	.	1.4211	0.02312	0.3225:0.2371:0.0:0.4404	.	1611	B5ME49	.	A	1611	ENSP00000381008:T1611A	ENSP00000381008:T1611A	T	-	1	0	MUC16	8947984	0.000000	0.05858	0.000000	0.03702	0.280000	0.26924	-1.076000	0.03420	-0.501000	0.06605	0.260000	0.18958	ACA	.	.	none		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OR10H2	26538	hgsc.bcm.edu	37	19	15838967	15838967	+	Silent	SNP	G	G	A	rs2285955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15838967G>A	ENST00000305899.3	+	1	134	c.114G>A	c.(112-114)acG>acA	p.T38T		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	38						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					ACCTGTTCACGCTGCTGGGCA	0.587													G|||	1755	0.350439	0.233	0.3112	5008	,	,		22410	0.3135		0.4394	False		,,,				2504	0.4836				p.T38T		Atlas-SNP	.											OR10H2,NS,carcinoma,+1,1	OR10H2	59	1	0			c.G114A						PASS	.	G		1225,3181		174,877,1152	237.0	198.0	211.0		114	-5.8	1.0	19	dbSNP_100	211	3845,4751		870,2105,1323	no	coding-synonymous	OR10H2	NM_013939.2		1044,2982,2475	AA,AG,GG		44.7301,27.803,38.994		38/316	15838967	5070,7932	2203	4298	6501	SO:0001819	synonymous_variant	26538	exon1			GTTCACGCTGCTG	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.114G>A	19.37:g.15838967G>A		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	357	145	0.406162	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			G|0.611;A|0.389	0.389	strong		0.587	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
METTL22	79091	hgsc.bcm.edu	37	16	8722629	8722629	+	Missense_Mutation	SNP	G	G	C	rs2270286	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:8722629G>C	ENST00000381920.3	+	3	434	c.176G>C	c.(175-177)tGg>tCg	p.W59S	METTL22_ENST00000561758.1_Missense_Mutation_p.W59S	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	59			W -> S (in dbSNP:rs2270286).			nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						CAAGACTCTTGGACAGATTCA	0.488													G|||	880	0.175719	0.0076	0.2061	5008	,	,		20032	0.3105		0.1889	False		,,,				2504	0.229				p.W59S		Atlas-SNP	.											.	METTL22	23	.	0			c.G176C						PASS	.	G	SER/TRP	160,3688		2,156,1766	57.0	59.0	58.0		176	-2.2	0.0	16	dbSNP_100	58	1560,6748		154,1252,2748	yes	missense	METTL22	NM_024109.2	177	156,1408,4514	CC,CG,GG		18.7771,4.158,14.1494	benign	59/405	8722629	1720,10436	1924	4154	6078	SO:0001583	missense	79091	exon3			ACTCTTGGACAGA	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"""chromosome 16 open reading frame 68"""	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.176G>C	16.37:g.8722629G>C	ENSP00000371345:p.Trp59Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	170	75	0.441176	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	37	CCDS10533.2	405	0.18543956043956045	8	0.016260162601626018	69	0.19060773480662985	176	0.3076923076923077	152	0.20052770448548812	G	6.561	0.471814	0.12461	0.04158	0.187771	ENSG00000067365	ENST00000381920;ENST00000163678	T;T	0.41758	2.37;0.99	5.0	-2.18	0.07037	.	1.766790	0.03076	N	0.157894	T	0.00012	0.0000	L	0.40543	1.245	0.33131	P	0.45687999999999995	B	0.14438	0.01	B	0.09377	0.004	T	0.23297	-1.0192	9	0.11485	T	0.65	-12.35	5.5293	0.16974	0.5345:0.0:0.3172:0.1483	rs2270286;rs17746596;rs52824520;rs2270286	59	Q9BUU2	MET22_HUMAN	S	59	ENSP00000371345:W59S;ENSP00000163678:W59S	ENSP00000163678:W59S	W	+	2	0	METTL22	8630130	0.000000	0.05858	0.009000	0.14445	0.639000	0.38242	-0.392000	0.07314	-0.770000	0.04614	0.561000	0.74099	TGG	G|0.810;C|0.190	0.190	strong		0.488	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109	
TTF1	7270	hgsc.bcm.edu	37	9	135277130	135277130	+	Missense_Mutation	SNP	C	C	A	rs3739915	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135277130C>A	ENST00000334270.2	-	2	1118	c.1079G>T	c.(1078-1080)gGa>gTa	p.G360V		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	360			G -> V (in dbSNP:rs3739915).		chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		CACCTGTGATCCTTCAGGGTA	0.448													C|||	481	0.0960463	0.0408	0.0807	5008	,	,		20873	0.246		0.0527	False		,,,				2504	0.0716				p.G360V		Atlas-SNP	.											.	TTF1	82	.	0			c.G1079T						PASS	.	C	,VAL/GLY	215,4191	130.6+/-167.2	0,215,1988	155.0	140.0	145.0		,1079	1.1	0.0	9	dbSNP_107	145	404,8196	128.8+/-187.0	7,390,3903	yes	intron,missense	TTF1	NM_001205296.1,NM_007344.3	,109	7,605,5891	AA,AC,CC		4.6977,4.8797,4.7593	,probably-damaging	,360/906	135277130	619,12387	2203	4300	6503	SO:0001583	missense	7270	exon2			TGTGATCCTTCAG	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.1079G>T	9.37:g.135277130C>A	ENSP00000333920:p.Gly360Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	189	86	0.455026	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	235	0.10760073260073261	21	0.042682926829268296	26	0.0718232044198895	148	0.25874125874125875	40	0.052770448548812667	C	14.18	2.459471	0.43736	0.048797	0.046977	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.11063	2.81	5.09	1.12	0.20585	.	1.518420	0.03910	N	0.281816	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	P	0.50943	0.94	P	0.46144	0.505	T	0.35475	-0.9787	9	0.22706	T	0.39	.	4.2753	0.10806	0.0:0.5508:0.1695:0.2797	rs3739915;rs52828446;rs57984098;rs3739915	360	Q15361	TTF1_HUMAN	V	360	ENSP00000333920:G360V	ENSP00000245588:G360V	G	-	2	0	TTF1	134266951	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.088000	0.11198	0.255000	0.21593	-0.140000	0.14226	GGA	C|0.927;A|0.073	0.073	strong		0.448	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344	
CES1	1066	hgsc.bcm.edu	37	16	55862720	55862720	+	Silent	SNP	T	T	C	rs74019278	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55862720T>C	ENST00000361503.4	-	2	346	c.216A>G	c.(214-216)gaA>gaG	p.E72E	CES1_ENST00000422046.2_Silent_p.E72E|CES1_ENST00000360526.3_Silent_p.E73E|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	72					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	AGCTCCATGGTTCTGCAGGCT	0.532																																					p.E73E	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,caecum,carcinoma,0,2	CES1	78	2	0			c.A219G						PASS	.						108.0	108.0	108.0					16																	55862720		2198	4300	6498	SO:0001819	synonymous_variant	1066	exon2			CCATGGTTCTGCA	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.216A>G	16.37:g.55862720T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	124	29	0.233871	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																			T|0.634;C|0.366	0.366	strong		0.532	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
NBAS	51594	hgsc.bcm.edu	37	2	15607842	15607842	+	Missense_Mutation	SNP	T	T	C	rs4668909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:15607842T>C	ENST00000281513.5	-	18	1989	c.1964A>G	c.(1963-1965)aAg>aGg	p.K655R	NBAS_ENST00000441750.1_Missense_Mutation_p.K655R	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	655			K -> R (in dbSNP:rs4668909). {ECO:0000269|PubMed:12706883, ECO:0000269|PubMed:15815621}.		negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CTCCTTTTCCTTTTTATTCTT	0.338													T|||	1806	0.360623	0.1135	0.5677	5008	,	,		17006	0.1617		0.6879	False		,,,				2504	0.4162				p.K655R		Atlas-SNP	.											.	NBAS	246	.	0			c.A1964G						PASS	.	T	ARG/LYS	971,3433	354.4+/-312.6	118,735,1349	110.0	101.0	104.0		1964	-1.3	0.0	2	dbSNP_111	104	5853,2747	673.3+/-403.0	1997,1859,444	yes	missense	NBAS	NM_015909.2	26	2115,2594,1793	CC,CT,TT		31.9419,22.0481,47.5238	benign	655/2372	15607842	6824,6180	2202	4300	6502	SO:0001583	missense	51594	exon18			TTTTCCTTTTTAT	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1964A>G	2.37:g.15607842T>C	ENSP00000281513:p.Lys655Arg	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	216	124	0.574074	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	877	0.4015567765567766	61	0.12398373983739837	206	0.569060773480663	103	0.18006993006993008	507	0.6688654353562006	T	10.91	1.485579	0.26686	0.220481	0.680581	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.10382	2.88;3.02	5.33	-1.26	0.09376	.	0.193529	0.53938	N	0.000051	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.33803	-0.9854	9	0.87932	D	0	.	12.0186	0.53329	0.0:0.5073:0.0:0.4927	rs4668909;rs52815017;rs57221916;rs4668909	655	A2RRP1	NBAS_HUMAN	R	655	ENSP00000413201:K655R;ENSP00000281513:K655R	ENSP00000281513:K655R	K	-	2	0	NBAS	15525293	0.996000	0.38824	0.000000	0.03702	0.513000	0.34164	1.492000	0.35594	-0.370000	0.08016	-0.256000	0.11100	AAG	T|0.539;C|0.461	0.461	strong		0.338	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
UBAP2	55833	hgsc.bcm.edu	37	9	33971740	33971740	+	Silent	SNP	A	A	G	rs3739690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:33971740A>G	ENST00000379238.1	-	8	705	c.588T>C	c.(586-588)ccT>ccC	p.P196P	UBAP2_ENST00000418786.2_Intron|UBAP2_ENST00000539807.1_Intron|UBAP2_ENST00000360802.1_Silent_p.P196P|UBAP2_ENST00000449054.1_Silent_p.P196P|UBAP2_ENST00000379239.4_Intron					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		AATAGTCTGCAGGATTAAATG	0.388													A|||	1427	0.284944	0.0923	0.2824	5008	,	,		19743	0.6101		0.2396	False		,,,				2504	0.2587				p.P196P		Atlas-SNP	.											.	UBAP2	82	.	0			c.T588C						PASS	.	A		509,3897	234.9+/-247.6	31,447,1725	86.0	88.0	87.0		588	4.5	1.0	9	dbSNP_107	87	1860,6740	329.7+/-318.9	212,1436,2652	no	coding-synonymous	UBAP2	NM_018449.2		243,1883,4377	GG,GA,AA		21.6279,11.5524,18.2147		196/1120	33971740	2369,10637	2203	4300	6503	SO:0001819	synonymous_variant	55833	exon8			GTCTGCAGGATTA	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.588T>C	9.37:g.33971740A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_018449		Silent	SNP	ENST00000379238.1	37	CCDS6547.1																																																																																			A|0.762;G|0.238	0.238	strong		0.388	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
PCLO	27445	hgsc.bcm.edu	37	7	82785097	82785097	+	Missense_Mutation	SNP	T	T	C	rs61741659	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82785097T>C	ENST00000333891.9	-	2	1197	c.860A>G	c.(859-861)gAc>gGc	p.D287G	PCLO_ENST00000423517.2_Missense_Mutation_p.D287G	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCTTACTATGTCTGCCTGTTT	0.507													T|||	768	0.153355	0.1225	0.147	5008	,	,		18860	0.0675		0.2664	False		,,,				2504	0.1718				p.D287G		Atlas-SNP	.											.	PCLO	1506	.	0			c.A860G						PASS	.	T	GLY/ASP,GLY/ASP	525,3621		39,447,1587	121.0	110.0	114.0		860,860	4.1	0.7	7	dbSNP_129	114	1914,6508		223,1468,2520	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	94,94	262,1915,4107	CC,CT,TT		22.7262,12.6628,19.4064	benign,benign	287/5143,287/4936	82785097	2439,10129	2073	4211	6284	SO:0001583	missense	27445	exon2			ACTATGTCTGCCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.860A>G	7.37:g.82785097T>C	ENSP00000334319:p.Asp287Gly	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	253	128	0.505929	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	368	0.1684981684981685	69	0.1402439024390244	57	0.1574585635359116	47	0.08216783216783216	195	0.25725593667546176	T	8.676	0.903995	0.17760	0.126628	0.227262	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.20463	2.07;2.08	5.26	4.08	0.47627	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B;B	0.17268	0.021;0.021	B;B	0.15484	0.013;0.013	T	0.26849	-1.0091	8	0.87932	D	0	.	9.6854	0.40096	0.0:0.081:0.0:0.919	.	287;287	Q9Y6V0-5;Q9Y6V0-6	.;.	G	287	ENSP00000334319:D287G;ENSP00000388393:D287G	ENSP00000334319:D287G	D	-	2	0	PCLO	82623033	0.990000	0.36364	0.696000	0.30242	0.886000	0.51366	2.445000	0.44899	0.819000	0.34492	0.533000	0.62120	GAC	T|0.813;C|0.187	0.187	strong		0.507	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
MYH9	4627	hgsc.bcm.edu	37	22	36684358	36684358	+	Silent	SNP	C	C	A	rs2269530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:36684358C>A	ENST00000216181.5	-	34	5102	c.4872G>T	c.(4870-4872)gcG>gcT	p.A1624A	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1624					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						AGTCGATGTGCGCCTCCAGGT	0.657			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				.|||	1471	0.29373	0.0416	0.2118	5008	,	,		16160	0.5952		0.2078	False		,,,				2504	0.4703				p.A1624A		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.G4872T						PASS	.	C		315,4091	166.5+/-197.7	12,291,1900	124.0	99.0	107.0		4872	-10.3	0.4	22	dbSNP_100	107	1703,6897	310.9+/-310.1	195,1313,2792	no	coding-synonymous	MYH9	NM_002473.4		207,1604,4692	AA,AC,CC		19.8023,7.1493,15.5159		1624/1961	36684358	2018,10988	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon34	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GATGTGCGCCTCC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4872G>T	22.37:g.36684358C>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	121	49	0.404959	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			C|0.785;A|0.215	0.215	strong		0.657	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
POLR2B	5431	hgsc.bcm.edu	37	4	57881715	57881715	+	Silent	SNP	G	G	A	rs1713982	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57881715G>A	ENST00000381227.1	+	15	2261	c.1848G>A	c.(1846-1848)acG>acA	p.T616T	POLR2B_ENST00000431623.2_Silent_p.T541T|POLR2B_ENST00000314595.5_Silent_p.T616T|POLR2B_ENST00000441246.2_Silent_p.T609T|POLR2B_ENST00000510355.1_3'UTR			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	616					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GGATCTATACGGATGCAGGCC	0.333													A|||	1934	0.386182	0.4342	0.2954	5008	,	,		10572	0.2986		0.3469	False		,,,				2504	0.5164				p.T616T		Atlas-SNP	.											POLR2B,colon,carcinoma,0,1	POLR2B	108	1	0			c.G1848A						PASS	.	A		1882,2524	629.0+/-395.2	403,1076,724	119.0	125.0	123.0		1848	-2.7	1.0	4	dbSNP_89	123	2939,5661	667.8+/-402.5	487,1965,1848	no	coding-synonymous	POLR2B	NM_000938.1		890,3041,2572	AA,AG,GG		34.1744,42.7145,37.0675		616/1175	57881715	4821,8185	2203	4300	6503	SO:0001819	synonymous_variant	5431	exon14			CTATACGGATGCA		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1848G>A	4.37:g.57881715G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			G|0.634;A|0.366	0.366	strong		0.333	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
FAM129C	199786	hgsc.bcm.edu	37	19	17662616	17662616	+	Intron	SNP	G	G	A	rs76629753	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17662616G>A	ENST00000335393.4	+	16	1981				FAM129C_ENST00000599164.1_Missense_Mutation_p.R591Q|FAM129C_ENST00000600871.1_Missense_Mutation_p.R540Q|FAM129C_ENST00000599124.1_Missense_Mutation_p.R555Q|FAM129C_ENST00000332386.5_Missense_Mutation_p.R622Q|FAM129C_ENST00000601861.1_Intron|FAM129C_ENST00000449408.2_Intron|FAM129C_ENST00000352727.3_Missense_Mutation_p.R586Q	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C											autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						gaggctgagcgggaaggaggg	0.507													g|||	308	0.0615016	0.0885	0.0418	5008	,	,		14475	0.0317		0.0417	False		,,,				2504	0.09				p.R622Q		Atlas-SNP	.											.	FAM129C	110	.	0			c.G1865A						PASS	.	G	GLN/ARG,	258,3488		12,234,1627	40.0	43.0	42.0		1865,	0.6	0.1	19	dbSNP_131	42	440,7782		11,418,3682	yes	missense,intron	FAM129C	NM_001098524.1,NM_173544.4	43,	23,652,5309	AA,AG,GG		5.3515,6.8873,5.8322	,	622/652,	17662616	698,11270	1873	4111	5984	SO:0001627	intron_variant	199786	exon16			CTGAGCGGGAAGG	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1844-1506G>A	19.37:g.17662616G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	102	0.046703296703296704	34	0.06910569105691057	17	0.04696132596685083	19	0.033216783216783216	32	0.04221635883905013	G	3.985	-0.005567	0.07773	0.068873	0.053515	ENSG00000167483	ENST00000332386;ENST00000352727;ENST00000435646	T;T	0.26223	2.14;1.75	0.649	0.649	0.17806	.	.	.	.	.	T	0.00666	0.0022	N	0.08118	0	0.09310	N	1	P;P;P	0.45672	0.658;0.864;0.864	B;B;B	0.32724	0.107;0.151;0.151	T	0.18241	-1.0343	8	0.62326	D	0.03	.	.	.	.	.	540;622;586	E7ENP6;Q86XR2-3;Q86XR2-4	.;.;.	Q	622;586;540	ENSP00000333447:R622Q;ENSP00000341067:R586Q	ENSP00000333447:R622Q	R	+	2	0	FAM129C	17523616	0.062000	0.20869	0.051000	0.19133	0.016000	0.09150	0.342000	0.19926	0.598000	0.29829	0.462000	0.41574	CGG	G|0.953;A|0.047	0.047	strong		0.507	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
ABCB1	5243	hgsc.bcm.edu	37	7	87229440	87229440	+	Missense_Mutation	SNP	T	T	C	rs9282564|rs9332385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:87229440T>C	ENST00000265724.3	-	3	478	c.61A>G	c.(61-63)Aat>Gat	p.N21D	ABCB1_ENST00000543898.1_Missense_Mutation_p.N21D	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	21			N -> D (in dbSNP:rs9282564). {ECO:0000269|PubMed:10716719, ECO:0000269|PubMed:10790226, ECO:0000269|PubMed:11240981, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	TACCTTTTATTGTTCAGTTTA	0.378													T|||	130	0.0259585	0.0015	0.0317	5008	,	,		18389	0.0		0.0835	False		,,,				2504	0.0225				p.N21D		Atlas-SNP	.											ABCB1,NS,adenoma,0,1	ABCB1	263	1	0			c.A61G						PASS	.	T	ASP/ASN	119,4287	89.2+/-127.9	4,111,2088	100.0	95.0	96.0		61	-2.7	0.0	7	dbSNP_118	96	857,7743	194.9+/-240.2	52,753,3495	yes	missense	ABCB1	NM_000927.4	23	56,864,5583	CC,CT,TT		9.9651,2.7009,7.5042	benign	21/1281	87229440	976,12030	2203	4300	6503	SO:0001583	missense	5243	exon3			TTTTATTGTTCAG	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.61A>G	7.37:g.87229440T>C	ENSP00000265724:p.Asn21Asp	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	145	79	0.544828	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	83	0.038003663003663	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	69	0.09102902374670185	T	4.122	0.020862	0.08006	0.027009	0.099651	ENSG00000085563	ENST00000265724;ENST00000543898;ENST00000416177;ENST00000394661	D;D;T	0.86769	-2.15;-2.17;1.93	4.07	-2.74	0.05932	.	0.520681	0.20542	N	0.090297	T	0.04137	0.0115	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.09377	0.001;0.004	T	0.23297	-1.0192	10	0.15952	T	0.53	-1.4166	4.4301	0.11524	0.0:0.2864:0.3307:0.3829	rs9282564;rs13234342;rs61615398;rs9282564	21;21	B5AK60;P08183	.;MDR1_HUMAN	D	21	ENSP00000265724:N21D;ENSP00000444095:N21D;ENSP00000399419:N21D	ENSP00000265724:N21D	N	-	1	0	ABCB1	87067376	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.186000	0.09670	-0.487000	0.06735	-1.829000	0.00594	AAT	.	.	weak		0.378	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
ASUN	55726	hgsc.bcm.edu	37	12	27068983	27068983	+	Silent	SNP	A	A	T	rs35037404	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:27068983A>T	ENST00000261191.7	-	11	1736	c.1200T>A	c.(1198-1200)ccT>ccA	p.P400P	ASUN_ENST00000539625.1_Silent_p.P299P	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	400					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CACTAATTGAAGGTGGATCTT	0.378													A|||	45	0.00898562	0.0038	0.0072	5008	,	,		17714	0.0		0.0328	False		,,,				2504	0.002				p.P400P		Atlas-SNP	.											.	.	.	.	0			c.T1200A						PASS	.	A		38,4368	43.1+/-76.7	0,38,2165	80.0	74.0	76.0		1200	4.7	1.0	12	dbSNP_126	76	404,8196	128.2+/-186.4	4,396,3900	no	coding-synonymous	C12orf11	NM_018164.2		4,434,6065	TT,TA,AA		4.6977,0.8625,3.3984		400/707	27068983	442,12564	2203	4300	6503	SO:0001819	synonymous_variant	55726	exon11			AATTGAAGGTGGA	AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"""spermatogenesis associated 30"""	615079	"""chromosome 12 open reading frame 11"", ""asunder, spermatogenesis regulator homolog (Drosphila)"""	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.1200T>A	12.37:g.27068983A>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	64	0.969697	NM_018164	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Silent	SNP	ENST00000261191.7	37	CCDS8708.1	25	0.011446886446886446	0	0.0	1	0.0027624309392265192	0	0.0	24	0.0316622691292876	A	10.41	1.342144	0.24339	0.008625	0.046977	ENSG00000064102	ENST00000542392	.	.	.	5.85	4.71	0.59529	.	.	.	.	.	T	0.11836	0.0288	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23976	-1.0173	4	.	.	.	-19.1291	2.418	0.04441	0.6099:0.1295:0.1364:0.1242	rs35037404	.	.	.	I	114	.	.	F	-	1	0	C12orf11	26960250	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.417000	0.44653	1.160000	0.42584	0.533000	0.62120	TTC	A|0.972;T|0.028	0.028	strong		0.378	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164	
GRID2IP	392862	hgsc.bcm.edu	37	7	6547902	6547902	+	Missense_Mutation	SNP	G	G	A	rs112305062	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6547902G>A	ENST00000457091.2	-	13	2257	c.2258C>T	c.(2257-2259)cCg>cTg	p.P753L	GRID2IP_ENST00000435185.1_Missense_Mutation_p.P569L|GRID2IP_ENST00000452113.1_Missense_Mutation_p.P562L	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	753	Pro-rich.				long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						GGGGCTGAGCGGGGGTGGGGG	0.657													G|||	401	0.0800719	0.0098	0.196	5008	,	,		4499	0.0685		0.1054	False		,,,				2504	0.0787				p.P753L		Atlas-SNP	.											.	GRID2IP	82	.	0			c.C2258T						PASS	.						6.0	6.0	6.0					7																	6547902		684	1570	2254	SO:0001583	missense	392862	exon13			CTGAGCGGGGGTG		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.2258C>T	7.37:g.6547902G>A	ENSP00000397351:p.Pro753Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	148	135	0.912162	NM_001145118		Missense_Mutation	SNP	ENST00000457091.2	37	CCDS47537.1	210	0.09615384615384616	19	0.03861788617886179	78	0.2154696132596685	37	0.06468531468531469	76	0.10026385224274406	g	15.29	2.789692	0.50102	.	.	ENSG00000215045	ENST00000452113;ENST00000435185;ENST00000457091	T;T;T	0.57107	0.46;0.45;0.42	3.75	3.75	0.43078	.	0.000000	0.85682	U	0.000000	T	0.00073	0.0002	L	0.61218	1.895	0.09310	P	0.99999281359	D	0.89917	1.0	D	0.74023	0.982	T	0.02885	-1.1098	9	0.54805	T	0.06	.	13.4078	0.60924	0.0:0.0:1.0:0.0	.	753	A4D2P6	GRD2I_HUMAN	L	562;569;753	ENSP00000397887:P562L;ENSP00000408364:P569L;ENSP00000397351:P753L	ENSP00000408364:P569L	P	-	2	0	GRID2IP	6514427	1.000000	0.71417	0.614000	0.29051	0.845000	0.48019	5.766000	0.68843	1.814000	0.52955	0.558000	0.71614	CCG	G|0.908;A|0.092	0.092	strong		0.657	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
ASMTL	8623	hgsc.bcm.edu	37	X	1540706	1540706	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:1540706A>G	ENST00000381317.3	-	9	1122	c.1090T>C	c.(1090-1092)Tac>Cac	p.Y364H	ASMTL_ENST00000416733.2_Missense_Mutation_p.Y288H|ASMTL_ENST00000534940.1_Missense_Mutation_p.Y306H|ASMTL_ENST00000381333.4_Missense_Mutation_p.Y348H	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	364	ASMT-like.			Y -> H (in Ref. 2; BAG63287). {ECO:0000305}.		cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GATGCCAGGTAGACGTTCGCT	0.498													a|||	401	0.0800719	0.0204	0.0922	5008	,	,		22215	0.0972		0.164	False		,,,				2504	0.0481				p.Y364H		Atlas-SNP	.											.	ASMTL	56	.	0			c.T1090C						PASS	.		HIS/TYR,HIS/TYR,HIS/TYR	164,3892		7,150,1871	348.0	354.0	352.0		916,1042,1090	-1.5	0.0	X	dbSNP_134	352	1313,7073		115,1083,2995	yes	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	83,83,83	122,1233,4866	GG,GA,AA		15.657,4.0434,11.8711	benign,benign,benign	306/564,348/606,364/622	1540706	1477,10965	2028	4193	6221	SO:0001583	missense	8623	exon9			CCAGGTAGACGTT	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"""Pseudoautosomal regions / PAR1"""	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.1090T>C	X.37:g.1540706A>G	ENSP00000370718:p.Tyr364His	Somatic	762	1	0.00131234		WXS	Illumina HiSeq	Phase_I	751	367	0.488682	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	230	0.10531135531135531	21	0.042682926829268296	33	0.09116022099447514	65	0.11363636363636363	111	0.14643799472295516	a	4.900	0.167170	0.09339	0.040434	0.15657	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	1.58	-1.51	0.08664	O-methyltransferase, family 2 (1);	0.253860	0.31834	N	0.006989	T	0.00039	0.0001	N	0.25144	0.715	0.09310	N	1	B;B;B	0.22746	0.044;0.074;0.044	B;B;B	0.21360	0.025;0.034;0.024	T	0.34750	-0.9816	10	0.25106	T	0.35	.	6.4899	0.22109	0.8338:0.0:0.1662:0.0	.	288;348;364	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	H	288;306;348;364	ENSP00000410578:Y288H;ENSP00000446410:Y306H;ENSP00000370734:Y348H;ENSP00000370718:Y364H	ENSP00000370718:Y364H	Y	-	1	0	ASMTL	1500706	1.000000	0.71417	0.003000	0.11579	0.028000	0.11728	3.398000	0.52579	-0.341000	0.08376	0.084000	0.15446	TAC	A|0.834;G|0.166	0.166	strong		0.498	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
ING3	54556	hgsc.bcm.edu	37	7	120610901	120610901	+	Silent	SNP	C	C	T	rs2525725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:120610901C>T	ENST00000315870.5	+	10	1216	c.1068C>T	c.(1066-1068)gaC>gaT	p.D356D	ING3_ENST00000431467.1_Silent_p.D341D	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	356					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|positive regulation of apoptotic process (GO:0043065)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12	all_neural(327;0.117)					GGACTTACGACCCAAATGAAC	0.338													C|||	699	0.139577	0.2118	0.1095	5008	,	,		17479	0.0337		0.2127	False		,,,				2504	0.0971				p.D356D		Atlas-SNP	.											.	ING3	36	.	0			c.C1068T						PASS	.	C		930,3476	353.8+/-312.3	90,750,1363	86.0	75.0	78.0		1068	5.2	1.0	7	dbSNP_100	78	1718,6882	312.9+/-311.0	165,1388,2747	no	coding-synonymous	ING3	NM_019071.2		255,2138,4110	TT,TC,CC		19.9767,21.1076,20.3598		356/419	120610901	2648,10358	2203	4300	6503	SO:0001819	synonymous_variant	54556	exon10			TTACGACCCAAAT	AF074968	CCDS5778.1, CCDS35497.1	7q31	2013-01-28			ENSG00000071243	ENSG00000071243		"""Zinc fingers, PHD-type"""	14587	protein-coding gene	gene with protein product		607493				12080476	Standard	NM_019071		Approved	p47ING3, FLJ20089, Eaf4, MEAF4	uc003vjn.3	Q9NXR8	OTTHUMG00000141270	ENST00000315870.5:c.1068C>T	7.37:g.120610901C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_019071	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	Silent	SNP	ENST00000315870.5	37	CCDS5778.1																																																																																			C|0.812;A|0.001	.	strong		0.338	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071	
ADCY9	115	hgsc.bcm.edu	37	16	4033436	4033436	+	Missense_Mutation	SNP	T	T	C	rs2230739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4033436T>C	ENST00000294016.3	-	7	2854	c.2316A>G	c.(2314-2316)atA>atG	p.I772M		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	772			I -> M (in 37.5% of the Asian population, in 30% of the Caucasian population and in 16.3% of the African-American population; reduced adenylyl cyclase activity in response to stimulation of the beta- adregnergic receptor by the agonists Mn(2+), isoproteronol and NaF; increased albuterol-stimulated adenylyl cyclase activity in the presence of corticosteroid; dbSNP:rs2230739). {ECO:0000269|PubMed:12972952, ECO:0000269|PubMed:15879435}.		activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGGAGTTCTTTATGACCTGTG	0.572													T|||	1304	0.260383	0.1172	0.2334	5008	,	,		19237	0.3819		0.341	False		,,,				2504	0.2648				p.I772M		Atlas-SNP	.											ADCY9,NS,carcinoma,0,1	ADCY9	151	1	0			c.A2316G	GRCh37	CM034003	ADCY9	M	rs2230739	PASS	.	T	MET/ILE	649,3745		40,569,1588	71.0	60.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2316	-7.9	0.0	16	dbSNP_98	64	2688,5912		445,1798,2057	yes	missense	ADCY9	NM_001116.3	10	485,2367,3645	CC,CT,TT		31.2558,14.7701,25.6811	benign	772/1354	4033436	3337,9657	2197	4300	6497	SO:0001583	missense	115	exon7			GTTCTTTATGACC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2316A>G	16.37:g.4033436T>C	ENSP00000294016:p.Ile772Met	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	118	51	0.432203	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	610	0.2793040293040293	50	0.1016260162601626	91	0.2513812154696133	228	0.3986013986013986	241	0.3179419525065963	T	6.786	0.513906	0.12944	0.147701	0.312558	ENSG00000162104	ENST00000294016	D	0.82433	-1.61	5.94	-7.94	0.01152	.	0.557796	0.20751	N	0.086357	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.11717	-1.0576	9	0.19590	T	0.45	.	11.3789	0.49746	0.0:0.3363:0.4723:0.1914	rs2230739;rs2531981;rs17184038;rs60378382;rs2230739	772	O60503	ADCY9_HUMAN	M	772	ENSP00000294016:I772M	ENSP00000294016:I772M	I	-	3	3	ADCY9	3973437	0.000000	0.05858	0.005000	0.12908	0.081000	0.17604	-1.685000	0.01930	-1.914000	0.01078	-0.429000	0.05907	ATA	T|0.736;C|0.264	0.264	strong		0.572	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
VAV2	7410	hgsc.bcm.edu	37	9	136633699	136633699	+	Missense_Mutation	SNP	G	G	C	rs61751477	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136633699G>C	ENST00000371850.3	-	29	2485	c.2454C>G	c.(2452-2454)atC>atG	p.I818M	VAV2_ENST00000371851.1_Missense_Mutation_p.I808M|VAV2_ENST00000406606.3_Missense_Mutation_p.I779M	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	818	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		CAGCTGTGCCGATGACGCGGG	0.627													G|||	53	0.0105831	0.0091	0.0231	5008	,	,		20442	0.002		0.0169	False		,,,				2504	0.0061				p.I818M		Atlas-SNP	.											VAV2_ENST00000371850,NS,carcinoma,-1,2	VAV2	165	2	0			c.C2454G						PASS	.	G	MET/ILE,MET/ILE	35,4371	40.0+/-72.8	0,35,2168	68.0	57.0	61.0		2454,2337	1.0	1.0	9	dbSNP_129	61	119,8481	60.2+/-122.0	1,117,4182	yes	missense,missense	VAV2	NM_001134398.1,NM_003371.3	10,10	1,152,6350	CC,CG,GG		1.3837,0.7944,1.1841	benign,benign	818/879,779/840	136633699	154,12852	2203	4300	6503	SO:0001583	missense	7410	exon29			TGTGCCGATGACG		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2454C>G	9.37:g.136633699G>C	ENSP00000360916:p.Ile818Met	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Missense_Mutation	SNP	ENST00000371850.3	37	CCDS48053.1	26	0.011904761904761904	6	0.012195121951219513	8	0.022099447513812154	2	0.0034965034965034965	10	0.013192612137203167	G	14.32	2.500060	0.44455	0.007944	0.013837	ENSG00000160293	ENST00000371850;ENST00000371851;ENST00000406606;ENST00000325440	T;T;D	0.82619	2.27;2.27;-1.63	4.98	0.998	0.19857	Src homology-3 domain (2);	0.061924	0.64402	D	0.000002	T	0.66237	0.2769	L	0.33624	1.015	0.35581	D	0.806302	D;B	0.62365	0.991;0.411	P;B	0.55545	0.778;0.33	T	0.74788	-0.3546	10	0.66056	D	0.02	.	4.4133	0.11443	0.3831:0.0:0.395:0.2219	rs61751477	818;779	P52735;P52735-3	VAV2_HUMAN;.	M	818;808;779;808	ENSP00000360916:I818M;ENSP00000360917:I808M;ENSP00000385362:I779M	ENSP00000317258:I808M	I	-	3	3	VAV2	135623520	0.330000	0.24705	1.000000	0.80357	0.522000	0.34438	-0.406000	0.07187	0.152000	0.19188	-0.244000	0.11960	ATC	G|0.989;C|0.011	0.011	strong		0.627	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
NHLRC3	387921	hgsc.bcm.edu	37	13	39618302	39618302	+	Missense_Mutation	SNP	T	T	G	rs9603498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:39618302T>G	ENST00000379600.3	+	5	984	c.662T>G	c.(661-663)cTt>cGt	p.L221R	NHLRC3_ENST00000379599.2_Missense_Mutation_p.L154R|NHLRC3_ENST00000470258.1_Missense_Mutation_p.L24R	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	221			L -> R (in dbSNP:rs9603498).			extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		AGTGTTACACTTGATTCAGCT	0.428													T|||	34	0.00678914	0.0	0.0058	5008	,	,		17200	0.001		0.0189	False		,,,				2504	0.0102				p.L221R		Atlas-SNP	.											.	NHLRC3	35	.	0			c.T662G						PASS	.	T	ARG/LEU,ARG/LEU	16,4390	24.3+/-50.5	0,16,2187	245.0	227.0	233.0		662,461	5.7	1.0	13	dbSNP_119	233	169,8431	79.8+/-142.4	1,167,4132	yes	missense,missense	NHLRC3	NM_001012754.2,NM_001017370.1	102,102	1,183,6319	GG,GT,TT		1.9651,0.3631,1.4224	probably-damaging,probably-damaging	221/348,154/281	39618302	185,12821	2203	4300	6503	SO:0001583	missense	387921	exon5			TTACACTTGATTC		CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.662T>G	13.37:g.39618302T>G	ENSP00000368920:p.Leu221Arg	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	245	118	0.481633	NM_001012754	B2RTZ2|B4DTL0|Q69YI9	Missense_Mutation	SNP	ENST00000379600.3	37	CCDS31961.1	18	0.008241758241758242	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	14	0.018469656992084433	T	25.6	4.659822	0.88154	0.003631	0.019651	ENSG00000188811	ENST00000470258;ENST00000379600;ENST00000379599	T;T;T	0.73469	-0.75;-0.75;-0.75	5.67	5.67	0.87782	Six-bladed beta-propeller, TolB-like (1);	0.393126	0.28042	N	0.016839	T	0.67841	0.2936	L	0.47716	1.5	0.42971	D	0.994433	D;P;P	0.53312	0.959;0.953;0.949	P;P;P	0.59761	0.802;0.863;0.745	T	0.74414	-0.3673	9	.	.	.	-5.0962	15.1039	0.72306	0.0:0.0:0.0:1.0	rs9603498;rs52797563;rs9603498	154;221;221	B4DTL0;Q5JS37;B4DRC8	.;NHLC3_HUMAN;.	R	24;221;154	ENSP00000418127:L24R;ENSP00000368920:L221R;ENSP00000368919:L154R	.	L	+	2	0	NHLRC3	38516302	1.000000	0.71417	0.970000	0.41538	0.912000	0.54170	6.976000	0.76135	2.157000	0.67596	0.528000	0.53228	CTT	T|0.989;G|0.011	0.011	strong		0.428	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	NM_001012754	
LRBA	987	hgsc.bcm.edu	37	4	151199080	151199080	+	Missense_Mutation	SNP	G	G	A	rs2290846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:151199080G>A	ENST00000357115.3	-	57	8669	c.8426C>T	c.(8425-8427)tCg>tTg	p.S2809L	LRBA_ENST00000510413.1_Missense_Mutation_p.S2797L|LRBA_ENST00000535741.1_Missense_Mutation_p.S2798L|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2809			S -> L (in dbSNP:rs2290846).			cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					CTTGAGGTCCGACACCTGCCG	0.572													G|||	712	0.142173	0.0121	0.1326	5008	,	,		15649	0.2371		0.2704	False		,,,				2504	0.0951				p.S2809L		Atlas-SNP	.											.	LRBA	253	.	0			c.C8426T						PASS	.	G	LEU/SER,LEU/SER	234,4172	137.3+/-173.1	8,218,1977	103.0	94.0	97.0		8426,8426	4.4	1.0	4	dbSNP_100	97	2302,6298	387.9+/-342.4	306,1690,2304	yes	missense,missense	LRBA	NM_001199282.2,NM_006726.4	145,145	314,1908,4281	AA,AG,GG		26.7674,5.3109,19.4987	benign,benign	2809/2864,2809/2864	151199080	2536,10470	2203	4300	6503	SO:0001583	missense	987	exon57			AGGTCCGACACCT	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.8426C>T	4.37:g.151199080G>A	ENSP00000349629:p.Ser2809Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	422|422	0.19322344322344323|0.19322344322344323	10|10	0.02032520325203252|0.02032520325203252	61|61	0.1685082872928177|0.1685082872928177	147|147	0.256993006993007|0.256993006993007	204|204	0.2691292875989446|0.2691292875989446	G|G	12.53|12.53	1.965397|1.965397	0.34659|0.34659	0.053109|0.053109	0.267674|0.267674	ENSG00000198589|ENSG00000198589	ENST00000509835|ENST00000535741;ENST00000510413;ENST00000357115	.|T;T;T	.|0.38401	.|1.14;1.14;1.14	5.23|5.23	4.37|4.37	0.52481|0.52481	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.|0.443064	.|0.26140	.|N	.|0.026119	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.34521|0.34521	1.04|1.04	0.29298|0.29298	P|P	0.868857|0.868857	.|B;B;B;B	.|0.28880	.|0.226;0.036;0.049;0.048	.|B;B;B;B	.|0.26094	.|0.028;0.012;0.066;0.029	T|T	0.24190|0.24190	-1.0167|-1.0167	4|9	.|0.10902	.|T	.|0.67	.|.	13.9559|13.9559	0.64147|0.64147	0.0:0.2529:0.7471:0.0|0.0:0.2529:0.7471:0.0	rs2290846;rs17632102;rs52824408;rs61057580;rs2290846|rs2290846;rs17632102;rs52824408;rs61057580;rs2290846	.|2809;2798;2797;704	.|P50851;F5H1X8;P50851-2;Q68D03	.|LRBA_HUMAN;.;.;.	W|L	1451|2798;2797;2809	.|ENSP00000446299:S2798L;ENSP00000421552:S2797L;ENSP00000349629:S2809L	.|ENSP00000349629:S2809L	R|S	-|-	1|2	2|0	LRBA|LRBA	151418530|151418530	0.976000|0.976000	0.34144|0.34144	0.997000|0.997000	0.53966|0.53966	0.748000|0.748000	0.42578|0.42578	2.360000|2.360000	0.44151|0.44151	2.441000|2.441000	0.82636|0.82636	0.655000|0.655000	0.94253|0.94253	CGG|TCG	G|0.803;A|0.197	0.197	strong		0.572	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
RPL3L	6123	hgsc.bcm.edu	37	16	2002960	2002960	+	Missense_Mutation	SNP	C	C	T	rs118144581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2002960C>T	ENST00000268661.7	-	3	374	c.280G>A	c.(280-282)Gcc>Acc	p.A94T	RPL3L_ENST00000566484.1_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	94					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						CGAGGGGTGGCCACGTAGCCC	0.592													C|||	19	0.00379393	0.0015	0.0058	5008	,	,		17359	0.0		0.0129	False		,,,				2504	0.0				p.A94T		Atlas-SNP	.											.	RPL3L	42	.	0			c.G280A						PASS	.	C	THR/ALA	3,4395	6.2+/-15.9	0,3,2196	72.0	66.0	68.0		280	4.3	1.0	16	dbSNP_132	68	59,8541	37.8+/-93.5	0,59,4241	yes	missense	RPL3L	NM_005061.2	58	0,62,6437	TT,TC,CC		0.686,0.0682,0.477	benign	94/408	2002960	62,12936	2199	4300	6499	SO:0001583	missense	6123	exon3			GGGTGGCCACGTA	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"""L ribosomal proteins"""	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.280G>A	16.37:g.2002960C>T	ENSP00000268661:p.Ala94Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	50	0.617284	NM_005061		Missense_Mutation	SNP	ENST00000268661.7	37	CCDS10450.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	11.69	1.713498	0.30413	6.82E-4	0.00686	ENSG00000140986	ENST00000268661	T	0.21932	1.98	5.28	4.33	0.51752	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.519934	0.20912	N	0.083458	T	0.14485	0.0350	L	0.44542	1.39	0.30156	N	0.802631	B	0.06786	0.001	B	0.06405	0.002	T	0.08086	-1.0739	10	0.72032	D	0.01	-24.4315	12.7616	0.57367	0.0:0.9211:0.0:0.0789	.	94	Q92901	RL3L_HUMAN	T	94	ENSP00000268661:A94T	ENSP00000268661:A94T	A	-	1	0	RPL3L	1942961	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	1.833000	0.39161	1.238000	0.43771	0.609000	0.83330	GCC	C|0.996;T|0.004	0.004	strong		0.592	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061	
AMPD3	272	hgsc.bcm.edu	37	11	10503736	10503736	+	Missense_Mutation	SNP	C	C	T	rs11042836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:10503736C>T	ENST00000396554.3	+	4	921	c.580C>T	c.(580-582)Cgg>Tgg	p.R194W	AMPD3_ENST00000444303.2_Missense_Mutation_p.R26W	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	185					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		GGGTCATCCGCGGGCGGATAC	0.622													C|||	115	0.0229633	0.003	0.0346	5008	,	,		16919	0.0		0.0755	False		,,,				2504	0.0112				p.R194W		Atlas-SNP	.											.	AMPD3	68	.	0			c.C580T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	72,4330	63.5+/-100.7	1,70,2130	49.0	56.0	54.0		580,553,574,553,76	-1.5	0.0	11	dbSNP_120	54	729,7859	173.2+/-223.7	37,655,3602	yes	missense,missense,missense,missense,missense	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	101,101,101,101,101	38,725,5732	TT,TC,CC		8.4886,1.6356,6.1663	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	194/777,185/768,192/775,185/768,26/609	10503736	801,12189	2201	4294	6495	SO:0001583	missense	272	exon4			CATCCGCGGGCGG	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.580C>T	11.37:g.10503736C>T	ENSP00000379802:p.Arg194Trp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Missense_Mutation	SNP	ENST00000396554.3	37	CCDS7802.1	76	0.0347985347985348	4	0.008130081300813009	16	0.04419889502762431	0	0.0	56	0.07387862796833773	C	15.69	2.909453	0.52439	0.016356	0.084886	ENSG00000133805	ENST00000444303;ENST00000396554;ENST00000524866;ENST00000396553;ENST00000528723;ENST00000529507	T;T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27;1.27	5.88	-1.45	0.08828	.	0.829016	0.11383	N	0.569647	T	0.01189	0.0039	L	0.29908	0.895	0.09310	N	1	P;P;D	0.56746	0.921;0.592;0.977	B;B;P	0.44860	0.339;0.058;0.462	T	0.05053	-1.0909	10	0.66056	D	0.02	-0.3438	3.2802	0.06912	0.2074:0.5028:0.097:0.1928	rs11042836;rs52815732;rs11042836	192;185;194	B7Z763;Q01432;A0AUX0	.;AMPD3_HUMAN;.	W	26;194;185;185;192;185	ENSP00000396000:R26W;ENSP00000379802:R194W;ENSP00000433284:R185W;ENSP00000379801:R185W;ENSP00000436987:R192W;ENSP00000431648:R185W	ENSP00000379801:R185W	R	+	1	2	AMPD3	10460312	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.216000	0.09266	-0.101000	0.12219	-0.140000	0.14226	CGG	C|0.954;T|0.046	0.046	strong		0.622	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
THOC5	8563	hgsc.bcm.edu	37	22	29913272	29913272	+	Missense_Mutation	SNP	C	C	T	rs737976	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29913272C>T	ENST00000490103.1	-	16	1695	c.1573G>A	c.(1573-1575)Gtt>Att	p.V525I	THOC5_ENST00000397871.1_Missense_Mutation_p.V525I|THOC5_ENST00000397872.1_Missense_Mutation_p.V525I|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397873.2_Missense_Mutation_p.V525I	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	525			V -> I (in dbSNP:rs737976). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8242058}.		blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCATGGGCAACTGTCACCCAT	0.502													T|||	2232	0.445687	0.3298	0.379	5008	,	,		23280	0.7242		0.5129	False		,,,				2504	0.2935				p.V525I		Atlas-SNP	.											.	THOC5	58	.	0			c.G1573A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1556,2850	668.9+/-402.1	277,1002,924	132.0	107.0	116.0		1573,1573,1573,1573	-2.5	0.0	22	dbSNP_86	116	4320,4280	576.4+/-390.4	1046,2228,1026	yes	missense,missense,missense,missense	THOC5	NM_001002877.1,NM_001002878.1,NM_001002879.1,NM_003678.4	29,29,29,29	1323,3230,1950	TT,TC,CC		49.7674,35.3155,45.1791	benign,benign,benign,benign	525/684,525/684,525/684,525/684	29913272	5876,7130	2203	4300	6503	SO:0001583	missense	8563	exon17			GGGCAACTGTCAC	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1573G>A	22.37:g.29913272C>T	ENSP00000420306:p.Val525Ile	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	182	83	0.456044	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	1135	0.5196886446886447	180	0.36585365853658536	147	0.40607734806629836	417	0.7290209790209791	391	0.5158311345646438	T	0.016	-1.518513	0.00967	0.353155	0.502326	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.35	-2.49	0.06403	.	0.472153	0.26338	N	0.024946	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27331	-1.0077	9	0.02654	T	1	-25.8597	7.0418	0.25025	0.0:0.1903:0.3011:0.5086	rs737976;rs1130637;rs3189712;rs11546950;rs17416425;rs17536969;rs17856090;rs52793971;rs60269391;rs737976	525	Q13769	THOC5_HUMAN	I	525	ENSP00000420306:V525I;ENSP00000380970:V525I;ENSP00000380969:V525I;ENSP00000380971:V525I	ENSP00000380969:V525I	V	-	1	0	THOC5	28243272	0.040000	0.19996	0.005000	0.12908	0.283000	0.27025	0.249000	0.18216	-1.032000	0.03304	-2.134000	0.00341	GTT	C|0.516;T|0.484	0.484	strong		0.502	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
COL6A5	256076	hgsc.bcm.edu	37	3	130125116	130125116	+	Missense_Mutation	SNP	G	G	C	rs1497312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130125116G>C	ENST00000432398.2	+	17	4924	c.4430G>C	c.(4429-4431)tGt>tCt	p.C1477S	COL6A5_ENST00000265379.6_Missense_Mutation_p.C1477S	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1477	Triple-helical region.		C -> S (in dbSNP:rs1497312).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						TTTTAGGGCTGTCATGGATTT	0.343													C|||	2264	0.452077	0.3389	0.4885	5008	,	,		19056	0.1855		0.7664	False		,,,				2504	0.5307				p.C1477S		Atlas-SNP	.											.	COL6A5	205	.	0			c.G4430C						PASS	.						143.0	105.0	117.0					3																	130125116		692	1591	2283	SO:0001583	missense	256076	exon17			AGGGCTGTCATGG	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.4430G>C	3.37:g.130125116G>C	ENSP00000390895:p.Cys1477Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		1083	0.4958791208791209	189	0.38414634146341464	198	0.5469613259668509	96	0.16783216783216784	600	0.7915567282321899	C	7.821	0.717721	0.15372	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.94046	-3.34;-3.34	5.56	0.227	0.15359	.	.	.	.	.	T	0.00012	0.0000	N	0.03917	-0.325	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40403	-0.9565	8	0.10111	T	0.7	.	0.9297	0.01332	0.2359:0.311:0.1289:0.3242	rs1497312;rs59992209;rs1497312	1477	A8TX70-2	.	S	1477	ENSP00000390895:C1477S;ENSP00000265379:C1477S	ENSP00000265379:C1477S	C	+	2	0	COL6A5	131607806	0.000000	0.05858	0.000000	0.03702	0.364000	0.29643	-0.617000	0.05584	-0.070000	0.12908	-1.104000	0.02111	TGT	G|0.545;C|0.455	0.455	strong		0.343	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
SSPO	23145	hgsc.bcm.edu	37	7	149486382	149486382	+	RNA	SNP	C	C	G	rs2074704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149486382C>G	ENST00000378016.2	+	0	4358							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TATCCGTGCCCCCAGGGCTTG	0.672													C|||	299	0.0597045	0.031	0.0519	5008	,	,		16691	0.0933		0.0666	False		,,,				2504	0.0624				p.P1453R		Atlas-SNP	.											.	.	.	.	0			c.C4358G						PASS	.	C		151,4245		2,147,2049	23.0	27.0	26.0		4362	4.8	0.5	7	dbSNP_96	26	557,8033		28,501,3766	no	coding-notMod3	SSPO	NM_198455.2		30,648,5815	GG,GC,CC		6.4843,3.4349,5.452			149486382	708,12278	2198	4295	6493			23145	exon30			CGTGCCCCCAGGG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149486382C>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	71	24	0.338028	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.891;G|0.109	0.109	strong		0.672	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
MST1L	11223	hgsc.bcm.edu	37	1	17084021	17084021	+	RNA	SNP	C	C	G	rs2446543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17084021C>G	ENST00000455405.2	-	0	691							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.A634P(1)									ACCTCACAGGCCCCCACAGGG	0.572																																					p.A634P		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	kidney(1)	c.G1900C						PASS	.																																					11223	exon14			CACAGGCCCCCAC	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17084021C>G		Somatic	877	1	0.00114025		WXS	Illumina HiSeq	Phase_I	786	311	0.395674	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	9.021	0.984781	0.18889	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41938	D	0.000787	T	0.57431	0.2053	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.61426	-0.7065	6	0.15499	T	0.54	.	6.7402	0.23431	0.0:0.9998:0.0:2.0E-4	rs2446543	634;660	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	P	634;660	.	ENSP00000439273:A634P	A	-	1	0	MST1P9	16956608	0.997000	0.39634	0.867000	0.34043	0.000000	0.00434	4.380000	0.59581	0.502000	0.28037	0.000000	0.15137	GCC	C|0.750;G|0.250	0.250	strong		0.572	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499228	59499228	+	Missense_Mutation	SNP	C	C	T	rs3809529	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:59499228C>T	ENST00000307144.4	+	1	187	c.89C>T	c.(88-90)cCg>cTg	p.P30L	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	30			P -> L (in dbSNP:rs3809529). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						GCCCTGTGTCCGCGTCAAGCA	0.597													C|||	2460	0.491214	0.4735	0.4409	5008	,	,		20601	0.6131		0.34	False		,,,				2504	0.5808				p.P30L		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.C89T						PASS	.	C	,LEU/PRO	1879,2503	542.2+/-376.0	414,1051,726	61.0	55.0	57.0		,89	1.5	0.0	15	dbSNP_107	57	2756,5824	439.8+/-359.3	438,1880,1972	yes	intron,missense	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,98	852,2931,2698	TT,TC,CC		32.1212,42.88,35.7584	,benign	,30/382	59499228	4635,8327	2191	4290	6481	SO:0001583	missense	92483	exon1			TGTGTCCGCGTCA	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.89C>T	15.37:g.59499228C>T	ENSP00000302393:p.Pro30Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	37	CCDS10171.1	984	0.45054945054945056	217	0.4410569105691057	146	0.40331491712707185	363	0.6346153846153846	258	0.3403693931398417	C	7.523	0.657174	0.14580	0.4288	0.321212	ENSG00000171989	ENST00000307144	T	0.68765	-0.35	1.49	1.49	0.22878	.	0.733878	0.10584	U	0.657625	T	0.00012	0.0000	L	0.29908	0.895	0.45946	P	0.0012299999999999534	B	0.15719	0.014	B	0.06405	0.002	T	0.47005	-0.9150	9	0.30854	T	0.27	.	6.8004	0.23748	0.0:1.0:0.0:0.0	rs3809529;rs17856654;rs52793037;rs57306412;rs3809529	30	Q9BYZ2	LDH6B_HUMAN	L	30	ENSP00000302393:P30L	ENSP00000302393:P30L	P	+	2	0	LDHAL6B	57286520	0.011000	0.17503	0.018000	0.16275	0.036000	0.12997	1.945000	0.40273	0.710000	0.31997	0.305000	0.20034	CCG	C|0.613;T|0.387	0.387	strong		0.597	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
AKAP9	10142	hgsc.bcm.edu	37	7	91632286	91632286	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:91632286T>G	ENST00000359028.2	+	9	3316	c.3091T>G	c.(3091-3093)Tta>Gta	p.L1031V	AKAP9_ENST00000358100.2_Missense_Mutation_p.L1031V|AKAP9_ENST00000356239.3_Missense_Mutation_p.L1019V			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1031					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGTAAGCTCTTTATTAGATGG	0.358			T	BRAF	papillary thyroid																																p.L1019V		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.T3055G						PASS	.						84.0	85.0	85.0					7																	91632286		2203	4300	6503	SO:0001583	missense	10142	exon8			AGCTCTTTATTAG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.3091T>G	7.37:g.91632286T>G	ENSP00000351922:p.Leu1031Val	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	T	12.35	1.911886	0.33721	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.03358	3.96;3.96;3.96	5.72	3.2	0.36748	.	0.556233	0.13630	N	0.373796	T	0.05364	0.0142	L	0.54323	1.7	0.09310	N	1	B;P;B;P	0.46220	0.094;0.874;0.152;0.493	B;B;B;B	0.41723	0.039;0.365;0.085;0.085	T	0.32348	-0.9910	10	0.56958	D	0.05	.	8.3792	0.32461	0.0:0.0687:0.1325:0.7988	.	1031;1019;1019;1031	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	V	1019;1031;1031;1031;1031	ENSP00000348573:L1019V;ENSP00000351922:L1031V;ENSP00000350813:L1031V	ENSP00000348573:L1019V	L	+	1	2	AKAP9	91470222	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.085000	0.14912	1.091000	0.41335	0.528000	0.53228	TTA	.	.	none		0.358	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
SCAP	22937	hgsc.bcm.edu	37	3	47459679	47459679	+	Missense_Mutation	SNP	C	C	T	rs12487736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:47459679C>T	ENST00000265565.5	-	16	2804	c.2392G>A	c.(2392-2394)Gtc>Atc	p.V798I	SCAP_ENST00000545718.1_Missense_Mutation_p.V406I|SCAP_ENST00000465628.1_5'Flank|SCAP_ENST00000441517.2_Missense_Mutation_p.V543I	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	798	Interaction with SREBF2. {ECO:0000250}.		V -> I (in dbSNP:rs12487736). {ECO:0000269|PubMed:10570919}.		aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CACACGCAGACGTGGCCTGCC	0.687													c|||	2265	0.452276	0.233	0.5245	5008	,	,		9125	0.4583		0.5905	False		,,,				2504	0.5491				p.V798I	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.G2392A						PASS	.		ILE/VAL	1178,3170		206,766,1202	19.0	21.0	20.0		2392	3.6	0.9	3	dbSNP_120	20	4846,3680		1440,1966,857	no	missense	SCAP	NM_012235.2	29	1646,2732,2059	TT,TC,CC		43.1621,27.0929,46.792	benign	798/1280	47459679	6024,6850	2174	4263	6437	SO:0001583	missense	22937	exon16			CGCAGACGTGGCC	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.2392G>A	3.37:g.47459679C>T	ENSP00000265565:p.Val798Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_012235	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	1039|1039	0.4757326007326007|0.4757326007326007	137|137	0.2784552845528455|0.2784552845528455	191|191	0.5276243093922652|0.5276243093922652	265|265	0.4632867132867133|0.4632867132867133	446|446	0.5883905013192612|0.5883905013192612	c|c	3.908|3.908	-0.020663|-0.020663	0.07634|0.07634	0.270929|0.270929	0.568379|0.568379	ENSG00000114650|ENSG00000114650	ENST00000383739|ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718	.|T;T;T	.|0.41758	.|1.61;2.2;0.99	4.59|4.59	3.62|3.62	0.41486|0.41486	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.|0.054283	.|0.64402	.|D	.|0.000001	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01705|0.01705	-0.755|-0.755	0.26338|0.26338	P|P	0.9774169|0.9774169	.|B;B	.|0.13594	.|0.005;0.008	.|B;B	.|0.12156	.|0.003;0.007	T|T	0.48525|0.48525	-0.9028|-0.9028	5|9	0.87932|0.02654	D|T	0|1	-31.7751|-31.7751	3.9583|3.9583	0.09399|0.09399	0.0:0.6739:0.0:0.3261|0.0:0.6739:0.0:0.3261	rs12487736;rs17845631;rs17849135;rs17858562|rs12487736;rs17845631;rs17849135;rs17858562	.|543;798	.|F8W921;Q12770	.|.;SCAP_HUMAN	H|I	322|425;798;543;406	.|ENSP00000265565:V798I;ENSP00000416847:V543I;ENSP00000438956:V406I	ENSP00000373245:R322H|ENSP00000265565:V798I	R|V	-|-	2|1	0|0	SCAP|SCAP	47434683|47434683	1.000000|1.000000	0.71417|0.71417	0.905000|0.905000	0.35620|0.35620	0.192000|0.192000	0.23643|0.23643	3.194000|3.194000	0.51005|0.51005	2.393000|2.393000	0.81446|0.81446	0.556000|0.556000	0.70494|0.70494	CGT|GTC	C|0.531;T|0.469	0.469	strong		0.687	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	
NOTCH3	4854	hgsc.bcm.edu	37	19	15295134	15295134	+	Silent	SNP	G	G	A	rs1043996	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15295134G>A	ENST00000263388.2	-	16	2613	c.2538C>T	c.(2536-2538)tgC>tgT	p.C846C		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	846	EGF-like 21; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TGTCCTGATCGCAGGAAGGGC	0.597													G|||	2604	0.519968	0.1997	0.562	5008	,	,		17319	0.5933		0.6928	False		,,,				2504	0.6697				p.C846C		Atlas-SNP	.											NOTCH3_ENST00000263388,colon,carcinoma,-2,2	NOTCH3	340	2	0			c.C2538T						PASS	.	G		1217,3189	422.5+/-339.8	184,849,1170	75.0	56.0	62.0		2538	-1.0	0.9	19	dbSNP_86	62	6150,2450	695.4+/-404.8	2210,1730,360	yes	coding-synonymous	NOTCH3	NM_000435.2		2394,2579,1530	AA,AG,GG		28.4884,27.6214,43.3569		846/2322	15295134	7367,5639	2203	4300	6503	SO:0001819	synonymous_variant	4854	exon16			CTGATCGCAGGAA	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.2538C>T	19.37:g.15295134G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	37	CCDS12326.1																																																																																			G|0.460;T|0.004	.	strong		0.597	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
GAPDHS	26330	hgsc.bcm.edu	37	19	36033460	36033460	+	Silent	SNP	C	C	T	rs2239945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36033460C>T	ENST00000222286.4	+	6	725	c.609C>T	c.(607-609)gtC>gtT	p.V203V	AD000090.2_ENST00000588286.1_RNA|AD000090.2_ENST00000589137.1_RNA|AD000090.2_ENST00000444728.1_RNA|AD000090.2_ENST00000590717.1_RNA|AD000090.2_ENST00000590125.1_RNA	NM_014364.4	NP_055179.1	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	203					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	cytosol (GO:0005829)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|NAD binding (GO:0051287)|NADP binding (GO:0050661)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)	11	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CAATGTTCGTCATGGGTGTCA	0.547													C|||	1029	0.205471	0.0234	0.33	5008	,	,		23417	0.3651		0.1382	False		,,,				2504	0.2679				p.V203V		Atlas-SNP	.											.	GAPDHS	34	.	0			c.C609T						PASS	.	C		208,4198	127.8+/-164.7	4,200,1999	138.0	107.0	118.0		609	5.0	1.0	19	dbSNP_98	118	1198,7402	242.2+/-272.3	96,1006,3198	no	coding-synonymous	GAPDHS	NM_014364.4		100,1206,5197	TT,TC,CC		13.9302,4.7208,10.8104		203/409	36033460	1406,11600	2203	4300	6503	SO:0001819	synonymous_variant	26330	exon6			GTTCGTCATGGGT	AJ005371	CCDS12465.1	19q13.1	2008-02-05		2005-05-06		ENSG00000105679			24864	protein-coding gene	gene with protein product		609169		GAPDS		10714828	Standard	NM_014364		Approved	GAPDH-2, GAPD2	uc002oaf.1	O14556		ENST00000222286.4:c.609C>T	19.37:g.36033460C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_014364	B2RC82|O60823|Q6JTT9|Q9HCU6	Silent	SNP	ENST00000222286.4	37	CCDS12465.1																																																																																			C|0.850;T|0.150	0.150	strong		0.547	GAPDHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460423.1	NM_014364	
XRCC1	7515	hgsc.bcm.edu	37	19	44057574	44057574	+	Missense_Mutation	SNP	G	G	A	rs1799782	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44057574G>A	ENST00000262887.5	-	6	1127	c.580C>T	c.(580-582)Cgg>Tgg	p.R194W	XRCC1_ENST00000543982.1_Missense_Mutation_p.R163W|L34079.3_ENST00000597119.1_RNA			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	194			R -> W (in dbSNP:rs1799782). {ECO:0000269|PubMed:9485007, ECO:0000269|Ref.2}.		base-excision repair (GO:0006284)|DNA repair (GO:0006281)|hippocampus development (GO:0021766)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to organic substance (GO:0010033)|single strand break repair (GO:0000012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Prostate(69;0.0153)				TTGTTGATCCGGCTGAAGAAG	0.597								Other BER factors					G|||	620	0.123802	0.0719	0.1167	5008	,	,		18638	0.2817		0.0517	False		,,,				2504	0.1104				p.R194W		Atlas-SNP	.											.	XRCC1	47	.	0			c.C580T	GRCh37	CM033678	XRCC1	M	rs1799782	PASS	.	G	TRP/ARG	247,4159	144.2+/-179.2	7,233,1963	81.0	76.0	78.0		580	1.0	1.0	19	dbSNP_89	78	555,8045	151.9+/-206.6	16,523,3761	yes	missense	XRCC1	NM_006297.2	101	23,756,5724	AA,AG,GG		6.4535,5.606,6.1664	probably-damaging	194/634	44057574	802,12204	2203	4300	6503	SO:0001583	missense	7515	exon6			TGATCCGGCTGAA	M36089	CCDS12624.1	19q13.2	2014-09-17				ENSG00000073050			12828	protein-coding gene	gene with protein product		194360		RCC		2247054	Standard	NM_006297		Approved		uc002owt.2	P18887		ENST00000262887.5:c.580C>T	19.37:g.44057574G>A	ENSP00000262887:p.Arg194Trp	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	148	79	0.533784	NM_006297	Q6IBS4|Q9HCB1	Missense_Mutation	SNP	ENST00000262887.5	37	CCDS12624.1	283	0.1295787545787546	36	0.07317073170731707	38	0.10497237569060773	165	0.28846153846153844	44	0.05804749340369393	G	19.83	3.900060	0.72754	0.05606	0.064535	ENSG00000073050	ENST00000458471;ENST00000262887;ENST00000543982;ENST00000538738	T;T	0.03772	3.83;3.81	4.73	1.03	0.20045	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.72894	2.215	0.19575	P	0.9999696885	P;D	0.89917	0.912;1.0	P;P	0.62184	0.574;0.899	T	0.39961	-0.9588	9	0.45353	T	0.12	-6.33	6.6426	0.22917	0.0899:0.0:0.599:0.3111	rs1799782;rs2229674;rs3213359;rs3826914;rs11553655	163;194	F5H8D7;P18887	.;XRCC1_HUMAN	W	208;194;163;194	ENSP00000262887:R194W;ENSP00000443671:R163W	ENSP00000262887:R194W	R	-	1	2	XRCC1	48749414	1.000000	0.71417	0.986000	0.45419	0.972000	0.66771	1.506000	0.35747	0.645000	0.30675	0.655000	0.94253	CGG	G|0.905;A|0.095	0.095	strong		0.597	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297	
FFAR4	338557	hgsc.bcm.edu	37	10	95326676	95326676	+	Missense_Mutation	SNP	C	C	T	rs61866610	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:95326676C>T	ENST00000371483.4	+	1	255	c.199C>T	c.(199-201)Cgc>Tgc	p.R67C	FFAR4_ENST00000371481.4_Missense_Mutation_p.R67C|FFAR4_ENST00000604414.1_Missense_Mutation_p.R67C	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	67	Poly-Arg.		R -> C (in dbSNP:rs61866610). {ECO:0000269|PubMed:15619630, ECO:0000269|PubMed:22343897}.	Missing (in Ref. 1; AAP72126). {ECO:0000305}.	hormone secretion (GO:0046879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of inflammatory response (GO:0050728)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of glucose transport (GO:0010827)	endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fatty acid binding (GO:0005504)|taste receptor activity (GO:0008527)										GCTGGTGGCGCGCCGACGACG	0.682													C|||	784	0.15655	0.0378	0.2277	5008	,	,		15030	0.3591		0.0447	False		,,,				2504	0.1728				p.R67C		Atlas-SNP	.											.	.	.	.	0			c.C199T						PASS	.	C	CYS/ARG,CYS/ARG	173,4227		4,165,2031	27.0	27.0	27.0		199,199	5.2	1.0	10	dbSNP_129	27	386,8208		10,366,3921	yes	missense,missense	O3FAR1	NM_001195755.1,NM_181745.3	180,180	14,531,5952	TT,TC,CC		4.4915,3.9318,4.302	probably-damaging,probably-damaging	67/362,67/378	95326676	559,12435	2200	4297	6497	SO:0001583	missense	338557	exon1			GTGGCGCGCCGAC		CCDS31248.1, CCDS55720.1	10q23.33	2012-11-16	2012-11-16	2012-11-16	ENSG00000186188	ENSG00000186188		"""GPCR / Class A : Fatty acid receptors"""	19061	protein-coding gene	gene with protein product		609044	"""G protein-coupled receptor 129"", ""G protein-coupled receptor 120"", ""omega-3 fatty acid receptor 1"""	GPR129, GPR120, O3FAR1		20471368, 19723586, 15619630, 20813258	Standard	NM_181745		Approved	PGR4	uc010qnt.2	Q5NUL3	OTTHUMG00000034409	ENST00000371483.4:c.199C>T	10.37:g.95326676C>T	ENSP00000360538:p.Arg67Cys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	68	46	0.676471	NM_001195755	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Missense_Mutation	SNP	ENST00000371483.4	37	CCDS31248.1	326	0.14926739926739926	27	0.054878048780487805	58	0.16022099447513813	205	0.3583916083916084	36	0.047493403693931395	C	15.14	2.746101	0.49151	0.039318	0.044915	ENSG00000186188	ENST00000371481;ENST00000371483	T;T	0.41400	1.0;1.0	5.22	5.22	0.72569	GPCR, rhodopsin-like superfamily (1);	0.093954	0.45126	D	0.000390	T	0.00012	0.0000	M	0.72118	2.19	0.21967	P	0.999441626	D;D	0.61697	0.988;0.99	P;P	0.55011	0.654;0.766	T	0.29488	-1.0010	9	0.72032	D	0.01	-27.4849	13.3065	0.60355	0.2729:0.7271:0.0:0.0	rs61866610	67;67	Q5NUL3-2;Q5NUL3	.;O3FA1_HUMAN	C	67	ENSP00000360536:R67C;ENSP00000360538:R67C	ENSP00000360536:R67C	R	+	1	0	O3FAR1	95316666	0.987000	0.35691	1.000000	0.80357	0.747000	0.42532	1.540000	0.36115	2.714000	0.92807	0.561000	0.74099	CGC	C|0.920;T|0.080	0.080	strong		0.682	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745	
SYNE3	161176	hgsc.bcm.edu	37	14	95910933	95910933	+	Silent	SNP	T	T	C	rs9919918	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:95910933T>C	ENST00000334258.5	-	9	1679	c.1665A>G	c.(1663-1665)gcA>gcG	p.A555A	SYNE3_ENST00000553340.1_Silent_p.A555A|SYNE3_ENST00000554873.1_Silent_p.A312A|SYNE3_ENST00000557275.1_Silent_p.A555A	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	555					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.A555A(1)		breast(1)|endometrium(2)|lung(25)	28						GCTCAAAAGCTGCTCCAAAGT	0.577													C|||	1410	0.28155	0.3427	0.4035	5008	,	,		19740	0.3155		0.2078	False		,,,				2504	0.1534				p.A555A		Atlas-SNP	.											C14orf49,NS,carcinoma,0,1	SYNE3	130	1	1	Substitution - coding silent(1)	stomach(1)	c.A1665G						PASS	.	C		1436,2970	682.6+/-404.1	244,948,1011	52.0	51.0	51.0		1665	-10.8	0.0	14	dbSNP_119	51	1620,6980	742.8+/-407.2	171,1278,2851	no	coding-synonymous	C14orf49	NM_152592.3		415,2226,3862	CC,CT,TT		18.8372,32.5919,23.4968		555/976	95910933	3056,9950	2203	4300	6503	SO:0001819	synonymous_variant	161176	exon9			AAAAGCTGCTCCA	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1665A>G	14.37:g.95910933T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	CCDS9935.1																																																																																			C|0.242;N|0.000	0.242	strong		0.577	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
PRDM9	56979	hgsc.bcm.edu	37	5	23527724	23527724	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:23527724A>G	ENST00000296682.3	+	11	2709	c.2527A>G	c.(2527-2529)Aat>Gat	p.N843D		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	843					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.N843D(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGCTTTCGCAATAAGTCACA	0.587										HNSCC(3;0.000094)																											p.N843D		Atlas-SNP	.											PRDM9,trunk,malignant_melanoma,0,2	PRDM9	344	2	2	Substitution - Missense(2)	skin(2)	c.A2527G						scavenged	.						66.0	76.0	72.0					5																	23527724		2183	4295	6478	SO:0001583	missense	56979	exon11			TTTCGCAATAAGT	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2527A>G	5.37:g.23527724A>G	ENSP00000296682:p.Asn843Asp	Somatic	200	3	0.015		WXS	Illumina HiSeq	Phase_I	247	10	0.0404858	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.847213	0.00067	.	.	ENSG00000164256	ENST00000296682	T	0.07444	3.19	2.67	-5.34	0.02705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02848	0.0085	N	0.04355	-0.22	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.30208	-0.9986	9	0.32370	T	0.25	.	1.9842	0.03433	0.2035:0.1472:0.4036:0.2457	.	843	Q9NQV7	PRDM9_HUMAN	D	843	ENSP00000296682:N843D	ENSP00000296682:N843D	N	+	1	0	PRDM9	23563481	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-14.808000	0.00000	-5.282000	0.00017	-3.452000	0.00036	AAT	.	.	none		0.587	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
ARSD	414	hgsc.bcm.edu	37	X	2836238	2836238	+	Missense_Mutation	SNP	G	G	A	rs73632978	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836238G>A	ENST00000381154.1	-	5	545	c.470C>T	c.(469-471)tCc>tTc	p.S157F	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	157					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ATCCCCGCGGGATGCACAATT	0.552																																					p.S157F		Atlas-SNP	.											.	ARSD	47	.	0			c.C470T						PASS	.						29.0	17.0	21.0					X																	2836238		2191	4278	6469	SO:0001583	missense	414	exon5			CCGCGGGATGCAC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.470C>T	X.37:g.2836238G>A	ENSP00000370546:p.Ser157Phe	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	137	0.08257986738999397	30	0.06726457399103139	29	0.0838150289017341	41	0.07536764705882353	57	0.0782967032967033	g	1.697	-0.502464	0.04261	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.94330	-3.4	3.47	1.08	0.20341	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.645437	0.15182	U	0.276051	T	0.44201	0.1282	L	0.53249	1.67	0.80722	P	0.0	B;B	0.23377	0.045;0.084	B;B	0.29598	0.104;0.059	T	0.76027	-0.3109	9	0.59425	D	0.04	.	8.5841	0.33646	0.112:0.1547:0.7333:0.0	.	157;157	E9PAW5;P51689	.;ARSD_HUMAN	F	157	ENSP00000370546:S157F	ENSP00000217890:S157F	S	-	2	0	ARSD	2846238	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.383000	0.20651	0.371000	0.24564	0.420000	0.28162	TCC	G|0.916;A|0.084	0.084	strong		0.552	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
VSX1	30813	hgsc.bcm.edu	37	20	25059442	25059442	+	Intron	SNP	C	C	T	rs6138482	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:25059442C>T	ENST00000376709.4	-	3	891				VSX1_ENST00000429762.3_Intron|VSX1_ENST00000451258.1_Intron|VSX1_ENST00000424574.1_Intron|VSX1_ENST00000376707.3_Missense_Mutation_p.R217H|VSX1_ENST00000444511.2_Intron	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1						neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(3)|lung(2)	6						ATCTTTGGAGCGGAGAAAAGG	0.527													c|||	1080	0.215655	0.0098	0.2147	5008	,	,		17699	0.5268		0.2137	False		,,,				2504	0.1759				p.R217H		Atlas-SNP	.											.	VSX1	20	.	0			c.G650A						PASS	.	T	,HIS/ARG	191,4215	120.4+/-158.0	4,183,2016	204.0	203.0	203.0		,650	-4.9	0.0	20	dbSNP_114	203	1700,6900	312.0+/-310.6	161,1378,2761	yes	intron,missense	VSX1	NM_014588.4,NM_199425.1	,29	165,1561,4777	TT,TC,CC		19.7674,4.335,14.5394	,	,217/240	25059442	1891,11115	2203	4300	6503	SO:0001627	intron_variant	30813	exon3			TTGGAGCGGAGAA	AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"""Homeoboxes / PRD class"""	12723	protein-coding gene	gene with protein product		605020	"""posterior polymorphous corneal dystrophy"", ""visual system homeobox 1 homolog, CHX10-like (zebrafish)"""	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.627+22G>A	20.37:g.25059442C>T		Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	232	109	0.469828	NM_199425	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Missense_Mutation	SNP	ENST00000376709.4	37	CCDS13168.1	578	0.26465201465201466	14	0.028455284552845527	86	0.23756906077348067	321	0.5611888111888111	157	0.20712401055408972	c	11.23	1.577349	0.28180	0.04335	0.197674	ENSG00000100987	ENST00000376707	D	0.93366	-3.21	4.23	-4.87	0.03123	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.13594	0.008	B	0.04013	0.001	T	0.39722	-0.9600	7	0.87932	D	0	.	0.4641	0.00521	0.3084:0.1187:0.2286:0.3443	rs6138482;rs58752432;rs6138482	217	Q9NZR4-2	.	H	217	ENSP00000365897:R217H	ENSP00000365897:R217H	R	-	2	0	VSX1	25007442	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.065000	0.11617	-1.182000	0.02727	-1.590000	0.00845	CGC	C|0.759;T|0.241	0.241	strong		0.527	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3		
USH1C	10083	hgsc.bcm.edu	37	11	17542439	17542439	+	Silent	SNP	T	T	C	rs2240487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:17542439T>C	ENST00000318024.4	-	14	1296	c.1188A>G	c.(1186-1188)ccA>ccG	p.P396P	USH1C_ENST00000005226.7_Silent_p.P396P|USH1C_ENST00000527720.1_Silent_p.P365P|USH1C_ENST00000527020.1_Silent_p.P377P	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	396					auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						GAAGGGGTACTGGGTGTACCT	0.517													T|||	2586	0.516374	0.3018	0.6527	5008	,	,		18761	0.6716		0.5338	False		,,,				2504	0.5317				p.P396P		Atlas-SNP	.											.	USH1C	157	.	0			c.A1188G						PASS	.	T	,	1569,2831	490.8+/-361.9	270,1029,901	294.0	274.0	281.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1188,1188	-10.6	0.0	11	dbSNP_98	281	4976,3610	625.8+/-397.8	1442,2092,759	no	coding-synonymous,coding-synonymous	USH1C	NM_005709.3,NM_153676.3	,	1712,3121,1660	CC,CT,TT		42.0452,35.6591,49.5996	,	396/553,396/900	17542439	6545,6441	2200	4293	6493	SO:0001819	synonymous_variant	10083	exon14			GGGTACTGGGTGT	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"""harmonin"""	605242	"""deafness, autosomal recessive 18"""	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1188A>G	11.37:g.17542439T>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	248	120	0.483871	NM_005709	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			C|0.518;T|0.482	0.518	strong		0.517	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
FANCB	2187	hgsc.bcm.edu	37	X	14877404	14877404	+	Missense_Mutation	SNP	C	C	T	rs41309679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:14877404C>T	ENST00000324138.3	-	3	1157	c.1004G>A	c.(1003-1005)gGa>gAa	p.G335E	FANCB_ENST00000398334.1_Missense_Mutation_p.G335E	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	335					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					AGTTCCACTTCCAATAAAGTC	0.358								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	138	0.0365563	0.0023	0.0331	3775	,	,		10355	0.0		0.0626	False		,,,				2504	0.0501				p.G335E		Atlas-SNP	.											.	FANCB	78	.	0			c.G1004A						PASS	.	C	GLU/GLY,GLU/GLY	57,3778		0,52,5,1580,566	77.0	69.0	72.0		1004,1004	5.8	0.2	X	dbSNP_127	72	566,6159		18,369,161,2041,1708	yes	missense,missense	FANCB	NM_001018113.1,NM_152633.2	98,98	18,421,166,3621,2274	TT,TC,T,CC,C		8.4164,1.4863,5.8996	probably-damaging,probably-damaging	335/860,335/860	14877404	623,9937	2203	4297	6500	SO:0001583	missense	2187	exon3	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCACTTCCAATAA	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"""Fanconi anemia, complementation groups"""	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1004G>A	X.37:g.14877404C>T	ENSP00000326819:p.Gly335Glu	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Missense_Mutation	SNP	ENST00000324138.3	37	CCDS14161.1	62	0.037371910789632305	2	0.004081632653061225	8	0.02247191011235955	0	0.0	32	0.04419889502762431	C	13.99	2.403010	0.42613	0.014863	0.084164	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	5.82	5.82	0.92795	.	0.230064	0.44902	D	0.000418	T	0.19725	0.0474	M	0.71581	2.175	0.27753	P	0.9440976	D	0.89917	1.0	D	0.97110	1.0	T	0.61048	-0.7141	8	0.87932	D	0	-20.4655	16.8235	0.85924	0.0:1.0:0.0:0.0	rs41309679	335	Q8NB91	FANCB_HUMAN	E	335	.	ENSP00000326819:G335E	G	-	2	0	FANCB	14787325	0.998000	0.40836	0.194000	0.23346	0.125000	0.20455	4.231000	0.58639	2.455000	0.83008	0.594000	0.82650	GGA	C|0.950;T|0.050	0.050	strong		0.358	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633	
KCNMB3	27094	hgsc.bcm.edu	37	3	178968634	178968634	+	Missense_Mutation	SNP	C	C	T	rs7645550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:178968634C>T	ENST00000314235.5	-	2	668	c.157G>A	c.(157-159)Gct>Act	p.A53T	KCNMB3_ENST00000392685.2_Missense_Mutation_p.A49T|KCNMB3_ENST00000485523.1_Missense_Mutation_p.A31T|KCNMB3_ENST00000497599.1_Missense_Mutation_p.A51T|KCNMB3_ENST00000349697.2_Missense_Mutation_p.A51T	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	53			A -> T (in dbSNP:rs7645550). {ECO:0000269|PubMed:10585773, ECO:0000269|PubMed:10692449, ECO:0000269|PubMed:10766764, ECO:0000269|PubMed:10792058, ECO:0000269|PubMed:10828459}.		action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)	p.A53T(1)		NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	TCCTCTCCAGCACTGGATGGC	0.517													C|||	1579	0.315296	0.416	0.3127	5008	,	,		18625	0.123		0.3708	False		,,,				2504	0.3221				p.A53T		Atlas-SNP	.											KCNMB3,NS,carcinoma,0,1	KCNMB3	46	1	1	Substitution - Missense(1)	stomach(1)	c.G157A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	1710,2696	514.5+/-368.7	332,1046,825	101.0	94.0	96.0		151,157,151,91,145	6.1	1.0	3	dbSNP_116	96	3284,5316	492.8+/-373.4	622,2040,1638	yes	missense,missense,missense,missense,missense	KCNMB3	NM_001163677.1,NM_014407.3,NM_171828.1,NM_171829.2,NM_171830.1	58,58,58,58,58	954,3086,2463	TT,TC,CC		38.186,38.8107,38.3977	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	51/174,53/280,51/278,31/258,49/276	178968634	4994,8012	2203	4300	6503	SO:0001583	missense	27094	exon2			CTCCAGCACTGGA	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"""Potassium channels"""	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.157G>A	3.37:g.178968634C>T	ENSP00000319370:p.Ala53Thr	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	285	167	0.585965	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000314235.5	37	CCDS3226.1	640	0.29304029304029305	201	0.40853658536585363	113	0.31215469613259667	48	0.08391608391608392	278	0.36675461741424803	C	18.08	3.544434	0.65198	0.388107	0.38186	ENSG00000171121	ENST00000497599;ENST00000392685;ENST00000349697;ENST00000314235;ENST00000485523	T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89	6.08	6.08	0.98989	.	0.117706	0.56097	D	0.000026	T	0.00012	0.0000	M	0.76574	2.34	0.23950	P	0.99637341	D;D;D;D;D	0.89917	1.0;0.997;0.993;0.998;1.0	D;D;D;D;D	0.83275	0.996;0.942;0.91;0.957;0.99	T	0.46331	-0.9199	9	0.39692	T	0.17	-13.1111	18.1573	0.89696	0.0:1.0:0.0:0.0	rs7645550;rs17565626;rs52829256;rs61485480;rs7645550	51;51;31;49;53	E9PER5;Q9NPA1-2;Q9NPA1-4;Q9NPA1-3;Q9NPA1	.;.;.;.;KCMB3_HUMAN	T	51;49;51;53;31	ENSP00000417091:A51T;ENSP00000376451:A49T;ENSP00000327866:A51T;ENSP00000319370:A53T;ENSP00000418536:A31T	ENSP00000319370:A53T	A	-	1	0	KCNMB3	180451328	1.000000	0.71417	0.999000	0.59377	0.099000	0.18886	4.589000	0.61006	2.894000	0.99253	0.655000	0.94253	GCT	C|0.649;T|0.351	0.351	strong		0.517	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1		
GPRC5D	55507	hgsc.bcm.edu	37	12	13102605	13102605	+	Silent	SNP	G	G	A	rs4630382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:13102605G>A	ENST00000228887.1	-	1	713	c.714C>T	c.(712-714)gaC>gaT	p.D238D	RP11-392P7.6_ENST00000540198.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000394742.3_RNA|RP11-392P7.6_ENST00000542078.1_RNA|GPRC5D_ENST00000396333.3_Silent_p.D238D|RP11-392P7.6_ENST00000538231.1_RNA	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			kidney(2)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		CGACCGGGTCGTCCCACTGGG	0.552													g|||	1035	0.206669	0.0204	0.2046	5008	,	,		20154	0.1865		0.3817	False		,,,				2504	0.3006				p.D238D		Atlas-SNP	.											.	GPRC5D	23	.	0			c.C714T						PASS	.	A		350,4056	180.8+/-209.0	12,326,1865	97.0	99.0	98.0		714	-3.6	0.9	12	dbSNP_111	98	3395,5205	502.3+/-375.6	674,2047,1579	no	coding-synonymous	GPRC5D	NM_018654.1		686,2373,3444	AA,AG,GG		39.4767,7.9437,28.7944		238/346	13102605	3745,9261	2203	4300	6503	SO:0001819	synonymous_variant	55507	exon1			CGGGTCGTCCCAC	AF209923	CCDS8658.1	12p13.3	2014-01-30	2014-01-30		ENSG00000111291	ENSG00000111291		"""GPCR / Class C : Orphans"""	13310	protein-coding gene	gene with protein product		607437	"""G protein-coupled receptor, family C, group 5, member D"""				Standard	XM_005253421		Approved		uc010shp.2	Q9NZD1	OTTHUMG00000168711	ENST00000228887.1:c.714C>T	12.37:g.13102605G>A		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_018654	Q3KNV3|Q7Z5J9|Q8TDS6	Silent	SNP	ENST00000228887.1	37	CCDS8658.1																																																																																			G|0.739;A|0.261	0.261	strong		0.552	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1		
KCNJ15	3772	hgsc.bcm.edu	37	21	39671476	39671476	+	Missense_Mutation	SNP	G	G	A	rs2230033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:39671476G>A	ENST00000328656.4	+	4	596	c.293G>A	c.(292-294)gGt>gAt	p.G98D	KCNJ15_ENST00000398932.1_Missense_Mutation_p.G98D|KCNJ15_ENST00000398930.1_Missense_Mutation_p.G98D|KCNJ15_ENST00000398938.2_Missense_Mutation_p.G98D|KCNJ15_ENST00000398934.1_Missense_Mutation_p.G98D	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	98			G -> D (in dbSNP:rs2230033). {ECO:0000269|PubMed:8995301, ECO:0000269|Ref.3}.		potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	TTAGAACCCGGTGAGCCCATT	0.483													G|||	1446	0.288738	0.0363	0.4625	5008	,	,		20529	0.253		0.497	False		,,,				2504	0.3292				p.L98X		Atlas-SNP	.											KCNJ15,colon,carcinoma,+1,1	KCNJ15	43	1	0			c.T293A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY	533,3873	244.7+/-253.9	32,469,1702	118.0	117.0	117.0		293,293,293	4.2	0.0	21	dbSNP_98	117	4707,3893	606.8+/-395.1	1302,2103,895	yes	missense,missense,missense	KCNJ15	NM_002243.3,NM_170736.1,NM_170737.1	94,94,94	1334,2572,2597	AA,AG,GG		45.2674,12.0971,40.2891	benign,benign,benign	98/376,98/376,98/376	39671476	5240,7766	2203	4300	6503	SO:0001583	missense	3772	exon3			AACCCGGTGAGCC	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.293G>A	21.37:g.39671476G>A	ENSP00000331698:p.Gly98Asp	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	159	67	0.421384	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Nonsense_Mutation	SNP	ENST00000328656.4	37	CCDS13656.1	727	0.33287545787545786	25	0.0508130081300813	167	0.4613259668508287	159	0.27797202797202797	376	0.49604221635883905	G	0.011	-1.728508	0.00694	0.120971	0.547326	ENSG00000157551	ENST00000328656;ENST00000398928;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934;ENST00000398927;ENST00000419868	D;D;D;D;D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27	5.13	4.22	0.49857	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.593826	0.15252	U	0.272284	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B	0.23891	0.093	B	0.27380	0.079	T	0.42865	-0.9426	8	.	.	.	.	2.9987	0.06007	0.1131:0.1737:0.5343:0.1789	rs2230033;rs3746877;rs61521838;rs2230033	98	Q99712	IRK15_HUMAN	D	98	ENSP00000331698:G98D;ENSP00000381902:G98D;ENSP00000381911:G98D;ENSP00000381905:G98D;ENSP00000414487:G98D;ENSP00000381904:G98D;ENSP00000381907:G98D;ENSP00000381901:G98D;ENSP00000400849:G98D	.	G	+	2	0	KCNJ15	38593346	0.001000	0.12720	0.005000	0.12908	0.019000	0.09904	1.174000	0.31932	1.249000	0.43950	0.655000	0.94253	GGT	G|0.642;A|0.358	0.358	strong		0.483	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
RIOK2	55781	hgsc.bcm.edu	37	5	96513471	96513471	+	Missense_Mutation	SNP	G	G	C	rs2544773	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:96513471G>C	ENST00000283109.3	-	3	355	c.287C>G	c.(286-288)tCt>tGt	p.S96C	RNU1-73P_ENST00000383971.1_RNA|CTD-2215E18.1_ENST00000509481.1_Intron|RIOK2_ENST00000508447.1_Missense_Mutation_p.S96C	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	96			S -> C (in dbSNP:rs2544773). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		GTTTCCAACAGACTCAACTAC	0.388													G|||	1709	0.341254	0.0749	0.4308	5008	,	,		19950	0.4782		0.4095	False		,,,				2504	0.4264				p.S96C		Atlas-SNP	.											.	RIOK2	82	.	0			c.C287G						PASS	.	G	CYS/SER,CYS/SER	584,3822	258.0+/-262.2	45,494,1664	119.0	109.0	113.0		287,287	5.7	1.0	5	dbSNP_100	113	3418,5182	505.0+/-376.3	680,2058,1562	yes	missense,missense	RIOK2	NM_001159749.1,NM_018343.2	112,112	725,2552,3226	CC,CG,GG		39.7442,13.2547,30.7704	probably-damaging,probably-damaging	96/475,96/553	96513471	4002,9004	2203	4300	6503	SO:0001583	missense	55781	exon3			CCAACAGACTCAA	AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"""RIO kinase 2 (yeast)"""				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.287C>G	5.37:g.96513471G>C	ENSP00000283109:p.Ser96Cys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	141	58	0.411348	NM_001159749	D6RDI3|Q9NUT0	Missense_Mutation	SNP	ENST00000283109.3	37	CCDS4089.1	781	0.3576007326007326	56	0.11382113821138211	151	0.4171270718232044	254	0.44405594405594406	320	0.42216358839050133	G	26.9	4.785840	0.90282	0.132547	0.397442	ENSG00000058729	ENST00000283109;ENST00000508447	T;T	0.05717	3.49;3.4	5.7	5.7	0.88788	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.92317	3.295	0.09310	P	0.9999999999536962	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.971	T	0.36016	-0.9765	9	0.87932	D	0	-15.9783	19.4334	0.94781	0.0:0.0:1.0:0.0	rs2544773;rs52835076;rs2544773	96;96	D6RDI3;Q9BVS4	.;RIOK2_HUMAN	C	96	ENSP00000283109:S96C;ENSP00000420932:S96C	ENSP00000283109:S96C	S	-	2	0	RIOK2	96539227	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.230000	0.95299	2.683000	0.91414	0.650000	0.86243	TCT	G|0.673;C|0.327	0.327	strong		0.388	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343	
CYP4F11	57834	hgsc.bcm.edu	37	19	16025176	16025176	+	Missense_Mutation	SNP	C	C	T	rs1060463	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:16025176C>T	ENST00000402119.4	-	11	1762	c.1336G>A	c.(1336-1338)Gac>Aac	p.D446N	CYP4F11_ENST00000591841.1_Missense_Mutation_p.D121N|CYP4F11_ENST00000326742.8_Missense_Mutation_p.R424Q|CYP4F11_ENST00000248041.8_Missense_Mutation_p.D446N	NM_021187.3	NP_067010.3			cytochrome P450, family 4, subfamily F, polypeptide 11											NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						TTCTCTTGGTCGAAACGGAAG	0.582													.|||	2504	0.5	0.4735	0.5245	5008	,	,		17534	0.381		0.5835	False		,,,				2504	0.5552				p.D446N		Atlas-SNP	.											.	CYP4F11	83	.	0			c.G1336A						PASS	.	C	ASN/ASP,ASN/ASP	2038,2368		491,1056,656	147.0	147.0	147.0		1336,1336	0.7	0.5	19	dbSNP_86	147	5145,3455		1544,2057,699	yes	missense,missense	CYP4F11	NM_001128932.1,NM_021187.3	23,23	2035,3113,1355	TT,TC,CC		40.1744,46.2551,44.7716	possibly-damaging,possibly-damaging	446/525,446/525	16025176	7183,5823	2203	4300	6503	SO:0001583	missense	57834	exon12			CTTGGTCGAAACG	AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"""Cytochrome P450s"""	13265	protein-coding gene	gene with protein product		611517	"""cytochrome P450, subfamily IVF, polypeptide 11"""			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000402119.4:c.1336G>A	19.37:g.16025176C>T	ENSP00000384588:p.Asp446Asn	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	172	86	0.5	NM_001128932		Missense_Mutation	SNP	ENST00000402119.4	37	CCDS12337.1	1105|1105	0.5059523809523809|0.5059523809523809	254|254	0.516260162601626|0.516260162601626	181|181	0.5|0.5	212|212	0.3706293706293706|0.3706293706293706	458|458	0.604221635883905|0.604221635883905	N|N	0.879|0.879	-0.729481|-0.729481	0.03135|0.03135	0.462551|0.462551	0.598256|0.598256	ENSG00000171903|ENSG00000171903	ENST00000402119;ENST00000248041|ENST00000326742	T;T|T	0.68624|0.59906	-0.34;-0.34|0.23	2.93|2.93	0.696|0.696	0.18075|0.18075	.|.	0.145456|.	0.42821|.	U|.	0.000641|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.27053|0.27053	0.805|0.805	0.28533|0.28533	P|P	0.9124901|0.9124901	B|P	0.30021|0.45531	0.265|0.86	B|B	0.33890|0.38428	0.172|0.273	T|T	0.46775|0.46775	-0.9167|-0.9167	9|8	0.52906|0.87932	T|D	0.07|0	.|.	7.3839|7.3839	0.26872|0.26872	0.1684:0.7228:0.0:0.1088|0.1684:0.7228:0.0:0.1088	rs1060463;rs3201353;rs52825646;rs60995218;rs1060463|rs1060463;rs3201353;rs52825646;rs60995218;rs1060463	446|424	Q9HBI6|F8W978	CP4FB_HUMAN|.	N|Q	446|424	ENSP00000384588:D446N;ENSP00000248041:D446N|ENSP00000319859:R424Q	ENSP00000248041:D446N|ENSP00000319859:R424Q	D|R	-|-	1|2	0|0	CYP4F11|CYP4F11	15886176|15886176	0.433000|0.433000	0.25562|0.25562	0.530000|0.530000	0.27963|0.27963	0.001000|0.001000	0.01503|0.01503	0.916000|0.916000	0.28651|0.28651	-0.168000|-0.168000	0.10853|0.10853	-2.048000|-2.048000	0.00412|0.00412	GAC|CGA	C|0.473;T|0.527	0.527	strong		0.582	CYP4F11-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460385.2	NM_021187	
HOXB1	3211	hgsc.bcm.edu	37	17	46607817	46607817	+	Silent	SNP	C	C	T	rs7207109	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46607817C>T	ENST00000239174.6	-	1	542	c.450G>A	c.(448-450)gcG>gcA	p.A150A	HOXB1_ENST00000577092.1_Silent_p.A150A	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	150					anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GTGCAAAGCTCGCGGTCTGCT	0.637													C|||	660	0.131789	0.1082	0.1225	5008	,	,		16178	0.0972		0.2048	False		,,,				2504	0.1309				p.A150A		Atlas-SNP	.											.	HOXB1	67	.	0			c.G450A						PASS	.	C		547,3859	248.1+/-256.1	32,483,1688	64.0	65.0	65.0		450	-4.2	0.0	17	dbSNP_116	65	1786,6814	321.2+/-315.0	184,1418,2698	no	coding-synonymous	HOXB1	NM_002144.3		216,1901,4386	TT,TC,CC		20.7674,12.4149,17.9379		150/302	46607817	2333,10673	2203	4300	6503	SO:0001819	synonymous_variant	3211	exon1			AAAGCTCGCGGTC		CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.450G>A	17.37:g.46607817C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_002144	Q4VB03	Silent	SNP	ENST00000239174.6	37	CCDS32675.1																																																																																			C|0.838;T|0.162	0.162	strong		0.637	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
ASTN2	23245	hgsc.bcm.edu	37	9	119770480	119770480	+	Silent	SNP	C	C	T	rs3761845	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:119770480C>T	ENST00000313400.4	-	7	1582	c.1482G>A	c.(1480-1482)ccG>ccA	p.P494P	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Silent_p.P494P|ASTN2_ENST00000361209.2_Silent_p.P443P			O75129	ASTN2_HUMAN	astrotactin 2	494					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						AAAGCTTGGCCGGGTTTAACC	0.527													C|||	2453	0.489816	0.1377	0.7075	5008	,	,		20120	0.748		0.5656	False		,,,				2504	0.4673				p.P443P		Atlas-SNP	.											.	ASTN2	307	.	0			c.G1329A						PASS	.	C		866,3540	337.3+/-304.8	95,676,1432	116.0	99.0	105.0		1329	-10.9	0.3	9	dbSNP_107	105	4773,3827	612.5+/-396.0	1348,2077,875	no	coding-synonymous	ASTN2	NM_014010.4		1443,2753,2307	TT,TC,CC		44.5,19.655,43.3569		443/1289	119770480	5639,7367	2203	4300	6503	SO:0001819	synonymous_variant	23245	exon6			CTTGGCCGGGTTT	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1482G>A	9.37:g.119770480C>T		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	226	224	0.99115	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37																																																																																				C|0.527;N|0.000	.	strong		0.527	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
AMT	275	hgsc.bcm.edu	37	3	49455330	49455330	+	Silent	SNP	C	C	T	rs11715915	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49455330C>T	ENST00000273588.3	-	8	1256	c.954G>A	c.(952-954)cgG>cgA	p.R318R	AMT_ENST00000538581.1_Silent_p.R262R|AMT_ENST00000395338.2_Silent_p.R318R|AMT_ENST00000458307.2_Silent_p.R274R|AMT_ENST00000546031.1_Silent_p.R221R|AMT_ENST00000476226.1_5'UTR	NM_000481.3	NP_000472.2	P48728	GCST_HUMAN	aminomethyltransferase	318					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|transaminase activity (GO:0008483)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Tetrahydrofolic acid(DB00116)	CCACACGCCTCCGCTGCACCC	0.602													C|||	1008	0.201278	0.2126	0.17	5008	,	,		18422	0.0734		0.336	False		,,,				2504	0.2014				p.R318R		Atlas-SNP	.											.	AMT	22	.	0			c.G954A						PASS	.	C	,,,	1061,3345	382.3+/-324.4	127,807,1269	43.0	43.0	43.0		954,822,786,954	2.7	1.0	3	dbSNP_120	43	2697,5903	427.7+/-355.7	449,1799,2052	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMT	NM_000481.3,NM_001164710.1,NM_001164711.1,NM_001164712.1	,,,	576,2606,3321	TT,TC,CC		31.3605,24.0808,28.8944	,,,	318/404,274/360,262/348,318/387	49455330	3758,9248	2203	4300	6503	SO:0001819	synonymous_variant	275	exon8			ACGCCTCCGCTGC	D13811	CCDS2797.1, CCDS54583.1, CCDS54584.1, CCDS54585.1	3p21.2-p21.1	2014-09-17	2006-05-22		ENSG00000145020	ENSG00000145020	2.1.2.10		473	protein-coding gene	gene with protein product	"""glycine cleavage system protein T"""	238310	"""aminomethyltransferase (glycine cleavage system protein T)"""			1993704, 8188235	Standard	NM_000481		Approved	GCST, NKH	uc003cww.3	P48728	OTTHUMG00000156847	ENST00000273588.3:c.954G>A	3.37:g.49455330C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_001164712	A8K3I5|B4DE61|B4DJQ0|E9PBG1|Q96IG6	Silent	SNP	ENST00000273588.3	37	CCDS2797.1	513	0.2348901098901099	123	0.25	81	0.22375690607734808	51	0.08916083916083917	258	0.3403693931398417	C	9.326	1.059402	0.19987	0.240808	0.313605	ENSG00000145020	ENST00000427987	.	.	.	4.77	2.73	0.32206	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999197068	.	.	.	.	.	.	T	0.39143	-0.9628	3	.	.	.	-7.9714	6.953	0.24556	0.2441:0.6572:0.0:0.0987	rs11715915;rs11715915	.	.	.	K	316	.	.	E	-	1	0	AMT	49430334	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	0.849000	0.27723	1.011000	0.39340	0.462000	0.41574	GAG	C|0.736;T|0.264	0.264	strong		0.602	AMT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346216.2	NM_000481	
MUC4	4585	hgsc.bcm.edu	37	3	195515003	195515003	+	Missense_Mutation	SNP	T	T	C	rs76196931	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515003T>C	ENST00000463781.3	-	2	3907	c.3448A>G	c.(3448-3450)Acc>Gcc	p.T1150A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1150A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	624					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T1150A(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGTGTGACCTGTG	0.567													.|||	585	0.116813	0.0363	0.1023	5008	,	,		12213	0.2054		0.1352	False		,,,				2504	0.1258				p.T1150A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	endometrium(1)	c.A3448G						scavenged	.						12.0	6.0	8.0					3																	195515003		680	1518	2198	SO:0001583	missense	4585	exon2			GGGTGGTGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3448A>G	3.37:g.195515003T>C	ENSP00000417498:p.Thr1150Ala	Somatic	424	8	0.0188679		WXS	Illumina HiSeq	Phase_I	92	87	0.945652	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	649	0.29716117216117216	49	0.09959349593495935	108	0.2983425414364641	260	0.45454545454545453	232	0.30606860158311344	-	4.336	0.061717	0.08339	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.54;1.53	0.814	0.814	0.18756	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.31837	0.342	B	0.20384	0.029	T	0.48768	-0.9006	7	.	.	.	.	5.9543	0.19265	0.0:0.0:0.0:1.0	.	1150	E7ESK3	.	A	1150	ENSP00000417498:T1150A;ENSP00000420243:T1150A	.	T	-	1	0	MUC4	196999398	0.000000	0.05858	0.002000	0.10522	0.033000	0.12548	-0.827000	0.04424	0.647000	0.30713	0.055000	0.15244	ACC	T|0.702;C|0.298	0.298	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HSP90AB1	3326	hgsc.bcm.edu	37	6	44221265	44221265	+	Missense_Mutation	SNP	C	C	A	rs200104342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44221265C>A	ENST00000371554.1	+	12	2319	c.2105C>A	c.(2104-2106)gCt>gAt	p.A702D	SLC35B2_ENST00000495706.1_5'Flank|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000371646.5_Missense_Mutation_p.A702D|HSP90AB1_ENST00000353801.3_Missense_Mutation_p.A702D			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	702					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GAACCCAATGCTGCAGTTCCT	0.458											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A702D		Atlas-SNP	.											.	HSP90AB1	83	.	0			c.C2105A						PASS	.						75.0	76.0	76.0					6																	44221265		2203	4300	6503	SO:0001583	missense	3326	exon12			CCAATGCTGCAGT	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2105C>A	6.37:g.44221265C>A	ENSP00000360609:p.Ala702Asp	Somatic	122	0	0	922	WXS	Illumina HiSeq	Phase_I	173	17	0.0982659	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	ENST00000371554.1	37	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920870	0.52653	.	.	ENSG00000096384	ENST00000371646;ENST00000353801;ENST00000371554	T;T;T	0.09350	2.99;2.99;2.99	3.9	3.9	0.45041	.	0.750751	0.11539	U	0.553976	T	0.07188	0.0182	M	0.68593	2.085	0.51767	D	0.999931	B;B;B	0.10296	0.0;0.003;0.0	B;B;B	0.20577	0.03;0.013;0.005	T	0.05354	-1.0890	10	0.33940	T	0.23	-11.1759	12.1165	0.53868	0.0:0.9118:0.0:0.0882	.	664;692;702	B4DMA2;B4DGL0;P08238	.;.;HS90B_HUMAN	D	702	ENSP00000360709:A702D;ENSP00000325875:A702D;ENSP00000360609:A702D	ENSP00000325875:A702D	A	+	2	0	HSP90AB1	44329243	0.999000	0.42202	1.000000	0.80357	0.877000	0.50540	3.853000	0.55941	2.183000	0.69458	0.603000	0.83216	GCT	C|0.991;A|0.009	0.009	strong		0.458	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
SHFM1	7979	hgsc.bcm.edu	37	7	96339061	96339061	+	Silent	SNP	C	C	T	rs4733	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:96339061C>T	ENST00000248566.2	-	1	142	c.15G>A	c.(13-15)aaG>aaA	p.K5K	SHFM1_ENST00000413065.1_Silent_p.K5K|SHFM1_ENST00000444799.1_Silent_p.K5K|SHFM1_ENST00000417009.1_Silent_p.K5K	NM_006304.1	NP_006295.1	P60896	DSS1_HUMAN	split hand/foot malformation (ectrodactyly) type 1	5					double-strand break repair via homologous recombination (GO:0000724)	proteasome complex (GO:0000502)				breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_cancers(62;4.24e-09)|all_epithelial(64;5.59e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0353)|Lung NSC(181;0.0987)					CTACCGGCTGCTTTTTCTCTG	0.552								Homologous recombination					C|||	164	0.0327476	0.0469	0.0187	5008	,	,		17053	0.0149		0.0348	False		,,,				2504	0.0399				p.K5K		Atlas-SNP	.											.	SHFM1	12	.	0			c.G15A						PASS	.	C		194,4212	118.4+/-156.1	4,186,2013	125.0	133.0	130.0		15	2.4	1.0	7	dbSNP_52	130	287,8313	103.8+/-164.8	3,281,4016	no	coding-synonymous	SHFM1	NM_006304.1		7,467,6029	TT,TC,CC		3.3372,4.4031,3.6983		5/71	96339061	481,12525	2203	4300	6503	SO:0001819	synonymous_variant	7979	exon1			CGGCTGCTTTTTC	U41515	CCDS5646.1	7q21.3	2010-04-22			ENSG00000127922	ENSG00000127922			10845	protein-coding gene	gene with protein product	"""deleted in split-hand/foot 1"""	601285		SHFD1		1895319, 8733122	Standard	NM_006304		Approved	DSS1, Shfdg1, ECD, SEM1, SHSF1	uc003uoi.3	P60896	OTTHUMG00000150680	ENST00000248566.2:c.15G>A	7.37:g.96339061C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_006304	Q13437|Q61067	Silent	SNP	ENST00000248566.2	37	CCDS5646.1																																																																																			C|0.958;T|0.042	0.042	strong		0.552	SHFM1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319595.1	NM_006304	
BTN2A1	11120	hgsc.bcm.edu	37	6	26463574	26463574	+	Missense_Mutation	SNP	G	G	T	rs34505465|rs13195401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26463574G>T	ENST00000312541.5	+	4	781	c.533G>T	c.(532-534)tGg>tTg	p.W178L	BTN2A1_ENST00000469185.1_Missense_Mutation_p.W178L|BTN2A1_ENST00000541522.1_Missense_Mutation_p.W117L|BTN2A1_ENST00000429381.1_Missense_Mutation_p.W178L	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	178			W -> C (in dbSNP:rs13195402).|W -> L (in dbSNP:rs13195401).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						CTCACAGTGTGGAGGGACCCC	0.592													G|||	120	0.0239617	0.0227	0.0303	5008	,	,		17970	0.0		0.0686	False		,,,				2504	0.0				p.W178L		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G533T						PASS	.	G	LEU/TRP,LEU/TRP,LEU/TRP,LEU/TRP	137,4269	87.8+/-126.4	3,131,2069	82.0	77.0	79.0		350,533,533,533	2.0	0.4	6	dbSNP_121	79	689,7911	159.7+/-212.9	29,631,3640	no	missense,missense,missense,missense	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	61,61,61,61	32,762,5709	TT,TG,GG		8.0116,3.1094,6.3509	probably-damaging,probably-damaging,probably-damaging,probably-damaging	117/467,178/331,178/528,178/335	26463574	826,12180	2203	4300	6503	SO:0001583	missense	11120	exon4			CAGTGTGGAGGGA	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.533G>T	6.37:g.26463574G>T	ENSP00000312158:p.Trp178Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	61	0.027930402930402932	8	0.016260162601626018	10	0.027624309392265192	0	0.0	43	0.05672823218997362	G	12.77	2.038076	0.35989	0.031094	0.080116	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	2.88	2.0	0.26442	CD80-like, immunoglobulin C2-set (1);	0.000000	0.50627	D	0.000118	T	0.80248	0.4588	H	0.95950	3.745	0.32048	N	0.59732	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78086	-0.2341	10	0.87932	D	0	.	8.118	0.30955	0.1282:0.0:0.8718:0.0	rs13195401	178;178	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	L	178;117;178;178;178	ENSP00000312158:W178L;ENSP00000443909:W117L;ENSP00000416945:W178L;ENSP00000419043:W178L	ENSP00000265424:W178L	W	+	2	0	BTN2A1	26571553	1.000000	0.71417	0.362000	0.25862	0.137000	0.21094	3.741000	0.55090	0.764000	0.33197	0.561000	0.74099	TGG	.	.	alt		0.592	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
GCC2	9648	hgsc.bcm.edu	37	2	109106381	109106381	+	Silent	SNP	A	A	G	rs12104502	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:109106381A>G	ENST00000309863.6	+	18	4854	c.4140A>G	c.(4138-4140)caA>caG	p.Q1380Q		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	1380					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						CTGAACTTCAAACATTGCAGT	0.383													A|||	2286	0.45647	0.1679	0.5879	5008	,	,		17454	0.8899		0.3757	False		,,,				2504	0.3896				p.Q1380Q		Atlas-SNP	.											.	GCC2	129	.	0			c.A4140G						PASS	.	A		970,3436	362.6+/-316.2	101,768,1334	66.0	60.0	62.0		4140	-2.3	0.0	2	dbSNP_120	62	3495,5105	510.0+/-377.4	714,2067,1519	no	coding-synonymous	GCC2	NM_181453.3		815,2835,2853	GG,GA,AA		40.6395,22.0154,34.3303		1380/1685	109106381	4465,8541	2203	4300	6503	SO:0001819	synonymous_variant	9648	exon18			ACTTCAAACATTG	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.4140A>G	2.37:g.109106381A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	188	90	0.478723	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Silent	SNP	ENST00000309863.6	37	CCDS33268.1																																																																																			A|0.618;G|0.382	0.382	strong		0.383	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720540	135720540	+	Missense_Mutation	SNP	A	A	G	rs9814557	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:135720540A>G	ENST00000264977.3	+	2	817	c.200A>G	c.(199-201)gAt>gGt	p.D67G	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	67			D -> G (in dbSNP:rs9814557).|D -> N (in dbSNP:rs57374999).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAAGATGCAGATCTGAACTCT	0.488													A|||	713	0.142372	0.0567	0.1369	5008	,	,		20072	0.0268		0.2773	False		,,,				2504	0.2423				p.D67G		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A200G						PASS	.	A	,GLY/ASP	448,3958	214.5+/-233.7	22,404,1777	111.0	91.0	98.0		,200	3.3	0.5	3	dbSNP_119	98	2694,5906	431.6+/-356.9	412,1870,2018	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,94	434,2274,3795	GG,GA,AA		31.3256,10.168,24.1581	,benign	,67/1151	135720540	3142,9864	2203	4300	6503	SO:0001583	missense	5523	exon2			ATGCAGATCTGAA	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.200A>G	3.37:g.135720540A>G	ENSP00000264977:p.Asp67Gly	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	212	85	0.400943	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	299	0.13690476190476192	29	0.05894308943089431	56	0.15469613259668508	11	0.019230769230769232	203	0.2678100263852243	A	9.131	1.011458	0.19277	0.10168	0.313256	ENSG00000073711	ENST00000264977	T	0.14391	2.51	5.79	3.3	0.37823	.	0.350012	0.31461	N	0.007608	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	1.999999999946489E-6	B	0.23442	0.085	B	0.19666	0.026	T	0.41875	-0.9484	9	0.56958	D	0.05	.	8.4145	0.32664	0.7085:0.2165:0.0751:0.0	rs9814557;rs52807842;rs57498404;rs9814557	67	Q06190	P2R3A_HUMAN	G	67	ENSP00000264977:D67G	ENSP00000264977:D67G	D	+	2	0	PPP2R3A	137203230	1.000000	0.71417	0.534000	0.28014	0.980000	0.70556	3.716000	0.54904	1.032000	0.39892	0.523000	0.50628	GAT	A|0.801;G|0.199	0.199	strong		0.488	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
PDXDC1	23042	hgsc.bcm.edu	37	16	15129940	15129940	+	Silent	SNP	C	C	T	rs3198697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15129940C>T	ENST00000396410.4	+	23	2272	c.2175C>T	c.(2173-2175)caC>caT	p.H725H	PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000447912.2_Silent_p.H634H|PDXDC1_ENST00000569715.1_Silent_p.H698H|PDXDC1_ENST00000450288.2_Silent_p.H697H|PDXDC1_ENST00000563679.1_Silent_p.H743H|PDXDC1_ENST00000325823.7_Silent_p.H710H	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	725					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CAGTCAGTCACATTGAAGACT	0.567													C|||	813	0.16234	0.0227	0.2133	5008	,	,		18967	0.003		0.3976	False		,,,				2504	0.2372				p.H725H		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C2175T						PASS	.	C		378,4016	190.2+/-216.2	20,338,1839	138.0	134.0	135.0		2175	1.3	0.8	16	dbSNP_105	135	3603,4997	521.2+/-379.8	748,2107,1445	no	coding-synonymous	PDXDC1	NM_015027.2		768,2445,3284	TT,TC,CC		41.8953,8.6026,30.6372		725/789	15129940	3981,9013	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon23			CAGTCACATTGAA	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.2175C>T	16.37:g.15129940C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			C|0.746;T|0.254	0.254	strong		0.567	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
SKA3	221150	hgsc.bcm.edu	37	13	21750538	21750538	+	Nonsense_Mutation	SNP	G	G	A	rs61950356	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:21750538G>A	ENST00000314759.5	-	1	203	c.79C>T	c.(79-81)Cga>Tga	p.R27*	MRP63_ENST00000309594.4_5'Flank|SKA3_ENST00000400018.3_Nonsense_Mutation_p.R27*	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	27					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TCCAGCGCTCGCTGCAGCCGG	0.721																																					p.R27X		Atlas-SNP	.											.	SKA3	76	.	0			c.C79T						PASS	.	G	stop/ARG,,stop/ARG	131,4131		1,129,2001	7.0	8.0	7.0		79,,79	4.8	1.0	13	dbSNP_129	7	771,7687		2,767,3460	no	stop-gained,utr-5,stop-gained	MRP63,SKA3	NM_001166017.1,NM_024026.4,NM_145061.5	,,	3,896,5461	AA,AG,GG		9.1156,3.0737,7.0912	,,	27/389,,27/413	21750538	902,11818	2131	4229	6360	SO:0001587	stop_gained	221150	exon1			GCGCTCGCTGCAG	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.79C>T	13.37:g.21750538G>A	ENSP00000319417:p.Arg27*	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Nonsense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	273	0.125	17	0.034552845528455285	50	0.13812154696132597	116	0.20279720279720279	90	0.11873350923482849	G	39	7.647652	0.98409	0.030737	0.091156	ENSG00000165480	ENST00000314759;ENST00000400018	.	.	.	5.68	4.83	0.62350	.	0.260691	0.32231	N	0.006397	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.4477	13.3101	0.60376	0.0:0.0:0.8422:0.1578	rs61950356	.	.	.	X	27	.	ENSP00000298260:R27X	R	-	1	2	SKA3	20648538	0.997000	0.39634	0.997000	0.53966	0.803000	0.45373	2.774000	0.47694	1.372000	0.46190	0.591000	0.81541	CGA	G|0.877;A|0.123	0.123	strong		0.721	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
COG2	22796	hgsc.bcm.edu	37	1	230810858	230810858	+	Silent	SNP	T	T	C	rs113173809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:230810858T>C	ENST00000366669.4	+	9	1129	c.1014T>C	c.(1012-1014)gaT>gaC	p.D338D	COG2_ENST00000366668.3_Silent_p.D338D|COG2_ENST00000534989.1_Silent_p.D279D|COG2_ENST00000535166.1_Silent_p.D222D	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	338					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GGAATCCCGATGCATTTCATG	0.418													T|||	6	0.00119808	0.0	0.0014	5008	,	,		14495	0.0		0.002	False		,,,				2504	0.0031				p.D338D		Atlas-SNP	.											.	COG2	61	.	0			c.T1014C						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	103.0	104.0	103.0		1014,1014	-0.5	0.2	1	dbSNP_132	103	48,8552	31.2+/-83.2	0,48,4252	no	coding-synonymous,coding-synonymous	COG2	NM_001145036.1,NM_007357.2	,	0,52,6451	CC,CT,TT		0.5581,0.0908,0.3998	,	338/738,338/739	230810858	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	22796	exon9			TCCCGATGCATTT	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.1014T>C	1.37:g.230810858T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	184	95	0.516304	NM_007357	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																			T|0.997;C|0.003	0.003	strong		0.418	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
ARFGEF1	10565	hgsc.bcm.edu	37	8	68130265	68130265	+	Missense_Mutation	SNP	C	C	A	rs142342517	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:68130265C>A	ENST00000262215.3	-	31	4836	c.4447G>T	c.(4447-4449)Gct>Tct	p.A1483S	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.A937S|ARFGEF1_ENST00000518230.1_Missense_Mutation_p.A321S	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1483					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TAGAGCTGAGCAAAAATGTCA	0.373													C|||	8	0.00159744	0.0	0.0014	5008	,	,		11866	0.0		0.007	False		,,,				2504	0.0				p.A1483S		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.G4447T						PASS	.	C	SER/ALA	8,4398	12.9+/-30.5	0,8,2195	108.0	96.0	100.0		4447	4.6	1.0	8	dbSNP_134	100	79,8521	46.3+/-105.2	0,79,4221	yes	missense	ARFGEF1	NM_006421.4	99	0,87,6416	AA,AC,CC		0.9186,0.1816,0.6689	benign	1483/1850	68130265	87,12919	2203	4300	6503	SO:0001583	missense	10565	exon31			GCTGAGCAAAAAT	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.4447G>T	8.37:g.68130265C>A	ENSP00000262215:p.Ala1483Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	10.81	1.455699	0.26161	0.001816	0.009186	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518230	T;T;T	0.63913	0.07;-0.07;-0.03	5.48	4.59	0.56863	Armadillo-like helical (1);Armadillo-type fold (1);	0.052243	0.85682	D	0.000000	T	0.39784	0.1091	N	0.25890	0.77	0.44254	D	0.997101	B;B;B	0.12013	0.005;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.002	T	0.34700	-0.9818	10	0.11182	T	0.66	.	15.9776	0.80083	0.136:0.864:0.0:0.0	.	1483;961;937	Q9Y6D6;Q59FY5;E5RIF2	BIG1_HUMAN;.;.	S	937;1483;321	ENSP00000428429:A937S;ENSP00000262215:A1483S;ENSP00000430891:A321S	ENSP00000262215:A1483S	A	-	1	0	ARFGEF1	68292819	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.366000	0.44204	1.427000	0.47276	0.655000	0.94253	GCT	C|0.995;A|0.005	0.005	strong		0.373	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
ALCAM	214	hgsc.bcm.edu	37	3	105260520	105260520	+	Missense_Mutation	SNP	C	C	T	rs1044243	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:105260520C>T	ENST00000306107.5	+	8	1402	c.902C>T	c.(901-903)aCg>aTg	p.T301M	ALCAM_ENST00000481337.1_3'UTR|ALCAM_ENST00000472644.2_Missense_Mutation_p.T301M|ALCAM_ENST00000486979.2_Missense_Mutation_p.T250M|ALCAM_ENST00000389927.4_Intron	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	301	Ig-like C2-type 1.		T -> M (in dbSNP:rs1044243). {ECO:0000269|PubMed:7760007}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TACACACTGACGGATGTGAGG	0.423													C|||	261	0.0521166	0.0091	0.049	5008	,	,		19991	0.0466		0.1074	False		,,,				2504	0.0613				p.T301M		Atlas-SNP	.											.	ALCAM	71	.	0			c.C902T						PASS	.	C	MET/THR	125,4281	92.0+/-130.7	3,119,2081	164.0	132.0	143.0		902	5.3	1.0	3	dbSNP_86	143	1012,7588	216.4+/-255.5	67,878,3355	no	missense	ALCAM	NM_001627.3	81	70,997,5436	TT,TC,CC		11.7674,2.837,8.7421	probably-damaging	301/584	105260520	1137,11869	2203	4300	6503	SO:0001583	missense	214	exon8			CACTGACGGATGT	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.902C>T	3.37:g.105260520C>T	ENSP00000305988:p.Thr301Met	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Missense_Mutation	SNP	ENST00000306107.5	37	CCDS33810.1	133	0.060897435897435896	4	0.008130081300813009	23	0.06353591160220995	26	0.045454545454545456	80	0.10554089709762533	C	15.03	2.711023	0.48517	0.02837	0.117674	ENSG00000170017	ENST00000306107;ENST00000472644;ENST00000486979	T;T;T	0.12879	2.64;2.64;2.64	6.17	5.3	0.74995	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.286912	0.43747	D	0.000532	T	0.00210	0.0006	L	0.59912	1.85	0.09310	P	0.9999999999999829	B;B	0.27951	0.195;0.195	B;B	0.24541	0.054;0.054	T	0.02933	-1.1092	9	0.59425	D	0.04	-3.6835	12.1962	0.54298	0.0:0.8715:0.0:0.1285	rs1044243;rs17189213;rs1044243	301;301	B4DTU0;Q13740	.;CD166_HUMAN	M	301;301;250	ENSP00000305988:T301M;ENSP00000419236:T301M;ENSP00000418213:T250M	ENSP00000305988:T301M	T	+	2	0	ALCAM	106743210	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.804000	0.47931	2.941000	0.99782	0.655000	0.94253	ACG	C|0.920;T|0.080	0.080	strong		0.423	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
TTC3	7267	hgsc.bcm.edu	37	21	38538736	38538736	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:38538736T>G	ENST00000399017.2	+	33	6967	c.4220T>G	c.(4219-4221)cTt>cGt	p.L1407R	TTC3_ENST00000355666.1_Missense_Mutation_p.L1407R|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.L1407R	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1407					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				ACACAGATCCTTGAGGGCTCT	0.438																																					p.L1407R	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.T4220G						PASS	.						121.0	114.0	117.0					21																	38538736		2203	4300	6503	SO:0001583	missense	7267	exon33			AGATCCTTGAGGG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.4220T>G	21.37:g.38538736T>G	ENSP00000381981:p.Leu1407Arg	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	193	90	0.466321	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	T	9.860	1.196029	0.22037	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.08807	3.05;3.05;3.05	4.85	-5.58	0.02512	.	1.732930	0.03051	N	0.154594	T	0.06690	0.0171	L	0.51422	1.61	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.09377	0.004;0.003	T	0.37454	-0.9705	9	.	.	.	0.1757	0.2964	0.00266	0.2464:0.163:0.2518:0.3389	.	465;1407	Q5GIT6;P53804	.;TTC3_HUMAN	R	1407	ENSP00000347889:L1407R;ENSP00000381981:L1407R;ENSP00000346791:L1407R	.	L	+	2	0	TTC3	37460606	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.249000	0.02888	-0.672000	0.05266	-0.290000	0.09829	CTT	.	.	none		0.438	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118364967	118364967	+	Missense_Mutation	SNP	G	G	C	rs2305204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:118364967G>C	ENST00000528052.1	+	12	1313	c.1242G>C	c.(1240-1242)gaG>gaC	p.E414D	PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.E414D|PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.E414D			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	414	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.		E -> D (in dbSNP:rs2305204). {ECO:0000269|PubMed:15489334}.		lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		GAACAATTGAGAAAGTCAAGT	0.423													-|||	628	0.125399	0.0091	0.0576	5008	,	,		18441	0.4107		0.0567	False		,,,				2504	0.1074				p.E414D		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.G1242C						PASS	.		ASP/GLU	83,4323		1,81,2121	138.0	137.0	138.0		1242	4.6	1.0	10	dbSNP_100	138	590,8010		20,550,3730	yes	missense	PNLIPRP1	NM_006229.2	45	21,631,5851	CC,CG,GG		6.8605,1.8838,5.1745	benign	414/468	118364967	673,12333	2203	4300	6503	SO:0001583	missense	5407	exon12			AATTGAGAAAGTC	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.1242G>C	10.37:g.118364967G>C	ENSP00000433933:p.Glu414Asp	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	37	CCDS7595.1	306	0.1401098901098901	9	0.018292682926829267	18	0.049723756906077346	241	0.42132867132867136	38	0.05013192612137203	-	11.16	1.556195	0.27827	0.018838	0.068605	ENSG00000187021	ENST00000358834;ENST00000528052;ENST00000534537	T;T;T	0.64803	-0.12;-0.12;-0.12	5.53	4.63	0.57726	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.406518	0.25288	N	0.031749	T	0.00012	0.0000	L	0.41632	1.29	0.09310	P	0.999999999708388	B	0.02656	0.0	B	0.04013	0.001	T	0.39583	-0.9607	9	0.15499	T	0.54	-15.4607	7.0954	0.25307	0.0818:0.0:0.649:0.2692	rs2305204;rs17848308;rs17855511;rs52801749;rs2305204	414	P54315	LIPR1_HUMAN	D	414	ENSP00000351695:E414D;ENSP00000433933:E414D;ENSP00000434159:E414D	ENSP00000351695:E414D	E	+	3	2	PNLIPRP1	118354957	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.781000	0.26774	1.331000	0.45412	0.550000	0.68814	GAG	G|0.919;C|0.081	0.081	strong		0.423	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229	
COL1A2	1278	hgsc.bcm.edu	37	7	94041937	94041937	+	Silent	SNP	A	A	C	rs412777	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:94041937A>C	ENST00000297268.6	+	25	1917	c.1446A>C	c.(1444-1446)ccA>ccC	p.P482P		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	482					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CAATTGGCCCAGCTGGAGCAA	0.517										HNSCC(75;0.22)			A|||	1639	0.327276	0.3396	0.2882	5008	,	,		17908	0.3085		0.3837	False		,,,				2504	0.2996				p.P482P		Atlas-SNP	.											COL1A2,caecum,carcinoma,0,1	COL1A2	240	1	0			c.A1446C						PASS	.	A		1508,2898	478.5+/-358.2	254,1000,949	51.0	50.0	50.0		1446	-5.1	1.0	7	dbSNP_80	50	3188,5412	479.0+/-370.0	591,2006,1703	no	coding-synonymous	COL1A2	NM_000089.3		845,3006,2652	CC,CA,AA		37.0698,34.2261,36.1064		482/1367	94041937	4696,8310	2203	4300	6503	SO:0001819	synonymous_variant	1278	exon25			TGGCCCAGCTGGA	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1446A>C	7.37:g.94041937A>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	28	0.383562	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	37	CCDS34682.1																																																																																			A|0.642;C|0.358	0.358	strong		0.517	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
PCCA	5095	hgsc.bcm.edu	37	13	100888122	100888122	+	Silent	SNP	A	A	G	rs538229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:100888122A>G	ENST00000376285.1	+	8	665	c.627A>G	c.(625-627)gcA>gcG	p.A209A	PCCA_ENST00000376279.3_Silent_p.A209A|PCCA_ENST00000376286.4_Silent_p.A183A	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	209	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	TCAGAATTGCAAGGGAAATTG	0.388													A|||	516	0.103035	0.0885	0.1455	5008	,	,		19089	0.0159		0.174	False		,,,				2504	0.1094				p.A209A		Atlas-SNP	.											PCCA,colon,carcinoma,+2,1	PCCA	59	1	0			c.A627G						PASS	.	A	,,	493,3913	231.4+/-245.2	26,441,1736	158.0	135.0	143.0		627,549,627	4.3	1.0	13	dbSNP_83	143	1478,7122	281.0+/-294.8	133,1212,2955	no	coding-synonymous,coding-synonymous,coding-synonymous	PCCA	NM_000282.3,NM_001127692.2,NM_001178004.1	,,	159,1653,4691	GG,GA,AA		17.186,11.1893,15.1545	,,	209/729,183/703,209/682	100888122	1971,11035	2203	4300	6503	SO:0001819	synonymous_variant	5095	exon8			AATTGCAAGGGAA	X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"""propionyl Coenzyme A carboxylase, alpha polypeptide"""			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.627A>G	13.37:g.100888122A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	134	69	0.514925	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Silent	SNP	ENST00000376285.1	37	CCDS9496.2																																																																																			A|0.862;G|0.138	0.138	strong		0.388	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2		
SLC25A32	81034	hgsc.bcm.edu	37	8	104417045	104417045	+	Missense_Mutation	SNP	C	C	T	rs17803441	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:104417045C>T	ENST00000297578.4	-	3	516	c.350G>A	c.(349-351)cGt>cAt	p.R117H	SLC25A32_ENST00000523701.1_5'Flank|SLC25A32_ENST00000543107.1_Intron	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32	117			R -> H (in dbSNP:rs17803441). {ECO:0000269|PubMed:10978331}.		folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TGCCTCTAAACGTTCAGCTCT	0.343													C|||	124	0.0247604	0.0098	0.0447	5008	,	,		20061	0.005		0.0616	False		,,,				2504	0.0133				p.R117H		Atlas-SNP	.											.	SLC25A32	36	.	0			c.G350A						PASS	.	C	HIS/ARG	106,4300	82.4+/-120.9	4,98,2101	150.0	121.0	131.0		350	-2.2	0.1	8	dbSNP_123	131	676,7924	169.3+/-220.7	30,616,3654	yes	missense	SLC25A32	NM_030780.3	29	34,714,5755	TT,TC,CC		7.8605,2.4058,6.0126	possibly-damaging	117/316	104417045	782,12224	2203	4300	6503	SO:0001583	missense	81034	exon3			TCTAAACGTTCAG	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.350G>A	8.37:g.104417045C>T	ENSP00000297578:p.Arg117His	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	120	46	0.383333	NM_030780	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	CCDS6300.1	70	0.03205128205128205	4	0.008130081300813009	17	0.04696132596685083	0	0.0	49	0.06464379947229551	C	15.49	2.849539	0.51270	0.024058	0.078605	ENSG00000164933	ENST00000297578;ENST00000424899	T	0.78246	-1.16	6.06	-2.19	0.07015	Mitochondrial carrier domain (2);	0.592881	0.18862	N	0.129107	T	0.05731	0.0150	N	0.12569	0.235	0.09310	N	1	B	0.22746	0.074	B	0.26202	0.067	T	0.14980	-1.0453	10	0.45353	T	0.12	-19.4225	7.3207	0.26526	0.0:0.3715:0.116:0.5126	rs17803441;rs52813171;rs17803441	117	Q9H2D1	MFTC_HUMAN	H	117;101	ENSP00000297578:R117H	ENSP00000297578:R117H	R	-	2	0	SLC25A32	104486221	0.015000	0.18098	0.069000	0.20011	0.979000	0.70002	0.059000	0.14322	-0.161000	0.10983	0.655000	0.94253	CGT	C|0.952;T|0.048	0.048	strong		0.343	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
TMEM8A	58986	hgsc.bcm.edu	37	16	427516	427516	+	Silent	SNP	T	T	C	rs11649031	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:427516T>C	ENST00000431232.2	-	3	529	c.369A>G	c.(367-369)gtA>gtG	p.V123V	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	123					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						AGGAGGGCTGTACCGCGGTGT	0.692											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2859	0.570887	0.736	0.4885	5008	,	,		15299	0.3036		0.5437	False		,,,				2504	0.7096				p.V123V		Atlas-SNP	.											TMEM8A,colon,carcinoma,0,2	TMEM8A	49	2	0			c.A369G						PASS	.	C		3129,1243		1125,879,182	19.0	19.0	19.0		369	-0.5	0.0	16	dbSNP_120	19	4870,3712		1419,2032,840	no	coding-synonymous	TMEM8A	NM_021259.2		2544,2911,1022	CC,CT,TT		43.2533,28.4309,38.2507		123/772	427516	7999,4955	2186	4291	6477	SO:0001819	synonymous_variant	58986	exon3			GGGCTGTACCGCG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.369A>G	16.37:g.427516T>C		Somatic	123	0	0	588	WXS	Illumina HiSeq	Phase_I	62	62	1	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			T|0.429;C|0.571	0.571	strong		0.692	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
HOOK2	29911	hgsc.bcm.edu	37	19	12876964	12876964	+	Missense_Mutation	SNP	G	G	C	rs897804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12876964G>C	ENST00000397668.3	-	15	1537	c.1464C>G	c.(1462-1464)caC>caG	p.H488Q	HOOK2_ENST00000264827.5_Missense_Mutation_p.H488Q|HOOK2_ENST00000589965.1_Intron	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	488	Sufficient for interaction with microtubules.		H -> Q (in dbSNP:rs897804). {ECO:0000269|PubMed:15489334}.		early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						CATCCTCCAGGTGGCGCTGCA	0.706											OREG0025273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1086	0.216853	0.0325	0.2939	5008	,	,		12044	0.2321		0.4394	False		,,,				2504	0.1667				p.H488Q		Atlas-SNP	.											HOOK2,NS,carcinoma,0,1	HOOK2	73	1	0			c.C1464G						scavenged	.	G	GLN/HIS,GLN/HIS	323,3541		20,283,1629	10.0	13.0	12.0		1464,1464	3.7	1.0	19	dbSNP_87	12	3246,5000		672,1902,1549	no	missense,missense	HOOK2	NM_001100176.1,NM_013312.2	24,24	692,2185,3178	CC,CG,GG		39.3645,8.3592,29.4715	benign,benign	488/718,488/720	12876964	3569,8541	1932	4123	6055	SO:0001583	missense	29911	exon15			CTCCAGGTGGCGC	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"""hook homolog 2 (Drosophila)"""			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.1464C>G	19.37:g.12876964G>C	ENSP00000380785:p.His488Gln	Somatic	46	0	0	683	WXS	Illumina HiSeq	Phase_I	10	3	0.3	NM_001100176	O60562	Missense_Mutation	SNP	ENST00000397668.3	37	CCDS42508.1	599	0.2742673992673993	19	0.03861788617886179	120	0.3314917127071823	121	0.21153846153846154	339	0.4472295514511873	G	13.50	2.255926	0.39896	0.083592	0.393645	ENSG00000095066	ENST00000397668;ENST00000264827	T;T	0.15718	2.4;2.4	4.77	3.69	0.42338	.	0.449885	0.22723	N	0.056436	T	0.00012	0.0000	N	0.04959	-0.14	0.32618	P	0.5237350000000001	B;B	0.15473	0.01;0.013	B;B	0.14023	0.006;0.01	T	0.47935	-0.9078	9	0.20046	T	0.44	-30.7248	6.3	0.21107	0.1135:0.3067:0.5798:0.0	rs897804;rs17850914;rs897804	488;488	Q96ED9-2;Q96ED9	.;HOOK2_HUMAN	Q	488	ENSP00000380785:H488Q;ENSP00000264827:H488Q	ENSP00000264827:H488Q	H	-	3	2	HOOK2	12737964	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.363000	0.34159	2.174000	0.68829	0.467000	0.42956	CAC	G|0.729;C|0.271	0.271	strong		0.706	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312	
FUS	2521	hgsc.bcm.edu	37	16	31193942	31193942	+	Silent	SNP	C	C	A	rs741810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31193942C>A	ENST00000254108.7	+	3	252	c.147C>A	c.(145-147)ggC>ggA	p.G49G	FUS_ENST00000568685.1_Silent_p.G49G|FUS_ENST00000380244.3_Silent_p.G49G|RP11-388M20.6_ENST00000564743.1_RNA	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	49	Gln/Gly/Ser/Tyr-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		ACACTTCAGGCTATGGCCAGA	0.532			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""								C|||	1397	0.278954	0.028	0.3617	5008	,	,		19513	0.253		0.3062	False		,,,				2504	0.5583				p.G49G		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	FUS,caecum,carcinoma,0,1	FUS	52	1	0			c.C147A						PASS	.	C	,,	321,4073	169.4+/-200.1	16,289,1892	101.0	95.0	97.0		147,147,147	4.1	1.0	16	dbSNP_86	97	2495,6105	410.1+/-350.0	357,1781,2162	no	coding-synonymous,coding-synonymous,coding-synonymous	FUS	NM_001170634.1,NM_001170937.1,NM_004960.3	,,	373,2070,4054	AA,AC,CC		29.0116,7.3054,21.6715	,,	49/526,49/523,49/527	31193942	2816,10178	2197	4300	6497	SO:0001819	synonymous_variant	2521	exon3			TTCAGGCTATGGC	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.147C>A	16.37:g.31193942C>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	202	119	0.589109	NM_001170634	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																			C|0.783;A|0.217	0.217	strong		0.532	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
PRR5	55615	hgsc.bcm.edu	37	22	45132853	45132853	+	Missense_Mutation	SNP	C	C	T	rs187629442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45132853C>T	ENST00000336985.6	+	8	1170	c.893C>T	c.(892-894)cCg>cTg	p.P298L	ARHGAP8_ENST00000517296.3_Intron|PRR5-ARHGAP8_ENST00000361473.5_Intron|ARHGAP8_ENST00000389773.5_Intron|PRR5_ENST00000477331.1_3'UTR|PRR5_ENST00000006251.7_Missense_Mutation_p.P289L|PRR5_ENST00000403581.1_Missense_Mutation_p.P321L|PRR5-ARHGAP8_ENST00000352766.7_Intron	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	298					cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		TTCTCCGACCCGCCCGGCCAG	0.741													C|||	19	0.00379393	0.0008	0.0086	5008	,	,		12627	0.0		0.0099	False		,,,				2504	0.002				p.P321L		Atlas-SNP	.											.	PRR5	75	.	0			c.C962T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,	7,4311		0,7,2152	10.0	12.0	11.0		866,608,608,962,866,893,	0.9	0.0	22		11	91,8381		0,91,4145	yes	missense,missense,missense,missense,missense,missense,intron	PRR5,PRR5-ARHGAP8	NM_001017528.2,NM_001017529.2,NM_001017530.1,NM_001198721.1,NM_015366.3,NM_181333.3,NM_181334.4	98,98,98,98,98,98,	0,98,6297	TT,TC,CC		1.0741,0.1621,0.7662	,,,,,,	289/380,203/294,203/294,321/412,289/380,298/389,	45132853	98,12692	2159	4236	6395	SO:0001583	missense	55615	exon10			CCGACCCGCCCGG	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"""protein observed with Rictor-1"""	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000336985.6:c.893C>T	22.37:g.45132853C>T	ENSP00000337464:p.Pro298Leu	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000336985.6	37	CCDS14058.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	C|C	4.489|4.489	0.090760|0.090760	0.08632|0.08632	0.001621|0.001621	0.010741|0.010741	ENSG00000186654|ENSG00000186654	ENST00000006251;ENST00000404016;ENST00000403581;ENST00000336985|ENST00000455389	T;T;T|.	0.27557|.	1.68;1.66;1.68|.	4.27|4.27	0.846|0.846	0.18955|0.18955	.|.	.|.	.|.	.|.	.|.	T|T	0.03095|0.03095	0.0091|0.0091	N|N	0.00368|0.00368	-1.59|-1.59	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0|.	T|T	0.38045|0.38045	-0.9679|-0.9679	8|5	.|.	.|.	.|.	.|.	1.0823|1.0823	0.01645|0.01645	0.1926:0.4208:0.128:0.2586|0.1926:0.4208:0.128:0.2586	.|.	262;321;197;298;298|.	B1AHF5;B1AHF6;P85299-2;P85299;A8K699|.	.;.;.;PRR5_HUMAN;.|.	L|C	289;262;321;298|258	ENSP00000006251:P289L;ENSP00000384848:P321L;ENSP00000337464:P298L|.	.|.	P|R	+|+	2|1	0|0	PRR5|PRR5	43511517|43511517	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.040000|0.040000	0.13550|0.13550	0.061000|0.061000	0.14366|0.14366	0.270000|0.270000	0.21984|0.21984	-0.680000|-0.680000	0.03767|0.03767	CCG|CGC	C|0.996;T|0.004	0.004	strong		0.741	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528	
LBR	3930	hgsc.bcm.edu	37	1	225600169	225600169	+	Silent	SNP	C	C	T	rs112582692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:225600169C>T	ENST00000338179.2	-	8	1196	c.1071G>A	c.(1069-1071)tcG>tcA	p.S357S	LBR_ENST00000272163.4_Silent_p.S357S|AC092811.1_ENST00000366845.2_5'Flank	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	357					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		AGCTGGCAGGCGACAGGTCAT	0.483													C|||	148	0.0295527	0.0136	0.0259	5008	,	,		15015	0.0208		0.0417	False		,,,				2504	0.0501				p.S357S		Atlas-SNP	.											.	LBR	54	.	0			c.G1071A						PASS	.	C	,	71,4335	63.5+/-100.7	0,71,2132	67.0	68.0	68.0		1071,1071	-12.1	0.0	1	dbSNP_132	68	430,8170	132.6+/-190.3	7,416,3877	no	coding-synonymous,coding-synonymous	LBR	NM_002296.3,NM_194442.2	,	7,487,6009	TT,TC,CC		5.0,1.6114,3.8521	,	357/616,357/616	225600169	501,12505	2203	4300	6503	SO:0001819	synonymous_variant	3930	exon8			GGCAGGCGACAGG	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"""Tudor domain containing"""	6518	protein-coding gene	gene with protein product	"""tudor domain containing 18"""	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.1071G>A	1.37:g.225600169C>T		Somatic	410	1	0.00243902		WXS	Illumina HiSeq	Phase_I	414	202	0.487923	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Silent	SNP	ENST00000338179.2	37	CCDS1545.1																																																																																			C|0.965;T|0.035	0.035	strong		0.483	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296	
NOX5	79400	hgsc.bcm.edu	37	15	69328226	69328226	+	Missense_Mutation	SNP	C	C	T	rs12907196	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:69328226C>T	ENST00000388866.3	+	7	1179	c.1138C>T	c.(1138-1140)Ctc>Ttc	p.L380F	NOX5_ENST00000448182.3_Missense_Mutation_p.L334F|NOX5_ENST00000530406.2_Missense_Mutation_p.L352F|NOX5_ENST00000455873.3_Missense_Mutation_p.L345F|RP11-809H16.4_ENST00000559495.1_RNA|NOX5_ENST00000260364.5_Missense_Mutation_p.L362F	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	380	Ferric oxidoreductase.|Poly-Leu.			L -> F (in Ref. 2; BAB84884/BAB84897, 3; BAB15319/BAG37241, 6; EAW77830 and 7; AAI25098/AAI25099). {ECO:0000305}.	angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						GCTGCTCCTCCTCATGTTCAT	0.607													C|||	1358	0.271166	0.1135	0.33	5008	,	,		18072	0.124		0.5358	False		,,,				2504	0.3221				p.L380F		Atlas-SNP	.											.	NOX5	60	.	0			c.C1138T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU	756,3644	309.1+/-290.9	69,618,1513	130.0	105.0	113.0		1054,1033,1138	1.2	0.4	15	dbSNP_121	113	4772,3824	611.8+/-395.9	1312,2148,838	yes	missense,missense,missense	NOX5	NM_001184779.1,NM_001184780.1,NM_024505.3	22,22,22	1381,2766,2351	TT,TC,CC		44.4858,17.1818,42.5362	possibly-damaging,possibly-damaging,possibly-damaging	352/738,345/731,380/766	69328226	5528,7468	2200	4298	6498	SO:0001583	missense	79400	exon7			CTCCTCCTCATGT	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"""EF-hand domain containing"""	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1138C>T	15.37:g.69328226C>T	ENSP00000373518:p.Leu380Phe	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Missense_Mutation	SNP	ENST00000388866.3	37	CCDS32276.2	673	0.30815018315018317	54	0.10975609756097561	128	0.35359116022099446	79	0.1381118881118881	412	0.5435356200527705	C	14.65	2.599053	0.46318	0.171818	0.555142	ENSG00000255346	ENST00000455873;ENST00000448182;ENST00000388866;ENST00000530406	D;D;D	0.92965	-3.14;-3.14;-3.14	3.38	1.18	0.20946	Flavoprotein transmembrane component (1);	0.376029	0.24347	N	0.039319	T	0.00012	0.0000	M	0.69248	2.105	0.24350	P	0.99492859	B;D;P	0.56287	0.303;0.975;0.886	B;P;P	0.56088	0.158;0.791;0.598	T	0.22312	-1.0220	9	0.45353	T	0.12	-12.2301	6.6006	0.22699	0.1777:0.5554:0.2669:0.0	rs12907196;rs35425174;rs60520952;rs12907196	345;380;352	Q96PH1-6;Q96PH1;Q96PH1-3	.;NOX5_HUMAN;.	F	345;362;380;352	ENSP00000416828:L345F;ENSP00000373518:L380F;ENSP00000432440:L352F	ENSP00000373518:L380F	L	+	1	0	NOX5	67115280	0.609000	0.26975	0.434000	0.26772	0.448000	0.32197	0.984000	0.29565	1.433000	0.47394	0.313000	0.20887	CTC	C|0.650;T|0.350	0.350	strong		0.607	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505	
ATAD3B	83858	hgsc.bcm.edu	37	1	1431165	1431165	+	Missense_Mutation	SNP	C	C	T	rs9792879		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1431165C>T	ENST00000308647.7	+	16	2031	c.1915C>T	c.(1915-1917)Ccg>Tcg	p.P639S		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	639						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)	p.P639S(1)		endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TGGCGGTCGGCCGTTCTGCCC	0.647																																					p.P639S		Atlas-SNP	.											ATAD3B,NS,carcinoma,0,2	ATAD3B	68	2	1	Substitution - Missense(1)	skin(1)	c.C1915T						PASS	.						33.0	33.0	33.0					1																	1431165		2202	4300	6502	SO:0001583	missense	83858	exon16			GGTCGGCCGTTCT	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1915C>T	1.37:g.1431165C>T	ENSP00000311766:p.Pro639Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	88	20	0.227273	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	476	0.21794871794871795	147	0.29878048780487804	60	0.16574585635359115	170	0.2972027972027972	99	0.13060686015831136	c	11.49	1.652810	0.29336	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.93811	-3.29	1.39	0.415	0.16411	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	8.000000000008E-6	B;B	0.22604	0.072;0.024	B;B	0.12156	0.007;0.002	T	0.11324	-1.0592	8	0.87932	D	0	.	3.748	0.08555	0.0:0.7411:0.0:0.2589	rs9792879	593;639	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	S	473;639	ENSP00000311766:P639S	ENSP00000311766:P639S	P	+	1	0	ATAD3B	1421028	0.034000	0.19679	0.001000	0.08648	0.022000	0.10575	0.000000	0.12993	0.145000	0.18977	0.194000	0.17425	CCG	C|0.782;T|0.218	0.218	strong		0.647	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
OR1E2	8388	hgsc.bcm.edu	37	17	3336260	3336260	+	Silent	SNP	A	A	G	rs61739591	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3336260A>G	ENST00000248384.1	-	1	875	c.876T>C	c.(874-876)ccT>ccC	p.P292P		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	292					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						GGGTCAGCATAGGGGTCACCA	0.458													G|||	876	0.17492	0.0643	0.2464	5008	,	,		16415	0.002		0.4543	False		,,,				2504	0.1646				p.P292P		Atlas-SNP	.											.	OR1E2	25	.	0			c.T876C						PASS	.	G		611,3795	767.1+/-413.5	57,497,1649	85.0	73.0	77.0		876	4.2	1.0	17	dbSNP_129	77	4171,4429	579.3+/-390.9	1038,2095,1167	no	coding-synonymous	OR1E2	NM_003554.1		1095,2592,2816	GG,GA,AA		48.5,13.8675,36.7676		292/324	3336260	4782,8224	2203	4300	6503	SO:0001819	synonymous_variant	8388	exon1			CAGCATAGGGGTC	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"""GPCR / Class A : Olfactory receptors"""	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.876T>C	17.37:g.3336260A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Silent	SNP	ENST00000248384.1	37	CCDS11026.1																																																																																			A|0.674;G|0.326	0.326	strong		0.458	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1		
PARP9	83666	hgsc.bcm.edu	37	3	122274757	122274757	+	Silent	SNP	G	G	C	rs73192127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122274757G>C	ENST00000360356.2	-	4	593	c.366C>G	c.(364-366)gtC>gtG	p.V122V	PARP9_ENST00000471785.1_Silent_p.V87V|PARP9_ENST00000462315.1_Silent_p.V87V|PARP9_ENST00000492382.1_Intron|PARP9_ENST00000477522.2_Silent_p.V87V	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	122	Macro 1. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		CATCTTTCCAGACTGATAACT	0.498													G|||	938	0.1873	0.0651	0.2046	5008	,	,		17635	0.2312		0.2594	False		,,,				2504	0.2209				p.V122V		Atlas-SNP	.											PARP9,caecum,carcinoma,+2,1	PARP9	72	1	0			c.C366G						PASS	.	G	,,,,,	428,3978	208.2+/-229.3	18,392,1793	106.0	92.0	97.0		366,261,261,261,261,366	2.5	1.0	3	dbSNP_130	97	2252,6348	381.6+/-340.1	297,1658,2345	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PARP9	NM_001146102.1,NM_001146103.1,NM_001146104.1,NM_001146105.1,NM_001146106.1,NM_031458.2	,,,,,	315,2050,4138	CC,CG,GG		26.186,9.714,20.6059	,,,,,	122/855,87/820,87/820,87/820,87/711,122/855	122274757	2680,10326	2203	4300	6503	SO:0001819	synonymous_variant	83666	exon4			TTTCCAGACTGAT	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"""Poly (ADP-ribose) polymerases"""	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.366C>G	3.37:g.122274757G>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	115	65	0.565217	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Silent	SNP	ENST00000360356.2	37	CCDS3014.1																																																																																			G|0.793;C|0.207	0.207	strong		0.498	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458	
PRRC2A	7916	hgsc.bcm.edu	37	6	31605278	31605278	+	Missense_Mutation	SNP	C	C	T	rs1046756	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31605278C>T	ENST00000376033.2	+	31	6623	c.6389C>T	c.(6388-6390)cCg>cTg	p.P2130L	PRRC2A_ENST00000376007.4_Missense_Mutation_p.P2130L	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	2130			P -> L (in dbSNP:rs1046756). {ECO:0000269|PubMed:14656967}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CGGACAGGGCCGCCACCTCGA	0.657													C|||	410	0.081869	0.1362	0.0519	5008	,	,		11513	0.122		0.0278	False		,,,				2504	0.044				p.P2130L		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C6389T						PASS	.	C	LEU/PRO,LEU/PRO	363,2653		30,303,1175	81.0	97.0	91.0		6389,6389	5.8	1.0	6	dbSNP_86	91	145,5273		1,143,2565	no	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	98,98	31,446,3740	TT,TC,CC		2.6763,12.0358,6.0232	probably-damaging,probably-damaging	2130/2158,2130/2158	31605278	508,7926	1508	2709	4217	SO:0001583	missense	7916	exon31			CAGGGCCGCCACC	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.6389C>T	6.37:g.31605278C>T	ENSP00000365201:p.Pro2130Leu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	145	0.06639194139194139	58	0.11788617886178862	17	0.04696132596685083	51	0.08916083916083917	19	0.025065963060686015	C	12.78	2.040453	0.35989	0.120358	0.026763	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.02498	4.27;4.27	5.84	5.84	0.93424	.	0.000000	0.53938	D	0.000050	T	0.01695	0.0054	N	0.19112	0.55	0.20489	P	0.999895857	D	0.58268	0.982	P	0.44732	0.459	T	0.57289	-0.7837	9	0.87932	D	0	-7.0051	15.638	0.76970	0.0:1.0:0.0:0.0	rs1046756;rs3177480;rs17137794;rs17857496	2130	P48634	PRC2A_HUMAN	L	2122;2111;2130;2130;1355	ENSP00000365175:P2130L;ENSP00000365201:P2130L	ENSP00000365175:P2130L	P	+	2	0	PRRC2A	31713257	0.966000	0.33281	0.998000	0.56505	0.865000	0.49528	2.123000	0.41996	2.779000	0.95612	0.655000	0.94253	CCG	C|0.943;T|0.057	0.057	strong		0.657	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
C11orf74	119710	hgsc.bcm.edu	37	11	36680719	36680719	+	Missense_Mutation	SNP	G	G	A	rs61753861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:36680719G>A	ENST00000334307.5	+	6	764	c.649G>A	c.(649-651)Gag>Aag	p.E217K	C11orf74_ENST00000534635.1_Missense_Mutation_p.E143K|C11orf74_ENST00000446510.2_Intron|C11orf74_ENST00000347206.4_Missense_Mutation_p.E143K	NM_138787.2	NP_620142.2	Q86VG3	CK074_HUMAN	chromosome 11 open reading frame 74	217										breast(1)|kidney(1)|large_intestine(1)|lung(5)	8	all_lung(20;0.226)	all_hematologic(20;0.0118)				CCCAGACTTAGAGAAATCCTG	0.383													g|||	38	0.00758786	0.0008	0.0101	5008	,	,		17815	0.0		0.0249	False		,,,				2504	0.0051				p.F217I		Atlas-SNP	.											.	C11orf74	22	.	0			c.T649A						PASS	.	A	LYS/GLU	17,4387	24.3+/-50.5	0,17,2185	128.0	123.0	125.0		649	1.5	0.0	11	dbSNP_129	125	216,8380	90.9+/-153.0	0,216,4082	yes	missense	C11orf74	NM_138787.2	56	0,233,6267	AA,AG,GG		2.5128,0.386,1.7923	benign	217/222	36680719	233,12767	2202	4298	6500	SO:0001583	missense	119710	exon6			GACTTAGAGAAAT	AK095997, BC009561	CCDS7904.1, CCDS60762.1	11p12	2012-08-10			ENSG00000166352	ENSG00000166352			25142	protein-coding gene	gene with protein product						12477932	Standard	NM_001276722		Approved	FLJ38678, HEPIS	uc031pzr.1	Q86VG3	OTTHUMG00000166397	ENST00000334307.5:c.649G>A	11.37:g.36680719G>A	ENSP00000334848:p.Glu217Lys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_138787	D3DR18|Q96DD6	Missense_Mutation	SNP	ENST00000334307.5	37	CCDS7904.1	23	0.010531135531135532	0	0.0	3	0.008287292817679558	0	0.0	20	0.026385224274406333	g	17.46	3.394733	0.62066	0.00386	0.025128	ENSG00000166352	ENST00000334307;ENST00000347206;ENST00000534635	.	.	.	5.78	1.45	0.22620	.	0.787972	0.11529	N	0.554917	T	0.08802	0.0218	L	0.50333	1.59	0.09310	N	1	P;P	0.38597	0.639;0.639	B;B	0.32928	0.155;0.155	T	0.10989	-1.0606	8	.	.	.	-0.0861	2.2694	0.04086	0.2005:0.1686:0.4845:0.1463	rs61753861	217;143	Q86VG3;Q86VG3-2	CK074_HUMAN;.	K	217;143;143	.	.	E	+	1	0	C11orf74	36637295	0.001000	0.12720	0.001000	0.08648	0.007000	0.05969	0.158000	0.16422	0.626000	0.30322	-0.127000	0.14921	GAG	G|0.985;A|0.015	0.015	strong		0.383	C11orf74-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389567.1	NM_138787	
DUOX2	50506	hgsc.bcm.edu	37	15	45392075	45392075	+	Missense_Mutation	SNP	G	G	A	rs269868	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45392075G>A	ENST00000603300.1	-	25	3402	c.3200C>T	c.(3199-3201)tCg>tTg	p.S1067L	DUOX2_ENST00000389039.6_Missense_Mutation_p.S1067L	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1067	Interaction with TXNDC11. {ECO:0000250}.		S -> L (in dbSNP:rs269868). {ECO:0000269|PubMed:10601291, ECO:0000269|PubMed:10806195, ECO:0000269|PubMed:11514595}.		adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CGAGGGTGGCGAGGCAAAGCC	0.597													G|||	3607	0.720248	0.1604	0.804	5008	,	,		20104	0.9514		0.9304	False		,,,				2504	0.9632				p.S1067L		Atlas-SNP	.											.	DUOX2	137	.	0			c.C3200T	GRCh37	CM085371	DUOX2	M	rs269868	PASS	.	G	LEU/SER	1182,3214	413.0+/-336.3	180,822,1196	82.0	86.0	85.0		3200	5.6	0.9	15	dbSNP_79	85	7948,648	788.8+/-407.6	3681,586,31	yes	missense	DUOX2	NM_014080.4	145	3861,1408,1227	AA,AG,GG		7.5384,26.8881,29.726	benign	1067/1549	45392075	9130,3862	2198	4298	6496	SO:0001583	missense	50506	exon25			GGTGGCGAGGCAA	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.3200C>T	15.37:g.45392075G>A	ENSP00000475084:p.Ser1067Leu	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	205	205	1	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	1649	0.75503663003663	95	0.19308943089430894	309	0.8535911602209945	539	0.9423076923076923	706	0.9313984168865436	G	17.52	3.410266	0.62399	0.268881	0.924616	ENSG00000140279	ENST00000389039	.	.	.	5.6	5.6	0.85130	.	0.054964	0.64402	D	0.000001	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	0.999999845329	B	0.18013	0.025	B	0.17979	0.02	T	0.43163	-0.9408	8	0.62326	D	0.03	-6.6702	18.6061	0.91266	0.0:0.0:1.0:0.0	rs269868;rs52813379;rs57566884;rs269868	1067	Q9NRD8	DUOX2_HUMAN	L	1067	.	ENSP00000373691:S1067L	S	-	2	0	DUOX2	43179367	1.000000	0.71417	0.889000	0.34880	0.334000	0.28698	7.934000	0.87649	2.653000	0.90120	0.563000	0.77884	TCG	G|0.281;T|0.002	.	strong		0.597	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
GM2A	2760	hgsc.bcm.edu	37	5	150647012	150647012	+	Silent	SNP	A	A	G	rs1048723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150647012A>G	ENST00000357164.3	+	4	907	c.582A>G	c.(580-582)taA>taG	p.*194*		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	0					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGGCATATAACATGGCATCT	0.552													A|||	1330	0.265575	0.0885	0.4524	5008	,	,		21786	0.2698		0.3171	False		,,,				2504	0.3149				p.X194X		Atlas-SNP	.											.	GM2A	24	.	0			c.A582G						PASS	.	A	,	585,3821	256.1+/-261.0	41,503,1659	94.0	93.0	93.0		582,	-2.1	0.0	5	dbSNP_86	93	2395,6205	397.7+/-345.9	338,1719,2243	no	coding-synonymous,intron	GM2A	NM_000405.4,NM_001167607.1	,	379,2222,3902	GG,GA,AA		27.8488,13.2773,22.9125	,	194/194,	150647012	2980,10026	2203	4300	6503	SO:0001819	synonymous_variant	2760	exon4			CATATAACATGGC		CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"""cerebroside sulfate activator protein"", ""sphingolipid activator protein 3"""	613109	"""GM2 ganglioside activator protein"""			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.582A>G	5.37:g.150647012A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	143	46	0.321678	NM_000405	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Silent	SNP	ENST00000357164.3	37	CCDS4313.1																																																																																			A|0.762;G|0.238;T|0.000	0.238	strong		0.552	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405	
DDR1	780	hgsc.bcm.edu	37	6	30862423	30862423	+	Silent	SNP	C	C	T	rs1264319	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30862423C>T	ENST00000324771.8	+	13	2036	c.1488C>T	c.(1486-1488)tcC>tcT	p.S496S	DDR1_ENST00000452441.1_Silent_p.S496S|DDR1_ENST00000376567.2_Silent_p.S496S|DDR1_ENST00000361741.4_Missense_Mutation_p.P200L|DDR1_ENST00000376570.4_Silent_p.S496S|DDR1_ENST00000376569.3_Silent_p.S496S|DDR1_ENST00000376568.3_Silent_p.S496S|DDR1_ENST00000508312.1_Silent_p.S514S|DDR1_ENST00000376575.3_Silent_p.S496S|DDR1_ENST00000418800.2_Silent_p.S496S|DDR1_ENST00000454612.2_Silent_p.S496S|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000513240.1_Silent_p.S496S			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	496	Gly/Pro-rich.		S -> A (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CGCCCCACTCCGCTCCCTGTG	0.582													C|||	642	0.128195	0.177	0.0951	5008	,	,		19738	0.0585		0.162	False		,,,				2504	0.1227				p.P469L		Atlas-SNP	.											.	DDR1	213	.	0			c.C1406T						PASS	.	C	,LEU/PRO,,,,	858,3548	335.7+/-304.0	90,678,1435	75.0	75.0	75.0		1488,1406,1542,1488,1488,1488	2.7	1.0	6	dbSNP_87	75	1699,6901	311.0+/-310.2	162,1375,2763	yes	coding-synonymous,missense,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,98,,,,	252,2053,4198	TT,TC,CC		19.7558,19.4734,19.6602	,,,,,	496/509,469/768,514/895,496/877,496/914,496/920	30862423	2557,10449	2203	4300	6503	SO:0001819	synonymous_variant	780	exon10			CCACTCCGCTCCC	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1488C>T	6.37:g.30862423C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_001202522	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	341|341	0.15613553113553114|0.15613553113553114	127|127	0.258130081300813|0.258130081300813	44|44	0.12154696132596685|0.12154696132596685	39|39	0.06818181818181818|0.06818181818181818	131|131	0.17282321899736147|0.17282321899736147	C|C	7.986|7.986	0.752226|0.752226	0.15778|0.15778	0.194734|0.194734	0.197558|0.197558	ENSG00000204580|ENSG00000204580	ENST00000417521;ENST00000361741;ENST00000451954|ENST00000514434	T;T|.	0.79454|.	-1.19;-1.27|.	5.24|5.24	2.73|2.73	0.32206|0.32206	.|.	.|.	.|.	.|.	.|.	T|T	0.26268|0.26268	0.0641|0.0641	.|.	.|.	.|.	0.26362|0.26362	P|P	0.9770315|0.9770315	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.08207|0.08207	-1.0733|-1.0733	7|3	0.20519|.	T|.	0.43|.	.|.	7.4808|7.4808	0.27404|0.27404	0.0:0.1817:0.0:0.8183|0.0:0.1817:0.0:0.8183	rs1264319;rs1264319|rs1264319;rs1264319	265|.	A2ABM8|.	.|.	L|C	265;200;152|25	ENSP00000398682:P265L;ENSP00000354844:P200L|.	ENSP00000354844:P200L|.	P|R	+|+	2|1	0|0	DDR1|DDR1	30970402|30970402	0.976000|0.976000	0.34144|0.34144	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	0.405000|0.405000	0.21015|0.21015	0.837000|0.837000	0.34925|0.34925	-0.455000|-0.455000	0.05494|0.05494	CCG|CGC	C|0.820;T|0.180	0.180	strong		0.582	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
LARS2	23395	hgsc.bcm.edu	37	3	45557707	45557707	+	Silent	SNP	G	G	A	rs11549809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:45557707G>A	ENST00000415258.1	+	16	2124	c.1983G>A	c.(1981-1983)acG>acA	p.T661T	LARS2_ENST00000414984.1_Silent_p.T618T|LARS2_ENST00000467936.1_3'UTR|LARS2_ENST00000265537.3_Silent_p.T661T			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	661					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	GGATCGACACGATTCGGCTCT	0.483													G|||	1233	0.246206	0.1982	0.2536	5008	,	,		20280	0.1935		0.332	False		,,,				2504	0.272				p.T661T		Atlas-SNP	.											.	LARS2	48	.	0			c.G1983A						PASS	.	G		957,3449	363.1+/-316.4	100,757,1346	253.0	202.0	219.0		1983	-6.6	0.0	3	dbSNP_120	219	2733,5867	437.2+/-358.5	431,1871,1998	no	coding-synonymous	LARS2	NM_015340.3		531,2628,3344	AA,AG,GG		31.7791,21.7204,28.3715		661/904	45557707	3690,9316	2203	4300	6503	SO:0001819	synonymous_variant	23395	exon17			CGACACGATTCGG	AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	17095	protein-coding gene	gene with protein product	"""leucine tRNA ligase 2, mitochondrial"""	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.1983G>A	3.37:g.45557707G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_015340		Silent	SNP	ENST00000415258.1	37	CCDS2728.1																																																																																			G|0.727;A|0.273	0.273	strong		0.483	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340	
ARMC3	219681	hgsc.bcm.edu	37	10	23297252	23297252	+	Missense_Mutation	SNP	G	G	A	rs10828395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:23297252G>A	ENST00000298032.5	+	15	1961	c.1877G>A	c.(1876-1878)cGa>cAa	p.R626Q	ARMC3_ENST00000409983.3_Missense_Mutation_p.R626Q|ARMC3_ENST00000409049.3_Missense_Mutation_p.R626Q|ARMC3_ENST00000376528.4_Missense_Mutation_p.R363Q	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	626			R -> Q (in dbSNP:rs10828395). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GGTTATGGACGAAGTATTTCT	0.279													g|||	944	0.188498	0.2821	0.0951	5008	,	,		16534	0.12		0.1859	False		,,,				2504	0.2014				p.R626Q		Atlas-SNP	.											.	ARMC3	102	.	0			c.G1877A						PASS	.	G	GLN/ARG	1197,3185		171,855,1165	36.0	32.0	34.0		1877	5.6	1.0	10	dbSNP_120	34	1544,6994		144,1256,2869	yes	missense	ARMC3	NM_173081.3	43	315,2111,4034	AA,AG,GG		18.0839,27.3163,21.2152	benign	626/873	23297252	2741,10179	2191	4269	6460	SO:0001583	missense	219681	exon15			ATGGACGAAGTAT	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1877G>A	10.37:g.23297252G>A	ENSP00000298032:p.Arg626Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	37	CCDS7142.1	359	0.16437728937728938	120	0.24390243902439024	37	0.10220994475138122	64	0.11188811188811189	138	0.1820580474934037	g	13.55	2.271992	0.40194	0.273163	0.180839	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000409049;ENST00000376528	T;T;T;T	0.37752	1.19;1.18;1.2;2.42	5.56	5.56	0.83823	.	1.341930	0.04522	N	0.384715	T	0.00012	0.0000	N	0.20986	0.625	0.35374	P	0.210704	B;B	0.30605	0.236;0.287	B;B	0.21708	0.036;0.024	T	0.10064	-1.0646	9	0.11182	T	0.66	-12.0527	15.0276	0.71682	0.0:0.0:1.0:0.0	rs10828395;rs17538475;rs17853918;rs52807337;rs59139275;rs10828395	626;626	Q5W041-4;Q5W041	.;ARMC3_HUMAN	Q	626;626;626;363	ENSP00000298032:R626Q;ENSP00000386943:R626Q;ENSP00000387288:R626Q;ENSP00000365711:R363Q	ENSP00000298032:R626Q	R	+	2	0	ARMC3	23337258	0.997000	0.39634	0.999000	0.59377	0.877000	0.50540	2.748000	0.47483	2.603000	0.88011	0.563000	0.77884	CGA	G|0.805;A|0.194	0.194	strong		0.279	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081	
TTI2	80185	hgsc.bcm.edu	37	8	33361280	33361280	+	Silent	SNP	C	C	T	rs17850186	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:33361280C>T	ENST00000431156.2	-	5	1719	c.1101G>A	c.(1099-1101)ccG>ccA	p.P367P	TTI2_ENST00000360742.5_Silent_p.P367P|TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000520636.1_Silent_p.P336P	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	367																	TCACGAAAGCCGGCAGGTTTC	0.527													C|||	43	0.00858626	0.0023	0.0058	5008	,	,		17510	0.002		0.0229	False		,,,				2504	0.0112				p.P367P		Atlas-SNP	.											C8orf41,rectum,carcinoma,0,2	.	.	2	0			c.G1101A						PASS	.	C	,	17,4389	24.3+/-50.5	0,17,2186	33.0	31.0	32.0		1101,1101	-8.6	0.2	8	dbSNP_123	32	172,8428	78.4+/-141.0	3,166,4131	no	coding-synonymous,coding-synonymous	TTI2	NM_001102401.1,NM_025115.2	,	3,183,6317	TT,TC,CC		2.0,0.3858,1.4532	,	367/509,367/509	33361280	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	80185	exon5			GAAAGCCGGCAGG	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"""chromosome 8 open reading frame 41"", ""Tel2 interacting protein 2 homolog (S. pombe)"""	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1101G>A	8.37:g.33361280C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	37	CCDS6090.1																																																																																			C|0.986;T|0.014	0.014	strong		0.527	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	
JUN	3725	hgsc.bcm.edu	37	1	59247993	59247993	+	Silent	SNP	C	C	T	rs11688	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:59247993C>T	ENST00000371222.2	-	1	1792	c.750G>A	c.(748-750)caG>caA	p.Q250Q	RP4-794H19.2_ENST00000419531.2_lincRNA	NM_002228.3	NP_002219.1	P05412	JUN_HUMAN	jun proto-oncogene	250					aging (GO:0007568)|angiogenesis (GO:0001525)|axon regeneration (GO:0031103)|cellular response to calcium ion (GO:0071277)|cellular response to potassium ion starvation (GO:0051365)|circadian rhythm (GO:0007623)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leading edge cell differentiation (GO:0035026)|learning (GO:0007612)|liver development (GO:0001889)|membrane depolarization (GO:0051899)|microglial cell activation (GO:0001774)|monocyte differentiation (GO:0030224)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA binding (GO:0043392)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990441)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|SMAD protein import into nucleus (GO:0007184)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nuclear chromosome (GO:0000228)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|R-SMAD binding (GO:0070412)|Rho GTPase activator activity (GO:0005100)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|kidney(2)|lung(5)|skin(1)	10	all_cancers(7;8.55e-07)				Arsenic trioxide(DB01169)|Irbesartan(DB01029)|Pseudoephedrine(DB00852)|Vinblastine(DB00570)	TGATCCGCTCCTGGGACTCCA	0.642			A		sarcoma								C|||	445	0.0888578	0.2481	0.0548	5008	,	,		16477	0.0238		0.0388	False		,,,				2504	0.0164				p.Q250Q		Atlas-SNP	.		Dom	yes		1	1p32-p31	3725	jun oncogene		M	.	JUN	26	.	0			c.G750A						PASS	.	C		875,3531	328.3+/-300.5	97,681,1425	46.0	49.0	48.0		750	2.3	1.0	1	dbSNP_52	48	431,8169	130.3+/-188.3	9,413,3878	no	coding-synonymous	JUN	NM_002228.3		106,1094,5303	TT,TC,CC		5.0116,19.8593,10.0415		250/332	59247993	1306,11700	2203	4300	6503	SO:0001819	synonymous_variant	3725	exon1			CCGCTCCTGGGAC	AY217548	CCDS610.1	1p32-p31	2013-01-10	2010-08-27		ENSG00000177606	ENSG00000177606		"""basic leucine zipper proteins"""	6204	protein-coding gene	gene with protein product		165160	"""v-jun avian sarcoma virus 17 oncogene homolog"", ""v-jun sarcoma virus 17 oncogene homolog (avian)"", ""jun oncogene"""			3194415	Standard	NM_002228		Approved	c-Jun, AP-1	uc001cze.3	P05412	OTTHUMG00000008376	ENST00000371222.2:c.750G>A	1.37:g.59247993C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	82	51	0.621951	NM_002228	Q6FHM7|Q96G93	Silent	SNP	ENST00000371222.2	37	CCDS610.1																																																																																			C|0.908;T|0.092	0.092	strong		0.642	JUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023042.1	NM_002228	
OR13C3	138803	hgsc.bcm.edu	37	9	107298444	107298444	+	Silent	SNP	C	C	T	rs41305445	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107298444C>T	ENST00000374781.2	-	1	693	c.651G>A	c.(649-651)ctG>ctA	p.L217L		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						CAGCACAGGCCAGCTTGAGGA	0.383													T|||	630	0.125799	0.2322	0.072	5008	,	,		23022	0.0764		0.0815	False		,,,				2504	0.1166				p.L217L	GBM(86;1248 1274 14222 15028 46219)	Atlas-SNP	.											.	OR13C3	45	.	0			c.G651A						PASS	.	T		920,3486	739.5+/-411.1	95,730,1378	108.0	107.0	107.0		651	-4.2	0.9	9	dbSNP_127	107	789,7811	783.0+/-407.6	38,713,3549	no	coding-synonymous	OR13C3	NM_001001961.1		133,1443,4927	TT,TC,CC		9.1744,20.8806,13.1401		217/348	107298444	1709,11297	2203	4300	6503	SO:0001819	synonymous_variant	138803	exon1			ACAGGCCAGCTTG		CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"""GPCR / Class A : Olfactory receptors"""	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.651G>A	9.37:g.107298444C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_001001961	Q5VVG1|Q6IF52	Silent	SNP	ENST00000374781.2	37	CCDS35089.1																																																																																			C|0.875;T|0.125	0.125	strong		0.383	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2		
C16orf46	123775	hgsc.bcm.edu	37	16	81095099	81095099	+	Silent	SNP	C	C	G	rs2287995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81095099C>G	ENST00000299578.5	-	4	1090	c.855G>C	c.(853-855)gcG>gcC	p.A285A	C16orf46_ENST00000378611.4_Silent_p.A285A|RP11-303E16.8_ENST00000564536.1_RNA|C16orf46_ENST00000444657.3_5'Flank	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	285						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						ATATCTGGGCCGCTGGGGAAG	0.577													C|||	541	0.108027	0.0514	0.1066	5008	,	,		17352	0.1944		0.0934	False		,,,				2504	0.1115				p.A285A		Atlas-SNP	.											C16orf46_ENST00000378611,right_upper_lobe,carcinoma,-1,2	C16orf46	57	2	0			c.G855C						PASS	.	C	,	215,4189	122.9+/-160.3	7,201,1994	117.0	111.0	113.0		855,855	-0.8	0.0	16	dbSNP_100	113	662,7938	161.6+/-214.5	25,612,3663	no	coding-synonymous,coding-synonymous	C16orf46	NM_001100873.1,NM_152337.2	,	32,813,5657	GG,GC,CC		7.6977,4.8819,6.7441	,	285/389,285/396	81095099	877,12127	2202	4300	6502	SO:0001819	synonymous_variant	123775	exon3			CTGGGCCGCTGGG	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.855G>C	16.37:g.81095099C>G		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	250	124	0.496	NM_001100873	Q96MA7	Silent	SNP	ENST00000299578.5	37	CCDS10932.1																																																																																			C|0.916;G|0.084	0.084	strong		0.577	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337	
MCF2L2	23101	hgsc.bcm.edu	37	3	183017965	183017965	+	Missense_Mutation	SNP	T	T	A	rs2293203	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183017965T>A	ENST00000328913.3	-	11	1430	c.1133A>T	c.(1132-1134)cAg>cTg	p.Q378L	MCF2L2_ENST00000473233.1_Missense_Mutation_p.Q378L|MCF2L2_ENST00000414362.2_Missense_Mutation_p.Q378L|MCF2L2_ENST00000447025.2_Missense_Mutation_p.Q378L	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	378			Q -> L (in dbSNP:rs2293203). {ECO:0000269|PubMed:15489334}.				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TGCCAGCAGCTGGGCCTTTTC	0.587													T|||	510	0.101837	0.2292	0.0231	5008	,	,		17855	0.1498		0.0159	False		,,,				2504	0.0245				p.Q378L		Atlas-SNP	.											.	MCF2L2	164	.	0			c.A1133T						PASS	.	T	LEU/GLN	848,3558	333.6+/-303.0	75,698,1430	42.0	41.0	42.0		1133	2.1	1.0	3	dbSNP_100	42	112,8488	58.7+/-120.3	0,112,4188	yes	missense	MCF2L2	NM_015078.2	113	75,810,5618	AA,AT,TT		1.3023,19.2465,7.3812	benign	378/1115	183017965	960,12046	2203	4300	6503	SO:0001583	missense	23101	exon11			AGCAGCTGGGCCT	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.1133A>T	3.37:g.183017965T>A	ENSP00000328118:p.Gln378Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	204	0.09340659340659341	109	0.22154471544715448	14	0.03867403314917127	69	0.12062937062937062	12	0.0158311345646438	T	14.67	2.603818	0.46423	0.192465	0.013023	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	4.59	2.1	0.27182	.	0.069175	0.64402	D	0.000015	T	0.00012	0.0000	M	0.62723	1.935	0.27167	P	0.9610247	B;D	0.57257	0.063;0.979	B;P	0.51833	0.03;0.681	T	0.11108	-1.0601	9	0.48119	T	0.1	.	6.9782	0.24688	0.0:0.0787:0.1497:0.7716	rs2293203;rs17855920;rs52819071;rs61177995;rs2293203	378;378	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	L	378	ENSP00000328118:Q378L;ENSP00000420070:Q378L;ENSP00000388190:Q378L;ENSP00000414131:Q378L	ENSP00000328118:Q378L	Q	-	2	0	MCF2L2	184500659	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.169000	0.42434	0.250000	0.21479	0.533000	0.62120	CAG	T|0.913;A|0.087	0.087	strong		0.587	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
PDCD4	27250	hgsc.bcm.edu	37	10	112647433	112647433	+	Missense_Mutation	SNP	G	G	A	rs41292600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:112647433G>A	ENST00000280154.7	+	6	840	c.566G>A	c.(565-567)aGa>aAa	p.R189K	PDCD4_ENST00000481353.1_3'UTR|PDCD4_ENST00000393104.2_Missense_Mutation_p.R178K	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	189	MI 1. {ECO:0000255|PROSITE- ProRule:PRU00698}.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GAAATGTTAAGAGATTTAAAT	0.299													G|||	11	0.00219649	0.0	0.0014	5008	,	,		18117	0.0		0.005	False		,,,				2504	0.0051				p.R189K	Ovarian(115;1498 1603 9363 40056 40885)	Atlas-SNP	.											.	PDCD4	39	.	0			c.G566A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	7,4399	12.9+/-30.5	0,7,2196	87.0	85.0	86.0		524,566,533	3.9	1.0	10	dbSNP_127	86	88,8512	43.6+/-101.6	1,86,4213	no	missense,missense,missense	PDCD4	NM_001199492.1,NM_014456.4,NM_145341.3	26,26,26	1,93,6409	AA,AG,GG		1.0233,0.1589,0.7304	benign,benign,benign	175/456,189/470,178/459	112647433	95,12911	2203	4300	6503	SO:0001583	missense	27250	exon6			TGTTAAGAGATTT	U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"""nuclear antigen H731"""	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.566G>A	10.37:g.112647433G>A	ENSP00000280154:p.Arg189Lys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_014456	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Missense_Mutation	SNP	ENST00000280154.7	37	CCDS7567.1	17	0.007783882783882784	4	0.008130081300813009	5	0.013812154696132596	1	0.0017482517482517483	7	0.009234828496042216	G	5.092	0.202557	0.09652	0.001589	0.010233	ENSG00000150593	ENST00000280154;ENST00000393104;ENST00000444997	T;T;T	0.38887	1.11;1.11;1.11	5.72	3.87	0.44632	Initiation factor eIF-4 gamma, MA3 (3);Armadillo-type fold (1);	0.306707	0.41396	N	0.000893	T	0.10766	0.0263	N	0.03071	-0.42	0.31940	N	0.611103	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.20273	-1.0280	10	0.07482	T	0.82	-16.6869	7.2204	0.25983	0.3582:0.0:0.6418:0.0	rs41292600;rs61753065	175;189;178	B4DKX4;Q53EL6;B5ME91	.;PDCD4_HUMAN;.	K	189;178;175	ENSP00000280154:R189K;ENSP00000376816:R178K;ENSP00000394668:R175K	ENSP00000280154:R189K	R	+	2	0	PDCD4	112637423	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.509000	0.35780	0.884000	0.36064	0.650000	0.86243	AGA	G|0.993;A|0.007	0.007	strong		0.299	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456	
OR11H1	81061	hgsc.bcm.edu	37	22	16449784	16449784	+	Missense_Mutation	SNP	C	C	A	rs200562384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:16449784C>A	ENST00000252835.4	-	1	21	c.21G>T	c.(19-21)caG>caT	p.Q7H		NM_001005239.1	NP_001005239.1	Q8NG94	O11H1_HUMAN	olfactory receptor, family 11, subfamily H, member 1	7						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|skin(1)	11	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.208)		Kidney(3;0.00216)|KIRC - Kidney renal clear cell carcinoma(3;0.00244)|Lung(27;0.0724)|COAD - Colon adenocarcinoma(3;0.211)		GGCCAGTGACCTGCAAGGTCA	0.358																																					p.Q7H		Atlas-SNP	.											OR11H1,NS,carcinoma,0,2	OR11H1	44	2	0			c.G21T						scavenged	.						1.0	1.0	1.0					22																	16449784		475	1076	1551	SO:0001583	missense	81061	exon1			AGTGACCTGCAAG	AP000535, AF399611	CCDS74807.1	22q11.1	2012-08-09			ENSG00000130538	ENSG00000130538		"""GPCR / Class A : Olfactory receptors"""	15404	protein-coding gene	gene with protein product						12213199	Standard	NM_001005239		Approved	OR22-1	uc011agd.2	Q8NG94	OTTHUMG00000030069	ENST00000252835.4:c.21G>T	22.37:g.16449784C>A	ENSP00000252835:p.Gln7His	Somatic	439	2	0.00455581		WXS	Illumina HiSeq	Phase_I	490	140	0.285714	NM_001005239	Q6IEX0|Q96R32	Missense_Mutation	SNP	ENST00000252835.4	37	CCDS33594.1	.	.	.	.	.	.	.	.	.	.	c	0.080	-1.186114	0.01620	.	.	ENSG00000130538	ENST00000252835	T	0.00004	9.8	1.41	0.267	0.15622	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.09310	N	1	B	0.33637	0.42	B	0.31869	0.137	T	0.00000	-1.2848	9	0.30078	T	0.28	.	4.0282	0.09697	0.0:0.752:0.0:0.248	.	7	Q8NG94	O11H1_HUMAN	H	7	ENSP00000252835:Q7H	ENSP00000252835:Q7H	Q	-	3	2	OR11H1	14829784	0.000000	0.05858	0.037000	0.18230	0.126000	0.20510	-1.911000	0.01583	0.153000	0.19213	0.064000	0.15345	CAG	.	.	weak		0.358	OR11H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074923.2	NM_001005239	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3686436	3686436	+	Missense_Mutation	SNP	C	C	T	rs6037651	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:3686436C>T	ENST00000344754.4	-	3	660	c.661G>A	c.(661-663)Gtg>Atg	p.V221M	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.V221M	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	221	Ig-like C2-type 1.		V -> M (in dbSNP:rs6037651).		cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						TGATTGGCCACGGAGAGCTGG	0.622													C|||	3460	0.690895	0.7375	0.5865	5008	,	,		19266	0.747		0.5726	False		,,,				2504	0.7658				p.V221M		Atlas-SNP	.											SIGLEC1,colon,carcinoma,0,1	SIGLEC1	210	1	0			c.G661A						PASS	.	C	MET/VAL	3143,1263	701.3+/-406.7	1105,933,165	66.0	68.0	67.0		661	0.3	0.0	20	dbSNP_114	67	5108,3492	633.3+/-398.7	1498,2112,690	yes	missense	SIGLEC1	NM_023068.3	21	2603,3045,855	TT,TC,CC		40.6047,28.6655,36.56	benign	221/1710	3686436	8251,4755	2203	4300	6503	SO:0001583	missense	6614	exon3			TGGCCACGGAGAG	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.661G>A	20.37:g.3686436C>T	ENSP00000341141:p.Val221Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	37	CCDS13060.1	1435	0.657051282051282	385	0.782520325203252	199	0.5497237569060773	409	0.715034965034965	442	0.58311345646438	C	8.586	0.883473	0.17467	0.713345	0.593953	ENSG00000088827	ENST00000344754;ENST00000202578	D;D	0.86230	-2.09;-2.09	4.68	0.33	0.15929	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.457645	0.16266	N	0.222010	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B;B	0.27971	0.076;0.196;0.163	B;B;B	0.28139	0.03;0.086;0.051	T	0.38351	-0.9665	9	0.33940	T	0.23	.	4.3209	0.11016	0.1498:0.4923:0.2731:0.0848	rs6037651;rs17724439;rs60531979;rs6037651	221;221;221	Q9BZZ2-2;Q9BZZ2;Q9BZZ2-3	.;SN_HUMAN;.	M	221	ENSP00000341141:V221M;ENSP00000202578:V221M	ENSP00000202578:V221M	V	-	1	0	SIGLEC1	3634436	0.000000	0.05858	0.003000	0.11579	0.025000	0.11179	-0.625000	0.05534	-0.069000	0.12931	-0.448000	0.05591	GTG	C|0.350;N|0.000	.	strong		0.622	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
KIAA1671	85379	hgsc.bcm.edu	37	22	25577688	25577688	+	Silent	SNP	G	G	A	rs763279	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:25577688G>A	ENST00000406486.4	+	11	5484	c.5097G>A	c.(5095-5097)gaG>gaA	p.E1699E	KIAA1671_ENST00000358431.3_Silent_p.E1699E|KIAA1671_ENST00000401395.1_Silent_p.E206E			Q9BY89	K1671_HUMAN	KIAA1671	1699								p.E1699E(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						CCAGGAAGGAGGAGTCGGATG	0.527													A|||	1802	0.359824	0.2269	0.4769	5008	,	,		19327	0.496		0.3658	False		,,,				2504	0.3098				p.E1699E		Atlas-SNP	.											KIAA1671,NS,carcinoma,0,1	KIAA1671	28	1	1	Substitution - coding silent(1)	stomach(1)	c.G5097A						PASS	.	A		349,1035		46,257,389	65.0	68.0	67.0		5097	-3.1	0.3	22	dbSNP_86	67	1081,2101		189,703,699	no	coding-synonymous	KIAA1671	NM_001145206.1		235,960,1088	AA,AG,GG		33.9723,25.2168,31.3184		1699/1807	25577688	1430,3136	692	1591	2283	SO:0001819	synonymous_variant	85379	exon8			GAAGGAGGAGTCG		CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077			29345	protein-coding gene	gene with protein product						15289310	Standard	NM_001145206		Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.5097G>A	22.37:g.25577688G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	116	66	0.568965	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			G|0.654;A|0.346	0.346	strong		0.527	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388724	1388724	+	Missense_Mutation	SNP	C	C	G	rs76728908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388724C>G	ENST00000324803.4	+	1	3385	c.425C>G	c.(424-426)cCa>cGa	p.P142R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	142					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P142R(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACGTGCCCATGCGGAGTG	0.697													N|||	556	0.111022	0.0658	0.1657	5008	,	,		14551	0.0238		0.1968	False		,,,				2504	0.135				p.P142R		Atlas-SNP	.											CRIPAK,NS,other,0,1	CRIPAK	185	1	1	Substitution - Missense(1)	pancreas(1)	c.C425G						scavenged	.						38.0	36.0	36.0					4																	1388724		1907	3680	5587	SO:0001583	missense	285464	exon1			CGTGCCCATGCGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.425C>G	4.37:g.1388724C>G	ENSP00000323978:p.Pro142Arg	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	0.221	-1.028683	0.02045	.	.	ENSG00000179979	ENST00000324803	T	0.19250	2.16	0.948	-1.9	0.07665	Post-SET domain (1);	.	.	.	.	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.28364	-1.0046	9	0.09843	T	0.71	.	0.6802	0.00873	0.2336:0.357:0.2313:0.1781	.	142	Q8N1N5	CRPAK_HUMAN	R	142	ENSP00000323978:P142R	ENSP00000323978:P142R	P	+	2	0	CRIPAK	1378724	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.476000	0.02333	-2.809000	0.00348	-3.729000	0.00022	CCA	C|0.500;G|0.500	0.500	weak		0.697	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
CUX2	23316	hgsc.bcm.edu	37	12	111760251	111760251	+	Silent	SNP	G	G	C	rs3742006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:111760251G>C	ENST00000261726.6	+	18	2947	c.2793G>C	c.(2791-2793)gtG>gtC	p.V931V		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	931					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						AGGGCAGCGTGAGCGACATGC	0.692													.|||	1757	0.350839	0.3676	0.17	5008	,	,		14063	0.6577		0.167	False		,,,				2504	0.3292				p.V931V		Atlas-SNP	.											.	CUX2	145	.	0			c.G2793C						PASS	.	C		1478,2888		258,962,963	10.0	12.0	12.0		2793	3.8	1.0	12	dbSNP_107	12	1285,7259		122,1041,3109	no	coding-synonymous	CUX2	NM_015267.3		380,2003,4072	CC,CG,GG		15.0398,33.8525,21.402		931/1487	111760251	2763,10147	2183	4272	6455	SO:0001819	synonymous_variant	23316	exon18			CAGCGTGAGCGAC	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.2793G>C	12.37:g.111760251G>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	78	30	0.384615	NM_015267	A7E2Y4	Silent	SNP	ENST00000261726.6	37	CCDS41837.1																																																																																			G|0.649;C|0.351	0.351	strong		0.692	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
ARMC5	79798	hgsc.bcm.edu	37	16	31476458	31476458	+	Intron	SNP	C	C	T	rs11150624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31476458C>T	ENST00000563544.1	+	5	2410				ARMC5_ENST00000408912.3_Intron|ARMC5_ENST00000457010.2_Missense_Mutation_p.A705V|ARMC5_ENST00000268314.4_Intron|ARMC5_ENST00000538189.1_Intron|ARMC5_ENST00000412665.2_Intron			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5											central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						TGCAGCCCCGCGCCCAGGATC	0.622													C|||	1523	0.304113	0.0507	0.5735	5008	,	,		20389	0.4494		0.4463	False		,,,				2504	0.1595				p.A705V		Atlas-SNP	.											ARMC5_ENST00000457010,brain,glioma,0,1	ARMC5	94	1	0			c.C2114T						PASS	.	C	,VAL/ALA	443,3739		26,391,1674	49.0	55.0	53.0		,2114	-7.3	0.0	16	dbSNP_120	53	3593,4857		780,2033,1412	yes	intron,missense	ARMC5	NM_001105247.1,NM_024742.2	,64	806,2424,3086	TT,TC,CC		42.5207,10.593,31.9506	,	,705/726	31476458	4036,8596	2091	4225	6316	SO:0001627	intron_variant	79798	exon4			GCCCCGCGCCCAG	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.1864+250C>T	16.37:g.31476458C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_024742	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	858	0.39285714285714285	28	0.056910569105691054	209	0.5773480662983426	277	0.48426573426573427	344	0.45382585751978893	C	8.087	0.773579	0.16051	0.10593	0.425207	ENSG00000140691	ENST00000457010	T	0.21543	2.0	3.63	-7.27	0.01461	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.20261	0.043	B	0.14578	0.011	T	0.45101	-0.9284	6	.	.	.	.	4.3423	0.11115	0.1614:0.4832:0.2508:0.1046	rs11150624;rs56855049;rs11150624	704	Q96C12-4	.	V	705	ENSP00000399561:A705V	.	A	+	2	0	ARMC5	31383959	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.168000	0.03123	-1.705000	0.01406	-1.359000	0.01217	GCG	C|0.636;T|0.364	0.364	strong		0.622	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
FAM172A	83989	hgsc.bcm.edu	37	5	93410379	93410379	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:93410379A>T	ENST00000395965.3	-	2	220	c.78T>A	c.(76-78)gaT>gaA	p.D26E	FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509739.1_5'UTR|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000504768.2_5'UTR	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	26						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						TTTCTTTTTCATCTGGACCTC	0.368																																					p.D26E		Atlas-SNP	.											.	FAM172A	38	.	0			c.T78A						PASS	.						145.0	131.0	136.0					5																	93410379		2203	4300	6503	SO:0001583	missense	83989	exon2			TTTTTCATCTGGA		CCDS4069.1, CCDS54879.1, CCDS54880.1	5q15	2008-06-16	2008-06-16	2008-06-16	ENSG00000113391	ENSG00000113391			25365	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 21"""	C5orf21		11230166	Standard	NM_032042		Approved	DKFZP564D172	uc010jbd.3	Q8WUF8	OTTHUMG00000131329	ENST00000395965.3:c.78T>A	5.37:g.93410379A>T	ENSP00000379294:p.Asp26Glu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	143	16	0.111888	NM_032042	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Missense_Mutation	SNP	ENST00000395965.3	37	CCDS4069.1	.	.	.	.	.	.	.	.	.	.	A	14.71	2.617897	0.46736	.	.	ENSG00000113391	ENST00000395965	T	0.41400	1.0	5.88	5.88	0.94601	.	0.370321	0.31495	N	0.007554	T	0.22666	0.0547	N	0.20685	0.6	0.80722	D	1	B;P	0.43094	0.01;0.799	B;B	0.35278	0.013;0.199	T	0.17107	-1.0380	10	0.02654	T	1	-0.91	13.8025	0.63208	1.0:0.0:0.0:0.0	.	26;26	Q8WUF8;Q8WUF8-2	F172A_HUMAN;.	E	26	ENSP00000379294:D26E	ENSP00000379294:D26E	D	-	3	2	FAM172A	93436135	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.859000	0.55987	2.243000	0.73865	0.533000	0.62120	GAT	.	.	none		0.368	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042	
WDR91	29062	hgsc.bcm.edu	37	7	134871775	134871775	+	Silent	SNP	C	C	T	rs292557	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:134871775C>T	ENST00000354475.4	-	14	2059	c.2028G>A	c.(2026-2028)tcG>tcA	p.S676S	WDR91_ENST00000423565.1_Silent_p.S641S|WDR91_ENST00000344400.5_3'UTR	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	676										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						AATTTCCCTCCGAGTCAAAAG	0.577													C|||	3566	0.712061	0.4962	0.8372	5008	,	,		19133	0.8214		0.7068	False		,,,				2504	0.8078				p.S676S		Atlas-SNP	.											.	WDR91	82	.	0			c.G2028A						PASS	.	C		2436,1970	619.7+/-393.4	683,1070,450	122.0	125.0	124.0		2028	-10.8	0.1	7	dbSNP_79	124	6247,2353	702.9+/-405.3	2279,1689,332	no	coding-synonymous	WDR91	NM_014149.3		2962,2759,782	TT,TC,CC		27.3605,44.7118,33.2385		676/748	134871775	8683,4323	2203	4300	6503	SO:0001819	synonymous_variant	29062	exon14			TCCCTCCGAGTCA	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"""WD repeat domain containing"""	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.2028G>A	7.37:g.134871775C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	138	55	0.398551	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Silent	SNP	ENST00000354475.4	37	CCDS34758.1																																																																																			C|0.315;N|0.000	.	strong		0.577	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149	
GJB3	2707	hgsc.bcm.edu	37	1	35250720	35250720	+	Silent	SNP	C	C	T	rs41310442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:35250720C>T	ENST00000373366.2	+	2	972	c.357C>T	c.(355-357)aaC>aaT	p.N119N	GJB3_ENST00000373362.3_Silent_p.N119N|RP1-34M23.5_ENST00000542839.1_RNA	NM_024009.2	NP_076872.1	O75712	CXB3_HUMAN	gap junction protein, beta 3, 31kDa	119					cell communication (GO:0007154)|in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|sensory perception of sound (GO:0007605)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	connexon complex (GO:0005922)|cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|prostate(3)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGTACGACAACGCAGGCAAGA	0.612													c|||	489	0.0976438	0.1051	0.0331	5008	,	,		20994	0.122		0.0457	False		,,,				2504	0.1616				p.N119N		Atlas-SNP	.											.	GJB3	40	.	0			c.C357T						PASS	.		,	439,3967	211.2+/-231.4	25,389,1789	210.0	215.0	214.0		357,357	2.8	0.0	1	dbSNP_127	214	432,8168	133.6+/-191.1	11,410,3879	no	coding-synonymous,coding-synonymous	GJB3	NM_001005752.1,NM_024009.2	,	36,799,5668	TT,TC,CC		5.0233,9.9637,6.6969	,	119/271,119/271	35250720	871,12135	2203	4300	6503	SO:0001819	synonymous_variant	2707	exon2			CGACAACGCAGGC	BC012918	CCDS384.1	1p34	2008-05-14	2007-01-16		ENSG00000188910	ENSG00000188910		"""Ion channels / Gap junction proteins (connexins)"""	4285	protein-coding gene	gene with protein product	"""connexin 31"""	603324	"""gap junction protein, beta 3, 31kD (connexin 31)"", ""gap junction protein, beta 3, 31kDa (connexin 31)"", ""erythrokeratodermia variabilis"""	DFNA2, EKV		9843210, 9704026	Standard	NM_024009		Approved	CX31	uc001bxy.3	O75712	OTTHUMG00000004051	ENST00000373366.2:c.357C>T	1.37:g.35250720C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	140	89	0.635714	NM_001005752	B2R790|Q2TAZ8	Silent	SNP	ENST00000373366.2	37	CCDS384.1																																																																																			C|0.936;T|0.064	0.064	strong		0.612	GJB3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011559.1	NM_024009	
LCE2D	353141	hgsc.bcm.edu	37	1	152636843	152636843	+	Missense_Mutation	SNP	A	A	T	rs9793541	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152636843A>T	ENST00000368784.1	+	2	317	c.262A>T	c.(262-264)Agc>Tgc	p.S88C		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	88	Cys-rich.				keratinization (GO:0031424)					large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCGGCACCAGAGCCCCGATTG	0.672													A|||	624	0.124601	0.0159	0.1585	5008	,	,		12797	0.0298		0.3032	False		,,,				2504	0.1616				p.S88C		Atlas-SNP	.											LCE2D,NS,carcinoma,-1,1	LCE2D	26	1	0			c.A262T						PASS	.	A	CYS/SER	289,4099		24,241,1929	40.0	52.0	48.0		262	0.3	0.0	1	dbSNP_119	48	2484,6092		395,1694,2199	no	missense	LCE2D	NM_178430.2	112	419,1935,4128	TT,TA,AA		28.9646,6.5861,21.39	possibly-damaging	88/111	152636843	2773,10191	2194	4288	6482	SO:0001583	missense	353141	exon2			CACCAGAGCCCCG	BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"""Late cornified envelopes"""	16518	protein-coding gene	gene with protein product		612612	"""small proline rich-like (epidermal differentiation complex) 1A"""	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.262A>T	1.37:g.152636843A>T	ENSP00000357773:p.Ser88Cys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_178430	A1L4M8	Missense_Mutation	SNP	ENST00000368784.1	37	CCDS1018.1	314	0.14377289377289376	4	0.008130081300813009	67	0.1850828729281768	17	0.02972027972027972	226	0.29815303430079154	a	4.613	0.113868	0.08831	0.065861	0.289646	ENSG00000187223	ENST00000368784	T	0.06068	3.35	2.75	0.291	0.15732	.	.	.	.	.	T	0.02193	0.0068	M	0.76328	2.33	0.80722	P	0.0	P	0.43392	0.805	B	0.31016	0.123	T	0.37888	-0.9686	8	0.87932	D	0	.	4.6936	0.12793	0.6844:0.0:0.3156:0.0	rs9793541	88	Q5TA82	LCE2D_HUMAN	C	88	ENSP00000357773:S88C	ENSP00000357773:S88C	S	+	1	0	LCE2D	150903467	0.001000	0.12720	0.003000	0.11579	0.074000	0.17049	0.682000	0.25335	-0.181000	0.10619	-0.756000	0.03474	AGC	A|0.803;T|0.197	0.197	strong		0.672	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430	
KIF27	55582	hgsc.bcm.edu	37	9	86518433	86518433	+	Missense_Mutation	SNP	A	A	G	rs144003628		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:86518433A>G	ENST00000297814.2	-	4	1143	c.1000T>C	c.(1000-1002)Tat>Cat	p.Y334H	KIF27_ENST00000334204.2_Missense_Mutation_p.Y334H|KIF27_ENST00000413982.1_Missense_Mutation_p.Y334H	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	334	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						CTGTTGGCATATTTGAGAGAA	0.433																																					p.Y334H		Atlas-SNP	.											.	KIF27	103	.	0			c.T1000C						PASS	.						95.0	95.0	95.0					9																	86518433		2203	4300	6503	SO:0001583	missense	55582	exon4			TGGCATATTTGAG	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.1000T>C	9.37:g.86518433A>G	ENSP00000297814:p.Tyr334His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.979561	0.74360	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.81415	-1.49;-1.49;-1.49	5.56	4.44	0.53790	Kinesin, motor domain (3);	0.000000	0.52532	D	0.000072	D	0.93475	0.7918	H	0.99156	4.45	0.40294	D	0.978531	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.987;0.998;0.999	D	0.95040	0.8177	10	0.87932	D	0	.	10.909	0.47097	0.9271:0.0:0.0729:0.0	.	334;334;334	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	H	334	ENSP00000297814:Y334H;ENSP00000401688:Y334H;ENSP00000333928:Y334H	ENSP00000297814:Y334H	Y	-	1	0	KIF27	85708253	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.531000	0.81973	2.125000	0.65367	0.533000	0.62120	TAT	A|1.000;T|0.000	.	alt		0.433	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
SVOPL	136306	hgsc.bcm.edu	37	7	138305806	138305806	+	Silent	SNP	T	T	C	rs3734944	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:138305806T>C	ENST00000419765.3	-	13	1371	c.1338A>G	c.(1336-1338)gcA>gcG	p.A446A	SVOPL_ENST00000288513.5_Silent_p.A294A|SVOPL_ENST00000463557.1_Intron|SVOPL_ENST00000436657.1_Silent_p.A294A|SVOPL_ENST00000421622.1_Silent_p.A326A	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	446						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						ATATAAATGGTGCCACCATTG	0.577													C|||	1319	0.263379	0.0915	0.3444	5008	,	,		16962	0.3919		0.3141	False		,,,				2504	0.2536				p.A446A		Atlas-SNP	.											.	SVOPL	111	.	0			c.A1338G						PASS	.	C	,	544,3862	774.8+/-414.1	34,476,1693	65.0	55.0	58.0		1338,882	-10.7	0.0	7	dbSNP_107	58	2739,5861	680.3+/-403.6	441,1857,2002	no	coding-synonymous,coding-synonymous	SVOPL	NM_001139456.1,NM_174959.2	,	475,2333,3695	CC,CT,TT		31.8488,12.3468,25.2422	,	446/493,294/341	138305806	3283,9723	2203	4300	6503	SO:0001819	synonymous_variant	136306	exon13			AAATGGTGCCACC	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"""SV2 related protein homolog (rat)-like"""				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1338A>G	7.37:g.138305806T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	NM_001139456		Silent	SNP	ENST00000419765.3	37	CCDS47721.1																																																																																			T|0.741;C|0.259	0.259	strong		0.577	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959	
PTK2B	2185	hgsc.bcm.edu	37	8	27255146	27255146	+	Silent	SNP	G	G	A	rs1045511	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:27255146G>A	ENST00000397501.1	+	7	853	c.45G>A	c.(43-45)acG>acA	p.T15T	PTK2B_ENST00000517339.1_Silent_p.T15T|PTK2B_ENST00000346049.5_Silent_p.T15T|PTK2B_ENST00000338238.4_Silent_p.T15T|PTK2B_ENST00000420218.2_Silent_p.T15T|PTK2B_ENST00000544172.1_Silent_p.T15T	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	15					activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	AGTTGGGCACGTTACGCCGGC	0.572													G|||	1560	0.311502	0.1823	0.3818	5008	,	,		19285	0.2748		0.4304	False		,,,				2504	0.3517				p.T15T		Atlas-SNP	.											.	PTK2B	304	.	0			c.G45A						PASS	.	G	,,,	939,3467	357.1+/-313.8	113,713,1377	138.0	116.0	123.0		45,45,45,45	-8.1	0.5	8	dbSNP_86	123	3839,4761	540.9+/-383.9	867,2105,1328	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	980,2818,2705	AA,AG,GG		44.6395,21.3118,36.7369	,,,	15/1010,15/1010,15/968,15/1010	27255146	4778,8228	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon7			GGGCACGTTACGC	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.45G>A	8.37:g.27255146G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			G|0.645;A|0.355	0.355	strong		0.572	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520254	72520254	+	Missense_Mutation	SNP	C	C	T	rs61736607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:72520254C>T	ENST00000373207.1	+	22	3317	c.3317C>T	c.(3316-3318)cCt>cTt	p.P1106L	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.P1109L	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1106	Pro-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						ggcccagaccctggcccaacc	0.637													C|||	140	0.0279553	0.0038	0.0461	5008	,	,		15277	0.001		0.0805	False		,,,				2504	0.0215				p.P1109L		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.C3326T						PASS	.	C	LEU/PRO,LEU/PRO	62,4344	57.4+/-93.9	1,60,2142	54.0	52.0	53.0		3317,3326	3.5	0.0	10	dbSNP_129	53	733,7867	177.2+/-226.9	35,663,3602	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	98,98	36,723,5744	TT,TC,CC		8.5233,1.4072,6.1126	benign,benign	1106/1224,1109/1227	72520254	795,12211	2203	4300	6503	SO:0001583	missense	140766	exon22			CAGACCCTGGCCC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3317C>T	10.37:g.72520254C>T	ENSP00000362303:p.Pro1106Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	78	0.03571428571428571	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	55	0.07255936675461741	C	9.658	1.143274	0.21205	0.014072	0.085233	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.61859	0.07;0.1	4.44	3.53	0.40419	.	0.685543	0.12145	N	0.495514	T	0.01189	0.0039	N	0.02916	-0.46	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.08055	0.003;0.003	T	0.01591	-1.1317	10	0.15066	T	0.55	.	12.2683	0.54691	0.0:0.9166:0.0:0.0834	rs61736607	1106;1109	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	L	1109;1106	ENSP00000362304:P1109L;ENSP00000362303:P1106L	ENSP00000362303:P1106L	P	+	2	0	ADAMTS14	72190260	0.002000	0.14202	0.017000	0.16124	0.263000	0.26337	1.076000	0.30729	1.220000	0.43490	0.655000	0.94253	CCT	C|0.944;T|0.056	0.056	strong		0.637	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
MUC4	4585	hgsc.bcm.edu	37	3	195506245	195506245	+	Missense_Mutation	SNP	C	C	A	rs150394536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506245C>A	ENST00000463781.3	-	2	12665	c.12206G>T	c.(12205-12207)aGc>aTc	p.S4069I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S4069I	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGCTGGTGACATG	0.577													.|||	15	0.00299521	0.0038	0.0	5008	,	,		11185	0.001		0.0	False		,,,				2504	0.0092				p.S4069I		Atlas-SNP	.											.	MUC4	1505	.	0			c.G12206T						PASS	.						34.0	19.0	24.0					3																	195506245		535	1210	1745	SO:0001583	missense	4585	exon2			GAAGGGCTGGTGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12206G>T	3.37:g.195506245C>A	ENSP00000417498:p.Ser4069Ile	Somatic	280	2	0.00714286		WXS	Illumina HiSeq	Phase_I	143	117	0.818182	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	405	0.18543956043956045	69	0.1402439024390244	65	0.17955801104972377	150	0.26223776223776224	121	0.15963060686015831	N	4.718	0.133419	0.09032	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.51574	0.95;0.7	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.44694	P	0.00231899999999996	B	0.13145	0.007	B	0.09377	0.004	T	0.30937	-0.9961	6	.	.	.	.	3.4513	0.07499	0.4478:0.552:1.0E-4:1.0E-4	.	3941	E7ESK3	.	I	4069	ENSP00000417498:S4069I;ENSP00000420243:S4069I	.	S	-	2	0	MUC4	196991024	0.000000	0.05858	0.020000	0.16555	0.080000	0.17528	-0.936000	0.03946	0.488000	0.27723	0.064000	0.15345	AGC	C|0.814;A|0.186	0.186	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NTN5	126147	hgsc.bcm.edu	37	19	49168005	49168005	+	Silent	SNP	G	G	A	rs17851884	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49168005G>A	ENST00000270235.4	-	3	746	c.651C>T	c.(649-651)caC>caT	p.H217H	SEC1P_ENST00000430145.2_RNA	NM_145807.1	NP_665806.1	Q8WTR8	NET5_HUMAN	netrin 5	217	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	10						AGCGTCGGGCGTGCTGGTTGC	0.662													G|||	235	0.0469249	0.0151	0.0591	5008	,	,		12172	0.001		0.1272	False		,,,				2504	0.046				p.H217H		Atlas-SNP	.											.	NTN5	27	.	0			c.C651T						PASS	.	G		135,4205		4,127,2039	10.0	11.0	10.0		651	-1.4	1.0	19	dbSNP_123	10	1001,7529		58,885,3322	no	coding-synonymous	NTN5	NM_145807.1		62,1012,5361	AA,AG,GG		11.7351,3.1106,8.8267		217/490	49168005	1136,11734	2170	4265	6435	SO:0001819	synonymous_variant	126147	exon3			TCGGGCGTGCTGG		CCDS33068.1	19q13.33	2013-03-01			ENSG00000142233	ENSG00000142233		"""Netrins"""	25208	protein-coding gene	gene with protein product	"""Netrin-5"""					12477932	Standard	NM_145807		Approved		uc002pkb.3	Q8WTR8		ENST00000270235.4:c.651C>T	19.37:g.49168005G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	70	0.636364	NM_145807	Q8N4X9|Q8WU63	Silent	SNP	ENST00000270235.4	37	CCDS33068.1																																																																																			G|0.937;A|0.063	0.063	strong		0.662	NTN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466176.1	NM_145807	
SMARCC1	6599	hgsc.bcm.edu	37	3	47712202	47712202	+	Silent	SNP	T	T	C	rs1141601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:47712202T>C	ENST00000254480.5	-	19	1964	c.1845A>G	c.(1843-1845)aaA>aaG	p.K615K	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	615					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		CACTAGCACCTTTACTCTAAG	0.413													T|||	926	0.184904	0.0113	0.2795	5008	,	,		19467	0.251		0.3221	False		,,,				2504	0.1431				p.K615K		Atlas-SNP	.											.	SMARCC1	85	.	0			c.A1845G						PASS	.	T		257,4149	145.4+/-180.2	9,239,1955	119.0	103.0	108.0		1845	4.3	1.0	3	dbSNP_86	108	2428,6172	392.3+/-344.0	367,1694,2239	no	coding-synonymous	SMARCC1	NM_003074.3		376,1933,4194	CC,CT,TT		28.2326,5.833,20.6443		615/1106	47712202	2685,10321	2203	4300	6503	SO:0001819	synonymous_variant	6599	exon19			AGCACCTTTACTC	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1845A>G	3.37:g.47712202T>C		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	279	143	0.512545	NM_003074	Q17RS0|Q6P172|Q8IWH2	Silent	SNP	ENST00000254480.5	37	CCDS2758.1																																																																																			T|0.639;G|0.036	.	strong		0.413	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1		
SLC30A9	10463	hgsc.bcm.edu	37	4	41992677	41992677	+	Silent	SNP	C	C	G	rs2581434	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:41992677C>G	ENST00000264451.7	+	1	189	c.9C>G	c.(7-9)ccC>ccG	p.P3P	RP11-814H16.2_ENST00000608029.1_lincRNA	NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	3					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GGATGTTACCCGGCTTGGCCG	0.682													G|||	3540	0.706869	0.2458	0.8401	5008	,	,		13696	0.9593		0.8151	False		,,,				2504	0.864				p.P3P		Atlas-SNP	.											.	SLC30A9	58	.	0			c.C9G						PASS	.	G		1457,2921		278,901,1010	20.0	20.0	20.0		9	2.8	1.0	4	dbSNP_100	20	7007,1573		2888,1231,171	no	coding-synonymous	SLC30A9	NM_006345.3		3166,2132,1181	GG,GC,CC		18.3333,33.28,34.6813		3/569	41992677	8464,4494	2189	4290	6479	SO:0001819	synonymous_variant	10463	exon1			GTTACCCGGCTTG	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"""Solute carriers"""	1329	protein-coding gene	gene with protein product	"""GRIP1-dependent nuclear receptor coactivator"""	604604	"""chromosome 4 open reading frame 1"""	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.9C>G	4.37:g.41992677C>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Silent	SNP	ENST00000264451.7	37	CCDS3465.1																																																																																			C|0.328;G|0.672	0.672	strong		0.682	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3		
NUFIP1	26747	hgsc.bcm.edu	37	13	45563464	45563464	+	Missense_Mutation	SNP	G	G	C	rs1140993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:45563464G>C	ENST00000379161.4	-	1	154	c.108C>G	c.(106-108)agC>agG	p.S36R	GPALPP1_ENST00000379151.4_5'Flank|GPALPP1_ENST00000361121.2_5'Flank|RP11-321C24.1_ENST00000437748.2_lincRNA	NM_012345.2	NP_036477.2	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein interacting protein 1	36	Pro-rich.		S -> R (in dbSNP:rs1140993). {ECO:0000269|PubMed:10556305}.		box C/D snoRNP assembly (GO:0000492)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA processing (GO:0006396)	cytosolic ribosome (GO:0022626)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|pre-snoRNP complex (GO:0070761)|presynaptic active zone (GO:0048786)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(4)|skin(3)	18		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		AGAACATCCAGCTGTCCCGCG	0.652													G|||	2567	0.51258	0.1286	0.6441	5008	,	,		14873	0.5575		0.7744	False		,,,				2504	0.6227				p.S36R		Atlas-SNP	.											.	NUFIP1	41	.	0			c.C108G						PASS	.	G	ARG/SER	998,3388		136,726,1331	15.0	18.0	17.0		108	1.3	0.0	13	dbSNP_86	17	6578,2002		2543,1492,255	no	missense	NUFIP1	NM_012345.2	110	2679,2218,1586	CC,CG,GG		23.3333,22.7542,41.5703	benign	36/496	45563464	7576,5390	2193	4290	6483	SO:0001583	missense	26747	exon1			CATCCAGCTGTCC	AF159548	CCDS9393.1	13q14	2008-02-05			ENSG00000083635	ENSG00000083635			8057	protein-coding gene	gene with protein product		604354				10556305, 10894927	Standard	NM_012345		Approved	NUFIP	uc001uzp.2	Q9UHK0	OTTHUMG00000016842	ENST00000379161.4:c.108C>G	13.37:g.45563464G>C	ENSP00000368459:p.Ser36Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	85	83	0.976471	NM_012345	Q8WVM5|Q96SG1	Missense_Mutation	SNP	ENST00000379161.4	37	CCDS9393.1	1205	0.5517399267399268	58	0.11788617886178862	227	0.6270718232044199	334	0.583916083916084	586	0.7730870712401056	G	10.62	1.400964	0.25291	0.227542	0.766667	ENSG00000083635	ENST00000379161	T	0.43294	0.95	3.96	1.29	0.21616	.	0.926496	0.09036	N	0.857946	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.26400	0.148	B	0.22152	0.038	T	0.29458	-1.0011	9	0.46703	T	0.11	-2.1681	5.7108	0.17933	0.3445:0.0:0.6555:0.0	rs1140993	36	Q9UHK0	NUFP1_HUMAN	R	36	ENSP00000368459:S36R	ENSP00000368459:S36R	S	-	3	2	NUFIP1	44461464	0.017000	0.18338	0.018000	0.16275	0.006000	0.05464	0.105000	0.15333	0.253000	0.21552	0.563000	0.77884	AGC	G|0.431;C|0.569	0.569	strong		0.652	NUFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044755.2	NM_012345	
TNS1	7145	hgsc.bcm.edu	37	2	218683368	218683368	+	Silent	SNP	C	C	T	rs34144104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:218683368C>T	ENST00000171887.4	-	24	3827	c.3375G>A	c.(3373-3375)ccG>ccA	p.P1125P	TNS1_ENST00000419504.1_Silent_p.P1112P|TNS1_ENST00000430930.1_Silent_p.P1104P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1125	Ser-rich.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.P1125P(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TCTGGGCAGACGGGCTGGGCT	0.632													C|||	1078	0.215256	0.0643	0.3156	5008	,	,		17264	0.2292		0.2654	False		,,,				2504	0.2822				p.P1125P		Atlas-SNP	.											TNS1,NS,carcinoma,0,2	TNS1	251	2	1	Substitution - coding silent(1)	prostate(1)	c.G3375A						PASS	.	C		401,4005	197.1+/-221.3	19,363,1821	45.0	50.0	48.0		3375	-1.6	0.3	2	dbSNP_126	48	2547,6053	413.0+/-351.0	376,1795,2129	no	coding-synonymous	TNS1	NM_022648.4		395,2158,3950	TT,TC,CC		29.6163,9.1012,22.6665		1125/1736	218683368	2948,10058	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon24			GGCAGACGGGCTG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.3375G>A	2.37:g.218683368C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	189	98	0.518519	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			C|0.774;T|0.226	0.226	strong		0.632	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
AGPAT4	56895	hgsc.bcm.edu	37	6	161557662	161557662	+	Silent	SNP	G	G	A	rs3734462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:161557662G>A	ENST00000320285.4	-	9	1259	c.1047C>T	c.(1045-1047)tcC>tcT	p.S349S	AGPAT4_ENST00000366911.5_3'UTR|AGPAT4_ENST00000457520.2_Silent_p.S187S	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	349					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		GAACTCCCACGGAGGCTGCAG	0.542													G|||	687	0.137181	0.0204	0.33	5008	,	,		19489	0.1825		0.1899	False		,,,				2504	0.0573				p.S349S		Atlas-SNP	.											AGPAT4,brain,glioma,-1,1	AGPAT4	50	1	0			c.C1047T						PASS	.	G		214,4192	130.6+/-167.2	5,204,1994	102.0	88.0	93.0		1047	-1.3	0.8	6	dbSNP_107	93	1631,6969	301.4+/-305.4	159,1313,2828	no	coding-synonymous	AGPAT4	NM_020133.2		164,1517,4822	AA,AG,GG		18.9651,4.857,14.1858		349/379	161557662	1845,11161	2203	4300	6503	SO:0001819	synonymous_variant	56895	exon9			TCCCACGGAGGCT	AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20885	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, delta"""	614795	"""1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"""				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.1047C>T	6.37:g.161557662G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_020133	B4DSF9|Q5TEF0	Silent	SNP	ENST00000320285.4	37	CCDS5280.1																																																																																			G|0.858;A|0.142	0.142	strong		0.542	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133	
OBSCN	84033	hgsc.bcm.edu	37	1	228520973	228520973	+	Missense_Mutation	SNP	C	C	G	rs369909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228520973C>G	ENST00000422127.1	+	58	15849	c.15805C>G	c.(15805-15807)Ctc>Gtc	p.L5269V	OBSCN_ENST00000284548.11_Missense_Mutation_p.L5269V|OBSCN_ENST00000570156.2_Missense_Mutation_p.L6226V|OBSCN_ENST00000366709.4_Missense_Mutation_p.L2388V|OBSCN_ENST00000366707.4_Missense_Mutation_p.L2903V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5269	Ig-like 50.		L -> V (in dbSNP:rs369909).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTGAGAGACCTCCAGGTGGC	0.627													C|||	1678	0.335064	0.4183	0.3847	5008	,	,		17947	0.249		0.4205	False		,,,				2504	0.1881				p.L6226V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C18676G						PASS	.	C	VAL/LEU,VAL/LEU	1383,2607		266,851,878	12.0	15.0	14.0		15805,15805	2.0	1.0	1	dbSNP_80	14	3469,4833		793,1883,1475	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	32,32	1059,2734,2353	GG,GC,CC		41.7851,34.6617,39.4728	possibly-damaging,possibly-damaging	5269/7969,5269/6621	228520973	4852,7440	1995	4151	6146	SO:0001583	missense	84033	exon69			AGAGACCTCCAGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15805C>G	1.37:g.228520973C>G	ENSP00000409493:p.Leu5269Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	780	0.35714285714285715	196	0.3983739837398374	133	0.3674033149171271	135	0.23601398601398602	316	0.41688654353562005	C	21.3	4.126247	0.77549	0.346617	0.417851	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.29	2.01	0.26516	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.253964	0.32028	N	0.006689	T	0.00012	0.0000	N	0.16201	0.385	0.39043	P	0.03983800000000004	B;B	0.20550	0.046;0.037	B;B	0.22152	0.038;0.022	T	0.36962	-0.9726	9	0.07482	T	0.82	.	7.164	0.25679	0.3498:0.4202:0.23:0.0	rs369909;rs1697610;rs3795806;rs57264919;rs369909	5269;5269	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	V	5269;5269;2903;2388	ENSP00000284548:L5269V;ENSP00000409493:L5269V;ENSP00000355668:L2903V;ENSP00000355670:L2388V	ENSP00000284548:L5269V	L	+	1	0	OBSCN	226587596	1.000000	0.71417	0.982000	0.44146	0.933000	0.57130	1.457000	0.35212	0.721000	0.32231	0.561000	0.74099	CTC	C|0.669;G|0.331	0.331	strong		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
APOA5	116519	hgsc.bcm.edu	37	11	116662331	116662331	+	Silent	SNP	G	G	T	rs12287066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:116662331G>T	ENST00000227665.4	-	2	166	c.132C>A	c.(130-132)atC>atA	p.I44I	APOA5_ENST00000542499.1_Silent_p.I44I			Q6Q788	APOA5_HUMAN	apolipoprotein A-V	44					acylglycerol homeostasis (GO:0055090)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|organ regeneration (GO:0031100)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)	chylomicron (GO:0042627)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|lipase activator activity (GO:0060229)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|lipoprotein particle receptor binding (GO:0070325)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylcholine binding (GO:0031210)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	14	all_hematologic(175;0.0487)	all_cancers(61;3.31e-09)|all_epithelial(67;8.03e-06)|Breast(348;0.0126)|Melanoma(852;0.0153)|Acute lymphoblastic leukemia(157;0.0257)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0433)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;4.93e-06)|all cancers(92;0.000123)|OV - Ovarian serous cystadenocarcinoma(223;0.149)		TCTGCTGATGGATCTGCTCCA	0.627											OREG0021366	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	454	0.090655	0.1899	0.1369	5008	,	,		18305	0.0		0.0676	False		,,,				2504	0.0409				p.I44I		Atlas-SNP	.											.	APOA5	34	.	0			c.C132A						PASS	.	G	,	749,3649	292.1+/-281.9	75,599,1525	82.0	72.0	76.0		132,132	1.9	1.0	11	dbSNP_120	76	581,8011	146.3+/-201.9	21,539,3736	no	coding-synonymous,coding-synonymous	APOA5	NM_001166598.1,NM_052968.4	,	96,1138,5261	TT,TG,GG		6.7621,17.0305,10.2386	,	44/367,44/367	116662331	1330,11660	2199	4296	6495	SO:0001819	synonymous_variant	116519	exon3			CTGATGGATCTGC	AF202889	CCDS8376.2	11q23	2013-01-24			ENSG00000110243	ENSG00000110243		"""Apolipoproteins"""	17288	protein-coding gene	gene with protein product		606368				11588264, 11577099	Standard	NM_001166598		Approved	RAP3, APOA-V	uc009yzf.3	Q6Q788	OTTHUMG00000046116	ENST00000227665.4:c.132C>A	11.37:g.116662331G>T		Somatic	205	0	0	1475	WXS	Illumina HiSeq	Phase_I	189	91	0.481481	NM_001166598	B0YIV9|Q3MIK6|Q6UWK9|Q9UBJ3	Silent	SNP	ENST00000227665.4	37	CCDS8376.2																																																																																			G|0.901;T|0.099	0.099	strong		0.627	APOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106285.2		
PKD1L2	114780	hgsc.bcm.edu	37	16	81242194	81242194	+	RNA	SNP	T	T	C	rs6564838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81242194T>C	ENST00000525539.1	-	0	661				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGACTGTAGCTCCTGGCACTG	0.547													C|||	3667	0.732228	0.5749	0.745	5008	,	,		20530	0.8839		0.8469	False		,,,				2504	0.6616				p.E221G		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A662G						PASS	.	C	GLY/GLU,GLY/GLU	2645,1567		845,955,306	68.0	66.0	67.0		662,662	4.3	1.0	16	dbSNP_116	67	7120,1322		3003,1114,104	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	98,98	3848,2069,410	CC,CT,TT		15.6598,37.2032,22.8307	benign,benign	221/992,221/2460	81242194	9765,2889	2106	4221	6327			114780	exon4			TGTAGCTCCTGGC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242194T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1714	0.7847985347985348	282	0.573170731707317	289	0.7983425414364641	495	0.8653846153846154	648	0.8548812664907651	C	2.293	-0.362040	0.05103	0.627968	0.843402	ENSG00000166473	ENST00000337114	T	0.14144	2.53	4.31	4.31	0.51392	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.070422	0.56097	N	0.000031	T	0.00012	0.0000	.	.	.	0.39873	P	0.026468000000000047	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36504	-0.9745	8	0.02654	T	1	-11.4682	11.9836	0.53133	0.0:0.9136:0.0:0.0864	rs6564838;rs59152870;rs6564838	221;221	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	G	221	ENSP00000337397:E221G	ENSP00000337397:E221G	E	-	2	0	PKD1L2	79799695	0.999000	0.42202	1.000000	0.80357	0.451000	0.32288	4.255000	0.58804	0.824000	0.34613	-0.642000	0.03964	GAG	T|0.231;C|0.769	0.769	strong		0.547	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
CARD8	22900	hgsc.bcm.edu	37	19	48715153	48715153	+	Silent	SNP	T	T	C	rs3745718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48715153T>C	ENST00000359009.4	-	10	1422	c.1110A>G	c.(1108-1110)caA>caG	p.Q370Q	CARD8_ENST00000521613.1_Silent_p.Q426Q|CARD8_ENST00000391898.3_Silent_p.Q476Q|CARD8_ENST00000357778.5_Intron|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000520153.1_Silent_p.Q426Q|CARD8_ENST00000447740.2_Silent_p.Q426Q|CTC-453G23.8_ENST00000595201.1_RNA|CARD8_ENST00000520015.1_3'UTR|CARD8_ENST00000520753.1_3'UTR|CARD8_ENST00000519940.1_Silent_p.Q476Q			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	370	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		CCTCATTGTCTTGGAGATCAT	0.532													T|||	1948	0.388978	0.2186	0.5533	5008	,	,		20355	0.2282		0.5199	False		,,,				2504	0.5337				p.Q476Q		Atlas-SNP	.											CARD8_ENST00000391898,colon,carcinoma,0,1	CARD8	53	1	0			c.A1428G						PASS	.	T	,,,,	1188,3218	415.0+/-337.0	160,868,1175	185.0	173.0	177.0		1428,1278,,,1278	0.9	0.2	19	dbSNP_107	177	4800,3800	612.6+/-396.0	1370,2060,870	no	coding-synonymous,coding-synonymous,utr-3,utr-3,coding-synonymous	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	,,,,	1530,2928,2045	CC,CT,TT		44.186,26.9632,46.0403	,,,,	476/538,426/488,,,426/488	48715153	5988,7018	2203	4300	6503	SO:0001819	synonymous_variant	22900	exon11			ATTGTCTTGGAGA	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.1110A>G	19.37:g.48715153T>C		Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	253	124	0.490119	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Silent	SNP	ENST00000359009.4	37																																																																																				T|0.588;C|0.412	0.412	strong		0.532	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
S100Z	170591	hgsc.bcm.edu	37	5	76171252	76171252	+	Missense_Mutation	SNP	A	A	C	rs1320308	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:76171252A>C	ENST00000317593.4	+	3	300	c.68A>C	c.(67-69)gAa>gCa	p.E23A	S100Z_ENST00000513010.1_Missense_Mutation_p.E23A	NM_130772.3	NP_570128.2	Q8WXG8	S100Z_HUMAN	S100 calcium binding protein Z	23	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.		E -> A (in dbSNP:rs1320308). {ECO:0000269|PubMed:11747429, ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			large_intestine(1)|ovary(1)	2		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;8.91e-51)|Epithelial(54;5.43e-45)|all cancers(79;1.82e-40)		TCTGGCAAGGAAAGGAAGAGA	0.532													A|||	2768	0.552716	0.5741	0.6628	5008	,	,		18098	0.5615		0.6958	False		,,,				2504	0.2894				p.E23A		Atlas-SNP	.											S100Z,NS,carcinoma,+1,1	S100Z	14	1	0			c.A68C						PASS	.	A	ALA/GLU	2253,1681		665,923,379	80.0	84.0	83.0		68	5.6	1.0	5	dbSNP_88	83	5598,2692		1882,1834,429	yes	missense	S100Z	NM_130772.3	107	2547,2757,808	CC,CA,AA		32.4729,42.73,35.7739	probably-damaging	23/100	76171252	7851,4373	1967	4145	6112	SO:0001583	missense	170591	exon3			GCAAGGAAAGGAA	AF437876	CCDS43333.1	5q13.3	2014-08-12	2006-09-11		ENSG00000171643	ENSG00000171643		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	30367	protein-coding gene	gene with protein product		610103	"""S100 calcium binding protein, zeta"""			11747429	Standard	NM_130772		Approved	Gm625, S100-zeta	uc003keq.4	Q8WXG8	OTTHUMG00000162441	ENST00000317593.4:c.68A>C	5.37:g.76171252A>C	ENSP00000320430:p.Glu23Ala	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_130772		Missense_Mutation	SNP	ENST00000317593.4	37	CCDS43333.1	1351	0.6185897435897436	283	0.5752032520325203	251	0.6933701657458563	291	0.5087412587412588	526	0.6939313984168866	A	17.13	3.311833	0.60414	0.5727	0.675271	ENSG00000171643	ENST00000513010;ENST00000317593	T;T	0.12255	2.7;2.7	5.58	5.58	0.84498	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.046090	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.19300	P	0.9999735892	D	0.89917	1.0	D	0.75484	0.986	T	0.28839	-1.0031	8	0.51188	T	0.08	.	15.4177	0.74983	1.0:0.0:0.0:0.0	rs1320308;rs17749716;rs17851986;rs52819823;rs57560961;rs1320308	23	Q8WXG8	S100Z_HUMAN	A	23	ENSP00000426768:E23A;ENSP00000320430:E23A	ENSP00000320430:E23A	E	+	2	0	S100Z	76207008	1.000000	0.71417	1.000000	0.80357	0.054000	0.15201	5.881000	0.69706	2.118000	0.64928	0.533000	0.62120	GAA	C|0.618;N|0.001;A|0.381	0.618	strong		0.532	S100Z-002	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368927.1	NM_130772	
WDR17	116966	hgsc.bcm.edu	37	4	177100644	177100644	+	Missense_Mutation	SNP	G	G	A	rs11736872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:177100644G>A	ENST00000280190.4	+	31	4039	c.3883G>A	c.(3883-3885)Gct>Act	p.A1295T	WDR17_ENST00000507824.2_Missense_Mutation_p.A1270T|WDR17_ENST00000393643.2_Missense_Mutation_p.A1271T|WDR17_ENST00000508596.1_Missense_Mutation_p.A1256T			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1295			A -> T (in dbSNP:rs11736872). {ECO:0000269|PubMed:12401215}.							breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CGGGAAATCTGCTATCTCCTT	0.388													G|||	1037	0.207069	0.1369	0.2104	5008	,	,		12251	0.13		0.2783	False		,,,				2504	0.3057				p.A1295T		Atlas-SNP	.											.	WDR17	198	.	0			c.G3883A						PASS	.	G	THR/ALA,THR/ALA	678,3728	285.7+/-278.4	58,562,1583	152.0	138.0	143.0		3883,3766	-0.9	0.3	4	dbSNP_120	143	2558,6042	417.4+/-352.4	365,1828,2107	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	58,58	423,2390,3690	AA,AG,GG		29.7442,15.3881,24.8808	benign,benign	1295/1323,1256/1284	177100644	3236,9770	2203	4300	6503	SO:0001583	missense	116966	exon31			AAATCTGCTATCT	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"""WD repeat domain containing"""	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3883G>A	4.37:g.177100644G>A	ENSP00000280190:p.Ala1295Thr	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	241	122	0.506224	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	428|428	0.19597069597069597|0.19597069597069597	68|68	0.13821138211382114|0.13821138211382114	85|85	0.23480662983425415|0.23480662983425415	63|63	0.11013986013986014|0.11013986013986014	212|212	0.2796833773087071|0.2796833773087071	G|G	12.85|12.85	2.060188|2.060188	0.36373|0.36373	0.153881|0.153881	0.297442|0.297442	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.58210|.	0.37;0.4;0.35|.	5.51|5.51	-0.869|-0.869	0.10649|0.10649	.|.	0.254658|.	0.38058|.	N|.	0.001838|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11927|0.11927	0.2|0.2	0.23381|0.23381	P|P	0.99779477|0.99779477	B;B;B|.	0.17038|.	0.02;0.001;0.003|.	B;B;B|.	0.13407|.	0.009;0.006;0.006|.	T|T	0.39354|0.39354	-0.9618|-0.9618	9|4	0.16896|.	T|.	0.51|.	-5.5383|-5.5383	10.6133|10.6133	0.45434|0.45434	0.3901:0.0:0.6099:0.0|0.3901:0.0:0.6099:0.0	rs11736872;rs17671753;rs52832800;rs60810877;rs11736872|rs11736872;rs17671753;rs52832800;rs60810877;rs11736872	1271;1256;1295|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	T|Y	1256;1271;1295;1271|529	ENSP00000422763:A1256T;ENSP00000377258:A1271T;ENSP00000280190:A1295T|.	ENSP00000280190:A1295T|.	A|C	+|+	1|2	0|0	WDR17|WDR17	177337638|177337638	0.202000|0.202000	0.23423|0.23423	0.315000|0.315000	0.25238|0.25238	0.997000|0.997000	0.91878|0.91878	0.596000|0.596000	0.24044|0.24044	-0.180000|-0.180000	0.10637|0.10637	0.655000|0.655000	0.94253|0.94253	GCT|TGC	G|0.774;A|0.226	0.226	strong		0.388	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
SVIL	6840	hgsc.bcm.edu	37	10	29821089	29821089	+	Silent	SNP	C	C	T	rs17756919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29821089C>T	ENST00000355867.4	-	9	2603	c.1851G>A	c.(1849-1851)gtG>gtA	p.V617V	SVIL_ENST00000375398.2_Silent_p.V617V|SVIL_ENST00000375400.3_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	617					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CCGACCTCTCCACCCGTGATT	0.498													C|||	1436	0.286741	0.3313	0.3617	5008	,	,		20324	0.0764		0.3926	False		,,,				2504	0.2812				p.V617V		Atlas-SNP	.											.	SVIL	226	.	0			c.G1851A						PASS	.	C	,	1520,2886	480.4+/-358.8	273,974,956	56.0	54.0	55.0		,1851	0.4	0.8	10	dbSNP_123	55	3531,5069	514.6+/-378.4	732,2067,1501	no	intron,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	1005,3041,2457	TT,TC,CC		41.0581,34.4984,38.8359	,	,617/2215	29821089	5051,7955	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon9			CCTCTCCACCCGT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1851G>A	10.37:g.29821089C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			C|0.659;T|0.341	0.341	strong		0.498	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
SMCO4	56935	hgsc.bcm.edu	37	11	93212245	93212245	+	Silent	SNP	C	C	T	rs3207348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:93212245C>T	ENST00000298966.2	-	3	496	c.111G>A	c.(109-111)acG>acA	p.T37T	SMCO4_ENST00000525141.1_Silent_p.T37T|SMCO4_ENST00000527149.1_Silent_p.T37T	NM_020179.2	NP_064564.1	Q9NRQ5	SMCO4_HUMAN	single-pass membrane protein with coiled-coil domains 4	37						integral component of membrane (GO:0016021)											CCACGGCCAGCGTGGGCAGCA	0.637													c|||	390	0.0778754	0.0113	0.0764	5008	,	,		14773	0.0397		0.159	False		,,,				2504	0.1247				p.T37T		Atlas-SNP	.											.	.	.	.	0			c.G111A						PASS	.	T		157,4245	106.0+/-144.5	1,155,2045	100.0	84.0	90.0		111	-3.5	1.0	11	dbSNP_105	90	1373,7223	267.4+/-287.2	114,1145,3039	no	coding-synonymous	C11orf75	NM_020179.2		115,1300,5084	TT,TC,CC		15.9725,3.5666,11.771		37/60	93212245	1530,11468	2201	4298	6499	SO:0001819	synonymous_variant	0	exon3			GGCCAGCGTGGGC	BC031564	CCDS8292.1	11q21	2013-03-11	2013-03-11	2013-03-11	ENSG00000166002	ENSG00000166002			24810	protein-coding gene	gene with protein product		609477	"""chromosome 11 open reading frame 75"""	C11orf75		10863097	Standard	NM_020179		Approved	FN5	uc001pds.4	Q9NRQ5	OTTHUMG00000167442	ENST00000298966.2:c.111G>A	11.37:g.93212245C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_020179		Silent	SNP	ENST00000298966.2	37	CCDS8292.1																																																																																			C|0.891;T|0.109	0.109	strong		0.637	SMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394630.1	NM_020179	
TRPA1	8989	hgsc.bcm.edu	37	8	72981318	72981318	+	Silent	SNP	G	G	A	rs28546865	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:72981318G>A	ENST00000262209.4	-	3	591	c.384C>T	c.(382-384)aaC>aaT	p.N128N		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	128					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TCATGTTGAAGTTTCGGAGAT	0.473													G|||	999	0.199481	0.295	0.0793	5008	,	,		19479	0.2847		0.1252	False		,,,				2504	0.1442				p.N128N		Atlas-SNP	.											.	TRPA1	256	.	0			c.C384T						PASS	.	G		1224,3182	424.2+/-340.4	157,910,1136	229.0	243.0	238.0		384	3.9	0.5	8	dbSNP_125	238	936,7664	206.1+/-248.3	62,812,3426	no	coding-synonymous	TRPA1	NM_007332.2		219,1722,4562	AA,AG,GG		10.8837,27.7803,16.6077		128/1120	72981318	2160,10846	2203	4300	6503	SO:0001819	synonymous_variant	8989	exon3			GTTGAAGTTTCGG	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.384C>T	8.37:g.72981318G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			G|0.819;A|0.181	0.181	strong		0.473	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
SIPA1	6494	hgsc.bcm.edu	37	11	65408937	65408937	+	Missense_Mutation	SNP	C	C	T	rs3741378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65408937C>T	ENST00000394224.3	+	2	841	c.545C>T	c.(544-546)tCc>tTc	p.S182F	SIPA1_ENST00000394227.3_Missense_Mutation_p.S182F|SIPA1_ENST00000534313.1_Missense_Mutation_p.S182F|SIPA1_ENST00000527525.1_Missense_Mutation_p.S182F	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	182			S -> F (in dbSNP:rs3741378). {ECO:0000269|PubMed:9346962}.		cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						GGACCAGCATCCCCACCTGTG	0.677													C|||	1050	0.209665	0.3048	0.1412	5008	,	,		16826	0.3522		0.1312	False		,,,				2504	0.0634				p.S182F		Atlas-SNP	.											.	SIPA1	45	.	0			c.C545T						PASS	.	C	PHE/SER,PHE/SER	1167,3233	404.9+/-333.3	156,855,1189	50.0	52.0	51.0		545,545	2.7	0.1	11	dbSNP_107	51	1126,7468	231.1+/-265.2	78,970,3249	yes	missense,missense	SIPA1	NM_006747.3,NM_153253.29	155,155	234,1825,4438	TT,TC,CC		13.1022,26.5227,17.6466	possibly-damaging,possibly-damaging	182/1043,182/1043	65408937	2293,10701	2200	4297	6497	SO:0001583	missense	6494	exon2			CAGCATCCCCACC	AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.545C>T	11.37:g.65408937C>T	ENSP00000377771:p.Ser182Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_006747	O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	37	CCDS8108.1	504	0.23076923076923078	158	0.32113821138211385	50	0.13812154696132597	201	0.3513986013986014	95	0.12532981530343007	C	11.84	1.758463	0.31137	0.265227	0.131022	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	D;D;D;D	0.83250	-1.69;-1.7;-1.69;-1.7	4.78	2.65	0.31530	.	0.828298	0.10021	U	0.726013	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B;B	0.31351	0.32;0.214	B;B	0.34931	0.192;0.094	T	0.04930	-1.0917	9	0.72032	D	0.01	-10.8171	12.2808	0.54762	0.0:0.6725:0.3275:0.0	rs3741378;rs3741378	182;182	F6RY50;Q96FS4	.;SIPA1_HUMAN	F	182	ENSP00000436269:S182F;ENSP00000433686:S182F;ENSP00000377771:S182F;ENSP00000377774:S182F	ENSP00000377771:S182F	S	+	2	0	SIPA1	65165513	0.004000	0.15560	0.104000	0.21259	0.212000	0.24457	1.961000	0.40432	1.071000	0.40834	0.555000	0.69702	TCC	C|0.800;T|0.200	0.200	strong		0.677	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747	
RBMXL1	494115	hgsc.bcm.edu	37	1	89448646	89448646	+	Silent	SNP	A	A	G	rs138129402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89448646A>G	ENST00000321792.5	-	2	1291	c.864T>C	c.(862-864)taT>taC	p.Y288Y	RBMXL1_ENST00000413769.1_5'Flank|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Silent_p.Y288Y	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	288	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										GTGAGTTACCATAACTCTCAT	0.473																																					p.Y288Y		Atlas-SNP	.											CCBL2,NS,haematopoietic_neoplasm,0,1	.	.	1	0			c.T864C						scavenged	.						201.0	195.0	197.0					1																	89448646		2203	4300	6503	SO:0001819	synonymous_variant	494115	exon3			GTTACCATAACTC	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.864T>C	1.37:g.89448646A>G		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	296	9	0.0304054	NM_001162536		Silent	SNP	ENST00000321792.5	37	CCDS716.1																																																																																			A|0.995;G|0.005	0.005	strong		0.473	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
GEMIN4	50628	hgsc.bcm.edu	37	17	649505	649505	+	Missense_Mutation	SNP	T	T	A	rs4968104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:649505T>A	ENST00000319004.5	-	2	1896	c.1778A>T	c.(1777-1779)gAg>gTg	p.E593V	GEMIN4_ENST00000576778.1_Missense_Mutation_p.E582V	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	593				E -> V (in Ref. 1; AAF35283 and 3; CAB45743). {ECO:0000305}.	gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GGGACCCTGCTCTTCCACAAA	0.498													T|||	795	0.158746	0.0545	0.1772	5008	,	,		19029	0.122		0.2465	False		,,,				2504	0.2342				p.E593V		Atlas-SNP	.											GEMIN4_ENST00000319004,NS,carcinoma,0,4	GEMIN4	116	4	0			c.A1778T						PASS	.	T	VAL/GLU	361,3573		17,327,1623	98.0	102.0	101.0		1778	5.5	0.9	17	dbSNP_111	101	2103,6257		286,1531,2363	yes	missense	GEMIN4	NM_015721.2	121	303,1858,3986	AA,AT,TT		25.1555,9.1764,20.0423	possibly-damaging	593/1059	649505	2464,9830	1967	4180	6147	SO:0001583	missense	50628	exon2			CCCTGCTCTTCCA	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.1778A>T	17.37:g.649505T>A	ENSP00000321706:p.Glu593Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	358	0.16391941391941392	26	0.052845528455284556	72	0.19889502762430938	75	0.13111888111888112	185	0.24406332453825857	T	2.280	-0.364930	0.05103	0.091764	0.251555	ENSG00000179409	ENST00000319004	T	0.16597	2.33	5.46	5.46	0.80206	.	0.885835	0.09880	N	0.743765	T	0.00012	0.0000	L	0.57536	1.79	0.09310	P	0.9999999547019	B	0.30439	0.279	B	0.28139	0.086	T	0.34850	-0.9812	9	0.36615	T	0.2	-13.2991	5.9152	0.19052	0.0:0.0844:0.168:0.7476	rs4968104;rs52822209;rs4968104	593	P57678	GEMI4_HUMAN	V	593	ENSP00000321706:E593V	ENSP00000321706:E593V	E	-	2	0	GEMIN4	596255	0.000000	0.05858	0.900000	0.35374	0.022000	0.10575	0.530000	0.23036	2.079000	0.62486	0.482000	0.46254	GAG	T|0.816;A|0.184	0.184	strong		0.498	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
FCGBP	8857	hgsc.bcm.edu	37	19	40368358	40368358	+	Silent	SNP	G	G	A	rs146289015	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40368358G>A	ENST00000221347.6	-	28	12997	c.12990C>T	c.(12988-12990)gcC>gcT	p.A4330A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4330						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCTGGCAGGCGGCCACGTAGG	0.642																																					p.A4330A		Atlas-SNP	.											.	FCGBP	416	.	0			c.C12990T						PASS	.	G		20,4386	27.2+/-55.0	0,20,2183	189.0	196.0	194.0		12990	-8.2	0.0	19	dbSNP_134	194	199,8401	83.1+/-145.7	0,199,4101	no	coding-synonymous	FCGBP	NM_003890.2		0,219,6284	AA,AG,GG		2.314,0.4539,1.6838		4330/5406	40368358	219,12787	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon28			GCAGGCGGCCACG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12990C>T	19.37:g.40368358G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	386	90	0.233161	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.987;A|0.013	0.013	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
OR13C2	392376	hgsc.bcm.edu	37	9	107367612	107367612	+	Silent	SNP	C	C	T	rs55706329	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107367612C>T	ENST00000542196.1	-	1	339	c.297G>A	c.(295-297)gtG>gtA	p.V99V		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GGAACATCTGCACTGCACAGC	0.517													C|||	1853	0.370008	0.4962	0.2089	5008	,	,		23529	0.5129		0.175	False		,,,				2504	0.3671				p.V99V		Atlas-SNP	.											.	OR13C2	46	.	0			c.G297A						PASS	.	C		2203,2203		462,1279,462	141.0	129.0	133.0		297	-7.1	0.0	9	dbSNP_129	133	1617,6983		132,1353,2815	no	coding-synonymous	OR13C2	NM_001004481.1		594,2632,3277	TT,TC,CC		18.8023,50.0,29.3711		99/319	107367612	3820,9186	2203	4300	6503	SO:0001819	synonymous_variant	392376	exon1			CATCTGCACTGCA		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.297G>A	9.37:g.107367612C>T		Somatic	557	0	0		WXS	Illumina HiSeq	Phase_I	639	265	0.41471	NM_001004481	B9EGV8|Q6IF54	Silent	SNP	ENST00000542196.1	37	CCDS35092.1																																																																																			C|0.652;T|0.348	0.348	strong		0.517	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
WDR5B	54554	hgsc.bcm.edu	37	3	122133830	122133830	+	Silent	SNP	T	T	G	rs3749213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122133830T>G	ENST00000330689.4	-	1	1052	c.546A>C	c.(544-546)atA>atC	p.I182I	RP11-299J3.8_ENST00000608465.1_RNA|RP11-299J3.8_ENST00000609469.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA	NM_019069.3	NP_061942.2	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	182										kidney(2)|large_intestine(4)|lung(2)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.0704)		TACCTGACACTATCAAGGACC	0.428													T|||	983	0.196286	0.1089	0.2118	5008	,	,		20763	0.2192		0.2584	False		,,,				2504	0.2157				p.I182I		Atlas-SNP	.											.	WDR5B	36	.	0			c.A546C						PASS	.	T		542,3864	244.3+/-253.7	26,490,1687	81.0	80.0	80.0		546	0.8	1.0	3	dbSNP_107	80	2239,6361	376.6+/-338.2	295,1649,2356	no	coding-synonymous	WDR5B	NM_019069.3		321,2139,4043	GG,GT,TT		26.0349,12.3014,21.3824		182/331	122133830	2781,10225	2203	4300	6503	SO:0001819	synonymous_variant	54554	exon1			TGACACTATCAAG	AK002149	CCDS3012.1	3q21.1	2013-01-09			ENSG00000196981	ENSG00000196981		"""WD repeat domain containing"""	17826	protein-coding gene	gene with protein product						10369878	Standard	NM_019069		Approved	FLJ11287	uc003efa.1	Q86VZ2	OTTHUMG00000159489	ENST00000330689.4:c.546A>C	3.37:g.122133830T>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	167	72	0.431138	NM_019069	B2RCM9|Q9NUL4	Silent	SNP	ENST00000330689.4	37	CCDS3012.1																																																																																			T|0.790;G|0.210	0.210	strong		0.428	WDR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355753.1	NM_019069	
GEMIN4	50628	hgsc.bcm.edu	37	17	648157	648157	+	Silent	SNP	G	G	A	rs1045481	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:648157G>A	ENST00000319004.5	-	2	3244	c.3126C>T	c.(3124-3126)atC>atT	p.I1042I	GEMIN4_ENST00000576778.1_Silent_p.I1031I	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	1042					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CTTCAGGGCCGATGCCCTCAG	0.572													G|||	794	0.158546	0.0545	0.1772	5008	,	,		19937	0.122		0.2455	False		,,,				2504	0.2342				p.I1042I		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C3126T						PASS	.	G		363,3619		17,329,1645	45.0	44.0	44.0		3126	-2.2	1.0	17	dbSNP_86	44	2088,6240		281,1526,2357	no	coding-synonymous	GEMIN4	NM_015721.2		298,1855,4002	AA,AG,GG		25.072,9.116,19.9106		1042/1059	648157	2451,9859	1991	4164	6155	SO:0001819	synonymous_variant	50628	exon2			AGGGCCGATGCCC	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.3126C>T	17.37:g.648157G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			G|0.829;A|0.172	0.172	strong		0.572	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
ITM2C	81618	hgsc.bcm.edu	37	2	231738168	231738168	+	Missense_Mutation	SNP	G	G	A	rs2289235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231738168G>A	ENST00000326427.6	+	2	283	c.157G>A	c.(157-159)Ggc>Agc	p.G53S	ITM2C_ENST00000335005.6_Intron|ITM2C_ENST00000409704.2_5'UTR|ITM2C_ENST00000492029.1_3'UTR|ITM2C_ENST00000326407.6_Missense_Mutation_p.G53S	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	53			G -> S (in dbSNP:rs2289235). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1, ECO:0000269|Ref.7}.		negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		CAAGAGGGGGGGCTCAGTGGG	0.617													G|||	2557	0.510583	0.233	0.5303	5008	,	,		17865	0.8135		0.503	False		,,,				2504	0.5675				p.G53S		Atlas-SNP	.											.	ITM2C	17	.	0			c.G157A						PASS	.	G	,SER/GLY,SER/GLY	1122,3284	397.2+/-330.3	143,836,1224	87.0	68.0	74.0		,157,157	-2.6	0.7	2	dbSNP_100	74	4152,4448	563.2+/-388.1	1020,2112,1168	yes	intron,missense,missense	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,56,56	1163,2948,2392	AA,AG,GG		48.2791,25.4653,40.5505	,benign,benign	,53/231,53/268	231738168	5274,7732	2203	4300	6503	SO:0001583	missense	81618	exon2			AGGGGGGGCTCAG	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.157G>A	2.37:g.231738168G>A	ENSP00000322730:p.Gly53Ser	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	177	174	0.983051	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Missense_Mutation	SNP	ENST00000326427.6	37	CCDS2479.1	1175	0.538003663003663	139	0.28252032520325204	177	0.4889502762430939	471	0.8234265734265734	388	0.5118733509234829	G	0.012	-1.673453	0.00758	0.254653	0.482791	ENSG00000135916	ENST00000457215;ENST00000326427;ENST00000326407	T;T;T	0.28255	1.62;2.01;2.03	4.85	-2.61	0.06171	.	0.677726	0.14983	N	0.287104	T	0.00012	0.0000	N	0.05124	-0.11	0.53688	P	2.6999999999999247E-5	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.36578	-0.9742	9	0.02654	T	1	-29.8811	4.6856	0.12755	0.5479:0.0:0.2897:0.1624	rs2289235;rs17849577;rs17852294;rs61461656;rs2289235	53;53	Q9NQX7-3;Q9NQX7	.;ITM2C_HUMAN	S	53	ENSP00000390655:G53S;ENSP00000322730:G53S;ENSP00000322100:G53S	ENSP00000322100:G53S	G	+	1	0	ITM2C	231446412	0.611000	0.26992	0.739000	0.30968	0.006000	0.05464	0.093000	0.15086	-0.144000	0.11314	-0.783000	0.03347	GGC	G|0.531;A|0.469	0.469	strong		0.617	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
SORCS2	57537	hgsc.bcm.edu	37	4	7717012	7717012	+	Silent	SNP	G	G	A	rs2285781	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:7717012G>A	ENST00000507866.2	+	17	2335	c.2226G>A	c.(2224-2226)ctG>ctA	p.L742L	SORCS2_ENST00000329016.9_Silent_p.L570L	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	742					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						ACTGTGCCCTGGGCCAGACCT	0.612													G|||	1629	0.32528	0.1301	0.4193	5008	,	,		18871	0.2639		0.5736	False		,,,				2504	0.3303				p.L742L		Atlas-SNP	.											.	SORCS2	98	.	0			c.G2226A						PASS	.	G		805,3207		80,645,1281	93.0	100.0	98.0		2226	1.9	0.9	4	dbSNP_100	98	4799,3519		1409,1981,769	no	coding-synonymous	SORCS2	NM_020777.2		1489,2626,2050	AA,AG,GG		42.3058,20.0648,45.4501		742/1160	7717012	5604,6726	2006	4159	6165	SO:0001819	synonymous_variant	57537	exon17			TGCCCTGGGCCAG	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2226G>A	4.37:g.7717012G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_020777	Q9P2L7	Silent	SNP	ENST00000507866.2	37	CCDS47008.1																																																																																			G|0.628;A|0.372	0.372	strong		0.612	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
ZMYM4	9202	hgsc.bcm.edu	37	1	35853073	35853073	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:35853073T>A	ENST00000314607.6	+	13	2211	c.2131T>A	c.(2131-2133)Tgt>Agt	p.C711S	ZMYM4_ENST00000373297.2_Missense_Mutation_p.C622S	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	711					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTTTCAGTTCTGTGGCAAGAA	0.299																																					p.C711S		Atlas-SNP	.											.	ZMYM4	143	.	0			c.T2131A						PASS	.						55.0	61.0	59.0					1																	35853073		2203	4300	6503	SO:0001583	missense	9202	exon13			CAGTTCTGTGGCA	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.2131T>A	1.37:g.35853073T>A	ENSP00000322915:p.Cys711Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	82	4	0.0487805	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.9|20.9	4.064116|4.064116	0.76187|0.76187	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000314607;ENST00000373297|ENST00000457946	T;T|.	0.39787|.	1.16;1.06|.	5.36|5.36	5.36|5.36	0.76844|0.76844	TRASH (1);Zinc finger, MYM-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75324|0.75324	0.3834|0.3834	M|M	0.79258|0.79258	2.445|2.445	0.54753|0.54753	D|D	0.999988|0.999988	D|.	0.71674|.	0.998|.	D|.	0.79784|.	0.993|.	T|T	0.76955|0.76955	-0.2767|-0.2767	10|5	0.66056|.	D|.	0.02|.	-8.763|-8.763	14.5294|14.5294	0.67915|0.67915	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	711|.	Q5VZL5|.	ZMYM4_HUMAN|.	S|Q	711;622|370	ENSP00000322915:C711S;ENSP00000362394:C622S|.	ENSP00000322915:C711S|.	C|L	+|+	1|2	0|0	ZMYM4|ZMYM4	35625660|35625660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.706000|5.706000	0.68362|0.68362	2.021000|2.021000	0.59480|0.59480	0.533000|0.533000	0.62120|0.62120	TGT|CTG	.	.	none		0.299	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	
IGSF3	3321	hgsc.bcm.edu	37	1	117158772	117158772	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:117158772C>T	ENST00000369486.3	-	3	1116	c.351G>A	c.(349-351)gaG>gaA	p.E117E	IGSF3_ENST00000369483.1_Silent_p.E117E|IGSF3_ENST00000318837.6_Silent_p.E117E	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	117	Ig-like C2-type 1.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.E117E(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GGCATTCATACTCCCCGGCAT	0.527																																					p.E117E		Atlas-SNP	.											IGSF3_ENST00000369483,NS,carcinoma,0,2	IGSF3	294	2	2	Substitution - coding silent(2)	endometrium(2)	c.G351A						scavenged	.						56.0	51.0	53.0					1																	117158772		2203	4300	6503	SO:0001819	synonymous_variant	3321	exon3			TTCATACTCCCCG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.351G>A	1.37:g.117158772C>T		Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	413	8	0.0193705	NM_001542	A6NJZ6|A6NMC7	Silent	SNP	ENST00000369486.3	37	CCDS30813.1																																																																																			.	.	none		0.527	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
COL6A3	1293	hgsc.bcm.edu	37	2	238249108	238249108	+	Silent	SNP	T	T	C	rs61729844	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:238249108T>C	ENST00000295550.4	-	38	8903	c.8451A>G	c.(8449-8451)ccA>ccG	p.P2817P	COL6A3_ENST00000346358.4_Silent_p.P2617P|COL6A3_ENST00000472056.1_Silent_p.P2210P|COL6A3_ENST00000409809.1_Silent_p.P2611P|COL6A3_ENST00000347401.3_Silent_p.P2616P|COL6A3_ENST00000353578.4_Silent_p.P2611P	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2817	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGACGAAGGATGGCAACAGCC	0.547													t|||	218	0.0435304	0.003	0.0432	5008	,	,		21534	0.0089		0.1133	False		,,,				2504	0.0624				p.P2817P		Atlas-SNP	.											.	COL6A3	608	.	0			c.A8451G						PASS	.	C	,,	79,4327	70.3+/-108.2	1,77,2125	68.0	62.0	64.0		8451,6630,7833	-11.3	0.0	2	dbSNP_129	64	855,7745	194.9+/-240.2	43,769,3488	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	44,846,5613	CC,CT,TT		9.9419,1.793,7.1813	,,	2817/3178,2210/2571,2611/2972	238249108	934,12072	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			GAAGGATGGCAAC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8451A>G	2.37:g.238249108T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			A|0.000;C|0.070;T|0.930	0.070	strong		0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
CDH3	1001	hgsc.bcm.edu	37	16	68725783	68725783	+	Silent	SNP	G	G	A	rs2274239	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:68725783G>A	ENST00000264012.4	+	13	2500	c.1956G>A	c.(1954-1956)aaG>aaA	p.K652K	CDH3_ENST00000581171.1_Silent_p.K597K|CDH3_ENST00000429102.2_Silent_p.K652K	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	652					adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		GACCCTGGAAGGGAGGTTTCA	0.602													G|||	2877	0.574481	0.6452	0.5461	5008	,	,		19650	0.4732		0.6153	False		,,,				2504	0.5613				p.K652K		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G1956A						PASS	.	G		2825,1571	666.9+/-401.8	903,1019,276	96.0	85.0	89.0		1956	-1.3	0.3	16	dbSNP_100	89	5303,3297	646.4+/-400.3	1631,2041,628	no	coding-synonymous	CDH3	NM_001793.4		2534,3060,904	AA,AG,GG		38.3372,35.737,37.4577		652/830	68725783	8128,4868	2198	4300	6498	SO:0001819	synonymous_variant	1001	exon13			CTGGAAGGGAGGT	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1956G>A	16.37:g.68725783G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_001793	B2R6F4|Q05DI6	Silent	SNP	ENST00000264012.4	37	CCDS10868.1																																																																																			G|0.389;A|0.611	0.611	strong		0.602	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
CR2	1380	hgsc.bcm.edu	37	1	207646923	207646923	+	Intron	SNP	G	G	A	rs17616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207646923G>A	ENST00000367058.3	+	11	2167				CR2_ENST00000367057.3_Missense_Mutation_p.R671H|CR2_ENST00000458541.2_Intron|CR2_ENST00000367059.3_Intron	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2						B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CACCATGGTCGTCATACAGGT	0.453													G|||	1290	0.257588	0.4228	0.2017	5008	,	,		21002	0.1071		0.2903	False		,,,				2504	0.1953				p.R671H		Atlas-SNP	.											CR2,NS,carcinoma,+1,1	CR2	164	1	0			c.G2012A						PASS	.	G	HIS/ARG,	1672,2734	508.4+/-367.0	334,1004,865	126.0	126.0	126.0		2012,	-8.6	0.0	1	dbSNP_63	126	2707,5893	433.4+/-357.4	420,1867,2013	yes	missense,intron	CR2	NM_001006658.2,NM_001877.4	29,	754,2871,2878	AA,AG,GG		31.4767,37.9483,33.6691	,	671/1093,	207646923	4379,8627	2203	4300	6503	SO:0001627	intron_variant	1380	exon11			ATGGTCGTCATAC	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.1979-223G>A	1.37:g.207646923G>A		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	230	229	0.995652	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	584	0.2673992673992674	205	0.4166666666666667	90	0.24861878453038674	65	0.11363636363636363	224	0.2955145118733509	G	18.79	3.697997	0.68386	0.379483	0.314767	ENSG00000117322	ENST00000367057	T	0.64803	-0.12	5.11	-8.57	0.00900	.	.	.	.	.	T	0.00012	0.0000	L	0.31664	0.95	0.80722	P	0.0	D	0.63046	0.992	P	0.51582	0.674	T	0.04165	-1.0972	8	0.40728	T	0.16	.	9.1856	0.37168	0.6537:0.0:0.2436:0.1026	rs17616;rs4328074;rs52802875;rs61243177;rs17616	671	P20023-3	.	H	671	ENSP00000356024:R671H	ENSP00000356024:R671H	R	+	2	0	CR2	205713546	0.000000	0.05858	0.000000	0.03702	0.347000	0.29111	-1.366000	0.02585	-1.688000	0.01435	-1.127000	0.01993	CGT	G|0.694;A|0.306	0.306	strong		0.453	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
OR2G2	81470	hgsc.bcm.edu	37	1	247751731	247751731	+	Missense_Mutation	SNP	C	C	G	rs12737801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247751731C>G	ENST00000320065.1	+	1	70	c.70C>G	c.(70-72)Cct>Gct	p.P24A	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	24			P -> A (in dbSNP:rs12737801).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TTCTGATTATCCTCAGTTACA	0.413													C|||	382	0.076278	0.0673	0.0865	5008	,	,		20844	0.005		0.1223	False		,,,				2504	0.1074				p.P24A		Atlas-SNP	.											.	OR2G2	88	.	0			c.C70G						PASS	.	C	ALA/PRO	347,4059	179.0+/-207.6	16,315,1872	195.0	187.0	190.0		70	2.8	0.7	1	dbSNP_121	190	1214,7386	246.1+/-274.7	86,1042,3172	yes	missense	OR2G2	NM_001001915.1	27	102,1357,5044	GG,GC,CC		14.1163,7.8756,12.0022	probably-damaging	24/318	247751731	1561,11445	2203	4300	6503	SO:0001583	missense	81470	exon1			GATTATCCTCAGT	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.70C>G	1.37:g.247751731C>G	ENSP00000326349:p.Pro24Ala	Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	370	180	0.486486	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	170	0.07783882783882784	32	0.06504065040650407	38	0.10497237569060773	2	0.0034965034965034965	98	0.12928759894459102	C	14.94	2.686342	0.47991	0.078756	0.141163	ENSG00000177489	ENST00000320065	T	0.00428	7.44	3.79	2.81	0.32909	.	0.000000	0.33235	U	0.005126	T	0.00012	0.0000	M	0.86420	2.815	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.33471	-0.9867	9	0.72032	D	0.01	.	5.2644	0.15591	0.0:0.6714:0.2115:0.1171	rs12737801;rs52798143;rs12737801	24	Q8NGZ5	OR2G2_HUMAN	A	24	ENSP00000326349:P24A	ENSP00000326349:P24A	P	+	1	0	OR2G2	245818354	0.000000	0.05858	0.686000	0.30086	0.928000	0.56348	0.253000	0.18296	1.925000	0.55765	0.591000	0.81541	CCT	C|0.897;G|0.103	0.103	strong		0.413	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
SLC52A3	113278	hgsc.bcm.edu	37	20	744382	744382	+	Missense_Mutation	SNP	G	G	A	rs3746803	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:744382G>A	ENST00000217254.7	-	3	1074	c.833C>T	c.(832-834)aCg>aTg	p.T278M	SLC52A3_ENST00000473664.1_Intron|SLC52A3_ENST00000381944.3_Missense_Mutation_p.T278M	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	278			T -> M (in dbSNP:rs3746803). {ECO:0000269|PubMed:15489334}.		cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										GCTGTCCACCGTGCCTGCAGG	0.642													G|||	453	0.0904553	0.0651	0.0533	5008	,	,		19281	0.0833		0.1093	False		,,,				2504	0.1391				p.T278M		Atlas-SNP	.											C20orf54,colon,carcinoma,+1,1	.	.	1	0			c.C833T						PASS	.	G	MET/THR	347,4059	178.0+/-206.8	16,315,1872	50.0	49.0	49.0		833	2.4	0.0	20	dbSNP_107	49	943,7657	206.6+/-248.6	49,845,3406	yes	missense	C20orf54	NM_033409.3	81	65,1160,5278	AA,AG,GG		10.9651,7.8756,9.9185	possibly-damaging	278/470	744382	1290,11716	2203	4300	6503	SO:0001583	missense	113278	exon3			TCCACCGTGCCTG	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.833C>T	20.37:g.744382G>A	ENSP00000217254:p.Thr278Met	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	37	CCDS13007.1	204	0.09340659340659341	40	0.08130081300813008	18	0.049723756906077346	57	0.09965034965034965	89	0.11741424802110818	G	10.57	1.385885	0.25031	0.078756	0.109651	ENSG00000101276	ENST00000217254;ENST00000381944	T;T	0.72835	-0.64;-0.69	4.39	2.39	0.29439	.	2.651000	0.01081	N	0.004996	T	0.00967	0.0032	N	0.08118	0	0.80722	P	0.0	P;P	0.45531	0.86;0.467	B;B	0.38712	0.28;0.054	T	0.17684	-1.0361	9	0.48119	T	0.1	-5.8559	4.9955	0.14237	0.1841:0.0:0.6506:0.1653	rs3746803;rs17773890;rs17855410;rs52826273;rs61325762;rs3746803	278;278	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	M	278	ENSP00000217254:T278M;ENSP00000371370:T278M	ENSP00000217254:T278M	T	-	2	0	C20orf54	692382	0.001000	0.12720	0.000000	0.03702	0.020000	0.10135	1.068000	0.30629	0.303000	0.22785	0.313000	0.20887	ACG	G|0.903;A|0.097	0.097	strong		0.642	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
LGR6	59352	hgsc.bcm.edu	37	1	202276494	202276494	+	Silent	SNP	C	C	T	rs896551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202276494C>T	ENST00000367278.3	+	14	1334	c.1245C>T	c.(1243-1245)ccC>ccT	p.P415P	LGR6_ENST00000439764.2_Silent_p.P276P|LGR6_ENST00000255432.7_Silent_p.P363P	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	415					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						CCATCCACCCCGAGGCCTTCT	0.602													C|||	2674	0.533946	0.2738	0.6427	5008	,	,		20510	0.7173		0.5447	False		,,,				2504	0.6084				p.P415P		Atlas-SNP	.											.	LGR6	102	.	0			c.C1245T						PASS	.	C	,,	1385,3021	457.1+/-351.5	216,953,1034	181.0	138.0	153.0		1245,828,1089	-10.3	0.6	1	dbSNP_86	153	4312,4288	578.0+/-390.6	1065,2182,1053	no	coding-synonymous,coding-synonymous,coding-synonymous	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	,,	1281,3135,2087	TT,TC,CC		49.8605,31.4344,43.8029	,,	415/968,276/829,363/916	202276494	5697,7309	2203	4300	6503	SO:0001819	synonymous_variant	59352	exon14			CCACCCCGAGGCC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.1245C>T	1.37:g.202276494C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	228	225	0.986842	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																			C|0.532;T|0.468	0.468	strong		0.602	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
OR7A17	26333	hgsc.bcm.edu	37	19	14992042	14992042	+	Silent	SNP	A	A	G	rs10405136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14992042A>G	ENST00000327462.2	-	1	222	c.126T>C	c.(124-126)aaT>aaC	p.N42N		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					TGATGAGCAGATTCCCGAGCA	0.498													.|||	2815	0.562101	0.3737	0.5591	5008	,	,		14102	0.6984		0.5149	False		,,,				2504	0.727				p.N42N		Atlas-SNP	.											.	OR7A17	37	.	0			c.T126C						PASS	.	A		1800,2606	632.7+/-395.9	367,1066,770	60.0	51.0	54.0		126	0.5	0.9	19	dbSNP_119	54	4390,4208	553.8+/-386.4	1163,2064,1072	no	coding-synonymous	OR7A17	NM_030901.1		1530,3130,1842	GG,GA,AA		48.9416,40.8534,47.6007		42/310	14992042	6190,6814	2203	4299	6502	SO:0001819	synonymous_variant	26333	exon1			GAGCAGATTCCCG	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"""GPCR / Class A : Olfactory receptors"""	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.126T>C	19.37:g.14992042A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			.	.	weak		0.498	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
ZNF862	643641	hgsc.bcm.edu	37	7	149543269	149543269	+	Missense_Mutation	SNP	C	C	T	rs62621204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149543269C>T	ENST00000223210.4	+	3	411	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C		NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	56	KRAB 1. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						TGAGCTGTTCCGCAAGTTCGG	0.557													T|||	886	0.176917	0.2368	0.1427	5008	,	,		16376	0.2361		0.1024	False		,,,				2504	0.136				p.R56C		Atlas-SNP	.											.	ZNF862	97	.	0			c.C166T						PASS	.	T	CYS/ARG	763,3173		84,595,1289	30.0	31.0	31.0		166	2.3	0.0	7	dbSNP_129	31	1004,7308		50,904,3202	yes	missense	ZNF862	NM_001099220.1	180	134,1499,4491	TT,TC,CC		12.0789,19.3852,14.4268	benign	56/1170	149543269	1767,10481	1968	4156	6124	SO:0001583	missense	643641	exon3			CTGTTCCGCAAGT	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.166C>T	7.37:g.149543269C>T	ENSP00000223210:p.Arg56Cys	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_001099220	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	37	CCDS47741.1	393	0.17994505494505494	133	0.2703252032520325	51	0.1408839779005525	130	0.22727272727272727	79	0.10422163588390501	T	0.015	-1.546478	0.00926	0.193852	0.120789	ENSG00000106479	ENST00000223210	T	0.00824	5.65	4.78	2.32	0.28847	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.02391	-0.57	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27226	-1.0080	8	0.20519	T	0.43	-19.474	4.1655	0.10305	0.0:0.1888:0.1749:0.6364	rs62621204	56	O60290	ZN862_HUMAN	C	56	ENSP00000223210:R56C	ENSP00000223210:R56C	R	+	1	0	ZNF862	149174202	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	-0.096000	0.11059	-0.081000	0.12662	-1.044000	0.02363	CGC	C|0.834;T|0.166	0.166	strong		0.557	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
WDR90	197335	hgsc.bcm.edu	37	16	711429	711429	+	Missense_Mutation	SNP	C	C	T	rs199527716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:711429C>T	ENST00000293879.4	+	30	3601	c.3601C>T	c.(3601-3603)Ctc>Ttc	p.L1201F	WDR90_ENST00000549091.1_Missense_Mutation_p.L1201F			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1201										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CTGCCAGCATCTCATTTTCCC	0.642													C|||	4	0.000798722	0.0	0.0	5008	,	,		15642	0.0		0.003	False		,,,				2504	0.001				p.L1201F		Atlas-SNP	.											.	WDR90	107	.	0			c.C3601T						PASS	.	C	PHE/LEU	2,4106		0,2,2052	44.0	51.0	48.0		3601	2.3	0.0	16		48	33,8345		0,33,4156	yes	missense	WDR90	NM_145294.4	22	0,35,6208	TT,TC,CC		0.3939,0.0487,0.2803	probably-damaging	1201/1749	711429	35,12451	2054	4189	6243	SO:0001583	missense	197335	exon30			CAGCATCTCATTT	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3601C>T	16.37:g.711429C>T	ENSP00000293879:p.Leu1201Phe	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	12.40	1.927260	0.34002	4.87E-4	0.003939	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.29917	1.55;3.54	5.51	2.27	0.28462	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.521846	0.19207	N	0.120035	T	0.33702	0.0872	M	0.67953	2.075	0.09310	N	0.999991	D;D	0.56035	0.974;0.964	P;P	0.49140	0.601;0.504	T	0.20042	-1.0287	10	0.56958	D	0.05	.	3.7409	0.08530	0.1417:0.3854:0.3779:0.0949	.	1201;1201	F8VUX9;Q96KV7	.;WDR90_HUMAN	F	1201	ENSP00000448122:L1201F;ENSP00000293879:L1201F	ENSP00000293879:L1201F	L	+	1	0	WDR90	651430	0.002000	0.14202	0.002000	0.10522	0.026000	0.11368	1.451000	0.35145	0.647000	0.30713	0.555000	0.69702	CTC	C|0.998;T|0.002	0.002	strong		0.642	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
NOP9	161424	hgsc.bcm.edu	37	14	24769663	24769663	+	Silent	SNP	T	T	G	rs11158632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24769663T>G	ENST00000267425.3	+	2	390	c.297T>G	c.(295-297)gcT>gcG	p.A99A	DHRS1_ENST00000288111.7_5'Flank|NOP9_ENST00000396802.3_Silent_p.A99A|DHRS1_ENST00000396813.1_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	99							poly(A) RNA binding (GO:0044822)										AGGCCCTAGCTTTGTCCACGA	0.478													T|||	753	0.150359	0.1581	0.3473	5008	,	,		19252	0.004		0.1849	False		,,,				2504	0.1155				p.A99A		Atlas-SNP	.											.	.	.	.	0			c.T297G						PASS	.	T		736,3670	303.2+/-287.8	63,610,1530	102.0	88.0	93.0		297	-0.8	1.0	14	dbSNP_120	93	1780,6820	321.5+/-315.1	189,1402,2709	no	coding-synonymous	C14orf21	NM_174913.1		252,2012,4239	GG,GT,TT		20.6977,16.7045,19.3449		99/637	24769663	2516,10490	2203	4300	6503	SO:0001819	synonymous_variant	161424	exon2			CCTAGCTTTGTCC		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.297T>G	14.37:g.24769663T>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			T|0.838;G|0.162	0.162	strong		0.478	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978587	45978587	+	Silent	SNP	A	A	G	rs448908|rs67272426	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45978587A>G	ENST00000391620.1	-	1	56	c.12T>C	c.(10-12)tcT>tcC	p.S4S	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	4						keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						CGGACATGGTAGACGTGGCCA	0.652													.|||	1049	0.209465	0.1399	0.2579	5008	,	,		17625	0.1964		0.33	False		,,,				2504	0.1585				p.S4S		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.T12C						PASS	.	A	,	689,3717	737.0+/-410.8	58,573,1572	63.0	63.0	63.0		,12	-2.2	0.1	21	dbSNP_80	63	2788,5812	664.1+/-402.1	463,1862,1975	no	intron,coding-synonymous	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,	521,2435,3547	GG,GA,AA		32.4186,15.6378,26.7338	,	,4/222	45978587	3477,9529	2203	4300	6503	SO:0001819	synonymous_variant	386682	exon1			CATGGTAGACGTG	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.12T>C	21.37:g.45978587A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	201	100	0.497512	NM_198696	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	37	CCDS42956.1																																																																																			AGACAT|0.500;GGACGC|0.500	.	alt		0.652	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
PHLDB3	653583	hgsc.bcm.edu	37	19	44006256	44006256	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44006256G>A	ENST00000292140.5	-	3	753	c.393C>T	c.(391-393)atC>atT	p.I131I	PHLDB3_ENST00000599242.1_Silent_p.I131I	NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	131							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GCCTCACCTCGATCCTCAGCT	0.622																																					p.I131I		Atlas-SNP	.											Q96HZ0_HUMAN,NS,carcinoma,0,2	PHLDB3	30	2	0			c.C393T						scavenged	.						27.0	29.0	29.0					19																	44006256		2202	4295	6497	SO:0001819	synonymous_variant	653583	exon3			CACCTCGATCCTC		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.393C>T	19.37:g.44006256G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	201	4	0.0199005	NM_198850	Q8N7Z4	Silent	SNP	ENST00000292140.5	37	CCDS12621.2																																																																																			.	.	none		0.622	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
RRP1	8568	hgsc.bcm.edu	37	21	45209559	45209559	+	Silent	SNP	C	C	T	rs78489660	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45209559C>T	ENST00000497547.1	+	1	166	c.49C>T	c.(49-51)Ctg>Ttg	p.L17L		NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		GGCTCAGCGCCTGGCGGGGAA	0.697													C|||	331	0.0660942	0.0159	0.0259	5008	,	,		12101	0.0863		0.0457	False		,,,				2504	0.1626				p.L17L		Atlas-SNP	.											.	RRP1	23	.	0			c.C49T						PASS	.	C		90,3924		2,86,1919	10.0	16.0	14.0		49	4.4	0.9	21	dbSNP_131	14	467,7841		14,439,3701	yes	coding-synonymous	RRP1	NM_003683.5		16,525,5620	TT,TC,CC		5.6211,2.2422,4.5204		17/462	45209559	557,11765	2007	4154	6161	SO:0001819	synonymous_variant	8568	exon1			CAGCGCCTGGCGG	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"""DNA segment on chromosome 21 (unique) 2056 expressed sequence"", ""Nnp1 homolog, nucleolar protein (Drosophila)"""	610653	"""ribosomal RNA processing 1 homolog (S. cerevisiae)"""			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.49C>T	21.37:g.45209559C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_003683	A6NIB2	Silent	SNP	ENST00000497547.1	37	CCDS42951.1																																																																																			C|0.949;T|0.051	0.051	strong		0.697	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
SMC1B	27127	hgsc.bcm.edu	37	22	45767421	45767421	+	Missense_Mutation	SNP	C	C	T	rs56174639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45767421C>T	ENST00000357450.4	-	14	2242	c.2243G>A	c.(2242-2244)tGt>tAt	p.C748Y	SMC1B_ENST00000404354.3_Missense_Mutation_p.C748Y	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	748					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CAACATAATACATTGAGACTC	0.279													C|||	434	0.0866613	0.0908	0.0908	5008	,	,		18743	0.003		0.1889	False		,,,				2504	0.0593				p.C748Y		Atlas-SNP	.											.	SMC1B	215	.	0			c.G2243A						PASS	.	C	TYR/CYS	313,3313		11,291,1511	95.0	85.0	88.0		2243	3.3	0.4	22	dbSNP_129	88	1329,6801		115,1099,2851	yes	missense	SMC1B	NM_148674.3	194	126,1390,4362	TT,TC,CC		16.3469,8.6321,13.9673	benign	748/1236	45767421	1642,10114	1813	4065	5878	SO:0001583	missense	27127	exon14			ATAATACATTGAG	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.2243G>A	22.37:g.45767421C>T	ENSP00000350036:p.Cys748Tyr	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	184	55	0.298913	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	243	0.11126373626373626	49	0.09959349593495935	39	0.10773480662983426	3	0.005244755244755245	152	0.20052770448548812	C	4.996	0.184893	0.09495	0.086321	0.163469	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.78003	-1.14;-0.97	5.66	3.35	0.38373	RecF/RecN/SMC (1);	0.372163	0.24518	N	0.037825	T	0.00073	0.0002	N	0.01729	-0.75	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.03443	-1.1036	9	0.18710	T	0.47	.	6.1198	0.20148	0.1837:0.6861:0.0:0.1302	rs56174639;rs61748561	748;748;748	Q8NDV3;Q8NDV3-2;Q8NDV3-3	SMC1B_HUMAN;.;.	Y	748	ENSP00000350036:C748Y;ENSP00000385902:C748Y	ENSP00000350036:C748Y	C	-	2	0	SMC1B	44146085	0.022000	0.18835	0.436000	0.26797	0.345000	0.29048	0.560000	0.23500	2.669000	0.90835	0.655000	0.94253	TGT	C|0.874;T|0.126	0.126	strong		0.279	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100820663	100820663	+	Missense_Mutation	SNP	G	G	A	rs17647207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100820663G>A	ENST00000298815.8	+	12	1141	c.1138G>A	c.(1138-1140)Gcc>Acc	p.A380T	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.A346T	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	380	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TACTCTGCCTGCCATTATAAG	0.294													G|||	156	0.0311502	0.0023	0.0346	5008	,	,		15251	0.0		0.0994	False		,,,				2504	0.0297				p.A380T		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G1138A						PASS	.	G	THR/ALA	30,1354		4,22,666	140.0	138.0	139.0		1138	5.2	1.0	11	dbSNP_123	139	304,2878		18,268,1305	yes	missense	ARHGAP42	NM_152432.2	58	22,290,1971	AA,AG,GG		9.5537,2.1676,7.3149	benign	380/875	100820663	334,4232	692	1591	2283	SO:0001583	missense	143872	exon12			CTGCCTGCCATTA			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.1138G>A	11.37:g.100820663G>A	ENSP00000298815:p.Ala380Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_152432	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	37		91	0.041666666666666664	1	0.0020325203252032522	15	0.04143646408839779	0	0.0	75	0.09894459102902374	G	16.75	3.209747	0.58343	0.021676	0.095537	ENSG00000165895	ENST00000524892;ENST00000298815	T;T	0.07114	3.22;3.31	5.23	5.23	0.72850	Rho GTPase-activating protein domain (1);	1.291020	0.06034	N	0.653550	T	0.00300	0.0009	L	0.33485	1.01	0.09310	P	0.999999897393	B	0.16396	0.017	B	0.20184	0.028	T	0.28138	-1.0053	9	0.25106	T	0.35	.	16.6609	0.85240	0.0:0.0:1.0:0.0	rs17647207;rs52820744;rs60330976;rs17647207	380	A6NI28	RHG42_HUMAN	T	346;380	ENSP00000431776:A346T;ENSP00000298815:A380T	ENSP00000298815:A380T	A	+	1	0	ARHGAP42	100325873	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.371000	0.73119	2.596000	0.87737	0.491000	0.48974	GCC	G|0.949;A|0.051	0.051	strong		0.294	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
TMPRSS4	56649	hgsc.bcm.edu	37	11	117965530	117965530	+	Splice_Site	SNP	A	A	G	rs2276122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:117965530A>G	ENST00000437212.3	+	2	217		c.e2-1		TMPRSS4_ENST00000522307.1_Intron|TMPRSS4_ENST00000534111.1_Intron|TMPRSS4_ENST00000523251.1_Intron|TMPRSS4_ENST00000522824.1_Splice_Site			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4						proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		TTTTCCTTCAATTACAGGATC	0.517													A|||	1536	0.306709	0.0408	0.402	5008	,	,		20301	0.3502		0.3499	False		,,,				2504	0.5092				.		Atlas-SNP	.											.	TMPRSS4	46	.	0			c.4-1A>G						PASS	.	A	,,,	485,3915	221.3+/-238.5	34,417,1749	109.0	84.0	92.0		,,,	0.6	0.1	11	dbSNP_100	92	3154,5438	466.9+/-366.9	588,1978,1730	yes	splice-3,intron,intron,splice-3	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	,,,	622,2395,3479	GG,GA,AA		36.7086,11.0227,28.0095	,,,	,,,	117965530	3639,9353	2200	4296	6496	SO:0001630	splice_region_variant	56649	exon2			CCTTCAATTACAG	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.4-1A>G	11.37:g.117965530A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	189	98	0.518519	NM_001083947	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Splice_Site	SNP	ENST00000437212.3	37	CCDS31684.1	639	0.2925824175824176	23	0.046747967479674794	117	0.32320441988950277	230	0.4020979020979021	269	0.3548812664907652	A	7.233	0.599624	0.13939	0.110227	0.367086	ENSG00000137648	ENST00000437212;ENST00000522824	.	.	.	4.73	0.624	0.17659	.	.	.	.	.	.	.	.	.	.	.	0.46874	P	7.660000000000444E-4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.3643	0.02198	0.5141:0.2168:0.1023:0.1667	rs2276122;rs2276122	.	.	.	.	-1	.	.	.	+	.	.	TMPRSS4	117470740	0.374000	0.25081	0.108000	0.21378	0.178000	0.23041	0.032000	0.13732	0.329000	0.23460	0.460000	0.39030	.	A|0.721;G|0.278	0.278	strong		0.517	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894	Intron
BFAR	51283	hgsc.bcm.edu	37	16	14742400	14742400	+	Missense_Mutation	SNP	T	T	G	rs11546303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:14742400T>G	ENST00000261658.2	+	3	696	c.419T>G	c.(418-420)aTg>aGg	p.M140R	BFAR_ENST00000426842.2_Intron|BFAR_ENST00000563971.1_Intron	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	140			M -> R (in dbSNP:rs11546303).		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						AATCAGCAGATGGGAGGGGGA	0.507													G|||	1262	0.251997	0.1172	0.4049	5008	,	,		17221	0.1558		0.3917	False		,,,				2504	0.2812				p.M140R		Atlas-SNP	.											BFAR,colon,carcinoma,0,1	BFAR	38	1	0			c.T419G						PASS	.	G	ARG/MET	775,3619	752.4+/-412.3	65,645,1487	207.0	204.0	205.0		419	6.1	1.0	16	dbSNP_120	205	3346,5254	643.3+/-399.9	658,2030,1612	yes	missense	BFAR	NM_016561.2	91	723,2675,3099	GG,GT,TT		38.907,17.6377,31.7146	benign	140/451	14742400	4121,8873	2197	4300	6497	SO:0001583	missense	51283	exon3			AGCAGATGGGAGG	AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"""RING-type (C3HC4) zinc fingers"", ""Sterile alpha motif (SAM) domain containing"""	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.419T>G	16.37:g.14742400T>G	ENSP00000261658:p.Met140Arg	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	204	204	1	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	37	CCDS10554.1	592	0.27106227106227104	64	0.13008130081300814	136	0.3756906077348066	90	0.15734265734265734	302	0.39841688654353563	G	2.593	-0.294767	0.05568	0.176377	0.38907	ENSG00000103429	ENST00000261658	T	0.05855	3.38	6.08	6.08	0.98989	.	0.094567	0.64402	N	0.000001	T	0.00012	0.0000	N	0.01048	-1.04	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45877	-0.9231	9	0.02654	T	1	.	16.121	0.81357	0.0:0.0:0.8652:0.1348	rs11546303;rs52806449;rs11546303	140	Q9NZS9	BFAR_HUMAN	R	140	ENSP00000261658:M140R	ENSP00000261658:M140R	M	+	2	0	BFAR	14649901	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	3.507000	0.53371	1.599000	0.50093	-0.121000	0.15023	ATG	T|0.708;G|0.292	0.292	strong		0.507	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561	
GOLGA3	2802	hgsc.bcm.edu	37	12	133393323	133393323	+	Missense_Mutation	SNP	C	C	T	rs2291256	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133393323C>T	ENST00000450791.2	-	2	392	c.209G>A	c.(208-210)gGg>gAg	p.G70E	GOLGA3_ENST00000456883.2_Missense_Mutation_p.G70E|GOLGA3_ENST00000545875.1_Missense_Mutation_p.G70E|GOLGA3_ENST00000537452.1_Missense_Mutation_p.G70E|GOLGA3_ENST00000204726.3_Missense_Mutation_p.G70E			Q08378	GOGA3_HUMAN	golgin A3	70	Pro-rich.		G -> E (in dbSNP:rs2291256).		intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		TGGCGTTGGCCCGTTCTGACA	0.627													C|||	291	0.058107	0.0	0.0634	5008	,	,		17764	0.129		0.0696	False		,,,				2504	0.0481				p.G70E		Atlas-SNP	.											.	GOLGA3	234	.	0			c.G209A						PASS	.	C	GLU/GLY,GLU/GLY	64,4342	62.3+/-99.4	0,64,2139	91.0	91.0	91.0		209,209	5.0	0.9	12	dbSNP_100	91	737,7863	178.3+/-227.7	35,667,3598	yes	missense,missense	GOLGA3	NM_001172557.1,NM_005895.3	98,98	35,731,5737	TT,TC,CC		8.5698,1.4526,6.1587	probably-damaging,probably-damaging	70/1135,70/1499	133393323	801,12205	2203	4300	6503	SO:0001583	missense	2802	exon3			GTTGGCCCGTTCT	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.209G>A	12.37:g.133393323C>T	ENSP00000410378:p.Gly70Glu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	165	68	0.412121	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	153	0.07005494505494506	0	0.0	19	0.052486187845303865	77	0.1346153846153846	57	0.07519788918205805	C	19.99	3.928431	0.73327	0.014526	0.085698	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.62232	0.57;0.57;0.55;0.04;0.04	5.91	5.02	0.67125	.	0.048742	0.85682	N	0.000000	T	0.01387	0.0045	M	0.66939	2.045	0.09310	P	1.0	P;B;B	0.38078	0.617;0.36;0.36	B;B;B	0.42959	0.403;0.181;0.181	T	0.43278	-0.9401	9	0.87932	D	0	.	14.9478	0.71047	0.0:0.9316:0.0:0.0684	rs2291256;rs52803888;rs56627172;rs60184311;rs2291256	70;70;70	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	E	70	ENSP00000204726:G70E;ENSP00000410378:G70E;ENSP00000409303:G70E;ENSP00000442143:G70E;ENSP00000442603:G70E	ENSP00000204726:G70E	G	-	2	0	GOLGA3	131903396	1.000000	0.71417	0.950000	0.38849	0.253000	0.25986	2.565000	0.45939	1.498000	0.48600	0.462000	0.41574	GGG	C|0.932;T|0.068	0.068	strong		0.627	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
QSOX2	169714	hgsc.bcm.edu	37	9	139100805	139100805	+	Silent	SNP	T	T	C	rs9696116	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139100805T>C	ENST00000358701.5	-	12	1903	c.1866A>G	c.(1864-1866)ccA>ccG	p.P622P		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	622					cell redox homeostasis (GO:0045454)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	thiol oxidase activity (GO:0016972)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		GCAAGCTCTCTGGAAGGGCAG	0.647													T|||	803	0.160343	0.0227	0.2147	5008	,	,		17725	0.12		0.2932	False		,,,				2504	0.2127				p.P622P		Atlas-SNP	.											.	QSOX2	63	.	0			c.A1866G						PASS	.	T		365,4041	184.7+/-212.0	14,337,1852	68.0	67.0	68.0		1866	-6.7	0.0	9	dbSNP_119	68	2574,6026	418.3+/-352.7	373,1828,2099	no	coding-synonymous	QSOX2	NM_181701.3		387,2165,3951	CC,CT,TT		29.9302,8.2842,22.5973		622/699	139100805	2939,10067	2203	4300	6503	SO:0001819	synonymous_variant	169714	exon12			GCTCTCTGGAAGG	AJ318051	CCDS35178.1	9q34.3	2008-02-05	2007-04-23	2007-04-23	ENSG00000165661	ENSG00000165661			30249	protein-coding gene	gene with protein product		612860	"""quiescin Q6-like 1"""	QSCN6L1		12176051	Standard	NM_181701		Approved	SOXN, DKFZp762A2013	uc010nbi.2	Q6ZRP7	OTTHUMG00000020923	ENST00000358701.5:c.1866A>G	9.37:g.139100805T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Silent	SNP	ENST00000358701.5	37	CCDS35178.1																																																																																			T|0.789;C|0.211	0.211	strong		0.647	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701	
PDGFC	56034	hgsc.bcm.edu	37	4	157684248	157684248	+	Silent	SNP	T	T	C	rs3815861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:157684248T>C	ENST00000502773.1	-	6	1522	c.1032A>G	c.(1030-1032)ggA>ggG	p.G344G	PDGFC_ENST00000504672.1_5'UTR|PDGFC_ENST00000422544.2_Silent_p.G281G|PDGFC_ENST00000541126.1_Silent_p.G181G|PDGFC_ENST00000542208.1_Silent_p.G189G	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	344					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)	p.G344G(1)		central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		GCGGCTATCCTCCTGTGCTCC	0.542													T|||	1176	0.234824	0.2307	0.1686	5008	,	,		16765	0.1716		0.165	False		,,,				2504	0.4243				p.G344G		Atlas-SNP	.											PDGFC,NS,carcinoma,0,1	PDGFC	46	1	1	Substitution - coding silent(1)	prostate(1)	c.A1032G						scavenged	.	T		870,3536	337.6+/-304.9	98,674,1431	125.0	94.0	105.0		1032	-2.2	0.9	4	dbSNP_107	105	1329,7271	261.0+/-283.6	113,1103,3084	no	coding-synonymous	PDGFC	NM_016205.2		211,1777,4515	CC,CT,TT		15.4535,19.7458,16.9076		344/346	157684248	2199,10807	2203	4300	6503	SO:0001819	synonymous_variant	56034	exon6			CTATCCTCCTGTG	AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.1032A>G	4.37:g.157684248T>C		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_016205	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Silent	SNP	ENST00000502773.1	37	CCDS3795.1																																																																																			A|0.000;C|0.171;T|0.829	0.171	strong		0.542	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1		
GOLGB1	2804	hgsc.bcm.edu	37	3	121415720	121415720	+	Missense_Mutation	SNP	T	T	C	rs3732410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121415720T>C	ENST00000340645.5	-	13	3760	c.3635A>G	c.(3634-3636)tAt>tGt	p.Y1212C	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Y1217C	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1212			Y -> C (in dbSNP:rs3732410). {ECO:0000269|PubMed:18487259}.		Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CAAGCGATTATAGTCATCTTT	0.428													T|||	1101	0.219848	0.0522	0.1585	5008	,	,		22709	0.4841		0.2505	False		,,,				2504	0.1861				p.Y1217C		Atlas-SNP	.											GOLGB1,NS,carcinoma,0,1	GOLGB1	319	1	0			c.A3650G						PASS	.	T	CYS/TYR	327,4079	171.9+/-202.1	11,305,1887	221.0	217.0	219.0		3635	4.6	0.9	3	dbSNP_107	219	2113,6487	365.1+/-333.8	277,1559,2464	yes	missense	GOLGB1	NM_004487.3	194	288,1864,4351	CC,CT,TT		24.5698,7.4217,18.7606	probably-damaging	1212/3260	121415720	2440,10566	2203	4300	6503	SO:0001583	missense	2804	exon13			CGATTATAGTCAT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.3635A>G	3.37:g.121415720T>C	ENSP00000341848:p.Tyr1212Cys	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	364	179	0.491758	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	563	0.25778388278388276	33	0.06707317073170732	70	0.19337016574585636	267	0.46678321678321677	193	0.2546174142480211	T	10.43	1.349415	0.24426	0.074217	0.245698	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	T;T;T	0.32515	2.09;2.09;1.45	5.81	4.59	0.56863	.	0.000000	0.56097	D	0.000036	T	0.00012	0.0000	L	0.32530	0.975	0.29624	P	0.845993	D;P;P;D	0.76494	0.999;0.936;0.936;0.999	D;P;P;D	0.70487	0.912;0.609;0.609;0.969	T	0.49113	-0.8973	9	0.39692	T	0.17	.	10.852	0.46775	0.0:0.0:0.1579:0.8421	rs3732410;rs52794344;rs61628092;rs3732410	1137;1176;1217;1212	F1T0J2;E7EU81;E7EP74;Q14789	.;.;.;GOGB1_HUMAN	C	1212;1217;1176	ENSP00000341848:Y1212C;ENSP00000377275:Y1217C;ENSP00000418231:Y1176C	ENSP00000341848:Y1212C	Y	-	2	0	GOLGB1	122898410	1.000000	0.71417	0.911000	0.35937	0.780000	0.44128	1.966000	0.40481	2.210000	0.71456	0.533000	0.62120	TAT	T|0.787;C|0.213	0.213	strong		0.428	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
ZMYND15	84225	hgsc.bcm.edu	37	17	4645324	4645324	+	Silent	SNP	T	T	C	rs3826517	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4645324T>C	ENST00000433935.1	+	4	999	c.942T>C	c.(940-942)caT>caC	p.H314H	CXCL16_ENST00000293778.6_5'Flank|ZMYND15_ENST00000592813.1_Silent_p.H314H|CXCL16_ENST00000574412.1_5'Flank|ZMYND15_ENST00000573751.2_Silent_p.H314H|ZMYND15_ENST00000269289.6_Silent_p.H314H	NM_001136046.2|NM_001267822.1	NP_001129518.1|NP_001254751.1	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15	314					negative regulation of transcription, DNA-templated (GO:0045892)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)	18						GAACCTGCCATGTGTGTCACA	0.567													T|||	1285	0.256589	0.0408	0.3271	5008	,	,		18356	0.1438		0.4642	False		,,,				2504	0.4008				p.H314H		Atlas-SNP	.											.	ZMYND15	87	.	0			c.T942C						PASS	.	T	,	505,3901	232.3+/-245.9	30,445,1728	73.0	76.0	75.0		942,942	-2.6	1.0	17	dbSNP_107	75	3853,4747	539.9+/-383.7	852,2149,1299	no	coding-synonymous,coding-synonymous	ZMYND15	NM_001136046.1,NM_032265.1	,	882,2594,3027	CC,CT,TT		44.8023,11.4616,33.5076	,	314/743,314/704	4645324	4358,8648	2203	4300	6503	SO:0001819	synonymous_variant	84225	exon4			CTGCCATGTGTGT	AL136893	CCDS11053.1, CCDS45584.1, CCDS58506.1	17p13.3	2008-05-02			ENSG00000141497	ENSG00000141497		"""Zinc fingers, MYND-type"""	20997	protein-coding gene	gene with protein product		614312				11230166	Standard	NM_001136046		Approved	DKFZp434N127	uc002fyu.3	Q9H091	OTTHUMG00000090760	ENST00000433935.1:c.942T>C	17.37:g.4645324T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_001136046	B4DXY5|I3L296	Silent	SNP	ENST00000433935.1	37	CCDS45584.1																																																																																			T|0.693;C|0.307	0.307	strong		0.567	ZMYND15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439580.1	NM_032265	
GGA2	23062	hgsc.bcm.edu	37	16	23504719	23504719	+	Missense_Mutation	SNP	G	G	C	rs143003037		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23504719G>C	ENST00000309859.4	-	4	395	c.313C>G	c.(313-315)Cgt>Ggt	p.R105G	GGA2_ENST00000567468.1_Missense_Mutation_p.R105G	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	105	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		TTCAGGAAACGAAATTTGGCC	0.552																																					p.R105G		Atlas-SNP	.											GGA2,mucosal,malignant_melanoma,0,3	GGA2	49	3	0			c.C313G						PASS	.	G	GLY/ARG	0,4394		0,0,2197	183.0	135.0	151.0		313	5.6	1.0	16	dbSNP_134	151	4,8596	3.7+/-12.6	0,4,4296	no	missense	GGA2	NM_015044.4	125	0,4,6493	CC,CG,GG		0.0465,0.0,0.0308	probably-damaging	105/614	23504719	4,12990	2197	4300	6497	SO:0001583	missense	23062	exon4			GGAAACGAAATTT	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.313C>G	16.37:g.23504719G>C	ENSP00000311962:p.Arg105Gly	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	37	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.556060	0.86231	0.0	4.65E-4	ENSG00000103365	ENST00000309859	T	0.23348	1.91	5.58	5.58	0.84498	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60657	-0.7220	10	0.72032	D	0.01	-16.2173	17.0743	0.86582	0.0:0.0:1.0:0.0	.	105	Q9UJY4	GGA2_HUMAN	G	105	ENSP00000311962:R105G	ENSP00000311962:R105G	R	-	1	0	GGA2	23412220	1.000000	0.71417	1.000000	0.80357	0.572000	0.35998	6.105000	0.71505	2.638000	0.89438	0.448000	0.29417	CGT	G|1.000;C|0.000	0.000	weak		0.552	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		
CROCC	9696	hgsc.bcm.edu	37	1	17257840	17257840	+	Missense_Mutation	SNP	C	C	G	rs143501240	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17257840C>G	ENST00000375541.5	+	8	973	c.904C>G	c.(904-906)Cag>Gag	p.Q302E	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CCTCTGGAGGCAGGTGGTGGG	0.642													c|||	99	0.0197684	0.0038	0.0331	5008	,	,		30269	0.0		0.0567	False		,,,				2504	0.0143				p.Q302E		Atlas-SNP	.											.	CROCC	185	.	0			c.C904G						PASS	.	C	GLU/GLN	37,4369	37.6+/-69.7	0,37,2166	102.0	85.0	91.0		904	3.7	1.0	1	dbSNP_134	91	340,8260	107.4+/-168.2	0,340,3960	yes	missense	CROCC	NM_014675.3	29	0,377,6126	GG,GC,CC		3.9535,0.8398,2.8987	probably-damaging	302/2018	17257840	377,12629	2203	4300	6503	SO:0001583	missense	9696	exon8			TGGAGGCAGGTGG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.904C>G	1.37:g.17257840C>G	ENSP00000364691:p.Gln302Glu	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	312	151	0.483974	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	48	0.02197802197802198	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	38	0.05013192612137203	C	14.52	2.560483	0.45590	0.008398	0.039535	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09630	2.96	4.6	3.67	0.42095	.	.	.	.	.	T	0.01940	0.0061	L	0.41632	1.29	0.44798	D	0.997801	P;D	0.54601	0.907;0.967	P;P	0.53035	0.547;0.716	T	0.05835	-1.0861	9	0.06494	T	0.89	.	13.0557	0.58980	0.1624:0.8376:0.0:0.0	.	165;302	A1L0S8;Q5TZA2	.;CROCC_HUMAN	E	302;183	ENSP00000364691:Q302E	ENSP00000364691:Q302E	Q	+	1	0	CROCC	17130427	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	3.247000	0.51422	1.253000	0.44018	0.561000	0.74099	CAG	C|0.968;G|0.032	0.032	strong		0.642	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
SNX18	112574	hgsc.bcm.edu	37	5	53815495	53815495	+	Missense_Mutation	SNP	A	A	C	rs2548612	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:53815495A>C	ENST00000326277.3	+	1	1903	c.1713A>C	c.(1711-1713)gaA>gaC	p.E571D	SNX18_ENST00000381410.4_Intron|SNX18_ENST00000343017.6_Missense_Mutation_p.E571D	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	571	BAR.		E -> D (in dbSNP:rs2548612). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.		cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				GGGTTTCAGAATCATATTCTA	0.512													N|||	2437	0.486621	0.4501	0.5303	5008	,	,		20299	0.4524		0.5666	False		,,,				2504	0.4581				p.E571D		Atlas-SNP	.											.	SNX18	102	.	0			c.A1713C						PASS	.	C	,ASP/GLU,ASP/GLU	2132,2274	598.9+/-389.2	525,1082,596	96.0	92.0	94.0		,1713,1713	-0.6	0.0	5	dbSNP_100	94	4749,3851	541.6+/-384.0	1294,2161,845	yes	intron,missense,missense	SNX18	NM_001102575.1,NM_001145427.1,NM_052870.2	,45,45	1819,3243,1441	CC,CA,AA		44.7791,48.3886,47.0936	,,	,571/592,571/629	53815495	6881,6125	2203	4300	6503	SO:0001583	missense	112574	exon1			TTCAGAATCATAT	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1713A>C	5.37:g.53815495A>C	ENSP00000317332:p.Glu571Asp	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	153	73	0.477124	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000326277.3	37	CCDS3962.1	1129	0.516941391941392	214	0.4349593495934959	205	0.5662983425414365	272	0.4755244755244755	438	0.5778364116094987	C	0.071	-1.201963	0.01581	0.483886	0.552209	ENSG00000178996	ENST00000343017;ENST00000326277	T;T	0.13307	2.6;2.71	2.61	-0.586	0.11694	.	0.447401	0.22024	N	0.065697	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41431	-0.9509	9	0.02654	T	1	-0.8049	0.4701	0.00530	0.1768:0.3098:0.2216:0.2918	rs2548612;rs52803321;rs59271712;rs2548612	571	Q96RF0	SNX18_HUMAN	D	571	ENSP00000342276:E571D;ENSP00000317332:E571D	ENSP00000317332:E571D	E	+	3	2	SNX18	53851252	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.800000	0.04555	-0.498000	0.06632	-0.217000	0.12591	GAA	A|0.480;C|0.520	0.520	strong		0.512	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
VPS13B	157680	hgsc.bcm.edu	37	8	100454804	100454804	+	Missense_Mutation	SNP	A	A	G	rs61759485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:100454804A>G	ENST00000358544.2	+	23	3497	c.3386A>G	c.(3385-3387)aAg>aGg	p.K1129R	VPS13B_ENST00000395996.1_Missense_Mutation_p.K1129R|VPS13B_ENST00000357162.2_Missense_Mutation_p.K1129R	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1129					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GCTGGGCACAAGTATATGGAA	0.398													A|||	7	0.00139776	0.0	0.0058	5008	,	,		17905	0.0		0.003	False		,,,				2504	0.0				p.K1129R	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A3386G						PASS	.	A	ARG/LYS,ARG/LYS	16,4390	24.3+/-50.5	0,16,2187	100.0	96.0	97.0		3386,3386	3.3	0.9	8	dbSNP_129	97	35,8565	22.8+/-68.1	0,35,4265	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	26,26	0,51,6452	GG,GA,AA		0.407,0.3631,0.3921	probably-damaging,probably-damaging	1129/4023,1129/3998	100454804	51,12955	2203	4300	6503	SO:0001583	missense	157680	exon23			GGCACAAGTATAT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3386A>G	8.37:g.100454804A>G	ENSP00000351346:p.Lys1129Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	150	75	0.5	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	7	0.003205128205128205	0	0.0	4	0.011049723756906077	0	0.0	3	0.00395778364116095	A	19.74	3.883056	0.72410	0.003631	0.00407	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.25912	1.77;1.77;1.77	5.71	3.34	0.38264	.	0.105634	0.64402	N	0.000012	T	0.32852	0.0843	L	0.49350	1.555	0.41967	D	0.990735	D;D;B;D	0.76494	0.999;0.998;0.125;0.989	D;D;B;D	0.78314	0.991;0.937;0.028;0.967	T	0.05321	-1.0892	10	0.51188	T	0.08	.	10.0017	0.41933	0.8633:0.0:0.1367:0.0	rs61759485	1128;1129;1129;1129	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	R	1129	ENSP00000349685:K1129R;ENSP00000351346:K1129R;ENSP00000379318:K1129R	ENSP00000349685:K1129R	K	+	2	0	VPS13B	100523980	1.000000	0.71417	0.933000	0.37362	0.815000	0.46073	4.769000	0.62300	0.447000	0.26695	-0.326000	0.08463	AAG	A|0.996;G|0.004	0.004	strong		0.398	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
FCGBP	8857	hgsc.bcm.edu	37	19	40406019	40406019	+	Silent	SNP	G	G	A	rs2355719	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40406019G>A	ENST00000221347.6	-	10	4834	c.4827C>T	c.(4825-4827)tgC>tgT	p.C1609C		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1609	Cys-rich.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CATGGCACGTGCACTGCTGCC	0.632													A|||	1308	0.261182	0.1566	0.402	5008	,	,		20345	0.2163		0.3419	False		,,,				2504	0.2658				p.C1609C		Atlas-SNP	.											.	FCGBP	416	.	0			c.C4827T						PASS	.						77.0	55.0	62.0					19																	40406019		2203	4298	6501	SO:0001819	synonymous_variant	8857	exon10			GCACGTGCACTGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4827C>T	19.37:g.40406019G>A		Somatic	554	1	0.00180505		WXS	Illumina HiSeq	Phase_I	881	374	0.424518	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.717;A|0.283	0.283	strong		0.632	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
GPR50	9248	hgsc.bcm.edu	37	X	150349649	150349649	+	Missense_Mutation	SNP	A	A	G	rs561077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:150349649A>G	ENST00000218316.3	+	2	1663	c.1594A>G	c.(1594-1596)Act>Gct	p.T532A	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	532	Pro-rich.		T -> A (higher fasting circulating triglyceride levels; dbSNP:rs561077). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8647286, ECO:0000269|Ref.2}.		cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)	p.N532D(1)|p.T532A(1)		breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					CCCTAAGCCCACTGCTGCTGA	0.617													G|||	1620	0.429139	0.3986	0.4121	3775	,	,		15435	0.1984		0.335	False		,,,				2504	0.2761				p.T532A		Atlas-SNP	.											.	GPR50	195	.	2	Substitution - Missense(2)	stomach(2)	c.A1594G						PASS	.	G	ALA/THR	1892,1897		427,748,290,434,281	77.0	88.0	84.0		1594	-3.2	0.0	X	dbSNP_83	84	2782,3903		455,1129,743,836,1102	yes	missense	GPR50	NM_004224.3	58	882,1877,1033,1270,1383	GG,GA,G,AA,A		41.6156,49.934,44.6248	benign	532/618	150349649	4674,5800	2180	4265	6445	SO:0001583	missense	9248	exon2			AAGCCCACTGCTG	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1594A>G	X.37:g.150349649A>G	ENSP00000218316:p.Thr532Ala	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	138	135	0.978261	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	743	0.4478601567209162	138	0.3812154696132597	114	0.3986013986013986	81	0.16598360655737704	184	0.30976430976430974	G	3.343	-0.134242	0.06711	0.49934	0.416156	ENSG00000102195	ENST00000218316	T	0.73897	-0.79	2.63	-3.21	0.05140	.	1.162070	0.06802	N	0.788946	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18935	-1.0321	9	0.05721	T	0.95	-0.0027	6.6426	0.22917	0.2539:0.0:0.5933:0.1528	rs561077;rs3827433;rs561077	532	Q13585	MTR1L_HUMAN	A	532	ENSP00000218316:T532A	ENSP00000218316:T532A	T	+	1	0	GPR50	150100307	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.842000	0.01681	-1.307000	0.02321	-2.432000	0.00214	ACT	A|0.574;G|0.426	0.426	strong		0.617	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
DNASE2B	58511	hgsc.bcm.edu	37	1	84864256	84864256	+	Missense_Mutation	SNP	G	G	C	rs3738573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:84864256G>C	ENST00000370665.3	+	1	42	c.9G>C	c.(7-9)caG>caC	p.Q3H		NM_021233.2	NP_067056.2	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta	3			Q -> H (in dbSNP:rs3738573).		apoptotic DNA fragmentation (GO:0006309)	extracellular region (GO:0005576)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)			endometrium(1)|lung(4)|skin(1)	6				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)		AAATGAAACAGAAAATGATGG	0.468													G|||	1473	0.294129	0.1755	0.3156	5008	,	,		20991	0.4038		0.334	False		,,,				2504	0.2853				p.Q3H	Pancreas(54;788 1175 11852 16034 30034)	Atlas-SNP	.											DNASE2B_ENST00000370665,NS,carcinoma,0,1	DNASE2B	40	1	0			c.G9C						PASS	.	G	HIS/GLN	778,3356		79,620,1368	166.0	174.0	171.0		9	3.0	0.8	1	dbSNP_107	171	2894,5546		499,1896,1825	yes	missense	DNASE2B	NM_021233.2	24	578,2516,3193	CC,CG,GG		34.2891,18.8195,29.2031	benign	3/362	84864256	3672,8902	2067	4220	6287	SO:0001583	missense	58511	exon1			GAAACAGAAAATG	AF274571	CCDS694.1, CCDS44167.1	1p22.3	2008-02-05			ENSG00000137976	ENSG00000137976			28875	protein-coding gene	gene with protein product		608057				12594037, 11376952	Standard	NM_021233		Approved	DLAD	uc001djt.1	Q8WZ79	OTTHUMG00000009860	ENST00000370665.3:c.9G>C	1.37:g.84864256G>C	ENSP00000359699:p.Gln3His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_021233	Q5VXD0|Q5VXD1|Q8WZ80|Q9NQW3	Missense_Mutation	SNP	ENST00000370665.3	37	CCDS44167.1	658	0.30128205128205127	94	0.1910569105691057	107	0.2955801104972376	211	0.3688811188811189	246	0.3245382585751979	G	0.349	-0.945820	0.02304	0.188195	0.342891	ENSG00000137976	ENST00000370665	T	0.11821	2.74	4.91	2.99	0.34606	.	0.945862	0.08788	N	0.893617	T	0.02083	0.0065	N	0.08118	0	0.09310	P	0.9999999400257	P	0.37864	0.61	B	0.35550	0.205	T	0.44421	-0.9329	9	0.26408	T	0.33	2.9062	7.0606	0.25123	0.2131:0.0:0.7869:0.0	rs3738573;rs17479406;rs3738573	3	Q8WZ79	DNS2B_HUMAN	H	3	ENSP00000359699:Q3H	ENSP00000359699:Q3H	Q	+	3	2	DNASE2B	84636844	0.616000	0.27035	0.798000	0.32154	0.152000	0.21847	0.646000	0.24797	0.742000	0.32697	0.655000	0.94253	CAG	G|0.694;C|0.306	0.306	strong		0.468	DNASE2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027248.1	NM_021233	
KLHL38	340359	hgsc.bcm.edu	37	8	124664130	124664130	+	Missense_Mutation	SNP	C	C	T	rs11780509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:124664130C>T	ENST00000325995.7	-	1	1060	c.1037G>A	c.(1036-1038)aGg>aAg	p.R346K	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	346			R -> K (in dbSNP:rs11780509). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.							breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						GACCAGACTCCTCCCTGAGCT	0.587													C|||	3540	0.706869	0.6604	0.6902	5008	,	,		21053	0.7113		0.8022	False		,,,				2504	0.6789				p.R346K		Atlas-SNP	.											.	KLHL38	81	.	0			c.G1037A						PASS	.	C	LYS/ARG	2886,1184		1030,826,179	64.0	65.0	65.0		1037	-0.1	0.0	8	dbSNP_120	65	6609,1771		2616,1377,197	yes	missense	KLHL38	NM_001081675.2	26	3646,2203,376	TT,TC,CC		21.1337,29.0909,23.7349	benign	346/582	124664130	9495,2955	2035	4190	6225	SO:0001583	missense	340359	exon1			AGACTCCTCCCTG		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1037G>A	8.37:g.124664130C>T	ENSP00000321475:p.Arg346Lys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	1575	0.7211538461538461	316	0.6422764227642277	249	0.6878453038674033	400	0.6993006993006993	610	0.8047493403693932	C	5.860	0.342830	0.11069	0.709091	0.788663	ENSG00000175946	ENST00000325995	T	0.65732	-0.17	5.18	-0.0604	0.13789	Kelch-type beta propeller (1);	0.516863	0.23252	N	0.050226	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41360	-0.9513	9	0.02654	T	1	.	4.7156	0.12893	0.0:0.2558:0.2902:0.454	rs11780509;rs59307986;rs11780509	346	Q2WGJ6	KLH38_HUMAN	K	346	ENSP00000321475:R346K	ENSP00000321475:R346K	R	-	2	0	KLHL38	124733311	0.494000	0.26043	0.005000	0.12908	0.953000	0.61014	1.274000	0.33132	0.034000	0.15491	0.561000	0.74099	AGG	C|0.260;T|0.740	0.740	strong		0.587	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
ACPP	55	hgsc.bcm.edu	37	3	132075707	132075707	+	Silent	SNP	A	A	G	rs2071505	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:132075707A>G	ENST00000336375.5	+	10	1236	c.1146A>G	c.(1144-1146)gaA>gaG	p.E382E	ACPP_ENST00000475741.1_Silent_p.E349E|ACPP_ENST00000351273.7_Intron	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	382					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						AAGGTACTGAAGACAGTACAG	0.512													G|||	1984	0.396166	0.3608	0.4827	5008	,	,		18799	0.119		0.5378	False		,,,				2504	0.5225				p.E382E		Atlas-SNP	.											.	ACPP	118	.	0			c.A1146G						PASS	.	G	,	1709,2697	651.7+/-399.3	341,1027,835	112.0	100.0	104.0		1146,	3.8	0.0	3	dbSNP_96	104	4801,3799	537.7+/-383.3	1332,2137,831	no	coding-synonymous,intron	ACPP	NM_001099.4,NM_001134194.1	,	1673,3164,1666	GG,GA,AA		44.1744,38.788,49.9462	,	382/387,	132075707	6510,6496	2203	4300	6503	SO:0001819	synonymous_variant	55	exon10			TACTGAAGACAGT		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.1146A>G	3.37:g.132075707A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	111	64	0.576577	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Silent	SNP	ENST00000336375.5	37	CCDS3073.1																																																																																			A|0.554;G|0.446	0.446	strong		0.512	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099	
TNFRSF25	8718	hgsc.bcm.edu	37	1	6524688	6524688	+	Silent	SNP	T	T	C	rs3170675	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:6524688T>C	ENST00000356876.3	-	4	474	c.387A>G	c.(385-387)caA>caG	p.Q129Q	TNFRSF25_ENST00000351959.5_Silent_p.Q129Q|TNFRSF25_ENST00000377782.3_Silent_p.Q129Q|TNFRSF25_ENST00000348333.3_Silent_p.Q84Q|TNFRSF25_ENST00000351748.3_Intron|TNFRSF25_ENST00000461703.2_5'UTR	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	129					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		TGCTGACACATTGGCTGACCT	0.632													t|||	101	0.0201677	0.003	0.0317	5008	,	,		17533	0.0		0.0726	False		,,,				2504	0.002				p.Q129Q		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.A387G						PASS	.	T	,,,,,	44,4362	46.7+/-81.2	0,44,2159	65.0	66.0	66.0		387,387,387,387,252,	-11.0	0.0	1	dbSNP_105	66	445,8155	134.7+/-192.1	20,405,3875	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	TNFRSF25	NM_001039664.1,NM_003790.2,NM_148965.1,NM_148966.1,NM_148967.1,NM_148970.1	,,,,,	20,449,6034	CC,CT,TT		5.1744,0.9986,3.7598	,,,,,	129/182,129/418,129/427,129/381,84/373,	6524688	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	8718	exon4			GACACATTGGCTG	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"""Tumor necrosis factor receptor superfamily"""	11910	protein-coding gene	gene with protein product		603366	"""tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"""	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.387A>G	1.37:g.6524688T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	81	57	0.703704	NM_148966	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Silent	SNP	ENST00000356876.3	37	CCDS71.1																																																																																			T|0.965;C|0.035	0.035	strong		0.632	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965	
TNR	7143	hgsc.bcm.edu	37	1	175335234	175335234	+	Silent	SNP	C	C	T	rs1385541	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:175335234C>T	ENST00000367674.2	-	11	2802	c.2094G>A	c.(2092-2094)tcG>tcA	p.S698S	TNR_ENST00000263525.2_Silent_p.S698S			Q92752	TENR_HUMAN	tenascin R	698	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TGGAGGTCTCCGAGGAGGCTG	0.522													C|||	832	0.166134	0.1483	0.1974	5008	,	,		22079	0.1042		0.2445	False		,,,				2504	0.1513				p.S698S		Atlas-SNP	.											.	TNR	399	.	0			c.G2094A						PASS	.	C		604,3802	264.1+/-265.8	53,498,1652	116.0	94.0	102.0		2094	-11.8	0.5	1	dbSNP_88	102	2089,6511	360.6+/-332.0	258,1573,2469	no	coding-synonymous	TNR	NM_003285.2		311,2071,4121	TT,TC,CC		24.2907,13.7086,20.7058		698/1359	175335234	2693,10313	2203	4300	6503	SO:0001819	synonymous_variant	7143	exon11			GGTCTCCGAGGAG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2094G>A	1.37:g.175335234C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	226	116	0.513274	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																			C|0.809;T|0.191	0.191	strong		0.522	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
PCLO	27445	hgsc.bcm.edu	37	7	82544987	82544987	+	Silent	SNP	A	A	G	rs17156844	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82544987A>G	ENST00000333891.9	-	7	12652	c.12315T>C	c.(12313-12315)caT>caC	p.H4105H	PCLO_ENST00000423517.2_Silent_p.H4105H|PCLO_ENST00000437081.1_Silent_p.H825H	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCACATAACTATGCAATCTAG	0.453													A|||	2137	0.426717	0.5023	0.4986	5008	,	,		20097	0.5466		0.2028	False		,,,				2504	0.3804				p.H4105H		Atlas-SNP	.											.	PCLO	1506	.	0			c.T12315C						PASS	.	A	,	1540,2230		305,930,650	58.0	53.0	55.0		12315,12315	-0.8	1.0	7	dbSNP_123	55	1814,6384		213,1388,2498	no	coding-synonymous,coding-synonymous	PCLO	NM_014510.2,NM_033026.5	,	518,2318,3148	GG,GA,AA		22.1273,40.8488,28.0247	,	4105/4936,4105/5143	82544987	3354,8614	1885	4099	5984	SO:0001819	synonymous_variant	27445	exon7			ATAACTATGCAAT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.12315T>C	7.37:g.82544987A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	186	92	0.494624	NM_014510		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			A|0.591;G|0.409	0.409	strong		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
OXCT1	5019	hgsc.bcm.edu	37	5	41862819	41862819	+	Missense_Mutation	SNP	G	G	A	rs76956231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:41862819G>A	ENST00000196371.5	-	2	272	c.112C>T	c.(112-114)Cgc>Tgc	p.R38C		NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	38					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	TTGGTATGGCGATGAGCACTG	0.378													G|||	15	0.00299521	0.0008	0.0029	5008	,	,		14176	0.0		0.0099	False		,,,				2504	0.002				p.R38C		Atlas-SNP	.											OXCT1,NS,carcinoma,+1,1	OXCT1	54	1	0			c.C112T						PASS	.	G	CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	120.0	107.0	112.0		112	3.8	0.0	5	dbSNP_132	112	83,8517	47.6+/-106.9	0,83,4217	yes	missense	OXCT1	NM_000436.3	180	0,87,6416	AA,AG,GG		0.9651,0.0908,0.6689	possibly-damaging	38/521	41862819	87,12919	2203	4300	6503	SO:0001583	missense	5019	exon2			TATGGCGATGAGC	U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"""3-oxoacid CoA transferase"""	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.112C>T	5.37:g.41862819G>A	ENSP00000196371:p.Arg38Cys	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_000436	B2R5V2|B7Z528	Missense_Mutation	SNP	ENST00000196371.5	37	CCDS3937.1	10	0.004578754578754579	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	11.72	1.723995	0.30593	9.08E-4	0.009651	ENSG00000083720	ENST00000196371	D	0.86164	-2.08	5.56	3.8	0.43715	.	0.298519	0.35495	N	0.003180	T	0.67411	0.2890	N	0.08118	0	0.21473	N	0.999674	B	0.09022	0.002	B	0.08055	0.003	T	0.60949	-0.7161	10	0.44086	T	0.13	0.7598	11.4381	0.50081	0.1494:0.0:0.8506:0.0	.	38	P55809	SCOT1_HUMAN	C	38	ENSP00000196371:R38C	ENSP00000196371:R38C	R	-	1	0	OXCT1	41898576	0.439000	0.25610	0.027000	0.17364	0.805000	0.45488	3.805000	0.55575	0.725000	0.32318	-0.216000	0.12614	CGC	G|0.994;A|0.006	0.006	strong		0.378	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436	
TYRO3	7301	hgsc.bcm.edu	37	15	41865525	41865525	+	Missense_Mutation	SNP	G	G	T	rs62001448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41865525G>T	ENST00000263798.3	+	17	2229	c.2005G>T	c.(2005-2007)Gtg>Ttg	p.V669L	TYRO3_ENST00000559066.1_Missense_Mutation_p.V624L	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	669	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GGACATGACAGTGTGTGTGGC	0.562																																					p.V669L		Atlas-SNP	.											.	TYRO3	169	.	0			c.G2005T						PASS	.						209.0	211.0	211.0					15																	41865525		2203	4300	6503	SO:0001583	missense	7301	exon17			ATGACAGTGTGTG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.2005G>T	15.37:g.41865525G>T	ENSP00000263798:p.Val669Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	117	10	0.0854701	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	177	0.08104395604395605	12	0.024390243902439025	34	0.09392265193370165	11	0.019230769230769232	120	0.158311345646438	G	28.2	4.901936	0.92035	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	D	0.85861	-2.04	5.55	5.55	0.83447	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.436224	0.16821	N	0.198144	T	0.03136	0.0092	L	0.41027	1.25	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.54715	-0.8252	10	0.87932	D	0	-8.3883	19.5084	0.95130	0.0:0.0:1.0:0.0	rs62001448	669	Q06418	TYRO3_HUMAN	L	601;669	ENSP00000263798:V669L	ENSP00000263798:V669L	V	+	1	0	TYRO3	39652817	1.000000	0.71417	0.964000	0.40570	0.975000	0.68041	9.869000	0.99810	2.612000	0.88384	0.655000	0.94253	GTG	G|0.915;T|0.085	0.085	strong		0.562	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		
POLL	27343	hgsc.bcm.edu	37	10	103340144	103340144	+	Silent	SNP	A	A	G	rs3730476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:103340144A>G	ENST00000370162.3	-	8	1718	c.1224T>C	c.(1222-1224)tcT>tcC	p.S408S	POLL_ENST00000339310.3_Silent_p.S131S|POLL_ENST00000370158.3_Silent_p.S133S|DPCD_ENST00000416979.2_Intron|POLL_ENST00000370168.3_Silent_p.S81S|DPCD_ENST00000470165.1_Intron|POLL_ENST00000370169.1_Silent_p.S408S|POLL_ENST00000463515.1_5'UTR|POLL_ENST00000299206.4_Silent_p.S408S|POLL_ENST00000456836.2_Silent_p.S145S|POLL_ENST00000370172.1_Silent_p.S320S	NM_001174084.1|NM_001174085.1|NM_013274.3	NP_001167555.1|NP_001167556.1|NP_037406.1	Q9UGP5	DPOLL_HUMAN	polymerase (DNA directed), lambda	408					DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|nucleotide-excision repair (GO:0006289)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		ACAGCAGCCCAGAGTTAAAGG	0.622								DNA polymerases (catalytic subunits)					G|||	817	0.163139	0.1649	0.183	5008	,	,		18428	0.0377		0.2982	False		,,,				2504	0.137				p.S408S		Atlas-SNP	.											.	POLL	43	.	0			c.T1224C						PASS	.	G	,,	835,3571	746.4+/-411.7	83,669,1451	68.0	70.0	70.0		1224,948,1224	-5.8	0.8	10	dbSNP_107	70	2617,5983	686.6+/-404.1	410,1797,2093	no	coding-synonymous,coding-synonymous,coding-synonymous	POLL	NM_001174084.1,NM_001174085.1,NM_013274.3	,,	493,2466,3544	GG,GA,AA		30.4302,18.9514,26.5416	,,	408/576,316/484,408/576	103340144	3452,9554	2203	4300	6503	SO:0001819	synonymous_variant	27343	exon8			CAGCCCAGAGTTA	AF161019	CCDS7513.1	10q23	2012-05-18			ENSG00000166169	ENSG00000166169		"""DNA polymerases"""	9184	protein-coding gene	gene with protein product		606343				17686665	Standard	NM_001174084		Approved		uc001kti.2	Q9UGP5	OTTHUMG00000018933	ENST00000370162.3:c.1224T>C	10.37:g.103340144A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	206	205	0.995146	NM_013274	D3DR76|Q5JQP5|Q6NUM2|Q9BTN8|Q9HA10|Q9HB35	Silent	SNP	ENST00000370162.3	37	CCDS7513.1																																																																																			A|0.771;G|0.229	0.229	strong		0.622	POLL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049946.1	NM_013274	
ZNF318	24149	hgsc.bcm.edu	37	6	43305520	43305520	+	Silent	SNP	C	C	T	rs35650765	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43305520C>T	ENST00000361428.2	-	10	6293	c.6216G>A	c.(6214-6216)ccG>ccA	p.P2072P	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	2072					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			GAGAATCTAACGGAAACCCAG	0.443													C|||	94	0.01877	0.003	0.0202	5008	,	,		20560	0.0129		0.0487	False		,,,				2504	0.0143				p.P2072P		Atlas-SNP	.											ZNF318,colon,carcinoma,0,1	ZNF318	175	1	0			c.G6216A						scavenged	.	C		40,4366	44.6+/-78.6	0,40,2163	80.0	76.0	78.0		6216	-11.7	0.2	6	dbSNP_126	78	413,8187	130.0+/-188.0	10,393,3897	no	coding-synonymous	ZNF318	NM_014345.2		10,433,6060	TT,TC,CC		4.8023,0.9079,3.483		2072/2280	43305520	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	24149	exon10			ATCTAACGGAAAC	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.6216G>A	6.37:g.43305520C>T		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	187	88	0.470588	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Silent	SNP	ENST00000361428.2	37	CCDS4895.2																																																																																			C|0.970;T|0.030	0.030	strong		0.443	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
APOL3	80833	hgsc.bcm.edu	37	22	36537871	36537871	+	Missense_Mutation	SNP	C	C	T	rs140252051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:36537871C>T	ENST00000349314.2	-	3	623	c.586G>A	c.(586-588)Gct>Act	p.A196T	APOL3_ENST00000487423.1_5'UTR|APOL3_ENST00000397293.2_Missense_Mutation_p.A125T|APOL3_ENST00000397287.2_5'UTR|APOL3_ENST00000361710.2_5'UTR|APOL3_ENST00000424878.2_5'UTR	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	196					inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(1)|lung(1)|stomach(1)	5						CCAGAGGCAGCGCCAGTGGAG	0.562													C|||	5	0.000998403	0.0015	0.0014	5008	,	,		21116	0.0		0.002	False		,,,				2504	0.0				p.A196T		Atlas-SNP	.											APOL3_ENST00000349314,caecum,carcinoma,0,4	APOL3	60	4	0			c.G586A						PASS	.	C	THR/ALA,,	8,4398	14.3+/-33.2	0,8,2195	93.0	85.0	88.0		586,,	-0.3	0.0	22	dbSNP_134	88	44,8556	29.0+/-79.6	0,44,4256	yes	missense,utr-5,utr-5	APOL3	NM_145640.2,NM_145641.2,NM_145642.2	58,,	0,52,6451	TT,TC,CC		0.5116,0.1816,0.3998	benign,,	196/403,,	36537871	52,12954	2203	4300	6503	SO:0001583	missense	80833	exon3			AGGCAGCGCCAGT	AF305227	CCDS13922.1, CCDS13924.1	22q13.1	2013-01-24			ENSG00000128284	ENSG00000128284		"""Apolipoproteins"""	14868	protein-coding gene	gene with protein product		607253				11374903	Standard	NM_145640		Approved	CG12-1, APOLIII	uc003aot.3	O95236	OTTHUMG00000150632	ENST00000349314.2:c.586G>A	22.37:g.36537871C>T	ENSP00000344577:p.Ala196Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Missense_Mutation	SNP	ENST00000349314.2	37	CCDS13922.1	5	0.0022893772893772895	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	9.409	1.080032	0.20309	0.001816	0.005116	ENSG00000128284	ENST00000397293;ENST00000349314	T;T	0.04156	3.69;3.69	4.3	-0.295	0.12828	.	0.919146	0.09404	N	0.806779	T	0.01558	0.0050	N	0.02708	-0.52	0.09310	N	0.999997	D;D	0.57571	0.98;0.975	P;B	0.44897	0.463;0.236	T	0.46275	-0.9203	10	0.16420	T	0.52	.	7.5658	0.27879	0.0:0.5334:0.0:0.4666	.	196;125	O95236;O95236-2	APOL3_HUMAN;.	T	125;196	ENSP00000380461:A125T;ENSP00000344577:A196T	ENSP00000344577:A196T	A	-	1	0	APOL3	34867817	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-2.685000	0.00834	-0.030000	0.13804	-0.556000	0.04195	GCT	C|0.997;T|0.003	0.003	strong		0.562	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641	
SLC38A8	146167	hgsc.bcm.edu	37	16	84063130	84063130	+	Missense_Mutation	SNP	C	C	G	rs11862366	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84063130C>G	ENST00000299709.3	-	5	658	c.659G>C	c.(658-660)aGt>aCt	p.S220T		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	220			S -> T (in dbSNP:rs11862366).		amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GGGGAAGACACTGAACACAGA	0.522													C|||	279	0.0557109	0.171	0.0144	5008	,	,		18537	0.0		0.0189	False		,,,				2504	0.0245				p.S220T		Atlas-SNP	.											.	SLC38A8	60	.	0			c.G659C						PASS	.	C	THR/SER	624,3776	270.7+/-269.8	34,556,1610	93.0	89.0	91.0		659	4.1	0.7	16	dbSNP_120	91	174,8426	78.4+/-141.0	4,166,4130	yes	missense	SLC38A8	NM_001080442.1	58	38,722,5740	GG,GC,CC		2.0233,14.1818,6.1385	benign	220/436	84063130	798,12202	2200	4300	6500	SO:0001583	missense	146167	exon5			AAGACACTGAACA		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.659G>C	16.37:g.84063130C>G	ENSP00000299709:p.Ser220Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	113	0.051739926739926737	92	0.18699186991869918	4	0.011049723756906077	0	0.0	17	0.022427440633245383	C	13.96	2.394329	0.42410	0.141818	0.020233	ENSG00000166558	ENST00000299709	T	0.02177	4.41	5.25	4.07	0.47477	.	0.087359	0.85682	D	0.000000	T	0.00012	0.0000	M	0.76002	2.32	0.20975	P	0.999818287	P	0.42620	0.785	B	0.43508	0.422	T	0.53251	-0.8465	9	0.28530	T	0.3	.	12.3155	0.54953	0.0:0.8818:0.0:0.1182	rs11862366	220	A6NNN8	S38A8_HUMAN	T	220	ENSP00000299709:S220T	ENSP00000299709:S220T	S	-	2	0	SLC38A8	82620631	0.263000	0.24083	0.730000	0.30809	0.806000	0.45545	0.840000	0.27600	2.621000	0.88768	0.643000	0.83706	AGT	C|0.939;G|0.061	0.061	strong		0.522	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
CAMK2G	818	hgsc.bcm.edu	37	10	75632760	75632760	+	Silent	SNP	C	C	T	rs2675671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:75632760C>T	ENST00000351293.3	-	2	204	c.147G>A	c.(145-147)aaG>aaA	p.K49K	CAMK2G_ENST00000372765.1_Silent_p.K49K|CAMK2G_ENST00000305762.7_Silent_p.K49K|CAMK2G_ENST00000423381.1_Silent_p.K49K|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000322680.3_Silent_p.K49K|CAMK2G_ENST00000322635.3_Silent_p.K49K|CAMK2G_ENST00000394762.2_Silent_p.K49K|CAMK2G_ENST00000444854.2_Silent_p.K49K	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	49	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	GGGCAGACAACTTCTTGGTAT	0.547													C|||	1424	0.284345	0.1936	0.3386	5008	,	,		18209	0.1121		0.5785	False		,,,				2504	0.2434				p.K49K		Atlas-SNP	.											CAMK2G_ENST00000322680,colon,carcinoma,0,2	CAMK2G	79	2	0			c.G147A						PASS	.	C	,,,,,	1173,3233	411.5+/-335.8	154,865,1184	261.0	238.0	246.0		147,147,147,147,147,147	4.1	1.0	10	dbSNP_100	246	4866,3734	617.6+/-396.7	1356,2154,790	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2G	NM_001204492.1,NM_001222.3,NM_172169.2,NM_172170.4,NM_172171.2,NM_172173.2	,,,,,	1510,3019,1974	TT,TC,CC		43.4186,26.6228,46.4324	,,,,,	49/540,49/496,49/528,49/519,49/557,49/505	75632760	6039,6967	2203	4300	6503	SO:0001819	synonymous_variant	818	exon2			AGACAACTTCTTG	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"""	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.147G>A	10.37:g.75632760C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_172170	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Silent	SNP	ENST00000351293.3	37	CCDS7336.1																																																																																			C|0.601;T|0.399	0.399	strong		0.547	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169	
MON2	23041	hgsc.bcm.edu	37	12	62894636	62894636	+	Silent	SNP	T	T	A	rs17120341	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:62894636T>A	ENST00000393632.2	+	6	1030	c.639T>A	c.(637-639)gcT>gcA	p.A213A	MON2_ENST00000546600.1_Silent_p.A213A|MON2_ENST00000393630.3_Silent_p.A213A|MON2_ENST00000280379.6_Silent_p.A213A|MON2_ENST00000552738.1_Silent_p.A213A|MON2_ENST00000549378.1_3'UTR|MON2_ENST00000393629.2_Silent_p.A213A|MON2_ENST00000552115.1_Silent_p.A213A	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	213					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		AACCTTGTGCTAAAGATGCAT	0.313													T|||	911	0.181909	0.1172	0.2349	5008	,	,		12472	0.2649		0.1133	False		,,,				2504	0.2168				p.A213A		Atlas-SNP	.											.	MON2	160	.	0			c.T639A						PASS	.	T		486,3920	223.9+/-240.3	29,428,1746	96.0	93.0	94.0		639	-0.5	1.0	12	dbSNP_123	94	905,7691	201.3+/-244.8	41,823,3434	no	coding-synonymous	MON2	NM_015026.2		70,1251,5180	AA,AT,TT		10.5282,11.0304,10.6984		213/1718	62894636	1391,11611	2203	4298	6501	SO:0001819	synonymous_variant	23041	exon6			TTGTGCTAAAGAT		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.639T>A	12.37:g.62894636T>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	134	49	0.365672	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Silent	SNP	ENST00000393632.2	37	CCDS31849.1																																																																																			T|0.868;A|0.132	0.132	strong		0.313	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
QRICH2	84074	hgsc.bcm.edu	37	17	74289648	74289648	+	Missense_Mutation	SNP	G	G	A	rs118098530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74289648G>A	ENST00000262765.5	-	4	841	c.662C>T	c.(661-663)cCa>cTa	p.P221L		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	221										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						ACGACGATCTGGCCTTAGATG	0.547													G|||	31	0.0061901	0.0	0.0086	5008	,	,		23912	0.0		0.0239	False		,,,				2504	0.001				p.P221L		Atlas-SNP	.											.	QRICH2	143	.	0			c.C662T						PASS	.	G	LEU/PRO	21,4385	28.1+/-56.4	0,21,2182	136.0	102.0	113.0		662	-0.7	0.0	17	dbSNP_132	113	226,8374	95.0+/-156.8	1,224,4075	yes	missense	QRICH2	NM_032134.1	98	1,245,6257	AA,AG,GG		2.6279,0.4766,1.8991	benign	221/1664	74289648	247,12759	2203	4300	6503	SO:0001583	missense	84074	exon4			CGATCTGGCCTTA	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.662C>T	17.37:g.74289648G>A	ENSP00000262765:p.Pro221Leu	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	375	190	0.506667	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	22	0.010073260073260074	0	0.0	3	0.008287292817679558	0	0.0	19	0.025065963060686015	G	7.287	0.610371	0.14066	0.004766	0.026279	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.20069	2.1	3.93	-0.743	0.11105	.	.	.	.	.	T	0.03390	0.0098	L	0.39020	1.185	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.11329	0.006;0.005	T	0.37911	-0.9685	9	0.02654	T	1	-0.3034	4.0087	0.09613	0.2955:0.0:0.5197:0.1848	.	221;221	B5MD94;Q9H0J4	.;QRIC2_HUMAN	L	221	ENSP00000262765:P221L	ENSP00000262765:P221L	P	-	2	0	QRICH2	71801243	0.297000	0.24408	0.003000	0.11579	0.059000	0.15707	0.061000	0.14366	-0.173000	0.10761	0.563000	0.77884	CCA	G|0.984;A|0.016	0.016	strong		0.547	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
CAPN10	11132	hgsc.bcm.edu	37	2	241537421	241537421	+	Silent	SNP	G	G	A	rs3749166	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:241537421G>A	ENST00000391984.2	+	10	2056	c.1860G>A	c.(1858-1860)gcG>gcA	p.A620A	CAPN10_ENST00000270364.7_Intron|CAPN10_ENST00000404753.3_Silent_p.A620A|CAPN10_ENST00000352879.4_Silent_p.A86A|CAPN10_ENST00000354082.4_Silent_p.A465A	NM_023083.3	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10	620	Domain III 2.				actin cytoskeleton reorganization (GO:0031532)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to insulin stimulus (GO:0032869)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin secretion (GO:0032024)|positive regulation of intracellular transport (GO:0032388)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteolysis (GO:0006508)|type B pancreatic cell apoptotic process (GO:0097050)	cell (GO:0005623)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cytoskeletal protein binding (GO:0008092)|SNARE binding (GO:0000149)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|urinary_tract(1)	27		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)		TCCTGCCTGCGGGCACCTACA	0.662													G|||	2563	0.511781	0.2897	0.5634	5008	,	,		17488	0.6488		0.6074	False		,,,				2504	0.5358				p.A620A		Atlas-SNP	.											.	CAPN10	105	.	0			c.G1860A						PASS	.	G	,	1389,3015	428.7+/-342.0	213,963,1026	40.0	41.0	40.0		1860,1395	-8.9	0.0	2	dbSNP_107	40	5324,3276	616.0+/-396.4	1642,2040,618	no	coding-synonymous,coding-synonymous	CAPN10	NM_023083.3,NM_023085.3	,	1855,3003,1644	AA,AG,GG		38.093,31.5395,48.3774	,	620/673,465/518	241537421	6713,6291	2202	4300	6502	SO:0001819	synonymous_variant	11132	exon10			GCCTGCGGGCACC	AF089088	CCDS33420.1, CCDS42838.1	2q37.3	2008-05-22			ENSG00000142330	ENSG00000142330			1477	protein-coding gene	gene with protein product		605286				11017071, 11018080	Standard	NM_023083		Approved		uc002vzk.2	Q9HC96	OTTHUMG00000133358	ENST00000391984.2:c.1860G>A	2.37:g.241537421G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	188	185	0.984043	NM_023083	A8MVS7|Q4ZFV1|Q8NCD4|Q96IG4|Q96JI2|Q9HC89|Q9HC90|Q9HC91|Q9HC92|Q9HC93|Q9HC94|Q9HC95	Silent	SNP	ENST00000391984.2	37	CCDS42838.1																																																																																			G|0.469;A|0.531	0.531	strong		0.662	CAPN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257191.3	NM_023083	
UGT2B7	7364	hgsc.bcm.edu	37	4	69962610	69962610	+	Silent	SNP	A	A	G	rs28365063	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69962610A>G	ENST00000508661.1	+	1	399	c.372A>G	c.(370-372)agA>agG	p.R124R	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Silent_p.R124R			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	124					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	ACATAACTAGAAAGTTCTGTA	0.313													A|||	669	0.133586	0.0749	0.0908	5008	,	,		20982	0.1706		0.1909	False		,,,				2504	0.1462				p.R124R		Atlas-SNP	.											.	UGT2B7	79	.	0			c.A372G						PASS	.	A		329,4045	151.0+/-185.0	13,303,1871	52.0	53.0	52.0		372	-0.4	0.0	4	dbSNP_126	52	1508,7086	272.6+/-290.2	137,1234,2926	no	coding-synonymous	UGT2B7	NM_001074.2		150,1537,4797	GG,GA,AA		17.5471,7.5217,14.1656		124/530	69962610	1837,11131	2187	4297	6484	SO:0001819	synonymous_variant	7364	exon1			AACTAGAAAGTTC	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.372A>G	4.37:g.69962610A>G		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	205	92	0.44878	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000508661.1	37																																																																																				A|0.850;G|0.150	0.150	strong		0.313	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
LOXL2	4017	hgsc.bcm.edu	37	8	23225745	23225745	+	Silent	SNP	C	C	T	rs2294133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:23225745C>T	ENST00000389131.3	-	2	489	c.120G>A	c.(118-120)ccG>ccA	p.P40P	RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	40					aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		ACTCAGGAGCCGGTTGCTGGA	0.662													C|||	802	0.160144	0.2352	0.0591	5008	,	,		17572	0.2212		0.0755	False		,,,				2504	0.1544				p.P40P		Atlas-SNP	.											.	LOXL2	97	.	0			c.G120A						PASS	.	C		890,3516	331.0+/-301.8	94,702,1407	42.0	47.0	46.0		120	-11.3	0.0	8	dbSNP_100	46	511,8089	139.5+/-196.2	14,483,3803	no	coding-synonymous	LOXL2	NM_002318.2		108,1185,5210	TT,TC,CC		5.9419,20.1997,10.772		40/775	23225745	1401,11605	2203	4300	6503	SO:0001819	synonymous_variant	4017	exon2			AGGAGCCGGTTGC	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.120G>A	8.37:g.23225745C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_002318	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Silent	SNP	ENST00000389131.3	37	CCDS34864.1																																																																																			C|0.872;T|0.128	0.128	strong		0.662	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1		
FAM57B	83723	hgsc.bcm.edu	37	16	30037128	30037128	+	Silent	SNP	A	A	C	rs11544328	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:30037128A>C	ENST00000380495.4	-	4	1190	c.459T>G	c.(457-459)ggT>ggG	p.G153G	FAM57B_ENST00000564806.1_Silent_p.G103G|FAM57B_ENST00000279389.4_Silent_p.G103G	NM_031478.4	NP_113666.2	Q71RH2	FA57B_HUMAN	family with sequence similarity 57, member B	153	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|negative regulation of fat cell differentiation (GO:0045599)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sphingosine N-acyltransferase activity (GO:0050291)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						AGTCTCCCTTACCCTGTCGCC	0.612													C|||	2205	0.440296	0.472	0.3833	5008	,	,		19898	0.377		0.4652	False		,,,				2504	0.4775				p.G153G		Atlas-SNP	.											.	FAM57B	26	.	0			c.T459G						PASS	.	C		2072,2322	603.2+/-390.1	488,1096,613	119.0	113.0	115.0		459	0.7	1.0	16	dbSNP_120	115	4009,4591	595.3+/-393.4	942,2125,1233	no	coding-synonymous	FAM57B	NM_031478.4		1430,3221,1846	CC,CA,AA		46.6163,47.1552,46.7985		153/275	30037128	6081,6913	2197	4300	6497	SO:0001819	synonymous_variant	83723	exon4			TCCCTTACCCTGT	AF370365	CCDS10667.2	16p11.2	2013-02-19			ENSG00000149926	ENSG00000149926			25295	protein-coding gene	gene with protein product		615175				11230166, 23275342	Standard	NM_031478		Approved	DKFZP434I2117	uc002dvt.3	Q71RH2	OTTHUMG00000132105	ENST00000380495.4:c.459T>G	16.37:g.30037128A>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_031478	Q9H0J1	Silent	SNP	ENST00000380495.4	37	CCDS10667.2	931	0.42628205128205127	224	0.45528455284552843	152	0.4198895027624309	207	0.3618881118881119	348	0.45910290237467016	C	6.837	0.523609	0.13066	0.471552	0.466163	ENSG00000149926	ENST00000279389	.	.	.	5.17	0.696	0.18075	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999063034	.	.	.	.	.	.	T	0.48445	-0.9035	3	.	.	.	-11.4479	6.491	0.22115	0.2189:0.3997:0.3813:0.0	rs11544328;rs11642480;rs57043294	.	.	.	G	120	.	.	V	-	2	0	FAM57B	29944629	0.397000	0.25270	1.000000	0.80357	0.608000	0.37181	-0.388000	0.07352	0.200000	0.20447	-1.165000	0.01757	GTA	A|0.543;C|0.457	0.457	strong		0.612	FAM57B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255142.2	NM_031478	
OR56A1	120796	hgsc.bcm.edu	37	11	6048056	6048056	+	Silent	SNP	T	T	C	rs11040335	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6048056T>C	ENST00000316650.5	-	1	915	c.879A>G	c.(877-879)gcA>gcG	p.A293A		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAGGGTTCAATGCAGGAGGAA	0.458													.|||	1352	0.269968	0.2572	0.3689	5008	,	,		23031	0.0516		0.3966	False		,,,				2504	0.3119				p.A293A		Atlas-SNP	.											.	OR56A1	73	.	0			c.A879G						PASS	.	T		1183,3219	416.7+/-337.7	150,883,1168	109.0	100.0	103.0		879	1.2	0.9	11	dbSNP_120	103	3187,5405	482.3+/-370.9	596,1995,1705	no	coding-synonymous	OR56A1	NM_001001917.2		746,2878,2873	CC,CT,TT		37.0926,26.8741,33.6309		293/319	6048056	4370,8624	2201	4296	6497	SO:0001819	synonymous_variant	120796	exon1			GTTCAATGCAGGA	AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"""GPCR / Class A : Olfactory receptors"""	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.879A>G	11.37:g.6048056T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	107	104	0.971963	NM_001001917	B2RNI2|Q6IFL0	Silent	SNP	ENST00000316650.5	37	CCDS31405.1																																																																																			T|0.695;C|0.305	0.305	strong		0.458	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847069	100847069	+	Missense_Mutation	SNP	G	G	A	rs569336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100847069G>A	ENST00000298815.8	+	20	2140	c.2137G>A	c.(2137-2139)Gtt>Att	p.V713I	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.V679I	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	713	Ser-rich.			V -> I (in Ref. 3; BAB71456). {ECO:0000305}.	signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						CCCAGGAGACGTTTCCCCACC	0.488													G|||	2485	0.496206	0.1505	0.5274	5008	,	,		21331	0.997		0.2883	False		,,,				2504	0.6391				p.V713I		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G2137A						PASS	.	G	ILE/VAL	307,1077		34,239,419	64.0	49.0	54.0		2137	2.4	0.0	11	dbSNP_83	54	987,2195		160,667,764	yes	missense	ARHGAP42	NM_152432.2	29	194,906,1183	AA,AG,GG		31.0182,22.1821,28.3399	benign	713/875	100847069	1294,3272	692	1591	2283	SO:0001583	missense	143872	exon20			GGAGACGTTTCCC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2137G>A	11.37:g.100847069G>A	ENSP00000298815:p.Val713Ile	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	175	79	0.451429	NM_152432	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	37		1052	0.4816849816849817	87	0.17682926829268292	168	0.46408839779005523	572	1.0	225	0.29683377308707126	G	3.367	-0.129186	0.06753	0.221821	0.310182	ENSG00000165895	ENST00000524892;ENST00000298815	T;T	0.06849	3.25;3.34	5.7	2.36	0.29203	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37753	-0.9692	8	0.33141	T	0.24	.	12.4883	0.55885	0.2148:0.0:0.7852:0.0	rs569336;rs52827090;rs58116702;rs569336	713	A6NI28	RHG42_HUMAN	I	679;713	ENSP00000431776:V679I;ENSP00000298815:V713I	ENSP00000298815:V713I	V	+	1	0	ARHGAP42	100352279	0.011000	0.17503	0.008000	0.14137	0.397000	0.30659	1.390000	0.34464	0.760000	0.33108	0.655000	0.94253	GTT	G|0.552;A|0.448	0.448	strong		0.488	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
TP53BP1	7158	hgsc.bcm.edu	37	15	43733730	43733730	+	Missense_Mutation	SNP	A	A	G	rs45482998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43733730A>G	ENST00000263801.3	-	15	3329	c.3077T>C	c.(3076-3078)gTt>gCt	p.V1026A	TP53BP1_ENST00000382044.4_Missense_Mutation_p.V1031A|TP53BP1_ENST00000450115.2_Missense_Mutation_p.V1031A|TP53BP1_ENST00000382039.3_Missense_Mutation_p.V1031A	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1026			V -> A (in dbSNP:rs45482998). {ECO:0000269|Ref.4}.		cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		TTACCTGGCAACAGACTCAGC	0.373								Other conserved DNA damage response genes					A|||	28	0.00559105	0.0	0.0086	5008	,	,		15995	0.0		0.0179	False		,,,				2504	0.0041				p.V1031A		Atlas-SNP	.											.	TP53BP1	157	.	0			c.T3092C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	10,4392	16.8+/-37.8	0,10,2191	140.0	138.0	139.0		3092,3092,3077	5.8	1.0	15	dbSNP_127	139	111,8485	58.7+/-120.3	0,111,4187	yes	missense,missense,missense	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	64,64,64	0,121,6378	GG,GA,AA		1.2913,0.2272,0.9309	probably-damaging,probably-damaging,probably-damaging	1031/1976,1031/1978,1026/1973	43733730	121,12877	2201	4298	6499	SO:0001583	missense	7158	exon15			CTGGCAACAGACT	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.3077T>C	15.37:g.43733730A>G	ENSP00000263801:p.Val1026Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	A	21.3	4.129115	0.77549	0.002272	0.012913	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.16073	3.16;3.16;3.07;3.14;2.37	5.82	5.82	0.92795	.	0.183825	0.38111	N	0.001802	T	0.20861	0.0502	M	0.72894	2.215	0.47153	D	0.999333	D;D;D;D	0.67145	0.995;0.994;0.996;0.996	D;D;D;D	0.76071	0.978;0.97;0.987;0.987	T	0.08764	-1.0706	10	0.17832	T	0.49	-14.4302	10.214	0.43158	0.9224:0.0:0.0776:0.0	rs45482998;rs61757242	1031;1026;1031;1031	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	A	1026;1031;1031;1031;991	ENSP00000263801:V1026A;ENSP00000371475:V1031A;ENSP00000371470:V1031A;ENSP00000393497:V1031A;ENSP00000388028:V991A	ENSP00000263801:V1026A	V	-	2	0	TP53BP1	41521022	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.923000	0.56469	2.232000	0.73038	0.528000	0.53228	GTT	A|0.991;G|0.009	0.009	strong		0.373	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
CYP1A1	1543	hgsc.bcm.edu	37	15	75012939	75012939	+	Missense_Mutation	SNP	C	C	T	rs140680363		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75012939C>T	ENST00000379727.3	-	7	1628	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q	CYP1A1_ENST00000395049.4_Missense_Mutation_p.R448Q|CYP1A1_ENST00000567032.1_Missense_Mutation_p.R477Q|CYP1A1_ENST00000395048.2_Missense_Mutation_p.R477Q			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	477			R -> W (in allele CYP1A1*10; dbSNP:rs56240201). {ECO:0000269|PubMed:15618738, ECO:0000269|PubMed:16959974}.		9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)			autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	GAATTCCACCCGTTGCAGCAG	0.547									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.R477Q		Atlas-SNP	.											CYP1A1,colon,carcinoma,0,3	CYP1A1	60	3	0			c.G1430A						scavenged	.	C	GLN/ARG	0,4394		0,0,2197	113.0	99.0	104.0		1430	-2.3	0.0	15	dbSNP_134	104	1,8591	1.2+/-3.3	0,1,4295	no	missense	CYP1A1	NM_000499.3	43	0,1,6492	TT,TC,CC		0.0116,0.0,0.0077	benign	477/513	75012939	1,12985	2197	4296	6493	SO:0001583	missense	1543	exon7	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	TCCACCCGTTGCA	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"""Cytochrome P450s"""	2595	protein-coding gene	gene with protein product		108330	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"""	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.1430G>A	15.37:g.75012939C>T	ENSP00000369050:p.Arg477Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	136	3	0.0220588	NM_000499	A4F3V9|A4F3W0|Q53G18	Missense_Mutation	SNP	ENST00000379727.3	37	CCDS10268.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.443673	0.01089	0.0	1.16E-4	ENSG00000140465	ENST00000379727;ENST00000395048;ENST00000395049;ENST00000268062	T;T;T	0.70399	-0.48;-0.48;-0.48	5.65	-2.35	0.06684	.	0.335977	0.35407	N	0.003227	T	0.40423	0.1116	N	0.05383	-0.06	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.12156	0.007;0.003	T	0.38845	-0.9642	10	0.02654	T	1	.	11.5324	0.50618	0.0:0.3318:0.0:0.6682	.	448;477	E7EMT5;P04798	.;CP1A1_HUMAN	Q	477;477;448;449	ENSP00000369050:R477Q;ENSP00000378488:R477Q;ENSP00000378489:R448Q	ENSP00000268062:R449Q	R	-	2	0	CYP1A1	72799992	0.628000	0.27138	0.014000	0.15608	0.005000	0.04900	0.963000	0.29293	-0.358000	0.08162	-1.044000	0.02363	CGG	C|1.000;T|0.000	0.000	weak		0.547	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57081197	57081197	+	Missense_Mutation	SNP	G	G	C	rs4939134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57081197G>C	ENST00000532437.1	-	4	1276	c.965C>G	c.(964-966)aCt>aGt	p.T322S	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.T322S|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	322	Acidic.|Pro-rich.		T -> S (in dbSNP:rs4939134). {ECO:0000269|PubMed:11854288}.		gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				AGCTTCAGGAGTCTGGGCTTC	0.662													g|||	2438	0.486821	0.0711	0.6268	5008	,	,		14414	0.7063		0.5457	False		,,,				2504	0.6626				p.T322S		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.C965G						PASS	.	G	SER/THR	648,3744		59,530,1607	19.0	25.0	23.0		965	2.2	0.8	11	dbSNP_111	23	4530,4062		1212,2106,978	yes	missense	TNKS1BP1	NM_033396.2	58	1271,2636,2585	CC,CG,GG		47.2765,14.7541,39.8799	benign	322/1730	57081197	5178,7806	2196	4296	6492	SO:0001583	missense	85456	exon5			TCAGGAGTCTGGG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.965C>G	11.37:g.57081197G>C	ENSP00000437271:p.Thr322Ser	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	185	90	0.486486	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	1091	0.49954212454212454	50	0.1016260162601626	211	0.5828729281767956	397	0.6940559440559441	433	0.5712401055408971	g	2.298	-0.360917	0.05103	0.147541	0.527235	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.26810	1.71;1.71	4.11	2.23	0.28157	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41556	-0.9502	8	0.02654	T	1	-0.9643	3.5604	0.07880	0.157:0.4422:0.3082:0.0926	rs4939134	322	Q9C0C2	TB182_HUMAN	S	322	ENSP00000350990:T322S;ENSP00000437271:T322S	ENSP00000350990:T322S	T	-	2	0	TNKS1BP1	56837773	0.001000	0.12720	0.786000	0.31890	0.504000	0.33889	0.130000	0.15850	0.348000	0.23949	-0.364000	0.07487	ACT	G|0.586;C|0.414	0.414	strong		0.662	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
FBN3	84467	hgsc.bcm.edu	37	19	8159362	8159362	+	Missense_Mutation	SNP	G	G	T	rs7245429	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8159362G>T	ENST00000600128.1	-	47	6287	c.5873C>A	c.(5872-5874)cCt>cAt	p.P1958H	FBN3_ENST00000270509.2_Missense_Mutation_p.P1958H|FBN3_ENST00000601739.1_Missense_Mutation_p.P1958H			Q75N90	FBN3_HUMAN	fibrillin 3	1958	EGF-like 31; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		P -> H (in dbSNP:rs7245429).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CTGGAAGCCAGGGGGACAGAT	0.587													G|||	2433	0.485823	0.2209	0.5403	5008	,	,		20228	0.7331		0.4006	False		,,,				2504	0.638				p.P1958H		Atlas-SNP	.											.	FBN3	300	.	0			c.C5873A						PASS	.	G	HIS/PRO	1034,3372	379.7+/-323.4	134,766,1303	77.0	58.0	64.0		5873	1.4	0.6	19	dbSNP_116	64	3332,5268	494.1+/-373.7	654,2024,1622	yes	missense	FBN3	NM_032447.3	77	788,2790,2925	TT,TG,GG		38.7442,23.468,33.5691	probably-damaging	1958/2810	8159362	4366,8640	2203	4300	6503	SO:0001583	missense	84467	exon46			AAGCCAGGGGGAC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5873C>A	19.37:g.8159362G>T	ENSP00000470498:p.Pro1958His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	1031|1031	0.47206959706959706|0.47206959706959706	114|114	0.23170731707317074|0.23170731707317074	190|190	0.5248618784530387|0.5248618784530387	422|422	0.7377622377622378|0.7377622377622378	305|305	0.4023746701846966|0.4023746701846966	G|G	18.00|18.00	3.525861|3.525861	0.64860|0.64860	0.23468|0.23468	0.387442|0.387442	ENSG00000142449|ENSG00000142449	ENST00000341066|ENST00000270509	.|D	.|0.92199	.|-2.99	4.69|4.69	1.38|1.38	0.22167|0.22167	.|EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|0.061519	.|0.64402	.|U	.|0.000003	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.55213|0.55213	1.73|1.73	0.19945|0.19945	P|P	0.9999416979|0.9999416979	.|D	.|0.53151	.|0.958	.|P	.|0.50440	.|0.641	T|T	0.49725|0.49725	-0.8909|-0.8909	5|9	0.34782|0.66056	T|D	0.22|0.02	.|.	9.8691|9.8691	0.41164|0.41164	0.2158:0.0:0.7842:0.0|0.2158:0.0:0.7842:0.0	rs7245429;rs17395421;rs52835316;rs60633933;rs7245429|rs7245429;rs17395421;rs52835316;rs60633933;rs7245429	.|1958	.|Q75N90	.|FBN3_HUMAN	M|H	78|1958	.|ENSP00000270509:P1958H	ENSP00000341317:L78M|ENSP00000270509:P1958H	L|P	-|-	1|2	2|0	FBN3|FBN3	8065362|8065362	1.000000|1.000000	0.71417|0.71417	0.566000|0.566000	0.28421|0.28421	0.913000|0.913000	0.54294|0.54294	5.137000|5.137000	0.64789|0.64789	0.085000|0.085000	0.17107|0.17107	-0.355000|-0.355000	0.07637|0.07637	CTG|CCT	G|0.603;T|0.397	0.397	strong		0.587	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
NOX5	79400	hgsc.bcm.edu	37	15	69327825	69327825	+	Silent	SNP	C	C	T	rs311889	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:69327825C>T	ENST00000388866.3	+	6	1028	c.987C>T	c.(985-987)acC>acT	p.T329T	NOX5_ENST00000448182.3_Silent_p.T283T|NOX5_ENST00000530406.2_Silent_p.T301T|NOX5_ENST00000455873.3_Silent_p.T294T|RP11-809H16.4_ENST00000559495.1_RNA|NOX5_ENST00000260364.5_Silent_p.T311T	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	329	Ferric oxidoreductase.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						TCGTGCACACCGTGGCTCACA	0.612													c|||	4039	0.80651	0.6142	0.9395	5008	,	,		20220	0.7391		0.9573	False		,,,				2504	0.8865				p.T329T		Atlas-SNP	.											.	NOX5	60	.	0			c.C987T						PASS	.	T	,,	2940,1460	679.6+/-403.7	995,950,255	95.0	63.0	74.0		903,882,987	-6.9	0.0	15	dbSNP_79	74	8230,366	802.5+/-407.3	3944,342,12	no	coding-synonymous,coding-synonymous,coding-synonymous	NOX5	NM_001184779.1,NM_001184780.1,NM_024505.3	,,	4939,1292,267	TT,TC,CC		4.2578,33.1818,14.0505	,,	301/738,294/731,329/766	69327825	11170,1826	2200	4298	6498	SO:0001819	synonymous_variant	79400	exon6			GCACACCGTGGCT	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"""EF-hand domain containing"""	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.987C>T	15.37:g.69327825C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Silent	SNP	ENST00000388866.3	37	CCDS32276.2																																																																																			T|0.832;G|0.000	0.832	strong		0.612	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505	
C1orf106	55765	hgsc.bcm.edu	37	1	200880869	200880869	+	Missense_Mutation	SNP	A	A	C	rs45547233	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:200880869A>C	ENST00000367342.4	+	9	1703	c.1503A>C	c.(1501-1503)agA>agC	p.R501S	C1orf106_ENST00000413687.2_Missense_Mutation_p.R416S	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	501										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						CCGGCAGCAGAGAGCTGGTCG	0.701													A|||	298	0.0595048	0.0091	0.0461	5008	,	,		13338	0.1091		0.1054	False		,,,				2504	0.0389				p.R515S		Atlas-SNP	.											C1orf106,caecum,carcinoma,0,1	C1orf106	59	1	0			c.A1545C						PASS	.	A	SER/ARG,SER/ARG	113,4291		3,107,2092	25.0	28.0	27.0		1248,1503	-3.0	0.5	1	dbSNP_127	27	990,7602		57,876,3363	no	missense,missense	C1orf106	NM_001142569.2,NM_018265.3	110,110	60,983,5455	CC,CA,AA		11.5223,2.5658,8.4872	benign,benign	416/579,501/664	200880869	1103,11893	2202	4296	6498	SO:0001583	missense	55765	exon9			CAGCAGAGAGCTG	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.1503A>C	1.37:g.200880869A>C	ENSP00000356311:p.Arg501Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Missense_Mutation	SNP	ENST00000367342.4	37		173	0.07921245421245421	3	0.006097560975609756	18	0.049723756906077346	65	0.11363636363636363	87	0.11477572559366754	A	7.865	0.726990	0.15439	0.025658	0.115223	ENSG00000163362	ENST00000367342;ENST00000413687	T;T	0.31247	1.5;1.5	3.45	-2.97	0.05530	.	1.399470	0.04811	N	0.435289	T	0.00178	0.0005	N	0.19112	0.55	0.39169	P	0.037437000000000054	P	0.37781	0.608	B	0.32289	0.143	T	0.06499	-1.0823	9	0.09084	T	0.74	-3.9784	4.1724	0.10336	0.5046:0.0:0.33:0.1654	rs45547233;rs61743890	501	Q3KP66	CA106_HUMAN	S	501;416	ENSP00000356311:R501S;ENSP00000392105:R416S	ENSP00000356311:R501S	R	+	3	2	C1orf106	199147492	0.978000	0.34361	0.487000	0.27428	0.184000	0.23303	0.652000	0.24888	-0.319000	0.08652	-0.385000	0.06624	AGA	A|0.921;C|0.079	0.079	strong		0.701	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
RIMS1	22999	hgsc.bcm.edu	37	6	72892796	72892796	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:72892796C>T	ENST00000521978.1	+	6	1622	c.1622C>T	c.(1621-1623)cCc>cTc	p.P541L	RIMS1_ENST00000518273.1_Missense_Mutation_p.P541L|RIMS1_ENST00000264839.7_Missense_Mutation_p.P541L|RIMS1_ENST00000491071.2_Missense_Mutation_p.P541L|RIMS1_ENST00000348717.5_Missense_Mutation_p.P541L|RIMS1_ENST00000522291.1_Missense_Mutation_p.P541L|RIMS1_ENST00000517960.1_Missense_Mutation_p.P541L|RIMS1_ENST00000520567.1_Missense_Mutation_p.P541L	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	541					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GTGTCGACGCCCGAGTACACC	0.682																																					p.P541L		Atlas-SNP	.											RIMS1,caecum,carcinoma,0,1	RIMS1	278	1	0			c.C1622T						scavenged	.						9.0	10.0	10.0					6																	72892796		1995	4142	6137	SO:0001583	missense	22999	exon6			CGACGCCCGAGTA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.1622C>T	6.37:g.72892796C>T	ENSP00000428417:p.Pro541Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	56	3	0.0535714	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.088952	0.76756	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.30714	1.57;1.72;1.63;1.73;1.65;1.67;1.74;1.52	4.05	3.16	0.36331	.	0.200172	0.34110	N	0.004245	T	0.43166	0.1235	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.94;0.966;0.999	T	0.49978	-0.8881	10	0.87932	D	0	-4.1408	13.4986	0.61440	0.0:0.8416:0.1584:0.0	.	541;541;541	E9PHR1;C9JNW6;Q86UR5	.;.;RIMS1_HUMAN	L	541	ENSP00000430101:P541L;ENSP00000275037:P541L;ENSP00000264839:P541L;ENSP00000429959:P541L;ENSP00000430408:P541L;ENSP00000430502:P541L;ENSP00000430932:P541L;ENSP00000428417:P541L	ENSP00000264839:P541L	P	+	2	0	RIMS1	72949517	1.000000	0.71417	0.681000	0.30009	0.907000	0.53573	7.468000	0.80943	0.657000	0.30906	-0.519000	0.04390	CCC	.	.	none		0.682	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
MAGEB16	139604	hgsc.bcm.edu	37	X	35820425	35820425	+	Missense_Mutation	SNP	C	C	T	rs1410961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:35820425C>T	ENST00000399989.1	+	2	391	c.112C>T	c.(112-114)Ctc>Ttc	p.L38F	MAGEB16_ENST00000399987.1_Missense_Mutation_p.L38F|MAGEB16_ENST00000399985.1_Missense_Mutation_p.L38F|MAGEB16_ENST00000399988.1_Missense_Mutation_p.L38F|MAGEB16_ENST00000399992.1_Missense_Mutation_p.L70F	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	38			L -> F (in dbSNP:rs1410961).							breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						GGAGAAGACCCTCCTCTCCTC	0.557													T|||	2340	0.619868	0.4455	0.4121	3775	,	,		14272	0.5694		0.4195	False		,,,				2504	0.4796				p.L38F		Atlas-SNP	.											.	MAGEB16	64	.	0			c.C112T						PASS	.	T	PHE/LEU	2045,1435		530,678,307,247,263	42.0	42.0	42.0		112	-5.7	0.0	X	dbSNP_88	42	3496,3018		687,1164,958,504,846	yes	missense	MAGEB16	NM_001099921.1	22	1217,1842,1265,751,1109	TT,TC,T,CC,C		46.331,41.2356,44.5567	benign	38/325	35820425	5541,4453	2025	4159	6184	SO:0001583	missense	139604	exon2			AAGACCCTCCTCT		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.112C>T	X.37:g.35820425C>T	ENSP00000382871:p.Leu38Phe	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	1012	0.6100060277275468	149	0.43567251461988304	102	0.4146341463414634	212	0.5792349726775956	230	0.3885135135135135	T	0.782	-0.761910	0.02996	0.587644	0.53669	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04454	3.62;3.62;3.62;3.62;3.62	3.02	-5.68	0.02436	Melanoma associated antigen, MAGE, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43605	-0.9381	8	0.08837	T	0.75	.	0.3947	0.00416	0.2901:0.216:0.2919:0.2021	rs1410961;rs17311172;rs1410961	38	A2A368	MAGBG_HUMAN	F	38;70;38;38;38	ENSP00000382870:L38F;ENSP00000382874:L70F;ENSP00000382869:L38F;ENSP00000382871:L38F;ENSP00000382867:L38F	ENSP00000382867:L38F	L	+	1	0	MAGEB16	35730346	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.364000	0.02590	-2.022000	0.00938	-2.348000	0.00243	CTC	C|0.371;0|0.010	.	strong		0.557	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
C17orf70	80233	hgsc.bcm.edu	37	17	79511135	79511135	+	Silent	SNP	A	A	G	rs8077430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79511135A>G	ENST00000327787.8	-	7	2368	c.2322T>C	c.(2320-2322)acT>acC	p.T774T	C17orf70_ENST00000537152.1_Silent_p.T623T|C17orf70_ENST00000425898.2_Silent_p.T423T			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	774					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GGCACAGGTCAGTCATGGCCA	0.657													G|||	3528	0.704473	0.5212	0.8156	5008	,	,		18480	0.7371		0.7406	False		,,,				2504	0.8027				p.T774T		Atlas-SNP	.											C17orf70_ENST00000327787,NS,adenoma,0,1	C17orf70	79	1	0			c.T2322C						PASS	.	G		2464,1936	536.8+/-374.6	682,1100,418	53.0	47.0	49.0		2322	-9.5	0.0	17	dbSNP_116	49	6596,2000	345.0+/-325.6	2534,1528,236	no	coding-synonymous	C17orf70	NM_025161.5		3216,2628,654	GG,GA,AA		23.2666,44.0,30.2862		774/882	79511135	9060,3936	2200	4298	6498	SO:0001819	synonymous_variant	80233	exon7			CAGGTCAGTCATG	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 100kDa"""	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.2322T>C	17.37:g.79511135A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Silent	SNP	ENST00000327787.8	37	CCDS32765.2																																																																																			A|0.314;G|0.686	0.686	strong		0.657	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161	
MUC20	200958	hgsc.bcm.edu	37	3	195453288	195453288	+	Missense_Mutation	SNP	A	A	C	rs3828405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195453288A>C	ENST00000447234.2	+	2	1940	c.1814A>C	c.(1813-1815)gAc>gCc	p.D605A	MUC20_ENST00000320736.6_Missense_Mutation_p.D434A|MUC20_ENST00000436408.1_Missense_Mutation_p.D605A|MUC20_ENST00000445522.2_Missense_Mutation_p.D570A	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	605	Involved in oligomerization.|Thr-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.D605A(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ACCAGCAGGGACCCTCTTCCT	0.597																																					p.D434A		Atlas-SNP	.											MUC20,NS,carcinoma,0,1	MUC20	84	1	1	Substitution - Missense(1)	stomach(1)	c.A1301C						PASS	.						62.0	67.0	65.0					3																	195453288		2096	4204	6300	SO:0001583	missense	200958	exon3			GCAGGGACCCTCT	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1814A>C	3.37:g.195453288A>C	ENSP00000414350:p.Asp605Ala	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	129	33	0.255814	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		165	0.07554945054945054	35	0.07113821138211382	19	0.052486187845303865	66	0.11538461538461539	45	0.059366754617414245	A	9.201	1.028502	0.19512	.	.	ENSG00000176945	ENST00000381954;ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.13657	2.99;2.99;3.16;2.57	4.81	-2.05	0.07321	.	1.913230	0.02235	N	0.065225	T	0.00144	0.0004	N	0.24115	0.695	0.09310	N	1	B	0.19331	0.035	B	0.19946	0.027	T	0.31779	-0.9931	10	0.24483	T	0.36	4.6485	5.3684	0.16127	0.4954:0.1476:0.357:0.0	rs3828405;rs60077383	434	E9PH32	.	A	416;605;434;605;570	ENSP00000414350:D605A;ENSP00000325431:D434A;ENSP00000396774:D605A;ENSP00000405629:D570A	ENSP00000325431:D434A	D	+	2	0	MUC20	196938959	0.000000	0.05858	0.000000	0.03702	0.150000	0.21749	-0.537000	0.06128	-0.538000	0.06281	-0.468000	0.05107	GAC	A|0.928;C|0.072	0.072	strong		0.597	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
KIF2C	11004	hgsc.bcm.edu	37	1	45224998	45224998	+	Missense_Mutation	SNP	A	A	C	rs4342887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45224998A>C	ENST00000372224.4	+	14	1458	c.1345A>C	c.(1345-1347)Atc>Ctc	p.I449L	KIF2C_ENST00000372217.1_Missense_Mutation_p.I395L|RP11-269F19.2_ENST00000440985.1_RNA|KIF2C_ENST00000372218.4_Missense_Mutation_p.I408L|KIF2C_ENST00000372222.3_Missense_Mutation_p.I336L|RP11-269F19.2_ENST00000428791.1_RNA	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	449	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.		I -> L (in dbSNP:rs4342887). {ECO:0000269|PubMed:12383881, ECO:0000269|PubMed:9434124, ECO:0000269|Ref.5}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					CATCAAGATGATCGACATGGG	0.547													A|||	1017	0.203075	0.1808	0.2507	5008	,	,		21901	0.2857		0.1382	False		,,,				2504	0.181				p.I449L		Atlas-SNP	.											.	KIF2C	68	.	0			c.A1345C						PASS	.	A	LEU/ILE	841,3565	332.0+/-302.3	82,677,1444	111.0	89.0	97.0		1345	4.7	1.0	1	dbSNP_111	97	1449,7151	276.9+/-292.6	128,1193,2979	yes	missense	KIF2C	NM_006845.3	5	210,1870,4423	CC,CA,AA		16.8488,19.0876,17.6073	benign	449/726	45224998	2290,10716	2203	4300	6503	SO:0001583	missense	11004	exon14			AAGATGATCGACA	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"""Kinesins"""	6393	protein-coding gene	gene with protein product		604538	"""kinesin-like 6 (mitotic centromere-associated kinesin)"""	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.1345A>C	1.37:g.45224998A>C	ENSP00000361298:p.Ile449Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	116	67	0.577586	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	37	CCDS512.1	426	0.19505494505494506	92	0.18699186991869918	73	0.20165745856353592	151	0.263986013986014	110	0.14511873350923482	A	18.34	3.603032	0.66445	0.190876	0.168488	ENSG00000142945	ENST00000372224;ENST00000372218;ENST00000372222;ENST00000372217	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.87	4.72	0.59763	Kinesin, motor domain (4);	0.179339	0.49916	N	0.000140	T	0.00012	0.0000	N	0.13352	0.335	0.09310	P	0.999999790191	B;B;B	0.21520	0.002;0.019;0.057	B;B;B	0.37015	0.155;0.044;0.239	T	0.15809	-1.0424	9	0.66056	D	0.02	.	13.045	0.58920	0.8655:0.1345:0.0:0.0	rs4342887;rs59548070;rs4342887	408;395;449	B7Z6Q6;Q99661-2;Q99661	.;.;KIF2C_HUMAN	L	449;408;336;395	ENSP00000361298:I449L;ENSP00000361292:I408L;ENSP00000361296:I336L;ENSP00000361291:I395L	ENSP00000361291:I395L	I	+	1	0	KIF2C	44997585	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	5.178000	0.65037	1.017000	0.39495	0.533000	0.62120	ATC	A|0.816;C|0.184	0.184	strong		0.547	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	
FOXD4	2298	hgsc.bcm.edu	37	9	116832	116832	+	Missense_Mutation	SNP	T	T	C	rs4742632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:116832T>C	ENST00000382500.2	-	1	1585	c.1288A>G	c.(1288-1290)Agt>Ggt	p.S430G		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	430					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GCCAGGGAACTGGGCGTGGGC	0.672																																					p.S430G		Atlas-SNP	.											.	FOXD4	75	.	0			c.A1288G						PASS	.	T	GLY/SER	786,3362		65,656,1353	15.0	20.0	19.0		1288	-4.8	0.0	9	dbSNP_111	19	2141,6135		228,1685,2225	no	missense	FOXD4	NM_207305.3	56	293,2341,3578	CC,CT,TT		25.87,18.9489,23.5592	benign	430/440	116832	2927,9497	2074	4138	6212	SO:0001583	missense	2298	exon1			GGGAACTGGGCGT	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.1288A>G	9.37:g.116832T>C	ENSP00000371940:p.Ser430Gly	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	176	109	0.619318	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	566	0.2591575091575092	95	0.19308943089430894	70	0.19337016574585636	182	0.3181818181818182	219	0.28891820580474936	.	0.106	-1.144682	0.01714	0.189489	0.2587	ENSG00000170122	ENST00000382500	D	0.95137	-3.62	2.41	-4.82	0.03171	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.35895	-0.9770	8	0.07644	T	0.81	.	1.4812	0.02437	0.1871:0.1494:0.422:0.2414	rs4742632	430	Q12950	FOXD4_HUMAN	G	430	ENSP00000371940:S430G	ENSP00000371940:S430G	S	-	1	0	FOXD4	106832	0.000000	0.05858	0.000000	0.03702	0.205000	0.24178	-2.099000	0.01346	-0.973000	0.03555	0.388000	0.25769	AGT	T|0.743;C|0.257	0.257	strong		0.672	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
CCDC9	26093	hgsc.bcm.edu	37	19	47774572	47774572	+	Silent	SNP	C	C	T	rs60930438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47774572C>T	ENST00000221922.6	+	12	1455	c.1233C>T	c.(1231-1233)gaC>gaT	p.D411D		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	411	Glu-rich.						poly(A) RNA binding (GO:0044822)	p.N416_E420delNEGEE(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		CTCCTgaagacgagggggaag	0.607													C|||	2566	0.51238	0.3411	0.5836	5008	,	,		18840	0.6825		0.4304	False		,,,				2504	0.6022				p.D411D		Atlas-SNP	.											.	CCDC9	37	.	1	Deletion - In frame(1)	ovary(1)	c.C1233T						PASS	.	C		1400,3006		233,934,1036	51.0	49.0	50.0		1233	-0.9	0.9	19	dbSNP_129	50	3755,4843		833,2089,1377	no	coding-synonymous	CCDC9	NM_015603.2		1066,3023,2413	TT,TC,CC		43.6729,31.7749,39.6416		411/532	47774572	5155,7849	2203	4299	6502	SO:0001819	synonymous_variant	26093	exon12			TGAAGACGAGGGG	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1233C>T	19.37:g.47774572C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_015603		Silent	SNP	ENST00000221922.6	37	CCDS12698.1																																																																																			C|0.569;G|0.000;T|0.431	0.431	strong		0.607	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
C5orf60	285679	hgsc.bcm.edu	37	5	179069468	179069468	+	Missense_Mutation	SNP	A	A	G	rs62405726	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:179069468A>G	ENST00000448248.2	-	5	731	c.706T>C	c.(706-708)Tgg>Cgg	p.W236R	C5orf60_ENST00000506142.1_5'Flank	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	0	Ser-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						CCCTGCCTCCACCTGCCTGCA	0.572													a|||	2302	0.459665	0.2935	0.5548	5008	,	,		17330	0.6806		0.2753	False		,,,				2504	0.5787				p.W236R		Atlas-SNP	.											C5orf60,caecum,carcinoma,+1,1	C5orf60	24	1	0			c.T706C						PASS	.						60.0	54.0	56.0					5																	179069468		692	1589	2281	SO:0001583	missense	285679	exon5			GCCTCCACCTGCC	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.706T>C	5.37:g.179069468A>G	ENSP00000404583:p.Trp236Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	26	0.238532	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	.	.	.	.	.	.	.	.	.	.	a	0.017	-1.489861	0.01018	.	.	ENSG00000204661	ENST00000448248	T	0.19938	2.11	0.517	-1.03	0.10102	.	.	.	.	.	T	0.21347	0.0514	.	.	.	0.80722	P	0.0	D;D	0.58268	0.982;0.982	P;P	0.61592	0.891;0.891	T	0.25745	-1.0123	6	0.07175	T	0.84	.	.	.	.	rs62405726	240;236	A6NFR6-2;A6NFR6-4	.;.	R	236	ENSP00000404583:W236R	ENSP00000404583:W236R	W	-	1	0	C5orf60	179002074	0.006000	0.16342	0.002000	0.10522	0.006000	0.05464	0.475000	0.22164	-0.672000	0.05266	-0.967000	0.02615	TGG	A|0.713;G|0.287	0.287	strong		0.572	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
POP1	10940	hgsc.bcm.edu	37	8	99153088	99153088	+	Missense_Mutation	SNP	A	A	C	rs17184326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:99153088A>C	ENST00000401707.2	+	11	1647	c.1566A>C	c.(1564-1566)aaA>aaC	p.K522N	POP1_ENST00000349693.3_Missense_Mutation_p.K522N	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	522			K -> N (in dbSNP:rs17184326).		RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			AGAAGTCCAAAGCTTTGCCCA	0.418													A|||	515	0.102835	0.1641	0.0951	5008	,	,		17452	0.001		0.1392	False		,,,				2504	0.093				p.K522N		Atlas-SNP	.											.	POP1	85	.	0			c.A1566C	GRCh37	CM067452	POP1	M	rs17184326	PASS	.	A	ASN/LYS,ASN/LYS,ASN/LYS	776,3630	309.4+/-291.0	72,632,1499	83.0	86.0	85.0		1566,1566,1566	4.2	0.8	8	dbSNP_123	85	1224,7376	246.5+/-274.9	77,1070,3153	yes	missense,missense,missense	POP1	NM_001145860.1,NM_001145861.1,NM_015029.2	94,94,94	149,1702,4652	CC,CA,AA		14.2326,17.6123,15.3775	possibly-damaging,possibly-damaging,possibly-damaging	522/1025,522/1025,522/1025	99153088	2000,11006	2203	4300	6503	SO:0001583	missense	10940	exon11			GTCCAAAGCTTTG	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"""processing of precursors 1"""	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.1566A>C	8.37:g.99153088A>C	ENSP00000385787:p.Lys522Asn	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	228	0.1043956043956044	90	0.18292682926829268	32	0.08839779005524862	0	0.0	106	0.13984168865435356	A	16.88	3.244265	0.59103	0.176123	0.142326	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.44482	0.92;0.92	5.59	4.23	0.50019	.	0.248471	0.40640	N	0.001052	T	0.00109	0.0003	M	0.78456	2.415	0.28215	P	0.9267864	P	0.41597	0.756	B	0.36289	0.221	T	0.15694	-1.0428	9	0.54805	T	0.06	-9.6686	9.0274	0.36239	0.8558:0.0:0.1442:0.0	rs17184326;rs17856354;rs52808856;rs17184326	522	Q99575	POP1_HUMAN	N	522	ENSP00000385787:K522N;ENSP00000339529:K522N	ENSP00000339529:K522N	K	+	3	2	POP1	99222264	1.000000	0.71417	0.779000	0.31741	0.922000	0.55478	5.790000	0.69038	2.127000	0.65507	0.529000	0.55759	AAA	A|0.859;C|0.141	0.141	strong		0.418	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029	
ACAP1	9744	hgsc.bcm.edu	37	17	7246851	7246851	+	Silent	SNP	C	C	T	rs3809828	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7246851C>T	ENST00000158762.3	+	6	704	c.498C>T	c.(496-498)taC>taT	p.Y166Y	ACAP1_ENST00000573893.1_3'UTR	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	166	BAR.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						GAGCTGGGTACCGGGGACGGG	0.657													C|||	267	0.0533147	0.0023	0.0231	5008	,	,		14038	0.127		0.0656	False		,,,				2504	0.0552				p.Y166Y		Atlas-SNP	.											.	ACAP1	66	.	0			c.C498T						PASS	.	C		50,4356	49.6+/-84.7	0,50,2153	44.0	52.0	50.0		498	5.1	1.0	17	dbSNP_107	50	506,8094	141.9+/-198.1	15,476,3809	no	coding-synonymous	ACAP1	NM_014716.3		15,526,5962	TT,TC,CC		5.8837,1.1348,4.275		166/741	7246851	556,12450	2203	4300	6503	SO:0001819	synonymous_variant	9744	exon6			TGGGTACCGGGGA	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.498C>T	17.37:g.7246851C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	121	67	0.553719	NM_014716	Q53XN9	Silent	SNP	ENST00000158762.3	37	CCDS11101.1																																																																																			C|0.944;T|0.056	0.056	strong		0.657	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
SLC47A2	146802	hgsc.bcm.edu	37	17	19584752	19584752	+	Silent	SNP	G	G	C	rs34416664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:19584752G>C	ENST00000325411.5	-	15	1478	c.1428C>G	c.(1426-1428)gcC>gcG	p.A476A	SLC47A2_ENST00000463318.1_5'UTR|SLC47A2_ENST00000350657.5_Silent_p.A454A	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	476					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	GGAAGACACAGGCCAGCATGC	0.592													G|||	22	0.00439297	0.0	0.0058	5008	,	,		19756	0.0		0.0139	False		,,,				2504	0.0041				p.A476A		Atlas-SNP	.											.	SLC47A2	61	.	0			c.C1428G						PASS	.	G	,	10,4396	17.9+/-39.9	0,10,2193	57.0	48.0	51.0		1320,1428	0.9	0.0	17	dbSNP_126	51	97,8503	52.7+/-113.3	1,95,4204	no	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	1,105,6397	CC,CG,GG		1.1279,0.227,0.8227	,	440/567,476/603	19584752	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon15			GACACAGGCCAGC	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.1428C>G	17.37:g.19584752G>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			G|0.993;C|0.007	0.007	strong		0.592	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
OR2D3	120775	hgsc.bcm.edu	37	11	6942476	6942476	+	Missense_Mutation	SNP	C	C	A	rs10839658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6942476C>A	ENST00000317834.3	+	1	272	c.244C>A	c.(244-246)Ctc>Atc	p.L82I		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	82			L -> I (in dbSNP:rs10839658).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TCTTAGAAATCTCTCCTTTGC	0.408													C|||	2022	0.403754	0.2716	0.4942	5008	,	,		19364	0.3383		0.6471	False		,,,				2504	0.3354				p.L82I		Atlas-SNP	.											.	OR2D3	51	.	0			c.C244A						PASS	.	C	ILE/LEU	1380,3022	454.0+/-350.5	211,958,1032	119.0	118.0	118.0		244	1.1	0.3	11	dbSNP_120	118	5357,3235	650.0+/-400.7	1683,1991,622	yes	missense	OR2D3	NM_001004684.1	5	1894,2949,1654	AA,AC,CC		37.6513,31.3494,48.153	probably-damaging	82/331	6942476	6737,6257	2201	4296	6497	SO:0001583	missense	120775	exon1			AGAAATCTCTCCT	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.244C>A	11.37:g.6942476C>A	ENSP00000320560:p.Leu82Ile	Somatic	288	1	0.00347222		WXS	Illumina HiSeq	Phase_I	296	156	0.527027	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	37	CCDS31417.1	1005	0.46016483516483514	148	0.3008130081300813	185	0.511049723756906	188	0.32867132867132864	484	0.6385224274406333	C	12.83	2.055315	0.36277	0.313494	0.623487	ENSG00000178358	ENST00000317834	T	0.00587	6.38	5.07	1.15	0.20763	GPCR, rhodopsin-like superfamily (1);	0.000000	0.28436	N	0.015359	T	0.00012	0.0000	H	0.96970	3.915	0.32904	P	0.486432	D	0.76494	0.999	D	0.71656	0.974	T	0.37103	-0.9720	9	0.87932	D	0	-35.2363	8.516	0.33246	0.0:0.6589:0.0:0.3411	rs10839658;rs17275930;rs52795055;rs56681860;rs10839658	82	Q8NGH3	OR2D3_HUMAN	I	82	ENSP00000320560:L82I	ENSP00000320560:L82I	L	+	1	0	OR2D3	6899052	0.001000	0.12720	0.319000	0.25293	0.068000	0.16541	-0.012000	0.12699	0.415000	0.25817	0.655000	0.94253	CTC	C|0.509;A|0.491	0.491	strong		0.408	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
PATZ1	23598	hgsc.bcm.edu	37	22	31741067	31741067	+	Silent	SNP	G	G	A	rs714909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:31741067G>A	ENST00000266269.5	-	1	1151	c.522C>T	c.(520-522)ctC>ctT	p.L174L	PATZ1_ENST00000405309.3_Silent_p.L174L|AC005003.1_ENST00000504184.2_5'Flank|PATZ1_ENST00000351933.4_Silent_p.L174L|PATZ1_ENST00000215919.3_Silent_p.L174L	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	174					male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						GGGGGCGAAAGAGCATTATAT	0.587													G|||	777	0.155152	0.0144	0.2536	5008	,	,		17894	0.121		0.2763	False		,,,				2504	0.1861				p.L174L		Atlas-SNP	.											.	PATZ1	24	.	0			c.C522T						PASS	.	G	,,,	241,4165	136.9+/-172.8	8,225,1970	84.0	92.0	89.0		522,522,522,522	-2.0	1.0	22	dbSNP_86	89	2371,6229	388.6+/-342.6	320,1731,2249	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PATZ1	NM_014323.2,NM_032050.1,NM_032051.1,NM_032052.1	,,,	328,1956,4219	AA,AG,GG		27.5698,5.4698,20.083	,,,	174/688,174/642,174/538,174/538	31741067	2612,10394	2203	4300	6503	SO:0001819	synonymous_variant	23598	exon1			GCGAAAGAGCATT	AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13071	protein-coding gene	gene with protein product		605165	"""zinc finger protein 278"""	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.522C>T	22.37:g.31741067G>A		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_032050	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Silent	SNP	ENST00000266269.5	37	CCDS13894.1																																																																																			G|0.818;A|0.182	0.182	strong		0.587	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383073	39383073	+	Missense_Mutation	SNP	G	G	C	rs9902235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39383073G>C	ENST00000377721.3	+	1	174	c.167G>C	c.(166-168)tGc>tCc	p.C56S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.C56S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	56	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].		C -> S (in dbSNP:rs9902235). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CGCCCAACTTGCTGTCAAAAC	0.652													.|||	3551	0.709065	0.6044	0.8329	5008	,	,		21802	0.6319		0.7455	False		,,,				2504	0.8047				p.C56S		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.G167C						PASS	.						71.0	63.0	66.0					17																	39383073		2203	4300	6503	SO:0001583	missense	83899	exon1			CAACTTGCTGTCA	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.167G>C	17.37:g.39383073G>C	ENSP00000366950:p.Cys56Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	124	120	0.967742	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	1526	0.6987179487179487	300	0.6097560975609756	297	0.8204419889502762	366	0.6398601398601399	563	0.7427440633245382	.	10.45	1.352814	0.24512	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.02323	4.46;4.34	2.89	1.92	0.25849	.	.	.	.	.	T	0.00012	0.0000	M	0.78637	2.42	0.33658	P	0.39071599999999995	B	0.25351	0.124	B	0.25614	0.062	T	0.08371	-1.0725	8	0.45353	T	0.12	.	4.9649	0.14085	0.2821:0.0:0.7179:0.0	rs9902235;rs60513024	56	Q9BYQ4	KRA92_HUMAN	S	56	ENSP00000366950:C56S;ENSP00000398325:C56S	ENSP00000366950:C56S	C	+	2	0	KRTAP9-2	36636599	0.077000	0.21312	0.247000	0.24249	0.193000	0.23685	0.915000	0.28638	0.793000	0.33875	0.552000	0.68991	TGC	G|0.287;C|0.713	0.713	strong		0.652	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
TSHZ1	10194	hgsc.bcm.edu	37	18	72998886	72998886	+	Silent	SNP	T	T	C	rs3809997	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72998886T>C	ENST00000580243.1	+	2	1872	c.1524T>C	c.(1522-1524)ccT>ccC	p.P508P	TSHZ1_ENST00000322038.5_Silent_p.P463P			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	508					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		AGAAGCCGCCTGTGGCTGGCG	0.602													C|||	1714	0.342252	0.3865	0.3732	5008	,	,		17539	0.1687		0.4115	False		,,,				2504	0.3681				p.P463P		Atlas-SNP	.											.	TSHZ1	104	.	0			c.T1389C						PASS	.	C		1701,2705	632.5+/-395.8	345,1011,847	80.0	95.0	90.0		1389	-9.0	0.0	18	dbSNP_107	90	3465,5135	613.6+/-396.1	702,2061,1537	no	coding-synonymous	TSHZ1	NM_005786.4		1047,3072,2384	CC,CT,TT		40.2907,38.6064,39.7201		463/1033	72998886	5166,7840	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GCCGCCTGTGGCT	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1524T>C	18.37:g.72998886T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				T|0.630;C|0.370	0.370	strong		0.602	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
PDPR	55066	hgsc.bcm.edu	37	16	70154480	70154480	+	Missense_Mutation	SNP	A	A	G	rs587776506|rs200469748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70154480A>G	ENST00000288050.4	+	3	1042	c.85A>G	c.(85-87)Acg>Gcg	p.T29A	PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Missense_Mutation_p.T29A	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	29				T -> A (in Ref. 3; CAH10555). {ECO:0000305}.	cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)	p.T29A(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		AAGAAACAGCACGTCAGCTGC	0.572																																					p.T29A		Atlas-SNP	.											PDPR,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PDPR	66	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A85G						scavenged	.						51.0	53.0	52.0					16																	70154480		2117	4237	6354	SO:0001583	missense	55066	exon3			AACAGCACGTCAG		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.85A>G	16.37:g.70154480A>G	ENSP00000288050:p.Thr29Ala	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	316	31	0.0981013	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	G	1.592	-0.528814	0.04112	.	.	ENSG00000090857	ENST00000288050	T	0.69435	-0.4	4.13	-5.16	0.02857	.	1.037440	0.07658	N	0.933150	T	0.37320	0.0999	N	0.14661	0.345	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	10	0.06494	T	0.89	.	5.1635	0.15073	0.443:0.0:0.2448:0.3121	.	29	Q8NCN5	PDPR_HUMAN	A	29	ENSP00000288050:T29A	ENSP00000288050:T29A	T	+	1	0	PDPR	68711981	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.944000	0.03913	-0.959000	0.03618	-0.318000	0.08688	ACG	A|0.741;G|0.260	0.260	strong		0.572	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
DCAF17	80067	hgsc.bcm.edu	37	2	172330393	172330393	+	Silent	SNP	A	A	G	rs3731983	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:172330393A>G	ENST00000375255.3	+	10	1326	c.999A>G	c.(997-999)caA>caG	p.Q333Q	DCAF17_ENST00000468592.1_3'UTR|DCAF17_ENST00000539783.1_Intron	NM_025000.3	NP_079276.2	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17	333					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)	17						ATGGGATCCAAGAAATGGATT	0.338													A|||	1035	0.206669	0.146	0.2767	5008	,	,		20111	0.1885		0.1948	False		,,,				2504	0.2699				p.Q333Q		Atlas-SNP	.											.	DCAF17	41	.	0			c.A999G						PASS	.	A	,	772,3634	303.0+/-287.7	78,616,1509	80.0	77.0	78.0		,999	1.8	1.0	2	dbSNP_107	78	1719,6881	308.4+/-308.9	164,1391,2745	no	intron,coding-synonymous	DCAF17	NM_001164821.1,NM_025000.3	,	242,2007,4254	GG,GA,AA		19.9884,17.5216,19.1527	,	,333/521	172330393	2491,10515	2203	4300	6503	SO:0001819	synonymous_variant	80067	exon10			GATCCAAGAAATG	AK023158	CCDS2243.2, CCDS54419.1	2q31.1	2014-01-28	2009-07-17	2009-07-17	ENSG00000115827	ENSG00000115827		"""DDB1 and CUL4 associated factors"""	25784	protein-coding gene	gene with protein product	"""Woodhouse-Sakati syndrome"""	612515	"""chromosome 2 open reading frame 37"""	C2orf37			Standard	NM_001164821		Approved	FLJ13096	uc002ugx.3	Q5H9S7	OTTHUMG00000132259	ENST00000375255.3:c.999A>G	2.37:g.172330393A>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	178	69	0.38764	NM_025000	B2RTW5|Q53TN3|Q9H908	Silent	SNP	ENST00000375255.3	37	CCDS2243.2	432	0.1978021978021978	75	0.1524390243902439	88	0.2430939226519337	134	0.23426573426573427	135	0.17810026385224276	A	0.948	-0.707301	0.03230	0.175216	0.199884	ENSG00000115827	ENST00000339506;ENST00000431110	.	.	.	5.53	1.75	0.24633	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999993463	.	.	.	.	.	.	T	0.07501	-1.0769	3	.	.	.	-10.5591	11.8954	0.52654	0.6933:0.0:0.3067:0.0	rs3731983;rs61472742;rs3731983	.	.	.	R	84;35	.	.	K	+	2	0	DCAF17	172038639	0.996000	0.38824	0.996000	0.52242	0.277000	0.26821	0.496000	0.22499	-0.190000	0.10465	-1.139000	0.01908	AAG	A|0.804;G|0.196	0.196	strong		0.338	DCAF17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255342.2	NM_025000	
ZNF641	121274	hgsc.bcm.edu	37	12	48736985	48736985	+	Missense_Mutation	SNP	T	T	G	rs2732481	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48736985T>G	ENST00000544117.2	-	6	1796	c.1088A>C	c.(1087-1089)cAg>cCg	p.Q363P	ZNF641_ENST00000448928.3_Missense_Mutation_p.Q340P|ZNF641_ENST00000547026.1_Missense_Mutation_p.Q349P|ZNF641_ENST00000301042.3_Missense_Mutation_p.Q363P			Q96N77	ZN641_HUMAN	zinc finger protein 641	363			Q -> P (in dbSNP:rs2732481). {ECO:0000269|PubMed:17974005}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(2)|kidney(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	12						TGGGGCACGCTGCCGTTTCCT	0.587													T|||	845	0.16873	0.0189	0.1859	5008	,	,		20204	0.0109		0.325	False		,,,				2504	0.3609				p.Q363P		Atlas-SNP	.											.	ZNF641	28	.	0			c.A1088C						PASS	.	T	PRO/GLN,PRO/GLN,PRO/GLN	275,4131	153.7+/-187.2	12,251,1940	96.0	85.0	89.0		1046,1019,1088	3.0	1.0	12	dbSNP_100	89	2909,5691	456.3+/-364.0	482,1945,1873	yes	missense,missense,missense	ZNF641	NM_001172681.1,NM_001172682.1,NM_152320.2	76,76,76	494,2196,3813	GG,GT,TT		33.8256,6.2415,24.481	benign,benign,benign	349/425,340/416,363/439	48736985	3184,9822	2203	4300	6503	SO:0001583	missense	121274	exon7			GCACGCTGCCGTT	BC018090	CCDS8763.1, CCDS53787.1, CCDS53788.1	12q13.11	2013-01-08				ENSG00000167528		"""Zinc fingers, C2H2-type"", ""-"""	31834	protein-coding gene	gene with protein product		613906					Standard	NM_152320		Approved	FLJ31295	uc001rro.2	Q96N77		ENST00000544117.2:c.1088A>C	12.37:g.48736985T>G	ENSP00000437832:p.Gln363Pro	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	230	105	0.456522	NM_152320	B3KS43|B4DNU5|Q8TCQ7|Q8WVE1	Missense_Mutation	SNP	ENST00000544117.2	37	CCDS8763.1	338	0.15476190476190477	14	0.028455284552845527	76	0.20994475138121546	3	0.005244755244755245	245	0.3232189973614776	T	14.30	2.493219	0.44352	0.062415	0.338256	ENSG00000167528	ENST00000301042;ENST00000544117;ENST00000448928;ENST00000547026	T;T;T;T	0.07444	3.3;3.3;3.19;3.28	5.47	3.04	0.35103	.	0.212636	0.33650	N	0.004693	T	0.00012	0.0000	M	0.79343	2.45	0.58432	P	1.0000000000287557E-6	B;B	0.33073	0.396;0.261	B;B	0.31614	0.133;0.064	T	0.46428	-0.9192	9	0.87932	D	0	.	3.6945	0.08358	0.0:0.1735:0.1975:0.6289	rs2732481;rs52811983;rs58167054;rs2732481	340;363	B4DNU5;Q96N77	.;ZN641_HUMAN	P	363;363;340;349	ENSP00000301042:Q363P;ENSP00000437832:Q363P;ENSP00000394627:Q340P;ENSP00000449974:Q349P	ENSP00000301042:Q363P	Q	-	2	0	ZNF641	47023252	0.124000	0.22315	0.995000	0.50966	0.929000	0.56500	0.062000	0.14389	2.191000	0.70037	0.533000	0.62120	CAG	T|0.801;G|0.199	0.199	strong		0.587	ZNF641-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000406518.1	NM_152320	
KMT2C	58508	hgsc.bcm.edu	37	7	151962257	151962257	+	Silent	SNP	C	C	T	rs62478357		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151962257C>T	ENST00000262189.6	-	8	1268	c.1050G>A	c.(1048-1050)ccG>ccA	p.P350P	KMT2C_ENST00000355193.2_Silent_p.P350P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	350					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AGAGGTCTCCCGGGCTGTCGC	0.398																																					p.P350P		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,-1,2	MLL3	1564	2	0			c.G1050A						scavenged	.						146.0	134.0	138.0					7																	151962257		2203	4296	6499	SO:0001819	synonymous_variant	58508	exon8			GTCTCCCGGGCTG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1050G>A	7.37:g.151962257C>T		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	389	24	0.0616967	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			.	.	weak		0.398	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
MUC4	4585	hgsc.bcm.edu	37	3	195509955	195509955	+	Silent	SNP	A	A	C	rs71635078		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509955A>C	ENST00000463781.3	-	2	8955	c.8496T>G	c.(8494-8496)tcT>tcG	p.S2832S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S2832S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGACAGGAAGAGAGGTGGCAT	0.592																																					p.S2832S		Atlas-SNP	.											.	MUC4	1505	.	0			c.T8496G						PASS	.						95.0	61.0	71.0					3																	195509955		685	1545	2230	SO:0001819	synonymous_variant	4585	exon2			AGGAAGAGAGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8496T>G	3.37:g.195509955A>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	441	296	0.671202	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			C|1.000;|0.000	1.000	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489825	32489825	+	Missense_Mutation	SNP	T	T	A	rs148834340	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32489825T>A	ENST00000374975.3	-	2	289	c.227A>T	c.(226-228)tAc>tTc	p.Y76F		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CACCGCCCGGTACTCCCCCAC	0.617													T|||	708	0.141374	0.1846	0.0778	5008	,	,		4676	0.1667		0.1312	False		,,,				2504	0.1125				p.Y76F		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.A227T						PASS	.						37.0	34.0	35.0					6																	32489825		2158	4211	6369	SO:0001583	missense	3127	exon2			GCCCGGTACTCCC		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.227A>T	6.37:g.32489825T>A	ENSP00000364114:p.Tyr76Phe	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	53	42	0.792453	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	135	0.061813186813186816	42	0.08536585365853659	28	0.07734806629834254	28	0.04895104895104895	37	0.048812664907651716	.	8.312	0.822355	0.16678	.	.	ENSG00000198502	ENST00000374975	T	0.00235	8.48	4.72	-9.43	0.00607	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	0.724315	0.13812	N	0.361053	T	0.00039	0.0001	N	0.12569	0.235	0.09310	N	1	B;B	0.21905	0.002;0.062	B;B	0.32393	0.014;0.145	T	0.34725	-0.9817	10	0.11182	T	0.66	.	9.9706	0.41752	0.6738:0.0:0.1796:0.1466	.	3;76	Q29973;Q30154	.;DRB5_HUMAN	F	76	ENSP00000364114:Y76F	ENSP00000364114:Y76F	Y	-	2	0	HLA-DRB5	32597803	0.000000	0.05858	0.000000	0.03702	0.920000	0.55202	-6.497000	0.00064	-2.805000	0.00350	0.352000	0.21897	TAC	T|0.917;A|0.083	0.083	strong		0.617	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
ZNF302	55900	hgsc.bcm.edu	37	19	35175208	35175208	+	Missense_Mutation	SNP	A	A	G	rs2290652	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35175208A>G	ENST00000446502.2	+	6	606	c.398A>G	c.(397-399)tAt>tGt	p.Y133C	ZNF302_ENST00000509528.1_Missense_Mutation_p.M21V|ZNF302_ENST00000423823.2_Missense_Mutation_p.Y89C|ZNF302_ENST00000505242.1_Missense_Mutation_p.Y89C|ZNF302_ENST00000457781.2_Missense_Mutation_p.Y89C|ZNF302_ENST00000507959.1_3'UTR|ZNF302_ENST00000505365.2_3'UTR			Q9NR11	ZN302_HUMAN	zinc finger protein 302	73					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			AAGGATATTTATGATGAAGAT	0.289													A|||	1255	0.250599	0.1369	0.2075	5008	,	,		15422	0.3006		0.3767	False		,,,				2504	0.2536				p.Y89C		Atlas-SNP	.											.	ZNF302	27	.	0			c.A266G						PASS	.	A	CYS/TYR,CYS/TYR	726,3476		68,590,1443	47.0	51.0	50.0		266,266	1.0	0.7	19	dbSNP_100	50	3012,5452		533,1946,1753	no	missense,missense	ZNF302	NM_001012320.1,NM_018443.2	194,194	601,2536,3196	GG,GA,AA		35.586,17.2775,29.5121	probably-damaging,probably-damaging	89/400,89/400	35175208	3738,8928	2101	4232	6333	SO:0001583	missense	55900	exon5			ATATTTATGATGA	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.398A>G	19.37:g.35175208A>G	ENSP00000396379:p.Tyr133Cys	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	266	128	0.481203	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	37		615	0.2815934065934066	74	0.15040650406504066	83	0.2292817679558011	174	0.3041958041958042	284	0.37467018469656993	A	10.21	1.288432	0.23478	0.172775	0.35586	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000505163;ENST00000423823;ENST00000446502	T;T;T;T;T	0.04654	3.59;3.59;6.05;3.59;3.58	0.967	0.967	0.19674	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.41825	P	0.009959999999999969	D;D	0.89917	0.999;1.0	D;D	0.87578	0.99;0.998	T	0.48410	-0.9038	7	0.45353	T	0.12	.	4.1694	0.10322	1.0:0.0:0.0:0.0	rs2290652;rs17649399;rs52790156;rs60043199;rs2290652	133;89	E7EVR1;Q9NR11-2	.;.	C	89;89;89;89;133	ENSP00000391067:Y89C;ENSP00000421028:Y89C;ENSP00000421696:Y89C;ENSP00000405219:Y89C;ENSP00000396379:Y133C	ENSP00000405219:Y89C	Y	+	2	0	ZNF302	39867048	0.989000	0.36119	0.678000	0.29963	0.054000	0.15201	0.223000	0.17719	0.686000	0.31488	0.383000	0.25322	TAT	A|0.726;G|0.274	0.274	strong		0.289	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
PRKRIP1	79706	hgsc.bcm.edu	37	7	102036877	102036877	+	Missense_Mutation	SNP	T	T	G	rs6951185	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:102036877T>G	ENST00000496391.1	+	5	1329	c.19T>G	c.(19-21)Tcc>Gcc	p.S7A	PRKRIP1_ENST00000482465.1_Intron|PRKRIP1_ENST00000462601.1_Intron|PRKRIP1_ENST00000397912.3_Missense_Mutation_p.S7A|PRKRIP1_ENST00000354783.4_5'Flank			Q9H875	PKRI1_HUMAN	PRKR interacting protein 1 (IL11 inducible)	7	Interaction with EIF2AK2. {ECO:0000250}.		S -> A (in dbSNP:rs6951185).		negative regulation of phosphorylation (GO:0042326)|negative regulation of protein kinase activity (GO:0006469)|renal system process (GO:0003014)	extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|lung(4)|ovary(1)	6						CCCAGCCGCCTCCTCGGTGCG	0.662													T|||	245	0.0489217	0.0908	0.0476	5008	,	,		12427	0.002		0.0686	False		,,,				2504	0.0215				p.S7A		Atlas-SNP	.											.	PRKRIP1	25	.	0			c.T19G						PASS	.	T	ALA/SER	308,3994		15,278,1858	8.0	10.0	10.0		19	-4.7	0.0	7	dbSNP_116	10	446,8002		10,426,3788	yes	missense	PRKRIP1	NM_024653.3	99	25,704,5646	GG,GT,TT		5.2794,7.1595,5.9137	benign	7/185	102036877	754,11996	2151	4224	6375	SO:0001583	missense	79706	exon1			GCCGCCTCCTCGG	AK023964	CCDS34714.1	7q22.1	2013-01-09			ENSG00000128563	ENSG00000128563		"""Zinc fingers, C2H2-type"", ""-"""	21894	protein-coding gene	gene with protein product	"""likely ortholog of mouse C114 dsRNA-binding protein"", ""KRAB box domain containing 3"""					12679338	Standard	NM_024653		Approved	C114, FLJ13902, KRBOX3	uc003uzh.2	Q9H875	OTTHUMG00000157717	ENST00000496391.1:c.19T>G	7.37:g.102036877T>G	ENSP00000419270:p.Ser7Ala	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_024653	B4DGM2|Q8NDM6|Q96CF8	Missense_Mutation	SNP	ENST00000496391.1	37	CCDS34714.1	120	0.054945054945054944	45	0.09146341463414634	25	0.06906077348066299	1	0.0017482517482517483	49	0.06464379947229551	t	17.54	3.415228	0.62511	0.071595	0.052794	ENSG00000128563	ENST00000496391;ENST00000397912	T;T	0.28255	1.62;1.62	5.17	-4.72	0.03269	.	0.816710	0.12034	N	0.505733	T	0.00328	0.0010	N	0.08118	0	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24333	-1.0163	9	0.06891	T	0.86	-13.1401	0.8194	0.01109	0.2447:0.1563:0.3454:0.2535	rs6951185;rs11556161;rs6951185	7	Q9H875	PKRI1_HUMAN	A	7	ENSP00000419270:S7A;ENSP00000381010:S7A	ENSP00000381010:S7A	S	+	1	0	PRKRIP1	101823882	0.000000	0.05858	0.001000	0.08648	0.455000	0.32408	-0.205000	0.09411	-1.009000	0.03400	0.450000	0.29827	TCC	T|0.938;G|0.062	0.062	strong		0.662	PRKRIP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349489.1	NM_024653	
POLR3B	55703	hgsc.bcm.edu	37	12	106838340	106838340	+	Silent	SNP	T	T	C	rs10861607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:106838340T>C	ENST00000228347.4	+	19	2277	c.2055T>C	c.(2053-2055)taT>taC	p.Y685Y	POLR3B_ENST00000539066.1_Silent_p.Y627Y	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	685					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GAAACACTTATCAGTGTGCCA	0.438													T|||	1592	0.317891	0.0144	0.3631	5008	,	,		18053	0.6984		0.2694	False		,,,				2504	0.3538				p.Y685Y		Atlas-SNP	.											POLR3B,caecum,carcinoma,0,1	POLR3B	123	1	0			c.T2055C						PASS	.	T	,	263,4143	149.2+/-183.4	6,251,1946	139.0	110.0	119.0		1881,2055	-5.0	0.4	12	dbSNP_120	119	2221,6379	378.1+/-338.8	287,1647,2366	no	coding-synonymous,coding-synonymous	POLR3B	NM_001160708.1,NM_018082.5	,	293,1898,4312	CC,CT,TT		25.8256,5.9691,19.0989	,	627/1076,685/1134	106838340	2484,10522	2203	4300	6503	SO:0001819	synonymous_variant	55703	exon19			CACTTATCAGTGT	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.2055T>C	12.37:g.106838340T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	NM_018082	A8K6H0|B3KV73|F5H1E6|Q9NW59	Silent	SNP	ENST00000228347.4	37	CCDS9105.1																																																																																			T|0.752;C|0.248	0.248	strong		0.438	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082	
VCPKMT	79609	hgsc.bcm.edu	37	14	50583083	50583083	+	Missense_Mutation	SNP	G	G	T	rs11157729	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50583083G>T	ENST00000395860.2	-	1	192	c.188C>A	c.(187-189)gCc>gAc	p.A63D	VCPKMT_ENST00000395859.2_Missense_Mutation_p.A63D	NM_024558.2	NP_078834.2	Q9H867	MT21D_HUMAN	valosin containing protein lysine (K) methyltransferase	63			A -> D (in dbSNP:rs11157729).		peptidyl-lysine trimethylation (GO:0018023)	cytoplasm (GO:0005737)	protein-lysine N-methyltransferase activity (GO:0016279)										CAGCGCGTGGGCCCCGTCGCC	0.667													G|||	1252	0.25	0.2216	0.245	5008	,	,		12014	0.4603		0.1461	False		,,,				2504	0.182				p.A63D		Atlas-SNP	.											.	METTL21D	11	.	0			c.C188A						PASS	.	G	ASP/ALA,ASP/ALA	876,3530	312.2+/-292.5	86,704,1413	22.0	27.0	25.0		188,188	4.2	0.4	14	dbSNP_120	25	1343,7257	252.3+/-278.5	107,1129,3064	yes	missense,missense	METTL21D	NM_001040662.1,NM_024558.2	126,126	193,1833,4477	TT,TG,GG		15.6163,19.882,17.0614	benign,benign	63/195,63/230	50583083	2219,10787	2203	4300	6503	SO:0001583	missense	79609	exon1			GCGTGGGCCCCGT	AK023982	CCDS9696.2, CCDS41951.1	14q21.3	2013-09-30	2013-09-30	2013-09-30	ENSG00000100483	ENSG00000100483			20352	protein-coding gene	gene with protein product		615260	"""chromosome 14 open reading frame 138"", ""methyltransferase like 21D"""	C14orf138, METTL21D		22948820	Standard	NR_049738		Approved	VCP-KMT	uc001wxo.1	Q9H867	OTTHUMG00000029531	ENST00000395860.2:c.188C>A	14.37:g.50583083G>T	ENSP00000379201:p.Ala63Asp	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	34	12	0.352941	NM_024558	B7ZLA3|B7ZLA4|Q2M2X3|Q86T12	Missense_Mutation	SNP	ENST00000395860.2	37	CCDS9696.2	527	0.2413003663003663	93	0.18902439024390244	72	0.19889502762430938	252	0.4405594405594406	110	0.14511873350923482	G	13.02	2.111626	0.37242	0.19882	0.156163	ENSG00000100483	ENST00000395859;ENST00000395860	T;T	0.06933	3.24;3.24	6.06	4.2	0.49525	.	0.741259	0.12068	N	0.502470	T	0.00012	0.0000	L	0.35288	1.05	0.80722	P	0.0	B;B	0.21381	0.055;0.055	B;B	0.21546	0.023;0.035	T	0.42582	-0.9443	9	0.15499	T	0.54	0.0014	6.6147	0.22771	0.0678:0.1304:0.6662:0.1355	rs11157729;rs57168136	63;63	B7ZLA4;Q9H867	.;MT21D_HUMAN	D	63	ENSP00000379200:A63D;ENSP00000379201:A63D	ENSP00000379200:A63D	A	-	2	0	METTL21D	49652833	0.008000	0.16893	0.394000	0.26270	0.985000	0.73830	0.585000	0.23879	0.849000	0.35215	0.650000	0.86243	GCC	G|0.812;T|0.188	0.188	strong		0.667	VCPKMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276877.1	NM_024558	
COX4I2	84701	hgsc.bcm.edu	37	20	30232673	30232673	+	Missense_Mutation	SNP	G	G	A	rs11907253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:30232673G>A	ENST00000376075.3	+	5	557	c.482G>A	c.(481-483)cGc>cAc	p.R161H		NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	161			R -> H (in dbSNP:rs11907253). {ECO:0000269|PubMed:11311561}.		cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			CTGGCCTCCCGCTGGGACTAT	0.627													G|||	287	0.0573083	0.0961	0.0764	5008	,	,		16625	0.001		0.0815	False		,,,				2504	0.0245				p.R161H		Atlas-SNP	.											.	COX4I2	18	.	0			c.G482A						PASS	.	G	HIS/ARG	411,3995	201.1+/-224.2	12,387,1804	73.0	64.0	67.0		482	-1.1	0.6	20	dbSNP_120	67	702,7898	172.9+/-223.5	33,636,3631	yes	missense	COX4I2	NM_032609.2	29	45,1023,5435	AA,AG,GG		8.1628,9.3282,8.5576	benign	161/172	30232673	1113,11893	2203	4300	6503	SO:0001583	missense	84701	exon5			CCTCCCGCTGGGA	AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"""Mitochondrial respiratory chain complex / Complex IV"""	16232	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit IV-like 2"""	607976	"""cytochrome c oxidase subunit IV isoform 2"""	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.482G>A	20.37:g.30232673G>A	ENSP00000365243:p.Arg161His	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	NM_032609	Q6GTF4|Q9H0Z4	Missense_Mutation	SNP	ENST00000376075.3	37	CCDS13187.1	164	0.07509157509157509	55	0.11178861788617886	41	0.1132596685082873	1	0.0017482517482517483	67	0.08839050131926121	G	11.36	1.615359	0.28801	0.093282	0.081628	ENSG00000131055	ENST00000376075	T	0.55930	0.49	4.38	-1.06	0.10002	.	0.324544	0.28442	N	0.015337	T	0.00412	0.0013	N	0.02916	-0.46	0.39291	P	0.035267999999999966	B	0.06786	0.001	B	0.04013	0.001	T	0.06127	-1.0844	9	0.35671	T	0.21	-17.387	7.746	0.28869	0.4725:0.0:0.5275:0.0	rs11907253;rs57114915;rs11907253	161	Q96KJ9	COX42_HUMAN	H	161	ENSP00000365243:R161H	ENSP00000365243:R161H	R	+	2	0	COX4I2	29696334	0.997000	0.39634	0.583000	0.28640	0.836000	0.47400	1.246000	0.32803	-0.361000	0.08125	-1.305000	0.01319	CGC	G|0.919;A|0.081	0.081	strong		0.627	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609	
PRM2	5620	hgsc.bcm.edu	37	16	11367195	11367195	+	IGR	SNP	G	G	C	rs35598356	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11367195G>C	ENST00000241808.4	-	0	680				SNORA48_ENST00000390926.1_RNA|PRM3_ENST00000327157.2_Missense_Mutation_p.H86Q|RMI2_ENST00000572173.1_Intron	NM_002762.2	NP_002753.2	P04554	PRM2_HUMAN	protamine 2						cell differentiation (GO:0030154)|chromosome condensation (GO:0030261)|DNA packaging (GO:0006323)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.0?(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)	7						CGTTGTCCTTGTGGCCCTCCT	0.682													C|||	471	0.0940495	0.0121	0.1585	5008	,	,		15515	0.0387		0.2008	False		,,,				2504	0.1063				p.H86Q		Atlas-SNP	.											.	PRM3	8	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C258G						PASS	.	C	GLN/HIS	136,3782		2,132,1825	22.0	34.0	30.0		258	-9.6	0.0	16	dbSNP_126	30	1370,6246		110,1150,2548	yes	missense	PRM3	NM_021247.1	24	112,1282,4373	CC,CG,GG		17.9884,3.4712,13.057	possibly-damaging	86/104	11367195	1506,10028	1959	3808	5767	SO:0001628	intergenic_variant	58531	exon1			GTCCTTGTGGCCC		CCDS42118.1, CCDS66944.1	16p13.13	2013-10-17			ENSG00000122304	ENSG00000122304			9448	protein-coding gene	gene with protein product	"""cancer/testis antigen family 94, member 2"""	182890				16632464	Standard	NM_001286356		Approved	CT94.2	uc002dau.1	P04554	OTTHUMG00000172317		16.37:g.11367195G>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_021247	Q6ZMM0	Missense_Mutation	SNP	ENST00000241808.4	37	CCDS42118.1	252	0.11538461538461539	9	0.018292682926829267	69	0.19060773480662985	33	0.057692307692307696	141	0.18601583113456466	C	2.075	-0.412073	0.04799	0.034712	0.179884	ENSG00000178257	ENST00000327157	T	0.40225	1.04	4.82	-9.63	0.00544	.	0.616036	0.13669	N	0.371033	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.10109	-1.0644	6	0.15499	T	0.54	-13.405	0.7477	0.00985	0.3975:0.162:0.2007:0.2398	rs35598356	.	.	.	Q	86	ENSP00000325638:H86Q	ENSP00000325638:H86Q	H	-	3	2	PRM3	11274696	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.559000	0.00431	-2.916000	0.00306	-3.196000	0.00055	CAC	G|0.884;C|0.116	0.116	strong		0.682	PRM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417808.1		
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73944185	73944185	+	Silent	SNP	T	T	C	rs2240357	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73944185T>C	ENST00000265755.3	+	9	1605	c.1212T>C	c.(1210-1212)taT>taC	p.Y404Y	GTF2IRD1_ENST00000455841.2_Silent_p.Y436Y|GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000476977.1_Silent_p.Y404Y|GTF2IRD1_ENST00000424337.2_Silent_p.Y404Y	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	404					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CCTGCACTTATGGAGTCCCCA	0.602													C|||	1419	0.283347	0.2466	0.2968	5008	,	,		17167	0.4663		0.2107	False		,,,				2504	0.2096				p.Y436Y		Atlas-SNP	.											GTF2IRD1,caecum,carcinoma,+1,1	GTF2IRD1	91	1	0			c.T1308C						PASS	.	C	,,	1050,3356	724.9+/-409.6	120,810,1273	55.0	54.0	54.0		1308,1212,1212	-6.7	0.8	7	dbSNP_98	54	1993,6607	722.5+/-406.4	224,1545,2531	no	coding-synonymous,coding-synonymous,coding-synonymous	GTF2IRD1	NM_001199207.1,NM_005685.3,NM_016328.2	,,	344,2355,3804	CC,CT,TT		23.1744,23.8311,23.3969	,,	436/977,404/945,404/960	73944185	3043,9963	2203	4300	6503	SO:0001819	synonymous_variant	9569	exon9			CACTTATGGAGTC	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1212T>C	7.37:g.73944185T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Silent	SNP	ENST00000265755.3	37	CCDS5571.1																																																																																			T|0.735;C|0.265	0.265	strong		0.602	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
PLEC	5339	hgsc.bcm.edu	37	8	144993069	144993069	+	Silent	SNP	G	G	A	rs28455570	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144993069G>A	ENST00000322810.4	-	32	11500	c.11331C>T	c.(11329-11331)taC>taT	p.Y3777Y	PLEC_ENST00000357649.2_Silent_p.Y3644Y|PLEC_ENST00000527096.1_Silent_p.Y3663Y|PLEC_ENST00000398774.2_Silent_p.Y3608Y|PLEC_ENST00000354958.2_Silent_p.Y3618Y|PLEC_ENST00000436759.2_Silent_p.Y3667Y|PLEC_ENST00000345136.3_Silent_p.Y3640Y|PLEC_ENST00000354589.3_Silent_p.Y3640Y|PLEC_ENST00000356346.3_Silent_p.Y3626Y	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3777	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCACGTAGTCGTAGGAGGCCA	0.607													G|||	167	0.0333466	0.0015	0.0375	5008	,	,		19251	0.001		0.1173	False		,,,				2504	0.0204				p.Y3777Y		Atlas-SNP	.											.	PLEC	1144	.	0			c.C11331T						PASS	.	G	,,,,,,,	88,4174		0,88,2043	55.0	63.0	60.0		11001,10878,10854,11331,10824,10920,10932,10920	-0.4	1.0	8	dbSNP_125	60	816,7676		48,720,3478	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	48,808,5521	AA,AG,GG		9.609,2.0648,7.088	,,,,,,,	3667/4575,3626/4534,3618/4526,3777/4685,3608/4516,3640/4548,3644/4552,3640/4548	144993069	904,11850	2131	4246	6377	SO:0001819	synonymous_variant	5339	exon32			GTAGTCGTAGGAG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11331C>T	8.37:g.144993069G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.941;A|0.059	0.059	strong		0.607	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
LRG1	116844	hgsc.bcm.edu	37	19	4538599	4538599	+	Missense_Mutation	SNP	G	G	A	rs966384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4538599G>A	ENST00000306390.6	-	2	857	c.397C>T	c.(397-399)Ccg>Tcg	p.P133S	LRG1_ENST00000586883.1_5'UTR|CTB-50L17.14_ENST00000586020.1_Intron	NM_052972.2	NP_443204.1	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1	133			P -> S (in dbSNP:rs966384). {ECO:0000269|PubMed:15489334}.		brown fat cell differentiation (GO:0050873)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				NS(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGAGGCCCGGGGGCAGCCCG	0.632													G|||	1604	0.320288	0.0862	0.4467	5008	,	,		16078	0.5308		0.3618	False		,,,				2504	0.2873				p.P133S		Atlas-SNP	.											.	LRG1	25	.	0			c.C397T						PASS	.	G	SER/PRO	566,3826		41,484,1671	24.0	30.0	28.0		397	0.9	0.0	19	dbSNP_86	28	2767,5779		455,1857,1961	yes	missense	LRG1	NM_052972.2	74	496,2341,3632	AA,AG,GG		32.3777,12.8871,25.7613	benign	133/348	4538599	3333,9605	2196	4273	6469	SO:0001583	missense	116844	exon2			GGCCCGGGGGCAG		CCDS12130.1	19p13.3	2013-09-20			ENSG00000171236	ENSG00000171236			29480	protein-coding gene	gene with protein product	"""leucine rich alpha 2 glycoprotein"""	611289				3856868, 12223515	Standard	NM_052972		Approved	LRG	uc002mau.3	P02750	OTTHUMG00000182010	ENST00000306390.6:c.397C>T	19.37:g.4538599G>A	ENSP00000302621:p.Pro133Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_052972	Q8N4F5|Q96QZ4	Missense_Mutation	SNP	ENST00000306390.6	37	CCDS12130.1	770	0.3525641025641026	39	0.07926829268292683	168	0.46408839779005523	290	0.506993006993007	273	0.36015831134564646	.	4.933	0.173269	0.09391	0.128871	0.323777	ENSG00000171236	ENST00000306390	T	0.03524	3.9	4.71	0.948	0.19561	.	0.000000	0.40469	N	0.001098	T	0.00012	0.0000	L	0.38733	1.17	0.80722	P	0.0	B	0.30068	0.267	B	0.30495	0.116	T	0.32214	-0.9915	9	0.22109	T	0.4	-22.3111	6.9139	0.24349	0.0:0.3445:0.4527:0.2027	rs966384;rs17846084;rs17859086;rs57205193;rs966384	133	P02750	A2GL_HUMAN	S	133	ENSP00000302621:P133S	ENSP00000302621:P133S	P	-	1	0	LRG1	4489599	0.091000	0.21658	0.009000	0.14445	0.001000	0.01503	0.022000	0.13511	0.527000	0.28560	0.655000	0.94253	CCG	G|0.705;A|0.295	0.295	strong		0.632	LRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458654.2	NM_052972	
UROC1	131669	hgsc.bcm.edu	37	3	126207049	126207049	+	Silent	SNP	G	G	A	rs139120643	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126207049G>A	ENST00000290868.2	-	18	1835	c.1782C>T	c.(1780-1782)ggC>ggT	p.G594G	UROC1_ENST00000383579.3_Silent_p.G654G	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	594					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)	p.G594G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		ACCAGCCCACGCCCCCTCCGT	0.602													G|||	3	0.000599042	0.0	0.0014	5008	,	,		19645	0.0		0.001	False		,,,				2504	0.001				p.G654G		Atlas-SNP	.											UROC1,NS,carcinoma,0,1	UROC1	150	1	1	Substitution - coding silent(1)	lung(1)	c.C1962T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	166.0	159.0	161.0		1962,1782	-3.2	1.0	3	dbSNP_134	161	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous,coding-synonymous	UROC1	NM_001165974.1,NM_144639.2	,	0,24,6479	AA,AG,GG		0.2209,0.1135,0.1845	,	654/737,594/677	126207049	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	131669	exon19			GCCCACGCCCCCT	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1782C>T	3.37:g.126207049G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	136	71	0.522059	NM_001165974	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	37	CCDS3038.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639	
PTCHD3	374308	hgsc.bcm.edu	37	10	27687225	27687225	+	Nonstop_Mutation	SNP	A	A	G	rs2505323	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:27687225A>G	ENST00000438700.3	-	4	2419	c.2302T>C	c.(2302-2304)Taa>Caa	p.*768Q		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	0					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						CGTCGTAATTAGAATAACAAT	0.338													G|||	2755	0.55012	0.5257	0.5202	5008	,	,		18410	0.37		0.6829	False		,,,				2504	0.6534				p.X768Q		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T2302C						PASS	.	G	GLN/stop	2355,2049	536.8+/-374.6	626,1103,473	29.0	31.0	30.0		2302	3.5	0.0	10	dbSNP_100	30	5857,2737	422.1+/-353.9	2008,1841,448	yes	stop-lost	PTCHD3	NM_001034842.3		2634,2944,921	GG,GA,AA		31.8478,46.5259,36.821		768/768	27687225	8212,4786	2202	4297	6499	SO:0001578	stop_lost	374308	exon4			GTAATTAGAATAA	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.2302T>C	10.37:g.27687225A>G	ENSP00000417658:p.*768Gluext*?	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	137	71	0.518248	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	1160	0.5311355311355311	264	0.5365853658536586	203	0.5607734806629834	178	0.3111888111888112	515	0.679419525065963	G	0.487	-0.877239	0.02550	0.534741	0.681522	ENSG00000182077	ENST00000438700	.	.	.	4.39	3.46	0.39613	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2224	0.43205	0.0771:0.3383:0.5846:0.0	rs2505323;rs17479111;rs17560874;rs52821138;rs59797391;rs2505323	.	.	.	Q	768	.	.	X	-	1	0	PTCHD3	27727231	0.000000	0.05858	0.007000	0.13788	0.023000	0.10783	0.032000	0.13732	0.465000	0.27167	-0.263000	0.10527	TAA	A|0.419;G|0.581	0.581	strong		0.338	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
NOTCH1	4851	hgsc.bcm.edu	37	9	139397707	139397707	+	Silent	SNP	G	G	A	rs10521	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139397707G>A	ENST00000277541.6	-	27	5169	c.5094C>T	c.(5092-5094)gaC>gaT	p.D1698D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1698					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1699D(11)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATGCGGCCACGTCGGTGGCAC	0.632			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2772	0.553514	0.5552	0.5115	5008	,	,		17626	0.9018		0.4046	False		,,,				2504	0.3753				p.D1698D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1_ENST00000277541,colon,carcinoma,0,19	NOTCH1	1980	19	11	Substitution - coding silent(11)	haematopoietic_and_lymphoid_tissue(11)	c.C5094T						PASS	.	G		2208,2062		587,1034,514	57.0	67.0	64.0		5094	-4.9	0.8	9	dbSNP_52	64	3010,5508		545,1920,1794	no	coding-synonymous	NOTCH1	NM_017617.3		1132,2954,2308	AA,AG,GG		35.3369,48.2904,40.8039		1698/2556	139397707	5218,7570	2135	4259	6394	SO:0001819	synonymous_variant	4851	exon27			GGCCACGTCGGTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5094C>T	9.37:g.139397707G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.466;A|0.534	0.534	strong		0.632	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
ZCCHC2	54877	hgsc.bcm.edu	37	18	60241333	60241333	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:60241333T>C	ENST00000269499.5	+	13	2437	c.2019T>C	c.(2017-2019)acT>acC	p.T673T	ZCCHC2_ENST00000586834.1_Silent_p.T352T	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	673						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						CATCAACAACTAGGTTTACAG	0.403																																					p.T673T		Atlas-SNP	.											ZCCHC2,NS,carcinoma,+1,1	ZCCHC2	64	1	0			c.T2019C						scavenged	.						112.0	102.0	106.0					18																	60241333		1860	4102	5962	SO:0001819	synonymous_variant	54877	exon13			AACAACTAGGTTT	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"""Zinc fingers, CCHC domain containing"""	22916	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 49"""	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.2019T>C	18.37:g.60241333T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	149	2	0.0134228	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Silent	SNP	ENST00000269499.5	37	CCDS45880.1																																																																																			.	.	none		0.403	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742	
WDR66	144406	hgsc.bcm.edu	37	12	122372176	122372176	+	Silent	SNP	C	C	T	rs78614343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:122372176C>T	ENST00000288912.4	+	5	1766	c.912C>T	c.(910-912)tgC>tgT	p.C304C	WDR66_ENST00000397454.2_Silent_p.C304C	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	304							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TTATCTCCTGCCTCTGCGTCA	0.542													C|||	244	0.048722	0.056	0.0403	5008	,	,		17609	0.0496		0.0457	False		,,,				2504	0.047				p.C304C	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,caecum,carcinoma,0,1	WDR66	143	1	0			c.C912T						PASS	.	C	,	222,3828		6,210,1809	73.0	75.0	74.0		912,912	4.0	1.0	12	dbSNP_131	74	381,7967		14,353,3807	no	coding-synonymous,coding-synonymous	WDR66	NM_001178003.1,NM_144668.5	,	20,563,5616	TT,TC,CC		4.564,5.4815,4.8637	,	304/942,304/1150	122372176	603,11795	2025	4174	6199	SO:0001819	synonymous_variant	144406	exon5			CTCCTGCCTCTGC	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.912C>T	12.37:g.122372176C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	52	17	0.326923	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	37	CCDS41853.1																																																																																			C|0.951;T|0.049	0.049	strong		0.542	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
RAI1	10743	hgsc.bcm.edu	37	17	17707105	17707105	+	Silent	SNP	T	T	C	rs3818717	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17707105T>C	ENST00000353383.1	+	4	6070	c.5601T>C	c.(5599-5601)atT>atC	p.I1867I	RAI1_ENST00000261641.6_Intron	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1867					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GGGCCACCATTGGGTGCTGCC	0.597													T|||	1205	0.240615	0.1248	0.3847	5008	,	,		19451	0.0754		0.5318	False		,,,				2504	0.1656				p.I1867I		Atlas-SNP	.											.	RAI1	121	.	0			c.T5601C						PASS	.	T		836,3570	325.6+/-299.2	77,682,1444	91.0	76.0	81.0		5601	-7.0	0.9	17	dbSNP_107	81	4832,3768	611.6+/-395.8	1361,2110,829	no	coding-synonymous	RAI1	NM_030665.3		1438,2792,2273	CC,CT,TT		43.814,18.9741,43.5799		1867/1907	17707105	5668,7338	2203	4300	6503	SO:0001819	synonymous_variant	10743	exon4			CACCATTGGGTGC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.5601T>C	17.37:g.17707105T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1	649	0.29716117216117216	57	0.11585365853658537	153	0.42265193370165743	35	0.06118881118881119	404	0.5329815303430079	T	10.79	1.450792	0.26074	0.189741	0.56186	ENSG00000108557	ENST00000395776;ENST00000315321	.	.	.	5.46	-6.98	0.01611	.	0.293540	0.29760	N	0.011262	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999982953	.	.	.	.	.	.	T	0.30001	-0.9993	5	0.39692	T	0.17	.	6.6284	0.22843	0.0819:0.5328:0.1606:0.2247	rs3818717;rs52832780;rs57642502;rs3818717	.	.	.	S	1911;1780	.	ENSP00000322928:L1780S	L	+	2	0	RAI1	17647830	0.036000	0.19791	0.900000	0.35374	0.987000	0.75469	-1.200000	0.03029	-1.125000	0.02932	-0.256000	0.11100	TTG	T|0.635;C|0.365	0.365	strong		0.597	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
HLA-A	3105	hgsc.bcm.edu	37	6	29912326	29912326	+	Silent	SNP	G	G	A	rs1059846	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29912326G>A	ENST00000396634.1	+	7	1286	c.945G>A	c.(943-945)ctG>ctA	p.L315L	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376806.5_Silent_p.L315L|HLA-A_ENST00000376809.5_Silent_p.L315L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	315					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TTGCTGGCCTGGTTCTCCTTG	0.597									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.L315L		Atlas-SNP	.											.	HLA-A	89	.	0			c.G945A						PASS	.						109.0	103.0	105.0					6																	29912326		1510	2709	4219	SO:0001819	synonymous_variant	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TGGCCTGGTTCTC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.945G>A	6.37:g.29912326G>A		Somatic	524	0	0		WXS	Illumina HiSeq	Phase_I	527	99	0.187856	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.880;A|0.120	0.120	strong		0.597	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
COL6A6	131873	hgsc.bcm.edu	37	3	130284284	130284284	+	Missense_Mutation	SNP	G	G	A	rs9830253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130284284G>A	ENST00000358511.6	+	3	1139	c.1108G>A	c.(1108-1110)Gcc>Acc	p.A370T	COL6A6_ENST00000453409.2_Missense_Mutation_p.A370T	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	370	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.		A -> T (in dbSNP:rs9830253).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CATAGAGGGCGCCAGCGACAC	0.552													G|||	2599	0.51897	0.1354	0.7522	5008	,	,		18957	0.4435		0.8221	False		,,,				2504	0.638				p.A370T		Atlas-SNP	.											COL6A6_ENST00000358511,right_upper_lobe,carcinoma,-1,2	COL6A6	497	2	0			c.G1108A						PASS	.	G	THR/ALA	1198,2902		194,810,1046	117.0	131.0	126.0		1108	4.1	0.5	3	dbSNP_119	126	7102,1308		3008,1086,111	yes	missense	COL6A6	NM_001102608.1	58	3202,1896,1157	AA,AG,GG		15.5529,29.2195,33.6531	probably-damaging	370/2264	130284284	8300,4210	2050	4205	6255	SO:0001583	missense	131873	exon3			GAGGGCGCCAGCG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1108G>A	3.37:g.130284284G>A	ENSP00000351310:p.Ala370Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	1266	0.5796703296703297	90	0.18292682926829268	278	0.7679558011049724	262	0.458041958041958	636	0.8390501319261213	G	15.48	2.845762	0.51164	0.292195	0.844471	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.80304	-1.36;-1.36	5.01	4.08	0.47627	von Willebrand factor, type A (3);	0.103399	0.42821	D	0.000652	T	0.00012	0.0000	M	0.82132	2.575	0.26570	P	0.9735732	D	0.71674	0.998	P	0.61275	0.886	T	0.48547	-0.9026	9	0.31617	T	0.26	.	8.0369	0.30496	0.0858:0.0:0.7548:0.1593	rs9830253;rs52830761;rs59475116;rs9830253	370	A6NMZ7	CO6A6_HUMAN	T	370	ENSP00000351310:A370T;ENSP00000399236:A370T	ENSP00000351310:A370T	A	+	1	0	COL6A6	131766974	0.989000	0.36119	0.529000	0.27951	0.050000	0.14768	3.264000	0.51553	2.492000	0.84095	0.561000	0.74099	GCC	G|0.446;A|0.554	0.554	strong		0.552	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
GRHL3	57822	hgsc.bcm.edu	37	1	24680915	24680915	+	Intron	SNP	C	C	T	rs12030057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:24680915C>T	ENST00000350501.5	+	15	1821				GRHL3_ENST00000236255.4_Silent_p.V587V|GRHL3_ENST00000342072.4_Silent_p.V489V|GRHL3_ENST00000361548.4_Silent_p.V582V|STPG1_ENST00000468303.1_5'Flank|GRHL3_ENST00000356046.2_Silent_p.V536V	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)						central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GCAACCACGTCGCCTTCCTGC	0.517													C|||	1352	0.269968	0.0703	0.3818	5008	,	,		22287	0.4127		0.2982	False		,,,				2504	0.2843				p.V587V		Atlas-SNP	.											.	GRHL3	69	.	0			c.C1761T						PASS	.	C	,,,	480,3926	224.6+/-240.7	26,428,1749	162.0	132.0	142.0		1608,1761,1746,	-10.4	0.3	1	dbSNP_120	142	2320,6280	389.1+/-342.8	311,1698,2291	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	GRHL3	NM_001195010.1,NM_021180.3,NM_198173.2,NM_198174.2	,,,	337,2126,4040	TT,TC,CC		26.9767,10.8942,21.5285	,,,	536/557,587/608,582/603,	24680915	2800,10206	2203	4300	6503	SO:0001627	intron_variant	57822	exon16			CCACGTCGCCTTC	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.1694+4303C>T	1.37:g.24680915C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Silent	SNP	ENST00000350501.5	37	CCDS252.2																																																																																			C|0.754;T|0.246	0.246	strong		0.517	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
TBC1D26	353149	hgsc.bcm.edu	37	17	15645289	15645289	+	Missense_Mutation	SNP	G	G	A	rs17855672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:15645289G>A	ENST00000437605.2	+	11	950	c.700G>A	c.(700-702)Ggc>Agc	p.G234S	AC005324.6_ENST00000433873.1_RNA|AC005324.6_ENST00000580194.1_RNA|ZNF286A_ENST00000413242.2_3'UTR|AC005324.6_ENST00000434017.1_RNA	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	234	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		G -> S (in dbSNP:rs17855672). {ECO:0000269|PubMed:15489334}.				Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		TGGCTCGAGAGGCTCCTATCG	0.572													.|||	1233	0.246206	0.0809	0.2651	5008	,	,		18897	0.254		0.3946	False		,,,				2504	0.2955				p.G234S		Atlas-SNP	.											.	TBC1D26	16	.	0			c.G700A						PASS	.	G	SER/GLY	516,3532		35,446,1543	57.0	57.0	57.0		700	-0.5	0.0	17	dbSNP_123	57	3324,5042		636,2052,1495	yes	missense	TBC1D26	NM_178571.4	56	671,2498,3038	AA,AG,GG		39.7322,12.747,30.9328	probably-damaging	234/251	15645289	3840,8574	2024	4183	6207	SO:0001583	missense	353149	exon11			TCGAGAGGCTCCT		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.700G>A	17.37:g.15645289G>A	ENSP00000410111:p.Gly234Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_178571	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	37	CCDS42265.1																																																																																			G|0.722;A|0.278	0.278	strong		0.572	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571	
XYLT2	64132	hgsc.bcm.edu	37	17	48432324	48432324	+	Missense_Mutation	SNP	G	G	C	rs12451299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48432324G>C	ENST00000017003.2	+	4	963	c.914G>C	c.(913-915)aGg>aCg	p.R305T	XYLT2_ENST00000507602.1_Missense_Mutation_p.R305T	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	305			R -> T (in dbSNP:rs12451299). {ECO:0000269|PubMed:11099377, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16571645}.		chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					AGCCTCCTGAGGATGTACCTG	0.637													g|||	658	0.13139	0.0408	0.2795	5008	,	,		19087	0.0784		0.2127	False		,,,				2504	0.1196				p.R305T		Atlas-SNP	.											XYLT2,NS,carcinoma,+1,1	XYLT2	51	1	0			c.G914C						PASS	.		THR/ARG	328,4078	174.1+/-203.8	19,290,1894	73.0	72.0	72.0		914	3.6	1.0	17	dbSNP_120	72	1917,6683	339.5+/-323.2	210,1497,2593	yes	missense	XYLT2	NM_022167.2	71	229,1787,4487	CC,CG,GG		22.2907,7.4444,17.2613	benign	305/866	48432324	2245,10761	2203	4300	6503	SO:0001583	missense	64132	exon4			TCCTGAGGATGTA	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.914G>C	17.37:g.48432324G>C	ENSP00000017003:p.Arg305Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_022167	Q6UY41|Q86V00	Missense_Mutation	SNP	ENST00000017003.2	37	CCDS11563.1	310	0.14194139194139194	19	0.03861788617886179	90	0.24861878453038674	43	0.07517482517482517	158	0.20844327176781002	g	2.759	-0.258362	0.05791	0.074444	0.222907	ENSG00000015532	ENST00000017003;ENST00000507602	T;T	0.11385	2.78;2.78	4.61	3.57	0.40892	.	0.179563	0.47093	D	0.000258	T	0.00012	0.0000	N	0.01109	-1.01	0.39741	P	0.02824899999999997	B	0.06786	0.001	B	0.11329	0.006	T	0.48559	-0.9025	9	0.07175	T	0.84	-16.396	3.2345	0.06760	0.1848:0.2897:0.5255:0.0	rs12451299	305	Q9H1B5	XYLT2_HUMAN	T	305	ENSP00000017003:R305T;ENSP00000426501:R305T	ENSP00000017003:R305T	R	+	2	0	XYLT2	45787323	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.212000	0.42835	2.399000	0.81585	0.306000	0.20318	AGG	G|0.835;C|0.165	0.165	strong		0.637	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
LRR1	122769	hgsc.bcm.edu	37	14	50074520	50074520	+	Missense_Mutation	SNP	C	C	T	rs7148147	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50074520C>T	ENST00000298288.6	+	3	1009	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	LRR1_ENST00000318317.4_Intron	NM_152329.3	NP_689542.2	Q96L50	LLR1_HUMAN	leucine rich repeat protein 1	229			R -> W (in dbSNP:rs7148147).		protein ubiquitination (GO:0016567)					kidney(2)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GAAGTCACTTCGGAGTTTGGA	0.408													C|||	863	0.172324	0.2625	0.3156	5008	,	,		19416	0.0268		0.2296	False		,,,				2504	0.0399				p.R229W		Atlas-SNP	.											.	LRR1	35	.	0			c.C685T						PASS	.	C	TRP/ARG,	1124,3282	401.5+/-332.0	138,848,1217	68.0	69.0	69.0		685,	5.1	1.0	14	dbSNP_116	69	1880,6720	333.7+/-320.7	218,1444,2638	yes	missense,intron	LRR1	NM_152329.3,NM_203467.1	101,	356,2292,3855	TT,TC,CC		21.8605,25.5107,23.097	possibly-damaging,	229/415,	50074520	3004,10002	2203	4300	6503	SO:0001583	missense	122769	exon3			TCACTTCGGAGTT	BC030142	CCDS9686.1, CCDS9687.1	14q21.3	2011-02-02	2011-02-02	2011-02-02	ENSG00000165501	ENSG00000165501			19742	protein-coding gene	gene with protein product	"""LRR-repeat protein 1"""	609193	"""peptidylprolyl isomerase (cyclophilin)-like 5"""	PPIL5		11804328, 21074724	Standard	NR_037792		Approved	MGC20689, LRR-1	uc001wwn.3	Q96L50	OTTHUMG00000140273	ENST00000298288.6:c.685C>T	14.37:g.50074520C>T	ENSP00000298288:p.Arg229Trp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_152329	A5D6X3|B4DDE0|Q52M24|Q86SZ1|Q8N6H9	Missense_Mutation	SNP	ENST00000298288.6	37	CCDS9686.1	417	0.19093406593406592	120	0.24390243902439024	106	0.292817679558011	27	0.0472027972027972	164	0.21635883905013192	C	20.8	4.057746	0.76074	0.255107	0.218605	ENSG00000165501	ENST00000298288;ENST00000361579	T	0.20738	2.05	5.98	5.1	0.69264	.	0.495374	0.23999	N	0.042485	T	0.00012	0.0000	M	0.85542	2.76	0.09310	P	1.0	D;D	0.61697	0.99;0.99	P;P	0.54210	0.53;0.745	T	0.21381	-1.0247	9	0.52906	T	0.07	-0.0624	11.5755	0.50858	0.0:0.8641:0.0:0.1359	rs7148147;rs52803719;rs58585267;rs7148147	251;229	A8MSW2;Q96L50	.;LLR1_HUMAN	W	229;251	ENSP00000298288:R229W	ENSP00000298288:R229W	R	+	1	2	LRR1	49144270	1.000000	0.71417	0.990000	0.47175	0.966000	0.64601	4.636000	0.61339	1.571000	0.49722	-0.131000	0.14894	CGG	C|0.792;T|0.208	0.208	strong		0.408	LRR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410790.1	NM_203467	
CFAP46	54777	hgsc.bcm.edu	37	10	134649709	134649709	+	Missense_Mutation	SNP	C	C	T	rs76581191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134649709C>T	ENST00000368586.5	-	46	6650	c.6550G>A	c.(6550-6552)Ggc>Agc	p.G2184S	TTC40_ENST00000263170.5_Missense_Mutation_p.G345S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TAGGCAGCGCCGTACAGACGG	0.647													c|||	33	0.00658946	0.0015	0.0043	5008	,	,		11914	0.0		0.0129	False		,,,				2504	0.0153				p.G2184S		Atlas-SNP	.											TTC40,NS,carcinoma,0,2	TTC40	100	2	0			c.G6550A						PASS	.		SER/GLY	11,4391	16.8+/-37.8	0,11,2190	76.0	58.0	64.0		1486	0.1	0.0	10	dbSNP_131	64	145,8453	70.7+/-133.2	0,145,4154	yes	missense	C10orf92	NM_001200049.1	56	0,156,6344	TT,TC,CC		1.6864,0.2499,1.2	benign	496/1028	134649709	156,12844	2201	4299	6500	SO:0001583	missense	54777	exon46			CAGCGCCGTACAG																												ENST00000368586.5:c.6550G>A	10.37:g.134649709C>T	ENSP00000357575:p.Gly2184Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	85	55	0.647059	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	c	4.026	0.002278	0.07819	0.002499	0.016864	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.25912	2.01;1.77	4.17	0.0804	0.14420	.	0.210433	0.27535	N	0.018933	T	0.06005	0.0156	N	0.25647	0.755	0.09310	N	0.999999	B	0.24132	0.098	B	0.15870	0.014	T	0.11966	-1.0566	10	0.40728	T	0.16	.	3.0641	0.06209	0.1917:0.4861:0.0:0.3222	.	345	Q8IYW2	CJ092_HUMAN	S	2184;345	ENSP00000357575:G2184S;ENSP00000263170:G345S	ENSP00000263170:G345S	G	-	1	0	C10orf93	134499699	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.167000	0.09940	0.040000	0.15660	-0.251000	0.11542	GGC	C|0.990;T|0.010	0.010	strong		0.647	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
KRT2	3849	hgsc.bcm.edu	37	12	53045777	53045777	+	Silent	SNP	G	G	A	rs11835758	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53045777G>A	ENST00000309680.3	-	1	171	c.150C>T	c.(148-150)ggC>ggT	p.G50G		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	50	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		CGAAGCCCCCGCCACCACCAC	0.617													G|||	1393	0.278155	0.1233	0.451	5008	,	,		16281	0.0437		0.4423	False		,,,				2504	0.4376				p.G50G		Atlas-SNP	.											.	KRT2	94	.	0			c.C150T						PASS	.	G		743,3663	299.6+/-285.9	53,637,1513	39.0	41.0	40.0		150	-10.0	0.0	12	dbSNP_120	40	3919,4681	538.8+/-383.5	899,2121,1280	no	coding-synonymous	KRT2	NM_000423.2		952,2758,2793	AA,AG,GG		45.5698,16.8634,35.845		50/640	53045777	4662,8344	2203	4300	6503	SO:0001819	synonymous_variant	3849	exon1			GCCCCCGCCACCA		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.150C>T	12.37:g.53045777G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_000423	Q4VAQ2	Silent	SNP	ENST00000309680.3	37	CCDS8835.1																																																																																			G|0.659;A|0.341	0.341	strong		0.617	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	
LILRA6	79168	hgsc.bcm.edu	37	19	54745682	54745682	+	Missense_Mutation	SNP	C	C	T	rs111666280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54745682C>T	ENST00000396365.2	-	4	467	c.428G>A	c.(427-429)cGa>cAa	p.R143Q	LILRA6_ENST00000270464.5_Missense_Mutation_p.R143Q|LILRA6_ENST00000245621.5_Missense_Mutation_p.R143Q|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Missense_Mutation_p.R143Q|LILRA6_ENST00000419410.2_Missense_Mutation_p.R143Q|LILRA6_ENST00000440558.2_Missense_Mutation_p.R143Q	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	143					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGAGCCACATCGGAGGGTCAT	0.567																																					p.R143Q		Atlas-SNP	.											.	LILRA6	75	.	0			c.G428A						PASS	.						29.0	50.0	43.0					19																	54745682		2122	4289	6411	SO:0001583	missense	79168	exon4			CCACATCGGAGGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.428G>A	19.37:g.54745682C>T	ENSP00000379651:p.Arg143Gln	Somatic	719	0	0		WXS	Illumina HiSeq	Phase_I	768	101	0.13151	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	0.554	-0.848058	0.02651	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.12774	2.65;2.65;2.65;4.09;2.65;2.65	3.38	-6.77	0.01727	Immunoglobulin-like fold (1);	0.513077	0.18054	N	0.153187	T	0.02047	0.0064	N	0.01640	-0.785	0.09310	N	1	B;B;B;B;B;B	0.33000	0.046;0.003;0.332;0.049;0.046;0.393	B;B;B;B;B;B	0.32342	0.008;0.002;0.144;0.015;0.015;0.014	T	0.37454	-0.9705	10	0.02654	T	1	.	0.493	0.00567	0.2783:0.2174:0.3072:0.1971	.	143;143;143;143;143;143	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	Q	143	ENSP00000390120:R143Q;ENSP00000270464:R143Q;ENSP00000411227:R143Q;ENSP00000375615:R143Q;ENSP00000379651:R143Q;ENSP00000245621:R143Q	ENSP00000245621:R143Q	R	-	2	0	LILRA6	59437494	0.000000	0.05858	0.001000	0.08648	0.096000	0.18686	-1.554000	0.02172	-1.307000	0.02321	0.162000	0.16502	CGA	C|0.904;T|0.096	0.096	strong		0.567	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209815	84209815	+	Missense_Mutation	SNP	C	C	G	rs2288021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84209815C>G	ENST00000378553.5	+	11	2099	c.1975C>G	c.(1975-1977)Cta>Gta	p.L659V	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	659			L -> P (in dbSNP:rs2288022). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.|L -> V (in dbSNP:rs2288021).		axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						CTCTGGCCAGCTACTGATGCC	0.557													C|||	658	0.13139	0.0068	0.2406	5008	,	,		16998	0.0972		0.2078	False		,,,				2504	0.1789				p.L659V		Atlas-SNP	.											.	DNAAF1	81	.	0			c.C1975G						PASS	.	C	VAL/LEU	192,4208	119.2+/-156.9	6,180,2014	35.0	33.0	34.0		1975	0.3	0.0	16	dbSNP_100	34	1878,6722	329.9+/-319.0	234,1410,2656	yes	missense	DNAAF1	NM_178452.4	32	240,1590,4670	GG,GC,CC		21.8372,4.3636,15.9231	benign	659/726	84209815	2070,10930	2200	4300	6500	SO:0001583	missense	123872	exon11			GGCCAGCTACTGA	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1975C>G	16.37:g.84209815C>G	ENSP00000367815:p.Leu659Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	167	81	0.48503	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	305	0.13965201465201466	5	0.01016260162601626	94	0.2596685082872928	50	0.08741258741258741	156	0.20580474934036938	C	9.473	1.096043	0.20552	0.043636	0.218372	ENSG00000154099	ENST00000378553	T	0.24350	1.86	4.67	0.294	0.15747	.	1.269100	0.05886	N	0.627428	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B	0.15473	0.013;0.013	B;B	0.21917	0.025;0.037	T	0.41270	-0.9518	9	0.40728	T	0.16	1.8768	2.8722	0.05620	0.1997:0.4697:0.0:0.3306	rs2288021	423;659	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	V	659	ENSP00000367815:L659V	ENSP00000367815:L659V	L	+	1	2	DNAAF1	82767316	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.449000	0.06812	0.214000	0.20742	-0.360000	0.07572	CTA	C|0.848;G|0.152	0.152	strong		0.557	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
GPLD1	2822	hgsc.bcm.edu	37	6	24445829	24445829	+	Silent	SNP	G	G	A	rs9358767	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:24445829G>A	ENST00000230036.1	-	20	2075	c.1965C>T	c.(1963-1965)caC>caT	p.H655H		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	655					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						TCATCAGTACGTGGCCACTGG	0.483													C|||	1012	0.202077	0.0643	0.2392	5008	,	,		19922	0.4524		0.0905	False		,,,				2504	0.2188				p.H655H		Atlas-SNP	.											.	GPLD1	91	.	0			c.C1965T						PASS	.	C		343,4063		14,315,1874	158.0	135.0	143.0		1965	-9.6	0.0	6	dbSNP_119	143	831,7769		39,753,3508	no	coding-synonymous	GPLD1	NM_001503.2		53,1068,5382	AA,AG,GG		9.6628,7.7848,9.0266		655/841	24445829	1174,11832	2203	4300	6503	SO:0001819	synonymous_variant	2822	exon20			CAGTACGTGGCCA	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1965C>T	6.37:g.24445829G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	168	75	0.446429	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Silent	SNP	ENST00000230036.1	37	CCDS4553.1																																																																																			G|0.859;A|0.140	0.140	strong		0.483	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	
CCL8	6355	hgsc.bcm.edu	37	17	32647831	32647831	+	Missense_Mutation	SNP	A	A	C	rs1133763	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:32647831A>C	ENST00000394620.1	+	3	671	c.205A>C	c.(205-207)Aaa>Caa	p.K69Q		NM_005623.2	NP_005614.2	P80075	CCL8_HUMAN	chemokine (C-C motif) ligand 8	69			K -> Q (in dbSNP:rs1133763). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9070881, ECO:0000269|PubMed:9119400}.		calcium ion transport (GO:0006816)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|exocytosis (GO:0006887)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)|heparin binding (GO:0008201)|phospholipase activator activity (GO:0016004)|protein kinase activity (GO:0004672)			NS(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Ovarian(249;0.0443)|Breast(31;0.151)				CTTCAAGACCAAACGGGGCAA	0.512													A|||	1138	0.227236	0.0658	0.2939	5008	,	,		15216	0.2986		0.1511	False		,,,				2504	0.4029				p.K69Q		Atlas-SNP	.											.	CCL8	12	.	0			c.A205C						PASS	.	A	GLN/LYS	318,4088	162.2+/-194.2	12,294,1897	72.0	60.0	64.0		205	3.1	0.0	17	dbSNP_86	64	1384,7216	253.4+/-279.1	118,1148,3034	yes	missense	CCL8	NM_005623.2	53	130,1442,4931	CC,CA,AA		16.093,7.2174,13.0863	probably-damaging	69/100	32647831	1702,11304	2203	4300	6503	SO:0001583	missense	6355	exon3			AAGACCAAACGGG	X99886	CCDS11280.1	17q11.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000108700	ENSG00000108700		"""Chemokine ligands"", ""Endogenous ligands"""	10635	protein-coding gene	gene with protein product		602283	"""small inducible cytokine subfamily A (Cys-Cys), member 8 (monocyte chemotactic protein 2)"""	SCYA8		9119400	Standard	NM_005623		Approved	MCP-2, HC14	uc002hib.3	P80075	OTTHUMG00000132883	ENST00000394620.1:c.205A>C	17.37:g.32647831A>C	ENSP00000378118:p.Lys69Gln	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	217	217	1	NM_005623	A0AV77|P78388	Missense_Mutation	SNP	ENST00000394620.1	37	CCDS11280.1	427	0.1955128205128205	48	0.0975609756097561	103	0.2845303867403315	163	0.28496503496503495	113	0.14907651715039577	A	16.50	3.140975	0.56936	0.072174	0.16093	ENSG00000108700	ENST00000394620;ENST00000225840	T	0.05580	3.42	5.34	3.09	0.35607	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.330523	0.21877	N	0.067797	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.46020	0.871	P	0.48738	0.588	T	0.46679	-0.9174	8	0.54805	T	0.06	.	6.482	0.22067	0.8092:0.0:0.1908:0.0	rs1133763;rs3138038;rs52819306;rs56696873;rs1133763	69	P80075	CCL8_HUMAN	Q	79;69	ENSP00000378118:K79Q	ENSP00000225840:K69Q	K	+	1	0	CCL8	29671944	0.027000	0.19231	0.042000	0.18584	0.132000	0.20833	2.066000	0.41452	0.829000	0.34733	0.460000	0.39030	AAA	A|0.839;C|0.161	0.161	strong		0.512	CCL8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256376.2	NM_005623	
PTCHD2	57540	hgsc.bcm.edu	37	1	11596455	11596455	+	Silent	SNP	C	C	T	rs2594310	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11596455C>T	ENST00000294484.6	+	21	4029	c.3891C>T	c.(3889-3891)gcC>gcT	p.A1297A	PTCHD2_ENST00000389575.3_Silent_p.A1297A|PTCHD2_ENST00000304391.6_Missense_Mutation_p.P184S	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1297					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		TCTCCAGTGCCCTCACCACGG	0.652													C|||	1219	0.243411	0.612	0.0865	5008	,	,		18018	0.0645		0.0626	False		,,,				2504	0.227				p.A1297A		Atlas-SNP	.											.	PTCHD2	193	.	0			c.C3891T						PASS	.	C		2232,2172	542.4+/-376.0	579,1074,549	98.0	103.0	101.0		3891	-7.5	1.0	1	dbSNP_100	101	568,8002	151.2+/-206.0	21,526,3738	no	coding-synonymous	PTCHD2	NM_020780.1		600,1600,4287	TT,TC,CC		6.6278,49.3188,21.5816		1297/1393	11596455	2800,10174	2202	4285	6487	SO:0001819	synonymous_variant	57540	exon21			CAGTGCCCTCACC	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.3891C>T	1.37:g.11596455C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	54	12	0.222222	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	37	CCDS41247.1	415	0.190018315018315	301	0.6117886178861789	39	0.10773480662983426	27	0.0472027972027972	48	0.0633245382585752	C	14.85	2.658334	0.47467	0.506812	0.066278	ENSG00000204624	ENST00000304391	.	.	.	4.89	-7.54	0.01332	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999814757	.	.	.	.	.	.	T	0.44205	-0.9343	4	0.87932	D	0	-29.2968	1.6823	0.02834	0.312:0.1843:0.3325:0.1713	rs2594310;rs2594310	.	.	.	S	184	.	ENSP00000303400:P184S	P	+	1	0	PTCHD2	11519042	0.006000	0.16342	0.955000	0.39395	0.969000	0.65631	-0.965000	0.03829	-0.787000	0.04510	-0.868000	0.02995	CCT	C|0.842;T|0.158	0.158	strong		0.652	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
RBM23	55147	hgsc.bcm.edu	37	14	23375564	23375564	+	Missense_Mutation	SNP	G	G	A	rs72681969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:23375564G>A	ENST00000359890.3	-	5	436	c.241C>T	c.(241-243)Cgg>Tgg	p.R81W	RBM23_ENST00000542016.2_5'UTR|RBM23_ENST00000556984.1_5'UTR|RBM23_ENST00000399922.2_Missense_Mutation_p.R65W|RBM23_ENST00000555209.1_5'UTR|RBM23_ENST00000346528.5_Missense_Mutation_p.R65W	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23	81	Arg-rich.				mRNA processing (GO:0006397)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|lung(3)|prostate(1)|skin(1)	10	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		TACCGATCCCGATCTCGACTA	0.512													G|||	72	0.014377	0.003	0.0259	5008	,	,		21445	0.0		0.0437	False		,,,				2504	0.0061				p.R81W		Atlas-SNP	.											.	RBM23	44	.	0			c.C241T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	44,4080		1,42,2019	70.0	70.0	70.0		241,193,193	4.8	1.0	14	dbSNP_130	70	317,8085		7,303,3891	yes	missense,missense,missense	RBM23	NM_001077351.1,NM_001077352.1,NM_018107.4	101,101,101	8,345,5910	AA,AG,GG		3.7729,1.0669,2.882	probably-damaging,probably-damaging,probably-damaging	81/440,65/406,65/424	23375564	361,12165	2062	4201	6263	SO:0001583	missense	55147	exon5			GATCCCGATCTCG	AF275678	CCDS41919.1, CCDS41920.1, CCDS41921.1	14q11.1	2014-07-03	2004-04-23	2004-04-23		ENSG00000100461		"""RNA binding motif (RRM) containing"""	20155	protein-coding gene	gene with protein product	"""coactivator of activating protein-1 and estrogen recep- tors beta"""		"""RNA-binding region (RNP1, RRM) containing 4"""	RNPC4		15694343	Standard	NM_018107		Approved	FLJ10482, CAPERbeta	uc001whg.3	Q86U06		ENST00000359890.3:c.241C>T	14.37:g.23375564G>A	ENSP00000352956:p.Arg81Trp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_001077351	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Missense_Mutation	SNP	ENST00000359890.3	37	CCDS41921.1	44	0.020146520146520148	3	0.006097560975609756	8	0.022099447513812154	0	0.0	33	0.04353562005277045	G	21.6	4.170582	0.78452	0.010669	0.037729	ENSG00000100461	ENST00000359890;ENST00000399922;ENST00000346528;ENST00000554256;ENST00000557549;ENST00000555676;ENST00000557571;ENST00000556862;ENST00000557464	T;T;T	0.79940	-1.32;3.27;3.34	4.83	4.83	0.62350	.	0.213810	0.30302	N	0.009932	T	0.57257	0.2041	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.998;0.997	P;P;P;P	0.59643	0.861;0.738;0.738;0.551	T	0.76686	-0.2868	10	0.87932	D	0	-6.2082	15.1845	0.72989	0.0:0.0:1.0:0.0	.	81;65;65;81	Q86U06-3;Q86U06-4;Q86U06-2;Q86U06	.;.;.;RBM23_HUMAN	W	81;65;65;81;65;65;65;81;65	ENSP00000352956:R81W;ENSP00000382806:R65W;ENSP00000339220:R65W	ENSP00000305783:R81W	R	-	1	2	RBM23	22445404	0.988000	0.35896	0.978000	0.43139	0.610000	0.37248	2.301000	0.43628	2.398000	0.81561	0.561000	0.74099	CGG	G|0.971;A|0.029	0.029	strong		0.512	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		
APCDD1	147495	hgsc.bcm.edu	37	18	10487918	10487918	+	Silent	SNP	C	C	T	rs3185480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:10487918C>T	ENST00000355285.5	+	5	1782	c.1428C>T	c.(1426-1428)ctC>ctT	p.L476L		NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CAGAGGACCTCGCAGAAGACA	0.647													C|||	2053	0.409944	0.205	0.4769	5008	,	,		14532	0.6181		0.4304	False		,,,				2504	0.4039				p.L476L		Atlas-SNP	.											.	APCDD1	57	.	0			c.C1428T						PASS	.	C		1073,3333	373.7+/-320.9	132,809,1262	62.0	63.0	63.0		1428	-3.8	0.0	18	dbSNP_105	63	3515,5085	490.0+/-372.7	713,2089,1498	no	coding-synonymous	APCDD1	NM_153000.4		845,2898,2760	TT,TC,CC		40.8721,24.3532,35.276		476/515	10487918	4588,8418	2203	4300	6503	SO:0001819	synonymous_variant	147495	exon5			GGACCTCGCAGAA	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1428C>T	18.37:g.10487918C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_153000		Silent	SNP	ENST00000355285.5	37	CCDS11849.1																																																																																			C|0.613;T|0.387	0.387	strong		0.647	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
PSMB6	5694	hgsc.bcm.edu	37	17	4699552	4699552	+	Silent	SNP	G	G	A	rs3169950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4699552G>A	ENST00000270586.3	+	1	114	c.63G>A	c.(61-63)gcG>gcA	p.A21A		NM_001270481.1|NM_002798.2	NP_001257410.1|NP_002789.1	P28072	PSB6_HUMAN	proteasome (prosome, macropain) subunit, beta type, 6	21					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	endopeptidase activity (GO:0004175)|threonine-type endopeptidase activity (GO:0004298)			endometrium(3)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11						GGCCGGAGGCGTTCACTCCAG	0.592													C|||	1348	0.269169	0.2368	0.4078	5008	,	,		14486	0.0982		0.4125	False		,,,				2504	0.2434				p.A21A		Atlas-SNP	.											.	PSMB6	20	.	0			c.G63A						PASS	.	C		1344,3042		215,914,1064	22.0	21.0	22.0		63	-5.4	0.0	17	dbSNP_105	22	3771,4819		847,2077,1371	no	coding-synonymous	PSMB6	NM_002798.1		1062,2991,2435	AA,AG,GG		43.8999,30.643,39.4189		21/240	4699552	5115,7861	2193	4295	6488	SO:0001819	synonymous_variant	5694	exon1			GGAGGCGTTCACT	BC000835	CCDS11056.1, CCDS73944.1	17p13	2004-02-18			ENSG00000142507	ENSG00000142507		"""Proteasome (prosome, macropain) subunits"""	9543	protein-coding gene	gene with protein product		600307				8066462, 1888762	Standard	NM_002798		Approved	Y, DELTA	uc002fzb.4	P28072	OTTHUMG00000090777	ENST00000270586.3:c.63G>A	17.37:g.4699552G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	NM_002798	Q96J55	Silent	SNP	ENST00000270586.3	37	CCDS11056.1																																																																																			A|0.322;C|0.010;G|0.668;T|0.000	0.322	strong		0.592	PSMB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207559.2	NM_002798	
CDC27	996	hgsc.bcm.edu	37	17	45216115	45216115	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45216115T>A	ENST00000066544.3	-	13	1787	c.1694A>T	c.(1693-1695)aAt>aTt	p.N565I	CDC27_ENST00000527547.1_Missense_Mutation_p.N564I|CDC27_ENST00000446365.2_Missense_Mutation_p.N504I|CDC27_ENST00000531206.1_Missense_Mutation_p.N571I	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	565					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.N565I(1)|p.N571I(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTCTGGCGAATTTTTATCCAT	0.353																																					p.N571I		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	2	2	Substitution - Missense(2)	ovary(2)	c.A1712T						scavenged	.						50.0	55.0	54.0					17																	45216115		2201	4299	6500	SO:0001583	missense	996	exon13			GGCGAATTTTTAT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1694A>T	17.37:g.45216115T>A	ENSP00000066544:p.Asn565Ile	Somatic	45	1	0.0222222		WXS	Illumina HiSeq	Phase_I	33	2	0.0606061	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.271461	0.80469	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.62	5.62	0.85841	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.041764	0.85682	D	0.000000	T	0.53997	0.1831	L	0.58810	1.83	0.58432	D	0.999999	D;P;D;P	0.57257	0.979;0.952;0.978;0.914	P;P;P;B	0.56788	0.806;0.546;0.645;0.36	T	0.52019	-0.8631	10	0.37606	T	0.19	-4.6177	13.77	0.63019	0.0:0.0:0.0:1.0	.	504;564;571;565	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	I	565;571;504;564	ENSP00000066544:N565I;ENSP00000434614:N571I;ENSP00000392802:N504I;ENSP00000437339:N564I	ENSP00000066544:N565I	N	-	2	0	CDC27	42571114	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.893000	0.56243	2.141000	0.66446	0.528000	0.53228	AAT	.	.	none		0.353	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548544	32548544	+	Missense_Mutation	SNP	T	T	G	rs199873800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32548544T>G	ENST00000360004.5	-	4	847	c.742A>C	c.(742-744)Atc>Ctc	p.I248L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	248					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CTGAAGTAGATGAACAGCCCG	0.547										Multiple Myeloma(14;0.17)																											p.I248L		Atlas-SNP	.											HLA-DRB1,NS,haematopoietic_neoplasm,0,1	HLA-DRB1	41	1	0			c.A742C						PASS	.						86.0	100.0	95.0					6																	32548544		1511	2709	4220	SO:0001583	missense	3123	exon4			AGTAGATGAACAG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.742A>C	6.37:g.32548544T>G	ENSP00000353099:p.Ile248Leu	Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	716	55	0.0768156	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	16.04	3.009505	0.54361	.	.	ENSG00000196126	ENST00000360004	T	0.00638	6.04	3.98	-6.48	0.01896	.	0.413267	0.26923	N	0.021810	T	0.00552	0.0018	L	0.58510	1.815	0.19300	N	0.99997	B;B;D	0.59357	0.009;0.002;0.985	B;B;D	0.66716	0.021;0.005;0.946	T	0.51252	-0.8729	10	0.87932	D	0	.	1.2914	0.02061	0.2749:0.3631:0.1397:0.2223	.	248;248;248	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	L	248	ENSP00000353099:I248L	ENSP00000353099:I248L	I	-	1	0	HLA-DRB1	32656522	0.003000	0.15002	0.067000	0.19924	0.641000	0.38312	-1.853000	0.01666	-0.703000	0.05049	0.372000	0.22366	ATC	T|0.954;G|0.046	0.046	strong		0.547	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PIK3CG	5294	hgsc.bcm.edu	37	7	106513011	106513011	+	Silent	SNP	C	C	T	rs1129293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:106513011C>T	ENST00000359195.3	+	3	2335	c.2025C>T	c.(2023-2025)agC>agT	p.S675S	PIK3CG_ENST00000440650.2_Silent_p.S675S|PIK3CG_ENST00000496166.1_Silent_p.S675S	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	675	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						ACCATGATAGCGCCCTTGCCA	0.398													C|||	1271	0.253794	0.0787	0.428	5008	,	,		21884	0.2897		0.3141	False		,,,				2504	0.2679				p.S675S		Atlas-SNP	.											PIK3CG,rectum,carcinoma,+1,1	PIK3CG	279	1	0			c.C2025T						PASS	.	C		570,3836	253.0+/-259.1	43,484,1676	205.0	195.0	198.0		2025	-5.9	0.9	7	dbSNP_86	198	2537,6063	413.6+/-351.2	379,1779,2142	no	coding-synonymous	PIK3CG	NM_002649.2		422,2263,3818	TT,TC,CC		29.5,12.9369,23.889		675/1103	106513011	3107,9899	2203	4300	6503	SO:0001819	synonymous_variant	5294	exon3			TGATAGCGCCCTT		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2025C>T	7.37:g.106513011C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	181	82	0.453039	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Silent	SNP	ENST00000359195.3	37	CCDS5739.1																																																																																			C|0.757;T|0.243	0.243	strong		0.398	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
MUC16	94025	hgsc.bcm.edu	37	19	9077060	9077060	+	Silent	SNP	C	C	T	rs2591596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9077060C>T	ENST00000397910.4	-	3	10589	c.10386G>A	c.(10384-10386)gtG>gtA	p.V3462V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3463	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGGCAGAGACACTAGTGAGG	0.498													T|||	1244	0.248403	0.2012	0.2118	5008	,	,		22404	0.249		0.3121	False		,,,				2504	0.272				p.V3462V		Atlas-SNP	.											.	MUC16	4315	.	0			c.G10386A						PASS	.	T		893,3339		107,679,1330	131.0	128.0	129.0		10386	-0.7	0.0	19	dbSNP_100	129	2433,6021		353,1727,2147	no	coding-synonymous	MUC16	NM_024690.2		460,2406,3477	TT,TC,CC		28.7793,21.1011,26.2179		3462/14508	9077060	3326,9360	2116	4227	6343	SO:0001819	synonymous_variant	94025	exon3			CAGAGACACTAGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10386G>A	19.37:g.9077060C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.743;T|0.257	0.257	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FIGLA	344018	hgsc.bcm.edu	37	2	71012734	71012734	+	Missense_Mutation	SNP	C	C	G	rs71647804|rs7566476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71012734C>G	ENST00000332372.6	-	3	426	c.422G>C	c.(421-423)aGt>aCt	p.S141T		NM_001004311.3	NP_001004311.2	Q6QHK4	FIGLA_HUMAN	folliculogenesis specific basic helix-loop-helix	141			S -> T (in dbSNP:rs7566476). {ECO:0000269|PubMed:15044608, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			endometrium(2)|lung(3)	5						TGATTCAGAACTGTTGTTACT	0.403													G|||	3821	0.762979	0.882	0.6873	5008	,	,		19278	0.9077		0.5626	False		,,,				2504	0.7127				p.S141T		Atlas-SNP	.											.	FIGLA	23	.	0			c.G422C						PASS	.	G	THR/SER	3225,739		1309,607,66	414.0	403.0	406.0		422	3.2	0.0	2	dbSNP_116	406	4492,3858		1216,2060,899	yes	missense	FIGLA	NM_001004311.3	58	2525,2667,965	GG,GC,CC		46.2036,18.6428,37.3315	benign	141/220	71012734	7717,4597	1982	4175	6157	SO:0001583	missense	344018	exon3			TCAGAACTGTTGT	BC039536	CCDS46320.1	2p13.3	2013-05-21			ENSG00000183733	ENSG00000183733		"""Basic helix-loop-helix proteins"""	24669	protein-coding gene	gene with protein product	"""factor in the germline alpha"""	608697				12468641	Standard	NM_001004311		Approved	bHLHc8	uc002she.1	Q6QHK4	OTTHUMG00000153440	ENST00000332372.6:c.422G>C	2.37:g.71012734C>G	ENSP00000333097:p.Ser141Thr	Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	196	195	0.994898	NM_001004311		Missense_Mutation	SNP	ENST00000332372.6	37	CCDS46320.1	1641	0.7513736263736264	432	0.8780487804878049	238	0.6574585635359116	538	0.9405594405594405	433	0.5712401055408971	G	0.012	-1.681187	0.00745	0.813572	0.537964	ENSG00000183733	ENST00000332372	D	0.95447	-3.71	4.12	3.24	0.37175	Helix-loop-helix DNA-binding (1);	1.058040	0.07402	N	0.890934	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42999	-0.9418	9	0.05721	T	0.95	.	6.0393	0.19726	0.1021:0.191:0.7069:0.0	rs7566476;rs17717676;rs52819463;rs61154013;rs7566476	141	Q6QHK4	FIGLA_HUMAN	T	141	ENSP00000333097:S141T	ENSP00000333097:S141T	S	-	2	0	FIGLA	70866242	0.310000	0.24527	0.010000	0.14722	0.009000	0.06853	1.504000	0.35726	0.701000	0.31803	-0.127000	0.14921	AGT	C|0.255;G|0.745	0.745	strong		0.403	FIGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331214.1	NM_001004311	
UGT1A7	54577	hgsc.bcm.edu	37	2	234590616	234590616	+	Silent	SNP	C	C	A	rs7577677	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234590616C>A	ENST00000373426.3	+	1	33	c.33C>A	c.(31-33)ccC>ccA	p.P11P	UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	11					cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	GCCTCCTTCCCCTATATGTGT	0.547											OREG0003832	type=REGULATORY REGION|Gene=UGT1A7|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	1489	0.297324	0.2481	0.2637	5008	,	,		18471	0.1964		0.3598	False		,,,				2504	0.4274				p.P11P		Atlas-SNP	.											.	UGT1A7	74	.	0			c.C33A						PASS	.	C	,,,	1205,3201	420.8+/-339.2	179,847,1177	135.0	129.0	131.0		,,33,	-3.0	0.0	2	dbSNP_116	131	3332,5268	496.3+/-374.3	653,2026,1621	no	intron,intron,coding-synonymous,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A9	NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2	,,,	832,2873,2798	AA,AC,CC		38.7442,27.3491,34.8839	,,,	,,11/531,	234590616	4537,8469	2203	4300	6503	SO:0001819	synonymous_variant	54577	exon1			CCTTCCCCTATAT	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.33C>A	2.37:g.234590616C>A		Somatic	196	0	0	2374	WXS	Illumina HiSeq	Phase_I	236	111	0.470339	NM_019077	B8K293|O00473	Silent	SNP	ENST00000373426.3	37	CCDS2506.1																																																																																			C|0.686;A|0.314	0.314	strong		0.547	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
MAATS1	89876	hgsc.bcm.edu	37	3	119426307	119426307	+	Silent	SNP	T	T	C	rs9848716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:119426307T>C	ENST00000273390.5	+	3	335	c.258T>C	c.(256-258)taT>taC	p.Y86Y	MAATS1_ENST00000463700.1_Silent_p.Y86Y	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	86						mitochondrion (GO:0005739)											ATCCAAGATATTCTCTATATT	0.433													T|||	2931	0.585264	0.1785	0.6369	5008	,	,		13328	0.8095		0.7286	False		,,,				2504	0.7198				p.Y86Y		Atlas-SNP	.											.	.	.	.	0			c.T258C						PASS	.	T		1134,3272	402.8+/-332.5	150,834,1219	68.0	72.0	71.0		258	3.5	1.0	3	dbSNP_119	71	6222,2378	701.4+/-405.2	2228,1766,306	no	coding-synonymous	C3orf15	NM_033364.3		2378,2600,1525	CC,CT,TT		27.6512,25.7376,43.4415		86/768	119426307	7356,5650	2203	4300	6503	SO:0001819	synonymous_variant	89876	exon3			AAGATATTCTCTA	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.258T>C	3.37:g.119426307T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Silent	SNP	ENST00000273390.5	37	CCDS2994.1																																																																																			T|0.424;C|0.576	0.576	strong		0.433	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
LTBP1	4052	hgsc.bcm.edu	37	2	33540307	33540307	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33540307C>T	ENST00000404816.2	+	24	4054	c.3701C>T	c.(3700-3702)tCa>tTa	p.S1234L	LTBP1_ENST00000404525.1_Missense_Mutation_p.S855L|LTBP1_ENST00000407925.1_Missense_Mutation_p.S908L|LTBP1_ENST00000272273.5_Missense_Mutation_p.S174L|LTBP1_ENST00000402934.1_Missense_Mutation_p.S855L|LTBP1_ENST00000418533.2_Missense_Mutation_p.S908L|LTBP1_ENST00000390003.4_Missense_Mutation_p.S909L|LTBP1_ENST00000354476.3_Missense_Mutation_p.S1235L			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1234	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CAGGGTTTCTCAATCTCTGCA	0.433																																					p.S1234L		Atlas-SNP	.											.	LTBP1	317	.	0			c.C3701T						PASS	.						115.0	102.0	107.0					2																	33540307		2203	4300	6503	SO:0001583	missense	4052	exon24			GTTTCTCAATCTC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3701C>T	2.37:g.33540307C>T	ENSP00000386043:p.Ser1234Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	129	21	0.162791	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.2|20.2	3.943601|3.943601	0.73672|0.73672	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273;ENST00000422669	.|D;D;D;D;D;D;D;D;D	.|0.86865	.|-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	4.98|4.98	4.98|4.98	0.66077|0.66077	.|EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|.	.|.	.|.	.|.	.|D	.|0.85885	.|0.5801	L|L	0.38531|0.38531	1.155|1.155	0.40185|0.40185	D|D	0.977332|0.977332	.|B;B;P;B;P;P;P	.|0.41624	.|0.005;0.343;0.757;0.078;0.746;0.58;0.47	.|B;B;B;B;P;B;B	.|0.45610	.|0.027;0.392;0.293;0.087;0.487;0.407;0.341	.|D	.|0.86865	.|0.2032	.|9	.|0.46703	.|T	.|0.11	.|.	18.2782|18.2782	0.90089|0.90089	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|174;1234;908;855;908;909;1235	.|E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;LTBP1_HUMAN;.;.;.;.;.	X|L	196|1234;1235;909;908;855;855;908;174;112	.|ENSP00000386043:S1234L;ENSP00000346467:S1235L;ENSP00000374653:S909L;ENSP00000393057:S908L;ENSP00000384373:S855L;ENSP00000385359:S855L;ENSP00000384091:S908L;ENSP00000272273:S174L;ENSP00000395211:S112L	.|ENSP00000272273:S174L	Q|S	+|+	1|2	0|0	LTBP1|LTBP1	33393811|33393811	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.886000|0.886000	0.51366|0.51366	5.677000|5.677000	0.68142|0.68142	2.295000|2.295000	0.77249|0.77249	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.	none		0.433	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
ZNF354A	6940	hgsc.bcm.edu	37	5	178140090	178140090	+	Silent	SNP	C	C	T	rs1132336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178140090C>T	ENST00000335815.2	-	5	986	c.789G>A	c.(787-789)acG>acA	p.T263T		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	263					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T263T(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		CTCCAGTATGCGTTATTTGAT	0.353													C|||	1318	0.263179	0.09	0.2464	5008	,	,		19499	0.3333		0.2813	False		,,,				2504	0.4182				p.T263T		Atlas-SNP	.											ZNF354A,NS,carcinoma,0,1	ZNF354A	74	1	1	Substitution - coding silent(1)	stomach(1)	c.G789A						scavenged	.	C		570,3836	251.5+/-258.2	38,494,1671	98.0	98.0	98.0		789	-5.9	0.9	5	dbSNP_86	98	2355,6245	392.0+/-343.8	322,1711,2267	no	coding-synonymous	ZNF354A	NM_005649.2		360,2205,3938	TT,TC,CC		27.3837,12.9369,22.4896		263/606	178140090	2925,10081	2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			AGTATGCGTTATT	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.789G>A	5.37:g.178140090C>T		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	101	35	0.346535	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			C|0.762;T|0.238	0.238	strong		0.353	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
MST1R	4486	hgsc.bcm.edu	37	3	49940078	49940078	+	Missense_Mutation	SNP	C	C	T	rs2230593	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49940078C>T	ENST00000296474.3	-	1	992	c.965G>A	c.(964-966)cGg>cAg	p.R322Q	CTD-2330K9.2_ENST00000435478.1_RNA|CTD-2330K9.3_ENST00000419183.1_5'Flank|MST1R_ENST00000344206.4_Missense_Mutation_p.R322Q	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	322	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		R -> Q (in dbSNP:rs2230593). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8386824}.		cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		GTGGGCCACCCGCAGCACAGG	0.627													C|||	102	0.0203674	0.0061	0.0346	5008	,	,		16340	0.0		0.0626	False		,,,				2504	0.0072				p.R322Q		Atlas-SNP	.											.	MST1R	205	.	0			c.G965A						PASS	.	C	GLN/ARG	78,4328	67.0+/-104.6	2,74,2127	90.0	99.0	96.0		965	-0.9	0.4	3	dbSNP_98	96	583,8017	153.1+/-207.6	18,547,3735	yes	missense	MST1R	NM_002447.2	43	20,621,5862	TT,TC,CC		6.7791,1.7703,5.0823	benign	322/1401	49940078	661,12345	2203	4300	6503	SO:0001583	missense	4486	exon1			GCCACCCGCAGCA	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"""CD molecules"""	7381	protein-coding gene	gene with protein product		600168	"""PTK8 protein tyrosine kinase 8"""	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.965G>A	3.37:g.49940078C>T	ENSP00000296474:p.Arg322Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	137	80	0.583942	NM_001244937	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	37	CCDS2807.1	65	0.02976190476190476	3	0.006097560975609756	11	0.03038674033149171	0	0.0	51	0.06728232189973615	C	1.784	-0.481188	0.04383	0.017703	0.067791	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.02837	4.14;4.14	4.92	-0.886	0.10590	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.325300	0.33161	N	0.005217	T	0.00109	0.0003	N	0.02120	-0.675	0.28818	N	0.897843	B;B;B;B;B	0.24823	0.013;0.112;0.013;0.013;0.041	B;B;B;B;B	0.15484	0.003;0.011;0.002;0.002;0.013	T	0.46205	-0.9208	10	0.02654	T	1	-8.7513	9.8282	0.40925	0.0:0.1883:0.0:0.8117	rs2230593;rs52807012;rs2230593	322;322;322;322;322	Q04912-3;Q04912-4;Q04912-6;Q04912-5;Q04912	.;.;.;.;RON_HUMAN	Q	322	ENSP00000296474:R322Q;ENSP00000341325:R322Q	ENSP00000296474:R322Q	R	-	2	0	MST1R	49915082	0.973000	0.33851	0.449000	0.26957	0.085000	0.17905	1.141000	0.31528	-0.050000	0.13356	-0.367000	0.07326	CGG	C|0.956;T|0.044	0.044	strong		0.627	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
SERPINA11	256394	hgsc.bcm.edu	37	14	94912896	94912896	+	Missense_Mutation	SNP	T	T	G	rs1885137	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94912896T>G	ENST00000334708.3	-	3	753	c.689A>C	c.(688-690)gAa>gCa	p.E230A	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	230			E -> A (in dbSNP:rs1885137).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		AAAGAAACTTTCCTGCTTCTG	0.488													T|||	1304	0.260383	0.0613	0.2695	5008	,	,		21655	0.1835		0.4503	False		,,,				2504	0.407				p.E230A		Atlas-SNP	.											.	SERPINA11	53	.	0			c.A689C						PASS	.	T	ALA/GLU	587,3819	258.6+/-262.5	46,495,1662	154.0	145.0	148.0		689	-6.3	0.1	14	dbSNP_92	148	3525,5075	515.2+/-378.5	700,2125,1475	yes	missense	SERPINA11	NM_001080451.1	107	746,2620,3137	GG,GT,TT		40.9884,13.3227,31.6162	benign	230/423	94912896	4112,8894	2203	4300	6503	SO:0001583	missense	256394	exon3			AAACTTTCCTGCT	BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"""Serine (or cysteine) peptidase inhibitors"""	19193	protein-coding gene	gene with protein product			"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"""			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.689A>C	14.37:g.94912896T>G	ENSP00000335024:p.Glu230Ala	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	190	99	0.521053	NM_001080451	B2RV07	Missense_Mutation	SNP	ENST00000334708.3	37	CCDS32149.1	613	0.2806776556776557	45	0.09146341463414634	108	0.2983425414364641	105	0.18356643356643357	355	0.4683377308707124	T	1.786	-0.480780	0.04383	0.133227	0.409884	ENSG00000186910	ENST00000334708	D	0.87887	-2.31	5.01	-6.34	0.01982	Serpin domain (3);	1.038600	0.07607	N	0.924607	T	0.00012	0.0000	L	0.58669	1.825	0.80722	P	0.0	B	0.24721	0.11	B	0.29077	0.098	T	0.35325	-0.9793	9	0.39692	T	0.17	.	3.0149	0.06057	0.1042:0.3435:0.2876:0.2647	rs57740714	230	Q86U17	SPA11_HUMAN	A	230	ENSP00000335024:E230A	ENSP00000335024:E230A	E	-	2	0	SERPINA11	93982649	0.000000	0.05858	0.091000	0.20842	0.252000	0.25951	-1.228000	0.02948	-0.657000	0.05373	0.454000	0.30748	GAA	G|0.312;N|0.000	0.312	strong		0.488	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451	
C6orf15	29113	hgsc.bcm.edu	37	6	31079644	31079644	+	Silent	SNP	G	G	A	rs2233980	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31079644G>A	ENST00000259870.3	-	2	495	c.492C>T	c.(490-492)ccC>ccT	p.P164P	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	164					extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GTGAAGCCTTGGGTGAGAGGC	0.617													G|||	119	0.023762	0.0083	0.0317	5008	,	,		16520	0.0		0.0855	False		,,,				2504	0.0				p.P164P		Atlas-SNP	.											.	C6orf15	29	.	0			c.C492T						PASS	.	G		103,3523		2,99,1712	32.0	36.0	34.0		492	-9.1	0.0	6	dbSNP_98	34	726,6374		42,642,2866	no	coding-synonymous	C6orf15	NM_014070.2		44,741,4578	AA,AG,GG		10.2254,2.8406,7.7289		164/326	31079644	829,9897	1813	3550	5363	SO:0001819	synonymous_variant	29113	exon2			AGCCTTGGGTGAG	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.492C>T	6.37:g.31079644G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			G|0.926;A|0.074	0.074	strong		0.617	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
PFKM	5213	hgsc.bcm.edu	37	12	48539482	48539482	+	Silent	SNP	T	T	G	rs8716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48539482T>G	ENST00000312352.7	+	23	2373	c.2334T>G	c.(2332-2334)gcT>gcG	p.A778A	PFKM_ENST00000359794.5_Silent_p.A778A|PFKM_ENST00000395233.2_Silent_p.A747A|PFKM_ENST00000551804.1_Silent_p.A747A|PFKM_ENST00000340802.6_Silent_p.A849A|PFKM_ENST00000547587.1_Silent_p.A778A	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	778	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						CCGGGGAAGCTGCCGTCTAAA	0.502													T|||	1023	0.204273	0.1051	0.2089	5008	,	,		18791	0.0139		0.3877	False		,,,				2504	0.3425				p.A849A		Atlas-SNP	.											.	PFKM	117	.	0			c.T2547G						PASS	.	T	,,,	555,3851	248.7+/-256.4	35,485,1683	82.0	73.0	76.0		2334,2547,2334,2334	-9.0	0.0	12	dbSNP_52	76	3249,5351	489.4+/-372.6	598,2053,1649	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PFKM	NM_000289.5,NM_001166686.1,NM_001166687.1,NM_001166688.1	,,,	633,2538,3332	GG,GT,TT		37.7791,12.5965,29.248	,,,	778/781,849/852,778/781,778/781	48539482	3804,9202	2203	4300	6503	SO:0001819	synonymous_variant	5213	exon25			GGAAGCTGCCGTC	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 122"""	610681	"""phosphofructokinase, polypeptide X"""	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.2334T>G	12.37:g.48539482T>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_001166686	J3KNX3|Q16814|Q16815|Q6ZTT1	Silent	SNP	ENST00000312352.7	37	CCDS8760.1																																																																																			T|0.746;G|0.254	0.254	strong		0.502	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289	
ADCK4	79934	hgsc.bcm.edu	37	19	41211056	41211056	+	Missense_Mutation	SNP	T	T	C	rs3865452	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41211056T>C	ENST00000324464.3	-	7	822	c.521A>G	c.(520-522)cAc>cGc	p.H174R	ADCK4_ENST00000243583.6_Missense_Mutation_p.H133R|ADCK4_ENST00000450541.1_Missense_Mutation_p.H133R|RNU6-195P_ENST00000411352.1_RNA	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	174			H -> R (in dbSNP:rs3865452). {ECO:0000269|PubMed:17344846}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)	p.H174R(2)		NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CTCAAAGATGTGCTGCAGCTG	0.622													C|||	2391	0.477436	0.3381	0.6441	5008	,	,		20444	0.4782		0.4901	False		,,,				2504	0.5337				p.H174R		Atlas-SNP	.											ADCK4_ENST00000324464,NS,carcinoma,0,4	ADCK4	92	4	2	Substitution - Missense(2)	stomach(2)	c.A521G						PASS	.	C	ARG/HIS,ARG/HIS	1636,2770	651.5+/-399.2	317,1002,884	39.0	36.0	37.0		398,521	2.9	1.0	19	dbSNP_108	37	4249,4351	575.6+/-390.2	1051,2147,1102	yes	missense,missense	ADCK4	NM_001142555.2,NM_024876.3	29,29	1368,3149,1986	CC,CT,TT		49.407,37.1312,45.2483	benign,benign	133/504,174/545	41211056	5885,7121	2203	4300	6503	SO:0001583	missense	79934	exon7			AAGATGTGCTGCA	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.521A>G	19.37:g.41211056T>C	ENSP00000315118:p.His174Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_024876	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	37	CCDS12562.1	1009	0.461996336996337	147	0.29878048780487804	218	0.6022099447513812	269	0.47027972027972026	375	0.4947229551451187	C	3.325	-0.137935	0.06711	0.371312	0.49407	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.73047	-0.71;-0.32;-0.32	5.04	2.89	0.33648	.	0.120557	0.53938	N	0.000041	T	0.00012	0.0000	N	0.00413	-1.525	0.54753	P	1.6000000000016E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46610	-0.9179	9	0.15066	T	0.55	-6.3523	8.2791	0.31889	0.0:0.6747:0.0:0.3253	rs3865452;rs52828684;rs61182676;rs3865452	174;133	Q96D53;Q96D53-2	ADCK4_HUMAN;.	R	174;133;133	ENSP00000315118:H174R;ENSP00000412839:H133R;ENSP00000243583:H133R	ENSP00000243583:H133R	H	-	2	0	ADCK4	45902896	0.996000	0.38824	0.995000	0.50966	0.293000	0.27360	0.735000	0.26115	0.544000	0.28883	-0.215000	0.12644	CAC	T|0.557;C|0.443	0.443	strong		0.622	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
CCDC180	100499483	hgsc.bcm.edu	37	9	100074446	100074446	+	Silent	SNP	C	C	T	rs3747504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100074446C>T	ENST00000357054.1	+	18	1796	c.861C>T	c.(859-861)atC>atT	p.I287I	CCDC180_ENST00000529487.1_Silent_p.I148I|CCDC180_ENST00000411667.2_Silent_p.I148I|CCDC180_ENST00000395220.1_Silent_p.I287I|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_Silent_p.I148I			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	287						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.I287I(1)									AGAACACCATCGCTGCCCGAG	0.567													C|||	1380	0.275559	0.2965	0.353	5008	,	,		21122	0.2907		0.1869	False		,,,				2504	0.2679				p.I148I		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C444T						PASS	.	C		1188,3218	416.1+/-337.4	155,878,1170	119.0	120.0	119.0		444	-10.4	0.0	9	dbSNP_107	119	1592,7008	299.0+/-304.2	146,1300,2854	no	coding-synonymous	C9orf174	NM_020893.2		301,2178,4024	TT,TC,CC		18.5116,26.9632,21.3748		148/1702	100074446	2780,10226	2203	4300	6503	SO:0001819	synonymous_variant	0	exon4			CACCATCGCTGCC	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.861C>T	9.37:g.100074446C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				C|0.766;T|0.234	0.234	strong		0.567	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
DOPEY2	9980	hgsc.bcm.edu	37	21	37609571	37609571	+	Silent	SNP	T	T	C	rs2835322	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:37609571T>C	ENST00000399151.3	+	16	2719	c.2634T>C	c.(2632-2634)cgT>cgC	p.R878R		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	878					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GGGTGGCTCGTGTGCTTTGGA	0.592													T|||	2203	0.439896	0.2882	0.5072	5008	,	,		18081	0.4276		0.5447	False		,,,				2504	0.502				p.R878R		Atlas-SNP	.											DOPEY2,right_upper_lobe,carcinoma,+1,1	DOPEY2	184	1	0			c.T2634C						scavenged	.	T		1585,2821	495.8+/-363.4	271,1043,889	94.0	80.0	85.0		2634	-4.1	1.0	21	dbSNP_100	85	4583,4017	596.7+/-393.6	1253,2077,970	no	coding-synonymous	DOPEY2	NM_005128.2		1524,3120,1859	CC,CT,TT		46.7093,35.9737,47.4243		878/2299	37609571	6168,6838	2203	4300	6503	SO:0001819	synonymous_variant	9980	exon16			GGCTCGTGTGCTT	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.2634T>C	21.37:g.37609571T>C		Somatic	110	2	0.0181818		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	37	CCDS13643.1																																																																																			C|0.464;N|0.001	0.464	strong		0.592	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
WFIKKN1	117166	hgsc.bcm.edu	37	16	681280	681280	+	Silent	SNP	G	G	T	rs4984905	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:681280G>T	ENST00000319070.2	+	1	349	c.27G>T	c.(25-27)ccG>ccT	p.P9P		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	9					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Hepatocellular(780;0.00335)				CACTCCTGCCGCTCCTGCTCC	0.741													g|||	1569	0.313299	0.0825	0.3833	5008	,	,		10832	0.62		0.2485	False		,,,				2504	0.3262				p.P9P		Atlas-SNP	.											.	WFIKKN1	30	.	0			c.G27T						PASS	.			455,3849		22,411,1719	9.0	10.0	10.0		27	-3.1	0.0	16	dbSNP_111	10	1798,6714		183,1432,2641	no	coding-synonymous	WFIKKN1	NM_053284.2		205,1843,4360	TT,TG,GG		21.1231,10.5716,17.5796		9/549	681280	2253,10563	2152	4256	6408	SO:0001819	synonymous_variant	117166	exon1			CCTGCCGCTCCTG	AK075356	CCDS10414.1	16p13	2013-01-21			ENSG00000127578	ENSG00000127578		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30912	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20A"""	608021	"""chromosome 16 open reading frame 12"""	C16orf12		11274388, 11928817	Standard	NM_053284		Approved	RJD2, WFIKKN, WFDC20A	uc002cht.1	Q96NZ8	OTTHUMG00000090359	ENST00000319070.2:c.27G>T	16.37:g.681280G>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	17	13	0.764706	NM_053284	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																			G|0.669;T|0.331	0.331	strong		0.741	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284	
CHRDL1	91851	hgsc.bcm.edu	37	X	109931856	109931856	+	Silent	SNP	T	T	C	rs5943053	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:109931856T>C	ENST00000372045.1	-	9	1064	c.933A>G	c.(931-933)aaA>aaG	p.K311K	CHRDL1_ENST00000434224.1_Silent_p.K238K|CHRDL1_ENST00000394797.4_Silent_p.K317K|CHRDL1_ENST00000372042.1_Silent_p.K318K|CHRDL1_ENST00000444321.2_Silent_p.K317K|CHRDL1_ENST00000482160.1_Silent_p.K238K|CHRDL1_ENST00000218054.4_Silent_p.K317K			Q9BU40	CRDL1_HUMAN	chordin-like 1	311	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						CCTTGCAGCATTTTCCGTCTA	0.433													c|||	1464	0.387815	0.6339	0.2003	3775	,	,		12311	0.0079		0.3211	False		,,,				2504	0.1595				p.K318K		Atlas-SNP	.											.	CHRDL1	78	.	0			c.A954G						PASS	.		,,,	3008,827		998,560,452,74,119	187.0	173.0	178.0		954,951,714,951	2.1	1.0	X	dbSNP_114	178	2670,4058		395,1166,714,867,1158	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CHRDL1	NM_001143981.1,NM_001143982.1,NM_001143983.2,NM_145234.3	,,,	1393,1726,1166,941,1277	CC,CT,C,TT,T		39.6849,21.5645,46.2463	,,,	318/459,317/458,238/379,317/457	109931856	5678,4885	2203	4300	6503	SO:0001819	synonymous_variant	91851	exon9			GCAGCATTTTCCG	AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"""megalocornea 1 (X-linked)"""	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.933A>G	X.37:g.109931856T>C		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_001143981	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Silent	SNP	ENST00000372045.1	37																																																																																				C|0.491;G|0.000;T|0.508	0.491	strong		0.433	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234	
F2RL3	9002	hgsc.bcm.edu	37	19	17004049	17004049	+	IGR	SNP	T	T	C	rs1054533	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:17004049T>C	ENST00000248076.3	+	0	3473				CPAMD8_ENST00000443236.1_Missense_Mutation_p.Q1890R|CPAMD8_ENST00000597335.1_5'Flank	NM_003950.2	NP_003941.2	Q96RI0	PAR4_HUMAN	coagulation factor II (thrombin) receptor-like 3						blood coagulation (GO:0007596)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			cervix(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						ACTATGTCTCTGAGGGGCCGG	0.662													C|||	1059	0.211462	0.0961	0.2968	5008	,	,		15498	0.126		0.333	False		,,,				2504	0.2699				p.Q1890R		Atlas-SNP	.											.	CPAMD8	192	.	0			c.A5669G						PASS	.	C	ARG/GLN	493,3217		31,431,1393	16.0	17.0	16.0		5669	-1.7	0.0	19	dbSNP_86	16	2683,5451		476,1731,1860	yes	missense	CPAMD8	NM_015692.2	43	507,2162,3253	CC,CT,TT		32.985,13.2884,26.8153	benign	1890/1933	17004049	3176,8668	1855	4067	5922	SO:0001628	intergenic_variant	27151	exon42			TGTCTCTGAGGGG	AF055917	CCDS12350.1	19p12	2012-08-08						"""GPCR / Class A : Protease activated receptors"""	3540	protein-coding gene	gene with protein product	"""proteinase-activated receptor-4"""	602779				9618465	Standard	XM_005260139		Approved	PAR4	uc002nfa.3	Q96RI0			19.37:g.17004049T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	48	0.55814	NM_015692	O76067|Q6DK42	Missense_Mutation	SNP	ENST00000248076.3	37	CCDS12350.1	493|493	0.22573260073260074|0.22573260073260074	56|56	0.11382113821138211|0.11382113821138211	111|111	0.30662983425414364|0.30662983425414364	81|81	0.14160839160839161|0.14160839160839161	245|245	0.3232189973614776|0.3232189973614776	C|C	1.789|1.789	-0.479931|-0.479931	0.04383|0.04383	0.132884|0.132884	0.32985|0.32985	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|T	.|0.34859	.|1.34	0.871|0.871	-1.74|-1.74	0.08056|0.08056	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.58432|0.58432	P|P	4.000000000004E-6|4.000000000004E-6	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.43180|0.43180	-0.9407|-0.9407	7|5	0.07030|.	T|.	0.85|.	.|.	6.3721|6.3721	0.21487|0.21487	0.0:0.2314:0.0:0.7686|0.0:0.2314:0.0:0.7686	rs1054533;rs3195070;rs3745323;rs60433400;rs1054533|rs1054533;rs3195070;rs3745323;rs60433400;rs1054533	1843|.	Q8IZJ3|.	CPMD8_HUMAN|.	R|G	1890|1901	.|ENSP00000402505:R1901G	ENSP00000291440:Q1890R|.	Q|R	-|-	2|1	0|2	CPAMD8|CPAMD8	16865049|16865049	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.459000|-2.459000	0.01000|0.01000	-2.277000|-2.277000	0.00677|0.00677	-2.753000|-2.753000	0.00124|0.00124	CAG|AGA	T|0.770;C|0.230	0.230	strong		0.662	F2RL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462875.1		
PCDHGA2	56113	hgsc.bcm.edu	37	5	140719090	140719090	+	Silent	SNP	G	G	A	rs6861047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140719090G>A	ENST00000394576.2	+	1	552	c.552G>A	c.(550-552)agG>agA	p.R184R	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	184	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGTGCGAAGGGGAGCTGATG	0.562													N|||	533	0.10643	0.0809	0.1124	5008	,	,		19274	0.0605		0.174	False		,,,				2504	0.1145				p.R184R		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.G552A						PASS	.	C	,,	416,3990		18,380,1805	92.0	89.0	90.0		,552,552	-0.5	0.0	5	dbSNP_116	90	1365,7235		97,1171,3032	no	intron,coding-synonymous,coding-synonymous	PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_032009.1	,,	115,1551,4837	AA,AG,GG		15.8721,9.4417,13.6937	,,	,184/933,184/824	140719090	1781,11225	2203	4300	6503	SO:0001819	synonymous_variant	56113	exon1			GCGAAGGGGAGCT	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.552G>A	5.37:g.140719090G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	30	0.326087	NM_018915	Q52LL6|Q9Y5D5	Silent	SNP	ENST00000394576.2	37	CCDS47289.1																																																																																			G|0.884;A|0.116	0.116	strong		0.562	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133670073	133670073	+	Silent	SNP	T	T	C	rs6767412	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:133670073T>C	ENST00000310926.4	-	6	1113	c.840A>G	c.(838-840)cgA>cgG	p.R280R	SLCO2A1_ENST00000493729.1_Silent_p.R204R	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	280					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)	p.R280R(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	TGGGCATTGCTCGAGGGAAGA	0.488													T|||	1274	0.254393	0.3215	0.2421	5008	,	,		19409	0.2827		0.1909	False		,,,				2504	0.2086				p.R280R		Atlas-SNP	.											SLCO2A1,NS,carcinoma,0,1	SLCO2A1	72	1	1	Substitution - coding silent(1)	stomach(1)	c.A840G						PASS	.	T		1395,3011	456.5+/-351.3	220,955,1028	87.0	96.0	93.0		840	1.0	0.0	3	dbSNP_116	93	1627,6973	300.6+/-305.0	154,1319,2827	no	coding-synonymous	SLCO2A1	NM_005630.2		374,2274,3855	CC,CT,TT		18.9186,31.6614,23.2354		280/644	133670073	3022,9984	2203	4300	6503	SO:0001819	synonymous_variant	6578	exon6			CATTGCTCGAGGG		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.840A>G	3.37:g.133670073T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	37	CCDS3084.1																																																																																			T|0.773;C|0.227	0.227	strong		0.488	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
DPCR1	135656	hgsc.bcm.edu	37	6	30919391	30919391	+	Silent	SNP	G	G	A	rs3094086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30919391G>A	ENST00000462446.1	+	2	3178	c.3150G>A	c.(3148-3150)tcG>tcA	p.S1050S	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	0						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TGACCCCATCGGCCAATGAGA	0.488													a|||	193	0.0385383	0.0386	0.0288	5008	,	,		26019	0.0159		0.0964	False		,,,				2504	0.0092				p.S1050S		Atlas-SNP	.											.	DPCR1	99	.	0			c.G3150A						PASS	.	G		98,1286		2,94,596	194.0	172.0	179.0		3150	-6.0	0.0	6	dbSNP_103	179	431,2751		28,375,1188	no	coding-synonymous	DPCR1	NM_080870.3		30,469,1784	AA,AG,GG		13.5449,7.0809,11.5856		1050/1394	30919391	529,4037	692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			CCCATCGGCCAAT	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3150G>A	6.37:g.30919391G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	194	77	0.396907	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	37	CCDS4692.2																																																																																			G|0.932;A|0.068	0.068	strong		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
PKD1L2	114780	hgsc.bcm.edu	37	16	81241100	81241100	+	RNA	SNP	G	G	C	rs386792899|rs11150370	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81241100G>C	ENST00000525539.1	-	0	900				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TACCTCGGCGGGTTGTAGGGA	0.453													G|||	2372	0.473642	0.177	0.4784	5008	,	,		18125	0.8661		0.4384	False		,,,				2504	0.5031				p.P301A		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C901G						PASS	.	G	ALA/PRO,ALA/PRO	788,3012		102,584,1214	97.0	96.0	96.0		901,901	4.9	1.0	16	dbSNP_120	96	3522,4718		826,1870,1424	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	27,27	928,2454,2638	CC,CG,GG		42.7427,20.7368,35.7973	probably-damaging,probably-damaging	301/992,301/2460	81241100	4310,7730	1900	4120	6020			114780	exon5			TCGGCGGGTTGTA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81241100G>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	53	32	0.603774	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1108	0.5073260073260073	107	0.21747967479674796	172	0.47513812154696133	482	0.8426573426573427	347	0.4577836411609499	G	15.13	2.741991	0.49151	0.207368	0.427427	ENSG00000166473	ENST00000337114	T	0.66280	-0.2	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.33489	P	0.411547	P;D	0.89917	0.951;1.0	P;D	0.72338	0.639;0.977	T	0.36432	-0.9748	8	0.62326	D	0.03	-15.1939	18.1543	0.89686	0.0:0.0:1.0:0.0	rs11150370;rs11150370	301;301	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	A	301	ENSP00000337397:P301A	ENSP00000337397:P301A	P	-	1	0	PKD1L2	79798601	1.000000	0.71417	0.976000	0.42696	0.032000	0.12392	6.049000	0.71053	2.277000	0.76020	0.563000	0.77884	CCG	G|0.506;C|0.494	0.494	strong		0.453	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
DNAH14	127602	hgsc.bcm.edu	37	1	225328440	225328440	+	Intron	SNP	T	T	G	rs75827633|rs138066581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:225328440T>G	ENST00000445597.2	+	17	3051				DNAH14_ENST00000439375.2_Missense_Mutation_p.Y1392D|DNAH14_ENST00000430092.1_Missense_Mutation_p.Y1392D			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.Y1392D(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TAGAGAGAGATATATATATAA	0.239													T|||	321	0.0640974	0.1384	0.0418	5008	,	,		13956	0.0		0.0696	False		,,,				2504	0.0399				p.Y1392D		Atlas-SNP	.											DNAH14_ENST00000430092,NS,carcinoma,0,1	DNAH14	300	1	1	Substitution - Missense(1)	endometrium(1)	c.T4174G						PASS	.						9.0	7.0	8.0					1																	225328440		688	1555	2243	SO:0001627	intron_variant	127602	exon27			GAGAGATATATAT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.3052-30T>G	1.37:g.225328440T>G		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		132	0.06043956043956044	55	0.11178861788617886	18	0.049723756906077346	4	0.006993006993006993	55	0.07255936675461741	T	10.21	1.288261	0.23478	.	.	ENSG00000185842	ENST00000430092;ENST00000439375	T;T	0.31247	1.5;1.5	5.29	-3.14	0.05250	.	.	.	.	.	T	0.00815	0.0027	M	0.93720	3.45	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30995	-0.9959	8	0.54805	T	0.06	.	6.4099	0.21686	0.0:0.1916:0.3392:0.4692	.	1392	Q0VDD8-4	.	D	1392	ENSP00000414402:Y1392D;ENSP00000392061:Y1392D	ENSP00000414402:Y1392D	Y	+	1	0	DNAH14	223395063	0.001000	0.12720	0.000000	0.03702	0.017000	0.09413	0.655000	0.24933	-0.306000	0.08818	0.491000	0.48974	TAT	T|0.939;G|0.061	0.061	strong		0.239	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
LAMA2	3908	hgsc.bcm.edu	37	6	129807714	129807714	+	Silent	SNP	G	G	A	rs2229850	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:129807714G>A	ENST00000421865.2	+	56	7894	c.7845G>A	c.(7843-7845)ccG>ccA	p.P2615P		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2615	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GACCAGAGCCGAATCTGTTTC	0.438													G|||	2022	0.403754	0.5877	0.3646	5008	,	,		19969	0.3631		0.2565	False		,,,				2504	0.3763				p.P2615P		Atlas-SNP	.											.	LAMA2	481	.	0			c.G7845A						PASS	.	G	,	2311,2095	604.3+/-390.3	620,1071,512	114.0	94.0	101.0		7845,7833	-4.0	0.6	6	dbSNP_98	101	2140,6460	367.3+/-334.7	275,1590,2435	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	895,2661,2947	AA,AG,GG		24.8837,47.5488,34.2227	,	2615/3123,2611/3119	129807714	4451,8555	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon56			AGAGCCGAATCTG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.7845G>A	6.37:g.129807714G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	57	0.398601	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			A|0.356;G|0.644;T|0.000	0.356	strong		0.438	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
ALOX15B	247	hgsc.bcm.edu	37	17	7950377	7950377	+	Silent	SNP	C	C	T	rs11541083	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7950377C>T	ENST00000380183.4	+	10	1579	c.1440C>T	c.(1438-1440)atC>atT	p.I480I	ALOX15B_ENST00000572022.1_Silent_p.I480I|ALOX15B_ENST00000380173.2_Silent_p.I451I|ALOX15B_ENST00000573359.1_Silent_p.I451I	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	480	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GGATGCAGATCTGGGGTGCAG	0.602													C|||	1244	0.248403	0.0711	0.4294	5008	,	,		18794	0.2192		0.3598	False		,,,				2504	0.2751				p.I480I		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C1440T						PASS	.	C	,,	519,3887	238.4+/-249.8	41,437,1725	70.0	69.0	69.0		1353,1353,1440	1.2	1.0	17	dbSNP_120	69	2916,5684	454.5+/-363.5	507,1902,1891	no	coding-synonymous,coding-synonymous,coding-synonymous	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	,,	548,2339,3616	TT,TC,CC		33.907,11.7794,26.4109	,,	451/648,451/603,480/677	7950377	3435,9571	2203	4300	6503	SO:0001819	synonymous_variant	247	exon10			GCAGATCTGGGGT	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1440C>T	17.37:g.7950377C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Silent	SNP	ENST00000380183.4	37	CCDS11128.1																																																																																			C|0.735;T|0.265	0.265	strong		0.602	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
PRKCA	5578	hgsc.bcm.edu	37	17	64685078	64685078	+	Silent	SNP	G	G	A	rs2227857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:64685078G>A	ENST00000413366.3	+	8	857	c.831G>A	c.(829-831)ttG>ttA	p.L277L		NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	277					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	GGTACAAGTTGCTTAACCAAG	0.478													G|||	1150	0.229633	0.0908	0.3473	5008	,	,		17492	0.1081		0.3658	False		,,,				2504	0.319				p.L277L		Atlas-SNP	.											.	PRKCA	82	.	0			c.G831A						PASS	.	G		599,3807	260.1+/-263.5	50,499,1654	89.0	70.0	76.0		831	4.5	1.0	17	dbSNP_98	76	3146,5454	475.0+/-369.0	559,2028,1713	no	coding-synonymous	PRKCA	NM_002737.2		609,2527,3367	AA,AG,GG		36.5814,13.5951,28.7944		277/673	64685078	3745,9261	2203	4300	6503	SO:0001819	synonymous_variant	5578	exon8			CAAGTTGCTTAAC		CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.831G>A	17.37:g.64685078G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_002737	B5BU22|Q15137|Q32M72|Q96RE4	Silent	SNP	ENST00000413366.3	37	CCDS11664.1																																																																																			G|0.741;A|0.259	0.259	strong		0.478	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1		
TMCC2	9911	hgsc.bcm.edu	37	1	205238275	205238275	+	Silent	SNP	A	A	G	rs1768586	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205238275A>G	ENST00000358024.3	+	3	1334	c.945A>G	c.(943-945)gcA>gcG	p.A315A	TMCC2_ENST00000330675.7_Silent_p.A90A|TMCC2_ENST00000545499.1_Silent_p.A237A|TMCC2_ENST00000329800.7_Silent_p.A75A|TMCC2_ENST00000495538.1_3'UTR	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	315						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			ACAATGTGGCAGAGTATCTGA	0.562													a|||	750	0.14976	0.1036	0.1902	5008	,	,		18858	0.0516		0.3549	False		,,,				2504	0.0736				p.A315A		Atlas-SNP	.											.	TMCC2	89	.	0			c.A945G						PASS	.	G	,	655,3751	280.2+/-275.2	54,547,1602	76.0	62.0	67.0		711,945	-11.4	0.0	1	dbSNP_89	67	3051,5549	469.6+/-367.6	543,1965,1792	no	coding-synonymous,coding-synonymous	TMCC2	NM_001242925.1,NM_014858.3	,	597,2512,3394	GG,GA,AA		35.4767,14.8661,28.4945	,	237/632,315/710	205238275	3706,9300	2203	4300	6503	SO:0001819	synonymous_variant	9911	exon3			TGTGGCAGAGTAT	AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"""Transmembrane and coiled-coil domain containing"""	24239	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 2"""			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.945A>G	1.37:g.205238275A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	183	183	1	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Silent	SNP	ENST00000358024.3	37	CCDS30984.1																																																																																			A|0.748;G|0.252	0.252	strong		0.562	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858	
C14orf37	145407	hgsc.bcm.edu	37	14	58604730	58604730	+	Silent	SNP	T	T	C	rs137871178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:58604730T>C	ENST00000267485.7	-	2	1541	c.1347A>G	c.(1345-1347)caA>caG	p.Q449Q	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	449						integral component of membrane (GO:0016021)		p.Q449Q(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TTCCCAACAGTTGGTCTGCCT	0.343													T|||	22	0.00439297	0.0	0.0043	5008	,	,		18899	0.001		0.0109	False		,,,				2504	0.0072				p.Q449Q		Atlas-SNP	.											C14orf37,NS,carcinoma,0,1	C14orf37	87	1	1	Substitution - coding silent(1)	pancreas(1)	c.A1347G						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	71.0	73.0	73.0		1347	-7.0	0.0	14	dbSNP_134	73	101,8499	54.8+/-115.7	1,99,4200	no	coding-synonymous	C14orf37	NM_001001872.2		1,102,6400	CC,CT,TT		1.1744,0.0681,0.7996		449/775	58604730	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	145407	exon2			CAACAGTTGGTCT		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1347A>G	14.37:g.58604730T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																			T|0.992;C|0.008	0.008	strong		0.343	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
MAD1L1	8379	hgsc.bcm.edu	37	7	1976457	1976457	+	Missense_Mutation	SNP	C	C	T	rs1801368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:1976457C>T	ENST00000406869.1	-	17	2230	c.1673G>A	c.(1672-1674)cGc>cAc	p.R558H	MAD1L1_ENST00000265854.7_Missense_Mutation_p.R558H|MAD1L1_ENST00000399654.2_Missense_Mutation_p.R558H|MAD1L1_ENST00000402746.1_Missense_Mutation_p.R466H			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	558			R -> H (in a cancer cell line; dbSNP:rs1801368). {ECO:0000269|PubMed:10366450, ECO:0000269|PubMed:10597320, ECO:0000269|PubMed:11423979}.		mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GTGGTCCTCGCGCAGGCGCTG	0.667													C|||	1526	0.304712	0.0295	0.4366	5008	,	,		17568	0.4454		0.3877	False		,,,				2504	0.3528				p.R558H		Atlas-SNP	.											.	MAD1L1	81	.	0			c.G1673A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	398,3902		30,338,1782	21.0	27.0	25.0		1673,1673,1673	0.0	0.0	7	dbSNP_89	25	3114,5360		559,1996,1682	yes	missense,missense,missense	MAD1L1	NM_001013836.1,NM_001013837.1,NM_003550.2	29,29,29	589,2334,3464	TT,TC,CC		36.7477,9.2558,27.4933	benign,benign,benign	558/719,558/719,558/719	1976457	3512,9262	2150	4237	6387	SO:0001583	missense	8379	exon17			TCCTCGCGCAGGC	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"""MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"""			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.1673G>A	7.37:g.1976457C>T	ENSP00000385334:p.Arg558His	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_003550	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	37	CCDS43539.1	712	0.326007326007326	17	0.034552845528455285	157	0.43370165745856354	251	0.4388111888111888	287	0.3786279683377309	C	10.34	1.322527	0.23994	0.092558	0.367477	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235;ENST00000437877	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01	4.77	-0.00151	0.14034	.	0.592432	0.18541	N	0.138191	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B;B;B	0.11235	0.003;0.004;0.003	B;B;B	0.06405	0.002;0.001;0.001	T	0.47661	-0.9100	9	0.45353	T	0.12	-4.9239	8.2117	0.31488	0.0:0.5493:0.0:0.4507	rs1801368;rs2280551;rs11557346;rs61400777	557;466;558	A4D218;B3KR41;Q9Y6D9	.;.;MD1L1_HUMAN	H	466;558;558;109;558;109;14	ENSP00000384155:R466H;ENSP00000382562:R558H;ENSP00000385334:R558H;ENSP00000265854:R558H;ENSP00000394886:R109H;ENSP00000394069:R14H	ENSP00000265854:R558H	R	-	2	0	MAD1L1	1942983	0.000000	0.05858	0.002000	0.10522	0.579000	0.36224	-0.301000	0.08232	0.085000	0.17107	0.555000	0.69702	CGC	T|0.328;G|0.000;C|0.671	0.328	strong		0.667	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
TMC8	147138	hgsc.bcm.edu	37	17	76130576	76130576	+	Silent	SNP	C	C	T	rs149203228		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76130576C>T	ENST00000318430.5	+	8	1292	c.918C>T	c.(916-918)aaC>aaT	p.N306N	TMC6_ENST00000322914.3_5'Flank|TMC8_ENST00000589691.1_Silent_p.N83N	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	306			N -> I (in dbSNP:rs7208422). {ECO:0000269|Ref.3}.		ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)	p.N306N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			ACGTACTCAACGGGCTCCTGG	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		17681	0.0		0.001	False		,,,				2504	0.0				p.N306N		Atlas-SNP	.											TMC8,NS,carcinoma,0,1	TMC8	44	1	1	Substitution - coding silent(1)	lung(1)	c.C918T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	51.0	56.0	54.0		918	-6.5	0.5	17	dbSNP_134	54	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	TMC8	NM_152468.4		0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153		306/727	76130576	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	147138	exon8			ACTCAACGGGCTC	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"""epidermodysplasia verruciformis 2"""	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.918C>T	17.37:g.76130576C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	37	CCDS32749.1																																																																																			C|0.998;T|0.002	0.002	strong		0.612	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3		
TTN	7273	hgsc.bcm.edu	37	2	179432185	179432185	+	Missense_Mutation	SNP	A	A	G	rs12463674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179432185A>G	ENST00000591111.1	-	276	73975	c.73751T>C	c.(73750-73752)aTt>aCt	p.I24584T	TTN_ENST00000589042.1_Missense_Mutation_p.I26225T|TTN_ENST00000342175.6_Missense_Mutation_p.I17352T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I17285T|TTN_ENST00000342992.6_Missense_Mutation_p.I23657T|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I17160T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000438095.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24584	Ig-like 122.		I -> T. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAACCACTCAATGGTAGGTAG	0.368													A|||	651	0.129992	0.0053	0.1124	5008	,	,		22267	0.0427		0.3091	False		,,,				2504	0.2168				p.I26225T		Atlas-SNP	.											.	TTN	18412	.	0			c.T78674C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE	200,3480		5,190,1645	102.0	98.0	99.0		51479,70970,51854,52055	5.7	1.0	2	dbSNP_120	99	2480,5706		365,1750,1978	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	89,89,89,89	370,1940,3623	GG,GA,AA		30.2956,5.4348,22.5855	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	17160/26927,23657/33424,17285/27052,17352/27119	179432185	2680,9186	1840	4093	5933	SO:0001583	missense	7273	exon326			CACTCAATGGTAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.73751T>C	2.37:g.179432185A>G	ENSP00000465570:p.Ile24584Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	111	47	0.423423	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		332	0.152014652014652	7	0.014227642276422764	56	0.15469613259668508	25	0.043706293706293704	244	0.32189973614775724	A	15.58	2.875811	0.51695	0.054348	0.302956	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	5.65	5.65	0.86999	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.76574	2.34	0.20307	P	0.9999138412	P;P;P;P	0.43231	0.801;0.801;0.801;0.684	B;B;B;B	0.34931	0.192;0.192;0.192;0.138	T	0.04005	-1.0985	8	0.87932	D	0	.	15.874	0.79148	1.0:0.0:0.0:0.0	rs12463674;rs52811439;rs60217524;rs12463674	17160;17285;17352;24584	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	23657;17160;17352;17285;17158	ENSP00000343764:I23657T;ENSP00000434586:I17160T;ENSP00000340554:I17352T;ENSP00000352154:I17285T	ENSP00000340554:I17352T	I	-	2	0	TTN	179140431	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.989000	0.70587	2.140000	0.66376	0.459000	0.35465	ATT	A|0.847;G|0.153	0.153	strong		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
GALT	2592	hgsc.bcm.edu	37	9	34649442	34649442	+	Missense_Mutation	SNP	A	A	G	rs2070074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:34649442A>G	ENST00000378842.3	+	10	982	c.940A>G	c.(940-942)Aac>Gac	p.N314D	GALT_ENST00000450095.2_Missense_Mutation_p.N205D|IL11RA_ENST00000555003.1_5'Flank|GALT_ENST00000488412.2_3'UTR|GALT_ENST00000556278.1_Intron|IL11RA_ENST00000441545.2_5'Flank	NM_000155.3	NP_000146.2	P07902	GALT_HUMAN	galactose-1-phosphate uridylyltransferase	314			N -> D (in Duarte; exists in two different types, D-1 with normal or increased activity and D-2 with an activity reduced to about 35-45% of normal; dbSNP:rs2070074). {ECO:0000269|PubMed:11754113, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18956253, ECO:0000269|PubMed:2011574, ECO:0000269|PubMed:23022339, ECO:0000269|PubMed:7550229, ECO:0000269|Ref.4}.		carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)|UDP-glucose catabolic process (GO:0006258)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	UDP-glucose:hexose-1-phosphate uridylyltransferase activity (GO:0008108)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(2)|lung(5)|upper_aerodigestive_tract(1)	16	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		GGCCAACTGGAACCATTGGCA	0.552									Galactosemia				G|||	365	0.0728834	0.0151	0.0576	5008	,	,		18730	0.0188		0.1024	False		,,,				2504	0.1871				p.N314D		Atlas-SNP	.											.	GALT	29	.	0			c.A940G	GRCh37	CM940804	GALT	M	rs2070074	PASS	.	G	ASP/ASN	127,4279	814.5+/-416.2	1,125,2077	99.0	97.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	940	4.4	1.0	9	dbSNP_96	98	803,7797	782.2+/-407.6	38,727,3535	yes	missense	GALT	NM_000155.2	23	39,852,5612	GG,GA,AA		9.3372,2.8824,7.1505	benign	314/380	34649442	930,12076	2203	4300	6503	SO:0001583	missense	2592	exon10	Familial Cancer Database	Galactose-1-Phosphate Uridyltransferase Deficiency	AACTGGAACCATT	M60091	CCDS6565.1, CCDS59122.1	9p13	2013-01-08			ENSG00000213930	ENSG00000213930	2.7.7.12		4135	protein-coding gene	gene with protein product		606999					Standard	NM_000155		Approved		uc003zve.4	P07902	OTTHUMG00000019836	ENST00000378842.3:c.940A>G	9.37:g.34649442A>G	ENSP00000368119:p.Asn314Asp	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_000155	B4E097|E7ET32|Q14355|Q14356|Q14357|Q14358|Q14359|Q14360|Q14361|Q14363|Q14364|Q14365|Q14369|Q14370|Q14371|Q14372|Q14373|Q14374|Q14375|Q14377|Q14378|Q14380|Q14381|Q14382|Q14383|Q14384|Q14385|Q14386|Q14387|Q14389|Q16766|Q53XK1|Q5VZ81|Q96BY1	Missense_Mutation	SNP	ENST00000378842.3	37	CCDS6565.1	119	0.05448717948717949	8	0.016260162601626018	23	0.06353591160220995	9	0.015734265734265736	79	0.10422163588390501	G	5.939	0.357315	0.11239	0.028824	0.093372	ENSG00000213930	ENST00000450095;ENST00000378842	D;D	0.99089	-5.41;-5.41	5.3	4.4	0.53042	Histidine triad motif (1);Galactose-1-phosphate uridyl transferase, C-terminal (1);Histidine triad-like motif (1);	0.363282	0.26560	N	0.023682	T	0.34164	0.0888	N	0.01454	-0.855	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.75068	-0.3448	10	0.02654	T	1	-8.4461	7.8294	0.29334	0.3139:0.0:0.6861:0.0	rs2070074;rs17845454;rs17858327;rs57246392;rs2070074	205;314	E7ET32;P07902	.;GALT_HUMAN	D	205;314	ENSP00000401956:N205D;ENSP00000368119:N314D	ENSP00000368119:N314D	N	+	1	0	GALT	34639442	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	1.578000	0.36525	1.256000	0.44068	-0.227000	0.12334	AAC	A|0.934;G|0.066	0.066	strong		0.552	GALT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052231.1	NM_000155	
MELK	9833	hgsc.bcm.edu	37	9	36597284	36597284	+	Silent	SNP	C	C	G	rs139481227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:36597284C>G	ENST00000298048.2	+	6	655	c.471C>G	c.(469-471)ccC>ccG	p.P157P	MELK_ENST00000536860.1_Silent_p.P109P|MELK_ENST00000536987.1_Silent_p.P26P|MELK_ENST00000543751.1_Silent_p.P125P|MELK_ENST00000536329.1_Silent_p.P86P|MELK_ENST00000545008.1_Intron|MELK_ENST00000487398.1_3'UTR|MELK_ENST00000538311.1_5'UTR|MELK_ENST00000541717.1_Silent_p.P157P	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	157	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			GTGCAAAACCCAAGGTAAGTG	0.318																																					p.P157P	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.C471G						PASS	.	C		0,4406		0,0,2203	105.0	109.0	108.0		471	1.4	1.0	9	dbSNP_134	108	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	MELK	NM_014791.2		0,6,6497	GG,GC,CC		0.0698,0.0,0.0461		157/652	36597284	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	9833	exon6			AAAACCCAAGGTA	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.471C>G	9.37:g.36597284C>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Silent	SNP	ENST00000298048.2	37	CCDS6606.1																																																																																			C|0.999;G|0.001	0.001	strong		0.318	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791	
CEMIP	57214	hgsc.bcm.edu	37	15	81173354	81173354	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:81173354A>G	ENST00000394685.3	+	6	913	c.494A>G	c.(493-495)aAc>aGc	p.N165S	KIAA1199_ENST00000220244.3_Missense_Mutation_p.N165S|KIAA1199_ENST00000356249.5_Missense_Mutation_p.N165S			Q8WUJ3	CEMIP_HUMAN		165	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						ACATTTCTGAACAAGACCCTT	0.488																																					p.N165S		Atlas-SNP	.											.	KIAA1199	118	.	0			c.A494G						PASS	.						131.0	126.0	128.0					15																	81173354		2203	4300	6503	SO:0001583	missense	57214	exon5			TTCTGAACAAGAC																												ENST00000394685.3:c.494A>G	15.37:g.81173354A>G	ENSP00000378177:p.Asn165Ser	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	187	78	0.417112	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	A	7.211	0.595402	0.13875	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	D;D;D	0.88509	-2.39;-2.39;-2.39	5.95	-0.988	0.10245	G8 domain (2);	0.111999	0.56097	N	0.000025	T	0.79191	0.4404	L	0.46157	1.445	0.41440	D	0.987918	B	0.02656	0.0	B	0.12156	0.007	T	0.61705	-0.7008	10	0.07813	T	0.8	-42.3377	6.5765	0.22569	0.6185:0.1162:0.2653:0.0	.	165	Q8WUJ3	K1199_HUMAN	S	165	ENSP00000220244:N165S;ENSP00000378177:N165S;ENSP00000348583:N165S	ENSP00000220244:N165S	N	+	2	0	KIAA1199	78960409	1.000000	0.71417	0.778000	0.31720	0.594000	0.36715	3.502000	0.53332	-0.411000	0.07530	0.533000	0.62120	AAC	.	.	none		0.488	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
USP25	29761	hgsc.bcm.edu	37	21	17236674	17236674	+	Missense_Mutation	SNP	G	G	C	rs142929561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:17236674G>C	ENST00000285679.6	+	19	2794	c.2425G>C	c.(2425-2427)Gtc>Ctc	p.V809L	USP25_ENST00000400183.2_Missense_Mutation_p.V879L|USP25_ENST00000351097.5_Intron|USP25_ENST00000285681.2_Missense_Mutation_p.V841L	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	809					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		TCATGTAGTGGTCTACTTTAT	0.363													G|||	6	0.00119808	0.0	0.0029	5008	,	,		13115	0.0		0.004	False		,,,				2504	0.0				p.V809L		Atlas-SNP	.											USP25,NS,carcinoma,-1,1	USP25	156	1	0			c.G2425C						PASS	.	G	LEU/VAL	3,4403	6.2+/-15.9	0,3,2200	82.0	78.0	80.0		2425	5.6	1.0	21	dbSNP_134	80	6,8594	5.0+/-18.6	0,6,4294	yes	missense	USP25	NM_013396.3	32	0,9,6494	CC,CG,GG		0.0698,0.0681,0.0692	benign	809/1056	17236674	9,12997	2203	4300	6503	SO:0001583	missense	29761	exon19			GTAGTGGTCTACT	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2425G>C	21.37:g.17236674G>C	ENSP00000285679:p.Val809Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	73	26	0.356164	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	G|G	21.6|21.6	4.175610|4.175610	0.78564|0.78564	6.81E-4|6.81E-4	6.98E-4|6.98E-4	ENSG00000155313|ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183|ENST00000449491	T;T;T|.	0.33438|.	1.54;1.7;1.41|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.053961|.	0.64402|.	D|.	0.000001|.	T|T	0.68183|0.68183	0.2973|0.2973	M|M	0.62723|0.62723	1.935|1.935	0.50813|0.50813	D|D	0.999893|0.999893	D;P;B|.	0.55172|.	0.97;0.83;0.214|.	P;B;B|.	0.53224|.	0.721;0.202;0.055|.	T|T	0.68394|0.68394	-0.5420|-0.5420	10|5	0.72032|.	D|.	0.01|.	.|.	20.0114|20.0114	0.97452|0.97452	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	879;841;809|.	Q9UHP3-3;Q9UHP3-1;Q9UHP3|.	.;.;UBP25_HUMAN|.	L|C	841;809;879|107	ENSP00000285681:V841L;ENSP00000285679:V809L;ENSP00000383044:V879L|.	ENSP00000285679:V809L|.	V|W	+|+	1|3	0|0	USP25|USP25	16158545|16158545	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.987000|0.987000	0.75469|0.75469	6.352000|6.352000	0.73027|0.73027	2.795000|2.795000	0.96236|0.96236	0.655000|0.655000	0.94253|0.94253	GTC|TGG	G|0.999;C|0.001	0.001	strong		0.363	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
THSD1	55901	hgsc.bcm.edu	37	13	52951802	52951802	+	Missense_Mutation	SNP	T	T	C	rs9536041	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:52951802T>C	ENST00000258613.4	-	5	2481	c.2303A>G	c.(2302-2304)aAg>aGg	p.K768R	THSD1_ENST00000544466.1_Missense_Mutation_p.K389R|THSD1_ENST00000349258.4_Missense_Mutation_p.K715R	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	768			K -> R (in dbSNP:rs9536041).		hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		TGAGACACTCTTGTGACTGGG	0.527													t|||	150	0.0299521	0.0174	0.0231	5008	,	,		19167	0.0079		0.0388	False		,,,				2504	0.0654				p.K768R		Atlas-SNP	.											.	THSD1	89	.	0			c.A2303G						PASS	.	T	ARG/LYS,ARG/LYS	119,4287	89.7+/-128.4	0,119,2084	131.0	138.0	136.0		2303,2144	2.7	1.0	13	dbSNP_119	136	438,8162	134.3+/-191.7	12,414,3874	yes	missense,missense	THSD1	NM_018676.3,NM_199263.2	26,26	12,533,5958	CC,CT,TT		5.093,2.7009,4.2826	benign,benign	768/853,715/800	52951802	557,12449	2203	4300	6503	SO:0001583	missense	55901	exon5			ACACTCTTGTGAC	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.2303A>G	13.37:g.52951802T>C	ENSP00000258613:p.Lys768Arg	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	199	100	0.502513	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Missense_Mutation	SNP	ENST00000258613.4	37	CCDS9432.1	53	0.024267399267399268	7	0.014227642276422764	10	0.027624309392265192	7	0.012237762237762238	29	0.03825857519788918	T	2.570	-0.299932	0.05532	0.027009	0.05093	ENSG00000136114	ENST00000349258;ENST00000544466;ENST00000258613	T;T;T	0.26660	2.48;1.72;2.66	5.38	2.66	0.31614	.	0.188222	0.56097	N	0.000029	T	0.00936	0.0031	N	0.01209	-0.955	0.29665	N	0.842941	B;B	0.11235	0.0;0.004	B;B	0.10450	0.002;0.005	T	0.35251	-0.9796	10	0.02654	T	1	-24.553	7.4276	0.27109	0.0:0.5901:0.0:0.4099	rs9536041;rs52807033;rs9536041	715;768	Q9NS62-2;Q9NS62	.;THSD1_HUMAN	R	715;389;768	ENSP00000340650:K715R;ENSP00000438512:K389R;ENSP00000258613:K768R	ENSP00000258613:K768R	K	-	2	0	THSD1	51849803	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.465000	0.35299	0.760000	0.33108	-0.459000	0.05422	AAG	T|0.965;C|0.035	0.035	strong		0.527	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
PPP2R4	5524	hgsc.bcm.edu	37	9	131909736	131909736	+	Missense_Mutation	SNP	C	C	T	rs2480452	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131909736C>T	ENST00000337738.1	+	11	1337	c.1070C>T	c.(1069-1071)tCg>tTg	p.S357L	PPP2R4_ENST00000348141.5_Missense_Mutation_p.S328L|PPP2R4_ENST00000414510.1_Missense_Mutation_p.S60L|PPP2R4_ENST00000432651.1_Missense_Mutation_p.S60L|PPP2R4_ENST00000355007.3_Missense_Mutation_p.S280L|PPP2R4_ENST00000358994.4_Missense_Mutation_p.S322L|PPP2R4_ENST00000357197.4_Missense_Mutation_p.S293L|PPP2R4_ENST00000434095.1_Missense_Mutation_p.S60L|PPP2R4_ENST00000419582.1_Missense_Mutation_p.S60L|PPP2R4_ENST00000423100.1_Missense_Mutation_p.S60L|PPP2R4_ENST00000393370.2_Missense_Mutation_p.S322L|PPP2R4_ENST00000435132.1_Missense_Mutation_p.S60L|PPP2R4_ENST00000347048.4_Missense_Mutation_p.S103L	NM_178001.2	NP_821068.1	Q15257	PTPA_HUMAN	protein phosphatase 2A activator, regulatory subunit 4	357			S -> L (in dbSNP:rs2480452). {ECO:0000269|Ref.6}.	S -> V (in Ref. 1; AA sequence). {ECO:0000305}.	ATP catabolic process (GO:0006200)|mitotic spindle organization in nucleus (GO:0030472)|negative regulation of phosphoprotein phosphatase activity (GO:0032515)|negative regulation of protein dephosphorylation (GO:0035308)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein dephosphorylation (GO:0035307)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of phosphoprotein phosphatase activity (GO:0043666)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	ATP binding (GO:0005524)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein tyrosine phosphatase activator activity (GO:0008160)|receptor binding (GO:0005102)			breast(3)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CCTGTCACGTCGGGCTAGGAG	0.637													C|||	397	0.0792732	0.0015	0.0375	5008	,	,		14335	0.1855		0.0666	False		,,,				2504	0.1176				p.S357L	Colon(158;2158 2504 4450 20433)	Atlas-SNP	.											.	PPP2R4	32	.	0			c.C1070T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	87,4319	72.0+/-110.0	2,83,2118	59.0	47.0	51.0		860,965,965,1070,839	4.3	0.0	9	dbSNP_100	51	637,7963	162.7+/-215.4	27,583,3690	yes	missense,missense,missense,missense,missense	PPP2R4	NM_001193397.1,NM_021131.4,NM_178000.2,NM_178001.2,NM_178003.2	145,145,145,145,145	29,666,5808	TT,TC,CC		7.407,1.9746,5.5667	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	287/289,322/324,322/324,357/359,280/282	131909736	724,12282	2203	4300	6503	SO:0001583	missense	5524	exon11			TCACGTCGGGCTA	X73478	CCDS6920.1, CCDS65156.1, CCDS75917.1	9q34	2010-06-18	2007-01-22		ENSG00000119383	ENSG00000119383		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9308	protein-coding gene	gene with protein product	"""phosphotyrosyl phosphatase activator"", ""PP2A phosphatase activator"""	600756	"""protein phosphatase 2A, regulatory subunit B' (PR 53)"""			8530035	Standard	NM_021131		Approved	PTPA, PR53	uc004bxm.2	Q15257	OTTHUMG00000020774	ENST00000337738.1:c.1070C>T	9.37:g.131909736C>T	ENSP00000337448:p.Ser357Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_178001	A2A347|A9IZU4|B4DXM4|Q15258|Q53GZ3|Q5TZQ2|Q9BUK1|Q9NNZ7|Q9NNZ8|Q9NNZ9	Missense_Mutation	SNP	ENST00000337738.1	37		176	0.08058608058608059	2	0.0040650406504065045	17	0.04696132596685083	110	0.19230769230769232	47	0.06200527704485488	C	36	5.642491	0.96704	0.019746	0.07407	ENSG00000119383	ENST00000358994;ENST00000393370;ENST00000337738;ENST00000348141;ENST00000347048;ENST00000357197;ENST00000355007;ENST00000423100;ENST00000414510;ENST00000419582;ENST00000432651;ENST00000435132;ENST00000434095	T;T;T;T;T;T;T;T;T;T;T;T;T	0.45276	1.94;1.94;1.91;1.93;1.49;1.94;1.93;0.9;0.9;0.9;0.9;0.9;0.9	5.16	4.26	0.50523	.	0.276731	0.36409	N	0.002607	T	0.00109	0.0003	M	0.63843	1.955	0.09310	P	1.0	D;P;D;D;P	0.64830	0.993;0.923;0.994;0.994;0.942	P;P;P;P;B	0.55965	0.686;0.452;0.668;0.788;0.208	T	0.03910	-1.0993	9	0.62326	D	0.03	.	12.7509	0.57308	0.0:0.9205:0.0:0.0795	rs2480452;rs3739844;rs17455922;rs17481867;rs61179358;rs2480452	293;103;280;357;322	Q15257-3;Q68CR8;Q15257-4;Q15257;Q15257-2	.;.;.;PTPA_HUMAN;.	L	322;322;357;328;103;293;280;60;60;60;60;60;60	ENSP00000351885:S322L;ENSP00000377036:S322L;ENSP00000337448:S357L;ENSP00000335200:S328L;ENSP00000337412:S103L;ENSP00000349726:S293L;ENSP00000347109:S280L;ENSP00000408316:S60L;ENSP00000408726:S60L;ENSP00000394001:S60L;ENSP00000416661:S60L;ENSP00000387726:S60L;ENSP00000411604:S60L	ENSP00000337448:S357L	S	+	2	0	PPP2R4	130949557	0.959000	0.32827	0.013000	0.15412	0.788000	0.44548	4.088000	0.57678	1.168000	0.42723	0.561000	0.74099	TCG	C|0.931;T|0.069	0.069	strong		0.637	PPP2R4-201	KNOWN	basic	protein_coding	protein_coding		NM_021131	
MUC2	4583	hgsc.bcm.edu	37	11	1075747	1075747	+	Missense_Mutation	SNP	T	T	C	rs2856111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1075747T>C	ENST00000441003.2	+	2	200	c.173T>C	c.(172-174)cTc>cCc	p.L58P	MUC2_ENST00000359061.5_Missense_Mutation_p.L58P	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	58	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.		L -> P (in dbSNP:rs2856111).		cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TTCCCCGGCCTCTGCGACTAC	0.647													T|||	1359	0.271366	0.4062	0.1052	5008	,	,		16777	0.4375		0.1362	False		,,,				2504	0.1748				p.L58P		Atlas-SNP	.											.	MUC2	614	.	0			c.T173C						PASS	.	T	PRO/LEU	1396,2748		255,886,931	24.0	29.0	27.0		173	3.9	1.0	11	dbSNP_100	27	1082,7336		79,924,3206	yes	missense	MUC2	NM_002457.2	98	334,1810,4137	CC,CT,TT		12.8534,33.6873,19.7262	probably-damaging	58/2813	1075747	2478,10084	2072	4209	6281	SO:0001583	missense	4583	exon2			CCGGCCTCTGCGA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.173T>C	11.37:g.1075747T>C	ENSP00000415183:p.Leu58Pro	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	141	58	0.411348	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		589	0.2696886446886447	214	0.4349593495934959	33	0.09116022099447514	237	0.4143356643356643	105	0.13852242744063326	T	11.43	1.637716	0.29157	0.336873	0.128534	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.58210	0.35;0.35	3.94	3.94	0.45596	.	0.806126	0.10627	U	0.652652	T	0.00012	0.0000	M	0.78456	2.415	0.22199	P	0.999297546	D	0.69078	0.997	D	0.75484	0.986	T	0.31447	-0.9943	9	0.46703	T	0.11	.	12.7996	0.57578	0.0:0.0:0.0:1.0	rs2856111;rs60177945;rs2856111	58	E7EUV1	.	P	58	ENSP00000415183:L58P;ENSP00000351956:L58P	ENSP00000351956:L58P	L	+	2	0	MUC2	1065747	0.013000	0.17824	0.998000	0.56505	0.622000	0.37654	1.613000	0.36900	1.429000	0.47314	0.459000	0.35465	CTC	T|0.739;C|0.261	0.261	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FLNC	2318	hgsc.bcm.edu	37	7	128477547	128477547	+	Silent	SNP	T	T	C	rs2291561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128477547T>C	ENST00000325888.8	+	4	1056	c.795T>C	c.(793-795)ggT>ggC	p.G265G	FLNC_ENST00000346177.6_Silent_p.G265G	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	265					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCAAACCTGGTGCCCCTGTTC	0.597													C|||	606	0.121006	0.1218	0.062	5008	,	,		14951	0.121		0.1093	False		,,,				2504	0.1738				p.G265G		Atlas-SNP	.											FLNC,NS,carcinoma,0,1	FLNC	339	1	0			c.T795C						scavenged	.	C	,	529,3827	714.4+/-408.4	36,457,1685	133.0	144.0	141.0		795,795	-5.9	0.9	7	dbSNP_100	141	952,7638	757.3+/-407.5	49,854,3392	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	85,1311,5077	CC,CT,TT		11.0827,12.1442,11.4398	,	265/2693,265/2726	128477547	1481,11465	2178	4295	6473	SO:0001819	synonymous_variant	2318	exon4			ACCTGGTGCCCCT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.795T>C	7.37:g.128477547T>C		Somatic	71	2	0.028169		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			T|0.881;C|0.119	0.119	strong		0.597	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
ZNF618	114991	hgsc.bcm.edu	37	9	116770785	116770785	+	Silent	SNP	G	G	A	rs3748182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:116770785G>A	ENST00000374126.5	+	9	804	c.705G>A	c.(703-705)acG>acA	p.T235T	ZNF618_ENST00000288466.7_Silent_p.T203T			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	235					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						TCGTGGCCACGGACGAGGTGA	0.672													G|||	1522	0.303914	0.062	0.2565	5008	,	,		17362	0.5962		0.3439	False		,,,				2504	0.3221				p.T203T		Atlas-SNP	.											.	ZNF618	184	.	0			c.G609A						PASS	.	G		422,3470		25,372,1549	47.0	55.0	53.0		609	-4.4	1.0	9	dbSNP_107	53	2692,5546		451,1790,1878	no	coding-synonymous	ZNF618	NM_133374.2		476,2162,3427	AA,AG,GG		32.6778,10.8428,25.6719		203/862	116770785	3114,9016	1946	4119	6065	SO:0001819	synonymous_variant	114991	exon8			GGCCACGGACGAG	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.705G>A	9.37:g.116770785G>A		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				G|0.655;A|0.345	0.345	strong		0.672	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
RMDN1	51115	hgsc.bcm.edu	37	8	87497176	87497176	+	Silent	SNP	G	G	A	rs11539113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:87497176G>A	ENST00000406452.3	-	5	669	c.510C>T	c.(508-510)tgC>tgT	p.C170C	RMDN1_ENST00000523911.1_Silent_p.C126C|RMDN1_ENST00000519966.1_Intron|RMDN1_ENST00000430676.2_Intron|CPNE3_ENST00000198765.4_Intron	NM_016033.2	NP_057117.2	Q96DB5	RMD1_HUMAN	regulator of microtubule dynamics 1	170						microtubule (GO:0005874)|mitochondrion (GO:0005739)											CATCACTAAGGCAGATTGCAT	0.289													G|||	1782	0.355831	0.1641	0.5072	5008	,	,		16591	0.5327		0.2694	False		,,,				2504	0.4141				p.C170C		Atlas-SNP	.											.	.	.	.	0			c.C510T						PASS	.	G		746,3660	298.7+/-285.4	69,608,1526	67.0	62.0	64.0		510	1.4	1.0	8	dbSNP_120	64	2115,6477	360.0+/-331.8	268,1579,2449	no	coding-synonymous	FAM82B	NM_016033.2		337,2187,3975	AA,AG,GG		24.6159,16.9315,22.0111		170/315	87497176	2861,10137	2203	4296	6499	SO:0001819	synonymous_variant	51115	exon5			ACTAAGGCAGATT	AK000672	CCDS34918.1, CCDS69509.1, CCDS69510.1	8q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000176623	ENSG00000176623			24285	protein-coding gene	gene with protein product		611871	"""family with sequence similarity 82, member B"""	FAM82B		10810093	Standard	NM_016033		Approved	CGI-90, FLJ20665, RMD1	uc003ydu.3	Q96DB5	OTTHUMG00000163692	ENST00000406452.3:c.510C>T	8.37:g.87497176G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	NM_016033	A9UMZ8|B4DNF5|B4DZW6|B5MC61|C9JSC6|E7EVI2|Q9Y398	Silent	SNP	ENST00000406452.3	37	CCDS34918.1	755|755	0.3456959706959707|0.3456959706959707	81|81	0.16463414634146342|0.16463414634146342	163|163	0.45027624309392267|0.45027624309392267	308|308	0.5384615384615384|0.5384615384615384	203|203	0.2678100263852243|0.2678100263852243	G|G	9.069|9.069	0.996302|0.996302	0.19043|0.19043	0.169315|0.169315	0.246159|0.246159	ENSG00000176623|ENSG00000176623	ENST00000519639|ENST00000519789	.|.	.|.	.|.	5.63|5.63	1.36|1.36	0.22044|0.22044	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49513|0.49513	-0.8932|-0.8932	3|3	.|.	.|.	.|.	-14.3246|-14.3246	13.866|13.866	0.63590|0.63590	0.217:0.0:0.783:0.0|0.217:0.0:0.783:0.0	rs11539113;rs13259590;rs13259590|rs11539113;rs13259590;rs13259590	.|.	.|.	.|.	V|S	16|116	.|.	.|.	A|P	-|-	2|1	0|0	FAM82B|FAM82B	87566292|87566292	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.670000|0.670000	0.25157|0.25157	0.239000|0.239000	0.21243|0.21243	0.655000|0.655000	0.94253|0.94253	GCC|CCT	G|0.596;T|0.065	.	strong		0.289	RMDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374770.2	NM_016033	
SPAG16	79582	hgsc.bcm.edu	37	2	214354811	214354811	+	Missense_Mutation	SNP	G	G	A	rs61752199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:214354811G>A	ENST00000331683.5	+	10	1162	c.1067G>A	c.(1066-1068)aGc>aAc	p.S356N	SPAG16_ENST00000374309.3_Missense_Mutation_p.S262N	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	356					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		CTTCCAGTGAGCTGGTAGGAT	0.318													G|||	62	0.0123802	0.0053	0.0058	5008	,	,		16436	0.004		0.0159	False		,,,				2504	0.0317				p.S356N		Atlas-SNP	.											.	SPAG16	134	.	0			c.G1067A						PASS	.	G	ASN/SER	33,4369	38.4+/-70.7	0,33,2168	51.0	55.0	54.0		1067	5.0	1.0	2	dbSNP_129	54	154,8440	72.9+/-135.5	2,150,4145	yes	missense	SPAG16	NM_024532.3	46	2,183,6313	AA,AG,GG		1.7919,0.7497,1.4389	probably-damaging	356/632	214354811	187,12809	2201	4297	6498	SO:0001583	missense	79582	exon10			CAGTGAGCTGGTA	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1067G>A	2.37:g.214354811G>A	ENSP00000332592:p.Ser356Asn	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	251	119	0.474104	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	24	0.01098901098901099	6	0.012195121951219513	3	0.008287292817679558	2	0.0034965034965034965	13	0.017150395778364115	G	17.80	3.477248	0.63849	0.007497	0.017919	ENSG00000144451	ENST00000331683;ENST00000374309;ENST00000451561	T;T;T	0.59364	0.27;0.27;0.27	5.93	5.03	0.67393	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.106321	0.64402	D	0.000016	T	0.57695	0.2071	M	0.72894	2.215	0.34970	D	0.753049	P;D;P;P	0.89917	0.951;1.0;0.599;0.872	P;D;P;P	0.87578	0.636;0.998;0.574;0.636	T	0.73145	-0.4075	10	0.22109	T	0.4	.	12.9132	0.58190	0.0:0.1628:0.8372:0.0	rs61752199	262;207;296;356	B4DYB5;Q8N0X2-2;Q4G1A2;Q8N0X2	.;.;.;SPG16_HUMAN	N	356;262;42	ENSP00000332592:S356N;ENSP00000363428:S262N;ENSP00000416600:S42N	ENSP00000332592:S356N	S	+	2	0	SPAG16	214063056	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	2.442000	0.44873	1.454000	0.47793	0.555000	0.69702	AGC	G|0.984;A|0.016	0.016	strong		0.318	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
CCDC6	8030	hgsc.bcm.edu	37	10	61665886	61665886	+	Silent	SNP	C	C	A	rs1171830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:61665886C>A	ENST00000263102.6	-	1	528	c.297G>T	c.(295-297)gtG>gtT	p.V99V		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	99						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		TCACGATGGTCACGCTGGCTT	0.657			T	RET	NSCLC								C|||	1880	0.375399	0.0393	0.4726	5008	,	,		12230	0.627		0.4523	False		,,,				2504	0.4223				p.V99V		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44	.	0			c.G297T						PASS	.	C		501,3905	230.4+/-244.6	46,409,1748	58.0	55.0	56.0		297	2.5	1.0	10	dbSNP_87	56	4054,4546	556.5+/-386.9	955,2144,1201	no	coding-synonymous	CCDC6	NM_005436.4		1001,2553,2949	AA,AC,CC		47.1395,11.3709,35.0223		99/475	61665886	4555,8451	2203	4300	6503	SO:0001819	synonymous_variant	8030	exon1			GATGGTCACGCTG	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.297G>T	10.37:g.61665886C>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	29	0.617021	NM_005436	Q15250|Q6GSG7	Silent	SNP	ENST00000263102.6	37	CCDS7257.1																																																																																			C|0.638;A|0.362	0.362	strong		0.657	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
SVEP1	79987	hgsc.bcm.edu	37	9	113209195	113209195	+	Missense_Mutation	SNP	T	T	G	rs1889323	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:113209195T>G	ENST00000401783.2	-	25	4582	c.4246A>C	c.(4246-4248)Aaa>Caa	p.K1416Q	SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.K1393Q|SVEP1_ENST00000302728.8_Missense_Mutation_p.K1416Q	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1416	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		K -> Q (in dbSNP:rs1889323).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TCACACCTTTTGCCTGAAAAT	0.343													T|||	568	0.113419	0.0401	0.1037	5008	,	,		19021	0.0327		0.1561	False		,,,				2504	0.2587				p.K1416Q		Atlas-SNP	.											.	SVEP1	326	.	0			c.A4246C						PASS	.	T	GLN/LYS	152,2988		5,142,1423	87.0	79.0	82.0		4246	4.8	1.0	9	dbSNP_92	82	1038,5840		81,876,2482	yes	missense	SVEP1	NM_153366.3	53	86,1018,3905	GG,GT,TT		15.0916,4.8408,11.8786	benign	1416/3572	113209195	1190,8828	1570	3439	5009	SO:0001583	missense	79987	exon25			ACCTTTTGCCTGA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.4246A>C	9.37:g.113209195T>G	ENSP00000384917:p.Lys1416Gln	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	185	0.08470695970695971	17	0.034552845528455285	36	0.09944751381215469	17	0.02972027972027972	115	0.1517150395778364	T	13.99	2.401177	0.42613	0.048408	0.150916	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	D;D;D	0.86562	-2.14;-2.14;-2.14	5.95	4.8	0.61643	EGF (1);EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.351938	0.39407	N	0.001370	T	0.01661	0.0053	L	0.42744	1.35	0.40196	P	0.022534000000000054	B;B	0.15719	0.014;0.007	B;B	0.18871	0.023;0.003	T	0.50206	-0.8855	9	0.13108	T	0.6	.	13.096	0.59192	0.0:0.0:0.1385:0.8615	rs1889323;rs52835560;rs57327200;rs1889323	1416;1416	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	Q	1416;1393;1416	ENSP00000384917:K1416Q;ENSP00000363593:K1393Q;ENSP00000304118:K1416Q	ENSP00000304118:K1416Q	K	-	1	0	SVEP1	112249016	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.923000	0.56469	1.057000	0.40506	0.533000	0.62120	AAA	T|0.902;G|0.098	0.098	strong		0.343	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
RHPN2	85415	hgsc.bcm.edu	37	19	33490585	33490585	+	Nonsense_Mutation	SNP	G	G	A	rs78615454	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33490585G>A	ENST00000254260.3	-	10	1167	c.1132C>T	c.(1132-1134)Cag>Tag	p.Q378*	RHPN2_ENST00000400226.4_Nonsense_Mutation_p.Q227*	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	378	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					CACTTCTCCTGGTGGTCCAGA	0.572																																					p.Q378X		Atlas-SNP	.											RHPN2,NS,haematopoietic_neoplasm,0,1	RHPN2	107	1	0			c.C1132T						PASS	.						96.0	76.0	83.0					19																	33490585		2203	4300	6503	SO:0001587	stop_gained	85415	exon10			TCTCCTGGTGGTC	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1132C>T	19.37:g.33490585G>A	ENSP00000254260:p.Gln378*	Somatic	864	1	0.00115741		WXS	Illumina HiSeq	Phase_I	1168	250	0.214041	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Nonsense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	G	40	8.339731	0.98767	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	.	.	.	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-23.5746	17.6847	0.88253	0.0:0.0:1.0:0.0	.	.	.	.	X	378;108;227	.	ENSP00000254260:Q378X	Q	-	1	0	RHPN2	38182425	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	8.944000	0.92980	2.174000	0.68829	0.484000	0.47621	CAG	G|0.856;A|0.144	0.144	strong		0.572	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
OBSCN	84033	hgsc.bcm.edu	37	1	228468458	228468458	+	Missense_Mutation	SNP	G	G	A	rs1188697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228468458G>A	ENST00000422127.1	+	30	8202	c.8158G>A	c.(8158-8160)Gtg>Atg	p.V2720M	OBSCN_ENST00000359599.6_Missense_Mutation_p.V1567M|OBSCN_ENST00000284548.11_Missense_Mutation_p.V2720M|OBSCN_ENST00000570156.2_Missense_Mutation_p.V3149M|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2720	Ig-like 26.		V -> M (in dbSNP:rs1188697).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CACCTGCCACGTGGGCTCCGA	0.697													g|||	1597	0.31889	0.469	0.3343	5008	,	,		14985	0.247		0.2962	False		,,,				2504	0.2025				p.V3149M		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	0			c.G9445A						PASS	.		MET/VAL,MET/VAL	1350,2712		242,866,923	15.0	20.0	19.0		8158,8158	0.4	0.3	1	dbSNP_87	19	2308,5980		341,1626,2177	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	21,21	583,2492,3100	AA,AG,GG		27.8475,33.2349,29.6194	probably-damaging,probably-damaging	2720/7969,2720/6621	228468458	3658,8692	2031	4144	6175	SO:0001583	missense	84033	exon35			TGCCACGTGGGCT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.8158G>A	1.37:g.228468458G>A	ENSP00000409493:p.Val2720Met	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	672	0.3076923076923077	211	0.42886178861788615	113	0.31215469613259667	133	0.23251748251748253	215	0.2836411609498681	g	12.51	1.958266	0.34565	0.332349	0.278475	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706;ENST00000366704	T;T;T	0.71934	-0.61;-0.61;-0.61	5.39	0.451	0.16629	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.699445	0.13181	N	0.407521	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.99999679775	D;D;D	0.71674	0.998;0.972;0.998	P;B;P	0.59703	0.862;0.343;0.789	T	0.30268	-0.9984	9	0.48119	T	0.1	.	8.5592	0.33501	0.1296:0.5629:0.3075:0.0	rs1188697;rs1188723;rs1757126;rs1188697	2720;2720;2720	Q5VST9;Q5VST9-2;Q5VST9-3	OBSCN_HUMAN;.;.	M	2720;2720;1567;419;126	ENSP00000284548:V2720M;ENSP00000409493:V2720M;ENSP00000352613:V1567M	ENSP00000284548:V2720M	V	+	1	0	OBSCN	226535081	0.047000	0.20315	0.253000	0.24343	0.628000	0.37860	0.459000	0.21908	0.186000	0.20125	0.457000	0.33378	GTG	G|0.696;A|0.304	0.304	strong		0.697	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SERPINA9	327657	hgsc.bcm.edu	37	14	94929541	94929541	+	Silent	SNP	G	G	A	rs2224418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94929541G>A	ENST00000380365.3	-	5	1221	c.1143C>T	c.(1141-1143)ggC>ggT	p.G381G	SERPINA9_ENST00000298845.7_Silent_p.G299G|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000424550.2_Silent_p.G250G|SERPINA9_ENST00000337425.5_Silent_p.G399G|SERPINA9_ENST00000448305.2_Silent_p.G301G			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	381					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		AGTAAGAGGGGCCATCCTTCG	0.498													A|||	3386	0.676118	0.3752	0.7507	5008	,	,		21303	0.6478		0.8529	False		,,,				2504	0.8773				p.G399G		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C1197T						PASS	.	A	,	2025,2163		479,1067,548	152.0	154.0	154.0		897,1197	-1.9	0.0	14	dbSNP_96	154	7018,1388		2918,1182,103	no	coding-synonymous,coding-synonymous	SERPINA9	NM_001042518.1,NM_175739.3	,	3397,2249,651	AA,AG,GG		16.512,48.3524,28.196	,	299/336,399/436	94929541	9043,3551	2094	4203	6297	SO:0001819	synonymous_variant	327657	exon5			AGAGGGGCCATCC	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.1143C>T	14.37:g.94929541G>A		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	246	243	0.987805	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Silent	SNP	ENST00000380365.3	37																																																																																				G|0.310;A|0.690	0.690	strong		0.498	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
CDH12	1010	hgsc.bcm.edu	37	5	21760731	21760731	+	Silent	SNP	T	T	C	rs2303749	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:21760731T>C	ENST00000382254.1	-	13	2655	c.1569A>G	c.(1567-1569)caA>caG	p.Q523Q	CDH12_ENST00000504376.2_Silent_p.Q523Q|CDH12_ENST00000522262.1_Silent_p.Q483Q|RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000521384.1_5'UTR	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	523	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TAAAGGAGAATTGTTGCCCAG	0.393										HNSCC(59;0.17)			T|||	296	0.0591054	0.0227	0.1225	5008	,	,		16792	0.0169		0.0606	False		,,,				2504	0.1053				p.Q523Q		Atlas-SNP	.											CDH12,right_upper_lobe,carcinoma,-2,1	CDH12	238	1	0			c.A1569G						PASS	.	T		144,4262	100.7+/-139.4	0,144,2059	134.0	140.0	138.0		1569	-3.9	1.0	5	dbSNP_100	138	574,8026	154.0+/-208.3	18,538,3744	no	coding-synonymous	CDH12	NM_004061.3		18,682,5803	CC,CT,TT		6.6744,3.2683,5.5205		523/795	21760731	718,12288	2203	4300	6503	SO:0001819	synonymous_variant	1010	exon13			GGAGAATTGTTGC	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.1569A>G	5.37:g.21760731T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	131	42	0.320611	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Silent	SNP	ENST00000382254.1	37	CCDS3890.1																																																																																			T|0.949;C|0.051	0.051	strong		0.393	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061	
PRDM5	11107	hgsc.bcm.edu	37	4	121706201	121706201	+	Silent	SNP	A	A	G	rs12499000	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:121706201A>G	ENST00000264808.3	-	11	1474	c.1234T>C	c.(1234-1236)Ttg>Ctg	p.L412L	PRDM5_ENST00000428209.2_Silent_p.L381L|PRDM5_ENST00000515109.1_Silent_p.L381L	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	412					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L412L(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GTCCGGAACAAAGCTTTACAT	0.408													A|||	688	0.13738	0.0113	0.1931	5008	,	,		15439	0.1895		0.2674	False		,,,				2504	0.0808				p.L412L		Atlas-SNP	.											PRDM5,NS,carcinoma,0,1	PRDM5	76	1	1	Substitution - coding silent(1)	stomach(1)	c.T1234C						PASS	.	A		255,4151	146.9+/-181.5	11,233,1959	108.0	97.0	101.0		1234	-1.3	0.8	4	dbSNP_120	101	2344,6256	392.4+/-344.0	329,1686,2285	no	coding-synonymous	PRDM5	NM_018699.2		340,1919,4244	GG,GA,AA		27.2558,5.7876,19.9831		412/631	121706201	2599,10407	2203	4300	6503	SO:0001819	synonymous_variant	11107	exon11			GGAACAAAGCTTT	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"""Zinc fingers, C2H2-type"""	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.1234T>C	4.37:g.121706201A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Silent	SNP	ENST00000264808.3	37	CCDS3716.1																																																																																			A|0.807;G|0.193	0.193	strong		0.408	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
FUCA1	2517	hgsc.bcm.edu	37	1	24180962	24180962	+	Missense_Mutation	SNP	T	T	C	rs13551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:24180962T>C	ENST00000374479.3	-	5	864	c.857A>G	c.(856-858)cAg>cGg	p.Q286R		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	286			Q -> R (in allele FUCA1*2; dbSNP:rs13551). {ECO:0000269|PubMed:12408193, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7815431, ECO:0000269|PubMed:8399358, ECO:0000269|PubMed:8504303}.		fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		TGGCAAGCTCTGTGGCTTGAA	0.463													t|||	1058	0.211262	0.1021	0.2464	5008	,	,		17166	0.2808		0.332	False		,,,				2504	0.138				p.Q286R		Atlas-SNP	.											.	FUCA1	24	.	0			c.A857G						PASS	.		ARG/GLN	643,3763	276.9+/-273.4	46,551,1606	140.0	133.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	857	3.6	0.0	1	dbSNP_52	135	2845,5755	447.0+/-361.4	457,1931,1912	yes	missense	FUCA1	NM_000147.4	43	503,2482,3518	CC,CT,TT		33.0814,14.5937,26.8184	benign	286/467	24180962	3488,9518	2203	4300	6503	SO:0001583	missense	2517	exon5			AAGCTCTGTGGCT	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.857A>G	1.37:g.24180962T>C	ENSP00000363603:p.Gln286Arg	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	219	126	0.575342	NM_000147	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Missense_Mutation	SNP	ENST00000374479.3	37	CCDS244.2	549	0.25137362637362637	63	0.12804878048780488	97	0.26795580110497236	141	0.2465034965034965	248	0.32717678100263853	t	7.821	0.717720	0.15372	0.145937	0.330814	ENSG00000179163	ENST00000374479;ENST00000374475	T	0.56444	0.46	4.74	3.6	0.41247	Glycoside hydrolase, family 29, conserved site (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	1.038340	0.07550	N	0.915237	T	0.00012	0.0000	L	0.35487	1.065	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.22871	-1.0204	9	0.87932	D	0	-18.2834	3.1357	0.06438	0.0:0.2037:0.2751:0.5212	rs13551;rs1126515;rs2228423;rs3181585;rs11549094;rs52796281;rs13551	286	P04066	FUCO_HUMAN	R	286;75	ENSP00000363603:Q286R	ENSP00000363599:Q75R	Q	-	2	0	FUCA1	24053549	0.000000	0.05858	0.002000	0.10522	0.148000	0.21650	0.652000	0.24888	0.839000	0.34971	0.515000	0.50301	CAG	.	.	none		0.463	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147	
ZNF726	730087	hgsc.bcm.edu	37	19	24115369	24115369	+	Silent	SNP	T	T	C	rs56014490	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:24115369T>C	ENST00000594466.1	+	4	556	c.451T>C	c.(451-453)Ttg>Ctg	p.L151L	ZNF726_ENST00000322487.7_Silent_p.L151L|CTB-92J24.3_ENST00000596326.1_RNA|ZNF726_ENST00000575986.1_Intron|ZNF726_ENST00000334589.5_Intron	NM_001244038.1	NP_001230967.1	A6NNF4	ZN726_HUMAN	zinc finger protein 726	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGGTAAATATTTGAAAGTCtt	0.294													.|||	535	0.106829	0.1104	0.0922	5008	,	,		13215	0.0139		0.1461	False		,,,				2504	0.1677				p.L151L		Atlas-SNP	.											.	.	.	.	0			c.T451C						PASS	.																																			SO:0001819	synonymous_variant	730087	exon4			AAATATTTGAAAG	DQ036016, BC046415	CCDS59372.1	19p12	2013-01-08			ENSG00000213967	ENSG00000213967		"""Zinc fingers, C2H2-type"", ""-"""	32462	protein-coding gene	gene with protein product							Standard	NM_001244038		Approved		uc021urw.1	A6NNF4	OTTHUMG00000167681	ENST00000594466.1:c.451T>C	19.37:g.24115369T>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	15	6	0.4	NM_001244038	M0R0X8|Q86Y87	Silent	SNP	ENST00000594466.1	37	CCDS59372.1																																																																																			T|0.891;C|0.109	0.109	strong		0.294	ZNF726-005	PUTATIVE	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466443.1	XM_001715134	
IGIP	492311	hgsc.bcm.edu	37	5	139508064	139508064	+	Start_Codon_SNP	SNP	G	G	A	rs141663065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139508064G>A	ENST00000333305.3	+	1	2544	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_001007189.1	NP_001007190.1	A6NJ69	IGIP_HUMAN	IgA-inducing protein	1						extracellular region (GO:0005576)											TATTAAATATGTGCAGTTATT	0.378													G|||	2	0.000399361	0.0	0.0	5008	,	,		18171	0.0		0.002	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	.	.	.	0			c.G3A						PASS	.	G	ILE/MET	4,4402	8.1+/-20.4	0,4,2199	114.0	105.0	108.0		3	4.2	1.0	5	dbSNP_134	108	16,8584	11.9+/-42.8	0,16,4284	yes	missense	IGIP	NM_001007189.1	10	0,20,6483	AA,AG,GG		0.186,0.0908,0.1538	benign	1/54	139508064	20,12986	2203	4300	6503	SO:0001582	initiator_codon_variant	492311	exon1			AAATATGTGCAGT	AB073888, BC017422, BC041380	CCDS34244.1	5q31	2013-08-06	2013-08-06	2011-09-22	ENSG00000182700	ENSG00000182700			33847	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 53"", ""IgA-inducing protein homolog (Bos taurus)"""	C5orf53		19201837, 12874223, 21074276	Standard	NM_001007189		Approved	LOC492311	uc003lfb.1	A6NJ69	OTTHUMG00000163359	ENST00000333305.3:c.3G>A	5.37:g.139508064G>A	ENSP00000327344:p.Met1Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_001007189		Missense_Mutation	SNP	ENST00000333305.3	37	CCDS34244.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	5.979	0.364590	0.11296	9.08E-4	0.00186	ENSG00000182700	ENST00000333305	.	.	.	5.28	4.18	0.49190	.	0.136380	0.33875	N	0.004466	T	0.44808	0.1311	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48937	-0.8990	8	0.87932	D	0	-1.909	6.7874	0.23682	0.1523:0.0:0.8477:0.0	.	1	A6NJ69	IGIP_HUMAN	I	1	.	ENSP00000327344:M1I	M	+	3	0	C5orf53	139488248	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.200000	0.51051	2.648000	0.89879	0.650000	0.86243	ATG	G|0.999;A|0.001	0.001	strong		0.378	IGIP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372850.1	NM_001007189	Missense_Mutation
UGT8	7368	hgsc.bcm.edu	37	4	115544713	115544713	+	Missense_Mutation	SNP	C	C	T	rs4148254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:115544713C>T	ENST00000310836.6	+	2	1199	c.677C>T	c.(676-678)cCa>cTa	p.P226L	UGT8_ENST00000394511.3_Missense_Mutation_p.P226L	NM_001128174.1	NP_001121646	Q16880	CGT_HUMAN	UDP glycosyltransferase 8	226			P -> L (in dbSNP:rs4148254).		axon cargo transport (GO:0008088)|central nervous system development (GO:0007417)|cytoskeleton organization (GO:0007010)|galactosylceramide biosynthetic process (GO:0006682)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to paranode region of axon (GO:0002175)	integral component of membrane (GO:0016021)	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity (GO:0003851)|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity (GO:0008489)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		AACCTGCTGCCAGAGAAGTCC	0.453													C|||	250	0.0499201	0.0045	0.0562	5008	,	,		17354	0.121		0.0328	False		,,,				2504	0.0511				p.P226L		Atlas-SNP	.											.	UGT8	82	.	0			c.C677T						PASS	.	C	LEU/PRO,LEU/PRO	39,4367	41.6+/-74.8	0,39,2164	102.0	102.0	102.0		677,677	5.5	1.0	4	dbSNP_110	102	273,8327	103.1+/-164.3	7,259,4034	yes	missense,missense	UGT8	NM_001128174.1,NM_003360.3	98,98	7,298,6198	TT,TC,CC		3.1744,0.8852,2.3989	probably-damaging,probably-damaging	226/542,226/542	115544713	312,12694	2203	4300	6503	SO:0001583	missense	7368	exon1			TGCTGCCAGAGAA	AK127970	CCDS3705.1	4q26	2013-02-21	2008-07-31	2005-07-20	ENSG00000174607	ENSG00000174607	2.4.1.45	"""UDP glucuronosyltransferases"""	12555	protein-coding gene	gene with protein product	"""2-hydroxyacylsphingosine 1-beta-galactosyltransferase"""	601291	"""UDP-galactose ceramide galactosyltransferase"""	CGT		8661025	Standard	NM_003360		Approved		uc003ibs.2	Q16880	OTTHUMG00000132915	ENST00000310836.6:c.677C>T	4.37:g.115544713C>T	ENSP00000311648:p.Pro226Leu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	179	88	0.49162	NM_003360	B3KXU7|O00196	Missense_Mutation	SNP	ENST00000310836.6	37	CCDS3705.1	95	0.043498168498168496	1	0.0020325203252032522	17	0.04696132596685083	62	0.10839160839160839	15	0.01978891820580475	C	22.3	4.264929	0.80358	0.008852	0.031744	ENSG00000174607	ENST00000310836;ENST00000394511	T;T	0.63744	-0.06;-0.06	5.46	5.46	0.80206	.	0.146885	0.64402	D	0.000006	T	0.02970	0.0088	L	0.58428	1.81	0.09310	P	0.999999999830677	B	0.32893	0.389	B	0.38921	0.285	T	0.40232	-0.9574	9	0.72032	D	0.01	.	19.6567	0.95845	0.0:1.0:0.0:0.0	rs4148254;rs56419563;rs4148254	226	Q16880	CGT_HUMAN	L	226	ENSP00000311648:P226L;ENSP00000378019:P226L	ENSP00000311648:P226L	P	+	2	0	UGT8	115764162	1.000000	0.71417	0.955000	0.39395	0.848000	0.48234	7.749000	0.85096	2.725000	0.93324	0.585000	0.79938	CCA	C|0.963;T|0.037	0.037	strong		0.453	UGT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256426.2	NM_003360	
MOK	5891	hgsc.bcm.edu	37	14	102729886	102729886	+	Nonsense_Mutation	SNP	G	G	A	rs34931752	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:102729886G>A	ENST00000361847.2	-	4	511	c.280C>T	c.(280-282)Cga>Tga	p.R94*	MOK_ENST00000193029.6_De_novo_Start_OutOfFrame|MOK_ENST00000524214.1_Nonsense_Mutation_p.R64*|MOK_ENST00000522874.1_Nonsense_Mutation_p.R94*	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	94	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										TACGTACCTCGTATTAGCTCA	0.308													G|||	254	0.0507188	0.0991	0.0288	5008	,	,		18323	0.0298		0.0318	False		,,,				2504	0.0419				p.R94X		Atlas-SNP	.											.	.	.	.	0			c.C280T	GRCh37	CM071966	MOK	M	rs34931752	PASS	.	G	stop/ARG	392,4012	192.6+/-218.0	12,368,1822	105.0	106.0	106.0		280	5.8	1.0	14	dbSNP_126	106	335,8265	115.0+/-174.9	4,327,3969	yes	stop-gained	MOK	NM_014226.1		16,695,5791	AA,AG,GG		3.8953,8.901,5.5906		94/420	102729886	727,12277	2202	4300	6502	SO:0001587	stop_gained	5891	exon4			TACCTCGTATTAG	AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"""renal tumor antigen"""	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.280C>T	14.37:g.102729886G>A	ENSP00000355304:p.Arg94*	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Nonsense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	95	0.043498168498168496	45	0.09146341463414634	12	0.03314917127071823	12	0.02097902097902098	26	0.03430079155672823	G	34	5.364007	0.95877	0.08901	0.038953	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	.	.	.	5.8	5.8	0.92144	.	0.357359	0.26404	N	0.024564	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	.	12.6279	0.56640	0.0:0.0:0.7939:0.2061	rs34931752	.	.	.	X	94;94;64	.	ENSP00000355304:R94X	R	-	1	2	RAGE	101799639	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	2.592000	0.46171	2.735000	0.93741	0.655000	0.94253	CGA	G|0.950;A|0.050	0.050	strong		0.308	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
OR51A2	401667	hgsc.bcm.edu	37	11	4976768	4976768	+	Missense_Mutation	SNP	C	C	T	rs112749434	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4976768C>T	ENST00000380371.1	-	1	175	c.176G>A	c.(175-177)gGg>gAg	p.G59E	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	59			G -> E (in dbSNP:rs1817206).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTACATGGGCCCATGCAAGGA	0.438																																					p.G59E		Atlas-SNP	.											OR51A2,NS,carcinoma,0,1	OR51A2	40	1	0			c.G176A						scavenged	.		GLU/GLY	1112,3190		453,206,1492	96.0	62.0	73.0		176	1.8	0.5	11	dbSNP_132	73	3436,4990		1480,476,2257	no	missense	OR51A2	NM_001004748.1	98	1933,682,3749	TT,TC,CC		40.7785,25.8484,35.7322	benign	59/314	4976768	4548,8180	2151	4213	6364	SO:0001583	missense	401667	exon1			ATGGGCCCATGCA	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.176G>A	11.37:g.4976768C>T	ENSP00000369729:p.Gly59Glu	Somatic	623	0	0		WXS	Illumina HiSeq	Phase_I	174	172	0.988506	NM_001004748		Missense_Mutation	SNP	ENST00000380371.1	37	CCDS31368.1	1147	0.5251831501831502	193	0.39227642276422764	202	0.5580110497237569	320	0.5594405594405595	432	0.5699208443271768	-	0.003	-2.538872	0.00143	0.258484	0.407785	ENSG00000205496	ENST00000380371	T	0.00492	7.01	2.94	1.75	0.24633	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00003	-3.455	0.51233	P	8.699999999994823E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.36138	-0.9760	8	0.02654	T	1	.	4.0946	0.09985	0.0:0.1203:0.208:0.6718	rs1817206;rs2959191;rs34314376;rs1817206	59	Q8NGJ7	O51A2_HUMAN	E	59	ENSP00000369729:G59E	ENSP00000369729:G59E	G	-	2	0	OR51A2	4933344	0.000000	0.05858	0.488000	0.27440	0.027000	0.11550	0.179000	0.16840	-0.051000	0.13334	-1.224000	0.01588	GGG	C|1.000;|0.000	.	weak		0.438	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
TRAPPC9	83696	hgsc.bcm.edu	37	8	140998945	140998945	+	Silent	SNP	G	G	A	rs2614718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:140998945G>A	ENST00000438773.2	-	19	2932	c.2799C>T	c.(2797-2799)ggC>ggT	p.G933G	TRAPPC9_ENST00000389328.4_Silent_p.G1031G|TRAPPC9_ENST00000389327.3_Silent_p.G924G	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	933					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						GCTGGCACTCGCCGGCGTGCA	0.637													G|||	466	0.0930511	0.1286	0.1916	5008	,	,		16704	0.0635		0.0408	False		,,,				2504	0.0593				p.G1031G		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3093T						PASS	.	G	,	361,3507		14,333,1587	28.0	25.0	26.0		2799,3093	1.3	1.0	8	dbSNP_100	26	354,6894		4,346,3274	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	18,679,4861	AA,AG,GG		4.8841,9.333,6.4322	,	933/1149,1031/1247	140998945	715,10401	1934	3624	5558	SO:0001819	synonymous_variant	83696	exon19			GCACTCGCCGGCG	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.2799C>T	8.37:g.140998945G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	191	0.08745421245421245	66	0.13414634146341464	59	0.16298342541436464	37	0.06468531468531469	29	0.03825857519788918	G	10.95	1.495014	0.26774	0.09333	0.048841	ENSG00000167632	ENST00000520857	.	.	.	5.48	1.34	0.21922	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.337	0.04250	0.095:0.2087:0.3125:0.3838	rs2614718;rs60012718	.	.	.	X	777	.	.	R	-	1	2	TRAPPC9	141068127	0.963000	0.33076	0.997000	0.53966	0.960000	0.62799	0.010000	0.13242	0.622000	0.30249	0.655000	0.94253	CGA	G|0.921;A|0.079	0.079	strong		0.637	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
GPR183	1880	hgsc.bcm.edu	37	13	99948097	99948097	+	Silent	SNP	A	A	G	rs2230343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:99948097A>G	ENST00000376414.4	-	2	386	c.303T>C	c.(301-303)gaT>gaC	p.D101D	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	101					G-protein coupled receptor signaling pathway (GO:0007186)|humoral immune response (GO:0006959)|immune response (GO:0006955)|mature B cell differentiation involved in immune response (GO:0002313)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|oxysterol binding (GO:0008142)			cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						TACACAAGGCATCTCCGATTC	0.428													A|||	363	0.072484	0.0885	0.0461	5008	,	,		21657	0.123		0.0527	False		,,,				2504	0.0378				p.D101D		Atlas-SNP	.											.	GPR183	38	.	0			c.T303C						PASS	.	A	,,	385,4021	194.7+/-219.5	18,349,1836	150.0	126.0	134.0		,303,	-11.6	0.1	13	dbSNP_98	134	588,8012	156.3+/-210.2	23,542,3735	no	intron,coding-synonymous,intron	GPR183,UBAC2	NM_001144072.1,NM_004951.4,NM_177967.3	,,	41,891,5571	GG,GA,AA		6.8372,8.7381,7.4812	,,	,101/362,	99948097	973,12033	2203	4300	6503	SO:0001819	synonymous_variant	1880	exon2			CAAGGCATCTCCG	L08177	CCDS9492.1	13q32.3	2012-08-21	2008-07-21	2008-07-21	ENSG00000169508	ENSG00000169508		"""GPCR / Class A : Orphans"""	3128	protein-coding gene	gene with protein product	"""EBV-induced G-protein coupled receptor 2"""	605741	"""Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor)"""	EBI2		8383238	Standard	NM_004951		Approved		uc001vog.3	P32249	OTTHUMG00000017263	ENST00000376414.4:c.303T>C	13.37:g.99948097A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_004951	B2R8N5|Q53F99|Q5JUH7	Silent	SNP	ENST00000376414.4	37	CCDS9492.1																																																																																			A|0.921;G|0.079	0.079	strong		0.428	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951	
ANK2	287	hgsc.bcm.edu	37	4	114274519	114274519	+	Missense_Mutation	SNP	G	G	A	rs138842207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:114274519G>A	ENST00000357077.4	+	38	4798	c.4745G>A	c.(4744-4746)cGg>cAg	p.R1582Q	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.R1549Q|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1582					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CAGAGCTCTCGGTCTGAGAGA	0.408													G|||	2	0.000399361	0.0	0.0	5008	,	,		21338	0.0		0.002	False		,,,				2504	0.0				p.R1582Q		Atlas-SNP	.											ANK2,rectum,carcinoma,+1,1	ANK2	576	1	0			c.G4745A						PASS	.	G	,GLN/ARG,	0,4406		0,0,2203	82.0	88.0	86.0		,4745,	0.9	0.0	4	dbSNP_134	86	11,8589	9.1+/-34.3	0,11,4289	yes	intron,missense,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,43,	0,11,6492	AA,AG,GG		0.1279,0.0,0.0846	,benign,	,1582/3958,	114274519	11,12995	2203	4300	6503	SO:0001583	missense	287	exon38			GCTCTCGGTCTGA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.4745G>A	4.37:g.114274519G>A	ENSP00000349588:p.Arg1582Gln	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	211	101	0.478673	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	0	-2.736183	0.00088	0.0	0.001279	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.65364	0.08;-0.02;-0.11;-0.15	4.9	0.954	0.19595	.	1.073890	0.07232	N	0.862650	T	0.28732	0.0712	N	0.02539	-0.55	0.19575	N	0.999967	B;B	0.10296	0.001;0.003	B;B	0.06405	0.001;0.002	T	0.22661	-1.0210	10	0.11182	T	0.66	.	1.566	0.02605	0.549:0.1302:0.1777:0.143	.	1549;1582	Q01484;Q01484-4	ANK2_HUMAN;.	Q	1495;1597;1582;1549	ENSP00000421011:R1495Q;ENSP00000424722:R1597Q;ENSP00000349588:R1582Q;ENSP00000264366:R1549Q	ENSP00000264366:R1549Q	R	+	2	0	ANK2	114493968	0.622000	0.27085	0.017000	0.16124	0.013000	0.08279	0.864000	0.27926	0.340000	0.23745	0.557000	0.71058	CGG	G|0.999;A|0.001	0.001	strong		0.408	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
BPI	671	hgsc.bcm.edu	37	20	36932660	36932660	+	Missense_Mutation	SNP	C	C	T	rs1341023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:36932660C>T	ENST00000262865.4	+	1	136	c.47C>T	c.(46-48)gCg>gTg	p.A16V	CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	16			A -> V (in dbSNP:rs1341023). {ECO:0000269|PubMed:2722846, ECO:0000269|Ref.3}.		defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				CCGAGATGGGCGTCCCTGATG	0.612													C|||	2160	0.43131	0.1573	0.5245	5008	,	,		16490	0.5764		0.5437	False		,,,				2504	0.4703				p.A16V		Atlas-SNP	.											.	BPI	67	.	0			c.C47T						PASS	.	C	VAL/ALA	954,3452	352.1+/-311.5	103,748,1352	73.0	70.0	71.0		47	2.8	0.1	20	dbSNP_88	71	4605,3995	590.0+/-392.6	1239,2127,934	yes	missense	BPI	NM_001725.2	64	1342,2875,2286	TT,TC,CC		46.4535,21.6523,42.7418	benign	16/488	36932660	5559,7447	2203	4300	6503	SO:0001583	missense	671	exon1			GATGGGCGTCCCT	J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"""BPI fold containing"""	1095	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 1"""	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.47C>T	20.37:g.36932660C>T	ENSP00000262865:p.Ala16Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	96	94	0.979167	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Missense_Mutation	SNP	ENST00000262865.4	37	CCDS13303.1	1026	0.4697802197802198	98	0.1991869918699187	201	0.5552486187845304	331	0.5786713286713286	396	0.5224274406332454	C	13.18	2.161549	0.38119	0.216523	0.535465	ENSG00000101425	ENST00000418004;ENST00000262865	T;T	0.31769	1.48;3.29	3.78	2.84	0.33178	.	0.517115	0.16616	N	0.206700	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	P	0.43169	0.8	B	0.29077	0.098	T	0.41963	-0.9479	9	0.12430	T	0.62	-5.5247	7.6199	0.28179	0.0:0.8846:0.0:0.1154	rs1341023;rs3746474;rs17790384;rs59096690;rs1341023	16	P17213	BPI_HUMAN	V	99;16	ENSP00000393126:A99V;ENSP00000262865:A16V	ENSP00000262865:A16V	A	+	2	0	BPI	36366074	0.821000	0.29204	0.055000	0.19348	0.001000	0.01503	1.496000	0.35638	1.190000	0.43042	-0.126000	0.14955	GCG	C|0.551;T|0.449	0.449	strong		0.612	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	
USP4	7375	hgsc.bcm.edu	37	3	49362369	49362369	+	Silent	SNP	C	C	T	rs56038006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49362369C>T	ENST00000265560.4	-	5	637	c.591G>A	c.(589-591)aaG>aaA	p.K197K	USP4_ENST00000351842.4_Silent_p.K197K|USP4_ENST00000416417.1_Silent_p.K197K|USP4_ENST00000415188.1_Silent_p.K197K	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	197	Necessary for interaction with SART3. {ECO:0000269|PubMed:20595234}.|Ubiquitin-like 1.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.K197K(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		TGTTGTCTAGCTTGCTCAACT	0.557													C|||	461	0.0920527	0.0651	0.098	5008	,	,		21404	0.0546		0.1988	False		,,,				2504	0.0532				p.K197K		Atlas-SNP	.											USP4,NS,carcinoma,0,1	USP4	72	1	1	Substitution - coding silent(1)	stomach(1)	c.G591A						PASS	.	C	,	428,3978	208.2+/-229.3	17,394,1792	170.0	170.0	170.0		591,591	-0.3	0.3	3	dbSNP_129	170	1489,7111	283.7+/-296.3	130,1229,2941	no	coding-synonymous,coding-synonymous	USP4	NM_003363.3,NM_199443.2	,	147,1623,4733	TT,TC,CC		17.314,9.714,14.7394	,	197/964,197/917	49362369	1917,11089	2203	4300	6503	SO:0001819	synonymous_variant	7375	exon5			GTCTAGCTTGCTC	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.591G>A	3.37:g.49362369C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	217	124	0.571429	NM_001251877	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1																																																																																			C|0.855;T|0.145	0.145	strong		0.557	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
NOS2	4843	hgsc.bcm.edu	37	17	26096597	26096597	+	Missense_Mutation	SNP	G	G	A	rs2297518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:26096597G>A	ENST00000313735.6	-	16	2056	c.1823C>T	c.(1822-1824)tCg>tTg	p.S608L		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	608	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.		S -> L (in dbSNP:rs2297518). {ECO:0000269|PubMed:7528017, ECO:0000269|PubMed:7531687, ECO:0000269|Ref.10}.		arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	CATGAAGAGCGATTTCTTCAG	0.453													G|||	828	0.165335	0.1271	0.1744	5008	,	,		22198	0.1518		0.2316	False		,,,				2504	0.1564				p.S608L		Atlas-SNP	.											NOS2,right_upper_lobe,carcinoma,+1,1	NOS2	113	1	0			c.C1823T	GRCh37	CM066586	NOS2	M	rs2297518	PASS	.	G	LEU/SER	500,3906	231.7+/-245.5	25,450,1728	109.0	99.0	103.0		1823	5.3	1.0	17	dbSNP_100	103	1680,6920	307.3+/-308.3	191,1298,2811	yes	missense	NOS2	NM_000625.4	145	216,1748,4539	AA,AG,GG		19.5349,11.3482,16.7615	benign	608/1154	26096597	2180,10826	2203	4300	6503	SO:0001583	missense	4843	exon16			AAGAGCGATTTCT	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1823C>T	17.37:g.26096597G>A	ENSP00000327251:p.Ser608Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	167	161	0.964072	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	37	CCDS11223.1	378	0.17307692307692307	63	0.12804878048780488	70	0.19337016574585636	74	0.12937062937062938	171	0.22559366754617413	G	17.52	3.409541	0.62399	0.113482	0.195349	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.74315	-0.83	5.27	5.27	0.74061	Flavodoxin/nitric oxide synthase (2);	0.220362	0.41194	D	0.000940	T	0.00073	0.0002	L	0.42008	1.315	0.22489	P	0.999053807	B;P	0.48998	0.066;0.918	B;P	0.49829	0.016;0.623	T	0.00228	-1.1899	9	0.40728	T	0.16	.	17.4604	0.87619	0.0:0.0:1.0:0.0	rs2297518;rs17718046;rs56509075;rs56740958;rs2297518	573;608	F8WEM3;P35228	.;NOS2_HUMAN	L	608;569;573	ENSP00000327251:S608L	ENSP00000305638:S573L	S	-	2	0	NOS2	23120724	1.000000	0.71417	0.997000	0.53966	0.399000	0.30720	6.204000	0.72143	2.464000	0.83262	0.462000	0.41574	TCG	G|0.830;A|0.170	0.170	strong		0.453	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
HLA-A	3105	hgsc.bcm.edu	37	6	29911307	29911307	+	Silent	SNP	G	G	A	rs199474578	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29911307G>A	ENST00000396634.1	+	5	947	c.606G>A	c.(604-606)acG>acA	p.T202T	HLA-A_ENST00000376802.2_Silent_p.T202T|HLA-A_ENST00000376806.5_Silent_p.T202T|HLA-A_ENST00000376809.5_Silent_p.T202T			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	202	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.T202T(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GGAAGGAGACGCTGCAGCGCA	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.T202T		Atlas-SNP	.											HLA-A,NS,adenoma,+1,2	HLA-A	89	2	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G606A						PASS	.						48.0	42.0	44.0					6																	29911307		1508	2706	4214	SO:0001819	synonymous_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGAGACGCTGCAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.606G>A	6.37:g.29911307G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	322	25	0.0776398	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			A|0.028;G|0.972	0.028	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
GLDC	2731	hgsc.bcm.edu	37	9	6620216	6620216	+	Silent	SNP	C	C	T	rs13289273	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:6620216C>T	ENST00000321612.6	-	3	588	c.438G>A	c.(436-438)acG>acA	p.T146T		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	146					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TCCGCAAAATCGTCTGTGGCA	0.418													C|||	149	0.0297524	0.0038	0.0447	5008	,	,		20847	0.0		0.1004	False		,,,				2504	0.0123				p.T146T		Atlas-SNP	.											.	GLDC	118	.	0			c.G438A						PASS	.	C		80,4326	69.2+/-107.0	0,80,2123	166.0	138.0	147.0		438	-4.3	1.0	9	dbSNP_121	147	798,7802	186.9+/-234.3	46,706,3548	no	coding-synonymous	GLDC	NM_000170.2		46,786,5671	TT,TC,CC		9.2791,1.8157,6.7507		146/1021	6620216	878,12128	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon3			CAAAATCGTCTGT	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"""glycine cleavage system protein P"", ""glycine decarboxylase"""	238300	"""glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"""			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.438G>A	9.37:g.6620216C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	148	46	0.310811	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			C|0.941;T|0.059	0.059	strong		0.418	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
ARHGAP28	79822	hgsc.bcm.edu	37	18	6890434	6890434	+	Silent	SNP	A	A	G	rs1116757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:6890434A>G	ENST00000383472.4	+	14	1844	c.1740A>G	c.(1738-1740)ccA>ccG	p.P580P	ARHGAP28_ENST00000262227.3_Silent_p.P528P|ARHGAP28_ENST00000314319.3_Silent_p.P421P|ARHGAP28_ENST00000532996.1_Silent_p.P403P|ARHGAP28_ENST00000531294.1_Silent_p.P416P|ARHGAP28_ENST00000418986.1_Silent_p.P421P|ARHGAP28_ENST00000400091.2_Silent_p.P580P|ARHGAP28_ENST00000419673.2_Silent_p.P421P			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	580					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				TCCAGGTTCCATCTTTCTTAA	0.458													G|||	2820	0.563099	0.5719	0.5331	5008	,	,		19204	0.6052		0.5686	False		,,,				2504	0.5235				p.P421P		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.A1263G						PASS	.	G		2530,1876	540.2+/-375.5	711,1108,384	76.0	74.0	74.0		1263	-7.3	0.4	18	dbSNP_86	74	4832,3768	532.5+/-382.2	1327,2178,795	no	coding-synonymous	ARHGAP28	NM_001010000.2		2038,3286,1179	GG,GA,AA		43.814,42.5783,43.3954		421/571	6890434	7362,5644	2203	4300	6503	SO:0001819	synonymous_variant	79822	exon13			GGTTCCATCTTTC	BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1740A>G	18.37:g.6890434A>G		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	235	129	0.548936	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Silent	SNP	ENST00000383472.4	37																																																																																				A|0.426;G|0.574	0.574	strong		0.458	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
HOXA7	3204	hgsc.bcm.edu	37	7	27196113	27196113	+	Missense_Mutation	SNP	C	C	T	rs2301721	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:27196113C>T	ENST00000242159.3	-	1	185	c.52G>A	c.(52-54)Gct>Act	p.A18T	HOXA7_ENST00000523796.2_5'Flank|HOXA-AS3_ENST00000518947.2_RNA|RP1-170O19.21_ENST00000602610.1_lincRNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	18			A -> T (in dbSNP:rs2301721). {ECO:0000269|PubMed:10911612, ECO:0000269|PubMed:11435435, ECO:0000269|PubMed:9804983, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.		angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						AACAGAGAAGCCCCCGCCGTA	0.532													C|||	3097	0.618411	0.1014	0.6499	5008	,	,		11557	0.8581		0.83	False		,,,				2504	0.8303				p.A18T		Atlas-SNP	.											.	HOXA7	34	.	0			c.G52A						PASS	.	C	THR/ALA	924,3476		117,690,1393	62.0	77.0	72.0		52	4.3	1.0	7	dbSNP_100	72	7180,1414		3008,1164,125	yes	missense	HOXA7	NM_006896.3	58	3125,1854,1518	TT,TC,CC		16.4533,21.0,37.6328	benign	18/231	27196113	8104,4890	2200	4297	6497	SO:0001583	missense	3204	exon1			GAGAAGCCCCCGC		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"""Homeoboxes / ANTP class : HOXL subclass"""	5108	protein-coding gene	gene with protein product		142950	"""homeo box A7"""	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.52G>A	7.37:g.27196113C>T	ENSP00000242159:p.Ala18Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	37	CCDS5408.1	1439	0.6588827838827839	81	0.16463414634146342	243	0.6712707182320442	483	0.8444055944055944	632	0.8337730870712401	C	13.23	2.173748	0.38413	0.21	0.835467	ENSG00000122592	ENST00000242159;ENST00000519842	T;T	0.63096	1.58;-0.02	5.21	4.34	0.51931	.	0.190595	0.43919	N	0.000503	T	0.00012	0.0000	N	0.19112	0.55	0.25878	P	0.9836271	B	0.23128	0.08	B	0.16289	0.015	T	0.25433	-1.0132	9	0.21540	T	0.41	.	13.6625	0.62376	0.0:0.9241:0.0:0.0759	rs2301721;rs58981696;rs2301721	18	P31268	HXA7_HUMAN	T	18	ENSP00000242159:A18T;ENSP00000428563:A18T	ENSP00000242159:A18T	A	-	1	0	HOXA7	27162638	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.781000	0.47750	1.341000	0.45600	0.561000	0.74099	GCT	C|0.328;T|0.672	0.672	strong		0.532	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1		
SAMD9	54809	hgsc.bcm.edu	37	7	92733766	92733766	+	Missense_Mutation	SNP	C	C	A	rs10279499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:92733766C>A	ENST00000379958.2	-	3	1914	c.1645G>T	c.(1645-1647)Gtg>Ttg	p.V549L		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	549			V -> L (in dbSNP:rs10279499).			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			GGGTCATCCACAGAGGACAGT	0.403													C|||	485	0.096845	0.1195	0.0994	5008	,	,		19903	0.1359		0.0974	False		,,,				2504	0.0235				p.V549L		Atlas-SNP	.											.	SAMD9	239	.	0			c.G1645T						PASS	.	C	LEU/VAL,LEU/VAL	581,3825	245.6+/-254.5	41,499,1663	87.0	90.0	89.0		1645,1645	3.4	0.5	7	dbSNP_119	89	879,7719	194.8+/-240.1	50,779,3470	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	32,32	91,1278,5133	AA,AC,CC		10.2233,13.1866,11.2273	possibly-damaging,possibly-damaging	549/1590,549/1590	92733766	1460,11544	2203	4299	6502	SO:0001583	missense	54809	exon2			CATCCACAGAGGA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1645G>T	7.37:g.92733766C>A	ENSP00000369292:p.Val549Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	256	0.11721611721611722	55	0.11178861788617886	38	0.10497237569060773	94	0.16433566433566432	69	0.09102902374670185	C	9.680	1.148940	0.21288	0.131866	0.102233	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.17213	2.29;2.29	4.25	3.37	0.38596	.	0.000000	0.51477	U	0.000083	T	0.00109	0.0003	M	0.76002	2.32	0.30847	P	0.7349859999999999	D	0.58268	0.982	P	0.45660	0.489	T	0.11518	-1.0584	9	0.72032	D	0.01	.	11.0892	0.48106	0.0:0.9068:0.0:0.0932	rs10279499;rs10279499	549	Q5K651	SAMD9_HUMAN	L	549	ENSP00000369292:V549L;ENSP00000414529:V549L	ENSP00000369292:V549L	V	-	1	0	SAMD9	92571702	0.999000	0.42202	0.539000	0.28077	0.069000	0.16628	3.695000	0.54749	1.147000	0.42369	0.603000	0.83216	GTG	C|0.882;A|0.118	0.118	strong		0.403	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
CDH20	28316	hgsc.bcm.edu	37	18	59174759	59174759	+	Missense_Mutation	SNP	C	C	A	rs1943330	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:59174759C>A	ENST00000262717.4	+	6	1381	c.983C>A	c.(982-984)cCc>cAc	p.P328H	CDH20_ENST00000538374.1_Missense_Mutation_p.P328H|CDH20_ENST00000536675.2_Missense_Mutation_p.P328H			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	328	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> H (in dbSNP:rs1943330).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				AGCACAGATCCCAATTTCCAA	0.393													C|||	297	0.0593051	0.0121	0.0793	5008	,	,		17704	0.0317		0.1461	False		,,,				2504	0.0481				p.P328H		Atlas-SNP	.											CDH20,right_upper_lobe,carcinoma,-1,1	CDH20	117	1	0			c.C983A						PASS	.	C	HIS/PRO	124,4282	92.0+/-130.7	1,122,2080	167.0	141.0	150.0		983	4.9	1.0	18	dbSNP_92	150	1220,7380	246.1+/-274.7	87,1046,3167	yes	missense	CDH20	NM_031891.2	77	88,1168,5247	AA,AC,CC		14.186,2.8143,10.3337	probably-damaging	328/802	59174759	1344,11662	2203	4300	6503	SO:0001583	missense	28316	exon5			CAGATCCCAATTT	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.983C>A	18.37:g.59174759C>A	ENSP00000262717:p.Pro328His	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	165	0.07554945054945054	10	0.02032520325203252	33	0.09116022099447514	18	0.03146853146853147	104	0.13720316622691292	C	16.95	3.263748	0.59431	0.028143	0.14186	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.53640	0.61;0.61;0.61	5.76	4.89	0.63831	Cadherin (4);Cadherin-like (1);	0.053678	0.85682	D	0.000000	T	0.01156	0.0038	M	0.81341	2.54	0.22581	P	0.99896011	D	0.76494	0.999	D	0.73708	0.981	T	0.14504	-1.0470	9	0.52906	T	0.07	.	16.4267	0.83816	0.132:0.868:0.0:0.0	rs1943330;rs17749069;rs52809328;rs57072012;rs1943330	328	Q9HBT6	CAD20_HUMAN	H	328	ENSP00000444767:P328H;ENSP00000442226:P328H;ENSP00000262717:P328H	ENSP00000262717:P328H	P	+	2	0	CDH20	57325739	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.904000	0.56325	1.411000	0.46957	0.555000	0.69702	CCC	C|0.911;A|0.089	0.089	strong		0.393	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
BDH1	622	hgsc.bcm.edu	37	3	197241286	197241286	+	Splice_Site	SNP	G	G	C	rs35089738	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:197241286G>C	ENST00000392378.2	-	6	721	c.411C>G	c.(409-411)ggC>ggG	p.G137G	BDH1_ENST00000392379.1_Splice_Site_p.G137G|BDH1_ENST00000358186.2_Splice_Site_p.G137G|BDH1_ENST00000441275.1_Splice_Site_p.G50G	NM_004051.4	NP_004042.1	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	137					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|response to cadmium ion (GO:0046686)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to growth hormone (GO:0060416)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|phospholipid binding (GO:0005543)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)		GGCCCCACATGCCTGGACAGG	0.572													C|||	391	0.0780751	0.1687	0.0634	5008	,	,		20500	0.001		0.0656	False		,,,				2504	0.0583				p.G137G		Atlas-SNP	.											.	BDH1	24	.	0			c.C411G						PASS	.	C	,,	624,3782	768.3+/-413.6	48,528,1627	114.0	104.0	107.0		411,411,411	-3.8	0.3	3	dbSNP_126	107	555,8045	794.2+/-407.5	22,511,3767	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	BDH1	NM_004051.4,NM_203314.2,NM_203315.2	,,	70,1039,5394	CC,CG,GG		6.4535,14.1625,9.065	,,	137/344,137/344,137/344	197241286	1179,11827	2203	4300	6503	SO:0001630	splice_region_variant	622	exon6			CCACATGCCTGGA	M93107	CCDS3328.1	3q29	2011-09-14	2005-11-15	2005-11-15	ENSG00000161267	ENSG00000161267	1.1.1.30	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	1027	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 1"""	603063	"""3-hydroxybutyrate dehydrogenase (heart, mitochondrial)"""	BDH		1639787, 19027726	Standard	XM_005269352		Approved	SDR9C1	uc003fxs.3	Q02338	OTTHUMG00000155478	ENST00000392378.2:c.410-1C>G	3.37:g.197241286G>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	115	69	0.6	NM_004051	D3DXC0|Q96ET1|Q9BRZ4	Silent	SNP	ENST00000392378.2	37	CCDS3328.1																																																																																			G|0.909;C|0.091	0.091	strong		0.572	BDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340267.1	NM_004051	Silent
KDM5B	10765	hgsc.bcm.edu	37	1	202710733	202710733	+	Missense_Mutation	SNP	C	C	G	rs112284833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202710733C>G	ENST00000367265.3	-	19	3871	c.2707G>C	c.(2707-2709)Gaa>Caa	p.E903Q	KDM5B_ENST00000367264.2_Missense_Mutation_p.E939Q	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	903					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						TGTGGAAGTTCAACATCAAAT	0.483													C|||	57	0.0113818	0.0015	0.0216	5008	,	,		19289	0.0		0.0388	False		,,,				2504	0.001				p.E903Q		Atlas-SNP	.											.	KDM5B	166	.	0			c.G2707C						PASS	.	C	GLN/GLU	28,4378	33.5+/-64.1	0,28,2175	92.0	82.0	85.0		2707	5.9	1.0	1	dbSNP_132	85	249,8351	99.3+/-160.8	5,239,4056	yes	missense	KDM5B	NM_006618.3	29	5,267,6231	GG,GC,CC		2.8953,0.6355,2.1298	possibly-damaging	903/1545	202710733	277,12729	2203	4300	6503	SO:0001583	missense	10765	exon19			GAAGTTCAACATC	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.2707G>C	1.37:g.202710733C>G	ENSP00000356234:p.Glu903Gln	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	40	0.018315018315018316	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	28	0.036939313984168866	C	28.1	4.894029	0.91889	0.006355	0.028953	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790;ENST00000543924	T;T;T	0.50001	0.76;0.76;0.76	5.95	5.95	0.96441	Lysine-specific demethylase-like domain (1);	0.178327	0.64402	D	0.000012	T	0.37210	0.0995	M	0.72894	2.215	0.58432	D	0.999996	D;P	0.55605	0.972;0.934	P;P	0.62885	0.675;0.908	T	0.58584	-0.7611	10	0.72032	D	0.01	-19.1952	20.3789	0.98926	0.0:1.0:0.0:0.0	.	939;903	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	Q	903;745;939;745;272	ENSP00000356234:E903Q;ENSP00000356233:E939Q;ENSP00000235790:E745Q	ENSP00000235790:E745Q	E	-	1	0	KDM5B	200977356	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.554000	0.60760	2.826000	0.97356	0.563000	0.77884	GAA	C|0.980;G|0.020	0.020	strong		0.483	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
IFNAR2	3455	hgsc.bcm.edu	37	21	34614255	34614255	+	Missense_Mutation	SNP	T	T	G	rs1051393	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:34614255T>G	ENST00000342136.4	+	2	354	c.28T>G	c.(28-30)Ttc>Gtc	p.F10V	IFNAR2_ENST00000420068.1_3'UTR|IFNAR2_ENST00000413881.1_Intron|IFNAR2_ENST00000382241.3_Missense_Mutation_p.F10V|IFNAR2_ENST00000404220.3_Missense_Mutation_p.F10V|IFNAR2_ENST00000342101.3_Missense_Mutation_p.F10V|IFNAR2_ENST00000382264.3_Missense_Mutation_p.F10V			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	10			F -> V (in dbSNP:rs1051393). {ECO:0000269|PubMed:16757563, ECO:0000269|PubMed:7759950, ECO:0000269|PubMed:8181059, ECO:0000269|Ref.5, ECO:0000269|Ref.6}.		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	TGCCTTCATCTTCAGATCACT	0.393													G|||	1962	0.391773	0.171	0.4481	5008	,	,		20781	0.5754		0.333	False		,,,				2504	0.5215				p.F10V		Atlas-SNP	.											.	IFNAR2	44	.	0			c.T28G	GRCh37	CM057711	IFNAR2	M	rs1051393	PASS	.	G	VAL/PHE,VAL/PHE,VAL/PHE	828,3578	747.1+/-411.8	86,656,1461	191.0	170.0	177.0		28,28,28	-7.2	0.0	21	dbSNP_86	177	2726,5874	681.0+/-403.7	408,1910,1982	yes	missense,missense,missense	IFNAR2	NM_000874.3,NM_207584.1,NM_207585.1	50,50,50	494,2566,3443	GG,GT,TT		31.6977,18.7926,27.3258	benign,benign,benign	10/332,10/332,10/516	34614255	3554,9452	2203	4300	6503	SO:0001583	missense	3455	exon2			TTCATCTTCAGAT		CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110		"""Interferons"""	5433	protein-coding gene	gene with protein product		602376		IFNABR		8181059	Standard	NM_207585		Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.28T>G	21.37:g.34614255T>G	ENSP00000343957:p.Phe10Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_207585	A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	Missense_Mutation	SNP	ENST00000342136.4	37	CCDS13621.1	835	0.3823260073260073	82	0.16666666666666666	158	0.43646408839779005	342	0.5979020979020979	253	0.3337730870712401	G	5.665	0.307370	0.10733	0.187926	0.316977	ENSG00000159110	ENST00000382264;ENST00000404220;ENST00000382241;ENST00000342136;ENST00000342101;ENST00000447980	T;T;T;T;T;T	0.26810	2.14;2.14;2.19;2.19;2.18;1.71	4.51	-7.2	0.01495	.	1.247330	0.05490	N	0.556450	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38436	-0.9661	9	0.02654	T	1	.	6.9718	0.24652	0.2442:0.0:0.513:0.2429	rs1051393;rs2229208;rs3191789;rs4986955;rs7279064;rs17413985;rs17856075;rs17860177;rs52819787;rs7279064	10;10;10	P48551-3;P48551;P48551-2	.;INAR2_HUMAN;.	V	10;10;10;10;10;34	ENSP00000371699:F10V;ENSP00000384309:F10V;ENSP00000371676:F10V;ENSP00000343957:F10V;ENSP00000343289:F10V;ENSP00000402311:F34V	ENSP00000343289:F10V	F	+	1	0	IFNAR2	33536125	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.080000	0.01368	-1.939000	0.01044	-1.389000	0.01157	TTC	A|0.000;G|0.315;T|0.685	0.315	strong		0.393	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139825.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13865980	13865980	+	Silent	SNP	T	T	C	rs7703349	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13865980T>C	ENST00000265104.4	-	27	4256	c.4152A>G	c.(4150-4152)acA>acG	p.T1384T	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1384	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T1384T(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTCCAGTATATGTGATGTATT	0.318									Kartagener syndrome				C|||	2347	0.46865	0.5968	0.3401	5008	,	,		18627	0.3323		0.4652	False		,,,				2504	0.5307				p.T1384T		Atlas-SNP	.											DNAH5,NS,carcinoma,0,1	DNAH5	868	1	1	Substitution - coding silent(1)	stomach(1)	c.A4152G						PASS	.	C		2506,1892		718,1070,411	49.0	55.0	53.0		4152	1.8	1.0	5	dbSNP_116	53	4011,4581		985,2041,1270	no	coding-synonymous	DNAH5	NM_001369.2		1703,3111,1681	CC,CT,TT		46.683,43.0196,49.8306		1384/4625	13865980	6517,6473	2199	4296	6495	SO:0001819	synonymous_variant	1767	exon27	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTATATGTGATG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.4152A>G	5.37:g.13865980T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.533;C|0.467	0.467	strong		0.318	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
PIEZO1	9780	hgsc.bcm.edu	37	16	88779032	88779032	+	IGR	SNP	G	G	C	rs2290896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88779032G>C	ENST00000301015.9	-	0	8072				CTU2_ENST00000312060.5_Silent_p.V152V|CTU2_ENST00000453996.2_Silent_p.V152V|CTU2_ENST00000378384.3_Silent_p.V65V|CTU2_ENST00000567949.1_Silent_p.V223V	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						CCCGGAAGGTGTTCAGCCTGC	0.692													G|||	474	0.0946486	0.0318	0.1556	5008	,	,		12054	0.127		0.1243	False		,,,				2504	0.0726				p.V152V		Atlas-SNP	.											CTU2_ENST00000453996,NS,carcinoma,0,2	CTU2	66	2	0			c.G456C						PASS	.	G	,	212,4180		4,204,1988	27.0	33.0	31.0		456,456	3.1	1.0	16	dbSNP_100	31	1191,7405		74,1043,3181	no	coding-synonymous,coding-synonymous	CTU2	NM_001012759.1,NM_001012762.1	,	78,1247,5169	CC,CG,GG		13.8553,4.827,10.8023	,	152/516,152/486	88779032	1403,11585	2196	4298	6494	SO:0001628	intergenic_variant	348180	exon7			GAAGGTGTTCAGC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776		16.37:g.88779032G>C		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	159	72	0.45283	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1																																																																																			G|0.895;C|0.105	0.105	strong		0.692	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
C4orf47	441054	hgsc.bcm.edu	37	4	186366181	186366181	+	Missense_Mutation	SNP	G	G	A	rs74560263	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:186366181G>A	ENST00000378850.4	+	6	800	c.778G>A	c.(778-780)Gct>Act	p.A260T		NM_001114357.1	NP_001107829.1	A7E2U8	CD047_HUMAN	chromosome 4 open reading frame 47	260										breast(2)|endometrium(1)	3						CCCTTATGTGGCTAAATTGGC	0.403													G|||	349	0.0696885	0.0363	0.0908	5008	,	,		17154	0.0109		0.1034	False		,,,				2504	0.1258				p.A260T		Atlas-SNP	.											.	C4orf47	13	.	0			c.G778A						PASS	.	G	THR/ALA	54,1330		2,50,640	149.0	125.0	132.0		778	-1.6	0.0	4	dbSNP_131	132	291,2891		13,265,1313	yes	missense	C4orf47	NM_001114357.1	58	15,315,1953	AA,AG,GG		9.1452,3.9017,7.5558	benign	260/310	186366181	345,4221	692	1591	2283	SO:0001583	missense	441054	exon6			TATGTGGCTAAAT	AY947525, BC127739, BC141967	CCDS47169.1	4q35.1	2008-07-18			ENSG00000205129	ENSG00000205129			34346	protein-coding gene	gene with protein product						12477932	Standard	NM_001114357		Approved	LOC441054	uc003ixt.2	A7E2U8	OTTHUMG00000160458	ENST00000378850.4:c.778G>A	4.37:g.186366181G>A	ENSP00000368127:p.Ala260Thr	Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	251	134	0.533865	NM_001114357	Q5BLP7	Missense_Mutation	SNP	ENST00000378850.4	37	CCDS47169.1	132	0.06043956043956044	12	0.024390243902439025	34	0.09392265193370165	4	0.006993006993006993	82	0.10817941952506596	G	0.152	-1.090902	0.01858	0.039017	0.091452	ENSG00000205129	ENST00000378850	.	.	.	5.68	-1.63	0.08345	.	.	.	.	.	T	0.00210	0.0006	N	0.02916	-0.46	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.30416	-0.9979	7	0.10377	T	0.69	-0.0288	3.3421	0.07122	0.3937:0.105:0.3953:0.106	.	260	A7E2U8	CD047_HUMAN	T	260	.	ENSP00000368127:A260T	A	+	1	0	C4orf47	186603175	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.285000	0.18883	-0.250000	0.09555	-1.012000	0.02466	GCT	G|0.938;A|0.062	0.062	strong		0.403	C4orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360667.1	NM_001114357	
POP1	10940	hgsc.bcm.edu	37	8	99170404	99170404	+	Missense_Mutation	SNP	C	C	G	rs17856355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:99170404C>G	ENST00000401707.2	+	16	3061	c.2980C>G	c.(2980-2982)Ctg>Gtg	p.L994V	POP1_ENST00000349693.3_Missense_Mutation_p.L994V	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	994			L -> V (in dbSNP:rs17856355).		RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			GCTGGATATGCTGTCCAGCCA	0.547													C|||	191	0.038139	0.0507	0.0504	5008	,	,		14398	0.003		0.0577	False		,,,				2504	0.0286				p.L994V		Atlas-SNP	.											.	POP1	85	.	0			c.C2980G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU	223,4183	131.4+/-167.9	4,215,1984	75.0	74.0	74.0		2980,2980,2980	3.8	0.6	8	dbSNP_123	74	379,8221	122.7+/-181.7	11,357,3932	yes	missense,missense,missense	POP1	NM_001145860.1,NM_001145861.1,NM_015029.2	32,32,32	15,572,5916	GG,GC,CC		4.407,5.0613,4.6286	probably-damaging,probably-damaging,probably-damaging	994/1025,994/1025,994/1025	99170404	602,12404	2203	4300	6503	SO:0001583	missense	10940	exon16			GATATGCTGTCCA	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"""processing of precursors 1"""	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.2980C>G	8.37:g.99170404C>G	ENSP00000385787:p.Leu994Val	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	29	0.828571	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	71	0.03250915750915751	15	0.03048780487804878	14	0.03867403314917127	1	0.0017482517482517483	41	0.05408970976253298	C	18.20	3.571746	0.65765	0.050613	0.04407	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.14640	2.49;2.49	5.67	3.85	0.44370	.	0.000000	0.64402	D	0.000001	T	0.06781	0.0173	M	0.80847	2.515	0.43287	D	0.995263	D	0.89917	1.0	D	0.83275	0.996	T	0.00157	-1.1977	10	0.56958	D	0.05	-10.4741	6.7226	0.23338	0.0:0.6611:0.0:0.3389	rs17856355	994	Q99575	POP1_HUMAN	V	994	ENSP00000385787:L994V;ENSP00000339529:L994V	ENSP00000339529:L994V	L	+	1	2	POP1	99239580	1.000000	0.71417	0.579000	0.28588	0.939000	0.58152	3.796000	0.55507	0.720000	0.32209	0.557000	0.71058	CTG	C|0.954;G|0.046	0.046	strong		0.547	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029	
MTG2	26164	hgsc.bcm.edu	37	20	60768573	60768573	+	Missense_Mutation	SNP	C	C	T	rs41284984	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60768573C>T	ENST00000370823.3	+	2	115	c.97C>T	c.(97-99)Cgg>Tgg	p.R33W	MTG2_ENST00000436421.2_Missense_Mutation_p.R33W|MTG2_ENST00000536470.1_Intron	NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	33	Localized in the mitochondria.|Not localized in the mitochondria.				GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)										GAAGCCCAGCCGGCTACTGCC	0.627													C|||	66	0.0131789	0.0008	0.0231	5008	,	,		18183	0.0		0.0447	False		,,,				2504	0.0041				p.R33W		Atlas-SNP	.											.	GTPBP5	43	.	0			c.C97T						PASS	.	C	TRP/ARG	36,4370	40.8+/-73.8	0,36,2167	65.0	69.0	68.0		97	-5.4	0.0	20	dbSNP_127	68	369,8231	121.8+/-180.9	9,351,3940	yes	missense	GTPBP5	NM_015666.3	101	9,387,6107	TT,TC,CC		4.2907,0.8171,3.1139	benign	33/407	60768573	405,12601	2203	4300	6503	SO:0001583	missense	26164	exon2			CCCAGCCGGCTAC	AK001603	CCDS13492.1	20q13.33	2013-05-24	2013-05-24	2013-05-24	ENSG00000101181	ENSG00000101181			16239	protein-coding gene	gene with protein product		610919	"""GTP-binding protein 5 (putative)"", ""GTP binding protein 5 (putative)"""	GTPBP5		17054726, 23396448	Standard	NM_015666		Approved	FLJ10741, dJ1005F21.2, ObgH1		Q9H4K7	OTTHUMG00000032897	ENST00000370823.3:c.97C>T	20.37:g.60768573C>T	ENSP00000359859:p.Arg33Trp	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	178	90	0.505618	NM_015666	A6NDR3|B4DR85|Q96I17|Q9NVG9|Q9UFR4	Missense_Mutation	SNP	ENST00000370823.3	37	CCDS13492.1	44	0.020146520146520148	0	0.0	11	0.03038674033149171	0	0.0	33	0.04353562005277045	C	12.21	1.869502	0.32977	0.008171	0.042907	ENSG00000101181	ENST00000436421;ENST00000370823;ENST00000448254	T;T;T	0.24350	1.86;2.68;2.18	4.17	-5.4	0.02656	.	3.317530	0.00654	N	0.000566	T	0.02380	0.0073	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.14337	-1.0476	10	0.36615	T	0.2	-0.151	3.8869	0.09102	0.398:0.1715:0.0:0.4305	rs41284984	33;33;33	Q5JXJ0;E7EU10;Q9H4K7	.;.;GTPB5_HUMAN	W	33	ENSP00000392267:R33W;ENSP00000359859:R33W;ENSP00000414693:R33W	ENSP00000359859:R33W	R	+	1	2	GTPBP5	60201968	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.749000	0.04813	-0.992000	0.03472	-0.203000	0.12734	CGG	A|0.000;C|0.973;T|0.027	0.027	strong		0.627	MTG2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079989.1	NM_015666	
AP4B1	10717	hgsc.bcm.edu	37	1	114443899	114443899	+	Silent	SNP	G	G	A	rs17464525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:114443899G>A	ENST00000369569.1	-	4	856	c.576C>T	c.(574-576)ggC>ggT	p.G192G	AP4B1_ENST00000369566.3_Intron|AP4B1_ENST00000256658.4_Silent_p.G192G|AP4B1_ENST00000369567.1_Intron|AP4B1-AS1_ENST00000419536.1_RNA	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	192					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGATGACAACGCCTCCTTCCT	0.433													G|||	613	0.122404	0.0605	0.1124	5008	,	,		17226	0.1776		0.1819	False		,,,				2504	0.0951				p.G192G		Atlas-SNP	.											.	AP4B1	72	.	0			c.C576T						PASS	.	G		417,3989	204.5+/-226.7	20,377,1806	113.0	110.0	111.0		576	-4.8	0.9	1	dbSNP_123	111	1635,6965	303.4+/-306.4	148,1339,2813	no	coding-synonymous	AP4B1	NM_006594.2		168,1716,4619	AA,AG,GG		19.0116,9.4644,15.7773		192/740	114443899	2052,10954	2203	4300	6503	SO:0001819	synonymous_variant	10717	exon5			GACAACGCCTCCT	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"""beta 4 subunit of AP-4"""	607245	"""spastic paraplegia 47"""	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.576C>T	1.37:g.114443899G>A		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	223	129	0.578475	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Silent	SNP	ENST00000369569.1	37	CCDS865.1																																																																																			G|0.856;A|0.144	0.144	strong		0.433	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594	
ENO3	2027	hgsc.bcm.edu	37	17	4856376	4856376	+	Missense_Mutation	SNP	A	A	G	rs238238	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4856376A>G	ENST00000323997.6	+	4	344	c.212A>G	c.(211-213)aAt>aGt	p.N71S	ENO3_ENST00000519584.1_Intron|ENO3_ENST00000518175.1_Missense_Mutation_p.N71S	NM_001976.4|NM_053013.3	NP_001967.3|NP_443739.3	P13929	ENOB_HUMAN	enolase 3 (beta, muscle)	71			N -> S (in dbSNP:rs238238). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8513787}.		aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to drug (GO:0042493)|skeletal muscle tissue regeneration (GO:0043403)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			cervix(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)	15						AACATCAACAATACTCTGGGC	0.602													A|||	2825	0.564097	0.5499	0.7795	5008	,	,		17474	0.3988		0.6809	False		,,,				2504	0.4806				p.N71S		Atlas-SNP	.											ENO3,NS,carcinoma,0,1	ENO3	36	1	0			c.A212G						PASS	.	A	,SER/ASN,SER/ASN	2639,1767	644.5+/-398.0	780,1079,344	79.0	75.0	76.0		,212,212	5.4	1.0	17	dbSNP_79	76	6063,2537	692.7+/-404.6	2127,1809,364	yes	intron,missense,missense	ENO3	NM_001193503.1,NM_001976.4,NM_053013.3	,46,46	2907,2888,708	GG,GA,AA		29.5,40.1044,33.0924	,benign,benign	,71/435,71/435	4856376	8702,4304	2203	4300	6503	SO:0001583	missense	2027	exon4			TCAACAATACTCT	X16504	CCDS11062.1, CCDS54070.1	17p13.2	2013-09-19	2004-11-22		ENSG00000108515	ENSG00000108515	4.2.1.11		3354	protein-coding gene	gene with protein product		131370	"""enolase 3, (beta, muscle)"""				Standard	NM_001976		Approved		uc002gab.4	P13929	OTTHUMG00000099394	ENST00000323997.6:c.212A>G	17.37:g.4856376A>G	ENSP00000324105:p.Asn71Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	156	84	0.538462	NM_001976	B4DUI6|B4DUM6|D3DTL2|E7ENK8|Q96AE2	Missense_Mutation	SNP	ENST00000323997.6	37	CCDS11062.1	1308	0.5989010989010989	292	0.5934959349593496	279	0.7707182320441989	221	0.38636363636363635	516	0.6807387862796834	A	13.59	2.282795	0.40394	0.598956	0.705	ENSG00000108515	ENST00000522798;ENST00000519602;ENST00000323997;ENST00000522249;ENST00000518175	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.4	5.4	0.78164	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.40295	P	0.02145600000000003	B	0.02656	0.0	B	0.04013	0.001	T	0.22312	-1.0220	7	0.33141	T	0.24	-15.9177	13.6512	0.62312	1.0:0.0:0.0:0.0	rs238238;rs2230256;rs3180329;rs3209189;rs11537779;rs58818159;rs238238	71	D3DTL2	.	S	71	ENSP00000428502:N71S;ENSP00000430055:N71S;ENSP00000324105:N71S;ENSP00000428811:N71S;ENSP00000431087:N71S	ENSP00000324105:N71S	N	+	2	0	ENO3	4797122	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.651000	0.54431	2.176000	0.68965	0.533000	0.62120	AAT	A|0.376;G|0.624	0.624	strong		0.602	ENO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216851.2		
FHIT	2272	hgsc.bcm.edu	37	3	59997112	59997112	+	Silent	SNP	G	G	A	rs1130972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:59997112G>A	ENST00000468189.1	-	7	634	c.264C>T	c.(262-264)gcC>gcT	p.A88A	FHIT_ENST00000476844.1_Silent_p.A88A|FHIT_ENST00000341848.4_Silent_p.A88A|FHIT_ENST00000466788.1_5'UTR|FHIT_ENST00000492590.1_Silent_p.A88A			P49789	FHIT_HUMAN	fragile histidine triad	88	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.				DNA replication (GO:0006260)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide metabolic process (GO:0009117)|purine nucleotide metabolic process (GO:0006163)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|catalytic activity (GO:0003824)|hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)	12		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		CAGTCTGTCCGGCTTCGGGGC	0.378			T	HMGA2	pleomorphic salivary gland adenoma				Renal Cell Cancer associated with constitutional translocation of chromosome 3				g|||	411	0.0820687	0.0681	0.1571	5008	,	,		19215	0.0		0.1491	False		,,,				2504	0.0634				p.A88A		Atlas-SNP	.		Dom	yes		3	3p14.2	2272	fragile histidine triad gene		E	.	FHIT	44	.	0			c.C264T						PASS	.	A	,	337,4069	175.5+/-204.9	14,309,1880	76.0	81.0	79.0		264,264	-11.1	0.4	3	dbSNP_123	79	1371,7229	266.3+/-286.6	115,1141,3044	no	coding-synonymous,coding-synonymous	FHIT	NM_001166243.1,NM_002012.2	,	129,1450,4924	AA,AG,GG		15.9419,7.6487,13.1324	,	88/148,88/148	59997112	1708,11298	2203	4300	6503	SO:0001819	synonymous_variant	2272	exon7	Familial Cancer Database		CTGTCCGGCTTCG	BC032336	CCDS2894.1	3p14.2	2012-02-27	2012-02-27		ENSG00000189283	ENSG00000189283			3701	protein-coding gene	gene with protein product		601153	"""fragile histidine triad gene"""			8598045, 9671749	Standard	NM_002012		Approved	FRA3B, AP3Aase	uc003dky.3	P49789	OTTHUMG00000158591	ENST00000468189.1:c.264C>T	3.37:g.59997112G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	179	98	0.547486	NM_002012	A2IAS9|A2IAT0|A2IAT6|A8K1A9|Q45QG9|Q6IU12	Silent	SNP	ENST00000468189.1	37	CCDS2894.1																																																																																			G|0.893;A|0.107	0.107	strong		0.378	FHIT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351648.1	NM_002012	
SEMA6D	80031	hgsc.bcm.edu	37	15	48053229	48053229	+	Silent	SNP	C	C	A	rs501916	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:48053229C>A	ENST00000316364.5	+	4	715	c.276C>A	c.(274-276)ccC>ccA	p.P92P	SEMA6D_ENST00000537942.1_Silent_p.P92P|SEMA6D_ENST00000355997.3_Silent_p.P92P|SEMA6D_ENST00000354744.4_Silent_p.P92P|SEMA6D_ENST00000389432.2_Silent_p.P92P|SEMA6D_ENST00000389428.3_Silent_p.P92P|SEMA6D_ENST00000536845.2_Silent_p.P92P|SEMA6D_ENST00000558014.1_Silent_p.P92P|SEMA6D_ENST00000358066.4_Silent_p.P92P|SEMA6D_ENST00000558816.1_Silent_p.P92P|SEMA6D_ENST00000389425.3_Silent_p.P92P|SEMA6D_ENST00000389433.2_Silent_p.P92P	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	92	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AAGTAATACCCAACAAGGTGA	0.353													A|||	2403	0.479832	0.5552	0.4107	5008	,	,		18970	0.6339		0.3469	False		,,,				2504	0.4049				p.P92P		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C276A						PASS	.	A	,,,,,,	2322,2074	565.1+/-381.6	599,1124,475	82.0	79.0	80.0		276,276,276,276,276,276,276	3.4	1.0	15	dbSNP_83	80	2785,5809	675.4+/-403.2	456,1873,1968	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEMA6D	NM_001198999.1,NM_020858.1,NM_024966.2,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	,,,,,,	1055,2997,2443	AA,AC,CC		32.4063,47.1793,39.3149	,,,,,,	92/1012,92/1012,92/477,92/999,92/1018,92/1074,92/598	48053229	5107,7883	2198	4297	6495	SO:0001819	synonymous_variant	80031	exon4			AATACCCAACAAG	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.276C>A	15.37:g.48053229C>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	205	86	0.419512	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																			C|0.567;A|0.433	0.433	strong		0.353	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
OR5F1	338674	hgsc.bcm.edu	37	11	55762060	55762060	+	Silent	SNP	T	T	C	rs71490418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55762060T>C	ENST00000278409.1	-	1	41	c.42A>G	c.(40-42)ctA>ctG	p.L14L		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	14					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					CTAATCCCAATAGGACGAACT	0.348													T|||	673	0.134385	0.0303	0.2089	5008	,	,		18031	0.1419		0.1789	False		,,,				2504	0.1687				p.L14L		Atlas-SNP	.											OR5F1,rectum,carcinoma,-2,2	OR5F1	116	2	0			c.A42G						PASS	.	T		248,4154	139.2+/-174.8	6,236,1959	59.0	61.0	60.0		42	-2.7	0.3	11	dbSNP_130	60	1660,6932	302.8+/-306.1	180,1300,2816	no	coding-synonymous	OR5F1	NM_003697.1		186,1536,4775	CC,CT,TT		19.3203,5.6338,14.6837		14/315	55762060	1908,11086	2201	4296	6497	SO:0001819	synonymous_variant	338674	exon1			TCCCAATAGGACG	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.42A>G	11.37:g.55762060T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	NM_003697	Q495D1|Q6IFB9	Silent	SNP	ENST00000278409.1	37	CCDS31515.1																																																																																			T|0.844;C|0.156	0.156	strong		0.348	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
LARS	51520	hgsc.bcm.edu	37	5	145539996	145539996	+	Silent	SNP	T	T	G	rs11540214	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145539996T>G	ENST00000394434.2	-	7	814	c.648A>C	c.(646-648)tcA>tcC	p.S216S	LARS_ENST00000545646.1_Silent_p.S170S|LARS_ENST00000274562.9_Silent_p.S189S|LARS_ENST00000511505.1_5'UTR|LARS_ENST00000510191.1_Silent_p.S162S	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	216					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.S216S(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	ATCTGACAAATGAATCATAGT	0.308																																					p.S216S		Atlas-SNP	.											LARS,NS,carcinoma,0,2	LARS	100	2	1	Substitution - coding silent(1)	stomach(1)	c.A648C						PASS	.	T		266,4140	145.7+/-180.5	12,242,1949	53.0	50.0	51.0		648	-11.4	0.6	5	dbSNP_120	51	2395,6205	388.3+/-342.5	350,1695,2255	no	coding-synonymous	LARS	NM_020117.9		362,1937,4204	GG,GT,TT		27.8488,6.0372,20.4598		216/1177	145539996	2661,10345	2203	4300	6503	SO:0001819	synonymous_variant	51520	exon7			GACAAATGAATCA	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.648A>C	5.37:g.145539996T>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	44	0.325926	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			T|0.793;G|0.207	0.207	strong		0.308	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
OR2B11	127623	hgsc.bcm.edu	37	1	247615252	247615252	+	Silent	SNP	G	G	A	rs12028142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247615252G>A	ENST00000318749.6	-	1	56	c.33C>T	c.(31-33)gaC>gaT	p.D11D		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CTTTAGGGGAGTCCCCTAAGA	0.488													G|||	510	0.101837	0.0061	0.1556	5008	,	,		21395	0.1935		0.1382	False		,,,				2504	0.0613				p.D11D		Atlas-SNP	.											.	OR2B11	102	.	0			c.C33T						PASS	.	G		123,4283	92.0+/-130.7	0,123,2080	111.0	125.0	120.0		33	-9.6	0.0	1	dbSNP_120	120	1118,7482	231.4+/-265.4	79,960,3261	no	coding-synonymous	OR2B11	NM_001004492.1		79,1083,5341	AA,AG,GG		13.0,2.7916,9.5417		11/318	247615252	1241,11765	2203	4300	6503	SO:0001819	synonymous_variant	127623	exon1			AGGGGAGTCCCCT		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"""GPCR / Class A : Olfactory receptors"""	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.33C>T	1.37:g.247615252G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_001004492	B2RP03	Silent	SNP	ENST00000318749.6	37	CCDS31090.1																																																																																			G|0.898;A|0.102	0.102	strong		0.488	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
IFNB1	3456	hgsc.bcm.edu	37	9	21077716	21077716	+	Silent	SNP	G	G	A	rs1051922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:21077716G>A	ENST00000380232.2	-	1	227	c.153C>T	c.(151-153)taC>taT	p.Y51Y		NM_002176.2	NP_002167.1	P01574	IFNB_HUMAN	interferon, beta 1, fibroblast	51					adaptive immune response (GO:0002250)|B cell activation involved in immune response (GO:0002312)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of viral genome replication (GO:0045071)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	12				GBM - Glioblastoma multiforme(5;7.45e-142)|Lung(24;2.42e-17)|LUSC - Lung squamous cell carcinoma(38;7.17e-11)		CCTTGAGGCAGTATTCAAGCC	0.483													A|||	1644	0.328275	0.3979	0.2608	5008	,	,		20472	0.3204		0.3579	False		,,,				2504	0.2597				p.Y51Y		Atlas-SNP	.											.	IFNB1	33	.	0			c.C153T						PASS	.	A		1651,2755	657.8+/-400.3	300,1051,852	69.0	68.0	68.0		153	-8.9	0.0	9	dbSNP_86	68	2819,5781	674.9+/-403.2	472,1875,1953	no	coding-synonymous	IFNB1	NM_002176.2		772,2926,2805	AA,AG,GG		32.7791,37.4716,34.3688		51/188	21077716	4470,8536	2203	4300	6503	SO:0001819	synonymous_variant	3456	exon1			GAGGCAGTATTCA		CCDS6495.1	9p22	2008-07-21			ENSG00000171855	ENSG00000171855		"""Interferons"""	5434	protein-coding gene	gene with protein product		147640		IFNB			Standard	NM_002176		Approved	IFB, IFF	uc003zok.3	P01574	OTTHUMG00000019652	ENST00000380232.2:c.153C>T	9.37:g.21077716G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_002176	Q5VWC9	Silent	SNP	ENST00000380232.2	37	CCDS6495.1																																																																																			G|0.656;N|0.000	.	strong		0.483	IFNB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051881.1	NM_002176	
FUT5	2527	hgsc.bcm.edu	37	19	5866724	5866724	+	Missense_Mutation	SNP	G	G	A	rs4807054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:5866724G>A	ENST00000588525.1	-	2	1100	c.1013C>T	c.(1012-1014)aCg>aTg	p.T338M	FUT5_ENST00000252675.5_Missense_Mutation_p.T338M	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	338			T -> M (in dbSNP:rs4807054).		carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						AGGCCGCAGCGTCTCCCGCCA	0.637													G|||	2004	0.40016	0.2254	0.5317	5008	,	,		12655	0.5516		0.3837	False		,,,				2504	0.4039				p.T338M		Atlas-SNP	.											FUT5,colon,carcinoma,0,1	FUT5	29	1	0			c.C1013T						PASS	.	G	MET/THR	1061,3341		148,765,1288	24.0	32.0	29.0		1013	0.9	0.7	19	dbSNP_111	29	3181,5417		624,1933,1742	no	missense	FUT5	NM_002034.2	81	772,2698,3030	AA,AG,GG		36.997,24.1027,32.6308	probably-damaging	338/375	5866724	4242,8758	2201	4299	6500	SO:0001583	missense	2527	exon2			CGCAGCGTCTCCC		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.1013C>T	19.37:g.5866724G>A	ENSP00000466880:p.Thr338Met	Somatic	393	0	0		WXS	Illumina HiSeq	Phase_I	389	114	0.293059	NM_002034	A8K4X2	Missense_Mutation	SNP	ENST00000588525.1	37	CCDS12154.1	896	0.41025641025641024	110	0.22357723577235772	186	0.5138121546961326	333	0.5821678321678322	267	0.35224274406332456	G	11.71	1.720979	0.30503	0.241027	0.36997	ENSG00000130383	ENST00000252675	T	0.24350	1.86	2.17	0.912	0.19349	.	0.954591	0.08565	N	0.926994	T	0.00012	0.0000	M	0.77486	2.375	0.52099	P	5.500000000002725E-5	P	0.38617	0.64	B	0.36186	0.219	T	0.46965	-0.9153	9	0.51188	T	0.08	.	7.4831	0.27417	0.0:0.0:0.7459:0.254	rs4807054;rs17748869;rs59555759;rs4807054	338	Q11128	FUT5_HUMAN	M	338	ENSP00000252675:T338M	ENSP00000252675:T338M	T	-	2	0	FUT5	5817724	0.000000	0.05858	0.661000	0.29709	0.253000	0.25986	0.495000	0.22483	1.211000	0.43351	0.407000	0.27541	ACG	G|0.603;A|0.397	0.397	strong		0.637	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
OR4B1	119765	hgsc.bcm.edu	37	11	48238880	48238880	+	Silent	SNP	C	C	T	rs10838833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:48238880C>T	ENST00000309562.2	+	1	537	c.519C>T	c.(517-519)gaC>gaT	p.D173D		NM_001005470.1	NP_001005470.1	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B, member 1	173						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						ATGTGATTGACCACTATTTCT	0.483													c|||	865	0.172724	0.2859	0.121	5008	,	,		21159	0.1637		0.1233	False		,,,				2504	0.1166				p.D173D		Atlas-SNP	.											.	OR4B1	52	.	0			c.C519T						PASS	.	C		1174,3228	412.8+/-336.2	167,840,1194	146.0	142.0	143.0		519	1.5	1.0	11	dbSNP_120	143	1142,7454	235.3+/-267.9	74,994,3230	no	coding-synonymous	OR4B1	NM_001005470.1		241,1834,4424	TT,TC,CC		13.2852,26.6697,17.8181		173/310	48238880	2316,10682	2201	4298	6499	SO:0001819	synonymous_variant	119765	exon1			GATTGACCACTAT	AB065848	CCDS31485.1	11p11.2	2012-08-09			ENSG00000175619	ENSG00000175619		"""GPCR / Class A : Olfactory receptors"""	8290	protein-coding gene	gene with protein product							Standard	NM_001005470		Approved	OST208	uc010rhs.2	Q8NGF8	OTTHUMG00000166576	ENST00000309562.2:c.519C>T	11.37:g.48238880C>T		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	283	136	0.480565	NM_001005470	Q6IF75|Q96R64	Silent	SNP	ENST00000309562.2	37	CCDS31485.1																																																																																			C|0.829;T|0.171	0.171	strong		0.483	OR4B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390554.1	NM_001005470	
ACSBG2	81616	hgsc.bcm.edu	37	19	6187657	6187657	+	Silent	SNP	C	C	T	rs16993453	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6187657C>T	ENST00000586696.1	+	13	2004	c.1728C>T	c.(1726-1728)ttC>ttT	p.F576F	ACSBG2_ENST00000591741.1_3'UTR|RFX2_ENST00000587700.1_5'Flank|ACSBG2_ENST00000591403.1_Silent_p.F576F|ACSBG2_ENST00000252669.5_Silent_p.F576F|ACSBG2_ENST00000588304.1_Silent_p.F526F|ACSBG2_ENST00000588485.1_Silent_p.F389F			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	576					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGCTGAACTTCGAGGCCATCA	0.582													C|||	475	0.0948482	0.23	0.0346	5008	,	,		17857	0.0417		0.0338	False		,,,				2504	0.0726				p.F576F		Atlas-SNP	.											.	ACSBG2	83	.	0			c.C1728T						PASS	.	C		803,3603	322.3+/-297.6	76,651,1476	133.0	97.0	109.0		1728	-1.9	0.1	19	dbSNP_123	109	298,8302	109.6+/-170.1	3,292,4005	no	coding-synonymous	ACSBG2	NM_030924.3		79,943,5481	TT,TC,CC		3.4651,18.2251,8.4653		576/667	6187657	1101,11905	2203	4300	6503	SO:0001819	synonymous_variant	81616	exon13			GAACTTCGAGGCC		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1728C>T	19.37:g.6187657C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Silent	SNP	ENST00000586696.1	37	CCDS12159.1																																																																																			C|0.909;T|0.091	0.091	strong		0.582	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
FBN3	84467	hgsc.bcm.edu	37	19	8160334	8160334	+	Missense_Mutation	SNP	G	G	A	rs12608849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8160334G>A	ENST00000600128.1	-	46	6124	c.5710C>T	c.(5710-5712)Ctc>Ttc	p.L1904F	FBN3_ENST00000270509.2_Missense_Mutation_p.L1904F|FBN3_ENST00000601739.1_Missense_Mutation_p.L1904F			Q75N90	FBN3_HUMAN	fibrillin 3	1904	EGF-like 30; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		L -> F (in dbSNP:rs12608849).|L -> P (in dbSNP:rs12608849). {ECO:0000269|PubMed:15221638}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GCTGTGTTGAGGCAATGGCCA	0.552													G|||	1550	0.309505	0.0613	0.2767	5008	,	,		18064	0.4881		0.2843	False		,,,				2504	0.5102				p.L1904F		Atlas-SNP	.											.	FBN3	300	.	0			c.C5710T						PASS	.	G	PHE/LEU	413,3993	203.1+/-225.7	22,369,1812	118.0	83.0	95.0		5710	-0.7	1.0	19	dbSNP_120	95	2173,6427	371.5+/-336.3	289,1595,2416	yes	missense	FBN3	NM_032447.3	22	311,1964,4228	AA,AG,GG		25.2674,9.3736,19.8831	benign	1904/2810	8160334	2586,10420	2203	4300	6503	SO:0001583	missense	84467	exon45			TGTTGAGGCAATG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5710C>T	19.37:g.8160334G>A	ENSP00000470498:p.Leu1904Phe	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	155	86	0.554839	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	629	0.288003663003663	34	0.06910569105691057	105	0.2900552486187845	275	0.4807692307692308	215	0.2836411609498681	G	1.717	-0.497540	0.04291	0.093736	0.252674	ENSG00000142449	ENST00000270509	D	0.87809	-2.3	4.68	-0.659	0.11424	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.119782	0.53938	U	0.000046	T	0.00012	0.0000	N	0.25789	0.76	0.37245	P	0.09371399999999996	B	0.21688	0.059	B	0.23275	0.045	T	0.33033	-0.9884	9	0.27082	T	0.32	.	3.9566	0.09393	0.0885:0.1042:0.416:0.3914	rs12608849;rs52826951;rs60158242;rs12608849	1904	Q75N90	FBN3_HUMAN	F	1904	ENSP00000270509:L1904F	ENSP00000270509:L1904F	L	-	1	0	FBN3	8066334	0.022000	0.18835	0.960000	0.40013	0.804000	0.45430	0.137000	0.15995	0.053000	0.16036	-0.211000	0.12701	CTC	G|0.757;A|0.243	0.243	strong		0.552	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
PRG4	10216	hgsc.bcm.edu	37	1	186276291	186276291	+	Silent	SNP	A	A	G	rs151267614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:186276291A>G	ENST00000445192.2	+	7	1485	c.1440A>G	c.(1438-1440)aaA>aaG	p.K480K	PRG4_ENST00000367485.4_Silent_p.K387K|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_Silent_p.K439K|PRG4_ENST00000367486.3_Silent_p.K437K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	480	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.K480K(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCACTCCCAAAGAGCCTGCAC	0.662													-|||	610	0.121805	0.1051	0.072	5008	,	,		8182	0.1319		0.1541	False		,,,				2504	0.136				p.K480K		Atlas-SNP	.											PRG4,NS,carcinoma,0,1	PRG4	259	1	1	Substitution - coding silent(1)	prostate(1)	c.A1440G						scavenged	.						89.0	94.0	92.0					1																	186276291		2198	4275	6473	SO:0001819	synonymous_variant	10216	exon7			TCCCAAAGAGCCT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1440A>G	1.37:g.186276291A>G		Somatic	232	15	0.0646552		WXS	Illumina HiSeq	Phase_I	303	22	0.0726073	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			A|0.906;G|0.094	0.094	strong		0.662	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
UBN1	29855	hgsc.bcm.edu	37	16	4930100	4930100	+	Silent	SNP	C	C	T	rs1876359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4930100C>T	ENST00000396658.4	+	17	4075	c.3372C>T	c.(3370-3372)caC>caT	p.H1124H	UBN1_ENST00000590769.1_Silent_p.H1094H|UBN1_ENST00000262376.6_Silent_p.H1124H|UBN1_ENST00000545171.1_Silent_p.H1094H	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	1124					chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						CTCAGCTTCACGGGAAAGGGC	0.488													C|||	1901	0.379593	0.2852	0.4582	5008	,	,		21591	0.3343		0.3767	False		,,,				2504	0.501				p.H1124H		Atlas-SNP	.											.	UBN1	88	.	0			c.C3372T						PASS	.	C	,	1305,3089	442.0+/-346.6	167,971,1059	132.0	129.0	130.0		3372,3372	-3.0	1.0	16	dbSNP_92	130	3073,5527	470.7+/-367.9	547,1979,1774	no	coding-synonymous,coding-synonymous	UBN1	NM_001079514.1,NM_016936.3	,	714,2950,2833	TT,TC,CC		35.7326,29.6996,33.6925	,	1124/1135,1124/1135	4930100	4378,8616	2197	4300	6497	SO:0001819	synonymous_variant	29855	exon18			GCTTCACGGGAAA	AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.3372C>T	16.37:g.4930100C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Silent	SNP	ENST00000396658.4	37	CCDS10525.1																																																																																			C|0.650;T|0.350	0.350	strong		0.488	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936	
FDX1L	112812	hgsc.bcm.edu	37	19	10426422	10426422	+	Silent	SNP	A	A	C	rs378395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10426422A>C	ENST00000393708.3	-	2	177	c.159T>G	c.(157-159)gcT>gcG	p.A53A	CTD-2369P2.12_ENST00000586529.1_3'UTR|FDX1L_ENST00000494368.1_5'UTR|FDX1L_ENST00000541276.1_Silent_p.A56A|FDX1L_ENST00000492239.1_5'UTR|CTD-2369P2.10_ENST00000452032.2_Silent_p.A53A	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	53					oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			NS(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(20;9.5e-10)|Epithelial(33;2.11e-06)|all cancers(31;5.06e-06)			CCTCCTCTCCAGCCGGGCGCG	0.726													C|||	2468	0.492812	0.6097	0.5576	5008	,	,		9095	0.3403		0.4781	False		,,,				2504	0.4611				p.A53A		Atlas-SNP	.											FDX1L,NS,carcinoma,0,1	FDX1L	21	1	0			c.T159G						scavenged	.	C		2227,1909		667,893,508	4.0	6.0	6.0		159	-3.4	0.0	19	dbSNP_80	6	3532,4618		870,1792,1413	no	coding-synonymous	FDX1L	NM_001031734.2		1537,2685,1921	CC,CA,AA		43.3374,46.1557,46.8745		53/184	10426422	5759,6527	2068	4075	6143	SO:0001819	synonymous_variant	112812	exon2			CTCTCCAGCCGGG	AK097022	CCDS32905.1	19p13.2	2012-10-09			ENSG00000267673	ENSG00000267673			30546	protein-coding gene	gene with protein product		614585				12477932	Standard	NM_001031734		Approved	MGC19604	uc002mny.1	Q6P4F2	OTTHUMG00000141299	ENST00000393708.3:c.159T>G	19.37:g.10426422A>C		Somatic	41	1	0.0243902		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_001031734	Q8N8B8	Silent	SNP	ENST00000393708.3	37	CCDS32905.1																																																																																			A|0.532;C|0.468	0.468	strong		0.726	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2		
VPS8	23355	hgsc.bcm.edu	37	3	184700426	184700426	+	Missense_Mutation	SNP	C	C	T	rs11555405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:184700426C>T	ENST00000437079.3	+	41	3664	c.3493C>T	c.(3493-3495)Cac>Tac	p.H1165Y	VPS8_ENST00000446204.2_Missense_Mutation_p.H1073Y|VPS8_ENST00000436792.2_Missense_Mutation_p.H1163Y|VPS8_ENST00000287546.4_Missense_Mutation_p.H1165Y	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1165			H -> Y (in dbSNP:rs11555405). {ECO:0000269|PubMed:17974005}.				zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TCCTCATCTACACTCTGAAGG	0.398													C|||	1432	0.285942	0.0174	0.3285	5008	,	,		16904	0.506		0.2883	False		,,,				2504	0.3896				p.H1165Y		Atlas-SNP	.											.	VPS8	109	.	0			c.C3493T						PASS	.	C	TYR/HIS,TYR/HIS	184,3598		2,180,1709	77.0	68.0	71.0		3493,3487	5.1	0.0	3	dbSNP_120	71	2082,6166		255,1572,2297	yes	missense,missense	VPS8	NM_001009921.2,NM_015303.3	83,83	257,1752,4006	TT,TC,CC		25.2425,4.8652,18.8362	benign,benign	1165/1429,1163/1427	184700426	2266,9764	1891	4124	6015	SO:0001583	missense	23355	exon40			CATCTACACTCTG	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.3493C>T	3.37:g.184700426C>T	ENSP00000397879:p.His1165Tyr	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	288	159	0.552083	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	659	0.3017399267399267	11	0.022357723577235773	127	0.35082872928176795	290	0.506993006993007	231	0.30474934036939316	C	4.147	0.025712	0.08054	0.048652	0.252425	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	6.05	5.09	0.68999	.	0.413977	0.28983	N	0.013505	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.13145	0.0;0.007;0.0	B;B;B	0.15870	0.0;0.014;0.0	T	0.41413	-0.9510	9	0.02654	T	1	-17.2505	9.2184	0.37362	0.0:0.824:0.0:0.176	rs11555405;rs13095607;rs52814306;rs61568357;rs11555405	1165;1073;1163	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	Y	1165;1165;1163;1073	ENSP00000287546:H1165Y;ENSP00000397879:H1165Y;ENSP00000404704:H1163Y;ENSP00000405483:H1073Y	ENSP00000287546:H1165Y	H	+	1	0	VPS8	186183120	0.000000	0.05858	0.008000	0.14137	0.700000	0.40528	0.339000	0.19875	1.408000	0.46895	0.650000	0.86243	CAC	C|0.726;T|0.274	0.274	strong		0.398	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
TRPM6	140803	hgsc.bcm.edu	37	9	77377410	77377410	+	Missense_Mutation	SNP	C	C	T	rs3750425	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:77377410C>T	ENST00000360774.1	-	26	4414	c.4177G>A	c.(4177-4179)Gtt>Att	p.V1393I	TRPM6_ENST00000449912.2_Missense_Mutation_p.V1388I|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000451710.3_Missense_Mutation_p.V1393I|TRPM6_ENST00000361255.3_Missense_Mutation_p.V1388I|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.V1393I	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1393			V -> I (in dbSNP:rs3750425). {ECO:0000269|PubMed:17344846}.		calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TCAGAGACAACTGGGGTCTGC	0.527													c|||	883	0.176318	0.2958	0.0879	5008	,	,		19160	0.1548		0.0785	False		,,,				2504	0.2004				p.V1393I		Atlas-SNP	.											.	TRPM6	377	.	0			c.G4177A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL	1138,3268	405.1+/-333.4	166,806,1231	93.0	86.0	89.0		4162,4162,4177	0.4	0.0	9	dbSNP_107	89	732,7868	177.9+/-227.4	30,672,3598	yes	missense,missense,missense	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	29,29,29	196,1478,4829	TT,TC,CC		8.5116,25.8284,14.378	benign,benign,benign	1388/2018,1388/2018,1393/2023	77377410	1870,11136	2203	4300	6503	SO:0001583	missense	140803	exon26			AGACAACTGGGGT	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.4177G>A	9.37:g.77377410C>T	ENSP00000354006:p.Val1393Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	303	0.13873626373626374	119	0.241869918699187	30	0.08287292817679558	89	0.1555944055944056	65	0.08575197889182058	c	8.299	0.819541	0.16607	0.258284	0.085116	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.55052	0.64;0.64;0.64;0.64;0.54	5.68	0.442	0.16582	.	2.390330	0.01144	N	0.006262	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B;B	0.30973	0.029;0.302;0.05	B;B;B	0.27500	0.016;0.08;0.037	T	0.06516	-1.0822	9	0.09843	T	0.71	.	1.2411	0.01963	0.2303:0.4003:0.1124:0.257	rs3750425;rs52794331;rs56518046;rs59790880;rs3750425	1393;1388;1388	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	I	1393;1393;1388;1388;1393;1056;1056	ENSP00000354006:V1393I;ENSP00000407341:V1393I;ENSP00000396672:V1388I;ENSP00000354962:V1388I;ENSP00000366060:V1393I	ENSP00000309693:V1056I	V	-	1	0	TRPM6	76567230	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-0.484000	0.06528	0.080000	0.16959	-1.618000	0.00794	GTT	C|0.855;T|0.145	0.145	strong		0.527	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
SLC12A3	6559	hgsc.bcm.edu	37	16	56928555	56928555	+	Splice_Site	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:56928555G>A	ENST00000563236.1	+	22	2658		c.e22+1		SLC12A3_ENST00000438926.2_Splice_Site|SLC12A3_ENST00000566786.1_Splice_Site|SLC12A3_ENST00000262502.5_Splice_Site			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	AGAGAAAGGCGTAAGTGTGGA	0.577																																					.		Atlas-SNP	.											.	SLC12A3	99	.	0			c.2633+1G>A	GRCh37	CD077781|CS066650|CS076679	SLC12A3	D|S		PASS	.						111.0	82.0	92.0					16																	56928555		2198	4300	6498	SO:0001630	splice_region_variant	6559	exon22			AAAGGCGTAAGTG		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"""Solute carriers"""	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.2633+1G>A	16.37:g.56928555G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_001126108	A8MSJ2|C9JNN9	Splice_Site	SNP	ENST00000563236.1	37	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126969	0.37533	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	4.76	4.76	0.60689	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6949	0.85333	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A3	55486056	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	7.659000	0.83766	2.350000	0.79820	0.561000	0.74099	.	.	.	none		0.577	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		Intron
SVEP1	79987	hgsc.bcm.edu	37	9	113234507	113234507	+	Missense_Mutation	SNP	T	T	C	rs10817025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:113234507T>C	ENST00000401783.2	-	15	3032	c.2696A>G	c.(2695-2697)aAg>aGg	p.K899R	SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.K876R|SVEP1_ENST00000302728.8_Missense_Mutation_p.K899R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	899			K -> R (in dbSNP:rs10817025).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CCGTGAGGACTTGGCATTGCC	0.423													C|||	997	0.199081	0.1354	0.2147	5008	,	,		18190	0.0754		0.2893	False		,,,				2504	0.3088				p.K899R		Atlas-SNP	.											.	SVEP1	326	.	0			c.A2696G						PASS	.	C	ARG/LYS	644,3256		58,528,1364	153.0	156.0	155.0		2696	4.2	1.0	9	dbSNP_120	155	2497,5801		391,1715,2043	yes	missense	SVEP1	NM_153366.3	26	449,2243,3407	CC,CT,TT		30.0916,16.5128,25.7501	benign	899/3572	113234507	3141,9057	1950	4149	6099	SO:0001583	missense	79987	exon15			GAGGACTTGGCAT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.2696A>G	9.37:g.113234507T>C	ENSP00000384917:p.Lys899Arg	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	198	113	0.570707	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	418	0.19139194139194138	76	0.15447154471544716	88	0.2430939226519337	36	0.06293706293706294	218	0.287598944591029	C	0.012	-1.676236	0.00751	0.165128	0.300916	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.77877	-1.01;-1.02;-1.13	5.25	4.15	0.48705	.	0.396625	0.29438	N	0.012160	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10291	-1.0636	9	0.11794	T	0.64	.	7.1732	0.25730	0.0:0.5639:0.2523:0.1837	rs10817025;rs17806789;rs52830999;rs56677016;rs10817025	899;899	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	R	899;876;899	ENSP00000384917:K899R;ENSP00000363593:K876R;ENSP00000304118:K899R	ENSP00000304118:K899R	K	-	2	0	SVEP1	112274328	0.926000	0.31397	0.960000	0.40013	0.121000	0.20230	0.716000	0.25836	1.247000	0.43917	-0.128000	0.14901	AAG	T|0.798;C|0.202	0.202	strong		0.423	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FABP1	2168	hgsc.bcm.edu	37	2	88424066	88424066	+	Missense_Mutation	SNP	T	T	C	rs2241883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:88424066T>C	ENST00000295834.3	-	3	378	c.280A>G	c.(280-282)Act>Gct	p.T94A	FABP1_ENST00000393750.3_Missense_Mutation_p.T94A|FABP1_ENST00000495375.1_5'UTR	NM_001443.2	NP_001434.1	P07148	FABPL_HUMAN	fatty acid binding protein 1, liver	94			T -> A (in dbSNP:rs2241883). {ECO:0000269|PubMed:3838313}.		cellular lipid metabolic process (GO:0044255)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|intestinal absorption (GO:0050892)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)	apical cortex (GO:0045179)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|peroxisomal matrix (GO:0005782)	antioxidant activity (GO:0016209)|bile acid binding (GO:0032052)|chromatin binding (GO:0003682)|drug binding (GO:0008144)|fatty acid binding (GO:0005504)|long-chain fatty acid transporter activity (GO:0005324)|phospholipid binding (GO:0005543)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|stomach(1)	6						TTTTTGAAAGTTGTCACCAGT	0.517													T|||	1118	0.223243	0.1392	0.3458	5008	,	,		20701	0.2073		0.3479	False		,,,				2504	0.138				p.T94A		Atlas-SNP	.											.	FABP1	23	.	0			c.A280G	GRCh37	CM042701	FABP1	M	rs2241883	PASS	.	T	ALA/THR	736,3670	304.4+/-288.4	68,600,1535	197.0	154.0	168.0		280	1.4	0.9	2	dbSNP_98	168	2774,5826	439.8+/-359.3	473,1828,1999	yes	missense	FABP1	NM_001443.2	58	541,2428,3534	CC,CT,TT		32.2558,16.7045,26.9875	benign	94/128	88424066	3510,9496	2203	4300	6503	SO:0001583	missense	2168	exon3			TGAAAGTTGTCAC	M10617	CCDS2001.1	2p11	2013-03-01			ENSG00000163586	ENSG00000163586		"""Fatty acid binding protein family"""	3555	protein-coding gene	gene with protein product		134650				3012800, 17698986	Standard	NM_001443		Approved	L-FABP	uc002sst.2	P07148	OTTHUMG00000130312	ENST00000295834.3:c.280A>G	2.37:g.88424066T>C	ENSP00000295834:p.Thr94Ala	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_001443		Missense_Mutation	SNP	ENST00000295834.3	37	CCDS2001.1	577	0.2641941391941392	61	0.12398373983739837	130	0.35911602209944754	127	0.22202797202797203	259	0.341688654353562	T	7.875	0.729033	0.15507	0.167045	0.322558	ENSG00000163586	ENST00000295834;ENST00000393750	T;T	0.13196	2.61;2.61	5.5	1.35	0.21983	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.647546	0.17155	N	0.184882	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.13407	0.009;0.002	T	0.44892	-0.9298	9	0.10636	T	0.68	.	6.2319	0.20740	0.3971:0.0:0.1367:0.4662	rs2241883;rs59305633;rs2241883	94;94	A8MW49;P07148	.;FABPL_HUMAN	A	94	ENSP00000295834:T94A;ENSP00000377351:T94A	ENSP00000295834:T94A	T	-	1	0	FABP1	88205181	0.001000	0.12720	0.885000	0.34714	0.923000	0.55619	0.541000	0.23207	0.404000	0.25506	0.533000	0.62120	ACT	A|0.004;C|0.254	0.254	strong		0.517	FABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252660.1	NM_001443	
USP35	57558	hgsc.bcm.edu	37	11	77909014	77909014	+	Missense_Mutation	SNP	G	G	A	rs2510044	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:77909014G>A	ENST00000529308.1	+	3	967	c.706G>A	c.(706-708)Gtg>Atg	p.V236M	USP35_ENST00000441408.2_5'UTR|USP35_ENST00000530267.1_Intron|USP35_ENST00000530535.1_Intron|USP35_ENST00000526425.1_5'Flank	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	236			V -> M (in dbSNP:rs2510044).		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			CCTGGCCAGCGTGGTCCAGCA	0.612													G|||	1022	0.204073	0.0325	0.2968	5008	,	,		21718	0.3591		0.1561	False		,,,				2504	0.2597				p.V236M		Atlas-SNP	.											.	USP35	179	.	0			c.G706A						PASS	.	G	MET/VAL	179,4141		7,165,1988	64.0	69.0	67.0		706	4.8	1.0	11	dbSNP_100	67	1165,7347		80,1005,3171	yes	missense	USP35	NM_020798.2	21	87,1170,5159	AA,AG,GG		13.6866,4.1435,10.4738	probably-damaging	236/1019	77909014	1344,11488	2160	4256	6416	SO:0001583	missense	57558	exon3			GCCAGCGTGGTCC	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.706G>A	11.37:g.77909014G>A	ENSP00000431876:p.Val236Met	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	105	68	0.647619	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	442	0.20238095238095238	21	0.042682926829268296	88	0.2430939226519337	209	0.36538461538461536	124	0.16358839050131926	G	11.80	1.745434	0.30955	0.041435	0.136866	ENSG00000118369	ENST00000529308	T	0.46451	0.87	4.82	4.82	0.62117	Armadillo-like helical (1);	0.311212	0.22400	N	0.060547	T	0.00012	0.0000	L	0.48642	1.525	0.09310	P	1.0	D	0.76494	0.999	P	0.59703	0.862	T	0.26815	-1.0092	9	0.72032	D	0.01	-35.837	18.1059	0.89520	0.0:0.0:1.0:0.0	rs2510044;rs58071390;rs2510044	236	Q9P2H5	UBP35_HUMAN	M	236	ENSP00000431876:V236M	ENSP00000431876:V236M	V	+	1	0	USP35	77586662	1.000000	0.71417	0.992000	0.48379	0.090000	0.18270	5.378000	0.66190	2.506000	0.84524	0.561000	0.74099	GTG	G|0.802;A|0.198	0.198	strong		0.612	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
PRRC2C	23215	hgsc.bcm.edu	37	1	171483717	171483717	+	Silent	SNP	A	A	C	rs1055417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:171483717A>C	ENST00000338920.4	+	4	564	c.327A>C	c.(325-327)gcA>gcC	p.A109A	PRRC2C_ENST00000367742.3_Silent_p.A111A|PRRC2C_ENST00000392078.3_Silent_p.A111A|PRRC2C_ENST00000426496.2_Silent_p.A109A|PRRC2C_ENST00000476522.1_3'UTR	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	109					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										CTGGGGTTGCAGCTCCCCCAG	0.443													A|||	642	0.128195	0.1089	0.1167	5008	,	,		16176	0.0625		0.1859	False		,,,				2504	0.1708				p.A109A		Atlas-SNP	.											.	.	.	.	0			c.A327C						PASS	.	A		515,3869		22,471,1699	54.0	43.0	47.0		327	3.6	1.0	1	dbSNP_86	47	1331,7223		107,1117,3053	no	coding-synonymous	PRRC2C	NM_015172.3		129,1588,4752	CC,CA,AA		15.56,11.7473,14.268		109/2818	171483717	1846,11092	2192	4277	6469	SO:0001819	synonymous_variant	23215	exon4			GGTTGCAGCTCCC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.327A>C	1.37:g.171483717A>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	203	203	1	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2																																																																																			A|0.870;C|0.130	0.130	strong		0.443	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
HOXB7	3217	hgsc.bcm.edu	37	17	46688135	46688135	+	Missense_Mutation	SNP	G	G	A	rs79247310	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46688135G>A	ENST00000239165.7	-	1	244	c.146C>T	c.(145-147)gCt>gTt	p.A49V	HOXB7_ENST00000567101.2_Intron	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	49				A -> V (in Ref. 2; BAF83342 and 3; BAD96969). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						GGCGAAGGAAGCGCCCGAACC	0.687													G|||	429	0.0856629	0.0469	0.0216	5008	,	,		12239	0.2341		0.0497	False		,,,				2504	0.0675				p.A49V		Atlas-SNP	.											.	HOXB7	15	.	0			c.C146T						PASS	.	G	VAL/ALA	175,4173		1,173,2000	12.0	15.0	14.0		146	4.3	0.9	17	dbSNP_132	14	241,8277		3,235,4021	no	missense	HOXB7	NM_004502.3	64	4,408,6021	AA,AG,GG		2.8293,4.0248,3.2333	possibly-damaging	49/218	46688135	416,12450	2174	4259	6433	SO:0001583	missense	3217	exon1			AAGGAAGCGCCCG		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"""Homeoboxes / ANTP class : HOXL subclass"""	5118	protein-coding gene	gene with protein product		142962	"""homeo box B7"""	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.146C>T	17.37:g.46688135G>A	ENSP00000239165:p.Ala49Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	37	25	0.675676	NM_004502	A8K3N8|Q15957|Q53FN3|Q96BQ6	Missense_Mutation	SNP	ENST00000239165.7	37	CCDS11532.1	218	0.09981684981684982	22	0.044715447154471545	8	0.022099447513812154	148	0.25874125874125875	40	0.052770448548812667	G	16.68	3.190187	0.58017	0.040248	0.028293	ENSG00000120087	ENST00000239165	T	0.34275	1.37	4.26	4.26	0.50523	.	0.286515	0.33401	N	0.004954	T	0.00012	0.0000	M	0.81239	2.535	0.32650	P	0.5194840000000001	B	0.22003	0.063	B	0.19666	0.026	T	0.12344	-1.0551	9	0.62326	D	0.03	.	14.6281	0.68638	0.0:0.0:1.0:0.0	.	49	P09629	HXB7_HUMAN	V	49	ENSP00000239165:A49V	ENSP00000239165:A49V	A	-	2	0	HOXB7	44043134	0.001000	0.12720	0.922000	0.36590	0.967000	0.64934	1.156000	0.31712	2.207000	0.71202	0.555000	0.69702	GCT	G|0.917;A|0.083	0.083	strong		0.687	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3		
CNTRL	11064	hgsc.bcm.edu	37	9	123850770	123850770	+	Missense_Mutation	SNP	G	G	A	rs10818503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:123850770G>A	ENST00000373855.1	+	3	426	c.166G>A	c.(166-168)Gtt>Att	p.V56I	CNTRL_ENST00000373865.2_Missense_Mutation_p.V56I|CNTRL_ENST00000238341.5_Missense_Mutation_p.V56I			Q7Z7A1	CNTRL_HUMAN	centriolin	56			V -> I (in dbSNP:rs10818503). {ECO:0000269|PubMed:12732615}.		cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						GTGTGAGCAAGTTGAGATTGC	0.378													G|||	3203	0.639577	0.2557	0.7421	5008	,	,		19334	0.7788		0.6958	False		,,,				2504	0.8845				p.V56I		Atlas-SNP	.											.	CNTRL	161	.	0			c.G166A						PASS	.	G	ILE/VAL	1479,2927	473.3+/-356.6	259,961,983	138.0	114.0	122.0		166	2.6	0.1	9	dbSNP_120	122	5930,2670	684.5+/-404.0	2060,1810,430	yes	missense	CNTRL	NM_007018.4	29	2319,2771,1413	AA,AG,GG		31.0465,33.5679,43.034	benign	56/2326	123850770	7409,5597	2203	4300	6503	SO:0001583	missense	11064	exon1			GAGCAAGTTGAGA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.166G>A	9.37:g.123850770G>A	ENSP00000362962:p.Val56Ile	Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	293	145	0.494881	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	1389	0.635989010989011	131	0.266260162601626	273	0.7541436464088398	458	0.8006993006993007	527	0.6952506596306068	G	11.56	1.676337	0.29783	0.335679	0.689535	ENSG00000119397	ENST00000373865;ENST00000373855;ENST00000238341;ENST00000454238	T;T	0.25414	1.8;1.8	6.15	2.62	0.31277	.	.	.	.	.	T	0.00012	0.0000	L	0.33753	1.03	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.24548	-1.0157	8	0.35671	T	0.21	.	4.3018	0.10928	0.2427:0.2733:0.4839:0.0	rs10818503;rs59041611;rs10818503	56	Q7Z7A1	CNTRL_HUMAN	I	56	ENSP00000362962:V56I;ENSP00000238341:V56I	ENSP00000238341:V56I	V	+	1	0	CNTRL	122890591	0.307000	0.24500	0.128000	0.21923	0.683000	0.39861	0.766000	0.26560	1.360000	0.45960	0.643000	0.83706	GTT	G|0.403;A|0.597	0.597	strong		0.378	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
BBS12	166379	hgsc.bcm.edu	37	4	123664109	123664109	+	Silent	SNP	G	G	C	rs34296401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:123664109G>C	ENST00000314218.3	+	2	1255	c.1062G>C	c.(1060-1062)gtG>gtC	p.V354V	BBS12_ENST00000542236.1_Silent_p.V354V	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	354					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						ATCAGCCTGTGCGAATAGTTC	0.408									Bardet-Biedl syndrome				C|||	145	0.0289537	0.0809	0.0231	5008	,	,		22038	0.0		0.0219	False		,,,				2504	0.0				p.V354V		Atlas-SNP	.											.	BBS12	63	.	0			c.G1062C						PASS	.	C	,	306,4100	797.4+/-415.4	10,286,1907	75.0	69.0	71.0		1062,1062	0.2	0.0	4	dbSNP_126	71	167,8433	811.4+/-407.1	2,163,4135	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	12,449,6042	CC,CG,GG		1.9419,6.9451,3.6368	,	354/711,354/711	123664109	473,12533	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCCTGTGCGAATA	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1062G>C	4.37:g.123664109G>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	50	0.381679	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			G|0.964;C|0.036	0.036	strong		0.408	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
FCAR	2204	hgsc.bcm.edu	37	19	55401170	55401170	+	Missense_Mutation	SNP	A	A	G	rs16986050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55401170A>G	ENST00000355524.3	+	5	815	c.805A>G	c.(805-807)Agc>Ggc	p.S269G	FCAR_ENST00000391726.3_Missense_Mutation_p.S161G|FCAR_ENST00000353758.4_Missense_Mutation_p.S160G|FCAR_ENST00000391723.3_3'UTR|FCAR_ENST00000345937.4_Missense_Mutation_p.S173G|FCAR_ENST00000391725.3_Missense_Mutation_p.S247G|FCAR_ENST00000482092.2_3'UTR|CTB-61M7.2_ENST00000594721.1_lincRNA|FCAR_ENST00000391724.3_Missense_Mutation_p.S235G|FCAR_ENST00000359272.4_Missense_Mutation_p.S257G	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	269			S -> G (in dbSNP:rs16986050). {ECO:0000269|PubMed:17548632}.		immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		ACCGAGCTGGAGCCAACAGAT	0.547													.|||	778	0.155351	0.3434	0.1081	5008	,	,		18910	0.0198		0.1839	False		,,,				2504	0.045				p.S269G		Atlas-SNP	.											FCAR,NS,carcinoma,-2,1	FCAR	110	1	0			c.A805G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,,GLY/SER,GLY/SER	1384,3022	454.9+/-350.8	206,972,1025	154.0	155.0	155.0		805,739,517,769,481,,478,703	0.9	0.0	19	dbSNP_123	155	1522,7078	287.7+/-298.4	135,1252,2913	yes	missense,missense,missense,missense,missense,utr-3,missense,missense	FCAR	NM_002000.2,NM_133269.2,NM_133271.2,NM_133272.2,NM_133273.2,NM_133274.2,NM_133277.2,NM_133278.2	56,56,56,56,56,,56,56	341,2224,3938	GG,GA,AA		17.6977,31.4117,22.3435	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	269/288,247/266,173/192,257/276,161/180,,160/179,235/254	55401170	2906,10100	2203	4300	6503	SO:0001583	missense	2204	exon5			AGCTGGAGCCAAC	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.805A>G	19.37:g.55401170A>G	ENSP00000347714:p.Ser269Gly	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	28	10	0.357143	NM_002000	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	37	CCDS12907.1	363	0.1662087912087912	170	0.34552845528455284	48	0.13259668508287292	10	0.017482517482517484	135	0.17810026385224276	A	9.725	1.160659	0.21538	0.314117	0.176977	ENSG00000186431	ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000353758;ENST00000359272;ENST00000391724	T;T;T;T;T;T;T	0.04406	3.63;6.77;6.35;4.65;6.45;6.61;6.22	2.95	0.854	0.19007	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B;B;B	0.34372	0.451;0.307;0.101;0.0;0.199;0.053;0.311	B;B;B;B;B;B;B	0.30179	0.112;0.097;0.039;0.003;0.097;0.021;0.103	T	0.49062	-0.8978	8	0.34782	T	0.22	.	4.7474	0.13043	0.7178:0.0:0.2822:0.0	rs16986050;rs52827522;rs60168829;rs16986050	160;235;161;257;247;173;269	Q92592;Q92593;Q92587;Q9UEK0;Q53X39;P24071-3;P24071	.;.;.;.;.;.;FCAR_HUMAN	G	161;269;247;173;160;257;235	ENSP00000375606:S161G;ENSP00000347714:S269G;ENSP00000375605:S247G;ENSP00000338257:S173G;ENSP00000338058:S160G;ENSP00000352218:S257G;ENSP00000375604:S235G	ENSP00000338257:S173G	S	+	1	0	FCAR	60092982	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	1.154000	0.31688	0.108000	0.17862	-0.379000	0.06801	AGC	A|0.795;G|0.205	0.205	strong		0.547	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000	
MYO7B	4648	hgsc.bcm.edu	37	2	128394955	128394955	+	Missense_Mutation	SNP	A	A	G	rs11686946	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:128394955A>G	ENST00000409816.2	+	46	6346	c.6314A>G	c.(6313-6315)cAg>cGg	p.Q2105R	MYO7B_ENST00000389524.4_Missense_Mutation_p.Q2106R|MYO7B_ENST00000409090.1_Missense_Mutation_p.Q958R|LIMS2_ENST00000494613.1_5'Flank|MYO7B_ENST00000428314.1_Missense_Mutation_p.Q2105R			Q6PIF6	MYO7B_HUMAN	myosin VIIB	2105			Q -> R (in dbSNP:rs11686946).			extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.Q2105R(1)|p.Q2349R(1)		breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		ATGAACAAGCAGCGGGGCTCC	0.652													A|||	1035	0.206669	0.1135	0.1239	5008	,	,		16620	0.1865		0.1968	False		,,,				2504	0.4223				p.Q2105R		Atlas-SNP	.											MYO7B_ENST00000428314,NS,carcinoma,0,4	MYO7B	359	4	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.A6314G						PASS	.	A	ARG/GLN	493,3485		34,425,1530	24.0	28.0	26.0		6314	2.7	0.3	2	dbSNP_120	26	1554,6772		130,1294,2739	yes	missense	MYO7B	NM_001080527.1	43	164,1719,4269	GG,GA,AA		18.6644,12.3932,16.6369	possibly-damaging	2105/2117	128394955	2047,10257	1989	4163	6152	SO:0001583	missense	4648	exon47			ACAAGCAGCGGGG		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.6314A>G	2.37:g.128394955A>G	ENSP00000386461:p.Gln2105Arg	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	161	80	0.496894	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	358	0.16391941391941392	46	0.09349593495934959	48	0.13259668508287292	114	0.1993006993006993	150	0.19788918205804748	N	14.00	2.406269	0.42715	0.123932	0.186644	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816;ENST00000409090	D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.1	3.81	2.65	0.31530	.	0.678240	0.13839	N	0.359206	T	0.00300	0.0009	L	0.53249	1.67	0.40000	P	0.024843999999999977	P	0.36282	0.546	B	0.30401	0.115	T	0.04347	-1.0958	9	0.37606	T	0.19	.	8.2599	0.31779	0.9062:0.0:0.0938:0.0	rs11686946;rs11686946	2105	Q6PIF6	MYO7B_HUMAN	R	2106;2105;2105;958	ENSP00000374175:Q2106R;ENSP00000415090:Q2105R;ENSP00000386461:Q2105R;ENSP00000386850:Q958R	ENSP00000374175:Q2106R	Q	+	2	0	MYO7B	128111425	1.000000	0.71417	0.259000	0.24435	0.041000	0.13682	6.232000	0.72313	0.819000	0.34492	0.528000	0.53228	CAG	A|0.835;G|0.165	0.165	strong		0.652	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
SPEG	10290	hgsc.bcm.edu	37	2	220331911	220331911	+	Missense_Mutation	SNP	G	G	A	rs34861443	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220331911G>A	ENST00000312358.7	+	10	3029	c.2897G>A	c.(2896-2898)cGg>cAg	p.R966Q	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	966	Ig-like 4.		R -> Q (in dbSNP:rs34861443). {ECO:0000269|PubMed:17344846}.		cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CCTGAAAGCCGGTCCCTGGCC	0.677											OREG0004000	type=REGULATORY REGION|Gene=APEG1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	25	0.00499201	0.0008	0.0043	5008	,	,		15110	0.0		0.0209	False		,,,				2504	0.0				p.R966Q		Atlas-SNP	.											.	SPEG	272	.	0			c.G2897A						PASS	.	G	GLN/ARG	28,4056		0,28,2014	40.0	49.0	46.0		2897	4.8	1.0	2	dbSNP_126	46	203,8143		4,195,3974	yes	missense	SPEG	NM_005876.4	43	4,223,5988	AA,AG,GG		2.4323,0.6856,1.8584	probably-damaging	966/3268	220331911	231,12199	2042	4173	6215	SO:0001583	missense	10290	exon10			AAAGCCGGTCCCT	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2897G>A	2.37:g.220331911G>A	ENSP00000311684:p.Arg966Gln	Somatic	78	0	0	2265	WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	18	0.008241758241758242	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	13	0.017150395778364115	G	11.23	1.576809	0.28092	0.006856	0.024323	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.65732	-0.17	4.75	4.75	0.60458	Immunoglobulin-like (1);	0.000000	0.36628	N	0.002490	T	0.23370	0.0565	L	0.27053	0.805	0.80722	D	1	B	0.31077	0.307	B	0.17722	0.019	T	0.16928	-1.0386	10	0.19590	T	0.45	.	5.3131	0.15841	0.1326:0.2:0.6674:0.0	rs34861443	966	Q15772	SPEG_HUMAN	Q	966	ENSP00000311684:R966Q	ENSP00000265327:R966Q	R	+	2	0	SPEG	220040155	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.907000	0.28531	2.465000	0.83290	0.655000	0.94253	CGG	G|0.988;A|0.012	0.012	strong		0.677	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
HUWE1	10075	hgsc.bcm.edu	37	X	53654402	53654402	+	Missense_Mutation	SNP	T	T	C	rs41307640	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:53654402T>C	ENST00000342160.3	-	16	1905	c.1448A>G	c.(1447-1449)aAt>aGt	p.N483S	HUWE1_ENST00000218328.8_Missense_Mutation_p.N483S|HUWE1_ENST00000262854.6_Missense_Mutation_p.N483S			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	483			N -> S (in dbSNP:rs41307640).		base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TTGTGTAGTATTGGGTCTCTG	0.368													t|||	34	0.00900662	0.003	0.0173	3775	,	,		10299	0.0		0.0179	False		,,,				2504	0.0				p.N483S		Atlas-SNP	.											.	HUWE1	724	.	0			c.A1448G						PASS	.		SER/ASN	15,3820		0,12,3,1620,568	191.0	160.0	171.0		1448	3.1	1.0	X	dbSNP_127	171	185,6543		4,127,50,2297,1822	yes	missense	HUWE1	NM_031407.4	46	4,139,53,3917,2390	CC,CT,C,TT,T		2.7497,0.3911,1.8934	benign	483/4375	53654402	200,10363	2203	4300	6503	SO:0001583	missense	10075	exon17			GTAGTATTGGGTC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.1448A>G	X.37:g.53654402T>C	ENSP00000340648:p.Asn483Ser	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	22	0.013261000602772756	2	0.0040650406504065045	4	0.0111731843575419	0	0.0	11	0.014627659574468085	t	0.090	-1.169288	0.01660	0.003911	0.027497	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328;ENST00000396323	T;T;T	0.42900	0.96;0.96;0.96	4.89	3.09	0.35607	E3 ubiquitin ligase, domain of unknown function DUF913 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.291697	0.30979	N	0.008486	T	0.04724	0.0128	N	0.02960	-0.455	0.21697	N	0.999585	B	0.06786	0.001	B	0.06405	0.002	T	0.29579	-1.0007	10	0.02654	T	1	.	7.9684	0.30113	0.0:0.4667:0.4405:0.0928	rs41307640;rs61752441	483	Q7Z6Z7	HUWE1_HUMAN	S	483;483;483;109	ENSP00000340648:N483S;ENSP00000262854:N483S;ENSP00000218328:N483S	ENSP00000218328:N483S	N	-	2	0	HUWE1	53671127	1.000000	0.71417	0.999000	0.59377	0.739000	0.42172	0.945000	0.29056	0.327000	0.23409	-1.244000	0.01528	AAT	T|0.984;C|0.016	0.016	strong		0.368	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
LRCH1	23143	hgsc.bcm.edu	37	13	47243196	47243196	+	Missense_Mutation	SNP	C	C	G	rs41284185	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:47243196C>G	ENST00000389798.3	+	3	681	c.484C>G	c.(484-486)Ctg>Gtg	p.L162V	LRCH1_ENST00000311191.6_Missense_Mutation_p.L162V|LRCH1_ENST00000389797.3_Missense_Mutation_p.L162V	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	162										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		GCCTGCCTGCCTGTGTGGTCT	0.448													C|||	77	0.0153754	0.0023	0.0159	5008	,	,		15377	0.0		0.0596	False		,,,				2504	0.0031				p.L162V		Atlas-SNP	.											.	LRCH1	104	.	0			c.C484G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU	62,4344	58.7+/-95.3	0,62,2141	171.0	159.0	163.0		484,484,484	6.0	1.0	13	dbSNP_127	163	608,7992	159.1+/-212.4	22,564,3714	yes	missense,missense,missense	LRCH1	NM_001164211.1,NM_001164213.1,NM_015116.2	32,32,32	22,626,5855	GG,GC,CC		7.0698,1.4072,5.1515	benign,benign,benign	162/764,162/697,162/729	47243196	670,12336	2203	4300	6503	SO:0001583	missense	23143	exon3			GCCTGCCTGTGTG	AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"""calponin homology (CH) domain containing 1"""	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.484C>G	13.37:g.47243196C>G	ENSP00000374448:p.Leu162Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	150	69	0.46	NM_015116	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	ENST00000389798.3	37	CCDS31972.1	58	0.026556776556776556	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	50	0.06596306068601583	C	13.90	2.375778	0.42105	0.014072	0.070698	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.66995	-0.24;-0.24;-0.24	5.98	5.98	0.97165	.	0.079486	0.52532	D	0.000075	T	0.07908	0.0198	L	0.28115	0.83	0.52099	D	0.999942	B;B;B;B	0.33748	0.008;0.423;0.013;0.103	B;B;B;B	0.31946	0.009;0.138;0.021;0.034	T	0.09818	-1.0657	10	0.33940	T	0.23	-15.3883	14.9718	0.71241	0.0:0.8579:0.1421:0.0	rs41284185	162;162;162;162	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	V	162	ENSP00000308493:L162V;ENSP00000374448:L162V;ENSP00000374447:L162V	ENSP00000308493:L162V	L	+	1	2	LRCH1	46141197	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.994000	0.40757	2.838000	0.97847	0.655000	0.94253	CTG	C|0.959;G|0.041	0.041	strong		0.448	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116	
SH3YL1	26751	hgsc.bcm.edu	37	2	224919	224919	+	Splice_Site	SNP	A	A	G	rs2290911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:224919A>G	ENST00000405430.1	-	11	1159	c.783T>C	c.(781-783)agT>agC	p.S261S	SH3YL1_ENST00000403657.1_Intron|SH3YL1_ENST00000415006.2_Splice_Site_p.S165S|SH3YL1_ENST00000403658.1_Intron|SH3YL1_ENST00000468321.1_5'UTR|SH3YL1_ENST00000356150.5_Splice_Site_p.S261S|SH3YL1_ENST00000403712.2_Intron			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	261					phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)			large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		CATTTCTGTTACCTGCCAAAA	0.323													A|||	1280	0.255591	0.1747	0.2291	5008	,	,		17201	0.248		0.331	False		,,,				2504	0.3139				p.S261S		Atlas-SNP	.											.	SH3YL1	49	.	0			c.T783C						PASS	.	A	,	733,2907		71,591,1158	119.0	111.0	114.0		,783	2.6	0.7	2	dbSNP_100	114	2797,5365		459,1879,1743	yes	intron,coding-synonymous-near-splice	SH3YL1	NM_001159597.1,NM_015677.2	,	530,2470,2901	GG,GA,AA		34.2686,20.1374,29.9102	,	,261/343	224919	3530,8272	1820	4081	5901	SO:0001630	splice_region_variant	26751	exon9			TCTGTTACCTGCC		CCDS42646.1, CCDS42646.2, CCDS54332.1, CCDS62841.1	2p25.3	2013-10-18	2013-10-18		ENSG00000035115	ENSG00000035115			29546	protein-coding gene	gene with protein product			"""SH3 domain containing, Ysc84-like 1 (S. cerevisiae)"""			21624956	Standard	NM_001282687		Approved	Ray, DKFZP586F1318	uc002qvx.3	Q96HL8	OTTHUMG00000151359	ENST00000405430.1:c.782-1T>C	2.37:g.224919A>G		Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	300	134	0.446667	NM_015677	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Silent	SNP	ENST00000405430.1	37																																																																																				A|0.752;G|0.248	0.248	strong		0.323	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677	Silent
ATP4A	495	hgsc.bcm.edu	37	19	36048741	36048741	+	Silent	SNP	G	G	T	rs2230181	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36048741G>T	ENST00000262623.3	-	11	1537	c.1509C>A	c.(1507-1509)atC>atA	p.I503I		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	503					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CCAGCGTATGGATGGACAGCT	0.721													G|||	1406	0.280751	0.174	0.2277	5008	,	,		8328	0.2659		0.4105	False		,,,				2504	0.3446				p.I503I		Atlas-SNP	.											.	ATP4A	123	.	0			c.C1509A						PASS	.	G		705,3255		72,561,1347	7.0	8.0	8.0		1509	1.5	1.0	19	dbSNP_98	8	2729,5079		474,1781,1649	no	coding-synonymous	ATP4A	NM_000704.2		546,2342,2996	TT,TG,GG		34.9513,17.803,29.1808		503/1036	36048741	3434,8334	1980	3904	5884	SO:0001819	synonymous_variant	495	exon11			CGTATGGATGGAC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"""ATPases / P-type"""	819	protein-coding gene	gene with protein product	"""gastric H,K-ATPase alpha subunit"", ""H(+)-K(+)-ATPase alpha subunit"", ""proton pump"""	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.1509C>A	19.37:g.36048741G>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	71	48	0.676056	NM_000704	O00738	Silent	SNP	ENST00000262623.3	37	CCDS12467.1																																																																																			G|0.705;T|0.295	0.295	strong		0.721	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704	
ARHGAP12	94134	hgsc.bcm.edu	37	10	32120678	32120678	+	Silent	SNP	C	C	T	rs2808100	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:32120678C>T	ENST00000344936.2	-	10	1671	c.1437G>A	c.(1435-1437)ggG>ggA	p.G479G	ARHGAP12_ENST00000311380.4_Silent_p.G427G|ARHGAP12_ENST00000375250.5_Silent_p.G449G|ARHGAP12_ENST00000375245.4_Silent_p.G427G|ARHGAP12_ENST00000396144.4_Silent_p.G474G	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	479	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				GAACCTTTTTCCCATTTTCAG	0.274													C|||	1211	0.241813	0.0908	0.2983	5008	,	,		16121	0.4127		0.2048	False		,,,				2504	0.2679				p.G479G		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.G1437A						PASS	.	C		476,3924	189.2+/-215.4	28,420,1752	116.0	109.0	111.0		1437	0.1	1.0	10	dbSNP_100	111	1747,6849	274.5+/-291.2	190,1367,2741	no	coding-synonymous	ARHGAP12	NM_018287.5		218,1787,4493	TT,TC,CC		20.3234,10.8182,17.1053		479/847	32120678	2223,10773	2200	4298	6498	SO:0001819	synonymous_variant	94134	exon10			CTTTTTCCCATTT	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1437G>A	10.37:g.32120678C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	249	122	0.48996	NM_018287	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Silent	SNP	ENST00000344936.2	37	CCDS7170.1	522	0.23901098901098902	44	0.08943089430894309	90	0.24861878453038674	219	0.38286713286713286	169	0.22295514511873352	c	9.190	1.025724	0.19512	0.108182	0.203234	ENSG00000165322	ENST00000454919	.	.	.	5.51	0.0976	0.14494	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999265	.	.	.	.	.	.	T	0.43572	-0.9383	3	.	.	.	.	5.5115	0.16884	0.1213:0.5113:0.0:0.3674	rs2808100;rs17582188;rs2808100	.	.	.	K	150	.	.	E	-	1	0	ARHGAP12	32160684	0.897000	0.30589	0.995000	0.50966	0.995000	0.86356	-0.141000	0.10327	-0.165000	0.10908	0.580000	0.79431	GAA	C|0.799;T|0.201	0.201	strong		0.274	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
SLC25A2	83884	hgsc.bcm.edu	37	5	140682757	140682757	+	Missense_Mutation	SNP	C	C	T	rs3749780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140682757C>T	ENST00000239451.4	-	1	855	c.676G>A	c.(676-678)Gtc>Atc	p.V226I		NM_031947.2	NP_114153.1	Q9BXI2	ORNT2_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 2	226			V -> I (in dbSNP:rs3749780).		cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(500;0.000249)|Lung NSC(810;0.0011)|Ovarian(839;0.00556)|Breast(839;0.0173)|all_hematologic(541;0.152)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00204)	L-Ornithine(DB00129)	GGGAACACGACAAGCCACAGG	0.433													C|||	641	0.127995	0.1346	0.1282	5008	,	,		19537	0.0645		0.1978	False		,,,				2504	0.1125				p.V226I		Atlas-SNP	.											.	SLC25A2	68	.	0			c.G676A						PASS	.	C	ILE/VAL	709,3697	295.9+/-283.9	54,601,1548	96.0	96.0	96.0		676	1.9	0.7	5	dbSNP_107	96	1605,6995	299.3+/-304.4	145,1315,2840	yes	missense	SLC25A2	NM_031947.2	29	199,1916,4388	TT,TC,CC		18.6628,16.0917,17.7918	benign	226/302	140682757	2314,10692	2203	4300	6503	SO:0001583	missense	83884	exon1			ACACGACAAGCCA	AF332005	CCDS4258.1	5q31.3	2013-05-22			ENSG00000120329	ENSG00000120329		"""Solute carriers"""	22921	protein-coding gene	gene with protein product		608157				11004451	Standard	NM_031947		Approved	ORNT2	uc003ljf.3	Q9BXI2	OTTHUMG00000129604	ENST00000239451.4:c.676G>A	5.37:g.140682757C>T	ENSP00000239451:p.Val226Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	141	36	0.255319	NM_031947	Q496C1|Q6XUI0|Q8NFZ2	Missense_Mutation	SNP	ENST00000239451.4	37	CCDS4258.1	298	0.13644688644688643	55	0.11178861788617886	49	0.13535911602209943	35	0.06118881118881119	159	0.20976253298153033	C	13.41	2.228145	0.39399	0.160917	0.186628	ENSG00000120329	ENST00000239451	T	0.80304	-1.36	3.78	1.89	0.25635	Mitochondrial carrier domain (2);	0.311720	0.30611	N	0.009259	T	0.00109	0.0003	L	0.42581	1.335	0.30575	P	0.763076	B	0.10296	0.003	B	0.12837	0.008	T	0.04115	-1.0976	9	0.16896	T	0.51	-17.3111	7.0946	0.25303	0.0:0.7465:0.0:0.2535	rs3749780;rs17524256;rs52815335;rs57086938;rs3749780	226	Q9BXI2	ORNT2_HUMAN	I	226	ENSP00000239451:V226I	ENSP00000239451:V226I	V	-	1	0	SLC25A2	140662941	1.000000	0.71417	0.732000	0.30844	0.988000	0.76386	3.889000	0.56212	0.526000	0.28541	0.650000	0.86243	GTC	T|0.148;C|0.852	0.148	strong		0.433	SLC25A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251799.2	NM_031947	
FAM3D	131177	hgsc.bcm.edu	37	3	58625875	58625875	+	Missense_Mutation	SNP	C	C	A	rs33966924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58625875C>A	ENST00000358781.2	-	7	662	c.352G>T	c.(352-354)Gca>Tca	p.A118S		NM_138805.2	NP_620160.1	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	118			A -> S (in dbSNP:rs33966924).		negative regulation of insulin secretion (GO:0046676)	extracellular region (GO:0005576)	cytokine activity (GO:0005125)			large_intestine(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)		ATGTCAAATGCCTTCTGTCCC	0.552													C|||	398	0.0794728	0.0552	0.1297	5008	,	,		21088	0.001		0.1769	False		,,,				2504	0.0573				p.A118S		Atlas-SNP	.											.	FAM3D	29	.	0			c.G352T						PASS	.	C	SER/ALA	361,4045	185.7+/-212.7	13,335,1855	257.0	213.0	228.0		352	-4.4	0.0	3	dbSNP_126	228	1567,7033	293.0+/-301.1	156,1255,2889	yes	missense	FAM3D	NM_138805.2	99	169,1590,4744	AA,AC,CC		18.2209,8.1934,14.8239	benign	118/225	58625875	1928,11078	2203	4300	6503	SO:0001583	missense	131177	exon7			CAAATGCCTTCTG	AF494381	CCDS2893.1	3p21.1	2008-07-18			ENSG00000198643	ENSG00000198643			18665	protein-coding gene	gene with protein product		608619				12160727	Standard	NM_138805		Approved	EF7, OIT1	uc003dkq.3	Q96BQ1	OTTHUMG00000159148	ENST00000358781.2:c.352G>T	3.37:g.58625875C>A	ENSP00000351632:p.Ala118Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	76	0.571429	NM_138805	Q547G2	Missense_Mutation	SNP	ENST00000358781.2	37	CCDS2893.1	215	0.09844322344322344	29	0.05894308943089431	55	0.15193370165745856	1	0.0017482517482517483	130	0.17150395778364116	C	8.959	0.969981	0.18659	0.081934	0.182209	ENSG00000198643	ENST00000358781;ENST00000483787;ENST00000489857	T;T;T	0.51325	0.71;1.99;1.55	5.49	-4.43	0.03568	.	1.461070	0.03576	N	0.229351	T	0.00039	0.0001	N	0.01576	-0.805	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.07751	-1.0756	9	0.20046	T	0.44	-0.4704	6.4739	0.22024	0.2845:0.2233:0.0:0.4922	rs33966924	118	Q96BQ1	FAM3D_HUMAN	S	118;117;81	ENSP00000351632:A118S;ENSP00000417099:A117S;ENSP00000417453:A81S	ENSP00000351632:A118S	A	-	1	0	FAM3D	58600915	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.939000	0.03933	-0.496000	0.06650	-0.302000	0.09304	GCA	C|0.868;A|0.132	0.132	strong		0.552	FAM3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353494.1	NM_138805	
THBS2	7058	hgsc.bcm.edu	37	6	169637763	169637763	+	Silent	SNP	G	G	C	rs9766671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:169637763G>C	ENST00000366787.3	-	9	1506	c.1257C>G	c.(1255-1257)tcC>tcG	p.S419S	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	419	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GTGTCTGGATGGAGGGCCCCA	0.662													g|||	1270	0.253594	0.2526	0.2478	5008	,	,		17747	0.2679		0.1968	False		,,,				2504	0.3027				p.S419S	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	1	0			c.C1257G						PASS	.			1069,3337	387.5+/-326.5	123,823,1257	87.0	79.0	81.0		1257	2.5	1.0	6	dbSNP_119	81	1601,6999	295.8+/-302.6	167,1267,2866	no	coding-synonymous	THBS2	NM_003247.2		290,2090,4123	CC,CG,GG		18.6163,24.2624,20.529		419/1173	169637763	2670,10336	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon9			CTGGATGGAGGGC		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.1257C>G	6.37:g.169637763G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|0.786;C|0.214	0.214	strong		0.662	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
PCDHA3	56145	hgsc.bcm.edu	37	5	140183058	140183058	+	Missense_Mutation	SNP	G	G	A	rs2240694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140183058G>A	ENST00000522353.2	+	1	2276	c.2276G>A	c.(2275-2277)tGc>tAc	p.C759Y	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.C759Y|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	759	6 X 4 AA repeats of P-X-X-P.		C -> Y (in dbSNP:rs2240694).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAGGGTGTGCTCTGGAGAG	0.622													.|||	2631	0.525359	0.4788	0.5893	5008	,	,		15605	0.5317		0.5378	False		,,,				2504	0.5235				p.C759Y		Atlas-SNP	.											PCDHA3,NS,carcinoma,+1,1	PCDHA3	396	1	0			c.G2276A						scavenged	.	G	,,TYR/CYS,,TYR/CYS	2185,2221	585.8+/-386.3	533,1119,551	97.0	103.0	101.0		,,2276,,2276	3.3	1.0	5	dbSNP_98	101	4540,4060	594.5+/-393.3	1192,2156,952	yes	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,194,,194	1725,3275,1503	AA,AG,GG		47.2093,49.5915,48.2931	,,,,	,,759/951,,759/825	140183058	6725,6281	2203	4300	6503	SO:0001583	missense	56145	exon1			GGGTGTGCTCTGG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.2276G>A	5.37:g.140183058G>A	ENSP00000429808:p.Cys759Tyr	Somatic	369	3	0.00813008		WXS	Illumina HiSeq	Phase_I	280	95	0.339286	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	1163	0.5325091575091575	252	0.5121951219512195	194	0.5359116022099447	311	0.5437062937062938	406	0.5356200527704486	g	12.10	1.836155	0.32421	0.495915	0.527907	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.14640	2.49;2.49	4.16	3.26	0.37387	.	0.338457	0.20695	U	0.087381	T	0.00012	0.0000	M	0.90019	3.08	0.39490	P	0.03197799999999995	B;B	0.19331	0.035;0.009	B;B	0.22880	0.042;0.013	T	0.35624	-0.9781	9	0.72032	D	0.01	.	13.8703	0.63615	0.0:0.1545:0.8455:0.0	rs2240694;rs17844263;rs52836725;rs2240694	759;759	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	Y	759	ENSP00000429808:C759Y;ENSP00000434086:C759Y	ENSP00000429808:C759Y	C	+	2	0	PCDHA3	140163242	.	.	0.987000	0.45799	0.619000	0.37552	.	.	0.828000	0.34709	0.467000	0.42956	TGC	G|0.476;A|0.524	0.524	strong		0.622	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
USH2A	7399	hgsc.bcm.edu	37	1	215914826	215914826	+	Missense_Mutation	SNP	T	T	C	rs35309576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:215914826T>C	ENST00000307340.3	-	60	11988	c.11602A>G	c.(11602-11604)Atg>Gtg	p.M3868V	USH2A_ENST00000366943.2_Missense_Mutation_p.M3868V	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3868	Fibronectin type-III 24. {ECO:0000255|PROSITE-ProRule:PRU00316}.		M -> V (in dbSNP:rs35309576). {ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.M3868V(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTAAGATCCATTGGGGCTGCT	0.383										HNSCC(13;0.011)			T|||	798	0.159345	0.2027	0.196	5008	,	,		15397	0.0843		0.2356	False		,,,				2504	0.0736				p.M3868V		Atlas-SNP	.											USH2A,NS,carcinoma,0,2	USH2A	1168	2	1	Substitution - Missense(1)	stomach(1)	c.A11602G						PASS	.	T	VAL/MET	835,3571	328.0+/-300.3	82,671,1450	115.0	116.0	116.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11602	-9.7	0.0	1	dbSNP_126	116	2006,6594	350.3+/-327.8	238,1530,2532	yes	missense	USH2A	NM_206933.2	21	320,2201,3982	CC,CT,TT		23.3256,18.9514,21.8438	benign	3868/5203	215914826	2841,10165	2203	4300	6503	SO:0001583	missense	7399	exon60			GATCCATTGGGGC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.11602A>G	1.37:g.215914826T>C	ENSP00000305941:p.Met3868Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	44	41	0.931818	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	425	0.1945970695970696	114	0.23170731707317074	81	0.22375690607734808	57	0.09965034965034965	173	0.22823218997361477	T	5.460	0.270032	0.10349	0.189514	0.233256	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.12361	2.69;2.69	5.38	-9.68	0.00528	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.951410	0.08631	N	0.917001	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	9	0.24483	T	0.36	.	7.5708	0.27907	0.1504:0.535:0.1184:0.1961	rs35309576	3868	O75445	USH2A_HUMAN	V	3868	ENSP00000305941:M3868V;ENSP00000355910:M3868V	ENSP00000305941:M3868V	M	-	1	0	USH2A	213981449	0.000000	0.05858	0.000000	0.03702	0.757000	0.42996	-2.392000	0.01056	-1.693000	0.01427	-1.303000	0.01326	ATG	T|0.785;C|0.215	0.215	strong		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
CARD11	84433	hgsc.bcm.edu	37	7	2962293	2962293	+	Silent	SNP	C	C	G	rs3735131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2962293C>G	ENST00000396946.4	-	17	2647	c.2244G>C	c.(2242-2244)acG>acC	p.T748T		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	748	PDZ.				Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TGTAGTGCAGCGTGACGGGGC	0.622			Mis		DLBCL								C|||	766	0.152955	0.2481	0.1542	5008	,	,		18721	0.1558		0.0268	False		,,,				2504	0.1503				p.T748T		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	CARD11,NS,carcinoma,-2,1	CARD11	339	1	0			c.G2244C						PASS	.	C		1025,3381	377.8+/-322.6	120,785,1298	135.0	97.0	110.0		2244	-8.0	0.9	7	dbSNP_107	110	180,8420	80.9+/-143.5	1,178,4121	no	coding-synonymous	CARD11	NM_032415.4		121,963,5419	GG,GC,CC		2.093,23.2637,9.265		748/1155	2962293	1205,11801	2203	4300	6503	SO:0001819	synonymous_variant	84433	exon17			GTGCAGCGTGACG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2244G>C	7.37:g.2962293C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	104	61	0.586538	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			C|0.887;G|0.113	0.113	strong		0.622	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
ITPR2	3709	hgsc.bcm.edu	37	12	26868322	26868322	+	Silent	SNP	T	T	C	rs1900941	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:26868322T>C	ENST00000381340.3	-	8	1181	c.765A>G	c.(763-765)gaA>gaG	p.E255E		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	255	MIR 3. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TTTTCTCATATTCATCACAAG	0.393													T|||	1086	0.216853	0.0295	0.2435	5008	,	,		17553	0.1944		0.492	False		,,,				2504	0.1912				p.E255E		Atlas-SNP	.											ITPR2,colon,carcinoma,-2,1	ITPR2	270	1	0			c.A765G						PASS	.	T		310,3448		13,284,1582	128.0	125.0	126.0		765	1.0	1.0	12	dbSNP_92	126	3870,4360		918,2034,1163	no	coding-synonymous	ITPR2	NM_002223.2		931,2318,2745	CC,CT,TT		47.0231,8.2491,34.8682		255/2702	26868322	4180,7808	1879	4115	5994	SO:0001819	synonymous_variant	3709	exon8			CTCATATTCATCA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.765A>G	12.37:g.26868322T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.714;C|0.286	0.286	strong		0.393	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
ATP10D	57205	hgsc.bcm.edu	37	4	47538044	47538044	+	Missense_Mutation	SNP	G	G	A	rs35012290	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:47538044G>A	ENST00000273859.3	+	7	1278	c.1009G>A	c.(1009-1011)Gca>Aca	p.A337T	ATP10D_ENST00000504445.1_Missense_Mutation_p.A337T	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	337			A -> T (in dbSNP:rs35012290).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						CTTAACTGGCGCAGTAGGTAG	0.363													G|||	268	0.0535144	0.003	0.1023	5008	,	,		19096	0.0516		0.0726	False		,,,				2504	0.0695				p.A337T		Atlas-SNP	.											.	ATP10D	168	.	0			c.G1009A						PASS	.	G	THR/ALA	63,4343	56.2+/-92.4	0,63,2140	118.0	114.0	116.0		1009	4.5	0.8	4	dbSNP_126	116	676,7922	168.4+/-220.0	19,638,3642	yes	missense	ATP10D	NM_020453.3	58	19,701,5782	AA,AG,GG		7.8623,1.4299,5.6829	probably-damaging	337/1427	47538044	739,12265	2203	4299	6502	SO:0001583	missense	57205	exon7			ACTGGCGCAGTAG	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.1009G>A	4.37:g.47538044G>A	ENSP00000273859:p.Ala337Thr	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	204	97	0.47549	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	132	0.06043956043956044	3	0.006097560975609756	36	0.09944751381215469	36	0.06293706293706294	57	0.07519788918205805	G	13.65	2.300657	0.40694	0.014299	0.078623	ENSG00000145246	ENST00000273859;ENST00000504445	D;D	0.88664	-2.41;-2.41	5.31	4.47	0.54385	ATPase, P-type, ATPase-associated domain (1);	0.126462	0.52532	D	0.000064	T	0.38453	0.1041	L	0.58810	1.83	0.25564	P	0.9869698	D;D	0.89917	1.0;1.0	D;D	0.81914	0.982;0.995	T	0.70908	-0.4744	9	0.48119	T	0.1	-10.9917	17.6256	0.88093	0.0:0.0:0.874:0.126	rs35012290	337;337	Q9P241;Q6PEW3	AT10D_HUMAN;.	T	337	ENSP00000273859:A337T;ENSP00000420909:A337T	ENSP00000273859:A337T	A	+	1	0	ATP10D	47232801	1.000000	0.71417	0.848000	0.33437	0.002000	0.02628	6.608000	0.74168	0.732000	0.32470	-1.357000	0.01221	GCA	G|0.944;A|0.056	0.056	strong		0.363	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
DDX52	11056	hgsc.bcm.edu	37	17	35988672	35988672	+	Silent	SNP	C	C	T	rs7224513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:35988672C>T	ENST00000349699.2	-	6	835	c.792G>A	c.(790-792)agG>agA	p.R264R	DDX52_ENST00000394367.3_Silent_p.R156R	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	264	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				TCATGTGTATCCTGAATCCTG	0.343													C|||	2844	0.567891	0.3986	0.7133	5008	,	,		15639	0.5526		0.7535	False		,,,				2504	0.5184				p.R264R		Atlas-SNP	.											.	DDX52	40	.	0			c.G792A						PASS	.	C		2118,2288	576.4+/-384.2	522,1074,607	134.0	125.0	128.0		792	-1.6	1.0	17	dbSNP_116	128	6828,1772	734.1+/-406.9	2714,1400,186	no	coding-synonymous	DDX52	NM_007010.3		3236,2474,793	TT,TC,CC		20.6047,48.0708,31.2164		264/600	35988672	8946,4060	2203	4300	6503	SO:0001819	synonymous_variant	11056	exon6			GTGTATCCTGAAT	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.792G>A	17.37:g.35988672C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Silent	SNP	ENST00000349699.2	37	CCDS11323.1																																																																																			C|0.357;T|0.643	0.643	strong		0.343	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	
SPTBN5	51332	hgsc.bcm.edu	37	15	42171654	42171654	+	Silent	SNP	G	G	A	rs56379301	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42171654G>A	ENST00000320955.6	-	16	3213	c.2986C>T	c.(2986-2988)Ctg>Ttg	p.L996L		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	996					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTGTGTGCCAGCTGCACGGCC	0.637													G|||	154	0.0307508	0.0	0.0519	5008	,	,		21436	0.0129		0.0368	False		,,,				2504	0.0695				p.L961L		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C2881T						PASS	.	G		27,4013		0,27,1993	18.0	20.0	19.0		2881	3.9	0.6	15	dbSNP_129	19	301,8013		9,283,3865	no	coding-synonymous	SPTBN5	NM_016642.2		9,310,5858	AA,AG,GG		3.6204,0.6683,2.655		961/3640	42171654	328,12026	2020	4157	6177	SO:0001819	synonymous_variant	51332	exon16			GTGCCAGCTGCAC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.2986C>T	15.37:g.42171654G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_016642		Silent	SNP	ENST00000320955.6	37																																																																																				G|0.972;A|0.028	0.028	strong		0.637	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
MUC4	4585	hgsc.bcm.edu	37	3	195509689	195509689	+	Missense_Mutation	SNP	G	G	A	rs59620726		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509689G>A	ENST00000463781.3	-	2	9221	c.8762C>T	c.(8761-8763)gCa>gTa	p.A2921V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2921V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A2921V(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.577																																					p.A2921V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	stomach(2)	c.C8762T						scavenged	.						13.0	9.0	10.0					3																	195509689		673	1544	2217	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8762C>T	3.37:g.195509689G>A	ENSP00000417498:p.Ala2921Val	Somatic	183	10	0.0546448		WXS	Illumina HiSeq	Phase_I	520	202	0.388462	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	1.188	-0.636095	0.03557	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.54;1.59	.	.	.	.	.	.	.	.	T	0.14442	0.0349	N	0.19112	0.55	0.09310	N	1	B	0.28128	0.201	B	0.24848	0.056	T	0.25187	-1.0139	7	.	.	.	.	2.1665	0.03838	0.3292:0.3381:0.3327:0.0	rs59620726	2793	E7ESK3	.	V	2921	ENSP00000417498:A2921V;ENSP00000420243:A2921V	.	A	-	2	0	MUC4	196994468	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.843000	0.01680	-0.000000	0.14550	0.000000	0.15137	GCA	G|0.997;A|0.003	0.003	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CUX1	1523	hgsc.bcm.edu	37	7	101848404	101848404	+	Silent	SNP	C	C	T	rs144081584	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:101848404C>T	ENST00000292535.7	+	20	3122	c.3084C>T	c.(3082-3084)tcC>tcT	p.S1028S	CUX1_ENST00000437600.4_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000360264.3_Silent_p.S1039S|CUX1_ENST00000549414.2_Silent_p.S1006S|CUX1_ENST00000550008.2_Silent_p.S972S|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Silent_p.S926S|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Silent_p.S870S|CUX1_ENST00000292538.4_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	1028					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						TCCTCCACTCCGTGACATCGC	0.512													c|||	36	0.0071885	0.0	0.0173	5008	,	,		16567	0.0		0.0179	False		,,,				2504	0.0061				p.S1039S		Atlas-SNP	.											CUX1,caecum,carcinoma,0,2	CUX1	253	2	0			c.C3117T						PASS	.	T	,,,,,,	13,4393	20.2+/-43.8	1,11,2191	124.0	112.0	116.0		3117,,,,,,3084	-11.4	0.3	7	dbSNP_134	116	143,8457	71.6+/-134.2	2,139,4159	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	3,150,6350	TT,TC,CC		1.6628,0.2951,1.1994	,,,,,,	1039/1517,,,,,,1028/1506	101848404	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	1523	exon20			CCACTCCGTGACA	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.3084C>T	7.37:g.101848404C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	183	97	0.530055	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																			C|0.989;T|0.011	0.011	strong		0.512	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
TNFAIP8	25816	hgsc.bcm.edu	37	5	118728953	118728953	+	Silent	SNP	G	G	C	rs3203922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:118728953G>C	ENST00000503646.1	+	3	1162	c.474G>C	c.(472-474)gtG>gtC	p.V158V	TNFAIP8_ENST00000504771.2_Silent_p.V158V|TNFAIP8_ENST00000274456.6_Silent_p.V148V|TNFAIP8_ENST00000513374.1_Silent_p.V170V|TNFAIP8_ENST00000504642.1_Silent_p.V160V|TNFAIP8_ENST00000415806.2_3'UTR			O95379	TFIP8_HUMAN	tumor necrosis factor, alpha-induced protein 8	158					defense response to Gram-positive bacterium (GO:0050830)|interleukin-1 beta production (GO:0032611)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)	cytoplasm (GO:0005737)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)		TTAATAATGTGTTTGATCATT	0.388													C|||	1348	0.269169	0.4039	0.2767	5008	,	,		19648	0.1151		0.2604	False		,,,				2504	0.2495				p.V158V		Atlas-SNP	.											.	TNFAIP8	12	.	0			c.G474C						PASS	.	C	,	1543,2325		302,939,693	99.0	101.0	101.0		444,474	3.8	1.0	5	dbSNP_105	101	2189,6151		266,1657,2247	no	coding-synonymous,coding-synonymous	TNFAIP8	NM_001077654.1,NM_014350.2	,	568,2596,2940	CC,CG,GG		26.247,39.8914,30.5701	,	148/189,158/199	118728953	3732,8476	1934	4170	6104	SO:0001819	synonymous_variant	25816	exon2			TAATGTGTTTGAT	AF070671	CCDS47257.1, CCDS47258.1, CCDS68933.1	5q23.1	2008-02-05			ENSG00000145779	ENSG00000145779			17260	protein-coding gene	gene with protein product		612111				10233894, 10644768	Standard	NM_001286813		Approved	GG2-1, MDC-3.13, SCC-S2	uc003ksi.3	O95379	OTTHUMG00000162949	ENST00000503646.1:c.474G>C	5.37:g.118728953G>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	178	91	0.511236	NM_014350	B3KMH1|B3KMI2|B7Z713|Q9P1Q1|Q9UER5|Q9UP47	Silent	SNP	ENST00000503646.1	37	CCDS47258.1																																																																																			G|0.745;C|0.255	0.255	strong		0.388	TNFAIP8-002	PUTATIVE	alternative_5_UTR|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000371134.2	NM_014350	
FN1	2335	hgsc.bcm.edu	37	2	216242917	216242917	+	Silent	SNP	T	T	A	rs1132741	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:216242917T>A	ENST00000359671.1	-	34	5683	c.5418A>T	c.(5416-5418)ggA>ggT	p.G1806G	FN1_ENST00000356005.4_Silent_p.G1716G|FN1_ENST00000421182.1_Silent_p.G1716G|FN1_ENST00000443816.1_Silent_p.G1716G|FN1_ENST00000323926.6_Silent_p.G1897G|FN1_ENST00000446046.1_Silent_p.G1806G|FN1_ENST00000354785.4_Silent_p.G1897G|FN1_ENST00000345488.5_Silent_p.G1806G|FN1_ENST00000432072.2_Silent_p.G1807G|FN1_ENST00000357009.2_Silent_p.G1806G|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000336916.4_Silent_p.G1806G|FN1_ENST00000346544.3_Silent_p.G1806G|FN1_ENST00000357867.4_Silent_p.G1716G			P02751	FINC_HUMAN	fibronectin 1	1806	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Heparin-binding 2.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.G1806G(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TGGTGACAACTCCCTGAGCTG	0.418													T|||	1626	0.324681	0.0598	0.3919	5008	,	,		15294	0.7659		0.2505	False		,,,				2504	0.2566				p.G1897G		Atlas-SNP	.											FN1,NS,carcinoma,0,1	FN1	521	1	1	Substitution - coding silent(1)	stomach(1)	c.A5691T						PASS	.	T	,,,,	400,4006	200.1+/-223.5	10,380,1813	146.0	125.0	132.0		5418,5148,5148,5418,5691	-4.2	0.9	2	dbSNP_86	132	2070,6530	360.9+/-332.1	251,1568,2481	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FN1	NM_002026.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	,,,,	261,1948,4294	AA,AT,TT		24.0698,9.0785,18.9912	,,,,	1806/2356,1716/2177,1716/2297,1806/2331,1897/2478	216242917	2470,10536	2203	4300	6503	SO:0001819	synonymous_variant	2335	exon35			GACAACTCCCTGA		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.5418A>T	2.37:g.216242917T>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																				T|0.728;A|0.272	0.272	strong		0.418	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
TTN	7273	hgsc.bcm.edu	37	2	179545859	179545859	+	Missense_Mutation	SNP	C	C	T	rs36051007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179545859C>T	ENST00000591111.1	-	136	32560	c.32336G>A	c.(32335-32337)cGt>cAt	p.R10779H	TTN_ENST00000589042.1_Missense_Mutation_p.R11096H|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R9852H|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.			R -> H (in Ref. 1; CAA62189). {ECO:0000305}.	adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATTGAAATACGTATTTTTTC	0.328													C|||	631	0.125998	0.0068	0.1124	5008	,	,		17999	0.0357		0.3062	False		,,,				2504	0.2045				p.R11096H		Atlas-SNP	.											.	TTN	18412	.	0			c.G33287A						PASS	.	C	,,,HIS/ARG	190,3410		4,182,1614	85.0	79.0	81.0		,,,29555	-2.8	0.1	2	dbSNP_126	81	2467,5671		363,1741,1965	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,29	367,1923,3579	TT,TC,CC		30.3146,5.2778,22.6359	,,,benign	,,,9852/33424	179545859	2657,9081	1800	4069	5869	SO:0001583	missense	7273	exon138			GAAATACGTATTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32336G>A	2.37:g.179545859C>T	ENSP00000465570:p.Arg10779His	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		329	0.15064102564102563	9	0.018292682926829267	56	0.15469613259668508	21	0.03671328671328671	243	0.32058047493403696	C	12.26	1.884919	0.33255	0.052778	0.303146	ENSG00000155657	ENST00000342992	T	0.62788	-0.0	5.92	-2.76	0.05896	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.40571	P	0.018691000000000013	B	0.02656	0.0	B	0.01281	0.0	T	0.21827	-1.0234	8	0.87932	D	0	.	4.6237	0.12467	0.1064:0.4398:0.109:0.3448	rs36051007	10779	Q8WZ42	TITIN_HUMAN	H	9852	ENSP00000343764:R9852H	ENSP00000343764:R9852H	R	-	2	0	TTN	179254104	0.001000	0.12720	0.090000	0.20809	0.962000	0.63368	-0.518000	0.06267	-0.660000	0.05352	-0.300000	0.09419	CGT	C|0.821;T|0.179	0.179	strong		0.328	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF142	7701	hgsc.bcm.edu	37	2	219520895	219520895	+	Silent	SNP	T	T	C	rs3731872	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219520895T>C	ENST00000449707.1	-	4	679	c.258A>G	c.(256-258)ccA>ccG	p.P86P	ZNF142_ENST00000411696.2_Silent_p.P86P	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	86					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CAGGAGCACCTGGGGTCAGGG	0.532													T|||	563	0.11242	0.2564	0.0317	5008	,	,		18480	0.122		0.0258	False		,,,				2504	0.0542				p.P86P	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A258G						PASS	.	T		856,3132		85,686,1223	58.0	61.0	60.0		258	0.1	1.0	2	dbSNP_107	60	273,8045		4,265,3890	no	coding-synonymous	ZNF142	NM_001105537.1		89,951,5113	CC,CT,TT		3.282,21.4644,9.1744		86/1688	219520895	1129,11177	1994	4159	6153	SO:0001819	synonymous_variant	7701	exon4			AGCACCTGGGGTC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.258A>G	2.37:g.219520895T>C		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	276	132	0.478261	NM_001105537	Q92510	Silent	SNP	ENST00000449707.1	37	CCDS42817.1	243	0.11126373626373626	130	0.26422764227642276	15	0.04143646408839779	81	0.14160839160839161	17	0.022427440633245383	T	10.61	1.398166	0.25205	0.214644	0.03282	ENSG00000115568	ENST00000440934	.	.	.	5.28	0.0464	0.14233	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999595341	.	.	.	.	.	.	T	0.32481	-0.9905	3	.	.	.	-5.8235	4.1445	0.10209	0.0:0.3393:0.1834:0.4773	rs3731872;rs61514357;rs3731872	.	.	.	G	78	.	.	R	-	1	2	ZNF142	219229139	0.976000	0.34144	1.000000	0.80357	0.990000	0.78478	0.182000	0.16900	0.446000	0.26666	0.533000	0.62120	AGG	T|0.896;C|0.104	0.104	strong		0.532	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
PARP10	84875	hgsc.bcm.edu	37	8	145059425	145059425	+	Missense_Mutation	SNP	T	T	C	rs11136344	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145059425T>C	ENST00000313028.7	-	5	839	c.745A>G	c.(745-747)Atc>Gtc	p.I249V	PARP10_ENST00000524918.1_Missense_Mutation_p.I249V|PARP10_ENST00000525773.1_Missense_Mutation_p.I261V|PARP10_ENST00000533665.1_5'UTR	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	249			I -> V (in dbSNP:rs11136344).		negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGCTCCAGgatgtcgtagtgg	0.627													C|||	1959	0.391174	0.6165	0.2795	5008	,	,		18107	0.1458		0.4314	False		,,,				2504	0.3773				p.I249V		Atlas-SNP	.											.	PARP10	57	.	0			c.A745G						PASS	.		VAL/ILE	2628,1778	516.2+/-369.1	781,1066,356	40.0	42.0	41.0		745	-0.6	0.0	8	dbSNP_120	41	3640,4960	614.2+/-396.2	796,2048,1456	yes	missense	PARP10	NM_032789.3	29	1577,3114,1812	CC,CT,TT		42.3256,40.3541,48.1931	benign	249/1026	145059425	6268,6738	2203	4300	6503	SO:0001583	missense	84875	exon5			CCAGGATGTCGTA	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.745A>G	8.37:g.145059425T>C	ENSP00000325618:p.Ile249Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	40	0.555556	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	37	CCDS34960.1	832	0.38095238095238093	308	0.6260162601626016	116	0.32044198895027626	88	0.15384615384615385	320	0.42216358839050133	C	0.003	-2.464539	0.00171	0.596459	0.423256	ENSG00000178685	ENST00000524918;ENST00000313028;ENST00000525773;ENST00000313059	T;T;T;T	0.24908	3.14;3.15;3.15;1.83	3.8	-0.575	0.11734	.	0.572735	0.14302	N	0.328229	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36407	-0.9749	9	0.02654	T	1	.	3.4917	0.07639	0.179:0.3745:0.0:0.4465	rs11136344;rs57845841;rs11136344	261;249;249	E9PNI7;E9PK67;Q53GL7	.;.;PAR10_HUMAN	V	249;249;261;164	ENSP00000431620:I249V;ENSP00000325618:I249V;ENSP00000434776:I261V;ENSP00000314320:I164V	ENSP00000325618:I249V	I	-	1	0	PARP10	145131413	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.973000	0.01500	-0.436000	0.07254	-1.016000	0.02456	ATC	T|0.554;C|0.446	0.446	strong		0.627	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
BAI3	577	hgsc.bcm.edu	37	6	70071173	70071173	+	Silent	SNP	G	G	A	rs913543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:70071173G>A	ENST00000370598.1	+	29	4829	c.4008G>A	c.(4006-4008)ccG>ccA	p.P1336P	BAI3_ENST00000238918.8_Silent_p.P542P|BAI3_ENST00000546190.1_Silent_p.P300P	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1336					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AAACCTTGCCGCATGAAAGGC	0.403													G|||	2435	0.486222	0.1747	0.4568	5008	,	,		20805	0.8304		0.4463	False		,,,				2504	0.6145				p.P1336P		Atlas-SNP	.											.	BAI3	451	.	0			c.G4008A						PASS	.	G		1019,3387	373.7+/-320.9	120,779,1304	76.0	72.0	73.0		4008	-2.2	1.0	6	dbSNP_86	73	3768,4830	533.9+/-382.5	832,2104,1363	no	coding-synonymous	BAI3	NM_001704.2		952,2883,2667	AA,AG,GG		43.8241,23.1276,36.8118		1336/1523	70071173	4787,8217	2203	4299	6502	SO:0001819	synonymous_variant	577	exon29			CTTGCCGCATGAA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.4008G>A	6.37:g.70071173G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																			G|0.585;A|0.415	0.415	strong		0.403	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
MET	4233	hgsc.bcm.edu	37	7	116339282	116339282	+	Silent	SNP	G	G	A	rs11762213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:116339282G>A	ENST00000318493.6	+	2	331	c.144G>A	c.(142-144)gcG>gcA	p.A48A	MET_ENST00000397752.3_Silent_p.A48A|MET_ENST00000436117.2_Silent_p.A48A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			ACTTCACCGCGGAAACACCCA	0.433			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	77	0.0153754	0.0023	0.0346	5008	,	,		21839	0.0		0.0398	False		,,,				2504	0.0102				p.A48A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,adenocarcinoma,+1,2	MET	412	2	0			c.G144A						PASS	.	G	,	42,3886		0,42,1922	100.0	99.0	99.0		144,144	-11.8	0.0	7	dbSNP_120	99	391,7915		6,379,3768	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	6,421,5690	AA,AG,GG		4.7074,1.0692,3.5393	,	48/1391,48/1409	116339282	433,11801	1964	4153	6117	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CACCGCGGAAACA	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.144G>A	7.37:g.116339282G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	174	98	0.563218	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
CMAS	55907	hgsc.bcm.edu	37	12	22213786	22213786	+	Silent	SNP	C	C	T	rs10841930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:22213786C>T	ENST00000229329.2	+	5	844	c.714C>T	c.(712-714)taC>taT	p.Y238Y		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	238					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						TGGCATACTACGAAATGCGAG	0.303													C|||	1268	0.253195	0.1452	0.1902	5008	,	,		15496	0.4524		0.0885	False		,,,				2504	0.408				p.Y238Y		Atlas-SNP	.											.	CMAS	45	.	0			c.C714T						PASS	.	C		681,3725	287.2+/-279.2	46,589,1568	118.0	123.0	121.0		714	-11.1	0.4	12	dbSNP_120	121	865,7731	197.5+/-242.1	39,787,3472	no	coding-synonymous	CMAS	NM_018686.3		85,1376,5040	TT,TC,CC		10.0628,15.4562,11.8905		238/435	22213786	1546,11456	2203	4298	6501	SO:0001819	synonymous_variant	55907	exon5			ATACTACGAAATG	AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"""CMP-Neu5Ac synthetase"""	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.714C>T	12.37:g.22213786C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_018686	Q96AX5|Q9NQZ0	Silent	SNP	ENST00000229329.2	37	CCDS8696.1																																																																																			C|0.831;G|0.000;T|0.169	0.169	strong		0.303	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686	
ACTN1	87	hgsc.bcm.edu	37	14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	rs11557769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:69341653T>A	ENST00000193403.6	-	21	2985	c.2602A>T	c.(2602-2604)Acc>Tcc	p.T868S	ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S|ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S|ACTN1_ENST00000394419.4_Missense_Mutation_p.T890S	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	868			T -> S (in dbSNP:rs11557769).		actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TCGGGGCCGGTGTAGGGGGCC	0.662													t|||	31	0.0061901	0.0	0.0159	5008	,	,		14509	0.0		0.0189	False		,,,				2504	0.001				p.T890S		Atlas-SNP	.											ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	0			c.A2668T						scavenged	.	T	SER/THR,SER/THR,SER/THR	16,4390	25.3+/-52.1	0,16,2187	42.0	41.0	41.0		2602,2668,2587	-2.7	0.9	14	dbSNP_120	41	142,8458	70.3+/-132.9	0,142,4158	yes	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	58,58,58	0,158,6345	AA,AT,TT		1.6512,0.3631,1.2148	benign,benign,benign	868/893,890/915,863/888	69341653	158,12848	2203	4300	6503	SO:0001583	missense	87	exon22			GGCCGGTGTAGGG	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.2602A>T	14.37:g.69341653T>A	ENSP00000193403:p.Thr868Ser	Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	80	32	0.4	NM_001130004	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	18	0.008241758241758242	0	0.0	8	0.022099447513812154	0	0.0	10	0.013192612137203167	T	9.571	1.121108	0.20877	0.003631	0.016512	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.39229	1.6;1.09;1.09;1.09;1.09	4.68	-2.72	0.05968	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.656003	0.15664	N	0.250756	T	0.09642	0.0237	L	0.28556	0.865	0.22185	N	0.999308	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.21690	-1.0238	10	0.08381	T	0.77	.	2.1866	0.03888	0.1289:0.3501:0.1331:0.3879	rs11557769	863;890;868;510	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	S	868;890;863;798;906	ENSP00000193403:T868S;ENSP00000377941:T890S;ENSP00000414272:T863S;ENSP00000366035:T798S;ENSP00000439828:T906S	ENSP00000193403:T868S	T	-	1	0	ACTN1	68411406	0.003000	0.15002	0.930000	0.37139	0.998000	0.95712	-0.007000	0.12810	-0.578000	0.05959	0.528000	0.53228	ACC	T|0.988;A|0.012	0.012	strong		0.662	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
IL32	9235	hgsc.bcm.edu	37	16	3119167	3119167	+	Silent	SNP	T	T	C	rs34184287	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3119167T>C	ENST00000534507.1	+	6	727	c.516T>C	c.(514-516)gtT>gtC	p.V172V	IL32_ENST00000552356.1_Silent_p.V106V|IL32_ENST00000325568.5_Silent_p.V126V|IL32_ENST00000530890.1_Silent_p.V106V|IL32_ENST00000529699.1_Silent_p.V106V|IL32_ENST00000525643.2_Silent_p.V126V|IL32_ENST00000440815.3_Silent_p.V126V|IL32_ENST00000396890.2_Silent_p.V172V|IL32_ENST00000396887.3_Intron|IL32_ENST00000548476.1_Silent_p.V172V|IL32_ENST00000548246.1_Silent_p.V86V|IL32_ENST00000530538.2_Silent_p.V126V|IL32_ENST00000382213.3_Silent_p.V117V|IL32_ENST00000548652.1_Silent_p.V117V|IL32_ENST00000444393.3_Silent_p.V126V|IL32_ENST00000551122.1_Intron|IL32_ENST00000008180.9_Silent_p.V106V|IL32_ENST00000552664.1_Silent_p.V126V|IL32_ENST00000552936.1_Silent_p.V150V|IL32_ENST00000528163.2_Silent_p.V126V|IL32_ENST00000526464.2_Silent_p.V126V|IL32_ENST00000531965.1_Silent_p.V116V|IL32_ENST00000549213.1_Intron|IL32_ENST00000551513.1_Silent_p.V163V|IL32_ENST00000529550.1_Silent_p.V126V|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000533097.2_Silent_p.V126V			P24001	IL32_HUMAN	interleukin 32	172					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						GGCACGGGGTTCTGGCCTGGG	0.597													T|||	1775	0.354433	0.2307	0.366	5008	,	,		18195	0.3839		0.4046	False		,,,				2504	0.4315				p.V126V		Atlas-SNP	.											.	IL32	32	.	0			c.T378C						PASS	.						21.0	25.0	24.0					16																	3119167		2192	4276	6468	SO:0001819	synonymous_variant	9235	exon7			CGGGGTTCTGGCC	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.516T>C	16.37:g.3119167T>C		Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	382	108	0.282723	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Silent	SNP	ENST00000534507.1	37																																																																																				T|0.235;C|0.765	0.765	strong		0.597	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
EML5	161436	hgsc.bcm.edu	37	14	89205265	89205265	+	Missense_Mutation	SNP	T	T	C	rs17188228	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:89205265T>C	ENST00000380664.5	-	6	804	c.805A>G	c.(805-807)Att>Gtt	p.I269V	EML5_ENST00000352093.5_Missense_Mutation_p.I269V|EML5_ENST00000554922.1_Missense_Mutation_p.I269V			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	269			I -> V (in dbSNP:rs17188228).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						ATCACAGTAATTGGTTTAAAA	0.373													T|||	1232	0.246006	0.1619	0.2291	5008	,	,		15501	0.3909		0.2256	False		,,,				2504	0.2434				p.I269V		Atlas-SNP	.											.	EML5	141	.	0			c.A805G						PASS	.	T	VAL/ILE	651,3069		60,531,1269	73.0	65.0	68.0		805	5.5	1.0	14	dbSNP_123	68	2066,6144		259,1548,2298	yes	missense	EML5	NM_183387.2	29	319,2079,3567	CC,CT,TT		25.1644,17.5,22.7745	benign	269/1978	89205265	2717,9213	1860	4105	5965	SO:0001583	missense	161436	exon6			CAGTAATTGGTTT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.805A>G	14.37:g.89205265T>C	ENSP00000370039:p.Ile269Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	593	0.2715201465201465	101	0.20528455284552846	86	0.23756906077348067	230	0.4020979020979021	176	0.23218997361477572	T	14.85	2.659503	0.47467	0.175	0.251644	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.01287	5.05;5.05;5.05	5.5	5.5	0.81552	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.52266	1.64	0.09310	P	0.99999262538	D	0.61080	0.989	P	0.58577	0.841	T	0.64681	-0.6350	9	0.14252	T	0.57	-17.9194	15.5946	0.76569	0.0:0.0:0.0:1.0	rs17188228;rs52811369;rs17188228	269	Q05BV3	EMAL5_HUMAN	V	269	ENSP00000451998:I269V;ENSP00000298315:I269V;ENSP00000370039:I269V	ENSP00000298315:I269V	I	-	1	0	EML5	88275018	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.091000	0.63221	0.454000	0.30748	ATT	T|0.733;C|0.267	0.267	strong		0.373	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
FAM8A1	51439	hgsc.bcm.edu	37	6	17608511	17608511	+	Nonsense_Mutation	SNP	C	C	T	rs200041366		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:17608511C>T	ENST00000259963.3	+	5	1238	c.1183C>T	c.(1183-1185)Cga>Tga	p.R395*		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	395	RDD.					integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			TCAGCATAATCGAACAGCTTA	0.383																																					p.R395X		Atlas-SNP	.											FAM8A1,lower_third,carcinoma,-1,1	FAM8A1	26	1	0			c.C1183T						scavenged	.						109.0	104.0	106.0					6																	17608511		2203	4300	6503	SO:0001587	stop_gained	51439	exon5			CATAATCGAACAG	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.1183C>T	6.37:g.17608511C>T	ENSP00000259963:p.Arg395*	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	213	8	0.0375587	NM_016255	B2R725	Nonsense_Mutation	SNP	ENST00000259963.3	37	CCDS4540.1	.	.	.	.	.	.	.	.	.	.	C	36	5.927702	0.97110	.	.	ENSG00000137414	ENST00000542476;ENST00000259963	.	.	.	5.63	4.76	0.60689	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0172	8.5079	0.33199	0.2528:0.6721:0.0:0.0751	.	.	.	.	X	145;395	.	ENSP00000259963:R395X	R	+	1	2	FAM8A1	17716490	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.235000	0.51328	1.373000	0.46208	0.557000	0.71058	CGA	.	.	weak		0.383	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1		
SULT2B1	6820	hgsc.bcm.edu	37	19	49096065	49096065	+	Silent	SNP	C	C	T	rs2302948	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49096065C>T	ENST00000201586.2	+	5	815	c.637C>T	c.(637-639)Ctg>Ttg	p.L213L	SULT2B1_ENST00000594274.1_3'UTR|SULT2B1_ENST00000323090.4_Silent_p.L198L	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	213					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		CTACGAGGAGCTGCAGCAGGT	0.602													C|||	838	0.167332	0.1914	0.1671	5008	,	,		17330	0.0883		0.2406	False		,,,				2504	0.1411				p.L213L		Atlas-SNP	.											.	SULT2B1	72	.	0			c.C637T						PASS	.	C	,	837,3569		81,675,1447	88.0	60.0	69.0		592,637	2.3	0.9	19	dbSNP_100	69	1952,6638		205,1542,2548	no	coding-synonymous,coding-synonymous	SULT2B1	NM_004605.2,NM_177973.1	,	286,2217,3995	TT,TC,CC		22.7241,18.9968,21.4604	,	198/351,213/366	49096065	2789,10207	2203	4295	6498	SO:0001819	synonymous_variant	6820	exon5			GAGGAGCTGCAGC	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.637C>T	19.37:g.49096065C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_177973	O00205|O75814	Silent	SNP	ENST00000201586.2	37	CCDS12723.1																																																																																			C|0.814;T|0.186	0.186	strong		0.602	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
TCN1	6947	hgsc.bcm.edu	37	11	59623479	59623479	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59623479T>G	ENST00000257264.3	-	6	904	c.800A>C	c.(799-801)cAa>cCa	p.Q267P	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	267	Globular N-terminal alpha domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATTCAGAGTTTGTTGGCAATT	0.473																																					p.Q267P		Atlas-SNP	.											.	TCN1	64	.	0			c.A800C						PASS	.						122.0	124.0	124.0					11																	59623479		2201	4295	6496	SO:0001583	missense	6947	exon6			AGAGTTTGTTGGC	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"""haptocorin"", ""haptocorrin"""	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.800A>C	11.37:g.59623479T>G	ENSP00000257264:p.Gln267Pro	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	194	34	0.175258	NM_001062	A8KAC5|Q8WV77	Missense_Mutation	SNP	ENST00000257264.3	37	CCDS7978.1	.	.	.	.	.	.	.	.	.	.	t	11.77	1.737860	0.30774	.	.	ENSG00000134827	ENST00000257264	T	0.35973	1.28	4.44	3.21	0.36854	.	0.874076	0.09641	N	0.775035	T	0.29423	0.0733	L	0.29908	0.895	0.09310	N	1	B	0.33919	0.432	B	0.39119	0.291	T	0.23511	-1.0186	10	0.45353	T	0.12	.	6.5473	0.22412	0.2145:0.0:0.0:0.7855	.	267	P20061	TCO1_HUMAN	P	267	ENSP00000257264:Q267P	ENSP00000257264:Q267P	Q	-	2	0	TCN1	59380055	0.622000	0.27085	0.497000	0.27552	0.055000	0.15305	1.583000	0.36579	1.638000	0.50547	0.473000	0.43528	CAA	.	.	none		0.473	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062	
PPP1R21	129285	hgsc.bcm.edu	37	2	48713777	48713777	+	Silent	SNP	C	C	T	rs33994624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:48713777C>T	ENST00000294952.8	+	14	1483	c.1326C>T	c.(1324-1326)tcC>tcT	p.S442S	PPP1R21_ENST00000449090.2_Silent_p.S442S|PPP1R21_ENST00000281394.4_Silent_p.S442S	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	442						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						TAGATATTTCCAAACATTATA	0.328													C|||	450	0.0898562	0.0113	0.0965	5008	,	,		16802	0.0248		0.1203	False		,,,				2504	0.227				p.S442S		Atlas-SNP	.											.	PPP1R21	47	.	0			c.C1326T						PASS	.	C	,,	109,4297	78.3+/-116.7	0,109,2094	44.0	43.0	43.0		1326,1326,1326	1.5	1.0	2	dbSNP_126	43	1091,7509	221.5+/-258.9	61,969,3270	no	coding-synonymous,coding-synonymous,coding-synonymous	KLRAQ1	NM_001135629.2,NM_001193475.1,NM_152994.4	,,	61,1078,5364	TT,TC,CC		12.686,2.4739,9.2265	,,	442/781,442/739,442/770	48713777	1200,11806	2203	4300	6503	SO:0001819	synonymous_variant	129285	exon14			TATTTCCAAACAT	AY134855	CCDS1839.1, CCDS46278.1, CCDS54358.1	2p16.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000162869	ENSG00000162869		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30595	protein-coding gene	gene with protein product			"""coiled-coil domain containing 128"", ""KLRAQ motif containing 1"""	CCDC128, KLRAQ1		12477932	Standard	NM_001135629		Approved	FLJ16566	uc002rwm.3	Q6ZMI0	OTTHUMG00000129167	ENST00000294952.8:c.1326C>T	2.37:g.48713777C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	138	58	0.42029	NM_152994	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Silent	SNP	ENST00000294952.8	37	CCDS46278.1																																																																																			C|0.914;T|0.086	0.086	strong		0.328	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994	
USP6	9098	hgsc.bcm.edu	37	17	5072316	5072316	+	Silent	SNP	C	C	T	rs11658877	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5072316C>T	ENST00000574788.1	+	35	5713	c.3483C>T	c.(3481-3483)tcC>tcT	p.S1161S	USP6_ENST00000304328.5_Silent_p.S844S|USP6_ENST00000250066.6_Silent_p.S1161S|USP6_ENST00000332776.4_3'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1161	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AAAGCCCATCCTCACTCAGCG	0.522			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								C|||	1608	0.321086	0.1369	0.5994	5008	,	,		19117	0.1706		0.6024	False		,,,				2504	0.2382				p.S1161S		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C3483T						PASS	.	C		1043,3363	382.1+/-324.3	123,797,1283	45.0	44.0	44.0		3483	-2.8	0.5	17	dbSNP_120	44	5472,3128	655.0+/-401.2	1743,1986,571	no	coding-synonymous	USP6	NM_004505.2		1866,2783,1854	TT,TC,CC		36.3721,23.6723,49.9077		1161/1407	5072316	6515,6491	2203	4300	6503	SO:0001819	synonymous_variant	9098	exon27			CCCATCCTCACTC	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.3483C>T	17.37:g.5072316C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	288	279	0.96875	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			C|0.530;T|0.470	0.470	strong		0.522	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
HAUS6	54801	hgsc.bcm.edu	37	9	19058743	19058743	+	Missense_Mutation	SNP	G	G	C	rs10511670	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:19058743G>C	ENST00000380502.3	-	16	2489	c.2022C>G	c.(2020-2022)caC>caG	p.H674Q	HAUS6_ENST00000380496.1_Missense_Mutation_p.H538Q	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	674			H -> Q (in dbSNP:rs10511670). {ECO:0000269|PubMed:14702039}.		centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GTTCATCTATGTGACTGGTCA	0.378													G|||	387	0.0772764	0.0666	0.0476	5008	,	,		20189	0.13		0.0855	False		,,,				2504	0.0501				p.H674Q		Atlas-SNP	.											.	HAUS6	66	.	0			c.C2022G						PASS	.	G	GLN/HIS	290,4116	160.3+/-192.7	12,266,1925	120.0	119.0	119.0		2022	-4.4	0.0	9	dbSNP_119	119	777,7823	184.5+/-232.4	46,685,3569	yes	missense	HAUS6	NM_017645.3	24	58,951,5494	CC,CG,GG		9.0349,6.5819,8.2039	benign	674/956	19058743	1067,11939	2203	4300	6503	SO:0001583	missense	54801	exon16			ATCTATGTGACTG	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.2022C>G	9.37:g.19058743G>C	ENSP00000369871:p.His674Gln	Somatic	421	0	0		WXS	Illumina HiSeq	Phase_I	368	170	0.461957	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	181	0.08287545787545787	23	0.046747967479674794	17	0.04696132596685083	71	0.12412587412587413	70	0.09234828496042216	G	1.349	-0.591964	0.03799	0.065819	0.090349	ENSG00000147874	ENST00000380502;ENST00000380496	T;T	0.23552	1.91;1.9	5.06	-4.36	0.03645	.	1.075000	0.07015	N	0.825785	T	0.00210	0.0006	L	0.42245	1.32	0.09310	N	1	B;B;B	0.13594	0.008;0.003;0.008	B;B;B	0.13407	0.009;0.009;0.009	T	0.33059	-0.9883	10	0.13470	T	0.59	13.9473	3.0345	0.06117	0.4343:0.3174:0.146:0.1023	rs10511670;rs10511670	639;538;674	Q7Z4H7-3;Q5VY60;Q7Z4H7	.;.;HAUS6_HUMAN	Q	674;538	ENSP00000369871:H674Q;ENSP00000369865:H538Q	ENSP00000369865:H538Q	H	-	3	2	HAUS6	19048743	0.000000	0.05858	0.000000	0.03702	0.202000	0.24057	-0.161000	0.10026	-0.856000	0.04120	0.467000	0.42956	CAC	G|1.000;|0.000	.	weak		0.378	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
GAK	2580	hgsc.bcm.edu	37	4	877187	877187	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:877187C>A	ENST00000314167.4	-	13	1430	c.1320G>T	c.(1318-1320)ttG>ttT	p.L440F	GAK_ENST00000511163.1_Missense_Mutation_p.L361F	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	440	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		AGTCCAGGAACAACCGCACAT	0.577																																					p.L440F		Atlas-SNP	.											.	GAK	104	.	0			c.G1320T						PASS	.						208.0	174.0	185.0					4																	877187		2203	4300	6503	SO:0001583	missense	2580	exon13			CAGGAACAACCGC	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.1320G>T	4.37:g.877187C>A	ENSP00000314499:p.Leu440Phe	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	118	18	0.152542	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.910103	0.33721	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	D;D	0.98602	-5.02;-5.02	5.34	1.53	0.23141	Phosphatase tensin type (1);	0.171640	0.38663	N	0.001620	D	0.95965	0.8686	L	0.48642	1.525	0.58432	D	0.999996	P;P;P;P	0.48640	0.913;0.848;0.849;0.849	P;P;B;B	0.47891	0.56;0.56;0.379;0.288	D	0.91526	0.5238	10	0.30854	T	0.27	-4.0961	5.1519	0.15015	0.139:0.515:0.2693:0.0766	.	361;361;440;336	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	F	440;361	ENSP00000314499:L440F;ENSP00000421361:L361F	ENSP00000314499:L440F	L	-	3	2	GAK	867187	0.927000	0.31430	0.089000	0.20774	0.004000	0.04260	0.128000	0.15810	-0.028000	0.13850	-1.047000	0.02352	TTG	.	.	none		0.577	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
ZNF419	79744	hgsc.bcm.edu	37	19	58004346	58004346	+	Missense_Mutation	SNP	G	G	C	rs2074076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58004346G>C	ENST00000221735.7	+	5	607	c.421G>C	c.(421-423)Gag>Cag	p.E141Q	ZNF419_ENST00000426954.2_Missense_Mutation_p.E129Q|ZNF419_ENST00000354197.4_Missense_Mutation_p.E129Q|ZNF419_ENST00000442920.2_Missense_Mutation_p.E128Q|ZNF419_ENST00000424930.2_Missense_Mutation_p.E142Q|ZNF419_ENST00000347466.6_Missense_Mutation_p.E109Q|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000415379.2_Missense_Mutation_p.E95Q			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	141			E -> Q (in dbSNP:rs2074076). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		AAAAAGACAAGAGGGCAGGGT	0.507													G|||	3484	0.695687	0.5794	0.7262	5008	,	,		19751	0.6984		0.6839	False		,,,				2504	0.8405				p.E142Q		Atlas-SNP	.											.	ZNF419	134	.	0			c.G424C						PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU,GLN/GLU,GLN/GLU,GLN/GLU,GLN/GLU	2618,1788	628.1+/-395.0	781,1056,366	60.0	63.0	62.0		424,385,382,325,286,283,421	0.3	0.0	19	dbSNP_96	62	5967,2633	681.2+/-403.7	2035,1897,368	no	missense,missense,missense,missense,missense,missense,missense	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	29,29,29,29,29,29,29	2816,2953,734	CC,CG,GG		30.6163,40.581,33.992	benign,benign,benign,benign,benign,benign,benign	142/512,129/499,128/498,109/479,96/466,95/465,141/511	58004346	8585,4421	2203	4300	6503	SO:0001583	missense	79744	exon5			AGACAAGAGGGCA	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.421G>C	19.37:g.58004346G>C	ENSP00000221735:p.Glu141Gln	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	217	92	0.423963	NM_001098491	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	1477	0.6762820512820513	290	0.5894308943089431	258	0.712707182320442	410	0.7167832167832168	519	0.6846965699208444	G	2.762	-0.257605	0.05791	0.59419	0.693837	ENSG00000105136	ENST00000284020;ENST00000524372;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000521754;ENST00000221735;ENST00000521137	T;T;T;T;T;T;T;T;T	0.06849	3.37;3.38;3.32;3.38;3.25;3.25;5.4;3.36;6.97	2.48	0.261	0.15592	.	.	.	.	.	T	0.00012	0.0000	L	0.35793	1.09	0.80722	P	0.0	P;B;B;P;P;B	0.45827	0.596;0.0;0.0;0.743;0.867;0.0	B;B;B;B;P;B	0.44897	0.099;0.002;0.003;0.356;0.463;0.001	T	0.08953	-1.0697	8	0.21014	T	0.42	.	6.0755	0.19913	0.3047:0.0:0.6953:0.0	rs2074076;rs12983132;rs58731055	95;128;129;142;109;141	E9PFX9;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;ZN419_HUMAN	Q	144;129;142;129;129;128;142;109;95;96;141;108	ENSP00000388864:E142Q;ENSP00000390916:E129Q;ENSP00000346136:E129Q;ENSP00000414709:E128Q;ENSP00000299860:E109Q;ENSP00000392129:E95Q;ENSP00000428523:E96Q;ENSP00000221735:E141Q;ENSP00000429628:E108Q	ENSP00000221735:E141Q	E	+	1	0	ZNF419	62696158	0.029000	0.19370	0.008000	0.14137	0.319000	0.28217	0.923000	0.28757	0.353000	0.24079	0.205000	0.17691	GAG	G|0.324;C|0.676	0.676	strong		0.507	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
GSTA2	2939	hgsc.bcm.edu	37	6	52617731	52617731	+	Missense_Mutation	SNP	C	C	G	rs2180314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:52617731C>G	ENST00000493422.1	-	5	490	c.335G>C	c.(334-336)aGt>aCt	p.S112T		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	112	GST C-terminal.		S -> T (in dbSNP:rs2180314). {ECO:0000269|PubMed:11668220, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3036131}.		epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Chloroquine(DB00608)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Vitamin E(DB00163)	CTCAGGTTGACTAAAGGGCAG	0.378													.|||	2686	0.536342	0.2882	0.6772	5008	,	,		19143	0.6845		0.5835	False		,,,				2504	0.5706				p.S112T		Atlas-SNP	.											.	GSTA2	33	.	0			c.G335C						PASS	.	C	THR/SER	1445,2961	465.9+/-354.3	255,935,1013	220.0	207.0	211.0		335	-4.5	0.0	6	dbSNP_96	211	5062,3538	630.9+/-398.4	1505,2052,743	yes	missense	GSTA2	NM_000846.4	58	1760,2987,1756	GG,GC,CC		41.1395,32.7962,49.9692	benign	112/223	52617731	6507,6499	2203	4300	6503	SO:0001583	missense	2939	exon5			GGTTGACTAAAGG	AL109918	CCDS4944.1	6p12.2	2012-06-21	2008-11-26		ENSG00000244067	ENSG00000244067	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4627	protein-coding gene	gene with protein product		138360	"""glutathione S-transferase A2"""	GST2			Standard	NM_000846		Approved		uc003pay.3	P09210	OTTHUMG00000016263	ENST00000493422.1:c.335G>C	6.37:g.52617731C>G	ENSP00000420168:p.Ser112Thr	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	263	262	0.996198	NM_000846	Q12759|Q16491|Q9NTY6	Missense_Mutation	SNP	ENST00000493422.1	37	CCDS4944.1	1211	0.5544871794871795	135	0.27439024390243905	242	0.6685082872928176	400	0.6993006993006993	434	0.5725593667546174	c	0.145	-1.097912	0.01843	0.327962	0.588605	ENSG00000244067	ENST00000493422	T	0.01981	4.52	2.26	-4.51	0.03483	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	2.024820	0.01875	N	0.037467	T	0.00271	0.0008	N	0.02202	-0.64	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48175	-0.9058	9	0.13470	T	0.59	.	1.6058	0.02684	0.3837:0.1768:0.3188:0.1206	rs2180314;rs3178048;rs17605670;rs17849682;rs52806894;rs57248371;rs2180314	112	P09210	GSTA2_HUMAN	T	112	ENSP00000420168:S112T	ENSP00000420168:S112T	S	-	2	0	GSTA2	52725690	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-3.139000	0.00587	-1.211000	0.02624	0.306000	0.20318	AGT	C|0.477;G|0.523	0.523	strong		0.378	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846	
ASCL3	56676	hgsc.bcm.edu	37	11	8959545	8959545	+	Missense_Mutation	SNP	C	C	A	rs4909951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8959545C>A	ENST00000531618.1	-	1	213	c.164G>T	c.(163-165)cGg>cTg	p.R55L	ASCL3_ENST00000325884.1_Missense_Mutation_p.R55L			Q9NQ33	ASCL3_HUMAN	achaete-scute family bHLH transcription factor 3	54					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(5)|stomach(1)	9				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)		AAAAGGCAGCCGTGGCAGCTC	0.562													A|||	2733	0.545727	0.3003	0.6916	5008	,	,		16224	0.7113		0.6392	False		,,,				2504	0.5072				p.R55L		Atlas-SNP	.											.	ASCL3	19	.	0			c.G164T						PASS	.	A	LEU/ARG	1572,2830	667.1+/-401.8	285,1002,914	69.0	74.0	72.0		164	4.6	0.6	11	dbSNP_111	72	5533,3057	469.0+/-367.5	1789,1955,551	yes	missense	ASCL3	NM_020646.1	102	2074,2957,1465	AA,AC,CC		35.5879,35.711,45.3125	probably-damaging	55/182	8959545	7105,5887	2201	4295	6496	SO:0001583	missense	56676	exon2			GGCAGCCGTGGCA	AJ400877	CCDS7795.1	11p15.3	2013-10-17	2013-10-17			ENSG00000176009		"""Basic helix-loop-helix proteins"""	740	protein-coding gene	gene with protein product		609154	"""achaete-scute complex (Drosophila) homolog-like 3"", ""achaete-scute complex homolog 3 (Drosophila)"""			11528127	Standard	NM_020646		Approved	bHLHa42, HASH3, Sgn1	uc001mhd.1	Q9NQ33	OTTHUMG00000165679	ENST00000531618.1:c.164G>T	11.37:g.8959545C>A	ENSP00000435770:p.Arg55Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_020646	Q8WYQ6	Missense_Mutation	SNP	ENST00000531618.1	37	CCDS7795.1	1303	0.5966117216117216	160	0.3252032520325203	230	0.6353591160220995	430	0.7517482517482518	483	0.637203166226913	A	2.974	-0.211794	0.06140	0.35711	0.644121	ENSG00000176009	ENST00000325884;ENST00000531618	D;D	0.97016	-4.21;-4.21	5.72	4.57	0.56435	.	0.644897	0.12420	N	0.470549	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43376	-0.9395	9	0.06494	T	0.89	-2.2751	11.7315	0.51739	0.7189:0.2811:0.0:0.0	rs4909951;rs52797401;rs58010219;rs4909951	54	Q9NQ33	ASCL3_HUMAN	L	55	ENSP00000318846:R55L;ENSP00000435770:R55L	ENSP00000318846:R55L	R	-	2	0	ASCL3	8916121	0.686000	0.27661	0.637000	0.29366	0.896000	0.52359	2.572000	0.45999	0.424000	0.26061	-0.264000	0.10439	CGG	C|0.449;A|0.551	0.551	strong		0.562	ASCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385773.1		
TRAK1	22906	hgsc.bcm.edu	37	3	42251263	42251263	+	Silent	SNP	C	C	T	rs2290134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:42251263C>T	ENST00000327628.5	+	14	2149	c.1749C>T	c.(1747-1749)tcC>tcT	p.S583S	TRAK1_ENST00000396175.1_Silent_p.S525S|TRAK1_ENST00000341421.3_Silent_p.S525S|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	583					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						tGCAAGGTTCCGCCACACTTC	0.592													T|||	2579	0.514976	0.4342	0.6499	5008	,	,		15727	0.504		0.499	False		,,,				2504	0.5562				p.S583S	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.C1749T						PASS	.	T	,	1982,2424	617.8+/-393.0	467,1048,688	64.0	60.0	61.0		1749,1575	-1.6	1.0	3	dbSNP_100	61	4374,4226	570.6+/-389.4	1125,2124,1051	no	coding-synonymous,coding-synonymous	TRAK1	NM_001042646.1,NM_014965.3	,	1592,3172,1739	TT,TC,CC		49.1395,44.9841,48.8698	,	583/954,525/687	42251263	6356,6650	2203	4300	6503	SO:0001819	synonymous_variant	22906	exon14			AGGTTCCGCCACA		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1749C>T	3.37:g.42251263C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	42	10	0.238095	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Silent	SNP	ENST00000327628.5	37	CCDS43072.1																																																																																			C|0.503;T|0.497	0.497	strong		0.592	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
OR51D1	390038	hgsc.bcm.edu	37	11	4661285	4661285	+	Missense_Mutation	SNP	A	A	G	rs905871	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4661285A>G	ENST00000357605.2	+	1	341	c.265A>G	c.(265-267)Atc>Gtc	p.I89V		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	89			I -> V (in dbSNP:rs905871). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCTCTCCTCTATCACCATGCC	0.522													A|||	597	0.119209	0.0182	0.2046	5008	,	,		23192	0.003		0.2992	False		,,,				2504	0.1299				p.I89V		Atlas-SNP	.											.	OR51D1	49	.	0			c.A265G						PASS	.	A	VAL/ILE	373,4029	189.2+/-215.4	16,341,1844	161.0	123.0	136.0		265	-4.4	0.0	11	dbSNP_86	136	2913,5683	455.3+/-363.7	509,1895,1894	yes	missense	OR51D1	NM_001004751.2	29	525,2236,3738	GG,GA,AA		33.8879,8.4734,25.2808	benign	89/325	4661285	3286,9712	2201	4298	6499	SO:0001583	missense	390038	exon1			TCCTCTATCACCA	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"""GPCR / Class A : Olfactory receptors"""	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.265A>G	11.37:g.4661285A>G	ENSP00000350222:p.Ile89Val	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	283	132	0.466431	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	37	CCDS31357.1	316	0.1446886446886447	14	0.028455284552845527	80	0.22099447513812154	3	0.005244755244755245	219	0.28891820580474936	A	0.120	-1.126930	0.01770	0.084734	0.338879	ENSG00000197428	ENST00000357605	T	0.00375	7.71	4.62	-4.42	0.03579	GPCR, rhodopsin-like superfamily (1);	1.077760	0.07339	N	0.880470	T	0.00012	0.0000	N	0.01257	-0.925	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06427	-1.0827	9	0.59425	D	0.04	.	5.3083	0.15815	0.4484:0.0:0.3376:0.214	rs905871;rs52794998;rs905871	89	Q8NGF3	O51D1_HUMAN	V	89	ENSP00000350222:I89V	ENSP00000350222:I89V	I	+	1	0	OR51D1	4617861	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.347000	0.02632	-1.020000	0.03354	-2.403000	0.00223	ATC	A|0.794;G|0.206	0.206	strong		0.522	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751	
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100452027	100452027	+	Missense_Mutation	SNP	T	T	C	rs60592197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:100452027T>C	ENST00000279907.7	-	14	3240	c.3028A>G	c.(3028-3030)Atc>Gtc	p.I1010V	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.I660V	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	1010										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						TAGTTTAAGATACTACTTGAA	0.308													T|||	183	0.0365415	0.0537	0.049	5008	,	,		17680	0.001		0.0696	False		,,,				2504	0.0072				p.I1010V		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.A3028G						PASS	.	T	VAL/ILE	252,4148	138.4+/-174.2	10,232,1958	62.0	68.0	66.0		3028	3.5	0.8	12	dbSNP_129	66	575,8013	152.5+/-207.1	26,523,3745	yes	missense	UHRF1BP1L	NM_015054.1	29	36,755,5703	CC,CT,TT		6.6954,5.7273,6.3674	benign	1010/1465	100452027	827,12161	2200	4294	6494	SO:0001583	missense	23074	exon14			TTAAGATACTACT		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.3028A>G	12.37:g.100452027T>C	ENSP00000279907:p.Ile1010Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	143	85	0.594406	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	37	CCDS31882.1	100	0.045787545787545784	31	0.06300813008130081	19	0.052486187845303865	0	0.0	50	0.06596306068601583	T	0	-2.675521	0.00104	0.057273	0.066954	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.08896	3.04;3.04	5.37	3.49	0.39957	.	0.673381	0.15097	N	0.280755	T	0.00271	0.0008	N	0.04880	-0.145	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37731	-0.9693	10	0.02654	T	1	-2.1075	5.7392	0.18083	0.0:0.5964:0.0:0.4036	rs60592197;rs61744301	1010	A0JNW5	UH1BL_HUMAN	V	1010;660	ENSP00000279907:I1010V;ENSP00000444824:I660V	ENSP00000279907:I1010V	I	-	1	0	UHRF1BP1L	98976158	0.985000	0.35326	0.797000	0.32132	0.364000	0.29643	0.533000	0.23082	0.756000	0.33013	0.455000	0.32223	ATC	T|0.937;C|0.063	0.063	strong		0.308	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947	
OR2T4	127074	hgsc.bcm.edu	37	1	248524992	248524992	+	Missense_Mutation	SNP	A	A	G	rs45552134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248524992A>G	ENST00000366475.1	+	1	110	c.110A>G	c.(109-111)aAc>aGc	p.N37S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N37S(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGGATGGCCAACCACACTGGA	0.488																																					p.N37S		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	1	1	Substitution - Missense(1)	liver(1)	c.A110G						scavenged	.	A	SER/ASN	19,4385		2,15,2185	124.0	108.0	113.0		110	0.2	0.1	1	dbSNP_127	113	273,8265		42,189,4038	yes	missense	OR2T4	NM_001004696.1	46	44,204,6223	GG,GA,AA		3.1975,0.4314,2.2562	benign	37/349	248524992	292,12650	2202	4269	6471	SO:0001583	missense	127074	exon1			TGGCCAACCACAC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.110A>G	1.37:g.248524992A>G	ENSP00000355431:p.Asn37Ser	Somatic	793	2	0.00252207		WXS	Illumina HiSeq	Phase_I	549	86	0.156648	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	A	7.617	0.676086	0.14841	0.004314	0.031975	ENSG00000196944	ENST00000366475	T	0.63913	-0.07	1.6	0.248	0.15526	.	0.853037	0.09884	N	0.743276	T	0.34629	0.0904	M	0.78285	2.405	0.44798	P	0.0021959999999999757	B	0.18461	0.028	B	0.20184	0.028	T	0.51865	-0.8651	9	0.72032	D	0.01	.	4.5644	0.12175	0.8044:0.0:0.1956:0.0	rs45552134	37	Q8NH00	OR2T4_HUMAN	S	37	ENSP00000355431:N37S	ENSP00000355431:N37S	N	+	2	0	OR2T4	246591615	0.199000	0.23386	0.064000	0.19789	0.029000	0.11900	3.897000	0.56273	-0.469000	0.06911	-0.956000	0.02647	AAC	A|0.973;G|0.027	0.027	strong		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
RRM1	6240	hgsc.bcm.edu	37	11	4159457	4159457	+	Silent	SNP	A	A	G	rs9937	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4159457A>G	ENST00000300738.5	+	19	2427	c.2223A>G	c.(2221-2223)acA>acG	p.T741T	RRM1_ENST00000537197.1_Silent_p.T403T|RRM1-AS1_ENST00000529323.1_RNA|RRM1_ENST00000534285.1_Silent_p.T519T|RRM1_ENST00000423050.2_Silent_p.T644T	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	741					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	ATTTAAGGACAAGACCAGCGG	0.373													A|||	1726	0.344649	0.0953	0.4424	5008	,	,		15831	0.3819		0.5239	False		,,,				2504	0.3896				p.T741T	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.A2223G						PASS	.	A		733,3669	299.6+/-285.9	48,637,1516	65.0	66.0	66.0		2223	3.0	1.0	11	dbSNP_52	66	4612,3984	600.6+/-394.2	1226,2160,912	no	coding-synonymous	RRM1	NM_001033.3		1274,2797,2428	GG,GA,AA		46.3471,16.6515,41.1217		741/793	4159457	5345,7653	2201	4298	6499	SO:0001819	synonymous_variant	6240	exon19			AAGGACAAGACCA	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"""ribonucleotide reductase M1 polypeptide"""			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.2223A>G	11.37:g.4159457A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_001033	Q9UNN2	Silent	SNP	ENST00000300738.5	37	CCDS7750.1																																																																																			A|0.587;G|0.413	0.413	strong		0.373	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033	
DDX1	1653	hgsc.bcm.edu	37	2	15735648	15735648	+	Silent	SNP	T	T	C	rs2302929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:15735648T>C	ENST00000381341.2	+	4	492	c.103T>C	c.(103-105)Ttg>Ctg	p.L35L	DDX1_ENST00000233084.3_Silent_p.L35L			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	35	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with HNRNPK.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		ATCTATCCCATTGATCTTAGG	0.383													T|||	876	0.17492	0.0333	0.1354	5008	,	,		18132	0.371		0.164	False		,,,				2504	0.2035				p.L35L		Atlas-SNP	.											.	DDX1	70	.	0			c.T103C						PASS	.	T		272,4134	154.0+/-187.5	8,256,1939	130.0	122.0	125.0		103	-5.1	0.0	2	dbSNP_100	125	1624,6976	301.6+/-305.5	162,1300,2838	no	coding-synonymous	DDX1	NM_004939.1		170,1556,4777	CC,CT,TT		18.8837,6.1734,14.5779		35/741	15735648	1896,11110	2203	4300	6503	SO:0001819	synonymous_variant	1653	exon3			ATCCCATTGATCT	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"""DEAD-boxes"""	2734	protein-coding gene	gene with protein product		601257	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"""			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.103T>C	2.37:g.15735648T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_004939	B4DME8|B4DPN6	Silent	SNP	ENST00000381341.2	37	CCDS1686.1																																																																																			T|0.830;C|0.170	0.170	strong		0.383	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939	
ANO7	50636	hgsc.bcm.edu	37	2	242141719	242141719	+	Splice_Site	SNP	C	C	T	rs2074840	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242141719C>T	ENST00000274979.8	+	8	988	c.885C>T	c.(883-885)gaC>gaT	p.D295D	ANO7_ENST00000402430.3_Splice_Site_p.D294D	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	295					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						CCCTGCATGACGTGAGCTCGG	0.657													C|||	2077	0.414736	0.4796	0.5086	5008	,	,		17915	0.0794		0.6829	False		,,,				2504	0.3303				p.D295D		Atlas-SNP	.											ANO7,NS,carcinoma,+2,1	ANO7	136	1	0			c.C885T						PASS	.	C		2330,2076	601.1+/-389.6	642,1046,515	51.0	49.0	50.0		885	-7.5	0.0	2	dbSNP_96	50	5930,2670	682.1+/-403.8	2039,1852,409	yes	coding-synonymous-near-splice	ANO7	NM_001001891.3		2681,2898,924	TT,TC,CC		31.0465,47.1176,36.4909		295/934	242141719	8260,4746	2203	4300	6503	SO:0001630	splice_region_variant	50636	exon8			GCATGACGTGAGC	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.885+1C>T	2.37:g.242141719C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			C|0.452;T|0.548	0.548	strong		0.657	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	Silent
APOBEC1	339	hgsc.bcm.edu	37	12	7803646	7803646	+	Silent	SNP	G	G	A	rs10431309	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7803646G>A	ENST00000229304.4	-	4	554	c.534C>T	c.(532-534)taC>taT	p.Y178Y		NM_001644.3	NP_001635.2	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	178					cellular response to insulin stimulus (GO:0032869)|cytidine deamination (GO:0009972)|cytidine to uridine editing (GO:0016554)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|gene expression (GO:0010467)|lipid metabolic process (GO:0006629)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein transport (GO:0042953)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to osmotic stress (GO:0006970)|response to zinc ion (GO:0010043)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	AU-rich element binding (GO:0017091)|cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.Y178Y(1)		kidney(2)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						GCTCCAGTGCGTACAACATCA	0.433													G|||	1212	0.242013	0.1483	0.1916	5008	,	,		-128	0.2312		0.2594	False		,,,				2504	0.3978				p.Y178Y	Pancreas(135;929 1826 4531 10527 41012)	Atlas-SNP	.											APOBEC1,caecum,carcinoma,0,2	APOBEC1	43	2	1	Substitution - coding silent(1)	stomach(1)	c.C534T						PASS	.	G		629,3777	270.7+/-269.8	51,527,1625	154.0	139.0	144.0		534	-3.2	0.5	12	dbSNP_119	144	2082,6518	360.6+/-332.0	236,1610,2454	no	coding-synonymous	APOBEC1	NM_001644.3		287,2137,4079	AA,AG,GG		24.2093,14.276,20.8442		178/237	7803646	2711,10295	2203	4300	6503	SO:0001819	synonymous_variant	339	exon4			CAGTGCGTACAAC	U72891	CCDS8579.1	12p13.1	2007-02-01			ENSG00000111701	ENSG00000111701		"""Apolipoprotein B mRNA editing enzymes"""	604	protein-coding gene	gene with protein product		600130					Standard	XM_005253355		Approved	BEDP, CDAR1, APOBEC-1, HEPR	uc001qtb.3	P41238	OTTHUMG00000141288	ENST00000229304.4:c.534C>T	12.37:g.7803646G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	157	77	0.490446	NM_001644	Q9UE64|Q9UM71	Silent	SNP	ENST00000229304.4	37	CCDS8579.1																																																																																			G|0.779;A|0.221	0.221	strong		0.433	APOBEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280523.1	NM_001644	
TMEM8A	58986	hgsc.bcm.edu	37	16	427479	427479	+	Missense_Mutation	SNP	T	T	C	rs11248931	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:427479T>C	ENST00000431232.2	-	3	566	c.406A>G	c.(406-408)Aca>Gca	p.T136A	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	136			T -> A (in dbSNP:rs11248931). {ECO:0000269|PubMed:11006113, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						CTTCTCGGTGTGGTGCTCAGC	0.682											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2677	0.534545	0.6188	0.4755	5008	,	,		15166	0.3006		0.5408	False		,,,				2504	0.6973				p.T136A		Atlas-SNP	.											TMEM8A,colon,carcinoma,0,1	TMEM8A	49	1	0			c.A406G						PASS	.	C	ALA/THR	2729,1649		847,1035,307	22.0	22.0	22.0		406	1.0	0.0	16	dbSNP_120	22	4876,3718		1417,2042,838	yes	missense	TMEM8A	NM_021259.2	58	2264,3077,1145	CC,CT,TT		43.2627,37.6656,41.3737	benign	136/772	427479	7605,5367	2189	4297	6486	SO:0001583	missense	58986	exon3			TCGGTGTGGTGCT	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.406A>G	16.37:g.427479T>C	ENSP00000401338:p.Thr136Ala	Somatic	144	0	0	588	WXS	Illumina HiSeq	Phase_I	81	81	1	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	1089	0.49862637362637363	335	0.6808943089430894	181	0.5	163	0.28496503496503495	410	0.5408970976253298	C	0.003	-2.441316	0.00180	0.623344	0.567373	ENSG00000129925	ENST00000431232	T	0.23147	1.92	3.34	0.981	0.19756	.	3.558320	0.02310	N	0.072046	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40590	-0.9555	9	0.06099	T	0.92	-8.0545	4.5877	0.12291	0.15:0.2114:0.0:0.6386	rs11248931;rs17845652;rs17858586;rs57237473;rs11248931	136	Q9HCN3	TMM8A_HUMAN	A	136	ENSP00000401338:T136A	ENSP00000401338:T136A	T	-	1	0	TMEM8A	367480	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.411000	0.02478	-0.100000	0.12241	-1.309000	0.01313	ACA	T|0.463;C|0.537	0.537	strong		0.682	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
APOA4	337	hgsc.bcm.edu	37	11	116691634	116691634	+	Missense_Mutation	SNP	C	C	A	rs5110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:116691634C>A	ENST00000357780.3	-	3	1254	c.1140G>T	c.(1138-1140)caG>caT	p.Q380H		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	380	Gln/Glu-rich.		Q -> H (in allele APOA-IV*2 and allele APOA-IV*0A; associated with E-187 in allele APOA-IV*0A; dbSNP:rs5110). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15108119, ECO:0000269|PubMed:1677358, ECO:0000269|PubMed:2065039, ECO:0000269|PubMed:2351649, ECO:0000269|PubMed:3036793, ECO:0000269|PubMed:3080432}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		gctgctcctgctgctgttcct	0.612													C|||	119	0.023762	0.0038	0.0418	5008	,	,		19562	0.0		0.0656	False		,,,				2504	0.0194				p.Q380H		Atlas-SNP	.											APOA4,rectum,carcinoma,0,1	APOA4	51	1	0			c.G1140T	GRCh37	CM984162	APOA4	M	rs5110	scavenged	.	C	HIS/GLN	78,4324	68.7+/-106.4	1,76,2124	54.0	47.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1140	0.1	0.1	11	dbSNP_52	50	712,7876	174.9+/-225.1	24,664,3606	yes	missense	APOA4	NM_000482.3	24	25,740,5730	AA,AC,CC		8.2906,1.7719,6.0816	benign	380/397	116691634	790,12200	2201	4294	6495	SO:0001583	missense	337	exon3			CTCCTGCTGCTGT		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.1140G>T	11.37:g.116691634C>A	ENSP00000350425:p.Gln380His	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	152	69	0.453947	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	37	CCDS31681.1	72	0.03296703296703297	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	49	0.06464379947229551	C	4.510	0.094555	0.08632	0.017719	0.082906	ENSG00000110244	ENST00000357780	T	0.74106	-0.81	1.25	0.139	0.14798	.	.	.	.	.	T	0.05090	0.0136	N	0.22421	0.69	0.09310	N	1	B	0.24533	0.105	B	0.20955	0.032	T	0.02471	-1.1154	9	0.20046	T	0.44	.	4.2239	0.10572	0.4256:0.5744:0.0:0.0	rs5110;rs3181830;rs9282881;rs17250981;rs5110	380	P06727	APOA4_HUMAN	H	380	ENSP00000350425:Q380H	ENSP00000350425:Q380H	Q	-	3	2	APOA4	116196844	0.000000	0.05858	0.111000	0.21465	0.022000	0.10575	-0.722000	0.04958	0.041000	0.15688	0.460000	0.39030	CAG	C|0.956;A|0.044	0.044	strong		0.612	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
LRP5L	91355	hgsc.bcm.edu	37	22	25753231	25753231	+	Silent	SNP	G	G	A	rs133194	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:25753231G>A	ENST00000402785.2	-	2	525	c.429C>T	c.(427-429)gaC>gaT	p.D143D	LRP5L_ENST00000402859.2_Silent_p.D143D|LRP5L_ENST00000444995.3_Silent_p.D143D			A4QPB2	LRP5L_HUMAN	low density lipoprotein receptor-related protein 5-like	143					canonical Wnt signaling pathway (GO:0060070)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)		Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	6						CCTCGATCTTGTCTGTCTTGG	0.657													G|||	2099	0.419129	0.2572	0.2781	5008	,	,		19362	0.4097		0.5507	False		,,,				2504	0.6125				p.D143D		Atlas-SNP	.											.	LRP5L	23	.	0			c.C429T						PASS	.	G	,	1347,3055	449.8+/-349.2	204,939,1058	117.0	91.0	100.0		429,429	1.2	1.0	22	dbSNP_78	100	4588,4012	598.5+/-393.9	1228,2132,940	no	coding-synonymous,coding-synonymous	LRP5L	NM_001135772.1,NM_182492.2	,	1432,3071,1998	AA,AG,GG		46.6512,30.5997,45.6468	,	143/253,143/253	25753231	5935,7067	2201	4300	6501	SO:0001819	synonymous_variant	91355	exon4			GATCTTGTCTGTC	AL137651	CCDS33626.1	22q11.23	2013-05-30			ENSG00000100068	ENSG00000100068			25323	protein-coding gene	gene with protein product							Standard	NM_182492		Approved	DKFZp434O0213	uc011ajz.2	A4QPB2	OTTHUMG00000150900	ENST00000402785.2:c.429C>T	22.37:g.25753231G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	178	90	0.505618	NM_001135772	B0QYF3|B0QYF4|B2RPI5	Silent	SNP	ENST00000402785.2	37	CCDS33626.1																																																																																			G|0.556;A|0.444	0.444	strong		0.657	LRP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320477.2	NM_182492	
SEC23B	10483	hgsc.bcm.edu	37	20	18523002	18523002	+	Missense_Mutation	SNP	C	C	G	rs2273526	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:18523002C>G	ENST00000336714.3	+	13	1899	c.1467C>G	c.(1465-1467)caC>caG	p.H489Q	SEC23B_ENST00000377465.1_Missense_Mutation_p.H489Q|SEC23B_ENST00000262544.2_Missense_Mutation_p.H489Q|SEC23B_ENST00000377475.3_Missense_Mutation_p.H489Q	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	489			H -> Q (in dbSNP:rs2273526). {ECO:0000269|PubMed:19621418, ECO:0000269|PubMed:8898360}.		ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						ATTATCAGCACTCCAGCACCC	0.532													C|||	578	0.115415	0.1225	0.1628	5008	,	,		19833	0.1597		0.1113	False		,,,				2504	0.0307				p.H489Q		Atlas-SNP	.											.	SEC23B	70	.	0			c.C1467G						PASS	.	C	GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS	531,3875	240.3+/-251.1	34,463,1706	235.0	197.0	210.0		1467,1413,1467,1467,1467	0.6	1.0	20	dbSNP_100	210	1012,7588	217.0+/-255.8	52,908,3340	yes	missense,missense,missense,missense,missense	SEC23B	NM_001172745.1,NM_001172746.1,NM_006363.4,NM_032985.4,NM_032986.3	24,24,24,24,24	86,1371,5046	GG,GC,CC		11.7674,12.0517,11.8638	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	489/768,471/750,489/768,489/768,489/768	18523002	1543,11463	2203	4300	6503	SO:0001583	missense	10483	exon13			TCAGCACTCCAGC	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"""Sec23 (S. cerevisiae) homolog B"", ""congenital dyserythropoietic anemia, type II"""	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.1467C>G	20.37:g.18523002C>G	ENSP00000338844:p.His489Gln	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	37	CCDS13137.1	321	0.14697802197802198	75	0.1524390243902439	63	0.17403314917127072	92	0.16083916083916083	91	0.12005277044854881	C	18.28	3.588170	0.66105	0.120517	0.117674	ENSG00000101310	ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	4.93	0.578	0.17391	Sec23/Sec24 beta-sandwich (1);	0.000000	0.85682	D	0.000000	T	0.01029	0.0034	M	0.93420	3.415	0.09310	P	0.9999999287442	P;B	0.42248	0.774;0.447	P;B	0.48089	0.566;0.316	T	0.50841	-0.8780	9	0.72032	D	0.01	-21.7711	8.1498	0.31134	0.0:0.5325:0.0:0.4675	rs2273526;rs59439358;rs2273526	471;489	B4DJW8;Q15437	.;SC23B_HUMAN	Q	489	ENSP00000338844:H489Q;ENSP00000262544:H489Q;ENSP00000366695:H489Q;ENSP00000366685:H489Q	ENSP00000262544:H489Q	H	+	3	2	SEC23B	18471002	0.969000	0.33509	1.000000	0.80357	0.940000	0.58332	0.078000	0.14761	0.272000	0.22027	0.655000	0.94253	CAC	C|0.873;G|0.127	0.127	strong		0.532	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5		
MTMR2	8898	hgsc.bcm.edu	37	11	95657111	95657111	+	Missense_Mutation	SNP	T	T	G	rs3824874	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:95657111T>G	ENST00000346299.5	-	1	348	c.8A>C	c.(7-9)aAg>aCg	p.K3T	MTMR2_ENST00000484818.1_5'Flank|MTMR2_ENST00000352297.7_5'UTR|MTMR2_ENST00000393223.3_5'UTR|MTMR2_ENST00000409459.1_5'UTR	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	3			K -> T (in dbSNP:rs3824874). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCTCGAGCTCTTCTCCATCGC	0.711													T|||	1066	0.212859	0.0681	0.2406	5008	,	,		14532	0.2688		0.3857	False		,,,				2504	0.1534				p.K3T		Atlas-SNP	.											.	MTMR2	79	.	0			c.A8C						PASS	.	T	THR/LYS,,	384,3908		20,344,1782	6.0	6.0	6.0		8,,	0.8	1.0	11	dbSNP_107	6	2643,5687		423,1797,1945	yes	missense,utr-5,utr-5	MTMR2	NM_016156.5,NM_201278.2,NM_201281.2	78,,	443,2141,3727	GG,GT,TT		31.7287,8.9469,23.9819	benign,,	3/644,,	95657111	3027,9595	2146	4165	6311	SO:0001583	missense	8898	exon1			GAGCTCTTCTCCA	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.8A>C	11.37:g.95657111T>G	ENSP00000345752:p.Lys3Thr	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_016156	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	37	CCDS8305.1	601	0.2751831501831502	37	0.07520325203252033	102	0.281767955801105	171	0.29895104895104896	291	0.3839050131926121	T	10.82	1.456942	0.26161	0.089469	0.317287	ENSG00000087053	ENST00000346299	D	0.95342	-3.68	4.49	0.819	0.18785	.	0.802256	0.11114	N	0.598149	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	0.999999999999761	B	0.19817	0.039	B	0.15870	0.014	T	0.05386	-1.0888	9	0.72032	D	0.01	.	7.154	0.25626	0.0:0.2881:0.0:0.7119	rs3824874;rs17230839;rs17854793;rs3824874	3	Q13614	MTMR2_HUMAN	T	3	ENSP00000345752:K3T	ENSP00000345752:K3T	K	-	2	0	MTMR2	95296759	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	1.345000	0.33953	0.264000	0.21851	0.459000	0.35465	AAG	G|0.251;N|0.000	0.251	strong		0.711	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156	
OR2G2	81470	hgsc.bcm.edu	37	1	247752367	247752367	+	Missense_Mutation	SNP	A	A	G	rs869111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247752367A>G	ENST00000320065.1	+	1	706	c.706A>G	c.(706-708)Agg>Ggg	p.R236G	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	236			R -> G (in dbSNP:rs869111).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			GTCAGCTACCAGGAGACAGAA	0.483													G|||	1947	0.388778	0.3116	0.3444	5008	,	,		19344	0.4444		0.5159	False		,,,				2504	0.3364				p.R236G		Atlas-SNP	.											.	OR2G2	88	.	0			c.A706G						PASS	.	G	GLY/ARG	1377,3029	690.5+/-405.3	220,937,1046	146.0	134.0	138.0		706	4.3	0.0	1	dbSNP_86	138	4290,4310	577.6+/-390.6	1074,2142,1084	yes	missense	OR2G2	NM_001001915.1	125	1294,3079,2130	GG,GA,AA		49.8837,31.2528,43.5722	benign	236/318	247752367	5667,7339	2203	4300	6503	SO:0001583	missense	81470	exon1			GCTACCAGGAGAC	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.706A>G	1.37:g.247752367A>G	ENSP00000326349:p.Arg236Gly	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	265	263	0.992453	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	928	0.4249084249084249	145	0.29471544715447157	143	0.39502762430939226	252	0.4405594405594406	388	0.5118733509234829	G	0.006	-2.051580	0.00394	0.312528	0.498837	ENSG00000177489	ENST00000320065	T	0.00013	9.24	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36972	N	0.002316	T	0.00012	0.0000	N	0.00012	-2.96	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	9	0.02654	T	1	.	10.1869	0.43002	0.0989:0.0:0.9011:0.0	rs869111;rs17318855;rs52811386;rs58487812;rs869111	236	Q8NGZ5	OR2G2_HUMAN	G	236	ENSP00000326349:R236G	ENSP00000326349:R236G	R	+	1	2	OR2G2	245818990	0.290000	0.24343	0.038000	0.18304	0.008000	0.06430	0.583000	0.23849	1.023000	0.39654	-0.186000	0.12905	AGG	A|0.573;G|0.426	0.426	strong		0.483	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
TXK	7294	hgsc.bcm.edu	37	4	48115264	48115264	+	Missense_Mutation	SNP	C	C	T	rs7658300	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:48115264C>T	ENST00000264316.4	-	3	219	c.134G>A	c.(133-135)cGt>cAt	p.R45H	TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	45			R -> H (in dbSNP:rs7658300). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7951233}.		activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						CGGCCTGCGACGCTGGGTGTA	0.403													c|||	865	0.172724	0.0257	0.3429	5008	,	,		18748	0.0685		0.3658	False		,,,				2504	0.1595				p.R45H		Atlas-SNP	.											.	TXK	58	.	0			c.G134A						PASS	.	T	HIS/ARG	354,4052	182.2+/-210.1	14,326,1863	146.0	148.0	147.0		134	-7.5	0.0	4	dbSNP_116	147	3146,5454	479.8+/-370.2	602,1942,1756	yes	missense	TXK	NM_003328.2	29	616,2268,3619	TT,TC,CC		36.5814,8.0345,26.9107	benign	45/528	48115264	3500,9506	2203	4300	6503	SO:0001583	missense	7294	exon3			CTGCGACGCTGGG	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"""SH2 domain containing"""	12434	protein-coding gene	gene with protein product		600058	"""PTK4 protein tyrosine kinase 4"""	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.134G>A	4.37:g.48115264C>T	ENSP00000264316:p.Arg45His	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	218	117	0.536697	NM_003328	Q14220	Missense_Mutation	SNP	ENST00000264316.4	37	CCDS3480.1	454	0.2078754578754579	18	0.036585365853658534	118	0.3259668508287293	37	0.06468531468531469	281	0.370712401055409	c	9.127	1.010474	0.19277	0.080345	0.365814	ENSG00000074966	ENST00000264316;ENST00000506073	T;T	0.74526	-0.85;0.23	5.03	-7.49	0.01355	.	1.279830	0.05322	N	0.526822	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07462	-1.0771	9	0.36615	T	0.2	.	9.2889	0.37775	0.0:0.1692:0.2098:0.621	rs7658300;rs56561099;rs61166743;rs7658300	45;45	E7EQN8;P42681	.;TXK_HUMAN	H	45	ENSP00000264316:R45H;ENSP00000422798:R45H	ENSP00000264316:R45H	R	-	2	0	TXK	47810021	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.757000	0.00374	-2.472000	0.00529	-0.906000	0.02833	CGT	C|0.766;T|0.234	0.234	strong		0.403	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328	
UAP1L1	91373	hgsc.bcm.edu	37	9	139973820	139973820	+	Missense_Mutation	SNP	C	C	T	rs7037849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139973820C>T	ENST00000409858.3	+	5	988	c.956C>T	c.(955-957)gCc>gTc	p.A319V	UAP1L1_ENST00000360271.3_Missense_Mutation_p.A196V	NM_207309.2	NP_997192.2	Q3KQV9	UAP1L_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1 like 1	319			A -> V (in dbSNP:rs7037849). {ECO:0000269|PubMed:14702039}.				uridylyltransferase activity (GO:0070569)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CAGCTACGTGCCTCCGACGGG	0.637													C|||	2450	0.489217	0.4834	0.4452	5008	,	,		14974	0.6528		0.3996	False		,,,				2504	0.4519				p.A319V		Atlas-SNP	.											.	UAP1L1	46	.	0			c.C956T						PASS	.	C	VAL/ALA	2072,2334	570.2+/-382.8	489,1094,620	134.0	115.0	122.0		956	0.1	0.0	9	dbSNP_116	122	3320,5280	494.2+/-373.8	648,2024,1628	yes	missense	UAP1L1	NM_207309.2	64	1137,3118,2248	TT,TC,CC		38.6047,47.0268,41.4578	benign	319/508	139973820	5392,7614	2203	4300	6503	SO:0001583	missense	91373	exon5			TACGTGCCTCCGA	AK022632	CCDS7028.2	9q34.3	2014-07-31	2014-07-31		ENSG00000197355	ENSG00000197355			28082	protein-coding gene	gene with protein product							Standard	NM_207309		Approved		uc010ncb.3	Q3KQV9	OTTHUMG00000020962	ENST00000409858.3:c.956C>T	9.37:g.139973820C>T	ENSP00000386935:p.Ala319Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_207309	A2AMJ8|Q5SPZ2|Q69YQ3|Q6ZR38	Missense_Mutation	SNP	ENST00000409858.3	37	CCDS7028.2	1056	0.4835164835164835	216	0.43902439024390244	165	0.4558011049723757	377	0.6590909090909091	298	0.39313984168865435	C	10.17	1.276808	0.23307	0.470268	0.386047	ENSG00000197355	ENST00000409858;ENST00000360271	T;T	0.17691	2.26;2.26	4.91	0.0909	0.14465	.	0.722083	0.13651	N	0.372274	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B;P	0.42692	0.173;0.787	B;B	0.40782	0.158;0.34	T	0.28522	-1.0041	9	0.59425	D	0.04	.	11.7893	0.52059	0.1378:0.1826:0.6796:0.0	rs7037849;rs60377984;rs7037849	319;196	Q3KQV9;Q3KQV9-2	UAP1L_HUMAN;.	V	319;196	ENSP00000386935:A319V;ENSP00000353409:A196V	ENSP00000353409:A196V	A	+	2	0	UAP1L1	139093641	0.000000	0.05858	0.000000	0.03702	0.136000	0.21042	1.006000	0.29847	0.092000	0.17331	0.491000	0.48974	GCC	C|0.558;T|0.442	0.442	strong		0.637	UAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055216.2	XM_038063	
ANK2	287	hgsc.bcm.edu	37	4	114257201	114257201	+	Silent	SNP	C	C	T	rs3736575	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:114257201C>T	ENST00000357077.4	+	30	3632	c.3579C>T	c.(3577-3579)cgC>cgT	p.R1193R	ANK2_ENST00000264366.6_Silent_p.R1160R|ANK2_ENST00000394537.3_Silent_p.R1193R|ANK2_ENST00000509550.1_Silent_p.R369R|ANK2_ENST00000506722.1_Silent_p.R1184R	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1193	ZU5 2. {ECO:0000255|PROSITE- ProRule:PRU00485}.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		AGCGGATCCGCGTAGGCCTGC	0.498													C|||	1304	0.260383	0.6241	0.2017	5008	,	,		17320	0.1161		0.1014	False		,,,				2504	0.1227				p.R1193R		Atlas-SNP	.											.	ANK2	576	.	0			c.C3579T						PASS	.	C	,,	2372,2034	610.6+/-391.6	645,1082,476	64.0	64.0	64.0		3552,3579,3579	-10.5	0.2	4	dbSNP_107	64	893,7707	200.4+/-244.2	34,825,3441	no	coding-synonymous,coding-synonymous,coding-synonymous	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,,	679,1907,3917	TT,TC,CC		10.3837,46.1643,25.1038	,,	1184/1864,1193/3958,1193/1873	114257201	3265,9741	2203	4300	6503	SO:0001819	synonymous_variant	287	exon30			GATCCGCGTAGGC	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.3579C>T	4.37:g.114257201C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1	517	0.2367216117216117	320	0.6504065040650406	62	0.1712707182320442	68	0.11888111888111888	67	0.08839050131926121	C	5.678	0.309745	0.10733	0.538357	0.103837	ENSG00000145362	ENST00000514960	T	0.73258	-0.73	5.27	-10.5	0.00291	.	0.000000	0.49916	D	0.000136	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999966	.	.	.	.	.	.	T	0.10245	-1.0638	5	.	.	.	.	7.0199	0.24908	0.1679:0.1308:0.0634:0.6379	rs3736575;rs58099055;rs3736575	.	.	.	C	206	ENSP00000422853:R206C	.	R	+	1	0	ANK2	114476650	0.000000	0.05858	0.204000	0.23530	0.750000	0.42670	-3.979000	0.00321	-3.279000	0.00197	-0.743000	0.03520	CGT	C|0.741;T|0.259	0.259	strong		0.498	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
KRT5	3852	hgsc.bcm.edu	37	12	52911401	52911401	+	Silent	SNP	T	T	G	rs4761924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52911401T>G	ENST00000252242.4	-	5	1455	c.1065A>C	c.(1063-1065)acA>acC	p.T355T		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	355	Coil 2.|Rod.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		ACTCGGCTTCTGTCCGGCTGC	0.562													G|||	644	0.128594	0.1793	0.1859	5008	,	,		18148	0.0377		0.1481	False		,,,				2504	0.093				p.T355T		Atlas-SNP	.											.	KRT5	88	.	0			c.A1065C						PASS	.	G		767,3639	754.0+/-412.4	59,649,1495	139.0	134.0	136.0		1065	-12.1	0.0	12	dbSNP_111	136	1205,7395	763.3+/-407.6	86,1033,3181	no	coding-synonymous	KRT5	NM_000424.3		145,1682,4676	GG,GT,TT		14.0116,17.4081,15.1622		355/591	52911401	1972,11034	2203	4300	6503	SO:0001819	synonymous_variant	3852	exon5			GGCTTCTGTCCGG		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1065A>C	12.37:g.52911401T>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	37	CCDS8830.1																																																																																			T|0.856;G|0.144	0.144	strong		0.562	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
BCAM	4059	hgsc.bcm.edu	37	19	45322744	45322744	+	Missense_Mutation	SNP	A	A	G	rs1135062	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45322744A>G	ENST00000270233.6	+	12	1637	c.1615A>G	c.(1615-1617)Acc>Gcc	p.T539A	BCAM_ENST00000589651.1_Missense_Mutation_p.T539A	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	539	Ig-like C2-type 3.		T -> A (in dbSNP:rs1135062). {ECO:0000269|PubMed:7777537, ECO:0000269|PubMed:7954395, ECO:0000269|Ref.7}.		cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CCACTTCGGCACCGGTGAGTG	0.642													a|||	1354	0.270367	0.4349	0.2305	5008	,	,		15269	0.1131		0.3002	False		,,,				2504	0.2076				p.T539A		Atlas-SNP	.											BCAM,NS,adenoma,0,1	BCAM	53	1	0			c.A1615G	GRCh37	CM973377	BCAM	M	rs1135062	scavenged	.		ALA/THR,ALA/THR	1803,2603		376,1051,776	55.0	61.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1615,1615	-8.3	0.0	19	dbSNP_86	59	2588,6012		384,1820,2096	yes	missense,missense	BCAM	NM_001013257.1,NM_005581.3	58,58	760,2871,2872	GG,GA,AA		30.093,40.9215,33.7613	benign,benign	539/589,539/629	45322744	4391,8615	2203	4300	6503	SO:0001583	missense	4059	exon12			TTCGGCACCGGTG	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1615A>G	19.37:g.45322744A>G	ENSP00000270233:p.Thr539Ala	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	579	0.2651098901098901	205	0.4166666666666667	88	0.2430939226519337	55	0.09615384615384616	231	0.30474934036939316	.	5.337	0.247523	0.10130	0.409215	0.30093	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.59364	0.27;0.29	4.24	-8.33	0.00992	Immunoglobulin subtype (1);Immunoglobulin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29731	-1.0002	8	0.05620	T	0.96	0.1002	1.2179	0.01918	0.1523:0.2382:0.3376:0.2719	rs1135062;rs11548861;rs11880954;rs16979448;rs58063257;rs1135062	539	P50895	BCAM_HUMAN	A	539	ENSP00000270233:T539A;ENSP00000375817:T539A	ENSP00000270233:T539A	T	+	1	0	BCAM	50014584	0.000000	0.05858	0.001000	0.08648	0.187000	0.23431	-0.967000	0.03821	-1.683000	0.01444	0.434000	0.28630	ACC	A|0.703;G|0.297	0.297	strong		0.642	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
RNF123	63891	hgsc.bcm.edu	37	3	49749976	49749976	+	Missense_Mutation	SNP	G	G	A	rs34823813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49749976G>A	ENST00000327697.6	+	27	2705	c.2561G>A	c.(2560-2562)cGc>cAc	p.R854H	RNF123_ENST00000432042.1_Missense_Mutation_p.R708H|RNF123_ENST00000433785.1_5'Flank	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	854			R -> H (in dbSNP:rs34823813). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CACGGTGATCGCACAGGGTCT	0.582													G|||	229	0.0457268	0.0023	0.0648	5008	,	,		20720	0.0298		0.1113	False		,,,				2504	0.0399				p.R854H		Atlas-SNP	.											.	RNF123	100	.	0			c.G2561A						PASS	.	G	HIS/ARG	92,4314	76.8+/-115.0	0,92,2111	162.0	123.0	136.0		2561	5.0	1.0	3	dbSNP_126	136	880,7720	199.3+/-243.4	42,796,3462	yes	missense	RNF123	NM_022064.2	29	42,888,5573	AA,AG,GG		10.2326,2.0881,7.4735	probably-damaging	854/1315	49749976	972,12034	2203	4300	6503	SO:0001583	missense	63891	exon27			GTGATCGCACAGG	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.2561G>A	3.37:g.49749976G>A	ENSP00000328287:p.Arg854His	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	134	0.06135531135531135	3	0.006097560975609756	31	0.0856353591160221	16	0.027972027972027972	84	0.11081794195250659	G	16.64	3.179625	0.57800	0.020881	0.102326	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.75821	-0.68;-0.97	5.91	5.04	0.67666	.	0.317981	0.37955	N	0.001863	T	0.03053	0.0090	L	0.29908	0.895	0.09310	P	0.9999999999999286	D;D	0.60160	0.987;0.987	P;P	0.45232	0.474;0.474	T	0.49103	-0.8974	9	0.45353	T	0.12	-27.8134	14.4717	0.67521	0.0702:0.0:0.9298:0.0	rs34823813;rs34823813	708;854	C9J266;Q5XPI4	.;RN123_HUMAN	H	854;854;708	ENSP00000328287:R854H;ENSP00000392443:R708H	ENSP00000328287:R854H	R	+	2	0	RNF123	49724980	1.000000	0.71417	0.999000	0.59377	0.313000	0.28021	3.578000	0.53892	1.521000	0.48983	-0.133000	0.14855	CGC	G|0.933;A|0.067	0.067	strong		0.582	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
DMKN	93099	hgsc.bcm.edu	37	19	36002389	36002389	+	Missense_Mutation	SNP	C	C	T	rs56743379|rs142519211		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36002389C>T	ENST00000339686.3	-	5	1018	c.842G>A	c.(841-843)aGc>aAc	p.S281N	DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.S281N|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.S281N|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000440396.1_Missense_Mutation_p.S281N|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.S281N|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.S281N|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000492341.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	281	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			gccgccactgctgccgccact	0.632																																					p.S281N		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.G842A						PASS	.						26.0	20.0	22.0					19																	36002389		2188	4250	6438	SO:0001583	missense	93099	exon5			CCACTGCTGCCGC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.842G>A	19.37:g.36002389C>T	ENSP00000342012:p.Ser281Asn	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	21	0.259259	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	3.259	-0.151610	0.06585	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	3.03	1.94	0.25998	.	0.972189	0.08437	N	0.945978	T	0.22742	0.0549	N	0.12746	0.255	0.09310	N	1	B;B;B;B;B	0.20550	0.046;0.046;0.046;0.046;0.017	B;B;B;B;B	0.12837	0.008;0.008;0.008;0.008;0.005	T	0.22173	-1.0224	10	0.23302	T	0.38	.	6.4474	0.21883	0.0:0.86:0.0:0.14	.	281;281;281;281;281	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	N	281	ENSP00000342012:S281N;ENSP00000394908:S281N;ENSP00000415277:S281N;ENSP00000414743:S281N;ENSP00000388404:S281N;ENSP00000409513:S281N	ENSP00000342012:S281N	S	-	2	0	DMKN	40694229	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.000000	0.12993	0.834000	0.34852	0.561000	0.74099	AGC	.	.	weak		0.632	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
CAPZA3	93661	hgsc.bcm.edu	37	12	18891318	18891318	+	Missense_Mutation	SNP	G	G	A	rs117330813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:18891318G>A	ENST00000317658.3	+	1	274	c.116G>A	c.(115-117)cGt>cAt	p.R39H	RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000539875.1_5'Flank|PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000447925.2_5'Flank|PLCZ1_ENST00000435379.1_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	39					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)		p.R39H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				CTGCTTATCCGTGATGAAAAA	0.458													G|||	11	0.00219649	0.0	0.0029	5008	,	,		19990	0.001		0.007	False		,,,				2504	0.001				p.R39H		Atlas-SNP	.											CAPZA3,NS,carcinoma,0,1	CAPZA3	51	1	1	Substitution - Missense(1)	breast(1)	c.G116A						scavenged	.	G	HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	121.0	111.0	115.0		116	3.8	1.0	12	dbSNP_132	115	67,8531	41.2+/-98.3	0,67,4232	yes	missense	CAPZA3	NM_033328.2	29	0,79,6423	AA,AG,GG		0.7793,0.2724,0.6075	possibly-damaging	39/300	18891318	79,12925	2203	4299	6502	SO:0001583	missense	93661	exon1			TTATCCGTGATGA	AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.116G>A	12.37:g.18891318G>A	ENSP00000326238:p.Arg39His	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	181	77	0.425414	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	37	CCDS8681.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	5	0.006596306068601583	G	13.90	2.375049	0.42105	0.002724	0.007793	ENSG00000177938	ENST00000317658	.	.	.	4.8	3.83	0.44106	.	0.346611	0.27415	N	0.019461	T	0.38506	0.1043	L	0.36672	1.1	0.34727	D	0.72938	D	0.60575	0.988	P	0.56916	0.809	T	0.55108	-0.8192	9	0.51188	T	0.08	-1.6784	5.836	0.18607	0.1725:0.0:0.8275:0.0	.	39	Q96KX2	CAZA3_HUMAN	H	39	.	ENSP00000326238:R39H	R	+	2	0	CAPZA3	18782585	0.150000	0.22732	1.000000	0.80357	0.998000	0.95712	1.795000	0.38784	2.498000	0.84270	0.563000	0.77884	CGT	G|0.995;A|0.005	0.005	strong		0.458	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328	
MTHFSD	64779	hgsc.bcm.edu	37	16	86585743	86585743	+	Missense_Mutation	SNP	G	G	C	rs34005514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:86585743G>C	ENST00000360900.6	-	3	158	c.133C>G	c.(133-135)Ctg>Gtg	p.L45V	MTHFSD_ENST00000568037.1_Intron|MTHFSD_ENST00000543303.2_Intron|MTHFSD_ENST00000381214.5_Intron|MTHFSD_ENST00000322911.6_Missense_Mutation_p.L44V|MTHFSD_ENST00000546093.1_Intron	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	45			L -> V (in dbSNP:rs34005514).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						TGGCAAGCCAGATAAGACCCC	0.473													G|||	95	0.0189696	0.0053	0.0274	5008	,	,		19532	0.004		0.0517	False		,,,				2504	0.0133				p.L45V		Atlas-SNP	.											.	MTHFSD	52	.	0			c.C133G						PASS	.	G	VAL/LEU,,,VAL/LEU,VAL/LEU	43,3753		0,43,1855	151.0	153.0	152.0		133,,,73,130	-0.4	0.6	16	dbSNP_126	152	398,7840		14,370,3735	yes	missense,intron,intron,missense,missense	MTHFSD	NM_001159377.1,NM_001159378.1,NM_001159379.1,NM_001159380.1,NM_022764.2	32,,,32,32	14,413,5590	CC,CG,GG		4.8313,1.1328,3.6646	,,,,	45/384,,,25/364,44/383	86585743	441,11593	1898	4119	6017	SO:0001583	missense	64779	exon3			AAGCCAGATAAGA	AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"""RNA binding motif (RRM) containing"""	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.133C>G	16.37:g.86585743G>C	ENSP00000354152:p.Leu45Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	37	CCDS54047.1	55	0.025183150183150184	2	0.0040650406504065045	8	0.022099447513812154	4	0.006993006993006993	41	0.05408970976253298	G	10.80	1.453214	0.26161	0.011328	0.048313	ENSG00000103248	ENST00000543303;ENST00000360900;ENST00000322911	T;T	0.41400	1.0;1.0	5.93	-0.438	0.12268	5-formyltetrahydrofolate cyclo-ligase-like domain (1);	1.474430	0.04126	N	0.317098	T	0.04724	0.0128	N	0.04297	-0.235	0.09310	N	1	B;B	0.17465	0.022;0.017	B;B	0.23852	0.049;0.029	T	0.23726	-1.0180	10	0.35671	T	0.21	-11.0693	14.9226	0.70851	0.0:0.419:0.4829:0.0981	rs34005514	45;44	Q2M296;Q2M296-2	MTHSD_HUMAN;.	V	43;45;44	ENSP00000354152:L45V;ENSP00000326777:L44V	ENSP00000326777:L44V	L	-	1	2	MTHFSD	85143244	0.057000	0.20700	0.564000	0.28396	0.964000	0.63967	0.453000	0.21811	0.070000	0.16634	0.655000	0.94253	CTG	G|0.968;C|0.032	0.032	strong		0.473	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764	
ARSE	415	hgsc.bcm.edu	37	X	2852951	2852951	+	Silent	SNP	G	G	A	rs11222	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2852951G>A	ENST00000381134.3	-	11	1758	c.1692C>T	c.(1690-1692)aaC>aaT	p.N564N	ARSE_ENST00000545496.1_Silent_p.N589N|ARSE_ENST00000540563.1_Silent_p.N519N	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	564					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GTCTCCAGATGTTGCCCAGCC	0.592													G|||	2136	0.565828	0.0575	0.4092	3775	,	,		12608	0.6796		0.503	False		,,,				2504	0.5982				p.N564N		Atlas-SNP	.											.	ARSE	43	.	0			c.C1692T						PASS	.	G		666,3169		57,473,79,1102,492	43.0	31.0	36.0		1692	3.5	0.0	X	dbSNP_52	36	4170,2552		948,1085,1189,393,681	no	coding-synonymous	ARSE	NM_000047.2		1005,1558,1268,1495,1173	AA,AG,A,GG,G		37.9649,17.3664,45.8085		564/590	2852951	4836,5721	2203	4296	6499	SO:0001819	synonymous_variant	415	exon11			CCAGATGTTGCCC	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1692C>T	X.37:g.2852951G>A		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	117	115	0.982906	NM_000047	Q53FT2|Q53FU8	Silent	SNP	ENST00000381134.3	37	CCDS14122.1																																																																																			.	.	weak		0.592	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
CHPT1	56994	hgsc.bcm.edu	37	12	102117589	102117589	+	Silent	SNP	C	C	T	rs11082	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:102117589C>T	ENST00000229266.3	+	7	1264	c.1029C>T	c.(1027-1029)aaC>aaT	p.N343N	CHPT1_ENST00000549872.1_Silent_p.N343N	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	343					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						ACTTTAATAACTTTATAGACG	0.313													T|||	3500	0.698882	0.8086	0.5504	5008	,	,		16960	0.8879		0.5239	False		,,,				2504	0.6411				p.N343N		Atlas-SNP	.											.	CHPT1	27	.	0			c.C1029T						PASS	.	T		3375,1029	375.1+/-321.5	1308,759,135	82.0	90.0	87.0		1029	4.9	1.0	12	dbSNP_52	87	4500,4096	558.3+/-387.2	1176,2148,974	no	coding-synonymous	CHPT1	NM_020244.2		2484,2907,1109	TT,TC,CC		47.6501,23.3651,39.4231		343/407	102117589	7875,5125	2202	4298	6500	SO:0001819	synonymous_variant	56994	exon7			TAATAACTTTATA		CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"""phosphatidylcholine synthesizing enzyme"""					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.1029C>T	12.37:g.102117589C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_020244	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Silent	SNP	ENST00000229266.3	37	CCDS9086.1																																																																																			C|0.344;T|0.656	0.656	strong		0.313	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244	
Unknown	0	hgsc.bcm.edu	37	13	103400729	103400729	+	IGR	SNP	G	G	A	rs12583104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103400729G>A								LINC00283 (3155 upstream) : TEX30 (17610 downstream)																							TTTGCTTCCTGGGGAAATGAG	0.353													A|||	3597	0.718251	0.6324	0.7536	5008	,	,		20444	0.5883		0.826	False		,,,				2504	0.8323				p.P773L		Atlas-SNP	.											.	.	.	.	0			c.C2318T						PASS	.	A	LEU/PRO	898,486		293,312,87	87.0	67.0	73.0		2318	0.6	0.0	13	dbSNP_120	73	2546,634		1026,494,70	yes	missense	CCDC168	NM_001146197.1	98	1319,806,157	AA,AG,GG		19.9371,35.1156,24.5399		773/7082	103400729	3444,1120	692	1590	2282	SO:0001628	intergenic_variant	643677	exon4			CTTCCTGGGGAAA																													13.37:g.103400729G>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	240	101	0.420833	NM_001146197		Missense_Mutation	SNP		37																																																																																				G|0.314;A|0.686	0.686	strong	0	0.353								
PPP2R5E	5529	hgsc.bcm.edu	37	14	63920601	63920601	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63920601C>T	ENST00000337537.3	-	3	762	c.160G>A	c.(160-162)Gtt>Att	p.V54I	PPP2R5E_ENST00000553266.1_Intron|PPP2R5E_ENST00000555899.1_Missense_Mutation_p.V54I|PPP2R5E_ENST00000422769.2_5'UTR	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	54					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		GAGGATGGAACGTCTAAGAAA	0.368																																					p.V54I		Atlas-SNP	.											PPP2R5E,NS,carcinoma,0,1	PPP2R5E	43	1	0			c.G160A						scavenged	.						59.0	55.0	56.0					14																	63920601		2203	4300	6503	SO:0001583	missense	5529	exon3			ATGGAACGTCTAA	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9313	protein-coding gene	gene with protein product		601647	"""protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"""			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.160G>A	14.37:g.63920601C>T	ENSP00000337641:p.Val54Ile	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	2	0.03125	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Missense_Mutation	SNP	ENST00000337537.3	37	CCDS9758.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.187557	0.57909	.	.	ENSG00000154001	ENST00000337537;ENST00000555899	.	.	.	6.03	6.03	0.97812	.	0.055575	0.64402	D	0.000001	T	0.65544	0.2701	M	0.80332	2.49	0.80722	D	1	P;P;B	0.35575	0.51;0.51;0.276	B;B;B	0.26517	0.07;0.047;0.047	T	0.68633	-0.5357	9	0.54805	T	0.06	-9.5887	20.5666	0.99351	0.0:1.0:0.0:0.0	.	54;54;54	B7ZKK9;B7Z5X1;Q16537	.;.;2A5E_HUMAN	I	54	.	ENSP00000337641:V54I	V	-	1	0	PPP2R5E	62990354	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.084000	0.71335	2.854000	0.98071	0.655000	0.94253	GTT	.	.	none		0.368	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246	
PYY	5697	hgsc.bcm.edu	37	17	42030531	42030531	+	Missense_Mutation	SNP	G	G	C	rs1058046	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42030531G>C	ENST00000360085.2	-	6	755	c.215C>G	c.(214-216)aCg>aGg	p.T72R	PYY_ENST00000592796.1_Missense_Mutation_p.T72R	NM_004160.4	NP_004151	P10082	PYY_HUMAN	peptide YY	72			T -> R (in dbSNP:rs1058046). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8318545, ECO:0000269|Ref.3}.		cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|digestion (GO:0007586)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			endometrium(1)|ovary(1)	2		Breast(137;0.00314)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.12)		GGAAAGAAGCGTGTCCGGGCC	0.662													G|||	2723	0.54373	0.4508	0.5519	5008	,	,		16057	0.3343		0.6909	False		,,,				2504	0.728				p.T72R		Atlas-SNP	.											.	PYY	11	.	0			c.C215G	GRCh37	CM052359	PYY	M	rs1058046	PASS	.	G	ARG/THR	1988,2414	512.9+/-368.2	457,1074,670	50.0	54.0	53.0		215	1.6	0.0	17	dbSNP_86	53	5717,2883	652.0+/-400.9	1908,1901,491	yes	missense	PYY	NM_004160.4	71	2365,2975,1161	CC,CG,GG		33.5233,45.1613,40.7399	benign	72/98	42030531	7705,5297	2201	4300	6501	SO:0001583	missense	5697	exon6			AGAAGCGTGTCCG		CCDS32662.1	17q21.1	2013-02-28				ENSG00000131096		"""Endogenous ligands"""	9748	protein-coding gene	gene with protein product	"""prepro-PYY"""	600781				7782089	Standard	NM_004160		Approved	PYY1	uc002ieq.3	P10082		ENST00000360085.2:c.215C>G	17.37:g.42030531G>C	ENSP00000353198:p.Thr72Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_004160	Q5U5Q6|Q6FGH8	Missense_Mutation	SNP	ENST00000360085.2	37	CCDS32662.1	1166	0.5338827838827839	235	0.47764227642276424	221	0.6104972375690608	181	0.31643356643356646	529	0.6978891820580475	G	11.17	1.560590	0.27827	0.451613	0.664767	ENSG00000131096	ENST00000360085	T	0.14640	2.49	3.75	1.58	0.23477	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.23650	0.089	B	0.20384	0.029	T	0.13980	-1.0489	7	0.52906	T	0.07	.	5.9892	0.19452	0.0:0.2133:0.5669:0.2198	rs1058046;rs1662756;rs3198643;rs57522456;rs1058046	72	P10082	PYY_HUMAN	R	72	ENSP00000353198:T72R	ENSP00000353198:T72R	T	-	2	0	PYY	39386057	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.144000	0.16135	0.211000	0.20683	0.561000	0.74099	ACG	G|0.439;C|0.561	0.561	strong		0.662	PYY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000457658.1	NM_004160	
PTPN21	11099	hgsc.bcm.edu	37	14	88946622	88946622	+	Missense_Mutation	SNP	G	G	A	rs2401751	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:88946622G>A	ENST00000556564.1	-	13	1437	c.1153C>T	c.(1153-1155)Ctc>Ttc	p.L385F	PTPN21_ENST00000328736.3_Missense_Mutation_p.L385F	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	385			L -> F (in dbSNP:rs2401751). {ECO:0000269|PubMed:7519780}.		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CGACCGTTGAGGTCAATCTGG	0.478													G|||	1785	0.35643	0.3835	0.2651	5008	,	,		18536	0.38		0.2962	False		,,,				2504	0.4223				p.L385F		Atlas-SNP	.											.	PTPN21	113	.	0			c.C1153T						PASS	.	G	PHE/LEU	1636,2770	502.5+/-365.3	299,1038,866	87.0	76.0	79.0		1153	1.0	0.0	14	dbSNP_100	79	2931,5669	457.5+/-364.3	489,1953,1858	yes	missense	PTPN21	NM_007039.3	22	788,2991,2724	AA,AG,GG		34.0814,37.1312,35.1146	benign	385/1175	88946622	4567,8439	2203	4300	6503	SO:0001583	missense	11099	exon13			CGTTGAGGTCAAT	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.1153C>T	14.37:g.88946622G>A	ENSP00000452414:p.Leu385Phe	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	735	0.33653846153846156	198	0.4024390243902439	99	0.27348066298342544	205	0.3583916083916084	233	0.3073878627968338	G	8.490	0.861786	0.17178	0.371312	0.340814	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.73681	-0.77;-0.77	5.5	0.973	0.19710	.	0.264843	0.38778	N	0.001564	T	0.00012	0.0000	L	0.27053	0.805	0.49130	P	2.4400000000002198E-4	B	0.29188	0.236	B	0.20577	0.03	T	0.33189	-0.9878	9	0.23891	T	0.37	.	3.566	0.07900	0.4895:0.2061:0.3044:0.0	rs2401751;rs3742685;rs17203670;rs52826621;rs58090049;rs2401751	385	Q16825	PTN21_HUMAN	F	385	ENSP00000330276:L385F;ENSP00000452414:L385F	ENSP00000330276:L385F	L	-	1	0	PTPN21	88016375	1.000000	0.71417	0.008000	0.14137	0.488000	0.33401	4.629000	0.61290	0.284000	0.22305	-1.077000	0.02231	CTC	G|0.651;N|0.000	.	strong		0.478	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
MAG	4099	hgsc.bcm.edu	37	19	35786868	35786868	+	Silent	SNP	C	C	T	rs2301600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35786868C>T	ENST00000392213.3	+	4	558	c.399C>T	c.(397-399)agC>agT	p.S133S	MAG_ENST00000361922.4_Silent_p.S133S|MAG_ENST00000597035.1_Intron|MAG_ENST00000537831.2_Silent_p.S108S	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	133					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGAGCACAGCGTCCTGGATA	0.662													C|||	1450	0.289537	0.0998	0.3746	5008	,	,		17137	0.4226		0.2416	False		,,,				2504	0.3978				p.S133S		Atlas-SNP	.											.	MAG	172	.	0			c.C399T						PASS	.	C	,,	519,3887		28,463,1712	88.0	86.0	87.0		324,399,399	2.8	1.0	19	dbSNP_100	87	1857,6739		199,1459,2640	no	coding-synonymous,coding-synonymous,coding-synonymous	MAG	NM_001199216.1,NM_002361.3,NM_080600.2	,,	227,1922,4352	TT,TC,CC		21.6031,11.7794,18.2741	,,	108/602,133/627,133/583	35786868	2376,10626	2203	4298	6501	SO:0001819	synonymous_variant	4099	exon4			GCACAGCGTCCTG	M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.399C>T	19.37:g.35786868C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_080600	B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																			C|0.780;T|0.220	0.220	strong		0.662	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600	
SLC22A20	440044	hgsc.bcm.edu	37	11	64990041	64990041	+	RNA	SNP	G	G	C	rs514076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64990041G>C	ENST00000525437.1	+	0	939							A6NK97	S22AK_HUMAN	solute carrier family 22, member 20						ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)	8						CGGGAGGAAGGAGGAAGGGGA	0.552													G|||	2865	0.572085	0.1876	0.719	5008	,	,		18386	0.6776		0.7783	False		,,,				2504	0.6667				p.G246A		Atlas-SNP	.											.	SLC22A20	36	.	0			c.G737C						PASS	.	G	ALA/GLY	1267,2847		212,843,1002	67.0	63.0	64.0		737	3.8	0.9	11	dbSNP_83	64	6604,1812		2580,1444,184	yes	missense	SLC22A20	NM_001004326.4	60	2792,2287,1186	CC,CG,GG		21.5304,30.7973,37.1828	probably-damaging	246/350	64990041	7871,4659	2057	4208	6265			440044	exon4			AGGAAGGAGGAAG	DQ053017		11q13.1	2014-02-20			ENSG00000197847	ENSG00000197847		"""Solute carriers"""	29867	other	unknown		611696				15369770, 16478971	Standard	NM_001004326		Approved	Oat6, FLJ16331	uc021qlh.1	A6NK97	OTTHUMG00000165615		11.37:g.64990041G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001004326	B9EJB2|Q6ZN88	Missense_Mutation	SNP	ENST00000525437.1	37																																																																																				G|0.371;C|0.629	0.629	strong		0.552	SLC22A20-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000385336.1	NM_001004326	
KIR3DL3	115653	hgsc.bcm.edu	37	19	55246731	55246731	+	Missense_Mutation	SNP	C	C	A	rs602444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55246731C>A	ENST00000291860.1	+	6	979	c.961C>A	c.(961-963)Cac>Aac	p.H321N	KIR2DL4_ENST00000396284.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000402254.2_Intron	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	321			H -> N (in allele KIR3DL3*00101, allele KIR3DL3*00102, allele KIR3DL3*00103, allele KIR3DL3*00601, allele KIR3DL3*00602, allele KIR3DL3*01302, allele KIR3DL3*01305, allele KIR3DL3*01306, allele KIR3DL3*01307, allele KIR3DL3*017 and allele KIR3DL3*026; dbSNP:rs77241525). {ECO:0000269|PubMed:9862332}.|H -> Y (in allele KIR3DL3*00101, allele KIR3DL3*0030101, allele KIR3DL3*00401, allele KIR3DL3*00402, allele KIR3DL3*007, allele KIR3DL3*01404, allele KIR3DL3*01405, allele KIR3DL3*01601 and allele KIR3DL3*028; dbSNP:rs602444). {ECO:0000269|PubMed:11513144}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		TAACTCCAGACACCTGCACGT	0.448													.|||	1177	0.235024	0.0318	0.2118	5008	,	,		15547	0.1339		0.4801	False		,,,				2504	0.3783				p.H321N		Atlas-SNP	.											KIR3DL3,NS,carcinoma,0,1	KIR3DL3	46	1	0			c.C961A						PASS	.	C	ASN/HIS	382,3632		96,190,1721	289.0	223.0	245.0		961	-0.6	0.0	19	dbSNP_83	245	3917,3999		1412,1093,1453	no	missense	KIR3DL3	NM_153443.3	68	1508,1283,3174	AA,AC,CC		49.4821,9.5167,36.0352	probably-damaging	321/411	55246731	4299,7631	2007	3958	5965	SO:0001583	missense	115653	exon6			TCCAGACACCTGC	AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.961C>A	19.37:g.55246731C>A	ENSP00000291860:p.His321Asn	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	342	159	0.464912	NM_153443	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Missense_Mutation	SNP	ENST00000291860.1	37	CCDS12903.1	546	0.25	25	0.0508130081300813	88	0.2430939226519337	69	0.12062937062937062	364	0.48021108179419525	c	2.032	-0.422252	0.04734	0.095167	0.494821	ENSG00000242019	ENST00000291860	T	0.00468	7.22	0.929	-0.622	0.11560	Immunoglobulin subtype (1);	.	.	.	.	T	0.00012	0.0000	M	0.76938	2.355	0.80722	P	0.0	B	0.24258	0.1	B	0.26864	0.074	T	0.26815	-1.0092	8	0.66056	D	0.02	.	3.6449	0.08181	0.4353:0.5647:0.0:0.0	.	321	Q8N743	KI3L3_HUMAN	N	321	ENSP00000291860:H321N	ENSP00000291860:H321N	H	+	1	0	KIR3DL3	59938543	0.000000	0.05858	0.002000	0.10522	0.026000	0.11368	0.011000	0.13264	-0.127000	0.11661	0.184000	0.17185	CAC	A|0.254;C|0.746	0.254	strong		0.448	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443	
RNF212	285498	hgsc.bcm.edu	37	4	1090625	1090625	+	Silent	SNP	G	G	A	rs4045481	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1090625G>A	ENST00000433731.2	-	3	235	c.174C>T	c.(172-174)acC>acT	p.T58T	RNF212_ENST00000333673.5_Silent_p.T58T|RNF212_ENST00000382968.5_Silent_p.T58T			Q495C1	RN212_HUMAN	ring finger protein 212	58					chiasma assembly (GO:0051026)|meiotic gene conversion (GO:0006311)|protein sumoylation (GO:0016925)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		TATCTGCGTCGGTCTGAAAGA	0.443													G|||	2738	0.546725	0.2988	0.5432	5008	,	,		25036	0.6498		0.6481	False		,,,				2504	0.6738				p.T58T		Atlas-SNP	.											.	RNF212	69	.	0			c.C174T						PASS	.	G	,,	1514,2892	481.4+/-359.1	268,978,957	271.0	265.0	267.0		174,174,174	-8.4	0.0	4	dbSNP_108	267	5905,2695	683.4+/-403.9	2024,1857,419	no	coding-synonymous,coding-synonymous,coding-synonymous	RNF212	NM_001131034.3,NM_001193318.2,NM_194439.4	,,	2292,2835,1376	AA,AG,GG		31.3372,34.3622,42.9571	,,	58/298,58/274,58/233	1090625	7419,5587	2203	4300	6503	SO:0001819	synonymous_variant	285498	exon3			TGCGTCGGTCTGA	AK096160	CCDS3345.1, CCDS46996.1, CCDS54704.1	4p16.3	2013-02-27	2007-01-19	2007-01-19	ENSG00000178222	ENSG00000178222		"""RING-type (C3HC4) zinc fingers"""	27729	protein-coding gene	gene with protein product		612041	"""hypothetical protein LOC285498"""	LOC285498		23396135	Standard	NM_001131034		Approved	FLJ38841	uc003gcj.3	Q495C1	OTTHUMG00000118997	ENST00000433731.2:c.174C>T	4.37:g.1090625G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_194439	C9J8N0|Q495C0|Q86W82|Q8IY99|Q8N8U7	Silent	SNP	ENST00000433731.2	37	CCDS46996.1																																																																																			G|0.444;A|0.556	0.556	strong		0.443	RNF212-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359124.2	NM_194439	
CFAP57	149465	hgsc.bcm.edu	37	1	43638457	43638457	+	Silent	SNP	T	T	A	rs1782387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43638457T>A	ENST00000372492.4	+	2	357	c.33T>A	c.(31-33)gtT>gtA	p.V11V	EBNA1BP2_ENST00000236051.2_5'Flank|WDR65_ENST00000528956.1_Silent_p.V11V|EBNA1BP2_ENST00000472982.1_5'Flank|EBNA1BP2_ENST00000431635.2_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		11										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CGCTGCATGTTTTTGGTCTTC	0.498													T|||	713	0.142372	0.1309	0.1513	5008	,	,		10879	0.0		0.2903	False		,,,				2504	0.1462				p.V11V		Atlas-SNP	.											.	WDR65	76	.	0			c.T33A						PASS	.	T	,,	520,3886	237.7+/-249.4	29,462,1712	138.0	123.0	128.0		33,33,33	-2.8	1.0	1	dbSNP_89	128	2212,6388	377.1+/-338.4	292,1628,2380	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	321,2090,4092	AA,AT,TT		25.7209,11.8021,21.0057	,,	11/699,11/699,11/699	43638457	2732,10274	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon2			GCATGTTTTTGGT																												ENST00000372492.4:c.33T>A	1.37:g.43638457T>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				T|0.803;A|0.197	0.197	strong		0.498	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
FANCI	55215	hgsc.bcm.edu	37	15	89804043	89804043	+	Missense_Mutation	SNP	C	C	T	rs17803620	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89804043C>T	ENST00000310775.7	+	4	343	c.257C>T	c.(256-258)gCg>gTg	p.A86V	FANCI_ENST00000451393.2_5'UTR|FANCI_ENST00000567996.1_Missense_Mutation_p.A86V|FANCI_ENST00000300027.8_Missense_Mutation_p.A86V	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	86			A -> V (in dbSNP:rs17803620). {ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					AAAGAAATAGCGTCTGAGATC	0.438								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	1301	0.259784	0.0393	0.3458	5008	,	,		17597	0.3036		0.3787	False		,,,				2504	0.3292				p.A86V		Atlas-SNP	.											.	FANCI	129	.	0			c.C257T						PASS	.	C	VAL/ALA,VAL/ALA	417,3983	205.2+/-227.1	19,379,1802	124.0	118.0	120.0		257,257	4.4	1.0	15	dbSNP_123	120	3304,5294	493.6+/-373.6	635,2034,1630	yes	missense,missense	FANCI	NM_001113378.1,NM_018193.2	64,64	654,2413,3432	TT,TC,CC		38.4275,9.4773,28.6275	benign,benign	86/1329,86/1269	89804043	3721,9277	2200	4299	6499	SO:0001583	missense	55215	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAATAGCGTCTGA	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.257C>T	15.37:g.89804043C>T	ENSP00000310842:p.Ala86Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	163	80	0.490798	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	623	0.28525641025641024	29	0.05894308943089431	120	0.3314917127071823	173	0.30244755244755245	301	0.3970976253298153	C	15.55	2.866199	0.51588	0.094773	0.384275	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	T;T;T	0.43294	0.95;0.95;0.95	5.43	4.45	0.53987	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	L	0.38838	1.175	0.09310	P	1.0	B;P	0.41345	0.191;0.746	B;B	0.25614	0.055;0.062	T	0.39375	-0.9617	9	0.08381	T	0.77	-8.5811	9.6142	0.39681	0.0:0.7708:0.1457:0.0835	rs17803620;rs17803620	86;86	Q9NVI1;Q9NVI1-1	FANCI_HUMAN;.	V	86	ENSP00000300027:A86V;ENSP00000310842:A86V;ENSP00000413249:A86V	ENSP00000300027:A86V	A	+	2	0	FANCI	87605047	0.997000	0.39634	1.000000	0.80357	0.955000	0.61496	1.970000	0.40520	2.534000	0.85438	0.655000	0.94253	GCG	C|0.726;T|0.274	0.274	strong		0.438	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
DPPA4	55211	hgsc.bcm.edu	37	3	109052732	109052732	+	Missense_Mutation	SNP	T	T	C	rs3762648	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:109052732T>C	ENST00000335658.6	-	2	217	c.163A>G	c.(163-165)Atc>Gtc	p.I55V	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	55			I -> V (in dbSNP:rs3762648). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						CTGCCTTTGATAGACATTTTT	0.418													C|||	2424	0.484026	0.2231	0.4697	5008	,	,		20137	0.751		0.4831	False		,,,				2504	0.5726				p.I55V		Atlas-SNP	.											DPPA4,NS,carcinoma,+2,1	DPPA4	56	1	0			c.A163G						PASS	.	C	VAL/ILE	1104,3302	718.9+/-408.9	151,802,1250	246.0	234.0	238.0		163	-6.0	0.0	3	dbSNP_107	238	4023,4577	597.5+/-393.8	946,2131,1223	yes	missense	DPPA4	NM_018189.3	29	1097,2933,2473	CC,CT,TT		46.7791,25.0567,39.4203	benign	55/305	109052732	5127,7879	2203	4300	6503	SO:0001583	missense	55211	exon2			CTTTGATAGACAT	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.163A>G	3.37:g.109052732T>C	ENSP00000335306:p.Ile55Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Missense_Mutation	SNP	ENST00000335658.6	37	CCDS33814.1	1081	0.49496336996337	135	0.27439024390243905	167	0.4613259668508287	420	0.7342657342657343	359	0.4736147757255937	C	0.010	-1.753635	0.00663	0.250567	0.467791	ENSG00000121570	ENST00000335658;ENST00000477303	T;T	0.59083	2.01;0.29	3.37	-6.02	0.02192	.	3.611190	0.00735	N	0.000974	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.24941	-1.0146	8	.	.	.	7.0679	6.7032	0.23236	0.1207:0.4535:0.0:0.4259	rs3762648;rs52798077;rs56492819;rs60833201;rs3762648	55	Q7L190	DPPA4_HUMAN	V	55;3	ENSP00000335306:I55V;ENSP00000418313:I3V	.	I	-	1	0	DPPA4	110535422	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.085000	0.03390	-1.950000	0.01030	-0.233000	0.12211	ATC	T|0.557;C|0.443	0.443	strong		0.418	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	
ZNF606	80095	hgsc.bcm.edu	37	19	58491382	58491382	+	Silent	SNP	G	G	A	rs142503772	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58491382G>A	ENST00000341164.4	-	7	1286	c.666C>T	c.(664-666)aaC>aaT	p.N222N	ZNF606_ENST00000536132.1_Silent_p.N132N	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		CAAAGTTTAAGTTCTGGCTAA	0.423													G|||	17	0.00339457	0.0	0.0115	5008	,	,		19562	0.0		0.0089	False		,,,				2504	0.0				p.N222N		Atlas-SNP	.											.	ZNF606	155	.	0			c.C666T						PASS	.	G		12,4394	20.2+/-43.8	0,12,2191	103.0	101.0	101.0		666	-0.5	0.4	19	dbSNP_134	101	95,8505	52.7+/-113.3	1,93,4206	no	coding-synonymous	ZNF606	NM_025027.3		1,105,6397	AA,AG,GG		1.1047,0.2724,0.8227		222/793	58491382	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	80095	exon7			GTTTAAGTTCTGG	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.666C>T	19.37:g.58491382G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_025027	A8KAN2|Q8NE04|Q96JH5	Silent	SNP	ENST00000341164.4	37	CCDS12968.1																																																																																			G|0.991;A|0.009	0.009	strong		0.423	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027	
OVCH2	341277	hgsc.bcm.edu	37	11	7713176	7713176	+	RNA	SNP	G	G	A	rs74054133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7713176G>A	ENST00000533663.1	-	0	182				OVCH2_ENST00000534193.2_RNA|OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		CTGTCACATAGTCGGAAGTGC	0.443													G|||	526	0.105032	0.2481	0.0922	5008	,	,		21681	0.0129		0.0596	False		,,,				2504	0.0624				p.D488D		Atlas-SNP	.											.	OVCH2	47	.	0			c.C1464T						PASS	.	G		819,3079		90,639,1220	89.0	97.0	95.0		1464	3.0	0.8	11	dbSNP_130	95	667,7609		30,607,3501	no	coding-synonymous	OVCH2	NM_198185.2		120,1246,4721	AA,AG,GG		8.0594,21.0108,12.2063		488/565	7713176	1486,10688	1949	4138	6087			341277	exon14			CACATAGTCGGAA	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"""ovochymase 2"""			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		11.37:g.7713176G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_198185		Silent	SNP	ENST00000533663.1	37																																																																																				G|0.912;A|0.088	0.088	strong		0.443	OVCH2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000383928.1	NM_198185	
RTEL1	51750	hgsc.bcm.edu	37	20	62321189	62321189	+	Silent	SNP	C	C	T	rs61753459	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62321189C>T	ENST00000360203.5	+	24	2437	c.2112C>T	c.(2110-2112)gaC>gaT	p.D704D	RTEL1_ENST00000370003.1_5'Flank|RTEL1_ENST00000508582.2_Silent_p.D728D|RTEL1_ENST00000318100.4_Silent_p.D704D|RTEL1_ENST00000370018.3_Silent_p.D704D|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.D704D					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			ACCGCCAGGACTACGGAGCTG	0.697													C|||	268	0.0535144	0.003	0.0605	5008	,	,		13614	0.0		0.1113	False		,,,				2504	0.1125				p.D728D		Atlas-SNP	.											.	RTEL1	114	.	0			c.C2184T						PASS	.	C	,	74,4304	64.1+/-101.4	0,74,2115	35.0	34.0	34.0		2112,2184	4.6	1.0	20	dbSNP_129	34	818,7760	180.8+/-229.6	25,768,3496	no	coding-synonymous,coding-synonymous	RTEL1	NM_016434.3,NM_032957.4	,	25,842,5611	TT,TC,CC		9.536,1.6903,6.8848	,	704/1220,728/1244	62321189	892,12064	2189	4289	6478	SO:0001819	synonymous_variant	51750	exon24			CCAGGACTACGGA	AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"""chromosome 20 open reading frame 41"""	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.2112C>T	20.37:g.62321189C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_032957		Silent	SNP	ENST00000360203.5	37																																																																																				C|0.939;G|0.000;T|0.061	0.061	strong		0.697	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
PTDSS2	81490	hgsc.bcm.edu	37	11	488609	488609	+	Silent	SNP	G	G	T	rs11539814	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:488609G>T	ENST00000308020.5	+	8	992	c.816G>T	c.(814-816)acG>acT	p.T272T		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	272					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	CCCTGAAGACGTACAAGTGGC	0.637													G|||	82	0.0163738	0.0015	0.0576	5008	,	,		16279	0.0		0.0328	False		,,,				2504	0.0072				p.T272T		Atlas-SNP	.											.	PTDSS2	27	.	0			c.G816T						PASS	.	G		36,4370	39.2+/-71.8	0,36,2167	105.0	85.0	92.0		816	-8.3	0.8	11	dbSNP_120	92	243,8357	97.9+/-159.5	5,233,4062	no	coding-synonymous	PTDSS2	NM_030783.1		5,269,6229	TT,TG,GG		2.8256,0.8171,2.1452		272/488	488609	279,12727	2203	4300	6503	SO:0001819	synonymous_variant	81490	exon8			GAAGACGTACAAG	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.816G>T	11.37:g.488609G>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	163	77	0.472393	NM_030783		Silent	SNP	ENST00000308020.5	37	CCDS7696.1																																																																																			G|0.980;T|0.020	0.020	strong		0.637	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2		
SPTBN5	51332	hgsc.bcm.edu	37	15	42149472	42149472	+	Missense_Mutation	SNP	T	T	C	rs1456235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42149472T>C	ENST00000320955.6	-	51	8812	c.8585A>G	c.(8584-8586)cAa>cGa	p.Q2862R		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2862			Q -> R (in dbSNP:rs1456235).		actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TTCCACATCTTGGGCAAGGCA	0.662													T|||	2626	0.524361	0.0855	0.647	5008	,	,		18275	0.9544		0.5467	False		,,,				2504	0.5644				p.Q2827R		Atlas-SNP	.											.	SPTBN5	171	.	0			c.A8480G						PASS	.	T	ARG/GLN	660,3422		84,492,1465	12.0	15.0	14.0		8480	-3.4	0.0	15	dbSNP_88	14	4536,3818		1273,1990,914	yes	missense	SPTBN5	NM_016642.2	43	1357,2482,2379	CC,CT,TT		45.7027,16.1685,41.7819	benign	2827/3640	42149472	5196,7240	2041	4177	6218	SO:0001583	missense	51332	exon51			ACATCTTGGGCAA	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8585A>G	15.37:g.42149472T>C	ENSP00000317790:p.Gln2862Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		1255	0.5746336996336996	49	0.09959349593495935	231	0.638121546961326	551	0.9632867132867133	424	0.5593667546174143	.	0.024	-1.392953	0.01185	0.161685	0.542973	ENSG00000137877	ENST00000320955	T	0.50548	0.74	3.76	-3.38	0.04883	.	1.017260	0.07908	N	0.973790	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B	0.12630	0.006	B	0.09377	0.004	T	0.31194	-0.9952	9	0.44086	T	0.13	.	1.4134	0.02296	0.128:0.1717:0.2953:0.405	rs1456235;rs17680095;rs57418386;rs1456235	2862	Q9NRC6	SPTN5_HUMAN	R	2862	ENSP00000317790:Q2862R	ENSP00000317790:Q2862R	Q	-	2	0	SPTBN5	39936764	0.003000	0.15002	0.002000	0.10522	0.042000	0.13812	0.010000	0.13242	-0.198000	0.10333	0.383000	0.25322	CAA	T|0.464;C|0.536	0.536	strong		0.662	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
SERAC1	84947	hgsc.bcm.edu	37	6	158571501	158571501	+	Silent	SNP	G	G	A	rs6929274	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:158571501G>A	ENST00000367104.3	-	4	380	c.249C>T	c.(247-249)gaC>gaT	p.D83D	SERAC1_ENST00000367101.1_Silent_p.D83D|SERAC1_ENST00000607000.1_Silent_p.D83D|SERAC1_ENST00000367102.2_Silent_p.D83D	NM_032861.3	NP_116250.3	Q96JX3	SRAC1_HUMAN	serine active site containing 1	83					extracellular matrix organization (GO:0030198)|GPI anchor metabolic process (GO:0006505)|intracellular protein transport (GO:0006886)|phospholipid biosynthetic process (GO:0008654)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	15		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		TTTCTCCTTTGTCTAAAGAAA	0.328													A|||	3575	0.713858	0.705	0.8242	5008	,	,		18440	0.7262		0.6948	False		,,,				2504	0.6544				p.D83D		Atlas-SNP	.											.	SERAC1	31	.	0			c.C249T						PASS	.	A		3113,1291	437.4+/-345.0	1088,937,177	95.0	96.0	96.0		249	3.6	0.1	6	dbSNP_116	96	6051,2541	413.5+/-351.2	2122,1807,367	no	coding-synonymous	SERAC1	NM_032861.3		3210,2744,544	AA,AG,GG		29.574,29.3143,29.486		83/655	158571501	9164,3832	2202	4296	6498	SO:0001819	synonymous_variant	84947	exon4			TCCTTTGTCTAAA	BC001705	CCDS5255.1	6q25.3	2003-05-12			ENSG00000122335	ENSG00000122335			21061	protein-coding gene	gene with protein product		614725					Standard	NM_032861		Approved	FLJ14917	uc003qrc.2	Q96JX3	OTTHUMG00000015905	ENST00000367104.3:c.249C>T	6.37:g.158571501G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_032861	Q49AT1|Q5VTX3|Q6PKF3	Silent	SNP	ENST00000367104.3	37	CCDS5255.1																																																																																			G|0.279;A|0.721	0.721	strong		0.328	SERAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042862.1	NM_032861	
NELL1	4745	hgsc.bcm.edu	37	11	20805335	20805335	+	Silent	SNP	C	C	T	rs2280363	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:20805335C>T	ENST00000357134.5	+	3	446	c.294C>T	c.(292-294)tcC>tcT	p.S98S	NELL1_ENST00000325319.5_Silent_p.S98S|NELL1_ENST00000298925.5_Silent_p.S126S|NELL1_ENST00000532434.1_Silent_p.S98S	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	98	Laminin G-like.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AGAAGCCATCCACTTCAGGAG	0.428													C|||	1374	0.274361	0.4523	0.1513	5008	,	,		20056	0.1607		0.2575	False		,,,				2504	0.2556				p.S98S		Atlas-SNP	.											NELL1,NS,carcinoma,0,1	NELL1	179	1	0			c.C294T						PASS	.	C	,	1934,2472	550.2+/-378.0	418,1098,687	118.0	106.0	110.0		294,294	-11.8	0.0	11	dbSNP_100	110	2072,6528	360.5+/-332.0	253,1566,2481	no	coding-synonymous,coding-synonymous	NELL1	NM_006157.3,NM_201551.1	,	671,2664,3168	TT,TC,CC		24.093,43.8947,30.8012	,	98/811,98/764	20805335	4006,9000	2203	4300	6503	SO:0001819	synonymous_variant	4745	exon3			GCCATCCACTTCA	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.294C>T	11.37:g.20805335C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	37	CCDS7855.1																																																																																			C|0.716;T|0.284	0.284	strong		0.428	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383041	39383041	+	Silent	SNP	C	C	T	rs71371479		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39383041C>T	ENST00000377721.3	+	1	142	c.135C>T	c.(133-135)tcC>tcT	p.S45S	KRTAP9-2_ENST00000455970.2_Silent_p.S45S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	45	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)		p.S45S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GCTGTGTGTCCAGCTGCTGCC	0.647																																					p.S45S		Atlas-SNP	.											KRTAP9-2,NS,carcinoma,0,1	KRTAP9-2	24	1	1	Substitution - coding silent(1)	prostate(1)	c.C135T						scavenged	.						62.0	56.0	58.0					17																	39383041		2203	4299	6502	SO:0001819	synonymous_variant	83899	exon1			TGTGTCCAGCTGC	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.135C>T	17.37:g.39383041C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	126	8	0.0634921	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Silent	SNP	ENST00000377721.3	37	CCDS32651.1																																																																																			C|0.500;T|0.500	0.500	weak		0.647	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
DGCR6L	85359	hgsc.bcm.edu	37	22	20307256	20307256	+	Silent	SNP	G	G	A	rs7235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20307256G>A	ENST00000248879.3	-	2	268	c.177C>T	c.(175-177)acC>acT	p.T59T	DGCR6L_ENST00000405465.3_Missense_Mutation_p.P55L|XXbac-B444P24.13_ENST00000608275.1_RNA|XXbac-B444P24.14_ENST00000609632.1_lincRNA	NM_033257.3	NP_150282.2	Q9BY27	DGC6L_HUMAN	DiGeorge syndrome critical region gene 6-like	59						nucleus (GO:0005634)		p.T59T(1)		endometrium(1)|kidney(1)|lung(2)|stomach(1)	5	Colorectal(54;0.0993)					TTTCGAACACGGTGCCGTCGA	0.667													.|||	1198	0.239217	0.1271	0.2205	5008	,	,		14674	0.1766		0.4314	False		,,,				2504	0.271				p.T59T		Atlas-SNP	.											DGCR6L,NS,carcinoma,0,1	DGCR6L	9	1	1	Substitution - coding silent(1)	stomach(1)	c.C177T						scavenged	.	G		717,3689	281.4+/-275.9	69,579,1555	32.0	29.0	30.0		177	-2.3	1.0	22	dbSNP_52	30	3774,4824	507.0+/-376.7	825,2124,1350	no	coding-synonymous	DGCR6L	NM_033257.3		894,2703,2905	AA,AG,GG		43.8939,16.2733,34.5355		59/221	20307256	4491,8513	2203	4299	6502	SO:0001819	synonymous_variant	85359	exon2			GAACACGGTGCCG	AF228708	CCDS13778.1	22q11.21	2013-02-19			ENSG00000128185	ENSG00000128185			18551	protein-coding gene	gene with protein product		609459				11157784	Standard	NM_033257		Approved	FLJ10666	uc002zrx.3	Q9BY27	OTTHUMG00000150583	ENST00000248879.3:c.177C>T	22.37:g.20307256G>A		Somatic	289	2	0.00692042		WXS	Illumina HiSeq	Phase_I	289	128	0.442907	NM_033257	A8K1N7|B3KMC0|D3DX29|Q9BW33	Silent	SNP	ENST00000248879.3	37	CCDS13778.1	579	0.2651098901098901	53	0.10772357723577236	83	0.2292817679558011	108	0.1888111888111888	335	0.4419525065963061	G	1.110	-0.658346	0.03454	0.162733	0.438939	ENSG00000128185	ENST00000405465	T	0.35789	1.29	1.83	-2.34	0.06704	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.41946	P	0.009368000000000043	.	.	.	.	.	.	T	0.40553	-0.9557	5	0.02654	T	1	-24.4417	6.2719	0.20959	0.151:0.6029:0.2461:0.0	rs7235;rs1056851;rs3197470;rs13058126;rs17349310	.	.	.	L	55	ENSP00000386052:P55L	ENSP00000386052:P55L	P	-	2	0	DGCR6L	18687256	0.019000	0.18553	0.989000	0.46669	0.808000	0.45660	-1.230000	0.02942	-0.496000	0.06650	0.306000	0.20318	CCG	G|0.703;A|0.297	0.297	strong		0.667	DGCR6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318970.3	NM_033257	
KLF17	128209	hgsc.bcm.edu	37	1	44595113	44595113	+	Missense_Mutation	SNP	G	G	C	rs2429051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:44595113G>C	ENST00000372299.3	+	2	228	c.170G>C	c.(169-171)aGc>aCc	p.S57T	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	57			S -> T (in dbSNP:rs2429051). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					GGCCTACCAAGCATTCAGCAC	0.537													G|||	2486	0.496406	0.2231	0.5159	5008	,	,		18838	0.628		0.6928	False		,,,				2504	0.5143				p.S57T		Atlas-SNP	.											.	KLF17	92	.	0			c.G170C						PASS	.	G	THR/SER	1311,3095	442.7+/-346.8	204,903,1096	96.0	84.0	88.0		170	-3.9	0.0	1	dbSNP_100	88	5710,2890	671.8+/-402.9	1918,1874,508	yes	missense	KLF17	NM_173484.3	58	2122,2777,1604	CC,CG,GG		33.6047,29.7549,46.0172	benign	57/390	44595113	7021,5985	2203	4300	6503	SO:0001583	missense	128209	exon2			TACCAAGCATTCA	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.170G>C	1.37:g.44595113G>C	ENSP00000361373:p.Ser57Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	1199	0.548992673992674	111	0.22560975609756098	197	0.5441988950276243	377	0.6590909090909091	514	0.6781002638522428	G	10.97	1.500537	0.26861	0.297549	0.663953	ENSG00000171872	ENST00000372299	T	0.09723	2.95	4.58	-3.88	0.04205	.	1.187530	0.06029	N	0.652786	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.27625	0.183	B	0.24394	0.053	T	0.32640	-0.9899	9	0.22109	T	0.4	.	1.6635	0.02797	0.4229:0.1764:0.276:0.1246	rs2429051;rs12734854;rs17854588;rs2429051	57	Q5JT82	KLF17_HUMAN	T	57	ENSP00000361373:S57T	ENSP00000361373:S57T	S	+	2	0	KLF17	44367700	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.374000	0.07484	-0.722000	0.04922	-0.806000	0.03193	AGC	G|0.456;C|0.544	0.544	strong		0.537	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
RP1L1	94137	hgsc.bcm.edu	37	8	10469233	10469233	+	Missense_Mutation	SNP	A	A	G	rs35602868	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:10469233A>G	ENST00000382483.3	-	4	2598	c.2375T>C	c.(2374-2376)cTg>cCg	p.L792P		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	792			L -> P (in dbSNP:rs35602868). {ECO:0000269|PubMed:12724644}.		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTCTTCCCCCAGGCTGGCAGC	0.692													A|||	1577	0.314896	0.3525	0.3602	5008	,	,		15992	0.0218		0.5567	False		,,,				2504	0.2853				p.L792P		Atlas-SNP	.											.	RP1L1	453	.	0			c.T2375C						PASS	.	A	PRO/LEU	1358,2534		220,918,808	53.0	58.0	57.0		2375	-0.8	0.0	8	dbSNP_126	57	4444,3826		1223,1998,914	yes	missense	RP1L1	NM_178857.5	98	1443,2916,1722	GG,GA,AA		46.2636,34.8921,47.706	probably-damaging	792/2401	10469233	5802,6360	1946	4135	6081	SO:0001583	missense	94137	exon4			TCCCCCAGGCTGG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2375T>C	8.37:g.10469233A>G	ENSP00000371923:p.Leu792Pro	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	721	0.3301282051282051	167	0.3394308943089431	138	0.3812154696132597	13	0.022727272727272728	403	0.5316622691292876	A	12.25	1.881182	0.33255	0.348921	0.537364	ENSG00000183638	ENST00000382483	T	0.07908	3.15	5.11	-0.8	0.10897	.	2.282260	0.02877	U	0.132403	T	0.00012	0.0000	N	0.19112	0.55	0.53688	P	2.6999999999999247E-5	P	0.38827	0.649	B	0.36186	0.219	T	0.41088	-0.9528	9	0.33940	T	0.23	-2.9284	5.5366	0.17016	0.4338:0.1325:0.0:0.4337	rs35602868	792	A6NKC6	.	P	792	ENSP00000371923:L792P	ENSP00000371923:L792P	L	-	2	0	RP1L1	10506643	0.000000	0.05858	0.018000	0.16275	0.014000	0.08584	-0.052000	0.11865	0.226000	0.20979	-0.695000	0.03696	CTG	A|0.605;G|0.395	0.395	strong		0.692	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234923	26234923	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26234923C>A	ENST00000244534.5	-	1	293	c.239G>T	c.(238-240)cGt>cTt	p.R80L		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	80	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)	p.R80H(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AAGCTTGATACGGCTGTTGTT	0.537																																					p.R80L		Atlas-SNP	.											HIST1H1D,NS,lymphoid_neoplasm,0,1	HIST1H1D	40	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G239T						PASS	.						88.0	96.0	93.0					6																	26234923		2203	4300	6503	SO:0001583	missense	3007	exon1			TTGATACGGCTGT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"""Histones / Replication-dependent"""	4717	protein-coding gene	gene with protein product		142210	"""H1 histone family, member 3"", ""histone 1, H1d"""	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.239G>T	6.37:g.26234923C>A	ENSP00000244534:p.Arg80Leu	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	289	57	0.197232	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	22.8	4.340881	0.81911	.	.	ENSG00000124575	ENST00000244534	T	0.09445	2.98	5.23	5.23	0.72850	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.18002	0.0432	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.04509	-1.0946	10	0.15499	T	0.54	-17.6271	18.1633	0.89717	0.0:1.0:0.0:0.0	.	80	P16402	H13_HUMAN	L	80	ENSP00000244534:R80L	ENSP00000244534:R80L	R	-	2	0	HIST1H1D	26342902	1.000000	0.71417	1.000000	0.80357	0.221000	0.24807	4.921000	0.63397	2.623000	0.88846	0.655000	0.94253	CGT	.	.	none		0.537	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320	
NCR2	9436	hgsc.bcm.edu	37	6	41309552	41309552	+	Missense_Mutation	SNP	T	T	C	rs2236369	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41309552T>C	ENST00000373089.5	+	3	503	c.415T>C	c.(415-417)Tcc>Ccc	p.S139P	NCR2_ENST00000373086.3_Missense_Mutation_p.S139P|NCR2_ENST00000373083.4_Missense_Mutation_p.S139P	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	139			S -> P (in dbSNP:rs2236369). {ECO:0000269|PubMed:10049942, ECO:0000269|Ref.2}.		cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					CACACAGACCTCCTGGACTCC	0.622													T|||	2452	0.489617	0.1846	0.6787	5008	,	,		17573	0.5764		0.5885	False		,,,				2504	0.5767				p.S139P		Atlas-SNP	.											NCR2,colon,carcinoma,0,1	NCR2	44	1	0			c.T415C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER	1075,3331	387.0+/-326.3	130,815,1258	80.0	76.0	77.0		415,415,415	-1.5	0.2	6	dbSNP_98	77	5106,3494	631.1+/-398.4	1562,1982,756	yes	missense,missense,missense	NCR2	NM_001199509.1,NM_001199510.1,NM_004828.3	74,74,74	1692,2797,2014	CC,CT,TT		40.6279,24.3985,47.5242	benign,benign,benign	139/271,139/259,139/277	41309552	6181,6825	2203	4300	6503	SO:0001583	missense	9436	exon3			CAGACCTCCTGGA	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	6732	protein-coding gene	gene with protein product		604531	"""lymphocyte antigen 95 (activating NK-receptor; NK-p44)"""	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.415T>C	6.37:g.41309552T>C	ENSP00000362181:p.Ser139Pro	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_004828	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Missense_Mutation	SNP	ENST00000373089.5	37	CCDS4855.1	1108	0.5073260073260073	118	0.23983739837398374	240	0.6629834254143646	308	0.5384615384615384	442	0.58311345646438	T	6.341	0.431064	0.12045	0.243985	0.593721	ENSG00000096264	ENST00000373083;ENST00000373089;ENST00000373086	T;T;T	0.14766	2.53;2.7;2.48	1.69	-1.52	0.08637	.	.	.	.	.	T	0.01592	0.0051	N	0.14661	0.345	0.80722	P	0.0	B;B;P	0.35363	0.396;0.34;0.497	B;B;B	0.34242	0.178;0.093;0.062	T	0.43621	-0.9380	8	0.20046	T	0.44	.	2.3519	0.04286	0.443:0.2713:0.0:0.2858	rs2236369;rs61406687;rs2236369	139;139;139	O95944-3;O95944-2;O95944	.;.;NCTR2_HUMAN	P	139	ENSP00000362175:S139P;ENSP00000362181:S139P;ENSP00000362178:S139P	ENSP00000362175:S139P	S	+	1	0	NCR2	41417530	0.005000	0.15991	0.214000	0.23707	0.212000	0.24457	-0.192000	0.09587	-0.289000	0.09038	-0.878000	0.02970	TCC	A|0.004;C|0.466	0.466	strong		0.622	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3		
ALPK2	115701	hgsc.bcm.edu	37	18	56203120	56203120	+	Silent	SNP	C	C	T	rs3809981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56203120C>T	ENST00000361673.3	-	5	4512	c.4299G>A	c.(4297-4299)ggG>ggA	p.G1433G	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1433						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TTGATTGACCCCCTTCTCTGG	0.502													C|||	1652	0.329872	0.2103	0.3847	5008	,	,		18692	0.2391		0.5308	False		,,,				2504	0.3395				p.G1433G		Atlas-SNP	.											ALPK2_ENST00000361673,NS,carcinoma,-1,4	ALPK2	487	4	0			c.G4299A						scavenged	.	C		1144,3262	397.0+/-330.2	141,862,1200	55.0	55.0	55.0		4299	1.0	0.0	18	dbSNP_107	55	4171,4429	542.7+/-384.2	1015,2141,1144	no	coding-synonymous	ALPK2	NM_052947.3		1156,3003,2344	TT,TC,CC		48.5,25.9646,40.8658		1433/2171	56203120	5315,7691	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			TTGACCCCCTTCT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4299G>A	18.37:g.56203120C>T		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.606;T|0.394	0.394	strong		0.502	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
GNPAT	8443	hgsc.bcm.edu	37	1	231408091	231408091	+	Missense_Mutation	SNP	A	A	G	rs11558492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:231408091A>G	ENST00000366647.4	+	11	1725	c.1556A>G	c.(1555-1557)gAt>gGt	p.D519G	GNPAT_ENST00000366646.3_Missense_Mutation_p.D458G	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	519			D -> G (in RCDP2; 70% reduction in activity; dbSNP:rs11558492). {ECO:0000269|PubMed:11152660}.		cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				TTCCTACGTGATGTTTTTGCA	0.383													A|||	679	0.135583	0.0688	0.1729	5008	,	,		20615	0.1002		0.2127	False		,,,				2504	0.1564				p.D519G		Atlas-SNP	.											.	GNPAT	73	.	0			c.A1556G						PASS	.	A	GLY/ASP	404,4002	199.8+/-223.2	16,372,1815	288.0	271.0	277.0		1556	-0.3	0.0	1	dbSNP_120	277	1770,6830	320.4+/-314.6	170,1430,2700	yes	missense	GNPAT	NM_014236.3	94	186,1802,4515	GG,GA,AA		20.5814,9.1693,16.7154	benign	519/681	231408091	2174,10832	2203	4300	6503	SO:0001583	missense	8443	exon11			TACGTGATGTTTT	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1556A>G	1.37:g.231408091A>G	ENSP00000355607:p.Asp519Gly	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	175	81	0.462857	NM_014236	B4DNM9|Q5TBH7|Q9BWC2	Missense_Mutation	SNP	ENST00000366647.4	37	CCDS1592.1	313	0.1433150183150183	37	0.07520325203252033	71	0.19613259668508287	59	0.10314685314685315	146	0.19261213720316622	A	11.88	1.770311	0.31320	0.091693	0.205814	ENSG00000116906	ENST00000366647;ENST00000366646;ENST00000416000	T;T;T	0.64618	-0.11;-0.1;-0.11	4.71	-0.263	0.12954	.	0.487719	0.24583	N	0.037281	T	0.00039	0.0001	L	0.34521	1.04	0.44871	P	0.0021200000000000108	B;B	0.22800	0.075;0.019	B;B	0.21360	0.034;0.028	T	0.06570	-1.0819	9	0.56958	D	0.05	.	9.158	0.37005	0.6427:0.0:0.3573:0.0	rs11558492;rs17387913;rs52834016;rs59486675;rs11558492	458;519	B4DNM9;O15228	.;GNPAT_HUMAN	G	519;458;509	ENSP00000355607:D519G;ENSP00000355606:D458G;ENSP00000411640:D509G	ENSP00000355606:D458G	D	+	2	0	GNPAT	229474714	0.814000	0.29104	0.006000	0.13384	0.976000	0.68499	1.947000	0.40293	-0.134000	0.11516	0.460000	0.39030	GAT	G|0.155;N|0.000	0.155	strong		0.383	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1		
PFN4	375189	hgsc.bcm.edu	37	2	24342532	24342532	+	Silent	SNP	G	G	A	rs1134516	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:24342532G>A	ENST00000313213.4	-	4	647	c.276C>T	c.(274-276)gtC>gtT	p.V92V	PFN4_ENST00000465360.1_5'UTR	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	92					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	lipid binding (GO:0008289)			breast(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGTCTTCACGACAACCACAC	0.463													g|||	643	0.128395	0.1278	0.0793	5008	,	,		18773	0.0456		0.1561	False		,,,				2504	0.2209				p.V92V		Atlas-SNP	.											.	PFN4	16	.	0			c.C276T						PASS	.	A		556,3850	248.7+/-256.4	26,504,1673	110.0	101.0	104.0		276	-5.6	0.1	2	dbSNP_86	104	1382,7218	267.9+/-287.5	110,1162,3028	no	coding-synonymous	PFN4	NM_199346.1		136,1666,4701	AA,AG,GG		16.0698,12.6192,14.9008		92/130	24342532	1938,11068	2203	4300	6503	SO:0001819	synonymous_variant	375189	exon4			CTTCACGACAACC	BC029523	CCDS1709.1	2p24.1	2008-02-05			ENSG00000176732	ENSG00000176732			31103	protein-coding gene	gene with protein product							Standard	NM_199346		Approved		uc002rfa.1	Q8NHR9	OTTHUMG00000090816	ENST00000313213.4:c.276C>T	2.37:g.24342532G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_199346	Q53TL9	Silent	SNP	ENST00000313213.4	37	CCDS1709.1																																																																																			G|0.866;A|0.134	0.134	strong		0.463	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346	
GPR56	9289	hgsc.bcm.edu	37	16	57689805	57689805	+	Missense_Mutation	SNP	A	A	C	rs1801255	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:57689805A>C	ENST00000388812.4	+	7	1358	c.918A>C	c.(916-918)caA>caC	p.Q306H	GPR56_ENST00000544297.1_Missense_Mutation_p.Q131H|GPR56_ENST00000540164.2_Missense_Mutation_p.Q306H|GPR56_ENST00000567835.1_Missense_Mutation_p.Q306H|GPR56_ENST00000379694.4_Missense_Mutation_p.Q136H|GPR56_ENST00000568909.1_Missense_Mutation_p.Q306H|GPR56_ENST00000379696.3_Missense_Mutation_p.Q306H|GPR56_ENST00000568908.1_Missense_Mutation_p.Q306H|GPR56_ENST00000562558.1_Missense_Mutation_p.Q306H|GPR56_ENST00000562631.1_Missense_Mutation_p.Q306H|GPR56_ENST00000538815.1_Missense_Mutation_p.Q306H|GPR56_ENST00000456916.1_Missense_Mutation_p.Q306H|GPR56_ENST00000388813.5_Missense_Mutation_p.Q306H			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	306			Q -> H (in dbSNP:rs1801255). {ECO:0000269|PubMed:10049584, ECO:0000269|PubMed:10100861, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.7}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						ATTCCAGCCAAGTCCTGGGTG	0.552													A|||	566	0.113019	0.0734	0.1484	5008	,	,		18820	0.006		0.2843	False		,,,				2504	0.0757				p.Q311H		Atlas-SNP	.											.	GPR56	44	.	0			c.A933C						PASS	.	A	HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN	430,3966	209.5+/-230.2	32,366,1800	119.0	117.0	118.0		918,918,918,933,918,918,918,918	-0.6	1.0	16	dbSNP_89	118	2284,6316	385.1+/-341.3	340,1604,2356	yes	missense,missense,missense,missense,missense,missense,missense,missense	GPR56	NM_001145770.1,NM_001145771.1,NM_001145772.1,NM_001145773.1,NM_001145774.1,NM_005682.5,NM_201524.2,NM_201525.2	24,24,24,24,24,24,24,24	372,1970,4156	CC,CA,AA		26.5581,9.7816,20.8833	benign,benign,benign,benign,benign,benign,benign,benign	306/688,306/694,306/688,311/693,306/688,306/694,306/688,306/688	57689805	2714,10282	2198	4300	6498	SO:0001583	missense	9289	exon7			CAGCCAAGTCCTG	AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"""-"", ""GPCR / Class B : Orphans"""	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.918A>C	16.37:g.57689805A>C	ENSP00000373464:p.Gln306His	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_001145773	A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Missense_Mutation	SNP	ENST00000388812.4	37	CCDS32460.1	309	0.14148351648351648	40	0.08130081300813008	57	0.1574585635359116	5	0.008741258741258742	207	0.27308707124010556	A	10.03	1.237897	0.22711	0.097816	0.265581	ENSG00000205336	ENST00000388813;ENST00000388812;ENST00000538815;ENST00000456916;ENST00000540164;ENST00000544297;ENST00000379694;ENST00000379696	T;T;T;T;T;T;T;T	0.44881	0.92;0.91;0.92;0.91;0.92;1.76;1.17;0.91	5.59	-0.618	0.11576	.	0.199890	0.35646	N	0.003069	T	0.00012	0.0000	L	0.42245	1.32	0.38031	P	0.06483099999999997	B;B;B;B	0.33964	0.028;0.012;0.016;0.434	B;B;B;B	0.28232	0.027;0.012;0.007;0.087	T	0.28490	-1.0042	9	0.35671	T	0.21	.	6.5868	0.22624	0.4196:0.1564:0.424:0.0	rs1801255;rs17326320;rs17855398;rs52830657;rs60204048;rs1801255	131;306;306;136	F5H144;Q9Y653-2;Q9Y653;E7ENB2	.;.;GPR56_HUMAN;.	H	306;306;306;306;306;131;136;306	ENSP00000373465:Q306H;ENSP00000373464:Q306H;ENSP00000444415:Q306H;ENSP00000398034:Q306H;ENSP00000444911:Q306H;ENSP00000438006:Q131H;ENSP00000369016:Q136H;ENSP00000369018:Q306H	ENSP00000369016:Q136H	Q	+	3	2	GPR56	56247306	0.808000	0.29022	0.993000	0.49108	0.811000	0.45836	-0.205000	0.09411	-0.161000	0.10983	-0.290000	0.09829	CAA	A|0.834;C|0.166	0.166	strong		0.552	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3		
HRAS	3265	hgsc.bcm.edu	37	11	534242	534242	+	Silent	SNP	A	A	G	rs12628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000417302.1_Silent_p.H27H|HRAS_ENST00000397596.2_Silent_p.H27H|HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"""E, L, M"""	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135.0	123.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1.0	1.0	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	102	59	0.578431	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242151	81242151	+	RNA	SNP	T	T	C	rs5818326|rs532218091|rs386792900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81242151T>C	ENST00000525539.1	-	0	704				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.G235G(2)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GACACAGGTTTCCAAAGTAGG	0.562													T|||	2211	0.441494	0.1717	0.4625	5008	,	,		20463	0.8026		0.4205	False		,,,				2504	0.4407				p.G235G		Atlas-SNP	.											PKD1L2_ENST00000525539,NS,carcinoma,0,4	PKD1L2	361	4	2	Substitution - coding silent(2)	lung(2)	c.A705G						scavenged	.						86.0	82.0	83.0					16																	81242151		2123	4226	6349			114780	exon4			CAGGTTTCCAAAG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242151T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	21	1	0.047619	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																				T|0.561;C|0.439	0.439	strong		0.562	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
ETV1	2115	hgsc.bcm.edu	37	7	13950864	13950864	+	Splice_Site	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:13950864C>T	ENST00000430479.1	-	10	1538	c.871G>A	c.(871-873)Ggc>Agc	p.G291S	ETV1_ENST00000403527.1_Splice_Site_p.G251S|ETV1_ENST00000405358.4_Splice_Site_p.G305S|ETV1_ENST00000420159.2_Splice_Site_p.G233S|ETV1_ENST00000405218.2_Splice_Site_p.G291S|ETV1_ENST00000242066.5_Splice_Site_p.G273S|ETV1_ENST00000476720.2_5'Flank|ETV1_ENST00000343495.5_Splice_Site_p.G273S|ETV1_ENST00000399357.3_Splice_Site_p.G188S|ETV1_ENST00000403685.1_Splice_Site_p.G273S|ETV1_ENST00000405192.2_Intron	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	291					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						GACAACTTAACTTCTGTTCTG	0.383			T	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""	"""Ewing sarcoma, prostate"""																																p.G291S		Atlas-SNP	.		Dom	yes		7	7p22	2115	ets variant gene 1		"""M, E"""	.	ETV1	138	.	0			c.G871A						PASS	.						81.0	80.0	81.0					7																	13950864		1904	4108	6012	SO:0001630	splice_region_variant	2115	exon10			ACTTAACTTCTGT		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"""ets variant gene 1"""			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.871+1G>A	7.37:g.13950864C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	115	14	0.121739	NM_004956	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	CCDS55088.1	.	.	.	.	.	.	.	.	.	.	C	36	5.733116	0.96856	.	.	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000399357;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956	T;T;T;T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.26	5.26	0.73747	.	2.792530	0.00481	N	0.000121	T	0.54464	0.1860	L	0.60067	1.865	0.80722	D	1	.	.	.	.	.	.	T	0.39820	-0.9595	7	.	.	.	.	19.7471	0.96257	0.0:1.0:0.0:0.0	.	.	.	.	S	291;273;273;233;188;305;251;291;273;233	ENSP00000405327:G291S;ENSP00000242066:G273S;ENSP00000340853:G273S;ENSP00000411626:G233S;ENSP00000382293:G188S;ENSP00000384085:G305S;ENSP00000384138:G251S;ENSP00000385551:G291S;ENSP00000385686:G273S;ENSP00000393078:G233S	.	G	-	1	0	ETV1	13917389	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.776000	0.85560	2.838000	0.97847	0.591000	0.81541	GGC	.	.	none		0.383	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956	Missense_Mutation
CHGB	1114	hgsc.bcm.edu	37	20	5903323	5903323	+	Missense_Mutation	SNP	G	G	A	rs910122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:5903323G>A	ENST00000378961.4	+	4	737	c.533G>A	c.(532-534)cGa>cAa	p.R178Q		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	178			R -> Q (in dbSNP:rs910122). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						AAAGGGGAGCGAGGGGAAGAT	0.473													G|||	2086	0.416534	0.2995	0.4942	5008	,	,		20215	0.5288		0.3489	False		,,,				2504	0.4734				p.R178Q		Atlas-SNP	.											CHGB,colon,carcinoma,+1,1	CHGB	112	1	0			c.G533A						PASS	.	G	GLN/ARG	1478,2928	473.5+/-356.7	260,958,985	88.0	89.0	89.0		533	-11.1	0.0	20	dbSNP_86	89	3075,5525	469.6+/-367.6	549,1977,1774	yes	missense	CHGB	NM_001819.2	43	809,2935,2759	AA,AG,GG		35.7558,33.5452,35.0069	benign	178/678	5903323	4553,8453	2203	4300	6503	SO:0001583	missense	1114	exon4			GGGAGCGAGGGGA		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.533G>A	20.37:g.5903323G>A	ENSP00000368244:p.Arg178Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	142	65	0.457746	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	886	0.4056776556776557	171	0.3475609756097561	155	0.4281767955801105	295	0.5157342657342657	265	0.3496042216358839	G	5.054	0.195656	0.09599	0.335452	0.357558	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.01821	4.62;4.62	5.57	-11.1	0.00147	.	1.782560	0.03085	N	0.159015	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48570	-0.9024	9	0.19147	T	0.46	3.7714	1.6706	0.02810	0.4906:0.1907:0.1291:0.1896	rs910122;rs52803541;rs57501504;rs910122	178	P05060	SCG1_HUMAN	Q	178;158	ENSP00000368244:R178Q;ENSP00000416643:R158Q	ENSP00000368244:R178Q	R	+	2	0	CHGB	5851323	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.898000	0.01602	-4.738000	0.00034	-2.619000	0.00157	CGA	G|0.631;A|0.369	0.369	strong		0.473	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
LUZP2	338645	hgsc.bcm.edu	37	11	25098938	25098938	+	Missense_Mutation	SNP	G	G	C	rs7930185	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:25098938G>C	ENST00000336930.6	+	11	988	c.922G>C	c.(922-924)Gag>Cag	p.E308Q	LUZP2_ENST00000533227.1_Missense_Mutation_p.E222Q			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	308			E -> Q (in dbSNP:rs7930185).			extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						TGCAGAAACCGAGCCTATCCC	0.333													G|||	2195	0.438299	0.1195	0.4712	5008	,	,		12587	0.7808		0.4553	False		,,,				2504	0.4755				p.E308Q		Atlas-SNP	.											.	LUZP2	90	.	0			c.G922C						PASS	.	G	GLN/GLU	741,3665	304.4+/-288.4	65,611,1527	142.0	142.0	142.0		922	3.1	0.0	11	dbSNP_116	142	3621,4979	522.4+/-380.1	766,2089,1445	yes	missense	LUZP2	NM_001009909.2	29	831,2700,2972	CC,CG,GG		42.1047,16.818,33.5384	benign	308/347	25098938	4362,8644	2203	4300	6503	SO:0001583	missense	338645	exon11			GAAACCGAGCCTA	AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.922G>C	11.37:g.25098938G>C	ENSP00000336817:p.Glu308Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_001009909	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Missense_Mutation	SNP	ENST00000336930.6	37	CCDS31446.1	1042	0.47710622710622713	56	0.11382113821138211	169	0.46685082872928174	468	0.8181818181818182	349	0.4604221635883905	G	6.284	0.420420	0.11928	0.16818	0.421047	ENSG00000187398	ENST00000336930;ENST00000533227	T;T	0.51574	0.71;0.7	5.05	3.09	0.35607	.	0.612081	0.15151	N	0.277731	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P;B	0.42556	0.783;0.325	B;B	0.41723	0.365;0.133	T	0.11665	-1.0578	9	0.48119	T	0.1	-0.1151	6.8141	0.23820	0.0972:0.1785:0.7243:0.0	rs7930185;rs17235288;rs52806551;rs7930185	222;308	E9PN53;Q86TE4	.;LUZP2_HUMAN	Q	308;222	ENSP00000336817:E308Q;ENSP00000432952:E222Q	ENSP00000336817:E308Q	E	+	1	0	LUZP2	25055514	0.000000	0.05858	0.005000	0.12908	0.269000	0.26545	0.240000	0.18042	0.581000	0.29539	0.551000	0.68910	GAG	G|0.600;C|0.400	0.400	strong		0.333	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909	
SEC16B	89866	hgsc.bcm.edu	37	1	177902725	177902725	+	Missense_Mutation	SNP	C	C	T	rs3813649	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177902725C>T	ENST00000308284.6	-	21	2707	c.2618G>A	c.(2617-2619)aGt>aAt	p.S873N	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	873			S -> N (in dbSNP:rs3813649). {ECO:0000269|PubMed:17974005}.		COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CTTGGCTGAACTGGCGGAACT	0.478													T|||	1098	0.219249	0.2352	0.2594	5008	,	,		19789	0.1052		0.2604	False		,,,				2504	0.2444				p.S873N		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2618A						PASS	.	T	ASN/SER	985,2803		117,751,1026	74.0	73.0	74.0		2618	-10.2	0.0	1	dbSNP_107	74	1950,6310		237,1476,2417	yes	missense	SEC16B	NM_033127.2	46	354,2227,3443	TT,TC,CC		23.6077,26.0032,24.3609	benign	873/1061	177902725	2935,9113	1894	4130	6024	SO:0001583	missense	89866	exon21			GCTGAACTGGCGG	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2618G>A	1.37:g.177902725C>T	ENSP00000308339:p.Ser873Asn	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	168	89	0.529762	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	450	0.20604395604395603	96	0.1951219512195122	90	0.24861878453038674	71	0.12412587412587413	193	0.2546174142480211	T	3.674	-0.066930	0.07273	0.260032	0.236077	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.14022	2.54	5.11	-10.2	0.00374	.	3.603110	0.00508	N	0.000175	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.25433	-1.0132	9	0.15952	T	0.53	15.6611	2.8549	0.05569	0.1716:0.1967:0.404:0.2277	rs3813649;rs52834956;rs3813649	428;874;873;570	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	N	873;557;588	ENSP00000308339:S873N	ENSP00000239472:S588N	S	-	2	0	AL359075.1	176169348	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.654000	0.01984	-4.241000	0.00062	-3.232000	0.00051	AGT	C|0.799;T|0.201	0.201	strong		0.478	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
ABCB5	340273	hgsc.bcm.edu	37	7	20762646	20762646	+	Missense_Mutation	SNP	G	G	T	rs62453384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:20762646G>T	ENST00000404938.2	+	21	3081	c.2429G>T	c.(2428-2430)gGt>gTt	p.G810V	ABCB5_ENST00000258738.6_Missense_Mutation_p.G365V	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	810	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						TAGGCAACAGGTTCCAGGATT	0.353													G|||	1163	0.232228	0.1142	0.1945	5008	,	,		16136	0.1855		0.3608	False		,,,				2504	0.3344				p.G810V		Atlas-SNP	.											ABCB5,NS,carcinoma,+1,1	ABCB5	357	1	0			c.G2429T						PASS	.	G	VAL/GLY,VAL/GLY	621,3785	268.0+/-268.2	47,527,1629	142.0	138.0	140.0		2429,1094	3.8	1.0	7	dbSNP_129	140	3269,5331	489.7+/-372.7	606,2057,1637	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	109,109	653,2584,3266	TT,TG,GG		38.0116,14.0944,29.9093	possibly-damaging,possibly-damaging	810/1258,365/813	20762646	3890,9116	2203	4300	6503	SO:0001583	missense	340273	exon21			CAACAGGTTCCAG	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2429G>T	7.37:g.20762646G>T	ENSP00000384881:p.Gly810Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	515	0.2358058608058608	56	0.11382113821138211	84	0.23204419889502761	116	0.20279720279720279	259	0.341688654353562	G	17.37	3.371456	0.61624	0.140944	0.380116	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90900	-2.75;-2.75	4.75	3.84	0.44239	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.224289	0.30401	N	0.009703	T	0.00012	0.0000	M	0.91300	3.195	0.09310	P	0.9999999509414	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.992	T	0.00000	-1.5246	9	0.87932	D	0	.	12.6345	0.56675	0.0:0.1751:0.8249:0.0	rs62453384	810;365	A7BKA4;Q2M3G0	.;ABCB5_HUMAN	V	810;365	ENSP00000384881:G810V;ENSP00000258738:G365V	ENSP00000258738:G365V	G	+	2	0	ABCB5	20729171	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	3.961000	0.56759	1.318000	0.45170	0.655000	0.94253	GGT	G|0.714;T|0.286	0.286	strong		0.353	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
SULT2B1	6820	hgsc.bcm.edu	37	19	49102599	49102599	+	Missense_Mutation	SNP	C	C	T	rs17842463	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49102599C>T	ENST00000201586.2	+	7	1212	c.1034C>T	c.(1033-1035)cCc>cTc	p.P345L	SULT2B1_ENST00000323090.4_Missense_Mutation_p.P330L	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	345	Pro/Ser-rich.		P -> L (in dbSNP:rs17842463).		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		GAGcccagacccaactccagc	0.662													C|||	43	0.00858626	0.0	0.0187	5008	,	,		10930	0.0		0.0278	False		,,,				2504	0.002				p.P345L		Atlas-SNP	.											.	SULT2B1	72	.	0			c.C1034T						PASS	.	C	LEU/PRO,LEU/PRO	10,4364		0,10,2177	28.0	20.0	23.0		989,1034	1.8	0.0	19	dbSNP_126	23	160,8420		0,160,4130	yes	missense,missense	SULT2B1	NM_004605.2,NM_177973.1	98,98	0,170,6307	TT,TC,CC		1.8648,0.2286,1.3123	probably-damaging,probably-damaging	330/351,345/366	49102599	170,12784	2187	4290	6477	SO:0001583	missense	6820	exon7			CCAGACCCAACTC	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.1034C>T	19.37:g.49102599C>T	ENSP00000201586:p.Pro345Leu	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	276	149	0.539855	NM_177973	O00205|O75814	Missense_Mutation	SNP	ENST00000201586.2	37	CCDS12723.1	30	0.013736263736263736	0	0.0	8	0.022099447513812154	0	0.0	22	0.029023746701846966	C	13.73	2.323169	0.41096	0.002286	0.018648	ENSG00000088002	ENST00000201586;ENST00000323090	T;T	0.58060	0.36;0.36	1.83	1.83	0.25207	.	.	.	.	.	T	0.29223	0.0727	N	0.19112	0.55	0.09310	N	0.999999	D;D	0.76494	0.999;0.999	D;D	0.76575	0.988;0.972	T	0.18304	-1.0341	9	0.87932	D	0	.	7.3051	0.26443	0.0:1.0:0.0:0.0	rs17842463;rs45514997;rs58865188	330;345	O00204-2;O00204	.;ST2B1_HUMAN	L	345;330	ENSP00000201586:P345L;ENSP00000312880:P330L	ENSP00000201586:P345L	P	+	2	0	SULT2B1	53794411	0.000000	0.05858	0.020000	0.16555	0.052000	0.14988	-0.366000	0.07563	0.702000	0.31825	0.454000	0.30748	CCC	C|0.989;T|0.011	0.011	strong		0.662	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
NPC1	4864	hgsc.bcm.edu	37	18	21124945	21124945	+	Missense_Mutation	SNP	C	C	G	rs1788799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21124945C>G	ENST00000269228.5	-	12	2480	c.1926G>C	c.(1924-1926)atG>atC	p.M642I	NPC1_ENST00000412552.2_Missense_Mutation_p.M324I|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	642	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.		M -> I (in dbSNP:rs1788799). {ECO:0000269|PubMed:11479732, ECO:0000269|PubMed:11754101, ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:12408188, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15774455, ECO:0000269|PubMed:16098014, ECO:0000269|PubMed:9211849}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GACAGCTTTTCATGTGCCCCA	0.438													G|||	4165	0.831669	0.9607	0.7795	5008	,	,		13605	0.9226		0.6521	False		,,,				2504	0.7853				p.M642I		Atlas-SNP	.											.	NPC1	114	.	0			c.G1926C						PASS	.	G	ILE/MET	4008,398	200.4+/-223.7	1820,368,15	71.0	68.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1926	5.9	1.0	18	dbSNP_89	69	5547,3053	468.5+/-367.3	1805,1937,558	yes	missense	NPC1	NM_000271.4	10	3625,2305,573	GG,GC,CC		35.5,9.0331,26.5339	benign	642/1279	21124945	9555,3451	2203	4300	6503	SO:0001583	missense	4864	exon12			GCTTTTCATGTGC	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1926G>C	18.37:g.21124945C>G	ENSP00000269228:p.Met642Ile	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	117	31	0.264957	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	1787	0.8182234432234432	472	0.959349593495935	277	0.7651933701657458	536	0.9370629370629371	502	0.662269129287599	G	6.557	0.470967	0.12461	0.909669	0.645	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.92348	-3.02;-2.93	5.91	5.91	0.95273	Sterol-sensing domain (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00389	-1.56	0.53005	P	3.399999999997849E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43861	-0.9365	9	0.02654	T	1	-28.8558	7.8687	0.29552	0.1345:0.1368:0.7287:0.0	rs1788799;rs17797480;rs17855818;rs58087863;rs1788799	653;642	Q59GR1;O15118	.;NPC1_HUMAN	I	642;324;487	ENSP00000269228:M642I;ENSP00000408606:M324I	ENSP00000269228:M642I	M	-	3	0	NPC1	19378943	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.301000	0.51842	1.514000	0.48869	-0.120000	0.15030	ATG	.	.	none		0.438	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
UGT2A1	10941	hgsc.bcm.edu	37	4	70460328	70460328	+	Missense_Mutation	SNP	C	C	T	rs4148304	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70460328C>T	ENST00000503640.1	-	5	1226	c.1171G>A	c.(1171-1173)Gtt>Att	p.V391I	UGT2A1_ENST00000286604.4_Missense_Mutation_p.V391I|UGT2A2_ENST00000457664.2_Missense_Mutation_p.V400I|UGT2A1_ENST00000514019.1_Missense_Mutation_p.V557I|UGT2A1_ENST00000502343.1_5'UTR|UGT2A1_ENST00000512704.1_Missense_Mutation_p.V347I	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	391			V -> I (in dbSNP:rs4148304). {ECO:0000269|PubMed:14702039}.		cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.V391I(1)|p.V400I(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						AACATGGGAACTCCCACCATA	0.448													c|||	593	0.118411	0.1256	0.1513	5008	,	,		17734	0.0288		0.17	False		,,,				2504	0.1247				p.V557I		Atlas-SNP	.											UGT2A1_ENST00000457664,NS,carcinoma,0,2	UGT2A1	131	2	2	Substitution - Missense(2)	prostate(2)	c.G1669A						PASS	.	T	ILE/VAL,ILE/VAL	453,3953	214.1+/-233.5	20,413,1770	115.0	98.0	104.0		1198,1171	-2.7	0.0	4	dbSNP_110	104	1506,7094	286.1+/-297.5	143,1220,2937	yes	missense,missense	UGT2A1,UGT2A2	NM_001105677.2,NM_006798.2	29,29	163,1633,4707	TT,TC,CC		17.5116,10.2814,15.0623	benign,benign	400/537,391/528	70460328	1959,11047	2203	4300	6503	SO:0001583	missense	10941	exon6			TGGGAACTCCCAC	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"""UDP glucuronosyltransferases"""	12542	protein-coding gene	gene with protein product		604716	"""UDP glycosyltransferase 2 family, polypeptide A1"", ""UDP glucuronosyltransferase 2 family, polypeptide A1"""			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.1171G>A	4.37:g.70460328C>T	ENSP00000424478:p.Val391Ile	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	301	153	0.508306	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	231	0.10576923076923077	44	0.08943089430894309	52	0.143646408839779	8	0.013986013986013986	127	0.16754617414248021	c	0.337	-0.952667	0.02285	0.102814	0.175116	ENSG00000173610	ENST00000457664;ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.33	4.53	-2.67	0.06059	.	0.590343	0.17077	N	0.187942	T	0.00039	0.0001	N	0.00510	-1.415	.	.	.	B;B;B;B	0.17268	0.021;0.003;0.006;0.014	B;B;B;B	0.16722	0.014;0.015;0.005;0.016	T	0.10753	-1.0616	9	0.02654	T	1	.	7.051	0.25073	0.0:0.3199:0.1282:0.5519	rs4148304;rs4148304	557;347;400;391	E9PDM7;D6RFW5;Q9Y4X1-2;Q9Y4X1	.;.;.;UD2A1_HUMAN	I	400;391;347;557;391	ENSP00000387888:V400I;ENSP00000424478:V391I;ENSP00000421432:V347I;ENSP00000425497:V557I;ENSP00000286604:V391I	ENSP00000286604:V391I	V	-	1	0	UGT2A1	70494917	0.051000	0.20477	0.001000	0.08648	0.944000	0.59088	0.340000	0.19892	-0.819000	0.04323	-0.133000	0.14855	GTT	C|0.876;T|0.124	0.124	strong		0.448	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
NUP210L	91181	hgsc.bcm.edu	37	1	154072601	154072601	+	Missense_Mutation	SNP	G	G	A	rs139838869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154072601G>A	ENST00000368559.3	-	14	1909	c.1838C>T	c.(1837-1839)cCa>cTa	p.P613L	NUP210L_ENST00000271854.3_Missense_Mutation_p.P613L	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	613					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			ACAATGCATTGGTCCAGGTCT	0.468													G|||	35	0.00698882	0.0	0.0101	5008	,	,		20531	0.0		0.0199	False		,,,				2504	0.0082				p.P613L		Atlas-SNP	.											.	NUP210L	181	.	0			c.C1838T						PASS	.	G	LEU/PRO,LEU/PRO	24,3820		0,24,1898	149.0	139.0	142.0		1838,1838	4.2	0.0	1	dbSNP_134	142	204,8072		3,198,3937	yes	missense,missense	NUP210L	NM_001159484.1,NM_207308.2	98,98	3,222,5835	AA,AG,GG		2.465,0.6243,1.8812	benign,benign	613/1737,613/1889	154072601	228,11892	1922	4138	6060	SO:0001583	missense	91181	exon14			TGCATTGGTCCAG	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.1838C>T	1.37:g.154072601G>A	ENSP00000357547:p.Pro613Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	173	104	0.601156	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	8.733	0.917097	0.17907	0.006243	0.02465	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.07567	3.43;3.18	5.15	4.24	0.50183	.	0.900642	0.09517	N	0.791444	T	0.02767	0.0083	L	0.58101	1.795	0.09310	N	1	B;B	0.28713	0.22;0.1	B;B	0.25140	0.058;0.036	T	0.46275	-0.9203	10	0.11485	T	0.65	-21.3824	8.695	0.34289	0.0832:0.1513:0.7655:0.0	.	613;613	E7EP56;Q5VU65	.;P210L_HUMAN	L	613	ENSP00000357547:P613L;ENSP00000271854:P613L	ENSP00000271854:P613L	P	-	2	0	NUP210L	152339225	0.346000	0.24844	0.019000	0.16419	0.774000	0.43823	1.068000	0.30629	1.162000	0.42619	0.462000	0.41574	CCA	G|0.986;A|0.014	0.014	strong		0.468	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
FILIP1L	11259	hgsc.bcm.edu	37	3	99643176	99643176	+	Missense_Mutation	SNP	C	C	T	rs793440	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:99643176C>T	ENST00000354552.3	-	4	973	c.503G>A	c.(502-504)cGt>cAt	p.R168H	CMSS1_ENST00000421999.2_Intron|CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000398326.2_Missense_Mutation_p.R168H|FILIP1L_ENST00000331335.5_Missense_Mutation_p.R168H	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	168			R -> H (in dbSNP:rs793440). {ECO:0000269|Ref.3, ECO:0000269|Ref.4}.			cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						GGTTTGCCTACGGGATTTTTC	0.373													T|||	1269	0.253395	0.1558	0.3545	5008	,	,		19145	0.1954		0.3111	False		,,,				2504	0.3139				p.R168H		Atlas-SNP	.											.	FILIP1L	154	.	0			c.G503A						PASS	.	T	HIS/ARG,,HIS/ARG	713,2967		61,591,1188	248.0	227.0	233.0		503,,503	5.5	0.9	3	dbSNP_86	233	2720,5448		463,1794,1827	yes	missense,intron,missense	FILIP1L,C3orf26	NM_001042459.1,NM_032359.3,NM_182909.2	29,,29	524,2385,3015	TT,TC,CC		33.3007,19.375,28.9754	benign,,benign	168/1134,,168/1136	99643176	3433,8415	1840	4084	5924	SO:0001583	missense	11259	exon4			TGCCTACGGGATT		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"""downregulated in ovarian cancer 1"", ""GPBP-interacting protein of 130 kDa"""	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.503G>A	3.37:g.99643176C>T	ENSP00000346560:p.Arg168His	Somatic	376	1	0.00265957		WXS	Illumina HiSeq	Phase_I	383	203	0.530026	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Missense_Mutation	SNP	ENST00000354552.3	37	CCDS43117.1	527	0.2413003663003663	80	0.16260162601626016	120	0.3314917127071823	80	0.13986013986013987	247	0.3258575197889182	T	4.956	0.177581	0.09443	0.19375	0.333007	ENSG00000168386	ENST00000354552;ENST00000331335;ENST00000398326	T;T;T	0.41400	1.0;1.0;1.0	5.5	5.5	0.81552	Cortactin-binding protein-2, N-terminal (1);	0.277746	0.25073	N	0.033358	T	0.00012	0.0000	N	0.00030	-2.605	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38112	-0.9676	9	0.02654	T	1	-5.2185	11.5161	0.50522	0.0:0.0703:0.0:0.9297	rs793440;rs1680276;rs17379418;rs52794044;rs60414686;rs793440	168;168	Q4L180-2;Q4L180	.;FIL1L_HUMAN	H	168	ENSP00000346560:R168H;ENSP00000327880:R168H;ENSP00000381371:R168H	ENSP00000327880:R168H	R	-	2	0	FILIP1L	101125866	1.000000	0.71417	0.927000	0.36925	0.478000	0.33099	5.664000	0.68045	0.931000	0.37242	-0.352000	0.07741	CGT	C|0.763;T|0.237	0.237	strong		0.373	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890	
PAQR8	85315	hgsc.bcm.edu	37	6	52268890	52268890	+	Silent	SNP	G	G	A	rs17591381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:52268890G>A	ENST00000442253.2	+	2	1053	c.879G>A	c.(877-879)acG>acA	p.T293T	PAQR8_ENST00000360726.3_Silent_p.T293T	NM_133367.4	NP_588608.1	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member VIII	293					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(2)	17	Lung NSC(77;0.0875)					CCATCTGTACGCTCTCCCAGC	0.587													G|||	495	0.0988419	0.0068	0.1225	5008	,	,		22026	0.0744		0.164	False		,,,				2504	0.1646				p.T293T		Atlas-SNP	.											.	PAQR8	31	.	0			c.G879A						PASS	.	G		184,4222	117.1+/-155.0	5,174,2024	84.0	81.0	82.0		879	-3.9	0.9	6	dbSNP_123	82	1443,7157	276.7+/-292.4	128,1187,2985	no	coding-synonymous	PAQR8	NM_133367.4		133,1361,5009	AA,AG,GG		16.7791,4.1761,12.5096		293/355	52268890	1627,11379	2203	4300	6503	SO:0001819	synonymous_variant	85315	exon2			CTGTACGCTCTCC	AF347029	CCDS4941.1	6p12	2012-08-10	2005-05-20	2005-05-20	ENSG00000170915	ENSG00000170915			15708	protein-coding gene	gene with protein product		607780	"""chromosome 6 open reading frame 33"""	C6orf33		11676489, 12574519	Standard	NM_133367		Approved	LMPB1, MPRB	uc003pao.4	Q8TEZ7	OTTHUMG00000014846	ENST00000442253.2:c.879G>A	6.37:g.52268890G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	127	75	0.590551	NM_133367	B2RCF6|Q86WL0|Q8N6D3|Q9HD02	Silent	SNP	ENST00000442253.2	37	CCDS4941.1																																																																																			G|0.883;A|0.117	0.117	strong		0.587	PAQR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040903.2	NM_133367	
KCNH2	3757	hgsc.bcm.edu	37	7	150644428	150644428	+	Missense_Mutation	SNP	C	C	A	rs36210421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150644428C>A	ENST00000262186.5	-	13	3541	c.3140G>T	c.(3139-3141)cGc>cTc	p.R1047L	KCNH2_ENST00000392968.2_Missense_Mutation_p.R951L|KCNH2_ENST00000330883.4_Missense_Mutation_p.R707L	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	1047					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GTTGAGCTGGCGCTGGAGGGC	0.716													C|||	45	0.00898562	0.0	0.0043	5008	,	,		8790	0.001		0.0378	False		,,,				2504	0.0031				p.R1047L	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.G3140T	GRCh37	CM045797	KCNH2	M	rs36210421	PASS	.	C	LEU/ARG,LEU/ARG	16,3806		0,16,1895	5.0	7.0	6.0		3140,2120	4.1	1.0	7	dbSNP_126	6	139,7661		0,139,3761	no	missense,missense	KCNH2	NM_000238.3,NM_172057.2	102,102	0,155,5656	AA,AC,CC		1.7821,0.4186,1.3337	possibly-damaging,possibly-damaging	1047/1160,707/820	150644428	155,11467	1911	3900	5811	SO:0001583	missense	3757	exon13			AGCTGGCGCTGGA	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.3140G>T	7.37:g.150644428C>A	ENSP00000262186:p.Arg1047Leu	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	15	10	0.666667	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	C	19.00	3.741960	0.69418	0.004186	0.017821	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186	D;D;D	0.87256	-2.23;-2.23;-2.23	4.97	4.09	0.47781	.	0.140191	0.45867	D	0.000324	T	0.52500	0.1738	L	0.40543	1.245	0.80722	D	1	B;B;B	0.22146	0.039;0.039;0.065	B;B;B	0.23275	0.028;0.02;0.045	T	0.64922	-0.6293	10	0.36615	T	0.2	.	7.6627	0.28413	0.0:0.8092:0.0:0.1908	rs36210421;rs41313758	951;1047;707	C4PFH9;Q12809;Q12809-2	.;KCNH2_HUMAN;.	L	707;951;1047	ENSP00000328531:R707L;ENSP00000376695:R951L;ENSP00000262186:R1047L	ENSP00000262186:R1047L	R	-	2	0	KCNH2	150275361	0.000000	0.05858	0.998000	0.56505	0.966000	0.64601	-0.090000	0.11163	1.094000	0.41399	0.555000	0.69702	CGC	C|0.983;A|0.017	0.017	strong		0.716	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
OR2M2	391194	hgsc.bcm.edu	37	1	248343945	248343945	+	Missense_Mutation	SNP	C	C	G	rs4244171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248343945C>G	ENST00000359682.2	+	1	658	c.658C>G	c.(658-660)Cga>Gga	p.R220G		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	220			R -> G (in dbSNP:rs4244171).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TTCCTATGCTCGAGTTATTCT	0.438													c|||	2878	0.574681	0.6051	0.6037	5008	,	,		22034	0.4306		0.6382	False		,,,				2504	0.5961				p.R220G		Atlas-SNP	.											OR2M2,NS,adenoma,0,1	OR2M2	149	1	0			c.C658G						PASS	.	C	GLY/ARG	2575,1831		801,973,429	199.0	183.0	189.0		658	-2.0	0.0	1	dbSNP_111	189	5443,3155		1823,1797,679	no	missense	OR2M2	NM_001004688.1	125	2624,2770,1108	GG,GC,CC		36.6946,41.557,38.342	probably-damaging	220/348	248343945	8018,4986	2203	4299	6502	SO:0001583	missense	391194	exon1			TATGCTCGAGTTA	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"""GPCR / Class A : Olfactory receptors"""	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.658C>G	1.37:g.248343945C>G	ENSP00000352710:p.Arg220Gly	Somatic	453	0	0		WXS	Illumina HiSeq	Phase_I	322	320	0.993789	NM_001004688	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	1111	0.5086996336996337	250	0.508130081300813	201	0.5552486187845304	220	0.38461538461538464	440	0.5804749340369393	c	6.844	0.524908	0.13066	0.58443	0.633054	ENSG00000198601	ENST00000359682	T	0.00123	8.7	2.03	-2.0	0.07433	GPCR, rhodopsin-like superfamily (1);	1.563310	0.05152	U	0.496260	T	0.00012	0.0000	M	0.70275	2.135	0.80722	P	0.0	D	0.55385	0.971	P	0.58391	0.838	T	0.16217	-1.0410	9	0.26408	T	0.33	.	3.4291	0.07421	0.1778:0.45:0.0:0.3722	rs4244171;rs59366045	220	Q96R28	OR2M2_HUMAN	G	220	ENSP00000352710:R220G	ENSP00000352710:R220G	R	+	1	2	OR2M2	246410568	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.965000	0.03829	-0.160000	0.11002	0.454000	0.30748	CGA	C|0.400;G|0.600	0.600	strong		0.438	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688	
NUBPL	80224	hgsc.bcm.edu	37	14	32319354	32319354	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:32319354G>T	ENST00000281081.7	+	10	889	c.844G>T	c.(844-846)Gaa>Taa	p.E282*	NUBPL_ENST00000536705.1_Nonsense_Mutation_p.E186*|NUBPL_ENST00000418681.2_3'UTR	NM_001201573.1|NM_001201574.1|NM_025152.2	NP_001188502.1|NP_001188503.1|NP_079428.2	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like	282					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrion morphogenesis (GO:0070584)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		TAATATAAGGGAAGCTTCAGA	0.358																																					p.E282X		Atlas-SNP	.											.	NUBPL	21	.	0			c.G844T						PASS	.						95.0	89.0	91.0					14																	32319354		1811	4084	5895	SO:0001587	stop_gained	80224	exon10			ATAAGGGAAGCTT	AK022722	CCDS41940.1	14q12	2012-10-12	2005-01-07	2005-01-07	ENSG00000151413	ENSG00000151413		"""Mitochondrial respiratory chain complex assembly factors"""	20278	protein-coding gene	gene with protein product	"""iron-sulfur protein required for NADH dehydrogenase"""	613621	"""chromosome 14 open reading frame 127"""	C14orf127			Standard	NM_025152		Approved	FLJ12660, IND1, huInd1	uc001wrk.4	Q8TB37	OTTHUMG00000170521	ENST00000281081.7:c.844G>T	14.37:g.32319354G>T	ENSP00000281081:p.Glu282*	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	138	10	0.0724638	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Nonsense_Mutation	SNP	ENST00000281081.7	37	CCDS41940.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524580	0.85600	.	.	ENSG00000151413	ENST00000550649;ENST00000281081;ENST00000536705	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-10.7882	18.1531	0.89682	0.0:0.0:1.0:0.0	.	.	.	.	X	148;282;186	.	ENSP00000281081:E282X	E	+	1	0	NUBPL	31389105	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	4.773000	0.62331	2.885000	0.99019	0.655000	0.94253	GAA	.	.	none		0.358	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152	
PLEKHG3	26030	hgsc.bcm.edu	37	14	65208026	65208026	+	Silent	SNP	T	T	C	rs229650	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:65208026T>C	ENST00000394691.1	+	16	1938	c.1791T>C	c.(1789-1791)tcT>tcC	p.S597S	PLEKHG3_ENST00000247226.7_Silent_p.S541S|PLEKHG3_ENST00000484731.2_Silent_p.S102S|PLEKHG3_ENST00000471182.2_Silent_p.S130S			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	597							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		TGCCACCCTCTGTGCTGGACC	0.617													C|||	1154	0.230431	0.4002	0.1499	5008	,	,		19780	0.0367		0.2147	False		,,,				2504	0.274				p.S541S		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.T1623C						PASS	.	C		1611,2795	659.7+/-400.6	300,1011,892	61.0	57.0	59.0		1623	-6.9	0.4	14	dbSNP_79	59	1978,6622	721.7+/-406.4	214,1550,2536	no	coding-synonymous	PLEKHG3	NM_015549.1		514,2561,3428	CC,CT,TT		23.0,36.5638,27.595		541/1164	65208026	3589,9417	2203	4300	6503	SO:0001819	synonymous_variant	26030	exon14			ACCCTCTGTGCTG	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20364	protein-coding gene	gene with protein product			"""KIAA0599"""	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.1791T>C	14.37:g.65208026T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Silent	SNP	ENST00000394691.1	37																																																																																				T|0.756;C|0.244	0.244	strong		0.617	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549	
EPHA8	2046	hgsc.bcm.edu	37	1	22915753	22915753	+	Intron	SNP	T	T	C	rs606002	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22915753T>C	ENST00000166244.3	+	5	1387				EPHA8_ENST00000374644.4_Missense_Mutation_p.S457P|EPHA8_ENST00000538803.1_Missense_Mutation_p.S457P	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTCCCCTGCCTCAGACCCATC	0.672													C|||	2413	0.481829	0.7126	0.3761	5008	,	,		17459	0.2907		0.3777	False		,,,				2504	0.5491				p.S457P		Atlas-SNP	.											.	EPHA8	221	.	0			c.T1369C						PASS	.	C	PRO/SER,	2884,1520	454.2+/-350.6	938,1008,256	34.0	36.0	36.0		1369,	-0.5	0.0	1	dbSNP_83	36	3067,5533	632.9+/-398.7	536,1995,1769	yes	missense,intron	EPHA8	NM_001006943.1,NM_020526.3	74,	1474,3003,2025	CC,CT,TT		35.6628,34.5141,45.7628	,	457/496,	22915753	5951,7053	2202	4300	6502	SO:0001627	intron_variant	2046	exon5			CCTGCCTCAGACC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1315+54T>C	1.37:g.22915753T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001006943	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	931	0.42628205128205127	338	0.6869918699186992	141	0.38950276243093923	167	0.291958041958042	285	0.3759894459102902	C	7.448	0.641996	0.14451	0.654859	0.356628	ENSG00000070886	ENST00000374644;ENST00000538803	T;T	0.01335	5.0;5.0	1.67	-0.495	0.12030	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02950	-1.1090	6	.	.	.	.	2.7548	0.05290	0.0:0.3927:0.2509:0.3564	rs606002;rs61099646;rs606002	457	P29322-2	.	P	457	ENSP00000363775:S457P;ENSP00000440274:S457P	.	S	+	1	0	EPHA8	22788340	0.001000	0.12720	0.000000	0.03702	0.029000	0.11900	-0.993000	0.03720	-0.528000	0.06366	-0.971000	0.02607	TCA	T|0.543;C|0.457	0.457	strong		0.672	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
PKD1L2	114780	hgsc.bcm.edu	37	16	81253759	81253759	+	RNA	SNP	A	A	G	rs9924371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81253759A>G	ENST00000525539.1	-	0	216				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGCAGAAACCACTGGGTGCCT	0.572													G|||	2677	0.534545	0.5983	0.562	5008	,	,		22265	0.4405		0.6511	False		,,,				2504	0.4059				p.W73R		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T217C						PASS	.	G	ARG/TRP,ARG/TRP	2615,1463		849,917,273	103.0	101.0	101.0		217,217	-0.1	0.0	16	dbSNP_119	101	5314,3088		1668,1978,555	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	101,101	2517,2895,828	GG,GA,AA		36.7532,35.8754,36.4663	benign,benign	73/992,73/2460	81253759	7929,4551	2039	4201	6240			114780	exon1			GAAACCACTGGGT	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81253759A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	157	73	0.464968	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1248	0.5714285714285714	298	0.6056910569105691	225	0.6215469613259669	233	0.40734265734265734	492	0.6490765171503958	G	0.003	-2.430925	0.00184	0.641246	0.632468	ENSG00000166473	ENST00000337114	T	0.16597	2.33	4.17	-0.109	0.13584	C-type lectin fold (1);C-type lectin (3);	0.543965	0.16764	N	0.200499	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34329	-0.9833	8	0.15499	T	0.54	0.6019	0.212	0.00157	0.2358:0.2029:0.2363:0.3249	rs9924371;rs58449243;rs9924371	73;73	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	R	73	ENSP00000337397:W73R	ENSP00000337397:W73R	W	-	1	0	PKD1L2	79811260	0.984000	0.35163	0.022000	0.16811	0.214000	0.24535	0.397000	0.20883	-0.436000	0.07254	-0.930000	0.02707	TGG	A|0.425;G|0.575	0.575	strong		0.572	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
LRP6	4040	hgsc.bcm.edu	37	12	12334006	12334006	+	Silent	SNP	G	G	C	rs10082834	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:12334006G>C	ENST00000261349.4	-	6	1420	c.1344C>G	c.(1342-1344)ccC>ccG	p.P448P	LRP6_ENST00000543091.1_Silent_p.P448P	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	448	Beta-propeller 2.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CAATAGCCCGGGGTTCCTCTA	0.428													.|||	244	0.048722	0.0212	0.147	5008	,	,		20171	0.002		0.0815	False		,,,				2504	0.0307				p.P448P		Atlas-SNP	.											.	LRP6	170	.	0			c.C1344G						PASS	.	G		168,4238	109.1+/-147.4	4,160,2039	68.0	66.0	66.0		1344	2.8	1.0	12	dbSNP_119	66	777,7821	180.3+/-229.3	40,697,3562	no	coding-synonymous	LRP6	NM_002336.2		44,857,5601	CC,CG,GG		9.037,3.813,7.267		448/1614	12334006	945,12059	2203	4299	6502	SO:0001819	synonymous_variant	4040	exon6			AGCCCGGGGTTCC	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.1344C>G	12.37:g.12334006G>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																			G|0.935;C|0.065	0.065	strong		0.428	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
ZBBX	79740	hgsc.bcm.edu	37	3	167051769	167051769	+	Missense_Mutation	SNP	T	T	C	rs11923054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167051769T>C	ENST00000392766.2	-	10	873	c.533A>G	c.(532-534)aAa>aGa	p.K178R	ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000307529.5_Missense_Mutation_p.K178R|ZBBX_ENST00000392764.1_Missense_Mutation_p.K149R|ZBBX_ENST00000392767.2_Missense_Mutation_p.K178R|ZBBX_ENST00000455345.2_Missense_Mutation_p.K178R	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	178			K -> R (in dbSNP:rs11923054).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TATTTGAGATTTTGCCTATTA	0.289													T|||	1283	0.25619	0.0711	0.3343	5008	,	,		14277	0.1786		0.4115	False		,,,				2504	0.3712				p.K178R		Atlas-SNP	.											.	ZBBX	299	.	0			c.A533G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	457,3111		29,399,1356	62.0	55.0	57.0		533,446,533	1.1	1.0	3	dbSNP_120	57	3454,4662		724,2006,1328	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	26,26,26	753,2405,2684	CC,CT,TT		42.5579,12.8083,33.4731	probably-damaging,probably-damaging,probably-damaging	178/840,149/772,178/801	167051769	3911,7773	1784	4058	5842	SO:0001583	missense	79740	exon10			TGAGATTTTGCCT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.533A>G	3.37:g.167051769T>C	ENSP00000376519:p.Lys178Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	88	24	0.272727	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	586	0.2683150183150183	50	0.1016260162601626	128	0.35359116022099446	101	0.17657342657342656	307	0.4050131926121372	T	7.602	0.673020	0.14776	0.128083	0.425579	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	4.79	1.08	0.20341	.	0.000000	0.34025	U	0.004322	T	0.00012	0.0000	L	0.59436	1.845	0.40911	P	0.015764	B;B	0.28552	0.215;0.064	B;B	0.28991	0.097;0.02	T	0.45716	-0.9242	9	0.34782	T	0.22	-17.7062	6.8506	0.24012	0.0:0.3027:0.0:0.6973	rs11923054;rs17853282;rs52807714;rs58791197;rs11923054	178;178	A8MT70-2;A8MT70	.;ZBBX_HUMAN	R	178;178;178;178;149	ENSP00000376519:K178R;ENSP00000376520:K178R;ENSP00000390232:K178R;ENSP00000305065:K178R;ENSP00000376517:K149R	ENSP00000305065:K178R	K	-	2	0	ZBBX	168534463	1.000000	0.71417	0.999000	0.59377	0.382000	0.30200	1.631000	0.37092	0.287000	0.22375	-0.256000	0.11100	AAA	T|0.719;C|0.281	0.281	strong		0.289	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
PLA2G12A	81579	hgsc.bcm.edu	37	4	110638810	110638810	+	Silent	SNP	C	C	T	rs2285714	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110638810C>T	ENST00000243501.5	-	3	612	c.345G>A	c.(343-345)gaG>gaA	p.E115E	PLA2G12A_ENST00000502283.1_Silent_p.E113E|PLA2G12A_ENST00000502772.1_5'UTR	NM_030821.4	NP_110448.2	Q9BZM1	PG12A_HUMAN	phospholipase A2, group XIIA	115					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			kidney(1)|lung(1)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000268)		TGCCACAGGTCTCATAGCACC	0.438													C|||	1264	0.252396	0.0234	0.3703	5008	,	,		19834	0.2014		0.3926	False		,,,				2504	0.3865				p.E115E		Atlas-SNP	.											.	PLA2G12A	11	.	0			c.G345A						PASS	.	C		372,4034	188.1+/-214.6	14,344,1845	189.0	157.0	168.0	http://www.ncbi.nlm.nih.gov/pubmed?term	345	4.6	1.0	4	dbSNP_100	168	3717,4883	529.7+/-381.6	827,2063,1410	no	coding-synonymous	PLA2G12A	NM_030821.4		841,2407,3255	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	43.2209,8.443,31.4393		115/190	110638810	4089,8917	2203	4300	6503	SO:0001819	synonymous_variant	81579	exon3			ACAGGTCTCATAG		CCDS3686.1	4q25	2010-11-24	2004-01-13	2004-01-14	ENSG00000123739	ENSG00000123739	3.1.1.4		18554	protein-coding gene	gene with protein product		611652	"""phospholipase A2, group XII"""	PLA2G12		11031251	Standard	NM_030821		Approved		uc003hzp.3	Q9BZM1	OTTHUMG00000131915	ENST00000243501.5:c.345G>A	4.37:g.110638810C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	215	90	0.418605	NM_030821	Q9BZ89	Silent	SNP	ENST00000243501.5	37	CCDS3686.1																																																																																			C|0.718;T|0.282	0.282	strong		0.438	PLA2G12A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254868.3		
DSEL	92126	hgsc.bcm.edu	37	18	65179829	65179829	+	Missense_Mutation	SNP	G	G	A	rs2279269	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:65179829G>A	ENST00000310045.7	-	2	3520	c.2047C>T	c.(2047-2049)Ccc>Tcc	p.P683S	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	673					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				GTGATTGTGGGTTCCATCTGA	0.388													A|||	2181	0.435503	0.3041	0.4294	5008	,	,		18126	0.498		0.5686	False		,,,				2504	0.4162				p.P683S		Atlas-SNP	.											.	DSEL	196	.	0			c.C2047T						PASS	.	A	SER/PRO	1427,2979	682.4+/-404.1	245,937,1021	77.0	80.0	79.0		2047	2.9	1.0	18	dbSNP_100	79	4444,4156	566.2+/-388.6	1167,2110,1023	yes	missense	DSEL	NM_032160.2	74	1412,3047,2044	AA,AG,GG		48.3256,32.3877,45.1407	benign	683/1223	65179829	5871,7135	2203	4300	6503	SO:0001583	missense	92126	exon2			TTGTGGGTTCCAT	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2047C>T	18.37:g.65179829G>A	ENSP00000310565:p.Pro683Ser	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	1025	0.4693223443223443	132	0.2682926829268293	166	0.4585635359116022	294	0.513986013986014	433	0.5712401055408971	A	6.141	0.394297	0.11638	0.323877	0.516744	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.15139	2.45	5.4	2.92	0.33932	.	0.380247	0.25094	N	0.033200	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44802	-0.9304	9	0.02654	T	1	.	1.1721	0.01827	0.4319:0.244:0.0915:0.2326	rs2279269;rs52806269;rs56523437;rs58927058;rs2279269	673	Q8IZU8	DSEL_HUMAN	S	683;673	ENSP00000310565:P683S	ENSP00000310565:P683S	P	-	1	0	DSEL	63330809	0.888000	0.30383	0.987000	0.45799	0.671000	0.39405	1.602000	0.36783	0.905000	0.36596	-0.521000	0.04368	CCC	G|0.545;A|0.455	0.455	strong		0.388	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
RBM6	10180	hgsc.bcm.edu	37	3	50103917	50103917	+	Silent	SNP	G	G	A	rs2023953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50103917G>A	ENST00000266022.4	+	17	3184	c.2925G>A	c.(2923-2925)caG>caA	p.Q975Q	RBM6_ENST00000442092.1_Silent_p.Q453Q|RBM6_ENST00000422955.1_Silent_p.Q453Q|RBM6_ENST00000443081.1_Silent_p.Q843Q|RBM6_ENST00000421682.1_De_novo_Start_OutOfFrame|RBM6_ENST00000539992.1_Silent_p.Q317Q	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	975					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		AACACCAGCAGCTGTCAGACC	0.468													G|||	366	0.0730831	0.0514	0.1268	5008	,	,		16835	0.0516		0.1133	False		,,,				2504	0.045				p.Q975Q		Atlas-SNP	.											.	RBM6	85	.	0			c.G2925A						PASS	.	G	,	362,4044	186.0+/-213.0	9,344,1850	120.0	130.0	126.0		1359,2925	3.3	1.0	3	dbSNP_94	126	926,7674	205.6+/-248.0	48,830,3422	no	coding-synonymous,coding-synonymous	RBM6	NM_001167582.1,NM_005777.2	,	57,1174,5272	AA,AG,GG		10.7674,8.2161,9.9031	,	453/602,975/1124	50103917	1288,11718	2203	4300	6503	SO:0001819	synonymous_variant	10180	exon17			CCAGCAGCTGTCA	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.2925G>A	3.37:g.50103917G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	35	12	0.342857	NM_005777	O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	37	CCDS2809.1																																																																																			G|0.907;N|0.000	.	strong		0.468	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
DDX11	1663	hgsc.bcm.edu	37	12	31244716	31244716	+	Silent	SNP	C	C	T	rs35588475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:31244716C>T	ENST00000407793.2	+	10	1404	c.1153C>T	c.(1153-1155)Ctg>Ttg	p.L385L	DDX11_ENST00000350437.4_Silent_p.L385L|DDX11_ENST00000228264.6_Silent_p.L359L|DDX11_ENST00000545668.1_Silent_p.L385L|DDX11_ENST00000542838.1_Silent_p.L385L|DDX11_ENST00000251758.5_3'UTR	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	385	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GGGCATCCGGCTGCAGGACCA	0.677										Multiple Myeloma(12;0.14)																											p.L385L		Atlas-SNP	.											.	DDX11	188	.	0			c.C1153T						PASS	.						43.0	42.0	42.0					12																	31244716		2203	4298	6501	SO:0001819	synonymous_variant	1663	exon10			ATCCGGCTGCAGG	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1153C>T	12.37:g.31244716C>T		Somatic	624	0	0		WXS	Illumina HiSeq	Phase_I	640	202	0.315625	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																			T|1.000;|0.000	1.000	weak		0.677	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111545670	111545670	+	Missense_Mutation	SNP	C	C	G	rs890757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:111545670C>G	ENST00000261486.5	-	13	1373	c.1097G>C	c.(1096-1098)aGc>aCc	p.S366T	CTC-459M5.2_ENST00000505825.1_RNA|CTC-459M5.2_ENST00000506875.1_RNA|EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	366				S -> T (in Ref. 3; BAB17229). {ECO:0000305}.		cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		CCTACTGATGCTGTTTGATTC	0.343													C|||	3812	0.761182	0.5605	0.8055	5008	,	,		18587	0.9871		0.6928	False		,,,				2504	0.8384				p.S366T		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.G1097C						PASS	.	C	THR/SER	2322,1384		706,910,237	166.0	155.0	158.0		1097	4.1	0.6	5	dbSNP_86	158	5721,2467		2007,1707,380	yes	missense	EPB41L4A	NM_022140.3	58	2713,2617,617	GG,GC,CC		30.1295,37.3448,32.3777	benign	366/687	111545670	8043,3851	1853	4094	5947	SO:0001583	missense	64097	exon13			CTGATGCTGTTTG	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1097G>C	5.37:g.111545670C>G	ENSP00000261486:p.Ser366Thr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	179	76	0.424581	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	1667	0.7632783882783882	289	0.5873983739837398	278	0.7679558011049724	571	0.9982517482517482	529	0.6978891820580475	C	10.80	1.453922	0.26161	0.626552	0.698705	ENSG00000129595	ENST00000261486	D	0.82344	-1.6	5.87	4.08	0.47627	.	0.213084	0.50627	D	0.000116	T	0.00012	0.0000	N	0.14661	0.345	0.44092	P	0.0031480000000000397	B	0.12630	0.006	B	0.10450	0.005	T	0.38200	-0.9672	9	0.13470	T	0.59	.	10.9187	0.47152	0.0:0.8494:0.0:0.1506	rs890757;rs56484717;rs61090528;rs890757	366	Q9HCS5	E41LA_HUMAN	T	366	ENSP00000261486:S366T	ENSP00000261486:S366T	S	-	2	0	EPB41L4A	111573569	0.155000	0.22806	0.610000	0.28997	0.415000	0.31203	0.188000	0.17018	0.920000	0.36970	0.655000	0.94253	AGC	C|0.252;G|0.748	0.748	strong		0.343	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
KIF13A	63971	hgsc.bcm.edu	37	6	17764530	17764530	+	Silent	SNP	C	C	T	rs9371018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:17764530C>T	ENST00000259711.6	-	39	5334	c.5229G>A	c.(5227-5229)gaG>gaA	p.E1743E	KIF13A_ENST00000378814.5_Silent_p.E1695E|KIF13A_ENST00000378843.2_Silent_p.E1695E|KIF13A_ENST00000378816.5_Silent_p.E1708E|KIF13A_ENST00000378826.2_Silent_p.E1708E	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1743					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			AATCTTTTCCCTCTGACACTC	0.502													C|||	1517	0.302915	0.1006	0.3343	5008	,	,		18534	0.5347		0.3072	False		,,,				2504	0.3108				p.E1743E		Atlas-SNP	.											.	KIF13A	276	.	0			c.G5229A						PASS	.	C	,,,	453,3283		30,393,1445	64.0	60.0	61.0		5124,5085,5085,5229	-8.6	0.3	6	dbSNP_119	61	2572,5640		409,1754,1943	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	439,2147,3388	TT,TC,CC		31.32,12.1253,25.318	,,,	1708/1771,1695/1758,1695/1750,1743/1806	17764530	3025,8923	1868	4106	5974	SO:0001819	synonymous_variant	63971	exon39			TTTTCCCTCTGAC	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.5229G>A	6.37:g.17764530C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	178	77	0.432584	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			C|0.684;T|0.316	0.316	strong		0.502	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
TLK2	11011	hgsc.bcm.edu	37	17	60637441	60637441	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:60637441G>A	ENST00000326270.9	+	10	1053	c.785G>A	c.(784-786)cGa>cAa	p.R262Q	TLK2_ENST00000346027.5_Missense_Mutation_p.R262Q|TLK2_ENST00000343388.7_Missense_Mutation_p.R230Q|TLK2_ENST00000542523.1_Missense_Mutation_p.R230Q|TLK2_ENST00000582809.1_Missense_Mutation_p.R113Q	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	262			R -> Q. {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R262Q(17)|p.R261Q(9)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						TACAAGGAACGATTAAATAGA	0.358																																					p.R262Q		Atlas-SNP	.											TLK2_ENST00000346027,NS,carcinoma,0,31	TLK2	223	31	26	Substitution - Missense(26)	endometrium(15)|kidney(9)|central_nervous_system(2)	c.G785A						scavenged	.						72.0	74.0	73.0					17																	60637441		2203	4298	6501	SO:0001583	missense	11011	exon10			AGGAACGATTAAA	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.785G>A	17.37:g.60637441G>A	ENSP00000316512:p.Arg262Gln	Somatic	545	3	0.00550459		WXS	Illumina HiSeq	Phase_I	580	7	0.012069	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	37		.	.	.	.	.	.	.	.	.	.	G	17.31	3.356600	0.61293	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.66460	-0.16;-0.21;-0.13;-0.21	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.70474	0.3228	N	0.26092	0.79	0.80722	D	1	D;B;B;B	0.89917	1.0;0.369;0.031;0.135	D;B;B;B	0.85130	0.997;0.074;0.016;0.012	T	0.64896	-0.6299	10	0.17369	T	0.5	.	16.8221	0.85835	0.0:0.0:1.0:0.0	.	262;230;262;262	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	Q	262;230;262;230	ENSP00000275780:R262Q;ENSP00000340800:R230Q;ENSP00000316512:R262Q;ENSP00000442311:R230Q	ENSP00000316512:R262Q	R	+	2	0	TLK2	57991173	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.504000	0.97986	2.516000	0.84829	0.655000	0.94253	CGA	.	.	none		0.358	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852	
OSGIN1	29948	hgsc.bcm.edu	37	16	83999548	83999548	+	Missense_Mutation	SNP	T	T	C	rs62640905	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:83999548T>C	ENST00000343939.2	+	7	2002	c.1619T>C	c.(1618-1620)gTg>gCg	p.V540A	NECAB2_ENST00000305202.4_5'Flank|OSGIN1_ENST00000361711.3_Missense_Mutation_p.V457A|OSGIN1_ENST00000393306.1_Missense_Mutation_p.V457A			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	540					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						GTGAGGTTTGTGCAGGGGGGC	0.662													T|||	40	0.00798722	0.0	0.013	5008	,	,		17559	0.0		0.0278	False		,,,				2504	0.0031				p.V457A		Atlas-SNP	.											.	OSGIN1	33	.	0			c.T1370C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	14,4370		0,14,2178	14.0	15.0	15.0		1619,1370,1370	4.4	1.0	16	dbSNP_129	15	218,8354		5,208,4073	yes	missense,missense,missense	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	64,64,64	5,222,6251	CC,CT,TT		2.5432,0.3193,1.7907	possibly-damaging,possibly-damaging,possibly-damaging	540/561,457/478,457/478	83999548	232,12724	2192	4286	6478	SO:0001583	missense	29948	exon6			GGTTTGTGCAGGG	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.1619T>C	16.37:g.83999548T>C	ENSP00000343376:p.Val540Ala	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	57	20	0.350877	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	37		27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	T	16.86	3.238732	0.58995	0.003193	0.025432	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.37411	1.2;1.2;1.2	4.37	4.37	0.52481	.	0.065516	0.64402	D	0.000009	T	0.15739	0.0379	M	0.63428	1.95	0.80722	D	1	D	0.58268	0.982	B	0.44315	0.446	T	0.04811	-1.0925	10	0.24483	T	0.36	-26.2537	12.7349	0.57218	0.0:0.0:0.0:1.0	rs62640905	540	Q9UJX0	OSGI1_HUMAN	A	540;457;457	ENSP00000343376:V540A;ENSP00000355374:V457A;ENSP00000376983:V457A	ENSP00000343376:V540A	V	+	2	0	OSGIN1	82557049	1.000000	0.71417	0.954000	0.39281	0.681000	0.39784	7.645000	0.83430	1.606000	0.50161	0.260000	0.18958	GTG	T|0.985;C|0.015	0.015	strong		0.662	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
SEZ6	124925	hgsc.bcm.edu	37	17	27286750	27286750	+	Silent	SNP	G	G	A	rs9907950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:27286750G>A	ENST00000317338.12	-	8	2165	c.1737C>T	c.(1735-1737)gaC>gaT	p.D579D	SEZ6_ENST00000360295.9_Silent_p.D579D|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000442608.3_Silent_p.D579D|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	579	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			TCCACTGGGGGTCGTGGGGGT	0.602													G|||	709	0.141573	0.2632	0.1268	5008	,	,		18719	0.0506		0.1402	False		,,,				2504	0.0828				p.D579D		Atlas-SNP	.											SEZ6,NS,lymphoid_neoplasm,-2,1	SEZ6	61	1	0			c.C1737T						scavenged	.	G	,	933,3183		106,721,1231	50.0	53.0	52.0		1737,1737	-2.8	0.9	17	dbSNP_119	52	1159,7293		80,999,3147	no	coding-synonymous,coding-synonymous	SEZ6	NM_001098635.1,NM_178860.4	,	186,1720,4378	AA,AG,GG		13.7127,22.6676,16.6454	,	579/994,579/995	27286750	2092,10476	2058	4226	6284	SO:0001819	synonymous_variant	124925	exon8			CTGGGGGTCGTGG	AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"""seizure related gene 6 (mouse) homolog"""			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.1737C>T	17.37:g.27286750G>A		Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Silent	SNP	ENST00000317338.12	37	CCDS45639.1																																																																																			G|0.841;A|0.159	0.159	strong		0.602	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3		
NBAS	51594	hgsc.bcm.edu	37	2	15615910	15615910	+	Silent	SNP	A	A	G	rs1990754	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:15615910A>G	ENST00000281513.5	-	14	1267	c.1242T>C	c.(1240-1242)tcT>tcC	p.S414S	NBAS_ENST00000441750.1_Silent_p.S414S	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	414					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.S414S(1)		NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						AAGTTTTCACAGATGAAACAG	0.418													G|||	2468	0.492812	0.5174	0.6009	5008	,	,		13316	0.1696		0.6909	False		,,,				2504	0.5123				p.S414S		Atlas-SNP	.											NBAS,NS,carcinoma,0,2	NBAS	246	2	1	Substitution - coding silent(1)	stomach(1)	c.T1242C						PASS	.	G		2397,2009	558.9+/-380.1	634,1129,440	70.0	72.0	72.0		1242	-12.2	0.0	2	dbSNP_92	72	5879,2721	434.1+/-357.6	2010,1859,431	no	coding-synonymous	NBAS	NM_015909.2		2644,2988,871	GG,GA,AA		31.6395,45.5969,36.3678		414/2372	15615910	8276,4730	2203	4300	6503	SO:0001819	synonymous_variant	51594	exon14			TTTCACAGATGAA	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1242T>C	2.37:g.15615910A>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	259	127	0.490348	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			A|0.445;G|0.555	0.555	strong		0.418	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
NKX2-3	159296	hgsc.bcm.edu	37	10	101293035	101293035	+	Silent	SNP	C	C	A	rs41290504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:101293035C>A	ENST00000344586.7	+	1	346	c.147C>A	c.(145-147)gcC>gcA	p.A49A	RP11-129J12.2_ENST00000548010.1_RNA	NM_145285.2	NP_660328.2	Q8TAU0	NKX23_HUMAN	NK2 homeobox 3	49					CD4-positive, alpha-beta T cell differentiation (GO:0043367)|gland morphogenesis (GO:0022612)|leukocyte homeostasis (GO:0001776)|leukocyte migration (GO:0050900)|lymph node development (GO:0048535)|macrophage differentiation (GO:0030225)|odontogenesis of dentin-containing tooth (GO:0042475)|Peyer's patch development (GO:0048541)|plasma cell differentiation (GO:0002317)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic digestive tract morphogenesis (GO:0048621)|regulation of cell proliferation (GO:0042127)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)|triglyceride metabolic process (GO:0006641)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.45e-08)		TGCTGGCCGCCGCTGAGGGGA	0.592													A|||	2761	0.551318	0.5628	0.5994	5008	,	,		17122	0.5546		0.503	False		,,,				2504	0.5481				p.A49A	Pancreas(173;2021 2035 19403 19989 27291)	Atlas-SNP	.											NKX2-3,NS,carcinoma,0,1	NKX2-3	11	1	0			c.C147A						PASS	.	A		2326,1750		653,1020,365	32.0	37.0	35.0		147	-11.2	0.0	10	dbSNP_127	35	4376,4028		1130,2116,956	no	coding-synonymous	NKX2-3	NM_145285.2		1783,3136,1321	AA,AC,CC		47.9296,42.9342,46.2981		49/365	101293035	6702,5778	2038	4202	6240	SO:0001819	synonymous_variant	159296	exon1			GGCCGCCGCTGAG		CCDS41558.1	10q24.2	2013-09-20	2011-06-01	2002-10-04	ENSG00000119919	ENSG00000119919		"""Homeoboxes / ANTP class : NKL subclass"""	7836	protein-coding gene	gene with protein product		606727	"""NK-2 (Drosophila) homolog C"", ""NK2 transcription factor related, locus 3 (Drosophila)"""	NKX2C		1346742, 9142493	Standard	NM_145285		Approved	NKX2.3, CSX3, NKX4-3	uc009xwj.3	Q8TAU0	OTTHUMG00000018887	ENST00000344586.7:c.147C>A	10.37:g.101293035C>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_145285	B4DUZ4|Q9NYS6	Silent	SNP	ENST00000344586.7	37	CCDS41558.1																																																																																			C|0.494;A|0.506	0.506	strong		0.592	NKX2-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049808.2		
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1605992	1605992	+	Missense_Mutation	SNP	G	G	C	rs60899198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1605992G>C	ENST00000382171.2	-	1	521	c.488C>G	c.(487-489)tCc>tGc	p.S163C	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	163	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GGCCCCCTTGGAGCACCCACA	0.652													g|||	4	0.000798722	0.0	0.0014	5008	,	,		8301	0.002		0.0	False		,,,				2504	0.001				p.S163C		Atlas-SNP	.											KRTAP5-1,NS,carcinoma,0,1	KRTAP5-1	74	1	0			c.C488G						scavenged	.						69.0	84.0	79.0					11																	1605992		2202	4299	6501	SO:0001583	missense	387264	exon1			CCCTTGGAGCACC	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.488C>G	11.37:g.1605992G>C	ENSP00000371606:p.Ser163Cys	Somatic	248	12	0.0483871		WXS	Illumina HiSeq	Phase_I	259	20	0.0772201	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	-	2.030	-0.422638	0.04734	.	.	ENSG00000205869	ENST00000382171	T	0.04809	3.55	3.69	-5.66	0.02451	.	.	.	.	.	T	0.04588	0.0125	N	0.25992	0.78	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.30736	-0.9968	9	0.62326	D	0.03	.	17.1666	0.86818	0.0:0.7049:0.2951:0.0	rs60899198	163	Q6L8H4	KRA51_HUMAN	C	163	ENSP00000371606:S163C	ENSP00000371606:S163C	S	-	2	0	KRTAP5-1	1562568	0.000000	0.05858	0.150000	0.22450	0.017000	0.09413	-1.717000	0.01876	-1.045000	0.03250	-0.974000	0.02594	TCC	G|0.500;C|0.500	0.500	weak		0.652	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
MUC4	4585	hgsc.bcm.edu	37	3	195506315	195506315	+	Missense_Mutation	SNP	T	T	C	rs62282465	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506315T>C	ENST00000463781.3	-	2	12595	c.12136A>G	c.(12136-12138)Acc>Gcc	p.T4046A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T4046A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4046A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGTGTCACCTGTG	0.587													.|||	561	0.112021	0.0817	0.0951	5008	,	,		10183	0.0595		0.1998	False		,,,				2504	0.1288				p.T4046A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	kidney(2)	c.A12136G						scavenged	.						32.0	17.0	22.0					3																	195506315		597	1263	1860	SO:0001583	missense	4585	exon2			GGGTGGTGTCACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12136A>G	3.37:g.195506315T>C	ENSP00000417498:p.Thr4046Ala	Somatic	259	4	0.015444		WXS	Illumina HiSeq	Phase_I	102	31	0.303922	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	t	5.814	0.334415	0.11013	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.64	0.613	0.613	0.17597	.	0.326178	0.13539	N	0.380396	T	0.12944	0.0314	N	0.19112	0.55	0.09310	N	1	B	0.33494	0.414	B	0.22386	0.039	T	0.15321	-1.0441	9	.	.	.	.	3.4823	0.07607	1.0E-4:0.0:0.427:0.5729	rs62282465	3918	E7ESK3	.	A	4046	ENSP00000417498:T4046A;ENSP00000420243:T4046A	.	T	-	1	0	MUC4	196991094	0.001000	0.12720	0.008000	0.14137	0.095000	0.18619	0.338000	0.19858	0.522000	0.28464	0.055000	0.15244	ACC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195510194	195510194	+	Missense_Mutation	SNP	G	G	C	rs200763896		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195510194G>C	ENST00000463781.3	-	2	8716	c.8257C>G	c.(8257-8259)Ctt>Gtt	p.L2753V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L2753V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L2753V(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGACAGGAAGAGGGGTGGTG	0.562																																					p.L2753V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C8257G						scavenged	.						13.0	8.0	10.0					3																	195510194		668	1470	2138	SO:0001583	missense	4585	exon2			CAGGAAGAGGGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8257C>G	3.37:g.195510194G>C	ENSP00000417498:p.Leu2753Val	Somatic	129	2	0.0155039		WXS	Illumina HiSeq	Phase_I	185	28	0.151351	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	1.135	-0.651152	0.03506	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34859	1.39;1.34	.	.	.	.	.	.	.	.	T	0.17534	0.0421	N	0.19112	0.55	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.23261	-1.0193	7	.	.	.	.	2.1461	0.03788	0.0:0.3259:0.3502:0.324	.	2625	E7ESK3	.	V	2753	ENSP00000417498:L2753V;ENSP00000420243:L2753V	.	L	-	1	0	MUC4	196994973	0.001000	0.12720	0.038000	0.18304	0.064000	0.16182	-1.239000	0.02916	0.073000	0.16731	0.074000	0.15403	CTT	.	.	weak		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
P2RY8	286530	hgsc.bcm.edu	37	X	1585079	1585079	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:1585079C>T	ENST00000381297.4	-	2	583	c.373G>A	c.(373-375)Gtc>Atc	p.V125I	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGGTACAGGACCCCCAGGAAG	0.647			T	CRLF2	"""B-ALL, Downs associated ALL"""								c|||	657	0.13119	0.2254	0.1527	5008	,	,		17726	0.004		0.171	False		,,,				2504	0.0787				p.V125I		Atlas-SNP	.		Dom	yes		"""X,Y"""	Xp22.3; Yp11.3	286530	"""purinergic receptor P2Y, G-protein coupled, 8"""		L	.	P2RY8	53	.	0			c.G373A						PASS	.	C	ILE/VAL	1033,3371		112,809,1281	85.0	83.0	84.0		373	2.3	1.0	X	dbSNP_134	84	1622,6968		157,1308,2830	no	missense	P2RY8	NM_178129.4	29	269,2117,4111	TT,TC,CC		18.8824,23.4559,20.4325	possibly-damaging	125/360	1585079	2655,10339	2202	4295	6497	SO:0001583	missense	286530	exon2			ACAGGACCCCCAG	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"""Pseudoautosomal regions / PAR1"", ""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.373G>A	X.37:g.1585079C>T	ENSP00000370697:p.Val125Ile	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	293	0.13415750915750915	103	0.20934959349593496	57	0.1574585635359116	1	0.0017482517482517483	132	0.1741424802110818	c	0.231	-1.020709	0.02061	0.234559	0.188824	ENSG00000182162	ENST00000381297	T	0.65364	-0.15	2.26	2.26	0.28386	GPCR, rhodopsin-like superfamily (1);	0.086698	0.46442	U	0.000296	T	0.00012	0.0000	N	0.12569	0.235	0.09310	N	1	P	0.43169	0.8	B	0.39660	0.306	T	0.00617	-1.1642	10	0.23891	T	0.37	.	12.6106	0.56547	0.0:1.0:0.0:0.0	.	125	Q86VZ1	P2RY8_HUMAN	I	125	ENSP00000370697:V125I	ENSP00000370697:V125I	V	-	1	0	P2RY8	1545079	1.000000	0.71417	0.954000	0.39281	0.305000	0.27757	3.923000	0.56469	0.740000	0.32651	0.279000	0.19357	GTC	C|0.801;T|0.199	0.199	strong		0.647	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129	
ZSCAN4	201516	hgsc.bcm.edu	37	19	58189287	58189287	+	Silent	SNP	C	C	T	rs9676604	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58189287C>T	ENST00000318203.5	+	4	1099	c.402C>T	c.(400-402)caC>caT	p.H134H		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	134					telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H134H(1)		endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TACAGGTCCACGTCCACATGC	0.443													C|||	798	0.159345	0.1664	0.134	5008	,	,		20895	0.2629		0.164	False		,,,				2504	0.0562				p.H134H		Atlas-SNP	.											ZSCAN4,NS,carcinoma,0,1	ZSCAN4	72	1	1	Substitution - coding silent(1)	stomach(1)	c.C402T						PASS	.	C		694,3712	289.5+/-280.5	48,598,1557	119.0	104.0	109.0		402	-8.0	0.0	19	dbSNP_119	109	1414,7186	272.2+/-289.9	117,1180,3003	no	coding-synonymous	ZSCAN4	NM_152677.2		165,1778,4560	TT,TC,CC		16.4419,15.7512,16.2079		134/434	58189287	2108,10898	2203	4300	6503	SO:0001819	synonymous_variant	201516	exon4			GGTCCACGTCCAC	AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"""-"", ""Zinc fingers, C2H2-type"""	23709	protein-coding gene	gene with protein product		613419	"""zinc finger protein 494"""	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.402C>T	19.37:g.58189287C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_152677	Q3MIQ2	Silent	SNP	ENST00000318203.5	37	CCDS12958.1																																																																																			C|0.827;T|0.173	0.173	strong		0.443	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677	
OLAH	55301	hgsc.bcm.edu	37	10	15106441	15106441	+	Silent	SNP	A	A	G	rs10906818	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:15106441A>G	ENST00000378228.3	+	5	596	c.342A>G	c.(340-342)ctA>ctG	p.L114L	OLAH_ENST00000378217.3_Silent_p.L167L	NM_001039702.2	NP_001034791.1	Q9NV23	SAST_HUMAN	oleoyl-ACP hydrolase	114					fatty acid biosynthetic process (GO:0006633)		myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)			endometrium(2)|large_intestine(1)|lung(14)|stomach(1)	18						CACTAGGTCTAAAAGAAAACA	0.383													A|||	2379	0.47504	0.4198	0.3429	5008	,	,		20305	0.5744		0.4165	False		,,,				2504	0.6012				p.L167L		Atlas-SNP	.											.	OLAH	45	.	0			c.A501G						PASS	.	A	,	1822,2584	532.2+/-373.4	367,1088,748	155.0	135.0	142.0		342,501	-3.1	0.0	10	dbSNP_120	142	3618,4982	522.3+/-380.1	738,2142,1420	no	coding-synonymous,coding-synonymous	OLAH	NM_001039702.2,NM_018324.2	,	1105,3230,2168	GG,GA,AA		42.0698,41.3527,41.8268	,	114/266,167/319	15106441	5440,7566	2203	4300	6503	SO:0001819	synonymous_variant	55301	exon6			AGGTCTAAAAGAA	AK001844	CCDS7106.1, CCDS31152.1	10p13	2010-11-23	2006-07-07	2006-07-07	ENSG00000152463	ENSG00000152463	3.1.2.14		25625	protein-coding gene	gene with protein product			"""thioesterase domain containing 1"""	THEDC1			Standard	NM_018324		Approved	FLJ11106, SAST	uc001inu.2	Q9NV23	OTTHUMG00000017724	ENST00000378228.3:c.342A>G	10.37:g.15106441A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_018324	Q5VUB6|Q9NUW1	Silent	SNP	ENST00000378228.3	37	CCDS31152.1																																																																																			A|0.563;G|0.437	0.437	strong		0.383	OLAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046964.1	NM_018324	
CLEC4M	10332	hgsc.bcm.edu	37	19	7828277	7828277	+	Splice_Site	SNP	A	A	G	rs62623420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7828277A>G	ENST00000327325.5	+	2	164		c.e2-1		CLEC4M_ENST00000359059.5_Splice_Site|CLEC4M_ENST00000248228.4_Splice_Site|CLEC4M_ENST00000596363.1_Intron|CLEC4M_ENST00000597522.1_Splice_Site|CLEC4M_ENST00000394122.2_Splice_Site|CLEC4M_ENST00000595496.1_Splice_Site|CLEC4M_ENST00000596707.1_Splice_Site|CLEC4M_ENST00000357361.2_Splice_Site|CLEC4M_ENST00000334806.5_Intron	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M						antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						CTGTCAATTCAGAAGAAGATC	0.522													A|||	5	0.000998403	0.0	0.0	5008	,	,		18184	0.0		0.005	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CLEC4M	58	.	0			c.47-2A>G						PASS	.	A	,,,,,,,,	6,4400	11.4+/-27.6	0,6,2197	129.0	124.0	126.0		,,,,,,,,	2.5	0.1	19	dbSNP_129	126	50,8550	31.7+/-84.0	0,50,4250	yes	intron,intron,splice-3,splice-3,splice-3,splice-3,splice-3,intron,splice-3	CLEC4M	NM_001144904.1,NM_001144905.1,NM_001144906.1,NM_001144907.1,NM_001144908.1,NM_001144909.1,NM_001144910.1,NM_001144911.1,NM_014257.4	,,,,,,,,	0,56,6447	GG,GA,AA		0.5814,0.1362,0.4306	,,,,,,,,	,,,,,,,,	7828277	56,12950	2203	4300	6503	SO:0001630	splice_region_variant	10332	exon2			CAATTCAGAAGAA	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.47-1A>G	19.37:g.7828277A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	134	69	0.514925	NM_001144907	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Splice_Site	SNP	ENST00000327325.5	37	CCDS12187.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	7.317	0.616157	0.14129	0.001362	0.005814	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000359059;ENST00000357361	.	.	.	2.5	2.5	0.30297	.	.	.	.	.	.	.	.	.	.	.	0.53688	D	0.99997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3238	0.26542	1.0:0.0:0.0:0.0	rs62623420	.	.	.	.	-1	.	.	.	+	.	.	CLEC4M	7734277	0.022000	0.18835	0.128000	0.21923	0.082000	0.17680	1.015000	0.29963	1.134000	0.42165	0.344000	0.21773	.	A|0.997;G|0.003	0.003	strong		0.522	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	Intron
WDR90	197335	hgsc.bcm.edu	37	16	708275	708275	+	Missense_Mutation	SNP	C	C	A	rs45613635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:708275C>A	ENST00000293879.4	+	22	2697	c.2697C>A	c.(2695-2697)caC>caA	p.H899Q	WDR90_ENST00000549091.1_Missense_Mutation_p.H899Q|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	899				H -> Q (in Ref. 1; BAD18654). {ECO:0000305}.						endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CTCTGGGCCACCTGCTGGTGT	0.667													C|||	1707	0.340855	0.0968	0.3804	5008	,	,		18278	0.6766		0.2565	False		,,,				2504	0.3834				p.H899Q		Atlas-SNP	.											.	WDR90	107	.	0			c.C2697A						PASS	.	C	GLN/HIS	490,3792		27,436,1678	57.0	63.0	61.0		2697	3.1	1.0	16	dbSNP_127	61	1923,6587		206,1511,2538	yes	missense	WDR90	NM_145294.4	24	233,1947,4216	AA,AC,CC		22.5969,11.4433,18.8634	possibly-damaging	899/1749	708275	2413,10379	2141	4255	6396	SO:0001583	missense	197335	exon22			GGGCCACCTGCTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2697C>A	16.37:g.708275C>A	ENSP00000293879:p.His899Gln	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	775	0.35485347985347987	47	0.09552845528455285	135	0.3729281767955801	385	0.6730769230769231	208	0.27440633245382584	C	15.64	2.893432	0.52121	0.114433	0.225969	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.49720	0.77;3.6	5.28	3.07	0.35406	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.126543	0.51477	U	0.000100	T	0.00012	0.0000	L	0.52759	1.655	0.09310	P	0.9999999999999999	D;P	0.67145	0.996;0.852	P;B	0.62089	0.898;0.314	T	0.43212	-0.9405	9	0.13108	T	0.6	.	5.1499	0.15004	0.0:0.5613:0.1906:0.2481	rs45613635;rs62032462	899;899	F8VUX9;Q96KV7	.;WDR90_HUMAN	Q	899	ENSP00000448122:H899Q;ENSP00000293879:H899Q	ENSP00000293879:H899Q	H	+	3	2	WDR90	648276	0.999000	0.42202	0.998000	0.56505	0.836000	0.47400	0.623000	0.24447	1.194000	0.43101	0.555000	0.69702	CAC	C|0.694;A|0.306	0.306	strong		0.667	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
CDHR5	53841	hgsc.bcm.edu	37	11	618998	618998	+	Missense_Mutation	SNP	G	G	A	rs2740375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:618998G>A	ENST00000358353.3	-	14	1883	c.1561C>T	c.(1561-1563)Ccc>Tcc	p.P521S	CDHR5_ENST00000397542.2_Missense_Mutation_p.P521S|CDHR5_ENST00000349570.7_Intron|IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000397574.2_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	521			P -> S (in dbSNP:rs2740375). {ECO:0000269|PubMed:11031102, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						GCACCCGGGGGCCCCCCGGGT	0.682													G|||	2503	0.4998	0.2436	0.4669	5008	,	,		14947	0.7024		0.5586	False		,,,				2504	0.6002				p.P521S		Atlas-SNP	.											CDHR5,NS,carcinoma,+2,1	CDHR5	77	1	0			c.C1561T						PASS	.	G	SER/PRO,SER/PRO,	1270,3136	412.8+/-336.2	187,896,1120	53.0	70.0	64.0		1543,1561,	1.6	0.0	11	dbSNP_100	64	4629,3969	578.4+/-390.7	1245,2139,915	yes	missense,missense,intron	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	74,74,	1432,3035,2035	AA,AG,GG		46.1619,28.8243,45.363	benign,benign,	515/840,521/846,	618998	5899,7105	2203	4299	6502	SO:0001583	missense	53841	exon13			CCGGGGGCCCCCC	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1561C>T	11.37:g.618998G>A	ENSP00000351118:p.Pro521Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Missense_Mutation	SNP	ENST00000358353.3	37	CCDS7707.1	1118	0.5119047619047619	121	0.2459349593495935	170	0.4696132596685083	406	0.7097902097902098	421	0.5554089709762533	G	8.544	0.873997	0.17395	0.288243	0.538381	ENSG00000099834	ENST00000397542;ENST00000358353	T;T	0.41065	1.01;1.01	3.63	1.56	0.23342	.	0.911619	0.08818	N	0.889226	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.23891	0.093;0.093	B;B	0.20955	0.032;0.032	T	0.38286	-0.9668	9	0.22109	T	0.4	-11.4476	4.8444	0.13507	0.3383:0.0:0.6617:0.0	rs2740375;rs60576746	515;521	Q9HBB8-4;Q9HBB8	.;CDHR5_HUMAN	S	521	ENSP00000380676:P521S;ENSP00000351118:P521S	ENSP00000351118:P521S	P	-	1	0	CDHR5	608998	0.002000	0.14202	0.003000	0.11579	0.009000	0.06853	-0.038000	0.12144	0.255000	0.21593	0.561000	0.74099	CCC	G|0.538;A|0.462	0.462	strong		0.682	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135722264	135722264	+	Missense_Mutation	SNP	A	A	G	rs17197552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:135722264A>G	ENST00000264977.3	+	2	2541	c.1924A>G	c.(1924-1926)Agt>Ggt	p.S642G	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	642			S -> G (in dbSNP:rs17197552).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGTCTGTAGAAGTCCTGTTGG	0.423													A|||	865	0.172724	0.1505	0.1412	5008	,	,		17582	0.0288		0.2783	False		,,,				2504	0.2648				p.S642G		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A1924G						PASS	.	A	,GLY/SER	770,3634	291.0+/-281.2	64,642,1496	82.0	77.0	79.0		,1924	3.5	1.0	3	dbSNP_123	79	2708,5892	418.8+/-352.9	415,1878,2007	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,56	479,2520,3503	GG,GA,AA		31.4884,17.4841,26.7456	,benign	,642/1151	135722264	3478,9526	2202	4300	6502	SO:0001583	missense	5523	exon2			TGTAGAAGTCCTG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.1924A>G	3.37:g.135722264A>G	ENSP00000264977:p.Ser642Gly	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	208	105	0.504808	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	340	0.15567765567765568	66	0.13414634146341464	57	0.1574585635359116	13	0.022727272727272728	204	0.2691292875989446	A	9.126	1.010279	0.19277	0.174841	0.314884	ENSG00000073711	ENST00000264977	T	0.06218	3.33	5.83	3.47	0.39725	.	0.643751	0.17330	N	0.178150	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.999999999742355	B	0.02656	0.0	B	0.04013	0.001	T	0.47636	-0.9102	9	0.44086	T	0.13	.	8.2194	0.31532	0.8457:0.0:0.1543:0.0	rs17197552;rs52827295;rs17197552	642	Q06190	P2R3A_HUMAN	G	642	ENSP00000264977:S642G	ENSP00000264977:S642G	S	+	1	0	PPP2R3A	137204954	0.878000	0.30173	0.996000	0.52242	0.962000	0.63368	1.520000	0.35899	0.481000	0.27557	0.460000	0.39030	AGT	A|0.779;G|0.221	0.221	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653177	121653177	+	Silent	SNP	A	A	G	rs61732006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:121653177A>G	ENST00000393386.2	+	12	4488	c.4077A>G	c.(4075-4077)acA>acG	p.T1359T	PTPRZ1_ENST00000483028.1_3'UTR|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1359					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						CTTCTGATACATTTGTATCTA	0.378													A|||	528	0.105431	0.1528	0.0562	5008	,	,		22427	0.2093		0.0557	False		,,,				2504	0.0204				p.T1359T		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.A4077G						PASS	.	A	,,	698,3708	292.7+/-282.2	63,572,1568	179.0	179.0	179.0		,,4077	-1.4	0.0	7	dbSNP_129	179	650,7950	165.9+/-218.0	23,604,3673	no	intron,intron,coding-synonymous	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,	86,1176,5241	GG,GA,AA		7.5581,15.842,10.3644	,,	,,1359/2316	121653177	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			TGATACATTTGTA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4077A>G	7.37:g.121653177A>G		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	196	92	0.469388	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			A|0.902;G|0.098	0.098	strong		0.378	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
DEFB127	140850	hgsc.bcm.edu	37	20	139456	139456	+	Missense_Mutation	SNP	G	G	A	rs12624954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:139456G>A	ENST00000382388.3	+	2	166	c.91G>A	c.(91-93)Gga>Aga	p.G31R		NM_139074.3	NP_620713.1	Q9H1M4	DB127_HUMAN	defensin, beta 127	31			G -> R (in dbSNP:rs12624954). {ECO:0000269|PubMed:11854508}.		defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CTATGTACAAGGACATTGCAG	0.403													G|||	1624	0.324281	0.0424	0.3487	5008	,	,		22136	0.5446		0.3419	False		,,,				2504	0.4427				p.G31R		Atlas-SNP	.											DEFB127,NS,carcinoma,-1,1	DEFB127	15	1	0			c.G91A						PASS	.	G	ARG/GLY	395,4011	195.3+/-220.0	18,359,1826	92.0	82.0	85.0		91	3.1	0.1	20	dbSNP_120	85	3023,5577	463.2+/-365.9	518,1987,1795	yes	missense	DEFB127	NM_139074.2	125	536,2346,3621	AA,AG,GG		35.1512,8.965,26.2802	probably-damaging	31/100	139456	3418,9588	2203	4300	6503	SO:0001583	missense	140850	exon2			GTACAAGGACATT	AY358796	CCDS12991.1	20p13	2008-02-01	2002-05-09	2002-05-10	ENSG00000088782	ENSG00000088782		"""Defensins, beta"""	16206	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 73"""	C20orf73		11854508	Standard	NM_139074		Approved	bA530N10.2, DEF-27	uc002wcy.2	Q9H1M4	OTTHUMG00000031617	ENST00000382388.3:c.91G>A	20.37:g.139456G>A	ENSP00000371825:p.Gly31Arg	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	200	99	0.495	NM_139074	Q14DW7	Missense_Mutation	SNP	ENST00000382388.3	37	CCDS12991.1	702	0.32142857142857145	19	0.03861788617886179	135	0.3729281767955801	287	0.5017482517482518	261	0.34432717678100266	G	10.22	1.289992	0.23478	0.08965	0.351512	ENSG00000088782	ENST00000382388	T	0.62639	0.01	3.12	3.12	0.35913	.	0.000000	0.33834	N	0.004506	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	D	0.89917	1.0	D	0.97110	1.0	T	0.47849	-0.9085	8	0.56958	D	0.05	-21.6232	9.9776	0.41793	0.0:0.0:1.0:0.0	rs12624954;rs52796717;rs61481484;rs12624954	31	Q9H1M4	DB127_HUMAN	R	31	ENSP00000371825:G31R	ENSP00000371825:G31R	G	+	1	0	DEFB127	87456	0.951000	0.32395	0.140000	0.22221	0.028000	0.11728	3.236000	0.51336	2.059000	0.61396	0.305000	0.20034	GGA	G|0.719;A|0.281	0.281	strong		0.403	DEFB127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077429.1	NM_139074	
HRNR	388697	hgsc.bcm.edu	37	1	152193286	152193286	+	Missense_Mutation	SNP	G	G	T	rs7545406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152193286G>T	ENST00000368801.2	-	3	894	c.819C>A	c.(817-819)caC>caA	p.H273Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	273			H -> Q (in dbSNP:rs7545406).		establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.H273Q(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCTAGATCTGTGTCGTTCAC	0.567													G|||	1732	0.345847	0.2088	0.2795	5008	,	,		21880	0.2917		0.5855	False		,,,				2504	0.3875				p.H273Q		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	1	Substitution - Missense(1)	stomach(1)	c.C819A						PASS	.	G	GLN/HIS	1161,3245	410.0+/-335.2	154,853,1196	312.0	282.0	292.0		819	-8.8	0.0	1	dbSNP_116	292	5083,3517	632.9+/-398.7	1502,2079,719	no	missense	HRNR	NM_001009931.1	24	1656,2932,1915	TT,TG,GG		40.8953,26.3504,48.0086	benign	273/2851	152193286	6244,6762	2203	4300	6503	SO:0001583	missense	388697	exon3			AGATCTGTGTCGT	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.819C>A	1.37:g.152193286G>T	ENSP00000357791:p.His273Gln	Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	183	183	1	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	869	0.39789377289377287	109	0.22154471544715448	131	0.36187845303867405	182	0.3181818181818182	447	0.5897097625329816	G	4.913	0.169574	0.09339	0.263504	0.591047	ENSG00000197915	ENST00000368801	T	0.02974	4.09	4.41	-8.81	0.00813	.	.	.	.	.	T	0.00300	0.0009	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.48768	-0.9006	8	0.10902	T	0.67	.	0.9813	0.01437	0.1922:0.1758:0.306:0.326	rs7545406	273	Q86YZ3	HORN_HUMAN	Q	273	ENSP00000357791:H273Q	ENSP00000357791:H273Q	H	-	3	2	HRNR	150459910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.851000	0.00178	-3.578000	0.00138	-1.517000	0.00937	CAC	G|0.544;T|0.456	0.456	strong		0.567	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
SLC11A1	6556	hgsc.bcm.edu	37	2	219249013	219249013	+	Silent	SNP	C	C	T	rs2276631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219249013C>T	ENST00000233202.6	+	3	538	c.198C>T	c.(196-198)ttC>ttT	p.F66F	SLC11A1_ENST00000473367.1_Intron|SLC11A1_ENST00000539932.1_5'UTR	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	66	Pro/Ser-rich.				activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGCCTGGCTTCCTCATGAGCA	0.597													C|||	841	0.167931	0.1452	0.2695	5008	,	,		14695	0.0982		0.2505	False		,,,				2504	0.1135				p.F66F		Atlas-SNP	.											.	SLC11A1	41	.	0			c.C198T	GRCh37	CM057841	SLC11A1	M	rs2276631	PASS	.	C		758,3648	311.1+/-291.9	69,620,1514	110.0	105.0	107.0		198	2.0	1.0	2	dbSNP_100	107	2313,6287	389.5+/-342.9	323,1667,2310	no	coding-synonymous	SLC11A1	NM_000578.3		392,2287,3824	TT,TC,CC		26.8953,17.2038,23.6122		66/551	219249013	3071,9935	2203	4300	6503	SO:0001819	synonymous_variant	6556	exon3			TGGCTTCCTCATG	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"""Solute carriers"""	10907	protein-coding gene	gene with protein product	"""natural resistance-associated macrophage protein 1"""	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.198C>T	2.37:g.219249013C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_000578	C0H5Y3	Silent	SNP	ENST00000233202.6	37	CCDS2415.1																																																																																			C|0.789;T|0.211	0.211	strong		0.597	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578	
HEG1	57493	hgsc.bcm.edu	37	3	124728626	124728626	+	Missense_Mutation	SNP	A	A	G	rs6438869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:124728626A>G	ENST00000311127.4	-	8	3183	c.3116T>C	c.(3115-3117)aTg>aCg	p.M1039T		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	1039	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		M -> T (in dbSNP:rs6438869).		cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						ATTGTTGCACATGGCTGTGGA	0.448													G|||	3146	0.628195	0.5113	0.7233	5008	,	,		19897	0.5982		0.6491	False		,,,				2504	0.728				p.M1039T		Atlas-SNP	.											.	HEG1	109	.	0			c.T3116C						PASS	.	G	THR/MET	2158,1698		611,936,381	78.0	78.0	78.0		3116	-7.7	0.0	3	dbSNP_116	78	5431,2849		1786,1859,495	yes	missense	HEG1	NM_020733.1	81	2397,2795,876	GG,GA,AA		34.4082,44.0353,37.467	benign	1039/1382	124728626	7589,4547	1928	4140	6068	SO:0001583	missense	57493	exon8			TTGCACATGGCTG	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.3116T>C	3.37:g.124728626A>G	ENSP00000311502:p.Met1039Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	1405	0.6433150183150184	276	0.5609756097560976	273	0.7541436464088398	347	0.6066433566433567	509	0.6715039577836411	G	0.001	-3.164122	0.00028	0.559647	0.655918	ENSG00000173706	ENST00000311127	D	0.91351	-2.83	3.87	-7.74	0.01241	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.394007	0.17862	N	0.159492	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50575	-0.8812	9	0.02654	T	1	.	19.5521	0.95324	0.2373:0.0:0.7627:0.0	rs6438869;rs57260092;rs6438869	1039	Q9ULI3	HEG1_HUMAN	T	1039	ENSP00000311502:M1039T	ENSP00000311502:M1039T	M	-	2	0	HEG1	126211316	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-0.837000	0.04377	-3.321000	0.00188	-1.073000	0.02249	ATG	A|0.361;G|0.638	0.638	strong		0.448	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
DGKG	1608	hgsc.bcm.edu	37	3	186006618	186006618	+	Missense_Mutation	SNP	G	G	C	rs1004588	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186006618G>C	ENST00000265022.3	-	6	964	c.425C>G	c.(424-426)aCc>aGc	p.T142S	DGKG_ENST00000544847.1_Missense_Mutation_p.T142S|DGKG_ENST00000382164.4_Missense_Mutation_p.T142S|DGKG_ENST00000344484.4_Missense_Mutation_p.T142S	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	142			T -> S (in dbSNP:rs1004588). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TTCCAGGGGGGTCGCAGCCAC	0.522													G|||	2599	0.51897	0.4387	0.5101	5008	,	,		16155	0.6081		0.5318	False		,,,				2504	0.5286				p.T142S		Atlas-SNP	.											.	DGKG	98	.	0			c.C425G						PASS	.	G	SER/THR,SER/THR,SER/THR	1929,2477	539.3+/-375.2	420,1089,694	123.0	137.0	132.0		425,425,425	2.2	0.0	3	dbSNP_86	132	4447,4153	580.4+/-391.1	1167,2113,1020	yes	missense,missense,missense	DGKG	NM_001080744.1,NM_001080745.1,NM_001346.2	58,58,58	1587,3202,1714	CC,CG,GG		48.2907,43.7812,49.0235	benign,benign,benign	142/767,142/753,142/792	186006618	6376,6630	2203	4300	6503	SO:0001583	missense	1608	exon6			AGGGGGGTCGCAG	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"""EF-hand domain containing"""	2853	protein-coding gene	gene with protein product		601854	"""diacylglycerol kinase, gamma (90kD)"""	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.425C>G	3.37:g.186006618G>C	ENSP00000265022:p.Thr142Ser	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	203	92	0.453202	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	37	CCDS3274.1	1183	0.5416666666666666	243	0.49390243902439024	173	0.47790055248618785	358	0.6258741258741258	409	0.5395778364116095	G	3.558	-0.090221	0.07053	0.437812	0.517093	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.87	2.16	0.27623	.	0.961737	0.08649	N	0.914365	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B	0.09022	0.002;0.001;0.0;0.001	B;B;B;B	0.13407	0.006;0.009;0.003;0.004	T	0.46076	-0.9217	9	0.05620	T	0.96	.	5.3794	0.16183	0.3513:0.1326:0.5161:0.0	rs1004588;rs2228941;rs52831315;rs57454656;rs1004588	142;142;142;142	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	S	142;142;142;142;145	ENSP00000265022:T142S;ENSP00000339777:T142S;ENSP00000371599:T142S;ENSP00000440507:T142S	ENSP00000265022:T142S	T	-	2	0	DGKG	187489312	.	.	0.000000	0.03702	0.002000	0.02628	.	.	0.191000	0.20236	-0.137000	0.14449	ACC	G|0.460;C|0.540	0.540	strong		0.522	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3		
HSD17B13	345275	hgsc.bcm.edu	37	4	88231429	88231429	+	Missense_Mutation	SNP	G	G	A	rs62305723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88231429G>A	ENST00000328546.4	-	6	842	c.778C>T	c.(778-780)Cca>Tca	p.P260S	HSD17B13_ENST00000302219.6_Missense_Mutation_p.P224S	NM_178135.3	NP_835236.2	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13	260				P -> S (in Ref. 1; AAO72313). {ECO:0000305}.		extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)		ATATACGATGGAACAAAAATC	0.323													G|||	111	0.0221645	0.0038	0.0389	5008	,	,		15464	0.0		0.0616	False		,,,				2504	0.0174				p.P260S		Atlas-SNP	.											.	HSD17B13	27	.	0			c.C778T						PASS	.	G	SER/PRO,SER/PRO	52,4352	50.9+/-86.3	0,52,2150	101.0	104.0	103.0		670,778	5.1	1.0	4	dbSNP_129	103	572,8028	154.2+/-208.4	21,530,3749	yes	missense,missense	HSD17B13	NM_001136230.1,NM_178135.3	74,74	21,582,5899	AA,AG,GG		6.6512,1.1807,4.7985	probably-damaging,probably-damaging	224/265,260/301	88231429	624,12380	2202	4300	6502	SO:0001583	missense	345275	exon6			ACGATGGAACAAA		CCDS3618.1, CCDS47097.1	4q22.1	2011-09-20			ENSG00000170509	ENSG00000170509	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	18685	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 3"""	612127				19027726	Standard	NM_178135		Approved	SCDR9, SDR16C3	uc003hqo.2	Q7Z5P4	OTTHUMG00000130602	ENST00000328546.4:c.778C>T	4.37:g.88231429G>A	ENSP00000333300:p.Pro260Ser	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	246	108	0.439024	NM_178135	A8K9R9|Q2M1L5|Q86W22|Q86W23	Missense_Mutation	SNP	ENST00000328546.4	37	CCDS3618.1	66	0.03021978021978022	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	46	0.06068601583113457	G	19.06	3.753468	0.69648	0.011807	0.066512	ENSG00000170509	ENST00000302219;ENST00000328546	D;D	0.89875	-2.58;-2.58	5.08	5.08	0.68730	.	0.195954	0.34725	N	0.003734	T	0.70351	0.3214	M	0.86573	2.825	0.43242	D	0.995157	D;D	0.71674	0.998;0.998	D;D	0.72625	0.978;0.937	T	0.81814	-0.0760	10	0.72032	D	0.01	.	17.3259	0.87246	0.0:0.0:1.0:0.0	rs62305723	224;260	Q7Z5P4-2;Q7Z5P4	.;DHB13_HUMAN	S	224;260	ENSP00000305438:P224S;ENSP00000333300:P260S	ENSP00000305438:P224S	P	-	1	0	HSD17B13	88450453	1.000000	0.71417	0.970000	0.41538	0.652000	0.38707	5.652000	0.67959	2.358000	0.79984	0.650000	0.86243	CCA	G|0.956;A|0.044	0.044	strong		0.323	HSD17B13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253052.1	NM_178135	
MAPK15	225689	hgsc.bcm.edu	37	8	144803785	144803785	+	Missense_Mutation	SNP	T	T	C	rs35986760	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144803785T>C	ENST00000338033.4	+	12	1390	c.1271T>C	c.(1270-1272)cTa>cCa	p.L424P	RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	424					MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)	p.L443P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			ACTGCTCTCCTAGGGAATGGG	0.657													t|||	101	0.0201677	0.0015	0.0605	5008	,	,		14902	0.0308		0.0249	False		,,,				2504	0.001				p.L424P		Atlas-SNP	.											MAPK15,NS,carcinoma,0,1	MAPK15	32	1	1	Substitution - Missense(1)	stomach(1)	c.T1271C						PASS	.	T	PRO/LEU	24,3792		1,22,1885	78.0	90.0	87.0		1271	0.1	0.0	8	dbSNP_126	87	139,8103		1,137,3983	yes	missense	MAPK15	NM_139021.2	98	2,159,5868	CC,CT,TT		1.6865,0.6289,1.3518	benign	424/545	144803785	163,11895	1908	4121	6029	SO:0001583	missense	225689	exon12			CTCTCCTAGGGAA	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"""Mitogen-activated protein kinase cascade / Kinases"""	24667	protein-coding gene	gene with protein product	"""extracellular signal regulated kinase 8"""					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.1271T>C	8.37:g.144803785T>C	ENSP00000337691:p.Leu424Pro	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	242	118	0.487603	NM_139021	Q2TCF9|Q8N362	Missense_Mutation	SNP	ENST00000338033.4	37	CCDS6409.2	57	0.0260989010989011	2	0.0040650406504065045	14	0.03867403314917127	20	0.03496503496503497	21	0.027704485488126648	t	4.832	0.154620	0.09236	0.006289	0.016865	ENSG00000181085	ENST00000338033	T	0.72835	-0.69	2.06	0.0782	0.14411	.	1.128040	0.06824	N	0.792726	T	0.13970	0.0338	N	0.02916	-0.46	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.09314	-1.0680	10	0.35671	T	0.21	-25.4672	4.1892	0.10413	0.0:0.589:0.0:0.411	rs35986760	424	Q8TD08	MK15_HUMAN	P	424	ENSP00000337691:L424P	ENSP00000337691:L424P	L	+	2	0	MAPK15	144875773	0.020000	0.18652	0.036000	0.18154	0.032000	0.12392	1.054000	0.30455	-0.005000	0.14395	0.255000	0.18592	CTA	T|0.977;C|0.023	0.023	strong		0.657	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	
NUSAP1	51203	hgsc.bcm.edu	37	15	41634588	41634588	+	Missense_Mutation	SNP	C	C	A	rs386783399|rs7178777	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41634588C>A	ENST00000559596.1	+	2	185	c.98C>A	c.(97-99)aCc>aAc	p.T33N	NUSAP1_ENST00000450318.1_Missense_Mutation_p.T33N|NUSAP1_ENST00000260359.6_Missense_Mutation_p.T33N|NUSAP1_ENST00000558123.1_3'UTR|NUSAP1_ENST00000414849.2_Missense_Mutation_p.T33N|RP11-16O9.2_ENST00000559959.1_RNA|NUSAP1_ENST00000560747.1_Missense_Mutation_p.T33N|NUSAP1_ENST00000560177.1_Missense_Mutation_p.T33N|NUSAP1_ENST00000450592.2_Intron			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	33			T -> A (in dbSNP:rs7178634).|T -> N (in dbSNP:rs7178777).	T -> D (in Ref. 6; AL833611). {ECO:0000305}.	establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.T33N(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		TTGCAGGCAACCAAGTTGTTA	0.343													A|||	1714	0.342252	0.5938	0.2781	5008	,	,		23702	0.1548		0.337	False		,,,				2504	0.2464				p.T33N		Atlas-SNP	.											NUSAP1,NS,carcinoma,+1,2	NUSAP1	32	2	1	Substitution - Missense(1)	prostate(1)	c.C98A						PASS	.	A	ASN/THR,ASN/THR,ASN/THR	49,3671		8,33,1819	69.0	66.0	67.0		98,98,98	3.1	1.0	15	dbSNP_116	67	30,8164		6,18,4073	yes	missense,missense,missense	NUSAP1	NM_001129897.1,NM_016359.4,NM_018454.7	65,65,65	14,51,5892	AA,AC,CC		0.3661,1.3172,0.6631	benign,benign,benign	33/403,33/442,33/441	41634588	79,11835	1860	4097	5957	SO:0001583	missense	51203	exon2			AGGCAACCAAGTT	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.98C>A	15.37:g.41634588C>A	ENSP00000453403:p.Thr33Asn	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	136	58	0.426471	NM_018454	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Missense_Mutation	SNP	ENST00000559596.1	37	CCDS45234.1	569	0.26053113553113555	215	0.4369918699186992	95	0.26243093922651933	73	0.12762237762237763	186	0.24538258575197888	A	10.11	1.261328	0.23051	0.013172	0.003661	ENSG00000137804	ENST00000260359;ENST00000414849;ENST00000450318	T;T;T	0.32272	1.46;1.46;1.46	5.47	3.09	0.35607	.	0.426017	0.27797	N	0.017808	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	1.0000000000287557E-6	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.46091	-0.9216	9	0.59425	D	0.04	.	6.8139	0.23819	0.6362:0.2882:0.0756:0.0	rs7178777;rs60176502;rs7178777	33;33;33;33;33	E9PB35;Q9BXS6-3;Q9BXS6-5;Q9BXS6;Q9BXS6-2	.;.;.;NUSAP_HUMAN;.	N	33	ENSP00000260359:T33N;ENSP00000400746:T33N;ENSP00000401351:T33N	ENSP00000260359:T33N	T	+	2	0	NUSAP1	39421880	1.000000	0.71417	0.997000	0.53966	0.243000	0.25628	1.044000	0.30329	0.105000	0.17753	-0.375000	0.07067	ACC	C|0.686;A|0.314	0.314	strong		0.343	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359	
FAM179A	165186	hgsc.bcm.edu	37	2	29240060	29240060	+	Missense_Mutation	SNP	A	A	G	rs11127202	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29240060A>G	ENST00000379558.4	+	9	1436	c.1085A>G	c.(1084-1086)cAg>cGg	p.Q362R	FAM179A_ENST00000465300.1_Intron|FAM179A_ENST00000403861.2_Missense_Mutation_p.Q362R	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	362			Q -> R (in dbSNP:rs11127202).							breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GAGAAGATGCAGCTGAAGCAG	0.542													G|||	1065	0.21266	0.267	0.1859	5008	,	,		16571	0.1567		0.2485	False		,,,				2504	0.1789				p.Q362R		Atlas-SNP	.											.	FAM179A	106	.	0			c.A1085G						PASS	.	G	ARG/GLN	920,3124		106,708,1208	108.0	112.0	110.0		1085	3.8	1.0	2	dbSNP_120	110	1979,6397		243,1493,2452	yes	missense	FAM179A	NM_199280.2	43	349,2201,3660	GG,GA,AA		23.627,22.7498,23.3414	benign	362/1020	29240060	2899,9521	2022	4188	6210	SO:0001583	missense	165186	exon9			AGATGCAGCTGAA	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.1085A>G	2.37:g.29240060A>G	ENSP00000368876:p.Gln362Arg	Somatic	349	1	0.00286533		WXS	Illumina HiSeq	Phase_I	367	178	0.485014	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	463	0.211996336996337	126	0.25609756097560976	69	0.19060773480662985	80	0.13986013986013987	188	0.24802110817941952	G	0.634	-0.815920	0.02776	0.227498	0.23627	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.14766	3.73;2.48	4.75	3.85	0.44370	.	.	.	.	.	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44544	-0.9321	8	0.02654	T	1	.	10.3911	0.44168	0.1669:0.0:0.8331:0.0	rs11127202;rs59508471;rs11127202	362;362	F8W8E4;Q6ZUX3	.;F179A_HUMAN	R	362	ENSP00000368876:Q362R;ENSP00000384699:Q362R	ENSP00000368876:Q362R	Q	+	2	0	FAM179A	29093564	1.000000	0.71417	0.999000	0.59377	0.396000	0.30629	1.748000	0.38308	0.510000	0.28216	-0.186000	0.12905	CAG	A|0.778;G|0.222	0.222	strong		0.542	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
TIMELESS	8914	hgsc.bcm.edu	37	12	56822378	56822378	+	Missense_Mutation	SNP	T	T	A	rs774027	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56822378T>A	ENST00000553532.1	-	12	1513	c.1363A>T	c.(1363-1365)Ata>Tta	p.I455L	TIMELESS_ENST00000229201.4_Missense_Mutation_p.I454L|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						TCTGGAGATATGTCCATCTCA	0.557													T|||	2537	0.506589	0.2534	0.683	5008	,	,		18483	0.746		0.4513	False		,,,				2504	0.5337				p.I455L		Atlas-SNP	.											.	TIMELESS	107	.	0			c.A1363T						PASS	.	T	LEU/ILE	1188,3218	413.7+/-336.6	150,888,1165	80.0	66.0	71.0		1363	-2.3	0.3	12	dbSNP_86	71	3907,4693	546.8+/-385.0	872,2163,1265	yes	missense	TIMELESS	NM_003920.3	5	1022,3051,2430	AA,AT,TT		45.4302,26.9632,39.1742	benign	455/1209	56822378	5095,7911	2203	4300	6503	SO:0001583	missense	8914	exon12			GAGATATGTCCAT	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.1363A>T	12.37:g.56822378T>A	ENSP00000450607:p.Ile455Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	1081	0.49496336996337	115	0.23373983739837398	221	0.6104972375690608	402	0.7027972027972028	343	0.4525065963060686	T	3.196	-0.164811	0.06502	0.269632	0.454302	ENSG00000111602	ENST00000229201;ENST00000553532	T;T	0.06068	3.35;3.35	5.13	-2.3	0.06785	.	0.643166	0.16789	N	0.199479	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.99999894515	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.11108	-1.0601	9	0.28530	T	0.3	-0.0721	2.3831	0.04359	0.0947:0.1834:0.1921:0.5298	rs774027;rs1063961;rs3204991;rs17441804;rs52789933;rs774027	454;455	Q9UNS1-2;Q9UNS1	.;TIM_HUMAN	L	454;455	ENSP00000229201:I454L;ENSP00000450607:I455L	ENSP00000229201:I455L	I	-	1	0	TIMELESS	55108645	0.098000	0.21812	0.273000	0.24645	0.427000	0.31564	0.322000	0.19576	-0.517000	0.06461	-2.479000	0.00199	ATA	T|0.566;A|0.434	0.434	strong		0.557	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
CYB5R4	51167	hgsc.bcm.edu	37	6	84618792	84618792	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:84618792A>G	ENST00000369681.5	+	4	535	c.395A>G	c.(394-396)aAa>aGa	p.K132R	CYB5R4_ENST00000369679.4_Missense_Mutation_p.K98R	NM_016230.3	NP_057314.2	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	132					cell development (GO:0048468)|detection of oxygen (GO:0003032)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NAD(P)H oxidase activity (GO:0016174)|NADPH-hemoprotein reductase activity (GO:0003958)|oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor (GO:0016653)			breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	23		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		ATGGCCATTAAACCTGCTGTT	0.398																																					p.K132R	Esophageal Squamous(86;1289 1332 25971 40349 52675)	Atlas-SNP	.											.	CYB5R4	72	.	0			c.A395G						PASS	.						133.0	118.0	123.0					6																	84618792		2203	4300	6503	SO:0001583	missense	51167	exon4			CCATTAAACCTGC	AF169803	CCDS5000.2	6q14.2	2012-09-19		2005-07-13	ENSG00000065615	ENSG00000065615	1.6.2.2		20147	protein-coding gene	gene with protein product		608343	"""NADPH cytochrome B5 oxidoreductase"""	NCB5OR		10611283	Standard	NM_016230		Approved	b5+b5R, dJ676J13.1	uc003pkf.3	Q7L1T6	OTTHUMG00000015118	ENST00000369681.5:c.395A>G	6.37:g.84618792A>G	ENSP00000358695:p.Lys132Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_016230	B1AEM2|Q5TGI9|Q9NUE4|Q9UHI9	Missense_Mutation	SNP	ENST00000369681.5	37	CCDS5000.2	.	.	.	.	.	.	.	.	.	.	A	18.22	3.576672	0.65878	.	.	ENSG00000065615	ENST00000369681;ENST00000369679	D;D	0.84944	-1.92;-1.68	5.74	5.74	0.90152	Cytochrome b5 (1);	0.206931	0.48767	D	0.000169	T	0.62720	0.2451	N	0.19112	0.55	0.44862	D	0.99787	B	0.27910	0.193	B	0.22386	0.039	T	0.64689	-0.6348	10	0.31617	T	0.26	.	12.4249	0.55540	1.0:0.0:0.0:0.0	.	132	Q7L1T6	NB5R4_HUMAN	R	132;98	ENSP00000358695:K132R;ENSP00000358693:K98R	ENSP00000358693:K98R	K	+	2	0	CYB5R4	84675511	1.000000	0.71417	0.173000	0.22940	0.007000	0.05969	5.761000	0.68801	2.182000	0.69389	0.482000	0.46254	AAA	.	.	none		0.398	CYB5R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041362.4	NM_016230	
MOV10L1	54456	hgsc.bcm.edu	37	22	50546666	50546666	+	Missense_Mutation	SNP	C	C	T	rs3810971	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50546666C>T	ENST00000262794.5	+	4	627	c.544C>T	c.(544-546)Cgc>Tgc	p.R182C	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.R182C|MOV10L1_ENST00000545383.1_Missense_Mutation_p.R182C|MOV10L1_ENST00000540615.1_Missense_Mutation_p.R162C	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	182			R -> C (in dbSNP:rs3810971).		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GAGATACAAGCGCGTGGACAA	0.617													C|||	1236	0.246805	0.1225	0.3833	5008	,	,		18174	0.248		0.2346	False		,,,				2504	0.3292				p.R182C		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C544T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	665,3741	278.7+/-274.4	55,555,1593	51.0	42.0	45.0		544,484,544	4.2	1.0	22	dbSNP_107	45	2052,6548	353.0+/-328.9	248,1556,2496	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	180,180,180	303,2111,4089	TT,TC,CC		23.8605,15.0931,20.8904	probably-damaging,probably-damaging,probably-damaging	182/1166,162/1166,182/1212	50546666	2717,10289	2203	4300	6503	SO:0001583	missense	54456	exon4			TACAAGCGCGTGG	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.544C>T	22.37:g.50546666C>T	ENSP00000262794:p.Arg182Cys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	129	83	0.643411	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	525	0.2403846153846154	54	0.10975609756097561	122	0.3370165745856354	177	0.3094405594405594	172	0.22691292875989447	C	18.20	3.570145	0.65765	0.150931	0.238605	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615;ENST00000428564	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.28	4.2	0.49525	.	0.055074	0.64402	D	0.000001	T	0.00012	0.0000	M	0.72894	2.215	0.09310	P	0.9999999999998017	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.68765	0.96;0.938;0.912;0.912	T	0.23762	-1.0179	9	0.87932	D	0	-10.4023	10.4014	0.44231	0.3131:0.6869:0.0:0.0	rs3810971;rs17836603;rs52835906;rs61218086;rs3810971	162;162;182;182	F5H403;E7EPK8;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	C	182;182;182;162;162	ENSP00000438978:R182C;ENSP00000262794:R182C;ENSP00000379199:R182C;ENSP00000438542:R162C	ENSP00000262794:R182C	R	+	1	0	MOV10L1	48888793	1.000000	0.71417	0.951000	0.38953	0.563000	0.35712	2.470000	0.45119	2.480000	0.83734	0.644000	0.83932	CGC	C|0.782;T|0.218	0.218	strong		0.617	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
DSG2	1829	hgsc.bcm.edu	37	18	29104714	29104714	+	Missense_Mutation	SNP	A	A	G	rs2230234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:29104714A>G	ENST00000261590.8	+	8	1086	c.877A>G	c.(877-879)Ata>Gta	p.I293V		NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	293	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> V (in dbSNP:rs2230234). {ECO:0000269|PubMed:18678517, ECO:0000269|PubMed:19863551}.		apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			AGTTACGCGCATAAAAGTGTT	0.343													A|||	162	0.0323482	0.003	0.036	5008	,	,		19637	0.001		0.0954	False		,,,				2504	0.0368				p.I293V		Atlas-SNP	.											.	DSG2	115	.	0			c.A877G						PASS	.	A	VAL/ILE	53,3661		0,53,1804	94.0	92.0	92.0		877	5.3	1.0	18	dbSNP_98	92	706,7514		30,646,3434	yes	missense	DSG2	NM_001943.3	29	30,699,5238	GG,GA,AA		8.5888,1.427,6.36	benign	293/1119	29104714	759,11175	1857	4110	5967	SO:0001583	missense	1829	exon8			ACGCGCATAAAAG	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"""Cadherins / Major cadherins"""	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.877A>G	18.37:g.29104714A>G	ENSP00000261590:p.Ile293Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	146	62	0.424658	NM_001943	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	37	CCDS42423.1	84	0.038461538461538464	2	0.0040650406504065045	12	0.03314917127071823	1	0.0017482517482517483	69	0.09102902374670185	A	14.27	2.485911	0.44147	0.01427	0.085888	ENSG00000046604	ENST00000261590	T	0.42131	0.98	5.35	5.35	0.76521	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000003	T	0.02455	0.0075	L	0.35593	1.075	0.09310	P	1.0	D	0.61697	0.99	P	0.60236	0.871	T	0.14227	-1.0480	9	0.30078	T	0.28	.	12.0796	0.53663	0.8565:0.1434:0.0:0.0	rs2230234;rs17664666;rs52789264;rs56627729;rs59246039;rs2230234	293	Q14126	DSG2_HUMAN	V	293	ENSP00000261590:I293V	ENSP00000261590:I293V	I	+	1	0	DSG2	27358712	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	2.066000	0.41452	2.243000	0.73865	0.533000	0.62120	ATA	A|0.952;G|0.048	0.048	strong		0.343	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943	
LRBA	987	hgsc.bcm.edu	37	4	151207127	151207127	+	Missense_Mutation	SNP	C	C	T	rs3749574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:151207127C>T	ENST00000357115.3	-	55	8353	c.8110G>A	c.(8110-8112)Gcg>Acg	p.A2704T	LRBA_ENST00000510413.1_Missense_Mutation_p.A2692T|LRBA_ENST00000535741.1_Missense_Mutation_p.A2693T|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2704			A -> T (in dbSNP:rs3749574).			cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					GCACACACCGCAGCACATGTG	0.448													C|||	812	0.162141	0.0363	0.1556	5008	,	,		15875	0.2371		0.3022	False		,,,				2504	0.1155				p.A2704T		Atlas-SNP	.											.	LRBA	253	.	0			c.G8110A						PASS	.	C	THR/ALA,THR/ALA	349,4057	168.7+/-199.5	11,327,1865	68.0	55.0	59.0		8110,8110	4.8	0.6	4	dbSNP_107	59	2554,6046	379.3+/-339.2	380,1794,2126	yes	missense,missense	LRBA	NM_001199282.2,NM_006726.4	58,58	391,2121,3991	TT,TC,CC		29.6977,7.921,22.3205	benign,benign	2704/2864,2704/2864	151207127	2903,10103	2203	4300	6503	SO:0001583	missense	987	exon55			ACACCGCAGCACA	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.8110G>A	4.37:g.151207127C>T	ENSP00000349629:p.Ala2704Thr	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	239	104	0.435146	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	459	0.21016483516483517	15	0.03048780487804878	72	0.19889502762430938	147	0.256993006993007	225	0.29683377308707126	C	9.955	1.221347	0.22457	0.07921	0.296977	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115	T;T;T	0.50548	0.74;0.89;0.75	5.78	4.83	0.62350	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.103999	0.64402	D	0.000005	T	0.00012	0.0000	N	0.17474	0.49	0.44048	P	0.0032170000000000254	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.10450	0.001;0.003;0.005;0.002	T	0.12142	-1.0559	9	0.38643	T	0.18	.	9.3169	0.37939	0.0:0.7762:0.0:0.2238	rs3749574;rs17588321;rs52792932;rs57711446;rs3749574	2704;2693;2692;599	P50851;F5H1X8;P50851-2;Q68D03	LRBA_HUMAN;.;.;.	T	2693;2692;2704	ENSP00000446299:A2693T;ENSP00000421552:A2692T;ENSP00000349629:A2704T	ENSP00000349629:A2704T	A	-	1	0	LRBA	151426577	0.917000	0.31117	0.598000	0.28837	0.793000	0.44817	1.932000	0.40143	2.717000	0.92951	0.650000	0.86243	GCG	C|0.798;T|0.202	0.202	strong		0.448	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
HERC2	8924	hgsc.bcm.edu	37	15	28419695	28419695	+	Silent	SNP	T	T	C	rs149592795	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28419695T>C	ENST00000261609.7	-	65	10011	c.9903A>G	c.(9901-9903)acA>acG	p.T3301T		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.T3301T(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTTGCACGAGTGTGGGCTTCC	0.562													t|||	336	0.0670927	0.0598	0.0634	5008	,	,		22598	0.0198		0.1183	False		,,,				2504	0.0757				p.T3301T		Atlas-SNP	.											HERC2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	HERC2	501	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A9903G						scavenged	.						87.0	58.0	68.0					15																	28419695		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon65			CACGAGTGTGGGC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9903A>G	15.37:g.28419695T>C		Somatic	797	6	0.00752823		WXS	Illumina HiSeq	Phase_I	747	153	0.204819	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			T|0.915;C|0.085	0.085	strong		0.562	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
VEZF1	7716	hgsc.bcm.edu	37	17	56060215	56060215	+	Silent	SNP	T	T	C	rs2228270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56060215T>C	ENST00000581208.1	-	2	613	c.573A>G	c.(571-573)cgA>cgG	p.R191R	VEZF1_ENST00000584396.1_Silent_p.R182R	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	191					angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						AGAGCTTGTGTCGATTGAGAT	0.483													C|||	380	0.0758786	0.1626	0.0461	5008	,	,		22038	0.0099		0.0557	False		,,,				2504	0.0685				p.R191R		Atlas-SNP	.											.	VEZF1	50	.	0			c.A573G						PASS	.	C		707,3699	760.1+/-412.9	63,581,1559	86.0	74.0	78.0		573	3.5	1.0	17	dbSNP_98	78	564,8036	794.1+/-407.5	24,516,3760	no	coding-synonymous	VEZF1	NM_007146.2		87,1097,5319	CC,CT,TT		6.5581,16.0463,9.7724		191/522	56060215	1271,11735	2203	4300	6503	SO:0001819	synonymous_variant	7716	exon2			CTTGTGTCGATTG	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"""Zinc fingers, C2H2-type"""	12949	protein-coding gene	gene with protein product		606747	"""zinc finger protein 161"""	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.573A>G	17.37:g.56060215T>C		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	287	145	0.505226	NM_007146		Silent	SNP	ENST00000581208.1	37	CCDS32687.1																																																																																			T|0.916;C|0.084	0.084	strong		0.483	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
CST2	1470	hgsc.bcm.edu	37	20	23805952	23805952	+	Silent	SNP	G	G	C	rs146039211	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23805952G>C	ENST00000304725.2	-	2	307	c.237C>G	c.(235-237)ggC>ggG	p.G79G		NM_001322.2	NP_001313.1	P09228	CYTT_HUMAN	cystatin SA	79					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|cervix(1)|large_intestine(1)|liver(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	10						AATTCACCCCGCCCACGATCT	0.542																																					p.G79G	Pancreas(193;496 3017 22514 29918)	Atlas-SNP	.											CST2,NS,adenoma,-1,1	CST2	39	1	0			c.C237G						scavenged	.						226.0	176.0	193.0					20																	23805952		2203	4300	6503	SO:0001819	synonymous_variant	1470	exon2			CACCCCGCCCACG	M19671	CCDS13161.1	20p11.2	2007-11-29			ENSG00000170369	ENSG00000170369			2474	protein-coding gene	gene with protein product	"""cystatin 2"""	123856					Standard	NM_001322		Approved		uc002wtq.1	P09228	OTTHUMG00000032086	ENST00000304725.2:c.237C>G	20.37:g.23805952G>C		Somatic	145	3	0.0206897		WXS	Illumina HiSeq	Phase_I	160	6	0.0375	NM_001322	Q9UCQ7	Silent	SNP	ENST00000304725.2	37	CCDS13161.1																																																																																			G|0.999;A|0.001	.	alt		0.542	CST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078352.2		
CENPM	79019	hgsc.bcm.edu	37	22	42342462	42342462	+	Silent	SNP	C	C	T	rs34730141	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:42342462C>T	ENST00000215980.5	-	2	183	c.96G>A	c.(94-96)gcG>gcA	p.A32A	CENPM_ENST00000402338.1_5'UTR|CENPM_ENST00000402420.1_5'UTR|CENPM_ENST00000407253.3_Silent_p.A32A|CENPM_ENST00000404067.1_5'UTR	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	32					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						GCATCGAGTCCGCCAGCTGCT	0.657											OREG0026600	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	73	0.0145767	0.0514	0.0072	5008	,	,		17483	0.0		0.0	False		,,,				2504	0.0				p.A32A		Atlas-SNP	.											.	CENPM	8	.	0			c.G96A						PASS	.	C	,	203,4203	121.7+/-159.2	7,189,2007	35.0	31.0	32.0		96,96	-1.8	1.0	22	dbSNP_126	32	2,8596	4.3+/-15.6	0,2,4297	no	coding-synonymous,coding-synonymous	CENPM	NM_001002876.1,NM_024053.3	,	7,191,6304	TT,TC,CC		0.0233,4.6074,1.5764	,	32/108,32/181	42342462	205,12799	2203	4299	6502	SO:0001819	synonymous_variant	79019	exon2			CGAGTCCGCCAGC	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"""chromosome 22 open reading frame 18"""	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.96G>A	22.37:g.42342462C>T		Somatic	230	0	0	908	WXS	Illumina HiSeq	Phase_I	288	152	0.527778	NM_024053	A7LM22|B1AHQ9|Q6I9W3	Silent	SNP	ENST00000215980.5	37	CCDS14025.1																																																																																			C|0.983;T|0.017	0.017	strong		0.657	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053	
REST	5978	hgsc.bcm.edu	37	4	57798174	57798174	+	Silent	SNP	C	C	G	rs3796528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57798174C>G	ENST00000309042.7	+	4	3464	c.3150C>G	c.(3148-3150)gcC>gcG	p.A1050A		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1050	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A1050A(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAAAGGAAGCCTTGGCAGTCA	0.448													C|||	596	0.11901	0.1256	0.2522	5008	,	,		20562	0.2024		0.0328	False		,,,				2504	0.0184				p.A1050A		Atlas-SNP	.											REST,NS,carcinoma,0,1	REST	104	1	1	Substitution - coding silent(1)	stomach(1)	c.C3150G						PASS	.	C	,	531,3875	241.5+/-251.9	29,473,1701	78.0	74.0	75.0		3150,3150	-1.1	0.0	4	dbSNP_107	75	351,8249	117.6+/-177.1	9,333,3958	yes	coding-synonymous,coding-synonymous	REST	NM_001193508.1,NM_005612.4	,	38,806,5659	GG,GC,CC		4.0814,12.0517,6.7815	,	1050/1098,1050/1098	57798174	882,12124	2203	4300	6503	SO:0001819	synonymous_variant	5978	exon4			GGAAGCCTTGGCA	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3150C>G	4.37:g.57798174C>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	172	75	0.436047	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Silent	SNP	ENST00000309042.7	37	CCDS3509.1																																																																																			C|0.914;G|0.086	0.086	strong		0.448	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
CCND3	896	hgsc.bcm.edu	37	6	41903783	41903783	+	Silent	SNP	G	G	A	rs386700585|rs3218102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41903783G>A	ENST00000372991.4	-	5	972	c.774C>T	c.(772-774)gcC>gcT	p.A258A	CCND3_ENST00000511642.1_Silent_p.A177A|CCND3_ENST00000372987.4_Silent_p.A208A|CCND3_ENST00000511686.1_5'UTR|CCND3_ENST00000372988.4_Silent_p.A177A|CCND3_ENST00000414200.2_Silent_p.A186A|CCND3_ENST00000510503.1_Missense_Mutation_p.L132F|CCND3_ENST00000415497.2_Silent_p.A62A	NM_001760.3	NP_001751.1	P30281	CCND3_HUMAN	cyclin D3	258					cell cycle (GO:0007049)|cell division (GO:0051301)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(13)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	20	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGGTCTGAGAGGCTTCCCTGA	0.637			T	IGH@	MM								G|||	322	0.0642971	0.1195	0.1513	5008	,	,		14932	0.002		0.0209	False		,,,				2504	0.0368				p.A258A		Atlas-SNP	.		Dom	yes		6	6p21	896	cyclin D3		L	.	CCND3	40	.	0			c.C774T						PASS	.						44.0	49.0	47.0					6																	41903783		2203	4300	6503	SO:0001819	synonymous_variant	896	exon5			CTGAGAGGCTTCC		CCDS4863.1, CCDS47425.1, CCDS47426.1, CCDS47427.1, CCDS75452.1	6p21	2008-08-26			ENSG00000112576	ENSG00000112576			1585	protein-coding gene	gene with protein product		123834				1386335	Standard	NM_001136125		Approved		uc003orn.3	P30281	OTTHUMG00000014690	ENST00000372991.4:c.774C>T	6.37:g.41903783G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_001760	B2RD63|B3KQ22|E9PAS4|E9PB36|Q5T8J0|Q6FG62|Q96F49	Silent	SNP	ENST00000372991.4	37	CCDS4863.1	78	0.03571428571428571	36	0.07317073170731707	30	0.08287292817679558	0	0.0	12	0.0158311345646438	g	9.151	1.016271	0.19355	.	.	ENSG00000112576	ENST00000510503	T	0.36878	1.23	5.29	-10.4	0.00318	.	.	.	.	.	T	0.11324	0.0276	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.35549	-0.9784	6	0.52906	T	0.07	.	6.9935	0.24767	0.612:0.0829:0.2216:0.0836	rs3218102	.	.	.	F	132	ENSP00000425986:L132F	ENSP00000425986:L132F	L	-	1	0	CCND3	42011761	0.000000	0.05858	0.003000	0.11579	0.256000	0.26092	-1.673000	0.01951	-2.526000	0.00494	-1.446000	0.01064	CTC	G|0.956;A|0.044	0.044	strong		0.637	CCND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040540.2	NM_001760	
WDFY4	57705	hgsc.bcm.edu	37	10	50184949	50184949	+	Silent	SNP	C	C	T	rs2271565	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50184949C>T	ENST00000325239.5	+	58	9243	c.9216C>T	c.(9214-9216)tgC>tgT	p.C3072C	RP11-523O18.5_ENST00000428825.4_RNA|WDFY4_ENST00000465910.1_3'UTR|WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	3072						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CCATAACCTGCTGCTGCCTGA	0.597													C|||	1674	0.334265	0.062	0.402	5008	,	,		16207	0.3502		0.4871	False		,,,				2504	0.4806				p.C3072C		Atlas-SNP	.											WDFY4,NS,carcinoma,+1,2	WDFY4	205	2	0			c.C9216T						PASS	.	C		184,1200		14,156,522	73.0	76.0	75.0		9216	3.8	1.0	10	dbSNP_100	75	1568,1614		398,772,421	no	coding-synonymous	WDFY4	NM_020945.1		412,928,943	TT,TC,CC		49.2772,13.2948,38.3706		3072/3185	50184949	1752,2814	692	1591	2283	SO:0001819	synonymous_variant	57705	exon59			AACCTGCTGCTGC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.9216C>T	10.37:g.50184949C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	201	200	0.995025	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	729	0.33379120879120877	37	0.07520325203252033	147	0.40607734806629836	171	0.29895104895104896	374	0.49340369393139843	C	13.59	2.281938	0.40394	0.132948	0.492772	ENSG00000128815	ENST00000265453	.	.	.	4.74	3.84	0.44239	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.49995	-0.8879	3	.	.	.	.	12.3839	0.55322	0.0:0.9184:0.0:0.0816	rs2271565;rs17772905;rs2271565	.	.	.	V	1159	.	.	A	+	2	0	WDFY4	49854955	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	1.643000	0.37217	1.351000	0.45789	-0.251000	0.11542	GCT	C|0.685;T|0.315	0.315	strong		0.597	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
ZNF573	126231	hgsc.bcm.edu	37	19	38230720	38230720	+	Missense_Mutation	SNP	C	C	G	rs3752365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38230720C>G	ENST00000590414.2	-	4	692	c.671G>C	c.(670-672)gGg>gCg	p.G224A	ZNF573_ENST00000392138.1_Missense_Mutation_p.G137A|ZNF573_ENST00000339503.4_Missense_Mutation_p.G166A|ZNF573_ENST00000357309.3_Missense_Mutation_p.G136A|ZNF573_ENST00000536220.1_Missense_Mutation_p.G136A			Q86YE8	ZN573_HUMAN	zinc finger protein 573	224			G -> A (in dbSNP:rs3752365).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			AAAGGCCTTCCCACACTGCCT	0.438													c|||	498	0.0994409	0.0189	0.1254	5008	,	,		20686	0.0694		0.2167	False		,,,				2504	0.1002				p.G224A		Atlas-SNP	.											.	ZNF573	63	.	0			c.G671C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY,ALA/GLY,ALA/GLY	261,4145	147.6+/-182.1	7,247,1949	116.0	107.0	110.0		407,671,665,407,497	2.6	0.7	19	dbSNP_107	110	1808,6792	324.5+/-316.5	217,1374,2709	yes	missense,missense,missense,missense,missense	ZNF573	NM_001172689.1,NM_001172690.1,NM_001172691.1,NM_001172692.1,NM_152360.3	60,60,60,60,60	224,1621,4658	GG,GC,CC		21.0233,5.9237,15.908	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	136/578,224/666,222/664,136/578,166/608	38230720	2069,10937	2203	4300	6503	SO:0001583	missense	126231	exon5			GCCTTCCCACACT	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"""Zinc fingers, C2H2-type"", ""-"""	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.671G>C	19.37:g.38230720C>G	ENSP00000465020:p.Gly224Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_001172690	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Missense_Mutation	SNP	ENST00000590414.2	37	CCDS59381.1	270	0.12362637362637363	15	0.03048780487804878	57	0.1574585635359116	43	0.07517482517482517	155	0.20448548812664907	c	13.65	2.299980	0.40694	0.059237	0.210233	ENSG00000189144	ENST00000392138;ENST00000536220;ENST00000357309;ENST00000339503;ENST00000427026	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	2.62	2.62	0.31277	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00109	0.0003	M	0.89414	3.03	0.41481	P	0.011831000000000036	D;D;D;D	0.61080	0.987;0.957;0.989;0.987	B;B;P;B	0.47891	0.342;0.342;0.56;0.424	T	0.21143	-1.0254	8	0.72032	D	0.01	.	12.0468	0.53485	0.0:1.0:0.0:0.0	rs3752365;rs17663719;rs3752365	137;166;204;136	Q86YE8-4;Q86YE8-3;Q86YE8;Q86YE8-2	.;.;ZN573_HUMAN;.	A	137;136;136;166;136	ENSP00000375983:G137A;ENSP00000440464:G136A;ENSP00000349861:G136A;ENSP00000340171:G166A	ENSP00000340171:G166A	G	-	2	0	ZNF573	42922560	0.846000	0.29590	0.685000	0.30070	0.396000	0.30629	1.580000	0.36547	1.300000	0.44818	0.645000	0.84053	GGG	C|0.852;G|0.148	0.148	strong		0.438	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360	
SIPA1L1	26037	hgsc.bcm.edu	37	14	72169130	72169130	+	Missense_Mutation	SNP	T	T	C	rs79937396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:72169130T>C	ENST00000555818.1	+	12	3902	c.3554T>C	c.(3553-3555)aTt>aCt	p.I1185T	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.I1185T|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.I1185T|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.I660T	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1185					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CCAGCCTCCATTGACAGGCAG	0.527													T|||	52	0.0103834	0.0008	0.0101	5008	,	,		20441	0.0		0.0328	False		,,,				2504	0.0112				p.I1185T		Atlas-SNP	.											SIPA1L1,NS,carcinoma,-1,1	SIPA1L1	219	1	0			c.T3554C						PASS	.	T	THR/ILE	35,4371	39.2+/-71.8	0,35,2168	140.0	118.0	125.0		3554	6.0	0.9	14	dbSNP_131	125	335,8265	116.1+/-175.8	6,323,3971	yes	missense	SIPA1L1	NM_015556.1	89	6,358,6139	CC,CT,TT		3.8953,0.7944,2.8448	benign	1185/1805	72169130	370,12636	2203	4300	6503	SO:0001583	missense	26037	exon12			CCTCCATTGACAG	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.3554T>C	14.37:g.72169130T>C	ENSP00000450832:p.Ile1185Thr	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	194	98	0.505155	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	51	0.023351648351648352	2	0.0040650406504065045	5	0.013812154696132596	8	0.013986013986013986	36	0.047493403693931395	T	9.237	1.037297	0.19669	0.007944	0.038953	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	6.02	6.02	0.97574	.	0.399694	0.28549	N	0.014944	T	0.08582	0.0213	N	0.22421	0.69	0.46798	D	0.999206	B;B;B;B;B	0.29805	0.257;0.0;0.012;0.257;0.0	B;B;B;B;B	0.29077	0.098;0.001;0.013;0.074;0.001	T	0.05435	-1.0885	10	0.20046	T	0.44	-6.7229	15.1131	0.72375	0.0:0.0:0.0:1.0	.	660;1185;660;1185;1185	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	T	1185;1185;1185;660	ENSP00000370630:I1185T;ENSP00000450832:I1185T;ENSP00000351352:I1185T;ENSP00000440682:I660T	ENSP00000351352:I1185T	I	+	2	0	SIPA1L1	71238883	1.000000	0.71417	0.938000	0.37757	0.159000	0.22180	4.942000	0.63547	2.304000	0.77564	0.528000	0.53228	ATT	T|0.974;C|0.026	0.026	strong		0.527	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
CAPG	822	hgsc.bcm.edu	37	2	85622059	85622059	+	Missense_Mutation	SNP	T	T	C	rs6886	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85622059T>C	ENST00000409921.1	-	10	1025	c.959A>G	c.(958-960)cAt>cGt	p.H320R	CAPG_ENST00000409724.1_Missense_Mutation_p.H335R|CAPG_ENST00000483659.1_5'Flank|CAPG_ENST00000409670.1_Missense_Mutation_p.H335R|CAPG_ENST00000263867.4_Missense_Mutation_p.H335R			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						GGGACTCTCATGGCCCTGAGG	0.602													C|||	2930	0.585064	0.7489	0.3977	5008	,	,		19490	0.504		0.6551	False		,,,				2504	0.5082				p.H335R		Atlas-SNP	.											.	CAPG	32	.	0			c.A1004G						PASS	.	C	ARG/HIS	3228,1178	413.0+/-336.3	1184,860,159	56.0	54.0	55.0		1004	3.9	0.9	2	dbSNP_52	55	5543,3057	469.4+/-367.6	1807,1929,564	yes	missense	CAPG	NM_001747.2	29	2991,2789,723	CC,CT,TT		35.5465,26.7363,32.5619	benign	335/349	85622059	8771,4235	2203	4300	6503	SO:0001583	missense	822	exon10			CTCTCATGGCCCT	M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"""macrophage capping protein"""	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.959A>G	2.37:g.85622059T>C	ENSP00000387063:p.His320Arg	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	211	209	0.990521	NM_001256139	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000409921.1	37	CCDS58715.1	1340	0.6135531135531136	389	0.790650406504065	159	0.43922651933701656	287	0.5017482517482518	505	0.6662269129287599	C	11.37	1.618331	0.28801	0.732637	0.644535	ENSG00000042493	ENST00000542681;ENST00000263867;ENST00000453973;ENST00000409921;ENST00000409670;ENST00000409724	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	5.69	3.9	0.45041	Gelsolin domain (1);	0.200680	0.41823	N	0.000809	T	0.00012	0.0000	N	0.03967	-0.31	0.53688	P	2.1000000000048757E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27571	-1.0070	9	0.26408	T	0.33	.	8.0924	0.30807	0.0:0.7496:0.0:0.2504	rs6886;rs1131551;rs2271627;rs3191581;rs3209744;rs17294682;rs17764992;rs17856020;rs17856462;rs57062873;rs6886	320;335	B8ZZS7;P40121	.;CAPG_HUMAN	R	314;335;90;320;335;335	ENSP00000263867:H335R;ENSP00000397381:H90R;ENSP00000387063:H320R;ENSP00000386315:H335R;ENSP00000386965:H335R	ENSP00000263867:H335R	H	-	2	0	CAPG	85475570	0.947000	0.32204	0.876000	0.34364	0.961000	0.63080	2.004000	0.40854	0.368000	0.24481	-0.733000	0.03571	CAT	T|0.353;C|0.647	0.647	strong		0.602	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747	
SVEP1	79987	hgsc.bcm.edu	37	9	113261483	113261483	+	Missense_Mutation	SNP	C	C	T	rs872665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:113261483C>T	ENST00000401783.2	-	7	1855	c.1519G>A	c.(1519-1521)Gtc>Atc	p.V507I	SVEP1_ENST00000374469.1_Missense_Mutation_p.V484I|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374461.1_Missense_Mutation_p.V484I|SVEP1_ENST00000302728.8_Missense_Mutation_p.V507I	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	507	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.		V -> I (in dbSNP:rs872665).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GATATGATGACATCTTTGGGC	0.463													C|||	1340	0.267572	0.3533	0.2622	5008	,	,		18368	0.1825		0.2535	False		,,,				2504	0.2577				p.V507I		Atlas-SNP	.											.	SVEP1	326	.	0			c.G1519A						PASS	.	C	ILE/VAL	1226,2836		190,846,995	54.0	53.0	54.0		1519	5.9	1.0	9	dbSNP_86	54	2174,6228		277,1620,2304	yes	missense	SVEP1	NM_153366.3	29	467,2466,3299	TT,TC,CC		25.8748,30.1822,27.2786	probably-damaging	507/3572	113261483	3400,9064	2031	4201	6232	SO:0001583	missense	79987	exon7			TGATGACATCTTT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1519G>A	9.37:g.113261483C>T	ENSP00000384917:p.Val507Ile	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	166	164	0.987952	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	553	0.2532051282051282	170	0.34552845528455284	90	0.24861878453038674	102	0.17832167832167833	191	0.2519788918205805	C	6.191	0.403446	0.11754	0.301822	0.258748	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.91	5.91	0.95273	Complement control module (2);Sushi/SCR/CCP (2);	0.116309	0.64402	D	0.000020	T	0.00012	0.0000	L	0.36672	1.1	0.27382	P	0.9553831	D;B;D	0.67145	0.983;0.355;0.996	P;B;D	0.77557	0.753;0.1;0.99	T	0.03433	-1.1037	9	0.02654	T	1	.	19.0678	0.93119	0.0:1.0:0.0:0.0	rs872665;rs3818765;rs52802511;rs60471347;rs872665	507;507;507	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	I	507;484;507;484	ENSP00000384917:V507I;ENSP00000363593:V484I;ENSP00000304118:V507I;ENSP00000363585:V484I	ENSP00000304118:V507I	V	-	1	0	SVEP1	112301304	1.000000	0.71417	1.000000	0.80357	0.214000	0.24535	2.265000	0.43311	2.813000	0.96785	0.655000	0.94253	GTC	C|0.731;T|0.269	0.269	strong		0.463	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ABCA7	10347	hgsc.bcm.edu	37	19	1055191	1055191	+	Missense_Mutation	SNP	G	G	A	rs3745842	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1055191G>A	ENST00000263094.6	+	30	4277	c.4046G>A	c.(4045-4047)cGg>cAg	p.R1349Q	ABCA7_ENST00000435683.2_Missense_Mutation_p.R1211Q|ABCA7_ENST00000433129.1_Missense_Mutation_p.R1349Q	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1349			R -> Q (in dbSNP:rs3745842). {ECO:0000269|PubMed:10873640, ECO:0000269|PubMed:11355874, ECO:0000269|PubMed:12111378}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGTGTAGCCGGCCCGGTGCC	0.677													g|||	1956	0.390575	0.3585	0.4121	5008	,	,		14407	0.3482		0.4205	False		,,,				2504	0.4315				p.R1349Q		Atlas-SNP	.											.	ABCA7	174	.	0			c.G4046A						PASS	.	G	GLN/ARG	1653,2743		312,1029,857	14.0	17.0	16.0		4046	-5.3	0.1	19	dbSNP_107	16	3614,4948		786,2042,1453	yes	missense	ABCA7	NM_019112.3	43	1098,3071,2310	AA,AG,GG		42.2098,37.6024,40.6467	benign	1349/2147	1055191	5267,7691	2198	4281	6479	SO:0001583	missense	10347	exon30			GTAGCCGGCCCGG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.4046G>A	19.37:g.1055191G>A	ENSP00000263094:p.Arg1349Gln	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	862	0.3946886446886447	159	0.3231707317073171	156	0.430939226519337	215	0.3758741258741259	332	0.43799472295514513	G	3.615	-0.078683	0.07141	0.376024	0.422098	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.94576	-3.46;-3.46	3.68	-5.26	0.02772	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.13594	0.008;0.002	B;B	0.09377	0.004;0.002	T	0.10064	-1.0646	8	0.12766	T	0.61	.	10.5156	0.44887	0.3354:0.0:0.6646:0.0	rs3745842	1211;1349	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	Q	1349	ENSP00000263094:R1349Q;ENSP00000414062:R1349Q	ENSP00000263094:R1349Q	R	+	2	0	ABCA7	1006191	0.000000	0.05858	0.077000	0.20336	0.045000	0.14185	-2.995000	0.00655	-1.084000	0.03092	-1.464000	0.01018	CGG	G|0.594;A|0.406	0.406	strong		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
DNAH10	196385	hgsc.bcm.edu	37	12	124298030	124298030	+	Missense_Mutation	SNP	G	G	A	rs143713799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124298030G>A	ENST00000409039.3	+	19	3135	c.3110G>A	c.(3109-3111)cGc>cAc	p.R1037H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1037	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GAGGTTATGCGCCACCCTCTA	0.438													G|||	65	0.0129792	0.0151	0.0058	5008	,	,		20812	0.0		0.008	False		,,,				2504	0.0337				p.R1037H		Atlas-SNP	.											DNAH10_ENST00000409039,colon,carcinoma,+1,7	DNAH10	888	7	0			c.G3110A						PASS	.	G	HIS/ARG	73,4333	64.7+/-102.0	1,71,2131	90.0	84.0	86.0		3110	0.7	0.0	12	dbSNP_134	86	125,8475	64.6+/-126.8	1,123,4176	yes	missense	DNAH10	NM_207437.3	29	2,194,6307	AA,AG,GG		1.4535,1.6568,1.5224	benign	1037/4472	124298030	198,12808	2203	4300	6503	SO:0001583	missense	196385	exon19			TTATGCGCCACCC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.3110G>A	12.37:g.124298030G>A	ENSP00000386770:p.Arg1037His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	18	0.008241758241758242	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	5.489	0.275238	0.10403	0.016568	0.014535	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.83	0.742	0.18341	.	0.186131	0.36200	N	0.002740	T	0.04137	0.0115	N	0.04959	-0.14	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.001	T	0.25572	-1.0128	10	0.44086	T	0.13	.	8.8463	0.35172	0.5998:0.0:0.4002:0.0	.	1037;912;1037	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	H	1037	ENSP00000386770:R1037H	ENSP00000386770:R1037H	R	+	2	0	DNAH10	122863983	0.001000	0.12720	0.035000	0.18076	0.004000	0.04260	0.637000	0.24659	0.067000	0.16545	-0.244000	0.11960	CGC	G|0.987;A|0.013	0.013	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
RNF175	285533	hgsc.bcm.edu	37	4	154631587	154631587	+	Missense_Mutation	SNP	C	C	G	rs1337	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:154631587C>G	ENST00000347063.4	-	9	1293	c.921G>C	c.(919-921)ttG>ttC	p.L307F		NM_173662.2	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	307			L -> F (in dbSNP:rs1337).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	13	all_hematologic(180;0.093)	Renal(120;0.118)				GCCAGGCCACCAAATAACGAA	0.458													C|||	399	0.0796725	0.0053	0.147	5008	,	,		16752	0.004		0.1889	False		,,,				2504	0.0982				p.L307F		Atlas-SNP	.											.	RNF175	40	.	0			c.G921C						PASS	.	C	PHE/LEU	142,3706		3,136,1785	83.0	75.0	78.0		921	2.5	1.0	4	dbSNP_36	78	1648,6620		155,1338,2641	yes	missense	RNF175	NM_173662.2	22	158,1474,4426	GG,GC,CC		19.9323,3.6902,14.7739	probably-damaging	307/329	154631587	1790,10326	1924	4134	6058	SO:0001583	missense	285533	exon9			GGCCACCAAATAA	BC034385	CCDS47149.1	4q31.3	2008-02-05			ENSG00000145428	ENSG00000145428		"""RING-type (C3HC4) zinc fingers"""	27735	protein-coding gene	gene with protein product							Standard	NM_173662		Approved	FLJ34190	uc003int.3	Q8N4F7	OTTHUMG00000161557	ENST00000347063.4:c.921G>C	4.37:g.154631587C>G	ENSP00000340979:p.Leu307Phe	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_173662	C9JL66|Q8NB61	Missense_Mutation	SNP	ENST00000347063.4	37	CCDS47149.1	213	0.09752747252747253	1	0.0020325203252032522	54	0.14917127071823205	1	0.0017482517482517483	157	0.20712401055408972	C	17.39	3.378453	0.61735	0.036902	0.199323	ENSG00000145428	ENST00000347063	T	0.30182	1.54	4.26	2.52	0.30459	.	0.103637	0.39146	N	0.001441	T	0.00039	0.0001	M	0.82193	2.58	0.09310	P	0.9999999999999867	D	0.59357	0.985	P	0.53518	0.728	T	0.04103	-1.0977	9	0.39692	T	0.17	-16.9333	3.9719	0.09457	0.1867:0.6155:0.0:0.1978	rs1337;rs17370770;rs1337	307	Q8N4F7	RN175_HUMAN	F	307	ENSP00000340979:L307F	ENSP00000340979:L307F	L	-	3	2	RNF175	154851037	1.000000	0.71417	0.963000	0.40424	0.988000	0.76386	1.070000	0.30653	0.720000	0.32209	0.655000	0.94253	TTG	C|0.896;G|0.104	0.104	strong		0.458	RNF175-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365286.1	NM_173662	
MUC4	4585	hgsc.bcm.edu	37	3	195508523	195508523	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508523C>T	ENST00000463781.3	-	2	10387	c.9928G>A	c.(9928-9930)Gcc>Acc	p.A3310T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3310T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3310T(2)|p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGAGTGGCGTGACCTGTG	0.567																																					p.A3310T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	4	Substitution - Missense(2)|Deletion - In frame(2)	stomach(4)	c.G9928A						scavenged	.																																			SO:0001583	missense	4585	exon2			GAGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9928G>A	3.37:g.195508523C>T	ENSP00000417498:p.Ala3310Thr	Somatic	101	2	0.019802		WXS	Illumina HiSeq	Phase_I	109	30	0.275229	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	7.818	0.717189	0.15372	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.55;1.46	0.743	-1.49	0.08718	.	.	.	.	.	T	0.14056	0.0340	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.01281	0.0	T	0.24119	-1.0169	8	.	.	.	.	1.46	0.02394	0.3334:0.3286:0.0:0.338	.	3182	E7ESK3	.	T	3310	ENSP00000417498:A3310T;ENSP00000420243:A3310T	.	A	-	1	0	MUC4	196993302	0.000000	0.05858	0.015000	0.15790	0.015000	0.08874	-2.317000	0.01122	-1.984000	0.00985	-2.041000	0.00417	GCC	.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TEX13A	56157	hgsc.bcm.edu	37	X	104464360	104464360	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:104464360G>A	ENST00000413579.1	-	3	629	c.518C>T	c.(517-519)gCa>gTa	p.A173V	IL1RAPL2_ENST00000372582.1_Intron|IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372578.3_Missense_Mutation_p.A173V|TEX13A_ENST00000372575.1_Missense_Mutation_p.A173V			Q9BXU3	TX13A_HUMAN	testis expressed 13A	173							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						CTCCTCAGCTGCTCCTTCTGT	0.642																																					p.A173V		Atlas-SNP	.											.	TEX13A	55	.	0			c.C518T						PASS	.						28.0	33.0	32.0					X																	104464360		2123	4174	6297	SO:0001583	missense	56157	exon3			TCAGCTGCTCCTT	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.518C>T	X.37:g.104464360G>A	ENSP00000399753:p.Ala173Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	38	8	0.210526	NM_031274	B1B1G8|Q32NB6	Missense_Mutation	SNP	ENST00000413579.1	37		.	.	.	.	.	.	.	.	.	.	G	14.16	2.452266	0.43531	.	.	ENSG00000133149	ENST00000372578;ENST00000372575;ENST00000413579	.	.	.	3.02	-0.0125	0.13988	.	2.067560	0.02469	N	0.087303	T	0.29256	0.0728	.	.	.	0.09310	N	1	B;B	0.17852	0.024;0.024	B;B	0.15052	0.012;0.012	T	0.16897	-1.0387	8	0.49607	T	0.09	.	2.3339	0.04242	0.3036:0.0:0.4237:0.2727	.	173;173	C9JWK0;Q9BXU3	.;TX13A_HUMAN	V	173	.	ENSP00000361656:A173V	A	-	2	0	TEX13A	104351016	0.011000	0.17503	0.000000	0.03702	0.009000	0.06853	1.241000	0.32743	-0.119000	0.11830	-0.312000	0.09012	GCA	.	.	none		0.642	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	
TNXB	7148	hgsc.bcm.edu	37	6	32025980	32025980	+	Silent	SNP	G	G	A	rs12196385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32025980G>A	ENST00000375244.3	-	22	7881	c.7680C>T	c.(7678-7680)gaC>gaT	p.D2560D	TNXB_ENST00000375247.2_Silent_p.D2560D			P22105	TENX_HUMAN	tenascin XB	2620	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGGGCCGCCCGTCCCTGTCCT	0.652													G|||	564	0.11262	0.1626	0.0432	5008	,	,		15128	0.0347		0.0994	False		,,,				2504	0.1881				p.D2560D		Atlas-SNP	.											.	TNXB	553	.	0			c.C7680T						PASS	.	G		418,2146		33,352,897	55.0	63.0	60.0		7680	-8.4	0.1	6	dbSNP_120	60	448,4642		25,398,2122	no	coding-synonymous	TNXB	NM_019105.6		58,750,3019	AA,AG,GG		8.8016,16.3027,11.3143		2560/4243	32025980	866,6788	1282	2545	3827	SO:0001819	synonymous_variant	7148	exon22			CCGCCCGTCCCTG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7680C>T	6.37:g.32025980G>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	251	123	0.49004	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.900;A|0.100	0.100	strong		0.652	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
PRKG1	5592	hgsc.bcm.edu	37	10	52751177	52751177	+	Missense_Mutation	SNP	G	G	A	rs202017913		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:52751177G>A	ENST00000401604.2	+	1	233	c.39G>A	c.(37-39)atG>atA	p.M13I	PRKG1_ENST00000373985.1_Start_Codon_SNP_p.M1I			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	13	Leucine-zipper.|Required for dimerization.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		AGATTCTCATGCTCAAGGAGG	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		10226	0.0		0.001	False		,,,				2504	0.0				p.M13I		Atlas-SNP	.											.	PRKG1	167	.	0			c.G39A						PASS	.	G	ILE/MET	1,3781		0,1,1890	22.0	28.0	26.0		39	4.8	1.0	10		26	8,8204		0,8,4098	yes	missense	PRKG1	NM_001098512.2	10	0,9,5988	AA,AG,GG		0.0974,0.0264,0.075	benign	13/672	52751177	9,11985	1891	4106	5997	SO:0001583	missense	5592	exon1			TCTCATGCTCAAG		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.39G>A	10.37:g.52751177G>A	ENSP00000384200:p.Met13Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	106	43	0.40566	NM_001098512	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.956344	0.34565	2.64E-4	9.74E-4	ENSG00000185532	ENST00000401604;ENST00000373985	T;T	0.66638	-0.22;-0.13	4.76	4.76	0.60689	.	.	.	.	.	T	0.48466	0.1501	N	0.08118	0	0.27645	N	0.947607	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.33369	-0.9871	9	0.30854	T	0.27	.	15.5982	0.76602	0.0:0.0:1.0:0.0	.	13;13	B4DT93;Q13976	.;KGP1_HUMAN	I	13;1	ENSP00000384200:M13I;ENSP00000363097:M1I	ENSP00000363097:M1I	M	+	3	0	PRKG1	52421183	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.962000	0.63687	2.349000	0.79799	0.462000	0.41574	ATG	.	.	weak		0.567	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OVGP1	5016	hgsc.bcm.edu	37	1	111957245	111957245	+	Silent	SNP	G	G	A	rs9629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111957245G>A	ENST00000369732.3	-	11	1933	c.1878C>T	c.(1876-1878)ccC>ccT	p.P626P		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	626					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		GCTGGATGACGGGGCTGGAGG	0.507													A|||	960	0.191693	0.115	0.1945	5008	,	,		17829	0.1885		0.2724	False		,,,				2504	0.2137				p.P626P		Atlas-SNP	.											.	OVGP1	177	.	0			c.C1878T						PASS	.	A		629,3777	767.7+/-413.5	40,549,1614	89.0	85.0	86.0		1878	0.7	0.1	1	dbSNP_52	86	2474,6126	695.9+/-404.8	331,1812,2157	no	coding-synonymous	OVGP1	NM_002557.3		371,2361,3771	AA,AG,GG		28.7674,14.276,23.8582		626/679	111957245	3103,9903	2203	4300	6503	SO:0001819	synonymous_variant	5016	exon11			GATGACGGGGCTG	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1878C>T	1.37:g.111957245G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_002557	A0AV19|B9EGE1|Q15841	Silent	SNP	ENST00000369732.3	37	CCDS834.1																																																																																			G|0.784;A|0.216	0.216	strong		0.507	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
OR5L1	219437	hgsc.bcm.edu	37	11	55579643	55579643	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55579643G>T	ENST00000333973.2	+	1	790	c.701G>T	c.(700-702)aGg>aTg	p.R234M		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	234						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R234K(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				GCAGAGGGCAGGCACAAAGCC	0.507																																					p.R234M		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	1	1	Substitution - Missense(1)	prostate(1)	c.G701T						scavenged	.						190.0	155.0	167.0					11																	55579643		2200	4296	6496	SO:0001583	missense	219437	exon1			AGGGCAGGCACAA	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.701G>T	11.37:g.55579643G>T	ENSP00000335529:p.Arg234Met	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	166	2	0.0120482	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	g	20.6	4.012501	0.75161	.	.	ENSG00000186117	ENST00000333973	T	0.00333	8.07	4.12	2.2	0.27929	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000027	T	0.00906	0.0030	M	0.92604	3.325	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.24261	-1.0165	10	0.87932	D	0	-25.907	8.4084	0.32629	0.1987:0.0:0.8013:0.0	.	234	Q8NGL2	OR5L1_HUMAN	M	234	ENSP00000335529:R234M	ENSP00000335529:R234M	R	+	2	0	OR5L1	55336219	0.000000	0.05858	0.001000	0.08648	0.869000	0.49853	0.630000	0.24553	0.736000	0.32559	0.428000	0.28381	AGG	.	.	none		0.507	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
RNF126	55658	hgsc.bcm.edu	37	19	648173	648173	+	Silent	SNP	G	G	C	rs2072104	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:648173G>C	ENST00000292363.5	-	9	1046	c.891C>G	c.(889-891)tcC>tcG	p.S297S		NM_194460.2	NP_919442.1			ring finger protein 126											lung(1)	1		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCTGGAGGAGGACGATGACG	0.657													g|||	151	0.0301518	0.003	0.0303	5008	,	,		8959	0.0179		0.0616	False		,,,				2504	0.047				p.S297S		Atlas-SNP	.											.	RNF126	15	.	0			c.C891G						PASS	.	G		43,4351		1,41,2155	97.0	78.0	84.0		891	-0.3	0.8	19	dbSNP_96	84	442,8150		3,436,3857	no	coding-synonymous	RNF126	NM_194460.2		4,477,6012	CC,CG,GG		5.1443,0.9786,3.7348		297/312	648173	485,12501	2197	4296	6493	SO:0001819	synonymous_variant	55658	exon9			GGAGGAGGACGAT	BC025374	CCDS12039.1	19p13.3	2013-01-09				ENSG00000070423		"""RING-type (C3HC4) zinc fingers"""	21151	protein-coding gene	gene with protein product		615177					Standard	NM_194460		Approved	FLJ20552	uc010drs.3	Q9BV68		ENST00000292363.5:c.891C>G	19.37:g.648173G>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	77	0.616	NM_194460		Silent	SNP	ENST00000292363.5	37	CCDS12039.1																																																																																			G|0.964;C|0.036	0.036	strong		0.657	RNF126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452104.2	NM_017876	
MCCC1	56922	hgsc.bcm.edu	37	3	182755209	182755209	+	Missense_Mutation	SNP	T	T	G	rs2270968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:182755209T>G	ENST00000265594.4	-	13	1537	c.1391A>C	c.(1390-1392)cAc>cCc	p.H464P	MCCC1_ENST00000492597.1_Missense_Mutation_p.H355P|MCCC1_ENST00000539926.1_Missense_Mutation_p.H329P|MCCC1_ENST00000489909.1_5'Flank	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	464	Biotin carboxylation.		H -> P (in dbSNP:rs2270968). {ECO:0000269|PubMed:11181649, ECO:0000269|PubMed:11406611, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	AATGTTGGTGTGCAGTCCAAC	0.433													T|||	2328	0.464856	0.1929	0.6297	5008	,	,		20070	0.3323		0.7346	False		,,,				2504	0.5746				p.H464P		Atlas-SNP	.											.	MCCC1	87	.	0			c.A1391C						PASS	.	T	PRO/HIS	1267,3139	433.7+/-343.7	204,859,1140	91.0	81.0	84.0		1391	3.5	1.0	3	dbSNP_100	84	6339,2261	707.6+/-405.6	2336,1667,297	yes	missense	MCCC1	NM_020166.3	77	2540,2526,1437	GG,GT,TT		26.2907,28.7562,41.5193	benign	464/726	182755209	7606,5400	2203	4300	6503	SO:0001583	missense	56922	exon13			TTGGTGTGCAGTC	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1391A>C	3.37:g.182755209T>G	ENSP00000265594:p.His464Pro	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	1043	0.4775641025641026	109	0.22154471544715448	209	0.5773480662983426	182	0.3181818181818182	543	0.716358839050132	T	9.294	1.051243	0.19827	0.287562	0.737093	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176;ENST00000448585	T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43	5.93	3.51	0.40186	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.212673	0.64402	D	0.000020	T	0.00012	0.0000	N	0.00175	-1.925	0.36830	P	0.11313200000000001	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.003;0.001;0.004	T	0.46582	-0.9181	9	0.28530	T	0.3	.	8.3092	0.32060	0.0:0.3158:0.0:0.6842	rs2270968;rs3207461;rs11540929;rs17408941;rs17845000;rs17857761;rs17857766;rs52791788;rs2270968	417;355;464	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	P	464;355;314;329;417;417	ENSP00000265594:H464P;ENSP00000419898:H355P;ENSP00000441253:H329P;ENSP00000420433:H417P	ENSP00000265594:H464P	H	-	2	0	MCCC1	184237903	1.000000	0.71417	0.990000	0.47175	0.990000	0.78478	1.118000	0.31246	0.474000	0.27392	0.459000	0.35465	CAC	T|0.479;G|0.521	0.521	strong		0.433	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
SERPINF2	5345	hgsc.bcm.edu	37	17	1648294	1648294	+	Missense_Mutation	SNP	C	C	T	rs2070862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1648294C>T	ENST00000324015.3	+	2	82	c.5C>T	c.(4-6)gCg>gTg	p.A2V	SERPINF2_ENST00000450523.2_Missense_Mutation_p.A2V|SERPINF2_ENST00000382061.4_Missense_Mutation_p.A2V	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	2			A -> V (in dbSNP:rs2070862). {ECO:0000269|PubMed:15489334}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	AGGAACATGGCGCTGCTCTGG	0.642													C|||	991	0.197883	0.236	0.245	5008	,	,		13572	0.1716		0.2237	False		,,,				2504	0.1135				p.A2V		Atlas-SNP	.											SERPINF2,NS,carcinoma,-1,1	SERPINF2	33	1	0			c.C5T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	1065,3341	386.3+/-326.1	140,785,1278	50.0	47.0	48.0		5,5,5	-0.9	0.8	17	dbSNP_96	48	1902,6698	335.9+/-321.6	222,1458,2620	yes	missense,missense,missense	SERPINF2	NM_000934.3,NM_001165920.1,NM_001165921.1	64,64,64	362,2243,3898	TT,TC,CC		22.1163,24.1716,22.8125	possibly-damaging,possibly-damaging,possibly-damaging	2/492,2/492,2/428	1648294	2967,10039	2203	4300	6503	SO:0001583	missense	5345	exon2			ACATGGCGCTGCT	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"""Serine (or cysteine) peptidase inhibitors"""	9075	protein-coding gene	gene with protein product	"""alpha-2-plasmin inhibitor"", ""alpha-2-antiplasmin"""	613168	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"""	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.5C>T	17.37:g.1648294C>T	ENSP00000321853:p.Ala2Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Missense_Mutation	SNP	ENST00000324015.3	37	CCDS11011.1	475	0.2174908424908425	109	0.22154471544715448	84	0.23204419889502761	102	0.17832167832167833	180	0.23746701846965698	C	12.20	1.866016	0.32977	0.241716	0.221163	ENSG00000167711	ENST00000453066;ENST00000324015;ENST00000450523;ENST00000423861;ENST00000453723;ENST00000382061	D;D;D;D;D	0.86230	-1.78;-1.91;-2.09;-1.6;-1.91	4.85	-0.868	0.10652	.	1.218600	0.05399	N	0.540414	T	0.00073	0.0002	N	0.14661	0.345	0.45528	P	0.0015140000000000153	B;B	0.10296	0.003;0.003	B;B	0.06405	0.002;0.002	T	0.02126	-1.1209	9	0.32370	T	0.25	.	8.9521	0.35796	0.0:0.4852:0.0:0.5148	rs2070862;rs57053177;rs2070862	2;2	B4E1B7;P08697	.;A2AP_HUMAN	V	2	ENSP00000402286:A2V;ENSP00000321853:A2V;ENSP00000403877:A2V;ENSP00000402056:A2V;ENSP00000371493:A2V	ENSP00000321853:A2V	A	+	2	0	SERPINF2	1595044	0.401000	0.25303	0.840000	0.33206	0.798000	0.45092	-0.536000	0.06135	-0.288000	0.09051	-0.263000	0.10527	GCG	C|0.780;T|0.220	0.220	strong		0.642	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934	
NALCN	259232	hgsc.bcm.edu	37	13	101735211	101735211	+	Silent	SNP	G	G	A	rs17677552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:101735211G>A	ENST00000251127.6	-	33	3795	c.3714C>T	c.(3712-3714)acC>acT	p.T1238T		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1238					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CCAAAGGTACGGTCACCGGGT	0.512													G|||	1633	0.326078	0.118	0.2536	5008	,	,		19082	0.506		0.3668	False		,,,				2504	0.4315				p.T1238T		Atlas-SNP	.											.	NALCN	431	.	0			c.C3714T						PASS	.	G		573,3833	254.9+/-260.3	33,507,1663	127.0	114.0	118.0		3714	-11.3	0.0	13	dbSNP_123	118	3015,5585	465.4+/-366.5	532,1951,1817	no	coding-synonymous	NALCN	NM_052867.2		565,2458,3480	AA,AG,GG		35.0581,13.005,27.5873		1238/1739	101735211	3588,9418	2203	4300	6503	SO:0001819	synonymous_variant	259232	exon33			AGGTACGGTCACC	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.3714C>T	13.37:g.101735211G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			G|0.699;A|0.301	0.301	strong		0.512	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
LARS	51520	hgsc.bcm.edu	37	5	145508637	145508637	+	Silent	SNP	A	A	C	rs61732382|rs35977062	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145508637A>C	ENST00000394434.2	-	26	2839	c.2673T>G	c.(2671-2673)gtT>gtG	p.V891V	LARS_ENST00000545646.1_Silent_p.V845V|LARS_ENST00000274562.9_Silent_p.V864V|LARS_ENST00000510191.1_Silent_p.V837V	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	891					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.V891V(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	AAACTTCATTAACAGGACCTG	0.353													C|||	910	0.181709	0.0076	0.3775	5008	,	,		14540	0.1984		0.2525	False		,,,				2504	0.1881				p.V891V		Atlas-SNP	.											LARS,NS,carcinoma,0,1	LARS	100	1	1	Substitution - coding silent(1)	stomach(1)	c.T2673G						PASS	.	C		260,4146	793.6+/-415.2	12,236,1955	68.0	77.0	74.0		2673	4.8	1.0	5	dbSNP_129	74	2381,6217	691.9+/-404.5	352,1677,2270	no	coding-synonymous	LARS	NM_020117.9		364,1913,4225	CC,CA,AA		27.6925,5.901,20.3091		891/1177	145508637	2641,10363	2203	4299	6502	SO:0001819	synonymous_variant	51520	exon26			TTCATTAACAGGA	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2673T>G	5.37:g.145508637A>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			A|0.808;C|0.192	0.192	strong		0.353	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
PATE4	399968	hgsc.bcm.edu	37	11	125707761	125707761	+	Splice_Site	SNP	A	A	C	rs11220236	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:125707761A>C	ENST00000457514.2	+	2	102		c.e2-1		PATE4_ENST00000534411.1_Intron	NM_001144874.1	NP_001138346.1	P0C8F1	PATE4_HUMAN	prostate and testis expressed 4						regulation of synaptic transmission (GO:0050804)|response to wounding (GO:0009611)	acrosomal vesicle (GO:0001669)|extracellular space (GO:0005615)				breast(1)	1						TCCACCCTGCAGTTATGGGTC	0.428													a|||	2468	0.492812	0.4017	0.4553	5008	,	,		21069	0.5308		0.5775	False		,,,				2504	0.5164				.		Atlas-SNP	.											.	PATE4	10	.	0			c.59-2A>C						PASS	.						71.0	63.0	65.0					11																	125707761		692	1591	2283	SO:0001630	splice_region_variant	399968	exon2			CCCTGCAGTTATG	AK123042	CCDS44765.1	11q24.2	2010-07-14			ENSG00000237353	ENSG00000237353		"""PATE family"""	35427	protein-coding gene	gene with protein product						18390568	Standard	NM_001144874		Approved	FLJ41047, PATE-B	uc001qcv.3	P0C8F1	OTTHUMG00000165235	ENST00000457514.2:c.59-1A>C	11.37:g.125707761A>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_001144874		Splice_Site	SNP	ENST00000457514.2	37	CCDS44765.1	1130	0.5173992673992674	197	0.40040650406504064	168	0.46408839779005523	319	0.5576923076923077	446	0.5883905013192612	a	13.30	2.195114	0.38806	.	.	ENSG00000237353	ENST00000457514	.	.	.	1.33	1.33	0.21861	.	.	.	.	.	.	.	.	.	.	.	0.44469	P	0.002595000000000014	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8024	0.13303	1.0:0.0:0.0:0.0	rs11220236;rs57766539;rs11220236	.	.	.	.	-1	.	.	.	+	.	.	PATE4	125212971	0.033000	0.19621	0.006000	0.13384	0.784000	0.44337	1.272000	0.33109	0.862000	0.35528	0.378000	0.23410	.	A|0.479;C|0.521	0.521	strong		0.428	PATE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382865.1	NM_001144874	Intron
PKHD1	5314	hgsc.bcm.edu	37	6	51875250	51875250	+	Missense_Mutation	SNP	A	A	C	rs2435322	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:51875250A>C	ENST00000371117.3	-	35	5883	c.5608T>G	c.(5608-5610)Ttg>Gtg	p.L1870V	PKHD1_ENST00000340994.4_Missense_Mutation_p.L1870V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1870			L -> V (in dbSNP:rs2435322). {ECO:0000269|PubMed:11898128, ECO:0000269|PubMed:12846734, ECO:0000269|PubMed:12874454}.		cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TCTCTTTCCAATTTAGGGCTG	0.398													C|||	4787	0.955871	0.8374	0.9914	5008	,	,		17314	1.0		1.0	False		,,,				2504	1.0				p.L1870V		Atlas-SNP	.											PKHD1,NS,carcinoma,+2,1	PKHD1	927	1	0			c.T5608G						PASS	.	C	VAL/LEU,VAL/LEU	3814,592	260.4+/-263.7	1650,514,39	118.0	112.0	114.0		5608,5608	5.6	1.0	6	dbSNP_100	114	8592,8	7.1+/-27.0	4292,8,0	yes	missense,missense	PKHD1	NM_138694.3,NM_170724.2	32,32	5942,522,39	CC,CA,AA		0.093,13.4362,4.6133	benign,benign	1870/4075,1870/3397	51875250	12406,600	2203	4300	6503	SO:0001583	missense	5314	exon35			TTTCCAATTTAGG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.5608T>G	6.37:g.51875250A>C	ENSP00000360158:p.Leu1870Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	182	182	1	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	2113	0.9674908424908425	422	0.8577235772357723	361	0.9972375690607734	572	1.0	758	1.0	C	3.145	-0.175481	0.06421	0.865638	0.99907	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.84442	-1.58;-1.85	5.63	5.63	0.86233	.	0.000000	0.64402	N	0.000004	T	0.41305	0.1153	N	0.01048	-1.04	0.43308	P	0.0046840000000000215	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42050	-0.9474	9	0.02654	T	1	.	16.157	0.81675	0.1346:0.8654:0.0:0.0	rs2435322;rs52810648;rs60052625	1870;1870	P08F94-2;P08F94	.;PKHD1_HUMAN	V	1870	ENSP00000360158:L1870V;ENSP00000341097:L1870V	ENSP00000341097:L1870V	L	-	1	2	PKHD1	51983209	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.050000	0.64251	1.396000	0.46663	-0.224000	0.12420	TTG	A|0.049;C|0.951	0.951	strong		0.398	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
FILIP1	27145	hgsc.bcm.edu	37	6	76018475	76018475	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:76018475A>G	ENST00000237172.7	-	6	3904	c.3574T>C	c.(3574-3576)Tct>Cct	p.S1192P	FILIP1_ENST00000370020.1_Missense_Mutation_p.S1093P|FILIP1_ENST00000393004.2_Intron|FILIP1_ENST00000498523.1_5'UTR	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1192										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						ATTTTCATAGACTGAGTCTCA	0.532																																					p.S1192P		Atlas-SNP	.											FILIP1,colon,carcinoma,+2,1	FILIP1	173	1	0			c.T3574C						scavenged	.						88.0	85.0	86.0					6																	76018475		2203	4300	6503	SO:0001583	missense	27145	exon6			TCATAGACTGAGT	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.3574T>C	6.37:g.76018475A>G	ENSP00000237172:p.Ser1192Pro	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	217	3	0.0138249	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.720765	0.89205	.	.	ENSG00000118407	ENST00000237172;ENST00000370020	T;T	0.22743	1.94;1.96	6.06	6.06	0.98353	.	0.746995	0.13869	N	0.357140	T	0.35128	0.0921	L	0.53249	1.67	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.78314	0.991;0.991	T	0.03829	-1.1000	10	0.62326	D	0.03	-11.4081	16.6154	0.84909	1.0:0.0:0.0:0.0	.	1192;1192	A8K2G7;Q7Z7B0	.;FLIP1_HUMAN	P	1192;1093	ENSP00000237172:S1192P;ENSP00000359037:S1093P	ENSP00000237172:S1192P	S	-	1	0	FILIP1	76075195	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.047000	0.76599	2.315000	0.78130	0.533000	0.62120	TCT	.	.	none		0.532	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179	
MYH11	4629	hgsc.bcm.edu	37	16	15820863	15820863	+	Missense_Mutation	SNP	C	C	T	rs16967494|rs587781052	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15820863C>T	ENST00000300036.5	-	28	3809	c.3700G>A	c.(3700-3702)Gca>Aca	p.A1234T	MYH11_ENST00000396324.3_Missense_Mutation_p.A1241T|MYH11_ENST00000576790.2_Missense_Mutation_p.A1234T|AF001548.5_ENST00000574212.1_RNA|MYH11_ENST00000452625.2_Missense_Mutation_p.A1241T	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1234			A -> T (in dbSNP:rs16967494).		axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GCCAGGTCTGCGTTCTCTTTC	0.607			T	CBFB	AML								C|||	1021	0.203874	0.0575	0.2349	5008	,	,		15848	0.2728		0.2883	False		,,,				2504	0.2219				p.A1241T		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G3721A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	434,3960	210.5+/-231.0	22,390,1785	150.0	162.0	158.0		3721,3721,3700,3700	4.7	1.0	16	dbSNP_123	158	2253,6347	379.3+/-339.2	314,1625,2361	yes	missense,missense,missense,missense	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	58,58,58,58	336,2015,4146	TT,TC,CC		26.1977,9.8771,20.6788	benign,benign,benign,benign	1241/1946,1241/1980,1234/1973,1234/1939	15820863	2687,10307	2197	4300	6497	SO:0001583	missense	4629	exon29			GGTCTGCGTTCTC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.3700G>A	16.37:g.15820863C>T	ENSP00000300036:p.Ala1234Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	517	0.2367216117216117	39	0.07926829268292683	84	0.23204419889502761	173	0.30244755244755245	221	0.29155672823219	C	10.49	1.365018	0.24684	0.098771	0.261977	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15	4.68	4.68	0.58851	Myosin tail (1);	0.149078	0.46758	D	0.000279	T	0.00012	0.0000	N	0.12961	0.28	0.26208	P	0.9793493	B;B;B;B;B	0.21225	0.053;0.013;0.013;0.013;0.013	B;B;B;B;B	0.19391	0.025;0.015;0.015;0.015;0.025	T	0.05582	-1.0876	9	0.72032	D	0.01	.	12.1208	0.53889	0.1712:0.8288:0.0:0.0	rs16967494;rs52835098;rs57715348;rs16967494	1241;1234;1241;1234;1241	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	T	1234;1234;1241;1241;1241	ENSP00000300036:A1234T;ENSP00000345136:A1234T;ENSP00000379616:A1241T;ENSP00000407821:A1241T	ENSP00000300036:A1234T	A	-	1	0	MYH11	15728364	0.184000	0.23200	0.998000	0.56505	0.595000	0.36748	0.783000	0.26802	2.311000	0.77944	0.655000	0.94253	GCA	C|0.787;N|0.000	.	strong		0.607	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
PTCHD3	374308	hgsc.bcm.edu	37	10	27687965	27687965	+	Missense_Mutation	SNP	A	A	G	rs2505327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:27687965A>G	ENST00000438700.3	-	4	1679	c.1562T>C	c.(1561-1563)aTg>aCg	p.M521T		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	521	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.		M -> T (in dbSNP:rs2505327). {ECO:0000269|PubMed:14702039}.		spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TAACAGGGTCATTCCTGTATA	0.378													G|||	2754	0.54992	0.5257	0.5202	5008	,	,		17467	0.37		0.6829	False		,,,				2504	0.6524				p.M521T		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T1562C						PASS	.	G	THR/MET	2356,2050	566.8+/-382.0	623,1110,470	88.0	83.0	85.0		1562	4.1	1.0	10	dbSNP_100	85	5860,2738	434.5+/-357.7	2005,1850,444	yes	missense	PTCHD3	NM_001034842.3	81	2628,2960,914	GG,GA,AA		31.8446,46.5275,36.8194	benign	521/768	27687965	8216,4788	2203	4299	6502	SO:0001583	missense	374308	exon4			AGGGTCATTCCTG	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1562T>C	10.37:g.27687965A>G	ENSP00000417658:p.Met521Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	1160	0.5311355311355311	264	0.5365853658536586	203	0.5607734806629834	178	0.3111888111888112	515	0.679419525065963	G	0.049	-1.256648	0.01457	0.534725	0.681554	ENSG00000182077	ENST00000438700	D	0.85171	-1.95	4.08	4.08	0.47627	Sterol-sensing domain (1);	0.309039	0.33670	N	0.004672	T	0.00012	0.0000	N	0.00074	-2.255	0.41104	P	0.014306999999999959	B	0.02656	0.0	B	0.04013	0.001	T	0.44112	-0.9349	9	0.06891	T	0.86	-7.2652	11.7298	0.51730	0.0888:0.0:0.9112:0.0	rs2505327;rs17560889;rs17681915;rs52836106;rs59351710;rs2505327	521	Q3KNS1	PTHD3_HUMAN	T	521	ENSP00000417658:M521T	ENSP00000417658:M521T	M	-	2	0	PTCHD3	27727971	1.000000	0.71417	0.970000	0.41538	0.248000	0.25809	3.946000	0.56644	0.934000	0.37316	-0.338000	0.08134	ATG	A|0.411;G|0.589	0.589	strong		0.378	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
MST1L	11223	hgsc.bcm.edu	37	1	17085780	17085780	+	RNA	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17085780G>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GCCGCACGTCGTCTGTACAAC	0.692																																					p.D347D		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,6	.	.	6	0			c.C1041T						scavenged	.																																					11223	exon8			CACGTCGTCTGTA	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17085780G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	162	21	0.12963	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				.	.	none		0.692	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
SMYD3	64754	hgsc.bcm.edu	37	1	246670481	246670481	+	Missense_Mutation	SNP	C	C	G	rs7520453	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:246670481C>G	ENST00000388985.4	-	1	38	c.39G>C	c.(37-39)aaG>aaC	p.K13N	SMYD3_ENST00000403792.3_Missense_Mutation_p.K13N|SMYD3_ENST00000490107.1_5'UTR			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	13	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.			K -> N (in Ref. 1; BAB86333 and 6; AAH31010). {ECO:0000305}.	cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)			breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		CGTTTCCCCTCTTGGCGGTTG	0.687													G|||	3749	0.748602	0.472	0.8329	5008	,	,		11891	0.9028		0.8618	False		,,,				2504	0.7873				p.K13N		Atlas-SNP	.											.	SMYD3	77	.	0			c.G39C						PASS	.	G	ASN/LYS	757,627		204,349,139	31.0	42.0	38.0		39	2.1	0.0	1	dbSNP_116	38	2789,393		1216,357,18	yes	missense	SMYD3	NM_001167740.1	94	1420,706,157	GG,GC,CC		12.3507,45.3035,22.339		13/429	246670481	3546,1020	692	1591	2283	SO:0001583	missense	64754	exon1			TCCCCTCTTGGCG	AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	15513	protein-coding gene	gene with protein product		608783	"""zinc finger, MYND domain containing 1"""	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.39G>C	1.37:g.246670481C>G	ENSP00000373637:p.Lys13Asn	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Missense_Mutation	SNP	ENST00000388985.4	37	CCDS53486.1	1709	0.7825091575091575	239	0.48577235772357724	303	0.8370165745856354	514	0.8986013986013986	653	0.8614775725593667	G	9.680	1.149145	0.21288	0.546965	0.876493	ENSG00000185420	ENST00000388985;ENST00000403792	T;T	0.13196	2.61;2.61	5.31	2.13	0.27403	SET domain (1);	0.788812	0.11174	N	0.591676	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.14448	-1.0472	9	0.17369	T	0.5	-0.0363	8.0023	0.30304	0.09:0.4822:0.4278:0.0	rs7520453;rs59425251;rs7520453	13	Q9H7B4	SMYD3_HUMAN	N	13	ENSP00000373637:K13N;ENSP00000385380:K13N	ENSP00000373637:K13N	K	-	3	2	SMYD3	244737104	0.004000	0.15560	0.006000	0.13384	0.609000	0.37215	0.597000	0.24059	0.222000	0.20900	-0.322000	0.08575	AAG	C|0.219;G|0.781	0.781	strong		0.687	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743	
RNF166	115992	hgsc.bcm.edu	37	16	88767769	88767769	+	Silent	SNP	G	G	C	rs2306049	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88767769G>C	ENST00000312838.4	-	2	308	c.213C>G	c.(211-213)ctC>ctG	p.L71L	RP5-1142A6.5_ENST00000561699.1_RNA|RNF166_ENST00000568683.1_5'Flank|RNF166_ENST00000541206.2_5'UTR|RNF166_ENST00000537718.2_5'Flank|RNF166_ENST00000562499.1_5'UTR|RNF166_ENST00000567844.1_Intron	NM_178841.3	NP_849163.1	Q96A37	RN166_HUMAN	ring finger protein 166	71							zinc ion binding (GO:0008270)			endometrium(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		GCAGGCGGCAGAGTGGGCACA	0.662													G|||	1945	0.388379	0.2995	0.4265	5008	,	,		14677	0.3194		0.5417	False		,,,				2504	0.3947				p.L71L		Atlas-SNP	.											.	RNF166	3	.	0			c.C213G						PASS	.	G	,,	1501,2893	473.5+/-356.7	248,1005,944	67.0	62.0	64.0		,,213	1.2	1.0	16	dbSNP_100	64	4917,3683	618.8+/-396.8	1433,2051,816	no	intron,utr-5,coding-synonymous	RNF166	NM_001171815.1,NM_001171816.1,NM_178841.3	,,	1681,3056,1760	CC,CG,GG		42.8256,34.1602,49.392	,,	,,71/238	88767769	6418,6576	2197	4300	6497	SO:0001819	synonymous_variant	115992	exon2			GCGGCAGAGTGGG	AK057106	CCDS10969.1, CCDS54056.1, CCDS54057.1	16q24.3	2013-01-09			ENSG00000158717	ENSG00000158717		"""RING-type (C3HC4) zinc fingers"""	28856	protein-coding gene	gene with protein product						12477932	Standard	NM_178841		Approved	MGC2647, MGC14381	uc002flk.3	Q96A37	OTTHUMG00000137863	ENST00000312838.4:c.213C>G	16.37:g.88767769G>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_178841	B3KQ03|D3DX75|H3BTU8|Q96DM0	Silent	SNP	ENST00000312838.4	37	CCDS10969.1																																																																																			G|0.537;C|0.463	0.463	strong		0.662	RNF166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269544.1	NM_178841	
SH2D1B	117157	hgsc.bcm.edu	37	1	162367071	162367071	+	Silent	SNP	C	C	T	rs17852003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:162367071C>T	ENST00000367929.2	-	4	507	c.398G>A	c.(397-399)tGa>tAa	p.*133*	SH2D1B_ENST00000359567.3_Silent_p.*78*	NM_053282.4	NP_444512.2	O14796	SH21B_HUMAN	SH2 domain containing 1B	0					leukocyte activation involved in immune response (GO:0002366)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of innate immune response (GO:0045089)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of natural killer cell activation (GO:0032814)	intracellular (GO:0005622)	protein binding, bridging (GO:0030674)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			GCCTTATCTTCAAGGCAAGAC	0.458													C|||	1539	0.307308	0.4418	0.2925	5008	,	,		19423	0.2063		0.3171	False		,,,				2504	0.2301				p.X133X		Atlas-SNP	.											.	SH2D1B	19	.	0			c.G398A						PASS	.	C		1827,2579	532.8+/-373.5	377,1073,753	93.0	85.0	88.0		398	2.9	1.0	1	dbSNP_123	88	2620,5980	423.6+/-354.4	384,1852,2064	no	coding-synonymous	SH2D1B	NM_053282.4		761,2925,2817	TT,TC,CC		30.4651,41.4662,34.1919		133/133	162367071	4447,8559	2203	4300	6503	SO:0001819	synonymous_variant	117157	exon4			TATCTTCAAGGCA	AF484964	CCDS30928.1	1q23.3	2013-02-14			ENSG00000198574	ENSG00000198574		"""SH2 domain containing"""	30416	protein-coding gene	gene with protein product		608510				9000139, 11689425	Standard	NM_053282		Approved	EAT2	uc001gbz.1	O14796	OTTHUMG00000031377	ENST00000367929.2:c.398G>A	1.37:g.162367071C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_053282	B2RBN6|Q5T0L1|Q8NI18|Q969K9	Silent	SNP	ENST00000367929.2	37	CCDS30928.1																																																																																			C|0.671;T|0.329	0.329	strong		0.458	SH2D1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076794.1	NM_053282	
DNAH12	201625	hgsc.bcm.edu	37	3	57414097	57414097	+	Missense_Mutation	SNP	T	T	A	rs17793014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:57414097T>A	ENST00000351747.2	-	35	5442	c.5262A>T	c.(5260-5262)aaA>aaT	p.K1754N		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1754			K -> N (in dbSNP:rs17793014).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GAGGCACATATTTAAAATAAT	0.259													T|||	1189	0.23742	0.1157	0.2651	5008	,	,		17345	0.0853		0.4423	False		,,,				2504	0.3282				p.K1754N		Atlas-SNP	.											.	DNAH12	182	.	0			c.A5262T						PASS	.						10.0	10.0	10.0					3																	57414097		692	1562	2254	SO:0001583	missense	201625	exon35			CACATATTTAAAA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.5262A>T	3.37:g.57414097T>A	ENSP00000295937:p.Lys1754Asn	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		581	0.266025641025641	77	0.1565040650406504	110	0.30386740331491713	42	0.07342657342657342	352	0.46437994722955145	T	3.072	-0.190912	0.06299	.	.	ENSG00000174844	ENST00000351747	T	0.20738	2.05	3.21	-2.61	0.06171	.	.	.	.	.	T	0.00012	0.0000	N	0.20986	0.625	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.48811	-0.9002	8	0.23302	T	0.38	.	3.1973	0.06637	0.1889:0.3487:0.0:0.4624	rs17793014;rs17793014	1754	Q6ZR08	DYH12_HUMAN	N	1754	ENSP00000295937:K1754N	ENSP00000295937:K1754N	K	-	3	2	DNAH12	57389137	0.145000	0.22656	0.001000	0.08648	0.019000	0.09904	0.906000	0.28517	-0.524000	0.06400	-1.542000	0.00909	AAA	T|0.739;A|0.261	0.261	strong		0.259	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
C6orf195	154386	hgsc.bcm.edu	37	6	2623960	2623960	+	Missense_Mutation	SNP	T	T	C	rs201134793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:2623960T>C	ENST00000296847.3	-	3	620	c.97A>G	c.(97-99)Atg>Gtg	p.M33V		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	33										cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				AGTGGCTCCATGCCATCAAAT	0.592													T|||	5	0.000998403	0.0	0.0043	5008	,	,		17886	0.0		0.002	False		,,,				2504	0.0				p.M33V		Atlas-SNP	.											.	C6orf195	10	.	0			c.A97G						PASS	.	T	VAL/MET	0,4034		0,0,2017	38.0	45.0	42.0		97	-0.6	0.0	6		42	25,8323		0,25,4149	yes	missense	C6orf195	NM_152554.2	21	0,25,6166	CC,CT,TT		0.2995,0.0,0.2019	benign	33/128	2623960	25,12357	2017	4174	6191	SO:0001583	missense	154386	exon3			GCTCCATGCCATC	AK056496	CCDS43416.1	6p25.2	2008-10-21			ENSG00000164385	ENSG00000164385			21600	protein-coding gene	gene with protein product							Standard	NM_152554		Approved	FLJ31934, bA145H9.2	uc003mtw.2	Q96MT4	OTTHUMG00000014122	ENST00000296847.3:c.97A>G	6.37:g.2623960T>C	ENSP00000296847:p.Met33Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_152554	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Missense_Mutation	SNP	ENST00000296847.3	37	CCDS43416.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	5.297	0.240255	0.10023	0.0	0.002995	ENSG00000164385	ENST00000296847	T	0.33438	1.41	3.3	-0.649	0.11461	.	.	.	.	.	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38222	-0.9671	9	0.87932	D	0	.	2.698	0.05140	0.2349:0.433:0.0:0.3322	.	33	Q96MT4	CF195_HUMAN	V	33	ENSP00000296847:M33V	ENSP00000296847:M33V	M	-	1	0	C6orf195	2568959	0.001000	0.12720	0.000000	0.03702	0.129000	0.20672	-0.866000	0.04245	-0.105000	0.12132	0.482000	0.46254	ATG	T|0.999;C|0.001	0.001	strong		0.592	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554	
LONRF2	164832	hgsc.bcm.edu	37	2	100917109	100917109	+	Silent	SNP	C	C	T	rs13006224	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:100917109C>T	ENST00000393437.3	-	4	1701	c.1062G>A	c.(1060-1062)tcG>tcA	p.S354S	LONRF2_ENST00000409647.1_Silent_p.S111S	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	354							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						GTCATACCTCCGAGCTCCCTG	0.413													C|||	1896	0.378594	0.0325	0.4467	5008	,	,		16541	0.7252		0.498	False		,,,				2504	0.318				p.S354S		Atlas-SNP	.											.	LONRF2	62	.	0			c.G1062A						PASS	.	C		499,3907	231.4+/-245.2	27,445,1731	134.0	118.0	124.0		1062	1.9	0.0	2	dbSNP_121	124	4167,4433	568.9+/-389.1	1031,2105,1164	no	coding-synonymous	LONRF2	NM_198461.3		1058,2550,2895	TT,TC,CC		48.4535,11.3255,35.8757		354/755	100917109	4666,8340	2203	4300	6503	SO:0001819	synonymous_variant	164832	exon4			TACCTCCGAGCTC	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1062G>A	2.37:g.100917109C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	37	CCDS2046.2																																																																																			C|0.610;T|0.390	0.390	strong		0.413	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
SLC15A4	121260	hgsc.bcm.edu	37	12	129293346	129293346	+	Silent	SNP	C	C	T	rs11059924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:129293346C>T	ENST00000266771.5	-	5	1284	c.1245G>A	c.(1243-1245)tcG>tcA	p.S415S	SLC15A4_ENST00000539703.1_5'Flank|SLC15A4_ENST00000544112.1_Silent_p.S78S	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	415					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		CAGCAAAGGCCGAGCACATGA	0.552													C|||	2339	0.467053	0.4425	0.3588	5008	,	,		20756	0.5893		0.4414	False		,,,				2504	0.4775				p.S415S		Atlas-SNP	.											.	SLC15A4	41	.	0			c.G1245A						PASS	.	C		1864,2542	538.8+/-375.1	401,1062,740	100.0	79.0	86.0		1245	-11.0	0.0	12	dbSNP_120	86	4035,4565	556.5+/-386.9	942,2151,1207	no	coding-synonymous	SLC15A4	NM_145648.3		1343,3213,1947	TT,TC,CC		46.9186,42.3059,45.356		415/578	129293346	5899,7107	2203	4300	6503	SO:0001819	synonymous_variant	121260	exon5			AAAGGCCGAGCAC	AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"""Solute carriers"""	23090	protein-coding gene	gene with protein product		615806	"""solute carrier family 15, member 4"""			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1245G>A	12.37:g.129293346C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_145648	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Silent	SNP	ENST00000266771.5	37	CCDS9264.1																																																																																			C|0.525;T|0.475	0.475	strong		0.552	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648	
CCDC129	223075	hgsc.bcm.edu	37	7	31594508	31594508	+	Silent	SNP	C	C	T	rs2286711	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:31594508C>T	ENST00000407970.3	+	4	287	c.249C>T	c.(247-249)gaC>gaT	p.D83D	CCDC129_ENST00000319386.3_Silent_p.D83D|CCDC129_ENST00000409210.1_5'UTR|CCDC129_ENST00000482748.1_3'UTR|CCDC129_ENST00000451887.2_Silent_p.D109D	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	83										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AAGTCATTGACCGCACTGGTA	0.318													C|||	1146	0.228834	0.1551	0.1671	5008	,	,		17987	0.3313		0.2435	False		,,,				2504	0.2515				p.D109D		Atlas-SNP	.											.	CCDC129	127	.	0			c.C327T						PASS	.	C		788,3618		83,622,1498	49.0	45.0	46.0		249	3.2	0.1	7	dbSNP_100	46	2031,6567		263,1505,2531	no	coding-synonymous	CCDC129	NM_194300.2		346,2127,4029	TT,TC,CC		23.6218,17.8847,21.6779		83/1045	31594508	2819,10185	2203	4299	6502	SO:0001819	synonymous_variant	223075	exon4			CATTGACCGCACT	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.249C>T	7.37:g.31594508C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			C|0.772;T|0.228	0.228	strong		0.318	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
STX1B	112755	hgsc.bcm.edu	37	16	31004169	31004169	+	Silent	SNP	T	T	C	rs17855121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31004169T>C	ENST00000215095.5	-	10	1071	c.840A>G	c.(838-840)tcA>tcG	p.S280S	STX1B_ENST00000565419.1_3'UTR	NM_052874.3	NP_443106.1	P61266	STX1B_HUMAN	syntaxin 1B	280					intracellular protein transport (GO:0006886)|neurotransmitter transport (GO:0006836)|regulation of exocytosis (GO:0017157)|regulation of gene expression (GO:0010468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|large_intestine(5)|lung(5)	13						CCCCAATGGATGACGCCAAGA	0.577													T|||	764	0.152556	0.118	0.2939	5008	,	,		9775	0.002		0.2893	False		,,,				2504	0.1135				p.S280S		Atlas-SNP	.											.	STX1B	26	.	0			c.A840G						PASS	.	T		635,3759	274.0+/-271.7	49,537,1611	71.0	57.0	61.0		840	2.2	1.0	16	dbSNP_123	61	2587,6013	420.6+/-353.4	407,1773,2120	no	coding-synonymous	STX1B	NM_052874.3		456,2310,3731	CC,CT,TT		30.0814,14.4515,24.7961		280/289	31004169	3222,9772	2197	4300	6497	SO:0001819	synonymous_variant	112755	exon10			AATGGATGACGCC	AY028792	CCDS10699.1	16p12-p11	2008-02-05	2007-06-20	2007-06-20	ENSG00000099365	ENSG00000099365			18539	protein-coding gene	gene with protein product		601485	"""syntaxin 1B1"", ""syntaxin 1B2"""	STX1B1, STX1B2			Standard	NM_052874		Approved		uc010cad.2	P61266	OTTHUMG00000132391	ENST00000215095.5:c.840A>G	16.37:g.31004169T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	216	95	0.439815	NM_052874	Q15531|Q2VPS2	Silent	SNP	ENST00000215095.5	37	CCDS10699.1																																																																																			T|0.788;C|0.212	0.212	strong		0.577	STX1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255521.2		
MUC4	4585	hgsc.bcm.edu	37	3	195513758	195513758	+	Missense_Mutation	SNP	G	G	C	rs202045385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513758G>C	ENST00000463781.3	-	2	5152	c.4693C>G	c.(4693-4695)Cac>Gac	p.H1565D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H1565D	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H1565D(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGTGTGACCTGTGGAT	0.572													.|||	11	0.00219649	0.0053	0.0014	5008	,	,		12530	0.002		0.001	False		,,,				2504	0.0				p.H1565D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C4693G						scavenged	.																																			SO:0001583	missense	4585	exon2			TGGTGTGACCTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4693C>G	3.37:g.195513758G>C	ENSP00000417498:p.His1565Asp	Somatic	241	4	0.0165975		WXS	Illumina HiSeq	Phase_I	324	31	0.095679	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	0.012	-1.677435	0.00751	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.53	.	.	.	.	.	.	.	.	T	0.13286	0.0322	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22836	-1.0205	7	.	.	.	.	2.1349	0.03759	0.3255:0.3453:0.3292:0.0	.	1565	E7ESK3	.	D	1565	ENSP00000417498:H1565D;ENSP00000420243:H1565D	.	H	-	1	0	MUC4	196998153	0.001000	0.12720	0.012000	0.15200	0.012000	0.07955	-0.789000	0.04609	-1.943000	0.01039	-1.898000	0.00530	CAC	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PVRIG	79037	hgsc.bcm.edu	37	7	99817585	99817585	+	Nonsense_Mutation	SNP	G	G	T	rs7786505	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99817585G>T	ENST00000317271.2	+	2	415	c.52G>T	c.(52-54)Gag>Tag	p.E18*	AC005071.1_ENST00000410550.1_RNA|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA	NM_024070.3	NP_076975.2	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin domain containing	18						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)	11	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACCTGGACTGGAGGGGGCCAT	0.647													G|||	772	0.154153	0.205	0.1225	5008	,	,		18246	0.0605		0.2276	False		,,,				2504	0.1288				p.E18X		Atlas-SNP	.											.	PVRIG	20	.	0			c.G52T						PASS	.	G	stop/GLU,	918,3482		106,706,1388	21.0	21.0	21.0		52,	-3.1	0.0	7	dbSNP_116	21	1974,6612		236,1502,2555	no	stop-gained,intron	PVRIG,GATS	NM_024070.3,NM_178831.6	,	342,2208,3943	TT,TG,GG		22.9909,20.8636,22.2701	,	18/327,	99817585	2892,10094	2200	4293	6493	SO:0001587	stop_gained	79037	exon2			GGACTGGAGGGGG	BC001129	CCDS5690.1	7q22.1	2013-06-26			ENSG00000213413	ENSG00000213413			32190	protein-coding gene	gene with protein product						16926269	Standard	NM_024070		Approved	MGC2463, C7orf15	uc003uuf.1	Q6DKI7	OTTHUMG00000156798	ENST00000317271.2:c.52G>T	7.37:g.99817585G>T	ENSP00000316675:p.Glu18*	Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	315	155	0.492063	NM_024070	D6W5U9|Q9BVK3	Nonsense_Mutation	SNP	ENST00000317271.2	37	CCDS5690.1	346	0.15842490842490842	99	0.20121951219512196	37	0.10220994475138122	33	0.057692307692307696	177	0.23350923482849603	g	14.41	2.527143	0.44969	0.208636	0.229909	ENSG00000213413	ENST00000317271	.	.	.	1.54	-3.09	0.05331	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999999580667	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	3.5359	0.07794	0.3015:0.2419:0.4566:0.0	rs7786505;rs11553413;rs60522857	.	.	.	X	18	.	ENSP00000316675:E18X	E	+	1	0	PVRIG	99655521	0.000000	0.05858	0.010000	0.14722	0.019000	0.09904	0.235000	0.17948	-1.041000	0.03266	0.423000	0.28283	GAG	G|0.814;T|0.186	0.186	strong		0.647	PVRIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345870.2	NM_024070	
OR5A1	219982	hgsc.bcm.edu	37	11	59211421	59211421	+	Silent	SNP	C	C	T	rs17591107	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59211421C>T	ENST00000302030.2	+	1	805	c.780C>T	c.(778-780)ttC>ttT	p.F260F		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						CAGCCCTTTTCGTGTACTTGC	0.537													C|||	630	0.125799	0.0242	0.1326	5008	,	,		21088	0.1111		0.2525	False		,,,				2504	0.1431				p.F260F		Atlas-SNP	.											OR5A1,NS,adenoma,0,1	OR5A1	72	1	0			c.C780T						scavenged	.	C		251,4151	146.9+/-181.5	10,231,1960	265.0	215.0	232.0		780	6.0	1.0	11	dbSNP_123	232	2264,6326	383.3+/-340.7	283,1698,2314	no	coding-synonymous	OR5A1	NM_001004728.1		293,1929,4274	TT,TC,CC		26.3562,5.702,19.3581		260/316	59211421	2515,10477	2201	4295	6496	SO:0001819	synonymous_variant	219982	exon1			CCTTTTCGTGTAC	AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"""GPCR / Class A : Olfactory receptors"""	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.780C>T	11.37:g.59211421C>T		Somatic	313	2	0.00638978		WXS	Illumina HiSeq	Phase_I	358	175	0.488827	NM_001004728	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																			C|0.815;T|0.185	0.185	strong		0.537	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728	
DBT	1629	hgsc.bcm.edu	37	1	100672060	100672060	+	Missense_Mutation	SNP	T	T	C	rs12021720	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:100672060T>C	ENST00000370132.4	-	9	1163	c.1150A>G	c.(1150-1152)Agt>Ggt	p.S384G		NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	384			G -> S (in MSUD2; dbSNP:rs12021720). {ECO:0000269|PubMed:16710414, ECO:0000269|PubMed:9621512}.		branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		CTGAGCTGACTCACAGAGCCC	0.408													C|||	4466	0.891773	0.7443	0.9481	5008	,	,		15527	0.9494		0.9215	False		,,,				2504	0.9611				p.S384G		Atlas-SNP	.											.	DBT	39	.	0			c.A1150G	GRCh37	CM983430	DBT	M	rs12021720	PASS	.	C	GLY/SER	3414,992	370.8+/-319.7	1319,776,108	186.0	189.0	188.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1150	4.4	0.4	1	dbSNP_120	188	7761,839	193.4+/-239.1	3503,755,42	yes	missense	DBT	NM_001918.2	56	4822,1531,150	CC,CT,TT		9.7558,22.5148,14.0781	benign	384/483	100672060	11175,1831	2203	4300	6503	SO:0001583	missense	1629	exon9			GCTGACTCACAGA	BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992			2698	protein-coding gene	gene with protein product		248610	"""dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)"""			1420314, 1429740	Standard	NM_001918		Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.1150A>G	1.37:g.100672060T>C	ENSP00000359151:p.Ser384Gly	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_001918	B2R811|Q5VVL8	Missense_Mutation	SNP	ENST00000370132.4	37	CCDS767.1	1963	0.8988095238095238	382	0.7764227642276422	341	0.9419889502762431	553	0.9667832167832168	687	0.9063324538258575	C	1.014	-0.687087	0.03328	0.774852	0.902442	ENSG00000137992	ENST00000543138;ENST00000370132	T	0.37584	1.19	5.54	4.4	0.53042	.	0.147709	0.64402	N	0.000010	T	0.05227	0.0139	.	.	.	0.46678	P	8.439999999999559E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.25813	-1.0121	8	0.02654	T	1	-15.7957	9.6265	0.39754	0.0:0.729:0.0:0.271	rs12021720;rs17856511;rs52821474;rs58080948;rs12021720	203	F5H1F9	.	G	203;384	ENSP00000359151:S384G	ENSP00000359151:S384G	S	-	1	0	DBT	100444648	0.551000	0.26497	0.356000	0.25785	0.611000	0.37282	1.905000	0.39878	1.495000	0.48549	-0.215000	0.12644	AGT	T|0.126;C|0.874	0.874	strong		0.408	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030101.2	NM_001918	
SLC17A2	10246	hgsc.bcm.edu	37	6	25914853	25914853	+	Silent	SNP	G	G	A	rs34525648	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:25914853G>A	ENST00000265425.3	-	10	1277	c.1257C>T	c.(1255-1257)atC>atT	p.I419I	SLC17A2_ENST00000377850.3_Silent_p.I419I|SLC17A2_ENST00000360488.3_Missense_Mutation_p.S370L			O00624	NPT3_HUMAN	solute carrier family 17, member 2	419					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						TGATTCCTGCGATGAGCCCAA	0.423													G|||	414	0.0826677	0.174	0.0692	5008	,	,		18873	0.0149		0.0885	False		,,,				2504	0.0327				p.S370L		Atlas-SNP	.											.	SLC17A2	70	.	0			c.C1109T						PASS	.	G	LEU/SER	788,3618	317.2+/-295.0	67,654,1482	129.0	107.0	115.0		1109	-1.0	0.9	6	dbSNP_126	115	836,7764	191.8+/-238.0	39,758,3503	yes	missense	SLC17A2	NM_005835.2	145	106,1412,4985	AA,AG,GG		9.7209,17.8847,12.4865	benign	370/437	25914853	1624,11382	2203	4300	6503	SO:0001819	synonymous_variant	10246	exon10			TCCTGCGATGAGC	U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"""Solute carriers"""	10930	protein-coding gene	gene with protein product		611049	"""solute carrier family 17 (sodium phosphate), member 2"""			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.1257C>T	6.37:g.25914853G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	186	186	1	NM_005835	A6NK81|A6NLD6|Q5TB84|Q76P85	Missense_Mutation	SNP	ENST00000265425.3	37		177	0.08104395604395605	70	0.14227642276422764	28	0.07734806629834254	10	0.017482517482517484	69	0.09102902374670185	G	14.75	2.628265	0.46944	0.178847	0.097209	ENSG00000112337	ENST00000360488	T	0.70282	-0.47	4.5	-0.974	0.10293	.	.	.	.	.	T	0.26882	0.0658	.	.	.	0.09310	P	0.9999999781991	B	0.10296	0.003	B	0.04013	0.001	T	0.03121	-1.1070	7	0.26408	T	0.33	.	3.6505	0.08201	0.4972:0.0:0.324:0.1788	rs34525648	370	O00624-2	.	L	370	ENSP00000353677:S370L	ENSP00000353677:S370L	S	-	2	0	SLC17A2	26022832	0.092000	0.21681	0.924000	0.36721	0.901000	0.52897	-0.542000	0.06091	-0.175000	0.10725	0.650000	0.86243	TCG	G|0.895;A|0.105	0.105	strong		0.423	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1		
SLC26A10	65012	hgsc.bcm.edu	37	12	58014864	58014864	+	Missense_Mutation	SNP	G	G	C	rs190472657	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:58014864G>C	ENST00000320442.4	+	2	690	c.379G>C	c.(379-381)Ggg>Cgg	p.G127R	AC025165.8_ENST00000593846.1_RNA|SLC26A10_ENST00000379218.2_Missense_Mutation_p.G127R	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	127						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					CTTCGGGAGCGGGGCGTTGAT	0.687													G|||	4	0.000798722	0.0	0.0029	5008	,	,		15675	0.0		0.002	False		,,,				2504	0.0				p.G127R		Atlas-SNP	.											.	SLC26A10	89	.	0			c.G379C						PASS	.	G	ARG/GLY	3,4335		0,3,2166	7.0	8.0	7.0		379	4.3	1.0	12		7	14,8482		1,12,4235	no	missense	SLC26A10	NM_133489.2	125	1,15,6401	CC,CG,GG		0.1648,0.0692,0.1325	probably-damaging	127/564	58014864	17,12817	2169	4248	6417	SO:0001583	missense	65012	exon2			GGGAGCGGGGCGT		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"""Solute carriers"""	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.379G>C	12.37:g.58014864G>C	ENSP00000320217:p.Gly127Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	.	25.7	4.667641	0.88348	6.92E-4	0.001648	ENSG00000135502	ENST00000320442;ENST00000379218	D;D	0.97209	-4.18;-4.29	4.29	4.29	0.51040	.	.	.	.	.	D	0.98134	0.9384	M	0.78049	2.395	0.48288	D	0.999622	D	0.89917	1.0	D	0.80764	0.994	D	0.98725	1.0710	9	0.87932	D	0	.	14.6462	0.68762	0.0:0.0:1.0:0.0	.	127	Q8NG04	S2610_HUMAN	R	127	ENSP00000320217:G127R;ENSP00000368520:G127R	ENSP00000320217:G127R	G	+	1	0	SLC26A10	56301131	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	1.928000	0.40104	2.401000	0.81631	0.561000	0.74099	GGG	G|0.999;C|0.001	0.001	strong		0.687	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		
MFSD9	84804	hgsc.bcm.edu	37	2	103335512	103335512	+	Silent	SNP	G	G	C	rs33988363	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:103335512G>C	ENST00000258436.5	-	6	835	c.792C>G	c.(790-792)gcC>gcG	p.A264A	MFSD9_ENST00000496253.1_5'Flank	NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	264					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						CCCAGGGCTGGGCAGTCTTCT	0.577													G|||	39	0.00778754	0.0008	0.013	5008	,	,		19816	0.0		0.0249	False		,,,				2504	0.0041				p.A264A		Atlas-SNP	.											.	MFSD9	56	.	0			c.C792G						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	97.0	84.0	88.0		792	-2.1	0.0	2	dbSNP_126	88	169,8431	77.8+/-140.4	0,169,4131	no	coding-synonymous	MFSD9	NM_032718.3		0,184,6319	CC,CG,GG		1.9651,0.3404,1.4147		264/475	103335512	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	84804	exon6			GGGCTGGGCAGTC		CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.792C>G	2.37:g.103335512G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_032718	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Silent	SNP	ENST00000258436.5	37	CCDS2063.1																																																																																			G|0.985;C|0.015	0.015	strong		0.577	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718	
SLC25A23	79085	hgsc.bcm.edu	37	19	6458240	6458240	+	Silent	SNP	G	G	C	rs2289784	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6458240G>C	ENST00000301454.4	-	2	358	c.252C>G	c.(250-252)ctC>ctG	p.L84L	SLC25A23_ENST00000334510.5_Silent_p.L84L	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	84	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						TGTGAAACATGAGCAGCAGAC	0.607													G|||	232	0.0463259	0.0121	0.0259	5008	,	,		19373	0.0456		0.0547	False		,,,				2504	0.0992				p.L84L		Atlas-SNP	.											SLC25A23,NS,carcinoma,0,1	SLC25A23	43	1	0			c.C252G						PASS	.	G		117,4289	86.8+/-125.4	1,115,2087	54.0	44.0	48.0		252	-0.6	1.0	19	dbSNP_100	48	560,8040	152.1+/-206.7	13,534,3753	no	coding-synonymous	SLC25A23	NM_024103.2		14,649,5840	CC,CG,GG		6.5116,2.6555,5.2053		84/469	6458240	677,12329	2203	4300	6503	SO:0001819	synonymous_variant	79085	exon2			AAACATGAGCAGC	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.252C>G	19.37:g.6458240G>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Silent	SNP	ENST00000301454.4	37	CCDS32882.1																																																																																			G|0.946;C|0.054	0.054	strong		0.607	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
NAT2	10	hgsc.bcm.edu	37	8	18257795	18257795	+	Silent	SNP	C	C	T	rs1041983	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:18257795C>T	ENST00000286479.3	+	2	389	c.282C>T	c.(280-282)taC>taT	p.Y94Y	NAT2_ENST00000520116.1_Intron	NM_000015.2	NP_000006.2	P11245	ARY2_HUMAN	N-acetyltransferase 2 (arylamine N-acetyltransferase)	94					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	arylamine N-acetyltransferase activity (GO:0004060)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(2)	12				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)	Acetaminophen(DB00316)|Clonazepam(DB01068)|Dapsone(DB00250)|Ezogabine(DB04953)|Isoniazid(DB00951)|Sulfamethoxazole(DB01015)	GGTATTTTTACATCCCTCCAG	0.493									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				C|||	1990	0.397364	0.4682	0.2911	5008	,	,		18016	0.4395		0.3052	False		,,,				2504	0.4284				p.Y94Y		Atlas-SNP	.											.	NAT2	34	.	0			c.C282T	GRCh37	CM001251	NAT2	M	rs1041983	PASS	.	C		1951,2455	551.8+/-378.4	421,1109,673	91.0	95.0	94.0		282	1.5	0.0	8	dbSNP_86	94	2697,5903	431.2+/-356.7	418,1861,2021	yes	coding-synonymous	NAT2	NM_000015.2		839,2970,2694	TT,TC,CC		31.3605,44.2805,35.7374		94/291	18257795	4648,8358	2203	4300	6503	SO:0001819	synonymous_variant	10	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TTTTTACATCCCT	D90042	CCDS6008.1	8p22	2012-01-18			ENSG00000156006	ENSG00000156006	2.3.1.5		7646	protein-coding gene	gene with protein product		612182		AAC2		7773298	Standard	NM_000015		Approved		uc003wyw.1	P11245	OTTHUMG00000130826	ENST00000286479.3:c.282C>T	8.37:g.18257795C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_000015	O43637|O60654|O60655|Q13146|Q16697|Q2MLE4|Q2MLF5|Q2MLG8|Q2MLJ6|Q2MLK4|Q2MLK6|Q2MLN7|Q6LET4|Q86XS0|Q86XS1|Q96KY8|Q96T64|Q96T65|Q9H220	Silent	SNP	ENST00000286479.3	37	CCDS6008.1																																																																																			C|0.637;T|0.363	0.363	strong		0.493	NAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253380.1	NM_000015	
SP110	3431	hgsc.bcm.edu	37	2	231042276	231042276	+	Missense_Mutation	SNP	A	A	G	rs1135791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231042276A>G	ENST00000358662.4	-	14	1646	c.1568T>C	c.(1567-1569)aTg>aCg	p.M523T	SP110_ENST00000338556.3_Missense_Mutation_p.M225T|SP110_ENST00000258382.5_Missense_Mutation_p.M523T|SP110_ENST00000258381.6_Missense_Mutation_p.M523T|SP110_ENST00000392048.3_Missense_Mutation_p.M521T|SP110_ENST00000540870.1_Missense_Mutation_p.M529T	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	523	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.		M -> T (in dbSNP:rs1135791). {ECO:0000269|PubMed:10913195, ECO:0000269|PubMed:16803959}.		regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		TCCTAGGGTCATTCCTTCACA	0.423													G|||	1627	0.32488	0.208	0.3545	5008	,	,		20126	0.1677		0.496	False		,,,				2504	0.4479				p.M529T		Atlas-SNP	.											.	SP110	105	.	0			c.T1586C						PASS	.	G	THR/MET,THR/MET,THR/MET,THR/MET	1124,3282	717.8+/-408.8	128,868,1207	370.0	347.0	355.0		1586,1568,1568,1568	-0.8	0.0	2	dbSNP_86	355	4306,4294	577.4+/-390.5	1110,2086,1104	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	81,81,81,81	1238,2954,2311	GG,GA,AA		49.9302,25.5107,41.75	benign,benign,benign,benign	529/556,523/690,523/550,523/714	231042276	5430,7576	2203	4300	6503	SO:0001583	missense	3431	exon15			AGGGTCATTCCTT	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"""interferon-induced protein 41, 30kD"""	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.1568T>C	2.37:g.231042276A>G	ENSP00000351488:p.Met523Thr	Somatic	387	0	0		WXS	Illumina HiSeq	Phase_I	340	151	0.444118	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	738	0.33791208791208793	120	0.24390243902439024	146	0.40331491712707185	97	0.16958041958041958	375	0.4947229551451187	G	3.063	-0.192867	0.06259	0.255107	0.500698	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	4.61	-0.782	0.10961	SAND domain-like (2);SAND domain (3);	0.977573	0.08310	N	0.965581	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.41928	-0.9481	9	0.21014	T	0.42	.	0.2939	0.00262	0.2799:0.1726:0.15:0.3975	rs1135791;rs1804027;rs3198703;rs11556889;rs17327944;rs59171471;rs1135791	521;225;529;523;523	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	T	523;523;521;523;529;225	ENSP00000258381:M523T;ENSP00000351488:M523T;ENSP00000375902:M521T;ENSP00000258382:M523T;ENSP00000439558:M529T;ENSP00000344049:M225T	ENSP00000258381:M523T	M	-	2	0	SP110	230750520	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.527000	0.06200	-0.498000	0.06632	-1.974000	0.00461	ATG	A|0.640;G|0.360	0.360	strong		0.423	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
TCTE1	202500	hgsc.bcm.edu	37	6	44253765	44253765	+	Missense_Mutation	SNP	A	A	G	rs2297336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44253765A>G	ENST00000371505.4	-	3	904	c.782T>C	c.(781-783)tTc>tCc	p.F261S	RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_Missense_Mutation_p.F108S|TMEM151B_ENST00000438774.2_Intron|TCTE1_ENST00000371503.3_Missense_Mutation_p.F108S	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	261			F -> S (in dbSNP:rs2297336).							breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGTGAAGAGGAAGAGATTCCA	0.587													A|||	998	0.199281	0.0242	0.134	5008	,	,		18717	0.3998		0.1769	False		,,,				2504	0.2986				p.F261S		Atlas-SNP	.											.	TCTE1	77	.	0			c.T782C						PASS	.	A	SER/PHE	237,4169	137.7+/-173.5	8,221,1974	118.0	104.0	109.0		782	4.9	1.0	6	dbSNP_100	109	1351,7249	265.2+/-286.0	115,1121,3064	yes	missense	TCTE1	NM_182539.3	155	123,1342,5038	GG,GA,AA		15.7093,5.379,12.2097	probably-damaging	261/502	44253765	1588,11418	2203	4300	6503	SO:0001583	missense	202500	exon3			AAGAGGAAGAGAT	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.782T>C	6.37:g.44253765A>G	ENSP00000360560:p.Phe261Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	108	38	0.351852	NM_182539	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	37	CCDS4910.1	424	0.19413919413919414	18	0.036585365853658534	47	0.1298342541436464	223	0.38986013986013984	136	0.17941952506596306	A	19.76	3.888394	0.72524	0.05379	0.157093	ENSG00000146221	ENST00000371505;ENST00000371503;ENST00000371504	T;T;T	0.54479	1.79;0.57;0.57	4.89	4.89	0.63831	.	0.094392	0.85682	D	0.000000	T	0.65417	0.2689	M	0.78456	2.415	0.20074	P	0.9999334244	D	0.89917	1.0	D	0.71414	0.973	T	0.73119	-0.4083	9	0.72032	D	0.01	-35.9923	14.4897	0.67642	1.0:0.0:0.0:0.0	rs2297336;rs52795123;rs59287625;rs2297336	261	Q5JU00	TCTE1_HUMAN	S	261;108;108	ENSP00000360560:F261S;ENSP00000360558:F108S;ENSP00000360559:F108S	ENSP00000360558:F108S	F	-	2	0	TCTE1	44361743	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.054000	0.76649	1.832000	0.53329	0.379000	0.24179	TTC	A|0.842;G|0.158	0.158	strong		0.587	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
AQP4	361	hgsc.bcm.edu	37	18	24441215	24441215	+	Silent	SNP	C	C	T	rs1839318	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:24441215C>T	ENST00000383168.4	-	3	620	c.492G>A	c.(490-492)ttG>ttA	p.L164L	AQP4-AS1_ENST00000579964.1_RNA|AQP4_ENST00000440832.3_Silent_p.L142L|AQP4-AS1_ENST00000582605.1_RNA|AQP4_ENST00000581374.1_Silent_p.L142L|AQP4_ENST00000583022.1_5'UTR	NM_001650.4|NM_004028.3	NP_001641.1|NP_004019.1	P55087	AQP4_HUMAN	aquaporin 4	164					carbon dioxide transport (GO:0015670)|cellular response to estradiol stimulus (GO:0071392)|cellular response to interferon-gamma (GO:0071346)|female pregnancy (GO:0007565)|hyperosmotic salinity response (GO:0042538)|multicellular organismal water homeostasis (GO:0050891)|protein homooligomerization (GO:0051260)|renal water absorption (GO:0070295)|response to glucocorticoid (GO:0051384)|response to radiation (GO:0009314)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)	porin activity (GO:0015288)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(2)|large_intestine(3)|lung(5)|skin(1)	11	all_cancers(21;0.0172)|Lung NSC(5;0.00299)|all_lung(6;0.00747)|Ovarian(20;0.124)					ATGTGATTATCAACTCAACCA	0.383													C|||	206	0.0411342	0.0439	0.0173	5008	,	,		20686	0.004		0.0219	False		,,,				2504	0.1125				p.L164L		Atlas-SNP	.											.	AQP4	27	.	0			c.G492A						PASS	.	C	,	151,4255	103.8+/-142.4	4,143,2056	104.0	97.0	99.0		492,426	3.8	1.0	18	dbSNP_92	99	140,8460	69.4+/-131.9	1,138,4161	no	coding-synonymous,coding-synonymous	AQP4	NM_001650.4,NM_004028.3	,	5,281,6217	TT,TC,CC		1.6279,3.4271,2.2374	,	164/324,142/302	24441215	291,12715	2203	4300	6503	SO:0001819	synonymous_variant	361	exon3			GATTATCAACTCA	U63622	CCDS11889.1, CCDS58617.1	18q11.2-q12.1	2005-09-20			ENSG00000171885	ENSG00000171885		"""Ion channels / Aquaporins"""	637	protein-coding gene	gene with protein product		600308				7528931	Standard	NM_001650		Approved	MIWC	uc002kwa.3	P55087	OTTHUMG00000131955	ENST00000383168.4:c.492G>A	18.37:g.24441215C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	131	42	0.320611	NM_001650	P78564	Silent	SNP	ENST00000383168.4	37	CCDS11889.1																																																																																			C|0.977;T|0.023	0.023	strong		0.383	AQP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254914.2	NM_001650, NM_004028	
PCLO	27445	hgsc.bcm.edu	37	7	82435033	82435033	+	Silent	SNP	C	C	T	rs12668093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82435033C>T	ENST00000333891.9	-	21	15241	c.14904G>A	c.(14902-14904)ggG>ggA	p.G4968G		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GATTAGTCTCCCCTGCAGTGC	0.498													C|||	1049	0.209465	0.3381	0.0965	5008	,	,		17481	0.2837		0.1412	False		,,,				2504	0.1094				p.G4968G		Atlas-SNP	.											.	PCLO	1506	.	0			c.G14904A						PASS	.	C		1160,2876		172,816,1030	63.0	66.0	65.0		14904	3.9	1.0	7	dbSNP_120	65	1135,7253		77,981,3136	no	coding-synonymous	PCLO	NM_033026.5		249,1797,4166	TT,TC,CC		13.5312,28.7413,18.4723		4968/5143	82435033	2295,10129	2018	4194	6212	SO:0001819	synonymous_variant	27445	exon21			AGTCTCCCCTGCA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14904G>A	7.37:g.82435033C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	163	81	0.496933	NM_033026		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			C|0.773;T|0.227	0.227	strong		0.498	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
CTAGE9	643854	hgsc.bcm.edu	37	6	132030966	132030966	+	Missense_Mutation	SNP	G	G	C	rs202051647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:132030966G>C	ENST00000314099.8	-	1	1240	c.1192C>G	c.(1192-1194)Ctc>Gtc	p.L398V	ENPP3_ENST00000358229.5_Intron|ENPP3_ENST00000414305.1_Intron|ENPP3_ENST00000357639.3_Intron	NM_001145659.1|NM_001278507.1	NP_001139131.1|NP_001265436.1	A4FU28	CTGE9_HUMAN	CTAGE family, member 9	398						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)	2						TTCCTGTAGAGTTTCATTTCA	0.343													g|||	1659	0.33127	0.6316	0.2997	5008	,	,		19300	0.3204		0.0825	False		,,,				2504	0.2147				p.L398V		Atlas-SNP	.											.	CTAGE9	56	.	0			c.C1192G						PASS	.						18.0	14.0	15.0					6																	132030966		692	1574	2266	SO:0001583	missense	643854	exon1			TGTAGAGTTTCAT		CCDS47475.1	6q23.2	2010-06-23			ENSG00000236761	ENSG00000236761			37275	protein-coding gene	gene with protein product							Standard	NM_001145659		Approved		uc011ece.2	A4FU28	OTTHUMG00000047966	ENST00000314099.8:c.1192C>G	6.37:g.132030966G>C	ENSP00000395587:p.Leu398Val	Somatic	575	0	0		WXS	Illumina HiSeq	Phase_I	588	156	0.265306	NM_001145659		Missense_Mutation	SNP	ENST00000314099.8	37	CCDS47475.1	.	.	.	.	.	.	.	.	.	.	-	7.709	0.694789	0.15039	.	.	ENSG00000236761	ENST00000314099	T	0.37915	1.17	.	.	.	.	.	.	.	.	T	0.48447	0.1500	M	0.91561	3.22	0.32510	P	0.537709	D	0.76494	0.999	D	0.74023	0.982	T	0.44159	-0.9346	7	0.87932	D	0	.	5.8178	0.18506	0.001:0.0:0.999:0.0	.	398	A4FU28	CTGE9_HUMAN	V	398	ENSP00000395587:L398V	ENSP00000395587:L398V	L	-	1	0	CTAGE9	132072659	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	0.675000	0.25232	-0.000000	0.14550	0.000000	0.15137	CTC	.	.	weak		0.343	CTAGE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109220.1	NM_001145659	
KRT76	51350	hgsc.bcm.edu	37	12	53162528	53162528	+	Missense_Mutation	SNP	G	G	A	rs2280480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53162528G>A	ENST00000332411.2	-	9	1939	c.1886C>T	c.(1885-1887)aCg>aTg	p.T629M		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	629	Tail.		T -> M (in dbSNP:rs2280480).		cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GCTTGAGCTCGTGGTCTGGGA	0.542													G|||	831	0.165935	0.0401	0.2795	5008	,	,		17508	0.1538		0.2644	False		,,,				2504	0.1667				p.T629M		Atlas-SNP	.											.	KRT76	72	.	0			c.C1886T						PASS	.	G	MET/THR	279,4127	156.6+/-189.7	8,263,1932	163.0	161.0	161.0		1886	2.2	1.0	12	dbSNP_100	161	2334,6266	390.9+/-343.5	308,1718,2274	yes	missense	KRT76	NM_015848.4	81	316,1981,4206	AA,AG,GG		27.1395,6.3323,20.0907	probably-damaging	629/639	53162528	2613,10393	2203	4300	6503	SO:0001583	missense	51350	exon9			GAGCTCGTGGTCT	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.1886C>T	12.37:g.53162528G>A	ENSP00000330101:p.Thr629Met	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	NM_015848	B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	37	CCDS8838.1	400	0.18315018315018314	32	0.06504065040650407	90	0.24861878453038674	86	0.15034965034965034	192	0.2532981530343008	g	9.686	1.150608	0.21371	0.063323	0.271395	ENSG00000185069	ENST00000332411	D	0.83837	-1.77	4.14	2.21	0.28008	.	0.639211	0.13003	N	0.421514	T	0.00012	0.0000	N	0.08118	0	0.29465	P	0.857477	D	0.54047	0.964	B	0.37422	0.249	T	0.04153	-1.0973	9	0.87932	D	0	.	12.4355	0.55596	0.0:0.4951:0.5049:0.0	rs2280480;rs17370790;rs52796754;rs59105661;rs2280480	629	Q01546	K22O_HUMAN	M	629	ENSP00000330101:T629M	ENSP00000330101:T629M	T	-	2	0	KRT76	51448795	0.998000	0.40836	0.989000	0.46669	0.439000	0.31926	0.746000	0.26275	0.446000	0.26666	-0.181000	0.13052	ACG	G|0.811;A|0.189	0.189	strong		0.542	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
ERCC6L2	375748	hgsc.bcm.edu	37	9	98691137	98691137	+	Missense_Mutation	SNP	T	T	C	rs2274654	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:98691137T>C	ENST00000288985.7	+	11	2080	c.1775T>C	c.(1774-1776)gTc>gCc	p.V592A	ERCC6L2_ENST00000437817.1_Missense_Mutation_p.V403A|ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	592	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		V -> A (in dbSNP:rs2274654).		DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										ATTTGCCTTGTCTCTACAATG	0.284													T|||	1137	0.227037	0.1936	0.2637	5008	,	,		15669	0.2639		0.1332	False		,,,				2504	0.3047				p.V592A		Atlas-SNP	.											.	.	.	.	0			c.T1775C						PASS	.	T	ALA/VAL	793,3613	314.7+/-293.7	73,647,1483	97.0	90.0	93.0		1775	5.1	1.0	9	dbSNP_100	93	1316,7284	257.5+/-281.5	89,1138,3073	yes	missense	C9orf102	NM_001010895.2	64	162,1785,4556	CC,CT,TT		15.3023,17.9982,16.2156	probably-damaging	592/713	98691137	2109,10897	2203	4300	6503	SO:0001583	missense	375748	exon11			GCCTTGTCTCTAC	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"""chromosome 9 open reading frame 102"", ""excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"""	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.1775T>C	9.37:g.98691137T>C	ENSP00000288985:p.Val592Ala	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	37	CCDS35072.1	439	0.20100732600732601	86	0.17479674796747968	95	0.26243093922651933	152	0.26573426573426573	106	0.13984168865435356	T	23.1	4.377977	0.82682	0.179982	0.153023	ENSG00000182150	ENST00000405401;ENST00000288985;ENST00000437817;ENST00000426805	T;T;T	0.81078	-1.45;-1.45;-1.45	5.09	5.09	0.68999	Helicase, C-terminal (3);	0.000000	0.47455	D	0.000234	T	0.00039	0.0001	L	0.39147	1.195	0.09310	P	1.0	D;D;D	0.76494	0.993;0.996;0.999	P;D;D	0.70487	0.84;0.946;0.969	T	0.00647	-1.1628	9	0.87932	D	0	-14.9419	15.019	0.71613	0.0:0.0:0.0:1.0	rs2274654;rs52819942;rs58407137;rs2274654	403;274;592	Q5T890-2;F2Z2R4;Q5T890	.;.;RAD26_HUMAN	A	274;592;403;79	ENSP00000288985:V592A;ENSP00000416286:V403A;ENSP00000395345:V79A	ENSP00000288985:V592A	V	+	2	0	C9orf102	97730958	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.229000	0.78088	2.142000	0.66516	0.477000	0.44152	GTC	T|0.816;C|0.184	0.184	strong		0.284	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895	
ATP9A	10079	hgsc.bcm.edu	37	20	50287790	50287790	+	Silent	SNP	A	A	G	rs2255342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:50287790A>G	ENST00000338821.5	-	12	1308	c.1044T>C	c.(1042-1044)cgT>cgC	p.R348R	ATP9A_ENST00000311637.5_Silent_p.R212R|ATP9A_ENST00000402822.1_Silent_p.R227R	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	348					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CCAGGTTCACACGCAAACTAG	0.502													G|||	3526	0.704073	0.5091	0.7046	5008	,	,		20600	0.7976		0.7942	False		,,,				2504	0.7781				p.R348R		Atlas-SNP	.											ATP9A,colon,carcinoma,-1,1	ATP9A	135	1	0			c.T1044C						scavenged	.	G		2609,1797	528.2+/-372.3	771,1067,365	78.0	65.0	69.0		1044	-7.5	0.7	20	dbSNP_100	69	6918,1682	307.8+/-308.6	2777,1364,159	no	coding-synonymous	ATP9A	NM_006045.1		3548,2431,524	GG,GA,AA		19.5581,40.7853,26.7492		348/1048	50287790	9527,3479	2203	4300	6503	SO:0001819	synonymous_variant	10079	exon12			GTTCACACGCAAA	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1044T>C	20.37:g.50287790A>G		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																			A|0.278;G|0.722	0.722	strong		0.502	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
DIDO1	11083	hgsc.bcm.edu	37	20	61512376	61512376	+	Silent	SNP	G	G	A	rs114534878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61512376G>A	ENST00000266070.4	-	16	5257	c.4932C>T	c.(4930-4932)ccC>ccT	p.P1644P	DIDO1_ENST00000395343.1_Silent_p.P1644P	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1644					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CAACCGTGGCGGGGCGGGTGC	0.726													G|||	150	0.0299521	0.0832	0.0231	5008	,	,		13284	0.0		0.0219	False		,,,				2504	0.002				p.P1644P	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C4932T						PASS	.	G	,	261,3851		6,249,1801	8.0	10.0	10.0		4932,4932	-9.9	0.0	20	dbSNP_132	10	144,8044		1,142,3951	no	coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_033081.2	,	7,391,5752	AA,AG,GG		1.7587,6.3473,3.2927	,	1644/2241,1644/2241	61512376	405,11895	2056	4094	6150	SO:0001819	synonymous_variant	11083	exon16			CGTGGCGGGGCGG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.4932C>T	20.37:g.61512376G>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	14	11	0.785714	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			G|0.975;A|0.025	0.025	strong		0.726	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
SEMA5A	9037	hgsc.bcm.edu	37	5	9154659	9154659	+	Silent	SNP	G	G	C	rs1806151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:9154659G>C	ENST00000382496.5	-	12	2087	c.1422C>G	c.(1420-1422)ggC>ggG	p.G474G		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	474	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GCTCCCGCAGGCCCACGAACA	0.612													G|||	1372	0.273962	0.0371	0.3199	5008	,	,		17575	0.2312		0.5676	False		,,,				2504	0.3037				p.G474G		Atlas-SNP	.											SEMA5A,lymph_node,lymphoid_neoplasm,-1,1	SEMA5A	236	1	0			c.C1422G						PASS	.	G		506,3900	232.3+/-245.9	29,448,1726	82.0	75.0	78.0		1422	-2.8	1.0	5	dbSNP_92	78	4728,3872	607.0+/-395.2	1306,2116,878	no	coding-synonymous	SEMA5A	NM_003966.2		1335,2564,2604	CC,CG,GG		45.0233,11.4843,40.243		474/1075	9154659	5234,7772	2203	4300	6503	SO:0001819	synonymous_variant	9037	exon12			CCGCAGGCCCACG	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1422C>G	5.37:g.9154659G>C		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	286	170	0.594406	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			G|0.619;C|0.381	0.381	strong		0.612	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
C6orf15	29113	hgsc.bcm.edu	37	6	31080016	31080016	+	Missense_Mutation	SNP	C	C	G	rs2233974	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31080016C>G	ENST00000259870.3	-	2	123	c.120G>C	c.(118-120)ttG>ttC	p.L40F	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	40			L -> F (in dbSNP:rs2233974). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						AGTTGGTCCCCAAGTTTTGGG	0.557													C|||	527	0.105232	0.1218	0.1066	5008	,	,		19205	0.0466		0.1461	False		,,,				2504	0.1002				p.L40F		Atlas-SNP	.											.	C6orf15	29	.	0			c.G120C						PASS	.	C	PHE/LEU	569,3753		41,487,1633	127.0	149.0	142.0		120	2.7	0.0	6	dbSNP_98	142	1529,6989		138,1253,2868	yes	missense	C6orf15	NM_014070.2	22	179,1740,4501	GG,GC,CC		17.9502,13.1652,16.3396	possibly-damaging	40/326	31080016	2098,10742	2161	4259	6420	SO:0001583	missense	29113	exon2			GGTCCCCAAGTTT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.120G>C	6.37:g.31080016C>G	ENSP00000259870:p.Leu40Phe	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	246	0.11263736263736264	71	0.1443089430894309	45	0.12430939226519337	19	0.033216783216783216	111	0.14643799472295516	C	13.84	2.357554	0.41801	0.131652	0.179502	ENSG00000204542	ENST00000259870	T	0.07114	3.22	4.44	2.65	0.31530	.	1.477720	0.05072	N	0.481790	T	0.08626	0.0214	L	0.51422	1.61	0.80722	P	0.0	D	0.61697	0.99	P	0.59487	0.858	T	0.14671	-1.0464	9	0.44086	T	0.13	.	6.7339	0.23399	0.0:0.7832:0.0:0.2168	rs2233974;rs52811515;rs2233974	40	Q6UXA7	CF015_HUMAN	F	40	ENSP00000259870:L40F	ENSP00000259870:L40F	L	-	3	2	C6orf15	31187995	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.062000	0.11674	0.492000	0.27815	-0.275000	0.10095	TTG	C|0.832;G|0.168	0.168	strong		0.557	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
MLC1	23209	hgsc.bcm.edu	37	22	50502469	50502469	+	Silent	SNP	A	A	G	rs11568189|rs11568190	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50502469A>G	ENST00000311597.5	-	11	1659	c.1053T>C	c.(1051-1053)gcT>gcC	p.A351A	MLC1_ENST00000395876.2_Silent_p.A351A|MLC1_ENST00000431262.2_Silent_p.A321A|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000538737.1_Silent_p.A317A|MLC1_ENST00000535444.1_Silent_p.A272A|MLC1_ENST00000450140.2_Silent_p.A299A	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	351					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		TCACCTCCCCAGCCAGGCGCT	0.697																																					p.A351A		Atlas-SNP	.											MLC1,caecum,carcinoma,0,2	MLC1	48	2	0			c.T1053C						PASS	.						24.0	24.0	24.0					22																	50502469		2199	4295	6494	SO:0001819	synonymous_variant	23209	exon11			CTCCCCAGCCAGG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.1053T>C	22.37:g.50502469A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	40	10	0.25	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			A|0.901;G|0.099	0.099	strong		0.697	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
SMAP1	60682	hgsc.bcm.edu	37	6	71546702	71546702	+	Missense_Mutation	SNP	C	C	T	rs2273566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:71546702C>T	ENST00000370455.3	+	7	883	c.635C>T	c.(634-636)gCg>gTg	p.A212V	SMAP1_ENST00000316999.5_Missense_Mutation_p.A185V|SMAP1_ENST00000370452.3_Missense_Mutation_p.A185V	NM_001044305.1|NM_001281440.1	NP_001037770.1|NP_001268369.1	Q8IYB5	SMAP1_HUMAN	small ArfGAP 1	212			A -> V (in dbSNP:rs2273566). {ECO:0000269|Ref.4}.		positive regulation of erythrocyte differentiation (GO:0045648)|regulation of ARF GTPase activity (GO:0032312)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(1)	15						AAAAAAGCTGCGGAGCCCACT	0.333													C|||	1362	0.271965	0.3313	0.1873	5008	,	,		15522	0.5516		0.0726	False		,,,				2504	0.1687				p.A212V		Atlas-SNP	.											.	SMAP1	77	.	0			c.C635T						PASS	.	C	VAL/ALA,VAL/ALA	1280,3126	408.4+/-334.6	182,916,1105	35.0	39.0	37.0		635,554	3.3	1.0	6	dbSNP_100	37	646,7954	155.4+/-209.4	27,592,3681	yes	missense,missense	SMAP1	NM_001044305.1,NM_021940.3	64,64	209,1508,4786	TT,TC,CC		7.5116,29.0513,14.8085	benign,benign	212/468,185/441	71546702	1926,11080	2203	4300	6503	SO:0001583	missense	60682	exon7			AAGCTGCGGAGCC	AK023221	CCDS4973.1, CCDS43478.1, CCDS64459.1, CCDS75478.1	6q12-q13	2009-11-30	2008-09-05		ENSG00000112305	ENSG00000112305		"""ADP-ribosylation factor GTPase activating proteins"""	19651	protein-coding gene	gene with protein product		611372	"""stromal membrane-associated protein 1"", ""stromal membrane-associated GTPase-activating protein 1"""			9644265, 12119110	Standard	NM_001044305		Approved	FLJ13159, SMAP-1	uc003pfr.3	Q8IYB5	OTTHUMG00000014996	ENST00000370455.3:c.635C>T	6.37:g.71546702C>T	ENSP00000359484:p.Ala212Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_001044305	Q53H70|Q5SYQ2|Q6PK24|Q8NDH4|Q96L38|Q96L39|Q9H8X4	Missense_Mutation	SNP	ENST00000370455.3	37	CCDS43478.1	596	0.27289377289377287	164	0.3333333333333333	52	0.143646408839779	322	0.5629370629370629	58	0.07651715039577836	C	5.181	0.218975	0.09810	0.290513	0.075116	ENSG00000112305	ENST00000370452;ENST00000316999;ENST00000370455;ENST00000370442	T;T;T	0.23147	2.14;2.18;1.92	5.12	3.35	0.38373	.	0.597462	0.17728	N	0.163990	T	0.03564	0.0102	N	0.12182	0.205	0.09310	P	0.99999999611323	P;B;B	0.39022	0.655;0.012;0.006	B;B;B	0.28709	0.093;0.003;0.001	T	0.39292	-0.9621	9	0.27082	T	0.32	-2.8523	7.5831	0.27976	0.133:0.7207:0.0:0.1463	rs2273566;rs52811178;rs58157895;rs2273566	185;185;212	Q8IYB5-3;Q8IYB5-2;Q8IYB5	.;.;SMAP1_HUMAN	V	185;185;212;124	ENSP00000359481:A185V;ENSP00000313382:A185V;ENSP00000359484:A212V	ENSP00000313382:A185V	A	+	2	0	SMAP1	71603423	0.927000	0.31430	1.000000	0.80357	0.007000	0.05969	0.463000	0.21972	0.671000	0.31185	-0.751000	0.03497	GCG	C|0.773;T|0.227	0.227	strong		0.333	SMAP1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041149.1	NM_001044305	
ACER3	55331	hgsc.bcm.edu	37	11	76637680	76637680	+	Silent	SNP	G	G	A	rs4479014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76637680G>A	ENST00000532485.1	+	2	287	c.183G>A	c.(181-183)aaG>aaA	p.K61K	ACER3_ENST00000533873.1_Intron|ACER3_ENST00000526597.1_5'UTR|ACER3_ENST00000538157.1_Silent_p.K19K|ACER3_ENST00000530182.1_3'UTR	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	61					ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						GTCTGGAAAAGCGGTACATTG	0.363													A|||	2523	0.503794	0.1876	0.4726	5008	,	,		15568	0.5903		0.7127	False		,,,				2504	0.6493				p.K61K		Atlas-SNP	.											.	ACER3	19	.	0			c.G183A						PASS	.	A		1274,3126	699.8+/-406.5	205,864,1131	154.0	130.0	138.0		183	1.6	1.0	11	dbSNP_111	138	6292,2292	384.5+/-341.1	2313,1666,313	no	coding-synonymous	ACER3	NM_018367.5		2518,2530,1444	AA,AG,GG		26.7008,28.9545,41.7283		61/268	76637680	7566,5418	2200	4292	6492	SO:0001819	synonymous_variant	55331	exon2			GGAAAAGCGGTAC	AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	3.5.1.23	"""Alkaline ceramidase"""	16066	protein-coding gene	gene with protein product	"""alkaline phytoceramidase"""		"""phytoceramidase, alkaline"""	PHCA		11356846, 18619555	Standard	XM_005274090		Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.183G>A	11.37:g.76637680G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_018367	B2RC99	Silent	SNP	ENST00000532485.1	37	CCDS8247.1																																																																																			G|0.422;A|0.578	0.578	strong		0.363	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382770.2	NM_018367	
PADI4	23569	hgsc.bcm.edu	37	1	17662662	17662662	+	Silent	SNP	T	T	C	rs1748033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17662662T>C	ENST00000375448.4	+	4	375	c.349T>C	c.(349-351)Ttg>Ctg	p.L117L	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	117					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	AGAAATCTCCTTGTGCGCAGA	0.562											OREG0013149	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2964	0.591853	0.5401	0.585	5008	,	,		15912	0.6151		0.661	False		,,,				2504	0.5716				p.L117L		Atlas-SNP	.											.	PADI4	70	.	0			c.T349C						PASS	.	C		2561,1845		735,1091,377	73.0	64.0	67.0		349	2.4	1.0	1	dbSNP_89	67	5714,2886		1890,1934,476	no	coding-synonymous	PADI4	NM_012387.2		2625,3025,853	CC,CT,TT		33.5581,41.8747,36.3755		117/664	17662662	8275,4731	2203	4300	6503	SO:0001819	synonymous_variant	23569	exon4			ATCTCCTTGTGCG	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.349T>C	1.37:g.17662662T>C		Somatic	85	0	0	719	WXS	Illumina HiSeq	Phase_I	89	89	1	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Silent	SNP	ENST00000375448.4	37	CCDS180.1																																																																																			T|0.370;C|0.630	0.630	strong		0.562	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
CUL4A	8451	hgsc.bcm.edu	37	13	113909339	113909339	+	Missense_Mutation	SNP	A	A	G	rs2302757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:113909339A>G	ENST00000375440.4	+	18	2015	c.1931A>G	c.(1930-1932)aAa>aGa	p.K644R	CUL4A_ENST00000375441.3_Missense_Mutation_p.K544R|CUL4A_ENST00000451881.1_Missense_Mutation_p.K544R|CUL4A_ENST00000326335.4_Missense_Mutation_p.K544R	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	644			K -> R (in dbSNP:rs2302757).		cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			AAAAGTCCCAAAGGAAAGGAA	0.428													A|||	1260	0.251597	0.0136	0.3228	5008	,	,		19800	0.3353		0.2326	False		,,,				2504	0.456				p.K644R		Atlas-SNP	.											.	CUL4A	50	.	0			c.A1931G						PASS	.	A	ARG/LYS,ARG/LYS	218,4188	132.9+/-169.3	3,212,1988	95.0	97.0	96.0		1931,1631	3.8	1.0	13	dbSNP_100	96	1984,6616	348.9+/-327.2	246,1492,2562	yes	missense,missense	CUL4A	NM_001008895.1,NM_003589.2	26,26	249,1704,4550	GG,GA,AA		23.0698,4.9478,16.9306	benign,benign	644/760,544/660	113909339	2202,10804	2203	4300	6503	SO:0001583	missense	8451	exon18			GTCCCAAAGGAAA	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.1931A>G	13.37:g.113909339A>G	ENSP00000364589:p.Lys644Arg	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	486	0.22252747252747251	12	0.024390243902439025	108	0.2983425414364641	181	0.31643356643356646	185	0.24406332453825857	A	8.608	0.888485	0.17540	0.049478	0.230698	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87	4.99	3.77	0.43336	Cullin, N-terminal (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Cullin homology (1);	0.051557	0.85682	D	0.000000	T	0.00012	0.0000	L	0.46567	1.45	0.21967	P	0.999444887	B;B	0.14012	0.004;0.009	B;B	0.24541	0.027;0.054	T	0.08493	-1.0719	9	0.40728	T	0.16	-26.3384	9.1672	0.37058	0.849:0.0:0.151:0.0	rs2302757;rs17693437;rs52821043;rs2302757	644;644	Q13619;A8MSH7	CUL4A_HUMAN;.	R	544;544;544;644	ENSP00000364590:K544R;ENSP00000389118:K544R;ENSP00000322132:K544R;ENSP00000364589:K644R	ENSP00000322132:K544R	K	+	2	0	CUL4A	112957340	1.000000	0.71417	0.998000	0.56505	0.124000	0.20399	3.974000	0.56852	0.817000	0.34445	0.379000	0.24179	AAA	A|0.806;G|0.194	0.194	strong		0.428	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589	
PGR	5241	hgsc.bcm.edu	37	11	100998771	100998771	+	Missense_Mutation	SNP	C	C	G	rs3740753	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100998771C>G	ENST00000325455.5	-	1	2484	c.1031G>C	c.(1030-1032)aGt>aCt	p.S344T	PGR_ENST00000534013.1_Intron|PGR_ENST00000263463.5_Missense_Mutation_p.S344T	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	344	Modulating, Pro-Rich.		S -> T (in dbSNP:rs3740753). {ECO:0000269|PubMed:2328727, ECO:0000269|Ref.8}.		cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	ACAGGGTGAACTCCGCGGCGG	0.682													C|||	361	0.0720847	0.0061	0.1398	5008	,	,		11093	0.0099		0.1769	False		,,,				2504	0.0695				p.S344T	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.G1031C						PASS	.	C	THR/SER,THR/SER	106,4056		1,104,1976	14.0	19.0	18.0		1031,539	1.8	1.0	11	dbSNP_107	18	1244,7046		88,1068,2989	yes	missense,missense	PGR	NM_000926.4,NM_001202474.1	58,58	89,1172,4965	GG,GC,CC		15.006,2.5469,10.8416	benign,benign	344/934,180/770	100998771	1350,11102	2081	4145	6226	SO:0001583	missense	5241	exon1			GGTGAACTCCGCG	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1031G>C	11.37:g.100998771C>G	ENSP00000325120:p.Ser344Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	208	0.09523809523809523	6	0.012195121951219513	55	0.15193370165745856	4	0.006993006993006993	143	0.18865435356200527	C	7.606	0.673794	0.14841	0.025469	0.15006	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	T;T	0.10288	2.89;2.89	3.84	1.76	0.24704	.	1.096570	0.07012	N	0.825310	T	0.00012	0.0000	L	0.27053	0.805	0.53688	P	2.1000000000048757E-5	B;B	0.26483	0.094;0.15	B;B	0.24394	0.034;0.053	T	0.43766	-0.9371	9	0.34782	T	0.22	.	5.4483	0.16548	0.0:0.5358:0.2446:0.2196	rs3740753	344;344	Q8TDS3;P06401	.;PRGR_HUMAN	T	344	ENSP00000325120:S344T;ENSP00000263463:S344T	ENSP00000263463:S344T	S	-	2	0	PGR	100503981	0.000000	0.05858	0.978000	0.43139	0.038000	0.13279	-0.179000	0.09768	0.816000	0.34421	0.561000	0.74099	AGT	C|0.884;G|0.116	0.116	strong		0.682	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
TTC13	79573	hgsc.bcm.edu	37	1	231042732	231042732	+	Silent	SNP	T	T	A	rs3811502	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:231042732T>A	ENST00000366661.4	-	23	2509	c.2502A>T	c.(2500-2502)gtA>gtT	p.V834V	TTC13_ENST00000366662.4_Silent_p.V780V|TTC13_ENST00000414259.1_Silent_p.V781V	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	834										central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		ACGTTTCTGATACTGATGGAA	0.358													T|||	2582	0.515575	0.4198	0.6556	5008	,	,		15841	0.5446		0.5338	False		,,,				2504	0.4969				p.V834V		Atlas-SNP	.											.	TTC13	74	.	0			c.A2502T						PASS	.	T	,	1789,2617	528.6+/-372.4	353,1083,767	82.0	80.0	81.0		2340,2502	-2.0	0.9	1	dbSNP_107	81	4480,4120	589.4+/-392.5	1167,2146,987	no	coding-synonymous,coding-synonymous	TTC13	NM_001122835.2,NM_024525.4	,	1520,3229,1754	AA,AT,TT		47.907,40.6037,48.2008	,	780/807,834/861	231042732	6269,6737	2203	4300	6503	SO:0001819	synonymous_variant	79573	exon23			TTCTGATACTGAT		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"""Tetratricopeptide (TTC) repeat domain containing"""	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.2502A>T	1.37:g.231042732T>A		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	221	221	1	NM_024525	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Silent	SNP	ENST00000366661.4	37	CCDS1588.1																																																																																			T|0.505;A|0.495	0.495	strong		0.358	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525	
CSPG5	10675	hgsc.bcm.edu	37	3	47618953	47618953	+	Missense_Mutation	SNP	C	C	A	rs3732530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:47618953C>A	ENST00000383738.2	-	2	2661	c.563G>T	c.(562-564)gGg>gTg	p.G188V	CSPG5_ENST00000456150.1_Missense_Mutation_p.G50V|CSPG5_ENST00000264723.4_Missense_Mutation_p.G188V|CSPG5_ENST00000465441.1_5'Flank	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	188			G -> V (in dbSNP:rs3732530). {ECO:0000269|PubMed:9950058, ECO:0000269|Ref.2}.		axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		CAGCTCTGGCCCTTGAGGGTC	0.607													C|||	2610	0.521166	0.3593	0.4784	5008	,	,		16133	0.5992		0.664	False		,,,				2504	0.5429				p.G188V		Atlas-SNP	.											.	CSPG5	46	.	0			c.G563T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	1711,2695	496.2+/-363.5	343,1025,835	42.0	47.0	46.0		149,563,563,149,563	0.8	0.9	3	dbSNP_107	46	5653,2947	657.8+/-401.5	1851,1951,498	yes	missense,missense,missense,missense,missense	CSPG5	NM_001206942.1,NM_001206943.1,NM_001206944.1,NM_001206945.1,NM_006574.3	109,109,109,109,109	2194,2976,1333	AA,AC,CC		34.2674,38.8334,43.38	benign,benign,benign,benign,benign	50/402,188/567,188/478,50/429,188/540	47618953	7364,5642	2203	4300	6503	SO:0001583	missense	10675	exon2			TCTGGCCCTTGAG	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.563G>T	3.37:g.47618953C>A	ENSP00000373244:p.Gly188Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_006574	Q71M39|Q71M40	Missense_Mutation	SNP	ENST00000383738.2	37	CCDS56253.1	1253	0.5737179487179487	210	0.4268292682926829	182	0.5027624309392266	353	0.6171328671328671	508	0.6701846965699209	C	11.00	1.509864	0.27036	0.388334	0.657326	ENSG00000114646	ENST00000456150;ENST00000383738;ENST00000264723	T;T;T	0.44083	0.93;0.93;0.93	3.93	0.844	0.18943	Chondroitin sulphate attachment (1);	0.601598	0.15689	N	0.249504	T	0.00012	0.0000	N	0.12182	0.205	0.25702	P	0.985573	B;B	0.18461	0.028;0.005	B;B	0.15052	0.012;0.005	T	0.35151	-0.9800	9	0.33141	T	0.24	-5.9554	2.953	0.05868	0.2162:0.5428:0.0:0.2409	rs3732530;rs59534820;rs3732530	188;188	O95196;O95196-2	CSPG5_HUMAN;.	V	50;188;188	ENSP00000392096:G50V;ENSP00000373244:G188V;ENSP00000264723:G188V	ENSP00000264723:G188V	G	-	2	0	CSPG5	47593957	0.042000	0.20092	0.922000	0.36590	0.989000	0.77384	0.166000	0.16583	0.429000	0.26202	0.643000	0.83706	GGG	C|0.433;A|0.567	0.567	strong		0.607	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574	
E2F4	1874	hgsc.bcm.edu	37	16	67233243	67233243	+	IGR	SNP	G	G	A	rs75193761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:67233243G>A	ENST00000379378.3	+	0	2096				MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000360833.1_Missense_Mutation_p.R58Q|ELMO3_ENST00000393997.2_Missense_Mutation_p.R58Q|ELMO3_ENST00000477898.1_5'Flank	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		GCGCCTCCGCGGAACGTGGTG	0.687													G|||	151	0.0301518	0.0219	0.0173	5008	,	,		10643	0.0		0.0308	False		,,,				2504	0.0808				p.R58Q		Atlas-SNP	.											.	ELMO3	41	.	0			c.G173A						PASS	.	G	GLN/ARG	101,4101		0,101,2000	27.0	35.0	32.0		173	5.2	1.0	16	dbSNP_131	32	266,8168		3,260,3954	yes	missense	ELMO3	NM_024712.3	43	3,361,5954	AA,AG,GG		3.1539,2.4036,2.9044	possibly-damaging	58/774	67233243	367,12269	2101	4217	6318	SO:0001628	intergenic_variant	79767	exon1			CTCCGCGGAACGT	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975		16.37:g.67233243G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	21	13	0.619048	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	51	0.023351648351648352	14	0.028455284552845527	11	0.03038674033149171	0	0.0	26	0.03430079155672823	G	25.5	4.641692	0.87859	0.024036	0.031539	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.14144	2.54;2.53	5.19	5.19	0.71726	.	0.308861	0.24915	U	0.034595	T	0.04998	0.0134	L	0.43152	1.355	0.80722	D	1	D;D	0.57899	0.981;0.981	B;B	0.43916	0.436;0.436	T	0.02020	-1.1228	10	0.36615	T	0.2	-23.8447	14.2244	0.65848	0.0:0.0:1.0:0.0	.	58;58	F8W9E7;Q96BJ8-3	.;.	Q	58	ENSP00000354077:R58Q;ENSP00000377566:R58Q	ENSP00000354077:R58Q	R	+	2	0	ELMO3	65790744	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.645000	0.46621	2.416000	0.81992	0.563000	0.77884	CGG	G|0.976;A|0.024	0.024	strong		0.687	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
HR	55806	hgsc.bcm.edu	37	8	21974427	21974427	+	Silent	SNP	G	G	T	rs112173147	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:21974427G>T	ENST00000381418.4	-	17	4819	c.3339C>A	c.(3337-3339)ccC>ccA	p.P1113P	HR_ENST00000312841.8_Intron	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	1113	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CGGCCTCTCCGGGGGCCTGGA	0.716													G|||	179	0.0357428	0.0045	0.0346	5008	,	,		12686	0.001		0.0755	False		,,,				2504	0.0736				p.P1113P		Atlas-SNP	.											.	HR	71	.	0			c.C3339A						PASS	.	G	,	66,3664		1,64,1800	4.0	4.0	4.0		3339,	-9.2	0.6	8	dbSNP_132	4	500,7108		6,488,3310	no	coding-synonymous,intron	HR	NM_005144.4,NM_018411.4	,	7,552,5110	TT,TG,GG		6.572,1.7694,4.9921	,	1113/1190,	21974427	566,10772	1865	3804	5669	SO:0001819	synonymous_variant	55806	exon17			CTCTCCGGGGGCC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.3339C>A	8.37:g.21974427G>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_005144	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			G|0.962;T|0.038	0.038	strong		0.716	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
VPS13C	54832	hgsc.bcm.edu	37	15	62223303	62223303	+	Missense_Mutation	SNP	C	C	G	rs78071599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:62223303C>G	ENST00000261517.5	-	50	6097	c.6024G>C	c.(6022-6024)gaG>gaC	p.E2008D	VPS13C_ENST00000249837.3_Missense_Mutation_p.E1965D|VPS13C_ENST00000395898.3_Missense_Mutation_p.E1965D|VPS13C_ENST00000395896.4_Missense_Mutation_p.E2008D	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ATGTTGCTCTCTCAATTCCTT	0.443													C|||	35	0.00698882	0.0	0.0101	5008	,	,		17268	0.002		0.0199	False		,,,				2504	0.0061				p.E2008D		Atlas-SNP	.											.	VPS13C	506	.	0			c.G6024C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	26,4380	32.6+/-62.9	0,26,2177	141.0	120.0	127.0		6024,5895,5895,6024	3.5	1.0	15	dbSNP_132	127	174,8426	79.8+/-142.4	3,168,4129	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	45,45,45,45	3,194,6306	GG,GC,CC		2.0233,0.5901,1.5378	benign,benign,benign,benign	2008/3629,1965/3711,1965/3586,2008/3754	62223303	200,12806	2203	4300	6503	SO:0001583	missense	54832	exon50			TGCTCTCTCAATT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6024G>C	15.37:g.62223303C>G	ENSP00000261517:p.Glu2008Asp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	C	15.37	2.812416	0.50527	0.005901	0.020233	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.46451	0.87;0.87;1.04	5.41	3.49	0.39957	.	0.454224	0.24937	N	0.034409	T	0.21186	0.0510	L	0.57536	1.79	0.32706	N	0.512236	B;B;P;B	0.36048	0.321;0.321;0.534;0.215	B;B;B;B	0.38842	0.205;0.205;0.283;0.101	T	0.34254	-0.9836	10	0.18276	T	0.48	.	7.8042	0.29191	0.1368:0.7269:0.0:0.1363	.	1965;2008;1965;2008	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	D	1965;2008;2008;2008	ENSP00000249837:E1965D;ENSP00000261517:E2008D;ENSP00000379233:E2008D	ENSP00000249837:E1965D	E	-	3	2	VPS13C	60010595	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.312000	0.43726	1.395000	0.46643	0.650000	0.86243	GAG	C|0.986;G|0.014	0.014	strong		0.443	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
C1QTNF9	338872	hgsc.bcm.edu	37	13	24895631	24895631	+	Missense_Mutation	SNP	T	T	A	rs78083136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:24895631T>A	ENST00000382071.2	+	4	812	c.727T>A	c.(727-729)Tgc>Agc	p.C243S	AL359736.1_ENST00000422229.2_5'Flank|C1QTNF9-AS1_ENST00000449656.1_RNA|C1QTNF9_ENST00000332018.4_Missense_Mutation_p.C243S			P0C862	C1T9A_HUMAN	C1q and tumor necrosis factor related protein 9	243	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				endometrium(1)|kidney(2)|lung(6)	9		all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159)		GAAATTCACGTGCCACATTGC	0.408																																					p.C243S		Atlas-SNP	.											.	C1QTNF9	22	.	0			c.T727A						PASS	.						193.0	170.0	178.0					13																	24895631		2203	4300	6503	SO:0001583	missense	338872	exon4			TTCACGTGCCACA	BC040438	CCDS9306.1	13q12.12	2010-08-18			ENSG00000240654	ENSG00000240654			28732	protein-coding gene	gene with protein product		614285				12975309, 18787108	Standard	NM_178540		Approved	MGC48915, CTRP9, C1QTNF9A, AQL1	uc001upj.3	P0C862	OTTHUMG00000016576	ENST00000382071.2:c.727T>A	13.37:g.24895631T>A	ENSP00000371503:p.Cys243Ser	Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	371	71	0.191375	NM_178540	A2A3T6|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	Missense_Mutation	SNP	ENST00000382071.2	37	CCDS9306.1	148	0.06776556776556776	29	0.05894308943089431	19	0.052486187845303865	1	0.0017482517482517483	99	0.13060686015831136	N	14.79	2.640291	0.47153	.	.	ENSG00000240654	ENST00000382071;ENST00000332018	T;T	0.79454	-1.27;-1.27	3.96	3.96	0.45880	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.000000	0.85682	D	0.000000	T	0.06645	0.0170	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.53085	-0.8488	10	0.62326	D	0.03	.	8.8982	0.35479	0.0:0.0:0.1885:0.8115	.	243	P0C862	C1T9A_HUMAN	S	243	ENSP00000371503:C243S;ENSP00000333737:C243S	ENSP00000333737:C243S	C	+	1	0	C1QTNF9	23793631	1.000000	0.71417	0.988000	0.46212	0.363000	0.29612	7.715000	0.84713	1.768000	0.52137	0.352000	0.21897	TGC	T|0.930;A|0.070	0.070	strong		0.408	C1QTNF9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044177.1	NM_178540	
MUC4	4585	hgsc.bcm.edu	37	3	195513345	195513345	+	Silent	SNP	A	A	C	rs71321841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513345A>C	ENST00000463781.3	-	2	5565	c.5106T>G	c.(5104-5106)gtT>gtG	p.V1702V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V1702V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ATGCCGAGGAAACGTCGGTGA	0.597																																					p.V1702V		Atlas-SNP	.											.	MUC4	1505	.	0			c.T5106G						PASS	.						31.0	33.0	33.0					3																	195513345		690	1583	2273	SO:0001819	synonymous_variant	4585	exon2			CGAGGAAACGTCG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5106T>G	3.37:g.195513345A>C		Somatic	552	0	0		WXS	Illumina HiSeq	Phase_I	660	275	0.416667	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.500;C|0.500	0.500	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PCDHA4	56144	hgsc.bcm.edu	37	5	140186937	140186937	+	Missense_Mutation	SNP	G	G	T	rs11167605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140186937G>T	ENST00000530339.1	+	1	165	c.165G>T	c.(163-165)gaG>gaT	p.E55D	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.E55D|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.E55D|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	55	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> D (in dbSNP:rs11167605).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGGACTGGAGCTGGCGGAGC	0.637													.|||	1662	0.331869	0.0151	0.415	5008	,	,		15300	0.5139		0.3738	False		,,,				2504	0.4703				p.E55D		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G165T						PASS	.	G	,,,ASP/GLU,,ASP/GLU	339,4065		16,307,1879	49.0	55.0	53.0		,,,165,,165	4.7	1.0	5	dbSNP_120	53	3130,5468		562,2006,1731	no	intron,intron,intron,missense,intron,missense	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,45,,45	578,2313,3610	TT,TG,GG		36.4038,7.6975,26.6805	,,,,,	,,,55/948,,55/799	140186937	3469,9533	2202	4299	6501	SO:0001583	missense	56144	exon1			ACTGGAGCTGGCG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.165G>T	5.37:g.140186937G>T	ENSP00000435300:p.Glu55Asp	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	81	31	0.382716	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	699	0.32005494505494503	10	0.02032520325203252	129	0.356353591160221	297	0.5192307692307693	263	0.3469656992084433	g	9.328	1.059892	0.19987	0.076975	0.364038	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.27720	1.65;1.65;1.65	4.73	4.73	0.59995	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.41001	U	0.000965	T	0.00012	0.0000	N	0.25825	0.765	0.49213	P	2.3700000000004273E-4	B;B;B	0.14805	0.011;0.003;0.003	B;B;B	0.20184	0.028;0.006;0.012	T	0.44952	-0.9294	9	0.40728	T	0.16	.	7.8007	0.29172	0.0827:0.0:0.7555:0.1618	rs11167605;rs17844266	55;55;55	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	D	55	ENSP00000423470:E55D;ENSP00000349344:E55D;ENSP00000435300:E55D	ENSP00000349344:E55D	E	+	3	2	PCDHA4	140167121	0.027000	0.19231	1.000000	0.80357	0.936000	0.57629	0.274000	0.18680	2.369000	0.80426	0.461000	0.40582	GAG	G|0.714;T|0.286	0.286	strong		0.637	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
HLA-B	3106	hgsc.bcm.edu	37	6	31324143	31324143	+	Nonsense_Mutation	SNP	G	G	T	rs12697944	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31324143G>T	ENST00000412585.2	-	3	448	c.420C>A	c.(418-420)taC>taA	p.Y140*		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	140	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGTCGTAGGCGTACTGGTCAT	0.711									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				G|||	485	0.096845	0.0802	0.0764	5008	,	,		9016	0.121		0.0994	False		,,,				2504	0.1063				p.Y140X		Atlas-SNP	.											HLA-B,colon,carcinoma,-1,1	HLA-B	54	1	0			c.C420A						scavenged	.						26.0	21.0	23.0					6																	31324143		2088	4190	6278	SO:0001587	stop_gained	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GTAGGCGTACTGG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.420C>A	6.37:g.31324143G>T	ENSP00000399168:p.Tyr140*	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	132	23	0.174242	NM_005514	Q29764	Nonsense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	13.76	2.331843	0.41297	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	.	.	.	3.18	-2.31	0.06765	.	1.609830	0.05070	U	0.481455	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.2996	0.02076	0.292:0.1494:0.3998:0.1588	rs12697944	.	.	.	X	140;19;19;151	.	ENSP00000399168:Y140X	Y	-	3	2	HLA-B	31432122	0.000000	0.05858	0.045000	0.18777	0.003000	0.03518	-5.040000	0.00157	-0.425000	0.07371	-0.929000	0.02709	TAC	T|0.046;G|0.954	0.046	strong		0.711	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
OR4Q3	441669	hgsc.bcm.edu	37	14	20216298	20216298	+	Missense_Mutation	SNP	T	T	C	rs12896533	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20216298T>C	ENST00000331723.1	+	1	712	c.712T>C	c.(712-714)Ttc>Ctc	p.F238L		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	238			F -> L (in dbSNP:rs12896533).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GAACAAGGTCTTCTCTACCTG	0.478													C|||	3555	0.709864	0.5537	0.6744	5008	,	,		27679	0.7768		0.7465	False		,,,				2504	0.8395				p.F238L		Atlas-SNP	.											.	OR4Q3	117	.	0			c.T712C						PASS	.		LEU/PHE	2508,1898		588,1332,283	164.0	150.0	155.0		712	2.2	1.0	14	dbSNP_121	155	6268,2332		2073,2122,105	yes	missense	OR4Q3	NM_172194.1	22	2661,3454,388	CC,CT,TT		27.1163,43.0776,32.5235	benign	238/314	20216298	8776,4230	2203	4300	6503	SO:0001583	missense	441669	exon1			AAGGTCTTCTCTA	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.712T>C	14.37:g.20216298T>C	ENSP00000330049:p.Phe238Leu	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	37	CCDS32020.1	1520	0.6959706959706959	269	0.5467479674796748	239	0.6602209944751382	438	0.7657342657342657	574	0.7572559366754618	.	0.006	-2.091199	0.00367	0.569224	0.728837	ENSG00000182652	ENST00000331723	T	0.00269	8.37	4.1	2.21	0.28008	GPCR, rhodopsin-like superfamily (1);	0.470384	0.15683	N	0.249837	T	0.00012	0.0000	N	0.11427	0.14	0.52501	P	4.700000000001925E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40534	-0.9558	9	0.02654	T	1	.	6.6167	0.22780	0.0:0.583:0.0:0.417	rs12896533;rs61086986;rs12896533	238	Q8NH05	OR4Q3_HUMAN	L	238	ENSP00000330049:F238L	ENSP00000330049:F238L	F	+	1	0	OR4Q3	19286138	0.000000	0.05858	0.974000	0.42286	0.026000	0.11368	-0.322000	0.08007	0.389000	0.25086	-0.291000	0.09656	TTC	T|0.298;C|0.702	0.702	strong		0.478	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2		
ZNF117	51351	hgsc.bcm.edu	37	7	64439701	64439701	+	Missense_Mutation	SNP	C	C	T	rs3807069	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:64439701C>T	ENST00000282869.6	-	4	1532	c.248G>A	c.(247-249)tGt>tAt	p.C83Y		NM_015852.3	NP_056936.2	Q03924	ZN117_HUMAN	zinc finger protein 117	83			C -> Y (in dbSNP:rs3807069).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(1)|skin(1)	22		Lung NSC(55;0.0295)|all_lung(88;0.0691)				ATATTTATTACATTGAAATAT	0.289													C|||	1939	0.387181	0.3964	0.2637	5008	,	,		17591	0.4058		0.4016	False		,,,				2504	0.4284				p.C83Y		Atlas-SNP	.											.	ZNF117	56	.	0			c.G248A						PASS	.	C	TYR/CYS	1446,2376		281,884,746	43.0	41.0	42.0		248	0.2	0.0	7	dbSNP_107	42	3086,5238		576,1934,1652	no	missense	ZNF117	NM_015852.3	194	857,2818,2398	TT,TC,CC		37.0735,37.8336,37.3127	benign	83/484	64439701	4532,7614	1911	4162	6073	SO:0001583	missense	51351	exon4			TTATTACATTGAA	M27879	CCDS43593.1	7q11.2	2013-01-08	2006-06-12		ENSG00000152926	ENSG00000152926		"""Zinc fingers, C2H2-type"""	12897	protein-coding gene	gene with protein product		194624	"""zinc finger protein 117 (HPF9)"""			1427907	Standard	NM_015852		Approved	HPF9, H-plk	uc003ttr.2	Q03924	OTTHUMG00000156631	ENST00000282869.6:c.248G>A	7.37:g.64439701C>T	ENSP00000282869:p.Cys83Tyr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_015852	Q02313|Q7Z7Q7	Missense_Mutation	SNP	ENST00000282869.6	37	CCDS43593.1	856	0.39194139194139194	196	0.3983739837398374	116	0.32044198895027626	223	0.38986013986013984	321	0.4234828496042216	.	10.52	1.374106	0.24857	0.378336	0.370735	ENSG00000152926	ENST00000398695;ENST00000282869	T	0.35421	1.31	1.29	0.163	0.14986	.	.	.	.	.	T	0.00012	0.0000	M	0.91561	3.22	0.80722	P	0.0	B	0.26672	0.156	B	0.24701	0.055	T	0.20806	-1.0264	8	0.59425	D	0.04	.	5.9854	0.19432	0.3063:0.6937:0.0:0.0	rs3807069;rs59205936;rs3807069	83	Q03924	ZN117_HUMAN	Y	83	ENSP00000282869:C83Y	ENSP00000282869:C83Y	C	-	2	0	ZNF117	64077136	0.094000	0.21725	0.000000	0.03702	0.018000	0.09664	1.008000	0.29872	-0.224000	0.09928	0.305000	0.20034	TGT	C|0.612;T|0.388	0.388	strong		0.289	ZNF117-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344863.3	NM_024498	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951657	130951657	+	Missense_Mutation	SNP	G	G	A	rs561879037		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130951657G>A	ENST00000312988.7	-	4	858	c.758C>T	c.(757-759)aCg>aTg	p.T253M		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	253					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.T253M(1)		endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					CTGGAATTCCGTCAAGTCCAC	0.602													.|||	1	0.000199681	0.0	0.0	5008	,	,		23562	0.0		0.0	False		,,,				2504	0.001				p.T253M		Atlas-SNP	.											TUBA3E,ear,carcinoma,0,1	TUBA3E	73	1	1	Substitution - Missense(1)	skin(1)	c.C758T						scavenged	.						213.0	151.0	172.0					2																	130951657		2203	4300	6503	SO:0001583	missense	112714	exon4			AATTCCGTCAAGT	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.758C>T	2.37:g.130951657G>A	ENSP00000318197:p.Thr253Met	Somatic	506	1	0.00197628		WXS	Illumina HiSeq	Phase_I	514	6	0.0116732	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	.	.	.	.	.	.	.	.	.	.	g	5.862	0.343297	0.11069	.	.	ENSG00000152086	ENST00000312988	D	0.84070	-1.8	2.92	1.06	0.20224	Tubulin/FtsZ, 2-layer sandwich domain (1);Tubulin/FtsZ, GTPase domain (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.51477	U	0.000095	D	0.86502	0.5948	M	0.85462	2.755	0.40861	D	0.98383	D	0.59357	0.985	P	0.54759	0.76	D	0.84266	0.0486	10	0.87932	D	0	.	5.8408	0.18633	0.1204:0.1981:0.6816:0.0	.	253	Q6PEY2	TBA3E_HUMAN	M	253	ENSP00000318197:T253M	ENSP00000318197:T253M	T	-	2	0	TUBA3E	130668127	1.000000	0.71417	0.493000	0.27502	0.700000	0.40528	3.667000	0.54547	0.137000	0.18759	-0.382000	0.06688	ACG	.	.	none		0.602	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
ABCC8	6833	hgsc.bcm.edu	37	11	17496516	17496516	+	Silent	SNP	A	A	G	rs1048099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:17496516A>G	ENST00000389817.3	-	2	275	c.207T>C	c.(205-207)ccT>ccC	p.P69P	ABCC8_ENST00000302539.4_Silent_p.P69P			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	69					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	GGTTGTGCCCAGGGAAATGAA	0.572													A|||	2200	0.439297	0.3729	0.5432	5008	,	,		22889	0.3611		0.497	False		,,,				2504	0.4765				p.P69P		Atlas-SNP	.											.	ABCC8	170	.	0			c.T207C						PASS	.	A		1811,2589	531.9+/-373.3	372,1067,761	223.0	141.0	169.0		207	-7.8	0.9	11	dbSNP_86	169	4381,4205	582.5+/-391.4	1152,2077,1064	no	coding-synonymous	ABCC8	NM_000352.3		1524,3144,1825	GG,GA,AA		48.9751,41.1591,47.6821		69/1582	17496516	6192,6794	2200	4293	6493	SO:0001819	synonymous_variant	6833	exon2			GTGCCCAGGGAAA	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.207T>C	11.37:g.17496516A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	236	236	1	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Silent	SNP	ENST00000389817.3	37	CCDS31437.1																																																																																			A|0.541;G|0.459	0.459	strong		0.572	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
EEF1G	1937	hgsc.bcm.edu	37	11	62334908	62334908	+	Silent	SNP	G	G	C	rs1061093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62334908G>C	ENST00000329251.4	-	6	745	c.615C>G	c.(613-615)ggC>ggG	p.G205G	EEF1G_ENST00000378019.3_Silent_p.G255G|MIR3654_ENST00000496634.2_3'UTR	NM_001404.4	NP_001395.1	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1 gamma	205	GST C-terminal.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to virus (GO:0009615)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	translation elongation factor activity (GO:0003746)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GTTTCACTTCGCCCAAGACAG	0.557													C|||	892	0.178115	0.1309	0.2061	5008	,	,		19172	0.0437		0.3201	False		,,,				2504	0.2147				p.G205G		Atlas-SNP	.											.	EEF1G	33	.	0			c.C615G						PASS	.	C		617,3263		55,507,1378	44.0	42.0	43.0		615	0.6	1.0	11	dbSNP_86	43	2991,5291		529,1933,1679	no	coding-synonymous	EEF1G	NM_001404.4		584,2440,3057	CC,CG,GG		36.1145,15.9021,29.6662		205/438	62334908	3608,8554	1940	4141	6081	SO:0001819	synonymous_variant	1937	exon6			CACTTCGCCCAAG	X63526	CCDS44626.1	11q12.3	2008-02-05			ENSG00000254772	ENSG00000254772			3213	protein-coding gene	gene with protein product		130593				1598220, 1461723	Standard	NM_001404		Approved	EF1G	uc001ntm.1	P26641	OTTHUMG00000167567	ENST00000329251.4:c.615C>G	11.37:g.62334908G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001404	B4DTG2|Q6PJ62|Q6PK31|Q96CU2|Q9P196	Silent	SNP	ENST00000329251.4	37	CCDS44626.1																																																																																			G|0.681;C|0.319	0.319	strong		0.557	EEF1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395047.1	NM_001404	
KLRC4	8302	hgsc.bcm.edu	37	12	10560957	10560957	+	Missense_Mutation	SNP	T	T	C	rs2617170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10560957T>C	ENST00000309384.1	-	3	492	c.311A>G	c.(310-312)aAt>aGt	p.N104S	KLRC4-KLRK1_ENST00000539300.1_Silent_p.Q95Q	NM_013431.2	NP_038459.1	O43908	NKG2F_HUMAN	killer cell lectin-like receptor subfamily C, member 4	104			N -> S (in allele NKG2-F*02; dbSNP:rs2617170). {ECO:0000269|PubMed:11751968, ECO:0000269|PubMed:9394807, ECO:0000269|PubMed:9598306, ECO:0000269|PubMed:9683661}.		cellular defense response (GO:0006968)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						CAGGGAAAAATTGTTCTGCTC	0.284													T|||	2788	0.556709	0.4327	0.6671	5008	,	,		13575	0.5496		0.663	False		,,,				2504	0.544				p.N104S		Atlas-SNP	.											KLRC4,caecum,carcinoma,0,1	KLRC4	23	1	0			c.A311G						PASS	.	T	,SER/ASN	2102,2298	566.5+/-381.9	516,1070,614	71.0	68.0	69.0		,311	2.9	0.0	12	dbSNP_100	69	5820,2756	669.6+/-402.7	1999,1822,467	yes	utr-5,missense	KLRC4,KLRC4-KLRK1	NM_001199805.1,NM_013431.2	,46	2515,2892,1081	CC,CT,TT		32.1362,47.7727,38.9488	,benign	,104/159	10560957	7922,5054	2200	4288	6488	SO:0001583	missense	8302	exon3			GAAAAATTGTTCT	U96846	CCDS8624.1	12p13.2-p12.3	2008-08-05			ENSG00000183542	ENSG00000183542		"""Killer cell lectin-like receptors"""	6377	protein-coding gene	gene with protein product		602893				9598306	Standard	NM_013431		Approved	NKG2-F	uc001qye.3	O43908	OTTHUMG00000168575	ENST00000309384.1:c.311A>G	12.37:g.10560957T>C	ENSP00000310216:p.Asn104Ser	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_013431	O60851	Missense_Mutation	SNP	ENST00000309384.1	37	CCDS8624.1	1308	0.5989010989010989	231	0.4695121951219512	239	0.6602209944751382	339	0.5926573426573427	499	0.658311345646438	T	9.629	1.135782	0.21123	0.477727	0.678638	ENSG00000183542	ENST00000309384	T	0.10005	2.92	2.89	2.89	0.33648	C-type lectin fold (1);	0.475829	0.17871	N	0.159163	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B	0.26445	0.149	B	0.25759	0.063	T	0.21109	-1.0255	9	0.19590	T	0.45	.	7.5748	0.27928	0.0:0.0:0.0:1.0	rs2617170;rs56530830;rs61074071;rs2617170	104	O43908	NKG2F_HUMAN	S	104	ENSP00000310216:N104S	ENSP00000310216:N104S	N	-	2	0	KLRC4	10452224	0.001000	0.12720	0.004000	0.12327	0.009000	0.06853	1.074000	0.30703	1.567000	0.49668	0.477000	0.44152	AAT	T|0.395;C|0.605	0.605	strong		0.284	KLRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400108.1	NM_013431	
NACA	4666	hgsc.bcm.edu	37	12	57114307	57114307	+	Missense_Mutation	SNP	A	A	T	rs2958127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57114307A>T	ENST00000454682.1	-	3	1288	c.1007T>A	c.(1006-1008)gTg>gAg	p.V336E	NACA_ENST00000393891.4_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.V336E|NACA_ENST00000552540.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000546392.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	336	Pro-rich.		V -> E (in dbSNP:rs2958127). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						AATGGTCTTCACTGTAGGGTC	0.448			T	BCL6	NHL								A|||	3044	0.607827	0.3343	0.6657	5008	,	,		20399	0.7401		0.6252	False		,,,				2504	0.7822				p.V336E		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	NACA_ENST00000550952,caecum,carcinoma,+1,1	NACA	131	1	0			c.T1007A						PASS	.	A	,,,GLU/VAL	1292,1844		271,750,547	69.0	62.0	64.0		,,,1007	-4.8	0.0	12	dbSNP_101	64	4451,2713		1388,1675,519	yes	intron,intron,intron,missense	NACA	NM_001113201.1,NM_001113202.1,NM_005594.4,NM_001113203.2	,,,121	1659,2425,1066	TT,TA,AA		37.8699,41.199,44.2427	,,,benign	,,,336/926	57114307	5743,4557	1568	3582	5150	SO:0001583	missense	4666	exon3			GTCTTCACTGTAG	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1007T>A	12.37:g.57114307A>T	ENSP00000403817:p.Val336Glu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		1313	0.6011904761904762	173	0.3516260162601626	248	0.6850828729281768	427	0.7465034965034965	465	0.6134564643799473	A	13.81	2.347203	0.41599	0.41199	0.621301	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.51325	0.71;0.95	4.09	-4.83	0.03161	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.21225	0.053;0.002	B;B	0.14578	0.011;0.005	T	0.40627	-0.9553	8	0.87932	D	0	.	1.7965	0.03062	0.3004:0.149:0.3915:0.1591	rs2958127;rs58365009;rs2958127	336;336	E9PAV3;F8VU71	.;.	E	336	ENSP00000403817:V336E;ENSP00000448035:V336E	ENSP00000403817:V336E	V	-	2	0	NACA	55400574	0.000000	0.05858	0.000000	0.03702	0.282000	0.26991	-0.114000	0.10757	-0.683000	0.05190	0.254000	0.18369	GTG	A|0.412;T|0.588	0.588	strong		0.448	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
KLK11	11012	hgsc.bcm.edu	37	19	51530741	51530741	+	Missense_Mutation	SNP	C	C	G	rs61752567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51530741C>G	ENST00000594768.1	-	1	218	c.33G>C	c.(31-33)aaG>aaC	p.K11N	KLK11_ENST00000594458.1_5'Flank|CTC-518B2.9_ENST00000594910.1_RNA|KLK11_ENST00000319720.7_Intron|KLK11_ENST00000453757.3_5'Flank|KLK11_ENST00000600362.1_5'Flank|KLK11_ENST00000391804.3_Intron	NM_144947.1	NP_659196.1	Q9UBX7	KLK11_HUMAN	kallikrein-related peptidase 11	11						extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		TGCCCGATGACTTCCAGTCCC	0.607													C|||	261	0.0521166	0.0734	0.0648	5008	,	,		17689	0.0		0.0805	False		,,,				2504	0.0389				p.K11N		Atlas-SNP	.											.	KLK11	28	.	0			c.G33C						PASS	.	C	,,ASN/LYS	307,4099	166.5+/-197.7	16,275,1912	92.0	93.0	92.0		,,33	1.7	0.1	19	dbSNP_129	92	707,7893	174.2+/-224.5	24,659,3617	yes	intron,intron,missense	KLK11	NM_001167605.1,NM_006853.2,NM_144947.1	,,94	40,934,5529	GG,GC,CC		8.2209,6.9678,7.7964	,,possibly-damaging	,,11/283	51530741	1014,11992	2203	4300	6503	SO:0001583	missense	11012	exon1			CGATGACTTCCAG	AB012917	CCDS12818.1, CCDS12819.1, CCDS54297.1	19q13.33	2011-09-07	2006-10-27			ENSG00000167757		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6359	protein-coding gene	gene with protein product		604434	"""kallikrein 11"""	PRSS20		9765601, 10662548, 16800724, 16800723	Standard	NM_006853		Approved	TLSP	uc002pvb.2	Q9UBX7		ENST00000594768.1:c.33G>C	19.37:g.51530741C>G	ENSP00000473047:p.Lys11Asn	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	62	38	0.612903	NM_144947	O75837|Q0WXX5|Q8IXD7|Q9NS65	Missense_Mutation	SNP	ENST00000594768.1	37	CCDS12818.1	125	0.05723443223443223	36	0.07317073170731707	26	0.0718232044198895	0	0.0	63	0.08311345646437995	c	10.13	1.265469	0.23136	0.069678	0.082209	ENSG00000167757	ENST00000319756	D	0.88277	-2.36	2.76	1.71	0.24356	.	.	.	.	.	T	0.17662	0.0424	N	0.22421	0.69	0.18873	N	0.999988	P	0.48162	0.906	B	0.38056	0.264	T	0.49360	-0.8948	9	0.48119	T	0.1	.	4.9789	0.14155	0.0:0.8224:0.0:0.1776	rs61752567	11	Q9UBX7	KLK11_HUMAN	N	11	ENSP00000324414:K11N	ENSP00000324414:K11N	K	-	3	2	KLK11	56222553	0.008000	0.16893	0.051000	0.19133	0.137000	0.21094	0.546000	0.23284	0.694000	0.31654	0.467000	0.42956	AAG	C|0.927;G|0.073	0.073	strong		0.607	KLK11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464314.2	NM_006853	
DISP2	85455	hgsc.bcm.edu	37	15	40660566	40660566	+	Silent	SNP	G	G	A	rs72733420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40660566G>A	ENST00000267889.3	+	8	2340	c.2253G>A	c.(2251-2253)gcG>gcA	p.A751A	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	751					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GCTTCGACGCGGAGTATCGCC	0.721													G|||	543	0.108427	0.087	0.1354	5008	,	,		11032	0.0188		0.1968	False		,,,				2504	0.1196				p.A751A		Atlas-SNP	.											DISP2,NS,carcinoma,0,1	DISP2	86	1	0			c.G2253A						scavenged	.	G		423,3975		25,373,1801	24.0	28.0	26.0		2253	-9.6	0.0	15	dbSNP_132	26	1823,6771		193,1437,2667	no	coding-synonymous	DISP2	NM_033510.1		218,1810,4468	AA,AG,GG		21.2125,9.618,17.2876		751/1402	40660566	2246,10746	2199	4297	6496	SO:0001819	synonymous_variant	85455	exon8			CGACGCGGAGTAT	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2253G>A	15.37:g.40660566G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	37	CCDS10056.1																																																																																			G|0.847;A|0.153	0.153	strong		0.721	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
PTPN23	25930	hgsc.bcm.edu	37	3	47452786	47452786	+	Silent	SNP	G	G	A	rs1531875	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:47452786G>A	ENST00000265562.4	+	20	3575	c.3498G>A	c.(3496-3498)gaG>gaA	p.E1166E	PTPN23_ENST00000431726.1_Silent_p.E1040E	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1166					cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACCCCTATGAGCATCCTGAGA	0.672													G|||	2298	0.458866	0.2405	0.5202	5008	,	,		15089	0.4633		0.6024	False		,,,				2504	0.5583				p.E1166E		Atlas-SNP	.											PTPN23,colon,carcinoma,0,1	PTPN23	85	1	0			c.G3498A						PASS	.	G		1234,3168		196,842,1163	25.0	26.0	26.0		3498	2.0	0.9	3	dbSNP_88	26	5072,3522		1520,2032,745	no	coding-synonymous	PTPN23	NM_015466.2		1716,2874,1908	AA,AG,GG		40.9821,28.0327,48.5226		1166/1637	47452786	6306,6690	2201	4297	6498	SO:0001819	synonymous_variant	25930	exon20			CTATGAGCATCCT	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.3498G>A	3.37:g.47452786G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Silent	SNP	ENST00000265562.4	37	CCDS2754.1																																																																																			G|0.529;A|0.471	0.471	strong		0.672	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
SLC22A25	387601	hgsc.bcm.edu	37	11	62931484	62931484	+	Missense_Mutation	SNP	T	T	C	rs6591771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62931484T>C	ENST00000306494.6	-	9	1455	c.1456A>G	c.(1456-1458)Atg>Gtg	p.M486V	SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						AGGATCATCATGAGGGAAGCC	0.473													C|||	2720	0.543131	0.6377	0.5	5008	,	,		19828	0.5337		0.4473	False		,,,				2504	0.5542				p.M486V		Atlas-SNP	.											.	SLC22A25	87	.	0			c.A1456G						PASS	.	C	VAL/MET	2736,1666	507.6+/-366.7	847,1042,312	145.0	156.0	152.0		1456	-9.1	0.0	11	dbSNP_116	152	3752,4844	616.4+/-396.5	824,2104,1370	yes	missense	SLC22A25	NM_199352.3	21	1671,3146,1682	CC,CT,TT		43.6482,37.8464,49.9154	benign	486/548	62931484	6488,6510	2201	4298	6499	SO:0001583	missense	387601	exon9			TCATCATGAGGGA	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.1456A>G	11.37:g.62931484T>C	ENSP00000307443:p.Met486Val	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	282	278	0.985816	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	1108	0.5073260073260073	296	0.6016260162601627	150	0.4143646408839779	334	0.583916083916084	328	0.43271767810026385	C	0.016	-1.521232	0.00967	0.621536	0.436482	ENSG00000196600	ENST00000306494	T	0.55234	0.53	4.56	-9.12	0.00707	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.731034	0.12480	N	0.465234	T	0.00012	0.0000	N	0.00483	-1.445	0.53005	P	3.500000000000725E-5	B	0.06786	0.001	B	0.06405	0.002	T	0.19778	-1.0295	9	0.08381	T	0.77	.	3.3572	0.07173	0.1046:0.2737:0.3903:0.2314	rs6591771;rs17646973;rs57023289;rs6591771	486	Q6T423	S22AP_HUMAN	V	486	ENSP00000307443:M486V	ENSP00000307443:M486V	M	-	1	0	SLC22A25	62688060	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.285000	0.01153	-4.095000	0.00074	-3.042000	0.00070	ATG	T|0.486;C|0.514	0.514	strong		0.473	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
SLC6A17	388662	hgsc.bcm.edu	37	1	110735290	110735290	+	Silent	SNP	C	C	T	rs62636569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110735290C>T	ENST00000331565.4	+	8	1754	c.1269C>T	c.(1267-1269)gaC>gaT	p.D423D	SLC6A17_ENST00000465159.1_3'UTR	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	423					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		TGGGCCTTGACCCCTGCCTTC	0.607													C|||	75	0.014976	0.003	0.0115	5008	,	,		21238	0.0		0.0398	False		,,,				2504	0.0235				p.D423D		Atlas-SNP	.											.	SLC6A17	86	.	0			c.C1269T						PASS	.	C		47,4359	48.2+/-83.0	0,47,2156	101.0	79.0	86.0		1269	-4.6	0.3	1	dbSNP_129	86	412,8188	128.7+/-186.9	17,378,3905	no	coding-synonymous	SLC6A17	NM_001010898.2		17,425,6061	TT,TC,CC		4.7907,1.0667,3.5291		423/728	110735290	459,12547	2203	4300	6503	SO:0001819	synonymous_variant	388662	exon8			CCTTGACCCCTGC		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1269C>T	1.37:g.110735290C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	CCDS30799.1																																																																																			C|0.969;T|0.031	0.031	strong		0.607	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
OR52I2	143502	hgsc.bcm.edu	37	11	4608542	4608542	+	Missense_Mutation	SNP	C	C	T	rs1847632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4608542C>T	ENST00000312614.4	+	1	522	c.500C>T	c.(499-501)aCg>aTg	p.T167M		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	167			T -> M (in dbSNP:rs1847632).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGAATTCTCACGCCTCAAGTG	0.512													C|||	2061	0.411542	0.2852	0.4121	5008	,	,		23130	0.5585		0.326	False		,,,				2504	0.5184				p.T167M		Atlas-SNP	.											.	OR52I2	50	.	0			c.C500T						PASS	.	C	MET/THR	1210,3192	413.5+/-336.5	186,838,1177	64.0	65.0	65.0		500	3.3	0.8	11	dbSNP_92	65	2416,6180	398.8+/-346.2	348,1720,2230	no	missense	OR52I2	NM_001005170.2	81	534,2558,3407	TT,TC,CC		28.1061,27.4875,27.8966	probably-damaging	167/351	4608542	3626,9372	2201	4298	6499	SO:0001583	missense	143502	exon1			TTCTCACGCCTCA	BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"""GPCR / Class A : Olfactory receptors"""	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.500C>T	11.37:g.4608542C>T	ENSP00000308764:p.Thr167Met	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	247	127	0.51417	NM_001005170	B2RNJ5|B9EKV8|Q6IFJ8	Missense_Mutation	SNP	ENST00000312614.4	37	CCDS31355.1	851	0.38965201465201466	118	0.23983739837398374	140	0.3867403314917127	330	0.5769230769230769	263	0.3469656992084433	C	8.772	0.926203	0.18056	0.274875	0.281061	ENSG00000226288	ENST00000312614	T	0.45668	0.89	4.18	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000314	T	0.00012	0.0000	H	0.95679	3.705	0.40828	P	0.016430999999999973	D	0.89917	1.0	D	0.68943	0.961	T	0.48175	-0.9058	9	0.87932	D	0	-12.5133	6.9968	0.24786	0.0:0.7261:0.1779:0.0959	rs1847632;rs61277460;rs1847632	167	Q8NH67	O52I2_HUMAN	M	167	ENSP00000308764:T167M	ENSP00000308764:T167M	T	+	2	0	OR52I2	4565118	0.055000	0.20627	0.810000	0.32431	0.089000	0.18198	0.878000	0.28126	0.984000	0.38629	-0.168000	0.13345	ACG	C|0.676;T|0.324	0.324	strong		0.512	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170	
ESR1	2099	hgsc.bcm.edu	37	6	152129077	152129077	+	Silent	SNP	T	T	C	rs2077647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152129077T>C	ENST00000206249.3	+	1	392	c.30T>C	c.(28-30)tcT>tcC	p.S10S	ESR1_ENST00000406599.1_Silent_p.S10S|ESR1_ENST00000440973.1_Silent_p.S10S|ESR1_ENST00000338799.5_Silent_p.S10S|ESR1_ENST00000456483.2_Silent_p.S10S|ESR1_ENST00000443427.1_Silent_p.S10S|ESR1_ENST00000427531.2_5'Flank	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	10	Modulating (transactivation AF-1); mediates interaction with MACROD1.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	CCAAAGCATCTGGGATGGCCC	0.667													C|||	2336	0.466454	0.5212	0.4654	5008	,	,		14556	0.378		0.4414	False		,,,				2504	0.5102				p.S10S		Atlas-SNP	.											.	ESR1	94	.	0			c.T30C						PASS	.	C	,,,	2127,2279	583.6+/-385.9	519,1089,595	35.0	33.0	34.0		30,30,30,30	-6.6	0.0	6	dbSNP_96	34	4101,4499	579.7+/-390.9	1006,2089,1205	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR1	NM_000125.3,NM_001122740.1,NM_001122741.1,NM_001122742.1	,,,	1525,3178,1800	CC,CT,TT		47.686,48.2751,47.8856	,,,	10/596,10/596,10/596,10/596	152129077	6228,6778	2203	4300	6503	SO:0001819	synonymous_variant	2099	exon1			AGCATCTGGGATG	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.30T>C	6.37:g.152129077T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1																																																																																			T|0.538;C|0.462	0.462	strong		0.667	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388508	1388508	+	Missense_Mutation	SNP	T	T	C	rs55703801		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388508T>C	ENST00000324803.4	+	1	3169	c.209T>C	c.(208-210)gTc>gCc	p.V70A		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	70					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACACGTGTCCATGTGGAG	0.632																																					p.V70A		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,1	CRIPAK	185	1	0			c.T209C						scavenged	.						283.0	245.0	257.0					4																	1388508		2203	4300	6503	SO:0001583	missense	285464	exon1			CACGTGTCCATGT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.209T>C	4.37:g.1388508T>C	ENSP00000323978:p.Val70Ala	Somatic	294	2	0.00680272		WXS	Illumina HiSeq	Phase_I	291	47	0.161512	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	8.717	0.913380	0.17907	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.24350	1.86	1.09	-2.19	0.07015	.	.	.	.	.	T	0.08714	0.0216	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.25257	-1.0137	9	0.16896	T	0.51	.	0.4342	0.00476	0.19:0.3247:0.1898:0.2955	rs55703801	70	Q8N1N5	CRPAK_HUMAN	A	70;63	ENSP00000323978:V70A	ENSP00000323978:V70A	V	+	2	0	CRIPAK	1378508	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-1.991000	0.01478	-2.302000	0.00657	-1.823000	0.00598	GTC	.	.	weak		0.632	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
PSMB4	5692	hgsc.bcm.edu	37	1	151374025	151374025	+	Missense_Mutation	SNP	T	T	C	rs4603	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151374025T>C	ENST00000290541.6	+	6	755	c.701T>C	c.(700-702)aTc>aCc	p.I234T		NM_002796.2	NP_002787.2	P28070	PSB4_HUMAN	proteasome (prosome, macropain) subunit, beta type, 4	234			I -> T (in dbSNP:rs4603). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7918633, ECO:0000269|PubMed:8013624, ECO:0000269|Ref.4, ECO:0000269|Ref.6}.		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	lipopolysaccharide binding (GO:0001530)|threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|lung(9)|ovary(2)|prostate(1)|skin(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CAGTTTCAAATCGCCACTGTC	0.438													T|||	962	0.192093	0.0666	0.3026	5008	,	,		20253	0.3165		0.1461	False		,,,				2504	0.2025				p.I234T		Atlas-SNP	.											.	PSMB4	18	.	0			c.T701C						PASS	.	T	THR/ILE	415,3991	200.8+/-224.0	21,373,1809	170.0	166.0	167.0		701	6.0	0.9	1	dbSNP_52	167	1486,7114	278.9+/-293.6	139,1208,2953	yes	missense	PSMB4	NM_002796.2	89	160,1581,4762	CC,CT,TT		17.2791,9.419,14.6163	probably-damaging	234/265	151374025	1901,11105	2203	4300	6503	SO:0001583	missense	5692	exon6			TTCAAATCGCCAC	D26600	CCDS996.1	1q21	2008-02-05			ENSG00000159377	ENSG00000159377		"""Proteasome (prosome, macropain) subunits"""	9541	protein-coding gene	gene with protein product		602177				7918633	Standard	NM_002796		Approved	HN3, PROS26	uc001eyc.1	P28070	OTTHUMG00000012494	ENST00000290541.6:c.701T>C	1.37:g.151374025T>C	ENSP00000290541:p.Ile234Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_002796	B2R9L3|P31148|Q5SZS5|Q6IBI4|Q969L6	Missense_Mutation	SNP	ENST00000290541.6	37	CCDS996.1	437	0.2000915750915751	25	0.0508130081300813	101	0.27900552486187846	198	0.34615384615384615	113	0.14907651715039577	T	20.3	3.972373	0.74246	0.09419	0.172791	ENSG00000159377	ENST00000290541	T	0.26373	1.74	5.99	5.99	0.97316	.	0.160708	0.56097	D	0.000035	T	0.42449	0.1203	M	0.86864	2.845	0.09310	P	0.999999382411	P	0.44478	0.836	P	0.55455	0.776	T	0.53683	-0.8404	9	0.87932	D	0	-8.657	13.8675	0.63598	0.0:0.0:0.0:1.0	rs4603;rs17601;rs1132311;rs2479383;rs3209768;rs3818560;rs11557383;rs17349275;rs52831382;rs56626133;rs57894623;rs4603	234	P28070	PSB4_HUMAN	T	234	ENSP00000290541:I234T	ENSP00000290541:I234T	I	+	2	0	PSMB4	149640649	1.000000	0.71417	0.903000	0.35520	0.519000	0.34347	7.791000	0.85805	2.291000	0.77112	0.533000	0.62120	ATC	T|0.835;C|0.165	0.165	strong		0.438	PSMB4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034885.1	NM_002796	
ZC2HC1A	51101	hgsc.bcm.edu	37	8	79609647	79609647	+	Silent	SNP	G	G	A	rs35904168	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:79609647G>A	ENST00000263849.4	+	6	612	c.510G>A	c.(508-510)aaG>aaA	p.K170K	ZC2HC1A_ENST00000521176.1_3'UTR	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	170							metal ion binding (GO:0046872)										TTTAGTATAAGCCACCCGCAC	0.363													G|||	153	0.0305511	0.0242	0.0389	5008	,	,		15369	0.0		0.0736	False		,,,				2504	0.0204				p.K170K		Atlas-SNP	.											.	.	.	.	0			c.G510A						PASS	.	G		128,4278	93.0+/-131.7	2,124,2077	57.0	58.0	58.0		510	-0.5	0.8	8	dbSNP_126	58	578,8022	155.4+/-209.4	23,532,3745	no	coding-synonymous	FAM164A	NM_016010.2		25,656,5822	AA,AG,GG		6.7209,2.9051,5.4283		170/326	79609647	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	51101	exon6			GTATAAGCCACCC		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"""Zinc fingers, C2HC-type containing"""	24277	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 70"", ""family with sequence similarity 164, member A"""	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.510G>A	8.37:g.79609647G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_016010	Q9Y372	Silent	SNP	ENST00000263849.4	37	CCDS6223.1	89	0.04075091575091575	17	0.034552845528455285	12	0.03314917127071823	0	0.0	60	0.079155672823219	G	2.794	-0.250565	0.05867	0.029051	0.067209	ENSG00000104427	ENST00000519307	.	.	.	5.48	-0.47	0.12131	.	.	.	.	.	T	0.04407	0.0121	.	.	.	0.09310	P	0.9999999999993069	.	.	.	.	.	.	T	0.39663	-0.9603	3	.	.	.	-15.1026	11.4129	0.49935	0.4266:0.0:0.5734:0.0	rs35904168;rs62518983	.	.	.	T	3	.	.	A	+	1	0	FAM164A	79772202	1.000000	0.71417	0.804000	0.32291	0.364000	0.29643	0.417000	0.21214	-0.318000	0.08665	-0.732000	0.03574	GCC	G|0.946;A|0.054	0.054	strong		0.363	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010	
TNRC18	84629	hgsc.bcm.edu	37	7	5410425	5410425	+	Missense_Mutation	SNP	G	G	C	rs12671708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5410425G>C	ENST00000430969.1	-	11	4148	c.3800C>G	c.(3799-3801)gCg>gGg	p.A1267G	TNRC18_ENST00000399537.4_Missense_Mutation_p.A1267G	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1267				A -> G (in Ref. 3; BAB47485). {ECO:0000305}.			chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CACGGGCACCGCCACAGGCAC	0.701													G|||	1718	0.343051	0.059	0.487	5008	,	,		14580	0.4236		0.4175	False		,,,				2504	0.4652				p.A1267G		Atlas-SNP	.											.	TNRC18	311	.	0			c.C3800G						PASS	.	G	GLY/ALA	485,3603		52,381,1611	8.0	10.0	9.0		3800	-0.1	0.0	7	dbSNP_120	9	3710,4648		915,1880,1384	no	missense	TNRC18	NM_001080495.2	60	967,2261,2995	CC,CG,GG		44.3886,11.864,33.7056	benign	1267/2969	5410425	4195,8251	2044	4179	6223	SO:0001583	missense	84629	exon11			GGCACCGCCACAG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.3800C>G	7.37:g.5410425G>C	ENSP00000395538:p.Ala1267Gly	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	777	0.3557692307692308	42	0.08536585365853659	172	0.47513812154696133	246	0.43006993006993005	317	0.4182058047493404	G	4.511	0.094781	0.08681	0.11864	0.443886	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000327499	T;T	0.11712	2.75;2.75	3.63	-0.141	0.13452	.	0.807460	0.10346	N	0.685646	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43988	-0.9357	9	0.15952	T	0.53	.	6.8614	0.24069	0.0:0.0925:0.4794:0.428	rs12671708	1267	O15417	TNC18_HUMAN	G	1267;1267;322;322	ENSP00000382452:A1267G;ENSP00000395538:A1267G	ENSP00000330383:A322G	A	-	2	0	TNRC18	5376951	0.000000	0.05858	0.033000	0.17914	0.638000	0.38207	-0.160000	0.10041	-0.021000	0.14009	-0.521000	0.04368	GCG	G|0.632;C|0.368	0.368	strong		0.701	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
RALB	5899	hgsc.bcm.edu	37	2	121036333	121036333	+	Silent	SNP	G	G	A	rs11545293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:121036333G>A	ENST00000272519.5	+	2	363	c.93G>A	c.(91-93)acG>acA	p.T31T	RALB_ENST00000470417.1_Intron|RALB_ENST00000420510.1_Silent_p.T31T|RALB_ENST00000404963.3_Silent_p.T31T|RALB_ENST00000474855.2_Silent_p.T53T	NM_002881.2	NP_002872.1	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B	31					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of exocyst assembly (GO:0001928)|regulation of exocyst localization (GO:0060178)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(154;0.122)				CAGCCCTGACGCTTCAGTTCA	0.592													g|||	221	0.0441294	0.0008	0.0634	5008	,	,		19749	0.003		0.1064	False		,,,				2504	0.0675				p.T31T		Atlas-SNP	.											.	RALB	27	.	0			c.G93A						PASS	.			88,4318	75.2+/-113.4	1,86,2116	104.0	80.0	88.0		93	-10.3	0.3	2	dbSNP_120	88	933,7667	205.1+/-247.6	65,803,3432	no	coding-synonymous	RALB	NM_002881.2		66,889,5548	AA,AG,GG		10.8488,1.9973,7.8502		31/207	121036333	1021,11985	2203	4300	6503	SO:0001819	synonymous_variant	5899	exon2			CCTGACGCTTCAG		CCDS2131.1	2q14.2	2014-05-09	2013-07-09		ENSG00000144118	ENSG00000144118			9840	protein-coding gene	gene with protein product	"""ras related GTP binding protein B"""	179551					Standard	NM_002881		Approved		uc002tmk.3	P11234	OTTHUMG00000131435	ENST00000272519.5:c.93G>A	2.37:g.121036333G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_002881	B4E040|Q53T32|Q6ZS74	Silent	SNP	ENST00000272519.5	37	CCDS2131.1																																																																																			G|0.926;A|0.074	0.074	strong		0.592	RALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254232.3	NM_002881	
DAXX	1616	hgsc.bcm.edu	37	6	33288271	33288271	+	Silent	SNP	A	A	G	rs1059231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33288271A>G	ENST00000374542.5	-	4	1341	c.1137T>C	c.(1135-1137)taT>taC	p.Y379Y	DAXX_ENST00000266000.6_Silent_p.Y379Y|DAXX_ENST00000414083.2_Silent_p.Y304Y|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000477162.1_5'UTR|ZBTB22_ENST00000431845.2_5'Flank	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	379	Interaction with histone H3.3.|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						GCAACATTGCATATTTGGAGA	0.552			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM								A|||	1106	0.220847	0.0182	0.3415	5008	,	,		18188	0.2619		0.2922	False		,,,				2504	0.2935				p.Y391Y		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.T1173C						PASS	.	A	,,	277,4129	154.4+/-187.8	5,267,1931	94.0	87.0	90.0		1137,1173,1137	2.1	1.0	6	dbSNP_86	90	2570,6030	417.9+/-352.6	398,1774,2128	no	coding-synonymous,coding-synonymous,coding-synonymous	DAXX	NM_001141969.1,NM_001141970.1,NM_001350.4	,,	403,2041,4059	GG,GA,AA		29.8837,6.2869,21.8899	,,	379/741,391/753,379/741	33288271	2847,10159	2203	4300	6503	SO:0001819	synonymous_variant	1616	exon4			CATTGCATATTTG	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1137T>C	6.37:g.33288271A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	44	0.721311	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	37	CCDS4776.1																																																																																			A|0.778;G|0.222	0.222	strong		0.552	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1		
POU4F3	5459	hgsc.bcm.edu	37	5	145718765	145718765	+	Silent	SNP	C	C	T	rs28994879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145718765C>T	ENST00000230732.4	+	1	179	c.90C>T	c.(88-90)gcC>gcT	p.A30A	CTC-359M8.1_ENST00000515598.1_RNA|RBM27_ENST00000506502.1_Missense_Mutation_p.H1016Y	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	30					auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTCCGAGGCCATGCGCCGAG	0.542													C|||	89	0.0177716	0.003	0.0331	5008	,	,		17870	0.0		0.0537	False		,,,				2504	0.0082				p.A30A		Atlas-SNP	.											.	POU4F3	47	.	0			c.C90T						PASS	.	C		25,4381	30.8+/-60.4	0,25,2178	103.0	93.0	97.0		90	3.3	1.0	5	dbSNP_125	97	364,8236	121.8+/-180.9	9,346,3945	no	coding-synonymous	POU4F3	NM_002700.2		9,371,6123	TT,TC,CC		4.2326,0.5674,2.9909		30/339	145718765	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	5459	exon1			CGAGGCCATGCGC	U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"""Homeoboxes / POU class"""	9220	protein-coding gene	gene with protein product		602460	"""POU domain class 4, transcription factor 3"""	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.90C>T	5.37:g.145718765C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	124	83	0.669355	NM_002700	O60557|Q2M3F8	Silent	SNP	ENST00000230732.4	37	CCDS4281.1																																																																																			C|0.969;T|0.031	0.031	strong		0.542	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700	
SCIMP	388325	hgsc.bcm.edu	37	17	5126689	5126689	+	Silent	SNP	G	G	A	rs2585271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5126689G>A	ENST00000574081.1	-	2	188	c.84C>T	c.(82-84)atC>atT	p.I28I	RP11-333E1.1_ENST00000573772.1_RNA|SCIMP_ENST00000399600.4_Silent_p.I28I|SCIMP_ENST00000571800.1_Silent_p.I28I|SCIMP_ENST00000574297.1_Silent_p.I28I|RP11-333E1.1_ENST00000575601.1_RNA|RP11-333E1.1_ENST00000571689.1_RNA	NM_001271842.1|NM_207103.3	NP_001258771.1|NP_996986.1	Q6UWF3	SCIMP_HUMAN	SLP adaptor and CSK interacting membrane protein	28					positive regulation of ERK1 and ERK2 cascade (GO:0070374)	immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|tetraspanin-enriched microdomain (GO:0097197)|uropod membrane (GO:0031259)											CAGAGACAACGATGATGGCCA	0.493													G|||	1680	0.335463	0.1831	0.5937	5008	,	,		21331	0.1984		0.6014	False		,,,				2504	0.226				p.I28I		Atlas-SNP	.											.	.	.	.	0			c.C84T						PASS	.	G		1054,3100		146,762,1169	282.0	267.0	272.0		84	-1.1	0.0	17	dbSNP_100	272	5348,3068		1708,1932,568	no	coding-synonymous	C17orf87	NM_207103.2		1854,2694,1737	AA,AG,GG		36.4544,25.3731,49.0692		28/146	5126689	6402,6168	2077	4208	6285	SO:0001819	synonymous_variant	388325	exon2			GACAACGATGATG	AY358809	CCDS42242.1, CCDS62044.1	17p13.2	2011-11-24	2011-11-23	2011-11-23	ENSG00000161929	ENSG00000161929			33504	protein-coding gene	gene with protein product	"""SLP65/SLP76, Csk-interacting membrane protein"""	614406	"""chromosome 17 open reading frame 87"""	C17orf87		21930792	Standard	NM_207103		Approved	DTFT5783, UNQ5783, FLJ32580, MGC163426, MGC163428	uc002gbh.3	Q6UWF3	OTTHUMG00000132914	ENST00000574081.1:c.84C>T	17.37:g.5126689G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_207103	A6XGL4|B4DLK1|Q96MD0	Silent	SNP	ENST00000574081.1	37	CCDS42242.1																																																																																			G|0.593;N|0.000	.	strong		0.493	SCIMP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256425.2	NM_207103	
TNRC18	84629	hgsc.bcm.edu	37	7	5347914	5347914	+	Silent	SNP	G	G	A	rs11554710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:5347914G>A	ENST00000430969.1	-	30	9078	c.8730C>T	c.(8728-8730)gaC>gaT	p.D2910D	TNRC18_ENST00000399537.4_Silent_p.D2910D	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2910	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.						chromatin binding (GO:0003682)	p.D2910D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CGTCATTTTCGTCCACATGCG	0.637													G|||	516	0.103035	0.0477	0.1758	5008	,	,		19611	0.0982		0.1521	False		,,,				2504	0.0808				p.D2910D		Atlas-SNP	.											TNRC18_ENST00000430969,caecum,carcinoma,0,3	TNRC18	311	3	1	Substitution - coding silent(1)	stomach(1)	c.C8730T						PASS	.	G		253,3923		5,243,1840	38.0	38.0	38.0		8730	1.2	1.0	7	dbSNP_120	38	1457,6947		132,1193,2877	no	coding-synonymous	TNRC18	NM_001080495.2		137,1436,4717	AA,AG,GG		17.337,6.0584,13.593		2910/2969	5347914	1710,10870	2088	4202	6290	SO:0001819	synonymous_variant	84629	exon30			ATTTTCGTCCACA	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.8730C>T	7.37:g.5347914G>A		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	278	122	0.438849	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.862;A|0.138	0.138	strong		0.637	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
NAA40	79829	hgsc.bcm.edu	37	11	63713317	63713317	+	Silent	SNP	G	G	A	rs3740637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:63713317G>A	ENST00000377793.4	+	2	113	c.12G>A	c.(10-12)aaG>aaA	p.K4K	NAA40_ENST00000456907.2_5'UTR|NAA40_ENST00000539656.1_Silent_p.K4K|NAA40_ENST00000536939.1_3'UTR|NAA40_ENST00000542163.1_5'UTR	NM_024771.2	NP_079047.2	Q86UY6	NAA40_HUMAN	N(alpha)-acetyltransferase 40, NatD catalytic subunit	4					lipid metabolic process (GO:0006629)		N-acetyltransferase activity (GO:0008080)			NS(1)|endometrium(1)|lung(2)|prostate(1)	5						TGCAGAGAAAGTCAAGCAAAG	0.537											OREG0021041	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	852	0.170128	0.0189	0.1499	5008	,	,		21146	0.0565		0.3946	False		,,,				2504	0.2751				p.K4K		Atlas-SNP	.											.	NAA40	13	.	0			c.G12A						PASS	.	G		359,4043	183.6+/-211.2	23,313,1865	184.0	149.0	161.0		12	5.0	1.0	11	dbSNP_107	161	3425,5169	504.9+/-376.3	658,2109,1530	no	coding-synonymous	NAA40	NM_024771.2		681,2422,3395	AA,AG,GG		39.8534,8.1554,29.1167		4/238	63713317	3784,9212	2201	4297	6498	SO:0001819	synonymous_variant	79829	exon2			GAGAAAGTCAAGC	AK023910	CCDS8053.1, CCDS73311.1	11q13.1	2013-10-11	2013-08-28	2010-01-14	ENSG00000110583	ENSG00000110583		"""N(alpha)-acetyltransferase subunits"""	25845	protein-coding gene	gene with protein product			"""N-acetyltransferase 11"", ""N-acetyltransferase 11 (GCN5-related, putative)"", ""N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae)"""	NAT11		19660095	Standard	XM_005274296		Approved	FLJ13848	uc009yoz.3	Q86UY6	OTTHUMG00000167784	ENST00000377793.4:c.12G>A	11.37:g.63713317G>A		Somatic	109	0	0	1071	WXS	Illumina HiSeq	Phase_I	128	128	1	NM_024771	B4DR03|B4DU10|Q5HYL5|Q9H897	Silent	SNP	ENST00000377793.4	37	CCDS8053.1																																																																																			G|0.756;A|0.244	0.244	strong		0.537	NAA40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396266.1	NM_024771	
PUS3	83480	hgsc.bcm.edu	37	11	125766173	125766173	+	Missense_Mutation	SNP	A	A	C	rs622756	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:125766173A>C	ENST00000530811.1	-	1	52	c.7T>G	c.(7-9)Tat>Gat	p.Y3D	PUS3_ENST00000227474.3_Missense_Mutation_p.Y3D|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron|HYLS1_ENST00000425380.2_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	3			Y -> D (in dbSNP:rs622756). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		GTGTCATTATAAGCCATGATA	0.418													C|||	4020	0.802716	0.6339	0.889	5008	,	,		19660	0.8542		0.8569	False		,,,				2504	0.8609				p.Y3D		Atlas-SNP	.											.	PUS3	33	.	0			c.T7G						PASS	.	C	,ASP/TYR,	2983,1419	458.2+/-351.9	988,1007,206	97.0	94.0	95.0		,7,	5.0	1.0	11	dbSNP_83	95	7479,1119	230.7+/-264.9	3259,961,79	yes	intron,missense,intron	PUS3,HYLS1	NM_001134793.1,NM_031307.3,NM_145014.2	,160,	4247,1968,285	CC,CA,AA		13.0147,32.2353,19.5231	,benign,	,3/482,	125766173	10462,2538	2201	4299	6500	SO:0001583	missense	83480	exon2			CATTATAAGCCAT	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.7T>G	11.37:g.125766173A>C	ENSP00000432386:p.Tyr3Asp	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	230	230	1	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Missense_Mutation	SNP	ENST00000530811.1	37	CCDS8466.1	1796	0.8223443223443223	318	0.6463414634146342	324	0.8950276243093923	504	0.8811188811188811	650	0.8575197889182058	C	0.181	-1.062392	0.01950	0.677647	0.869853	ENSG00000110060	ENST00000227474;ENST00000530811;ENST00000534158;ENST00000529801	T;T;T;T	0.54279	1.58;1.58;0.58;1.57	5.93	5.02	0.67125	.	0.328338	0.26200	N	0.025741	T	0.00012	0.0000	N	0.08118	0	0.48632	P	3.1800000000004047E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	9	0.16420	T	0.52	-11.2711	4.1188	0.10095	0.1332:0.6013:0.1285:0.137	rs622756;rs1285317;rs1285710;rs17845028;rs17857797;rs56918725;rs622756	3	Q9BZE2	PUS3_HUMAN	D	3	ENSP00000227474:Y3D;ENSP00000432386:Y3D;ENSP00000432272:Y3D;ENSP00000437077:Y3D	ENSP00000227474:Y3D	Y	-	1	0	PUS3	125271383	0.963000	0.33076	1.000000	0.80357	0.306000	0.27790	0.899000	0.28417	0.862000	0.35528	-0.121000	0.15023	TAT	A|0.194;C|0.806	0.806	strong		0.418	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307	
EZH2	2146	hgsc.bcm.edu	37	7	148525904	148525904	+	Missense_Mutation	SNP	C	C	G	rs2302427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:148525904C>G	ENST00000460911.1	-	6	641	c.553G>C	c.(553-555)Gac>Cac	p.D185H	EZH2_ENST00000536783.1_Missense_Mutation_p.D76H|EZH2_ENST00000483967.1_Missense_Mutation_p.D176H|EZH2_ENST00000541220.1_Missense_Mutation_p.D176H|EZH2_ENST00000350995.2_Missense_Mutation_p.D146H|EZH2_ENST00000478654.1_Missense_Mutation_p.D176H|EZH2_ENST00000320356.2_Missense_Mutation_p.D185H|EZH2_ENST00000476773.1_Missense_Mutation_p.D176H			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	185	Interaction with DNMT1, DNMT3A and DNMT3B.		D -> H (in dbSNP:rs2302427).		cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			tcatcatcgtcatcatcatta	0.393			Mis		DLBCL								C|||	400	0.0798722	0.0038	0.0461	5008	,	,		19098	0.2063		0.0696	False		,,,				2504	0.0869				p.D185H		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,NS,carcinoma,+2,2	EZH2	823	2	0			c.G553C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	66,4340	60.5+/-97.4	0,66,2137	178.0	146.0	157.0		553,526,526,553,436	5.7	0.9	7	dbSNP_100	157	719,7881	175.3+/-225.4	30,659,3611	yes	missense,missense,missense,missense,missense	EZH2	NM_001203247.1,NM_001203248.1,NM_001203249.1,NM_004456.4,NM_152998.2	81,81,81,81,81	30,725,5748	GG,GC,CC		8.3605,1.498,6.0357	benign,benign,benign,benign,benign	185/747,176/738,176/696,185/752,146/708	148525904	785,12221	2203	4300	6503	SO:0001583	missense	2146	exon6			CATCGTCATCATC		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.553G>C	7.37:g.148525904C>G	ENSP00000419711:p.Asp185His	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	141	83	0.588652	NM_001203247	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	161	0.07371794871794872	3	0.006097560975609756	21	0.058011049723756904	83	0.1451048951048951	54	0.0712401055408971	C	19.43	3.826662	0.71143	0.01498	0.083605	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.94828	-3.46;-3.5;-3.46;-3.5;-3.46;-3.46;-3.53;0.81	5.69	5.69	0.88448	SANT domain, DNA binding (1);	0.168733	0.49916	D	0.000127	T	0.08980	0.0222	L	0.34521	1.04	0.09310	P	0.99999641944	P;B;B;B;P;P	0.47604	0.898;0.348;0.348;0.41;0.659;0.676	P;B;B;B;B;P	0.49226	0.553;0.393;0.393;0.299;0.393;0.603	T	0.59161	-0.7506	9	0.72032	D	0.01	.	19.4235	0.94732	0.0:1.0:0.0:0.0	rs2302427;rs52833659	185;176;176;185;146;185	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	H	176;185;185;146;176;176;176;76	ENSP00000417062:D176H;ENSP00000320147:D185H;ENSP00000419711:D185H;ENSP00000223193:D146H;ENSP00000443219:D176H;ENSP00000419050:D176H;ENSP00000419856:D176H;ENSP00000439305:D76H	ENSP00000320147:D185H	D	-	1	0	EZH2	148156837	1.000000	0.71417	0.919000	0.36401	0.821000	0.46438	7.538000	0.82048	2.682000	0.91365	0.585000	0.79938	GAC	C|0.926;G|0.074	0.074	strong		0.393	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
FAM187B	148109	hgsc.bcm.edu	37	19	35718891	35718891	+	Nonsense_Mutation	SNP	C	C	T	rs35001809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:35718891C>T	ENST00000324675.3	-	1	741	c.693G>A	c.(691-693)tgG>tgA	p.W231*		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	231						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						GACAGTCGAGCCACACAAATT	0.507													C|||	86	0.0171725	0.0	0.0115	5008	,	,		19197	0.001		0.0398	False		,,,				2504	0.0378				p.W231X		Atlas-SNP	.											.	FAM187B	28	.	0			c.G693A						PASS	.	C	stop/TRP	41,4365	44.6+/-78.6	0,41,2162	82.0	68.0	73.0		693	3.8	0.8	19	dbSNP_126	73	252,8348	98.6+/-160.1	3,246,4051	yes	stop-gained	FAM187B	NM_152481.1		3,287,6213	TT,TC,CC		2.9302,0.9305,2.2528		231/370	35718891	293,12713	2203	4300	6503	SO:0001587	stop_gained	148109	exon1			GTCGAGCCACACA	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"""transmembrane protein 162"""	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.693G>A	19.37:g.35718891C>T	ENSP00000323355:p.Trp231*	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	164	55	0.335366	NM_152481	Q8N7G6	Nonsense_Mutation	SNP	ENST00000324675.3	37	CCDS12448.1	33	0.01510989010989011	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	29	0.03825857519788918	C	15.73	2.918681	0.52546	0.009305	0.029302	ENSG00000177558	ENST00000324675	.	.	.	4.91	3.85	0.44370	.	0.693744	0.12668	N	0.449031	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-6.6331	10.6862	0.45843	0.1915:0.8085:0.0:0.0	rs35001809;rs61744928	.	.	.	X	231	.	ENSP00000323355:W231X	W	-	3	0	FAM187B	40410731	0.905000	0.30787	0.764000	0.31436	0.016000	0.09150	1.334000	0.33827	1.142000	0.42291	0.655000	0.94253	TGG	C|0.978;T|0.022	0.022	strong		0.507	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
FGF21	26291	hgsc.bcm.edu	37	19	49261267	49261267	+	Silent	SNP	C	C	T	rs3745710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49261267C>T	ENST00000593756.1	+	4	992	c.420C>T	c.(418-420)caC>caT	p.H140H	FUT1_ENST00000310160.3_5'Flank|FGF21_ENST00000222157.3_Silent_p.H140H			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	140					cell-cell signaling (GO:0007267)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		CCGAAGCCCACGGCCTCCCGC	0.632													C|||	209	0.0417332	0.0083	0.1297	5008	,	,		9454	0.0089		0.0924	False		,,,				2504	0.0061				p.H140H		Atlas-SNP	.											.	FGF21	21	.	0			c.C420T						PASS	.	C		132,4274	89.7+/-128.4	1,130,2072	79.0	86.0	83.0		420	-8.9	0.0	19	dbSNP_107	83	690,7908	165.5+/-217.6	30,630,3639	no	coding-synonymous	FGF21	NM_019113.2		31,760,5711	TT,TC,CC		8.0251,2.9959,6.3211		140/210	49261267	822,12182	2203	4299	6502	SO:0001819	synonymous_variant	26291	exon3			AGCCCACGGCCTC	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.420C>T	19.37:g.49261267C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	NM_019113	Q8N683	Silent	SNP	ENST00000593756.1	37	CCDS12734.1																																																																																			C|0.943;T|0.057	0.057	strong		0.632	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1		
PRIMPOL	201973	hgsc.bcm.edu	37	4	185615768	185615768	+	Silent	SNP	T	T	G	rs3184982	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:185615768T>G	ENST00000314970.6	+	14	1951	c.1518T>G	c.(1516-1518)ggT>ggG	p.G506G	PRIMPOL_ENST00000512834.1_Silent_p.G505G|PRIMPOL_ENST00000515774.1_Silent_p.G377G|PRIMPOL_ENST00000503752.1_Silent_p.G506G|PRIMPOL_ENST00000510864.1_3'UTR	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	506	Interaction with RPA1.				mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										TGTCAACAGGTGCATCTGCTG	0.413													T|||	733	0.146366	0.3011	0.1369	5008	,	,		19993	0.001		0.1481	False		,,,				2504	0.092				p.G506G		Atlas-SNP	.											.	CCDC111	43	.	0			c.T1518G						PASS	.	T	,	1219,3187	418.3+/-338.2	165,889,1149	99.0	102.0	101.0		,1518	-4.1	0.0	4	dbSNP_105	101	1407,7193	270.4+/-288.9	117,1173,3010	no	utr-3,coding-synonymous	MLF1IP,CCDC111	NM_024629.3,NM_152683.2	,	282,2062,4159	GG,GT,TT		16.3605,27.6668,20.1907	,	,506/561	185615768	2626,10380	2203	4300	6503	SO:0001819	synonymous_variant	201973	exon14			AACAGGTGCATCT	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.1518T>G	4.37:g.185615768T>G		Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	217	105	0.483871	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Silent	SNP	ENST00000314970.6	37	CCDS3837.1																																																																																			T|0.822;G|0.178	0.178	strong		0.413	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
FAM105A	54491	hgsc.bcm.edu	37	5	14610309	14610309	+	Missense_Mutation	SNP	C	C	G	rs16903574	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:14610309C>G	ENST00000274217.3	+	8	1077	c.957C>G	c.(955-957)ttC>ttG	p.F319L		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	319	OTU.		F -> L (in dbSNP:rs16903574).							large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					TCAGACTGTTCAAGTTTAACT	0.468													C|||	109	0.0217652	0.0015	0.0317	5008	,	,		18153	0.0		0.0726	False		,,,				2504	0.0123				p.F319L		Atlas-SNP	.											.	FAM105A	32	.	0			c.C957G						PASS	.	C	LEU/PHE	59,4347	58.1+/-94.6	0,59,2144	102.0	106.0	105.0		957	4.2	1.0	5	dbSNP_123	105	641,7959	164.6+/-216.9	25,591,3684	yes	missense	FAM105A	NM_019018.2	22	25,650,5828	GG,GC,CC		7.4535,1.3391,5.3821	benign	319/357	14610309	700,12306	2203	4300	6503	SO:0001583	missense	54491	exon8			ACTGTTCAAGTTT		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"""OTU domain containing"""	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.957C>G	5.37:g.14610309C>G	ENSP00000274217:p.Phe319Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	90	52	0.577778	NM_019018	Q53H50|Q9H037	Missense_Mutation	SNP	ENST00000274217.3	37	CCDS3884.1	68	0.031135531135531136	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	57	0.07519788918205805	C	11.86	1.765141	0.31228	0.013391	0.074535	ENSG00000145569	ENST00000274217	T	0.14766	2.48	5.14	4.15	0.48705	.	0.467586	0.21827	N	0.068531	T	0.00468	0.0015	L	0.44542	1.39	0.33258	P	0.440623	P	0.36837	0.571	B	0.33392	0.163	T	0.08680	-1.0710	9	0.11485	T	0.65	-25.5093	7.4991	0.27507	0.0:0.6813:0.1688:0.1499	rs16903574;rs52818857;rs56541622;rs16903574	319	Q9NUU6	F105A_HUMAN	L	319	ENSP00000274217:F319L	ENSP00000274217:F319L	F	+	3	2	FAM105A	14663309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.867000	0.39499	2.381000	0.81170	0.655000	0.94253	TTC	C|0.954;G|0.046	0.046	strong		0.468	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018	
HTRA4	203100	hgsc.bcm.edu	37	8	38835666	38835666	+	Splice_Site	SNP	T	T	C	rs4733961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:38835666T>C	ENST00000302495.4	+	4	1066	c.966T>C	c.(964-966)aaT>aaC	p.N322N		NM_153692.3	NP_710159.1	P83105	HTRA4_HUMAN	HtrA serine peptidase 4	322	Serine protease.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)	11		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			CCACAATTAATGTAAGTCACT	0.532													T|||	3916	0.781949	0.6778	0.8559	5008	,	,		23584	0.9494		0.8012	False		,,,				2504	0.6779				p.N322N		Atlas-SNP	.											.	HTRA4	25	.	0			c.T966C						PASS	.	T		3054,1352	692.7+/-405.6	1055,944,204	72.0	64.0	66.0		966	-3.2	1.0	8	dbSNP_111	66	6575,2025	719.7+/-406.3	2499,1577,224	yes	coding-synonymous-near-splice	HTRA4	NM_153692.3		3554,2521,428	CC,CT,TT		23.5465,30.6854,25.9649		322/477	38835666	9629,3377	2203	4300	6503	SO:0001630	splice_region_variant	203100	exon4			AATTAATGTAAGT	AK075205	CCDS6110.1	8p11.23	2008-02-05			ENSG00000169495	ENSG00000169495			26909	protein-coding gene	gene with protein product		610700					Standard	NM_153692		Approved	FLJ90724	uc003xmj.3	P83105	OTTHUMG00000164070	ENST00000302495.4:c.966+1T>C	8.37:g.38835666T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_153692	Q542Z4|Q6PF13	Silent	SNP	ENST00000302495.4	37	CCDS6110.1																																																																																			T|0.228;C|0.772	0.772	strong		0.532	HTRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377077.1	NM_153692	Silent
OR5W2	390148	hgsc.bcm.edu	37	11	55681865	55681865	+	Missense_Mutation	SNP	T	T	C	rs12419022	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55681865T>C	ENST00000344514.1	-	1	193	c.194A>G	c.(193-195)cAt>cGt	p.H65R		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	65			H -> R (in dbSNP:rs12419022).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GAAAGACAGATGACTGAGGAA	0.393													T|||	512	0.102236	0.0477	0.0965	5008	,	,		21019	0.1448		0.1233	False		,,,				2504	0.1145				p.H65R	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.A194G						PASS	.	T	ARG/HIS	241,4161	141.1+/-176.5	7,227,1967	124.0	119.0	120.0		194	5.0	1.0	11	dbSNP_120	120	1022,7570	218.7+/-257.0	57,908,3331	yes	missense	OR5W2	NM_001001960.1	29	64,1135,5298	CC,CT,TT		11.8948,5.4748,9.7199	benign	65/311	55681865	1263,11731	2201	4296	6497	SO:0001583	missense	390148	exon1			GACAGATGACTGA	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.194A>G	11.37:g.55681865T>C	ENSP00000342448:p.His65Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	69	0.466216	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	250	0.11446886446886446	29	0.05894308943089431	33	0.09116022099447514	87	0.1520979020979021	101	0.13324538258575197	T	11.80	1.745930	0.30955	0.054748	0.118948	ENSG00000187612	ENST00000344514	T	0.02916	4.11	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.172191	0.27816	N	0.017733	T	0.00039	0.0001	M	0.89214	3.015	0.29591	P	0.848406	B	0.13145	0.007	B	0.18263	0.021	T	0.03957	-1.0989	9	0.66056	D	0.02	.	12.6788	0.56910	0.0:0.0:0.0:1.0	rs12419022;rs52804851;rs59891570;rs12419022	65	Q8NH69	OR5W2_HUMAN	R	65	ENSP00000342448:H65R	ENSP00000342448:H65R	H	-	2	0	OR5W2	55438441	0.045000	0.20229	0.990000	0.47175	0.405000	0.30901	2.454000	0.44979	1.874000	0.54306	0.448000	0.29417	CAT	T|0.900;C|0.100	0.100	strong		0.393	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
ASMTL	8623	hgsc.bcm.edu	37	X	1531687	1531687	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:1531687T>C	ENST00000381317.3	-	12	1615	c.1583A>G	c.(1582-1584)cAt>cGt	p.H528R	ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL_ENST00000416733.2_Missense_Mutation_p.H452R|ASMTL-AS1_ENST00000425740.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL_ENST00000534940.1_Missense_Mutation_p.H470R|ASMTL_ENST00000381333.4_Missense_Mutation_p.H512R	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	528	ASMT-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGGCCAGTCATGCAGGATCCG	0.542													t|||	69	0.013778	0.0053	0.0101	5008	,	,		17057	0.0		0.0537	False		,,,				2504	0.001				p.H528R		Atlas-SNP	.											.	ASMTL	56	.	0			c.A1583G						PASS	.		ARG/HIS,ARG/HIS,ARG/HIS	65,4009		1,63,1973	178.0	189.0	186.0		1409,1535,1583	1.4	0.1	X	dbSNP_134	186	651,7731		26,599,3566	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	29,29,29	27,662,5539	CC,CT,TT		7.7666,1.5955,5.7482	probably-damaging,probably-damaging,probably-damaging	470/564,512/606,528/622	1531687	716,11740	2037	4191	6228	SO:0001583	missense	8623	exon12			CAGTCATGCAGGA	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"""Pseudoautosomal regions / PAR1"""	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.1583A>G	X.37:g.1531687T>C	ENSP00000370718:p.His528Arg	Somatic	483	0	0		WXS	Illumina HiSeq	Phase_I	462	220	0.47619	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	52	0.023809523809523808	0	0.0	4	0.011049723756906077	0	0.0	48	0.0633245382585752	N	9.505	1.104249	0.20632	0.015955	0.077666	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	1.43	1.43	0.22495	O-methyltransferase, family 2 (1);	0.218384	0.37437	U	0.002092	T	0.05731	0.0150	M	0.88775	2.98	0.34823	D	0.738929	D;D;D	0.89917	1.0;0.994;0.995	D;P;P	0.81914	0.995;0.836;0.898	T	0.48559	-0.9025	10	0.87932	D	0	.	8.1988	0.31413	0.0:0.0:0.0:1.0	.	452;512;528	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	R	452;470;512;528	ENSP00000410578:H452R;ENSP00000446410:H470R;ENSP00000370734:H512R;ENSP00000370718:H528R	ENSP00000370718:H528R	H	-	2	0	ASMTL	1491687	1.000000	0.71417	0.077000	0.20336	0.000000	0.00434	3.601000	0.54059	0.431000	0.26258	0.000000	0.15137	CAT	T|0.962;C|0.038	0.038	strong		0.542	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
LRIG1	26018	hgsc.bcm.edu	37	3	66434674	66434674	+	Silent	SNP	C	C	T	rs140903952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:66434674C>T	ENST00000273261.3	-	14	2336	c.1812G>A	c.(1810-1812)acG>acA	p.T604T	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000383703.3_Silent_p.T628T|LRIG1_ENST00000496559.2_5'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	604	Ig-like C2-type 2.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)		p.T604T(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TGTCGTGGGGCGTTTTGGTGA	0.547													c|||	7	0.00139776	0.0	0.0029	5008	,	,		18000	0.0		0.001	False		,,,				2504	0.0041				p.T604T		Atlas-SNP	.											LRIG1,colon,carcinoma,0,1	LRIG1	138	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1812A						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	233.0	225.0	228.0		1812	-1.0	0.8	3	dbSNP_134	228	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	LRIG1	NM_015541.2		0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		604/1094	66434674	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon14			GTGGGGCGTTTTG	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1812G>A	3.37:g.66434674C>T		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	341	147	0.431085	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
DENND4C	55667	hgsc.bcm.edu	37	9	19290732	19290732	+	5'Flank	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:19290732A>G	ENST00000380432.2	+	0	0				RP11-146N23.4_ENST00000417577.2_RNA|DENND4C_ENST00000602925.1_Missense_Mutation_p.Y220C|DENND4C_ENST00000434457.2_Missense_Mutation_p.Y220C			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C						cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GAAGAGGACTATGAGTCATTT	0.343																																					p.Y220C		Atlas-SNP	.											.	DENND4C	120	.	0			c.A659G						PASS	.						96.0	85.0	88.0					9																	19290732		1829	4075	5904	SO:0001631	upstream_gene_variant	55667	exon5			AGGACTATGAGTC	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627		9.37:g.19290732A>G	Exception_encountered	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	45	31	0.688889	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37																																																																																				.	.	none		0.343	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
OR52W1	120787	hgsc.bcm.edu	37	11	6221305	6221305	+	Missense_Mutation	SNP	C	C	G	rs374054864		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6221305C>G	ENST00000311352.2	+	1	930	c.852C>G	c.(850-852)aaC>aaG	p.N284K	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, member 1	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCTCTCCAACATCTACTTGC	0.527																																					p.N284K		Atlas-SNP	.											.	OR52W1	33	.	0			c.C852G						PASS	.	C	LYS/ASN	0,4402		0,0,2201	338.0	328.0	332.0		852	-0.5	1.0	11		332	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR52W1	NM_001005178.1	94	0,1,6496	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging	284/321	6221305	1,12993	2201	4296	6497	SO:0001583	missense	120787	exon1			CTCCAACATCTAC	AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"""GPCR / Class A : Olfactory receptors"""	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.852C>G	11.37:g.6221305C>G	ENSP00000309673:p.Asn284Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.954305	0.53293	0.0	1.16E-4	ENSG00000175485	ENST00000311352	T	0.00115	8.71	5.11	-0.514	0.11958	GPCR, rhodopsin-like superfamily (1);	0.173838	0.27245	N	0.020242	T	0.00241	0.0007	M	0.87971	2.92	0.22226	N	0.999278	P	0.47191	0.891	P	0.45377	0.478	T	0.42632	-0.9440	10	0.87932	D	0	.	6.437	0.21829	0.0:0.5957:0.1217:0.2826	.	284	Q6IF63	O52W1_HUMAN	K	284	ENSP00000309673:N284K	ENSP00000309673:N284K	N	+	3	2	OR52W1	6177881	0.000000	0.05858	0.995000	0.50966	0.975000	0.68041	-0.511000	0.06321	0.003000	0.14656	-0.253000	0.11424	AAC	.	.	weak		0.527	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178	
SERPINA9	327657	hgsc.bcm.edu	37	14	94933473	94933473	+	Missense_Mutation	SNP	C	C	A	rs28618118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94933473C>A	ENST00000380365.3	-	3	953	c.875G>T	c.(874-876)aGa>aTa	p.R292I	SERPINA9_ENST00000298845.7_Missense_Mutation_p.R210I|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000424550.2_Missense_Mutation_p.R161I|SERPINA9_ENST00000546329.1_Missense_Mutation_p.R274I|SERPINA9_ENST00000337425.5_Missense_Mutation_p.R310I|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000448305.2_Missense_Mutation_p.R212I			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	292			R -> I (in dbSNP:rs28618118). {ECO:0000269|PubMed:12975309}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		GCTCCACTTTCTCAGTGTTCT	0.537													C|||	1614	0.322284	0.1452	0.3847	5008	,	,		21972	0.4643		0.3101	False		,,,				2504	0.3834				p.R310I		Atlas-SNP	.											.	SERPINA9	105	.	0			c.G929T						PASS	.	C	ILE/ARG,ILE/ARG	641,3347		54,533,1407	116.0	110.0	112.0		629,929	2.6	0.1	14	dbSNP_125	112	2518,5864		381,1756,2054	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	97,97	435,2289,3461	AA,AC,CC		30.0406,16.0732,25.5376	probably-damaging,probably-damaging	210/336,310/436	94933473	3159,9211	1994	4191	6185	SO:0001583	missense	327657	exon3			CACTTTCTCAGTG	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.875G>T	14.37:g.94933473C>A	ENSP00000369723:p.Arg292Ile	Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	217	117	0.539171	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		721	0.3301282051282051	79	0.16056910569105692	127	0.35082872928176795	275	0.4807692307692308	240	0.316622691292876	C	11.91	1.778992	0.31502	0.160732	0.300406	ENSG00000170054	ENST00000448305;ENST00000298845;ENST00000424550;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87;-1.87	3.48	2.57	0.30868	Serpin domain (3);	0.260319	0.31976	N	0.006767	T	0.00012	0.0000	L	0.37697	1.125	0.51233	P	8.799999999997699E-5	B;B;B;B;B	0.18741	0.004;0.002;0.0;0.0;0.03	B;B;B;B;B	0.17979	0.008;0.018;0.004;0.003;0.02	T	0.36841	-0.9731	9	0.22109	T	0.4	.	9.3187	0.37950	0.0:0.8933:0.0:0.1067	rs28618118	274;292;212;310;210	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7;Q86WD7-2	.;SPA9_HUMAN;.;.;.	I	212;210;161;310;292;274	ENSP00000414092:R212I;ENSP00000298845:R210I;ENSP00000409012:R161I;ENSP00000337133:R310I;ENSP00000369723:R292I;ENSP00000445476:R274I	ENSP00000298845:R210I	R	-	2	0	SERPINA9	94003226	0.000000	0.05858	0.103000	0.21229	0.961000	0.63080	-0.880000	0.04183	0.790000	0.33803	0.462000	0.41574	AGA	C|0.677;A|0.323	0.323	strong		0.537	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
MUC16	94025	hgsc.bcm.edu	37	19	9077264	9077264	+	Silent	SNP	T	T	G	rs1862461	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9077264T>G	ENST00000397910.4	-	3	10385	c.10182A>C	c.(10180-10182)gtA>gtC	p.V3394V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3395	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.V3394V(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGTGGTGCTTACCCATGTCT	0.438													G|||	1250	0.249601	0.202	0.2133	5008	,	,		21618	0.251		0.3121	False		,,,				2504	0.274				p.V3394V		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - coding silent(2)	stomach(2)	c.A10182C						PASS	.	G		852,3122		101,650,1236	265.0	251.0	256.0		10182	2.0	0.1	19	dbSNP_92	256	2409,5935		349,1711,2112	no	coding-synonymous	MUC16	NM_024690.2		450,2361,3348	GG,GT,TT		28.871,21.4394,26.4735		3394/14508	9077264	3261,9057	1987	4172	6159	SO:0001819	synonymous_variant	94025	exon3			GGTGCTTACCCAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.10182A>C	19.37:g.9077264T>G		Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	302	141	0.466887	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.748;G|0.252	0.252	strong		0.438	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PLXNA3	55558	hgsc.bcm.edu	37	X	153689643	153689643	+	Missense_Mutation	SNP	G	G	A	rs145244142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153689643G>A	ENST00000369682.3	+	3	974	c.799G>A	c.(799-801)Gcg>Acg	p.A267T		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	267	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCGCATGTGCGCGGGAGACTC	0.607																																					p.A267T		Atlas-SNP	.											.	PLXNA3	156	.	0			c.G799A						PASS	.	G	THR/ALA	3,3832		0,3,1629,571	95.0	88.0	90.0		799	3.5	0.0	X	dbSNP_134	90	2,6726		0,2,2426,1872	yes	missense	PLXNA3	NM_017514.3	58	0,5,4055,2443	AA,AG,GG,G		0.0297,0.0782,0.0473	benign	267/1872	153689643	5,10558	2203	4300	6503	SO:0001583	missense	55558	exon3			ATGTGCGCGGGAG	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.799G>A	X.37:g.153689643G>A	ENSP00000358696:p.Ala267Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	G	8.118	0.780273	0.16120	7.82E-4	2.97E-4	ENSG00000130827	ENST00000369682	T	0.10960	2.82	5.29	3.5	0.40072	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.124679	0.56097	D	0.000036	T	0.08133	0.0203	L	0.43152	1.355	0.23816	N	0.996762	B	0.24258	0.1	B	0.26202	0.067	T	0.40534	-0.9558	10	0.09338	T	0.73	.	6.5277	0.22310	0.087:0.0:0.5809:0.3321	.	267	P51805	PLXA3_HUMAN	T	267	ENSP00000358696:A267T	ENSP00000358696:A267T	A	+	1	0	PLXNA3	153342837	0.000000	0.05858	0.019000	0.16419	0.256000	0.26092	0.639000	0.24690	0.584000	0.29591	0.594000	0.82650	GCG	G|0.999;A|0.001	0.001	strong		0.607	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
ZNF416	55659	hgsc.bcm.edu	37	19	58084588	58084588	+	Missense_Mutation	SNP	G	G	C	rs145794172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58084588G>C	ENST00000196489.3	-	4	906	c.684C>G	c.(682-684)caC>caG	p.H228Q		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	228					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		GAAAAAAAGTGTGTTTGTGGC	0.443													G|||	22	0.00439297	0.0	0.0029	5008	,	,		21218	0.0		0.0109	False		,,,				2504	0.0092				p.H228Q		Atlas-SNP	.											.	ZNF416	50	.	0			c.C684G						PASS	.	G	GLN/HIS	3,4403	8.1+/-20.4	0,3,2200	160.0	162.0	161.0		684	-7.1	0.0	19	dbSNP_134	161	72,8528	42.6+/-100.3	1,70,4229	yes	missense	ZNF416	NM_017879.1	24	1,73,6429	CC,CG,GG		0.8372,0.0681,0.5767	benign	228/595	58084588	75,12931	2203	4300	6503	SO:0001583	missense	55659	exon4			AAAAGTGTGTTTG	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"""Zinc fingers, C2H2-type"", ""-"""	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.684C>G	19.37:g.58084588G>C	ENSP00000196489:p.His228Gln	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	194	94	0.484536	NM_017879	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	37	CCDS12954.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	3.259	-0.151587	0.06585	6.81E-4	0.008372	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	T	0.06933	3.24	3.55	-7.09	0.01553	.	.	.	.	.	T	0.02807	0.0084	L	0.31476	0.935	0.09310	N	1	B	0.19331	0.035	B	0.09377	0.004	T	0.31447	-0.9943	9	0.21540	T	0.41	.	4.0091	0.09615	0.1783:0.2491:0.4888:0.0837	.	228	Q9BWM5	ZN416_HUMAN	Q	228;214;208	ENSP00000196489:H228Q	ENSP00000196489:H228Q	H	-	3	2	ZNF416	62776400	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.685000	0.01930	-3.127000	0.00237	-2.333000	0.00248	CAC	G|0.994;C|0.006	0.006	strong		0.443	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879	
SLC13A5	284111	hgsc.bcm.edu	37	17	6597480	6597480	+	Silent	SNP	G	G	A	rs55698160	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6597480G>A	ENST00000433363.2	-	8	1325	c.1092C>T	c.(1090-1092)gcC>gcT	p.A364A	SLC13A5_ENST00000381074.4_Silent_p.A321A|SLC13A5_ENST00000293800.6_Silent_p.A347A|SLC13A5_ENST00000573648.1_Silent_p.A364A	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5	364					transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						ATAGCAGGGTGGCCACAAAGA	0.517													G|||	344	0.0686901	0.1256	0.0533	5008	,	,		18691	0.003		0.0885	False		,,,				2504	0.0501				p.A364A		Atlas-SNP	.											.	SLC13A5	57	.	0			c.C1092T						PASS	.	G	,	516,3890	239.6+/-250.7	35,446,1722	84.0	70.0	75.0		1092,1092	2.0	0.7	17	dbSNP_129	75	785,7815	183.3+/-231.6	43,699,3558	no	coding-synonymous,coding-synonymous	SLC13A5	NM_001143838.1,NM_177550.3	,	78,1145,5280	AA,AG,GG		9.1279,11.7113,10.0031	,	364/523,364/569	6597480	1301,11705	2203	4300	6503	SO:0001819	synonymous_variant	284111	exon8			CAGGGTGGCCACA	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"""Solute carriers"""	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.1092C>T	17.37:g.6597480G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	36	0.75	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Silent	SNP	ENST00000433363.2	37	CCDS11079.1																																																																																			G|0.908;A|0.092	0.092	strong		0.517	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550	
BRF1	2972	hgsc.bcm.edu	37	14	105688082	105688082	+	Silent	SNP	C	C	T	rs28406206	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105688082C>T	ENST00000546474.1	-	11	16177	c.1218G>A	c.(1216-1218)ccG>ccA	p.P406P	BRF1_ENST00000440513.3_Silent_p.P291P|BRF1_ENST00000327359.3_Silent_p.P291P|BRF1_ENST00000379937.2_Silent_p.P379P|BRF1_ENST00000392557.4_Silent_p.P202P|BRF1_ENST00000547530.1_5'UTR|BRF1_ENST00000379932.4_Intron|BRF1_ENST00000446501.2_Silent_p.P168P|BRF1_ENST00000551787.1_Intron|BRF1_ENST00000549044.1_5'Flank	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	406					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		ACCCCAGGGCCGGAGGTCTGC	0.672													C|||	245	0.0489217	0.0719	0.0476	5008	,	,		15085	0.0		0.0905	False		,,,				2504	0.0266				p.P406P		Atlas-SNP	.											.	BRF1	102	.	0			c.G1218A						PASS	.	C	,,,,,	350,4044		18,314,1865	14.0	18.0	17.0		873,873,1137,504,1218,606	-9.3	0.0	14	dbSNP_125	17	751,7829		34,683,3573	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRF1	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001242789.1,NM_001519.3,NM_145685.2	,,,,,	52,997,5438	TT,TC,CC		8.7529,7.9654,8.4862	,,,,,	291/585,291/563,379/651,168/440,406/678,202/474	105688082	1101,11873	2197	4290	6487	SO:0001819	synonymous_variant	2972	exon11			CAGGGCCGGAGGT	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.1218G>A	14.37:g.105688082C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Silent	SNP	ENST00000546474.1	37	CCDS10001.1																																																																																			C|0.927;T|0.073	0.073	strong		0.672	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519	
KSR1	8844	hgsc.bcm.edu	37	17	25909816	25909816	+	Missense_Mutation	SNP	C	C	T	rs2293180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:25909816C>T	ENST00000319524.6	+	4	665	c.665C>T	c.(664-666)gCc>gTc	p.A222V	KSR1_ENST00000398988.3_Missense_Mutation_p.A85V|KSR1_ENST00000509603.2_Missense_Mutation_p.A222V|KSR1_ENST00000268763.6_Missense_Mutation_p.A85V			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	222					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		GGCAACAGCGCCCAGGGCCCA	0.687													C|||	850	0.169728	0.1142	0.2536	5008	,	,		12452	0.1935		0.1223	False		,,,				2504	0.2096				p.A85V	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-SNP	.											.	KSR1	151	.	0			c.C254T						PASS	.	C	VAL/ALA	541,3649		43,455,1597	27.0	33.0	31.0		254	1.2	0.6	17	dbSNP_100	31	990,7424		69,852,3286	yes	missense	KSR1	NM_014238.1	64	112,1307,4883	TT,TC,CC		11.7661,12.9117,12.1469	benign	85/763	25909816	1531,11073	2095	4207	6302	SO:0001583	missense	8844	exon5			ACAGCGCCCAGGG	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"""kinase suppressor of ras"""	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.665C>T	17.37:g.25909816C>T	ENSP00000323178:p.Ala222Val	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	168	86	0.511905	NM_014238	F8WEA9|H7BYU0|Q13476	Missense_Mutation	SNP	ENST00000319524.6	37		341	0.15613553113553114	55	0.11178861788617886	83	0.2292817679558011	116	0.20279720279720279	87	0.11477572559366754	C	9.370	1.070225	0.20147	0.129117	0.117661	ENSG00000141068	ENST00000319524;ENST00000509603;ENST00000268763;ENST00000398982	T;T;T	0.00457	7.29;7.29;7.29	5.7	1.18	0.20946	.	0.665569	0.15469	N	0.260716	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.20887	0.049	B	0.16722	0.016	T	0.20174	-1.0283	9	0.34782	T	0.22	.	4.2194	0.10551	0.2408:0.4774:0.2036:0.0781	rs2293180;rs52831133;rs2293180	220	Q8IVT5	KSR1_HUMAN	V	222;222;85;85	ENSP00000323178:A222V;ENSP00000438795:A222V;ENSP00000268763:A85V	ENSP00000268763:A85V	A	+	2	0	KSR1	22933943	0.035000	0.19736	0.626000	0.29213	0.160000	0.22226	0.263000	0.18478	0.745000	0.32763	0.455000	0.32223	GCC	C|0.840;T|0.160	0.160	strong		0.687	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238	
KLHL3	26249	hgsc.bcm.edu	37	5	136969793	136969793	+	Silent	SNP	C	C	T	rs2301708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:136969793C>T	ENST00000309755.4	-	12	1826	c.1383G>A	c.(1381-1383)gaG>gaA	p.E461E	KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000506491.1_Silent_p.E379E|KLHL3_ENST00000508657.1_Silent_p.E429E	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	461					distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)	p.E461E(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		GGTTGTACTGCTCCACAGTGC	0.567													C|||	1134	0.226438	0.0855	0.2118	5008	,	,		16929	0.4583		0.175	False		,,,				2504	0.2413				p.E461E		Atlas-SNP	.											KLHL3,NS,carcinoma,0,1	KLHL3	54	1	1	Substitution - coding silent(1)	stomach(1)	c.G1383A						PASS	.	C		398,4008	198.4+/-222.2	17,364,1822	119.0	106.0	110.0		1383	2.3	1.0	5	dbSNP_100	110	1623,6977	303.2+/-306.3	167,1289,2844	no	coding-synonymous	KLHL3	NM_017415.2		184,1653,4666	TT,TC,CC		18.8721,9.0331,15.539		461/588	136969793	2021,10985	2203	4300	6503	SO:0001819	synonymous_variant	26249	exon12			GTACTGCTCCACA	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"""Kelch-like"", ""BTB/POZ domain containing"""	6354	protein-coding gene	gene with protein product		605775	"""kelch (Drosophila)-like 3"", ""kelch-like 3 (Drosophila)"""			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.1383G>A	5.37:g.136969793C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	91	62	0.681319	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	37	CCDS4192.1																																																																																			C|0.814;T|0.186	0.186	strong		0.567	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2		
ZNF100	163227	hgsc.bcm.edu	37	19	21909875	21909875	+	Silent	SNP	G	G	A	rs115256934	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:21909875G>A	ENST00000358296.6	-	5	1437	c.1239C>T	c.(1237-1239)tcC>tcT	p.S413S	ZNF100_ENST00000305570.6_Silent_p.S349S	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						TGAGGGCTGAGGACCAGTTAA	0.388													N|||	108	0.0215655	0.0779	0.0072	5008	,	,		20815	0.0		0.0	False		,,,				2504	0.0				p.S413S		Atlas-SNP	.											.	ZNF100	62	.	0			c.C1239T						PASS	.	G		228,4080		6,216,1932	71.0	79.0	76.0		1239	0.8	0.0	19	dbSNP_132	76	10,8550		0,10,4270	no	coding-synonymous	ZNF100	NM_173531.3		6,226,6202	AA,AG,GG		0.1168,5.2925,1.8495		413/543	21909875	238,12630	2154	4280	6434	SO:0001819	synonymous_variant	163227	exon5			GGCTGAGGACCAG	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"""Zinc fingers, C2H2-type"", ""-"""	12880	protein-coding gene	gene with protein product		603982	"""zinc finger protein 100 (Y1)"""			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.1239C>T	19.37:g.21909875G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			G|0.990;A|0.010	0.010	strong		0.388	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
CAPSL	133690	hgsc.bcm.edu	37	5	35910529	35910529	+	Missense_Mutation	SNP	C	C	T	rs1445898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:35910529C>T	ENST00000397367.2	-	3	380	c.254G>A	c.(253-255)cGg>cAg	p.R85Q	CAPSL_ENST00000514524.1_Missense_Mutation_p.R85Q|CAPSL_ENST00000397366.1_Missense_Mutation_p.R85Q	NM_144647.3	NP_653248.3	Q8WWF8	CAPSL_HUMAN	calcyphosine-like	85	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		R -> Q (in dbSNP:rs1445898).			cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(10)|skin(1)|urinary_tract(1)	19	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			ATCAAACCTCCGGAAAAGTTC	0.358													c|||	2631	0.525359	0.2277	0.5937	5008	,	,		18925	0.7609		0.4523	False		,,,				2504	0.7117				p.R85Q		Atlas-SNP	.											.	CAPSL	68	.	0			c.G254A						PASS	.	T	GLN/ARG,GLN/ARG	1220,3186	423.8+/-340.2	172,876,1155	117.0	115.0	115.0	http://www.ncbi.nlm.nih.gov/pubmed?term	254,254	0.5	1.0	5	dbSNP_88	115	3821,4779	538.4+/-383.4	854,2113,1333	yes	missense,missense	CAPSL	NM_001042625.1,NM_144647.3	43,43	1026,2989,2488	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	44.4302,27.6895,38.759	benign,benign	85/209,85/209	35910529	5041,7965	2203	4300	6503	SO:0001583	missense	133690	exon3			AACCTCCGGAAAA	BC017586	CCDS3912.2	5p13.2	2013-01-10			ENSG00000152611	ENSG00000152611		"""EF-hand domain containing"""	28375	protein-coding gene	gene with protein product						12477932	Standard	NM_001042625		Approved	MGC26610	uc003jju.1	Q8WWF8	OTTHUMG00000131109	ENST00000397367.2:c.254G>A	5.37:g.35910529C>T	ENSP00000380524:p.Arg85Gln	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	206	206	1	NM_144647		Missense_Mutation	SNP	ENST00000397367.2	37	CCDS3912.2	1124	0.5146520146520146	124	0.25203252032520324	202	0.5580110497237569	455	0.7954545454545454	343	0.4525065963060686	c	2.980	-0.210599	0.06140	0.276895	0.444302	ENSG00000152611	ENST00000397367;ENST00000397366;ENST00000513623;ENST00000514524	T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67	5.38	0.531	0.17108	EF-hand-like domain (1);	0.583831	0.19450	N	0.113949	T	0.00012	0.0000	L	0.33137	0.985	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.35895	-0.9770	9	0.22109	T	0.4	-2.3175	6.8704	0.24117	0.0:0.4281:0.117:0.4549	rs1445898;rs17643269;rs52822159;rs58733553;rs1445898	85	Q8WWF8	CAPSL_HUMAN	Q	85	ENSP00000380524:R85Q;ENSP00000380523:R85Q;ENSP00000424806:R85Q;ENSP00000421018:R85Q	ENSP00000380523:R85Q	R	-	2	0	CAPSL	35946286	0.000000	0.05858	0.995000	0.50966	0.133000	0.20885	-1.012000	0.03649	0.016000	0.14998	-1.212000	0.01626	CGG	C|0.556;T|0.444	0.444	strong		0.358	CAPSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253772.2	NM_144647	
DBN1	1627	hgsc.bcm.edu	37	5	176885499	176885499	+	Missense_Mutation	SNP	T	T	C	rs2544809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176885499T>C	ENST00000309007.5	-	12	1555	c.1336A>G	c.(1336-1338)Atc>Gtc	p.I446V	DBN1_ENST00000393565.1_Missense_Mutation_p.I492V|DBN1_ENST00000292385.5_Missense_Mutation_p.I448V|DBN1_ENST00000393563.4_Missense_Mutation_p.I178V|DBN1_ENST00000512501.1_Missense_Mutation_p.I178V	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	446			I -> V (in dbSNP:rs2544809). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:8216329, ECO:0000269|Ref.2}.		actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCATCGTGGATCTCCGTGGCG	0.612													C|||	1980	0.395367	0.4894	0.3732	5008	,	,		17876	0.2609		0.5249	False		,,,				2504	0.2894				p.I448V		Atlas-SNP	.											.	DBN1	122	.	0			c.A1342G						PASS	.	C	VAL/ILE,VAL/ILE	2120,2286	600.8+/-389.6	516,1088,599	115.0	134.0	128.0		1336,1342	2.8	0.0	5	dbSNP_100	128	4782,3818	538.6+/-383.4	1318,2146,836	yes	missense,missense	DBN1	NM_004395.3,NM_080881.2	29,29	1834,3234,1435	CC,CT,TT		44.3953,48.1162,46.9322	benign,benign	446/650,448/652	176885499	6902,6104	2203	4300	6503	SO:0001583	missense	1627	exon13			CGTGGATCTCCGT		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.1336A>G	5.37:g.176885499T>C	ENSP00000308532:p.Ile446Val	Somatic	797	2	0.00250941		WXS	Illumina HiSeq	Phase_I	626	625	0.998403	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	908	0.4157509157509158	215	0.4369918699186992	151	0.4171270718232044	138	0.24125874125874125	404	0.5329815303430079	C	0.001	-3.106167	0.00033	0.481162	0.556047	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563	T;T;T;T;T	0.28666	1.65;1.64;1.63;1.6;1.63	3.63	2.76	0.32466	.	1.387540	0.04762	N	0.426468	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.42120	-0.9470	9	0.05959	T	0.93	-1.3584	7.0039	0.24826	0.0:0.6972:0.0:0.3028	rs2544809;rs3204645;rs57246022;rs2544809	396;492;446;448	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	V	446;448;492;178;178	ENSP00000308532:I446V;ENSP00000292385:I448V;ENSP00000377195:I492V;ENSP00000423208:I178V;ENSP00000377193:I178V	ENSP00000292385:I448V	I	-	1	0	DBN1	176818105	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-0.209000	0.09358	0.354000	0.24105	-0.642000	0.03964	ATC	T|0.522;C|0.478	0.478	strong		0.612	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881	
SAMD7	344658	hgsc.bcm.edu	37	3	169644710	169644710	+	Missense_Mutation	SNP	G	G	C	rs10513680	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:169644710G>C	ENST00000428432.2	+	6	1049	c.660G>C	c.(658-660)gaG>gaC	p.E220D	SAMD7_ENST00000335556.3_Missense_Mutation_p.E220D	NM_182610.2	NP_872416.1	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	220			E -> D (in dbSNP:rs10513680).							NS(1)|biliary_tract(1)|breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			CCTATGAAGAGGATCATTATG	0.443													G|||	733	0.146366	0.1377	0.1744	5008	,	,		20196	0.1687		0.1223	False		,,,				2504	0.1401				p.E220D		Atlas-SNP	.											.	SAMD7	69	.	0			c.G660C						PASS	.	G	ASP/GLU	560,3846	251.2+/-258.0	39,482,1682	97.0	96.0	96.0		660	2.7	0.7	3	dbSNP_119	96	1034,7566	220.4+/-258.1	62,910,3328	yes	missense	SAMD7	NM_182610.2	45	101,1392,5010	CC,CG,GG		12.0233,12.7099,12.2559	possibly-damaging	220/447	169644710	1594,11412	2203	4300	6503	SO:0001583	missense	344658	exon6			TGAAGAGGATCAT	BX537903	CCDS3209.1	3q26.31	2013-01-10			ENSG00000187033	ENSG00000187033		"""Sterile alpha motif (SAM) domain containing"""	25394	protein-coding gene	gene with protein product							Standard	NM_182610		Approved	DKFZp686E1583	uc003fgd.3	Q7Z3H4	OTTHUMG00000158730	ENST00000428432.2:c.660G>C	3.37:g.169644710G>C	ENSP00000391299:p.Glu220Asp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	127	76	0.598425	NM_182610		Missense_Mutation	SNP	ENST00000428432.2	37	CCDS3209.1	313	0.1433150183150183	67	0.13617886178861788	54	0.14917127071823205	102	0.17832167832167833	90	0.11873350923482849	G	18.88	3.717056	0.68844	0.127099	0.120233	ENSG00000187033	ENST00000428432;ENST00000335556	T;T	0.64438	-0.1;-0.1	6.16	2.72	0.32119	.	0.045570	0.85682	D	0.000000	T	0.00356	0.0011	M	0.66939	2.045	0.27516	P	0.9515344	D	0.67145	0.996	P	0.59948	0.866	T	0.20472	-1.0274	9	0.56958	D	0.05	-18.0646	12.5792	0.56381	0.2235:0.0:0.7765:0.0	rs10513680;rs17289453;rs10513680	220	Q7Z3H4	SAMD7_HUMAN	D	220	ENSP00000391299:E220D;ENSP00000334668:E220D	ENSP00000334668:E220D	E	+	3	2	SAMD7	171127404	0.996000	0.38824	0.695000	0.30226	0.009000	0.06853	1.485000	0.35519	0.810000	0.34279	0.650000	0.86243	GAG	G|0.864;C|0.136	0.136	strong		0.443	SAMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351959.1	NM_182610	
ZNF853	54753	hgsc.bcm.edu	37	7	6660790	6660790	+	Silent	SNP	G	G	A	rs940873	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6660790G>A	ENST00000457543.3	+	3	726	c.168G>A	c.(166-168)gaG>gaA	p.E56E		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	56							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						AGGAGGAAGAGCCTCAGGAGA	0.607													G|||	2052	0.409744	0.4395	0.2651	5008	,	,		16821	0.5208		0.2147	False		,,,				2504	0.5583				p.E56E		Atlas-SNP	.											.	ZNF853	32	.	0			c.G168A						PASS	.	G		609,775		136,337,219	24.0	27.0	26.0		168	2.6	1.0	7	dbSNP_86	26	763,2419		88,587,916	no	coding-synonymous	ZNF853	NM_017560.1		224,924,1135	AA,AG,GG		23.9786,44.0029,30.0482		56/660	6660790	1372,3194	692	1591	2283	SO:0001819	synonymous_variant	54753	exon3			GGAAGAGCCTCAG	AL133055	CCDS59048.1	7p22.1	2013-01-08				ENSG00000236609		"""Zinc fingers, C2H2-type"""	21767	protein-coding gene	gene with protein product							Standard	NM_017560		Approved	DKFZp434J1015	uc011jwz.2	P0CG23		ENST00000457543.3:c.168G>A	7.37:g.6660790G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_017560		Silent	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			G|0.644;A|0.356	0.356	strong		0.607	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
TMEM132C	92293	hgsc.bcm.edu	37	12	129190474	129190474	+	Silent	SNP	G	G	A	rs3812792	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:129190474G>A	ENST00000435159.2	+	9	2961	c.2961G>A	c.(2959-2961)gcG>gcA	p.A987A	TMEM132C_ENST00000537538.1_Silent_p.A372A|TMEM132C_ENST00000315208.8_Silent_p.A603A	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	987						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						TGGGGGATGCGCCGCCGCCCC	0.642													G|||	2433	0.485823	0.1899	0.6542	5008	,	,		14093	0.5744		0.5626	False		,,,				2504	0.5961				p.A987A		Atlas-SNP	.											TMEM132C_ENST00000435159,NS,carcinoma,+1,4	TMEM132C	142	4	0			c.G2961A						PASS	.	G		326,1058		46,234,412	23.0	32.0	29.0		2961	-1.1	0.0	12	dbSNP_107	29	1820,1362		533,754,304	no	coding-synonymous	TMEM132C	NM_001136103.2		579,988,716	AA,AG,GG		42.8033,23.5549,46.9996		987/1109	129190474	2146,2420	692	1591	2283	SO:0001819	synonymous_variant	92293	exon9			GGATGCGCCGCCG	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.2961G>A	12.37:g.129190474G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	80	0.97561	NM_001136103	Q69YX8	Silent	SNP	ENST00000435159.2	37																																																																																				G|0.497;A|0.503	0.503	strong		0.642	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
CNR2	1269	hgsc.bcm.edu	37	1	24201162	24201162	+	Missense_Mutation	SNP	G	G	A	rs2229579	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:24201162G>A	ENST00000374472.4	-	2	1107	c.946C>T	c.(946-948)Cac>Tac	p.H316Y	CNR2_ENST00000536471.1_Missense_Mutation_p.H316Y	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	316			H -> Y (in dbSNP:rs2229579). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18286196, ECO:0000269|Ref.5}.		G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	TTCTTCCAGTGAGCCAGGCAG	0.552													G|||	538	0.107428	0.0045	0.1081	5008	,	,		21093	0.2143		0.0885	False		,,,				2504	0.1554				p.H316Y		Atlas-SNP	.											.	CNR2	78	.	0			c.C946T						PASS	.	G	TYR/HIS	105,4301	80.9+/-119.3	2,101,2100	93.0	95.0	94.0		946	0.7	0.0	1	dbSNP_98	94	859,7741	197.3+/-242.0	34,791,3475	yes	missense	CNR2	NM_001841.2	83	36,892,5575	AA,AG,GG		9.9884,2.3831,7.412	benign	316/361	24201162	964,12042	2203	4300	6503	SO:0001583	missense	1269	exon2			TCCAGTGAGCCAG	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.946C>T	1.37:g.24201162G>A	ENSP00000363596:p.His316Tyr	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	238	88	0.369748	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Missense_Mutation	SNP	ENST00000374472.4	37	CCDS245.1	219	0.10027472527472528	1	0.0020325203252032522	30	0.08287292817679558	119	0.20804195804195805	69	0.09102902374670185	G	0.505	-0.868974	0.02570	0.023831	0.099884	ENSG00000188822	ENST00000374472;ENST00000536471	T;T	0.36878	1.23;1.23	5.21	0.728	0.18260	.	1.823760	0.02519	N	0.092394	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.30870	0.298	B	0.24974	0.057	T	0.11397	-1.0589	9	0.12430	T	0.62	.	4.3273	0.11046	0.0722:0.2569:0.4207:0.2501	rs2229579;rs3820021;rs52824290;rs2229579	316	P34972	CNR2_HUMAN	Y	316	ENSP00000363596:H316Y;ENSP00000442830:H316Y	ENSP00000363596:H316Y	H	-	1	0	CNR2	24073749	0.000000	0.05858	0.006000	0.13384	0.092000	0.18411	0.023000	0.13533	0.151000	0.19162	0.563000	0.77884	CAC	G|0.906;T|0.006	.	strong		0.552	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
NXPE3	91775	hgsc.bcm.edu	37	3	101540387	101540387	+	Missense_Mutation	SNP	T	T	G	rs35598292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:101540387T>G	ENST00000491511.2	+	8	2225	c.1269T>G	c.(1267-1269)caT>caG	p.H423Q	NXPE3_ENST00000422132.1_Missense_Mutation_p.H423Q|NXPE3_ENST00000273347.5_Missense_Mutation_p.H423Q|NXPE3_ENST00000477909.1_Missense_Mutation_p.H423Q|RP11-49I4.3_ENST00000490324.2_RNA	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	423						extracellular region (GO:0005576)											ATGAGCTCCATTATGTGGCGA	0.512													T|||	57	0.0113818	0.0	0.0231	5008	,	,		20493	0.001		0.0368	False		,,,				2504	0.0031				p.H423Q		Atlas-SNP	.											.	.	.	.	0			c.T1269G						PASS	.	T	GLN/HIS,GLN/HIS	34,4372	39.2+/-71.8	0,34,2169	130.0	98.0	109.0		1269,1269	-5.0	0.1	3	dbSNP_126	109	404,8196	128.5+/-186.7	11,382,3907	yes	missense,missense	FAM55C	NM_001134456.1,NM_145037.2	24,24	11,416,6076	GG,GT,TT		4.6977,0.7717,3.3677	benign,benign	423/560,423/560	101540387	438,12568	2203	4300	6503	SO:0001583	missense	91775	exon8			GCTCCATTATGTG	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member C"""	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.1269T>G	3.37:g.101540387T>G	ENSP00000417485:p.His423Gln	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	172	90	0.523256	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	37	CCDS2945.1	33	0.01510989010989011	0	0.0	10	0.027624309392265192	0	0.0	23	0.030343007915567283	T	9.492	1.100921	0.20552	0.007717	0.046977	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.25085	1.82;1.82;1.82;1.82	5.83	-4.96	0.03038	.	0.366329	0.36066	N	0.002814	T	0.02230	0.0069	L	0.46157	1.445	0.19945	N	0.999941	B	0.26258	0.145	B	0.23419	0.046	T	0.29822	-0.9999	10	0.15066	T	0.55	-0.2416	9.7523	0.40483	0.2155:0.5939:0.0:0.1906	rs35598292;rs35598292	423	Q969Y0	FA55C_HUMAN	Q	423	ENSP00000273347:H423Q;ENSP00000417485:H423Q;ENSP00000418369:H423Q;ENSP00000396421:H423Q	ENSP00000273347:H423Q	H	+	3	2	FAM55C	103023077	0.014000	0.17966	0.084000	0.20598	0.359000	0.29487	-0.414000	0.07114	-0.655000	0.05387	-0.899000	0.02877	CAT	T|0.974;G|0.026	0.026	strong		0.512	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037	
MEP1A	4224	hgsc.bcm.edu	37	6	46801092	46801092	+	Missense_Mutation	SNP	A	A	G	rs12197930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46801092A>G	ENST00000230588.4	+	11	1435	c.1426A>G	c.(1426-1428)Aga>Gga	p.R476G		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	476	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.		R -> G (in dbSNP:rs12197930). {ECO:0000269|PubMed:15489334}.		digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			CCCAAATAGCAGAGAAAGCTC	0.468													A|||	235	0.0469249	0.0908	0.0259	5008	,	,		20600	0.0119		0.0278	False		,,,				2504	0.0583				p.R476G		Atlas-SNP	.											.	MEP1A	93	.	0			c.A1426G						PASS	.	A	GLY/ARG	328,4078	173.0+/-202.9	12,304,1887	92.0	96.0	95.0		1426	0.1	0.0	6	dbSNP_120	95	299,8301	109.6+/-170.1	6,287,4007	yes	missense	MEP1A	NM_005588.2	125	18,591,5894	GG,GA,AA		3.4767,7.4444,4.8209	benign	476/747	46801092	627,12379	2203	4300	6503	SO:0001583	missense	4224	exon11			AATAGCAGAGAAA		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.1426A>G	6.37:g.46801092A>G	ENSP00000230588:p.Arg476Gly	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	68	0.561983	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	37	CCDS4918.1	68	0.031135531135531136	33	0.06707317073170732	10	0.027624309392265192	7	0.012237762237762238	18	0.023746701846965697	A	0.365	-0.937143	0.02340	0.074444	0.034767	ENSG00000112818	ENST00000230588	T	0.39997	1.05	5.61	0.122	0.14702	TRAF-type (1);TRAF-like (1);MATH (3);	0.443943	0.29631	N	0.011614	T	0.10937	0.0267	L	0.43701	1.375	0.09310	N	1	B;B	0.13594	0.008;0.004	B;B	0.16289	0.015;0.01	T	0.33240	-0.9876	10	0.22706	T	0.39	0.391	5.145	0.14979	0.3225:0.4882:0.0707:0.1186	rs12197930;rs52802550;rs12197930	504;476	B7ZL91;Q16819	.;MEP1A_HUMAN	G	476	ENSP00000230588:R476G	ENSP00000230588:R476G	R	+	1	2	MEP1A	46909051	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	1.053000	0.30442	-0.189000	0.10482	-0.297000	0.09499	AGA	A|0.957;G|0.043	0.043	strong		0.468	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588	
MUC6	4588	hgsc.bcm.edu	37	11	1026048	1026048	+	Silent	SNP	G	G	A	rs55965773	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1026048G>A	ENST00000421673.2	-	21	2690	c.2640C>T	c.(2638-2640)gaC>gaT	p.D880D		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	880	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCGCTGGCCGTCGAAGGTGA	0.677													g|||	419	0.0836661	0.0182	0.1254	5008	,	,		18109	0.0198		0.1839	False		,,,				2504	0.1053				p.D880D		Atlas-SNP	.											.	MUC6	408	.	0			c.C2640T						PASS	.	G		147,4171		2,143,2014	41.0	48.0	45.0		2640	-7.8	0.6	11	dbSNP_129	45	1573,6901		148,1277,2812	no	coding-synonymous	MUC6	NM_005961.2		150,1420,4826	AA,AG,GG		18.5627,3.4044,13.4459		880/2440	1026048	1720,11072	2159	4237	6396	SO:0001819	synonymous_variant	4588	exon21			CTGGCCGTCGAAG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.2640C>T	11.37:g.1026048G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			G|0.902;A|0.098	0.098	strong		0.677	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
MUC4	4585	hgsc.bcm.edu	37	3	195509525	195509525	+	Missense_Mutation	SNP	G	G	A	rs550606134		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509525G>A	ENST00000463781.3	-	2	9385	c.8926C>T	c.(8926-8928)Cct>Tct	p.P2976S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2976S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P2976S(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TCAGGAAGAGGGGTGGCGTGA	0.587													.|||	1	0.000199681	0.0008	0.0	5008	,	,		9881	0.0		0.0	False		,,,				2504	0.0				p.P2976S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	endometrium(2)	c.C8926T						scavenged	.						18.0	10.0	12.0					3																	195509525		663	1548	2211	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8926C>T	3.37:g.195509525G>A	ENSP00000417498:p.Pro2976Ser	Somatic	133	4	0.0300752		WXS	Illumina HiSeq	Phase_I	274	12	0.0437956	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	5.257	0.232935	0.09969	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28069	1.63;1.63	.	.	.	.	.	.	.	.	T	0.24392	0.0591	N	0.08118	0	0.09310	N	1	D	0.63880	0.993	D	0.70227	0.968	T	0.10428	-1.0630	7	.	.	.	.	1.6626	0.02795	0.4559:0.0:0.2522:0.2919	.	2848	E7ESK3	.	S	2976	ENSP00000417498:P2976S;ENSP00000420243:P2976S	.	P	-	1	0	MUC4	196994304	.	.	0.004000	0.12327	0.000000	0.00434	.	.	-0.437000	0.07243	0.000000	0.15137	CCT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
WDR91	29062	hgsc.bcm.edu	37	7	134879830	134879830	+	Silent	SNP	G	G	A	rs292575	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:134879830G>A	ENST00000354475.4	-	9	1282	c.1251C>T	c.(1249-1251)gaC>gaT	p.D417D	WDR91_ENST00000423565.1_Silent_p.D382D|WDR91_ENST00000485942.1_5'Flank|WDR91_ENST00000344400.5_Silent_p.D417D	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	417										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						TCCCAGAGCAGTCCACTCTGA	0.512													A|||	3284	0.655751	0.497	0.804	5008	,	,		16779	0.6131		0.7078	False		,,,				2504	0.7556				p.D417D		Atlas-SNP	.											.	WDR91	82	.	0			c.C1251T						PASS	.	A		2426,1980	554.2+/-379.0	675,1076,452	74.0	58.0	63.0		1251	-2.7	1.0	7	dbSNP_79	63	6220,2380	394.9+/-344.9	2260,1700,340	no	coding-synonymous	WDR91	NM_014149.3		2935,2776,792	AA,AG,GG		27.6744,44.9387,33.523		417/748	134879830	8646,4360	2203	4300	6503	SO:0001819	synonymous_variant	29062	exon9			AGAGCAGTCCACT	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"""WD repeat domain containing"""	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.1251C>T	7.37:g.134879830G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Silent	SNP	ENST00000354475.4	37	CCDS34758.1																																																																																			G|0.346;A|0.654	0.654	strong		0.512	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149	
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58350631	58350631	+	Silent	SNP	C	C	T	rs10122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:58350631C>T	ENST00000300145.3	+	6	824	c.699C>T	c.(697-699)caC>caT	p.H233H	XRCC6BP1_ENST00000546709.1_3'UTR	NM_033276.2	NP_150592.1	Q9Y6H3	ATP23_HUMAN	XRCC6 binding protein 1	233					double-strand break repair via nonhomologous end joining (GO:0006303)|protein phosphorylation (GO:0006468)	DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)	DNA-dependent protein kinase activity (GO:0004677)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	11						GATATGCTCACAGAGACTTTG	0.333													T|||	2763	0.551717	0.556	0.5447	5008	,	,		16308	0.7262		0.3668	False		,,,				2504	0.5613				p.H233H		Atlas-SNP	.											.	XRCC6BP1	22	.	0			c.C699T						PASS	.	T		1976,1670		558,860,405	107.0	99.0	101.0		699	-0.2	1.0	12	dbSNP_52	101	3063,5089		568,1927,1581	no	coding-synonymous	XRCC6BP1	NM_033276.2		1126,2787,1986	TT,TC,CC		37.5736,45.8036,42.7106		233/247	58350631	5039,6759	1823	4076	5899	SO:0001819	synonymous_variant	91419	exon6			TGCTCACAGAGAC	AF078164	CCDS41802.1	12q14.1	2006-01-09				ENSG00000166896			29452	protein-coding gene	gene with protein product	"""Ku70 binding protein 3"""					10219089	Standard	XM_005269223		Approved	KUB3	uc001sqp.3	Q9Y6H3	OTTHUMG00000170493	ENST00000300145.3:c.699C>T	12.37:g.58350631C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_033276	Q1RLM4|Q96E81	Silent	SNP	ENST00000300145.3	37	CCDS41802.1																																																																																			C|0.485;T|0.515	0.515	strong		0.333	XRCC6BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409390.1	NM_033276	
PLTP	5360	hgsc.bcm.edu	37	20	44540037	44540037	+	Missense_Mutation	SNP	A	A	G	rs151157782	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:44540037A>G	ENST00000477313.1	-	1	649	c.55T>C	c.(55-57)Ttc>Ctc	p.F19L	PLTP_ENST00000372420.1_5'Flank|PLTP_ENST00000372431.3_Missense_Mutation_p.F19L|PLTP_ENST00000420868.2_Missense_Mutation_p.F19L|PLTP_ENST00000542937.1_Missense_Mutation_p.F39L|PLTP_ENST00000354050.4_Missense_Mutation_p.F19L			P55058	PLTP_HUMAN	phospholipid transfer protein	19					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				CAGCCTGGGAACTCTGCATGT	0.697																																					p.F19L		Atlas-SNP	.											.	PLTP	49	.	0			c.T55C						PASS	.	A	LEU/PHE,LEU/PHE,LEU/PHE	0,4406		0,0,2203	47.0	52.0	50.0		55,55,55	0.2	1.0	20	dbSNP_134	50	14,8586	8.4+/-32.0	0,14,4286	yes	missense,missense,missense	PLTP	NM_001242920.1,NM_006227.3,NM_182676.2	22,22,22	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	benign,benign,benign	19/399,19/494,19/442	44540037	14,12992	2203	4300	6503	SO:0001583	missense	5360	exon2			CTGGGAACTCTGC	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"""BPI fold containing"""	9093	protein-coding gene	gene with protein product	"""BPI fold containing family E"""	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.55T>C	20.37:g.44540037A>G	ENSP00000417138:p.Phe19Leu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_182676	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	37	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	A	9.612	1.131600	0.21041	0.0	0.001628	ENSG00000100979	ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T	0.08282	3.18;3.32;3.18;3.23;3.11	5.2	0.154	0.14901	Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.584072	0.18973	N	0.126087	T	0.02533	0.0077	N	0.02011	-0.69	0.23411	N	0.99774	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.48031	-0.9070	10	0.11794	T	0.64	-7.2857	8.8452	0.35166	0.0773:0.0:0.4171:0.5056	.	19;19;19;19;19;39	E7EV16;B4DRB4;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;PLTP_HUMAN;.	L	19;19;19;39;19	ENSP00000361508:F19L;ENSP00000335290:F19L;ENSP00000417138:F19L;ENSP00000440296:F39L;ENSP00000411671:F19L	ENSP00000335290:F19L	F	-	1	0	PLTP	43973444	0.987000	0.35691	1.000000	0.80357	0.757000	0.42996	0.505000	0.22642	0.248000	0.21435	-0.313000	0.08912	TTC	A|0.999;G|0.001	0.001	strong		0.697	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227	
BAI1	575	hgsc.bcm.edu	37	8	143623459	143623459	+	Silent	SNP	G	G	T	rs34364916	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143623459G>T	ENST00000517894.1	+	28	4758	c.3864G>T	c.(3862-3864)ctG>ctT	p.L1288L	BAI1_ENST00000323289.5_Silent_p.L1288L			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1288					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					AGCTGCACCTGCACGGCTCAC	0.667													g|||	742	0.148163	0.0416	0.0836	5008	,	,		11568	0.25		0.1302	False		,,,				2504	0.2515				p.L1288L		Atlas-SNP	.											.	BAI1	146	.	0			c.G3864T						PASS	.			230,3950		6,218,1866	29.0	34.0	32.0		3864	2.1	1.0	8	dbSNP_126	32	1174,7248		86,1002,3123	no	coding-synonymous	BAI1	NM_001702.2		92,1220,4989	TT,TG,GG		13.9397,5.5024,11.1411		1288/1585	143623459	1404,11198	2090	4211	6301	SO:0001819	synonymous_variant	575	exon27			GCACCTGCACGGC	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"""-"", ""GPCR / Class B : Orphans"""	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3864G>T	8.37:g.143623459G>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_001702		Silent	SNP	ENST00000517894.1	37																																																																																				G|0.865;T|0.135	0.135	strong		0.667	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702	
TLR3	7098	hgsc.bcm.edu	37	4	187004074	187004074	+	Missense_Mutation	SNP	C	C	T	rs3775291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187004074C>T	ENST00000296795.3	+	4	1338	c.1234C>T	c.(1234-1236)Ctc>Ttc	p.L412F	TLR3_ENST00000504367.1_Missense_Mutation_p.L135F	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	412			L -> F (in dbSNP:rs3775291). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18753640, ECO:0000269|PubMed:22174453, ECO:0000269|Ref.4}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.L412F(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		CTTACACATACTCAACCTAAC	0.378													C|||	1161	0.231829	0.0265	0.3055	5008	,	,		19216	0.3284		0.3241	False		,,,				2504	0.2628				p.L412F		Atlas-SNP	.											TLR3,NS,carcinoma,0,1	TLR3	83	1	1	Substitution - Missense(1)	stomach(1)	c.C1234T	GRCh37	CM073380	TLR3	M	rs3775291	PASS	.	C	PHE/LEU	313,4093	163.3+/-195.1	12,289,1902	62.0	57.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1234	4.9	1.0	4	dbSNP_107	59	2496,6104	406.7+/-348.9	361,1774,2165	yes	missense	TLR3	NM_003265.2	22	373,2063,4067	TT,TC,CC		29.0233,7.1039,21.5977	probably-damaging	412/905	187004074	2809,10197	2203	4300	6503	SO:0001583	missense	7098	exon4			CACATACTCAACC	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"""CD molecules"""	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1234C>T	4.37:g.187004074C>T	ENSP00000296795:p.Leu412Phe	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	37	CCDS3846.1	548	0.2509157509157509	20	0.04065040650406504	108	0.2983425414364641	177	0.3094405594405594	243	0.32058047493403696	C	15.62	2.888156	0.52014	0.071039	0.290233	ENSG00000164342	ENST00000296795;ENST00000513189;ENST00000542020;ENST00000504367	T;T;T	0.80304	-1.36;0.95;-1.36	5.78	4.95	0.65309	.	0.054971	0.85682	N	0.000000	T	0.00039	0.0001	H	0.99336	4.52	0.09310	P	0.999999867741	D	0.89917	1.0	D	0.97110	1.0	T	0.00000	-1.3545	9	0.66056	D	0.02	.	14.7982	0.69894	0.0:0.9309:0.0:0.0691	rs3775291;rs52805499;rs56463237;rs60096761;rs3775291	412	O15455	TLR3_HUMAN	F	412;348;412;135	ENSP00000296795:L412F;ENSP00000423386:L348F;ENSP00000423684:L135F	ENSP00000296795:L412F	L	+	1	0	TLR3	187241068	0.999000	0.42202	0.965000	0.40720	0.296000	0.27459	4.031000	0.57267	1.458000	0.47871	0.557000	0.71058	CTC	C|0.781;T|0.219	0.219	strong		0.378	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4		
ATP8B2	57198	hgsc.bcm.edu	37	1	154317153	154317153	+	Silent	SNP	C	C	T	rs1194587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154317153C>T	ENST00000368489.3	+	21	2277	c.2277C>T	c.(2275-2277)tcC>tcT	p.S759S		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	745					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CATCCCGCTCCGTAGGCAACG	0.547											OREG0013835	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2103	0.419928	0.1203	0.4899	5008	,	,		19944	0.624		0.4523	False		,,,				2504	0.5317				p.S759S		Atlas-SNP	.											.	ATP8B2	158	.	0			c.C2277T						PASS	.	C		789,3617	317.7+/-295.3	68,653,1482	133.0	126.0	128.0		2277	-11.5	0.0	1	dbSNP_87	128	4064,4536	559.9+/-387.5	964,2136,1200	no	coding-synonymous	ATP8B2	NM_020452.3		1032,2789,2682	TT,TC,CC		47.2558,17.9074,37.3135		759/1224	154317153	4853,8153	2203	4300	6503	SO:0001819	synonymous_variant	57198	exon21			CCGCTCCGTAGGC	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"""ATPases / P-type"""	13534	protein-coding gene	gene with protein product		605867	"""ATPase, class I, type 8B, member 2"""			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.2277C>T	1.37:g.154317153C>T		Somatic	118	0	0	1762	WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368489.3	37	CCDS1066.1																																																																																			C|0.608;T|0.392	0.392	strong		0.547	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452	
ARSD	414	hgsc.bcm.edu	37	X	2836041	2836041	+	Missense_Mutation	SNP	A	A	T	rs67272620		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836041A>T	ENST00000381154.1	-	5	742	c.667T>A	c.(667-669)Ttc>Atc	p.F223I	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	223					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GAGACAGAGAAGAAACCGCAG	0.642																																					p.F223I		Atlas-SNP	.											.	ARSD	47	.	0			c.T667A						PASS	.						18.0	22.0	21.0					X																	2836041		2203	4298	6501	SO:0001583	missense	414	exon5			CAGAGAAGAAACC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.667T>A	X.37:g.2836041A>T	ENSP00000370546:p.Phe223Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	111	45	0.405405	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	a	2.915	-0.224509	0.06061	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.93366	-3.21	3.47	-2.84	0.05751	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.212178	0.30510	N	0.009474	T	0.68805	0.3041	N	0.00652	-1.29	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.002	T	0.68610	-0.5363	10	0.10377	T	0.69	.	1.9766	0.03417	0.2278:0.2384:0.3921:0.1417	.	223;223	E9PAW5;P51689	.;ARSD_HUMAN	I	223	ENSP00000370546:F223I	ENSP00000217890:F223I	F	-	1	0	ARSD	2846041	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-4.118000	0.00291	-1.381000	0.02112	-0.663000	0.03849	TTC	A|0.500;T|0.500	0.500	strong		0.642	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
TTLL3	26140	hgsc.bcm.edu	37	3	9870857	9870857	+	Silent	SNP	G	G	A	rs2290303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:9870857G>A	ENST00000547186.1	+	10	1548	c.1332G>A	c.(1330-1332)caG>caA	p.Q444Q	TTLL3_ENST00000466245.1_3'UTR|TTLL3_ENST00000426895.4_Silent_p.Q587Q|TTLL3_ENST00000427853.3_Silent_p.Q232Q|TTLL3_ENST00000383827.1_Silent_p.Q232Q|TTLL3_ENST00000455274.1_Silent_p.Q232Q|TTLL3_ENST00000430793.1_Silent_p.Q232Q|TTLL3_ENST00000397241.1_Silent_p.Q232Q|ARPC4-TTLL3_ENST00000397256.1_Silent_p.Q505Q	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	444	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					ACACCGTGCAGTGTCGGAAGG	0.592													G|||	1367	0.272963	0.1286	0.3112	5008	,	,		22011	0.1577		0.5746	False		,,,				2504	0.2495				p.Q587Q		Atlas-SNP	.											.	TTLL3	51	.	0			c.G1761A						PASS	.	G	,	794,3612	319.6+/-296.2	81,632,1490	118.0	89.0	99.0		1761,1515	0.7	0.6	3	dbSNP_100	99	4342,4258	579.8+/-391.0	1109,2124,1067	no	coding-synonymous,coding-synonymous	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	,	1190,2756,2557	AA,AG,GG		49.5116,18.0209,39.4895	,	587/916,505/626	9870857	5136,7870	2203	4300	6503	SO:0001819	synonymous_variant	26140	exon10			CGTGCAGTGTCGG		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"""Tubulin tyrosine ligase-like family"""	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1332G>A	3.37:g.9870857G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Silent	SNP	ENST00000547186.1	37		722	0.3305860805860806	67	0.13617886178861788	126	0.34806629834254144	89	0.1555944055944056	440	0.5804749340369393	G	7.645	0.681788	0.14907	0.180209	0.504884	ENSG00000214021	ENST00000310252	.	.	.	4.93	0.73	0.18271	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27062	P	0.9635391	.	.	.	.	.	.	T	0.47071	-0.9145	3	.	.	.	.	5.6426	0.17572	0.2252:0.0:0.5736:0.2012	rs2290303;rs17319071	.	.	.	M	400	.	.	V	+	1	0	TTLL3	9845857	0.050000	0.20438	0.650000	0.29550	0.977000	0.68977	0.301000	0.19174	0.489000	0.27749	0.563000	0.77884	GTG	G|0.623;A|0.377	0.377	strong		0.592	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119859	38119859	+	Silent	SNP	C	C	T	rs66505048	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38119859C>T	ENST00000406386.3	+	7	1551	c.1296C>T	c.(1294-1296)tgC>tgT	p.C432C		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	432					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.C432C(6)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GAACATCCTGCGCCCAGCGGG	0.582																																					p.C432C		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,8	TRIOBP	262	8	6	Substitution - coding silent(6)	kidney(3)|cervix(1)|lung(1)|endometrium(1)	c.C1296T						scavenged	.																																			SO:0001819	synonymous_variant	11078	exon7			ATCCTGCGCCCAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1296C>T	22.37:g.38119859C>T		Somatic	307	1	0.00325733		WXS	Illumina HiSeq	Phase_I	320	7	0.021875	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.500;T|0.500	0.500	strong		0.582	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
TRUB2	26995	hgsc.bcm.edu	37	9	131073842	131073842	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131073842C>T	ENST00000372890.4	-	6	832	c.499G>A	c.(499-501)Gtt>Att	p.V167I	TRUB2_ENST00000460320.1_5'UTR|TRUB2_ENST00000546104.1_Missense_Mutation_p.V111I	NM_015679.1	NP_056494.1	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase family member 2	167					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(2)|large_intestine(2)|lung(3)|ovary(1)	8						CCTTGGATAACGGCCAGAATG	0.577																																					p.V167I		Atlas-SNP	.											.	TRUB2	26	.	0			c.G499A						PASS	.						121.0	102.0	108.0					9																	131073842		2203	4300	6503	SO:0001583	missense	26995	exon6			GGATAACGGCCAG	AK001956	CCDS6897.1	9q34.11	2014-01-28	2013-09-02		ENSG00000167112	ENSG00000167112			17170	protein-coding gene	gene with protein product		610727	"""TruB pseudouridine (psi) synthase homolog 2 (E. coli)"""			12736709	Standard	NM_015679		Approved	CLONE24922	uc004buq.1	O95900	OTTHUMG00000020741	ENST00000372890.4:c.499G>A	9.37:g.131073842C>T	ENSP00000361982:p.Val167Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	137	20	0.145985	NM_015679	B7Z7G5	Missense_Mutation	SNP	ENST00000372890.4	37	CCDS6897.1	.	.	.	.	.	.	.	.	.	.	C	5.380	0.255372	0.10185	.	.	ENSG00000167112	ENST00000372890;ENST00000546104	T;T	0.51071	0.72;0.72	5.58	-2.46	0.06461	Pseudouridine synthase, catalytic domain (1);	0.527930	0.21014	N	0.081636	T	0.40398	0.1115	L	0.54323	1.7	0.21020	N	0.999806	B	0.10296	0.003	B	0.09377	0.004	T	0.25433	-1.0132	10	0.38643	T	0.18	-1.9214	15.1301	0.72517	0.0:0.7555:0.0944:0.1501	.	167	O95900	TRUB2_HUMAN	I	167;111	ENSP00000361982:V167I;ENSP00000438084:V111I	ENSP00000361982:V167I	V	-	1	0	TRUB2	130113663	0.001000	0.12720	0.009000	0.14445	0.593000	0.36681	-0.332000	0.07904	-0.900000	0.03896	-1.317000	0.01298	GTT	.	.	none		0.577	TRUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054419.1	NM_015679	
URGCP	55665	hgsc.bcm.edu	37	7	43916727	43916727	+	Missense_Mutation	SNP	T	T	G	rs2232108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43916727T>G	ENST00000453200.1	-	6	2828	c.2335A>C	c.(2335-2337)Atg>Ctg	p.M779L	URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_Missense_Mutation_p.M736L|URGCP_ENST00000336086.6_Missense_Mutation_p.M736L|URGCP_ENST00000223341.7_Missense_Mutation_p.M736L|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000402306.3_Missense_Mutation_p.M770L|URGCP_ENST00000443736.1_Missense_Mutation_p.M736L			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	779	VLIG-type G.		M -> L (in dbSNP:rs2232108). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CTCAGTCCCATGAGCAGAGTG	0.527													T|||	2559	0.510982	0.3933	0.5231	5008	,	,		20920	0.5764		0.4602	False		,,,				2504	0.6462				p.M779L		Atlas-SNP	.											.	URGCP	170	.	0			c.A2335C						PASS	.	T	LEU/MET,LEU/MET,,LEU/MET	1544,2518		301,942,788	79.0	78.0	79.0		2335,2206,,2308	3.0	1.0	7	dbSNP_98	79	3973,4427		962,2049,1189	yes	missense,missense,intron,missense	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	15,15,,15	1263,2991,1977	GG,GT,TT		47.2976,38.0108,44.2706	benign,benign,,benign	779/932,736/889,,770/923	43916727	5517,6945	2031	4200	6231	SO:0001583	missense	55665	exon6			GTCCCATGAGCAG		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2335A>C	7.37:g.43916727T>G	ENSP00000396918:p.Met779Leu	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	158	80	0.506329	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	37	CCDS47578.1	1042	0.47710622710622713	185	0.37601626016260165	191	0.5276243093922652	308	0.5384615384615384	358	0.47229551451187335	T	14.29	2.491278	0.44249	0.380108	0.472976	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27;0.27	5.41	3.0	0.34707	.	0.351075	0.32719	N	0.005730	T	0.00012	0.0000	L	0.44542	1.39	0.42695	P	0.006406000000000023	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.42120	-0.9470	9	0.62326	D	0.03	-45.4448	3.0295	0.06102	0.1831:0.1741:0.0:0.6428	rs2232108;rs3735264;rs11551793;rs17654527;rs52829585;rs58683263;rs2232108	770;779	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	L	736;736;770;736;779;736	ENSP00000223341:M736L;ENSP00000336872:M736L;ENSP00000384955:M770L;ENSP00000392136:M736L;ENSP00000396918:M779L;ENSP00000402803:M736L	ENSP00000223341:M736L	M	-	1	0	URGCP	43883252	0.219000	0.23619	0.979000	0.43373	0.991000	0.79684	0.607000	0.24209	0.854000	0.35336	0.482000	0.46254	ATG	T|0.515;G|0.485	0.485	strong		0.527	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
C2orf71	388939	hgsc.bcm.edu	37	2	29294754	29294754	+	Missense_Mutation	SNP	G	G	C	rs17744093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29294754G>C	ENST00000331664.5	-	1	2373	c.2374C>G	c.(2374-2376)Ctc>Gtc	p.L792V		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	792			L -> V (in dbSNP:rs17744093). {ECO:0000269|PubMed:21412943}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CCCATTTTGAGAGATTCTCTG	0.527													G|||	626	0.125	0.0303	0.1571	5008	,	,		19258	0.1637		0.2137	False		,,,				2504	0.0992				p.L792V		Atlas-SNP	.											.	C2orf71	146	.	0			c.C2374G						PASS	.	G	VAL/LEU	270,3554		9,252,1651	64.0	65.0	64.0		2374	0.5	0.0	2	dbSNP_123	64	1852,6442		191,1470,2486	yes	missense	C2orf71	NM_001029883.1	32	200,1722,4137	CC,CG,GG		22.3294,7.0607,17.5111	probably-damaging	792/1289	29294754	2122,9996	1912	4147	6059	SO:0001583	missense	388939	exon1			TTTTGAGAGATTC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.2374C>G	2.37:g.29294754G>C	ENSP00000332809:p.Leu792Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	117	60	0.512821	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	323	0.1478937728937729	22	0.044715447154471545	59	0.16298342541436464	93	0.16258741258741258	149	0.19656992084432717	G	11.65	1.703088	0.30232	0.070607	0.223294	ENSG00000179270	ENST00000331664	T	0.25085	1.82	5.39	0.524	0.17066	.	0.696719	0.13076	N	0.415662	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P	0.37276	0.589	B	0.33392	0.163	T	0.22977	-1.0201	9	0.33940	T	0.23	-1.8564	2.3117	0.04188	0.4334:0.1197:0.3243:0.1226	rs17744093;rs17744093	792	A6NGG8	CB071_HUMAN	V	792	ENSP00000332809:L792V	ENSP00000332809:L792V	L	-	1	0	C2orf71	29148258	0.033000	0.19621	0.000000	0.03702	0.001000	0.01503	1.734000	0.38166	-0.205000	0.10219	-0.806000	0.03193	CTC	G|0.836;C|0.164	0.164	strong		0.527	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
DAB2	1601	hgsc.bcm.edu	37	5	39376988	39376988	+	Missense_Mutation	SNP	C	C	T	rs3733801	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:39376988C>T	ENST00000320816.6	-	12	2368	c.1901G>A	c.(1900-1902)aGt>aAt	p.S634N	DAB2_ENST00000509337.1_Missense_Mutation_p.S613N|DAB2_ENST00000545653.1_Missense_Mutation_p.S613N|DAB2_ENST00000339788.6_Missense_Mutation_p.S416N	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	634	Sufficient for interaction with GRB2. {ECO:0000250}.		S -> N (in dbSNP:rs3733801).		activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			GAAGGCATCACTGGAGATGTC	0.562											OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	573	0.114417	0.0295	0.1715	5008	,	,		19642	0.0694		0.1103	False		,,,				2504	0.2393				p.S634N		Atlas-SNP	.											.	DAB2	124	.	0			c.G1901A						PASS	.	C	ASN/SER	213,4193	131.0+/-167.6	6,201,1996	71.0	82.0	78.0		1901	3.0	0.6	5	dbSNP_107	78	1034,7566	219.9+/-257.8	62,910,3328	yes	missense	DAB2	NM_001343.3	46	68,1111,5324	TT,TC,CC		12.0233,4.8343,9.5879	possibly-damaging	634/771	39376988	1247,11759	2203	4300	6503	SO:0001583	missense	1601	exon12			GCATCACTGGAGA	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1901G>A	5.37:g.39376988C>T	ENSP00000313391:p.Ser634Asn	Somatic	137	0	0	885	WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	202	0.0924908424908425	11	0.022357723577235773	61	0.1685082872928177	46	0.08041958041958042	84	0.11081794195250659	C	12.59	1.983072	0.34942	0.048343	0.120233	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.38722	1.15;1.21;1.12;1.12	4.85	2.98	0.34508	.	0.566631	0.20034	N	0.100652	T	0.00144	0.0004	M	0.61703	1.905	0.34155	P	0.332017	B;B	0.17038	0.009;0.02	B;B	0.26416	0.008;0.069	T	0.05750	-1.0866	9	0.38643	T	0.18	-0.6023	9.2483	0.37541	0.0:0.7572:0.1593:0.0835	rs3733801;rs52819300;rs58689740;rs3733801	634;613	P98082;P98082-3	DAB2_HUMAN;.	N	634;416;613;613	ENSP00000313391:S634N;ENSP00000345508:S416N;ENSP00000439919:S613N;ENSP00000426245:S613N	ENSP00000313391:S634N	S	-	2	0	DAB2	39412745	0.979000	0.34478	0.577000	0.28562	0.979000	0.70002	1.379000	0.34340	0.386000	0.24997	0.655000	0.94253	AGT	C|0.904;T|0.096	0.096	strong		0.562	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
C17orf49	124944	hgsc.bcm.edu	37	17	6919093	6919093	+	Splice_Site	SNP	T	T	C	rs14309	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6919093T>C	ENST00000439424.2	+	3	193	c.117T>C	c.(115-117)ggT>ggC	p.G39G	C17orf49_ENST00000546495.1_Splice_Site_p.G39G|MIR497HG_ENST00000385056.1_RNA|AC040977.1_ENST00000593646.1_5'Flank|RNASEK-C17orf49_ENST00000547302.2_Splice_Site_p.V80A|MIR497HG_ENST00000443997.1_RNA|C17orf49_ENST00000546760.1_Splice_Site_p.G39G|MIR497HG_ENST00000572453.1_RNA|RP11-589P10.7_ENST00000572547.1_RNA|C17orf49_ENST00000552402.1_Intron|MIR497HG_ENST00000385194.1_RNA|C17orf49_ENST00000552775.1_Splice_Site_p.G13G	NM_001142798.2|NM_174893.3	NP_001136270.1|NP_777553.1	Q8IXM2	BAP18_HUMAN	chromosome 17 open reading frame 49	39	SANT.				chromatin modification (GO:0016568)	MLL1 complex (GO:0071339)|NURF complex (GO:0016589)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|ovary(1)	4						CTTCTGACAGTGCGAAGTGGA	0.577													T|||	3793	0.757388	0.5628	0.5908	5008	,	,		16868	0.877		0.8569	False		,,,				2504	0.9131				p.G39G		Atlas-SNP	.											.	C17orf49	28	.	0			c.T117C						PASS	.	T	,,	2699,1707	651.8+/-399.3	831,1037,335	63.0	56.0	58.0		117,,117	3.6	1.0	17	dbSNP_52	58	7345,1255	760.4+/-407.6	3140,1065,95	yes	coding-synonymous-near-splice,intron,coding-synonymous-near-splice	C17orf49	NM_001142798.2,NM_001142799.2,NM_174893.3	,,	3971,2102,430	CC,CT,TT		14.593,38.7426,22.7741	,,	39/193,,39/173	6919093	10044,2962	2203	4300	6503	SO:0001630	splice_region_variant	124944	exon3			TGACAGTGCGAAG	AK055800	CCDS32542.1, CCDS45595.1, CCDS45596.1	17p13.1	2013-02-11			ENSG00000258315	ENSG00000258315			28737	protein-coding gene	gene with protein product	"""BPTF associated protein of 18 kDa"", ""human embryo lung cellular protein interacting with SARS-CoV nsp-10"""						Standard	NM_174893		Approved	MGC49942, BAP18, HEPIS		Q8IXM2	OTTHUMG00000170147	ENST00000439424.2:c.117-1T>C	17.37:g.6919093T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_174893	B4DIV3|C9J4G0|E9PB29	Silent	SNP	ENST00000439424.2	37	CCDS32542.1	1646	0.7536630036630036	290	0.5894308943089431	227	0.6270718232044199	483	0.8444055944055944	646	0.8522427440633246	T	16.08	3.022526	0.54683	0.612574	0.85407	ENSG00000161939	ENST00000547302	.	.	.	4.73	3.62	0.41486	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.31099	P	0.710612	.	.	.	.	.	.	T	0.15694	-1.0428	3	.	.	.	.	5.2785	0.15663	0.1794:0.0:0.1867:0.6339	rs14309;rs312465;rs1128043;rs11548332;rs17343670;rs17358432;rs14309	.	.	.	A	80	.	.	V	+	2	0	C17orf49	6859817	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.113000	0.31184	0.790000	0.33803	0.460000	0.39030	GTG	T|0.229;C|0.771	0.771	strong		0.577	C17orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407666.1	NM_174893	Silent
MDM2	4193	hgsc.bcm.edu	37	12	69233215	69233215	+	Silent	SNP	A	A	G	rs769412	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:69233215A>G	ENST00000350057.5	+	9	987	c.987A>G	c.(985-987)gaA>gaG	p.E329E	MDM2_ENST00000478070.1_3'UTR|MDM2_ENST00000517852.1_Intron|MDM2_ENST00000428863.2_Silent_p.E133E|MDM2_ENST00000356290.4_Silent_p.E184E|MDM2_ENST00000393410.1_Silent_p.E106E|MDM2_ENST00000258149.5_Silent_p.E299E|MDM2_ENST00000393412.3_Silent_p.E81E|MDM2_ENST00000360430.2_Silent_p.E159E|MDM2_ENST00000462284.1_Silent_p.E360E|MDM2_ENST00000540827.1_Silent_p.E159E|MDM2_ENST00000258148.7_Silent_p.E305E|MDM2_ENST00000544561.1_Intron|MDM2_ENST00000348801.2_Silent_p.E128E|MDM2_ENST00000545204.1_Intron|RP11-611O2.5_ENST00000553141.1_RNA|MDM2_ENST00000393413.3_Silent_p.E81E|MDM2_ENST00000299252.4_Silent_p.E184E			Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	354	Necessary for interaction with USP2.|Region II.				cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			CACAAGCTGAAGAGGGCTTTG	0.388			A		"""sarcoma, glioma, colorectal, other"""								A|||	391	0.0780751	0.1505	0.072	5008	,	,		20089	0.0179		0.0676	False		,,,				2504	0.0573				p.E360E		Atlas-SNP	.		Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		"""M, O, E, L"""	.	MDM2	92	.	0			c.A1080G						PASS	.	A		453,3245		29,395,1425	102.0	96.0	98.0		1080	1.7	0.7	12	dbSNP_86	98	485,7673		16,453,3610	no	coding-synonymous	MDM2	NM_002392.3		45,848,5035	GG,GA,AA		5.9451,12.2499,7.9116		360/498	69233215	938,10918	1849	4079	5928	SO:0001819	synonymous_variant	4193	exon11			AGCTGAAGAGGGC		CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679			6973	protein-coding gene	gene with protein product		164785	"""mouse double minute 2, human homolog of; p53-binding protein"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)"", ""Mdm2 p53 binding protein homolog (mouse)"""			1614537, 16905769	Standard	NM_002392		Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000350057.5:c.987A>G	12.37:g.69233215A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	NM_002392	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	Silent	SNP	ENST00000350057.5	37																																																																																				A|0.927;G|0.073	0.073	strong		0.388	MDM2-033	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000402665.1	NM_006880	
DAGLA	747	hgsc.bcm.edu	37	11	61511133	61511133	+	Silent	SNP	G	G	A	rs3741251	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:61511133G>A	ENST00000257215.5	+	20	2417	c.2301G>A	c.(2299-2301)gcG>gcA	p.A767A	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	767					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		AGCGGCTGGCGGCGGAGCTGC	0.716													G|||	902	0.180112	0.0772	0.2176	5008	,	,		9840	0.1478		0.163	False		,,,				2504	0.3436				p.A767A		Atlas-SNP	.											.	DAGLA	109	.	0			c.G2301A						PASS	.	G		307,3765		11,285,1740	17.0	22.0	20.0		2301	-6.2	0.0	11	dbSNP_107	20	1129,6939		80,969,2985	no	coding-synonymous	DAGLA	NM_006133.2		91,1254,4725	AA,AG,GG		13.9936,7.5393,11.8287		767/1043	61511133	1436,10704	2036	4034	6070	SO:0001819	synonymous_variant	747	exon20			GCTGGCGGCGGAG	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.2301G>A	11.37:g.61511133G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.868;A|0.132	0.132	strong		0.716	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
TBC1D8	11138	hgsc.bcm.edu	37	2	101644855	101644855	+	Silent	SNP	G	G	A	rs11683877	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:101644855G>A	ENST00000376840.4	-	13	2216	c.2217C>T	c.(2215-2217)ccC>ccT	p.P739P	TBC1D8_ENST00000409318.1_Silent_p.P754P			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	739					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.P739P(1)		breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						TGCCAACTGGGGGCCCTGGGC	0.557													G|||	1078	0.215256	0.0356	0.2853	5008	,	,		13355	0.1667		0.2744	False		,,,				2504	0.3978				p.P739P		Atlas-SNP	.											TBC1D8_ENST00000376840,NS,carcinoma,0,1	TBC1D8	169	1	1	Substitution - coding silent(1)	stomach(1)	c.C2217T						PASS	.	G		302,3652		13,276,1688	75.0	86.0	82.0		2217	-1.0	0.0	2	dbSNP_120	82	2398,5900		358,1682,2109	no	coding-synonymous	TBC1D8	NM_001102426.1		371,1958,3797	AA,AG,GG		28.8985,7.6378,22.0372		739/1141	101644855	2700,9552	1977	4149	6126	SO:0001819	synonymous_variant	11138	exon13			AACTGGGGGCCCT	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.2217C>T	2.37:g.101644855G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	37	CCDS46375.1																																																																																			G|0.795;A|0.205	0.205	strong		0.557	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
ST14	6768	hgsc.bcm.edu	37	11	130068491	130068491	+	Silent	SNP	G	G	C	rs11827924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130068491G>C	ENST00000278742.5	+	14	2077	c.1659G>C	c.(1657-1659)ggG>ggC	p.G553G		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	553	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	GTGGGGACGGGTCCGACGAGG	0.657													g|||	589	0.117612	0.1029	0.0749	5008	,	,		13855	0.1974		0.1133	False		,,,				2504	0.09				p.G553G		Atlas-SNP	.											ST14,NS,malignant_melanoma,+1,1	ST14	82	1	0			c.G1659C						scavenged	.			480,3922	222.0+/-238.9	26,428,1747	46.0	47.0	47.0		1659	-3.3	0.6	11	dbSNP_120	47	1206,7388	241.7+/-271.9	85,1036,3176	no	coding-synonymous	ST14	NM_021978.3		111,1464,4923	CC,CG,GG		14.033,10.9041,12.9732		553/856	130068491	1686,11310	2201	4297	6498	SO:0001819	synonymous_variant	6768	exon14			GGACGGGTCCGAC	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.1659G>C	11.37:g.130068491G>C		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	184	92	0.5	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	CCDS8487.1																																																																																			G|0.868;C|0.132	0.132	strong		0.657	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
EFHB	151651	hgsc.bcm.edu	37	3	19975215	19975215	+	Missense_Mutation	SNP	C	C	A	rs17795400	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:19975215C>A	ENST00000295824.9	-	1	457	c.296G>T	c.(295-297)gGa>gTa	p.G99V	EFHB_ENST00000498089.1_5'UTR|EFHB_ENST00000344838.4_Intron	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	99			G -> V (in dbSNP:rs17795400).				calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						AGGTTTTGTTCCCTGTGAAGC	0.458													C|||	950	0.189696	0.0809	0.1686	5008	,	,		21397	0.2192		0.2376	False		,,,				2504	0.272				p.G99V		Atlas-SNP	.											.	EFHB	186	.	0			c.G296T						PASS	.	C	VAL/GLY	400,3646		22,356,1645	147.0	146.0	146.0		296	-1.2	0.0	3	dbSNP_123	146	2188,6190		279,1630,2280	yes	missense	EFHB	NM_144715.3	109	301,1986,3925	AA,AC,CC		26.116,9.8863,20.8307	possibly-damaging	99/834	19975215	2588,9836	2023	4189	6212	SO:0001583	missense	151651	exon1			TTTGTTCCCTGTG	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.296G>T	3.37:g.19975215C>A	ENSP00000295824:p.Gly99Val	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	277	171	0.617329	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	436	0.19963369963369965	53	0.10772357723577236	67	0.1850828729281768	127	0.22202797202797203	189	0.24934036939313983	C	9.672	1.146992	0.21288	0.098863	0.26116	ENSG00000163576	ENST00000295824;ENST00000389256	T;T	0.25579	1.79;2.04	3.6	-1.22	0.09494	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.15141	0.012	B	0.09377	0.004	T	0.42999	-0.9418	7	.	.	.	-3.0822	7.0131	0.24873	0.0:0.3945:0.0:0.6055	rs17795400;rs52807659;rs17795400	99	Q8N7U6	EFHB_HUMAN	V	99	ENSP00000295824:G99V;ENSP00000373908:G99V	.	G	-	2	0	EFHB	19950219	0.001000	0.12720	0.000000	0.03702	0.154000	0.21943	-0.159000	0.10056	-0.238000	0.09724	0.555000	0.69702	GGA	C|0.797;A|0.202	0.202	strong		0.458	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
COL6A5	256076	hgsc.bcm.edu	37	3	130124491	130124491	+	Silent	SNP	G	G	A	rs10934940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130124491G>A	ENST00000432398.2	+	14	4835	c.4341G>A	c.(4339-4341)gcG>gcA	p.A1447A	COL6A5_ENST00000265379.6_Silent_p.A1447A	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1447	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GTCCAGGGGCGTGGGGTCAGA	0.478													G|||	2245	0.448283	0.3343	0.4885	5008	,	,		18453	0.1736		0.7654	False		,,,				2504	0.5307				p.A1447A		Atlas-SNP	.											COL6A5,colon,carcinoma,0,1	COL6A5	205	1	0			c.G4341A						PASS	.	G		583,801		123,337,232	128.0	124.0	125.0		4341	-3.6	0.0	3	dbSNP_120	125	2403,779		924,555,112	no	coding-synonymous	COL6A5	NM_153264.5		1047,892,344	AA,AG,GG		24.4815,42.1243,34.6036		1447/2527	130124491	2986,1580	692	1591	2283	SO:0001819	synonymous_variant	256076	exon14			AGGGGCGTGGGGT	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.4341G>A	3.37:g.130124491G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	165	163	0.987879	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				G|0.508;A|0.492	0.492	strong		0.478	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
SLC2A11	66035	hgsc.bcm.edu	37	22	24224659	24224659	+	Silent	SNP	C	C	A	rs9612499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:24224659C>A	ENST00000345044.6	+	7	967	c.699C>A	c.(697-699)ctC>ctA	p.L233L	SLC2A11_ENST00000467660.1_3'UTR|AP000350.10_ENST00000433835.3_Intron|RN7SL268P_ENST00000491172.2_RNA|SLC2A11_ENST00000316185.8_Silent_p.L236L|SLC2A11_ENST00000398356.2_Silent_p.L240L			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	233					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						TACGGCGGCTCCGGGGCTCCG	0.711													a|||	1721	0.34365	0.1899	0.3689	5008	,	,		13300	0.3194		0.4076	False		,,,				2504	0.4928				p.L240L		Atlas-SNP	.											.	SLC2A11	32	.	0			c.C720A						PASS	.		,,	723,2953		132,459,1247	3.0	4.0	3.0		699,708,720	1.7	1.0	22	dbSNP_119	3	2732,4606		630,1472,1567	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC2A11	NM_001024938.2,NM_001024939.2,NM_030807.3	,,	762,1931,2814	AA,AC,CC		37.2309,19.6681,31.3692	,,	233/497,236/500,240/504	24224659	3455,7559	1838	3669	5507	SO:0001819	synonymous_variant	66035	exon8			GCGGCTCCGGGGC	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.699C>A	22.37:g.24224659C>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Silent	SNP	ENST00000345044.6	37	CCDS46673.1	712|712	0.326007326007326|0.326007326007326	102|102	0.2073170731707317|0.2073170731707317	114|114	0.3149171270718232|0.3149171270718232	183|183	0.31993006993006995|0.31993006993006995	313|313	0.4129287598944591|0.4129287598944591	a|a	3.415|3.415	-0.119334|-0.119334	0.06838|0.06838	0.196681|0.196681	0.372309|0.372309	ENSG00000133460|ENSG00000251357	ENST00000398363|ENST00000502845	.|.	.|.	.|.	3.92|3.92	1.69|1.69	0.24217|0.24217	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999999996|0.999999999999996	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44802|0.44802	-0.9304|-0.9304	4|3	0.44086|.	T|.	0.13|.	.|.	1.5873|1.5873	0.02647|0.02647	0.1956:0.1662:0.4674:0.1708|0.1956:0.1662:0.4674:0.1708	rs9612499|rs9612499	.|.	.|.	.|.	T|Y	184|5	.|.	ENSP00000381404:P184T|.	P|S	+|+	1|2	0|0	SLC2A11|AP000350.10	22554659|22554659	0.903000|0.903000	0.30736|0.30736	0.970000|0.970000	0.41538|0.41538	0.002000|0.002000	0.02628|0.02628	-0.016000|-0.016000	0.12613|0.12613	0.069000|0.069000	0.16605|0.16605	-0.938000|-0.938000	0.02693|0.02693	CCG|TCC	C|0.674;A|0.326	0.326	strong		0.711	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
OR8B8	26493	hgsc.bcm.edu	37	11	124310622	124310622	+	Silent	SNP	A	A	G	rs4296049	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124310622A>G	ENST00000328064.2	-	1	432	c.360T>C	c.(358-360)taT>taC	p.Y120Y		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	120					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CATAGCGGTCATACGCCATTG	0.473													A|||	1244	0.248403	0.0303	0.33	5008	,	,		23587	0.5317		0.2644	False		,,,				2504	0.1769				p.Y120Y		Atlas-SNP	.											.	OR8B8	76	.	0			c.T360C						PASS	.	A		300,4102	164.0+/-195.7	8,284,1909	93.0	86.0	88.0		360	1.2	0.9	11	dbSNP_111	88	2499,6099	410.5+/-350.2	360,1779,2160	no	coding-synonymous	OR8B8	NM_012378.1		368,2063,4069	GG,GA,AA		29.0649,6.8151,21.5308		120/312	124310622	2799,10201	2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			GCGGTCATACGCC	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"""GPCR / Class A : Olfactory receptors"""	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.360T>C	11.37:g.124310622A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	91	52	0.571429	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	37	CCDS8446.1																																																																																			A|0.756;G|0.244	0.244	strong		0.473	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378	
PBOV1	59351	hgsc.bcm.edu	37	6	138539315	138539315	+	Missense_Mutation	SNP	A	A	G	rs6927706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138539315A>G	ENST00000527246.2	-	1	312	c.218T>C	c.(217-219)aTa>aCa	p.I73T	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	73			I -> T (in dbSNP:rs6927706).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		TGACTGTTCTATGGAATAATC	0.378													A|||	781	0.15595	0.1498	0.1556	5008	,	,		21690	0.3581		0.0616	False		,,,				2504	0.0532				p.I73T		Atlas-SNP	.											.	PBOV1	12	.	0			c.T218C						PASS	.	A	,THR/ILE	668,3738	284.3+/-277.5	52,564,1587	277.0	274.0	275.0		,218	-6.2	0.0	6	dbSNP_116	275	589,8011	157.5+/-211.1	18,553,3729	yes	intron,missense	KIAA1244,PBOV1	NM_020340.4,NM_021635.2	,89	70,1117,5316	GG,GA,AA		6.8488,15.1611,9.6648	,benign	,73/136	138539315	1257,11749	2203	4300	6503	SO:0001583	missense	59351	exon1			TGTTCTATGGAAT	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.218T>C	6.37:g.138539315A>G	ENSP00000432353:p.Ile73Thr	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	270	85	0.314815	NM_021635		Missense_Mutation	SNP	ENST00000527246.2	37	CCDS5190.1	408	0.18681318681318682	89	0.18089430894308944	51	0.1408839779005525	218	0.3811188811188811	50	0.06596306068601583	A	0.276	-0.989605	0.02162	0.151611	0.068488	ENSG00000254440	ENST00000527246	T	0.43294	0.95	3.1	-6.21	0.02065	.	.	.	.	.	T	0.07458	0.0188	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32079	-0.9920	8	0.87932	D	0	.	11.5379	0.50648	0.196:0.1308:0.6731:0.0	rs6927706;rs52793958;rs61006697;rs6927706	73	Q9GZY1	PBOV1_HUMAN	T	73	ENSP00000432353:I73T	ENSP00000432353:I73T	I	-	2	0	PBOV1	138581008	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.868000	0.00346	-2.939000	0.00298	-1.948000	0.00487	ATA	A|0.855;G|0.145	0.145	strong		0.378	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635	
SPTA1	6708	hgsc.bcm.edu	37	1	158582646	158582646	+	Silent	SNP	T	T	C	rs2251969	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158582646T>C	ENST00000368147.4	-	51	7275	c.7095A>G	c.(7093-7095)gcA>gcG	p.A2365A	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2365	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ACTTGCCCTCTGCCAGGGCTT	0.443													C|||	2528	0.504792	0.4183	0.5202	5008	,	,		19129	0.6319		0.5626	False		,,,				2504	0.4202				p.A2365A		Atlas-SNP	.											SPTA1,NS,carcinoma,-2,2	SPTA1	720	2	0			c.A7095G						PASS	.	C		1681,2167		361,959,604	130.0	125.0	126.0		7095	0.2	1.0	1	dbSNP_100	126	4498,3782		1247,2004,889	no	coding-synonymous	SPTA1	NM_003126.2		1608,2963,1493	CC,CT,TT		45.6763,43.685,49.0518		2365/2420	158582646	6179,5949	1924	4140	6064	SO:0001819	synonymous_variant	6708	exon51			GCCCTCTGCCAGG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.7095A>G	1.37:g.158582646T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			T|0.458;C|0.542	0.542	strong		0.443	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
KIAA1429	25962	hgsc.bcm.edu	37	8	95541302	95541302	+	Silent	SNP	A	A	G	rs957448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95541302A>G	ENST00000297591.5	-	7	951	c.876T>C	c.(874-876)ggT>ggC	p.G292G	KIAA1429_ENST00000437199.1_Silent_p.G292G|KIAA1429_ENST00000421249.2_Silent_p.G292G	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	292	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ACCCACCTTCACcttcttcat	0.403													A|||	1768	0.353035	0.2723	0.438	5008	,	,		22682	0.4861		0.3101	False		,,,				2504	0.3088				p.G292G		Atlas-SNP	.											.	KIAA1429	176	.	0			c.T876C						PASS	.	A	,	1242,3164	427.0+/-341.4	189,864,1150	412.0	345.0	368.0		876,876	4.0	1.0	8	dbSNP_86	368	2131,6469	366.1+/-334.2	271,1589,2440	no	coding-synonymous,coding-synonymous	KIAA1429	NM_015496.4,NM_183009.2	,	460,2453,3590	GG,GA,AA		24.7791,28.1888,25.9342	,	292/1813,292/1148	95541302	3373,9633	2203	4300	6503	SO:0001819	synonymous_variant	25962	exon7			ACCTTCACCTTCT	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.876T>C	8.37:g.95541302A>G		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	211	103	0.488152	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			A|0.691;G|0.309	0.309	strong		0.403	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
ABCA7	10347	hgsc.bcm.edu	37	19	1042809	1042809	+	Missense_Mutation	SNP	A	A	G	rs3764645	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1042809A>G	ENST00000263094.6	+	7	794	c.563A>G	c.(562-564)gAg>gGg	p.E188G	ABCA7_ENST00000435683.2_Missense_Mutation_p.E50G|ABCA7_ENST00000433129.1_Missense_Mutation_p.E188G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	188			E -> G (in dbSNP:rs3764645). {ECO:0000269|PubMed:11435699, ECO:0000269|PubMed:12111378}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGCCGCTGAGGACCTGGCC	0.657													A|||	2001	0.399561	0.1657	0.6268	5008	,	,		17314	0.4355		0.4463	False		,,,				2504	0.4693				p.E188G		Atlas-SNP	.											.	ABCA7	174	.	0			c.A563G						PASS	.	A	GLY/GLU	979,3427	364.9+/-317.2	113,753,1337	58.0	57.0	58.0		563	-0.6	0.0	19	dbSNP_107	58	4076,4524	556.1+/-386.8	998,2080,1222	yes	missense	ABCA7	NM_019112.3	98	1111,2833,2559	GG,GA,AA		47.3953,22.2197,38.8667	benign	188/2147	1042809	5055,7951	2203	4300	6503	SO:0001583	missense	10347	exon7			CCGCTGAGGACCT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.563A>G	19.37:g.1042809A>G	ENSP00000263094:p.Glu188Gly	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	901	0.4125457875457875	71	0.1443089430894309	219	0.6049723756906077	269	0.47027972027972026	342	0.45118733509234826	A	7.460	0.644520	0.14451	0.222197	0.473953	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.86497	-2.13;-2.13	4.3	-0.62	0.11567	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.32160	0.358;0.244	B;B	0.25140	0.058;0.037	T	0.41106	-0.9527	8	0.17832	T	0.49	.	4.1058	0.10037	0.4862:0.1825:0.3312:0.0	rs3764645	50;188	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	G	188	ENSP00000263094:E188G;ENSP00000414062:E188G	ENSP00000263094:E188G	E	+	2	0	ABCA7	993809	0.000000	0.05858	0.000000	0.03702	0.396000	0.30629	-1.730000	0.01855	-0.436000	0.07254	0.379000	0.24179	GAG	A|0.609;G|0.391	0.391	strong		0.657	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
LILRB3	11025	hgsc.bcm.edu	37	19	54726241	54726241	+	Missense_Mutation	SNP	C	C	T	rs77279742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54726241C>T	ENST00000391750.1	-	4	400	c.264G>A	c.(262-264)atG>atA	p.M88I	LILRB3_ENST00000424807.1_Missense_Mutation_p.M88I|LILRB3_ENST00000469273.1_5'Flank|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000245620.9_Missense_Mutation_p.M88I|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000346401.6_Missense_Mutation_p.M88I|LILRA6_ENST00000419410.2_Intron|LILRA6_ENST00000440558.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	88	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGTGCTCTGTCATGGATGGGA	0.562													.|||	2272	0.453674	0.5325	0.4265	5008	,	,		12679	0.4871		0.4046	False		,,,				2504	0.3824				p.M88I		Atlas-SNP	.											LILRB3,NS,haematopoietic_neoplasm,0,2	LILRB3	67	2	0			c.G264A						PASS	.	C	ILE/MET,ILE/MET	2307,1735		841,625,555	85.0	121.0	109.0		264,264	0.8	0.0	19	dbSNP_131	109	3530,4528		697,2136,1196	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	10,10	1538,2761,1751	TT,TC,CC		43.8074,42.9243,48.2397	benign,benign	88/633,88/632	54726241	5837,6263	2021	4029	6050	SO:0001583	missense	11025	exon3			CTCTGTCATGGAT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.264G>A	19.37:g.54726241C>T	ENSP00000375630:p.Met88Ile	Somatic	471	1	0.00212314		WXS	Illumina HiSeq	Phase_I	756	245	0.324074	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	930	0.4258241758241758	254	0.516260162601626	141	0.38950276243093923	263	0.4597902097902098	272	0.35883905013192613	C	4.046	0.006136	0.07866	0.570757	0.438074	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000445347	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	3.08	0.77	0.18497	Immunoglobulin-like fold (1);	0.442058	0.21614	N	0.071749	T	0.00012	0.0000	M	0.75884	2.315	0.80722	P	0.0	P;B	0.43352	0.804;0.06	B;B	0.35655	0.087;0.207	T	0.38993	-0.9635	9	0.23891	T	0.37	.	8.9029	0.35505	0.0:0.5451:0.4549:0.0	.	88;88	O75022;O75022-3	LIRB3_HUMAN;.	I	88	ENSP00000375630:M88I;ENSP00000412771:M88I;ENSP00000345184:M88I;ENSP00000245620:M88I;ENSP00000388199:M88I	ENSP00000245620:M88I	M	-	3	0	LILRB3	59418053	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.092000	0.15066	0.300000	0.22699	0.573000	0.79308	ATG	C|0.581;T|0.419	0.419	strong		0.562	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
IL31RA	133396	hgsc.bcm.edu	37	5	55206444	55206444	+	Missense_Mutation	SNP	G	G	A	rs161704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:55206444G>A	ENST00000447346.2	+	12	1651	c.1586G>A	c.(1585-1587)aGc>aAc	p.S529N	IL31RA_ENST00000354961.4_Missense_Mutation_p.S510N|IL31RA_ENST00000490985.1_Missense_Mutation_p.S387N|IL31RA_ENST00000396834.1_Missense_Mutation_p.S510N|IL31RA_ENST00000359040.5_Missense_Mutation_p.S529N	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	497					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GTCATGGCCAGCACCAGTGCT	0.468													G|||	1552	0.309904	0.3321	0.2176	5008	,	,		22564	0.3254		0.2962	False		,,,				2504	0.3436				p.S529N		Atlas-SNP	.											.	IL31RA	84	.	0			c.G1586A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	1511,2895	480.3+/-358.8	262,987,954	163.0	141.0	148.0		1529,1586,1529,1160,1586	3.3	1.0	5	dbSNP_79	148	2503,6097	410.3+/-350.1	354,1795,2151	yes	missense,missense,missense,missense,missense	IL31RA	NM_001242636.1,NM_001242637.1,NM_001242638.1,NM_001242639.1,NM_139017.5	46,46,46,46,46	616,2782,3105	AA,AG,GG		29.1047,34.2941,30.8627	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	510/746,529/682,510/663,387/623,529/765	55206444	4014,8992	2203	4300	6503	SO:0001583	missense	133396	exon12			TGGCCAGCACCAG	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1586G>A	5.37:g.55206444G>A	ENSP00000415900:p.Ser529Asn	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	255	126	0.494118	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	669	0.30631868131868134	147	0.29878048780487804	82	0.2265193370165746	205	0.3583916083916084	235	0.3100263852242744	G	3.877	-0.026766	0.07589	0.342941	0.291047	ENSG00000164509	ENST00000396834;ENST00000447346;ENST00000359040;ENST00000490985;ENST00000354961	T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41	5.11	3.33	0.38152	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.372887	0.31685	N	0.007222	T	0.00012	0.0000	M	0.71871	2.18	0.09310	P	0.9999999999994192	B;B;B;B	0.27166	0.17;0.037;0.141;0.141	B;B;B;B	0.26310	0.068;0.028;0.041;0.041	T	0.31861	-0.9928	9	0.25751	T	0.34	-19.8536	6.2045	0.20595	0.2609:0.0:0.7391:0.0	rs161704;rs327251;rs52803246;rs58671636;rs161704	497;529;510;529	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2	IL31R_HUMAN;.;.;.	N	510;529;529;387;510	ENSP00000380046:S510N;ENSP00000415900:S529N;ENSP00000351935:S529N;ENSP00000427533:S387N;ENSP00000347047:S510N	ENSP00000347047:S510N	S	+	2	0	IL31RA	55242201	0.982000	0.34865	1.000000	0.80357	0.987000	0.75469	0.168000	0.16622	1.521000	0.48983	0.557000	0.71058	AGC	G|0.694;N|0.000	.	strong		0.468	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
THBS4	7060	hgsc.bcm.edu	37	5	79361265	79361265	+	Missense_Mutation	SNP	G	G	C	rs1866389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:79361265G>C	ENST00000350881.2	+	9	1349	c.1159G>C	c.(1159-1161)Gcg>Ccg	p.A387P	CTD-2201I18.1_ENST00000514042.1_RNA|CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000511733.1_Missense_Mutation_p.A296P	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	387	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		A -> P (gain of function mutation; resulting in a pro-atherogenic phenotype; dbSNP:rs1866389). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		TCGAAATGGAGCGTGCGTTCC	0.378													G|||	630	0.125799	0.0688	0.1311	5008	,	,		18658	0.0506		0.2326	False		,,,				2504	0.1667				p.A387P		Atlas-SNP	.											.	THBS4	82	.	0			c.G1159C	GRCh37	CM054868	THBS4	M	rs1866389	PASS	.	G	PRO/ALA	438,3968	212.8+/-232.6	25,388,1790	225.0	192.0	203.0		1159	5.2	1.0	5	dbSNP_92	203	1903,6697	339.8+/-323.3	188,1527,2585	yes	missense	THBS4	NM_003248.4	27	213,1915,4375	CC,CG,GG		22.1279,9.941,17.9994	benign	387/962	79361265	2341,10665	2203	4300	6503	SO:0001583	missense	7060	exon9			AATGGAGCGTGCG		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.1159G>C	5.37:g.79361265G>C	ENSP00000339730:p.Ala387Pro	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	133	71	0.533835	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	37	CCDS4049.1	297	0.13598901098901098	31	0.06300813008130081	57	0.1574585635359116	34	0.05944055944055944	175	0.23087071240105542	G	14.44	2.535439	0.45176	0.09941	0.221279	ENSG00000113296	ENST00000350881;ENST00000511733	D;D	0.92249	-3.0;-3.0	5.19	5.19	0.71726	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.105026	0.64402	D	0.000005	T	0.00109	0.0003	N	0.01003	-1.06	0.29022	P	0.886245	P	0.36753	0.568	B	0.41271	0.352	T	0.48525	-0.9028	9	0.07813	T	0.8	-12.6373	15.9889	0.80183	0.0:0.1342:0.8658:0.0	rs1866389;rs2228290;rs17257691;rs17884905;rs1866389	387	P35443	TSP4_HUMAN	P	387;296	ENSP00000339730:A387P;ENSP00000422298:A296P	ENSP00000339730:A387P	A	+	1	0	THBS4	79397021	0.995000	0.38212	0.989000	0.46669	0.026000	0.11368	2.875000	0.48491	2.711000	0.92665	0.655000	0.94253	GCG	G|0.840;C|0.160	0.160	strong		0.378	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
CR1L	1379	hgsc.bcm.edu	37	1	207872595	207872595	+	Missense_Mutation	SNP	A	A	G	rs12729569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207872595A>G	ENST00000508064.2	+	8	1264	c.1204A>G	c.(1204-1206)Aat>Gat	p.N402D	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	402	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.		N -> D (in dbSNP:rs12729569). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						AAGCCTTTGGAATAGCAGTGT	0.418											OREG0014195	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	559	0.111621	0.053	0.1441	5008	,	,		19328	0.0317		0.2535	False		,,,				2504	0.1043				p.N402D		Atlas-SNP	.											.	CR1L	97	.	0			c.A1204G						PASS	.	A	ASP/ASN	337,3427		18,301,1563	243.0	220.0	227.0		1204	1.6	0.8	1	dbSNP_121	227	2159,6055		278,1603,2226	no	missense	CR1L	NM_175710.1	23	296,1904,3789	GG,GA,AA		26.2844,8.9532,20.8382	probably-damaging	402/570	207872595	2496,9482	1882	4107	5989	SO:0001583	missense	1379	exon8			CTTTGGAATAGCA	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1204A>G	1.37:g.207872595A>G	ENSP00000421736:p.Asn402Asp	Somatic	469	0	0	2170	WXS	Illumina HiSeq	Phase_I	553	275	0.497288	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	309	0.14148351648351648	24	0.04878048780487805	66	0.18232044198895028	24	0.04195804195804196	195	0.25725593667546176	.	14.04	2.416352	0.42918	0.089532	0.262844	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.63255	-0.03	1.65	1.65	0.23941	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.41027	1.25	0.58432	P	2.9999999999752447E-6	D	0.64830	0.994	D	0.70227	0.968	T	0.06409	-1.0828	8	0.28530	T	0.3	.	5.4429	0.16519	1.0:0.0:0.0:0.0	rs12729569	402	Q2VPA4	CR1L_HUMAN	D	402	ENSP00000421736:N402D	ENSP00000434864:N346D	N	+	1	0	CR1L	205939218	1.000000	0.71417	0.843000	0.33291	0.860000	0.49131	3.166000	0.50785	1.027000	0.39758	0.242000	0.17961	AAT	A|0.831;G|0.169	0.169	strong		0.418	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
ANG	283	hgsc.bcm.edu	37	14	21162053	21162053	+	Silent	SNP	T	T	G	rs11701	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21162053T>G	ENST00000336811.6	+	2	930	c.330T>G	c.(328-330)ggT>ggG	p.G110G	ANG_ENST00000397990.4_Silent_p.G110G|AL163636.6_ENST00000553909.1_Intron|RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000397995.2_Intron|ANG_ENST00000554073.1_Intron|RNASE4_ENST00000304704.4_Intron|RNASE4_ENST00000555835.1_Intron|RNASE4_ENST00000555597.1_Intron	NM_001145.4	NP_001136.1	P03950	ANGI_HUMAN	angiogenin, ribonuclease, RNase A family, 5	110					actin filament polymerization (GO:0030041)|activation of phospholipase A2 activity (GO:0032431)|activation of phospholipase C activity (GO:0007202)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|cell communication (GO:0007154)|cell death (GO:0008219)|cell migration (GO:0016477)|diacylglycerol biosynthetic process (GO:0006651)|homeostatic process (GO:0042592)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of translation (GO:0017148)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oocyte maturation (GO:0001556)|ovarian follicle development (GO:0001541)|placenta development (GO:0001890)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein secretion (GO:0050714)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|RNA phosphodiester bond hydrolysis (GO:0090501)|rRNA transcription (GO:0009303)	angiogenin-PRI complex (GO:0032311)|basal lamina (GO:0005605)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	actin binding (GO:0003779)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|heparin binding (GO:0008201)|peptide binding (GO:0042277)|receptor binding (GO:0005102)|ribonuclease activity (GO:0004540)|rRNA binding (GO:0019843)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)	5	all_cancers(95;0.00387)	all_cancers(140;0.196)|all_epithelial(140;0.156)	Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	OV - Ovarian serous cystadenocarcinoma(311;3.25e-17)|GBM - Glioblastoma multiforme(265;5.56e-07)		TACATGGAGGTTCCCCCTGGC	0.478													G|||	575	0.114816	0.1256	0.1844	5008	,	,		19948	0.0089		0.1372	False		,,,				2504	0.137				p.G110G		Atlas-SNP	.											.	ANG	8	.	0			c.T330G	GRCh37	CM045634	ANG	M	rs11701	PASS	.	G	,,,	567,3839	774.1+/-414.0	45,477,1681	107.0	102.0	103.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	330,330,,	0.7	0.7	14	dbSNP_52	103	1145,7455	766.1+/-407.6	74,997,3229	no	coding-synonymous,coding-synonymous,intron,intron	ANG,RNASE4	NM_001097577.2,NM_001145.4,NM_002937.3,NM_194431.1	,,,	119,1474,4910	GG,GT,TT		13.314,12.8688,13.1632	,,,	110/148,110/148,,	21162053	1712,11294	2203	4300	6503	SO:0001819	synonymous_variant	283	exon2			TGGAGGTTCCCCC		CCDS9554.1	14q11.1-q11.2	2014-09-17			ENSG00000214274	ENSG00000214274	3.1.27.-	"""Ribonucleases, RNase A"""	483	protein-coding gene	gene with protein product		105850				1978563	Standard	NM_001145		Approved	RNASE5	uc001vxw.4	P03950	OTTHUMG00000029576	ENST00000336811.6:c.330T>G	14.37:g.21162053T>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_001097577	Q05CV1|Q53X86|Q6P5T2|Q8WXE7	Silent	SNP	ENST00000336811.6	37	CCDS9554.1																																																																																			T|0.871;G|0.129	0.129	strong		0.478	ANG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073731.3	NM_001097577	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558314	140558314	+	Silent	SNP	T	T	C	rs17844487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140558314T>C	ENST00000239444.2	+	1	944	c.699T>C	c.(697-699)gtT>gtC	p.V233V	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	233	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACATTGAAGTTGTCGATGTCA	0.512													T|||	673	0.134385	0.0136	0.1441	5008	,	,		25997	0.3333		0.0805	False		,,,				2504	0.1411				p.V233V		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T699C						PASS	.						177.0	223.0	207.0					5																	140558314		2200	4217	6417	SO:0001819	synonymous_variant	56128	exon1			TGAAGTTGTCGAT	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.699T>C	5.37:g.140558314T>C		Somatic	359	0	0		WXS	Illumina HiSeq	Phase_I	491	47	0.095723	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			T|0.929;C|0.071	0.071	strong		0.512	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
NLRC5	84166	hgsc.bcm.edu	37	16	57060724	57060724	+	Silent	SNP	G	G	A	rs13339199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:57060724G>A	ENST00000262510.6	+	6	2094	c.1869G>A	c.(1867-1869)caG>caA	p.Q623Q	NLRC5_ENST00000539144.1_Silent_p.Q623Q|NLRC5_ENST00000436936.1_Silent_p.Q623Q|NLRC5_ENST00000308149.7_Silent_p.Q623Q	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	623					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				ATGAGACACAGGAGCCTGAGC	0.577													G|||	543	0.108427	0.2958	0.0461	5008	,	,		19707	0.0		0.0487	False		,,,				2504	0.0726				p.Q623Q		Atlas-SNP	.											.	NLRC5	186	.	0			c.G1869A						PASS	.	G		1047,3349	385.8+/-325.9	127,793,1278	116.0	87.0	97.0		1869	5.5	1.0	16	dbSNP_121	97	434,8166	132.5+/-190.1	11,412,3877	no	coding-synonymous	NLRC5	NM_032206.3		138,1205,5155	AA,AG,GG		5.0465,23.8171,11.3958		623/1867	57060724	1481,11515	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon5			GACACAGGAGCCT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1869G>A	16.37:g.57060724G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	172	89	0.517442	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	200	0.09157509157509157	144	0.2926829268292683	15	0.04143646408839779	3	0.005244755244755245	38	0.05013192612137203	G	6.139	0.393896	0.11638	0.238171	0.050465	ENSG00000140853	ENST00000538805	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33240	-0.9876	3	.	.	.	.	8.0878	0.30782	0.1725:0.0:0.8275:0.0	rs13339199;rs13339199	.	.	.	R	376	.	.	G	+	1	0	NLRC5	55618225	1.000000	0.71417	0.972000	0.41901	0.756000	0.42949	3.034000	0.49751	2.594000	0.87642	0.561000	0.74099	GGA	G|0.895;A|0.105	0.105	strong		0.577	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
CFAP46	54777	hgsc.bcm.edu	37	10	134726621	134726621	+	Silent	SNP	G	G	C	rs4880467	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134726621G>C	ENST00000368586.5	-	18	2362	c.2262C>G	c.(2260-2262)gcC>gcG	p.A754A	TTC40_ENST00000368582.2_Silent_p.A754A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCTGCCGCCCGGCCAGGATCA	0.637													G|||	1435	0.286542	0.264	0.3429	5008	,	,		18941	0.1498		0.34	False		,,,				2504	0.363				p.A754A		Atlas-SNP	.											.	TTC40	100	.	0			c.C2262G						PASS	.																																			SO:0001819	synonymous_variant	54777	exon18			CCGCCCGGCCAGG																												ENST00000368586.5:c.2262C>G	10.37:g.134726621G>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	161	161	1	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			G|0.740;C|0.260	0.260	strong		0.637	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
TPTE	7179	hgsc.bcm.edu	37	21	10942756	10942756	+	Nonsense_Mutation	SNP	G	G	A	rs1810540	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:10942756G>A	ENST00000361285.4	-	13	1014	c.685C>T	c.(685-687)Cga>Tga	p.R229*	TPTE_ENST00000342420.5_Nonsense_Mutation_p.R191*|TPTE_ENST00000298232.7_Nonsense_Mutation_p.R211*|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	229	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTTGTGTATCGCCTTTTGTTT	0.323																																					p.R229X		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,+1,4	TPTE	513	4	0			c.C685T						scavenged	.						460.0	404.0	423.0					21																	10942756		2203	4300	6503	SO:0001587	stop_gained	7179	exon13			TGTATCGCCTTTT	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.685C>T	21.37:g.10942756G>A	ENSP00000355208:p.Arg229*	Somatic	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	577	147	0.254766	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Nonsense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	37	6.526122	0.97637	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	.	.	.	2.73	0.513	0.17000	.	0.060960	0.64402	U	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.0328	8.5255	0.33302	0.0:0.0:0.5862:0.4138	rs1810540;rs3761314;rs59614997;rs1810540	.	.	.	X	211;229;191	.	ENSP00000298232:R211X	R	-	1	2	TPTE	9964627	0.999000	0.42202	0.858000	0.33744	0.576000	0.36127	2.540000	0.45727	-0.040000	0.13580	0.194000	0.17425	CGA	G|0.905;A|0.095	0.095	strong		0.323	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
TVP23C	201158	hgsc.bcm.edu	37	17	15406197	15406197	+	Missense_Mutation	SNP	A	A	T	rs12150518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:15406197A>T	ENST00000225576.3	-	6	907	c.812T>A	c.(811-813)cTg>cAg	p.L271Q	TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Intron	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	271			L -> Q (in dbSNP:rs12150518).			integral component of membrane (GO:0016021)											TCCGGATGCCAGATGAAATTT	0.562													A|||	154	0.0307508	0.0038	0.0389	5008	,	,		14672	0.0218		0.0666	False		,,,				2504	0.0337				p.L271Q		Atlas-SNP	.											.	.	.	.	0			c.T812A						PASS	.	A	,GLN/LEU	66,4338	58.1+/-94.6	1,64,2137	31.0	36.0	34.0		,812	-1.9	0.1	17	dbSNP_120	34	614,7986	159.5+/-212.8	24,566,3710	yes	intron,missense	FAM18B2,FAM18B2-CDRT4	NM_001204478.1,NM_145301.2	,113	25,630,5847	TT,TA,AA		7.1395,1.4986,5.2292	,benign	,271/277	15406197	680,12324	2202	4300	6502	SO:0001583	missense	201158	exon6			GATGCCAGATGAA	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.812T>A	17.37:g.15406197A>T	ENSP00000225576:p.Leu271Gln	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	NM_145301	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	37	CCDS11170.1	85	0.03891941391941392	2	0.0040650406504065045	18	0.049723756906077346	6	0.01048951048951049	59	0.07783641160949868	A	7.851	0.723912	0.15439	0.014986	0.071395	ENSG00000175106	ENST00000225576	T	0.30981	1.51	3.25	-1.86	0.07760	.	.	.	.	.	T	0.00580	0.0019	N	0.08118	0	0.34736	D	0.730257	B	0.19200	0.034	B	0.12156	0.007	T	0.23440	-1.0188	9	0.87932	D	0	-9.5616	0.3328	0.00321	0.384:0.194:0.2335:0.1885	rs12150518;rs12150518	271	Q96ET8	F18B2_HUMAN	Q	271	ENSP00000225576:L271Q	ENSP00000225576:L271Q	L	-	2	0	FAM18B2	15346922	0.983000	0.35010	0.124000	0.21820	0.386000	0.30323	0.065000	0.14466	-0.437000	0.07243	-0.621000	0.04028	CTG	A|0.951;T|0.049	0.049	strong		0.562	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301	
LLGL2	3993	hgsc.bcm.edu	37	17	73568055	73568055	+	Silent	SNP	C	C	T	rs1661714	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73568055C>T	ENST00000392550.3	+	19	2487	c.2370C>T	c.(2368-2370)ccC>ccT	p.P790P	LLGL2_ENST00000577200.1_Silent_p.P790P|LLGL2_ENST00000167462.5_Silent_p.P790P	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	790			P -> L (in dbSNP:rs1661714).		cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			TACCCCTTCCCGAGCCCCTCG	0.637													C|||	1089	0.217452	0.2995	0.2133	5008	,	,		15679	0.1508		0.2346	False		,,,				2504	0.1605				p.P790P		Atlas-SNP	.											.	LLGL2	155	.	0			c.C2370T						PASS	.	C	,	1133,3273	397.0+/-330.2	148,837,1218	41.0	38.0	39.0		2370,2370	-9.6	0.4	17	dbSNP_89	39	2297,6303	381.7+/-340.1	319,1659,2322	no	coding-synonymous,coding-synonymous	LLGL2	NM_001031803.1,NM_004524.2	,	467,2496,3540	TT,TC,CC		26.7093,25.7149,26.3724	,	790/1021,790/1016	73568055	3430,9576	2203	4300	6503	SO:0001819	synonymous_variant	3993	exon19			CCTTCCCGAGCCC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2370C>T	17.37:g.73568055C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			C|0.747;T|0.253	0.253	strong		0.637	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
APBB3	10307	hgsc.bcm.edu	37	5	139936760	139936760	+	IGR	SNP	G	G	T	rs250426	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139936760G>T	ENST00000357560.4	-	0	2218				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Silent_p.V53V	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGTGCGGCGACCCTCTTGG	0.672													G|||	3165	0.631989	0.292	0.7248	5008	,	,		11754	0.8254		0.7167	False		,,,				2504	0.7393				p.S93X		Atlas-SNP	.											.	SRA1	24	.	0			c.C278A						PASS	.	G		1616,2784		306,1004,890	40.0	49.0	46.0		159	-4.0	1.0	5	dbSNP_79	46	5988,2602		2111,1766,418	no	coding-synonymous	SRA1	NM_001035235.2		2417,2770,1308	TT,TG,GG		30.291,36.7273,41.4627		53/237	139936760	7604,5386	2200	4295	6495	SO:0001628	intergenic_variant	10011	exon1			TGCGGCGACCCTC	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504		5.37:g.139936760G>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	150	45	0.3	NM_001253764	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Nonsense_Mutation	SNP	ENST00000357560.4	37	CCDS4229.1																																																																																			A|0.000;G|0.374;T|0.626	0.626	strong		0.672	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
MICAL3	57553	hgsc.bcm.edu	37	22	18300879	18300879	+	Silent	SNP	G	G	A	rs11704809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:18300879G>A	ENST00000441493.2	-	26	4900	c.4548C>T	c.(4546-4548)agC>agT	p.S1516S	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1516					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TCTCCTCCACGCTCTCCACAA	0.637													G|||	761	0.151957	0.034	0.1844	5008	,	,		9836	0.0843		0.3161	False		,,,				2504	0.1892				p.S1516S		Atlas-SNP	.											.	MICAL3	53	.	0			c.C4548T						PASS	.	G		287,3845		9,269,1788	45.0	44.0	44.0		4548	-8.1	0.7	22	dbSNP_120	44	2758,5634		453,1852,1891	no	coding-synonymous	MICAL3	NM_015241.2		462,2121,3679	AA,AG,GG		32.8646,6.9458,24.3133		1516/2003	18300879	3045,9479	2066	4196	6262	SO:0001819	synonymous_variant	57553	exon26			CTCCACGCTCTCC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.4548C>T	22.37:g.18300879G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	80	51	0.6375	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1	372	0.17032967032967034	19	0.03861788617886179	75	0.20718232044198895	49	0.08566433566433566	229	0.3021108179419525	G	2.932	-0.220901	0.06061	0.069458	0.328646	ENSG00000093100	ENST00000252134	.	.	.	4.9	-8.09	0.01090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999519218	.	.	.	.	.	.	T	0.05370	-1.0889	3	.	.	.	.	15.7355	0.77839	0.6563:0.0:0.3437:0.0	rs11704809;rs17339582	.	.	.	V	498	.	.	A	-	2	0	XXbac-B461K10.4	16680879	0.145000	0.22656	0.749000	0.31150	0.370000	0.29829	-0.400000	0.07241	-1.838000	0.01187	-0.291000	0.09656	GCG	G|0.800;A|0.200	0.200	strong		0.637	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
SAG	6295	hgsc.bcm.edu	37	2	234255547	234255547	+	Missense_Mutation	SNP	G	G	A	rs1046974	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234255547G>A	ENST00000409110.1	+	16	1437	c.1207G>A	c.(1207-1209)Gtt>Att	p.V403I		NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	403			V -> A (in dbSNP:rs1046976). {ECO:0000269|PubMed:3164688, ECO:0000269|PubMed:9020843}.|V -> I (in dbSNP:rs1046974).		cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		CAAGAATGACGTTGATGAGTG	0.453													A|||	1517	0.302915	0.0545	0.245	5008	,	,		20836	0.3988		0.4344	False		,,,				2504	0.4458				p.V403I		Atlas-SNP	.											.	SAG	77	.	0			c.G1207A						PASS	.	A	ILE/VAL	462,3554		25,412,1571	91.0	96.0	95.0		1207	-2.7	0.0	2	dbSNP_86	95	3350,5002		661,2028,1487	yes	missense	SAG	NM_000541.4	29	686,2440,3058	AA,AG,GG		40.1102,11.504,30.8215	benign	403/406	234255547	3812,8556	2008	4176	6184	SO:0001583	missense	6295	exon16			AATGACGTTGATG		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.1207G>A	2.37:g.234255547G>A	ENSP00000386444:p.Val403Ile	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	30	0.333333	NM_000541	A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	37	CCDS46545.1	683	0.31272893772893773	31	0.06300813008130081	104	0.287292817679558	224	0.3916083916083916	324	0.42744063324538256	g	4.826	0.153569	0.09185	0.11504	0.401102	ENSG00000130561	ENST00000252857;ENST00000409110	T	0.06849	3.25	4.39	-2.67	0.06059	.	2.199560	0.02549	N	0.095496	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.48234	-0.9053	9	0.36615	T	0.2	6.8364	6.9618	0.24601	0.5946:0.0:0.2798:0.1255	rs1046974;rs3172176;rs52832638;rs57908936;rs1046974	403	P10523	ARRS_HUMAN	I	403	ENSP00000386444:V403I	ENSP00000252857:V403I	V	+	1	0	SAG	233920286	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.089000	0.15002	-0.720000	0.04935	-0.934000	0.02701	GTT	G|0.696;A|0.304	0.304	strong		0.453	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541	
SERPINA9	327657	hgsc.bcm.edu	37	14	94933640	94933640	+	Missense_Mutation	SNP	A	A	T	rs28583900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94933640A>T	ENST00000380365.3	-	3	786	c.708T>A	c.(706-708)caT>caA	p.H236Q	SERPINA9_ENST00000298845.7_Missense_Mutation_p.H154Q|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000424550.2_Missense_Mutation_p.H105Q|SERPINA9_ENST00000546329.1_Missense_Mutation_p.H218Q|SERPINA9_ENST00000337425.5_Missense_Mutation_p.H254Q|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000448305.2_Missense_Mutation_p.H156Q			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	236			H -> Q (in dbSNP:rs28583900). {ECO:0000269|PubMed:12975309}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TCATGGGGACATGCACAGTGA	0.507													A|||	1615	0.322484	0.146	0.3847	5008	,	,		21179	0.4643		0.3101	False		,,,				2504	0.3834				p.H254Q		Atlas-SNP	.											.	SERPINA9	105	.	0			c.T762A						PASS	.	A	GLN/HIS,GLN/HIS	638,3366		54,530,1418	73.0	71.0	72.0		462,762	-6.9	0.0	14	dbSNP_125	72	2511,5847		374,1763,2042	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	24,24	428,2293,3460	TT,TA,AA		30.0431,15.9341,25.4732	benign,benign	154/336,254/436	94933640	3149,9213	2002	4179	6181	SO:0001583	missense	327657	exon3			GGGGACATGCACA	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.708T>A	14.37:g.94933640A>T	ENSP00000369723:p.His236Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	101	65	0.643564	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		721	0.3301282051282051	79	0.16056910569105692	127	0.35082872928176795	275	0.4807692307692308	240	0.316622691292876	A	1.410	-0.575794	0.03882	0.159341	0.300431	ENSG00000170054	ENST00000448305;ENST00000298845;ENST00000424550;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	3.89	-6.94	0.01633	Serpin domain (3);	1.031920	0.07716	N	0.942849	T	0.00012	0.0000	N	0.00890	-1.11	0.58432	P	4.000000000004E-6	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.0;0.002	B;B;B;B;B	0.12156	0.004;0.0;0.003;0.0;0.007	T	0.21348	-1.0248	9	0.12766	T	0.61	.	1.5507	0.02574	0.5155:0.1089:0.2329:0.1427	rs28583900	218;236;156;254;154	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7;Q86WD7-2	.;SPA9_HUMAN;.;.;.	Q	156;154;105;254;236;218	ENSP00000414092:H156Q;ENSP00000298845:H154Q;ENSP00000409012:H105Q;ENSP00000337133:H254Q;ENSP00000369723:H236Q;ENSP00000445476:H218Q	ENSP00000298845:H154Q	H	-	3	2	SERPINA9	94003393	0.005000	0.15991	0.002000	0.10522	0.028000	0.11728	-0.058000	0.11750	-1.227000	0.02571	-0.464000	0.05259	CAT	A|0.681;T|0.319	0.319	strong		0.507	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
GSDMC	56169	hgsc.bcm.edu	37	8	130789767	130789767	+	Missense_Mutation	SNP	G	G	A	rs10090835	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:130789767G>A	ENST00000276708.4	-	2	948	c.67C>T	c.(67-69)Cct>Tct	p.P23S		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	23			P -> S (in dbSNP:rs10090835). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						TATTTGACAGGTGTCAGGTCT	0.403													G|||	68	0.0135783	0.0053	0.0231	5008	,	,		22250	0.0		0.0398	False		,,,				2504	0.0051				p.P23S		Atlas-SNP	.											.	GSDMC	71	.	0			c.C67T						PASS	.	G	SER/PRO	38,4368	41.6+/-74.8	0,38,2165	188.0	174.0	179.0		67	4.0	0.0	8	dbSNP_119	179	428,8172	132.2+/-189.8	8,412,3880	yes	missense	GSDMC	NM_031415.2	74	8,450,6045	AA,AG,GG		4.9767,0.8625,3.583	probably-damaging	23/509	130789767	466,12540	2203	4300	6503	SO:0001583	missense	56169	exon2			TGACAGGTGTCAG	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.67C>T	8.37:g.130789767G>A	ENSP00000276708:p.Pro23Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	37	CCDS6360.1	41	0.018772893772893772	5	0.01016260162601626	6	0.016574585635359115	0	0.0	30	0.0395778364116095	G	15.75	2.925135	0.52759	0.008625	0.049767	ENSG00000147697	ENST00000276708	T	0.43294	0.95	4.01	4.01	0.46588	.	0.000000	0.53938	D	0.000046	T	0.23846	0.0577	M	0.80332	2.49	0.09310	N	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.27400	-1.0075	10	0.66056	D	0.02	.	11.8128	0.52192	0.0:0.0:1.0:0.0	rs10090835;rs52809615;rs10090835	23	Q9BYG8	GSDMC_HUMAN	S	23	ENSP00000276708:P23S	ENSP00000276708:P23S	P	-	1	0	GSDMC	130858949	0.700000	0.27796	0.046000	0.18839	0.008000	0.06430	2.220000	0.42908	2.251000	0.74343	0.491000	0.48974	CCT	G|0.973;A|0.027	0.027	strong		0.403	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
OR51S1	119692	hgsc.bcm.edu	37	11	4870269	4870269	+	Missense_Mutation	SNP	A	A	T	rs12417164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4870269A>T	ENST00000322101.2	-	1	245	c.170T>A	c.(169-171)aTt>aAt	p.I57N	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	57			I -> N (in dbSNP:rs12417164).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTGCAGGGCAATGATCCAGAG	0.567													A|||	715	0.142772	0.0666	0.1297	5008	,	,		20054	0.0308		0.1998	False		,,,				2504	0.3119				p.I57N		Atlas-SNP	.											.	OR51S1	83	.	0			c.T170A						PASS	.	A	ASN/ILE	395,4007	195.7+/-220.2	18,359,1824	112.0	89.0	97.0		170	4.8	0.9	11	dbSNP_120	97	1666,6930	307.4+/-308.4	173,1320,2805	yes	missense	OR51S1	NM_001004758.1	149	191,1679,4629	TT,TA,AA		19.3811,8.9732,15.8563	probably-damaging	57/324	4870269	2061,10937	2201	4298	6499	SO:0001583	missense	119692	exon1			AGGGCAATGATCC	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.170T>A	11.37:g.4870269A>T	ENSP00000322754:p.Ile57Asn	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	296	146	0.493243	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	240	0.10989010989010989	29	0.05894308943089431	50	0.13812154696132597	20	0.03496503496503497	141	0.18601583113456466	A	14.01	2.407778	0.42715	0.089732	0.193811	ENSG00000176922	ENST00000322101	T	0.08720	3.06	4.85	4.85	0.62838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	D	0.000848	T	0.00073	0.0002	H	0.94582	3.555	0.54753	P	1.4999999999987246E-5	D	0.76494	0.999	D	0.75020	0.985	T	0.05954	-1.0854	9	0.87932	D	0	-10.3652	13.4094	0.60933	1.0:0.0:0.0:0.0	rs12417164;rs12417164	57	Q8NGJ8	O51S1_HUMAN	N	57	ENSP00000322754:I57N	ENSP00000322754:I57N	I	-	2	0	OR51S1	4826845	0.357000	0.24938	0.924000	0.36721	0.236000	0.25371	4.873000	0.63057	2.031000	0.59945	0.460000	0.39030	ATT	A|0.842;T|0.158	0.158	strong		0.567	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
PADI4	23569	hgsc.bcm.edu	37	1	17660499	17660499	+	Missense_Mutation	SNP	G	G	C	rs874881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17660499G>C	ENST00000375448.4	+	3	361	c.335G>C	c.(334-336)gGg>gCg	p.G112A	PADI4_ENST00000375453.1_Missense_Mutation_p.G112A|AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	112			G -> A (does not catalytic activity; dbSNP:rs874881). {ECO:0000269|PubMed:10488123, ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	TACCTCACCGGGGTGGGTAAG	0.512													G|||	2614	0.521965	0.4607	0.5403	5008	,	,		17445	0.5585		0.5537	False		,,,				2504	0.5215				p.G112A		Atlas-SNP	.											.	PADI4	70	.	0			c.G335C						PASS	.	G	ALA/GLY	2143,2263	580.0+/-385.0	511,1121,571	92.0	76.0	81.0		335	4.7	0.9	1	dbSNP_86	81	4738,3862	609.5+/-395.5	1295,2148,857	yes	missense	PADI4	NM_012387.2	60	1806,3269,1428	CC,CG,GG		44.907,48.6382,47.0936	benign	112/664	17660499	6881,6125	2203	4300	6503	SO:0001583	missense	23569	exon3			TCACCGGGGTGGG	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.335G>C	1.37:g.17660499G>C	ENSP00000364597:p.Gly112Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	37	CCDS180.1	1110	0.5082417582417582	204	0.4146341463414634	185	0.511049723756906	315	0.5506993006993007	406	0.5356200527704486	g	10.46	1.355764	0.24598	0.486382	0.55093	ENSG00000159339	ENST00000375453;ENST00000358829;ENST00000375448	T;T	0.07800	3.16;3.16	4.74	4.74	0.60224	Cupredoxin (1);	0.155963	0.43747	D	0.000534	T	0.00012	0.0000	L	0.42744	1.35	0.31107	P	0.710423	P;P	0.38597	0.639;0.639	B;B	0.34824	0.19;0.19	T	0.20638	-1.0269	9	0.11182	T	0.66	-16.8479	13.6003	0.62015	0.0:0.0:1.0:0.0	rs874881;rs3737763;rs17852289;rs52816356;rs874881	112;112	A8K392;Q9UM07	.;PADI4_HUMAN	A	112	ENSP00000364602:G112A;ENSP00000364597:G112A	ENSP00000351690:G112A	G	+	2	0	PADI4	17533086	0.810000	0.29049	0.885000	0.34714	0.983000	0.72400	3.212000	0.51145	2.339000	0.79563	0.557000	0.71058	GGG	G|0.467;C|0.533	0.533	strong		0.512	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
CENPQ	55166	hgsc.bcm.edu	37	6	49439805	49439805	+	Missense_Mutation	SNP	G	G	A	rs4267943	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:49439805G>A	ENST00000335783.3	+	4	281	c.187G>A	c.(187-189)Gga>Aga	p.G63R		NM_018132.3	NP_060602.2	Q7L2Z9	CENPQ_HUMAN	centromere protein Q	63			G -> R (in dbSNP:rs4267943).		CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(4)|ovary(2)|prostate(1)	11	Lung NSC(77;0.0128)					CCTAAAACACGGAAAGACAGC	0.378													G|||	1674	0.334265	0.4191	0.2305	5008	,	,		14881	0.2103		0.332	False		,,,				2504	0.4233				p.G63R		Atlas-SNP	.											.	CENPQ	23	.	0			c.G187A						PASS	.	G	ARG/GLY	1724,2682	516.8+/-369.3	331,1062,810	121.0	124.0	123.0		187	-6.5	0.0	6	dbSNP_111	123	3158,5442	479.9+/-370.2	584,1990,1726	yes	missense	CENPQ	NM_018132.3	125	915,3052,2536	AA,AG,GG		36.7209,39.1285,37.5365	benign	63/269	49439805	4882,8124	2203	4300	6503	SO:0001583	missense	55166	exon4			AAACACGGAAAGA	AK001407	CCDS4925.1	6p12.3	2013-11-05	2006-06-15	2006-06-15	ENSG00000031691	ENSG00000031691			21347	protein-coding gene	gene with protein product		611506	"""chromosome 6 open reading frame 139"""	C6orf139		16622420, 16622419	Standard	NM_018132		Approved	FLJ10545, CENP-Q	uc003ozh.1	Q7L2Z9	OTTHUMG00000014815	ENST00000335783.3:c.187G>A	6.37:g.49439805G>A	ENSP00000337289:p.Gly63Arg	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_018132	A8KAF1|Q6IN61|Q9NVS5	Missense_Mutation	SNP	ENST00000335783.3	37	CCDS4925.1	690	0.3159340659340659	205	0.4166666666666667	89	0.24585635359116023	112	0.1958041958041958	284	0.37467018469656993	G	4.427	0.079036	0.08533	0.391285	0.367209	ENSG00000031691	ENST00000335783;ENST00000371200	T	0.29142	1.58	4.44	-6.48	0.01896	.	0.695143	0.13866	N	0.357330	T	0.04363	0.0120	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.33954	-0.9848	9	0.87932	D	0	-0.2957	9.5128	0.39087	0.5713:0.0989:0.3297:0.0	rs4267943;rs17186767;rs56644708;rs58394552;rs4267943	63	Q7L2Z9	CENPQ_HUMAN	R	63	ENSP00000337289:G63R	ENSP00000337289:G63R	G	+	1	0	CENPQ	49547764	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.832000	0.04400	-1.779000	0.01280	-1.345000	0.01243	GGA	G|0.653;A|0.347	0.347	strong		0.378	CENPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040855.2	NM_018132	
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs41307110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:22102293C>T	ENST00000542433.1	-	1	803	c.706G>A	c.(706-708)Gct>Act	p.A236T		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		CTCCCATCAGCGGTGCGTATC	0.542																																					p.A236T		Atlas-SNP	.											OR10G2,NS,carcinoma,0,1	OR10G2	35	1	0			c.G706A						scavenged	.						39.0	41.0	40.0					14																	22102293		2179	4246	6425	SO:0001583	missense	26534	exon1			CATCAGCGGTGCG		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.706G>A	14.37:g.22102293C>T	ENSP00000445383:p.Ala236Thr	Somatic	424	0	0		WXS	Illumina HiSeq	Phase_I	223	21	0.0941704	NM_001005466	B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	37	CCDS32047.1	347	0.15888278388278387	55	0.11178861788617886	40	0.11049723756906077	137	0.2395104895104895	115	0.1517150395778364	c	2.861	-0.236170	0.05944	.	.	ENSG00000255582	ENST00000542433	T	0.00174	8.62	3.92	2.07	0.26955	GPCR, rhodopsin-like superfamily (1);	0.146443	0.31134	N	0.008190	T	0.00012	0.0000	L	0.41236	1.265	0.80722	P	0.0	B	0.29378	0.243	B	0.25506	0.061	T	0.41305	-0.9516	9	0.41790	T	0.15	-5.7356	13.1106	0.59270	0.0:0.9007:0.0:0.0993	rs41307110;rs41428047;rs61753936;rs41307110	236	Q8NGC3	O10G2_HUMAN	T	236	ENSP00000445383:A236T	ENSP00000445383:A236T	A	-	1	0	OR10G2	21172133	0.000000	0.05858	0.819000	0.32651	0.005000	0.04900	-0.178000	0.09782	0.045000	0.15804	-2.571000	0.00171	GCT	C|0.750;T|0.250	0.250	weak		0.542	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
ERAP1	51752	hgsc.bcm.edu	37	5	96129535	96129535	+	Missense_Mutation	SNP	T	T	C	rs2287987	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:96129535T>C	ENST00000443439.2	-	6	1111	c.1045A>G	c.(1045-1047)Atg>Gtg	p.M349V	ERAP1_ENST00000296754.3_Missense_Mutation_p.M349V	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	349			M -> V (in dbSNP:rs2287987). {ECO:0000269|PubMed:11481040, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:9628581}.		angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		GCCACAGTCATTGTGATGCCA	0.398													T|||	526	0.105032	0.0658	0.1268	5008	,	,		18025	0.0575		0.2247	False		,,,				2504	0.0685				p.M349V		Atlas-SNP	.											.	ERAP1	59	.	0			c.A1045G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	462,3944	217.8+/-236.0	21,420,1762	62.0	56.0	58.0		1045,1045,1045	4.6	1.0	5	dbSNP_100	58	1822,6778	326.6+/-317.4	202,1418,2680	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	21,21,21	223,1838,4442	CC,CT,TT		21.186,10.4857,17.5611	benign,benign,benign	349/942,349/942,349/949	96129535	2284,10722	2203	4300	6503	SO:0001583	missense	51752	exon6			CAGTCATTGTGAT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.1045A>G	5.37:g.96129535T>C	ENSP00000406304:p.Met349Val	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	191	191	1	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	285	0.1304945054945055	27	0.054878048780487805	48	0.13259668508287292	40	0.06993006993006994	170	0.22427440633245382	T	10.79	1.450308	0.26074	0.104857	0.21186	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.02498	4.27;4.27	5.82	4.64	0.57946	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.125717	0.64402	D	0.000001	T	0.00012	0.0000	N	0.17872	0.535	0.28558	P	0.9112808	B;B;B	0.28208	0.002;0.157;0.203	B;B;B	0.33121	0.001;0.158;0.098	T	0.54990	-0.8210	9	0.23302	T	0.38	.	10.4738	0.44652	0.272:0.0:0.0:0.728	rs2287987;rs17404429;rs2287987	349;349;349	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	V	349	ENSP00000296754:M349V;ENSP00000406304:M349V	ENSP00000296754:M349V	M	-	1	0	ERAP1	96155291	0.989000	0.36119	0.998000	0.56505	0.827000	0.46813	2.125000	0.42016	1.010000	0.39314	0.533000	0.62120	ATG	T|0.857;C|0.143	0.143	strong		0.398	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
ACOX2	8309	hgsc.bcm.edu	37	3	58512375	58512375	+	Silent	SNP	T	T	C	rs1127743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58512375T>C	ENST00000302819.5	-	10	1455	c.1164A>G	c.(1162-1164)gcA>gcG	p.A388A	ACOX2_ENST00000459701.2_Silent_p.A374A	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	388					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		CCGTGCTCAGTGCGTGGAGCT	0.592													T|||	818	0.163339	0.3041	0.1066	5008	,	,		19469	0.2282		0.0427	False		,,,				2504	0.0706				p.A388A		Atlas-SNP	.											.	ACOX2	53	.	0			c.A1164G						PASS	.	T		1245,3161	427.6+/-341.6	171,903,1129	72.0	67.0	69.0		1164	-2.9	0.6	3	dbSNP_86	69	444,8156	134.1+/-191.5	10,424,3866	yes	coding-synonymous	ACOX2	NM_003500.3		181,1327,4995	CC,CT,TT		5.1628,28.2569,12.9863		388/682	58512375	1689,11317	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon10			GCTCAGTGCGTGG	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.1164A>G	3.37:g.58512375T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	167	74	0.443114	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			T|0.826;G|0.008	.	strong		0.592	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
MYH7B	57644	hgsc.bcm.edu	37	20	33581955	33581955	+	Silent	SNP	G	G	A	rs2425012	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:33581955G>A	ENST00000262873.7	+	25	2669	c.2577G>A	c.(2575-2577)gcG>gcA	p.A859A		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	817						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CTAGGGATGCGCTGTTCACCA	0.557													G|||	1987	0.396765	0.171	0.621	5008	,	,		20265	0.5546		0.4861	False		,,,				2504	0.2883				p.A859A		Atlas-SNP	.											.	MYH7B	145	.	0			c.G2577A						PASS	.	G		922,3332		107,708,1312	91.0	97.0	95.0		2577	0.1	1.0	20	dbSNP_100	95	3623,4885		760,2103,1391	no	coding-synonymous	MYH7B	NM_020884.3		867,2811,2703	AA,AG,GG		42.5835,21.6737,35.6135		859/1984	33581955	4545,8217	2127	4254	6381	SO:0001819	synonymous_variant	57644	exon27			GGATGCGCTGTTC	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.2577G>A	20.37:g.33581955G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	163	75	0.460123	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			G|0.585;A|0.415	0.415	strong		0.557	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
B4GALT5	9334	hgsc.bcm.edu	37	20	48259034	48259034	+	Silent	SNP	A	A	G	rs2235855	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:48259034A>G	ENST00000371711.4	-	5	764	c.577T>C	c.(577-579)Ttg>Ctg	p.L193L		NM_004776.3	NP_004767.1	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5	193					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			GCAAACTGCAAGCGCTGGCGC	0.502													G|||	2237	0.446685	0.267	0.4395	5008	,	,		22474	0.3948		0.5547	False		,,,				2504	0.637				p.L193L		Atlas-SNP	.											.	B4GALT5	40	.	0			c.T577C						PASS	.	G		1455,2951	681.3+/-404.0	251,953,999	93.0	88.0	90.0		577	5.8	1.0	20	dbSNP_98	90	4750,3850	542.0+/-384.1	1315,2120,865	no	coding-synonymous	B4GALT5	NM_004776.3		1566,3073,1864	GG,GA,AA		44.7674,33.0232,47.7087		193/389	48259034	6205,6801	2203	4300	6503	SO:0001819	synonymous_variant	9334	exon5			ACTGCAAGCGCTG	AB004550	CCDS13420.1	20q13.1-q13.2	2013-02-19			ENSG00000158470	ENSG00000158470		"""Beta 4-glycosyltransferases"""	928	protein-coding gene	gene with protein product	"""beta4-GalT IV"""	604016				9597550, 9435216	Standard	NM_004776		Approved	beta4GalT-V	uc002xuu.4	O43286	OTTHUMG00000033086	ENST00000371711.4:c.577T>C	20.37:g.48259034A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	86	48	0.55814	NM_004776	E1P625|Q2M394|Q9UJQ8	Silent	SNP	ENST00000371711.4	37	CCDS13420.1																																																																																			A|0.541;G|0.459	0.459	strong		0.502	B4GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080543.3	NM_004776	
QSOX1	5768	hgsc.bcm.edu	37	1	180159657	180159657	+	Silent	SNP	C	C	T	rs1050154	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180159657C>T	ENST00000367602.3	+	10	1304	c.1230C>T	c.(1228-1230)ctC>ctT	p.L410L	QSOX1_ENST00000367600.5_Silent_p.L410L			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	410	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						TGTGGGTCCTCTTCCACTTCT	0.597													C|||	629	0.125599	0.0832	0.1556	5008	,	,		18905	0.0734		0.1581	False		,,,				2504	0.182				p.L410L		Atlas-SNP	.											.	QSOX1	79	.	0			c.C1230T						PASS	.	C	,	390,4016		27,336,1840	134.0	120.0	125.0		1230,1230	-1.8	1.0	1	dbSNP_86	125	1353,7247		121,1111,3068	no	coding-synonymous,coding-synonymous	QSOX1	NM_001004128.2,NM_002826.4	,	148,1447,4908	TT,TC,CC		15.7326,8.8516,13.4015	,	410/605,410/748	180159657	1743,11263	2203	4300	6503	SO:0001819	synonymous_variant	5768	exon10			GGTCCTCTTCCAC	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1230C>T	1.37:g.180159657C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	169	93	0.550296	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Silent	SNP	ENST00000367602.3	37	CCDS1337.1																																																																																			C|0.864;T|0.136	0.136	strong		0.597	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
HECW1	23072	hgsc.bcm.edu	37	7	43506059	43506059	+	Silent	SNP	A	A	G	rs2304329	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43506059A>G	ENST00000395891.2	+	15	3410	c.2805A>G	c.(2803-2805)gaA>gaG	p.E935E	HECW1_ENST00000453890.1_Silent_p.E901E	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	935					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TAAGGAGAGAAGGGTCACTTT	0.473													A|||	2781	0.555312	0.5098	0.5533	5008	,	,		16370	0.3879		0.6352	False		,,,				2504	0.7086				p.E935E		Atlas-SNP	.											.	HECW1	540	.	0			c.A2805G						PASS	.	A		2032,1862		531,970,446	110.0	103.0	105.0		2805	-0.8	1.0	7	dbSNP_100	105	5225,3043		1676,1873,585	no	coding-synonymous	HECW1	NM_015052.3		2207,2843,1031	GG,GA,AA		36.8045,47.8172,40.3305		935/1607	43506059	7257,4905	1947	4134	6081	SO:0001819	synonymous_variant	23072	exon15			GAGAGAAGGGTCA	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.2805A>G	7.37:g.43506059A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			A|0.416;G|0.584	0.584	strong		0.473	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
HEPACAM	220296	hgsc.bcm.edu	37	11	124793716	124793716	+	Silent	SNP	G	G	A	rs10790716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124793716G>A	ENST00000298251.4	-	3	1023	c.618C>T	c.(616-618)cgC>cgT	p.R206R		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		CCATGAGCACGCGGGTGATGG	0.587													G|||	681	0.135982	0.1074	0.1513	5008	,	,		20947	0.0714		0.2624	False		,,,				2504	0.1002				p.R206R		Atlas-SNP	.											.	HEPACAM	64	.	0			c.C618T						PASS	.	G		602,3800	264.4+/-266.0	42,518,1641	112.0	86.0	95.0		618	-11.3	0.1	11	dbSNP_120	95	2292,6306	385.3+/-341.4	319,1654,2326	no	coding-synonymous	HEPACAM	NM_152722.4		361,2172,3967	AA,AG,GG		26.6574,13.6756,22.2615		206/417	124793716	2894,10106	2201	4299	6500	SO:0001819	synonymous_variant	220296	exon3			GAGCACGCGGGTG	AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26361	protein-coding gene	gene with protein product	"""glial cell adhesion molecule"""	611642	"""hepatocyte cell adhesion molecule"""			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.618C>T	11.37:g.124793716G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	37	0.37	NM_152722		Silent	SNP	ENST00000298251.4	37	CCDS8456.1																																																																																			G|0.814;A|0.186	0.186	strong		0.587	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722	
FN3KRP	79672	hgsc.bcm.edu	37	17	80684843	80684843	+	Silent	SNP	G	G	A	rs146293327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80684843G>A	ENST00000269373.6	+	6	799	c.726G>A	c.(724-726)tcG>tcA	p.S242S	RP11-388C12.5_ENST00000570919.1_lincRNA|FN3KRP_ENST00000535965.1_Silent_p.S192S	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	242							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			ACGGCCACTCGGAATATGAGC	0.557													G|||	2	0.000399361	0.0008	0.0	5008	,	,		16728	0.0		0.001	False		,,,				2504	0.0				p.S242S		Atlas-SNP	.											FN3KRP,right_upper_lobe,carcinoma,+1,2	FN3KRP	31	2	0			c.G726A						PASS	.	G		0,4406		0,0,2203	61.0	64.0	63.0		726	-8.8	0.9	17	dbSNP_134	63	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	FN3KRP	NM_024619.3		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		242/310	80684843	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	79672	exon6			CCACTCGGAATAT	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.726G>A	17.37:g.80684843G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_024619	Q969F4|Q9H0U7	Silent	SNP	ENST00000269373.6	37	CCDS11817.1																																																																																			G|0.999;A|0.001	0.001	strong		0.557	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619	
CEP192	55125	hgsc.bcm.edu	37	18	13068109	13068109	+	Missense_Mutation	SNP	G	G	A	rs7228940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:13068109G>A	ENST00000325971.8	+	21	4436	c.2843G>A	c.(2842-2844)cGc>cAc	p.R948H	CEP192_ENST00000506447.1_Missense_Mutation_p.R1544H|CEP192_ENST00000430049.2_Missense_Mutation_p.R1069H			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	948			R -> H (in dbSNP:rs7228940). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15498874}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GTAGCCTGGCGCTGTTTCACG	0.458													G|||	937	0.187101	0.1354	0.121	5008	,	,		18333	0.2986		0.1262	False		,,,				2504	0.2515				p.R1544H		Atlas-SNP	.											.	CEP192	340	.	0			c.G4631A						PASS	.	G	HIS/ARG	503,3903	231.7+/-245.5	25,453,1725	100.0	107.0	105.0		4631	4.5	1.0	18	dbSNP_116	105	1095,7505	226.1+/-261.9	84,927,3289	yes	missense	CEP192	NM_032142.3	29	109,1380,5014	AA,AG,GG		12.7326,11.4163,12.2866	probably-damaging	1544/2538	13068109	1598,11408	2203	4300	6503	SO:0001583	missense	55125	exon23			CCTGGCGCTGTTT	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.2843G>A	18.37:g.13068109G>A	ENSP00000317156:p.Arg948His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		365	0.1671245421245421	79	0.16056910569105692	45	0.12430939226519337	150	0.26223776223776224	91	0.12005277044854881	G	17.38	3.375821	0.61735	0.114163	0.127326	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.80653	-1.4;-1.4;-1.4	5.37	4.48	0.54585	.	0.137803	0.47852	D	0.000215	T	0.00039	0.0001	L	0.47016	1.485	0.20703	P	0.999861796	D;P	0.53151	0.958;0.923	B;P	0.45558	0.404;0.485	T	0.00583	-1.1659	9	0.87932	D	0	-1.8284	16.2157	0.82217	0.0:0.1333:0.8667:0.0	rs7228940;rs52809530;rs58206101;rs7228940	1069;1544	C9JT09;E9PF99	.;.	H	1544;948;948;1069	ENSP00000427550:R1544H;ENSP00000317156:R948H;ENSP00000389190:R1069H	ENSP00000317156:R948H	R	+	2	0	CEP192	13058109	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	3.990000	0.56965	1.357000	0.45904	0.655000	0.94253	CGC	G|0.852;A|0.148	0.148	strong		0.458	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
OR2T2	401992	hgsc.bcm.edu	37	1	248616749	248616749	+	Silent	SNP	C	C	G	rs151176830		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248616749C>G	ENST00000342927.3	+	1	673	c.651C>G	c.(649-651)gtC>gtG	p.V217V		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCATCTCTGTCTCCTACACGC	0.542																																					p.V217V		Atlas-SNP	.											OR2T2,NS,carcinoma,0,1	OR2T2	73	1	0			c.C651G						scavenged	.						255.0	173.0	201.0					1																	248616749		2189	4267	6456	SO:0001819	synonymous_variant	401992	exon1			CTCTGTCTCCTAC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.651C>G	1.37:g.248616749C>G		Somatic	535	11	0.0205607		WXS	Illumina HiSeq	Phase_I	315	11	0.0349206	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			C|0.500;G|0.500	0.500	strong		0.542	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
ANKUB1	389161	hgsc.bcm.edu	37	3	149488442	149488442	+	Silent	SNP	A	A	G	rs7630153	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:149488442A>G	ENST00000383050.3	-	4	927	c.471T>C	c.(469-471)gaT>gaC	p.D157D	ANKUB1_ENST00000446160.1_Silent_p.D157D|ANKUB1_ENST00000462519.2_Silent_p.D157D			A6NFN9	ANKUB_HUMAN	ankyrin repeat and ubiquitin domain containing 1	157										breast(1)|kidney(1)|lung(1)|skin(1)	4						CATCCCAGACATCCAAGCGAA	0.433													G|||	1645	0.328474	0.6452	0.3573	5008	,	,		18502	0.0248		0.2922	False		,,,				2504	0.2301				p.D157D		Atlas-SNP	.											ANKUB1,NS,carcinoma,-2,1	ANKUB1	27	1	0			c.T471C						PASS	.	G		815,569		246,323,123	164.0	146.0	151.0		471	-3.3	1.0	3	dbSNP_116	151	965,2217		152,661,778	no	coding-synonymous	ANKUB1	NM_001144960.1		398,984,901	GG,GA,AA		30.3268,41.1127,38.9838		157/545	149488442	1780,2786	692	1591	2283	SO:0001819	synonymous_variant	389161	exon4			CCAGACATCCAAG	AK027233		3q25.1	2013-01-11	2011-05-10	2011-05-10	ENSG00000206199	ENSG00000206199		"""Ankyrin repeat domain containing"""	29642	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 16"""	C3orf16			Standard	NM_001144960		Approved		uc003exl.3	A6NFN9	OTTHUMG00000159615	ENST00000383050.3:c.471T>C	3.37:g.149488442A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	41	0.621212	NM_001144960	B4E2N8	Silent	SNP	ENST00000383050.3	37																																																																																				A|0.690;G|0.310	0.310	strong		0.433	ANKUB1-201	KNOWN	basic	protein_coding	protein_coding		NM_001144960	
DZIP1	22873	hgsc.bcm.edu	37	13	96239805	96239805	+	Missense_Mutation	SNP	G	G	A	rs11070136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:96239805G>A	ENST00000376829.2	-	20	3057	c.2206C>T	c.(2206-2208)Ccc>Tcc	p.P736S	DZIP1_ENST00000347108.3_Missense_Mutation_p.P736S|DZIP1_ENST00000361156.3_Missense_Mutation_p.P717S|DZIP1_ENST00000361396.2_Missense_Mutation_p.P717S	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	736			P -> S (in dbSNP:rs11070136). {ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.P717S(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			GCGGGCTTGGGAGAATCATCA	0.542													G|||	1346	0.26877	0.3207	0.2248	5008	,	,		19768	0.1558		0.3618	False		,,,				2504	0.2505				p.P736S		Atlas-SNP	.											DZIP1,NS,carcinoma,0,1	DZIP1	195	1	1	Substitution - Missense(1)	stomach(1)	c.C2206T						scavenged	.	G	SER/PRO,SER/PRO	1323,3083	444.7+/-347.4	190,943,1070	161.0	140.0	147.0		2149,2206	2.6	1.0	13	dbSNP_120	147	2927,5673	456.3+/-364.0	498,1931,1871	yes	missense,missense	DZIP1	NM_014934.3,NM_198968.2	74,74	688,2874,2941	AA,AG,GG		34.0349,30.0272,32.6772	benign,benign	717/849,736/868	96239805	4250,8756	2203	4300	6503	SO:0001583	missense	22873	exon20			GCTTGGGAGAATC	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"""Zinc fingers, C2H2-type"""	20908	protein-coding gene	gene with protein product		608671	"""DAZ interacting protein 1"""				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2206C>T	13.37:g.96239805G>A	ENSP00000366025:p.Pro736Ser	Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_198968	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	37	CCDS9478.1	619	0.2834249084249084	160	0.3252032520325203	103	0.2845303867403315	80	0.13986013986013987	276	0.3641160949868074	G	0.013	-1.609554	0.00842	0.300272	0.340349	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	5.34	2.63	0.31362	.	0.434403	0.26116	N	0.026258	T	0.00012	0.0000	L	0.43923	1.385	0.50467	P	1.2900000000004574E-4	B;B	0.12013	0.005;0.003	B;B	0.12837	0.008;0.004	T	0.44081	-0.9351	9	0.17369	T	0.5	-9.4551	4.96	0.14061	0.2465:0.1776:0.5759:0.0	rs11070136;rs52809482;rs56641201;rs60157457;rs11070136	717;736	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	S	736;717;717;736	ENSP00000257312:P736S;ENSP00000355018:P717S;ENSP00000355175:P717S;ENSP00000366025:P736S	ENSP00000257312:P736S	P	-	1	0	DZIP1	95037806	0.995000	0.38212	0.968000	0.41197	0.094000	0.18550	0.739000	0.26173	1.244000	0.43870	0.650000	0.86243	CCC	G|0.704;A|0.296	0.296	strong		0.542	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
CHDH	55349	hgsc.bcm.edu	37	3	53855738	53855738	+	Silent	SNP	G	G	C	rs35064726	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:53855738G>C	ENST00000315251.6	-	5	1358	c.921C>G	c.(919-921)ctC>ctG	p.L307L		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	307					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	CGATGCCAGAGAGCATGAGCA	0.562													G|||	123	0.0245607	0.0023	0.0216	5008	,	,		19271	0.0		0.0527	False		,,,				2504	0.0532				p.L307L		Atlas-SNP	.											.	CHDH	34	.	0			c.C921G						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	142.0	126.0	131.0		921	-2.7	0.6	3	dbSNP_126	131	472,8128	138.7+/-195.5	17,438,3845	no	coding-synonymous	CHDH	NM_018397.4		17,488,5998	CC,CG,GG		5.4884,1.1348,4.0135		307/595	53855738	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon5			GCCAGAGAGCATG	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.921C>G	3.37:g.53855738G>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			G|0.958;C|0.042	0.042	strong		0.562	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
CCDC169	728591	hgsc.bcm.edu	37	13	36828237	36828237	+	Missense_Mutation	SNP	T	T	C	rs9546897	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:36828237T>C	ENST00000239859.7	-	5	390	c.359A>G	c.(358-360)aAg>aGg	p.K120R	CCDC169_ENST00000239860.6_Missense_Mutation_p.K20R|CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.K20R|SOHLH2_ENST00000554962.1_Missense_Mutation_p.K20R|CCDC169_ENST00000510088.1_Missense_Mutation_p.K18R|CCDC169_ENST00000379864.2_Missense_Mutation_p.K18R|CCDC169_ENST00000503173.1_Missense_Mutation_p.K120R|CCDC169_ENST00000379862.2_Missense_Mutation_p.K18R|CCDC169_ENST00000491049.2_Missense_Mutation_p.K18R			A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	120			K -> R (in dbSNP:rs9546897).							breast(1)|endometrium(1)	2						TTCAAGAGTCTTCTTTTCTTC	0.274													C|||	1882	0.375799	0.2231	0.4755	5008	,	,		15496	0.373		0.4712	False		,,,				2504	0.4162				p.K120R		Atlas-SNP	.											.	CCDC169	20	.	0			c.A359G						PASS	.						189.0	156.0	166.0					13																	36828237		692	1588	2280	SO:0001583	missense	728591	exon5			AGAGTCTTCTTTT		CCDS45027.1, CCDS45028.1, CCDS45029.1, CCDS53863.1, CCDS55897.1	13q13.3	2011-08-09	2011-08-09	2011-08-09	ENSG00000242715	ENSG00000242715			34361	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 38"""	C13orf38			Standard	NM_001144981		Approved	RP11-251J8.1, LOC728591		A6NNP5	OTTHUMG00000016731	ENST00000239859.7:c.359A>G	13.37:g.36828237T>C	ENSP00000239859:p.Lys120Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	NM_001144981	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Missense_Mutation	SNP	ENST00000239859.7	37	CCDS45028.1	830	0.38003663003663	110	0.22357723577235772	166	0.4585635359116022	207	0.3618881118881119	347	0.4577836411609499	C	2.085	-0.409739	0.04799	.	.	ENSG00000120669;ENSG00000250709;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715	ENST00000554962;ENST00000511166;ENST00000491049;ENST00000503173;ENST00000239860;ENST00000379864;ENST00000510088;ENST00000379862;ENST00000239859	T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	4.78	3.05	0.35203	.	0.212888	0.31884	N	0.006914	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	2.9999999999752447E-6	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.0	T	0.45454	-0.9260	9	0.07175	T	0.84	-13.7239	6.8623	0.24074	0.0:0.633:0.0:0.367	rs9546897;rs52836889;rs56836767;rs9546897	120;20;18;20;120	A6NNP5-4;B7ZW49;A6NNP5-3;B4DX90;A6NNP5	.;.;.;.;CC169_HUMAN	R	20;20;18;120;20;18;18;18;120	ENSP00000451542:K20R;ENSP00000421868:K20R;ENSP00000425252:K18R;ENSP00000426174:K120R;ENSP00000239860:K20R;ENSP00000369193:K18R;ENSP00000427495:K18R;ENSP00000369191:K18R;ENSP00000239859:K120R	ENSP00000239859:K120R	K	-	2	0	CCDC169-SOHLH2;SOHLH2;CCDC169	35726237	0.999000	0.42202	0.995000	0.50966	0.967000	0.64934	0.877000	0.28106	0.333000	0.23563	-0.119000	0.15052	AAG	T|0.629;C|0.371	0.371	strong		0.274	CCDC169-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368255.1	NM_001144981	
IL33	90865	hgsc.bcm.edu	37	9	6253571	6253571	+	Silent	SNP	C	C	T	rs10975519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:6253571C>T	ENST00000381434.3	+	5	502	c.489C>T	c.(487-489)taC>taT	p.Y163Y	IL33_ENST00000417746.2_Silent_p.Y37Y|IL33_ENST00000456383.2_Silent_p.Y121Y	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	163					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)			breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		TACTGAGTTACTATGAGTCTC	0.373													C|||	2029	0.405152	0.4175	0.4524	5008	,	,		16658	0.4375		0.3231	False		,,,				2504	0.4059				p.Y163Y		Atlas-SNP	.											.	IL33	27	.	0			c.C489T						PASS	.	C	,,	1678,2728	511.2+/-367.7	313,1052,838	139.0	133.0	135.0		363,111,489	2.5	0.0	9	dbSNP_120	135	2602,5998	421.7+/-353.8	423,1756,2121	no	coding-synonymous,coding-synonymous,coding-synonymous	IL33	NM_001199640.1,NM_001199641.1,NM_033439.3	,,	736,2808,2959	TT,TC,CC		30.2558,38.0844,32.9079	,,	121/229,37/145,163/271	6253571	4280,8726	2203	4300	6503	SO:0001819	synonymous_variant	90865	exon6			GAGTTACTATGAG	AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.489C>T	9.37:g.6253571C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_033439	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Silent	SNP	ENST00000381434.3	37	CCDS6468.1																																																																																			C|0.633;T|0.367	0.367	strong		0.373	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439	
DNAH14	127602	hgsc.bcm.edu	37	1	225580093	225580093	+	Missense_Mutation	SNP	G	G	C	rs61738690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:225580093G>C	ENST00000445597.2	+	59	10101	c.10101G>C	c.(10099-10101)aaG>aaC	p.K3367N	DNAH14_ENST00000439375.2_Missense_Mutation_p.K4375N|DNAH14_ENST00000430092.1_Missense_Mutation_p.K4375N			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	3367					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CCACTGACAAGGATGAGAAGT	0.463													G|||	133	0.0265575	0.0015	0.0259	5008	,	,		21175	0.0208		0.0427	False		,,,				2504	0.0501				p.K4375N		Atlas-SNP	.											.	DNAH14	300	.	0			c.G13125C						PASS	.	G	ASN/LYS	12,1372		0,12,680	156.0	138.0	143.0		13125	-9.8	0.0	1	dbSNP_129	143	156,3026		1,154,1436	yes	missense	DNAH14	NM_001373.1	94	1,166,2116	CC,CG,GG		4.9026,0.8671,3.6794	benign	4375/4516	225580093	168,4398	692	1591	2283	SO:0001583	missense	127602	exon82			TGACAAGGATGAG	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.10101G>C	1.37:g.225580093G>C	ENSP00000409472:p.Lys3367Asn	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	184	80	0.434783	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		56|56	0.02564102564102564|0.02564102564102564	3|3	0.006097560975609756|0.006097560975609756	10|10	0.027624309392265192|0.027624309392265192	9|9	0.015734265734265736|0.015734265734265736	34|34	0.044854881266490766|0.044854881266490766	G|G	4.746|4.746	0.138681|0.138681	0.09083|0.09083	0.008671|0.008671	0.049026|0.049026	ENSG00000185842|ENSG00000185842	ENST00000428003|ENST00000445597;ENST00000430092;ENST00000439375	.|T;T;T	.|0.08720	.|3.06;3.06;3.06	4.92|4.92	-9.84|-9.84	0.00479|0.00479	.|.	.|.	.|.	.|.	.|.	T|T	0.00524|0.00524	0.0017|0.0017	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.13145	.|0.007	.|B	.|0.13407	.|0.009	T|T	0.43637|0.43637	-0.9379|-0.9379	5|9	.|0.46703	.|T	.|0.11	.|.	5.6053|5.6053	0.17377|0.17377	0.1138:0.094:0.4884:0.3038|0.1138:0.094:0.4884:0.3038	rs61738690|rs61738690	.|4375	.|Q0VDD8-4	.|.	R|N	79|3367;4375;4375	.|ENSP00000409472:K3367N;ENSP00000414402:K4375N;ENSP00000392061:K4375N	.|ENSP00000414402:K4375N	G|K	+|+	1|3	0|2	DNAH14|DNAH14	223646716|223646716	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-3.172000|-3.172000	0.00572|0.00572	-2.912000|-2.912000	0.00307|0.00307	-1.238000|-1.238000	0.01547|0.01547	GGA|AAG	G|0.969;C|0.031	0.031	strong		0.463	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
OR2T5	401993	hgsc.bcm.edu	37	1	248652049	248652049	+	Missense_Mutation	SNP	C	C	T	rs554643879		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248652049C>T	ENST00000366473.2	+	1	165	c.160C>T	c.(160-162)Cac>Tac	p.H54Y		NM_001004697.1	NP_001004697.1	Q6IEZ7	OR2T5_HUMAN	olfactory receptor, family 2, subfamily T, member 5	54						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(2)|pancreas(1)|skin(2)	9	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCTTCTGATACACTGTGACGC	0.478													.|||	1	0.000199681	0.0	0.0	5008	,	,		22734	0.0		0.001	False		,,,				2504	0.0				p.H54Y		Atlas-SNP	.											.	OR2T5	17	.	0			c.C160T						PASS	.						26.0	58.0	47.0					1																	248652049		2151	4276	6427	SO:0001583	missense	401993	exon1			CTGATACACTGTG	BK004465	CCDS31118.1	1q44	2012-08-09			ENSG00000203661	ENSG00000203661		"""GPCR / Class A : Olfactory receptors"""	15017	protein-coding gene	gene with protein product							Standard	NM_001004697		Approved		uc001iem.1	Q6IEZ7	OTTHUMG00000040481	ENST00000366473.2:c.160C>T	1.37:g.248652049C>T	ENSP00000355429:p.His54Tyr	Somatic	702	0	0		WXS	Illumina HiSeq	Phase_I	1045	302	0.288995	NM_001004697		Missense_Mutation	SNP	ENST00000366473.2	37	CCDS31118.1	.	.	.	.	.	.	.	.	.	.	c	0.003	-2.443662	0.00178	.	.	ENSG00000203661	ENST00000366473	T	0.02863	4.13	2.64	-5.28	0.02755	GPCR, rhodopsin-like superfamily (1);	0.834465	0.10259	N	0.696179	T	0.01353	0.0044	N	0.26092	0.79	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.49579	-0.8925	10	0.02654	T	1	.	0.9068	0.01286	0.1456:0.2245:0.233:0.3969	.	54	Q6IEZ7	OR2T5_HUMAN	Y	54	ENSP00000355429:H54Y	ENSP00000355429:H54Y	H	+	1	0	OR2T5	246718672	0.000000	0.05858	0.093000	0.20910	0.019000	0.09904	-3.180000	0.00569	-0.589000	0.05874	-0.506000	0.04501	CAC	.	.	none		0.478	OR2T5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097422.1	NM_001004697	
TNK2	10188	hgsc.bcm.edu	37	3	195594950	195594950	+	Missense_Mutation	SNP	G	G	A	rs56260729	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195594950G>A	ENST00000333602.6	-	12	2791	c.2174C>T	c.(2173-2175)cCg>cTg	p.P725L	TNK2_ENST00000392400.1_Missense_Mutation_p.P725L|TNK2_ENST00000428187.1_Missense_Mutation_p.P757L|TNK2_ENST00000381916.2_Missense_Mutation_p.P803L	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	725	Pro-rich.		P -> L (in dbSNP:rs56260729). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.	Missing (in Ref. 4; AAH08884). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	AGAGGGGGCCGGGGAGCCGGC	0.716													g|||	620	0.123802	0.0166	0.2349	5008	,	,		12164	0.0367		0.2366	False		,,,				2504	0.1636				p.P803L		Atlas-SNP	.											.	TNK2	246	.	0			c.C2408T						PASS	.		LEU/PRO,LEU/PRO	187,4111		7,173,1969	8.0	11.0	10.0		2408,2174	1.4	0.0	3	dbSNP_129	10	1796,6674		195,1406,2634	yes	missense,missense	TNK2	NM_001010938.1,NM_005781.4	98,98	202,1579,4603	AA,AG,GG		21.2043,4.3509,15.531	benign,benign	803/1087,725/1039	195594950	1983,10785	2149	4235	6384	SO:0001583	missense	10188	exon13			GGGGCCGGGGAGC	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"""activated Cdc42-associated kinase 1"""	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.2174C>T	3.37:g.195594950G>A	ENSP00000329425:p.Pro725Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	37	CCDS33928.1	275	0.1259157509157509	12	0.024390243902439025	63	0.17403314917127072	20	0.03496503496503497	180	0.23746701846965698	G	0.221	-1.028459	0.02045	0.043509	0.212043	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000416152;ENST00000428187;ENST00000392400	T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73	5.04	1.38	0.22167	.	0.708126	0.13524	N	0.381455	T	0.00012	0.0000	N	0.00583	-1.355	0.44123	P	0.0030970000000000164	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.43782	-0.9370	9	0.02654	T	1	.	8.5498	0.33444	0.788:0.0:0.212:0.0	rs56260729;rs61749507	725;803;757;250	Q07912;Q07912-3;C9J1X3;B3KXJ4	ACK1_HUMAN;.;.;.	L	725;803;292;757;725	ENSP00000329425:P725L;ENSP00000371341:P803L;ENSP00000398614:P292L;ENSP00000392546:P757L;ENSP00000376201:P725L	ENSP00000329425:P725L	P	-	2	0	TNK2	197079347	0.147000	0.22687	0.006000	0.13384	0.002000	0.02628	1.514000	0.35834	0.008000	0.14787	-1.292000	0.01352	CCG	G|0.858;A|0.142	0.142	strong		0.716	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
NLGN2	57555	hgsc.bcm.edu	37	17	7318935	7318935	+	Silent	SNP	C	C	T	rs12947017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7318935C>T	ENST00000302926.2	+	6	1216	c.1143C>T	c.(1141-1143)ggC>ggT	p.G381G	NLGN2_ENST00000575301.1_Silent_p.G381G	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	381					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				TGCTCATCGGCGTCAACCAGG	0.587													C|||	963	0.192292	0.1036	0.2464	5008	,	,		21553	0.1835		0.3827	False		,,,				2504	0.0869				p.G381G		Atlas-SNP	.											.	NLGN2	61	.	0			c.C1143T						PASS	.	C		663,3743	282.5+/-276.6	50,563,1590	204.0	159.0	175.0		1143	-10.8	0.0	17	dbSNP_121	175	3366,5234	499.1+/-374.9	642,2082,1576	no	coding-synonymous	NLGN2	NM_020795.2		692,2645,3166	TT,TC,CC		39.1395,15.0477,30.978		381/836	7318935	4029,8977	2203	4300	6503	SO:0001819	synonymous_variant	57555	exon6			CATCGGCGTCAAC	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.1143C>T	17.37:g.7318935C>T		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	223	221	0.991031	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	37	CCDS11103.1																																																																																			C|0.720;T|0.280	0.280	strong		0.587	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
ANKRD12	23253	hgsc.bcm.edu	37	18	9258537	9258537	+	Missense_Mutation	SNP	T	T	C	rs3744822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:9258537T>C	ENST00000262126.4	+	9	5512	c.5272T>C	c.(5272-5274)Tca>Cca	p.S1758P	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Missense_Mutation_p.S1735P|ANKRD12_ENST00000383440.2_Missense_Mutation_p.S1735P	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1758			S -> P (in dbSNP:rs3744822).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						TACACTATTATCAGAAAAAGA	0.368													T|||	311	0.0621006	0.0991	0.049	5008	,	,		22075	0.0446		0.0706	False		,,,				2504	0.0307				p.S1758P		Atlas-SNP	.											.	ANKRD12	167	.	0			c.T5272C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER	440,3966	211.8+/-231.9	22,396,1785	86.0	81.0	83.0		5203,5203,5272	-10.7	0.0	18	dbSNP_107	83	653,7947	163.9+/-216.4	27,599,3674	yes	missense,missense,missense	ANKRD12	NM_001083625.2,NM_001204056.1,NM_015208.4	74,74,74	49,995,5459	CC,CT,TT		7.593,9.9864,8.4038	benign,benign,benign	1735/2040,1735/2040,1758/2063	9258537	1093,11913	2203	4300	6503	SO:0001583	missense	23253	exon9			CTATTATCAGAAA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5272T>C	18.37:g.9258537T>C	ENSP00000262126:p.Ser1758Pro	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	154	0.07051282051282051	48	0.0975609756097561	19	0.052486187845303865	29	0.050699300699300696	58	0.07651715039577836	T	11.73	1.726145	0.30593	0.099864	0.07593	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.46451	0.87;0.87	5.33	-10.7	0.00240	.	1.241720	0.05335	N	0.529159	T	0.00384	0.0012	N	0.04508	-0.205	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.06110	-1.0845	9	0.30078	T	0.28	1.1165	3.9872	0.09521	0.0871:0.1045:0.2638:0.5446	rs3744822;rs57612578;rs3744822	1735;1758	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	P	1735;1758	ENSP00000372932:S1735P;ENSP00000262126:S1758P	ENSP00000262126:S1758P	S	+	1	0	ANKRD12	9248537	0.000000	0.05858	0.001000	0.08648	0.998000	0.95712	-1.099000	0.03343	-1.779000	0.01280	0.533000	0.62120	TCA	T|0.923;C|0.077	0.077	strong		0.368	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
CDCA2	157313	hgsc.bcm.edu	37	8	25364960	25364960	+	Silent	SNP	A	A	G	rs6990278	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:25364960A>G	ENST00000330560.3	+	15	3255	c.2778A>G	c.(2776-2778)acA>acG	p.T926T	CDCA2_ENST00000380665.3_Silent_p.T911T|CDCA2_ENST00000521098.2_3'UTR	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	926					mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		CAATATGTACATTTGACAGCA	0.428													A|||	964	0.192492	0.1687	0.1931	5008	,	,		19672	0.2351		0.2147	False		,,,				2504	0.1575				p.T926T		Atlas-SNP	.											.	CDCA2	78	.	0			c.A2778G						PASS	.	A		769,3637	311.9+/-292.3	73,623,1507	184.0	196.0	192.0		2778	-4.6	0.0	8	dbSNP_116	192	1729,6871	313.5+/-311.4	178,1373,2749	no	coding-synonymous	CDCA2	NM_152562.2		251,1996,4256	GG,GA,AA		20.1047,17.4535,19.2065		926/1024	25364960	2498,10508	2203	4300	6503	SO:0001819	synonymous_variant	157313	exon15			ATGTACATTTGAC	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 81"""					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.2778A>G	8.37:g.25364960A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Silent	SNP	ENST00000330560.3	37	CCDS6049.1																																																																																			A|0.800;G|0.200	0.200	strong		0.428	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562	
MON1B	22879	hgsc.bcm.edu	37	16	77228971	77228971	+	Silent	SNP	C	C	T	rs2232506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:77228971C>T	ENST00000248248.3	+	4	1565	c.1215C>T	c.(1213-1215)gtC>gtT	p.V405V	MON1B_ENST00000439557.2_Silent_p.V296V|MON1B_ENST00000320859.6_Intron|MON1B_ENST00000545553.1_Silent_p.V259V	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	405										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						TGCAGGCTGTCGGGGCGCCGG	0.637													C|||	657	0.13119	0.0076	0.1052	5008	,	,		16646	0.2857		0.1123	False		,,,				2504	0.1769				p.V405V		Atlas-SNP	.											.	MON1B	55	.	0			c.C1215T						PASS	.	C		104,4292	77.8+/-116.1	1,102,2095	21.0	19.0	20.0		1215	1.6	1.0	16	dbSNP_98	20	827,7773	174.6+/-224.8	54,719,3527	no	coding-synonymous	MON1B	NM_014940.2		55,821,5622	TT,TC,CC		9.6163,2.3658,7.1637		405/548	77228971	931,12065	2198	4300	6498	SO:0001819	synonymous_variant	22879	exon4			GGCTGTCGGGGCG	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"""MON1 homolog B (yeast)"""			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.1215C>T	16.37:g.77228971C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_014940	B4DDZ0|O94949	Silent	SNP	ENST00000248248.3	37	CCDS10925.1																																																																																			C|0.912;T|0.088	0.088	strong		0.637	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940	
MUC4	4585	hgsc.bcm.edu	37	3	195506410	195506410	+	Missense_Mutation	SNP	G	G	A	rs79037473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506410G>A	ENST00000463781.3	-	2	12500	c.12041C>T	c.(12040-12042)gCc>gTc	p.A4014V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A4014V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4014I(1)|p.A4014V(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGAGGGGTGGCGTGACCTGT	0.602													.|||	6	0.00119808	0.0038	0.0014	5008	,	,		10366	0.0		0.0	False		,,,				2504	0.0				p.A4014V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	stomach(2)	c.C12041T						scavenged	.						17.0	14.0	15.0					3																	195506410		653	1470	2123	SO:0001583	missense	4585	exon2			GGGGTGGCGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12041C>T	3.37:g.195506410G>A	ENSP00000417498:p.Ala4014Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	39	25	0.641026	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.670	0.492161	0.12702	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.48836	1.09;0.8	.	.	.	.	0.000000	0.25514	U	0.030158	T	0.32164	0.0820	N	0.14661	0.345	0.09310	N	1	D	0.55385	0.971	P	0.49752	0.621	T	0.13575	-1.0504	8	.	.	.	.	6.5141	0.22239	2.0E-4:0.0:0.9998:0.0	.	3886	E7ESK3	.	V	4014	ENSP00000417498:A4014V;ENSP00000420243:A4014V	.	A	-	2	0	MUC4	196991189	0.207000	0.23482	0.003000	0.11579	0.017000	0.09413	1.130000	0.31393	0.419000	0.25927	0.064000	0.15345	GCC	.	.	weak		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DYRK1A	1859	hgsc.bcm.edu	37	21	38884589	38884589	+	Missense_Mutation	SNP	C	C	T	rs201554841		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:38884589C>T	ENST00000398960.2	+	11	2122	c.2047C>T	c.(2047-2049)Cgc>Tgc	p.R683C	DYRK1A_ENST00000339659.4_Missense_Mutation_p.R674C|DYRK1A_ENST00000338785.3_3'UTR|DYRK1A_ENST00000455387.2_Missense_Mutation_p.R455C	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	683					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CTACCAGAATCGCCCAGTGGC	0.517																																					p.R683C	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											DYRK1A,NS,malignant_melanoma,0,1	DYRK1A	85	1	0			c.C2047T						PASS	.						142.0	128.0	133.0					21																	38884589		2203	4300	6503	SO:0001583	missense	1859	exon11			CAGAATCGCCCAG	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.2047C>T	21.37:g.38884589C>T	ENSP00000381932:p.Arg683Cys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.272816	0.59649	.	.	ENSG00000157540	ENST00000339659;ENST00000398960;ENST00000455387	T;T;T	0.58652	0.32;0.35;0.88	5.73	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.45597	0.1350	N	0.24115	0.695	0.80722	D	1	B;B	0.17465	0.013;0.022	B;B	0.08055	0.001;0.003	T	0.40869	-0.9540	10	0.87932	D	0	.	14.9122	0.70767	0.0:0.9311:0.0:0.0689	.	683;674	Q13627;Q13627-2	DYR1A_HUMAN;.	C	674;683;455	ENSP00000340373:R674C;ENSP00000381932:R683C;ENSP00000407854:R455C	ENSP00000340373:R674C	R	+	1	0	DYRK1A	37806459	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.398000	0.79919	1.433000	0.47394	-0.150000	0.13652	CGC	C|0.999;T|0.001	0.001	weak		0.517	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	
NUP210	23225	hgsc.bcm.edu	37	3	13399786	13399786	+	Missense_Mutation	SNP	G	G	A	rs6795271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:13399786G>A	ENST00000254508.5	-	16	2346	c.2264C>T	c.(2263-2265)gCg>gTg	p.A755V		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	755			A -> V (in dbSNP:rs6795271).		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					GTAGACAGGCGCGAGGGTGAG	0.652													G|||	908	0.18131	0.2269	0.2104	5008	,	,		19901	0.0139		0.325	False		,,,				2504	0.1237				p.A755V		Atlas-SNP	.											.	NUP210	182	.	0			c.C2264T						PASS	.	G	VAL/ALA	1061,3345	386.8+/-326.2	130,801,1272	84.0	83.0	83.0		2264	-1.6	0.0	3	dbSNP_116	83	2973,5627	462.0+/-365.6	512,1949,1839	yes	missense	NUP210	NM_024923.2	64	642,2750,3111	AA,AG,GG		34.5698,24.0808,31.0165	benign	755/1888	13399786	4034,8972	2203	4300	6503	SO:0001583	missense	23225	exon16			ACAGGCGCGAGGG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.2264C>T	3.37:g.13399786G>A	ENSP00000254508:p.Ala755Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	213	114	0.535211	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	458	0.2097069597069597	118	0.23983739837398374	93	0.2569060773480663	10	0.017482517482517484	237	0.31266490765171506	G	2.929	-0.221390	0.06061	0.240808	0.345698	ENSG00000132182	ENST00000254508	T	0.16597	2.33	5.05	-1.59	0.08453	.	0.621103	0.17582	N	0.169078	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.04013	0.001;0.001	T	0.42832	-0.9428	9	0.02654	T	1	.	10.2615	0.43430	0.5834:0.0:0.4166:0.0	rs6795271;rs57991742;rs6795271	755;755	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	V	755	ENSP00000254508:A755V	ENSP00000254508:A755V	A	-	2	0	NUP210	13374786	0.505000	0.26131	0.011000	0.14972	0.064000	0.16182	1.087000	0.30865	-0.784000	0.04528	0.609000	0.83330	GCG	G|0.734;A|0.266	0.266	strong		0.652	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
CNTN3	5067	hgsc.bcm.edu	37	3	74413676	74413676	+	Silent	SNP	T	T	C	rs6549590	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:74413676T>C	ENST00000263665.6	-	9	1182	c.1155A>G	c.(1153-1155)caA>caG	p.Q385Q		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	385	Ig-like C2-type 4.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CTGCTATGCATTGGAACATGC	0.358													T|||	2254	0.45008	0.3147	0.5173	5008	,	,		17968	0.4653		0.5586	False		,,,				2504	0.4581				p.Q385Q		Atlas-SNP	.											.	CNTN3	174	.	0			c.A1155G						PASS	.	T		1454,2952	469.8+/-355.6	236,982,985	200.0	179.0	186.0		1155	0.1	1.0	3	dbSNP_116	186	4690,3910	605.8+/-395.0	1290,2110,900	no	coding-synonymous	CNTN3	NM_020872.1		1526,3092,1885	CC,CT,TT		45.4651,33.0005,47.2397		385/1029	74413676	6144,6862	2203	4300	6503	SO:0001819	synonymous_variant	5067	exon9			TATGCATTGGAAC	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1155A>G	3.37:g.74413676T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_020872	B9EK50|Q9H039	Silent	SNP	ENST00000263665.6	37	CCDS33790.1																																																																																			T|0.536;C|0.464	0.464	strong		0.358	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
FCGR3A	2214	hgsc.bcm.edu	37	1	161514542	161514542	+	Missense_Mutation	SNP	A	A	C	rs396991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161514542A>C	ENST00000436743.1	-	5	680	c.526T>G	c.(526-528)Ttt>Gtt	p.F176V	FCGR3A_ENST00000540048.1_Missense_Mutation_p.F176V|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'Flank|FCGR3A_ENST00000443193.1_Missense_Mutation_p.F211V|FCGR3A_ENST00000367969.3_Missense_Mutation_p.F212V	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	176	Ig-like C2-type 2.		F -> V (shows a higher binding capacity of IgG1, IgG3 and IgG4; dbSNP:rs396991). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7700021, ECO:0000269|PubMed:9242542, ECO:0000269|PubMed:9276722, ECO:0000269|Ref.3}.		Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TTACTCCCAAAAAGCCCCCTG	0.478																																					p.F212V		Atlas-SNP	.											.	FCGR3A	38	.	0			c.T634G	GRCh37	CM992625	FCGR3A	M	rs396991	PASS	.	C	VAL/PHE,VAL/PHE,VAL/PHE,VAL/PHE,VAL/PHE	1150,3256		243,664,1296	74.0	75.0	75.0		523,526,526,631,634	-0.1	0.0	1	dbSNP_80	75	2412,6188		505,1402,2393	no	missense,missense,missense,missense,missense	FCGR3A	NM_001127596.1,NM_001127595.1,NM_001127593.1,NM_001127592.1,NM_000569.6	50,50,50,50,50	748,2066,3689	CC,CA,AA		28.0465,26.1008,27.3874	benign,benign,benign,benign,benign	175/254,176/255,176/255,211/290,212/291	161514542	3562,9444	2203	4300	6503	SO:0001583	missense	2214	exon4			TCCCAAAAAGCCC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.526T>G	1.37:g.161514542A>C	ENSP00000416607:p.Phe176Val	Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	339	336	0.99115	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	535|535	0.24496336996336995|0.24496336996336995	106|106	0.21544715447154472|0.21544715447154472	71|71	0.19613259668508287|0.19613259668508287	154|154	0.2692307692307692|0.2692307692307692	204|204	0.2691292875989446|0.2691292875989446	N|N	8.451|8.451	0.853189|0.853189	0.17106|0.17106	0.261008|0.261008	0.280465|0.280465	ENSG00000203747|ENSG00000203747	ENST00000426740|ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048	.|T;T;T;T;T	.|0.11604	.|2.76;2.76;2.76;2.76;2.76	5.03|5.03	-0.103|-0.103	0.13609|0.13609	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.285436|0.285436	0.25027|0.25027	N|N	0.033707|0.033707	T|T	0.00998|0.00998	0.0033|0.0033	N|N	0.04355|0.04355	-0.22|-0.22	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.46925|0.46925	-0.9156|-0.9156	5|9	.|0.44086	.|T	.|0.13	.|.	0.3561|0.3561	0.00357|0.00357	0.2836:0.1629:0.1472:0.4063|0.2836:0.1629:0.1472:0.4063	rs396991;rs2229097;rs3171040;rs4151086;rs17857127;rs61228128|rs396991;rs2229097;rs3171040;rs4151086;rs17857127;rs61228128	.|176;211	.|P08637;E9PG94	.|FCG3A_HUMAN;.	L|V	192|212;211;176;176;176	.|ENSP00000356946:F212V;ENSP00000392047:F211V;ENSP00000416607:F176V;ENSP00000356944:F176V;ENSP00000444971:F176V	.|ENSP00000356944:F176V	F|F	-|-	3|1	2|0	FCGR3A|FCGR3A	159781166|159781166	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.208000|-0.208000	0.09371|0.09371	-0.464000|-0.464000	0.06963|0.06963	-5.115000|-5.115000	0.00001|0.00001	TTT|TTT	A|0.681;C|0.319	0.319	strong		0.478	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
RHOBTB3	22836	hgsc.bcm.edu	37	5	95084131	95084131	+	Silent	SNP	G	G	A	rs34896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:95084131G>A	ENST00000379982.3	+	4	1018	c.510G>A	c.(508-510)gcG>gcA	p.A170A		NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	170	Rho-like.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		AACTAGGAGCGACCTATCTTG	0.418													G|||	2269	0.453075	0.2784	0.3343	5008	,	,		15976	0.6905		0.4294	False		,,,				2504	0.5532				p.A170A		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.G510A						PASS	.	G		1347,3059	448.1+/-348.6	202,943,1058	116.0	109.0	111.0		510	-12.1	0.4	5	dbSNP_76	111	3574,5026	518.5+/-379.3	731,2112,1457	no	coding-synonymous	RHOBTB3	NM_014899.3		933,3055,2515	AA,AG,GG		41.5581,30.5719,37.8364		170/612	95084131	4921,8085	2203	4300	6503	SO:0001819	synonymous_variant	22836	exon4			AGGAGCGACCTAT	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"""BTB/POZ domain containing"""	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.510G>A	5.37:g.95084131G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_014899	A0PJA4|A8K1W9|Q8IW06	Silent	SNP	ENST00000379982.3	37	CCDS4077.1																																																																																			A|0.416;C|0.001	0.416	strong		0.418	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
SNX19	399979	hgsc.bcm.edu	37	11	130776524	130776524	+	Missense_Mutation	SNP	T	T	C	rs4414223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130776524T>C	ENST00000265909.4	-	6	2827	c.2258A>G	c.(2257-2259)aAt>aGt	p.N753S	SNX19_ENST00000533318.1_5'UTR|SNX19_ENST00000545537.1_5'UTR|SNX19_ENST00000539184.1_Missense_Mutation_p.N196S|SNX19_ENST00000533214.1_Missense_Mutation_p.N753S|SNX19_ENST00000528555.1_Missense_Mutation_p.N133S|SNX19_ENST00000534726.1_5'UTR|SNX19_ENST00000530356.1_Missense_Mutation_p.N133S	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	753			N -> S (in dbSNP:rs4414223). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9039502, ECO:0000269|Ref.1}.		protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TCTTACCACATTGCCTTCCTG	0.418													T|||	3321	0.663139	0.5537	0.6916	5008	,	,		20237	0.6468		0.6372	False		,,,				2504	0.8344				p.N753S		Atlas-SNP	.											.	SNX19	84	.	0			c.A2258G						PASS	.	T	SER/ASN	2508,1894	627.8+/-395.0	722,1064,415	103.0	90.0	95.0		2258	0.5	0.0	11	dbSNP_111	95	5696,2898	670.9+/-402.8	1885,1926,486	yes	missense	SNX19	NM_014758.2	46	2607,2990,901	CC,CT,TT		33.7212,43.0259,36.8729	benign	753/993	130776524	8204,4792	2201	4297	6498	SO:0001583	missense	399979	exon6			ACCACATTGCCTT	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.2258A>G	11.37:g.130776524T>C	ENSP00000265909:p.Asn753Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	1357	0.6213369963369964	267	0.5426829268292683	240	0.6629834254143646	362	0.6328671328671329	488	0.6437994722955145	T	0.288	-0.981589	0.02197	0.569741	0.662788	ENSG00000120451	ENST00000265909;ENST00000528555;ENST00000530356;ENST00000539184;ENST00000533214	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.6	0.523	0.17060	.	0.984852	0.08313	N	0.965024	T	0.00012	0.0000	N	0.16098	0.37	0.50813	P	1.100000000000545E-4	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.44513	-0.9323	9	0.07175	T	0.84	-1.0623	6.2822	0.21013	0.0:0.3467:0.2417:0.4117	rs4414223;rs17852967;rs52819866;rs58727162;rs4414223	196;753;753	F5H5D1;E9PKB9;Q92543	.;.;SNX19_HUMAN	S	753;133;133;196;753	ENSP00000265909:N753S;ENSP00000435122:N133S;ENSP00000432307:N133S;ENSP00000443480:N196S;ENSP00000435390:N753S	ENSP00000265909:N753S	N	-	2	0	SNX19	130281734	0.001000	0.12720	0.001000	0.08648	0.625000	0.37756	-0.119000	0.10676	-0.154000	0.11118	0.533000	0.62120	AAT	T|0.378;C|0.622	0.622	strong		0.418	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
TTC27	55622	hgsc.bcm.edu	37	2	32983526	32983526	+	Silent	SNP	C	C	T	rs2273665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:32983526C>T	ENST00000317907.4	+	13	1851	c.1620C>T	c.(1618-1620)aaC>aaT	p.N540N		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	540								p.N540N(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						ATCTTCGGAACAAGGAGTTTC	0.527													C|||	1467	0.292931	0.1536	0.3718	5008	,	,		17491	0.3671		0.4125	False		,,,				2504	0.226				p.N540N		Atlas-SNP	.											TTC27,NS,carcinoma,0,1	TTC27	71	1	1	Substitution - coding silent(1)	stomach(1)	c.C1620T						PASS	.	C	,	923,3483	351.3+/-311.2	88,747,1368	100.0	92.0	94.0		1470,1620	5.9	0.7	2	dbSNP_100	94	3528,5072	514.7+/-378.4	732,2064,1504	no	coding-synonymous,coding-synonymous	TTC27	NM_001193509.1,NM_017735.4	,	820,2811,2872	TT,TC,CC		41.0233,20.9487,34.2227	,	490/794,540/844	32983526	4451,8555	2203	4300	6503	SO:0001819	synonymous_variant	55622	exon13			TCGGAACAAGGAG	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"""Tetratricopeptide (TTC) repeat domain containing"""	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1620C>T	2.37:g.32983526C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Silent	SNP	ENST00000317907.4	37	CCDS33176.1																																																																																			C|0.676;N|0.000	.	strong		0.527	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	
CIITA	4261	hgsc.bcm.edu	37	16	11016045	11016045	+	Silent	SNP	C	C	T	rs2229322	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11016045C>T	ENST00000324288.8	+	17	3304	c.3171C>T	c.(3169-3171)tgC>tgT	p.C1057C	CIITA_ENST00000381835.5_Silent_p.C473C	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	1057					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)	p.C1057C(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						ACTGCATCTGCGACGTGGGAG	0.612			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								C|||	525	0.104832	0.0787	0.1081	5008	,	,		17922	0.1865		0.0994	False		,,,				2504	0.0593				p.C1057C		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	CIITA,NS,carcinoma,0,1	CIITA	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C3171T						PASS	.	C		342,4052	179.7+/-208.2	8,326,1863	150.0	143.0	145.0		3171	-6.7	0.3	16	dbSNP_98	145	932,7668	205.1+/-247.6	49,834,3417	no	coding-synonymous	CIITA	NM_000246.3		57,1160,5280	TT,TC,CC		10.8372,7.7833,9.8045		1057/1131	11016045	1274,11720	2197	4300	6497	SO:0001819	synonymous_variant	4261	exon17			CATCTGCGACGTG	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.3171C>T	16.37:g.11016045C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			C|0.893;T|0.107	0.107	strong		0.612	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
ZNF354A	6940	hgsc.bcm.edu	37	5	178139379	178139379	+	Silent	SNP	C	C	G	rs201342253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178139379C>G	ENST00000335815.2	-	5	1697	c.1500G>C	c.(1498-1500)ggG>ggC	p.G500G		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	500					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		TGAATGTTTTCCCACACTCGT	0.393													C|||	14	0.00279553	0.0008	0.0029	5008	,	,		20195	0.0		0.0089	False		,,,				2504	0.002				p.G500G		Atlas-SNP	.											.	ZNF354A	74	.	0			c.G1500C						PASS	.						122.0	119.0	120.0					5																	178139379		2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			TGTTTTCCCACAC	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.1500G>C	5.37:g.178139379C>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	126	7	0.0555556	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			C|0.999;G|0.001	0.001	weak		0.393	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
OBSCN	84033	hgsc.bcm.edu	37	1	228475848	228475848	+	Missense_Mutation	SNP	G	G	A	rs437129	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228475848G>A	ENST00000422127.1	+	37	9942	c.9898G>A	c.(9898-9900)Gca>Aca	p.A3300T	OBSCN_ENST00000284548.11_Missense_Mutation_p.A3300T|OBSCN_ENST00000570156.2_Missense_Mutation_p.A3729T|OBSCN_ENST00000366707.4_Missense_Mutation_p.A419T|OBSCN_ENST00000359599.6_Missense_Mutation_p.A2147T|OBSCN_ENST00000366709.4_Missense_Mutation_p.A419T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3300	Ig-like 33.		A -> T (in dbSNP:rs437129). {ECO:0000269|PubMed:11448995}.		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTGAGCAAGGCAGCCCCTGT	0.617													G|||	1516	0.302716	0.4153	0.3242	5008	,	,		20091	0.247		0.2932	False		,,,				2504	0.2025				p.A3729T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G11185A						PASS	.	G	THR/ALA,THR/ALA	1321,2779		209,903,938	95.0	100.0	98.0		9898,9898	5.0	1.0	1	dbSNP_80	98	2490,5884		384,1722,2081	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	58,58	593,2625,3019	AA,AG,GG		29.7349,32.2195,30.5515	benign,benign	3300/7969,3300/6621	228475848	3811,8663	2050	4187	6237	SO:0001583	missense	84033	exon42			AGCAAGGCAGCCC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9898G>A	1.37:g.228475848G>A	ENSP00000409493:p.Ala3300Thr	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	222	93	0.418919	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	645	0.29532967032967034	194	0.3943089430894309	106	0.292817679558011	133	0.23251748251748253	212	0.2796833773087071	G	21.9	4.212602	0.79240	0.322195	0.297349	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	4.99	4.99	0.66335	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.774326	0.12172	N	0.492955	T	0.00012	0.0000	M	0.73217	2.22	0.46823	P	7.859999999999534E-4	P;D	0.54772	0.947;0.968	P;P	0.59288	0.855;0.637	T	0.37150	-0.9718	9	0.20519	T	0.43	.	10.7007	0.45926	0.0:0.1412:0.7127:0.1461	rs437129	3300;3300	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	T	3300;3300;419;419;2147	ENSP00000284548:A3300T;ENSP00000409493:A3300T;ENSP00000355668:A419T;ENSP00000355670:A419T;ENSP00000352613:A2147T	ENSP00000284548:A3300T	A	+	1	0	OBSCN	226542471	0.000000	0.05858	0.957000	0.39632	0.808000	0.45660	-0.084000	0.11268	2.605000	0.88082	0.561000	0.74099	GCA	G|0.702;A|0.298	0.298	strong		0.617	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ZNF638	27332	hgsc.bcm.edu	37	2	71633389	71633389	+	Silent	SNP	C	C	T	rs6714975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71633389C>T	ENST00000409544.1	+	19	3762	c.3132C>T	c.(3130-3132)aaC>aaT	p.N1044N	ZNF638_ENST00000409407.1_5'Flank|ZNF638_ENST00000264447.4_Silent_p.N1044N|ZNF638_ENST00000355812.3_Silent_p.N1044N	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1044					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GTAATAGAAACAAGGTAACAA	0.353													C|||	2127	0.42472	0.2201	0.6225	5008	,	,		18856	0.2927		0.5527	False		,,,				2504	0.5654				p.N1044N		Atlas-SNP	.											.	ZNF638	179	.	0			c.C3132T						PASS	.	C	,	1193,3211	414.6+/-336.9	160,873,1169	118.0	107.0	111.0		3132,3132	3.6	1.0	2	dbSNP_116	111	4982,3618	625.1+/-397.7	1437,2108,755	yes	coding-synonymous,coding-synonymous	ZNF638	NM_001014972.1,NM_014497.3	,	1597,2981,1924	TT,TC,CC		42.0698,27.089,47.4854	,	1044/1979,1044/1979	71633389	6175,6829	2202	4300	6502	SO:0001819	synonymous_variant	27332	exon19			TAGAAACAAGGTA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3132C>T	2.37:g.71633389C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	133	47	0.353383	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	37	CCDS1917.1																																																																																			C|0.545;T|0.455	0.455	strong		0.353	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
LOXL4	84171	hgsc.bcm.edu	37	10	100017453	100017453	+	Missense_Mutation	SNP	T	T	G	rs1983864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:100017453T>G	ENST00000260702.3	-	8	1364	c.1214A>C	c.(1213-1215)gAt>gCt	p.D405A	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	405	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.		D -> A (in dbSNP:rs1983864). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GACAGCAGCATCATTCTCATG	0.597													T|||	1814	0.36222	0.0575	0.5231	5008	,	,		21368	0.6081		0.341	False		,,,				2504	0.4284				p.D405A		Atlas-SNP	.											.	LOXL4	60	.	0			c.A1214C						PASS	.	T	ALA/ASP	462,3944	221.3+/-238.5	35,392,1776	166.0	136.0	146.0		1214	5.6	1.0	10	dbSNP_92	146	2808,5792	443.7+/-360.5	448,1912,1940	yes	missense	LOXL4	NM_032211.6	126	483,2304,3716	GG,GT,TT		32.6512,10.4857,25.1422	probably-damaging	405/757	100017453	3270,9736	2203	4300	6503	SO:0001583	missense	84171	exon8			GCAGCATCATTCT	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1214A>C	10.37:g.100017453T>G	ENSP00000260702:p.Asp405Ala	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	37	CCDS7473.1	795	0.364010989010989	38	0.07723577235772358	158	0.43646408839779005	335	0.5856643356643356	264	0.3482849604221636	T	25.5	4.648533	0.87958	0.104857	0.326512	ENSG00000138131	ENST00000260702	T	0.53423	0.62	5.55	5.55	0.83447	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.82433	2.59	0.09310	P	0.9999999102462	D	0.89917	1.0	D	0.97110	1.0	T	0.51317	-0.8721	9	0.87932	D	0	.	15.6918	0.77461	0.0:0.0:0.0:1.0	rs1983864;rs3750600;rs17851004;rs61640819;rs1983864	405	Q96JB6	LOXL4_HUMAN	A	405	ENSP00000260702:D405A	ENSP00000260702:D405A	D	-	2	0	LOXL4	100007443	1.000000	0.71417	0.978000	0.43139	0.956000	0.61745	6.298000	0.72763	2.104000	0.64026	0.454000	0.30748	GAT	T|0.706;G|0.294	0.294	strong		0.597	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
KCNH5	27133	hgsc.bcm.edu	37	14	63175013	63175013	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63175013C>T	ENST00000322893.7	-	11	2448	c.2180G>A	c.(2179-2181)gGt>gAt	p.G727D	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	727					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CTCAGGGTCACCCTGTGTTGA	0.557																																					p.G727D		Atlas-SNP	.											KCNH5,NS,carcinoma,0,1	KCNH5	320	1	0			c.G2180A						PASS	.						115.0	107.0	110.0					14																	63175013		2203	4300	6503	SO:0001583	missense	27133	exon11			GGGTCACCCTGTG	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2180G>A	14.37:g.63175013C>T	ENSP00000321427:p.Gly727Asp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	161	68	0.42236	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	0.402	-0.917791	0.02396	.	.	ENSG00000140015	ENST00000322893	D	0.98849	-5.18	5.52	2.7	0.31948	.	0.410001	0.25494	N	0.030283	D	0.95191	0.8441	L	0.34521	1.04	0.34981	D	0.754079	B	0.10296	0.003	B	0.17098	0.017	D	0.91085	0.4902	10	0.19147	T	0.46	.	6.6545	0.22981	0.3021:0.5555:0.0:0.1423	.	727	Q8NCM2	KCNH5_HUMAN	D	727	ENSP00000321427:G727D	ENSP00000321427:G727D	G	-	2	0	KCNH5	62244766	0.000000	0.05858	0.065000	0.19835	0.001000	0.01503	0.059000	0.14322	0.297000	0.22615	-0.181000	0.13052	GGT	.	.	none		0.557	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
PLIN4	729359	hgsc.bcm.edu	37	19	4511575	4511575	+	Silent	SNP	C	C	G	rs62115185	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4511575C>G	ENST00000301286.3	-	3	2354	c.2355G>C	c.(2353-2355)gtG>gtC	p.V785V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	785	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CCCCACTGCACACAGCATCCT	0.597													C|||	1336	0.266773	0.1407	0.2334	5008	,	,		27617	0.3204		0.2684	False		,,,				2504	0.4039				p.V785V		Atlas-SNP	.											PLIN4_ENST00000301286,caecum,carcinoma,0,2	PLIN4	191	2	0			c.G2355C						scavenged	.						108.0	114.0	112.0					19																	4511575		2146	4239	6385	SO:0001819	synonymous_variant	729359	exon3			ACTGCACACAGCA	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2355G>C	19.37:g.4511575C>G		Somatic	420	7	0.0166667		WXS	Illumina HiSeq	Phase_I	305	42	0.137705	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			C|0.978;G|0.022	0.022	strong		0.597	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
RBM5	10181	hgsc.bcm.edu	37	3	50144951	50144951	+	Silent	SNP	T	T	C	rs1061474	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50144951T>C	ENST00000347869.3	+	12	1165	c.990T>C	c.(988-990)gcT>gcC	p.A330A	RBM5_ENST00000441812.2_3'UTR	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	330	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCGTCAGCGCTTTCTCTGTAG	0.488													C|||	3743	0.747404	0.7458	0.6945	5008	,	,		16513	0.881		0.5686	False		,,,				2504	0.8333				p.A330A		Atlas-SNP	.											.	RBM5	76	.	0			c.T990C						PASS	.	C		3175,1231	424.2+/-340.4	1144,887,172	169.0	147.0	154.0		990	5.0	1.0	3	dbSNP_86	154	4901,3699	529.7+/-381.6	1368,2165,767	no	coding-synonymous	RBM5	NM_005778.2		2512,3052,939	CC,CT,TT		43.0116,27.9392,37.9056		330/816	50144951	8076,4930	2203	4300	6503	SO:0001819	synonymous_variant	10181	exon12			CAGCGCTTTCTCT	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.990T>C	3.37:g.50144951T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	222	107	0.481982	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	37	CCDS2810.1																																																																																			T|0.327;C|0.673	0.673	strong		0.488	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
ERICH5	203111	hgsc.bcm.edu	37	8	99101976	99101976	+	Missense_Mutation	SNP	A	A	C	rs35368005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:99101976A>C	ENST00000318528.3	+	2	1090	c.731A>C	c.(730-732)cAa>cCa	p.Q244P	C8orf47_ENST00000545282.1_Intron	NM_173549.2	NP_775820.2	Q6P6B1	ERIC5_HUMAN		244	Glu-rich.		Q -> P (in dbSNP:rs35368005).							kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(2)	13	Breast(36;2.31e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			GAAGAGCAGCAACTTCAGGCA	0.443													A|||	57	0.0113818	0.0015	0.0274	5008	,	,		21301	0.0		0.0328	False		,,,				2504	0.0031				p.Q244P		Atlas-SNP	.											.	C8orf47	34	.	0			c.A731C						PASS	.	A	,PRO/GLN	13,4393	19.1+/-41.9	0,13,2190	42.0	42.0	42.0		,731	2.4	0.0	8	dbSNP_126	42	141,8459	67.0+/-129.4	3,135,4162	yes	intron,missense	C8orf47	NM_001170806.1,NM_173549.2	,76	3,148,6352	CC,CA,AA		1.6395,0.2951,1.1841	,probably-damaging	,244/375	99101976	154,12852	2203	4300	6503	SO:0001583	missense	203111	exon2			AGCAGCAACTTCA																												ENST00000318528.3:c.731A>C	8.37:g.99101976A>C	ENSP00000315614:p.Gln244Pro	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_173549	G3V1K4|Q8N1L8	Missense_Mutation	SNP	ENST00000318528.3	37	CCDS34929.1	34	0.015567765567765568	0	0.0	9	0.024861878453038673	0	0.0	25	0.032981530343007916	A	16.08	3.022370	0.54683	0.002951	0.016395	ENSG00000177459	ENST00000318528	T	0.53423	0.62	4.93	2.41	0.29592	.	0.551444	0.16660	N	0.204836	T	0.18425	0.0442	L	0.55834	1.745	0.09310	N	1	B	0.24882	0.113	B	0.21917	0.037	T	0.20773	-1.0265	10	0.59425	D	0.04	-17.2464	9.0696	0.36484	0.6359:0.3641:0.0:0.0	rs35368005	244	Q6P6B1	CH047_HUMAN	P	244	ENSP00000315614:Q244P	ENSP00000315614:Q244P	Q	+	2	0	C8orf47	99171152	0.004000	0.15560	0.001000	0.08648	0.981000	0.71138	1.848000	0.39309	0.403000	0.25479	0.533000	0.62120	CAA	A|0.987;C|0.013	0.013	strong		0.443	C8orf47-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380465.1		
C8G	733	hgsc.bcm.edu	37	9	139839904	139839904	+	Silent	SNP	T	T	G	rs2071006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139839904T>G	ENST00000224181.3	+	1	192	c.132T>G	c.(130-132)gcT>gcG	p.A44A	FBXW5_ENST00000483559.1_5'Flank|FBXW5_ENST00000325285.3_5'Flank	NM_000606.2	NP_000597.2	P07360	CO8G_HUMAN	complement component 8, gamma polypeptide	44					complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	retinol binding (GO:0019841)			NS(1)|prostate(1)|skin(1)	3	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.88e-06)|Epithelial(140;0.000107)		ATTTTGATGCTCAGCAGGTAG	0.627											OREG0019623	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2843	0.567692	0.5832	0.4179	5008	,	,		16109	0.6954		0.5417	False		,,,				2504	0.5481				p.A44A		Atlas-SNP	.											.	C8G	9	.	0			c.T132G						PASS	.	T		2475,1885		742,991,447	13.0	14.0	14.0		132	-3.5	0.0	9	dbSNP_96	14	4603,3957		1299,2005,976	no	coding-synonymous	C8G	NM_000606.2		2041,2996,1423	GG,GT,TT		46.2266,43.2339,45.2167		44/203	139839904	7078,5842	2180	4280	6460	SO:0001819	synonymous_variant	733	exon1			TGATGCTCAGCAG	X06465	CCDS7017.1	9q	2011-11-15			ENSG00000176919	ENSG00000176919		"""Complement system"", ""Lipocalins"""	1354	protein-coding gene	gene with protein product		120930					Standard	NM_000606		Approved		uc004cka.2	P07360	OTTHUMG00000020955	ENST00000224181.3:c.132T>G	9.37:g.139839904T>G		Somatic	91	0	0	1651	WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_000606	Q14CT8|Q14CU0|Q5SQ07	Silent	SNP	ENST00000224181.3	37	CCDS7017.1																																																																																			T|0.438;G|0.562	0.562	strong		0.627	C8G-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055178.1		
LHX9	56956	hgsc.bcm.edu	37	1	197896728	197896728	+	Silent	SNP	T	T	C	rs12046958	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197896728T>C	ENST00000367387.4	+	4	1166	c.741T>C	c.(739-741)aaT>aaC	p.N247N	LHX9_ENST00000367391.1_Silent_p.N238N|LHX9_ENST00000561173.1_Silent_p.N253N|LHX9_ENST00000367390.3_Silent_p.N238N|LHX9_ENST00000337020.2_Silent_p.N247N	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	247					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.N247N(1)		endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						CAGGTTGTAATGAGAATGAGG	0.493													T|||	1342	0.267971	0.1959	0.3545	5008	,	,		18498	0.4067		0.1859	False		,,,				2504	0.2454				p.N247N		Atlas-SNP	.											LHX9,NS,carcinoma,0,1	LHX9	144	1	1	Substitution - coding silent(1)	stomach(1)	c.T741C						PASS	.	T	,	819,3587	326.7+/-299.7	80,659,1464	286.0	288.0	288.0		714,741	-3.6	1.0	1	dbSNP_120	288	1625,6975	301.4+/-305.4	151,1323,2826	no	coding-synonymous,coding-synonymous	LHX9	NM_001014434.1,NM_020204.2	,	231,1982,4290	CC,CT,TT		18.8953,18.5883,18.7913	,	238/389,247/398	197896728	2444,10562	2203	4300	6503	SO:0001819	synonymous_variant	56956	exon4			TTGTAATGAGAAT	AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"""Homeoboxes / LIM class"""	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.741T>C	1.37:g.197896728T>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	NM_020204	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Silent	SNP	ENST00000367387.4	37	CCDS1393.1																																																																																			T|0.773;C|0.227	0.227	strong		0.493	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204	
RAI1	10743	hgsc.bcm.edu	37	17	17697102	17697102	+	Silent	SNP	G	G	A	rs398124422|rs34083643|rs398124421|rs587780431		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17697102G>A	ENST00000353383.1	+	3	1309	c.840G>A	c.(838-840)caG>caA	p.Q280Q	RAI1_ENST00000261641.6_Silent_p.Q280Q	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	280	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)	p.Q280fs*84(1)		breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ACcagcagcagcagcagcagc	0.627																																					p.Q280Q		Atlas-SNP	.											RAI1,colon,carcinoma,0,3	RAI1	121	3	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.G840A						PASS	.						20.0	25.0	23.0					17																	17697102		2038	4033	6071	SO:0001819	synonymous_variant	10743	exon3			GCAGCAGCAGCAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.840G>A	17.37:g.17697102G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	8	0.0941176	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	none		0.627	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
SDC1	6382	hgsc.bcm.edu	37	2	20403949	20403949	+	Silent	SNP	C	C	T	rs2230924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:20403949C>T	ENST00000254351.4	-	3	496	c.252G>A	c.(250-252)gaG>gaA	p.E84E	SDC1_ENST00000403076.1_Silent_p.E84E|SDC1_ENST00000381150.1_Silent_p.E84E|SDC1_ENST00000482879.1_5'UTR	NM_002997.4	NP_002988	P18827	SDC1_HUMAN	syndecan 1	84					canonical Wnt signaling pathway (GO:0060070)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|myoblast development (GO:0048627)|odontogenesis (GO:0042476)|phototransduction, visible light (GO:0007603)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to toxic substance (GO:0009636)|retinoid metabolic process (GO:0001523)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|striated muscle cell development (GO:0055002)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|skin(2)	21	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)		CAGCTGTAGCCTCCAGGCCGG	0.642													c|||	871	0.173922	0.1513	0.2421	5008	,	,		14341	0.0843		0.2634	False		,,,				2504	0.1564				p.E84E		Atlas-SNP	.											.	SDC1	32	.	0			c.G252A						PASS	.		,	745,3661		65,615,1523	56.0	63.0	61.0		252,252	-7.7	0.0	2	dbSNP_98	61	2307,6291		327,1653,2319	no	coding-synonymous,coding-synonymous	SDC1	NM_001006946.1,NM_002997.4	,	392,2268,3842	TT,TC,CC		26.8318,16.9088,23.4697	,	84/311,84/311	20403949	3052,9952	2203	4299	6502	SO:0001819	synonymous_variant	6382	exon3			TGTAGCCTCCAGG	AJ551176	CCDS1697.1	2p24.1	2008-02-05			ENSG00000115884	ENSG00000115884		"""CD molecules"", ""Proteoglycans / Cell Surface : Syndecans"""	10658	protein-coding gene	gene with protein product	"""syndecan proteoglycan 1"""	186355		SDC			Standard	XM_005262621		Approved	CD138, syndecan, SYND1	uc002rdo.1	P18827	OTTHUMG00000090751	ENST00000254351.4:c.252G>A	2.37:g.20403949C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	25	11	0.44	NM_002997	D6W523|Q53QV0|Q546D3|Q96HB7	Silent	SNP	ENST00000254351.4	37	CCDS1697.1																																																																																			T|0.225;G|0.000;C|0.775	0.225	strong		0.642	SDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207495.1	NM_001006946	
DISC1	27185	hgsc.bcm.edu	37	1	231954101	231954101	+	Missense_Mutation	SNP	C	C	T	rs6675281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:231954101C>T	ENST00000602281.1	+	9	1872	c.1819C>T	c.(1819-1821)Ctc>Ttc	p.L607F	DISC1_ENST00000539444.1_Silent_p.T572T|DISC1_ENST00000366636.4_Missense_Mutation_p.L607F|DISC1_ENST00000439617.2_Missense_Mutation_p.L607F|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000602873.1_3'UTR|DISC1_ENST00000535983.1_Missense_Mutation_p.L607F|DISC1_ENST00000537876.1_Intron|DISC1_ENST00000366633.3_Missense_Mutation_p.L607F	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	607	Interaction with ATF4 and ATF5.|Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.		L -> F (associated with susceptibility to schizoaffective disorder; dbSNP:rs6675281). {ECO:0000269|PubMed:15386212}.		canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GGCTAAAGACCTCACCGAGGA	0.483													C|||	480	0.0958466	0.1884	0.0821	5008	,	,		20772	0.003		0.1243	False		,,,				2504	0.047				p.L639F		Atlas-SNP	.											.	DISC1	207	.	0			c.C1915T	GRCh37	CM042974	DISC1	M	rs6675281	PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,,,,,,PHE/LEU	781,3625	314.7+/-293.7	53,675,1475	107.0	108.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1819,1819,1915,1819,1819,1453,1819,1819,1819,1716,,,,,1819	4.3	1.0	1	dbSNP_116	107	1218,7382	246.0+/-274.6	86,1046,3168	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,coding-synonymous,intron,intron,utr-3,utr-3,missense	DISC1	NM_001012957.1,NM_001012959.1,NM_001164537.1,NM_001164538.1,NM_001164539.1,NM_001164540.1,NM_001164541.1,NM_001164542.1,NM_001164544.1,NM_001164545.1,NM_001164546.1,NM_001164547.1,NM_001164548.1,NM_001164556.1,NM_018662.2	22,22,22,22,22,22,22,22,22,,,,,,22	139,1721,4643	TT,TC,CC		14.1628,17.7258,15.3698	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,,,,,probably-damaging	607/833,607/679,639/887,607/804,607/756,485/733,607/696,607/682,607/663,572/580,,,,,607/855	231954101	1999,11007	2203	4300	6503	SO:0001583	missense	27185	exon10			AAAGACCTCACCG	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1819C>T	1.37:g.231954101C>T	ENSP00000473425:p.Leu607Phe	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	204	0.09340659340659341	84	0.17073170731707318	29	0.08011049723756906	0	0.0	91	0.12005277044854881	C	20.8	4.051022	0.75960	0.177258	0.141628	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000366633	T;T;T;T	0.24151	2.01;1.88;1.87;2.03	5.23	4.32	0.51571	.	0.178636	0.36591	N	0.002514	T	0.00144	0.0004	.	.	.	0.09310	P	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.994;1.0;0.994;1.0;0.986;0.994;1.0;1.0;1.0;0.994;1.0;0.986;1.0	D;P;D;P;D;P;P;D;D;D;P;D;P;D	0.91635	0.999;0.799;0.999;0.683;0.999;0.799;0.683;0.999;0.999;0.999;0.683;0.999;0.683;0.999	T	0.04915	-1.0918	8	0.87932	D	0	-8.5446	11.9831	0.53131	0.0:0.9205:0.0:0.0795	rs6675281;rs52801396;rs59116826;rs6675281	639;485;639;607;607;485;607;607;607;607;607;607;607;607	C4P096;C4P094;E2QRA4;C4P0A3;C4P098;F5H1F1;C4P0A4;A6NLH2;C4P0B6;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	F	607;607;607;639;485;607;607	ENSP00000403888:L607F;ENSP00000355596:L607F;ENSP00000443996:L607F;ENSP00000355593:L607F	ENSP00000355593:L607F	L	+	1	0	DISC1	230020724	1.000000	0.71417	0.977000	0.42913	0.978000	0.69477	3.306000	0.51881	1.425000	0.47237	0.591000	0.81541	CTC	C|0.877;T|0.123	0.123	strong		0.483	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
RGAG1	57529	hgsc.bcm.edu	37	X	109694685	109694685	+	Silent	SNP	T	T	A	rs2073787	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:109694685T>A	ENST00000465301.2	+	3	1086	c.840T>A	c.(838-840)ggT>ggA	p.G280G	RGAG1_ENST00000540313.1_Silent_p.G280G	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	280										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CTTCTGGAGGTACATCACCCC	0.478													A|||	1412	0.37404	0.5915	0.2075	3775	,	,		16051	0.0129		0.333	False		,,,				2504	0.1411				p.G280G		Atlas-SNP	.											.	RGAG1	168	.	0			c.T840A						PASS	.	A		2908,927		948,591,421,93,150	141.0	119.0	127.0		840	2.7	0.0	X	dbSNP_96	127	2788,3940		422,1194,750,812,1122	no	coding-synonymous	RGAG1	NM_020769.2		1370,1785,1171,905,1272	AA,AT,A,TT,T		41.4388,24.1721,46.0759		280/1389	109694685	5696,4867	2203	4300	6503	SO:0001819	synonymous_variant	57529	exon3			TGGAGGTACATCA	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.840T>A	X.37:g.109694685T>A		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_020769	Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																			T|0.511;0|0.003	.	strong		0.478	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769	
ITIH5	80760	hgsc.bcm.edu	37	10	7621771	7621771	+	Silent	SNP	A	A	G	rs17431370	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:7621771A>G	ENST00000256861.6	-	9	1443	c.1365T>C	c.(1363-1365)tgT>tgC	p.C455C	ITIH5_ENST00000298441.6_Silent_p.C241C|ITIH5_ENST00000446830.2_Silent_p.C237C|ITIH5_ENST00000397145.2_Silent_p.C455C|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397146.2_Silent_p.C455C	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	455	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						GTGTGAGGCCACAGTTCTCCA	0.617													G|||	676	0.134984	0.1006	0.1988	5008	,	,		20020	0.006		0.2763	False		,,,				2504	0.1237				p.C455C		Atlas-SNP	.											.	ITIH5	343	.	0			c.T1365C						PASS	.	G	,,	543,3863	776.5+/-414.2	40,463,1700	113.0	102.0	106.0		1365,1365,723	-0.2	1.0	10	dbSNP_123	106	2192,6408	712.3+/-405.9	263,1666,2371	no	coding-synonymous,coding-synonymous,coding-synonymous	ITIH5	NM_001001851.2,NM_030569.6,NM_032817.5	,,	303,2129,4071	GG,GA,AA		25.4884,12.3241,21.0288	,,	455/703,455/943,241/729	7621771	2735,10271	2203	4300	6503	SO:0001819	synonymous_variant	80760	exon9			GAGGCCACAGTTC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1365T>C	10.37:g.7621771A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																				A|0.807;G|0.193	0.193	strong		0.617	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
SMARCA4	6597	hgsc.bcm.edu	37	19	11145752	11145752	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11145752C>T	ENST00000429416.3	+	30	4395	c.4114C>T	c.(4114-4116)Cgc>Tgc	p.R1372C	SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1372C|SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1372C|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1339C|SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1339C|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1339C|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1339C|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1339C|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1339C	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1372					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCGTGGCTCCCGCCACCGCAA	0.652			"""F, N, Mis"""		NSCLC																																p.R1372C		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.C4114T						PASS	.						44.0	36.0	39.0					19																	11145752		2203	4299	6502	SO:0001583	missense	6597	exon29			GGCTCCCGCCACC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4114C>T	19.37:g.11145752C>T	ENSP00000395654:p.Arg1372Cys	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	163	28	0.171779	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	25.0|25.0	4.593820|4.593820	0.86953|0.86953	.|.	.|.	ENSG00000127616|ENSG00000127616	ENST00000538456|ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.|D;D;D;D;D;D;D	.|0.95724	.|-3.77;-3.79;-3.77;-3.03;-3.0;-3.07;-3.03	4.59|4.59	3.56|3.56	0.40772|0.40772	.|.	.|0.065843	.|0.64402	.|D	.|0.000006	D|D	0.98239|0.98239	0.9417|0.9417	H|H	0.96239|0.96239	3.79|3.79	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D	.|0.97110	.|1.0;1.0;1.0;1.0;0.999;1.0;1.0	D|D	0.98554|0.98554	1.0638|1.0638	5|10	.|0.87932	.|D	.|0	-29.8756|-29.8756	11.6252|11.6252	0.51139|0.51139	0.0:0.9121:0.0:0.0879|0.0:0.9121:0.0:0.0879	.|.	.|1339;1339;1339;1372;1339;559;1372	.|B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.|.;.;.;.;.;.;SMCA4_HUMAN	L|C	108|1372;1372;1403;1372;1339;1339;1339;1339	.|ENSP00000395654:R1372C;ENSP00000350720:R1372C;ENSP00000343896:R1372C;ENSP00000445036:R1339C;ENSP00000392837:R1339C;ENSP00000397783:R1339C;ENSP00000414727:R1339C	.|ENSP00000343896:R1372C	P|R	+|+	2|1	0|0	SMARCA4|SMARCA4	11006752|11006752	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.546000|7.546000	0.82137|0.82137	1.164000|1.164000	0.42652|0.42652	0.558000|0.558000	0.71614|0.71614	CCG|CGC	.	.	none		0.652	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
ZNF275	10838	hgsc.bcm.edu	37	X	152610985	152610985	+	Silent	SNP	T	T	C	rs3213466	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:152610985T>C	ENST00000421401.3	+	3	216	c.39T>C	c.(37-39)ccT>ccC	p.P13P	ZNF275_ENST00000370251.3_Silent_p.P13P|ZNF275_ENST00000440091.1_Silent_p.P43P|ZNF275_ENST00000370249.2_5'UTR			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	13					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGCGTTCCTGTTTTAAATC	0.517													T|||	1776	0.470464	0.503	0.317	3775	,	,		15111	0.4286		0.2386	False		,,,				2504	0.2239				p.P13P		Atlas-SNP	.											.	ZNF275	44	.	0			c.T39C						PASS	.	T		2064,1512		536,655,337,312,233	81.0	79.0	80.0		39	2.3	0.9	X	dbSNP_106	80	2017,4563		244,971,558,1166,1260	no	coding-synonymous	ZNF275	NM_001080485.3		780,1626,895,1478,1493	CC,CT,C,TT,T		30.6535,42.2819,40.1831		13/330	152610985	4081,6075	2073	4199	6272	SO:0001819	synonymous_variant	10838	exon3			CGTTCCTGTTTTA	BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"""Zinc fingers, C2H2-type"", ""-"""	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.39T>C	X.37:g.152610985T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001080485	A6NE92	Silent	SNP	ENST00000421401.3	37																																																																																				0|0.006;C|0.479	0.479	strong		0.517	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485	
HELZ2	85441	hgsc.bcm.edu	37	20	62191558	62191558	+	Silent	SNP	G	G	A	rs3810479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62191558G>A	ENST00000467148.1	-	17	7692	c.7623C>T	c.(7621-7623)gcC>gcT	p.A2541A	HELZ2_ENST00000427522.2_Silent_p.A1972A	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2541	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CGGCCACCCCGGCGATGCCCT	0.716													g|||	786	0.156949	0.0083	0.0821	5008	,	,		12764	0.3433		0.16	False		,,,				2504	0.2157				p.A2541A		Atlas-SNP	.											.	.	.	.	0			c.C7623T						PASS	.	A	,	161,4179		4,153,2013	24.0	19.0	21.0		7623,5916	-7.9	0.0	20	dbSNP_107	21	1308,7220		111,1086,3067	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	115,1239,5080	AA,AG,GG		15.3377,3.7097,11.4159	,	2541/2650,1972/2081	62191558	1469,11399	2170	4264	6434	SO:0001819	synonymous_variant	85441	exon18			CACCCCGGCGATG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.7623C>T	20.37:g.62191558G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			G|0.863;A|0.137	0.137	strong		0.716	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
SVIL	6840	hgsc.bcm.edu	37	10	29821475	29821475	+	Silent	SNP	G	G	A	rs41284748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29821475G>A	ENST00000355867.4	-	8	2573	c.1821C>T	c.(1819-1821)gcC>gcT	p.A607A	SVIL_ENST00000375398.2_Silent_p.A607A|SVIL_ENST00000375400.3_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	607					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GTCTCCTGCAGGCGTTGGCAG	0.567													G|||	292	0.0583067	0.0386	0.1138	5008	,	,		20702	0.0		0.1044	False		,,,				2504	0.0583				p.A607A		Atlas-SNP	.											.	SVIL	226	.	0			c.C1821T						PASS	.	G	,	196,4210	123.7+/-161.0	4,188,2011	68.0	52.0	57.0		,1821	4.8	1.0	10	dbSNP_127	57	728,7872	177.5+/-227.1	29,670,3601	no	intron,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	33,858,5612	AA,AG,GG		8.4651,4.4485,7.1044	,	,607/2215	29821475	924,12082	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			CCTGCAGGCGTTG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1821C>T	10.37:g.29821475G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			G|0.928;A|0.072	0.072	strong		0.567	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
CNDP2	55748	hgsc.bcm.edu	37	18	72178161	72178161	+	Silent	SNP	T	T	C	rs2278159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72178161T>C	ENST00000324262.4	+	6	886	c.570T>C	c.(568-570)taT>taC	p.Y190Y	CNDP2_ENST00000324301.8_Silent_p.Y106Y|CNDP2_ENST00000579847.1_Silent_p.Y190Y	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	190					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.Y190Y(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		ATGTGGACTATGTCTGCATTT	0.507													T|||	1013	0.202276	0.0779	0.3026	5008	,	,		23053	0.2986		0.162	False		,,,				2504	0.2413				p.Y190Y		Atlas-SNP	.											CNDP2,NS,carcinoma,0,1	CNDP2	55	1	1	Substitution - coding silent(1)	stomach(1)	c.T570C						PASS	.	T	,	493,3913	230.4+/-244.6	34,425,1744	146.0	127.0	134.0		318,570	1.8	0.9	18	dbSNP_100	134	1634,6966	303.4+/-306.4	133,1368,2799	no	coding-synonymous,coding-synonymous	CNDP2	NM_001168499.1,NM_018235.2	,	167,1793,4543	CC,CT,TT		19.0,11.1893,16.354	,	106/392,190/476	72178161	2127,10879	2203	4300	6503	SO:0001819	synonymous_variant	55748	exon6			GGACTATGTCTGC	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.570T>C	18.37:g.72178161T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	101	64	0.633663	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Silent	SNP	ENST00000324262.4	37	CCDS12006.1																																																																																			T|0.825;C|0.175	0.175	strong		0.507	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
CAND2	23066	hgsc.bcm.edu	37	3	12875443	12875443	+	Missense_Mutation	SNP	G	G	A	rs12629133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:12875443G>A	ENST00000456430.2	+	15	3714	c.3673G>A	c.(3673-3675)Gct>Act	p.A1225T	CAND2_ENST00000295989.5_Missense_Mutation_p.A1108T|RP11-767C1.2_ENST00000606447.1_RNA	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	1225			A -> T (in dbSNP:rs12629133). {ECO:0000269|PubMed:15489334}.		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GAAGGATTCCGCTTCAGCCCC	0.577													G|||	2258	0.450879	0.2852	0.5187	5008	,	,		18560	0.4474		0.6332	False		,,,				2504	0.4427				p.A1225T	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.G3673A						PASS	.	G	THR/ALA,THR/ALA	1386,2480		251,884,798	77.0	81.0	79.0		3673,3322	2.0	0.0	3	dbSNP_120	79	5191,3085		1628,1935,575	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	58,58	1879,2819,1373	AA,AG,GG		37.2765,35.851,45.8326	benign,benign	1225/1237,1108/1120	12875443	6577,5565	1933	4138	6071	SO:0001583	missense	23066	exon15			GATTCCGCTTCAG		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.3673G>A	3.37:g.12875443G>A	ENSP00000387641:p.Ala1225Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	100	58	0.58	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1060	0.48534798534798534	144	0.2926829268292683	196	0.5414364640883977	255	0.4458041958041958	465	0.6134564643799473	G	1.657	-0.512544	0.04200	0.35851	0.627235	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.04194	3.69;3.68	5.11	2.05	0.26809	.	0.848123	0.10399	N	0.679423	T	0.00012	0.0000	N	0.13098	0.295	0.58432	P	1.999999999946489E-6	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.10314	-1.0635	9	0.19590	T	0.45	-2.9374	11.2764	0.49170	0.2491:0.0:0.7509:0.0	rs12629133;rs58909666;rs12629133	1225;1108	O75155;O75155-2	CAND2_HUMAN;.	T	1108;1225	ENSP00000295989:A1108T;ENSP00000387641:A1225T	ENSP00000295989:A1108T	A	+	1	0	CAND2	12850443	0.052000	0.20516	0.003000	0.11579	0.316000	0.28119	0.948000	0.29096	0.001000	0.14605	-1.094000	0.02160	GCT	A|0.499;C|0.000;G|0.500;T|0.000	0.499	strong		0.577	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
IVL	3713	hgsc.bcm.edu	37	1	152882979	152882979	+	Missense_Mutation	SNP	C	C	T	rs17855670		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152882979C>T	ENST00000368764.3	+	2	770	c.706C>T	c.(706-708)Cca>Tca	p.P236S	IVL_ENST00000392667.2_Missense_Mutation_p.P90S			P07476	INVO_HUMAN	involucrin	236	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		P -> S (in dbSNP:rs17855670). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2873896}.		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gctggagctcccacagcagca	0.677																																					p.P236S		Atlas-SNP	.											IVL,colon,carcinoma,0,2	IVL	100	2	0			c.C706T						scavenged	.																																			SO:0001583	missense	3713	exon2			GAGCTCCCACAGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.706C>T	1.37:g.152882979C>T	ENSP00000357753:p.Pro236Ser	Somatic	91	2	0.021978		WXS	Illumina HiSeq	Phase_I	156	37	0.237179	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	126	0.057692307692307696	14	0.028455284552845527	19	0.052486187845303865	65	0.11363636363636363	28	0.036939313984168866	C	0.481	-0.879883	0.02530	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10960	3.06;2.82	3.86	-2.86	0.05717	.	.	.	.	.	T	0.01387	0.0045	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.48198	-0.9056	9	0.09590	T	0.72	.	4.7558	0.13082	0.3537:0.2977:0.3486:0.0	rs17855670	236	P07476	INVO_HUMAN	S	236;90	ENSP00000357753:P236S;ENSP00000376435:P90S	ENSP00000357753:P236S	P	+	1	0	IVL	151149603	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.107000	0.15375	-0.341000	0.08376	-0.883000	0.02948	CCA	C|0.943;T|0.057	0.057	strong		0.677	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
FBN3	84467	hgsc.bcm.edu	37	19	8159409	8159409	+	Silent	SNP	G	G	T	rs7245552	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8159409G>T	ENST00000600128.1	-	47	6240	c.5826C>A	c.(5824-5826)ccC>ccA	p.P1942P	FBN3_ENST00000270509.2_Silent_p.P1942P|FBN3_ENST00000601739.1_Silent_p.P1942P			Q75N90	FBN3_HUMAN	fibrillin 3	1942	EGF-like 31; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GGCAAGTGCCGGGTAGGCAGG	0.602													T|||	3436	0.686102	0.4266	0.7536	5008	,	,		21056	0.9018		0.6471	False		,,,				2504	0.8067				p.P1942P		Atlas-SNP	.											FBN3,NS,carcinoma,0,1	FBN3	300	1	0			c.C5826A						PASS	.	T		1993,2413	615.6+/-392.6	456,1081,666	100.0	69.0	80.0		5826	1.0	1.0	19	dbSNP_116	80	5295,3305	492.7+/-373.4	1634,2027,639	no	coding-synonymous	FBN3	NM_032447.3		2090,3108,1305	TT,TG,GG		38.4302,45.2338,43.9643		1942/2810	8159409	7288,5718	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon46			AGTGCCGGGTAGG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5826C>A	19.37:g.8159409G>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1	1469	0.6726190476190477	200	0.4065040650406504	263	0.7265193370165746	514	0.8986013986013986	492	0.6490765171503958	T	5.247	0.230947	0.09969	0.452338	0.615698	ENSG00000142449	ENST00000341066	.	.	.	4.82	1.01	0.19927	.	0.000000	0.85682	U	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.10870	-1.0611	5	0.41790	T	0.15	.	0.8827	0.01237	0.2011:0.148:0.2041:0.4468	rs7245552;rs59338233;rs7245552	.	.	.	Q	62	.	ENSP00000341317:P62Q	P	-	2	0	FBN3	8065409	0.000000	0.05858	0.971000	0.41717	0.533000	0.34776	-2.665000	0.00848	-0.083000	0.12618	-1.477000	0.00996	CCG	G|0.395;T|0.605	0.605	strong		0.602	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
SLC28A2	9153	hgsc.bcm.edu	37	15	45561551	45561551	+	Missense_Mutation	SNP	C	C	T	rs17222057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:45561551C>T	ENST00000347644.3	+	14	1449	c.1384C>T	c.(1384-1386)Ctc>Ttc	p.L462F	CTD-2651B20.3_ENST00000561404.1_RNA|CTD-2651B20.3_ENST00000560344.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	462			L -> F (in dbSNP:rs17222057). {ECO:0000269|PubMed:15861032}.		nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Mercaptopurine(DB01033)	CTGCTCCTATCTCCTAAGGCC	0.473													C|||	11	0.00219649	0.0	0.0058	5008	,	,		18573	0.0		0.006	False		,,,				2504	0.001				p.L462F	NSCLC(92;493 1501 26361 28917 47116)	Atlas-SNP	.											.	SLC28A2	64	.	0			c.C1384T						PASS	.	C	PHE/LEU	5,4391	8.1+/-20.4	0,5,2193	179.0	164.0	169.0		1384	-7.6	0.0	15	dbSNP_126	169	64,8532	39.3+/-95.6	0,64,4234	yes	missense	SLC28A2	NM_004212.3	22	0,69,6427	TT,TC,CC		0.7445,0.1137,0.5311	benign	462/659	45561551	69,12923	2198	4298	6496	SO:0001583	missense	9153	exon14			TCCTATCTCCTAA	U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"""Solute carriers"""	11002	protein-coding gene	gene with protein product		606208	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"""			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.1384C>T	15.37:g.45561551C>T	ENSP00000315006:p.Leu462Phe	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	223	82	0.367713	NM_004212	A8K7F9|O43239|Q52LZ0	Missense_Mutation	SNP	ENST00000347644.3	37	CCDS10121.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	13.53	2.263359	0.39995	0.001137	0.007445	ENSG00000137860	ENST00000347644	T	0.09073	3.02	6.04	-7.62	0.01294	Na dependent nucleoside transporter, C-terminal (1);	0.405704	0.30159	N	0.010277	T	0.04272	0.0118	L	0.47016	1.485	0.09310	N	0.999998	B	0.21147	0.052	B	0.28784	0.094	T	0.20974	-1.0259	10	0.87932	D	0	-0.5401	7.6923	0.28575	0.4656:0.2783:0.2561:0.0	rs17222057;rs45511902;rs60414556	462	O43868	S28A2_HUMAN	F	462	ENSP00000315006:L462F	ENSP00000315006:L462F	L	+	1	0	SLC28A2	43348843	0.000000	0.05858	0.005000	0.12908	0.861000	0.49209	-0.249000	0.08842	-1.440000	0.01960	-1.109000	0.02080	CTC	C|0.996;T|0.004	0.004	strong		0.473	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212	
IFI16	3428	hgsc.bcm.edu	37	1	159002377	159002377	+	Missense_Mutation	SNP	C	C	A	rs1057027	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:159002377C>A	ENST00000295809.7	+	7	1480	c.1225C>A	c.(1225-1227)Cgt>Agt	p.R409S	IFI16_ENST00000368131.4_Missense_Mutation_p.R409S|IFI16_ENST00000430894.2_Missense_Mutation_p.R357S|IFI16_ENST00000359709.3_Missense_Mutation_p.R353S|IFI16_ENST00000448393.2_Missense_Mutation_p.R409S|IFI16_ENST00000368132.3_Missense_Mutation_p.R409S|IFI16_ENST00000340979.6_Missense_Mutation_p.R409S			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	409			R -> S (in dbSNP:rs1057027). {ECO:0000269|PubMed:12894224, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					CCAGGAACAGCGTCAGCTTCC	0.448													A|||	3160	0.63099	0.3207	0.8689	5008	,	,		18161	0.5883		0.838	False		,,,				2504	0.7127				p.R409S		Atlas-SNP	.											.	IFI16	111	.	0			c.C1225A						PASS	.	A	SER/ARG,SER/ARG	1895,2511	628.5+/-395.1	413,1069,721	122.0	115.0	117.0		1057,1225	2.2	0.1	1	dbSNP_86	117	7028,1572	293.1+/-301.2	2881,1266,153	yes	missense,missense	IFI16	NM_001206567.1,NM_005531.2	110,110	3294,2335,874	AA,AC,CC		18.2791,43.0095,31.3932	benign,benign	353/730,409/730	159002377	8923,4083	2203	4300	6503	SO:0001583	missense	3428	exon7			GAACAGCGTCAGC	M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.1225C>A	1.37:g.159002377C>A	ENSP00000295809:p.Arg409Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	174	70	0.402299	NM_005531	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	ENST00000295809.7	37		1485|1485	0.679945054945055|0.679945054945055	149|149	0.30284552845528456|0.30284552845528456	314|314	0.8674033149171271|0.8674033149171271	379|379	0.6625874125874126|0.6625874125874126	643|643	0.8482849604221636|0.8482849604221636	A|A	0.009|0.009	-1.803729|-1.803729	0.00611|0.00611	0.430095|0.430095	0.817209|0.817209	ENSG00000163565|ENSG00000163565	ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894|ENST00000448393	T;T;T;T;T|.	0.03889|.	3.77;3.87;3.8;3.8;3.8|.	2.15|2.15	2.15|2.15	0.27550|0.27550	.|.	.|.	.|.	.|.	.|.	T|T	0.01870|0.01870	0.0059|0.0059	N|N	0.00483|0.00483	-1.445|-1.445	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.0;0.001;0.0|.	T|T	0.45789|0.45789	-0.9237|-0.9237	8|4	0.02654|.	T|.	1|.	.|.	5.2195|5.2195	0.15362|0.15362	0.6949:0.3051:0.0:0.0|0.6949:0.3051:0.0:0.0	rs1057027;rs3197638;rs17838196;rs17856525;rs52834589;rs58402778;rs1057027|rs1057027;rs3197638;rs17838196;rs17856525;rs52834589;rs58402778;rs1057027	357;409;409|.	E7EPR3;Q16666-3;Q16666-2|.	.;.;.|.	S|R	409;409;409;409;357|229	ENSP00000295809:R409S;ENSP00000342741:R409S;ENSP00000357113:R409S;ENSP00000357114:R409S;ENSP00000394935:R357S|.	ENSP00000295809:R409S|.	R|S	+|+	1|3	0|2	IFI16|IFI16	157269001|157269001	0.001000|0.001000	0.12720|0.12720	0.135000|0.135000	0.22099|0.22099	0.003000|0.003000	0.03518|0.03518	0.250000|0.250000	0.18235|0.18235	0.257000|0.257000	0.21650|0.21650	-0.525000|-0.525000	0.04345|0.04345	CGT|AGC	C|0.328;A|0.672	0.672	strong		0.448	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458765	39458765	+	Silent	SNP	A	A	G	rs1005197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39458765A>G	ENST00000391353.1	-	1	338	c.339T>C	c.(337-339)tcT>tcC	p.S113S		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	113	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											GACAACAAGTAGATTCCGAGC	0.542													A|||	3397	0.678315	0.5166	0.8012	5008	,	,		24206	0.629		0.7336	False		,,,				2504	0.8037				p.S113S		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.T339C						PASS	.																																			SO:0001819	synonymous_variant	100533177	exon1			ACAAGTAGATTCC		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.339T>C	17.37:g.39458765A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001257309		Silent	SNP	ENST00000391353.1	37																																																																																				A|0.331;G|0.669	0.669	strong		0.542	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
FAM214B	80256	hgsc.bcm.edu	37	9	35107765	35107765	+	Silent	SNP	C	C	A	rs13287211	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35107765C>A	ENST00000378561.1	-	2	3562	c.507G>T	c.(505-507)ggG>ggT	p.G169G	FAM214B_ENST00000605244.1_Silent_p.G169G|FAM214B_ENST00000603301.1_Silent_p.G169G|FAM214B_ENST00000378566.1_Intron|FAM214B_ENST00000378554.2_Silent_p.G169G|FAM214B_ENST00000605392.1_5'Flank|FAM214B_ENST00000488109.2_Silent_p.G169G|FAM214B_ENST00000378557.1_Silent_p.G169G|FAM214B_ENST00000322813.5_Silent_p.G169G			Q7L5A3	F214B_HUMAN	family with sequence similarity 214, member B	169						nucleus (GO:0005634)											CCCCCAGGGACCCCTGTCCCC	0.627													C|||	937	0.187101	0.0197	0.4424	5008	,	,		16091	0.003		0.3936	False		,,,				2504	0.2096				p.G169G		Atlas-SNP	.											.	.	.	.	0			c.G507T						PASS	.	C		319,4069		15,289,1890	33.0	42.0	39.0		507	3.0	1.0	9	dbSNP_121	39	3388,5212		670,2048,1582	no	coding-synonymous	KIAA1539	NM_025182.2		685,2337,3472	AA,AC,CC		39.3953,7.2698,28.5417		169/539	35107765	3707,9281	2194	4300	6494	SO:0001819	synonymous_variant	80256	exon3			CAGGGACCCCTGT	AB040972	CCDS6578.1	9p13.2	2011-12-01	2011-12-01	2011-12-01	ENSG00000005238	ENSG00000005238			25666	protein-coding gene	gene with protein product			"""KIAA1539"""	KIAA1539		10819331	Standard	NM_025182		Approved	FLJ11560, bA182N22.6	uc003zwo.3	Q7L5A3	OTTHUMG00000019847	ENST00000378561.1:c.507G>T	9.37:g.35107765C>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_025182	B1AML4|B1AML5|D3DRN5|O60377|Q9BQ60|Q9HAI9|Q9P1Y9	Silent	SNP	ENST00000378561.1	37	CCDS6578.1																																																																																			C|0.718;A|0.282	0.282	strong		0.627	FAM214B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052261.1	NM_025182	
SLC28A1	9154	hgsc.bcm.edu	37	15	85447431	85447431	+	Missense_Mutation	SNP	G	G	A	rs2290272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85447431G>A	ENST00000286749.3	+	6	655	c.565G>A	c.(565-567)Gtc>Atc	p.V189I	SLC28A1_ENST00000537216.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000394573.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000538177.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000537624.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000537703.1_Missense_Mutation_p.V111I			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	189			V -> I (in A; dbSNP:rs2290272). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.V189I(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	CTGCGTGTTCGTCGCTCTCCT	0.587													A|||	1919	0.383187	0.1914	0.5058	5008	,	,		20264	0.375		0.3638	False		,,,				2504	0.5838				p.V189I		Atlas-SNP	.											SLC28A1,NS,carcinoma,0,1	SLC28A1	118	1	1	Substitution - Missense(1)	stomach(1)	c.G565A	GRCh37	CM045806	SLC28A1	M	rs2290272	PASS	.	A	ILE/VAL	962,3444	734.2+/-410.6	104,754,1345	171.0	146.0	155.0		565	-5.9	0.0	15	dbSNP_100	155	3013,5585	663.4+/-402.1	524,1965,1810	yes	missense	SLC28A1	NM_004213.3	29	628,2719,3155	AA,AG,GG		35.043,21.8339,30.5675	benign	189/650	85447431	3975,9029	2203	4299	6502	SO:0001583	missense	9154	exon7			GTGTTCGTCGCTC	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.565G>A	15.37:g.85447431G>A	ENSP00000286749:p.Val189Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	148	85	0.574324	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	762	0.3489010989010989	93	0.18902439024390244	175	0.48342541436464087	208	0.36363636363636365	286	0.37730870712401055	A	0.006	-2.043950	0.00398	0.218339	0.35043	ENSG00000156222	ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573;ENST00000537703	T;T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7;2.7	4.38	-5.87	0.02297	Na dependent nucleoside transporter (1);	0.579854	0.17850	N	0.159890	T	0.00012	0.0000	N	0.02357	-0.585	0.80722	P	0.0	B;B;B;B;B	0.19331	0.005;0.001;0.035;0.001;0.002	B;B;B;B;B	0.19148	0.006;0.003;0.024;0.004;0.006	T	0.16808	-1.0390	9	0.02654	T	1	3.2539	9.4688	0.38829	0.2123:0.2511:0.5366:0.0	rs2290272;rs17222253;rs17536477;rs52799974;rs58773874;rs2290272	189;189;189;111;189	B7Z533;F5H560;B7Z3L6;B7Z3M4;O00337	.;.;.;.;S28A1_HUMAN	I	189;189;189;189;189;111	ENSP00000440546:V189I;ENSP00000443752:V189I;ENSP00000444700:V189I;ENSP00000286749:V189I;ENSP00000378074:V189I;ENSP00000443764:V111I	ENSP00000286749:V189I	V	+	1	0	SLC28A1	83248435	0.142000	0.22610	0.003000	0.11579	0.001000	0.01503	-0.604000	0.05667	-1.600000	0.01603	-1.157000	0.01802	GTC	G|0.674;A|0.326	0.326	strong		0.587	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
CUX1	1523	hgsc.bcm.edu	37	7	101917521	101917521	+	Missense_Mutation	SNP	G	G	A	rs803064	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:101917521G>A	ENST00000437600.4	+	16	1736	c.1384G>A	c.(1384-1386)Gct>Act	p.A462T	CUX1_ENST00000547394.2_Missense_Mutation_p.A448T|CUX1_ENST00000292538.4_Missense_Mutation_p.A464T|CUX1_ENST00000425244.2_Missense_Mutation_p.A418T|CUX1_ENST00000393824.3_Missense_Mutation_p.A425T|CUX1_ENST00000560541.1_3'UTR	NM_181500.2	NP_852477.1	P39880	CUX1_HUMAN	cut-like homeobox 1	0					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						GCAGGGTGCCGCTGAGCACCG	0.607													G|||	2800	0.559105	0.6172	0.5072	5008	,	,		19921	0.498		0.5358	False		,,,				2504	0.6043				p.A464T		Atlas-SNP	.											.	CUX1	253	.	0			c.G1390A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	2609,1797	641.4+/-397.5	776,1057,370	96.0	88.0	90.0		1342,1252,1273,1390,1384	-0.1	0.0	7	dbSNP_86	90	4869,3731	618.5+/-396.8	1369,2131,800	yes	missense,missense,missense,missense,missense	CUX1	NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2	58,58,58,58,58	2145,3188,1170	AA,AG,GG		43.3837,40.7853,42.5035	,,,,	448/663,418/633,425/640,464/679,462/677	101917521	7478,5528	2203	4300	6503	SO:0001583	missense	1523	exon16			GGTGCCGCTGAGC	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000437600.4:c.1384G>A	7.37:g.101917521G>A	ENSP00000414091:p.Ala462Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_001913	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000437600.4	37	CCDS47672.1	1228	0.5622710622710623	321	0.6524390243902439	202	0.5580110497237569	277	0.48426573426573427	428	0.5646437994722955	G	6.651	0.488701	0.12641	0.592147	0.566163	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000425244;ENST00000437600	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.64	-0.106	0.13596	CASP, C-terminal (1);	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B;B;B;B	0.28971	0.127;0.229;0.229;0.001	B;B;B;B	0.24269	0.021;0.052;0.041;0.006	T	0.41070	-0.9529	8	0.12766	T	0.61	.	7.499	0.27507	0.1446:0.0:0.6019:0.2535	rs803064;rs1725585;rs2230106;rs10375045;rs17135114;rs52803548;rs803064	418;448;462;464	B3KV79;G3V1Z6;Q13948-2;Q13948	.;.;.;CASP_HUMAN	T	464;448;418;462	ENSP00000292538:A464T;ENSP00000449371:A448T;ENSP00000409745:A418T;ENSP00000414091:A462T	ENSP00000292538:A464T	A	+	1	0	CUX1	101704241	0.807000	0.29009	0.020000	0.16555	0.029000	0.11900	2.486000	0.45259	0.064000	0.16427	-0.918000	0.02743	GCT	G|0.431;A|0.569	0.569	strong		0.607	CUX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347534.3	NM_001913	
USP10	9100	hgsc.bcm.edu	37	16	84778762	84778762	+	Silent	SNP	C	C	T	rs4553618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84778762C>T	ENST00000219473.7	+	4	788	c.675C>T	c.(673-675)gaC>gaT	p.D225D	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Silent_p.D229D	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	225					autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						TTGTGCCTGACAGTCCTTTCC	0.597													C|||	1160	0.231629	0.0507	0.3934	5008	,	,		17012	0.4018		0.2107	False		,,,				2504	0.2076				p.D229D		Atlas-SNP	.											.	USP10	51	.	0			c.C687T						PASS	.	C		313,3549		5,303,1623	20.0	20.0	20.0		675	-9.7	0.0	16	dbSNP_111	20	1784,6442		201,1382,2530	no	coding-synonymous	USP10	NM_005153.2		206,1685,4153	TT,TC,CC		21.6873,8.1046,17.3478		225/799	84778762	2097,9991	1931	4113	6044	SO:0001819	synonymous_variant	9100	exon5			GCCTGACAGTCCT	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.675C>T	16.37:g.84778762C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	164	95	0.579268	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			C|0.779;T|0.221	0.221	strong		0.597	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
ZNF805	390980	hgsc.bcm.edu	37	19	57764770	57764770	+	Missense_Mutation	SNP	G	G	A	rs10421632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57764770G>A	ENST00000414468.2	+	4	583	c.583G>A	c.(583-585)Gtt>Att	p.V195I	ZNF805_ENST00000354309.4_Missense_Mutation_p.V62I|ZNF805_ENST00000535550.1_Missense_Mutation_p.V62I	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	195					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(3)|lung(1)|stomach(1)	9						TAAAAATCCAGTTATTCAGGA	0.413													.|||	1831	0.365615	0.2421	0.4481	5008	,	,		22087	0.1766		0.5746	False		,,,				2504	0.454				p.V195I		Atlas-SNP	.											.	ZNF805	30	.	0			c.G583A						PASS	.	A	ILE/VAL,ILE/VAL	375,1009		49,277,366	122.0	105.0	110.0		583,184	-8.7	0.0	19	dbSNP_119	110	1647,1535		429,789,373	yes	missense,missense	ZNF805	NM_001023563.3,NM_001145078.1	29,29	478,1066,739	AA,AG,GG		48.2401,27.0954,44.2838	benign,benign	195/628,62/495	57764770	2022,2544	692	1591	2283	SO:0001583	missense	390980	exon4			AATCCAGTTATTC	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.583G>A	19.37:g.57764770G>A	ENSP00000412999:p.Val195Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_001023563	B4DNM5	Missense_Mutation	SNP	ENST00000414468.2	37	CCDS46207.1	848	0.3882783882783883	129	0.2621951219512195	174	0.48066298342541436	112	0.1958041958041958	433	0.5712401055408971	g	6.573	0.474080	0.12521	0.270954	0.517599	ENSG00000204524	ENST00000535550;ENST00000414468;ENST00000354309	T;T;T	0.06371	3.31;3.47;3.31	4.35	-8.7	0.00851	.	.	.	.	.	T	0.00012	0.0000	N	0.05050	-0.12	0.80722	P	0.0	B	0.18166	0.026	B	0.12837	0.008	T	0.43702	-0.9375	8	0.54805	T	0.06	.	2.344	0.04267	0.3727:0.0955:0.3431:0.1887	rs10421632;rs52822092;rs10421632	195	Q5CZA5	ZN805_HUMAN	I	62;195;62	ENSP00000440067:V62I;ENSP00000412999:V195I;ENSP00000365414:V62I	ENSP00000365414:V62I	V	+	1	0	ZNF805	62456582	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.992000	0.00657	-3.127000	0.00237	-2.384000	0.00231	GTT	G|0.634;A|0.366	0.366	strong		0.413	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563	
SALL1	6299	hgsc.bcm.edu	37	16	51173559	51173559	+	Silent	SNP	G	G	A	rs1965024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:51173559G>A	ENST00000251020.4	-	2	2607	c.2574C>T	c.(2572-2574)ctC>ctT	p.L858L	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.L761L	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	858					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L858L(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TCGACATCTCGAGGGGCAAAG	0.527													G|||	2698	0.538738	0.1006	0.634	5008	,	,		21471	0.7173		0.6223	False		,,,				2504	0.7935				p.L858L	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											SALL1,NS,carcinoma,0,1	SALL1	301	1	1	Substitution - coding silent(1)	prostate(1)	c.C2574T						PASS	.	G	,	890,3506	343.8+/-307.8	97,696,1405	96.0	94.0	95.0		2283,2574	-10.7	0.7	16	dbSNP_92	95	5503,3097	659.0+/-401.6	1761,1981,558	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	1858,2677,1963	AA,AG,GG		36.0116,20.2457,49.1921	,	761/1228,858/1325	51173559	6393,6603	2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			CATCTCGAGGGGC	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2574C>T	16.37:g.51173559G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	163	160	0.981595	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			.	.	weak		0.527	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
PGBD1	84547	hgsc.bcm.edu	37	6	28268824	28268824	+	Missense_Mutation	SNP	A	A	G	rs33932084	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28268824A>G	ENST00000405948.2	+	7	1613	c.1193A>G	c.(1192-1194)aAt>aGt	p.N398S	PGBD1_ENST00000259883.3_Missense_Mutation_p.N398S	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	398			N -> S (in dbSNP:rs33932084).			membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						ATTAAACCCAATTTTCCAAGC	0.383													A|||	121	0.0241613	0.0257	0.0216	5008	,	,		19621	0.001		0.0706	False		,,,				2504	0.0				p.N398S		Atlas-SNP	.											.	PGBD1	106	.	0			c.A1193G						PASS	.	A	SER/ASN,SER/ASN	250,4156	140.4+/-175.9	6,238,1959	66.0	71.0	69.0		1193,1193	-0.6	1.0	6	dbSNP_126	69	755,7845	176.3+/-226.2	35,685,3580	yes	missense,missense	PGBD1	NM_001184743.1,NM_032507.3	46,46	41,923,5539	GG,GA,AA		8.7791,5.6741,7.7272	benign,benign	398/810,398/810	28268824	1005,12001	2203	4300	6503	SO:0001583	missense	84547	exon7			AACCCAATTTTCC	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1193A>G	6.37:g.28268824A>G	ENSP00000385213:p.Asn398Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	83	0.038003663003663	18	0.036585365853658534	7	0.019337016574585635	0	0.0	58	0.07651715039577836	A	8.244	0.807549	0.16467	0.056741	0.087791	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01388	4.95;4.95	4.54	-0.61	0.11604	.	0.439561	0.19459	N	0.113751	T	0.00271	0.0008	N	0.12182	0.205	0.25988	N	0.982283	B	0.10296	0.003	B	0.06405	0.002	T	0.31364	-0.9946	10	0.10902	T	0.67	-19.5486	7.3919	0.26915	0.5566:0.0:0.4434:0.0	rs33932084	398	Q96JS3	PGBD1_HUMAN	S	398	ENSP00000385213:N398S;ENSP00000259883:N398S	ENSP00000259883:N398S	N	+	2	0	PGBD1	28376803	0.064000	0.20934	0.992000	0.48379	0.995000	0.86356	-0.220000	0.09215	-0.170000	0.10816	0.533000	0.62120	AAT	A|0.939;G|0.061	0.061	strong		0.383	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
DSE	29940	hgsc.bcm.edu	37	6	116720487	116720487	+	Missense_Mutation	SNP	C	C	T	rs10485183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116720487C>T	ENST00000331677.3	+	3	518	c.74C>T	c.(73-75)aCc>aTc	p.T25I	DSE_ENST00000452085.3_Missense_Mutation_p.T25I|DSE_ENST00000359564.2_Missense_Mutation_p.T25I|DSE_ENST00000537543.1_Missense_Mutation_p.T44I|DSE_ENST00000540275.1_3'UTR			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	25			T -> I (in dbSNP:rs10485183).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		GCCTACATCACCGACGAGAAC	0.512													C|||	684	0.136581	0.0908	0.2046	5008	,	,		18041	0.0169		0.2734	False		,,,				2504	0.1329				p.T25I		Atlas-SNP	.											DSE,rectum,carcinoma,-1,1	DSE	98	1	0			c.C74T						PASS	.	C	ILE/THR,ILE/THR	607,3799	264.7+/-266.2	39,529,1635	89.0	78.0	82.0		74,74	4.8	0.2	6	dbSNP_119	82	2783,5817	441.7+/-359.9	455,1873,1972	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	89,89	494,2402,3607	TT,TC,CC		32.3605,13.7767,26.0649	benign,benign	25/959,25/959	116720487	3390,9616	2203	4300	6503	SO:0001583	missense	29940	exon2			ACATCACCGACGA	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.74C>T	6.37:g.116720487C>T	ENSP00000332151:p.Thr25Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	95	33	0.347368	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	361	0.1652930402930403	48	0.0975609756097561	90	0.24861878453038674	17	0.02972027972027972	206	0.2717678100263852	C	12.67	2.007432	0.35415	0.137767	0.323605	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.65	4.77	0.60923	.	0.345981	0.33610	N	0.004734	T	0.14141	0.0342	L	0.36672	1.1	0.29795	P	0.832921	B;B	0.27791	0.189;0.062	B;B	0.33254	0.16;0.048	T	0.06267	-1.0836	9	0.52906	T	0.07	-9.9049	16.6514	0.85203	0.0:0.8702:0.1298:0.0	rs10485183;rs10485183	44;25	B7Z765;Q9UL01	.;DSE_HUMAN	I	25;25;44;25;25	ENSP00000397597:T25I;ENSP00000404049:T25I;ENSP00000441152:T44I;ENSP00000332151:T25I;ENSP00000352567:T25I	ENSP00000332151:T25I	T	+	2	0	DSE	116827180	0.001000	0.12720	0.234000	0.24042	0.710000	0.40934	0.555000	0.23422	1.593000	0.50029	0.655000	0.94253	ACC	C|0.500;T|0.500	0.500	strong		0.512	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
MAMLD1	10046	hgsc.bcm.edu	37	X	149638920	149638920	+	Missense_Mutation	SNP	C	C	T	rs41313406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:149638920C>T	ENST00000370401.2	+	4	1385	c.1075C>T	c.(1075-1077)Cca>Tca	p.P359S	MAMLD1_ENST00000432680.2_Missense_Mutation_p.P334S|MAMLD1_ENST00000426613.2_Missense_Mutation_p.P334S|MAMLD1_ENST00000262858.5_Missense_Mutation_p.P359S|MAMLD1_ENST00000455522.2_5'Flank			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	359	Poly-Pro.		P -> S (in dbSNP:rs41313406). {ECO:0000269|PubMed:17086185}.		male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					accaccacccccaTTCAGCCC	0.612													C|||	154	0.0407947	0.003	0.049	3775	,	,		13714	0.001		0.1004	False		,,,				2504	0.0143				p.P359S		Atlas-SNP	.											.	MAMLD1	263	.	0			c.C1075T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	68,3766		0,58,10,1574,560	83.0	66.0	72.0		1000,1000,1075	0.3	0.0	X	dbSNP_127	72	846,5882		33,550,230,1845,1642	yes	missense,missense,missense	MAMLD1	NM_001177465.1,NM_001177466.1,NM_005491.3	74,74,74	33,608,240,3419,2202	TT,TC,T,CC,C		12.5743,1.7736,8.6537	probably-damaging,probably-damaging,probably-damaging	334/999,334/750,359/775	149638920	914,9648	2202	4300	6502	SO:0001583	missense	10046	exon3			CCACCCCCATTCA	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1075C>T	X.37:g.149638920C>T	ENSP00000359428:p.Pro359Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_005491	B2RCQ4|B4DG93|B9EGA5	Missense_Mutation	SNP	ENST00000370401.2	37	CCDS14693.2	108	0.0650994575045208	3	0.006122448979591836	18	0.05142857142857143	0	0.0	49	0.07040229885057471	C	2.468	-0.322517	0.05350	0.017736	0.125743	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000432680;ENST00000262858;ENST00000426613	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	1.18	0.275	0.15659	.	0.161882	0.29699	N	0.011432	T	0.02047	0.0064	M	0.71581	2.175	0.80722	P	0.0	D;D;B;P	0.89917	1.0;1.0;0.341;0.775	D;D;B;B	0.87578	0.998;0.998;0.086;0.306	T	0.45991	-0.9223	8	.	.	.	-0.7732	3.3336	0.07093	0.0:0.6971:0.0:0.3029	rs41313406	321;334;334;359	F6WVG1;Q13495-4;Q13495-3;Q13495	.;.;.;MAMD1_HUMAN	S	321;359;334;359;334	ENSP00000359428:P359S;ENSP00000414517:P334S;ENSP00000262858:P359S;ENSP00000397438:P334S	.	P	+	1	0	MAMLD1	149389578	0.049000	0.20398	0.000000	0.03702	0.032000	0.12392	1.043000	0.30316	0.019000	0.15079	-0.191000	0.12829	CCA	C|0.927;T|0.073	0.073	strong		0.612	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491	
IGSF10	285313	hgsc.bcm.edu	37	3	151155620	151155620	+	Silent	SNP	G	G	A	rs6781302	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:151155620G>A	ENST00000282466.3	-	6	6728	c.6729C>T	c.(6727-6729)aaC>aaT	p.N2243N	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2243	Ig-like C2-type 9.			N -> S (in Ref. 3; AAH31063). {ECO:0000305}.	cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TAACAGTTCTGTTTGTATACA	0.438													G|||	2964	0.591853	0.5015	0.5937	5008	,	,		22139	0.5169		0.7565	False		,,,				2504	0.6207				p.N2243N		Atlas-SNP	.											.	IGSF10	279	.	0			c.C6729T						PASS	.	G	,,	2340,2066	605.2+/-390.5	628,1084,491	110.0	98.0	102.0		810,666,6729	3.7	0.1	3	dbSNP_116	102	6549,2051	720.2+/-406.3	2496,1557,247	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	3124,2641,738	AA,AG,GG		23.8488,46.8906,31.6546	,,	270/651,222/603,2243/2624	151155620	8889,4117	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			AGTTCTGTTTGTA	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6729C>T	3.37:g.151155620G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			G|0.352;A|0.648	0.648	strong		0.438	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
HMHA1	23526	hgsc.bcm.edu	37	19	1079959	1079959	+	Missense_Mutation	SNP	G	G	A	rs36084354	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1079959G>A	ENST00000313093.2	+	13	1776	c.1545G>A	c.(1543-1545)atG>atA	p.M515I	HMHA1_ENST00000539243.2_Missense_Mutation_p.M531I|HMHA1_ENST00000543365.1_Missense_Mutation_p.M398I|HMHA1_ENST00000586866.1_Missense_Mutation_p.M519I|HMHA1_ENST00000590577.1_Missense_Mutation_p.M150I|HMHA1_ENST00000590214.1_Missense_Mutation_p.M542I|HMHA1_ENST00000536472.1_Missense_Mutation_p.M355I	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	515			M -> I (in dbSNP:rs36084354).		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGATGCATATGCAGACGGCGC	0.682													G|||	146	0.0291534	0.0045	0.0548	5008	,	,		15433	0.0069		0.0855	False		,,,				2504	0.0092				p.M531I		Atlas-SNP	.											HMHA1,NS,carcinoma,0,2	HMHA1	78	2	0			c.G1593A						PASS	.	G	ILE/MET	82,4324	68.1+/-105.8	2,78,2123	74.0	83.0	80.0		1545	4.4	1.0	19	dbSNP_126	80	706,7894	170.9+/-221.9	37,632,3631	yes	missense	HMHA1	NM_012292.2	10	39,710,5754	AA,AG,GG		8.2093,1.8611,6.0587	benign	515/1137	1079959	788,12218	2203	4300	6503	SO:0001583	missense	23526	exon13			GCATATGCAGACG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.1545G>A	19.37:g.1079959G>A	ENSP00000316772:p.Met515Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	42	0.646154	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	37	CCDS32863.1	95	0.043498168498168496	7	0.014227642276422764	27	0.07458563535911603	4	0.006993006993006993	57	0.07519788918205805	G	17.24	3.339832	0.60963	0.018611	0.082093	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	4.41	4.41	0.53225	.	0.044760	0.85682	U	0.000000	T	0.02688	0.0081	M	0.66939	2.045	0.54753	D	0.999981	P;B;B;B;B	0.38827	0.649;0.4;0.215;0.4;0.172	B;B;B;B;B	0.35770	0.21;0.173;0.062;0.077;0.035	T	0.01608	-1.1313	10	0.29301	T	0.29	-21.4743	14.4939	0.67670	0.0:0.0:1.0:0.0	rs36084354;rs62131203	355;531;150;398;515	F5H4A3;F6QP70;B3KVA9;F5H1R4;Q92619	.;.;.;.;HMHA1_HUMAN	I	531;515;515;355;509;398	ENSP00000439601:M531I;ENSP00000316772:M515I;ENSP00000445109:M355I;ENSP00000438979:M398I	ENSP00000316772:M515I	M	+	3	0	HMHA1	1030959	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.741000	0.47426	2.021000	0.59480	0.561000	0.74099	ATG	G|0.948;A|0.052	0.052	strong		0.682	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
OR4K1	79544	hgsc.bcm.edu	37	14	20404735	20404735	+	Missense_Mutation	SNP	C	C	T	rs34394400	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20404735C>T	ENST00000285600.4	+	1	969	c.910C>T	c.(910-912)Cgt>Tgt	p.R304C		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, member 1	304			R -> H (in dbSNP:rs2792146). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		GCTGAGAAACCGTCATGTGAA	0.428													C|||	1174	0.234425	0.1195	0.2363	5008	,	,		22691	0.1974		0.3211	False		,,,				2504	0.3374				p.R304C		Atlas-SNP	.											.	OR4K1	108	.	0			c.C910T						PASS	.	C	CYS/ARG	636,3770		28,580,1595	72.0	79.0	77.0		910	0.6	0.0	14	dbSNP_126	77	2688,5912		287,2114,1899	yes	missense	OR4K1	NM_001004063.2	180	315,2694,3494	TT,TC,CC		31.2558,14.4349,25.5574	possibly-damaging	304/312	20404735	3324,9682	2203	4300	6503	SO:0001583	missense	79544	exon1			AGAAACCGTCATG		CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"""GPCR / Class A : Olfactory receptors"""	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.910C>T	14.37:g.20404735C>T	ENSP00000285600:p.Arg304Cys	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_001004063	B9EKV9|Q8NGD6|Q96R73	Missense_Mutation	SNP	ENST00000285600.4	37	CCDS32025.1	519	0.23763736263736263	63	0.12804878048780488	94	0.2596685082872928	103	0.18006993006993008	259	0.341688654353562	.	7.788	0.711016	0.15239	0.144349	0.312558	ENSG00000155249	ENST00000285600	T	0.35048	1.33	5.17	0.607	0.17564	.	0.609210	0.15670	N	0.250404	T	0.00012	0.0000	L	0.39692	1.235	0.80722	P	0.0	D	0.59767	0.986	B	0.41510	0.359	T	0.41538	-0.9503	9	0.72032	D	0.01	.	7.8378	0.29380	0.4734:0.4492:0.0:0.0774	rs34394400	304	Q8NGD4	OR4K1_HUMAN	C	304	ENSP00000285600:R304C	ENSP00000285600:R304C	R	+	1	0	OR4K1	19474575	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.468000	0.22051	0.209000	0.20645	-0.136000	0.14681	CGT	C|0.733;T|0.267	0.267	strong		0.428	OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1		
GNL1	2794	hgsc.bcm.edu	37	6	30515043	30515043	+	Silent	SNP	T	T	C	rs3130247	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30515043T>C	ENST00000376621.3	-	10	2257	c.1287A>G	c.(1285-1287)gcA>gcG	p.A429A		NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	429					cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GGTAGATCCCTGCCAGAACCT	0.597													T|||	110	0.0219649	0.0121	0.0216	5008	,	,		19418	0.0		0.0785	False		,,,				2504	0.0				p.A429A		Atlas-SNP	.											.	GNL1	47	.	0			c.A1287G						PASS	.	T		103,2919		1,101,1409	195.0	185.0	189.0		1287	-10.0	0.3	6	dbSNP_103	189	578,4840		35,508,2166	yes	coding-synonymous	GNL1	NM_005275.3		36,609,3575	CC,CT,TT		10.6681,3.4083,8.0687		429/608	30515043	681,7759	1511	2709	4220	SO:0001819	synonymous_variant	2794	exon10			GATCCCTGCCAGA		CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590			4413	protein-coding gene	gene with protein product		143024				8180467	Standard	NM_005275		Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.1287A>G	6.37:g.30515043T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	175	69	0.394286	NM_005275	B0S838|Q96CT5	Silent	SNP	ENST00000376621.3	37	CCDS4680.1																																																																																			T|0.939;C|0.061	0.061	strong		0.597	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076241.2		
PER3	8863	hgsc.bcm.edu	37	1	7890024	7890024	+	Missense_Mutation	SNP	T	T	G	rs201662971|rs57875989		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:7890024T>G	ENST00000361923.2	+	18	3165	c.2990T>G	c.(2989-2991)aTg>aGg	p.M997R	PER3_ENST00000377532.3_Missense_Mutation_p.M1006R|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	997	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.M997R(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TCGCCTCCCATGAAGAATCCA	0.582																																					p.M997R		Atlas-SNP	.											PER3,NS,carcinoma,0,3	PER3	95	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.T2990G						scavenged	.						85.0	70.0	75.0					1																	7890024		2001	3894	5895	SO:0001583	missense	8863	exon18			CTCCCATGAAGAA	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2990T>G	1.37:g.7890024T>G	ENSP00000355031:p.Met997Arg	Somatic	278	2	0.00719424		WXS	Illumina HiSeq	Phase_I	105	19	0.180952	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	T	0.033	-1.321421	0.01320	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.14640	2.49;2.49	.	.	.	Period circadian-like, C-terminal (1);	31.945600	0.01768	N	0.031022	T	0.04861	0.0131	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.25152	-1.0140	8	0.11485	T	0.65	.	.	.	.	.	997;1006;1006;997	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	R	1006;997	ENSP00000366755:M1006R;ENSP00000355031:M997R	ENSP00000355031:M997R	M	+	2	0	PER3	7812611	0.004000	0.15560	0.012000	0.15200	0.013000	0.08279	-1.043000	0.03535	-1.402000	0.02056	-1.459000	0.01027	ATG	.	.	weak		0.582	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
ESPNL	339768	hgsc.bcm.edu	37	2	239038912	239038912	+	Silent	SNP	T	T	C	rs57813708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:239038912T>C	ENST00000343063.3	+	9	1820	c.1557T>C	c.(1555-1557)ctT>ctC	p.L519L	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Silent_p.L151L|ESPNL_ENST00000409169.1_Silent_p.L475L	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	519										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		ACCTGCAGCTTCGGCGCCGCT	0.632													T|||	1243	0.248203	0.3215	0.2709	5008	,	,		17111	0.1835		0.2386	False		,,,				2504	0.2096				p.L519L		Atlas-SNP	.											.	ESPNL	63	.	0			c.T1557C						PASS	.	T		1358,3038		206,946,1046	24.0	24.0	24.0		1557	0.8	1.0	2	dbSNP_129	24	1944,6650		230,1484,2583	yes	coding-synonymous	ESPNL	NM_194312.2		436,2430,3629	CC,CT,TT		22.6204,30.8917,25.4196		519/1006	239038912	3302,9688	2198	4297	6495	SO:0001819	synonymous_variant	339768	exon9			GCAGCTTCGGCGC	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1557T>C	2.37:g.239038912T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			T|0.748;C|0.252	0.252	strong		0.632	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
ZNF174	7727	hgsc.bcm.edu	37	16	3454480	3454480	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3454480C>T	ENST00000268655.4	+	2	1042	c.457C>T	c.(457-459)Ctt>Ttt	p.L153F	ZNF174_ENST00000572544.1_Missense_Mutation_p.L153F|ZNF174_ENST00000575752.1_Missense_Mutation_p.L153F|ZNF174_ENST00000344823.5_Missense_Mutation_p.L153F|ZNF174_ENST00000571936.1_Missense_Mutation_p.L153F	NM_003450.2	NP_003441.1	Q15697	ZN174_HUMAN	zinc finger protein 174	153					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|urinary_tract(2)	12						TGGATCTCAGCTTGGAGAACA	0.537																																					p.L153F		Atlas-SNP	.											.	ZNF174	32	.	0			c.C457T						PASS	.						115.0	126.0	122.0					16																	3454480		2197	4300	6497	SO:0001583	missense	7727	exon2			TCTCAGCTTGGAG	U31248	CCDS10504.1, CCDS32380.1	16p13	2013-01-09			ENSG00000103343	ENSG00000103343		"""-"", ""Zinc fingers, C2H2-type"""	12963	protein-coding gene	gene with protein product		603900					Standard	NM_003450		Approved	ZSCAN8	uc002cvc.3	Q15697	OTTHUMG00000129358	ENST00000268655.4:c.457C>T	16.37:g.3454480C>T	ENSP00000268655:p.Leu153Phe	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_001032292	Q53Y68|Q9BQ34	Missense_Mutation	SNP	ENST00000268655.4	37	CCDS10504.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508223	0.44660	.	.	ENSG00000103343	ENST00000344823;ENST00000268655	T;T	0.07444	4.06;3.19	5.32	3.34	0.38264	Transcription regulator SCAN (1);	0.161847	0.29631	N	0.011620	T	0.11153	0.0272	L	0.29908	0.895	0.29888	N	0.825478	P;D;P	0.53619	0.761;0.961;0.935	B;P;P	0.56700	0.36;0.804;0.642	T	0.02345	-1.1173	10	0.56958	D	0.05	.	5.9089	0.19016	0.1921:0.7141:0.0:0.0937	.	153;153;153	Q15697;Q15697-2;Q8IZN5	ZN174_HUMAN;.;.	F	153	ENSP00000339781:L153F;ENSP00000268655:L153F	ENSP00000268655:L153F	L	+	1	0	ZNF174	3394481	0.994000	0.37717	1.000000	0.80357	0.984000	0.73092	0.526000	0.22971	1.542000	0.49330	0.563000	0.77884	CTT	.	.	none		0.537	ZNF174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251510.1	NM_003450	
FKBP6	8468	hgsc.bcm.edu	37	7	72754645	72754645	+	Silent	SNP	G	G	A	rs56301507	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:72754645G>A	ENST00000252037.4	+	6	663	c.594G>A	c.(592-594)ctG>ctA	p.L198L	RNU6-1080P_ENST00000383982.1_RNA|FKBP6_ENST00000413573.2_Silent_p.L168L|FKBP6_ENST00000431982.2_Silent_p.L193L	NM_003602.3	NP_003593.3	O75344	FKBP6_HUMAN	FK506 binding protein 6, 36kDa	198					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|piRNA metabolic process (GO:0034587)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|synaptonemal complex (GO:0000795)	FK506 binding (GO:0005528)|Hsp90 protein binding (GO:0051879)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	16		Lung NSC(55;0.0908)|all_lung(88;0.198)				CACAGGCCCTGTTGCTTCTGC	0.517													G|||	239	0.0477236	0.003	0.1124	5008	,	,		16721	0.0784		0.0686	False		,,,				2504	0.0092				p.L198L		Atlas-SNP	.											.	FKBP6	35	.	0			c.G594A						PASS	.	G	,	63,3877		1,61,1908	46.0	51.0	49.0		579,594	4.0	0.7	7	dbSNP_129	49	471,7827		12,447,3690	no	coding-synonymous,coding-synonymous	FKBP6	NM_001135211.1,NM_003602.3	,	13,508,5598	AA,AG,GG		5.6761,1.599,4.3635	,	193/323,198/328	72754645	534,11704	1970	4149	6119	SO:0001819	synonymous_variant	8468	exon6			GGCCCTGTTGCTT	AF038847	CCDS43595.1, CCDS47604.1, CCDS64670.1	7q11.23	2009-01-05	2002-08-29		ENSG00000077800	ENSG00000077800			3722	protein-coding gene	gene with protein product	"""FK506 binding protein 6 (36kD)"", ""peptidylprolyl cis-trans isomerase"", ""rotamase"", ""immunophilin FKBP36"""	604839	"""FK506-binding protein 6 (36kD)"""			9782077, 19001379	Standard	NM_003602		Approved	PPIase, FKBP36	uc003tya.2	O75344	OTTHUMG00000150520	ENST00000252037.4:c.594G>A	7.37:g.72754645G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_003602	B4DXT7|G3V0I2|Q7Z4T4|Q9UDS0	Silent	SNP	ENST00000252037.4	37	CCDS43595.1																																																																																			G|0.937;A|0.063	0.063	strong		0.517	FKBP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318723.1	NM_003602	
GPR139	124274	hgsc.bcm.edu	37	16	20043330	20043330	+	Silent	SNP	T	T	C	rs2147865	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20043330T>C	ENST00000570682.1	-	2	1089	c.789A>G	c.(787-789)gtA>gtG	p.V263V		NM_001002911.2	NP_001002911.1	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	263					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	30						ACATGATGTGTACCAGCCAGC	0.532													C|||	2594	0.517971	0.6029	0.4092	5008	,	,		19887	0.7827		0.328	False		,,,				2504	0.4029				p.V263V		Atlas-SNP	.											.	GPR139	75	.	0			c.A789G						PASS	.	C		2400,2006	561.5+/-380.7	651,1098,454	71.0	74.0	73.0		789	4.8	1.0	16	dbSNP_96	73	2609,5991	689.1+/-404.3	386,1837,2077	no	coding-synonymous	GPR139	NM_001002911.2		1037,2935,2531	CC,CT,TT		30.3372,45.5288,38.513		263/354	20043330	5009,7997	2203	4300	6503	SO:0001819	synonymous_variant	124274	exon2			GATGTGTACCAGC	AY255545	CCDS32398.1	16p13.11	2012-08-21						"""GPCR / Class A : Orphans"""	19995	protein-coding gene	gene with protein product						12679517	Standard	XM_005255114		Approved	PGR3	uc002dgu.1	Q6DWJ6		ENST00000570682.1:c.789A>G	16.37:g.20043330T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	171	79	0.461988	NM_001002911	A8K5R9|Q86SP2|Q8TDU8	Silent	SNP	ENST00000570682.1	37	CCDS32398.1																																																																																			T|0.549;C|0.451	0.451	strong		0.532	GPR139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438522.1	NM_001002911	
PAPL	390928	hgsc.bcm.edu	37	19	39589189	39589189	+	Silent	SNP	C	C	T	rs55878600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39589189C>T	ENST00000331256.5	+	3	487	c.213C>T	c.(211-213)ccC>ccT	p.P71P	PAPL_ENST00000594229.1_Silent_p.P71P	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		71						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										GGCCCCTGCCCCTCCGCGCCC	0.647													c|||	1149	0.229433	0.0348	0.2709	5008	,	,		13054	0.4077		0.2306	False		,,,				2504	0.2781				p.P71P		Atlas-SNP	.											.	.	.	.	0			c.C213T						PASS	.	C		372,4034	187.4+/-214.1	14,344,1845	36.0	34.0	35.0		213	-0.2	0.3	19	dbSNP_129	35	2109,6491	351.2+/-328.2	258,1593,2449	no	coding-synonymous	PAPL	NM_001004318.2		272,1937,4294	TT,TC,CC		24.5233,8.443,19.0758		71/439	39589189	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			CCTGCCCCTCCGC																												ENST00000331256.5:c.213C>T	19.37:g.39589189C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_001004318	B2RN68	Silent	SNP	ENST00000331256.5	37	CCDS33018.1																																																																																			C|0.796;T|0.204	0.204	strong		0.647	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
ASTN2	23245	hgsc.bcm.edu	37	9	119491277	119491277	+	Missense_Mutation	SNP	C	C	T	rs72765708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:119491277C>T	ENST00000313400.4	-	15	2720	c.2620G>A	c.(2620-2622)Gca>Aca	p.A874T	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.A870T|ASTN2_ENST00000361209.2_Missense_Mutation_p.A823T			O75129	ASTN2_HUMAN	astrotactin 2	874					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TCACCTGCTGCGAGGGTGATG	0.572													A|||	209	0.0417332	0.0053	0.0447	5008	,	,		15673	0.0		0.1282	False		,,,				2504	0.0429				p.A823T		Atlas-SNP	.											.	ASTN2	307	.	0			c.G2467A						PASS	.	A	THR/ALA	112,4292		1,110,2091	43.0	30.0	34.0		2467	5.5	1.0	9	dbSNP_130	34	1117,7479		76,965,3257	yes	missense	ASTN2	NM_014010.4	58	77,1075,5348	TT,TC,CC		12.9944,2.5431,9.4538	benign	823/1289	119491277	1229,11771	2202	4298	6500	SO:0001583	missense	23245	exon14			CTGCTGCGAGGGT	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.2620G>A	9.37:g.119491277C>T	ENSP00000314038:p.Ala874Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		130	0.05952380952380952	3	0.006097560975609756	19	0.052486187845303865	0	0.0	108	0.1424802110817942	A	35	5.527528	0.96431	0.025431	0.129944	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72	5.54	5.54	0.83059	Membrane attack complex component/perforin (MACPF) domain (2);	0.000000	0.85682	D	0.000000	T	0.00666	0.0022	N	0.03608	-0.345	0.45005	P	0.0019759999999999778	P;B;B	0.42757	0.789;0.003;0.022	B;B;B	0.28465	0.09;0.006;0.006	T	0.33727	-0.9857	8	.	.	.	-5.4616	13.1401	0.59430	0.8662:0.1338:0.0:0.0	.	823;874;870	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	T	874;870;597;823	ENSP00000314038:A874T;ENSP00000363108:A870T;ENSP00000363098:A597T;ENSP00000354504:A823T	.	A	-	1	0	ASTN2	118531098	1.000000	0.71417	0.965000	0.40720	0.943000	0.58893	6.143000	0.71756	1.037000	0.40024	-0.269000	0.10298	GCA	C|0.925;T|0.075	0.075	strong		0.572	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
ADH7	131	hgsc.bcm.edu	37	4	100349669	100349669	+	Missense_Mutation	SNP	C	C	G	rs543158429|rs1573496	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:100349669C>G	ENST00000209665.4	-	3	515	c.275G>C	c.(274-276)gGa>gCa	p.G92A	ADH7_ENST00000476959.1_Missense_Mutation_p.G100A|ADH7_ENST00000482593.1_Missense_Mutation_p.G23A|ADH7_ENST00000437033.2_Missense_Mutation_p.G80A	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	92			G -> A (in dbSNP:rs1573496).		ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		TGTAGTCACTCCTTCTCCAAT	0.423																																					p.G100A		Atlas-SNP	.											ADH7_ENST00000476959,NS,malignant_melanoma,-1,2	ADH7	76	2	0			c.G299C						PASS	.	C	ALA/GLY,ALA/GLY	80,4326	68.7+/-106.4	3,74,2126	260.0	214.0	230.0	http://omim.org/entry/103720	275,299	3.4	0.5	4	dbSNP_88	230	950,7650	208.4+/-249.9	62,826,3412	yes	missense,missense	ADH7	NM_000673.4,NM_001166504.1	60,60	65,900,5538	GG,GC,CC		11.0465,1.8157,7.9194	possibly-damaging,possibly-damaging	92/387,100/395	100349669	1030,11976	2203	4300	6503	SO:0001583	missense	131	exon3			GTCACTCCTTCTC	X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"""Alcohol dehydrogenases"""	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.275G>C	4.37:g.100349669C>G	ENSP00000209665:p.Gly92Ala	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_001166504	A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Missense_Mutation	SNP	ENST00000209665.4	37	CCDS34034.1	127	0.05815018315018315	0	0.0	39	0.10773480662983426	0	0.0	88	0.11609498680738786	C	18.53	3.644194	0.67244	0.018157	0.110465	ENSG00000196344	ENST00000437033;ENST00000209665;ENST00000482593;ENST00000476959;ENST00000474027	T;T;T;T;T	0.04049	3.72;3.72;3.72;3.72;3.72	4.24	3.39	0.38822	GroES-like (1);Alcohol dehydrogenase GroES-like (1);Alcohol dehydrogenase, zinc-type, conserved site (1);	0.296303	0.36338	N	0.002660	T	0.00210	0.0006	M	0.62266	1.93	0.18873	P	0.9999810684	D	0.55800	0.973	D	0.63033	0.91	T	0.04115	-1.0976	9	0.87932	D	0	-16.7579	10.8069	0.46522	0.0:0.8377:0.0:0.1623	rs1573496;rs52814989;rs56770102;rs1573496	92	P40394	ADH7_HUMAN	A	80;92;23;100;23	ENSP00000414254:G80A;ENSP00000209665:G92A;ENSP00000420613:G23A;ENSP00000420269:G100A;ENSP00000420300:G23A	ENSP00000209665:G92A	G	-	2	0	ADH7	100568692	0.904000	0.30761	0.496000	0.27539	0.945000	0.59286	3.253000	0.51469	0.973000	0.38340	0.655000	0.94253	GGA	C|0.933;G|0.067	0.067	strong		0.423	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673	
ADCK4	79934	hgsc.bcm.edu	37	19	41209477	41209477	+	Silent	SNP	C	C	T	rs11538385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41209477C>T	ENST00000324464.3	-	9	1069	c.768G>A	c.(766-768)gcG>gcA	p.A256A	ADCK4_ENST00000243583.6_Silent_p.A215A|ADCK4_ENST00000450541.1_Silent_p.A215A	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	256	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			TCTTGAGTACCGCCAGCAGGT	0.622													C|||	1149	0.229433	0.084	0.196	5008	,	,		17506	0.2361		0.3032	False		,,,				2504	0.3671				p.A256A		Atlas-SNP	.											ADCK4_ENST00000324464,colon,carcinoma,-1,6	ADCK4	92	6	0			c.G768A						PASS	.	C	,	543,3863	240.9+/-251.5	35,473,1695	55.0	57.0	56.0		645,768	-10.1	0.5	19	dbSNP_120	56	2474,6126	404.1+/-348.0	353,1768,2179	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	388,2241,3874	TT,TC,CC		28.7674,12.3241,23.197	,	215/504,256/545	41209477	3017,9989	2203	4300	6503	SO:0001819	synonymous_variant	79934	exon9			GAGTACCGCCAGC	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.768G>A	19.37:g.41209477C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	NM_024876	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			C|0.773;T|0.227	0.227	strong		0.622	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
CCDC79	283847	hgsc.bcm.edu	37	16	66792714	66792714	+	Missense_Mutation	SNP	T	T	C	rs363156	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:66792714T>C	ENST00000558713.2	-	17	2030	c.1958A>G	c.(1957-1959)cAa>cGa	p.Q653R	CCDC79_ENST00000415744.1_3'UTR|CCDC79_ENST00000433574.1_3'UTR|CCDC79_ENST00000432602.1_Missense_Mutation_p.Q606R|CCDC79_ENST00000433154.1_Missense_Mutation_p.Q653R			Q8NA31	TERB1_HUMAN	coiled-coil domain containing 79	653	Interaction with TERF1. {ECO:0000250}.				meiotic telomere clustering (GO:0045141)|synapsis (GO:0007129)	chromosome, telomeric region (GO:0000781)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|skin(2)	7						ACTGAGTCGTTGTCTTCTACG	0.348													T|||	1722	0.34385	0.0681	0.3963	5008	,	,		17640	0.6161		0.3479	False		,,,				2504	0.3947				p.Q653R		Atlas-SNP	.											.	CCDC79	32	.	0			c.A1958G						PASS	.	T	ARG/GLN	172,1212		16,140,536	213.0	172.0	185.0		1958	-7.6	0.0	16	dbSNP_79	185	1152,2030		210,732,649	yes	missense	CCDC79	NM_001136505.1	43	226,872,1185	CC,CT,TT		36.2036,12.4277,28.9969	benign	653/728	66792714	1324,3242	692	1591	2283	SO:0001583	missense	283847	exon18			AGTCGTTGTCTTC	AK093213		16q22.1	2012-10-03			ENSG00000249961	ENSG00000249961			26675	protein-coding gene	gene with protein product							Standard	NM_001136505		Approved	FLJ35894	uc010viv.2	Q8NA31	OTTHUMG00000133562	ENST00000558713.2:c.1958A>G	16.37:g.66792714T>C	ENSP00000462883:p.Gln653Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	41	12	0.292683	NM_001136505	A0AUW1	Missense_Mutation	SNP	ENST00000558713.2	37		804	0.36813186813186816	38	0.07723577235772358	148	0.4088397790055249	360	0.6293706293706294	258	0.3403693931398417	T	7.896	0.733318	0.15574	0.124277	0.362036	ENSG00000177461	ENST00000433154;ENST00000432602	.	.	.	4.96	-7.59	0.01308	.	.	.	.	.	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45848	-0.9233	7	0.02654	T	1	-2.038	14.4873	0.67626	0.0:0.2195:0.0:0.7805	rs363156;rs17700107;rs61213912;rs363156	653	Q8NA31	CCD79_HUMAN	R	653;606	.	ENSP00000446376:Q606R	Q	-	2	0	CCDC79	65350215	0.013000	0.17824	0.000000	0.03702	0.728000	0.41692	-1.224000	0.02959	-1.282000	0.02396	-1.010000	0.02471	CAA	T|0.651;C|0.349	0.349	strong		0.348	CCDC79-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000418864.2		
FAM184B	27146	hgsc.bcm.edu	37	4	17636638	17636638	+	Silent	SNP	G	G	C	rs61745212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:17636638G>C	ENST00000265018.3	-	16	3095	c.2883C>G	c.(2881-2883)tcC>tcG	p.S961S		NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	961										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						TTACCTTCATGGAAGGGGTCA	0.428													G|||	65	0.0129792	0.0295	0.0115	5008	,	,		18359	0.0		0.0149	False		,,,				2504	0.0031				p.S961S		Atlas-SNP	.											.	FAM184B	38	.	0			c.C2883G						PASS	.	G		29,1355		0,29,663	102.0	92.0	95.0		2883	5.3	1.0	4	dbSNP_129	95	48,3134		1,46,1544	no	coding-synonymous	FAM184B	NM_015688.1		1,75,2207	CC,CG,GG		1.5085,2.0954,1.6864		961/1061	17636638	77,4489	692	1591	2283	SO:0001819	synonymous_variant	27146	exon16			CTTCATGGAAGGG		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.2883C>G	4.37:g.17636638G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_015688		Silent	SNP	ENST00000265018.3	37	CCDS47033.1																																																																																			G|0.960;C|0.040	0.040	strong		0.428	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
NUP210	23225	hgsc.bcm.edu	37	3	13368892	13368892	+	Silent	SNP	G	G	A	rs2271509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:13368892G>A	ENST00000254508.5	-	32	4414	c.4332C>T	c.(4330-4332)tgC>tgT	p.C1444C		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1444					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TGCGGACAACGCAGGTGTTGT	0.612													G|||	1985	0.396366	0.4592	0.3775	5008	,	,		19707	0.3016		0.4891	False		,,,				2504	0.3272				p.C1444C		Atlas-SNP	.											NUP210,NS,carcinoma,0,2	NUP210	182	2	0			c.C4332T						PASS	.	G		2074,2332	564.7+/-381.5	474,1126,603	53.0	41.0	45.0		4332	1.7	0.1	3	dbSNP_100	45	4402,4198	577.9+/-390.6	1134,2134,1032	no	coding-synonymous	NUP210	NM_024923.2		1608,3260,1635	AA,AG,GG		48.814,47.0722,49.7924		1444/1888	13368892	6476,6530	2203	4300	6503	SO:0001819	synonymous_variant	23225	exon32			GACAACGCAGGTG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.4332C>T	3.37:g.13368892G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	158	82	0.518987	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1																																																																																			G|0.541;A|0.459	0.459	strong		0.612	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
PDK1	5163	hgsc.bcm.edu	37	2	173460640	173460640	+	Silent	SNP	T	T	C	rs12693005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:173460640T>C	ENST00000282077.3	+	11	1436	c.1254T>C	c.(1252-1254)gaT>gaC	p.D418D	PDK1_ENST00000544863.1_Silent_p.D263D|PDK1_ENST00000543905.1_Silent_p.D342D|PDK1_ENST00000392571.2_Silent_p.D438D|PDK1_ENST00000410055.1_Silent_p.D418D			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1	418					cell proliferation (GO:0008283)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			ACGAGGCTGATGACTGGTGCG	0.473									Autosomal Dominant Polycystic Kidney Disease				T|||	349	0.0696885	0.0628	0.0807	5008	,	,		16058	0.0218		0.1074	False		,,,				2504	0.0818				p.D418D		Atlas-SNP	.											.	PDK1	39	.	0			c.T1254C						PASS	.	T		303,4103	164.4+/-196.0	9,285,1909	80.0	66.0	71.0		1254	-4.3	0.9	2	dbSNP_121	71	1035,7565	219.1+/-257.3	54,927,3319	no	coding-synonymous	PDK1	NM_002610.3		63,1212,5228	CC,CT,TT		12.0349,6.877,10.2876		418/437	173460640	1338,11668	2203	4300	6503	SO:0001819	synonymous_variant	5163	exon11	Familial Cancer Database	ADPKD	GGCTGATGACTGG	L42450	CCDS2250.1, CCDS63059.1	2q31.1	2008-05-23	2005-11-16		ENSG00000152256	ENSG00000152256			8809	protein-coding gene	gene with protein product		602524	"""pyruvate dehydrogenase kinase, isoenzyme 1"""			7499431	Standard	NR_103731		Approved		uc002uhs.3	Q15118	OTTHUMG00000132285	ENST00000282077.3:c.1254T>C	2.37:g.173460640T>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	202	96	0.475248	NM_002610	B2R6T1|B7Z937|D3DPD8|E9PD65|Q308M4	Silent	SNP	ENST00000282077.3	37	CCDS2250.1																																																																																			T|0.907;C|0.093	0.093	strong		0.473	PDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255380.3	NM_002610	
CCDC186	55088	hgsc.bcm.edu	37	10	115922492	115922492	+	Missense_Mutation	SNP	C	C	T	rs12782946	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115922492C>T	ENST00000369287.3	-	2	802	c.536G>A	c.(535-537)cGa>cAa	p.R179Q	C10orf118_ENST00000369286.1_Missense_Mutation_p.R179Q|C10orf118_ENST00000369285.3_Missense_Mutation_p.R179Q	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		179			R -> Q (in dbSNP:rs12782946). {ECO:0000269|PubMed:14996095}.							NS(1)|autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(2)	24		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		ATTTGGTACTCGATGTTCTGC	0.338													C|||	156	0.0311502	0.0015	0.0706	5008	,	,		18398	0.0		0.0974	False		,,,				2504	0.0072				p.R179Q		Atlas-SNP	.											.	C10orf118	70	.	0			c.G536A						PASS	.	C	GLN/ARG	92,4312	76.2+/-114.5	0,92,2110	77.0	74.0	75.0		536	-1.3	1.0	10	dbSNP_121	75	710,7888	174.6+/-224.8	25,660,3614	yes	missense	C10orf118	NM_018017.2	43	25,752,5724	TT,TC,CC		8.2577,2.089,6.1683	benign	179/899	115922492	802,12200	2202	4299	6501	SO:0001583	missense	55088	exon2			GGTACTCGATGTT																												ENST00000369287.3:c.536G>A	10.37:g.115922492C>T	ENSP00000358293:p.Arg179Gln	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	167	88	0.526946	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	103	0.04716117216117216	1	0.0020325203252032522	28	0.07734806629834254	0	0.0	74	0.09762532981530343	C	13.05	2.121216	0.37436	0.02089	0.082577	ENSG00000165813	ENST00000369287;ENST00000430353;ENST00000369286;ENST00000369285	T;T;T	0.29142	1.58;1.58;1.58	5.48	-1.27	0.09347	.	0.498560	0.21829	N	0.068507	T	0.00328	0.0010	N	0.04508	-0.205	0.09310	P	0.9999999999589961	B	0.02656	0.0	B	0.01281	0.0	T	0.28396	-1.0045	9	0.19147	T	0.46	.	11.2522	0.49032	0.0:0.2126:0.0:0.7874	rs12782946;rs17703540;rs56560159;rs61469075;rs12782946	179	Q7Z3E2	CJ118_HUMAN	Q	179;285;179;179	ENSP00000358293:R179Q;ENSP00000358292:R179Q;ENSP00000358291:R179Q	ENSP00000358291:R179Q	R	-	2	0	C10orf118	115912482	0.005000	0.15991	0.988000	0.46212	0.990000	0.78478	-0.072000	0.11486	-0.272000	0.09259	0.650000	0.86243	CGA	C|0.948;T|0.052	0.052	strong		0.338	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1		
CD163	9332	hgsc.bcm.edu	37	12	7649653	7649653	+	Silent	SNP	T	T	C	rs4883264	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7649653T>C	ENST00000359156.4	-	5	1057	c.855A>G	c.(853-855)ggA>ggG	p.G285G	CD163_ENST00000541972.1_Silent_p.G273G|CD163_ENST00000396620.3_Silent_p.G285G|CD163_ENST00000432237.2_Silent_p.G285G	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	285	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	TCCCCCATTCTCCTTGGAATC	0.507													T|||	2410	0.48123	0.1241	0.7233	5008	,	,		-128	0.3839		0.7694	False		,,,				2504	0.5961				p.G285G		Atlas-SNP	.											.	CD163	221	.	0			c.A855G						PASS	.	T	,	988,3418	370.5+/-319.6	123,742,1338	209.0	165.0	180.0		855,855	2.5	1.0	12	dbSNP_111	180	6547,2053	719.5+/-406.3	2496,1555,249	no	coding-synonymous,coding-synonymous	CD163	NM_004244.5,NM_203416.3	,	2619,2297,1587	CC,CT,TT		23.8721,22.424,42.0652	,	285/1157,285/1122	7649653	7535,5471	2203	4300	6503	SO:0001819	synonymous_variant	9332	exon5			CCATTCTCCTTGG	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.855A>G	12.37:g.7649653T>C		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1																																																																																			T|0.460;C|0.540	0.540	strong		0.507	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416	
EIF3F	8665	hgsc.bcm.edu	37	11	8009241	8009241	+	Silent	SNP	C	C	T	rs12421289	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8009241C>T	ENST00000533626.1	+	3	968	c.342C>T	c.(340-342)gcC>gcT	p.A114A	EIF3F_ENST00000309828.4_Silent_p.A114A|EIF3F_ENST00000449102.2_5'UTR|EIF3F_ENST00000537635.1_Silent_p.A129A					eukaryotic translation initiation factor 3, subunit F											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)	13				Epithelial(150;1.44e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGGGTGCTGCCCGAGTTATCG	0.542											OREG0020726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	338	0.067492	0.0424	0.0994	5008	,	,		19051	0.001		0.1829	False		,,,				2504	0.0286				p.A114A		Atlas-SNP	.											.	EIF3F	23	.	0			c.C342T						PASS	.	C		253,4147		8,237,1955	14.0	15.0	15.0		342	2.9	1.0	11	dbSNP_120	15	1506,7080		132,1242,2919	no	coding-synonymous	EIF3F	NM_003754.2		140,1479,4874	TT,TC,CC		17.5402,5.75,13.5454		114/358	8009241	1759,11227	2200	4293	6493	SO:0001819	synonymous_variant	8665	exon1			TGCTGCCCGAGTT	U94855, AK093511	CCDS7785.1	11p15.4	2010-03-10	2007-07-27	2007-07-27	ENSG00000175390	ENSG00000175390			3275	protein-coding gene	gene with protein product		603914	"""eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa"""	EIF3S5		9341143	Standard	NM_003754		Approved	eIF3-epsilon, eIF3-p47, eIF3f	uc001mfw.3	O00303		ENST00000533626.1:c.342C>T	11.37:g.8009241C>T		Somatic	142	0	0	646	WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_003754		Silent	SNP	ENST00000533626.1	37	CCDS7785.1																																																																																			C|0.889;T|0.111	0.111	strong		0.542	EIF3F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385713.2	NM_003754	
C1orf101	257044	hgsc.bcm.edu	37	1	244735858	244735858	+	Silent	SNP	A	A	G	rs10927267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:244735858A>G	ENST00000366534.4	+	11	1788	c.1734A>G	c.(1732-1734)acA>acG	p.T578T	C1orf101_ENST00000366531.3_Silent_p.T427T|C1orf101_ENST00000473875.1_3'UTR|C1orf101_ENST00000366533.4_Silent_p.T578T	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	578						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			TAGCTTTCACAACAAAAGACA	0.393													a|||	1362	0.271965	0.4289	0.2464	5008	,	,		18269	0.373		0.0785	False		,,,				2504	0.1728				p.T578T		Atlas-SNP	.											C1orf101_ENST00000366534,NS,carcinoma,0,2	C1orf101	158	2	0			c.A1734G						PASS	.	A	,,	1693,2713	512.9+/-368.2	326,1041,836	120.0	107.0	111.0		1734,1281,1734	-4.1	0.0	1	dbSNP_120	111	765,7835	181.3+/-230.0	26,713,3561	no	coding-synonymous,coding-synonymous,coding-synonymous	C1orf101	NM_001130957.1,NM_001242340.1,NM_173807.4	,,	352,1754,4397	GG,GA,AA		8.8953,38.4249,18.899	,,	578/952,427/801,578/833	244735858	2458,10548	2203	4300	6503	SO:0001819	synonymous_variant	257044	exon11			TTTCACAACAAAA	BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.1734A>G	1.37:g.244735858A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																			A|0.783;G|0.217	0.217	strong		0.393	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807	
SPEF2	79925	hgsc.bcm.edu	37	5	35759812	35759812	+	Missense_Mutation	SNP	G	G	T	rs201517270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:35759812G>T	ENST00000356031.3	+	25	3765	c.3611G>T	c.(3610-3612)aGc>aTc	p.S1204I	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000440995.2_Missense_Mutation_p.S1199I	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1204					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AATTCTGAAAGCCAGCTTAGG	0.348													G|||	3	0.000599042	0.0	0.0	5008	,	,		16893	0.0		0.003	False		,,,				2504	0.0				p.S1204I		Atlas-SNP	.											.	SPEF2	324	.	0			c.G3611T						PASS	.	G	ILE/SER	2,3688		0,2,1843	90.0	87.0	88.0		3611	-10.7	0.0	5		88	10,8146		0,10,4068	yes	missense	SPEF2	NM_024867.3	142	0,12,5911	TT,TG,GG		0.1226,0.0542,0.1013	benign	1204/1823	35759812	12,11834	1845	4078	5923	SO:0001583	missense	79925	exon25			CTGAAAGCCAGCT	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"""cancer/testis antigen 122"""	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.3611G>T	5.37:g.35759812G>T	ENSP00000348314:p.Ser1204Ile	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	3.572	-0.087472	0.07097	5.42E-4	0.001226	ENSG00000152582	ENST00000356031;ENST00000440995	T;T	0.36520	1.25;1.25	5.33	-10.7	0.00240	.	1.448510	0.03545	N	0.224510	T	0.27278	0.0669	L	0.50333	1.59	0.24410	N	0.994669	B;B	0.20261	0.043;0.014	B;B	0.20955	0.032;0.005	T	0.04870	-1.0921	10	0.19147	T	0.46	.	10.1477	0.42774	0.5976:0.0:0.229:0.1733	.	1199;1204	Q9C093-2;Q9C093	.;SPEF2_HUMAN	I	1204;1199	ENSP00000348314:S1204I;ENSP00000412125:S1199I	ENSP00000348314:S1204I	S	+	2	0	SPEF2	35795569	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.033000	0.03571	-2.982000	0.00282	-0.793000	0.03317	AGC	G|0.999;T|0.001	0.001	strong		0.348	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
OVGP1	5016	hgsc.bcm.edu	37	1	111957517	111957517	+	Missense_Mutation	SNP	T	T	C	rs3767609|rs201350653|rs549398942	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111957517T>C	ENST00000369732.3	-	11	1661	c.1606A>G	c.(1606-1608)Agt>Ggt	p.S536G		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	536			S -> G (in dbSNP:rs3767609).		binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)	p.T597_V604delTPVSHQSV(2)|p.T533_V540delTPVSHQSV(2)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		GACTGATGACTCACAGGGGTC	0.547													T|||	1503	0.30012	0.4092	0.2291	5008	,	,		16183	0.2044		0.2972	False		,,,				2504	0.3047				p.S536G		Atlas-SNP	.											.	OVGP1	177	.	4	Deletion - In frame(4)	haematopoietic_and_lymphoid_tissue(2)|stomach(2)	c.A1606G						PASS	.	T	GLY/SER	1138,3170		242,654,1258	58.0	69.0	66.0		1606	-4.5	0.0	1	dbSNP_107	66	2424,6110		368,1688,2211	yes	missense	OVGP1	NM_002557.3	56	610,2342,3469	CC,CT,TT		28.404,26.416,27.7371	benign	536/679	111957517	3562,9280	2154	4267	6421	SO:0001583	missense	5016	exon11			GATGACTCACAGG	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1606A>G	1.37:g.111957517T>C	ENSP00000358747:p.Ser536Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	66	64	0.969697	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	.	.	.	.	.	.	.	.	.	.	T	6.657	0.489649	0.12702	0.26416	0.28404	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.02787	4.16	2.23	-4.46	0.03536	.	.	.	.	.	T	0.00524	0.0017	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.44982	-0.9292	8	0.31617	T	0.26	0.2049	3.9657	0.09431	0.0:0.2687:0.3546:0.3767	rs3767609;rs3767609	536;600	Q12889;Q59HH5	OVGP1_HUMAN;.	G	536;600;344	ENSP00000358747:S536G	ENSP00000358743:S600G	S	-	1	0	OVGP1	111759040	0.017000	0.18338	0.000000	0.03702	0.168000	0.22595	0.634000	0.24614	-1.729000	0.01364	0.254000	0.18369	AGT	T|0.776;C|0.224	0.224	strong		0.547	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
CD101	9398	hgsc.bcm.edu	37	1	117560929	117560929	+	Silent	SNP	C	C	A	rs3736907	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:117560929C>A	ENST00000256652.4	+	6	1822	c.1764C>A	c.(1762-1764)atC>atA	p.I588I	CD101_ENST00000369470.1_Silent_p.I588I	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	588	Ig-like C2-type 5.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GCTCTCACATCTTCCACCAGC	0.507													C|||	1050	0.209665	0.0129	0.3876	5008	,	,		18282	0.2054		0.2326	False		,,,				2504	0.3303				p.I588I		Atlas-SNP	.											.	CD101	95	.	0			c.C1764A						PASS	.	C		240,4166	140.4+/-175.9	10,220,1973	136.0	104.0	115.0		1764	3.2	0.0	1	dbSNP_107	115	2046,6554	355.9+/-330.1	240,1566,2494	no	coding-synonymous	CD101	NM_004258.3		250,1786,4467	AA,AC,CC		23.7907,5.4471,17.5765		588/1022	117560929	2286,10720	2203	4300	6503	SO:0001819	synonymous_variant	9398	exon6			TCACATCTTCCAC	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1764C>A	1.37:g.117560929C>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001256109	Q15856	Silent	SNP	ENST00000256652.4	37	CCDS891.1																																																																																			C|0.812;N|0.000	.	strong		0.507	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
C10orf71	118461	hgsc.bcm.edu	37	10	50534350	50534350	+	Missense_Mutation	SNP	G	G	A	rs11101095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50534350G>A	ENST00000374144.3	+	3	4048	c.3760G>A	c.(3760-3762)Gtc>Atc	p.V1254I	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1254			V -> I (in dbSNP:rs11101095).							endometrium(1)	1						CTCGGAGCCTGTCGGGAGGCG	0.711													g|||	516	0.103035	0.0779	0.0735	5008	,	,		12166	0.122		0.1193	False		,,,				2504	0.1217				p.V1254I		Atlas-SNP	.											C10orf71_ENST00000374144,NS,carcinoma,0,1	C10orf71	179	1	0			c.G3760A						PASS	.						2.0	4.0	4.0					10																	50534350		476	1307	1783	SO:0001583	missense	118461	exon3			GAGCCTGTCGGGA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.3760G>A	10.37:g.50534350G>A	ENSP00000363259:p.Val1254Ile	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	233	0.10668498168498168	53	0.10772357723577236	31	0.0856353591160221	60	0.1048951048951049	89	0.11741424802110818	g	4.860	0.159868	0.09287	.	.	ENSG00000177354	ENST00000374144	T	0.04119	3.7	5.81	-10.0	0.00425	.	2.286840	0.02567	N	0.097430	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.23297	-1.0192	7	0.17369	T	0.5	.	12.0882	0.53710	0.7132:0.1795:0.1073:0.0	rs11101095;rs58564182;rs11101095	.	.	.	I	1254	ENSP00000363259:V1254I	ENSP00000363259:V1254I	V	+	1	0	C10orf71	50204356	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	0.235000	0.17948	-1.922000	0.01067	0.479000	0.44913	GTC	G|0.909;A|0.091	0.091	strong		0.711	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
EVA1C	59271	hgsc.bcm.edu	37	21	33887131	33887131	+	Silent	SNP	G	G	A	rs1129157	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:33887131G>A	ENST00000300255.2	+	8	1430	c.957G>A	c.(955-957)ccG>ccA	p.P319P	EVA1C_ENST00000382699.3_Silent_p.P316P|EVA1C_ENST00000485488.1_3'UTR|EVA1C_ENST00000401402.3_Silent_p.P271P	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	319						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										CAGCCCACCCGGAGAGAGCTG	0.617													G|||	2458	0.490815	0.5976	0.5072	5008	,	,		17369	0.631		0.2922	False		,,,				2504	0.3947				p.P319P		Atlas-SNP	.											.	.	.	.	0			c.G957A						PASS	.	G		2457,1949	584.9+/-386.1	698,1061,444	38.0	39.0	39.0		957	-11.2	0.2	21	dbSNP_105	39	2363,6237	365.7+/-334.0	328,1707,2265	no	coding-synonymous	C21orf63	NM_058187.3		1026,2768,2709	AA,AG,GG		27.4767,44.2351,37.0598		319/442	33887131	4820,8186	2203	4300	6503	SO:0001819	synonymous_variant	59271	exon8			CCACCCGGAGAGA	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 64"", ""chromosome 21 open reading frame 63"", ""family with sequence similarity 176, member C"""	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.957G>A	21.37:g.33887131G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	87	50	0.574713	NM_058187	A6ND58|Q8IXZ0	Silent	SNP	ENST00000300255.2	37	CCDS13614.1																																																																																			G|0.575;A|0.425	0.425	strong		0.617	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187	
HIVEP3	59269	hgsc.bcm.edu	37	1	42047208	42047208	+	Missense_Mutation	SNP	C	C	G	rs17363472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:42047208C>G	ENST00000372583.1	-	4	4146	c.3261G>C	c.(3259-3261)caG>caC	p.Q1087H	HIVEP3_ENST00000372584.1_Missense_Mutation_p.Q1087H|HIVEP3_ENST00000247584.5_Missense_Mutation_p.Q1087H|HIVEP3_ENST00000429157.2_Missense_Mutation_p.Q1087H|HIVEP3_ENST00000460604.1_5'Flank	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1087			Q -> H (in dbSNP:rs17363472).		positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CAGAGGAAATCTGGGACAATG	0.607													C|||	245	0.0489217	0.0038	0.1153	5008	,	,		17657	0.002		0.0427	False		,,,				2504	0.1176				p.Q1087H		Atlas-SNP	.											.	HIVEP3	235	.	0			c.G3261C						PASS	.	C	HIS/GLN,HIS/GLN	64,4342	59.9+/-96.7	0,64,2139	58.0	66.0	63.0		3261,3261	3.9	0.7	1	dbSNP_123	63	499,8101	142.8+/-198.9	12,475,3813	yes	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	24,24	12,539,5952	GG,GC,CC		5.8023,1.4526,4.3288	possibly-damaging,possibly-damaging	1087/2406,1087/2407	42047208	563,12443	2203	4300	6503	SO:0001583	missense	59269	exon4			GGAAATCTGGGAC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.3261G>C	1.37:g.42047208C>G	ENSP00000361664:p.Gln1087His	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	151	91	0.602649	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	77	0.035256410256410256	2	0.0040650406504065045	39	0.10773480662983426	1	0.0017482517482517483	35	0.04617414248021108	C	0.012	-1.671318	0.00758	0.014526	0.058023	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.05996	3.37;3.36;3.36;3.37	4.77	3.86	0.44501	.	0.388790	0.19076	N	0.123374	T	0.00144	0.0004	N	0.24115	0.695	0.38461	P	0.05277699999999996	P;P	0.41569	0.755;0.641	B;B	0.44224	0.444;0.259	T	0.52185	-0.8609	9	0.19590	T	0.45	0.4506	12.7726	0.57429	0.0:0.9196:0.0:0.0804	rs17363472;rs52801254;rs17363472	1087;1087	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	H	1087	ENSP00000361665:Q1087H;ENSP00000361664:Q1087H;ENSP00000247584:Q1087H;ENSP00000410828:Q1087H	ENSP00000247584:Q1087H	Q	-	3	2	HIVEP3	41819795	0.009000	0.17119	0.653000	0.29593	0.119000	0.20118	0.192000	0.17096	1.233000	0.43693	0.313000	0.20887	CAG	C|0.961;G|0.039	0.039	strong		0.607	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
CES1	1066	hgsc.bcm.edu	37	16	55862791	55862791	+	Missense_Mutation	SNP	T	T	C	rs3826193	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55862791T>C	ENST00000361503.4	-	2	275	c.145A>G	c.(145-147)Att>Gtt	p.I49V	CES1_ENST00000422046.2_Missense_Mutation_p.I49V|CES1_ENST00000360526.3_Missense_Mutation_p.I50V|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	49					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	CCCAGGAAAATGGCCACAGGC	0.572																																					p.I50V	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.A148G						PASS	.						86.0	75.0	79.0					16																	55862791		2198	4300	6498	SO:0001583	missense	1066	exon2			GGAAAATGGCCAC	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.145A>G	16.37:g.55862791T>C	ENSP00000355193:p.Ile49Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	126	22	0.174603	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	0.005	-2.119403	0.00346	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.64438	-0.1;-0.1;-0.1	4.48	2.48	0.30137	Carboxylesterase, type B (1);	0.166939	0.28382	N	0.015560	T	0.19287	0.0463	N	0.00260	-1.75	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.38866	-0.9641	10	0.02654	T	1	.	8.5586	0.33496	0.0:0.727:0.0:0.273	rs3826193	49;49;50	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	V	50;49;49	ENSP00000353720:I50V;ENSP00000355193:I49V;ENSP00000390492:I49V	ENSP00000353720:I50V	I	-	1	0	CES1	54420292	0.001000	0.12720	0.534000	0.28014	0.060000	0.15804	0.503000	0.22610	0.358000	0.24211	-0.534000	0.04291	ATT	.	.	weak		0.572	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449383	89449383	+	Missense_Mutation	SNP	G	G	A	rs147771633	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89449383G>A	ENST00000321792.5	-	2	554	c.127C>T	c.(127-129)Cgt>Tgt	p.R43C	RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.R43C	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	43	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										TTGGTTTCACGGTCTTTTATC	0.413											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R43C		Atlas-SNP	.											CCBL2,NS,carcinoma,0,1	.	.	1	0			c.C127T						scavenged	.	G	,,CYS/ARG,CYS/ARG	2,4404	2.1+/-5.4	0,2,2201	208.0	196.0	200.0		,,127,127	-0.9	1.0	1	dbSNP_134	200	13,8587	6.4+/-24.3	0,13,4287	no	intron,intron,missense,missense	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	,,180,180	0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153	,,probably-damaging,probably-damaging	,,43/391,43/391	89449383	15,12991	2203	4300	6503	SO:0001583	missense	494115	exon3			TTTCACGGTCTTT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.127C>T	1.37:g.89449383G>A	ENSP00000318415:p.Arg43Cys	Somatic	483	2	0.00414079	1267	WXS	Illumina HiSeq	Phase_I	432	67	0.155093	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008797	0.75046	4.54E-4	0.001512	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.85702	-2.02;-2.02	1.59	-0.931	0.10438	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	U	0.000000	D	0.84938	0.5583	M	0.80616	2.505	0.49687	D	0.999813	D	0.71674	0.998	D	0.65987	0.94	T	0.81988	-0.0680	10	0.87932	D	0	-3.8545	4.2107	0.10510	0.4537:0.0:0.5463:0.0	.	43	Q96E39	RBMXL_HUMAN	C	43	ENSP00000318415:R43C;ENSP00000446099:R43C	ENSP00000318415:R43C	R	-	1	0	RBMXL1	89221971	1.000000	0.71417	0.976000	0.42696	0.893000	0.52053	3.231000	0.51294	-0.417000	0.07461	0.306000	0.20318	CGT	G|0.500;A|0.500	0.500	weak		0.413	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
ZNF91	7644	hgsc.bcm.edu	37	19	23543078	23543078	+	Silent	SNP	C	C	T	rs117657695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:23543078C>T	ENST00000300619.7	-	4	2908	c.2703G>A	c.(2701-2703)aaG>aaA	p.K901K	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Silent_p.K869K	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	901					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TATGAATTCTCTTATGTTCAG	0.388													C|||	12	0.00239617	0.0023	0.0029	5008	,	,		21504	0.0		0.007	False		,,,				2504	0.0				p.K901K		Atlas-SNP	.											.	ZNF91	349	.	0			c.G2703A						PASS	.	C		6,4362	9.9+/-24.2	0,6,2178	59.0	65.0	63.0		2703	-1.5	0.0	19	dbSNP_132	63	70,8512	41.7+/-99.0	1,68,4222	no	coding-synonymous	ZNF91	NM_003430.2		1,74,6400	TT,TC,CC		0.8157,0.1374,0.5869		901/1192	23543078	76,12874	2184	4291	6475	SO:0001819	synonymous_variant	7644	exon4			AATTCTCTTATGT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.2703G>A	19.37:g.23543078C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			C|0.995;T|0.005	0.005	strong		0.388	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
ZNF284	342909	hgsc.bcm.edu	37	19	44590558	44590558	+	Silent	SNP	C	C	T	rs7255701	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44590558C>T	ENST00000421176.3	+	5	1143	c.927C>T	c.(925-927)caC>caT	p.H309H	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				CCATGGTCCACATGCAAGAGA	0.368													C|||	2180	0.435304	0.2436	0.3631	5008	,	,		22949	0.2986		0.665	False		,,,				2504	0.6503				p.H309H		Atlas-SNP	.											.	ZNF284	38	.	0			c.C927T						PASS	.	C		1433,2825		277,879,973	83.0	85.0	84.0		927	0.4	0.0	19	dbSNP_116	84	5572,2966		1827,1918,524	no	coding-synonymous	ZNF284	NM_001037813.2		2104,2797,1497	TT,TC,CC		34.7388,33.6543,45.2563		309/594	44590558	7005,5791	2129	4269	6398	SO:0001819	synonymous_variant	342909	exon5			GGTCCACATGCAA	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"""Zinc fingers, C2H2-type"", ""-"""	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.927C>T	19.37:g.44590558C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001037813	Q86WM1	Silent	SNP	ENST00000421176.3	37	CCDS46099.1																																																																																			C|0.510;T|0.490	0.490	strong		0.368	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813	
ZNF211	10520	hgsc.bcm.edu	37	19	58153000	58153000	+	Silent	SNP	T	T	C	rs3746218	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58153000T>C	ENST00000347302.3	+	3	1325	c.1146T>C	c.(1144-1146)ttT>ttC	p.F382F	ZNF211_ENST00000240731.4_Silent_p.F395F|ZNF211_ENST00000254182.7_Silent_p.F373F|ZNF211_ENST00000544273.1_Silent_p.F394F|ZNF211_ENST00000541801.1_Silent_p.F373F|ZNF211_ENST00000299871.5_Silent_p.F447F|ZNF211_ENST00000420680.1_Silent_p.F386F|ZNF211_ENST00000391703.3_Silent_p.F321F	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GCCAAAACTTTAGCCTGATCT	0.468													t|||	1072	0.214058	0.2352	0.1297	5008	,	,		22300	0.3214		0.159	False		,,,				2504	0.1912				p.F447F		Atlas-SNP	.											.	ZNF211	78	.	0			c.T1341C						PASS	.	C	,	979,3427	730.9+/-410.2	117,745,1341	70.0	76.0	74.0		1185,1146	-4.8	0.0	19	dbSNP_107	74	1346,7254	756.1+/-407.5	97,1152,3051	no	coding-synonymous,coding-synonymous	ZNF211	NM_006385.3,NM_198855.2	,	214,1897,4392	CC,CT,TT		15.6512,22.2197,17.8764	,	395/578,382/565	58153000	2325,10681	2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			AAACTTTAGCCTG	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1146T>C	19.37:g.58153000T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	37	CCDS12957.1	485	0.22206959706959706	135	0.27439024390243905	52	0.143646408839779	180	0.3146853146853147	118	0.15567282321899736	c	7.735	0.700102	0.15106	0.222197	0.156512	ENSG00000121417	ENST00000407202	.	.	.	3.57	-4.82	0.03171	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.8423	0.05533	0.1604:0.184:0.1095:0.5462	rs3746218;rs3746218	.	.	.	Q	386	.	.	X	+	1	0	ZNF211	62844812	0.000000	0.05858	0.000000	0.03702	0.974000	0.67602	-2.277000	0.01160	-0.956000	0.03631	-0.197000	0.12766	TAG	T|0.792;C|0.208	0.208	strong		0.468	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549531	32549531	+	Missense_Mutation	SNP	T	T	C	rs112796209	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549531T>C	ENST00000360004.5	-	3	560	c.455A>G	c.(454-456)tAt>tGt	p.Y152C		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	152	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCTGCCTGGATAGAAACCACT	0.532										Multiple Myeloma(14;0.17)																											p.Y152C		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A455G						PASS	.						101.0	120.0	113.0					6																	32549531		1511	2709	4220	SO:0001583	missense	3123	exon3			CCTGGATAGAAAC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.455A>G	6.37:g.32549531T>C	ENSP00000353099:p.Tyr152Cys	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	557	78	0.140036	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	15.26	2.782128	0.49891	.	.	ENSG00000196126	ENST00000360004	T	0.04317	3.65	3.87	3.87	0.44632	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.113906	0.64402	D	0.000009	T	0.18882	0.0453	H	0.96398	3.815	0.44275	D	0.997133	D	0.89917	1.0	D	0.97110	1.0	T	0.02813	-1.1107	10	0.87932	D	0	.	6.8165	0.23833	0.2079:0.0:0.0:0.7921	.	152	P01911	2B1F_HUMAN	C	152	ENSP00000353099:Y152C	ENSP00000353099:Y152C	Y	-	2	0	HLA-DRB1	32657509	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.404000	0.44539	1.535000	0.49220	0.372000	0.22366	TAT	T|0.921;C|0.079	0.079	strong		0.532	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SULT1A2	6799	hgsc.bcm.edu	37	16	28603655	28603655	+	Missense_Mutation	SNP	T	T	G	rs1059491	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28603655T>G	ENST00000395630.1	-	7	1054	c.704A>C	c.(703-705)aAc>aCc	p.N235T	SULT1A2_ENST00000335715.4_Missense_Mutation_p.N235T|SULT1A2_ENST00000533150.1_Missense_Mutation_p.N202T	NM_177528.2	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	235			N -> T (in dbSNP:rs1059491). {ECO:0000269|PubMed:10762004, ECO:0000269|PubMed:8697101, ECO:0000269|PubMed:8912648, ECO:0000269|PubMed:9119390}.		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine biosynthetic process (GO:0009309)|catecholamine metabolic process (GO:0006584)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|sulfotransferase activity (GO:0008146)			NS(2)|breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|skin(2)	14						GGTCATAGGGTTCTTCTTCAT	0.567													.|||	1126	0.22484	0.2209	0.3977	5008	,	,		18966	0.0744		0.3171	False		,,,				2504	0.1677				p.N235T		Atlas-SNP	.											SULT1A2,lymph_node,lymphoid_neoplasm,0,1	SULT1A2	27	1	0			c.A704C						scavenged	.	T	THR/ASN,THR/ASN	1083,3311	390.0+/-327.5	145,793,1259	224.0	198.0	207.0		704,704	5.0	1.0	16	dbSNP_86	207	3103,5497	474.1+/-368.8	573,1957,1770	yes	missense,missense	SULT1A2	NM_001054.3,NM_177528.2	65,65	718,2750,3029	GG,GT,TT		36.0814,24.6472,32.2149	probably-damaging,probably-damaging	235/296,235/296	28603655	4186,8808	2197	4300	6497	SO:0001583	missense	6799	exon7			ATAGGGTTCTTCT	U34804	CCDS10636.1	16p12.1	2008-02-05			ENSG00000197165	ENSG00000197165	2.8.2.1	"""Sulfotransferases, cytosolic"""	11454	protein-coding gene	gene with protein product		601292		STP2		8661000, 8912648	Standard	NM_001054		Approved	HAST4	uc002dqh.2	P50226	OTTHUMG00000048082	ENST00000395630.1:c.704A>C	16.37:g.28603655T>G	ENSP00000378992:p.Asn235Thr	Somatic	402	2	0.00497512		WXS	Illumina HiSeq	Phase_I	382	177	0.463351	NM_001054	A9QY25|P78393|Q14CJ7	Missense_Mutation	SNP	ENST00000395630.1	37	CCDS10636.1	527	0.2413003663003663	106	0.21544715447154472	117	0.32320441988950277	53	0.09265734265734266	251	0.3311345646437995	t	20.2	3.950088	0.73787	0.246472	0.360814	ENSG00000197165	ENST00000533150;ENST00000335715;ENST00000395630	T;T;T	0.02103	4.45;4.45;4.45	4.98	4.98	0.66077	Sulfotransferase domain (1);	0.068979	0.64402	D	0.000019	T	0.00012	0.0000	M	0.86502	2.82	0.29114	P	0.880686	D	0.89917	1.0	D	0.97110	1.0	T	0.42599	-0.9442	9	0.72032	D	0.01	.	12.659	0.56803	0.0:0.0:0.0:1.0	rs1059491;rs3174702;rs16940488	235	P50226	ST1A2_HUMAN	T	202;235;235	ENSP00000435271:N202T;ENSP00000338742:N235T;ENSP00000378992:N235T	ENSP00000338742:N235T	N	-	2	0	SULT1A2	28511156	1.000000	0.71417	0.997000	0.53966	0.624000	0.37722	7.957000	0.87870	1.864000	0.54056	0.374000	0.22700	AAC	T|0.705;G|0.295	0.295	strong		0.567	SULT1A2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109415.2	NM_001054	
EVC	2121	hgsc.bcm.edu	37	4	5800494	5800494	+	Missense_Mutation	SNP	G	G	A	rs2279252	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:5800494G>A	ENST00000264956.6	+	15	2463	c.2279G>A	c.(2278-2280)cGg>cAg	p.R760Q	EVC_ENST00000515113.1_3'UTR|EVC_ENST00000382674.2_Missense_Mutation_p.R760Q	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	760			R -> Q (in dbSNP:rs2279252). {ECO:0000269|PubMed:10700184}.		cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				ACCAAGAGCCGGGCCAAGGAC	0.632													G|||	138	0.0275559	0.0008	0.0231	5008	,	,		19605	0.0556		0.0119	False		,,,				2504	0.0542				p.R760Q		Atlas-SNP	.											EVC,right_upper_lobe,carcinoma,-1,1	EVC	90	1	0			c.G2279A						PASS	.	G	GLN/ARG	11,4351		0,11,2170	23.0	20.0	21.0		2279	4.2	1.0	4	dbSNP_100	21	121,8417		1,119,4149	yes	missense	EVC	NM_153717.2	43	1,130,6319	AA,AG,GG		1.4172,0.2522,1.0233	probably-damaging	760/993	5800494	132,12768	2181	4269	6450	SO:0001583	missense	2121	exon15			AGAGCCGGGCCAA	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.2279G>A	4.37:g.5800494G>A	ENSP00000264956:p.Arg760Gln	Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	259	138	0.532819	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	51	0.023351648351648352	0	0.0	8	0.022099447513812154	31	0.05419580419580419	12	0.0158311345646438	G	9.827	1.187415	0.21870	0.002522	0.014172	ENSG00000072840	ENST00000264956;ENST00000382674	T;T	0.52754	0.65;0.65	5.08	4.22	0.49857	.	0.389162	0.26331	N	0.024982	T	0.09113	0.0225	M	0.62723	1.935	0.33377	D	0.574385	P	0.50272	0.933	B	0.44044	0.439	T	0.30794	-0.9966	10	0.11794	T	0.64	.	6.9767	0.24679	0.0917:0.0:0.7384:0.1699	rs2279252;rs52809221;rs2279252	760	P57679	EVC_HUMAN	Q	760	ENSP00000264956:R760Q;ENSP00000372120:R760Q	ENSP00000264956:R760Q	R	+	2	0	EVC	5851395	0.590000	0.26815	0.984000	0.44739	0.594000	0.36715	2.223000	0.42936	2.355000	0.79922	0.561000	0.74099	CGG	G|0.980;A|0.020	0.020	strong		0.632	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
RPUSD2	27079	hgsc.bcm.edu	37	15	40862064	40862064	+	Silent	SNP	C	C	T	rs1058734	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40862064C>T	ENST00000315616.7	+	1	566	c.528C>T	c.(526-528)gcC>gcT	p.A176A	RPUSD2_ENST00000559271.1_Intron	NM_152260.1	NP_689473.1	Q8IZ73	RUSD2_HUMAN	RNA pseudouridylate synthase domain containing 2	176					pseudouridine synthesis (GO:0001522)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(4)|lung(4)|skin(3)	11		all_cancers(109;2.74e-14)|all_epithelial(112;1.64e-11)|Lung NSC(122;6.69e-09)|all_lung(180;1.22e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3.1e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0786)		AGCCCCTGGCCTACTATGAGG	0.627													C|||	1323	0.264177	0.2247	0.2939	5008	,	,		13198	0.0942		0.4712	False		,,,				2504	0.2587				p.A176A		Atlas-SNP	.											.	RPUSD2	28	.	0			c.C528T						PASS	.	C		1165,3241		168,829,1206	16.0	15.0	15.0		528	-1.0	1.0	15	dbSNP_86	15	3813,4787		847,2119,1334	no	coding-synonymous	RPUSD2	NM_152260.1		1015,2948,2540	TT,TC,CC		44.3372,26.4412,38.2746		176/546	40862064	4978,8028	2203	4300	6503	SO:0001819	synonymous_variant	27079	exon1			CCTGGCCTACTAT	AK055971	CCDS10061.1, CCDS66737.1	15q13.3	2013-02-11	2005-01-31	2005-02-07	ENSG00000166133	ENSG00000166133		"""RNA pseudouridylate synthase domain containing"""	24180	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 19"""	C15orf19		12477932	Standard	NM_001286407		Approved	C18B11, FLJ31409	uc001zmd.1	Q8IZ73	OTTHUMG00000130031	ENST00000315616.7:c.528C>T	15.37:g.40862064C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	42	24	0.571429	NM_152260	B4DDD1|Q7L989|Q92939|Q96IA7|Q96N50	Silent	SNP	ENST00000315616.7	37	CCDS10061.1																																																																																			C|0.669;T|0.331	0.331	strong		0.627	RPUSD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252308.2	NM_152260	
TNFRSF18	8784	hgsc.bcm.edu	37	1	1140871	1140871	+	Splice_Site	SNP	G	G	A	rs142770542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1140871G>A	ENST00000379268.2	-	2	308	c.189C>T	c.(187-189)ggC>ggT	p.G63G	TNFRSF18_ENST00000379265.5_Splice_Site_p.G63G|TNFRSF18_ENST00000328596.6_Splice_Site_p.G63G|TNFRSF18_ENST00000486728.1_5'UTR	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	63					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			lung(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGCACTCCTCGCCTGGGCAGG	0.682													g|||	4	0.000798722	0.0015	0.0014	5008	,	,		16517	0.0		0.001	False		,,,				2504	0.0				p.G63G	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.C189T						PASS	.	G	,,	0,4394		0,0,2197	42.0	37.0	39.0		189,189,189	-4.2	0.0	1	dbSNP_134	39	21,8573	16.0+/-53.3	0,21,4276	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	TNFRSF18	NM_004195.2,NM_148901.1,NM_148902.1	,,	0,21,6473	AA,AG,GG		0.2444,0.0,0.1617	,,	63/242,63/256,63/235	1140871	21,12967	2197	4297	6494	SO:0001630	splice_region_variant	8784	exon2			CTCCTCGCCTGGG	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.188-1C>T	1.37:g.1140871G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	132	71	0.537879	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Silent	SNP	ENST00000379268.2	37	CCDS10.1																																																																																			G|0.998;A|0.002	0.002	strong		0.682	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195	Silent
MMP8	4317	hgsc.bcm.edu	37	11	102584135	102584135	+	Nonsense_Mutation	SNP	G	G	A	rs35231465	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:102584135G>A	ENST00000236826.3	-	10	1446	c.1348C>T	c.(1348-1350)Cag>Tag	p.Q450*		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	450					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	GTAACTCTCTGAGCAATAAGA	0.343													G|||	32	0.00638978	0.0008	0.013	5008	,	,		21321	0.0		0.0219	False		,,,				2504	0.0				p.Q450X		Atlas-SNP	.											.	MMP8	68	.	0			c.C1348T						PASS	.	G	stop/GLN	20,4386	27.2+/-55.0	0,20,2183	181.0	157.0	165.0		1348	-2.5	0.0	11	dbSNP_126	165	194,8404	85.6+/-148.0	1,192,4106	yes	stop-gained	MMP8	NM_002424.2		1,212,6289	AA,AG,GG		2.2563,0.4539,1.6456		450/468	102584135	214,12790	2203	4299	6502	SO:0001587	stop_gained	4317	exon10			CTCTCTGAGCAAT	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.1348C>T	11.37:g.102584135G>A	ENSP00000236826:p.Gln450*	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_002424	Q45F99	Nonsense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	23	0.010531135531135532	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	16	0.021108179419525065	G	14.94	2.684696	0.47991	0.004539	0.022563	ENSG00000118113	ENST00000236826;ENST00000544383	.	.	.	5.44	-2.53	0.06326	.	2.032460	0.02278	N	0.069177	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.2365	0.43286	0.0:0.1875:0.4109:0.4016	rs35231465	.	.	.	X	450;427	.	ENSP00000236826:Q450X	Q	-	1	0	MMP8	102089345	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	1.371000	0.34250	-0.538000	0.06281	-3.056000	0.00068	CAG	G|0.985;A|0.015	0.015	strong		0.343	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
ITPR2	3709	hgsc.bcm.edu	37	12	26732987	26732987	+	Silent	SNP	G	G	A	rs2230376	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:26732987G>A	ENST00000381340.3	-	33	4898	c.4482C>T	c.(4480-4482)ccC>ccT	p.P1494P		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1494					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TGTCTGAAAAGGGAGAATTAA	0.363													G|||	935	0.186701	0.0923	0.2248	5008	,	,		16444	0.0744		0.332	False		,,,				2504	0.2536				p.P1494P		Atlas-SNP	.											.	ITPR2	270	.	0			c.C4482T						PASS	.	G		475,3141		30,415,1363	116.0	104.0	108.0		4482	-10.1	0.0	12	dbSNP_98	108	2587,5565		428,1731,1917	no	coding-synonymous	ITPR2	NM_002223.2		458,2146,3280	AA,AG,GG		31.7345,13.1361,26.0197		1494/2702	26732987	3062,8706	1808	4076	5884	SO:0001819	synonymous_variant	3709	exon33			TGAAAAGGGAGAA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4482C>T	12.37:g.26732987G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.794;A|0.206	0.206	strong		0.363	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
HBP1	26959	hgsc.bcm.edu	37	7	106826381	106826381	+	Silent	SNP	C	C	T	rs201145168|rs7794598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:106826381C>T	ENST00000222574.4	+	4	720	c.534C>T	c.(532-534)caC>caT	p.H178H	HBP1_ENST00000485846.1_Silent_p.H178H|HBP1_ENST00000468410.1_Silent_p.H178H	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	178					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						CAGTAAGACACGAAAGGGTAA	0.413														792	0.158147	0.1483	0.1282	5008	,	,		18826	0.124		0.2018	False		,,,				2504	0.183				p.H188H		Atlas-SNP	.											.	HBP1	31	.	0			c.C564T						PASS	.	T		637,3769	767.1+/-413.5	61,515,1627	96.0	88.0	91.0		534	-0.4	1.0	7	dbSNP_116	91	1850,6750	730.1+/-406.7	206,1438,2656	no	coding-synonymous	HBP1	NM_012257.3		267,1953,4283	TT,TC,CC		21.5116,14.4576,19.1219		178/515	106826381	2487,10519	2203	4300	6503	SO:0001819	synonymous_variant	26959	exon4			AAGACACGAAAGG	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.534C>T	7.37:g.106826381C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	37	CCDS5741.1																																																																																			C|0.818;T|0.182	0.182	strong		0.413	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257	
CACNA1A	773	hgsc.bcm.edu	37	19	13470522	13470522	+	Silent	SNP	T	T	C	rs16006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:13470522T>C	ENST00000360228.5	-	6	875	c.876A>G	c.(874-876)gaA>gaG	p.E292E	CACNA1A_ENST00000573710.2_Silent_p.E292E	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	292					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGTTGGGCCCTTCCCAGTAGG	0.542													T|||	561	0.112021	0.1974	0.0288	5008	,	,		19652	0.1429		0.0308	False		,,,				2504	0.1074				p.E292E		Atlas-SNP	.											.	CACNA1A	715	.	0			c.A876G						PASS	.	T	,,,,	618,3392		34,550,1421	88.0	82.0	84.0		876,876,876,876,876	2.2	1.0	19	dbSNP_54	84	249,8089		4,241,3924	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	38,791,5345	CC,CT,TT		2.9863,15.4115,7.0214	,,,,	292/2267,292/2262,292/2507,292/2264,292/2513	13470522	867,11481	2005	4169	6174	SO:0001819	synonymous_variant	773	exon6			GGGCCCTTCCCAG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.876A>G	19.37:g.13470522T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	209	111	0.5311	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			T|0.909;C|0.089	0.089	strong		0.542	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
PRRC2A	7916	hgsc.bcm.edu	37	6	31602967	31602967	+	Missense_Mutation	SNP	G	G	A	rs1046089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31602967G>A	ENST00000376033.2	+	22	5453	c.5219G>A	c.(5218-5220)cGt>cAt	p.R1740H	PRRC2A_ENST00000376007.4_Missense_Mutation_p.R1740H	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1740	4 X 57 AA type A repeats.		R -> H (in dbSNP:rs1046089). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14656967, ECO:0000269|Ref.6}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CGATCACAGCGTACAGACCGA	0.622													G|||	1954	0.390176	0.5431	0.3646	5008	,	,		17959	0.3512		0.3449	False		,,,				2504	0.2883				p.R1740H		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G5219A	GRCh37	CM090830	PRRC2A	M	rs1046089	PASS	.	G	HIS/ARG,HIS/ARG	2245,2161	594.2+/-388.2	578,1089,536	85.0	82.0	83.0	http://www.ncbi.nlm.nih.gov/pubmed?term	5219,5219	5.5	1.0	6	dbSNP_86	83	2971,5629	460.2+/-365.1	516,1939,1845	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	29,29	1094,3028,2381	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.5465,49.0468,40.1046	probably-damaging,probably-damaging	1740/2158,1740/2158	31602967	5216,7790	2203	4300	6503	SO:0001583	missense	7916	exon22			CACAGCGTACAGA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5219G>A	6.37:g.31602967G>A	ENSP00000365201:p.Arg1740His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	862	0.3946886446886447	262	0.532520325203252	127	0.35082872928176795	202	0.3531468531468531	271	0.3575197889182058	G	15.40	2.822060	0.50739	0.509532	0.345465	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01745	4.66;4.66	5.51	5.51	0.81932	.	0.218848	0.33075	N	0.005319	T	0.01592	0.0051	L	0.36672	1.1	0.27289	P	0.9578908	D	0.52996	0.957	P	0.46339	0.513	T	0.60131	-0.7323	9	0.87932	D	0	0.17	16.4508	0.83990	0.0:0.0:1.0:0.0	rs1046089;rs6913649;rs17207246;rs17845914;rs17857495;rs17858890;rs59917316;rs1046089	1740	P48634	PRC2A_HUMAN	H	1734;1723;1740;1740;965	ENSP00000365175:R1740H;ENSP00000365201:R1740H	ENSP00000365175:R1740H	R	+	2	0	PRRC2A	31710946	0.999000	0.42202	0.983000	0.44433	0.993000	0.82548	3.354000	0.52254	2.873000	0.98535	0.561000	0.74099	CGT	G|0.611;A|0.389	0.389	strong		0.622	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
MDN1	23195	hgsc.bcm.edu	37	6	90397132	90397132	+	Missense_Mutation	SNP	G	G	C	rs34766278	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90397132G>C	ENST00000369393.3	-	68	11496	c.11381C>G	c.(11380-11382)gCt>gGt	p.A3794G	MDN1_ENST00000428876.1_Missense_Mutation_p.A3794G			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3794			A -> G (in dbSNP:rs34766278).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CAAAGACAAAGCTCGACTTGC	0.393													g|||	521	0.104034	0.0613	0.085	5008	,	,		19927	0.0486		0.1551	False		,,,				2504	0.18				p.A3794G		Atlas-SNP	.											.	MDN1	478	.	0			c.C11381G						PASS	.	A	GLY/ALA	279,4127	153.7+/-187.2	11,257,1935	103.0	92.0	96.0		11381	3.4	0.0	6	dbSNP_126	96	1241,7359	248.5+/-276.1	102,1037,3161	yes	missense	MDN1	NM_014611.1	60	113,1294,5096	CC,CG,GG		14.4302,6.3323,11.6869	possibly-damaging	3794/5597	90397132	1520,11486	2203	4300	6503	SO:0001583	missense	23195	exon68			GACAAAGCTCGAC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.11381C>G	6.37:g.90397132G>C	ENSP00000358400:p.Ala3794Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	188	0.08608058608058608	28	0.056910569105691054	27	0.07458563535911603	24	0.04195804195804196	109	0.1437994722955145	g	4.930	0.172802	0.09391	0.063323	0.144302	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03301	3.98;3.98	6.07	3.36	0.38483	.	0.715195	0.13782	N	0.363178	T	0.00784	0.0026	N	0.19112	0.55	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.48328	-0.9045	9	0.23302	T	0.38	.	4.6655	0.12664	0.1292:0.1219:0.6224:0.1266	rs34766278	3794	Q9NU22	MDN1_HUMAN	G	3794	ENSP00000358400:A3794G;ENSP00000413970:A3794G	ENSP00000358400:A3794G	A	-	2	0	MDN1	90453853	0.981000	0.34729	0.039000	0.18376	0.075000	0.17131	4.792000	0.62467	0.455000	0.26910	-0.119000	0.15052	GCT	G|0.889;C|0.111	0.111	strong		0.393	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
MUC16	94025	hgsc.bcm.edu	37	19	9086819	9086819	+	Silent	SNP	G	G	A	rs1823056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9086819G>A	ENST00000397910.4	-	1	5199	c.4996C>T	c.(4996-4998)Ctg>Ttg	p.L1666L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1666	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTTCTTTCCAGTGCCATGTTT	0.512													G|||	952	0.190096	0.0711	0.2709	5008	,	,		22140	0.3036		0.172	False		,,,				2504	0.1953				p.L1666L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C4996T						PASS	.	G		282,3728		5,272,1728	109.0	105.0	106.0		4996	-1.9	0.0	19	dbSNP_92	106	1490,6868		127,1236,2816	no	coding-synonymous	MUC16	NM_024690.2		132,1508,4544	AA,AG,GG		17.8272,7.0324,14.3273		1666/14508	9086819	1772,10596	2005	4179	6184	SO:0001819	synonymous_variant	94025	exon1			TTTCCAGTGCCAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4996C>T	19.37:g.9086819G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	209	108	0.516746	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.811;A|0.189	0.189	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DNAH5	1767	hgsc.bcm.edu	37	5	13701525	13701525	+	Silent	SNP	T	T	C	rs3734111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13701525T>C	ENST00000265104.4	-	77	13463	c.13359A>G	c.(13357-13359)acA>acG	p.T4453T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4453					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGAAACCCAGTGTACTAGAAA	0.368									Kartagener syndrome				T|||	2242	0.447684	0.3449	0.4928	5008	,	,		16114	0.4435		0.5398	False		,,,				2504	0.4642				p.T4453T		Atlas-SNP	.											.	DNAH5	868	.	0			c.A13359G						PASS	.	T		1615,2791	484.4+/-360.0	330,955,918	68.0	76.0	73.0		13359	-11.6	0.0	5	dbSNP_107	73	4706,3894	602.6+/-394.5	1263,2180,857	no	coding-synonymous	DNAH5	NM_001369.2		1593,3135,1775	CC,CT,TT		45.2791,36.6546,48.6006		4453/4625	13701525	6321,6685	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon77	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ACCCAGTGTACTA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13359A>G	5.37:g.13701525T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	78	0.666667	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.537;C|0.463	0.463	strong		0.368	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
ZFP36	7538	hgsc.bcm.edu	37	19	39899177	39899177	+	Silent	SNP	T	T	C	rs17885410	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39899177T>C	ENST00000248673.3	+	2	877	c.819T>C	c.(817-819)tcT>tcC	p.S273S	MIR4530_ENST00000581459.1_RNA|ZFP36_ENST00000597629.1_Silent_p.S279S	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	273					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GGACCCCCTCTGTACAGTCCC	0.647													T|||	113	0.0225639	0.0151	0.0259	5008	,	,		15422	0.0169		0.0378	False		,,,				2504	0.0204				p.S279S	NSCLC(67;1164 1324 12056 21056 30097)	Atlas-SNP	.											.	ZFP36	19	.	0			c.T837C						PASS	.	T		63,4343	56.2+/-92.4	0,63,2140	31.0	35.0	34.0		819	-0.4	1.0	19	dbSNP_124	34	261,8339	99.7+/-161.2	5,251,4044	no	coding-synonymous	ZFP36	NM_003407.2		5,314,6184	CC,CT,TT		3.0349,1.4299,2.4912		273/327	39899177	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	7538	exon2			CCCCTCTGTACAG	M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"""RING-type (C3HC4) zinc fingers"""	12862	protein-coding gene	gene with protein product		190700	"""zinc finger protein 36, C3H type, homolog (mouse)"""			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.819T>C	19.37:g.39899177T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	116	65	0.560345	NM_003407	B2RA54	Silent	SNP	ENST00000248673.3	37																																																																																				T|0.975;C|0.025	0.025	strong		0.647	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
CLEC4F	165530	hgsc.bcm.edu	37	2	71044211	71044211	+	Missense_Mutation	SNP	C	C	T	rs2075221	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71044211C>T	ENST00000272367.2	-	4	378	c.302G>A	c.(301-303)cGa>cAa	p.R101Q	CLEC4F_ENST00000426626.1_Missense_Mutation_p.R101Q	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	101			R -> Q (in dbSNP:rs2075221).		endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						GATAAGCTCTCGCATTTCTGC	0.488													C|||	1655	0.330471	0.028	0.402	5008	,	,		21486	0.5248		0.3817	False		,,,				2504	0.4356				p.R101Q	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											CLEC4F,caecum,carcinoma,-1,1	CLEC4F	95	1	0			c.G302A						PASS	.	C	GLN/ARG	423,3983	204.5+/-226.7	30,363,1810	58.0	53.0	55.0		302	3.9	0.0	2	dbSNP_96	55	3155,5445	479.6+/-370.2	611,1933,1756	yes	missense	CLEC4F	NM_173535.2	43	641,2296,3566	TT,TC,CC		36.686,9.6005,27.5104	benign	101/590	71044211	3578,9428	2203	4300	6503	SO:0001583	missense	165530	exon4			AGCTCTCGCATTT	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.302G>A	2.37:g.71044211C>T	ENSP00000272367:p.Arg101Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	768	0.3516483516483517	15	0.03048780487804878	123	0.3397790055248619	343	0.5996503496503497	287	0.3786279683377309	C	1.674	-0.508202	0.04231	0.096005	0.36686	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.01397	5.0;4.94	5.04	3.88	0.44766	.	0.366890	0.20087	N	0.099533	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.18935	-1.0321	9	0.02654	T	1	.	7.7138	0.28692	0.0:0.0975:0.0:0.9025	rs2075221;rs52820023;rs57574782;rs2075221	101;101	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	Q	101	ENSP00000272367:R101Q;ENSP00000390581:R101Q	ENSP00000272367:R101Q	R	-	2	0	CLEC4F	70897719	0.678000	0.27586	0.026000	0.17262	0.084000	0.17831	0.690000	0.25451	0.878000	0.35920	-0.483000	0.04790	CGA	C|0.692;T|0.308	0.308	strong		0.488	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
PARP4	143	hgsc.bcm.edu	37	13	25043207	25043207	+	Silent	SNP	G	G	A	rs116339023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25043207G>A	ENST00000381989.3	-	17	2193	c.2088C>T	c.(2086-2088)gcC>gcT	p.A696A		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	696	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CCTGGGTCACGGCTTCTAGGT	0.473																																					p.A696A		Atlas-SNP	.											PARP4,colon,carcinoma,0,1	PARP4	142	1	0			c.C2088T						scavenged	.						132.0	124.0	127.0					13																	25043207		2203	4300	6503	SO:0001819	synonymous_variant	143	exon17			GGTCACGGCTTCT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2088C>T	13.37:g.25043207G>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	150	6	0.04	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			G|0.975;A|0.026	0.026	strong		0.473	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
MUC4	4585	hgsc.bcm.edu	37	3	195509622	195509622	+	Silent	SNP	G	G	C	rs199744021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509622G>C	ENST00000463781.3	-	2	9288	c.8829C>G	c.(8827-8829)acC>acG	p.T2943T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2943T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T2943T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CAGGAAGAGGGGTGGTGTCAC	0.597													.|||	7	0.00139776	0.003	0.0014	5008	,	,		9829	0.0		0.0	False		,,,				2504	0.002				p.T2943T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.C8829G						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			AAGAGGGGTGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8829C>G	3.37:g.195509622G>C		Somatic	174	2	0.0114943		WXS	Illumina HiSeq	Phase_I	481	36	0.0748441	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CASD1	64921	hgsc.bcm.edu	37	7	94173803	94173803	+	Silent	SNP	T	T	C	rs13242090	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:94173803T>C	ENST00000297273.4	+	11	1724	c.1437T>C	c.(1435-1437)ttT>ttC	p.F479F		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	479						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			TCTCATACTTTTGGATAAAAG	0.358													T|||	599	0.119609	0.0038	0.1297	5008	,	,		16417	0.2103		0.0944	False		,,,				2504	0.2014				p.F479F		Atlas-SNP	.											.	CASD1	70	.	0			c.T1437C						PASS	.	T		77,4329	68.1+/-105.8	1,75,2127	124.0	119.0	120.0		1437	-0.4	1.0	7	dbSNP_121	120	703,7895	173.6+/-224.1	27,649,3623	no	coding-synonymous	CASD1	NM_022900.4		28,724,5750	CC,CT,TT		8.1763,1.7476,5.9982		479/798	94173803	780,12224	2203	4299	6502	SO:0001819	synonymous_variant	64921	exon11			ATACTTTTGGATA	AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 12"""	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1437T>C	7.37:g.94173803T>C		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	279	141	0.505376	NM_022900	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Silent	SNP	ENST00000297273.4	37	CCDS5636.1																																																																																			T|0.913;C|0.087	0.087	strong		0.358	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900	
SRRM5	100170229	hgsc.bcm.edu	37	19	44117582	44117582	+	Missense_Mutation	SNP	T	T	C	rs10410000	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44117582T>C	ENST00000607544.1	+	3	1631	c.1309T>C	c.(1309-1311)Tgc>Cgc	p.C437R	SRRM5_ENST00000526798.1_Missense_Mutation_p.C452R|ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000417606.1_Missense_Mutation_p.C437R			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	437	Ser-rich.			C -> R (in Ref. 1; BAG60212). {ECO:0000305}.				p.C437R(1)		endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						GGCGAGAGATTGCAGCCGATC	0.527													C|||	1056	0.210863	0.2814	0.2666	5008	,	,		15615	0.2698		0.1481	False		,,,				2504	0.0798				p.C437R		Atlas-SNP	.											SRRM5,colon,carcinoma,0,3	SRRM5	38	3	1	Substitution - Missense(1)	endometrium(1)	c.T1309C						PASS	.						53.0	65.0	62.0					19																	44117582		692	1591	2283	SO:0001583	missense	100170229	exon1			AGAGATTGCAGCC	AK297891	CCDS46095.1	19q13.31	2013-09-20			ENSG00000226763	ENSG00000226763			37248	protein-coding gene	gene with protein product							Standard	NM_001145641		Approved		uc010xwr.2	B3KS81	OTTHUMG00000165480	ENST00000607544.1:c.1309T>C	19.37:g.44117582T>C	ENSP00000476253:p.Cys437Arg	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_001145641	B4DNF0	Missense_Mutation	SNP	ENST00000607544.1	37	CCDS46095.1	.	.	.	.	.	.	.	.	.	.	C	4.598	0.111134	0.08831	.	.	ENSG00000226763	ENST00000526798;ENST00000417606	.	.	.	3.92	-3.58	0.04597	.	.	.	.	.	T	0.17704	0.0425	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27839	-1.0062	7	0.20519	T	0.43	.	6.7094	0.23268	0.1388:0.2466:0.0:0.6145	rs10410000	437	B3KS81	SRRM5_HUMAN	R	452;437	.	ENSP00000414512:C437R	C	+	1	0	SRRM5	48809422	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.651000	0.05372	-0.877000	0.04012	-0.801000	0.03215	TGC	C|1.000;|0.000	1.000	weak		0.527	SRRM5-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000384398.2	NM_001145641	
OR4D6	219983	hgsc.bcm.edu	37	11	59224885	59224885	+	Missense_Mutation	SNP	G	G	C	rs1453542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59224885G>C	ENST00000300127.2	+	1	475	c.452G>C	c.(451-453)aGt>aCt	p.S151T		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	151			S -> T (in dbSNP:rs1453542).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						TCTTGGGTGAGTGGTGGTTTG	0.517													G|||	888	0.177316	0.0477	0.2305	5008	,	,		19531	0.1746		0.2793	False		,,,				2504	0.2127				p.S151T		Atlas-SNP	.											.	OR4D6	65	.	0			c.G452C						PASS	.	G	THR/SER	329,4073	176.2+/-205.4	11,307,1883	283.0	250.0	261.0		452	5.0	1.0	11	dbSNP_88	261	2540,6050	415.1+/-351.7	365,1810,2120	yes	missense	OR4D6	NM_001004708.1	58	376,2117,4003	CC,CG,GG		29.5693,7.4739,22.0828	benign	151/315	59224885	2869,10123	2201	4295	6496	SO:0001583	missense	219983	exon1			GGGTGAGTGGTGG	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.452G>C	11.37:g.59224885G>C	ENSP00000300127:p.Ser151Thr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	204	102	0.5	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	460	0.21062271062271062	28	0.056910569105691054	95	0.26243093922651933	114	0.1993006993006993	223	0.2941952506596306	G	12.41	1.928327	0.34002	0.074739	0.295693	ENSG00000166884	ENST00000300127	T	0.36699	1.24	6.0	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.374604	0.22876	N	0.054573	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.17465	0.022	B	0.28305	0.088	T	0.27400	-1.0075	9	0.87932	D	0	-5.4983	15.5056	0.75739	0.0:0.1386:0.8614:0.0	rs1453542;rs17500408;rs1453542	151	Q8NGJ1	OR4D6_HUMAN	T	151	ENSP00000300127:S151T	ENSP00000300127:S151T	S	+	2	0	OR4D6	58981461	0.000000	0.05858	0.956000	0.39512	0.935000	0.57460	-0.059000	0.11731	2.846000	0.97976	0.650000	0.86243	AGT	G|0.782;C|0.218	0.218	strong		0.517	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
CCNT1	904	hgsc.bcm.edu	37	12	49087656	49087656	+	Silent	SNP	G	G	C	rs3013	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49087656G>C	ENST00000261900.3	-	9	1563	c.1341C>G	c.(1339-1341)ccC>ccG	p.P447P		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	447					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						AAGGCCGCTCGGGGTTTTCTG	0.443													G|||	617	0.123203	0.0794	0.121	5008	,	,		19212	0.004		0.2744	False		,,,				2504	0.1513				p.P447P		Atlas-SNP	.											.	CCNT1	55	.	0			c.C1341G						PASS	.	G		460,3946	196.4+/-220.7	25,410,1768	56.0	62.0	60.0		1341	-2.5	1.0	12	dbSNP_36	60	2794,5806	415.8+/-351.9	481,1832,1987	no	coding-synonymous	CCNT1	NM_001240.2		506,2242,3755	CC,CG,GG		32.4884,10.4403,25.0192		447/727	49087656	3254,9752	2203	4300	6503	SO:0001819	synonymous_variant	904	exon9			CCGCTCGGGGTTT	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1341C>G	12.37:g.49087656G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_001240	A9XU13|E7EX76|O60581	Silent	SNP	ENST00000261900.3	37	CCDS8766.1																																																																																			G|0.788;C|0.212	0.212	strong		0.443	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240	
HOPX	84525	hgsc.bcm.edu	37	4	57516896	57516896	+	Intron	SNP	G	G	A	rs4371677	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57516896G>A	ENST00000337881.7	-	3	801				HOPX_ENST00000381260.3_Missense_Mutation_p.P76L|HOPX_ENST00000317745.7_Intron|HOPX_ENST00000555760.2_Intron|HOPX_ENST00000503639.3_Intron|HOPX_ENST00000553379.2_Intron|HOPX_ENST00000556614.2_Intron|HOPX_ENST00000420433.1_Intron|HOPX_ENST00000381255.3_Intron|HOPX_ENST00000508121.1_Intron|HOPX_ENST00000556376.2_Intron|HOPX_ENST00000554144.1_Missense_Mutation_p.P94L	NM_139212.3	NP_631958.1	Q9BPY8	HOP_HUMAN	HOP homeobox						heart development (GO:0007507)|histone deacetylation (GO:0016575)|lung alveolus development (GO:0048286)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of heart contraction (GO:0008016)|regulation of protein binding (GO:0043393)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P94L(1)		large_intestine(2)|lung(5)|skin(1)	8	Glioma(25;0.08)|all_neural(26;0.101)					AGCCAAGCACGGCAGACTATC	0.458													A|||	2435	0.486222	0.6725	0.3617	5008	,	,		19278	0.4712		0.4791	False		,,,				2504	0.3456				p.P94L		Atlas-SNP	.											HOPX_ENST00000554144,NS,carcinoma,0,1	HOPX	28	1	1	Substitution - Missense(1)	stomach(1)	c.C281T						PASS	.	A	,LEU/PRO,,,	894,490		280,334,78	75.0	69.0	71.0		,281,,,	0.5	0.0	4	dbSNP_111	71	1438,1744		323,792,476	yes	intron,missense,intron,intron,intron	HOPX	NM_001145459.1,NM_001145460.1,NM_032495.5,NM_139211.4,NM_139212.3	,98,,,	603,1126,554	AA,AG,GG		45.1917,35.4046,48.9269	,,,,	,94/113,,,	57516896	2332,2234	692	1591	2283	SO:0001627	intron_variant	84525	exon4			AAGCACGGCAGAC		CCDS3507.1, CCDS47062.1, CCDS54767.1	4q12	2011-06-20			ENSG00000171476	ENSG00000171476		"""Homeoboxes / PRD class"""	24961	protein-coding gene	gene with protein product	"""homeobox only domain"""	607275				12297045	Standard	NM_032495		Approved	LAGY, HOP, OB1, NECC1, SMAP31	uc003hbz.2	Q9BPY8	OTTHUMG00000128768	ENST00000337881.7:c.145-1933C>T	4.37:g.57516896G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	130	73	0.561538	NM_001145460	A8K0Z2|E9PB55|G3V294|Q8N0V6|Q96CI1	Missense_Mutation	SNP	ENST00000337881.7	37	CCDS3507.1	1076	0.4926739926739927	340	0.6910569105691057	138	0.3812154696132597	246	0.43006993006993005	352	0.46437994722955145	A	0.011	-1.702512	0.00719	0.645954	0.451917	ENSG00000171476	ENST00000554144;ENST00000381260;ENST00000503864;ENST00000509435	.	.	.	3.22	0.473	0.16763	.	.	.	.	.	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39901	-0.9591	7	0.02654	T	1	.	3.3623	0.07192	0.5528:0.2065:0.2407:0.0	rs4371677;rs52837923;rs59676692;rs4371677	94	G3V294	.	L	94;76;76;76	.	ENSP00000370659:P94L	P	-	2	0	HOPX	57211653	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.278000	0.08490	-0.146000	0.11274	-0.269000	0.10298	CCG	G|0.501;A|0.499	0.499	strong		0.458	HOPX-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250689.4		
ELF3	1999	hgsc.bcm.edu	37	1	201981862	201981862	+	Silent	SNP	T	T	C	rs2819362	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201981862T>C	ENST00000359651.3	+	4	3765	c.573T>C	c.(571-573)ccT>ccC	p.P191P	RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000367284.5_Silent_p.P191P|ELF3_ENST00000367283.3_Silent_p.P191P|RP11-510N19.5_ENST00000504773.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						CCCCCTCCCCTGGCAGCTCTG	0.667													t|||	3527	0.704273	0.8464	0.6009	5008	,	,		15478	0.7758		0.5467	False		,,,				2504	0.6738				p.P191P		Atlas-SNP	.											.	ELF3	92	.	0			c.T573C						PASS	.	T	,	3421,985		1335,751,117	27.0	33.0	31.0		573,573	-9.9	0.0	1	dbSNP_100	31	4458,4140		1166,2126,1007	no	coding-synonymous,coding-synonymous	ELF3	NM_001114309.1,NM_004433.4	,	2501,2877,1124	CC,CT,TT		48.1507,22.3559,39.411	,	191/372,191/372	201981862	7879,5125	2203	4299	6502	SO:0001819	synonymous_variant	1999	exon5			CTCCCCTGGCAGC	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.573T>C	1.37:g.201981862T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_001114309		Silent	SNP	ENST00000359651.3	37	CCDS1419.1																																																																																			T|0.353;C|0.647	0.647	strong		0.667	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433	
NEO1	4756	hgsc.bcm.edu	37	15	73541513	73541513	+	Silent	SNP	A	A	G	rs3736510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:73541513A>G	ENST00000339362.5	+	11	2166	c.1719A>G	c.(1717-1719)aaA>aaG	p.K573K	NEO1_ENST00000558964.1_Silent_p.K573K|NEO1_ENST00000560262.1_Silent_p.K573K|NEO1_ENST00000560352.1_3'UTR|NEO1_ENST00000261908.6_Silent_p.K573K			Q92859	NEO1_HUMAN	neogenin 1	573	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						AGAATTATAAATTGTACTACA	0.408													A|||	1755	0.350439	0.143	0.5562	5008	,	,		17725	0.2976		0.4722	False		,,,				2504	0.4141				p.K573K		Atlas-SNP	.											.	NEO1	102	.	0			c.A1719G						PASS	.	A	,,	834,3562	329.1+/-300.9	82,670,1446	81.0	83.0	83.0		1719,1719,1719	0.6	1.0	15	dbSNP_107	83	4317,4277	578.6+/-390.8	1093,2131,1073	no	coding-synonymous,coding-synonymous,coding-synonymous	NEO1	NM_001172623.1,NM_001172624.1,NM_002499.3	,,	1175,2801,2519	GG,GA,AA		49.7673,18.9718,39.6536	,,	573/1409,573/1451,573/1462	73541513	5151,7839	2198	4297	6495	SO:0001819	synonymous_variant	4756	exon10			TTATAAATTGTAC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7754	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 2"""	601907	"""neogenin (chicken) homolog 1"""			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.1719A>G	15.37:g.73541513A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Silent	SNP	ENST00000339362.5	37	CCDS10247.1																																																																																			A|0.621;G|0.379	0.379	strong		0.408	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499	
NOS1	4842	hgsc.bcm.edu	37	12	117685270	117685270	+	Silent	SNP	G	G	A	rs1047735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:117685270G>A	ENST00000338101.4	-	18	2812	c.2808C>T	c.(2806-2808)caC>caT	p.H936H	NOS1_ENST00000317775.6_Silent_p.H902H|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TGTCCACAGCGTGTCCGAAGG	0.562													g|||	1735	0.346446	0.1982	0.5231	5008	,	,		16579	0.502		0.3151	False		,,,				2504	0.2935				p.H936H	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C2808T						PASS	.	G	,,,	692,3256		63,566,1345	87.0	87.0	87.0		2706,1698,1698,2808	-9.2	0.2	12	dbSNP_86	87	2511,5805		390,1731,2037	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	453,2297,3382	AA,AG,GG		30.1948,17.5279,26.1171	,,,	902/1435,566/1099,566/1099,936/1469	117685270	3203,9061	1974	4158	6132	SO:0001819	synonymous_variant	4842	exon19			CACAGCGTGTCCG		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2808C>T	12.37:g.117685270G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.652;A|0.348	0.348	strong		0.562	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
DSPP	1834	hgsc.bcm.edu	37	4	88536917	88536917	+	Missense_Mutation	SNP	G	G	A	rs199901845		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536917G>A	ENST00000282478.7	+	4	3136	c.3103G>A	c.(3103-3105)Gat>Aat	p.D1035N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1035N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1035N(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacagcagcgatagcagtga	0.522																																					p.D1035N		Atlas-SNP	.											DSPP,NS,carcinoma,-2,3	DSPP	174	3	1	Substitution - Missense(1)	kidney(1)	c.G3103A						PASS	.						62.0	68.0	66.0					4																	88536917		1560	2750	4310	SO:0001583	missense	1834	exon5			AGCAGCGATAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3103G>A	4.37:g.88536917G>A	ENSP00000282478:p.Asp1035Asn	Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	282	54	0.191489	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	5.819	0.335399	0.11013	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88664	-2.41;-2.41	1.43	0.544	0.17185	.	.	.	.	.	T	0.73999	0.3659	L	0.29908	0.895	0.18873	N	0.999989	B	0.30542	0.284	B	0.13407	0.009	T	0.59783	-0.7389	9	0.06494	T	0.89	-6.585	4.0989	0.10004	0.2347:0.0:0.7653:0.0	.	1035	Q9NZW4	DSPP_HUMAN	N	1035	ENSP00000382213:D1035N;ENSP00000282478:D1035N	ENSP00000282478:D1035N	D	+	1	0	DSPP	88755941	0.238000	0.23825	0.544000	0.28141	0.014000	0.08584	1.337000	0.33862	0.180000	0.19960	-0.791000	0.03333	GAT	.	.	weak		0.522	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
CNBP	7555	hgsc.bcm.edu	37	3	128890350	128890350	+	Silent	SNP	G	G	A	rs4303883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:128890350G>A	ENST00000422453.2	-	3	316	c.156C>T	c.(154-156)gaC>gaT	p.D52D	CNBP_ENST00000451728.2_Silent_p.D52D|CNBP_ENST00000500450.2_Splice_Site_p.D35D|CNBP_ENST00000502976.1_Silent_p.D45D|CNBP_ENST00000446936.2_Silent_p.D45D|CNBP_ENST00000441626.2_Silent_p.D52D|CNBP_ENST00000504813.1_Splice_Site_p.D42D	NM_001127192.1|NM_001127193.1|NM_003418.4	NP_001120664.1|NP_001120665.1|NP_003409.1	P62633	CNBP_HUMAN	CCHC-type zinc finger, nucleic acid binding protein	52					cholesterol biosynthetic process (GO:0006695)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			biliary_tract(1)|endometrium(1)|kidney(1)|lung(2)	5						GATAACAAATGTCTGGAAGAG	0.413													G|||	3792	0.757188	0.3555	0.8674	5008	,	,		20065	0.8879		0.9821	False		,,,				2504	0.8558				p.D52D		Atlas-SNP	.											.	CNBP	12	.	0			c.C156T						PASS	.	G	,,,,,	1953,2453	552.3+/-378.5	447,1059,697	105.0	95.0	98.0		156,156,135,135,135,156	5.8	1.0	3	dbSNP_111	98	8338,262	807.7+/-407.2	4044,250,6	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CNBP	NM_001127192.1,NM_001127193.1,NM_001127194.1,NM_001127195.1,NM_001127196.1,NM_003418.4	,,,,,	4491,1309,703	AA,AG,GG		3.0465,44.3259,20.875	,,,,,	52/180,52/179,45/173,45/172,45/171,52/178	128890350	10291,2715	2203	4300	6503	SO:0001819	synonymous_variant	7555	exon3			ACAAATGTCTGGA	U19765	CCDS3056.1, CCDS46906.1, CCDS46907.1, CCDS46908.1, CCDS54637.1	3q21	2013-01-09	2006-06-29	2006-06-29				"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCHC domain containing"""	13164	protein-coding gene	gene with protein product		116955	"""zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)"", ""zinc finger protein 9"""	DM2, ZNF9		2249857, 11486088	Standard	NM_003418		Approved	RNF163, ZCCHC22, CNBP1	uc021xdw.1	P62633		ENST00000422453.2:c.156C>T	3.37:g.128890350G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_003418	A8K7V4|B2RAV9|B4DP17|D3DNB9|D3DNC0|D3DNC1|E9PDR7|P20694|Q4JGY0|Q4JGY1|Q5QJR0|Q5U0E9|Q6PJI7|Q96NV3	Silent	SNP	ENST00000422453.2	37	CCDS3056.1																																																																																			G|0.213;A|0.787	0.787	strong		0.413	CNBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358419.1	NM_003418	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086457	46086457	+	Missense_Mutation	SNP	G	G	A	rs12483730	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46086457G>A	ENST00000360770.3	-	1	387	c.347C>T	c.(346-348)gCg>gTg	p.A116V	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	116	23 X 5 AA approximate repeats.		A -> V (in dbSNP:rs12483730).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						GGACGGAGCCGCATACACGAC	0.627													G|||	723	0.144369	0.0877	0.1657	5008	,	,		18686	0.0923		0.2078	False		,,,				2504	0.1943				p.A116V		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.C347T						PASS	.	G	,VAL/ALA	387,3947		21,345,1801	55.0	64.0	61.0		,347	0.4	0.0	21	dbSNP_120	61	1745,6771		173,1399,2686	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,64	194,1744,4487	AA,AG,GG		20.4908,8.9294,16.5914	,possibly-damaging	,116/147	46086457	2132,10718	2167	4258	6425	SO:0001583	missense	353323	exon1			GGAGCCGCATACA	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.347C>T	21.37:g.46086457G>A	ENSP00000354001:p.Ala116Val	Somatic	324	1	0.00308642		WXS	Illumina HiSeq	Phase_I	381	184	0.48294	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	320	0.14652014652014653	44	0.08943089430894309	61	0.1685082872928177	56	0.0979020979020979	159	0.20976253298153033	g	0.632	-0.816857	0.02776	0.089294	0.204908	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.02944	4.1	2.9	0.394	0.16299	.	.	.	.	.	T	0.00012	0.0000	N	0.00507	-1.42	0.58432	P	1.0000000000287557E-6	B	0.12630	0.006	B	0.04013	0.001	T	0.44267	-0.9339	8	0.27082	T	0.32	.	4.4209	0.11479	0.6485:0.0:0.3515:0.0	rs12483730	116	P59991	KR122_HUMAN	V	116;66	ENSP00000354001:A116V	ENSP00000354001:A116V	A	-	2	0	KRTAP12-2	44910885	0.002000	0.14202	0.006000	0.13384	0.001000	0.01503	0.492000	0.22435	0.175000	0.19841	-0.481000	0.04817	GCG	G|0.846;A|0.154	0.154	strong		0.627	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
CHIA	27159	hgsc.bcm.edu	37	1	111861974	111861974	+	Missense_Mutation	SNP	T	T	C	rs2275254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:111861974T>C	ENST00000369740.1	+	11	1164	c.1061T>C	c.(1060-1062)tTt>tCt	p.F354S	CHIA_ENST00000483391.1_Missense_Mutation_p.F193S|CHIA_ENST00000353665.6_Missense_Mutation_p.F193S|CHIA_ENST00000430615.1_Missense_Mutation_p.F246S|CHIA_ENST00000343320.6_Missense_Mutation_p.F354S|CHIA_ENST00000451398.2_Missense_Mutation_p.F193S|RP5-1125M8.2_ENST00000426321.1_RNA	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	354			F -> S (in dbSNP:rs2275254). {ECO:0000269|PubMed:19435888}.		apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		CACAACAAATTTGGAGGCGCC	0.502													T|||	2215	0.442292	0.3154	0.3098	5008	,	,		19337	0.38		0.5954	False		,,,				2504	0.6145				p.F354S		Atlas-SNP	.											.	CHIA	115	.	0			c.T1061C						PASS	.	T	SER/PHE,SER/PHE	1541,2865	484.0+/-359.9	262,1017,924	84.0	78.0	80.0		737,1061	3.8	0.6	1	dbSNP_100	80	4956,3644	623.4+/-397.5	1446,2064,790	yes	missense,missense	CHIA	NM_021797.2,NM_201653.2	155,155	1708,3081,1714	CC,CT,TT		42.3721,34.975,49.9539	probably-damaging,probably-damaging	246/369,354/477	111861974	6497,6509	2203	4300	6503	SO:0001583	missense	27159	exon11			ACAAATTTGGAGG	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.1061T>C	1.37:g.111861974T>C	ENSP00000358755:p.Phe354Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	943	0.4317765567765568	152	0.3089430894308943	136	0.3756906077348066	187	0.3269230769230769	468	0.6174142480211082	T	14.39	2.521585	0.44866	0.34975	0.576279	ENSG00000134216	ENST00000422815;ENST00000483391;ENST00000369740;ENST00000343320;ENST00000451398;ENST00000353665;ENST00000489524;ENST00000430615	T;T;T;T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4;3.4;3.4;3.4	4.96	3.8	0.43715	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.417964	0.20116	N	0.098901	T	0.19248	0.0462	M	0.92122	3.275	0.30347	P	0.785122	D	0.89917	1.0	D	0.85130	0.997	T	0.12268	-1.0554	9	0.66056	D	0.02	-7.9225	9.3552	0.38161	0.1605:0.0:0.0:0.8395	rs2275254;rs17718176;rs52821641;rs58142838;rs2275254	354	Q9BZP6	CHIA_HUMAN	S	298;193;354;354;193;193;193;246	ENSP00000387671:F298S;ENSP00000436946:F193S;ENSP00000358755:F354S;ENSP00000341828:F354S;ENSP00000390476:F193S;ENSP00000338970:F193S;ENSP00000433309:F193S;ENSP00000391132:F246S	ENSP00000341828:F354S	F	+	2	0	CHIA	111663497	1.000000	0.71417	0.620000	0.29132	0.296000	0.27459	3.465000	0.53064	0.796000	0.33947	0.533000	0.62120	TTT	T|0.537;C|0.463	0.463	strong		0.502	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
SALL1	6299	hgsc.bcm.edu	37	16	51173912	51173912	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:51173912G>A	ENST00000251020.4	-	2	2254	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.R644W	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	741					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R741W(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GTGAAAGCCCGGCCACAGATC	0.547																																					p.R741W	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											SALL1,NS,carcinoma,0,2	SALL1	301	2	1	Substitution - Missense(1)	prostate(1)	c.C2221T						scavenged	.						57.0	58.0	58.0					16																	51173912		2198	4300	6498	SO:0001583	missense	6299	exon2			AAGCCCGGCCACA	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2221C>T	16.37:g.51173912G>A	ENSP00000251020:p.Arg741Trp	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	151	3	0.0198676	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.862360	0.51482	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.19806	2.12;2.12	5.3	4.31	0.51392	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.42854	0.1221	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36817	-0.9732	10	0.87932	D	0	.	15.3926	0.74758	0.0:0.0:0.8603:0.1397	.	741	Q9NSC2	SALL1_HUMAN	W	741;644;705	ENSP00000251020:R741W;ENSP00000407914:R644W	ENSP00000251020:R741W	R	-	1	2	SALL1	49731413	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	4.955000	0.63638	2.490000	0.84030	0.454000	0.30748	CGG	.	.	none		0.547	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
PLEC	5339	hgsc.bcm.edu	37	8	144995494	144995494	+	Missense_Mutation	SNP	C	C	T	rs6558407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144995494C>T	ENST00000322810.4	-	32	9075	c.8906G>A	c.(8905-8907)cGc>cAc	p.R2969H	PLEC_ENST00000357649.2_Missense_Mutation_p.R2836H|PLEC_ENST00000527096.1_Missense_Mutation_p.R2855H|PLEC_ENST00000398774.2_Missense_Mutation_p.R2800H|PLEC_ENST00000354958.2_Missense_Mutation_p.R2810H|PLEC_ENST00000436759.2_Missense_Mutation_p.R2859H|PLEC_ENST00000345136.3_Missense_Mutation_p.R2832H|PLEC_ENST00000354589.3_Missense_Mutation_p.R2832H|PLEC_ENST00000356346.3_Missense_Mutation_p.R2818H	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2969	Globular 2.		R -> H (in dbSNP:rs6558407).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GAAGTAGCCGCGCCGGTAGGC	0.682													C|||	1155	0.230631	0.028	0.2939	5008	,	,		19137	0.1419		0.4294	False		,,,				2504	0.3466				p.R2969H		Atlas-SNP	.											.	PLEC	1144	.	0			c.G8906A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	368,3618		24,320,1649	60.0	66.0	64.0		8576,8453,8429,8906,8399,8495,8507,8495	2.1	1.0	8	dbSNP_116	64	3412,4876		720,1972,1452	no	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	29,29,29,29,29,29,29,29	744,2292,3101	TT,TC,CC		41.168,9.2323,30.7968	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	2859/4575,2818/4534,2810/4526,2969/4685,2800/4516,2832/4548,2836/4552,2832/4548	144995494	3780,8494	1993	4144	6137	SO:0001583	missense	5339	exon32			TAGCCGCGCCGGT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8906G>A	8.37:g.144995494C>T	ENSP00000323856:p.Arg2969His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	538	0.24633699633699635	15	0.03048780487804878	108	0.2983425414364641	94	0.16433566433566432	321	0.4234828496042216	C	9.838	1.190145	0.21954	0.092323	0.41168	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25	4.95	2.11	0.27256	.	0.205118	0.33591	U	0.004744	T	0.00012	0.0000	M	0.92412	3.305	0.30565	P	0.76412	B;B;B;B;B;B;B;B	0.25007	0.095;0.095;0.095;0.116;0.095;0.095;0.095;0.095	B;B;B;B;B;B;B;B	0.14023	0.006;0.006;0.006;0.01;0.006;0.006;0.006;0.006	T	0.09015	-1.0694	9	0.54805	T	0.06	.	7.3802	0.26851	0.1365:0.7151:0.0:0.1483	rs6558407;rs6558407	2859;2818;2810;2969;2800;2832;2836;2832	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	H	2832;2836;2832;2800;2969;2810;2818;2859;2855	ENSP00000344848:R2832H;ENSP00000350277:R2836H;ENSP00000346602:R2832H;ENSP00000381756:R2800H;ENSP00000323856:R2969H;ENSP00000347044:R2810H;ENSP00000348702:R2818H;ENSP00000388180:R2859H;ENSP00000434583:R2855H	ENSP00000323856:R2969H	R	-	2	0	PLEC	145067482	0.993000	0.37304	0.985000	0.45067	0.496000	0.33645	2.910000	0.48766	0.222000	0.20900	-0.538000	0.04264	CGC	.	.	weak		0.682	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
MYO5A	4644	hgsc.bcm.edu	37	15	52667552	52667552	+	Silent	SNP	G	G	A	rs2414145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:52667552G>A	ENST00000399231.3	-	20	2769	c.2526C>T	c.(2524-2526)atC>atT	p.I842I	MYO5A_ENST00000553916.1_Silent_p.I842I|MYO5A_ENST00000358212.6_Silent_p.I842I|MYO5A_ENST00000356338.6_Silent_p.I842I|MYO5A_ENST00000399233.2_Silent_p.I842I	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	842	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ACTGAAGAACGATAGTGGCAG	0.438													g|||	4230	0.844649	0.5242	0.9697	5008	,	,		18023	0.9633		0.996	False		,,,				2504	0.911				p.I842I		Atlas-SNP	.											.	MYO5A	145	.	0			c.C2526T						PASS	.	A	,	2365,1465		722,921,272	99.0	94.0	95.0		2526,2526	-9.4	0.0	15	dbSNP_100	95	8211,39		4086,39,0	no	coding-synonymous,coding-synonymous	MYO5A	NM_000259.3,NM_001142495.1	,	4808,960,272	AA,AG,GG		0.4727,38.2507,12.4503	,	842/1856,842/1829	52667552	10576,1504	1915	4125	6040	SO:0001819	synonymous_variant	4644	exon20			AAGAACGATAGTG		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.2526C>T	15.37:g.52667552G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	37	CCDS42037.1																																																																																			G|0.127;A|0.873	0.873	strong		0.438	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
SVIL	6840	hgsc.bcm.edu	37	10	29783885	29783885	+	Silent	SNP	A	A	G	rs1056782	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29783885A>G	ENST00000355867.4	-	20	4551	c.3799T>C	c.(3799-3801)Ttg>Ctg	p.L1267L	SVIL_ENST00000375398.2_Silent_p.L1267L|SVIL_ENST00000375400.3_Silent_p.L841L|SVIL_ENST00000538146.1_Silent_p.L59L|SVIL_ENST00000535393.1_Silent_p.L181L	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1267					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AGCCTGTCCAACTTCAGGTCC	0.448																																					p.L1267L		Atlas-SNP	.											.	SVIL	226	.	0			c.T3799C						PASS	.	A	,	1110,3296		84,942,1177	185.0	180.0	181.0		2521,3799	-2.0	1.0	10	dbSNP_86	181	3424,5176		495,2434,1371	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	579,3376,2548	GG,GA,AA		39.814,25.1929,34.8608	,	841/1789,1267/2215	29783885	4534,8472	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon20			TGTCCAACTTCAG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3799T>C	10.37:g.29783885A>G		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	195	78	0.4	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			A|0.589;G|0.411	0.411	strong		0.448	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
NHLRC2	374354	hgsc.bcm.edu	37	10	115644040	115644040	+	Missense_Mutation	SNP	G	G	A	rs7913176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115644040G>A	ENST00000369301.3	+	5	1152	c.940G>A	c.(940-942)Gta>Ata	p.V314I		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	314			V -> I (in dbSNP:rs7913176).							breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		GGTGAGCACTGTAGCTGGTAT	0.388													G|||	1119	0.223442	0.121	0.2291	5008	,	,		15051	0.3125		0.2932	False		,,,				2504	0.1943				p.V314I		Atlas-SNP	.											NHLRC2,NS,carcinoma,0,1	NHLRC2	56	1	0			c.G940A						PASS	.	G	ILE/VAL	684,3722	289.8+/-280.6	64,556,1583	137.0	126.0	130.0		940	5.0	1.0	10	dbSNP_116	130	2422,6178	400.6+/-346.9	361,1700,2239	yes	missense	NHLRC2	NM_198514.3	29	425,2256,3822	AA,AG,GG		28.1628,15.5243,23.8813	benign	314/727	115644040	3106,9900	2203	4300	6503	SO:0001583	missense	374354	exon5			AGCACTGTAGCTG	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.940G>A	10.37:g.115644040G>A	ENSP00000358307:p.Val314Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	NM_198514	Q8N1H1|Q8N5A6	Missense_Mutation	SNP	ENST00000369301.3	37	CCDS7585.1	525	0.2403846153846154	59	0.11991869918699187	71	0.19613259668508287	178	0.3111888111888112	217	0.2862796833773087	G	13.78	2.338147	0.41398	0.155243	0.281628	ENSG00000196865	ENST00000369301	D	0.89939	-2.59	5.03	5.03	0.67393	Six-bladed beta-propeller, TolB-like (1);	0.155986	0.44285	D	0.000462	T	0.00012	0.0000	L	0.35723	1.085	0.27849	P	0.9408216	P	0.36412	0.552	B	0.25884	0.064	T	0.33599	-0.9862	9	0.07990	T	0.79	-18.5562	16.5886	0.84759	0.0:0.0:1.0:0.0	rs7913176;rs52796392;rs56430477;rs61476386;rs7913176	314	Q8NBF2	NHLC2_HUMAN	I	314	ENSP00000358307:V314I	ENSP00000358307:V314I	V	+	1	0	NHLRC2	115634030	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.574000	0.46016	2.345000	0.79718	0.479000	0.44913	GTA	G|0.771;A|0.229	0.229	strong		0.388	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	
SP2	6668	hgsc.bcm.edu	37	17	46000406	46000406	+	Missense_Mutation	SNP	T	T	C	rs62067380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46000406T>C	ENST00000376741.4	+	4	1275	c.1138T>C	c.(1138-1140)Tct>Cct	p.S380P	AC003665.1_ENST00000451140.2_RNA|AC003665.1_ENST00000585280.1_RNA|AC003665.1_ENST00000411573.2_RNA|AC003665.1_ENST00000433001.1_RNA	NM_003110.5	NP_003101.3	Q02086	SP2_HUMAN	Sp2 transcription factor	380					cardiovascular system development (GO:0072358)|embryonic organ development (GO:0048568)|fibroblast proliferation (GO:0048144)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						TGCAGCCACCTCTAACACCAC	0.597													T|||	478	0.0954473	0.0204	0.1398	5008	,	,		18745	0.0605		0.1511	False		,,,				2504	0.1442				p.S380P		Atlas-SNP	.											.	SP2	38	.	0			c.T1138C						PASS	.	T	PRO/SER	180,4226	115.0+/-153.0	4,172,2027	82.0	78.0	79.0		1138	3.8	1.0	17	dbSNP_129	79	1212,7388	243.3+/-273.0	83,1046,3171	yes	missense	SP2	NM_003110.5	74	87,1218,5198	CC,CT,TT		14.093,4.0853,10.7028	benign	380/614	46000406	1392,11614	2203	4300	6503	SO:0001583	missense	6668	exon4			GCCACCTCTAACA		CCDS11521.2	17q21.3-q22	2013-01-08			ENSG00000167182	ENSG00000167182		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11207	protein-coding gene	gene with protein product		601801				1341900, 9730617	Standard	NM_003110		Approved	KIAA0048	uc002imk.3	Q02086	OTTHUMG00000150196	ENST00000376741.4:c.1138T>C	17.37:g.46000406T>C	ENSP00000365931:p.Ser380Pro	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_003110	A6NK74	Missense_Mutation	SNP	ENST00000376741.4	37	CCDS11521.2	214	0.09798534798534798	12	0.024390243902439025	54	0.14917127071823205	30	0.05244755244755245	118	0.15567282321899736	T	15.74	2.922421	0.52653	0.040853	0.14093	ENSG00000167182	ENST00000376741	T	0.10382	2.88	6.17	3.84	0.44239	.	0.294876	0.32802	N	0.005632	T	0.00039	0.0001	L	0.36672	1.1	0.25600	P	0.9866029	B	0.06786	0.001	B	0.06405	0.002	T	0.34453	-0.9828	9	0.25751	T	0.34	.	3.6607	0.08237	0.1331:0.0707:0.1394:0.6568	rs62067380	380	Q02086	SP2_HUMAN	P	380	ENSP00000365931:S380P	ENSP00000365931:S380P	S	+	1	0	SP2	43355405	0.844000	0.29557	0.985000	0.45067	0.987000	0.75469	1.773000	0.38563	1.116000	0.41820	0.533000	0.62120	TCT	T|0.895;C|0.105	0.105	strong		0.597	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
F5	2153	hgsc.bcm.edu	37	1	169551682	169551682	+	Silent	SNP	T	T	C	rs6028	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169551682T>C	ENST00000367797.3	-	2	438	c.237A>G	c.(235-237)caA>caG	p.Q79Q	F5_ENST00000367796.3_Silent_p.Q79Q|F5_ENST00000546081.1_Intron	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	79	F5/8 type A 1.|Plastocyanin-like 1.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.Q79Q(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	AAATGGTAGATTGTGGTTTTT	0.269													t|||	1134	0.226438	0.028	0.3501	5008	,	,		15692	0.2044		0.2942	False		,,,				2504	0.3599				p.Q79Q		Atlas-SNP	.											F5,NS,carcinoma,0,1	F5	301	1	1	Substitution - coding silent(1)	stomach(1)	c.A237G						PASS	.	C		311,4043		14,283,1880	32.0	32.0	32.0		237	3.3	0.2	1	dbSNP_52	32	2331,6177		315,1701,2238	no	coding-synonymous	F5	NM_000130.4		329,1984,4118	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	27.3977,7.1429,20.5411		79/2225	169551682	2642,10220	2177	4254	6431	SO:0001819	synonymous_variant	2153	exon2			GGTAGATTGTGGT	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.237A>G	1.37:g.169551682T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	173	43	0.248555	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			C|0.214;N|0.000	0.214	strong		0.269	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
TTN	7273	hgsc.bcm.edu	37	2	179613651	179613651	+	Intron	SNP	G	G	A	rs72648904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179613651G>A	ENST00000591111.1	-	45	10585				TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Silent_p.D4492D			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAAAGGCTTTGTCATCAATCT	0.313													G|||	55	0.0109824	0.0015	0.0231	5008	,	,		19218	0.0		0.0239	False		,,,				2504	0.0133				p.D4492D		Atlas-SNP	.											.	TTN	18412	.	0			c.C13476T						PASS	.	G	,,,,	32,4374	37.6+/-69.7	0,32,2171	96.0	95.0	96.0		,,13476,,	0.9	0.0	2	dbSNP_130	96	306,8290	110.2+/-170.6	13,280,4005	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	13,312,6176	AA,AG,GG		3.5598,0.7263,2.5996	,,,,	,,4492/5605,,	179613651	338,12664	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			GGCTTTGTCATCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+4199C>T	2.37:g.179613651G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.977;A|0.023	0.023	strong		0.313	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
BTBD16	118663	hgsc.bcm.edu	37	10	124096061	124096061	+	Missense_Mutation	SNP	A	A	C	rs1048347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124096061A>C	ENST00000260723.4	+	15	1567	c.1316A>C	c.(1315-1317)cAc>cCc	p.H439P	BTBD16_ENST00000368994.2_Missense_Mutation_p.H440P|BTBD16_ENST00000495370.2_3'UTR	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	439			H -> P (in dbSNP:rs1048347).							breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				GAGCACAACCACGTCAGCCTG	0.557													C|||	2300	0.459265	0.3956	0.487	5008	,	,		17696	0.6935		0.325	False		,,,				2504	0.4223				p.H439P		Atlas-SNP	.											.	BTBD16	44	.	0			c.A1316C						PASS	.	C	PRO/HIS	1583,2823	661.8+/-401.0	293,997,913	89.0	73.0	78.0		1316	1.4	0.0	10	dbSNP_86	78	2766,5834	676.0+/-403.3	446,1874,1980	yes	missense	BTBD16	NM_144587.2	77	739,2871,2893	CC,CA,AA		32.1628,35.9283,33.4384	benign	439/507	124096061	4349,8657	2203	4300	6503	SO:0001583	missense	118663	exon15			ACAACCACGTCAG	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1316A>C	10.37:g.124096061A>C	ENSP00000260723:p.His439Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	1023	0.4684065934065934	208	0.42276422764227645	165	0.4558011049723757	403	0.7045454545454546	247	0.3258575197889182	C	0.040	-1.289364	0.01387	0.359283	0.321628	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.16073	2.37;2.37	5.5	1.38	0.22167	.	0.189287	0.32852	N	0.005580	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33574	-0.9863	9	0.05721	T	0.95	-2.4471	4.2236	0.10570	0.1484:0.4976:0.0:0.354	rs1048347;rs3167835;rs3817283;rs17642636;rs58942580;rs1048347	440;439	Q32M84-2;Q32M84	.;BTBDG_HUMAN	P	439;440	ENSP00000260723:H439P;ENSP00000357990:H440P	ENSP00000260723:H439P	H	+	2	0	BTBD16	124086051	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.113000	0.15499	-0.223000	0.09943	-0.729000	0.03580	CAC	A|0.608;C|0.392	0.392	strong		0.557	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
KANK1	23189	hgsc.bcm.edu	37	9	710818	710818	+	Missense_Mutation	SNP	A	A	G	rs61737970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:710818A>G	ENST00000382303.1	+	7	704	c.52A>G	c.(52-54)Att>Gtt	p.I18V	KANK1_ENST00000382293.3_5'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.I18V|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	18					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		AGCAGGTGATATTCTCAGTGG	0.378													A|||	37	0.00738818	0.0008	0.013	5008	,	,		19639	0.0		0.0199	False		,,,				2504	0.0072				p.I18V		Atlas-SNP	.											.	KANK1	231	.	0			c.A52G						PASS	.	A	VAL/ILE,	18,4388	22.3+/-47.3	0,18,2185	90.0	94.0	92.0		52,	2.1	0.0	9	dbSNP_129	92	169,8431	78.6+/-141.3	2,165,4133	yes	missense,utr-5	KANK1	NM_015158.2,NM_153186.3	29,	2,183,6318	GG,GA,AA		1.9651,0.4085,1.4378	benign,	18/1353,	710818	187,12819	2203	4300	6503	SO:0001583	missense	23189	exon7			GGTGATATTCTCA	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.52A>G	9.37:g.710818A>G	ENSP00000371740:p.Ile18Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	100	60	0.6	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	16	0.007326007326007326	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	A	0.001	-3.647191	0.00006	0.004085	0.019651	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297	T;T	0.36520	1.25;1.25	5.95	2.1	0.27182	.	0.629214	0.13985	N	0.349186	T	0.06872	0.0175	N	0.04297	-0.235	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27434	-1.0074	10	0.05620	T	0.96	-3.2263	9.5209	0.39135	0.4368:0.0:0.5632:0.0	rs61737970	18;18	Q5W0W1;Q14678	.;KANK1_HUMAN	V	18	ENSP00000371740:I18V;ENSP00000371734:I18V	ENSP00000346479:I18V	I	+	1	0	KANK1	700818	0.015000	0.18098	0.011000	0.14972	0.126000	0.20510	0.402000	0.20965	0.126000	0.18424	-0.899000	0.02877	ATT	A|0.989;G|0.011	0.011	strong		0.378	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
FBN3	84467	hgsc.bcm.edu	37	19	8168545	8168545	+	Missense_Mutation	SNP	C	C	T	rs33967815	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8168545C>T	ENST00000600128.1	-	39	5254	c.4840G>A	c.(4840-4842)Ggc>Agc	p.G1614S	FBN3_ENST00000601739.1_Missense_Mutation_p.G1614S|FBN3_ENST00000270509.2_Missense_Mutation_p.G1614S			Q75N90	FBN3_HUMAN	fibrillin 3	1614	EGF-like 25; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		G -> S (in dbSNP:rs33967815). {ECO:0000269|PubMed:14962672, ECO:0000269|PubMed:15221638}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCACAGATGCCGGAGTGTGTG	0.557													C|||	690	0.13778	0.0507	0.1888	5008	,	,		19067	0.0476		0.2952	False		,,,				2504	0.1503				p.G1614S		Atlas-SNP	.											.	FBN3	300	.	0			c.G4840A						PASS	.	C	SER/GLY	377,4029	191.2+/-216.9	25,327,1851	114.0	98.0	103.0		4840	3.6	0.9	19	dbSNP_126	103	2900,5700	454.0+/-363.4	492,1916,1892	yes	missense	FBN3	NM_032447.3	56	517,2243,3743	TT,TC,CC		33.7209,8.5565,25.1961	possibly-damaging	1614/2810	8168545	3277,9729	2203	4300	6503	SO:0001583	missense	84467	exon38			AGATGCCGGAGTG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.4840G>A	19.37:g.8168545C>T	ENSP00000470498:p.Gly1614Ser	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	178	99	0.55618	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	359	0.16437728937728938	30	0.06097560975609756	79	0.21823204419889503	28	0.04895104895104895	222	0.2928759894459103	C	18.38	3.610916	0.66558	0.085565	0.337209	ENSG00000142449	ENST00000270509	D	0.91631	-2.88	3.61	3.61	0.41365	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	T	0.00012	0.0000	L	0.31752	0.955	0.19300	P	0.9999791011	D	0.89917	1.0	D	0.91635	0.999	T	0.00025	-1.2319	9	0.24483	T	0.36	.	15.6061	0.76672	0.0:1.0:0.0:0.0	rs33967815	1614	Q75N90	FBN3_HUMAN	S	1614	ENSP00000270509:G1614S	ENSP00000270509:G1614S	G	-	1	0	FBN3	8074545	1.000000	0.71417	0.943000	0.38184	0.440000	0.31957	5.475000	0.66787	1.724000	0.51502	0.491000	0.48974	GGC	C|0.769;T|0.231	0.231	strong		0.557	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
USP21	27005	hgsc.bcm.edu	37	1	161132821	161132821	+	Missense_Mutation	SNP	C	C	A	rs1127525	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161132821C>A	ENST00000289865.8	+	6	1227	c.1006C>A	c.(1006-1008)Cca>Aca	p.P336T	USP21_ENST00000368002.3_Missense_Mutation_p.P336T|USP21_ENST00000368001.1_Missense_Mutation_p.P336T	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	336	USP.		P -> T (in dbSNP:rs1127525).		histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AGTTCCCTCTCCACCCCGCCG	0.562													C|||	82	0.0163738	0.0008	0.0447	5008	,	,		18247	0.0		0.0427	False		,,,				2504	0.0072				p.P336T		Atlas-SNP	.											.	USP21	63	.	0			c.C1006A						PASS	.	C	THR/PRO,THR/PRO	31,4375	36.8+/-68.6	0,31,2172	83.0	90.0	88.0		1006,1006	3.8	0.2	1	dbSNP_86	88	375,8225	122.2+/-181.2	9,357,3934	yes	missense,missense	USP21	NM_001014443.2,NM_012475.4	38,38	9,388,6106	AA,AC,CC		4.3605,0.7036,3.1216	benign,benign	336/566,336/566	161132821	406,12600	2203	4300	6503	SO:0001583	missense	27005	exon6			CCCTCTCCACCCC	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"""Ubiquitin-specific peptidases"""	12620	protein-coding gene	gene with protein product		604729	"""ubiquitin specific protease 21"""	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.1006C>A	1.37:g.161132821C>A	ENSP00000289865:p.Pro336Thr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	177	103	0.581921	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Missense_Mutation	SNP	ENST00000289865.8	37	CCDS30920.1	44	0.020146520146520148	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	26	0.03430079155672823	C	3.473	-0.107462	0.06924	0.007036	0.043605	ENSG00000143258	ENST00000368002;ENST00000289865;ENST00000368001	T;T;T	0.15256	2.59;2.59;2.44	4.72	3.77	0.43336	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	3.051530	0.00695	N	0.000758	T	0.04543	0.0124	N	0.11870	0.19	0.26414	N	0.976213	B	0.21688	0.059	B	0.30316	0.114	T	0.37776	-0.9691	10	0.25106	T	0.35	.	10.456	0.44550	0.0:0.8024:0.1976:0.0	rs1127525;rs3183622;rs17392327	336	Q9UK80	UBP21_HUMAN	T	336	ENSP00000356981:P336T;ENSP00000289865:P336T;ENSP00000356980:P336T	ENSP00000289865:P336T	P	+	1	0	USP21	159399445	0.001000	0.12720	0.161000	0.22692	0.641000	0.38312	0.929000	0.28844	1.146000	0.42352	0.455000	0.32223	CCA	C|0.972;A|0.028	0.028	strong		0.562	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1		
LINGO1	84894	hgsc.bcm.edu	37	15	77907145	77907145	+	Silent	SNP	G	G	A	rs3743481	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:77907145G>A	ENST00000355300.6	-	2	1278	c.1104C>T	c.(1102-1104)tcC>tcT	p.S368S	LINGO1_ENST00000561030.1_Silent_p.S362S	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	368					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						CCAGCGGGTTGGAGTCCAGGA	0.637													G|||	2604	0.519968	0.5666	0.4164	5008	,	,		17828	0.5952		0.4056	False		,,,				2504	0.5706				p.S368S		Atlas-SNP	.											LINGO1,rectum,carcinoma,0,1	LINGO1	76	1	0			c.C1104T						PASS	.	G		2162,2064		575,1012,526	42.0	45.0	44.0		1104	4.9	1.0	15	dbSNP_107	44	3157,5271		564,2029,1621	no	coding-synonymous	LINGO1	NM_032808.5		1139,3041,2147	AA,AG,GG		37.4585,48.8405,42.0341		368/621	77907145	5319,7335	2113	4214	6327	SO:0001819	synonymous_variant	84894	exon2			CGGGTTGGAGTCC	AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"""Immunoglobulin superfamily / I-set domain containing"""	21205	protein-coding gene	gene with protein product		609791	"""leucine rich repeat neuronal 6A"""	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.1104C>T	15.37:g.77907145G>A		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																			G|0.496;A|0.504	0.504	strong		0.637	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
IL22RA2	116379	hgsc.bcm.edu	37	6	137482840	137482840	+	Missense_Mutation	SNP	A	A	G	rs28385692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:137482840A>G	ENST00000296980.2	-	2	347	c.47T>C	c.(46-48)cTt>cCt	p.L16P	IL22RA2_ENST00000349184.4_Missense_Mutation_p.L16P|IL22RA2_ENST00000339602.3_Missense_Mutation_p.L16P	NM_052962.2	NP_443194.1	Q969J5	I22R2_HUMAN	interleukin 22 receptor, alpha 2	16			L -> P (in dbSNP:rs28385692). {ECO:0000269|Ref.6}.		cytokine-mediated signaling pathway (GO:0019221)|negative regulation of inflammatory response (GO:0050728)|regulation of tyrosine phosphorylation of Stat3 protein (GO:0042516)	cytosol (GO:0005829)|extracellular space (GO:0005615)	interleukin-22 binding (GO:0042017)|interleukin-22 receptor activity (GO:0042018)			endometrium(1)|large_intestine(1)|lung(3)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000313)|OV - Ovarian serous cystadenocarcinoma(155;0.00407)		TACACCAGTAAGGAAGAAACT	0.428													A|||	89	0.0177716	0.0023	0.0159	5008	,	,		17508	0.001		0.0318	False		,,,				2504	0.0429				p.L16P		Atlas-SNP	.											IL22RA2,NS,malignant_melanoma,-1,1	IL22RA2	17	1	0			c.T47C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	30,4376	36.0+/-67.5	0,30,2173	119.0	92.0	101.0		47,47,47	3.3	0.7	6	dbSNP_125	101	295,8305	106.0+/-166.9	8,279,4013	yes	missense,missense,missense	IL22RA2	NM_052962.2,NM_181309.1,NM_181310.1	98,98,98	8,309,6186	GG,GA,AA		3.4302,0.6809,2.4988	benign,benign,benign	16/264,16/232,16/131	137482840	325,12681	2203	4300	6503	SO:0001583	missense	116379	exon2			CCAGTAAGGAAGA	AY044429	CCDS5182.1, CCDS5183.1, CCDS5184.1	6q24.1-q24.2	2008-02-05			ENSG00000164485	ENSG00000164485		"""Interleukins and interleukin receptors"""	14901	protein-coding gene	gene with protein product		606648				11481447, 11390454	Standard	NM_181309		Approved	CRF2-S1, IL-22BP	uc003qhl.3	Q969J5	OTTHUMG00000015655	ENST00000296980.2:c.47T>C	6.37:g.137482840A>G	ENSP00000296980:p.Leu16Pro	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	104	36	0.346154	NM_181309	Q08AH7|Q6UWM1|Q96A41|Q96QR0	Missense_Mutation	SNP	ENST00000296980.2	37	CCDS5182.1	29	0.013278388278388278	0	0.0	4	0.011049723756906077	0	0.0	25	0.032981530343007916	A	11.51	1.659956	0.29515	0.006809	0.034302	ENSG00000164485	ENST00000349184;ENST00000296980;ENST00000339602	T;T;T	0.79653	-1.29;-1.29;-1.29	4.55	3.3	0.37823	.	.	.	.	.	T	0.71879	0.3392	M	0.83384	2.64	0.38674	D	0.952373	B;B;P	0.45634	0.125;0.224;0.863	B;B;B	0.42112	0.037;0.097;0.376	T	0.72593	-0.4246	9	0.33141	T	0.24	.	7.7806	0.29062	0.7873:0.2127:0.0:0.0	rs28385692;rs35818500;rs28385692	16;16;16	Q969J5-3;Q969J5-2;Q969J5	.;.;I22R2_HUMAN	P	16	ENSP00000296979:L16P;ENSP00000296980:L16P;ENSP00000340920:L16P	ENSP00000296980:L16P	L	-	2	0	IL22RA2	137524533	0.004000	0.15560	0.734000	0.30879	0.386000	0.30323	0.318000	0.19504	2.060000	0.61445	0.524000	0.50904	CTT	A|0.974;G|0.026	0.026	strong		0.428	IL22RA2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042399.1		
NGF	4803	hgsc.bcm.edu	37	1	115829313	115829313	+	Missense_Mutation	SNP	G	G	A	rs6330	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:115829313G>A	ENST00000369512.2	-	3	272	c.104C>T	c.(103-105)gCc>gTc	p.A35V	RP4-663N10.1_ENST00000425449.1_RNA	NM_002506.2	NP_002497.2	P01138	NGF_HUMAN	nerve growth factor (beta polypeptide)	35			A -> V (in dbSNP:rs6330). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:15014171, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2374737, ECO:0000269|PubMed:6327169, ECO:0000269|PubMed:6688123, ECO:0000269|Ref.10}.		activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|adult locomotory behavior (GO:0008344)|apoptotic signaling pathway (GO:0097190)|circadian rhythm (GO:0007623)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|nerve growth factor processing (GO:0032455)|neuron apoptotic process (GO:0051402)|neuron projection morphogenesis (GO:0048812)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axon extension (GO:0045773)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotrophin TRK receptor signaling pathway (GO:0051388)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|Ras protein signal transduction (GO:0007265)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of neurotransmitter secretion (GO:0046928)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to peptide hormone (GO:0043434)|response to radiation (GO:0009314)|sensory perception of pain (GO:0019233)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)	nerve growth factor receptor binding (GO:0005163)|receptor signaling protein activity (GO:0005057)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13	Lung SC(450;0.211)	all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)	Clenbuterol(DB01407)	AGTCCAGTGGGCTTGGGGGAT	0.602													G|||	1239	0.247404	0.1551	0.3228	5008	,	,		18467	0.1637		0.4563	False		,,,				2504	0.1902				p.A35V		Atlas-SNP	.											.	NGF	43	.	0			c.C104T	GRCh37	CM086294	NGF	M	rs6330	PASS	.	G	VAL/ALA	911,3495	349.5+/-310.4	95,721,1387	114.0	90.0	98.0		104	4.4	1.0	1	dbSNP_52	98	3890,4710	544.1+/-384.5	857,2176,1267	yes	missense	NGF	NM_002506.2	64	952,2897,2654	AA,AG,GG		45.2326,20.6764,36.9137	benign	35/242	115829313	4801,8205	2203	4300	6503	SO:0001583	missense	4803	exon3			CAGTGGGCTTGGG		CCDS882.1	1p13.1	2014-09-17	2008-02-07	2008-02-07	ENSG00000134259	ENSG00000134259		"""Endogenous ligands"""	7808	protein-coding gene	gene with protein product		162030		NGFB			Standard	XM_006710663		Approved		uc001efu.1	P01138	OTTHUMG00000011880	ENST00000369512.2:c.104C>T	1.37:g.115829313G>A	ENSP00000358525:p.Ala35Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	114	69	0.605263	NM_002506	A1A4E5|Q6FHA0|Q96P60|Q9P2Q8|Q9UKL8	Missense_Mutation	SNP	ENST00000369512.2	37	CCDS882.1	667	0.30540293040293043	81	0.16463414634146342	142	0.39226519337016574	88	0.15384615384615385	356	0.46965699208443273	G	15.76	2.927347	0.52759	0.206764	0.452326	ENSG00000134259	ENST00000369512	T	0.61627	0.09	5.36	4.45	0.53987	.	0.578915	0.18573	N	0.137281	T	0.32675	0.0837	L	0.57536	1.79	0.30744	P	0.745886	B	0.09022	0.002	B	0.08055	0.003	T	0.29336	-1.0015	9	0.62326	D	0.03	-26.7795	5.8933	0.18925	0.1689:0.1588:0.6723:0.0	rs6330;rs3182218;rs3729539;rs52795215;rs60014358;rs6330	35	P01138	NGF_HUMAN	V	35	ENSP00000358525:A35V	ENSP00000358525:A35V	A	-	2	0	NGF	115630836	0.997000	0.39634	0.977000	0.42913	0.986000	0.74619	2.298000	0.43602	1.264000	0.44198	0.467000	0.42956	GCC	G|0.664;A|0.336	0.336	strong		0.602	NGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032832.1	NM_002506	
SBSN	374897	hgsc.bcm.edu	37	19	36017928	36017928	+	Missense_Mutation	SNP	G	G	C	rs10775583	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36017928G>C	ENST00000452271.2	-	1	1284	c.1256C>G	c.(1255-1257)gCg>gGg	p.A419G	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	419	Ala/Gly/His-rich.		A -> G (in dbSNP:rs10775583). {ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AAACTGCCCCGCCTCCCTTCC	0.617													G|||	2088	0.416933	0.2065	0.4683	5008	,	,		17406	0.6567		0.3559	False		,,,				2504	0.4806				p.A419G		Atlas-SNP	.											.	SBSN	58	.	0			c.C1256G						PASS	.	G	GLY/ALA,,	316,1068		34,248,410	85.0	76.0	79.0		1256,,	-2.4	0.0	19	dbSNP_120	79	1106,2076		209,688,694	yes	missense,intron,intron	SBSN	NM_001166034.1,NM_001166035.1,NM_198538.3	60,,	243,936,1104	CC,CG,GG		34.758,22.8324,31.1432	possibly-damaging,,	419/591,,	36017928	1422,3144	692	1591	2283	SO:0001583	missense	374897	exon1			TGCCCCGCCTCCC	AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05							24950	protein-coding gene	gene with protein product		609969				12228223	Standard	NM_198538		Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.1256C>G	19.37:g.36017928G>C	ENSP00000430242:p.Ala419Gly	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_001166034	A8K5J0|E9PBV3	Missense_Mutation	SNP	ENST00000452271.2	37	CCDS54253.1	917	0.4198717948717949	101	0.20528455284552846	164	0.4530386740331492	386	0.6748251748251748	266	0.35092348284960423	G	3.759	-0.049935	0.07407	0.228324	0.34758	ENSG00000189001	ENST00000452271	T	0.51071	0.72	4.17	-2.36	0.06663	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	1.0000000000287557E-6	P	0.45768	0.866	B	0.43331	0.416	T	0.37596	-0.9699	8	0.05351	T	0.99	.	7.8143	0.29249	0.6501:0.0:0.3499:0.0	rs10775583	419	E9PBV3	.	G	419	ENSP00000430242:A419G	ENSP00000430242:A419G	A	-	2	0	SBSN	40709768	0.000000	0.05858	0.007000	0.13788	0.048000	0.14542	-1.005000	0.03674	-0.296000	0.08947	0.407000	0.27541	GCG	G|0.577;C|0.423	0.423	strong		0.617	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538	
MYRF	745	hgsc.bcm.edu	37	11	61551356	61551356	+	Silent	SNP	T	T	C	rs174535	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:61551356T>C	ENST00000278836.5	+	24	3249	c.3153T>C	c.(3151-3153)agT>agC	p.S1051S	MYRF_ENST00000265460.5_Silent_p.S1011S|MYRF_ENST00000389602.4_Silent_p.S437S|TMEM258_ENST00000535042.1_Intron	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	1051					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCCCTGTCAGTAGTGGCACCC	0.637													C|||	1703	0.340056	0.1467	0.6037	5008	,	,		18016	0.5694		0.3549	False		,,,				2504	0.1626				p.S1051S		Atlas-SNP	.											C11orf9,colon,carcinoma,0,1	.	.	1	0			c.T3153C						scavenged	.	C	,	894,3510	726.5+/-409.7	107,680,1415	53.0	39.0	44.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3153,3033	1.3	0.9	11	dbSNP_79	44	2860,5738	657.4+/-401.5	498,1864,1937	no	coding-synonymous,coding-synonymous	C11orf9	NM_001127392.1,NM_013279.2	,	605,2544,3352	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	33.2635,20.2997,28.8725	,	1051/1152,1011/1112	61551356	3754,9248	2202	4299	6501	SO:0001819	synonymous_variant	745	exon24			TGTCAGTAGTGGC		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"""myelin gene regulatory factor"""	608329	"""chromosome 11 open reading frame 9"""	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.3153T>C	11.37:g.61551356T>C		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	171	72	0.421053	NM_001127392	O43582|Q9P1Q6	Silent	SNP	ENST00000278836.5	37	CCDS44622.1																																																																																			T|0.705;C|0.295	0.295	strong		0.637	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279	
CDH3	1001	hgsc.bcm.edu	37	16	68721470	68721470	+	Silent	SNP	T	T	C	rs2296405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:68721470T>C	ENST00000264012.4	+	12	2170	c.1626T>C	c.(1624-1626)aaT>aaC	p.N542N	CDH3_ENST00000581171.1_Silent_p.N487N|CDH3_ENST00000429102.2_Silent_p.N542N	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	542	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TTGATGTCAATGACCATGGCC	0.562													C|||	2992	0.597444	0.6657	0.5476	5008	,	,		21060	0.5536		0.6173	False		,,,				2504	0.5654				p.N542N		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.T1626C						PASS	.	C		2947,1449	468.9+/-355.3	985,977,236	124.0	112.0	116.0		1626	-8.0	0.4	16	dbSNP_100	116	5319,3281	491.6+/-373.1	1641,2037,622	yes	coding-synonymous	CDH3	NM_001793.4		2626,3014,858	CC,CT,TT		38.1512,32.9618,36.3958		542/830	68721470	8266,4730	2198	4300	6498	SO:0001819	synonymous_variant	1001	exon12			TGTCAATGACCAT	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1626T>C	16.37:g.68721470T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	171	168	0.982456	NM_001793	B2R6F4|Q05DI6	Silent	SNP	ENST00000264012.4	37	CCDS10868.1																																																																																			T|0.373;G|0.004	.	strong		0.562	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
EXOSC3	51010	hgsc.bcm.edu	37	9	37782111	37782111	+	Silent	SNP	C	C	T	rs7158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37782111C>T	ENST00000327304.5	-	3	510	c.498G>A	c.(496-498)caG>caA	p.Q166Q	RP11-613M10.9_ENST00000540557.1_Intron|EXOSC3_ENST00000396521.3_Intron|EXOSC3_ENST00000490516.1_Intron	NM_016042.3	NP_057126.2	Q9NQT5	EXOS3_HUMAN	exosome component 3	166					CUT catabolic process (GO:0071034)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of isotype switching (GO:0045830)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(1)	4				GBM - Glioblastoma multiforme(29;0.00771)|Lung(182;0.221)		CAACCACAAACTGGCCATAGA	0.433													T|||	2825	0.564097	0.612	0.5908	5008	,	,		18244	0.5337		0.4841	False		,,,				2504	0.5941				p.Q166Q		Atlas-SNP	.											.	EXOSC3	8	.	0			c.G498A						PASS	.	T	,	2606,1800	529.2+/-372.6	793,1020,390	78.0	74.0	75.0		,498	-7.3	0.2	9	dbSNP_52	75	4276,4324	578.7+/-390.8	1073,2130,1097	no	intron,coding-synonymous	EXOSC3	NM_001002269.1,NM_016042.2	,	1866,3150,1487	TT,TC,CC		49.7209,40.8534,47.086	,	,166/276	37782111	6882,6124	2203	4300	6503	SO:0001819	synonymous_variant	51010	exon3			CACAAACTGGCCA	BC002437	CCDS35016.1, CCDS43805.1	9p11	2009-01-20			ENSG00000107371	ENSG00000107371			17944	protein-coding gene	gene with protein product	"""exosome component Rrp40"", ""CGI-102 protein"""	606489				10810093, 11110791	Standard	NM_016042		Approved	hRrp40p, Rrp40p, RRP40, CGI-102, p10, hRrp-40	uc004aal.3	Q9NQT5	OTTHUMG00000019932	ENST00000327304.5:c.498G>A	9.37:g.37782111C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_016042	A8K0K6|Q5QP85|Q9Y3A8	Silent	SNP	ENST00000327304.5	37	CCDS35016.1																																																																																			C|0.471;T|0.529	0.529	strong		0.433	EXOSC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052478.3	NM_016042	
ZNF404	342908	hgsc.bcm.edu	37	19	44377669	44377669	+	Missense_Mutation	SNP	G	G	A	rs12977303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44377669G>A	ENST00000587539.1	-	3	696	c.697C>T	c.(697-699)Cat>Tat	p.H233Y	ZNF404_ENST00000324394.6_Missense_Mutation_p.H231Y	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	233			H -> Y (in dbSNP:rs12977303). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				ATTTTCTGATGTTCTGTAAGG	0.373													G|||	1953	0.389976	0.0855	0.5692	5008	,	,		20854	0.5536		0.507	False		,,,				2504	0.3855				p.H230Y		Atlas-SNP	.											.	ZNF404	46	.	0			c.C688T						PASS	.	G	TYR/HIS	589,3619		55,479,1570	107.0	108.0	108.0		697	2.6	1.0	19	dbSNP_121	108	4199,4311		1058,2083,1114	yes	missense	ZNF404	NM_001033719.2	83	1113,2562,2684	AA,AG,GG		49.342,13.9971,37.6474	possibly-damaging	233/553	44377669	4788,7930	2104	4255	6359	SO:0001583	missense	342908	exon2			TCTGATGTTCTGT	XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"""Zinc fingers, C2H2-type"", ""-"""	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.697C>T	19.37:g.44377669G>A	ENSP00000466051:p.His233Tyr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_001033719	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	37	CCDS59394.1	943	0.4317765567765568	53	0.10772357723577236	181	0.5	326	0.5699300699300699	383	0.5052770448548812	G	12.88	2.070859	0.36566	0.139971	0.49342	ENSG00000176222	ENST00000324394	D	0.86769	-2.17	2.56	2.56	0.30785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	H	0.97365	3.99	0.36459	P	0.13344199999999995	D	0.89917	1.0	D	0.91635	0.999	T	0.03000	-1.1084	8	0.87932	D	0	.	12.2572	0.54631	0.0:0.0:1.0:0.0	rs12977303;rs52824820;rs59071427;rs12977303	233	Q494X3	ZN404_HUMAN	Y	231	ENSP00000319479:H231Y	ENSP00000319479:H231Y	H	-	1	0	ZNF404	49069509	1.000000	0.71417	0.981000	0.43875	0.212000	0.24457	5.111000	0.64628	1.444000	0.47605	0.404000	0.27445	CAT	G|0.588;A|0.412	0.412	strong		0.373	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
BACE2	25825	hgsc.bcm.edu	37	21	42551270	42551270	+	Intron	SNP	A	A	G	rs199893430		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:42551270A>G	ENST00000330333.6	+	1	775				PLAC4_ENST00000440221.2_RNA|BACE2_ENST00000328735.6_Intron|BACE2-IT1_ENST00000433378.1_RNA|PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000414699.1_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000536486.1_RNA	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				gagtgagggtatccagggtga	0.607																																					p.Y96H		Atlas-SNP	.											.	.	.	.	0			c.T286C						PASS	.						147.0	128.0	134.0					21																	42551270		2184	4258	6442	SO:0001627	intron_variant	191585	exon1			GAGGGTATCCAGG	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10768A>G	21.37:g.42551270A>G		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	283	21	0.0742049	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			.	.	weak		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
ZNF222	7673	hgsc.bcm.edu	37	19	44535999	44535999	+	Missense_Mutation	SNP	G	G	T	rs7258517	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44535999G>T	ENST00000187879.8	+	4	334	c.172G>T	c.(172-174)Gtt>Ttt	p.V58F	ZNF222_ENST00000391960.3_Missense_Mutation_p.V98F|ZNF223_ENST00000591793.1_Intron	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	58	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> F (in dbSNP:rs7258517). {ECO:0000269|PubMed:12743021}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GATGGAGACTGTTCCAGAAGC	0.453													G|||	2084	0.416134	0.1543	0.3559	5008	,	,		20780	0.2897		0.7068	False		,,,				2504	0.6442				p.V98F		Atlas-SNP	.											.	ZNF222	90	.	0			c.G292T						PASS	.	G	PHE/VAL,PHE/VAL	1078,3328	391.0+/-327.9	130,818,1255	86.0	82.0	83.0		172,292	-3.1	0.0	19	dbSNP_116	83	5991,2609	687.8+/-404.2	2076,1839,385	yes	missense,missense	ZNF222	NM_013360.2,NM_001129996.1	50,50	2206,2657,1640	TT,TG,GG		30.3372,24.4666,45.6482	benign,benign	58/452,98/492	44535999	7069,5937	2203	4300	6503	SO:0001583	missense	7673	exon4			GAGACTGTTCCAG	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"""Zinc fingers, C2H2-type"", ""-"""	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.172G>T	19.37:g.44535999G>T	ENSP00000187879:p.Val58Phe	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	249	112	0.449799	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Missense_Mutation	SNP	ENST00000187879.8	37	CCDS33045.1	948	0.4340659340659341	70	0.14227642276422764	152	0.4198895027624309	183	0.31993006993006995	543	0.716358839050132	G	11.18	1.563133	0.27915	0.244666	0.696628	ENSG00000159885	ENST00000391960;ENST00000187879;ENST00000251272	T;T	0.05996	3.36;3.4	2.14	-3.06	0.05379	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B;B	0.20261	0.035;0.043	B;B	0.21151	0.033;0.025	T	0.19031	-1.0318	8	0.09590	T	0.72	.	4.3188	0.11007	0.2565:0.2687:0.4748:0.0	rs7258517;rs52824298;rs59933403;rs7258517	98;58	G5E9B9;Q9UK12	.;ZN222_HUMAN	F	98;58;4	ENSP00000375822:V98F;ENSP00000187879:V58F	ENSP00000187879:V58F	V	+	1	0	ZNF222	49227839	0.000000	0.05858	0.000000	0.03702	0.707000	0.40811	-3.161000	0.00577	-0.521000	0.06426	0.205000	0.17691	GTT	G|0.510;T|0.490	0.490	strong		0.453	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2		
KIAA1755	85449	hgsc.bcm.edu	37	20	36841756	36841756	+	Silent	SNP	T	T	C	rs1534967	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:36841756T>C	ENST00000279024.4	-	14	3562	c.3291A>G	c.(3289-3291)tcA>tcG	p.S1097S		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1097								p.S1097S(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CCATGCCCAGTGAGTCTAGTG	0.607													C|||	1970	0.393371	0.2436	0.4424	5008	,	,		18755	0.5238		0.4344	False		,,,				2504	0.3845				p.S1097S		Atlas-SNP	.											KIAA1755,NS,carcinoma,0,1	KIAA1755	145	1	1	Substitution - coding silent(1)	stomach(1)	c.A3291G						PASS	.	C		1169,3237	690.7+/-405.3	162,845,1196	41.0	30.0	34.0		3291	-10.6	0.0	20	dbSNP_88	34	3941,4657	580.1+/-391.0	907,2127,1265	no	coding-synonymous	KIAA1755	NM_001029864.1		1069,2972,2461	CC,CT,TT		45.8362,26.532,39.2956		1097/1201	36841756	5110,7894	2203	4299	6502	SO:0001819	synonymous_variant	85449	exon14			GCCCAGTGAGTCT	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.3291A>G	20.37:g.36841756T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			T|0.603;C|0.397	0.397	strong		0.607	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
BAZ2B	29994	hgsc.bcm.edu	37	2	160182302	160182302	+	Missense_Mutation	SNP	C	C	T	rs415793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160182302C>T	ENST00000392783.2	-	35	6566	c.6071G>A	c.(6070-6072)aGt>aAt	p.S2024N	BAZ2B_ENST00000355831.2_Missense_Mutation_p.S1990N|BAZ2B_ENST00000392782.1_Missense_Mutation_p.S1988N|BAZ2B_ENST00000343439.5_Missense_Mutation_p.S1924N	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	2024			S -> N (in dbSNP:rs415793).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						TTTTAGTGAACTACTTGTAGA	0.323													C|||	1255	0.250599	0.329	0.1801	5008	,	,		15308	0.2321		0.2097	False		,,,				2504	0.2556				p.S2024N		Atlas-SNP	.											.	BAZ2B	196	.	0			c.G6071A						PASS	.	C	ASN/SER	1037,2615		143,751,932	153.0	141.0	145.0		6071	5.8	1.0	2	dbSNP_80	145	1786,6372		189,1408,2482	yes	missense	BAZ2B	NM_013450.2	46	332,2159,3414	TT,TC,CC		21.8926,28.3954,23.9035	benign	2024/2169	160182302	2823,8987	1826	4079	5905	SO:0001583	missense	29994	exon35			AGTGAACTACTTG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.6071G>A	2.37:g.160182302C>T	ENSP00000376534:p.Ser2024Asn	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	220	104	0.472727	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	545	0.24954212454212454	180	0.36585365853658536	77	0.212707182320442	118	0.2062937062937063	170	0.22427440633245382	C	12.94	2.089690	0.36855	0.283954	0.218926	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.78	5.78	0.91487	.	0.000000	0.43110	U	0.000601	T	0.00012	0.0000	N	0.24115	0.695	0.27458	P	0.9532378	P;B	0.41848	0.763;0.209	B;B	0.36608	0.229;0.062	T	0.40590	-0.9555	9	0.26408	T	0.33	-12.2975	11.376	0.49728	0.1272:0.6343:0.2384:0.0	rs415793;rs52792009;rs58271129;rs415793	1988;2024	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	N	1988;2024;1990;1924	ENSP00000376533:S1988N;ENSP00000376534:S2024N;ENSP00000348087:S1990N;ENSP00000339670:S1924N	ENSP00000339670:S1924N	S	-	2	0	BAZ2B	159890548	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	2.956000	0.49129	2.730000	0.93505	0.650000	0.86243	AGT	T|0.249;G|0.012	0.249	strong		0.323	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
IP6K3	117283	hgsc.bcm.edu	37	6	33690796	33690796	+	Missense_Mutation	SNP	C	C	T	rs4713668|rs34332988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33690796C>T	ENST00000293756.4	-	6	1260	c.934G>A	c.(934-936)Gtc>Atc	p.V312I	IP6K3_ENST00000451316.1_Missense_Mutation_p.V312I	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	312			V -> I (in dbSNP:rs4713668). {ECO:0000269|PubMed:14702039}.		inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						CTCCTAATGACAGAGAGGAGG	0.577													C|||	2567	0.51258	0.1021	0.5778	5008	,	,		16130	0.8442		0.4702	False		,,,				2504	0.7229				p.V312I		Atlas-SNP	.											.	IP6K3	52	.	0			c.G934A						PASS	.	C	ILE/VAL,ILE/VAL	787,3619		69,649,1485	51.0	57.0	55.0		934,934	5.1	0.9	6	dbSNP_111	55	3734,4866		868,1998,1434	yes	missense,missense	IP6K3	NM_001142883.1,NM_054111.4	29,29	937,2647,2919	TT,TC,CC		43.4186,17.862,34.7609	probably-damaging,probably-damaging	312/411,312/411	33690796	4521,8485	2203	4300	6503	SO:0001583	missense	117283	exon7			TAATGACAGAGAG	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"""inositol hexaphosphate kinase 3"""	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.934G>A	6.37:g.33690796C>T	ENSP00000293756:p.Val312Ile	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	187	75	0.40107	NM_001142883	Q96MQ9	Missense_Mutation	SNP	ENST00000293756.4	37	CCDS34435.1	901	0.4125457875457875	37	0.07520325203252033	178	0.49171270718232046	405	0.708041958041958	281	0.370712401055409	C	14.58	2.577765	0.45902	0.17862	0.434186	ENSG00000161896	ENST00000451316;ENST00000293756	T;T	0.17854	2.25;2.25	5.99	5.12	0.69794	.	0.106716	0.41823	N	0.000815	T	0.06508	0.0167	L	0.41492	1.28	0.29232	P	0.873246	B	0.32283	0.362	B	0.33568	0.166	T	0.24799	-1.0150	9	0.22706	T	0.39	-43.3953	11.8663	0.52495	0.0:0.8588:0.0:0.1412	rs4713668;rs59117943;rs4713668	312	Q96PC2	IP6K3_HUMAN	I	312	ENSP00000398861:V312I;ENSP00000293756:V312I	ENSP00000293756:V312I	V	-	1	0	IP6K3	33798774	0.999000	0.42202	0.899000	0.35326	0.291000	0.27294	4.011000	0.57124	1.534000	0.49203	0.655000	0.94253	GTC	C|0.610;T|0.390	0.390	strong		0.577	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
HSD17B1	3292	hgsc.bcm.edu	37	17	40706596	40706596	+	Missense_Mutation	SNP	C	C	T	rs147402365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:40706596C>T	ENST00000585807.1	+	5	4433	c.713C>T	c.(712-714)gCg>gTg	p.A238V	HSD17B1_ENST00000225929.5_Missense_Mutation_p.A239V|RP11-400F19.6_ENST00000590513.1_RNA|RP11-400F19.8_ENST00000585572.1_RNA	NM_000413.2	NP_000404.2	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	238			A -> V. {ECO:0000269|PubMed:8389226}.		bone development (GO:0060348)|cellular response to metal ion (GO:0071248)|estrogen biosynthetic process (GO:0006703)|estrogen metabolic process (GO:0008210)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			NS(1)|endometrium(1)|kidney(1)|lung(2)	5		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Equilin(DB02187)	GAGGAGGTGGCGGAGGTGAGC	0.687													C|||	14	0.00279553	0.0008	0.0	5008	,	,		12600	0.0		0.0129	False		,,,				2504	0.0				p.A238V		Atlas-SNP	.											.	HSD17B1	24	.	0			c.C713T						PASS	.	C	VAL/ALA	9,4395	15.5+/-35.6	0,9,2193	39.0	31.0	34.0		713	-0.4	0.0	17	dbSNP_134	34	70,8530	42.2+/-99.7	0,70,4230	yes	missense	HSD17B1	NM_000413.2	64	0,79,6423	TT,TC,CC		0.814,0.2044,0.6075	benign	238/329	40706596	79,12925	2202	4300	6502	SO:0001583	missense	3292	exon5			AGGTGGCGGAGGT		CCDS11428.1	17q11-q21	2011-09-14					1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5210	protein-coding gene	gene with protein product	"""Estradiol 17-beta-dehydrogenase-1"", ""short chain dehydrogenase/reductase family 28CE, member 1"""	109684		EDHB17, EDH17B2		2330005, 19027726	Standard	NM_000413		Approved	HSD17, MGC138140, SDR28C1	uc002hzw.3	P14061		ENST00000585807.1:c.713C>T	17.37:g.40706596C>T	ENSP00000466799:p.Ala238Val	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_000413	B3KXS1|Q2M2L8	Missense_Mutation	SNP	ENST00000585807.1	37	CCDS11428.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	8.655	0.899159	0.17686	0.002044	0.00814	ENSG00000108786	ENST00000225929	.	.	.	4.16	-0.383	0.12477	NAD(P)-binding domain (1);	1.163550	0.06218	N	0.686122	T	0.07503	0.0189	N	0.04636	-0.2	0.09310	N	1	B;P	0.41102	0.002;0.738	B;B	0.28553	0.002;0.091	T	0.15065	-1.0450	9	0.30854	T	0.27	.	6.1916	0.20528	0.0:0.5144:0.0:0.4856	.	269;238	B3RFR9;P14061	.;DHB1_HUMAN	V	238	.	ENSP00000225929:A238V	A	+	2	0	HSD17B1	37960122	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.067000	0.14510	0.095000	0.17434	-0.658000	0.03865	GCG	C|0.996;T|0.004	0.004	strong		0.687	HSD17B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450392.1	NM_000413	
PIEZO2	63895	hgsc.bcm.edu	37	18	10681711	10681711	+	Missense_Mutation	SNP	C	C	T	rs3748428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:10681711C>T	ENST00000503781.3	-	47	7386	c.7387G>A	c.(7387-7389)Gtt>Att	p.V2463I	PIEZO2_ENST00000581680.1_5'Flank|PIEZO2_ENST00000580640.1_Missense_Mutation_p.V2488I|PIEZO2_ENST00000538948.1_Missense_Mutation_p.V420I|PIEZO2_ENST00000285141.4_Missense_Mutation_p.V255I|PIEZO2_ENST00000302079.6_Missense_Mutation_p.V2400I	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2463			V -> I (in dbSNP:rs3748428). {ECO:0000269|Ref.1}.		cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TGGTCCATAACTTTCAACTGG	0.408													C|||	579	0.115615	0.0219	0.1427	5008	,	,		18706	0.1786		0.1491	False		,,,				2504	0.1237				p.V2463I		Atlas-SNP	.											.	.	.	.	0			c.G7387A						PASS	.	C	ILE/VAL	123,4283	92.0+/-130.7	1,121,2081	157.0	152.0	153.0		7387	5.1	1.0	18	dbSNP_107	153	1124,7476	231.9+/-265.7	69,986,3245	yes	missense	PIEZO2	NM_022068.2	29	70,1107,5326	TT,TC,CC		13.0698,2.7916,9.5879	benign	2463/2753	10681711	1247,11759	2203	4300	6503	SO:0001583	missense	63895	exon47			CCATAACTTTCAA	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.7387G>A	18.37:g.10681711C>T	ENSP00000421377:p.Val2463Ile	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	94	35	0.37234	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Missense_Mutation	SNP	ENST00000503781.3	37		310	0.14194139194139194	18	0.036585365853658534	56	0.15469613259668508	125	0.21853146853146854	111	0.14643799472295516	C	10.17	1.277813	0.23307	0.027916	0.130698	ENSG00000154864	ENST00000503781;ENST00000302079;ENST00000538948;ENST00000285141	T;T	0.72725	-0.68;-0.68	5.12	5.12	0.69794	.	0.275088	0.30850	N	0.008741	T	0.00039	0.0001	N	0.22421	0.69	0.42504	P	0.007051999999999947	B	0.29481	0.245	B	0.31101	0.124	T	0.04678	-1.0934	9	0.22109	T	0.4	.	11.9455	0.52926	0.0:0.8729:0.0:0.1271	rs3748428;rs17550999;rs56544279;rs61174242;rs3748428	357	D6RFZ0	.	I	357;2463;420;255	ENSP00000443129:V420I;ENSP00000285141:V255I	ENSP00000285141:V255I	V	-	1	0	FAM38B	10671711	0.025000	0.19082	1.000000	0.80357	0.786000	0.44442	0.205000	0.17356	2.549000	0.85964	0.561000	0.74099	GTT	C|0.882;T|0.118	0.118	strong		0.408	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068	
LAMB1	3912	hgsc.bcm.edu	37	7	107591763	107591763	+	Missense_Mutation	SNP	G	G	A	rs145485632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:107591763G>A	ENST00000222399.6	-	24	3529	c.3299C>T	c.(3298-3300)aCg>aTg	p.T1100M	LAMB1_ENST00000393561.1_Missense_Mutation_p.T1124M	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1100	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GCACTGCCCCGTGAACTGCGG	0.572													G|||	5	0.000998403	0.0	0.0029	5008	,	,		16910	0.0		0.003	False		,,,				2504	0.0				p.T1100M		Atlas-SNP	.											.	LAMB1	185	.	0			c.C3299T						PASS	.	G	MET/THR	3,4403	6.2+/-15.9	0,3,2200	42.0	38.0	39.0		3299	5.0	1.0	7	dbSNP_134	39	1,8599	1.2+/-3.3	0,1,4299	yes	missense	LAMB1	NM_002291.2	81	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	possibly-damaging	1100/1787	107591763	4,13002	2203	4300	6503	SO:0001583	missense	3912	exon24			TGCCCCGTGAACT	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3299C>T	7.37:g.107591763G>A	ENSP00000222399:p.Thr1100Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	17.85	3.489271	0.64074	6.81E-4	1.16E-4	ENSG00000091136	ENST00000393561;ENST00000222399	T;T	0.66099	-0.19;-0.19	5.0	5.0	0.66597	EGF-like, laminin (3);	.	.	.	.	T	0.77532	0.4144	M	0.92507	3.315	0.80722	D	1	D;D	0.65815	0.995;0.991	P;B	0.59115	0.852;0.424	D	0.84831	0.0802	9	0.66056	D	0.02	.	18.8361	0.92164	0.0:0.0:1.0:0.0	.	1100;1124	P07942;G3XAI2	LAMB1_HUMAN;.	M	1124;1100	ENSP00000377191:T1124M;ENSP00000222399:T1100M	ENSP00000222399:T1100M	T	-	2	0	LAMB1	107378999	0.986000	0.35501	0.976000	0.42696	0.899000	0.52679	2.037000	0.41174	2.748000	0.94277	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.572	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79057989	79057989	+	Missense_Mutation	SNP	C	C	T	rs200769684		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79057989C>T	ENST00000388820.4	-	19	4474	c.4264G>A	c.(4264-4266)Gag>Aag	p.E1422K	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1422	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E1422K(3)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CCACTTGCCTCGCTCCAGTTT	0.657																																					p.E1422K		Atlas-SNP	.											ADAMTS7,face,carcinoma,0,3	ADAMTS7	142	3	3	Substitution - Missense(3)	skin(2)|NS(1)	c.G4264A						scavenged	.						31.0	34.0	33.0					15																	79057989		2188	4275	6463	SO:0001583	missense	11173	exon19			TTGCCTCGCTCCA	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.4264G>A	15.37:g.79057989C>T	ENSP00000373472:p.Glu1422Lys	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	168	7	0.0416667	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	c	8.994	0.978370	0.18812	.	.	ENSG00000136378	ENST00000388820	T	0.54279	0.58	4.21	-8.41	0.00961	.	0.609972	0.15843	N	0.241932	T	0.35248	0.0925	L	0.51914	1.62	0.19775	N	0.999954	B	0.14012	0.009	B	0.10450	0.005	T	0.45483	-0.9258	10	0.07325	T	0.83	.	13.64	0.62243	0.0:0.6736:0.1359:0.1905	.	1422	Q9UKP4	ATS7_HUMAN	K	1422	ENSP00000373472:E1422K	ENSP00000373472:E1422K	E	-	1	0	ADAMTS7	76845044	0.010000	0.17322	0.706000	0.30403	0.289000	0.27227	-0.206000	0.09398	-1.547000	0.01715	-2.551000	0.00177	GAG	C|0.999;T|0.001	0.001	weak		0.657	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
CHST15	51363	hgsc.bcm.edu	37	10	125780759	125780759	+	Intron	SNP	G	G	C	rs4072194	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:125780759G>C	ENST00000346248.5	-	6	1990				CHST15_ENST00000421115.1_Missense_Mutation_p.P454A|CHST15_ENST00000435907.1_Intron	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15						carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						GTACGGGGGGGGGGGGTACAC	0.542													-|||	4042	0.807109	0.764	0.8429	5008	,	,		7867	0.874		0.829	False		,,,				2504	0.7485				p.P454A		Atlas-SNP	.											.	CHST15	134	.	0			c.C1360G						PASS	.						17.0	17.0	17.0					10																	125780759		2200	4294	6494	SO:0001627	intron_variant	51363	exon6			GGGGGGGGGGGGT	AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"""Sulfotransferases, membrane-bound"""	18137	protein-coding gene	gene with protein product	"""B cell RAG associated protein"", ""N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"""	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1347+12C>G	10.37:g.125780759G>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	75	71	0.946667	NM_014863	O60338|O60474|Q86VM4	Missense_Mutation	SNP	ENST00000346248.5	37	CCDS7638.1	.	.	.	.	.	.	.	.	.	.	-	6.715	0.500693	0.12822	.	.	ENSG00000182022	ENST00000421115	.	.	.	.	.	.	.	.	.	.	.	T	0.18635	0.0447	N	0.08118	0	0.19945	N	0.999945	.	.	.	.	.	.	T	0.23833	-1.0177	4	0.87932	D	0	.	.	.	.	rs4072194	454	Q7LFX5-2	.	A	454	.	ENSP00000412477:P454A	P	-	1	0	CHST15	125770749	0.087000	0.21565	0.962000	0.40283	0.629000	0.37895	-0.227000	0.09126	0.000000	0.14550	0.000000	0.15137	CCC	G|0.996;A|0.004	.	strong		0.542	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892	
DLK2	65989	hgsc.bcm.edu	37	6	43418528	43418528	+	Missense_Mutation	SNP	C	C	T	rs35192247	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43418528C>T	ENST00000357338.3	-	6	1601	c.901G>A	c.(901-903)Ggg>Agg	p.G301R	DLK2_ENST00000414245.1_Missense_Mutation_p.G295R|DLK2_ENST00000372488.3_Missense_Mutation_p.G301R|DLK2_ENST00000372485.1_Missense_Mutation_p.G295R	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	301			G -> R (in dbSNP:rs35192247).		negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			TCACCTAGCCCAGCCTCTTGC	0.667													C|||	100	0.0199681	0.0121	0.0202	5008	,	,		19294	0.0		0.0507	False		,,,				2504	0.0194				p.G301R		Atlas-SNP	.											.	DLK2	22	.	0			c.G901A						PASS	.	C	ARG/GLY,ARG/GLY	59,4347	56.8+/-93.2	0,59,2144	75.0	75.0	75.0		901,901	3.3	0.8	6	dbSNP_126	75	434,8166	130.5+/-188.4	11,412,3877	yes	missense,missense	DLK2	NM_023932.2,NM_206539.1	125,125	11,471,6021	TT,TC,CC		5.0465,1.3391,3.7906	probably-damaging,probably-damaging	301/384,301/384	43418528	493,12513	2203	4300	6503	SO:0001583	missense	65989	exon6			CTAGCCCAGCCTC	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"""EGF-like-domain, multiple 9"""	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.901G>A	6.37:g.43418528C>T	ENSP00000349893:p.Gly301Arg	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	286	101	0.353147	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Missense_Mutation	SNP	ENST00000357338.3	37	CCDS4897.1	52	0.023809523809523808	4	0.008130081300813009	9	0.024861878453038673	0	0.0	39	0.051451187335092345	C	14.84	2.655420	0.47467	0.013391	0.050465	ENSG00000171462	ENST00000372485;ENST00000372488;ENST00000357338;ENST00000414245	D;D;D;D	0.89681	-2.55;-2.52;-2.52;-2.55	5.09	3.3	0.37823	.	0.269104	0.36519	N	0.002554	T	0.67487	0.2898	L	0.27053	0.805	0.40627	D	0.981829	B	0.14805	0.011	B	0.13407	0.009	T	0.59144	-0.7509	10	0.22706	T	0.39	.	9.1141	0.36746	0.0:0.7721:0.0:0.2279	rs35192247;rs35192247	301	Q6UY11	DLK2_HUMAN	R	295;301;301;295	ENSP00000361563:G295R;ENSP00000361566:G301R;ENSP00000349893:G301R;ENSP00000398906:G295R	ENSP00000349893:G301R	G	-	1	0	DLK2	43526506	0.959000	0.32827	0.799000	0.32177	0.623000	0.37688	2.096000	0.41738	0.546000	0.28920	0.462000	0.41574	GGG	C|0.967;T|0.033	0.033	strong		0.667	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932	
C7orf57	136288	hgsc.bcm.edu	37	7	48086151	48086151	+	Missense_Mutation	SNP	G	G	A	rs111480809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:48086151G>A	ENST00000348904.3	+	5	657	c.445G>A	c.(445-447)Gac>Aac	p.D149N	C7orf57_ENST00000430738.1_Missense_Mutation_p.D194N|C7orf57_ENST00000435376.1_Missense_Mutation_p.D27N|C7orf57_ENST00000539619.1_Missense_Mutation_p.D149N|C7orf57_ENST00000420324.1_Missense_Mutation_p.D194N	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	149										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						AGGGCCCTTCGACTTCGACAT	0.493													G|||	26	0.00519169	0.0	0.0101	5008	,	,		19923	0.0		0.0169	False		,,,				2504	0.002				p.D149N		Atlas-SNP	.											C7orf57_ENST00000348904,colon,carcinoma,0,2	C7orf57	59	2	0			c.G445A						PASS	.	G	ASN/ASP	5,3889		0,5,1942	61.0	57.0	59.0		445	4.6	1.0	7	dbSNP_132	59	103,8171		0,103,4034	yes	missense	C7orf57	NM_001100159.1	23	0,108,5976	AA,AG,GG		1.2449,0.1284,0.8876	probably-damaging	149/296	48086151	108,12060	1947	4137	6084	SO:0001583	missense	136288	exon5			CCCTTCGACTTCG	BC031107	CCDS47583.1, CCDS59054.1, CCDS75594.1	7p12.3	2011-11-25			ENSG00000164746	ENSG00000164746			22247	protein-coding gene	gene with protein product							Standard	NM_001100159		Approved		uc003toh.5	Q8NEG2	OTTHUMG00000155808	ENST00000348904.3:c.445G>A	7.37:g.48086151G>A	ENSP00000335500:p.Asp149Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_001100159	C9JBJ8	Missense_Mutation	SNP	ENST00000348904.3	37	CCDS47583.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	G	17.67	3.447949	0.63178	0.001284	0.012449	ENSG00000164746	ENST00000420324;ENST00000435376;ENST00000430738;ENST00000348904;ENST00000539619	T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36	5.44	4.56	0.56223	.	0.056720	0.64402	D	0.000001	T	0.55016	0.1894	M	0.76574	2.34	0.40682	D	0.982317	D;P	0.89917	1.0;0.638	D;B	0.73380	0.98;0.167	T	0.69022	-0.5255	10	0.59425	D	0.04	-23.6274	12.28	0.54759	0.0829:0.0:0.9171:0.0	.	27;149	C9JBJ8;Q8NEG2	.;CG057_HUMAN	N	194;27;194;149;149	ENSP00000394648:D194N;ENSP00000391652:D27N;ENSP00000410944:D194N;ENSP00000335500:D149N;ENSP00000442474:D149N	ENSP00000335500:D149N	D	+	1	0	C7orf57	48052676	1.000000	0.71417	0.965000	0.40720	0.991000	0.79684	4.434000	0.59935	1.425000	0.47237	0.655000	0.94253	GAC	G|0.989;A|0.011	0.011	strong		0.493	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159	
ZNF142	7701	hgsc.bcm.edu	37	2	219508263	219508263	+	Silent	SNP	G	G	T	rs3770212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219508263G>T	ENST00000449707.1	-	8	3397	c.2976C>A	c.(2974-2976)ccC>ccA	p.P992P	ZNF142_ENST00000411696.2_Silent_p.P992P	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	992					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGGCCTCCGTGGGTGAGGAGT	0.597													G|||	384	0.0766773	0.1256	0.0231	5008	,	,		16385	0.122		0.0258	False		,,,				2504	0.0542				p.P992P	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.C2976A						PASS	.	G		376,3454		16,344,1555	108.0	116.0	114.0		2976	0.9	0.0	2	dbSNP_107	114	265,7971		4,257,3857	no	coding-synonymous	ZNF142	NM_001105537.1		20,601,5412	TT,TG,GG		3.2176,9.8172,5.3124		992/1688	219508263	641,11425	1915	4118	6033	SO:0001819	synonymous_variant	7701	exon8			CTCCGTGGGTGAG	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.2976C>A	2.37:g.219508263G>T		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	316	161	0.509494	NM_001105537	Q92510	Silent	SNP	ENST00000449707.1	37	CCDS42817.1																																																																																			G|0.931;T|0.069	0.069	strong		0.597	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
ATP11A	23250	hgsc.bcm.edu	37	13	113510230	113510230	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:113510230C>T	ENST00000487903.1	+	20	2337	c.2249C>T	c.(2248-2250)tCa>tTa	p.S750L	ATP11A_ENST00000283558.8_Missense_Mutation_p.S750L|ATP11A_ENST00000375645.3_Missense_Mutation_p.S750L|ATP11A_ENST00000375630.2_Missense_Mutation_p.S750L			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	750					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				AACAGACTTTCAGCAGATATG	0.423																																					p.S750L		Atlas-SNP	.											ATP11A_ENST00000375630,lower_third,carcinoma,+1,2	ATP11A	225	2	0			c.C2249T						scavenged	.						97.0	101.0	99.0					13																	113510230		2203	4300	6503	SO:0001583	missense	23250	exon20			GACTTTCAGCAGA	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.2249C>T	13.37:g.113510230C>T	ENSP00000420387:p.Ser750Leu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	138	2	0.0144928	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.40|18.40	3.616363|3.616363	0.66672|0.66672	.|.	.|.	ENSG00000068650|ENSG00000068650	ENST00000418678|ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000432166	.|T;T;T;T	.|0.45668	.|0.89;0.89;0.89;0.89	5.11|5.11	5.11|5.11	0.69529|0.69529	.|HAD-like domain (1);	.|0.362054	.|0.29745	.|N	.|0.011307	.|T	.|0.38321	.|0.1036	L|L	0.38692|0.38692	1.165|1.165	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.25169	.|0.011;0.099;0.119	.|B;B;B	.|0.29267	.|0.039;0.057;0.1	.|T	.|0.13282	.|-1.0515	.|10	.|0.28530	.|T	.|0.3	.|.	18.5563|18.5563	0.91086|0.91086	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|750;750;750	.|E9PCW5;E9PEJ6;P98196	.|.;.;AT11A_HUMAN	X|L	725|750;750;750;750;191	.|ENSP00000420387:S750L;ENSP00000364781:S750L;ENSP00000364796:S750L;ENSP00000283558:S750L	.|ENSP00000283558:S750L	Q|S	+|+	1|2	0|0	ATP11A|ATP11A	112558231|112558231	1.000000|1.000000	0.71417|0.71417	0.037000|0.037000	0.18230|0.18230	0.082000|0.082000	0.17680|0.17680	6.931000|6.931000	0.75863|0.75863	2.375000|2.375000	0.81037|0.81037	0.561000|0.561000	0.74099|0.74099	CAG|TCA	.	.	none		0.423	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
LRBA	987	hgsc.bcm.edu	37	4	151793903	151793903	+	Missense_Mutation	SNP	T	T	C	rs72719663	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:151793903T>C	ENST00000357115.3	-	18	2413	c.2170A>G	c.(2170-2172)Atc>Gtc	p.I724V	LRBA_ENST00000507224.1_Missense_Mutation_p.I724V|LRBA_ENST00000510413.1_Missense_Mutation_p.I724V|LRBA_ENST00000535741.1_Missense_Mutation_p.I724V	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	724						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AGTTTGTAGATAACACTGAAT	0.279													T|||	48	0.00958466	0.0008	0.0173	5008	,	,		13099	0.0		0.0159	False		,,,				2504	0.0194				p.I724V		Atlas-SNP	.											.	LRBA	253	.	0			c.A2170G						PASS	.	T	VAL/ILE,VAL/ILE	26,4380	31.7+/-61.6	0,26,2177	69.0	69.0	69.0		2170,2170	4.6	1.0	4	dbSNP_130	69	263,8337	101.2+/-162.5	3,257,4040	yes	missense,missense	LRBA	NM_001199282.2,NM_006726.4	29,29	3,283,6217	CC,CT,TT		3.0581,0.5901,2.2221	benign,benign	724/2864,724/2864	151793903	289,12717	2203	4300	6503	SO:0001583	missense	987	exon18			TGTAGATAACACT	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.2170A>G	4.37:g.151793903T>C	ENSP00000349629:p.Ile724Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	172	78	0.453488	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	21	0.009615384615384616	0	0.0	8	0.022099447513812154	0	0.0	13	0.017150395778364115	T	9.446	1.089271	0.20390	0.005901	0.030581	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.81	4.6	0.57074	Armadillo-like helical (1);Armadillo-type fold (1);	0.311295	0.30667	N	0.009136	T	0.21145	0.0509	N	0.17312	0.475	0.34945	D	0.750677	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.33777	-0.9855	10	0.24483	T	0.36	.	5.4566	0.16594	0.0:0.1452:0.1555:0.6992	.	724;724	P50851;P50851-2	LRBA_HUMAN;.	V	724	ENSP00000446299:I724V;ENSP00000421552:I724V;ENSP00000349629:I724V;ENSP00000422180:I724V	ENSP00000349629:I724V	I	-	1	0	LRBA	152013353	0.735000	0.28153	1.000000	0.80357	0.981000	0.71138	1.086000	0.30853	0.993000	0.38866	0.477000	0.44152	ATC	T|0.983;C|0.017	0.017	strong		0.279	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
ZBTB4	57659	hgsc.bcm.edu	37	17	7366651	7366651	+	Missense_Mutation	SNP	C	C	G	rs871990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7366651C>G	ENST00000311403.4	-	4	1989	c.1650G>C	c.(1648-1650)atG>atC	p.M550I	ZBTB4_ENST00000380599.4_Missense_Mutation_p.M550I	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	550			M -> I (in dbSNP:rs871990).		cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		TGGTGGTGGCCATGGCTGGCC	0.662													C|||	938	0.1873	0.1203	0.2277	5008	,	,		13827	0.1944		0.1571	False		,,,				2504	0.273				p.M550I		Atlas-SNP	.											.	ZBTB4	163	.	0			c.G1650C						PASS	.	C	ILE/MET,ILE/MET	586,3814		44,498,1658	14.0	17.0	16.0		1650,1650	-9.8	0.0	17	dbSNP_96	16	1227,7365		93,1041,3162	yes	missense,missense	ZBTB4	NM_001128833.1,NM_020899.3	10,10	137,1539,4820	GG,GC,CC		14.2807,13.3182,13.9547	benign,benign	550/1014,550/1014	7366651	1813,11179	2200	4296	6496	SO:0001583	missense	57659	exon4			GGTGGCCATGGCT	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.1650G>C	17.37:g.7366651C>G	ENSP00000307858:p.Met550Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	135	53	0.392593	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	37	CCDS11107.1	373	0.1707875457875458	56	0.11382113821138211	85	0.23480662983425415	116	0.20279720279720279	116	0.15303430079155672	C	4.476	0.088158	0.08583	0.133182	0.142807	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.03524	3.9;3.9	4.9	-9.81	0.00487	.	1.029510	0.07893	U	0.971512	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49370	-0.8947	9	0.46703	T	0.11	.	4.0539	0.09808	0.1796:0.515:0.1813:0.1241	rs871990;rs3744546;rs3892359;rs871990	550	Q9P1Z0	ZBTB4_HUMAN	I	550	ENSP00000307858:M550I;ENSP00000369973:M550I	ENSP00000307858:M550I	M	-	3	0	ZBTB4	7307375	0.000000	0.05858	0.006000	0.13384	0.509000	0.34042	-3.455000	0.00465	-2.294000	0.00663	-0.448000	0.05591	ATG	C|0.861;G|0.139	0.139	strong		0.662	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
OR10G4	390264	hgsc.bcm.edu	37	11	123886307	123886307	+	Missense_Mutation	SNP	C	C	T	rs113664910|rs79057843|rs386758378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123886307C>T	ENST00000320891.4	+	1	26	c.26C>T	c.(25-27)gCa>gTa	p.A9V		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A9V(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CTCGTGACAGCATTCATCCTC	0.537													N|||	1550	0.309505	0.2587	0.3357	5008	,	,		19587	0.2093		0.4334	False		,,,				2504	0.3354				p.A9V		Atlas-SNP	.											OR10G4,NS,carcinoma,0,1	OR10G4	77	1	1	Substitution - Missense(1)	stomach(1)	c.C26T						PASS	.	T	VAL/ALA	1313,3091		219,875,1108	147.0	104.0	118.0		26	-5.4	0.0	11	dbSNP_131	118	3678,4920		878,1922,1499	no	missense	OR10G4	NM_001004462.1	64	1097,2797,2607	TT,TC,CC		42.7774,29.8138,38.3864	benign	9/312	123886307	4991,8011	2202	4299	6501	SO:0001583	missense	390264	exon1			TGACAGCATTCAT	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.26C>T	11.37:g.123886307C>T	ENSP00000325076:p.Ala9Val	Somatic	369	1	0.00271003		WXS	Illumina HiSeq	Phase_I	290	172	0.593103	NM_001004462	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	605	0.27701465201465203	95	0.19308943089430894	118	0.3259668508287293	127	0.22202797202797203	265	0.3496042216358839	c	9.683	1.149889	0.21371	0.298138	0.427774	ENSG00000254737	ENST00000320891	T	0.01099	5.34	3.49	-5.4	0.02656	.	1.466740	0.04179	N	0.326156	T	0.00012	0.0000	N	0.02842	-0.48	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42849	-0.9427	9	0.66056	D	0.02	.	2.0899	0.03655	0.2112:0.362:0.0864:0.3405	.	9	Q8NGN3	O10G4_HUMAN	V	9	ENSP00000325076:A9V	ENSP00000325076:A9V	A	+	2	0	OR10G4	123391517	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.071000	0.01378	-2.100000	0.00848	-4.499000	0.00005	GCA	C|0.622;T|0.378	0.378	strong		0.537	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
CCDC7	79741	hgsc.bcm.edu	37	10	32745248	32745248	+	Missense_Mutation	SNP	A	A	C	rs371686762|rs56391924	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:32745248A>C	ENST00000362006.5	+	4	985	c.442A>C	c.(442-444)Aaa>Caa	p.K148Q	CCDC7_ENST00000535327.1_Missense_Mutation_p.K148Q|CCDC7_ENST00000537047.1_Missense_Mutation_p.K148Q|CCDC7_ENST00000545067.1_Missense_Mutation_p.K148Q|CCDC7_ENST00000539197.1_Missense_Mutation_p.K148Q|CCDC7_ENST00000277657.6_Missense_Mutation_p.K148Q	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	148			K -> Q (in dbSNP:rs56391924).							NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				AGAAGCACTTAAAGAAGAACA	0.313													A|||	706	0.140974	0.0038	0.2305	5008	,	,		15305	0.1696		0.0875	False		,,,				2504	0.2883				p.K148Q		Atlas-SNP	.											.	CCDC7	47	.	0			c.A442C						PASS	.	A	GLN/LYS,GLN/LYS	88,4316	74.1+/-112.3	1,86,2115	82.0	80.0	81.0		442,442	2.4	0.1	10	dbSNP_129	81	720,7872	173.7+/-224.2	39,642,3615	yes	missense,missense	CCDC7	NM_001026383.1,NM_145023.4	53,53	40,728,5730	CC,CA,AA		8.3799,1.9982,6.2173	probably-damaging,probably-damaging	148/487,148/487	32745248	808,12188	2202	4296	6498	SO:0001583	missense	221016	exon4			GCACTTAAAGAAG	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 68"""	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.442A>C	10.37:g.32745248A>C	ENSP00000355078:p.Lys148Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	37	CCDS7173.1	232	0.10622710622710622	4	0.008130081300813009	64	0.17679558011049723	96	0.16783216783216784	68	0.08970976253298153	A	10.64	1.406881	0.25378	0.019982	0.083799	ENSG00000216937	ENST00000324147;ENST00000277657;ENST00000362006;ENST00000545067;ENST00000539197;ENST00000537047;ENST00000535327	T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13	4.94	2.44	0.29823	.	.	.	.	.	T	0.00109	0.0003	L	0.34521	1.04	0.80722	P	0.0	P;P	0.41102	0.496;0.738	B;B	0.42593	0.269;0.392	T	0.03993	-1.0986	8	0.48119	T	0.1	-5.3104	4.545	0.12076	0.7013:0.1966:0.1021:0.0	rs56391924	148;148	A6YT98;Q96M83	.;CCDC7_HUMAN	Q	148	ENSP00000277657:K148Q;ENSP00000355078:K148Q;ENSP00000439930:K148Q;ENSP00000441041:K148Q;ENSP00000440632:K148Q;ENSP00000442531:K148Q	ENSP00000277657:K148Q	K	+	1	0	CCDC7	32785254	0.995000	0.38212	0.073000	0.20177	0.097000	0.18754	1.280000	0.33202	0.735000	0.32537	0.533000	0.62120	AAA	A|0.920;C|0.080	0.080	strong		0.313	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	
PFAS	5198	hgsc.bcm.edu	37	17	8166458	8166458	+	Missense_Mutation	SNP	T	T	A	rs35217368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8166458T>A	ENST00000314666.6	+	13	1575	c.1442T>A	c.(1441-1443)tTt>tAt	p.F481Y	PFAS_ENST00000545834.1_Missense_Mutation_p.F57Y|PFAS_ENST00000585319.1_3'UTR	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	481			F -> Y (in dbSNP:rs35217368).		'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	GACCTGGACTTTGGGGCTGTG	0.582													T|||	154	0.0307508	0.0023	0.0548	5008	,	,		18309	0.0		0.1034	False		,,,				2504	0.0092				p.F481Y		Atlas-SNP	.											.	PFAS	91	.	0			c.T1442A						PASS	.	T	TYR/PHE	60,4346	57.4+/-93.9	2,56,2145	114.0	114.0	114.0		1442	4.8	0.8	17	dbSNP_126	114	617,7983	161.0+/-214.0	25,567,3708	yes	missense	PFAS	NM_012393.2	22	27,623,5853	AA,AT,TT		7.1744,1.3618,5.2053	benign	481/1339	8166458	677,12329	2203	4300	6503	SO:0001583	missense	5198	exon13			TGGACTTTGGGGC	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.1442T>A	17.37:g.8166458T>A	ENSP00000313490:p.Phe481Tyr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	103	0.04716117216117216	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	79	0.10422163588390501	T	14.99	2.699938	0.48307	0.013618	0.071744	ENSG00000178921	ENST00000545834;ENST00000314666	T;T	0.32272	1.46;1.46	5.91	4.82	0.62117	AIR synthase-related protein, C-terminal (2);	0.184978	0.48286	N	0.000195	T	0.01320	0.0043	M	0.86953	2.85	0.44302	D	0.997172	B;B	0.21309	0.003;0.054	B;B	0.28638	0.007;0.092	T	0.01468	-1.1347	10	0.66056	D	0.02	-8.494	10.2394	0.43303	0.1602:0.0:0.0:0.8398	rs35217368	57;481	F5GWT9;O15067	.;PUR4_HUMAN	Y	57;481	ENSP00000441706:F57Y;ENSP00000313490:F481Y	ENSP00000313490:F481Y	F	+	2	0	PFAS	8107183	1.000000	0.71417	0.813000	0.32504	0.921000	0.55340	3.439000	0.52878	1.022000	0.39626	0.533000	0.62120	TTT	T|0.955;A|0.045	0.045	strong		0.582	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
ZNF846	162993	hgsc.bcm.edu	37	19	9868404	9868404	+	Missense_Mutation	SNP	C	C	T	rs10414485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9868404C>T	ENST00000397902.2	-	6	1762	c.1349G>A	c.(1348-1350)tGt>tAt	p.C450Y	ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_Intron|ZNF846_ENST00000588267.1_Intron	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	450			C -> Y (in dbSNP:rs10414485).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						CTTACATTCACAGGCCTTTTC	0.428													N|||	1379	0.275359	0.4728	0.3804	5008	,	,		21932	0.0714		0.2127	False		,,,				2504	0.2086				p.C450Y		Atlas-SNP	.											.	ZNF846	61	.	0			c.G1349A						PASS	.	T	TYR/CYS	1577,2711		336,905,903	84.0	96.0	92.0		1349	-0.4	0.0	19	dbSNP_119	92	1694,6864		171,1352,2756	yes	missense	ZNF846	NM_001077624.1	194	507,2257,3659	TT,TC,CC		19.7943,36.7771,25.4632	benign	450/534	9868404	3271,9575	2144	4279	6423	SO:0001583	missense	162993	exon6			CATTCACAGGCCT	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"""Zinc fingers, C2H2-type"", ""-"""	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.1349G>A	19.37:g.9868404C>T	ENSP00000380999:p.Cys450Tyr	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	190	99	0.521053	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	546	0.25	231	0.4695121951219512	122	0.3370165745856354	31	0.05419580419580419	162	0.21372031662269128	.	0.003	-2.444505	0.00178	0.367771	0.197943	ENSG00000196605	ENST00000397902	T	0.12039	2.72	2.04	-0.357	0.12579	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00068	-2.285	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38499	-0.9658	7	.	.	.	.	3.3875	0.07277	0.5722:0.1347:0.0:0.2931	rs10414485;rs52801835;rs59999512;rs10414485	450	Q147U1	ZN846_HUMAN	Y	450	ENSP00000380999:C450Y	.	C	-	2	0	ZNF846	9729404	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.861000	0.04268	-0.578000	0.05959	-0.369000	0.07265	TGT	C|0.749;T|0.251	0.251	strong		0.428	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624	
MOV10L1	54456	hgsc.bcm.edu	37	22	50530501	50530501	+	Missense_Mutation	SNP	A	A	T	rs9617066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50530501A>T	ENST00000262794.5	+	2	252	c.169A>T	c.(169-171)Atg>Ttg	p.M57L	MOV10L1_ENST00000540615.1_Missense_Mutation_p.M37L|MOV10L1_ENST00000395843.1_De_novo_Start_InFrame|MOV10L1_ENST00000395858.3_Missense_Mutation_p.M57L|MOV10L1_ENST00000475190.1_3'UTR|MOV10L1_ENST00000545383.1_Missense_Mutation_p.M57L	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	57			M -> L (in dbSNP:rs9617066).		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.M57L(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GATTGATGATATGATCTACTT	0.428													T|||	1255	0.250599	0.1301	0.3833	5008	,	,		21379	0.255		0.2356	False		,,,				2504	0.3303				p.M57L		Atlas-SNP	.											MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	1	Substitution - Missense(1)	stomach(1)	c.A169T						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	699,3707	760.7+/-413.0	60,579,1564	336.0	276.0	297.0		169,109,169	-1.0	0.1	22	dbSNP_119	297	2048,6552	718.9+/-406.2	247,1554,2499	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	15,15,15	307,2133,4063	TT,TA,AA		23.814,15.8647,21.121	benign,benign,benign	57/1166,37/1166,57/1212	50530501	2747,10259	2203	4300	6503	SO:0001583	missense	54456	exon2			GATGATATGATCT	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.169A>T	22.37:g.50530501A>T	ENSP00000262794:p.Met57Leu	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	197	125	0.634518	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	530	0.24267399267399267	58	0.11788617886178862	121	0.3342541436464088	178	0.3111888111888112	173	0.22823218997361477	T	1.958	-0.439463	0.04636	0.158647	0.23814	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615;ENST00000428564	D;D;T;D	0.83992	-1.6;-1.6;-1.18;-1.79	5.21	-0.971	0.10303	.	0.589282	0.17323	N	0.178429	T	0.00012	0.0000	N	0.00389	-1.56	0.58432	P	4.000000000004E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.11867	-1.0570	9	0.02654	T	1	-6.8196	4.8754	0.13653	0.3029:0.3448:0.0:0.3523	rs9617066;rs17846341;rs17859375;rs52817043;rs9617066	37;37;57;57	F5H403;E7EPK8;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	L	57;57;57;37;37	ENSP00000438978:M57L;ENSP00000262794:M57L;ENSP00000379199:M57L;ENSP00000438542:M37L	ENSP00000262794:M57L	M	+	1	0	MOV10L1	48872628	0.000000	0.05858	0.117000	0.21633	0.988000	0.76386	-1.156000	0.03160	-0.198000	0.10333	-0.265000	0.10407	ATG	A|0.776;T|0.224	0.224	strong		0.428	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
TOE1	114034	hgsc.bcm.edu	37	1	45808863	45808863	+	Missense_Mutation	SNP	G	G	A	rs9429157	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45808863G>A	ENST00000372090.5	+	8	1605	c.1022G>A	c.(1021-1023)cGt>cAt	p.R341H	MUTYH_ENST00000372110.3_5'Flank|TESK2_ENST00000486676.1_5'Flank|MUTYH_ENST00000529984.1_5'Flank|MUTYH_ENST00000372098.3_5'Flank|TOE1_ENST00000539779.1_Missense_Mutation_p.R261H|TOE1_ENST00000495703.1_3'UTR|MUTYH_ENST00000450313.1_5'Flank|MUTYH_ENST00000372115.3_5'Flank|MUTYH_ENST00000528332.2_5'Flank	NM_025077.3	NP_079353.3	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	341			R -> H (in dbSNP:rs9429157).			nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	11	Acute lymphoblastic leukemia(166;0.155)					CGGCGACGACGTAGGGAAAAA	0.567													G|||	48	0.00958466	0.0015	0.0086	5008	,	,		18981	0.0		0.0328	False		,,,				2504	0.0072				p.R341H		Atlas-SNP	.											.	TOE1	27	.	0			c.G1022A						PASS	.	G	HIS/ARG	33,4373	38.4+/-70.7	0,33,2170	111.0	112.0	112.0		1022	3.8	0.1	1	dbSNP_119	112	297,8303	107.2+/-168.0	10,277,4013	yes	missense	TOE1	NM_025077.3	29	10,310,6183	AA,AG,GG		3.4535,0.749,2.5373	probably-damaging	341/511	45808863	330,12676	2203	4300	6503	SO:0001583	missense	114034	exon8			GACGACGTAGGGA		CCDS521.1	1p33	2011-02-03			ENSG00000132773	ENSG00000132773			15954	protein-coding gene	gene with protein product		613931				12562764	Standard	NM_025077		Approved		uc009vxq.3	Q96GM8	OTTHUMG00000007678	ENST00000372090.5:c.1022G>A	1.37:g.45808863G>A	ENSP00000361162:p.Arg341His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	77	25	0.324675	NM_025077	B4DEM6|Q6IA35|Q8IWN5|Q9H846	Missense_Mutation	SNP	ENST00000372090.5	37	CCDS521.1	28	0.01282051282051282	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	25	0.032981530343007916	G	14.07	2.424405	0.43020	0.00749	0.034535	ENSG00000132773	ENST00000372090;ENST00000539779	T;T	0.37058	1.22;1.22	5.66	3.78	0.43462	.	0.165148	0.52532	D	0.000077	T	0.24470	0.0593	L	0.55743	1.74	0.33987	D	0.64863	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.52931	-0.8509	10	0.48119	T	0.1	-4.1231	5.7095	0.17927	0.1598:0.0:0.6823:0.158	rs9429157;rs9429157	261;341	B4DEM6;Q96GM8	.;TOE1_HUMAN	H	341;261	ENSP00000361162:R341H;ENSP00000438900:R261H	ENSP00000361162:R341H	R	+	2	0	TOE1	45581450	0.096000	0.21769	0.147000	0.22382	0.467000	0.32768	2.340000	0.43974	0.861000	0.35504	-0.140000	0.14226	CGT	G|0.981;A|0.019	0.019	strong		0.567	TOE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020517.1	NM_025077	
ANGPT2	285	hgsc.bcm.edu	37	8	6378763	6378763	+	Silent	SNP	C	C	T	rs3020221	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:6378763C>T	ENST00000325203.5	-	4	1209	c.735G>A	c.(733-735)caG>caA	p.Q245Q	ANGPT2_ENST00000523120.1_Silent_p.Q245Q|ANGPT2_ENST00000415216.1_Silent_p.Q245Q|ANGPT2_ENST00000338312.6_Silent_p.Q193Q|MCPH1_ENST00000344683.5_Intron			O15123	ANGP2_HUMAN	angiopoietin 2	245					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		GTTGCTGCTTCTGAAGAACTG	0.353													T|||	1551	0.309704	0.3139	0.2767	5008	,	,		18482	0.2331		0.3837	False		,,,				2504	0.3303				p.Q245Q		Atlas-SNP	.											ANGPT2_ENST00000325203,NS,carcinoma,-2,2	ANGPT2	126	2	0			c.G735A						PASS	.	T	,,,	1477,2929	678.8+/-403.6	248,981,974	156.0	149.0	151.0		735,579,735,	-2.7	0.8	8	dbSNP_101	151	3274,5326	647.3+/-400.4	603,2068,1629	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ANGPT2,MCPH1	NM_001118887.1,NM_001118888.1,NM_001147.2,NM_024596.3	,,,	851,3049,2603	TT,TC,CC		38.0698,33.5225,36.5293	,,,	245/496,193/445,245/497,	6378763	4751,8255	2203	4300	6503	SO:0001819	synonymous_variant	285	exon4			CTGCTTCTGAAGA	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"""Fibrinogen C domain containing"""	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.735G>A	8.37:g.6378763C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	177	177	1	NM_001118887	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Silent	SNP	ENST00000325203.5	37	CCDS5958.1																																																																																			C|0.666;T|0.334	0.334	strong		0.353	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489792	32489792	+	Missense_Mutation	SNP	G	G	T	rs41562816	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32489792G>T	ENST00000374975.3	-	2	322	c.260C>A	c.(259-261)gCt>gAt	p.A87D		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CCAGTACTCAGCGTCAGGCCG	0.612													G|||	386	0.0770767	0.1104	0.062	5008	,	,		4380	0.0427		0.0974	False		,,,				2504	0.0573				p.A87D		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.C260A						PASS	.	G	ASP/ALA	24,4310		1,22,2144	41.0	38.0	39.0		260	1.8	0.0	6	dbSNP_127	39	25,8437		0,25,4206	no	missense	HLA-DRB5	NM_002125.3	126	1,47,6350	TT,TG,GG		0.2954,0.5538,0.3829	possibly-damaging	87/267	32489792	49,12747	2167	4231	6398	SO:0001583	missense	3127	exon2			TACTCAGCGTCAG		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.260C>A	6.37:g.32489792G>T	ENSP00000364114:p.Ala87Asp	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	67	56	0.835821	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	19.01	3.743850	0.69418	0.005538	0.002954	ENSG00000198502	ENST00000374975	T	0.00420	7.47	4.72	1.79	0.24919	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	0.288263	0.31554	N	0.007451	T	0.00936	0.0031	H	0.99507	4.6	0.09310	N	0.999996	D;D	0.76494	0.977;0.999	D;D	0.77557	0.99;0.982	T	0.43605	-0.9381	10	0.87932	D	0	.	6.4918	0.22119	0.1765:0.1492:0.6743:0.0	rs41562816	14;87	Q29973;Q30154	.;DRB5_HUMAN	D	87	ENSP00000364114:A87D	ENSP00000364114:A87D	A	-	2	0	HLA-DRB5	32597770	0.019000	0.18553	0.000000	0.03702	0.427000	0.31564	1.458000	0.35223	0.051000	0.15978	0.430000	0.28490	GCT	G|0.928;T|0.072	0.072	strong		0.612	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859816	144859816	+	Missense_Mutation	SNP	T	T	C	rs587702923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859816T>C	ENST00000369354.3	-	38	6457	c.6268A>G	c.(6268-6270)Att>Gtt	p.I2090V	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.I2226V|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.I2175V|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.I1984V|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.I2090V|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2090					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTCTGGTTAATGGAGGAGGGG	0.577			T	PDGFRB	MPD																																p.I2090V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6268G						PASS	.						65.0	63.0	63.0					1																	144859816		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTTAATGGAGGA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6268A>G	1.37:g.144859816T>C	ENSP00000358360:p.Ile2090Val	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	409	26	0.0635697	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.760839	0.00657	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01685	4.69;4.78;4.78;4.8;4.79	4.63	-9.26	0.00662	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47058	-0.9146	9	0.02654	T	1	.	5.9795	0.19399	0.0819:0.4615:0.1653:0.2913	.	1984;2090	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	V	1984;2090;2090;2175;2226	ENSP00000327209:I1984V;ENSP00000358360:I2090V;ENSP00000358363:I2090V;ENSP00000435654:I2175V;ENSP00000358366:I2226V	ENSP00000327209:I1984V	I	-	1	0	PDE4DIP	143571173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.249000	0.00266	-3.114000	0.00240	-1.162000	0.01777	ATT	.	.	none		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
HLA-C	3107	hgsc.bcm.edu	37	6	31239622	31239622	+	Missense_Mutation	SNP	C	C	G	rs9264668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31239622C>G	ENST00000376228.5	-	2	111	c.97G>C	c.(97-99)Gac>Cac	p.D33H	HLA-C_ENST00000383329.3_Missense_Mutation_p.D33H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	33	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACGGCGGTGTCGAAATACCTC	0.726													a|||	20	0.00399361	0.0113	0.0	5008	,	,		11654	0.001		0.003	False		,,,				2504	0.001				p.D33H		Atlas-SNP	.											HLA-C_ENST00000383329,NS,neuroblastoma,0,2	HLA-C	92	2	0			c.G97C						scavenged	.						16.0	17.0	17.0					6																	31239622		1477	2676	4153	SO:0001583	missense	3107	exon2			CGGTGTCGAAATA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.97G>C	6.37:g.31239622C>G	ENSP00000365402:p.Asp33His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	12	0.157895	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.003|0.003	-2.468672|-2.468672	0.00169|0.00169	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.5;9.5|.	2.16|2.16	-4.32|-4.32	0.03688|0.03688	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	10.311600|.	0.00879|.	N|.	0.002109|.	T|T	0.03390|0.03390	0.0098|0.0098	L|L	0.31578|0.31578	0.945|0.945	0.09310|0.09310	N|N	1|1	P;P;P;P|.	0.51351|.	0.944;0.822;0.822;0.888|.	P;P;P;D|.	0.68483|.	0.904;0.904;0.829;0.958|.	T|T	0.58504|0.58504	-0.7625|-0.7625	10|5	0.42905|.	T|.	0.14|.	.|.	0.4543|0.4543	0.00506|0.00506	0.2454:0.267:0.2544:0.2332|0.2454:0.267:0.2544:0.2332	.|.	33;33;33;33|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	H|P	33;33;33;70|32	ENSP00000365402:D33H;ENSP00000372819:D33H|.	ENSP00000365402:D33H|.	D|R	-|-	1|2	0|0	HLA-C|HLA-C	31347601|31347601	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-13.217000|-13.217000	0.00001|0.00001	-7.736000|-7.736000	0.00000|0.00000	-4.008000|-4.008000	0.00013|0.00013	GAC|CGA	A|0.575;C|0.423;G|0.002	0.002	strong		0.726	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PAH	5053	hgsc.bcm.edu	37	12	103288554	103288554	+	Missense_Mutation	SNP	G	G	T	rs398123291|rs62642929|rs199475570		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:103288554G>T	ENST00000553106.1	-	3	783	c.311C>A	c.(310-312)gCc>gAc	p.A104D	PAH_ENST00000307000.2_Missense_Mutation_p.A99D|PAH_ENST00000551988.1_5'UTR	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	104	ACT. {ECO:0000255|PROSITE- ProRule:PRU01007}.		A -> D (in PKU; mild; haplotype 1).		catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	ATGGACAGTGGCACCAATGTC	0.383																																					p.A104D		Atlas-SNP	.											.	PAH	77	.	0			c.C311A	GRCh37	CM920543	PAH	M	rs62642929	PASS	.						150.0	143.0	146.0					12																	103288554		2203	4300	6503	SO:0001583	missense	5053	exon3			ACAGTGGCACCAA	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.311C>A	12.37:g.103288554G>T	ENSP00000448059:p.Ala104Asp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	123	49	0.398374	NM_000277	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.418471	0.42918	.	.	ENSG00000171759	ENST00000553106;ENST00000307000;ENST00000551337;ENST00000546844	D;D;D;D	0.98280	-4.84;-4.84;-4.84;-4.84	6.17	5.29	0.74685	.	0.098719	0.64402	D	0.000002	D	0.95153	0.8429	L	0.29908	0.895	0.49299	D	0.999774	B;B	0.15930	0.015;0.002	B;B	0.11329	0.006;0.002	D	0.92907	0.6344	10	0.19147	T	0.46	-15.3988	13.5379	0.61657	0.1288:0.0:0.8712:0.0	rs62642929	104;104	B4DPN2;P00439	.;PH4H_HUMAN	D	104;99;104;104	ENSP00000448059:A104D;ENSP00000303500:A99D;ENSP00000447620:A104D;ENSP00000446658:A104D	ENSP00000303500:A99D	A	-	2	0	PAH	101812684	1.000000	0.71417	0.996000	0.52242	0.829000	0.46940	2.755000	0.47540	1.625000	0.50366	0.655000	0.94253	GCC	.	.	weak		0.383	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
RASSF6	166824	hgsc.bcm.edu	37	4	74451073	74451073	+	Missense_Mutation	SNP	A	A	G	rs12507775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:74451073A>G	ENST00000342081.3	-	6	617	c.487T>C	c.(487-489)Tct>Cct	p.S163P	RASSF6_ENST00000335049.5_Missense_Mutation_p.S119P|RASSF6_ENST00000395777.2_Missense_Mutation_p.S131P|RASSF6_ENST00000307439.5_Missense_Mutation_p.S131P	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	163			S -> P (in dbSNP:rs12507775). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)					breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			CTGTGATAAGATAAATAGTCT	0.418													A|||	1319	0.263379	0.2761	0.4712	5008	,	,		17888	0.1141		0.2833	False		,,,				2504	0.2321				p.S163P		Atlas-SNP	.											.	RASSF6	68	.	0			c.T487C						PASS	.	A	PRO/SER,PRO/SER	1307,3099	443.1+/-346.9	188,931,1084	102.0	95.0	97.0		391,487	4.7	1.0	4	dbSNP_120	97	2374,6224	394.4+/-344.7	322,1730,2247	yes	missense,missense	RASSF6	NM_177532.3,NM_201431.1	74,74	510,2661,3331	GG,GA,AA		27.6111,29.6641,28.3067	benign,benign	131/338,163/370	74451073	3681,9323	2203	4299	6502	SO:0001583	missense	166824	exon6			GATAAGATAAATA	AY217664	CCDS3558.1, CCDS3559.1, CCDS58904.1, CCDS58905.1	4q21.1	2008-02-22	2008-02-22		ENSG00000169435	ENSG00000169435			20796	protein-coding gene	gene with protein product		612620					Standard	NM_177532		Approved		uc003hhd.2	Q6ZTQ3	OTTHUMG00000130007	ENST00000342081.3:c.487T>C	4.37:g.74451073A>G	ENSP00000340578:p.Ser163Pro	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	139	73	0.52518	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Missense_Mutation	SNP	ENST00000342081.3	37	CCDS3558.1	549	0.25137362637362637	123	0.25	150	0.4143646408839779	64	0.11188811188811189	212	0.2796833773087071	A	9.003	0.980560	0.18812	0.296641	0.276111	ENSG00000169435	ENST00000307439;ENST00000342081;ENST00000395777;ENST00000335049	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	5.91	4.74	0.60224	.	0.456851	0.26788	N	0.022498	T	0.00012	0.0000	L	0.31664	0.95	0.32144	P	0.5851740000000001	B;B;B	0.19200	0.034;0.006;0.009	B;B;B	0.22152	0.038;0.014;0.012	T	0.43798	-0.9369	9	0.34782	T	0.22	-4.3402	4.8405	0.13487	0.7508:0.0:0.0844:0.1648	rs12507775;rs17854967;rs59189514;rs12507775	119;131;163	Q6ZTQ3-3;Q6ZTQ3-4;Q6ZTQ3	.;.;RASF6_HUMAN	P	131;163;131;119	ENSP00000303877:S131P;ENSP00000340578:S163P;ENSP00000379123:S131P;ENSP00000335582:S119P	ENSP00000303877:S131P	S	-	1	0	RASSF6	74669937	0.988000	0.35896	1.000000	0.80357	0.463000	0.32649	1.490000	0.35573	2.254000	0.74563	0.533000	0.62120	TCT	A|0.733;G|0.267	0.267	strong		0.418	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532	
SLCO4A1	28231	hgsc.bcm.edu	37	20	61288355	61288355	+	Silent	SNP	G	G	T	rs3195701	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61288355G>T	ENST00000370507.1	+	1	645	c.549G>T	c.(547-549)ggG>ggT	p.G183G	SLCO4A1_ENST00000217159.1_Silent_p.G183G			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	183					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TGGGCACGGGGTCGCTGGTGT	0.687													G|||	771	0.153954	0.0159	0.1599	5008	,	,		16750	0.1706		0.2913	False		,,,				2504	0.1779				p.G183G	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											SLCO4A1,caecum,carcinoma,0,1	SLCO4A1	65	1	0			c.G549T						PASS	.	G		254,4150	142.3+/-177.5	9,236,1957	44.0	41.0	42.0		549	2.5	0.7	20	dbSNP_105	42	2311,6285	379.5+/-339.3	308,1695,2295	no	coding-synonymous	SLCO4A1	NM_016354.3		317,1931,4252	TT,TG,GG		26.8846,5.7675,19.7308		183/723	61288355	2565,10435	2202	4298	6500	SO:0001819	synonymous_variant	28231	exon2			CACGGGGTCGCTG	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"""Solute carriers"""	10953	protein-coding gene	gene with protein product		612436	"""solute carrier family 21 (organic anion transporter), member 12"""	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.549G>T	20.37:g.61288355G>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	59	37	0.627119	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Silent	SNP	ENST00000370507.1	37	CCDS13501.1																																																																																			G|0.820;T|0.180	0.180	strong		0.687	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	
ABCF3	55324	hgsc.bcm.edu	37	3	183904049	183904049	+	Silent	SNP	A	A	G	rs11539876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183904049A>G	ENST00000429586.2	+	1	239	c.54A>G	c.(52-54)caA>caG	p.Q18Q	ABCF3_ENST00000292808.5_Silent_p.Q18Q|EIF2B5_ENST00000444495.1_Intron	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	18					defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TTGACGGACAAGTCTTCGACT	0.627													A|||	864	0.172524	0.0242	0.3343	5008	,	,		14981	0.3075		0.1918	False		,,,				2504	0.0992				p.Q18Q		Atlas-SNP	.											.	ABCF3	72	.	0			c.A54G						PASS	.	A		235,4171	138.0+/-173.8	7,221,1975	68.0	65.0	66.0		54	3.5	1.0	3	dbSNP_120	66	1618,6982	300.6+/-305.0	158,1302,2840	no	coding-synonymous	ABCF3	NM_018358.2		165,1523,4815	GG,GA,AA		18.814,5.3336,14.2473		18/710	183904049	1853,11153	2203	4300	6503	SO:0001819	synonymous_variant	55324	exon1			CGGACAAGTCTTC	U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"""ATP binding cassette transporters / subfamily F"""	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.54A>G	3.37:g.183904049A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	160	71	0.44375	NM_018358	A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Silent	SNP	ENST00000429586.2	37	CCDS3254.1																																																																																			A|0.835;G|0.165	0.165	strong		0.627	ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358	
TMEM143	55260	hgsc.bcm.edu	37	19	48863386	48863386	+	Silent	SNP	C	C	T	rs438767	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48863386C>T	ENST00000293261.3	-	3	628	c.312G>A	c.(310-312)tcG>tcA	p.S104S	TMEM143_ENST00000377431.2_Intron|TMEM143_ENST00000436660.2_Silent_p.S104S|TMEM143_ENST00000435956.3_Intron|TMEM143_ENST00000598012.1_5'Flank|TMEM143_ENST00000541566.1_Intron	NM_018273.2	NP_060743.2	Q96AN5	TM143_HUMAN	transmembrane protein 143	104					hematopoietic progenitor cell differentiation (GO:0002244)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	14		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)		CCACGTGGGCCGAGAACGCCT	0.602													C|||	2697	0.538538	0.3404	0.6614	5008	,	,		17097	0.6052		0.5924	False		,,,				2504	0.5951				p.S104S		Atlas-SNP	.											TMEM143,NS,carcinoma,0,1	TMEM143	29	1	0			c.G312A						PASS	.	C		1641,2765	504.4+/-365.8	311,1019,873	94.0	88.0	90.0		312	-6.8	0.2	19	dbSNP_80	90	5265,3335	643.8+/-400.0	1640,1985,675	no	coding-synonymous	TMEM143	NM_018273.2		1951,3004,1548	TT,TC,CC		38.7791,37.2447,46.9014		104/460	48863386	6906,6100	2203	4300	6503	SO:0001819	synonymous_variant	55260	exon3			GTGGGCCGAGAAC	AK129801	CCDS12716.1	19q13.32	2008-02-05				ENSG00000161558			25603	protein-coding gene	gene with protein product						12975309	Standard	NM_018273		Approved	FLJ10922	uc002pix.1	Q96AN5		ENST00000293261.3:c.312G>A	19.37:g.48863386C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_018273	A8K656|Q6UXY4|Q9NV49	Silent	SNP	ENST00000293261.3	37	CCDS12716.1																																																																																			C|0.462;T|0.538	0.538	strong		0.602	TMEM143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465622.1	NM_018273	
EXPH5	23086	hgsc.bcm.edu	37	11	108381247	108381247	+	Missense_Mutation	SNP	C	C	T	rs2640779	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108381247C>T	ENST00000265843.4	-	6	5097	c.4987G>A	c.(4987-4989)Gga>Aga	p.G1663R	EXPH5_ENST00000428840.1_Missense_Mutation_p.G1587R|EXPH5_ENST00000443411.1_Missense_Mutation_p.G1475R|EXPH5_ENST00000525344.1_Missense_Mutation_p.G1656R|EXPH5_ENST00000524840.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1663			G -> R (in dbSNP:rs2640779). {ECO:0000269|PubMed:12062444, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.G1663R(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		ACATGCTTTCCGTTCTCACTC	0.478													C|||	1434	0.286342	0.028	0.3689	5008	,	,		21940	0.6419		0.2465	False		,,,				2504	0.2515				p.G1663R		Atlas-SNP	.											EXPH5,NS,adenoma,0,2	EXPH5	193	2	1	Substitution - Missense(1)	stomach(1)	c.G4987A						PASS	.	C	ARG/GLY	276,4126	155.9+/-189.0	4,268,1929	207.0	200.0	202.0		4987	3.4	0.0	11	dbSNP_100	202	2037,6559	355.4+/-329.9	265,1507,2526	yes	missense	EXPH5	NM_015065.2	125	269,1775,4455	TT,TC,CC		23.6971,6.2699,17.795	possibly-damaging	1663/1990	108381247	2313,10685	2201	4298	6499	SO:0001583	missense	23086	exon6			GCTTTCCGTTCTC		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4987G>A	11.37:g.108381247C>T	ENSP00000265843:p.Gly1663Arg	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	248	119	0.479839	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	708	0.3241758241758242	18	0.036585365853658534	115	0.31767955801104975	373	0.6520979020979021	202	0.26649076517150394	C	11.38	1.622865	0.28889	0.062699	0.236971	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312	T;T;T;T;T	0.02787	4.38;4.31;4.16;4.38;4.23	4.36	3.44	0.39384	.	0.571316	0.16944	N	0.193156	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.20887	0.049	B	0.17098	0.017	T	0.02860	-1.1101	9	0.17369	T	0.5	-0.3997	11.0934	0.48130	0.0:0.9131:0.0:0.0869	rs2640779;rs3802835;rs52819961;rs60165688;rs2640779	1663	Q8NEV8	EXPH5_HUMAN	R	1663;1587;1475;1656;1587	ENSP00000265843:G1663R;ENSP00000391966:G1587R;ENSP00000411390:G1475R;ENSP00000432546:G1656R;ENSP00000432683:G1587R	ENSP00000265843:G1663R	G	-	1	0	EXPH5	107886457	0.005000	0.15991	0.004000	0.12327	0.012000	0.07955	1.616000	0.36933	1.178000	0.42870	0.650000	0.86243	GGA	C|0.760;T|0.240	0.240	strong		0.478	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
BICD1	636	hgsc.bcm.edu	37	12	32480886	32480886	+	Silent	SNP	T	T	C	rs12369637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32480886T>C	ENST00000281474.5	+	5	1600	c.1497T>C	c.(1495-1497)agT>agC	p.S499S	BICD1_ENST00000548411.1_Silent_p.S499S	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	499					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AAAATCACAGTACCCTTAATA	0.468													T|||	27	0.00539137	0.0008	0.0058	5008	,	,		20862	0.0		0.0189	False		,,,				2504	0.0031				p.S499S		Atlas-SNP	.											.	BICD1	89	.	0			c.T1497C						PASS	.	T	,	21,4385	28.1+/-56.4	0,21,2182	143.0	119.0	127.0		1497,1497	-1.3	1.0	12	dbSNP_120	127	208,8392	89.2+/-151.4	5,198,4097	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	5,219,6279	CC,CT,TT		2.4186,0.4766,1.7607	,	499/836,499/976	32480886	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	636	exon5			TCACAGTACCCTT	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1497T>C	12.37:g.32480886T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	174	69	0.396552	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			T|0.987;C|0.013	0.013	strong		0.468	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
RANBP9	10048	hgsc.bcm.edu	37	6	13711279	13711279	+	Silent	SNP	A	A	G	rs6905991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:13711279A>G	ENST00000011619.3	-	1	517	c.459T>C	c.(457-459)cgT>cgC	p.R153R		NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	153	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			CCGGGTAGAGACGCTTCAGCC	0.677													G|||	2173	0.433906	0.4796	0.4179	5008	,	,		7364	0.2847		0.4622	False		,,,				2504	0.5082				p.R153R		Atlas-SNP	.											RANBP9,NS,carcinoma,0,1	RANBP9	42	1	0			c.T459C						PASS	.	G		1906,2464		464,978,743	12.0	14.0	13.0		459	2.6	1.0	6	dbSNP_116	13	3907,4663		916,2075,1294	no	coding-synonymous	RANBP9	NM_005493.2		1380,3053,2037	GG,GA,AA		45.5893,43.6156,44.9227		153/730	13711279	5813,7127	2185	4285	6470	SO:0001819	synonymous_variant	10048	exon1			GTAGAGACGCTTC	AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"""Ran Binding Protein in the Microtubule organizing center"""	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.459T>C	6.37:g.13711279A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_005493	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Silent	SNP	ENST00000011619.3	37	CCDS4529.1																																																																																			A|0.575;C|0.000;G|0.424;T|0.000	0.424	strong		0.677	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1		
C6orf15	29113	hgsc.bcm.edu	37	6	31079350	31079350	+	Silent	SNP	T	T	C	rs146335336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31079350T>C	ENST00000259870.3	-	2	789	c.786A>G	c.(784-786)ggA>ggG	p.G262G		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	262	Gly-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GATTAATATTTCCCCAGCTGC	0.502																																					p.G262G		Atlas-SNP	.											.	C6orf15	29	.	0			c.A786G						PASS	.						64.0	75.0	71.0					6																	31079350		1739	3348	5087	SO:0001819	synonymous_variant	29113	exon2			AATATTTCCCCAG	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.786A>G	6.37:g.31079350T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	184	63	0.342391	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			T|0.998;C|0.002	0.002	strong		0.502	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
IRAK1BP1	134728	hgsc.bcm.edu	37	6	79595097	79595097	+	Silent	SNP	A	A	G	rs6908105	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:79595097A>G	ENST00000369940.2	+	2	423	c.318A>G	c.(316-318)gcA>gcG	p.A106A	IRAK1BP1_ENST00000607739.1_Silent_p.A19A	NM_001010844.2	NP_001010844.1	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1 binding protein 1	106					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(3)	12		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		TGTTTCAGGCAGAAAATATAA	0.303													a|||	1330	0.265575	0.292	0.3112	5008	,	,		15573	0.1855		0.3668	False		,,,				2504	0.1759				p.A106A		Atlas-SNP	.											.	IRAK1BP1	18	.	0			c.A318G						PASS	.	A		1361,3045	445.3+/-347.6	198,965,1040	93.0	101.0	98.0		318	5.3	1.0	6	dbSNP_116	98	2994,5604	458.5+/-364.6	528,1938,1833	no	coding-synonymous	IRAK1BP1	NM_001010844.1		726,2903,2873	GG,GA,AA		34.8221,30.8897,33.4897		106/261	79595097	4355,8649	2203	4299	6502	SO:0001819	synonymous_variant	134728	exon2			TCAGGCAGAAAAT	AI478629	CCDS34488.1	6q14-q15	2006-04-12				ENSG00000146243			17368	protein-coding gene	gene with protein product		615375				11096118	Standard	XM_005248654		Approved	AIP70, SIMPL	uc003pim.4	Q5VVH5		ENST00000369940.2:c.318A>G	6.37:g.79595097A>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	154	96	0.623377	NM_001010844		Silent	SNP	ENST00000369940.2	37	CCDS34488.1																																																																																			A|0.684;G|0.316	0.316	strong		0.303	IRAK1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041296.2	XM_059729	
KCNQ4	9132	hgsc.bcm.edu	37	1	41296828	41296828	+	Missense_Mutation	SNP	T	T	G	rs34287852	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:41296828T>G	ENST00000347132.5	+	10	1447	c.1365T>G	c.(1363-1365)caT>caG	p.H455Q	KCNQ4_ENST00000509682.2_Missense_Mutation_p.H401Q|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	455			H -> Q (in dbSNP:rs34287852). {ECO:0000269|PubMed:10025409}.		inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	CCAAGCAGCATCTGGCACCTC	0.642													T|||	471	0.0940495	0.0061	0.1124	5008	,	,		14942	0.0516		0.2167	False		,,,				2504	0.1176				p.H455Q		Atlas-SNP	.											.	KCNQ4	58	.	0			c.T1365G	GRCh37	CM062786	KCNQ4	M	rs34287852	PASS	.	T	GLN/HIS,GLN/HIS	215,4187		3,209,1989	43.0	34.0	37.0		1365,1203	2.0	1.0	1	dbSNP_126	37	2062,6538		256,1550,2494	yes	missense,missense	KCNQ4	NM_004700.3,NM_172163.2	24,24	259,1759,4483	GG,GT,TT		23.9767,4.8841,17.5127	benign,benign	455/696,401/642	41296828	2277,10725	2201	4300	6501	SO:0001583	missense	9132	exon10			GCAGCATCTGGCA	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.1365T>G	1.37:g.41296828T>G	ENSP00000262916:p.His455Gln	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	260	142	0.546154	NM_004700	O96025	Missense_Mutation	SNP	ENST00000347132.5	37	CCDS456.1	244|244	0.11172161172161173|0.11172161172161173	5|5	0.01016260162601626|0.01016260162601626	48|48	0.13259668508287292|0.13259668508287292	33|33	0.057692307692307696|0.057692307692307696	158|158	0.20844327176781002|0.20844327176781002	T|T	10.83|10.83	1.461499|1.461499	0.26248|0.26248	0.048841|0.048841	0.239767|0.239767	ENSG00000117013|ENSG00000117013	ENST00000347132;ENST00000509682|ENST00000443478	D;D|.	0.98717|.	-5.09;-4.95|.	5.02|5.02	2.05|2.05	0.26809|0.26809	.|.	0.530165|.	0.18743|.	N|.	0.132418|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.35098|0.35098	P|P	0.23502900000000004|0.23502900000000004	B;B|.	0.17465|.	0.001;0.022|.	B;B|.	0.10450|.	0.001;0.005|.	T|T	0.35251|0.35251	-0.9796|-0.9796	9|4	0.17832|.	T|.	0.49|.	-13.1202|-13.1202	7.873|7.873	0.29578|0.29578	0.0:0.7067:0.0:0.2933|0.0:0.7067:0.0:0.2933	rs34287852|rs34287852	401;455|.	P56696-2;P56696|.	.;KCNQ4_HUMAN|.	Q|A	455;401|316	ENSP00000262916:H455Q;ENSP00000423756:H401Q|.	ENSP00000262916:H455Q|.	H|S	+|+	3|1	2|0	KCNQ4|KCNQ4	41069415|41069415	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	0.412000|0.412000	0.21131|0.21131	0.215000|0.215000	0.20761|0.20761	-0.394000|-0.394000	0.06481|0.06481	CAT|TCT	T|0.858;G|0.142	0.142	strong		0.642	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
ALDH8A1	64577	hgsc.bcm.edu	37	6	135263557	135263557	+	Silent	SNP	C	C	A	rs3813342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:135263557C>A	ENST00000265605.2	-	3	500	c.432G>T	c.(430-432)ccG>ccT	p.P144P	ALDH8A1_ENST00000367845.2_Silent_p.P144P|ALDH8A1_ENST00000367847.2_Silent_p.P144P|RP11-349J5.2_ENST00000416448.2_RNA	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	144					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		CGACTCCCACCGGGGCCCGCA	0.567													C|||	693	0.138379	0.0045	0.196	5008	,	,		17672	0.2867		0.0646	False		,,,				2504	0.2014				p.P144P		Atlas-SNP	.											ALDH8A1,right_upper_lobe,carcinoma,-2,1	ALDH8A1	68	1	0			c.G432T						PASS	.	C	,,	65,4341	60.5+/-97.4	0,65,2138	73.0	70.0	71.0		432,432,432	-10.6	0.0	6	dbSNP_107	71	490,8110	141.7+/-198.0	16,458,3826	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	,,	16,523,5964	AA,AC,CC		5.6977,1.4753,4.2673	,,	144/438,144/488,144/434	135263557	555,12451	2203	4300	6503	SO:0001819	synonymous_variant	64577	exon3			TCCCACCGGGGCC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.432G>T	6.37:g.135263557C>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Silent	SNP	ENST00000265605.2	37	CCDS5171.1																																																																																			C|0.916;A|0.084	0.084	strong		0.567	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
PREX2	80243	hgsc.bcm.edu	37	8	68993014	68993014	+	Silent	SNP	T	T	C	rs368406603|rs12680555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:68993014T>C	ENST00000288368.4	+	17	2096	c.1819T>C	c.(1819-1821)Tta>Cta	p.L607L	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	607	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGGCTTTGGATTAGAAGACAA	0.279													C|||	2624	0.523962	0.5318	0.4524	5008	,	,		18488	0.4722		0.5696	False		,,,				2504	0.5706				p.L607L		Atlas-SNP	.											.	PREX2	614	.	0			c.T1819C						PASS	.	C	,	2362,2042	531.2+/-373.1	653,1056,493	66.0	71.0	69.0		1819,1819	3.7	0.9	8	dbSNP_120	69	4665,3929	530.9+/-381.9	1289,2087,921	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	1942,3143,1414	CC,CT,TT		45.7179,46.3669,45.9378	,	607/1607,607/980	68993014	7027,5971	2202	4297	6499	SO:0001819	synonymous_variant	80243	exon17			TTTGGATTAGAAG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1819T>C	8.37:g.68993014T>C		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	201	201	1	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			T|0.502;C|0.498	0.498	strong		0.279	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
CUL9	23113	hgsc.bcm.edu	37	6	43154017	43154017	+	Missense_Mutation	SNP	C	C	G	rs150188923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43154017C>G	ENST00000252050.4	+	4	1159	c.1075C>G	c.(1075-1077)Caa>Gaa	p.Q359E	CUL9_ENST00000372647.2_Missense_Mutation_p.Q359E|CUL9_ENST00000354495.3_Missense_Mutation_p.Q359E	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	359					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CCCCAGAAGACAAGGGTGGGT	0.587													C|||	15	0.00299521	0.0008	0.0029	5008	,	,		17488	0.0		0.0119	False		,,,				2504	0.0				p.Q359E		Atlas-SNP	.											.	CUL9	248	.	0			c.C1075G						PASS	.	C	GLU/GLN	8,4398	14.3+/-33.2	0,8,2195	78.0	82.0	81.0		1075	4.6	0.3	6	dbSNP_134	81	75,8525	44.5+/-102.8	1,73,4226	yes	missense	CUL9	NM_015089.2	29	1,81,6421	GG,GC,CC		0.8721,0.1816,0.6382	benign	359/2518	43154017	83,12923	2203	4300	6503	SO:0001583	missense	23113	exon4			AGAAGACAAGGGT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.1075C>G	6.37:g.43154017C>G	ENSP00000252050:p.Gln359Glu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	C	12.56	1.974769	0.34848	0.001816	0.008721	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.72942	-0.7;-0.69;-0.6	5.5	4.63	0.57726	.	1.075350	0.07089	N	0.838384	T	0.49457	0.1558	L	0.42245	1.32	0.22001	N	0.999429	B;B;B	0.23937	0.094;0.094;0.044	B;B;B	0.21360	0.034;0.034;0.019	T	0.52601	-0.8554	10	0.45353	T	0.12	0.0071	14.0214	0.64558	0.0:0.9271:0.0:0.0729	.	359;359;359	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	E	359	ENSP00000252050:Q359E;ENSP00000346490:Q359E;ENSP00000361730:Q359E	ENSP00000252050:Q359E	Q	+	1	0	CUL9	43261995	1.000000	0.71417	0.272000	0.24630	0.923000	0.55619	2.022000	0.41030	1.317000	0.45149	0.467000	0.42956	CAA	C|0.995;G|0.005	0.005	strong		0.587	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
DPF3	8110	hgsc.bcm.edu	37	14	73220020	73220020	+	Silent	SNP	A	A	G	rs3742836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:73220020A>G	ENST00000556509.1	-	3	252	c.253T>C	c.(253-255)Ttg>Ctg	p.L85L	DPF3_ENST00000541685.1_Silent_p.L85L|DPF3_ENST00000546183.1_Silent_p.L95L	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	85					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GGTGGGTGCAATCGTCTCTTC	0.562													A|||	1118	0.223243	0.0764	0.2205	5008	,	,		19283	0.2907		0.2744	False		,,,				2504	0.3016				p.L85L		Atlas-SNP	.											.	DPF3	117	.	0			c.T253C						PASS	.	A		401,3395		29,343,1526	58.0	59.0	59.0		253	3.2	1.0	14	dbSNP_107	59	2312,5912		328,1656,2128	yes	coding-synonymous	DPF3	NM_012074.3		357,1999,3654	GG,GA,AA		28.1128,10.5638,22.5707		85/358	73220020	2713,9307	1898	4112	6010	SO:0001819	synonymous_variant	8110	exon3			GGTGCAATCGTCT	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"""Zinc fingers, PHD-type"""	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.253T>C	14.37:g.73220020A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Silent	SNP	ENST00000556509.1	37																																																																																				A|0.773;G|0.227	0.227	strong		0.562	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2		
TBC1D1	23216	hgsc.bcm.edu	37	4	38023302	38023302	+	Silent	SNP	C	C	G	rs34119528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38023302C>G	ENST00000261439.4	+	6	1528	c.1173C>G	c.(1171-1173)ccC>ccG	p.P391P	TBC1D1_ENST00000508802.1_Silent_p.P391P	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	391	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						AGGGCTGCCCCCTGCAAAGCC	0.547													C|||	929	0.185503	0.0061	0.1686	5008	,	,		17929	0.3978		0.1521	False		,,,				2504	0.2556				p.P391P		Atlas-SNP	.											.	TBC1D1	94	.	0			c.C1173G						PASS	.	C		124,4282	87.8+/-126.4	1,122,2080	33.0	32.0	32.0		1173	-2.5	0.6	4	dbSNP_126	32	1319,7281	241.8+/-272.0	100,1119,3081	no	coding-synonymous	TBC1D1	NM_015173.2		101,1241,5161	GG,GC,CC		15.3372,2.8143,11.0949		391/1169	38023302	1443,11563	2203	4300	6503	SO:0001819	synonymous_variant	23216	exon6			CTGCCCCCTGCAA	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.1173C>G	4.37:g.38023302C>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Silent	SNP	ENST00000261439.4	37	CCDS33972.1	431	0.19734432234432234	2	0.0040650406504065045	54	0.14917127071823205	256	0.44755244755244755	119	0.15699208443271767	C	3.672	-0.067280	0.07273	0.028143	0.153372	ENSG00000065882	ENST00000510573	.	.	.	5.76	-2.5	0.06384	.	0.000000	0.56097	D	0.000021	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41360	-0.9513	5	0.87932	D	0	-23.8283	7.0043	0.24828	0.1686:0.5047:0.0:0.3267	rs34119528	.	.	.	A	39	.	ENSP00000421641:P39A	P	+	1	0	TBC1D1	37699697	0.470000	0.25854	0.563000	0.28383	0.351000	0.29236	-0.065000	0.11617	-0.522000	0.06417	-1.338000	0.01255	CCT	C|0.867;G|0.133	0.133	strong		0.547	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
TSHR	7253	hgsc.bcm.edu	37	14	81558919	81558919	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:81558919C>G	ENST00000541158.2	+	7	834	c.512C>G	c.(511-513)gCt>gGt	p.A171G	TSHR_ENST00000554435.1_Missense_Mutation_p.A171G|TSHR_ENST00000298171.2_Missense_Mutation_p.A171G|TSHR_ENST00000342443.6_Missense_Mutation_p.A171G|TSHR_ENST00000554263.1_Missense_Mutation_p.A171G			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	171					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)			breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	CCTGTGAATGCTTTTCAGGGA	0.388			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.A171G		Atlas-SNP	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	TSHR_ENST00000554435,NS,carcinoma,+1,2	TSHR	462	2	0			c.C512G						PASS	.						204.0	181.0	189.0					14																	81558919		2203	4300	6503	SO:0001583	missense	7253	exon6			TGAATGCTTTTCA	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.512C>G	14.37:g.81558919C>G	ENSP00000441235:p.Ala171Gly	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	201	26	0.129353	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.074553	0.76415	.	.	ENSG00000165409	ENST00000541158;ENST00000342443;ENST00000298171;ENST00000554263;ENST00000554435	D;D;D;D;D	0.93659	-3.26;-3.26;-3.26;-3.26;-3.26	5.28	5.28	0.74379	.	0.104905	0.64402	D	0.000003	D	0.97235	0.9096	H	0.94264	3.515	0.58432	D	0.999992	P;D;P;P	0.54207	0.918;0.965;0.953;0.852	P;P;P;P	0.61533	0.88;0.789;0.89;0.502	D	0.98083	1.0405	10	0.87932	D	0	.	14.4086	0.67101	0.0:1.0:0.0:0.0	.	171;171;171;171	G3V2A9;F5GYU5;P16473-2;P16473	.;.;.;TSHR_HUMAN	G	171	ENSP00000441235:A171G;ENSP00000340113:A171G;ENSP00000298171:A171G;ENSP00000451202:A171G;ENSP00000450549:A171G	ENSP00000298171:A171G	A	+	2	0	TSHR	80628672	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.359000	0.52292	2.483000	0.83821	0.655000	0.94253	GCT	.	.	none		0.388	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369	
PSMD12	5718	hgsc.bcm.edu	37	17	65362552	65362552	+	Silent	SNP	T	T	A	rs11079691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:65362552T>A	ENST00000356126.3	-	1	191	c.84A>T	c.(82-84)ctA>ctT	p.L28L	PSMD12_ENST00000581618.1_5'UTR|PSMD12_ENST00000357146.4_Silent_p.L28L	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	28					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					CACACTCGGGTAGGCGCTGAT	0.701													T|||	1084	0.216454	0.2595	0.1859	5008	,	,		13937	0.1696		0.2644	False		,,,				2504	0.1789				p.L28L		Atlas-SNP	.											PSMD12,NS,carcinoma,0,2	PSMD12	32	2	0			c.A84T						PASS	.	T	,	1198,3208	393.7+/-329.0	167,864,1172	41.0	32.0	35.0		84,84	3.5	1.0	17	dbSNP_120	35	2064,6534	340.7+/-323.7	260,1544,2495	no	coding-synonymous,coding-synonymous	PSMD12	NM_002816.3,NM_174871.2	,	427,2408,3667	AA,AT,TT		24.0056,27.1902,25.0846	,	28/457,28/437	65362552	3262,9742	2203	4299	6502	SO:0001819	synonymous_variant	5718	exon1			CTCGGGTAGGCGC	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"""Proteasome (prosome, macropain) subunits"""	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.84A>T	17.37:g.65362552T>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_174871	A6NP15|Q53HA2|Q6P053	Silent	SNP	ENST00000356126.3	37	CCDS11669.1																																																																																			T|0.752;A|0.248	0.248	strong		0.701	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871	
IGFN1	91156	hgsc.bcm.edu	37	1	201183402	201183402	+	Silent	SNP	T	T	C	rs1568810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201183402T>C	ENST00000335211.4	+	13	8956	c.8826T>C	c.(8824-8826)ccT>ccC	p.P2942P	IGFN1_ENST00000295591.8_Silent_p.P102P|IGFN1_ENST00000451870.2_Silent_p.P485P	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	485						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACCTGGGACCTGGCACCTGGT	0.617													C|||	1581	0.315695	0.1891	0.3256	5008	,	,		16461	0.3403		0.3509	False		,,,				2504	0.4182				p.P2942P		Atlas-SNP	.											.	IGFN1	220	.	0			c.T8826C						PASS	.	C		966,3440	727.6+/-409.9	100,766,1337	69.0	54.0	59.0		8826	-4.1	0.2	1	dbSNP_88	59	2869,5731	666.2+/-402.3	494,1881,1925	no	coding-synonymous	IGFN1	NM_001164586.1		594,2647,3262	CC,CT,TT		33.3605,21.9246,29.4864		2942/3709	201183402	3835,9171	2203	4300	6503	SO:0001819	synonymous_variant	91156	exon13			GGGACCTGGCACC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.8826T>C	1.37:g.201183402T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	710	0.3250915750915751	114	0.23170731707317074	115	0.31767955801104975	214	0.3741258741258741	267	0.35224274406332456	C	12.92	2.083537	0.36758	0.219246	0.333605	ENSG00000163395	ENST00000412892	.	.	.	3.39	-4.06	0.03986	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999858896	.	.	.	.	.	.	T	0.20273	-1.0280	3	.	.	.	.	11.6598	0.51339	0.0:0.1592:0.0:0.8408	rs1568810;rs17424132;rs58560287;rs1568810	.	.	.	R	360	.	.	W	+	1	0	IGFN1	199450025	0.001000	0.12720	0.205000	0.23548	0.697000	0.40408	-0.981000	0.03766	-1.670000	0.01468	-0.642000	0.03964	TGG	T|0.698;C|0.302	0.302	strong		0.617	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
MAOA	4128	hgsc.bcm.edu	37	X	43603391	43603391	+	Silent	SNP	T	T	C	rs1137070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:43603391T>C	ENST00000338702.3	+	14	1533	c.1410T>C	c.(1408-1410)gaT>gaC	p.D470D	MAOA_ENST00000542639.1_Silent_p.D337D	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	470					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	CCGAGAAAGATATCTGGGTAC	0.423													C|||	2083	0.551788	0.4879	0.4597	3775	,	,		15525	0.3214		0.5388	False		,,,				2504	0.2587				p.D470D		Atlas-SNP	.											.	MAOA	48	.	0			c.T1410C						PASS	.	C		2378,1457		621,781,355,230,216	132.0	119.0	123.0		1410	-0.1	0.0	X	dbSNP_86	123	4733,1995		1214,976,1329,238,543	no	coding-synonymous	MAOA	NM_000240.2		1835,1757,1684,468,759	CC,CT,C,TT,T		29.6522,37.9922,32.6801		470/528	43603391	7111,3452	2203	4300	6503	SO:0001819	synonymous_variant	4128	exon14			GAAAGATATCTGG		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.1410T>C	X.37:g.43603391T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_000240	B4DF46|Q16426	Silent	SNP	ENST00000338702.3	37	CCDS14260.1																																																																																			0|0.014;C|0.615	0.615	strong		0.423	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240	
GNAT2	2780	hgsc.bcm.edu	37	1	110148974	110148974	+	Silent	SNP	C	C	T	rs1799875	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110148974C>T	ENST00000351050.3	-	5	732	c.546G>A	c.(544-546)acG>acA	p.T182T		NM_005272.3	NP_005263.1	P19087	GNAT2_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 2	182					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of light stimulus involved in visual perception (GO:0050908)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to light intensity (GO:0009642)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	14		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0422)|Colorectal(144;0.108)|Epithelial(280;0.125)|all cancers(265;0.129)|LUSC - Lung squamous cell carcinoma(189;0.227)		CAATGATGCCCGTGGTTTTGA	0.458													C|||	1896	0.378594	0.056	0.5375	5008	,	,		21137	0.626		0.4602	False		,,,				2504	0.363				p.T182T		Atlas-SNP	.											.	GNAT2	31	.	0			c.G546A						PASS	.	C		495,3911	229.1+/-243.8	26,443,1734	152.0	139.0	143.0		546	-1.3	1.0	1	dbSNP_89	143	3805,4795	538.7+/-383.5	837,2131,1332	no	coding-synonymous	GNAT2	NM_005272.3		863,2574,3066	TT,TC,CC		44.2442,11.2347,33.0617		182/355	110148974	4300,8706	2203	4300	6503	SO:0001819	synonymous_variant	2780	exon5			GATGCCCGTGGTT	BC000233	CCDS803.1	1p13	2013-01-08			ENSG00000134183	ENSG00000134183			4394	protein-coding gene	gene with protein product		139340				8406495	Standard	NM_005272		Approved	ACHM4	uc001dya.3	P19087	OTTHUMG00000011639	ENST00000351050.3:c.546G>A	1.37:g.110148974C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	179	176	0.98324	NM_005272		Silent	SNP	ENST00000351050.3	37	CCDS803.1																																																																																			C|0.630;T|0.370	0.370	strong		0.458	GNAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032181.1	NM_005272	
ALKBH7	84266	hgsc.bcm.edu	37	19	6374890	6374890	+	Missense_Mutation	SNP	G	G	A	rs7540	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6374890G>A	ENST00000245812.3	+	4	960	c.572G>A	c.(571-573)cGg>cAg	p.R191Q	ALKBH7_ENST00000596657.1_Missense_Mutation_p.R49Q|ALKBH7_ENST00000599849.1_Missense_Mutation_p.R130Q	NM_032306.3	NP_115682.1	Q9BT30	ALKB7_HUMAN	alkB, alkylation repair homolog 7 (E. coli)	191			R -> Q (in dbSNP:rs7540).		cellular response to DNA damage stimulus (GO:0006974)|fatty acid metabolic process (GO:0006631)|regulation of lipid storage (GO:0010883)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)	mitochondrial matrix (GO:0005759)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						GGGGAACGCCGGATTCCCCGG	0.647													G|||	136	0.0271565	0.0038	0.0274	5008	,	,		15582	0.001		0.0885	False		,,,				2504	0.0225				p.R191Q		Atlas-SNP	.											.	ALKBH7	18	.	0			c.G572A						PASS	.	G	GLN/ARG	82,4324	72.5+/-110.5	1,80,2122	61.0	62.0	62.0		572	3.0	0.0	19	dbSNP_52	62	780,7820	184.6+/-232.5	35,710,3555	yes	missense	ALKBH7	NM_032306.3	43	36,790,5677	AA,AG,GG		9.0698,1.8611,6.6277	possibly-damaging	191/222	6374890	862,12144	2203	4300	6503	SO:0001583	missense	84266	exon4			AACGCCGGATTCC	AY427650	CCDS12163.1	19p13.3	2008-02-05	2006-02-09	2006-02-09		ENSG00000125652		"""Alkylation repair homologs"""	21306	protein-coding gene	gene with protein product		613305	"""spermatogenesis associated 11"""	SPATA11		12477932	Standard	NM_032306		Approved	MGC10974	uc002meo.2	Q9BT30		ENST00000245812.3:c.572G>A	19.37:g.6374890G>A	ENSP00000245812:p.Arg191Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_032306	B2R4U9|Q53FF3	Missense_Mutation	SNP	ENST00000245812.3	37	CCDS12163.1	82	0.037545787545787544	6	0.012195121951219513	12	0.03314917127071823	1	0.0017482517482517483	63	0.08311345646437995	G	11.34	1.608980	0.28623	0.018611	0.090698	ENSG00000125652	ENST00000245812	T	0.45668	0.89	5.15	3.03	0.35002	.	0.244180	0.39210	N	0.001437	T	0.00998	0.0033	L	0.46157	1.445	0.33102	P	0.46068699999999996	B	0.30281	0.275	B	0.21151	0.033	T	0.12528	-1.0544	9	0.11794	T	0.64	-18.278	7.4476	0.27219	0.3331:0.0:0.6669:0.0	rs7540;rs3203434;rs58564048;rs7540	191	Q9BT30	ALKB7_HUMAN	Q	191	ENSP00000245812:R191Q	ENSP00000245812:R191Q	R	+	2	0	ALKBH7	6325890	0.964000	0.33143	0.021000	0.16686	0.871000	0.50021	0.738000	0.26158	0.695000	0.31675	-0.463000	0.05309	CGG	G|0.943;A|0.057	0.057	strong		0.647	ALKBH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453036.1	NM_032306	
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56703248	56703248	+	Missense_Mutation	SNP	G	G	A	rs527025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56703248G>A	ENST00000586855.2	-	3	872	c.559C>T	c.(559-561)Ccc>Tcc	p.P187S	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.P187S			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	187			P -> S (in dbSNP:rs527025).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GCGACCCTGGGCAGGATCTGC	0.622													G|||	1232	0.246006	0.1936	0.2032	5008	,	,		14284	0.2798		0.2932	False		,,,				2504	0.2638				p.P187S		Atlas-SNP	.											.	ZSCAN5B	160	.	0			c.C559T						PASS	.	G	SER/PRO	899,3507	327.2+/-299.9	90,719,1394	35.0	36.0	35.0		559	-2.5	0.0	19	dbSNP_83	35	2700,5900	402.8+/-347.6	427,1846,2027	yes	missense	ZSCAN5B	NM_001080456.2	74	517,2565,3421	AA,AG,GG		31.3953,20.404,27.6718	probably-damaging	187/496	56703248	3599,9407	2203	4300	6503	SO:0001583	missense	342933	exon2			CCCTGGGCAGGAT		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"""-"", ""Zinc fingers, C2H2-type"""	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.559C>T	19.37:g.56703248G>A	ENSP00000466072:p.Pro187Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	111	67	0.603604	NM_001080456		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	556	0.25457875457875456	95	0.19308943089430894	78	0.2154696132596685	160	0.27972027972027974	223	0.2941952506596306	G	11.85	1.762444	0.31228	0.20404	0.313953	ENSG00000197213	ENST00000358992	T	0.06449	3.3	1.9	-2.51	0.06365	.	.	.	.	.	T	0.00012	0.0000	M	0.82517	2.595	0.80722	P	0.0	D	0.89917	1.0	D	0.83275	0.996	T	0.20140	-1.0284	8	0.32370	T	0.25	.	3.8942	0.09131	0.1953:0.4955:0.3092:0.0	rs527025;rs527025	187	A6NJL1	ZSA5B_HUMAN	S	187	ENSP00000351883:P187S	ENSP00000351883:P187S	P	-	1	0	ZSCAN5B	61395060	0.001000	0.12720	0.000000	0.03702	0.041000	0.13682	-0.393000	0.07305	-0.516000	0.06470	0.306000	0.20318	CCC	G|0.725;A|0.275	0.275	strong		0.622	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456	
CROCC	9696	hgsc.bcm.edu	37	1	17275018	17275018	+	Splice_Site	SNP	C	C	A	rs114863724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17275018C>A	ENST00000375541.5	+	18	2776	c.2707C>A	c.(2707-2709)Cgc>Agc	p.R903S	CROCC_ENST00000467938.1_Intron	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CACACGCCTGCGGTAAGGCCT	0.687													c|||	95	0.0189696	0.003	0.0303	5008	,	,		24307	0.0		0.0557	False		,,,				2504	0.0143				p.R903S		Atlas-SNP	.											.	CROCC	185	.	0			c.C2707A						PASS	.	C	SER/ARG	40,4168		0,40,2064	9.0	8.0	8.0		2707	3.0	1.0	1	dbSNP_132	8	327,7921		0,327,3797	no	missense-near-splice	CROCC	NM_014675.3	110	0,367,5861	AA,AC,CC		3.9646,0.9506,2.9464	probably-damaging	903/2018	17275018	367,12089	2104	4124	6228	SO:0001630	splice_region_variant	9696	exon18			CGCCTGCGGTAAG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2708+1C>A	1.37:g.17275018C>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	39	0.661017	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	44	0.020146520146520148	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	37	0.048812664907651716	C	15.46	2.839765	0.51057	0.009506	0.039646	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.24151	1.87	3.97	3.02	0.34903	.	.	.	.	.	T	0.07728	0.0194	L	0.39514	1.22	0.43667	D	0.996096	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.00299	-1.1836	9	0.44086	T	0.13	.	9.3999	0.38426	0.3842:0.6158:0.0:0.0	.	206;903	Q5TZA2-2;Q5TZA2	.;CROCC_HUMAN	S	903;784	ENSP00000364691:R903S	ENSP00000364691:R903S	R	+	1	0	CROCC	17147605	0.965000	0.33210	1.000000	0.80357	0.970000	0.65996	1.131000	0.31406	0.945000	0.37605	0.449000	0.29647	CGC	C|0.981;A|0.019	0.019	strong		0.687	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	Missense_Mutation
AFAP1	60312	hgsc.bcm.edu	37	4	7802292	7802292	+	Silent	SNP	G	G	A	rs11728778	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:7802292G>A	ENST00000360265.4	-	9	1377	c.1143C>T	c.(1141-1143)acC>acT	p.T381T	AFAP1_ENST00000358461.2_Silent_p.T381T|AFAP1_ENST00000420658.1_Silent_p.T381T|AFAP1_ENST00000513842.1_5'Flank|AFAP1_ENST00000382543.3_Silent_p.T381T			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	381	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TCTTCAGGTCGGTCCTGTCCT	0.562													G|||	559	0.111621	0.0106	0.1484	5008	,	,		19505	0.0615		0.3042	False		,,,				2504	0.0757				p.T381T		Atlas-SNP	.											.	AFAP1	93	.	0			c.C1143T						PASS	.	G	,	246,4160	144.2+/-179.2	7,232,1964	134.0	122.0	126.0		1143,1143	-8.9	0.1	4	dbSNP_120	126	2607,5993	423.4+/-354.3	421,1765,2114	no	coding-synonymous,coding-synonymous	AFAP1	NM_001134647.1,NM_198595.2	,	428,1997,4078	AA,AG,GG		30.314,5.5833,21.936	,	381/815,381/731	7802292	2853,10153	2203	4300	6503	SO:0001819	synonymous_variant	60312	exon10			CAGGTCGGTCCTG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1143C>T	4.37:g.7802292G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	189	89	0.470899	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			G|0.812;A|0.188	0.188	strong		0.562	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
NPBWR2	2832	hgsc.bcm.edu	37	20	62737318	62737318	+	Silent	SNP	G	G	A	rs13036542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62737318G>A	ENST00000369768.1	-	1	1206	c.867C>T	c.(865-867)ccC>ccT	p.P289P		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	289					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					GTGGGGTCTGGGGCAGGTCCG	0.617													G|||	2247	0.448682	0.348	0.5245	5008	,	,		14518	0.6091		0.4821	False		,,,				2504	0.3313				p.P289P		Atlas-SNP	.											.	NPBWR2	36	.	0			c.C867T						PASS	.	G		1589,2815	492.0+/-362.3	282,1025,895	147.0	102.0	117.0		867	-0.2	0.0	20	dbSNP_121	117	4045,4551	554.9+/-386.6	969,2107,1222	no	coding-synonymous	NPBWR2	NM_005286.2		1251,3132,2117	AA,AG,GG		47.0568,36.0808,43.3385		289/334	62737318	5634,7366	2202	4298	6500	SO:0001819	synonymous_variant	2832	exon1			GGTCTGGGGCAGG	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4530	protein-coding gene	gene with protein product		600731	"""G protein-coupled receptor 8"""	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.867C>T	20.37:g.62737318G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_005286	Q6NWQ6|Q9H4K3	Silent	SNP	ENST00000369768.1	37	CCDS13557.1																																																																																			G|0.545;A|0.455	0.455	strong		0.617	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286	
CIDEB	27141	hgsc.bcm.edu	37	14	24775287	24775287	+	Silent	SNP	G	G	A	rs139893717	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24775287G>A	ENST00000336557.5	-	7	1695	c.393C>T	c.(391-393)atC>atT	p.I131I	CIDEB_ENST00000258807.5_Silent_p.I131I|LTB4R2_ENST00000528054.1_5'Flank|CIDEB_ENST00000554411.1_Silent_p.I131I|NOP9_ENST00000267425.3_3'UTR			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	131					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		TGAATCGGGCGATGTCCTTGC	0.527													G|||	8	0.00159744	0.0	0.0072	5008	,	,		21522	0.0		0.002	False		,,,				2504	0.001				p.I131I		Atlas-SNP	.											.	CIDEB	17	.	0			c.C393T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	196.0	166.0	176.0		393	0.1	1.0	14	dbSNP_134	176	72,8528	43.1+/-100.9	1,70,4229	no	coding-synonymous	CIDEB	NM_014430.2		1,79,6423	AA,AG,GG		0.8372,0.2043,0.6228		131/220	24775287	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	27141	exon6			TCGGGCGATGTCC	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.393C>T	14.37:g.24775287G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_014430	D3DS73|Q546V8|Q9NNW9	Silent	SNP	ENST00000336557.5	37	CCDS32056.1																																																																																			G|0.995;A|0.005	0.005	strong		0.527	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1		
KCNH5	27133	hgsc.bcm.edu	37	14	63174960	63174960	+	Missense_Mutation	SNP	C	C	T	rs4902176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63174960C>T	ENST00000322893.7	-	11	2501	c.2233G>A	c.(2233-2235)Gcc>Acc	p.A745T	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	745			A -> T (in dbSNP:rs4902176). {ECO:0000269|PubMed:11943152, ECO:0000269|PubMed:12135768, ECO:0000269|PubMed:15489334}.		potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GTGATGGAGGCTCCATTCTGT	0.527													c|||	1108	0.221246	0.1936	0.2997	5008	,	,		18594	0.1478		0.3479	False		,,,				2504	0.1483				p.A745T		Atlas-SNP	.											.	KCNH5	320	.	0			c.G2233A						PASS	.	C	THR/ALA,	906,3500	350.0+/-310.6	98,710,1395	107.0	95.0	99.0		2233,	5.5	1.0	14	dbSNP_111	99	2985,5615	462.4+/-365.7	517,1951,1832	yes	missense,utr-3	KCNH5	NM_139318.3,NM_172375.1	58,	615,2661,3227	TT,TC,CC		34.7093,20.5629,29.917	benign,	745/989,	63174960	3891,9115	2203	4300	6503	SO:0001583	missense	27133	exon11			TGGAGGCTCCATT	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2233G>A	14.37:g.63174960C>T	ENSP00000321427:p.Ala745Thr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	552	0.25274725274725274	97	0.19715447154471544	120	0.3314917127071823	87	0.1520979020979021	248	0.32717678100263853	C	2.888	-0.230279	0.05983	0.205629	0.347093	ENSG00000140015	ENST00000322893	D	0.98901	-5.22	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	1.0	B	0.16396	0.017	B	0.08055	0.003	T	0.47824	-0.9087	9	0.13470	T	0.59	.	19.4558	0.94889	0.0:1.0:0.0:0.0	rs4902176;rs17256625;rs52818800;rs58489583;rs4902176	745	Q8NCM2	KCNH5_HUMAN	T	745	ENSP00000321427:A745T	ENSP00000321427:A745T	A	-	1	0	KCNH5	62244713	0.997000	0.39634	0.997000	0.53966	0.521000	0.34408	3.750000	0.55157	2.611000	0.88343	0.655000	0.94253	GCC	C|0.730;T|0.270	0.270	strong		0.527	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
TRIM54	57159	hgsc.bcm.edu	37	2	27521506	27521506	+	Silent	SNP	G	G	A	rs540676343		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:27521506G>A	ENST00000380075.2	+	2	580	c.240G>A	c.(238-240)tcG>tcA	p.S80S	TRIM54_ENST00000296098.4_Silent_p.S80S	NM_187841.2	NP_912730.2	Q9BYV2	TRI54_HUMAN	tripartite motif containing 54	80					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|negative regulation of microtubule depolymerization (GO:0007026)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTGCCCATCGTGCAGGCATG	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		19839	0.0		0.0	False		,,,				2504	0.001				p.S80S		Atlas-SNP	.											.	TRIM54	35	.	0			c.G240A						PASS	.						85.0	70.0	75.0					2																	27521506		2203	4300	6503	SO:0001819	synonymous_variant	57159	exon2			CCCATCGTGCAGG	AJ291714	CCDS1745.2, CCDS1746.2	2p23.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000138100	ENSG00000138100		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16008	protein-coding gene	gene with protein product		606474	"""ring finger protein 30"", ""tripartite motif-containing 54"""	RNF30		11243782	Standard	NM_032546		Approved	MURF, MURF-3	uc002rjn.3	Q9BYV2	OTTHUMG00000097078	ENST00000380075.2:c.240G>A	2.37:g.27521506G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	190	25	0.131579	NM_187841	A5D8T7|Q53SY4|Q9BYV3	Silent	SNP	ENST00000380075.2	37	CCDS1746.2																																																																																			.	.	none		0.567	TRIM54-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214199.2	NM_187841	
PKD1L2	114780	hgsc.bcm.edu	37	16	81232294	81232294	+	RNA	SNP	T	T	C	rs61734110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81232294T>C	ENST00000525539.1	-	0	1515				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGGCGGCAAATCCCAAATGGC	0.582													T|||	154	0.0307508	0.0325	0.0317	5008	,	,		20196	0.004		0.0716	False		,,,				2504	0.0133				p.I506V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A1516G						PASS	.	T	VAL/ILE,VAL/ILE	168,3844		1,166,1839	51.0	52.0	51.0		1516,1516	2.8	0.5	16	dbSNP_129	51	526,7782		17,492,3645	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	29,29	18,658,5484	CC,CT,TT		6.3312,4.1874,5.6331	benign,benign	506/992,506/2460	81232294	694,11626	2006	4154	6160			114780	exon7			GGCAAATCCCAAA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81232294T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	101	60	0.594059	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		85|85	0.03891941391941392|0.03891941391941392	17|17	0.034552845528455285|0.034552845528455285	16|16	0.04419889502762431|0.04419889502762431	1|1	0.0017482517482517483|0.0017482517482517483	51|51	0.06728232189973615|0.06728232189973615	T|T	0.006|0.006	-2.058861|-2.058861	0.00390|0.00390	0.041874|0.041874	0.063312|0.063312	ENSG00000166473|ENSG00000166473	ENST00000526632|ENST00000337114	.|T	.|0.01279	.|5.06	5.08|5.08	2.75|2.75	0.32379|0.32379	.|Egg jelly receptor, REJ-like (1);	.|1.001100	.|0.08058	.|N	.|0.997623	T|T	0.00144|0.00144	0.0004|0.0004	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B	.|0.16603	.|0.018;0.006	.|B;B	.|0.17722	.|0.019;0.004	T|T	0.50127|0.50127	-0.8864|-0.8864	4|9	.|0.22706	.|T	.|0.39	-3.0E-4|-3.0E-4	8.8296|8.8296	0.35076|0.35076	0.0:0.2087:0.0:0.7913|0.0:0.2087:0.0:0.7913	.|.	.|506;506	.|Q7Z442-3;Q7Z442	.|.;PK1L2_HUMAN	G|V	33|506	.|ENSP00000337397:I506V	.|ENSP00000337397:I506V	D|I	-|-	2|1	0|0	PKD1L2|PKD1L2	79789795|79789795	0.000000|0.000000	0.05858|0.05858	0.487000|0.487000	0.27428|0.27428	0.041000|0.041000	0.13682|0.13682	0.422000|0.422000	0.21296|0.21296	0.790000|0.790000	0.33803|0.33803	-0.398000|-0.398000	0.06409|0.06409	GAT|ATT	T|0.956;C|0.044	0.044	strong		0.582	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
MUC4	4585	hgsc.bcm.edu	37	3	195489067	195489067	+	Silent	SNP	C	C	G	rs2246980	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195489067C>G	ENST00000346145.4	-	13	1734	c.1695G>C	c.(1693-1695)tcG>tcC	p.S565S	MUC4_ENST00000349607.4_Silent_p.S514S|MUC4_ENST00000463781.3_Silent_p.S4801S|MUC4_ENST00000475231.1_Silent_p.S4749S	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1558					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGAAGCTGGCCGAGACCTCAG	0.687													.|||	2125	0.424321	0.1513	0.415	5008	,	,		11346	0.7599		0.4533	False		,,,				2504	0.4243				p.S4801S		Atlas-SNP	.											MUC4_ENST00000463781,colon,carcinoma,0,3	MUC4	1505	3	0			c.G14403C						scavenged	.	C	,,	923,3469		101,721,1374	27.0	24.0	25.0		1695,14403,1542	-4.3	0.9	3	dbSNP_100	25	3919,4669		941,2037,1316	no	coding-synonymous,coding-synonymous,coding-synonymous	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	1042,2758,2690	GG,GC,CC		45.6334,21.0155,37.3035	,,	565/1177,4801/5413,514/1126	195489067	4842,8138	2196	4294	6490	SO:0001819	synonymous_variant	4585	exon14			GCTGGCCGAGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.1695G>C	3.37:g.195489067C>G		Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																			C|0.619;G|0.381	0.381	strong		0.687	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
CNTNAP3	79937	hgsc.bcm.edu	37	9	39085764	39085764	+	Silent	SNP	G	G	A	rs2150942		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:39085764G>A	ENST00000297668.6	-	21	3484	c.3411C>T	c.(3409-3411)gcC>gcT	p.A1137A	CNTNAP3_ENST00000377656.2_Silent_p.A1056A|CNTNAP3_ENST00000358144.2_3'UTR	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	1137	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GAGATTTGACGGCGTTGAATT	0.398																																					p.A1137A		Atlas-SNP	.											CNTNAP3,NS,carcinoma,-1,1	CNTNAP3	82	1	0			c.C3411T						scavenged	.						66.0	84.0	78.0					9																	39085764		2168	4238	6406	SO:0001819	synonymous_variant	79937	exon21			TTTGACGGCGTTG	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.3411C>T	9.37:g.39085764G>A		Somatic	819	0	0		WXS	Illumina HiSeq	Phase_I	148	145	0.97973	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			.	.	weak		0.398	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
GABRA4	2557	hgsc.bcm.edu	37	4	46995366	46995366	+	Missense_Mutation	SNP	G	G	T	rs2229940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:46995366G>T	ENST00000264318.3	-	1	1058	c.76C>A	c.(76-78)Ctg>Atg	p.L26M	GABRA4_ENST00000509316.1_5'UTR	NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	26			L -> M (in dbSNP:rs2229940).		central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.L26M(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CAAACCGCCAGGCACAGGAAG	0.607													G|||	1506	0.300719	0.2526	0.2968	5008	,	,		16875	0.3879		0.3668	False		,,,				2504	0.2106				p.L26M	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											GABRA4,NS,carcinoma,0,1	GABRA4	129	1	1	Substitution - Missense(1)	prostate(1)	c.C76A						PASS	.	G	MET/LEU,,	1132,3274	403.5+/-332.8	127,878,1198	109.0	105.0	106.0		76,,	3.0	1.0	4	dbSNP_98	106	3154,5446	479.1+/-370.0	599,1956,1745	yes	missense,intron,intron	GABRA4	NM_000809.3,NM_001204266.1,NM_001204267.1	15,,	726,2834,2943	TT,TG,GG		36.6744,25.6922,32.954	probably-damaging,,	26/555,,	46995366	4286,8720	2203	4300	6503	SO:0001583	missense	2557	exon1			CCGCCAGGCACAG		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.76C>A	4.37:g.46995366G>T	ENSP00000264318:p.Leu26Met	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	178	84	0.47191	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	742	0.33974358974358976	138	0.2804878048780488	107	0.2955801104972376	214	0.3741258741258741	283	0.3733509234828496	G	13.24	2.178732	0.38511	0.256922	0.366744	ENSG00000109158	ENST00000264318	D	0.81996	-1.56	4.72	2.98	0.34508	.	0.473208	0.19701	N	0.108022	T	0.00012	0.0000	N	0.24115	0.695	0.35598	P	0.19235199999999997	B	0.23806	0.091	B	0.29524	0.103	T	0.13045	-1.0524	9	0.49607	T	0.09	.	6.8007	0.23750	0.2113:0.0:0.7887:0.0	rs2229940;rs2280071;rs16859834;rs52790560;rs2229940	26	P48169	GBRA4_HUMAN	M	26	ENSP00000264318:L26M	ENSP00000264318:L26M	L	-	1	2	GABRA4	46690123	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	2.533000	0.45667	0.588000	0.29660	0.585000	0.79938	CTG	G|0.672;T|0.328	0.328	strong		0.607	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
ASCL3	56676	hgsc.bcm.edu	37	11	8959455	8959455	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8959455C>T	ENST00000531618.1	-	1	303	c.254G>A	c.(253-255)gGg>gAg	p.G85E	ASCL3_ENST00000325884.1_Missense_Mutation_p.G85E			Q9NQ33	ASCL3_HUMAN	achaete-scute family bHLH transcription factor 3	84					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(5)|stomach(1)	9				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)		GTACTCGCACCCTCTGTAATT	0.557																																					p.G85E		Atlas-SNP	.											ASCL3,NS,carcinoma,+1,1	ASCL3	19	1	0			c.G254A						scavenged	.						62.0	65.0	64.0					11																	8959455		2201	4295	6496	SO:0001583	missense	56676	exon2			TCGCACCCTCTGT	AJ400877	CCDS7795.1	11p15.3	2013-10-17	2013-10-17			ENSG00000176009		"""Basic helix-loop-helix proteins"""	740	protein-coding gene	gene with protein product		609154	"""achaete-scute complex (Drosophila) homolog-like 3"", ""achaete-scute complex homolog 3 (Drosophila)"""			11528127	Standard	NM_020646		Approved	bHLHa42, HASH3, Sgn1	uc001mhd.1	Q9NQ33	OTTHUMG00000165679	ENST00000531618.1:c.254G>A	11.37:g.8959455C>T	ENSP00000435770:p.Gly85Glu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	119	2	0.0168067	NM_020646	Q8WYQ6	Missense_Mutation	SNP	ENST00000531618.1	37	CCDS7795.1	.	.	.	.	.	.	.	.	.	.	C	2.864	-0.235422	0.05983	.	.	ENSG00000176009	ENST00000325884;ENST00000531618	D;D	0.97161	-4.27;-4.27	5.72	4.76	0.60689	.	0.588227	0.16920	N	0.194110	D	0.89389	0.6701	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.75682	-0.3233	10	0.02654	T	1	-5.6034	9.2075	0.37298	0.1449:0.78:0.0:0.0751	.	84	Q9NQ33	ASCL3_HUMAN	E	85	ENSP00000318846:G85E;ENSP00000435770:G85E	ENSP00000318846:G85E	G	-	2	0	ASCL3	8916031	0.841000	0.29509	0.993000	0.49108	0.087000	0.18053	2.974000	0.49272	2.717000	0.92951	0.650000	0.86243	GGG	.	.	none		0.557	ASCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385773.1		
ANO5	203859	hgsc.bcm.edu	37	11	22271870	22271870	+	Missense_Mutation	SNP	A	A	T	rs7481951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:22271870A>T	ENST00000324559.8	+	10	1283	c.966A>T	c.(964-966)ttA>ttT	p.L322F		NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	322			L -> F (in dbSNP:rs7481951).		chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TAGTTGGCTTAGCTTGTTTTA	0.343																																					p.L322F		Atlas-SNP	.											.	ANO5	162	.	0			c.A966T						PASS	.	A	PHE/LEU,PHE/LEU	794,3612	316.3+/-294.6	74,646,1483	152.0	134.0	140.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	963,966	3.0	1.0	11	dbSNP_116	140	5041,3559	627.3+/-398.0	1487,2067,746	yes	missense,missense	ANO5	NM_001142649.1,NM_213599.2	22,22	1561,2713,2229	TT,TA,AA		41.3837,18.0209,44.8639	benign,benign	321/913,322/914	22271870	5835,7171	2203	4300	6503	SO:0001583	missense	203859	exon10			TGGCTTAGCTTGT	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	27337	protein-coding gene	gene with protein product		608662	"""transmembrane protein 16E"", ""limb girdle muscular dystrophy 2L (autosomal recessive)"""	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.966A>T	11.37:g.22271870A>T	ENSP00000315371:p.Leu322Phe	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_213599		Missense_Mutation	SNP	ENST00000324559.8	37	CCDS31444.1	762	0.3489010989010989	51	0.10365853658536585	152	0.4198895027624309	117	0.20454545454545456	442	0.58311345646438	A	12.13	1.844660	0.32606	0.180209	0.586163	ENSG00000171714	ENST00000324559	T	0.66099	-0.19	5.42	3.01	0.34805	.	0.672331	0.14951	N	0.288911	T	0.00012	0.0000	L	0.41824	1.3	0.80722	P	0.0	B	0.14805	0.011	B	0.18561	0.022	T	0.44236	-0.9341	9	0.34782	T	0.22	.	5.3272	0.15913	0.654:0.0:0.0732:0.2728	rs7481951;rs7481951	322	Q75V66	ANO5_HUMAN	F	322	ENSP00000315371:L322F	ENSP00000315371:L322F	L	+	3	2	ANO5	22228446	0.001000	0.12720	0.999000	0.59377	0.984000	0.73092	-0.001000	0.12947	0.317000	0.23160	0.455000	0.32223	TTA	A|0.607;T|0.393	0.393	strong		0.343	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599	
CYP1B1	1545	hgsc.bcm.edu	37	2	38298150	38298150	+	Silent	SNP	A	A	G	rs1056837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:38298150A>G	ENST00000260630.3	-	3	1748	c.1347T>C	c.(1345-1347)gaT>gaC	p.D449D	CYP1B1_ENST00000407341.1_Silent_p.D449D|CYP1B1_ENST00000494864.1_5'UTR	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	449			D -> E (in dbSNP:rs1056837).		angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	TGATGAGGCCATCCTTGTCCA	0.478													G|||	3106	0.620208	0.2012	0.7277	5008	,	,		20544	0.9087		0.6024	False		,,,				2504	0.8313				p.D449D		Atlas-SNP	.											.	CYP1B1	39	.	0			c.T1347C						PASS	.	G		1119,3287	718.6+/-408.9	159,801,1243	84.0	77.0	79.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1347	-7.2	0.2	2	dbSNP_86	79	4782,3818	538.6+/-383.4	1344,2094,862	no	coding-synonymous	CYP1B1	NM_000104.3		1503,2895,2105	GG,GA,AA		44.3953,25.3972,45.3714		449/544	38298150	5901,7105	2203	4300	6503	SO:0001819	synonymous_variant	1545	exon3			GAGGCCATCCTTG	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.1347T>C	2.37:g.38298150A>G		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_000104	Q5TZW8|Q93089|Q9H316	Silent	SNP	ENST00000260630.3	37	CCDS1793.1																																																																																			G|0.522;A|0.478	0.522	strong		0.478	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
ZNF462	58499	hgsc.bcm.edu	37	9	109692820	109692820	+	Silent	SNP	A	A	G	rs139184113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:109692820A>G	ENST00000277225.5	+	4	6151	c.5862A>G	c.(5860-5862)ttA>ttG	p.L1954L	ZNF462_ENST00000457913.1_Silent_p.L1954L|ZNF462_ENST00000497489.1_3'UTR|ZNF462_ENST00000441147.2_Silent_p.L799L|ZNF462_ENST00000542028.1_5'Flank			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1954					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						TTGGTCACTTAGAAGAGGTGC	0.453																																					p.L1954L		Atlas-SNP	.											.	ZNF462	322	.	0			c.A5862G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	102.0	95.0	97.0		5862	5.4	1.0	9	dbSNP_134	97	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	ZNF462	NM_021224.4		0,29,6474	GG,GA,AA		0.314,0.0454,0.223		1954/2507	109692820	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	58499	exon4			TCACTTAGAAGAG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5862A>G	9.37:g.109692820A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	149	67	0.449664	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			A|0.999;G|0.001	0.001	strong		0.453	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
DDAH1	23576	hgsc.bcm.edu	37	1	85816134	85816134	+	Silent	SNP	T	T	C	rs2230820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:85816134T>C	ENST00000284031.8	-	4	655	c.561A>G	c.(559-561)gcA>gcG	p.A187A	DDAH1_ENST00000426972.3_Silent_p.A94A|DDAH1_ENST00000539042.1_Silent_p.A187A|DDAH1_ENST00000535924.2_Silent_p.A84A|RP11-131L23.1_ENST00000426125.1_RNA|DDAH1_ENST00000483110.1_5'UTR|DDAH1_ENST00000542148.1_Silent_p.A87A|RP11-131L23.1_ENST00000427819.1_RNA	NM_012137.3	NP_036269.1	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1	187					arginine catabolic process (GO:0006527)|citrulline metabolic process (GO:0000052)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of angiogenesis (GO:0045766)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of systemic arterial blood pressure (GO:0003073)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|catalytic activity (GO:0003824)|dimethylargininase activity (GO:0016403)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|skin(1)	5				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	TAGACCCAATTGCGATCAGGT	0.483													T|||	624	0.124601	0.0204	0.1974	5008	,	,		18538	0.1567		0.2038	False		,,,				2504	0.0992				p.A187A		Atlas-SNP	.											.	DDAH1	19	.	0			c.A561G						PASS	.	T	,	209,4197	128.2+/-165.1	10,189,2004	158.0	148.0	151.0		252,561	-1.8	0.8	1	dbSNP_119	151	1718,6882	316.1+/-312.6	183,1352,2765	no	coding-synonymous,coding-synonymous	DDAH1	NM_001134445.1,NM_012137.3	,	193,1541,4769	CC,CT,TT		19.9767,4.7435,14.8162	,	84/183,187/286	85816134	1927,11079	2203	4300	6503	SO:0001819	synonymous_variant	23576	exon4			CCCAATTGCGATC	AB001915	CCDS705.1, CCDS44170.1	1p22	2008-02-05			ENSG00000153904	ENSG00000153904	3.5.3.18		2715	protein-coding gene	gene with protein product		604743				9874257	Standard	NM_012137		Approved	DDAH	uc001dlb.3	O94760	OTTHUMG00000010578	ENST00000284031.8:c.561A>G	1.37:g.85816134T>C		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_012137	Q5HYC8|Q86XK5	Silent	SNP	ENST00000284031.8	37	CCDS705.1																																																																																			T|0.860;C|0.140	0.140	strong		0.483	DDAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029189.1		
AGBL1	123624	hgsc.bcm.edu	37	15	86807843	86807843	+	Missense_Mutation	SNP	T	T	C	rs11857527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:86807843T>C	ENST00000441037.2	+	10	1398	c.1303T>C	c.(1303-1305)Tcc>Ccc	p.S435P	AGBL1_ENST00000389298.3_Missense_Mutation_p.S166P|AGBL1_ENST00000421325.2_Missense_Mutation_p.S435P	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	435			S -> P (in dbSNP:rs11857527).		C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GATGAGTGCCTCCTTTTCTAA	0.453													T|||	669	0.133586	0.1029	0.1988	5008	,	,		20466	0.0288		0.1799	False		,,,				2504	0.1892				p.S435P		Atlas-SNP	.											AGBL1,NS,carcinoma,-1,1	AGBL1	151	1	0			c.T1303C						PASS	.	T	PRO/SER	442,3326		24,394,1466	113.0	113.0	113.0		1303	2.9	0.0	15	dbSNP_120	113	1586,6646		156,1274,2686	yes	missense	AGBL1	NM_152336.2	74	180,1668,4152	CC,CT,TT		19.2663,11.7304,16.9	possibly-damaging	435/1067	86807843	2028,9972	1884	4116	6000	SO:0001583	missense	123624	exon10			AGTGCCTCCTTTT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.1303T>C	15.37:g.86807843T>C	ENSP00000413001:p.Ser435Pro	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	95	34	0.357895	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	267	0.12225274725274725	57	0.11585365853658537	61	0.1685082872928177	14	0.024475524475524476	135	0.17810026385224276	T	15.22	2.770289	0.49680	0.117304	0.192663	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.11712	2.77;2.75	5.23	2.89	0.33648	Armadillo-type fold (1);	0.550372	0.19529	N	0.112097	T	0.00012	0.0000	M	0.74258	2.255	0.80722	P	0.0	B;B;B	0.25955	0.138;0.138;0.001	B;B;B	0.24701	0.055;0.037;0.003	T	0.23297	-1.0192	9	0.25751	T	0.34	-2.8611	6.399	0.21628	0.0:0.0806:0.1584:0.7609	rs11857527;rs17602437;rs52833441;rs58891646;rs11857527	134;166;435	Q96MI9-2;Q96MI9-3;Q96MI9	.;.;CBPC4_HUMAN	P	464;435;166	ENSP00000397173:S435P;ENSP00000373949:S166P	ENSP00000373949:S166P	S	+	1	0	AGBL1	84608847	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	0.589000	0.23939	0.389000	0.25086	-0.323000	0.08544	TCC	T|0.872;C|0.128	0.128	strong		0.453	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
MRPL9	65005	hgsc.bcm.edu	37	1	151735913	151735913	+	Missense_Mutation	SNP	G	G	A	rs199630729		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151735913G>A	ENST00000368830.3	-	1	127	c.43C>T	c.(43-45)Cgg>Tgg	p.R15W	RP11-98D18.2_ENST00000420382.1_RNA|OAZ3_ENST00000453029.2_5'Flank|RP11-98D18.3_ENST00000512280.1_RNA|OAZ3_ENST00000479764.1_5'Flank|MRPL9_ENST00000467306.1_5'UTR|OAZ3_ENST00000315067.8_Intron|MRPL9_ENST00000368829.3_Missense_Mutation_p.R15W|OAZ3_ENST00000321531.5_Intron	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	15					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCGCCCGCCCGCAGCAGAGCT	0.692													G|||	1	0.000199681	0.0	0.0	5008	,	,		10868	0.0		0.001	False		,,,				2504	0.0				p.R15W		Atlas-SNP	.											.	MRPL9	21	.	0			c.C43T						PASS	.	G	,TRP/ARG	0,4330		0,0,2165	8.0	10.0	9.0		,43	0.8	0.0	1		9	13,8467		0,13,4227	yes	intron,missense	OAZ3,MRPL9	NM_001134939.1,NM_031420.2	,101	0,13,6392	AA,AG,GG		0.1533,0.0,0.1015	,probably-damaging	,15/268	151735913	13,12797	2165	4240	6405	SO:0001583	missense	65005	exon1			CCGCCCGCAGCAG	AK026363	CCDS1003.1, CCDS72916.1	1q21	2012-09-13			ENSG00000143436	ENSG00000143436		"""Mitochondrial ribosomal proteins / large subunits"""	14277	protein-coding gene	gene with protein product		611824					Standard	XM_005245455		Approved		uc001eyv.3	Q9BYD2	OTTHUMG00000013063	ENST00000368830.3:c.43C>T	1.37:g.151735913G>A	ENSP00000357823:p.Arg15Trp	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	46	31	0.673913	NM_031420	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.285275	0.59867	0.0	0.001533	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.31510	1.5;1.49	4.93	0.779	0.18550	.	0.716541	0.14023	N	0.346675	T	0.04588	0.0125	N	0.12746	0.255	0.09310	N	1	B;B;B	0.19331	0.013;0.035;0.001	B;B;B	0.10450	0.002;0.005;0.001	T	0.37033	-0.9723	10	0.42905	T	0.14	-0.4378	3.2367	0.06767	0.3201:0.0:0.4969:0.183	.	15;15;15	B4DDZ7;B4DUJ1;Q9BYD2	.;.;RM09_HUMAN	W	15	ENSP00000357823:R15W;ENSP00000357822:R15W	ENSP00000357822:R15W	R	-	1	2	MRPL9	150002537	0.005000	0.15991	0.002000	0.10522	0.008000	0.06430	0.245000	0.18142	-0.015000	0.14150	-0.140000	0.14226	CGG	.	.	weak		0.692	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420	
KRT6B	3854	hgsc.bcm.edu	37	12	52844243	52844243	+	Silent	SNP	A	A	G	rs28414881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52844243A>G	ENST00000252252.3	-	2	749	c.702T>C	c.(700-702)cgT>cgC	p.R234R		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	234	Coil 1B.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		CCGAGTCCAGACGACCCCGTT	0.552													A|||	394	0.0786741	0.0061	0.0821	5008	,	,		24489	0.1875		0.0875	False		,,,				2504	0.0532				p.R234R		Atlas-SNP	.											KRT6B,NS,carcinoma,-1,1	KRT6B	90	1	0			c.T702C						scavenged	.						211.0	184.0	193.0					12																	52844243		2203	4300	6503	SO:0001819	synonymous_variant	3854	exon2			GTCCAGACGACCC	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.702T>C	12.37:g.52844243A>G		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	522	100	0.191571	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			A|0.959;G|0.041	0.041	strong		0.552	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
OR6N1	128372	hgsc.bcm.edu	37	1	158735595	158735595	+	Missense_Mutation	SNP	C	C	T	rs857824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158735595C>T	ENST00000335094.2	-	1	897	c.878G>A	c.(877-879)cGc>cAc	p.R293H		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	293			R -> H (in dbSNP:rs857824).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					CTCCTTGTTGCGCAAGCTGTA	0.547													C|||	3345	0.667931	0.7784	0.7839	5008	,	,		21103	0.6171		0.7217	False		,,,				2504	0.4335				p.R293H		Atlas-SNP	.											OR6N1,NS,adenoma,0,1	OR6N1	96	1	0			c.G878A						PASS	.	C	HIS/ARG	3435,971	733.7+/-410.5	1328,779,96	156.0	151.0	153.0		878	4.0	1.0	1	dbSNP_86	153	6163,2437	698.7+/-405.0	2218,1727,355	yes	missense	OR6N1	NM_001005185.1	29	3546,2506,451	TT,TC,CC		28.3372,22.0381,26.2033	benign	293/313	158735595	9598,3408	2203	4300	6503	SO:0001583	missense	128372	exon1			TTGTTGCGCAAGC	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.878G>A	1.37:g.158735595C>T	ENSP00000335535:p.Arg293His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	161	161	1	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	1561	0.7147435897435898	376	0.7642276422764228	286	0.7900552486187845	344	0.6013986013986014	555	0.7321899736147758	C	13.99	2.401976	0.42613	0.779619	0.716628	ENSG00000197403	ENST00000335094	T	0.41065	1.01	4.92	4.01	0.46588	.	0.144113	0.32518	N	0.005981	T	0.33059	0.0850	M	0.91561	3.22	0.33801	P	0.373286	B	0.28605	0.217	B	0.22753	0.041	T	0.44574	-0.9319	9	0.66056	D	0.02	-13.5884	8.7382	0.34541	0.0:0.8249:0.0:0.1751	rs857824;rs1633199;rs52807313;rs60646728;rs857824	293	Q8NGY5	OR6N1_HUMAN	H	293	ENSP00000335535:R293H	ENSP00000335535:R293H	R	-	2	0	OR6N1	157002219	0.143000	0.22626	1.000000	0.80357	0.995000	0.86356	1.872000	0.39549	1.279000	0.44446	0.643000	0.83706	CGC	C|0.286;T|0.714	0.714	strong		0.547	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
OR2C1	4993	hgsc.bcm.edu	37	16	3406838	3406838	+	Missense_Mutation	SNP	G	G	A	rs62000975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3406838G>A	ENST00000304936.2	+	1	950	c.898G>A	c.(898-900)Gca>Aca	p.A300T		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	300					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)	cell cortex (GO:0005938)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						AGTGAAGGGCGCACTGAGGAG	0.493													G|||	39	0.00778754	0.0	0.0	5008	,	,		20025	0.0		0.0169	False		,,,				2504	0.0225				p.A300T		Atlas-SNP	.											.	OR2C1	38	.	0			c.G898A						PASS	.		THR/ALA	8,4384		0,8,2188	29.0	24.0	26.0		898	4.0	1.0	16	dbSNP_129	26	114,8484		1,112,4186	yes	missense	OR2C1	NM_012368.2	58	1,120,6374	AA,AG,GG		1.3259,0.1821,0.9392	possibly-damaging	300/313	3406838	122,12868	2196	4299	6495	SO:0001583	missense	4993	exon1			AAGGGCGCACTGA	AF098664	CCDS10502.1	16p13.3	2012-08-09			ENSG00000168158	ENSG00000168158		"""GPCR / Class A : Olfactory receptors"""	8242	protein-coding gene	gene with protein product				OR2C2P		9847080	Standard	NM_012368		Approved	OLFmf3	uc002cuw.1	O95371	OTTHUMG00000090505	ENST00000304936.2:c.898G>A	16.37:g.3406838G>A	ENSP00000307726:p.Ala300Thr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	NM_012368	A0AVA4|Q6IF34|Q6IF55	Missense_Mutation	SNP	ENST00000304936.2	37	CCDS10502.1	13	0.005952380952380952	0	0.0	0	0.0	0	0.0	13	0.017150395778364115	g	16.22	3.062779	0.55432	0.001821	0.013259	ENSG00000168158	ENST00000304936	T	0.42131	0.98	5.0	4.03	0.46877	.	0.000000	0.40222	N	0.001150	T	0.48077	0.1480	M	0.86740	2.835	0.30161	N	0.802197	D	0.76494	0.999	P	0.60609	0.877	T	0.65109	-0.6248	10	0.87932	D	0	.	12.4744	0.55805	0.0:0.0:0.8314:0.1685	rs62000975	300	O95371	OR2C1_HUMAN	T	300	ENSP00000307726:A300T	ENSP00000307726:A300T	A	+	1	0	OR2C1	3346839	0.793000	0.28825	0.986000	0.45419	0.529000	0.34654	1.915000	0.39976	1.301000	0.44836	0.604000	0.83254	GCA	G|0.992;A|0.008	0.008	strong		0.493	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3		
KIAA0141	9812	hgsc.bcm.edu	37	5	141309152	141309152	+	Nonsense_Mutation	SNP	C	C	T	rs114623503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141309152C>T	ENST00000432126.2	+	5	552	c.418C>T	c.(418-420)Cga>Tga	p.R140*	KIAA0141_ENST00000194118.4_Nonsense_Mutation_p.R140*	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	140					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGCACTGCGACAACACAT	0.632													C|||	2	0.000399361	0.0	0.0	5008	,	,		17987	0.0		0.002	False		,,,				2504	0.0				p.R140X		Atlas-SNP	.											.	KIAA0141	44	.	0			c.C418T						PASS	.	C	stop/ARG,stop/ARG	2,4404	4.2+/-10.8	0,2,2201	68.0	71.0	70.0		418,418	1.9	0.7	5	dbSNP_132	70	16,8584	11.2+/-40.8	0,16,4284	yes	stop-gained,stop-gained	KIAA0141	NM_001142603.1,NM_014773.3	,	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	,	140/516,140/516	141309152	18,12988	2203	4300	6503	SO:0001587	stop_gained	9812	exon5			GCACTGCGACAAC	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.418C>T	5.37:g.141309152C>T	ENSP00000396225:p.Arg140*	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	109	40	0.366972	NM_001142603	Q969R4|Q96EU9	Nonsense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	14.47	2.543632	0.45280	4.54E-4	0.00186	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	.	.	.	3.95	1.87	0.25490	.	0.181406	0.33040	N	0.005360	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.4383	8.0362	0.30493	0.4754:0.5246:0.0:0.0	.	.	.	.	X	140	.	ENSP00000194118:R140X	R	+	1	2	KIAA0141	141289336	0.059000	0.20769	0.661000	0.29709	0.048000	0.14542	0.121000	0.15667	0.827000	0.34685	0.305000	0.20034	CGA	C|0.999;T|0.001	0.001	strong		0.632	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
CCRL2	9034	hgsc.bcm.edu	37	3	46449978	46449978	+	Silent	SNP	A	A	C	rs11266744	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46449978A>C	ENST00000399036.3	+	2	760	c.408A>C	c.(406-408)ggA>ggC	p.G136G	CCRL2_ENST00000357392.4_Silent_p.G148G|CCRL2_ENST00000400880.3_Silent_p.G136G|RP11-24F11.2_ENST00000451485.1_RNA|CCRL2_ENST00000400882.2_Silent_p.G136G	NM_003965.4	NP_003956.2	O00421	CCRL2_HUMAN	chemokine (C-C motif) receptor-like 2	136					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CCR chemokine receptor binding (GO:0048020)|chemokine receptor activity (GO:0004950)|chemokine receptor binding (GO:0042379)			lung(3)|ovary(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)		TGCACAAGGGAAACTTTTTCT	0.468													A|||	1691	0.33766	0.0477	0.3703	5008	,	,		19839	0.5605		0.4026	False		,,,				2504	0.41				p.G148G		Atlas-SNP	.											.	CCRL2	23	.	0			c.A444C						PASS	.	A	,	337,3557		11,315,1621	96.0	88.0	91.0		444,408	-3.8	0.0	3	dbSNP_120	91	3272,5004		669,1934,1535	no	coding-synonymous,coding-synonymous	CCRL2	NM_001130910.1,NM_003965.4	,	680,2249,3156	CC,CA,AA		39.536,8.6543,29.6549	,	148/357,136/345	46449978	3609,8561	1947	4138	6085	SO:0001819	synonymous_variant	9034	exon2			CAAGGGAAACTTT	AF014958	CCDS43079.1, CCDS46814.1	3p21	2013-07-18	2013-07-18	2013-07-18	ENSG00000121797	ENSG00000121797		"""GPCR / Class A : Chemokine receptors : Atypical"""	1612	protein-coding gene	gene with protein product	"""atypical chemokine receptor 5"""	608379				9473515	Standard	NM_001130910		Approved	HCR, CRAM-B, CKRX, CRAM-A, ACKR5	uc003cpp.4	O00421	OTTHUMG00000156318	ENST00000399036.3:c.408A>C	3.37:g.46449978A>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	182	84	0.461538	NM_001130910	B4DKQ8|O75307|Q4VBB0|Q6IPX0|Q7KYQ9|Q96KP5|Q9UPG0	Silent	SNP	ENST00000399036.3	37	CCDS43079.1																																																																																			A|0.645;C|0.355	0.355	strong		0.468	CCRL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343909.2		
NSUN5	55695	hgsc.bcm.edu	37	7	72717933	72717933	+	Silent	SNP	C	C	T	rs11544043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:72717933C>T	ENST00000252594.6	-	8	1050	c.1035G>A	c.(1033-1035)gcG>gcA	p.A345A	NSUN5_ENST00000310326.8_Silent_p.A345A|NSUN5_ENST00000428206.1_Silent_p.A307A|NSUN5_ENST00000438747.2_Silent_p.A345A			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	345					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				GGAAAGTGAGCGCGTGGCACA	0.662													.|||	1253	0.2502	0.2595	0.3228	5008	,	,		16894	0.2381		0.2197	False		,,,				2504	0.2301				p.A345A		Atlas-SNP	.											NSUN5_ENST00000438747,NS,carcinoma,0,2	NSUN5	47	2	0			c.G1035A						PASS	.	C	,,,	1103,3303		141,821,1241	36.0	39.0	38.0		1035,921,1035,1035	-4.2	0.0	7	dbSNP_120	38	2086,6512		247,1592,2460	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	,,,	388,2413,3701	TT,TC,CC		24.2615,25.034,24.5232	,,,	345/471,307/392,345/430,345/467	72717933	3189,9815	2203	4299	6502	SO:0001819	synonymous_variant	55695	exon8			AGTGAGCGCGTGG	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.1035G>A	7.37:g.72717933C>T		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	238	237	0.995798	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Silent	SNP	ENST00000252594.6	37	CCDS5547.1																																																																																			C|0.714;T|0.286	0.286	strong		0.662	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
STX17	55014	hgsc.bcm.edu	37	9	102677589	102677589	+	Missense_Mutation	SNP	T	T	C	rs41305451	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:102677589T>C	ENST00000259400.6	+	2	204	c.68T>C	c.(67-69)aTa>aCa	p.I23T	RP11-60I3.4_ENST00000524512.1_RNA|STX17_ENST00000534052.1_Missense_Mutation_p.I23T|STX17_ENST00000525640.1_Missense_Mutation_p.I23T	NM_017919.2	NP_060389.2	P56962	STX17_HUMAN	syntaxin 17	23					autophagic vacuole fusion (GO:0000046)|endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111)|ER to Golgi vesicle-mediated transport (GO:0006888)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|protein localization to pre-autophagosomal structure (GO:0034497)	autophagic vacuole membrane (GO:0000421)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle (GO:0030134)|ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|smooth endoplasmic reticulum membrane (GO:0030868)|SNARE complex (GO:0031201)	protein phosphatase binding (GO:0019903)|SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				TTCATTAAGATAGTAATCCCA	0.363													T|||	153	0.0305511	0.0038	0.036	5008	,	,		16231	0.001		0.0924	False		,,,				2504	0.0297				p.I23T		Atlas-SNP	.											.	STX17	17	.	0			c.T68C						PASS	.	T	THR/ILE	63,4343	59.3+/-96.0	1,61,2141	99.0	102.0	101.0		68	5.3	1.0	9	dbSNP_127	101	770,7830	182.2+/-230.7	35,700,3565	yes	missense	STX17	NM_017919.2	89	36,761,5706	CC,CT,TT		8.9535,1.4299,6.4047	benign	23/303	102677589	833,12173	2203	4300	6503	SO:0001583	missense	55014	exon2			TTAAGATAGTAAT	AL834371	CCDS6745.1	9q31.1	2008-02-05			ENSG00000136874	ENSG00000136874			11432	protein-coding gene	gene with protein product		604204				9852078	Standard	NM_017919		Approved	FLJ20651	uc004bal.4	P56962	OTTHUMG00000020359	ENST00000259400.6:c.68T>C	9.37:g.102677589T>C	ENSP00000259400:p.Ile23Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_017919	Q4VXC2	Missense_Mutation	SNP	ENST00000259400.6	37	CCDS6745.1	94	0.04304029304029304	4	0.008130081300813009	13	0.03591160220994475	1	0.0017482517482517483	76	0.10026385224274406	T	16.64	3.180517	0.57800	0.014299	0.089535	ENSG00000136874	ENST00000259400;ENST00000531035;ENST00000525640;ENST00000534052;ENST00000526607	T;T;T	0.21734	1.99;1.99;1.99	5.32	5.32	0.75619	t-SNARE (1);	0.108846	0.64402	D	0.000007	T	0.00356	0.0011	N	0.19112	0.55	0.35359	D	0.78806	B;P	0.38504	0.309;0.634	B;B	0.34242	0.039;0.178	T	0.17653	-1.0362	10	0.66056	D	0.02	-5.6625	12.974	0.58527	0.0:0.0:0.0:1.0	rs41305451	23;23	P56962;B4DJ69	STX17_HUMAN;.	T	23	ENSP00000259400:I23T;ENSP00000435981:I23T;ENSP00000433484:I23T	ENSP00000259400:I23T	I	+	2	0	STX17	101717410	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.766000	0.68843	2.150000	0.67090	0.533000	0.62120	ATA	T|0.945;C|0.055	0.055	strong		0.363	STX17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053398.3	NM_017919	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136291361	136291361	+	Silent	SNP	C	C	T	rs34054981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136291361C>T	ENST00000371929.3	+	6	1026	c.582C>T	c.(580-582)ggC>ggT	p.G194G	ADAMTS13_ENST00000371911.3_Silent_p.G194G|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000536611.1_5'Flank|ADAMTS13_ENST00000355699.2_Silent_p.G194G|ADAMTS13_ENST00000356589.2_Silent_p.G194G|ADAMTS13_ENST00000371916.1_Silent_p.G194G	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	194	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		AGGTGCGGGGCGTCACCCAGC	0.627													C|||	139	0.0277556	0.0053	0.036	5008	,	,		18895	0.001		0.0805	False		,,,				2504	0.0256				p.G194G		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C582T						PASS	.	C	,,	74,4332	65.8+/-103.3	1,72,2130	73.0	65.0	68.0		582,582,582	-4.6	0.9	9	dbSNP_126	68	734,7866	177.5+/-227.1	35,664,3601	yes	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	36,736,5731	TT,TC,CC		8.5349,1.6795,6.2125	,,	194/1428,194/1341,194/1372	136291361	808,12198	2203	4300	6503	SO:0001819	synonymous_variant	11093	exon6			GCGGGGCGTCACC	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.582C>T	9.37:g.136291361C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_139026	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			C|0.942;T|0.058	0.058	strong		0.627	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
FETUB	26998	hgsc.bcm.edu	37	3	186370333	186370333	+	Silent	SNP	G	G	T	rs1131364	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186370333G>T	ENST00000265029.3	+	7	1163	c.1062G>T	c.(1060-1062)gtG>gtT	p.V354V	FETUB_ENST00000382136.3_Silent_p.V317V|RP11-134F2.2_ENST00000428501.1_RNA|FETUB_ENST00000450521.1_Silent_p.V354V|FETUB_ENST00000382134.3_Silent_p.V289V|RP11-134F2.2_ENST00000455926.1_RNA|FETUB_ENST00000539949.1_Silent_p.V206V	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	354					binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		AGAAGCTGGTGGTCCTGCCTT	0.562													T|||	3284	0.655751	0.798	0.5879	5008	,	,		18847	0.746		0.4592	False		,,,				2504	0.6207				p.V354V		Atlas-SNP	.											.	FETUB	53	.	0			c.G1062T						PASS	.	T		3219,1187	415.0+/-337.0	1176,867,160	60.0	65.0	64.0		1062	2.3	0.3	3	dbSNP_86	64	3978,4622	595.8+/-393.5	937,2104,1259	no	coding-synonymous	FETUB	NM_014375.2		2113,2971,1419	TT,TG,GG		46.2558,26.9405,44.664		354/383	186370333	7197,5809	2203	4300	6503	SO:0001819	synonymous_variant	26998	exon7			GCTGGTGGTCCTG	AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.1062G>T	3.37:g.186370333G>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	74	0.592	NM_014375	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Silent	SNP	ENST00000265029.3	37	CCDS3279.1																																																																																			G|0.402;T|0.598	0.598	strong		0.562	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375	
SMG6	23293	hgsc.bcm.edu	37	17	2203025	2203025	+	Missense_Mutation	SNP	T	T	G	rs1885987	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:2203025T>G	ENST00000263073.6	-	2	1072	c.1022A>C	c.(1021-1023)aAc>aCc	p.N341T	SMG6_ENST00000544865.1_Missense_Mutation_p.N310T	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	341	Interaction with telomeric DNA.		N -> T (in dbSNP:rs1885987). {ECO:0000269|PubMed:12676087, ECO:0000269|PubMed:9872452}.		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTTAGCACTGTTTTTCTGCTC	0.473													T|||	1149	0.229433	0.0469	0.438	5008	,	,		19830	0.1716		0.3827	False		,,,				2504	0.2301				p.N341T	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											SMG6,NS,carcinoma,+1,1	SMG6	97	1	0			c.A1022C						PASS	.	T	THR/ASN,THR/ASN	414,3992	201.5+/-224.5	24,366,1813	132.0	115.0	121.0		929,1022	2.3	1.0	17	dbSNP_92	121	3325,5275	492.6+/-373.4	640,2045,1615	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	65,65	664,2411,3428	GG,GT,TT		38.6628,9.3963,28.7483	benign,benign	310/1389,341/1420	2203025	3739,9267	2203	4300	6503	SO:0001583	missense	23293	exon2			GCACTGTTTTTCT	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.1022A>C	17.37:g.2203025T>G	ENSP00000263073:p.Asn341Thr	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	298	146	0.489933	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	569	0.26053113553113555	30	0.06097560975609756	162	0.44751381215469616	99	0.17307692307692307	278	0.36675461741424803	T	8.744	0.919722	0.17982	0.093963	0.386628	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.07908	3.15;3.15	5.35	2.3	0.28687	.	0.902977	0.09887	N	0.742929	T	0.00012	0.0000	N	0.08118	0	0.46279	P	0.0010320000000000329	B	0.06786	0.001	B	0.09377	0.004	T	0.43426	-0.9392	9	0.21540	T	0.41	-2.6793	10.1357	0.42706	0.0:0.7847:0.0:0.2153	rs1885987;rs56772408;rs1885987	341	Q86US8	EST1A_HUMAN	T	341;310	ENSP00000263073:N341T;ENSP00000443920:N310T	ENSP00000263073:N341T	N	-	2	0	SMG6	2149775	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.302000	0.51849	0.252000	0.21531	-0.146000	0.13790	AAC	T|0.736;G|0.264	0.264	strong		0.473	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
KREMEN1	83999	hgsc.bcm.edu	37	22	29533499	29533499	+	Silent	SNP	G	G	A	rs35612970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29533499G>A	ENST00000407188.1	+	6	795	c.795G>A	c.(793-795)gcG>gcA	p.A265A	KREMEN1_ENST00000400335.4_Silent_p.A267A|KREMEN1_ENST00000327813.5_Silent_p.A267A|KREMEN1_ENST00000400338.2_Silent_p.A267A			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	265	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						GGGACTCGGCGGACATGGTGG	0.622													G|||	543	0.108427	0.0726	0.111	5008	,	,		15598	0.0427		0.1958	False		,,,				2504	0.1329				p.A267A		Atlas-SNP	.											.	KREMEN1	46	.	0			c.G801A						PASS	.	G	,	317,3549		11,295,1627	64.0	64.0	64.0		801,801	0.2	1.0	22	dbSNP_126	64	1432,6822		129,1174,2824	no	coding-synonymous,coding-synonymous	KREMEN1	NM_001039570.2,NM_032045.4	,	140,1469,4451	AA,AG,GG		17.3492,8.1997,14.4307	,	267/459,267/493	29533499	1749,10371	1933	4127	6060	SO:0001819	synonymous_variant	83999	exon6			CTCGGCGGACATG	AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762			17550	protein-coding gene	gene with protein product		609898	"""kringle containing transmembrane protein"""	KREMEN		11267660	Standard	NM_001039570		Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.795G>A	22.37:g.29533499G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_001039570	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Silent	SNP	ENST00000407188.1	37	CCDS43000.2																																																																																			G|0.861;A|0.139	0.139	strong		0.622	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1		
KRT71	112802	hgsc.bcm.edu	37	12	52938364	52938364	+	Silent	SNP	T	T	C	rs2292507	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52938364T>C	ENST00000267119.5	-	9	1593	c.1524A>G	c.(1522-1524)ctA>ctG	p.L508L		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	508	Tail.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		AACCCTTCCCTAGGGTGTCTT	0.617													C|||	1639	0.327276	0.028	0.4712	5008	,	,		16109	0.5		0.507	False		,,,				2504	0.2669				p.L508L		Atlas-SNP	.											.	KRT71	70	.	0			c.A1524G						PASS	.	C		451,3955	784.4+/-414.7	32,387,1784	152.0	162.0	159.0		1524	3.3	0.4	12	dbSNP_100	159	4423,4177	567.7+/-388.9	1126,2171,1003	no	coding-synonymous	KRT71	NM_033448.2		1158,2558,2787	CC,CT,TT		48.5698,10.236,37.475		508/524	52938364	4874,8132	2203	4300	6503	SO:0001819	synonymous_variant	112802	exon9			CTTCCCTAGGGTG	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.1524A>G	12.37:g.52938364T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_033448	B3KVC1|Q3SY85|Q96DU2	Silent	SNP	ENST00000267119.5	37	CCDS8831.1																																																																																			T|0.620;C|0.380	0.380	strong		0.617	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448	
GLP1R	2740	hgsc.bcm.edu	37	6	39041502	39041502	+	Missense_Mutation	SNP	A	A	C	rs1042044	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:39041502A>C	ENST00000373256.4	+	7	823	c.780A>C	c.(778-780)ttA>ttC	p.L260F		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	260			L -> F (in dbSNP:rs1042044). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7843404, ECO:0000269|PubMed:8216285, ECO:0000269|PubMed:8404634, ECO:0000269|PubMed:8405712, ECO:0000269|Ref.7}.		activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)			breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	TCTCGGTCTTATCTGAGCAAT	0.577													C|||	2897	0.578474	0.5885	0.5937	5008	,	,		21418	0.5506		0.5626	False		,,,				2504	0.5992				p.L260F		Atlas-SNP	.											.	GLP1R	64	.	0			c.A780C						PASS	.	C	PHE/LEU	2557,1849	537.6+/-374.8	752,1053,398	168.0	140.0	150.0		780	3.9	1.0	6	dbSNP_86	150	4806,3794	537.8+/-383.3	1356,2094,850	yes	missense	GLP1R	NM_002062.3	22	2108,3147,1248	CC,CA,AA		44.1163,41.9655,43.3877	benign	260/464	39041502	7363,5643	2203	4300	6503	SO:0001583	missense	2740	exon7			GGTCTTATCTGAG		CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"""GPCR / Class B : Glucagon receptors"""	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.780A>C	6.37:g.39041502A>C	ENSP00000362353:p.Leu260Phe	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_002062	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	37	CCDS4839.1	1246	0.5705128205128205	310	0.6300813008130082	218	0.6022099447513812	299	0.5227272727272727	419	0.5527704485488126	C	0.350	-0.945358	0.02304	0.580345	0.558837	ENSG00000112164	ENST00000373256	T	0.41400	1.0	5.66	3.88	0.44766	GPCR, family 2-like (1);	0.088005	0.50627	N	0.000106	T	0.02455	0.0075	N	0.00317	-1.655	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.11329	0.006	T	0.42327	-0.9458	9	0.02654	T	1	.	6.3679	0.21465	0.134:0.6301:0.0:0.2358	rs1042044;rs3181520;rs17848969;rs52791180;rs61208251;rs1042044	260	P43220	GLP1R_HUMAN	F	260	ENSP00000362353:L260F	ENSP00000362353:L260F	L	+	3	2	GLP1R	39149480	1.000000	0.71417	0.967000	0.41034	0.378000	0.30076	0.906000	0.28517	0.766000	0.33244	-0.121000	0.15023	TTA	A|0.423;C|0.577;T|0.000	0.577	strong		0.577	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1		
ERICH6	131831	hgsc.bcm.edu	37	3	150421419	150421419	+	Silent	SNP	G	G	A	rs17281287	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:150421419G>A	ENST00000295910.6	-	1	319	c.267C>T	c.(265-267)gaC>gaT	p.D89D	RP11-103G8.2_ENST00000471093.1_RNA|RP11-103G8.2_ENST00000475393.1_RNA|FAM194A_ENST00000491361.1_Intron	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CTGGGAAGTCGTCGTCGTAGT	0.622													G|||	1618	0.323083	0.2179	0.4597	5008	,	,		13460	0.3591		0.4632	False		,,,				2504	0.1871				p.D89D		Atlas-SNP	.											FAM194A,NS,adenoma,0,1	FAM194A	91	1	0			c.C267T						PASS	.	G		1162,3244	409.5+/-335.0	152,858,1193	197.0	162.0	174.0		267	-4.4	0.0	3	dbSNP_123	174	4105,4495	562.1+/-387.9	985,2135,1180	no	coding-synonymous	FAM194A	NM_152394.3		1137,2993,2373	AA,AG,GG		47.7326,26.3731,40.4967		89/664	150421419	5267,7739	2203	4300	6503	SO:0001819	synonymous_variant	131831	exon1			GAAGTCGTCGTCG																												ENST00000295910.6:c.267C>T	3.37:g.150421419G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	152	81	0.532895	NM_152394		Silent	SNP	ENST00000295910.6	37	CCDS3151.2																																																																																			G|0.601;A|0.399	0.399	strong		0.622	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
USP36	57602	hgsc.bcm.edu	37	17	76799898	76799898	+	Silent	SNP	A	A	G	rs9302885	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76799898A>G	ENST00000542802.3	-	16	2822	c.2379T>C	c.(2377-2379)tcT>tcC	p.S793S	USP36_ENST00000312010.6_Silent_p.S793S|USP36_ENST00000449938.2_Intron			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	793					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			GGTGTGGAAGAGACACAAGGT	0.617													G|||	2836	0.566294	0.59	0.4914	5008	,	,		13946	0.6081		0.5477	False		,,,				2504	0.5634				p.S793S		Atlas-SNP	.											USP36_ENST00000312010,NS,carcinoma,0,2	USP36	243	2	0			c.T2379C						scavenged	.	G		2497,1893		735,1027,433	43.0	49.0	47.0		2379	4.3	0.1	17	dbSNP_119	47	4692,3874		1322,2048,913	no	coding-synonymous	USP36	NM_025090.3		2057,3075,1346	GG,GA,AA		45.2253,43.1207,44.5122		793/1124	76799898	7189,5767	2195	4283	6478	SO:0001819	synonymous_variant	57602	exon16			TGGAAGAGACACA	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2379T>C	17.37:g.76799898A>G		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	37	CCDS32755.1																																																																																			A|0.445;G|0.555	0.555	strong		0.617	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117779305	117779305	+	Missense_Mutation	SNP	C	C	A	rs80264810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:117779305C>A	ENST00000526090.1	-	9	1455	c.1304G>T	c.(1303-1305)cGc>cTc	p.R435L	TMPRSS13_ENST00000528626.1_Intron|TMPRSS13_ENST00000445164.2_Intron|TMPRSS13_ENST00000524993.1_Intron|TMPRSS13_ENST00000430170.2_Intron	NM_001206790.1	NP_001193719.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	0	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GGCAGGAGAGCGGGGAGTGCA	0.602													C|||	98	0.0195687	0.0023	0.0303	5008	,	,		15493	0.001		0.0547	False		,,,				2504	0.0184				p.R435L		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.G1304T						PASS	.	C	,,LEU/ARG	60,4008		0,60,1974	19.0	21.0	20.0		,,1304	-6.7	0.0	11	dbSNP_132	20	531,7773		20,491,3641	yes	intron,intron,missense	TMPRSS13	NM_001077263.2,NM_001206789.1,NM_001206790.1	,,102	20,551,5615	AA,AC,CC		6.3945,1.4749,4.7769	,,	,,435/492	117779305	591,11781	2034	4152	6186	SO:0001583	missense	84000	exon9			GGAGAGCGGGGAG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000526090.1:c.1304G>T	11.37:g.117779305C>A	ENSP00000436502:p.Arg435Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000526090.1	37	CCDS55789.1	61	0.027930402930402932	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	46	0.06068601583113457	C	4.101	0.016804	0.07959	0.014749	0.063945	ENSG00000137747	ENST00000526090	D	0.88896	-2.44	3.34	-6.69	0.01772	.	.	.	.	.	T	0.26846	0.0657	.	.	.	0.09310	N	1	B	0.17465	0.022	B	0.17722	0.019	T	0.51521	-0.8695	8	0.18276	T	0.48	.	3.6166	0.08079	0.1116:0.3185:0.4182:0.1516	.	430	Q9BYE2-4	.	L	435	ENSP00000436502:R435L	ENSP00000436502:R435L	R	-	2	0	TMPRSS13	117284515	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.386000	0.02537	-1.208000	0.02634	-0.463000	0.05309	CGC	C|0.971;A|0.029	0.029	strong		0.602	TMPRSS13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000392320.1	NM_032046	
CNTN3	5067	hgsc.bcm.edu	37	3	74344356	74344356	+	Silent	SNP	T	T	G	rs10490832	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:74344356T>G	ENST00000263665.6	-	18	2460	c.2433A>C	c.(2431-2433)gcA>gcC	p.A811A		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	811	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ATAGGCTATTTGCAGAGACTT	0.388													T|||	445	0.0888578	0.0068	0.0706	5008	,	,		18103	0.0288		0.1421	False		,,,				2504	0.2198				p.A811A		Atlas-SNP	.											.	CNTN3	174	.	0			c.A2433C						PASS	.	T		139,4267	98.0+/-136.7	4,131,2068	100.0	93.0	95.0		2433	-2.5	0.2	3	dbSNP_119	95	1410,7190	270.5+/-289.0	131,1148,3021	yes	coding-synonymous	CNTN3	NM_020872.1		135,1279,5089	GG,GT,TT		16.3953,3.1548,11.9099		811/1029	74344356	1549,11457	2203	4300	6503	SO:0001819	synonymous_variant	5067	exon18			GCTATTTGCAGAG	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.2433A>C	3.37:g.74344356T>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_020872	B9EK50|Q9H039	Silent	SNP	ENST00000263665.6	37	CCDS33790.1																																																																																			T|0.912;G|0.088	0.088	strong		0.388	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
OR2T3	343173	hgsc.bcm.edu	37	1	248637543	248637543	+	Missense_Mutation	SNP	C	C	T	rs139993642	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248637543C>T	ENST00000359594.2	+	1	917	c.892C>T	c.(892-894)Cgc>Tgc	p.R298C		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTACAGTCTCCGCAACAAAGA	0.488																																					p.R298C		Atlas-SNP	.											OR2T3,NS,carcinoma,-2,1	OR2T3	79	1	0			c.C892T						PASS	.	C	CYS/ARG	537,3867		11,515,1676	123.0	127.0	125.0		892	-0.6	0.2	1	dbSNP_134	125	673,7913		0,673,3620	no	missense	OR2T3	NM_001005495.1	180	11,1188,5296	TT,TC,CC		7.8383,12.1935,9.3149	probably-damaging	298/319	248637543	1210,11780	2202	4293	6495	SO:0001583	missense	343173	exon1			AGTCTCCGCAACA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.892C>T	1.37:g.248637543C>T	ENSP00000352604:p.Arg298Cys	Somatic	1087	0	0		WXS	Illumina HiSeq	Phase_I	1264	300	0.237342	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	626	0.2866300366300366	125	0.2540650406504065	93	0.2569060773480663	233	0.40734265734265734	175	0.23087071240105542	c	13.85	2.361258	0.41801	0.121935	0.078383	ENSG00000196539	ENST00000359594	T	0.40476	1.03	2.37	-0.64	0.11493	.	.	.	.	.	T	0.00012	0.0000	M	0.77820	2.39	0.36159	P	0.15204600000000001	D	0.89917	1.0	D	0.74348	0.983	T	0.32771	-0.9894	8	0.72032	D	0.01	.	7.4986	0.27505	0.5605:0.4394:0.0:0.0	.	298	Q8NH03	OR2T3_HUMAN	C	298	ENSP00000352604:R298C	ENSP00000352604:R298C	R	+	1	0	OR2T3	246704166	0.005000	0.15991	0.198000	0.23420	0.152000	0.21847	0.085000	0.14912	-0.543000	0.06240	0.186000	0.17326	CGC	C|0.500;T|0.500	0.500	strong		0.488	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
TRPV1	7442	hgsc.bcm.edu	37	17	3480447	3480447	+	Missense_Mutation	SNP	T	T	C	rs8065080	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3480447T>C	ENST00000571088.1	-	12	1966	c.1753A>G	c.(1753-1755)Atc>Gtc	p.I585V	TRPV1_ENST00000174621.6_Missense_Mutation_p.I583V|RP11-235E17.3_ENST00000573568.1_RNA|TRPV1_ENST00000425167.2_Missense_Mutation_p.I596V|TRPV1_ENST00000576351.1_Missense_Mutation_p.I575V|TRPV1_ENST00000399756.4_Missense_Mutation_p.I585V|SHPK_ENST00000572705.1_Missense_Mutation_p.I585V|TRPV1_ENST00000310522.5_Missense_Mutation_p.I525V|TRPV1_ENST00000399759.3_Missense_Mutation_p.I585V	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	585			I -> V (in dbSNP:rs8065080). {ECO:0000269|PubMed:11050376}.		calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	AAGAAGACGATGTAGACAAAC	0.582													C|||	1591	0.317692	0.1067	0.3343	5008	,	,		18230	0.5883		0.4085	False		,,,				2504	0.2188				p.I585V	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.A1753G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	616,3428		48,520,1454	43.0	42.0	42.0		1753,1753,1753,1753	-1.9	0.0	17	dbSNP_116	42	3103,5237		579,1945,1646	yes	missense,missense,missense,missense	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	29,29,29,29	627,2465,3100	CC,CT,TT		37.2062,15.2324,30.0307	benign,benign,benign,benign	585/840,585/840,585/840,585/840	3480447	3719,8665	2022	4170	6192	SO:0001583	missense	7442	exon12			AGACGATGTAGAC	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1753A>G	17.37:g.3480447T>C	ENSP00000461007:p.Ile585Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	37	CCDS45576.1	851	0.38965201465201466	54	0.10975609756097561	140	0.3867403314917127	341	0.5961538461538461	316	0.41688654353562005	C	1.501	-0.552161	0.03996	0.152324	0.372062	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	5.14	-1.93	0.07594	Ion transport (1);	0.755076	0.13129	N	0.411637	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B	0.09022	0.0;0.002;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.47169	-0.9138	9	0.36615	T	0.2	-6.2838	10.1969	0.43060	0.0:0.2668:0.2895:0.4437	rs8065080;rs57404253;rs8065080	585;583;525;596	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	V	585;585;583;596;525	ENSP00000382661:I585V;ENSP00000382659:I585V;ENSP00000174621:I583V;ENSP00000409627:I596V;ENSP00000311692:I525V	ENSP00000174621:I583V	I	-	1	0	TRPV1	3427196	0.195000	0.23338	0.017000	0.16124	0.004000	0.04260	-0.245000	0.08890	-0.324000	0.08589	-2.015000	0.00435	ATC	T|0.625;C|0.375	0.375	strong		0.582	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
ZXDC	79364	hgsc.bcm.edu	37	3	126194076	126194076	+	Silent	SNP	T	T	C	rs812367	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126194076T>C	ENST00000389709.3	-	1	686	c.633A>G	c.(631-633)ccA>ccG	p.P211P	ZXDC_ENST00000336332.5_Silent_p.P211P	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	211					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		AGCCCTCCAGTGGGCACTTGA	0.682													C|||	2741	0.547324	0.2753	0.5749	5008	,	,		11019	0.5724		0.673	False		,,,				2504	0.7403				p.P211P		Atlas-SNP	.											.	ZXDC	87	.	0			c.A633G						PASS	.	C	,	1522,2592		316,890,851	11.0	13.0	13.0		633,633	-2.2	1.0	3	dbSNP_86	13	5693,2645		2000,1693,476	no	coding-synonymous,coding-synonymous	ZXDC	NM_001040653.2,NM_025112.4	,	2316,2583,1327	CC,CT,TT		31.7222,36.9956,42.0575	,	211/711,211/859	126194076	7215,5237	2057	4169	6226	SO:0001819	synonymous_variant	79364	exon1			CTCCAGTGGGCAC	AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"""Zinc fingers, C2H2-type"""	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.633A>G	3.37:g.126194076T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Silent	SNP	ENST00000389709.3	37	CCDS43145.1																																																																																			T|0.442;C|0.558	0.558	strong		0.682	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112	
GPATCH8	23131	hgsc.bcm.edu	37	17	42475983	42475983	+	Silent	SNP	G	G	C	rs936019	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42475983G>C	ENST00000591680.1	-	8	3492	c.3462C>G	c.(3460-3462)acC>acG	p.T1154T	GPATCH8_ENST00000434000.1_Silent_p.T1076T	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1154							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		TGGGCTTTCGGGTAGCTGGGA	0.562													G|||	2462	0.491613	0.4009	0.5937	5008	,	,		18050	0.497		0.6014	False		,,,				2504	0.4233				p.T1154T		Atlas-SNP	.											GPATCH8,NS,adenoma,0,1	GPATCH8	114	1	0			c.C3462G						scavenged	.	G		1816,2588	505.6+/-366.2	383,1050,769	134.0	140.0	138.0		3462	1.7	1.0	17	dbSNP_86	138	5354,3246	638.5+/-399.3	1659,2036,605	no	coding-synonymous	GPATCH8	NM_001002909.2		2042,3086,1374	CC,CG,GG		37.7442,41.2352,44.8631		1154/1503	42475983	7170,5834	2202	4300	6502	SO:0001819	synonymous_variant	23131	exon8			CTTTCGGGTAGCT	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.3462C>G	17.37:g.42475983G>C		Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_001002909	B9EGP9|O60300|Q8TB99	Silent	SNP	ENST00000591680.1	37	CCDS32666.1																																																																																			G|0.435;C|0.565	0.565	strong		0.562	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
KLB	152831	hgsc.bcm.edu	37	4	39450229	39450229	+	Missense_Mutation	SNP	C	C	A	rs4975017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:39450229C>A	ENST00000257408.4	+	5	3155	c.3058C>A	c.(3058-3060)Cag>Aag	p.Q1020K		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	1020			Q -> K (in dbSNP:rs4975017).		carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						TTTTCAAAGGCAGAAGAGAAG	0.388													C|||	1644	0.328275	0.118	0.402	5008	,	,		22119	0.3819		0.3201	False		,,,				2504	0.5133				p.Q1020K		Atlas-SNP	.											.	KLB	95	.	0			c.C3058A						PASS	.	C	LYS/GLN	684,3722	285.7+/-278.4	54,576,1573	107.0	102.0	104.0		3058	2.8	0.0	4	dbSNP_111	104	2792,5808	436.5+/-358.3	441,1910,1949	yes	missense	KLB	NM_175737.3	53	495,2486,3522	AA,AC,CC		32.4651,15.5243,26.7261	benign	1020/1045	39450229	3476,9530	2203	4300	6503	SO:0001583	missense	152831	exon5			CAAAGGCAGAAGA	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.3058C>A	4.37:g.39450229C>A	ENSP00000257408:p.Gln1020Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	37	CCDS3451.1	713	0.32646520146520147	57	0.11585365853658537	150	0.4143646408839779	243	0.42482517482517484	263	0.3469656992084433	C	0.005	-2.212627	0.00289	0.155243	0.324651	ENSG00000134962	ENST00000257408	T	0.25250	1.81	5.78	2.81	0.32909	.	0.900332	0.09745	N	0.761361	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.20887	0.049;0.049	B;B	0.14023	0.01;0.01	T	0.46816	-0.9164	9	0.02654	T	1	-0.5786	5.2329	0.15432	0.4452:0.385:0.0:0.1697	rs4975017;rs17584864;rs52837022;rs60465305;rs4975017	1011;1020	B7ZL50;Q86Z14	.;KLOTB_HUMAN	K	1020	ENSP00000257408:Q1020K	ENSP00000257408:Q1020K	Q	+	1	0	KLB	39126624	1.000000	0.71417	0.015000	0.15790	0.104000	0.19210	1.848000	0.39309	0.786000	0.33708	0.313000	0.20887	CAG	C|0.717;A|0.282	0.282	strong		0.388	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737	
MOGAT1	116255	hgsc.bcm.edu	37	2	223559089	223559089	+	Missense_Mutation	SNP	T	T	C	rs1868024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:223559089T>C	ENST00000446656.3	+	4	487	c.487T>C	c.(487-489)Tca>Cca	p.S163P		NM_058165.2	NP_477513.2	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	163			S -> P (in dbSNP:rs1868024).		diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)			breast(1)|cervix(1)|endometrium(1)|lung(5)|urinary_tract(1)	9		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)		AGGGCTGGTTTCAGTTTCCAA	0.358													T|||	1151	0.229832	0.3654	0.2349	5008	,	,		19517	0.1161		0.2336	False		,,,				2504	0.1564				p.S163P	Ovarian(93;205 1446 2385 11581 25911)	Atlas-SNP	.											.	MOGAT1	47	.	0			c.T487C						PASS	.	T	PRO/SER	1281,2449		236,809,820	64.0	65.0	65.0		487	3.0	1.0	2	dbSNP_92	65	1786,6392		202,1382,2505	yes	missense	MOGAT1	NM_058165.2	74	438,2191,3325	CC,CT,TT		21.8391,34.3432,25.7558	benign	163/336	223559089	3067,8841	1865	4089	5954	SO:0001583	missense	116255	exon4			CTGGTTTCAGTTT	AF384163	CCDS46524.1	2q36.2	2006-10-06	2004-05-28	2004-05-28	ENSG00000124003	ENSG00000124003			18210	protein-coding gene	gene with protein product		610268	"""diacylglycerol O-acyltransferase 2 like 1"""	DGAT2L1		14970677	Standard	NM_058165		Approved	DGAT2L, MGAT1	uc010fws.1	Q96PD6	OTTHUMG00000153394	ENST00000446656.3:c.487T>C	2.37:g.223559089T>C	ENSP00000406674:p.Ser163Pro	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_058165	Q6IEE5	Missense_Mutation	SNP	ENST00000446656.3	37	CCDS46524.1	494	0.2261904761904762	165	0.3353658536585366	94	0.2596685082872928	65	0.11363636363636363	170	0.22427440633245382	T	0.052	-1.247371	0.01481	0.343432	0.218391	ENSG00000124003	ENST00000446656	D	0.91894	-2.93	5.42	2.96	0.34315	.	0.086801	0.49916	D	0.000132	T	0.00012	0.0000	L	0.33710	1.025	0.20873	P	0.999830245	B	0.17465	0.022	B	0.29598	0.104	T	0.03433	-1.1037	9	0.23891	T	0.37	-7.6214	7.6937	0.28581	0.1246:0.0686:0.0:0.8067	rs1868024;rs17507996;rs52814175;rs61034242;rs1868024	163	Q96PD6	MOGT1_HUMAN	P	163	ENSP00000406674:S163P	ENSP00000406674:S163P	S	+	1	0	MOGAT1	223267333	1.000000	0.71417	0.985000	0.45067	0.321000	0.28281	2.651000	0.46674	1.049000	0.40321	0.523000	0.50628	TCA	C|0.221;N|0.001	0.221	strong		0.358	MOGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331010.3	NM_058165	
COL11A1	1301	hgsc.bcm.edu	37	1	103379918	103379918	+	Missense_Mutation	SNP	G	G	A	rs3753841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:103379918G>A	ENST00000370096.3	-	52	4280	c.3968C>T	c.(3967-3969)cCt>cTt	p.P1323L	COL11A1_ENST00000512756.1_Missense_Mutation_p.P1207L|COL11A1_ENST00000358392.2_Missense_Mutation_p.P1335L|COL11A1_ENST00000353414.4_Missense_Mutation_p.P1284L	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1323	Triple-helical region.		P -> L (in dbSNP:rs3753841). {ECO:0000269|PubMed:10486316, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1690726}.		cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TGCAGGGCCAGGTTCCCCAGG	0.318													G|||	2487	0.496605	0.0492	0.755	5008	,	,		14366	0.7034		0.6123	False		,,,				2504	0.5859				p.P1335L		Atlas-SNP	.											.	COL11A1	972	.	0			c.C4004T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	615,3791	245.0+/-254.1	51,513,1639	33.0	34.0	34.0		3851,3968,4004,3620	5.8	1.0	1	dbSNP_107	34	5260,3340	623.3+/-397.4	1623,2014,663	yes	missense,missense,missense,missense	COL11A1	NM_001190709.1,NM_001854.3,NM_080629.2,NM_080630.3	98,98,98,98	1674,2527,2302	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	38.8372,13.9582,45.1715	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1284/1768,1323/1807,1335/1819,1207/1691	103379918	5875,7131	2203	4300	6503	SO:0001583	missense	1301	exon52			GGGCCAGGTTCCC	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3968C>T	1.37:g.103379918G>A	ENSP00000359114:p.Pro1323Leu	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	1163	0.5325091575091575	29	0.05894308943089431	266	0.7348066298342542	406	0.7097902097902098	462	0.6094986807387863	G	21.2	4.107244	0.77096	0.139582	0.611628	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.96685	-4.09;-4.09;-4.09;-4.09	5.75	5.75	0.90469	.	0.058834	0.64402	D	0.000001	D	0.97417	0.9155	M	0.85373	2.75	0.09310	P	0.999999999630763	B;B;P;B;B	0.50443	0.104;0.073;0.935;0.044;0.167	B;B;P;B;B	0.53006	0.024;0.053;0.715;0.024;0.053	D	0.96950	0.9694	9	0.49607	T	0.09	.	19.9598	0.97242	0.0:0.0:1.0:0.0	rs3753841;rs17446207;rs52824780;rs59687016;rs3753841	1207;1284;1335;1323;543	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	L	1323;1335;1284;543;1207	ENSP00000359114:P1323L;ENSP00000351163:P1335L;ENSP00000302551:P1284L;ENSP00000426533:P1207L	ENSP00000302551:P1284L	P	-	2	0	COL11A1	103152506	1.000000	0.71417	0.991000	0.47740	0.996000	0.88848	9.365000	0.97139	2.716000	0.92895	0.655000	0.94253	CCT	G|0.517;A|0.483	0.483	strong		0.318	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
ZNF208	7757	hgsc.bcm.edu	37	19	22156482	22156482	+	Missense_Mutation	SNP	G	G	T	rs12975751	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:22156482G>T	ENST00000397126.4	-	4	1502	c.1354C>A	c.(1354-1356)Ccc>Acc	p.P452T	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	452					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				CATTTGTAGGGTGTCTCTCCA	0.378													g|||	1500	0.299521	0.1014	0.3948	5008	,	,		21461	0.504		0.4553	False		,,,				2504	0.1288				p.P452T		Atlas-SNP	.											.	ZNF208	817	.	0			c.C1354A						PASS	.	G	THR/PRO	660,3628		43,574,1527	79.0	87.0	84.0		1354	-1.3	0.0	19	dbSNP_121	84	3523,4999		715,2093,1453	no	missense	ZNF208	NM_007153.3	38	758,2667,2980	TT,TG,GG		41.3401,15.3918,32.6542	probably-damaging	452/1281	22156482	4183,8627	2144	4261	6405	SO:0001583	missense	7757	exon4			TGTAGGGTGTCTC	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1354C>A	19.37:g.22156482G>T	ENSP00000380315:p.Pro452Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	830	0.38003663003663	53	0.10772357723577236	132	0.36464088397790057	292	0.5104895104895105	353	0.4656992084432718	G	12.04	1.819574	0.32145	0.153918	0.413401	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.28895	1.59	2.83	-1.26	0.09376	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	D	0.54047	0.964	D	0.63381	0.914	T	0.44345	-0.9334	7	0.62326	D	0.03	.	4.155	0.10256	0.2256:0.0:0.5945:0.1799	rs12975751;rs60247420	452	O43345	ZN208_HUMAN	T	452	ENSP00000380315:P452T	ENSP00000380315:P452T	P	-	1	0	ZNF208	21948322	0.203000	0.23435	0.001000	0.08648	0.002000	0.02628	1.383000	0.34385	-0.684000	0.05183	-0.667000	0.03836	CCC	G|0.624;T|0.376	0.376	strong		0.378	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
ADA	100	hgsc.bcm.edu	37	20	43252915	43252915	+	Silent	SNP	T	T	C	rs244076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43252915T>C	ENST00000372874.4	-	6	668	c.534A>G	c.(532-534)gtA>gtG	p.V178V	ADA_ENST00000464097.1_5'UTR|ADA_ENST00000537820.1_Silent_p.V178V	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	178					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	GGTCAATGGCTACCACGGTCT	0.597									Adenosine Deaminase Deficiency				C|||	1331	0.265775	0.4735	0.1585	5008	,	,		19918	0.1548		0.1829	False		,,,				2504	0.2607				p.V178V		Atlas-SNP	.											.	ADA	42	.	0			c.A534G						PASS	.	C		1770,2636	642.7+/-397.7	340,1090,773	103.0	83.0	90.0		534	3.5	1.0	20	dbSNP_79	90	1463,7137	750.6+/-407.4	122,1219,2959	yes	coding-synonymous	ADA	NM_000022.2		462,2309,3732	CC,CT,TT		17.0116,40.1725,24.8578		178/364	43252915	3233,9773	2203	4300	6503	SO:0001819	synonymous_variant	100	exon6	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	AATGGCTACCACG	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.534A>G	20.37:g.43252915T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_000022	Q53F92|Q6LA59	Silent	SNP	ENST00000372874.4	37	CCDS13335.1																																																																																			T|0.751;C|0.249	0.249	strong		0.597	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
WDR1	9948	hgsc.bcm.edu	37	4	10099340	10099340	+	Missense_Mutation	SNP	T	T	C	rs13441	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:10099340T>C	ENST00000499869.2	-	5	746	c.553A>G	c.(553-555)Att>Gtt	p.I185V	WDR1_ENST00000382451.2_Intron|WDR1_ENST00000502702.1_Intron|WDR1_ENST00000382452.2_Missense_Mutation_p.I185V			O75083	WDR1_HUMAN	WD repeat domain 1	185			I -> V (in dbSNP:rs13441). {ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CTTACGCCAATTGTGAACTTG	0.512													T|||	2881	0.57528	0.3941	0.7147	5008	,	,		20083	0.6538		0.7097	False		,,,				2504	0.502				p.I185V		Atlas-SNP	.											.	WDR1	93	.	0			c.A553G						PASS	.	T	,VAL/ILE	1813,2119		434,945,587	64.0	68.0	67.0		,553	4.3	0.7	4	dbSNP_52	67	5804,2484		2040,1724,380	yes	intron,missense	WDR1	NM_005112.4,NM_017491.3	,29	2474,2669,967	CC,CT,TT		29.971,46.1089,37.6678	,benign	,185/607	10099340	7617,4603	1966	4144	6110	SO:0001583	missense	9948	exon5			CGCCAATTGTGAA	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"""WD repeat domain containing"""	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.553A>G	4.37:g.10099340T>C	ENSP00000427687:p.Ile185Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	99	58	0.585859	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Missense_Mutation	SNP	ENST00000499869.2	37	CCDS54740.1	1347	0.6167582417582418	198	0.4024390243902439	266	0.7348066298342542	356	0.6223776223776224	527	0.6952506596306068	T	9.102	1.004302	0.19199	0.461089	0.70029	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000508079	T;T;T	0.60299	0.2;0.2;0.2	5.56	4.35	0.52113	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.258408	0.32785	N	0.005649	T	0.00012	0.0000	N	0.20845	0.615	0.47094	P	6.850000000000467E-4	B	0.16802	0.019	B	0.19666	0.026	T	0.35699	-0.9778	9	0.36615	T	0.2	-12.9695	10.3924	0.44181	0.0:0.0:0.3423:0.6577	rs13441;rs1131629;rs2241481;rs3191683;rs17844834;rs17857545;rs52825858;rs13441	185	O75083	WDR1_HUMAN	V	185;185;189	ENSP00000427687:I185V;ENSP00000371890:I185V;ENSP00000425481:I189V	ENSP00000371890:I185V	I	-	1	0	WDR1	9708438	0.871000	0.30034	0.741000	0.31004	0.736000	0.42039	1.162000	0.31786	0.917000	0.36895	0.460000	0.39030	ATT	T|0.401;C|0.599	0.599	strong		0.512	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1		
HRG	3273	hgsc.bcm.edu	37	3	186390627	186390627	+	Missense_Mutation	SNP	C	C	T	rs9898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186390627C>T	ENST00000232003.4	+	5	690	c.610C>T	c.(610-612)Ccc>Tcc	p.P204S		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	204	Cystatin 2.		P -> S (in dbSNP:rs9898).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GCGGAACTGCCCCAGACACCA	0.443													T|||	2461	0.491414	0.6278	0.3977	5008	,	,		17738	0.5724		0.327	False		,,,				2504	0.4591				p.P204S		Atlas-SNP	.											HRG,NS,adenoma,0,1	HRG	81	1	0			c.C610T						PASS	.	T	SER/PRO	2615,1791	528.1+/-372.3	781,1053,369	97.0	94.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	610	4.3	1.0	3	dbSNP_52	95	2945,5655	668.1+/-402.5	523,1899,1878	yes	missense	HRG	NM_000412.2	74	1304,2952,2247	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	34.2442,40.6491,42.7495	benign	204/526	186390627	5560,7446	2203	4300	6503	SO:0001583	missense	3273	exon5			AACTGCCCCAGAC		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.610C>T	3.37:g.186390627C>T	ENSP00000232003:p.Pro204Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	139	74	0.532374	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	1012	0.4633699633699634	309	0.6280487804878049	153	0.42265193370165743	308	0.5384615384615384	242	0.31926121372031663	T	0.012	-1.670189	0.00758	0.593509	0.342442	ENSG00000113905	ENST00000232003	T	0.12879	2.64	4.35	4.35	0.52113	Proteinase inhibitor I25, cystatin (1);	0.000000	0.42294	N	0.000735	T	0.00012	0.0000	N	0.00170	-1.935	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41466	-0.9507	9	0.02654	T	1	-16.0271	7.2132	0.25945	0.0:0.1061:0.0:0.8939	rs9898;rs1042439;rs1468076;rs3181917;rs3733013;rs52820836;rs58677142;rs9898	204	P04196	HRG_HUMAN	S	204	ENSP00000232003:P204S	ENSP00000232003:P204S	P	+	1	0	HRG	187873321	0.993000	0.37304	0.977000	0.42913	0.017000	0.09413	2.157000	0.42320	0.779000	0.33543	-0.361000	0.07541	CCC	C|0.544;T|0.456	0.456	strong		0.443	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
DOPEY2	9980	hgsc.bcm.edu	37	21	37584331	37584331	+	Silent	SNP	C	C	T	rs147659226	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:37584331C>T	ENST00000399151.3	+	7	925	c.840C>T	c.(838-840)gcC>gcT	p.A280A	RN7SL73P_ENST00000585239.1_RNA|DOPEY2_ENST00000492760.1_3'UTR	NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	280					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TTCTCTCAGCCGCCACCCAGA	0.468													c|||	8	0.00159744	0.0045	0.0029	5008	,	,		20397	0.0		0.0	False		,,,				2504	0.0				p.A280A		Atlas-SNP	.											DOPEY2,NS,carcinoma,+2,1	DOPEY2	184	1	0			c.C840T						scavenged	.	T		14,4392	21.2+/-45.6	0,14,2189	101.0	89.0	93.0		840	-10.2	0.0	21	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DOPEY2	NM_005128.2		0,15,6488	TT,TC,CC		0.0116,0.3177,0.1153		280/2299	37584331	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	9980	exon7			CTCAGCCGCCACC	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.840C>T	21.37:g.37584331C>T		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	37	CCDS13643.1																																																																																			C|0.999;T|0.001	0.001	strong		0.468	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
PLG	5340	hgsc.bcm.edu	37	6	161137779	161137779	+	Silent	SNP	T	T	C	rs14224	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:161137779T>C	ENST00000308192.9	+	7	834	c.771T>C	c.(769-771)tgT>tgC	p.C257C		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	257	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	GGGAACTTTGTGACATCCCCC	0.502													C|||	2253	0.44988	0.5537	0.3329	5008	,	,		18453	0.4563		0.3976	False		,,,				2504	0.4397				p.C257C		Atlas-SNP	.											.	PLG	150	.	0			c.T771C						PASS	.	C		2301,2105	575.2+/-383.9	590,1121,492	66.0	62.0	64.0		771	-6.8	0.4	6	dbSNP_52	64	3595,5005	626.7+/-397.9	759,2077,1464	no	coding-synonymous	PLG	NM_000301.3		1349,3198,1956	CC,CT,TT		41.8023,47.7758,45.3329		257/811	161137779	5896,7110	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon7			ACTTTGTGACATC	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.771T>C	6.37:g.161137779T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	29	0.329545	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			T|0.540;C|0.460	0.460	strong		0.502	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
TRIM49B	283116	hgsc.bcm.edu	37	11	49053390	49053390	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49053390T>C	ENST00000332682.7	+	2	267	c.239T>C	c.(238-240)gTc>gCc	p.V80A		NM_001206626.1	NP_001193555.1	A6NDI0	TR49B_HUMAN	tripartite motif containing 49B	80						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			lung(8)	8						GCTAGAAAAGTCAGTCTCTGG	0.458																																					p.V80A		Atlas-SNP	.											TRIM49B,NS,NS,-1,1	TRIM49B	27	1	0			c.T239C						scavenged	.																																			SO:0001583	missense	283116	exon1			GAAAAGTCAGTCT		CCDS55762.1	11p11.12	2014-02-17			ENSG00000182053	ENSG00000182053		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	42955	protein-coding gene	gene with protein product							Standard	NM_001206626		Approved		uc021qix.1	A6NDI0		ENST00000332682.7:c.239T>C	11.37:g.49053390T>C	ENSP00000330216:p.Val80Ala	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	303	5	0.0165017	NM_001206626		Missense_Mutation	SNP	ENST00000332682.7	37	CCDS55762.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.970469	0.00048	.	.	ENSG00000182053	ENST00000332682	D	0.84516	-1.86	0.49	-0.979	0.10276	.	.	.	.	.	T	0.62258	0.2413	N	0.08118	0	0.09310	N	0.999994	.	.	.	.	.	.	T	0.43327	-0.9398	7	0.09590	T	0.72	.	3.3156	0.07032	0.0:0.4841:0.2642:0.2517	.	.	.	.	A	80	ENSP00000330216:V80A	ENSP00000330216:V80A	V	+	2	0	AC084851.1	49009966	0.001000	0.12720	0.043000	0.18650	0.016000	0.09150	0.032000	0.13732	-1.832000	0.01196	-1.194000	0.01681	GTC	.	.	none		0.458	TRIM49B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
KCTD17	79734	hgsc.bcm.edu	37	22	37458586	37458586	+	Silent	SNP	C	C	T	rs116956945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:37458586C>T	ENST00000403888.3	+	9	919	c.918C>T	c.(916-918)ccC>ccT	p.P306P	KCTD17_ENST00000402077.3_Silent_p.P282P	NM_001282684.1	NP_001269613.1	Q8N5Z5	KCD17_HUMAN	potassium channel tetramerization domain containing 17	306	Pro-rich.				protein homooligomerization (GO:0051260)		identical protein binding (GO:0042802)			NS(1)|breast(1)|endometrium(1)|lung(1)|prostate(1)	5						CAGAGGCACCCGGATGTGAGG	0.587													C|||	106	0.0211661	0.0045	0.0259	5008	,	,		12259	0.001		0.0447	False		,,,				2504	0.0368				p.P282P		Atlas-SNP	.											KCTD17,NS,carcinoma,0,1	KCTD17	17	1	0			c.C846T						PASS	.	C		42,4364	44.6+/-78.6	0,42,2161	55.0	56.0	55.0		846	1.5	1.0	22	dbSNP_132	55	472,8128	134.3+/-191.7	15,442,3843	no	coding-synonymous	KCTD17	NM_024681.2		15,484,6004	TT,TC,CC		5.4884,0.9532,3.952		282/298	37458586	514,12492	2203	4300	6503	SO:0001819	synonymous_variant	79734	exon8			GGCACCCGGATGT	BC025403	CCDS13940.2, CCDS74854.1, CCDS74855.1	22q12.3	2013-06-20	2013-06-20		ENSG00000100379	ENSG00000100379			25705	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 17"""			12477932	Standard	XM_005261741		Approved	FLJ12242	uc011amv.2	Q8N5Z5	OTTHUMG00000150532	ENST00000403888.3:c.918C>T	22.37:g.37458586C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	81	29	0.358025	NM_024681	B0QYA9|B0QYB0|O95517	Silent	SNP	ENST00000403888.3	37																																																																																				C|0.965;T|0.035	0.035	strong		0.587	KCTD17-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318781.1	NM_024681	
LARS	51520	hgsc.bcm.edu	37	5	145499996	145499996	+	Missense_Mutation	SNP	C	C	T	rs10988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145499996C>T	ENST00000394434.2	-	31	3429	c.3263G>A	c.(3262-3264)aGg>aAg	p.R1088K	LARS_ENST00000545646.1_Missense_Mutation_p.R1042K|LARS_ENST00000274562.9_Missense_Mutation_p.R1061K|LARS_ENST00000510191.1_Missense_Mutation_p.R1034K|RP11-118M9.3_ENST00000514002.1_RNA	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	1088			R -> K (in dbSNP:rs10988). {ECO:0000269|Ref.1}.		gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.R1088K(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	ATCTCCTTGCCTGATTTCAAT	0.403													C|||	926	0.184904	0.0189	0.3775	5008	,	,		19608	0.1984		0.2535	False		,,,				2504	0.1881				p.R1088K		Atlas-SNP	.											LARS,NS,carcinoma,0,1	LARS	100	1	1	Substitution - Missense(1)	stomach(1)	c.G3263A						PASS	.	C	LYS/ARG	299,4107	161.8+/-193.9	15,269,1919	134.0	129.0	131.0		3263	4.5	1.0	5	dbSNP_52	131	2397,6203	398.2+/-346.0	352,1693,2255	yes	missense	LARS	NM_020117.9	26	367,1962,4174	TT,TC,CC		27.8721,6.7862,20.7289	benign	1088/1177	145499996	2696,10310	2203	4300	6503	SO:0001583	missense	51520	exon31			CCTTGCCTGATTT	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.3263G>A	5.37:g.145499996C>T	ENSP00000377954:p.Arg1088Lys	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	150	41	0.273333	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	ENST00000394434.2	37	CCDS34265.1	438	0.20054945054945056	20	0.04065040650406504	110	0.30386740331491713	117	0.20454545454545456	191	0.2519788918205805	C	15.39	2.819804	0.50633	0.067862	0.278721	ENSG00000133706	ENST00000394434;ENST00000545646;ENST00000540713;ENST00000510191;ENST00000274562	T;T;T;T	0.62788	0.0;-0.0;0.0;-0.0	5.32	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.63428	1.95	0.19300	P	0.9999771666	B;B;B	0.22683	0.016;0.002;0.073	B;B;B	0.23275	0.012;0.006;0.045	T	0.09684	-1.0663	9	0.28530	T	0.3	.	14.3862	0.66947	0.0:0.9285:0.0:0.0715	rs10988;rs3183233;rs3763369;rs17426951;rs52800413;rs58213459;rs10988	1061;1042;1088	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	K	1088;1042;397;1034;1061	ENSP00000377954:R1088K;ENSP00000437791:R1042K;ENSP00000426005:R1034K;ENSP00000274562:R1061K	ENSP00000274562:R1061K	R	-	2	0	LARS	145480189	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.941000	0.63540	1.371000	0.46172	0.650000	0.86243	AGG	C|0.802;N|0.000	.	strong		0.403	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
IL37	27178	hgsc.bcm.edu	37	2	113671378	113671378	+	Missense_Mutation	SNP	G	G	T	rs3811046	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113671378G>T	ENST00000263326.3	+	2	134	c.92G>T	c.(91-93)gGa>gTa	p.G31V	IL37_ENST00000349806.3_Intron|IL37_ENST00000353225.3_Missense_Mutation_p.G31V|IL37_ENST00000352179.3_Intron|IL37_ENST00000311328.2_5'Flank	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	31			G -> V (in dbSNP:rs3811046). {ECO:0000269|PubMed:11145836, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						GACCCGGCTGGAAGCCCCCTG	0.537													g|||	3005	0.60004	0.1755	0.7997	5008	,	,		13804	0.8115		0.6998	False		,,,				2504	0.7117				p.G31V		Atlas-SNP	.											.	IL37	56	.	0			c.G92T						PASS	.		VAL/GLY,,,VAL/GLY	1234,3172	424.2+/-340.4	192,850,1161	102.0	91.0	95.0		92,,,92	1.9	0.0	2	dbSNP_107	95	6080,2520	692.4+/-404.6	2154,1772,374	yes	missense,intron,intron,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1	109,,,109	2346,2622,1535	TT,TG,GG		29.3023,28.0073,43.7644	possibly-damaging,,,possibly-damaging	31/219,,,31/179	113671378	7314,5692	2203	4300	6503	SO:0001583	missense	27178	exon2			CGGCTGGAAGCCC	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"""Interleukins and interleukin receptors"""	15563	protein-coding gene	gene with protein product	"""interleukin 1, zeta"", ""interleukin-1 homolog 4"", ""interleukin-1-related protein"""	605510	"""interleukin 1 family, member 7 (zeta)"""	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.92G>T	2.37:g.113671378G>T	ENSP00000263326:p.Gly31Val	Somatic	378	0	0		WXS	Illumina HiSeq	Phase_I	305	299	0.980328	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	1386	0.6346153846153846	103	0.20934959349593496	287	0.7928176795580111	466	0.8146853146853147	530	0.6992084432717678	g	6.398	0.441596	0.12164	0.280073	0.706977	ENSG00000125571	ENST00000263326;ENST00000353225	T;T	0.59772	0.24;0.24	2.78	1.89	0.25635	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	P;P	0.49185	0.92;0.87	P;P	0.55391	0.775;0.601	T	0.43228	-0.9404	8	0.07325	T	0.83	-2.6833	5.5971	0.17333	0.155:0.0:0.845:0.0	rs3811046;rs52811134;rs3811046	31;31	Q9NZH6-3;Q9NZH6	.;IL37_HUMAN	V	31	ENSP00000263326:G31V;ENSP00000309208:G31V	ENSP00000263326:G31V	G	+	2	0	IL37	113387849	0.016000	0.18221	0.002000	0.10522	0.024000	0.10985	1.500000	0.35682	0.749000	0.32854	0.552000	0.68991	GGA	G|0.425;T|0.575	0.575	strong		0.537	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439	
TNFSF12	8742	hgsc.bcm.edu	37	17	7453505	7453505	+	Silent	SNP	C	C	A	rs62059804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7453505C>A	ENST00000293825.6	+	3	539	c.276C>A	c.(274-276)cgC>cgA	p.R92R	TNFSF12_ENST00000557233.1_Silent_p.R92R|TNFSF12-TNFSF13_ENST00000293826.4_Silent_p.R92R|TNFSF12_ENST00000462811.1_3'UTR	NM_003809.2	NP_003800.1	O43508	TNF12_HUMAN	tumor necrosis factor (ligand) superfamily, member 12	92					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|endothelial cell migration (GO:0043542)|immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|prostate(2)	11		Prostate(122;0.157)				TTCGGCCTCGCAGAAGTGGTG	0.542													C|||	612	0.122204	0.1203	0.1628	5008	,	,		19975	0.001		0.2535	False		,,,				2504	0.0859				p.R92R		Atlas-SNP	.											.	TNFSF12	20	.	0			c.C276A						PASS	.	C	,	657,3749	281.4+/-275.9	41,575,1587	104.0	92.0	96.0		276,276	1.6	1.0	17	dbSNP_129	96	2163,6437	371.9+/-336.4	265,1633,2402	no	coding-synonymous,coding-synonymous	TNFSF12,TNFSF12-TNFSF13	NM_003809.2,NM_172089.3	,	306,2208,3989	AA,AC,CC		25.1512,14.9115,21.6823	,	92/250,92/331	7453505	2820,10186	2203	4300	6503	SO:0001819	synonymous_variant	8742	exon3			GCCTCGCAGAAGT	AF030099	CCDS11109.1	17p13.1	2008-02-01			ENSG00000239697	ENSG00000239697		"""Tumor necrosis factor (ligand) superfamily"""	11927	protein-coding gene	gene with protein product		602695				9405449, 9560343	Standard	NM_003809		Approved	TWEAK, DR3LG, APO3L		O43508	OTTHUMG00000108148	ENST00000293825.6:c.276C>A	17.37:g.7453505C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_003809	Q8IZK7|Q8WUZ7	Silent	SNP	ENST00000293825.6	37	CCDS11109.1																																																																																			C|0.800;A|0.200	0.200	strong		0.542	TNFSF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226951.2	NM_003809	
CHGA	1113	hgsc.bcm.edu	37	14	93399101	93399101	+	Missense_Mutation	SNP	C	C	T	rs729940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:93399101C>T	ENST00000216492.5	+	7	1475	c.1195C>T	c.(1195-1197)Cgg>Tgg	p.R399W	CHGA_ENST00000334654.4_Missense_Mutation_p.R248W	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	399			R -> W (in dbSNP:rs729940). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2445752, ECO:0000269|PubMed:8120054}.		regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		GCCATCCTCCCGGGAGGACAG	0.687													C|||	623	0.124401	0.0121	0.2061	5008	,	,		14971	0.2004		0.164	False		,,,				2504	0.0992				p.R399W	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.C1195T						PASS	.	C	TRP/ARG	148,4206		7,134,2036	11.0	13.0	12.0		1195	1.2	0.1	14	dbSNP_86	12	1200,7320		80,1040,3140	no	missense	CHGA	NM_001275.3	101	87,1174,5176	TT,TC,CC		14.0845,3.3992,10.4707	possibly-damaging	399/458	93399101	1348,11526	2177	4260	6437	SO:0001583	missense	1113	exon7			TCCTCCCGGGAGG		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"""vasostatin"", ""pancreastatin"", ""parastatin"""	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.1195C>T	14.37:g.93399101C>T	ENSP00000216492:p.Arg399Trp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	45	30	0.666667	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	37	CCDS9906.1	332	0.152014652014652	9	0.018292682926829267	84	0.23204419889502761	114	0.1993006993006993	125	0.16490765171503957	C	13.08	2.129737	0.37630	0.033992	0.140845	ENSG00000100604	ENST00000216492;ENST00000334654	T;T	0.01821	4.62;4.62	4.71	1.2	0.21068	.	0.839077	0.10441	N	0.674355	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	D;D	0.89917	1.0;0.997	D;D	0.70935	0.971;0.913	T	0.45440	-0.9261	9	0.59425	D	0.04	-3.6408	6.2358	0.20762	0.4752:0.2822:0.2426:0.0	rs729940;rs1058460;rs17847003;rs729940	248;399	G5E968;P10645	.;CMGA_HUMAN	W	399;248	ENSP00000216492:R399W;ENSP00000334023:R248W	ENSP00000216492:R399W	R	+	1	2	CHGA	92468854	0.000000	0.05858	0.140000	0.22221	0.387000	0.30353	0.516000	0.22817	0.327000	0.23409	0.555000	0.69702	CGG	C|0.876;T|0.124	0.124	strong		0.687	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275	
TNS4	84951	hgsc.bcm.edu	37	17	38640744	38640744	+	Missense_Mutation	SNP	C	C	T	rs2290207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38640744C>T	ENST00000254051.6	-	6	1651	c.1493G>A	c.(1492-1494)aGt>aAt	p.S498N		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	498	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		S -> N (in dbSNP:rs2290207). {ECO:0000269|PubMed:12154022, ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			ACCTGGTCGACTCTGAGCAGA	0.597													T|||	1386	0.276757	0.1248	0.2954	5008	,	,		19494	0.3562		0.2594	False		,,,				2504	0.4049				p.S498N		Atlas-SNP	.											.	TNS4	72	.	0			c.G1493A						PASS	.	T	ASN/SER	731,3675	757.5+/-412.7	68,595,1540	71.0	60.0	64.0		1493	0.6	0.1	17	dbSNP_100	64	2111,6489	716.5+/-406.1	257,1597,2446	yes	missense	TNS4	NM_032865.5	46	325,2192,3986	TT,TC,CC		24.5465,16.591,21.8515	benign	498/716	38640744	2842,10164	2203	4300	6503	SO:0001583	missense	84951	exon6			GGTCGACTCTGAG	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"""SH2 domain containing"""	24352	protein-coding gene	gene with protein product	"""C terminal tensin like"""	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.1493G>A	17.37:g.38640744C>T	ENSP00000254051:p.Ser498Asn	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Missense_Mutation	SNP	ENST00000254051.6	37	CCDS11368.1	556	0.25457875457875456	60	0.12195121951219512	99	0.27348066298342544	201	0.3513986013986014	196	0.25857519788918204	T	1.181	-0.638024	0.03557	0.16591	0.245465	ENSG00000131746	ENST00000377816;ENST00000254051	T	0.19105	2.17	5.6	0.651	0.17817	SH2 motif (4);	0.738911	0.12343	N	0.477279	T	0.00012	0.0000	N	0.13235	0.315	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.48801	-0.9003	9	0.11485	T	0.65	-11.1851	6.0639	0.19852	0.0:0.4904:0.2062:0.3034	rs2290207;rs57765426;rs2290207	498	Q8IZW8	TENS4_HUMAN	N	498	ENSP00000254051:S498N	ENSP00000254051:S498N	S	-	2	0	TNS4	35894270	0.982000	0.34865	0.073000	0.20177	0.023000	0.10783	0.553000	0.23391	-0.112000	0.11979	-0.361000	0.07541	AGT	C|0.761;T|0.239	0.239	strong		0.597	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865	
PDHX	8050	hgsc.bcm.edu	37	11	34937813	34937813	+	5'Flank	SNP	G	G	A	rs2956114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34937813G>A	ENST00000227868.4	+	0	0				APIP_ENST00000278359.5_5'UTR|APIP_ENST00000527830.1_5'UTR|PDHX_ENST00000430469.2_5'Flank|PDHX_ENST00000448838.3_5'UTR|APIP_ENST00000395787.3_Missense_Mutation_p.R7W			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X						cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TCTCCCTCCCGAGCATCACAG	0.716													G|||	2177	0.434704	0.2239	0.3977	5008	,	,		10339	0.7371		0.3539	False		,,,				2504	0.5174				p.R7W		Atlas-SNP	.											.	APIP	21	.	0			c.C19T						PASS	.	G	,,,TRP/ARG	1067,3329		142,783,1273	17.0	19.0	18.0		,,,19	2.5	0.0	11	dbSNP_101	18	3045,5543		555,1935,1804	yes	utr-5,utr-5,utr-5,missense	PDHX,APIP	NM_001135024.1,NM_001166158.1,NM_003477.2,NM_015957.2	,,,101	697,2718,3077	AA,AG,GG		35.4565,24.2721,31.6697	,,,benign	,,,7/243	34937813	4112,8872	2198	4294	6492	SO:0001631	upstream_gene_variant	51074	exon1			CCTCCCGAGCATC	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491		11.37:g.34937813G>A	Exception_encountered	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_015957	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	37	CCDS7896.1	947	0.4336080586080586	128	0.2601626016260163	142	0.39226519337016574	406	0.7097902097902098	271	0.3575197889182058	G	14.24	2.476444	0.44044	0.242721	0.354565	ENSG00000149089	ENST00000395787	T	0.18810	2.19	4.48	2.5	0.30297	.	1.377040	0.04518	N	0.384034	T	0.00012	0.0000	N	0.08118	0	0.47441	P	5.789999999999962E-4	P	0.41159	0.74	B	0.26969	0.075	T	0.42565	-0.9444	9	0.56958	D	0.05	.	10.8523	0.46777	0.0:0.3704:0.6296:0.0	rs2956114;rs17348273;rs17851547;rs52829807;rs57274539;rs2956114	7	Q96GX9	MTNB_HUMAN	W	7	ENSP00000379133:R7W	ENSP00000379133:R7W	R	-	1	2	APIP	34894389	0.138000	0.22547	0.032000	0.17829	0.005000	0.04900	0.295000	0.19065	0.561000	0.29186	0.491000	0.48974	CGG	G|0.630;A|0.370	0.370	strong		0.716	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
FOLH1B	219595	hgsc.bcm.edu	37	11	89413781	89413781	+	RNA	SNP	C	C	G	rs10830339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:89413781C>G	ENST00000532352.1	+	0	1266							Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48						TTTCAGGAAACTACACTCTGA	0.299													C|||	1130	0.225639	0.1619	0.2478	5008	,	,		17371	0.1319		0.3718	False		,,,				2504	0.2423				p.N151K		Atlas-SNP	.											.	FOLH1B	93	.	0			c.C453G						PASS	.	C	LYS/ASN	939,3463	318.5+/-295.7	88,763,1350	33.0	34.0	34.0		453	3.2	1.0	11	dbSNP_120	34	3199,5385	442.5+/-360.1	587,2025,1680	no	missense	FOLH1B	NM_153696.2	94	675,2788,3030	GG,GC,CC		37.267,21.3312,31.8651	possibly-damaging	151/443	89413781	4138,8848	2201	4292	6493			219595	exon8			AGGAAACTACACT	AF261715		11q14.3	2014-03-18			ENSG00000134612	ENSG00000134612			13636	protein-coding gene	gene with protein product	"""prostate specific membrane antigen like protein"", ""Cell growth-inhibiting gene 26 protein"", ""glutamate carboxypeptidase III"""	609020	"""folate hydrolase 2"""	FOLH2, FOLHP		9838072, 14716746	Standard	NM_153696		Approved	PSMAL, GCPIII	uc001pda.3	Q9HBA9	OTTHUMG00000167376		11.37:g.89413781C>G		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	213	67	0.314554	NM_153696		Missense_Mutation	SNP	ENST00000532352.1	37																																																																																				C|0.717;G|0.283	0.283	strong		0.299	FOLH1B-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000395421.1	NM_153696	
ZNF280A	129025	hgsc.bcm.edu	37	22	22868776	22868776	+	Silent	SNP	G	G	A	rs362173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22868776G>A	ENST00000302097.3	-	2	1431	c.1179C>T	c.(1177-1179)ccC>ccT	p.P393P		NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		GGCACACGTAGGGCATTTCGC	0.443													G|||	2379	0.47504	0.2405	0.7334	5008	,	,		19167	0.4137		0.7068	False		,,,				2504	0.4335				p.P393P		Atlas-SNP	.											ZNF280A,NS,adenoma,0,1	ZNF280A	67	1	0			c.C1179T						scavenged	.	G		1355,3051	449.8+/-349.2	220,915,1068	123.0	102.0	109.0		1179	0.5	0.7	22	dbSNP_79	109	5846,2748	677.3+/-403.4	2005,1836,456	no	coding-synonymous	ZNF280A	NM_080740.3		2225,2751,1524	AA,AG,GG		31.9758,30.7535,44.6077		393/543	22868776	7201,5799	2203	4297	6500	SO:0001819	synonymous_variant	129025	exon2			CACGTAGGGCATT	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.1179C>T	22.37:g.22868776G>A		Somatic	310	2	0.00645161		WXS	Illumina HiSeq	Phase_I	279	128	0.458781	NM_080740		Silent	SNP	ENST00000302097.3	37	CCDS13800.1																																																																																			G|0.454;A|0.546	0.546	strong		0.443	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
PADI1	29943	hgsc.bcm.edu	37	1	17555508	17555508	+	Silent	SNP	G	G	T	rs2977234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17555508G>T	ENST00000375471.4	+	8	983	c.891G>T	c.(889-891)acG>acT	p.T297T		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	297					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	GGATCATGACGCCCAACACTC	0.622													G|||	1074	0.214457	0.1831	0.1902	5008	,	,		15507	0.0585		0.3539	False		,,,				2504	0.2914				p.T297T	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											PADI1,NS,carcinoma,0,1	PADI1	77	1	0			c.G891T						PASS	.	G		921,3483		95,731,1376	40.0	31.0	34.0		891	-0.3	1.0	1	dbSNP_101	34	2761,5839		451,1859,1990	no	coding-synonymous	PADI1	NM_013358.2		546,2590,3366	TT,TG,GG		32.1047,20.9128,28.3144		297/664	17555508	3682,9322	2202	4300	6502	SO:0001819	synonymous_variant	29943	exon8			CATGACGCCCAAC	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.891G>T	1.37:g.17555508G>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_013358	A1L4K6|Q70SX6	Silent	SNP	ENST00000375471.4	37	CCDS178.1																																																																																			G|0.762;T|0.238	0.238	strong		0.622	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
PKD1L2	114780	hgsc.bcm.edu	37	16	81253917	81253917	+	RNA	SNP	A	A	G	rs533693628|rs9924530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81253917A>G	ENST00000525539.1	-	0	58				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTCTGGCTTAACAGTGGTGGC	0.567													G|||	2680	0.535144	0.6014	0.562	5008	,	,		20950	0.4405		0.6501	False		,,,				2504	0.4059				p.V20A		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T59C						PASS	.	G	ALA/VAL,ALA/VAL	2630,1446		865,900,273	69.0	69.0	69.0		59,59	3.2	0.0	16	dbSNP_119	69	5299,3093		1657,1985,554	yes	missense,missense	PKD1L2	NM_052892.3,NM_001076780.1	64,64	2522,2885,827	GG,GA,AA		36.8565,35.476,36.4052	benign,benign	20/2460,20/992	81253917	7929,4539	2038	4196	6234			114780	exon1			GGCTTAACAGTGG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81253917A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1251	0.5728021978021978	301	0.6117886178861789	226	0.6243093922651933	233	0.40734265734265734	491	0.6477572559366754	G	0.019	-1.453081	0.01071	0.64524	0.631435	ENSG00000166473	ENST00000337114	T	0.16196	2.36	4.17	3.22	0.36961	.	0.335569	0.23343	N	0.049204	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43861	-0.9365	8	0.02654	T	1	-0.5748	3.3619	0.07189	0.2937:0.0:0.5103:0.196	rs9924530;rs52790816;rs61536671;rs9924530	20;20	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	A	20	ENSP00000337397:V20A	ENSP00000337397:V20A	V	-	2	0	PKD1L2	79811418	0.009000	0.17119	0.001000	0.08648	0.013000	0.08279	1.062000	0.30555	0.426000	0.26116	-0.213000	0.12676	GTT	A|0.429;G|0.571	0.571	strong		0.567	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
IL16	3603	hgsc.bcm.edu	37	15	81584925	81584925	+	Silent	SNP	C	C	T	rs61752774	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:81584925C>T	ENST00000302987.4	+	11	1449	c.1449C>T	c.(1447-1449)caC>caT	p.H483H	IL16_ENST00000394660.2_Silent_p.H483H			Q14005	IL16_HUMAN	interleukin 16	483					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GCAGTTGGCACGGGCGGCCCA	0.557													C|||	837	0.167133	0.0673	0.1931	5008	,	,		19115	0.1885		0.0994	False		,,,				2504	0.3313				p.H483H		Atlas-SNP	.											IL16_ENST00000302987,caecum,carcinoma,0,2	IL16	254	2	0			c.C1449T						PASS	.	C	,	274,3694		11,252,1721	54.0	60.0	58.0		1449,1449	-8.4	0.5	15	dbSNP_129	58	870,7440		43,784,3328	no	coding-synonymous,coding-synonymous	IL16	NM_001172128.1,NM_172217.3	,	54,1036,5049	TT,TC,CC		10.4693,6.9052,9.3175	,	483/1332,483/1333	81584925	1144,11134	1984	4155	6139	SO:0001819	synonymous_variant	3603	exon12			TTGGCACGGGCGG	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1449C>T	15.37:g.81584925C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	43	0.651515	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			C|0.881;T|0.119	0.119	strong		0.557	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
PITRM1	10531	hgsc.bcm.edu	37	10	3189380	3189380	+	Silent	SNP	C	C	T	rs3740607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:3189380C>T	ENST00000224949.4	-	20	2332	c.2298G>A	c.(2296-2298)ccG>ccA	p.P766P	PITRM1_ENST00000464395.1_5'UTR|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380994.1_Silent_p.P324P|PITRM1_ENST00000380989.2_Silent_p.P767P|PITRM1-AS1_ENST00000441377.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000451104.2_Silent_p.P668P			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	766					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TCTTGATACGCGGGAGCTTCC	0.403													C|||	2731	0.545327	0.4508	0.5403	5008	,	,		19192	0.6865		0.5239	False		,,,				2504	0.5532				p.P767P		Atlas-SNP	.											.	PITRM1	109	.	0			c.G2301A						PASS	.	C	,,	1779,2027		416,947,540	149.0	145.0	146.0		2301,2004,2298	-9.1	0.0	10	dbSNP_107	146	4065,4195		977,2111,1042	no	coding-synonymous,coding-synonymous,coding-synonymous	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	,,	1393,3058,1582	TT,TC,CC		49.2131,46.742,48.4336	,,	767/1039,668/940,766/1038	3189380	5844,6222	1903	4130	6033	SO:0001819	synonymous_variant	10531	exon20			GATACGCGGGAGC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.2298G>A	10.37:g.3189380C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	99	65	0.656566	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	37	CCDS59208.1	1251	0.5728021978021978	227	0.4613821138211382	210	0.580110497237569	411	0.7185314685314685	403	0.5316622691292876	c	0.495	-0.873550	0.02570	0.46742	0.492131	ENSG00000107959	ENST00000451454	.	.	.	5.66	-9.12	0.00707	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19945	P	0.9999408251	.	.	.	.	.	.	T	0.41378	-0.9512	3	.	.	.	-13.8849	1.1031	0.01688	0.2755:0.0973:0.289:0.3382	rs3740607;rs17849430;rs17849901;rs60129773;rs3740607	.	.	.	T	100	.	.	A	-	1	0	PITRM1	3179380	0.360000	0.24964	0.027000	0.17364	0.004000	0.04260	-0.493000	0.06459	-1.269000	0.02436	-1.077000	0.02231	GCG	C|0.430;T|0.570	0.570	strong		0.403	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
KDM1B	221656	hgsc.bcm.edu	37	6	18208415	18208415	+	Missense_Mutation	SNP	G	G	A	rs72840622	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:18208415G>A	ENST00000297792.5	+	13	1325	c.1148G>A	c.(1147-1149)gGc>gAc	p.G383D	KDM1B_ENST00000397244.1_Missense_Mutation_p.G384D|KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000388870.2_Missense_Mutation_p.G616D			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	615					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						ACTACAGATGGCACAGGGTAT	0.458													G|||	21	0.00419329	0.0008	0.0043	5008	,	,		19075	0.0		0.0129	False		,,,				2504	0.0041				p.G383D		Atlas-SNP	.											.	KDM1B	58	.	0			c.G1148A						PASS	.	G	ASP/GLY	20,4386	27.2+/-55.0	0,20,2183	170.0	161.0	165.0		1148	5.2	0.2	6	dbSNP_130	165	200,8400	86.9+/-149.2	4,192,4104	yes	missense	KDM1B	NM_153042.3	94	4,212,6287	AA,AG,GG		2.3256,0.4539,1.6915	probably-damaging	383/591	18208415	220,12786	2203	4300	6503	SO:0001583	missense	221656	exon13			CAGATGGCACAGG	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"""Chromatin-modifying enzymes / K-demethylases"""	21577	protein-coding gene	gene with protein product		613081	"""amine oxidase, flavin containing 1"", ""chromosome 6 open reading frame 193"", ""amine oxidase (flavin containing) domain 1"""	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.1148G>A	6.37:g.18208415G>A	ENSP00000297792:p.Gly383Asp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Missense_Mutation	SNP	ENST00000297792.5	37	CCDS34343.1	12|12	0.005494505494505495|0.005494505494505495	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	G|G	32|32	5.176462|5.176462	0.94846|0.94846	0.004539|0.004539	0.023256|0.023256	ENSG00000165097|ENSG00000165097	ENST00000449850|ENST00000388870;ENST00000397244;ENST00000297792;ENST00000388869	.|T;T;T	.|0.19250	.|2.16;2.16;2.16	5.16|5.16	5.16|5.16	0.70880|0.70880	.|Amine oxidase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.42017|0.42017	0.1184|0.1184	M|M	0.75615|0.75615	2.305|2.305	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.993	.|D;D	.|0.76575	.|0.988;0.977	T|T	0.35773|0.35773	-0.9775|-0.9775	5|10	.|0.72032	.|D	.|0.01	-3.398|-3.398	18.8307|18.8307	0.92137|0.92137	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|615;383	.|Q8NB78;A2A2C6	.|KDM1B_HUMAN;.	T|D	433|616;384;383;615	.|ENSP00000373522:G616D;ENSP00000380419:G384D;ENSP00000297792:G383D	.|ENSP00000297792:G383D	A|G	+|+	1|2	0|0	KDM1B|KDM1B	18316394|18316394	1.000000|1.000000	0.71417|0.71417	0.211000|0.211000	0.23655|0.23655	0.481000|0.481000	0.33189|0.33189	8.531000|8.531000	0.90610|0.90610	2.689000|2.689000	0.91719|0.91719	0.655000|0.655000	0.94253|0.94253	GCA|GGC	G|0.986;A|0.014	0.014	strong		0.458	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042	
TNXB	7148	hgsc.bcm.edu	37	6	32025863	32025863	+	Silent	SNP	C	C	T	rs369637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32025863C>T	ENST00000375244.3	-	22	7998	c.7797G>A	c.(7795-7797)ctG>ctA	p.L2599L	TNXB_ENST00000375247.2_Silent_p.L2599L			P22105	TENX_HUMAN	tenascin XB	2659	Fibronectin type-III 18. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						ACACCGGGCCCAGGCGCCGCC	0.627													C|||	248	0.0495208	0.0469	0.0432	5008	,	,		16728	0.0169		0.1113	False		,,,				2504	0.0276				p.L2599L		Atlas-SNP	.											.	TNXB	553	.	0			c.G7797A						PASS	.	C		132,2518		4,124,1197	40.0	49.0	46.0		7797	4.1	1.0	6	dbSNP_80	46	710,4442		51,608,1917	no	coding-synonymous	TNXB	NM_019105.6		55,732,3114	TT,TC,CC		13.7811,4.9811,10.7921		2599/4243	32025863	842,6960	1325	2576	3901	SO:0001819	synonymous_variant	7148	exon22			CGGGCCCAGGCGC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7797G>A	6.37:g.32025863C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	141	69	0.489362	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				C|0.927;T|0.073	0.073	strong		0.627	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
PLEC	5339	hgsc.bcm.edu	37	8	144995736	144995736	+	Silent	SNP	G	G	A	rs11777402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144995736G>A	ENST00000322810.4	-	32	8833	c.8664C>T	c.(8662-8664)aaC>aaT	p.N2888N	PLEC_ENST00000357649.2_Silent_p.N2755N|PLEC_ENST00000527096.1_Silent_p.N2774N|PLEC_ENST00000398774.2_Silent_p.N2719N|PLEC_ENST00000354958.2_Silent_p.N2729N|PLEC_ENST00000436759.2_Silent_p.N2778N|PLEC_ENST00000345136.3_Silent_p.N2751N|PLEC_ENST00000354589.3_Silent_p.N2751N|PLEC_ENST00000356346.3_Silent_p.N2737N	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2888	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TCACAGCCTCGTTGACGGTCA	0.697													G|||	1153	0.230232	0.0272	0.2968	5008	,	,		14387	0.1419		0.4284	False		,,,				2504	0.3446				p.N2888N		Atlas-SNP	.											.	PLEC	1144	.	0			c.C8664T						PASS	.	G	,,,,,,,	365,3783		25,315,1734	28.0	35.0	33.0		8334,8211,8187,8664,8157,8253,8265,8253	-8.6	0.0	8	dbSNP_120	33	3418,4956		715,1988,1484	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	740,2303,3218	AA,AG,GG		40.8168,8.7994,30.2108	,,,,,,,	2778/4575,2737/4534,2729/4526,2888/4685,2719/4516,2751/4548,2755/4552,2751/4548	144995736	3783,8739	2074	4187	6261	SO:0001819	synonymous_variant	5339	exon32			AGCCTCGTTGACG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8664C>T	8.37:g.144995736G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	128	69	0.539062	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.681;A|0.319	0.319	strong		0.697	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
CDKN2C	1031	hgsc.bcm.edu	37	1	51439777	51439777	+	Silent	SNP	C	C	T	rs1043141	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:51439777C>T	ENST00000262662.1	+	4	2376	c.342C>T	c.(340-342)ggC>ggT	p.G114G	CDKN2C_ENST00000371761.3_Silent_p.G114G|CDKN2C_ENST00000396148.1_Silent_p.G114G			P42773	CDN2C_HUMAN	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	114					cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|oligodendrocyte differentiation (GO:0048709)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0?(11)|p.?(1)		central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|thyroid(1)	23				GBM - Glioblastoma multiforme(3;3.61e-13)|all cancers(3;0.00151)		CCAAAGAAGGCCACCTCCGGG	0.542			D		"""glioma, MM"""								C|||	220	0.0439297	0.0038	0.0591	5008	,	,		18193	0.0417		0.0964	False		,,,				2504	0.0358				p.G114G	Melanoma(47;50 1155 4767 22863 47597)	Atlas-SNP	.		Rec	yes		1	1p32	1031	"""cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)"""		"""O, L"""	.	CDKN2C	24	.	12	Whole gene deletion(11)|Unknown(1)	central_nervous_system(6)|haematopoietic_and_lymphoid_tissue(5)|thyroid(1)	c.C342T						PASS	.	C	,	88,4318	73.6+/-111.7	1,86,2116	68.0	66.0	66.0		342,342	2.7	1.0	1	dbSNP_86	66	777,7823	183.9+/-232.0	44,689,3567	no	coding-synonymous,coding-synonymous	CDKN2C	NM_001262.2,NM_078626.2	,	45,775,5683	TT,TC,CC		9.0349,1.9973,6.6508	,	114/169,114/169	51439777	865,12141	2203	4300	6503	SO:0001819	synonymous_variant	1031	exon3			AGAAGGCCACCTC	BC000598	CCDS555.1	1p32.3	2013-01-10			ENSG00000123080	ENSG00000123080		"""Ankyrin repeat domain containing"""	1789	protein-coding gene	gene with protein product		603369				8001816, 9636670	Standard	NM_001262		Approved	INK4C, p18	uc001csg.3	P42773	OTTHUMG00000008046	ENST00000262662.1:c.342C>T	1.37:g.51439777C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_001262	Q8TB83	Silent	SNP	ENST00000262662.1	37	CCDS555.1																																																																																			C|0.933;T|0.067	0.067	strong		0.542	CDKN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022058.1	NM_001262	
SMYD4	114826	hgsc.bcm.edu	37	17	1686737	1686737	+	Missense_Mutation	SNP	C	C	T	rs374639152		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1686737C>T	ENST00000305513.7	-	9	2221	c.2054G>A	c.(2053-2055)cGt>cAt	p.R685H		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	685							metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						CTCGGCGTCACGCTGGCACCC	0.607																																					p.R685H		Atlas-SNP	.											.	SMYD4	50	.	0			c.G2054A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	24.0	24.0	24.0		2054	-10.0	0.0	17		24	1,8599		0,1,4299	no	missense	SMYD4	NM_052928.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	685/805	1686737	1,13005	2203	4300	6503	SO:0001583	missense	114826	exon9			GCGTCACGCTGGC	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.2054G>A	17.37:g.1686737C>T	ENSP00000304360:p.Arg685His	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	185	102	0.551351	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	.	.	.	.	.	.	.	.	.	.	C	9.257	1.042180	0.19748	0.0	1.16E-4	ENSG00000186532	ENST00000305513	T	0.64260	-0.09	5.75	-10.0	0.00425	Tetratricopeptide-like helical (1);	1.666840	0.02239	N	0.065610	T	0.29850	0.0746	N	0.01352	-0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34229	-0.9837	10	0.14252	T	0.57	1.9281	14.6337	0.68673	0.1008:0.6859:0.0:0.2133	.	685	Q8IYR2	SMYD4_HUMAN	H	685	ENSP00000304360:R685H	ENSP00000304360:R685H	R	-	2	0	SMYD4	1633487	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-1.683000	0.01934	-2.027000	0.00932	-0.474000	0.04947	CGT	.	.	weak		0.607	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
GRHL3	57822	hgsc.bcm.edu	37	1	24668667	24668667	+	Silent	SNP	C	C	G	rs11576645	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:24668667C>G	ENST00000350501.5	+	9	1237	c.1110C>G	c.(1108-1110)gtC>gtG	p.V370V	GRHL3_ENST00000236255.4_Silent_p.V375V|GRHL3_ENST00000342072.4_Silent_p.V277V|GRHL3_ENST00000361548.4_Silent_p.V370V|GRHL3_ENST00000356046.2_Silent_p.V324V	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	370					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		TGAAGGGTGTCCCCCTGAACC	0.572													C|||	790	0.157748	0.0772	0.1527	5008	,	,		20035	0.123		0.2068	False		,,,				2504	0.2556				p.V375V		Atlas-SNP	.											.	GRHL3	69	.	0			c.C1125G						PASS	.	C	,,,	424,3982	206.5+/-228.1	21,382,1800	105.0	106.0	106.0		972,1125,1110,1110	3.7	1.0	1	dbSNP_120	106	1942,6658	342.3+/-324.4	219,1504,2577	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRHL3	NM_001195010.1,NM_021180.3,NM_198173.2,NM_198174.2	,,,	240,1886,4377	GG,GC,CC		22.5814,9.6232,18.1916	,,,	324/557,375/608,370/603,370/627	24668667	2366,10640	2203	4300	6503	SO:0001819	synonymous_variant	57822	exon9			GGGTGTCCCCCTG	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.1110C>G	1.37:g.24668667C>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	112	44	0.392857	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Silent	SNP	ENST00000350501.5	37	CCDS252.2																																																																																			C|0.832;G|0.168	0.168	strong		0.572	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
CIAPIN1	57019	hgsc.bcm.edu	37	16	57464236	57464236	+	Nonsense_Mutation	SNP	G	G	A	rs170358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:57464236G>A	ENST00000565961.1	-	6	684	c.565C>T	c.(565-567)Cga>Tga	p.R189*	CIAPIN1_ENST00000394391.4_Silent_p.A254A|CIAPIN1_ENST00000567518.1_Silent_p.A241A|CIAPIN1_ENST00000569246.1_5'Flank|CIAPIN1_ENST00000568940.1_Nonsense_Mutation_p.R216*|CIAPIN1_ENST00000569979.1_Intron|CIAPIN1_ENST00000569370.1_Nonsense_Mutation_p.R216*					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						CCAGTTCTTCGGCAAGGCCAC	0.448													G|||	107	0.0213658	0.0257	0.0216	5008	,	,		21458	0.002		0.0398	False		,,,				2504	0.0164				p.A254A		Atlas-SNP	.											CIAPIN1,colon,carcinoma,-1,1	CIAPIN1	17	1	0			c.C762T						PASS	.	G		106,3730		0,106,1812	108.0	99.0	102.0		762	-5.4	0.9	16	dbSNP_79	102	284,8008		5,274,3867	no	coding-synonymous	CIAPIN1	NM_020313.2		5,380,5679	AA,AG,GG		3.425,2.7633,3.2157		254/313	57464236	390,11738	1918	4146	6064	SO:0001587	stop_gained	57019	exon8			TTCTTCGGCAAGG	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000565961.1:c.565C>T	16.37:g.57464236G>A	ENSP00000455309:p.Arg189*	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_020313		Silent	SNP	ENST00000565961.1	37																																																																																				G|0.978;A|0.022	0.022	strong		0.448	CIAPIN1-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000431014.1	NM_020313	
OR2T35	403244	hgsc.bcm.edu	37	1	248801897	248801897	+	Silent	SNP	G	G	A	rs79303917	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248801897G>A	ENST00000317450.3	-	1	662	c.663C>T	c.(661-663)atC>atT	p.I221I		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I221I(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CAGTCAGGAGGATGTGCGTGT	0.542																																					p.I221I		Atlas-SNP	.											OR2T35,NS,carcinoma,0,1	OR2T35	19	1	1	Substitution - coding silent(1)	ovary(1)	c.C663T						PASS	.	G		125,3975		2,121,1927	102.0	89.0	93.0		663	-0.2	0.0	1	dbSNP_131	93	877,7621		4,869,3376	no	coding-synonymous	OR2T35	NM_001001827.1		6,990,5303	AA,AG,GG		10.3201,3.0488,7.9536		221/324	248801897	1002,11596	2050	4249	6299	SO:0001819	synonymous_variant	403244	exon1			CAGGAGGATGTGC	BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"""GPCR / Class A : Olfactory receptors"""	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.663C>T	1.37:g.248801897G>A		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	574	266	0.463415	NM_001001827	Q6IEY7	Silent	SNP	ENST00000317450.3	37	CCDS31123.1																																																																																			G|0.895;A|0.105	0.105	strong		0.542	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827	
TOX4	9878	hgsc.bcm.edu	37	14	21960969	21960969	+	Silent	SNP	G	G	A	rs7617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21960969G>A	ENST00000405508.1	+	8	1470	c.1194G>A	c.(1192-1194)cgG>cgA	p.R398R	TOX4_ENST00000448790.2_Silent_p.R375R|TOX4_ENST00000262709.3_Silent_p.R398R			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	398						chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)			large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		TGACCTCCCGGGGGCTCCAAC	0.512													G|||	2480	0.495208	0.4274	0.3746	5008	,	,		18365	0.6488		0.502	False		,,,				2504	0.5072				p.R398R		Atlas-SNP	.											.	TOX4	50	.	0			c.G1194A						PASS	.	G		2060,2346	569.2+/-382.6	473,1114,616	92.0	100.0	98.0		1194	1.9	1.0	14	dbSNP_52	98	4322,4278	579.2+/-390.9	1127,2068,1105	no	coding-synonymous	TOX4	NM_014828.2		1600,3182,1721	AA,AG,GG		49.7442,46.7544,49.0697		398/622	21960969	6382,6624	2203	4300	6503	SO:0001819	synonymous_variant	9878	exon7			CTCCCGGGGGCTC	AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"""chromosome 14 open reading frame 92"", ""KIAA0737"""	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.1194G>A	14.37:g.21960969G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	182	106	0.582418	NM_014828	B4DPY8|B4DSM0|E7EV69	Silent	SNP	ENST00000405508.1	37	CCDS32043.1																																																																																			G|0.511;A|0.489	0.489	strong		0.512	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828	
MAGEA1	4100	hgsc.bcm.edu	37	X	152482917	152482917	+	Missense_Mutation	SNP	T	T	C	rs2008160	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:152482917T>C	ENST00000356661.5	-	3	312	c.94A>G	c.(94-96)Acc>Gcc	p.T32A		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	32			T -> A (probable polymorphism; dbSNP:rs2008160). {ECO:0000269|PubMed:15059299, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GAGGAGGAGGTGGCAGCCTGC	0.627													c|||	1347	0.356821	0.2867	0.2723	3775	,	,		13567	0.4534		0.1252	False		,,,				2504	0.2004				p.T32A		Atlas-SNP	.											.	MAGEA1	57	.	0			c.A94G						PASS	.		ALA/THR	1329,2506		183,768,195,681,376	65.0	75.0	71.0		94	-1.6	0.0	X	dbSNP_92	71	1272,5456		82,752,356,1594,1516	no	missense	MAGEA1	NM_004988.4	58	265,1520,551,2275,1892	CC,CT,C,TT,T		18.9061,34.6545,24.6237	benign	32/310	152482917	2601,7962	2203	4300	6503	SO:0001583	missense	4100	exon3			AGGAGGTGGCAGC		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"""melanoma-associated antigen 1"", ""melanoma-associated antigen MZ2-E"", ""melanoma antigen MAGE-1"", ""melanoma antigen family A 1"", ""cancer/testis antigen family 1, member 1"""	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.94A>G	X.37:g.152482917T>C	ENSP00000349085:p.Thr32Ala	Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_004988	B2RC81|O00346	Missense_Mutation	SNP	ENST00000356661.5	37	CCDS14720.1	594	0.35804701627486435	98	0.24873096446700507	69	0.23154362416107382	161	0.4045226130653266	72	0.10198300283286119	c	0.003	-2.459661	0.00171	0.346545	0.189061	ENSG00000198681	ENST00000356661	T	0.04317	3.65	0.779	-1.56	0.08532	Melanoma associated antigen, MAGE, N-terminal (1);	2.563400	0.01613	N	0.022635	T	0.00012	0.0000	N	0.05031	-0.125	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.46205	-0.9208	8	0.02654	T	1	.	.	.	.	rs2008160;rs16996899;rs17855474;rs60036418;rs2008160	32	P43355	MAGA1_HUMAN	A	32	ENSP00000349085:T32A	ENSP00000349085:T32A	T	-	1	0	MAGEA1	152136111	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.564000	0.05936	-1.829000	0.01201	-1.119000	0.02030	ACC	T|0.710;C|0.290	0.290	strong		0.627	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988	
TMEM2	23670	hgsc.bcm.edu	37	9	74355028	74355028	+	Silent	SNP	A	A	G	rs25690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:74355028A>G	ENST00000377044.4	-	5	1694	c.1155T>C	c.(1153-1155)acT>acC	p.T385T	TMEM2_ENST00000377066.5_Silent_p.T385T	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	385					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GGCCATCCACAGTATAAAATT	0.408													G|||	407	0.08127	0.0393	0.0476	5008	,	,		15182	0.0198		0.0815	False		,,,				2504	0.2249				p.T385T		Atlas-SNP	.											.	TMEM2	112	.	0			c.T1155C						PASS	.	G	,	174,4232	810.7+/-416.0	6,162,2035	114.0	110.0	111.0		1155,1155	-4.1	0.3	9	dbSNP_72	111	722,7878	786.7+/-407.6	31,660,3609	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	37,822,5644	GG,GA,AA		8.3953,3.9492,6.8891	,	385/1321,385/1384	74355028	896,12110	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon5			ATCCACAGTATAA		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1155T>C	9.37:g.74355028A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			A|0.936;G|0.064	0.064	strong		0.408	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
MYEOV	26579	hgsc.bcm.edu	37	11	69063728	69063728	+	Missense_Mutation	SNP	G	G	C	rs11228610	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:69063728G>C	ENST00000308946.3	+	3	1261	c.811G>C	c.(811-813)Ggg>Cgg	p.G271R	MYEOV_ENST00000535407.1_Missense_Mutation_p.G213R|MYEOV_ENST00000441339.2_Missense_Mutation_p.G271R	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	271			G -> R (in dbSNP:rs11228610). {ECO:0000269|PubMed:10753852}.							endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		GGCCCTGGGGGGGTGGCGCAT	0.677													G|||	901	0.179912	0.1785	0.0922	5008	,	,		15476	0.2153		0.1083	False		,,,				2504	0.2812				p.G271R		Atlas-SNP	.											.	MYEOV	42	.	0			c.G811C						PASS	.	G	ARG/GLY	687,3713	285.2+/-278.0	45,597,1558	47.0	49.0	48.0		811	-0.2	0.0	11	dbSNP_120	48	929,7659	202.0+/-245.4	48,833,3413	yes	missense	MYEOV	NM_138768.2	125	93,1430,4971	CC,CG,GG		10.8174,15.6136,12.4423	possibly-damaging	271/314	69063728	1616,11372	2200	4294	6494	SO:0001583	missense	26579	exon3			CTGGGGGGGTGGC	AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"""myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"""			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.811G>C	11.37:g.69063728G>C	ENSP00000308330:p.Gly271Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	328	0.15018315018315018	97	0.19715447154471544	38	0.10497237569060773	114	0.1993006993006993	79	0.10422163588390501	G	6.945	0.544246	0.13312	0.156136	0.108174	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.28895	1.61;1.61;1.59	0.866	-0.159	0.13379	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.47910	0.902	B	0.38655	0.278	T	0.26258	-1.0108	8	0.87932	D	0	.	3.2233	0.06723	0.3288:0.0:0.6712:0.0	rs11228610;rs11228610	271	Q96EZ4	MYEOV_HUMAN	R	271;271;213	ENSP00000412482:G271R;ENSP00000308330:G271R;ENSP00000438100:G213R	ENSP00000308330:G271R	G	+	1	0	MYEOV	68820304	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.360000	0.07622	-0.078000	0.12730	0.491000	0.48974	GGG	G|0.859;C|0.141	0.141	strong		0.677	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
KPTN	11133	hgsc.bcm.edu	37	19	47980153	47980153	+	Silent	SNP	G	G	A	rs2293424	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47980153G>A	ENST00000338134.3	-	10	1013	c.906C>T	c.(904-906)ccC>ccT	p.P302P	KPTN_ENST00000536339.1_Silent_p.P62P	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	302					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		GGTCACTGCCGGGCAGGAGAA	0.597													G|||	1733	0.346046	0.0159	0.3775	5008	,	,		18859	0.5427		0.503	False		,,,				2504	0.4059				p.P302P		Atlas-SNP	.											.	KPTN	34	.	0			c.C906T						PASS	.	G		389,3607		29,331,1638	17.0	19.0	18.0		906	-10.6	0.0	19	dbSNP_100	18	3937,4393		961,2015,1189	no	coding-synonymous	KPTN	NM_007059.2		990,2346,2827	AA,AG,GG		47.2629,9.7347,35.0965		302/437	47980153	4326,8000	1998	4165	6163	SO:0001819	synonymous_variant	11133	exon10			ACTGCCGGGCAGG	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"""kaptin (actin-binding protein)"""			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.906C>T	19.37:g.47980153G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	62	0.607843	NM_007059	B3KN86|B4DQ76|Q96GT1	Silent	SNP	ENST00000338134.3	37	CCDS42583.1																																																																																			G|0.633;A|0.367	0.367	strong		0.597	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2		
SLC6A17	388662	hgsc.bcm.edu	37	1	110709720	110709720	+	Missense_Mutation	SNP	G	G	A	rs12737742|rs35600013	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110709720G>A	ENST00000331565.4	+	2	654	c.169G>A	c.(169-171)Gca>Aca	p.A57T	RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000443008.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	57			A -> T (in dbSNP:rs12737742). {ECO:0000269|PubMed:15489334}.		alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GGAGCTGGATGCAGAGGACCG	0.612													G|||	1253	0.2502	0.0333	0.2608	5008	,	,		14238	0.2143		0.4652	False		,,,				2504	0.3517				p.A57T		Atlas-SNP	.											.	SLC6A17	86	.	0			c.G169A						PASS	.	G	THR/ALA,	477,3929		30,417,1756	71.0	58.0	62.0		169,291	2.6	0.0	1	dbSNP_121	62	3831,4769		935,1961,1404	yes	missense,coding-synonymous	SLC6A17,LOC100130800	NM_001010898.2,XM_001719118.1	58,	965,2378,3160	AA,AG,GG		44.5465,10.8261,33.1232	benign,	57/728,97/154	110709720	4308,8698	2203	4300	6503	SO:0001583	missense	388662	exon2			CTGGATGCAGAGG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.169G>A	1.37:g.110709720G>A	ENSP00000330199:p.Ala57Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	106	43	0.40566	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	500	0.22893772893772893	15	0.03048780487804878	100	0.27624309392265195	108	0.1888111888111888	277	0.3654353562005277	G	13.10	2.134875	0.37728	0.108261	0.445465	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.74209	-0.82	4.44	2.57	0.30868	.	0.616662	0.17593	N	0.168698	T	0.28830	0.0715	N	0.08118	0	0.80722	P	0.0	B	0.20887	0.049	B	0.23275	0.045	T	0.03325	-1.1048	9	0.22706	T	0.39	.	6.0414	0.19736	0.1679:0.1554:0.6768:0.0	rs12737742	57	Q9H1V8	S6A17_HUMAN	T	57	ENSP00000330199:A57T	ENSP00000330199:A57T	A	+	1	0	SLC6A17	110511243	0.000000	0.05858	0.042000	0.18584	0.914000	0.54420	0.538000	0.23160	0.504000	0.28082	0.655000	0.94253	GCA	A|0.305;C|0.000;G|0.695	0.305	strong		0.612	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
TTF2	8458	hgsc.bcm.edu	37	1	117617705	117617705	+	Missense_Mutation	SNP	A	A	G	rs998532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:117617705A>G	ENST00000369466.4	+	5	543	c.499A>G	c.(499-501)Aaa>Gaa	p.K167E		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	167			K -> E (in dbSNP:rs998532). {ECO:0000269|PubMed:14702039}.		ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		CGATCAAAAGAAAGAACAGAA	0.428													A|||	2577	0.514577	0.1157	0.6671	5008	,	,		18261	0.7679		0.5934	False		,,,				2504	0.6033				p.K167E		Atlas-SNP	.											.	TTF2	92	.	0			c.A499G						PASS	.	A	GLU/LYS	910,3496	348.2+/-309.8	102,706,1395	85.0	89.0	88.0		499	0.4	0.0	1	dbSNP_86	88	5194,3406	636.6+/-399.1	1610,1974,716	yes	missense	TTF2	NM_003594.3	56	1712,2680,2111	GG,GA,AA		39.6047,20.6537,46.9322	benign	167/1163	117617705	6104,6902	2203	4300	6503	SO:0001583	missense	8458	exon5			CAAAAGAAAGAAC	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.499A>G	1.37:g.117617705A>G	ENSP00000358478:p.Lys167Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	111	80	0.720721	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	1169	0.5352564102564102	55	0.11178861788617886	240	0.6629834254143646	434	0.7587412587412588	440	0.5804749340369393	A	8.352	0.831161	0.16820	0.206537	0.603953	ENSG00000116830	ENST00000369466	D	0.87966	-2.32	5.59	0.438	0.16560	.	0.175261	0.27636	N	0.018493	T	0.60011	0.2236	N	0.25890	0.77	0.80722	P	0.0	B;B	0.28350	0.006;0.208	B;B	0.25759	0.004;0.063	T	0.44483	-0.9325	9	0.51188	T	0.08	-2.8154	5.315	0.15850	0.5612:0.2837:0.1552:0.0	rs998532;rs1289674;rs17523198;rs52796029;rs58084515;rs998532	167;167	Q9UNY4;Q9UNY4-2	TTF2_HUMAN;.	E	167	ENSP00000358478:K167E	ENSP00000358478:K167E	K	+	1	0	TTF2	117419228	0.972000	0.33761	0.003000	0.11579	0.004000	0.04260	0.349000	0.20055	0.102000	0.17638	0.455000	0.32223	AAA	A|0.499;G|0.501	0.501	strong		0.428	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
HLA-A	3105	hgsc.bcm.edu	37	6	29911271	29911271	+	Missense_Mutation	SNP	G	G	C	rs3098019	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29911271G>C	ENST00000396634.1	+	5	911	c.570G>C	c.(568-570)gaG>gaC	p.E190D	HLA-A_ENST00000376802.2_Missense_Mutation_p.E190D|HLA-A_ENST00000376806.5_Missense_Mutation_p.E190D|HLA-A_ENST00000376809.5_Missense_Mutation_p.E190D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	190	Alpha-2.		EW -> DG (in allele A*31:05).		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CGTGCGTGGAGTGGCTCCGCA	0.677									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	1082	0.216054	0.1679	0.2089	5008	,	,		13958	0.2183		0.2167	False		,,,				2504	0.2832				p.E190D		Atlas-SNP	.											HLA-A,colon,carcinoma,0,1	HLA-A	89	1	0			c.G570C						PASS	.	G	ASP/GLU	8,3012		1,6,1503	48.0	39.0	42.0		570	0.6	0.0	6	dbSNP_131	42	10,5400		1,8,2696	no	missense	HLA-A	NM_002116.7	45	2,14,4199	CC,CG,GG		0.1848,0.2649,0.2135	benign	190/366	29911271	18,8412	1510	2705	4215	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGTGGAGTGGCTC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.570G>C	6.37:g.29911271G>C	ENSP00000379873:p.Glu190Asp	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	367	75	0.20436	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	419	0.19184981684981686	56	0.11382113821138211	78	0.2154696132596685	139	0.243006993006993	146	0.19261213720316622	.	9.897	1.205898	0.22205	0.002649	0.001848	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00995	5.46;5.46;5.46;5.46	3.78	0.557	0.17260	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	1.991270	0.03551	U	0.225458	T	0.00637	0.0021	M	0.78916	2.43	0.80722	P	0.0	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.001;0.0;0.001;0.001	T	0.46582	-0.9181	9	0.62326	D	0.03	.	4.9635	0.14078	0.111:0.0:0.5236:0.3654	rs3129016;rs9260160;rs41553132	69;190;190;190;190;190;190	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	D	190	ENSP00000379873:E190D;ENSP00000366002:E190D;ENSP00000366005:E190D;ENSP00000365998:E190D	ENSP00000365998:E190D	E	+	3	2	HLA-A	30019250	0.578000	0.26717	0.003000	0.11579	0.119000	0.20118	1.433000	0.34947	-0.016000	0.14127	0.485000	0.47835	GAG	C|0.644;G|0.356	0.644	strong		0.677	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
FGFR4	2264	hgsc.bcm.edu	37	5	176516631	176516631	+	Missense_Mutation	SNP	G	G	A	rs1966265	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176516631G>A	ENST00000292408.4	+	2	273	c.28G>A	c.(28-30)Gtc>Atc	p.V10I	FGFR4_ENST00000393648.2_Missense_Mutation_p.V10I|FGFR4_ENST00000502906.1_Missense_Mutation_p.V10I|FGFR4_ENST00000292410.3_Missense_Mutation_p.V10I|FGFR4_ENST00000393637.1_Missense_Mutation_p.V10I|FGFR4_ENST00000507708.1_3'UTR	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	10			V -> I (in dbSNP:rs1966265). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:21882254, ECO:0000269|Ref.8}.		alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	CCTGTTGGGGGTCCTGCTGAG	0.607										TSP Lung(9;0.080)			g|||	1146	0.228834	0.0182	0.3184	5008	,	,		17888	0.5069		0.1799	False		,,,				2504	0.2137				p.V10I		Atlas-SNP	.											.	FGFR4	174	.	0			c.G28A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	269,4137	148.8+/-183.1	6,257,1940	59.0	54.0	55.0		28,28,28	-2.2	0.6	5	dbSNP_92	55	1952,6648	332.9+/-320.3	235,1482,2583	yes	missense,missense,missense	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	29,29,29	241,1739,4523	AA,AG,GG		22.6977,6.1053,17.0767	benign,benign,benign	10/803,10/763,10/803	176516631	2221,10785	2203	4300	6503	SO:0001583	missense	2264	exon1			TTGGGGGTCCTGC	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.28G>A	5.37:g.176516631G>A	ENSP00000292408:p.Val10Ile	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	253	85	0.335968	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	545	0.24954212454212454	13	0.026422764227642278	95	0.26243093922651933	304	0.5314685314685315	133	0.17546174142480211	g	0.003	-2.512008	0.00153	0.061053	0.226977	ENSG00000160867	ENST00000292408;ENST00000503708;ENST00000393648;ENST00000514472;ENST00000502906;ENST00000292410;ENST00000510911;ENST00000513166;ENST00000393637	T;T;T;D;T;T;T;D;T	0.88509	-1.17;-0.84;-1.13;-2.39;-1.17;-1.17;0.9;-2.32;-1.17	4.63	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	6.999999999979245E-6	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0	T	0.36648	-0.9739	8	0.31617	T	0.26	.	1.5311	0.02536	0.3612:0.135:0.3665:0.1373	rs1966265;rs2230268;rs17839798;rs59346453;rs1966265	10;10;10;10;10	B5A965;B4DVP5;P22455-2;E7EWF4;P22455	.;.;.;.;FGFR4_HUMAN	I	10	ENSP00000292408:V10I;ENSP00000424905:V10I;ENSP00000377259:V10I;ENSP00000426492:V10I;ENSP00000424960:V10I;ENSP00000292410:V10I;ENSP00000427222:V10I;ENSP00000422889:V10I;ENSP00000377254:V10I	ENSP00000292408:V10I	V	+	1	0	FGFR4	176449237	0.864000	0.29904	0.612000	0.29024	0.022000	0.10575	-0.136000	0.10405	-0.406000	0.07588	-1.652000	0.00757	GTC	G|0.804;A|0.196	0.196	strong		0.607	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
TLK2	11011	hgsc.bcm.edu	37	17	60650660	60650660	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:60650660T>C	ENST00000326270.9	+	12	1321	c.1053T>C	c.(1051-1053)ggT>ggC	p.G351G	TLK2_ENST00000346027.5_Silent_p.G351G|TLK2_ENST00000343388.7_Silent_p.G319G|TLK2_ENST00000542523.1_Silent_p.G319G|TLK2_ENST00000582809.1_Silent_p.G202G	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	351					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.G351G(2)|p.G350G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						CTGCCATGGGTCAGGCCCCTC	0.443																																					p.G351G		Atlas-SNP	.											TLK2_ENST00000346027,NS,carcinoma,0,3	TLK2	223	3	3	Substitution - coding silent(3)	endometrium(3)	c.T1053C						scavenged	.						58.0	54.0	56.0					17																	60650660		2203	4300	6503	SO:0001819	synonymous_variant	11011	exon12			CATGGGTCAGGCC	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.1053T>C	17.37:g.60650660T>C		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	395	5	0.0126582	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Silent	SNP	ENST00000326270.9	37																																																																																				.	.	none		0.443	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852	
OR51I2	390064	hgsc.bcm.edu	37	11	5474838	5474838	+	Silent	SNP	G	G	T	rs2030094	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5474838G>T	ENST00000341449.2	+	1	201	c.120G>T	c.(118-120)ggG>ggT	p.G40G	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	40					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGCCCTTGGGGGAAATACAG	0.567													G|||	2014	0.402157	0.4516	0.4539	5008	,	,		20631	0.2589		0.5	False		,,,				2504	0.3456				p.G40G		Atlas-SNP	.											OR51I2,colon,carcinoma,0,1	OR51I2	76	1	0			c.G120T						scavenged	.	G		2053,2349	568.3+/-382.3	479,1095,627	105.0	90.0	95.0		120	-1.4	0.0	11	dbSNP_94	95	4350,4244	581.8+/-391.3	1089,2172,1036	no	coding-synonymous	OR51I2	NM_001004754.2		1568,3267,1663	TT,TG,GG		49.3833,46.6379,49.269		40/313	5474838	6403,6593	2201	4297	6498	SO:0001819	synonymous_variant	390064	exon1			CCTTGGGGGAAAT	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"""GPCR / Class A : Olfactory receptors"""	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.120G>T	11.37:g.5474838G>T		Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_001004754	Q6IF81	Silent	SNP	ENST00000341449.2	37	CCDS31383.1																																																																																			G|0.552;T|0.448	0.448	strong		0.567	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
DNAH7	56171	hgsc.bcm.edu	37	2	196825402	196825402	+	Missense_Mutation	SNP	T	T	C	rs6719500	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:196825402T>C	ENST00000312428.6	-	18	2573	c.2473A>G	c.(2473-2475)Aaa>Gaa	p.K825E		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	825	Stem. {ECO:0000250}.		K -> E (in dbSNP:rs6719500).		cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CTTACTTTTTTTGTCATTGCC	0.418													T|||	781	0.15595	0.298	0.1239	5008	,	,		20877	0.0744		0.1402	False		,,,				2504	0.0869				p.K825E		Atlas-SNP	.											DNAH7,NS,carcinoma,+1,1	DNAH7	512	1	0			c.A2473G						PASS	.	T	GLU/LYS	1017,2753		128,761,996	163.0	158.0	159.0		2473	5.7	0.6	2	dbSNP_116	159	1118,7112		76,966,3073	yes	missense	DNAH7	NM_018897.2	56	204,1727,4069	CC,CT,TT		13.5844,26.9761,17.7917	benign	825/4025	196825402	2135,9865	1885	4115	6000	SO:0001583	missense	56171	exon18			CTTTTTTTGTCAT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.2473A>G	2.37:g.196825402T>C	ENSP00000311273:p.Lys825Glu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	180	87	0.483333	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	343	0.15705128205128205	158	0.32113821138211385	48	0.13259668508287292	31	0.05419580419580419	106	0.13984168865435356	T	0.008	-1.905870	0.00512	0.269761	0.135844	ENSG00000118997	ENST00000312428	T	0.60299	0.2	5.74	5.74	0.90152	Dynein heavy chain, domain-2 (1);	0.192711	0.39687	N	0.001289	T	0.00012	0.0000	N	0.05554	-0.025	0.58432	P	5.000000000032756E-6	B	0.10296	0.003	B	0.12156	0.007	T	0.15925	-1.0420	9	0.02654	T	1	.	7.6395	0.28286	0.0:0.0711:0.1416:0.7872	rs6719500;rs52822107;rs60531815;rs6719500	825	Q8WXX0	DYH7_HUMAN	E	825	ENSP00000311273:K825E	ENSP00000311273:K825E	K	-	1	0	DNAH7	196533647	0.942000	0.31987	0.593000	0.28771	0.213000	0.24496	2.786000	0.47790	2.187000	0.69744	0.528000	0.53228	AAA	T|0.836;C|0.164	0.164	strong		0.418	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
NLRP13	126204	hgsc.bcm.edu	37	19	56424443	56424443	+	Missense_Mutation	SNP	T	T	C	rs303997	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56424443T>C	ENST00000342929.3	-	5	739	c.740A>G	c.(739-741)cAg>cGg	p.Q247R	NLRP13_ENST00000588751.1_Missense_Mutation_p.Q247R	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	247	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		Q -> R (in dbSNP:rs303997). {ECO:0000269|PubMed:12563287}.				ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CAGCATAGCCTGCATTGCCAA	0.507													T|||	3329	0.664736	0.7405	0.5101	5008	,	,		17398	0.7302		0.5924	False		,,,				2504	0.6789				p.Q247R		Atlas-SNP	.											NLRP13,colon,carcinoma,0,2	NLRP13	220	2	0			c.A740G						PASS	.	T	ARG/GLN	3145,1261	702.3+/-406.9	1126,893,184	105.0	106.0	105.0		740	2.8	0.0	19	dbSNP_79	105	5241,3359	642.8+/-399.9	1600,2041,659	yes	missense	NLRP13	NM_176810.2	43	2726,2934,843	CC,CT,TT		39.0581,28.6201,35.5221	benign	247/1044	56424443	8386,4620	2203	4300	6503	SO:0001583	missense	126204	exon5			ATAGCCTGCATTG	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.740A>G	19.37:g.56424443T>C	ENSP00000343891:p.Gln247Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	56	0.408759	NM_176810	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	1395	0.6387362637362637	357	0.725609756097561	194	0.5359116022099447	406	0.7097902097902098	438	0.5778364116094987	T	11.93	1.785132	0.31593	0.713799	0.609419	ENSG00000173572	ENST00000342929	T	0.76839	-1.05	2.81	2.81	0.32909	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.00012	0.0000	N	0.05487	-0.04	0.80722	P	0.0	B	0.25609	0.13	B	0.28305	0.088	T	0.43180	-0.9407	8	0.39692	T	0.17	.	7.7212	0.28733	0.0:0.0:0.0:1.0	rs303997;rs306517;rs17668358;rs52826226;rs58328755;rs303997	247	Q86W25	NAL13_HUMAN	R	247	ENSP00000343891:Q247R	ENSP00000343891:Q247R	Q	-	2	0	NLRP13	61116255	0.947000	0.32204	0.006000	0.13384	0.103000	0.19146	4.167000	0.58209	1.271000	0.44313	0.482000	0.46254	CAG	C|0.641;N|0.000	0.641	strong		0.507	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
PRRC2A	7916	hgsc.bcm.edu	37	6	31603770	31603770	+	Silent	SNP	A	A	G	rs11229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31603770A>G	ENST00000376033.2	+	25	5802	c.5568A>G	c.(5566-5568)caA>caG	p.Q1856Q	PRRC2A_ENST00000376007.4_Silent_p.Q1856Q	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1856						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TGGACTCTCAATTACATCCAA	0.512													A|||	668	0.133387	0.2126	0.0793	5008	,	,		13510	0.0714		0.1461	False		,,,				2504	0.1155				p.Q1856Q		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A5568G						PASS	.	A	,	880,3526	343.1+/-307.5	85,710,1408	67.0	60.0	63.0		5568,5568	0.3	1.0	6	dbSNP_52	63	1542,7058	289.6+/-299.4	146,1250,2904	yes	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	231,1960,4312	GG,GA,AA		17.9302,19.9728,18.6222	,	1856/2158,1856/2158	31603770	2422,10584	2203	4300	6503	SO:0001819	synonymous_variant	7916	exon25			CTCTCAATTACAT	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5568A>G	6.37:g.31603770A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	215	91	0.423256	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1	286	0.13095238095238096	112	0.22764227642276422	30	0.08287292817679558	33	0.057692307692307696	111	0.14643799472295516	A	7.453	0.642991	0.14451	0.199728	0.179302	ENSG00000204469	ENST00000424184;ENST00000435052	.	.	.	5.24	0.33	0.15929	.	.	.	.	.	T	0.32255	0.0823	.	.	.	0.09310	P	0.9999999855904	.	.	.	.	.	.	T	0.20438	-1.0275	4	0.87932	D	0	-4.865	7.5454	0.27764	0.2257:0.1228:0.6515:0.0	rs11229;rs1046090;rs3173343;rs9267522;rs17354367;rs17398279;rs52803694;rs61060019;rs9267522	.	.	.	V	1850;1839	.	ENSP00000407986:I1850V	I	+	1	0	PRRC2A	31711749	0.999000	0.42202	0.987000	0.45799	0.746000	0.42486	0.221000	0.17680	-0.122000	0.11766	-1.811000	0.00612	ATT	A|0.841;G|0.159	0.159	strong		0.512	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
FCGR2A	2212	hgsc.bcm.edu	37	1	161487863	161487863	+	Silent	SNP	C	C	T	rs143182858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161487863C>T	ENST00000271450.6	+	7	917	c.879C>T	c.(877-879)ccC>ccT	p.P293P	FCGR2A_ENST00000367972.4_Silent_p.P292P|RP11-25K21.6_ENST00000537821.2_RNA|FCGR2A_ENST00000486608.1_3'UTR	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	293					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTCTGAACCCCAGGGCACCTA	0.453													C|||	607	0.121206	0.0242	0.1239	5008	,	,		19315	0.2758		0.1183	False		,,,				2504	0.0941				p.P293P		Atlas-SNP	.											.	FCGR2A	38	.	0			c.C879T						PASS	.	C	,	150,4256		2,146,2055	69.0	72.0	71.0		879,876	0.6	0.0	1	dbSNP_134	71	982,7612		48,886,3363	no	coding-synonymous,coding-synonymous	FCGR2A	NM_001136219.1,NM_021642.3	,	50,1032,5418	TT,TC,CC		11.4266,3.4044,8.7077	,	293/318,292/317	161487863	1132,11868	2203	4297	6500	SO:0001819	synonymous_variant	2212	exon7			GAACCCCAGGGCA	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3616	protein-coding gene	gene with protein product	"""Immunoglobulin G Fc receptor II"""	146790	"""Fc fragment of IgG, low affinity IIa, receptor for (CD32)"""	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.879C>T	1.37:g.161487863C>T		Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	450	138	0.306667	NM_001136219	Q8WUN1|Q8WW64	Silent	SNP	ENST00000271450.6	37	CCDS44264.1																																																																																			C|0.901;T|0.099	0.099	strong		0.453	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48603434	48603434	+	Missense_Mutation	SNP	C	C	T	rs61753813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48603434C>T	ENST00000323776.5	+	14	2266	c.2104C>T	c.(2104-2106)Cgg>Tgg	p.R702W	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.R665W	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			TCAAGTGCCCCGGCCTGAGAA	0.597													C|||	56	0.0111821	0.0008	0.0115	5008	,	,		17022	0.0		0.0378	False		,,,				2504	0.0092				p.R702W		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C2104T						PASS	.	C	TRP/ARG	26,4380	33.5+/-64.1	0,26,2177	61.0	52.0	55.0		2104	3.2	0.0	17	dbSNP_129	55	333,8267	113.1+/-173.2	4,325,3971	yes	missense	MYCBPAP	NM_032133.4	101	4,351,6148	TT,TC,CC		3.8721,0.5901,2.7603	benign	702/985	48603434	359,12647	2203	4300	6503	SO:0001583	missense	84073	exon14			GTGCCCCGGCCTG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.2104C>T	17.37:g.48603434C>T	ENSP00000323184:p.Arg702Trp	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	38	0.0173992673992674	0	0.0	7	0.019337016574585635	0	0.0	31	0.040897097625329816	C	10.48	1.360907	0.24684	0.005901	0.038721	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.22336	1.98;1.96	5.26	3.15	0.36227	.	1.911610	0.02198	N	0.062024	T	0.03136	0.0092	N	0.13043	0.29	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.16424	-1.0403	10	0.33141	T	0.24	-0.9009	6.6489	0.22951	0.3715:0.543:0.0:0.0855	rs61753813	665	Q8TBZ2	MYBPP_HUMAN	W	702;665	ENSP00000323184:R702W;ENSP00000397209:R665W	ENSP00000323184:R702W	R	+	1	2	MYCBPAP	45958433	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.485000	0.06520	0.732000	0.32470	0.655000	0.94253	CGG	C|0.974;T|0.026	0.026	strong		0.597	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
RBM19	9904	hgsc.bcm.edu	37	12	114377885	114377885	+	Silent	SNP	G	G	C	rs2290790	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:114377885G>C	ENST00000545145.2	-	15	1896	c.1818C>G	c.(1816-1818)acC>acG	p.T606T	RBM19_ENST00000261741.5_Silent_p.T606T|RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000392561.3_Silent_p.T606T	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	606	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					AATGGCCGAAGGTCTCCTGCA	0.632													G|||	1099	0.219449	0.0688	0.2565	5008	,	,		17610	0.1756		0.3191	False		,,,				2504	0.3395				p.T606T		Atlas-SNP	.											.	RBM19	117	.	0			c.C1818G						PASS	.	G	,,	469,3937	221.0+/-238.3	31,407,1765	67.0	72.0	70.0		1818,1818,1818	0.1	0.2	12	dbSNP_100	70	2825,5775	441.5+/-359.8	470,1885,1945	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	501,2292,3710	CC,CG,GG		32.8488,10.6446,25.3268	,,	606/961,606/961,606/961	114377885	3294,9712	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon15			GCCGAAGGTCTCC	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1818C>G	12.37:g.114377885G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.761;C|0.239	0.239	strong		0.632	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
DOCK5	80005	hgsc.bcm.edu	37	8	25159885	25159885	+	Silent	SNP	G	G	A	rs907157	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:25159885G>A	ENST00000276440.7	+	10	935	c.891G>A	c.(889-891)gtG>gtA	p.V297V	DOCK5_ENST00000481100.1_Silent_p.V297V	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	297					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TCAGCCTTGTGTGCCAGATTG	0.582													G|||	1392	0.277955	0.0514	0.3646	5008	,	,		18282	0.244		0.498	False		,,,				2504	0.3313				p.V297V	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.G891A						PASS	.	G		485,3921	227.5+/-242.7	24,437,1742	93.0	71.0	79.0		891	4.7	1.0	8	dbSNP_86	79	4017,4583	547.9+/-385.3	924,2169,1207	no	coding-synonymous	DOCK5	NM_024940.6		948,2606,2949	AA,AG,GG		46.7093,11.0077,34.6148		297/1871	25159885	4502,8504	2203	4300	6503	SO:0001819	synonymous_variant	80005	exon10			CCTTGTGTGCCAG		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.891G>A	8.37:g.25159885G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1	681	0.3118131868131868	28	0.056910569105691054	145	0.4005524861878453	138	0.24125874125874125	370	0.48812664907651715	G	10.41	1.341314	0.24339	0.110077	0.467093	ENSG00000147459	ENST00000444569	T	0.18502	2.21	5.55	4.67	0.58626	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48681	-0.9014	6	0.87932	D	0	.	10.5137	0.44876	0.1514:0.0:0.8486:0.0	rs907157;rs17775605;rs17845314;rs17858153;rs61496588;rs907157	.	.	.	M	69	ENSP00000414125:V69M	ENSP00000414125:V69M	V	+	1	0	DOCK5	25215802	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	1.503000	0.35715	1.332000	0.45431	0.650000	0.86243	GTG	G|0.698;N|0.000	.	strong		0.582	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
LPHN3	23284	hgsc.bcm.edu	37	4	62845326	62845326	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:62845326G>A	ENST00000514591.1	+	17	2976	c.2647G>A	c.(2647-2649)Gtt>Att	p.V883I	LPHN3_ENST00000514996.1_Missense_Mutation_p.V883I|LPHN3_ENST00000509896.1_Missense_Mutation_p.V951I|LPHN3_ENST00000514157.1_Missense_Mutation_p.V883I|LPHN3_ENST00000512091.2_Missense_Mutation_p.V883I|LPHN3_ENST00000507164.1_Missense_Mutation_p.V951I|LPHN3_ENST00000507625.1_Missense_Mutation_p.V951I|LPHN3_ENST00000506720.1_Missense_Mutation_p.V951I|LPHN3_ENST00000504896.1_Missense_Mutation_p.V883I|LPHN3_ENST00000506746.1_Missense_Mutation_p.V951I|LPHN3_ENST00000508946.1_Missense_Mutation_p.V883I|LPHN3_ENST00000545650.1_Missense_Mutation_p.V883I|LPHN3_ENST00000506700.1_Missense_Mutation_p.V883I|LPHN3_ENST00000508693.1_Missense_Mutation_p.V951I|LPHN3_ENST00000511324.1_Missense_Mutation_p.V951I			Q9HAR2	LPHN3_HUMAN	latrophilin 3	870					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GATCACGTGGGTTGGAATTTT	0.458																																					p.V883I		Atlas-SNP	.											.	LPHN3	800	.	0			c.G2647A						PASS	.						321.0	314.0	316.0					4																	62845326		1998	4191	6189	SO:0001583	missense	23284	exon15			ACGTGGGTTGGAA	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2647G>A	4.37:g.62845326G>A	ENSP00000422533:p.Val883Ile	Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	435	66	0.151724	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.8|25.8	4.679692|4.679692	0.88542|0.88542	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000502815|ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.54279	.|0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.5|5.5	5.5|5.5	0.81552|0.81552	.|GPCR, family 2-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64789|0.64789	0.2630|0.2630	L|L	0.37800|0.37800	1.135|1.135	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.69078	.|0.997;0.997;0.996	.|D;D;D	.|0.79108	.|0.992;0.992;0.987	T|T	0.61207|0.61207	-0.7109|-0.7109	5|10	.|0.35671	.|T	.|0.21	.|.	19.0068|19.0068	0.92854|0.92854	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|883;870;883	.|E9PE04;Q9HAR2;Q9HAR2-2	.|.;LPHN3_HUMAN;.	D|I	340|883;883;951;951;883;883;870;883;951;951;951;883;883;883;951;951;883	.|ENSP00000423388:V883I;ENSP00000422533:V883I;ENSP00000423787:V951I;ENSP00000425033:V951I;ENSP00000424120:V883I;ENSP00000439831:V883I;ENSP00000421476:V951I;ENSP00000424030:V951I;ENSP00000421372:V951I;ENSP00000425201:V883I;ENSP00000423434:V883I;ENSP00000421627:V883I;ENSP00000420931:V951I;ENSP00000425884:V951I;ENSP00000424258:V883I	.|ENSP00000280009:V883I	G|V	+|+	2|1	0|0	LPHN3|LPHN3	62527921|62527921	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.808000|9.808000	0.99193|0.99193	2.580000|2.580000	0.87095|0.87095	0.467000|0.467000	0.42956|0.42956	GGT|GTT	.	.	none		0.458	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
EME1	146956	hgsc.bcm.edu	37	17	48455985	48455985	+	Silent	SNP	A	A	T	rs2189712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48455985A>T	ENST00000338165.4	+	4	1015	c.933A>T	c.(931-933)acA>acT	p.T311T	EME1_ENST00000393271.2_Silent_p.T311T|EME1_ENST00000511648.2_Silent_p.T311T	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	311					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.T311T(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			AGGAGCCAACAGTACTGGTGT	0.587								Direct reversal of damage;Homologous recombination					A|||	715	0.142772	0.0416	0.2911	5008	,	,		18564	0.0794		0.2465	False		,,,				2504	0.1329				p.T311T		Atlas-SNP	.											EME1,NS,carcinoma,0,1	EME1	39	1	1	Substitution - coding silent(1)	stomach(1)	c.A933T						PASS	.	A	,	356,4050	184.0+/-211.4	21,314,1868	150.0	148.0	149.0		933,933	-1.3	0.1	17	dbSNP_96	149	2244,6356	380.3+/-339.6	297,1650,2353	no	coding-synonymous,coding-synonymous	EME1	NM_001166131.1,NM_152463.2	,	318,1964,4221	TT,TA,AA		26.093,8.0799,19.9908	,	311/584,311/571	48455985	2600,10406	2203	4300	6503	SO:0001819	synonymous_variant	146956	exon4			GCCAACAGTACTG	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"""	610885	"""essential meiotic endonuclease 1 homolog 1 (S. pombe)"""			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.933A>T	17.37:g.48455985A>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	161	86	0.534162	NM_152463	Q96N62	Silent	SNP	ENST00000338165.4	37	CCDS11565.1	340	0.15567765567765568	19	0.03861788617886179	94	0.2596685082872928	43	0.07517482517482517	184	0.24274406332453827	A	2.611	-0.290728	0.05568	0.080799	0.26093	ENSG00000154920	ENST00000511519	T	0.19394	2.15	5.32	-1.3	0.09259	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41124	-0.9526	5	0.87932	D	0	-20.2006	0.2198	0.00167	0.331:0.212:0.2412:0.2157	rs2189712;rs2189712	.	.	.	C	153	ENSP00000423029:S153C	ENSP00000423029:S153C	S	+	1	0	EME1	45810984	0.000000	0.05858	0.071000	0.20095	0.004000	0.04260	-0.478000	0.06575	0.137000	0.18759	-0.366000	0.07423	AGT	A|0.812;T|0.188	0.188	strong		0.587	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
COL11A1	1301	hgsc.bcm.edu	37	1	103352451	103352451	+	Silent	SNP	A	A	G	rs2229783	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:103352451A>G	ENST00000370096.3	-	63	5082	c.4770T>C	c.(4768-4770)atT>atC	p.I1590I	COL11A1_ENST00000512756.1_Silent_p.I1474I|COL11A1_ENST00000358392.2_Silent_p.I1602I|COL11A1_ENST00000353414.4_Silent_p.I1551I	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1590	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TCATATGCTCAATGTCTTGTT	0.408													G|||	2427	0.484625	0.0499	0.7478	5008	,	,		17459	0.6647		0.6064	False		,,,				2504	0.5746				p.I1602I		Atlas-SNP	.											.	COL11A1	972	.	0			c.T4806C						PASS	.	G	,,,	615,3791	769.4+/-413.7	55,505,1643	201.0	191.0	194.0		4653,4770,4806,4422	-5.2	0.8	1	dbSNP_98	194	5217,3383	501.1+/-375.4	1598,2021,681	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL11A1	NM_001190709.1,NM_001854.3,NM_080629.2,NM_080630.3	,,,	1653,2526,2324	GG,GA,AA		39.3372,13.9582,44.8408	,,,	1551/1768,1590/1807,1602/1819,1474/1691	103352451	5832,7174	2203	4300	6503	SO:0001819	synonymous_variant	1301	exon63			ATGCTCAATGTCT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.4770T>C	1.37:g.103352451A>G		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	201	201	1	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	37	CCDS778.1																																																																																			A|0.534;G|0.466	0.466	strong		0.408	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
MYO15A	51168	hgsc.bcm.edu	37	17	18058521	18058521	+	Silent	SNP	C	C	T	rs712272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18058521C>T	ENST00000205890.5	+	46	8660	c.8322C>T	c.(8320-8322)tcC>tcT	p.S2774S	MYO15A_ENST00000418233.3_Silent_p.S38S|MYO15A_ENST00000585180.1_Silent_p.S38S	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2774	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TCTACTTCTCCCGCATCTTCC	0.602													C|||	1078	0.215256	0.1846	0.2983	5008	,	,		17398	0.0675		0.3907	False		,,,				2504	0.1697				p.S2774S		Atlas-SNP	.											.	MYO15A	268	.	0			c.C8322T						PASS	.	C		956,3260		106,744,1258	40.0	49.0	46.0		8322	-0.5	1.0	17	dbSNP_86	46	3446,4990		723,2000,1495	no	coding-synonymous	MYO15A	NM_016239.3		829,2744,2753	TT,TC,CC		40.8487,22.6755,34.7929		2774/3531	18058521	4402,8250	2108	4218	6326	SO:0001819	synonymous_variant	51168	exon45			CTTCTCCCGCATC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8322C>T	17.37:g.18058521C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																			C|0.696;T|0.304	0.304	strong		0.602	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
RTP4	64108	hgsc.bcm.edu	37	3	187089031	187089031	+	Missense_Mutation	SNP	C	C	A	rs1003995|rs3926263	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:187089031C>A	ENST00000259030.2	+	2	721	c.611C>A	c.(610-612)gCt>gAt	p.A204D		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	204				A -> D (in Ref. 1; AAT70683, 2; CAC14309 and 4; AAH13161). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		AACCAGTCAGCTGAGGCAAAA	0.493													C|||	1442	0.287939	0.0348	0.4524	5008	,	,		19751	0.4504		0.3419	False		,,,				2504	0.2904				p.A204D		Atlas-SNP	.											.	RTP4	20	.	0			c.C611A						PASS	.	C	ASP/ALA	449,3957	215.1+/-234.2	22,405,1776	85.0	69.0	74.0		611	0.7	0.0	3	dbSNP_86	74	2973,5627	462.3+/-365.7	509,1955,1836	yes	missense	RTP4	NM_022147.2	126	531,2360,3612	AA,AC,CC		34.5698,10.1906,26.3109	possibly-damaging	204/247	187089031	3422,9584	2203	4300	6503	SO:0001583	missense	64108	exon2			AGTCAGCTGAGGC	BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"""Receptor transporter proteins"""	23992	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 4"""	609350	"""receptor transporter protein 4"""			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.611C>A	3.37:g.187089031C>A	ENSP00000259030:p.Ala204Asp	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_022147	Q9H4F3	Missense_Mutation	SNP	ENST00000259030.2	37	CCDS33910.1	684	0.3131868131868132	29	0.05894308943089431	145	0.4005524861878453	252	0.4405594405594406	258	0.3403693931398417	C	11.95	1.790253	0.31685	0.101906	0.345698	ENSG00000136514	ENST00000259030	T	0.19806	2.12	2.56	0.673	0.17941	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.40476	0.718	B	0.36244	0.22	T	0.45702	-0.9243	8	0.28530	T	0.3	1.011	3.5252	0.07757	0.0:0.5711:0.2697:0.1592	rs3926263;rs3926264	204	Q96DX8	RTP4_HUMAN	D	204	ENSP00000259030:A204D	ENSP00000259030:A204D	A	+	2	0	RTP4	188571725	0.002000	0.14202	0.000000	0.03702	0.021000	0.10359	0.841000	0.27613	0.154000	0.19237	0.655000	0.94253	GCT	C|0.721;A|0.278	0.278	strong		0.493	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
CSMD2	114784	hgsc.bcm.edu	37	1	34038214	34038214	+	Missense_Mutation	SNP	T	T	C	rs2641962	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:34038214T>C	ENST00000373381.4	-	50	7830	c.7654A>G	c.(7654-7656)Atg>Gtg	p.M2552V		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2554	Sushi 15. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CAGCTGTACATGGCCTTGGTT	0.552													C|||	2554	0.509984	0.5424	0.6542	5008	,	,		17034	0.4087		0.494	False		,,,				2504	0.4847				p.M2554V		Atlas-SNP	.											.	CSMD2	946	.	0			c.A7660G						PASS	.	C	VAL/MET	2281,2125	578.8+/-384.8	606,1069,528	144.0	122.0	130.0		7660	1.7	0.8	1	dbSNP_100	130	4026,4574	596.6+/-393.6	938,2150,1212	yes	missense	CSMD2	NM_052896.3	21	1544,3219,1740	CC,CT,TT		46.814,48.2297,48.493	benign	2554/3488	34038214	6307,6699	2203	4300	6503	SO:0001583	missense	114784	exon51			TGTACATGGCCTT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.7654A>G	1.37:g.34038214T>C	ENSP00000362479:p.Met2552Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		1094	0.5009157509157509	281	0.5711382113821138	218	0.6022099447513812	229	0.40034965034965037	366	0.48284960422163586	C	0.024	-1.389467	0.01185	0.517703	0.46814	ENSG00000121904	ENST00000373381	T	0.62788	-0.0	5.65	1.67	0.24075	Complement control module (2);Sushi/SCR/CCP (3);	0.437433	0.24698	N	0.036329	T	0.00012	0.0000	N	0.00149	-1.99	0.26660	P	0.9719208	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44345	-0.9334	9	0.10636	T	0.68	.	6.1601	0.20360	0.1202:0.5973:0.0:0.2824	rs2641962;rs52795195;rs58510459;rs2641962	2554;2552	Q7Z408;E7EUA6	CSMD2_HUMAN;.	V	2552	ENSP00000362479:M2552V	ENSP00000241312:M2554V	M	-	1	0	CSMD2	33810801	0.095000	0.21747	0.819000	0.32651	0.299000	0.27559	0.282000	0.18829	-0.127000	0.11661	-1.886000	0.00541	ATG	C|0.495;N|0.000	0.495	strong		0.552	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
SLC1A5	6510	hgsc.bcm.edu	37	19	47278859	47278859	+	Missense_Mutation	SNP	C	C	G	rs3027961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47278859C>G	ENST00000542575.2	-	8	2162	c.1534G>C	c.(1534-1536)Gtc>Ctc	p.V512L	SLC1A5_ENST00000434726.2_Missense_Mutation_p.V310L|FKRP_ENST00000600646.1_Intron|SLC1A5_ENST00000412532.2_Missense_Mutation_p.V284L|SLC1A5_ENST00000594991.1_Missense_Mutation_p.V336L	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	512			V -> L (in dbSNP:rs3027961). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:19690332}.		amino acid transport (GO:0006865)|extracellular amino acid transport (GO:0006860)|glutamine transport (GO:0006868)|ion transport (GO:0006811)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-glutamine transmembrane transporter activity (GO:0015186)|L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)|receptor activity (GO:0004872)|sodium:dicarboxylate symporter activity (GO:0017153)|virus receptor activity (GO:0001618)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(2)|stomach(1)	13		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	TCAGTGGGGACTGGCAGCGGA	0.587													-|||	660	0.131789	0.146	0.1254	5008	,	,		14789	0.001		0.2306	False		,,,				2504	0.1503				p.V512L		Atlas-SNP	.											.	SLC1A5	31	.	0			c.G1534C						PASS	.		LEU/VAL,LEU/VAL,LEU/VAL	768,3638		60,648,1495	146.0	145.0	146.0		850,928,1534	-2.1	0.0	19	dbSNP_102	146	2255,6345		302,1651,2347	yes	missense,missense,missense	SLC1A5	NM_001145144.1,NM_001145145.1,NM_005628.2	32,32,32	362,2299,3842	GG,GC,CC		26.2209,17.4308,23.2431	benign,benign,benign	284/314,310/340,512/542	47278859	3023,9983	2203	4300	6503	SO:0001583	missense	6510	exon8			TGGGGACTGGCAG	U53347	CCDS12692.1, CCDS46125.1, CCDS46126.1	19q13.32	2013-07-15			ENSG00000105281	ENSG00000105281		"""Solute carriers"""	10943	protein-coding gene	gene with protein product		109190		RDRC, M7V1		8702519, 10051606	Standard	NM_005628		Approved	AAAT, ASCT2	uc002pfs.3	Q15758	OTTHUMG00000183434	ENST00000542575.2:c.1534G>C	19.37:g.47278859C>G	ENSP00000444408:p.Val512Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	210	97	0.461905	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Missense_Mutation	SNP	ENST00000542575.2	37	CCDS12692.1	303	0.13873626373626374	68	0.13821138211382114	53	0.1464088397790055	2	0.0034965034965034965	180	0.23746701846965698	-	11.76	1.734189	0.30684	0.174308	0.262209	ENSG00000105281	ENST00000542575;ENST00000434726;ENST00000412532;ENST00000306894	T;T;T	0.63096	0.81;-0.02;-0.01	4.58	-2.11	0.07187	.	1.994340	0.02456	N	0.086045	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.09185	-1.0686	9	0.02654	T	1	-3.983	6.1016	0.20051	0.0:0.373:0.3862:0.2408	rs3027961;rs17855343;rs52803135;rs3027961	310;512;512	E9PC01;Q15758;Q71UA6	.;AAAT_HUMAN;.	L	512;310;284;519	ENSP00000444408:V512L;ENSP00000406532:V310L;ENSP00000397924:V284L	ENSP00000303623:V519L	V	-	1	0	SLC1A5	51970699	0.000000	0.05858	0.000000	0.03702	0.339000	0.28857	-0.180000	0.09754	-0.280000	0.09154	0.550000	0.68814	GTC	C|0.796;G|0.204	0.204	strong		0.587	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
SERPINA9	327657	hgsc.bcm.edu	37	14	94936062	94936062	+	Missense_Mutation	SNP	G	G	A	rs45438596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94936062G>A	ENST00000380365.3	-	2	194	c.116C>T	c.(115-117)aCc>aTc	p.T39I	SERPINA9_ENST00000298845.7_Missense_Mutation_p.T57I|SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000546329.1_Intron|SERPINA9_ENST00000337425.5_Missense_Mutation_p.T57I|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000448305.2_Intron			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	39					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TGAGGCAGGGGTGCTCTTTGT	0.567													G|||	93	0.0185703	0.0393	0.0144	5008	,	,		17740	0.0		0.0278	False		,,,				2504	0.0031				p.T57I		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C170T						PASS	.	G	ILE/THR,ILE/THR	176,3872		7,162,1855	86.0	89.0	88.0		170,170	-8.0	0.0	14	dbSNP_127	88	245,8115		2,241,3937	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	89,89	9,403,5792	AA,AG,GG		2.9306,4.3478,3.393	possibly-damaging,possibly-damaging	57/336,57/436	94936062	421,11987	2024	4180	6204	SO:0001583	missense	327657	exon2			GCAGGGGTGCTCT	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.116C>T	14.37:g.94936062G>A	ENSP00000369723:p.Thr39Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	92	51	0.554348	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		40	0.018315018315018316	16	0.032520325203252036	4	0.011049723756906077	0	0.0	20	0.026385224274406333	G	11.98	1.800787	0.31869	0.043478	0.029306	ENSG00000170054	ENST00000298845;ENST00000337425;ENST00000380365	D;D;D	0.87571	-2.27;-2.27;-2.27	3.99	-7.98	0.01135	Serpin domain (1);	1.422810	0.05300	U	0.522890	T	0.41558	0.1164	N	0.08118	0	0.09310	N	1	B;B;B	0.18968	0.007;0.032;0.021	B;B;B	0.22386	0.01;0.039;0.025	T	0.57825	-0.7744	10	0.54805	T	0.06	.	9.7894	0.40697	0.0:0.3432:0.454:0.2028	rs45438596;rs61743375	39;57;57	Q86WD7;Q86WD7-7;Q86WD7-2	SPA9_HUMAN;.;.	I	57;57;39	ENSP00000298845:T57I;ENSP00000337133:T57I;ENSP00000369723:T39I	ENSP00000298845:T57I	T	-	2	0	SERPINA9	94005815	0.000000	0.05858	0.000000	0.03702	0.438000	0.31896	-1.284000	0.02793	-1.491000	0.01840	0.313000	0.20887	ACC	G|0.979;A|0.021	0.021	strong		0.567	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
ZPBP2	124626	hgsc.bcm.edu	37	17	38031674	38031674	+	Silent	SNP	C	C	T	rs10852935	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38031674C>T	ENST00000348931.4	+	7	1067	c.876C>T	c.(874-876)tgC>tgT	p.C292C	ZPBP2_ENST00000377940.3_Silent_p.C270C|ZPBP2_ENST00000584588.1_Silent_p.C219C	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	292					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)		p.C292C(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			ACAGTAATTGCGCTAGCTGTT	0.358													C|||	1453	0.290136	0.1135	0.3415	5008	,	,		15697	0.2827		0.4722	False		,,,				2504	0.3129				p.C292C		Atlas-SNP	.											ZPBP2,colon,carcinoma,0,2	ZPBP2	33	2	1	Substitution - coding silent(1)	stomach(1)	c.C876T						PASS	.	C	,	652,3754	276.9+/-273.4	46,560,1597	57.0	52.0	54.0		810,876	-9.6	0.6	17	dbSNP_120	54	3869,4731	535.7+/-382.9	859,2151,1290	no	coding-synonymous,coding-synonymous	ZPBP2	NM_198844.2,NM_199321.2	,	905,2711,2887	TT,TC,CC		44.9884,14.798,34.7609	,	270/317,292/339	38031674	4521,8485	2203	4300	6503	SO:0001819	synonymous_variant	124626	exon7			TAATTGCGCTAGC	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.876C>T	17.37:g.38031674C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_199321	A8K8L8|Q6X783|Q86XL5	Silent	SNP	ENST00000348931.4	37	CCDS11352.1																																																																																			C|0.654;T|0.346	0.346	strong		0.358	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844	
SAMSN1	64092	hgsc.bcm.edu	37	21	15954528	15954528	+	Missense_Mutation	SNP	G	G	A	rs2822785	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:15954528G>A	ENST00000285670.2	-	2	364	c.190C>T	c.(190-192)Cac>Tac	p.H64Y	SAMSN1-AS1_ENST00000449214.1_RNA	NM_001256370.1	NP_001243299.1	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	0					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		GAGGAGCAGTGGTCCCAGGGT	0.468													G|||	1439	0.28734	0.1974	0.4654	5008	,	,		19067	0.1458		0.4384	False		,,,				2504	0.273				p.H64Y		Atlas-SNP	.											.	SAMSN1	112	.	0			c.C190T						PASS	.																																			SO:0001583	missense	64092	exon2			AGCAGTGGTCCCA	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	10528	protein-coding gene	gene with protein product	"""nuclear localization signals, SAM and SH3 domain containing 1"", ""SAM and SH3 domain containing 2"", ""hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1"", ""Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"""	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000285670.2:c.190C>T	21.37:g.15954528G>A	ENSP00000285670:p.His64Tyr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000285670.2	37	CCDS58786.1	687|687	0.31456043956043955|0.31456043956043955	98|98	0.1991869918699187|0.1991869918699187	174|174	0.48066298342541436|0.48066298342541436	89|89	0.1555944055944056|0.1555944055944056	326|326	0.43007915567282323|0.43007915567282323	G|G	8.528|8.528	0.870416|0.870416	0.17322|0.17322	.|.	.|.	ENSG00000155307|ENSG00000243440	ENST00000285670|ENST00000442499;ENST00000389438	T|.	0.42513|.	0.97|.	5.65|5.65	-2.47|-2.47	0.06442|0.06442	.|.	0.518762|.	0.17792|.	N|.	0.161851|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	8.000000000008E-6|8.000000000008E-6	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.47368|0.47368	-0.9123|-0.9123	8|3	0.59425|.	D|.	0.04|.	-8.5588|-8.5588	1.9003|1.9003	0.03266|0.03266	0.1033:0.2036:0.2507:0.4425|0.1033:0.2036:0.2507:0.4425	rs2822785;rs17274353;rs52815372;rs60384084;rs2822785|rs2822785;rs17274353;rs52815372;rs60384084;rs2822785	64|.	F8WAA1|.	.|.	Y|L	64|271;150	ENSP00000285670:H64Y|.	ENSP00000285670:H64Y|.	H|P	-|-	1|2	0|0	SAMSN1|AF165138.7	14876399|14876399	0.801000|0.801000	0.28930|0.28930	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.372000|0.372000	0.20467|0.20467	-0.604000|-0.604000	0.05760|0.05760	-0.136000|-0.136000	0.14681|0.14681	CAC|CCA	G|0.692;A|0.307	0.307	strong		0.468	SAMSN1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157913.1		
TMEM43	79188	hgsc.bcm.edu	37	3	14175262	14175262	+	Missense_Mutation	SNP	T	T	C	rs2340917	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14175262T>C	ENST00000306077.4	+	7	790	c.536T>C	c.(535-537)aTg>aCg	p.M179T	RP11-434D12.1_ENST00000608606.1_5'Flank	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	179			M -> T (in dbSNP:rs2340917). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						GAGTCATTCATGGCAACAGCC	0.587													C|||	2320	0.463259	0.4508	0.5058	5008	,	,		17856	0.6756		0.2624	False		,,,				2504	0.4376				p.M179T		Atlas-SNP	.											.	TMEM43	33	.	0			c.T536C						PASS	.	C	THR/MET	1787,2619	643.1+/-397.8	369,1049,785	183.0	174.0	177.0		536	5.3	0.3	3	dbSNP_100	177	2541,6059	692.5+/-404.6	389,1763,2148	yes	missense	TMEM43	NM_024334.2	81	758,2812,2933	CC,CT,TT		29.5465,40.5583,33.2769	benign	179/401	14175262	4328,8678	2203	4300	6503	SO:0001583	missense	79188	exon7			CATTCATGGCAAC	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"""arrhythmogenic right ventricular dysplasia 5"""	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.536T>C	3.37:g.14175262T>C	ENSP00000303992:p.Met179Thr	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	207	123	0.594203	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	37	CCDS2618.1	994	0.4551282051282051	243	0.49390243902439024	177	0.4889502762430939	375	0.6555944055944056	199	0.262532981530343	C	2.349	-0.349307	0.05173	0.405583	0.295465	ENSG00000170876	ENST00000306077	T	0.28666	1.6	5.32	5.32	0.75619	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00368	-1.59	0.47441	P	5.760000000000209E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	9	0.02654	T	1	-14.0095	14.2173	0.65802	0.0:0.9278:0.0:0.0722	rs2340917;rs3796313;rs17856368;rs52809893;rs58039334;rs2340917	179	Q9BTV4	TMM43_HUMAN	T	179	ENSP00000303992:M179T	ENSP00000303992:M179T	M	+	2	0	TMEM43	14150263	0.992000	0.36948	0.348000	0.25681	0.370000	0.29829	3.048000	0.49862	1.246000	0.43901	-0.186000	0.12905	ATG	T|0.607;C|0.393	0.393	strong		0.587	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334	
GTF3C1	2975	hgsc.bcm.edu	37	16	27474910	27474910	+	Missense_Mutation	SNP	A	A	G	rs12919017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:27474910A>G	ENST00000356183.4	-	35	5891	c.5876T>C	c.(5875-5877)tTc>tCc	p.F1959S	GTF3C1_ENST00000567806.1_5'Flank|GTF3C1_ENST00000561623.1_Missense_Mutation_p.F1934S	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1959			F -> S (in dbSNP:rs12919017).		5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						ACTCTCTGTGAACCCTGAGGG	0.602													A|||	344	0.0686901	0.0098	0.1844	5008	,	,		16004	0.001		0.161	False		,,,				2504	0.0409				p.F1959S		Atlas-SNP	.											.	GTF3C1	210	.	0			c.T5876C						PASS	.	A	SER/PHE	175,4219	114.2+/-152.2	1,173,2023	97.0	94.0	95.0		5876	-2.3	0.0	16	dbSNP_121	95	1311,7289	256.3+/-280.9	92,1127,3081	yes	missense	GTF3C1	NM_001520.3	155	93,1300,5104	GG,GA,AA		15.2442,3.9827,11.436	benign	1959/2110	27474910	1486,11508	2197	4300	6497	SO:0001583	missense	2975	exon35			TCTGTGAACCCTG	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.5876T>C	16.37:g.27474910A>G	ENSP00000348510:p.Phe1959Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	191	0.08745421245421245	6	0.012195121951219513	59	0.16298342541436464	0	0.0	126	0.1662269129287599	A	11.04	1.522915	0.27211	0.039827	0.152442	ENSG00000077235	ENST00000356183	T	0.20598	2.06	4.58	-2.26	0.06867	.	3.038090	0.00807	N	0.001467	T	0.00039	0.0001	L	0.36672	1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.23976	-1.0173	9	0.19147	T	0.46	-19.9669	5.7354	0.18063	0.3476:0.1927:0.4597:0.0	rs12919017;rs12919017	1959;1934	Q12789;Q12789-3	TF3C1_HUMAN;.	S	1959	ENSP00000348510:F1959S	ENSP00000348510:F1959S	F	-	2	0	GTF3C1	27382411	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.195000	0.17155	-0.496000	0.06650	0.459000	0.35465	TTC	A|0.904;G|0.096	0.096	strong		0.602	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
FAM189A1	23359	hgsc.bcm.edu	37	15	29415560	29415560	+	Silent	SNP	G	G	A	rs3751562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:29415560G>A	ENST00000261275.4	-	11	1601	c.1602C>T	c.(1600-1602)gaC>gaT	p.D534D		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	534						integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						GGTCCAGAACGTCAGCGCCGA	0.612													G|||	3020	0.603035	0.2973	0.6427	5008	,	,		18966	0.5774		0.829	False		,,,				2504	0.7822				p.D534D		Atlas-SNP	.											FAM189A1,NS,carcinoma,0,1	FAM189A1	20	1	0			c.C1602T						PASS	.	G		472,912		70,332,290	35.0	31.0	32.0		1602	-2.8	0.0	15	dbSNP_107	32	2663,519		1129,405,57	no	coding-synonymous	FAM189A1	NM_015307.1		1199,737,347	AA,AG,GG		16.3105,34.104,31.3403		534/540	29415560	3135,1431	692	1591	2283	SO:0001819	synonymous_variant	23359	exon11			CAGAACGTCAGCG		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.1602C>T	15.37:g.29415560G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_015307	A0PK09	Silent	SNP	ENST00000261275.4	37	CCDS45198.1																																																																																			G|0.381;A|0.619	0.619	strong		0.612	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
FAM209B	388799	hgsc.bcm.edu	37	20	55108418	55108418	+	Silent	SNP	C	C	T	rs41311045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55108418C>T	ENST00000371325.1	+	1	117	c.21C>T	c.(19-21)tcC>tcT	p.S7S		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	7						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TGAAATCGTCCCTGGTCCTGC	0.567													C|||	231	0.0461262	0.0023	0.0476	5008	,	,		20936	0.0446		0.0974	False		,,,				2504	0.0532				p.S7S		Atlas-SNP	.											.	.	.	.	0			c.C21T						PASS	.	C		50,4354	49.6+/-84.7	1,48,2153	92.0	85.0	88.0		21	0.7	0.0	20	dbSNP_127	88	600,7958	158.3+/-211.8	23,554,3702	no	coding-synonymous	C20orf107	NM_001013646.2		24,602,5855	TT,TC,CC		7.011,1.1353,5.0147		7/172	55108418	650,12312	2202	4279	6481	SO:0001819	synonymous_variant	388799	exon1			ATCGTCCCTGGTC	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.21C>T	20.37:g.55108418C>T		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	245	135	0.55102	NM_001013646	Q3KRB5	Silent	SNP	ENST00000371325.1	37	CCDS33494.1																																																																																			.	.	weak		0.567	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
C5orf45	51149	hgsc.bcm.edu	37	5	179285752	179285752	+	Silent	SNP	G	G	A	rs10060182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:179285752G>A	ENST00000292586.6	-	1	135	c.45C>T	c.(43-45)tgC>tgT	p.C15C	C5orf45_ENST00000520698.1_Silent_p.C15C|C5orf45_ENST00000518235.1_Silent_p.C15C|C5orf45_ENST00000518219.1_Silent_p.C15C|CTC-241N9.1_ENST00000499601.2_5'Flank|C5orf45_ENST00000376931.2_Silent_p.C15C|C5orf45_ENST00000521333.1_Silent_p.C15C|C5orf45_ENST00000523084.1_5'UTR|C5orf45_ENST00000403396.2_Missense_Mutation_p.P31S	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	15										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GGAAGAGGCGGCAGCTGCAGC	0.706													G|||	2240	0.447284	0.1687	0.5706	5008	,	,		14354	0.7589		0.2982	False		,,,				2504	0.5685				p.C15C		Atlas-SNP	.											C5orf45,colon,carcinoma,0,1	C5orf45	23	1	0			c.C45T						PASS	.	G	,	760,3204		108,544,1330	10.0	11.0	11.0		45,45	1.6	1.0	5	dbSNP_119	11	2081,5543		332,1417,2063	no	coding-synonymous,coding-synonymous	C5orf45	NM_001017987.2,NM_016175.3	,	440,1961,3393	AA,AG,GG		27.2954,19.1726,24.5167	,	15/289,15/344	179285752	2841,8747	1982	3812	5794	SO:0001819	synonymous_variant	51149	exon1			GAGGCGGCAGCTG		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.45C>T	5.37:g.179285752G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	43	35	0.813953	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Silent	SNP	ENST00000292586.6	37	CCDS34319.1	936	0.42857142857142855	86	0.17479674796747968	182	0.5027624309392266	453	0.791958041958042	215	0.2836411609498681	G	11.87	1.766751	0.31320	0.191726	0.272954	ENSG00000161010	ENST00000403396	T	0.30182	1.54	3.43	1.62	0.23740	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.43172	P	0.005027000000000004	.	.	.	.	.	.	T	0.11717	-1.0576	5	0.87932	D	0	-12.471	8.1787	0.31298	0.1954:0.0:0.8046:0.0	rs10060182;rs56833977;rs10060182	.	.	.	S	31	ENSP00000384599:P31S	ENSP00000384599:P31S	P	-	1	0	C5orf45	179218358	1.000000	0.71417	0.998000	0.56505	0.719000	0.41307	1.018000	0.30002	0.445000	0.26639	0.561000	0.74099	CCG	G|0.579;A|0.421	0.421	strong		0.706	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
PDZRN4	29951	hgsc.bcm.edu	37	12	41967677	41967677	+	Silent	SNP	G	G	A	rs3747556	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:41967677G>A	ENST00000402685.2	+	10	3104	c.3096G>A	c.(3094-3096)tcG>tcA	p.S1032S	PDZRN4_ENST00000539469.2_Silent_p.S774S|PDZRN4_ENST00000298919.7_Silent_p.S772S	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	1032							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				CCTTCTTGTCGGTGACCACTG	0.463													G|||	710	0.141773	0.1157	0.1916	5008	,	,		17226	0.2837		0.0944	False		,,,				2504	0.044				p.S1032S		Atlas-SNP	.											.	PDZRN4	346	.	0			c.G3096A						PASS	.	G	,	541,3865	244.0+/-253.5	30,481,1692	82.0	70.0	74.0		3096,2322	-9.6	0.7	12	dbSNP_107	74	964,7636	209.4+/-250.6	47,870,3383	no	coding-synonymous,coding-synonymous	PDZRN4	NM_001164595.1,NM_013377.3	,	77,1351,5075	AA,AG,GG		11.2093,12.2787,11.5716	,	1032/1037,774/779	41967677	1505,11501	2203	4300	6503	SO:0001819	synonymous_variant	29951	exon10			CTTGTCGGTGACC	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.3096G>A	12.37:g.41967677G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	114	48	0.421053	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																			G|0.870;A|0.130	0.130	strong		0.463	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
SNUPN	10073	hgsc.bcm.edu	37	15	75901899	75901899	+	Splice_Site	SNP	C	C	G	rs148983993	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75901899C>G	ENST00000564644.1	-	6	1080	c.502G>C	c.(502-504)Gac>Cac	p.D168H	SNUPN_ENST00000564675.1_Splice_Site_p.D168H|SNUPN_ENST00000371091.5_Splice_Site_p.D210H|SNUPN_ENST00000308588.5_Splice_Site_p.D168H|SNUPN_ENST00000567134.1_Splice_Site_p.D168H			O95149	SPN1_HUMAN	snurportin 1	168					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein import into nucleus (GO:0006606)|RNA metabolic process (GO:0016070)|snRNA import into nucleus (GO:0061015)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear pore (GO:0005643)	protein transporter activity (GO:0008565)|RNA cap binding (GO:0000339)			endometrium(2)|large_intestine(3)|lung(2)|pancreas(1)	8						ATGTAGGTACCTTTTGCTGTT	0.488													c|||	3	0.000599042	0.0	0.0	5008	,	,		20574	0.0		0.003	False		,,,				2504	0.0				p.D168H		Atlas-SNP	.											.	SNUPN	26	.	0			c.G502C						PASS	.		HIS/ASP,HIS/ASP,HIS/ASP	4,4390	9.9+/-24.2	0,4,2193	112.0	108.0	109.0		502,502,502	3.9	1.0	15	dbSNP_134	109	56,8532	35.3+/-89.8	0,56,4238	yes	missense-near-splice,missense-near-splice,missense-near-splice	SNUPN	NM_001042581.1,NM_001042588.1,NM_005701.3	81,81,81	0,60,6431	GG,GC,CC		0.6521,0.091,0.4622	probably-damaging,probably-damaging,probably-damaging	168/361,168/361,168/361	75901899	60,12922	2197	4294	6491	SO:0001630	splice_region_variant	10073	exon5			AGGTACCTTTTGC	AF039029	CCDS10281.1	15q24.2	2008-02-05	2006-07-14	2006-07-14	ENSG00000169371	ENSG00000169371			14245	protein-coding gene	gene with protein product		607902	"""RNA, U transporter 1"""	RNUT1		9670026	Standard	NM_005701		Approved	SNURPORTIN-1, Snurportin1	uc002bas.3	O95149	OTTHUMG00000142833	ENST00000564644.1:c.502+1G>C	15.37:g.75901899C>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_001042581	A6NE34|A8K0B0|D3DW76	Missense_Mutation	SNP	ENST00000564644.1	37	CCDS10281.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	c	13.54	2.268020	0.40095	9.1E-4	0.006521	ENSG00000169371	ENST00000308588;ENST00000371091	T;T	0.59083	0.29;0.29	4.82	3.87	0.44632	.	0.257082	0.43110	D	0.000606	T	0.42040	0.1185	M	0.62016	1.91	0.58432	D	0.999996	B;P	0.50819	0.187;0.939	B;B	0.36766	0.024;0.232	T	0.50651	-0.8803	9	.	.	.	-15.817	13.2114	0.59828	0.1607:0.8393:0.0:0.0	.	210;168	C9K0X5;O95149	.;SPN1_HUMAN	H	168;210	ENSP00000309831:D168H;ENSP00000360132:D210H	.	D	-	1	0	SNUPN	73688954	1.000000	0.71417	0.997000	0.53966	0.682000	0.39822	6.399000	0.73248	1.111000	0.41721	0.444000	0.29173	GAC	C|0.996;G|0.004	0.004	strong		0.488	SNUPN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420332.1	NM_005701	Missense_Mutation
TDRD6	221400	hgsc.bcm.edu	37	6	46656557	46656557	+	Missense_Mutation	SNP	C	C	T	rs41273658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46656557C>T	ENST00000316081.6	+	1	692	c.692C>T	c.(691-693)cCg>cTg	p.P231L	RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000422284.2_RNA|RP11-446F17.3_ENST00000434329.2_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.P231L	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	231					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TCGCGAGTCCCGCTCAAGCAA	0.652													C|||	218	0.0435304	0.0666	0.036	5008	,	,		16665	0.0		0.0457	False		,,,				2504	0.0603				p.P231L		Atlas-SNP	.											.	TDRD6	205	.	0			c.C692T						PASS	.	C	LEU/PRO,LEU/PRO	251,4149		4,243,1953	21.0	23.0	22.0		692,692	-6.2	0.0	6	dbSNP_127	22	346,8250		9,328,3961	yes	missense,missense	TDRD6	NM_001010870.2,NM_001168359.1	98,98	13,571,5914	TT,TC,CC		4.0251,5.7045,4.5937	benign,benign	231/2097,231/2067	46656557	597,12399	2200	4298	6498	SO:0001583	missense	221400	exon1			GAGTCCCGCTCAA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.692C>T	6.37:g.46656557C>T	ENSP00000346065:p.Pro231Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	72	0.03296703296703297	21	0.042682926829268296	13	0.03591160220994475	0	0.0	38	0.05013192612137203	C	0.213	-1.034775	0.02029	0.057045	0.040251	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.15139	2.45;2.46	5.44	-6.21	0.02065	.	2.220440	0.01510	N	0.017883	T	0.02012	0.0063	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26573	-1.0099	10	0.08599	T	0.76	-7.1423	12.633	0.56667	0.1248:0.6709:0.0:0.2042	rs41273658;rs61730436	231;231	F5H5M3;O60522	.;TDRD6_HUMAN	L	231	ENSP00000443299:P231L;ENSP00000346065:P231L	ENSP00000346065:P231L	P	+	2	0	TDRD6	46764516	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-1.224000	0.02959	-1.162000	0.02797	-0.290000	0.09829	CCG	C|0.958;T|0.042	0.042	strong		0.652	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
ABCC5	10057	hgsc.bcm.edu	37	3	183699516	183699516	+	Splice_Site	SNP	T	T	C	rs7636910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183699516T>C	ENST00000334444.6	-	8	1386	c.1146A>G	c.(1144-1146)caA>caG	p.Q382Q	ABCC5_ENST00000265586.6_Splice_Site_p.Q382Q|ABCC5_ENST00000492216.1_5'UTR	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	382	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.Q382Q(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	TAAACTCACTTTGAACACTCT	0.378													T|||	1674	0.334265	0.2224	0.2925	5008	,	,		20737	0.4167		0.3867	False		,,,				2504	0.3763				p.Q382Q		Atlas-SNP	.											ABCC5,NS,carcinoma,0,1	ABCC5	142	1	1	Substitution - coding silent(1)	stomach(1)	c.A1146G						PASS	.	T		1026,2724		144,738,993	96.0	94.0	94.0		1146	4.6	1.0	3	dbSNP_116	94	3065,5149		562,1941,1604	yes	coding-synonymous-near-splice	ABCC5	NM_005688.2		706,2679,2597	CC,CT,TT		37.3143,27.36,34.1942		382/1438	183699516	4091,7873	1875	4107	5982	SO:0001630	splice_region_variant	10057	exon8			CTCACTTTGAACA	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.1147+1A>G	3.37:g.183699516T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			T|0.657;C|0.343	0.343	strong		0.378	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	Silent
GPR32	2854	hgsc.bcm.edu	37	19	51274851	51274851	+	Missense_Mutation	SNP	A	A	C	rs201404376		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:51274851A>C	ENST00000270590.4	+	1	1131	c.994A>C	c.(994-996)Act>Cct	p.T332P		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	332					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		CCAGTCTTTGACTTCTGCCCT	0.552																																					p.T332P	Esophageal Squamous(113;152 1581 5732 15840 44398)	Atlas-SNP	.											GPR32,NS,carcinoma,0,5	GPR32	68	5	0			c.A994C						scavenged	.						66.0	71.0	69.0					19																	51274851		2203	4298	6501	SO:0001583	missense	2854	exon1			TCTTTGACTTCTG	AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"""GPCR / Class A : Resolvin receptors"""	4487	protein-coding gene	gene with protein product	"""resolvin D1 receptor"""	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.994A>C	19.37:g.51274851A>C	ENSP00000270590:p.Thr332Pro	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	110	9	0.0818182	NM_001506	Q502U7|Q6NWS5	Missense_Mutation	SNP	ENST00000270590.4	37	CCDS12801.1	.	.	.	.	.	.	.	.	.	.	a	0.006	-2.066505	0.00382	.	.	ENSG00000142511	ENST00000270590	T	0.36699	1.24	2.71	-0.781	0.10965	.	.	.	.	.	T	0.12518	0.0304	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31138	-0.9954	9	0.02654	T	1	.	3.6506	0.08202	0.205:0.5623:0.0:0.2327	.	332	O75388	GPR32_HUMAN	P	332	ENSP00000270590:T332P	ENSP00000270590:T332P	T	+	1	0	GPR32	55966663	0.000000	0.05858	0.025000	0.17156	0.653000	0.38743	0.089000	0.15002	-0.262000	0.09392	-0.755000	0.03482	ACT	.	.	weak		0.552	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1		
CA13	377677	hgsc.bcm.edu	37	8	86180719	86180719	+	Missense_Mutation	SNP	A	A	G	rs75353219	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:86180719A>G	ENST00000321764.3	+	6	834	c.532A>G	c.(532-534)Aca>Gca	p.T178A	CA13_ENST00000517298.1_3'UTR	NM_198584.2	NP_940986.1	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	178					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|myelin sheath (GO:0043209)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)	7					Zonisamide(DB00909)	AACTCGATTCACAAATTTTGA	0.413													A|||	24	0.00479233	0.0015	0.0058	5008	,	,		17595	0.0		0.0139	False		,,,				2504	0.0041				p.T178A		Atlas-SNP	.											.	CA13	26	.	0			c.A532G						PASS	.	A	ALA/THR	8,4398	12.9+/-30.5	0,8,2195	171.0	159.0	163.0		532	5.5	1.0	8	dbSNP_131	163	132,8468	68.0+/-130.5	1,130,4169	yes	missense	CA13	NM_198584.2	58	1,138,6364	GG,GA,AA		1.5349,0.1816,1.0764	benign	178/263	86180719	140,12866	2203	4300	6503	SO:0001583	missense	377677	exon6			CGATTCACAAATT	BC052602	CCDS6236.1	8q21	2004-05-10				ENSG00000185015		"""Carbonic anhydrases"""	14914	protein-coding gene	gene with protein product		611436				14600151	Standard	NM_198584		Approved	CAXIII, FLJ37995, MGC59868	uc003ydg.2	Q8N1Q1		ENST00000321764.3:c.532A>G	8.37:g.86180719A>G	ENSP00000318912:p.Thr178Ala	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	187	98	0.524064	NM_198584		Missense_Mutation	SNP	ENST00000321764.3	37	CCDS6236.1	13	0.005952380952380952	0	0.0	0	0.0	0	0.0	13	0.017150395778364115	A	14.11	2.436542	0.43224	0.001816	0.015349	ENSG00000185015	ENST00000321764	T	0.63580	-0.05	5.5	5.5	0.81552	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.144213	0.64402	D	0.000006	T	0.35885	0.0947	L	0.38953	1.18	0.46849	D	0.999224	B	0.21381	0.055	B	0.21917	0.037	T	0.38001	-0.9681	10	0.21540	T	0.41	-11.4932	14.5856	0.68322	1.0:0.0:0.0:0.0	.	178	Q8N1Q1	CAH13_HUMAN	A	178	ENSP00000318912:T178A	ENSP00000318912:T178A	T	+	1	0	CA13	86367971	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.135000	0.42112	2.104000	0.64026	0.383000	0.25322	ACA	A|0.992;G|0.008	0.008	strong		0.413	CA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381066.1	NM_198584	
SLFN13	146857	hgsc.bcm.edu	37	17	33768383	33768383	+	Missense_Mutation	SNP	T	T	A	rs11657183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:33768383T>A	ENST00000285013.6	-	6	2200	c.1925A>T	c.(1924-1926)gAt>gTt	p.D642V	SLFN13_ENST00000533791.1_Missense_Mutation_p.D642V|SLFN13_ENST00000534689.1_Missense_Mutation_p.D324V|SLFN13_ENST00000360502.2_Missense_Mutation_p.D324V|SLFN13_ENST00000542635.1_Missense_Mutation_p.D642V|SLFN13_ENST00000526861.1_Missense_Mutation_p.D642V	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	642			D -> V (in dbSNP:rs11657183).			intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GATATTTCTATCACTGTAAAA	0.383													T|||	818	0.163339	0.1286	0.0865	5008	,	,		17186	0.1052		0.1123	False		,,,				2504	0.3773				p.D642V		Atlas-SNP	.											.	SLFN13	79	.	0			c.A1925T						PASS	.	T	VAL/ASP	432,3678		28,376,1651	38.0	44.0	42.0		1925	-2.3	0.0	17	dbSNP_120	42	967,7539		56,855,3342	no	missense	SLFN13	NM_144682.5	152	84,1231,4993	AA,AT,TT		11.3684,10.5109,11.0891	benign	642/898	33768383	1399,11217	2055	4253	6308	SO:0001583	missense	146857	exon6			TTTCTATCACTGT	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.1925A>T	17.37:g.33768383T>A	ENSP00000285013:p.Asp642Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	247	0.1130952380952381	83	0.16869918699186992	31	0.0856353591160221	50	0.08741258741258741	83	0.10949868073878628	a	5.074	0.199308	0.09652	0.105109	0.113684	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67	3.29	-2.27	0.06846	Domain of unknown function DUF2075 (1);	1.570860	0.03754	N	0.257015	T	0.00412	0.0013	N	0.22421	0.69	0.80722	P	0.0	B;B	0.33413	0.226;0.411	B;B	0.33890	0.076;0.172	T	0.09975	-1.0650	9	0.45353	T	0.12	.	0.4205	0.00455	0.1772:0.2366:0.1973:0.3889	rs11657183;rs52816132;rs59899591;rs11657183	324;642	Q68D06-2;Q68D06	.;SLN13_HUMAN	V	642;324;642;642;324	ENSP00000285013:D642V;ENSP00000353692:D324V;ENSP00000434439:D642V;ENSP00000444016:D642V;ENSP00000435442:D324V	ENSP00000285013:D642V	D	-	2	0	SLFN13	30792496	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.126000	0.10563	-0.669000	0.05289	-2.924000	0.00089	GAT	T|0.891;A|0.109	0.109	strong		0.383	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047925	46047925	+	Silent	SNP	G	G	T	rs9979457	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46047925G>T	ENST00000397911.3	+	1	886	c.837G>T	c.(835-837)ccG>ccT	p.P279P	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	279						keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GCTCCCGCCCGGCCTGCTACA	0.692													G|||	3169	0.632788	0.5212	0.6715	5008	,	,		17780	0.6627		0.7107	False		,,,				2504	0.6452				p.P279P		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.G837T						PASS	.	G	,	2373,1995		667,1039,478	60.0	74.0	70.0		,837	-5.6	0.0	21	dbSNP_119	70	5797,2777		1967,1863,457	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	2634,2902,935	TT,TG,GG		32.3886,45.6731,36.8722	,	,279/293	46047925	8170,4772	2184	4287	6471	SO:0001819	synonymous_variant	386676	exon1			CCGCCCGGCCTGC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.837G>T	21.37:g.46047925G>T		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	191	105	0.549738	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			G|0.347;T|0.653	0.653	strong		0.692	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
KIAA1614	57710	hgsc.bcm.edu	37	1	180905694	180905694	+	Silent	SNP	C	C	T	rs3795503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180905694C>T	ENST00000367588.4	+	5	2704	c.2649C>T	c.(2647-2649)aaC>aaT	p.N883N	KIAA1614_ENST00000367587.1_Silent_p.N504N	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	883										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						ACTGCAACAACAGCGCACCTC	0.697													C|||	1446	0.288738	0.1316	0.2738	5008	,	,		16039	0.495		0.3012	False		,,,				2504	0.2863				p.N883N		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C2649T						PASS	.	C		667,3347		63,541,1403	27.0	33.0	31.0		2649	2.4	0.0	1	dbSNP_107	31	2521,5791		392,1737,2027	no	coding-synonymous	KIAA1614	NM_020950.1		455,2278,3430	TT,TC,CC		30.3296,16.6168,25.864		883/1191	180905694	3188,9138	2007	4156	6163	SO:0001819	synonymous_variant	57710	exon5			CAACAACAGCGCA	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2649C>T	1.37:g.180905694C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	142	69	0.485915	NM_020950	Q5VZ45|Q9HCF8	Silent	SNP	ENST00000367588.4	37	CCDS41442.1																																																																																			C|0.696;T|0.304	0.304	strong		0.697	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
MYOM2	9172	hgsc.bcm.edu	37	8	2046700	2046700	+	Missense_Mutation	SNP	C	C	T	rs2294066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:2046700C>T	ENST00000262113.4	+	19	2468	c.2327C>T	c.(2326-2328)aCg>aTg	p.T776M	MYOM2_ENST00000523438.1_Missense_Mutation_p.T201M	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	776	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> M (in dbSNP:rs2294066). {ECO:0000269|PubMed:15489334}.		muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GACGGCTTGACGGAAGGCTCA	0.517													C|||	831	0.165935	0.1195	0.1945	5008	,	,		16148	0.2629		0.166	False		,,,				2504	0.1084				p.T776M		Atlas-SNP	.											.	MYOM2	251	.	0			c.C2327T						PASS	.	C	MET/THR	555,3851	244.7+/-253.9	34,487,1682	41.0	39.0	40.0		2327	3.7	0.6	8	dbSNP_100	40	1240,7360	245.3+/-274.2	99,1042,3159	yes	missense	MYOM2	NM_003970.2	81	133,1529,4841	TT,TC,CC		14.4186,12.5965,13.8013	probably-damaging	776/1466	2046700	1795,11211	2203	4300	6503	SO:0001583	missense	9172	exon19			GCTTGACGGAAGG		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2327C>T	8.37:g.2046700C>T	ENSP00000262113:p.Thr776Met	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	21	0.313433	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	413	0.1891025641025641	50	0.1016260162601626	85	0.23480662983425415	153	0.2674825174825175	125	0.16490765171503957	C	10.81	1.456847	0.26161	0.125965	0.144186	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.58652	0.32;0.32	5.5	3.72	0.42706	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.289558	0.38111	N	0.001820	T	0.00012	0.0000	M	0.76002	2.32	0.34133	P	0.33448100000000003	D	0.76494	0.999	D	0.70016	0.967	T	0.02491	-1.1151	9	0.59425	D	0.04	.	11.1141	0.48249	0.0:0.7936:0.0:0.2064	rs2294066;rs17719462;rs17857420;rs60334248;rs2294066	776	P54296	MYOM2_HUMAN	M	776;201	ENSP00000262113:T776M;ENSP00000428396:T201M	ENSP00000262113:T776M	T	+	2	0	MYOM2	2034107	0.005000	0.15991	0.578000	0.28575	0.016000	0.09150	0.029000	0.13666	0.700000	0.31782	-0.291000	0.09656	ACG	C|0.846;N|0.000	.	strong		0.517	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
NAT2	10	hgsc.bcm.edu	37	8	18257854	18257854	+	Missense_Mutation	SNP	T	T	C	rs1801280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:18257854T>C	ENST00000286479.3	+	2	448	c.341T>C	c.(340-342)aTt>aCt	p.I114T	NAT2_ENST00000520116.1_5'UTR	NM_000015.2	NP_000006.2	P11245	ARY2_HUMAN	N-acetyltransferase 2 (arylamine N-acetyltransferase)	114			I -> T (in allele NAT2*5A, allele NAT2*5B, allele NAT2*5C, allele NAT2*5D, allele NAT2*5E, allele NAT2*5F, allele NAT2*14B and allele NAT2*14E; a slow acetylator; dbSNP:rs1801280). {ECO:0000269|PubMed:16416399, ECO:0000269|PubMed:7915226, ECO:0000269|Ref.10, ECO:0000269|Ref.11, ECO:0000269|Ref.12, ECO:0000269|Ref.14, ECO:0000269|Ref.8, ECO:0000269|Ref.9}.		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	arylamine N-acetyltransferase activity (GO:0004060)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(2)	12				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)	Acetaminophen(DB00316)|Clonazepam(DB01068)|Dapsone(DB00250)|Ezogabine(DB04953)|Isoniazid(DB00951)|Sulfamethoxazole(DB01015)	CAGGTGACCATTGACGGCAGG	0.483									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				T|||	1466	0.292732	0.292	0.3617	5008	,	,		18553	0.0377		0.4493	False		,,,				2504	0.3466				p.I114T		Atlas-SNP	.											.	NAT2	34	.	0			c.T341C	GRCh37	CM910269	NAT2	M	rs1801280	PASS	.	T	THR/ILE	1311,3095	443.1+/-346.9	196,919,1088	93.0	95.0	94.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	341	0.5	0.0	8	dbSNP_89	94	3831,4769	540.8+/-383.9	834,2163,1303	yes	missense	NAT2	NM_000015.2	89	1030,3082,2391	CC,CT,TT		44.5465,29.7549,39.5356	benign	114/291	18257854	5142,7864	2203	4300	6503	SO:0001583	missense	10	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TGACCATTGACGG	D90042	CCDS6008.1	8p22	2012-01-18			ENSG00000156006	ENSG00000156006	2.3.1.5		7646	protein-coding gene	gene with protein product		612182		AAC2		7773298	Standard	NM_000015		Approved		uc003wyw.1	P11245	OTTHUMG00000130826	ENST00000286479.3:c.341T>C	8.37:g.18257854T>C	ENSP00000286479:p.Ile114Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	131	58	0.442748	NM_000015	O43637|O60654|O60655|Q13146|Q16697|Q2MLE4|Q2MLF5|Q2MLG8|Q2MLJ6|Q2MLK4|Q2MLK6|Q2MLN7|Q6LET4|Q86XS0|Q86XS1|Q96KY8|Q96T64|Q96T65|Q9H220	Missense_Mutation	SNP	ENST00000286479.3	37	CCDS6008.1	648	0.2967032967032967	153	0.31097560975609756	136	0.3756906077348066	16	0.027972027972027972	343	0.4525065963060686	T	9.050	0.991860	0.18966	0.297549	0.445465	ENSG00000156006	ENST00000286479	T	0.02525	4.26	2.95	0.537	0.17144	.	0.333219	0.30840	N	0.008775	T	0.00012	0.0000	L	0.51422	1.61	0.37630	P	0.07838	B	0.32409	0.37	P	0.45998	0.5	T	0.45086	-0.9285	9	0.54805	T	0.06	.	4.7527	0.13068	0.0:0.2853:0.0:0.7147	rs1801280;rs4134724;rs56935242;rs1801280	114	A4Z6T7	.	T	114	ENSP00000286479:I114T	ENSP00000286479:I114T	I	+	2	0	NAT2	18302134	0.980000	0.34600	0.008000	0.14137	0.230000	0.25150	3.744000	0.55112	0.102000	0.17638	0.358000	0.22013	ATT	T|0.652;C|0.348	0.348	strong		0.483	NAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253380.1	NM_000015	
PNPLA1	285848	hgsc.bcm.edu	37	6	36274153	36274153	+	Splice_Site	SNP	C	C	T	rs12197079	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:36274153C>T	ENST00000394571.2	+	7	1469	c.1469C>T	c.(1468-1470)aCg>aTg	p.T490M	PNPLA1_ENST00000388715.3_Splice_Site_p.T395M|PNPLA1_ENST00000312917.5_Splice_Site_p.T404M	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	490			T -> M (in dbSNP:rs12197079). {ECO:0000269|PubMed:15489334}.		lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						CCTTATGTAACGTAAGTTTCC	0.488													T|||	1204	0.240415	0.3238	0.1859	5008	,	,		19609	0.1032		0.2565	False		,,,				2504	0.2914				p.T490M		Atlas-SNP	.											.	PNPLA1	92	.	0			c.C1469T						PASS	.	T	MET/THR,MET/THR,MET/THR	1401,3005	687.2+/-404.8	225,951,1027	157.0	148.0	151.0		1211,1469,1184	-3.4	0.0	6	dbSNP_120	151	2464,6136	695.8+/-404.8	376,1712,2212	yes	missense-near-splice,missense-near-splice,missense-near-splice	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	81,81,81	601,2663,3239	TT,TC,CC		28.6512,31.7975,29.7171	benign,benign,benign	404/447,490/533,395/438	36274153	3865,9141	2203	4300	6503	SO:0001630	splice_region_variant	285848	exon7			ATGTAACGTAAGT		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.1469+1C>T	6.37:g.36274153C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	468	0.21428571428571427	148	0.3008130081300813	73	0.20165745856353592	54	0.0944055944055944	193	0.2546174142480211	T	9.014	0.983174	0.18889	0.317975	0.286512	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.27557	1.89;1.89;1.66;1.66	4.25	-3.36	0.04913	.	1.943300	0.02601	N	0.101010	T	0.03871	0.0109	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23762	-1.0179	9	0.30078	T	0.28	0.6036	6.6281	0.22841	0.1679:0.5507:0.0:0.2814	rs12197079;rs52834844;rs60801136;rs12197079	490;404	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	M	395;404;491;490	ENSP00000373367:T395M;ENSP00000321116:T404M;ENSP00000391868:T491M;ENSP00000378072:T490M	ENSP00000321116:T404M	T	+	2	0	PNPLA1	36382131	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.405000	0.00482	-0.715000	0.04968	-0.361000	0.07541	ACG	C|0.747;N|0.000	.	strong		0.488	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	Missense_Mutation
CAMK2B	816	hgsc.bcm.edu	37	7	44259871	44259871	+	Silent	SNP	C	C	T	rs1127065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:44259871C>T	ENST00000395749.2	-	23	1867	c.1791G>A	c.(1789-1791)ccG>ccA	p.P597P	CAMK2B_ENST00000350811.3_Silent_p.P473P|CAMK2B_ENST00000346990.4_Silent_p.P380P|CAMK2B_ENST00000347193.4_Silent_p.P423P|CAMK2B_ENST00000457475.1_Silent_p.P449P|CAMK2B_ENST00000502837.2_3'UTR|CAMK2B_ENST00000440254.2_Silent_p.P473P|CAMK2B_ENST00000395747.2_Silent_p.P449P|CAMK2B_ENST00000258682.6_Silent_p.P448P|CAMK2B_ENST00000489429.1_5'UTR|CAMK2B_ENST00000353625.4_Silent_p.P410P|CAMK2B_ENST00000358707.3_Silent_p.P434P	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	597					activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						TCGTGTGGATCGGCTTGCTGT	0.627													C|||	1711	0.341653	0.1694	0.3213	5008	,	,		16956	0.3998		0.4076	False		,,,				2504	0.4611				p.P597P		Atlas-SNP	.											CAMK2B,NS,carcinoma,0,1	CAMK2B	56	1	0			c.G1791A						PASS	.	C	,,,,,,,	1004,3402	352.8+/-311.9	125,754,1324	107.0	59.0	75.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1791,1419,1347,1344,1302,1269,1230,1140	-8.5	0.9	7	dbSNP_86	75	3673,4927	498.7+/-374.8	817,2039,1444	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2B	NM_001220.4,NM_172078.2,NM_172079.2,NM_172080.2,NM_172081.2,NM_172082.2,NM_172083.2,NM_172084.2	,,,,,,,	942,2793,2768	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	42.7093,22.7871,35.9603	,,,,,,,	597/667,473/543,449/519,448/518,434/504,423/493,410/480,380/450	44259871	4677,8329	2203	4300	6503	SO:0001819	synonymous_variant	816	exon23			GTGGATCGGCTTG	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"""CaM-kinase II beta chain"", ""calcium/calmodulin-dependent protein kinase type II beta chain"", ""CaM kinase II beta subunit"", ""proline rich calmodulin-dependent protein kinase"""	607707	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"""	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.1791G>A	7.37:g.44259871C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	178	82	0.460674	NM_001220	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Silent	SNP	ENST00000395749.2	37	CCDS5483.1																																																																																			T|0.361;G|0.004;C|0.635	0.361	strong		0.627	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
C11orf16	56673	hgsc.bcm.edu	37	11	8947283	8947283	+	Missense_Mutation	SNP	G	G	C	rs3751066	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8947283G>C	ENST00000326053.5	-	5	1037	c.931C>G	c.(931-933)Ccc>Gcc	p.P311A	C11orf16_ENST00000525780.1_Missense_Mutation_p.P311A|C11orf16_ENST00000528998.1_5'Flank	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	311				P -> A (in Ref. 2; BAD97097 and 4; AAH27865). {ECO:0000305}.						central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		TGTGCTGTGGGCTCCAACTCT	0.577													G|||	2658	0.530751	0.2935	0.6787	5008	,	,		21407	0.7093		0.6044	False		,,,				2504	0.4867				p.P311A		Atlas-SNP	.											.	C11orf16	43	.	0			c.C931G						PASS	.	G	ALA/PRO	1531,2871	484.0+/-359.9	267,997,937	85.0	84.0	85.0		931	0.0	0.1	11	dbSNP_107	85	5222,3370	640.5+/-399.6	1581,2060,655	yes	missense	C11orf16	NM_020643.2	27	1848,3057,1592	CC,CG,GG		39.2225,34.7796,48.0299	possibly-damaging	311/468	8947283	6753,6241	2201	4296	6497	SO:0001583	missense	56673	exon5			CTGTGGGCTCCAA	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.931C>G	11.37:g.8947283G>C	ENSP00000318999:p.Pro311Ala	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	135	67	0.496296	NM_020643	Q53FB2|Q8N6Y9	Missense_Mutation	SNP	ENST00000326053.5	37	CCDS7794.1	1261	0.5773809523809523	154	0.3130081300813008	225	0.6215469613259669	429	0.75	453	0.5976253298153035	G	10.20	1.283644	0.23392	0.347796	0.607775	ENSG00000176029	ENST00000525780;ENST00000326053	T;T	0.34859	1.39;1.34	5.67	0.0228	0.14134	.	0.488362	0.20971	N	0.082396	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	P;P	0.41673	0.525;0.759	B;B	0.41860	0.116;0.368	T	0.51371	-0.8714	9	0.02654	T	1	-4.7603	2.4899	0.04607	0.2922:0.1201:0.465:0.1227	rs3751066;rs17856776;rs3751066	311;311	Q9NQ32-2;Q9NQ32	.;CK016_HUMAN	A	311	ENSP00000436818:P311A;ENSP00000318999:P311A	ENSP00000318999:P311A	P	-	1	0	C11orf16	8903859	0.006000	0.16342	0.141000	0.22245	0.120000	0.20174	0.204000	0.17335	0.350000	0.24002	0.655000	0.94253	CCC	G|0.464;C|0.536	0.536	strong		0.577	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643	
CEACAM16	388551	hgsc.bcm.edu	37	19	45211407	45211407	+	Silent	SNP	C	C	T	rs61744497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45211407C>T	ENST00000405314.2	+	5	1312	c.1215C>T	c.(1213-1215)acC>acT	p.T405T	CTB-171A8.1_ENST00000590796.1_RNA|CEACAM16_ENST00000587331.1_Silent_p.T405T			Q2WEN9	CEA16_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 16	405					sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)|stereocilium bundle tip (GO:0032426)				endometrium(3)|large_intestine(2)|lung(3)|ovary(1)	9	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				CACTCAAGACCGTCACAGTGC	0.622													C|||	543	0.108427	0.0106	0.0447	5008	,	,		19901	0.2282		0.1551	False		,,,				2504	0.1145				p.T405T		Atlas-SNP	.											.	CEACAM16	56	.	0			c.C1215T						PASS	.	C		135,4095		2,131,1982	30.0	31.0	31.0		1215	-1.8	1.0	19	dbSNP_129	31	1185,7257		87,1011,3123	no	coding-synonymous	CEACAM16	NM_001039213.2		89,1142,5105	TT,TC,CC		14.037,3.1915,10.4167		405/426	45211407	1320,11352	2115	4221	6336	SO:0001819	synonymous_variant	388551	exon6			CAAGACCGTCACA		CCDS54278.1	19q13.31	2014-01-27			ENSG00000213892	ENSG00000213892		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31948	protein-coding gene	gene with protein product		614591				21368133	Standard	NM_001039213		Approved	DFNA4B	uc010xxd.2	Q2WEN9	OTTHUMG00000151519	ENST00000405314.2:c.1215C>T	19.37:g.45211407C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	177	76	0.429379	NM_001039213	A7LI12	Silent	SNP	ENST00000405314.2	37	CCDS54278.1																																																																																			C|0.867;T|0.133	0.133	strong		0.622	CEACAM16-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		XM_371177	
IDUA	3425	hgsc.bcm.edu	37	4	996165	996165	+	Missense_Mutation	SNP	G	G	A	rs6831280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:996165G>A	ENST00000247933.4	+	8	1169	c.1081G>A	c.(1081-1083)Gcg>Acg	p.A361T	IDUA_ENST00000453894.1_Missense_Mutation_p.A383T|IDUA_ENST00000514224.1_Missense_Mutation_p.A229T	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	361			A -> T (in dbSNP:rs6831280). {ECO:0000269|PubMed:15300847, ECO:0000269|PubMed:21394825, ECO:0000269|PubMed:8242073}.		carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GCACCCCTTCGCGCAGCGCAC	0.672													G|||	1090	0.217652	0.2481	0.1095	5008	,	,		13248	0.2133		0.166	False		,,,				2504	0.3108				p.A361T		Atlas-SNP	.											.	IDUA	33	.	0			c.G1081A						PASS	.	G	THR/ALA	880,3518	316.6+/-294.7	100,680,1419	62.0	60.0	60.0		1081	-6.4	0.2	4	dbSNP_116	60	1360,7230	254.1+/-279.5	109,1142,3044	yes	missense	IDUA	NM_000203.3	58	209,1822,4463	AA,AG,GG		15.8324,20.0091,17.2467	benign	361/654	996165	2240,10748	2199	4295	6494	SO:0001583	missense	3425	exon8			CCCTTCGCGCAGC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.1081G>A	4.37:g.996165G>A	ENSP00000247933:p.Ala361Thr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	148	80	0.540541	NM_000203	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	405	0.18543956043956045	120	0.24390243902439024	42	0.11602209944751381	119	0.20804195804195805	124	0.16358839050131926	G	1.283	-0.609829	0.03690	0.200091	0.158324	ENSG00000127415	ENST00000247933;ENST00000453894;ENST00000514224	D;D;D	0.93019	-3.15;-3.15;-3.15	5.35	-6.42	0.01932	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.644905	0.15664	N	0.250755	T	0.00039	0.0001	N	0.00595	-1.35	0.47009	P	7.200000000000539E-4	B;B	0.16802	0.019;0.004	B;B	0.09377	0.004;0.001	T	0.50750	-0.8791	9	0.05959	T	0.93	-1.0E-4	5.933	0.19150	0.4822:0.0:0.2105:0.3073	rs6831280;rs6831280	383;361	B3KWK6;P35475	.;IDUA_HUMAN	T	361;383;229	ENSP00000247933:A361T;ENSP00000396458:A383T;ENSP00000425081:A229T	ENSP00000247933:A361T	A	+	1	0	IDUA	986165	0.998000	0.40836	0.152000	0.22495	0.006000	0.05464	0.896000	0.28377	-0.673000	0.05259	-0.397000	0.06425	GCG	G|0.821;A|0.179	0.179	strong		0.672	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
CECR1	51816	hgsc.bcm.edu	37	22	17669306	17669306	+	Missense_Mutation	SNP	T	T	C	rs2231495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:17669306T>C	ENST00000399839.1	-	7	1274	c.1004A>G	c.(1003-1005)cAt>cGt	p.H335R	CECR1_ENST00000262607.3_Missense_Mutation_p.H335R|CECR1_ENST00000399837.2_Missense_Mutation_p.H335R|CECR1_ENST00000449907.2_Missense_Mutation_p.H293R|CECR1_ENST00000480276.1_5'Flank|CECR1_ENST00000330232.4_Missense_Mutation_p.H94R	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	335			H -> R (in dbSNP:rs2231495). {ECO:0000269|PubMed:10756095, ECO:0000269|PubMed:14702039}.		adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				CTTGTAGTCATGCAAGGAGTG	0.612													T|||	1826	0.364617	0.5696	0.3156	5008	,	,		18402	0.2262		0.3211	False		,,,				2504	0.3098				p.H335R		Atlas-SNP	.											.	CECR1	77	.	0			c.A1004G						PASS	.	T	ARG/HIS,ARG/HIS	2411,1995	615.3+/-392.5	659,1093,451	84.0	68.0	73.0		1004,281	0.3	0.0	22	dbSNP_98	73	2864,5736	449.2+/-362.0	478,1908,1914	yes	missense,missense	CECR1	NM_017424.2,NM_177405.1	29,29	1137,3001,2365	CC,CT,TT		33.3023,45.2792,40.5582	benign,benign	335/512,94/271	17669306	5275,7731	2203	4300	6503	SO:0001583	missense	51816	exon6			TAGTCATGCAAGG	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.1004A>G	22.37:g.17669306T>C	ENSP00000382733:p.His335Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Missense_Mutation	SNP	ENST00000399839.1	37	CCDS13742.1	728	0.3333333333333333	258	0.524390243902439	99	0.27348066298342544	121	0.21153846153846154	250	0.32981530343007914	T	2.455	-0.325573	0.05350	0.547208	0.333023	ENSG00000093072	ENST00000399839;ENST00000330232;ENST00000262607;ENST00000449907;ENST00000399837	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	4.24	0.283	0.15696	Adenosine/AMP deaminase (1);	0.345183	0.32640	N	0.005837	T	0.00012	0.0000	N	0.03948	-0.315	0.54753	P	1.3000000000040757E-5	B;B	0.29212	0.237;0.001	B;B	0.16289	0.015;0.0	T	0.46428	-0.9192	9	0.25751	T	0.34	.	2.3977	0.04394	0.5396:0.1884:0.0:0.272	rs2231495;rs61542193;rs2231495	335;94	Q9NZK5;Q9NZK5-2	CECR1_HUMAN;.	R	335;94;335;293;335	ENSP00000382733:H335R;ENSP00000332871:H94R;ENSP00000262607:H335R;ENSP00000406443:H293R;ENSP00000382731:H335R	ENSP00000262607:H335R	H	-	2	0	CECR1	16049306	0.974000	0.33945	0.000000	0.03702	0.005000	0.04900	2.520000	0.45554	0.033000	0.15463	-0.527000	0.04329	CAT	T|0.627;C|0.373	0.373	strong		0.612	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		
GBP4	115361	hgsc.bcm.edu	37	1	89652102	89652102	+	Missense_Mutation	SNP	A	A	T	rs655260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89652102A>T	ENST00000355754.6	-	10	1718	c.1621T>A	c.(1621-1623)Tac>Aac	p.Y541N	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	541			Y -> N (in dbSNP:rs655260).	YM -> NI (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TGGGCCATGTATTCCTGGAAG	0.488													A|||	1801	0.359625	0.1445	0.3141	5008	,	,		18800	0.3998		0.4891	False		,,,				2504	0.5082				p.Y541N		Atlas-SNP	.											.	GBP4	89	.	0			c.T1621A						PASS	.	A	ASN/TYR	435,3971		120,195,1888	167.0	106.0	127.0		1621	0.4	0.0	1	dbSNP_83	127	2958,5642		1090,778,2432	no	missense	GBP4	NM_052941.4	143	1210,973,4320	TT,TA,AA		34.3953,9.8729,26.088	benign	541/641	89652102	3393,9613	2203	4300	6503	SO:0001583	missense	115361	exon10			CCATGTATTCCTG	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1621T>A	1.37:g.89652102A>T	ENSP00000359490:p.Tyr541Asn	Somatic	468	0	0		WXS	Illumina HiSeq	Phase_I	150	147	0.98	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	630	0.28846153846153844	39	0.07926829268292683	115	0.31767955801104975	184	0.32167832167832167	292	0.38522427440633245	A	0.009	-1.824350	0.00589	0.098729	0.343953	ENSG00000162654	ENST00000355754	T	0.01804	4.63	4.29	0.417	0.16421	Guanylate-binding protein, C-terminal (3);	0.451332	0.23175	N	0.051084	T	0.00073	0.0002	N	0.00010	-3.05	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13737	-1.0498	9	0.02654	T	1	.	6.8128	0.23814	0.1531:0.0:0.4653:0.3816	rs655260;rs1142885;rs3180071;rs3206367;rs655260	541	Q96PP9	GBP4_HUMAN	N	541	ENSP00000359490:Y541N	ENSP00000359490:Y541N	Y	-	1	0	GBP4	89424690	0.025000	0.19082	0.002000	0.10522	0.043000	0.13939	0.002000	0.13061	-0.033000	0.13736	-2.024000	0.00429	TAC	A|0.677;T|0.323	0.323	strong		0.488	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
DKKL1	27120	hgsc.bcm.edu	37	19	49878196	49878196	+	Missense_Mutation	SNP	G	G	A	rs2288481	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49878196G>A	ENST00000221498.2	+	5	1045	c.640G>A	c.(640-642)Gaa>Aaa	p.E214K	DKKL1_ENST00000594268.1_Missense_Mutation_p.E72K|AC010524.2_ENST00000599433.1_RNA	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	214			E -> K (in dbSNP:rs2288481).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GGACGTCCTAGAAGAGGGGAC	0.662													G|||	1294	0.258387	0.1952	0.2003	5008	,	,		17220	0.3264		0.2068	False		,,,				2504	0.3681				p.E214K		Atlas-SNP	.											.	DKKL1	23	.	0			c.G640A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	887,3519	314.7+/-293.7	95,697,1411	33.0	35.0	34.0		547,415,640	3.1	0.0	19	dbSNP_100	34	1979,6621	320.3+/-314.5	240,1499,2561	yes	missense,missense,missense	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	56,56,56	335,2196,3972	AA,AG,GG		23.0116,20.1316,22.036	possibly-damaging,possibly-damaging,possibly-damaging	183/212,139/168,214/243	49878196	2866,10140	2203	4300	6503	SO:0001583	missense	27120	exon5			GTCCTAGAAGAGG	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.640G>A	19.37:g.49878196G>A	ENSP00000221498:p.Glu214Lys	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	490	0.22435897435897437	83	0.16869918699186992	73	0.20165745856353592	179	0.3129370629370629	155	0.20448548812664907	G	14.07	2.424616	0.43020	0.201316	0.230116	ENSG00000104901	ENST00000221498	T	0.14266	2.52	4.15	3.09	0.35607	.	0.449220	0.18957	N	0.126514	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P	0.36909	0.573	B	0.36666	0.23	T	0.47235	-0.9133	9	0.87932	D	0	-7.7924	10.0305	0.42099	0.0:0.2047:0.7953:0.0	rs2288481;rs3195289;rs61144855;rs2288481	214	Q9UK85	DKKL1_HUMAN	K	214	ENSP00000221498:E214K	ENSP00000221498:E214K	E	+	1	0	DKKL1	54570008	0.014000	0.17966	0.007000	0.13788	0.009000	0.06853	0.384000	0.20668	1.320000	0.45209	0.655000	0.94253	GAA	G|0.767;A|0.233	0.233	strong		0.662	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	
LPP	4026	hgsc.bcm.edu	37	3	188590446	188590446	+	Silent	SNP	A	A	G	rs1136644	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:188590446A>G	ENST00000312675.4	+	10	1851	c.1605A>G	c.(1603-1605)cgA>cgG	p.R535R	LPP_ENST00000543006.1_Silent_p.R535R	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	535	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TTGCCCCGCGATGTTCTGTGT	0.522			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								A|||	2005	0.400359	0.2602	0.3919	5008	,	,		21140	0.4345		0.5298	False		,,,				2504	0.4274				p.R535R		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	LPP_ENST00000312675,NS,carcinoma,+1,1	LPP	72	1	0			c.A1605G						scavenged	.	A	,,	1244,3162	429.5+/-342.2	184,876,1143	139.0	128.0	132.0		1605,1164,1605	0.0	1.0	3	dbSNP_86	132	4360,4240	582.0+/-391.3	1118,2124,1058	no	coding-synonymous,coding-synonymous,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	1302,3000,2201	GG,GA,AA		49.3023,28.2342,43.0878	,,	535/613,388/466,535/613	188590446	5604,7402	2203	4300	6503	SO:0001819	synonymous_variant	4026	exon10			CCCGCGATGTTCT	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1605A>G	3.37:g.188590446A>G		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	220	84	0.381818	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																			A|0.579;G|0.421	0.421	strong		0.522	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
CC2D1A	54862	hgsc.bcm.edu	37	19	14040896	14040896	+	Missense_Mutation	SNP	G	G	A	rs11669628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14040896G>A	ENST00000318003.7	+	27	2957	c.2716G>A	c.(2716-2718)Gca>Aca	p.A906T	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A905T	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	906				A -> T (in Ref. 2; BAC77355). {ECO:0000305}.	positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			CTCAGAATACGCAGCCCAGCT	0.687													G|||	667	0.133187	0.0151	0.111	5008	,	,		9448	0.255		0.1501	False		,,,				2504	0.1656				p.A906T		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G2716A						PASS	.	G	THR/ALA	131,3813		3,125,1844	18.0	21.0	20.0		2716	-4.5	0.0	19	dbSNP_120	20	1042,7240		61,920,3160	yes	missense	CC2D1A	NM_017721.4	58	64,1045,5004	AA,AG,GG		12.5815,3.3215,9.5943	benign	906/952	14040896	1173,11053	1972	4141	6113	SO:0001583	missense	54862	exon27			GAATACGCAGCCC	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.2716G>A	19.37:g.14040896G>A	ENSP00000313601:p.Ala906Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	325	0.1488095238095238	13	0.026422764227642278	50	0.13812154696132597	143	0.25	119	0.15699208443271767	g	10.36	1.329670	0.24167	0.033215	0.125815	ENSG00000132024	ENST00000318003;ENST00000254346	T	0.16897	2.31	4.97	-4.52	0.03472	.	1.156840	0.06362	N	0.711860	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.22746	0.074;0.003;0.002	B;B;B	0.08055	0.003;0.002;0.001	T	0.45906	-0.9229	9	0.27785	T	0.31	1.114	7.893	0.29688	0.4382:0.14:0.4219:0.0	rs11669628;rs11669628	527;905;906	Q9NX28;Q6P1N0-2;Q6P1N0	.;.;C2D1A_HUMAN	T	906;528	ENSP00000313601:A906T	ENSP00000254346:A528T	A	+	1	0	CC2D1A	13901896	0.000000	0.05858	0.008000	0.14137	0.188000	0.23474	-2.576000	0.00910	-0.388000	0.07797	-0.266000	0.10368	GCA	A|0.141;G|0.859;T|0.000	0.141	strong		0.687	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
MTMR7	9108	hgsc.bcm.edu	37	8	17169039	17169039	+	Missense_Mutation	SNP	C	C	T	rs147637471		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17169039C>T	ENST00000180173.5	-	9	1116	c.1082G>A	c.(1081-1083)cGg>cAg	p.R361Q	MTMR7_ENST00000521857.1_Missense_Mutation_p.R361Q|MTMR7_ENST00000398099.3_5'UTR	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	361	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		CTTCAGAGTCCGGTAGTGAGG	0.582																																					p.R361Q		Atlas-SNP	.											.	MTMR7	75	.	0			c.G1082A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	214.0	209.0	211.0		1082	4.9	1.0	8	dbSNP_134	211	3,8597	3.0+/-9.4	0,3,4297	no	missense	MTMR7	NM_004686.4	43	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	361/661	17169039	3,13003	2203	4300	6503	SO:0001583	missense	9108	exon9			AGAGTCCGGTAGT	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1082G>A	8.37:g.17169039C>T	ENSP00000180173:p.Arg361Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	C	34	5.299020	0.95574	0.0	3.49E-4	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.98135	-4.74;-4.74	4.86	4.86	0.63082	Myotubularin phosphatase domain (1);	0.047533	0.85682	D	0.000000	D	0.99405	0.9790	H	0.99516	4.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.98030	1.0376	10	0.87932	D	0	.	18.5539	0.91075	0.0:1.0:0.0:0.0	.	361;361	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	Q	361	ENSP00000180173:R361Q;ENSP00000429733:R361Q	ENSP00000180173:R361Q	R	-	2	0	MTMR7	17213410	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.697000	0.92050	0.655000	0.94253	CGG	C|1.000;T|0.000	0.000	weak		0.582	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
PER1	5187	hgsc.bcm.edu	37	17	8046680	8046680	+	Silent	SNP	G	G	A	rs112185134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8046680G>A	ENST00000317276.4	-	19	3213	c.2976C>T	c.(2974-2976)ctC>ctT	p.L992L	PER1_ENST00000581082.1_Silent_p.L969L|PER1_ENST00000578089.1_5'Flank	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	992	Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CAGCACGGGGGAGCTCCTCCA	0.682			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					G|||	42	0.00838658	0.0015	0.0187	5008	,	,		11238	0.0		0.0239	False		,,,				2504	0.0031				p.L992L		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.C2976T						PASS	.	G		19,4381		1,17,2182	26.0	28.0	27.0		2976	0.8	0.9	17	dbSNP_132	27	172,8418		2,168,4125	no	coding-synonymous	PER1	NM_002616.2		3,185,6307	AA,AG,GG		2.0023,0.4318,1.4704		992/1291	8046680	191,12799	2200	4295	6495	SO:0001819	synonymous_variant	5187	exon19			ACGGGGGAGCTCC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2976C>T	17.37:g.8046680G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	145	59	0.406897	NM_002616	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	37	CCDS11131.1																																																																																			G|0.986;A|0.014	0.014	strong		0.682	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
IL12RB1	3594	hgsc.bcm.edu	37	19	18180413	18180413	+	Missense_Mutation	SNP	C	C	G	rs401502	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18180413C>G	ENST00000600835.2	-	11	1430	c.1132G>C	c.(1132-1134)Ggg>Cgg	p.G378R	IL12RB1_ENST00000593993.2_Missense_Mutation_p.G378R			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	378	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		G -> R (in dbSNP:rs401502). {ECO:0000269|Ref.3}.		cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GCAAGGCCCCCGTCCTGGCCC	0.627													C|||	1260	0.251597	0.1747	0.1729	5008	,	,		18697	0.376		0.3121	False		,,,				2504	0.2209				p.G378R		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G1132C	GRCh37	CM030471	IL12RB1	M	rs401502	PASS	.	C	ARG/GLY	796,3248		76,644,1302	54.0	62.0	59.0		1132	-4.1	0.0	19	dbSNP_80	59	2582,5764		396,1790,1987	yes	missense	IL12RB1	NM_005535.1	125	472,2434,3289	GG,GC,CC		30.937,19.6835,27.2639	benign	378/663	18180413	3378,9012	2022	4173	6195	SO:0001583	missense	3594	exon10			GGCCCCCGTCCTG	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.1132G>C	19.37:g.18180413C>G	ENSP00000470788:p.Gly378Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	83	24	0.289157	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	598	0.27380952380952384	84	0.17073170731707318	72	0.19889502762430938	206	0.36013986013986016	236	0.3113456464379947	C	5.700	0.313642	0.10789	0.196835	0.30937	ENSG00000096996	ENST00000430026	T	0.79454	-1.27	4.2	-4.14	0.03892	.	1.317880	0.04893	N	0.449891	T	0.00012	0.0000	N	0.10874	0.06	0.80722	P	0.0	B;B	0.12013	0.005;0.003	B;B	0.12837	0.008;0.003	T	0.04128	-1.0975	9	0.12766	T	0.61	-1.3151	5.1974	0.15245	0.1609:0.2116:0.0:0.6276	rs401502;rs2230367;rs17885175;rs401502	378;378	P42701-2;P42701	.;I12R1_HUMAN	R	378	ENSP00000403103:G378R	ENSP00000403103:G378R	G	-	1	0	IL12RB1	18041413	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.856000	0.01662	-0.371000	0.08004	0.430000	0.28490	GGG	C|0.703;G|0.297	0.297	strong		0.627	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
HYAL4	23553	hgsc.bcm.edu	37	7	123514896	123514896	+	Missense_Mutation	SNP	G	G	T	rs6949082	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:123514896G>T	ENST00000223026.4	+	4	1674	c.1036G>T	c.(1036-1038)Gca>Tca	p.A346S	HYAL4_ENST00000476325.1_Missense_Mutation_p.A346S	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	346			A -> S (in dbSNP:rs6949082). {ECO:0000269|PubMed:15489334}.		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						GAATTTAACTGCATCCAAGGT	0.393													T|||	569	0.113618	0.1293	0.0994	5008	,	,		17605	0.001		0.1779	False		,,,				2504	0.1524				p.A346S		Atlas-SNP	.											.	HYAL4	65	.	0			c.G1036T						PASS	.	T	SER/ALA	660,3746	764.9+/-413.3	55,550,1598	117.0	109.0	112.0		1036	4.9	0.9	7	dbSNP_116	112	1464,7136	749.6+/-407.4	107,1250,2943	yes	missense	HYAL4	NM_012269.2	99	162,1800,4541	TT,TG,GG		17.0233,14.9796,16.3309	benign	346/482	123514896	2124,10882	2203	4300	6503	SO:0001583	missense	23553	exon4			TTAACTGCATCCA	AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"""hyaluronidase 4"""	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.1036G>T	7.37:g.123514896G>T	ENSP00000223026:p.Ala346Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_012269	D0VXG1|Q9UL99|Q9Y6T9	Missense_Mutation	SNP	ENST00000223026.4	37	CCDS5789.1	251	0.11492673992673992	79	0.16056910569105692	36	0.09944751381215469	1	0.0017482517482517483	135	0.17810026385224276	T	1.595	-0.528098	0.04112	0.149796	0.170233	ENSG00000106302	ENST00000223026;ENST00000476325	T;T	0.20738	2.05;2.05	6.06	4.89	0.63831	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.076912	0.53938	N	0.000044	T	0.00012	0.0000	N	0.00119	-2.075	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33163	-0.9879	9	0.02654	T	1	-5.186	7.8202	0.29284	0.0:0.065:0.266:0.669	rs6949082;rs17703276;rs52837968;rs60489599;rs6949082	346;346	F8WDH9;Q2M3T9	.;HYAL4_HUMAN	S	346	ENSP00000223026:A346S;ENSP00000417186:A346S	ENSP00000223026:A346S	A	+	1	0	HYAL4	123302132	0.998000	0.40836	0.929000	0.37066	0.879000	0.50718	2.040000	0.41203	0.508000	0.28173	-0.256000	0.11100	GCA	G|0.852;T|0.148	0.148	strong		0.393	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269	
HRNR	388697	hgsc.bcm.edu	37	1	152187554	152187554	+	Missense_Mutation	SNP	C	C	T	rs61814935		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152187554C>T	ENST00000368801.2	-	3	6626	c.6551G>A	c.(6550-6552)aGc>aAc	p.S2184N	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2184					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCGGCCGCGGCTAGGGGAATG	0.642																																					p.S2184N		Atlas-SNP	.											HRNR,NS,haematopoietic_neoplasm,0,1	HRNR	403	1	0			c.G6551A						scavenged	.						17.0	18.0	17.0					1																	152187554		2151	4271	6422	SO:0001583	missense	388697	exon3			CCGCGGCTAGGGG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6551G>A	1.37:g.152187554C>T	ENSP00000357791:p.Ser2184Asn	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	496	234	0.471774	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	7.548	0.662058	0.14645	.	.	ENSG00000197915	ENST00000368801	T	0.01933	4.55	3.24	2.29	0.28610	.	.	.	.	.	T	0.00666	0.0022	L	0.42245	1.32	0.80722	P	0.0	P	0.47409	0.895	B	0.38056	0.264	T	0.53151	-0.8479	8	0.21540	T	0.41	.	4.8473	0.13519	0.0:0.6514:0.223:0.1256	.	2184	Q86YZ3	HORN_HUMAN	N	2184	ENSP00000357791:S2184N	ENSP00000357791:S2184N	S	-	2	0	HRNR	150454178	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.142000	0.10311	0.666000	0.31087	0.650000	0.86243	AGC	.	.	weak		0.642	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
ZNF25	219749	hgsc.bcm.edu	37	10	38241067	38241067	+	Missense_Mutation	SNP	A	A	C	rs1208606	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:38241067A>C	ENST00000302609.7	-	6	1571	c.1359T>G	c.(1357-1359)aaT>aaG	p.N453K	ZNF25_ENST00000374633.1_5'UTR|AL117337.1_ENST00000582458.1_RNA	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	453			N -> K (in dbSNP:rs1208606). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				ACTTCTCAGCATTCCTCTTCT	0.418													C|||	158	0.0315495	0.0015	0.0648	5008	,	,		19419	0.0		0.1024	False		,,,				2504	0.0082				p.N453K		Atlas-SNP	.											.	ZNF25	66	.	0			c.T1359G						PASS	.	C	LYS/ASN	80,4326	819.0+/-416.3	1,78,2124	161.0	141.0	148.0		1359	-0.7	0.0	10	dbSNP_87	148	757,7843	784.7+/-407.6	32,693,3575	yes	missense	ZNF25	NM_145011.2	94	33,771,5699	CC,CA,AA		8.8023,1.8157,6.4355	benign	453/457	38241067	837,12169	2203	4300	6503	SO:0001583	missense	219749	exon6			CTCAGCATTCCTC	AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"""Zinc fingers, C2H2-type"", ""-"""	13043	protein-coding gene	gene with protein product		194528	"""zinc finger protein 25 (KOX 19)"""			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.1359T>G	10.37:g.38241067A>C	ENSP00000302222:p.Asn453Lys	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	211	98	0.464455	NM_145011	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Missense_Mutation	SNP	ENST00000302609.7	37	CCDS7195.1	107	0.04899267399267399	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	74	0.09762532981530343	C	1.557	-0.537804	0.04082	0.018157	0.088023	ENSG00000175395	ENST00000302609;ENST00000374633	T	0.04502	3.61	4.46	-0.696	0.11287	Zinc finger, C2H2 (1);	1.517950	0.04479	N	0.377442	T	0.00109	0.0003	N	0.17248	0.465	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46034	-0.9220	9	0.66056	D	0.02	14.094	1.1582	0.01800	0.1446:0.2805:0.1489:0.426	rs1208606;rs17608680;rs17857088;rs52833070;rs61682660;rs1208606	453	P17030	ZNF25_HUMAN	K	453;417	ENSP00000302222:N453K	ENSP00000302222:N453K	N	-	3	2	ZNF25	38281073	.	.	0.000000	0.03702	0.036000	0.12997	.	.	-0.512000	0.06505	-1.078000	0.02229	AAT	A|0.939;C|0.061	0.061	strong		0.418	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966	
TLR4	7099	hgsc.bcm.edu	37	9	120474891	120474891	+	Missense_Mutation	SNP	T	T	C	rs200168998		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:120474891T>C	ENST00000355622.6	+	3	586	c.485T>C	c.(484-486)aTc>aCc	p.I162T	TLR4_ENST00000394487.4_Missense_Mutation_p.I122T|TLR4_ENST00000472304.1_3'UTR	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	162					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	CACAATCTTATCCAATCTTTC	0.388																																					p.I162T		Atlas-SNP	.											.	TLR4	220	.	0			c.T485C						PASS	.	T	THR/ILE	0,4406		0,0,2203	94.0	98.0	97.0		485	5.1	0.3	9		97	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TLR4	NM_138554.3	89	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	162/840	120474891	1,13005	2203	4300	6503	SO:0001583	missense	7099	exon3			ATCTTATCCAATC	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.485T>C	9.37:g.120474891T>C	ENSP00000363089:p.Ile162Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	154	83	0.538961	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622678	0.46840	0.0	1.16E-4	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.21734	1.99;1.99	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000005	T	0.49236	0.1545	M	0.83012	2.62	0.40068	D	0.975989	D	0.76494	0.999	D	0.91635	0.999	T	0.53767	-0.8392	10	0.39692	T	0.17	.	14.8663	0.70419	0.0:0.0:0.0:1.0	.	162	O00206	TLR4_HUMAN	T	122;162	ENSP00000377997:I122T;ENSP00000363089:I162T	ENSP00000363089:I162T	I	+	2	0	TLR4	119514712	0.955000	0.32602	0.282000	0.24776	0.322000	0.28314	3.253000	0.51469	1.913000	0.55393	0.533000	0.62120	ATC	.	.	weak		0.388	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554	
MUC4	4585	hgsc.bcm.edu	37	3	195505867	195505867	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195505867A>T	ENST00000463781.3	-	2	13043	c.12584T>A	c.(12583-12585)gTc>gAc	p.V4195D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V4195D	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V4195D(6)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGTGTCGGTGACAGGAAGAGG	0.607																																					p.V4195D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,8	MUC4	1505	8	6	Substitution - Missense(6)	endometrium(3)|kidney(3)	c.T12584A						scavenged	.																																			SO:0001583	missense	4585	exon2			TCGGTGACAGGAA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12584T>A	3.37:g.195505867A>T	ENSP00000417498:p.Val4195Asp	Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	195	3	0.0153846	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	0.384	-0.927152	0.02377	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36157	1.42;1.27	.	.	.	.	.	.	.	.	T	0.34513	0.0900	N	0.19112	0.55	0.29126	N	0.879938	D	0.67145	0.996	D	0.69479	0.964	T	0.27938	-1.0059	7	.	.	.	.	4.4413	0.11575	0.3374:0.0:0.6626:0.0	.	4067	E7ESK3	.	D	4195	ENSP00000417498:V4195D;ENSP00000420243:V4195D	.	V	-	2	0	MUC4	196990646	0.000000	0.05858	0.033000	0.17914	0.055000	0.15305	-2.347000	0.01095	-0.475000	0.06852	0.063000	0.15292	GTC	.	.	none		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
POFUT2	23275	hgsc.bcm.edu	37	21	46705621	46705621	+	Silent	SNP	G	G	A	rs2297285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46705621G>A	ENST00000349485.5	-	2	380	c.354C>T	c.(352-354)ccC>ccT	p.P118P	BX322557.10_ENST00000454115.2_RNA|POFUT2_ENST00000331343.7_Silent_p.P118P|POFUT2_ENST00000471540.1_5'Flank	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	118					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		ACTCGATGACGGGGATGTTTT	0.547													G|||	818	0.163339	0.0159	0.1196	5008	,	,		21057	0.1776		0.2485	False		,,,				2504	0.2914				p.P118P		Atlas-SNP	.											POFUT2,NS,carcinoma,-1,1	POFUT2	77	1	0			c.C354T						PASS	.	G	,	227,4179	135.7+/-171.8	3,221,1979	81.0	88.0	85.0		354,354	-9.3	0.3	21	dbSNP_100	85	2116,6484	363.6+/-333.2	267,1582,2451	no	coding-synonymous,coding-synonymous	POFUT2	NM_015227.4,NM_133635.4	,	270,1803,4430	AA,AG,GG		24.6047,5.1521,18.0148	,	118/425,118/430	46705621	2343,10663	2203	4300	6503	SO:0001819	synonymous_variant	23275	exon2			GATGACGGGGATG	AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"""Fucosyltransferases"""	14683	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 2"""	610249	"""chromosome 21 open reading frame 80"""	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.354C>T	21.37:g.46705621G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_015227	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			G|0.821;A|0.179	0.179	strong		0.547	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227	
HCLS1	3059	hgsc.bcm.edu	37	3	121351338	121351338	+	Missense_Mutation	SNP	C	C	T	rs2070180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121351338C>T	ENST00000314583.3	-	12	1172	c.1081G>A	c.(1081-1083)Gaa>Aaa	p.E361K	HCLS1_ENST00000428394.2_Missense_Mutation_p.E324K|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	361			E -> K (in dbSNP:rs2070180).		actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		ggctcTGCTTCGTACACTGGC	0.592													C|||	733	0.146366	0.1271	0.1398	5008	,	,		13576	0.0913		0.2813	False		,,,				2504	0.0951				p.E361K		Atlas-SNP	.											.	HCLS1	78	.	0			c.G1081A						PASS	.	C	LYS/GLU	662,3744	280.2+/-275.2	49,564,1590	113.0	108.0	109.0		1081	4.1	0.9	3	dbSNP_96	109	2464,6136	404.2+/-348.1	369,1726,2205	yes	missense	HCLS1	NM_005335.4	56	418,2290,3795	TT,TC,CC		28.6512,15.025,24.0351	benign	361/487	121351338	3126,9880	2203	4300	6503	SO:0001583	missense	3059	exon12			CTGCTTCGTACAC		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.1081G>A	3.37:g.121351338C>T	ENSP00000320176:p.Glu361Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	126	72	0.571429	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Missense_Mutation	SNP	ENST00000314583.3	37	CCDS3003.1	373	0.1707875457875458	63	0.12804878048780488	49	0.13535911602209943	54	0.0944055944055944	207	0.27308707124010556	C	9.453	1.090966	0.20471	0.15025	0.286512	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.21031	2.03;2.03	5.06	4.14	0.48551	.	1.220880	0.05550	N	0.567392	T	0.00012	0.0000	L	0.46157	1.445	0.40396	P	0.02041000000000004	P;P	0.49635	0.926;0.926	B;B	0.31946	0.138;0.138	T	0.31447	-0.9943	9	0.37606	T	0.19	-27.1314	11.5842	0.50908	0.0:0.8212:0.1788:0.0	rs2070180;rs3184687;rs57559761;rs2070180	324;361	E7EVW7;P14317	.;HCLS1_HUMAN	K	361;324	ENSP00000320176:E361K;ENSP00000387645:E324K	ENSP00000320176:E361K	E	-	1	0	HCLS1	122834028	0.998000	0.40836	0.919000	0.36401	0.042000	0.13812	1.511000	0.35801	2.638000	0.89438	0.655000	0.94253	GAA	C|0.798;T|0.202	0.202	strong		0.592	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	
KCNMB3	27094	hgsc.bcm.edu	37	3	178968660	178968660	+	Missense_Mutation	SNP	T	T	C	rs1170672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:178968660T>C	ENST00000314235.5	-	2	642	c.131A>G	c.(130-132)gAt>gGt	p.D44G	KCNMB3_ENST00000392685.2_Missense_Mutation_p.D40G|KCNMB3_ENST00000497599.1_Missense_Mutation_p.D42G|KCNMB3_ENST00000349697.2_Missense_Mutation_p.D42G|KCNMB3_ENST00000485523.1_Missense_Mutation_p.D22G	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	44			D -> G (in dbSNP:rs1170672).		action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	CTTGTGCACATCTAGTGGGTC	0.542													T|||	347	0.0692891	0.0408	0.0375	5008	,	,		18388	0.005		0.0954	False		,,,				2504	0.1697				p.D44G		Atlas-SNP	.											.	KCNMB3	46	.	0			c.A131G						PASS	.	T	GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP	233,4173	137.3+/-173.1	6,221,1976	124.0	112.0	116.0		125,131,125,65,119	2.3	0.0	3	dbSNP_87	116	991,7609	214.5+/-254.1	63,865,3372	yes	missense,missense,missense,missense,missense	KCNMB3	NM_001163677.1,NM_014407.3,NM_171828.1,NM_171829.2,NM_171830.1	94,94,94,94,94	69,1086,5348	CC,CT,TT		11.5233,5.2882,9.411	benign,benign,benign,benign,benign	42/174,44/280,42/278,22/258,40/276	178968660	1224,11782	2203	4300	6503	SO:0001583	missense	27094	exon2			TGCACATCTAGTG	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"""Potassium channels"""	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.131A>G	3.37:g.178968660T>C	ENSP00000319370:p.Asp44Gly	Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	313	135	0.43131	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000314235.5	37	CCDS3226.1	120	0.054945054945054944	35	0.07113821138211382	12	0.03314917127071823	3	0.005244755244755245	70	0.09234828496042216	T	14.90	2.672063	0.47781	0.052882	0.115233	ENSG00000171121	ENST00000497599;ENST00000392685;ENST00000349697;ENST00000314235;ENST00000485523	T;T;T;T;T	0.20738	2.05;2.74;2.77;2.81;2.77	6.07	2.34	0.29019	.	1.479250	0.03645	N	0.240197	T	0.00241	0.0007	N	0.24115	0.695	0.09310	N	1	B;B;P;P;P	0.42248	0.006;0.041;0.628;0.774;0.665	B;B;B;B;B	0.40066	0.004;0.066;0.318;0.318;0.169	T	0.19353	-1.0308	10	0.66056	D	0.02	-8.1794	7.3861	0.26882	0.0:0.0714:0.2725:0.6561	rs1170672;rs17565640;rs57414713;rs1170672	42;42;22;40;44	E9PER5;Q9NPA1-2;Q9NPA1-4;Q9NPA1-3;Q9NPA1	.;.;.;.;KCMB3_HUMAN	G	42;40;42;44;22	ENSP00000417091:D42G;ENSP00000376451:D40G;ENSP00000327866:D42G;ENSP00000319370:D44G;ENSP00000418536:D22G	ENSP00000319370:D44G	D	-	2	0	KCNMB3	180451354	0.029000	0.19370	0.004000	0.12327	0.007000	0.05969	1.097000	0.30988	0.169000	0.19679	0.528000	0.53228	GAT	T|0.918;C|0.082	0.082	strong		0.542	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1		
PLA2R1	22925	hgsc.bcm.edu	37	2	160885442	160885442	+	Missense_Mutation	SNP	T	T	C	rs3749117	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160885442T>C	ENST00000283243.7	-	5	1080	c.874A>G	c.(874-876)Atg>Gtg	p.M292V	PLA2R1_ENST00000392771.1_Missense_Mutation_p.M292V	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	292	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.		M -> V (in dbSNP:rs3749117). {ECO:0000269|PubMed:7721806}.		cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						TTGAGGCCCATCCACACCTCC	0.458													T|||	1287	0.256989	0.0552	0.2695	5008	,	,		19362	0.3542		0.4742	False		,,,				2504	0.1973				p.M292V		Atlas-SNP	.											.	PLA2R1	153	.	0			c.A874G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	534,3872	243.1+/-252.9	31,472,1700	109.0	86.0	94.0		874,874,874	4.6	0.8	2	dbSNP_107	94	4212,4388	570.2+/-389.3	1062,2088,1150	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	21,21,21	1093,2560,2850	CC,CT,TT		48.9767,12.1198,36.4909	benign,benign,benign	292/1325,292/1462,292/1464	160885442	4746,8260	2203	4300	6503	SO:0001583	missense	22925	exon5			GGCCCATCCACAC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.874A>G	2.37:g.160885442T>C	ENSP00000283243:p.Met292Val	Somatic	298	1	0.0033557		WXS	Illumina HiSeq	Phase_I	248	248	1	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	710	0.3250915750915751	31	0.06300813008130081	110	0.30386740331491713	201	0.3513986013986014	368	0.48548812664907653	T	8.814	0.935883	0.18206	0.121198	0.489767	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15256	2.44;2.44	5.83	4.64	0.57946	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.833616	0.11223	N	0.586525	T	0.00012	0.0000	L	0.37697	1.125	0.43364	P	0.004554999999999976	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.14578	0.005;0.002;0.011	T	0.43909	-0.9362	9	0.59425	D	0.04	.	12.1668	0.54135	0.0:0.0:0.1431:0.8569	rs3749117;rs52812136;rs58475274;rs3749117	292;292;292	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	V	292	ENSP00000283243:M292V;ENSP00000376524:M292V	ENSP00000283243:M292V	M	-	1	0	PLA2R1	160593688	1.000000	0.71417	0.830000	0.32933	0.119000	0.20118	3.267000	0.51577	0.991000	0.38814	0.528000	0.53228	ATG	T|0.669;C|0.331	0.331	strong		0.458	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
CATIP	375307	hgsc.bcm.edu	37	2	219221846	219221846	+	Silent	SNP	G	G	A	rs4324314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219221846G>A	ENST00000289388.3	+	2	83	c.54G>A	c.(52-54)tcG>tcA	p.S18S	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		18					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACCAGCCCTCGGGTCCGGAGT	0.637													G|||	594	0.11861	0.0408	0.2421	5008	,	,		15900	0.1032		0.2117	False		,,,				2504	0.0562				p.S18S		Atlas-SNP	.											.	C2orf62	28	.	0			c.G54A						PASS	.	G		316,4090	167.6+/-198.6	9,298,1896	55.0	55.0	55.0		54	-3.9	0.0	2	dbSNP_111	55	1929,6671	338.5+/-322.8	219,1491,2590	no	coding-synonymous	C2orf62	NM_198559.1		228,1789,4486	AA,AG,GG		22.4302,7.172,17.2613		18/388	219221846	2245,10761	2203	4300	6503	SO:0001819	synonymous_variant	375307	exon2			GCCCTCGGGTCCG																												ENST00000289388.3:c.54G>A	2.37:g.219221846G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	58	0.617021	NM_198559		Silent	SNP	ENST00000289388.3	37	CCDS2414.1																																																																																			G|0.843;A|0.157	0.157	strong		0.637	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1		
SCNN1B	6338	hgsc.bcm.edu	37	16	23360174	23360174	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23360174T>C	ENST00000343070.2	+	2	430	c.254T>C	c.(253-255)gTa>gCa	p.V85A	SCNN1B_ENST00000569789.1_3'UTR|SCNN1B_ENST00000568923.1_Missense_Mutation_p.V85A|SCNN1B_ENST00000568085.1_Missense_Mutation_p.V85A|SCNN1B_ENST00000307331.5_Missense_Mutation_p.V130A	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	85					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	TCCCTCTCCGTAGGCTTCAAG	0.617																																					p.V85A		Atlas-SNP	.											SCNN1B_ENST00000307331,NS,carcinoma,+1,2	SCNN1B	81	2	0			c.T254C						scavenged	.						78.0	67.0	71.0					16																	23360174		2197	4300	6497	SO:0001583	missense	6338	exon2			TCTCCGTAGGCTT	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10600	protein-coding gene	gene with protein product	"""Liddle syndrome"""	600760	"""sodium channel, nonvoltage-gated 1, beta"", ""sodium channel, non-voltage-gated 1, beta"""				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.254T>C	16.37:g.23360174T>C	ENSP00000345751:p.Val85Ala	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	229	3	0.0131004	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	37	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	T	15.78	2.933501	0.52866	.	.	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.62788	-0.0;-0.0	4.92	4.92	0.64577	.	1.032170	0.07691	N	0.938686	T	0.60983	0.2311	L	0.47716	1.5	0.25186	N	0.990167	B	0.24317	0.101	B	0.25506	0.061	T	0.55611	-0.8114	10	0.87932	D	0	-7.5454	13.7288	0.62774	0.0:0.0:0.0:1.0	.	85	P51168	SCNNB_HUMAN	A	85;130	ENSP00000345751:V85A;ENSP00000302874:V130A	ENSP00000302874:V130A	V	+	2	0	SCNN1B	23267675	0.328000	0.24687	0.288000	0.24862	0.915000	0.54546	4.282000	0.58971	1.834000	0.53371	0.459000	0.35465	GTA	.	.	none		0.617	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2		
MYO18B	84700	hgsc.bcm.edu	37	22	26219605	26219605	+	Silent	SNP	G	G	A	rs4820658	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26219605G>A	ENST00000407587.2	+	13	2824	c.2655G>A	c.(2653-2655)ggG>ggA	p.G885G	MYO18B_ENST00000536101.1_Silent_p.G885G|MYO18B_ENST00000335473.7_Silent_p.G885G			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	885	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TGACGTTTGGGCCAAGCCGAT	0.607													G|||	797	0.159145	0.0136	0.3372	5008	,	,		17951	0.0258		0.3429	False		,,,				2504	0.1779				p.G885G		Atlas-SNP	.											.	MYO18B	322	.	0			c.G2655A						PASS	.	G		279,3877		14,251,1813	176.0	174.0	175.0		2655	2.5	0.2	22	dbSNP_111	175	3049,5359		561,1927,1716	no	coding-synonymous	MYO18B	NM_032608.5		575,2178,3529	AA,AG,GG		36.2631,6.7132,26.4884		885/2568	26219605	3328,9236	2078	4204	6282	SO:0001819	synonymous_variant	84700	exon13			GTTTGGGCCAAGC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2655G>A	22.37:g.26219605G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				G|0.815;A|0.185	0.185	strong		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
ACSS2	55902	hgsc.bcm.edu	37	20	33470694	33470694	+	Silent	SNP	C	C	T	rs4911163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:33470694C>T	ENST00000360596.2	+	2	487	c.276C>T	c.(274-276)ttC>ttT	p.F92F	ACSS2_ENST00000253382.5_Silent_p.F92F|ACSS2_ENST00000336325.4_Silent_p.F42F|ACSS2_ENST00000476922.1_3'UTR	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	92					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|lipid biosynthetic process (GO:0008610)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GGAAAATCTTCATTGAGTGGA	0.423													C|||	2565	0.512181	0.4304	0.3516	5008	,	,		19780	0.4355		0.5706	False		,,,				2504	0.7556				p.F92F		Atlas-SNP	.											.	ACSS2	75	.	0			c.C276T						PASS	.	C	,,	2050,2356	568.1+/-382.3	481,1088,634	123.0	113.0	117.0		276,,276	4.1	1.0	20	dbSNP_111	117	5307,3293	647.1+/-400.3	1627,2053,620	yes	coding-synonymous,utr-5,coding-synonymous	ACSS2	NM_001076552.2,NM_001242393.1,NM_018677.3	,,	2108,3141,1254	TT,TC,CC		38.2907,46.5275,43.4338	,,	92/715,,92/702	33470694	7357,5649	2203	4300	6503	SO:0001819	synonymous_variant	55902	exon2			AATCTTCATTGAG	AF263614	CCDS13243.1, CCDS42868.1, CCDS42868.2	20q11.22	2012-07-13	2005-09-08	2005-09-08	ENSG00000131069	ENSG00000131069	6.2.1.1	"""Acyl-CoA synthetase family"""	15814	protein-coding gene	gene with protein product		605832	"""acetyl-Coenzyme A synthetase 2 (ADP forming)"""	ACAS2		10843999	Standard	NM_018677		Approved	ACS, ACSA, AceCS, dJ1161H23.1	uc010gey.2	Q9NR19	OTTHUMG00000032317	ENST00000360596.2:c.276C>T	20.37:g.33470694C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	124	44	0.354839	NM_001076552	A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Silent	SNP	ENST00000360596.2	37	CCDS13243.1																																																																																			C|0.467;T|0.533	0.533	strong		0.423	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3	NM_018677	
MUS81	80198	hgsc.bcm.edu	37	11	65631167	65631167	+	Silent	SNP	C	C	T	rs648732	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65631167C>T	ENST00000308110.4	+	9	1285	c.936C>T	c.(934-936)gcC>gcT	p.A312A	MUS81_ENST00000533035.1_Silent_p.A237A|EFEMP2_ENST00000532648.1_5'Flank|CFL1_ENST00000534769.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	312	ERCC4.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		TGTGGGTGGCCCAGGAGACCA	0.662								Homologous recombination					C|||	2144	0.428115	0.2012	0.4063	5008	,	,		17571	0.3323		0.668	False		,,,				2504	0.6022				p.A312A		Atlas-SNP	.											.	MUS81	68	.	0			c.C936T						PASS	.	C		1150,3252	407.5+/-334.3	153,844,1204	63.0	68.0	66.0		936	-11.1	0.5	11	dbSNP_83	66	5739,2853	672.8+/-403.0	1894,1951,451	no	coding-synonymous	MUS81	NM_025128.4		2047,2795,1655	TT,TC,CC		33.2053,26.1245,46.9832		312/552	65631167	6889,6105	2201	4296	6497	SO:0001819	synonymous_variant	80198	exon9			GGTGGCCCAGGAG		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.936C>T	11.37:g.65631167C>T		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_025128	Q9H7D9	Silent	SNP	ENST00000308110.4	37	CCDS8115.1	976	0.4468864468864469	117	0.23780487804878048	176	0.4861878453038674	174	0.3041958041958042	509	0.6715039577836411	C	1.335	-0.595788	0.03771	0.261245	0.667947	ENSG00000172732	ENST00000529374	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999477	.	.	.	.	.	.	T	0.37572	-0.9700	3	.	.	.	-13.2162	1.7302	0.02930	0.2467:0.2533:0.323:0.177	rs648732;rs17850599;rs648732	.	.	.	S	237	.	.	P	+	1	0	MUS81	65387743	0.042000	0.20092	0.502000	0.27614	0.053000	0.15095	-1.084000	0.03393	-2.125000	0.00821	-1.095000	0.02154	CCA	C|0.515;T|0.485	0.485	strong		0.662	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
EP400	57634	hgsc.bcm.edu	37	12	132562126	132562126	+	Missense_Mutation	SNP	G	G	A	rs73164912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:132562126G>A	ENST00000333577.4	+	54	9497	c.9388G>A	c.(9388-9390)Gcc>Acc	p.A3130T	EP400_ENST00000389561.2_Missense_Mutation_p.A3094T|EP400_ENST00000332482.4_Missense_Mutation_p.A3057T|EP400_ENST00000330386.6_Missense_Mutation_p.A3013T|RP13-820C6.2_ENST00000542422.1_RNA|EP400_ENST00000389562.2_Missense_Mutation_p.A3093T			Q96L91	EP400_HUMAN	E1A binding protein p400	3130					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCAGGTGCCCGCCAGCTCCGA	0.632													G|||	409	0.0816693	0.143	0.072	5008	,	,		13730	0.0119		0.1213	False		,,,				2504	0.0368				p.A3094T		Atlas-SNP	.											.	EP400	370	.	0			c.G9280A						PASS	.	G	THR/ALA	584,3822	247.2+/-255.5	41,502,1660	25.0	29.0	28.0		9280	1.7	0.0	12	dbSNP_131	28	1201,7399	236.8+/-268.9	90,1021,3189	yes	missense	EP400	NM_015409.4	58	131,1523,4849	AA,AG,GG		13.9651,13.2547,13.7244	possibly-damaging	3094/3124	132562126	1785,11221	2203	4300	6503	SO:0001583	missense	57634	exon53			GTGCCCGCCAGCT	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.9388G>A	12.37:g.132562126G>A	ENSP00000333602:p.Ala3130Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	115	112	0.973913	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		201	0.09203296703296704	71	0.1443089430894309	29	0.08011049723756906	5	0.008741258741258742	96	0.1266490765171504	G	4.653	0.121436	0.08881	0.132547	0.139651	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.91068	-2.78;-2.77;-2.73;-2.75;-2.76	5.62	1.66	0.24008	.	0.251619	0.39407	N	0.001380	T	0.02649	0.0080	N	0.24115	0.695	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.19331	0.001;0.035;0.035;0.035	B;B;B;B	0.14023	0.001;0.01;0.01;0.01	T	0.47420	-0.9119	9	0.51188	T	0.08	.	9.7951	0.40731	0.1811:0.0:0.7155:0.1035	.	3130;3094;3013;3093	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	T	3130;3094;3093;3057;3013;3094	ENSP00000333602:A3130T;ENSP00000374212:A3094T;ENSP00000374213:A3093T;ENSP00000331737:A3057T;ENSP00000330620:A3013T	ENSP00000330620:A3013T	A	+	1	0	EP400	131128079	0.728000	0.28080	0.001000	0.08648	0.029000	0.11900	2.010000	0.40913	-0.162000	0.10964	-0.797000	0.03246	GCC	G|0.875;A|0.125	0.125	strong		0.632	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
COLEC12	81035	hgsc.bcm.edu	37	18	346821	346821	+	Silent	SNP	C	C	T	rs3826628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:346821C>T	ENST00000400256.3	-	5	1008	c.801G>A	c.(799-801)acG>acA	p.T267T		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	267					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TGGCAGCCAGCGTCTGCAAGC	0.498													C|||	1168	0.233227	0.177	0.2839	5008	,	,		21093	0.2153		0.2545	False		,,,				2504	0.2699				p.T267T		Atlas-SNP	.											COLEC12,colon,carcinoma,0,1	COLEC12	121	1	0			c.G801A						PASS	.	C		802,3604	324.2+/-298.5	93,616,1494	131.0	109.0	117.0		801	-7.0	0.6	18	dbSNP_107	117	2150,6450	369.5+/-335.5	270,1610,2420	no	coding-synonymous	COLEC12	NM_130386.2		363,2226,3914	TT,TC,CC		25.0,18.2025,22.6972		267/743	346821	2952,10054	2203	4300	6503	SO:0001819	synonymous_variant	81035	exon5			AGCCAGCGTCTGC	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"""Collectins"""	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.801G>A	18.37:g.346821C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	105	36	0.342857	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	37	CCDS32782.1																																																																																			C|0.763;T|0.237	0.237	strong		0.498	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1		
UGT2B17	7367	hgsc.bcm.edu	37	4	69433714	69433714	+	Silent	SNP	C	C	T	rs34664906	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:69433714C>T	ENST00000317746.2	-	1	531	c.489G>A	c.(487-489)gaG>gaA	p.E163E		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	163					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	TGTTAAGTAGCTCAGCCAGCA	0.443													C|||	1417	0.282947	0.3306	0.4798	5008	,	,		8754	0.0476		0.3549	False		,,,				2504	0.2474				p.E163E	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											UGT2B17,NS,carcinoma,-1,1	UGT2B17	34	1	0			c.G489A						scavenged	.	C		1402,2780		435,532,1124	177.0	173.0	174.0		489	1.8	0.3	4	dbSNP_126	174	3313,4597		1164,985,1806	no	coding-synonymous	UGT2B17	NM_001077.3		1599,1517,2930	TT,TC,CC		41.8837,33.5246,38.9927		163/531	69433714	4715,7377	2091	3955	6046	SO:0001819	synonymous_variant	7367	exon1			AAGTAGCTCAGCC	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.489G>A	4.37:g.69433714C>T		Somatic	1	1	1		WXS	Illumina HiSeq	Phase_I	396	179	0.45202	NM_001077		Silent	SNP	ENST00000317746.2	37	CCDS3523.1																																																																																			C|0.694;T|0.306	0.306	strong		0.443	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	
ICOSLG	23308	hgsc.bcm.edu	37	21	45656774	45656774	+	Missense_Mutation	SNP	C	C	T	rs11558819	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45656774C>T	ENST00000407780.3	-	3	509	c.382G>A	c.(382-384)Gtt>Att	p.V128I	ICOSLG_ENST00000400377.3_Intron|ICOSLG_ENST00000344330.4_Missense_Mutation_p.V128I|ICOSLG_ENST00000400379.3_Missense_Mutation_p.V128I	NM_001283052.1	NP_001269981.1	O75144	ICOSL_HUMAN	inducible T-cell co-stimulator ligand	128	Ig-like V-type.		V -> I (in dbSNP:rs11558819).		B cell activation (GO:0042113)|defense response (GO:0006952)|hyperosmotic response (GO:0006972)|positive regulation of activated T cell proliferation (GO:0042104)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.V128I(1)		endometrium(2)|lung(1)|stomach(1)|urinary_tract(1)	5				Colorectal(79;0.0163)|READ - Rectum adenocarcinoma(84;0.0772)		GTAACCTCAACGCTCAAAACC	0.572													c|||	1348	0.269169	0.3427	0.3271	5008	,	,		18992	0.1438		0.2873	False		,,,				2504	0.2393				p.V128I		Atlas-SNP	.											ICOSLG,NS,carcinoma,0,1	ICOSLG	20	1	1	Substitution - Missense(1)	stomach(1)	c.G382A						PASS	.	T	ILE/VAL	1318,2860		210,898,981	101.0	113.0	109.0		382	1.0	0.0	21	dbSNP_120	109	2320,6132		329,1662,2235	yes	missense	ICOSLG	NM_015259.4	29	539,2560,3216	TT,TC,CC		27.4491,31.5462,28.8044	possibly-damaging	128/303	45656774	3638,8992	2089	4226	6315	SO:0001583	missense	23308	exon3			CCTCAACGCTCAA	AB014553	CCDS42952.1, CCDS63377.1, CCDS63379.1	21q22.3	2014-01-30		2005-01-12	ENSG00000160223	ENSG00000160223		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Endogenous ligands"""	17087	protein-coding gene	gene with protein product	"""B7-related protein 1"", ""B7 homologue 2"", ""B7 homolog 2"""	605717		ICOSL		9734811, 11007762	Standard	NM_001283050		Approved	KIAA0653, GL50, B7-H2, B7RP-1, B7H2, B7RP1, ICOS-L, CD275	uc002zee.3	O75144	OTTHUMG00000086920	ENST00000407780.3:c.382G>A	21.37:g.45656774C>T	ENSP00000384432:p.Val128Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_015259	A8MUZ1|Q9HD18|Q9NRQ1	Missense_Mutation	SNP	ENST00000407780.3	37	CCDS42952.1	547	0.25045787545787546	150	0.3048780487804878	105	0.2900552486187845	77	0.1346153846153846	215	0.2836411609498681	c	8.707	0.911038	0.17833	0.315462	0.274491	ENSG00000160223	ENST00000344330;ENST00000407780;ENST00000400379	T;T;T	0.27557	1.66;1.66;1.66	5.01	1.05	0.20165	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.262160	0.05654	N	0.585727	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	P;P	0.39903	0.694;0.694	B;B	0.37550	0.253;0.253	T	0.32079	-0.9920	9	0.24483	T	0.36	.	4.0371	0.09735	0.0:0.5387:0.1755:0.2858	rs11558819;rs11575872	128;128	A0N0L8;O75144	.;ICOSL_HUMAN	I	128	ENSP00000339477:V128I;ENSP00000384432:V128I;ENSP00000383230:V128I	ENSP00000339477:V128I	V	-	1	0	ICOSLG	44481202	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.355000	0.07671	0.332000	0.23536	-0.766000	0.03442	GTT	C|0.738;T|0.262	0.262	strong		0.572	ICOSLG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195838.1	NM_015259	
KDM1B	221656	hgsc.bcm.edu	37	6	18161563	18161563	+	Silent	SNP	G	G	A	rs4716224	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:18161563G>A	ENST00000297792.5	+	4	270	c.93G>A	c.(91-93)aaG>aaA	p.K31K	KDM1B_ENST00000397244.1_Silent_p.K31K|KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000388870.2_Silent_p.K31K			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	31					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						CTTAGGCGAAGAAGAAAGCAA	0.433													G|||	1570	0.313498	0.146	0.3501	5008	,	,		20748	0.5258		0.3419	False		,,,				2504	0.2658				p.K31K		Atlas-SNP	.											.	KDM1B	58	.	0			c.G93A						PASS	.	G		860,3546	336.3+/-304.3	89,682,1432	181.0	147.0	159.0		93	5.8	1.0	6	dbSNP_111	159	3088,5512	471.5+/-368.1	575,1938,1787	no	coding-synonymous	KDM1B	NM_153042.3		664,2620,3219	AA,AG,GG		35.907,19.5188,30.3552		31/591	18161563	3948,9058	2203	4300	6503	SO:0001819	synonymous_variant	221656	exon4			GGCGAAGAAGAAA	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"""Chromatin-modifying enzymes / K-demethylases"""	21577	protein-coding gene	gene with protein product		613081	"""amine oxidase, flavin containing 1"", ""chromosome 6 open reading frame 193"", ""amine oxidase (flavin containing) domain 1"""	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.93G>A	6.37:g.18161563G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Silent	SNP	ENST00000297792.5	37	CCDS34343.1																																																																																			G|0.683;A|0.317	0.317	strong		0.433	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042	
MED29	55588	hgsc.bcm.edu	37	19	39880011	39880011	+	5'Flank	SNP	G	G	A	rs2074852	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39880011G>A	ENST00000599213.2	+	0	0				PAF1_ENST00000221266.7_Silent_p.H114H|PAF1_ENST00000595564.1_Silent_p.H114H|MED29_ENST00000315588.5_5'Flank|MED29_ENST00000594368.1_5'Flank|PAF1_ENST00000221265.3_Silent_p.H124H			Q9NX70	MED29_HUMAN	mediator complex subunit 29						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mediator complex (GO:0016592)|nucleus (GO:0005634)				lung(2)|ovary(1)|pancreas(1)	4	all_cancers(60;7.82e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;1.04e-26)|all cancers(26;7.68e-24)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			CCACCTTCGCGTGCTGCTGGG	0.537													G|||	328	0.0654952	0.1392	0.0403	5008	,	,		19638	0.0466		0.0348	False		,,,				2504	0.0348				p.H124H		Atlas-SNP	.											.	PAF1	43	.	0			c.C372T						PASS	.	G		504,3902	232.6+/-246.1	36,432,1735	85.0	79.0	81.0		372	-0.6	1.0	19	dbSNP_96	81	263,8337	101.9+/-163.1	3,257,4040	no	coding-synonymous	PAF1	NM_019088.2		39,689,5775	AA,AG,GG		3.0581,11.4389,5.8973		124/532	39880011	767,12239	2203	4300	6503	SO:0001631	upstream_gene_variant	54623	exon6			CTTCGCGTGCTGC	AL137304, AY729650	CCDS33021.1	19q13.2	2007-07-30	2007-07-30	2007-07-30		ENSG00000063322			23074	protein-coding gene	gene with protein product		612914	"""intersex-like (Drosophila)"""	IXL		15555573	Standard	NM_017592		Approved	DKFZp434H247	uc010xux.3	Q9NX70			19.37:g.39880011G>A	Exception_encountered	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	206	105	0.509709	NM_019088	B4DNQ6|M0R2E4|Q5XX09|Q9NTF4	Silent	SNP	ENST00000599213.2	37																																																																																				A|0.060;C|0.007	0.060	strong		0.537	MED29-011	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470870.1	XM_290829	
CHIT1	1118	hgsc.bcm.edu	37	1	203194186	203194186	+	Missense_Mutation	SNP	C	C	T	rs2297950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:203194186C>T	ENST00000367229.1	-	4	338	c.304G>A	c.(304-306)Ggc>Agc	p.G102S	CHIT1_ENST00000535569.1_Intron|CHIT1_ENST00000255427.3_Intron|CHIT1_ENST00000484834.1_5'UTR	NM_001270509.1|NM_003465.2	NP_001257438.1|NP_003456.1	Q13231	CHIT1_HUMAN	chitinase 1 (chitotriosidase)	102			G -> S (common variant detected in patients with Gaucher disease type 1 as well as healthy individuals; slightly reduced activity towards 4- methylumbelliferyl-chitotrioside but no effect on activity towards 4- methylumbelliferyl-deoxychitobioside; dbSNP:rs2297950). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17464953}.		chitin catabolic process (GO:0006032)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|lysosome (GO:0005764)	chitin binding (GO:0008061)|chitinase activity (GO:0004568)|endochitinase activity (GO:0008843)	p.G102S(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|stomach(2)	27						TTCTGAGTGCCGAAATTCCAG	0.572													C|||	1457	0.290935	0.2738	0.3271	5008	,	,		20255	0.2847		0.3231	False		,,,				2504	0.2618				p.G102S		Atlas-SNP	.											CHIT1,NS,carcinoma,0,1	CHIT1	61	1	1	Substitution - Missense(1)	stomach(1)	c.G304A	GRCh37	CM065066	CHIT1	M	rs2297950	PASS	.	C	SER/GLY	1188,3218	416.3+/-337.5	145,898,1160	74.0	66.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	304	2.6	0.3	1	dbSNP_100	69	2522,6078	412.3+/-350.8	349,1824,2127	yes	missense	CHIT1	NM_003465.2	56	494,2722,3287	TT,TC,CC		29.3256,26.9632,28.5253	possibly-damaging	102/467	203194186	3710,9296	2203	4300	6503	SO:0001583	missense	1118	exon4			GAGTGCCGAAATT	U29615	CCDS1436.1, CCDS58057.1	1q32.1	2013-06-06			ENSG00000133063	ENSG00000133063			1936	protein-coding gene	gene with protein product		600031				9748235, 9492324	Standard	NM_003465		Approved	CHIT, CHI3	uc001gzn.2	Q13231	OTTHUMG00000042126	ENST00000367229.1:c.304G>A	1.37:g.203194186C>T	ENSP00000356198:p.Gly102Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	58	0.651685	NM_001270509	B3KNW6|J3KN09|Q0VGG5|Q0VGG6|Q3ZAR1|Q6ISC2|Q9H3V8|Q9UDJ8	Missense_Mutation	SNP	ENST00000367229.1	37	CCDS1436.1	656	0.30036630036630035	143	0.29065040650406504	104	0.287292817679558	169	0.29545454545454547	240	0.316622691292876	C	20.4	3.985328	0.74474	0.269632	0.293256	ENSG00000133063	ENST00000367229	T	0.03772	3.81	4.5	2.59	0.31030	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.47093	D	0.000249	T	0.00012	0.0000	L	0.54965	1.715	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.42965	-0.9420	9	0.87932	D	0	-2.7183	7.7551	0.28919	0.0:0.7418:0.1646:0.0936	rs2297950;rs17532953;rs52810372;rs61547564;rs2297950	102	Q13231	CHIT1_HUMAN	S	102	ENSP00000356198:G102S	ENSP00000356198:G102S	G	-	1	0	CHIT1	201460809	1.000000	0.71417	0.309000	0.25155	0.887000	0.51463	4.997000	0.63921	0.319000	0.23209	0.655000	0.94253	GGC	C|0.715;N|0.000	.	strong		0.572	CHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100275.2	NM_003465	
NLRP13	126204	hgsc.bcm.edu	37	19	56423074	56423074	+	Silent	SNP	C	C	G	rs977070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56423074C>G	ENST00000342929.3	-	5	2108	c.2109G>C	c.(2107-2109)ctG>ctC	p.L703L	NLRP13_ENST00000588751.1_Silent_p.L703L	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	703							ATP binding (GO:0005524)	p.L703L(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		ATACTCACTCCAGAATTTCCA	0.393													C|||	2762	0.551518	0.7133	0.3674	5008	,	,		21051	0.5565		0.4573	False		,,,				2504	0.5552				p.L703L		Atlas-SNP	.											NLRP13,NS,carcinoma,0,1	NLRP13	220	1	1	Substitution - coding silent(1)	stomach(1)	c.G2109C						PASS	.	C		2969,1437	644.6+/-398.0	999,971,233	77.0	86.0	83.0		2109	-0.4	0.1	19	dbSNP_86	83	3975,4625	535.2+/-382.8	933,2109,1258	no	coding-synonymous	NLRP13	NM_176810.2		1932,3080,1491	GG,GC,CC		46.2209,32.6146,46.6093		703/1044	56423074	6944,6062	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon5			TCACTCCAGAATT	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2109G>C	19.37:g.56423074C>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			C|0.480;G|0.520	0.520	strong		0.393	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
CCDC146	57639	hgsc.bcm.edu	37	7	76871086	76871086	+	Silent	SNP	G	G	A	rs74783981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76871086G>A	ENST00000285871.4	+	4	445	c.318G>A	c.(316-318)ctG>ctA	p.L106L	CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	106										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				AGTTTCACCTGCAGCAAGCTG	0.418													G|||	347	0.0692891	0.0061	0.0663	5008	,	,		19920	0.0962		0.0885	False		,,,				2504	0.1094				p.L106L		Atlas-SNP	.											.	CCDC146	87	.	0			c.G318A						PASS	.	G		95,4311	78.3+/-116.7	2,91,2110	110.0	108.0	109.0		318	5.7	1.0	7	dbSNP_132	109	794,7806	186.6+/-234.0	26,742,3532	no	coding-synonymous	CCDC146	NM_020879.2		28,833,5642	AA,AG,GG		9.2326,2.1562,6.8353		106/956	76871086	889,12117	2203	4300	6503	SO:0001819	synonymous_variant	57639	exon4			TCACCTGCAGCAA	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.318G>A	7.37:g.76871086G>A		Somatic	308	1	0.00324675		WXS	Illumina HiSeq	Phase_I	334	162	0.48503	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	37	CCDS34671.1																																																																																			G|0.931;A|0.069	0.069	strong		0.418	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
MPND	84954	hgsc.bcm.edu	37	19	4352959	4352959	+	Silent	SNP	A	A	G	rs11882587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4352959A>G	ENST00000262966.8	+	4	664	c.597A>G	c.(595-597)gcA>gcG	p.A199A	MPND_ENST00000359935.4_Silent_p.A199A|MPND_ENST00000599840.1_Silent_p.A199A|AC007292.4_ENST00000594776.1_RNA	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	199							peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		aCGTTCTGGCAGGGGTCTCAG	0.657													g|||	3273	0.653554	0.6362	0.7176	5008	,	,		10991	0.7718		0.5328	False		,,,				2504	0.6339				p.A199A		Atlas-SNP	.											.	MPND	28	.	0			c.A597G						PASS	.		,	2498,1470		798,902,284	33.0	36.0	35.0		597,597	-6.4	0.2	19	dbSNP_120	35	4533,3785		1246,2041,872	no	coding-synonymous,coding-synonymous	MPND	NM_001159846.1,NM_032868.4	,	2044,2943,1156	GG,GA,AA		45.5037,37.0464,42.7723	,	199/452,199/472	4352959	7031,5255	1984	4159	6143	SO:0001819	synonymous_variant	84954	exon4			TCTGGCAGGGGTC		CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.597A>G	19.37:g.4352959A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	159	67	0.421384	NM_032868	Q96SJ0|Q9Y2P1|Q9Y2P2	Silent	SNP	ENST00000262966.8	37	CCDS42470.1																																																																																			A|0.386;G|0.614	0.614	strong		0.657	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1	NM_032868	
SLCO1B3	28234	hgsc.bcm.edu	37	12	21015760	21015760	+	Missense_Mutation	SNP	G	G	A	rs7311358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:21015760G>A	ENST00000381545.3	+	8	918	c.699G>A	c.(697-699)atG>atA	p.M233I	SLCO1B3_ENST00000261196.2_Missense_Mutation_p.M233I|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.M233I|LST3_ENST00000540229.1_Missense_Mutation_p.M233I|SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000381541.3_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	233			M -> I (in dbSNP:rs7311358).		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TTGCTAAAATGTACGTGGATA	0.353													.|||	3518	0.702476	0.3555	0.8372	5008	,	,		15110	0.6984		0.8648	False		,,,				2504	0.9131				p.M233I		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.G699A						PASS	.	G	ILE/MET	1972,2434	555.5+/-379.3	464,1044,695	169.0	144.0	153.0		699	-2.0	0.1	12	dbSNP_116	153	7429,1171	764.5+/-407.6	3210,1009,81	yes	missense	SLCO1B3	NM_019844.2	10	3674,2053,776	AA,AG,GG		13.6163,44.7571,27.718	benign	233/703	21015760	9401,3605	2203	4300	6503	SO:0001583	missense	28234	exon8			TAAAATGTACGTG		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.699G>A	12.37:g.21015760G>A	ENSP00000370956:p.Met233Ile	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	196	195	0.994898	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	1550	0.7097069597069597	185	0.37601626016260165	310	0.856353591160221	411	0.7185314685314685	644	0.8496042216358839	G	11.67	1.706783	0.30232	0.447571	0.863837	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000544370;ENST00000540229	T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31	3.9	-2.0	0.07433	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.365415	0.31145	N	0.008175	T	0.00012	0.0000	N	0.04994	-0.135	0.09310	P	0.999999826979	B;B	0.23854	0.092;0.007	B;B	0.20577	0.03;0.007	T	0.14896	-1.0456	9	0.23891	T	0.37	.	4.723	0.12927	0.3524:0.277:0.3706:0.0	rs7311358;rs60001963;rs7311358	233;233	Q5JAR4;Q9NPD5	.;SO1B3_HUMAN	I	233;233;233;233;57;233	ENSP00000442000:M233I;ENSP00000261196:M233I;ENSP00000370956:M233I;ENSP00000451758:M233I;ENSP00000443225:M57I;ENSP00000441269:M233I	ENSP00000441269:M233I	M	+	3	0	SLCO1B3;RP11-545J16.1	20907027	0.001000	0.12720	0.065000	0.19835	0.847000	0.48162	-1.540000	0.02200	-0.125000	0.11703	0.460000	0.39030	ATG	G|0.289;A|0.711	0.711	strong		0.353	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
CDH17	1015	hgsc.bcm.edu	37	8	95143172	95143172	+	Missense_Mutation	SNP	T	T	G	rs1051624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95143172T>G	ENST00000027335.3	-	16	2340	c.2216A>C	c.(2215-2217)gAg>gCg	p.E739A	CDH17_ENST00000450165.2_Missense_Mutation_p.E739A|CDH17_ENST00000441892.2_Missense_Mutation_p.E525A	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	739	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> A (in dbSNP:rs1051624).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			GACGACATACTCCCTCTCCTC	0.483													T|||	2217	0.442692	0.2753	0.3948	5008	,	,		18760	0.5327		0.5736	False		,,,				2504	0.4755				p.E739A		Atlas-SNP	.											.	CDH17	119	.	0			c.A2216C						PASS	.	T	ALA/GLU,ALA/GLU	1359,3047	451.4+/-349.7	191,977,1035	121.0	109.0	113.0		2216,2216	0.4	0.0	8	dbSNP_86	113	4801,3799	613.6+/-396.1	1340,2121,839	yes	missense,missense	CDH17	NM_001144663.1,NM_004063.3	107,107	1531,3098,1874	GG,GT,TT		44.1744,30.8443,47.3628	benign,benign	739/833,739/833	95143172	6160,6846	2203	4300	6503	SO:0001583	missense	1015	exon16			ACATACTCCCTCT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.2216A>C	8.37:g.95143172T>G	ENSP00000027335:p.Glu739Ala	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	47	12	0.255319	NM_004063	Q15336|Q2M2E0	Missense_Mutation	SNP	ENST00000027335.3	37	CCDS6260.1	1066	0.4880952380952381	174	0.35365853658536583	141	0.38950276243093923	305	0.5332167832167832	446	0.5883905013192612	T	0.013	-1.614376	0.00835	0.308443	0.558256	ENSG00000079112	ENST00000027335;ENST00000441892;ENST00000450165	T;T;T	0.38560	1.13;1.13;1.13	5.67	0.449	0.16619	Cadherin (1);Cadherin-like (1);	1.430150	0.04648	N	0.406534	T	0.00012	0.0000	L	0.41492	1.28	0.80722	P	0.0	B;B	0.25521	0.128;0.0	B;B	0.29353	0.101;0.001	T	0.44314	-0.9336	9	0.08837	T	0.75	-2.382	3.3153	0.07031	0.5413:0.0:0.1676:0.291	rs1051624;rs3192027;rs17414110;rs17788384;rs52819423;rs57157263;rs1051624	525;739	E7EN24;Q12864	.;CAD17_HUMAN	A	739;525;739	ENSP00000027335:E739A;ENSP00000392811:E525A;ENSP00000401468:E739A	ENSP00000027335:E739A	E	-	2	0	CDH17	95212348	0.021000	0.18746	0.001000	0.08648	0.001000	0.01503	0.256000	0.18351	-0.143000	0.11334	-0.691000	0.03719	GAG	T|0.524;G|0.476	0.476	strong		0.483	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
OR13C5	138799	hgsc.bcm.edu	37	9	107360826	107360826	+	Missense_Mutation	SNP	A	A	G	rs1851725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107360826A>G	ENST00000374779.2	-	1	962	c.869T>C	c.(868-870)aTg>aCg	p.M290T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	290			M -> T (in dbSNP:rs1851725).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AGGATTCATCATGGGAGTCAT	0.373													G|||	2184	0.436102	0.6475	0.2277	5008	,	,		20206	0.5754		0.1789	False		,,,				2504	0.4192				p.M290T		Atlas-SNP	.											.	OR13C5	60	.	0			c.T869C						PASS	.	G	THR/MET	2577,1829	532.5+/-373.5	762,1053,388	112.0	114.0	113.0		869	-0.1	0.0	9	dbSNP_92	113	1669,6931	739.5+/-407.1	183,1303,2814	yes	missense	OR13C5	NM_001004482.1	81	945,2356,3202	GG,GA,AA		19.407,41.5116,32.6465	benign	290/319	107360826	4246,8760	2203	4300	6503	SO:0001583	missense	138799	exon1			TTCATCATGGGAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.869T>C	9.37:g.107360826A>G	ENSP00000363911:p.Met290Thr	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	190	101	0.531579	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	839	0.3841575091575092	297	0.6036585365853658	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	G	9.506	1.104528	0.20632	0.584884	0.19407	ENSG00000255800	ENST00000374779	T	0.37411	1.2	4.03	-0.0854	0.13686	GPCR, rhodopsin-like superfamily (1);	0.153284	0.29660	N	0.011536	T	0.00012	0.0000	M	0.80508	2.5	0.49687	P	1.8499999999999073E-4	B	0.17268	0.021	B	0.20577	0.03	T	0.34675	-0.9819	9	0.45353	T	0.12	.	4.7671	0.13137	0.6686:0.0:0.191:0.1404	rs1851725;rs58161788;rs1851725	290	Q8NGS8	O13C5_HUMAN	T	290	ENSP00000363911:M290T	ENSP00000363911:M290T	M	-	2	0	OR13C5	106400647	0.002000	0.14202	0.005000	0.12908	0.202000	0.24057	1.919000	0.40015	-0.437000	0.07243	-2.339000	0.00246	ATG	A|0.634;G|0.366	0.366	strong		0.373	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
SLC36A2	153201	hgsc.bcm.edu	37	5	150723806	150723806	+	Silent	SNP	G	G	A	rs192192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150723806G>A	ENST00000335244.4	-	2	316	c.187C>T	c.(187-189)Ctg>Ttg	p.L63L	SLC36A2_ENST00000521967.1_Silent_p.L63L	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	63					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	CCTTTCACCAGGTGAATCAAG	0.557													G|||	3131	0.6252	0.3064	0.6369	5008	,	,		21922	0.9841		0.5348	False		,,,				2504	0.771				p.L63L		Atlas-SNP	.											.	SLC36A2	71	.	0			c.C187T						PASS	.	G		1606,2800	496.4+/-363.5	290,1026,887	99.0	83.0	88.0		187	0.2	1.0	5	dbSNP_79	88	4505,4095	590.4+/-392.7	1165,2175,960	no	coding-synonymous	SLC36A2	NM_181776.2		1455,3201,1847	AA,AG,GG		47.6163,36.4503,46.986		63/484	150723806	6111,6895	2203	4300	6503	SO:0001819	synonymous_variant	153201	exon2			TCACCAGGTGAAT	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.187C>T	5.37:g.150723806G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	237	78	0.329114	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Silent	SNP	ENST00000335244.4	37	CCDS4315.1																																																																																			G|0.470;A|0.530	0.530	strong		0.557	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
FAT1	2195	hgsc.bcm.edu	37	4	187538330	187538330	+	Silent	SNP	G	G	A	rs1280099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187538330G>A	ENST00000441802.2	-	11	9113	c.8904C>T	c.(8902-8904)gcC>gcT	p.A2968A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2968	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TAGTTTCAACGGCAAACTGTC	0.348										HNSCC(5;0.00058)			A|||	2084	0.416134	0.5424	0.4683	5008	,	,		17635	0.2808		0.4662	False		,,,				2504	0.2965				p.A2968A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C8904T						PASS	.	A		1961,1693		534,893,400	122.0	110.0	113.0		8904	0.3	0.9	4	dbSNP_87	113	3659,4507		820,2019,1244	no	coding-synonymous	FAT1	NM_005245.3		1354,2912,1644	AA,AG,GG		44.8077,46.3328,47.5465		2968/4589	187538330	5620,6200	1827	4083	5910	SO:0001819	synonymous_variant	2195	exon11			TTCAACGGCAAAC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8904C>T	4.37:g.187538330G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	148	79	0.533784	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.546;A|0.453	0.453	strong		0.348	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
GUCA2A	2980	hgsc.bcm.edu	37	1	42630364	42630364	+	Missense_Mutation	SNP	G	G	A	rs2071499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:42630364G>A	ENST00000357001.2	-	1	25	c.20C>T	c.(19-21)tCc>tTc	p.S7F		NM_033553.2	NP_291031.2	Q02747	GUC2A_HUMAN	guanylate cyclase activator 2A (guanylin)	7			S -> F (in dbSNP:rs2071499). {ECO:0000269|PubMed:1327879, ECO:0000269|PubMed:1409606, ECO:0000269|PubMed:7892222}.			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	guanylate cyclase activator activity (GO:0030250)|hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|pancreas(1)|skin(1)	5	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCACAGTGCGGAGAGCAGGAA	0.657													G|||	1928	0.384984	0.0772	0.572	5008	,	,		17289	0.4028		0.6113	False		,,,				2504	0.4172				p.S7F		Atlas-SNP	.											GUCA2A,trunk,malignant_melanoma,+1,1	GUCA2A	9	1	0			c.C20T						PASS	.	G	PHE/SER	701,3569		82,537,1516	53.0	38.0	43.0		20	2.8	0.1	1	dbSNP_96	43	4969,3361		1532,1905,728	yes	missense	GUCA2A	NM_033553.2	155	1614,2442,2244	AA,AG,GG		40.3481,16.4169,45.0	possibly-damaging	7/116	42630364	5670,6930	2135	4165	6300	SO:0001583	missense	2980	exon1			AGTGCGGAGAGCA	X74322	CCDS465.1	1p35-p34	2014-01-30			ENSG00000197273	ENSG00000197273		"""Endogenous ligands"""	4682	protein-coding gene	gene with protein product	"""prepro-guanylin"""	139392		GUCA2		1327879, 7892222	Standard	NM_033553		Approved	STARA	uc001chd.1	Q02747	OTTHUMG00000007023	ENST00000357001.2:c.20C>T	1.37:g.42630364G>A	ENSP00000349493:p.Ser7Phe	Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	279	279	1	NM_033553		Missense_Mutation	SNP	ENST00000357001.2	37	CCDS465.1	998	0.45695970695970695	46	0.09349593495934959	228	0.6298342541436464	254	0.44405594405594406	470	0.6200527704485488	G	8.260	0.811046	0.16537	0.164169	0.596519	ENSG00000197273	ENST00000357001	T	0.47177	0.85	4.7	2.79	0.32731	.	0.431115	0.22442	N	0.060004	T	0.00012	0.0000	M	0.68317	2.08	0.80722	P	0.0	P	0.44877	0.845	B	0.41813	0.367	T	0.45585	-0.9251	9	0.38643	T	0.18	-15.1715	6.1467	0.20289	0.1047:0.2141:0.6812:0.0	rs2071499;rs17368004;rs52817553;rs58257700;rs2071499	7	Q02747	GUC2A_HUMAN	F	7	ENSP00000349493:S7F	ENSP00000349493:S7F	S	-	2	0	GUCA2A	42402951	0.002000	0.14202	0.058000	0.19502	0.120000	0.20174	0.768000	0.26590	0.680000	0.31366	0.491000	0.48974	TCC	G|0.596;A|0.404	0.404	strong		0.657	GUCA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018306.1	NM_033553	
MUC4	4585	hgsc.bcm.edu	37	3	195509603	195509603	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509603T>C	ENST00000463781.3	-	2	9307	c.8848A>G	c.(8848-8850)Act>Gct	p.T2950A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2950A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGTGTCGGTGACA	0.587																																					p.T2950A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.A8848G						scavenged	.						10.0	8.0	9.0					3																	195509603		642	1496	2138	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8848A>G	3.37:g.195509603T>C	ENSP00000417498:p.Thr2950Ala	Somatic	170	7	0.0411765		WXS	Illumina HiSeq	Phase_I	446	59	0.132287	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	9.324	1.058736	0.19987	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.47;1.45	.	.	.	.	.	.	.	.	T	0.16041	0.0386	N	0.19112	0.55	0.09310	N	1	B	0.22346	0.068	B	0.23018	0.043	T	0.30736	-0.9968	7	.	.	.	.	5.3345	0.15949	0.0:1.0E-4:0.0:0.9999	.	2822	E7ESK3	.	A	2950	ENSP00000417498:T2950A;ENSP00000420243:T2950A	.	T	-	1	0	MUC4	196994382	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.312000	0.08113	0.000000	0.14550	0.000000	0.15137	ACT	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NAT2	10	hgsc.bcm.edu	37	8	18258316	18258316	+	Missense_Mutation	SNP	G	G	A	rs1208	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:18258316G>A	ENST00000286479.3	+	2	910	c.803G>A	c.(802-804)aGa>aAa	p.R268K	NAT2_ENST00000520116.1_Missense_Mutation_p.R138K	NM_000015.2	NP_000006.2	P11245	ARY2_HUMAN	N-acetyltransferase 2 (arylamine N-acetyltransferase)	268			K -> R (in allele NAT2*5B, allele NAT2*5C, allele NAT2*5F, allele NAT2*6C, allele NAT2*12A, allele NAT2*14B, allele NAT2*14C, allele NAT2*14E, allele NAT2*14F and allele NAT2*14G; dbSNP:rs1208). {ECO:0000269|PubMed:16416399, ECO:0000269|PubMed:7915226, ECO:0000269|Ref.10, ECO:0000269|Ref.11, ECO:0000269|Ref.12, ECO:0000269|Ref.14, ECO:0000269|Ref.7, ECO:0000269|Ref.8}.		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	arylamine N-acetyltransferase activity (GO:0004060)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(2)	12				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)	Acetaminophen(DB00316)|Clonazepam(DB01068)|Dapsone(DB00250)|Ezogabine(DB04953)|Isoniazid(DB00951)|Sulfamethoxazole(DB01015)	GAAGTGCTGAGAAATATATTT	0.378									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				A|||	3391	0.677117	0.6051	0.6268	5008	,	,		15994	0.9603		0.5616	False		,,,				2504	0.637				p.R268K		Atlas-SNP	.											.	NAT2	34	.	0			c.G803A	GRCh37	CM910271	NAT2	M	rs1208	PASS	.	A	LYS/ARG	2646,1760		802,1042,359	48.0	53.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	803	1.5	0.0	8	dbSNP_36	51	4951,3647		1421,2109,769	yes	missense	NAT2	NM_000015.2	26	2223,3151,1128	AA,AG,GG		42.4168,39.9455,41.5795	benign	268/291	18258316	7597,5407	2203	4299	6502	SO:0001583	missense	10	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TGCTGAGAAATAT	D90042	CCDS6008.1	8p22	2012-01-18			ENSG00000156006	ENSG00000156006	2.3.1.5		7646	protein-coding gene	gene with protein product		612182		AAC2		7773298	Standard	NM_000015		Approved		uc003wyw.1	P11245	OTTHUMG00000130826	ENST00000286479.3:c.803G>A	8.37:g.18258316G>A	ENSP00000286479:p.Arg268Lys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_000015	O43637|O60654|O60655|Q13146|Q16697|Q2MLE4|Q2MLF5|Q2MLG8|Q2MLJ6|Q2MLK4|Q2MLK6|Q2MLN7|Q6LET4|Q86XS0|Q86XS1|Q96KY8|Q96T64|Q96T65|Q9H220	Missense_Mutation	SNP	ENST00000286479.3	37	CCDS6008.1	1493	0.6836080586080586	295	0.5995934959349594	218	0.6022099447513812	555	0.9702797202797203	425	0.5606860158311345	A	0.001	-2.883121	0.00061	0.600545	0.575832	ENSG00000156006	ENST00000286479;ENST00000520116	T;T	0.01665	4.7;4.7	2.71	1.54	0.23209	.	0.490064	0.19833	N	0.105043	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.30765	-0.9967	8	0.02654	T	1	.	4.6966	0.12806	0.7038:0.0:0.2962:0.0	rs1208;rs3181478;rs17126586;rs17845485;rs17858365;rs52821724;rs56599719;rs58999469;rs1208	268	A4Z6T7	.	K	268;138	ENSP00000286479:R268K;ENSP00000428416:R138K	ENSP00000286479:R268K	R	+	2	0	NAT2	18302596	0.375000	0.25089	0.002000	0.10522	0.037000	0.13140	0.588000	0.23924	0.047000	0.15862	-0.665000	0.03846	AGA	G|0.370;A|0.630	0.630	strong		0.378	NAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253380.1	NM_000015	
SEC23A	10484	hgsc.bcm.edu	37	14	39517925	39517925	+	Silent	SNP	T	T	C	rs11556216	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:39517925T>C	ENST00000307712.6	-	15	2185	c.1668A>G	c.(1666-1668)aaA>aaG	p.K556K	SEC23A_ENST00000537403.1_Silent_p.K354K|SEC23A_ENST00000545328.2_Silent_p.K527K|SEC23A_ENST00000536508.1_Silent_p.K430K	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	556					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		ATTCTCCAAATTTCTGACACT	0.299													T|||	1241	0.247804	0.0673	0.281	5008	,	,		15501	0.3065		0.3509	False		,,,				2504	0.3016				p.K556K		Atlas-SNP	.											.	SEC23A	73	.	0			c.A1668G						PASS	.	T		506,3900	222.3+/-239.2	25,456,1722	55.0	62.0	60.0		1668	1.9	1.0	14	dbSNP_121	60	2946,5654	450.2+/-362.3	535,1876,1889	no	coding-synonymous	SEC23A	NM_006364.2		560,2332,3611	CC,CT,TT		34.2558,11.4843,26.5416		556/766	39517925	3452,9554	2203	4300	6503	SO:0001819	synonymous_variant	10484	exon15			TCCAAATTTCTGA	X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"""Sec23 (S. cerevisiae) homolog A"""			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.1668A>G	14.37:g.39517925T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	22	14	0.636364	NM_006364	B2R5P4|B3KXI2|Q8NE16	Silent	SNP	ENST00000307712.6	37	CCDS9668.1																																																																																			T|0.741;C|0.259	0.259	strong		0.299	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2		
KMT2D	8085	hgsc.bcm.edu	37	12	49439900	49439900	+	Silent	SNP	G	G	A	rs377048725		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49439900G>A	ENST00000301067.7	-	17	4640	c.4641C>T	c.(4639-4641)gcC>gcT	p.A1547A		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1547				EQAA -> DHAP (in Ref. 1; AAC51734/ AAC51735). {ECO:0000305}.	chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										AGCCTTCATCGGCTGCCTGCT	0.577																																					p.A1547A		Atlas-SNP	.											.	MLL2	1173	.	0			c.C4641T						PASS	.	G		1,4203		0,1,2101	39.0	47.0	44.0		4641	-10.7	0.2	12		44	1,8433		0,1,4216	no	coding-synonymous	MLL2	NM_003482.3		0,2,6317	AA,AG,GG		0.0119,0.0238,0.0158		1547/5538	49439900	2,12636	2102	4217	6319	SO:0001819	synonymous_variant	8085	exon17			TTCATCGGCTGCC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.4641C>T	12.37:g.49439900G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	weak		0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
BBS1	582	hgsc.bcm.edu	37	11	66282095	66282095	+	Silent	SNP	G	G	A	rs2298806	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66282095G>A	ENST00000318312.7	+	4	429	c.378G>A	c.(376-378)ctG>ctA	p.L126L	BBS1_ENST00000393994.2_Silent_p.L126L|CTD-3074O7.11_ENST00000419755.3_Silent_p.L163L|BBS1_ENST00000529766.1_3'UTR|BBS1_ENST00000537537.1_Missense_Mutation_p.C30Y|BBS1_ENST00000455748.2_Silent_p.L126L	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	126					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)	p.L126L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						AGTTCAGCCTGCCCCAATTGC	0.498									Bardet-Biedl syndrome				G|||	1060	0.211661	0.1475	0.1614	5008	,	,		20250	0.3036		0.2396	False		,,,				2504	0.2106				p.L126L	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											BBS1,NS,carcinoma,0,1	BBS1	58	1	1	Substitution - coding silent(1)	stomach(1)	c.G378A						PASS	.	G		586,3814	259.8+/-263.3	34,518,1648	103.0	99.0	101.0		378	2.2	1.0	11	dbSNP_100	101	1981,6609	348.1+/-326.9	222,1537,2536	no	coding-synonymous	BBS1	NM_024649.4		256,2055,4184	AA,AG,GG		23.0617,13.3182,19.7614		126/594	66282095	2567,10423	2200	4295	6495	SO:0001819	synonymous_variant	582	exon4	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CAGCCTGCCCCAA	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.378G>A	11.37:g.66282095G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_024649	Q32MM9|Q32MN0|Q96SN4	Silent	SNP	ENST00000318312.7	37	CCDS8142.1	497	0.22756410256410256	60	0.12195121951219512	73	0.20165745856353592	170	0.2972027972027972	194	0.2559366754617414	G	8.328	0.825914	0.16749	0.133182	0.230617	ENSG00000174483	ENST00000537537	D	0.85861	-2.04	5.09	2.16	0.27623	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.42316	P	0.007762000000000047	.	.	.	.	.	.	T	0.05402	-1.0887	5	0.02654	T	1	.	4.6187	0.12438	0.1659:0.0:0.5317:0.3024	rs2298806;rs17471805;rs58436150;rs2298806	.	.	.	Y	30	ENSP00000439873:C30Y	ENSP00000439873:C30Y	C	+	2	0	BBS1	66038671	1.000000	0.71417	0.966000	0.40874	0.938000	0.57974	1.113000	0.31184	0.261000	0.21753	-0.261000	0.10672	TGC	G|0.793;A|0.207	0.207	strong		0.498	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2		
IBSP	3381	hgsc.bcm.edu	37	4	88732918	88732918	+	Missense_Mutation	SNP	A	A	T	rs1054629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88732918A>T	ENST00000226284.5	+	7	877	c.810A>T	c.(808-810)gaA>gaT	p.E270D		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	270			E -> D (in dbSNP:rs1054629). {ECO:0000269|PubMed:8061918, ECO:0000269|PubMed:8406493}.		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		GCGCCAATGAATACGACAATG	0.473													A|||	941	0.187899	0.0083	0.2752	5008	,	,		19969	0.1062		0.329	False		,,,				2504	0.3078				p.E270D		Atlas-SNP	.											.	IBSP	53	.	0			c.A810T						PASS	.	A	ASP/GLU	265,4141	150.3+/-184.3	12,241,1950	68.0	63.0	65.0		810	0.1	0.6	4	dbSNP_86	65	2760,5840	439.4+/-359.2	442,1876,1982	yes	missense	IBSP	NM_004967.3	45	454,2117,3932	TT,TA,AA		32.093,6.0145,23.2585	benign	270/318	88732918	3025,9981	2203	4300	6503	SO:0001583	missense	3381	exon7			CAATGAATACGAC		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"""bone sialoprotein"", ""bone sialoprotein II"""	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.810A>T	4.37:g.88732918A>T	ENSP00000226284:p.Glu270Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_004967		Missense_Mutation	SNP	ENST00000226284.5	37	CCDS3624.1	403	0.18452380952380953	6	0.012195121951219513	96	0.26519337016574585	60	0.1048951048951049	241	0.3179419525065963	A	17.37	3.372643	0.61624	0.060145	0.32093	ENSG00000029559	ENST00000226284	T	0.14266	2.52	5.36	0.073	0.14389	.	0.286130	0.30419	N	0.009678	T	0.00012	0.0000	M	0.77616	2.38	0.44754	P	0.0022489999999999455	B	0.27791	0.189	B	0.35655	0.207	T	0.41858	-0.9485	9	0.09084	T	0.74	.	1.9131	0.03291	0.4035:0.1346:0.331:0.1309	rs1054629;rs17711813;rs1054629	270	P21815	SIAL_HUMAN	D	270	ENSP00000226284:E270D	ENSP00000226284:E270D	E	+	3	2	IBSP	88951942	0.245000	0.23899	0.597000	0.28824	0.898000	0.52572	-0.256000	0.08757	-0.197000	0.10350	0.482000	0.46254	GAA	A|0.771;T|0.229	0.229	strong		0.473	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2		
PCTP	58488	hgsc.bcm.edu	37	17	53828493	53828493	+	Missense_Mutation	SNP	A	A	C	rs12941739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:53828493A>C	ENST00000268896.5	+	1	154	c.29A>C	c.(28-30)gAg>gCg	p.E10A	PCTP_ENST00000573500.1_Missense_Mutation_p.E10A|PCTP_ENST00000325214.6_5'Flank|PCTP_ENST00000576183.1_Missense_Mutation_p.E10A	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	10	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.		E -> A (in dbSNP:rs12941739).		cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			AGCTTCTCGGAGGAGCAGTTC	0.716													A|||	506	0.101038	0.1823	0.0576	5008	,	,		13270	0.0129		0.1103	False		,,,				2504	0.1033				p.E10A		Atlas-SNP	.											.	PCTP	17	.	0			c.A29C						PASS	.	A	,ALA/GLU	370,3370		9,352,1509	4.0	6.0	5.0		,29	4.0	0.3	17	dbSNP_121	5	497,6687		18,461,3113	yes	utr-5,missense	PCTP	NM_001102402.2,NM_021213.3	,107	27,813,4622	CC,CA,AA		6.9182,9.893,7.9367	,benign	,10/215	53828493	867,10057	1870	3592	5462	SO:0001583	missense	58488	exon1			TCTCGGAGGAGCA	AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"""StAR-related lipid transfer (START) domain containing"""	8752	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 2"""	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.29A>C	17.37:g.53828493A>C	ENSP00000268896:p.Glu10Ala	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_021213	Q9BSC9|Q9UIT3|Q9UKW7	Missense_Mutation	SNP	ENST00000268896.5	37	CCDS11588.1	184	0.08424908424908426	85	0.17276422764227642	20	0.055248618784530384	4	0.006993006993006993	75	0.09894459102902374	A	8.931	0.963508	0.18583	0.09893	0.069182	ENSG00000141179	ENST00000268896	T	0.45668	0.89	5.05	3.97	0.46021	Lipid-binding START (2);START-like domain (1);	0.342285	0.31859	N	0.006953	T	0.00109	0.0003	L	0.39020	1.185	0.23082	P	0.99832733	B;B	0.23735	0.09;0.09	B;B	0.24541	0.054;0.054	T	0.07195	-1.0785	9	0.38643	T	0.18	-4.2269	9.9948	0.41893	0.9139:0.0:0.0861:0.0	rs12941739;rs12941739	10;10	Q549N3;Q9UKL6	.;PPCT_HUMAN	A	10	ENSP00000268896:E10A	ENSP00000268896:E10A	E	+	2	0	PCTP	51183492	0.879000	0.30193	0.289000	0.24876	0.382000	0.30200	1.289000	0.33307	0.469000	0.27268	-1.162000	0.01777	GAG	A|0.914;C|0.086	0.086	strong		0.716	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2	NM_021213	
ELL2	22936	hgsc.bcm.edu	37	5	95234091	95234091	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:95234091T>C	ENST00000237853.4	-	8	1727	c.1378A>G	c.(1378-1380)Aaa>Gaa	p.K460E	ELL2_ENST00000431061.2_Missense_Mutation_p.K210E	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	460					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		TTGGACTTTTTGTGAGACATT	0.378																																					p.K460E		Atlas-SNP	.											.	ELL2	63	.	0			c.A1378G						PASS	.						130.0	134.0	132.0					5																	95234091		2203	4300	6503	SO:0001583	missense	22936	exon8			ACTTTTTGTGAGA	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1378A>G	5.37:g.95234091T>C	ENSP00000237853:p.Lys460Glu	Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	330	165	0.5	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	37	CCDS4080.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381477	0.61845	.	.	ENSG00000118985	ENST00000237853;ENST00000431061	T;T	0.30981	1.83;1.51	5.5	5.5	0.81552	.	0.235233	0.50627	N	0.000120	T	0.43299	0.1241	M	0.64997	1.995	0.58432	D	0.999996	D	0.60575	0.988	P	0.52343	0.696	T	0.26052	-1.0114	10	0.32370	T	0.25	2.215	15.2489	0.73529	0.0:0.0:0.0:1.0	.	460	O00472	ELL2_HUMAN	E	460;210	ENSP00000237853:K460E;ENSP00000399704:K210E	ENSP00000237853:K460E	K	-	1	0	ELL2	95259847	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.564000	0.53791	2.073000	0.62155	0.482000	0.46254	AAA	.	.	none		0.378	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
MIB2	142678	hgsc.bcm.edu	37	1	1551927	1551927	+	Missense_Mutation	SNP	T	T	C	rs7418389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1551927T>C	ENST00000357210.4	+	2	259	c.43T>C	c.(43-45)Ttc>Ctc	p.F15L	MIB2_ENST00000504599.1_5'UTR|MIB2_ENST00000355826.5_Missense_Mutation_p.F72L|MIB2_ENST00000360522.4_Missense_Mutation_p.F15L|MIB2_ENST00000378712.1_5'UTR|RP11-345P4.9_ENST00000607222.1_RNA|MIB2_ENST00000520777.1_Missense_Mutation_p.F72L|MIB2_ENST00000518681.1_Missense_Mutation_p.F72L|MIB2_ENST00000378708.1_5'Flank|MIB2_ENST00000378710.3_Missense_Mutation_p.F15L|MIB2_ENST00000505820.2_Missense_Mutation_p.F72L	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	15			F -> L (in dbSNP:rs7418389). {ECO:0000269|PubMed:12761501, ECO:0000269|PubMed:14702039}.		Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GTCCCAAAGTTTCCAGGCATC	0.662													C|||	2389	0.477037	0.5378	0.4813	5008	,	,		12794	0.2054		0.7058	False		,,,				2504	0.4366				p.F72L		Atlas-SNP	.											.	MIB2	62	.	0			c.T214C						PASS	.	C	LEU/PHE,LEU/PHE,LEU/PHE,,LEU/PHE	2126,1670		610,906,382	21.0	26.0	24.0		214,214,214,,214	0.4	0.1	1	dbSNP_116	24	5960,2296		2173,1614,341	yes	missense,missense,missense,utr-5,missense	MIB2	NM_001170686.1,NM_001170687.1,NM_001170688.1,NM_001170689.1,NM_080875.2	22,22,22,,22	2783,2520,723	CC,CT,TT		27.8101,43.9937,32.9074	benign,benign,benign,,benign	72/1067,72/1057,72/1006,,72/1071	1551927	8086,3966	1898	4128	6026	SO:0001583	missense	142678	exon2			CAAAGTTTCCAGG	AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	30577	protein-coding gene	gene with protein product		611141	"""zinc finger, ZZ type with ankyrin repeat domain 1"", ""mindbomb homolog 2 (Drosophila)"""	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.43T>C	1.37:g.1551927T>C	ENSP00000349741:p.Phe15Leu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_001170687	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	Missense_Mutation	SNP	ENST00000357210.4	37		1112	0.5091575091575091	265	0.5386178861788617	206	0.569060773480663	106	0.1853146853146853	535	0.7058047493403694	C	1.975	-0.435458	0.04669	0.560063	0.721899	ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000355826;ENST00000518681;ENST00000505820	T;T;T;T;T;T;T	0.37752	1.41;1.45;1.44;1.44;1.18;1.4;1.41	2.73	0.364	0.16124	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.44651	-0.9314	8	0.02654	T	1	.	1.1038	0.01690	0.2284:0.4002:0.2244:0.147	rs7418389	72;72;15;15	E9PHQ1;E9PGU1;Q96AX9-2;Q96AX9	.;.;.;MIB2_HUMAN	L	72;15;15;15;72;72;72	ENSP00000428660:F72L;ENSP00000349741:F15L;ENSP00000353713:F15L;ENSP00000367982:F15L;ENSP00000348081:F72L;ENSP00000428264:F72L;ENSP00000426103:F72L	ENSP00000348081:F72L	F	+	1	0	MIB2	1541790	0.002000	0.14202	0.120000	0.21714	0.176000	0.22953	0.221000	0.17680	0.044000	0.15775	-0.674000	0.03794	TTC	T|0.464;C|0.536	0.536	strong		0.662	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875	
PARP4	143	hgsc.bcm.edu	37	13	25060313	25060313	+	Silent	SNP	A	A	G	rs73154350	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25060313A>G	ENST00000381989.3	-	11	1450	c.1345T>C	c.(1345-1347)Ttg>Ctg	p.L449L		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	449	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TACCGACACAAGATTCCCACG	0.373													.|||	194	0.038738	0.0083	0.0591	5008	,	,		17531	0.002		0.0934	False		,,,				2504	0.047				p.L449L		Atlas-SNP	.											.	PARP4	142	.	0			c.T1345C						PASS	.	A		115,4291	87.3+/-125.9	4,107,2092	97.0	85.0	89.0		1345	2.6	1.0	13	dbSNP_131	89	978,7622	212.1+/-252.5	65,848,3387	no	coding-synonymous	PARP4	NM_006437.3		69,955,5479	GG,GA,AA		11.3721,2.6101,8.4038		449/1725	25060313	1093,11913	2203	4300	6503	SO:0001819	synonymous_variant	143	exon11			GACACAAGATTCC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1345T>C	13.37:g.25060313A>G		Somatic	568	0	0		WXS	Illumina HiSeq	Phase_I	463	283	0.611231	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			A|0.924;G|0.076	0.076	strong		0.373	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
KPNA3	3839	hgsc.bcm.edu	37	13	50283819	50283819	+	Silent	SNP	T	T	C	rs17073322	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:50283819T>C	ENST00000261667.3	-	12	1335	c.921A>G	c.(919-921)gcA>gcG	p.A307A		NM_002267.3	NP_002258.2	O00505	IMA4_HUMAN	karyopherin alpha 3 (importin alpha 4)	307	NLS binding site (minor). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)|protein complex assembly (GO:0006461)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(4)	21		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		TGTTGCCAACTGCTCTGAGGG	0.398													T|||	930	0.185703	0.0567	0.1484	5008	,	,		14829	0.5982		0.0268	False		,,,				2504	0.1247				p.A307A		Atlas-SNP	.											.	KPNA3	53	.	0			c.A921G						PASS	.	T		289,4117	160.3+/-192.7	9,271,1923	126.0	115.0	119.0		921	-2.3	1.0	13	dbSNP_123	119	255,8345	100.1+/-161.6	5,245,4050	no	coding-synonymous	KPNA3	NM_002267.3		14,516,5973	CC,CT,TT		2.9651,6.5592,4.1827		307/522	50283819	544,12462	2203	4300	6503	SO:0001819	synonymous_variant	3839	exon12			GCCAACTGCTCTG	D89618	CCDS9421.1	13q14.3	2013-02-14			ENSG00000102753	ENSG00000102753		"""Importins"", ""Armadillo repeat containing"""	6396	protein-coding gene	gene with protein product		601892				9154134, 9435235	Standard	NM_002267		Approved	SRP1gamma, SRP4, hSRP1, IPOA4	uc001vdj.2	O00505	OTTHUMG00000016922	ENST00000261667.3:c.921A>G	13.37:g.50283819T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_002267	O00191|O43195|Q5JVM9|Q96AA7	Silent	SNP	ENST00000261667.3	37	CCDS9421.1																																																																																			T|0.881;C|0.119	0.119	strong		0.398	KPNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044939.2	NM_002267	
VWF	7450	hgsc.bcm.edu	37	12	6138595	6138595	+	Silent	SNP	C	C	T	rs1800380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6138595C>T	ENST00000261405.5	-	22	3134	c.2880G>A	c.(2878-2880)cgG>cgA	p.R960R		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	960	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GAATGATGTACCGGCCAGACT	0.557													C|||	897	0.179113	0.3079	0.1902	5008	,	,		20208	0.004		0.2555	False		,,,				2504	0.0992				p.R960R		Atlas-SNP	.											.	VWF	338	.	0			c.G2880A						PASS	.	C		1373,3033	456.9+/-351.5	210,953,1040	131.0	116.0	121.0		2880	-5.1	0.1	12	dbSNP_89	121	2162,6438	370.9+/-336.0	264,1634,2402	no	coding-synonymous	VWF	NM_000552.3		474,2587,3442	TT,TC,CC		25.1395,31.1621,27.1798		960/2814	6138595	3535,9471	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon22			GATGTACCGGCCA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2880G>A	12.37:g.6138595C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			C|0.766;T|0.234	0.234	strong		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
HNF1A	6927	hgsc.bcm.edu	37	12	121432117	121432117	+	Silent	SNP	G	G	C	rs56348580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121432117G>C	ENST00000257555.6	+	4	1090	c.864G>C	c.(862-864)ggG>ggC	p.G288G	HNF1A_ENST00000543427.1_Silent_p.G171G|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000541395.1_Silent_p.G288G|HNF1A_ENST00000400024.2_Silent_p.G288G|HNF1A_ENST00000402929.1_Silent_p.G288G|HNF1A_ENST00000544413.1_Silent_p.G288G			P20823	HNF1A_HUMAN	HNF1 homeobox A	288					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGTACAGCGGGCCCCCCCCAG	0.667									Hepatic Adenoma, Familial Clustering of				g|||	907	0.18111	0.1778	0.415	5008	,	,		17094	0.005		0.3032	False		,,,				2504	0.0757				p.G288G		Atlas-SNP	.											HNF1A,brain,glioma,0,1	HNF1A	302	1	0			c.G864C	GRCh37	CI064741|CM067044	HNF1A	I|M	rs56348580	PASS	.	G		802,3604		95,612,1496	24.0	24.0	24.0		864	2.3	1.0	12	dbSNP_129	24	2264,6334		374,1516,2409	no	coding-synonymous	HNF1A	NM_000545.5		469,2128,3905	CC,CG,GG		26.3317,18.2025,23.5774		288/632	121432117	3066,9938	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon4	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CAGCGGGCCCCCC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.864G>C	12.37:g.121432117G>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.754;C|0.246	0.246	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
FAM209A	200232	hgsc.bcm.edu	37	20	55100056	55100056	+	Silent	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55100056T>G	ENST00000371328.3	+	1	515	c.192T>G	c.(190-192)ctT>ctG	p.L64L	FAM209A_ENST00000481560.1_3'UTR|GCNT7_ENST00000243913.4_Intron	NM_001012971.3	NP_001012989.2	Q5JX71	F209A_HUMAN	family with sequence similarity 209, member A	64						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TCTGGCTTCTTTTTGTTGTTG	0.463																																					p.L64L		Atlas-SNP	.											C20orf106,caecum,carcinoma,+2,1	.	.	1	0			c.T192G						PASS	.						153.0	140.0	145.0					20																	55100056		2203	4300	6503	SO:0001819	synonymous_variant	200232	exon1			GCTTCTTTTTGTT	AL109806	CCDS33493.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000124103	ENSG00000124103			16100	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 106"""	C20orf106			Standard	NM_001012971		Approved	dJ1153D9.3		Q5JX71	OTTHUMG00000032799	ENST00000371328.3:c.192T>G	20.37:g.55100056T>G		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	293	25	0.0853242	NM_001012971	Q05C43	Silent	SNP	ENST00000371328.3	37	CCDS33493.1																																																																																			.	.	none		0.463	FAM209A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079815.2		
NUB1	51667	hgsc.bcm.edu	37	7	151074296	151074296	+	Silent	SNP	A	A	G	rs2159158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151074296A>G	ENST00000355851.4	+	15	1910	c.1833A>G	c.(1831-1833)gcA>gcG	p.A611A	NUB1_ENST00000568733.1_Silent_p.A635A|NUB1_ENST00000566856.1_Silent_p.A597A|NUB1_ENST00000413040.2_Silent_p.A621A|WDR86_ENST00000463000.1_Intron	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	611					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GGAAGTCAGCAACAAAGAAAA	0.333													A|||	1667	0.332867	0.1233	0.4035	5008	,	,		20987	0.4603		0.5249	False		,,,				2504	0.2372				p.A635A		Atlas-SNP	.											.	NUB1	31	.	0			c.A1905G						PASS	.	A		639,3053		58,523,1265	29.0	27.0	28.0		1791	1.1	0.1	7	dbSNP_96	28	4187,3983		1062,2063,960	no	coding-synonymous	NUB1	NM_016118.4		1120,2586,2225	GG,GA,AA		48.7515,17.3077,40.6845		597/602	151074296	4826,7036	1846	4085	5931	SO:0001819	synonymous_variant	51667	exon15			GTCAGCAACAAAG	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.1833A>G	7.37:g.151074296A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_001243351	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37		932	0.4267399267399267	75	0.1524390243902439	164	0.4530386740331492	294	0.513986013986014	399	0.5263852242744064	A	0.352	-0.944139	0.02322	0.173077	0.512485	ENSG00000013374	ENST00000460712	.	.	.	5.11	1.06	0.20224	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.8000000000048004E-5	.	.	.	.	.	.	T	0.48811	-0.9002	3	.	.	.	-18.3438	7.6126	0.28139	0.3371:0.5744:0.0885:0.0	rs2159158;rs3207510;rs10369514;rs11550340;rs2159158	.	.	.	R	198	.	.	Q	+	2	0	NUB1	150705229	0.005000	0.15991	0.118000	0.21660	0.142000	0.21351	0.018000	0.13422	0.019000	0.15079	0.482000	0.46254	CAA	A|0.597;G|0.403	0.403	strong		0.333	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
TAF4B	6875	hgsc.bcm.edu	37	18	23866349	23866349	+	Silent	SNP	G	G	A	rs3744961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:23866349G>A	ENST00000269142.5	+	7	2474	c.1476G>A	c.(1474-1476)ggG>ggA	p.G492G	TAF4B_ENST00000400466.2_Silent_p.G492G|TAF4B_ENST00000578121.1_Silent_p.G492G	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	492				SAGTTSD -> FCWDHIC (in Ref. 2; CAA70499). {ECO:0000305}.	gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CTTCTGCTGGGACCACATCTG	0.493													G|||	589	0.117612	0.1528	0.121	5008	,	,		17159	0.1121		0.1083	False		,,,				2504	0.0828				p.G492G		Atlas-SNP	.											.	TAF4B	71	.	0			c.G1476A						PASS	.	G		564,3156		36,492,1332	88.0	82.0	84.0		1476	0.8	1.0	18	dbSNP_107	84	883,7347		49,785,3281	no	coding-synonymous	TAF4B	NM_005640.1		85,1277,4613	AA,AG,GG		10.729,15.1613,12.1088		492/863	23866349	1447,10503	1860	4115	5975	SO:0001819	synonymous_variant	6875	exon7			TGCTGGGACCACA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1476G>A	18.37:g.23866349G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	CCDS42421.1	265	0.12133699633699634	73	0.1483739837398374	46	0.1270718232044199	57	0.09965034965034965	89	0.11741424802110818	G	5.134	0.210342	0.09757	0.151613	0.10729	ENSG00000141384	ENST00000418698	.	.	.	5.28	0.775	0.18527	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999698558	.	.	.	.	.	.	T	0.25257	-1.0137	4	0.17369	T	0.5	6.4391	2.3266	0.04224	0.1916:0.1519:0.5012:0.1553	rs3744961;rs52827702;rs56906477;rs3744961	.	.	.	N	492	.	ENSP00000389365:D492N	D	+	1	0	TAF4B	22120347	0.990000	0.36364	1.000000	0.80357	0.624000	0.37722	0.500000	0.22562	0.220000	0.20860	-0.319000	0.08680	GAC	G|0.879;A|0.121	0.121	strong		0.493	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
ALPK3	57538	hgsc.bcm.edu	37	15	85383145	85383145	+	Missense_Mutation	SNP	C	C	G	rs3803403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85383145C>G	ENST00000258888.5	+	5	1408	c.1241C>G	c.(1240-1242)aCt>aGt	p.T414S		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	414			T -> S (in dbSNP:rs3803403). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GAGGTCGACACTCTGCGCAAG	0.677													C|||	683	0.136382	0.0159	0.1628	5008	,	,		16453	0.1329		0.2575	False		,,,				2504	0.1595				p.T414S		Atlas-SNP	.											.	ALPK3	289	.	0			c.C1241G						PASS	.	C	SER/THR	247,4159	141.1+/-176.5	10,227,1966	38.0	40.0	40.0		1241	3.0	0.0	15	dbSNP_107	40	2334,6264	387.5+/-342.2	314,1706,2279	yes	missense	ALPK3	NM_020778.4	58	324,1933,4245	GG,GC,CC		27.1458,5.606,19.8477	benign	414/1908	85383145	2581,10423	2203	4299	6502	SO:0001583	missense	57538	exon5			TCGACACTCTGCG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.1241C>G	15.37:g.85383145C>G	ENSP00000258888:p.Thr414Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	359	0.16437728937728938	7	0.014227642276422764	72	0.19889502762430938	81	0.14160839160839161	199	0.262532981530343	C	2.744	-0.261585	0.05791	0.05606	0.271458	ENSG00000136383	ENST00000258888	T	0.59502	0.26	4.95	2.95	0.34219	.	0.880280	0.09710	N	0.765881	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.26318	0.146	B	0.24974	0.057	T	0.21042	-1.0257	9	0.22109	T	0.4	-2.83	4.2817	0.10836	0.1755:0.6128:0.0:0.2117	rs3803403;rs60827617;rs3803403	414	Q96L96	ALPK3_HUMAN	S	414	ENSP00000258888:T414S	ENSP00000258888:T414S	T	+	2	0	ALPK3	83184149	0.001000	0.12720	0.003000	0.11579	0.126000	0.20510	0.517000	0.22832	0.981000	0.38548	0.563000	0.77884	ACT	C|0.808;G|0.192	0.192	strong		0.677	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
ARSD	414	hgsc.bcm.edu	37	X	2836181	2836181	+	Missense_Mutation	SNP	A	A	T	rs73632975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836181A>T	ENST00000381154.1	-	5	602	c.527T>A	c.(526-528)aTg>aAg	p.M176K	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	176					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGTGAAGGGCATGCCGTAGAA	0.602																																					p.M176K		Atlas-SNP	.											.	ARSD	47	.	0			c.T527A						PASS	.						36.0	23.0	27.0					X																	2836181		2202	4298	6500	SO:0001583	missense	414	exon5			AAGGGCATGCCGT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.527T>A	X.37:g.2836181A>T	ENSP00000370546:p.Met176Lys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	158	69	0.436709	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	143	0.0861965039180229	34	0.07727272727272727	32	0.09302325581395349	35	0.06433823529411764	60	0.0821917808219178	a	16.17	3.048099	0.55110	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.93763	-3.28	3.47	3.47	0.39725	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.071270	0.64402	U	0.000010	T	0.52125	0.1715	M	0.90252	3.1	0.23186	P	0.99815953	B;B	0.31227	0.314;0.097	B;B	0.37387	0.248;0.114	T	0.80901	-0.1175	9	0.62326	D	0.03	.	11.4758	0.50297	1.0:0.0:0.0:0.0	.	176;176	E9PAW5;P51689	.;ARSD_HUMAN	K	176	ENSP00000370546:M176K	ENSP00000217890:M176K	M	-	2	0	ARSD	2846181	1.000000	0.71417	0.287000	0.24848	0.868000	0.49771	5.800000	0.69108	1.132000	0.42129	0.343000	0.21770	ATG	A|0.913;T|0.087	0.087	strong		0.602	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
OR2W3	343171	hgsc.bcm.edu	37	1	248059456	248059456	+	Missense_Mutation	SNP	G	G	A	rs12135078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248059456G>A	ENST00000360358.3	+	1	568	c.568G>A	c.(568-570)Gtc>Atc	p.V190I	OR2W3_ENST00000537741.1_Missense_Mutation_p.V190I	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	190			V -> I (in dbSNP:rs12135078).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GATGGCCTGCGTCAGCACTGT	0.607													G|||	1821	0.363618	0.0545	0.3357	5008	,	,		20126	0.5327		0.5507	False		,,,				2504	0.4346				p.V190I		Atlas-SNP	.											OR2W3,brain,glioma,0,1	OR2W3	113	1	0			c.G568A						PASS	.	G	ILE/VAL	597,3809	262.8+/-265.1	47,503,1653	138.0	117.0	124.0		568	0.0	0.1	1	dbSNP_120	124	4605,3995	599.8+/-394.1	1230,2145,925	yes	missense	OR2W3	NM_001001957.2	29	1277,2648,2578	AA,AG,GG		46.4535,13.5497,39.9969	benign	190/315	248059456	5202,7804	2203	4300	6503	SO:0001583	missense	343171	exon1			GCCTGCGTCAGCA	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.568G>A	1.37:g.248059456G>A	ENSP00000353516:p.Val190Ile	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	289	152	0.525952	NM_001001957	Q6IF06|Q8NG86	Missense_Mutation	SNP	ENST00000360358.3	37	CCDS31099.1	824	0.3772893772893773	32	0.06504065040650407	125	0.3453038674033149	271	0.4737762237762238	396	0.5224274406332454	G	7.848	0.723453	0.15439	0.135497	0.535465	ENSG00000238243	ENST00000537741;ENST00000360358	T;T	0.00076	8.76;8.76	5.28	0.041	0.14211	GPCR, rhodopsin-like superfamily (1);	0.481200	0.19196	N	0.120313	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	B	0.26258	0.145	B	0.29598	0.104	T	0.29701	-1.0003	9	0.51188	T	0.08	.	4.0481	0.09783	0.3336:0.0:0.3833:0.283	rs12135078;rs12135078	190	Q7Z3T1	OR2W3_HUMAN	I	190	ENSP00000445853:V190I;ENSP00000353516:V190I	ENSP00000353516:V190I	V	+	1	0	OR2W3	246126079	0.000000	0.05858	0.129000	0.21949	0.013000	0.08279	-1.678000	0.01942	0.382000	0.24878	-0.199000	0.12753	GTC	G|0.601;A|0.399	0.399	strong		0.607	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
FZD9	8326	hgsc.bcm.edu	37	7	72848499	72848499	+	Silent	SNP	G	G	C	rs61749861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:72848499G>C	ENST00000344575.3	+	1	391	c.162G>C	c.(160-162)ctG>ctC	p.L54L		NM_003508.2	NP_003499.1	O00144	FZD9_HUMAN	frizzled class receptor 9	54	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				B cell differentiation (GO:0030183)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuroblast proliferation (GO:0007405)|vasculature development (GO:0001944)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	14		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCTACAACCTGACCCGCATGC	0.731													G|||	89	0.0177716	0.0015	0.0216	5008	,	,		7311	0.0		0.0646	False		,,,				2504	0.0072				p.L54L	Pancreas(144;909 1878 36867 38226 39554)	Atlas-SNP	.											.	FZD9	51	.	0			c.G162C						PASS	.	G		51,4239		0,51,2094	12.0	11.0	11.0		162	2.6	1.0	7	dbSNP_129	11	401,8025		7,387,3819	no	coding-synonymous	FZD9	NM_003508.2		7,438,5913	CC,CG,GG		4.7591,1.1888,3.5546		54/592	72848499	452,12264	2145	4213	6358	SO:0001819	synonymous_variant	8326	exon1			CAACCTGACCCGC	U82169	CCDS5548.1	7q11.23	2014-01-29	2014-01-29		ENSG00000188763	ENSG00000188763		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4047	protein-coding gene	gene with protein product		601766	"""frizzled (Drosophila) homolog 9"", ""frizzled homolog 9 (Drosophila)"", ""frizzled 9, seven transmembrane spanning receptor"", ""frizzled family receptor 9"""			9147651, 10198163	Standard	NM_003508		Approved	FZD3, CD349	uc003tyb.3	O00144	OTTHUMG00000023051	ENST00000344575.3:c.162G>C	7.37:g.72848499G>C		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_003508		Silent	SNP	ENST00000344575.3	37	CCDS5548.1																																																																																			G|0.970;C|0.030	0.030	strong		0.731	FZD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252120.1		
CR1	1378	hgsc.bcm.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207787831G>T	ENST00000367049.4	+	40	6658	c.6658G>T	c.(6658-6660)Gaa>Taa	p.E2220*	CR1_ENST00000367051.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000400960.2_Nonsense_Mutation_p.E1770*|CR1_ENST00000367052.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000367053.1_Nonsense_Mutation_p.E1770*	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1770					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.E2220*(6)|p.E1775*(6)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TCCAGTGTGTGAACGTGAGTA	0.408																																					p.E2220X		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,0,12	CR1	354	12	12	Substitution - Nonsense(12)	kidney(8)|endometrium(4)	c.G6658T						scavenged	.						131.0	122.0	125.0					1																	207787831		1887	4127	6014	SO:0001587	stop_gained	1378	exon40			GTGTGTGAACGTG	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6658G>T	1.37:g.207787831G>T	ENSP00000356016:p.Glu2220*	Somatic	319	1	0.0031348		WXS	Illumina HiSeq	Phase_I	298	4	0.0134228	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Nonsense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	G	45	12.061806	0.99632	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	12.9543	0.58418	0.0:0.0:1.0:0.0	.	.	.	.	X	1770;1770;1770;1770;2220	.	ENSP00000356016:E2220X	E	+	1	0	CR1	205854454	1.000000	0.71417	0.999000	0.59377	0.893000	0.52053	2.536000	0.45693	2.316000	0.78162	0.436000	0.28706	GAA	.	.	none		0.408	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
NACAD	23148	hgsc.bcm.edu	37	7	45120248	45120248	+	Silent	SNP	G	G	A	rs1132130	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45120248G>A	ENST00000490531.2	-	7	4684	c.4665C>T	c.(4663-4665)aaC>aaT	p.N1555N		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1555					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						CCATGATGGCGTTGACGATGT	0.622													G|||	539	0.107628	0.0166	0.1657	5008	,	,		20196	0.1081		0.173	False		,,,				2504	0.1217				p.N1555N		Atlas-SNP	.											.	NACAD	44	.	0			c.C4665T						PASS	.	G		49,1335		0,49,643	191.0	195.0	194.0		4665	-4.9	1.0	7	dbSNP_86	194	595,2587		48,499,1044	no	coding-synonymous	NACAD	NM_001146334.1		48,548,1687	AA,AG,GG		18.6989,3.5405,14.1042		1555/1563	45120248	644,3922	692	1591	2283	SO:0001819	synonymous_variant	23148	exon7			GATGGCGTTGACG	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.4665C>T	7.37:g.45120248G>A		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	253	127	0.501976	NM_001146334		Silent	SNP	ENST00000490531.2	37	CCDS47582.1																																																																																			G|0.875;C|0.000;A|0.124	0.124	strong		0.622	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
KIAA1614	57710	hgsc.bcm.edu	37	1	180905448	180905448	+	Missense_Mutation	SNP	G	G	T	rs3795504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180905448G>T	ENST00000367588.4	+	5	2458	c.2403G>T	c.(2401-2403)ttG>ttT	p.L801F	KIAA1614_ENST00000367587.1_Missense_Mutation_p.L422F	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	801			L -> F (in dbSNP:rs3795504). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039}.							NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CAGCTTCCTTGTGTCCTGAAG	0.612													T|||	2021	0.403554	0.3548	0.428	5008	,	,		19313	0.2748		0.4533	False		,,,				2504	0.5337				p.L801F		Atlas-SNP	.											.	KIAA1614	75	.	0			c.G2403T						PASS	.	T	PHE/LEU	1469,2525		285,899,813	67.0	71.0	69.0		2403	2.4	0.0	1	dbSNP_107	69	3670,4648		807,2056,1296	yes	missense	KIAA1614	NM_020950.1	22	1092,2955,2109	TT,TG,GG		44.1212,36.7802,41.7398	benign	801/1191	180905448	5139,7173	1997	4159	6156	SO:0001583	missense	57710	exon5			TTCCTTGTGTCCT	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2403G>T	1.37:g.180905448G>T	ENSP00000356560:p.Leu801Phe	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	132	58	0.439394	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	842	0.38553113553113555	181	0.3678861788617886	175	0.48342541436464087	146	0.25524475524475526	340	0.44854881266490765	T	2.589	-0.295649	0.05532	0.367802	0.441212	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.42513	0.97;0.97	4.3	2.38	0.29361	.	0.948451	0.08769	N	0.896507	T	0.00012	0.0000	N	0.11560	0.145	0.20821	P	0.999844	B	0.02656	0.0	B	0.04013	0.001	T	0.48468	-0.9033	9	0.14252	T	0.57	-0.1445	4.419	0.11470	0.0:0.5393:0.1748:0.2859	rs3795504;rs17302221;rs59561360;rs3795504	801	Q5VZ46	K1614_HUMAN	F	801;422	ENSP00000356560:L801F;ENSP00000356559:L422F	ENSP00000356559:L422F	L	+	3	2	KIAA1614	179172071	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.066000	0.14489	0.277000	0.22141	-1.202000	0.01658	TTG	G|0.614;T|0.386	0.386	strong		0.612	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
ZDHHC24	254359	hgsc.bcm.edu	37	11	66313203	66313203	+	Missense_Mutation	SNP	T	T	C	rs2305534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66313203T>C	ENST00000310442.3	-	1	506	c.272A>G	c.(271-273)cAg>cGg	p.Q91R	ACTN3_ENST00000502692.1_RNA|ZDHHC24_ENST00000526986.1_Missense_Mutation_p.Q91R|ZDHHC24_ENST00000525925.1_5'UTR|ACTN3_ENST00000513398.1_RNA	NM_207340.1	NP_997223.1	Q6UX98	ZDH24_HUMAN	zinc finger, DHHC-type containing 24	91						integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|ovary(1)|prostate(1)|skin(1)	7						CGCCCAGCCCTGGCCCAGACC	0.687													T|||	1141	0.227835	0.1891	0.17	5008	,	,		12955	0.3165		0.2416	False		,,,				2504	0.2157				p.Q91R		Atlas-SNP	.											.	ZDHHC24	13	.	0			c.A272G						PASS	.	T	ARG/GLN	469,3061		23,423,1319	4.0	6.0	5.0		272	2.6	1.0	11	dbSNP_100	5	1334,5990		118,1098,2446	no	missense	ZDHHC24	NM_207340.1	43	141,1521,3765	CC,CT,TT		18.2141,13.2861,16.6114	benign	91/285	66313203	1803,9051	1765	3662	5427	SO:0001583	missense	254359	exon1			CAGCCCTGGCCCA	BC005015	CCDS8143.1	11q13.2	2008-05-02				ENSG00000174165		"""Zinc fingers, DHHC-type"""	27387	protein-coding gene	gene with protein product							Standard	NM_207340		Approved		uc001oin.1	Q6UX98		ENST00000310442.3:c.272A>G	11.37:g.66313203T>C	ENSP00000309429:p.Gln91Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	42	10	0.238095	NM_207340	Q6PEW7|Q9BSJ0	Missense_Mutation	SNP	ENST00000310442.3	37	CCDS8143.1	540	0.24725274725274726	88	0.17886178861788618	77	0.212707182320442	176	0.3076923076923077	199	0.262532981530343	T	15.80	2.941012	0.53079	0.132861	0.182141	ENSG00000174165	ENST00000526986;ENST00000310442	T;T	0.59364	0.27;0.92	4.94	2.62	0.31277	.	0.132078	0.51477	N	0.000085	T	0.00012	0.0000	N	0.16478	0.41	0.23838	P	0.99670126	B;P	0.37914	0.129;0.611	B;B	0.43623	0.103;0.425	T	0.22034	-1.0228	9	0.11182	T	0.66	-16.1725	5.8623	0.18754	0.0:0.2092:0.0:0.7908	rs2305534;rs11552042	91;91	E9PLR9;Q6UX98	.;ZDH24_HUMAN	R	91	ENSP00000431321:Q91R;ENSP00000309429:Q91R	ENSP00000309429:Q91R	Q	-	2	0	ZDHHC24	66069779	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.694000	0.37752	0.850000	0.35239	0.379000	0.24179	CAG	T|0.753;C|0.247	0.247	strong		0.687	ZDHHC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393089.1	NM_207340	
ATXN1	6310	hgsc.bcm.edu	37	6	16327903	16327903	+	Missense_Mutation	SNP	C	C	A	rs3817753		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:16327903C>A	ENST00000244769.4	-	8	1575	c.639G>T	c.(637-639)caG>caT	p.Q213H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q213H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	213	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgctgctgatgct	0.667																																					p.Q213H		Atlas-SNP	.											ATXN1,rectum,carcinoma,0,1	ATXN1	117	1	0			c.G639T						PASS	.						5.0	8.0	7.0					6																	16327903		1624	3504	5128	SO:0001583	missense	6310	exon7			CTGCTGCTGCTGA	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.639G>T	6.37:g.16327903C>A	ENSP00000244769:p.Gln213His	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	109	10	0.0917431	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	221	0.10119047619047619	38	0.07723577235772358	47	0.1298342541436464	89	0.1555944055944056	47	0.06200527704485488	C	4.787	0.146322	0.09134	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.62941	-0.01;-0.01	.	.	.	.	.	.	.	.	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.19582	-1.0301	5	0.45353	T	0.12	.	.	.	.	rs3817753	213	P54253	ATX1_HUMAN	H	213	ENSP00000244769:Q213H;ENSP00000416360:Q213H	ENSP00000244769:Q213H	Q	-	3	2	ATXN1	16435882	0.034000	0.19679	0.018000	0.16275	0.072000	0.16883	0.306000	0.19279	0.000000	0.14550	0.000000	0.15137	CAG	C|0.899;A|0.101	0.101	strong		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
INTS2	57508	hgsc.bcm.edu	37	17	59969000	59969000	+	Silent	SNP	T	T	C	rs753765	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59969000T>C	ENST00000444766.3	-	14	1848	c.1773A>G	c.(1771-1773)caA>caG	p.Q591Q	INTS2_ENST00000251334.6_Silent_p.Q583Q	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	591					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						AAGGAAGTAATTGAGGATGAA	0.368													T|||	669	0.133586	0.0136	0.0504	5008	,	,		15194	0.2381		0.0646	False		,,,				2504	0.318				p.Q591Q		Atlas-SNP	.											INTS2,NS,carcinoma,0,1	INTS2	89	1	0			c.A1773G						PASS	.	T		63,3675		1,61,1807	100.0	97.0	98.0		1773	-7.1	0.4	17	dbSNP_86	98	507,7695		20,467,3614	no	coding-synonymous	INTS2	NM_020748.2		21,528,5421	CC,CT,TT		6.1814,1.6854,4.7739		591/1205	59969000	570,11370	1869	4101	5970	SO:0001819	synonymous_variant	57508	exon14			AAGTAATTGAGGA	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"""KIAA1287"""	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1773A>G	17.37:g.59969000T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_020748	Q9ULD3	Silent	SNP	ENST00000444766.3	37	CCDS45750.1																																																																																			T|0.903;C|0.097	0.097	strong		0.368	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748	
OR10G4	390264	hgsc.bcm.edu	37	11	123886352	123886352	+	Missense_Mutation	SNP	T	T	C	rs547068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123886352T>C	ENST00000320891.4	+	1	71	c.71T>C	c.(70-72)cTc>cCc	p.L24P		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	24			L -> P (in dbSNP:rs547068).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CTGGACGCCCTCCTCTTTGGA	0.582																																					p.L24P		Atlas-SNP	.											OR10G4,NS,haematopoietic_neoplasm,-1,1	OR10G4	77	1	0			c.T71C						scavenged	.						166.0	114.0	132.0					11																	123886352		2202	4297	6499	SO:0001583	missense	390264	exon1			ACGCCCTCCTCTT	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.71T>C	11.37:g.123886352T>C	ENSP00000325076:p.Leu24Pro	Somatic	471	1	0.00212314		WXS	Illumina HiSeq	Phase_I	328	93	0.283537	NM_001004462	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	.	.	.	.	.	.	.	.	.	.	t	2.968	-0.213094	0.06140	.	.	ENSG00000254737	ENST00000320891	T	0.00644	6.01	3.49	-2.71	0.05986	.	1.870160	0.02665	N	0.107976	T	0.00695	0.0023	N	0.17674	0.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.25106	T	0.35	.	12.2552	0.54619	0.0:0.3248:0.0:0.6752	rs547068	24	Q8NGN3	O10G4_HUMAN	P	24	ENSP00000325076:L24P	ENSP00000325076:L24P	L	+	2	0	OR10G4	123391562	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.326000	0.07965	-1.205000	0.02645	-0.898000	0.02899	CTC	T|0.958;C|0.042	0.042	strong		0.582	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
SCN11A	11280	hgsc.bcm.edu	37	3	38936134	38936134	+	Missense_Mutation	SNP	C	C	T	rs33985936	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38936134C>T	ENST00000302328.3	-	15	2923	c.2725G>A	c.(2725-2727)Gtc>Atc	p.V909I	SCN11A_ENST00000450244.1_Missense_Mutation_p.V909I|SCN11A_ENST00000456224.3_Missense_Mutation_p.V909I|SCN11A_ENST00000444237.2_Missense_Mutation_p.V909I	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	909			V -> I (in dbSNP:rs33985936).		cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCATGCCTGACGCCCAGGGTC	0.507													C|||	769	0.153554	0.0749	0.2248	5008	,	,		20781	0.12		0.2376	False		,,,				2504	0.1575				p.V909I		Atlas-SNP	.											.	SCN11A	296	.	0			c.G2725A						PASS	.	C	ILE/VAL	553,3853	249.3+/-256.8	30,493,1680	137.0	130.0	132.0		2725	-9.1	0.0	3	dbSNP_126	132	2108,6492	363.0+/-333.0	272,1564,2464	yes	missense	SCN11A	NM_014139.2	29	302,2057,4144	TT,TC,CC		24.5116,12.5511,20.4598	benign	909/1792	38936134	2661,10345	2203	4300	6503	SO:0001583	missense	11280	exon15			GCCTGACGCCCAG	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.2725G>A	3.37:g.38936134C>T	ENSP00000307599:p.Val909Ile	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	211	138	0.654028	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	362	0.16575091575091574	41	0.08333333333333333	78	0.2154696132596685	62	0.10839160839160839	181	0.23878627968337732	C	6.773	0.511621	0.12944	0.125511	0.245116	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	4.53	-9.06	0.00727	Sodium ion transport-associated (1);	3.067170	0.00864	N	0.001956	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.05649	-1.0872	9	0.24483	T	0.36	.	9.7812	0.40649	0.0:0.6478:0.1818:0.1704	rs33985936;rs59878058	909	Q9UI33	SCNBA_HUMAN	I	909	ENSP00000307599:V909I;ENSP00000400945:V909I;ENSP00000416757:V909I;ENSP00000408028:V909I	ENSP00000307599:V909I	V	-	1	0	SCN11A	38911138	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.830000	0.00744	-1.817000	0.01219	-1.027000	0.02421	GTC	C|0.801;T|0.199	0.199	strong		0.507	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
GLI2	2736	hgsc.bcm.edu	37	2	121726447	121726447	+	Silent	SNP	G	G	A	rs2592595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:121726447G>A	ENST00000452319.1	+	6	861	c.801G>A	c.(799-801)tcG>tcA	p.S267S	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Silent_p.S267S|GLI2_ENST00000314490.11_5'UTR					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GAAGCAGCTCGGCGGCCAGCG	0.657													G|||	4143	0.827276	0.407	0.938	5008	,	,		13109	0.999		0.9801	False		,,,				2504	0.9826				p.S267S		Atlas-SNP	.											.	GLI2	187	.	0			c.G801A						PASS	.	G		2064,2342	565.2+/-381.6	503,1058,642	56.0	52.0	53.0		801	-9.8	0.1	2	dbSNP_100	53	8461,139	810.5+/-407.1	4162,137,1	no	coding-synonymous	GLI2	NM_005270.4		4665,1195,643	AA,AG,GG		1.6163,46.8452,19.0758		267/1587	121726447	10525,2481	2203	4300	6503	SO:0001819	synonymous_variant	2736	exon5			CAGCTCGGCGGCC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.801G>A	2.37:g.121726447G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1	1862	0.8525641025641025	208	0.42276422764227645	336	0.9281767955801105	572	1.0	746	0.9841688654353562	G	7.371	0.626728	0.14257	0.468452	0.983837	ENSG00000074047	ENST00000440937;ENST00000360874	.	.	.	4.91	-9.82	0.00484	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999986	B	0.12630	0.006	B	0.14023	0.01	T	0.33420	-0.9869	6	0.05351	T	0.99	.	9.2055	0.37287	0.6871:0.0729:0.1671:0.0729	rs2592595;rs2592595	138	F5H4D9	.	S	138;130	.	ENSP00000441454:G130S	G	+	1	0	GLI2	121442917	0.000000	0.05858	0.052000	0.19188	0.127000	0.20565	-5.509000	0.00117	-2.599000	0.00452	-0.782000	0.03352	GGC	G|0.177;A|0.823	0.823	strong		0.657	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
STX16	8675	hgsc.bcm.edu	37	20	57244493	57244493	+	Silent	SNP	G	G	A	rs2296524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57244493G>A	ENST00000371141.4	+	5	1264	c.540G>A	c.(538-540)caG>caA	p.Q180Q	STX16_ENST00000361830.3_Silent_p.Q180Q|STX16_ENST00000355957.5_Silent_p.Q163Q|STX16_ENST00000371132.4_Silent_p.Q159Q|STX16_ENST00000496003.1_Intron|STX16_ENST00000358029.4_Silent_p.Q176Q|STX16_ENST00000361770.5_Silent_p.Q163Q|STX16_ENST00000359617.4_Silent_p.Q127Q|STX16-NPEPL1_ENST00000530122.1_Silent_p.Q180Q	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	180					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			GGCACGCACAGTCAGGCTACC	0.562													G|||	2376	0.474441	0.5008	0.4553	5008	,	,		17396	0.4147		0.5	False		,,,				2504	0.4877				p.Q180Q		Atlas-SNP	.											.	STX16	36	.	0			c.G540A						PASS	.	G	,,,,	2120,2260		535,1050,605	16.0	18.0	18.0		540,528,489,381,477	3.9	1.0	20	dbSNP_100	18	4561,3997		1239,2083,957	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STX16	NM_001001433.2,NM_001134772.2,NM_001134773.2,NM_001204868.1,NM_003763.5	,,,,	1774,3133,1562	AA,AG,GG		46.7048,48.4018,48.3614	,,,,	180/326,176/322,163/309,127/273,159/305	57244493	6681,6257	2190	4279	6469	SO:0001819	synonymous_variant	8675	exon5			CGCACAGTCAGGC	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.540G>A	20.37:g.57244493G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	37	CCDS13468.1																																																																																			G|0.492;A|0.508	0.508	strong		0.562	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	
NRXN2	9379	hgsc.bcm.edu	37	11	64418900	64418900	+	Silent	SNP	G	G	A	rs526338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64418900G>A	ENST00000377551.1	-	13	2956	c.2745C>T	c.(2743-2745)atC>atT	p.I915I	AP001092.4_ENST00000433606.1_RNA|NRXN2_ENST00000265459.6_Silent_p.I915I|NRXN2_ENST00000377559.3_Silent_p.I875I|NRXN2_ENST00000409571.1_Silent_p.I908I			Q9P2S2	NRX2A_HUMAN	neurexin 2	915					adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GATCGGCCACGATGGCACGCA	0.572											OREG0021057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1912	0.381789	0.0635	0.415	5008	,	,		19799	0.2212		0.7137	False		,,,				2504	0.6125				p.I915I		Atlas-SNP	.											.	NRXN2	247	.	0			c.C2745T						PASS	.	G	,	727,3675	299.8+/-286.0	64,599,1538	125.0	80.0	95.0		2745,2625	-1.4	1.0	11	dbSNP_83	95	6085,2509	693.2+/-404.6	2169,1747,381	no	coding-synonymous,coding-synonymous	NRXN2	NM_015080.3,NM_138732.2	,	2233,2346,1919	AA,AG,GG		29.1948,16.5152,47.5839	,	915/1713,875/1643	64418900	6812,6184	2201	4297	6498	SO:0001819	synonymous_variant	9379	exon14			GGCCACGATGGCA		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.2745C>T	11.37:g.64418900G>A		Somatic	132	0	0	1076	WXS	Illumina HiSeq	Phase_I	125	125	1	NM_015080	A7E2C1|Q9Y2D6	Silent	SNP	ENST00000377551.1	37	CCDS8077.1																																																																																			G|0.542;A|0.458	0.458	strong		0.572	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
UBR1	197131	hgsc.bcm.edu	37	15	43256191	43256191	+	Missense_Mutation	SNP	T	T	C	rs3917223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43256191T>C	ENST00000290650.4	-	42	4720	c.4642A>G	c.(4642-4644)Aca>Gca	p.T1548A	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1548			T -> A (in dbSNP:rs3917223).		cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		AACAAATTTGTAGGTAAAGAT	0.373													T|||	166	0.033147	0.0023	0.0259	5008	,	,		18240	0.001		0.0736	False		,,,				2504	0.0716				p.T1548A		Atlas-SNP	.											.	UBR1	124	.	0			c.A4642G						PASS	.	T	ALA/THR	73,4333	65.3+/-102.7	1,71,2131	76.0	73.0	74.0		4642	4.7	1.0	15	dbSNP_108	74	632,7966	162.2+/-214.9	26,580,3693	yes	missense	UBR1	NM_174916.2	58	27,651,5824	CC,CT,TT		7.3505,1.6568,5.4214	benign	1548/1750	43256191	705,12299	2203	4299	6502	SO:0001583	missense	197131	exon42			AATTTGTAGGTAA		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.4642A>G	15.37:g.43256191T>C	ENSP00000290650:p.Thr1548Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	116	71	0.612069	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	71	0.03250915750915751	0	0.0	11	0.03038674033149171	1	0.0017482517482517483	59	0.07783641160949868	T	14.23	2.472063	0.43942	0.016568	0.073505	ENSG00000159459	ENST00000290650	T	0.48836	0.8	4.65	4.65	0.58169	.	0.113840	0.64402	D	0.000011	T	0.02012	0.0063	L	0.33245	0.995	0.80722	D	1	P	0.40083	0.702	B	0.36092	0.217	T	0.00878	-1.1530	10	0.28530	T	0.3	-28.0639	12.4581	0.55716	0.0:0.0:0.0:1.0	rs3917223;rs17719808;rs52813857;rs61722037;rs17719808	1548	Q8IWV7	UBR1_HUMAN	A	1548	ENSP00000290650:T1548A	ENSP00000290650:T1548A	T	-	1	0	UBR1	41043483	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.860000	0.55995	1.969000	0.57287	0.528000	0.53228	ACA	T|0.847;G|0.006;C|0.046;A|0.102	0.046	strong		0.373	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
SH2D4A	63898	hgsc.bcm.edu	37	8	19218745	19218745	+	Missense_Mutation	SNP	A	A	G	rs35647122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:19218745A>G	ENST00000265807.3	+	6	1037	c.626A>G	c.(625-627)gAa>gGa	p.E209G	SH2D4A_ENST00000519207.1_Missense_Mutation_p.E209G|SH2D4A_ENST00000518040.1_Missense_Mutation_p.E164G	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	209			E -> G (in dbSNP:rs35647122). {ECO:0000269|PubMed:14702039}.		negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AAACAAGATGAAGAAATAAAT	0.343													A|||	180	0.0359425	0.0023	0.0231	5008	,	,		17894	0.1141		0.0398	False		,,,				2504	0.0061				p.E209G		Atlas-SNP	.											.	SH2D4A	49	.	0			c.A626G						PASS	.	A	GLY/GLU,GLY/GLU,GLY/GLU	44,4362	40.8+/-73.8	0,44,2159	54.0	54.0	54.0		626,491,626	5.6	0.9	8	dbSNP_126	54	357,8243	110.0+/-170.5	7,343,3950	yes	missense,missense,missense	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	98,98,98	7,387,6109	GG,GA,AA		4.1512,0.9986,3.0832	probably-damaging,probably-damaging,probably-damaging	209/455,164/410,209/455	19218745	401,12605	2203	4300	6503	SO:0001583	missense	63898	exon6			AAGATGAAGAAAT	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.626A>G	8.37:g.19218745A>G	ENSP00000265807:p.Glu209Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	107	0.04899267399267399	3	0.006097560975609756	10	0.027624309392265192	67	0.11713286713286714	27	0.03562005277044855	A	15.96	2.988095	0.53934	0.009986	0.041512	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207;ENST00000523736	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	5.61	5.61	0.85477	.	0.594604	0.17751	N	0.163223	T	0.00637	0.0021	M	0.80847	2.515	0.26366	P	0.9769664	P;D	0.61080	0.877;0.989	B;P	0.55749	0.417;0.783	T	0.11275	-1.0594	9	0.45353	T	0.12	.	12.1915	0.54275	1.0:0.0:0.0:0.0	rs35647122	164;209	B4DDR1;Q9H788	.;SH24A_HUMAN	G	209;164;209;168	ENSP00000265807:E209G;ENSP00000429482:E164G;ENSP00000428684:E209G;ENSP00000428048:E168G	ENSP00000265807:E209G	E	+	2	0	SH2D4A	19263025	1.000000	0.71417	0.928000	0.36995	0.329000	0.28539	4.210000	0.58500	2.133000	0.65898	0.533000	0.62120	GAA	A|0.963;G|0.037	0.037	strong		0.343	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
OR5J2	282775	hgsc.bcm.edu	37	11	55944474	55944474	+	Silent	SNP	G	G	A	rs4489763	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55944474G>A	ENST00000312298.1	+	1	381	c.381G>A	c.(379-381)gtG>gtA	p.V127V		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	127						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V127V(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					TGGCCATTGTGAGTCCCTTGC	0.453													.|||	494	0.0986422	0.0499	0.0994	5008	,	,		23210	0.125		0.1163	False		,,,				2504	0.1186				p.V127V		Atlas-SNP	.											OR5J2,NS,carcinoma,0,1	OR5J2	98	1	1	Substitution - coding silent(1)	stomach(1)	c.G381A						PASS	.	G		239,4163	140.4+/-175.9	7,225,1969	159.0	144.0	149.0		381	-9.2	0.0	11	dbSNP_111	149	999,7593	215.5+/-254.8	53,893,3350	no	coding-synonymous	OR5J2	NM_001005492.1		60,1118,5319	AA,AG,GG		11.6271,5.4294,9.5275		127/313	55944474	1238,11756	2201	4296	6497	SO:0001819	synonymous_variant	282775	exon1			CATTGTGAGTCCC	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"""GPCR / Class A : Olfactory receptors"""	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.381G>A	11.37:g.55944474G>A		Somatic	371	1	0.00269542		WXS	Illumina HiSeq	Phase_I	390	190	0.487179	NM_001005492	Q6IEU5	Silent	SNP	ENST00000312298.1	37	CCDS31522.1																																																																																			G|0.903;A|0.097	0.097	strong		0.453	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492	
ZDHHC21	340481	hgsc.bcm.edu	37	9	14662260	14662260	+	Silent	SNP	A	A	G	rs17215796	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:14662260A>G	ENST00000380916.4	-	6	784	c.318T>C	c.(316-318)tgT>tgC	p.C106C		NM_178566.4	NP_848661.1	Q8IVQ6	ZDH21_HUMAN	zinc finger, DHHC-type containing 21	106					hair follicle development (GO:0001942)|nitric oxide metabolic process (GO:0046209)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)|regulation of nitric-oxide synthase activity (GO:0050999)|sebaceous gland development (GO:0048733)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9				GBM - Glioblastoma multiforme(50;4.31e-06)		CGCAGCGGCTACAGTGATGGG	0.393													A|||	360	0.071885	0.0265	0.1657	5008	,	,		16348	0.0129		0.164	False		,,,				2504	0.0327				p.C106C		Atlas-SNP	.											.	ZDHHC21	22	.	0			c.T318C						PASS	.	A		244,4162	142.3+/-177.5	7,230,1966	69.0	65.0	67.0		318	0.9	1.0	9	dbSNP_123	67	1399,7201	270.1+/-288.8	108,1183,3009	no	coding-synonymous	ZDHHC21	NM_178566.4		115,1413,4975	GG,GA,AA		16.2674,5.5379,12.6326		106/266	14662260	1643,11363	2203	4300	6503	SO:0001819	synonymous_variant	340481	exon6			GCGGCTACAGTGA	AF161360	CCDS6475.1	9p22.3	2010-02-09			ENSG00000175893	ENSG00000175893		"""Zinc fingers, DHHC-type"""	20750	protein-coding gene	gene with protein product		614605				19956733	Standard	NM_178566		Approved	HSPC097, DNZ1	uc003zlg.2	Q8IVQ6	OTTHUMG00000019573	ENST00000380916.4:c.318T>C	9.37:g.14662260A>G		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_178566	A8KA95|D3DRI7|Q5VWG1	Silent	SNP	ENST00000380916.4	37	CCDS6475.1																																																																																			A|0.899;G|0.101	0.101	strong		0.393	ZDHHC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051748.2	NM_178566	
CES1	1066	hgsc.bcm.edu	37	16	55862824	55862824	+	Missense_Mutation	SNP	C	C	T	rs3826192		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55862824C>T	ENST00000361503.4	-	2	242	c.112G>A	c.(112-114)Gtc>Atc	p.V38I	CES1_ENST00000422046.2_Missense_Mutation_p.V38I|CES1_ENST00000360526.3_Missense_Mutation_p.V39I|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	38					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	TCTAAGCTGACGAACTTCCCC	0.562																																					p.V39I	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.G115A						PASS	.						71.0	57.0	61.0					16																	55862824		2198	4300	6498	SO:0001583	missense	1066	exon2			AGCTGACGAACTT	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.112G>A	16.37:g.55862824C>T	ENSP00000355193:p.Val38Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	116	24	0.206897	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	4.259	0.047210	0.08243	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.69040	3.07;3.07;-0.37	4.48	3.5	0.40072	Carboxylesterase, type B (1);	0.385300	0.18328	N	0.144578	T	0.51907	0.1702	L	0.31526	0.94	0.09310	N	1	B;B;B	0.22211	0.066;0.03;0.053	B;B;B	0.15870	0.014;0.014;0.008	T	0.40384	-0.9566	10	0.36615	T	0.2	.	10.7143	0.46002	0.0:0.9016:0.0:0.0984	rs3826192;rs3826192	38;38;39	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	I	39;38;38	ENSP00000353720:V39I;ENSP00000355193:V38I;ENSP00000390492:V38I	ENSP00000353720:V39I	V	-	1	0	CES1	54420325	0.000000	0.05858	0.003000	0.11579	0.063000	0.16089	0.558000	0.23469	0.849000	0.35215	0.393000	0.25936	GTC	C|0.998;T|0.002	0.002	strong		0.562	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
ANTXR1	84168	hgsc.bcm.edu	37	2	69472476	69472476	+	Silent	SNP	G	G	A	rs147959058	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:69472476G>A	ENST00000303714.4	+	18	1876	c.1554G>A	c.(1552-1554)gcG>gcA	p.A518A		NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	518	Pro-rich.				actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						cacctcctgcgccccactgcc	0.692									Familial Infantile Hemangioma				G|||	66	0.0131789	0.0061	0.0187	5008	,	,		3811	0.0		0.0378	False		,,,				2504	0.0072				p.A518A		Atlas-SNP	.											ANTXR1,NS,lymphoid_neoplasm,+1,1	ANTXR1	128	1	0			c.G1554A						PASS	.	G		33,4369		0,33,2168	82.0	77.0	79.0		1554	-8.2	0.8	2	dbSNP_134	79	295,8299		5,285,4007	no	coding-synonymous	ANTXR1	NM_032208.2		5,318,6175	AA,AG,GG		3.4326,0.7497,2.5239		518/565	69472476	328,12668	2201	4297	6498	SO:0001819	synonymous_variant	84168	exon18	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	TCCTGCGCCCCAC	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"""anthrax toxin receptor"", ""tumor endothelial marker 8 precursor"""	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.1554G>A	2.37:g.69472476G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	167	79	0.473054	NM_032208	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Silent	SNP	ENST00000303714.4	37	CCDS1892.1																																																																																			G|0.980;A|0.020	0.020	strong		0.692	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208	
INPP5F	22876	hgsc.bcm.edu	37	10	121579040	121579040	+	Silent	SNP	T	T	C	rs17099318	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:121579040T>C	ENST00000369080.3	+	1	813	c.45T>C	c.(43-45)ttT>ttC	p.F15F	INPP5F_ENST00000490818.1_3'UTR|INPP5F_ENST00000361976.2_Intron	NM_001243194.1	NP_001230123.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	0	PH.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		AGCAACAATTTTCAGAGTGCA	0.343													T|||	561	0.112021	0.0023	0.0274	5008	,	,		15296	0.1746		0.0537	False		,,,				2504	0.316				p.F15F		Atlas-SNP	.											.	INPP5F	112	.	0			c.T45C						PASS	.	T		15,1737		0,15,861	32.0	33.0	33.0			1.2	0.0	10	dbSNP_123	33	225,3755		3,219,1768	no	intron	INPP5F	NM_014937.3		3,234,2629	CC,CT,TT		5.6533,0.8562,4.187			121579040	240,5492	876	1990	2866	SO:0001819	synonymous_variant	22876	exon1			ACAATTTTCAGAG	AB023183	CCDS7616.1, CCDS58098.1	10q26.13	2009-02-03			ENSG00000198825	ENSG00000198825			17054	protein-coding gene	gene with protein product		609389				10231032, 11274189	Standard	NM_014937		Approved	SAC2, KIAA0966, hSac2	uc001leo.3	Q9Y2H2	OTTHUMG00000019158	ENST00000369080.3:c.45T>C	10.37:g.121579040T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	143	77	0.538462	NM_001243194	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Silent	SNP	ENST00000369080.3	37	CCDS58098.1																																																																																			T|0.916;C|0.084	0.084	strong		0.343	INPP5F-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050680.1	NM_014937	
PROB1	389333	hgsc.bcm.edu	37	5	138732579	138732579	+	5'Flank	SNP	C	C	T	rs10900862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:138732579C>T	ENST00000434752.2	-	0	0					NM_001161546.1	NP_001155018.1	E7EW31	PROB1_HUMAN	proline-rich basic protein 1																		CCATGTAGCTCTCCTGCTGCT	0.597													C|||	1947	0.388778	0.0734	0.5994	5008	,	,		16449	0.3135		0.6223	False		,,,				2504	0.5031				p.E176E		Atlas-SNP	.											Q8N799_HUMAN,colon,carcinoma,0,1	.	.	1	0			c.G528A						PASS	.	C		234,1150		18,198,476	107.0	93.0	97.0		528	5.7	1.0	5	dbSNP_120	97	2067,1115		676,715,200	no	coding-synonymous	SPATA24	NM_194296.1		694,913,676	TT,TC,CC		35.0409,16.9075,49.6058		176/206	138732579	2301,2265	692	1591	2283	SO:0001631	upstream_gene_variant	202051	exon6			GTAGCTCTCCTGC	AK316483	CCDS54909.1	5q31.2	2012-10-01	2012-10-01	2012-10-01	ENSG00000228672	ENSG00000228672			41906	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 65"""	C5orf65			Standard	NM_001161546		Approved		uc011czc.1	E7EW31			5.37:g.138732579C>T	Exception_encountered	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	252	146	0.579365	NM_194296	B4E007	Silent	SNP	ENST00000434752.2	37	CCDS54909.1	906|906	0.41483516483516486|0.41483516483516486	46|46	0.09349593495934959|0.09349593495934959	217|217	0.5994475138121547|0.5994475138121547	171|171	0.29895104895104896|0.29895104895104896	472|472	0.6226912928759895|0.6226912928759895	C|C	19.23|19.23	3.787128|3.787128	0.70337|0.70337	0.169075|0.169075	0.649591|0.649591	ENSG00000170469|ENSG00000170469	ENST00000514983|ENST00000302091	.|.	.|.	.|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	.|1.121690	.|0.06529	.|N	.|0.741144	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|D	.|0.71674	.|0.998	.|P	.|0.60541	.|0.876	T|T	0.47995|0.47995	-0.9073|-0.9073	3|7	.|0.51188	.|T	.|0.08	-4.7387|-4.7387	15.2367|15.2367	0.73436|0.73436	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs10900862;rs52816305;rs58994621;rs10900862|rs10900862;rs52816305;rs58994621;rs10900862	.|185	.|Q8N799	.|.	K|K	139|185	.|.	.|ENSP00000302917:R185K	E|R	-|-	1|2	0|0	SPATA24|SPATA24	138760478|138760478	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.854000|3.854000	0.55949|0.55949	2.672000|2.672000	0.90937|0.90937	0.655000|0.655000	0.94253|0.94253	GAG|AGA	C|0.593;T|0.407	0.407	strong		0.597	PROB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470735.1	NM_001161546	
KRT39	390792	hgsc.bcm.edu	37	17	39116728	39116728	+	Missense_Mutation	SNP	G	G	A	rs17843021	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39116728G>A	ENST00000355612.2	-	6	1057	c.1022C>T	c.(1021-1023)aCg>aTg	p.T341M	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	341	Coil 2.|Rod.		T -> M (in dbSNP:rs17843021).			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				CTCTGTCTCCGTTAGGATGCA	0.493													G|||	585	0.116813	0.1452	0.0548	5008	,	,		18259	0.1399		0.1322	False		,,,				2504	0.0828				p.T341M		Atlas-SNP	.											.	KRT39	53	.	0			c.C1022T						PASS	.	G	MET/THR	630,3776	274.0+/-271.7	53,524,1626	137.0	135.0	135.0		1022	-1.1	0.0	17	dbSNP_123	135	1136,7456	235.1+/-267.8	71,994,3231	yes	missense	KRT39	NM_213656.3	81	124,1518,4857	AA,AG,GG		13.2216,14.2987,13.5867	possibly-damaging	341/492	39116728	1766,11232	2203	4296	6499	SO:0001583	missense	390792	exon6			GTCTCCGTTAGGA	AJ786657	CCDS11382.1	17q21.2	2013-01-16			ENSG00000196859	ENSG00000196859		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	32971	protein-coding gene	gene with protein product						16831889	Standard	NM_213656		Approved	KA35	uc002hvo.1	Q6A163	OTTHUMG00000133424	ENST00000355612.2:c.1022C>T	17.37:g.39116728G>A	ENSP00000347823:p.Thr341Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_213656	B2RXK6|Q6IFU6	Missense_Mutation	SNP	ENST00000355612.2	37	CCDS11382.1	273	0.125	69	0.1402439024390244	29	0.08011049723756906	75	0.13111888111888112	100	0.13192612137203166	G	6.273	0.418486	0.11870	0.142987	0.132216	ENSG00000196859	ENST00000355612	D	0.89050	-2.46	5.81	-1.12	0.09808	Filament (1);	1.437790	0.04585	N	0.395707	T	0.03651	0.0104	M	0.64170	1.965	0.80722	P	0.0	P	0.41947	0.766	B	0.37239	0.244	T	0.51655	-0.8678	9	0.62326	D	0.03	.	4.6774	0.12719	0.2521:0.0:0.3101:0.4378	rs17843021;rs17843021	341	Q6A163	K1C39_HUMAN	M	341	ENSP00000347823:T341M	ENSP00000347823:T341M	T	-	2	0	KRT39	36370254	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.117000	0.10708	-0.383000	0.07858	-0.218000	0.12543	ACG	G|0.868;A|0.132	0.132	strong		0.493	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	
ADRA1A	148	hgsc.bcm.edu	37	8	26721888	26721888	+	Missense_Mutation	SNP	A	A	C	rs2229125	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:26721888A>C	ENST00000519229.1	-	1	605	c.599T>G	c.(598-600)aTc>aGc	p.I200S	ADRA1A_ENST00000380587.1_Missense_Mutation_p.I200S|ADRA1A_ENST00000380573.3_Missense_Mutation_p.I200S|ADRA1A_ENST00000276393.4_Missense_Mutation_p.I200S|ADRA1A_ENST00000358857.5_Missense_Mutation_p.I200S|ADRA1A_ENST00000380582.3_Missense_Mutation_p.I200S|ADRA1A_ENST00000354550.4_Missense_Mutation_p.I200S|ADRA1A_ENST00000380581.2_Missense_Mutation_p.I200S|ADRA1A_ENST00000380572.3_Missense_Mutation_p.I200S|ADRA1A_ENST00000380586.1_Missense_Mutation_p.I200S			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	270					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	CATGACCAGGATGATGGCCAG	0.637													A|||	107	0.0213658	0.0015	0.0663	5008	,	,		18702	0.001		0.0219	False		,,,				2504	0.0368				p.I200S		Atlas-SNP	.											.	ADRA1A	337	.	0			c.T599G	GRCh37	CM057865	ADRA1A	M	rs2229125	PASS	.	A	SER/ILE,SER/ILE,SER/ILE,SER/ILE	19,4387	25.3+/-52.1	0,19,2184	28.0	29.0	29.0		599,599,599,599	5.1	1.0	8	dbSNP_98	29	211,8389	85.3+/-147.7	2,207,4091	yes	missense,missense,missense,missense	ADRA1A	NM_000680.2,NM_033302.2,NM_033303.3,NM_033304.2	142,142,142,142	2,226,6275	CC,CA,AA		2.4535,0.4312,1.7684	probably-damaging,probably-damaging,probably-damaging,probably-damaging	200/467,200/430,200/476,200/456	26721888	230,12776	2203	4300	6503	SO:0001583	missense	148	exon1			ACCAGGATGATGG	L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"""GPCR / Class A : Adrenoceptors : alpha"""	277	protein-coding gene	gene with protein product		104221	"""adrenergic, alpha-1A-, receptor"""	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.599T>G	8.37:g.26721888A>C	ENSP00000430793:p.Ile200Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_033303	Q9NPY0	Missense_Mutation	SNP	ENST00000519229.1	37		33	0.01510989010989011	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	16	0.021108179419525065	A	20.2	3.952146	0.73787	0.004312	0.024535	ENSG00000120907	ENST00000380586;ENST00000380587;ENST00000380582;ENST00000380581;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573;ENST00000380572;ENST00000358857	T;T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.12	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	H	0.95365	3.66	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D	0.91635	0.994;0.994;0.997;0.996;0.999;0.995	T	0.77563	-0.2541	10	0.87932	D	0	.	14.8856	0.70567	1.0:0.0:0.0:0.0	rs2229125;rs2229125	200;200;200;200;200;200	P35348-9;P35348-8;P35348;P35348-4;P35348-3;B0ZBD3	.;.;ADA1A_HUMAN;.;.;.	S	200	ENSP00000369960:I200S;ENSP00000369961:I200S;ENSP00000369956:I200S;ENSP00000369955:I200S;ENSP00000430793:I200S;ENSP00000346557:I200S;ENSP00000276393:I200S;ENSP00000369947:I200S;ENSP00000369946:I200S;ENSP00000351725:I200S	ENSP00000276393:I200S	I	-	2	0	ADRA1A	26777805	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	9.287000	0.95975	2.049000	0.60858	0.460000	0.39030	ATC	A|0.984;C|0.016	0.016	strong		0.637	ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1	NM_033303	
CD99	4267	hgsc.bcm.edu	37	X	2644302	2644302	+	Splice_Site	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2644302C>T	ENST00000381192.3	+	8	545	c.363C>T	c.(361-363)gcC>gcT	p.A121A	CD99_ENST00000381184.1_Splice_Site_p.A121A|CD99_ENST00000482405.2_3'UTR|CD99_ENST00000381187.3_Splice_Site_p.A105A	NM_001277710.1|NM_002414.3	NP_001264639.1|NP_002405.1	P14209	CD99_HUMAN	CD99 molecule	121					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11						CTCCTGCAGCCGACGCCCCAG	0.597													.|||	594	0.11861	0.0741	0.2075	5008	,	,		18276	0.0804		0.1362	False		,,,				2504	0.137				p.A121A		Atlas-SNP	.											.	CD99	12	.	0			c.C363T						PASS	.	C	,	405,4001		22,361,1820	72.0	72.0	72.0		315,363	-5.0	0.0	X	dbSNP_134	72	1289,7303		91,1107,3098	no	coding-synonymous-near-splice,coding-synonymous-near-splice	CD99	NM_001122898.1,NM_002414.3	,	113,1468,4918	TT,TC,CC		15.0023,9.192,13.0328	,	105/170,121/186	2644302	1694,11304	2203	4296	6499	SO:0001630	splice_region_variant	4267	exon8			TGCAGCCGACGCC	M16279	CCDS14119.1, CCDS48071.1, CCDS75947.1	Xp22.32 and Yp11.3	2012-10-02	2006-03-28	2003-02-14	ENSG00000002586	ENSG00000002586		"""Pseudoautosomal regions / PAR1"", ""CD molecules"""	7082	protein-coding gene	gene with protein product		313470, 450000	"""antigen identified by monoclonal antibodies 12E7, F21 and O13"", ""CD99 antigen"""	MIC2			Standard	NM_001122898		Approved		uc004cqm.3	P14209	OTTHUMG00000021073	ENST00000381192.3:c.362-1C>T	X.37:g.2644302C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	173	77	0.445087	NM_002414	A6NIW1|O00518|Q6ICV7	Silent	SNP	ENST00000381192.3	37	CCDS14119.1																																																																																			.	.	weak		0.597	CD99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055624.1	NM_001122898	Silent
SSTR4	6754	hgsc.bcm.edu	37	20	23016970	23016970	+	Missense_Mutation	SNP	T	T	G	rs3746726	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23016970T>G	ENST00000255008.3	+	1	914	c.850T>G	c.(850-852)Ttc>Gtc	p.F284V	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	284			F -> V (in dbSNP:rs3746726). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8483934, ECO:0000269|PubMed:8512564, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GCTGAACCTCTTCGTGACCAG	0.557													T|||	1530	0.305511	0.2179	0.281	5008	,	,		18337	0.2351		0.3698	False		,,,				2504	0.4479				p.F284V	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,colon,carcinoma,0,1	SSTR4	83	1	0			c.T850G						PASS	.	T	VAL/PHE	1031,3375	359.9+/-315.0	134,763,1306	197.0	205.0	202.0		850	3.4	0.5	20	dbSNP_107	202	3321,5279	483.4+/-371.1	672,1977,1651	yes	missense	SSTR4	NM_001052.2	50	806,2740,2957	GG,GT,TT		38.6163,23.3999,33.4615	benign	284/389	23016970	4352,8654	2203	4300	6503	SO:0001583	missense	6754	exon1			AACCTCTTCGTGA		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.850T>G	20.37:g.23016970T>G	ENSP00000255008:p.Phe284Val	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	175	79	0.451429	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	648	0.2967032967032967	113	0.22967479674796748	112	0.30939226519337015	148	0.25874125874125875	275	0.3627968337730871	T	7.979	0.750733	0.15778	0.233999	0.386163	ENSG00000132671	ENST00000255008	T	0.39406	1.08	3.36	3.36	0.38483	GPCR, rhodopsin-like superfamily (1);	0.090253	0.44483	U	0.000451	T	0.00012	0.0000	L	0.47190	1.495	0.37728	P	0.07484000000000002	B	0.11235	0.004	B	0.17098	0.017	T	0.38373	-0.9664	9	0.02654	T	1	.	6.6396	0.22901	0.0:0.1196:0.0:0.8804	rs3746726;rs60613961;rs3746726	284	P31391	SSR4_HUMAN	V	284	ENSP00000255008:F284V	ENSP00000255008:F284V	F	+	1	0	SSTR4	22964970	0.846000	0.29590	0.479000	0.27329	0.626000	0.37791	1.296000	0.33389	1.384000	0.46424	0.533000	0.62120	TTC	T|0.674;G|0.326	0.326	strong		0.557	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
NBPF3	84224	hgsc.bcm.edu	37	1	21795388	21795388	+	Missense_Mutation	SNP	A	A	G	rs1827293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:21795388A>G	ENST00000318249.5	+	3	691	c.341A>G	c.(340-342)tAc>tGc	p.Y114C	NBPF3_ENST00000342104.5_Missense_Mutation_p.Y114C|NBPF3_ENST00000454000.2_Intron|NBPF3_ENST00000318220.6_Missense_Mutation_p.Y58C	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	114			Y -> C (in dbSNP:rs1827293). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAAAATAATTACGGTAAGTTC	0.448											OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	2123	0.423922	0.1445	0.4755	5008	,	,		19838	0.5804		0.5417	False		,,,				2504	0.4826				p.A114G		Atlas-SNP	.											NBPF3,NS,carcinoma,0,1	NBPF3	55	1	0			c.C341G						PASS	.	A	CYS/TYR	970,3436		104,762,1337	48.0	53.0	51.0		341	-2.2	0.0	1	dbSNP_92	51	4756,3844		1332,2092,876	yes	missense	NBPF3	NM_032264.2	194	1436,2854,2213	GG,GA,AA		44.6977,22.0154,44.0258	probably-damaging	114/634	21795388	5726,7280	2203	4300	6503	SO:0001583	missense	84224	exon3			ATAATTACGGTAA	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.341A>G	1.37:g.21795388A>G	ENSP00000316782:p.Tyr114Cys	Somatic	185	0	0	751	WXS	Illumina HiSeq	Phase_I	180	104	0.577778	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Missense_Mutation	SNP	ENST00000318249.5	37	CCDS216.1	999	0.4574175824175824	88	0.17886178861788618	187	0.5165745856353591	318	0.5559440559440559	406	0.5356200527704486	.	10.34	1.323132	0.24080	0.220154	0.553023	ENSG00000142794	ENST00000318220;ENST00000318249;ENST00000417552;ENST00000342104;ENST00000434838	T;T;T;T	0.04970	3.69;3.52;3.55;3.69	1.08	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	M	0.72353	2.195	0.80722	P	0.0	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.979	T	0.48547	-0.9026	8	0.87932	D	0	.	1.9892	0.03442	0.3991:0.302:0.0:0.2989	rs1827293;rs3738102;rs17420230;rs17856707;rs52824093;rs58179675;rs1827293	114;114	Q9H094-3;Q9H094	.;NBPF3_HUMAN	C	58;114;58;114;58	ENSP00000316739:Y58C;ENSP00000316782:Y114C;ENSP00000340336:Y114C;ENSP00000391865:Y58C	ENSP00000316739:Y58C	Y	+	2	0	NBPF3	21667975	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.056000	0.11787	-0.776000	0.04578	0.327000	0.21459	TAC	A|0.554;G|0.446	0.446	strong		0.448	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
HERC1	8925	hgsc.bcm.edu	37	15	63932513	63932513	+	Silent	SNP	G	G	C	rs2228517	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63932513G>C	ENST00000443617.2	-	61	11826	c.11739C>G	c.(11737-11739)ctC>ctG	p.L3913L		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3913					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.L3913L(1)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CAGGGTCAGGGAGACAGTTCT	0.512													G|||	1610	0.321486	0.3056	0.428	5008	,	,		18060	0.0764		0.5268	False		,,,				2504	0.3088				p.L3913L		Atlas-SNP	.											HERC1_ENST00000443617,NS,carcinoma,0,1	HERC1	624	1	1	Substitution - coding silent(1)	stomach(1)	c.C11739G						PASS	.	G		1356,2760		240,876,942	142.0	143.0	143.0		11739	4.6	1.0	15	dbSNP_98	143	4476,3958		1187,2102,928	no	coding-synonymous	HERC1	NM_003922.3		1427,2978,1870	CC,CG,GG		46.9291,32.9446,46.4701		3913/4862	63932513	5832,6718	2058	4217	6275	SO:0001819	synonymous_variant	8925	exon61			GTCAGGGAGACAG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.11739C>G	15.37:g.63932513G>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																			G|0.631;C|0.369	0.369	strong		0.512	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
SLFN11	91607	hgsc.bcm.edu	37	17	33690466	33690466	+	Missense_Mutation	SNP	C	C	A	rs12453150	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:33690466C>A	ENST00000394566.1	-	4	633	c.361G>T	c.(361-363)Gtc>Ttc	p.V121F	SLFN11_ENST00000308377.4_Missense_Mutation_p.V121F	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	121			V -> F (in dbSNP:rs12453150). {ECO:0000269|PubMed:14702039}.		defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CGGGGCTTGACAGAGCGATCT	0.468													C|||	2084	0.416134	0.1543	0.5202	5008	,	,		18643	0.4821		0.5547	False		,,,				2504	0.4857				p.V121F		Atlas-SNP	.											.	SLFN11	112	.	0			c.G361T						PASS	.	C	PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL	1015,3391	373.9+/-321.0	101,813,1289	58.0	57.0	57.0		361,361,361,361,361	-8.4	0.0	17	dbSNP_120	57	4725,3875	605.0+/-394.9	1311,2103,886	yes	missense,missense,missense,missense,missense	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	50,50,50,50,50	1412,2916,2175	AA,AC,CC		45.0581,23.0368,44.1335	benign,benign,benign,benign,benign	121/902,121/902,121/902,121/902,121/902	33690466	5740,7266	2203	4300	6503	SO:0001583	missense	91607	exon2			GCTTGACAGAGCG	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.361G>T	17.37:g.33690466C>A	ENSP00000378067:p.Val121Phe	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	972	0.44505494505494503	76	0.15447154471544716	184	0.5082872928176796	287	0.5017482517482518	425	0.5606860158311345	C	6.914	0.538262	0.13188	0.230368	0.549419	ENSG00000172716	ENST00000308377;ENST00000394566	T;T	0.01981	4.52;4.52	4.18	-8.36	0.00980	.	3.322670	0.01114	N	0.005654	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.45906	-0.9229	9	0.08381	T	0.77	.	1.5129	0.02500	0.2034:0.4249:0.1856:0.1861	rs12453150;rs52821683;rs57680721;rs12453150	121	Q7Z7L1	SLN11_HUMAN	F	121	ENSP00000312402:V121F;ENSP00000378067:V121F	ENSP00000312402:V121F	V	-	1	0	SLFN11	30714579	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.838000	0.01687	-3.775000	0.00108	-0.150000	0.13652	GTC	C|0.564;A|0.436	0.436	strong		0.468	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
POLG	5428	hgsc.bcm.edu	37	15	89864987	89864987	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89864987G>A	ENST00000268124.5	-	16	2911	c.2578C>T	c.(2578-2580)Ctc>Ttc	p.L860F	POLG_ENST00000442287.2_Missense_Mutation_p.L860F	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	860					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			CTGGCGGTGAGCCATGTGGGC	0.617								DNA polymerases (catalytic subunits)																													p.L860F	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.C2578T						PASS	.						68.0	69.0	69.0					15																	89864987		2200	4299	6499	SO:0001583	missense	5428	exon16			CGGTGAGCCATGT	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.2578C>T	15.37:g.89864987G>A	ENSP00000268124:p.Leu860Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	111	20	0.18018	NM_002693	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	37	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	G	33	5.233367	0.95207	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.99089	-5.41;-5.41	5.24	5.24	0.73138	DNA-directed DNA polymerase, family A, palm domain (1);	0.000000	0.85682	D	0.000000	D	0.99429	0.9798	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98735	1.0714	10	0.72032	D	0.01	-22.7577	18.8187	0.92088	0.0:0.0:1.0:0.0	.	860	P54098	DPOG1_HUMAN	F	860	ENSP00000268124:L860F;ENSP00000399851:L860F	ENSP00000268124:L860F	L	-	1	0	POLG	87665991	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.553000	0.82203	2.448000	0.82819	0.655000	0.94253	CTC	.	.	none		0.617	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
MADCAM1	8174	hgsc.bcm.edu	37	19	501786	501786	+	Missense_Mutation	SNP	C	C	A	rs77264553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:501786C>A	ENST00000215637.3	+	4	831	c.785C>A	c.(784-786)cCg>cAg	p.P262Q	MADCAM1_ENST00000587541.1_Missense_Mutation_p.P43Q|MADCAM1_ENST00000382683.4_Intron|MADCAM1_ENST00000346144.4_Intron|AC005775.2_ENST00000592413.1_RNA	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	262	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCACCTCCCCGGAGCCTCCC	0.726																																					p.P262Q		Atlas-SNP	.											MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	0			c.C785A						scavenged	.						21.0	23.0	22.0					19																	501786		2174	4254	6428	SO:0001583	missense	8174	exon4			CCTCCCCGGAGCC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.785C>A	19.37:g.501786C>A	ENSP00000215637:p.Pro262Gln	Somatic	140	3	0.0214286		WXS	Illumina HiSeq	Phase_I	189	84	0.444444	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	c	9.375	1.071453	0.20147	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.12147	2.71	3.07	-3.57	0.04612	.	3.584140	0.00988	N	0.003486	T	0.04907	0.0132	N	0.03608	-0.345	0.80722	P	0.0	B	0.33073	0.396	B	0.12837	0.008	T	0.24584	-1.0156	9	0.72032	D	0.01	.	3.8366	0.08897	0.3193:0.4698:0.0:0.2109	.	262	Q13477	MADCA_HUMAN	Q	286;278;270;262	ENSP00000215637:P262Q	ENSP00000215637:P262Q	P	+	2	0	MADCAM1	452786	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.770000	0.04705	-0.633000	0.05545	-0.962000	0.02626	CCG	C|0.500;A|0.500	0.500	strong		0.726	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
CASP2	835	hgsc.bcm.edu	37	7	142991361	142991361	+	Missense_Mutation	SNP	G	G	C	rs4647297	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:142991361G>C	ENST00000310447.5	+	5	755	c.514G>C	c.(514-516)Gtc>Ctc	p.V172L	CASP2_ENST00000493642.1_3'UTR	NM_032982.3|NM_032983.3	NP_116764.2|NP_116765.2	P42575	CASP2_HUMAN	caspase 2, apoptosis-related cysteine peptidase	172			V -> L (in dbSNP:rs4647297). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5, ECO:0000269|Ref.9}.		aging (GO:0007568)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|ectopic germ cell programmed cell death (GO:0035234)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|luteolysis (GO:0001554)|neural retina development (GO:0003407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron apoptotic process (GO:0043525)|protein processing (GO:0016485)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(164;0.059)					AGATGGTCCTGTCTGCCTTCA	0.383													G|||	196	0.0391374	0.0439	0.0432	5008	,	,		21481	0.001		0.0547	False		,,,				2504	0.0532				p.V172L		Atlas-SNP	.											CASP2,NS,carcinoma,0,1	CASP2	55	1	0			c.G514C						PASS	.	G	LEU/VAL,LEU/VAL,	259,4147	149.5+/-183.7	11,237,1955	163.0	163.0	163.0		421,514,	4.9	1.0	7	dbSNP_111	163	479,8121	139.7+/-196.3	15,449,3836	yes	missense,missense,intron	CASP2	NM_001224.4,NM_032982.3,NM_032983.3	32,32,	26,686,5791	CC,CG,GG		5.5698,5.8783,5.6743	benign,benign,	141/313,172/453,	142991361	738,12268	2203	4300	6503	SO:0001583	missense	835	exon5			GGTCCTGTCTGCC	AK096245, BC002427, BM998653, BX537669, CB988674, U13021	CCDS5879.1, CCDS47733.1	7q34-q35	2014-01-20	2008-08-01		ENSG00000106144	ENSG00000106144		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1503	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 57"""	600639	"""neural precursor cell expressed, developmentally down-regulated 2"""	NEDD2		7789948, 8780721	Standard	NM_032982		Approved	ICH1, PPP1R57, MGC2181	uc003wco.3	P42575	OTTHUMG00000023641	ENST00000310447.5:c.514G>C	7.37:g.142991361G>C	ENSP00000312664:p.Val172Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_032982	A8K5F9|D3DXD6|E9PDN0|P42576|Q59F21|Q7KZL6|Q86UJ3|Q9BUP7|Q9BZK9|Q9BZL0	Missense_Mutation	SNP	ENST00000310447.5	37	CCDS5879.1	79	0.036172161172161175	13	0.026422764227642278	19	0.052486187845303865	0	0.0	47	0.06200527704485488	G	13.34	2.208472	0.39003	0.058783	0.055698	ENSG00000106144	ENST00000310447;ENST00000392923	T	0.01787	4.64	5.78	4.9	0.64082	.	0.491806	0.25060	N	0.033444	T	0.00210	0.0006	N	0.19112	0.55	0.80722	D	1	B	0.11235	0.004	B	0.12837	0.008	T	0.58160	-0.7685	10	0.11485	T	0.65	.	10.3394	0.43868	0.0:0.7862:0.1406:0.0733	rs4647297;rs17849580;rs4647297	172	P42575	CASP2_HUMAN	L	172;141	ENSP00000312664:V172L	ENSP00000312664:V172L	V	+	1	0	CASP2	142701483	0.002000	0.14202	0.993000	0.49108	0.907000	0.53573	0.993000	0.29680	1.460000	0.47911	-0.321000	0.08615	GTC	G|0.954;C|0.046	0.046	strong		0.383	CASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059962.3	NM_032982	
FAM114A1	92689	hgsc.bcm.edu	37	4	38945169	38945169	+	Silent	SNP	A	A	G	rs1060582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38945169A>G	ENST00000358869.2	+	15	1859	c.1683A>G	c.(1681-1683)gcA>gcG	p.A561A	FAM114A1_ENST00000515037.1_Silent_p.A354A	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	561						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						GTTTGAAAGCACAGCCGTGAC	0.527													A|||	535	0.106829	0.053	0.1787	5008	,	,		17632	0.0903		0.1233	False		,,,				2504	0.1288				p.A561A		Atlas-SNP	.											.	FAM114A1	42	.	0			c.A1683G						PASS	.	A		330,4076	175.9+/-205.1	13,304,1886	104.0	85.0	91.0		1683	-1.9	0.4	4	dbSNP_86	91	1287,7313	255.5+/-280.4	88,1111,3101	no	coding-synonymous	FAM114A1	NM_138389.2		101,1415,4987	GG,GA,AA		14.9651,7.4898,12.4327		561/564	38945169	1617,11389	2203	4300	6503	SO:0001819	synonymous_variant	92689	exon15			GAAAGCACAGCCG		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1683A>G	4.37:g.38945169A>G		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	206	206	1	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Silent	SNP	ENST00000358869.2	37	CCDS3447.1																																																																																			A|0.883;G|0.117	0.117	strong		0.527	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
LAD1	3898	hgsc.bcm.edu	37	1	201351421	201351421	+	Missense_Mutation	SNP	T	T	A	rs2275866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201351421T>A	ENST00000391967.2	-	9	1808	c.1507A>T	c.(1507-1509)Act>Tct	p.T503S	LAD1_ENST00000488842.1_5'Flank|LAD1_ENST00000367313.3_Missense_Mutation_p.T517S	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	503			T -> S (in dbSNP:rs2275866).			basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						CCCCACTGAGTCCTCTCGGTT	0.597													T|||	229	0.0457268	0.0076	0.0519	5008	,	,		18239	0.0605		0.0716	False		,,,				2504	0.0511				p.T503S		Atlas-SNP	.											.	LAD1	42	.	0			c.A1507T						PASS	.	T	SER/THR	100,4306	79.9+/-118.3	1,98,2104	217.0	176.0	190.0		1507	0.4	1.0	1	dbSNP_100	190	704,7896	173.7+/-224.2	34,636,3630	yes	missense	LAD1	NM_005558.3	58	35,734,5734	AA,AT,TT		8.186,2.2696,6.1818	benign	503/518	201351421	804,12202	2203	4300	6503	SO:0001583	missense	3898	exon9			ACTGAGTCCTCTC	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.1507A>T	1.37:g.201351421T>A	ENSP00000375829:p.Thr503Ser	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	233	98	0.420601	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	37	CCDS1410.1	117	0.05357142857142857	7	0.014227642276422764	23	0.06353591160220995	30	0.05244755244755245	57	0.07519788918205805	T	11.80	1.745742	0.30955	0.022696	0.08186	ENSG00000159166	ENST00000503578;ENST00000391967;ENST00000367313	T;T;T	0.42900	0.96;2.78;2.77	4.12	0.451	0.16629	.	0.507095	0.16571	N	0.208618	T	0.01454	0.0047	L	0.46157	1.445	0.21290	N	0.999731	B	0.28291	0.206	B	0.31101	0.124	T	0.09015	-1.0694	10	0.14656	T	0.56	-3.1856	3.2502	0.06811	0.0:0.2377:0.214:0.5483	rs2275866;rs52833503;rs2275866	503	O00515	LAD1_HUMAN	S	154;503;517	ENSP00000422687:T154S;ENSP00000375829:T503S;ENSP00000356282:T517S	ENSP00000356282:T517S	T	-	1	0	LAD1	199618044	0.930000	0.31532	0.954000	0.39281	0.104000	0.19210	0.043000	0.13971	-0.018000	0.14079	0.459000	0.35465	ACT	T|0.942;A|0.058	0.058	strong		0.597	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370707	26370707	+	Silent	SNP	T	T	C	rs9379862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26370707T>C	ENST00000356386.2	+	5	779	c.591T>C	c.(589-591)gaT>gaC	p.D197D	BTN3A2_ENST00000527422.1_Silent_p.D197D|BTN3A2_ENST00000508906.2_Silent_p.D155D|BTN3A2_ENST00000396934.3_Silent_p.D174D|BTN3A2_ENST00000396948.1_Silent_p.D197D|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000377708.2_Silent_p.D197D	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	197					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						TGGTTGCAGATGGAGTGGGCC	0.567													t|||	1182	0.236022	0.3109	0.1931	5008	,	,		18947	0.124		0.2396	False		,,,				2504	0.2771				p.D197D		Atlas-SNP	.											.	BTN3A2	44	.	0			c.T591C						PASS	.	C	,,,,	1355,3051		203,949,1051	153.0	143.0	146.0		591,591,522,465,591	-4.6	0.0	6	dbSNP_119	146	2112,6488		249,1614,2437	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	452,2563,3488	CC,CT,TT		24.5581,30.7535,26.6569	,,,,	197/335,197/335,174/312,155/293,197/335	26370707	3467,9539	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			TGCAGATGGAGTG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.591T>C	6.37:g.26370707T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	347	169	0.487032	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			T|0.752;C|0.248	0.248	strong		0.567	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
CMSS1	84319	hgsc.bcm.edu	37	3	99886662	99886662	+	Missense_Mutation	SNP	G	G	A	rs11537816	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:99886662G>A	ENST00000421999.2	+	6	642	c.496G>A	c.(496-498)Gtc>Atc	p.V166I	CMSS1_ENST00000489081.1_Missense_Mutation_p.V148I	NM_032359.3	NP_115735.2	Q9BQ75	CMS1_HUMAN	cms1 ribosomal small subunit homolog (yeast)	166			V -> I (in dbSNP:rs11537816).				poly(A) RNA binding (GO:0044822)										CAGCTCGGCCGTCCGAGCCCT	0.418													A|||	602	0.120208	0.0242	0.2233	5008	,	,		16980	0.0417		0.162	False		,,,				2504	0.2147				p.V166I		Atlas-SNP	.											.	.	.	.	0			c.G496A						PASS	.	A	ILE/VAL,ILE/VAL	203,4203	808.0+/-415.9	7,189,2007	133.0	138.0	137.0		442,496	-8.8	0.1	3	dbSNP_120	137	1526,7074	747.1+/-407.3	135,1256,2909	yes	missense,missense	C3orf26	NM_001167924.1,NM_032359.3	29,29	142,1445,4916	AA,AG,GG		17.7442,4.6074,13.2939	benign,benign	148/262,166/280	99886662	1729,11277	2203	4300	6503	SO:0001583	missense	84319	exon6			TCGGCCGTCCGAG		CCDS2935.1, CCDS54618.1	3q12.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000184220	ENSG00000184220			28666	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 26"""	C3orf26		12477932	Standard	NM_032359		Approved	MGC4308	uc003dtl.3	Q9BQ75	OTTHUMG00000159054	ENST00000421999.2:c.496G>A	3.37:g.99886662G>A	ENSP00000410396:p.Val166Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_032359	A8K5S7|B4DUM1|E9PHS3	Missense_Mutation	SNP	ENST00000421999.2	37	CCDS2935.1	235|235	0.10760073260073261|0.10760073260073261	21|21	0.042682926829268296|0.042682926829268296	67|67	0.1850828729281768|0.1850828729281768	18|18	0.03146853146853147|0.03146853146853147	129|129	0.17018469656992086|0.17018469656992086	A|A	11.24|11.24	1.581789|1.581789	0.28180|0.28180	0.046074|0.046074	0.177442|0.177442	ENSG00000184220|ENSG00000184220	ENST00000497345|ENST00000421999;ENST00000489081;ENST00000478909	.|T;T;T	.|0.31769	.|1.48;1.48;1.48	5.62|5.62	-8.83|-8.83	0.00806|0.00806	.|DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	.|0.617522	.|0.17485	.|N	.|0.172544	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11789|0.11789	0.175|0.175	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.12630	.|0.006	.|B	.|0.06405	.|0.002	T|T	0.23368|0.23368	-1.0190|-1.0190	4|8	.|.	.|.	.|.	.|.	14.5932|14.5932	0.68386|0.68386	0.1416:0.2756:0.5828:0.0|0.1416:0.2756:0.5828:0.0	rs11537816;rs11537816|rs11537816;rs11537816	.|166	.|Q9BQ75	.|CC026_HUMAN	H|I	74|166;148;122	.|ENSP00000410396:V166I;ENSP00000419161:V148I;ENSP00000417293:V122I	.|.	R|V	+|+	2|1	0|0	C3orf26|C3orf26	101369352|101369352	0.000000|0.000000	0.05858|0.05858	0.082000|0.082000	0.20525|0.20525	0.663000|0.663000	0.39108|0.39108	-0.461000|-0.461000	0.06712|0.06712	-1.984000|-1.984000	0.00985|0.00985	-1.760000|-1.760000	0.00671|0.00671	CGT|GTC	G|0.873;A|0.127	0.127	strong		0.418	CMSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353060.1	NM_032359	
OR6S1	341799	hgsc.bcm.edu	37	14	21109305	21109305	+	Silent	SNP	G	G	A	rs376650163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21109305G>A	ENST00000320704.3	-	1	545	c.546C>T	c.(544-546)tgC>tgT	p.C182C		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		GGCCACTGTCGCAGAAGAAGT	0.587													G|||	2	0.000399361	0.0	0.0	5008	,	,		21782	0.001		0.001	False		,,,				2504	0.0				p.C182C		Atlas-SNP	.											OR6S1,NS,carcinoma,0,1	OR6S1	49	1	0			c.C546T						scavenged	.	G		0,4406		0,0,2203	64.0	62.0	62.0		546	0.8	1.0	14		62	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	OR6S1	NM_001001968.1		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		182/332	21109305	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	341799	exon1			ACTGTCGCAGAAG	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.546C>T	14.37:g.21109305G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	122	2	0.0163934	NM_001001968	Q6IFJ9	Silent	SNP	ENST00000320704.3	37	CCDS32038.1																																																																																			.	.	weak		0.587	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
HEXB	3074	hgsc.bcm.edu	37	5	73992881	73992881	+	Missense_Mutation	SNP	A	A	G	rs10805890	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:73992881A>G	ENST00000261416.7	+	5	736	c.619A>G	c.(619-621)Att>Gtt	p.I207V	HEXB_ENST00000511181.1_5'UTR	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	207			I -> V (probable polymorphism; dbSNP:rs10805890). {ECO:0000269|PubMed:1720305, ECO:0000269|PubMed:8950198}.		astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		AGGAATTTTGATTGATACATC	0.303													A|||	643	0.128395	0.0091	0.1988	5008	,	,		17389	0.2609		0.1461	False		,,,				2504	0.0849				p.I207V	Melanoma(66;841 1270 13391 18706 27225)	Atlas-SNP	.											.	HEXB	34	.	0			c.A619G	GRCh37	CM910221	HEXB	M	rs10805890	PASS	.	A	VAL/ILE	160,4246	106.0+/-144.5	3,154,2046	92.0	95.0	94.0		619	4.8	1.0	5	dbSNP_120	94	1498,7102	283.2+/-296.0	141,1216,2943	yes	missense	HEXB	NM_000521.3	29	144,1370,4989	GG,GA,AA		17.4186,3.6314,12.748	benign	207/557	73992881	1658,11348	2203	4300	6503	SO:0001583	missense	3074	exon5			ATTTTGATTGATA	M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.619A>G	5.37:g.73992881A>G	ENSP00000261416:p.Ile207Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_000521		Missense_Mutation	SNP	ENST00000261416.7	37	CCDS4022.1	329	0.15064102564102563	7	0.014227642276422764	64	0.17679558011049723	147	0.256993006993007	111	0.14643799472295516	A	11.93	1.786183	0.31593	0.036314	0.174186	ENSG00000049860	ENST00000261416	D	0.90504	-2.68	6.07	4.85	0.62838	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);Glycoside hydrolase, family 20 (1);	0.055692	0.64402	D	0.000001	T	0.00073	0.0002	L	0.41124	1.26	0.09310	P	1.0	B	0.30482	0.281	B	0.35770	0.21	T	0.06899	-1.0801	9	0.33940	T	0.23	-33.5887	7.9195	0.29837	0.6433:0.2356:0.0:0.1211	rs10805890;rs56696079;rs10805890	207	P07686	HEXB_HUMAN	V	207	ENSP00000261416:I207V	ENSP00000261416:I207V	I	+	1	0	HEXB	74028637	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	1.232000	0.32636	2.330000	0.79161	0.477000	0.44152	ATT	A|0.860;G|0.140	0.140	strong		0.303	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521	
COL22A1	169044	hgsc.bcm.edu	37	8	139701209	139701209	+	Missense_Mutation	SNP	G	G	T	rs4909444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:139701209G>T	ENST00000303045.6	-	37	3259	c.2813C>A	c.(2812-2814)gCt>gAt	p.A938D	COL22A1_ENST00000435777.1_Missense_Mutation_p.A938D|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	938	Collagen-like 8.|Gly-rich.|Pro-rich.		A -> D (in dbSNP:rs4909444). {ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GAGGCCGGGAGCACCCTGTGG	0.517										HNSCC(7;0.00092)			G|||	1461	0.291733	0.2534	0.3012	5008	,	,		19616	0.1835		0.34	False		,,,				2504	0.3988				p.A938D		Atlas-SNP	.											.	COL22A1	390	.	0			c.C2813A						PASS	.	G	ASP/ALA	1269,3137	434.1+/-343.8	198,873,1132	130.0	118.0	122.0		2813	2.7	0.4	8	dbSNP_111	122	2821,5779	444.9+/-360.8	474,1873,1953	yes	missense	COL22A1	NM_152888.1	126	672,2746,3085	TT,TG,GG		32.8023,28.8016,31.447	benign	938/1627	139701209	4090,8916	2203	4300	6503	SO:0001583	missense	169044	exon37			CCGGGAGCACCCT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2813C>A	8.37:g.139701209G>T	ENSP00000303153:p.Ala938Asp	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	638	0.29212454212454214	142	0.2886178861788618	116	0.32044198895027626	119	0.20804195804195805	261	0.34432717678100266	G	0.686	-0.796225	0.02862	0.288016	0.328023	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.93488	-3.23;-3.23	3.63	2.74	0.32292	.	0.979358	0.08299	U	0.967174	T	0.00012	0.0000	N	0.10760	0.04	0.80722	P	0.0	B;B	0.21905	0.062;0.037	B;B	0.17098	0.017;0.007	T	0.17837	-1.0356	9	0.13470	T	0.59	.	6.2583	0.20885	0.138:0.0:0.862:0.0	rs4909444;rs17445739;rs52804110;rs60475514;rs4909444	938;938	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	D	938;938;651	ENSP00000303153:A938D;ENSP00000387655:A938D	ENSP00000303153:A938D	A	-	2	0	COL22A1	139770391	0.034000	0.19679	0.361000	0.25849	0.153000	0.21895	1.251000	0.32862	2.017000	0.59298	0.542000	0.68232	GCT	G|0.699;T|0.301	0.301	strong		0.517	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653250	121653250	+	Missense_Mutation	SNP	G	G	A	rs61732005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:121653250G>A	ENST00000393386.2	+	12	4561	c.4150G>A	c.(4150-4152)Gat>Aat	p.D1384N	PTPRZ1_ENST00000483028.1_3'UTR|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1384					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TCCCCACAGAGATGGTTCTGT	0.438													G|||	393	0.0784744	0.0567	0.0447	5008	,	,		22228	0.2093		0.0557	False		,,,				2504	0.0204				p.D1384N		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G4150A						PASS	.	G	,,ASN/ASP	342,4064	179.4+/-207.9	9,324,1870	169.0	160.0	163.0		,,4150	3.3	0.0	7	dbSNP_129	163	646,7954	165.5+/-217.6	23,600,3677	yes	intron,intron,missense	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,23	32,924,5547	AA,AG,GG		7.5116,7.7621,7.5965	,,benign	,,1384/2316	121653250	988,12018	2203	4300	6503	SO:0001583	missense	5803	exon12			CACAGAGATGGTT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4150G>A	7.37:g.121653250G>A	ENSP00000377047:p.Asp1384Asn	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	180	96	0.533333	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	196	0.08974358974358974	21	0.042682926829268296	18	0.049723756906077346	117	0.20454545454545456	40	0.052770448548812667	G	12.01	1.808443	0.31961	0.077621	0.075116	ENSG00000106278	ENST00000393386	T	0.45276	0.9	5.1	3.29	0.37713	.	0.832539	0.10667	N	0.648025	T	0.00039	0.0001	L	0.31294	0.92	0.54753	P	1.0999999999983245E-5	B	0.06786	0.001	B	0.04013	0.001	T	0.08391	-1.0724	9	0.46703	T	0.11	.	7.9809	0.30183	0.1449:0.1332:0.7218:0.0	rs61732005	1384	P23471	PTPRZ_HUMAN	N	1384	ENSP00000377047:D1384N	ENSP00000377047:D1384N	D	+	1	0	PTPRZ1	121440486	0.861000	0.29849	0.007000	0.13788	0.897000	0.52465	3.354000	0.52254	0.732000	0.32470	0.555000	0.69702	GAT	G|0.926;A|0.074	0.074	strong		0.438	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
GBP4	115361	hgsc.bcm.edu	37	1	89652071	89652071	+	Missense_Mutation	SNP	T	T	C	rs386633303|rs561042	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89652071T>C	ENST00000355754.6	-	10	1749	c.1652A>G	c.(1651-1653)gAg>gGg	p.E551G	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	551			E -> G (in dbSNP:rs561042).|E -> K (in dbSNP:rs561037).	LEE -> MER (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TTCCCTTTCCTCCTCCAACTT	0.493													T|||	1790	0.357428	0.143	0.3141	5008	,	,		18881	0.3978		0.4881	False		,,,				2504	0.502				p.E551G		Atlas-SNP	.											GBP4,NS,carcinoma,+1,1	GBP4	89	1	0			c.A1652G						PASS	.	T	GLY/GLU	34,4372		5,24,2174	194.0	136.0	156.0		1652	-6.3	0.0	1	dbSNP_83	156	186,8414		23,140,4137	yes	missense	GBP4	NM_052941.4	98	28,164,6311	CC,CT,TT		2.1628,0.7717,1.6915	benign	551/641	89652071	220,12786	2203	4300	6503	SO:0001583	missense	115361	exon10			CTTTCCTCCTCCA	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1652A>G	1.37:g.89652071T>C	ENSP00000359490:p.Glu551Gly	Somatic	427	2	0.00468384		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.484517	0.26598	0.007717	0.021628	ENSG00000162654	ENST00000355754	T	0.02216	4.39	4.14	-6.34	0.01982	Guanylate-binding protein, C-terminal (3);	1.061500	0.07205	N	0.858069	T	0.01156	0.0038	M	0.73962	2.25	0.80722	P	0.0	B	0.23990	0.095	B	0.33121	0.158	T	0.44697	-0.9311	9	0.52906	T	0.07	.	4.4945	0.11830	0.1154:0.1531:0.1208:0.6107	rs561042;rs34567676;rs52816340;rs561042	551	Q96PP9	GBP4_HUMAN	G	551	ENSP00000359490:E551G	ENSP00000359490:E551G	E	-	2	0	GBP4	89424659	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.078000	0.01370	-1.292000	0.02366	-0.232000	0.12228	GAG	T|0.620;C|0.380	0.380	strong		0.493	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
TDO2	6999	hgsc.bcm.edu	37	4	156830085	156830085	+	Missense_Mutation	SNP	G	G	A	rs375801975		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:156830085G>A	ENST00000536354.2	+	5	414	c.350G>A	c.(349-351)cGa>cAa	p.R117Q		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase											breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		CGGATGCACCGAGTGTCAGTG	0.443																																					p.R117Q	Colon(57;928 1036 2595 6946 26094)	Atlas-SNP	.											.	TDO2	51	.	0			c.G350A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	112.0	100.0	104.0		350	5.3	0.9	4		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	TDO2	NM_005651.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	117/407	156830085	1,13005	2203	4300	6503	SO:0001583	missense	6999	exon5			TGCACCGAGTGTC		CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.350G>A	4.37:g.156830085G>A	ENSP00000444788:p.Arg117Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_005651		Missense_Mutation	SNP	ENST00000536354.2	37	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453794	0.96223	0.0	1.16E-4	ENSG00000151790	ENST00000506072;ENST00000507590;ENST00000536354	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.89791	0.6817	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92677	0.6155	9	0.87932	D	0	-12.6575	19.4005	0.94627	0.0:0.0:1.0:0.0	.	117	P48775	T23O_HUMAN	Q	10;10;117	.	ENSP00000281525:R117Q	R	+	2	0	TDO2	157049535	1.000000	0.71417	0.852000	0.33557	0.908000	0.53690	9.388000	0.97237	2.663000	0.90544	0.650000	0.86243	CGA	.	.	weak		0.443	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651	
AQP4	361	hgsc.bcm.edu	37	18	24442227	24442227	+	Silent	SNP	C	C	T	rs72557968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:24442227C>T	ENST00000383168.4	-	2	494	c.366G>A	c.(364-366)caG>caA	p.Q122Q	AQP4-AS1_ENST00000579964.1_RNA|AQP4_ENST00000440832.3_Silent_p.Q100Q|AQP4-AS1_ENST00000582605.1_RNA|AQP4_ENST00000581374.1_Silent_p.Q100Q|AQP4_ENST00000583022.1_5'Flank	NM_001650.4|NM_004028.3	NP_001641.1|NP_004019.1	P55087	AQP4_HUMAN	aquaporin 4	122					carbon dioxide transport (GO:0015670)|cellular response to estradiol stimulus (GO:0071392)|cellular response to interferon-gamma (GO:0071346)|female pregnancy (GO:0007565)|hyperosmotic salinity response (GO:0042538)|multicellular organismal water homeostasis (GO:0050891)|protein homooligomerization (GO:0051260)|renal water absorption (GO:0070295)|response to glucocorticoid (GO:0051384)|response to radiation (GO:0009314)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)	porin activity (GO:0015288)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(2)|large_intestine(3)|lung(5)|skin(1)	11	all_cancers(21;0.0172)|Lung NSC(5;0.00299)|all_lung(6;0.00747)|Ovarian(20;0.124)					CCCCCAGGCACTGGGCTGCGA	0.562													C|||	158	0.0315495	0.0113	0.0173	5008	,	,		18992	0.004		0.0219	False		,,,				2504	0.1074				p.Q122Q		Atlas-SNP	.											.	AQP4	27	.	0			c.G366A						PASS	.	C	,	60,4346	57.4+/-93.9	0,60,2143	82.0	75.0	77.0		366,300	5.6	1.0	18	dbSNP_130	77	140,8460	69.0+/-131.5	1,138,4161	no	coding-synonymous,coding-synonymous	AQP4	NM_001650.4,NM_004028.3	,	1,198,6304	TT,TC,CC		1.6279,1.3618,1.5378	,	122/324,100/302	24442227	200,12806	2203	4300	6503	SO:0001819	synonymous_variant	361	exon2			CAGGCACTGGGCT	U63622	CCDS11889.1, CCDS58617.1	18q11.2-q12.1	2005-09-20			ENSG00000171885	ENSG00000171885		"""Ion channels / Aquaporins"""	637	protein-coding gene	gene with protein product		600308				7528931	Standard	NM_001650		Approved	MIWC	uc002kwa.3	P55087	OTTHUMG00000131955	ENST00000383168.4:c.366G>A	18.37:g.24442227C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001650	P78564	Silent	SNP	ENST00000383168.4	37	CCDS11889.1																																																																																			C|0.983;T|0.017	0.017	strong		0.562	AQP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254914.2	NM_001650, NM_004028	
SNAPC3	6619	hgsc.bcm.edu	37	9	15422888	15422888	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:15422888G>C	ENST00000380821.3	+	1	187	c.11G>C	c.(10-12)gGa>gCa	p.G4A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	4					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		ATGGCTGAAGGAAGCCGAGGT	0.632																																					p.G4A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.G11C						PASS	.						27.0	24.0	25.0					9																	15422888		2093	4148	6241	SO:0001583	missense	6619	exon1			CTGAAGGAAGCCG	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.11G>C	9.37:g.15422888G>C	ENSP00000370200:p.Gly4Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.977930	0.34942	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	T	0.41400	1.0	5.13	1.96	0.26148	.	0.722427	0.13995	N	0.348553	T	0.29620	0.0739	L	0.36672	1.1	0.18873	N	0.999989	B;B	0.19583	0.013;0.037	B;B	0.18561	0.022;0.02	T	0.22417	-1.0217	10	0.54805	T	0.06	-21.5863	5.523	0.16943	0.5091:0.0:0.4909:0.0	.	4;4	B4DDR9;Q92966	.;SNPC3_HUMAN	A	4	ENSP00000370200:G4A	ENSP00000370185:G4A	G	+	2	0	SNAPC3	15412888	0.013000	0.17824	0.128000	0.21923	0.010000	0.07245	1.978000	0.40598	0.594000	0.29761	0.462000	0.41574	GGA	.	.	none		0.632	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
DOCK6	57572	hgsc.bcm.edu	37	19	11326119	11326119	+	Silent	SNP	A	A	G	rs2304155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11326119A>G	ENST00000294618.7	-	32	4061	c.4050T>C	c.(4048-4050)aaT>aaC	p.N1350N	CTC-510F12.2_ENST00000588634.1_RNA|DOCK6_ENST00000319867.7_Silent_p.N689N	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1350					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCCAGCGCACATTCTCCGGAT	0.557													G|||	2508	0.500799	0.41	0.5101	5008	,	,		18057	0.5119		0.6292	False		,,,				2504	0.4734				p.N1350N		Atlas-SNP	.											.	DOCK6	104	.	0			c.T4050C						PASS	.	G		1911,2141		456,999,571	53.0	52.0	53.0		4050	-7.4	0.2	19	dbSNP_100	53	5217,3123		1623,1971,576	no	coding-synonymous	DOCK6	NM_020812.2		2079,2970,1147	GG,GA,AA		37.446,47.1619,42.479		1350/2048	11326119	7128,5264	2026	4170	6196	SO:0001819	synonymous_variant	57572	exon32			GCGCACATTCTCC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4050T>C	19.37:g.11326119A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			G|0.539;N|0.001	0.539	strong		0.557	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503002	140503002	+	Silent	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140503002C>A	ENST00000194152.1	+	1	1422	c.1422C>A	c.(1420-1422)gcC>gcA	p.A474A	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	474	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A474A(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTGTCAGCGCCACAGACAGAG	0.662																																					p.A474A		Atlas-SNP	.											PCDHB4,leg,malignant_melanoma,0,1	PCDHB4	177	1	1	Substitution - coding silent(1)	skin(1)	c.C1422A						scavenged	.						48.0	52.0	51.0					5																	140503002		2201	4295	6496	SO:0001819	synonymous_variant	56131	exon1			CAGCGCCACAGAC	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1422C>A	5.37:g.140503002C>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	180	16	0.0888889	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			C|0.912;A|0.088	0.088	strong		0.662	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
OR10H1	26539	hgsc.bcm.edu	37	19	15918201	15918201	+	Missense_Mutation	SNP	A	A	G	rs201868341	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15918201A>G	ENST00000334920.2	-	1	735	c.647T>C	c.(646-648)cTc>cCc	p.L216P		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	216						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L216P(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						ATAGGAGAGGAGGATGAGGAG	0.577																																					p.L216P		Atlas-SNP	.											OR10H1,NS,carcinoma,0,1	OR10H1	59	1	1	Substitution - Missense(1)	ovary(1)	c.T647C						scavenged	.						97.0	79.0	85.0					19																	15918201		2203	4294	6497	SO:0001583	missense	26539	exon1			GAGAGGAGGATGA	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.647T>C	19.37:g.15918201A>G	ENSP00000335596:p.Leu216Pro	Somatic	259	2	0.00772201		WXS	Illumina HiSeq	Phase_I	302	35	0.115894	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	19	0.0086996336996337	2	0.0040650406504065045	4	0.011049723756906077	3	0.005244755244755245	10	0.013192612137203167	.	13.80	2.346237	0.41599	.	.	ENSG00000186723	ENST00000334920	T	0.00277	8.34	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.158488	0.29660	N	0.011531	T	0.00580	0.0019	M	0.90814	3.15	0.38102	D	0.937307	D	0.69078	0.997	D	0.72075	0.976	T	0.62397	-0.6863	10	0.72032	D	0.01	.	12.5636	0.56297	1.0:0.0:0.0:0.0	.	216	Q9Y4A9	O10H1_HUMAN	P	216	ENSP00000335596:L216P	ENSP00000335596:L216P	L	-	2	0	OR10H1	15779201	0.049000	0.20398	0.996000	0.52242	0.682000	0.39822	3.435000	0.52849	1.853000	0.53794	0.523000	0.50628	CTC	A|0.897;G|0.103	0.103	strong		0.577	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
CHL1	10752	hgsc.bcm.edu	37	3	391100	391100	+	Missense_Mutation	SNP	A	A	G	rs13060847	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:391100A>G	ENST00000256509.2	+	10	1549	c.907A>G	c.(907-909)Aca>Gca	p.T303A	CHL1_ENST00000397491.2_Missense_Mutation_p.T287A	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	785	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GGGGAGAGAAACAAAAGAAAA	0.383													A|||	4262	0.851038	0.4644	0.951	5008	,	,		19394	1.0		0.996	False		,,,				2504	1.0				p.T303A		Atlas-SNP	.											.	CHL1	242	.	0			c.A907G						PASS	.	A	ALA/THR	2308,2098	601.5+/-389.7	599,1110,494	71.0	72.0	72.0		907	4.1	0.9	3	dbSNP_121	72	8587,13	818.4+/-406.9	4287,13,0	yes	missense	CHL1	NM_006614.2	58	4886,1123,494	GG,GA,AA		0.1512,47.6169,16.231	benign	303/1225	391100	10895,2111	2203	4300	6503	SO:0001583	missense	10752	exon8			AGAGAAACAAAAG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.907A>G	3.37:g.391100A>G	ENSP00000256509:p.Thr303Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	1910	0.8745421245421245	236	0.4796747967479675	344	0.9502762430939227	572	1.0	758	1.0	A	4.423	0.078292	0.08485	0.523831	0.998488	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.66460	-0.21;-0.21	5.22	4.05	0.47172	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.541980	0.21246	N	0.077721	T	0.00012	0.0000	L	0.49778	1.585	0.58432	P	5.000000000032756E-6	B;B	0.23990	0.095;0.016	B;B	0.29663	0.105;0.02	T	0.47032	-0.9148	9	0.14656	T	0.56	.	5.6283	0.17495	0.8278:0.0:0.1722:0.0	rs13060847;rs52817366;rs60322500;rs13060847	287;303	O00533;O00533-2	CHL1_HUMAN;.	A	303;287	ENSP00000256509:T303A;ENSP00000380628:T287A	ENSP00000256509:T303A	T	+	1	0	CHL1	366100	0.017000	0.18338	0.946000	0.38457	0.780000	0.44128	0.891000	0.28309	2.106000	0.64143	0.528000	0.53228	ACA	A|0.166;G|0.834	0.834	strong		0.383	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
XPO7	23039	hgsc.bcm.edu	37	8	21833965	21833965	+	Silent	SNP	C	C	T	rs2306641	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:21833965C>T	ENST00000252512.9	+	7	796	c.696C>T	c.(694-696)atC>atT	p.I232I	XPO7_ENST00000518017.1_3'UTR|XPO7_ENST00000434536.1_Silent_p.I241I|XPO7_ENST00000433566.4_Silent_p.I233I	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	232					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TTGACTTCATCGGCACTTCCA	0.478													C|||	1473	0.294129	0.2186	0.2104	5008	,	,		18198	0.4008		0.4563	False		,,,				2504	0.1789				p.I232I		Atlas-SNP	.											.	XPO7	79	.	0			c.C696T						PASS	.	C		1090,2952		163,764,1094	153.0	150.0	151.0		696	0.8	1.0	8	dbSNP_100	151	3545,4903		757,2031,1436	no	coding-synonymous	XPO7	NM_015024.4		920,2795,2530	TT,TC,CC		41.9626,26.9668,37.1097		232/1088	21833965	4635,7855	2021	4224	6245	SO:0001819	synonymous_variant	23039	exon7			CTTCATCGGCACT	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"""Exportins"""	14108	protein-coding gene	gene with protein product		606140	"""RAN binding protein 16"""	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.696C>T	8.37:g.21833965C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_015024	O94846|Q6PJK9|Q8NEK7	Silent	SNP	ENST00000252512.9	37	CCDS47818.1																																																																																			C|0.655;T|0.345	0.345	strong		0.478	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	
C5orf60	285679	hgsc.bcm.edu	37	5	179069912	179069912	+	Missense_Mutation	SNP	C	C	T	rs75942553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:179069912C>T	ENST00000448248.2	-	4	666	c.641G>A	c.(640-642)aGc>aAc	p.S214N	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	214	Ser-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						TGATAGGGTGCTCGCAGGTGG	0.602													-|||	305	0.0609026	0.0257	0.0663	5008	,	,		17687	0.0843		0.0755	False		,,,				2504	0.0654				p.S214N		Atlas-SNP	.											.	C5orf60	24	.	0			c.G641A						PASS	.	C	ASN/SER	39,1345		0,39,653	72.0	73.0	72.0		641	0.1	0.0	5	dbSNP_131	72	277,2905		14,249,1328	no	missense	C5orf60	NM_001142306.1	46	14,288,1981	TT,TC,CC		8.7052,2.8179,6.9207	probably-damaging	214/278	179069912	316,4250	692	1591	2283	SO:0001583	missense	285679	exon4			AGGGTGCTCGCAG	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.641G>A	5.37:g.179069912C>T	ENSP00000404583:p.Ser214Asn	Somatic	453	0	0		WXS	Illumina HiSeq	Phase_I	511	338	0.661448	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	132	0.06043956043956044	14	0.028455284552845527	22	0.06077348066298342	44	0.07692307692307693	52	0.06860158311345646	c	10.63	1.403766	0.25291	0.028179	0.087052	ENSG00000204661	ENST00000448248	T	0.24723	1.84	0.118	0.118	0.14667	.	.	.	.	.	T	0.00875	0.0029	L	0.42245	1.32	0.09310	N	1	P;P	0.51449	0.945;0.945	P;P	0.51866	0.682;0.682	T	0.07309	-1.0779	8	0.10902	T	0.67	.	.	.	.	.	214;214	A6NFR6-2;A6NFR6-4	.;.	N	214	ENSP00000404583:S214N	ENSP00000404583:S214N	S	-	2	0	C5orf60	179002518	0.065000	0.20965	0.044000	0.18714	0.025000	0.11179	0.197000	0.17197	0.191000	0.20236	0.194000	0.17425	AGC	C|0.934;T|0.066	0.066	strong		0.602	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
ARHGAP40	343578	hgsc.bcm.edu	37	20	37272551	37272551	+	Missense_Mutation	SNP	A	A	C	rs369137106		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:37272551A>C	ENST00000373345.4	+	11	1576	c.1408A>C	c.(1408-1410)Acg>Ccg	p.T470P		NM_001164431.1	NP_001157903.1	Q5TG30	RHG40_HUMAN	Rho GTPase activating protein 40	470					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)	1						TCTGCTGTGGACGGTGAGTGC	0.637																																					p.T522P		Atlas-SNP	.											.	ARHGAP40	50	.	0			c.A1564C						PASS	.	A	PRO/THR	0,1384		0,0,692	87.0	88.0	88.0		1564	2.0	1.0	20		88	2,3180		0,2,1589	no	missense	ARHGAP40	NM_001164431.1	38	0,2,2281	CC,CA,AA		0.0629,0.0,0.0438		522/675	37272551	2,4564	692	1591	2283	SO:0001583	missense	343578	exon11			CTGTGGACGGTGA	AL035419		20q11.23	2011-06-29	2010-04-14	2010-04-14	ENSG00000124143	ENSG00000124143		"""Rho GTPase activating proteins"""	16226	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 95"""	C20orf95			Standard	NM_001164431		Approved	dJ1100H13.4	uc021wdn.1	Q5TG30	OTTHUMG00000032453	ENST00000373345.4:c.1408A>C	20.37:g.37272551A>C	ENSP00000362442:p.Thr470Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001164431		Missense_Mutation	SNP	ENST00000373345.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.61|18.61	3.661798|3.661798	0.67700|0.67700	0.0|0.0	6.29E-4|6.29E-4	ENSG00000124143|ENSG00000124143	ENST00000243967;ENST00000373346|ENST00000373345	.|T	.|0.09350	.|2.99	4.36|4.36	1.97|1.97	0.26223|0.26223	.|.	.|0.231755	.|0.42964	.|D	.|0.000638	T|T	0.17577|0.17577	0.0422|0.0422	M|M	0.70595|0.70595	2.14|2.14	0.38013|0.38013	D|D	0.934613|0.934613	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.03112|0.03112	-1.1071|-1.1071	5|8	.|0.41790	.|T	.|0.15	.|.	5.382|5.382	0.16196|0.16196	0.7236:0.1768:0.0996:0.0|0.7236:0.1768:0.0996:0.0	.|.	.|.	.|.	.|.	A|P	410;1|470	.|ENSP00000362442:T470P	.|ENSP00000362442:T470P	D|T	+|+	2|1	0|0	ARHGAP40|ARHGAP40	36705965|36705965	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.858000|0.858000	0.48976|0.48976	5.511000|5.511000	0.67024|0.67024	0.082000|0.082000	0.17018|0.17018	0.397000|0.397000	0.26171|0.26171	GAC|ACG	.	.	weak		0.637	ARHGAP40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_293123	
LY6G6F	259215	hgsc.bcm.edu	37	6	31675297	31675297	+	Missense_Mutation	SNP	C	C	T	rs805295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31675297C>T	ENST00000375832.4	+	2	137	c.115C>T	c.(115-117)Cct>Tct	p.P39S	LY6G6F_ENST00000556581.1_Missense_Mutation_p.P39S|XXbac-BPG32J3.20_ENST00000461287.1_Intron|MEGT1_ENST00000503322.1_Missense_Mutation_p.P39S	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	39	Ig-like V-type.		P -> S (in dbSNP:rs805295). {ECO:0000269|PubMed:14656967}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						TCCCTCACCACCTACTCTACA	0.597													C|||	618	0.123403	0.233	0.0893	5008	,	,		19413	0.1488		0.0358	False		,,,				2504	0.0634				p.P39S		Atlas-SNP	.											.	LY6G6F	23	.	0			c.C115T						PASS	.	C	SER/PRO	883,3523	339.4+/-305.8	94,695,1414	53.0	43.0	47.0		115	2.9	0.3	6	dbSNP_86	47	290,8310	106.6+/-167.4	6,278,4016	yes	missense	LY6G6F	NM_001003693.1	74	100,973,5430	TT,TC,CC		3.3721,20.0409,9.0189	benign	39/298	31675297	1173,11833	2203	4300	6503	SO:0001583	missense	259215	exon2			TCACCACCTACTC		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"""Immunoglobulin superfamily / V-set domain containing"""	13933	protein-coding gene	gene with protein product		611404	"""chromosome 6 open reading frame 21"""	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.115C>T	6.37:g.31675297C>T	ENSP00000364992:p.Pro39Ser	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	261	163	0.624521	NM_001003693	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	214	0.09798534798534798	99	0.20121951219512196	26	0.0718232044198895	66	0.11538461538461539	23	0.030343007915567283	C	12.30	1.897390	0.33535	0.200409	0.033721	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.03951	3.75;3.75;3.75	4.82	2.89	0.33648	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.638875	0.14723	N	0.302235	T	0.02267	0.0070	M	0.64997	1.995	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.006	T	0.20806	-1.0264	9	0.66056	D	0.02	-5.5563	5.952	0.19253	0.0:0.6988:0.1952:0.106	rs805295;rs6904655;rs17207357;rs52810185;rs60327601;rs805295	39;39	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	S	39	ENSP00000452432:P39S;ENSP00000364992:P39S;ENSP00000421232:P39S	ENSP00000364992:P39S	P	+	1	0	XXbac-BPG32J3.19;LY6G6F	31783276	0.000000	0.05858	0.293000	0.24932	0.847000	0.48162	0.456000	0.21859	1.143000	0.42306	0.591000	0.81541	CCT	C|0.905;T|0.095	0.095	strong		0.597	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693	
AQP12B	653437	hgsc.bcm.edu	37	2	241621908	241621908	+	Missense_Mutation	SNP	G	G	A	rs190367401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:241621908G>A	ENST00000407834.3	-	1	409	c.347C>T	c.(346-348)gCg>gTg	p.A116V		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	104						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		CCCCTGTGCCGCCAGCTTCAG	0.697													N|||	50	0.00998403	0.0	0.0115	5008	,	,		17712	0.0		0.0298	False		,,,				2504	0.0123				p.A116V		Atlas-SNP	.											.	AQP12B	33	.	0			c.C347T						PASS	.		VAL/ALA	20,4386		0,20,2183	31.0	33.0	32.0		347	-1.6	0.7	2		32	197,8401		4,189,4106	no	missense	AQP12B	NM_001102467.1	64	4,209,6289	AA,AG,GG		2.2912,0.4539,1.6687	possibly-damaging	116/308	241621908	217,12787	2203	4299	6502	SO:0001583	missense	653437	exon1			TGTGCCGCCAGCT	BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.347C>T	2.37:g.241621908G>A	ENSP00000384894:p.Ala116Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	51	31	0.607843	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	28	0.01282051282051282	0	0.0	5	0.013812154696132596	0	0.0	23	0.030343007915567283	.	6.357	0.434000	0.12045	0.004539	0.022912	ENSG00000185176	ENST00000407834	T	0.11277	2.79	2.84	-1.64	0.08318	.	1.118960	0.06641	N	0.760999	T	0.02649	0.0080	M	0.64997	1.995	0.09310	N	1	B	0.22276	0.067	B	0.16722	0.016	T	0.42344	-0.9457	10	0.02654	T	1	0.1107	4.173	0.10339	0.465:0.1803:0.3547:0.0	.	116	A6NM10-2	.	V	116	ENSP00000384894:A116V	ENSP00000384894:A116V	A	-	2	0	AQP12B	241270581	0.000000	0.05858	0.676000	0.29932	0.273000	0.26683	0.088000	0.14979	-0.391000	0.07763	-0.370000	0.07254	GCG	G|0.987;A|0.013	0.013	strong		0.697	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
MUS81	80198	hgsc.bcm.edu	37	11	65629932	65629932	+	Silent	SNP	T	T	C	rs659857|rs386754402	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65629932T>C	ENST00000308110.4	+	6	886	c.537T>C	c.(535-537)gcT>gcC	p.A179A	MUS81_ENST00000533035.1_Silent_p.A104A|CFL1_ENST00000534769.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	179	Interaction with BLM.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		CTGGGAGTGCTCGACCCTGGC	0.617								Homologous recombination					T|||	2144	0.428115	0.2012	0.4063	5008	,	,		15874	0.3323		0.668	False		,,,				2504	0.6022				p.A179A		Atlas-SNP	.											.	MUS81	68	.	0			c.T537C						PASS	.	T		1117,3285	382.5+/-324.5	153,811,1237	76.0	62.0	67.0		537	-1.0	0.0	11	dbSNP_83	67	5701,2891	661.2+/-401.8	1893,1915,488	no	coding-synonymous	MUS81	NM_025128.4		2046,2726,1725	CC,CT,TT		33.6476,25.3748,47.5296		179/552	65629932	6818,6176	2201	4296	6497	SO:0001819	synonymous_variant	80198	exon6			GAGTGCTCGACCC		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.537T>C	11.37:g.65629932T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_025128	Q9H7D9	Silent	SNP	ENST00000308110.4	37	CCDS8115.1	974	0.445970695970696	117	0.23780487804878048	175	0.48342541436464087	174	0.3041958041958042	508	0.6701846965699209	T	12.54	1.967880	0.34754	0.253748	0.663524	ENSG00000172732	ENST00000529374;ENST00000530111	.	.	.	5.29	-0.966	0.10320	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.38542	-0.9656	3	.	.	.	4.4053	0.8643	0.01200	0.1549:0.2443:0.1596:0.4411	rs659857;rs17850597;rs659857	.	.	.	P	104;75	.	.	S	+	1	0	MUS81	65386508	0.000000	0.05858	0.000000	0.03702	0.804000	0.45430	-0.653000	0.05360	0.033000	0.15463	0.459000	0.35465	TCG	T|0.520;G|0.002	.	strong		0.617	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
PXMP2	5827	hgsc.bcm.edu	37	12	133272470	133272470	+	Splice_Site	SNP	G	G	T	rs74727297	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133272470G>T	ENST00000317479.3	+	3	302	c.237G>T	c.(235-237)ggG>ggT	p.G79G	PXMP2_ENST00000545677.1_Intron|PXMP2_ENST00000428960.2_5'UTR|PXMP2_ENST00000539093.1_Intron|PXMP2_ENST00000543589.1_Intron|RP13-672B3.2_ENST00000537262.1_Intron	NM_018663.1	NP_061133.1	Q9NR77	PXMP2_HUMAN	peroxisomal membrane protein 2, 22kDa	79						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|protein complex (GO:0043234)				large_intestine(1)|liver(2)|lung(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.86e-08)|Epithelial(86;2.47e-07)|all cancers(50;6.85e-06)		GGGGCCTCAGGTTCTTCTTCA	0.577													G|||	283	0.0565096	0.0045	0.0447	5008	,	,		16917	0.1032		0.1004	False		,,,				2504	0.0419				p.G79G		Atlas-SNP	.											.	PXMP2	15	.	0			c.G237T						PASS	.	G		70,4336	64.7+/-102.0	0,70,2133	54.0	54.0	54.0		237	-2.4	0.8	12	dbSNP_131	54	920,7680	204.7+/-247.3	60,800,3440	yes	coding-synonymous-near-splice	PXMP2	NM_018663.1		60,870,5573	TT,TG,GG		10.6977,1.5887,7.6119		79/196	133272470	990,12016	2203	4300	6503	SO:0001630	splice_region_variant	5827	exon3			CCTCAGGTTCTTC		CCDS9279.1	12q24	2010-08-18	2002-08-29		ENSG00000176894	ENSG00000176894			9716	protein-coding gene	gene with protein product			"""peroxisomal membrane protein 2 (22kD)"""			11590176	Standard	NM_018663		Approved	PMP22	uc001ukt.3	Q9NR77	OTTHUMG00000168019	ENST00000317479.3:c.237-1G>T	12.37:g.133272470G>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_018663		Silent	SNP	ENST00000317479.3	37	CCDS9279.1																																																																																			G|0.928;T|0.072	0.072	strong		0.577	PXMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397553.1	NM_018663	Silent
SBSN	374897	hgsc.bcm.edu	37	19	36018272	36018272	+	Silent	SNP	C	C	T	rs12461911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36018272C>T	ENST00000452271.2	-	1	940	c.912G>A	c.(910-912)gcG>gcA	p.A304A	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	304	Ala/Gly/His-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CGGCCTGCCCCGCAGCATGGT	0.652													c|||	1051	0.209864	0.0371	0.3401	5008	,	,		21069	0.3631		0.1392	False		,,,				2504	0.2658				p.A304A		Atlas-SNP	.											.	SBSN	58	.	0			c.G912A						PASS	.	A	,,	86,1298		3,80,609	29.0	37.0	34.0		912,,	-8.9	0.0	19	dbSNP_120	34	440,2742		33,374,1184	no	coding-synonymous,intron,intron	SBSN	NM_001166034.1,NM_001166035.1,NM_198538.3	,,	36,454,1793	TT,TC,CC		13.8278,6.2139,11.5199	,,	304/591,,	36018272	526,4040	692	1591	2283	SO:0001819	synonymous_variant	374897	exon1			CTGCCCCGCAGCA	AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05							24950	protein-coding gene	gene with protein product		609969				12228223	Standard	NM_198538		Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.912G>A	19.37:g.36018272C>T		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001166034	A8K5J0|E9PBV3	Silent	SNP	ENST00000452271.2	37	CCDS54253.1																																																																																			C|0.795;T|0.205	0.205	strong		0.652	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538	
FAM208A	23272	hgsc.bcm.edu	37	3	56680943	56680943	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:56680943G>A	ENST00000493960.2	-	14	1832	c.1822C>T	c.(1822-1824)Cgg>Tgg	p.R608W	FAM208A_ENST00000431842.2_Missense_Mutation_p.R212W|FAM208A_ENST00000355628.5_Missense_Mutation_p.R608W	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	608							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						ACTTCAGGCCGAAAAATATAG	0.308																																					p.R608W		Atlas-SNP	.											.	FAM208A	113	.	0			c.C1822T						PASS	.						33.0	34.0	34.0					3																	56680943		2199	4297	6496	SO:0001583	missense	23272	exon14			CAGGCCGAAAAAT	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1822C>T	3.37:g.56680943G>A	ENSP00000417509:p.Arg608Trp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	119	27	0.226891	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.944599	0.53079	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.12255	2.7;2.88;2.88	5.38	4.51	0.55191	.	1.076610	0.07180	N	0.853813	T	0.12433	0.0302	N	0.08118	0	0.26200	N	0.979465	D;D;D	0.71674	0.998;0.997;0.997	P;P;P	0.52856	0.711;0.533;0.648	T	0.21177	-1.0253	10	0.66056	D	0.02	1.8924	4.9438	0.13978	0.0785:0.2888:0.5061:0.1265	.	608;608;212	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	W	212;608;608	ENSP00000399410:R212W;ENSP00000417509:R608W;ENSP00000347845:R608W	ENSP00000347845:R608W	R	-	1	2	C3orf63	56655983	0.528000	0.26314	0.955000	0.39395	0.975000	0.68041	1.045000	0.30341	1.505000	0.48720	-0.140000	0.14226	CGG	.	.	none		0.308	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
UGT1A7	54577	hgsc.bcm.edu	37	2	234590970	234590970	+	Missense_Mutation	SNP	T	T	G	rs71405712|rs17868323	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234590970T>G	ENST00000373426.3	+	1	387	c.387T>G	c.(385-387)aaT>aaG	p.N129K	UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	129			N -> K (in allele UGT1A7*2 and allele UGT1A7*3; dbSNP:rs17868323). {ECO:0000269|PubMed:11037804, ECO:0000269|PubMed:11434514, ECO:0000269|PubMed:19204906, ECO:0000269|Ref.3}.		cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	GTTTGTTTAATGACCGAAAAT	0.368													G|||	2886	0.576278	0.6097	0.5072	5008	,	,		19279	0.4385		0.6034	False		,,,				2504	0.6943				p.N129K		Atlas-SNP	.											.	UGT1A7	74	.	0			c.T387G	GRCh37	CM024576	UGT1A7	M	rs17868323	PASS	.						70.0	76.0	74.0					2																	234590970		2201	4300	6501	SO:0001583	missense	54577	exon1			GTTTAATGACCGA	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.387T>G	2.37:g.234590970T>G	ENSP00000362525:p.Asn129Lys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	124	43	0.346774	NM_019077	B8K293|O00473	Missense_Mutation	SNP	ENST00000373426.3	37	CCDS2506.1	1095	0.5013736263736264	265	0.5386178861788617	185	0.511049723756906	220	0.38461538461538464	425	0.5606860158311345	G	0.103	-1.149935	0.01714	.	.	ENSG00000244122	ENST00000373426	T	0.05855	3.38	4.51	-9.01	0.00744	.	.	.	.	.	T	0.00012	0.0000	N	0.04994	-0.135	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42582	-0.9443	8	0.27785	T	0.31	.	8.2035	0.31438	0.0617:0.3453:0.391:0.202	rs17868323	129;129	Q5DSZ7;Q9HAW7	.;UD17_HUMAN	K	129	ENSP00000362525:N129K	ENSP00000362525:N129K	N	+	3	2	UGT1A7	234255709	0.000000	0.05858	0.001000	0.08648	0.037000	0.13140	-13.134000	0.00001	-3.135000	0.00235	-1.473000	0.01005	AAT	.	.	weak		0.368	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
LRRC8B	23507	hgsc.bcm.edu	37	1	90048248	90048248	+	Silent	SNP	C	C	T	rs12130207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:90048248C>T	ENST00000330947.2	+	5	399	c.39C>T	c.(37-39)gcC>gcT	p.A13A	LRRC8B_ENST00000439853.1_Silent_p.A13A|RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.A13A	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	13					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		TAGCAGATGCCCAGTCATCTT	0.463													C|||	738	0.147364	0.1573	0.1873	5008	,	,		21834	0.0407		0.2177	False		,,,				2504	0.1431				p.A13A		Atlas-SNP	.											LRRC8B,NS,neuroblastoma,+2,1	LRRC8B	49	1	0			c.C39T						PASS	.	C	,	692,3714	289.2+/-280.3	58,576,1569	146.0	137.0	140.0		39,39	3.5	1.0	1	dbSNP_120	140	1808,6792	325.9+/-317.1	195,1418,2687	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	253,1994,4256	TT,TC,CC		21.0233,15.7059,19.2219	,	13/804,13/804	90048248	2500,10506	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			AGATGCCCAGTCA	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"""T cell activation leucine repeat rich protein"""	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.39C>T	1.37:g.90048248C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	155	62	0.4	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			C|0.814;T|0.186	0.186	strong		0.463	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
MADCAM1	8174	hgsc.bcm.edu	37	19	501714	501714	+	Missense_Mutation	SNP	C	C	A	rs78071082	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:501714C>A	ENST00000215637.3	+	4	759	c.713C>A	c.(712-714)cCg>cAg	p.P238Q	MADCAM1_ENST00000587541.1_Missense_Mutation_p.P19Q|MADCAM1_ENST00000382683.4_Intron|MADCAM1_ENST00000346144.4_Intron|AC005775.2_ENST00000592413.1_RNA	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	238	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCACCTCCCCGGAGTCTCCC	0.667																																					p.P238Q		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C713A						PASS	.						27.0	42.0	37.0					19																	501714		2202	4299	6501	SO:0001583	missense	8174	exon4			CCTCCCCGGAGTC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.713C>A	19.37:g.501714C>A	ENSP00000215637:p.Pro238Gln	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	245	24	0.0979592	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	c	9.846	1.192318	0.21954	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.11495	2.77	3.69	-3.39	0.04868	.	.	.	.	.	T	0.05181	0.0138	N	0.24115	0.695	0.09310	N	1	P	0.45078	0.85	B	0.40134	0.32	T	0.23084	-1.0198	9	0.34782	T	0.22	.	1.1525	0.01789	0.1428:0.3186:0.2805:0.2581	.	238	Q13477	MADCA_HUMAN	Q	262;254;246;238	ENSP00000215637:P238Q	ENSP00000215637:P238Q	P	+	2	0	MADCAM1	452714	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.794000	0.04584	-0.567000	0.06046	-0.145000	0.13849	CCG	A|0.000;C|1.000;T|0.000	0.000	strong		0.667	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
FLII	2314	hgsc.bcm.edu	37	17	18156957	18156957	+	Silent	SNP	G	G	A	rs147128917		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18156957G>A	ENST00000327031.4	-	8	981	c.756C>T	c.(754-756)aaC>aaT	p.N252N	FLII_ENST00000545457.2_Silent_p.N198N|FLII_ENST00000584444.1_Intron|FLII_ENST00000579294.1_Silent_p.N241N|FLII_ENST00000578558.1_Silent_p.N252N|FLII_ENST00000379450.4_Silent_p.N167N	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	252	Interaction with LRRFIP1 and LRRFIP2.				multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					TGCTGCTGAGGTTGAGGCGGC	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		19548	0.0		0.001	False		,,,				2504	0.0				p.N252N		Atlas-SNP	.											.	FLII	79	.	0			c.C756T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	87.0	77.0	80.0		756	5.4	1.0	17	dbSNP_134	80	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FLII	NM_002018.2		0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308		252/1270	18156957	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon8			GCTGAGGTTGAGG	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.756C>T	17.37:g.18156957G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	171	75	0.438596	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
FBXO33	254170	hgsc.bcm.edu	37	14	39870594	39870594	+	Silent	SNP	T	T	C	rs61754302		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:39870594T>C	ENST00000298097.7	-	3	1519	c.1182A>G	c.(1180-1182)ctA>ctG	p.L394L	FBXO33_ENST00000554190.1_Intron	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	394					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		GAATCCTCTCTAGTGGTATAC	0.368																																					p.L394L		Atlas-SNP	.											.	FBXO33	21	.	0			c.A1182G						PASS	.	T		0,4406		0,0,2203	100.0	96.0	97.0		1182	0.4	1.0	14	dbSNP_129	97	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	FBXO33	NM_203301.3		0,3,6500	CC,CT,TT		0.0349,0.0,0.0231		394/556	39870594	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	254170	exon3			CCTCTCTAGTGGT	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"""F-boxes /  ""other"""""	19833	protein-coding gene	gene with protein product		609103	"""F-box only protein 33"""				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.1182A>G	14.37:g.39870594T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	37	CCDS9677.1																																																																																			T|1.000;C|0.000	0.000	weak		0.368	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2		
DIDO1	11083	hgsc.bcm.edu	37	20	61528306	61528306	+	Missense_Mutation	SNP	A	A	G	rs1883848	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61528306A>G	ENST00000266070.4	-	7	1956	c.1631T>C	c.(1630-1632)aTg>aCg	p.M544T	DIDO1_ENST00000395335.2_Missense_Mutation_p.M544T|DIDO1_ENST00000395340.1_Missense_Mutation_p.M544T|DIDO1_ENST00000395343.1_Missense_Mutation_p.M544T	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	544			M -> T (in dbSNP:rs1883848). {ECO:0000269|PubMed:16127461}.		apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					TGAGGCTGCCATGGCTGCCGC	0.567													G|||	2438	0.486821	0.4395	0.5014	5008	,	,		17658	0.629		0.3877	False		,,,				2504	0.4959				p.M544T	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,0,1	DIDO1	321	1	0			c.T1631C						PASS	.	G	THR/MET,THR/MET,THR/MET,THR/MET	1888,2518		409,1070,724	24.0	26.0	25.0		1631,1631,1631,1631	-1.2	0.0	20	dbSNP_92	25	3549,5045		754,2041,1502	yes	missense,missense,missense,missense	DIDO1	NM_001193369.1,NM_001193370.1,NM_033081.2,NM_080797.3	81,81,81,81	1163,3111,2226	GG,GA,AA		41.2963,42.8507,41.8231	benign,benign,benign,benign	544/2241,544/1190,544/2241,544/1190	61528306	5437,7563	2203	4297	6500	SO:0001583	missense	11083	exon7			GCTGCCATGGCTG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1631T>C	20.37:g.61528306A>G	ENSP00000266070:p.Met544Thr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	1026	0.4697802197802198	209	0.4247967479674797	189	0.5220994475138122	353	0.6171328671328671	275	0.3627968337730871	G	4.197	0.035244	0.08148	0.428507	0.412963	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.10477	3.23;3.23;2.87;2.87	5.12	-1.16	0.09678	.	1.282380	0.05904	N	0.630433	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38329	-0.9666	9	0.14656	T	0.56	-1.5461	10.4843	0.44713	0.5041:0.0:0.4959:0.0	rs1883848;rs58247654;rs1883848	544;544	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	T	544	ENSP00000266070:M544T;ENSP00000378752:M544T;ENSP00000378749:M544T;ENSP00000378744:M544T	ENSP00000266070:M544T	M	-	2	0	DIDO1	60998751	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.881000	0.28173	-0.468000	0.06922	-0.213000	0.12676	ATG	A|0.551;G|0.449	0.449	strong		0.567	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
YDJC	150223	hgsc.bcm.edu	37	22	21982892	21982892	+	Missense_Mutation	SNP	C	C	T	rs2298428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21982892C>T	ENST00000292778.6	-	5	836	c.787G>A	c.(787-789)Gct>Act	p.A263T	YDJC_ENST00000398873.3_3'UTR	NM_001017964.1	NP_001017964.1	A8MPS7	YDJC_HUMAN	YdjC homolog (bacterial)	263			A -> T (in dbSNP:rs2298428).		carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)					Colorectal(54;0.105)					CAAGAGAAAGCGTCGGGGCCT	0.701													C|||	1126	0.22484	0.0227	0.3631	5008	,	,		11576	0.4117		0.1769	False		,,,				2504	0.2566				p.A263T		Atlas-SNP	.											.	YDJC	8	.	0			c.G787A						PASS	.	C	THR/ALA	218,4160		4,210,1975	13.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/pubmed?term	787	4.3	0.7	22	dbSNP_100	13	1582,6978		142,1298,2840	yes	missense	YDJC	NM_001017964.1	58	146,1508,4815	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	18.4813,4.9794,13.9125	benign	263/324	21982892	1800,11138	2189	4280	6469	SO:0001583	missense	150223	exon5			AGAAAGCGTCGGG		CCDS33613.1	22q11.21	2008-02-26			ENSG00000161179	ENSG00000161179			27158	protein-coding gene	gene with protein product						18177738	Standard	XM_005261347		Approved		uc002zvb.2	A8MPS7	OTTHUMG00000150822	ENST00000292778.6:c.787G>A	22.37:g.21982892C>T	ENSP00000292778:p.Ala263Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_001017964	Q2YDT4|Q4V9R7	Missense_Mutation	SNP	ENST00000292778.6	37	CCDS33613.1	495	0.22664835164835165	20	0.04065040650406504	115	0.31767955801104975	223	0.38986013986013984	137	0.18073878627968337	C	24.5	4.541910	0.85917	0.049794	0.184813	ENSG00000161179	ENST00000292778	T	0.42131	0.98	4.32	4.32	0.51571	Polysaccharide deacetylase (1);	0.104489	0.64402	D	0.000007	T	0.00012	0.0000	L	0.54323	1.7	0.09310	P	1.0	P	0.46784	0.884	B	0.39068	0.289	T	0.47368	-0.9123	9	0.13470	T	0.59	-16.7508	14.3921	0.66986	0.0:1.0:0.0:0.0	rs2298428;rs52827392;rs56745961;rs2298428	263	A8MPS7	YDJC_HUMAN	T	263	ENSP00000292778:A263T	ENSP00000292778:A263T	A	-	1	0	YDJC	20312892	1.000000	0.71417	0.677000	0.29947	0.942000	0.58702	7.032000	0.76498	2.245000	0.73994	0.650000	0.86243	GCT	C|0.795;T|0.205	0.205	strong		0.701	YDJC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320213.1		
ZC3H14	79882	hgsc.bcm.edu	37	14	89061298	89061298	+	Intron	SNP	G	G	A	rs78648645	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:89061298G>A	ENST00000251038.5	+	10	1504				ZC3H14_ENST00000359301.3_Intron|ZC3H14_ENST00000555755.1_Intron|ZC3H14_ENST00000318308.6_Silent_p.K76K|ZC3H14_ENST00000555900.1_Silent_p.K76K|ZC3H14_ENST00000406216.3_Silent_p.K76K|ZC3H14_ENST00000556945.1_Intron|ZC3H14_ENST00000336693.4_Intron|ZC3H14_ENST00000393514.5_Intron|ZC3H14_ENST00000557607.1_Intron|ZC3H14_ENST00000302216.8_Intron	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14							cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						GAGTGTCCAAGAATGAAGCAA	0.303													G|||	51	0.0101837	0.0	0.0187	5008	,	,		20833	0.0		0.0348	False		,,,				2504	0.0031				p.K76K		Atlas-SNP	.											.	ZC3H14	71	.	0			c.G228A						PASS	.	G	,,,,,	22,4382	29.9+/-59.1	0,22,2180	49.0	48.0	48.0		,,,,,228	3.8	1.0	14	dbSNP_132	48	215,8385	87.9+/-150.2	4,207,4089	no	intron,intron,intron,intron,intron,coding-synonymous	ZC3H14	NM_001160103.1,NM_001160104.1,NM_024824.4,NM_207660.3,NM_207661.2,NM_207662.3	,,,,,	4,229,6269	AA,AG,GG		2.5,0.4995,1.8225	,,,,,	,,,,,76/307	89061298	237,12767	2202	4300	6502	SO:0001627	intron_variant	79882	exon1			GTCCAAGAATGAA	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"""Zinc fingers, CCCH-type domain containing"""	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.1280-1780G>A	14.37:g.89061298G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_207662	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Silent	SNP	ENST00000251038.5	37	CCDS32133.1																																																																																			G|0.983;A|0.017	0.017	strong		0.303	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824	
MTF1	4520	hgsc.bcm.edu	37	1	38289383	38289383	+	Splice_Site	SNP	T	T	C	rs12751325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:38289383T>C	ENST00000373036.4	-	8	1310	c.1170A>G	c.(1168-1170)acA>acG	p.T390T		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	390					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GTGACAAACCTGTCTGTTGAG	0.448													T|||	1059	0.211462	0.0628	0.2104	5008	,	,		17900	0.2639		0.2843	False		,,,				2504	0.2843				p.T390T		Atlas-SNP	.											.	MTF1	67	.	0			c.A1170G						PASS	.	T		461,3945	217.1+/-235.6	25,411,1767	159.0	121.0	134.0		1170	4.2	1.0	1	dbSNP_121	134	2492,6108	407.0+/-349.0	342,1808,2150	yes	coding-synonymous-near-splice	MTF1	NM_005955.2		367,2219,3917	CC,CT,TT		28.9767,10.463,22.7049		390/754	38289383	2953,10053	2203	4300	6503	SO:0001630	splice_region_variant	4520	exon8			CAAACCTGTCTGT	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1171+1A>G	1.37:g.38289383T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_005955	B2RAK6|Q96CB1	Silent	SNP	ENST00000373036.4	37	CCDS30676.1																																																																																			T|0.771;C|0.229	0.229	strong		0.448	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955	Silent
AKAP13	11214	hgsc.bcm.edu	37	15	86123364	86123364	+	Missense_Mutation	SNP	G	G	A	rs7177107	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:86123364G>A	ENST00000394518.2	+	7	2160	c.2065G>A	c.(2065-2067)Gag>Aag	p.E689K	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.E689K	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	689			E -> K (in dbSNP:rs7177107). {ECO:0000269|Ref.3}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CATAGTTAGCGAGTCCGAAAG	0.498													G|||	381	0.0760783	0.0091	0.098	5008	,	,		20905	0.001		0.1938	False		,,,				2504	0.1074				p.E689K	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G2065A						PASS	.	G	LYS/GLU,LYS/GLU	213,4191	128.6+/-165.4	8,197,1997	112.0	97.0	102.0		2065,2065	3.4	0.0	15	dbSNP_116	102	1894,6704	326.2+/-317.3	200,1494,2605	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	56,56	208,1691,4602	AA,AG,GG		22.0284,4.8365,16.2052	benign,benign	689/2818,689/2814	86123364	2107,10895	2202	4299	6501	SO:0001583	missense	11214	exon7			GTTAGCGAGTCCG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.2065G>A	15.37:g.86123364G>A	ENSP00000378026:p.Glu689Lys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	197	0.0902014652014652	8	0.016260162601626018	38	0.10497237569060773	1	0.0017482517482517483	150	0.19788918205804748	G	13.21	2.168651	0.38315	0.048365	0.220284	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.09445	2.98;2.98	5.38	3.38	0.38709	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.53688	P	2.2999999999995246E-5	B;B	0.16802	0.011;0.019	B;B	0.09377	0.002;0.004	T	0.38394	-0.9663	8	0.06625	T	0.88	.	11.9016	0.52687	0.0:0.657:0.343:0.0	rs7177107;rs52836676;rs7177107	689;689	Q12802;Q12802-2	AKP13_HUMAN;.	K	689;689;688;688	ENSP00000354718:E689K;ENSP00000378026:E689K	ENSP00000354718:E689K	E	+	1	0	AKAP13	83924368	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.321000	0.19558	1.405000	0.46838	-0.133000	0.14855	GAG	G|0.875;A|0.125	0.125	strong		0.498	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
STIM1	6786	hgsc.bcm.edu	37	11	4103524	4103524	+	Silent	SNP	A	A	G	rs2304891	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4103524A>G	ENST00000300737.4	+	8	1649	c.1080A>G	c.(1078-1080)caA>caG	p.Q360Q	STIM1_ENST00000533977.1_Silent_p.Q187Q|STIM1_ENST00000527651.1_Silent_p.Q360Q	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	360	SOAR/CAD.				activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		TGGAGGTGCAATATTACAACA	0.507													A|||	1948	0.388978	0.0976	0.4841	5008	,	,		19607	0.4425		0.5676	False		,,,				2504	0.4765				p.Q360Q		Atlas-SNP	.											STIM1,NS,carcinoma,0,2	STIM1	55	2	0			c.A1080G						scavenged	.	A		765,3637	309.4+/-291.0	79,607,1515	68.0	62.0	64.0		1080	1.5	1.0	11	dbSNP_100	64	4938,3658	623.1+/-397.4	1403,2132,763	no	coding-synonymous	STIM1	NM_003156.3		1482,2739,2278	GG,GA,AA		42.5547,17.3785,43.876		360/686	4103524	5703,7295	2201	4298	6499	SO:0001819	synonymous_variant	6786	exon8			GGTGCAATATTAC	BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"""Sterile alpha motif (SAM) domain containing"""	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.1080A>G	11.37:g.4103524A>G		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	156	78	0.5	NM_003156	E9PQJ4|Q8N382	Silent	SNP	ENST00000300737.4	37	CCDS7749.1	938	0.42948717948717946	51	0.10365853658536585	194	0.5359116022099447	272	0.4755244755244755	421	0.5554089709762533	A	10.06	1.246080	0.22796	0.173785	0.574453	ENSG00000167323	ENST00000526596	.	.	.	5.49	1.5	0.22942	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48570	-0.9024	3	.	.	.	-27.0925	9.4534	0.38741	0.2918:0.0:0.7082:0.0	rs2304891;rs17209912;rs57302968;rs2304891	.	.	.	S	91	.	.	N	+	2	0	STIM1	4060100	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	1.794000	0.38774	0.016000	0.14998	-0.375000	0.07067	AAT	A|0.576;G|0.424	0.424	strong		0.507	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156	
SGOL2	151246	hgsc.bcm.edu	37	2	201436555	201436555	+	Missense_Mutation	SNP	A	A	G	rs17448235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:201436555A>G	ENST00000357799.4	+	7	1584	c.1486A>G	c.(1486-1488)Ata>Gta	p.I496V		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	496			I -> V (in dbSNP:rs17448235). {ECO:0000269|Ref.1}.		meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						GGAGAAAAGAATAACAAATGA	0.363													A|||	495	0.0988419	0.1596	0.0735	5008	,	,		18424	0.001		0.1481	False		,,,				2504	0.0849				p.I496V		Atlas-SNP	.											.	SGOL2	126	.	0			c.A1486G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	546,3090		39,468,1311	115.0	117.0	116.0		1486,1486,1486	2.5	0.0	2	dbSNP_123	116	1284,6852		92,1100,2876	yes	missense,missense,missense	SGOL2	NM_001160033.1,NM_001160046.1,NM_152524.5	29,29,29	131,1568,4187	GG,GA,AA		15.7817,15.0165,15.5454	possibly-damaging,possibly-damaging,possibly-damaging	496/1261,496/1262,496/1266	201436555	1830,9942	1818	4068	5886	SO:0001583	missense	151246	exon7			AAAAGAATAACAA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1486A>G	2.37:g.201436555A>G	ENSP00000350447:p.Ile496Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	221	0.10119047619047619	81	0.16463414634146342	28	0.07734806629834254	1	0.0017482517482517483	111	0.14643799472295516	A	0.036	-1.305830	0.01353	0.150165	0.157817	ENSG00000163535	ENST00000357799	T	0.39406	1.08	4.93	2.46	0.29980	.	2.801810	0.01020	N	0.003977	T	0.00210	0.0006	L	0.57536	1.79	0.58432	P	2.9999999999752447E-6	B;B;B	0.33807	0.426;0.426;0.426	B;B;B	0.37692	0.256;0.256;0.256	T	0.04140	-1.0974	9	0.14656	T	0.56	0.5055	6.3925	0.21595	0.7609:0.1586:0.0805:0.0	rs17448235;rs52804876;rs58619980;rs17448235	496;496;496	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	V	496	ENSP00000350447:I496V	ENSP00000350447:I496V	I	+	1	0	SGOL2	201144800	0.001000	0.12720	0.000000	0.03702	0.157000	0.22087	1.263000	0.33004	0.422000	0.26005	0.477000	0.44152	ATA	A|0.888;G|0.112	0.112	strong		0.363	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
MELK	9833	hgsc.bcm.edu	37	9	36674842	36674842	+	Silent	SNP	C	C	T	rs2274473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:36674842C>T	ENST00000298048.2	+	17	1870	c.1686C>T	c.(1684-1686)aaC>aaT	p.N562N	MELK_ENST00000536860.1_Silent_p.N514N|MELK_ENST00000536987.1_Silent_p.N431N|MELK_ENST00000543751.1_Silent_p.N530N|MELK_ENST00000536329.1_Silent_p.N491N|MELK_ENST00000545008.1_Silent_p.N491N|MELK_ENST00000538311.1_Silent_p.N368N|MELK_ENST00000541717.1_Silent_p.N521N	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	562	Autoinhibitory region.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			TTCACTATAACGTGACTACAA	0.343													T|||	3752	0.749201	0.4244	0.8862	5008	,	,		19912	0.8859		0.8887	False		,,,				2504	0.8067				p.N562N	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.C1686T						PASS	.	T		2220,2186	584.7+/-386.1	568,1084,551	63.0	57.0	59.0		1686	2.2	1.0	9	dbSNP_100	59	7721,875	197.2+/-241.9	3465,791,42	no	coding-synonymous	MELK	NM_014791.2		4033,1875,593	TT,TC,CC		10.1792,49.6142,23.5425		562/652	36674842	9941,3061	2203	4298	6501	SO:0001819	synonymous_variant	9833	exon17			CTATAACGTGACT	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1686C>T	9.37:g.36674842C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Silent	SNP	ENST00000298048.2	37	CCDS6606.1																																																																																			C|0.234;T|0.766	0.766	strong		0.343	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791	
MUC16	94025	hgsc.bcm.edu	37	19	9058942	9058942	+	Missense_Mutation	SNP	C	C	T	rs1833778	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9058942C>T	ENST00000397910.4	-	3	28707	c.28504G>A	c.(28504-28506)Gct>Act	p.A9502T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9504	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCTTTAGAAGCGGCCAGACTC	0.478													c|||	2201	0.439497	0.2829	0.487	5008	,	,		21053	0.5546		0.4742	False		,,,				2504	0.4632				p.A9502T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G28504A						PASS	.	C	THR/ALA	1242,2732		191,860,936	161.0	157.0	158.0		28504	-4.6	0.0	19	dbSNP_92	158	3928,4420		946,2036,1192	yes	missense	MUC16	NM_024690.2	58	1137,2896,2128	TT,TC,CC		47.0532,31.2531,41.9575	benign	9502/14508	9058942	5170,7152	1987	4174	6161	SO:0001583	missense	94025	exon3			TAGAAGCGGCCAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28504G>A	19.37:g.9058942C>T	ENSP00000381008:p.Ala9502Thr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	168	0.988235	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	1022	0.46794871794871795	166	0.33739837398373984	179	0.494475138121547	321	0.5611888111888111	356	0.46965699208443273	c	2.488	-0.318202	0.05386	0.312531	0.470532	ENSG00000181143	ENST00000397910	T	0.19105	2.17	2.29	-4.58	0.03410	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.42207	-0.9465	7	0.87932	D	0	.	2.0581	0.03586	0.5546:0.1062:0.1212:0.218	rs1833778;rs1833778	9502	B5ME49	.	T	9502	ENSP00000381008:A9502T	ENSP00000381008:A9502T	A	-	1	0	MUC16	8919942	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.608000	0.00887	-3.882000	0.00095	-1.013000	0.02462	GCT	C|0.535;T|0.465	0.465	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
THSD7A	221981	hgsc.bcm.edu	37	7	11676377	11676377	+	Silent	SNP	G	G	A	rs2074598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:11676377G>A	ENST00000423059.4	-	2	653	c.402C>T	c.(400-402)ccC>ccT	p.P134P	THSD7A_ENST00000480061.1_5'UTR	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	134					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TTGAAATCACGGGCTGACACT	0.468										HNSCC(18;0.044)			A|||	1335	0.266573	0.1649	0.33	5008	,	,		18947	0.2837		0.2535	False		,,,				2504	0.3548				p.P134P		Atlas-SNP	.											.	THSD7A	219	.	0			c.C402T						PASS	.	A		564,3316		48,468,1424	81.0	80.0	80.0		402	-11.4	0.1	7	dbSNP_96	80	2112,6180		261,1590,2295	no	coding-synonymous	THSD7A	NM_015204.2		309,2058,3719	AA,AG,GG		25.4703,14.5361,21.9849		134/1658	11676377	2676,9496	1940	4146	6086	SO:0001819	synonymous_variant	221981	exon2			AATCACGGGCTGA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.402C>T	7.37:g.11676377G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	242	127	0.524793	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			G|0.745;N|0.000	.	strong		0.468	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035262	110035262	+	Silent	SNP	A	A	G	rs1026608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:110035262A>G	ENST00000278590.3	+	6	1503	c.1452A>G	c.(1450-1452)cgA>cgG	p.R484R	ZC3H12C_ENST00000453089.2_Silent_p.R453R|ZC3H12C_ENST00000528673.1_Silent_p.R485R	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	484							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		ATGTCAAACGAGGTGCTCCAA	0.458													A|||	1103	0.220248	0.2186	0.2161	5008	,	,		23480	0.2004		0.2724	False		,,,				2504	0.1922				p.R484R		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A1452G						PASS	.	A		807,3057		89,629,1214	106.0	104.0	105.0		1452	-2.8	1.0	11	dbSNP_86	105	2087,6189		246,1595,2297	no	coding-synonymous	ZC3H12C	NM_033390.1		335,2224,3511	GG,GA,AA		25.2175,20.8851,23.8386		484/884	110035262	2894,9246	1932	4138	6070	SO:0001819	synonymous_variant	85463	exon6			CAAACGAGGTGCT		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1452A>G	11.37:g.110035262A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			A|0.746;G|0.254	0.254	strong		0.458	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
C9orf57	138240	hgsc.bcm.edu	37	9	74671719	74671719	+	Silent	SNP	T	T	C	rs13295099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:74671719T>C	ENST00000377024.3	-	3	299	c.204A>G	c.(202-204)aaA>aaG	p.K68K	C9orf57_ENST00000424431.2_Silent_p.K34K	NM_001128618.1	NP_001122090.1	Q5W0N0	CI057_HUMAN	chromosome 9 open reading frame 57	68						integral component of membrane (GO:0016021)				endometrium(1)	1						GGACCTCTTCTTTCCAGTACT	0.368													T|||	1334	0.266374	0.1566	0.3228	5008	,	,		17668	0.0774		0.5467	False		,,,				2504	0.2812				p.K68K		Atlas-SNP	.											.	C9orf57	16	.	0			c.A204G						PASS	.	T		304,1080		30,244,418	94.0	75.0	80.0		204	-0.4	0.0	9	dbSNP_121	80	1785,1397		499,787,305	no	coding-synonymous	C9orf57	NM_001128618.1		529,1031,723	CC,CT,TT		43.9032,21.9653,45.7512		68/162	74671719	2089,2477	692	1591	2283	SO:0001819	synonymous_variant	138240	exon3			CTCTTCTTTCCAG	BC036255	CCDS47980.1	9q21.2	2012-03-15			ENSG00000204669	ENSG00000204669			27037	protein-coding gene	gene with protein product						12477932	Standard	NM_001128618		Approved		uc004aip.3	Q5W0N0	OTTHUMG00000020003	ENST00000377024.3:c.204A>G	9.37:g.74671719T>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_001128618	A1L456	Silent	SNP	ENST00000377024.3	37	CCDS47980.1																																																																																			.	.	alt		0.368	C9orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052631.1	NM_001128618	
MFSD1	64747	hgsc.bcm.edu	37	3	158538056	158538056	+	Silent	SNP	T	T	C	rs4680469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:158538056T>C	ENST00000264266.8	+	9	866	c.804T>C	c.(802-804)ctT>ctC	p.L268L	MFSD1_ENST00000415822.2_Silent_p.L317L|MFSD1_ENST00000392813.4_Silent_p.L278L			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	268					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CCCTGTGGCTTATATTTATCA	0.343													C|||	767	0.153155	0.0492	0.2176	5008	,	,		16270	0.1389		0.2296	False		,,,				2504	0.184				p.L317L	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.T951C						PASS	.	C	,	385,4021	790.9+/-415.1	19,347,1837	207.0	187.0	194.0		834,951	-2.7	0.2	3	dbSNP_111	194	1973,6625	721.9+/-406.4	229,1515,2555	no	coding-synonymous,coding-synonymous	MFSD1	NM_001167903.1,NM_022736.2	,	248,1862,4392	CC,CT,TT		22.9472,8.7381,18.1329	,	278/476,317/515	158538056	2358,10646	2203	4299	6502	SO:0001819	synonymous_variant	64747	exon9			GTGGCTTATATTT	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.804T>C	3.37:g.158538056T>C		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	252	101	0.400794	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Silent	SNP	ENST00000264266.8	37																																																																																				T|0.820;C|0.180	0.180	strong		0.343	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736	
IPO4	79711	hgsc.bcm.edu	37	14	24653954	24653954	+	Missense_Mutation	SNP	G	G	A	rs7146310	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24653954G>A	ENST00000354464.6	-	16	1714	c.1538C>T	c.(1537-1539)gCc>gTc	p.A513V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	513			A -> V (in dbSNP:rs7146310). {ECO:0000269|PubMed:11823430, ECO:0000269|PubMed:14702039}.		DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CAGCAGCGAGGCCTGGGCAGC	0.622													G|||	1592	0.317891	0.2163	0.2363	5008	,	,		18141	0.4206		0.2654	False		,,,				2504	0.4611				p.A513V		Atlas-SNP	.											IPO4,NS,carcinoma,+1,1	IPO4	74	1	0			c.C1538T						PASS	.	G	VAL/ALA	911,3223		105,701,1261	21.0	26.0	24.0		1538	3.3	1.0	14	dbSNP_116	24	2400,5978		321,1758,2110	yes	missense	IPO4	NM_024658.3	64	426,2459,3371	AA,AG,GG		28.6465,22.0368,26.4626	benign	513/1082	24653954	3311,9201	2067	4189	6256	SO:0001583	missense	79711	exon16			AGCGAGGCCTGGG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1538C>T	14.37:g.24653954G>A	ENSP00000346453:p.Ala513Val	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	240	125	0.520833	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	37	CCDS9616.1	648	0.2967032967032967	106	0.21544715447154472	94	0.2596685082872928	249	0.4353146853146853	199	0.262532981530343	G	14.34	2.506634	0.44558	0.220368	0.286465	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.04654	3.58	5.28	3.32	0.38043	Armadillo-like helical (1);Armadillo-type fold (1);	0.612691	0.17322	N	0.178468	T	0.00012	0.0000	N	0.17474	0.49	0.46317	P	0.0010149999999999881	B	0.09022	0.002	B	0.16722	0.016	T	0.43925	-0.9361	9	0.51188	T	0.08	-1.7252	7.6189	0.28173	0.0:0.1498:0.4235:0.4267	rs7146310;rs17256720;rs61234434;rs7146310	513	Q8TEX9	IPO4_HUMAN	V	513;189	ENSP00000346453:A513V	ENSP00000346453:A513V	A	-	2	0	IPO4	23723794	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	1.072000	0.30678	1.412000	0.46977	0.558000	0.71614	GCC	G|0.693;A|0.307	0.307	strong		0.622	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
KLHL38	340359	hgsc.bcm.edu	37	8	124664874	124664874	+	Missense_Mutation	SNP	T	T	C	rs7386562|rs71505429	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:124664874T>C	ENST00000325995.7	-	1	316	c.293A>G	c.(292-294)cAt>cGt	p.H98R	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	98	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.			H -> R (in Ref. 3; EAW92045 and 4; AAI27887). {ECO:0000305}.						breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						AGTGGCAATATGTGCCTCCCC	0.572													C|||	3641	0.727037	0.6672	0.7118	5008	,	,		20058	0.7113		0.8579	False		,,,				2504	0.7004				p.H98R		Atlas-SNP	.											.	KLHL38	81	.	0			c.A293G						PASS	.	C	ARG/HIS	2932,1164		1076,780,192	68.0	75.0	73.0		293	-10.7	0.0	8	dbSNP_116	73	7029,1361		3031,967,197	yes	missense	KLHL38	NM_001081675.2	29	4107,1747,389	CC,CT,TT		16.2217,28.418,20.2226	benign	98/582	124664874	9961,2525	2048	4195	6243	SO:0001583	missense	340359	exon1			GCAATATGTGCCT		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.293A>G	8.37:g.124664874T>C	ENSP00000321475:p.His98Arg	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	1387	0.63507326007326	252	0.5121951219512195	243	0.6712707182320442	347	0.6066433566433567	545	0.7189973614775725	C	0.042	-1.282167	0.01398	0.71582	0.837783	ENSG00000175946	ENST00000325995	T	0.66099	-0.19	5.37	-10.7	0.00240	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	1.497270	0.03427	N	0.207124	T	0.00012	0.0000	N	0.16708	0.43	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34725	-0.9817	9	0.09843	T	0.71	.	0.6835	0.00879	0.2783:0.2958:0.1531:0.2728	rs7386562;rs59281930	98	Q2WGJ6	KLH38_HUMAN	R	98	ENSP00000321475:H98R	ENSP00000321475:H98R	H	-	2	0	KLHL38	124734055	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.180000	0.09754	-2.417000	0.00567	-0.355000	0.07637	CAT	T|0.288;C|0.712	0.712	strong		0.572	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
CDYL2	124359	hgsc.bcm.edu	37	16	80718879	80718879	+	Silent	SNP	A	A	G	rs8049284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:80718879A>G	ENST00000570137.2	-	2	327	c.172T>C	c.(172-174)Ttg>Ctg	p.L58L	CDYL2_ENST00000562753.1_5'UTR|CDYL2_ENST00000562812.1_Silent_p.L58L|CDYL2_ENST00000563890.1_Silent_p.L58L|CDYL2_ENST00000566173.1_Silent_p.L58L	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	58	Chromo. {ECO:0000255|PROSITE- ProRule:PRU00053}.					nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						GACATGTGCAACCCATTGAAT	0.542													G|||	2291	0.457468	0.4017	0.4236	5008	,	,		20166	0.2867		0.662	False		,,,				2504	0.5225				p.L58L		Atlas-SNP	.											.	CDYL2	66	.	0			c.T172C						PASS	.	G		2041,2365	612.1+/-391.9	461,1119,623	144.0	119.0	127.0		172	3.1	1.0	16	dbSNP_116	127	5670,2930	457.6+/-364.4	1862,1946,492	yes	coding-synonymous	CDYL2	NM_152342.2		2323,3065,1115	GG,GA,AA		34.0698,46.3232,40.712		58/507	80718879	7711,5295	2203	4300	6503	SO:0001819	synonymous_variant	124359	exon2			TGTGCAACCCATT	AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"""chromodomain Y-like protein 2"""			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.172T>C	16.37:g.80718879A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_152342	Q7Z5I8	Silent	SNP	ENST00000570137.2	37	CCDS32493.1																																																																																			A|0.467;G|0.533	0.533	strong		0.542	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342	
MAGEB16	139604	hgsc.bcm.edu	37	X	35821056	35821056	+	Missense_Mutation	SNP	T	T	A	rs4829391|rs370444095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:35821056T>A	ENST00000399989.1	+	2	1022	c.743T>A	c.(742-744)aTg>aAg	p.M248K	MAGEB16_ENST00000399987.1_Missense_Mutation_p.M248K|MAGEB16_ENST00000399985.1_Missense_Mutation_p.M248K|MAGEB16_ENST00000399988.1_Missense_Mutation_p.M248K|MAGEB16_ENST00000399992.1_Missense_Mutation_p.M280K	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	248	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		M -> K (in dbSNP:rs4829391).|M -> V (in dbSNP:rs4829390).							breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						GAGCCCAGAATGCTCATCACC	0.502													A|||	2343	0.620662	0.4478	0.4121	3775	,	,		15958	0.5694		0.4205	False		,,,				2504	0.4785				p.M248K		Atlas-SNP	.											.	MAGEB16	64	.	0			c.T743A						PASS	.	A	LYS/MET	396,3363		64,150,118,1380,453	44.0	44.0	44.0		743	3.1	0.0	X	dbSNP_111	44	749,5958		102,225,320,2095,1543	yes	missense	MAGEB16	NM_001099921.1	95	166,375,438,3475,1996	AA,AT,A,TT,T		11.1674,10.5347,10.9402	benign	248/325	35821056	1145,9321	2165	4285	6450	SO:0001583	missense	139604	exon2			CCAGAATGCTCAT		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.743T>A	X.37:g.35821056T>A	ENSP00000382871:p.Met248Lys	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	895	0.5394816154309825	145	0.3835978835978836	92	0.36220472440944884	192	0.4948453608247423	202	0.33554817275747506	A	0.014	-1.583330	0.00872	0.105347	0.111674	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.03580	3.88;3.88;3.88;3.88;3.88	3.06	3.06	0.35304	.	0.726440	0.13630	N	0.373788	T	0.00012	0.0000	N	0.00002	-3.54	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.41305	-0.9516	9	0.02654	T	1	.	5.0116	0.14315	0.7301:0.0:0.0:0.2699	rs4829391;rs4829391	248	A2A368	MAGBG_HUMAN	K	248;280;248;248;248	ENSP00000382870:M248K;ENSP00000382874:M280K;ENSP00000382869:M248K;ENSP00000382871:M248K;ENSP00000382867:M248K	ENSP00000382867:M248K	M	+	2	0	MAGEB16	35730977	0.038000	0.19896	0.000000	0.03702	0.002000	0.02628	1.366000	0.34193	0.445000	0.26639	-0.541000	0.04245	ATG	T|0.434;A|0.566	0.566	strong		0.502	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499274	59499274	+	Silent	SNP	C	C	A	rs3809528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:59499274C>A	ENST00000307144.4	+	1	233	c.135C>A	c.(133-135)acC>acA	p.T45T	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	45					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						GGCTCTTCACCCCCGTGAGCA	0.562													C|||	2509	0.500998	0.5113	0.4409	5008	,	,		20835	0.6131		0.34	False		,,,				2504	0.5798				p.T45T		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.C135A						PASS	.	C	,	2053,2329	567.5+/-382.2	502,1049,640	78.0	70.0	72.0		,135	-0.3	0.0	15	dbSNP_107	72	2754,5826	439.4+/-359.2	437,1880,1973	no	intron,coding-synonymous	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,	939,2929,2613	AA,AC,CC		32.0979,46.8508,37.0853	,	,45/382	59499274	4807,8155	2191	4290	6481	SO:0001819	synonymous_variant	92483	exon1			CTTCACCCCCGTG	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.135C>A	15.37:g.59499274C>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	146	57	0.390411	NM_033195	Q6DUY4|Q96LI2	Silent	SNP	ENST00000307144.4	37	CCDS10171.1																																																																																			C|0.586;A|0.414	0.414	strong		0.562	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
LMO2	4005	hgsc.bcm.edu	37	11	33886294	33886294	+	Silent	SNP	A	A	G	rs2038602	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:33886294A>G	ENST00000395833.3	-	2	540	c.111T>C	c.(109-111)atT>atC	p.I37I	LMO2_ENST00000257818.2_Silent_p.I106I	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	37	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						AGCGGTCCCCAATGTTCTGCT	0.652			T	TRD@	T-ALL								G|||	2175	0.434305	0.5847	0.2839	5008	,	,		19179	0.4067		0.4185	False		,,,				2504	0.3824				p.I106I		Atlas-SNP	.		Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	.	LMO2	21	.	0			c.T318C						PASS	.	G	,,	2446,1958	546.4+/-377.0	674,1098,430	62.0	53.0	56.0		111,111,318	-4.5	0.9	11	dbSNP_94	56	3551,5045	623.2+/-397.4	762,2027,1509	no	coding-synonymous,coding-synonymous,coding-synonymous	LMO2	NM_001142315.1,NM_001142316.1,NM_005574.3	,,	1436,3125,1939	GG,GA,AA		41.3099,44.4596,46.1308	,,	37/159,37/159,106/228	33886294	5997,7003	2202	4298	6500	SO:0001819	synonymous_variant	4005	exon5			GTCCCCAATGTTC	X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"""T-cell translocation gene 2"", ""rhombotin-like 1"""	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.111T>C	11.37:g.33886294A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	150	66	0.44	NM_005574	Q9HD58	Silent	SNP	ENST00000395833.3	37	CCDS44567.1																																																																																			A|0.546;G|0.454	0.454	strong		0.652	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574	
SPINK5	11005	hgsc.bcm.edu	37	5	147480112	147480112	+	Silent	SNP	T	T	C	rs2303065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147480112T>C	ENST00000256084.7	+	13	1230	c.1188T>C	c.(1186-1188)caT>caC	p.H396H	SPINK5_ENST00000398454.1_Silent_p.H396H|SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Silent_p.H396H	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	396	Kazal-like 6. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.H396H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAAAGTGCATGGCAACACCT	0.478													t|||	2168	0.432907	0.1989	0.6167	5008	,	,		17745	0.4851		0.4861	False		,,,				2504	0.5102				p.H396H		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - coding silent(1)	stomach(1)	c.T1188C						scavenged	.	C	,,	994,2980		127,740,1120	155.0	154.0	155.0		1188,1188,1188	-0.5	0.6	5	dbSNP_100	155	4264,4084		1079,2106,989	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	1206,2846,2109	CC,CT,TT		48.9219,25.0126,42.6716	,,	396/1095,396/917,396/1065	147480112	5258,7064	1987	4174	6161	SO:0001819	synonymous_variant	11005	exon13			AGTGCATGGCAAC	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1188T>C	5.37:g.147480112T>C		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			T|0.546;C|0.454	0.454	strong		0.478	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
BTBD16	118663	hgsc.bcm.edu	37	10	124036305	124036305	+	Splice_Site	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124036305G>T	ENST00000260723.4	+	3	269		c.e3-1		BTBD16_ENST00000368994.2_Missense_Mutation_p.Q7H	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16											breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TTACCAAGCAGCACAAAGCTC	0.448																																					.		Atlas-SNP	.											BTBD16,bladder,carcinoma,0,1	BTBD16	44	1	0			c.19-1G>T						PASS	.						84.0	87.0	86.0					10																	124036305		2203	4300	6503	SO:0001630	splice_region_variant	118663	exon3			CAAGCAGCACAAA	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.19-1G>T	10.37:g.124036305G>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	134	18	0.134328	NM_144587	A6NM63|Q4VXL1|Q96LN0	Splice_Site	SNP	ENST00000260723.4	37	CCDS31301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.139|9.139	1.013409|1.013409	0.19277|0.19277	.|.	.|.	ENSG00000138152|ENSG00000138152	ENST00000260723|ENST00000368994	.|T	.|0.19250	.|2.16	4.66|4.66	3.76|3.76	0.43208|0.43208	.|.	.|.	.|.	.|.	.|.	.|T	.|0.34571	.|0.0902	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|D	.|0.61697	.|0.99	.|P	.|0.58873	.|0.847	.|T	.|0.07139	.|-1.0788	.|8	.|0.44086	.|T	.|0.13	.|-0.0759	8.8669|8.8669	0.35291|0.35291	0.1013:0.0:0.8987:0.0|0.1013:0.0:0.8987:0.0	.|.	.|7	.|Q32M84-2	.|.	.|H	-1|7	.|ENSP00000357990:Q7H	.|ENSP00000357990:Q7H	.|Q	+|+	.|3	.|2	BTBD16|BTBD16	124026295|124026295	0.605000|0.605000	0.26941|0.26941	0.007000|0.007000	0.13788|0.13788	0.006000|0.006000	0.05464|0.05464	2.406000|2.406000	0.44557|0.44557	1.332000|1.332000	0.45431|0.45431	0.650000|0.650000	0.86243|0.86243	.|CAG	.	.	none		0.448	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	Intron
CELA1	1990	hgsc.bcm.edu	37	12	51737562	51737562	+	Missense_Mutation	SNP	T	T	C	rs17860300	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51737562T>C	ENST00000293636.1	-	3	215	c.175A>G	c.(175-177)Atg>Gtg	p.M59V		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	59	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		M -> V (in dbSNP:rs17860300).		exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						GCAGCTGTCATCACCCAGTTC	0.507													T|||	720	0.14377	0.0809	0.1772	5008	,	,		19403	0.0417		0.2873	False		,,,				2504	0.1626				p.M59V		Atlas-SNP	.											CELA1,NS,carcinoma,+2,1	CELA1	39	1	0			c.A175G						PASS	.	T	VAL/MET	524,3882	237.1+/-249.0	26,472,1705	59.0	50.0	53.0		175	-0.8	1.0	12	dbSNP_123	53	2666,5934	425.1+/-354.9	418,1830,2052	yes	missense	CELA1	NM_001971.5	21	444,2302,3757	CC,CT,TT		31.0,11.8929,24.5271	benign	59/259	51737562	3190,9816	2203	4300	6503	SO:0001583	missense	1990	exon3			CTGTCATCACCCA		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.175A>G	12.37:g.51737562T>C	ENSP00000293636:p.Met59Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	37	CCDS8812.1	328	0.15018315018315018	42	0.08536585365853659	69	0.19060773480662985	19	0.033216783216783216	198	0.2612137203166227	T	12.72	2.021611	0.35701	0.118929	0.31	ENSG00000139610	ENST00000293636	D	0.91945	-2.94	5.03	-0.799	0.10901	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.246105	0.43260	N	0.000592	T	0.00012	0.0000	N	0.01686	-0.76	0.26678	P	0.9715944	B	0.14805	0.011	B	0.19148	0.024	T	0.15723	-1.0427	9	0.15066	T	0.55	-12.8783	3.4045	0.07336	0.1286:0.0785:0.3914:0.4014	rs17860300	59	Q9UNI1	CELA1_HUMAN	V	59	ENSP00000293636:M59V	ENSP00000293636:M59V	M	-	1	0	CELA1	50023829	0.027000	0.19231	0.998000	0.56505	0.995000	0.86356	-0.007000	0.12810	0.013000	0.14918	0.523000	0.50628	ATG	T|0.788;C|0.212	0.212	strong		0.507	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
VCAM1	7412	hgsc.bcm.edu	37	1	101203698	101203698	+	Silent	SNP	C	C	T	rs3176878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:101203698C>T	ENST00000294728.2	+	9	2180	c.2079C>T	c.(2077-2079)gaC>gaT	p.D693D	VCAM1_ENST00000347652.2_Silent_p.D601D|VCAM1_ENST00000370115.1_Silent_p.D494D|VCAM1_ENST00000370119.4_Silent_p.D631D	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	693					acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	ACAACAAAGACTATTTTTCTC	0.318													C|||	647	0.129193	0.1672	0.2435	5008	,	,		21950	0.0208		0.1531	False		,,,				2504	0.0838				p.D693D		Atlas-SNP	.											.	VCAM1	111	.	0			c.C2079T						PASS	.	C	,,	718,3688	298.7+/-285.4	63,592,1548	153.0	162.0	159.0		2079,1893,1803	1.5	0.9	1	dbSNP_105	159	1449,7151	276.8+/-292.5	144,1161,2995	no	coding-synonymous,coding-synonymous,coding-synonymous	VCAM1	NM_001078.3,NM_001199834.1,NM_080682.2	,,	207,1753,4543	TT,TC,CC		16.8488,16.296,16.6615	,,	693/740,631/678,601/648	101203698	2167,10839	2203	4300	6503	SO:0001819	synonymous_variant	7412	exon9			CAAAGACTATTTT	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.2079C>T	1.37:g.101203698C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	150	48	0.32	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Silent	SNP	ENST00000294728.2	37	CCDS773.1																																																																																			C|0.854;T|0.146	0.146	strong		0.318	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078	
KIRREL	55243	hgsc.bcm.edu	37	1	158045965	158045965	+	Missense_Mutation	SNP	G	G	A	rs191487619	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158045965G>A	ENST00000359209.6	+	2	182	c.115G>A	c.(115-117)Gtg>Atg	p.V39M	KIRREL_ENST00000392272.2_Missense_Mutation_p.V39M|KIRREL_ENST00000368173.3_Missense_Mutation_p.V39M|KIRREL_ENST00000416935.2_Intron|KIRREL_ENST00000360089.4_5'UTR			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	39	Ig-like C2-type 1.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					ACAGCGGGCCGTGCTCCCCTG	0.627													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18780	0.0		0.004	False		,,,				2504	0.002				p.V39M		Atlas-SNP	.											.	KIRREL	346	.	0			c.G115A						PASS	.	G	MET/VAL	0,1384		0,0,692	35.0	45.0	42.0		115	3.5	1.0	1		42	21,3161		0,21,1570	yes	missense	KIRREL	NM_018240.5	21	0,21,2262	AA,AG,GG		0.66,0.0,0.4599	possibly-damaging	39/758	158045965	21,4545	692	1591	2283	SO:0001583	missense	55243	exon2			CGGGCCGTGCTCC	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15734	protein-coding gene	gene with protein product	"""nephrin-like protein 1"""	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.115G>A	1.37:g.158045965G>A	ENSP00000352138:p.Val39Met	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	140	54	0.385714	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Missense_Mutation	SNP	ENST00000359209.6	37	CCDS1172.2	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	18.11	3.551931	0.65311	0.0	0.0066	ENSG00000183853	ENST00000368173;ENST00000392272;ENST00000359209	D;D;D	0.84516	-1.86;-1.86;-1.86	4.37	3.46	0.39613	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.32343	N	0.006240	D	0.85622	0.5739	M	0.74389	2.26	0.80722	D	1	D	0.63880	0.993	P	0.55923	0.787	D	0.86884	0.2044	10	0.72032	D	0.01	-11.7015	10.6834	0.45828	0.0975:0.0:0.9025:0.0	.	39	Q96J84	KIRR1_HUMAN	M	39	ENSP00000357155:V39M;ENSP00000376098:V39M;ENSP00000352138:V39M	ENSP00000352138:V39M	V	+	1	0	KIRREL	156312589	0.684000	0.27642	1.000000	0.80357	0.997000	0.91878	1.107000	0.31110	1.140000	0.42260	0.655000	0.94253	GTG	G|0.995;A|0.005	0.005	strong		0.627	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487170	32487170	+	Missense_Mutation	SNP	G	G	A	rs1136633	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32487170G>A	ENST00000374975.3	-	3	691	c.629C>T	c.(628-630)aCg>aTg	p.T210M		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						GAGAGGGCTCGTCACGCTTGG	0.488													A|||	1326	0.264776	0.1876	0.3184	5008	,	,		12433	0.2956		0.2604	False		,,,				2504	0.3037				p.T210M		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,+1,1	HLA-DRB5	31	1	0			c.C629T						scavenged	.	A	MET/THR	491,3289		88,315,1487	73.0	83.0	80.0		629	-8.7	0.0	6	dbSNP_86	80	1057,6447		111,835,2806	no	missense	HLA-DRB5	NM_002125.3	81	199,1150,4293	AA,AG,GG		14.0858,12.9894,13.7185	benign	210/267	32487170	1548,9736	1890	3752	5642	SO:0001583	missense	3127	exon3			GGGCTCGTCACGC		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.629C>T	6.37:g.32487170G>A	ENSP00000364114:p.Thr210Met	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	216	15	0.0694444	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	1.089	-0.664536	0.03428	0.129894	0.140858	ENSG00000198502	ENST00000374975	T	0.03124	4.04	4.36	-8.71	0.00848	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.255310	0.05108	N	0.488406	T	0.01254	0.0041	M	0.79011	2.435	0.80722	P	0.0	B;B	0.20459	0.045;0.007	B;B	0.13407	0.009;0.003	T	0.44421	-0.9329	9	0.42905	T	0.14	.	1.1219	0.01726	0.2262:0.1878:0.1331:0.4529	.	137;210	Q29973;Q30154	.;DRB5_HUMAN	M	210	ENSP00000364114:T210M	ENSP00000364114:T210M	T	-	2	0	HLA-DRB5	32595148	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.520000	0.00951	-1.663000	0.01481	-0.992000	0.02543	ACG	G|0.440;A|0.560	0.560	strong		0.488	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
TOP2A	7153	hgsc.bcm.edu	37	17	38545824	38545824	+	Missense_Mutation	SNP	C	C	A	rs11540720	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38545824C>A	ENST00000423485.1	-	35	4701	c.4543G>T	c.(4543-4545)Gca>Tca	p.A1515S	Y_RNA_ENST00000410949.1_RNA	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1515			A -> S (in dbSNP:rs11540720).		apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GGTTTCTTTGCCCGTACAGAT	0.413													C|||	171	0.0341454	0.0998	0.0173	5008	,	,		17081	0.0		0.0209	False		,,,				2504	0.0061				p.A1515S		Atlas-SNP	.											.	TOP2A	124	.	0			c.G4543T						PASS	.	C	SER/ALA	296,3402		10,276,1563	54.0	51.0	52.0		4543	2.2	0.0	17	dbSNP_120	52	181,7997		4,173,3912	yes	missense	TOP2A	NM_001067.3	99	14,449,5475	AA,AC,CC		2.2133,8.0043,4.0165	possibly-damaging	1515/1532	38545824	477,11399	1849	4089	5938	SO:0001583	missense	7153	exon35			TCTTTGCCCGTAC		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.4543G>T	17.37:g.38545824C>A	ENSP00000411532:p.Ala1515Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	82	0.037545787545787544	60	0.12195121951219512	9	0.024861878453038673	0	0.0	13	0.017150395778364115	C	10.07	1.250112	0.22880	0.080043	0.022133	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.53423	0.62	5.35	2.21	0.28008	DTHCT (1);	0.378221	0.30185	N	0.010201	T	0.00524	0.0017	L	0.53249	1.67	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.10450	0.005	T	0.06862	-1.0803	9	0.48119	T	0.1	.	2.2969	0.04153	0.2593:0.461:0.1266:0.1532	rs11540720;rs11540720	1515	P11388	TOP2A_HUMAN	S	1515;1595;1538;1552	ENSP00000411532:A1515S	ENSP00000269577:A1595S	A	-	1	0	TOP2A	35799350	0.031000	0.19500	0.044000	0.18714	0.511000	0.34104	0.139000	0.16036	0.439000	0.26476	0.655000	0.94253	GCA	C|0.957;A|0.043	0.043	strong		0.413	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
ECE1	1889	hgsc.bcm.edu	37	1	21573855	21573855	+	Splice_Site	SNP	G	G	A	rs1076669	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:21573855G>A	ENST00000374893.6	-	9	1096	c.1022C>T	c.(1021-1023)aCc>aTc	p.T341I	ECE1_ENST00000357071.4_Splice_Site_p.T329I|ECE1_ENST00000415912.2_Splice_Site_p.T325I|ECE1_ENST00000528294.1_5'UTR|ECE1_ENST00000264205.6_Splice_Site_p.T338I|ECE1_ENST00000436918.2_Splice_Site_p.T341I	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	341			T -> I (in dbSNP:rs1076669). {ECO:0000269|Ref.6}.		bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		GGGTGCCAAGGTCTGCAAGGG	0.537													G|||	143	0.0285543	0.0038	0.0317	5008	,	,		18119	0.0		0.0785	False		,,,				2504	0.0378				p.T341I		Atlas-SNP	.											.	ECE1	76	.	0			c.C1022T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	66,4340	62.3+/-99.4	1,64,2138	128.0	121.0	124.0		986,974,1013,1022	4.6	1.0	1	dbSNP_86	124	649,7951	165.9+/-218.0	25,599,3676	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	ECE1	NM_001113347.1,NM_001113348.1,NM_001113349.1,NM_001397.2	89,89,89,89	26,663,5814	AA,AG,GG		7.5465,1.498,5.4975	benign,benign,benign,benign	329/759,325/755,338/768,341/771	21573855	715,12291	2203	4300	6503	SO:0001630	splice_region_variant	1889	exon9			GCCAAGGTCTGCA	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.1021-1C>T	1.37:g.21573855G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	124	58	0.467742	NM_001397	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Missense_Mutation	SNP	ENST00000374893.6	37	CCDS215.1	83	0.038003663003663	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	65	0.08575197889182058	G	11.68	1.711809	0.30322	0.01498	0.075465	ENSG00000117298	ENST00000415912;ENST00000357071;ENST00000374893;ENST00000436918;ENST00000264205	T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81	5.48	4.56	0.56223	Peptidase M13 (1);	0.599354	0.18408	N	0.142134	T	0.05547	0.0146	L	0.35793	1.09	0.19575	N	0.999969	B;B;B;B;B	0.19935	0.04;0.011;0.007;0.013;0.009	B;B;B;B;B	0.25759	0.063;0.022;0.032;0.008;0.013	T	0.03566	-1.1024	10	0.38643	T	0.18	-15.5264	7.4439	0.27201	0.0819:0.0:0.6686:0.2494	rs1076669;rs17355495;rs58761677;rs1076669	341;325;341;329;338	B4DKB2;Q2Z2K8;P42892;P42892-2;P42892-4	.;.;ECE1_HUMAN;.;.	I	325;329;341;341;338	ENSP00000405088:T325I;ENSP00000349581:T329I;ENSP00000364028:T341I;ENSP00000388439:T341I;ENSP00000264205:T338I	ENSP00000264205:T338I	T	-	2	0	ECE1	21446442	0.005000	0.15991	0.994000	0.49952	0.855000	0.48748	0.811000	0.27198	2.561000	0.86390	0.555000	0.69702	ACC	G|0.955;A|0.045	0.045	strong		0.537	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397	Missense_Mutation
CEP89	84902	hgsc.bcm.edu	37	19	33414420	33414420	+	Missense_Mutation	SNP	A	A	G	rs4805825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33414420A>G	ENST00000305768.5	-	12	1281	c.1193T>C	c.(1192-1194)gTc>gCc	p.V398A		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	398			V -> A (in dbSNP:rs4805825). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CACTTCTTGGACTCGCATCCT	0.393													A|||	1446	0.288738	0.2194	0.2493	5008	,	,		17961	0.501		0.2167	False		,,,				2504	0.2658				p.V398A		Atlas-SNP	.											.	CEP89	82	.	0			c.T1193C						PASS	.	A	ALA/VAL	922,3482	353.1+/-312.0	90,742,1370	232.0	207.0	215.0		1193	3.0	1.0	19	dbSNP_111	215	1721,6879	314.1+/-311.6	172,1377,2751	yes	missense	CEP89	NM_032816.3	64	262,2119,4121	GG,GA,AA		20.0116,20.9355,20.3245	benign	398/784	33414420	2643,10361	2202	4300	6502	SO:0001583	missense	84902	exon12			TCTTGGACTCGCA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1193T>C	19.37:g.33414420A>G	ENSP00000306105:p.Val398Ala	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	180	77	0.427778	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	679	0.3108974358974359	122	0.24796747967479674	97	0.26795580110497236	306	0.534965034965035	154	0.20316622691292877	A	11.21	1.570529	0.28003	0.209355	0.200116	ENSG00000121289	ENST00000305768	T	0.51071	0.72	5.12	3.02	0.34903	.	0.478493	0.22998	N	0.053115	T	0.00012	0.0000	L	0.55481	1.735	0.09310	P	0.9999999999882019	B;B	0.12630	0.002;0.006	B;B	0.13407	0.006;0.009	T	0.45308	-0.9270	9	0.27082	T	0.32	-12.8387	7.8251	0.29311	0.8273:0.0:0.1727:0.0	rs4805825;rs52813011;rs58402097;rs4805825	151;398	Q96ST8-2;Q96ST8	.;CEP89_HUMAN	A	398	ENSP00000306105:V398A	ENSP00000306105:V398A	V	-	2	0	CEP89	38106260	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.189000	0.50965	0.817000	0.34445	0.529000	0.55759	GTC	A|0.745;G|0.255	0.255	strong		0.393	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
MTUS1	57509	hgsc.bcm.edu	37	8	17611886	17611886	+	Silent	SNP	G	G	A	rs2979788	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17611886G>A	ENST00000262102.6	-	2	1655	c.1431C>T	c.(1429-1431)ccC>ccT	p.P477P	MTUS1_ENST00000519263.1_Silent_p.P477P|MTUS1_ENST00000381869.3_Silent_p.P477P|MTUS1_ENST00000381862.3_Silent_p.P477P	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	477					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TTCCTAAACTGGGTTTACACA	0.403													A|||	3344	0.667732	0.3661	0.8228	5008	,	,		19432	0.5942		0.8519	False		,,,				2504	0.8517				p.P477P		Atlas-SNP	.											.	MTUS1	144	.	0			c.C1431T						PASS	.	A	,	1707,1981		386,935,523	157.0	148.0	151.0		1431,1431	-2.7	0.0	8	dbSNP_101	151	6879,1329		2867,1145,92	no	coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2	,	3253,2080,615	AA,AG,GG		16.1915,46.2852,27.8245	,	477/1271,477/1217	17611886	8586,3310	1844	4104	5948	SO:0001819	synonymous_variant	57509	exon2			TAAACTGGGTTTA	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1431C>T	8.37:g.17611886G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	225	224	0.995556	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			G|0.311;A|0.689	0.689	strong		0.403	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
PRSS3	5646	hgsc.bcm.edu	37	9	33796673	33796673	+	Missense_Mutation	SNP	G	G	A	rs76740888		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:33796673G>A	ENST00000361005.5	+	2	244	c.244G>A	c.(244-246)Gtt>Att	p.V82I	RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000342836.4_Missense_Mutation_p.V39I|PRSS3_ENST00000379405.3_Missense_Mutation_p.V25I|PRSS3_ENST00000429677.3_Missense_Mutation_p.V18I	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	82	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			TGACAAGATTGTTGGGGGCTA	0.557																																					p.V82I		Atlas-SNP	.											.	PRSS3	79	.	0			c.G244A						PASS	.						190.0	179.0	183.0					9																	33796673		2203	4300	6503	SO:0001583	missense	5646	exon2			AAGATTGTTGGGG		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.244G>A	9.37:g.33796673G>A	ENSP00000354280:p.Val82Ile	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	283	15	0.0530035	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	37	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	G	0.331	-0.956310	0.02267	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	D;D;D;D;D	0.93906	-2.54;-2.54;-3.31;-2.54;-3.31	3.21	1.32	0.21799	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.057900	0.64402	D	0.000002	D	0.88529	0.6461	L	0.41573	1.285	0.37860	D	0.929704	B;B;B	0.30542	0.122;0.266;0.284	B;B;B	0.40101	0.184;0.319;0.127	T	0.77464	-0.2578	10	0.11182	T	0.66	.	6.4881	0.22099	0.3388:0.0:0.6612:0.0	.	25;82;39	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	I	82;37;39;18;25	ENSP00000354280:V82I;ENSP00000401249:V37I;ENSP00000340889:V39I;ENSP00000401828:V18I;ENSP00000368715:V25I	ENSP00000340889:V39I	V	+	1	0	PRSS3	33786673	0.998000	0.40836	0.673000	0.29887	0.001000	0.01503	2.615000	0.46368	0.048000	0.15891	-2.635000	0.00153	GTT	.	.	weak		0.557	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549540	32549540	+	Missense_Mutation	SNP	C	C	T	rs74626234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549540C>T	ENST00000360004.5	-	3	551	c.446G>A	c.(445-447)aGt>aAt	p.S149N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	149	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						ATAGAAACCACTCACAGAGCA	0.532										Multiple Myeloma(14;0.17)																											p.S149N		Atlas-SNP	.											HLA-DRB1,NS,carcinoma,-1,1	HLA-DRB1	41	1	0			c.G446A						PASS	.						107.0	128.0	120.0					6																	32549540		1511	2709	4220	SO:0001583	missense	3123	exon3			AAACCACTCACAG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.446G>A	6.37:g.32549540C>T	ENSP00000353099:p.Ser149Asn	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	520	103	0.198077	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	0.502	-0.870320	0.02570	.	.	ENSG00000196126	ENST00000360004	T	0.02974	4.09	3.87	0.0265	0.14150	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.369240	0.34067	N	0.004292	T	0.00412	0.0013	N	0.17872	0.535	0.24042	N	0.996072	B	0.02656	0.0	B	0.08055	0.003	T	0.45498	-0.9257	10	0.02654	T	1	.	3.9566	0.09393	0.0:0.2842:0.2583:0.4575	rs2308765;rs17841952;rs17856294	149	P01911	2B1F_HUMAN	N	149	ENSP00000353099:S149N	ENSP00000353099:S149N	S	-	2	0	HLA-DRB1	32657518	0.000000	0.05858	0.997000	0.53966	0.962000	0.63368	-1.449000	0.02392	0.181000	0.19994	-0.389000	0.06534	AGT	C|0.844;T|0.156	0.156	strong		0.532	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
Unknown	0	hgsc.bcm.edu	37	X	71379702	71379702	+	IGR	SNP	T	T	C	rs7884806	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:71379702T>C								BX119917.1 (7438 upstream) : PIN4 (21823 downstream)																							ATCATGATTATCTACTGGGAC	0.562													T|||	1372	0.363444	0.2156	0.389	3775	,	,		14128	0.0317		0.5517	False		,,,				2504	0.2352				p.I8T		Atlas-SNP	.											.	FLJ44635	13	.	0			c.T23C						PASS	.	T	THR/ILE	1194,2597		164,686,180,760,391	60.0	54.0	56.0		23	0.5	0.2	X	dbSNP_116	56	4946,1758		1351,896,1348,175,512	yes	missense	FLJ44635	NM_207422.2	89	1515,1582,1528,935,903	CC,CT,C,TT,T		26.2232,31.4956,41.496	benign	8/141	71379702	6140,4355	2181	4282	6463	SO:0001628	intergenic_variant	0	exon2			TGATTATCTACTG																													X.37:g.71379702T>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_207422		Missense_Mutation	SNP		37																																																																																				0|0.005;C|0.369	0.369	strong	0	0.562								
LILRA3	11026	hgsc.bcm.edu	37	19	54802693	54802693	+	Missense_Mutation	SNP	C	C	T	rs73055462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54802693C>T	ENST00000251390.3	-	5	839	c.748G>A	c.(748-750)Gcc>Acc	p.A250T	LILRA3_ENST00000391744.3_Missense_Mutation_p.A186T|LILRA3_ENST00000391745.1_Missense_Mutation_p.A267T	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	250	Ig-like C2-type 3.			A -> T (in Ref. 6; AAM18037). {ECO:0000305}.	defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCGTAGCCGGCATCAGAGCCA	0.612													.|||	231	0.0461262	0.0507	0.0331	5008	,	,		10951	0.002		0.0577	False		,,,				2504	0.0828				p.A250T		Atlas-SNP	.											.	LILRA3	65	.	0			c.G748A						PASS	.	C	THR/ALA,THR/ALA	220,4166		22,176,1995	65.0	60.0	62.0		556,748	-4.1	0.0	19	dbSNP_130	62	638,7684		117,404,3640	no	missense,missense	LILRA3	NM_001172654.1,NM_006865.3	58,58	139,580,5635	TT,TC,CC		7.6664,5.016,6.7517	,	186/376,250/440	54802693	858,11850	2193	4161	6354	SO:0001583	missense	11026	exon5			AGCCGGCATCAGA	U91926		19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.748G>A	19.37:g.54802693C>T	ENSP00000251390:p.Ala250Thr	Somatic	343	1	0.00291545		WXS	Illumina HiSeq	Phase_I	165	163	0.987879	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	92	0.04212454212454213	21	0.042682926829268296	16	0.04419889502762431	0	0.0	55	0.07255936675461741	C	7.946	0.743724	0.15642	0.05016	0.076664	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.12672	2.66;2.66;2.66	2.03	-4.05	0.03998	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.581811	0.14052	N	0.344695	T	0.00384	0.0012	N	0.16066	0.365	0.09310	N	1	B;B	0.26041	0.021;0.14	B;B	0.36092	0.08;0.217	T	0.36529	-0.9744	10	0.51188	T	0.08	.	4.5512	0.12114	0.0:0.2539:0.1842:0.562	.	250;250	E7EU74;Q8N6C8	.;LIRA3_HUMAN	T	250;186;267	ENSP00000251390:A250T;ENSP00000375624:A186T;ENSP00000375625:A267T	ENSP00000251390:A250T	A	-	1	0	LILRA3	59494505	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.833000	0.00180	-1.396000	0.02071	-0.236000	0.12185	GCC	C|0.944;T|0.056	0.056	strong		0.612	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
LAPTM5	7805	hgsc.bcm.edu	37	1	31208042	31208042	+	Missense_Mutation	SNP	C	C	T	rs35351292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:31208042C>T	ENST00000294507.3	-	7	751	c.677G>A	c.(676-678)aGa>aAa	p.R226K		NM_006762.2	NP_006753.1	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5	226			R -> K (in dbSNP:rs35351292). {ECO:0000269|PubMed:15489334}.		transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)				large_intestine(2)|lung(7)|skin(1)	10		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		CTTGGAGTTTCTCTTCTCCTC	0.537													C|||	578	0.115415	0.0408	0.1124	5008	,	,		20260	0.0764		0.2664	False		,,,				2504	0.1033				p.R226K		Atlas-SNP	.											.	LAPTM5	30	.	0			c.G677A						PASS	.	C	LYS/ARG	363,4043	186.0+/-213.0	12,339,1852	307.0	269.0	282.0		677	-3.4	0.0	1	dbSNP_126	282	2178,6422	370.8+/-336.0	283,1612,2405	yes	missense	LAPTM5	NM_006762.2	26	295,1951,4257	TT,TC,CC		25.3256,8.2388,19.5371	benign	226/263	31208042	2541,10465	2203	4300	6503	SO:0001583	missense	7805	exon7			GAGTTTCTCTTCT	U51240	CCDS337.1	1p34	2009-07-20	2009-07-20		ENSG00000162511	ENSG00000162511			29612	protein-coding gene	gene with protein product		601476	"""lysosomal multispanning membrane protein 5"""			8661146, 12527926	Standard	NM_006762		Approved		uc001bsc.2	Q13571	OTTHUMG00000003707	ENST00000294507.3:c.677G>A	1.37:g.31208042C>T	ENSP00000294507:p.Arg226Lys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_006762	Q13240|Q14698|Q3KP54	Missense_Mutation	SNP	ENST00000294507.3	37	CCDS337.1	299	0.13690476190476192	23	0.046747967479674794	45	0.12430939226519337	37	0.06468531468531469	194	0.2559366754617414	C	3.338	-0.135257	0.06711	0.082388	0.253256	ENSG00000162511	ENST00000294507;ENST00000424259	T	0.42900	0.96	5.5	-3.43	0.04810	.	1.182330	0.05835	N	0.618151	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.18263	0.021	T	0.22312	-1.0220	9	0.06099	T	0.92	-0.9238	1.3828	0.02233	0.1734:0.2608:0.3426:0.2231	rs35351292;rs61750962	226	Q13571	LAPM5_HUMAN	K	226	ENSP00000294507:R226K	ENSP00000294507:R226K	R	-	2	0	LAPTM5	30980629	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.033000	0.03571	-0.202000	0.10268	-0.175000	0.13238	AGA	T|0.179;G|0.000;C|0.821	0.179	strong		0.537	LAPTM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010463.1	NM_006762	
PDXDC1	23042	hgsc.bcm.edu	37	16	15095675	15095675	+	Silent	SNP	C	C	A	rs9921162	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15095675C>A	ENST00000396410.4	+	4	301	c.204C>A	c.(202-204)ctC>ctA	p.L68L	PDXDC1_ENST00000535621.2_Silent_p.L68L|PDXDC1_ENST00000447912.2_Intron|PDXDC1_ENST00000455313.2_Silent_p.L68L|PDXDC1_ENST00000569715.1_Intron|PDXDC1_ENST00000450288.2_Intron|PDXDC1_ENST00000563679.1_Silent_p.L86L|PDXDC1_ENST00000325823.7_Silent_p.L53L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	68					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTCAGAATCTCATGCATGGAG	0.483																																					p.L68L		Atlas-SNP	.											PDXDC1,NS,carcinoma,0,1	PDXDC1	59	1	0			c.C204A						PASS	.	A		909,3485		55,799,1343	60.0	58.0	58.0		204	-1.9	1.0	16	dbSNP_119	58	1467,7133		37,1393,2870	no	coding-synonymous	PDXDC1	NM_015027.2		92,2192,4213	AA,AC,CC		17.0581,20.6873,18.2854		68/789	15095675	2376,10618	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon4			GAATCTCATGCAT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.204C>A	16.37:g.15095675C>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	193	67	0.34715	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			C|0.773;A|0.227	0.227	strong		0.483	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118231363	118231363	+	Missense_Mutation	SNP	A	A	G	rs1897519|rs386747985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:118231363A>G	ENST00000369230.3	+	10	1290	c.1144A>G	c.(1144-1146)Agg>Ggg	p.R382G		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	382	PLAT.		R -> G (in dbSNP:rs1897519). {ECO:0000269|PubMed:15489334}.		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		CGGGGCAGTTAGGAAAACTGG	0.483													G|||	4850	0.96845	0.885	0.9914	5008	,	,		14264	1.0		1.0	False		,,,				2504	1.0				p.R382G		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.A1144G						PASS	.	G	GLY/ARG	3938,468	220.4+/-237.8	1763,412,28	128.0	136.0	134.0		1144	4.2	0.0	10	dbSNP_92	134	8589,11	8.4+/-32.0	4289,11,0	yes	missense	PNLIPRP3	NM_001011709.2	125	6052,423,28	GG,GA,AA		0.1279,10.6219,3.6829	benign	382/468	118231363	12527,479	2203	4300	6503	SO:0001583	missense	119548	exon10			GCAGTTAGGAAAA	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1144A>G	10.37:g.118231363A>G	ENSP00000358232:p.Arg382Gly	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	172	171	0.994186	NM_001011709		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	2131	0.9757326007326007	443	0.9004065040650406	358	0.988950276243094	572	1.0	758	1.0	G	0.970	-0.700475	0.03279	0.893781	0.998721	ENSG00000203837	ENST00000369230	T	0.54071	0.59	4.18	4.18	0.49190	Lipoxygenase, LH2 (2);Lipase/lipooxygenase, PLAT/LH2 (1);	0.285017	0.22236	N	0.062759	T	0.00012	0.0000	N	0.00037	-2.525	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38628	-0.9652	9	0.02654	T	1	.	9.9547	0.41660	0.0996:0.0:0.9004:0.0	rs1897519;rs60531469;rs1897519	382	Q17RR3	LIPR3_HUMAN	G	382	ENSP00000358232:R382G	ENSP00000358232:R382G	R	+	1	2	PNLIPRP3	118221353	0.001000	0.12720	0.002000	0.10522	0.009000	0.06853	0.528000	0.23002	1.084000	0.41184	-0.186000	0.12905	AGG	A|0.029;G|0.971	0.971	strong		0.483	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
SELL	6402	hgsc.bcm.edu	37	1	169673838	169673838	+	Missense_Mutation	SNP	G	G	A	rs2229569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169673838G>A	ENST00000236147.4	-	5	836	c.676C>T	c.(676-678)Cct>Tct	p.P226S	SELL_ENST00000463108.1_5'UTR|C1orf112_ENST00000498289.1_Intron	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	213	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					TTTCCCAAAGGGTGAGTACAG	0.478													G|||	1222	0.24401	0.27	0.2752	5008	,	,		19408	0.254		0.175	False		,,,				2504	0.2474				p.P226S		Atlas-SNP	.											.	SELL	43	.	0			c.C676T						PASS	.	G	SER/PRO	809,2909		85,639,1135	47.0	47.0	47.0		676	5.3	0.9	1	dbSNP_98	47	1076,7044		73,930,3057	yes	missense	SELL	NM_000655.4	74	158,1569,4192	AA,AG,GG		13.2512,21.759,15.9233	probably-damaging	226/386	169673838	1885,9953	1859	4060	5919	SO:0001583	missense	6402	exon5			CCAAAGGGTGAGT	M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"""CD molecules"""	10720	protein-coding gene	gene with protein product		153240	"""lymphocyte adhesion molecule 1"""	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.676C>T	1.37:g.169673838G>A	ENSP00000236147:p.Pro226Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	138	82	0.594203	NM_000655	B2R6Q8|P15023|Q9UJ43	Missense_Mutation	SNP	ENST00000236147.4	37	CCDS53427.1	523	0.23946886446886448	139	0.28252032520325204	91	0.2513812154696133	163	0.28496503496503495	130	0.17150395778364116	G	18.76	3.692950	0.68271	0.21759	0.132512	ENSG00000188404	ENST00000236147	T	0.48201	0.82	5.31	5.31	0.75309	Complement control module (2);Sushi/SCR/CCP (3);	0.117810	0.38326	N	0.001734	T	0.56717	0.2004	M	0.63843	1.955	0.23533	P	0.99747012	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.61033	-0.7144	9	0.56958	D	0.05	-9.9883	12.5565	0.56257	0.0:0.1674:0.8325:0.0	rs2229569;rs4987310;rs52812496;rs58249723;rs4987310	226;213	Q8WW79;P14151	.;LYAM1_HUMAN	S	226	ENSP00000236147:P226S	ENSP00000236147:P226S	P	-	1	0	SELL	167940462	0.994000	0.37717	0.872000	0.34217	0.870000	0.49936	2.131000	0.42074	2.631000	0.89168	0.655000	0.94253	CCT	G|0.766;A|0.234	0.234	strong		0.478	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655	
SELE	6401	hgsc.bcm.edu	37	1	169695870	169695870	+	Missense_Mutation	SNP	G	G	A	rs5355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169695870G>A	ENST00000333360.7	-	11	1862	c.1723C>T	c.(1723-1725)Ctc>Ttc	p.L575F	SELE_ENST00000367776.1_Missense_Mutation_p.L512F|SELE_ENST00000367780.4_Missense_Mutation_p.L450F|SELE_ENST00000367779.4_Missense_Mutation_p.L449F|SELE_ENST00000367782.4_Missense_Mutation_p.L512F|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367774.1_Missense_Mutation_p.L449F|SELE_ENST00000367777.1_Missense_Mutation_p.L512F|SELE_ENST00000367775.1_Missense_Mutation_p.L450F|SELE_ENST00000367781.4_Missense_Mutation_p.L512F	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	575			L -> F (in dbSNP:rs5355). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:10982036, ECO:0000269|PubMed:8557254, ECO:0000269|Ref.4}.		actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)	p.L575I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	AGCCAGAGGAGAAATGGTGCT	0.418													G|||	231	0.0461262	0.0121	0.0274	5008	,	,		21738	0.0516		0.0477	False		,,,				2504	0.0982				p.L575F		Atlas-SNP	.											SELE,rectum,carcinoma,0,1	SELE	84	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1723T	GRCh37	CM961269	SELE	M	rs5355	PASS	.	G	PHE/LEU	76,4330	65.8+/-103.3	0,76,2127	85.0	72.0	76.0		1723	4.6	1.0	1	dbSNP_52	76	368,8232	122.9+/-181.8	6,356,3938	yes	missense	SELE	NM_000450.2	22	6,432,6065	AA,AG,GG		4.2791,1.7249,3.4138	benign	575/611	169695870	444,12562	2203	4300	6503	SO:0001583	missense	6401	exon11			AGAGGAGAAATGG	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"""CD molecules"""	10718	protein-coding gene	gene with protein product		131210	"""endothelial adhesion molecule 1"""	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.1723C>T	1.37:g.169695870G>A	ENSP00000331736:p.Leu575Phe	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_000450	A2RRD6|P16111	Missense_Mutation	SNP	ENST00000333360.7	37	CCDS1283.1	73	0.033424908424908424	4	0.008130081300813009	10	0.027624309392265192	29	0.050699300699300696	30	0.0395778364116095	G	10.68	1.417529	0.25552	0.017249	0.042791	ENSG00000007908	ENST00000367781;ENST00000367782;ENST00000367780;ENST00000367779;ENST00000333360;ENST00000367777;ENST00000367775;ENST00000367776;ENST00000367774	T;T;T;T;T;T;T;T;T	0.25414	1.8;1.83;1.91;1.84;1.83;1.83;1.91;1.8;1.84	5.52	4.6	0.57074	.	0.263488	0.20200	N	0.097120	T	0.13286	0.0322	M	0.71581	2.175	0.22866	N	0.99863	B	0.32939	0.391	B	0.33392	0.163	T	0.12016	-1.0564	10	0.23891	T	0.37	-14.6227	11.9311	0.52847	0.0:0.0:0.827:0.173	rs5355;rs17592301;rs56494597;rs5355	575	P16581	LYAM2_HUMAN	F	512;512;450;449;575;512;450;512;449	ENSP00000356755:L512F;ENSP00000356756:L512F;ENSP00000356754:L450F;ENSP00000356753:L449F;ENSP00000331736:L575F;ENSP00000356751:L512F;ENSP00000356749:L450F;ENSP00000356750:L512F;ENSP00000356748:L449F	ENSP00000331736:L575F	L	-	1	0	SELE	167962494	1.000000	0.71417	0.982000	0.44146	0.103000	0.19146	2.279000	0.43435	1.303000	0.44873	0.650000	0.86243	CTC	G|0.963;A|0.037	0.037	strong		0.418	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450	
KCNA5	3741	hgsc.bcm.edu	37	12	5154064	5154064	+	Missense_Mutation	SNP	G	G	A	rs12720442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:5154064G>A	ENST00000252321.3	+	1	980	c.751G>A	c.(751-753)Gcc>Acc	p.A251T		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	251					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	GTCCGCGCGGGCCATCGCCAT	0.587													G|||	41	0.0081869	0.0015	0.0274	5008	,	,		15304	0.0		0.0169	False		,,,				2504	0.0031				p.A251T		Atlas-SNP	.											KCNA5,brain,glioma,0,1	KCNA5	138	1	0			c.G751A						PASS	.	G	THR/ALA	14,4392	22.3+/-47.3	1,12,2190	109.0	118.0	115.0		751	4.8	0.9	12	dbSNP_126	115	109,8491	58.3+/-119.8	1,107,4192	yes	missense	KCNA5	NM_002234.2	58	2,119,6382	AA,AG,GG		1.2674,0.3177,0.9457	benign	251/614	5154064	123,12883	2203	4300	6503	SO:0001583	missense	3741	exon1			GCGCGGGCCATCG	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.751G>A	12.37:g.5154064G>A	ENSP00000252321:p.Ala251Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	37	CCDS8536.1	22	0.010073260073260074	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	13	0.017150395778364115	G	10.28	1.305403	0.23736	0.003177	0.012674	ENSG00000130037	ENST00000252321	T	0.65178	-0.14	4.77	4.77	0.60923	.	0.227351	0.34484	U	0.003922	T	0.38480	0.1042	L	0.38175	1.15	0.28718	N	0.90318	B	0.13145	0.007	B	0.17722	0.019	T	0.48603	-0.9021	10	0.48119	T	0.1	.	16.9696	0.86295	0.0:0.0:1.0:0.0	rs12720442;rs45573135	251	P22460	KCNA5_HUMAN	T	251	ENSP00000252321:A251T	ENSP00000252321:A251T	A	+	1	0	KCNA5	5024325	0.948000	0.32251	0.932000	0.37286	0.982000	0.71751	5.267000	0.65530	2.478000	0.83669	0.561000	0.74099	GCC	G|0.990;A|0.010	0.010	strong		0.587	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234	
ST14	6768	hgsc.bcm.edu	37	11	130060453	130060453	+	Missense_Mutation	SNP	G	G	A	rs35230546|rs144266633	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130060453G>A	ENST00000278742.5	+	7	1157	c.739G>A	c.(739-741)Gcc>Acc	p.A247T		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	247	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	CTGCCAGTGGGCCCTGCGGGG	0.687																																					p.A247T		Atlas-SNP	.											.	ST14	82	.	0			c.G739A						PASS	.	G	THR/ALA	0,4400		0,0,2200	27.0	25.0	26.0		739	1.3	1.0	11	dbSNP_134	26	7,8583		0,7,4288	yes	missense	ST14	NM_021978.3	58	0,7,6488	AA,AG,GG		0.0815,0.0,0.0539	benign	247/856	130060453	7,12983	2200	4295	6495	SO:0001583	missense	6768	exon7			CAGTGGGCCCTGC	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.739G>A	11.37:g.130060453G>A	ENSP00000278742:p.Ala247Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	45	29	0.644444	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	37	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.510543	0.27036	0.0	8.15E-4	ENSG00000149418	ENST00000278742;ENST00000525779	T	0.30714	1.52	5.45	1.26	0.21427	CUB (5);	1.014350	0.07937	N	0.978525	T	0.10035	0.0246	N	0.01188	-0.97	0.23271	N	0.998006	B;B	0.10296	0.003;0.002	B;B	0.12837	0.008;0.005	T	0.34625	-0.9821	10	0.08837	T	0.75	.	7.5637	0.27866	0.5136:0.0:0.4864:0.0	.	57;247	B4DYI7;Q9Y5Y6	.;ST14_HUMAN	T	247;149	ENSP00000278742:A247T	ENSP00000278742:A247T	A	+	1	0	ST14	129565663	0.025000	0.19082	0.997000	0.53966	0.915000	0.54546	0.259000	0.18405	-0.033000	0.13736	0.650000	0.86243	GCC	G|1.000;A|0.000	0.000	strong		0.687	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
MIA3	375056	hgsc.bcm.edu	37	1	222803204	222803204	+	Missense_Mutation	SNP	A	A	G	rs2936051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:222803204A>G	ENST00000344922.5	+	4	2667	c.2642A>G	c.(2641-2643)gAg>gGg	p.E881G	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Missense_Mutation_p.E881G|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	881			E -> G (in dbSNP:rs2936051). {ECO:0000269|PubMed:9039502}.		chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GAGGACCATGAGAACACAGAG	0.502													a|||	1609	0.321286	0.3374	0.4236	5008	,	,		19303	0.3998		0.168	False		,,,				2504	0.3037				p.E881G		Atlas-SNP	.											.	MIA3	167	.	0			c.A2642G						PASS	.		GLY/GLU	1144,2716		158,828,944	35.0	36.0	35.0		2642	3.8	0.0	1	dbSNP_101	35	1457,6799		136,1185,2807	yes	missense	MIA3	NM_198551.2	98	294,2013,3751	GG,GA,AA		17.6478,29.6373,21.4675	probably-damaging	881/1908	222803204	2601,9515	1930	4128	6058	SO:0001583	missense	375056	exon4			ACCATGAGAACAC		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.2642A>G	1.37:g.222803204A>G	ENSP00000340900:p.Glu881Gly	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	645|645	0.29532967032967034|0.29532967032967034	168|168	0.34146341463414637|0.34146341463414637	128|128	0.35359116022099446|0.35359116022099446	221|221	0.38636363636363635|0.38636363636363635	128|128	0.16886543535620052|0.16886543535620052	a|a	18.04|18.04	3.534540|3.534540	0.64972|0.64972	0.296373|0.296373	0.176478|0.176478	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831|ENST00000354906	T;T|.	0.06218|.	3.33;3.33|.	4.91|4.91	3.79|3.79	0.43588|0.43588	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	P|P	0.0|0.0	B;D|.	0.89917|.	0.385;1.0|.	B;D|.	0.74674|.	0.313;0.984|.	T|.	0.38499|.	-0.9658|.	8|.	0.66056|.	D|.	0.02|.	.|.	10.284|10.284	0.43556|0.43556	0.9215:0.0:0.0785:0.0|0.9215:0.0:0.0785:0.0	rs2936051;rs3748628;rs9441929;rs17163335|rs2936051;rs3748628;rs9441929;rs17163335	881;881|.	Q5JRA6-2;Q5JRA6|.	.;MIA3_HUMAN|.	G|W	881|463	ENSP00000340900:E881G;ENSP00000340587:E881G|.	ENSP00000325973:E881G|.	E|X	+|+	2|3	0|0	MIA3|MIA3	220869827|220869827	0.997000|0.997000	0.39634|0.39634	0.006000|0.006000	0.13384|0.13384	0.006000|0.006000	0.05464|0.05464	4.080000|4.080000	0.57620|0.57620	0.842000|0.842000	0.35045|0.35045	0.375000|0.375000	0.23000|0.23000	GAG|TGA	A|0.748;G|0.252	0.252	strong		0.502	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
RGAG4	340526	hgsc.bcm.edu	37	X	71349753	71349753	+	Silent	SNP	G	G	A	rs12397326		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:71349753G>A	ENST00000545866.1	-	1	2005	c.1638C>T	c.(1636-1638)cgC>cgT	p.R546R	RGAG4_ENST00000609883.1_Silent_p.R546R|NHSL2_ENST00000540800.1_Intron	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	546										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					GCACAGGGGGGCGTCTTCGAA	0.602													G|||	1160	0.307285	0.0386	0.3775	3775	,	,		13445	0.0298		0.5934	False		,,,				2504	0.2249				p.R546R		Atlas-SNP	.											.	RGAG4	63	.	0			c.C1638T						PASS	.	G	,	507,2759		47,335,78,966,492	38.0	43.0	41.0		,1638	-4.0	0.1	X	dbSNP_120	41	5072,1385		1458,749,1407,126,384	no	intron,coding-synonymous	RGAG4,NHSL2	NM_001013627.2,NM_001024455.3	,	1505,1084,1485,1092,876	AA,AG,A,GG,G		21.4496,15.5236,42.6206	,	,546/570	71349753	5579,4144	1918	4124	6042	SO:0001819	synonymous_variant	340526	exon1			AGGGGGGCGTCTT	AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.1638C>T	X.37:g.71349753G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Silent	SNP	ENST00000545866.1	37	CCDS55446.1																																																																																			G|0.616;A|0.384	0.384	strong		0.602	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
ATP8B3	148229	hgsc.bcm.edu	37	19	1806667	1806667	+	Missense_Mutation	SNP	C	C	T	rs45574836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1806667C>T	ENST00000310127.6	-	7	875	c.637G>A	c.(637-639)Gcc>Acc	p.A213T	ATP8B3_ENST00000525591.1_Missense_Mutation_p.A160T|ATP8B3_ENST00000539485.1_Missense_Mutation_p.A213T|ATP8B3_ENST00000526092.2_Missense_Mutation_p.A160T	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	213					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTGTTGATGGCTCTGTCACTC	0.667													c|||	310	0.061901	0.0136	0.0504	5008	,	,		13981	0.0942		0.0606	False		,,,				2504	0.1033				p.A213T		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G637A						PASS	.	C	THR/ALA,THR/ALA	49,4023		0,49,1987	42.0	49.0	47.0		478,637	-8.1	0.0	19	dbSNP_127	47	373,7911		8,357,3777	yes	missense,missense	ATP8B3	NM_001178002.1,NM_138813.2	58,58	8,406,5764	TT,TC,CC		4.5027,1.2033,3.4153	benign,benign	160/1264,213/1301	1806667	422,11934	2036	4142	6178	SO:0001583	missense	148229	exon7			TGATGGCTCTGTC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.637G>A	19.37:g.1806667C>T	ENSP00000311336:p.Ala213Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	36	0.349515	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	129	0.059065934065934064	7	0.014227642276422764	14	0.03867403314917127	61	0.10664335664335664	47	0.06200527704485488	c	9.701	1.154504	0.21371	0.012033	0.045027	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591;ENST00000526092;ENST00000382339	D;D;D;D	0.90197	-2.63;-2.63;-2.63;-2.63	4.08	-8.15	0.01065	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	2.158490	0.02032	N	0.048604	T	0.09598	0.0236	L	0.31752	0.955	0.09310	N	1	B;B;B	0.25719	0.132;0.01;0.03	B;B;B	0.23574	0.047;0.018;0.018	T	0.61686	-0.7012	10	0.33940	T	0.23	.	9.4352	0.38635	0.0939:0.3028:0.0:0.6033	rs45574836	160;213;160	F5H3R9;O60423;Q7Z485	.;AT8B3_HUMAN;.	T	213;213;160;160;160	ENSP00000311336:A213T;ENSP00000443574:A213T;ENSP00000437115:A160T;ENSP00000445204:A160T	ENSP00000311336:A213T	A	-	1	0	ATP8B3	1757667	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	-1.593000	0.02096	-1.983000	0.00987	-2.069000	0.00389	GCC	C|0.941;T|0.059	0.059	strong		0.667	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
SPATA13	221178	hgsc.bcm.edu	37	13	24823699	24823699	+	5'UTR	SNP	G	G	A	rs41287016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:24823699G>A	ENST00000382095.4	+	0	270				SPATA13_ENST00000424834.2_Missense_Mutation_p.G580S|RP11-307N16.6_ENST00000382141.4_Intron|SPATA13_ENST00000474317.1_3'UTR|SPATA13_ENST00000382108.3_Missense_Mutation_p.G580S	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		GAGGAGATGGGGCTCTGGGAG	0.592													G|||	168	0.0335463	0.0371	0.0504	5008	,	,		15704	0.0		0.0716	False		,,,				2504	0.0123				p.G580S		Atlas-SNP	.											.	SPATA13	92	.	0			c.G1738A						PASS	.	G	SER/GLY,	45,1339		1,43,648	30.0	35.0	34.0		1738,	4.1	0.9	13	dbSNP_127	34	185,2997		8,169,1414	yes	missense,utr-5	SPATA13	NM_001166271.1,NM_153023.2	56,	9,212,2062	AA,AG,GG		5.814,3.2514,5.0372	,	580/1278,	24823699	230,4336	692	1591	2283	SO:0001623	5_prime_UTR_variant	221178	exon3			AGATGGGGCTCTG	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-138G>A	13.37:g.24823699G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	138	81	0.586957	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	37	CCDS9305.1	89|89	0.04075091575091575|0.04075091575091575	16|16	0.032520325203252036|0.032520325203252036	23|23	0.06353591160220995|0.06353591160220995	0|0	0.0|0.0	50|50	0.06596306068601583|0.06596306068601583	G|G	19.19|19.19	3.779485|3.779485	0.70107|0.70107	0.032514|0.032514	0.05814|0.05814	ENSG00000182957|ENSG00000182957	ENST00000424834|ENST00000382108	.|T	.|0.77229	.|-1.08	5.8|5.8	4.08|4.08	0.47627|0.47627	.|.	.|.	.|.	.|.	.|.	T|T	0.28400|0.28400	0.0702|0.0702	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.58814|0.58814	-0.7570|-0.7570	4|6	.|0.49607	.|T	.|0.09	.|.	8.672|8.672	0.34156|0.34156	0.2275:0.0:0.7725:0.0|0.2275:0.0:0.7725:0.0	rs41287016|rs41287016	.|.	.|.	.|.	E|S	617|580	.|ENSP00000371542:G580S	.|ENSP00000371542:G580S	G|G	+|+	2|1	0|0	SPATA13|SPATA13	23721699|23721699	1.000000|1.000000	0.71417|0.71417	0.949000|0.949000	0.38748|0.38748	0.379000|0.379000	0.30106|0.30106	1.644000|1.644000	0.37228|0.37228	0.812000|0.812000	0.34326|0.34326	0.462000|0.462000	0.41574|0.41574	GGG|GGC	G|0.953;A|0.047	0.047	strong		0.592	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
ZNF107	51427	hgsc.bcm.edu	37	7	64166802	64166802	+	Missense_Mutation	SNP	G	G	T	rs73138709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:64166802G>T	ENST00000395391.1	+	4	1495	c.120G>T	c.(118-120)gaG>gaT	p.E40D	ZNF107_ENST00000344930.3_Missense_Mutation_p.E40D|ZNF107_ENST00000423627.1_Missense_Mutation_p.E40D			Q9UII5	ZN107_HUMAN	zinc finger protein 107	40					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				GTGAATATGAGAATTTACAGT	0.393													g|||	88	0.0175719	0.0023	0.0375	5008	,	,		16210	0.001		0.0427	False		,,,				2504	0.0153				p.E40D		Atlas-SNP	.											.	ZNF107	107	.	0			c.G120T						PASS	.	G	ASP/GLU,ASP/GLU	35,4371		0,35,2168	76.0	71.0	73.0		120,120	-0.2	0.0	7	dbSNP_130	73	396,8204		4,388,3908	yes	missense,missense	ZNF107	NM_001013746.1,NM_016220.3	45,45	4,423,6076	TT,TG,GG		4.6047,0.7944,3.3139	benign,benign	40/784,40/784	64166802	431,12575	2203	4300	6503	SO:0001583	missense	51427	exon7			ATATGAGAATTTA	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.120G>T	7.37:g.64166802G>T	ENSP00000378789:p.Glu40Asp	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_016220		Missense_Mutation	SNP	ENST00000395391.1	37	CCDS5527.1	44	0.020146520146520148	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	30	0.0395778364116095	.	4.715	0.132888	0.09032	0.007944	0.046047	ENSG00000196247	ENST00000541526;ENST00000360117;ENST00000344930;ENST00000423627;ENST00000395391	T;T;T;T	0.07567	4.76;3.18;3.18;3.18	1.13	-0.162	0.13367	.	.	.	.	.	T	0.00724	0.0024	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.17433	0.018	T	0.42120	-0.9470	9	0.41790	T	0.15	.	3.6105	0.08058	0.3231:0.0:0.6769:0.0	.	40	Q9UII5	ZN107_HUMAN	D	40	ENSP00000353234:E40D;ENSP00000343443:E40D;ENSP00000400037:E40D;ENSP00000378789:E40D	ENSP00000343443:E40D	E	+	3	2	ZNF107	63804237	0.000000	0.05858	0.005000	0.12908	0.030000	0.12068	-0.348000	0.07740	-0.264000	0.09365	0.305000	0.20034	GAG	G|0.969;T|0.031	0.031	strong		0.393	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
MCM7	4176	hgsc.bcm.edu	37	7	99696797	99696797	+	Missense_Mutation	SNP	T	T	C	rs2070215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99696797T>C	ENST00000303887.5	-	5	1076	c.431A>G	c.(430-432)aAc>aGc	p.N144S	AP4M1_ENST00000422582.1_5'Flank|AP4M1_ENST00000359593.4_5'Flank|AP4M1_ENST00000421755.1_5'Flank|AP4M1_ENST00000429084.1_5'Flank|MCM7_ENST00000354230.3_5'UTR|MCM7_ENST00000343023.6_Missense_Mutation_p.N144S	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	144			N -> S (in dbSNP:rs2070215). {ECO:0000269|PubMed:8626784}.		cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)	p.N144S(1)		endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACGAGGCTTGTTGCTGCTAGG	0.512													T|||	981	0.195887	0.0129	0.1902	5008	,	,		20215	0.2758		0.2734	False		,,,				2504	0.2853				p.N144S		Atlas-SNP	.											MCM7_ENST00000303887,NS,carcinoma,0,1	MCM7	136	1	1	Substitution - Missense(1)	stomach(1)	c.A431G						scavenged	.	T	SER/ASN,	287,4119	158.5+/-191.2	7,273,1923	110.0	105.0	107.0		431,	-3.6	0.9	7	dbSNP_96	107	2459,6141	405.7+/-348.6	355,1749,2196	yes	missense,utr-5	MCM7	NM_005916.3,NM_182776.1	46,	362,2022,4119	CC,CT,TT		28.593,6.5138,21.1133	benign,	144/720,	99696797	2746,10260	2203	4300	6503	SO:0001583	missense	4176	exon5			GGCTTGTTGCTGC		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 104"""	600592	"""minichromosome maintenance deficient (S. cerevisiae) 7"", ""MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"""	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.431A>G	7.37:g.99696797T>C	ENSP00000307288:p.Asn144Ser	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	37	CCDS5683.1	435	0.19917582417582416	10	0.02032520325203252	73	0.20165745856353592	147	0.256993006993007	205	0.2704485488126649	T	2.044	-0.419462	0.04766	0.065138	0.28593	ENSG00000166508	ENST00000343023;ENST00000303887;ENST00000542483;ENST00000362082;ENST00000425308	T;T;T	0.10382	2.88;2.88;2.88	4.58	-3.6	0.04570	Nucleic acid-binding, OB-fold-like (1);	0.790345	0.12308	N	0.480423	T	0.00012	0.0000	N	0.00729	-1.24	0.53005	P	3.2000000000032E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40572	-0.9556	9	0.06494	T	0.89	-10.0949	7.4761	0.27376	0.0:0.4978:0.2936:0.2086	rs2070215;rs17447420;rs17845219;rs17858032;rs57620700;rs2070215	144	P33993	MCM7_HUMAN	S	144;144;81;37;37	ENSP00000344006:N144S;ENSP00000307288:N144S;ENSP00000411295:N37S	ENSP00000307288:N144S	N	-	2	0	MCM7	99534733	0.002000	0.14202	0.910000	0.35882	0.915000	0.54546	-0.062000	0.11674	-0.576000	0.05974	0.379000	0.24179	AAC	T|0.798;C|0.202	0.202	strong		0.512	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3		
C3orf62	375341	hgsc.bcm.edu	37	3	49313978	49313978	+	Missense_Mutation	SNP	C	C	T	rs13077498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49313978C>T	ENST00000343010.3	-	1	1364	c.328G>A	c.(328-330)Gag>Aag	p.E110K	MIR4271_ENST00000582451.1_RNA	NM_198562.2	NP_940964.1	Q6ZUJ4	CC062_HUMAN	chromosome 3 open reading frame 62	110			E -> K (in dbSNP:rs13077498).							breast(1)|kidney(1)|large_intestine(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGTTTTCTCTCGGGGCACAGA	0.493													C|||	326	0.0650958	0.059	0.0706	5008	,	,		20835	0.0417		0.1133	False		,,,				2504	0.044				p.E110K		Atlas-SNP	.											.	C3orf62	23	.	0			c.G328A						PASS	.	C	LYS/GLU	384,4022	194.0+/-219.0	12,360,1831	135.0	130.0	132.0		328	-7.3	0.0	3	dbSNP_121	132	932,7668	206.6+/-248.6	52,828,3420	yes	missense	C3orf62	NM_198562.2	56	64,1188,5251	TT,TC,CC		10.8372,8.7154,10.1184	benign	110/268	49313978	1316,11690	2203	4300	6503	SO:0001583	missense	375341	exon1			TTCTCTCGGGGCA	AK125642	CCDS2792.1	3p21.31	2006-02-11			ENSG00000188315	ENSG00000188315			24771	protein-coding gene	gene with protein product						12477932	Standard	NM_198562		Approved	FLJ43654	uc003cwn.2	Q6ZUJ4	OTTHUMG00000156819	ENST00000343010.3:c.328G>A	3.37:g.49313978C>T	ENSP00000341139:p.Glu110Lys	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	247	101	0.408907	NM_198562	Q6P7E9|Q7Z3X6	Missense_Mutation	SNP	ENST00000343010.3	37	CCDS2792.1	187	0.08562271062271062	33	0.06707317073170732	33	0.09116022099447514	35	0.06118881118881119	86	0.11345646437994723	C	8.379	0.837036	0.16891	0.087154	0.108372	ENSG00000188315	ENST00000343010;ENST00000436325	T;T	0.37915	1.17;1.17	4.75	-7.32	0.01436	.	0.724870	0.12413	N	0.471107	T	0.00210	0.0006	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25676	-1.0125	9	0.02654	T	1	-0.1717	13.4186	0.60982	0.0:0.0827:0.7423:0.175	rs13077498;rs52829775;rs13077498	110	Q6ZUJ4	CC062_HUMAN	K	110;108	ENSP00000341139:E110K;ENSP00000413663:E108K	ENSP00000341139:E110K	E	-	1	0	C3orf62	49288982	0.000000	0.05858	0.001000	0.08648	0.798000	0.45092	-1.271000	0.02828	-1.626000	0.01552	-1.078000	0.02229	GAG	C|0.907;T|0.093	0.093	strong		0.493	C3orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345990.1	NM_198562	
CAMTA2	23125	hgsc.bcm.edu	37	17	4875566	4875566	+	Silent	SNP	T	T	C	rs238230	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4875566T>C	ENST00000348066.3	-	16	2892	c.2769A>G	c.(2767-2769)ccA>ccG	p.P923P	RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000361571.5_Silent_p.P922P|CAMTA2_ENST00000414043.3_Silent_p.P946P|CAMTA2_ENST00000572543.1_Silent_p.P928P|CAMTA2_ENST00000381311.5_Silent_p.P925P|CAMTA2_ENST00000358183.4_Silent_p.P923P	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	923					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						CAGCGTCCTCTGGAGCAGCCC	0.587													T|||	2889	0.576877	0.7882	0.6599	5008	,	,		17313	0.4028		0.5875	False		,,,				2504	0.4008				p.P946P		Atlas-SNP	.											.	CAMTA2	93	.	0			c.A2838G						PASS	.	T	,,,	3428,978	724.0+/-409.5	1338,752,113	67.0	72.0	71.0		2775,2838,2766,2769	-0.5	1.0	17	dbSNP_79	71	5334,3266	642.3+/-399.8	1650,2034,616	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMTA2	NM_001171166.1,NM_001171167.1,NM_001171168.1,NM_015099.3	,,,	2988,2786,729	CC,CT,TT		37.9767,22.197,32.6311	,,,	925/1198,946/1242,922/1202,923/1203	4875566	8762,4244	2203	4300	6503	SO:0001819	synonymous_variant	23125	exon16			GTCCTCTGGAGCA	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.2769A>G	17.37:g.4875566T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Silent	SNP	ENST00000348066.3	37	CCDS11063.1																																																																																			T|0.359;C|0.641	0.641	strong		0.587	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
AP5Z1	9907	hgsc.bcm.edu	37	7	4825307	4825307	+	Missense_Mutation	SNP	T	T	A	rs11772411	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4825307T>A	ENST00000348624.4	+	9	1218	c.1124T>A	c.(1123-1125)cTg>cAg	p.L375Q	AP5Z1_ENST00000401897.1_Missense_Mutation_p.L375Q|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	375					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CACTTCTTCCTGAGCCACGGT	0.592													T|||	359	0.0716853	0.0091	0.0317	5008	,	,		13424	0.0506		0.0676	False		,,,				2504	0.2106				p.L375Q		Atlas-SNP	.											.	.	.	.	0			c.T1124A						PASS	.	T	GLN/LEU	72,4098		0,72,2013	6.0	7.0	6.0		1124	5.6	0.9	7	dbSNP_120	6	528,7844		17,494,3675	no	missense	KIAA0415	NM_014855.2	113	17,566,5688	AA,AT,TT		6.3067,1.7266,4.7839	probably-damaging	375/808	4825307	600,11942	2085	4186	6271	SO:0001583	missense	9907	exon9			TCTTCCTGAGCCA	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1124T>A	7.37:g.4825307T>A	ENSP00000297562:p.Leu375Gln	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	98	0.04487179487179487	7	0.014227642276422764	15	0.04143646408839779	30	0.05244755244755245	46	0.06068601583113457	t	16.98	3.271083	0.59540	0.017266	0.063067	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.63417	-0.01;-0.04	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000002	T	0.36496	0.0969	M	0.83483	2.645	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.69457	-0.5140	10	0.87932	D	0	.	13.5539	0.61749	0.0:0.0:0.0:1.0	rs11772411	375	O43299	K0415_HUMAN	Q	375	ENSP00000297562:L375Q;ENSP00000384980:L375Q	ENSP00000297562:L375Q	L	+	2	0	KIAA0415	4791833	1.000000	0.71417	0.879000	0.34478	0.057000	0.15508	7.654000	0.83653	2.141000	0.66446	0.454000	0.30748	CTG	T|0.956;A|0.044	0.044	strong		0.592	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
OR2M2	391194	hgsc.bcm.edu	37	1	248343543	248343543	+	Silent	SNP	C	C	T	rs9435919|rs386641960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248343543C>T	ENST00000359682.2	+	1	256	c.256C>T	c.(256-258)Ctg>Ttg	p.L86L		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CTTCAACTACCTGTCTGGCAG	0.493													c|||	2897	0.578474	0.6188	0.6052	5008	,	,		20890	0.4306		0.6382	False		,,,				2504	0.5961				p.L86L		Atlas-SNP	.											.	OR2M2	149	.	0			c.C256T						PASS	.	C		2728,1678	654.4+/-399.7	843,1042,318	212.0	217.0	216.0		256	-4.1	0.0	1	dbSNP_119	216	5583,3015	664.4+/-402.2	1825,1933,541	no	coding-synonymous	OR2M2	NM_001004688.1		2668,2975,859	TT,TC,CC		35.0663,38.0844,36.0889		86/348	248343543	8311,4693	2203	4299	6502	SO:0001819	synonymous_variant	391194	exon1			AACTACCTGTCTG	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"""GPCR / Class A : Olfactory receptors"""	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.256C>T	1.37:g.248343543C>T		Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	412	409	0.992718	NM_001004688	A3KFT4	Silent	SNP	ENST00000359682.2	37	CCDS31106.1																																																																																			C|0.384;T|0.616	0.616	strong		0.493	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688	
PRSS55	203074	hgsc.bcm.edu	37	8	10383138	10383138	+	Missense_Mutation	SNP	G	G	A	rs35102108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:10383138G>A	ENST00000328655.3	+	1	83	c.43G>A	c.(43-45)Gga>Aga	p.G15R	PRSS51_ENST00000523024.1_RNA|PRSS55_ENST00000522210.1_Missense_Mutation_p.G15R	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	15				G -> R (in Ref. 3; BC033497). {ECO:0000305}.		cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						CCTGGTCACGGGAACTCAGCT	0.677													G|||	928	0.185304	0.0499	0.245	5008	,	,		17372	0.3204		0.1789	False		,,,				2504	0.1933				p.G15R		Atlas-SNP	.											.	PRSS55	67	.	0			c.G43A						PASS	.	G	ARG/GLY,ARG/GLY	333,4073	176.2+/-205.4	12,309,1882	93.0	75.0	81.0		43,43	-1.0	0.0	8	dbSNP_126	81	1710,6890	312.5+/-310.9	176,1358,2766	yes	missense,missense	PRSS55	NM_198464.3,NM_001197020.1	125,125	188,1667,4648	AA,AG,GG		19.8837,7.5579,15.7081	benign,benign	15/353,15/277	10383138	2043,10963	2203	4300	6503	SO:0001583	missense	203074	exon1			GTCACGGGAACTC	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"""Serine peptidases / Serine peptidases"""	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.43G>A	8.37:g.10383138G>A	ENSP00000333003:p.Gly15Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	NM_001197020	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	437	0.2000915750915751	21	0.042682926829268296	92	0.2541436464088398	186	0.32517482517482516	138	0.1820580474934037	G	10.04	1.241746	0.22711	0.075579	0.198837	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.88431	-2.38;-2.36	3.39	-0.977	0.10282	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.05099	-1.0906	8	0.66056	D	0.02	.	6.5712	0.22539	0.5624:0.0:0.4376:0.0	rs35102108;rs61067117	15	Q6UWB4	PRS55_HUMAN	R	15	ENSP00000333003:G15R;ENSP00000430459:G15R	ENSP00000333003:G15R	G	+	1	0	PRSS55	10420548	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.494000	0.22467	-0.219000	0.10003	-0.218000	0.12543	GGA	G|0.834;A|0.166	0.166	strong		0.677	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
FER1L6	654463	hgsc.bcm.edu	37	8	125035788	125035788	+	Silent	SNP	G	G	C	rs4358790	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:125035788G>C	ENST00000522917.1	+	18	2444	c.2238G>C	c.(2236-2238)gcG>gcC	p.A746A	FER1L6-AS1_ENST00000518567.1_RNA|FER1L6_ENST00000399018.1_Silent_p.A746A	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	746						integral component of membrane (GO:0016021)		p.A746A(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CCCCTGTCGCGGGGCAGATGG	0.493													G|||	2764	0.551917	0.68	0.3948	5008	,	,		19241	0.5198		0.5924	False		,,,				2504	0.4816				p.A746A		Atlas-SNP	.											FER1L6,NS,carcinoma,0,2	FER1L6	268	2	1	Substitution - coding silent(1)	stomach(1)	c.G2238C						PASS	.	G		2517,1369		793,931,219	72.0	75.0	74.0		2238	-2.0	0.0	8	dbSNP_111	74	4948,3330		1491,1966,682	no	coding-synonymous	FER1L6	NM_001039112.2		2284,2897,901	CC,CG,GG		40.2271,35.229,38.6304		746/1858	125035788	7465,4699	1943	4139	6082	SO:0001819	synonymous_variant	654463	exon18			TGTCGCGGGGCAG	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.2238G>C	8.37:g.125035788G>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_001039112		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																			G|0.427;C|0.573	0.573	strong		0.493	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
KRT76	51350	hgsc.bcm.edu	37	12	53167395	53167395	+	Missense_Mutation	SNP	C	C	T	rs11170271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53167395C>T	ENST00000332411.2	-	3	900	c.847G>A	c.(847-849)Gca>Aca	p.A283T		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	283	Coil 1B.|Rod.		A -> T (in dbSNP:rs11170271).		cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.A283T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TCATTCTCTGCGGCAGTGCGT	0.493													C|||	821	0.163938	0.028	0.2795	5008	,	,		19874	0.1587		0.2644	False		,,,				2504	0.1677				p.A283T		Atlas-SNP	.											KRT76,NS,carcinoma,0,1	KRT76	72	1	1	Substitution - Missense(1)	stomach(1)	c.G847A						PASS	.	C	THR/ALA	241,4165	141.9+/-177.2	6,229,1968	147.0	119.0	128.0		847	4.5	0.8	12	dbSNP_120	128	2340,6260	391.6+/-343.7	311,1718,2271	yes	missense	KRT76	NM_015848.4	58	317,1947,4239	TT,TC,CC		27.2093,5.4698,19.8447	possibly-damaging	283/639	53167395	2581,10425	2203	4300	6503	SO:0001583	missense	51350	exon3			TCTCTGCGGCAGT	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.847G>A	12.37:g.53167395C>T	ENSP00000330101:p.Ala283Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	123	60	0.487805	NM_015848	B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	37	CCDS8838.1	389	0.17811355311355312	21	0.042682926829268296	90	0.24861878453038674	86	0.15034965034965034	192	0.2532981530343008	C	15.41	2.826063	0.50739	0.054698	0.272093	ENSG00000185069	ENST00000332411	D	0.88586	-2.4	4.48	4.48	0.54585	Filament (1);	0.000000	0.44097	D	0.000486	T	0.00144	0.0004	M	0.75150	2.29	0.58432	P	5.999999999950489E-6	D	0.89917	1.0	D	0.76071	0.987	T	0.00000	-1.3632	9	0.87932	D	0	.	18.0452	0.89330	0.0:1.0:0.0:0.0	rs11170271;rs52799703;rs56756879;rs11170271	283	Q01546	K22O_HUMAN	T	283	ENSP00000330101:A283T	ENSP00000330101:A283T	A	-	1	0	KRT76	51453662	0.000000	0.05858	0.805000	0.32314	0.361000	0.29550	0.820000	0.27323	2.423000	0.82170	0.557000	0.71058	GCA	C|0.817;T|0.183	0.183	strong		0.493	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
RBM14	10432	hgsc.bcm.edu	37	11	66392880	66392880	+	Silent	SNP	C	C	T	rs11550057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66392880C>T	ENST00000310137.4	+	2	1672	c.1533C>T	c.(1531-1533)acC>acT	p.T511T	RBM14-RBM4_ENST00000511114.1_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM14_ENST00000393979.3_Intron|RBM4_ENST00000503028.2_Intron|RBM14_ENST00000409738.4_Intron|RBM4_ENST00000514361.3_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	511	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CTTCTGCCACCCTGGCAGCTC	0.647													C|||	399	0.0796725	0.0136	0.0793	5008	,	,		15624	0.0208		0.1531	False		,,,				2504	0.1544				p.T511T		Atlas-SNP	.											.	RBM14	59	.	0			c.C1533T						PASS	.	C	,,,,	155,4245	106.5+/-144.9	3,149,2048	50.0	46.0	47.0		,,,,1533	4.8	1.0	11	dbSNP_120	47	1377,7213	265.2+/-286.0	118,1141,3036	no	intron,intron,intron,intron,coding-synonymous	RBM14,RBM14-RBM4	NM_001198836.1,NM_001198837.1,NM_001198845.1,NM_001198846.1,NM_006328.3	,,,,	121,1290,5084	TT,TC,CC		16.0303,3.5227,11.7937	,,,,	,,,,511/670	66392880	1532,11458	2200	4295	6495	SO:0001819	synonymous_variant	10432	exon2			TGCCACCCTGGCA	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"""RNA binding motif (RRM) containing"""	14219	protein-coding gene	gene with protein product	"""coactivator activator"", ""SYT interacting protein"""	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1533C>T	11.37:g.66392880C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Silent	SNP	ENST00000310137.4	37	CCDS8147.1																																																																																			C|0.902;T|0.098	0.098	strong		0.647	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328	
ATG10	83734	hgsc.bcm.edu	37	5	81549240	81549240	+	Missense_Mutation	SNP	C	C	A	rs1864182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:81549240C>A	ENST00000282185.3	+	7	953	c.659C>A	c.(658-660)cCt>cAt	p.P220H	ATG10_ENST00000458350.3_Missense_Mutation_p.P220H|ATG10_ENST00000514253.2_Intron	NM_031482.4	NP_113670.1	Q9H0Y0	ATG10_HUMAN	autophagy related 10	220			P -> H (in dbSNP:rs1864182). {ECO:0000269|PubMed:15489334}.		autophagy (GO:0006914)|autophagy in response to ER overload (GO:0034263)|positive regulation of protein modification process (GO:0031401)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	Atg12 ligase activity (GO:0019777)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(2)	9		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		CGAAATGTCCCTTAACAAGGT	0.408													A|||	2814	0.561901	0.1785	0.611	5008	,	,		21595	0.9077		0.5537	False		,,,				2504	0.6973				p.P220H		Atlas-SNP	.											.	ATG10	23	.	0			c.C659A						PASS	.	A	HIS/PRO,HIS/PRO	986,3420	731.6+/-410.3	126,734,1343	113.0	100.0	105.0		659,659	-2.7	0.0	5	dbSNP_92	105	4809,3791	536.5+/-383.0	1329,2151,820	yes	missense,missense	ATG10	NM_031482.4,NM_001131028.1	77,77	1455,2885,2163	AA,AC,CC		44.0814,22.3786,44.5564	benign,benign	220/221,220/221	81549240	5795,7211	2203	4300	6503	SO:0001583	missense	83734	exon8			ATGTCCCTTAACA	AK024016	CCDS4057.1	5q14.1	2014-02-12	2012-06-06	2005-09-11	ENSG00000152348	ENSG00000152348			20315	protein-coding gene	gene with protein product		610800	"""APG10 autophagy 10-like (S. cerevisiae)"", ""ATG10 autophagy related 10 homolog (S. cerevisiae)"""	APG10L			Standard	NM_031482		Approved	DKFZP586I0418, FLJ13954	uc003khr.3	Q9H0Y0	OTTHUMG00000119041	ENST00000282185.3:c.659C>A	5.37:g.81549240C>A	ENSP00000282185:p.Pro220His	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_001131028	B2RE09|Q6PIX1|Q9H842	Missense_Mutation	SNP	ENST00000282185.3	37	CCDS4057.1	1276	0.5842490842490843	101	0.20528455284552846	205	0.5662983425414365	532	0.9300699300699301	438	0.5778364116094987	A	9.272	1.045998	0.19748	0.223786	0.559186	ENSG00000152348	ENST00000282185;ENST00000458350	T;T	0.23754	1.89;1.89	5.75	-2.66	0.06077	.	2.720220	0.01454	N	0.015598	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45934	-0.9227	9	0.87932	D	0	.	0.8103	0.01092	0.3887:0.1181:0.2654:0.2278	rs1864182;rs17305578;rs17856118;rs17856774;rs52800713;rs60536852;rs1864182	220	Q9H0Y0	ATG10_HUMAN	H	220	ENSP00000282185:P220H;ENSP00000404938:P220H	ENSP00000282185:P220H	P	+	2	0	ATG10	81584996	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.323000	0.07997	-0.968000	0.03578	-0.976000	0.02587	CCT	C|0.500;N|0.000	.	strong		0.408	ATG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239252.2	NM_001131028	
SEPT14	346288	hgsc.bcm.edu	37	7	55902230	55902230	+	Missense_Mutation	SNP	T	T	C	rs146004414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:55902230T>C	ENST00000388975.3	-	6	724	c.608A>G	c.(607-609)gAt>gGt	p.D203G		NM_207366.2	NP_997249.2	Q6ZU15	SEP14_HUMAN	septin 14	203	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|skin(2)	23	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CGTCTGTAAATCATTTTTAGA	0.348													.|||	23	0.00459265	0.0008	0.0072	5008	,	,		4554	0.0		0.0159	False		,,,				2504	0.001				p.D203G		Atlas-SNP	.											.	SEPT14	58	.	0			c.A608G						PASS	.	T	GLY/ASP	22,4384	29.0+/-57.7	0,22,2181	94.0	89.0	91.0		608	4.2	0.9	7	dbSNP_134	91	194,8406	85.3+/-147.7	1,192,4107	yes	missense	SEPT14	NM_207366.2	94	1,214,6288	CC,CT,TT		2.2558,0.4993,1.6608	probably-damaging	203/433	55902230	216,12790	2203	4300	6503	SO:0001583	missense	346288	exon6			TGTAAATCATTTT	AK126048	CCDS5519.2	7p11.2	2013-01-21			ENSG00000154997	ENSG00000154997		"""Septins"""	33280	protein-coding gene	gene with protein product		612140					Standard	NM_207366		Approved	FLJ44060	uc003tqz.2	Q6ZU15	OTTHUMG00000129341	ENST00000388975.3:c.608A>G	7.37:g.55902230T>C	ENSP00000373627:p.Asp203Gly	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_207366	A6NCC2|B4DXD6	Missense_Mutation	SNP	ENST00000388975.3	37	CCDS5519.2	18	0.008241758241758242	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	14	0.018469656992084433	t	21.2	4.107748	0.77096	0.004993	0.022558	ENSG00000154997	ENST00000388975	T	0.52057	0.68	4.19	4.19	0.49359	.	0.113304	0.36665	N	0.002465	T	0.39809	0.1092	L	0.58101	1.795	0.44439	D	0.997365	P	0.49862	0.929	P	0.54431	0.752	T	0.54721	-0.8251	10	0.87932	D	0	.	11.5397	0.50659	0.0:0.0:0.0:1.0	.	203	Q6ZU15	SEP14_HUMAN	G	203	ENSP00000373627:D203G	ENSP00000373627:D203G	D	-	2	0	SEPT14	55869724	1.000000	0.71417	0.942000	0.38095	0.982000	0.71751	6.442000	0.73443	1.888000	0.54679	0.528000	0.53228	GAT	T|0.988;C|0.012	0.012	strong		0.348	SEPT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251489.2	NM_207366	
KCNH5	27133	hgsc.bcm.edu	37	14	63175012	63175012	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63175012A>G	ENST00000322893.7	-	11	2449	c.2181T>C	c.(2179-2181)ggT>ggC	p.G727G	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	727					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TCTCAGGGTCACCCTGTGTTG	0.557																																					p.G727G		Atlas-SNP	.											KCNH5,NS,carcinoma,-1,1	KCNH5	320	1	0			c.T2181C						PASS	.						114.0	106.0	109.0					14																	63175012		2203	4300	6503	SO:0001819	synonymous_variant	27133	exon11			AGGGTCACCCTGT	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2181T>C	14.37:g.63175012A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	160	67	0.41875	NM_139318	C9JP98	Silent	SNP	ENST00000322893.7	37	CCDS9756.1																																																																																			.	.	none		0.557	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
SLC13A3	64849	hgsc.bcm.edu	37	20	45204266	45204266	+	Silent	SNP	G	G	A	rs1880898	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:45204266G>A	ENST00000279027.4	-	10	1296	c.1278C>T	c.(1276-1278)ccC>ccT	p.P426P	SLC13A3_ENST00000413164.2_Silent_p.P376P|SLC13A3_ENST00000495082.1_Silent_p.P379P|SLC13A3_ENST00000290317.5_Silent_p.P379P|SLC13A3_ENST00000396360.1_Silent_p.P344P|SLC13A3_ENST00000472148.1_Silent_p.P344P|SLC13A3_ENST00000435032.1_Intron	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	426					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	TGATGTTCCAGGGCACTGTCT	0.617													G|||	2774	0.553914	0.4796	0.5692	5008	,	,		19600	0.5625		0.6093	False		,,,				2504	0.5777				p.P426P		Atlas-SNP	.											.	SLC13A3	88	.	0			c.C1278T						PASS	.	G	,,,,	2183,2223	576.3+/-384.2	531,1121,551	90.0	71.0	77.0		1137,1128,1032,984,1278	0.4	1.0	20	dbSNP_92	77	5474,3126	645.5+/-400.2	1732,2010,558	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC13A3	NM_001011554.2,NM_001193339.1,NM_001193340.1,NM_001193342.1,NM_022829.5	,,,,	2263,3131,1109	AA,AG,GG		36.3488,49.5461,41.1272	,,,,	379/556,376/553,344/521,328/505,426/603	45204266	7657,5349	2203	4300	6503	SO:0001819	synonymous_variant	64849	exon10			GTTCCAGGGCACT	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"""Solute carriers"""	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1278C>T	20.37:g.45204266G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	37	CCDS13400.1																																																																																			G|0.419;T|0.006	.	strong		0.617	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2		
SEC11A	23478	hgsc.bcm.edu	37	15	85234858	85234858	+	Silent	SNP	T	T	C	rs369852123		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85234858T>C	ENST00000268220.7	-	2	709	c.69A>G	c.(67-69)ctA>ctG	p.L23L	SEC11A_ENST00000560266.1_Silent_p.L23L|SEC11A_ENST00000558134.1_Silent_p.L23L|SEC11A_ENST00000455959.3_5'UTR	NM_014300.2	NP_055115.1	P67812	SC11A_HUMAN	SEC11 homolog A (S. cerevisiae)	23					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	serine-type peptidase activity (GO:0008236)			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)			TTCCAAAATTTAGGACTTGAT	0.398																																					p.L23L		Atlas-SNP	.											.	SEC11A	8	.	0			c.A69G						PASS	.	T		0,3756		0,0,1878	75.0	69.0	71.0		69	-1.8	1.0	15		71	1,8227		0,1,4113	no	coding-synonymous	SEC11A	NM_014300.2		0,1,5991	CC,CT,TT		0.0122,0.0,0.0083		23/180	85234858	1,11983	1878	4114	5992	SO:0001819	synonymous_variant	23478	exon2			AAAATTTAGGACT	AF061737	CCDS45340.1, CCDS61742.1, CCDS61743.1, CCDS61744.1, CCDS73776.1	15q25.2	2006-11-07	2006-11-07	2006-11-07		ENSG00000140612			17718	protein-coding gene	gene with protein product			"""SEC11-like 1 (S. cerevisiae)"""	SEC11L1			Standard	NM_001271919		Approved	SPC18, sid2895, SPCS4A	uc031qtg.1	P67812		ENST00000268220.7:c.69A>G	15.37:g.85234858T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	77	45	0.584416	NM_014300	B2RAD7|B4DUL4|H0YK72|H0YK83|O75957|P21378|Q53FQ8	Silent	SNP	ENST00000268220.7	37	CCDS45340.1																																																																																			.	.	weak		0.398	SEC11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418777.1	NM_014300	
USP4	7375	hgsc.bcm.edu	37	3	49343175	49343175	+	Silent	SNP	G	G	A	rs2230929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49343175G>A	ENST00000265560.4	-	9	1147	c.1101C>T	c.(1099-1101)gaC>gaT	p.D367D	USP4_ENST00000488520.1_5'UTR|USP4_ENST00000351842.4_Silent_p.D320D	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	367	USP.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.D367D(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		CCACATGGGCGTCCCTTCCAG	0.468													G|||	459	0.0916534	0.0651	0.098	5008	,	,		19901	0.0546		0.1968	False		,,,				2504	0.0532				p.D367D		Atlas-SNP	.											USP4,NS,carcinoma,0,1	USP4	72	1	1	Substitution - coding silent(1)	stomach(1)	c.C1101T						PASS	.	G	,	426,3980	207.5+/-228.8	17,392,1794	113.0	99.0	104.0		1101,960	-11.4	0.0	3	dbSNP_98	104	1491,7109	283.7+/-296.3	132,1227,2941	no	coding-synonymous,coding-synonymous	USP4	NM_003363.3,NM_199443.2	,	149,1619,4735	AA,AG,GG		17.3372,9.6686,14.7394	,	367/964,320/917	49343175	1917,11089	2203	4300	6503	SO:0001819	synonymous_variant	7375	exon9			ATGGGCGTCCCTT	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.1101C>T	3.37:g.49343175G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	184	88	0.478261	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1	279	0.12774725274725274	36	0.07317073170731707	50	0.13812154696132597	41	0.07167832167832168	152	0.20052770448548812	G	4.516	0.095814	0.08681	0.096686	0.173372	ENSG00000114316	ENST00000431357	.	.	.	5.92	-11.4	0.00090	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.19775	P	0.9999511744	.	.	.	.	.	.	T	0.30937	-0.9961	3	.	.	.	-12.157	16.2274	0.82306	0.18:0.1428:0.6772:0.0	rs2230929;rs11130188;rs11130188	.	.	.	C	124	.	.	R	-	1	0	USP4	49318179	0.000000	0.05858	0.000000	0.03702	0.717000	0.41224	-0.668000	0.05268	-2.469000	0.00531	-2.040000	0.00418	CGC	G|0.864;C|0.000;A|0.136	0.136	strong		0.468	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
WDR81	124997	hgsc.bcm.edu	37	17	1640709	1640709	+	Silent	SNP	C	C	T	rs1045794|rs587780509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1640709C>T	ENST00000409644.1	+	10	5556	c.5556C>T	c.(5554-5556)acC>acT	p.T1852T	WDR81_ENST00000545662.1_Silent_p.T483T|WDR81_ENST00000437219.2_Silent_p.T649T|WDR81_ENST00000309182.5_Silent_p.T801T|WDR81_ENST00000419248.1_Silent_p.T625T|WDR81_ENST00000446363.1_Silent_p.T491T|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1852					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ATTCCTTGACCGTCTGGAAGG	0.617													C|||	739	0.147564	0.0545	0.2277	5008	,	,		20197	0.1726		0.2227	False		,,,				2504	0.1135				p.T1852T		Atlas-SNP	.											WDR81_ENST00000437219,NS,carcinoma,+1,3	WDR81	180	3	0			c.C5556T						scavenged	.	C	,,,	368,4034	185.0+/-212.2	22,324,1855	165.0	105.0	125.0		1947,5556,1875,2403	-7.2	0.7	17	dbSNP_86	125	1903,6695	335.1+/-321.3	224,1455,2620	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	246,1779,4475	TT,TC,CC		22.1331,8.3598,17.4692	,,,	649/739,1852/1942,625/715,801/891	1640709	2271,10729	2201	4299	6500	SO:0001819	synonymous_variant	124997	exon10			CTTGACCGTCTGG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5556C>T	17.37:g.1640709C>T		Somatic	120	2	0.0166667		WXS	Illumina HiSeq	Phase_I	173	88	0.508671	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.826;N|0.001	.	strong		0.617	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
HK3	3101	hgsc.bcm.edu	37	5	176309082	176309082	+	Silent	SNP	C	C	T	rs34127573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176309082C>T	ENST00000292432.5	-	16	2191	c.2100G>A	c.(2098-2100)gcG>gcA	p.A700A		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	700	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGGCACGCCCGCCACATTCC	0.597													C|||	20	0.00399361	0.003	0.0014	5008	,	,		18484	0.0		0.0139	False		,,,				2504	0.001				p.A700A		Atlas-SNP	.											.	HK3	210	.	0			c.G2100A						PASS	.	C		10,4396	12.9+/-30.5	0,10,2193	52.0	50.0	51.0		2100	-10.1	0.0	5	dbSNP_126	51	119,8479	55.6+/-116.7	1,117,4181	no	coding-synonymous	HK3	NM_002115.2		1,127,6374	TT,TC,CC		1.384,0.227,0.992		700/924	176309082	129,12875	2203	4299	6502	SO:0001819	synonymous_variant	3101	exon16			CACGCCCGCCACA		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.2100G>A	5.37:g.176309082C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	130	82	0.630769	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			C|0.992;T|0.008	0.008	strong		0.597	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
FOLH1	2346	hgsc.bcm.edu	37	11	49221885	49221885	+	Silent	SNP	T	T	A	rs202680	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49221885T>A	ENST00000256999.2	-	3	593	c.333A>T	c.(331-333)gcA>gcT	p.A111A	FOLH1_ENST00000343844.4_Intron|FOLH1_ENST00000356696.3_Silent_p.A111A|FOLH1_ENST00000340334.7_Silent_p.A96A|FOLH1_ENST00000533034.1_Silent_p.A96A	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	111					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	CATCATAATGTGCTAGCTCAA	0.353													A|||	2078	0.414936	0.6354	0.3156	5008	,	,		15587	0.3165		0.2753	False		,,,				2504	0.4325				p.A111A		Atlas-SNP	.											.	FOLH1	141	.	0			c.A333T						PASS	.	A	,,,,	2359,2039	528.2+/-372.3	663,1033,503	65.0	67.0	66.0		333,288,288,,333	-0.8	1.0	11	dbSNP_79	66	2297,6299	686.0+/-404.1	332,1633,2333	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	FOLH1	NM_001014986.1,NM_001193471.1,NM_001193472.1,NM_001193473.1,NM_004476.1	,,,,	995,2666,2836	AA,AT,TT		26.7217,46.362,35.8319	,,,,	111/720,96/736,96/705,,111/751	49221885	4656,8338	2199	4298	6497	SO:0001819	synonymous_variant	2346	exon3			ATAATGTGCTAGC	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.333A>T	11.37:g.49221885T>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Silent	SNP	ENST00000256999.2	37	CCDS7946.1																																																																																			T|0.646;A|0.354	0.354	strong		0.353	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
TBC1D5	9779	hgsc.bcm.edu	37	3	17255768	17255768	+	Silent	SNP	T	T	C	rs116772060	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:17255768T>C	ENST00000253692.7	-	18	3347	c.1683A>G	c.(1681-1683)aaA>aaG	p.K561K	TBC1D5_ENST00000446818.2_Silent_p.K583K|TBC1D5_ENST00000429924.2_Silent_p.K535K|TBC1D5_ENST00000429383.4_Silent_p.K561K|TBC1D5_ENST00000414318.2_5'UTR	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	561						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						AGGAATCTTTTTTAGTAGCAG	0.403													T|||	55	0.0109824	0.0008	0.0115	5008	,	,		16030	0.0		0.0398	False		,,,				2504	0.0061				p.K583K		Atlas-SNP	.											.	TBC1D5	69	.	0			c.A1749G						PASS	.	T	,,	23,4383	29.9+/-59.1	0,23,2180	76.0	82.0	80.0		1683,1749,1683	-2.5	0.9	3	dbSNP_132	80	214,8386	90.6+/-152.8	2,210,4088	no	coding-synonymous,coding-synonymous,coding-synonymous	TBC1D5	NM_001134380.1,NM_001134381.1,NM_014744.2	,,	2,233,6268	CC,CT,TT		2.4884,0.522,1.8222	,,	561/796,583/818,561/796	17255768	237,12769	2203	4300	6503	SO:0001819	synonymous_variant	9779	exon20			ATCTTTTTTAGTA	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.1683A>G	3.37:g.17255768T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_001134381	A6NP25|C9JP52	Silent	SNP	ENST00000253692.7	37	CCDS33714.1																																																																																			T|0.974;C|0.026	0.026	strong		0.403	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744	
PLA2G2C	391013	hgsc.bcm.edu	37	1	20501582	20501582	+	Nonsense_Mutation	SNP	G	G	A	rs12139100	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20501582G>A	ENST00000429261.2	-	2	157	c.97C>T	c.(97-99)Cga>Tga	p.R33*	PLA2G2C_ENST00000247992.5_Nonsense_Mutation_p.R36*|PLA2G2C_ENST00000495760.2_5'UTR			Q5R387	PA2GC_HUMAN	phospholipase A2, group IIC	33					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(1)	7		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.14e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.000528)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AAGGCACTTCGCCCCGTGATG	0.532													G|||	1203	0.240216	0.2829	0.121	5008	,	,		18086	0.1766		0.1839	False		,,,				2504	0.3906				p.R36X		Atlas-SNP	.											.	PLA2G2C	21	.	0			c.C106T						PASS	.	G	stop/ARG	979,2931		124,731,1100	99.0	103.0	101.0		106	-0.9	0.1	1	dbSNP_120	101	1469,6879		122,1225,2827	yes	stop-gained	PLA2G2C	NM_001105572.1		246,1956,3927	AA,AG,GG		17.597,25.0384,19.9706		36/151	20501582	2448,9810	1955	4174	6129	SO:0001587	stop_gained	391013	exon1			CACTTCGCCCCGT			1p36.12	2010-06-04	2003-10-13		ENSG00000187980	ENSG00000187980			9032	protein-coding gene	gene with protein product			"""phospholipase A2, group IIC (possible pseudogene)"""			8838795	Standard	NM_001105572		Approved		uc009vpq.1	Q5R387	OTTHUMG00000002705	ENST00000429261.2:c.97C>T	1.37:g.20501582G>A	ENSP00000389335:p.Arg33*	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	159	100	0.628931	NM_001105572	Q7M4M6	Nonsense_Mutation	SNP	ENST00000429261.2	37		403	0.18452380952380953	119	0.241869918699187	45	0.12430939226519337	94	0.16433566433566432	145	0.19129287598944592	G	18.40	3.615689	0.66672	0.250384	0.17597	ENSG00000187980	ENST00000429261;ENST00000247992	.	.	.	5.13	-0.89	0.10577	.	0.311359	0.23189	N	0.050933	.	.	.	.	.	.	0.09310	P	0.999999999909794	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	4.7511	0.13061	0.1801:0.0:0.3081:0.5118	rs12139100;rs57362211;rs12139100	.	.	.	X	33;36	.	ENSP00000247992:R36X	R	-	1	2	PLA2G2C	20374169	0.033000	0.19621	0.057000	0.19452	0.256000	0.26092	0.198000	0.17217	-0.055000	0.13244	-0.751000	0.03497	CGA	G|0.802;A|0.198	0.198	strong		0.532	PLA2G2C-001	PUTATIVE	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000007689.3	NM_001105572	
HTR5A	3361	hgsc.bcm.edu	37	7	154862652	154862652	+	Missense_Mutation	SNP	C	C	T	rs11575874	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:154862652C>T	ENST00000287907.2	+	1	619	c.43C>T	c.(43-45)Ccc>Tcc	p.P15S	HTR5A-AS1_ENST00000395731.2_Intron|HTR5A-AS1_ENST00000493904.1_Intron|HTR5A-AS1_ENST00000543018.1_Intron	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	15					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	CCTCTCCACCCCCTCCCCTTT	0.587													C|||	135	0.0269569	0.0136	0.0432	5008	,	,		17944	0.0		0.0676	False		,,,				2504	0.0194				p.P15S		Atlas-SNP	.											HTR5A,NS,carcinoma,-2,1	HTR5A	114	1	0			c.C43T	GRCh37	CM014359	HTR5A	M	rs11575874	PASS	.	C	SER/PRO	67,4339	61.7+/-98.7	0,67,2136	104.0	111.0	108.0		43	0.2	0.0	7	dbSNP_120	108	501,8099	142.3+/-198.5	10,481,3809	yes	missense	HTR5A	NM_024012.2	74	10,548,5945	TT,TC,CC		5.8256,1.5207,4.3672	benign	15/358	154862652	568,12438	2203	4300	6503	SO:0001583	missense	3361	exon1			TCCACCCCCTCCC		CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5300	protein-coding gene	gene with protein product		601305	"""5-hydroxytryptamine (serotonin) receptor 5A"""			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.43C>T	7.37:g.154862652C>T	ENSP00000287907:p.Pro15Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	47	35	0.744681	NM_024012	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	37	CCDS5936.1	75	0.034340659340659344	8	0.016260162601626018	21	0.058011049723756904	0	0.0	46	0.06068601583113457	C	2.270	-0.367277	0.05069	0.015207	0.058256	ENSG00000157219	ENST00000287907	T	0.37058	1.22	4.42	0.195	0.15151	.	0.402743	0.24980	N	0.034065	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19451	-1.0305	10	0.14656	T	0.56	.	5.2712	0.15627	0.0:0.4746:0.2675:0.2579	rs11575874	15	P47898	5HT5A_HUMAN	S	15	ENSP00000287907:P15S	ENSP00000287907:P15S	P	+	1	0	HTR5A	154493585	0.036000	0.19791	0.000000	0.03702	0.752000	0.42762	1.014000	0.29950	-0.169000	0.10834	0.467000	0.42956	CCC	C|0.956;T|0.044	0.044	strong		0.587	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012	
IL22RA1	58985	hgsc.bcm.edu	37	1	24447468	24447468	+	Missense_Mutation	SNP	G	G	C	rs3795299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:24447468G>C	ENST00000270800.1	-	7	1590	c.1552C>G	c.(1552-1554)Cgt>Ggt	p.R518G		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	518			R -> G (in dbSNP:rs3795299). {ECO:0000269|PubMed:10875937, ECO:0000269|PubMed:14702039}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		GAACATGGACGGGAAGGAGGT	0.627													G|||	2335	0.466254	0.2874	0.4035	5008	,	,		19250	0.7252		0.3996	False		,,,				2504	0.5542				p.R518G		Atlas-SNP	.											.	IL22RA1	62	.	0			c.C1552G						PASS	.	G	GLY/ARG	1339,3067	446.7+/-348.1	218,903,1082	82.0	71.0	75.0		1552	4.2	0.2	1	dbSNP_107	75	3507,5093	511.1+/-377.6	723,2061,1516	yes	missense	IL22RA1	NM_021258.3	125	941,2964,2598	CC,CG,GG		40.7791,30.3904,37.2597	benign	518/575	24447468	4846,8160	2203	4300	6503	SO:0001583	missense	58985	exon7			ATGGACGGGAAGG	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"""Interleukins and interleukin receptors"""	13700	protein-coding gene	gene with protein product		605457	"""interleukin 22 receptor"""	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.1552C>G	1.37:g.24447468G>C	ENSP00000270800:p.Arg518Gly	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	200	198	0.99	NM_021258	A8K839|B2R9Y9|Q9HB22	Missense_Mutation	SNP	ENST00000270800.1	37	CCDS247.1	961	0.440018315018315	140	0.2845528455284553	127	0.35082872928176795	407	0.7115384615384616	287	0.3786279683377309	G	7.672	0.687230	0.14973	0.303904	0.407791	ENSG00000142677	ENST00000270800	T	0.08282	3.11	5.17	4.24	0.50183	.	1.536800	0.03697	N	0.248041	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.27416	0.178	B	0.22386	0.039	T	0.36578	-0.9742	9	0.27082	T	0.32	-1.3849	11.3002	0.49300	0.0:0.1921:0.8079:0.0	rs3795299;rs17256862;rs3795299	518	Q8N6P7	I22R1_HUMAN	G	518	ENSP00000270800:R518G	ENSP00000270800:R518G	R	-	1	0	IL22RA1	24320055	0.973000	0.33851	0.173000	0.22940	0.006000	0.05464	1.837000	0.39201	1.394000	0.46624	0.650000	0.86243	CGT	G|0.599;C|0.401	0.401	strong		0.627	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
CCDC107	203260	hgsc.bcm.edu	37	9	35660872	35660872	+	Silent	SNP	C	C	T	rs141349284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35660872C>T	ENST00000426546.2	+	5	606	c.540C>T	c.(538-540)ggC>ggT	p.G180G	ARHGEF39_ENST00000378387.3_3'UTR|CCDC107_ENST00000378409.3_Intron|ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000421582.2_3'UTR|CCDC107_ENST00000327351.2_Intron|ARHGEF39_ENST00000343259.3_3'UTR|RMRP_ENST00000602361.1_lincRNA|CCDC107_ENST00000378407.3_3'UTR|ARHGEF39_ENST00000490970.1_5'Flank|CCDC107_ENST00000378406.1_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	180						integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCTCGGGAGGCGAGTCTGCTG	0.527													C|||	4	0.000798722	0.0	0.0029	5008	,	,		19570	0.001		0.001	False		,,,				2504	0.0				p.G180G		Atlas-SNP	.											.	CCDC107	12	.	0			c.C540T						PASS	.	C	,,,,	0,4406		0,0,2203	123.0	134.0	130.0		,,,,540	-4.9	0.0	9	dbSNP_134	130	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,utr-3,utr-3,coding-synonymous	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	,,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,,	,,,,180/284	35660872	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	203260	exon5			GGGAGGCGAGTCT	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.540C>T	9.37:g.35660872C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Silent	SNP	ENST00000426546.2	37	CCDS6583.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
PRG3	10394	hgsc.bcm.edu	37	11	57148175	57148175	+	Missense_Mutation	SNP	A	A	G	rs669661	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57148175A>G	ENST00000287143.2	-	2	116	c.7T>C	c.(7-9)Tgc>Cgc	p.C3R		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						AGCAAGAGGCATTGCATATCT	0.498													G|||	4797	0.957867	0.8593	0.9841	5008	,	,		19409	0.996		1.0	False		,,,				2504	0.9898				p.C3R	Melanoma(154;1456 2519 19358 45229)	Atlas-SNP	.											.	PRG3	35	.	0			c.T7C						PASS	.	G	ARG/CYS	3815,585	250.9+/-257.8	1650,515,35	205.0	156.0	173.0		7	-5.9	0.0	11	dbSNP_83	173	8583,9	6.4+/-24.3	4287,9,0	yes	missense	PRG3	NM_006093.3	180	5937,524,35	GG,GA,AA		0.1047,13.2955,4.572	probably-damaging	3/226	57148175	12398,594	2200	4296	6496	SO:0001583	missense	10394	exon2			AGAGGCATTGCAT	AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.7T>C	11.37:g.57148175A>G	ENSP00000287143:p.Cys3Arg	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	233	232	0.995708	NM_006093	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000287143.2	37	CCDS7954.1	2101	0.961996336996337	417	0.8475609756097561	356	0.9834254143646409	570	0.9965034965034965	758	1.0	G	13.61	2.287376	0.40494	0.867045	0.998953	ENSG00000156575	ENST00000287143	T	0.04049	3.72	5.76	-5.95	0.02241	.	3.603330	0.00531	N	0.000212	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36720	-0.9736	9	0.07813	T	0.8	1.6714	3.2173	0.06704	0.3935:0.3277:0.1885:0.0902	rs669661;rs52811925;rs60371144;rs669661	3	Q9Y2Y8	PRG3_HUMAN	R	3	ENSP00000287143:C3R	ENSP00000287143:C3R	C	-	1	0	PRG3	56904751	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.016000	0.03633	-2.247000	0.00703	-1.617000	0.00794	TGC	A|0.049;G|0.951	0.951	strong		0.498	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093	
UBE2D2	7322	hgsc.bcm.edu	37	5	139002976	139002976	+	Silent	SNP	T	T	C	rs61760192	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139002976T>C	ENST00000398733.3	+	6	954	c.328T>C	c.(328-330)Ttg>Ctg	p.L110L	UBE2D2_ENST00000511725.1_Silent_p.L81L|UBE2D2_ENST00000505548.1_Silent_p.L81L|UBE2D2_ENST00000253815.2_Silent_p.L81L	NM_003339.2	NP_003330.1	P62837	UB2D2_HUMAN	ubiquitin-conjugating enzyme E2D 2	110					cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTGTTCTCTGTTGTGTGATCC	0.388													T|||	8	0.00159744	0.0008	0.0029	5008	,	,		16072	0.0		0.005	False		,,,				2504	0.0				p.L110L		Atlas-SNP	.											.	UBE2D2	17	.	0			c.T328C						PASS	.	T	,	11,3797		0,11,1893	213.0	186.0	195.0		328,241	6.0	1.0	5	dbSNP_129	195	98,8182		0,98,4042	no	coding-synonymous,coding-synonymous	UBE2D2	NM_003339.2,NM_181838.1	,	0,109,5935	CC,CT,TT		1.1836,0.2889,0.9017	,	110/148,81/119	139002976	109,11979	1904	4140	6044	SO:0001819	synonymous_variant	7322	exon6			TCTCTGTTGTGTG	L40146	CCDS43369.1, CCDS47275.1	5q31.2	2013-10-18	2011-05-19		ENSG00000131508	ENSG00000131508		"""Ubiquitin-conjugating enzymes E2"""	12475	protein-coding gene	gene with protein product		602962	"""ubiquitin-conjugating enzyme E2D 2 (homologous to yeast UBC4/5)"", ""ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)"""			8530467	Standard	NM_181838		Approved	UbcH5B, UBC4	uc003ler.3	P62837	OTTHUMG00000163282	ENST00000398733.3:c.328T>C	5.37:g.139002976T>C		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	193	138	0.715026	NM_003339	D3DQC9|P51669|Q3MN78|Q96RP6	Silent	SNP	ENST00000398733.3	37	CCDS43369.1																																																																																			T|0.995;C|0.005	0.005	strong		0.388	UBE2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372454.3	NM_181838	
VPS37C	55048	hgsc.bcm.edu	37	11	60899815	60899815	+	Missense_Mutation	SNP	A	A	T	rs2232142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60899815A>T	ENST00000301765.5	-	5	777	c.545T>A	c.(544-546)gTc>gAc	p.V182D		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	182	Pro-rich.		V -> D (in dbSNP:rs2232142). {ECO:0000269|PubMed:17974005}.		endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						TCCCTGGGGGACTGGGCGCAC	0.677													A|||	172	0.034345	0.0053	0.0533	5008	,	,		11332	0.003		0.0815	False		,,,				2504	0.044				p.V182D		Atlas-SNP	.											VPS37C,colon,carcinoma,0,1	VPS37C	30	1	0			c.T545A						PASS	.	A	ASP/VAL	70,4324		2,66,2129	17.0	20.0	19.0		545	-6.6	0.0	11	dbSNP_98	19	763,7821		33,697,3562	yes	missense	VPS37C	NM_017966.4	152	35,763,5691	TT,TA,AA		8.8886,1.5931,6.4186	benign	182/356	60899815	833,12145	2197	4292	6489	SO:0001583	missense	55048	exon5			TGGGGGACTGGGC	AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"""vacuolar protein sorting 37C (yeast)"""			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.545T>A	11.37:g.60899815A>T	ENSP00000301765:p.Val182Asp	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	155	80	0.516129	NM_017966	Q8N3K4	Missense_Mutation	SNP	ENST00000301765.5	37	CCDS31573.1	92	0.04212454212454213	4	0.008130081300813009	21	0.058011049723756904	2	0.0034965034965034965	65	0.08575197889182058	A	1.833	-0.469258	0.04445	0.015931	0.088886	ENSG00000167987	ENST00000301765;ENST00000540084	T	0.45668	0.89	4.71	-6.59	0.01830	.	1.707430	0.03070	N	0.156996	T	0.00754	0.0025	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.04930	-1.0917	9	0.21014	T	0.42	2.7763	3.0749	0.06243	0.3376:0.3612:0.2053:0.0959	rs2232142	182	A5D8V6	VP37C_HUMAN	D	182	ENSP00000301765:V182D	ENSP00000301765:V182D	V	-	2	0	VPS37C	60656391	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.471000	0.00990	-1.467000	0.01895	-0.464000	0.05259	GTC	A|0.958;T|0.042	0.042	strong		0.677	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966	
MUTYH	4595	hgsc.bcm.edu	37	1	45800156	45800156	+	Missense_Mutation	SNP	C	C	T	rs3219484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45800156C>T	ENST00000372098.3	-	2	197	c.64G>A	c.(64-66)Gtg>Atg	p.V22M	MUTYH_ENST00000448481.1_Missense_Mutation_p.V8M|MUTYH_ENST00000354383.6_Missense_Mutation_p.V8M|MUTYH_ENST00000372110.3_Missense_Mutation_p.V22M|MUTYH_ENST00000529984.1_Missense_Mutation_p.V8M|MUTYH_ENST00000531105.1_Missense_Mutation_p.V8M|MUTYH_ENST00000450313.1_Missense_Mutation_p.V22M|MUTYH_ENST00000488731.2_Missense_Mutation_p.V8M|MUTYH_ENST00000372100.5_Missense_Mutation_p.V8M|MUTYH_ENST00000372104.1_Missense_Mutation_p.V8M|MUTYH_ENST00000355498.2_Missense_Mutation_p.V8M|MUTYH_ENST00000372115.3_Missense_Mutation_p.V22M|MUTYH_ENST00000528013.2_Missense_Mutation_p.V8M|MUTYH_ENST00000456914.2_Missense_Mutation_p.V8M|MUTYH_ENST00000528332.2_Missense_Mutation_p.V22M			Q9UIF7	MUTYH_HUMAN	mutY homolog	22			V -> M (in dbSNP:rs3219484). {ECO:0000269|PubMed:12606733, ECO:0000269|Ref.4}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					CCACTTCCCACGGCTGCTCGT	0.537			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis				C|||	102	0.0203674	0.0015	0.0231	5008	,	,		20713	0.002		0.0537	False		,,,				2504	0.0286				p.V22M		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.G64A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	54,4352	53.6+/-89.4	0,54,2149	127.0	102.0	110.0		64,22,22,22,64,64	1.7	0.8	1	dbSNP_106	110	597,8003	157.9+/-211.5	31,535,3734	yes	missense,missense,missense,missense,missense,missense	MUTYH	NM_001048171.1,NM_001048172.1,NM_001048173.1,NM_001048174.1,NM_001128425.1,NM_012222.2	21,21,21,21,21,21	31,589,5883	TT,TC,CC		6.9419,1.2256,5.0054	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	22/536,8/523,8/522,8/522,22/550,22/547	45800156	651,12355	2203	4300	6503	SO:0001583	missense	4595	exon2	Familial Cancer Database	MAP, MYH-associated polyposis	TTCCCACGGCTGC	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.64G>A	1.37:g.45800156C>T	ENSP00000361170:p.Val22Met	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	179	111	0.620112	NM_012222	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	37	CCDS520.1	56	0.02564102564102564	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	47	0.06200527704485488	C	12.19	1.864916	0.32977	0.012256	0.069419	ENSG00000132781	ENST00000529984;ENST00000528332;ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000488731;ENST00000450313;ENST00000372100;ENST00000531105;ENST00000435155;ENST00000528013;ENST00000483127	T;D;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.92495	1.96;-3.05;3.1;3.06;3.1;3.04;3.1;3.03;3.02;3.08;1.96;3.02;3.06;0.29;1.75;0.7;0.64	4.52	1.68	0.24146	.	0.406616	0.20456	N	0.091988	T	0.39253	0.1071	L	0.54323	1.7	0.27697	N	0.945914	B;B;B;P;B	0.36144	0.185;0.281;0.185;0.539;0.113	B;B;B;B;B	0.21546	0.015;0.035;0.015;0.025;0.01	T	0.64613	-0.6366	10	0.72032	D	0.01	-1.9465	6.5278	0.22310	0.0:0.7063:0.0:0.2937	rs3219484;rs17784895;rs52809192;rs61197742;rs3219484	22;22;22;22;8	E5KP25;Q9UIF7-2;Q9UIF7;E5KP27;E5KP28	.;.;MUTYH_HUMAN;.;.	M	8;22;8;8;8;8;8;22;22;22;8;22;8;8;8;8;14	ENSP00000437093:V8M;ENSP00000433076:V22M;ENSP00000361176:V8M;ENSP00000409718:V8M;ENSP00000407590:V8M;ENSP00000346354:V8M;ENSP00000347685:V8M;ENSP00000361170:V22M;ENSP00000361182:V22M;ENSP00000361187:V22M;ENSP00000432330:V8M;ENSP00000408176:V22M;ENSP00000361172:V8M;ENSP00000431292:V8M;ENSP00000403655:V8M;ENSP00000433130:V8M;ENSP00000436469:V14M	ENSP00000346354:V8M	V	-	1	0	MUTYH	45572743	0.000000	0.05858	0.831000	0.32960	0.790000	0.44656	-0.106000	0.10890	0.423000	0.26033	-0.806000	0.03193	GTG	T|0.042;G|0.006	0.042	strong		0.537	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222	
SLC22A9	114571	hgsc.bcm.edu	37	11	63175593	63175593	+	Missense_Mutation	SNP	C	C	T	rs61742518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:63175593C>T	ENST00000279178.3	+	8	1547	c.1298C>T	c.(1297-1299)aCg>aTg	p.T433M	SLC22A9_ENST00000310969.4_3'UTR	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	433					hormone transport (GO:0009914)|short-chain fatty acid import (GO:0015913)|sodium-independent organic anion transport (GO:0043252)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	anion:anion antiporter activity (GO:0015301)|short-chain fatty acid uptake transporter activity (GO:0015636)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						GAAATGCAGACGCTGCGTGAG	0.483													C|||	48	0.00958466	0.0008	0.0159	5008	,	,		20878	0.0		0.0298	False		,,,				2504	0.0061				p.T433M		Atlas-SNP	.											.	SLC22A9	77	.	0			c.C1298T						PASS	.	C	MET/THR	25,4377	31.7+/-61.6	0,25,2176	84.0	78.0	80.0		1298	1.5	0.3	11	dbSNP_129	80	241,8355	96.1+/-157.9	6,229,4063	yes	missense	SLC22A9	NM_080866.2	81	6,254,6239	TT,TC,CC		2.8036,0.5679,2.0465	probably-damaging	433/554	63175593	266,12732	2201	4298	6499	SO:0001583	missense	114571	exon8			TGCAGACGCTGCG	AP001880	CCDS8043.1	11q12.3	2014-05-20	2008-01-11		ENSG00000149742	ENSG00000149742		"""Solute carriers"""	16261	protein-coding gene	gene with protein product		607579				11327718, 17393504	Standard	NM_080866		Approved	OAT4, FLJ23666, UST3, OAT7	uc001nww.3	Q8IVM8	OTTHUMG00000167805	ENST00000279178.3:c.1298C>T	11.37:g.63175593C>T	ENSP00000279178:p.Thr433Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_080866	A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Missense_Mutation	SNP	ENST00000279178.3	37	CCDS8043.1	28	0.01282051282051282	0	0.0	7	0.019337016574585635	0	0.0	21	0.027704485488126648	C	15.20	2.762386	0.49468	0.005679	0.028036	ENSG00000149742	ENST00000279178	T	0.57436	0.4	2.46	1.51	0.23008	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.448480	0.24864	N	0.034999	T	0.44393	0.1291	M	0.87682	2.9	0.23063	N	0.998356	D	0.89917	1.0	D	0.77557	0.99	T	0.45731	-0.9241	10	0.34782	T	0.22	.	4.3887	0.11330	0.0:0.798:0.0:0.202	rs61742518	433	Q8IVM8	S22A9_HUMAN	M	433	ENSP00000279178:T433M	ENSP00000279178:T433M	T	+	2	0	SLC22A9	62932169	0.011000	0.17503	0.290000	0.24890	0.624000	0.37722	-0.231000	0.09069	0.572000	0.29383	0.205000	0.17691	ACG	C|0.982;T|0.018	0.018	strong		0.483	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866	
BARD1	580	hgsc.bcm.edu	37	2	215632256	215632256	+	Silent	SNP	A	A	G	rs113211432|rs2070093|rs386654966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:215632256A>G	ENST00000260947.4	-	6	1652	c.1518T>C	c.(1516-1518)caT>caC	p.H506H	BARD1_ENST00000449967.2_Silent_p.H362H	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	506					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTATATCCACATGCCCATTCT	0.408									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				a|||	3859	0.770567	0.5545	0.7594	5008	,	,		18610	0.9484		0.8181	False		,,,				2504	0.8384				p.H506H		Atlas-SNP	.											.	BARD1	138	.	0			c.T1518C						PASS	.	A		2571,1835		819,933,451	128.0	116.0	120.0		1518	-1.7	0.0	2	dbSNP_96	120	6713,1887		2726,1261,313	no	coding-synonymous	BARD1	NM_000465.2		3545,2194,764	GG,GA,AA		21.9419,41.6478,28.6176		506/778	215632256	9284,3722	2203	4300	6503	SO:0001819	synonymous_variant	580	exon6	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	ATCCACATGCCCA		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.1518T>C	2.37:g.215632256A>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	200	200	1	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Silent	SNP	ENST00000260947.4	37	CCDS2397.1																																																																																			A|0.259;G|0.741	0.741	strong		0.408	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
CGNL1	84952	hgsc.bcm.edu	37	15	57731384	57731384	+	Missense_Mutation	SNP	G	G	T	rs148544821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:57731384G>T	ENST00000281282.5	+	2	1265	c.1187G>T	c.(1186-1188)gGc>gTc	p.G396V		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	396	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TTTCCTTTTGGCCTCCAAGGG	0.527													G|||	4	0.000798722	0.0008	0.0014	5008	,	,		18234	0.0		0.002	False		,,,				2504	0.0				p.G396V		Atlas-SNP	.											.	CGNL1	125	.	0			c.G1187T						PASS	.	G	VAL/GLY	2,4382	4.2+/-10.8	0,2,2190	94.0	96.0	95.0		1187	5.8	0.3	15	dbSNP_134	95	14,8570	9.8+/-36.6	0,14,4278	yes	missense	CGNL1	NM_032866.3	109	0,16,6468	TT,TG,GG		0.1631,0.0456,0.1234	probably-damaging	396/1303	57731384	16,12952	2192	4292	6484	SO:0001583	missense	84952	exon2			CTTTTGGCCTCCA	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.1187G>T	15.37:g.57731384G>T	ENSP00000281282:p.Gly396Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	115	46	0.4	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	17.89	3.498940	0.64298	4.56E-4	0.001631	ENSG00000128849	ENST00000281282	T	0.58940	0.3	5.79	5.79	0.91817	.	0.000000	0.52532	D	0.000073	T	0.68723	0.3032	L	0.54323	1.7	0.58432	D	0.999999	D	0.65815	0.995	P	0.59357	0.856	T	0.70733	-0.4791	10	0.87932	D	0	-28.2427	15.212	0.73230	0.0689:0.0:0.9311:0.0	.	396	Q0VF96	CGNL1_HUMAN	V	396	ENSP00000281282:G396V	ENSP00000281282:G396V	G	+	2	0	CGNL1	55518676	1.000000	0.71417	0.255000	0.24374	0.477000	0.33069	6.194000	0.72082	2.722000	0.93159	0.655000	0.94253	GGC	G|0.998;T|0.002	0.002	strong		0.527	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
CAND1	55832	hgsc.bcm.edu	37	12	67706466	67706466	+	Silent	SNP	G	G	A	rs1060350	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:67706466G>A	ENST00000545606.1	+	15	3986	c.3549G>A	c.(3547-3549)ctG>ctA	p.L1183L		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	1183					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)		p.L1183L(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TAGCAGCACTGCTAACCATTC	0.433													G|||	2035	0.40635	0.2201	0.4899	5008	,	,		19555	0.3194		0.5905	False		,,,				2504	0.499				p.L1183L		Atlas-SNP	.											CAND1,NS,carcinoma,0,1	CAND1	100	1	1	Substitution - coding silent(1)	stomach(1)	c.G3549A						scavenged	.	G		1226,3180	425.3+/-340.8	171,884,1148	99.0	83.0	89.0		3549	2.7	1.0	12	dbSNP_86	89	5129,3471	635.2+/-398.9	1523,2083,694	no	coding-synonymous	CAND1	NM_018448.3		1694,2967,1842	AA,AG,GG		40.3605,27.8257,48.8621		1183/1231	67706466	6355,6651	2203	4300	6503	SO:0001819	synonymous_variant	55832	exon15			AGCACTGCTAACC		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"""TBP interacting protein"""	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.3549G>A	12.37:g.67706466G>A		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	145	79	0.544828	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	37	CCDS8977.1																																																																																			G|0.539;A|0.461	0.461	strong		0.433	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448	
UNC5C	8633	hgsc.bcm.edu	37	4	96171681	96171681	+	Silent	SNP	A	A	G	rs34875919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:96171681A>G	ENST00000453304.1	-	5	1080	c.732T>C	c.(730-732)atT>atC	p.I244I	UNC5C_ENST00000506749.1_Silent_p.I244I|UNC5C_ENST00000504962.1_Silent_p.I244I	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	244	Ig-like C2-type.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		TCTTGGCAACAATGTTTTTGG	0.413													A|||	192	0.0383387	0.0197	0.0317	5008	,	,		18255	0.001		0.0606	False		,,,				2504	0.0838				p.I244I		Atlas-SNP	.											.	UNC5C	141	.	0			c.T732C						PASS	.	A		104,4302	81.9+/-120.4	1,102,2100	148.0	140.0	143.0		732	-2.0	1.0	4	dbSNP_126	143	512,8088	146.3+/-201.9	13,486,3801	no	coding-synonymous	UNC5C	NM_003728.3		14,588,5901	GG,GA,AA		5.9535,2.3604,4.7363		244/932	96171681	616,12390	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon5			GGCAACAATGTTT	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.732T>C	4.37:g.96171681A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	244	113	0.463115	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			A|0.956;G|0.044	0.044	strong		0.413	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
BUD13	84811	hgsc.bcm.edu	37	11	116633862	116633862	+	Missense_Mutation	SNP	G	G	A	rs11820589	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:116633862G>A	ENST00000260210.4	-	4	466	c.443C>T	c.(442-444)cCg>cTg	p.P148L	BUD13_ENST00000375445.3_Missense_Mutation_p.P148L	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	148	Arg-rich.		P -> L (in dbSNP:rs11820589).		mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		AGATGGATCCGGGGTGTCATG	0.572													G|||	445	0.0888578	0.1808	0.134	5008	,	,		16456	0.0		0.0696	False		,,,				2504	0.044				p.P148L		Atlas-SNP	.											.	BUD13	41	.	0			c.C443T						PASS	.	G	LEU/PRO,LEU/PRO	725,3677	295.0+/-283.4	66,593,1542	99.0	106.0	104.0	http://www.ncbi.nlm.nih.gov/pubmed?term	443,443	4.1	0.4	11	dbSNP_120	104	586,8004	154.2+/-208.4	16,554,3725	yes	missense,missense	BUD13	NM_001159736.1,NM_032725.3	98,98	82,1147,5267	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	6.8219,16.4698,10.0908	benign,benign	148/486,148/620	116633862	1311,11681	2201	4295	6496	SO:0001583	missense	84811	exon4			GGATCCGGGGTGT	BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 71"""		"""BUD13 homolog (yeast)"""			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.443C>T	11.37:g.116633862G>A	ENSP00000260210:p.Pro148Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_001159736	A8K0S0|Q96LS7	Missense_Mutation	SNP	ENST00000260210.4	37	CCDS8374.1	170	0.07783882783882784	88	0.17886178861788618	36	0.09944751381215469	0	0.0	46	0.06068601583113457	G	10.42	1.346601	0.24426	0.164698	0.068219	ENSG00000137656	ENST00000375445;ENST00000260210	T;T	0.20069	2.15;2.1	5.01	4.08	0.47627	.	0.318031	0.37669	N	0.001982	T	0.00039	0.0001	M	0.75777	2.31	0.09310	P	0.99999896671	B;P;B	0.40931	0.084;0.733;0.047	B;B;B	0.36608	0.016;0.229;0.011	T	0.10870	-1.0611	9	0.87932	D	0	-0.6497	12.9589	0.58447	0.0794:0.0:0.9206:0.0	rs11820589;rs52824190;rs11820589	148;148;148	A8K4Z6;Q9BRD0-2;Q9BRD0	.;.;BUD13_HUMAN	L	148	ENSP00000364594:P148L;ENSP00000260210:P148L	ENSP00000260210:P148L	P	-	2	0	BUD13	116139072	1.000000	0.71417	0.358000	0.25811	0.036000	0.12997	4.403000	0.59729	2.597000	0.87782	0.609000	0.83330	CCG	G|0.905;A|0.095	0.095	strong		0.572	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000104864.1	NM_032725	
MIOX	55586	hgsc.bcm.edu	37	22	50926768	50926768	+	Silent	SNP	C	C	T	rs2232883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50926768C>T	ENST00000216075.6	+	5	479	c.405C>T	c.(403-405)ccC>ccT	p.P135P	MIOX_ENST00000395732.3_Silent_p.P135P|MIOX_ENST00000395733.3_Missense_Mutation_p.P146L	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	135					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCGGGGAGCCCCAGGTAAGAG	0.647													c|||	427	0.0852636	0.093	0.0908	5008	,	,		14186	0.0278		0.1392	False		,,,				2504	0.0746				p.P135P		Atlas-SNP	.											.	MIOX	21	.	0			c.C405T						PASS	.	C		450,3956	211.5+/-231.7	30,390,1783	55.0	57.0	56.0		405	-2.2	1.0	22	dbSNP_98	56	1244,7356	245.7+/-274.4	101,1042,3157	no	coding-synonymous	MIOX	NM_017584.5		131,1432,4940	TT,TC,CC		14.4651,10.2133,13.0248		135/286	50926768	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	55586	exon5			GGAGCCCCAGGTA	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"""kidney-specific protein 32"""	606774	"""aldehyde reductase (aldose reductase) like 6"""	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.405C>T	22.37:g.50926768C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	61	0.616162	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Silent	SNP	ENST00000216075.6	37	CCDS14092.1	212	0.09706959706959707	48	0.0975609756097561	38	0.10497237569060773	16	0.027972027972027972	110	0.14511873350923482	C	10.08	1.251662	0.22880	0.102133	0.144651	ENSG00000100253	ENST00000395733	.	.	.	4.29	-2.17	0.07059	.	0.057262	0.64402	D	0.000001	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	B	0.09022	0.002	B	0.09377	0.004	T	0.07366	-1.0776	7	0.72032	D	0.01	-9.7685	0.8144	0.01099	0.163:0.2381:0.3211:0.2778	rs2232883	146	Q9UGB7-2	.	L	146	.	ENSP00000379082:P146L	P	+	2	0	MIOX	49273634	0.009000	0.17119	1.000000	0.80357	0.751000	0.42716	-0.849000	0.04322	0.058000	0.16222	0.436000	0.28706	CCC	C|0.878;T|0.122	0.122	strong		0.647	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584	
NOX3	50508	hgsc.bcm.edu	37	6	155774608	155774608	+	Silent	SNP	C	C	T	rs34960420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:155774608C>T	ENST00000159060.2	-	4	372	c.270G>A	c.(268-270)ccG>ccA	p.P90P		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	90	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GCCTCCTCCACGGTCCTCTGC	0.378													C|||	638	0.127396	0.1059	0.2291	5008	,	,		19963	0.1121		0.1044	False		,,,				2504	0.1237				p.P90P		Atlas-SNP	.											.	NOX3	93	.	0			c.G270A						PASS	.	C		471,3935	221.7+/-238.7	29,413,1761	203.0	209.0	207.0		270	-5.3	0.8	6	dbSNP_126	207	968,7632	210.8+/-251.6	57,854,3389	no	coding-synonymous	NOX3	NM_015718.2		86,1267,5150	TT,TC,CC		11.2558,10.69,11.0641		90/569	155774608	1439,11567	2203	4300	6503	SO:0001819	synonymous_variant	50508	exon4			CCTCCACGGTCCT	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.270G>A	6.37:g.155774608C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	203	90	0.44335	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	37	CCDS5250.1																																																																																			C|0.888;T|0.112	0.112	strong		0.378	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
DSC1	1823	hgsc.bcm.edu	37	18	28734749	28734749	+	Silent	SNP	A	A	G	rs2249810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:28734749A>G	ENST00000257198.5	-	5	876	c.615T>C	c.(613-615)taT>taC	p.Y205Y	DSC1_ENST00000257197.3_Silent_p.Y205Y|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	205	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CAAACTGTTCATATTTCTCAC	0.328													A|||	2397	0.478634	0.2057	0.5749	5008	,	,		15175	0.6657		0.6183	False		,,,				2504	0.4427				p.Y205Y		Atlas-SNP	.											.	DSC1	240	.	0			c.T615C						PASS	.	A	,	1212,3194	419.3+/-338.6	165,882,1156	59.0	57.0	58.0		615,615	2.8	0.3	18	dbSNP_100	58	4955,3645	621.0+/-397.1	1412,2131,757	yes	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	1577,3013,1913	GG,GA,AA		42.3837,27.5079,47.4166	,	205/841,205/895	28734749	6167,6839	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon5			CTGTTCATATTTC	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.615T>C	18.37:g.28734749A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			G|0.484;N|0.000	0.484	strong		0.328	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
PLXDC1	57125	hgsc.bcm.edu	37	17	37224211	37224211	+	Splice_Site	SNP	C	C	T	rs75117355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:37224211C>T	ENST00000315392.4	-	14	1596	c.1385G>A	c.(1384-1386)cGt>cAt	p.R462H	CTD-2206N4.4_ENST00000583447.1_RNA|PLXDC1_ENST00000493200.1_5'UTR|PLXDC1_ENST00000444911.2_Splice_Site_p.R422H|PLXDC1_ENST00000539608.1_3'UTR	NM_020405.4	NP_065138.2	Q8IUK5	PLDX1_HUMAN	plexin domain containing 1	462			R -> H (in dbSNP:rs75117355). {ECO:0000269|PubMed:14702039}.		angiogenesis (GO:0001525)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)	receptor activity (GO:0004872)			kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						GTGAGGTCTACGCTGCAGAAG	0.602													c|||	358	0.0714856	0.0182	0.1124	5008	,	,		18457	0.1349		0.0746	False		,,,				2504	0.046				p.R462H		Atlas-SNP	.											.	PLXDC1	45	.	0			c.G1385A						PASS	.	C	HIS/ARG	113,4293	86.8+/-125.4	2,109,2092	83.0	71.0	75.0		1385	5.3	1.0	17	dbSNP_131	75	639,7961	164.8+/-217.1	19,601,3680	yes	missense-near-splice	PLXDC1	NM_020405.4	29	21,710,5772	TT,TC,CC		7.4302,2.5647,5.7819	probably-damaging	462/501	37224211	752,12254	2203	4300	6503	SO:0001630	splice_region_variant	57125	exon14			GGTCTACGCTGCA	AF279144	CCDS11333.1	17q21.1	2006-04-12			ENSG00000161381	ENSG00000161381			20945	protein-coding gene	gene with protein product	"""tumor endothelial marker 7 precursor"""	606826				10947988, 11559528	Standard	NM_020405		Approved	TEM3, TEM7	uc002hrg.2	Q8IUK5	OTTHUMG00000133183	ENST00000315392.4:c.1384-1G>A	17.37:g.37224211C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	189	80	0.42328	NM_020405	B2R7I8|Q5QCZ7|Q5QCZ8|Q5QCZ9|Q9HCT9	Missense_Mutation	SNP	ENST00000315392.4	37	CCDS11333.1	193	0.08836996336996338	8	0.016260162601626018	48	0.13259668508287292	77	0.1346153846153846	60	0.079155672823219	C	27.7	4.859336	0.91433	0.025647	0.074302	ENSG00000161381	ENST00000315392;ENST00000394318;ENST00000444911	T;T	0.26373	1.74;1.79	5.27	5.27	0.74061	.	0.276982	0.35013	N	0.003511	T	0.00608	0.0020	M	0.64404	1.975	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.00190	-1.1937	9	0.49607	T	0.09	-28.3849	15.9589	0.79910	0.0:1.0:0.0:0.0	.	422;462	B4E173;Q8IUK5	.;PXDC1_HUMAN	H	462;389;422	ENSP00000323927:R462H;ENSP00000409687:R422H	ENSP00000323927:R462H	R	-	2	0	PLXDC1	34477737	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	4.971000	0.63749	2.632000	0.89209	0.561000	0.74099	CGT	C|0.927;T|0.073	0.073	strong		0.602	PLXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256892.2	NM_020405	Missense_Mutation
CBWD6	644019	hgsc.bcm.edu	37	9	69256816	69256816	+	Silent	SNP	G	G	A	rs62557779	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:69256816G>A	ENST00000377457.5	-	3	420	c.315C>T	c.(313-315)aaC>aaT	p.N105N	CBWD6_ENST00000377441.1_Silent_p.N105N|CBWD6_ENST00000382399.4_Silent_p.N105N|CBWD6_ENST00000377449.1_Silent_p.N69N	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6	105							ATP binding (GO:0005524)			lung(4)	4						AGAGGCAACCGTTTCTAAGTT	0.378													.|||	1986	0.396565	0.1921	0.5288	5008	,	,		16370	0.4712		0.5686	False		,,,				2504	0.3252				p.N105N		Atlas-SNP	.											.	CBWD6	19	.	0			c.C315T						PASS	.						86.0	93.0	90.0					9																	69256816		2193	4267	6460	SO:0001819	synonymous_variant	644019	exon3			GCAACCGTTTCTA		CCDS43827.1	9q13	2006-06-30			ENSG00000204790	ENSG00000204790			31978	protein-coding gene	gene with protein product							Standard	NM_001085457		Approved	OTTHUMG00000066820	uc004afj.4	Q4V339	OTTHUMG00000066820	ENST00000377457.5:c.315C>T	9.37:g.69256816G>A		Somatic	2677	2	0.000747105		WXS	Illumina HiSeq	Phase_I	1626	523	0.321648	NM_001085457		Silent	SNP	ENST00000377457.5	37	CCDS43827.1																																																																																			G|0.525;A|0.475	0.475	strong		0.378	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822	
SCUBE2	57758	hgsc.bcm.edu	37	11	9069046	9069046	+	Missense_Mutation	SNP	G	G	A	rs3751055	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:9069046G>A	ENST00000309263.3	-	15	1844	c.1772C>T	c.(1771-1773)aCg>aTg	p.T591M	SCUBE2_ENST00000457346.2_Missense_Mutation_p.T620M|SCUBE2_ENST00000520467.1_Missense_Mutation_p.T620M|SCUBE2_ENST00000450649.2_Missense_Mutation_p.T465M|RP11-467K18.2_ENST00000531592.1_RNA			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	591			T -> M (in dbSNP:rs3751055). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.T591M(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		CTTTCTGAGCGTGCGGATGGC	0.562													G|||	773	0.154353	0.0507	0.062	5008	,	,		19886	0.256		0.1272	False		,,,				2504	0.2832				p.T620M		Atlas-SNP	.											SCUBE2,NS,carcinoma,0,1	SCUBE2	102	1	1	Substitution - Missense(1)	stomach(1)	c.C1859T						PASS	.	G	MET/THR,MET/THR	291,4111	160.0+/-192.4	11,269,1921	90.0	75.0	80.0		1394,1859	2.0	0.6	11	dbSNP_107	80	1204,7388	242.8+/-272.6	87,1030,3179	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	81,81	98,1299,5100	AA,AG,GG		14.013,6.6106,11.5053	benign,benign	465/808,620/972	9069046	1495,11499	2201	4296	6497	SO:0001583	missense	57758	exon16			CTGAGCGTGCGGA	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.1772C>T	11.37:g.9069046G>A	ENSP00000310658:p.Thr591Met	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	201	93	0.462687	NM_020974	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		311	0.1423992673992674	34	0.06910569105691057	33	0.09116022099447514	140	0.24475524475524477	104	0.13720316622691292	G	15.50	2.851660	0.51270	0.066106	0.14013	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	T;T;D;T	0.84370	-1.3;-1.41;-1.84;-1.48	5.07	2.03	0.26663	.	0.256195	0.44902	D	0.000419	T	0.00109	0.0003	L	0.45352	1.415	0.20926	P	0.999825555	P;P;P	0.46706	0.883;0.852;0.875	B;P;P	0.50162	0.407;0.633;0.534	T	0.01488	-1.1342	9	0.33141	T	0.24	.	7.8988	0.29723	0.1473:0.1337:0.719:0.0	rs3751055;rs52811192;rs58729419;rs3751055	465;620;591	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	M	620;591;465;620	ENSP00000390481:T620M;ENSP00000310658:T591M;ENSP00000415187:T465M;ENSP00000429969:T620M	ENSP00000310658:T591M	T	-	2	0	SCUBE2	9025622	1.000000	0.71417	0.556000	0.28293	0.935000	0.57460	4.686000	0.61700	0.594000	0.29761	0.655000	0.94253	ACG	G|0.865;A|0.135	0.135	strong		0.562	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
SLC6A15	55117	hgsc.bcm.edu	37	12	85277561	85277561	+	Intron	SNP	T	T	A	rs17183577	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:85277561T>A	ENST00000266682.5	-	5	1298				SLC6A15_ENST00000552192.1_Intron|SLC6A15_ENST00000450363.3_Missense_Mutation_p.D278V|SLC6A15_ENST00000551388.1_Intron	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15						amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						CCCACAGAAATCTGTAACAGA	0.348													T|||	374	0.0746805	0.0053	0.1599	5008	,	,		18044	0.0		0.2266	False		,,,				2504	0.0286				p.D278V		Atlas-SNP	.											.	SLC6A15	159	.	0			c.A833T						PASS	.	T	,VAL/ASP,	191,4215	121.3+/-158.8	7,177,2019	73.0	71.0	72.0		,833,	-0.4	0.0	12	dbSNP_123	72	1788,6812	314.9+/-312.0	196,1396,2708	yes	intron,missense,intron	SLC6A15	NM_001146335.1,NM_018057.5,NM_182767.4	,152,	203,1573,4727	AA,AT,TT		20.7907,4.335,15.2161	,,	,278/290,	85277561	1979,11027	2203	4300	6503	SO:0001627	intron_variant	55117	exon5			CAGAAATCTGTAA	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.756+76A>T	12.37:g.85277561T>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	238	0.10897435897435898	2	0.0040650406504065045	59	0.16298342541436464	0	0.0	177	0.23350923482849603	T	7.764	0.705915	0.15172	0.04335	0.207907	ENSG00000072041	ENST00000450363	T	0.68479	-0.33	4.95	-0.422	0.12329	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09907	-1.0653	7	0.87932	D	0	.	1.2642	0.02007	0.2154:0.1912:0.1092:0.4842	rs17183577;rs52796771;rs17183577	278	Q9H9F5	.	V	278	ENSP00000390706:D278V	ENSP00000390706:D278V	D	-	2	0	SLC6A15	83801692	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.510000	0.22723	-0.439000	0.07222	-1.427000	0.01099	GAT	T|0.862;A|0.138	0.138	strong		0.348	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
ZNF683	257101	hgsc.bcm.edu	37	1	26688181	26688181	+	Silent	SNP	G	G	C	rs11583897	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:26688181G>C	ENST00000436292.1	-	7	1656	c.1536C>G	c.(1534-1536)gcC>gcG	p.A512A	ZNF683_ENST00000403843.1_Silent_p.A512A|ZNF683_ENST00000349618.3_Silent_p.A492A|ZNF683_ENST00000374204.1_Silent_p.A492A			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	512					natural killer cell differentiation (GO:0001779)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		GGGGAGTCCCGGCACTGCTCA	0.522													G|||	407	0.08127	0.1346	0.0533	5008	,	,		21791	0.0278		0.0875	False		,,,				2504	0.0777				p.A492A		Atlas-SNP	.											.	ZNF683	51	.	0			c.C1476G						PASS	.	G	,	494,3912	227.8+/-242.9	18,458,1727	135.0	132.0	133.0		1476,1476	-0.2	0.0	1	dbSNP_120	133	788,7812	184.2+/-232.2	33,722,3545	no	coding-synonymous,coding-synonymous	ZNF683	NM_001114759.1,NM_173574.2	,	51,1180,5272	CC,CG,GG		9.1628,11.212,9.857	,	492/505,492/505	26688181	1282,11724	2203	4300	6503	SO:0001819	synonymous_variant	257101	exon6			AGTCCCGGCACTG	BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"""Zinc fingers, C2H2-type"""	28495	protein-coding gene	gene with protein product	"""hypothetical protein MGC33414"""					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.1536C>G	1.37:g.26688181G>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	56	42	0.75	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Silent	SNP	ENST00000436292.1	37																																																																																				G|0.907;C|0.093	0.093	strong		0.522	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574	
PHF19	26147	hgsc.bcm.edu	37	9	123632045	123632045	+	Intron	SNP	A	A	G	rs1056567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:123632045A>G	ENST00000373896.3	-	5	718				PHF19_ENST00000419155.1_5'Flank|PHF19_ENST00000312189.6_Silent_p.S181S|PHF19_ENST00000487555.1_5'Flank	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19						chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGGAGCTCAGACTCTGTGATG	0.602													G|||	3194	0.63778	0.5303	0.7824	5008	,	,		17905	0.501		0.6819	False		,,,				2504	0.7761				p.S181S		Atlas-SNP	.											PHF19_ENST00000312189,NS,carcinoma,0,1	PHF19	47	1	0			c.T543C						PASS	.	G	,	2553,1843		740,1073,385	47.0	37.0	40.0		543,	-3.0	0.0	9	dbSNP_86	40	5825,2769		1976,1873,448	no	coding-synonymous,intron	PHF19	NM_001009936.1,NM_015651.1	,	2716,2946,833	GG,GA,AA		32.2202,41.9245,35.5042	,	181/208,	123632045	8378,4612	2198	4297	6495	SO:0001627	intron_variant	26147	exon5			GCTCAGACTCTGT	BX640713	CCDS35116.1, CCDS35117.1, CCDS69648.1, CCDS75889.1	9q34.11	2013-01-28			ENSG00000119403	ENSG00000119403		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24566	protein-coding gene	gene with protein product	"""polycomb-like 3"", ""tudor domain containing 19B"""	609740				15563832	Standard	XM_005251906		Approved	DKFZP727G051, PCL3, MTF2L1, TDRD19B	uc004bks.1	Q5T6S3	OTTHUMG00000020577	ENST00000373896.3:c.465+77T>C	9.37:g.123632045A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	126	51	0.404762	NM_001009936	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	Silent	SNP	ENST00000373896.3	37	CCDS35116.1																																																																																			A|0.383;G|0.617	0.617	strong		0.602	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308	
APIP	51074	hgsc.bcm.edu	37	11	34910397	34910397	+	Missense_Mutation	SNP	C	C	T	rs1977420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34910397C>T	ENST00000395787.3	-	4	441	c.227G>A	c.(226-228)tGt>tAt	p.C76Y	APIP_ENST00000278359.5_Missense_Mutation_p.C93Y|APIP_ENST00000527830.1_5'UTR	NM_015957.2	NP_057041.2			APAF1 interacting protein											kidney(2)|lung(1)|skin(1)	4	all_epithelial(35;0.161)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.000425)			ATTTATATCACAAACAAACAT	0.333													C|||	2291	0.457468	0.3056	0.4035	5008	,	,		14661	0.7371		0.3559	False		,,,				2504	0.5174				p.C76Y		Atlas-SNP	.											.	APIP	21	.	0			c.G227A						PASS	.	C	TYR/CYS	1360,3042	448.7+/-348.8	223,914,1064	86.0	80.0	82.0		227	5.8	1.0	11	dbSNP_92	82	3072,5524	467.2+/-367.0	556,1960,1782	yes	missense	APIP	NM_015957.2	194	779,2874,2846	TT,TC,CC		35.7376,30.895,34.0976	benign	76/243	34910397	4432,8566	2201	4298	6499	SO:0001583	missense	51074	exon4			ATATCACAAACAA	AF132963	CCDS7895.1	11p13	2014-05-12				ENSG00000149089	4.2.1.109		17581	protein-coding gene	gene with protein product	"""methylthioribulose-1-phosphate dehydratase"""	612491				10810093, 15262985, 24367089	Standard	NM_015957		Approved	CGI-29, Mmrp19, APIP2	uc001mvs.2	Q96GX9		ENST00000395787.3:c.227G>A	11.37:g.34910397C>T	ENSP00000379133:p.Cys76Tyr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	53	0.946429	NM_015957		Missense_Mutation	SNP	ENST00000395787.3	37	CCDS7895.1	998	0.45695970695970695	176	0.35772357723577236	145	0.4005524861878453	406	0.7097902097902098	271	0.3575197889182058	C	15.65	2.895387	0.52121	0.30895	0.357376	ENSG00000149089	ENST00000278359;ENST00000395787	T;T	0.21031	2.03;2.03	5.85	5.85	0.93711	Class II aldolase/adducin, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.35723	1.085	0.09310	P	0.999999999737726	B;B	0.15141	0.012;0.01	B;B	0.21708	0.036;0.021	T	0.38585	-0.9654	9	0.27785	T	0.31	-14.1985	20.1775	0.98187	0.0:1.0:0.0:0.0	rs1977420;rs17845553;rs17858450;rs61147536;rs1977420	93;76	B4DY17;Q96GX9	.;MTNB_HUMAN	Y	93;76	ENSP00000278359:C93Y;ENSP00000379133:C76Y	ENSP00000278359:C93Y	C	-	2	0	APIP	34866973	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.655000	0.61476	2.771000	0.95319	0.561000	0.74099	TGT	C|0.611;T|0.389	0.389	strong		0.333	APIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389864.1	NM_015957	
EIF4ENIF1	56478	hgsc.bcm.edu	37	22	31836696	31836696	+	Missense_Mutation	SNP	G	G	A	rs554525025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:31836696G>A	ENST00000397525.1	-	18	2933	c.2710C>T	c.(2710-2712)Cgc>Tgc	p.R904C	EIF4ENIF1_ENST00000344710.5_Missense_Mutation_p.R730C|EIF4ENIF1_ENST00000441289.1_5'Flank|EIF4ENIF1_ENST00000382180.2_Missense_Mutation_p.R559C|EIF4ENIF1_ENST00000330125.5_Missense_Mutation_p.R904C|EIF4ENIF1_ENST00000397523.1_Missense_Mutation_p.R880C	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	904						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CTACCTGAGCGCTGTAGCTGC	0.502													G|||	2	0.000399361	0.0	0.0	5008	,	,		20715	0.0		0.0	False		,,,				2504	0.002				p.R904C		Atlas-SNP	.											EIF4ENIF1,colon,carcinoma,+1,1	EIF4ENIF1	80	1	0			c.C2710T						scavenged	.						118.0	108.0	111.0					22																	31836696		2203	4300	6503	SO:0001583	missense	56478	exon18			CTGAGCGCTGTAG	AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.2710C>T	22.37:g.31836696G>A	ENSP00000380659:p.Arg904Cys	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	132	3	0.0227273	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Missense_Mutation	SNP	ENST00000397525.1	37	CCDS13898.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.867658	0.72065	.	.	ENSG00000184708	ENST00000344710;ENST00000397525;ENST00000330125;ENST00000397523;ENST00000382180	.	.	.	5.59	5.59	0.84812	.	0.166619	0.53938	D	0.000047	T	0.74966	0.3786	L	0.56769	1.78	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;0.988	D;D;D;B	0.79784	0.988;0.993;0.949;0.295	T	0.76424	-0.2964	9	0.87932	D	0	-11.0544	13.3751	0.60734	0.0:0.0:0.7355:0.2644	.	730;904;729;880	B1AKL3;Q9NRA8;Q9NRA8-2;B1AKL4	.;4ET_HUMAN;.;.	C	730;904;904;880;559	.	ENSP00000328103:R904C	R	-	1	0	EIF4ENIF1	30166696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.597000	0.61062	2.763000	0.94921	0.655000	0.94253	CGC	.	.	none		0.502	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843	
BTN1A1	696	hgsc.bcm.edu	37	6	26509382	26509382	+	Missense_Mutation	SNP	C	C	T	rs35555795	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26509382C>T	ENST00000244513.6	+	7	1627	c.1561C>T	c.(1561-1563)Ccc>Tcc	p.P521S		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	521			P -> S (in dbSNP:rs35555795).			extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						CCCTACCCAACCCAGCCAAGG	0.527													C|||	191	0.038139	0.0348	0.0346	5008	,	,		14149	0.0089		0.0815	False		,,,				2504	0.0307				p.P521S		Atlas-SNP	.											.	BTN1A1	68	.	0			c.C1561T						PASS	.	C	SER/PRO	184,4220		4,176,2022	87.0	93.0	91.0		1561	-2.1	0.0	6	dbSNP_126	91	790,7806		38,714,3546	yes	missense	BTN1A1	NM_001732.2	74	42,890,5568	TT,TC,CC		9.1903,4.178,7.4923	possibly-damaging	521/527	26509382	974,12026	2202	4298	6500	SO:0001583	missense	696	exon7			ACCCAACCCAGCC	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.1561C>T	6.37:g.26509382C>T	ENSP00000244513:p.Pro521Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	37	CCDS4614.1	100	0.045787545787545784	18	0.036585365853658534	11	0.03038674033149171	7	0.012237762237762238	64	0.08443271767810026	C	8.290	0.817509	0.16607	0.04178	0.091903	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.36699	1.24	5.41	-2.07	0.07276	.	0.653000	0.14428	N	0.320212	T	0.07503	0.0189	L	0.32530	0.975	0.80722	P	0.0	P	0.35745	0.518	B	0.32149	0.141	T	0.14282	-1.0478	9	0.72032	D	0.01	.	1.5958	0.02663	0.1187:0.3669:0.2316:0.2829	rs35555795;rs61747505	521	Q13410	BT1A1_HUMAN	S	521;489	ENSP00000244513:P521S	ENSP00000244513:P521S	P	+	1	0	BTN1A1	26617361	0.000000	0.05858	0.001000	0.08648	0.155000	0.21991	-1.703000	0.01900	-0.673000	0.05259	-0.768000	0.03414	CCC	C|0.934;T|0.066	0.066	strong		0.527	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
SUMF2	25870	hgsc.bcm.edu	37	7	56136194	56136194	+	Silent	SNP	C	C	T	rs7808729	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:56136194C>T	ENST00000413756.1	+	2	110	c.87C>T	c.(85-87)agC>agT	p.S29S	SUMF2_ENST00000434526.2_Silent_p.S48S|SUMF2_ENST00000275607.9_Intron|SUMF2_ENST00000342190.6_Silent_p.S48S|SUMF2_ENST00000395435.2_Silent_p.S48S|SUMF2_ENST00000395436.2_Silent_p.S48S|SUMF2_ENST00000437307.2_Silent_p.S29S			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	29					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			AGGCTACTAGCATGGTCCAAC	0.453													C|||	763	0.152356	0.0734	0.2133	5008	,	,		15871	0.0724		0.2227	False		,,,				2504	0.226				p.S48S		Atlas-SNP	.											.	SUMF2	56	.	0			c.C144T						PASS	.	C	,,,,	375,4031	190.2+/-216.2	19,337,1847	48.0	47.0	47.0		144,144,144,,144	4.7	0.9	7	dbSNP_116	47	1922,6678	338.2+/-322.6	204,1514,2582	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	SUMF2	NM_001042469.1,NM_001042470.1,NM_001130069.2,NM_001146333.1,NM_015411.2	,,,,	223,1851,4429	TT,TC,CC		22.3488,8.5111,17.6611	,,,,	48/306,48/237,48/359,,48/321	56136194	2297,10709	2203	4300	6503	SO:0001819	synonymous_variant	25870	exon2			TACTAGCATGGTC	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.87C>T	7.37:g.56136194C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_015411	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Silent	SNP	ENST00000413756.1	37																																																																																				C|0.832;T|0.168	0.168	strong		0.453	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136305530	136305530	+	Missense_Mutation	SNP	C	C	G	rs28647808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136305530C>G	ENST00000371929.3	+	16	2296	c.1852C>G	c.(1852-1854)Ccc>Gcc	p.P618A	ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000536611.1_Missense_Mutation_p.P290A|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.P618A|ADAMTS13_ENST00000356589.2_Missense_Mutation_p.P587A|ADAMTS13_ENST00000371916.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	618	Spacer.		P -> A (in dbSNP:rs28647808). {ECO:0000269|PubMed:11586351, ECO:0000269|PubMed:19055667, ECO:0000269|Ref.6}.		cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CACCACCTACCCCTCCCTCCT	0.652													C|||	162	0.0323482	0.0053	0.036	5008	,	,		18262	0.0198		0.0825	False		,,,				2504	0.0276				p.P618A		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C1852G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	79,4327	68.7+/-106.4	1,77,2125	119.0	85.0	97.0		1852,1759,1852	5.1	1.0	9	dbSNP_125	97	742,7858	178.5+/-227.8	37,668,3595	yes	missense,missense,missense	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	27,27,27	38,745,5720	GG,GC,CC		8.6279,1.793,6.3125	probably-damaging,probably-damaging,probably-damaging	618/1428,587/1341,618/1372	136305530	821,12185	2203	4300	6503	SO:0001583	missense	11093	exon16			ACCTACCCCTCCC	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.1852C>G	9.37:g.136305530C>G	ENSP00000360997:p.Pro618Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	153	60	0.392157	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	96	0.04395604395604396	3	0.006097560975609756	14	0.03867403314917127	12	0.02097902097902098	67	0.08839050131926121	C	21.8	4.204993	0.79127	0.01793	0.086279	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589;ENST00000536611	T;T;T;T	0.67523	-0.26;-0.27;-0.25;0.22	5.12	5.12	0.69794	.	.	.	.	.	T	0.19927	0.0479	M	0.85945	2.785	0.20403	P	0.9999036639	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.997;0.998;0.985;0.996	T	0.63060	-0.6721	8	0.45353	T	0.12	.	17.1153	0.86687	0.0:1.0:0.0:0.0	rs28647808;rs36221218	618;587;618;290	Q76LX8;Q76LX8-3;Q76LX8-2;Q9UGQ1	ATS13_HUMAN;.;.;.	A	618;618;587;290	ENSP00000360997:P618A;ENSP00000347927:P618A;ENSP00000348997:P587A;ENSP00000444504:P290A	ENSP00000347927:P618A	P	+	1	0	ADAMTS13	135295351	1.000000	0.71417	0.996000	0.52242	0.617000	0.37484	6.389000	0.73199	2.377000	0.81083	0.491000	0.48974	CCC	C|0.939;G|0.061	0.061	strong		0.652	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
SLC5A11	115584	hgsc.bcm.edu	37	16	24918048	24918048	+	Missense_Mutation	SNP	C	C	T	rs17772929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:24918048C>T	ENST00000569071.1	+	9	944	c.679C>T	c.(679-681)Cgc>Tgc	p.R227C	SLC5A11_ENST00000347898.3_Silent_p.I359I|SLC5A11_ENST00000545376.1_Silent_p.I289I|SLC5A11_ENST00000567758.1_Silent_p.I324I|SLC5A11_ENST00000424767.2_Silent_p.I324I|SLC5A11_ENST00000539472.1_Silent_p.I295I|SLC5A11_ENST00000565769.1_Silent_p.I295I|SLC5A11_ENST00000568579.1_Silent_p.I289I|SLC5A11_ENST00000449109.2_Missense_Mutation_p.R227C					solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		GTTCGGACATCGCGTATCCCA	0.557											OREG0023688	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1187	0.237021	0.3026	0.2565	5008	,	,		18589	0.0169		0.4254	False		,,,				2504	0.1677				p.R227C		Atlas-SNP	.											SLC5A11,NS,carcinoma,0,1	SLC5A11	97	1	0			c.C679T						PASS	.	C		1472,2922	472.6+/-356.4	242,988,967	101.0	83.0	89.0		1077	-2.8	0.9	16	dbSNP_123	89	3702,4898	529.3+/-381.6	791,2120,1389	no	coding-synonymous	SLC5A11	NM_052944.2		1033,3108,2356	TT,TC,CC		43.0465,33.5002,39.8184		359/676	24918048	5174,7820	2197	4300	6497	SO:0001583	missense	115584	exon10			GGACATCGCGTAT	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000569071.1:c.679C>T	16.37:g.24918048C>T	ENSP00000456376:p.Arg227Cys	Somatic	103	0	0	775	WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_001258414		Missense_Mutation	SNP	ENST00000569071.1	37	CCDS58440.1	570	0.260989010989011	128	0.2601626016260163	103	0.2845303867403315	9	0.015734265734265736	330	0.43535620052770446	C	15.67	2.903209	0.52333	0.335002	0.430465	ENSG00000158865	ENST00000449109	D	0.83992	-1.79	5.73	-2.83	0.05769	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.13145	0.007	B	0.04013	0.001	T	0.35500	-0.9786	7	0.87932	D	0	.	11.6091	0.51049	0.0:0.3507:0.0:0.6493	rs17772929;rs17854934;rs59135221;rs17772929	227	Q05BF1	.	C	227	ENSP00000389606:R227C	ENSP00000389606:R227C	R	+	1	0	SLC5A11	24825549	0.031000	0.19500	0.939000	0.37840	0.958000	0.62258	-0.908000	0.04063	-0.302000	0.08869	0.563000	0.77884	CGC	C|0.678;T|0.322	0.322	strong		0.557	SLC5A11-006	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435852.1	NM_052944	
ZNF117	51351	hgsc.bcm.edu	37	7	64439613	64439613	+	Missense_Mutation	SNP	T	T	G	rs3807068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:64439613T>G	ENST00000282869.6	-	4	1620	c.336A>C	c.(334-336)aaA>aaC	p.K112N		NM_015852.3	NP_056936.2	Q03924	ZN117_HUMAN	zinc finger protein 117	112			K -> N (in dbSNP:rs3807068).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(1)|skin(1)	22		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TGCGACATTCTTTACATTTAA	0.279													T|||	1939	0.387181	0.3964	0.2637	5008	,	,		19187	0.4058		0.4016	False		,,,				2504	0.4284				p.K112N		Atlas-SNP	.											ZNF117,NS,carcinoma,0,1	ZNF117	56	1	0			c.A336C						PASS	.	T	ASN/LYS	1557,2601		297,963,819	61.0	59.0	60.0		336	-2.3	0.0	7	dbSNP_107	60	3190,5280		596,1998,1641	no	missense	ZNF117	NM_015852.3	94	893,2961,2460	GG,GT,TT		37.6623,37.4459,37.5911	benign	112/484	64439613	4747,7881	2079	4235	6314	SO:0001583	missense	51351	exon4			ACATTCTTTACAT	M27879	CCDS43593.1	7q11.2	2013-01-08	2006-06-12		ENSG00000152926	ENSG00000152926		"""Zinc fingers, C2H2-type"""	12897	protein-coding gene	gene with protein product		194624	"""zinc finger protein 117 (HPF9)"""			1427907	Standard	NM_015852		Approved	HPF9, H-plk	uc003ttr.2	Q03924	OTTHUMG00000156631	ENST00000282869.6:c.336A>C	7.37:g.64439613T>G	ENSP00000282869:p.Lys112Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_015852	Q02313|Q7Z7Q7	Missense_Mutation	SNP	ENST00000282869.6	37	CCDS43593.1	855	0.3914835164835165	196	0.3983739837398374	116	0.32044198895027626	223	0.38986013986013984	320	0.42216358839050133	.	8.568	0.879357	0.17467	0.374459	0.376623	ENSG00000152926	ENST00000398695;ENST00000282869	T	0.01209	5.17	1.49	-2.31	0.06765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.37750	1.13	0.80722	P	0.0	D	0.67145	0.996	D	0.72982	0.979	T	0.47837	-0.9086	8	0.25106	T	0.35	.	4.72	0.12913	0.4399:0.0:0.0:0.5601	rs3807068;rs3807068	112	Q03924	ZN117_HUMAN	N	112	ENSP00000282869:K112N	ENSP00000282869:K112N	K	-	3	2	ZNF117	64077048	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.380000	0.00068	-0.188000	0.10499	0.260000	0.18958	AAA	T|0.611;G|0.389	0.389	strong		0.279	ZNF117-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344863.3	NM_024498	
ATP5S	27109	hgsc.bcm.edu	37	14	50788213	50788213	+	Missense_Mutation	SNP	C	C	T	rs2275592	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50788213C>T	ENST00000311459.7	+	2	433	c.53C>T	c.(52-54)cCg>cTg	p.P18L	ATP5S_ENST00000426751.2_Missense_Mutation_p.P18L|ATP5S_ENST00000245448.6_Missense_Mutation_p.P18L|ATP5S_ENST00000554438.1_3'UTR|ATP5S_ENST00000358473.1_Intron	NM_001003803.2	NP_001003803.1	Q99766	ATP5S_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B)	18	N-terminal domain.		P -> L (in dbSNP:rs2275592). {ECO:0000269|PubMed:11744738, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9110174, ECO:0000269|Ref.5}.		ATP biosynthetic process (GO:0006754)|hydrogen ion transmembrane transport (GO:1902600)|proton transport (GO:0015992)	mitochondrial inner membrane (GO:0005743)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|metal ion binding (GO:0046872)	p.P18L(1)		breast(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	12	all_epithelial(31;0.000636)|Breast(41;0.0102)			OV - Ovarian serous cystadenocarcinoma(311;0.0685)		CAAATGATGCCGTTTGGAAAA	0.413													T|||	2849	0.56889	0.556	0.5821	5008	,	,		20204	0.6171		0.5606	False		,,,				2504	0.5358				p.P18L		Atlas-SNP	.											ATP5S,NS,carcinoma,0,1	ATP5S	28	1	1	Substitution - Missense(1)	stomach(1)	c.C53T						PASS	.	T	LEU/PRO,LEU/PRO,LEU/PRO	2414,1992	558.6+/-380.0	665,1084,454	160.0	151.0	154.0		53,53,53	5.6	1.0	14	dbSNP_100	154	4857,3743	532.9+/-382.3	1385,2087,828	yes	missense,missense,missense	ATP5S	NM_001003803.2,NM_001003805.2,NM_015684.3	98,98,98	2050,3171,1282	TT,TC,CC		43.5233,45.2111,44.095	benign,benign,benign	18/216,18/128,18/137	50788213	7271,5735	2203	4300	6503	SO:0001583	missense	27109	exon2			TGATGCCGTTTGG	U79253	CCDS32075.1, CCDS32076.1, CCDS45102.1	14q21.3	2011-04-13	2010-06-11			ENSG00000125375			18799	protein-coding gene	gene with protein product			"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B)"""			11744738, 8619474	Standard	NM_015684		Approved	HSU79253, ATPW	uc001wxw.2	Q99766		ENST00000311459.7:c.53C>T	14.37:g.50788213C>T	ENSP00000308334:p.Pro18Leu	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	193	100	0.518135	NM_015684	A8K1U3|D9N156|Q8WWX3|Q96F77	Missense_Mutation	SNP	ENST00000311459.7	37	CCDS32075.1	1235	0.5654761904761905	264	0.5365853658536586	202	0.5580110497237569	344	0.6013986013986014	425	0.5606860158311345	T	5.722	0.317754	0.10845	0.547889	0.564767	ENSG00000125375	ENST00000245448;ENST00000426751;ENST00000311459	T;T;T	0.38240	1.17;1.15;1.79	5.56	5.56	0.83823	.	.	.	.	.	T	0.00012	0.0000	N	0.00125	-2.05	0.09310	P	0.9999999999999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45249	-0.9274	8	0.02654	T	1	.	10.3135	0.43723	0.0:0.0756:0.0:0.9244	rs2275592;rs17845292;rs17858126;rs52805692;rs2275592	18;18;18	Q99766-3;Q99766;Q99766-2	.;ATP5S_HUMAN;.	L	18	ENSP00000245448:P18L;ENSP00000389246:P18L;ENSP00000308334:P18L	ENSP00000245448:P18L	P	+	2	0	ATP5S	49857963	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.614000	0.46359	1.049000	0.40321	-0.352000	0.07741	CCG	C|0.434;T|0.566	0.566	strong		0.413	ATP5S-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410761.1	NM_015684	
SLC39A8	64116	hgsc.bcm.edu	37	4	103189036	103189036	+	Silent	SNP	G	G	A	rs17823966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:103189036G>A	ENST00000394833.2	-	6	1517	c.1041C>T	c.(1039-1041)caC>caT	p.H347H	SLC39A8_ENST00000424970.2_Silent_p.H347H|SLC39A8_ENST00000356736.4_Silent_p.H347H	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	347					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)	p.H347H(1)		large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		TACCTAACTCGTGGGGAAACT	0.448													G|||	144	0.028754	0.0008	0.013	5008	,	,		19203	0.0		0.0427	False		,,,				2504	0.093				p.H347H		Atlas-SNP	.											SLC39A8,NS,carcinoma,0,1	SLC39A8	24	1	1	Substitution - coding silent(1)	prostate(1)	c.C1041T						PASS	.	G	,,,	37,4369	42.3+/-75.8	0,37,2166	55.0	50.0	52.0		1041,1041,840,1041	-2.9	1.0	4	dbSNP_123	52	361,8239	121.1+/-180.3	5,351,3944	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A8	NM_001135146.1,NM_001135147.1,NM_001135148.1,NM_022154.5	,,,	5,388,6110	AA,AG,GG		4.1977,0.8398,3.0601	,,,	347/461,347/445,280/394,347/461	103189036	398,12608	2203	4300	6503	SO:0001819	synonymous_variant	64116	exon6			TAACTCGTGGGGA		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"""Solute carriers"""	20862	protein-coding gene	gene with protein product		608732	"""solute carrier family 39 (metal ion transporter), member 8"""			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.1041C>T	4.37:g.103189036G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Silent	SNP	ENST00000394833.2	37	CCDS3656.1																																																																																			G|0.970;A|0.030	0.030	strong		0.448	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
CACNA1A	773	hgsc.bcm.edu	37	19	13482554	13482554	+	Silent	SNP	C	C	T	rs41276894	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:13482554C>T	ENST00000360228.5	-	4	578	c.579G>A	c.(577-579)acG>acA	p.T193T	CACNA1A_ENST00000573710.2_Silent_p.T193T	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	193					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CTGCCCTCAGCGTCCGTAGGT	0.592													C|||	20	0.00399361	0.0023	0.0029	5008	,	,		17505	0.0		0.0129	False		,,,				2504	0.002				p.T193T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G579A						PASS	.	C	,,,,	18,3972		0,18,1977	19.0	23.0	21.0		579,579,579,579,579	-5.9	0.9	19	dbSNP_127	21	151,8163		0,151,4006	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	0,169,5983	TT,TC,CC		1.8162,0.4511,1.3735	,,,,	193/2267,193/2262,193/2507,193/2264,193/2513	13482554	169,12135	1995	4157	6152	SO:0001819	synonymous_variant	773	exon4			CCTCAGCGTCCGT	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.579G>A	19.37:g.13482554C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.994;T|0.006	0.006	strong		0.592	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
ECD	11319	hgsc.bcm.edu	37	10	74894526	74894526	+	Missense_Mutation	SNP	A	A	C	rs35331959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:74894526A>C	ENST00000372979.4	-	14	1956	c.1750T>G	c.(1750-1752)Tct>Gct	p.S584A	ECD_ENST00000430082.2_Missense_Mutation_p.S617A|ECD_ENST00000454759.2_Missense_Mutation_p.S541A	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	584					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					CCCGTACCAGAATCTTCCTCA	0.428													A|||	14	0.00279553	0.0015	0.0029	5008	,	,		17074	0.0		0.0099	False		,,,				2504	0.0				p.S617A		Atlas-SNP	.											.	ECD	50	.	0			c.T1849G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER	13,4393	20.2+/-43.8	0,13,2190	114.0	111.0	112.0		1849,1621,1750	4.3	1.0	10	dbSNP_126	112	136,8464	68.7+/-131.2	2,132,4166	yes	missense,missense,missense	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	99,99,99	2,145,6356	CC,CA,AA		1.5814,0.2951,1.1456	benign,benign,benign	617/678,541/602,584/645	74894526	149,12857	2203	4300	6503	SO:0001583	missense	11319	exon15			TACCAGAATCTTC	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1750T>G	10.37:g.74894526A>C	ENSP00000362070:p.Ser584Ala	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	160	67	0.41875	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	4.002	-0.002418	0.07819	0.002951	0.015814	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.19394	2.15;2.15;2.15	5.48	4.29	0.51040	.	0.570097	0.19982	N	0.101760	T	0.04861	0.0131	N	0.12746	0.255	0.26648	N	0.972169	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.15484	0.01;0.003;0.013	T	0.24297	-1.0164	10	0.09590	T	0.72	-0.8007	10.5006	0.44804	0.7883:0.2116:0.0:0.0	rs35331959	541;617;584	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	A	584;617;541	ENSP00000362070:S584A;ENSP00000401566:S617A;ENSP00000395786:S541A	ENSP00000362070:S584A	S	-	1	0	ECD	74564532	1.000000	0.71417	1.000000	0.80357	0.242000	0.25591	2.625000	0.46452	2.063000	0.61619	0.460000	0.39030	TCT	A|0.991;C|0.009	0.009	strong		0.428	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792171	8792171	+	Silent	SNP	T	T	C	rs11650737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8792171T>C	ENST00000447110.1	-	10	1057	c.933A>G	c.(931-933)ctA>ctG	p.L311L	PIK3R5_ENST00000584803.1_Silent_p.L311L|PIK3R5_ENST00000581552.1_Silent_p.L311L	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	311				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)	p.L311L(2)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						CTGGCTGGAGTAGCTCCTGTT	0.582													C|||	1017	0.203075	0.2995	0.2839	5008	,	,		20122	0.001		0.2843	False		,,,				2504	0.1401				p.L311L	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											PIK3R5,NS,carcinoma,0,1	PIK3R5	79	1	2	Substitution - coding silent(2)	prostate(2)	c.A933G						PASS	.	C	,	1302,3104	692.1+/-405.5	204,894,1105	51.0	56.0	54.0		933,933	3.7	1.0	17	dbSNP_120	54	2695,5905	681.3+/-403.7	418,1859,2023	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	622,2753,3128	CC,CT,TT		31.3372,29.5506,30.732	,	311/881,311/881	8792171	3997,9009	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			CTGGAGTAGCTCC	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.933A>G	17.37:g.8792171T>C		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			T|0.722;C|0.278	0.278	strong		0.582	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
C11orf48	79081	hgsc.bcm.edu	37	11	62437422	62437422	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62437422G>A	ENST00000431002.2	-	1	1815	c.82C>T	c.(82-84)Ccc>Tcc	p.P28S	C11orf83_ENST00000377953.3_5'Flank|C11orf48_ENST00000354588.3_Missense_Mutation_p.P28S|C11orf83_ENST00000531323.1_5'Flank|C11orf48_ENST00000532208.1_Missense_Mutation_p.P28S			Q9BQE6	CK048_HUMAN	chromosome 11 open reading frame 48	28										endometrium(1)|lung(5)|urinary_tract(1)	7						GGCAGCCTGGGACTTTCTGGA	0.542																																					p.P28S		Atlas-SNP	.											.	C11orf48	18	.	0			c.C82T						PASS	.						101.0	94.0	96.0					11																	62437422		2202	4299	6501	SO:0001583	missense	79081	exon2			GCCTGGGACTTTC	BC001434	CCDS8028.1	11q12.3	2014-02-12			ENSG00000162194	ENSG00000162194			28351	protein-coding gene	gene with protein product						12477932	Standard	NM_024099		Approved	MGC2477	uc001nuf.3	Q9BQE6	OTTHUMG00000167588	ENST00000431002.2:c.82C>T	11.37:g.62437422G>A	ENSP00000416856:p.Pro28Ser	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	197	94	0.477157	NM_024099	Q96NA4	Missense_Mutation	SNP	ENST00000431002.2	37		.	.	.	.	.	.	.	.	.	.	G	13.80	2.346432	0.41599	.	.	ENSG00000162194	ENST00000354588;ENST00000431002;ENST00000532208;ENST00000377954;ENST00000526490	.	.	.	4.49	2.59	0.31030	.	0.201361	0.24988	N	0.034002	T	0.29288	0.0729	N	0.19112	0.55	0.32145	N	0.585027	P;B	0.46912	0.886;0.301	P;B	0.46275	0.51;0.184	T	0.37753	-0.9692	9	0.87932	D	0	-0.7818	5.6644	0.17687	0.1061:0.2021:0.6918:0.0	.	28;28	B4DYP8;Q9BQE6-2	.;.	S	28;28;28;53;28	.	ENSP00000346600:P28S	P	-	1	0	C11orf48	62193998	0.087000	0.21565	0.765000	0.31456	0.811000	0.45836	1.056000	0.30480	1.216000	0.43427	0.563000	0.77884	CCC	.	.	none		0.542	C11orf48-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000395233.1	NM_024099	
RSPH1	89765	hgsc.bcm.edu	37	21	43905887	43905887	+	Silent	SNP	C	C	T	rs2839536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43905887C>T	ENST00000291536.3	-	5	560	c.393G>A	c.(391-393)gcG>gcA	p.A131A	RSPH1_ENST00000398352.3_Silent_p.A93A	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	131					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)				large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						TGCCCGTCTCCGCGTATAAAT	0.517													C|||	1399	0.279353	0.0817	0.6182	5008	,	,		22217	0.1994		0.3728	False		,,,				2504	0.2924				p.A131A	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											.	RSPH1	36	.	0			c.G393A						PASS	.	C		626,3780	269.5+/-269.1	49,528,1626	162.0	139.0	147.0		393	-9.7	0.6	21	dbSNP_100	147	3379,5221	501.5+/-375.5	680,2019,1601	no	coding-synonymous	RSPH1	NM_080860.2		729,2547,3227	TT,TC,CC		39.2907,14.2079,30.7935		131/310	43905887	4005,9001	2203	4300	6503	SO:0001819	synonymous_variant	89765	exon5			CGTCTCCGCGTAT	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"""meichroacidin"""	609314	"""testis specific A2 homolog (mouse)"""	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.393G>A	21.37:g.43905887C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	120	118	0.983333	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Silent	SNP	ENST00000291536.3	37	CCDS13688.1																																																																																			C|0.704;T|0.296	0.296	strong		0.517	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		
C12orf54	121273	hgsc.bcm.edu	37	12	48888689	48888689	+	Silent	SNP	C	C	G	rs9268	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48888689C>G	ENST00000548364.1	+	7	408	c.351C>G	c.(349-351)ctC>ctG	p.L117L	RP11-722P11.4_ENST00000551847.1_RNA|C12orf54_ENST00000314014.2_Silent_p.L117L			Q6X4T0	CL054_HUMAN	chromosome 12 open reading frame 54	117										endometrium(1)|large_intestine(4)	5						AGACACAGCTCTTCAGTCAAT	0.512													C|||	1587	0.316893	0.1248	0.3689	5008	,	,		22147	0.1766		0.6421	False		,,,				2504	0.3497				p.L117L		Atlas-SNP	.											.	C12orf54	11	.	0			c.C351G						PASS	.			963,3443	363.1+/-316.4	124,715,1364	178.0	156.0	164.0		351	3.5	0.0	12	dbSNP_52	164	5654,2946	669.1+/-402.6	1846,1962,492	no	coding-synonymous	C12orf54	NM_152319.3		1970,2677,1856	GG,GC,CC		34.2558,21.8566,49.1235		117/128	48888689	6617,6389	2203	4300	6503	SO:0001819	synonymous_variant	121273	exon8			ACAGCTCTTCAGT	BC031670	CCDS8764.1	12q13.11	2011-01-31			ENSG00000177627	ENSG00000177627			28553	protein-coding gene	gene with protein product						12477932	Standard	NM_152319		Approved	MGC35033	uc001rrr.3	Q6X4T0	OTTHUMG00000170019	ENST00000548364.1:c.351C>G	12.37:g.48888689C>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_152319	Q6X4S9|Q8N5S2	Silent	SNP	ENST00000548364.1	37	CCDS8764.1																																																																																			C|0.533;G|0.467	0.467	strong		0.512	C12orf54-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406875.1	NM_152319	
LRRN1	57633	hgsc.bcm.edu	37	3	3887093	3887093	+	Silent	SNP	A	A	G	rs9844909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:3887093A>G	ENST00000319331.3	+	2	1529	c.768A>G	c.(766-768)caA>caG	p.Q256Q	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	256						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		AAGTCCCTCAACTTGCCCTGC	0.393													A|||	1262	0.251997	0.1422	0.2032	5008	,	,		17992	0.3224		0.2525	False		,,,				2504	0.362				p.Q256Q		Atlas-SNP	.											.	LRRN1	82	.	0			c.A768G						PASS	.	A		602,3802	237.4+/-249.2	42,518,1642	77.0	85.0	82.0		768	-1.2	1.0	3	dbSNP_119	82	2011,6589	346.7+/-326.3	237,1537,2526	no	coding-synonymous	LRRN1	NM_020873.5		279,2055,4168	GG,GA,AA		23.3837,13.6694,20.0938		256/717	3887093	2613,10391	2202	4300	6502	SO:0001819	synonymous_variant	57633	exon2			CCCTCAACTTGCC	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.768A>G	3.37:g.3887093A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			A|0.775;G|0.225	0.225	strong		0.393	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
CDH4	1002	hgsc.bcm.edu	37	20	60509209	60509209	+	Silent	SNP	C	C	T	rs3753045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60509209C>T	ENST00000360469.5	+	15	2563	c.2475C>T	c.(2473-2475)ggC>ggT	p.G825G	CDH4_ENST00000543233.1_Silent_p.G751G	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	825					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GGCCGGTGGGCGCTGAGCCCC	0.687													C|||	808	0.161342	0.0287	0.1988	5008	,	,		14233	0.1498		0.2535	False		,,,				2504	0.2311				p.G825G		Atlas-SNP	.											CDH4,colon,carcinoma,0,1	CDH4	172	1	0			c.C2475T						PASS	.	C		285,4119		8,269,1925	27.0	31.0	29.0		2475	-8.7	0.7	20	dbSNP_107	29	2147,6445		274,1599,2423	no	coding-synonymous	CDH4	NM_001794.2		282,1868,4348	TT,TC,CC		24.9884,6.4714,18.7135		825/917	60509209	2432,10564	2202	4296	6498	SO:0001819	synonymous_variant	1002	exon15			GGTGGGCGCTGAG	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.2475C>T	20.37:g.60509209C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	65	43	0.661538	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	37	CCDS13488.1																																																																																			C|0.826;T|0.174	0.174	strong		0.687	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
PRDM10	56980	hgsc.bcm.edu	37	11	129801124	129801124	+	Silent	SNP	T	T	C	rs2277032	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:129801124T>C	ENST00000360871.3	-	11	1548	c.1317A>G	c.(1315-1317)caA>caG	p.Q439Q	PRDM10_ENST00000304538.6_Silent_p.Q353Q|PRDM10_ENST00000358825.5_Silent_p.Q439Q|PRDM10_ENST00000526082.1_Silent_p.Q353Q|PRDM10_ENST00000423662.2_Silent_p.Q353Q|PRDM10_ENST00000528746.1_Silent_p.Q413Q	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	439					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		CCTCATCAAATTGCTCCTTTG	0.493													T|||	496	0.0990415	0.0976	0.1369	5008	,	,		13397	0.1101		0.0557	False		,,,				2504	0.1074				p.Q439Q		Atlas-SNP	.											.	PRDM10	120	.	0			c.A1317G						PASS	.	T	,,,	313,4089	168.7+/-199.5	7,299,1895	112.0	115.0	114.0		1317,1317,1059,1059	4.2	1.0	11	dbSNP_100	114	540,8054	149.1+/-204.2	19,502,3776	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	26,801,5671	CC,CT,TT		6.2835,7.1104,6.5636	,,,	439/1161,439/1157,353/1062,353/1024	129801124	853,12143	2201	4297	6498	SO:0001819	synonymous_variant	56980	exon11			ATCAAATTGCTCC	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.1317A>G	11.37:g.129801124T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	182	81	0.445055	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			T|0.928;C|0.072	0.072	strong		0.493	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
AHSA1	10598	hgsc.bcm.edu	37	14	77935520	77935520	+	Silent	SNP	G	G	A	rs7250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:77935520G>A	ENST00000216479.3	+	9	1105	c.945G>A	c.(943-945)acG>acA	p.T315T	AHSA1_ENST00000555457.1_3'UTR|SNORA46_ENST00000391069.1_RNA	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	315					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AAGAGCGGACGCGACAGGGCT	0.572													G|||	2401	0.479433	0.0946	0.513	5008	,	,		19856	0.9187		0.4871	False		,,,				2504	0.5153				p.T315T		Atlas-SNP	.											.	AHSA1	24	.	0			c.G945A						PASS	.	G		727,3679	299.3+/-285.7	62,603,1538	170.0	158.0	162.0		945	-4.8	0.9	14	dbSNP_52	162	4490,4110	592.7+/-393.0	1192,2106,1002	no	coding-synonymous	AHSA1	NM_012111.2		1254,2709,2540	AA,AG,GG		47.7907,16.5002,40.1123		315/339	77935520	5217,7789	2203	4300	6503	SO:0001819	synonymous_variant	10598	exon9			GCGGACGCGACAG	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"""chromosome 14 open reading frame 3"""	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.945G>A	14.37:g.77935520G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	194	95	0.489691	NM_012111	B2R9L2|B4DUR9|Q96IL6|Q9P060	Silent	SNP	ENST00000216479.3	37	CCDS9863.1	1121	0.5132783882783882	56	0.11382113821138211	164	0.4530386740331492	528	0.9230769230769231	373	0.4920844327176781	G	6.940	0.543292	0.13250	0.165002	0.522093	ENSG00000100591	ENST00000555729	.	.	.	5.46	-4.83	0.03161	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999824522	.	.	.	.	.	.	T	0.18053	-1.0349	3	.	.	.	-12.277	11.2432	0.48980	0.634:0.0907:0.2753:0.0	rs7250;rs3168946;rs17751382;rs7250	.	.	.	T	110	.	.	A	+	1	0	AHSA1	77005273	0.010000	0.17322	0.911000	0.35937	0.803000	0.45373	-0.993000	0.03720	-0.791000	0.04486	-0.218000	0.12543	GCG	G|0.558;A|0.442	0.442	strong		0.572	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111	
PUS3	83480	hgsc.bcm.edu	37	11	125766044	125766044	+	Missense_Mutation	SNP	C	C	A	rs549990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:125766044C>A	ENST00000530811.1	-	1	181	c.136G>T	c.(136-138)Gca>Tca	p.A46S	PUS3_ENST00000227474.3_Missense_Mutation_p.A46S|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron|HYLS1_ENST00000425380.2_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	46			A -> S (in dbSNP:rs549990). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.A46S(1)		NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		CCAGCTCCTGCTGAATTTTCT	0.448													A|||	3192	0.63738	0.6074	0.6023	5008	,	,		20694	0.6964		0.673	False		,,,				2504	0.6053				p.A46S		Atlas-SNP	.											PUS3,NS,carcinoma,0,1	PUS3	33	1	1	Substitution - Missense(1)	prostate(1)	c.G136T						PASS	.	A	,SER/ALA,	2755,1647	504.7+/-365.9	846,1063,292	225.0	224.0	224.0		,136,	3.9	0.6	11	dbSNP_83	224	5857,2741	436.6+/-358.4	2003,1851,445	yes	intron,missense,intron	PUS3,HYLS1	NM_001134793.1,NM_031307.3,NM_145014.2	,99,	2849,2914,737	AA,AC,CC		31.8795,37.4148,33.7538	,benign,	,46/482,	125766044	8612,4388	2201	4299	6500	SO:0001583	missense	83480	exon2			CTCCTGCTGAATT	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.136G>T	11.37:g.125766044C>A	ENSP00000432386:p.Ala46Ser	Somatic	344	1	0.00290698		WXS	Illumina HiSeq	Phase_I	380	377	0.992105	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Missense_Mutation	SNP	ENST00000530811.1	37	CCDS8466.1	1434	0.6565934065934066	301	0.6117886178861789	225	0.6215469613259669	402	0.7027972027972028	506	0.6675461741424802	A	0.006	-2.066169	0.00382	0.625852	0.681205	ENSG00000110060	ENST00000227474;ENST00000530811;ENST00000534158;ENST00000529801	T;T;T;T	0.55234	1.49;1.49;0.53;1.55	5.11	3.91	0.45181	.	0.627475	0.15533	N	0.257382	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43540	-0.9385	9	0.07175	T	0.84	-0.1633	2.1408	0.03775	0.5881:0.1507:0.116:0.1452	rs549990;rs1285175;rs1285316;rs1285709;rs17856119;rs52794946;rs61539703;rs549990	46	Q9BZE2	PUS3_HUMAN	S	46	ENSP00000227474:A46S;ENSP00000432386:A46S;ENSP00000432272:A46S;ENSP00000437077:A46S	ENSP00000227474:A46S	A	-	1	0	PUS3	125271254	0.000000	0.05858	0.629000	0.29254	0.303000	0.27691	0.706000	0.25690	1.082000	0.41137	-0.310000	0.09108	GCA	C|0.337;A|0.663	0.663	strong		0.448	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307	
ZNF79	7633	hgsc.bcm.edu	37	9	130206762	130206762	+	Silent	SNP	C	C	T	rs2248025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:130206762C>T	ENST00000342483.5	+	5	1189	c.783C>T	c.(781-783)aaC>aaT	p.N261N	ZNF79_ENST00000543471.1_Silent_p.N237N	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N261N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						TCAGCCAGAACGCCAACCTCA	0.537													C|||	1663	0.332069	0.3215	0.2853	5008	,	,		21490	0.1647		0.5318	False		,,,				2504	0.3466				p.N261N		Atlas-SNP	.											ZNF79,NS,carcinoma,0,1	ZNF79	47	1	1	Substitution - coding silent(1)	stomach(1)	c.C783T						PASS	.	C		1541,2865	487.8+/-361.0	259,1023,921	116.0	103.0	107.0		783	-5.3	0.9	9	dbSNP_100	107	4161,4439	567.3+/-388.8	1037,2087,1176	no	coding-synonymous	ZNF79	NM_007135.2		1296,3110,2097	TT,TC,CC		48.3837,34.975,43.8413		261/499	130206762	5702,7304	2203	4300	6503	SO:0001819	synonymous_variant	7633	exon5			CCAGAACGCCAAC	X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"""Zinc fingers, C2H2-type"""	13153	protein-coding gene	gene with protein product		194552	"""zinc finger protein 79 (pT7)"""			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.783C>T	9.37:g.130206762C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_007135	Q5VVW1|Q96NV1	Silent	SNP	ENST00000342483.5	37	CCDS6871.1																																																																																			C|0.612;T|0.388	0.388	strong		0.537	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135	
CHD2	1106	hgsc.bcm.edu	37	15	93567864	93567864	+	Silent	SNP	A	A	C	rs12906163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:93567864A>C	ENST00000394196.4	+	39	6484	c.5416A>C	c.(5416-5418)Agg>Cgg	p.R1806R		NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1806					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			CCTGGATCATAGGTCTCCTTT	0.463													A|||	934	0.186502	0.0855	0.2248	5008	,	,		21175	0.0575		0.3698	False		,,,				2504	0.2403				p.R1806R		Atlas-SNP	.											.	CHD2	280	.	0			c.A5416C						PASS	.	A		468,3276		26,416,1430	81.0	78.0	79.0		5416	3.3	0.7	15	dbSNP_121	79	3300,4930		648,2004,1463	no	coding-synonymous	CHD2	NM_001271.3		674,2420,2893	CC,CA,AA		40.0972,12.5,31.4682		1806/1829	93567864	3768,8206	1872	4115	5987	SO:0001819	synonymous_variant	1106	exon39			GATCATAGGTCTC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.5416A>C	15.37:g.93567864A>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	199	94	0.472362	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	37	CCDS10374.2																																																																																			A|0.767;C|0.233	0.233	strong		0.463	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33568789	33568789	+	Silent	SNP	T	T	G	rs10971566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:33568789T>G	ENST00000290943.6	+	15	2985	c.2889T>G	c.(2887-2889)ctT>ctG	p.L963L	ANKRD18B_ENST00000426460.2_3'UTR	NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	963										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						TTGAAAATCTTAATAGTATAG	0.393													.|||	1000	0.199681	0.0454	0.2695	5008	,	,		16912	0.2143		0.3161	False		,,,				2504	0.2239				p.L962L		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.T2886G						PASS	.																																			SO:0001819	synonymous_variant	441459	exon15			AAATCTTAATAGT			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2889T>G	9.37:g.33568789T>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	134	76	0.567164	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				T|0.756;G|0.244	0.244	strong		0.393	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
RBM47	54502	hgsc.bcm.edu	37	4	40428010	40428010	+	Missense_Mutation	SNP	T	T	C	rs278981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:40428010T>C	ENST00000381793.2	-	6	2089	c.1693A>G	c.(1693-1695)Atg>Gtg	p.M565V	RBM47_ENST00000381795.6_Missense_Mutation_p.M496V|RBM47_ENST00000295971.7_Missense_Mutation_p.M565V|RBM47_ENST00000319592.4_Missense_Mutation_p.M496V|RBM47_ENST00000514014.1_Missense_Mutation_p.M527V|RP11-588L15.2_ENST00000514187.1_RNA			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	565	Ala-rich.		M -> V (in dbSNP:rs278981). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						CCTCCATACATGGCGGCCGCG	0.607													C|||	3467	0.692292	0.6725	0.7767	5008	,	,		16051	0.5784		0.7843	False		,,,				2504	0.682				p.M565V		Atlas-SNP	.											.	RBM47	146	.	0			c.A1693G						PASS	.	C	VAL/MET,VAL/MET	3095,1311	440.4+/-346.0	1080,935,188	87.0	75.0	79.0		1693,1486	3.8	0.1	4	dbSNP_79	79	6573,2027	351.6+/-328.3	2504,1565,231	yes	missense,missense	RBM47	NM_001098634.1,NM_019027.3	21,21	3584,2500,419	CC,CT,TT		23.5698,29.7549,25.6651	benign,benign	565/594,496/525	40428010	9668,3338	2203	4300	6503	SO:0001583	missense	54502	exon7			CATACATGGCGGC	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"""RNA binding motif (RRM) containing"""	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.1693A>G	4.37:g.40428010T>C	ENSP00000371212:p.Met565Val	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	124	122	0.983871	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	37	CCDS43223.1	1409	0.6451465201465202	300	0.6097560975609756	263	0.7265193370165746	304	0.5314685314685315	542	0.7150395778364116	C	0.046	-1.264835	0.01433	0.702451	0.764302	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014	T;T;T;T;T	0.12569	2.7;2.68;2.7;2.68;2.67	5.53	3.82	0.43975	.	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46470	-0.9189	9	0.24483	T	0.36	-18.5301	10.6827	0.45823	0.0:0.7908:0.0:0.2092	rs278981;rs17606761;rs58465571;rs278981	496;565	A0AV96-2;A0AV96	.;RBM47_HUMAN	V	496;565;496;565;527	ENSP00000320108:M496V;ENSP00000371212:M565V;ENSP00000371214:M496V;ENSP00000295971:M565V;ENSP00000423243:M527V	ENSP00000295971:M565V	M	-	1	0	RBM47	40122767	0.945000	0.32115	0.115000	0.21578	0.139000	0.21198	2.476000	0.45171	0.322000	0.23283	-0.642000	0.03964	ATG	T|0.287;G|0.002	.	strong		0.607	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183286	11183286	+	Missense_Mutation	SNP	G	G	C	rs10845294	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:11183286G>C	ENST00000390675.2	-	1	720	c.649C>G	c.(649-651)Caa>Gaa	p.Q217E	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	217			Q -> E (in dbSNP:rs10845294).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						CTGGGATCTTGAGATCCTTTA	0.403													.|||	614	0.122604	0.1051	0.2161	5008	,	,		20987	0.0		0.2734	False		,,,				2504	0.0511				p.Q217E		Atlas-SNP	.											.	TAS2R31	24	.	0			c.C649G						PASS	.	G	GLU/GLN	590,3816		49,492,1662	152.0	159.0	157.0		649	-1.3	0.0	12	dbSNP_120	157	2206,6390		295,1616,2387	no	missense	TAS2R31	NM_176885.2	29	344,2108,4049	CC,CG,GG		25.6631,13.3908,21.5044	possibly-damaging	217/310	11183286	2796,10206	2203	4298	6501	SO:0001583	missense	259290	exon1			GATCTTGAGATCC	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.649C>G	12.37:g.11183286G>C	ENSP00000375093:p.Gln217Glu	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	233	98	0.420601	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	359	0.16437728937728938	70	0.14227642276422764	76	0.20994475138121546	0	0.0	213	0.28100263852242746	.	10.69	1.420493	0.25639	0.133908	0.256631	ENSG00000256436	ENST00000390675	T	0.00724	5.78	2.62	-1.26	0.09376	.	.	.	.	.	T	0.00012	0.0000	M	0.79805	2.47	0.80722	P	0.0	P	0.41041	0.736	B	0.44278	0.445	T	0.43442	-0.9391	8	0.72032	D	0.01	.	3.0067	0.06031	0.1566:0.0:0.3795:0.4638	rs10845294	217	P59538	T2R31_HUMAN	E	217	ENSP00000375093:Q217E	ENSP00000375093:Q217E	Q	-	1	0	TAS2R31	11074553	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	0.317000	0.19487	-0.006000	0.14370	0.194000	0.17425	CAA	G|0.834;C|0.166	0.166	strong		0.403	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
KANK1	23189	hgsc.bcm.edu	37	9	712137	712137	+	Silent	SNP	G	G	C	rs912175	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:712137G>C	ENST00000382303.1	+	7	2023	c.1371G>C	c.(1369-1371)ctG>ctC	p.L457L	KANK1_ENST00000382293.3_Silent_p.L299L|KANK1_ENST00000382297.2_Silent_p.L457L|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	457	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.L299L(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		AAATTGAGCTGCAACAGCAGA	0.463													G|||	918	0.183307	0.1823	0.2968	5008	,	,		21835	0.1925		0.2107	False		,,,				2504	0.0665				p.L457L		Atlas-SNP	.											KANK1,NS,carcinoma,0,1	KANK1	231	1	1	Substitution - coding silent(1)	stomach(1)	c.G1371C						PASS	.	G	,	793,3613	318.2+/-295.5	83,627,1493	95.0	92.0	93.0		1371,897	2.6	1.0	9	dbSNP_86	93	1891,6709	334.5+/-321.0	227,1437,2636	no	coding-synonymous,coding-synonymous	KANK1	NM_015158.2,NM_153186.3	,	310,2064,4129	CC,CG,GG		21.9884,17.9982,20.6366	,	457/1353,299/1195	712137	2684,10322	2203	4300	6503	SO:0001819	synonymous_variant	23189	exon7			TGAGCTGCAACAG	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1371G>C	9.37:g.712137G>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			G|0.771;C|0.229	0.229	strong		0.463	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
NDOR1	27158	hgsc.bcm.edu	37	9	140110555	140110555	+	Missense_Mutation	SNP	G	G	A	rs62587579	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140110555G>A	ENST00000344894.5	+	13	1647	c.1564G>A	c.(1564-1566)Gta>Ata	p.V522I	NDOR1_ENST00000427047.2_Missense_Mutation_p.V488I|NDOR1_ENST00000371521.4_Missense_Mutation_p.V531I|NDOR1_ENST00000458322.2_Missense_Mutation_p.V515I	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GGAGCAGAAAGTATATGTGCA	0.637													G|||	87	0.0173722	0.0023	0.0447	5008	,	,		17550	0.001		0.0398	False		,,,				2504	0.0123				p.V531I		Atlas-SNP	.											.	NDOR1	71	.	0			c.G1591A	GRCh37	CM056012	NDOR1	M	rs62587579	PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	45,4361	46.0+/-80.4	0,45,2158	50.0	57.0	54.0		1591,1462,1543,1564	2.0	0.1	9	dbSNP_129	54	468,8132	137.6+/-194.5	14,440,3846	yes	missense,missense,missense,missense	NDOR1	NM_001144026.1,NM_001144027.1,NM_001144028.1,NM_014434.2	29,29,29,29	14,485,6004	AA,AG,GG		5.4419,1.0213,3.9443	benign,benign,benign,benign	531/607,488/522,515/591,522/598	140110555	513,12493	2203	4300	6503	SO:0001583	missense	27158	exon13			CAGAAAGTATATG	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"""NADPH dependent FMN and FAD containing oxidoreductase"""	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.1564G>A	9.37:g.140110555G>A	ENSP00000343344:p.Val522Ile	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_001144026		Missense_Mutation	SNP	ENST00000344894.5	37	CCDS7036.1	51	0.023351648351648352	2	0.0040650406504065045	18	0.049723756906077346	1	0.0017482517482517483	30	0.0395778364116095	G	8.357	0.832158	0.16820	0.010213	0.054419	ENSG00000188566	ENST00000458322;ENST00000427047;ENST00000371521;ENST00000344894	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	4.06	2.0	0.26442	Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.152913	0.43747	N	0.000522	T	0.38665	0.1049	N	0.20574	0.59	0.54753	D	0.999985	B;B;B;B	0.18166	0.026;0.003;0.021;0.011	B;B;B;B	0.30495	0.116;0.042;0.071;0.075	T	0.53265	-0.8463	10	0.24483	T	0.36	-6.0513	7.5162	0.27602	0.2428:0.0:0.7572:0.0	rs62587579	515;488;531;522	D3YTG6;D3YTH9;Q9UHB4-2;Q9UHB4	.;.;.;NDOR1_HUMAN	I	515;488;531;522	ENSP00000389905:V515I;ENSP00000394309:V488I;ENSP00000360576:V531I;ENSP00000343344:V522I	ENSP00000343344:V522I	V	+	1	0	NDOR1	139230376	0.986000	0.35501	0.146000	0.22360	0.589000	0.36550	1.232000	0.32636	0.927000	0.37143	0.561000	0.74099	GTA	G|0.962;A|0.038	0.038	strong		0.637	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434	
HAUS3	79441	hgsc.bcm.edu	37	4	2233709	2233709	+	Missense_Mutation	SNP	A	A	G	rs11937432	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2233709A>G	ENST00000243706.4	-	5	1986	c.1757T>C	c.(1756-1758)aTt>aCt	p.I586T	POLN_ENST00000382865.1_5'Flank|POLN_ENST00000515357.1_Intron|POLN_ENST00000511885.2_Intron|HAUS3_ENST00000443786.2_Missense_Mutation_p.I586T|HAUS3_ENST00000506763.1_Intron	NM_024511.5	NP_078787.2	Q68CZ6	HAUS3_HUMAN	HAUS augmin-like complex, subunit 3	586			I -> T (in dbSNP:rs11937432).		centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				breast(3)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						ATTCTCCACAATATCTTTCAG	0.259													A|||	374	0.0746805	0.1536	0.0648	5008	,	,		13067	0.0317		0.0527	False		,,,				2504	0.0419				p.I586T		Atlas-SNP	.											.	HAUS3	54	.	0			c.T1757C						PASS	.	A	THR/ILE	620,3734		44,532,1601	27.0	28.0	28.0		1757	4.9	1.0	4	dbSNP_120	28	435,8045		8,419,3813	yes	missense	HAUS3	NM_024511.5	89	52,951,5414	GG,GA,AA		5.1297,14.2398,8.2204	benign	586/604	2233709	1055,11779	2177	4240	6417	SO:0001583	missense	79441	exon5			TCCACAATATCTT	AF040964	CCDS33941.1	4p16.3	2013-10-11	2009-04-20	2009-04-20	ENSG00000214367	ENSG00000214367		"""HAUS augmin-like complex subunits"""	28719	protein-coding gene	gene with protein product		613430	"""chromosome 4 open reading frame 15"""	C4orf15		19427217, 19812674	Standard	NM_024511		Approved	MGC4701, IT1, dgt3	uc003ges.1	Q68CZ6		ENST00000243706.4:c.1757T>C	4.37:g.2233709A>G	ENSP00000243706:p.Ile586Thr	Somatic	320	1	0.003125		WXS	Illumina HiSeq	Phase_I	317	147	0.463722	NM_024511	B4DF64|O43606|Q8TAZ5|Q9BTJ9	Missense_Mutation	SNP	ENST00000243706.4	37	CCDS33941.1	157	0.07188644688644688	76	0.15447154471544716	26	0.0718232044198895	16	0.027972027972027972	39	0.051451187335092345	A	13.91	2.377161	0.42105	0.142398	0.051297	ENSG00000214367	ENST00000243706;ENST00000443786	T;T	0.41758	0.99;0.99	6.03	4.86	0.63082	.	0.547632	0.17996	U	0.155041	T	0.00241	0.0007	L	0.50333	1.59	0.42460	P	0.0072149999999999714	B	0.16396	0.017	B	0.18871	0.023	T	0.04178	-1.0971	9	0.49607	T	0.09	-34.7787	11.4395	0.50088	0.9301:0.0:0.0699:0.0	rs11937432;rs52824107;rs59133563;rs11937432	586	Q68CZ6	HAUS3_HUMAN	T	586	ENSP00000243706:I586T;ENSP00000392903:I586T	ENSP00000243706:I586T	I	-	2	0	HAUS3	2203507	0.557000	0.26546	0.981000	0.43875	0.985000	0.73830	3.694000	0.54742	1.111000	0.41721	0.455000	0.32223	ATT	A|0.928;G|0.072	0.072	strong		0.259	HAUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357446.1	NM_024511	
NACAD	23148	hgsc.bcm.edu	37	7	45122723	45122723	+	Missense_Mutation	SNP	G	G	A	rs61740895	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45122723G>A	ENST00000490531.2	-	2	3075	c.3056C>T	c.(3055-3057)gCg>gTg	p.A1019V		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1019					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						AGTGGAATCCGCATCTTCCTG	0.622													G|||	1204	0.240415	0.0272	0.3833	5008	,	,		21118	0.2877		0.332	False		,,,				2504	0.2843				p.A1019V		Atlas-SNP	.											.	NACAD	44	.	0			c.C3056T						PASS	.	G	VAL/ALA	114,1270		8,98,586	19.0	18.0	19.0		3056	2.0	0.0	7	dbSNP_129	19	1117,2065		187,743,661	yes	missense	NACAD	NM_001146334.1	64	195,841,1247	AA,AG,GG		35.1037,8.237,26.9601	benign	1019/1563	45122723	1231,3335	692	1591	2283	SO:0001583	missense	23148	exon2			GAATCCGCATCTT	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.3056C>T	7.37:g.45122723G>A	ENSP00000420477:p.Ala1019Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	551	0.2522893772893773	13	0.026422764227642278	134	0.3701657458563536	150	0.26223776223776224	254	0.33509234828496043	G	7.346	0.621835	0.14193	0.08237	0.351037	ENSG00000136274	ENST00000490531	T	0.11385	2.78	3.79	1.97	0.26223	.	2.516370	0.03046	U	0.153903	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.15473	0.013	B	0.06405	0.002	T	0.41998	-0.9477	9	0.02654	T	1	0.6018	3.6281	0.08121	0.2167:0.0:0.5896:0.1937	.	1019	O15069	NACAD_HUMAN	V	1019	ENSP00000420477:A1019V	ENSP00000420477:A1019V	A	-	2	0	NACAD	45089248	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.103000	0.10940	0.395000	0.25257	-0.480000	0.04831	GCG	G|0.739;A|0.261	0.261	strong		0.622	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
CEP85L	387119	hgsc.bcm.edu	37	6	118887303	118887303	+	Missense_Mutation	SNP	T	T	C	rs3734381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:118887303T>C	ENST00000368491.3	-	3	1030	c.409A>G	c.(409-411)Agt>Ggt	p.S137G	CEP85L_ENST00000472713.1_5'UTR|CEP85L_ENST00000368488.5_Missense_Mutation_p.S140G|CEP85L_ENST00000360290.3_Missense_Mutation_p.S35G|CEP85L_ENST00000392500.3_Missense_Mutation_p.S140G|CEP85L_ENST00000419517.2_Missense_Mutation_p.S137G	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	137			S -> G (in dbSNP:rs3734381). {ECO:0000269|PubMed:15489334}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.S137G(1)									TCCCCCCTACTGTGGTTTCCC	0.493													T|||	2188	0.436901	0.5598	0.2939	5008	,	,		18807	0.248		0.5368	False		,,,				2504	0.4642				p.S140G		Atlas-SNP	.											C6orf204,NS,carcinoma,0,1	CEP85L	26	1	1	Substitution - Missense(1)	stomach(1)	c.A418G						PASS	.	T	GLY/SER,GLY/SER,GLY/SER	2432,1974	619.8+/-393.4	677,1078,448	118.0	107.0	111.0		409,418,409	-2.7	0.0	6	dbSNP_107	111	4529,4071	594.3+/-393.3	1189,2151,960	yes	missense,missense,missense	C6orf204	NM_001042475.2,NM_001178035.1,NM_206921.2	56,56,56	1866,3229,1408	CC,CT,TT		47.3372,44.8025,46.4785	benign,benign,benign	137/806,140/809,137/497	118887303	6961,6045	2203	4300	6503	SO:0001583	missense	387119	exon4			CCCTACTGTGGTT	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.409A>G	6.37:g.118887303T>C	ENSP00000357477:p.Ser137Gly	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	228	135	0.592105	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	936	0.42857142857142855	271	0.5508130081300813	121	0.3342541436464088	138	0.24125874125874125	406	0.5356200527704486	T	2.471	-0.321800	0.05386	0.551975	0.526628	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604;ENST00000392500;ENST00000360290;ENST00000419517	T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84	5.96	-2.65	0.06095	.	0.665589	0.15668	N	0.250545	T	0.02610	0.0079	N	0.24115	0.695	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.0;0.0	B;B;B;B;B	0.06405	0.0;0.002;0.001;0.0;0.002	T	0.39981	-0.9587	9	0.08837	T	0.75	3.0069	1.1076	0.01698	0.2062:0.2369:0.1067:0.4502	rs3734381;rs52837138;rs58829518;rs3734381	35;140;137;140;137	B4DYT2;Q5SZL2-2;G3V0H3;F8W6J2;Q5SZL2	.;.;.;.;CF204_HUMAN	G	137;140;140;140;35;137	ENSP00000357477:S137G;ENSP00000357474:S140G;ENSP00000392131:S140G;ENSP00000376288:S140G;ENSP00000353434:S35G;ENSP00000393317:S137G	ENSP00000353434:S35G	S	-	1	0	C6orf204	118993996	0.000000	0.05858	0.000000	0.03702	0.328000	0.28507	0.109000	0.15417	-0.699000	0.05077	-0.333000	0.08304	AGT	T|0.510;C|0.490	0.490	strong		0.493	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
OBP2A	29991	hgsc.bcm.edu	37	9	138440554	138440554	+	Splice_Site	SNP	G	G	C	rs55695858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:138440554G>C	ENST00000539850.1	+	5	415	c.389G>C	c.(388-390)gGt>gCt	p.G130A	OBP2A_ENST00000340780.3_Missense_Mutation_p.V152L|OBP2A_ENST00000371776.1_Splice_Site_p.G130A|OBP2A_ENST00000342114.4_Missense_Mutation_p.G107A			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	130			G -> A (in dbSNP:rs55695858).		response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		TCACCTGCAGGTAGGAATCCT	0.582													.|||	869	0.173522	0.1286	0.1369	5008	,	,		15862	0.1567		0.2525	False		,,,				2504	0.1963				p.G130A		Atlas-SNP	.											.	OBP2A	21	.	0			c.G389C						PASS	.	G	ALA/GLY	661,3745	280.5+/-275.4	58,545,1600	76.0	69.0	71.0		389	2.5	0.1	9	dbSNP_129	71	2275,6325	381.9+/-340.2	305,1665,2330	yes	missense-near-splice	OBP2A	NM_014582.2	60	363,2210,3930	CC,CG,GG		26.4535,15.0023,22.5742	probably-damaging	130/171	138440554	2936,10070	2203	4300	6503	SO:0001630	splice_region_variant	29991	exon5			CTGCAGGTAGGAA	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.389-1G>C	9.37:g.138440554G>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	162	74	0.45679	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	410|410	0.18772893772893773|0.18772893772893773	69|69	0.1402439024390244|0.1402439024390244	63|63	0.17403314917127072|0.17403314917127072	84|84	0.14685314685314685|0.14685314685314685	194|194	0.2559366754617414|0.2559366754617414	g|g	14.94|14.94	2.685917|2.685917	0.47991|0.47991	0.150023|0.150023	0.264535|0.264535	ENSG00000122136|ENSG00000122136	ENST00000342114;ENST00000371776;ENST00000539850|ENST00000340780	T;T;T|T	0.10382|0.28895	2.88;3.14;3.14|1.59	2.49|2.49	2.49|2.49	0.30216|0.30216	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.83483|0.83483	2.645|2.645	0.45979|0.45979	P|P	0.0012010000000000076|0.0012010000000000076	D;P|P	0.76494|0.36222	0.999;0.845|0.544	D;P|B	0.87578|0.34873	0.998;0.585|0.191	T|T	0.14671|0.14671	-1.0464|-1.0464	8|8	0.40728|0.27785	T|T	0.16|0.31	-1.3376|-1.3376	8.6552|8.6552	0.34060|0.34060	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs55695858;rs61739461|rs55695858;rs61739461	107;130|152	Q5T8A4;Q9NY56|Q5T8A5	.;OBP2A_HUMAN|.	A|L	107;130;130|152	ENSP00000340950:G107A;ENSP00000360841:G130A;ENSP00000441028:G130A|ENSP00000342097:V152L	ENSP00000340950:G107A|ENSP00000342097:V152L	G|V	+|+	2|1	0|0	OBP2A|OBP2A	137580375|137580375	0.056000|0.056000	0.20664|0.20664	0.127000|0.127000	0.21898|0.21898	0.498000|0.498000	0.33706|0.33706	1.149000|1.149000	0.31626|0.31626	1.711000|1.711000	0.51337|0.51337	0.480000|0.480000	0.44947|0.44947	GGT|GTA	G|0.790;C|0.210	0.210	strong		0.582	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	Missense_Mutation
CPEB1	64506	hgsc.bcm.edu	37	15	83215251	83215251	+	Silent	SNP	T	T	C	rs1267657	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:83215251T>C	ENST00000562019.1	-	11	1846	c.1530A>G	c.(1528-1530)ctA>ctG	p.L510L	CPEB1_ENST00000398592.2_Silent_p.L279L|CPEB1_ENST00000450751.2_Silent_p.L430L|CPEB1_ENST00000564522.1_Silent_p.L430L|CPEB1_ENST00000568128.1_Silent_p.L505L|CPEB1_ENST00000563800.1_Silent_p.L532L|CPEB1_ENST00000261723.6_Silent_p.L508L|CPEB1_ENST00000398591.2_Silent_p.L435L|CPEB1_ENST00000423133.2_Silent_p.L430L|CPEB1_ENST00000568757.1_Silent_p.L430L|RP11-152F13.10_ENST00000562833.1_Nonstop_Mutation_p.*240W|RP11-379H8.1_ENST00000568285.1_Intron			Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding protein 1	510	Necessary for stress granule assembly and correct localization in dcp1 bodies.|RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to amino acid stimulus (GO:0071230)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|mRNA processing (GO:0006397)|negative regulation of cytoplasmic translation (GO:2000766)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(1)|skin(1)	28			BRCA - Breast invasive adenocarcinoma(143;0.229)			GAGAATCTTCTAGGTAGGGGT	0.463													.|||	2211	0.441494	0.4418	0.3905	5008	,	,		20582	0.4663		0.4155	False		,,,				2504	0.4785				p.L505L		Atlas-SNP	.											.	CPEB1	114	.	0			c.A1515G						PASS	.	T	,,,	1571,2287		311,949,669	79.0	81.0	81.0		1305,1290,1290,1515	-5.5	0.9	15	dbSNP_87	81	3104,5176		573,1958,1609	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPEB1	NM_001079533.1,NM_001079534.1,NM_001079535.1,NM_030594.3	,,,	884,2907,2278	CC,CT,TT		37.4879,40.7206,38.5154	,,,	435/492,430/487,430/487,505/562	83215251	4675,7463	1929	4140	6069	SO:0001819	synonymous_variant	64506	exon11			ATCTTCTAGGTAG	AF329402	CCDS42072.1, CCDS45329.1, CCDS45330.1, CCDS42072.2, CCDS45329.2, CCDS45330.2	15q25.1	2008-02-05				ENSG00000214575			21744	protein-coding gene	gene with protein product		607342				11223249	Standard	NM_001079533		Approved	FLJ13203, CPEB	uc002biv.3	Q9BZB8		ENST00000562019.1:c.1530A>G	15.37:g.83215251T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	210	97	0.461905	NM_030594	B7Z6C6|Q86W46|Q8IV41|Q9BZB7|Q9H8V5	Silent	SNP	ENST00000562019.1	37																																																																																				T|0.579;C|0.421	0.421	strong		0.463	CPEB1-006	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000421102.1	NM_030594	
CCDC150	284992	hgsc.bcm.edu	37	2	197521496	197521496	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:197521496C>T	ENST00000389175.4	+	3	451	c.316C>T	c.(316-318)Cgt>Tgt	p.R106C	CCDC150_ENST00000272831.7_Intron|CCDC150_ENST00000472405.2_Missense_Mutation_p.R3C|CCDC150_ENST00000423093.2_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	106										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TCGAATGTGCCGTCTTGAAAG	0.383																																					p.R106C		Atlas-SNP	.											CCDC150,NS,carcinoma,-1,1	CCDC150	96	1	0			c.C316T						scavenged	.						121.0	117.0	118.0					2																	197521496		1850	4102	5952	SO:0001583	missense	284992	exon3			ATGTGCCGTCTTG		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.316C>T	2.37:g.197521496C>T	ENSP00000373827:p.Arg106Cys	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	133	2	0.0150376	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	37	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.959752	0.74016	.	.	ENSG00000144395	ENST00000389175;ENST00000536389;ENST00000472405	T;T	0.30714	1.52;1.52	5.03	4.14	0.48551	.	0.560593	0.15922	N	0.238095	T	0.36717	0.0977	L	0.48642	1.525	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.50896	0.653;0.534	T	0.13818	-1.0495	10	0.59425	D	0.04	-0.1759	11.6018	0.51008	0.0:0.9112:0.0:0.0888	.	106;106	Q8NCX0;F5H6M2	CC150_HUMAN;.	C	106;106;3	ENSP00000373827:R106C;ENSP00000441149:R3C	ENSP00000373827:R106C	R	+	1	0	CCDC150	197229741	0.939000	0.31865	0.979000	0.43373	0.960000	0.62799	2.235000	0.43044	1.334000	0.45468	0.655000	0.94253	CGT	.	.	none		0.383	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539	
FSD2	123722	hgsc.bcm.edu	37	15	83428193	83428193	+	Silent	SNP	G	G	A	rs1108135	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:83428193G>A	ENST00000334574.8	-	13	2338	c.2157C>T	c.(2155-2157)caC>caT	p.H719H	RP11-752G15.6_ENST00000558174.1_RNA|FSD2_ENST00000541889.1_Silent_p.H674H|RP11-752G15.6_ENST00000559366.1_RNA|RP11-752G15.6_ENST00000561107.1_RNA			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	719	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						GCACAAATTCGTGAAGCTGAC	0.353													g|||	913	0.182308	0.2496	0.196	5008	,	,		20305	0.2629		0.1213	False		,,,				2504	0.0613				p.H719H		Atlas-SNP	.											.	FSD2	45	.	0			c.C2157T						PASS	.			711,2981		74,563,1209	71.0	69.0	70.0		2157	0.5	0.0	15	dbSNP_86	70	855,7345		40,775,3285	no	coding-synonymous	FSD2	NM_001007122.2		114,1338,4494	AA,AG,GG		10.4268,19.2579,13.1685		719/750	83428193	1566,10326	1846	4100	5946	SO:0001819	synonymous_variant	123722	exon13			AAATTCGTGAAGC	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"""Fibronectin type III domain containing"""	18024	protein-coding gene	gene with protein product			"""SPRY domain containing 1"""	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.2157C>T	15.37:g.83428193G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_001007122	B3KVG1|B7ZM02	Silent	SNP	ENST00000334574.8	37	CCDS45332.1																																																																																			G|0.816;A|0.184	0.184	strong		0.353	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122	
COPS7A	50813	hgsc.bcm.edu	37	12	6839913	6839913	+	Silent	SNP	C	C	T	rs2286730	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6839913C>T	ENST00000543155.1	+	7	1197	c.715C>T	c.(715-717)Ctg>Ttg	p.L239L	COPS7A_ENST00000538410.1_Intron|COPS7A_ENST00000534947.1_Silent_p.L239L|COPS7A_ENST00000542150.1_3'UTR|COPS7A_ENST00000229251.3_Silent_p.L239L|COPS7A_ENST00000534877.1_Silent_p.L239L|COPS7A_ENST00000539735.1_Silent_p.L239L	NM_001164094.1	NP_001157566.1	Q9UBW8	CSN7A_HUMAN	COP9 signalosome subunit 7A	239					cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	10						TGAGCAACACCTGACTGAGCT	0.562													C|||	550	0.109824	0.2632	0.0591	5008	,	,		19356	0.0694		0.0656	False		,,,				2504	0.0256				p.L239L		Atlas-SNP	.											.	COPS7A	26	.	0			c.C715T						PASS	.	C	,,,	1026,3380	373.9+/-321.0	109,808,1286	43.0	45.0	44.0		715,715,715,715	3.7	1.0	12	dbSNP_100	44	783,7817	184.3+/-232.3	37,709,3554	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COPS7A	NM_001164093.1,NM_001164094.1,NM_001164095.1,NM_016319.2	,,,	146,1517,4840	TT,TC,CC		9.1047,23.2864,13.909	,,,	239/276,239/276,239/276,239/276	6839913	1809,11197	2203	4300	6503	SO:0001819	synonymous_variant	50813	exon7			CAACACCTGACTG	AF193844	CCDS8558.1	12p13.31	2013-03-14	2013-03-14		ENSG00000111652	ENSG00000111652			16758	protein-coding gene	gene with protein product			"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7A"", ""COP9 constitutive photomorphogenic homolog subunit 7A (Arabidopsis)"""				Standard	NM_001164093		Approved	CSN7A	uc001qqh.3	Q9UBW8	OTTHUMG00000169182	ENST00000543155.1:c.715C>T	12.37:g.6839913C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_001164094	A8K9A6|Q9NVX3|Q9UJW4	Silent	SNP	ENST00000543155.1	37	CCDS8558.1																																																																																			C|0.879;T|0.121	0.121	strong		0.562	COPS7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402740.1		
WDR41	55255	hgsc.bcm.edu	37	5	76734084	76734084	+	Missense_Mutation	SNP	C	C	T	rs33204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:76734084C>T	ENST00000296679.4	-	10	1360	c.985G>A	c.(985-987)Gtt>Att	p.V329I	WDR41_ENST00000414719.2_Missense_Mutation_p.V75I|WDR41_ENST00000507029.1_Missense_Mutation_p.V274I|WDR41_ENST00000512033.1_5'Flank	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	329			V -> I (in dbSNP:rs33204). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		AGTCTGGCAACGTGCAGGACA	0.463													T|||	2646	0.528355	0.6362	0.611	5008	,	,		21138	0.4603		0.4205	False		,,,				2504	0.5051				p.V329I		Atlas-SNP	.											.	WDR41	29	.	0			c.G985A						PASS	.	T	ILE/VAL	2590,1816	532.2+/-373.4	761,1068,374	228.0	214.0	218.0		985	-2.4	0.0	5	dbSNP_76	218	3902,4698	604.5+/-394.8	914,2074,1312	yes	missense	WDR41	NM_018268.2	29	1675,3142,1686	TT,TC,CC		45.3721,41.2165,49.9154	benign	329/460	76734084	6492,6514	2203	4300	6503	SO:0001583	missense	55255	exon10			TGGCAACGTGCAG	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"""WD repeat domain containing"""	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.985G>A	5.37:g.76734084C>T	ENSP00000296679:p.Val329Ile	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Missense_Mutation	SNP	ENST00000296679.4	37	CCDS4038.1	1102	0.5045787545787546	318	0.6463414634146342	212	0.585635359116022	270	0.47202797202797203	302	0.39841688654353563	T	0.196	-1.048825	0.01981	0.587835	0.453721	ENSG00000164253	ENST00000296679;ENST00000414719;ENST00000515253;ENST00000507029;ENST00000507654	T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14	5.75	-2.41	0.06562	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.335923	0.35096	N	0.003446	T	0.00012	0.0000	N	0.04387	-0.21	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.47548	-0.9109	9	0.34782	T	0.22	-1.4621	12.8081	0.57626	0.0:0.4274:0.0:0.5726	rs33204;rs1128214;rs3184901;rs11550077;rs17409156;rs17856058;rs52790159;rs59230263;rs33204	274;75;329	B4DT55;B4E2L4;Q9HAD4	.;.;WDR41_HUMAN	I	329;75;264;274;100	ENSP00000296679:V329I;ENSP00000392931:V75I;ENSP00000426499:V264I;ENSP00000424287:V274I;ENSP00000427291:V100I	ENSP00000296679:V329I	V	-	1	0	WDR41	76769840	0.999000	0.42202	0.031000	0.17742	0.239000	0.25481	0.529000	0.23019	-0.623000	0.05618	-1.007000	0.02485	GTT	C|0.490;T|0.510	0.510	strong		0.463	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
OR51F1	256892	hgsc.bcm.edu	37	11	4791111	4791111	+	Missense_Mutation	SNP	T	T	C	rs17324812	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4791111T>C	ENST00000380383.1	-	1	57	c.58A>G	c.(58-60)Acc>Gcc	p.T20A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.T13A			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	20			T -> A (in dbSNP:rs17324812).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		AACAAGAAGGTTGGAAATTTA	0.448													T|||	681	0.135982	0.0091	0.1427	5008	,	,		20080	0.0635		0.2485	False		,,,				2504	0.2618				p.T13A		Atlas-SNP	.											.	OR51F1	60	.	0			c.A37G						PASS	.	T	ALA/THR	213,4189		4,205,1992	40.0	44.0	43.0		37	0.8	0.9	11	dbSNP_123	43	2311,6285		308,1695,2295	yes	missense	OR51F1	NM_001004752.1	58	312,1900,4287	CC,CT,TT		26.8846,4.8387,19.4184	benign	13/313	4791111	2524,10474	2201	4298	6499	SO:0001583	missense	256892	exon1			AGAAGGTTGGAAA	BK004771	CCDS31359.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188069	ENSG00000188069		"""GPCR / Class A : Olfactory receptors"""	15196	protein-coding gene	gene with protein product				OR51F1P			Standard	NM_001004752		Approved		uc010qyl.2	A6NGY5	OTTHUMG00000066503	ENST00000380383.1:c.58A>G	11.37:g.4791111T>C	ENSP00000369744:p.Thr20Ala	Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	208	204	0.980769	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		284	0.13003663003663005	10	0.02032520325203252	56	0.15469613259668508	38	0.06643356643356643	180	0.23746701846965698	T	11.72	1.721629	0.30503	0.048387	0.268846	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00325	8.1;8.1	4.81	0.84	0.18912	.	0.270733	0.25848	N	0.027919	T	0.00012	0.0000	M	0.73372	2.23	0.45318	P	0.0016880000000000228	B	0.12013	0.005	B	0.11329	0.006	T	0.41342	-0.9514	9	0.39692	T	0.17	.	4.146	0.10215	0.1493:0.1733:0.0:0.6774	rs17324812;rs52822566;rs59975624;rs17324812	20	A6NGY5	O51F1_HUMAN	A	13;20	ENSP00000345163:T13A;ENSP00000369744:T20A	ENSP00000345163:T13A	T	-	1	0	OR51F1	4747687	0.000000	0.05858	0.888000	0.34837	0.934000	0.57294	-0.930000	0.03972	0.316000	0.23135	0.477000	0.44152	ACC	T|0.834;C|0.166	0.166	strong		0.448	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
ENPP5	59084	hgsc.bcm.edu	37	6	46135984	46135984	+	Missense_Mutation	SNP	G	G	T	rs3806995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:46135984G>T	ENST00000371383.2	-	3	276	c.16C>A	c.(16-18)Ctc>Atc	p.L6I	ENPP5_ENST00000492313.1_5'Flank|ENPP5_ENST00000230565.3_Missense_Mutation_p.L6I					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						GACACCAAGAGAAATTTCGAA	0.348													G|||	2225	0.444289	0.1899	0.4467	5008	,	,		17819	0.4494		0.5298	False		,,,				2504	0.6933				p.L6I		Atlas-SNP	.											.	ENPP5	44	.	0			c.C16A						PASS	.	G	ILE/LEU	943,3191		113,717,1237	65.0	67.0	66.0		16	3.4	0.0	6	dbSNP_107	66	4445,4071		1170,2105,983	yes	missense	ENPP5	NM_021572.4	5	1283,2822,2220	TT,TG,GG		47.8041,22.8108,42.5929	benign	6/478	46135984	5388,7262	2067	4258	6325	SO:0001583	missense	59084	exon2			CCAAGAGAAATTT	AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.16C>A	6.37:g.46135984G>T	ENSP00000360436:p.Leu6Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_021572		Missense_Mutation	SNP	ENST00000371383.2	37	CCDS4915.1	908	0.4157509157509158	95	0.19308943089430894	178	0.49171270718232046	231	0.40384615384615385	404	0.5329815303430079	G	5.728	0.318747	0.10845	0.228108	0.521959	ENSG00000112796	ENST00000371383;ENST00000230565	T;T	0.74632	-0.86;-0.86	5.26	3.41	0.39046	.	1.187990	0.05858	N	0.622403	T	0.39009	0.1062	N	0.19112	0.55	0.80722	P	0.0	B	0.13594	0.008	B	0.12837	0.008	T	0.17868	-1.0355	9	0.34782	T	0.22	-4.3671	5.3566	0.16065	0.0787:0.3349:0.4595:0.1268	rs3806995;rs52837713;rs60345511;rs3806995	6	Q9UJA9	ENPP5_HUMAN	I	6	ENSP00000360436:L6I;ENSP00000230565:L6I	ENSP00000230565:L6I	L	-	1	0	ENPP5	46243943	0.209000	0.23505	0.015000	0.15790	0.108000	0.19459	1.068000	0.30629	1.305000	0.44909	0.591000	0.81541	CTC	G|0.573;T|0.427	0.427	strong		0.348	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
SLC25A31	83447	hgsc.bcm.edu	37	4	128689936	128689936	+	Silent	SNP	A	A	G	rs2305958	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:128689936A>G	ENST00000281154.4	+	5	831	c.663A>G	c.(661-663)ccA>ccG	p.P221P		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	221					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)			NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						AGAAAACTCCATTTCTTGTCT	0.328													A|||	2684	0.535942	0.3298	0.6441	5008	,	,		16708	0.4067		0.659	False		,,,				2504	0.7444				p.P221P		Atlas-SNP	.											SLC25A31,colon,carcinoma,+1,1	SLC25A31	42	1	0			c.A663G						PASS	.	A		1767,2639	524.1+/-371.2	347,1073,783	107.0	99.0	102.0		663	0.3	1.0	4	dbSNP_100	102	5594,3002	661.6+/-401.9	1832,1930,536	no	coding-synonymous	SLC25A31	NM_031291.2		2179,3003,1319	GG,GA,AA		34.9232,40.1044,43.3856		221/316	128689936	7361,5641	2203	4298	6501	SO:0001819	synonymous_variant	83447	exon5			AACTCCATTTCTT	AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"""Solute carriers"""	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.663A>G	4.37:g.128689936A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_031291		Silent	SNP	ENST00000281154.4	37	CCDS3733.1																																																																																			A|0.472;G|0.528	0.528	strong		0.328	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257094.2	NM_031291	
KIAA0020	9933	hgsc.bcm.edu	37	9	2811505	2811505	+	Silent	SNP	G	G	A	rs2270888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:2811505G>A	ENST00000397885.2	-	15	1697	c.1491C>T	c.(1489-1491)caC>caT	p.H497H		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	497	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		CTTCTTGGGCGTGTTCTTGCA	0.502													G|||	2072	0.413738	0.2035	0.3746	5008	,	,		19076	0.496		0.4742	False		,,,				2504	0.5787				p.H497H		Atlas-SNP	.											.	KIAA0020	56	.	0			c.C1491T						PASS	.	G		1137,3269	406.6+/-333.9	132,873,1198	165.0	149.0	154.0		1491	-8.9	0.0	9	dbSNP_100	154	4300,4300	578.5+/-390.7	1081,2138,1081	no	coding-synonymous	KIAA0020	NM_014878.4		1213,3011,2279	AA,AG,GG		50.0,25.8057,41.8038		497/649	2811505	5437,7569	2203	4300	6503	SO:0001819	synonymous_variant	9933	exon15			TTGGGCGTGTTCT	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1491C>T	9.37:g.2811505G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Silent	SNP	ENST00000397885.2	37	CCDS6448.2																																																																																			A|0.416;C|0.000;G|0.584;T|0.000	0.416	strong		0.502	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
RALGDS	5900	hgsc.bcm.edu	37	9	135985796	135985796	+	Silent	SNP	C	C	T	rs3761824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135985796C>T	ENST00000372050.3	-	3	396	c.375G>A	c.(373-375)gtG>gtA	p.V125V	RALGDS_ENST00000393157.3_Silent_p.V124V|RALGDS_ENST00000542690.1_Silent_p.V196V|RALGDS_ENST00000393160.3_Silent_p.V70V|RALGDS_ENST00000372047.3_Silent_p.V125V|RALGDS_ENST00000372062.3_Silent_p.V108V|RALGDS_ENST00000469972.1_5'Flank	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	125	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		CCAGGTGCTCCACCAGCTTCT	0.592			T	CIITA	"""PMBL, Hodgkin Lymphona, """								C|||	1245	0.248602	0.1278	0.2161	5008	,	,		18066	0.3204		0.2704	False		,,,				2504	0.3384				p.V125V	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.G375A						PASS	.	C	,	687,3717	288.1+/-279.7	48,591,1563	93.0	81.0	85.0		210,375	4.1	1.0	9	dbSNP_107	85	2649,5951	427.2+/-355.5	405,1839,2056	no	coding-synonymous,coding-synonymous	RALGDS	NM_001042368.1,NM_006266.2	,	453,2430,3619	TT,TC,CC		30.8023,15.5995,25.6536	,	70/860,125/915	135985796	3336,9668	2202	4300	6502	SO:0001819	synonymous_variant	5900	exon3			GTGCTCCACCAGC	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.375G>A	9.37:g.135985796C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																			C|0.754;T|0.246	0.246	strong		0.592	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
ZNF665	79788	hgsc.bcm.edu	37	19	53667940	53667940	+	Silent	SNP	A	A	G	rs12459471	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53667940A>G	ENST00000600412.1	-	2	1723	c.1608T>C	c.(1606-1608)aaT>aaC	p.N536N	ZNF665_ENST00000396424.3_Silent_p.N601N|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	536					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TGCCACATTCATTACATTTGT	0.383													G|||	2592	0.517572	0.1543	0.6499	5008	,	,		20967	0.6448		0.5974	False		,,,				2504	0.7014				p.N601N		Atlas-SNP	.											.	ZNF665	136	.	0			c.T1803C						PASS	.	G		1025,3381	722.8+/-409.3	126,773,1304	113.0	115.0	115.0		1803	-0.0	0.0	19	dbSNP_120	115	5247,3353	496.1+/-374.2	1589,2069,642	no	coding-synonymous	ZNF665	NM_024733.3		1715,2842,1946	GG,GA,AA		38.9884,23.2637,48.2239		601/679	53667940	6272,6734	2203	4300	6503	SO:0001819	synonymous_variant	79788	exon4			ACATTCATTACAT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1608T>C	19.37:g.53667940A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_024733	A8K5T8	Silent	SNP	ENST00000600412.1	37																																																																																				A|0.473;G|0.527	0.527	strong		0.383	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
COMMD2	51122	hgsc.bcm.edu	37	3	149468530	149468530	+	Missense_Mutation	SNP	T	T	G	rs9843784	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:149468530T>G	ENST00000473414.1	-	4	391	c.337A>C	c.(337-339)Att>Ctt	p.I113L		NM_016094.3	NP_057178.2	Q86X83	COMD2_HUMAN	COMM domain containing 2	113			I -> L (in dbSNP:rs9843784). {ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15799966}.							NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TCACTCAGAATCGTTCTGATC	0.358													T|||	1197	0.239018	0.0446	0.268	5008	,	,		16341	0.25		0.4085	False		,,,				2504	0.2955				p.I113L		Atlas-SNP	.											.	COMMD2	21	.	0			c.A337C						PASS	.	T	LEU/ILE	491,3915	229.4+/-244.0	30,431,1742	153.0	148.0	149.0		337	2.7	0.8	3	dbSNP_119	149	3641,4959	523.4+/-380.3	786,2069,1445	yes	missense	COMMD2	NM_016094.3	5	816,2500,3187	GG,GT,TT		42.3372,11.1439,31.77	benign	113/200	149468530	4132,8874	2203	4300	6503	SO:0001583	missense	51122	exon4			TCAGAATCGTTCT	AY542158	CCDS3145.1	3q25.1	2004-02-20			ENSG00000114744	ENSG00000114744			24993	protein-coding gene	gene with protein product						15799966	Standard	NM_016094		Approved	HSPC042	uc003exj.2	Q86X83	OTTHUMG00000159616	ENST00000473414.1:c.337A>C	3.37:g.149468530T>G	ENSP00000419475:p.Ile113Leu	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	265	153	0.577358	NM_016094	Q561V4|Q9H3L5|Q9Y5V1	Missense_Mutation	SNP	ENST00000473414.1	37	CCDS3145.1	563	0.25778388278388276	21	0.042682926829268296	95	0.26243093922651933	130	0.22727272727272727	317	0.4182058047493404	T	14.86	2.662649	0.47572	0.111439	0.423372	ENSG00000114744	ENST00000473414	T	0.08634	3.07	5.36	2.7	0.31948	.	0.147086	0.64402	D	0.000009	T	0.00012	0.0000	L	0.46885	1.475	0.25896	P	0.9834196	B	0.16166	0.016	B	0.14578	0.011	T	0.47315	-0.9127	9	0.27785	T	0.31	-14.4315	11.8066	0.52158	0.0:0.0:0.2777:0.7223	rs9843784;rs17854390;rs52814071;rs59944079;rs9843784	113	Q86X83	COMD2_HUMAN	L	113	ENSP00000419475:I113L	ENSP00000419475:I113L	I	-	1	0	COMMD2	150951220	0.997000	0.39634	0.816000	0.32577	0.834000	0.47266	2.382000	0.44345	0.927000	0.37143	0.528000	0.53228	ATT	T|0.704;G|0.296	0.296	strong		0.358	COMMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356515.1	NM_016094	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240804	39240804	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39240804C>A	ENST00000391417.4	+	1	346	c.346C>A	c.(346-348)Cgc>Agc	p.R116S		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	141	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						cagctgctgccgcccctgctg	0.672																																					p.R116S		Atlas-SNP	.											KRTAP4-7,caecum,carcinoma,0,1	KRTAP4-7	49	1	0			c.C346A						scavenged	.						15.0	16.0	16.0					17																	39240804		692	1588	2280	SO:0001583	missense	100132476	exon1			TGCTGCCGCCCCT	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.346C>A	17.37:g.39240804C>A	ENSP00000375236:p.Arg116Ser	Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	108	9	0.0833333	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.016	-1.524493	0.00959	.	.	ENSG00000240871	ENST00000391417	T	0.00596	6.32	3.15	-6.29	0.02013	.	0.163808	0.19966	U	0.102091	T	0.00241	0.0007	.	.	.	0.09310	N	0.999997	B	0.33748	0.423	B	0.29524	0.103	T	0.47661	-0.9100	9	0.11794	T	0.64	.	1.8893	0.03244	0.1228:0.1811:0.2435:0.4526	.	171	Q9BYR0	KRA47_HUMAN	S	116	ENSP00000375236:R116S	ENSP00000375236:R116S	R	+	1	0	KRTAP4-7	36494330	0.000000	0.05858	0.002000	0.10522	0.468000	0.32798	-3.208000	0.00557	-2.496000	0.00513	-0.734000	0.03567	CGC	.	.	none		0.672	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
OR2D2	120776	hgsc.bcm.edu	37	11	6913127	6913127	+	Missense_Mutation	SNP	A	A	G	rs2741804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6913127A>G	ENST00000299459.2	-	1	703	c.605T>C	c.(604-606)aTg>aCg	p.M202T		NM_003700.1	NP_003691.1	Q9H210	OR2D2_HUMAN	olfactory receptor, family 2, subfamily D, member 2	202			M -> T (in dbSNP:rs2741804). {ECO:0000269|PubMed:11416212, ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:9787077}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	18		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CACAACCCCCATAAGAAAAAT	0.458													A|||	1892	0.377796	0.1195	0.5706	5008	,	,		21873	0.4306		0.502	False		,,,				2504	0.408				p.M202T		Atlas-SNP	.											.	OR2D2	52	.	0			c.T605C						PASS	.		THR/MET	814,3588	321.8+/-297.3	80,654,1467	82.0	78.0	79.0		605	4.0	0.9	11	dbSNP_100	79	4803,3789	611.1+/-395.8	1373,2057,866	yes	missense	OR2D2	NM_003700.1	81	1453,2711,2333	GG,GA,AA		44.0992,18.4916,43.2276	benign	202/309	6913127	5617,7377	2201	4296	6497	SO:0001583	missense	120776	exon1			ACCCCCATAAGAA	AB065824	CCDS31416.1	11p15.4	2012-08-09			ENSG00000166368	ENSG00000166368		"""GPCR / Class A : Olfactory receptors"""	8244	protein-coding gene	gene with protein product		608494		OR2D1		9787077	Standard	NM_003700		Approved	OR11-610, hg27	uc010rau.2	Q9H210	OTTHUMG00000165741	ENST00000299459.2:c.605T>C	11.37:g.6913127A>G	ENSP00000299459:p.Met202Thr	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	162	92	0.567901	NM_003700	B9EIL5|O95224|Q6IF28|Q8NGH4|Q96R52	Missense_Mutation	SNP	ENST00000299459.2	37	CCDS31416.1	930	0.4258241758241758	71	0.1443089430894309	203	0.5607734806629834	273	0.4772727272727273	383	0.5052770448548812	a	2.132	-0.398977	0.04865	0.184916	0.559008	ENSG00000166368	ENST00000299459	T	0.00063	8.78	5.08	3.96	0.45880	GPCR, rhodopsin-like superfamily (1);	0.219434	0.32416	N	0.006122	T	0.00012	0.0000	N	0.19112	0.55	0.37198	P	0.09576899999999999	B	0.09022	0.002	B	0.13407	0.009	T	0.04178	-1.0971	9	0.28530	T	0.3	-18.7375	5.6143	0.17422	0.7411:0.1714:0.0875:0.0	rs2741804;rs17183805;rs52796262;rs60656633;rs2741804	202	Q9H210	OR2D2_HUMAN	T	202	ENSP00000299459:M202T	ENSP00000299459:M202T	M	-	2	0	OR2D2	6869703	0.000000	0.05858	0.859000	0.33776	0.067000	0.16453	0.682000	0.25335	1.079000	0.41038	-0.294000	0.09567	ATG	G|0.425;N|0.001	0.425	strong		0.458	OR2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385986.1	NM_003700	
IFIT2	3433	hgsc.bcm.edu	37	10	91066977	91066977	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:91066977C>T	ENST00000371826.3	+	2	1433	c.1264C>T	c.(1264-1266)Cga>Tga	p.R422*	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	422					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				TGCCAAAATGCGACTTTCTAA	0.393																																					p.R422X		Atlas-SNP	.											IFIT2,colon,carcinoma,0,1	IFIT2	39	1	0			c.C1264T						scavenged	.						128.0	120.0	123.0					10																	91066977		1831	4085	5916	SO:0001587	stop_gained	3433	exon2			AAAATGCGACTTT	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"""Tetratricopeptide (TTC) repeat domain containing"""	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.1264C>T	10.37:g.91066977C>T	ENSP00000360891:p.Arg422*	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	124	3	0.0241935	NM_001547	Q5T767	Nonsense_Mutation	SNP	ENST00000371826.3	37	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.420645	0.83559	.	.	ENSG00000119922	ENST00000371826	.	.	.	4.58	1.48	0.22813	.	0.534254	0.16694	U	0.203422	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.1255	12.5012	0.55955	0.7486:0.2513:0.0:0.0	.	.	.	.	X	422	.	ENSP00000360891:R422X	R	+	1	2	IFIT2	91056957	0.000000	0.05858	0.039000	0.18376	0.059000	0.15707	0.363000	0.20301	0.312000	0.23038	-0.152000	0.13540	CGA	.	.	none		0.393	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547	
SPTBN1	6711	hgsc.bcm.edu	37	2	54858214	54858214	+	Silent	SNP	A	A	G	rs61730127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:54858214A>G	ENST00000356805.4	+	16	3311	c.3030A>G	c.(3028-3030)gcA>gcG	p.A1010A	SPTBN1_ENST00000333896.5_Silent_p.A997A	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1010					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CCATTGAGGCAAAGCTGAGTG	0.647													A|||	139	0.0277556	0.0038	0.0476	5008	,	,		20509	0.0		0.0825	False		,,,				2504	0.0184				p.A1010A		Atlas-SNP	.											.	SPTBN1	378	.	0			c.A3030G						PASS	.	A	,	58,4348	55.5+/-91.7	0,58,2145	60.0	70.0	67.0		3030,2991	-10.6	0.8	2	dbSNP_129	67	671,7929	167.8+/-219.5	41,589,3670	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	41,647,5815	GG,GA,AA		7.8023,1.3164,5.6051	,	1010/2365,997/2156	54858214	729,12277	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon16			TGAGGCAAAGCTG		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3030A>G	2.37:g.54858214A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			A|0.949;G|0.051;T|0.000	0.051	strong		0.647	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
TBX18	9096	hgsc.bcm.edu	37	6	85473758	85473758	+	Missense_Mutation	SNP	C	C	T	rs172562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:85473758C>T	ENST00000369663.5	-	1	479	c.142G>A	c.(142-144)Ggg>Agg	p.G48R	TBX18_ENST00000606784.1_5'Flank|TBX18_ENST00000606521.1_5'Flank	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	48			G -> R (in dbSNP:rs172562). {ECO:0000269|PubMed:15489334}.		anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.G48R(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		tccacggcccccgccgccTCT	0.711													C|||	2052	0.409744	0.0862	0.3847	5008	,	,		9197	0.4683		0.501	False		,,,				2504	0.7106				p.G48R		Atlas-SNP	.											TBX18,NS,carcinoma,0,1	TBX18	131	1	1	Substitution - Missense(1)	prostate(1)	c.G142A						PASS	.	C	ARG/GLY	558,3286		91,376,1455	3.0	4.0	4.0		142	4.4	0.1	6	dbSNP_79	4	3522,4434		896,1730,1352	yes	missense	TBX18	NM_001080508.1	125	987,2106,2807	TT,TC,CC		44.2685,14.5161,34.5763	benign	48/608	85473758	4080,7720	1922	3978	5900	SO:0001583	missense	9096	exon1			CGGCCCCCGCCGC	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.142G>A	6.37:g.85473758C>T	ENSP00000358677:p.Gly48Arg	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	22	14	0.636364	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	37	CCDS34495.1	861	0.3942307692307692	51	0.10365853658536585	152	0.4198895027624309	273	0.4772727272727273	385	0.5079155672823219	C	14.67	2.603923	0.46423	0.145161	0.442685	ENSG00000112837	ENST00000369663	D	0.86366	-2.11	5.33	4.45	0.53987	.	0.989186	0.08254	N	0.974149	T	0.62600	0.2441	N	0.08118	0	0.80722	P	0.0	B	0.14438	0.01	B	0.12156	0.007	T	0.16988	-1.0384	9	0.17369	T	0.5	.	14.0585	0.64786	0.0:0.9244:0.0:0.0756	rs172562	48	O95935	TBX18_HUMAN	R	48	ENSP00000358677:G48R	ENSP00000358677:G48R	G	-	1	0	TBX18	85530477	0.007000	0.16637	0.127000	0.21898	0.591000	0.36615	2.304000	0.43655	2.495000	0.84180	0.305000	0.20034	GGG	C|0.605;T|0.395	0.395	strong		0.711	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508	
MYBPC2	4606	hgsc.bcm.edu	37	19	50967640	50967640	+	Missense_Mutation	SNP	G	G	A	rs25667	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50967640G>A	ENST00000357701.5	+	27	3317	c.3266G>A	c.(3265-3267)cGt>cAt	p.R1089H		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	1089	Ig-like C2-type 7.		R -> H (in dbSNP:rs25667).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		ATGGAAATCCGTGAAGATCCC	0.537													G|||	705	0.140775	0.0136	0.2522	5008	,	,		20485	0.126		0.2207	False		,,,				2504	0.1667				p.R1089H		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G3266A						PASS	.	G	HIS/ARG	171,4039		2,167,1936	55.0	59.0	58.0		3266	-0.5	0.0	19	dbSNP_72	58	1622,6868		164,1294,2787	yes	missense	MYBPC2	NM_004533.3	29	166,1461,4723	AA,AG,GG		19.1048,4.0618,14.1181	benign	1089/1142	50967640	1793,10907	2105	4245	6350	SO:0001583	missense	4606	exon27			AAATCCGTGAAGA		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.3266G>A	19.37:g.50967640G>A	ENSP00000350332:p.Arg1089His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	339	0.15521978021978022	9	0.018292682926829267	88	0.2430939226519337	80	0.13986013986013987	162	0.21372031662269128	g	2.377	-0.342929	0.05243	0.040618	0.191048	ENSG00000086967	ENST00000357701	T	0.68331	-0.32	3.99	-0.521	0.11931	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.234288	0.17079	N	0.187854	T	0.00012	0.0000	N	0.16862	0.45	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.06679	-1.0813	9	0.45353	T	0.12	.	5.3863	0.16220	0.2583:0.1555:0.5862:0.0	rs25667;rs2230840;rs17403009;rs17718746;rs52798518;rs56519860;rs61720718;rs17403009	1089	Q14324	MYPC2_HUMAN	H	1089	ENSP00000350332:R1089H	ENSP00000350332:R1089H	R	+	2	0	MYBPC2	55659452	0.000000	0.05858	0.001000	0.08648	0.385000	0.30292	0.074000	0.14662	0.199000	0.20427	0.457000	0.33378	CGT	A|0.143;C|0.000;G|0.857	0.143	strong		0.537	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
ZNF280A	129025	hgsc.bcm.edu	37	22	22868493	22868493	+	Missense_Mutation	SNP	G	G	T	rs361666	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22868493G>T	ENST00000302097.3	-	2	1714	c.1462C>A	c.(1462-1464)Cgt>Agt	p.R488S		NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	488			R -> S (in dbSNP:rs361666). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9074928}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TTTGTTTCACGAGGGAACCCT	0.433													G|||	2362	0.471645	0.2375	0.732	5008	,	,		17316	0.4107		0.7018	False		,,,				2504	0.4294				p.R488S		Atlas-SNP	.											.	ZNF280A	67	.	0			c.C1462A						PASS	.	G	SER/ARG	1357,3049	446.9+/-348.2	220,917,1066	123.0	108.0	113.0		1462	3.8	0.4	22	dbSNP_79	113	5856,2744	679.0+/-403.5	2008,1840,452	yes	missense	ZNF280A	NM_080740.3	110	2228,2757,1518	TT,TG,GG		31.907,30.7989,44.541	benign	488/543	22868493	7213,5793	2203	4300	6503	SO:0001583	missense	129025	exon2			TTTCACGAGGGAA	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.1462C>A	22.37:g.22868493G>T	ENSP00000302855:p.Arg488Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	1156	0.5293040293040293	126	0.25609756097560976	254	0.7016574585635359	245	0.42832167832167833	531	0.7005277044854882	G	10.94	1.491486	0.26774	0.307989	0.68093	ENSG00000169548	ENST00000302097	T	0.01133	5.29	3.76	3.76	0.43208	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.33910	P	0.36043499999999995	B	0.17852	0.024	B	0.12837	0.008	T	0.04115	-1.0976	8	0.41790	T	0.15	-0.3875	13.8754	0.63648	0.0:0.0:1.0:0.0	rs361666;rs3747096;rs17173828;rs17854853	488	P59817	Z280A_HUMAN	S	488	ENSP00000302855:R488S	ENSP00000302855:R488S	R	-	1	0	ZNF280A	21198493	1.000000	0.71417	0.382000	0.26119	0.034000	0.12701	4.885000	0.63142	2.372000	0.80975	0.655000	0.94253	CGT	G|0.469;T|0.531	0.531	strong		0.433	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
PNPLA7	375775	hgsc.bcm.edu	37	9	140438216	140438216	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140438216G>A	ENST00000277531.4	-	4	436	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W	AL365502.1_ENST00000580317.1_RNA|PNPLA7_ENST00000406427.1_Missense_Mutation_p.R109W	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	84					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TTCCTGGCCCGCTGCCGGGGC	0.637																																					p.R109W		Atlas-SNP	.											.	PNPLA7	124	.	0			c.C325T						PASS	.						85.0	77.0	80.0					9																	140438216		2203	4300	6503	SO:0001583	missense	375775	exon5			TGGCCCGCTGCCG	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.250C>T	9.37:g.140438216G>A	ENSP00000277531:p.Arg84Trp	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	171	74	0.432749	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Missense_Mutation	SNP	ENST00000277531.4	37	CCDS7045.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.306502	0.60305	.	.	ENSG00000130653	ENST00000277531;ENST00000406427;ENST00000371451;ENST00000434090;ENST00000371450	T;T;T	0.62364	0.05;0.03;0.06	3.41	2.4	0.29515	.	0.066594	0.56097	D	0.000027	T	0.74966	0.3786	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.76767	-0.2838	10	0.87932	D	0	-14.0749	8.3027	0.32023	0.0:0.0:0.5617:0.4382	.	109;84	Q6ZV29-5;Q6ZV29	.;PLPL7_HUMAN	W	84;109;84;75;109	ENSP00000277531:R84W;ENSP00000384610:R109W;ENSP00000400582:R75W	ENSP00000277531:R84W	R	-	1	2	PNPLA7	139558037	1.000000	0.71417	0.954000	0.39281	0.848000	0.48234	1.656000	0.37355	1.907000	0.55213	0.462000	0.41574	CGG	.	.	none		0.637	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
SLC26A6	65010	hgsc.bcm.edu	37	3	48669447	48669447	+	Missense_Mutation	SNP	C	C	T	rs13324142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:48669447C>T	ENST00000395550.2	-	6	663	c.616G>A	c.(616-618)Gtg>Atg	p.V206M	SLC26A6_ENST00000337000.8_Intron|SLC26A6_ENST00000358747.6_Missense_Mutation_p.V185M|SLC26A6_ENST00000383733.3_Missense_Mutation_p.V206M|SLC26A6_ENST00000482282.1_5'UTR|SLC26A6_ENST00000455886.2_Missense_Mutation_p.R171H|SLC26A6_ENST00000420764.2_Missense_Mutation_p.V206M			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6	206			V -> M (in dbSNP:rs13324142). {ECO:0000269|PubMed:11247665}.		angiotensin-activated signaling pathway (GO:0038166)|anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular response to cAMP (GO:0071320)|cellular response to fructose stimulus (GO:0071332)|cellular response to interferon-gamma (GO:0071346)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|epithelial fluid transport (GO:0042045)|formate transport (GO:0015724)|intestinal absorption (GO:0050892)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|mannitol transport (GO:0015797)|oxalate transport (GO:0019532)|oxalic acid secretion (GO:0046724)|positive regulation of dipeptide transmembrane transport (GO:2001150)|protein kinase C signaling (GO:0070528)|regulation of intracellular pH (GO:0051453)|sperm capacitation (GO:0048240)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transepithelial chloride transport (GO:0030321)|transepithelial transport (GO:0070633)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|chloride channel complex (GO:0034707)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle membrane (GO:0012506)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|chloride transmembrane transporter activity (GO:0015108)|efflux transmembrane transporter activity (GO:0015562)|formate efflux transmembrane transporter activity (GO:0015660)|formate transmembrane transporter activity (GO:0015499)|formate uptake transmembrane transporter activity (GO:0015659)|oxalate transmembrane transporter activity (GO:0019531)|PDZ domain binding (GO:0030165)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)		SLC26A6/PRKAR2A(2)	NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		TAGGTGACCACGAAGCCGAAG	0.607													C|||	555	0.110823	0.1641	0.0821	5008	,	,		21000	0.127		0.1123	False		,,,				2504	0.0409				p.V206M	NSCLC(13;369 479 28271 30152 44026)	Atlas-SNP	.											.	SLC26A6	45	.	0			c.G616A	GRCh37	CM086000	SLC26A6	M	rs13324142	PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	586,3494		38,510,1492	63.0	71.0	68.0		553,616,616,616	3.0	0.7	3	dbSNP_121	68	903,7451		58,787,3332	yes	missense,missense,missense,missense	SLC26A6	NM_001040454.1,NM_022911.2,NM_134263.2,NM_134426.2	21,21,21,21	96,1297,4824	TT,TC,CC		10.8092,14.3627,11.9752	probably-damaging,probably-damaging,probably-damaging,probably-damaging	185/739,206/760,206/759,206/741	48669447	1489,10945	2040	4177	6217	SO:0001583	missense	65010	exon6			TGACCACGAAGCC	AF279265	CCDS43087.1, CCDS46824.1, CCDS46825.1, CCDS46826.1, CCDS63627.1, CCDS63628.1	3p21.31	2013-08-05	2013-07-18		ENSG00000225697	ENSG00000225697		"""Solute carriers"""	14472	protein-coding gene	gene with protein product	"""pendrin-like protein 1"", ""pendrin L1"", ""sulfate anion transporter"", ""anion transporter 1"""	610068	"""solute carrier family 26, member 6"""			11087667, 11247665	Standard	NM_022911		Approved	DKFZp586E1422		Q9BXS9	OTTHUMG00000186381	ENST00000395550.2:c.616G>A	3.37:g.48669447C>T	ENSP00000378920:p.Val206Met	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	145	82	0.565517	NM_022911	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Missense_Mutation	SNP	ENST00000395550.2	37	CCDS43087.1	253|253	0.11584249084249085|0.11584249084249085	76|76	0.15447154471544716|0.15447154471544716	28|28	0.07734806629834254|0.07734806629834254	63|63	0.11013986013986014|0.11013986013986014	86|86	0.11345646437994723|0.11345646437994723	C|C	17.64|17.64	3.439539|3.439539	0.63067|0.63067	0.143627|0.143627	0.108092|0.108092	ENSG00000225697|ENSG00000225697	ENST00000455886;ENST00000431739|ENST00000420764;ENST00000395550;ENST00000383733;ENST00000447978;ENST00000358747;ENST00000421649	D;D|D;D;D;D;D	0.92647|0.93604	-3.08;-2.72|-3.25;-3.25;-3.25;-3.25;-3.25	4.78|4.78	2.98|2.98	0.34508|0.34508	.|Sulphate transporter (1);	.|.	.|.	.|.	.|.	T|T	0.21227|0.21227	0.0511|0.0511	M|M	0.93808|0.93808	3.46|3.46	0.36497|0.36497	P|P	0.13119400000000003|0.13119400000000003	B|P;D;D;D;D	0.22604|0.76494	0.072|0.802;0.994;0.998;0.998;0.999	B|P;D;D;D;D	0.12837|0.68353	0.008|0.482;0.916;0.931;0.931;0.957	T|T	0.60286|0.60286	-0.7293|-0.7293	8|8	0.87932|0.87932	D|D	0|0	.|.	11.7948|11.7948	0.52093|0.52093	0.0:0.6963:0.2341:0.0696|0.0:0.6963:0.2341:0.0696	rs13324142;rs57651294;rs13324142|rs13324142;rs57651294;rs13324142	171|219;206;206;206;3611	B4DMZ1|Q86YZ4;Q9BXS9-2;Q548A7;Q9BXS9;Q5Y190	.|.;.;.;S26A6_HUMAN;.	H|M	171;155|206;206;206;219;185;52	ENSP00000401066:R171H;ENSP00000401813:R155H|ENSP00000404684:V206M;ENSP00000378920:V206M;ENSP00000373239:V206M;ENSP00000351597:V185M;ENSP00000389922:V52M	ENSP00000401813:R155H|ENSP00000351597:V185M	R|V	-|-	2|1	0|0	SLC26A6|SLC26A6	48644451|48644451	0.974000|0.974000	0.33945|0.33945	0.655000|0.655000	0.29622|0.29622	0.818000|0.818000	0.46254|0.46254	2.430000|2.430000	0.44766|0.44766	0.233000|0.233000	0.21120|0.21120	-1.255000|-1.255000	0.01485|0.01485	CGT|GTG	C|0.888;T|0.112	0.112	strong		0.607	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911	
SLC38A9	153129	hgsc.bcm.edu	37	5	54960687	54960687	+	Silent	SNP	C	C	T	rs4865616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:54960687C>T	ENST00000396865.2	-	8	1122	c.531G>A	c.(529-531)tcG>tcA	p.S177S	SLC38A9_ENST00000515629.1_Silent_p.S114S|SLC38A9_ENST00000416547.2_Silent_p.S53S|SLC38A9_ENST00000539768.1_Silent_p.S177S|SLC38A9_ENST00000512595.1_Silent_p.S150S|SLC38A9_ENST00000318672.3_Silent_p.S177S	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	177					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				TGGTATCCAACGAAACTAGAT	0.368													C|||	2797	0.558506	0.4297	0.585	5008	,	,		13519	0.4613		0.661	False		,,,				2504	0.7086				p.S177S		Atlas-SNP	.											SLC38A9,rectum,carcinoma,-1,1	SLC38A9	50	1	0			c.G531A						PASS	.	C		2109,2297	555.4+/-379.2	500,1109,594	31.0	28.0	29.0		531	-1.6	0.9	5	dbSNP_111	29	5617,2983	626.9+/-397.9	1830,1957,513	no	coding-synonymous	SLC38A9	NM_173514.2		2330,3066,1107	TT,TC,CC		34.686,47.8665,40.5966		177/562	54960687	7726,5280	2203	4300	6503	SO:0001819	synonymous_variant	153129	exon8			ATCCAACGAAACT		CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"""Solute carriers"""	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.531G>A	5.37:g.54960687C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	200	90	0.45	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Silent	SNP	ENST00000396865.2	37	CCDS3968.1																																																																																			C|0.428;T|0.572	0.572	strong		0.368	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514	
PCDHGB7	56099	hgsc.bcm.edu	37	5	140798639	140798639	+	Missense_Mutation	SNP	G	G	C	rs17208397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140798639G>C	ENST00000398594.2	+	1	1213	c.1213G>C	c.(1213-1215)Gta>Cta	p.V405L	PCDHGA8_ENST00000398604.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA6_ENST00000517434.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	405	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> L (in dbSNP:rs17208397).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTACAAGCTAGTAACAGATGA	0.488													g|||	434	0.0866613	0.0499	0.1081	5008	,	,		19013	0.0367		0.1779	False		,,,				2504	0.0787				p.V405L		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G1213C						PASS	.	G	,,,,,,,,,,,,,,,LEU/VAL,,LEU/VAL	280,3768		12,256,1756	43.0	46.0	45.0		,,,,,,,,,,,,,,,1213,,1213	2.5	0.9	5	dbSNP_123	45	1312,7010		91,1130,2940	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032101.2	,,,,,,,,,,,,,,,32,,32	103,1386,4696	CC,CG,GG		15.7654,6.917,12.8698	,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,405/930,,405/809	140798639	1592,10778	2024	4161	6185	SO:0001583	missense	56099	exon1			AAGCTAGTAACAG	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"""Cadherins / Protocadherins : Clustered"""	8714	other	protocadherin	"""cadherin ME6"""	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1213G>C	5.37:g.140798639G>C	ENSP00000381594:p.Val405Leu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	127	42	0.330709	NM_018927	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	219	0.10027472527472528	15	0.03048780487804878	48	0.13259668508287292	19	0.033216783216783216	137	0.18073878627968337	g	9.441	1.088102	0.20390	0.06917	0.157654	ENSG00000254122	ENST00000398594	T	0.51574	0.7	5.31	2.47	0.30058	Cadherin (4);Cadherin-like (1);	0.000000	0.30076	U	0.010477	T	0.00109	0.0003	L	0.58510	1.815	0.48571	P	3.300000000000525E-4	B;B	0.27498	0.18;0.149	B;B	0.37943	0.261;0.105	T	0.09952	-1.0651	9	0.26408	T	0.33	.	7.4728	0.27359	0.0706:0.1899:0.6288:0.1107	rs17208397;rs17208397	405;405	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	L	405	ENSP00000381594:V405L	ENSP00000381594:V405L	V	+	1	0	PCDHGB7	140778823	0.233000	0.23772	0.950000	0.38849	0.995000	0.86356	0.657000	0.24963	1.478000	0.48253	0.561000	0.74099	GTA	G|0.905;C|0.095	0.095	strong		0.488	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927	
SEPT12	124404	hgsc.bcm.edu	37	16	4837545	4837545	+	Silent	SNP	A	A	G	rs9673735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4837545A>G	ENST00000268231.8	-	2	365	c.102T>C	c.(100-102)gcT>gcC	p.A34A	SMIM22_ENST00000589721.1_5'Flank|SEPT12_ENST00000591861.1_5'UTR|SEPT12_ENST00000396693.5_Silent_p.A34A|SMIM22_ENST00000589327.1_5'Flank	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	34					cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.A34A(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						GGTCCAGCACAGCCTCAATGC	0.627													A|||	1520	0.303514	0.1536	0.3458	5008	,	,		18187	0.3026		0.328	False		,,,				2504	0.4519				p.A34A		Atlas-SNP	.											SEPT12,colon,carcinoma,0,2	SEPT12	40	2	1	Substitution - coding silent(1)	stomach(1)	c.T102C						PASS	.	A	,	704,3690	293.6+/-282.7	56,592,1549	200.0	146.0	164.0		102,102	-9.9	0.5	16	dbSNP_119	164	2371,6229	394.7+/-344.8	340,1691,2269	no	coding-synonymous,coding-synonymous	SEPT12	NM_001154458.2,NM_144605.4	,	396,2283,3818	GG,GA,AA		27.5698,16.0218,23.6648	,	34/313,34/359	4837545	3075,9919	2197	4300	6497	SO:0001819	synonymous_variant	124404	exon2			CAGCACAGCCTCA	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.102T>C	16.37:g.4837545A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	CCDS10522.1																																																																																			A|0.743;G|0.257	0.257	strong		0.627	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
WNK2	65268	hgsc.bcm.edu	37	9	96015256	96015256	+	Silent	SNP	C	C	T	rs4744201	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:96015256C>T	ENST00000297954.4	+	8	1926	c.1926C>T	c.(1924-1926)gaC>gaT	p.D642D	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Silent_p.D254D|WNK2_ENST00000395477.2_Silent_p.D642D|WNK2_ENST00000395475.2_Silent_p.D628D|WNK2_ENST00000349097.3_Silent_p.D254D	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	642					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CCCTTGCCGACGCAGCGCCGT	0.706													C|||	1583	0.316094	0.062	0.5115	5008	,	,		15328	0.4345		0.4712	False		,,,				2504	0.2393				p.D642D		Atlas-SNP	.											.	WNK2	277	.	0			c.C1926T						PASS	.	C		628,3760		50,528,1616	29.0	19.0	22.0		1926	-4.0	0.0	9	dbSNP_111	22	4207,4371		1046,2115,1128	no	coding-synonymous	WNK2	NM_006648.3		1096,2643,2744	TT,TC,CC		49.0441,14.3118,37.2898		642/2218	96015256	4835,8131	2194	4289	6483	SO:0001819	synonymous_variant	65268	exon8			TGCCGACGCAGCG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.1926C>T	9.37:g.96015256C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		834|834	0.38186813186813184|0.38186813186813184	34|34	0.06910569105691057|0.06910569105691057	184|184	0.5082872928176796|0.5082872928176796	253|253	0.4423076923076923|0.4423076923076923	363|363	0.4788918205804749|0.4788918205804749	C|C	0.038|0.038	-1.295186|-1.295186	0.01375|0.01375	0.143118|0.143118	0.490441|0.490441	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730	.|.	.|.	.|.	4.68|4.68	-3.95|-3.95	0.04118|0.04118	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.38418|0.38418	P|P	0.05389699999999997|0.05389699999999997	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.38607|0.38607	-0.9653|-0.9653	3|3	.|.	.|.	.|.	.|.	12.8604|12.8604	0.57910|0.57910	0.0:0.4563:0.0:0.5437|0.0:0.4563:0.0:0.5437	rs4744201;rs58280912;rs4744201|rs4744201;rs58280912;rs4744201	.|.	.|.	.|.	C|M	246|638	.|.	.|.	R|T	+|+	1|2	0|0	WNK2|WNK2	95055077|95055077	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.009000|0.009000	0.06853|0.06853	-2.814000|-2.814000	0.00753|0.00753	-0.624000|-0.624000	0.05611|0.05611	-1.020000|-1.020000	0.02445|0.02445	CGC|ACG	C|0.650;T|0.350	0.350	strong		0.706	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
YTHDC2	64848	hgsc.bcm.edu	37	5	112899573	112899573	+	Silent	SNP	T	T	C	rs6867579	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:112899573T>C	ENST00000161863.4	+	20	2673	c.2460T>C	c.(2458-2460)gaT>gaC	p.D820D		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	820					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		ATGCAATGGATACATGGGAAG	0.368													T|||	469	0.0936502	0.025	0.0908	5008	,	,		16509	0.0794		0.1759	False		,,,				2504	0.1186				p.D820D		Atlas-SNP	.											YTHDC2,NS,carcinoma,+1,1	YTHDC2	118	1	0			c.T2460C						PASS	.	T		217,4187	131.4+/-167.9	4,209,1989	160.0	146.0	151.0		2460	1.3	1.0	5	dbSNP_116	151	1476,7124	282.1+/-295.4	136,1204,2960	no	coding-synonymous	YTHDC2	NM_022828.3		140,1413,4949	CC,CT,TT		17.1628,4.9273,13.0191		820/1431	112899573	1693,11311	2202	4300	6502	SO:0001819	synonymous_variant	64848	exon20			AATGGATACATGG	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.2460T>C	5.37:g.112899573T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	181	78	0.430939	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			T|0.881;C|0.119	0.119	strong		0.368	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
TRIM49	57093	hgsc.bcm.edu	37	11	89531540	89531540	+	Missense_Mutation	SNP	C	C	T	rs12417980	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:89531540C>T	ENST00000329758.1	-	8	1445	c.1117G>A	c.(1117-1119)Gga>Aga	p.G373R	TRIM49_ENST00000532501.2_Missense_Mutation_p.G296R	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	373	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		G -> R (in dbSNP:rs12417980).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.G373R(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CCCGCCTTTCCATCTATCTTC	0.428													c|||	1372	0.273962	0.087	0.33	5008	,	,		18725	0.3958		0.3827	False		,,,				2504	0.2495				p.G373R		Atlas-SNP	.											TRIM49,NS,carcinoma,0,1	TRIM49	45	1	1	Substitution - Missense(1)	stomach(1)	c.G1117A						PASS	.	C	ARG/GLY	710,3652		161,388,1632	76.0	83.0	81.0		1117	-1.8	0.0	11	dbSNP_120	81	3282,5312		714,1854,1729	no	missense	TRIM49	NM_020358.2	125	875,2242,3361	TT,TC,CC		38.1894,16.2769,30.812	possibly-damaging	373/453	89531540	3992,8964	2181	4297	6478	SO:0001583	missense	57093	exon8			CCTTTCCATCTAT	AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13431	protein-coding gene	gene with protein product		606124	"""ring finger protein 18"", ""tripartite motif-containing 49"""	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.1117G>A	11.37:g.89531540C>T	ENSP00000327604:p.Gly373Arg	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	223	188	0.843049	NM_020358	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	ENST00000329758.1	37	CCDS8287.1	625	0.28617216117216115	46	0.09349593495934959	100	0.27624309392265195	222	0.3881118881118881	257	0.3390501319261214	C	8.805	0.933832	0.18206	0.162769	0.381894	ENSG00000168930	ENST00000329758;ENST00000532501	T	0.67865	-0.29	1.04	-1.8	0.07907	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.00012	0.0000	N	0.17248	0.465	0.80722	P	0.0	P	0.44380	0.834	P	0.52598	0.703	T	0.15065	-1.0450	7	.	.	.	.	1.806	0.03081	0.318:0.4353:0.0:0.2467	rs12417980	373	P0CI25	TRI49_HUMAN	R	373;296	ENSP00000327604:G373R	.	G	-	1	0	TRIM49	89171188	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.015000	0.12634	-0.534000	0.06315	0.194000	0.17425	GGA	C|0.707;T|0.293	0.293	strong		0.428	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358	
KIF17	57576	hgsc.bcm.edu	37	1	21031046	21031046	+	Silent	SNP	C	C	T	rs2296226	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:21031046C>T	ENST00000247986.2	-	5	1327	c.1017G>A	c.(1015-1017)ccG>ccA	p.P339P	KIF17_ENST00000400463.3_Silent_p.P339P|KIF17_ENST00000375044.1_Silent_p.P239P			Q9P2E2	KIF17_HUMAN	kinesin family member 17	339					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)	p.P339P(1)		NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CATTGATGCGCGGCTTGTTCC	0.602													C|||	930	0.185703	0.23	0.1354	5008	,	,		17402	0.3998		0.0507	False		,,,				2504	0.0798				p.P339P		Atlas-SNP	.											KIF17,colon,carcinoma,0,1	KIF17	130	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1017A						PASS	.	C	,	886,3520	346.2+/-308.9	103,680,1420	158.0	119.0	132.0		1017,1017	-10.5	0.1	1	dbSNP_100	132	415,8185	130.2+/-188.1	10,395,3895	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	113,1075,5315	TT,TC,CC		4.8256,20.1089,10.0031	,	339/1029,339/1030	21031046	1301,11705	2203	4300	6503	SO:0001819	synonymous_variant	57576	exon5			GATGCGCGGCTTG	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1017G>A	1.37:g.21031046C>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	239	138	0.577406	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			C|0.878;T|0.122	0.122	strong		0.602	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
TPGS1	91978	hgsc.bcm.edu	37	19	507731	507731	+	Silent	SNP	C	C	T	rs16990489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:507731C>T	ENST00000359315.5	+	1	433	c.225C>T	c.(223-225)ggC>ggT	p.G75G	AC005775.2_ENST00000592413.1_RNA	NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	75					adult behavior (GO:0030534)|multicellular organismal development (GO:0007275)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|synaptic transmission (GO:0007268)|vesicle localization (GO:0051648)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)	tubulin-glutamic acid ligase activity (GO:0070740)										AGAACATGGGCCTGCGCTCGC	0.711													C|||	93	0.0185703	0.0545	0.0173	5008	,	,		12412	0.0		0.0089	False		,,,				2504	0.0				p.G75G		Atlas-SNP	.											.	.	.	.	0			c.C225T						PASS	.	C		140,3414		1,138,1638	7.0	10.0	9.0		225	2.2	1.0	19	dbSNP_123	9	51,7895		0,51,3922	no	coding-synonymous	C19orf20	NM_033513.2		1,189,5560	TT,TC,CC		0.6418,3.9392,1.6609		75/291	507731	191,11309	1777	3973	5750	SO:0001819	synonymous_variant	91978	exon1			CATGGGCCTGCGC	BC009520	CCDS42454.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000141933	ENSG00000141933			25058	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 20"""	C19orf20		11441184, 12972506	Standard	NM_033513		Approved	GTRGEO22, PGs1	uc002lou.3	Q6ZTW0		ENST00000359315.5:c.225C>T	19.37:g.507731C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	24	14	0.583333	NM_033513	Q96GE2	Silent	SNP	ENST00000359315.5	37	CCDS42454.1																																																																																			C|0.974;T|0.026	0.026	strong		0.711	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513	
MSH4	4438	hgsc.bcm.edu	37	1	76344705	76344705	+	Silent	SNP	T	T	C	rs5745448	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:76344705T>C	ENST00000263187.3	+	12	1673	c.1569T>C	c.(1567-1569)taT>taC	p.Y523Y		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	523					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						GAGAAAAATATAGTCTACCTT	0.333								Mismatch excision repair (MMR)					T|||	1690	0.33746	0.0242	0.2349	5008	,	,		16425	0.6964		0.3022	False		,,,				2504	0.5				p.Y523Y		Atlas-SNP	.											.	MSH4	147	.	0			c.T1569C						PASS	.	T		380,4026	189.2+/-215.4	14,352,1837	85.0	86.0	85.0		1569	-3.1	0.3	1	dbSNP_114	85	2784,5814	440.8+/-359.6	452,1880,1967	no	coding-synonymous	MSH4	NM_002440.3		466,2232,3804	CC,CT,TT		32.3796,8.6246,24.331		523/937	76344705	3164,9840	2203	4299	6502	SO:0001819	synonymous_variant	4438	exon12			AAAATATAGTCTA	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"""mutS (E. coli) homolog 4"", ""mutS homolog 4 (E. coli)"""			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.1569T>C	1.37:g.76344705T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Silent	SNP	ENST00000263187.3	37	CCDS670.1																																																																																			T|0.728;C|0.272	0.272	strong		0.333	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	
MEFV	4210	hgsc.bcm.edu	37	16	3293922	3293922	+	Intron	SNP	A	A	T	rs1231123	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3293922A>T	ENST00000219596.1	-	9	1799				MEFV_ENST00000536379.1_Intron|MEFV_ENST00000339854.4_Intron|MEFV_ENST00000541159.1_Missense_Mutation_p.D424E	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever						inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						AGGGAAAAAAATCCTGAGCAT	0.502													G|||	1559	0.311302	0.2784	0.3646	5008	,	,		19521	0.2808		0.4414	False		,,,				2504	0.2157				p.D424E		Atlas-SNP	.											.	MEFV	170	.	0			c.T1272A						PASS	.	G	,GLU/ASP	1317,3077		193,931,1073	36.0	37.0	37.0		,1272	-1.4	0.0	16	dbSNP_87	37	3954,4646		950,2054,1296	yes	intron,missense	MEFV	NM_000243.2,NM_001198536.1	,45	1143,2985,2369	TT,TA,AA		45.9767,29.9727,40.5649	,	,424/446	3293922	5271,7723	2197	4300	6497	SO:0001627	intron_variant	4210	exon8			AAAAAAATCCTGA	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1760-30T>A	16.37:g.3293922A>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_001198536	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	37	CCDS10498.1	747	0.34203296703296704	118	0.23983739837398374	130	0.35911602209944754	164	0.2867132867132867	335	0.4419525065963061	G	16.71	3.199416	0.58126	0.299727	0.459767	ENSG00000103313	ENST00000541159	T	0.62232	0.04	4.99	-1.4	0.08968	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.42682	-0.9437	5	.	.	.	.	1.6153	0.02702	0.4923:0.1343:0.2325:0.1409	rs1231123;rs3843146;rs17609946;rs1231123	.	.	.	E	424	ENSP00000438711:D424E	.	D	-	3	2	MEFV	3233923	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.068000	0.11561	-0.780000	0.04553	-0.812000	0.03155	GAT	A|0.656;T|0.344	0.344	strong		0.502	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
BEND7	222389	hgsc.bcm.edu	37	10	13481427	13481427	+	Silent	SNP	T	T	A	rs12415754	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:13481427T>A	ENST00000396900.2	-	9	1304	c.1305A>T	c.(1303-1305)tcA>tcT	p.S435S	BEND7_ENST00000341083.3_Silent_p.S384S|BEND7_ENST00000486542.1_5'UTR			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	435						extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						TTGTCTGAGGTGAGCTCTGCA	0.537													T|||	1668	0.333067	0.0257	0.3401	5008	,	,		20712	0.6667		0.3559	False		,,,				2504	0.3763				p.S384S		Atlas-SNP	.											.	BEND7	85	.	0			c.A1152T						PASS	.	T		354,4052	182.6+/-210.3	12,330,1861	105.0	92.0	97.0		1152	-0.7	0.0	10	dbSNP_120	97	2890,5710	452.6+/-363.0	484,1922,1894	no	coding-synonymous	BEND7	NM_152751.2		496,2252,3755	AA,AT,TT		33.6047,8.0345,24.9423		384/469	13481427	3244,9762	2203	4300	6503	SO:0001819	synonymous_variant	222389	exon9			CTGAGGTGAGCTC	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.1305A>T	10.37:g.13481427T>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_152751	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				T|0.703;A|0.297	0.297	strong		0.537	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
ZNF485	220992	hgsc.bcm.edu	37	10	44104101	44104101	+	Missense_Mutation	SNP	C	C	T	rs45545532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:44104101C>T	ENST00000361807.3	+	3	258	c.64C>T	c.(64-66)Cgg>Tgg	p.R22W	ZNF485_ENST00000374437.2_Intron|ZNF485_ENST00000374435.3_Missense_Mutation_p.R22W	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	22	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GGCCTTTACCCGGATTGAGTG	0.562													C|||	312	0.0623003	0.056	0.0865	5008	,	,		17332	0.0119		0.1163	False		,,,				2504	0.0501				p.R22W		Atlas-SNP	.											.	ZNF485	102	.	0			c.C64T						PASS	.	C	TRP/ARG	98,1286		5,88,599	171.0	161.0	164.0		64	2.0	0.0	10	dbSNP_127	164	431,2751		33,365,1193	yes	missense	ZNF485	NM_145312.3	101	38,453,1792	TT,TC,CC		13.5449,7.0809,11.5856	possibly-damaging	22/442	44104101	529,4037	692	1591	2283	SO:0001583	missense	220992	exon3			TTTACCCGGATTG	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.64C>T	10.37:g.44104101C>T	ENSP00000354694:p.Arg22Trp	Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	331	160	0.483384	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	37	CCDS7205.2	165	0.07554945054945054	26	0.052845528455284556	40	0.11049723756906077	8	0.013986013986013986	91	0.12005277044854881	C	13.31	2.199318	0.38806	0.070809	0.135449	ENSG00000198298	ENST00000361807;ENST00000430885;ENST00000374435	T;T;T	0.01887	4.58;4.58;4.58	2.96	2.04	0.26737	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	N	0.04148	-0.265	0.51482	P	7.199999999996098E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.45440	-0.9261	8	0.45353	T	0.12	.	4.2694	0.10778	0.0:0.6208:0.2395:0.1397	rs45545532;rs61729737	22	Q8NCK3	ZN485_HUMAN	W	22	ENSP00000354694:R22W;ENSP00000393570:R22W;ENSP00000363558:R22W	ENSP00000354694:R22W	R	+	1	2	ZNF485	43424107	0.000000	0.05858	0.015000	0.15790	0.921000	0.55340	-0.817000	0.04472	0.567000	0.29293	0.462000	0.41574	CGG	C|0.915;T|0.085	0.085	strong		0.562	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
SORL1	6653	hgsc.bcm.edu	37	11	121475922	121475922	+	Silent	SNP	T	T	A	rs3824968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:121475922T>A	ENST00000260197.7	+	34	4881	c.4752T>A	c.(4750-4752)gcT>gcA	p.A1584A	SORL1_ENST00000534286.1_Silent_p.A494A|SORL1_ENST00000527934.1_Silent_p.A199A|SORL1_ENST00000525532.1_Silent_p.A528A|SORL1_ENST00000532694.1_Silent_p.A430A	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1584	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		TGCCCTCTGCTTCTTGTGTAT	0.433													T|||	1984	0.396166	0.1324	0.4899	5008	,	,		19405	0.5883		0.3032	False		,,,				2504	0.5838				p.A1584A		Atlas-SNP	.											.	SORL1	218	.	0			c.T4752A						PASS	.	T		644,3762	275.7+/-272.7	51,542,1610	139.0	137.0	138.0		4752	-1.7	1.0	11	dbSNP_107	138	2671,5927	430.8+/-356.6	392,1887,2020	no	coding-synonymous	SORL1	NM_003105.5		443,2429,3630	AA,AT,TT		31.0654,14.6164,25.4922		1584/2215	121475922	3315,9689	2203	4299	6502	SO:0001819	synonymous_variant	6653	exon34			CTCTGCTTCTTGT	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.4752T>A	11.37:g.121475922T>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	37	CCDS8436.1																																																																																			T|0.706;A|0.294	0.294	strong		0.433	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
KLRC4	8302	hgsc.bcm.edu	37	12	10562089	10562089	+	Missense_Mutation	SNP	A	A	C	rs1841958	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10562089A>C	ENST00000309384.1	-	1	267	c.86T>G	c.(85-87)aTc>aGc	p.I29S	KLRC4-KLRK1_ENST00000539300.1_Missense_Mutation_p.N20K	NM_013431.2	NP_038459.1	O43908	NKG2F_HUMAN	killer cell lectin-like receptor subfamily C, member 4	29			I -> S (in allele NKG2-F*02; dbSNP:rs1841958). {ECO:0000269|PubMed:11751968, ECO:0000269|PubMed:9394807, ECO:0000269|PubMed:9598306, ECO:0000269|PubMed:9683661}.		cellular defense response (GO:0006968)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						TGAAATGGAGATTTTATTGCC	0.413													C|||	3691	0.737021	0.6558	0.8012	5008	,	,		18416	0.7431		0.6789	False		,,,				2504	0.8548				p.I29S		Atlas-SNP	.											.	KLRC4	23	.	0			c.T86G						PASS	.	C	,SER/ILE	2870,1536	486.0+/-360.5	945,980,278	231.0	222.0	225.0		,86	-1.6	0.0	12	dbSNP_92	225	5880,2720	435.7+/-358.1	2036,1808,456	no	intron,missense	KLRC4,KLRC4-KLRK1	NM_001199805.1,NM_013431.2	,142	2981,2788,734	CC,CA,AA		31.6279,34.8616,32.7234	,benign	,29/159	10562089	8750,4256	2203	4300	6503	SO:0001583	missense	8302	exon1			ATGGAGATTTTAT	U96846	CCDS8624.1	12p13.2-p12.3	2008-08-05			ENSG00000183542	ENSG00000183542		"""Killer cell lectin-like receptors"""	6377	protein-coding gene	gene with protein product		602893				9598306	Standard	NM_013431		Approved	NKG2-F	uc001qye.3	O43908	OTTHUMG00000168575	ENST00000309384.1:c.86T>G	12.37:g.10562089A>C	ENSP00000310216:p.Ile29Ser	Somatic	366	0	0		WXS	Illumina HiSeq	Phase_I	463	463	1	NM_013431	O60851	Missense_Mutation	SNP	ENST00000309384.1	37	CCDS8624.1	1596	0.7307692307692307	355	0.7215447154471545	279	0.7707182320441989	450	0.7867132867132867	512	0.6754617414248021	C	0.007	-1.951907	0.00470	0.651384	0.683721	ENSG00000183542	ENST00000309384	T	0.04454	3.62	3.78	-1.6	0.08426	.	0.817801	0.11116	N	0.598017	T	0.00012	0.0000	N	0.00023	-2.71	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38802	-0.9644	9	0.02654	T	1	.	0.1569	0.00099	0.305:0.2537:0.1496:0.2917	rs1841958;rs17549011;rs52833411;rs1841958	29	O43908	NKG2F_HUMAN	S	29	ENSP00000310216:I29S	ENSP00000310216:I29S	I	-	2	0	KLRC4	10453356	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.559000	0.05971	-0.540000	0.06265	-2.648000	0.00150	ATC	A|0.302;C|0.698	0.698	strong		0.413	KLRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400108.1	NM_013431	
TTLL4	9654	hgsc.bcm.edu	37	2	219602499	219602499	+	Missense_Mutation	SNP	G	G	C	rs3731877	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219602499G>C	ENST00000392102.1	+	3	440	c.100G>C	c.(100-102)Gag>Cag	p.E34Q	TTLL4_ENST00000442769.1_Missense_Mutation_p.E34Q|TTLL4_ENST00000457313.1_Intron|TTLL4_ENST00000258398.4_Missense_Mutation_p.E34Q	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	34			E -> Q (in dbSNP:rs3731877). {ECO:0000269|PubMed:8724849}.		protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CACGCCACCTGAGAAACCCTC	0.557													G|||	2020	0.403355	0.6006	0.4222	5008	,	,		19525	0.1409		0.4662	False		,,,				2504	0.3292				p.E34Q	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											TTLL4,brain,glioma,0,1	TTLL4	96	1	0			c.G100C						PASS	.	G	GLN/GLU	2578,1828	637.9+/-396.8	756,1066,381	65.0	67.0	66.0		100	5.5	1.0	2	dbSNP_107	66	4082,4518	561.4+/-387.8	987,2108,1205	yes	missense	TTLL4	NM_014640.4	29	1743,3174,1586	CC,CG,GG		47.4651,41.4889,48.7929	probably-damaging	34/1200	219602499	6660,6346	2203	4300	6503	SO:0001583	missense	9654	exon3			CCACCTGAGAAAC		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"""Tubulin tyrosine ligase-like family"""	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.100G>C	2.37:g.219602499G>C	ENSP00000375951:p.Glu34Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	146	145	0.993151	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	910	0.4166666666666667	317	0.6443089430894309	151	0.4171270718232044	90	0.15734265734265734	352	0.46437994722955145	G	15.17	2.754812	0.49362	0.585111	0.474651	ENSG00000135912	ENST00000415717;ENST00000392102;ENST00000437755;ENST00000442769;ENST00000424644;ENST00000258398	T;T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75;1.75	5.53	5.53	0.82687	.	0.114147	0.39475	N	0.001342	T	0.00012	0.0000	L	0.34521	1.04	0.39370	P	0.03393400000000002	P;P	0.37330	0.59;0.59	B;B	0.33196	0.159;0.159	T	0.28808	-1.0032	9	0.66056	D	0.02	.	13.9947	0.64390	0.0:0.151:0.849:0.0	rs3731877;rs52824369;rs3731877	34;34	E7EX20;Q14679	.;TTLL4_HUMAN	Q	34	ENSP00000411228:E34Q;ENSP00000375951:E34Q;ENSP00000391342:E34Q;ENSP00000396555:E34Q;ENSP00000405485:E34Q;ENSP00000258398:E34Q	ENSP00000258398:E34Q	E	+	1	0	TTLL4	219310743	0.985000	0.35326	0.992000	0.48379	0.444000	0.32077	3.127000	0.50484	2.601000	0.87937	0.563000	0.77884	GAG	G|0.525;C|0.475	0.475	strong		0.557	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249829	3249829	+	Silent	SNP	G	G	A	rs11026040	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:3249829G>A	ENST00000389832.5	-	2	507	c.201C>T	c.(199-201)tgC>tgT	p.C67C	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Silent_p.C66C			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGAGATCCGCGCAGGCCACGT	0.637													G|||	1131	0.225839	0.2776	0.3213	5008	,	,		18071	0.13		0.1431	False		,,,				2504	0.272				p.C67C		Atlas-SNP	.											.	MRGPRE	35	.	0			c.C201T						PASS	.	G		1085,3169		138,809,1180	79.0	97.0	91.0		198	-7.0	0.0	11	dbSNP_120	91	1029,7463		57,915,3274	no	coding-synonymous	MRGPRE	NM_001039165.2		195,1724,4454	AA,AG,GG		12.1173,25.5054,16.5856		66/312	3249829	2114,10632	2127	4246	6373	SO:0001819	synonymous_variant	116534	exon2			ATCCGCGCAGGCC	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"""GPCR / Class A : Orphans"""	30694	protein-coding gene	gene with protein product		607232	"""G protein-coupled receptor 167"""	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.201C>T	11.37:g.3249829G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001039165	Q2M1V7	Silent	SNP	ENST00000389832.5	37																																																																																				A|0.172;G|0.828	0.172	strong		0.637	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
ITPR3	3710	hgsc.bcm.edu	37	6	33651129	33651129	+	Silent	SNP	C	C	T	rs942636	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33651129C>T	ENST00000374316.5	+	36	5803	c.4743C>T	c.(4741-4743)ccC>ccT	p.P1581P	ITPR3_ENST00000605930.1_Silent_p.P1581P			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1581					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GCGTCACCCCCACCGCCAACC	0.642													C|||	945	0.188698	0.1664	0.3357	5008	,	,		17048	0.1012		0.2008	False		,,,				2504	0.1922				p.P1581P		Atlas-SNP	.											.	ITPR3	409	.	0			c.C4743T						PASS	.	C		777,3615		74,629,1493	20.0	17.0	18.0		4743	2.7	1.0	6	dbSNP_86	18	1398,7194		115,1168,3013	no	coding-synonymous	ITPR3	NM_002224.3		189,1797,4506	TT,TC,CC		16.2709,17.6913,16.7514		1581/2672	33651129	2175,10809	2196	4296	6492	SO:0001819	synonymous_variant	3710	exon35			CACCCCCACCGCC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.4743C>T	6.37:g.33651129C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.835;T|0.165	0.165	strong		0.642	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
NRAP	4892	hgsc.bcm.edu	37	10	115389356	115389356	+	Silent	SNP	G	G	A	rs2286736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115389356G>A	ENST00000359988.3	-	19	2275	c.2031C>T	c.(2029-2031)ctC>ctT	p.L677L	NRAP_ENST00000369360.3_Silent_p.L650L|NRAP_ENST00000369358.4_Silent_p.L685L|NRAP_ENST00000360478.3_Silent_p.L642L	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CCTCGCTCTGGAGCCCATAGG	0.483													G|||	1376	0.27476	0.1823	0.3948	5008	,	,		20478	0.2817		0.2962	False		,,,				2504	0.2853				p.L677L		Atlas-SNP	.											.	NRAP	208	.	0			c.C2031T						PASS	.	G	,	940,3466	354.4+/-312.6	96,748,1359	110.0	92.0	98.0		1926,2031	-0.3	1.0	10	dbSNP_100	98	2620,5980	424.4+/-354.6	371,1878,2051	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	467,2626,3410	AA,AG,GG		30.4651,21.3345,27.372	,	642/1696,677/1731	115389356	3560,9446	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon19			GCTCTGGAGCCCA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2031C>T	10.37:g.115389356G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			G|0.727;A|0.273	0.273	strong		0.483	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
ZNRF3	84133	hgsc.bcm.edu	37	22	29446745	29446745	+	Missense_Mutation	SNP	G	G	A	rs200918833		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29446745G>A	ENST00000544604.2	+	8	2751	c.2576G>A	c.(2575-2577)cGa>cAa	p.R859Q	ZNRF3_ENST00000406323.3_Missense_Mutation_p.R759Q|ZNRF3_ENST00000402174.1_Missense_Mutation_p.R759Q|ZNRF3_ENST00000332811.4_Missense_Mutation_p.R759Q	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	859					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GGTGGGACGCGAGGCCCGGAT	0.697																																					p.R859Q		Atlas-SNP	.											ZNRF3,colon,carcinoma,+1,1	ZNRF3	75	1	0			c.G2576A						PASS	.	G	GLN/ARG,GLN/ARG	0,3800		0,0,1900	10.0	13.0	12.0		2576,2276	-3.9	0.0	22		12	2,8206		0,2,4102	no	missense,missense	ZNRF3	NM_001206998.1,NM_032173.3	43,43	0,2,6002	AA,AG,GG		0.0244,0.0,0.0167	benign,benign	859/937,759/837	29446745	2,12006	1900	4104	6004	SO:0001583	missense	84133	exon8			GGACGCGAGGCCC	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"""RING-type (C3HC4) zinc fingers"""	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.2576G>A	22.37:g.29446745G>A	ENSP00000443824:p.Arg859Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	97	60	0.618557	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	37	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	G	1.454	-0.564307	0.03939	0.0	2.44E-4	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	T;T;T;T	0.07908	3.3;3.15;3.15;3.15	5.83	-3.93	0.04143	.	1.507060	0.04173	N	0.325138	T	0.03564	0.0102	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.39272	-0.9622	10	0.20046	T	0.44	0.1821	2.947	0.05849	0.1045:0.5688:0.1319:0.1948	.	859	Q9ULT6	ZNRF3_HUMAN	Q	859;759;566;759;759	ENSP00000443824:R859Q;ENSP00000328614:R759Q;ENSP00000384456:R759Q;ENSP00000384553:R759Q	ENSP00000328614:R759Q	R	+	2	0	ZNRF3	27776745	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.676000	0.05221	-1.095000	0.03050	-1.114000	0.02060	CGA	.	.	weak		0.697	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972	
FMNL2	114793	hgsc.bcm.edu	37	2	153435434	153435434	+	Silent	SNP	C	C	T	rs16831399	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:153435434C>T	ENST00000288670.9	+	8	1105	c.738C>T	c.(736-738)caC>caT	p.H246H		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	246	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CTCATCCACACGCTGTCAATG	0.388													C|||	715	0.142772	0.2897	0.1268	5008	,	,		19052	0.0367		0.1312	False		,,,				2504	0.0767				p.H246H		Atlas-SNP	.											.	FMNL2	75	.	0			c.C738T						PASS	.	C		971,2891		126,719,1086	78.0	75.0	76.0		738	-0.8	1.0	2	dbSNP_123	76	1127,7203		75,977,3113	no	coding-synonymous	FMNL2	NM_052905.3		201,1696,4199	TT,TC,CC		13.5294,25.1424,17.208		246/1093	153435434	2098,10094	1931	4165	6096	SO:0001819	synonymous_variant	114793	exon8			TCCACACGCTGTC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.738C>T	2.37:g.153435434C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																			C|0.842;N|0.000	.	strong		0.388	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
TFEB	7942	hgsc.bcm.edu	37	6	41652514	41652514	+	Silent	SNP	C	C	T	rs2073158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41652514C>T	ENST00000230323.4	-	10	1555	c.1254G>A	c.(1252-1254)gcG>gcA	p.A418A	TFEB_ENST00000403298.4_Silent_p.A418A|TFEB_ENST00000358871.2_Silent_p.A432A|AL035588.1_ENST00000597468.1_5'Flank|TFEB_ENST00000373033.1_Silent_p.A418A|TFEB_ENST00000420312.1_Silent_p.A333A	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	418					autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			CATGCCCCGGCGCCAGGGGTT	0.647			T	ALPHA	renal (childhood epithelioid)								C|||	989	0.197484	0.0749	0.183	5008	,	,		14273	0.3194		0.1998	False		,,,				2504	0.2454				p.A432A		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"""E,M"""	TFEB,NS,carcinoma,-1,1	TFEB	37	1	0			c.G1296A						PASS	.	C	,	385,4019	183.6+/-211.2	14,357,1831	34.0	36.0	35.0		1254,1254	4.3	1.0	6	dbSNP_96	35	1681,6919	294.2+/-301.7	175,1331,2794	no	coding-synonymous,coding-synonymous	TFEB	NM_001167827.1,NM_007162.2	,	189,1688,4625	TT,TC,CC		19.5465,8.7421,15.8874	,	418/477,418/477	41652514	2066,10938	2202	4300	6502	SO:0001819	synonymous_variant	7942	exon9			CCCCGGCGCCAGG	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"""Basic helix-loop-helix proteins"""	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.1254G>A	6.37:g.41652514C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	179	100	0.558659	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Silent	SNP	ENST00000230323.4	37	CCDS4858.1																																																																																			C|0.832;T|0.168	0.168	strong		0.647	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		
FAM26D	221301	hgsc.bcm.edu	37	6	116875493	116875493	+	Silent	SNP	T	T	C	rs9387420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116875493T>C	ENST00000368596.3	+	1	581	c.537T>C	c.(535-537)ctT>ctC	p.L179L	FAM26D_ENST00000405399.1_Silent_p.L36L|FAM26D_ENST00000368597.2_Intron|FAM26D_ENST00000416171.2_Silent_p.L35L			Q5JW98	FA26D_HUMAN	family with sequence similarity 26, member D	179					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				endometrium(1)|lung(5)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0458)|OV - Ovarian serous cystadenocarcinoma(136;0.0694)|Epithelial(106;0.222)		AAATAGCTCTTCTGCACAGAT	0.408													T|||	1127	0.22504	0.1528	0.1542	5008	,	,		21118	0.3482		0.17	False		,,,				2504	0.3027				p.L36L		Atlas-SNP	.											.	FAM26D	29	.	0			c.T108C						PASS	.																																			SO:0001819	synonymous_variant	221301	exon3			AGCTCTTCTGCAC	AK056801	CCDS5109.1, CCDS59032.1	6q22.31	2008-02-05	2007-03-19	2007-03-19	ENSG00000164451	ENSG00000164451			21094	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 78"""	C6orf78			Standard	NM_153036		Approved	FLJ32239	uc010ked.4	Q5JW98	OTTHUMG00000015443	ENST00000368596.3:c.537T>C	6.37:g.116875493T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_001256887	B0QZ25|B0QZ27|B4DTQ0|Q96MK0	Silent	SNP	ENST00000368596.3	37																																																																																				C|0.205;N|0.000	0.205	strong		0.408	FAM26D-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000041958.1	NM_153036	
PREX2	80243	hgsc.bcm.edu	37	8	68993013	68993013	+	Silent	SNP	A	A	G	rs12682458|rs368406603	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:68993013A>G	ENST00000288368.4	+	17	2095	c.1818A>G	c.(1816-1818)ggA>ggG	p.G606G	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	606	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ATGGCTTTGGATTAGAAGACA	0.279													G|||	2624	0.523962	0.5318	0.4524	5008	,	,		18396	0.4722		0.5696	False		,,,				2504	0.5706				p.G606G		Atlas-SNP	.											.	PREX2	614	.	0			c.A1818G						PASS	.	G	,	2363,2041	529.8+/-372.8	653,1057,492	66.0	71.0	69.0		1818,1818	-4.0	0.9	8	dbSNP_120	69	4662,3932	529.9+/-381.7	1290,2082,925	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	1943,3139,1417	GG,GA,AA		45.7529,46.3442,45.9532	,	606/1607,606/980	68993013	7025,5973	2202	4297	6499	SO:0001819	synonymous_variant	80243	exon17			CTTTGGATTAGAA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1818A>G	8.37:g.68993013A>G		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	202	202	1	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			.	.	alt		0.279	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
FBN3	84467	hgsc.bcm.edu	37	19	8191401	8191401	+	Silent	SNP	G	G	A	rs3813778	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8191401G>A	ENST00000600128.1	-	20	2919	c.2505C>T	c.(2503-2505)tgC>tgT	p.C835C	FBN3_ENST00000601739.1_Silent_p.C835C|FBN3_ENST00000270509.2_Silent_p.C835C			Q75N90	FBN3_HUMAN	fibrillin 3	835	TB 4.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CGAGGGTGGCGCAGCACTCAG	0.647													G|||	1316	0.26278	0.1309	0.2637	5008	,	,		15115	0.2758		0.4404	False		,,,				2504	0.2444				p.C835C		Atlas-SNP	.											FBN3,NS,carcinoma,0,1	FBN3	300	1	0			c.C2505T						PASS	.	G		759,3645	298.1+/-285.1	77,605,1520	28.0	28.0	28.0		2505	-5.3	1.0	19	dbSNP_107	28	3876,4724	528.5+/-381.4	865,2146,1289	no	coding-synonymous	FBN3	NM_032447.3		942,2751,2809	AA,AG,GG		45.0698,17.2343,35.6429		835/2810	8191401	4635,8369	2202	4300	6502	SO:0001819	synonymous_variant	84467	exon19			GGTGGCGCAGCAC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.2505C>T	19.37:g.8191401G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	38	0.622951	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.684;A|0.316	0.316	strong		0.647	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
LRIG1	26018	hgsc.bcm.edu	37	3	66430811	66430811	+	Missense_Mutation	SNP	T	T	G	rs2279290	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:66430811T>G	ENST00000273261.3	-	19	3682	c.3158A>C	c.(3157-3159)cAg>cCg	p.Q1053P	SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.Q1030P|LRIG1_ENST00000496559.2_5'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	1053			Q -> P (in dbSNP:rs2279290).		innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AAGCAAGTACTGGGCTTCCGC	0.567													T|||	541	0.108027	0.084	0.1138	5008	,	,		18725	0.0556		0.1958	False		,,,				2504	0.1002				p.Q1053P		Atlas-SNP	.											.	LRIG1	138	.	0			c.A3158C						PASS	.	T	PRO/GLN	426,3980	206.5+/-228.1	21,384,1798	114.0	113.0	113.0		3158	3.1	1.0	3	dbSNP_100	113	1726,6874	315.0+/-312.1	181,1364,2755	yes	missense	LRIG1	NM_015541.2	76	202,1748,4553	GG,GT,TT		20.0698,9.6686,16.5462	possibly-damaging	1053/1094	66430811	2152,10854	2203	4300	6503	SO:0001583	missense	26018	exon19			AAGTACTGGGCTT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.3158A>C	3.37:g.66430811T>G	ENSP00000273261:p.Gln1053Pro	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	272	0.12454212454212454	42	0.08536585365853659	46	0.1270718232044199	30	0.05244755244755245	154	0.20316622691292877	T	10.08	1.252740	0.22965	0.096686	0.200698	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.67171	-0.21;-0.25	5.54	3.13	0.36017	.	0.119598	0.38272	N	0.001745	T	0.00109	0.0003	L	0.51422	1.61	0.80722	P	0.0	P;B;B	0.34757	0.467;0.347;0.229	B;B;B	0.31686	0.134;0.043;0.026	T	0.06180	-1.0841	9	0.51188	T	0.08	.	9.9676	0.41734	0.0:0.1399:0.0:0.8601	rs2279290;rs17774921;rs2279290	1030;1053;1053	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	P	1053;1030;956	ENSP00000273261:Q1053P;ENSP00000373208:Q1030P	ENSP00000273261:Q1053P	Q	-	2	0	LRIG1	66513501	1.000000	0.71417	0.984000	0.44739	0.036000	0.12997	2.859000	0.48364	0.931000	0.37242	0.533000	0.62120	CAG	T|0.854;G|0.146	0.146	strong		0.567	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
SEC14L2	23541	hgsc.bcm.edu	37	22	30793137	30793137	+	Missense_Mutation	SNP	G	G	A	rs757660	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30793137G>A	ENST00000312932.9	+	1	292	c.32G>A	c.(31-33)aGg>aAg	p.R11K	SEC14L2_ENST00000403484.1_5'UTR|SEC14L2_ENST00000459728.1_3'UTR|SEC14L2_ENST00000402592.3_Missense_Mutation_p.R11K|SEC14L2_ENST00000405717.3_Missense_Mutation_p.R11K	NM_012429.3	NP_036561.1	O76054	S14L2_HUMAN	SEC14-like 2 (S. cerevisiae)	11			R -> K (in dbSNP:rs757660). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.8}.		positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cholesterol biosynthetic process (GO:0045540)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	10					Vitamin E(DB00163)	CTGAGCCCCAGGCAGAAGGAG	0.716													A|||	1857	0.370807	0.4085	0.3617	5008	,	,		10837	0.3849		0.3121	False		,,,				2504	0.3722				p.R11K		Atlas-SNP	.											.	SEC14L2	24	.	0			c.G32A						PASS	.	A	LYS/ARG,LYS/ARG,LYS/ARG	1467,2675		287,893,891	17.0	13.0	14.0		32,32,32	0.6	1.0	22	dbSNP_86	14	2010,6066		255,1500,2283	yes	missense,missense,missense	SEC14L2	NM_001204204.1,NM_012429.3,NM_033382.2	26,26,26	542,2393,3174	AA,AG,GG		24.8886,35.4177,28.458	benign,benign,benign	11/321,11/404,11/393	30793137	3477,8741	2071	4038	6109	SO:0001583	missense	23541	exon1			GCCCCAGGCAGAA	AL096881	CCDS13876.1, CCDS46685.1, CCDS56228.1	22q12.2	2010-08-19	2001-11-28		ENSG00000100003	ENSG00000100003			10699	protein-coding gene	gene with protein product	"""supernatant protein factor"""	607558	"""SEC14 (S. cerevisiae)-like 2"""	C22orf6		10591208	Standard	NM_033382		Approved	TAP, SPF, KIAA1186, KIAA1658	uc003ahr.3	O76054	OTTHUMG00000151024	ENST00000312932.9:c.32G>A	22.37:g.30793137G>A	ENSP00000316203:p.Arg11Lys	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	102	41	0.401961	NM_001204204	B7Z8Q1|F5H3U4|Q53EQ2|Q6PD61|Q9ULN4	Missense_Mutation	SNP	ENST00000312932.9	37	CCDS13876.1	795	0.364010989010989	216	0.43902439024390244	118	0.3259668508287293	221	0.38636363636363635	240	0.316622691292876	A	6.498	0.460151	0.12342	0.354177	0.248886	ENSG00000100003	ENST00000312932;ENST00000416523;ENST00000405717;ENST00000402592	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	4.15	0.645	0.17782	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.138996	0.47852	N	0.000208	T	0.00012	0.0000	N	0.00521	-1.4	0.09310	P	0.99999999615629	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45804	-0.9236	9	0.05436	T	0.98	-2.7632	7.7743	0.29029	0.5955:0.0:0.4045:0.0	rs757660;rs11556717;rs52809732;rs60495705;rs757660	11;11;11	F5H3U4;O76054;O76054-4	.;S14L2_HUMAN;.	K	11	ENSP00000316203:R11K;ENSP00000400567:R11K;ENSP00000385186:R11K;ENSP00000383882:R11K	ENSP00000316203:R11K	R	+	2	0	SEC14L2	29123137	0.197000	0.23362	0.956000	0.39512	0.881000	0.50899	0.584000	0.23864	-0.099000	0.12263	-0.361000	0.07541	AGG	G|0.644;A|0.356	0.356	strong		0.716	SEC14L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321018.4	NM_012429	
ALS2CL	259173	hgsc.bcm.edu	37	3	46713457	46713457	+	Silent	SNP	C	C	G	rs7625303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46713457C>G	ENST00000318962.4	-	24	2684	c.2601G>C	c.(2599-2601)acG>acC	p.T867T	ALS2CL_ENST00000383742.3_Silent_p.T214T|ALS2CL_ENST00000415953.1_Silent_p.T867T	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	867	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CCCTCGACACCGTGCCCTCAA	0.642													C|||	1254	0.250399	0.1483	0.2968	5008	,	,		17491	0.38		0.2197	False		,,,				2504	0.2536				p.T867T		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G2601C						PASS	.	C	,,	723,3683	299.8+/-286.0	58,607,1538	124.0	103.0	110.0		2601,2601,642	-10.6	0.7	3	dbSNP_116	110	1848,6752	330.1+/-319.0	197,1454,2649	no	coding-synonymous,coding-synonymous,coding-synonymous	ALS2CL	NM_001190707.1,NM_147129.3,NM_182775.2	,,	255,2061,4187	GG,GC,CC		21.4884,16.4094,19.7678	,,	867/954,867/954,214/301	46713457	2571,10435	2203	4300	6503	SO:0001819	synonymous_variant	259173	exon24			CGACACCGTGCCC	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.2601G>C	3.37:g.46713457C>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Silent	SNP	ENST00000318962.4	37	CCDS2743.1																																																																																			C|0.780;G|0.220	0.220	strong		0.642	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
IL37	27178	hgsc.bcm.edu	37	2	113671410	113671410	+	Missense_Mutation	SNP	A	A	G	rs3811047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113671410A>G	ENST00000263326.3	+	2	166	c.124A>G	c.(124-126)Acc>Gcc	p.T42A	IL37_ENST00000349806.3_Intron|IL37_ENST00000353225.3_Missense_Mutation_p.T42A|IL37_ENST00000352179.3_Intron|IL37_ENST00000311328.2_5'Flank	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	42			T -> A (in dbSNP:rs3811047). {ECO:0000269|PubMed:11145836, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						AAGCCTCCCCACCATGAATTT	0.577													a|||	3092	0.617412	0.2375	0.8055	5008	,	,		14671	0.8115		0.7008	False		,,,				2504	0.7117				p.T42A		Atlas-SNP	.											IL37,NS,carcinoma,-1,1	IL37	56	1	0			c.A124G						PASS	.		ALA/THR,,,ALA/THR	1415,2991	445.1+/-347.6	251,913,1039	88.0	77.0	81.0		124,,,124	1.6	0.0	2	dbSNP_107	81	6032,2568	670.0+/-402.7	2158,1716,426	yes	missense,intron,intron,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1	58,,,58	2409,2629,1465	GG,GA,AA		29.8605,32.1153,42.7418	benign,,,benign	42/219,,,42/179	113671410	7447,5559	2203	4300	6503	SO:0001583	missense	27178	exon2			CTCCCCACCATGA	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"""Interleukins and interleukin receptors"""	15563	protein-coding gene	gene with protein product	"""interleukin 1, zeta"", ""interleukin-1 homolog 4"", ""interleukin-1-related protein"""	605510	"""interleukin 1 family, member 7 (zeta)"""	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.124A>G	2.37:g.113671410A>G	ENSP00000263326:p.Thr42Ala	Somatic	397	3	0.00755668		WXS	Illumina HiSeq	Phase_I	309	308	0.996764	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	1413	0.646978021978022	129	0.2621951219512195	287	0.7928176795580111	466	0.8146853146853147	531	0.7005277044854882	a	6.370	0.436359	0.12104	0.321153	0.701395	ENSG00000125571	ENST00000263326;ENST00000353225	T;T	0.55588	0.51;0.51	2.78	1.6	0.23607	.	0.554710	0.13684	N	0.369998	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39418	-0.9615	9	0.06494	T	0.89	-3.2296	3.5807	0.07952	0.2263:0.0:0.2349:0.5388	rs3811047;rs52828342;rs57284703;rs3811047	42;42	Q9NZH6-3;Q9NZH6	.;IL37_HUMAN	A	42	ENSP00000263326:T42A;ENSP00000309208:T42A	ENSP00000263326:T42A	T	+	1	0	IL37	113387881	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.665000	0.05286	0.068000	0.16574	-1.436000	0.01078	ACC	A|0.399;G|0.601	0.601	strong		0.577	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439	
QSOX2	169714	hgsc.bcm.edu	37	9	139110654	139110654	+	Splice_Site	SNP	C	C	T	rs12684650	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139110654C>T	ENST00000358701.5	-	8	994	c.957G>A	c.(955-957)aaG>aaA	p.K319K		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	319					cell redox homeostasis (GO:0045454)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	thiol oxidase activity (GO:0016972)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		ACAGCTTCGACCTAGGACGGG	0.647													C|||	767	0.153155	0.0098	0.2075	5008	,	,		16290	0.121		0.2873	False		,,,				2504	0.2035				p.K319K		Atlas-SNP	.											.	QSOX2	63	.	0			c.G957A						PASS	.	C		277,4129	154.4+/-187.8	10,257,1936	78.0	63.0	68.0		957	4.0	0.5	9	dbSNP_120	68	2552,6048	415.6+/-351.9	362,1828,2110	yes	coding-synonymous-near-splice	QSOX2	NM_181701.3		372,2085,4046	TT,TC,CC		29.6744,6.2869,21.7515		319/699	139110654	2829,10177	2203	4300	6503	SO:0001630	splice_region_variant	169714	exon8			CTTCGACCTAGGA	AJ318051	CCDS35178.1	9q34.3	2008-02-05	2007-04-23	2007-04-23	ENSG00000165661	ENSG00000165661			30249	protein-coding gene	gene with protein product		612860	"""quiescin Q6-like 1"""	QSCN6L1		12176051	Standard	NM_181701		Approved	SOXN, DKFZp762A2013	uc010nbi.2	Q6ZRP7	OTTHUMG00000020923	ENST00000358701.5:c.957-1G>A	9.37:g.139110654C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Silent	SNP	ENST00000358701.5	37	CCDS35178.1	379	0.17353479853479853	8	0.016260162601626018	75	0.20718232044198895	75	0.13111888111888112	221	0.29155672823219	C	5.417	0.262043	0.10239	0.062869	0.296744	ENSG00000165661	ENST00000455222	.	.	.	4.86	3.96	0.45880	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.19353	-1.0308	3	.	.	.	.	10.2325	0.43264	0.0:0.832:0.0:0.168	rs12684650;rs17602333;rs12684650	.	.	.	I	87	.	.	V	-	1	0	QSOX2	138250475	1.000000	0.71417	0.519000	0.27824	0.049000	0.14656	1.654000	0.37334	1.032000	0.39892	0.436000	0.28706	GTC	C|0.803;N|0.000	.	strong		0.647	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701	Silent
TMEM132C	92293	hgsc.bcm.edu	37	12	129028586	129028586	+	Silent	SNP	C	C	T	rs73426420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:129028586C>T	ENST00000435159.2	+	3	1059	c.1059C>T	c.(1057-1059)agC>agT	p.S353S	TMEM132C_ENST00000315208.8_5'UTR	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	353						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						AGGTGGGCAGCGGCGGAAAGC	0.662													C|||	681	0.135982	0.056	0.0821	5008	,	,		15052	0.2431		0.1302	False		,,,				2504	0.1779				p.S353S		Atlas-SNP	.											.	TMEM132C	142	.	0			c.C1059T						PASS	.	C		74,1310		1,72,619	29.0	41.0	37.0		1059	-4.6	0.0	12	dbSNP_130	37	439,2743		30,379,1182	no	coding-synonymous	TMEM132C	NM_001136103.2		31,451,1801	TT,TC,CC		13.7964,5.3468,11.2352		353/1109	129028586	513,4053	692	1591	2283	SO:0001819	synonymous_variant	92293	exon3			GGGCAGCGGCGGA	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.1059C>T	12.37:g.129028586C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	118	0.967213	NM_001136103	Q69YX8	Silent	SNP	ENST00000435159.2	37																																																																																				C|0.848;T|0.152	0.152	strong		0.662	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
PLA2R1	22925	hgsc.bcm.edu	37	2	160808075	160808075	+	Missense_Mutation	SNP	C	C	T	rs3828323	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160808075C>T	ENST00000283243.7	-	24	3522	c.3316G>A	c.(3316-3318)Ggt>Agt	p.G1106S	PLA2R1_ENST00000392771.1_Missense_Mutation_p.G1106S	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1106			G -> S (in dbSNP:rs3828323).		cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						GTATTTACACCGTGTCCAGAA	0.363													C|||	1249	0.249401	0.0401	0.2824	5008	,	,		22780	0.2917		0.5169	False		,,,				2504	0.1902				p.G1106S		Atlas-SNP	.											.	PLA2R1	153	.	0			c.G3316A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	468,3938	221.3+/-238.5	20,428,1755	116.0	104.0	108.0		3316,3316,3316	-3.0	0.0	2	dbSNP_107	108	4216,4384	570.1+/-389.3	1035,2146,1119	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	56,56,56	1055,2574,2874	TT,TC,CC		49.0233,10.6219,36.0141	benign,benign,benign	1106/1325,1106/1462,1106/1464	160808075	4684,8322	2203	4300	6503	SO:0001583	missense	22925	exon24			TTACACCGTGTCC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3316G>A	2.37:g.160808075C>T	ENSP00000283243:p.Gly1106Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	169	67	0.39645	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	686	0.3141025641025641	27	0.054878048780487805	107	0.2955801104972376	165	0.28846153846153844	387	0.5105540897097626	C	0.031	-1.336677	0.01287	0.106219	0.490233	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.06294	3.39;3.32	5.92	-3.0	0.05480	C-type lectin-like (1);	1.622470	0.03024	N	0.151168	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.44019	-0.9355	9	0.07482	T	0.82	.	4.5914	0.12307	0.0934:0.1082:0.2383:0.5601	rs3828323;rs17232626;rs56981515;rs3828323	1106;1106;1106	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	S	1106	ENSP00000283243:G1106S;ENSP00000376524:G1106S	ENSP00000283243:G1106S	G	-	1	0	PLA2R1	160516321	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.698000	0.05092	-0.402000	0.07633	-1.283000	0.01379	GGT	C|0.679;T|0.321	0.321	strong		0.363	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
CDH6	1004	hgsc.bcm.edu	37	5	31317952	31317952	+	Silent	SNP	T	T	C	rs2229575	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:31317952T>C	ENST00000265071.2	+	11	2068	c.1803T>C	c.(1801-1803)caT>caC	p.H601H	CDH6_ENST00000514738.1_Silent_p.H546H	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	601	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AATCCTGCCATGCGGAGGCGC	0.572													T|||	1950	0.389377	0.062	0.5043	5008	,	,		19805	0.4931		0.5616	False		,,,				2504	0.4663				p.H601H		Atlas-SNP	.											.	CDH6	175	.	0			c.T1803C						PASS	.	T		657,3749	276.9+/-273.4	53,551,1599	61.0	54.0	56.0		1803	-10.6	0.3	5	dbSNP_98	56	4623,3977	595.4+/-393.5	1279,2065,956	no	coding-synonymous	CDH6	NM_004932.3		1332,2616,2555	CC,CT,TT		46.2442,14.9115,40.5966		601/791	31317952	5280,7726	2203	4300	6503	SO:0001819	synonymous_variant	1004	exon11			CTGCCATGCGGAG	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.1803T>C	5.37:g.31317952T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	32	0.4	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			T|0.595;C|0.405	0.405	strong		0.572	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
SGCG	6445	hgsc.bcm.edu	37	13	23898509	23898509	+	Silent	SNP	T	T	C	rs1800353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:23898509T>C	ENST00000218867.3	+	8	829	c.705T>C	c.(703-705)ctT>ctC	p.L235L	SGCG_ENST00000545013.1_Silent_p.L235L|SGCG_ENST00000537476.1_Silent_p.L235L	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	235					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		CCAACCAGCTTGTGCTTGATG	0.522													T|||	3154	0.629792	0.3253	0.7493	5008	,	,		20308	0.748		0.6918	False		,,,				2504	0.771				p.L235L		Atlas-SNP	.											.	SGCG	64	.	0			c.T705C						PASS	.	T		1772,2634	526.2+/-371.8	354,1064,785	91.0	73.0	79.0		705	-4.4	0.9	13	dbSNP_89	79	5722,2878	672.5+/-402.9	1892,1938,470	no	coding-synonymous	SGCG	NM_000231.2		2246,3002,1255	CC,CT,TT		33.4651,40.2179,42.3804		235/292	23898509	7494,5512	2203	4300	6503	SO:0001819	synonymous_variant	6445	exon8			CCAGCTTGTGCTT	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.705T>C	13.37:g.23898509T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	37	CCDS9299.1																																																																																			T|0.406;C|0.594	0.594	strong		0.522	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
GMEB2	26205	hgsc.bcm.edu	37	20	62221766	62221766	+	Silent	SNP	C	C	T	rs2297428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62221766C>T	ENST00000266068.1	-	9	1747	c.1269G>A	c.(1267-1269)ccG>ccA	p.P423P	GMEB2_ENST00000370069.1_Silent_p.P372P|GMEB2_ENST00000370077.1_Silent_p.P423P			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	423					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			GCGGGGAGGCCGGGGAGCTGG	0.692													C|||	1126	0.22484	0.0091	0.1066	5008	,	,		15223	0.5159		0.2127	False		,,,				2504	0.3129				p.P423P		Atlas-SNP	.											.	GMEB2	44	.	0			c.G1269A						PASS	.	C		224,4138		12,200,1969	12.0	13.0	12.0		1269	-8.9	0.2	20	dbSNP_100	12	1750,6810		175,1400,2705	no	coding-synonymous	GMEB2	NM_012384.3		187,1600,4674	TT,TC,CC		20.4439,5.1353,15.2763		423/531	62221766	1974,10948	2181	4280	6461	SO:0001819	synonymous_variant	26205	exon10			GGAGGCCGGGGAG	AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.1269G>A	20.37:g.62221766C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_012384	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Silent	SNP	ENST00000266068.1	37	CCDS13528.1																																																																																			C|0.763;T|0.237	0.237	strong		0.692	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384	
VPS9D1	9605	hgsc.bcm.edu	37	16	89777761	89777761	+	Silent	SNP	C	C	T	rs12920315	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:89777761C>T	ENST00000389386.3	-	9	931	c.807G>A	c.(805-807)gtG>gtA	p.V269V	VPS9D1_ENST00000561976.1_Silent_p.V199V|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000565452.1_5'UTR	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	269					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCAGGCTGGTCACGAGTGACA	0.667													c|||	2815	0.562101	0.4546	0.5951	5008	,	,		12592	0.4623		0.5527	False		,,,				2504	0.7965				p.V269V		Atlas-SNP	.											C16orf7,NS,carcinoma,0,1	.	.	1	0			c.G807A						PASS	.			2075,1981		537,1001,490	62.0	77.0	73.0		807	1.8	1.0	16	dbSNP_121	73	4573,3759		1274,2025,867	no	coding-synonymous	C16orf7	NM_004913.2		1811,3026,1357	TT,TC,CC		45.1152,48.8412,46.3352		269/632	89777761	6648,5740	2028	4166	6194	SO:0001819	synonymous_variant	9605	exon9			GCTGGTCACGAGT	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.807G>A	16.37:g.89777761C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			A|0.000;C|0.471;G|0.000;T|0.529	0.529	strong		0.667	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
CXCR5	643	hgsc.bcm.edu	37	11	118764448	118764448	+	Silent	SNP	C	C	T	rs537787473		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118764448C>T	ENST00000292174.4	+	2	371	c.195C>T	c.(193-195)ggC>ggT	p.G65G		NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	65					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		TCCTCCTGGGCGTGATCGGCA	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19111	0.0		0.0	False		,,,				2504	0.0				p.G65G		Atlas-SNP	.											.	CXCR5	34	.	0			c.C195T						PASS	.						117.0	105.0	109.0					11																	118764448		2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGGGCGTGATC	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	1060	protein-coding gene	gene with protein product		601613	"""Burkitt lymphoma receptor 1, GTP-binding protein"", ""Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"""	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.195C>T	11.37:g.118764448C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			.	.	none		0.642	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
OR4N2	390429	hgsc.bcm.edu	37	14	20295779	20295779	+	Missense_Mutation	SNP	C	C	G	rs11621884	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20295779C>G	ENST00000315947.1	+	1	172	c.172C>G	c.(172-174)Ccc>Gcc	p.P58A	OR4N2_ENST00000568211.1_Missense_Mutation_p.P58A	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GCTCACAGCCCCCCTCTATTT	0.473													.|||	1039	0.207468	0.2663	0.1657	5008	,	,		25877	0.1161		0.2107	False		,,,				2504	0.2485				p.P58A		Atlas-SNP	.											OR4N2,NS,carcinoma,-2,1	OR4N2	125	1	0			c.C172G						PASS	.	C	ALA/PRO	76,4330		24,28,2151	178.0	213.0	201.0		172	4.3	0.2	14	dbSNP_120	201	114,8482		37,40,4221	no	missense	OR4N2	NM_001004723.1	27	61,68,6372	GG,GC,CC		1.3262,1.7249,1.4613	probably-damaging	58/308	20295779	190,12812	2203	4298	6501	SO:0001583	missense	390429	exon1			ACAGCCCCCCTCT		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.172C>G	14.37:g.20295779C>G	ENSP00000319601:p.Pro58Ala	Somatic	357	1	0.00280112		WXS	Illumina HiSeq	Phase_I	293	131	0.447099	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	266	0.12179487179487179	80	0.16260162601626016	41	0.1132596685082873	49	0.08566433566433566	96	0.1266490765171504	.	16.18	3.050174	0.55218	0.017249	0.013262	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.02015	4.5;4.5	4.3	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000189	T	0.00073	0.0002	M	0.93550	3.43	0.24376	P	0.99481913	D	0.89917	1.0	D	0.97110	1.0	T	0.01549	-1.1327	9	0.72032	D	0.01	-18.589	14.6285	0.68640	0.0:1.0:0.0:0.0	rs11621884	58	Q8NGD1	OR4N2_HUMAN	A	58	ENSP00000452022:P58A;ENSP00000319601:P58A	ENSP00000319601:P58A	P	+	1	0	OR4N2	19365619	0.998000	0.40836	0.248000	0.24265	0.439000	0.31926	4.629000	0.61290	2.374000	0.81015	0.591000	0.81541	CCC	C|0.886;G|0.114	0.114	strong		0.473	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
TRIOBP	11078	hgsc.bcm.edu	37	22	38129332	38129332	+	Silent	SNP	G	G	A	rs7284476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38129332G>A	ENST00000406386.3	+	8	4230	c.3975G>A	c.(3973-3975)caG>caA	p.Q1325Q		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1325					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GGGCCTTCCAGGCCCAGGACG	0.662													G|||	1689	0.33726	0.1573	0.2867	5008	,	,		14945	0.5843		0.3877	False		,,,				2504	0.3098				p.Q1325Q		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G3975A						PASS	.	G		735,3103		119,497,1303	10.0	16.0	14.0		3975	5.8	1.0	22	dbSNP_116	14	3389,4547		832,1725,1411	no	coding-synonymous	TRIOBP	NM_001039141.2		951,2222,2714	AA,AG,GG		42.7041,19.1506,35.0263		1325/2366	38129332	4124,7650	1919	3968	5887	SO:0001819	synonymous_variant	11078	exon8			CTTCCAGGCCCAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3975G>A	22.37:g.38129332G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	228	228	1	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			G|0.639;A|0.361	0.361	strong		0.662	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
ZNF19	7567	hgsc.bcm.edu	37	16	71509796	71509796	+	Missense_Mutation	SNP	C	C	G	rs8050871	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:71509796C>G	ENST00000288177.5	-	6	909	c.654G>C	c.(652-654)caG>caC	p.Q218H	ZNF19_ENST00000564230.1_Missense_Mutation_p.Q218H|ZNF19_ENST00000567225.1_Intron|ZNF19_ENST00000565637.1_Missense_Mutation_p.Q176H|ZNF19_ENST00000565100.2_Missense_Mutation_p.Q148H|AC010547.9_ENST00000561908.1_Intron	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	218			Q -> H (in dbSNP:rs8050871). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		ACTCCTCACACTGATAGGGTC	0.463													C|||	3275	0.653954	0.5946	0.585	5008	,	,		19714	0.6012		0.674	False		,,,				2504	0.817				p.Q218H		Atlas-SNP	.											.	ZNF19	46	.	0			c.G654C						PASS	.	C	HIS/GLN	2606,1790	638.7+/-397.0	781,1044,373	62.0	69.0	67.0		654	-2.1	0.5	16	dbSNP_116	67	5976,2624	685.5+/-404.1	2079,1818,403	yes	missense	ZNF19	NM_006961.3	24	2860,2862,776	GG,GC,CC		30.5116,40.7188,33.9643	probably-damaging	218/459	71509796	8582,4414	2198	4300	6498	SO:0001583	missense	7567	exon6			CTCACACTGATAG	X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"""Zinc fingers, C2H2-type"", ""-"""	12981	protein-coding gene	gene with protein product		194525	"""zinc finger protein 19 (KOX 12)"""			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.654G>C	16.37:g.71509796C>G	ENSP00000288177:p.Gln218His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_006961	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Missense_Mutation	SNP	ENST00000288177.5	37	CCDS10901.1	1372	0.6282051282051282	284	0.5772357723577236	241	0.6657458563535912	343	0.5996503496503497	504	0.6649076517150396	C	14.63	2.592560	0.46214	0.592812	0.694884	ENSG00000157429	ENST00000288177	T	0.19394	2.15	3.49	-2.11	0.07187	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.218239	0.23530	N	0.047196	T	0.00012	0.0000	L	0.56199	1.76	0.54753	P	1.799999999996249E-5	P	0.50710	0.938	P	0.54499	0.754	T	0.44590	-0.9318	9	0.66056	D	0.02	.	0.2239	0.00171	0.2965:0.2762:0.1454:0.2819	rs8050871;rs17854417;rs52838300;rs60426363;rs8050871	218	P17023	ZNF19_HUMAN	H	218	ENSP00000288177:Q218H	ENSP00000288177:Q218H	Q	-	3	2	ZNF19	70067297	0.000000	0.05858	0.500000	0.27589	0.896000	0.52359	-2.771000	0.00779	-0.382000	0.07870	-0.127000	0.14921	CAG	C|0.357;G|0.643	0.643	strong		0.463	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961	
ZFHX3	463	hgsc.bcm.edu	37	16	72822296	72822296	+	Silent	SNP	G	G	A	rs2228199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:72822296G>A	ENST00000268489.5	-	10	10551	c.9879C>T	c.(9877-9879)gcC>gcT	p.A3293A	ZFHX3_ENST00000397992.5_Silent_p.A2379A|AC004943.1_ENST00000584072.1_RNA|RP5-991G20.1_ENST00000563328.2_RNA|RP5-991G20.4_ENST00000569195.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	3293					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				AAGTCAACGCGGCCTGCAGGG	0.602													G|||	304	0.0607029	0.0121	0.0994	5008	,	,		14824	0.1141		0.0577	False		,,,				2504	0.047				p.A3293A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C9879T						PASS	.	G	,	103,4293	79.9+/-118.3	1,101,2096	55.0	57.0	57.0		7137,9879	-7.4	0.8	16	dbSNP_98	57	505,8095	144.3+/-200.2	25,455,3820	no	coding-synonymous,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	26,556,5916	AA,AG,GG		5.8721,2.343,4.6784	,	2379/2790,3293/3704	72822296	608,12388	2198	4300	6498	SO:0001819	synonymous_variant	463	exon10			CAACGCGGCCTGC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.9879C>T	16.37:g.72822296G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	230	116	0.504348	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			G|0.949;A|0.051	0.051	strong		0.602	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
PKD1L2	114780	hgsc.bcm.edu	37	16	81241098	81241098	+	RNA	SNP	C	C	T	rs386792899|rs11150369	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81241098C>T	ENST00000525539.1	-	0	902				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTTACCTCGGCGGGTTGTAGG	0.453													C|||	3514	0.701677	0.4561	0.7378	5008	,	,		18063	0.8839		0.8539	False		,,,				2504	0.6636				p.P301P		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G903A						PASS	.	C	,	1996,1792		558,880,456	93.0	93.0	93.0		903,903	-9.6	0.0	16	dbSNP_120	93	6940,1300		2939,1062,119	no	coding-synonymous,coding-synonymous	PKD1L2	NM_001076780.1,NM_052892.3	,	3497,1942,575	TT,TC,CC		15.7767,47.3073,25.7067	,	301/992,301/2460	81241098	8936,3092	1894	4120	6014			114780	exon5			CCTCGGCGGGTTG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81241098C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																				C|0.212;T|0.788	0.788	strong		0.453	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
SLC38A10	124565	hgsc.bcm.edu	37	17	79244802	79244802	+	Silent	SNP	T	T	C	rs2292184	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79244802T>C	ENST00000374759.3	-	10	1430	c.1047A>G	c.(1045-1047)acA>acG	p.T349T	SLC38A10_ENST00000546352.1_5'UTR|SLC38A10_ENST00000288439.5_Silent_p.T349T	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	349					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TGGTCGCTCCTGTGAGGCCCA	0.582													C|||	2149	0.429113	0.7837	0.4121	5008	,	,		16257	0.1825		0.4414	False		,,,				2504	0.2035				p.T349T		Atlas-SNP	.											SLC38A10_ENST00000374759,NS,carcinoma,0,2	SLC38A10	133	2	0			c.A1047G						PASS	.	C	,	3292,1114	397.4+/-330.4	1230,832,141	87.0	76.0	79.0		1047,1047	-5.6	0.4	17	dbSNP_100	79	3646,4954	623.5+/-397.5	807,2032,1461	no	coding-synonymous,coding-synonymous	SLC38A10	NM_001037984.1,NM_138570.2	,	2037,2864,1602	CC,CT,TT		42.3953,25.2837,46.6554	,	349/1120,349/781	79244802	6938,6068	2203	4300	6503	SO:0001819	synonymous_variant	124565	exon10			CGCTCCTGTGAGG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1047A>G	17.37:g.79244802T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	65	0.560345	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1																																																																																			T|0.518;C|0.482	0.482	strong		0.582	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
MAU2	23383	hgsc.bcm.edu	37	19	19446936	19446936	+	Silent	SNP	G	G	A	rs769267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19446936G>A	ENST00000392313.6	+	3	479	c.300G>A	c.(298-300)ccG>ccA	p.P100P	MAU2_ENST00000586189.3_3'UTR|MAU2_ENST00000262815.8_Silent_p.P100P	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	100	Sufficient for interaction with NIPBL.				maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						ACTAGATCCCGCAGTTCGAAG	0.463													G|||	2635	0.526158	0.3464	0.5432	5008	,	,		21505	0.6677		0.6829	False		,,,				2504	0.4499				p.P100P		Atlas-SNP	.											.	MAU2	38	.	0			c.G300A						PASS	.	G		1533,2333		299,935,699	126.0	115.0	119.0		300	-3.6	0.9	19	dbSNP_86	119	5510,2760		1839,1832,464	no	coding-synonymous	MAU2	NM_015329.3		2138,2767,1163	AA,AG,GG		33.3736,39.6534,41.9661		100/614	19446936	7043,5093	1933	4135	6068	SO:0001819	synonymous_variant	23383	exon3			GATCCCGCAGTTC	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"""sister chromatid cohesion 4"""	614560	"""KIAA0892"", ""MAU2 chromatid cohesion factor homolog (C. elegans)"""	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.300G>A	19.37:g.19446936G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	162	95	0.58642	NM_015329	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Silent	SNP	ENST00000392313.6	37	CCDS32969.2																																																																																			G|0.435;A|0.565	0.565	strong		0.463	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329	
AATK	9625	hgsc.bcm.edu	37	17	79095144	79095144	+	Silent	SNP	G	G	A	rs8073904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79095144G>A	ENST00000326724.4	-	11	2616	c.2592C>T	c.(2590-2592)gcC>gcT	p.A864A	AATK_ENST00000417379.1_Silent_p.A761A	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	864					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AGGTGGCCTCGGCCGTGTCCT	0.657													A|||	4033	0.805312	0.795	0.634	5008	,	,		17360	0.8611		0.8628	False		,,,				2504	0.8241				p.A864A		Atlas-SNP	.											.	AATK	102	.	0			c.C2592T						PASS	.	A	,	3419,801		1380,659,71	26.0	31.0	29.0		2592,2283	-8.9	0.0	17	dbSNP_116	29	7343,1087		3191,961,63	no	coding-synonymous,coding-synonymous	AATK	NM_001080395.2,NM_004920.2	,	4571,1620,134	AA,AG,GG		12.8944,18.981,14.9249	,	864/1375,761/1272	79095144	10762,1888	2110	4215	6325	SO:0001819	synonymous_variant	9625	exon11			GGCCTCGGCCGTG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.2592C>T	17.37:g.79095144G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	1749	0.8008241758241759	376	0.7642276422764228	245	0.6767955801104972	478	0.8356643356643356	650	0.8575197889182058	A	0.526	-0.859811	0.02610	0.81019	0.871056	ENSG00000181409	ENST00000417379	.	.	.	4.47	-8.95	0.00765	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999336698	.	.	.	.	.	.	T	0.04115	-1.0976	3	.	.	.	.	4.3982	0.11374	0.1161:0.2285:0.4282:0.2272	rs8073904;rs57097371;rs8073904	.	.	.	L	817	.	.	P	-	2	0	AATK	76709739	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-8.005000	0.00026	-4.297000	0.00058	-0.521000	0.04368	CCG	G|0.190;A|0.810	0.810	strong		0.657	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
FAM109B	150368	hgsc.bcm.edu	37	22	42473860	42473860	+	Missense_Mutation	SNP	C	C	G	rs1807493	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:42473860C>G	ENST00000321753.3	+	3	750	c.563C>G	c.(562-564)gCg>gGg	p.A188G	snoU13_ENST00000458891.1_RNA|SMDT1_ENST00000331479.3_5'Flank	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	188			A -> G (in dbSNP:rs1807493). {ECO:0000269|PubMed:15489334}.		endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|liver(2)|lung(1)|prostate(1)	8						GTTGAAGAAGCGGGCAGCAGG	0.667													C|||	808	0.161342	0.0484	0.2363	5008	,	,		17874	0.1101		0.2396	False		,,,				2504	0.2331				p.A188G		Atlas-SNP	.											.	FAM109B	22	.	0			c.C563G						PASS	.	C	GLY/ALA	308,4096		14,280,1908	28.0	29.0	29.0		563	-2.4	0.0	22	dbSNP_92	29	1915,6685		246,1423,2631	yes	missense	FAM109B	NM_001002034.2	60	260,1703,4539	GG,GC,CC		22.2674,6.9936,17.0947	benign	188/260	42473860	2223,10781	2202	4300	6502	SO:0001583	missense	150368	exon3			AAGAAGCGGGCAG	BX648402	CCDS33655.1	22q13.2	2013-01-10			ENSG00000177096	ENSG00000177096		"""Pleckstrin homology (PH) domain containing"""	27161	protein-coding gene	gene with protein product		614240				12477932	Standard	NM_001002034		Approved	DKFZp686J07229	uc003bbz.3	Q6ICB4	OTTHUMG00000151285	ENST00000321753.3:c.563C>G	22.37:g.42473860C>G	ENSP00000312753:p.Ala188Gly	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_001002034	Q3SXQ3|Q8N6L9	Missense_Mutation	SNP	ENST00000321753.3	37	CCDS33655.1	367	0.16804029304029305	28	0.056910569105691054	78	0.2154696132596685	78	0.13636363636363635	183	0.24142480211081793	C	0.005	-2.164310	0.00318	0.069936	0.222674	ENSG00000177096	ENST00000321753	T	0.42513	0.97	4.37	-2.38	0.06622	.	1.543610	0.05328	N	0.527815	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23226	-1.0194	9	0.17369	T	0.5	-8.7261	2.597	0.04856	0.1219:0.3229:0.3358:0.2193	rs1807493;rs17845905;rs17858880	188	Q6ICB4	SESQ2_HUMAN	G	188	ENSP00000312753:A188G	ENSP00000312753:A188G	A	+	2	0	FAM109B	40803806	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.591000	0.05753	-0.397000	0.07691	-4.145000	0.00010	GCG	C|0.837;G|0.163	0.163	strong		0.667	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034	
WDR16	146845	hgsc.bcm.edu	37	17	9515777	9515777	+	Missense_Mutation	SNP	G	G	A	rs6503235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:9515777G>A	ENST00000352665.5	+	8	1075	c.1006G>A	c.(1006-1008)Gag>Aag	p.E336K	WDR16_ENST00000396219.3_Missense_Mutation_p.E268K|WDR16_ENST00000299764.5_Missense_Mutation_p.E346K	NM_145054.4	NP_659491.4			WD repeat domain 16									p.E336K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						TGATGCTGTCGAGGATATTGT	0.398													G|||	3003	0.599641	0.3116	0.7594	5008	,	,		20591	0.5714		0.7594	False		,,,				2504	0.7403				p.E336K		Atlas-SNP	.											WDR16,NS,carcinoma,0,1	WDR16	67	1	1	Substitution - Missense(1)	stomach(1)	c.G1006A						PASS	.	G	LYS/GLU,LYS/GLU	1798,2608	529.3+/-372.6	361,1076,766	120.0	102.0	108.0		802,1006	0.8	0.2	17	dbSNP_116	108	6500,2100	717.8+/-406.2	2463,1574,263	yes	missense,missense	WDR16	NM_001080556.1,NM_145054.4	56,56	2824,2650,1029	AA,AG,GG		24.4186,40.808,36.1987	benign,benign	268/553,336/621	9515777	8298,4708	2203	4300	6503	SO:0001583	missense	146845	exon8			GCTGTCGAGGATA	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"""WD repeat domain containing"""	16053	protein-coding gene	gene with protein product	"""WD40-repeat protein upregulated in HCC"""	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.1006G>A	17.37:g.9515777G>A	ENSP00000339449:p.Glu336Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_145054		Missense_Mutation	SNP	ENST00000352665.5	37	CCDS11149.2	1326	0.6071428571428571	167	0.3394308943089431	263	0.7265193370165746	318	0.5559440559440559	578	0.762532981530343	G	6.556	0.470932	0.12461	0.40808	0.755814	ENSG00000166596	ENST00000352665;ENST00000396219;ENST00000299764	T;D;T	0.90069	2.58;-2.61;5.07	5.53	0.828	0.18841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.453160	0.26765	N	0.022601	T	0.00012	0.0000	N	0.00707	-1.245	0.58432	P	9.000000000036756E-6	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.47086	-0.9144	9	0.08837	T	0.75	-6.3495	13.1025	0.59228	0.1055:0.3838:0.5107:0.0	rs6503235;rs17207234;rs17852263;rs52807676;rs60055865;rs6503235	346;268;336	Q8N1V2-2;Q8N1V2-3;Q8N1V2	.;.;WDR16_HUMAN	K	336;268;346	ENSP00000339449:E336K;ENSP00000379521:E268K;ENSP00000299764:E346K	ENSP00000299764:E346K	E	+	1	0	WDR16	9456502	0.598000	0.26882	0.154000	0.22540	0.119000	0.20118	0.842000	0.27627	-0.055000	0.13244	-0.312000	0.09012	GAG	G|0.383;A|0.617	0.617	strong		0.398	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054	
OTOF	9381	hgsc.bcm.edu	37	2	26739423	26739423	+	Silent	SNP	T	T	C	rs11687696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:26739423T>C	ENST00000272371.2	-	5	498	c.372A>G	c.(370-372)acA>acG	p.T124T	OTOF_ENST00000403946.3_Silent_p.T124T	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	124					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGAGCCCACTGTGCCGTCAG	0.627													T|||	1279	0.255391	0.0272	0.2536	5008	,	,		18921	0.5248		0.3012	False		,,,				2504	0.2403				p.T124T	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.A372G						PASS	.	T		337,4069	176.6+/-205.7	16,305,1882	70.0	67.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	372	-9.7	0.0	2	dbSNP_120	68	2429,6171	399.4+/-346.4	318,1793,2189	no	coding-synonymous	OTOF	NM_194248.2		334,2098,4071	CC,CT,TT		28.2442,7.6487,21.2671		124/1998	26739423	2766,10240	2203	4300	6503	SO:0001819	synonymous_variant	9381	exon5			GCCCACTGTGCCG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.372A>G	2.37:g.26739423T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			T|0.761;C|0.239	0.239	strong		0.627	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
FAM120AOS	158293	hgsc.bcm.edu	37	9	96214928	96214928	+	Missense_Mutation	SNP	G	G	A	rs1055710	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:96214928G>A	ENST00000375412.5	-	1	946	c.64C>T	c.(64-66)Ctc>Ttc	p.L22F	FAM120A_ENST00000340893.4_Intron|FAM120AOS_ENST00000423591.1_5'Flank|FAM120A_ENST00000375389.3_Intron|FAM120A_ENST00000333936.5_Intron|FAM120AOS_ENST00000479094.1_5'Flank|FAM120A_ENST00000277165.6_Intron	NM_198841.2	NP_942138.2	Q5T036	F120S_HUMAN	family with sequence similarity 120A opposite strand	22			L -> F (in dbSNP:rs1055710). {ECO:0000269|PubMed:14702039}.							kidney(1)|large_intestine(1)|lung(3)|skin(1)	6						GGCTGGGAGAGAGCCCCGGAC	0.627													G|||	1451	0.289736	0.2247	0.33	5008	,	,		14673	0.4187		0.3509	False		,,,				2504	0.1534				p.L22F		Atlas-SNP	.											.	FAM120AOS	13	.	0			c.C64T						PASS	.	G	,PHE/LEU	862,3084		96,670,1207	22.0	25.0	24.0		,64	-6.6	0.0	9	dbSNP_86	24	2380,5512		372,1636,1938	yes	intron,missense	FAM120A,FAM120AOS	NM_014612.3,NM_198841.2	,22	468,2306,3145	AA,AG,GG		30.1571,21.8449,27.3864	,benign	,22/257	96214928	3242,8596	1973	3946	5919	SO:0001583	missense	158293	exon1			GGGAGAGAGCCCC	AK056096	CCDS6705.1	9q22.32	2008-02-05	2006-07-04	2006-07-04	ENSG00000188938	ENSG00000188938			23389	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 10 opposite strand"""	C9orf10OS		14585507	Standard	NM_198841		Approved		uc004atu.4	Q5T036	OTTHUMG00000020251	ENST00000375412.5:c.64C>T	9.37:g.96214928G>A	ENSP00000364561:p.Leu22Phe	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_198841	A6NN20	Missense_Mutation	SNP	ENST00000375412.5	37	CCDS6705.1	781	0.3576007326007326	114	0.23170731707317074	137	0.3784530386740331	258	0.45104895104895104	272	0.35883905013192613	G	13.52	2.262325	0.39995	0.218449	0.301571	ENSG00000188938	ENST00000375412	T	0.55588	0.51	3.32	-6.63	0.01807	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	2.9999999999752447E-6	B	0.20780	0.048	B	0.16289	0.015	T	0.41052	-0.9530	8	0.32370	T	0.25	.	2.1198	0.03723	0.1008:0.2486:0.2257:0.4248	rs1055710;rs3196205;rs58279967;rs1055710	22	Q5T036	F120S_HUMAN	F	22	ENSP00000364561:L22F	ENSP00000364561:L22F	L	-	1	0	FAM120AOS	95254749	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.624000	0.02038	-1.502000	0.01814	0.591000	0.81541	CTC	G|0.688;A|0.312	0.312	strong		0.627	FAM120AOS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053154.1		
FAM218A	152756	hgsc.bcm.edu	37	4	165878609	165878609	+	Silent	SNP	T	T	A	rs3196673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:165878609T>A	ENST00000513876.2	+	1	510	c.435T>A	c.(433-435)tcT>tcA	p.S145S	TRIM61_ENST00000329314.5_Intron	NM_153027.1	NP_694572.1	Q96MZ4	F218A_HUMAN	family with sequence similarity 218, member A	145																	GGTTTGGGTCTGCAGTGGGCT	0.547													t|||	1205	0.240615	0.2141	0.3487	5008	,	,		17509	0.0942		0.3091	False		,,,				2504	0.2802				p.S145S		Atlas-SNP	.											.	.	.	.	0			c.T435A						PASS	.		,	1013,3393	375.1+/-321.5	124,765,1314	61.0	63.0	62.0		,435	0.3	0.0	4	dbSNP_105	62	2709,5891	432.4+/-357.1	407,1895,1998	no	intron,coding-synonymous	C4orf39,TRIM61	NM_001012414.2,NM_153027.1	,	531,2660,3312	AA,AT,TT		31.5,22.9914,28.6176	,	,145/158	165878609	3722,9284	2203	4300	6503	SO:0001819	synonymous_variant	152756	exon1			TGGGTCTGCAGTG	AK056221	CCDS3807.1	4q32.3	2012-03-01	2012-03-01	2012-03-01	ENSG00000250486	ENSG00000250486			26466	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 39"""	C4orf39		12477932	Standard	NM_153027		Approved	FLJ31659	uc003iqx.1	Q96MZ4	OTTHUMG00000161252	ENST00000513876.2:c.435T>A	4.37:g.165878609T>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	268	144	0.537313	NM_153027		Silent	SNP	ENST00000513876.2	37	CCDS3807.1																																																																																			T|0.736;A|0.264	0.264	strong		0.547	FAM218A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364308.1	NM_153027	
ZSCAN9	7746	hgsc.bcm.edu	37	6	28195521	28195521	+	Silent	SNP	A	A	G	rs12197427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28195521A>G	ENST00000252207.5	+	3	622	c.474A>G	c.(472-474)ctA>ctG	p.L158L	ZSCAN9_ENST00000531979.1_Silent_p.L158L|ZSCAN9_ENST00000425468.2_Silent_p.L158L|ZSCAN9_ENST00000531981.1_3'UTR|ZSCAN9_ENST00000527436.1_Silent_p.L158L	NM_006299.4	NP_006290.1	O15535	ZSC9_HUMAN	zinc finger and SCAN domain containing 9	158					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGGTGCCTCTAGCAGAGCAGA	0.488													A|||	78	0.0155751	0.0	0.0274	5008	,	,		18815	0.0129		0.0278	False		,,,				2504	0.0184				p.L158L		Atlas-SNP	.											ZNF193,NS,carcinoma,+2,1	.	.	1	0			c.A474G						PASS	.	A	,,	26,4380	32.6+/-62.9	0,26,2177	70.0	64.0	66.0		474,474,474	-3.5	0.0	6	dbSNP_120	66	313,8287	112.0+/-172.2	8,297,3995	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF193	NM_001199479.1,NM_001199480.1,NM_006299.4	,,	8,323,6172	GG,GA,AA		3.6395,0.5901,2.6065	,,	158/446,158/395,158/395	28195521	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	7746	exon3			GCCTCTAGCAGAG	U62392	CCDS4646.1, CCDS56407.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000137185	ENSG00000137185		"""-"", ""Zinc fingers, C2H2-type"""	12984	protein-coding gene	gene with protein product		602246	"""zinc finger protein 193"""	ZNF193			Standard	NM_001199479		Approved	PRD51	uc003nkq.2	O15535	OTTHUMG00000014515	ENST00000252207.5:c.474A>G	6.37:g.28195521A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	213	125	0.586854	NM_006299	B4E1W6|E7EVQ2|Q2TTR1	Silent	SNP	ENST00000252207.5	37	CCDS4646.1																																																																																			A|0.971;G|0.029	0.029	strong		0.488	ZSCAN9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040183.2	NM_006299	
MB21D1	115004	hgsc.bcm.edu	37	6	74155346	74155346	+	Missense_Mutation	SNP	G	G	T	rs610913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:74155346G>T	ENST00000370315.3	-	2	876	c.782C>A	c.(781-783)cCt>cAt	p.P261H	MB21D1_ENST00000370318.1_Missense_Mutation_p.P261H	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	261			P -> H (in dbSNP:rs610913). {ECO:0000269|PubMed:15489334}.		activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						CTGACTCAGAGGATTTTCTTT	0.323													G|||	2518	0.502796	0.3691	0.389	5008	,	,		17037	0.502		0.6441	False		,,,				2504	0.6196				p.P261H		Atlas-SNP	.											.	MB21D1	33	.	0			c.C782A						PASS	.	G	HIS/PRO	1767,2633	503.4+/-365.5	356,1055,789	56.0	55.0	55.0		782	5.1	1.0	6	dbSNP_83	55	5337,3253	639.6+/-399.5	1658,2021,616	yes	missense	MB21D1	NM_138441.2	77	2014,3076,1405	TT,TG,GG		37.8696,40.1591,45.3118	probably-damaging	261/523	74155346	7104,5886	2200	4295	6495	SO:0001583	missense	115004	exon2			CTCAGAGGATTTT	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"""chromosome 6 open reading frame 150"""	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.782C>A	6.37:g.74155346G>T	ENSP00000359339:p.Pro261His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Missense_Mutation	SNP	ENST00000370315.3	37	CCDS4978.1	1123	0.5141941391941391	191	0.3882113821138211	155	0.4281767955801105	299	0.5227272727272727	478	0.6306068601583114	G	12.09	1.833903	0.32421	0.401591	0.621304	ENSG00000164430	ENST00000370318;ENST00000370315;ENST00000296913	T;T	0.07567	3.18;3.18	5.09	5.09	0.68999	.	0.156200	0.41823	D	0.000802	T	0.19087	0.0458	M	0.78916	2.43	0.32655	P	0.518833	D	0.89917	1.0	D	0.76575	0.988	T	0.00923	-1.1513	9	0.72032	D	0.01	-14.8394	11.4896	0.50373	0.0:0.0:0.8207:0.1793	rs610913;rs17718689;rs52790815;rs59873091;rs610913	261	Q8N884	M21D1_HUMAN	H	261	ENSP00000359342:P261H;ENSP00000359339:P261H	ENSP00000296913:P261H	P	-	2	0	MB21D1	74212067	1.000000	0.71417	0.994000	0.49952	0.085000	0.17905	1.979000	0.40608	2.525000	0.85131	0.462000	0.41574	CCT	G|0.477;T|0.523	0.523	strong		0.323	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441	
WISP3	8838	hgsc.bcm.edu	37	6	112382313	112382313	+	Missense_Mutation	SNP	G	G	T	rs1230345	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:112382313G>T	ENST00000368666.2	+	2	454	c.168G>T	c.(166-168)caG>caT	p.Q56H	WISP3_ENST00000368663.3_Missense_Mutation_p.Q34H|WISP3_ENST00000361714.1_Missense_Mutation_p.Q74H|WISP3_ENST00000409166.1_5'Flank|WISP3_ENST00000230529.5_Missense_Mutation_p.Q56H|WISP3_ENST00000604763.1_Missense_Mutation_p.Q56H	NM_198239.1	NP_937882.1	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	56	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.		Q -> H (common polymorphism; dbSNP:rs1230345). {ECO:0000269|PubMed:10471507}.		cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	13		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		AATGCCCTCAGCAGAAGCCCC	0.532													T|||	1497	0.298922	0.4705	0.2392	5008	,	,		19236	0.3313		0.2465	False		,,,				2504	0.1299				p.Q74H		Atlas-SNP	.											.	WISP3	33	.	0			c.G222T						PASS	.	T	HIS/GLN,HIS/GLN	1991,2415	616.9+/-392.9	462,1067,674	135.0	124.0	128.0		168,222	-7.2	0.0	6	dbSNP_87	128	2381,6219	701.1+/-405.2	311,1759,2230	yes	missense,missense	WISP3	NM_003880.3,NM_198239.1	24,24	773,2826,2904	TT,TG,GG		27.686,45.1884,33.6153	benign,benign	56/355,74/373	112382313	4372,8634	2203	4300	6503	SO:0001583	missense	8838	exon2			CCCTCAGCAGAAG	AF100781	CCDS5097.1, CCDS5098.1	6q21	2014-05-06			ENSG00000112761	ENSG00000112761			12771	protein-coding gene	gene with protein product		603400				9843955	Standard	NM_003880		Approved	CCN6	uc003pvo.3	O95389	OTTHUMG00000185101	ENST00000368666.2:c.168G>T	6.37:g.112382313G>T	ENSP00000357655:p.Gln56His	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	169	57	0.337278	NM_198239	Q3KR29|Q5H8W4|Q6UXH6	Missense_Mutation	SNP	ENST00000368666.2	37	CCDS5098.1	656	0.30036630036630035	220	0.44715447154471544	88	0.2430939226519337	172	0.3006993006993007	176	0.23218997361477572	T	0.324	-0.960165	0.02267	0.451884	0.27686	ENSG00000112761	ENST00000368666;ENST00000230529;ENST00000361714;ENST00000541400;ENST00000368663	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	3.77	-7.25	0.01470	Insulin-like growth factor-binding protein, IGFBP (3);	1.850360	0.02256	N	0.067100	T	0.10423	0.0255	N	0.12182	0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.05649	-1.0872	9	0.44086	T	0.13	5.8147	3.0603	0.06197	0.1172:0.3374:0.3572:0.1882	rs1230345;rs1709860;rs52826752;rs61572383;rs1230345	74;56	O95389-2;O95389	.;WISP3_HUMAN	H	56;56;74;56;34	ENSP00000357655:Q56H;ENSP00000230529:Q56H;ENSP00000354734:Q74H;ENSP00000357652:Q34H	ENSP00000230529:Q56H	Q	+	3	2	WISP3	112489006	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.729000	0.04920	-1.590000	0.01623	-0.362000	0.07510	CAG	G|0.673;T|0.321	0.321	strong		0.532	WISP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041873.2	NM_003880	
CLCN1	1180	hgsc.bcm.edu	37	7	143016928	143016928	+	Silent	SNP	C	C	T	rs6962852	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:143016928C>T	ENST00000343257.2	+	2	348	c.261C>T	c.(259-261)acC>acT	p.T87T		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	87					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					CCAGTTCTACCGTGGACAGCA	0.453													C|||	1617	0.322883	0.5961	0.2378	5008	,	,		20869	0.0427		0.328	False		,,,				2504	0.2975				p.T87T		Atlas-SNP	.											.	CLCN1	141	.	0			c.C261T						PASS	.	C		2504,1902		705,1094,404	201.0	165.0	177.0		261	-2.3	0.0	7	dbSNP_116	177	2802,5798		465,1872,1963	no	coding-synonymous	CLCN1	NM_000083.2		1170,2966,2367	TT,TC,CC		32.5814,43.1684,40.7966		87/989	143016928	5306,7700	2203	4300	6503	SO:0001819	synonymous_variant	1180	exon2			TTCTACCGTGGAC	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"""Ion channels / Chloride channels : Voltage-sensitive"""	2019	protein-coding gene	gene with protein product	"""Thomsen disease, autosomal dominant"""	118425	"""chloride channel 1, skeletal muscle"""			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.261C>T	7.37:g.143016928C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_000083	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																			C|0.646;T|0.354	0.354	strong		0.453	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	
SUSD2	56241	hgsc.bcm.edu	37	22	24581207	24581207	+	Silent	SNP	C	C	T	rs3752497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:24581207C>T	ENST00000358321.3	+	6	1189	c.928C>T	c.(928-930)Ctg>Ttg	p.L310L		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	310	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						CCTGGAGGAGCTGCCGGACTG	0.672													c|||	483	0.0964457	0.1044	0.1124	5008	,	,		15550	0.0764		0.0606	False		,,,				2504	0.1319				p.L310L		Atlas-SNP	.											.	SUSD2	68	.	0			c.C928T						PASS	.	C		476,3930	209.2+/-230.0	22,432,1749	26.0	26.0	26.0		928	0.6	1.0	22	dbSNP_107	26	539,8061	143.1+/-199.2	16,507,3777	no	coding-synonymous	SUSD2	NM_019601.3		38,939,5526	TT,TC,CC		6.2674,10.8034,7.8041		310/823	24581207	1015,11991	2203	4300	6503	SO:0001819	synonymous_variant	56241	exon6			GAGGAGCTGCCGG	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.928C>T	22.37:g.24581207C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	46	28	0.608696	NM_019601	Q9H5Y6	Silent	SNP	ENST00000358321.3	37	CCDS13824.1																																																																																			C|0.922;T|0.078	0.078	strong		0.672	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601	
MUC16	94025	hgsc.bcm.edu	37	19	9074073	9074073	+	Missense_Mutation	SNP	G	G	A	rs72486387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9074073G>A	ENST00000397910.4	-	3	13576	c.13373C>T	c.(13372-13374)cCt>cTt	p.P4458L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4460	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GACCAAGAAAGGTGTCAGGGA	0.512													G|||	934	0.186502	0.0923	0.2536	5008	,	,		21091	0.3254		0.1312	False		,,,				2504	0.18				p.P4458L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C13373T						PASS	.	G	LEU/PRO	379,3695		16,347,1674	109.0	106.0	107.0		13373	2.1	0.0	19	dbSNP_130	107	1159,7225		73,1013,3106	yes	missense	MUC16	NM_024690.2	98	89,1360,4780	AA,AG,GG		13.824,9.3029,12.3455	possibly-damaging	4458/14508	9074073	1538,10920	2037	4192	6229	SO:0001583	missense	94025	exon3			AAGAAAGGTGTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.13373C>T	19.37:g.9074073G>A	ENSP00000381008:p.Pro4458Leu	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	245	140	0.571429	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	439	0.20100732600732601	56	0.11382113821138211	80	0.22099447513812154	205	0.3583916083916084	98	0.12928759894459102	g	9.747	1.166313	0.21621	0.093029	0.13824	ENSG00000181143	ENST00000397910	T	0.21734	1.99	2.13	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	.	.	.	P	0.40282	0.711	B	0.29598	0.104	T	0.48305	-0.9047	8	0.87932	D	0	.	7.7927	0.29129	0.0:0.0:1.0:0.0	.	4458	B5ME49	.	L	4458	ENSP00000381008:P4458L	ENSP00000381008:P4458L	P	-	2	0	MUC16	8935073	0.007000	0.16637	0.002000	0.10522	0.513000	0.34164	2.389000	0.44407	1.499000	0.48617	0.305000	0.20034	CCT	G|0.808;A|0.192	0.192	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF253	56242	hgsc.bcm.edu	37	19	19989295	19989295	+	Silent	SNP	A	A	G	rs10406883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19989295A>G	ENST00000589717.1	+	2	101	c.9A>G	c.(7-9)ccA>ccG	p.P3P	ZNF253_ENST00000355650.4_Intron	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	3					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCCAGGGACCATTGCAATTTA	0.398													a|||	411	0.0820687	0.2587	0.0389	5008	,	,		14380	0.0129		0.0219	False		,,,				2504	0.0072				p.P3P		Atlas-SNP	.											.	ZNF253	99	.	0			c.A9G						PASS	.	G		648,2352		75,498,927	106.0	132.0	123.0		9	-1.9	0.0	19	dbSNP_119	123	140,5268		1,138,2565	no	coding-synonymous	ZNF253	NM_021047.2		76,636,3492	GG,GA,AA		2.5888,21.6,9.372		3/500	19989295	788,7620	1500	2704	4204	SO:0001819	synonymous_variant	56242	exon2			GGGACCATTGCAA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"""Zinc fingers, C2H2-type"", ""-"""	13497	protein-coding gene	gene with protein product		606954	"""zinc finger protein 411"""	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.9A>G	19.37:g.19989295A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	55	20	0.363636	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Silent	SNP	ENST00000589717.1	37	CCDS42532.1																																																																																			A|0.951;G|0.049	0.049	strong		0.398	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047	
BACE2	25825	hgsc.bcm.edu	37	21	42551432	42551432	+	Intron	SNP	T	T	A	rs5019194		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:42551432T>A	ENST00000330333.6	+	1	775				PLAC4_ENST00000440221.2_RNA|BACE2_ENST00000328735.6_Intron|BACE2-IT1_ENST00000433378.1_RNA|PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000414699.1_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000536486.1_RNA	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				TGACGGTGTCTGGGGTGAGTG	0.612																																					p.R42X		Atlas-SNP	.											.	.	.	.	0			c.A124T						PASS	.						123.0	106.0	112.0					21																	42551432		2195	4272	6467	SO:0001627	intron_variant	191585	exon1			GGTGTCTGGGGTG	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10930T>A	21.37:g.42551432T>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	221	33	0.149321	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Nonsense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			.	.	weak		0.612	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
SPTBN5	51332	hgsc.bcm.edu	37	15	42168400	42168400	+	Missense_Mutation	SNP	C	C	T	rs2290559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42168400C>T	ENST00000320955.6	-	21	4261	c.4034G>A	c.(4033-4035)cGc>cAc	p.R1345H		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1345			R -> H (in dbSNP:rs2290559).		actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GATGTTTCTGCGCGCTCCGGA	0.632													C|||	786	0.156949	0.0461	0.1888	5008	,	,		18058	0.0476		0.3121	False		,,,				2504	0.2372				p.R1310H		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G3929A						PASS	.	C	HIS/ARG	379,3911		21,337,1787	46.0	51.0	50.0		3929	3.0	0.0	15	dbSNP_100	50	2645,5891		408,1829,2031	yes	missense	SPTBN5	NM_016642.2	29	429,2166,3818	TT,TC,CC		30.9864,8.8345,23.5771	benign	1310/3640	42168400	3024,9802	2145	4268	6413	SO:0001583	missense	51332	exon21			TTTCTGCGCGCTC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4034G>A	15.37:g.42168400C>T	ENSP00000317790:p.Arg1345His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		340	0.15567765567765568	27	0.054878048780487805	69	0.19060773480662985	20	0.03496503496503497	224	0.2955145118733509	.	17.09	3.300924	0.60195	0.088345	0.309864	ENSG00000137877	ENST00000320955	T	0.49720	0.77	4.94	3.0	0.34707	.	0.710907	0.12920	N	0.428223	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.51791	0.948	P	0.45794	0.493	T	0.33599	-0.9862	9	0.72032	D	0.01	.	14.2271	0.65868	0.0:0.3011:0.6989:0.0	rs2290559;rs17686159;rs60823875;rs2290559	1345	Q9NRC6	SPTN5_HUMAN	H	1345	ENSP00000317790:R1345H	ENSP00000317790:R1345H	R	-	2	0	SPTBN5	39955692	0.979000	0.34478	0.000000	0.03702	0.000000	0.00434	4.573000	0.60893	0.562000	0.29204	-0.147000	0.13772	CGC	C|0.835;T|0.165	0.165	strong		0.632	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
ZHX2	22882	hgsc.bcm.edu	37	8	123964953	123964953	+	Silent	SNP	C	C	T	rs3808600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:123964953C>T	ENST00000314393.4	+	3	2038	c.1203C>T	c.(1201-1203)acC>acT	p.T401T		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	401	Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CAGGAGTCACCAACCATGGCC	0.632													C|||	1161	0.231829	0.0136	0.3314	5008	,	,		16083	0.131		0.3579	False		,,,				2504	0.4305				p.T401T	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.C1203T						PASS	.	C		308,4098	164.7+/-196.3	10,288,1905	50.0	57.0	55.0		1203	4.0	1.0	8	dbSNP_107	55	2985,5615	460.5+/-365.2	509,1967,1824	no	coding-synonymous	ZHX2	NM_014943.3		519,2255,3729	TT,TC,CC		34.7093,6.9905,25.3191		401/838	123964953	3293,9713	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			AGTCACCAACCAT	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1203C>T	8.37:g.123964953C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	107	63	0.588785	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			C|0.762;T|0.238	0.238	strong		0.632	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
ADAM21	8747	hgsc.bcm.edu	37	14	70924812	70924812	+	Missense_Mutation	SNP	C	C	T	rs370238293		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70924812C>T	ENST00000603540.1	+	2	854	c.596C>T	c.(595-597)tCt>tTt	p.S199F	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.S199F	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	199					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GAACCAAAATCTGCTGGTGAC	0.448																																					p.S199F		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,6	ADAM21	181	6	0			c.C596T						scavenged	.						74.0	76.0	75.0					14																	70924812		2203	4300	6503	SO:0001583	missense	8747	exon2			CAAAATCTGCTGG	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.596C>T	14.37:g.70924812C>T	ENSP00000474385:p.Ser199Phe	Somatic	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	244	13	0.0532787	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	C	9.262	1.043355	0.19748	.	.	ENSG00000139985	ENST00000267499	T	0.01215	5.16	3.49	3.49	0.39957	.	0.378699	0.19013	U	0.125029	T	0.02230	0.0069	M	0.68593	2.085	0.26948	N	0.966098	B	0.32876	0.388	B	0.37422	0.249	T	0.24764	-1.0151	10	0.40728	T	0.16	.	10.6601	0.45698	0.0:1.0:0.0:0.0	.	199	Q9UKJ8	ADA21_HUMAN	F	199	ENSP00000267499:S199F	ENSP00000267499:S199F	S	+	2	0	ADAM21	69994565	0.001000	0.12720	0.813000	0.32504	0.022000	0.10575	0.380000	0.20602	1.947000	0.56498	0.557000	0.71058	TCT	.	.	weak		0.448	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
PTPN7	5778	hgsc.bcm.edu	37	1	202124690	202124690	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202124690C>T	ENST00000308986.5	-	5	569	c.439G>A	c.(439-441)Gga>Aga	p.G147R	PTPN7_ENST00000543735.1_5'UTR|PTPN7_ENST00000492977.1_5'UTR|PTPN7_ENST00000309017.3_Missense_Mutation_p.G252R|PTPN7_ENST00000367279.4_Missense_Mutation_p.G186R|PTPN7_ENST00000544762.1_Intron			P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type 7	147	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	protein tyrosine phosphatase activity (GO:0004725)	p.G186*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|soft_tissue(1)|urinary_tract(1)	13						ATGTAATCTCCGTCCTCCTGG	0.542																																					p.G252R		Atlas-SNP	.											PTPN7,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PTPN7	31	1	1	Substitution - Nonsense(1)	central_nervous_system(1)	c.G754A						PASS	.						93.0	77.0	83.0					1																	202124690		2203	4300	6503	SO:0001583	missense	5778	exon5			AATCTCCGTCCTC	BC001746	CCDS1422.1, CCDS1423.1, CCDS1423.2	1q32.1	2011-06-09			ENSG00000143851	ENSG00000143851		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9659	protein-coding gene	gene with protein product		176889				1510684	Standard	NM_002832		Approved	HEPTP, LC-PTP	uc010ppx.2	P35236	OTTHUMG00000035931	ENST00000308986.5:c.439G>A	1.37:g.202124690C>T	ENSP00000311133:p.Gly147Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_002832	B3KXE1|Q53XK4|Q5SXQ0|Q5SXQ1|Q9BV05	Missense_Mutation	SNP	ENST00000308986.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.66|12.66	2.005836|2.005836	0.35415|0.35415	.|.	.|.	ENSG00000143851|ENSG00000143851	ENST00000367279;ENST00000309017;ENST00000308986;ENST00000477554;ENST00000476061;ENST00000467283;ENST00000464870|ENST00000477625;ENST00000435759	T;T;T;T;T;T;T|.	0.14022|.	2.54;2.54;2.54;2.54;2.75;2.75;2.75|.	5.26|5.26	4.33|4.33	0.51752|0.51752	Protein-tyrosine phosphatase, receptor/non-receptor type (3);|.	0.239923|.	0.29459|.	N|.	0.012088|.	T|T	0.49270|0.49270	0.1547|0.1547	M|M	0.62088|0.62088	1.915|1.915	0.19775|0.19775	N|N	0.999951|0.999951	P;B;B;B;P|.	0.43578|.	0.811;0.076;0.229;0.123;0.508|.	P;B;B;B;B|.	0.49561|.	0.615;0.223;0.256;0.223;0.314|.	T|T	0.44862|0.44862	-0.9300|-0.9300	10|6	0.87932|0.87932	D|D	0|0	-12.8237|-12.8237	9.366|9.366	0.38226|0.38226	0.0:0.8348:0.0:0.1652|0.0:0.8348:0.0:0.1652	.|.	221;95;99;147;186|.	B4DZD9;B4DVF0;Q8NFX3;P35236;P35236-2|.	.;.;.;PTN7_HUMAN;.|.	R|Q	186;252;147;228;146;146;147|78;153	ENSP00000356248:G186R;ENSP00000309116:G252R;ENSP00000311133:G147R;ENSP00000418416:G228R;ENSP00000419993:G146R;ENSP00000418837:G146R;ENSP00000420434:G147R|.	ENSP00000311133:G147R|ENSP00000406042:R153Q	G|R	-|-	1|2	0|0	PTPN7|PTPN7	200391313|200391313	0.005000|0.005000	0.15991|0.15991	0.011000|0.011000	0.14972|0.14972	0.665000|0.665000	0.39181|0.39181	1.125000|1.125000	0.31332|0.31332	1.180000|1.180000	0.42898|0.42898	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.	.	none		0.542	PTPN7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002832	
STON1	11037	hgsc.bcm.edu	37	2	48822381	48822381	+	Silent	SNP	G	G	A	rs2140551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:48822381G>A	ENST00000406226.1	+	5	2343	c.2148G>A	c.(2146-2148)aaG>aaA	p.K716K	STON1_ENST00000404752.1_Silent_p.K716K|STON1-GTF2A1L_ENST00000309827.2_Intron|STON1-GTF2A1L_ENST00000402114.2_Intron|STON1-GTF2A1L_ENST00000394751.3_Intron|STON1-GTF2A1L_ENST00000405008.1_Intron|STON1-GTF2A1L_ENST00000394754.1_Intron|STON1_ENST00000309835.3_Silent_p.K716K	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	716					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AAATAGAAAAGAAGTGGATTA	0.388													G|||	2432	0.485623	0.2814	0.5749	5008	,	,		20052	0.5575		0.5577	False		,,,				2504	0.5501				p.K716K		Atlas-SNP	.											.	STON1	100	.	0			c.G2148A						PASS	.	G	,,,,	1405,3001	457.5+/-351.6	213,979,1011	109.0	101.0	103.0		,,2148,2148,	3.0	1.0	2	dbSNP_96	103	4744,3856	606.3+/-395.1	1316,2112,872	yes	intron,intron,coding-synonymous,coding-synonymous,intron	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	1529,3091,1883	AA,AG,GG		44.8372,31.8883,47.2782	,,,,	,,716/736,716/736,	48822381	6149,6857	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon5			AGAAAAGAAGTGG	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.2148G>A	2.37:g.48822381G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			G|0.518;A|0.482	0.482	strong		0.388	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
SYMPK	8189	hgsc.bcm.edu	37	19	46341824	46341824	+	Silent	SNP	C	C	T	rs17850110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46341824C>T	ENST00000245934.7	-	10	1381	c.1137G>A	c.(1135-1137)ccG>ccA	p.P379P		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	379					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		AGGTCCCCGACGGGCCTGGCT	0.592													T|||	726	0.144968	0.1074	0.2334	5008	,	,		18331	0.0952		0.1571	False		,,,				2504	0.1718				p.P379P		Atlas-SNP	.											.	SYMPK	104	.	0			c.G1137A						PASS	.	T		476,3930	782.3+/-414.6	26,424,1753	66.0	58.0	60.0		1137	-11.7	0.0	19	dbSNP_123	60	1271,7329	759.8+/-407.6	98,1075,3127	no	coding-synonymous	SYMPK	NM_004819.2		124,1499,4880	TT,TC,CC		14.7791,10.8034,13.4323		379/1275	46341824	1747,11259	2203	4300	6503	SO:0001819	synonymous_variant	8189	exon10			CCCCGACGGGCCT	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.1137G>A	19.37:g.46341824C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			C|0.873;G|0.000;T|0.127	0.127	strong		0.592	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
SLC52A3	113278	hgsc.bcm.edu	37	20	746098	746098	+	Silent	SNP	G	G	A	rs3746808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:746098G>A	ENST00000217254.7	-	2	562	c.321C>T	c.(319-321)gcC>gcT	p.A107A	SLC52A3_ENST00000473664.1_5'UTR|SLC52A3_ENST00000381944.3_Silent_p.A107A	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	107					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										GGACCAAGAAGGCGATGCTGT	0.592													G|||	1284	0.25639	0.1362	0.3401	5008	,	,		19825	0.2014		0.3082	False		,,,				2504	0.363				p.A107A		Atlas-SNP	.											.	.	.	.	0			c.C321T						PASS	.	G		692,3714	275.4+/-272.5	54,584,1565	62.0	48.0	53.0		321	3.7	0.7	20	dbSNP_107	53	2633,5967	403.1+/-347.7	420,1793,2087	no	coding-synonymous	C20orf54	NM_033409.3		474,2377,3652	AA,AG,GG		30.6163,15.7059,25.5651		107/470	746098	3325,9681	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon2			CAAGAAGGCGATG	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.321C>T	20.37:g.746098G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	141	54	0.382979	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.754;A|0.246	0.246	strong		0.592	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
OR6N1	128372	hgsc.bcm.edu	37	1	158735740	158735740	+	Missense_Mutation	SNP	A	A	G	rs857826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158735740A>G	ENST00000335094.2	-	1	752	c.733T>C	c.(733-735)Ttc>Ctc	p.F245L		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	245			F -> L (in dbSNP:rs857826). {ECO:0000269|PubMed:12213199}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F245L(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					ACCACAGTGAAGTGGGAGGCA	0.537													G|||	3345	0.667931	0.7784	0.7839	5008	,	,		20507	0.6171		0.7217	False		,,,				2504	0.4335				p.F245L		Atlas-SNP	.											OR6N1,NS,carcinoma,0,3	OR6N1	96	3	2	Substitution - Missense(2)	prostate(2)	c.T733C						PASS	.	G	LEU/PHE	3436,970	365.1+/-317.3	1329,778,96	167.0	157.0	160.0		733	4.7	1.0	1	dbSNP_86	160	6162,2438	402.2+/-347.4	2217,1728,355	yes	missense	OR6N1	NM_001005185.1	22	3546,2506,451	GG,GA,AA		28.3488,22.0154,26.2033	benign	245/313	158735740	9598,3408	2203	4300	6503	SO:0001583	missense	128372	exon1			CAGTGAAGTGGGA	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.733T>C	1.37:g.158735740A>G	ENSP00000335535:p.Phe245Leu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	177	177	1	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	1561	0.7147435897435898	376	0.7642276422764228	286	0.7900552486187845	344	0.6013986013986014	555	0.7321899736147758	G	2.721	-0.266661	0.05754	0.779846	0.716512	ENSG00000197403	ENST00000335094	T	0.26810	1.71	4.74	4.74	0.60224	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41294	N	0.000915	T	0.01320	0.0043	N	0.00124	-2.055	0.46416	P	9.630000000000472E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	9	0.02654	T	1	-13.3645	12.1889	0.54257	0.0845:0.0:0.9155:0.0	rs857826;rs16841069;rs58086106;rs857826	245	Q8NGY5	OR6N1_HUMAN	L	245	ENSP00000335535:F245L	ENSP00000335535:F245L	F	-	1	0	OR6N1	157002364	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	3.015000	0.49599	1.211000	0.43351	-0.119000	0.15052	TTC	A|0.285;G|0.715	0.715	strong		0.537	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
AHNAK2	113146	hgsc.bcm.edu	37	14	105406235	105406235	+	Missense_Mutation	SNP	A	A	C	rs78014542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:105406235A>C	ENST00000333244.5	-	7	15672	c.15553T>G	c.(15553-15555)Tcg>Gcg	p.S5185A	AHNAK2_ENST00000557457.1_Missense_Mutation_p.S183A	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5185						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTTTCCTGCGAGTACTTGGTC	0.562													A|||	45	0.00898562	0.0008	0.0159	5008	,	,		21457	0.0		0.0258	False		,,,				2504	0.0072				p.S5185A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T15553G						PASS	.	A	ALA/SER	17,3929		0,17,1956	187.0	196.0	193.0		15553	-9.0	0.0	14	dbSNP_132	193	207,8131		2,203,3964	yes	missense	AHNAK2	NM_138420.2	99	2,220,5920	CC,CA,AA		2.4826,0.4308,1.8235	possibly-damaging	5185/5796	105406235	224,12060	1973	4169	6142	SO:0001583	missense	113146	exon7			CCTGCGAGTACTT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.15553T>G	14.37:g.105406235A>C	ENSP00000353114:p.Ser5185Ala	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	A	3.138	-0.176967	0.06380	0.004308	0.024826	ENSG00000185567	ENST00000557457;ENST00000333244	T;T	0.03553	3.89;6.01	4.51	-9.02	0.00741	.	0.849101	0.09521	U	0.790924	T	0.01124	0.0037	L	0.40543	1.245	0.09310	N	1	B	0.13145	0.007	B	0.15484	0.013	T	0.45877	-0.9231	10	0.08179	T	0.78	.	7.733	0.28797	0.1397:0.6082:0.1518:0.1004	.	5185	Q8IVF2	AHNK2_HUMAN	A	183;5185	ENSP00000450998:S183A;ENSP00000353114:S5185A	ENSP00000353114:S5185A	S	-	1	0	AHNAK2	104477280	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.909000	0.04058	-2.246000	0.00704	-0.379000	0.06801	TCG	A|0.988;C|0.012	0.012	strong		0.562	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR13C2	392376	hgsc.bcm.edu	37	9	107367704	107367704	+	Missense_Mutation	SNP	A	A	T	rs201900693	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107367704A>T	ENST00000542196.1	-	1	247	c.205T>A	c.(205-207)Ttg>Atg	p.L69M		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	69						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CAGATGTCCAAGAAGGAGAGG	0.483													A|||	215	0.0429313	0.0893	0.0115	5008	,	,		20012	0.0476		0.004	False		,,,				2504	0.0378				p.L69M		Atlas-SNP	.											OR13C2,NS,carcinoma,0,1	OR13C2	46	1	0			c.T205A						scavenged	.						16.0	18.0	18.0					9																	107367704		2196	4277	6473	SO:0001583	missense	392376	exon1			TGTCCAAGAAGGA		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.205T>A	9.37:g.107367704A>T	ENSP00000438815:p.Leu69Met	Somatic	804	71	0.0883085		WXS	Illumina HiSeq	Phase_I	782	56	0.0716113	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	.	.	.	.	.	.	.	.	.	.	A	13.36	2.214684	0.39102	.	.	ENSG00000257019	ENST00000542196	T	0.14391	2.51	3.39	-2.32	0.06745	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29948	U	0.010786	T	0.19208	0.0461	L	0.58302	1.8	0.09310	N	1	D	0.65815	0.995	P	0.53401	0.725	T	0.09058	-1.0692	10	0.56958	D	0.05	.	9.8961	0.41320	0.3456:0.0:0.6544:0.0	.	69	Q8NGS9	O13C2_HUMAN	M	69	ENSP00000438815:L69M	ENSP00000438815:L69M	L	-	1	2	OR13C2	106407525	0.000000	0.05858	0.993000	0.49108	0.979000	0.70002	-3.903000	0.00338	-0.393000	0.07739	0.379000	0.24179	TTG	A|0.222;T|0.778	0.778	strong		0.483	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
USP16	10600	hgsc.bcm.edu	37	21	30408670	30408670	+	Missense_Mutation	SNP	A	A	T	rs2274802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:30408670A>T	ENST00000334352.4	+	6	654	c.423A>T	c.(421-423)caA>caT	p.Q141H	USP16_ENST00000399975.3_Missense_Mutation_p.Q141H|USP16_ENST00000399976.2_Missense_Mutation_p.Q141H|USP16_ENST00000535828.1_Intron	NM_001032410.1	NP_001027582.1			ubiquitin specific peptidase 16											breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(2)	34						TCAGAAAACAAGCCAGCATTA	0.353													A|||	891	0.177915	0.0885	0.17	5008	,	,		19840	0.1131		0.2783	False		,,,				2504	0.2679				p.Q141H	Melanoma(92;625 1444 27493 34101 44971)	Atlas-SNP	.											.	USP16	65	.	0			c.A423T						PASS	.	A	HIS/GLN,HIS/GLN,HIS/GLN	508,3898	235.5+/-248.0	31,446,1726	144.0	137.0	139.0		423,423,423	2.0	1.0	21	dbSNP_100	139	2121,6479	367.5+/-334.7	264,1593,2443	yes	missense,missense,missense	USP16	NM_001001992.1,NM_001032410.1,NM_006447.2	24,24,24	295,2039,4169	TT,TA,AA		24.6628,11.5297,20.2137	possibly-damaging,possibly-damaging,possibly-damaging	141/823,141/824,141/824	30408670	2629,10377	2203	4300	6503	SO:0001583	missense	10600	exon5			AAAACAAGCCAGC	AF126736	CCDS13583.1, CCDS42912.1	21q21	2008-04-11	2005-08-08		ENSG00000156256	ENSG00000156256		"""Ubiquitin-specific peptidases"""	12614	protein-coding gene	gene with protein product		604735	"""ubiquitin specific protease 16"""			12838346	Standard	NM_006447		Approved	Ubp-M	uc002ymy.3	Q9Y5T5	OTTHUMG00000078802	ENST00000334352.4:c.423A>T	21.37:g.30408670A>T	ENSP00000334808:p.Gln141His	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	NM_006447		Missense_Mutation	SNP	ENST00000334352.4	37	CCDS13583.1	375	0.1717032967032967	43	0.08739837398373984	66	0.18232044198895028	61	0.10664335664335664	205	0.2704485488126649	A	8.584	0.883010	0.17467	0.115297	0.246628	ENSG00000156256	ENST00000399975;ENST00000399976;ENST00000334352	T;T;T	0.06294	3.32;3.35;3.35	5.85	2.02	0.26589	Zinc finger, RING/FYVE/PHD-type (1);	0.104153	0.64402	D	0.000002	T	0.00012	0.0000	N	0.11201	0.11	0.09310	P	0.9999999999999911	D;D;D	0.89917	0.996;1.0;1.0	D;D;D	0.77004	0.961;0.989;0.961	T	0.20240	-1.0281	9	0.06494	T	0.89	.	6.7394	0.23426	0.7366:0.1286:0.1349:0.0	rs2274802;rs17852823;rs52826900;rs2274802	127;141;141	Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5	.;.;UBP16_HUMAN	H	141	ENSP00000382857:Q141H;ENSP00000382858:Q141H;ENSP00000334808:Q141H	ENSP00000334808:Q141H	Q	+	3	2	USP16	29330541	1.000000	0.71417	0.969000	0.41365	0.293000	0.27360	3.760000	0.55235	0.478000	0.27488	0.533000	0.62120	CAA	A|0.804;T|0.196	0.196	strong		0.353	USP16-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171847.1		
THAP4	51078	hgsc.bcm.edu	37	2	242573211	242573211	+	Missense_Mutation	SNP	T	T	C	rs7424328	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242573211T>C	ENST00000407315.1	-	2	792	c.361A>G	c.(361-363)Agc>Ggc	p.S121G		NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	121			S -> G (in dbSNP:rs7424328). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874}.				DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		GCTCCTCTGCTGGTGGCGGCA	0.637													C|||	3055	0.610024	0.5257	0.5908	5008	,	,		18238	0.8889		0.4592	False		,,,				2504	0.6053				p.S121G		Atlas-SNP	.											.	THAP4	27	.	0			c.A361G						PASS	.	C	GLY/SER	2226,2180	580.5+/-385.1	555,1116,532	74.0	75.0	74.0		361	-1.9	0.0	2	dbSNP_116	74	3893,4699	602.4+/-394.5	893,2107,1296	yes	missense	THAP4	NM_015963.5	56	1448,3223,1828	CC,CT,TT		45.3096,49.478,47.0765	benign	121/578	242573211	6119,6879	2203	4296	6499	SO:0001583	missense	51078	exon2			CTCTGCTGGTGGC	AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"""THAP (C2CH-type zinc finger) domain containing"""	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.361A>G	2.37:g.242573211T>C	ENSP00000385006:p.Ser121Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Missense_Mutation	SNP	ENST00000407315.1	37	CCDS2551.1	1302	0.5961538461538461	258	0.524390243902439	198	0.5469613259668509	499	0.8723776223776224	347	0.4577836411609499	C	0.108	-1.141827	0.01728	0.50522	0.453096	ENSG00000176946	ENST00000407315	D	0.95690	-3.78	4.69	-1.86	0.07760	.	1.710450	0.03691	N	0.247116	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.32134	-0.9918	9	0.10636	T	0.68	-7.9501	5.9451	0.19213	0.1647:0.3858:0.0:0.4495	rs7424328	121	Q8WY91	THAP4_HUMAN	G	121	ENSP00000385006:S121G	ENSP00000385006:S121G	S	-	1	0	THAP4	242221884	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.450000	0.06803	-0.591000	0.05859	-1.557000	0.00889	AGC	T|0.492;C|0.508	0.508	strong		0.637	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963	
EEF1D	1936	hgsc.bcm.edu	37	8	144660046	144660046	+	IGR	SNP	G	G	A	rs896954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144660046G>A	ENST00000529272.1	-	0	1311				NAPRT1_ENST00000460623.1_5'Flank|NAPRT1_ENST00000426292.3_Silent_p.A98A|NAPRT1_ENST00000276844.7_Silent_p.A98A|RP11-661A12.7_ENST00000529247.1_RNA|NAPRT1_ENST00000449291.2_Silent_p.A98A|NAPRT1_ENST00000435154.3_Silent_p.A98A|RP11-661A12.9_ENST00000531730.1_RNA			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			AGCAGTCGAGGGCCCGAAGGT	0.697													G|||	777	0.155152	0.0749	0.255	5008	,	,		13421	0.0933		0.169	False		,,,				2504	0.2423				p.A98A		Atlas-SNP	.											NAPRT1,extremity,malignant_melanoma,-2,1	NAPRT1	47	1	0			c.C294T						PASS	.	G		426,3962		21,384,1789	34.0	32.0	33.0		294	2.3	0.2	8	dbSNP_86	33	1365,7205		104,1157,3024	no	coding-synonymous	NAPRT1	NM_145201.4		125,1541,4813	AA,AG,GG		15.9277,9.7083,13.8216		98/539	144660046	1791,11167	2194	4285	6479	SO:0001628	intergenic_variant	93100	exon2			GTCGAGGGCCCGA	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191		8.37:g.144660046G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	37	11	0.297297	NM_145201	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Silent	SNP	ENST00000529272.1	37	CCDS6405.1																																																																																			G|0.851;A|0.149	0.149	strong		0.697	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378	
APBB3	10307	hgsc.bcm.edu	37	5	139936980	139936980	+	IGR	SNP	A	A	G	rs250427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139936980A>G	ENST00000357560.4	-	0	2218				SRA1_ENST00000520427.1_Intron|SRA1_ENST00000336283.6_Intron	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGGGGCGACAACCTAGTGCC	0.667													G|||	3551	0.709065	0.5696	0.7493	5008	,	,		14128	0.8254		0.7187	False		,,,				2504	0.7393				p.C20R		Atlas-SNP	.											.	SRA1	24	.	0			c.T58C						PASS	.	G		2750,1578		886,978,300	8.0	10.0	9.0			-3.3	0.0	5	dbSNP_79	9	6054,2436		2195,1664,386	no	intron	SRA1	NM_001035235.2		3081,2642,686	GG,GA,AA		28.6926,36.4603,31.3153			139936980	8804,4014	2164	4245	6409	SO:0001628	intergenic_variant	10011	exon1			GGCGACAACCTAG	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504		5.37:g.139936980A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	69	15	0.217391	NM_001253764	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	37	CCDS4229.1																																																																																			A|0.290;G|0.710	0.710	strong		0.667	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
PGAM5	192111	hgsc.bcm.edu	37	12	133294333	133294333	+	Silent	SNP	C	C	T	rs61978651	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133294333C>T	ENST00000498926.2	+	4	592	c.534C>T	c.(532-534)ggC>ggT	p.G178G	PXMP2_ENST00000545677.1_3'UTR|PGAM5_ENST00000317555.2_Silent_p.G178G|PGAM5_ENST00000543955.1_Silent_p.G29G|PGAM5_ENST00000454808.2_Silent_p.G29G	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	178					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		TGCGGGAAGGCGCCCCCATCG	0.667													C|||	273	0.0545128	0.0015	0.0461	5008	,	,		11840	0.1081		0.0855	False		,,,				2504	0.045				p.G178G		Atlas-SNP	.											PGAM5,NS,carcinoma,+1,1	PGAM5	18	1	0			c.C534T						PASS	.	C	,,	57,4269		0,57,2106	20.0	26.0	24.0		534,534,534	-5.2	1.0	12	dbSNP_129	24	669,7871		29,611,3630	no	coding-synonymous,coding-synonymous,coding-synonymous	PGAM5	NM_001170543.1,NM_001170544.1,NM_138575.3	,,	29,668,5736	TT,TC,CC		7.8337,1.3176,5.6428	,,	178/290,178/289,178/256	133294333	726,12140	2163	4270	6433	SO:0001819	synonymous_variant	192111	exon4			GGAAGGCGCCCCC	BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.534C>T	12.37:g.133294333C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	47	32	0.680851	NM_138575	A9LN06|C9IZY7|Q96JB0	Silent	SNP	ENST00000498926.2	37	CCDS53845.1																																																																																			C|0.942;T|0.058	0.058	strong		0.667	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575	
SIGLEC12	89858	hgsc.bcm.edu	37	19	52001485	52001485	+	Missense_Mutation	SNP	G	G	A	rs11668530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52001485G>A	ENST00000291707.3	-	5	1247	c.1192C>T	c.(1192-1194)Cac>Tac	p.H398Y	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.H280Y	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	398	Ig-like C2-type 2.		H -> Y (in dbSNP:rs11668530).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CAGACAAGGTGCAGGGACTGG	0.597													g|||	1770	0.353435	0.0605	0.513	5008	,	,		17523	0.2728		0.498	False		,,,				2504	0.5706				p.H398Y		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.C1192T						PASS	.	G	TYR/HIS,TYR/HIS	631,3775		52,527,1624	39.0	35.0	36.0		838,1192	1.4	0.2	19	dbSNP_120	36	4457,4143		1169,2119,1012	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	83,83	1221,2646,2636	AA,AG,GG		48.1744,14.3214,39.1204	benign,benign	280/478,398/596	52001485	5088,7918	2203	4300	6503	SO:0001583	missense	89858	exon5			CAAGGTGCAGGGA	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1192C>T	19.37:g.52001485G>A	ENSP00000291707:p.His398Tyr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	740	0.33882783882783885	40	0.08130081300813008	174	0.48066298342541436	145	0.2534965034965035	381	0.5026385224274407	.	5.039	0.192805	0.09599	0.143214	0.518256	ENSG00000254521	ENST00000291707	T	0.11930	2.73	1.39	1.39	0.22231	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.407398	0.18126	U	0.150893	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.22983	0.078;0.024	B;B	0.30401	0.115;0.022	T	0.42103	-0.9471	9	0.27082	T	0.32	.	6.2185	0.20667	0.0:0.0:1.0:0.0	rs11668530;rs56924805;rs11668530	398;280	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	Y	398	ENSP00000291707:H398Y	ENSP00000291707:H398Y	H	-	1	0	SIGLEC12	56693297	0.087000	0.21565	0.164000	0.22755	0.025000	0.11179	0.197000	0.17197	1.076000	0.40961	0.393000	0.25936	CAC	G|0.640;A|0.360	0.360	strong		0.597	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
PIM3	415116	hgsc.bcm.edu	37	22	50354773	50354773	+	Splice_Site	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50354773C>T	ENST00000360612.4	+	2	521	c.86C>T	c.(85-87)gCc>gTc	p.A29V		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	29					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		CTCCCTGCAGCCAAGGCGGAC	0.786																																					p.A29V		Atlas-SNP	.											.	PIM3	15	.	0			c.C86T						PASS	.						5.0	5.0	5.0					22																	50354773		1996	4027	6023	SO:0001630	splice_region_variant	415116	exon2			CTGCAGCCAAGGC	BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"""pim-3 oncogene"""			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.86-1C>T	22.37:g.50354773C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	16	7	0.4375	NM_001001852	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Missense_Mutation	SNP	ENST00000360612.4	37	CCDS33678.1	.	.	.	.	.	.	.	.	.	.	c	7.065	0.567090	0.13560	.	.	ENSG00000198355	ENST00000360612	T	0.56611	0.45	2.28	-0.308	0.12773	Protein kinase-like domain (1);	0.177323	0.37393	U	0.002107	T	0.19485	0.0468	N	0.02802	-0.49	0.36106	D	0.844454	B	0.06786	0.001	B	0.09377	0.004	T	0.03910	-1.0993	10	0.21540	T	0.41	.	3.0393	0.06133	0.0:0.3221:0.2312:0.4467	.	29	Q86V86	PIM3_HUMAN	V	29	ENSP00000353824:A29V	ENSP00000353824:A29V	A	+	2	0	PIM3	48740777	1.000000	0.71417	0.559000	0.28332	0.795000	0.44927	1.317000	0.33631	-0.287000	0.09064	0.291000	0.19559	GCC	.	.	none		0.786	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852	Missense_Mutation
ZNF283	284349	hgsc.bcm.edu	37	19	44352639	44352639	+	Missense_Mutation	SNP	G	G	A	rs1061768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44352639G>A	ENST00000324461.7	+	7	2183	c.1886G>A	c.(1885-1887)cGt>cAt	p.R629H	ZNF283_ENST00000588797.1_Missense_Mutation_p.R490H	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	629			R -> H (in dbSNP:rs1061768).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				CTTTATCAACGTAAGGAATTC	0.398													G|||	750	0.14976	0.1316	0.1787	5008	,	,		20278	0.0744		0.2227	False		,,,				2504	0.1564				p.R629H		Atlas-SNP	.											.	ZNF283	83	.	0			c.G1886A						PASS	.	G	HIS/ARG	565,3571		23,519,1526	102.0	110.0	107.0		1886	2.6	0.2	19	dbSNP_86	107	1754,6704		175,1404,2650	yes	missense	ZNF283	NM_181845.1	29	198,1923,4176	AA,AG,GG		20.7378,13.6605,18.4135	benign	629/680	44352639	2319,10275	2068	4229	6297	SO:0001583	missense	284349	exon7			ATCAACGTAAGGA	AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"""Zinc fingers, C2H2-type"", ""-"""	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.1886G>A	19.37:g.44352639G>A	ENSP00000327314:p.Arg629His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	357	0.16346153846153846	83	0.16869918699186992	53	0.1464088397790055	45	0.07867132867132867	176	0.23218997361477572	G	12.00	1.805208	0.31961	0.136605	0.207378	ENSG00000167637	ENST00000324461	T	0.14766	2.48	2.61	2.61	0.31194	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.09310	P	1.0	P	0.36660	0.564	B	0.31337	0.128	T	0.42716	-0.9435	8	0.87932	D	0	.	12.3634	0.55215	0.0:0.0:1.0:0.0	rs1061768;rs3170394;rs56865400;rs1061768	629	Q8N7M2	ZN283_HUMAN	H	629	ENSP00000327314:R629H	ENSP00000327314:R629H	R	+	2	0	ZNF283	49044479	0.986000	0.35501	0.234000	0.24042	0.459000	0.32528	3.677000	0.54619	1.440000	0.47531	0.563000	0.77884	CGT	G|0.832;A|0.168	0.168	strong		0.398	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
MYH3	4621	hgsc.bcm.edu	37	17	10544416	10544416	+	Silent	SNP	G	G	T	rs876657	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:10544416G>T	ENST00000583535.1	-	19	2238	c.2151C>A	c.(2149-2151)ggC>ggA	p.G717G	MYH3_ENST00000226209.7_Silent_p.G717G	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	717	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						GTTTAAAATCGCCATAGAGAA	0.458																																					p.G717G		Atlas-SNP	.											.	MYH3	227	.	0			c.C2151A						PASS	.	T		1299,3107	696.8+/-406.1	197,905,1101	125.0	113.0	117.0		2151	-3.4	0.9	17	dbSNP_86	117	6267,2333	388.9+/-342.7	2259,1749,292	no	coding-synonymous	MYH3	NM_002470.3		2456,2654,1393	TT,TG,GG		27.1279,29.4825,41.8268		717/1941	10544416	7566,5440	2203	4300	6503	SO:0001819	synonymous_variant	4621	exon19			AAAATCGCCATAG		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2151C>A	17.37:g.10544416G>T		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	243	243	1	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	37	CCDS11157.1																																																																																			G|0.466;T|0.534	0.534	strong		0.458	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
SIM1	6492	hgsc.bcm.edu	37	6	100868721	100868721	+	Missense_Mutation	SNP	G	G	A	rs3734355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:100868721G>A	ENST00000369208.3	-	10	1894	c.1112C>T	c.(1111-1113)gCc>gTc	p.A371V	SIM1_ENST00000262901.4_Missense_Mutation_p.A371V			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	371	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.		A -> V (in dbSNP:rs3734355).		cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.A371V(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		CCGGGATTTGGCCCCCTTTCT	0.517													G|||	894	0.178514	0.0053	0.2089	5008	,	,		15370	0.4067		0.1471	False		,,,				2504	0.1881				p.A371V		Atlas-SNP	.											SIM1,NS,carcinoma,0,1	SIM1	173	1	1	Substitution - Missense(1)	stomach(1)	c.C1112T						PASS	.	G	VAL/ALA	139,4267	97.6+/-136.3	2,135,2066	111.0	104.0	106.0		1112	2.9	1.0	6	dbSNP_107	106	1172,7428	239.3+/-270.5	62,1048,3190	yes	missense	SIM1	NM_005068.2	64	64,1183,5256	AA,AG,GG		13.6279,3.1548,10.08	benign	371/767	100868721	1311,11695	2203	4300	6503	SO:0001583	missense	6492	exon9			GATTTGGCCCCCT	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1112C>T	6.37:g.100868721G>A	ENSP00000358210:p.Ala371Val	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	162	85	0.524691	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	432	0.1978021978021978	7	0.014227642276422764	76	0.20994475138121546	236	0.4125874125874126	113	0.14907651715039577	G	15.06	2.722664	0.48728	0.031548	0.136279	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.33438	1.41;1.41	5.8	2.86	0.33363	Single-minded, C-terminal (2);	0.916570	0.09543	N	0.788056	T	0.06645	0.0170	N	0.19112	0.55	0.35594	P	0.19266700000000003	B	0.10296	0.003	B	0.12156	0.007	T	0.30592	-0.9973	9	0.27785	T	0.31	.	4.3759	0.11270	0.0874:0.3246:0.4629:0.1251	rs3734355;rs3734355	371	P81133	SIM1_HUMAN	V	371	ENSP00000358210:A371V;ENSP00000262901:A371V	ENSP00000262901:A371V	A	-	2	0	SIM1	100975442	0.941000	0.31946	1.000000	0.80357	0.987000	0.75469	1.394000	0.34509	1.466000	0.48025	-0.157000	0.13467	GCC	G|0.857;A|0.143	0.143	strong		0.517	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
NEK11	79858	hgsc.bcm.edu	37	3	130947435	130947435	+	Missense_Mutation	SNP	A	A	T	rs3738000	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130947435A>T	ENST00000510769.1	+	11	1401	c.1148A>T	c.(1147-1149)gAa>gTa	p.E383V	NEK11_ENST00000412440.2_Missense_Mutation_p.E304V|NEK11_ENST00000429253.2_Missense_Mutation_p.E488V|NEK11_ENST00000510688.1_Missense_Mutation_p.E488V|NEK11_ENST00000508196.1_Missense_Mutation_p.E488V|NEK11_ENST00000383366.4_Missense_Mutation_p.E488V					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						TCCTATTGTGAAGAGAGTGAT	0.423													A|||	2474	0.49401	0.1838	0.5879	5008	,	,		19367	0.4058		0.7018	False		,,,				2504	0.7239				p.E488V		Atlas-SNP	.											.	NEK11	76	.	0			c.A1463T						PASS	.	A	VAL/GLU,VAL/GLU	1145,3261	406.9+/-334.0	145,855,1203	133.0	125.0	127.0		1463,1463	5.7	1.0	3	dbSNP_107	127	6092,2508	694.3+/-404.7	2134,1824,342	yes	missense,missense	NEK11	NM_001146003.1,NM_024800.4	121,121	2279,2679,1545	TT,TA,AA		29.1628,25.9873,44.3565	probably-damaging,probably-damaging	488/600,488/646	130947435	7237,5769	2203	4300	6503	SO:0001583	missense	79858	exon15			ATTGTGAAGAGAG	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.1148A>T	3.37:g.130947435A>T	ENSP00000421549:p.Glu383Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_024800		Missense_Mutation	SNP	ENST00000510769.1	37		1054	0.4826007326007326	90	0.18292682926829268	215	0.5939226519337016	219	0.38286713286713286	530	0.6992084432717678	A	17.75	3.467512	0.63625	0.259873	0.708372	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000510688;ENST00000383366;ENST00000412440;ENST00000508196	T;T;T;T;T;T	0.76186	-0.91;-0.73;-1.0;-0.73;-0.96;-0.73	5.67	5.67	0.87782	.	0.324438	0.22031	N	0.065583	T	0.00012	0.0000	L	0.55481	1.735	0.24132	P	0.9957671	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.999;0.997	T	0.51679	-0.8675	9	0.52906	T	0.07	.	13.4265	0.61028	1.0:0.0:0.0:0.0	rs3738000;rs57477185;rs3738000	383;304;488;488	E9PHI8;B4DDN2;Q8NG66-4;Q8NG66	.;.;.;NEK11_HUMAN	V	383;488;488;488;304;488	ENSP00000421549:E383V;ENSP00000397180:E488V;ENSP00000423458:E488V;ENSP00000372857:E488V;ENSP00000411888:E304V;ENSP00000421851:E488V	ENSP00000372857:E488V	E	+	2	0	NEK11	132430125	1.000000	0.71417	1.000000	0.80357	0.382000	0.30200	5.115000	0.64655	2.144000	0.66660	0.533000	0.62120	GAA	A|0.481;T|0.519	0.519	strong		0.423	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800	
PHACTR2	9749	hgsc.bcm.edu	37	6	144081768	144081768	+	Silent	SNP	C	C	A	rs2073215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:144081768C>A	ENST00000427704.2	+	5	782	c.652C>A	c.(652-654)Cga>Aga	p.R218R	PHACTR2_ENST00000367584.4_Intron|PHACTR2_ENST00000440869.2_Silent_p.R229R|PHACTR2_ENST00000367582.3_Intron|PHACTR2_ENST00000305766.6_Intron	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	218							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		AAACACGACCCGAGAGGCTGG	0.557													C|||	1098	0.219249	0.2247	0.183	5008	,	,		18438	0.3988		0.0964	False		,,,				2504	0.1789				p.R229R	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											.	PHACTR2	99	.	0			c.C685A						PASS	.	C	,,,	782,2942		89,604,1169	40.0	45.0	44.0		685,,,652	6.1	1.0	6	dbSNP_96	44	666,7516		30,606,3455	no	coding-synonymous,intron,intron,coding-synonymous	PHACTR2	NM_001100164.1,NM_001100165.1,NM_001100166.1,NM_014721.2	,,,	119,1210,4624	AA,AC,CC		8.1398,20.9989,12.1619	,,,	229/646,,,218/635	144081768	1448,10458	1862	4091	5953	SO:0001819	synonymous_variant	9749	exon5			ACGACCCGAGAGG	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"""Phosphatase and actin regulators"""	20956	protein-coding gene	gene with protein product		608724	"""chromosome 6 open reading frame 56"""	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.652C>A	6.37:g.144081768C>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Silent	SNP	ENST00000427704.2	37	CCDS47492.1																																																																																			C|0.800;A|0.200	0.200	strong		0.557	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721	
SYNJ2	8871	hgsc.bcm.edu	37	6	158502527	158502527	+	Silent	SNP	C	C	T	rs1744177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:158502527C>T	ENST00000355585.4	+	20	2925	c.2850C>T	c.(2848-2850)gaC>gaT	p.D950D	SYNJ2_ENST00000367112.1_Silent_p.D35D|SYNJ2_ENST00000367121.3_Silent_p.D950D|SYNJ2_ENST00000367122.2_Silent_p.D950D	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	950	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		GTGTCCTGGACGTGGACGGTA	0.502													C|||	332	0.0662939	0.0923	0.049	5008	,	,		17254	0.001		0.1004	False		,,,				2504	0.0757				p.D950D		Atlas-SNP	.											.	SYNJ2	111	.	0			c.C2850T						PASS	.	C	,	474,3932	223.3+/-239.8	25,424,1754	122.0	95.0	104.0		2139,2850	-6.9	0.8	6	dbSNP_89	104	909,7691	202.4+/-245.7	53,803,3444	no	coding-synonymous,coding-synonymous	SYNJ2	NM_001178088.1,NM_003898.3	,	78,1227,5198	TT,TC,CC		10.5698,10.7581,10.6336	,	713/1260,950/1497	158502527	1383,11623	2203	4300	6503	SO:0001819	synonymous_variant	8871	exon20			CCTGGACGTGGAC	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.2850C>T	6.37:g.158502527C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	37	CCDS5254.1																																																																																			C|0.911;T|0.089	0.089	strong		0.502	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2		
RYR3	6263	hgsc.bcm.edu	37	15	33905410	33905410	+	Missense_Mutation	SNP	A	A	G	rs2229116	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:33905410A>G	ENST00000389232.4	+	19	2261	c.2191A>G	c.(2191-2193)Atc>Gtc	p.I731V	RYR3_ENST00000415757.3_Missense_Mutation_p.I731V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	731	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.		I -> V (in dbSNP:rs2229116). {ECO:0000269|PubMed:9515741}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGTGGCTTCCATCAACCAGCA	0.602													A|||	1012	0.202077	0.1271	0.3314	5008	,	,		18103	0.1587		0.2247	False		,,,				2504	0.2331				p.I731V		Atlas-SNP	.											RYR3,colon,carcinoma,0,1	RYR3	760	1	0			c.A2191G						PASS	.	A	VAL/ILE	576,3604		30,516,1544	38.0	41.0	40.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2191	3.1	1.0	15	dbSNP_98	40	1824,6658		203,1418,2620	yes	missense	RYR3	NM_001036.3	29	233,1934,4164	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	21.5044,13.7799,18.9544	benign	731/4871	33905410	2400,10262	2090	4241	6331	SO:0001583	missense	6263	exon19			GCTTCCATCAACC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.2191A>G	15.37:g.33905410A>G	ENSP00000373884:p.Ile731Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	184	99	0.538043	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	477	0.2184065934065934	89	0.18089430894308944	114	0.3149171270718232	98	0.17132867132867133	176	0.23218997361477572	A	8.841	0.942258	0.18281	0.137799	0.215044	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.68331	-0.32;-0.32	5.4	3.06	0.35304	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.296753	0.33457	N	0.004896	T	0.00012	0.0000	N	0.19112	0.55	0.39187	P	0.037104000000000026	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18147	-1.0346	9	0.15952	T	0.53	.	2.9905	0.05981	0.4962:0.232:0.2718:0.0	rs2229116;rs2277889;rs8042362;rs17817397;rs52825179;rs58186010;rs2229116	731;731	Q15413-2;Q15413	.;RYR3_HUMAN	V	731	ENSP00000373884:I731V;ENSP00000399610:I731V	ENSP00000354735:I731V	I	+	1	0	RYR3	31692702	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.792000	0.26929	1.079000	0.41038	0.529000	0.55759	ATC	A|0.790;G|0.210	0.210	strong		0.602	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
SPATA22	84690	hgsc.bcm.edu	37	17	3352309	3352309	+	Missense_Mutation	SNP	T	T	C	rs11556563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3352309T>C	ENST00000573128.1	-	6	947	c.464A>G	c.(463-465)cAa>cGa	p.Q155R	SPATA22_ENST00000575375.1_Missense_Mutation_p.Q155R|SPATA22_ENST00000268981.5_Missense_Mutation_p.Q155R|SPATA22_ENST00000355380.4_Missense_Mutation_p.Q112R|SPATA22_ENST00000541913.1_Missense_Mutation_p.Q139R|SPATA22_ENST00000572969.1_Missense_Mutation_p.Q155R|SPATA22_ENST00000397168.3_Missense_Mutation_p.Q155R			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	155			Q -> R (in dbSNP:rs11556563).		fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						TAATTGTTTTTGTTGTTGAGC	0.363													t|||	859	0.171526	0.0643	0.2421	5008	,	,		15634	0.002		0.4523	False		,,,				2504	0.1524				p.Q155R		Atlas-SNP	.											.	SPATA22	49	.	0			c.A464G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	608,3798	264.7+/-266.2	58,492,1653	243.0	235.0	238.0		464,335,464,464,464,464	0.1	0.0	17	dbSNP_120	238	4152,4448	566.3+/-388.6	1020,2112,1168	yes	missense,missense,missense,missense,missense,missense	SPATA22	NM_001170695.1,NM_001170696.1,NM_001170697.1,NM_001170698.1,NM_001170699.1,NM_032598.4	43,43,43,43,43,43	1078,2604,2821	CC,CT,TT		48.2791,13.7994,36.5985	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	155/364,112/321,155/364,155/364,155/270,155/364	3352309	4760,8246	2203	4300	6503	SO:0001583	missense	84690	exon6			TGTTTTTGTTGTT	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.464A>G	17.37:g.3352309T>C	ENSP00000459580:p.Gln155Arg	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	308	308	1	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Missense_Mutation	SNP	ENST00000573128.1	37	CCDS11027.1	470	0.21520146520146521	31	0.06300813008130081	96	0.26519337016574585	2	0.0034965034965034965	341	0.449868073878628	t	8.804	0.933511	0.18206	0.137994	0.482791	ENSG00000141255	ENST00000355380;ENST00000397168;ENST00000268981;ENST00000541913	T;T;T;T	0.19250	2.16;2.18;2.18;2.18	5.07	0.123	0.14709	.	0.259602	0.25411	N	0.030870	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P;P;P;P	0.52061	0.718;0.933;0.95;0.718	B;P;P;B	0.49829	0.281;0.623;0.453;0.281	T	0.47849	-0.9085	9	0.41790	T	0.15	0.4278	5.2873	0.15708	0.0:0.2463:0.1424:0.6113	rs11556563;rs17175171;rs52810964;rs57028001;rs11556563	139;155;112;155	F5GWB9;B4DXB1;Q8NHS9-2;Q8NHS9	.;.;.;SPT22_HUMAN	R	112;155;155;139	ENSP00000347541:Q112R;ENSP00000380354:Q155R;ENSP00000268981:Q155R;ENSP00000441920:Q139R	ENSP00000268981:Q155R	Q	-	2	0	SPATA22	3299059	0.065000	0.20965	0.008000	0.14137	0.052000	0.14988	0.202000	0.17295	0.036000	0.15547	0.454000	0.30748	CAA	T|0.702;C|0.298	0.298	strong		0.363	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
LDLR	3949	hgsc.bcm.edu	37	19	11227602	11227602	+	Silent	SNP	C	C	T	rs688	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11227602C>T	ENST00000558518.1	+	12	1960	c.1773C>T	c.(1771-1773)aaC>aaT	p.N591N	LDLR_ENST00000557933.1_Silent_p.N591N|LDLR_ENST00000535915.1_Silent_p.N550N|LDLR_ENST00000558013.1_Silent_p.N591N|LDLR_ENST00000455727.2_Silent_p.N423N|LDLR_ENST00000545707.1_Silent_p.N464N	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	591					cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	TCGATGTCAACGGGGGCAACC	0.542													C|||	1381	0.275759	0.0439	0.4582	5008	,	,		17670	0.1835		0.4414	False		,,,				2504	0.3845				p.N591N	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.C1773T	GRCh37	CM984053	LDLR	M	rs688	PASS	.	C	,,,,,	486,3920	227.5+/-242.7	36,414,1753	234.0	208.0	217.0		1773,1773,1650,1269,1410,1392	-6.7	0.0	19	dbSNP_36	217	3874,4726	543.7+/-384.4	847,2180,1273	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	,,,,,	883,2594,3026	TT,TC,CC		45.0465,11.0304,33.523	,,,,,	591/861,591/859,550/820,423/693,470/740,464/683	11227602	4360,8646	2203	4300	6503	SO:0001819	synonymous_variant	3949	exon12			TGTCAACGGGGGC	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1773C>T	19.37:g.11227602C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	201	95	0.472637	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Silent	SNP	ENST00000558518.1	37	CCDS12254.1																																																																																			C|0.717;N|0.000	.	strong		0.542	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
DSCAM	1826	hgsc.bcm.edu	37	21	41559182	41559182	+	Silent	SNP	G	G	A	rs2297267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:41559182G>A	ENST00000400454.1	-	14	3132	c.2655C>T	c.(2653-2655)ccC>ccT	p.P885P		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	885	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GAGGGTCTGGGGGCTCTGTGC	0.483													G|||	211	0.0421326	0.0061	0.0389	5008	,	,		17522	0.127		0.0229	False		,,,				2504	0.0256				p.P885P	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C2655T						PASS	.	G		32,3852		0,32,1910	96.0	95.0	96.0		2655	2.3	1.0	21	dbSNP_100	96	160,8140		1,158,3991	no	coding-synonymous	DSCAM	NM_001389.3		1,190,5901	AA,AG,GG		1.9277,0.8239,1.5758		885/2013	41559182	192,11992	1942	4150	6092	SO:0001819	synonymous_variant	1826	exon14			GTCTGGGGGCTCT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.2655C>T	21.37:g.41559182G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	146	70	0.479452	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																			G|0.952;A|0.048	0.048	strong		0.483	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
SLC4A2	6522	hgsc.bcm.edu	37	7	150761314	150761314	+	Missense_Mutation	SNP	G	G	A	rs2303929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150761314G>A	ENST00000485713.1	+	3	1117	c.77G>A	c.(76-78)gGg>gAg	p.G26E	SLC4A2_ENST00000413384.2_Missense_Mutation_p.G26E|SLC4A2_ENST00000310317.5_Intron|SLC4A2_ENST00000392826.2_Missense_Mutation_p.G17E|SLC4A2_ENST00000461735.1_Missense_Mutation_p.G12E	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	26	Pro-rich.		G -> E (in dbSNP:rs2303929). {ECO:0000269|Ref.2}.		anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTGGGCCCTGGGACGCCTGGG	0.617													G|||	1191	0.237819	0.1089	0.4424	5008	,	,		12118	0.2877		0.2425	False		,,,				2504	0.2106				p.G26E		Atlas-SNP	.											SLC4A2,NS,carcinoma,0,1	SLC4A2	98	1	0			c.G77A						PASS	.	G	GLU/GLY,GLU/GLY,GLU/GLY,GLU/GLY	588,3818	259.5+/-263.1	40,508,1655	59.0	54.0	56.0		77,50,35,77	-0.4	0.0	7	dbSNP_100	56	1943,6657	341.8+/-324.2	220,1503,2577	yes	missense,missense,missense,missense	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	98,98,98,98	260,2011,4232	AA,AG,GG		22.593,13.3454,19.4602	probably-damaging,probably-damaging,probably-damaging,probably-damaging	26/1242,17/1233,12/1228,26/1242	150761314	2531,10475	2203	4300	6503	SO:0001583	missense	6522	exon3			GCCCTGGGACGCC		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.77G>A	7.37:g.150761314G>A	ENSP00000419412:p.Gly26Glu	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	175	88	0.502857	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	597	0.2733516483516483	62	0.12601626016260162	146	0.40331491712707185	184	0.32167832167832167	205	0.2704485488126649	g	4.728	0.135334	0.09032	0.133454	0.22593	ENSG00000164889	ENST00000483786;ENST00000485713;ENST00000413384;ENST00000490898;ENST00000482950;ENST00000463414;ENST00000488420;ENST00000392826;ENST00000461735	T;T;T;T;T;T;T;T;T	0.75050	0.87;-0.9;-0.9;1.46;0.88;0.88;0.65;-0.86;-0.88	4.28	-0.421	0.12332	.	0.696201	0.13322	N	0.396634	T	0.00012	0.0000	L	0.46157	1.445	0.58432	P	2.9999999999752447E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.29181	-1.0020	9	0.05833	T	0.94	.	1.1008	0.01683	0.1913:0.3358:0.2677:0.2053	rs2303929;rs60575044;rs2303929	17;12;26	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	E	26;26;26;26;26;26;26;17;12	ENSP00000417808:G26E;ENSP00000419412:G26E;ENSP00000405600:G26E;ENSP00000418114:G26E;ENSP00000419379:G26E;ENSP00000418584:G26E;ENSP00000417221:G26E;ENSP00000376571:G17E;ENSP00000419164:G12E	ENSP00000376571:G17E	G	+	2	0	SLC4A2	150392247	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.002000	0.13061	-0.328000	0.08539	-0.394000	0.06481	GGG	G|0.779;A|0.221	0.221	strong		0.617	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
DOC2A	8448	hgsc.bcm.edu	37	16	30021402	30021402	+	Missense_Mutation	SNP	C	C	T	rs1140239	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:30021402C>T	ENST00000350119.4	-	2	332	c.142G>A	c.(142-144)Ggc>Agc	p.G48S	DOC2A_ENST00000567824.1_5'Flank|DOC2A_ENST00000564944.1_Missense_Mutation_p.G48S|DOC2A_ENST00000564979.1_Missense_Mutation_p.G48S	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	48	Interaction with UNC13D and DYNLT1.		G -> S (in dbSNP:rs1140239). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7826360}.		nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						tccccgccgcccccgccgccc	0.731													C|||	1633	0.326078	0.1604	0.2954	5008	,	,		12182	0.376		0.3847	False		,,,				2504	0.4601				p.G48S		Atlas-SNP	.											.	DOC2A	40	.	0			c.G142A						PASS	.	C	SER/GLY	684,3516		73,538,1489	13.0	16.0	15.0		142	1.8	0.0	16	dbSNP_86	15	3170,5200		638,1894,1653	yes	missense	DOC2A	NM_003586.2	56	711,2432,3142	TT,TC,CC		37.8734,16.2857,30.6603	benign	48/401	30021402	3854,8716	2100	4185	6285	SO:0001583	missense	8448	exon2			CGCCGCCCCCGCC	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.142G>A	16.37:g.30021402C>T	ENSP00000340017:p.Gly48Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	37	CCDS10666.1	692	0.31684981684981683	80	0.16260162601626016	117	0.32320441988950277	206	0.36013986013986016	289	0.3812664907651715	C	4.206	0.036904	0.08148	0.162857	0.378734	ENSG00000149927	ENST00000350119	T	0.61040	0.14	3.79	1.81	0.25067	.	0.654184	0.12703	N	0.446200	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.35201	-0.9798	9	0.05721	T	0.95	.	5.7904	0.18357	0.0:0.7533:0.0:0.2467	rs1140239;rs3814879;rs17846636;rs17859727;rs1140239	48	Q14183	DOC2A_HUMAN	S	48	ENSP00000340017:G48S	ENSP00000340017:G48S	G	-	1	0	DOC2A	29928903	0.000000	0.05858	0.003000	0.11579	0.081000	0.17604	0.322000	0.19576	0.401000	0.25424	0.561000	0.74099	GGC	C|0.733;T|0.267	0.267	strong		0.731	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
RP1	6101	hgsc.bcm.edu	37	8	55542540	55542540	+	Missense_Mutation	SNP	G	G	A	rs61739567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:55542540G>A	ENST00000220676.1	+	4	6246	c.6098G>A	c.(6097-6099)tGt>tAt	p.C2033Y		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	2033			C -> Y (in dbSNP:rs61739567). {ECO:0000269|PubMed:10391212, ECO:0000269|PubMed:11527933, ECO:0000269|PubMed:20664799}.		axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			GAAAGGTTTTGTATGAATTTC	0.338													G|||	1080	0.215655	0.0696	0.245	5008	,	,		18653	0.0675		0.4264	False		,,,				2504	0.3282				p.C2033Y	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G6098A						PASS	.	G	TYR/CYS	516,3888	233.6+/-246.7	35,446,1721	83.0	87.0	86.0		6098	0.4	0.0	8	dbSNP_129	86	3577,5023	515.5+/-378.6	716,2145,1439	yes	missense	RP1	NM_006269.1	194	751,2591,3160	AA,AG,GG		41.593,11.7166,31.4749	benign	2033/2157	55542540	4093,8911	2202	4300	6502	SO:0001583	missense	6101	exon4			GGTTTTGTATGAA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.6098G>A	8.37:g.55542540G>A	ENSP00000220676:p.Cys2033Tyr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	516	0.23626373626373626	41	0.08333333333333333	105	0.2900552486187845	43	0.07517482517482517	327	0.4313984168865435	G	0.001	-3.520656	0.00010	0.117166	0.41593	ENSG00000104237	ENST00000220676	T	0.18960	2.18	5.25	0.404	0.16355	.	0.555464	0.16627	N	0.206202	T	0.00012	0.0000	L	0.28274	0.84	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.46289	-0.9202	9	0.02654	T	1	.	0.7012	0.00908	0.2659:0.3374:0.2093:0.1874	rs61739567	2033	P56715	RP1_HUMAN	Y	2033	ENSP00000220676:C2033Y	ENSP00000220676:C2033Y	C	+	2	0	RP1	55705093	0.493000	0.26035	0.014000	0.15608	0.012000	0.07955	-0.012000	0.12699	0.153000	0.19213	0.591000	0.81541	TGT	A|0.295;G|0.705	0.295	strong		0.338	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
HERC1	8925	hgsc.bcm.edu	37	15	63988357	63988357	+	Missense_Mutation	SNP	C	C	G	rs2255243	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63988357C>G	ENST00000443617.2	-	27	5174	c.5087G>C	c.(5086-5088)gGc>gCc	p.G1696A	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1696			G -> A (in dbSNP:rs2255243). {ECO:0000269|PubMed:8861955}.		cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.G1696A(1)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CTCTCCCTTGCCTCCTGTGTG	0.463													G|||	3185	0.635982	0.8744	0.647	5008	,	,		17469	0.0982		0.8956	False		,,,				2504	0.593				p.G1696A		Atlas-SNP	.											HERC1_ENST00000443617,NS,carcinoma,0,1	HERC1	624	1	1	Substitution - Missense(1)	stomach(1)	c.G5087C						PASS	.	G	ALA/GLY	3421,579		1466,489,45	88.0	86.0	87.0		5087	4.3	1.0	15	dbSNP_100	87	7336,1006		3216,904,51	yes	missense	HERC1	NM_003922.3	60	4682,1393,96	GG,GC,CC		12.0595,14.475,12.8423	benign	1696/4862	63988357	10757,1585	2000	4171	6171	SO:0001583	missense	8925	exon27			CCCTTGCCTCCTG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.5087G>C	15.37:g.63988357C>G	ENSP00000390158:p.Gly1696Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	1412	0.6465201465201466	435	0.8841463414634146	250	0.6906077348066298	54	0.0944055944055944	673	0.8878627968337731	G	1.312	-0.601842	0.03744	0.85525	0.879405	ENSG00000103657	ENST00000443617;ENST00000425434	T	0.21932	1.98	5.24	4.29	0.51040	.	0.534254	0.18868	N	0.128946	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.0999999999983245E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40289	-0.9571	9	0.02654	T	1	.	15.683	0.77388	0.0:0.2599:0.7401:0.0	rs63019465	680;1696	B4DKS2;Q15751	.;HERC1_HUMAN	A	1696;680	ENSP00000390158:G1696A	ENSP00000389613:G680A	G	-	2	0	HERC1	61775410	1.000000	0.71417	0.961000	0.40146	0.386000	0.30323	3.883000	0.56168	0.667000	0.31107	-0.127000	0.14921	GGC	C|0.305;G|0.695	0.695	strong		0.463	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
ZNF45	7596	hgsc.bcm.edu	37	19	44418680	44418680	+	Missense_Mutation	SNP	G	G	C	rs388685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44418680G>C	ENST00000269973.5	-	10	1998	c.908C>G	c.(907-909)cCa>cGa	p.P303R	RP11-15A1.2_ENST00000586247.1_RNA|ZNF45_ENST00000589703.1_Missense_Mutation_p.P303R	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	303			P -> R (in dbSNP:rs388685). {ECO:0000269|PubMed:15057824}.		gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						ACACTTATATGGTTTCTTTCC	0.463													G|||	2075	0.414337	0.174	0.5764	5008	,	,		21910	0.5486		0.5119	False		,,,				2504	0.3855				p.P303R		Atlas-SNP	.											.	ZNF45	51	.	0			c.C908G						PASS	.	G	ARG/PRO	994,3412	372.7+/-320.5	131,732,1340	87.0	73.0	78.0		908	3.4	0.2	19	dbSNP_80	78	4306,4294	577.4+/-390.6	1094,2118,1088	yes	missense	ZNF45	NM_003425.3	103	1225,2850,2428	CC,CG,GG		49.9302,22.5601,40.7504	possibly-damaging	303/683	44418680	5300,7706	2203	4300	6503	SO:0001583	missense	7596	exon10			TTATATGGTTTCT	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"""Zinc fingers, C2H2-type"", ""-"""	13111	protein-coding gene	gene with protein product		194554	"""zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)"", ""zinc finger protein 13"""	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.908C>G	19.37:g.44418680G>C	ENSP00000269973:p.Pro303Arg	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	1018	0.4661172161172161	125	0.2540650406504065	183	0.505524861878453	324	0.5664335664335665	386	0.5092348284960422	G	12.18	1.860140	0.32884	0.225601	0.500698	ENSG00000124459	ENST00000269973;ENST00000328762	T	0.17213	2.29	3.39	3.39	0.38822	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36134	N	0.002777	T	0.00012	0.0000	M	0.77486	2.375	0.20821	P	0.999846303	D	0.89917	1.0	D	0.91635	0.999	T	0.49523	-0.8931	9	0.72032	D	0.01	-5.3101	14.0503	0.64732	0.0:0.0:1.0:0.0	rs388685;rs17173169;rs17712965;rs56609263;rs60039409;rs388685	303	Q02386	ZNF45_HUMAN	R	303	ENSP00000269973:P303R	ENSP00000269973:P303R	P	-	2	0	ZNF45	49110520	0.999000	0.42202	0.248000	0.24265	0.125000	0.20455	2.850000	0.48294	1.915000	0.55452	0.462000	0.41574	CCA	G|0.566;C|0.433	0.433	strong		0.463	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
CACNA1H	8912	hgsc.bcm.edu	37	16	1252118	1252118	+	Silent	SNP	C	C	T	rs2407083	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1252118C>T	ENST00000348261.5	+	9	1916	c.1668C>T	c.(1666-1668)ccC>ccT	p.P556P	CACNA1H_ENST00000358590.4_Silent_p.P556P|CACNA1H_ENST00000565831.1_Silent_p.P556P	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	556					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CTGGCGCGCCCCCCTCGCCAC	0.716													C|||	420	0.0838658	0.0166	0.0793	5008	,	,		14275	0.0645		0.1203	False		,,,				2504	0.1605				p.P556P		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C1668T						PASS	.	C	,	67,2481		0,67,1207	2.0	2.0	2.0		1668,1668	-3.3	0.0	16	dbSNP_100	2	615,5447		14,587,2430	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	14,654,3637	TT,TC,CC		10.1452,2.6295,7.921	,	556/2348,556/2354	1252118	682,7928	1274	3031	4305	SO:0001819	synonymous_variant	8912	exon9			CGCGCCCCCCTCG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1668C>T	16.37:g.1252118C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	13	8	0.615385	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.919;T|0.081	0.081	strong		0.716	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TM4SF20	79853	hgsc.bcm.edu	37	2	228243905	228243905	+	Missense_Mutation	SNP	G	G	A	rs7574414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228243905G>A	ENST00000304568.3	-	1	117	c.80C>T	c.(79-81)gCg>gTg	p.A27V		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	27			A -> V (in dbSNP:rs7574414). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A27V(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		TAGAGGTATCGCATTGAGAAC	0.483													G|||	530	0.105831	0.0068	0.0807	5008	,	,		19698	0.1935		0.1511	False		,,,				2504	0.1207				p.A27V		Atlas-SNP	.											TM4SF20,NS,carcinoma,0,1	TM4SF20	24	1	1	Substitution - Missense(1)	stomach(1)	c.C80T						PASS	.	G	VAL/ALA	115,4291	87.8+/-126.4	0,115,2088	127.0	125.0	126.0		80	1.8	0.0	2	dbSNP_116	126	1209,7391	244.2+/-273.5	81,1047,3172	yes	missense	TM4SF20	NM_024795.3	64	81,1162,5260	AA,AG,GG		14.0581,2.6101,10.1799	benign	27/230	228243905	1324,11682	2203	4300	6503	SO:0001583	missense	79853	exon1			GGTATCGCATTGA	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.80C>T	2.37:g.228243905G>A	ENSP00000303028:p.Ala27Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	CCDS2466.1	275	0.1259157509157509	4	0.008130081300813009	32	0.08839779005524862	114	0.1993006993006993	125	0.16490765171503957	G	3.354	-0.131890	0.06753	0.026101	0.140581	ENSG00000168955	ENST00000304568	T	0.26518	1.73	5.77	1.78	0.24846	.	0.883848	0.09827	N	0.750664	T	0.00012	0.0000	L	0.41356	1.27	0.80722	P	0.0	D	0.53462	0.96	B	0.37047	0.24	T	0.10917	-1.0609	9	0.06891	T	0.86	-3.7897	5.2601	0.15567	0.1976:0.3385:0.4638:0.0	rs7574414;rs7574414	27	Q53R12	T4S20_HUMAN	V	27	ENSP00000303028:A27V	ENSP00000303028:A27V	A	-	2	0	TM4SF20	227952149	0.000000	0.05858	0.034000	0.17996	0.029000	0.11900	0.089000	0.15002	0.711000	0.32018	0.591000	0.81541	GCG	G|0.889;A|0.111	0.111	strong		0.483	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795	
TMEM8A	58986	hgsc.bcm.edu	37	16	427820	427820	+	Silent	SNP	C	C	T	rs12922073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:427820C>T	ENST00000431232.2	-	2	310	c.150G>A	c.(148-150)tcG>tcA	p.S50S	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_Intron	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	50					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GCGGGGCCTGCGAGAAGTGCT	0.672													C|||	2580	0.515176	0.5582	0.4683	5008	,	,		14226	0.2996		0.5368	False		,,,				2504	0.6902				p.S50S		Atlas-SNP	.											.	TMEM8A	49	.	0			c.G150A						PASS	.	C		2520,1808		745,1030,389	33.0	39.0	37.0		150	-8.8	0.7	16	dbSNP_121	37	4850,3678		1444,1962,858	no	coding-synonymous	TMEM8A	NM_021259.2		2189,2992,1247	TT,TC,CC		43.1285,41.7745,42.6727		50/772	427820	7370,5486	2164	4264	6428	SO:0001819	synonymous_variant	58986	exon2			GGCCTGCGAGAAG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.150G>A	16.37:g.427820C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			A|0.000;C|0.470;G|0.000;T|0.530	0.530	strong		0.672	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
COMMD5	28991	hgsc.bcm.edu	37	8	146076708	146076708	+	Missense_Mutation	SNP	C	C	T	rs1209879	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:146076708C>T	ENST00000305103.3	-	2	268	c.16G>A	c.(16-18)Gct>Act	p.A6T	COMMD5_ENST00000450361.2_Missense_Mutation_p.A6T|ZNF250_ENST00000543949.1_3'UTR|AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000402718.3_Missense_Mutation_p.A6T	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	6			A -> T (in dbSNP:rs1209879). {ECO:0000269|PubMed:10931946}.			nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			GGAGTTGCAGCCCCCACAGCA	0.592													C|||	1344	0.268371	0.0446	0.232	5008	,	,		19951	0.3254		0.3419	False		,,,				2504	0.4622				p.A6T		Atlas-SNP	.											.	COMMD5	18	.	0			c.G16A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	447,3959	212.8+/-232.6	26,395,1782	64.0	67.0	66.0		16,16,16	1.5	0.0	8	dbSNP_87	66	3126,5474	464.3+/-366.2	524,2078,1698	yes	missense,missense,missense	COMMD5	NM_001081003.1,NM_001081004.1,NM_014066.3	58,58,58	550,2473,3480	TT,TC,CC		36.3488,10.1453,27.4719	benign,benign,benign	6/225,6/225,6/225	146076708	3573,9433	2203	4300	6503	SO:0001583	missense	28991	exon2			TTGCAGCCCCCAC	AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.16G>A	8.37:g.146076708C>T	ENSP00000304544:p.Ala6Thr	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	249	112	0.449799	NM_001081004	D3DWN7|Q9NVN6|Q9UHX5	Missense_Mutation	SNP	ENST00000305103.3	37	CCDS6436.1	531	0.24313186813186813	26	0.052845528455284556	93	0.2569060773480663	148	0.25874125874125875	264	0.3482849604221636	C	9.609	1.130698	0.21041	0.101453	0.363488	ENSG00000170619	ENST00000402718;ENST00000450361;ENST00000305103;ENST00000529143;ENST00000533270	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	4.48	1.48	0.22813	.	1.416370	0.04663	N	0.409266	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	1.0000000000287557E-6	B	0.24186	0.099	B	0.19391	0.025	T	0.41770	-0.9490	9	0.18276	T	0.48	3.0506	7.9519	0.30019	0.1709:0.4976:0.3316:0.0	rs1209879;rs1622745;rs3199266;rs17816149;rs52798652;rs58731279;rs1209879	6	Q9GZQ3	COMD5_HUMAN	T	6	ENSP00000385793:A6T;ENSP00000394331:A6T;ENSP00000304544:A6T;ENSP00000435552:A6T;ENSP00000433758:A6T	ENSP00000304544:A6T	A	-	1	0	COMMD5	146047512	0.003000	0.15002	0.001000	0.08648	0.300000	0.27592	-0.806000	0.04525	0.062000	0.16340	0.557000	0.71058	GCT	T|0.254;G|0.001	0.254	strong		0.592	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066	
RIOK2	55781	hgsc.bcm.edu	37	5	96498783	96498783	+	Silent	SNP	G	G	A	rs8654	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:96498783G>A	ENST00000283109.3	-	10	1709	c.1641C>T	c.(1639-1641)gcC>gcT	p.A547A	CTD-2215E18.1_ENST00000509481.1_Intron	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	547	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		CCCAAAAGCTGGCTGCTTCCA	0.333													A|||	2776	0.554313	0.5076	0.5692	5008	,	,		17087	0.5208		0.5845	False		,,,				2504	0.6104				p.A547A		Atlas-SNP	.											RIOK2,colon,carcinoma,-1,1	RIOK2	82	1	0			c.C1641T						PASS	.	A		2308,2096	571.4+/-383.1	597,1114,491	127.0	114.0	119.0		1641	0.2	1.0	5	dbSNP_52	119	5142,3458	506.5+/-376.6	1548,2046,706	no	coding-synonymous	RIOK2	NM_018343.2		2145,3160,1197	AA,AG,GG		40.2093,47.5931,42.7099		547/553	96498783	7450,5554	2202	4300	6502	SO:0001819	synonymous_variant	55781	exon10			AAAGCTGGCTGCT	AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"""RIO kinase 2 (yeast)"""				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.1641C>T	5.37:g.96498783G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_018343	D6RDI3|Q9NUT0	Silent	SNP	ENST00000283109.3	37	CCDS4089.1	1201	0.549908424908425	267	0.5426829268292683	201	0.5552486187845304	288	0.5034965034965035	445	0.5870712401055409	A	9.511	1.105780	0.20632	0.524069	0.597907	ENSG00000058729	ENST00000511293	.	.	.	5.7	0.19	0.15125	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999123177	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.9061	9.4914	0.38962	0.2863:0.0:0.5915:0.1223	rs8654;rs3187842;rs56603502;rs8654	.	.	.	X	154	.	.	Q	-	1	0	RIOK2	96524539	0.941000	0.31946	0.985000	0.45067	0.990000	0.78478	0.119000	0.15626	-0.539000	0.06273	-0.254000	0.11334	CAG	G|0.438;A|0.562	0.562	strong		0.333	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343	
SPIB	6689	hgsc.bcm.edu	37	19	50926126	50926126	+	Silent	SNP	C	C	T	rs61729811	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50926126C>T	ENST00000595883.1	+	4	196	c.171C>T	c.(169-171)ccC>ccT	p.P57P	SPIB_ENST00000597855.1_Silent_p.P57P|SPIB_ENST00000270632.7_Silent_p.P57P|CTD-2545M3.6_ENST00000599632.1_Silent_p.L192L|SPIB_ENST00000439922.2_Intron|SPIB_ENST00000596074.1_Intron	NM_001243999.1|NM_001244000.1|NM_003121.4	NP_001230928.1|NP_001230929.1|NP_003112.2	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	57	TAD2.				cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)	14		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		CAGCCACCCCCTATGAAGCCT	0.657													C|||	92	0.0183706	0.0038	0.0245	5008	,	,		13885	0.0		0.0557	False		,,,				2504	0.0143				p.P38L		Atlas-SNP	.											.	SPIB	23	.	0			c.C113T						PASS	.	C		52,4354		0,52,2151	41.0	51.0	48.0		171	2.6	0.8	19	dbSNP_129	48	420,8178		14,392,3893	no	coding-synonymous	SPIB	NM_003121.4		14,444,6044	TT,TC,CC		4.8849,1.1802,3.6297		57/263	50926126	472,12532	2203	4299	6502	SO:0001819	synonymous_variant	6689	exon4			CACCCCCTATGAA		CCDS33080.1, CCDS58674.1, CCDS59412.1	19q13.3-q13.4	2008-07-22				ENSG00000269404			11242	protein-coding gene	gene with protein product		606802				1406622	Standard	NM_003121		Approved	SPI-B	uc002psd.3	Q01892		ENST00000595883.1:c.171C>T	19.37:g.50926126C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	199	100	0.502513	NM_001244000	A8K9C9|B4DUG6|Q15359	Missense_Mutation	SNP	ENST00000595883.1	37	CCDS33080.1																																																																																			C|0.962;T|0.038	0.038	strong		0.657	SPIB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464744.1	NM_003121	
PHIP	55023	hgsc.bcm.edu	37	6	79675701	79675701	+	Missense_Mutation	SNP	A	A	G	rs9350797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:79675701A>G	ENST00000275034.4	-	28	3445	c.3278T>C	c.(3277-3279)cTt>cCt	p.L1093P	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1093	Mediates interaction with IRS1. {ECO:0000250}.		L -> P (in dbSNP:rs9350797). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AGGGTACTCAAGTTGAAGAGG	0.398													A|||	1086	0.216853	0.1672	0.2824	5008	,	,		16263	0.1855		0.3211	False		,,,				2504	0.1626				p.L1093P		Atlas-SNP	.											.	PHIP	177	.	0			c.T3278C						PASS	.	A	PRO/LEU	869,3537	337.0+/-304.7	96,677,1430	146.0	153.0	151.0		3278	2.8	1.0	6	dbSNP_119	151	2594,6006	421.5+/-353.7	413,1768,2119	yes	missense	PHIP	NM_017934.5	98	509,2445,3549	GG,GA,AA		30.1628,19.7231,26.6262	benign	1093/1822	79675701	3463,9543	2203	4300	6503	SO:0001583	missense	55023	exon28			TACTCAAGTTGAA	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.3278T>C	6.37:g.79675701A>G	ENSP00000275034:p.Leu1093Pro	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	576	0.26373626373626374	90	0.18292682926829268	108	0.2983425414364641	126	0.2202797202797203	252	0.3324538258575198	A	3.253	-0.152753	0.06585	0.197231	0.301628	ENSG00000146247	ENST00000275034	T	0.41758	0.99	5.64	2.76	0.32466	.	0.314442	0.32503	N	0.006007	T	0.04137	0.0115	N	0.01242	-0.935	0.21933	P	0.999465749	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39078	-0.9631	8	.	.	.	-1.3565	6.8281	0.23895	0.1584:0.0:0.7019:0.1397	rs9350797;rs52802348;rs60889537;rs9350797	1093;1093	A7J992;Q8WWQ0	.;PHIP_HUMAN	P	1093	ENSP00000275034:L1093P	.	L	-	2	0	PHIP	79732420	0.998000	0.40836	0.996000	0.52242	0.985000	0.73830	2.470000	0.45119	0.347000	0.23924	-0.248000	0.11899	CTT	A|0.746;G|0.254	0.254	strong		0.398	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
OR1I1	126370	hgsc.bcm.edu	37	19	15198631	15198631	+	Missense_Mutation	SNP	A	A	C	rs8105737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198631A>C	ENST00000209540.2	+	1	841	c.755A>C	c.(754-756)tAt>tCt	p.Y252S		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	252			Y -> S (in dbSNP:rs8105737).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						TCACTGTCCTATGGGACCATC	0.542													A|||	2458	0.490815	0.354	0.5533	5008	,	,		22501	0.3849		0.659	False		,,,				2504	0.5675				p.Y252S		Atlas-SNP	.											.	OR1I1	58	.	0			c.A755C						PASS	.	A	SER/TYR	1727,2679	517.7+/-369.5	324,1079,800	128.0	98.0	108.0		755	3.6	0.7	19	dbSNP_116	108	5799,2801	677.4+/-403.4	1978,1843,479	yes	missense	OR1I1	NM_001004713.1	144	2302,2922,1279	CC,CA,AA		32.5698,39.1966,42.1344	probably-damaging	252/356	15198631	7526,5480	2203	4300	6503	SO:0001583	missense	126370	exon1			TGTCCTATGGGAC	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.755A>C	19.37:g.15198631A>C	ENSP00000209540:p.Tyr252Ser	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	1102	0.5045787545787546	172	0.34959349593495936	207	0.5718232044198895	231	0.40384615384615385	492	0.6490765171503958	A	10.32	1.318584	0.23994	0.391966	0.674302	ENSG00000094661	ENST00000209540	T	0.40756	1.02	4.6	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29529	U	0.011883	T	0.00012	0.0000	H	0.96208	3.785	0.33826	P	0.37030399999999997	D	0.76494	0.999	D	0.72982	0.979	T	0.47497	-0.9113	9	0.66056	D	0.02	.	8.4904	0.33098	0.906:0.0:0.094:0.0	rs8105737;rs52832629;rs58162341;rs8105737	252	O60431	OR1I1_HUMAN	S	252	ENSP00000209540:Y252S	ENSP00000209540:Y252S	Y	+	2	0	OR1I1	15059631	0.540000	0.26410	0.743000	0.31040	0.024000	0.10985	1.274000	0.33132	0.809000	0.34255	-0.434000	0.05882	TAT	A|0.453;C|0.547	0.547	strong		0.542	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
SCN10A	6336	hgsc.bcm.edu	37	3	38766701	38766701	+	Silent	SNP	C	C	T	rs6791171	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38766701C>T	ENST00000449082.2	-	17	3191	c.3192G>A	c.(3190-3192)acG>acA	p.T1064T		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1064					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CATCTTTCCACGTCTCACCCA	0.592													C|||	578	0.115415	0.1967	0.1383	5008	,	,		19183	0.002		0.1322	False		,,,				2504	0.089				p.T1064T		Atlas-SNP	.											.	SCN10A	359	.	0			c.G3192A						PASS	.	C		880,3526	343.8+/-307.8	98,684,1421	79.0	77.0	77.0		3192	-0.0	0.0	3	dbSNP_116	77	1216,7384	245.0+/-274.0	80,1056,3164	no	coding-synonymous	SCN10A	NM_006514.2		178,1740,4585	TT,TC,CC		14.1395,19.9728,16.1156		1064/1957	38766701	2096,10910	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon17			TTTCCACGTCTCA	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.3192G>A	3.37:g.38766701C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	135	47	0.348148	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			C|0.861;T|0.139	0.139	strong		0.592	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
SIGIRR	59307	hgsc.bcm.edu	37	11	408174	408174	+	Missense_Mutation	SNP	G	G	T	rs117739035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:408174G>T	ENST00000431843.2	-	4	545	c.239C>A	c.(238-240)tCc>tAc	p.S80Y	SIGIRR_ENST00000332725.3_Missense_Mutation_p.S80Y|SIGIRR_ENST00000531205.1_Missense_Mutation_p.S80Y|SIGIRR_ENST00000529486.1_5'UTR|SIGIRR_ENST00000382520.2_Missense_Mutation_p.S80Y|SIGIRR_ENST00000397632.3_Missense_Mutation_p.S80Y	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	80	Ig-like C2-type.				acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGACACTGGACACAAGCAC	0.587													g|||	81	0.0161741	0.0008	0.0576	5008	,	,		19868	0.0		0.0358	False		,,,				2504	0.0041				p.S80Y		Atlas-SNP	.											.	SIGIRR	22	.	0			c.C239A						PASS	.	G	TYR/SER,TYR/SER,TYR/SER	45,4359	45.3+/-79.5	0,45,2157	117.0	108.0	111.0		239,239,239	3.0	1.0	11	dbSNP_132	111	266,8334	102.7+/-163.9	4,258,4038	yes	missense,missense,missense	SIGIRR	NM_001135053.1,NM_001135054.1,NM_021805.2	144,144,144	4,303,6195	TT,TG,GG		3.093,1.0218,2.3916	probably-damaging,probably-damaging,probably-damaging	80/411,80/411,80/411	408174	311,12693	2202	4300	6502	SO:0001583	missense	59307	exon4			ACACTGGACACAA		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30575	protein-coding gene	gene with protein product	"""single immunoglobulin domain IL1R1 related"""	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.239C>A	11.37:g.408174G>T	ENSP00000403104:p.Ser80Tyr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_001135053	Q3KQY2|Q6UXI3|Q9H733	Missense_Mutation	SNP	ENST00000431843.2	37	CCDS31325.1	38	0.0173992673992674	0	0.0	13	0.03591160220994475	0	0.0	25	0.032981530343007916	g	14.41	2.525954	0.44969	0.010218	0.03093	ENSG00000185187	ENST00000431843;ENST00000397632;ENST00000332725;ENST00000531205;ENST00000382520	T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46	3.0	3.0	0.34707	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.579755	0.16764	N	0.200495	T	0.46776	0.1410	M	0.62723	1.935	0.53005	D	0.999961	D;D	0.76494	0.998;0.999	D;D	0.64042	0.921;0.921	T	0.67894	-0.5552	10	0.59425	D	0.04	.	12.2696	0.54697	0.0:0.0:1.0:0.0	.	80;80	C9JFX4;Q6IA17	.;SIGIR_HUMAN	Y	80	ENSP00000403104:S80Y;ENSP00000380756:S80Y;ENSP00000333656:S80Y;ENSP00000433022:S80Y;ENSP00000371960:S80Y	ENSP00000333656:S80Y	S	-	2	0	SIGIRR	398174	0.996000	0.38824	0.994000	0.49952	0.043000	0.13939	2.557000	0.45871	1.988000	0.58038	0.305000	0.20034	TCC	G|0.978;T|0.022	0.022	strong		0.587	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805	
CELF4	56853	hgsc.bcm.edu	37	18	34850846	34850846	+	Silent	SNP	G	G	A	rs1443638	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:34850846G>A	ENST00000591282.1	-	8	983	c.984C>T	c.(982-984)gcC>gcT	p.A328A	CELF4_ENST00000420428.2_Silent_p.A328A|CELF4_ENST00000361795.5_Silent_p.A326A|CELF4_ENST00000601019.1_Silent_p.A326A|CELF4_ENST00000588597.1_Silent_p.A317A|CELF4_ENST00000603232.1_Silent_p.A327A|CELF4_ENST00000591287.1_Silent_p.A327A|RP11-797E24.3_ENST00000588766.1_RNA|CELF4_ENST00000412753.1_Silent_p.A327A|CELF4_ENST00000334919.5_Silent_p.A318A			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4	328					alternative mRNA splicing, via spliceosome (GO:0000380)|embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA splice site selection (GO:0006376)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of translation (GO:0017148)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	44						TGCTAGGCACGGCTGGTGCAG	0.632													G|||	1079	0.215455	0.1324	0.17	5008	,	,		18519	0.2272		0.3529	False		,,,				2504	0.2065				p.A328A		Atlas-SNP	.											.	CELF4	90	.	0			c.C984T						PASS	.	G	,,,	818,3588	320.2+/-296.5	79,660,1464	39.0	34.0	36.0		981,978,954,984	-4.0	1.0	18	dbSNP_88	36	3152,5448	474.8+/-368.9	589,1974,1737	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CELF4	NM_001025087.1,NM_001025088.1,NM_001025089.1,NM_020180.3	,,,	668,2634,3201	AA,AG,GG		36.6512,18.5656,30.5244	,,,	327/486,326/485,318/449,328/487	34850846	3970,9036	2203	4300	6503	SO:0001819	synonymous_variant	56853	exon8			AGGCACGGCTGGT	AF248651	CCDS32818.1, CCDS45857.1, CCDS45858.1	18q12	2013-02-12	2010-02-19	2010-02-19				"""RNA binding motif (RRM) containing"""	14015	protein-coding gene	gene with protein product		612679	"""Bruno (Drosophila) -like 4, RNA binding protein"", ""bruno-like 4, RNA binding protein (Drosophila)"""	BRUNOL4		10893231	Standard	NM_020180		Approved		uc002lae.2	Q9BZC1		ENST00000591282.1:c.984C>T	18.37:g.34850846G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_020180	Q59EN7|Q86XB9|Q8N2M6|Q9BQ96|Q9NR84|Q9NR85	Silent	SNP	ENST00000591282.1	37	CCDS32818.1	535	0.24496336996336995	61	0.12398373983739837	71	0.19613259668508287	130	0.22727272727272727	273	0.36015831134564646	G	9.731	1.162181	0.21538	0.185656	0.366512	ENSG00000101489	ENST00000361683	.	.	.	4.66	-3.97	0.04094	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999956	.	.	.	.	.	.	T	0.39761	-0.9598	4	0.62326	D	0.03	-9.1122	13.6895	0.62537	0.7368:0.0:0.2632:0.0	rs1443638;rs52790871;rs59351053;rs1443638	.	.	.	C	211	.	ENSP00000355189:R211C	R	-	1	0	CELF4	33104844	0.169000	0.23002	0.977000	0.42913	0.946000	0.59487	-0.355000	0.07671	-0.730000	0.04869	-1.031000	0.02408	CGT	G|0.726;A|0.274	0.274	strong		0.632	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	NM_020180	
SPEG	10290	hgsc.bcm.edu	37	2	220354542	220354542	+	Silent	SNP	G	G	A	rs55969678	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220354542G>A	ENST00000312358.7	+	36	8934	c.8802G>A	c.(8800-8802)ccG>ccA	p.P2934P	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2934	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GCCTCAGCCCGGCCAAGGAGG	0.642													G|||	284	0.0567093	0.0121	0.1138	5008	,	,		12302	0.0833		0.0596	False		,,,				2504	0.046				p.P2934P		Atlas-SNP	.											.	SPEG	272	.	0			c.G8802A						PASS	.	G		97,3661		1,95,1783	40.0	43.0	42.0		8802	-2.8	0.6	2	dbSNP_129	42	573,7623		14,545,3539	no	coding-synonymous	SPEG	NM_005876.4		15,640,5322	AA,AG,GG		6.9912,2.5812,5.6048		2934/3268	220354542	670,11284	1879	4098	5977	SO:0001819	synonymous_variant	10290	exon36			CAGCCCGGCCAAG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8802G>A	2.37:g.220354542G>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	277	132	0.476534	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			G|0.917;A|0.083	0.083	strong		0.642	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59500116	59500116	+	Missense_Mutation	SNP	T	T	C	rs3825937	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:59500116T>C	ENST00000307144.4	+	1	1075	c.977T>C	c.(976-978)aTt>aCt	p.I326T	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	326			I -> T (in dbSNP:rs3825937). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						TCCACCATAATTAAGGGCCTC	0.393													T|||	1998	0.398962	0.2496	0.3934	5008	,	,		19264	0.5694		0.2734	False		,,,				2504	0.5583				p.I326T		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.T977C						PASS	.	T	,THR/ILE	1144,3238	380.4+/-323.7	168,808,1215	80.0	86.0	84.0		,977	1.5	1.0	15	dbSNP_107	84	2385,6191	388.1+/-342.4	328,1729,2231	no	intron,missense	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,89	496,2537,3446	CC,CT,TT		27.8102,26.1068,27.2341	,benign	,326/382	59500116	3529,9429	2191	4288	6479	SO:0001583	missense	92483	exon1			CCATAATTAAGGG	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.977T>C	15.37:g.59500116T>C	ENSP00000302393:p.Ile326Thr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	151	53	0.350993	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	37	CCDS10171.1	793	0.3630952380952381	120	0.24390243902439024	126	0.34806629834254144	340	0.5944055944055944	207	0.27308707124010556	T	18.32	3.597035	0.66332	0.261068	0.278102	ENSG00000171989	ENST00000307144	T	0.63255	-0.03	1.47	1.47	0.22746	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.099877	0.42964	U	0.000632	T	0.00012	0.0000	M	0.71581	2.175	0.37666	P	0.07706800000000003	B	0.22414	0.069	P	0.46320	0.512	T	0.48570	-0.9024	9	0.54805	T	0.06	.	4.9571	0.14048	0.0:0.0:0.0:1.0	rs3825937;rs17856652;rs59074481;rs3825937	326	Q9BYZ2	LDH6B_HUMAN	T	326	ENSP00000302393:I326T	ENSP00000302393:I326T	I	+	2	0	LDHAL6B	57287408	0.999000	0.42202	0.963000	0.40424	0.968000	0.65278	4.730000	0.62015	0.654000	0.30846	0.254000	0.18369	ATT	T|0.679;C|0.321	0.321	strong		0.393	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
DOCK5	80005	hgsc.bcm.edu	37	8	25230168	25230168	+	Silent	SNP	C	C	T	rs2271108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:25230168C>T	ENST00000276440.7	+	35	3662	c.3618C>T	c.(3616-3618)gaC>gaT	p.D1206D		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1206					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.D1206D(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		ACCTGCTGGACTATAGAACCA	0.537													C|||	2194	0.438099	0.382	0.464	5008	,	,		20146	0.3968		0.508	False		,,,				2504	0.4663				p.D1206D	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											DOCK5,NS,carcinoma,0,1	DOCK5	167	1	1	Substitution - coding silent(1)	stomach(1)	c.C3618T						PASS	.	C		1669,2737	507.8+/-366.8	322,1025,856	93.0	79.0	83.0		3618	3.5	1.0	8	dbSNP_100	83	4219,4381	570.7+/-389.4	1030,2159,1111	no	coding-synonymous	DOCK5	NM_024940.6		1352,3184,1967	TT,TC,CC		49.0581,37.8802,45.2714		1206/1871	25230168	5888,7118	2203	4300	6503	SO:0001819	synonymous_variant	80005	exon35			GCTGGACTATAGA		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3618C>T	8.37:g.25230168C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			C|0.562;T|0.438	0.438	strong		0.537	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
PMFBP1	83449	hgsc.bcm.edu	37	16	72184629	72184629	+	Missense_Mutation	SNP	C	C	T	rs217180	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:72184629C>T	ENST00000237353.10	-	5	775	c.514G>A	c.(514-516)Gcc>Acc	p.A172T	PMFBP1_ENST00000355636.6_Missense_Mutation_p.A27T|PMFBP1_ENST00000537465.1_Missense_Mutation_p.A172T	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	172			A -> T (in dbSNP:rs217180).			cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TCTAGAGAGGCGATCTTGTCC	0.507													C|||	430	0.0858626	0.003	0.1326	5008	,	,		19868	0.1736		0.0875	False		,,,				2504	0.0726				p.A172T		Atlas-SNP	.											.	PMFBP1	101	.	0			c.G514A						PASS	.	C	THR/ALA,THR/ALA	92,4304	75.7+/-113.9	1,90,2107	119.0	111.0	114.0		79,514	-4.6	0.0	16	dbSNP_79	114	731,7869	177.6+/-227.2	31,669,3600	yes	missense,missense	PMFBP1	NM_001160213.1,NM_031293.2	58,58	32,759,5707	TT,TC,CC		8.5,2.0928,6.3327	benign,benign	27/883,172/1008	72184629	823,12173	2198	4300	6498	SO:0001583	missense	83449	exon5			GAGAGGCGATCTT	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.514G>A	16.37:g.72184629C>T	ENSP00000237353:p.Ala172Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	216	0.0989010989010989	3	0.006097560975609756	46	0.1270718232044199	99	0.17307692307692307	68	0.08970976253298153	C	14.35	2.509389	0.44660	0.020928	0.085	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.78003	-1.14;-1.14;2.77	6.17	-4.61	0.03380	.	1.378430	0.04711	N	0.417677	T	0.00178	0.0005	N	0.14661	0.345	0.80722	P	0.0	P;P;P	0.42039	0.769;0.642;0.769	B;B;B	0.25614	0.062;0.062;0.062	T	0.09378	-1.0677	9	0.14656	T	0.56	0.0471	1.8798	0.03225	0.1193:0.2169:0.3507:0.313	rs217180;rs17667549;rs57451652;rs217180	172;172;172	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	T	172;172;27	ENSP00000443817:A172T;ENSP00000237353:A172T;ENSP00000347854:A27T	ENSP00000237353:A172T	A	-	1	0	PMFBP1	70742130	0.000000	0.05858	0.009000	0.14445	0.823000	0.46562	-2.843000	0.00736	-0.318000	0.08665	0.655000	0.94253	GCC	C|0.923;T|0.077	0.077	strong		0.507	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	
MROH7	374977	hgsc.bcm.edu	37	1	55119144	55119144	+	Missense_Mutation	SNP	A	A	G	rs11206407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55119144A>G	ENST00000421030.2	+	3	830	c.545A>G	c.(544-546)cAt>cGt	p.H182R	MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.H182R|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000395690.2_Missense_Mutation_p.H182R|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000339553.5_Missense_Mutation_p.H182R|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000454855.2_Intron	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	182			H -> R (in dbSNP:rs11206407). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											ATAAGGCACCATTCCAGAGAA	0.453													A|||	1556	0.310703	0.1596	0.268	5008	,	,		20536	0.5188		0.3708	False		,,,				2504	0.2689				p.H182R		Atlas-SNP	.											HEATR8_ENST00000421030,colon,carcinoma,0,2	.	.	2	0			c.A545G						scavenged	.	A	ARG/HIS	705,3091		67,571,1260	82.0	78.0	79.0		545	-3.6	0.0	1	dbSNP_120	79	2809,5439		456,1897,1771	yes	missense	HEATR8	NM_001039464.2	29	523,2468,3031	GG,GA,AA		34.0567,18.5722,29.1764	benign	182/1324	55119144	3514,8530	1898	4124	6022	SO:0001583	missense	374977	exon3			GGCACCATTCCAG	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.545A>G	1.37:g.55119144A>G	ENSP00000396622:p.His182Arg	Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	99	36	0.363636	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	757	0.3466117216117216	77	0.1565040650406504	96	0.26519337016574585	306	0.534965034965035	278	0.36675461741424803	A	8.507	0.865663	0.17250	0.185722	0.340567	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.02446	4.83;4.29;4.3	3.39	-3.58	0.04597	.	1.199260	0.06503	N	0.736707	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33420	-0.9869	9	0.37606	T	0.19	.	1.0236	0.01523	0.2638:0.1581:0.3633:0.2148	rs11206407;rs56541778;rs57235564;rs11206407	182;182;182	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	R	182	ENSP00000396622:H182R;ENSP00000343211:H182R;ENSP00000379044:H182R	ENSP00000343211:H182R	H	+	2	0	HEATR8	54891732	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-0.714000	0.05002	-0.805000	0.04404	-0.441000	0.05720	CAT	A|0.655;G|0.344	0.344	strong		0.453	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
TPM1	7168	hgsc.bcm.edu	37	15	63363291	63363291	+	Missense_Mutation	SNP	A	A	G	rs144045691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63363291A>G	ENST00000357980.4	+	10	980	c.901A>G	c.(901-903)Aaa>Gaa	p.K301E	RP11-244F12.2_ENST00000558905.1_RNA|TPM1_ENST00000267996.7_Missense_Mutation_p.K259E|TPM1_ENST00000358278.3_Missense_Mutation_p.K259E|TPM1_ENST00000404484.4_Missense_Mutation_p.K223E|TPM1_ENST00000559556.1_Missense_Mutation_p.K259E|TPM1_ENST00000559397.1_Missense_Mutation_p.K259E			P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	259					cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						CACCACAGAGAAAGTGGCTCA	0.413													A|||	3	0.000599042	0.0	0.0	5008	,	,		23023	0.0		0.003	False		,,,				2504	0.0				p.K259E		Atlas-SNP	.											.	TPM1	59	.	0			c.A775G						PASS	.	A	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	0,4406		0,0,2203	122.0	113.0	116.0		775,775,775,775	6.0	1.0	15	dbSNP_134	116	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense,missense	TPM1	NM_001018004.1,NM_001018006.1,NM_001018007.1,NM_001018020.1	56,56,56,56	0,4,6499	GG,GA,AA		0.0465,0.0,0.0308	benign,benign,benign,benign	259/285,259/285,259/285,259/285	63363291	4,13002	2203	4300	6503	SO:0001583	missense	7168	exon9			ACAGAGAAAGTGG	AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"""Tropomyosins"""	12010	protein-coding gene	gene with protein product		191010	"""chromosome 15 open reading frame 13"", ""cardiomyopathy, hypertrophic 3"""	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000357980.4:c.901A>G	15.37:g.63363291A>G	ENSP00000350667:p.Lys301Glu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_001018007	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Missense_Mutation	SNP	ENST00000357980.4	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	10.44	1.350695	0.24512	0.0	4.65E-4	ENSG00000140416	ENST00000267996;ENST00000358278;ENST00000357980	T;T;T	0.73897	-0.79;-0.79;-0.79	6.02	6.02	0.97574	.	0.000000	0.56097	D	0.000039	T	0.52869	0.1761	N	0.05467	-0.045	0.80722	D	1	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.15052	0.012;0.006;0.002;0.001;0.001;0.001	T	0.53858	-0.8379	10	0.02654	T	1	-4.6565	15.7258	0.77756	1.0:0.0:0.0:0.0	.	223;301;259;259;259;259	B7Z722;Q6ZN40;D9YZV8;D9YZV5;Q9Y427;D9YZV3	.;.;.;.;.;.	E	259;259;301	ENSP00000267996:K259E;ENSP00000351022:K259E;ENSP00000350667:K301E	ENSP00000267996:K259E	K	+	1	0	TPM1	61150344	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.122000	0.94380	2.311000	0.77944	0.533000	0.62120	AAA	A|0.999;G|0.001	0.001	strong		0.413	TPM1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000417087.2	NM_001018004	
KNOP1	400506	hgsc.bcm.edu	37	16	19726275	19726275	+	Missense_Mutation	SNP	C	C	T	rs11640454	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19726275C>T	ENST00000219837.7	-	2	161	c.83G>A	c.(82-84)cGa>cAa	p.R28Q	AC002550.5_ENST00000565916.1_RNA|IQCK_ENST00000320394.6_5'Flank|KNOP1_ENST00000568230.1_5'Flank	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	28			R -> Q (in dbSNP:rs11640454).			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										AACTGAGTATCGAGTCTCTGG	0.433													C|||	385	0.076877	0.0272	0.0937	5008	,	,		20248	0.003		0.1928	False		,,,				2504	0.089				p.R28Q		Atlas-SNP	.											C16orf88,NS,carcinoma,-1,1	C16orf88	41	1	0			c.G83A						PASS	.	C	GLN/ARG	199,3553		4,191,1681	91.0	88.0	89.0		83	0.8	0.1	16	dbSNP_120	89	1617,6587		159,1299,2644	yes	missense	C16orf88	NM_001012991.2	43	163,1490,4325	TT,TC,CC		19.7099,5.3038,15.189	benign	28/459	19726275	1816,10140	1876	4102	5978	SO:0001583	missense	400506	exon2			GAGTATCGAGTCT	BC047010	CCDS42127.1	16p12.3	2013-03-12	2013-03-12	2013-03-12	ENSG00000103550	ENSG00000103550			34404	protein-coding gene	gene with protein product	"""family with sequence similarity 191, member A"", ""testis-specific gene 118"""		"""chromosome 16 open reading frame 88"""	C16orf88			Standard	NM_001012991		Approved	101F10.1, FAM191A, TSG118	uc002dgq.3	Q1ED39		ENST00000219837.7:c.83G>A	16.37:g.19726275C>T	ENSP00000219837:p.Arg28Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_001012991	O43328|Q5FWF3	Missense_Mutation	SNP	ENST00000219837.7	37	CCDS42127.1	207	0.09478021978021978	13	0.026422764227642278	43	0.11878453038674033	1	0.0017482517482517483	150	0.19788918205804748	C	0.627	-0.818824	0.02776	0.053038	0.197099	ENSG00000103550	ENST00000219837	T	0.20738	2.05	4.6	0.767	0.18482	.	1.453810	0.04750	N	0.424454	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.37663	-0.9696	8	.	.	.	-0.0584	6.5268	0.22305	0.0:0.3079:0.0:0.6921	rs11640454	28	Q1ED39	CP088_HUMAN	Q	28	ENSP00000219837:R28Q	.	R	-	2	0	C16orf88	19633776	0.035000	0.19736	0.118000	0.21660	0.103000	0.19146	-0.166000	0.09954	0.040000	0.15660	-0.459000	0.05422	CGA	C|0.879;T|0.121	0.121	strong		0.433	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991	
OR2C3	81472	hgsc.bcm.edu	37	1	247694958	247694958	+	Silent	SNP	G	G	A	rs6702695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247694958G>A	ENST00000366487.3	-	2	1217	c.856C>T	c.(856-858)Ctg>Ttg	p.L286L	GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000531662.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	286						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			AGTGGGTTCAGCGCAGGAGTG	0.547													G|||	925	0.184704	0.1036	0.1268	5008	,	,		21934	0.1994		0.2107	False		,,,				2504	0.2935				p.L286L		Atlas-SNP	.											.	OR2C3	92	.	0			c.C856T						PASS	.	G		514,3892	236.1+/-248.4	35,444,1724	101.0	87.0	92.0		856	2.0	0.1	1	dbSNP_116	92	1645,6955	304.6+/-307.0	153,1339,2808	no	coding-synonymous	OR2C3	NM_198074.4		188,1783,4532	AA,AG,GG		19.1279,11.6659,16.6		286/321	247694958	2159,10847	2203	4300	6503	SO:0001819	synonymous_variant	81472	exon2			GGTTCAGCGCAGG	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"""GPCR / Class A : Olfactory receptors"""	15005	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily C, member 4"""	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.856C>T	1.37:g.247694958G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	177	76	0.429379	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	37	CCDS1634.2																																																																																			G|0.830;A|0.170	0.170	strong		0.547	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074	
USP20	10868	hgsc.bcm.edu	37	9	132637712	132637712	+	Silent	SNP	G	G	A	rs735115	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:132637712G>A	ENST00000315480.4	+	20	2330	c.2172G>A	c.(2170-2172)gcG>gcA	p.A724A	USP20_ENST00000372429.3_Silent_p.A724A|USP20_ENST00000358355.1_Silent_p.A724A			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	724	DUSP 1. {ECO:0000255|PROSITE- ProRule:PRU00613}.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				ACACCTTCGCGGAGCCAGGCC	0.682													G|||	1041	0.207867	0.0507	0.2522	5008	,	,		17874	0.1885		0.4066	False		,,,				2504	0.2045				p.A724A		Atlas-SNP	.											.	USP20	186	.	0			c.G2172A						PASS	.	G	,,	391,3755		20,351,1702	55.0	63.0	60.0		2172,2172,2172	-10.7	0.0	9	dbSNP_86	60	3070,5360		541,1988,1686	no	coding-synonymous,coding-synonymous,coding-synonymous	USP20	NM_001008563.3,NM_001110303.2,NM_006676.6	,,	561,2339,3388	AA,AG,GG		36.4176,9.4308,27.5207	,,	724/915,724/915,724/915	132637712	3461,9115	2073	4215	6288	SO:0001819	synonymous_variant	10868	exon20			CTTCGCGGAGCCA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.2172G>A	9.37:g.132637712G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Silent	SNP	ENST00000315480.4	37	CCDS43892.1																																																																																			G|0.730;A|0.270	0.270	strong		0.682	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		
FCGBP	8857	hgsc.bcm.edu	37	19	40389657	40389657	+	Missense_Mutation	SNP	T	T	G	rs3746010|rs148187888		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40389657T>G	ENST00000221347.6	-	18	8532	c.8525A>C	c.(8524-8526)aAc>aCc	p.N2842T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2842	Cys-rich.			N -> T (in Ref. 1; BAA19526). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)		p.N2842T(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			agcACCTTTGTTGACGCAGCT	0.637																																					p.N2842T		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	large_intestine(1)	c.A8525C						scavenged	.						47.0	40.0	42.0					19																	40389657		2103	3809	5912	SO:0001583	missense	8857	exon18			CCTTTGTTGACGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8525A>C	19.37:g.40389657T>G	ENSP00000221347:p.Asn2842Thr	Somatic	865	1	0.00115607		WXS	Illumina HiSeq	Phase_I	381	76	0.199475	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	t	0.013	-1.641107	0.00799	.	.	ENSG00000090920	ENST00000221347	T	0.19938	2.11	2.94	-3.79	0.04320	von Willebrand factor, type C (1);	0.689783	0.12210	N	0.489415	T	0.04952	0.0133	N	0.01219	-0.95	0.09310	N	1	B	0.19935	0.04	B	0.18871	0.023	T	0.41179	-0.9523	10	0.13108	T	0.6	.	6.0306	0.19679	0.0:0.1722:0.2977:0.5301	.	2842	Q9Y6R7	FCGBP_HUMAN	T	2842	ENSP00000221347:N2842T	ENSP00000221347:N2842T	N	-	2	0	FCGBP	45081497	0.511000	0.26179	0.068000	0.19968	0.025000	0.11179	-0.344000	0.07780	-0.736000	0.04831	-0.708000	0.03648	AAC	T|0.250;G|0.750	0.750	weak		0.637	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
TTC7A	57217	hgsc.bcm.edu	37	2	47220622	47220622	+	Silent	SNP	G	G	A	rs17480869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:47220622G>A	ENST00000319190.5	+	6	1166	c.798G>A	c.(796-798)gaG>gaA	p.E266E	TTC7A_ENST00000263737.6_De_novo_Start_OutOfFrame|TTC7A_ENST00000394850.2_Silent_p.E266E|TTC7A_ENST00000461601.1_3'UTR|TTC7A_ENST00000409245.1_Silent_p.E232E	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	266					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			AGCTCCGGGAGGTGCTGCGGA	0.537													G|||	685	0.136781	0.174	0.1513	5008	,	,		19358	0.0109		0.1978	False		,,,				2504	0.1431				p.E266E		Atlas-SNP	.											.	TTC7A	80	.	0			c.G798A						PASS	.	G		715,3691	296.1+/-284.1	53,609,1541	153.0	153.0	153.0		798	1.3	0.5	2	dbSNP_123	153	1423,7177	273.4+/-290.6	122,1179,2999	no	coding-synonymous	TTC7A	NM_020458.2		175,1788,4540	AA,AG,GG		16.5465,16.2279,16.4386		266/859	47220622	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	57217	exon6			CCGGGAGGTGCTG	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.798G>A	2.37:g.47220622G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	248	124	0.5	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			G|0.848;A|0.152	0.152	strong		0.537	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
STXBP3	6814	hgsc.bcm.edu	37	1	109338861	109338861	+	Silent	SNP	G	G	C	rs1127635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109338861G>C	ENST00000370008.3	+	14	1166	c.1116G>C	c.(1114-1116)ctG>ctC	p.L372L		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	372					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		TTAAGGACCTGGCACTTGGAA	0.353													G|||	1650	0.329473	0.2731	0.3213	5008	,	,		18139	0.1925		0.4334	False		,,,				2504	0.4458				p.L372L		Atlas-SNP	.											.	STXBP3	44	.	0			c.G1116C						PASS	.	G		1335,3071	440.4+/-346.0	212,911,1080	57.0	57.0	57.0		1116	4.9	1.0	1	dbSNP_86	57	3818,4782	536.8+/-383.1	825,2168,1307	no	coding-synonymous	STXBP3	NM_007269.2		1037,3079,2387	CC,CG,GG		44.3953,30.2996,39.6202		372/593	109338861	5153,7853	2203	4300	6503	SO:0001819	synonymous_variant	6814	exon14			GGACCTGGCACTT	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1116G>C	1.37:g.109338861G>C		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	237	236	0.995781	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Silent	SNP	ENST00000370008.3	37	CCDS790.1																																																																																			G|0.624;C|0.375	0.375	strong		0.353	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269	
CERS4	79603	hgsc.bcm.edu	37	19	8321937	8321937	+	Silent	SNP	C	C	T	rs1127912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8321937C>T	ENST00000251363.5	+	9	1017	c.717C>T	c.(715-717)caC>caT	p.H239H	CERS4_ENST00000559336.1_Silent_p.H239H|CERS4_ENST00000559450.1_Silent_p.H239H|CERS4_ENST00000558331.1_Silent_p.H188H|CERS4_ENST00000595722.1_3'UTR	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	239	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.H239H(1)									TGCTGTTACACGATTCCTCTG	0.602													C|||	1142	0.228035	0.3434	0.2291	5008	,	,		17567	0.1964		0.2117	False		,,,				2504	0.1207				p.H239H		Atlas-SNP	.											LASS4,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C717T						PASS	.	C		1378,3028	455.7+/-351.1	215,948,1040	241.0	226.0	231.0		717	-3.9	0.8	19	dbSNP_86	231	1642,6958	303.2+/-306.3	175,1292,2833	no	coding-synonymous	CERS4	NM_024552.2		390,2240,3873	TT,TC,CC		19.093,31.2755,23.2201		239/395	8321937	3020,9986	2203	4300	6503	SO:0001819	synonymous_variant	79603	exon9			GTTACACGATTCC		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.717C>T	19.37:g.8321937C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	NM_024552	D6W665	Silent	SNP	ENST00000251363.5	37	CCDS12197.1																																																																																			C|0.761;T|0.239	0.239	strong		0.602	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68812283	68812283	+	Silent	SNP	C	C	T	rs11930532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:68812283C>T	ENST00000334830.7	-	2	764	c.18G>A	c.(16-18)gtG>gtA	p.V6V	TMPRSS11A_ENST00000508048.1_Silent_p.V5V|UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000396188.2_Silent_p.V6V			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	6					cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						TGCCAAATCCCACTGTCCTGA	0.502													T|||	3109	0.620807	0.2458	0.6037	5008	,	,		15666	0.8105		0.7843	False		,,,				2504	0.7761				p.V6V	NSCLC(26;2 894 10941 14480 22546)	Atlas-SNP	.											.	TMPRSS11A	74	.	0			c.G18A						PASS	.	T	,	1482,2924	678.0+/-403.5	246,990,967	67.0	61.0	63.0		18,18	-0.9	0.0	4	dbSNP_120	63	7126,1474	279.5+/-294.0	2945,1236,119	no	coding-synonymous,coding-synonymous	TMPRSS11A	NM_001114387.1,NM_182606.3	,	3191,2226,1086	TT,TC,CC		17.1395,33.636,33.8152	,	6/419,6/422	68812283	8608,4398	2203	4300	6503	SO:0001819	synonymous_variant	339967	exon2			AAATCCCACTGTC	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"""Serine peptidases / Transmembrane"""	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.18G>A	4.37:g.68812283C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_001114387	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Silent	SNP	ENST00000334830.7	37	CCDS3519.1																																																																																			C|0.342;T|0.658	0.658	strong		0.502	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606	
RPN1	6184	hgsc.bcm.edu	37	3	128356852	128356852	+	Silent	SNP	C	C	T	rs1697	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:128356852C>T	ENST00000296255.3	-	3	471	c.423G>A	c.(421-423)ccG>ccA	p.P141P	RPN1_ENST00000497289.1_5'UTR	NM_002950.3	NP_002941.1	P04843	RPN1_HUMAN	ribophorin I	141					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|stomach(2)	13				GBM - Glioblastoma multiforme(114;0.189)		GGGTTGGATACGGATGAAGCA	0.473			T	EVI1	AML								C|||	3176	0.634185	0.615	0.5893	5008	,	,		22066	0.752		0.6312	False		,,,				2504	0.5736				p.P141P		Atlas-SNP	.		Dom	yes		3	3q21.3-q25.2	6184	ribophorin I		L	.	RPN1	39	.	0			c.G423A						PASS	.	C		2570,1836	635.3+/-396.4	743,1084,376	165.0	131.0	142.0		423	-11.4	0.1	3	dbSNP_36	142	5280,3320	645.6+/-400.2	1614,2052,634	no	coding-synonymous	RPN1	NM_002950.3		2357,3136,1010	TT,TC,CC		38.6047,41.6704,39.6432		141/608	128356852	7850,5156	2203	4300	6503	SO:0001819	synonymous_variant	6184	exon3			TGGATACGGATGA		CCDS3051.1	3q21.3	2013-03-06			ENSG00000163902	ENSG00000163902			10381	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 1 homolog (S. cerevisiae)"", ""oligosaccharyltransferase complex subunit (non-catalytic)"""	180470					Standard	NM_002950		Approved	OST1	uc003ekr.1	P04843	OTTHUMG00000159691	ENST00000296255.3:c.423G>A	3.37:g.128356852C>T		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	277	137	0.494585	NM_002950	B2R5Z0|D3DNB6|Q68DT1	Silent	SNP	ENST00000296255.3	37	CCDS3051.1																																																																																			C|0.375;T|0.625	0.625	strong		0.473	RPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356934.2	NM_002950	
TNIK	23043	hgsc.bcm.edu	37	3	171087469	171087469	+	Silent	SNP	G	G	A	rs3796295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:171087469G>A	ENST00000436636.2	-	2	407	c.63C>T	c.(61-63)ccC>ccT	p.P21P	TNIK_ENST00000357327.5_Silent_p.P21P|TNIK_ENST00000538048.1_Silent_p.P21P|TNIK_ENST00000369326.5_Silent_p.P21P|TNIK_ENST00000475336.1_Silent_p.P21P|TNIK_ENST00000341852.6_Silent_p.P21P|TNIK_ENST00000460047.1_Silent_p.P21P|TNIK_ENST00000488470.1_Silent_p.P21P|TNIK_ENST00000470834.1_Silent_p.P21P|TNIK_ENST00000465393.1_Silent_p.P21P|TNIK_ENST00000284483.8_Silent_p.P21P	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	21					actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			AGATCCCTGCGGGGTCCTGAA	0.338													G|||	2254	0.45008	0.0779	0.6282	5008	,	,		17476	0.4276		0.7306	False		,,,				2504	0.5613				p.P21P		Atlas-SNP	.											.	TNIK	313	.	0			c.C63T						PASS	.	G	,,,,,,,	713,2915		83,547,1184	48.0	43.0	44.0		63,63,63,63,63,63,63,63	1.8	1.0	3	dbSNP_107	44	6049,2081		2266,1517,282	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TNIK	NM_001161560.1,NM_001161561.1,NM_001161562.1,NM_001161563.1,NM_001161564.1,NM_001161565.1,NM_001161566.1,NM_015028.2	,,,,,,,	2349,2064,1466	AA,AG,GG		25.5966,19.6527,42.4902	,,,,,,,	21/1353,21/1332,21/1324,21/1306,21/1298,21/1277,21/1269,21/1361	171087469	6762,4996	1814	4065	5879	SO:0001819	synonymous_variant	23043	exon2			CCCTGCGGGGTCC	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.63C>T	3.37:g.171087469G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001161562	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Silent	SNP	ENST00000436636.2	37	CCDS46956.1																																																																																			G|0.509;A|0.491	0.491	strong		0.338	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
C18orf21	83608	hgsc.bcm.edu	37	18	33557466	33557466	+	Missense_Mutation	SNP	A	A	G	rs2276314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:33557466A>G	ENST00000592875.1	+	4	1040	c.394A>G	c.(394-396)Aca>Gca	p.T132A	C18orf21_ENST00000333234.5_Missense_Mutation_p.T44A	NM_031446.4	NP_113634.3	Q32NC0	CR021_HUMAN	chromosome 18 open reading frame 21	132			T -> A (in dbSNP:rs2276314). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							endometrium(1)|kidney(1)|large_intestine(1)|skin(2)	5						TGCCACTCCTACAAGTAAACT	0.438													A|||	1251	0.2498	0.323	0.1859	5008	,	,		18639	0.248		0.2137	False		,,,				2504	0.2352				p.T132A		Atlas-SNP	.											.	C18orf21	15	.	0			c.A394G						PASS	.	A	ALA/THR,ALA/THR,,ALA/THR	1390,3016	457.3+/-351.6	219,952,1032	106.0	95.0	99.0		130,130,,394	-9.5	0.0	18	dbSNP_100	99	1917,6683	339.1+/-323.0	222,1473,2605	yes	missense,missense,intron,missense	C18orf21	NM_001201474.1,NM_001201475.1,NM_001201476.1,NM_031446.4	58,58,,58	441,2425,3637	GG,GA,AA		22.2907,31.5479,25.4267	benign,benign,,benign	44/133,44/133,,132/221	33557466	3307,9699	2203	4300	6503	SO:0001583	missense	83608	exon4			ACTCCTACAAGTA	BC025950	CCDS11916.2, CCDS56064.1, CCDS74212.1	18q12.2	2004-05-05			ENSG00000141428	ENSG00000141428			28802	protein-coding gene	gene with protein product						12477932	Standard	NM_031446		Approved	PNAS-131, PNAS-124, HsT3108	uc002kzc.3	Q32NC0	OTTHUMG00000128531	ENST00000592875.1:c.394A>G	18.37:g.33557466A>G	ENSP00000465517:p.Thr132Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	81	48	0.592593	NM_031446	Q6GW03|Q9BXV6|Q9BXW2	Missense_Mutation	SNP	ENST00000592875.1	37	CCDS11916.2	528	0.24175824175824176	165	0.3353658536585366	56	0.15469613259668508	150	0.26223776223776224	157	0.20712401055408972	A	7.176	0.588546	0.13812	0.315479	0.222907	ENSG00000141428	ENST00000333234;ENST00000269194	T	0.41400	1.0	5.52	-9.47	0.00594	.	1.609950	0.02981	N	0.145670	T	0.00012	0.0000	N	0.16233	0.39	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.32241	-0.9914	9	0.02654	T	1	-2.0526	13.2713	0.60161	0.2449:0.1141:0.641:0.0	rs2276314;rs17845782;rs17858743;rs52824020;rs59707726;rs2276314	132	Q32NC0	CR021_HUMAN	A	132;44	ENSP00000269194:T44A	ENSP00000269194:T44A	T	+	1	0	C18orf21	31811464	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-1.358000	0.02604	-2.144000	0.00802	-0.379000	0.06801	ACA	A|0.742;G|0.258	0.258	strong		0.438	C18orf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250364.1	NM_031446	
GXYLT1	283464	hgsc.bcm.edu	37	12	42503467	42503467	+	Silent	SNP	T	T	C	rs7312933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:42503467T>C	ENST00000398675.3	-	4	745	c.513A>G	c.(511-513)acA>acG	p.T171T	GXYLT1_ENST00000280876.6_Silent_p.T140T	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	171					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						TATAATTAAATGTTTGTAGAA	0.328													T|||	1763	0.352037	0.2012	0.3012	5008	,	,		12711	0.4365		0.3787	False		,,,				2504	0.4775				p.T171T		Atlas-SNP	.											.	GXYLT1	47	.	0			c.A513G						PASS	.	T	,	839,2763		82,675,1044	39.0	38.0	38.0		420,513	3.2	1.0	12	dbSNP_116	38	3039,5089		541,1957,1566	no	coding-synonymous,coding-synonymous	GXYLT1	NM_001099650.1,NM_173601.1	,	623,2632,2610	CC,CT,TT		37.3893,23.2926,33.0605	,	140/410,171/441	42503467	3878,7852	1801	4064	5865	SO:0001819	synonymous_variant	283464	exon4			ATTAAATGTTTGT	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"""Glycosyltransferase family 8 domain containing"""	27482	protein-coding gene	gene with protein product		613321	"""glycosyltransferase 8 domain containing 3"""	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.513A>G	12.37:g.42503467T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Silent	SNP	ENST00000398675.3	37	CCDS41772.1																																																																																			T|0.670;C|0.330	0.330	strong		0.328	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597	
RAI1	10743	hgsc.bcm.edu	37	17	17697099	17697099	+	Silent	SNP	G	G	A	rs587780429|rs398124422|rs35068024|rs11078398|rs587780431	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17697099G>A	ENST00000353383.1	+	3	1306	c.837G>A	c.(835-837)caG>caA	p.Q279Q	RAI1_ENST00000261641.6_Silent_p.Q279Q	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	279	Gln-rich.|Poly-Gln.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ATGACcagcagcagcagcagc	0.637													G|||	2748	0.548722	0.4047	0.5	5008	,	,		14895	0.8333		0.333	False		,,,				2504	0.7065				p.Q279Q		Atlas-SNP	.											.	RAI1	121	.	0			c.G837A						PASS	.	G		1437,2657		231,975,841	20.0	25.0	23.0		837	0.2	0.5	17	dbSNP_120	23	2226,5860		298,1630,2115	no	coding-synonymous	RAI1	NM_030665.3		529,2605,2956	AA,AG,GG		27.5291,35.1001,30.0739		279/1907	17697099	3663,8517	2047	4043	6090	SO:0001819	synonymous_variant	10743	exon3			CCAGCAGCAGCAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.837G>A	17.37:g.17697099G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			G|0.495;A|0.505	0.505	strong		0.637	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
GRIPAP1	56850	hgsc.bcm.edu	37	X	48847497	48847497	+	Silent	SNP	T	T	C	rs11545861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:48847497T>C	ENST00000376441.1	-	7	517	c.483A>G	c.(481-483)gaA>gaG	p.E161E	GRIPAP1_ENST00000376423.4_Silent_p.E108E|GRIPAP1_ENST00000376444.3_Silent_p.E116E|GRIPAP1_ENST00000473581.1_5'UTR|GRIPAP1_ENST00000376425.3_Silent_p.E161E	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	161						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						ACTTCCCGGCTTCTTTCCCAT	0.617													t|||	957	0.25351	0.0144	0.3444	3775	,	,		13768	0.1825		0.3698	False		,,,				2504	0.1462				p.E161E		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.A483G						PASS	.	T	,	288,3545		12,218,46,1401,525	27.0	24.0	25.0		483,324	2.4	0.9	X	dbSNP_120	25	2989,3734		491,1171,836,765,1033	no	coding-synonymous,coding-synonymous	GRIPAP1	NM_020137.3,NM_207672.1	,	503,1389,882,2166,1558	CC,CT,C,TT,T		44.4593,7.5137,31.044	,	161/842,108/626	48847497	3277,7279	2202	4296	6498	SO:0001819	synonymous_variant	56850	exon7			CCCGGCTTCTTTC	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.483A>G	X.37:g.48847497T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Silent	SNP	ENST00000376441.1	37	CCDS35248.1																																																																																			T|0.713;C|0.287	0.287	strong		0.617	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
PTBP1	5725	hgsc.bcm.edu	37	19	808586	808586	+	Silent	SNP	C	C	G	rs13169	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:808586C>G	ENST00000349038.4	+	12	1282	c.1209C>G	c.(1207-1209)ccC>ccG	p.P403P	PTBP1_ENST00000350092.4_Silent_p.P69P|PTBP1_ENST00000356948.6_Silent_p.P429P|PTBP1_ENST00000394601.4_Silent_p.P422P	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	403	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)	p.P429P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGGGAAGCCCATCCGCATCA	0.697													C|||	805	0.160743	0.1339	0.2666	5008	,	,		9699	0.0218		0.1451	False		,,,				2504	0.2812				p.P429P		Atlas-SNP	.											PTBP1,NS,lymphoid_neoplasm,0,1	PTBP1	43	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1287G						scavenged	.	C	,,,	558,3840		44,470,1685	37.0	29.0	31.0		1287,1266,1209,207	-10.3	0.3	19	dbSNP_52	31	1250,7346		87,1076,3135	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	131,1546,4820	GG,GC,CC		14.5416,12.6876,13.9141	,,,	429/558,422/551,403/532,69/198	808586	1808,11186	2199	4298	6497	SO:0001819	synonymous_variant	5725	exon13			GAAGCCCATCCGC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.1209C>G	19.37:g.808586C>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	24	0.292683	NM_002819	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.867;G|0.133	0.133	strong		0.697	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
DAGLA	747	hgsc.bcm.edu	37	11	61505168	61505168	+	Silent	SNP	G	G	A	rs198444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:61505168G>A	ENST00000257215.5	+	15	1640	c.1524G>A	c.(1522-1524)gcG>gcA	p.A508A		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	508					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		GTGAGGATGCGATGGAGTATT	0.622													G|||	2461	0.491414	0.3631	0.4986	5008	,	,		15387	0.7986		0.4284	False		,,,				2504	0.408				p.A508A		Atlas-SNP	.											DAGLA,NS,carcinoma,+1,1	DAGLA	109	1	0			c.G1524A						PASS	.	G		1586,2818	492.9+/-362.5	275,1036,891	160.0	131.0	141.0		1524	-3.4	1.0	11	dbSNP_79	141	3767,4831	535.2+/-382.8	819,2129,1351	no	coding-synonymous	DAGLA	NM_006133.2		1094,3165,2242	AA,AG,GG		43.8125,36.0127,41.1706		508/1043	61505168	5353,7649	2202	4299	6501	SO:0001819	synonymous_variant	747	exon15			GGATGCGATGGAG	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.1524G>A	11.37:g.61505168G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	132	44	0.333333	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.536;A|0.464	0.464	strong		0.622	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
NMI	9111	hgsc.bcm.edu	37	2	152132130	152132130	+	Silent	SNP	A	A	G	rs289834	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:152132130A>G	ENST00000243346.5	-	6	972	c.502T>C	c.(502-504)Ttg>Ctg	p.L168L		NM_004688.2	NP_004679.2	Q13287	NMI_HUMAN	N-myc (and STAT) interactor	168					inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription cofactor activity (GO:0003712)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.0571)		TCTTCACGCAATGTGTCAGGA	0.413													A|||	837	0.167133	0.3162	0.1182	5008	,	,		18489	0.0516		0.1203	False		,,,				2504	0.1677				p.L168L		Atlas-SNP	.											.	NMI	21	.	0			c.T502C						PASS	.	A		1165,3241	412.2+/-336.0	161,843,1199	95.0	98.0	97.0		502	-9.2	0.0	2	dbSNP_79	97	1086,7514	227.6+/-262.9	73,940,3287	no	coding-synonymous	NMI	NM_004688.2		234,1783,4486	GG,GA,AA		12.6279,26.4412,17.3074		168/308	152132130	2251,10755	2203	4300	6503	SO:0001819	synonymous_variant	9111	exon6			CACGCAATGTGTC	U32849	CCDS2192.1	2q23	2008-05-23			ENSG00000123609	ENSG00000123609			7854	protein-coding gene	gene with protein product		603525				8668343, 9989503	Standard	NM_004688		Approved		uc002txi.2	Q13287	OTTHUMG00000131867	ENST00000243346.5:c.502T>C	2.37:g.152132130A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	160	87	0.54375	NM_004688	B5BU69|Q53TI8|Q9BVE5	Silent	SNP	ENST00000243346.5	37	CCDS2192.1																																																																																			A|0.833;G|0.167	0.167	strong		0.413	NMI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254817.2	NM_004688	
IL12RB1	3594	hgsc.bcm.edu	37	19	18191664	18191664	+	Silent	SNP	C	C	G	rs11086087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18191664C>G	ENST00000600835.2	-	5	685	c.387G>C	c.(385-387)gtG>gtC	p.V129V	IL12RB1_ENST00000322153.7_Silent_p.V129V|IL12RB1_ENST00000593993.2_Silent_p.V129V			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	129	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GCTGCAGGGTCACCTCAGGAG	0.572													C|||	651	0.129992	0.0537	0.0807	5008	,	,		18656	0.2857		0.1193	False		,,,				2504	0.1186				p.V129V		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G387C						PASS	.	C	,	244,4162	141.9+/-177.2	5,234,1964	100.0	91.0	94.0		387,387	-4.7	0.0	19	dbSNP_120	94	991,7609	215.0+/-254.5	55,881,3364	no	coding-synonymous,coding-synonymous	IL12RB1	NM_005535.1,NM_153701.1	,	60,1115,5328	GG,GC,CC		11.5233,5.5379,9.4956	,	129/663,129/382	18191664	1235,11771	2203	4300	6503	SO:0001819	synonymous_variant	3594	exon4			CAGGGTCACCTCA	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.387G>C	19.37:g.18191664C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	37	CCDS54232.1																																																																																			G|0.108;C|0.892	0.108	strong		0.572	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
FBXW10	10517	hgsc.bcm.edu	37	17	18682399	18682399	+	Missense_Mutation	SNP	A	A	G	rs1318979	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18682399A>G	ENST00000395665.4	+	14	3168	c.2947A>G	c.(2947-2949)Act>Gct	p.T983A	FBXW10_ENST00000301938.4_Missense_Mutation_p.T930A|TVP23B_ENST00000476139.1_5'Flank|TVP23B_ENST00000307767.8_5'Flank|FBXW10_ENST00000395667.1_Missense_Mutation_p.T982A|TVP23B_ENST00000574226.1_5'Flank|FBXW10_ENST00000308799.4_Missense_Mutation_p.T992A			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	983								p.T982A(1)		NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						TAGAGTGAACACTGAGTTCGT	0.527																																					p.T983A		Atlas-SNP	.											FBXW10,extremity,malignant_melanoma,0,1	FBXW10	82	1	1	Substitution - Missense(1)	skin(1)	c.A2947G						scavenged	.						61.0	55.0	57.0					17																	18682399		2015	3877	5892	SO:0001583	missense	10517	exon14			GTGAACACTGAGT	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.2947A>G	17.37:g.18682399A>G	ENSP00000379025:p.Thr983Ala	Somatic	651	5	0.00768049		WXS	Illumina HiSeq	Phase_I	372	15	0.0403226	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	409	0.18727106227106227	97	0.19715447154471544	81	0.22375690607734808	71	0.12412587412587413	160	0.21108179419525067	A	10.59	1.393102	0.25118	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	3.38	3.38	0.38709	.	0.586804	0.12753	U	0.441979	T	0.00210	0.0006	M	0.61703	1.905	0.47276	P	6.270000000000442E-4	D;D;D;D	0.71674	0.99;0.998;0.984;0.998	D;D;D;D	0.80764	0.98;0.994;0.956;0.994	T	0.05273	-1.0895	9	0.35671	T	0.21	.	9.7578	0.40513	1.0:0.0:0.0:0.0	.	930;992;983;982	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	A	982;992;930;983	ENSP00000379026:T982A;ENSP00000310382:T992A;ENSP00000306937:T930A;ENSP00000379025:T983A	ENSP00000306937:T930A	T	+	1	0	FBXW10	18623124	0.422000	0.25473	0.559000	0.28332	0.113000	0.19764	1.755000	0.38379	1.381000	0.46364	0.338000	0.21704	ACT	A|0.813;G|0.187	0.187	strong		0.527	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
WDR34	89891	hgsc.bcm.edu	37	9	131398636	131398636	+	Silent	SNP	C	C	T	rs10760570	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131398636C>T	ENST00000372715.2	-	4	687	c.627G>A	c.(625-627)caG>caA	p.Q209Q	WDR34_ENST00000483181.1_5'Flank	NM_052844.3	NP_443076.2	Q96EX3	WDR34_HUMAN	WD repeat domain 34	209						axoneme (GO:0005930)|centriole (GO:0005814)|ciliary basal body (GO:0036064)				central_nervous_system(2)|lung(5)|skin(1)|urinary_tract(1)	9						CGGCCGACGGCTGCTGGGGAC	0.677													C|||	3012	0.601438	0.2814	0.7795	5008	,	,		15874	0.5119		0.8698	False		,,,				2504	0.7239				p.Q209Q		Atlas-SNP	.											WDR34,NS,carcinoma,0,2	WDR34	29	2	0			c.G627A						PASS	.	C		1532,2870	455.3+/-351.0	276,980,945	57.0	51.0	53.0		627	4.7	1.0	9	dbSNP_120	53	7656,940	745.5+/-407.3	3417,822,59	no	coding-synonymous	WDR34	NM_052844.3		3693,1802,1004	TT,TC,CC		10.9353,34.8024,29.3122		209/537	131398636	9188,3810	2201	4298	6499	SO:0001819	synonymous_variant	89891	exon4			CGACGGCTGCTGG	BC011874	CCDS6906.2	9q34.11	2013-11-15	2013-02-19	2013-02-19	ENSG00000119333	ENSG00000119333		"""WD repeat domain containing"""	28296	protein-coding gene	gene with protein product		613363				19521662, 21953912, 24183451	Standard	NM_052844		Approved	DIC5, MGC20486, bA216B9.3, FAP133	uc004bvq.1	Q96EX3	OTTHUMG00000020750	ENST00000372715.2:c.627G>A	9.37:g.131398636C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_052844	Q5VXV4|Q9BV46	Silent	SNP	ENST00000372715.2	37	CCDS6906.2																																																																																			C|0.367;T|0.633	0.633	strong		0.677	WDR34-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054463.1	NM_052844	
POMGNT2	84892	hgsc.bcm.edu	37	3	43121559	43121559	+	Silent	SNP	C	C	T	rs604033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:43121559C>T	ENST00000344697.2	-	2	1710	c.1365G>A	c.(1363-1365)ccG>ccA	p.P455P	POMGNT2_ENST00000441964.1_Silent_p.P455P	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	455					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										GAATGAGGGACGGGATGTCCA	0.612													C|||	3920	0.782748	0.8275	0.8127	5008	,	,		21590	0.7401		0.7922	False		,,,				2504	0.7352				p.P455P		Atlas-SNP	.											.	.	.	.	0			c.G1365A						PASS	.	C		3589,817	745.7+/-411.7	1450,689,64	41.0	40.0	40.0		1365	-11.1	0.1	3	dbSNP_83	40	6872,1728	732.5+/-406.8	2730,1412,158	no	coding-synonymous	C3orf39	NM_032806.4		4180,2101,222	TT,TC,CC		20.093,18.5429,19.5679		455/581	43121559	10461,2545	2203	4300	6503	SO:0001819	synonymous_variant	84892	exon2			GAGGGACGGGATG	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1365G>A	3.37:g.43121559C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_032806	B3KWC3|Q96SY3	Silent	SNP	ENST00000344697.2	37	CCDS2709.1																																																																																			C|0.197;T|0.803	0.803	strong		0.612	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
BEST1	7439	hgsc.bcm.edu	37	11	61730553	61730553	+	Intron	SNP	T	T	C	rs17185413	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:61730553T>C	ENST00000378043.4	+	10	2382				BEST1_ENST00000301774.9_Missense_Mutation_p.S271P|FTH1_ENST00000529631.1_Intron|BEST1_ENST00000378042.3_Intron|BEST1_ENST00000449131.2_Missense_Mutation_p.S583P|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000534553.1_3'UTR	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						AGGGAAGTGTTCGGGACCTTT	0.537													T|||	523	0.104433	0.0151	0.1268	5008	,	,		21309	0.002		0.2247	False		,,,				2504	0.1912				p.S583P		Atlas-SNP	.											BEST1_ENST00000449131,colon,carcinoma,-1,2	BEST1	85	2	0			c.T1747C						PASS	.	T	PRO/SER,	73,1311		1,71,620	52.0	45.0	47.0		1747,	-2.9	0.0	11	dbSNP_123	47	798,2384		102,594,895	yes	missense,intron	BEST1	NM_001139443.1,NM_004183.3	74,	103,665,1515	CC,CT,TT		25.0786,5.2746,19.0758	,	583/605,	61730553	871,3695	692	1591	2283	SO:0001627	intron_variant	7439	exon9			AAGTGTTCGGGAC	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+188T>C	11.37:g.61730553T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	71	0.47651	NM_001139443	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Missense_Mutation	SNP	ENST00000378043.4	37	CCDS31580.1	230	0.10531135531135531	9	0.018292682926829267	60	0.16574585635359115	0	0.0	161	0.21240105540897097	T	17.59	3.427298	0.62733	0.052746	0.250786	ENSG00000167995	ENST00000301774;ENST00000449131	T;D	0.97209	-0.36;-4.29	4.35	-2.91	0.05631	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.50448	-0.8827	7	.	.	.	.	2.0384	0.03545	0.1365:0.3758:0.2746:0.2131	rs17185413	583	O76090-3	.	P	271;583	ENSP00000301774:S271P;ENSP00000399709:S583P	.	S	+	1	0	BEST1	61487129	0.000000	0.05858	0.000000	0.03702	0.259000	0.26198	-0.347000	0.07750	-0.344000	0.08338	0.459000	0.35465	TCG	T|0.906;C|0.094	0.094	strong		0.537	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
IP6K2	51447	hgsc.bcm.edu	37	3	48725707	48725707	+	Silent	SNP	C	C	T	rs1048940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:48725707C>T	ENST00000328631.5	-	6	1503	c.1280G>A	c.(1279-1281)tGa>tAa	p.*427*	NCKIPSD_ENST00000416649.2_5'Flank|NCKIPSD_ENST00000294129.2_5'Flank|NCKIPSD_ENST00000341520.4_5'Flank	NM_001005909.2|NM_016291.3	NP_001005909.1|NP_057375.2	Q9UHH9	IP6K2_HUMAN	inositol hexakisphosphate kinase 2	0					cytokine-mediated signaling pathway (GO:0019221)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell growth (GO:0030308)|phosphate ion transport (GO:0006817)|phosphatidylinositol phosphorylation (GO:0046854)|positive regulation of apoptotic process (GO:0043065)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	15						CTAGCAAGCTCACTCCCCACT	0.582													C|||	150	0.0299521	0.0023	0.0504	5008	,	,		19809	0.0		0.1014	False		,,,				2504	0.0102				p.X427X		Atlas-SNP	.											.	IP6K2	63	.	0			c.G1280A						PASS	.	C	,	93,4313	77.3+/-115.6	0,93,2110	116.0	114.0	115.0		1280,1280	4.4	1.0	3	dbSNP_86	115	812,7788	189.4+/-236.2	41,730,3529	no	coding-synonymous,coding-synonymous	IP6K2	NM_001005909.2,NM_016291.3	,	41,823,5639	TT,TC,CC		9.4419,2.1108,6.9583	,	427/427,427/427	48725707	905,12101	2203	4300	6503	SO:0001819	synonymous_variant	51447	exon6			CAAGCTCACTCCC	AF177145	CCDS2777.1, CCDS33752.1, CCDS54579.1, CCDS54580.1, CCDS54581.1	3p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000068745	ENSG00000068745			17313	protein-coding gene	gene with protein product		606992	"""inositol hexaphosphate kinase 2"""	IHPK2		10574768	Standard	NM_016291		Approved		uc003cup.3	Q9UHH9	OTTHUMG00000133543	ENST00000328631.5:c.1280G>A	3.37:g.48725707C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	183	97	0.530055	NM_016291	A8K3B1|B4E3G6|G8JLL6|Q6P0N8|Q9BSZ6|Q9BUW3|Q9H4P7|Q9NT63|Q9UFU6	Silent	SNP	ENST00000328631.5	37	CCDS2777.1																																																																																			T|0.062;G|0.000;C|0.937	0.062	strong		0.582	IP6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257521.2	NM_016291	
FAM160B2	64760	hgsc.bcm.edu	37	8	21960096	21960096	+	Missense_Mutation	SNP	C	C	T	rs117802113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:21960096C>T	ENST00000289921.7	+	16	2096	c.2050C>T	c.(2050-2052)Ctc>Ttc	p.L684F		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	684				L -> F (in Ref. 2; AAH12865/AAH13350). {ECO:0000305}.						endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						AGGCAAGCTGCTCCTGGTGCG	0.617													.|||	183	0.0365415	0.0076	0.0476	5008	,	,		14506	0.001		0.1233	False		,,,				2504	0.0153				p.L684F		Atlas-SNP	.											.	FAM160B2	35	.	0			c.C2050T						PASS	.	C	PHE/LEU	79,3821		1,77,1872	23.0	26.0	25.0		2050	5.0	1.0	8	dbSNP_132	25	999,7267		43,913,3177	yes	missense	FAM160B2	NM_022749.5	22	44,990,5049	TT,TC,CC		12.0857,2.0256,8.8608	benign	684/744	21960096	1078,11088	1950	4133	6083	SO:0001583	missense	64760	exon16			AAGCTGCTCCTGG	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"""retinoic acid induced 16"""	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.2050C>T	8.37:g.21960096C>T	ENSP00000289921:p.Leu684Phe	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Missense_Mutation	SNP	ENST00000289921.7	37	CCDS6021.2	116	0.05311355311355311	4	0.008130081300813009	17	0.04696132596685083	1	0.0017482517482517483	94	0.12401055408970976	C	21.7	4.182786	0.78677	0.020256	0.120857	ENSG00000158863	ENST00000289921;ENST00000356512	T	0.57107	0.42	4.98	4.98	0.66077	.	0.075316	0.52532	D	0.000062	T	0.01254	0.0041	M	0.63843	1.955	0.23381	P	0.99779929	P	0.42483	0.781	P	0.44732	0.459	T	0.23583	-1.0184	9	0.49607	T	0.09	-29.1676	15.7616	0.78087	0.0:1.0:0.0:0.0	.	684	Q86V87	F16B2_HUMAN	F	684;102	ENSP00000289921:L684F	ENSP00000289921:L684F	L	+	1	0	FAM160B2	22016041	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.353000	0.44089	2.318000	0.78349	0.561000	0.74099	CTC	C|0.945;T|0.055	0.055	strong		0.617	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2		
IL16	3603	hgsc.bcm.edu	37	15	81578139	81578139	+	Missense_Mutation	SNP	C	C	T	rs4072111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:81578139C>T	ENST00000302987.4	+	9	1300	c.1300C>T	c.(1300-1302)Ccc>Tcc	p.P434S	IL16_ENST00000394660.2_Missense_Mutation_p.P434S			Q14005	IL16_HUMAN	interleukin 16	434	Interaction with GRIN2A.|PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.		P -> S (in dbSNP:rs4072111).		immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P434S(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CGGTCCAGTCCCCATCATTGT	0.507													C|||	824	0.164537	0.0431	0.1888	5008	,	,		19338	0.2083		0.1024	False		,,,				2504	0.3303				p.P434S		Atlas-SNP	.											IL16,NS,carcinoma,0,1	IL16	254	1	1	Substitution - Missense(1)	stomach(1)	c.C1300T						PASS	.	C	SER/PRO,SER/PRO	214,3880		6,202,1839	179.0	179.0	179.0		1300,1300	5.2	1.0	15	dbSNP_108	179	886,7490		45,796,3347	yes	missense,missense	IL16	NM_001172128.1,NM_172217.3	74,74	51,998,5186	TT,TC,CC		10.5778,5.2272,8.8212	possibly-damaging,possibly-damaging	434/1332,434/1333	81578139	1100,11370	2047	4188	6235	SO:0001583	missense	3603	exon10			CCAGTCCCCATCA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1300C>T	15.37:g.81578139C>T	ENSP00000302935:p.Pro434Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	148	87	0.587838	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	279	0.12774725274725274	25	0.0508130081300813	59	0.16298342541436464	109	0.19055944055944055	86	0.11345646437994723	C	12.92	2.082011	0.36758	0.052272	0.105778	ENSG00000172349	ENST00000394655;ENST00000394660;ENST00000355368;ENST00000302987	T;T	0.15718	2.4;2.4	5.23	5.23	0.72850	PDZ/DHR/GLGF (2);	0.000000	0.45126	D	0.000386	T	0.00012	0.0000	N	0.01493	-0.835	0.09310	P	1.0	D;D	0.56287	0.958;0.975	P;P	0.51385	0.468;0.668	T	0.29610	-1.0006	9	0.07325	T	0.83	.	13.8975	0.63783	0.1521:0.8479:0.0:0.0	rs4072111;rs17846279;rs17859301;rs52792386;rs58547005;rs4072111	434;434	Q14005;Q14005-2	IL16_HUMAN;.	S	434;434;266;434	ENSP00000378155:P434S;ENSP00000302935:P434S	ENSP00000302935:P434S	P	+	1	0	IL16	79365194	1.000000	0.71417	0.997000	0.53966	0.713000	0.41058	3.714000	0.54889	2.717000	0.92951	0.655000	0.94253	CCC	C|0.870;T|0.130	0.130	strong		0.507	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
FGD4	121512	hgsc.bcm.edu	37	12	32777362	32777362	+	Silent	SNP	G	G	A	rs11052110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32777362G>A	ENST00000427716.2	+	12	1942	c.1518G>A	c.(1516-1518)gcG>gcA	p.A506A	FGD4_ENST00000381025.3_Silent_p.A258A|FGD4_ENST00000534526.2_Silent_p.A643A|FGD4_ENST00000525053.1_Silent_p.A618A|FGD4_ENST00000266482.3_Silent_p.A258A|FGD4_ENST00000546442.1_Silent_p.A413A|FGD4_ENST00000531134.1_Silent_p.A591A	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	506	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					TTAGTTCTGCGCAAGACAAAG	0.353													G|||	1260	0.251597	0.1536	0.268	5008	,	,		19635	0.1667		0.3191	False		,,,				2504	0.3906				p.A506A		Atlas-SNP	.											.	FGD4	86	.	0			c.G1518A						PASS	.	G		859,3547	324.0+/-298.4	85,689,1429	69.0	71.0	70.0		1518	0.1	1.0	12	dbSNP_120	70	2682,5918	417.3+/-352.4	441,1800,2059	no	coding-synonymous	FGD4	NM_139241.2		526,2489,3488	AA,AG,GG		31.186,19.4961,27.2259		506/767	32777362	3541,9465	2203	4300	6503	SO:0001819	synonymous_variant	121512	exon12			TTCTGCGCAAGAC	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.1518G>A	12.37:g.32777362G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	112	65	0.580357	NM_139241	Q6ULS2|Q8TCP6	Silent	SNP	ENST00000427716.2	37	CCDS8727.1																																																																																			G|0.744;A|0.256	0.256	strong		0.353	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241	
MGAT5B	146664	hgsc.bcm.edu	37	17	74936576	74936576	+	Silent	SNP	G	G	A	rs8081793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74936576G>A	ENST00000569840.2	+	14	2251	c.1677G>A	c.(1675-1677)ccG>ccA	p.P559P	MGAT5B_ENST00000301618.4_Silent_p.P557P|MGAT5B_ENST00000428789.2_Silent_p.P568P	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	559					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCTTCAGCCCGCCCCACAGCT	0.647													G|||	1327	0.264976	0.2451	0.1744	5008	,	,		16308	0.371		0.2674	False		,,,				2504	0.2444				p.P568P		Atlas-SNP	.											.	MGAT5B	98	.	0			c.G1704A						PASS	.	G	,,	1125,3281	401.3+/-331.9	145,835,1223	76.0	69.0	71.0		1677,1671,1704	-8.8	0.6	17	dbSNP_116	71	2155,6445	370.6+/-335.9	294,1567,2439	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	439,2402,3662	AA,AG,GG		25.0581,25.5334,25.2191	,,	559/793,557/791,568/802	74936576	3280,9726	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon12			CAGCCCGCCCCAC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1677G>A	17.37:g.74936576G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			G|0.734;A|0.266	0.266	strong		0.647	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
HSP90AB1	3326	hgsc.bcm.edu	37	6	44221262	44221262	+	Missense_Mutation	SNP	A	A	G	rs201760495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44221262A>G	ENST00000371554.1	+	12	2316	c.2102A>G	c.(2101-2103)aAt>aGt	p.N701S	SLC35B2_ENST00000495706.1_5'Flank|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000371646.5_Missense_Mutation_p.N701S|HSP90AB1_ENST00000353801.3_Missense_Mutation_p.N701S			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	701					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GAGGAACCCAATGCTGCAGTT	0.453											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N701S		Atlas-SNP	.											.	HSP90AB1	83	.	0			c.A2102G						PASS	.						75.0	76.0	76.0					6																	44221262		2203	4300	6503	SO:0001583	missense	3326	exon12			AACCCAATGCTGC	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2102A>G	6.37:g.44221262A>G	ENSP00000360609:p.Asn701Ser	Somatic	125	0	0	922	WXS	Illumina HiSeq	Phase_I	167	14	0.0838323	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	ENST00000371554.1	37	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	G	3.876	-0.026861	0.07589	.	.	ENSG00000096384	ENST00000371646;ENST00000353801;ENST00000371554	T;T;T	0.08807	3.05;3.05;3.05	3.91	3.91	0.45181	.	0.272984	0.27901	N	0.017393	T	0.00580	0.0019	N	0.01109	-1.01	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.47749	-0.9093	10	0.02654	T	1	-8.621	7.7636	0.28968	0.0881:0.2939:0.618:0.0	.	663;691;701	B4DMA2;B4DGL0;P08238	.;.;HS90B_HUMAN	S	701	ENSP00000360709:N701S;ENSP00000325875:N701S;ENSP00000360609:N701S	ENSP00000325875:N701S	N	+	2	0	HSP90AB1	44329240	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	2.913000	0.48790	1.010000	0.39314	-0.166000	0.13349	AAT	A|0.993;G|0.007	0.007	strong		0.453	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
MUC4	4585	hgsc.bcm.edu	37	3	195510192	195510192	+	Silent	SNP	A	A	C	rs367755087		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195510192A>C	ENST00000463781.3	-	2	8718	c.8259T>G	c.(8257-8259)ctT>ctG	p.L2753L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.L2753L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L2753L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGGTGACAGGAAGAGGGGTGG	0.562																																					p.L2753L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	1	Substitution - coding silent(1)	kidney(1)	c.T8259G						scavenged	.						13.0	8.0	10.0					3																	195510192		667	1473	2140	SO:0001819	synonymous_variant	4585	exon2			GACAGGAAGAGGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8259T>G	3.37:g.195510192A>C		Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	195	26	0.133333	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
INO80D	54891	hgsc.bcm.edu	37	2	206872126	206872126	+	Silent	SNP	C	C	T	rs116331438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:206872126C>T	ENST00000403263.1	-	10	2204	c.1800G>A	c.(1798-1800)ccG>ccA	p.P600P	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	600					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P600P(1)|p.P495P(1)		NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						CAATGTCATCCGGCAACTCAT	0.498													C|||	2	0.000399361	0.0	0.0	5008	,	,		19913	0.0		0.001	False		,,,				2504	0.001				p.P600P		Atlas-SNP	.											INO80D_ENST00000403263,NS,carcinoma,0,2	INO80D	134	2	2	Substitution - coding silent(2)	kidney(2)	c.G1800A						PASS	.	C		3,4115		0,3,2056	130.0	130.0	130.0		1800	2.8	1.0	2	dbSNP_132	130	22,8406		0,22,4192	no	coding-synonymous	INO80D	NM_017759.4		0,25,6248	TT,TC,CC		0.261,0.0729,0.1993		600/1028	206872126	25,12521	2059	4214	6273	SO:0001819	synonymous_variant	54891	exon10			GTCATCCGGCAAC		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"""INO80 complex subunits"""	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.1800G>A	2.37:g.206872126C>T		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	309	145	0.469256	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																			C|0.999;T|0.001	0.001	strong		0.498	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
EXPH5	23086	hgsc.bcm.edu	37	11	108409784	108409784	+	Missense_Mutation	SNP	T	T	A	rs2640785	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108409784T>A	ENST00000265843.4	-	3	520	c.410A>T	c.(409-411)gAg>gTg	p.E137V	EXPH5_ENST00000525344.1_Missense_Mutation_p.E130V|EXPH5_ENST00000428840.1_Missense_Mutation_p.E61V|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	137			E -> V (in dbSNP:rs2640785).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTTTGAAGTCTCCTTTCCAGA	0.433													T|||	1264	0.252396	0.0393	0.3501	5008	,	,		17701	0.5804		0.17	False		,,,				2504	0.2178				p.E137V		Atlas-SNP	.											.	EXPH5	193	.	0			c.A410T						PASS	.	T	VAL/GLU	281,4121	156.6+/-189.7	4,273,1924	144.0	141.0	142.0		410	5.0	0.8	11	dbSNP_100	142	1462,7134	279.8+/-294.2	141,1180,2977	yes	missense	EXPH5	NM_015065.2	121	145,1453,4901	AA,AT,TT		17.0079,6.3835,13.4098	probably-damaging	137/1990	108409784	1743,11255	2201	4298	6499	SO:0001583	missense	23086	exon3			GAAGTCTCCTTTC		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.410A>T	11.37:g.108409784T>A	ENSP00000265843:p.Glu137Val	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	638	0.29212454212454214	31	0.06300813008130081	111	0.30662983425414364	356	0.6223776223776224	140	0.18469656992084432	T	22.7	4.322784	0.81580	0.063835	0.170079	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000525344;ENST00000526312;ENST00000531386	T;T;T;T;T	0.40756	3.92;3.84;3.92;3.74;1.02	4.99	4.99	0.66335	.	0.347910	0.24755	N	0.035872	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	1.0	D	0.61080	0.989	P	0.58266	0.836	T	0.50013	-0.8877	9	0.87932	D	0	-6.9937	11.3852	0.49780	0.0:0.0:0.0:1.0	rs2640785;rs3741047;rs52819845;rs2640785	137	Q8NEV8	EXPH5_HUMAN	V	137;61;130;61;61	ENSP00000265843:E137V;ENSP00000391966:E61V;ENSP00000432546:E130V;ENSP00000432683:E61V;ENSP00000433909:E61V	ENSP00000265843:E137V	E	-	2	0	EXPH5	107914994	0.997000	0.39634	0.799000	0.32177	0.948000	0.59901	4.094000	0.57721	2.012000	0.59069	0.528000	0.53228	GAG	T|0.797;A|0.203	0.203	strong		0.433	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3469463	3469463	+	Silent	SNP	G	G	C	rs4971514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:3469463G>C	ENST00000324266.5	+	9	1968	c.1773G>C	c.(1771-1773)ctG>ctC	p.L591L	TRAPPC12_ENST00000469147.1_3'UTR|TRAPPC12_ENST00000382110.2_Silent_p.L591L	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	591					vesicle-mediated transport (GO:0016192)												GGATTTCCCTGCAGGTACCTG	0.488													G|||	2080	0.415335	0.4826	0.3285	5008	,	,		18864	0.3601		0.4473	False		,,,				2504	0.41				p.L591L		Atlas-SNP	.											.	.	.	.	0			c.G1773C						PASS	.	G		2006,2400	560.5+/-380.5	459,1088,656	74.0	75.0	75.0		1773	-10.7	0.4	2	dbSNP_111	75	3586,5014	519.3+/-379.4	751,2084,1465	no	coding-synonymous	TTC15	NM_016030.5		1210,3172,2121	CC,CG,GG		41.6977,45.5288,42.9955		591/736	3469463	5592,7414	2203	4300	6503	SO:0001819	synonymous_variant	51112	exon9			TTCCCTGCAGGTA	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1773G>C	2.37:g.3469463G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1	932|932	0.4267399267399267|0.4267399267399267	244|244	0.4959349593495935|0.4959349593495935	134|134	0.3701657458563536|0.3701657458563536	213|213	0.3723776223776224|0.3723776223776224	341|341	0.449868073878628|0.449868073878628	G|G	13.50|13.50	2.257146|2.257146	0.39896|0.39896	0.455288|0.455288	0.416977|0.416977	ENSG00000171853|ENSG00000171853	ENST00000433382|ENST00000416918	.|.	.|.	.|.	5.65|5.65	-10.7|-10.7	0.00240|0.00240	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.32640|0.32640	-0.9899|-0.9899	3|3	.|.	.|.	.|.	.|.	2.9671|2.9671	0.05911|0.05911	0.165:0.3251:0.3618:0.1481|0.165:0.3251:0.3618:0.1481	rs4971514;rs17851116;rs57881176;rs4971514|rs4971514;rs17851116;rs57881176;rs4971514	.|.	.|.	.|.	P|S	137|7	.|.	.|.	A|C	+|+	1|2	0|0	TTC15|TTC15	3448470|3448470	0.166000|0.166000	0.22962|0.22962	0.430000|0.430000	0.26722|0.26722	0.957000|0.957000	0.61999|0.61999	-0.650000|-0.650000	0.05378|0.05378	-2.368000|-2.368000	0.00604|0.00604	0.655000|0.655000	0.94253|0.94253	GCA|TGC	G|0.566;C|0.434	0.434	strong		0.488	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
OR51B2	79345	hgsc.bcm.edu	37	11	5344592	5344592	+	Missense_Mutation	SNP	A	A	C	rs11036814	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5344592A>C	ENST00000328813.2	-	1	990	c.936T>G	c.(934-936)agT>agG	p.S312R	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_033180.4	NP_149420.4	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B, member 2	312			S -> R (in dbSNP:rs11036814). {ECO:0000269|PubMed:10220430}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S312R(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|large_intestine(6)|lung(21)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCCGAGTTTAACTACTAAACC	0.378													A|||	491	0.0980431	0.0113	0.1182	5008	,	,		20745	0.123		0.165	False		,,,				2504	0.1063				p.S312R		Atlas-SNP	.											OR51B2,NS,carcinoma,0,1	OR51B2	69	1	1	Substitution - Missense(1)	stomach(1)	c.T936G						PASS	.	A	ARG/SER	178,4224	109.1+/-147.4	2,174,2025	60.0	58.0	59.0		936	1.8	0.0	11	dbSNP_120	59	1353,7241	256.2+/-280.8	97,1159,3041	yes	missense	OR51B2	NM_033180.4	110	99,1333,5066	CC,CA,AA		15.7435,4.0436,11.7805	possibly-damaging	312/313	5344592	1531,11465	2201	4297	6498	SO:0001583	missense	79345	exon1			AGTTTAACTACTA	AF399503	CCDS31377.1	11p15.4	2012-08-09			ENSG00000184881	ENSG00000184881		"""GPCR / Class A : Olfactory receptors"""	14703	protein-coding gene	gene with protein product				OR51B1P			Standard	NM_033180		Approved		uc001mao.1	Q9Y5P1	OTTHUMG00000066682	ENST00000328813.2:c.936T>G	11.37:g.5344592A>C	ENSP00000327540:p.Ser312Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_033180	Q96RD4	Missense_Mutation	SNP	ENST00000328813.2	37	CCDS31377.1	267	0.12225274725274725	9	0.018292682926829267	42	0.11602209944751381	91	0.1590909090909091	125	0.16490765171503957	A	11.46	1.645446	0.29246	0.040436	0.157435	ENSG00000184881	ENST00000328813	T	0.00005	9.79	4.1	1.78	0.24846	.	0.780759	0.10783	U	0.634602	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.08055	0.003	T	0.04165	-1.0972	9	0.87932	D	0	.	5.3809	0.16192	0.7866:0.0:0.2134:0.0	rs11036814;rs52827869;rs58407994;rs11036814	312	Q9Y5P1	O51B2_HUMAN	R	312	ENSP00000327540:S312R	ENSP00000327540:S312R	S	-	3	2	OR51B2	5301168	0.009000	0.17119	0.006000	0.13384	0.032000	0.12392	0.153000	0.16323	1.521000	0.48983	0.519000	0.50382	AGT	A|0.880;C|0.120	0.120	strong		0.378	OR51B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142983.1	NM_033180	
LAMA1	284217	hgsc.bcm.edu	37	18	6943264	6943264	+	Silent	SNP	G	G	A	rs2016639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:6943264G>A	ENST00000389658.3	-	62	9075	c.8982C>T	c.(8980-8982)gaC>gaT	p.D2994D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2994	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.D2994D(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTGCGTTCCCGTCAACAATCA	0.498													G|||	1433	0.286142	0.0204	0.4006	5008	,	,		20239	0.3413		0.331	False		,,,				2504	0.4611				p.D2994D		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	1	1	Substitution - coding silent(1)	stomach(1)	c.C8982T						PASS	.	G		303,4103	163.6+/-195.4	13,277,1913	308.0	234.0	259.0		8982	-5.8	0.2	18	dbSNP_92	259	2856,5744	448.1+/-361.7	487,1882,1931	no	coding-synonymous	LAMA1	NM_005559.3		500,2159,3844	AA,AG,GG		33.2093,6.877,24.2888		2994/3076	6943264	3159,9847	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon62			GTTCCCGTCAACA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.8982C>T	18.37:g.6943264G>A		Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.755;A|0.245	0.245	strong		0.498	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90503007	90503007	+	Missense_Mutation	SNP	A	A	G	rs11789780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:90503007A>G	ENST00000325643.5	+	4	3671	c.3605A>G	c.(3604-3606)gAc>gGc	p.D1202G		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1202			D -> G (in dbSNP:rs11789780). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGCTGTGCGGACAAGGGCGAG	0.652													.|||	2303	0.459864	0.5159	0.4049	5008	,	,		17260	0.3363		0.5169	False		,,,				2504	0.4918				p.D1202G		Atlas-SNP	.											C9orf79,NS,carcinoma,0,3	.	.	3	0			c.A3605G						PASS	.	A	GLY/ASP	2103,2275		533,1037,619	11.0	11.0	11.0		3605	1.5	0.0	9	dbSNP_120	11	4092,4468		1053,1986,1241	yes	missense	C9orf79	NM_178828.4	94	1586,3023,1860	GG,GA,AA		47.8037,48.0356,47.8822	probably-damaging	1202/1446	90503007	6195,6743	2189	4280	6469	SO:0001583	missense	286234	exon4			GTGCGGACAAGGG	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.3605A>G	9.37:g.90503007A>G	ENSP00000322640:p.Asp1202Gly	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	981	0.4491758241758242	245	0.49796747967479676	157	0.43370165745856354	192	0.3356643356643357	387	0.5105540897097626	a	11.24	1.581690	0.28180	0.480356	0.478037	ENSG00000177992	ENST00000325643	T	0.03772	3.81	2.71	1.51	0.23008	.	1.504920	0.04304	N	0.347788	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	D	0.60575	0.988	P	0.57960	0.83	T	0.45991	-0.9223	9	0.23891	T	0.37	.	5.7461	0.18120	0.7205:0.2795:0.0:0.0	rs11789780;rs11789780	1202	Q6ZUB1	CI079_HUMAN	G	1202	ENSP00000322640:D1202G	ENSP00000322640:D1202G	D	+	2	0	C9orf79	89692827	0.001000	0.12720	0.002000	0.10522	0.004000	0.04260	1.304000	0.33482	0.429000	0.26202	0.533000	0.62120	GAC	A|0.555;G|0.445	0.445	strong		0.652	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
ZNF280B	140883	hgsc.bcm.edu	37	22	22843118	22843118	+	Silent	SNP	C	C	T	rs2236730	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22843118C>T	ENST00000406426.1	-	4	1348	c.606G>A	c.(604-606)tcG>tcA	p.S202S	ZNF280B_ENST00000360412.2_Silent_p.S202S			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	202					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		CTGAAGGGAACGAAGCTGAAG	0.388													C|||	3739	0.746605	0.6611	0.8516	5008	,	,		18894	0.7421		0.8738	False		,,,				2504	0.6616				p.S202S		Atlas-SNP	.											.	ZNF280B	67	.	0			c.G606A						PASS	.	C		2989,1417	685.5+/-404.6	1022,945,236	114.0	110.0	112.0		606	-5.0	0.0	22	dbSNP_98	112	7431,1169	763.0+/-407.6	3221,989,90	no	coding-synonymous	ZNF280B	NM_080764.2		4243,1934,326	TT,TC,CC		13.593,32.1607,19.8831		202/544	22843118	10420,2586	2203	4300	6503	SO:0001819	synonymous_variant	140883	exon4			AGGGAACGAAGCT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"""zinc finger protein 279"", ""suppressor of hairy wing homolog 2 (Drosophila)"""	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.606G>A	22.37:g.22843118C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	136	133	0.977941	NM_080764		Silent	SNP	ENST00000406426.1	37	CCDS13799.1																																																																																			C|0.206;T|0.794	0.794	strong		0.388	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764	
MUC6	4588	hgsc.bcm.edu	37	11	1017316	1017316	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1017316G>T	ENST00000421673.2	-	31	5535	c.5485C>A	c.(5485-5487)Cca>Aca	p.P1829T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1829	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTGTGATGGGGTTGGATAG	0.547																																					p.P1829T		Atlas-SNP	.											MUC6_ENST00000421673,right_upper_lobe,carcinoma,+1,2	MUC6	408	2	0			c.C5485A						scavenged	.																																			SO:0001583	missense	4588	exon31			GTGATGGGGTTGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5485C>A	11.37:g.1017316G>T	ENSP00000406861:p.Pro1829Thr	Somatic	1307	59	0.0451415		WXS	Illumina HiSeq	Phase_I	1323	44	0.0332577	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.335327	0.24253	.	.	ENSG00000184956	ENST00000421673	T	0.24723	1.84	3.21	-0.343	0.12632	.	.	.	.	.	T	0.30355	0.0762	L	0.52126	1.63	0.09310	N	1	D	0.54964	0.969	P	0.61477	0.889	T	0.17531	-1.0366	9	0.02654	T	1	.	7.2552	0.26173	0.0:0.2939:0.4065:0.2996	.	1829	Q6W4X9	MUC6_HUMAN	T	1829	ENSP00000406861:P1829T	ENSP00000406861:P1829T	P	-	1	0	MUC6	1007316	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.664000	0.05292	-0.177000	0.10690	0.313000	0.20887	CCA	.	.	none		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90503451	90503451	+	Missense_Mutation	SNP	G	G	A	rs11142017	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:90503451G>A	ENST00000325643.5	+	4	4115	c.4049G>A	c.(4048-4050)cGc>cAc	p.R1350H		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1350			R -> H (in dbSNP:rs11142017). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGTGACTTCCGCGCCCAGGAG	0.592													.|||	2304	0.460064	0.5151	0.4049	5008	,	,		19039	0.3373		0.5179	False		,,,				2504	0.4918				p.R1350H		Atlas-SNP	.											.	.	.	.	0			c.G4049A						PASS	.	A	HIS/ARG	2192,2214	589.5+/-387.1	542,1108,553	86.0	77.0	80.0		4049	1.2	0.0	9	dbSNP_120	80	4226,4374	583.5+/-391.6	1067,2092,1141	yes	missense	C9orf79	NM_178828.4	29	1609,3200,1694	AA,AG,GG		49.1395,49.7503,49.3465	benign	1350/1446	90503451	6418,6588	2203	4300	6503	SO:0001583	missense	286234	exon4			ACTTCCGCGCCCA	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.4049G>A	9.37:g.90503451G>A	ENSP00000322640:p.Arg1350His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	982	0.44963369963369965	245	0.49796747967479676	157	0.43370165745856354	192	0.3356643356643357	388	0.5118733509234829	a	7.370	0.626610	0.14257	0.497503	0.491395	ENSG00000177992	ENST00000325643	T	0.03717	3.83	2.47	1.25	0.21368	.	2.244580	0.02369	N	0.077687	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43956	-0.9359	9	0.42905	T	0.14	.	2.9167	0.05755	0.586:0.2613:0.1527:0.0	rs11142017;rs11142017	1350	Q6ZUB1	CI079_HUMAN	H	1350	ENSP00000322640:R1350H	ENSP00000322640:R1350H	R	+	2	0	C9orf79	89693271	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.117000	0.15583	-0.023000	0.13963	-0.254000	0.11334	CGC	G|0.532;A|0.468	0.468	strong		0.592	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
SPRR1B	6699	hgsc.bcm.edu	37	1	153004983	153004983	+	Silent	SNP	C	C	T	rs12195	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:153004983C>T	ENST00000307098.4	+	2	227	c.162C>T	c.(160-162)ccC>ccT	p.P54P	SPRR1B_ENST00000392661.3_Intron	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	54	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCAAAGTGCCCGAGCCCTGCC	0.627													T|||	2492	0.497604	0.441	0.4265	5008	,	,		14910	0.5923		0.5179	False		,,,				2504	0.5061				p.P54P		Atlas-SNP	.											.	SPRR1B	18	.	1	Deletion - In frame(1)	ovary(1)	c.C162T						PASS	.	T		2076,2330	605.2+/-390.5	490,1096,617	113.0	114.0	113.0		162	0.6	1.0	1	dbSNP_52	113	4494,4102	561.2+/-387.7	1233,2028,1037	no	coding-synonymous	SPRR1B	NM_003125.2		1723,3124,1654	TT,TC,CC		47.7199,47.1176,49.4693		54/90	153004983	6570,6432	2203	4298	6501	SO:0001819	synonymous_variant	6699	exon2			AGTGCCCGAGCCC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.162C>T	1.37:g.153004983C>T		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	263	152	0.577947	NM_003125	B2R5H7|P22529|P22530|Q5T524	Silent	SNP	ENST00000307098.4	37	CCDS30863.1																																																																																			C|0.493;T|0.507	0.507	strong		0.627	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
ALPK2	115701	hgsc.bcm.edu	37	18	56196451	56196451	+	Silent	SNP	C	C	T	rs7236563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56196451C>T	ENST00000361673.3	-	6	5586	c.5373G>A	c.(5371-5373)aaG>aaA	p.K1791K		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1791	Ig-like 2.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CAGCTTGGATCTTTTTCAGTA	0.348													C|||	1868	0.373003	0.3169	0.415	5008	,	,		18894	0.2381		0.5815	False		,,,				2504	0.3436				p.K1791K		Atlas-SNP	.											ALPK2_ENST00000361673,colon,carcinoma,0,2	ALPK2	487	2	0			c.G5373A						PASS	.	C		1576,2830	488.3+/-361.2	281,1014,908	92.0	90.0	91.0		5373	2.7	1.0	18	dbSNP_116	91	4617,3983	597.5+/-393.8	1251,2115,934	no	coding-synonymous	ALPK2	NM_052947.3		1532,3129,1842	TT,TC,CC		46.314,35.7694,47.6165		1791/2171	56196451	6193,6813	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon6			TTGGATCTTTTTC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.5373G>A	18.37:g.56196451C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.554;T|0.446	0.446	strong		0.348	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
WTAP	9589	hgsc.bcm.edu	37	6	160169258	160169258	+	Silent	SNP	G	G	T	rs7766006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:160169258G>T	ENST00000358372.4	+	6	2066	c.309G>T	c.(307-309)ccG>ccT	p.P103P	WTAP_ENST00000337387.4_Silent_p.P103P|SOD2_ENST00000546087.1_Intron	NM_001270531.1|NM_004906.4	NP_001257460.1|NP_004897.2	Q15007	FL2D_HUMAN	Wilms tumor 1 associated protein	103					cell cycle (GO:0007049)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	MIS complex (GO:0036396)|nuclear membrane (GO:0031965)|nuclear speck (GO:0016607)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	18		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		TCCAGCAGCCGAGCGTTGCCC	0.423													G|||	1304	0.260383	0.1747	0.2161	5008	,	,		20479	0.4256		0.2097	False		,,,				2504	0.2894				p.P103P		Atlas-SNP	.											WTAP,NS,carcinoma,+2,1	WTAP	44	1	0			c.G309T						PASS	.	G	,,	843,3563	333.3+/-302.9	92,659,1452	63.0	63.0	63.0		309,309,309	2.3	1.0	6	dbSNP_116	63	1498,7102	284.0+/-296.4	138,1222,2940	no	coding-synonymous,coding-synonymous,coding-synonymous	WTAP	NM_004906.3,NM_152857.1,NM_152858.1	,,	230,1881,4392	TT,TG,GG		17.4186,19.133,17.9994	,,	103/397,103/152,103/152	160169258	2341,10665	2203	4300	6503	SO:0001819	synonymous_variant	9589	exon6			GCAGCCGAGCGTT	AJ276706	CCDS5266.1, CCDS5267.1, CCDS75542.1	6q25-q27	2008-02-05			ENSG00000146457	ENSG00000146457			16846	protein-coding gene	gene with protein product		605442				7788527, 11001926	Standard	NM_004906		Approved	KIAA0105, MGC3925	uc003qsl.4	Q15007	OTTHUMG00000015933	ENST00000358372.4:c.309G>T	6.37:g.160169258G>T		Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	339	144	0.424779	NM_001270533	Q5TCL8|Q5TCL9|Q96T28|Q9BYJ7|Q9H4E2	Silent	SNP	ENST00000358372.4	37	CCDS5266.1																																																																																			G|0.800;T|0.200	0.200	strong		0.423	WTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042905.1	NM_152857	
MUC4	4585	hgsc.bcm.edu	37	3	195507385	195507385	+	Missense_Mutation	SNP	G	G	A	rs199842409		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507385G>A	ENST00000463781.3	-	2	11525	c.11066C>T	c.(11065-11067)gCa>gTa	p.A3689V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3689V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3689V(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.572																																					p.A3689V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	stomach(1)	c.C11066T						scavenged	.						15.0	15.0	15.0					3																	195507385		598	1552	2150	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11066C>T	3.37:g.195507385G>A	ENSP00000417498:p.Ala3689Val	Somatic	19	1	0.0526316		WXS	Illumina HiSeq	Phase_I	119	75	0.630252	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	8.097	0.775840	0.16051	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27104	1.69;1.8	0.743	-0.753	0.11068	.	.	.	.	.	T	0.10165	0.0249	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.36335	-0.9752	7	.	.	.	.	4.7378	0.12997	0.3389:0.0:0.6611:0.0	.	3561	E7ESK3	.	V	3689	ENSP00000417498:A3689V;ENSP00000420243:A3689V	.	A	-	2	0	MUC4	196992164	0.004000	0.15560	0.010000	0.14722	0.010000	0.07245	0.039000	0.13884	-2.027000	0.00932	-2.047000	0.00414	GCA	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GAB4	128954	hgsc.bcm.edu	37	22	17469049	17469049	+	Nonsense_Mutation	SNP	C	C	A	rs28502153	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:17469049C>A	ENST00000400588.1	-	3	594	c.487G>T	c.(487-489)Gga>Tga	p.G163*	GAB4_ENST00000523144.1_Intron	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	163										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				GAAATGTTTCCCAGGAAGCCT	0.552													c|||	1771	0.353634	0.1982	0.4265	5008	,	,		19665	0.3938		0.3698	False		,,,				2504	0.454				p.G163X		Atlas-SNP	.											.	GAB4	95	.	0			c.G487T						PASS	.	-	stop/GLY	994,3258		126,742,1258	37.0	47.0	44.0		487	-0.5	0.1	22	dbSNP_125	44	3334,5200		694,1946,1627	yes	stop-gained	GAB4	NM_001037814.1		820,2688,2885	AA,AC,CC		39.0673,23.3772,33.8495		163/575	17469049	4328,8458	2126	4267	6393	SO:0001587	stop_gained	128954	exon3			TGTTTCCCAGGAA	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.487G>T	22.37:g.17469049C>A	ENSP00000383431:p.Gly163*	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001037814		Nonsense_Mutation	SNP	ENST00000400588.1	37	CCDS42976.1	734	0.3360805860805861	92	0.18699186991869918	140	0.3867403314917127	227	0.3968531468531469	275	0.3627968337730871	C	11.48	1.650227	0.29336	0.233772	0.390673	ENSG00000215568	ENST00000400588	.	.	.	1.9	-0.505	0.11993	.	238.900000	0.00166	U	0.000000	.	.	.	.	.	.	0.09310	P	0.9999999999999991	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	2.2739	0.04097	0.0:0.2171:0.3125:0.4705	rs28502153	.	.	.	X	163	.	ENSP00000383431:G163X	G	-	1	0	GAB4	15849049	1.000000	0.71417	0.141000	0.22245	0.007000	0.05969	1.798000	0.38814	-0.183000	0.10585	0.313000	0.20887	GGA	C|0.664;A|0.336	0.336	strong		0.552	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
SVOPL	136306	hgsc.bcm.edu	37	7	138312122	138312122	+	Missense_Mutation	SNP	A	A	C	rs2305816	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:138312122A>C	ENST00000419765.3	-	11	1187	c.1154T>G	c.(1153-1155)tTc>tGc	p.F385C	SVOPL_ENST00000288513.5_Missense_Mutation_p.F233C|SNORA40_ENST00000516379.1_RNA|SVOPL_ENST00000436657.1_Missense_Mutation_p.F233C|SVOPL_ENST00000463557.1_5'UTR|SVOPL_ENST00000421622.1_Missense_Mutation_p.F265C	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	385			F -> C (in dbSNP:rs2305816).			integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						GAGGAGAAGGAAGAATAAAGC	0.413													A|||	2386	0.476438	0.3533	0.5187	5008	,	,		21102	0.3452		0.7416	False		,,,				2504	0.4755				p.F385C		Atlas-SNP	.											.	SVOPL	111	.	0			c.T1154G						PASS	.	A	CYS/PHE,CYS/PHE	1775,2631	526.0+/-371.8	363,1049,791	112.0	101.0	105.0		1154,698	5.6	1.0	7	dbSNP_100	105	6365,2235	708.0+/-405.6	2356,1653,291	yes	missense,missense	SVOPL	NM_001139456.1,NM_174959.2	205,205	2719,2702,1082	CC,CA,AA		25.9884,40.286,37.4135	probably-damaging,probably-damaging	385/493,233/341	138312122	8140,4866	2203	4300	6503	SO:0001583	missense	136306	exon11			AGAAGGAAGAATA	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"""SV2 related protein homolog (rat)-like"""				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1154T>G	7.37:g.138312122A>C	ENSP00000405482:p.Phe385Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_001139456		Missense_Mutation	SNP	ENST00000419765.3	37	CCDS47721.1	1126	0.5155677655677655	193	0.39227642276422764	195	0.5386740331491713	176	0.3076923076923077	562	0.741424802110818	A	18.49	3.635035	0.67130	0.40286	0.740116	ENSG00000157703	ENST00000288513;ENST00000421622;ENST00000436657;ENST00000419765	T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86	5.61	5.61	0.85477	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.089556	0.85682	D	0.000000	T	0.00012	0.0000	L	0.58583	1.82	0.20821	P	0.999842922	D;D	0.89917	1.0;0.999	D;D	0.74348	0.983;0.912	T	0.50874	-0.8776	9	0.32370	T	0.25	-35.6448	15.8094	0.78547	1.0:0.0:0.0:0.0	rs2305816;rs10353447;rs52807130;rs61581409;rs2305816	385;233	Q8N434;Q8N434-2	SVOPL_HUMAN;.	C	233;265;233;385	ENSP00000288513:F233C;ENSP00000412830:F265C;ENSP00000417018:F233C;ENSP00000405482:F385C	ENSP00000288513:F233C	F	-	2	0	SVOPL	137962662	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	4.588000	0.60999	2.141000	0.66446	0.533000	0.62120	TTC	A|0.433;C|0.567	0.567	strong		0.413	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959	
PTPRT	11122	hgsc.bcm.edu	37	20	40743945	40743945	+	Missense_Mutation	SNP	A	A	G	rs41310016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:40743945A>G	ENST00000373187.1	-	22	2992	c.2993T>C	c.(2992-2994)gTg>gCg	p.V998A	PTPRT_ENST00000373201.1_Missense_Mutation_p.V988A|PTPRT_ENST00000373193.3_Missense_Mutation_p.V1001A|PTPRT_ENST00000373190.1_Missense_Mutation_p.V997A|PTPRT_ENST00000356100.2_Missense_Mutation_p.V1007A|PTPRT_ENST00000373184.1_Missense_Mutation_p.V1008A|PTPRT_ENST00000373198.4_Missense_Mutation_p.V1017A			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	998	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CCAGTATCGCACACATTTCAC	0.507													A|||	7	0.00139776	0.0	0.0	5008	,	,		21027	0.0		0.006	False		,,,				2504	0.001				p.V1017A		Atlas-SNP	.											.	PTPRT	372	.	0			c.T3050C						PASS	.	A	ALA/VAL,ALA/VAL	3,4193		0,3,2095	120.0	126.0	124.0		3050,2993	5.8	1.0	20	dbSNP_127	124	39,8425		0,39,4193	yes	missense,missense	PTPRT	NM_133170.3,NM_007050.5	64,64	0,42,6288	GG,GA,AA		0.4608,0.0715,0.3318	benign,benign	1017/1461,998/1442	40743945	42,12618	2098	4232	6330	SO:0001583	missense	11122	exon23			TATCGCACACATT	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2993T>C	20.37:g.40743945A>G	ENSP00000362283:p.Val998Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	14.50	2.553285	0.45487	7.15E-4	0.004608	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	D;D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.85	5.85	0.93711	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.66277	0.2773	N	0.04636	-0.2	0.58432	D	0.999998	P;B	0.39782	0.688;0.349	P;P	0.50378	0.639;0.516	T	0.71699	-0.4514	10	0.23302	T	0.38	.	16.2303	0.82332	1.0:0.0:0.0:0.0	rs41310016	1020;998	O14522-1;O14522	.;PTPRT_HUMAN	A	997;998;1001;1007;1020;1008;988	ENSP00000362286:V997A;ENSP00000362283:V998A;ENSP00000362289:V1001A;ENSP00000348408:V1007A;ENSP00000362294:V1020A;ENSP00000362280:V1008A;ENSP00000362297:V988A	ENSP00000348408:V1007A	V	-	2	0	PTPRT	40177359	1.000000	0.71417	0.994000	0.49952	0.972000	0.66771	4.153000	0.58118	2.233000	0.73108	0.533000	0.62120	GTG	A|0.997;G|0.003	0.003	strong		0.507	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
OTX1	5013	hgsc.bcm.edu	37	2	63283178	63283178	+	Silent	SNP	C	C	G	rs17850223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:63283178C>G	ENST00000282549.2	+	5	1068	c.792C>G	c.(790-792)ctC>ctG	p.L264L	OTX1_ENST00000366671.3_Silent_p.L264L	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	264					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.L264L(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					CGCACCAGCTCAGCCCCATGG	0.642													C|||	621	0.124002	0.0257	0.2161	5008	,	,		17931	0.1806		0.1362	False		,,,				2504	0.1207				p.L264L		Atlas-SNP	.											OTX1,NS,carcinoma,0,1	OTX1	49	1	1	Substitution - coding silent(1)	stomach(1)	c.C792G						PASS	.	C	,	194,4212	122.9+/-160.3	9,176,2018	136.0	121.0	126.0		792,792	0.4	1.0	2	dbSNP_123	126	1138,7462	233.9+/-267.0	73,992,3235	no	coding-synonymous,coding-synonymous	OTX1	NM_001199770.1,NM_014562.3	,	82,1168,5253	GG,GC,CC		13.2326,4.4031,10.2414	,	264/355,264/355	63283178	1332,11674	2203	4300	6503	SO:0001819	synonymous_variant	5013	exon5			CCAGCTCAGCCCC		CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"""Homeoboxes / PRD class"""	8521	protein-coding gene	gene with protein product		600036	"""orthodenticle (Drosophila) homolog 1"", ""orthodenticle homolog 1 (Drosophila)"""			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.792C>G	2.37:g.63283178C>G		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	276	121	0.438406	NM_014562	A6NHA2|B3KTJ4|Q53TG6	Silent	SNP	ENST00000282549.2	37	CCDS1873.1																																																																																			C|0.884;G|0.116	0.116	strong		0.642	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1		
APOA5	116519	hgsc.bcm.edu	37	11	116662407	116662407	+	Missense_Mutation	SNP	G	G	C	rs3135506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:116662407G>C	ENST00000227665.4	-	2	90	c.56C>G	c.(55-57)tCg>tGg	p.S19W	APOA5_ENST00000542499.1_Missense_Mutation_p.S19W			Q6Q788	APOA5_HUMAN	apolipoprotein A-V	19			S -> W (in allele APOA5*3; associated with high plasma triglyceride levels; dbSNP:rs3135506). {ECO:0000269|PubMed:12417524, ECO:0000269|PubMed:12920097, ECO:0000269|PubMed:15108119}.		acylglycerol homeostasis (GO:0055090)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|organ regeneration (GO:0031100)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)	chylomicron (GO:0042627)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|lipase activator activity (GO:0060229)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|lipoprotein particle receptor binding (GO:0070325)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylcholine binding (GO:0031210)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	14	all_hematologic(175;0.0487)	all_cancers(61;3.31e-09)|all_epithelial(67;8.03e-06)|Breast(348;0.0126)|Melanoma(852;0.0153)|Acute lymphoblastic leukemia(157;0.0257)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0433)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;4.93e-06)|all cancers(92;0.000123)|OV - Ovarian serous cystadenocarcinoma(223;0.149)		CTGGGTGGCCGAAAACGCTGT	0.637											OREG0021366	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	279	0.0557109	0.0673	0.1167	5008	,	,		19485	0.0		0.0676	False		,,,				2504	0.0419				p.S19W		Atlas-SNP	.											APOA5,colon,carcinoma,0,1	APOA5	34	1	0			c.C56G	GRCh37	CM023881	APOA5	M	rs3135506	PASS	.	G	TRP/SER,TRP/SER	269,4133	143.1+/-178.2	9,251,1941	65.0	57.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	56,56	5.4	0.0	11	dbSNP_103	60	558,8034	143.7+/-199.7	19,520,3757	yes	missense,missense	APOA5	NM_001166598.1,NM_052968.4	177,177	28,771,5698	CC,CG,GG		6.4944,6.1109,6.3645	probably-damaging,probably-damaging	19/367,19/367	116662407	827,12167	2201	4296	6497	SO:0001583	missense	116519	exon3			GTGGCCGAAAACG	AF202889	CCDS8376.2	11q23	2013-01-24			ENSG00000110243	ENSG00000110243		"""Apolipoproteins"""	17288	protein-coding gene	gene with protein product		606368				11588264, 11577099	Standard	NM_001166598		Approved	RAP3, APOA-V	uc009yzf.3	Q6Q788	OTTHUMG00000046116	ENST00000227665.4:c.56C>G	11.37:g.116662407G>C	ENSP00000227665:p.Ser19Trp	Somatic	143	0	0	1475	WXS	Illumina HiSeq	Phase_I	164	87	0.530488	NM_001166598	B0YIV9|Q3MIK6|Q6UWK9|Q9UBJ3	Missense_Mutation	SNP	ENST00000227665.4	37	CCDS8376.2	100	0.045787545787545784	24	0.04878048780487805	33	0.09116022099447514	0	0.0	43	0.05672823218997362	G	20.5	4.006633	0.74932	0.061109	0.064944	ENSG00000110243	ENST00000227665;ENST00000542499;ENST00000433069	T;T;T	0.74737	-0.46;-0.46;-0.87	5.41	5.41	0.78517	.	0.910838	0.09256	N	0.827241	T	0.19846	0.0477	M	0.67953	2.075	0.09310	N	1	D	0.63880	0.993	P	0.57548	0.823	T	0.53753	-0.8394	10	0.87932	D	0	0.0	14.5768	0.68255	0.0:0.0:1.0:0.0	rs3135506;rs28939090	19	Q6Q788	APOA5_HUMAN	W	19	ENSP00000227665:S19W;ENSP00000445002:S19W;ENSP00000399701:S19W	ENSP00000227665:S19W	S	-	2	0	APOA5	116167617	0.412000	0.25392	0.008000	0.14137	0.215000	0.24574	2.796000	0.47869	2.826000	0.97356	0.561000	0.74099	TCG	G|0.891;C|0.109	0.109	strong		0.637	APOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106285.2		
ANKRD12	23253	hgsc.bcm.edu	37	18	9221883	9221883	+	Missense_Mutation	SNP	C	C	G	rs2298548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:9221883C>G	ENST00000262126.4	+	8	1069	c.829C>G	c.(829-831)Cca>Gca	p.P277A	ANKRD12_ENST00000400020.3_Missense_Mutation_p.P254A|ANKRD12_ENST00000383440.2_Missense_Mutation_p.P254A|ANKRD12_ENST00000540578.2_3'UTR	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	277			P -> A (in dbSNP:rs2298548).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CGGTGGAAATCCATTTCAAGC	0.423													C|||	232	0.0463259	0.0408	0.0461	5008	,	,		19648	0.0446		0.0706	False		,,,				2504	0.0307				p.P277A		Atlas-SNP	.											.	ANKRD12	167	.	0			c.C829G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	218,4188	132.1+/-168.6	9,200,1994	160.0	136.0	144.0		760,760,829	4.9	1.0	18	dbSNP_100	144	653,7947	165.9+/-218.0	27,599,3674	yes	missense,missense,missense	ANKRD12	NM_001083625.2,NM_001204056.1,NM_015208.4	27,27,27	36,799,5668	GG,GC,CC		7.593,4.9478,6.6969	benign,benign,benign	254/2040,254/2040,277/2063	9221883	871,12135	2203	4300	6503	SO:0001583	missense	23253	exon8			GGAAATCCATTTC	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.829C>G	18.37:g.9221883C>G	ENSP00000262126:p.Pro277Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	104	62	0.596154	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	116	0.05311355311355311	16	0.032520325203252036	16	0.04419889502762431	27	0.0472027972027972	57	0.07519788918205805	C	12.30	1.896174	0.33442	0.049478	0.07593	ENSG00000101745	ENST00000383440;ENST00000546007;ENST00000262126;ENST00000540578	T;T	0.67698	-0.28;-0.28	5.79	4.9	0.64082	Ankyrin repeat-containing domain (3);	0.178700	0.48286	D	0.000183	T	0.07728	0.0194	L	0.48174	1.505	0.26639	P	0.9723126	B;B;B	0.17038	0.0;0.016;0.02	B;B;B	0.20184	0.002;0.016;0.028	T	0.44967	-0.9293	9	0.36615	T	0.2	-14.7786	16.5229	0.84322	0.0:0.7828:0.2172:0.0	rs2298548;rs57447041;rs2298548	277;254;277	Q6PG48;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	A	254;254;277;277	ENSP00000372932:P254A;ENSP00000262126:P277A	ENSP00000262126:P277A	P	+	1	0	ANKRD12	9211883	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.472000	0.60189	2.740000	0.93945	0.561000	0.74099	CCA	C|0.936;G|0.064	0.064	strong		0.423	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
DOK1	1796	hgsc.bcm.edu	37	2	74783100	74783100	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74783100G>A	ENST00000233668.5	+	4	1203	c.534G>A	c.(532-534)gtG>gtA	p.V178V	DOK1_ENST00000480318.1_3'UTR|DOK1_ENST00000340004.6_Intron|LOXL3_ENST00000264094.3_5'Flank|LOXL3_ENST00000409986.1_5'Flank|LOXL3_ENST00000393937.2_5'Flank|M1AP_ENST00000464686.1_5'Flank|DOK1_ENST00000409429.1_Silent_p.V39V|LOXL3_ENST00000409549.1_5'Flank	NM_001381.3	NP_001372.1	Q99704	DOK1_HUMAN	docking protein 1, 62kDa (downstream of tyrosine kinase 1)	178	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cell surface receptor signaling pathway (GO:0007166)|insulin receptor signaling pathway (GO:0008286)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor signaling protein activity (GO:0005057)			endometrium(3)|large_intestine(2)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						TGCTGAGGGTGGAGGCTGAAA	0.617																																					p.V178V	Esophageal Squamous(36;520 860 12502 33616 51270)	Atlas-SNP	.											.	DOK1	39	.	0			c.G534A						PASS	.						55.0	57.0	56.0					2																	74783100		2203	4300	6503	SO:0001819	synonymous_variant	1796	exon4			GAGGGTGGAGGCT	U70987	CCDS1954.1, CCDS56125.1	2p13	2008-05-21	2002-08-29		ENSG00000115325	ENSG00000115325			2990	protein-coding gene	gene with protein product		602919	"""docking protein 1, 62kD (downstream of tyrosine kinase 1)"""			9008160, 9790776, 15546884	Standard	NM_001381		Approved	p62dok	uc002sms.3	Q99704	OTTHUMG00000129956	ENST00000233668.5:c.534G>A	2.37:g.74783100G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	127	22	0.173228	NM_001381	O43204|Q53TY2|Q9UHG6	Silent	SNP	ENST00000233668.5	37	CCDS1954.1																																																																																			.	.	none		0.617	DOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252218.3	NM_001381	
MAP4	4134	hgsc.bcm.edu	37	3	47957996	47957996	+	Missense_Mutation	SNP	C	C	G	rs2230169	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:47957996C>G	ENST00000360240.6	-	7	1839	c.1321G>C	c.(1321-1323)Gaa>Caa	p.E441Q	MAP4_ENST00000383737.4_Intron|MAP4_ENST00000426837.2_Missense_Mutation_p.E458Q|MAP4_ENST00000395734.3_Missense_Mutation_p.E441Q	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	441	17 X 14 AA tandem repeats.		E -> Q (in dbSNP:rs2230169).		cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	ACCTCTGTTTCTGAGGACAAA	0.488													C|||	134	0.0267572	0.0008	0.0303	5008	,	,		22176	0.0		0.0676	False		,,,				2504	0.045				p.E441Q		Atlas-SNP	.											.	MAP4	176	.	0			c.G1321C						PASS	.	C	GLN/GLU,GLN/GLU	64,4342	59.9+/-96.7	0,64,2139	94.0	84.0	88.0		1321,1321	3.3	0.9	3	dbSNP_98	88	625,7975	161.0+/-214.0	20,585,3695	yes	missense,missense	MAP4	NM_001134364.1,NM_002375.4	29,29	20,649,5834	GG,GC,CC		7.2674,1.4526,5.2976	possibly-damaging,possibly-damaging	441/1136,441/1153	47957996	689,12317	2203	4300	6503	SO:0001583	missense	4134	exon7			CTGTTTCTGAGGA		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1321G>C	3.37:g.47957996C>G	ENSP00000353375:p.Glu441Gln	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	187	82	0.438503	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	69	0.03159340659340659	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	56	0.07387862796833773	C	16.75	3.210243	0.58343	0.014526	0.072674	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.09350	3.09;2.99;3.07	4.24	3.33	0.38152	.	.	.	.	.	T	0.02342	0.0072	M	0.79693	2.465	0.80722	D	1	D;D;D	0.71674	0.998;0.994;0.991	P;P;P	0.62089	0.898;0.869;0.732	T	0.00143	-1.1995	9	0.66056	D	0.02	-5.0369	11.8808	0.52574	0.0:0.822:0.178:0.0	rs2230169;rs17382387;rs2230169	418;441;441	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	Q	441;458;441	ENSP00000379083:E441Q;ENSP00000407602:E458Q;ENSP00000353375:E441Q	ENSP00000353375:E441Q	E	-	1	0	MAP4	47933000	0.046000	0.20272	0.949000	0.38748	0.254000	0.26022	2.207000	0.42788	1.082000	0.41137	0.561000	0.74099	GAA	C|0.951;G|0.049	0.049	strong		0.488	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375	
PRODH2	58510	hgsc.bcm.edu	37	19	36303664	36303664	+	Missense_Mutation	SNP	G	G	C	rs3848666	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36303664G>C	ENST00000301175.3	-	2	289	c.272C>G	c.(271-273)cCc>cGc	p.P91R		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	91			P -> R (in dbSNP:rs3848666).		proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCCCCTGGAGGGGGGACCAGC	0.637													g|||	272	0.0543131	0.0061	0.0965	5008	,	,		18695	0.0		0.1561	False		,,,				2504	0.0409				p.P91R		Atlas-SNP	.											.	PRODH2	68	.	0			c.C272G						PASS	.	A	ARG/PRO	147,4259	99.4+/-138.0	3,141,2059	42.0	42.0	42.0		272	0.6	0.0	19	dbSNP_108	42	1425,7175	267.9+/-287.5	126,1173,3001	yes	missense	PRODH2	NM_021232.1	103	129,1314,5060	CC,CG,GG		16.5698,3.3364,12.0867	benign	91/537	36303664	1572,11434	2203	4300	6503	SO:0001583	missense	58510	exon2			CTGGAGGGGGGAC	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.272C>G	19.37:g.36303664G>C	ENSP00000301175:p.Pro91Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	156	154	0.987179	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	166	0.076007326007326	5	0.01016260162601626	45	0.12430939226519337	0	0.0	116	0.15303430079155672	g	6.252	0.414685	0.11870	0.033364	0.165698	ENSG00000250799	ENST00000301175	T	0.23754	1.89	5.19	0.647	0.17796	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.58432	P	1.999999999946489E-6	B	0.11235	0.004	B	0.06405	0.002	T	0.31110	-0.9955	8	0.35671	T	0.21	.	6.956	0.24572	0.2961:0.1194:0.5845:0.0	rs3848666;rs52793092;rs3848666	91	Q9UF12	PROD2_HUMAN	R	91	ENSP00000301175:P91R	ENSP00000301175:P91R	P	-	2	0	PRODH2	40995504	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	0.765000	0.26546	0.103000	0.17682	-2.308000	0.00257	CCC	G|0.901;C|0.099	0.099	strong		0.637	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
USH2A	7399	hgsc.bcm.edu	37	1	215916563	215916563	+	Missense_Mutation	SNP	G	G	A	rs11120616	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:215916563G>A	ENST00000307340.3	-	59	11890	c.11504C>T	c.(11503-11505)aCt>aTt	p.T3835I	USH2A_ENST00000366943.2_Missense_Mutation_p.T3835I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3835	Fibronectin type-III 23. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> I (in dbSNP:rs11120616). {ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.T3835I(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGTGAATGGAGTCAAATTTTC	0.393										HNSCC(13;0.011)			G|||	724	0.144569	0.149	0.1931	5008	,	,		9956	0.0843		0.2346	False		,,,				2504	0.0736				p.T3835I		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	1	1	Substitution - Missense(1)	stomach(1)	c.C11504T						PASS	.	G	ILE/THR	628,3778	269.8+/-269.2	42,544,1617	139.0	133.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11504	4.9	1.0	1	dbSNP_120	135	2005,6595	351.9+/-328.4	237,1531,2532	yes	missense	USH2A	NM_206933.2	89	279,2075,4149	AA,AG,GG		23.314,14.2533,20.2445	benign	3835/5203	215916563	2633,10373	2203	4300	6503	SO:0001583	missense	7399	exon59			AATGGAGTCAAAT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.11504C>T	1.37:g.215916563G>A	ENSP00000305941:p.Thr3835Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	392	0.1794871794871795	83	0.16869918699186992	80	0.22099447513812154	57	0.09965034965034965	172	0.22691292875989447	G	12.76	2.036066	0.35893	0.142533	0.23314	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.58210	0.35;0.35	4.94	4.94	0.65067	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.047120	0.07615	N	0.926035	T	0.00039	0.0001	L	0.34521	1.04	0.50039	P	1.5399999999998748E-4	B	0.21381	0.055	B	0.24701	0.055	T	0.02244	-1.1189	9	0.35671	T	0.21	.	11.5737	0.50850	0.0:0.0:0.7026:0.2974	rs11120616;rs52823661;rs61208500;rs11120616	3835	O75445	USH2A_HUMAN	I	3835	ENSP00000305941:T3835I;ENSP00000355910:T3835I	ENSP00000305941:T3835I	T	-	2	0	USH2A	213983186	0.919000	0.31177	0.996000	0.52242	0.781000	0.44180	1.348000	0.33987	2.706000	0.92434	0.655000	0.94253	ACT	G|0.807;A|0.193	0.193	strong		0.393	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
RIPK4	54101	hgsc.bcm.edu	37	21	43162150	43162150	+	Silent	SNP	G	G	A	rs3746894	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43162150G>A	ENST00000352483.2	-	9	1411	c.1347C>T	c.(1345-1347)ggC>ggT	p.G449G	RIPK4_ENST00000542057.1_Silent_p.G338G|RIPK4_ENST00000332512.3_Silent_p.G401G|RIPK4_ENST00000544709.1_Silent_p.G338G|AP001615.9_ENST00000423276.1_RNA			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	449					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CGTCTGTGGTGCCCAGATCTG	0.617													G|||	2204	0.440096	0.2806	0.4654	5008	,	,		19302	0.5714		0.4811	False		,,,				2504	0.4601				p.G401G		Atlas-SNP	.											.	RIPK4	151	.	0			c.C1203T						PASS	.	G		1394,3008		215,964,1022	107.0	111.0	109.0		1203	2.1	0.4	21	dbSNP_107	109	3745,4847		852,2041,1403	yes	coding-synonymous	RIPK4	NM_020639.2		1067,3005,2425	AA,AG,GG		43.5871,31.6674,39.549		401/785	43162150	5139,7855	2201	4296	6497	SO:0001819	synonymous_variant	54101	exon8			TGTGGTGCCCAGA	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1347C>T	21.37:g.43162150G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				G|0.579;A|0.421	0.421	strong		0.617	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
UGGT1	56886	hgsc.bcm.edu	37	2	128870808	128870808	+	Silent	SNP	T	T	C	rs4662775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:128870808T>C	ENST00000259253.6	+	6	719	c.672T>C	c.(670-672)aaT>aaC	p.N224N	UGGT1_ENST00000375990.3_Silent_p.N200N	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	224					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GCAAAATCAATTATGTATTCA	0.333													T|||	4123	0.823283	0.6543	0.9035	5008	,	,		15404	0.8512		0.9801	False		,,,				2504	0.8047				p.N224N		Atlas-SNP	.											.	UGGT1	126	.	0			c.T672C						PASS	.	T		3196,1210	702.3+/-406.9	1174,848,181	59.0	61.0	60.0		672	3.2	1.0	2	dbSNP_111	60	8374,226	807.5+/-407.2	4078,218,4	no	coding-synonymous	UGGT1	NM_020120.3		5252,1066,185	CC,CT,TT		2.6279,27.4626,11.0411		224/1556	128870808	11570,1436	2203	4300	6503	SO:0001819	synonymous_variant	56886	exon6			AATCAATTATGTA	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.672T>C	2.37:g.128870808T>C		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	297	297	1	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			T|0.137;C|0.863	0.863	strong		0.333	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
ACAN	176	hgsc.bcm.edu	37	15	89415247	89415247	+	Missense_Mutation	SNP	C	C	G	rs3817428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89415247C>G	ENST00000561243.1	+	14	7119	c.7119C>G	c.(7117-7119)gaC>gaG	p.D2373E	ACAN_ENST00000439576.2_Missense_Mutation_p.D2373E|ACAN_ENST00000559004.1_Missense_Mutation_p.D2335E|ACAN_ENST00000352105.7_Missense_Mutation_p.D2335E			P16112	PGCA_HUMAN	aggrecan	2258	G3.|Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.D2259E(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			ATGCCCAAGACTACCAGTGGA	0.592													C|||	572	0.114217	0.0477	0.1268	5008	,	,		22065	0.123		0.2445	False		,,,				2504	0.0521				p.D2373E		Atlas-SNP	.											ACAN,NS,carcinoma,0,1	ACAN	220	1	1	Substitution - Missense(1)	stomach(1)	c.C7119G						PASS	.	C	GLU/ASP,GLU/ASP	307,4045	151.4+/-185.3	15,277,1884	110.0	114.0	112.0		7119,7005	3.9	1.0	15	dbSNP_107	112	2308,6282	380.0+/-339.5	298,1712,2285	yes	missense,missense	ACAN	NM_013227.3,NM_001135.3	45,45	313,1989,4169	GG,GC,CC		26.8685,7.0542,20.2055	benign,benign	2373/2531,2335/2432	89415247	2615,10327	2176	4295	6471	SO:0001583	missense	176	exon15			CCAAGACTACCAG	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.7119C>G	15.37:g.89415247C>G	ENSP00000453342:p.Asp2373Glu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_013227	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	342	0.1565934065934066	25	0.0508130081300813	57	0.1574585635359116	63	0.11013986013986014	197	0.2598944591029024	C	13.69	2.311104	0.40895	0.070542	0.268685	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.18338	2.22;2.22	5.76	3.89	0.44902	.	0.000000	0.34386	N	0.004011	T	0.00012	0.0000	N	0.04705	-0.18	0.38965	P	0.04137299999999999	P;B	0.35493	0.505;0.286	B;B	0.35607	0.161;0.206	T	0.50389	-0.8834	9	0.23891	T	0.37	-28.3785	11.615	0.51083	0.0:0.8564:0.0:0.1436	rs3817428;rs17201667;rs52795578;rs3817428	2335;2373	E7ENV9;E7EX88	.;.	E	2373;2335;2259	ENSP00000387356:D2373E;ENSP00000341615:D2335E	ENSP00000268134:D2259E	D	+	3	2	ACAN	87216251	0.991000	0.36638	1.000000	0.80357	0.979000	0.70002	0.384000	0.20668	0.796000	0.33947	-0.192000	0.12808	GAC	C|0.854;G|0.146	0.146	strong		0.592	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
FAAH2	158584	hgsc.bcm.edu	37	X	57475132	57475132	+	Silent	SNP	T	T	C	rs1367830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:57475132T>C	ENST00000374900.4	+	10	1524	c.1404T>C	c.(1402-1404)ccT>ccC	p.P468P	FAAH2_ENST00000491179.1_3'UTR	NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	468						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						TAACACGGCCTTTCAACTTTG	0.398										HNSCC(52;0.14)			T|||	1777	0.470728	0.0295	0.402	3775	,	,		9355	0.4663		0.5457	False		,,,				2504	0.4499				p.P468P		Atlas-SNP	.											.	FAAH2	66	.	0			c.T1404C						PASS	.	T		451,3384		30,328,63,1274,508	202.0	146.0	165.0		1404	1.3	1.0	X	dbSNP_88	165	4917,1811		1311,944,1351,173,521	no	coding-synonymous	FAAH2	NM_174912.3		1341,1272,1414,1447,1029	CC,CT,C,TT,T		26.9174,11.7601,49.1811		468/533	57475132	5368,5195	2203	4300	6503	SO:0001819	synonymous_variant	158584	exon10			ACGGCCTTTCAAC	AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"""amidase domain containing"""	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.1404T>C	X.37:g.57475132T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_174912	Q86VT2|Q96N98	Silent	SNP	ENST00000374900.4	37	CCDS14375.1																																																																																			T|0.496;0|0.015	.	strong		0.398	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912	
ZNF701	55762	hgsc.bcm.edu	37	19	53086598	53086598	+	Missense_Mutation	SNP	G	G	A	rs3745102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53086598G>A	ENST00000540331.1	+	5	1709	c.1484G>A	c.(1483-1485)cGt>cAt	p.R495H	ZNF701_ENST00000391785.3_Missense_Mutation_p.R429H|ZNF701_ENST00000301093.2_Missense_Mutation_p.R495H|CTD-3099C6.7_ENST00000599222.1_RNA	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	495			R -> H (in dbSNP:rs67702454). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		GCATGTCATCGTAGACTTCAT	0.363													g|||	1417	0.282947	0.0522	0.2839	5008	,	,		22708	0.3373		0.3598	False		,,,				2504	0.4591				p.R495H	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											.	ZNF701	44	.	0			c.G1484A						PASS	.						50.0	41.0	44.0					19																	53086598		2203	4291	6494	SO:0001583	missense	55762	exon5			GTCATCGTAGACT	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"""Zinc fingers, C2H2-type"", ""-"""	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.1484G>A	19.37:g.53086598G>A	ENSP00000444339:p.Arg495His	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	239	125	0.523013	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Missense_Mutation	SNP	ENST00000540331.1	37	CCDS54311.1	581	0.266025641025641	27	0.054878048780487805	106	0.292817679558011	182	0.3181818181818182	266	0.35092348284960423	N	4.277	0.050616	0.08243	.	.	ENSG00000167562	ENST00000391785;ENST00000301093;ENST00000540331	T;T;T	0.18502	2.21;2.21;2.21	1.98	-2.21	0.06973	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.42487	1.325	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.47275	-0.9130	8	0.24483	T	0.36	.	7.8679	0.29547	0.4668:0.0:0.5332:0.0	rs3745102	495;429	F5GZM6;Q9NV72	.;ZN701_HUMAN	H	429;495;495	ENSP00000375662:R429H;ENSP00000301093:R495H;ENSP00000444339:R495H	ENSP00000301093:R495H	R	+	2	0	ZNF701	57778410	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.539000	0.02202	-0.969000	0.03573	-0.598000	0.04106	CGT	G|0.686;A|0.314	0.314	strong		0.363	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
RBBP8	5932	hgsc.bcm.edu	37	18	20577669	20577669	+	Silent	SNP	G	G	A	rs17852769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:20577669G>A	ENST00000399722.2	+	14	2466	c.2115G>A	c.(2113-2115)aaG>aaA	p.K705K	RBBP8_ENST00000399725.2_Silent_p.K705K|RBBP8_ENST00000360790.5_Silent_p.K705K|RBBP8_ENST00000327155.5_Silent_p.K705K	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	705					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			AAATGAAGAAGCAAGAGCAGA	0.343								Homologous recombination					G|||	845	0.16873	0.3752	0.0778	5008	,	,		16068	0.003		0.1382	False		,,,				2504	0.1564				p.K705K		Atlas-SNP	.											.	RBBP8	138	.	0			c.G2115A						PASS	.	G	,,	1490,2916	458.0+/-351.8	241,1008,954	74.0	75.0	75.0		2115,2115,2115	-0.4	1.0	18	dbSNP_123	75	1037,7563	209.4+/-250.6	54,929,3317	no	coding-synonymous,coding-synonymous,coding-synonymous	RBBP8	NM_002894.2,NM_203291.1,NM_203292.1	,,	295,1937,4271	AA,AG,GG		12.0581,33.8175,19.4295	,,	705/898,705/898,705/868	20577669	2527,10479	2203	4300	6503	SO:0001819	synonymous_variant	5932	exon14			GAAGAAGCAAGAG	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"""CTBP-interacting protein"""	604124	"""retinoblastoma-binding protein 8"", ""Seckel syndrome 2"""	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.2115G>A	18.37:g.20577669G>A		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	228	76	0.333333	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Silent	SNP	ENST00000399722.2	37	CCDS11875.1																																																																																			G|0.821;A|0.179	0.179	strong		0.343	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291	
RBPJL	11317	hgsc.bcm.edu	37	20	43944958	43944958	+	Silent	SNP	G	G	T	rs2741500	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43944958G>T	ENST00000343694.3	+	10	1224	c.1152G>T	c.(1150-1152)ccG>ccT	p.P384P	RBPJL_ENST00000372741.3_Silent_p.P384P|RBPJL_ENST00000372743.1_Silent_p.P384P|RBPJL_ENST00000464504.1_3'UTR	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	384					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CGGTCACTCCGGTGCCTCTCA	0.637													G|||	557	0.111222	0.0961	0.1297	5008	,	,		17481	0.0169		0.1988	False		,,,				2504	0.1258				p.P384P		Atlas-SNP	.											.	RBPJL	67	.	0			c.G1152T						PASS	.	G		489,3917	227.2+/-242.5	25,439,1739	48.0	45.0	46.0		1152	-9.4	0.0	20	dbSNP_100	46	1843,6757	329.6+/-318.8	192,1459,2649	no	coding-synonymous	RBPJL	NM_014276.2		217,1898,4388	TT,TG,GG		21.4302,11.0985,17.9302		384/518	43944958	2332,10674	2203	4300	6503	SO:0001819	synonymous_variant	11317	exon10			CACTCCGGTGCCT	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1152G>T	20.37:g.43944958G>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Silent	SNP	ENST00000343694.3	37	CCDS13349.1																																																																																			G|0.853;T|0.147	0.147	strong		0.637	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
CRKL	1399	hgsc.bcm.edu	37	22	21272249	21272249	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21272249G>A	ENST00000354336.3	+	1	536	c.27G>A	c.(25-27)tcG>tcA	p.S9S		NM_005207.3	NP_005198.1	P46109	CRKL_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog-like	9					activation of MAPKK activity (GO:0000186)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|heart development (GO:0007507)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|parathyroid gland development (GO:0060017)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|thymus development (GO:0048538)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	poly(A) RNA binding (GO:0044822)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)	14	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			TCGACTCCTCGGACCGCTCCG	0.692																																					p.S9S	Pancreas(85;3 1441 23889 42519 42763)	Atlas-SNP	.											.	CRKL	28	.	0			c.G27A						PASS	.						27.0	27.0	27.0					22																	21272249		2202	4299	6501	SO:0001819	synonymous_variant	1399	exon1			CTCCTCGGACCGC		CCDS13785.1	22q11.21	2013-07-09	2013-07-09		ENSG00000099942	ENSG00000099942		"""SH2 domain containing"""	2363	protein-coding gene	gene with protein product		602007				8361759, 8798523	Standard	NM_005207		Approved		uc002ztf.2	P46109	OTTHUMG00000150807	ENST00000354336.3:c.27G>A	22.37:g.21272249G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_005207	A8KA44|D3DX35	Silent	SNP	ENST00000354336.3	37	CCDS13785.1																																																																																			.	.	none		0.692	CRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320158.1	NM_005207	
MED9	55090	hgsc.bcm.edu	37	17	17394611	17394611	+	Silent	SNP	G	G	A	rs1242489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17394611G>A	ENST00000268711.3	+	2	299	c.243G>A	c.(241-243)ccG>ccA	p.P81P		NM_018019.2	NP_060489.1	Q9NWA0	MED9_HUMAN	mediator complex subunit 9	81						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						AGGACAGCCCGGAGGTCCACC	0.597													G|||	801	0.159944	0.025	0.2925	5008	,	,		19957	0.1409		0.3211	False		,,,				2504	0.1022				p.P81P		Atlas-SNP	.											.	MED9	11	.	0			c.G243A						PASS	.	G		320,4086	169.8+/-200.3	10,300,1893	91.0	74.0	80.0		243	-9.5	0.0	17	dbSNP_87	80	2619,5981	424.1+/-354.6	400,1819,2081	no	coding-synonymous	MED9	NM_018019.2		410,2119,3974	AA,AG,GG		30.4535,7.2628,22.5973		81/147	17394611	2939,10067	2203	4300	6503	SO:0001819	synonymous_variant	55090	exon2			CAGCCCGGAGGTC	BC000647	CCDS11184.1	17p11.2	2007-07-30	2007-07-30		ENSG00000141026	ENSG00000141026			25487	protein-coding gene	gene with protein product		609878	"""mediator of RNA polymerase II transcription, subunit 9 homolog (S. cerevisiae)"""			11997338	Standard	NM_018019		Approved	FLJ10193, MED25	uc002grh.1	Q9NWA0	OTTHUMG00000059293	ENST00000268711.3:c.243G>A	17.37:g.17394611G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	64	23	0.359375	NM_018019		Silent	SNP	ENST00000268711.3	37	CCDS11184.1																																																																																			G|0.779;A|0.221	0.221	strong		0.597	MED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131669.2	NM_018019	
SIX6	4990	hgsc.bcm.edu	37	14	60976537	60976537	+	Missense_Mutation	SNP	C	C	A	rs33912345	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:60976537C>A	ENST00000327720.5	+	1	869	c.421C>A	c.(421-423)Cac>Aac	p.H141N		NM_007374.2	NP_031400.2	O95475	SIX6_HUMAN	SIX homeobox 6	141			H -> N (in dbSNP:rs33912345). {ECO:0000269|PubMed:10381575, ECO:0000269|PubMed:10512683, ECO:0000269|PubMed:15266624, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		organ morphogenesis (GO:0009887)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.088)		GCGCACGCGGCACCTGCTACG	0.602													C|||	1710	0.341454	0.0318	0.6599	5008	,	,		18691	0.2133		0.5974	False		,,,				2504	0.4029				p.H141N		Atlas-SNP	.											.	SIX6	27	.	0			c.C421A						PASS	.	C	ASN/HIS	514,3892	227.8+/-242.9	36,442,1725	58.0	53.0	54.0		421	5.4	1.0	14	dbSNP_126	54	5151,3447	615.2+/-396.3	1547,2057,695	yes	missense	SIX6	NM_007374.2	68	1583,2499,2420	AA,AC,CC		40.0907,11.6659,43.5635	benign	141/247	60976537	5665,7339	2203	4299	6502	SO:0001583	missense	4990	exon1			ACGCGGCACCTGC	AF141651	CCDS9747.1	14q23.1	2011-06-20	2007-07-13		ENSG00000184302	ENSG00000184302		"""Homeoboxes / SINE class"""	10892	protein-coding gene	gene with protein product		606326	"""sine oculis homeobox (Drosophila) homolog 6"", ""sine oculis homeobox homolog 6 (Drosophila)"""	OPTX2		10512683	Standard	NM_007374		Approved	Six9	uc001xfa.4	O95475	OTTHUMG00000152339	ENST00000327720.5:c.421C>A	14.37:g.60976537C>A	ENSP00000328596:p.His141Asn	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	86	48	0.55814	NM_007374	Q6NT42|Q9P1X8	Missense_Mutation	SNP	ENST00000327720.5	37	CCDS9747.1	842	0.38553113553113555	22	0.044715447154471545	219	0.6049723756906077	139	0.243006993006993	462	0.6094986807387863	C	8.731	0.916682	0.17907	0.116659	0.599093	ENSG00000184302	ENST00000327720	D	0.95949	-3.86	5.38	5.38	0.77491	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.00566	-1.37	0.09310	P	0.99999837833	B	0.02656	0.0	B	0.06405	0.002	T	0.39961	-0.9588	9	0.48119	T	0.1	.	14.8422	0.70233	0.1439:0.8561:0.0:0.0	rs33912345	141	O95475	SIX6_HUMAN	N	141	ENSP00000328596:H141N	ENSP00000328596:H141N	H	+	1	0	SIX6	60046290	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.798000	0.55522	2.804000	0.96469	0.462000	0.41574	CAC	C|0.576;A|0.424	0.424	strong		0.602	SIX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276952.2		
PARP4	143	hgsc.bcm.edu	37	13	25068808	25068808	+	Missense_Mutation	SNP	A	A	T	rs9318600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25068808A>T	ENST00000381989.3	-	7	749	c.644T>A	c.(643-645)tTt>tAt	p.F215Y		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	215			F -> Y (in dbSNP:rs9318600).		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GTAATTTTCAAAGTATTCACT	0.338													.|||	379	0.0756789	0.118	0.0634	5008	,	,		15488	0.0317		0.0944	False		,,,				2504	0.0532				p.F215Y		Atlas-SNP	.											.	PARP4	142	.	0			c.T644A						PASS	.	T	TYR/PHE	553,3851	774.1+/-414.0	40,473,1689	144.0	141.0	142.0		644	3.3	0.7	13	dbSNP_119	142	989,7611	772.9+/-407.7	67,855,3378	yes	missense	PARP4	NM_006437.3	22	107,1328,5067	TT,TA,AA		11.5,12.5568,11.8579	benign	215/1725	25068808	1542,11462	2202	4300	6502	SO:0001583	missense	143	exon7			TTTTCAAAGTATT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.644T>A	13.37:g.25068808A>T	ENSP00000371419:p.Phe215Tyr	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	165	76	0.460606	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	178	0.0815018315018315	66	0.13414634146341464	24	0.06629834254143646	8	0.013986013986013986	80	0.10554089709762533	T	0.016	-1.523172	0.00967	0.125568	0.115	ENSG00000102699	ENST00000381989	T	0.39787	1.06	4.52	3.26	0.37387	.	0.080006	0.52532	N	0.000078	T	0.00073	0.0002	N	0.00170	-1.935	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.25606	-1.0127	9	0.02654	T	1	-10.8909	8.2978	0.31995	0.3131:0.0:0.0:0.6869	rs9318600;rs17470108;rs52836352;rs9318600	215	Q9UKK3	PARP4_HUMAN	Y	215	ENSP00000371419:F215Y	ENSP00000371419:F215Y	F	-	2	0	PARP4	23966808	1.000000	0.71417	0.658000	0.29665	0.057000	0.15508	1.886000	0.39688	0.782000	0.33613	-0.383000	0.06682	TTT	A|0.889;T|0.111	0.111	strong		0.338	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
LYPD5	284348	hgsc.bcm.edu	37	19	44306482	44306482	+	Silent	SNP	C	C	T	rs11879355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44306482C>T	ENST00000377950.3	-	1	131	c.51G>A	c.(49-51)gcG>gcA	p.A17A	LYPD5_ENST00000594013.1_5'Flank|LYPD5_ENST00000414615.2_Intron	NM_001031749.2	NP_001026919.2	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5	17						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	8		Prostate(69;0.0352)				TCAGGCAGAGCGCAGCCCCAA	0.607													C|||	1074	0.214457	0.1823	0.2507	5008	,	,		13983	0.1101		0.3956	False		,,,				2504	0.1534				p.A17A		Atlas-SNP	.											LYPD5_ENST00000377950,colon,carcinoma,-1,1	LYPD5	22	1	0			c.G51A						PASS	.						65.0	71.0	69.0					19																	44306482		692	1591	2283	SO:0001819	synonymous_variant	284348	exon1			GCAGAGCGCAGCC	AK055031	CCDS12631.1, CCDS46096.1	19q13.31	2008-02-05				ENSG00000159871			26397	protein-coding gene	gene with protein product						12477932	Standard	NM_182573		Approved	FLJ30469	uc002oxm.4	Q6UWN5		ENST00000377950.3:c.51G>A	19.37:g.44306482C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	78	47	0.602564	NM_001031749	Q6PEX9|Q96DR2	Silent	SNP	ENST00000377950.3	37	CCDS46096.1																																																																																			C|0.728;T|0.272	0.272	strong		0.607	LYPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463611.1	NM_182573	
MDN1	23195	hgsc.bcm.edu	37	6	90499502	90499502	+	Silent	SNP	G	G	A	rs1036853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90499502G>A	ENST00000369393.3	-	7	1342	c.1227C>T	c.(1225-1227)gaC>gaT	p.D409D	MDN1_ENST00000428876.1_Silent_p.D409D			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	409					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GACATACCACGTCTAAGGGGG	0.433													G|||	453	0.0904553	0.0053	0.0922	5008	,	,		18907	0.0496		0.1581	False		,,,				2504	0.1769				p.D409D		Atlas-SNP	.											.	MDN1	478	.	0			c.C1227T						PASS	.	G		127,4279	91.1+/-129.8	5,117,2081	73.0	78.0	76.0		1227	-6.9	0.9	6	dbSNP_86	76	1243,7357	248.7+/-276.3	102,1039,3159	no	coding-synonymous	MDN1	NM_014611.1		107,1156,5240	AA,AG,GG		14.4535,2.8824,10.5336		409/5597	90499502	1370,11636	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon7			TACCACGTCTAAG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.1227C>T	6.37:g.90499502G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	97	34	0.350515	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			G|0.905;A|0.095	0.095	strong		0.433	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
OTUD3	23252	hgsc.bcm.edu	37	1	20233086	20233086	+	Missense_Mutation	SNP	G	G	A	rs10916668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20233086G>A	ENST00000375120.3	+	7	998	c.997G>A	c.(997-999)Gca>Aca	p.A333T		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	333			A -> T (in dbSNP:rs10916668).		protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAAACAAAGCAAATAAAAA	0.478													G|||	252	0.0503195	0.0091	0.1182	5008	,	,		19749	0.0208		0.0567	False		,,,				2504	0.0818				p.A333T		Atlas-SNP	.											OTUD3,NS,carcinoma,-2,1	OTUD3	25	1	0			c.G997A						PASS	.	G	THR/ALA	62,3844		1,60,1892	85.0	85.0	85.0		997	3.7	1.0	1	dbSNP_120	85	514,7752		14,486,3633	yes	missense	OTUD3	NM_015207.1	58	15,546,5525	AA,AG,GG		6.2182,1.5873,4.7322	benign	333/399	20233086	576,11596	1953	4133	6086	SO:0001583	missense	23252	exon7			AACAAAGCAAATA	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"""OTU domain containing"""	29038	protein-coding gene	gene with protein product		611758	"""OTU domain containing 3"""			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.997G>A	1.37:g.20233086G>A	ENSP00000364261:p.Ala333Thr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	117	45	0.384615	NM_015207	O75047	Missense_Mutation	SNP	ENST00000375120.3	37	CCDS41279.1	116	0.05311355311355311	4	0.008130081300813009	43	0.11878453038674033	18	0.03146853146853147	51	0.06728232189973615	G	13.74	2.328108	0.41197	0.015873	0.062182	ENSG00000169914	ENST00000375120	T	0.23147	1.92	5.88	3.67	0.42095	.	0.163049	0.53938	D	0.000057	T	0.00241	0.0007	L	0.31752	0.955	0.44048	D	0.996788	B	0.11235	0.004	B	0.10450	0.005	T	0.20672	-1.0268	10	0.19590	T	0.45	.	10.0034	0.41942	0.0855:0.1437:0.7708:0.0	rs10916668;rs52818455;rs57768647;rs10916668	333	Q5T2D3	OTUD3_HUMAN	T	333	ENSP00000364261:A333T	ENSP00000364261:A333T	A	+	1	0	OTUD3	20105673	1.000000	0.71417	0.991000	0.47740	0.704000	0.40688	1.730000	0.38125	1.482000	0.48325	0.650000	0.86243	GCA	G|0.948;A|0.052	0.052	strong		0.478	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1		
GBP7	388646	hgsc.bcm.edu	37	1	89599037	89599037	+	Silent	SNP	A	A	G	rs72728707	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89599037A>G	ENST00000294671.2	-	10	1704	c.1566T>C	c.(1564-1566)agT>agC	p.S522S		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	522						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TTTCCTGGAAACTTCTCTCTT	0.438																																					p.S522S		Atlas-SNP	.											.	GBP7	57	.	0			c.T1566C						PASS	.						270.0	250.0	257.0					1																	89599037		2202	4300	6502	SO:0001819	synonymous_variant	388646	exon10			CTGGAAACTTCTC	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1566T>C	1.37:g.89599037A>G		Somatic	497	0	0		WXS	Illumina HiSeq	Phase_I	550	89	0.161818	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			A|0.989;G|0.011	0.011	strong		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
NT5DC3	51559	hgsc.bcm.edu	37	12	104186946	104186946	+	Silent	SNP	G	G	T	rs1866295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:104186946G>T	ENST00000392876.3	-	9	1055	c.1015C>A	c.(1015-1017)Cgg>Agg	p.R339R		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	339						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						ACTCACCTCCGCTTATCATTA	0.403													G|||	2051	0.409545	0.2829	0.3199	5008	,	,		20518	0.6319		0.2406	False		,,,				2504	0.589				p.R339R		Atlas-SNP	.											.	NT5DC3	113	.	0			c.C1015A						PASS	.	G		1180,3226	414.4+/-336.8	152,876,1175	142.0	150.0	147.0		1015	5.0	1.0	12	dbSNP_92	147	2078,6522	361.9+/-332.5	254,1570,2476	no	coding-synonymous	NT5DC3	NM_001031701.2		406,2446,3651	TT,TG,GG		24.1628,26.7817,25.05		339/549	104186946	3258,9748	2203	4300	6503	SO:0001819	synonymous_variant	51559	exon9			ACCTCCGCTTATC	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.1015C>A	12.37:g.104186946G>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Silent	SNP	ENST00000392876.3	37	CCDS41824.1																																																																																			G|0.708;T|0.292	0.292	strong		0.403	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575	
SRRM2	23524	hgsc.bcm.edu	37	16	2812939	2812939	+	Missense_Mutation	SNP	C	C	A	rs2240140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2812939C>A	ENST00000301740.8	+	11	2959	c.2410C>A	c.(2410-2412)Cct>Act	p.P804T		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	804	Arg-rich.|Ser-rich.		P -> T (in dbSNP:rs2240140). {ECO:0000269|PubMed:9205841}.		mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						ATCCTCCCAACCTAAAGCTAA	0.517													C|||	2075	0.414337	0.0242	0.6873	5008	,	,		19376	0.372		0.6262	False		,,,				2504	0.5736				p.P804T		Atlas-SNP	.											.	SRRM2	263	.	0			c.C2410A						PASS	.	C	THR/PRO	583,3813	257.4+/-261.8	45,493,1660	215.0	213.0	213.0		2410	3.4	0.5	16	dbSNP_98	213	5246,3354	642.5+/-399.8	1607,2032,661	yes	missense	SRRM2	NM_016333.3	38	1652,2525,2321	AA,AC,CC		39.0,13.2621,44.8523	benign	804/2753	2812939	5829,7167	2198	4300	6498	SO:0001583	missense	23524	exon11			TCCCAACCTAAAG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2410C>A	16.37:g.2812939C>A	ENSP00000301740:p.Pro804Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	923	0.4226190476190476	10	0.02032520325203252	235	0.649171270718232	193	0.3374125874125874	485	0.6398416886543535	C	0.011	-1.693981	0.00731	0.132621	0.61	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933;ENST00000426305	T	0.26373	1.74	5.36	3.39	0.38822	.	0.428538	0.22611	N	0.057840	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40270	-0.9572	9	0.10377	T	0.69	-3.8004	4.3612	0.11203	0.1608:0.5989:0.1556:0.0847	rs2240140;rs59555258;rs2240140	804	Q9UQ35	SRRM2_HUMAN	T	804;804;56;769	ENSP00000301740:P804T	ENSP00000301740:P804T	P	+	1	0	SRRM2	2752940	0.049000	0.20398	0.462000	0.27118	0.749000	0.42624	0.748000	0.26305	0.628000	0.30357	-0.181000	0.13052	CCT	C|0.569;A|0.431	0.431	strong		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
PCDHB13	56123	hgsc.bcm.edu	37	5	140594442	140594442	+	Silent	SNP	A	A	G	rs17844607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140594442A>G	ENST00000341948.4	+	1	934	c.747A>G	c.(745-747)agA>agG	p.R249R		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	249	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTTCTATAGAGTGCAGATCT	0.512																																					p.R249R		Atlas-SNP	.											.	PCDHB13	142	.	0			c.A747G						PASS	.						182.0	185.0	184.0					5																	140594442		2203	4300	6503	SO:0001819	synonymous_variant	56123	exon1			CTATAGAGTGCAG	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.747A>G	5.37:g.140594442A>G		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	362	83	0.229282	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			.	.	weak		0.512	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
MRGPRX3	117195	hgsc.bcm.edu	37	11	18159668	18159668	+	Missense_Mutation	SNP	T	T	C	rs386751136|rs79562368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18159668T>C	ENST00000396275.2	+	3	1280	c.919T>C	c.(919-921)Tgg>Cgg	p.W307R		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	307				W -> Q (in Ref. 5; AAH67292). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						AGGTGGAGGGTGGCTTCCTCA	0.572													.|||	170	0.0339457	0.0083	0.0591	5008	,	,		19639	0.0079		0.0855	False		,,,				2504	0.0245				p.W307R		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.T919C						PASS	.	C	ARG/TRP	58,4342		1,56,2143	40.0	43.0	42.0		919	0.0	0.0	11	dbSNP_131	42	642,7944		39,564,3690	no	missense	MRGPRX3	NM_054031.3	101	40,620,5833	CC,CT,TT		7.4773,1.3182,5.3904	benign	307/323	18159668	700,12286	2200	4293	6493	SO:0001583	missense	117195	exon3			GGAGGGTGGCTTC		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.919T>C	11.37:g.18159668T>C	ENSP00000379571:p.Trp307Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	88	0.040293040293040296	5	0.01016260162601626	25	0.06906077348066299	5	0.008741258741258742	53	0.06992084432717678	C	0.013	-1.641348	0.00799	0.013182	0.074773	ENSG00000179826	ENST00000396275	T	0.21191	2.02	1.3	0.00275	0.14052	.	1.239230	0.05408	N	0.541893	T	0.00356	0.0011	N	0.00335	-1.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24048	-1.0171	9	0.14656	T	0.56	.	2.1566	0.03814	0.4143:0.3058:0.0:0.2799	.	307	Q96LB0	MRGX3_HUMAN	R	307	ENSP00000379571:W307R	ENSP00000379571:W307R	W	+	1	0	MRGPRX3	18116244	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.282000	0.08445	-0.806000	0.04398	-1.063000	0.02288	TGG	T|0.948;C|0.052	0.052	strong		0.572	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
PRRC2A	7916	hgsc.bcm.edu	37	6	31600304	31600304	+	Missense_Mutation	SNP	G	G	C	rs2736158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31600304G>C	ENST00000376033.2	+	16	4088	c.3854G>C	c.(3853-3855)gGa>gCa	p.G1285A	PRRC2A_ENST00000376007.4_Missense_Mutation_p.G1285A	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1285	4 X 57 AA type A repeats.		G -> A (in dbSNP:rs2736158). {ECO:0000269|PubMed:14656967}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TCCGCTCCTGGACCTGAGGAG	0.612													G|||	467	0.0932508	0.1536	0.0562	5008	,	,		16755	0.1369		0.0318	False		,,,				2504	0.0562				p.G1285A		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G3854C						PASS	.	G	ALA/GLY,ALA/GLY	401,2619		36,329,1145	72.0	79.0	77.0		3854,3854	3.2	0.0	6	dbSNP_100	77	161,5257		2,157,2550	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	60,60	38,486,3695	CC,CG,GG		2.9716,13.2781,6.6603	benign,benign	1285/2158,1285/2158	31600304	562,7876	1510	2709	4219	SO:0001583	missense	7916	exon16			CTCCTGGACCTGA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3854G>C	6.37:g.31600304G>C	ENSP00000365201:p.Gly1285Ala	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	165	0.07554945054945054	66	0.13414634146341464	18	0.049723756906077346	60	0.1048951048951049	21	0.027704485488126648	G	0.497	-0.872764	0.02570	0.132781	0.029716	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01804	4.63;4.63	5.08	3.24	0.37175	.	0.373747	0.22902	N	0.054242	T	0.00784	0.0026	L	0.45137	1.4	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.43278	-0.9401	9	0.87932	D	0	-1.1573	7.9453	0.29982	0.0:0.1573:0.5182:0.3245	rs2736158;rs3873422;rs17857494;rs2736158	1285	P48634	PRC2A_HUMAN	A	1279;1268;1285;1285;510	ENSP00000365175:G1285A;ENSP00000365201:G1285A	ENSP00000365175:G1285A	G	+	2	0	PRRC2A	31708283	0.369000	0.25039	0.012000	0.15200	0.339000	0.28857	1.941000	0.40233	0.659000	0.30945	0.561000	0.74099	GGA	G|0.935;C|0.065	0.065	strong		0.612	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
CYP2B6	1555	hgsc.bcm.edu	37	19	41512841	41512841	+	Missense_Mutation	SNP	G	G	T	rs3745274	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41512841G>T	ENST00000324071.4	+	4	523	c.516G>T	c.(514-516)caG>caT	p.Q172H	CYP2B6_ENST00000598834.1_3'UTR|CYP2B6_ENST00000593831.1_Intron|CYP2B6_ENST00000330446.5_Intron	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	172			Q -> H (in allele CYP2B6*6, allele CYP2B6*7, allele CYP2B6*9 and allele CYP2B6*13; dbSNP:rs3745274). {ECO:0000269|PubMed:11243870, ECO:0000269|PubMed:11470993, ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:14551287, ECO:0000269|PubMed:15469410, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	TCCTCTTCCAGTCCATTACCG	0.507													g|||	1581	0.315695	0.3744	0.3732	5008	,	,		19726	0.2153		0.2356	False		,,,				2504	0.3814				p.Q172H		Atlas-SNP	.											.	CYP2B6	79	.	0			c.G516T	GRCh37	CS080663	CYP2B6	S	rs3745274	PASS	.	G	HIS/GLN	1629,2777		311,1007,885	87.0	77.0	81.0		516	-9.0	0.0	19	dbSNP_107	81	2148,6452		267,1614,2419	yes	missense	CYP2B6	NM_000767.4	24	578,2621,3304	TT,TG,GG		24.9767,36.9723,29.0404	benign	172/492	41512841	3777,9229	2203	4300	6503	SO:0001583	missense	1555	exon4			CTTCCAGTCCATT	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"""Cytochrome P450s"""	2615	protein-coding gene	gene with protein product		123930	"""cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6"", ""cytochrome P450, family 2, subfamily B"", ""cytochrome P450, subfamily IIB (phenobarbital-inducible)"""	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.516G>T	19.37:g.41512841G>T	ENSP00000324648:p.Gln172His	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	225	87	0.386667	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	37	CCDS12570.1	583	0.26694139194139194	174	0.35365853658536583	131	0.36187845303867405	102	0.17832167832167833	176	0.23218997361477572	.	7.755	0.704176	0.15172	0.369723	0.249767	ENSG00000197408	ENST00000324071	T	0.69561	-0.41	4.48	-8.96	0.00761	.	0.221834	0.44285	N	0.000465	T	0.00012	0.0000	N	0.17838	0.53	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.18493	-1.0335	9	0.45353	T	0.12	.	1.071	0.01621	0.199:0.1663:0.3402:0.2946	rs3745274;rs57685583;rs3745274	172	P20813	CP2B6_HUMAN	H	172	ENSP00000324648:Q172H	ENSP00000324648:Q172H	Q	+	3	2	CYP2B6	46204681	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.320000	0.02700	-1.641000	0.01523	-1.412000	0.01120	CAG	.	.	weak		0.507	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
CXXC1	30827	hgsc.bcm.edu	37	18	47811374	47811374	+	Silent	SNP	G	G	A	rs17660776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:47811374G>A	ENST00000285106.6	-	7	1624	c.910C>T	c.(910-912)Ctg>Ttg	p.L304L	CXXC1_ENST00000412036.2_Silent_p.L304L|CXXC1_ENST00000589940.1_Silent_p.L304L|CXXC1_ENST00000587396.1_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	304	Asp/Glu-rich (acidic).				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						CTGCTCACCAGGCCATGGTCA	0.547													G|||	547	0.109225	0.0318	0.1052	5008	,	,		19404	0.0526		0.174	False		,,,				2504	0.2086				p.L304L		Atlas-SNP	.											.	CXXC1	50	.	0			c.C910T						PASS	.	G	,	258,4148	147.3+/-181.8	10,238,1955	71.0	76.0	74.0		910,910	2.2	1.0	18	dbSNP_123	74	1509,7091	284.4+/-296.6	129,1251,2920	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	139,1489,4875	AA,AG,GG		17.5465,5.8557,13.586	,	304/661,304/657	47811374	1767,11239	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon7			TCACCAGGCCATG	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.910C>T	18.37:g.47811374G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	146	143	0.979452	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			G|0.886;A|0.114	0.114	strong		0.547	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593	
LARP6	55323	hgsc.bcm.edu	37	15	71125093	71125093	+	Silent	SNP	G	G	A	rs3825970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:71125093G>A	ENST00000299213.8	-	3	844	c.774C>T	c.(772-774)tgC>tgT	p.C258C	RP11-138H8.7_ENST00000592096.1_lincRNA	NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	258	RRM.				regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						CCACGATGGCGCACTCCTGGG	0.557													G|||	2512	0.501597	0.3048	0.7594	5008	,	,		17404	0.503		0.5885	False		,,,				2504	0.4939				p.C258C		Atlas-SNP	.											LARP6,colon,carcinoma,0,1	LARP6	43	1	0			c.C774T						PASS	.	G		1575,2823	490.3+/-361.7	292,991,916	63.0	58.0	60.0		774	-9.5	0.5	15	dbSNP_107	60	5141,3453	635.7+/-399.0	1524,2093,680	no	coding-synonymous	LARP6	NM_018357.2		1816,3084,1596	AA,AG,GG		40.1792,35.8117,48.3067		258/492	71125093	6716,6276	2199	4297	6496	SO:0001819	synonymous_variant	55323	exon3			GATGGCGCACTCC	BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"""La ribonucleoprotein domain containing"""	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.774C>T	15.37:g.71125093G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	174	170	0.977012	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																			G|0.490;A|0.509	0.509	strong		0.557	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357	
GPR146	115330	hgsc.bcm.edu	37	7	1097430	1097430	+	Silent	SNP	G	G	A	rs61742514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:1097430G>A	ENST00000397095.1	+	2	502	c.279G>A	c.(277-279)gcG>gcA	p.A93A	GPR146_ENST00000297468.3_Silent_p.A93A|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000357429.6_Intron|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397100.2_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		CCCGGTGGGCGCTGTGGAGTG	0.667													g|||	45	0.00898562	0.0	0.0029	5008	,	,		18213	0.0		0.0318	False		,,,				2504	0.0112				p.A93A		Atlas-SNP	.											.	GPR146	20	.	0			c.G279A						PASS	.		,,,	30,4376	34.3+/-65.2	0,30,2173	35.0	37.0	36.0		,,,279	-10.2	0.0	7	dbSNP_129	36	313,8285	110.2+/-170.6	9,295,3995	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	9,325,6168	AA,AG,GG		3.6404,0.6809,2.6376	,,,	,,,93/334	1097430	343,12661	2203	4299	6502	SO:0001819	synonymous_variant	115330	exon1			GTGGGCGCTGTGG	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.279G>A	7.37:g.1097430G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			G|0.978;A|0.022	0.022	strong		0.667	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
GLT8D1	55830	hgsc.bcm.edu	37	3	52729264	52729264	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:52729264A>G	ENST00000407584.3	-	10	1717	c.867T>C	c.(865-867)ctT>ctC	p.L289L	GLT8D1_ENST00000491606.1_Silent_p.L289L|GLT8D1_ENST00000394783.3_Silent_p.L289L|GLT8D1_ENST00000478968.2_Silent_p.L289L|SNORD69_ENST00000391150.1_RNA|GLT8D1_ENST00000463827.1_5'UTR|GLT8D1_ENST00000266014.5_Silent_p.L289L	NM_001010983.1|NM_001278280.1	NP_001010983.1|NP_001265209.1	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	289						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)	8				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		AAAATACGATAAGCAGAGGAG	0.433																																					p.L289L		Atlas-SNP	.											GLT8D1,NS,carcinoma,-2,1	GLT8D1	28	1	0			c.T867C						scavenged	.						237.0	222.0	227.0					3																	52729264		2203	4300	6503	SO:0001819	synonymous_variant	55830	exon9			TACGATAAGCAGA	AY358579	CCDS2862.1	3p21.1	2013-02-22			ENSG00000016864	ENSG00000016864		"""Glycosyltransferase family 8 domain containing"""	24870	protein-coding gene	gene with protein product						12975309	Standard	NM_152932		Approved	AD-017, FLJ14611	uc003dfi.4	Q68CQ7	OTTHUMG00000158759	ENST00000407584.3:c.867T>C	3.37:g.52729264A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_152932	Q7Z4D1|Q8N2J6|Q9P0I5	Silent	SNP	ENST00000407584.3	37	CCDS2862.1																																																																																			.	.	none		0.433	GLT8D1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352065.3	NM_152932	
KCNH6	81033	hgsc.bcm.edu	37	17	61611502	61611502	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:61611502T>C	ENST00000583023.1	+	5	942	c.931T>C	c.(931-933)Ttc>Ctc	p.F311L	KCNH6_ENST00000580652.1_Missense_Mutation_p.F311L|KCNH6_ENST00000581784.1_Missense_Mutation_p.F311L|KCNH6_ENST00000456941.2_Missense_Mutation_p.F311L|KCNH6_ENST00000314672.5_Missense_Mutation_p.F311L	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	311					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GGACATCATGTTCGTCGTGGA	0.587																																					p.F311L		Atlas-SNP	.											KCNH6,bladder,carcinoma,-2,1	KCNH6	122	1	0			c.T931C						scavenged	.						248.0	209.0	222.0					17																	61611502		2203	4300	6503	SO:0001583	missense	81033	exon5			ATCATGTTCGTCG	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.931T>C	17.37:g.61611502T>C	ENSP00000463533:p.Phe311Leu	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	187	3	0.0160428	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.403515	0.42613	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.98987	-5.3;-5.3	4.14	4.14	0.48551	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99272	0.9746	M	0.86178	2.8	0.58432	D	0.999999	P;B;P;B;P	0.38711	0.643;0.121;0.591;0.241;0.535	P;B;P;B;B	0.62885	0.908;0.319;0.702;0.434;0.422	D	0.98968	1.0800	10	0.87932	D	0	.	13.3281	0.60471	0.0:0.0:0.0:1.0	.	188;311;311;311;311	B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3	.;.;.;KCNH6_HUMAN;.	L	311	ENSP00000318212:F311L;ENSP00000396900:F311L	ENSP00000318212:F311L	F	+	1	0	KCNH6	58965234	1.000000	0.71417	0.988000	0.46212	0.685000	0.39939	7.864000	0.87037	1.723000	0.51488	0.254000	0.18369	TTC	.	.	none		0.587	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
PRG4	10216	hgsc.bcm.edu	37	1	186275983	186275983	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:186275983C>A	ENST00000445192.2	+	7	1177	c.1132C>A	c.(1132-1134)Ccc>Acc	p.P378T	PRG4_ENST00000367483.4_Missense_Mutation_p.P337T|PRG4_ENST00000367485.4_Missense_Mutation_p.P285T|PRG4_ENST00000367484.3_Missense_Mutation_p.P337T|PRG4_ENST00000367486.3_Missense_Mutation_p.P335T	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	378	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ACCCACCACCCCCAAGGAGCC	0.637																																					p.P378T		Atlas-SNP	.											PRG4,NS,malignant_melanoma,0,1	PRG4	259	1	0			c.C1132A						scavenged	.						168.0	162.0	164.0					1																	186275983		2203	4300	6503	SO:0001583	missense	10216	exon7			ACCACCCCCAAGG	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1132C>A	1.37:g.186275983C>A	ENSP00000399679:p.Pro378Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	171	5	0.0292398	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	5.443	0.266920	0.10294	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.05081	3.5;3.57;3.61;3.5;3.6	2.42	-4.85	0.03142	.	.	.	.	.	T	0.03305	0.0096	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.24258	0.1;0.037;0.022;0.037	B;B;B;B	0.18263	0.021;0.012;0.005;0.012	T	0.46898	-0.9158	8	.	.	.	.	6.9592	0.24587	0.1804:0.4659:0.3536:0.0	.	244;285;378;337	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	T	335;337;244;337;285;378	ENSP00000356456:P335T;ENSP00000356454:P337T;ENSP00000356453:P337T;ENSP00000356455:P285T;ENSP00000399679:P378T	.	P	+	1	0	PRG4	184542606	0.000000	0.05858	0.011000	0.14972	0.044000	0.14063	-3.957000	0.00325	-0.405000	0.07599	0.154000	0.16183	CCC	.	.	none		0.637	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
MKRN1	23608	hgsc.bcm.edu	37	7	140158851	140158851	+	Missense_Mutation	SNP	C	C	G	rs2272095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:140158851C>G	ENST00000255977.2	-	4	951	c.727G>C	c.(727-729)Gtc>Ctc	p.V243L	MKRN1_ENST00000481705.1_5'Flank|MKRN1_ENST00000480552.1_Intron|MKRN1_ENST00000443720.2_Missense_Mutation_p.V243L|MKRN1_ENST00000437223.2_Intron|MKRN1_ENST00000474576.1_Missense_Mutation_p.V179L	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	243	Makorin-type Cys-His.		V -> L (in dbSNP:rs2272095). {ECO:0000269|PubMed:10843807, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					GGATGCAGGACCTGCAGCCCA	0.488													c|||	620	0.123802	0.0204	0.1527	5008	,	,		19731	0.0913		0.2893	False		,,,				2504	0.1063				p.V243L		Atlas-SNP	.											.	MKRN1	35	.	0			c.G727C						PASS	.	C	LEU/VAL,LEU/VAL	246,4160	143.8+/-178.8	10,226,1967	95.0	90.0	92.0		727,727	4.9	1.0	7	dbSNP_100	92	2247,6353	381.6+/-340.1	303,1641,2356	yes	missense,missense	MKRN1	NM_001145125.1,NM_013446.3	32,32	313,1867,4323	GG,GC,CC		26.1279,5.5833,19.1681	benign,benign	243/330,243/483	140158851	2493,10513	2203	4300	6503	SO:0001583	missense	23608	exon4			GCAGGACCTGCAG	AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"""RING-type (C3HC4) zinc fingers"""	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.727G>C	7.37:g.140158851C>G	ENSP00000255977:p.Val243Leu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	159	68	0.427673	NM_013446	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Missense_Mutation	SNP	ENST00000255977.2	37	CCDS5860.1	337	0.1543040293040293	15	0.03048780487804878	56	0.15469613259668508	61	0.10664335664335664	205	0.2704485488126649	C	24.5	4.534295	0.85812	0.055833	0.261279	ENSG00000133606	ENST00000255977;ENST00000539898;ENST00000474576;ENST00000443720;ENST00000471104	T;T;T;T	0.24723	2.87;2.22;2.45;1.84	4.91	4.91	0.64330	.	0.057098	0.64402	D	0.000001	T	0.00012	0.0000	M	0.74647	2.275	0.09310	P	1.0	P	0.38420	0.63	B	0.35770	0.21	T	0.17167	-1.0378	9	0.52906	T	0.07	.	18.2987	0.90155	0.0:1.0:0.0:0.0	rs2272095;rs9648841;rs17852313;rs2272095	243	Q9UHC7	MKRN1_HUMAN	L	243;179;179;243;179	ENSP00000255977:V243L;ENSP00000417863:V179L;ENSP00000416369:V243L;ENSP00000418864:V179L	ENSP00000255977:V243L	V	-	1	0	MKRN1	139805320	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.223000	0.78033	2.556000	0.86216	0.555000	0.69702	GTC	C|0.819;G|0.181	0.181	strong		0.488	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446	
EPPK1	83481	hgsc.bcm.edu	37	8	144940331	144940331	+	Missense_Mutation	SNP	C	C	T	rs200585601		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144940331C>T	ENST00000525985.1	-	2	7162	c.7091G>A	c.(7090-7092)cGg>cAg	p.R2364Q				P58107	EPIPL_HUMAN	epiplakin 1	2364						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)	p.R2364Q(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GTAGCCGCGCCGGTAGGCCAC	0.692																																					p.R2364Q		Atlas-SNP	.											EPPK1,NS,carcinoma,0,6	EPPK1	199	6	1	Substitution - Missense(1)	large_intestine(1)	c.G7091A						PASS	.	C	GLN/ARG	194,4166		0,194,1986	217.0	211.0	213.0		7091	0.7	1.0	8	dbSNP_134	213	66,8462		0,66,4198	no	missense	EPPK1	NM_031308.1	43	0,260,6184	TT,TC,CC		0.7739,4.4495,2.0174	benign	2364/2420	144940331	260,12628	2180	4264	6444	SO:0001583	missense	83481	exon1			CCGCGCCGGTAGG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.7091G>A	8.37:g.144940331C>T	ENSP00000436337:p.Arg2364Gln	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	151	17	0.112583	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	7.296	0.612142	0.14066	0.044495	0.007739	ENSG00000227184	ENST00000525985	T	0.74526	-0.85	4.42	0.661	0.17874	.	.	.	.	.	T	0.14184	0.0343	N	0.03903	-0.33	0.21579	N	0.999636	B	0.20550	0.046	B	0.12837	0.008	T	0.14254	-1.0479	9	0.02654	T	1	.	7.4216	0.27075	0.0:0.2871:0.0:0.7129	.	2364	E9PPU0	.	Q	2364	ENSP00000436337:R2364Q	ENSP00000436337:R2364Q	R	-	2	0	EPPK1	145012319	0.742000	0.28228	0.982000	0.44146	0.955000	0.61496	1.358000	0.34102	0.024000	0.15214	-0.482000	0.04802	CGG	C|0.997;T|0.003	0.003	weak		0.692	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
RNF25	64320	hgsc.bcm.edu	37	2	219533378	219533378	+	Silent	SNP	T	T	C	rs16859170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219533378T>C	ENST00000295704.2	-	2	506	c.66A>G	c.(64-66)gtA>gtG	p.V22V		NM_022453.2	NP_071898.2	Q96BH1	RNF25_HUMAN	ring finger protein 25	22	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|NF-kappaB binding (GO:0051059)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGGACTCCAATACTTCAACTT	0.478													C|||	738	0.147364	0.3729	0.0519	5008	,	,		16535	0.124		0.0278	False		,,,				2504	0.0573				p.V22V		Atlas-SNP	.											.	RNF25	40	.	0			c.A66G						PASS	.	C		1304,3102	697.2+/-406.2	193,918,1092	138.0	143.0	141.0		66	-0.7	1.0	2	dbSNP_123	141	324,8276	804.7+/-407.3	8,308,3984	no	coding-synonymous	RNF25	NM_022453.2		201,1226,5076	CC,CT,TT		3.7674,29.596,12.5173		22/460	219533378	1628,11378	2203	4300	6503	SO:0001819	synonymous_variant	64320	exon2			CTCCAATACTTCA		CCDS2420.1	2q35	2008-02-05			ENSG00000163481	ENSG00000163481		"""RING-type (C3HC4) zinc fingers"""	14662	protein-coding gene	gene with protein product						12748188	Standard	NM_022453		Approved	AO7, FLJ13906	uc002vit.3	Q96BH1	OTTHUMG00000133077	ENST00000295704.2:c.66A>G	2.37:g.219533378T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	29	0.358025	NM_022453	A8K0D6|Q53HQ5|Q9H874	Silent	SNP	ENST00000295704.2	37	CCDS2420.1																																																																																			T|0.857;C|0.143	0.143	strong		0.478	RNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256721.1	NM_022453	
DOK2	9046	hgsc.bcm.edu	37	8	21769432	21769432	+	Missense_Mutation	SNP	A	A	G	rs56094005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:21769432A>G	ENST00000276420.4	-	3	671	c.413T>C	c.(412-414)tTg>tCg	p.L138S	DOK2_ENST00000544659.1_Intron	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	138					blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GCTGCTGTACAATTCATTTTC	0.667													A|||	59	0.0117812	0.0023	0.013	5008	,	,		16263	0.0		0.0427	False		,,,				2504	0.0041				p.L138S		Atlas-SNP	.											.	DOK2	51	.	0			c.T413C						PASS	.	A	SER/LEU	36,4342		0,36,2153	69.0	62.0	64.0		413	4.6	0.9	8	dbSNP_129	64	322,8244		4,314,3965	yes	missense	DOK2	NM_003974.2	145	4,350,6118	GG,GA,AA		3.759,0.8223,2.7658	probably-damaging	138/413	21769432	358,12586	2189	4283	6472	SO:0001583	missense	9046	exon3			CTGTACAATTCAT	AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"""docking protein 2, 56kD"""			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.413T>C	8.37:g.21769432A>G	ENSP00000276420:p.Leu138Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_003974	Q8N5A4	Missense_Mutation	SNP	ENST00000276420.4	37	CCDS6016.1	46	0.021062271062271064	3	0.006097560975609756	4	0.011049723756906077	0	0.0	39	0.051451187335092345	A	16.84	3.233523	0.58886	0.008223	0.03759	ENSG00000147443	ENST00000276420;ENST00000523932	T;T	0.57273	1.38;0.41	4.64	4.64	0.57946	.	1.504630	0.03895	N	0.279388	T	0.25005	0.0607	M	0.81802	2.56	0.80722	D	1	D;P	0.55605	0.972;0.912	P;B	0.48304	0.573;0.356	T	0.55205	-0.8177	10	0.56958	D	0.05	.	8.3827	0.32481	0.8012:0.1988:0.0:0.0	rs56094005;rs61752039	138;138	O60496;A8K7W1	DOK2_HUMAN;.	S	138	ENSP00000276420:L138S;ENSP00000429224:L138S	ENSP00000276420:L138S	L	-	2	0	DOK2	21825378	0.057000	0.20700	0.884000	0.34674	0.655000	0.38815	0.817000	0.27281	1.951000	0.56629	0.533000	0.62120	TTG	A|0.975;G|0.025	0.025	strong		0.667	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253735.3	NM_003974	
CDON	50937	hgsc.bcm.edu	37	11	125831701	125831701	+	Silent	SNP	G	G	A	rs2276061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:125831701G>A	ENST00000392693.3	-	19	3676	c.3549C>T	c.(3547-3549)gtC>gtT	p.V1183V	CDON_ENST00000531738.1_Silent_p.V560V|CDON_ENST00000263577.7_Silent_p.V1183V	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1183					anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		GCTGAGTAGGGACTGGTTCCA	0.547													G|||	1213	0.242212	0.1014	0.2565	5008	,	,		20428	0.2837		0.3091	False		,,,				2504	0.3108				p.V1183V		Atlas-SNP	.											.	CDON	137	.	0			c.C3549T						PASS	.	G		583,3819	260.1+/-263.5	33,517,1651	110.0	82.0	91.0		3549	1.1	0.0	11	dbSNP_100	91	2707,5891	433.4+/-357.4	457,1793,2049	no	coding-synonymous	CDON	NM_016952.4		490,2310,3700	AA,AG,GG		31.4841,13.244,25.3077		1183/1265	125831701	3290,9710	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon19			AGTAGGGACTGGT	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.3549C>T	11.37:g.125831701G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			G|0.751;A|0.249	0.249	strong		0.547	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
UTP15	84135	hgsc.bcm.edu	37	5	72874907	72874907	+	Silent	SNP	A	A	C	rs343122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:72874907A>C	ENST00000296792.4	+	11	1467	c.1212A>C	c.(1210-1212)ggA>ggC	p.G404G	UTP15_ENST00000543251.1_Silent_p.G214G|UTP15_ENST00000508491.1_Silent_p.G385G	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	404					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		ATCGAAGAGGAGTCCTTGCAA	0.373													A|||	647	0.129193	0.0976	0.1527	5008	,	,		18085	0.0585		0.2187	False		,,,				2504	0.136				p.G404G		Atlas-SNP	.											.	UTP15	30	.	0			c.A1212C						PASS	.	A		566,3840	252.7+/-259.0	41,484,1678	119.0	124.0	122.0		1212	3.3	1.0	5	dbSNP_79	122	1917,6683	339.9+/-323.4	230,1457,2613	no	coding-synonymous	UTP15	NM_032175.2		271,1941,4291	CC,CA,AA		22.2907,12.8461,19.0912		404/519	72874907	2483,10523	2203	4300	6503	SO:0001819	synonymous_variant	84135	exon11			AAGAGGAGTCCTT	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"""WD repeat domain containing"""	25758	protein-coding gene	gene with protein product			"""UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.1212A>C	5.37:g.72874907A>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Silent	SNP	ENST00000296792.4	37	CCDS34186.1	296	0.13553113553113552	47	0.09552845528455285	64	0.17679558011049723	23	0.04020979020979021	162	0.21372031662269128	A	10.51	1.369190	0.24771	0.128461	0.222907	ENSG00000164338	ENST00000509005	.	.	.	5.68	3.27	0.37495	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.07790	-1.0754	3	.	.	.	.	8.4101	0.32638	0.7937:0.1372:0.0691:0.0	rs343122;rs1667442;rs17551643;rs17845364;rs17858217;rs343122	.	.	.	A	431	.	.	E	+	2	0	UTP15	72910663	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.317000	0.43770	0.503000	0.28060	0.533000	0.62120	GAG	A|0.839;C|0.161	0.161	strong		0.373	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175	
ESPL1	9700	hgsc.bcm.edu	37	12	53682457	53682457	+	Missense_Mutation	SNP	G	G	A	rs56358776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53682457G>A	ENST00000257934.4	+	20	4773	c.4682G>A	c.(4681-4683)cGg>cAg	p.R1561Q	ESPL1_ENST00000552462.1_Missense_Mutation_p.R1561Q	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1561				R -> Q (in Ref. 1; AAR18247 and 2; BAA11482). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						CCTCGGCTCCGGCTCCCCTCA	0.592													g|||	1190	0.23762	0.2632	0.3386	5008	,	,		17662	0.1319		0.341	False		,,,				2504	0.1339				p.R1561Q	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.G4682A						PASS	.	G	GLN/ARG	1263,3143		181,901,1121	47.0	47.0	47.0		4682	-7.1	0.0	12	dbSNP_129	47	2904,5694		498,1908,1893	yes	missense	ESPL1	NM_012291.4	43	679,2809,3014	AA,AG,GG		33.7753,28.6655,32.044	benign	1561/2121	53682457	4167,8837	2203	4299	6502	SO:0001583	missense	9700	exon20			GGCTCCGGCTCCC	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.4682G>A	12.37:g.53682457G>A	ENSP00000257934:p.Arg1561Gln	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	176	174	0.988636	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	634	0.2902930402930403	139	0.28252032520325204	123	0.3397790055248619	100	0.17482517482517482	272	0.35883905013192613	g	6.020	0.372128	0.11409	0.286655	0.337753	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.11604	2.76;2.76	5.34	-7.11	0.01542	.	1.494160	0.03591	N	0.231873	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43048	-0.9415	9	0.14656	T	0.56	.	9.7156	0.40272	0.6513:0.1114:0.2373:0.0	rs56358776;rs57423655;rs61741333	1561	Q14674	ESPL1_HUMAN	Q	1561;1236;1561	ENSP00000257934:R1561Q;ENSP00000449831:R1561Q	ENSP00000257934:R1561Q	R	+	2	0	ESPL1	51968724	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.550000	0.00929	-1.910000	0.01083	-1.723000	0.00705	CGG	G|0.698;A|0.302	0.302	strong		0.592	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
HLA-C	3107	hgsc.bcm.edu	37	6	31239544	31239544	+	Silent	SNP	G	G	T	rs281860356		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31239544G>T	ENST00000376228.5	-	2	189	c.175C>A	c.(175-177)Cgg>Agg	p.R59R	HLA-C_ENST00000383329.3_Silent_p.R59R	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	59	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTGTCGAACCGCACGAACTGC	0.677																																					p.R59R		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,0,2	HLA-C	92	2	0			c.C175A						scavenged	.						40.0	39.0	39.0					6																	31239544		1511	2707	4218	SO:0001819	synonymous_variant	3107	exon2			CGAACCGCACGAA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.175C>A	6.37:g.31239544G>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	153	21	0.137255	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	-	7.431	0.638746	0.14386	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	2.81	0.32909	.	.	.	.	.	T	0.46347	0.1388	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43065	-0.9414	4	.	.	.	.	9.2778	0.37709	0.0:0.0:1.0:0.0	.	.	.	.	E	58	.	.	A	-	2	0	HLA-C	31347523	0.000000	0.05858	1.000000	0.80357	0.308000	0.27856	0.040000	0.13905	1.886000	0.54624	0.305000	0.20034	GCG	.	.	weak		0.677	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
MUC6	4588	hgsc.bcm.edu	37	11	1017596	1017596	+	Missense_Mutation	SNP	T	T	G	rs201522029	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1017596T>G	ENST00000421673.2	-	31	5255	c.5205A>C	c.(5203-5205)caA>caC	p.Q1735H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1735	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.Q1735H(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCTTCGGGATTGGCTGGTCC	0.532													-|||	633	0.126398	0.0514	0.0461	5008	,	,		41573	0.1786		0.0845	False		,,,				2504	0.274				p.Q1735H		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,1	MUC6	408	1	1	Substitution - Missense(1)	prostate(1)	c.A5205C						PASS	.	T	HIS/GLN	131,4233		0,131,2051	549.0	551.0	550.0		5205	-4.1	0.0	11		550	400,8150		0,400,3875	yes	missense	MUC6	NM_005961.2	24	0,531,5926	GG,GT,TT		4.6784,3.0018,4.1118	probably-damaging	1735/2440	1017596	531,12383	2182	4275	6457	SO:0001583	missense	4588	exon31			TCGGGATTGGCTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5205A>C	11.37:g.1017596T>G	ENSP00000406861:p.Gln1735His	Somatic	1106	1	0.000904159		WXS	Illumina HiSeq	Phase_I	1122	188	0.167558	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	4.598	0.111210	0.08831	0.030018	0.046784	ENSG00000184956	ENST00000421673	T	0.20881	2.04	2.07	-4.14	0.03892	.	.	.	.	.	T	0.04003	0.0112	N	0.24115	0.695	0.09310	N	1	D	0.67145	0.996	D	0.69479	0.964	T	0.12477	-1.0546	9	0.45353	T	0.12	.	8.0645	0.30652	0.0:0.135:0.173:0.6921	.	1735	Q6W4X9	MUC6_HUMAN	H	1735	ENSP00000406861:Q1735H	ENSP00000406861:Q1735H	Q	-	3	2	MUC6	1007596	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.097000	0.01348	-2.302000	0.00657	-1.058000	0.02302	CAA	T|0.995;G|0.005	0.005	strong		0.532	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
FOCAD	54914	hgsc.bcm.edu	37	9	20948311	20948311	+	Silent	SNP	A	A	G	rs35470485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:20948311A>G	ENST00000380249.1	+	33	4081	c.3717A>G	c.(3715-3717)ggA>ggG	p.G1239G	FOCAD_ENST00000338382.6_Silent_p.G1239G|FOCAD_ENST00000605086.1_Silent_p.G675G	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1239						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											TAGTTCATGGATTGTCTGTGT	0.388													A|||	151	0.0301518	0.0015	0.0346	5008	,	,		15666	0.0		0.1153	False		,,,				2504	0.0092				p.G1239G		Atlas-SNP	.											.	.	.	.	0			c.A3717G						PASS	.	A		78,4328	68.1+/-105.8	1,76,2126	126.0	119.0	121.0		3717	-5.3	0.9	9	dbSNP_126	121	812,7788	189.7+/-236.4	36,740,3524	no	coding-synonymous	KIAA1797	NM_017794.3		37,816,5650	GG,GA,AA		9.4419,1.7703,6.843		1239/1802	20948311	890,12116	2203	4300	6503	SO:0001819	synonymous_variant	54914	exon33			TCATGGATTGTCT	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.3717A>G	9.37:g.20948311A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	37	CCDS34993.1																																																																																			A|0.933;G|0.067	0.067	strong		0.388	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
PTPN13	5783	hgsc.bcm.edu	37	4	87692393	87692393	+	Missense_Mutation	SNP	G	G	A	rs12500797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:87692393G>A	ENST00000411767.2	+	31	4936	c.4873G>A	c.(4873-4875)Gag>Aag	p.E1625K	PTPN13_ENST00000436978.1_Missense_Mutation_p.E1630K|PTPN13_ENST00000427191.2_Missense_Mutation_p.E1606K|PTPN13_ENST00000511467.1_Missense_Mutation_p.E1630K|PTPN13_ENST00000316707.6_Missense_Mutation_p.E1434K			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1625			E -> K (in dbSNP:rs12500797).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ATCATGTGTGGAGCAAAGCAC	0.443													G|||	222	0.0443291	0.0098	0.0663	5008	,	,		18384	0.0079		0.1133	False		,,,				2504	0.0419				p.E1630K		Atlas-SNP	.											PTPN13,NS,carcinoma,-2,1	PTPN13	203	1	0			c.G4888A	GRCh37	CM067710	PTPN13	M	rs12500797	PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	119,3839		3,113,1863	33.0	32.0	32.0		4816,4873,4300,4888	5.3	1.0	4	dbSNP_120	32	1002,7334		61,880,3227	yes	missense,missense,missense,missense	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	56,56,56,56	64,993,5090	AA,AG,GG		12.0202,3.0066,9.1183	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1606/2467,1625/2486,1434/2295,1630/2491	87692393	1121,11173	1979	4168	6147	SO:0001583	missense	5783	exon31			TGTGTGGAGCAAA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4873G>A	4.37:g.87692393G>A	ENSP00000407249:p.Glu1625Lys	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	361	154	0.426593	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	122	0.055860805860805864	6	0.012195121951219513	25	0.06906077348066299	4	0.006993006993006993	87	0.11477572559366754	G	10.86	1.469049	0.26335	0.030066	0.120202	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.52526	0.66;0.68;0.76;0.66;0.68	5.32	5.32	0.75619	.	0.134693	0.33217	N	0.005151	T	0.00784	0.0026	L	0.47716	1.5	0.27061	P	0.9635484	P;B;B;B	0.41848	0.763;0.21;0.215;0.057	B;B;B;B	0.42361	0.385;0.147;0.07;0.131	T	0.01532	-1.1331	9	0.16896	T	0.51	.	19.3643	0.94456	0.0:0.0:1.0:0.0	rs12500797;rs17454863;rs52799273;rs12500797	1434;1606;1625;1630	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	K	1606;1630;1434;1625;1630;1574	ENSP00000408368:E1606K;ENSP00000394794:E1630K;ENSP00000322675:E1434K;ENSP00000407249:E1625K;ENSP00000426626:E1630K	ENSP00000322675:E1434K	E	+	1	0	PTPN13	87911417	1.000000	0.71417	0.979000	0.43373	0.828000	0.46876	5.276000	0.65580	2.659000	0.90383	0.655000	0.94253	GAG	G|0.939;A|0.061	0.061	strong		0.443	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
NRAP	4892	hgsc.bcm.edu	37	10	115422474	115422474	+	Silent	SNP	A	A	G	rs3127122	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115422474A>G	ENST00000359988.3	-	3	463	c.219T>C	c.(217-219)aaT>aaC	p.N73N	NRAP_ENST00000369360.3_Silent_p.N73N|NRAP_ENST00000369358.4_Silent_p.N73N|NRAP_ENST00000360478.3_Silent_p.N73N	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.N73N(2)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TCACATTTAGATTTAATGGAG	0.363													G|||	1448	0.289137	0.289	0.4553	5008	,	,		15795	0.2143		0.3231	False		,,,				2504	0.2137				p.N73N		Atlas-SNP	.											NRAP,NS,carcinoma,0,2	NRAP	208	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.T219C						PASS	.	G	,	1328,3078	696.6+/-406.1	193,942,1068	137.0	129.0	132.0		219,219	0.5	0.4	10	dbSNP_103	132	2944,5656	668.0+/-402.5	502,1940,1858	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	695,2882,2926	GG,GA,AA		34.2326,30.1407,32.8464	,	73/1696,73/1731	115422474	4272,8734	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon3			ATTTAGATTTAAT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.219T>C	10.37:g.115422474A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			A|0.683;G|0.317	0.317	strong		0.363	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
ZNF519	162655	hgsc.bcm.edu	37	18	14105853	14105853	+	Missense_Mutation	SNP	C	C	A	rs8094412	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:14105853C>A	ENST00000590202.1	-	3	838	c.686G>T	c.(685-687)aGa>aTa	p.R229I	ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	229			R -> I (in dbSNP:rs8094412).		negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						AATATAAATTCTTTGATGTTG	0.308													C|||	827	0.165136	0.0106	0.2248	5008	,	,		17374	0.4454		0.1302	False		,,,				2504	0.0787				p.R229I		Atlas-SNP	.											.	ZNF519	53	.	0			c.G686T						PASS	.	C	ILE/ARG	148,4252		2,144,2054	47.0	51.0	50.0		686	-0.5	0.0	18	dbSNP_116	50	1302,7274		103,1096,3089	yes	missense	ZNF519	NM_145287.3	97	105,1240,5143	AA,AC,CC		15.1819,3.3636,11.1745	probably-damaging	229/541	14105853	1450,11526	2200	4288	6488	SO:0001583	missense	162655	exon3			TAAATTCTTTGAT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.686G>T	18.37:g.14105853C>A	ENSP00000464872:p.Arg229Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	433	0.19826007326007325	8	0.016260162601626018	70	0.19337016574585636	262	0.458041958041958	93	0.12269129287598944	C	6.374	0.437165	0.12104	0.033636	0.151819	ENSG00000175322	ENST00000309305	.	.	.	0.646	-0.517	0.11947	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.39566	1.225	0.29437	P	0.859452	P	0.38788	0.647	B	0.35859	0.212	T	0.47142	-0.9140	7	0.30854	T	0.27	.	4.7853	0.13222	0.0:0.7185:0.0:0.2815	rs8094412;rs59037945;rs8094412	229	Q8TB69	ZN519_HUMAN	I	229	.	ENSP00000307908:R229I	R	-	2	0	ZNF519	14095853	0.000000	0.05858	0.002000	0.10522	0.342000	0.28953	0.122000	0.15687	-0.192000	0.10432	0.089000	0.15464	AGA	C|0.863;A|0.137	0.137	strong		0.308	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
MUC4	4585	hgsc.bcm.edu	37	3	195507241	195507241	+	Missense_Mutation	SNP	G	G	A	rs74187968|rs370997210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507241G>A	ENST00000463781.3	-	2	11669	c.11210C>T	c.(11209-11211)gCa>gTa	p.A3737V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3737V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGG	0.572													.|||	4	0.000798722	0.0023	0.0014	5008	,	,		10160	0.0		0.0	False		,,,				2504	0.0				p.A3737V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.C11210T						scavenged	.						34.0	33.0	33.0					3																	195507241		619	1580	2199	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11210C>T	3.37:g.195507241G>A	ENSP00000417498:p.Ala3737Val	Somatic	64	2	0.03125		WXS	Illumina HiSeq	Phase_I	286	20	0.0699301	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	7.469	0.646185	0.14451	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.43;1.42	.	.	.	.	0.435754	0.11199	N	0.589055	T	0.11067	0.0270	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.24476	-1.0159	8	.	.	.	.	4.6376	0.12531	0.4334:0.0:0.5666:0.0	.	3609	E7ESK3	.	V	3737	ENSP00000417498:A3737V;ENSP00000420243:A3737V	.	A	-	2	0	MUC4	196992020	0.002000	0.14202	0.010000	0.14722	0.022000	0.10575	-2.011000	0.01452	-1.860000	0.01154	-2.092000	0.00371	GCA	G|0.500;A|0.500	0.500	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HHIP	64399	hgsc.bcm.edu	37	4	145659064	145659064	+	Silent	SNP	T	T	C	rs11727676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:145659064T>C	ENST00000296575.3	+	13	2713	c.2058T>C	c.(2056-2058)atT>atC	p.I686I		NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	686					carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		ATCAGATCATTGACATGACAT	0.388													T|||	130	0.0259585	0.0023	0.0533	5008	,	,		19218	0.001		0.0765	False		,,,				2504	0.0123				p.I686I		Atlas-SNP	.											.	HHIP	100	.	0			c.T2058C						PASS	.	T		79,4327	69.2+/-107.0	0,79,2124	174.0	153.0	160.0		2058	4.3	1.0	4	dbSNP_120	160	839,7761	192.3+/-238.3	40,759,3501	no	coding-synonymous	HHIP	NM_022475.2		40,838,5625	CC,CT,TT		9.7558,1.793,7.0583		686/701	145659064	918,12088	2203	4300	6503	SO:0001819	synonymous_variant	64399	exon13			GATCATTGACATG	AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"""hedgehog-interacting protein"""			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.2058T>C	4.37:g.145659064T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_022475	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Silent	SNP	ENST00000296575.3	37	CCDS3762.1																																																																																			T|0.939;C|0.061	0.061	strong		0.388	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2		
OR1L8	138881	hgsc.bcm.edu	37	9	125330739	125330739	+	Silent	SNP	G	G	A	rs1999182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:125330739G>A	ENST00000304865.2	-	1	99	c.18C>T	c.(16-18)caC>caT	p.H6H		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CACTGCTGGTGTGGTTGATTC	0.453													G|||	3167	0.632388	0.4811	0.6124	5008	,	,		20598	0.9792		0.5467	False		,,,				2504	0.5818				p.H6H		Atlas-SNP	.											.	OR1L8	90	.	0			c.C18T						PASS	.	G		2182,2224	585.1+/-386.2	544,1094,565	118.0	145.0	136.0		18	-0.1	0.9	9	dbSNP_92	136	4813,3787	614.2+/-396.2	1313,2187,800	yes	coding-synonymous	OR1L8	NM_001004454.1		1857,3281,1365	AA,AG,GG		44.0349,49.5234,46.2171		6/310	125330739	6995,6011	2203	4300	6503	SO:0001819	synonymous_variant	138881	exon1			GCTGGTGTGGTTG		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"""GPCR / Class A : Olfactory receptors"""	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.18C>T	9.37:g.125330739G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	130	54	0.415385	NM_001004454	A3KFM3|B9EIR6|Q6IF15|Q96R79	Silent	SNP	ENST00000304865.2	37	CCDS35124.1																																																																																			G|0.418;A|0.582	0.582	strong		0.453	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1		
ALDH16A1	126133	hgsc.bcm.edu	37	19	49964977	49964977	+	Missense_Mutation	SNP	C	C	G	rs1320303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49964977C>G	ENST00000293350.4	+	6	842	c.679C>G	c.(679-681)Ctc>Gtc	p.L227V	CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.L64V|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.L227V|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.L62V	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	227			L -> V (in dbSNP:rs1320303). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CCTGAATGTCCTCAGTGGCCC	0.726													A|||	2555	0.510184	0.5257	0.4222	5008	,	,		11636	0.3214		0.7107	False		,,,				2504	0.5399				p.L227V		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.C679G						PASS	.	A	VAL/LEU,VAL/LEU	2293,2101		626,1041,530	18.0	19.0	19.0		679,679	-9.2	0.2	19	dbSNP_88	19	6166,2430		2216,1734,348	yes	missense,missense	ALDH16A1	NM_001145396.1,NM_153329.3	32,32	2842,2775,878	GG,GC,CC		28.269,47.8152,34.8807	benign,benign	227/752,227/803	49964977	8459,4531	2197	4298	6495	SO:0001583	missense	126133	exon6			AATGTCCTCAGTG	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.679C>G	19.37:g.49964977C>G	ENSP00000293350:p.Leu227Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_001145396	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	1140	0.521978021978022	271	0.5508130081300813	176	0.4861878453038674	172	0.3006993006993007	521	0.6873350923482849	A	0.001	-3.956990	0.00002	0.521848	0.71731	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	4.61	-9.23	0.00672	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.899390	0.09742	N	0.761795	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.08055	0.002;0.0;0.003	T	0.35649	-0.9780	9	0.02654	T	1	-8.8278	13.2063	0.59798	0.1088:0.5911:0.3001:0.0	rs1320303;rs17845440;rs17858312;rs1320303	64;227;227	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	V	227;227;64;62	ENSP00000293350:L227V;ENSP00000410142:L227V;ENSP00000445088:L64V;ENSP00000398675:L62V	ENSP00000293350:L227V	L	+	1	0	ALDH16A1	54656789	0.000000	0.05858	0.184000	0.23157	0.060000	0.15804	-3.278000	0.00529	-2.738000	0.00380	-0.343000	0.07986	CTC	C|0.422;G|0.578	0.578	strong		0.726	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
ZNF83	55769	hgsc.bcm.edu	37	19	53116643	53116643	+	Missense_Mutation	SNP	T	T	C	rs11545619	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53116643T>C	ENST00000597597.1	-	2	3428	c.1175A>G	c.(1174-1176)cAc>cGc	p.H392R	ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000544146.1_Missense_Mutation_p.H392R|ZNF83_ENST00000301096.3_Missense_Mutation_p.H392R|ZNF83_ENST00000541777.2_Missense_Mutation_p.H392R|ZNF83_ENST00000545872.1_Missense_Mutation_p.H392R|ZNF83_ENST00000536937.1_Missense_Mutation_p.H392R|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000391789.4_Missense_Mutation_p.H364R			P51522	ZNF83_HUMAN	zinc finger protein 83	392			H -> R (in dbSNP:rs11545619). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		ATGGATTCTGTGATGTTGTAC	0.373													C|||	457	0.091254	0.1505	0.0562	5008	,	,		23594	0.0625		0.0964	False		,,,				2504	0.0603				p.H392R		Atlas-SNP	.											.	ZNF83	73	.	0			c.A1175G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	693,3713		52,589,1562	111.0	106.0	108.0		1175,1175,1175,1175,1091,1091,1091,1091,1175	-0.9	0.0	19	dbSNP_120	108	777,7823		33,711,3556	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	ZNF83	NM_001105549.1,NM_001105550.1,NM_001105551.1,NM_001105552.1,NM_001105553.1,NM_001105554.1,NM_001242531.1,NM_001242538.1,NM_018300.3	29,29,29,29,29,29,29,29,29	85,1300,5118	CC,CT,TT		9.0349,15.7286,11.3025	benign,benign,benign,benign,benign,benign,benign,benign,benign	392/517,392/517,392/517,392/517,364/489,364/489,364/489,364/489,392/517	53116643	1470,11536	2203	4300	6503	SO:0001583	missense	55769	exon3			ATTCTGTGATGTT	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.1175A>G	19.37:g.53116643T>C	ENSP00000472619:p.His392Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	37	CCDS12854.1	233	0.10668498168498168	95	0.19308943089430894	23	0.06353591160220995	39	0.06818181818181818	76	0.10026385224274406	-	0.027	-1.361672	0.01235	0.157286	0.090349	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000434535;ENST00000545872;ENST00000541777;ENST00000391789	T;T;T;T;T;T	0.07216	3.21;3.21;3.21;3.21;3.21;3.21	2.16	-0.898	0.10550	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45920	-0.9228	8	0.48119	T	0.1	.	7.5047	0.27538	0.0:0.2925:0.0:0.7075	rs11545619;rs17855685;rs52799426;rs60024569;rs11545619	364;392	P51522-2;P51522	.;ZNF83_HUMAN	R	392;392;392;364;392;392;364	ENSP00000445993:H392R;ENSP00000301096:H392R;ENSP00000445470:H392R;ENSP00000440713:H392R;ENSP00000439681:H392R;ENSP00000375666:H364R	ENSP00000301096:H392R	H	-	2	0	ZNF83	57808455	0.000000	0.05858	0.000000	0.03702	0.224000	0.24922	-1.005000	0.03674	-0.992000	0.03472	-0.492000	0.04666	CAC	T|0.885;C|0.115	0.115	strong		0.373	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
RPS4X	6191	hgsc.bcm.edu	37	X	71493691	71493691	+	Silent	SNP	C	C	T	rs7580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:71493691C>T	ENST00000316084.6	-	5	596	c.492G>A	c.(490-492)ttG>ttA	p.L164L	RPS4X_ENST00000486733.1_5'UTR	NM_001007.4	NP_000998.1	P62701	RS4X_HUMAN	ribosomal protein S4, X-linked	164					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of cell proliferation (GO:0008284)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			NS(1)|large_intestine(1)	2	Renal(35;0.156)					TGCCAGTCTCCAAATCAATCT	0.478													C|||	1144	0.303046	0.0726	0.3718	3775	,	,		14042	0.0089		0.5636	False		,,,				2504	0.2188				p.L164L		Atlas-SNP	.											.	RPS4X	20	.	0			c.G492A						PASS	.	C		624,3211		45,446,88,1141,483	60.0	45.0	50.0		492	2.5	1.0	X	dbSNP_52	50	5150,1576		1442,851,1415,134,457	no	coding-synonymous	RPS4X	NM_001007.4		1487,1297,1503,1275,940	TT,TC,T,CC,C		23.4315,16.2712,45.3271		164/264	71493691	5774,4787	2203	4299	6502	SO:0001819	synonymous_variant	6191	exon5			AGTCTCCAAATCA		CCDS14418.1	Xq13.1	2011-04-05			ENSG00000198034	ENSG00000198034		"""S ribosomal proteins"""	10424	protein-coding gene	gene with protein product	"""40S ribosomal protein S4, X isoform"", ""ribosomal protein S4X isoform"", ""single-copy abundant mRNA"", ""cell cycle gene 2"""	312760				1795030, 8139551	Standard	NM_001007		Approved	DXS306, CCG2, SCAR, SCR10, FLJ40595, RPS4, S4	uc004ear.3	P62701	OTTHUMG00000021813	ENST00000316084.6:c.492G>A	X.37:g.71493691C>T		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_001007	P12631|P12750|P27576|P55831|Q14727|Q6IPY4	Silent	SNP	ENST00000316084.6	37	CCDS14418.1																																																																																			C|0.526;T|0.474	0.474	strong		0.478	RPS4X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057188.1	NM_001007	
SH3RF3	344558	hgsc.bcm.edu	37	2	110065649	110065649	+	Missense_Mutation	SNP	C	C	G	rs201796718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:110065649C>G	ENST00000309415.6	+	8	1852	c.1852C>G	c.(1852-1854)Cag>Gag	p.Q618E		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	618							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						AGCCCAGGCTCAGGACCGGCC	0.647													C|||	4	0.000798722	0.0	0.0029	5008	,	,		16125	0.0		0.002	False		,,,				2504	0.0				p.Q618E		Atlas-SNP	.											.	SH3RF3	62	.	0			c.C1852G						PASS	.	C	GLU/GLN	7,4313		0,7,2153	18.0	24.0	22.0		1852	5.2	0.4	2		22	31,8479		0,31,4224	yes	missense	SH3RF3	NM_001099289.1	29	0,38,6377	GG,GC,CC		0.3643,0.162,0.2962	benign	618/883	110065649	38,12792	2160	4255	6415	SO:0001583	missense	344558	exon8			CAGGCTCAGGACC	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"""RING-type (C3HC4) zinc fingers"""	24699	protein-coding gene	gene with protein product			"""SH3 multiple domains 4"""	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.1852C>G	2.37:g.110065649C>G	ENSP00000309186:p.Gln618Glu	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	216	120	0.555556	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		.	.	.	.	.	.	.	.	.	.	C	10.24	1.295937	0.23564	0.00162	0.003643	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.58210	0.35;2.12	5.15	5.15	0.70609	.	0.409870	0.27294	N	0.020036	T	0.48732	0.1516	.	.	.	0.28576	N	0.910391	P	0.45428	0.858	P	0.46389	0.515	T	0.40384	-0.9566	9	0.13108	T	0.6	-22.3701	18.8174	0.92081	0.0:1.0:0.0:0.0	.	618	Q8TEJ3	SH3R3_HUMAN	E	618	ENSP00000414997:Q618E;ENSP00000309186:Q618E	ENSP00000309186:Q618E	Q	+	1	0	SH3RF3	109432081	0.996000	0.38824	0.421000	0.26609	0.136000	0.21042	3.743000	0.55104	2.680000	0.91292	0.655000	0.94253	CAG	C|0.999;G|0.001	0.001	weak		0.647	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289	
ANO9	338440	hgsc.bcm.edu	37	11	419706	419706	+	Missense_Mutation	SNP	T	T	C	rs114405390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:419706T>C	ENST00000332826.6	-	20	1894	c.1810A>G	c.(1810-1812)Acc>Gcc	p.T604A	SIGIRR_ENST00000332725.3_5'Flank|SIGIRR_ENST00000382520.2_5'Flank|SIGIRR_ENST00000397632.3_5'Flank	NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	604					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						ACACCGATGGTCTCCAGCACC	0.617													T|||	75	0.014976	0.0008	0.049	5008	,	,		19185	0.0		0.0328	False		,,,				2504	0.0072				p.T604A		Atlas-SNP	.											.	ANO9	61	.	0			c.A1810G						PASS	.	T	ALA/THR	42,4362	44.6+/-78.6	0,42,2160	110.0	88.0	96.0		1810	3.2	1.0	11	dbSNP_132	96	259,8339	100.1+/-161.6	4,251,4044	yes	missense	ANO9	NM_001012302.2	58	4,293,6204	CC,CT,TT		3.0123,0.9537,2.315	benign	604/783	419706	301,12701	2202	4299	6501	SO:0001583	missense	338440	exon20			CGATGGTCTCCAG	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	20679	protein-coding gene	gene with protein product			"""tumor protein p53 inducible protein 5"", ""transmembrane protein 16J"""	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.1810A>G	11.37:g.419706T>C	ENSP00000332788:p.Thr604Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	37	CCDS31326.1	34	0.015567765567765568	0	0.0	12	0.03314917127071823	0	0.0	22	0.029023746701846966	T	12.77	2.038447	0.35989	0.009537	0.030123	ENSG00000185101	ENST00000332826	T	0.61742	0.08	4.55	3.23	0.37069	.	0.323437	0.29314	N	0.012507	T	0.10035	0.0246	N	0.04959	-0.14	0.37837	D	0.928917	B;B	0.12013	0.001;0.005	B;B	0.15052	0.004;0.012	T	0.09509	-1.0671	10	0.13108	T	0.6	.	3.2512	0.06815	0.0:0.4065:0.0:0.5935	.	305;604	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	A	604	ENSP00000332788:T604A	ENSP00000332788:T604A	T	-	1	0	ANO9	409706	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	4.011000	0.57124	1.833000	0.53350	0.379000	0.24179	ACC	T|0.980;C|0.020	0.020	strong		0.617	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302	
OR1I1	126370	hgsc.bcm.edu	37	19	15198851	15198851	+	Silent	SNP	A	A	T	rs16980313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198851A>T	ENST00000209540.2	+	1	1061	c.975A>T	c.(973-975)ccA>ccT	p.P325P		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	325						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						atcatgttccaggatcactgt	0.517													A|||	912	0.182109	0.0242	0.219	5008	,	,		21835	0.2371		0.17	False		,,,				2504	0.3252				p.P325P		Atlas-SNP	.											.	OR1I1	58	.	0			c.A975T						PASS	.	A		203,4203	125.3+/-162.5	3,197,2003	81.0	59.0	66.0		975	-0.2	0.0	19	dbSNP_123	66	1455,7145	274.3+/-291.2	108,1239,2953	no	coding-synonymous	OR1I1	NM_001004713.1		111,1436,4956	TT,TA,AA		16.9186,4.6074,12.748		325/356	15198851	1658,11348	2203	4300	6503	SO:0001819	synonymous_variant	126370	exon1			TGTTCCAGGATCA	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.975A>T	19.37:g.15198851A>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	148	70	0.472973	NM_001004713	Q96R92	Silent	SNP	ENST00000209540.2	37	CCDS32937.1																																																																																			A|0.869;T|0.131	0.131	strong		0.517	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
ANKMY1	51281	hgsc.bcm.edu	37	2	241451350	241451350	+	Silent	SNP	C	C	T	rs10427348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:241451350C>T	ENST00000272972.3	-	10	2161	c.1947G>A	c.(1945-1947)acG>acA	p.T649T	ANKMY1_ENST00000406958.1_Silent_p.T410T|ANKMY1_ENST00000401804.1_Silent_p.T738T|ANKMY1_ENST00000391987.1_Silent_p.T649T|ANKMY1_ENST00000403283.1_Silent_p.T587T|ANKMY1_ENST00000361678.4_Intron|ANKMY1_ENST00000373320.4_Silent_p.T419T|ANKMY1_ENST00000373318.2_Silent_p.T508T	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	649			T -> M (in dbSNP:rs35044862).				metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		GGGCTGTGTCCGTGCTGTAGT	0.672													C|||	391	0.0780751	0.0658	0.098	5008	,	,		18680	0.0069		0.1541	False		,,,				2504	0.0757				p.T649T		Atlas-SNP	.											.	ANKMY1	112	.	0			c.G1947A						PASS	.	C	,	379,4027	191.2+/-216.9	18,343,1842	61.0	61.0	61.0		1947,	-6.3	0.0	2	dbSNP_119	61	1435,7165	275.6+/-291.8	119,1197,2984	no	coding-synonymous,intron	ANKMY1	NM_016552.2,NM_017844.2	,	137,1540,4826	TT,TC,CC		16.686,8.6019,13.9474	,	649/942,	241451350	1814,11192	2203	4300	6503	SO:0001819	synonymous_variant	51281	exon10			TGTGTCCGTGCTG	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1947G>A	2.37:g.241451350C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Silent	SNP	ENST00000272972.3	37	CCDS2536.1																																																																																			C|0.881;T|0.119	0.119	strong		0.672	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
PEX14	5195	hgsc.bcm.edu	37	1	10689942	10689942	+	Silent	SNP	G	G	T	rs11539794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:10689942G>T	ENST00000356607.4	+	9	1112	c.1032G>T	c.(1030-1032)ggG>ggT	p.G344G	PEX14_ENST00000538836.1_Silent_p.G280G	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	344					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		ACTGCCTGGGGGTGCAGAGGG	0.657													G|||	519	0.103634	0.0197	0.1326	5008	,	,		16747	0.0228		0.1948	False		,,,				2504	0.1861				p.G344G		Atlas-SNP	.											PEX14,NS,carcinoma,0,1	PEX14	40	1	0			c.G1032T						PASS	.	G		200,4202	123.7+/-161.0	3,194,2004	183.0	190.0	188.0		1032	0.2	1.0	1	dbSNP_120	188	1631,6969	298.5+/-303.9	148,1335,2817	no	coding-synonymous	PEX14	NM_004565.2		151,1529,4821	TT,TG,GG		18.9651,4.5434,14.0824		344/378	10689942	1831,11171	2201	4300	6501	SO:0001819	synonymous_variant	5195	exon9			CCTGGGGGTGCAG	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.1032G>T	1.37:g.10689942G>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			G|0.875;T|0.125	0.125	strong		0.657	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
LONRF3	79836	hgsc.bcm.edu	37	X	118108785	118108785	+	Silent	SNP	T	T	C	rs3813933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:118108785T>C	ENST00000371628.3	+	1	73	c.42T>C	c.(40-42)gcT>gcC	p.A14A	LONRF3_ENST00000422289.2_5'Flank|LONRF3_ENST00000304778.7_Silent_p.A14A	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	14							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GCTTGCCCGCTGAGGTCAGCA	0.647													C|||	1898	0.502781	0.2247	0.464	3775	,	,		12076	0.5923		0.327	False		,,,				2504	0.3609				p.A14A		Atlas-SNP	.											.	LONRF3	138	.	0			c.T42C						PASS	.	C	,	1211,2620		174,681,182,777,385	24.0	19.0	20.0		42,42	-1.1	0.5	X	dbSNP_107	20	2862,3854		444,1178,796,804,1068	no	coding-synonymous,coding-synonymous	LONRF3	NM_001031855.1,NM_024778.4	,	618,1859,978,1581,1453	CC,CT,C,TT,T		42.6147,31.6105,38.6176	,	14/760,14/719	118108785	4073,6474	2199	4290	6489	SO:0001819	synonymous_variant	79836	exon1			GCCCGCTGAGGTC	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.42T>C	X.37:g.118108785T>C		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Silent	SNP	ENST00000371628.3	37	CCDS35374.1																																																																																			T|0.560;C|0.440	0.440	strong		0.647	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
SULT1A1	6817	hgsc.bcm.edu	37	16	28617552	28617552	+	Silent	SNP	C	C	G	rs3176926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28617552C>G	ENST00000395607.1	-	7	873	c.600G>C	c.(598-600)ccG>ccC	p.P200P	SULT1A1_ENST00000314752.7_Silent_p.P200P|SULT1A1_ENST00000395609.1_Silent_p.P200P|SULT1A1_ENST00000350842.4_Silent_p.P122P|SULT1A1_ENST00000569554.1_Silent_p.P200P	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	200					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)			endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	TCTCCCTTTTCGGGTTCTGAG	0.547																																					p.P200P		Atlas-SNP	.											.	SULT1A1	53	.	0			c.G600C						PASS	.						82.0	61.0	68.0					16																	28617552		2197	4300	6497	SO:0001819	synonymous_variant	6817	exon6			CCTTTTCGGGTTC	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.600G>C	16.37:g.28617552C>G		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	631	143	0.226624	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Silent	SNP	ENST00000395607.1	37	CCDS32420.1																																																																																			C|0.646;G|0.354	0.354	strong		0.547	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
AURKB	9212	hgsc.bcm.edu	37	17	8108331	8108331	+	Missense_Mutation	SNP	A	A	G	rs1059476	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8108331A>G	ENST00000585124.1	-	9	986	c.893T>C	c.(892-894)aTg>aCg	p.M298T	AURKB_ENST00000534871.1_Missense_Mutation_p.M257T|AURKB_ENST00000316199.6_Missense_Mutation_p.M299T|AURKB_ENST00000578549.1_Missense_Mutation_p.M266T|AURKB_ENST00000535053.1_3'UTR	NM_004217.3	NP_004208.2	Q96GD4	AURKB_HUMAN	aurora kinase B	298	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		M -> T (in dbSNP:rs1059476). {ECO:0000269|PubMed:11471245, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16762494, ECO:0000269|PubMed:9514916, ECO:0000269|PubMed:9809983, ECO:0000269|PubMed:9858806, ECO:0000269|Ref.5, ECO:0000269|Ref.7}.		abscission (GO:0009838)|aging (GO:0007568)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|attachment of spindle microtubules to kinetochore (GO:0008608)|cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|cleavage furrow formation (GO:0036089)|cytokinesis checkpoint (GO:0031565)|histone H3-S28 phosphorylation (GO:0043988)|histone modification (GO:0016570)|mitotic cell cycle (GO:0000278)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytokinesis (GO:0032467)|protein autophosphorylation (GO:0046777)|protein localization to kinetochore (GO:0034501)|protein phosphorylation (GO:0006468)|regulation of chromosome segregation (GO:0051983)|spindle checkpoint (GO:0031577)|spindle midzone assembly involved in mitosis (GO:0051256)|spindle stabilization (GO:0043146)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|central_nervous_system(1)|lung(2)	4						CTGGGCTCCCATGGGCACGGA	0.592													G|||	3686	0.736022	0.6407	0.8141	5008	,	,		15155	0.5516		0.8827	False		,,,				2504	0.8487				p.M298T	NSCLC(134;1161 2470 43664 51568)	Atlas-SNP	.											AURKB_ENST00000316199,colon,carcinoma,+1,2	AURKB	47	2	0			c.T893C						PASS	.	G	THR/MET	3096,1310	441.6+/-346.4	1092,912,199	67.0	62.0	64.0		893	-1.9	0.0	17	dbSNP_86	64	7593,1007	216.7+/-255.6	3361,871,68	yes	missense	AURKB	NM_004217.2	81	4453,1783,267	GG,GA,AA		11.7093,29.7322,17.8149	benign	298/345	8108331	10689,2317	2203	4300	6503	SO:0001583	missense	9212	exon9			GCTCCCATGGGCA	AF004022	CCDS11134.1, CCDS58514.1, CCDS67162.1	17p13.1	2013-01-17	2003-07-21	2003-07-23	ENSG00000178999	ENSG00000178999		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	11390	protein-coding gene	gene with protein product	"""aurora-B"", ""aurora-1"", ""protein phosphatase 1, regulatory subunit 48"""	604970	"""serine/threonine kinase 12"""	STK12		9858806	Standard	NM_001256834		Approved	Aik2, IPL1, AurB, AIM-1, ARK2, STK5, PPP1R48	uc002gkm.4	Q96GD4	OTTHUMG00000108189	ENST00000585124.1:c.893T>C	17.37:g.8108331A>G	ENSP00000463999:p.Met298Thr	Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	191	191	1	NM_004217	B4DNM4|C7G533|C7G534|C7G535|D3DTR4|J9JID1|O14630|O60446|O95083|Q96DV5|Q9UQ46	Missense_Mutation	SNP	ENST00000585124.1	37	CCDS11134.1	1636	0.7490842490842491	301	0.6117886178861789	297	0.8204419889502762	354	0.6188811188811189	684	0.9023746701846965	G	0.092	-1.165487	0.01673	0.702678	0.882907	ENSG00000178999	ENST00000316199;ENST00000534871	T	0.63913	-0.07	4.91	-1.93	0.07594	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.618130	0.03306	N	0.189864	T	0.00012	0.0000	N	0.04245	-0.25	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32214	-0.9915	9	0.22706	T	0.39	-22.7558	4.479	0.11757	0.4618:0.0:0.2863:0.2519	rs1059476;rs3169876;rs17433751;rs58319271;rs1059476	298;298	C7G533;Q96GD4	.;AURKB_HUMAN	T	298;257	ENSP00000443869:M257T	ENSP00000313950:M298T	M	-	2	0	AURKB	8049056	0.001000	0.12720	0.000000	0.03702	0.153000	0.21895	1.251000	0.32862	-0.814000	0.04352	-1.234000	0.01563	ATG	A|0.222;G|0.778	0.778	strong		0.592	AURKB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000226995.2	NM_004217	
FYCO1	79443	hgsc.bcm.edu	37	3	46008790	46008790	+	Missense_Mutation	SNP	G	G	A	rs3796375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:46008790G>A	ENST00000296137.2	-	8	2241	c.2036C>T	c.(2035-2037)gCg>gTg	p.A679V	FYCO1_ENST00000535325.1_Missense_Mutation_p.A679V	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	679			A -> V (in dbSNP:rs3796375). {ECO:0000269|PubMed:17974005}.		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CAGCAAGCTCGCCTCCATCTG	0.617													G|||	1979	0.395168	0.093	0.5648	5008	,	,		18181	0.6607		0.4314	False		,,,				2504	0.3722				p.A679V		Atlas-SNP	.											.	FYCO1	115	.	0			c.C2036T						PASS	.	G	VAL/ALA	626,3780	268.6+/-268.5	47,532,1624	67.0	72.0	71.0		2036	3.5	0.9	3	dbSNP_107	71	3706,4892	521.8+/-380.0	808,2090,1401	yes	missense	FYCO1	NM_024513.2	64	855,2622,3025	AA,AG,GG		43.103,14.2079,33.3128	possibly-damaging	679/1479	46008790	4332,8672	2203	4299	6502	SO:0001583	missense	79443	exon8			AAGCTCGCCTCCA	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.2036C>T	3.37:g.46008790G>A	ENSP00000296137:p.Ala679Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	933	0.4271978021978022	45	0.09146341463414634	198	0.5469613259668509	363	0.6346153846153846	327	0.4313984168865435	G	15.03	2.711650	0.48517	0.142079	0.43103	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21031	2.03;2.03	5.53	3.55	0.40652	.	0.182612	0.45867	N	0.000338	T	0.00012	0.0000	L	0.57536	1.79	0.37551	P	0.08129600000000003	D;D	0.60160	0.984;0.987	B;B	0.43155	0.41;0.356	T	0.35475	-0.9787	9	0.33141	T	0.24	-16.3376	6.1101	0.20096	0.0989:0.0:0.5877:0.3134	rs3796375;rs57674943;rs3796375	679;679	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	V	679	ENSP00000296137:A679V;ENSP00000441178:A679V	ENSP00000296137:A679V	A	-	2	0	FYCO1	45983794	0.998000	0.40836	0.871000	0.34182	0.819000	0.46315	2.820000	0.48057	1.331000	0.45412	0.655000	0.94253	GCG	G|0.650;A|0.350	0.350	strong		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
NLRP8	126205	hgsc.bcm.edu	37	19	56467281	56467281	+	Silent	SNP	A	A	G	rs61750024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56467281A>G	ENST00000291971.3	+	3	1928	c.1857A>G	c.(1855-1857)gaA>gaG	p.E619E	NLRP8_ENST00000590542.1_Silent_p.E619E	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	619					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		TCCGGGAGGAAGCCTTTGTAA	0.458													A|||	273	0.0545128	0.062	0.0533	5008	,	,		19188	0.005		0.0736	False		,,,				2504	0.0767				p.E619E		Atlas-SNP	.											.	NLRP8	225	.	0			c.A1857G						PASS	.	A		302,4104	164.4+/-196.0	11,280,1912	94.0	88.0	90.0		1857	-2.7	0.1	19	dbSNP_129	90	532,8068	148.2+/-203.4	18,496,3786	no	coding-synonymous	NLRP8	NM_176811.2		29,776,5698	GG,GA,AA		6.186,6.8543,6.4124		619/1049	56467281	834,12172	2203	4300	6503	SO:0001819	synonymous_variant	126205	exon3			GGAGGAAGCCTTT	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.1857A>G	19.37:g.56467281A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	186	97	0.521505	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																			A|0.939;G|0.061	0.061	strong		0.458	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
JAKMIP2	9832	hgsc.bcm.edu	37	5	147012291	147012291	+	Silent	SNP	G	G	A	rs3763094	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147012291G>A	ENST00000265272.5	-	13	2195	c.1728C>T	c.(1726-1728)gaC>gaT	p.D576D	JAKMIP2_ENST00000333010.6_Silent_p.D534D|JAKMIP2_ENST00000507386.1_Silent_p.D555D	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	576						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCTCTGGCGTCCTGTAGTT	0.368													G|||	787	0.157149	0.0212	0.2233	5008	,	,		18120	0.2073		0.1551	False		,,,				2504	0.2444				p.D576D		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.C1728T						PASS	.	G		170,4236	111.2+/-149.4	3,164,2036	226.0	223.0	224.0		1728	3.4	1.0	5	dbSNP_107	224	1133,7467	234.2+/-267.2	69,995,3236	no	coding-synonymous	JAKMIP2	NM_014790.3		72,1159,5272	AA,AG,GG		13.1744,3.8584,10.0185		576/811	147012291	1303,11703	2203	4300	6503	SO:0001819	synonymous_variant	9832	exon13			TCTGGCGTCCTGT	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1728C>T	5.37:g.147012291G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	179	118	0.659218	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																			G|0.876;A|0.124	0.124	strong		0.368	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
POLQ	10721	hgsc.bcm.edu	37	3	121238863	121238863	+	Silent	SNP	C	C	T	rs35766343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121238863C>T	ENST00000264233.5	-	9	1451	c.1323G>A	c.(1321-1323)gcG>gcA	p.A441A	POLQ_ENST00000488282.1_5'Flank	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	441	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TAGAAGTTGCCGCCAAGACCC	0.398								DNA polymerases (catalytic subunits)					C|||	243	0.0485224	0.087	0.062	5008	,	,		16043	0.001		0.0537	False		,,,				2504	0.0307				p.A441A	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G1323A						PASS	.	C		404,4002	197.4+/-221.5	15,374,1814	90.0	99.0	96.0		1323	1.7	1.0	3	dbSNP_126	96	459,8141	137.6+/-194.5	12,435,3853	no	coding-synonymous	POLQ	NM_199420.3		27,809,5667	TT,TC,CC		5.3372,9.1693,6.6354		441/2591	121238863	863,12143	2203	4300	6503	SO:0001819	synonymous_variant	10721	exon9			AGTTGCCGCCAAG	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.1323G>A	3.37:g.121238863C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	207	106	0.512077	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																			C|0.939;T|0.061	0.061	strong		0.398	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
PIM3	415116	hgsc.bcm.edu	37	22	50354819	50354819	+	Silent	SNP	C	C	A	rs11541025	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50354819C>A	ENST00000360612.4	+	2	567	c.132C>A	c.(130-132)gcC>gcA	p.A44A		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	44	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		AGGTGGGCGCCGTGCTGGGTA	0.766													c|||	1862	0.371805	0.3676	0.2867	5008	,	,		6787	0.3383		0.2922	False		,,,				2504	0.5542				p.A44A		Atlas-SNP	.											.	PIM3	15	.	0			c.C132A						PASS	.	G		1402,2728		306,790,969	6.0	6.0	6.0		132	-4.2	0.3	22	dbSNP_120	6	2589,5681		503,1583,2049	no	coding-synonymous	PIM3	NM_001001852.3		809,2373,3018	AA,AC,CC		31.3059,33.9467,32.1855		44/327	50354819	3991,8409	2065	4135	6200	SO:0001819	synonymous_variant	415116	exon2			GGGCGCCGTGCTG	BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"""pim-3 oncogene"""			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.132C>A	22.37:g.50354819C>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_001001852	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Silent	SNP	ENST00000360612.4	37	CCDS33678.1																																																																																			C|0.669;A|0.331	0.331	strong		0.766	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852	
ASAP2	8853	hgsc.bcm.edu	37	2	9491017	9491017	+	Silent	SNP	C	C	T	rs4669385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:9491017C>T	ENST00000281419.3	+	12	1444	c.1104C>T	c.(1102-1104)ctC>ctT	p.L368L	ASAP2_ENST00000315273.4_Silent_p.L368L	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	368	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						GCTTTGACCTCATTTCACGTA	0.502													T|||	4412	0.88099	0.677	0.9611	5008	,	,		20584	0.9196		0.998	False		,,,				2504	0.9397				p.L368L		Atlas-SNP	.											.	ASAP2	91	.	0			c.C1104T						PASS	.	T	,	3242,1164	410.6+/-335.4	1204,834,165	83.0	65.0	72.0		1104,1104	-5.9	0.9	2	dbSNP_111	72	8577,23	14.6+/-50.1	4277,23,0	no	coding-synonymous,coding-synonymous	ASAP2	NM_001135191.1,NM_003887.2	,	5481,857,165	TT,TC,CC		0.2674,26.4185,9.1266	,	368/962,368/1007	9491017	11819,1187	2203	4300	6503	SO:0001819	synonymous_variant	8853	exon12			TGACCTCATTTCA	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2721	protein-coding gene	gene with protein product	"""centaurin, beta 3"""	603817	"""development and differentiation enhancing factor 2"""	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1104C>T	2.37:g.9491017C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001135191	D6W4Y8	Silent	SNP	ENST00000281419.3	37	CCDS1661.1																																																																																			C|0.109;T|0.891	0.891	strong		0.502	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887	
LARS	51520	hgsc.bcm.edu	37	5	145506100	145506100	+	Silent	SNP	G	G	A	rs11540216	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145506100G>A	ENST00000394434.2	-	28	3055	c.2889C>T	c.(2887-2889)aaC>aaT	p.N963N	LARS_ENST00000545646.1_Silent_p.N917N|LARS_ENST00000274562.9_Silent_p.N936N|LARS_ENST00000510191.1_Silent_p.N909N	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	963					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	GCAGTTTTCCGTTATTGGCCT	0.408													G|||	213	0.0425319	0.0582	0.0317	5008	,	,		21246	0.0		0.0726	False		,,,				2504	0.0419				p.N963N		Atlas-SNP	.											.	LARS	100	.	0			c.C2889T						PASS	.	G		244,4162	141.5+/-176.9	4,236,1963	130.0	108.0	116.0		2889	2.8	0.8	5	dbSNP_120	116	641,7957	163.8+/-216.2	32,577,3690	no	coding-synonymous	LARS	NM_020117.9		36,813,5653	AA,AG,GG		7.4552,5.5379,6.8056		963/1177	145506100	885,12119	2203	4299	6502	SO:0001819	synonymous_variant	51520	exon28			TTTTCCGTTATTG	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2889C>T	5.37:g.145506100G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	177	105	0.59322	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			G|0.767;T|0.009	.	strong		0.408	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
EGFL6	25975	hgsc.bcm.edu	37	X	13635937	13635937	+	Silent	SNP	C	C	T	rs5978653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:13635937C>T	ENST00000361306.1	+	8	1124	c.867C>T	c.(865-867)agC>agT	p.S289S	EGFL6_ENST00000380602.3_Silent_p.S289S	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	289					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						ACAAAAACAGCATGAAAAAGA	0.408													C|||	251	0.0664901	0.0461	0.0346	3775	,	,		13027	0.0962		0.0378	False		,,,				2504	0.0317				p.S289S		Atlas-SNP	.											.	EGFL6	111	.	0			c.C867T						PASS	.	C	,	194,3641		3,156,32,1473,539	103.0	102.0	102.0		867,867	3.7	1.0	X	dbSNP_114	102	429,6299		8,281,132,2139,1740	no	coding-synonymous,coding-synonymous	EGFL6	NM_001167890.1,NM_015507.3	,	11,437,164,3612,2279	TT,TC,T,CC,C		6.3763,5.0587,5.8979	,	289/555,289/554	13635937	623,9940	2203	4300	6503	SO:0001819	synonymous_variant	25975	exon8			AAACAGCATGAAA	AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"""MAM and EGF domain containing"""	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.867C>T	X.37:g.13635937C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Silent	SNP	ENST00000361306.1	37	CCDS14155.1																																																																																			C|0.938;T|0.062	0.062	strong		0.408	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507	
SYNPO2	171024	hgsc.bcm.edu	37	4	119944611	119944611	+	Silent	SNP	G	G	T	rs1459058	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:119944611G>T	ENST00000429713.2	+	2	314	c.132G>T	c.(130-132)ggG>ggT	p.G44G	SYNPO2_ENST00000434046.2_Silent_p.G44G|SYNPO2_ENST00000448416.2_Silent_p.G44G|SYNPO2_ENST00000307142.4_Silent_p.G44G	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	44	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AAGCCTCTGGGTCTGGGCTCT	0.433													G|||	2063	0.411941	0.1906	0.4784	5008	,	,		17996	0.4524		0.503	False		,,,				2504	0.5286				p.G44G		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G132T						PASS	.	G	,,	1018,3388	377.1+/-322.3	129,760,1314	92.0	77.0	82.0		132,132,132	0.8	0.7	4	dbSNP_88	82	4276,4324	575.3+/-390.2	1049,2178,1073	no	coding-synonymous,coding-synonymous,coding-synonymous	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	,,	1178,2938,2387	TT,TG,GG		49.7209,23.1049,40.7043	,,	44/1094,44/1110,44/1262	119944611	5294,7712	2203	4300	6503	SO:0001819	synonymous_variant	171024	exon2			CTCTGGGTCTGGG	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.132G>T	4.37:g.119944611G>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	196	103	0.52551	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Silent	SNP	ENST00000429713.2	37	CCDS47129.1																																																																																			G|0.594;T|0.406	0.406	strong		0.433	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
ESRP1	54845	hgsc.bcm.edu	37	8	95690579	95690579	+	Silent	SNP	T	T	C	rs12677519	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95690579T>C	ENST00000433389.2	+	13	1990	c.1800T>C	c.(1798-1800)aaT>aaC	p.N600N	ESRP1_ENST00000454170.2_Silent_p.N600N|ESRP1_ENST00000423620.2_Silent_p.N596N|ESRP1_ENST00000358397.5_Silent_p.N596N	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	600					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						TCTTCATGAATTACACAGCGT	0.502													C|||	2466	0.492412	0.1914	0.5346	5008	,	,		20607	0.5407		0.6223	False		,,,				2504	0.6861				p.N600N		Atlas-SNP	.											.	ESRP1	148	.	0			c.T1800C						PASS	.	C	,,,,	1101,3003		169,763,1120	83.0	79.0	80.0		1788,1800,1788,1788,1800	3.6	1.0	8	dbSNP_120	80	5055,3371		1542,1971,700	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	1711,2734,1820	CC,CT,TT		40.0071,26.8275,49.1301	,,,,	596/678,600/609,596/660,596/605,600/682	95690579	6156,6374	2052	4213	6265	SO:0001819	synonymous_variant	54845	exon13			CATGAATTACACA	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.1800T>C	8.37:g.95690579T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001122825	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1																																																																																			T|0.494;C|0.506	0.506	strong		0.502	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
SESN1	27244	hgsc.bcm.edu	37	6	109323519	109323519	+	Missense_Mutation	SNP	G	G	T	rs2273668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:109323519G>T	ENST00000356644.7	-	2	224	c.130C>A	c.(130-132)Cta>Ata	p.L44I	SESN1_ENST00000302071.2_5'UTR|SESN1_ENST00000436639.2_Missense_Mutation_p.L103I	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	44			L -> I (in dbSNP:rs2273668). {ECO:0000269|PubMed:12607115}.		cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		CCCTGTCCTAGTGGTCGAGGA	0.428													G|||	431	0.0860623	0.0053	0.072	5008	,	,		20704	0.0407		0.1352	False		,,,				2504	0.2014				p.L103I		Atlas-SNP	.											.	SESN1	29	.	0			c.C307A						PASS	.	G	ILE/LEU,,ILE/LEU	106,4300	80.9+/-119.3	3,100,2100	157.0	130.0	139.0		130,,307	5.6	1.0	6	dbSNP_100	139	1004,7596	215.7+/-255.0	72,860,3368	yes	missense,utr-5,missense	SESN1	NM_001199933.1,NM_001199934.1,NM_014454.2	5,,5	75,960,5468	TT,TG,GG		11.6744,2.4058,8.5345	benign,,benign	44/493,,103/552	109323519	1110,11896	2203	4300	6503	SO:0001583	missense	27244	exon2			GTCCTAGTGGTCG	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.130C>A	6.37:g.109323519G>T	ENSP00000349061:p.Leu44Ile	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_014454	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Missense_Mutation	SNP	ENST00000356644.7	37	CCDS56445.1	153	0.07005494505494506	4	0.008130081300813009	26	0.0718232044198895	23	0.04020979020979021	100	0.13192612137203166	G	14.18	2.458009	0.43634	0.024058	0.116744	ENSG00000080546	ENST00000436639;ENST00000356644	T;T	0.19394	2.18;2.15	5.58	5.58	0.84498	.	0.068247	0.64402	D	0.000011	T	0.06600	0.0169	N	0.08118	0	0.51482	D	0.999924	P;B	0.35348	0.496;0.243	B;B	0.34242	0.178;0.06	T	0.29882	-0.9997	10	0.27082	T	0.32	-8.8817	19.5825	0.95473	0.0:0.0:1.0:0.0	rs2273668;rs52836178;rs60044736;rs2273668	103;44	Q9Y6P5-2;Q9Y6P5	.;SESN1_HUMAN	I	103;44	ENSP00000393762:L103I;ENSP00000349061:L44I	ENSP00000349061:L44I	L	-	1	2	SESN1	109430212	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.365000	0.59486	2.624000	0.88883	0.655000	0.94253	CTA	G|0.927;T|0.073	0.073	strong		0.428	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454	
CHRNA3	1136	hgsc.bcm.edu	37	15	78894339	78894339	+	Silent	SNP	G	G	A	rs1051730	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78894339G>A	ENST00000326828.5	-	5	1029	c.645C>T	c.(643-645)taC>taT	p.Y215Y	CHRNA3_ENST00000348639.3_Silent_p.Y215Y	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	215					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	TGTCGTGTTTGTAGCCTGGGG	0.532													G|||	842	0.168131	0.087	0.2161	5008	,	,		17692	0.0268		0.3688	False		,,,				2504	0.183				p.Y215Y		Atlas-SNP	.											.	CHRNA3	56	.	0			c.C645T	GRCh37	CM078027	CHRNA3	M	rs1051730	PASS	.	G	,	529,3863	240.6+/-251.3	28,473,1695	163.0	139.0	147.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	645,645	5.3	1.0	15	dbSNP_86	147	3000,5586	463.5+/-366.0	555,1890,1848	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	583,2363,3543	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.9406,12.0446,27.1922	,	215/506,215/490	78894339	3529,9449	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			GTGTTTGTAGCCT		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.645C>T	15.37:g.78894339G>A		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	253	133	0.525692	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			G|0.754;A|0.246	0.246	strong		0.532	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
SLC12A4	6560	hgsc.bcm.edu	37	16	67979423	67979423	+	Silent	SNP	G	G	T	rs17851876	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:67979423G>T	ENST00000316341.3	-	22	3021	c.2881C>A	c.(2881-2883)Cgg>Agg	p.R961R	SLC12A4_ENST00000576616.1_Silent_p.R961R|SLC12A4_ENST00000572037.1_Silent_p.R913R|SLC12A4_ENST00000541864.2_Silent_p.R930R|LCAT_ENST00000264005.5_5'Flank|SLC12A4_ENST00000422611.2_Silent_p.R963R|CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000537830.2_Silent_p.R955R|SLC12A4_ENST00000338335.3_3'UTR	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	961					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CTCTCCAGCCGCAGGGCCGAG	0.592													G|||	151	0.0301518	0.0008	0.0245	5008	,	,		19721	0.0		0.0646	False		,,,				2504	0.0695				p.R963R		Atlas-SNP	.											.	SLC12A4	81	.	0			c.C2887A						PASS	.	G	,,,,	52,4342	52.9+/-88.7	0,52,2145	60.0	61.0	61.0		2863,2887,2863,2788,2881	3.4	0.9	16	dbSNP_123	61	603,7997	158.6+/-212.1	11,581,3708	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A4	NM_001145961.1,NM_001145962.1,NM_001145963.1,NM_001145964.1,NM_005072.4	,,,,	11,633,5853	TT,TG,GG		7.0116,1.1834,5.0408	,,,,	955/1080,963/1088,955/1080,930/1055,961/1086	67979423	655,12339	2197	4300	6497	SO:0001819	synonymous_variant	6560	exon21			CCAGCCGCAGGGC		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"""Solute carriers"""	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.2881C>A	16.37:g.67979423G>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Silent	SNP	ENST00000316341.3	37	CCDS10855.1																																																																																			G|0.959;T|0.041	0.041	strong		0.592	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072	
ANKRD36	375248	hgsc.bcm.edu	37	2	97860487	97860487	+	Missense_Mutation	SNP	T	T	C	rs59466168	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97860487T>C	ENST00000461153.2	+	39	2718	c.2474T>C	c.(2473-2475)tTg>tCg	p.L825S	ANKRD36_ENST00000420699.2_Missense_Mutation_p.L825S			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	825								p.L825S(1)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						AAACCAGCCTTGAAGGTAATG	0.338																																					p.L825S		Atlas-SNP	.											ANKRD36_ENST00000420699,NS,carcinoma,0,1	ANKRD36	170	1	1	Substitution - Missense(1)	stomach(1)	c.T2474C						scavenged	.																																			SO:0001583	missense	375248	exon39			CAGCCTTGAAGGT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.2474T>C	2.37:g.97860487T>C	ENSP00000419530:p.Leu825Ser	Somatic	22	1	0.0454545		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	6.237	0.411823	0.11812	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000461694	D;D	0.82255	-1.59;-1.59	0.649	-1.05	0.10036	.	.	.	.	.	T	0.66446	0.2790	L	0.34521	1.04	0.58432	P	1.0000000000287557E-6	B	0.31893	0.345	B	0.18871	0.023	T	0.56032	-0.8046	7	0.25751	T	0.34	.	.	.	.	rs59466168;rs62154812	825	A6QL64	AN36A_HUMAN	S	825;825;187	ENSP00000419530:L825S;ENSP00000391950:L825S	ENSP00000391950:L825S	L	+	2	0	ANKRD36	97224214	0.001000	0.12720	0.048000	0.18961	0.004000	0.04260	-0.718000	0.04980	-0.323000	0.08602	-1.634000	0.00779	TTG	T|0.500;C|0.500	0.500	strong		0.338	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
DENND1A	57706	hgsc.bcm.edu	37	9	126220114	126220114	+	Silent	SNP	C	C	T	rs61736953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126220114C>T	ENST00000373624.2	-	14	1257	c.1056G>A	c.(1054-1056)agG>agA	p.R352R	DENND1A_ENST00000542603.1_Silent_p.R94R|DENND1A_ENST00000373620.3_Silent_p.R352R|DENND1A_ENST00000394215.2_Silent_p.R322R|DENND1A_ENST00000394219.3_Silent_p.R320R|DENND1A_ENST00000473039.1_Intron|DENND1A_ENST00000373618.1_Silent_p.R320R	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	352	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						GCAGGAACTGCCTCATGGCTC	0.632													C|||	297	0.0593051	0.0946	0.0576	5008	,	,		15802	0.0		0.0686	False		,,,				2504	0.0644				p.R352R		Atlas-SNP	.											.	DENND1A	112	.	0			c.G1056A						PASS	.	C	,	385,4021	187.1+/-213.8	16,353,1834	50.0	44.0	46.0		1056,1056	2.0	1.0	9	dbSNP_129	46	760,7840	177.0+/-226.7	31,698,3571	no	coding-synonymous,coding-synonymous	DENND1A	NM_020946.1,NM_024820.2	,	47,1051,5405	TT,TC,CC		8.8372,8.7381,8.8036	,	352/1010,352/560	126220114	1145,11861	2203	4300	6503	SO:0001819	synonymous_variant	57706	exon14			GAACTGCCTCATG	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1056G>A	9.37:g.126220114C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_024820	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	37	CCDS35133.1																																																																																			C|0.921;T|0.079	0.079	strong		0.632	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
UPK3A	7380	hgsc.bcm.edu	37	22	45683246	45683246	+	Silent	SNP	C	C	T	rs2673088	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45683246C>T	ENST00000216211.4	+	3	434	c.402C>T	c.(400-402)gtC>gtT	p.V134V	UPK3A_ENST00000396082.2_Intron	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	134					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCTACCTGGTCAGGGTGGGTG	0.602													C|||	2745	0.548123	0.233	0.768	5008	,	,		16522	0.5417		0.7316	False		,,,				2504	0.636				p.V134V		Atlas-SNP	.											.	UPK3A	14	.	0			c.C402T						PASS	.	C	,	1400,3006	459.4+/-352.3	234,932,1037	71.0	58.0	62.0		,402	2.2	1.0	22	dbSNP_100	62	6558,2042	718.8+/-406.2	2494,1570,236	no	intron,coding-synonymous	UPK3A	NM_001167574.1,NM_006953.3	,	2728,2502,1273	TT,TC,CC		23.7442,31.7749,38.8129	,	,134/288	45683246	7958,5048	2203	4300	6503	SO:0001819	synonymous_variant	7380	exon3			CCTGGTCAGGGTG	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.402C>T	22.37:g.45683246C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			C|0.404;T|0.596	0.596	strong		0.602	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
DNHD1	144132	hgsc.bcm.edu	37	11	6554941	6554941	+	Missense_Mutation	SNP	C	C	A	rs4282961	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6554941C>A	ENST00000527990.2	+	12	2536	c.2536C>A	c.(2536-2538)Ctg>Atg	p.L846M	DNHD1_ENST00000254579.6_Missense_Mutation_p.L846M			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	846					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GTACGTCGAGCTGGAGGAGCG	0.532													C|||	1069	0.213458	0.1248	0.2882	5008	,	,		21748	0.131		0.3549	False		,,,				2504	0.2198				p.L846M		Atlas-SNP	.											.	DNHD1	198	.	0			c.C2536A						PASS	.	C	MET/LEU	200,1184		19,162,511	68.0	61.0	63.0		2536	4.1	0.7	11	dbSNP_111	63	1063,2119		181,701,709	yes	missense	DNHD1	NM_144666.2	15	200,863,1220	AA,AC,CC		33.4067,14.4509,27.661	probably-damaging	846/4754	6554941	1263,3303	692	1591	2283	SO:0001583	missense	144132	exon14			GTCGAGCTGGAGG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.2536C>A	11.37:g.6554941C>A	ENSP00000436180:p.Leu846Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	121	69	0.570248	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	521	0.23855311355311357	62	0.12601626016260162	111	0.30662983425414364	90	0.15734265734265734	258	0.3403693931398417	C	15.55	2.865728	0.51588	0.144509	0.334067	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.37915	1.17;1.17	5.92	4.05	0.47172	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.42629	P	0.006622000000000017	D	0.89917	1.0	D	0.87578	0.998	T	0.31916	-0.9926	8	0.66056	D	0.02	.	8.7938	0.34868	0.0:0.8283:0.0:0.1717	rs4282961;rs17833604;rs60785446;rs4282961	846	Q96M86	DNHD1_HUMAN	M	846;846;112	ENSP00000254579:L846M;ENSP00000436180:L846M	ENSP00000254579:L846M	L	+	1	2	DNHD1	6511517	0.754000	0.28360	0.699000	0.30290	0.467000	0.32768	1.070000	0.30653	0.829000	0.34733	0.655000	0.94253	CTG	C|0.773;A|0.227	0.227	strong		0.532	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
PLXNC1	10154	hgsc.bcm.edu	37	12	94645255	94645255	+	Silent	SNP	A	A	G	rs2230757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:94645255A>G	ENST00000258526.4	+	15	3081	c.2832A>G	c.(2830-2832)acA>acG	p.T944T		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	944					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TTCCTTCCACATGGTATTTTC	0.463													G|||	3048	0.608626	0.5439	0.6974	5008	,	,		19096	0.7411		0.5706	False		,,,				2504	0.5358				p.T944T		Atlas-SNP	.											.	PLXNC1	135	.	0			c.A2832G						PASS	.	G		2538,1868	538.2+/-374.9	717,1104,382	257.0	209.0	225.0		2832	-4.2	0.6	12	dbSNP_98	225	4750,3850	542.1+/-384.1	1278,2194,828	no	coding-synonymous	PLXNC1	NM_005761.2		1995,3298,1210	GG,GA,AA		44.7674,42.3967,43.9643		944/1569	94645255	7288,5718	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon15			TTCCACATGGTAT	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.2832A>G	12.37:g.94645255A>G		Somatic	290	1	0.00344828		WXS	Illumina HiSeq	Phase_I	348	170	0.488506	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			A|0.420;C|0.000;G|0.580;T|0.000	0.580	strong		0.463	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
CCDC88B	283234	hgsc.bcm.edu	37	11	64117106	64117106	+	Missense_Mutation	SNP	C	C	T	rs144037797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64117106C>T	ENST00000356786.5	+	16	2872	c.2828C>T	c.(2827-2829)aCc>aTc	p.T943I	CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000359902.2_Missense_Mutation_p.T95I	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	943				T -> I (in Ref. 5; AAI41867). {ECO:0000305}.		membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GAGCTCAAGACCAGGGCCCTG	0.662													c|||	37	0.00738818	0.0008	0.0159	5008	,	,		13030	0.0		0.0229	False		,,,				2504	0.002				p.T943I		Atlas-SNP	.											.	CCDC88B	89	.	0			c.C2828T						PASS	.	C	ILE/THR	22,4364		0,22,2171	31.0	37.0	35.0		2828	-5.0	0.0	11	dbSNP_134	35	221,8369		2,217,4076	yes	missense	CCDC88B	NM_032251.5	89	2,239,6247	TT,TC,CC		2.5728,0.5016,1.8727	benign	943/1477	64117106	243,12733	2193	4295	6488	SO:0001583	missense	283234	exon16			TCAAGACCAGGGC	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.2828C>T	11.37:g.64117106C>T	ENSP00000349238:p.Thr943Ile	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	213	103	0.483568	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	37	CCDS8072.2	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	c	12.02	1.812333	0.32053	0.005016	0.025728	ENSG00000168071	ENST00000377638;ENST00000356786;ENST00000359902	T;T	0.47528	1.88;0.84	3.9	-4.97	0.03029	.	.	.	.	.	T	0.08758	0.0217	N	0.22421	0.69	0.20489	N	0.999896	B;P;B;B	0.41910	0.201;0.764;0.358;0.201	B;B;B;B	0.37091	0.055;0.241;0.047;0.055	T	0.09773	-1.0659	9	0.45353	T	0.12	.	3.0486	0.06161	0.2784:0.2118:0.4129:0.0969	.	943;79;592;943	B2RTU8;A6NC98-5;A6NC98-3;A6NC98	.;.;.;CC88B_HUMAN	I	943;943;95	ENSP00000349238:T943I;ENSP00000352974:T95I	ENSP00000349238:T943I	T	+	2	0	CCDC88B	63873682	0.000000	0.05858	0.003000	0.11579	0.973000	0.67179	-1.071000	0.03437	-0.624000	0.05611	0.539000	0.68188	ACC	C|0.987;T|0.013	0.013	strong		0.662	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
PPHLN1	51535	hgsc.bcm.edu	37	12	42840082	42840082	+	Missense_Mutation	SNP	A	A	C	rs149559306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:42840082A>C	ENST00000395568.2	+	12	1424	c.1340A>C	c.(1339-1341)aAc>aCc	p.N447T	PPHLN1_ENST00000256678.8_Missense_Mutation_p.N352T|PPHLN1_ENST00000317560.9_Intron|PPHLN1_ENST00000432191.2_Missense_Mutation_p.N423T	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	447					keratinization (GO:0031424)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	16	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		gtacattgcaactcacgcaag	0.433													A|||	11	0.00219649	0.0	0.0043	5008	,	,		17538	0.0		0.008	False		,,,				2504	0.0				p.N447T		Atlas-SNP	.											.	PPHLN1	101	.	0			c.A1340C						PASS	.	A	THR/ASN,THR/ASN	9,4163		0,9,2077	32.0	34.0	33.0		1268,1340	0.2	0.1	12	dbSNP_134	33	69,8029		0,69,3980	yes	missense,missense	PPHLN1	NM_001143787.1,NM_016488.6	65,65	0,78,6057	CC,CA,AA		0.8521,0.2157,0.6357	possibly-damaging,possibly-damaging	423/435,447/459	42840082	78,12192	2086	4049	6135	SO:0001583	missense	51535	exon12			ATTGCAACTCACG	AY157850	CCDS8741.1, CCDS31777.1, CCDS41773.1, CCDS44860.1, CCDS44861.1, CCDS55817.1	12q12	2006-10-24				ENSG00000134283			19369	protein-coding gene	gene with protein product		608150					Standard	NM_016488		Approved		uc001rng.1	Q8NEY8		ENST00000395568.2:c.1340A>C	12.37:g.42840082A>C	ENSP00000378935:p.Asn447Thr	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	18	6	0.333333	NM_016488	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	37	CCDS31777.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	A	7.021	0.558783	0.13436	0.002157	0.008521	ENSG00000134283	ENST00000395568;ENST00000256678;ENST00000432191	.	.	.	0.158	0.158	0.14942	.	.	.	.	.	T	0.23492	0.0568	N	0.22421	0.69	0.09310	N	1	P;P;P;P	0.42039	0.769;0.659;0.769;0.659	P;B;P;B	0.49332	0.607;0.403;0.607;0.403	T	0.18398	-1.0338	7	0.87932	D	0	.	.	.	.	.	352;398;423;447	F8W6A0;B7Z695;Q8NEY8-3;Q8NEY8	.;.;.;PPHLN_HUMAN	T	447;352;423	.	ENSP00000256678:N352T	N	+	2	0	PPHLN1	41126349	0.169000	0.23002	0.075000	0.20258	0.076000	0.17211	0.241000	0.18065	0.175000	0.19841	0.172000	0.16884	AAC	A|0.992;C|0.008	0.008	strong		0.433	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515	
FAM178A	55719	hgsc.bcm.edu	37	10	102684380	102684380	+	Missense_Mutation	SNP	C	C	A	rs10883563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:102684380C>A	ENST00000238961.4	+	5	2164	c.1622C>A	c.(1621-1623)tCt>tAt	p.S541Y	FAM178A_ENST00000370269.3_Missense_Mutation_p.S541Y|FAM178A_ENST00000370271.3_Missense_Mutation_p.S541Y	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	541			S -> Y (in dbSNP:rs10883563). {ECO:0000269|PubMed:12459258}.			chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											GGGAAAATTTCTGGGGGACCT	0.458													C|||	1596	0.31869	0.1619	0.4769	5008	,	,		17842	0.0952		0.5746	False		,,,				2504	0.3855				p.S541Y		Atlas-SNP	.											.	FAM178A	9	.	0			c.C1622A						PASS	.	C	TYR/SER,TYR/SER	916,3490	353.1+/-312.0	102,712,1389	96.0	96.0	96.0		1622,1622	4.2	1.0	10	dbSNP_120	96	4653,3947	603.7+/-394.7	1293,2067,940	yes	missense,missense	FAM178A	NM_001136123.1,NM_018121.3	144,144	1395,2779,2329	AA,AC,CC		45.8953,20.7898,42.8187	possibly-damaging,possibly-damaging	541/1187,541/1174	102684380	5569,7437	2203	4300	6503	SO:0001583	missense	55719	exon5			AAATTTCTGGGGG	AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"""chromosome 10 open reading frame 6"""	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.1622C>A	10.37:g.102684380C>A	ENSP00000238961:p.Ser541Tyr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Missense_Mutation	SNP	ENST00000238961.4	37	CCDS7500.1	725	0.33195970695970695	61	0.12398373983739837	167	0.4613259668508287	59	0.10314685314685315	438	0.5778364116094987	C	14.21	2.468846	0.43839	0.207898	0.541047	ENSG00000119906	ENST00000370271;ENST00000238961;ENST00000370269	T;T;T	0.62105	0.05;0.77;0.75	6.03	4.17	0.49024	.	0.113200	0.40728	N	0.001031	T	0.00012	0.0000	L	0.27053	0.805	0.33336	P	0.430708	D;D;D;D	0.89917	1.0;0.988;0.999;1.0	D;D;D;D	0.70935	0.971;0.912;0.944;0.944	T	0.42766	-0.9432	9	0.16896	T	0.51	-7.7375	13.4906	0.61393	0.0:0.7011:0.2989:0.0	rs10883563;rs58241043;rs10883563	190;541;541;541	Q96LW0;Q8IX21;B1AL17;B1AL16	.;F178A_HUMAN;.;.	Y	541	ENSP00000359294:S541Y;ENSP00000238961:S541Y;ENSP00000359292:S541Y	ENSP00000238961:S541Y	S	+	2	0	FAM178A	102674370	0.746000	0.28272	0.983000	0.44433	0.818000	0.46254	0.681000	0.25320	0.874000	0.35823	0.655000	0.94253	TCT	C|0.621;A|0.379	0.379	strong		0.458	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3		
ACTR5	79913	hgsc.bcm.edu	37	20	37394988	37394988	+	Silent	SNP	G	G	A	rs151070334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:37394988G>A	ENST00000243903.4	+	7	1438	c.1401G>A	c.(1399-1401)ggG>ggA	p.G467G		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	467					DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				AACAGGCTGGGATTGCAGAGA	0.428													G|||	7	0.00139776	0.0	0.0029	5008	,	,		19343	0.0		0.005	False		,,,				2504	0.0				p.G467G		Atlas-SNP	.											.	ACTR5	44	.	0			c.G1401A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	109.0	111.0	110.0		1401	-0.5	0.0	20	dbSNP_134	110	43,8557	28.5+/-78.6	0,43,4257	no	coding-synonymous	ACTR5	NM_024855.3		0,53,6450	AA,AG,GG		0.5,0.227,0.4075		467/608	37394988	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	79913	exon7			GGCTGGGATTGCA	AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"""INO80 complex subunits"""	14671	protein-coding gene	gene with protein product	"""INO80 complex subunit M"""		"""ARP5 (actin-related protein 5, yeast) homolog"""			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.1401G>A	20.37:g.37394988G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	173	79	0.456647	NM_024855	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Silent	SNP	ENST00000243903.4	37	CCDS13308.1																																																																																			G|0.996;A|0.004	0.004	strong		0.428	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855	
SLC17A9	63910	hgsc.bcm.edu	37	20	61595636	61595636	+	Silent	SNP	C	C	T	rs2248900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61595636C>T	ENST00000370351.4	+	8	1010	c.879C>T	c.(877-879)agC>agT	p.S293S	SLC17A9_ENST00000488738.1_3'UTR|SLC17A9_ENST00000370349.3_Silent_p.S287S	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	293					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						GTCTATTCAGCGGGTTTCTCT	0.617													C|||	771	0.153954	0.0832	0.2118	5008	,	,		18199	0.1974		0.1958	False		,,,				2504	0.1207				p.S293S		Atlas-SNP	.											SLC17A9,caecum,carcinoma,0,1	SLC17A9	54	1	0			c.C879T						PASS	.	C		432,3608		21,390,1609	201.0	215.0	210.0		879	-10.1	0.0	20	dbSNP_100	210	1838,6506		208,1422,2542	yes	coding-synonymous	SLC17A9	NM_022082.3		229,1812,4151	TT,TC,CC		22.0278,10.6931,18.3301		293/437	61595636	2270,10114	2020	4172	6192	SO:0001819	synonymous_variant	63910	exon8			ATTCAGCGGGTTT	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"""Solute carriers"""	16192	protein-coding gene	gene with protein product		612107	"""chromosome 20 open reading frame 59"", ""solute carrier family 17, member 9"""	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.879C>T	20.37:g.61595636C>T		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	262	120	0.458015	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Silent	SNP	ENST00000370351.4	37	CCDS42901.1																																																																																			C|0.831;T|0.169	0.169	strong		0.617	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
WDR5	11091	hgsc.bcm.edu	37	9	137005023	137005023	+	Silent	SNP	C	C	T	rs11556390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:137005023C>T	ENST00000358625.3	+	2	195	c.24C>T	c.(22-24)ccC>ccT	p.P8P	WDR5_ENST00000425041.1_Silent_p.P8P	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	8					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|histone H3-K4 methylation (GO:0051568)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|positive regulation of gluconeogenesis (GO:0045722)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|histone acetyltransferase complex (GO:0000123)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)				endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)		AGAAGAAGCCCGAGACCGAGG	0.647													C|||	1600	0.319489	0.1982	0.438	5008	,	,		12500	0.3562		0.4185	False		,,,				2504	0.2597				p.P8P		Atlas-SNP	.											.	WDR5	29	.	0			c.C24T						PASS	.	C	,	941,3465	340.7+/-306.4	103,735,1365	57.0	53.0	55.0		24,24	-8.8	0.2	9	dbSNP_120	55	3809,4791	523.5+/-380.3	869,2071,1360	yes	coding-synonymous,coding-synonymous	WDR5	NM_017588.2,NM_052821.3	,	972,2806,2725	TT,TC,CC		44.2907,21.3572,36.5216	,	8/335,8/335	137005023	4750,8256	2203	4300	6503	SO:0001819	synonymous_variant	11091	exon1			GAAGCCCGAGACC	AJ011376	CCDS6981.1	9q34	2014-09-03			ENSG00000196363	ENSG00000196363		"""WD repeat domain containing"""	12757	protein-coding gene	gene with protein product	"""SWD3, Set1c WD40 repeat protein, homolog (S. cerevisiae)"", ""cilia and flagella associated protein 89"""	609012				11551928	Standard	XM_005272163		Approved	SWD3, CFAP89	uc004cey.3	P61964	OTTHUMG00000131707	ENST00000358625.3:c.24C>T	9.37:g.137005023C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_052821	Q91VA5|Q9NWX7|Q9UGP9	Silent	SNP	ENST00000358625.3	37	CCDS6981.1																																																																																			C|0.632;T|0.368	0.368	strong		0.647	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1	NM_052821	
FMO1	2326	hgsc.bcm.edu	37	1	171249933	171249933	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:171249933C>T	ENST00000354841.4	+	5	767	c.636C>T	c.(634-636)ctC>ctT	p.L212L	FMO1_ENST00000469112.1_3'UTR|FMO1_ENST00000402921.2_Silent_p.L149L|FMO1_ENST00000367750.3_Silent_p.L212L	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	212					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	AGGTGTTCCTCAGCACCACCG	0.498																																					p.L212L		Atlas-SNP	.											.	FMO1	79	.	0			c.C636T						PASS	.						82.0	70.0	74.0					1																	171249933		2203	4300	6503	SO:0001819	synonymous_variant	2326	exon6			GTTCCTCAGCACC	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.636C>T	1.37:g.171249933C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	160	24	0.15	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Silent	SNP	ENST00000354841.4	37	CCDS1294.1																																																																																			.	.	none		0.498	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021	
C22orf42	150297	hgsc.bcm.edu	37	22	32550293	32550293	+	Missense_Mutation	SNP	C	C	T	rs142906642	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:32550293C>T	ENST00000382097.3	-	2	317	c.245G>A	c.(244-246)cGc>cAc	p.R82H		NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	82										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						GCGCTTGGAGCGGGCGTCCAA	0.398													.|||	150	0.0299521	0.0053	0.036	5008	,	,		17663	0.0169		0.0527	False		,,,				2504	0.0491				p.R82H		Atlas-SNP	.											.	C22orf42	37	.	0			c.G245A						PASS	.	T	HIS/ARG	37,4353		0,37,2158	48.0	53.0	51.0		245	-0.3	0.0	22	dbSNP_134	51	426,8156		14,398,3879	no	missense	C22orf42	NM_001010859.1	29	14,435,6037	TT,TC,CC		4.9639,0.8428,3.5692	benign	82/252	32550293	463,12509	2195	4291	6486	SO:0001583	missense	150297	exon2			TTGGAGCGGGCGT	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.245G>A	22.37:g.32550293C>T	ENSP00000371529:p.Arg82His	Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	453	206	0.454746	NM_001010859	A4QPH5	Missense_Mutation	SNP	ENST00000382097.3	37	CCDS33639.1	67	0.030677655677655676	3	0.006097560975609756	18	0.049723756906077346	10	0.017482517482517484	36	0.047493403693931395	T	0.022	-1.416868	0.01136	0.008428	0.049639	ENSG00000205856	ENST00000382097	T	0.32023	1.47	0.167	-0.334	0.12666	.	.	.	.	.	T	0.01627	0.0052	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28202	-1.0051	8	0.16896	T	0.51	.	.	.	.	.	82	Q6IC83	CV042_HUMAN	H	82	ENSP00000371529:R82H	ENSP00000371529:R82H	R	-	2	0	C22orf42	30880293	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.447000	0.01010	-0.841000	0.04200	-0.849000	0.03036	CGC	.	.	weak		0.398	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859	
ZNF813	126017	hgsc.bcm.edu	37	19	53993923	53993923	+	Missense_Mutation	SNP	C	C	T	rs35712939	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53993923C>T	ENST00000396403.4	+	4	565	c.437C>T	c.(436-438)tCg>tTg	p.S146L	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		AGCTTTCATTCGCATCTGCCT	0.413													c|||	1002	0.20008	0.2133	0.2003	5008	,	,		20208	0.0615		0.2565	False		,,,				2504	0.2669				p.S146L		Atlas-SNP	.											.	ZNF813	81	.	0			c.C437T						PASS	.	C	LEU/SER	934,3472	349.3+/-310.3	98,738,1367	161.0	164.0	163.0		437	1.0	0.0	19	dbSNP_126	163	2201,6393	365.7+/-334.0	282,1637,2378	no	missense	ZNF813	NM_001004301.3	145	380,2375,3745	TT,TC,CC		25.6109,21.1984,24.1154	benign	146/618	53993923	3135,9865	2203	4297	6500	SO:0001583	missense	126017	exon4			TTCATTCGCATCT	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.437C>T	19.37:g.53993923C>T	ENSP00000379684:p.Ser146Leu	Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	334	144	0.431138	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	423	0.1936813186813187	114	0.23170731707317074	80	0.22099447513812154	31	0.05419580419580419	198	0.2612137203166227	C	7.752	0.703554	0.15172	0.211984	0.256109	ENSG00000198346	ENST00000468450;ENST00000396403	T;T	0.05996	3.76;3.36	0.961	0.961	0.19638	.	.	.	.	.	T	0.00012	0.0000	M	0.62088	1.915	0.32253	P	0.57116	B	0.32101	0.356	B	0.23852	0.049	T	0.42582	-0.9443	8	0.52906	T	0.07	.	5.2224	0.15375	0.0:1.0:0.0:0.0	rs35712939;rs58445793	146	Q6ZN06	ZN813_HUMAN	L	93;146	ENSP00000419821:S93L;ENSP00000379684:S146L	ENSP00000379684:S146L	S	+	2	0	ZNF813	58685735	0.000000	0.05858	0.002000	0.10522	0.055000	0.15305	-1.331000	0.02672	0.820000	0.34516	0.205000	0.17691	TCG	C|0.986;T|0.014	0.014	weak		0.413	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
NOTCH4	4855	hgsc.bcm.edu	37	6	32188383	32188383	+	Missense_Mutation	SNP	T	T	C	rs422951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32188383T>C	ENST00000375023.3	-	6	1096	c.958A>G	c.(958-960)Acc>Gcc	p.T320A		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	320	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		T -> A (in dbSNP:rs422951).		cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GGACCCTGGGTCTCACACTCA	0.637													T|||	1718	0.343051	0.2958	0.3112	5008	,	,		17396	0.2212		0.4553	False		,,,				2504	0.4397				p.T320A		Atlas-SNP	.											NOTCH4,NS,carcinoma,0,1	NOTCH4	201	1	0			c.A958G						scavenged	.	T	ALA/THR	942,2080		144,654,713	49.0	50.0	50.0		958	-5.0	0.0	6	dbSNP_80	50	2436,2982		538,1360,811	yes	missense	NOTCH4	NM_004557.3	58	682,2014,1524	CC,CT,TT		44.9612,31.1714,40.0237	benign	320/2004	32188383	3378,5062	1511	2709	4220	SO:0001583	missense	4855	exon6			CCTGGGTCTCACA		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.958A>G	6.37:g.32188383T>C	ENSP00000364163:p.Thr320Ala	Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	70	20	0.285714	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	730	0.3342490842490842	138	0.2804878048780488	125	0.3453038674033149	127	0.22202797202797203	340	0.44854881266490765	T	1.333	-0.596204	0.03771	0.311714	0.449612	ENSG00000204301	ENST00000375023	D	0.92149	-2.98	4.6	-4.96	0.03038	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	1.178960	0.06410	N	0.720517	T	0.72867	0.3514	L	0.31752	0.955	0.09310	P	0.99999999997133	B;B	0.02656	0.0;0.0	B;B	0.13407	0.009;0.003	T	0.58736	-0.7584	9	0.37606	T	0.19	.	7.561	0.27851	0.1143:0.3195:0.0:0.5662	rs422951;rs2229976;rs17422277;rs17855878;rs58507746;rs422951	320;320	Q6P3V5;Q99466	.;NOTC4_HUMAN	A	320	ENSP00000364163:T320A	ENSP00000364163:T320A	T	-	1	0	NOTCH4	32296361	0.007000	0.16637	0.009000	0.14445	0.286000	0.27126	0.081000	0.14823	-1.001000	0.03434	-1.194000	0.01681	ACC	T|0.625;C|0.375	0.375	strong		0.637	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
ZBBX	79740	hgsc.bcm.edu	37	3	167068256	167068256	+	Missense_Mutation	SNP	T	T	A	rs4619784	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167068256T>A	ENST00000392766.2	-	9	820	c.480A>T	c.(478-480)aaA>aaT	p.K160N	ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000307529.5_Missense_Mutation_p.K160N|ZBBX_ENST00000392764.1_Missense_Mutation_p.K131N|ZBBX_ENST00000392767.2_Missense_Mutation_p.K160N|ZBBX_ENST00000455345.2_Missense_Mutation_p.K160N	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	160			K -> N (in dbSNP:rs4619784).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TCTGGTGAACTTTAGCAAAGC	0.308													T|||	1278	0.255192	0.0756	0.3343	5008	,	,		13253	0.1756		0.4076	False		,,,				2504	0.3671				p.K160N		Atlas-SNP	.											.	ZBBX	299	.	0			c.A480T						PASS	.	T	ASN/LYS,ASN/LYS,ASN/LYS	474,3148		29,416,1366	190.0	182.0	184.0		480,393,480	5.5	1.0	3	dbSNP_111	184	3474,4674		723,2028,1323	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	94,94,94	752,2444,2689	AA,AT,TT		42.6362,13.0867,33.5429	probably-damaging,probably-damaging,probably-damaging	160/840,131/772,160/801	167068256	3948,7822	1811	4074	5885	SO:0001583	missense	79740	exon9			GTGAACTTTAGCA	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.480A>T	3.37:g.167068256T>A	ENSP00000376519:p.Lys160Asn	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	246	100	0.406504	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	591	0.2706043956043956	58	0.11788617886178862	128	0.35359116022099446	101	0.17657342657342656	304	0.40105540897097625	T	20.9	4.065775	0.76187	0.130867	0.426362	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764;ENST00000474464	T;T;T;T;T;T	0.33865	1.54;1.54;1.54;1.54;1.54;1.39	5.54	5.54	0.83059	Zinc finger, B-box (1);	0.235594	0.20612	U	0.088941	T	0.00012	0.0000	L	0.36672	1.1	0.26900	P	0.9671236	D;D	0.69078	0.996;0.997	D;D	0.71184	0.953;0.972	T	0.46261	-0.9204	9	0.72032	D	0.01	-11.1017	13.6397	0.62243	0.0:0.0:0.0:1.0	rs4619784;rs17857007;rs52831775;rs4619784	160;160	A8MT70-2;A8MT70	.;ZBBX_HUMAN	N	160;160;160;160;131;160	ENSP00000376519:K160N;ENSP00000376520:K160N;ENSP00000390232:K160N;ENSP00000305065:K160N;ENSP00000376517:K131N;ENSP00000419307:K160N	ENSP00000305065:K160N	K	-	3	2	ZBBX	168550950	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	2.674000	0.46867	2.101000	0.63845	0.377000	0.23210	AAA	T|0.693;A|0.307	0.307	strong		0.308	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
ALDH2	217	hgsc.bcm.edu	37	12	112230539	112230539	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:112230539C>T	ENST00000261733.2	+	9	1097	c.1036C>T	c.(1036-1038)Cgg>Tgg	p.R346W	ALDH2_ENST00000416293.3_Missense_Mutation_p.R299W	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	346					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)	p.R346W(2)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	GGCCAAGTCTCGGGTGGTCGG	0.632			T	HMGA2	leiomyoma																																p.R346W		Atlas-SNP	.		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	ALDH2_ENST00000261733,NS,malignant_melanoma,0,2	ALDH2	91	2	2	Substitution - Missense(2)	NS(2)	c.C1036T						scavenged	.						32.0	25.0	27.0					12																	112230539		2200	4294	6494	SO:0001583	missense	217	exon9			AAGTCTCGGGTGG	M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"""Aldehyde dehydrogenases"""	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.1036C>T	12.37:g.112230539C>T	ENSP00000261733:p.Arg346Trp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	132	2	0.0151515	NM_000690	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Missense_Mutation	SNP	ENST00000261733.2	37	CCDS9155.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.590906	0.66219	.	.	ENSG00000111275	ENST00000416293;ENST00000261733;ENST00000553044;ENST00000552234	T;T	0.75821	-0.97;-0.97	5.75	3.95	0.45737	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.68100	0.2964	N	0.04746	-0.17	0.46823	D	0.999211	D;B;D	0.89917	0.999;0.337;1.0	D;B;D	0.76071	0.969;0.033;0.987	T	0.70428	-0.4874	10	0.87932	D	0	.	5.9307	0.19138	0.2485:0.5966:0.0:0.155	.	299;270;346	E7EUE5;F8VXI5;P05091	.;.;ALDH2_HUMAN	W	299;346;270;206	ENSP00000403349:R299W;ENSP00000261733:R346W	ENSP00000261733:R346W	R	+	1	2	ALDH2	110714922	0.986000	0.35501	0.952000	0.39060	0.942000	0.58702	2.720000	0.47252	0.798000	0.33994	-0.136000	0.14681	CGG	.	.	none		0.632	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690	
OR4F17	81099	hgsc.bcm.edu	37	19	111016	111016	+	Missense_Mutation	SNP	T	T	G	rs200336441		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:111016T>G	ENST00000585993.1	+	2	477	c.338T>G	c.(337-339)tTt>tGt	p.F113C	OR4F17_ENST00000318050.3_Missense_Mutation_p.F113C			Q8NGA8	O4F17_HUMAN	olfactory receptor, family 4, subfamily F, member 17	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			lung(2)	2		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCATGGGCTTTGACAGATAT	0.463																																					p.F113C		Atlas-SNP	.											OR4F17,NS,carcinoma,0,2	OR4F17	5	2	0			c.T338G						scavenged	.						1.0	1.0	1.0					19																	111016		76	150	226	SO:0001583	missense	81099	exon1			TGGGCTTTGACAG	AC005605	CCDS32854.1	19p13.3	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15381	protein-coding gene	gene with protein product				OR4F19, OR4F11P, OR4F18			Standard	NM_001005240		Approved		uc002loc.1	Q8NGA8		ENST00000585993.1:c.338T>G	19.37:g.111016T>G	ENSP00000467301:p.Phe113Cys	Somatic	1793	1	0.000557725		WXS	Illumina HiSeq	Phase_I	1864	602	0.322961	NM_001005240	B2RNE8	Missense_Mutation	SNP	ENST00000585993.1	37	CCDS32854.1	.	.	.	.	.	.	.	.	.	.	.	9.777	1.174271	0.21704	.	.	ENSG00000176695	ENST00000442916;ENST00000318050	T	0.00520	6.85	2.55	2.55	0.30701	GPCR, rhodopsin-like superfamily (1);	0.156294	0.30193	N	0.010181	T	0.01189	0.0039	M	0.75884	2.315	0.31291	N	0.689393	D	0.76494	0.999	D	0.74674	0.984	T	0.24154	-1.0168	10	0.72032	D	0.01	.	4.9478	0.13999	0.2703:0.0:0.0:0.7297	.	113	Q8NGA8	O4F17_HUMAN	C	161;113	ENSP00000315047:F113C	ENSP00000315047:F113C	F	+	2	0	OR4F17	62016	0.698000	0.27777	1.000000	0.80357	0.325000	0.28411	0.344000	0.19962	1.410000	0.46936	0.346000	0.21813	TTT	T|0.500;G|0.500	0.500	strong		0.463	OR4F17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451410.1		
HFM1	164045	hgsc.bcm.edu	37	1	91782011	91782011	+	Silent	SNP	G	G	A	rs74843031	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:91782011G>A	ENST00000370425.3	-	26	2933	c.2835C>T	c.(2833-2835)atC>atT	p.I945I	HFM1_ENST00000370424.3_Silent_p.I624I|HFM1_ENST00000294696.5_Silent_p.I177I|HFM1_ENST00000462405.1_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	945	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.I945I(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		CAGCATTTACGATTGCATTTG	0.259													G|||	529	0.105631	0.1021	0.1167	5008	,	,		12740	0.1726		0.0746	False		,,,				2504	0.0654				p.I945I		Atlas-SNP	.											HFM1,NS,carcinoma,0,1	HFM1	188	1	1	Substitution - coding silent(1)	stomach(1)	c.C2835T						scavenged	.	G		470,3934	219.7+/-237.4	20,430,1752	85.0	88.0	87.0		2835	4.2	1.0	1	dbSNP_131	87	671,7909	167.8+/-219.5	28,615,3647	no	coding-synonymous	HFM1	NM_001017975.3		48,1045,5399	AA,AG,GG		7.8205,10.6721,8.7877		945/1436	91782011	1141,11843	2202	4290	6492	SO:0001819	synonymous_variant	164045	exon26			ATTTACGATTGCA	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2835C>T	1.37:g.91782011G>A		Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	134	57	0.425373	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2	243	0.11126373626373626	47	0.09552845528455285	53	0.1464088397790055	78	0.13636363636363635	65	0.08575197889182058	G	8.343	0.829136	0.16749	0.106721	0.078205	ENSG00000162669	ENST00000430465	.	.	.	5.07	4.16	0.48862	.	.	.	.	.	T	0.55305	0.1912	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.58255	-0.7668	3	.	.	.	.	15.3264	0.74168	0.0:0.8534:0.1466:0.0	.	.	.	.	L	157	.	.	S	-	2	0	HFM1	91554599	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.416000	0.59815	1.103000	0.41568	-0.357000	0.07601	TCG	G|0.908;A|0.092	0.092	strong		0.259	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
GRM6	2916	hgsc.bcm.edu	37	5	178416288	178416288	+	Silent	SNP	G	G	A	rs2071246	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178416288G>A	ENST00000517717.1	-	6	1169	c.1131C>T	c.(1129-1131)gaC>gaT	p.D377D	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.D377D			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	377					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		GGGTGGAATCGTCTGACTGGG	0.607													G|||	3614	0.721645	0.7791	0.6772	5008	,	,		9752	0.6974		0.7455	False		,,,				2504	0.6759				p.D377D		Atlas-SNP	.											.	GRM6	149	.	0			c.C1131T						PASS	.	G		3300,1106	720.2+/-409.0	1260,780,163	79.0	76.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1131	-10.3	0.0	5	dbSNP_96	77	6294,2306	705.3+/-405.5	2276,1742,282	no	coding-synonymous	GRM6	NM_000843.3		3536,2522,445	AA,AG,GG		26.814,25.1021,26.234		377/878	178416288	9594,3412	2203	4300	6503	SO:0001819	synonymous_variant	2916	exon5			GGAATCGTCTGAC	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1131C>T	5.37:g.178416288G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	163	161	0.98773	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			G|0.261;A|0.739	0.739	strong		0.607	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
ZNF653	115950	hgsc.bcm.edu	37	19	11594928	11594928	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11594928G>A	ENST00000293771.5	-	8	1735	c.1599C>T	c.(1597-1599)tgC>tgT	p.C533C	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	533					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						AGGACTTGCCGCAGGTCTCGC	0.647																																					p.C533C	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.C1599T						PASS	.						42.0	34.0	37.0					19																	11594928		2189	4255	6444	SO:0001819	synonymous_variant	115950	exon8			CTTGCCGCAGGTC	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.1599C>T	19.37:g.11594928G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	16	0.16	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			.	.	none		0.647	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
VMO1	284013	hgsc.bcm.edu	37	17	4689572	4689572	+	Missense_Mutation	SNP	T	T	C	rs4790706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4689572T>C	ENST00000328739.5	-	1	155	c.76A>G	c.(76-78)Aca>Gca	p.T26A	VMO1_ENST00000441199.2_Missense_Mutation_p.T26A|VMO1_ENST00000354194.4_Missense_Mutation_p.T26A|GLTPD2_ENST00000331264.7_5'Flank|VMO1_ENST00000416307.2_Missense_Mutation_p.T26A	NM_182566.2	NP_872372.1	Q7Z5L0	VMO1_HUMAN	vitelline membrane outer layer 1 homolog (chicken)	26			T -> A (in dbSNP:rs4790706). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			extracellular vesicular exosome (GO:0070062)				kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|pancreas(1)	11						CGGCCATCTGTCTGTGCACAT	0.642													C|||	2672	0.533546	0.407	0.4957	5008	,	,		15997	0.5516		0.5348	False		,,,				2504	0.7117				p.T26A		Atlas-SNP	.											.	VMO1	19	.	0			c.A76G						PASS	.	C	ALA/THR,ALA/THR,ALA/THR,ALA/THR	1970,2436		435,1100,668	25.0	28.0	27.0		76,76,76,76	-3.6	0.0	17	dbSNP_111	27	4576,4022		1212,2152,935	yes	missense,missense,missense,missense	VMO1	NM_001144939.1,NM_001144940.1,NM_001144941.1,NM_182566.2	58,58,58,58	1647,3252,1603	CC,CT,TT		46.7783,44.7118,49.6616	benign,benign,benign,benign	26/115,26/103,26/71,26/203	4689572	6546,6458	2203	4299	6502	SO:0001583	missense	284013	exon1			CATCTGTCTGTGC	AF521892	CCDS11055.1, CCDS45585.1, CCDS45586.1, CCDS45587.1	17p13.2	2013-03-07	2005-11-14						30387	protein-coding gene	gene with protein product						22025569	Standard	NM_182566		Approved		uc002fyx.3	Q7Z5L0		ENST00000328739.5:c.76A>G	17.37:g.4689572T>C	ENSP00000328397:p.Thr26Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_182566	C9JQ15|E9PAU9|E9PGP4|Q3SXP1|Q8IUY1	Missense_Mutation	SNP	ENST00000328739.5	37	CCDS11055.1	1109	0.5077838827838828	207	0.42073170731707316	184	0.5082872928176796	290	0.506993006993007	428	0.5646437994722955	C	2.909	-0.225681	0.06022	0.447118	0.532217	ENSG00000182853	ENST00000328739;ENST00000416307;ENST00000354194;ENST00000441199	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.57	-3.6	0.04570	.	1.617020	0.03169	N	0.170489	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.42258	-0.9462	9	0.13108	T	0.6	2.7273	1.4357	0.02343	0.2336:0.2382:0.3445:0.1837	rs4790706;rs17177719;rs17846231;rs17859248;rs60321209;rs4790706	26;26;26;26	C9JQ15;E9PAU9;E9PGP4;Q7Z5L0	.;.;.;VMO1_HUMAN	A	26	ENSP00000328397:T26A;ENSP00000390450:T26A;ENSP00000346133:T26A;ENSP00000408166:T26A	ENSP00000328397:T26A	T	-	1	0	VMO1	4636312	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.070000	0.14573	-0.778000	0.04566	-1.096000	0.02151	ACA	T|0.502;C|0.498	0.498	strong		0.642	VMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439587.1	NM_182566	
ZAK	51776	hgsc.bcm.edu	37	2	174128513	174128513	+	Missense_Mutation	SNP	C	C	T	rs3769148	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:174128513C>T	ENST00000375213.3	+	19	1670	c.1592C>T	c.(1591-1593)tCg>tTg	p.S531L	MLTK_ENST00000409176.2_Missense_Mutation_p.S531L|MLK7-AS1_ENST00000422703.1_RNA|MLK7-AS1_ENST00000423106.2_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		531			S -> L (in dbSNP:rs3769148). {ECO:0000269|PubMed:10924358, ECO:0000269|PubMed:11042189, ECO:0000269|PubMed:11836244, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.6}.		activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										CATGTCCATTCGATTCAGTGG	0.378													C|||	1229	0.245407	0.0219	0.2867	5008	,	,		20916	0.2123		0.4831	False		,,,				2504	0.3078				p.S531L		Atlas-SNP	.											.	ZAK	62	.	0			c.C1592T						PASS	.	C	LEU/SER	354,3406		19,316,1545	119.0	105.0	109.0		1592	0.3	0.0	2	dbSNP_107	109	4058,4184		1005,2048,1068	yes	missense	ZAK	NM_016653.2	145	1024,2364,2613	TT,TC,CC		49.2356,9.4149,36.7605	benign	531/801	174128513	4412,7590	1880	4121	6001	SO:0001583	missense	0	exon19			TCCATTCGATTCA																												ENST00000375213.3:c.1592C>T	2.37:g.174128513C>T	ENSP00000364361:p.Ser531Leu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	89	87	0.977528	NM_016653	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	CCDS42777.1	615	0.2815934065934066	13	0.026422764227642278	111	0.30662983425414364	122	0.21328671328671328	369	0.4868073878627968	C	7.512	0.654931	0.14580	0.094149	0.492356	ENSG00000091436	ENST00000409176;ENST00000375213	T;T	0.75938	-0.98;-0.98	5.74	0.342	0.15996	.	0.899151	0.09761	N	0.759278	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.40776	-0.9545	9	0.25106	T	0.35	.	2.4273	0.04462	0.1168:0.4507:0.2271:0.2054	rs3769148;rs17692053;rs52801304;rs61527137;rs3769148	531	Q9NYL2	MLTK_HUMAN	L	531	ENSP00000387259:S531L;ENSP00000364361:S531L	ENSP00000364361:S531L	S	+	2	0	AC013461.1	173836759	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.555000	0.23422	-0.223000	0.09943	-0.176000	0.13171	TCG	C|0.702;T|0.298	0.298	strong		0.378	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
B9D1	27077	hgsc.bcm.edu	37	17	19247075	19247075	+	Intron	SNP	G	G	A	rs4924987	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:19247075G>A	ENST00000261499.4	-	6	616				B9D1_ENST00000575403.1_Intron|B9D1_ENST00000395616.3_Intron|B9D1_ENST00000395615.1_Intron|B9D1_ENST00000461069.2_Intron|MIR1180_ENST00000408613.1_RNA|B9D1_ENST00000477478.2_Missense_Mutation_p.H143Y	NM_015681.3	NP_056496.1	Q9UPM9	B9D1_HUMAN	B9 protein domain 1						camera-type eye development (GO:0043010)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|in utero embryonic development (GO:0001701)|neuroepithelial cell differentiation (GO:0060563)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)|vasculature development (GO:0001944)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)	hedgehog receptor activity (GO:0008158)			large_intestine(3)|urinary_tract(1)	4	all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143)					TATGGGGGATGGGGGTAAGAG	0.642													G|||	1555	0.310503	0.0726	0.5173	5008	,	,		16653	0.004		0.8121	False		,,,				2504	0.2853				p.H187Y		Atlas-SNP	.											.	B9D1	8	.	0			c.C559T						PASS	.	G		860,3546	329.9+/-301.2	90,680,1433	38.0	44.0	42.0			-0.6	0.0	17	dbSNP_111	42	6938,1662	729.9+/-406.7	2794,1350,156	no	intron	B9D1	NM_015681.3		2884,2030,1589	AA,AG,GG		19.3256,19.5188,40.0431			19247075	7798,5208	2203	4300	6503	SO:0001627	intron_variant	27077	exon6			GGGGATGGGGGTA	BC002944	CCDS11205.1, CCDS58528.1	17p11.2	2014-09-17			ENSG00000108641	ENSG00000108641			24123	protein-coding gene	gene with protein product	"""endothelial precursor protein B9"""	614144				21493627	Standard	NM_015681		Approved	B9, EPPB9, MKS9	uc010vyr.2	Q9UPM9	OTTHUMG00000059586	ENST00000261499.4:c.472+27C>T	17.37:g.19247075G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_001243473	Q9BU22	Missense_Mutation	SNP	ENST00000261499.4	37	CCDS11205.1																																																																																			G|0.579;A|0.421	0.421	strong		0.642	B9D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132494.1	NM_015681	
ANKRD27	84079	hgsc.bcm.edu	37	19	33096786	33096786	+	Silent	SNP	G	G	A	rs7247420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33096786G>A	ENST00000306065.4	-	24	2606	c.2448C>T	c.(2446-2448)taC>taT	p.Y816Y	SNORA68_ENST00000364518.1_RNA	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	816					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CGGAGCAGGCGTAAATGAGGG	0.552													G|||	1175	0.234625	0.3434	0.1427	5008	,	,		13004	0.3393		0.1153	False		,,,				2504	0.1677				p.Y816Y		Atlas-SNP	.											.	ANKRD27	86	.	0			c.C2448T						PASS	.	G		1377,3029	454.9+/-350.8	223,931,1049	137.0	125.0	129.0		2448	-4.8	0.9	19	dbSNP_116	129	1049,7551	221.0+/-258.6	64,921,3315	no	coding-synonymous	ANKRD27	NM_032139.2		287,1852,4364	AA,AG,GG		12.1977,31.2528,18.6529		816/1051	33096786	2426,10580	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon24			GCAGGCGTAAATG	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2448C>T	19.37:g.33096786G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	222	99	0.445946	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			G|0.792;A|0.208	0.208	strong		0.552	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
ZBTB37	84614	hgsc.bcm.edu	37	1	173855208	173855208	+	Silent	SNP	A	A	G	rs16846520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:173855208A>G	ENST00000367701.5	+	4	1649	c.1458A>G	c.(1456-1458)acA>acG	p.T486T	ZBTB37_ENST00000427304.1_Silent_p.T486T|ZBTB37_ENST00000367704.1_3'UTR			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	486					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						AGGAAGAGACAGTTGCTCCTG	0.577													A|||	475	0.0948482	0.0083	0.121	5008	,	,		19240	0.0605		0.1511	False		,,,				2504	0.1708				p.T486T		Atlas-SNP	.											.	ZBTB37	38	.	0			c.A1458G						PASS	.	A		38,1346		0,38,654	17.0	16.0	16.0		1458	-0.5	0.3	1	dbSNP_123	16	426,2756		29,368,1194	no	coding-synonymous	ZBTB37	NM_001122770.1		29,406,1848	GG,GA,AA		13.3878,2.7457,10.1621		486/504	173855208	464,4102	692	1591	2283	SO:0001819	synonymous_variant	84614	exon5			AGAGACAGTTGCT	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.1458A>G	1.37:g.173855208A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_001122770	Q5TC80|Q96M87|Q9BQ88	Silent	SNP	ENST00000367701.5	37	CCDS44278.1																																																																																			A|0.907;G|0.093	0.093	strong		0.577	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522	
OR2T12	127064	hgsc.bcm.edu	37	1	248458760	248458760	+	Missense_Mutation	SNP	C	C	A	rs12135684	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248458760C>A	ENST00000317996.1	-	1	120	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	41			A -> S (in dbSNP:rs12135684).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			ATCATGAGGGCATTGCTAAAC	0.517													-|||	1258	0.251198	0.1316	0.2651	5008	,	,		15579	0.3591		0.1849	False		,,,				2504	0.3599				p.A41S		Atlas-SNP	.											OR2T12,caecum,carcinoma,0,1	OR2T12	113	1	0			c.G121T						PASS	.	C	SER/ALA	581,3825	248.4+/-256.2	45,491,1667	108.0	96.0	100.0		121	-3.1	0.0	1	dbSNP_120	100	1560,7040	288.6+/-298.9	144,1272,2884	yes	missense	OR2T12	NM_001004692.1	99	189,1763,4551	AA,AC,CC		18.1395,13.1866,16.4616	benign	41/321	248458760	2141,10865	2203	4300	6503	SO:0001583	missense	127064	exon1			TGAGGGCATTGCT	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.121G>T	1.37:g.248458760C>A	ENSP00000324583:p.Ala41Ser	Somatic	685	0	0		WXS	Illumina HiSeq	Phase_I	638	246	0.38558	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	523	0.23946886446886448	86	0.17479674796747968	86	0.23756906077348067	198	0.34615384615384615	153	0.20184696569920843	c	5.228	0.227590	0.09916	0.131866	0.181395	ENSG00000177201	ENST00000317996	T	0.00922	5.54	1.55	-3.09	0.05331	GPCR, rhodopsin-like superfamily (1);	0.508381	0.14656	U	0.306246	T	0.00012	0.0000	N	0.16066	0.365	0.80722	P	0.0	B	0.06786	0.001	B	0.12837	0.008	T	0.20306	-1.0279	9	0.09084	T	0.74	.	6.1685	0.20404	0.0:0.5253:0.3187:0.156	rs12135684	41	Q8NG77	O2T12_HUMAN	S	41	ENSP00000324583:A41S	ENSP00000324583:A41S	A	-	1	0	OR2T12	246525383	0.000000	0.05858	0.016000	0.15963	0.239000	0.25481	-7.823000	0.00029	-0.223000	0.09943	0.175000	0.17021	GCC	C|0.817;A|0.183	0.183	strong		0.517	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
RBP5	83758	hgsc.bcm.edu	37	12	7277236	7277236	+	Missense_Mutation	SNP	T	T	A	rs2290237	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7277236T>A	ENST00000266560.3	-	3	509	c.343A>T	c.(343-345)Atg>Ttg	p.M115L	C1RL-AS1_ENST00000535078.1_RNA|C1RL-AS1_ENST00000541775.1_RNA|C1RL-AS1_ENST00000545775.1_RNA	NM_031491.2	NP_113679.1	P29762	RABP1_HUMAN	retinol binding protein 5, cellular	118					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoic acid binding (GO:0001972)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			autonomic_ganglia(1)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)	10					Alitretinoin(DB00523)|Tretinoin(DB00755)	AGATACAGCATCTCTCCCTCC	0.582													T|||	1475	0.294529	0.1702	0.4827	5008	,	,		-128	0.1736		0.3738	False		,,,				2504	0.3722				p.M115L		Atlas-SNP	.											.	RBP5	20	.	0			c.A343T						PASS	.	T	LEU/MET	863,3543	335.5+/-303.9	85,693,1425	103.0	103.0	103.0		343	2.0	0.0	12	dbSNP_100	103	3341,5259	496.7+/-374.4	627,2087,1586	yes	missense	RBP5	NM_031491.2	15	712,2780,3011	AA,AT,TT		38.8488,19.5869,32.3235	benign	115/136	7277236	4204,8802	2203	4300	6503	SO:0001583	missense	83758	exon3			ACAGCATCTCTCC	AY007436	CCDS8574.1	12p13.31	2013-03-01	2001-11-28		ENSG00000139194	ENSG00000139194		"""Fatty acid binding protein family"""	15847	protein-coding gene	gene with protein product		611866	"""retinol-binding protein 5, cellular"""			11274389	Standard	NM_031491		Approved	CRBPIII	uc001qsq.3	P82980	OTTHUMG00000168165	ENST00000266560.3:c.343A>T	12.37:g.7277236T>A	ENSP00000266560:p.Met115Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	36	0.36	NM_031491	Q6IAY7|Q8WTV5	Missense_Mutation	SNP	ENST00000266560.3	37	CCDS8574.1	629	0.288003663003663	88	0.17886178861788618	167	0.4613259668508287	87	0.1520979020979021	287	0.3786279683377309	T	9.449	1.090168	0.20390	0.195869	0.388488	ENSG00000139194	ENST00000266560	T	0.07567	3.18	3.19	2.04	0.26737	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	2.671410	0.01367	N	0.012450	T	0.00012	0.0000	N	0.02916	-0.46	0.38416	P	0.053956000000000004	B	0.02656	0.0	B	0.01281	0.0	T	0.46133	-0.9213	9	0.45353	T	0.12	.	5.1611	0.15062	0.0:0.1163:0.3746:0.5091	rs2290237;rs11540814;rs59739778;rs2290237	115	P82980	RET5_HUMAN	L	115	ENSP00000266560:M115L	ENSP00000266560:M115L	M	-	1	0	RBP5	7168510	0.006000	0.16342	0.008000	0.14137	0.539000	0.34962	0.473000	0.22132	0.618000	0.30179	0.379000	0.24179	ATG	T|0.686;A|0.314	0.314	strong		0.582	RBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398554.1	NM_031491	
PASK	23178	hgsc.bcm.edu	37	2	242077496	242077496	+	Missense_Mutation	SNP	C	C	T	rs1470414	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:242077496C>T	ENST00000405260.1	-	6	1446	c.748G>A	c.(748-750)Gtc>Atc	p.V250I	PASK_ENST00000358649.4_Missense_Mutation_p.V250I|PASK_ENST00000234040.4_Missense_Mutation_p.V250I|PASK_ENST00000544142.1_Missense_Mutation_p.V64I|PASK_ENST00000539818.1_Missense_Mutation_p.V34I|PASK_ENST00000403638.3_Missense_Mutation_p.V250I	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	250			V -> I (in dbSNP:rs1470414). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.V250I(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CATGACGTGACGGTGCCCTGG	0.498													C|||	1114	0.222444	0.115	0.2983	5008	,	,		21641	0.1716		0.3728	False		,,,				2504	0.2117				p.V250I		Atlas-SNP	.											PASK_ENST00000234040,NS,carcinoma,0,2	PASK	230	2	2	Substitution - Missense(2)	stomach(2)	c.G748A						PASS	.	C	ILE/VAL	621,3785	268.9+/-268.7	45,531,1627	115.0	91.0	99.0		748	-2.5	0.0	2	dbSNP_88	99	3195,5405	484.5+/-371.4	539,2117,1644	yes	missense	PASK	NM_015148.2	29	584,2648,3271	TT,TC,CC		37.1512,14.0944,29.3403	benign	250/1324	242077496	3816,9190	2203	4300	6503	SO:0001583	missense	23178	exon6			ACGTGACGGTGCC	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.748G>A	2.37:g.242077496C>T	ENSP00000384016:p.Val250Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	550	0.2518315018315018	71	0.1443089430894309	111	0.30662983425414364	100	0.17482517482517482	268	0.35356200527704484	C	0.005	-2.163729	0.00318	0.140944	0.371512	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638;ENST00000415234	T;T;T;T;T;T;T	0.71222	1.32;-0.55;1.32;1.32;1.32;1.32;-0.55	4.63	-2.45	0.06481	.	0.279921	0.24608	N	0.037061	T	0.00012	0.0000	N	0.02721	-0.515	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.08055	0.001;0.001;0.003;0.0	T	0.15665	-1.0429	9	0.02654	T	1	.	9.5498	0.39304	0.0:0.4868:0.0:0.5132	rs1470414;rs17383924;rs52809637;rs56762868;rs1470414	64;250;250;250	F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;PASK_HUMAN	I	250;64;250;250;34;250;34	ENSP00000234040:V250I;ENSP00000441374:V64I;ENSP00000384016:V250I;ENSP00000351475:V250I;ENSP00000443083:V34I;ENSP00000384438:V250I;ENSP00000400734:V34I	ENSP00000234040:V250I	V	-	1	0	PASK	241726169	0.003000	0.15002	0.012000	0.15200	0.002000	0.02628	-0.265000	0.08644	-0.421000	0.07416	-1.148000	0.01847	GTC	C|0.729;T|0.271	0.271	strong		0.498	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
ZNF648	127665	hgsc.bcm.edu	37	1	182027022	182027022	+	Missense_Mutation	SNP	C	C	T	rs12564283	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:182027022C>T	ENST00000339948.3	-	2	331	c.124G>A	c.(124-126)Gag>Aag	p.E42K		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	42			E -> K (in dbSNP:rs12564283).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						TTTTCGGCCTCCCCACCATCT	0.587													C|||	880	0.175719	0.0862	0.121	5008	,	,		18447	0.2827		0.1471	False		,,,				2504	0.2546				p.E42K	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.G124A						PASS	.	C	LYS/GLU	412,3994	197.7+/-221.8	18,376,1809	95.0	91.0	93.0		124	0.8	0.0	1	dbSNP_120	93	1176,7424	236.9+/-269.0	82,1012,3206	yes	missense	ZNF648	NM_001009992.1	56	100,1388,5015	TT,TC,CC		13.6744,9.3509,12.2097	benign	42/569	182027022	1588,11418	2203	4300	6503	SO:0001583	missense	127665	exon2			CGGCCTCCCCACC	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"""Zinc fingers, C2H2-type"""	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.124G>A	1.37:g.182027022C>T	ENSP00000344129:p.Glu42Lys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	170	68	0.4	NM_001009992	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	37	CCDS30952.1	372	0.17032967032967034	56	0.11382113821138211	41	0.1132596685082873	159	0.27797202797202797	116	0.15303430079155672	C	9.404	1.078777	0.20227	0.093509	0.136744	ENSG00000179930	ENST00000339948	T	0.08102	3.13	2.76	0.787	0.18596	.	.	.	.	.	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.48917	-0.8992	8	0.18276	T	0.48	.	7.0419	0.25025	0.0:0.7496:0.0:0.2504	rs12564283;rs52816065;rs61040691;rs12564283	42	Q5T619	ZN648_HUMAN	K	42	ENSP00000344129:E42K	ENSP00000344129:E42K	E	-	1	0	ZNF648	180293645	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	0.313000	0.19415	0.218000	0.20820	0.655000	0.94253	GAG	C|0.857;T|0.143	0.143	strong		0.587	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597	
LANCL2	55915	hgsc.bcm.edu	37	7	55459563	55459563	+	Silent	SNP	A	A	G	rs2049497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:55459563A>G	ENST00000254770.2	+	2	860	c.282A>G	c.(280-282)acA>acG	p.T94T		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	94					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GGCTGAAGACAGCTGATCCCC	0.403													A|||	2040	0.407348	0.3109	0.5634	5008	,	,		18162	0.5694		0.337	False		,,,				2504	0.3323				p.T94T		Atlas-SNP	.											.	LANCL2	54	.	0			c.A282G						PASS	.	A		1484,2922	475.0+/-357.2	275,934,994	100.0	102.0	102.0		282	1.9	1.0	7	dbSNP_94	102	2989,5611	461.9+/-365.5	501,1987,1812	no	coding-synonymous	LANCL2	NM_018697.3		776,2921,2806	GG,GA,AA		34.7558,33.6813,34.3918		94/451	55459563	4473,8533	2203	4300	6503	SO:0001819	synonymous_variant	55915	exon2			GAAGACAGCTGAT	AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"""testis-specific adriamycin sensitivity protein"", ""G protein-coupled receptor 69B"""	612919	"""LanC (bacterial lantibiotic synthetase component C)-like 2"""	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.282A>G	7.37:g.55459563A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Silent	SNP	ENST00000254770.2	37	CCDS5517.1																																																																																			A|0.628;G|0.372	0.372	strong		0.403	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697	
CWH43	80157	hgsc.bcm.edu	37	4	49063872	49063872	+	Missense_Mutation	SNP	C	C	A	rs1051447	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:49063872C>A	ENST00000226432.4	+	16	2248	c.2065C>A	c.(2065-2067)Cat>Aat	p.H689N	CWH43_ENST00000513409.1_Missense_Mutation_p.H662N	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	689			H -> N (in dbSNP:rs1051447). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						AAACAACCATCATTTTCATAT	0.254													.|||	2387	0.476637	0.1967	0.7536	5008	,	,		15036	0.3681		0.7475	False		,,,				2504	0.4918				p.H689N		Atlas-SNP	.											.	CWH43	101	.	0			c.C2065A						PASS	.	C	ASN/HIS	1204,3162		177,850,1156	28.0	27.0	27.0		2065	4.6	1.0	4	dbSNP_86	27	6045,2429		2185,1675,377	yes	missense	CWH43	NM_025087.2	68	2362,2525,1533	AA,AC,CC		28.6641,27.5767,43.5436	probably-damaging	689/700	49063872	7249,5591	2183	4237	6420	SO:0001583	missense	80157	exon16			AACCATCATTTTC		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.2065C>A	4.37:g.49063872C>A	ENSP00000226432:p.His689Asn	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_025087	B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	37	CCDS3486.1	1195	0.5471611721611722	109	0.22154471544715448	284	0.7845303867403315	227	0.3968531468531469	575	0.758575197889182	C	14.38	2.518520	0.44763	0.275767	0.713359	ENSG00000109182	ENST00000226432;ENST00000513409	T;T	0.42513	1.55;0.97	4.59	4.59	0.56863	.	0.209202	0.34025	N	0.004323	T	0.00012	0.0000	M	0.66939	2.045	0.28466	P	0.9156359000000001	D	0.53619	0.961	P	0.52159	0.691	T	0.29671	-1.0004	8	.	.	.	.	13.2029	0.59778	0.0:1.0:0.0:0.0	rs1051447;rs2768949;rs3087790;rs52789586;rs58129284;rs1051447	689	Q9H720	PG2IP_HUMAN	N	689;662	ENSP00000226432:H689N;ENSP00000422802:H662N	.	H	+	1	0	CWH43	48758629	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.679000	0.54634	2.838000	0.97847	0.561000	0.74099	CAT	C|0.458;A|0.542	0.542	strong		0.254	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087	
ZNF628	89887	hgsc.bcm.edu	37	19	55995272	55995272	+	Silent	SNP	G	G	A	rs11550705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55995272G>A	ENST00000598519.1	+	3	3265	c.2712G>A	c.(2710-2712)ccG>ccA	p.P904P	ZNF628_ENST00000391718.2_Silent_p.P900P|NAT14_ENST00000591590.1_5'Flank|NAT14_ENST00000587400.1_5'Flank|NAT14_ENST00000205194.4_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	904					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TCACTGGCCCGGGCCCCGGGG	0.662													g|||	1181	0.235823	0.0825	0.2781	5008	,	,		13382	0.0149		0.4404	False		,,,				2504	0.4305				p.P904P		Atlas-SNP	.											.	ZNF628	75	.	0			c.G2712A						PASS	.	G		544,3850		32,480,1685	17.0	19.0	18.0		2700	-7.0	0.0	19	dbSNP_120	18	3972,4614		924,2124,1245	no	coding-synonymous	ZNF628	NM_033113.2		956,2604,2930	AA,AG,GG		46.2614,12.3805,34.792		900/1056	55995272	4516,8464	2197	4293	6490	SO:0001819	synonymous_variant	89887	exon3			TGGCCCGGGCCCC	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2712G>A	19.37:g.55995272G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																			G|0.723;A|0.277	0.277	strong		0.662	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
VNN2	8875	hgsc.bcm.edu	37	6	133073844	133073844	+	Silent	SNP	C	C	T	rs33980664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:133073844C>T	ENST00000326499.6	-	4	706	c.582G>A	c.(580-582)ccG>ccA	p.P194P	VNN2_ENST00000525289.1_Intron|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000526192.1_5'Flank|VNN2_ENST00000525270.1_Silent_p.P141P	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	194	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TCACCAACTCCGGCTTTTCAG	0.408													C|||	85	0.0169728	0.0023	0.049	5008	,	,		19553	0.004		0.0278	False		,,,				2504	0.0164				p.P194P		Atlas-SNP	.											.	VNN2	83	.	0			c.G582A						PASS	.	C	,,	24,4382	29.0+/-57.7	0,24,2179	119.0	115.0	116.0		,582,423	-10.8	0.0	6	dbSNP_126	116	294,8306	108.0+/-168.7	6,282,4012	no	intron,coding-synonymous,coding-synonymous	VNN2	NM_001242350.1,NM_004665.2,NM_078488.1	,,	6,306,6191	TT,TC,CC		3.4186,0.5447,2.445	,,	,194/521,141/468	133073844	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	8875	exon4			CAACTCCGGCTTT	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"""Vanins"""	12706	protein-coding gene	gene with protein product	"""pantetheinase"""	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.582G>A	6.37:g.133073844C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																			C|0.976;T|0.024	0.024	strong		0.408	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2		
RIN3	79890	hgsc.bcm.edu	37	14	93118669	93118669	+	Silent	SNP	G	G	A	rs3742716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:93118669G>A	ENST00000216487.7	+	6	1434	c.1275G>A	c.(1273-1275)acG>acA	p.T425T	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	425	Pro-rich.		T -> I (in dbSNP:rs3742717).|T -> M (in dbSNP:rs3742717). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CTGAGGACACGCCCCGGGAGA	0.652													g|||	1194	0.238419	0.0295	0.2594	5008	,	,		13370	0.4494		0.2883	False		,,,				2504	0.2372				p.T425T		Atlas-SNP	.											RIN3,rectum,carcinoma,0,1	RIN3	81	1	0			c.G1275A						PASS	.	A		330,4076	173.0+/-202.9	18,294,1891	56.0	64.0	62.0		1275	0.9	0.0	14	dbSNP_107	62	2738,5862	433.0+/-357.3	433,1872,1995	no	coding-synonymous	RIN3	NM_024832.3		451,2166,3886	AA,AG,GG		31.8372,7.4898,23.5891		425/986	93118669	3068,9938	2203	4300	6503	SO:0001819	synonymous_variant	79890	exon6			GGACACGCCCCGG	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1275G>A	14.37:g.93118669G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	153	86	0.562092	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent	SNP	ENST00000216487.7	37	CCDS32144.1																																																																																			G|0.748;A|0.252	0.252	strong		0.652	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
PODN	127435	hgsc.bcm.edu	37	1	53544439	53544439	+	Silent	SNP	G	G	A	rs1288388	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:53544439G>A	ENST00000312553.5	+	8	1408	c.1401G>A	c.(1399-1401)ccG>ccA	p.P467P	PODN_ENST00000371500.3_Silent_p.P448P|PODN_ENST00000395871.2_Silent_p.P325P|RP11-334A14.5_ENST00000447867.1_RNA	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	419					negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TCACCAGCCCGCAGGTGCACC	0.637													G|||	2056	0.410543	0.1528	0.4813	5008	,	,		20128	0.2937		0.7326	False		,,,				2504	0.498				p.P467P		Atlas-SNP	.											.	PODN	86	.	0			c.G1401A						PASS	.	G	,,,	1165,3241	410.6+/-335.4	170,825,1208	134.0	107.0	116.0		1344,1344,975,1401	-2.2	0.9	1	dbSNP_87	116	6261,2339	703.8+/-405.4	2291,1679,330	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	,,,	2461,2504,1538	AA,AG,GG		27.1977,26.4412,42.9033	,,,	448/643,448/643,325/520,467/662	53544439	7426,5580	2203	4300	6503	SO:0001819	synonymous_variant	127435	exon8			CAGCCCGCAGGTG	AY313607	CCDS573.1, CCDS55601.1, CCDS55602.1	1p32.3	2008-02-05			ENSG00000174348	ENSG00000174348		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	23174	protein-coding gene	gene with protein product	"""podocan proteoglycan"""	608661					Standard	NM_153703		Approved	PCAN, PODOCAN, MGC24995, SLRR5A	uc010onr.2	Q7Z5L7	OTTHUMG00000008934	ENST00000312553.5:c.1401G>A	1.37:g.53544439G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Silent	SNP	ENST00000312553.5	37	CCDS573.1																																																																																			G|0.495;A|0.504	0.504	strong		0.637	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703	
PSRC1	84722	hgsc.bcm.edu	37	1	109824250	109824250	+	Silent	SNP	G	G	A	rs35358959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109824250G>A	ENST00000438534.2	-	4	648	c.510C>T	c.(508-510)aaC>aaT	p.N170N	PSRC1_ENST00000369909.2_Silent_p.N170N|PSRC1_ENST00000369904.3_Silent_p.N170N|PSRC1_ENST00000409267.1_Silent_p.N170N|PSRC1_ENST00000409138.2_Silent_p.N170N|PSRC1_ENST00000369907.3_Silent_p.N170N|PSRC1_ENST00000369903.2_Silent_p.N170N	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	170	4 X 4 AA repeats of P-X-X-P.				microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CCCTCTTCATGTTGGAGGGCC	0.557													G|||	214	0.0427316	0.0166	0.0303	5008	,	,		18881	0.0308		0.0835	False		,,,				2504	0.0573				p.N170N		Atlas-SNP	.											.	PSRC1	12	.	0			c.C510T						PASS	.	G	,,	115,4291		0,115,2088	74.0	75.0	75.0		510,510,510	-2.6	0.0	1	dbSNP_126	75	633,7965		20,593,3686	no	coding-synonymous,coding-synonymous,coding-synonymous	PSRC1	NM_001005290.3,NM_001032291.2,NM_032636.7	,,	20,708,5774	AA,AG,GG		7.3622,2.6101,5.7521	,,	170/311,170/334,170/334	109824250	748,12256	2203	4299	6502	SO:0001819	synonymous_variant	84722	exon4			CTTCATGTTGGAG		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"""differential display and activated by p53"""	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.510C>T	1.37:g.109824250G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Silent	SNP	ENST00000438534.2	37																																																																																				G|0.944;A|0.056	0.056	strong		0.557	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636	
BCO1	53630	hgsc.bcm.edu	37	16	81314496	81314496	+	Missense_Mutation	SNP	C	C	T	rs7501331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81314496C>T	ENST00000258168.2	+	8	1597	c.1136C>T	c.(1135-1137)gCa>gTa	p.A379V	BCMO1_ENST00000425577.2_Missense_Mutation_p.A310V	NM_017429.2	NP_059125.2														breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						ATCAAAGTGGCATCTACAACA	0.388													C|||	762	0.152157	0.0091	0.1744	5008	,	,		18135	0.1875		0.2316	False		,,,				2504	0.2117				p.A379V		Atlas-SNP	.											.	BCMO1	53	.	0			c.C1136T						PASS	.	C	VAL/ALA	224,4180	133.7+/-170.0	1,222,1979	65.0	63.0	64.0		1136	4.6	0.3	16	dbSNP_116	64	2007,6593	350.7+/-328.0	243,1521,2536	yes	missense	BCMO1	NM_017429.2	64	244,1743,4515	TT,TC,CC		23.3372,5.0863,17.1563	benign	379/548	81314496	2231,10773	2202	4300	6502	SO:0001583	missense	53630	exon8			AAGTGGCATCTAC																												ENST00000258168.2:c.1136C>T	16.37:g.81314496C>T	ENSP00000258168:p.Ala379Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_017429		Missense_Mutation	SNP	ENST00000258168.2	37	CCDS10934.1	353	0.16163003663003664	8	0.016260162601626018	65	0.17955801104972377	96	0.16783216783216784	184	0.24274406332453827	C	15.85	2.954275	0.53293	0.050863	0.233372	ENSG00000135697	ENST00000258168;ENST00000425577	D;D	0.95103	-3.61;-3.23	5.61	4.6	0.57074	.	0.904678	0.09742	N	0.761746	T	0.00271	0.0008	L	0.40543	1.245	0.80722	P	0.0	P;B	0.45044	0.849;0.12	B;B	0.40982	0.345;0.114	T	0.06391	-1.0829	9	0.30078	T	0.28	-1.633	15.431	0.75099	0.1389:0.861:0.0:0.0	rs7501331;rs52800470;rs7501331	310;379	E7EM88;Q9HAY6	.;BCDO1_HUMAN	V	379;310	ENSP00000258168:A379V;ENSP00000400586:A310V	ENSP00000258168:A379V	A	+	2	0	BCMO1	79871997	0.052000	0.20516	0.265000	0.24526	0.986000	0.74619	1.730000	0.38125	2.793000	0.96121	0.655000	0.94253	GCA	C|0.837;T|0.163	0.163	strong		0.388	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269056.1		
DHRS11	79154	hgsc.bcm.edu	37	17	34951481	34951481	+	Silent	SNP	C	C	T	rs73993036	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34951481C>T	ENST00000251312.5	+	2	440	c.228C>T	c.(226-228)gaC>gaT	p.D76D	DHRS11_ENST00000394445.1_3'UTR|DHRS11_ENST00000590554.1_5'UTR	NM_024308.3	NP_077284.2	Q6UWP2	DHR11_HUMAN	dehydrogenase/reductase (SDR family) member 11	76						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(4)	5						ATGAAGAGGACATCCTCTCCA	0.537													C|||	104	0.0207668	0.0734	0.0101	5008	,	,		20188	0.0		0.0	False		,,,				2504	0.0				p.D76D		Atlas-SNP	.											.	DHRS11	10	.	0			c.C228T						PASS	.	C		278,4128	154.4+/-187.8	10,258,1935	146.0	126.0	133.0		228	3.7	1.0	17	dbSNP_130	133	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DHRS11	NM_024308.3		10,261,6232	TT,TC,CC		0.0349,6.3096,2.1605		76/261	34951481	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	79154	exon2			AGAGGACATCCTC		CCDS11315.2	17q12	2014-05-06			ENSG00000108272	ENSG00000278535		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	28639	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 24C, member 1"""					12975309, 19027726	Standard	NM_024308		Approved	MGC4172, SDR24C1	uc002hnd.3	Q6UWP2	OTTHUMG00000188442	ENST00000251312.5:c.228C>T	17.37:g.34951481C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	123	65	0.528455	NM_024308	B2RDZ3|Q9BUC7|Q9H674	Silent	SNP	ENST00000251312.5	37	CCDS11315.2																																																																																			C|0.977;T|0.023	0.023	strong		0.537	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308	
ZNF836	162962	hgsc.bcm.edu	37	19	52660783	52660783	+	Silent	SNP	A	A	G	rs17696575	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52660783A>G	ENST00000322146.8	-	5	674	c.153T>C	c.(151-153)ccT>ccC	p.P51P	ZNF836_ENST00000597252.1_Silent_p.P51P|CTC-471J1.8_ENST00000594362.1_RNA	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						TCATACATTTAGGAAGGATAC	0.393													A|||	979	0.195487	0.1029	0.2075	5008	,	,		18253	0.1716		0.1521	False		,,,				2504	0.3814				p.P51P		Atlas-SNP	.											ZNF836_ENST00000322146,colon,carcinoma,-1,2	ZNF836	158	2	0			c.T153C						PASS	.	A		408,3460		26,356,1552	61.0	50.0	54.0		153	0.2	0.0	19	dbSNP_123	54	1276,7032		110,1056,2988	no	coding-synonymous	ZNF836	NM_001102657.1		136,1412,4540	GG,GA,AA		15.3587,10.5481,13.8305		51/937	52660783	1684,10492	1934	4154	6088	SO:0001819	synonymous_variant	162962	exon5			ACATTTAGGAAGG	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"""Zinc fingers, C2H2-type"", ""-"""	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.153T>C	19.37:g.52660783A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	191	103	0.539267	NM_001102657		Silent	SNP	ENST00000322146.8	37	CCDS46162.1																																																																																			A|0.836;G|0.164	0.164	strong		0.393	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657	
ZNF419	79744	hgsc.bcm.edu	37	19	58004931	58004931	+	Missense_Mutation	SNP	A	A	G	rs2074077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58004931A>G	ENST00000221735.7	+	5	1192	c.1006A>G	c.(1006-1008)Att>Gtt	p.I336V	ZNF419_ENST00000426954.2_Missense_Mutation_p.I324V|ZNF419_ENST00000354197.4_Missense_Mutation_p.I324V|ZNF419_ENST00000442920.2_Missense_Mutation_p.I323V|ZNF419_ENST00000424930.2_Missense_Mutation_p.I337V|ZNF419_ENST00000347466.6_Missense_Mutation_p.I304V|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000415379.2_Missense_Mutation_p.I290V			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	336			I -> V (in dbSNP:rs2074077). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		ACATCAGAGAATTCACACTGG	0.403													G|||	3483	0.695487	0.5787	0.7262	5008	,	,		19805	0.6984		0.6839	False		,,,				2504	0.8405				p.I337V		Atlas-SNP	.											.	ZNF419	134	.	0			c.A1009G						PASS	.	G	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	2496,1904		772,952,476	67.0	65.0	66.0		1009,970,967,910,871,868,1006	-1.2	0.6	19	dbSNP_96	66	5837,2755		2025,1787,484	no	missense,missense,missense,missense,missense,missense,missense	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	29,29,29,29,29,29,29	2797,2739,960	GG,GA,AA		32.0647,43.2727,35.8605	benign,benign,benign,benign,benign,benign,benign	337/512,324/499,323/498,304/479,291/466,290/465,336/511	58004931	8333,4659	2200	4296	6496	SO:0001583	missense	79744	exon5			CAGAGAATTCACA	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.1006A>G	19.37:g.58004931A>G	ENSP00000221735:p.Ile336Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_001098491	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	1309	0.5993589743589743	232	0.4715447154471545	236	0.6519337016574586	377	0.6590909090909091	464	0.6121372031662269	G	0.009	-1.847078	0.00568	0.567273	0.679353	ENSG00000105136	ENST00000284020;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735	T;T;T;T;T;T;T	0.00986	5.47;5.47;5.47;5.47;5.47;5.47;5.47	2.36	-1.18	0.09617	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.28504	0.86	0.80722	P	0.0	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.001;0.0;0.001	T	0.02232	-1.1191	8	0.22109	T	0.4	.	5.3392	0.15974	0.6093:0.1722:0.2185:0.0	rs2074077;rs2074077	290;323;324;337;304;336	E9PFX9;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;ZN419_HUMAN	V	311;337;324;324;323;337;304;290;336	ENSP00000388864:I337V;ENSP00000390916:I324V;ENSP00000346136:I324V;ENSP00000414709:I323V;ENSP00000299860:I304V;ENSP00000392129:I290V;ENSP00000221735:I336V	ENSP00000221735:I336V	I	+	1	0	ZNF419	62696743	0.000000	0.05858	0.578000	0.28575	0.727000	0.41649	-0.608000	0.05641	-0.414000	0.07495	-0.971000	0.02607	ATT	A|0.171;G|0.829	0.829	strong		0.403	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
RHBDL1	9028	hgsc.bcm.edu	37	16	726301	726301	+	Missense_Mutation	SNP	G	G	A	rs139776304	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:726301G>A	ENST00000219551.2	+	1	227	c.200G>A	c.(199-201)cGc>cAc	p.R67H	LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Intron|LA16c-313D11.9_ENST00000571933.1_RNA			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	67					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				GGTCGGGCCCGCACTCAGGCC	0.667													G|||	3	0.000599042	0.0	0.0	5008	,	,		12129	0.0		0.003	False		,,,				2504	0.0				p.R67H		Atlas-SNP	.											.	RHBDL1	14	.	0			c.G200A						PASS	.	G	HIS/ARG	3,4303		0,3,2150	10.0	11.0	10.0		200	-5.9	0.0	16	dbSNP_134	10	33,8439		0,33,4203	yes	missense	RHBDL1	NM_003961.1	29	0,36,6353	AA,AG,GG		0.3895,0.0697,0.2817	benign	67/439	726301	36,12742	2153	4236	6389	SO:0001583	missense	9028	exon1			GGGCCCGCACTCA	Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"""rhomboid (veinlet, Drosophila)-like"""	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	ENST00000219551.2:c.200G>A	16.37:g.726301G>A	ENSP00000219551:p.Arg67His	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	160	86	0.5375	NM_003961	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Missense_Mutation	SNP	ENST00000219551.2	37	CCDS10418.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.462076	0.26248	6.97E-4	0.003895	ENSG00000103269	ENST00000219551	T	0.33216	1.42	3.75	-5.92	0.02261	.	3.088160	0.01236	N	0.008493	T	0.12944	0.0314	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14952	-1.0454	10	0.37606	T	0.19	-10.5783	1.9892	0.03442	0.1944:0.2915:0.3706:0.1436	.	67	O75783	RHBL1_HUMAN	H	67	ENSP00000219551:R67H	ENSP00000219551:R67H	R	+	2	0	RHBDL1	666302	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.123000	0.10611	-0.437000	0.07243	-0.672000	0.03802	CGC	G|0.999;A|0.001	0.001	strong		0.667	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961	
ZNF286B	729288	hgsc.bcm.edu	37	17	18584123	18584123	+	Silent	SNP	A	A	G	rs200143783	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18584123A>G	ENST00000545289.1	-	3	307	c.57T>C	c.(55-57)tcT>tcC	p.S19S	ZNF286B_ENST00000285274.5_Silent_p.S19S	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	19					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						GGAAATGGGGAGAATCCTGGG	0.463																																					p.S19S		Atlas-SNP	.											.	ZNF286B	75	.	0			c.T57C						PASS	.						92.0	99.0	97.0					17																	18584123		692	1591	2283	SO:0001819	synonymous_variant	729288	exon3			ATGGGGAGAATCC		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.57T>C	17.37:g.18584123A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	145	47	0.324138	NM_001145045		Silent	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			A|0.962;G|0.038	0.038	strong		0.463	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
MUC4	4585	hgsc.bcm.edu	37	3	195509498	195509498	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509498C>T	ENST00000463781.3	-	2	9412	c.8953G>A	c.(8953-8955)Gca>Aca	p.A2985T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2985T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A2985T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGTG	0.572																																					p.A2985T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	endometrium(2)	c.G8953A						scavenged	.						18.0	10.0	12.0					3																	195509498		655	1551	2206	SO:0001583	missense	4585	exon2			TGGATGCTGAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8953G>A	3.37:g.195509498C>T	ENSP00000417498:p.Ala2985Thr	Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	210	19	0.0904762	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	4.352	0.064824	0.08388	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.58;1.53	.	.	.	.	.	.	.	.	T	0.13500	0.0327	N	0.14661	0.345	0.09310	N	0.999999	B	0.22480	0.07	B	0.14023	0.01	T	0.25745	-1.0123	7	.	.	.	.	2.3265	0.04224	0.0:0.3925:0.3321:0.2754	.	2857	E7ESK3	.	T	2985	ENSP00000417498:A2985T;ENSP00000420243:A2985T	.	A	-	1	0	MUC4	196994277	.	.	0.014000	0.15608	0.000000	0.00434	.	.	0.482000	0.27582	0.000000	0.15137	GCA	.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DSE	29940	hgsc.bcm.edu	37	6	116720514	116720514	+	Missense_Mutation	SNP	C	C	T	rs35548455	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116720514C>T	ENST00000331677.3	+	3	545	c.101C>T	c.(100-102)cCc>cTc	p.P34L	DSE_ENST00000452085.3_Missense_Mutation_p.P34L|DSE_ENST00000359564.2_Missense_Mutation_p.P34L|DSE_ENST00000537543.1_Missense_Mutation_p.P53L|DSE_ENST00000540275.1_3'UTR			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	34			P -> L (in dbSNP:rs35548455).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		GTTATGATTCCCTTCACCAAT	0.532													C|||	110	0.0219649	0.0023	0.049	5008	,	,		18805	0.0		0.0477	False		,,,				2504	0.0256				p.P34L		Atlas-SNP	.											.	DSE	98	.	0			c.C101T						PASS	.	C	LEU/PRO,LEU/PRO	70,4336	63.5+/-100.7	0,70,2133	90.0	77.0	81.0		101,101	5.7	1.0	6	dbSNP_126	81	583,8017	156.4+/-210.3	20,543,3737	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	98,98	20,613,5870	TT,TC,CC		6.7791,1.5887,5.0208	possibly-damaging,possibly-damaging	34/959,34/959	116720514	653,12353	2203	4300	6503	SO:0001583	missense	29940	exon2			TGATTCCCTTCAC	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.101C>T	6.37:g.116720514C>T	ENSP00000332151:p.Pro34Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	61	0.027930402930402932	1	0.0020325203252032522	20	0.055248618784530384	0	0.0	40	0.052770448548812667	C	22.8	4.341742	0.81911	0.015887	0.067791	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	5.65	5.65	0.86999	.	0.112000	0.64402	D	0.000007	T	0.16938	0.0407	L	0.44542	1.39	0.80722	D	1	P;P	0.36535	0.557;0.557	B;B	0.34242	0.178;0.178	T	0.02417	-1.1162	10	0.59425	D	0.04	-19.329	19.9142	0.97043	0.0:1.0:0.0:0.0	rs35548455	53;34	B7Z765;Q9UL01	.;DSE_HUMAN	L	34;34;53;34;34	ENSP00000397597:P34L;ENSP00000404049:P34L;ENSP00000441152:P53L;ENSP00000332151:P34L;ENSP00000352567:P34L	ENSP00000332151:P34L	P	+	2	0	DSE	116827207	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.454000	0.66651	2.941000	0.99782	0.655000	0.94253	CCC	C|0.955;T|0.045	0.045	strong		0.532	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37438725	37438725	+	Missense_Mutation	SNP	C	C	G	rs200260827	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:37438725C>G	ENST00000602533.1	+	11	1524	c.1425C>G	c.(1423-1425)aaC>aaG	p.N475K	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.N475K|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.N475K			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	531					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N475K(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AAATGCAAAACTCTGTTCCAA	0.289													.|||	266	0.053115	0.0666	0.0836	5008	,	,		16587	0.0228		0.0586	False		,,,				2504	0.0389				p.N475K		Atlas-SNP	.											ANKRD30A,trunk,malignant_melanoma,0,1	ANKRD30A	448	1	1	Substitution - Missense(1)	skin(1)	c.C1425G						PASS	.						108.0	98.0	101.0					10																	37438725		1809	4067	5876	SO:0001583	missense	91074	exon11			GCAAAACTCTGTT	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1425C>G	10.37:g.37438725C>G	ENSP00000473551:p.Asn475Lys	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	412	40	0.0970874	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		21	0.009615384615384616	14	0.028455284552845527	4	0.011049723756906077	2	0.0034965034965034965	1	0.0013192612137203166	.	1.178	-0.639028	0.03557	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.05513	3.43;3.43	1.12	-0.157	0.13387	.	.	.	.	.	T	0.00666	0.0022	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44877	-0.9299	9	0.05525	T	0.97	.	3.0001	0.06011	0.0:0.3069:0.0:0.6931	.	531	Q9BXX3	AN30A_HUMAN	K	475	ENSP00000354432:N475K;ENSP00000363792:N475K	ENSP00000354432:N475K	N	+	3	2	ANKRD30A	37478731	0.020000	0.18652	0.005000	0.12908	0.010000	0.07245	-0.067000	0.11579	-0.051000	0.13334	0.162000	0.16502	AAC	C|0.993;G|0.007	0.007	strong		0.289	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
CDH23	64072	hgsc.bcm.edu	37	10	73434906	73434906	+	Missense_Mutation	SNP	G	G	A	rs10999947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:73434906G>A	ENST00000224721.6	+	14	1507	c.1502G>A	c.(1501-1503)aGc>aAc	p.S501N	CDH23_ENST00000299366.7_Missense_Mutation_p.S541N	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	496	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GGGGAAGTCAGCTACTTCTTC	0.577													A|||	1264	0.252396	0.2315	0.2738	5008	,	,		21316	0.2619		0.2555	False		,,,				2504	0.2526				p.S496N		Atlas-SNP	.											.	CDH23	365	.	0			c.G1487A						PASS	.	A	ASN/SER,ASN/SER,ASN/SER	963,3217		115,733,1242	94.0	97.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1487,1487,1487	-0.6	1.0	10	dbSNP_120	96	2193,6257		271,1651,2303	yes	missense,missense,missense	CDH23	NM_022124.5,NM_001171931.1,NM_001171930.1	46,46,46	386,2384,3545	AA,AG,GG		25.9527,23.0383,24.9881	benign,benign,benign	496/3355,496/1062,496/1382	73434906	3156,9474	2090	4225	6315	SO:0001583	missense	64072	exon14			AAGTCAGCTACTT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.1502G>A	10.37:g.73434906G>A	ENSP00000224721:p.Ser501Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		587	0.26877289377289376	125	0.2540650406504065	107	0.2955801104972376	160	0.27972027972027974	195	0.25725593667546176	A	6.694	0.496660	0.12762	0.230383	0.259527	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.72	-0.614	0.11590	Cadherin (4);Cadherin-like (1);	0.362307	0.27754	N	0.017987	T	0.00012	0.0000	L	0.33339	1.005	0.09310	P	0.9999999899995	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.005;0.0;0.001	T	0.33137	-0.9880	8	0.12430	T	0.62	.	13.7661	0.62995	0.3039:0.0:0.6961:0.0	rs10999947;rs61259887;rs10999947	496;499;496	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	N	501;496;496;499;499;13	.	ENSP00000224721:S501N	S	+	2	0	CDH23	73104912	0.961000	0.32948	0.991000	0.47740	0.813000	0.45954	0.400000	0.20932	-0.381000	0.07882	-1.213000	0.01624	AGC	G|0.725;A|0.275	0.275	strong		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
MCF2L2	23101	hgsc.bcm.edu	37	3	183006918	183006918	+	Missense_Mutation	SNP	A	A	G	rs3732602	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183006918A>G	ENST00000328913.3	-	14	2063	c.1766T>C	c.(1765-1767)tTt>tCt	p.F589S	B3GNT5_ENST00000462559.1_Intron|MCF2L2_ENST00000414362.2_Missense_Mutation_p.F589S|MCF2L2_ENST00000473233.1_Missense_Mutation_p.F589S|MCF2L2_ENST00000447025.2_Missense_Mutation_p.F589S	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	589			F -> S (in dbSNP:rs3732602). {ECO:0000269|PubMed:15489334}.				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CTTGACTTCAAATTTAGTCTC	0.393													A|||	152	0.0303514	0.0431	0.013	5008	,	,		18241	0.0506		0.0129	False		,,,				2504	0.0225				p.F589S		Atlas-SNP	.											.	MCF2L2	164	.	0			c.T1766C						PASS	.	A	SER/PHE	179,4227	115.9+/-153.8	0,179,2024	67.0	65.0	66.0		1766	-6.7	0.0	3	dbSNP_107	66	96,8504	52.3+/-112.8	0,96,4204	yes	missense	MCF2L2	NM_015078.2	155	0,275,6228	GG,GA,AA		1.1163,4.0626,2.1144	benign	589/1115	183006918	275,12731	2203	4300	6503	SO:0001583	missense	23101	exon14			ACTTCAAATTTAG	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.1766T>C	3.37:g.183006918A>G	ENSP00000328118:p.Phe589Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	63	0.028846153846153848	22	0.044715447154471545	8	0.022099447513812154	24	0.04195804195804196	9	0.011873350923482849	A	2.420	-0.333366	0.05278	0.040626	0.011163	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000437431;ENST00000414362	T;T;T;T	0.05081	4.69;4.71;3.83;3.5	3.36	-6.72	0.01755	.	3.710490	0.00166	N	0.000011	T	0.00580	0.0019	N	0.01297	-0.9	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.39165	-0.9627	10	0.19590	T	0.45	.	10.6738	0.45774	0.2141:0.0:0.6544:0.1314	rs3732602;rs17855921;rs52803000;rs3732602	589;589	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	S	589;589;589;125;589	ENSP00000328118:F589S;ENSP00000420070:F589S;ENSP00000388190:F589S;ENSP00000414131:F589S	ENSP00000328118:F589S	F	-	2	0	MCF2L2	184489612	0.001000	0.12720	0.007000	0.13788	0.109000	0.19521	-1.821000	0.01713	-2.431000	0.00556	-0.899000	0.02877	TTT	A|0.973;G|0.027	0.027	strong		0.393	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
OR4L1	122742	hgsc.bcm.edu	37	14	20528505	20528505	+	Missense_Mutation	SNP	T	T	A	rs2775253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20528505T>A	ENST00000315683.1	+	1	302	c.302T>A	c.(301-303)aTg>aAg	p.M101K		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	101			M -> K (in dbSNP:rs2775253).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		GTGACCCAGATGTTCTTCATG	0.473													t|||	2135	0.426318	0.3623	0.3934	5008	,	,		19257	0.5357		0.3221	False		,,,				2504	0.5307				p.M101K		Atlas-SNP	.											.	OR4L1	98	.	0			c.T302A						PASS	.		LYS/MET	1574,2832		284,1006,913	151.0	136.0	141.0		302	4.0	1.0	14	dbSNP_100	141	2755,5845		481,1793,2026	yes	missense	OR4L1	NM_001004717.1	95	765,2799,2939	AA,AT,TT		32.0349,35.724,33.2846	probably-damaging	101/313	20528505	4329,8677	2203	4300	6503	SO:0001583	missense	122742	exon1			CCCAGATGTTCTT		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.302T>A	14.37:g.20528505T>A	ENSP00000319217:p.Met101Lys	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_001004717	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	889	0.40705128205128205	184	0.37398373983739835	140	0.3867403314917127	303	0.5297202797202797	262	0.34564643799472294	.	19.10	3.761031	0.69763	0.35724	0.320349	ENSG00000176246	ENST00000315683	T	0.06687	3.27	3.97	3.97	0.46021	GPCR, rhodopsin-like superfamily (1);	0.164442	0.43110	D	0.000618	T	0.00012	0.0000	M	0.83312	2.635	0.29923	P	0.8226100000000001	P	0.49862	0.929	P	0.49012	0.598	T	0.44498	-0.9324	9	0.87932	D	0	.	11.1491	0.48447	0.0:0.0:0.0:1.0	rs2775253;rs2994401;rs2775253	101	Q8NH43	OR4L1_HUMAN	K	101	ENSP00000319217:M101K	ENSP00000319217:M101K	M	+	2	0	OR4L1	19598345	0.001000	0.12720	1.000000	0.80357	0.960000	0.62799	0.887000	0.28254	1.793000	0.52555	0.524000	0.50904	ATG	T|0.639;A|0.361	0.361	strong		0.473	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
OR8J3	81168	hgsc.bcm.edu	37	11	55904828	55904828	+	Missense_Mutation	SNP	A	A	G	rs11227321	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55904828A>G	ENST00000301529.1	-	1	366	c.367T>C	c.(367-369)Tat>Cat	p.Y123H		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y123H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					ATGGCCACATAGCGGTCATAG	0.507													A|||	517	0.103235	0.0499	0.098	5008	,	,		17549	0.1429		0.1213	False		,,,				2504	0.1196				p.Y123H		Atlas-SNP	.											OR8J3,NS,carcinoma,0,1	OR8J3	112	1	1	Substitution - Missense(1)	stomach(1)	c.T367C						PASS	.	A	HIS/TYR	240,4162	140.8+/-176.2	7,226,1968	150.0	137.0	141.0		367	3.3	1.0	11	dbSNP_120	141	1007,7585	216.6+/-255.6	54,899,3343	no	missense	OR8J3	NM_001004064.1	83	61,1125,5311	GG,GA,AA		11.7202,5.4521,9.5967	possibly-damaging	123/316	55904828	1247,11747	2201	4296	6497	SO:0001583	missense	81168	exon1			CCACATAGCGGTC		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.367T>C	11.37:g.55904828A>G	ENSP00000301529:p.Tyr123His	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	230	113	0.491304	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	253	0.11584249084249085	32	0.06504065040650407	33	0.09116022099447514	88	0.15384615384615385	100	0.13192612137203166	A	16.07	3.019022	0.54576	0.054521	0.117202	ENSG00000167822	ENST00000301529	T	0.57273	0.41	3.26	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000031	T	0.00580	0.0019	M	0.90759	3.145	0.30023	P	0.814203	B	0.34226	0.443	B	0.40285	0.325	T	0.39418	-0.9615	9	0.46703	T	0.11	.	11.5522	0.50726	1.0:0.0:0.0:0.0	rs11227321	123	Q8NGG0	OR8J3_HUMAN	H	123	ENSP00000301529:Y123H	ENSP00000301529:Y123H	Y	-	1	0	OR8J3	55661404	0.998000	0.40836	0.952000	0.39060	0.818000	0.46254	3.920000	0.56446	1.268000	0.44264	0.240000	0.17902	TAT	A|0.901;G|0.099	0.099	strong		0.507	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
FAM35A	54537	hgsc.bcm.edu	37	10	88930249	88930249	+	Missense_Mutation	SNP	A	A	T	rs11202365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88930249A>T	ENST00000298784.1	+	5	1762	c.1648A>T	c.(1648-1650)Agt>Tgt	p.S550C	FAM35A_ENST00000298786.4_Missense_Mutation_p.S550C	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	550			S -> C (in dbSNP:rs11202365).							endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						CAGTGTAGTTAGTGAAGTTGT	0.358													A|||	1379	0.275359	0.1785	0.255	5008	,	,		17119	0.1607		0.3638	False		,,,				2504	0.4479				p.S550C	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											.	FAM35A	48	.	0			c.A1648T						PASS	.	A	CYS/SER	881,3525	336.8+/-304.5	91,699,1413	75.0	70.0	72.0		1648	2.9	0.0	10	dbSNP_120	72	3341,5259	483.5+/-371.2	664,2013,1623	yes	missense	FAM35A	NM_019054.2	112	755,2712,3036	TT,TA,AA		38.8488,19.9955,32.4619	probably-damaging	550/836	88930249	4222,8784	2203	4300	6503	SO:0001583	missense	54537	exon5			GTAGTTAGTGAAG	BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.1648A>T	10.37:g.88930249A>T	ENSP00000298784:p.Ser550Cys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	577|577	0.2641941391941392|0.2641941391941392	103|103	0.20934959349593496|0.20934959349593496	104|104	0.287292817679558|0.287292817679558	85|85	0.1486013986013986|0.1486013986013986	285|285	0.3759894459102902|0.3759894459102902	a|a	11.73|11.73	1.727046|1.727046	0.30593|0.30593	0.199955|0.199955	0.388488|0.388488	ENSG00000122376|ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313|ENST00000342900	T;T;T|.	0.64991|.	-0.13;-0.13;-0.13|.	4.05|4.05	2.92|2.92	0.33932|0.33932	.|.	0.667425|.	0.13796|.	N|.	0.362154|.	T|.	0.00012|.	0.0000|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	P|P	0.0|0.0	D|.	0.65815|.	0.995|.	P|.	0.55824|.	0.785|.	T|.	0.44877|.	-0.9299|.	9|.	0.59425|.	D|.	0.04|.	-3.8081|-3.8081	4.8821|4.8821	0.13685|0.13685	0.6758:0.0:0.3242:0.0|0.6758:0.0:0.3242:0.0	rs11202365;rs11202365|rs11202365;rs11202365	550|.	Q86V20|.	FA35A_HUMAN|.	C|L	550|204	ENSP00000298786:S550C;ENSP00000298784:S550C;ENSP00000351064:S550C|.	ENSP00000298784:S550C|.	S|X	+|+	1|2	0|0	FAM35A|FAM35A	88920229|88920229	0.725000|0.725000	0.28048|0.28048	0.017000|0.017000	0.16124|0.16124	0.669000|0.669000	0.39330|0.39330	1.260000|1.260000	0.32968|0.32968	0.630000|0.630000	0.30394|0.30394	0.438000|0.438000	0.28831|0.28831	AGT|TAG	A|0.698;T|0.302	0.302	strong		0.358	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054	
UVSSA	57654	hgsc.bcm.edu	37	4	1369885	1369885	+	Silent	SNP	G	G	A	rs11724369	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1369885G>A	ENST00000389851.4	+	10	1944	c.1497G>A	c.(1495-1497)gcG>gcA	p.A499A	UVSSA_ENST00000511216.1_Silent_p.A499A|UVSSA_ENST00000512728.1_Silent_p.A50A|UVSSA_ENST00000511563.1_Silent_p.A50A|UVSSA_ENST00000507531.1_Silent_p.A499A	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	499					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										GGGCCCGGGCGCCTGTGGTGC	0.662													G|||	913	0.182308	0.0371	0.2896	5008	,	,		15144	0.0704		0.3827	False		,,,				2504	0.2117				p.A499A		Atlas-SNP	.											.	.	.	.	0			c.G1497A						PASS	.	G		375,3975		23,329,1823	18.0	19.0	19.0		1497	-10.6	0.0	4	dbSNP_120	19	3279,5307		648,1983,1662	no	coding-synonymous	KIAA1530	NM_020894.2		671,2312,3485	AA,AG,GG		38.1901,8.6207,28.2468		499/710	1369885	3654,9282	2175	4293	6468	SO:0001819	synonymous_variant	57654	exon10			CCGGGCGCCTGTG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.1497G>A	4.37:g.1369885G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			G|0.793;A|0.207	0.207	strong		0.662	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894	
DCHS2	54798	hgsc.bcm.edu	37	4	155219549	155219549	+	Missense_Mutation	SNP	T	T	G	rs74321456	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155219549T>G	ENST00000357232.4	-	18	4551	c.4552A>C	c.(4552-4554)Act>Cct	p.T1518P		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1518	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GCCTCATCAGTCAGAAAATAC	0.478													T|||	98	0.0195687	0.0023	0.0288	5008	,	,		20431	0.0		0.0706	False		,,,				2504	0.0041				p.T1518P		Atlas-SNP	.											.	DCHS2	594	.	0			c.A4552C						PASS	.	T	PRO/THR	52,4354	52.3+/-87.9	1,50,2152	131.0	126.0	128.0		4552	-4.2	0.0	4	dbSNP_131	128	557,8043	151.9+/-206.6	16,525,3759	yes	missense	DCHS2	NM_017639.3	38	17,575,5911	GG,GT,TT		6.4767,1.1802,4.6825	possibly-damaging	1518/2917	155219549	609,12397	2203	4300	6503	SO:0001583	missense	54798	exon18			CATCAGTCAGAAA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4552A>C	4.37:g.155219549T>G	ENSP00000349768:p.Thr1518Pro	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	71	0.03250915750915751	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	57	0.07519788918205805	T	14.15	2.448560	0.43429	0.011802	0.064767	ENSG00000197410	ENST00000357232	T	0.53640	0.61	5.76	-4.16	0.03869	Cadherin (4);Cadherin-like (1);	1.854830	0.02210	N	0.063130	T	0.02156	0.0067	L	0.28740	0.885	0.09310	N	1	P	0.49696	0.927	P	0.45998	0.5	T	0.09729	-1.0661	10	0.34782	T	0.22	.	3.9116	0.09205	0.1082:0.3942:0.1115:0.3861	.	1518	Q6V1P9	PCD23_HUMAN	P	1518	ENSP00000349768:T1518P	ENSP00000349768:T1518P	T	-	1	0	DCHS2	155438999	0.000000	0.05858	0.000000	0.03702	0.471000	0.32888	-0.327000	0.07955	-0.615000	0.05679	0.528000	0.53228	ACT	T|0.959;G|0.041	0.041	strong		0.478	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
UBQLN3	50613	hgsc.bcm.edu	37	11	5529139	5529139	+	Silent	SNP	T	T	C	rs2234456	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5529139T>C	ENST00000311659.4	-	2	1797	c.1650A>G	c.(1648-1650)gcA>gcG	p.A550A	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_5'Flank|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_5'Flank	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	550										NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TACCCGTCCCTGCTAGGCAAG	0.577													T|||	946	0.188898	0.0575	0.3314	5008	,	,		20260	0.0526		0.3837	False		,,,				2504	0.2055				p.A550A	Ovarian(72;684 1260 12332 41642 52180)	Atlas-SNP	.											.	UBQLN3	107	.	0			c.A1650G						PASS	.	T		460,3942	212.2+/-232.1	30,400,1771	54.0	49.0	50.0		1650	-1.6	0.0	11	dbSNP_98	50	3445,5149	492.7+/-373.4	705,2035,1557	no	coding-synonymous	UBQLN3	NM_017481.2		735,2435,3328	CC,CT,TT		40.0861,10.4498,30.0477		550/656	5529139	3905,9091	2201	4297	6498	SO:0001819	synonymous_variant	50613	exon2			CGTCCCTGCTAGG	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"""Ubiquilin family"""	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1650A>G	11.37:g.5529139T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_017481	Q9NRE0	Silent	SNP	ENST00000311659.4	37	CCDS7758.1																																																																																			T|0.748;C|0.252	0.252	strong		0.577	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481	
MUC4	4585	hgsc.bcm.edu	37	3	195509171	195509171	+	Missense_Mutation	SNP	G	G	A	rs71634716		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195509171G>A	ENST00000463781.3	-	2	9739	c.9280C>T	c.(9280-9282)Ctt>Ttt	p.L3094F	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L3094F	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L3094F(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAAGGCTGGTGACA	0.602																																					p.L3094F		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C9280T						scavenged	.						13.0	10.0	11.0					3																	195509171		666	1549	2215	SO:0001583	missense	4585	exon2			AGGAAAGGCTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9280C>T	3.37:g.195509171G>A	ENSP00000417498:p.Leu3094Phe	Somatic	254	3	0.011811		WXS	Illumina HiSeq	Phase_I	355	31	0.0873239	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	13.68	2.309979	0.40895	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36520	1.4;1.25	.	.	.	.	.	.	.	.	T	0.17280	0.0415	N	0.14661	0.345	0.09310	N	0.999996	P	0.47604	0.898	B	0.40165	0.321	T	0.07462	-1.0771	7	.	.	.	.	3.4791	0.07595	1.0E-4:1.0E-4:0.5545:0.4454	.	2966	E7ESK3	.	F	3094	ENSP00000417498:L3094F;ENSP00000420243:L3094F	.	L	-	1	0	MUC4	196993950	.	.	0.015000	0.15790	0.000000	0.00434	.	.	0.497000	0.27926	0.000000	0.15137	CTT	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MLC1	23209	hgsc.bcm.edu	37	22	50502491	50502491	+	Missense_Mutation	SNP	T	T	C	rs11568188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50502491T>C	ENST00000311597.5	-	11	1637	c.1031A>G	c.(1030-1032)aAc>aGc	p.N344S	MLC1_ENST00000395876.2_Missense_Mutation_p.N344S|MLC1_ENST00000431262.2_Missense_Mutation_p.N314S|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000538737.1_Missense_Mutation_p.N310S|MLC1_ENST00000535444.1_Missense_Mutation_p.N265S|MLC1_ENST00000450140.2_Missense_Mutation_p.N292S	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	344			N -> S (in dbSNP:rs11568188).		caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CTGCGGGCCGTTCTGGGTGTC	0.706													t|||	657	0.13119	0.059	0.1758	5008	,	,		11900	0.0923		0.1312	False		,,,				2504	0.2372				p.N344S		Atlas-SNP	.											MLC1,rectum,carcinoma,0,2	MLC1	48	2	0			c.A1031G						PASS	.		SER/ASN,SER/ASN	292,4112		14,264,1924	37.0	35.0	36.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1031,1031	1.7	0.0	22	dbSNP_120	36	1094,7506		84,926,3290	yes	missense,missense	MLC1	NM_015166.3,NM_139202.2	46,46	98,1190,5214	CC,CT,TT		12.7209,6.6303,10.6583	benign,benign	344/378,344/378	50502491	1386,11618	2202	4300	6502	SO:0001583	missense	23209	exon11			GGGCCGTTCTGGG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.1031A>G	22.37:g.50502491T>C	ENSP00000310375:p.Asn344Ser	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	60	15	0.25	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	245	0.11217948717948718	41	0.08333333333333333	58	0.16022099447513813	53	0.09265734265734266	93	0.12269129287598944	t	0.798	-0.756380	0.03019	0.066303	0.127209	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140	D;D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99;-1.99	3.83	1.67	0.24075	.	1.397770	0.04286	N	0.344697	T	0.00384	0.0012	N	0.02011	-0.69	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.30707	-0.9969	9	0.07644	T	0.81	-1.0819	2.0661	0.03603	0.1148:0.2091:0.4716:0.2045	rs11568188	310;314;344	F5H1B9;B7Z659;Q15049	.;.;MLC1_HUMAN	S	344;344;310;314;265;292	ENSP00000379216:N344S;ENSP00000310375:N344S;ENSP00000445805:N310S;ENSP00000415877:N314S;ENSP00000438910:N265S;ENSP00000412448:N292S	ENSP00000310375:N344S	N	-	2	0	MLC1	48844618	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.621000	0.24418	0.357000	0.24183	-1.438000	0.01074	AAC	T|0.905;C|0.095	0.095	strong		0.706	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
EPN3	55040	hgsc.bcm.edu	37	17	48619272	48619272	+	Silent	SNP	G	G	A	rs111678638	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48619272G>A	ENST00000268933.3	+	10	2232	c.1653G>A	c.(1651-1653)caG>caA	p.Q551Q	EPN3_ENST00000537145.1_Silent_p.Q579Q|EPN3_ENST00000541226.1_3'UTR	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	551	3 X 3 AA repeats of N-P-F.					clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CGCTAAACCAGATGCGCACCG	0.726													G|||	194	0.038738	0.003	0.0418	5008	,	,		11388	0.0188		0.0984	False		,,,				2504	0.044				p.Q551Q		Atlas-SNP	.											.	EPN3	32	.	0			c.G1653A						PASS	.	G		99,4275		4,91,2092	13.0	17.0	16.0		1653	4.2	1.0	17	dbSNP_132	16	864,7700		36,792,3454	no	coding-synonymous	EPN3	NM_017957.2		40,883,5546	AA,AG,GG		10.0887,2.2634,7.4432		551/633	48619272	963,11975	2187	4282	6469	SO:0001819	synonymous_variant	55040	exon10			AAACCAGATGCGC	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.1653G>A	17.37:g.48619272G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Silent	SNP	ENST00000268933.3	37	CCDS11570.1																																																																																			G|0.934;A|0.066	0.066	strong		0.726	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
SPTA1	6708	hgsc.bcm.edu	37	1	158597507	158597507	+	Missense_Mutation	SNP	G	G	C	rs3737515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158597507G>C	ENST00000368147.4	-	40	5752	c.5572C>G	c.(5572-5574)Cta>Gta	p.L1858V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1858			L -> V (in dbSNP:rs3737515). {ECO:0000269|PubMed:8486776}.		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGCTTCATTAGCAAGCTCTGC	0.403													G|||	1141	0.227835	0.1906	0.2133	5008	,	,		19212	0.2054		0.2863	False		,,,				2504	0.2515				p.L1858V		Atlas-SNP	.											.	SPTA1	720	.	0			c.C5572G						PASS	.	G	VAL/LEU	710,2988		63,584,1202	143.0	127.0	132.0		5572	2.7	0.7	1	dbSNP_107	132	2255,5929		309,1637,2146	yes	missense	SPTA1	NM_003126.2	32	372,2221,3348	CC,CG,GG		27.5538,19.1996,24.9537	benign	1858/2420	158597507	2965,8917	1849	4092	5941	SO:0001583	missense	6708	exon40			TCATTAGCAAGCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5572C>G	1.37:g.158597507G>C	ENSP00000357129:p.Leu1858Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	538	0.24633699633699635	104	0.21138211382113822	83	0.2292817679558011	124	0.21678321678321677	227	0.2994722955145119	G	13.00	2.107732	0.37242	0.191996	0.275538	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48201	0.82;0.82	5.55	2.68	0.31781	.	0.398187	0.14832	N	0.295829	T	0.37320	0.0999	M	0.75447	2.3	0.26869	P	0.9677948	P	0.37594	0.601	B	0.42692	0.395	T	0.28427	-1.0044	9	0.56958	D	0.05	.	10.2495	0.43360	0.2184:0.0:0.7816:0.0	rs3737515;rs52827684;rs56522116;rs59553946;rs3737515	1858	P02549	SPTA1_HUMAN	V	1858	ENSP00000357130:L1858V;ENSP00000357129:L1858V	ENSP00000357129:L1858V	L	-	1	2	SPTA1	156864131	1.000000	0.71417	0.678000	0.29963	0.560000	0.35617	2.457000	0.45005	0.451000	0.26802	-0.136000	0.14681	CTA	G|0.758;C|0.242	0.242	strong		0.403	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
STK31	56164	hgsc.bcm.edu	37	7	23757162	23757162	+	Missense_Mutation	SNP	G	G	C	rs6945306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:23757162G>C	ENST00000355870.3	+	4	332	c.213G>C	c.(211-213)caG>caC	p.Q71H	STK31_ENST00000354639.3_Missense_Mutation_p.Q48H|STK31_ENST00000433467.2_Missense_Mutation_p.Q71H|STK31_ENST00000428484.1_Missense_Mutation_p.Q48H	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	71			Q -> H (in dbSNP:rs6945306). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.			acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTTGCCCCCAGGCCAGTTCAG	0.358																																					p.Q71H		Atlas-SNP	.											.	STK31	175	.	0			c.G213C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN	731,3675	299.8+/-286.0	72,587,1544	65.0	66.0	66.0		144,213,144	3.0	0.9	7	dbSNP_116	66	2492,6108	404.5+/-348.2	368,1756,2176	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	24,24,24	440,2343,3720	CC,CG,GG		28.9767,16.591,24.7809	benign,benign,benign	48/997,71/1020,48/997	23757162	3223,9783	2203	4300	6503	SO:0001583	missense	56164	exon4			CCCCCAGGCCAGT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.213G>C	7.37:g.23757162G>C	ENSP00000348132:p.Gln71His	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	263	128	0.486692	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	552|552	0.25274725274725274|0.25274725274725274	66|66	0.13414634146341464|0.13414634146341464	66|66	0.18232044198895028|0.18232044198895028	203|203	0.3548951048951049|0.3548951048951049	217|217	0.2862796833773087|0.2862796833773087	G|G	5.213|5.213	0.224817|0.224817	0.09916|0.09916	0.16591|0.16591	0.289767|0.289767	ENSG00000196335|ENSG00000196335	ENST00000422637|ENST00000355870;ENST00000456014;ENST00000433467;ENST00000354639;ENST00000444333;ENST00000428484	.|T;T;T;T;T;T	.|0.09817	.|2.94;2.94;2.94;2.94;2.94;2.94	5.23|5.23	2.95|2.95	0.34219|0.34219	.|Maternal tudor protein (1);	.|0.983616	.|0.08296	.|N	.|0.967629	.|T	.|0.00012	.|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.48087|0.48087	P|P	4.1400000000002546E-4|4.1400000000002546E-4	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.10450	.|0.001;0.005	.|T	.|0.48514	.|-0.9029	.|9	.|0.27785	.|T	.|0.31	.|-0.6565	6.0676|6.0676	0.19871|0.19871	0.1394:0.0:0.4391:0.4215|0.1394:0.0:0.4391:0.4215	rs6945306;rs11558824;rs17854998;rs52815535;rs6945306|rs6945306;rs11558824;rs17854998;rs52815535;rs6945306	.|71;71	.|B4DZ06;Q9BXU1	.|.;STK31_HUMAN	.|H	-1|71;48;71;48;48;48	.|ENSP00000348132:Q71H;ENSP00000389340:Q48H;ENSP00000411852:Q71H;ENSP00000346660:Q48H;ENSP00000398413:Q48H;ENSP00000406146:Q48H	.|ENSP00000346660:Q48H	.|Q	+|+	.|3	.|2	STK31|STK31	23723687|23723687	0.998000|0.998000	0.40836|0.40836	0.888000|0.888000	0.34837|0.34837	0.163000|0.163000	0.22366|0.22366	1.356000|1.356000	0.34079|0.34079	0.838000|0.838000	0.34948|0.34948	-0.518000|-0.518000	0.04402|0.04402	.|CAG	G|0.742;C|0.258	0.258	strong		0.358	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
PDE1C	5137	hgsc.bcm.edu	37	7	31855569	31855569	+	Silent	SNP	G	G	A	rs2302450	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:31855569G>A	ENST00000396191.1	-	15	2237	c.1782C>T	c.(1780-1782)gcC>gcT	p.A594A	PDE1C_ENST00000396193.1_Silent_p.A654A|PDE1C_ENST00000396182.2_Silent_p.A594A|PDE1C_ENST00000396184.3_Silent_p.A594A|PDE1C_ENST00000321453.7_Silent_p.A594A|PDE1C_ENST00000479980.1_5'UTR	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	594					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.A594A(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	ATGACTTCTCGGCTTTGGAGT	0.448													A|||	1175	0.234625	0.2451	0.2046	5008	,	,		22184	0.1667		0.2704	False		,,,				2504	0.2751				p.A654A		Atlas-SNP	.											PDE1C_ENST00000396191,NS,carcinoma,0,2	PDE1C	465	2	2	Substitution - coding silent(2)	stomach(2)	c.C1962T						PASS	.	A	,,,,	1024,3382	727.8+/-409.9	133,758,1312	230.0	222.0	225.0		1782,1782,1962,1782,1782	-8.8	0.4	7	dbSNP_100	225	2092,6508	717.1+/-406.1	254,1584,2462	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE1C	NM_001191056.1,NM_001191057.1,NM_001191058.1,NM_001191059.1,NM_005020.2	,,,,	387,2342,3774	AA,AG,GG		24.3256,23.241,23.9582	,,,,	594/635,594/710,654/770,594/710,594/635	31855569	3116,9890	2203	4300	6503	SO:0001819	synonymous_variant	5137	exon16			CTTCTCGGCTTTG	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1782C>T	7.37:g.31855569G>A		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	292	124	0.424658	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396191.1	37	CCDS55099.1																																																																																			G|0.761;A|0.239	0.239	strong		0.448	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
SRD5A1	6715	hgsc.bcm.edu	37	5	6656210	6656210	+	Silent	SNP	G	G	A	rs3736316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:6656210G>A	ENST00000274192.5	+	3	714	c.480G>A	c.(478-480)acG>acA	p.T160T	SRD5A1_ENST00000537411.1_3'UTR|SRD5A1_ENST00000538824.1_Silent_p.T113T	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	160					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)	p.T160T(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TGTGGTTAACGGGCATGTTGA	0.388													G|||	1447	0.288938	0.3298	0.3919	5008	,	,		19956	0.1587		0.3897	False		,,,				2504	0.1912				p.T160T		Atlas-SNP	.											SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	1	Substitution - coding silent(1)	stomach(1)	c.G480A						PASS	.	G		1452,2954	468.7+/-355.2	244,964,995	116.0	110.0	112.0		480	-1.3	0.0	5	dbSNP_107	112	3218,5382	484.5+/-371.4	611,1996,1693	no	coding-synonymous	SRD5A1	NM_001047.2		855,2960,2688	AA,AG,GG		37.4186,32.9551,35.9065		160/260	6656210	4670,8336	2203	4300	6503	SO:0001819	synonymous_variant	6715	exon3			GTTAACGGGCATG	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.480G>A	5.37:g.6656210G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	162	85	0.524691	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Silent	SNP	ENST00000274192.5	37	CCDS3870.1																																																																																			.	.	weak		0.388	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
IPP	3652	hgsc.bcm.edu	37	1	46195375	46195375	+	Missense_Mutation	SNP	T	T	C	rs28375469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46195375T>C	ENST00000396478.3	-	4	893	c.791A>G	c.(790-792)aAa>aGa	p.K264R		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	264			K -> R (in dbSNP:rs28375469). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.			actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.K264R(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TTTGGGAGATTTGCATACTTC	0.373													T|||	1577	0.314896	0.2504	0.3473	5008	,	,		15649	0.3135		0.2833	False		,,,				2504	0.4131				p.K264R		Atlas-SNP	.											IPP,NS,carcinoma,0,1	IPP	66	1	1	Substitution - Missense(1)	stomach(1)	c.A791G						PASS	.	T	ARG/LYS,ARG/LYS	1088,3318	393.7+/-329.0	138,812,1253	110.0	112.0	111.0		791,791	5.8	1.0	1	dbSNP_125	111	2546,6054	415.3+/-351.7	384,1778,2138	yes	missense,missense	IPP	NM_001145349.1,NM_005897.2	26,26	522,2590,3391	CC,CT,TT		29.6047,24.6936,27.941	benign,benign	264/583,264/585	46195375	3634,9372	2203	4300	6503	SO:0001583	missense	3652	exon4			GGAGATTTGCATA	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"""Kelch-like"", ""BTB/POZ domain containing"""	6108	protein-coding gene	gene with protein product	"""kelch-like family member 27"""	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.791A>G	1.37:g.46195375T>C	ENSP00000379739:p.Lys264Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	133	46	0.345865	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	649	0.29716117216117216	130	0.26422764227642276	114	0.3149171270718232	182	0.3181818181818182	223	0.2941952506596306	T	16.43	3.121918	0.56613	0.246936	0.296047	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.74106	-0.63;-0.81	5.81	5.81	0.92471	.	0.197772	0.52532	D	0.000068	T	0.00012	0.0000	N	0.08118	0	0.20873	P	0.999833586	B;B	0.12630	0.003;0.006	B;B	0.10450	0.002;0.005	T	0.05354	-1.0890	9	0.59425	D	0.04	.	16.1671	0.81777	0.0:0.0:0.0:1.0	rs28375469;rs28375469	264;264	Q9Y573;A2A6V3	IPP_HUMAN;.	R	264	ENSP00000353024:K264R;ENSP00000379739:K264R	ENSP00000353024:K264R	K	-	2	0	IPP	45967962	1.000000	0.71417	0.994000	0.49952	0.629000	0.37895	7.623000	0.83113	2.226000	0.72624	0.459000	0.35465	AAA	T|0.709;C|0.291	0.291	strong		0.373	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897	
UBE2J1	51465	hgsc.bcm.edu	37	6	90047956	90047956	+	Silent	SNP	G	G	A	rs35213866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:90047956G>A	ENST00000435041.2	-	5	674	c.396C>T	c.(394-396)taC>taT	p.Y132Y		NM_016021.2	NP_057105.2	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	132					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(11)|stomach(1)	18		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		CCTCAGGAGTGTAATCTAGAG	0.378													G|||	13	0.00259585	0.0015	0.0029	5008	,	,		17857	0.0		0.0089	False		,,,				2504	0.0				p.Y132Y		Atlas-SNP	.											.	UBE2J1	28	.	0			c.C396T						PASS	.	G		9,4397	16.8+/-37.8	0,9,2194	133.0	135.0	134.0		396	1.5	1.0	6	dbSNP_126	134	80,8520	47.2+/-106.3	0,80,4220	no	coding-synonymous	UBE2J1	NM_016021.2		0,89,6414	AA,AG,GG		0.9302,0.2043,0.6843		132/319	90047956	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	51465	exon5			AGGAGTGTAATCT	AJ245898	CCDS5021.1	6q15	2014-01-28	2012-06-08		ENSG00000198833	ENSG00000198833		"""Ubiquitin-conjugating enzymes E2"""	17598	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)"""			10708578	Standard	NM_016021		Approved	HSPC153, CGI-76, NCUBE1, UBC6	uc003pnc.3	Q9Y385	OTTHUMG00000016337	ENST00000435041.2:c.396C>T	6.37:g.90047956G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_016021	A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10	Silent	SNP	ENST00000435041.2	37	CCDS5021.1																																																																																			G|0.993;A|0.007	0.007	strong		0.378	UBE2J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043742.2	NM_016021	
LMBRD2	92255	hgsc.bcm.edu	37	5	36142648	36142648	+	Silent	SNP	A	A	G	rs12658867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:36142648A>G	ENST00000296603.4	-	3	690	c.228T>C	c.(226-228)aaT>aaC	p.N76N		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	76						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.N76N(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TAATGTTGCTATTCTCAGGAG	0.358													A|||	1137	0.227037	0.0272	0.2493	5008	,	,		15180	0.2192		0.4056	False		,,,				2504	0.3057				p.N76N		Atlas-SNP	.											LMBRD2,NS,carcinoma,0,1	LMBRD2	89	1	1	Substitution - coding silent(1)	prostate(1)	c.T228C						PASS	.	A		406,4000	201.1+/-224.2	19,368,1816	158.0	148.0	151.0		228	-3.7	0.0	5	dbSNP_120	151	3496,5104	511.1+/-377.6	714,2068,1518	no	coding-synonymous	LMBRD2	NM_001007527.1		733,2436,3334	GG,GA,AA		40.6512,9.2147,30.0015		76/696	36142648	3902,9104	2203	4300	6503	SO:0001819	synonymous_variant	92255	exon3			GTTGCTATTCTCA		CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.228T>C	5.37:g.36142648A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001007527	B3KRB6|Q9NTC7	Silent	SNP	ENST00000296603.4	37	CCDS34145.1																																																																																			A|0.736;G|0.264	0.264	strong		0.358	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527	
GFM2	84340	hgsc.bcm.edu	37	5	74017590	74017590	+	Missense_Mutation	SNP	G	G	C	rs35080306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:74017590G>C	ENST00000296805.3	-	21	2687	c.2230C>G	c.(2230-2232)Cga>Gga	p.R744G	GFM2_ENST00000509430.1_Missense_Mutation_p.R744G|GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000345239.2_Missense_Mutation_p.R697G	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		GTTAGCGTTCGAAGCACAGTT	0.353													G|||	63	0.0125799	0.0038	0.0187	5008	,	,		16563	0.0129		0.0129	False		,,,				2504	0.0194				p.R744G		Atlas-SNP	.											GFM2,NS,carcinoma,+1,1	GFM2	38	1	0			c.C2230G						PASS	.	G	GLY/ARG,GLY/ARG	32,4374	36.8+/-68.6	0,32,2171	74.0	70.0	71.0		2230,2089	5.8	1.0	5	dbSNP_126	71	167,8433	77.5+/-140.1	1,165,4134	yes	missense,missense	GFM2	NM_032380.3,NM_170691.1	125,125	1,197,6305	CC,CG,GG		1.9419,0.7263,1.5301	probably-damaging,probably-damaging	744/780,697/733	74017590	199,12807	2203	4300	6503	SO:0001583	missense	84340	exon21			GCGTTCGAAGCAC	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.2230C>G	5.37:g.74017590G>C	ENSP00000296805:p.Arg744Gly	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	68	23	0.338235	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	30	0.013736263736263736	2	0.0040650406504065045	6	0.016574585635359115	11	0.019230769230769232	11	0.014511873350923483	G	25.3	4.624496	0.87560	0.007263	0.019419	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430	T;T;T	0.69435	-0.4;-0.4;-0.4	5.85	5.85	0.93711	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.81856	0.4911	H	0.96833	3.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88902	0.3353	10	0.87932	D	0	-11.8116	20.1736	0.98170	0.0:0.0:1.0:0.0	rs35080306	742;697;744	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	G	744;697;566;744	ENSP00000296805:R744G;ENSP00000296804:R697G;ENSP00000427004:R744G	ENSP00000296805:R744G	R	-	1	2	GFM2	74053346	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	9.439000	0.97543	2.767000	0.95098	0.557000	0.71058	CGA	G|0.984;C|0.016	0.016	strong		0.353	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
SLC36A2	153201	hgsc.bcm.edu	37	5	150696498	150696498	+	Silent	SNP	G	G	A	rs428064	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150696498G>A	ENST00000335244.4	-	10	1461	c.1332C>T	c.(1330-1332)gaC>gaT	p.D444D	SLC36A2_ENST00000450886.1_Silent_p.D168D	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	444					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	TGATCAGGGCGTCCTTGAAGA	0.612													G|||	1586	0.316693	0.0136	0.5173	5008	,	,		15015	0.4335		0.3678	False		,,,				2504	0.411				p.D444D		Atlas-SNP	.											.	SLC36A2	71	.	0			c.C1332T						PASS	.	G		360,4046	184.7+/-212.0	19,322,1862	79.0	70.0	73.0		1332	1.1	0.9	5	dbSNP_80	73	3155,5445	478.7+/-369.9	605,1945,1750	no	coding-synonymous	SLC36A2	NM_181776.2		624,2267,3612	AA,AG,GG		36.686,8.1707,27.026		444/484	150696498	3515,9491	2203	4300	6503	SO:0001819	synonymous_variant	153201	exon10			CAGGGCGTCCTTG	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.1332C>T	5.37:g.150696498G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	150	48	0.32	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Silent	SNP	ENST00000335244.4	37	CCDS4315.1																																																																																			G|0.708;A|0.292	0.292	strong		0.612	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
MAGEC1	9947	hgsc.bcm.edu	37	X	140993990	140993990	+	Missense_Mutation	SNP	C	C	T	rs386828015|rs80051600		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:140993990C>T	ENST00000285879.4	+	4	1086	c.800C>T	c.(799-801)tCt>tTt	p.S267F	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	267				S -> P (in Ref. 1 and 2). {ECO:0000305}.						breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					GCCCAGTCTTCTCTCCAGATT	0.493										HNSCC(15;0.026)			-|||	93	0.0246358	0.0015	0.0173	3775	,	,		9863	0.001		0.0656	False		,,,				2504	0.0123				p.S267F		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C800T						PASS	.						81.0	64.0	70.0					X																	140993990		2103	3835	5938	SO:0001583	missense	9947	exon4			AGTCTTCTCTCCA	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.800C>T	X.37:g.140993990C>T	ENSP00000285879:p.Ser267Phe	Somatic	729	0	0		WXS	Illumina HiSeq	Phase_I	127	114	0.897638	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	c	0.026	-1.374597	0.01214	.	.	ENSG00000155495	ENST00000285879;ENST00000370511;ENST00000370510	T;T	0.12569	4.21;2.67	.	.	.	.	.	.	.	.	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.34925	-0.9809	8	0.72032	D	0.01	.	3.6706	0.08272	2.0E-4:0.5073:0.4924:2.0E-4	rs57227275	267	O60732	MAGC1_HUMAN	F	267;69;68	ENSP00000285879:S267F;ENSP00000359542:S69F	ENSP00000285879:S267F	S	+	2	0	MAGEC1	140821656	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	-0.440000	0.06888	0.148000	0.19059	0.150000	0.16122	TCT	.	.	weak		0.493	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204403659	204403659	+	Silent	SNP	A	A	G	rs3747636	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204403659A>G	ENST00000367187.3	-	25	4150	c.3594T>C	c.(3592-3594)aaT>aaC	p.N1198N	PIK3C2B_ENST00000424712.2_Silent_p.N1170N|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1198	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TGATGTTGTCATTATGTCGGT	0.537													G|||	2028	0.404952	0.525	0.2666	5008	,	,		23776	0.5089		0.2594	False		,,,				2504	0.3834				p.N1198N		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.T3594C						PASS	.	G		2104,2302	601.4+/-389.7	495,1114,594	92.0	71.0	78.0		3594	-7.8	0.4	1	dbSNP_107	78	1876,6724	728.1+/-406.7	189,1498,2613	no	coding-synonymous	PIK3C2B	NM_002646.3		684,2612,3207	GG,GA,AA		21.814,47.7531,30.6013		1198/1635	204403659	3980,9026	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon25			GTTGTCATTATGT	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.3594T>C	1.37:g.204403659A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	223	93	0.41704	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			A|0.650;G|0.350	0.350	strong		0.537	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
PARP14	54625	hgsc.bcm.edu	37	3	122419083	122419083	+	Missense_Mutation	SNP	C	C	A	rs13093808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122419083C>A	ENST00000474629.2	+	6	1948	c.1682C>A	c.(1681-1683)gCa>gAa	p.A561E		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	561					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CTTTTCATAGCACAGAAGATT	0.398													C|||	389	0.0776757	0.0378	0.1066	5008	,	,		20965	0.126		0.0885	False		,,,				2504	0.0501				p.A561E		Atlas-SNP	.											.	PARP14	242	.	0			c.C1682A						PASS	.	C	GLU/ALA	150,3518		8,134,1692	42.0	37.0	39.0		1682	2.5	0.0	3	dbSNP_121	39	872,7308		42,788,3260	yes	missense	PARP14	NM_017554.2	107	50,922,4952	AA,AC,CC		10.6601,4.0894,8.6259	probably-damaging	561/1802	122419083	1022,10826	1834	4090	5924	SO:0001583	missense	54625	exon6			TCATAGCACAGAA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1682C>A	3.37:g.122419083C>A	ENSP00000418194:p.Ala561Glu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	190	0.08699633699633699	22	0.044715447154471545	42	0.11602209944751381	61	0.10664335664335664	65	0.08575197889182058	C	12.47	1.947858	0.34377	0.040894	0.106601	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.08807	3.05	5.34	2.52	0.30459	.	0.547984	0.17666	N	0.166130	T	0.00210	0.0006	M	0.69823	2.125	0.80722	P	0.0	P;D	0.55605	0.956;0.972	P;P	0.51016	0.656;0.573	T	0.09058	-1.0692	9	0.45353	T	0.12	.	8.2514	0.31724	0.2784:0.6477:0.0:0.0739	rs13093808;rs13093808	561;561	Q460N5-4;Q460N5	.;PAR14_HUMAN	E	561;480	ENSP00000418194:A561E	ENSP00000381228:A480E	A	+	2	0	PARP14	123901773	0.000000	0.05858	0.044000	0.18714	0.231000	0.25187	0.622000	0.24433	0.355000	0.24131	0.650000	0.86243	GCA	C|0.915;A|0.085	0.085	strong		0.398	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
CDKN2AIPNL	91368	hgsc.bcm.edu	37	5	133747354	133747354	+	Silent	SNP	C	C	G	rs141449831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:133747354C>G	ENST00000458198.2	-	1	235	c.192G>C	c.(190-192)ctG>ctC	p.L64L	CDKN2AIPNL_ENST00000395009.3_Silent_p.L64L	NM_080656.2	NP_542387.1	Q96HQ2	C2AIL_HUMAN	CDKN2A interacting protein N-terminal like	64										central_nervous_system(1)|kidney(2)|prostate(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAGGGAGAGCAGCTGGTCCA	0.657											OREG0016789	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	76	0.0151757	0.0008	0.0144	5008	,	,		14144	0.0		0.0398	False		,,,				2504	0.0256				p.L64L		Atlas-SNP	.											.	CDKN2AIPNL	5	.	0			c.G192C						PASS	.	C		22,4380		0,22,2179	18.0	22.0	20.0		192	3.6	1.0	5	dbSNP_134	20	241,8349		3,235,4057	no	coding-synonymous	CDKN2AIPNL	NM_080656.2		3,257,6236	GG,GC,CC		2.8056,0.4998,2.0243		64/117	133747354	263,12729	2201	4295	6496	SO:0001819	synonymous_variant	91368	exon1			GGAGAGCAGCTGG	BC008293	CCDS4175.1	5q31.1	2008-02-05			ENSG00000237190	ENSG00000237190			30545	protein-coding gene	gene with protein product						12477932	Standard	NM_080656		Approved	MGC13017	uc011cxs.2	Q96HQ2	OTTHUMG00000129123	ENST00000458198.2:c.192G>C	5.37:g.133747354C>G		Somatic	421	0	0	1605	WXS	Illumina HiSeq	Phase_I	476	161	0.338235	NM_080656	Q8WVE3	Silent	SNP	ENST00000458198.2	37	CCDS4175.1																																																																																			C|0.982;G|0.018	0.018	strong		0.657	CDKN2AIPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251171.2	NM_080656	
LILRA4	23547	hgsc.bcm.edu	37	19	54848741	54848741	+	Silent	SNP	T	T	C	rs12985462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54848741T>C	ENST00000291759.4	-	5	938	c.882A>G	c.(880-882)agA>agG	p.R294R	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	294	Ig-like C2-type 3.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CGCCGTAGCATCTGTACTGGC	0.692													T|||	872	0.174121	0.0204	0.2262	5008	,	,		13206	0.2143		0.1978	False		,,,				2504	0.2791				p.R294R		Atlas-SNP	.											LILRA4,NS,carcinoma,0,1	LILRA4	91	1	0			c.A882G						PASS	.	T		199,4207		5,189,2009	32.0	32.0	32.0		882	-0.7	0.0	19	dbSNP_121	32	1570,7030		144,1282,2874	no	coding-synonymous	LILRA4	NM_012276.3		149,1471,4883	CC,CT,TT		18.2558,4.5166,13.6014		294/500	54848741	1769,11237	2203	4300	6503	SO:0001819	synonymous_variant	23547	exon5			GTAGCATCTGTAC	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.882A>G	19.37:g.54848741T>C		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	196	82	0.418367	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			T|0.855;C|0.145	0.145	strong		0.692	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
OR4C46	119749	hgsc.bcm.edu	37	11	51516036	51516036	+	Missense_Mutation	SNP	G	G	A	rs11246608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:51516036G>A	ENST00000328188.1	+	1	755	c.755G>A	c.(754-756)tGc>tAc	p.C252Y		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	252			C -> Y (in dbSNP:rs11246608).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TTTGTGCCCTGCATATTTGTG	0.428													.|||	2191	0.4375	0.2171	0.5908	5008	,	,		19567	0.5427		0.5467	False		,,,				2504	0.4059				p.C252Y		Atlas-SNP	.											.	OR4C46	96	.	0			c.G755A						PASS	.	G	TYR/CYS	1211,3191		172,867,1162	117.0	97.0	104.0		755	2.5	0.1	11	dbSNP_120	104	4688,3904		1303,2082,911	no	missense	OR4C46	NM_001004703.1	194	1475,2949,2073	AA,AG,GG		45.4376,27.5102,45.3979	probably-damaging	252/310	51516036	5899,7095	2201	4296	6497	SO:0001583	missense	119749	exon1			TGCCCTGCATATT		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.755G>A	11.37:g.51516036G>A	ENSP00000329056:p.Cys252Tyr	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	284	119	0.419014	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	1033	0.47298534798534797	89	0.18089430894308944	218	0.6022099447513812	305	0.5332167832167832	421	0.5554089709762533	.	3.827	-0.036573	0.07497	0.275102	0.545624	ENSG00000185926	ENST00000328188	T	0.00069	8.77	2.47	2.47	0.30058	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000128	T	0.00012	0.0000	M	0.83223	2.63	0.80722	P	0.0	D	0.89917	1.0	D	0.78314	0.991	T	0.02625	-1.1132	9	0.87932	D	0	.	5.3536	0.16050	0.1676:0.0:0.8324:0.0	rs11246608;rs58821827;rs11246608	252	A6NHA9	O4C46_HUMAN	Y	252	ENSP00000329056:C252Y	ENSP00000329056:C252Y	C	+	2	0	OR4C46	51372612	0.000000	0.05858	0.070000	0.20053	0.015000	0.08874	0.197000	0.17197	1.433000	0.47394	0.121000	0.15741	TGC	G|0.535;A|0.465	0.465	strong		0.428	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
BCL7A	605	hgsc.bcm.edu	37	12	122468687	122468687	+	Splice_Site	SNP	C	C	T	rs2272132	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:122468687C>T	ENST00000261822.4	+	2	380	c.174C>T	c.(172-174)gaC>gaT	p.D58D	BCL7A_ENST00000538010.1_Splice_Site_p.D58D	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	58					negative regulation of transcription, DNA-templated (GO:0045892)					haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		AGGTTGATGACGTGAGTATGG	0.592			T	MYC	BNHL								C|||	173	0.0345447	0.0045	0.0375	5008	,	,		19084	0.0476		0.0487	False		,,,				2504	0.045				p.D58D	GBM(17;197 467 16477 23242 44349)	Atlas-SNP	.		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	.	BCL7A	31	.	0			c.C174T						PASS	.	C	,	55,4351	54.9+/-90.9	2,51,2150	141.0	109.0	120.0		174,174	-5.3	0.8	12	dbSNP_100	120	392,8208	126.3+/-184.8	15,362,3923	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	BCL7A	NM_001024808.1,NM_020993.3	,	17,413,6073	TT,TC,CC		4.5581,1.2483,3.4369	,	58/211,58/232	122468687	447,12559	2203	4300	6503	SO:0001630	splice_region_variant	605	exon2			TGATGACGTGAGT	X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.174+1C>T	12.37:g.122468687C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	167	62	0.371257	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Silent	SNP	ENST00000261822.4	37	CCDS53841.1																																																																																			C|0.964;T|0.036	0.036	strong		0.592	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		Silent
BTN2A1	11120	hgsc.bcm.edu	37	6	26468660	26468660	+	Silent	SNP	G	G	A	rs3734544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26468660G>A	ENST00000312541.5	+	8	1715	c.1467G>A	c.(1465-1467)agG>agA	p.R489R	BTN2A1_ENST00000429381.1_3'UTR|BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000541522.1_Silent_p.R428R	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	489	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						CCTTCTTCAGGTTGGGGTGTG	0.562													G|||	813	0.16234	0.2103	0.1081	5008	,	,		20145	0.1161		0.1759	False		,,,				2504	0.1697				p.R489R		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G1467A						PASS	.	G	,,,	861,3545	335.7+/-304.0	88,685,1430	153.0	121.0	132.0		1284,,1467,	-0.3	0.7	6	dbSNP_107	132	1481,7119	282.3+/-295.5	126,1229,2945	no	coding-synonymous,intron,coding-synonymous,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	,,,	214,1914,4375	AA,AG,GG		17.2209,19.5415,18.0071	,,,	428/467,,489/528,	26468660	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	11120	exon8			CTTCAGGTTGGGG	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1467G>A	6.37:g.26468660G>A		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	402	192	0.477612	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Silent	SNP	ENST00000312541.5	37	CCDS4613.1																																																																																			G|0.824;A|0.176	0.176	strong		0.562	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
DLEC1	9940	hgsc.bcm.edu	37	3	38080952	38080952	+	Missense_Mutation	SNP	T	T	G	rs7625806	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38080952T>G	ENST00000308059.6	+	1	257	c.236T>G	c.(235-237)cTg>cGg	p.L79R	DLEC1_ENST00000346219.3_Missense_Mutation_p.L79R|DLEC1_ENST00000452631.2_Missense_Mutation_p.L79R					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		GAGCCTCAGCTGCTTCGTCTG	0.652													G|||	2258	0.450879	0.5658	0.4092	5008	,	,		18071	0.6062		0.3429	False		,,,				2504	0.2761				p.L79R		Atlas-SNP	.											DLEC1_ENST00000346219,NS,carcinoma,0,2	DLEC1	278	2	0			c.T236G						PASS	.	G	ARG/LEU,ARG/LEU	2107,1909		567,973,468	35.0	40.0	39.0		236,236	0.3	0.0	3	dbSNP_116	39	2839,5501		509,1821,1840	yes	missense,missense	DLEC1	NM_007335.2,NM_007337.2	102,102	1076,2794,2308	GG,GT,TT		34.0408,47.5349,40.0291	probably-damaging,probably-damaging	79/1756,79/1779	38080952	4946,7410	2008	4170	6178	SO:0001583	missense	9940	exon1			CTCAGCTGCTTCG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.236T>G	3.37:g.38080952T>G	ENSP00000308597:p.Leu79Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	22	7	0.318182	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	988	0.4523809523809524	267	0.5426829268292683	142	0.39226519337016574	328	0.5734265734265734	251	0.3311345646437995	G	10.55	1.381461	0.24944	0.524651	0.340408	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.06528	3.32;3.29;3.54	5.47	0.309	0.15820	.	0.942952	0.08797	N	0.892317	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B;B	0.12630	0.006;0.006;0.006	B;B;B	0.17098	0.017;0.017;0.017	T	0.34725	-0.9817	9	0.30078	T	0.28	0.0241	2.3534	0.04290	0.1262:0.1483:0.132:0.5935	rs7625806;rs60689091;rs7625806	79;79;79	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	R	79	ENSP00000308597:L79R;ENSP00000315914:L79R;ENSP00000410427:L79R	ENSP00000308597:L79R	L	+	2	0	DLEC1	38055956	0.383000	0.25156	0.028000	0.17463	0.050000	0.14768	0.147000	0.16202	-0.457000	0.07033	-1.717000	0.00709	CTG	T|0.555;G|0.445	0.445	strong		0.652	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
HHLA2	11148	hgsc.bcm.edu	37	3	108081247	108081247	+	Silent	SNP	G	G	A	rs16854512	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108081247G>A	ENST00000357759.5	+	7	1476	c.1062G>A	c.(1060-1062)gcG>gcA	p.A354A	HHLA2_ENST00000467761.1_Silent_p.A354A|HHLA2_ENST00000489514.2_Silent_p.A354A|HHLA2_ENST00000491820.1_Silent_p.A354A|HHLA2_ENST00000467562.1_Silent_p.A290A	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	354					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						TGCCCTCTGCGATTTTGGCAG	0.418													G|||	773	0.154353	0.2292	0.1686	5008	,	,		18023	0.0536		0.1928	False		,,,				2504	0.1074				p.A354A		Atlas-SNP	.											.	HHLA2	95	.	0			c.G1062A						PASS	.	G		739,2921		83,573,1174	119.0	107.0	110.0		1062	0.4	0.0	3	dbSNP_123	110	1620,6564		143,1334,2615	no	coding-synonymous	HHLA2	NM_007072.2		226,1907,3789	AA,AG,GG		19.7947,20.1913,19.9173		354/415	108081247	2359,9485	1830	4092	5922	SO:0001819	synonymous_variant	11148	exon7			CTCTGCGATTTTG	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1062G>A	3.37:g.108081247G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	25	0.3125	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Silent	SNP	ENST00000357759.5	37	CCDS46883.1	331	0.15155677655677655	106	0.21544715447154472	71	0.19613259668508287	16	0.027972027972027972	138	0.1820580474934037	G	2.730	-0.264632	0.05754	0.201913	0.197947	ENSG00000114455	ENST00000482099	.	.	.	3.38	0.437	0.16555	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.25293	-1.0136	3	.	.	.	-15.2717	2.5227	0.04683	0.2695:0.0:0.4973:0.2332	rs16854512;rs60599253;rs16854512	.	.	.	N	257	.	.	D	+	1	0	HHLA2	109563937	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.619000	0.05572	0.067000	0.16545	-0.258000	0.10820	GAT	G|0.836;A|0.164	0.164	strong		0.418	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
CALCOCO2	10241	hgsc.bcm.edu	37	17	46939658	46939658	+	Missense_Mutation	SNP	C	C	G	rs10278	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46939658C>G	ENST00000258947.3	+	12	1266	c.1165C>G	c.(1165-1167)Ccc>Gcc	p.P389A	CALCOCO2_ENST00000508679.1_Missense_Mutation_p.P317A|CALCOCO2_ENST00000416445.2_Missense_Mutation_p.P347A|CALCOCO2_ENST00000448105.2_Missense_Mutation_p.P413A|CALCOCO2_ENST00000509507.1_Missense_Mutation_p.P410A	NM_001261390.1|NM_001261391.1|NM_001261393.1|NM_001261395.1|NM_005831.4	NP_001248319.1|NP_001248320.1|NP_001248322.1|NP_001248324.1|NP_005822.1	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2	389			P -> A (in dbSNP:rs10278). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4, ECO:0000269|Ref.6}.		response to interferon-gamma (GO:0034341)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	15						AAGTTCTTCCCCCAGCCCGGT	0.413																																					p.P413A		Atlas-SNP	.											.	CALCOCO2	29	.	0			c.C1237G						PASS	.	C	ALA/PRO	1475,2931	473.9+/-356.8	239,997,967	124.0	120.0	121.0		1165	-0.7	0.0	17	dbSNP_52	121	2601,5999	421.5+/-353.7	395,1811,2094	yes	missense	CALCOCO2	NM_005831.3	27	634,2808,3061	GG,GC,CC		30.2442,33.4771,31.3394	benign	389/447	46939658	4076,8930	2203	4300	6503	SO:0001583	missense	10241	exon13			TCTTCCCCCAGCC	BC004130	CCDS11538.1, CCDS58558.1, CCDS58559.1, CCDS58560.1, CCDS58561.1	17q21.32	2006-02-09				ENSG00000136436			29912	protein-coding gene	gene with protein product		604587				7540613	Standard	NM_001261390		Approved	MGC17318, NDP52	uc010wlr.3	Q13137		ENST00000258947.3:c.1165C>G	17.37:g.46939658C>G	ENSP00000258947:p.Pro389Ala	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	169	83	0.491124	NM_001261390	B2RBT0|B4DDC4|B4DDT4|B4DP36|B4E0C0|E7ENK0|E7ETP5|E9PBE5|Q53FQ5|Q53HB5|Q6IBN9|Q9BTF7	Missense_Mutation	SNP	ENST00000258947.3	37	CCDS11538.1	609	0.27884615384615385	157	0.31910569105691056	154	0.425414364640884	93	0.16258741258741258	205	0.2704485488126649	C	13.18	2.161292	0.38119	0.334771	0.302442	ENSG00000136436	ENST00000258947;ENST00000509507;ENST00000448105;ENST00000416445;ENST00000508679;ENST00000507306	T;T;T;T;T;T	0.71341	2.6;2.74;2.6;2.73;2.5;-0.56	5.05	-0.674	0.11369	.	0.533478	0.17025	N	0.189977	T	0.00012	0.0000	L	0.58101	1.795	0.80722	P	0.0	B;B;B;B	0.15141	0.012;0.007;0.006;0.006	B;B;B;B	0.11329	0.004;0.006;0.004;0.003	T	0.31861	-0.9928	9	0.33940	T	0.23	0.4464	4.5603	0.12158	0.0:0.4294:0.3067:0.2639	rs10278;rs1134989;rs1422645;rs3197407;rs11539409;rs17342409;rs17350096;rs52821500;rs1422645	347;413;410;389	E7ETP5;B4DP36;E9PBE5;Q13137	.;.;.;CACO2_HUMAN	A	389;410;413;347;317;57	ENSP00000258947:P389A;ENSP00000424352:P410A;ENSP00000398523:P413A;ENSP00000406974:P347A;ENSP00000423437:P317A;ENSP00000424083:P57A	ENSP00000258947:P389A	P	+	1	0	CALCOCO2	44294657	0.000000	0.05858	0.000000	0.03702	0.572000	0.35998	0.019000	0.13444	-0.118000	0.11851	0.655000	0.94253	CCC	C|0.673;G|0.327	0.327	strong		0.413	CALCOCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360866.1	NM_005831	
LRP4	4038	hgsc.bcm.edu	37	11	46893108	46893108	+	Missense_Mutation	SNP	T	T	C	rs2306029	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:46893108T>C	ENST00000378623.1	-	31	4902	c.4660A>G	c.(4660-4662)Agc>Ggc	p.S1554G	LRP4-AS1_ENST00000531719.1_RNA|LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1554			S -> G (in dbSNP:rs2306029). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9693030, ECO:0000269|Ref.1}.		dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GACACATGGCTGACCAAGACC	0.532													T|||	1841	0.367612	0.1142	0.4841	5008	,	,		17882	0.2569		0.5417	False		,,,				2504	0.5624				p.S1554G		Atlas-SNP	.											.	LRP4	160	.	0			c.A4660G						PASS	.	T	GLY/SER	858,3544		99,660,1442	113.0	91.0	98.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4660	5.8	1.0	11	dbSNP_100	98	4671,3927		1285,2101,913	yes	missense	LRP4	NM_002334.3	56	1384,2761,2355	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	45.6734,19.4911,42.5308	benign	1554/1906	46893108	5529,7471	2201	4299	6500	SO:0001583	missense	4038	exon31			CATGGCTGACCAA	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4660A>G	11.37:g.46893108T>C	ENSP00000367888:p.Ser1554Gly	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	767	0.35119047619047616	52	0.10569105691056911	163	0.45027624309392267	153	0.2674825174825175	399	0.5263852242744064	.	18.48	3.633739	0.67130	0.194911	0.543266	ENSG00000134569	ENST00000378623	D	0.95788	-3.81	5.81	5.81	0.92471	Six-bladed beta-propeller, TolB-like (1);	0.185823	0.64402	D	0.000020	T	0.00012	0.0000	M	0.65975	2.015	0.21290	P	0.999738373	B	0.29115	0.233	B	0.39465	0.3	T	0.02358	-1.1171	9	0.59425	D	0.04	.	12.391	0.55358	0.1258:0.0:0.0:0.8742	rs2306029;rs17787852;rs17848230;rs59459638;rs2306029	1554	O75096	LRP4_HUMAN	G	1554	ENSP00000367888:S1554G	ENSP00000367888:S1554G	S	-	1	0	LRP4	46849684	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	2.210000	0.71456	0.533000	0.62120	AGC	C|0.383;N|0.000	0.383	strong		0.532	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
THAP8	199745	hgsc.bcm.edu	37	19	36530332	36530332	+	Missense_Mutation	SNP	G	G	A	rs10420353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36530332G>A	ENST00000292894.1	-	3	1109	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	THAP8_ENST00000524106.1_5'Flank|AC002116.7_ENST00000586962.1_RNA|THAP8_ENST00000538849.1_Missense_Mutation_p.R44W	NM_152658.2	NP_689871.1	Q8NA92	THAP8_HUMAN	THAP domain containing 8	189			R -> W (in dbSNP:rs10420353). {ECO:0000269|PubMed:14702039}.				DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TCCTGGCACCGTTGCAGCCTC	0.701													g|||	1294	0.258387	0.2239	0.2233	5008	,	,		15161	0.3274		0.33	False		,,,				2504	0.1851				p.R189W		Atlas-SNP	.											.	THAP8	11	.	0			c.C565T						PASS	.	G	TRP/ARG	909,3421		107,695,1363	7.0	7.0	7.0		565	2.3	0.2	19	dbSNP_119	7	2503,5983		399,1705,2139	no	missense	THAP8	NM_152658.2	101	506,2400,3502	AA,AG,GG		29.4956,20.9931,26.623	benign	189/275	36530332	3412,9404	2165	4243	6408	SO:0001583	missense	199745	exon3			GGCACCGTTGCAG	AK057453	CCDS33000.1	19q13.13	2013-01-25			ENSG00000161277	ENSG00000161277		"""THAP (C2CH-type zinc finger) domain containing"""	23191	protein-coding gene	gene with protein product		612536				12575992	Standard	NM_152658		Approved	FLJ32891	uc002oda.1	Q8NA92	OTTHUMG00000048138	ENST00000292894.1:c.565C>T	19.37:g.36530332G>A	ENSP00000292894:p.Arg189Trp	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	15	13	0.866667	NM_152658	Q0P5Z7|Q96M21	Missense_Mutation	SNP	ENST00000292894.1	37	CCDS33000.1	661	0.30265567765567764	122	0.24796747967479674	90	0.24861878453038674	194	0.33916083916083917	255	0.33641160949868076	g	12.94	2.089001	0.36855	0.209931	0.294956	ENSG00000161277	ENST00000292894;ENST00000392182;ENST00000538849	D;T	0.89552	-2.53;1.67	4.54	2.33	0.28932	.	0.571368	0.14254	U	0.331258	T	0.00012	0.0000	N	0.17082	0.46	0.36517	P	0.13008200000000003	B	0.15930	0.015	B	0.08055	0.003	T	0.04915	-1.0918	9	0.32370	T	0.25	-7.5514	5.2732	0.15636	0.1082:0.0:0.6808:0.211	rs10420353;rs10420353	189	Q8NA92	THAP8_HUMAN	W	189;189;44	ENSP00000292894:R189W;ENSP00000445493:R44W	ENSP00000292894:R189W	R	-	1	2	THAP8	41222172	0.988000	0.35896	0.189000	0.23252	0.003000	0.03518	1.634000	0.37123	0.423000	0.26033	0.552000	0.68991	CGG	G|0.699;A|0.301	0.301	strong		0.701	THAP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379036.1	NM_152658	
SHROOM2	357	hgsc.bcm.edu	37	X	9859098	9859098	+	Silent	SNP	A	A	G	rs6640543	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:9859098A>G	ENST00000380913.3	+	3	489	c.399A>G	c.(397-399)ccA>ccG	p.P133P		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	133					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				CGGCCTCCCCATTCACCTCCA	0.637													A|||	3254	0.861987	0.4713	0.6844	3775	,	,		12174	0.754		0.7038	False		,,,				2504	0.7035				p.P133P		Atlas-SNP	.											.	SHROOM2	139	.	0			c.A399G						PASS	.	A		2571,1264		742,707,380,183,191	64.0	41.0	49.0		399	-3.6	0.0	X	dbSNP_116	49	6319,407		2146,270,1757,12,113	no	coding-synonymous	SHROOM2	NM_001649.2		2888,977,2137,195,304	GG,GA,G,AA,A		6.0511,32.9596,15.8224		133/1617	9859098	8890,1671	2203	4298	6501	SO:0001819	synonymous_variant	357	exon3			CTCCCCATTCACC	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.399A>G	X.37:g.9859098A>G		Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	160	159	0.99375	NM_001649	B9EIQ7	Silent	SNP	ENST00000380913.3	37	CCDS14135.1																																																																																			A|0.147;G|0.853	0.853	strong		0.637	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
RBMXL2	27288	hgsc.bcm.edu	37	11	7110548	7110548	+	Missense_Mutation	SNP	C	C	T	rs11041170	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7110548C>T	ENST00000306904.5	+	1	384	c.197C>T	c.(196-198)gCc>gTc	p.A66V		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	66	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.		A -> V (in dbSNP:rs11041170). {ECO:0000269|PubMed:10958650}.			nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAGGCCGCCGCCAGAGACATG	0.647													C|||	759	0.151558	0.2337	0.1628	5008	,	,		9247	0.0139		0.2316	False		,,,				2504	0.092				p.A66V		Atlas-SNP	.											.	RBMXL2	47	.	0			c.C197T						PASS	.	C	VAL/ALA	998,3396		105,788,1304	22.0	21.0	21.0		197	-0.5	1.0	11	dbSNP_120	21	1993,6599		240,1513,2543	no	missense	RBMXL2	NM_014469.4	64	345,2301,3847	TT,TC,CC		23.196,22.7128,23.0325	benign	66/393	7110548	2991,9995	2197	4296	6493	SO:0001583	missense	27288	exon1			CCGCCGCCAGAGA	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"""RNA binding motif (RRM) containing"""	17886	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G T"""	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.197C>T	11.37:g.7110548C>T	ENSP00000304139:p.Ala66Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_014469	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	37	CCDS7777.1	364	0.16666666666666666	119	0.241869918699187	62	0.1712707182320442	11	0.019230769230769232	172	0.22691292875989447	C	10.62	1.401357	0.25291	0.227128	0.23196	ENSG00000170748	ENST00000306904	T	0.13778	2.56	2.51	-0.49	0.12049	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.068562	0.64402	N	0.000014	T	0.00012	0.0000	N	0.00707	-1.245	0.29091	P	0.882081	B	0.06786	0.001	B	0.13407	0.009	T	0.46076	-0.9217	9	0.36615	T	0.2	.	6.1131	0.20112	0.0:0.4557:0.0:0.5443	rs11041170	66	O75526	HNRGT_HUMAN	V	66	ENSP00000304139:A66V	ENSP00000304139:A66V	A	+	2	0	RBMXL2	7067124	0.996000	0.38824	0.978000	0.43139	0.984000	0.73092	1.429000	0.34903	-0.131000	0.11578	-0.463000	0.05309	GCC	C|0.795;T|0.205	0.205	strong		0.647	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469	
SH2D2A	9047	hgsc.bcm.edu	37	1	156784982	156784982	+	Missense_Mutation	SNP	T	T	C	rs926103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156784982T>C	ENST00000368199.3	-	3	308	c.155A>G	c.(154-156)aAc>aGc	p.N52S	NTRK1_ENST00000392302.2_5'Flank|SH2D2A_ENST00000495306.1_5'UTR|SH2D2A_ENST00000368198.3_Missense_Mutation_p.N34S|SH2D2A_ENST00000392306.2_Missense_Mutation_p.N52S	NM_001161443.1|NM_001161444.1|NM_003975.3	NP_001154915.1|NP_001154916.1|NP_003966.2	Q9NP31	SH22A_HUMAN	SH2 domain containing 2A	52			N -> S (in dbSNP:rs926103). {ECO:0000269|PubMed:10692392, ECO:0000269|PubMed:10752626, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15592455, ECO:0000269|PubMed:9468509, ECO:0000269|Ref.4}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|large_intestine(2)|lung(15)	18	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ATTCCCTGTGTTGGAGGCAGC	0.617													T|||	2973	0.59365	0.3192	0.6297	5008	,	,		17540	0.8155		0.662	False		,,,				2504	0.6401				p.N52S		Atlas-SNP	.											SH2D2A_ENST00000392306,NS,carcinoma,0,2	SH2D2A	78	2	0			c.A155G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	1686,2720		330,1026,847	26.0	24.0	25.0		155,101,71,155,155	-9.9	0.0	1	dbSNP_86	25	5505,3095		1791,1923,586	yes	missense,missense,missense,missense,missense	SH2D2A	NM_001161441.1,NM_001161442.1,NM_001161443.1,NM_001161444.1,NM_003975.3	46,46,46,46,46	2121,2949,1433	CC,CT,TT		35.9884,38.266,44.7101	benign,benign,benign,benign,benign	52/400,34/372,24/362,52/390,52/390	156784982	7191,5815	2203	4300	6503	SO:0001583	missense	9047	exon3			CCTGTGTTGGAGG	AJ000553	CCDS1159.1, CCDS53380.1, CCDS53381.1	1q21	2013-02-14	2010-04-21		ENSG00000027869	ENSG00000027869		"""SH2 domain containing"""	10821	protein-coding gene	gene with protein product	"""T lymphocyte specific adaptor protein"", ""T cell specific adapter protein TSAd"", ""T cell specific adpater protein TSAd"""	604514	"""SH2 domain protein 2A"""			9468509	Standard	NM_003975		Approved	TSAd, F2771	uc009wsh.2	Q9NP31	OTTHUMG00000041305	ENST00000368199.3:c.155A>G	1.37:g.156784982T>C	ENSP00000357182:p.Asn52Ser	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	280	278	0.992857	NM_003975	O43817|Q5UBZ1|Q5VZS4|Q5VZS5|Q9UPA7	Missense_Mutation	SNP	ENST00000368199.3	37	CCDS1159.1	1349	0.6176739926739927	154	0.3130081300813008	234	0.6464088397790055	464	0.8111888111888111	497	0.6556728232189973	T	0.142	-1.101109	0.01843	0.38266	0.640116	ENSG00000027869	ENST00000368199;ENST00000368198;ENST00000392306	T;T;T	0.54866	0.59;0.55;1.01	4.94	-9.87	0.00470	.	3.198450	0.00760	N	0.001137	T	0.05135	0.0137	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.15780	-1.0425	9	0.06099	T	0.92	2.6197	0.9938	0.01462	0.1594:0.239:0.209:0.3925	rs926103;rs3748807;rs17850866;rs926103	52;34;52	Q9NP31-2;Q5VZS4;Q9NP31	.;.;SH22A_HUMAN	S	52;34;52	ENSP00000357182:N52S;ENSP00000357181:N34S;ENSP00000376123:N52S	ENSP00000357181:N34S	N	-	2	0	SH2D2A	155051606	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.442000	0.02407	-2.789000	0.00357	-1.847000	0.00572	AAC	T|0.445;C|0.555	0.555	strong		0.617	SH2D2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098982.1	NM_003975	
CCDC9	26093	hgsc.bcm.edu	37	19	47770015	47770015	+	Silent	SNP	A	A	C	rs10413121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47770015A>C	ENST00000221922.6	+	8	1090	c.868A>C	c.(868-870)Agg>Cgg	p.R290R		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	290							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		TGGCCAGTGGAGGCGCGAGTG	0.647													C|||	2564	0.511981	0.3411	0.5821	5008	,	,		15668	0.6825		0.4294	False		,,,				2504	0.6022				p.R290R		Atlas-SNP	.											CCDC9,NS,carcinoma,0,1	CCDC9	37	1	0			c.A868C						PASS	.	C		1379,3019		236,907,1056	41.0	31.0	34.0		868	4.3	1.0	19	dbSNP_119	34	3729,4865		829,2071,1397	no	coding-synonymous	CCDC9	NM_015603.2		1065,2978,2453	CC,CA,AA		43.3907,31.3552,39.3165		290/532	47770015	5108,7884	2199	4297	6496	SO:0001819	synonymous_variant	26093	exon8			CAGTGGAGGCGCG	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.868A>C	19.37:g.47770015A>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	191	88	0.460733	NM_015603		Silent	SNP	ENST00000221922.6	37	CCDS12698.1																																																																																			A|0.573;C|0.427	0.427	strong		0.647	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
MUC4	4585	hgsc.bcm.edu	37	3	195506482	195506482	+	Missense_Mutation	SNP	G	G	T	rs113936020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506482G>T	ENST00000463781.3	-	2	12428	c.11969C>A	c.(11968-11970)aCt>aAt	p.T3990N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3990N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TACTGAGGAAGTGTCGGTGAC	0.592																																					p.T3990N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.C11969A						scavenged	.						10.0	7.0	8.0					3																	195506482		623	1357	1980	SO:0001583	missense	4585	exon2			GAGGAAGTGTCGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11969C>A	3.37:g.195506482G>T	ENSP00000417498:p.Thr3990Asn	Somatic	38	1	0.0263158		WXS	Illumina HiSeq	Phase_I	24	6	0.25	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	0.405	-0.916416	0.02415	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.37;1.46	0.481	0.481	0.16809	.	0.562686	0.09843	U	0.748557	T	0.35913	0.0948	N	0.14661	0.345	0.09310	N	1	D	0.57257	0.979	D	0.68192	0.956	T	0.29852	-0.9998	9	.	.	.	.	6.8687	0.24108	1.0E-4:0.0:0.9999:0.0	.	3862	E7ESK3	.	N	3990	ENSP00000417498:T3990N;ENSP00000420243:T3990N	.	T	-	2	0	MUC4	196991261	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-0.001000	0.12947	0.537000	0.28751	0.064000	0.15345	ACT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CYP4A22	284541	hgsc.bcm.edu	37	1	47614434	47614434	+	Missense_Mutation	SNP	C	C	T	rs4926600	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:47614434C>T	ENST00000371891.3	+	12	1556	c.1525C>T	c.(1525-1527)Ctc>Ttc	p.L509F	CYP4A22_ENST00000371890.3_Missense_Mutation_p.L411F|CYP4A22_ENST00000485117.1_3'UTR|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	509			L -> F (in allele CYP4A22*7, allele CYP4A22*10, allele CYP4A22*11, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs4926600). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCTCAGGAGGCTCCCTAACCC	0.572													C|||	764	0.152556	0.0401	0.1023	5008	,	,		19061	0.3065		0.0805	False		,,,				2504	0.2556				p.L509F	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											CYP4A22,NS,carcinoma,-1,1	CYP4A22	60	1	0			c.C1525T						PASS	.	C	PHE/LEU	230,4176	137.3+/-173.1	6,218,1979	90.0	77.0	81.0		1525	0.6	0.0	1	dbSNP_111	81	758,7836	181.6+/-230.3	38,682,3577	no	missense	CYP4A22	NM_001010969.2	22	44,900,5556	TT,TC,CC		8.8201,5.2202,7.6	possibly-damaging	509/520	47614434	988,12012	2203	4297	6500	SO:0001583	missense	284541	exon12			AGGAGGCTCCCTA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.1525C>T	1.37:g.47614434C>T	ENSP00000360958:p.Leu509Phe	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	217	82	0.37788	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	279	0.12774725274725274	17	0.034552845528455285	39	0.10773480662983426	168	0.2937062937062937	55	0.07255936675461741	c	14.64	2.596638	0.46318	0.052202	0.088201	ENSG00000162365	ENST00000371890;ENST00000371891	T;T	0.73681	-0.77;-0.58	1.69	0.555	0.17247	.	0.379178	0.27725	N	0.018109	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	D	0.58620	0.983	D	0.63793	0.918	T	0.07927	-1.0747	9	0.72032	D	0.01	.	3.3575	0.07174	0.2617:0.5536:0.0:0.1847	rs4926600	509	Q5TCH4	CP4AM_HUMAN	F	411;509	ENSP00000360957:L411F;ENSP00000360958:L509F	ENSP00000360957:L411F	L	+	1	0	CYP4A22	47387021	0.846000	0.29590	0.007000	0.13788	0.443000	0.32047	1.006000	0.29847	0.011000	0.14865	0.194000	0.17425	CTC	C|0.949;T|0.051	0.051	strong		0.572	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
CAPNS2	84290	hgsc.bcm.edu	37	16	55601388	55601388	+	Silent	SNP	A	A	G	rs1502003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:55601388A>G	ENST00000457326.2	+	1	805	c.720A>G	c.(718-720)gaA>gaG	p.E240E	LPCAT2_ENST00000262134.5_Intron|LPCAT2_ENST00000565056.1_Intron	NM_032330.1	NP_115706.1	Q96L46	CPNS2_HUMAN	calpain, small subunit 2	240	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|large_intestine(1)|lung(3)|prostate(2)	7						CTATCAAAGAATGGCTGCAGT	0.478													A|||	2118	0.422923	0.3775	0.353	5008	,	,		19080	0.4087		0.4632	False		,,,				2504	0.5072				p.E240E		Atlas-SNP	.											.	CAPNS2	21	.	0			c.A720G						PASS	.	A	,	1577,2345		305,967,689	111.0	106.0	108.0		,720	-12.0	0.0	16	dbSNP_88	108	3866,4466		921,2024,1221	no	intron,coding-synonymous	LPCAT2,CAPNS2	NM_017839.4,NM_032330.1	,	1226,2991,1910	GG,GA,AA		46.3994,40.2091,44.4181	,	,240/249	55601388	5443,6811	1961	4166	6127	SO:0001819	synonymous_variant	84290	exon1			CAAAGAATGGCTG	AY052551	CCDS54010.1	16q12.2	2013-01-10						"""EF-hand domain containing"""	16371	protein-coding gene	gene with protein product						11853546	Standard	NM_032330		Approved	MGC12536, MGC14804	uc002eid.1	Q96L46		ENST00000457326.2:c.720A>G	16.37:g.55601388A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	131	129	0.984733	NM_032330	Q9BPV4	Silent	SNP	ENST00000457326.2	37	CCDS54010.1																																																																																			A|0.574;G|0.425	0.425	strong		0.478	CAPNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396391.1	NM_032330	
CHGB	1114	hgsc.bcm.edu	37	20	5904040	5904040	+	Missense_Mutation	SNP	G	G	A	rs742711	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:5904040G>A	ENST00000378961.4	+	4	1454	c.1250G>A	c.(1249-1251)cGc>cAc	p.R417H		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	417			R -> H (in dbSNP:rs742711). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)	p.R417H(1)		breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GGAAAGGGACGCCATCACAGA	0.527													G|||	1158	0.23123	0.0734	0.2334	5008	,	,		20807	0.379		0.2584	False		,,,				2504	0.2628				p.R417H		Atlas-SNP	.											CHGB,NS,carcinoma,0,1	CHGB	112	1	1	Substitution - Missense(1)	stomach(1)	c.G1250A	GRCh37	CM043991	CHGB	M	rs742711	PASS	.	G	HIS/ARG	521,3885	238.4+/-249.8	37,447,1719	80.0	80.0	80.0		1250	-10.8	0.0	20	dbSNP_86	80	2277,6323	378.7+/-339.0	302,1673,2325	yes	missense	CHGB	NM_001819.2	29	339,2120,4044	AA,AG,GG		26.4767,11.8248,21.5131	benign	417/678	5904040	2798,10208	2203	4300	6503	SO:0001583	missense	1114	exon4			AGGGACGCCATCA		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1250G>A	20.37:g.5904040G>A	ENSP00000368244:p.Arg417His	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	529	0.24221611721611722	49	0.09959349593495935	77	0.212707182320442	206	0.36013986013986016	197	0.2598944591029024	G	1.700	-0.501792	0.04261	0.118248	0.264767	ENSG00000089199	ENST00000378961	T	0.01963	4.53	5.4	-10.8	0.00216	.	2.054640	0.02189	N	0.061130	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.15473	0.013	B	0.06405	0.002	T	0.48536	-0.9027	9	0.10902	T	0.67	1.7578	6.6545	0.22981	0.2912:0.3742:0.2747:0.0599	rs742711;rs52814619;rs61667157;rs742711	417	P05060	SCG1_HUMAN	H	417	ENSP00000368244:R417H	ENSP00000368244:R417H	R	+	2	0	CHGB	5852040	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-2.806000	0.00758	-2.864000	0.00326	-1.788000	0.00630	CGC	G|0.775;A|0.225	0.225	strong		0.527	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
MX1	4599	hgsc.bcm.edu	37	21	42817930	42817930	+	Missense_Mutation	SNP	G	G	A	rs469390	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:42817930G>A	ENST00000398600.2	+	15	2160	c.1135G>A	c.(1135-1137)Gtt>Att	p.V379I	MX1_ENST00000455164.2_Missense_Mutation_p.V379I|MX1_ENST00000398598.3_Missense_Mutation_p.V379I|MX1_ENST00000288383.6_Missense_Mutation_p.V356I	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	379	Middle domain.|Stalk.		V -> I (in dbSNP:rs469390). {ECO:0000269|PubMed:10830953, ECO:0000269|PubMed:10942113, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2154602, ECO:0000269|PubMed:2481229}.		apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|response to type I interferon (GO:0034340)|response to virus (GO:0009615)|signal transduction (GO:0007165)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	27		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				TTGACAGAAAGTTAATGCCTT	0.463													g|||	2313	0.461861	0.444	0.4496	5008	,	,		22175	0.2857		0.5885	False		,,,				2504	0.546				p.V379I		Atlas-SNP	.											.	MX1	58	.	0			c.G1135A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	1976,2430	555.1+/-379.2	444,1088,671	92.0	81.0	85.0		1135,1135,1135	2.3	0.9	21	dbSNP_80	85	5065,3535	630.3+/-398.3	1456,2153,691	yes	missense,missense,missense	MX1	NM_001144925.1,NM_001178046.1,NM_002462.3	29,29,29	1900,3241,1362	AA,AG,GG		41.1047,44.8479,45.8634	benign,benign,benign	379/663,379/663,379/663	42817930	7041,5965	2203	4300	6503	SO:0001583	missense	4599	exon15			CAGAAAGTTAATG		CCDS13673.1, CCDS74796.1	21q22.3	2014-07-15	2014-07-15		ENSG00000157601	ENSG00000157601			7532	protein-coding gene	gene with protein product	"""interferon-inducible protein p78"""	147150	"""myxovirus (influenza) resistance 1, homolog of murine (interferon-inducible protein p78)"", ""myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)"""			17570575	Standard	XM_005260979		Approved	IFI-78K, MxA	uc010goq.3	P20591	OTTHUMG00000086755	ENST00000398600.2:c.1135G>A	21.37:g.42817930G>A	ENSP00000381601:p.Val379Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Missense_Mutation	SNP	ENST00000398600.2	37	CCDS13673.1	945	0.4326923076923077	216	0.43902439024390244	168	0.46408839779005523	134	0.23426573426573427	427	0.5633245382585752	g	0.119	-1.128583	0.01756	0.448479	0.588953	ENSG00000157601	ENST00000398600;ENST00000398598;ENST00000455164;ENST00000288383	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	4.72	2.29	0.28610	Dynamin central domain (1);	0.245514	0.40640	N	0.001046	T	0.00012	0.0000	N	0.00392	-1.555	0.33847	P	0.367781	B	0.02656	0.0	B	0.01281	0.0	T	0.46091	-0.9216	9	0.02654	T	1	-13.2937	6.626	0.22830	0.7612:0.154:0.0847:0.0	rs469390;rs1130854;rs1804114;rs2070231;rs2230453;rs3177819;rs3190226;rs11550654;rs11566221;rs17000967;rs17416634;rs52825961;rs56495964;rs61388665;rs469390	379	P20591	MX1_HUMAN	I	379;379;379;356	ENSP00000381601:V379I;ENSP00000381599:V379I;ENSP00000410523:V379I;ENSP00000288383:V356I	ENSP00000288383:V356I	V	+	1	0	MX1	41739800	1.000000	0.71417	0.912000	0.35992	0.352000	0.29268	0.915000	0.28638	0.350000	0.24002	-0.285000	0.09966	GTT	G|0.513;A|0.487	0.487	strong		0.463	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
MRPL12	6182	hgsc.bcm.edu	37	17	79671298	79671298	+	Silent	SNP	C	C	T	rs148659191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79671298C>T	ENST00000333676.3	+	2	244	c.99C>T	c.(97-99)gcC>gcT	p.A33A	SLC25A10_ENST00000571730.1_Silent_p.A33A|RP13-1032I1.7_ENST00000575312.1_RNA|SLC25A10_ENST00000541223.1_Silent_p.A33A	NM_002949.3	NP_002940.2	P52815	RM12_HUMAN	mitochondrial ribosomal protein L12	33				A -> T (in Ref. 1; CAA56249). {ECO:0000305}.	positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|lung(2)|urinary_tract(1)	4	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			GTGTCTGTGCCGTGCGACATA	0.607													C|||	10	0.00199681	0.0	0.0029	5008	,	,		17178	0.0		0.005	False		,,,				2504	0.0031				p.A33A		Atlas-SNP	.											.	MRPL12	12	.	0			c.C99T						PASS	.	C		4,4400	6.2+/-15.9	0,4,2198	55.0	51.0	52.0		99	-9.1	0.0	17	dbSNP_134	52	63,8537	38.8+/-94.9	0,63,4237	no	coding-synonymous	MRPL12	NM_002949.3		0,67,6435	TT,TC,CC		0.7326,0.0908,0.5152		33/199	79671298	67,12937	2202	4300	6502	SO:0001819	synonymous_variant	6182	exon2			CTGTGCCGTGCGA	X79865	CCDS11785.1	17q25	2012-11-14			ENSG00000262814	ENSG00000262814		"""Mitochondrial ribosomal proteins / large subunits"""	10378	protein-coding gene	gene with protein product		602375		RPML12		8626705, 9169145	Standard	NM_002949		Approved	MRPL7/L12, MRPL7		P52815	OTTHUMG00000178171	ENST00000333676.3:c.99C>T	17.37:g.79671298C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	100	60	0.6	NM_002949	Q969U0|Q9HCA2|Q9UQJ3	Silent	SNP	ENST00000333676.3	37	CCDS11785.1																																																																																			C|0.996;T|0.004	0.004	strong		0.607	MRPL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440812.1	NM_002949	
CLEC17A	388512	hgsc.bcm.edu	37	19	14705574	14705574	+	Missense_Mutation	SNP	T	T	C	rs78269670	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14705574T>C	ENST00000417570.1	+	7	403	c.365T>C	c.(364-366)cTg>cCg	p.L122P	CLEC17A_ENST00000547437.1_Missense_Mutation_p.L122P|CLEC17A_ENST00000397439.2_Missense_Mutation_p.L105P	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	122						cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)										CTTCTAGGCCTGGACCTCGCC	0.532													N|||	417	0.0832668	0.174	0.036	5008	,	,		18213	0.004		0.0676	False		,,,				2504	0.092				p.L122P		Atlas-SNP	.											.	CLEC17A	27	.	0			c.T365C						PASS	.		PRO/LEU,PRO/LEU	571,3429		39,493,1468	79.0	81.0	81.0		365,365	-0.2	0.0	19	dbSNP_131	81	555,7781		21,513,3634	yes	missense,missense	CLEC17A	NM_207390.3,NM_001204118.1	98,98	60,1006,5102	CC,CT,TT		6.6579,14.275,9.1278	benign,benign	122/307,122/379	14705574	1126,11210	2000	4168	6168	SO:0001583	missense	388512	exon7			TAGGCCTGGACCT	AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912		"""C-type lectin domain containing"""	34520	protein-coding gene	gene with protein product	"""prolectin"""					19419970	Standard	NM_207390		Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.365T>C	19.37:g.14705574T>C	ENSP00000393719:p.Leu122Pro	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_207390	A8MX68|B2RTX0|B7ZMM4	Missense_Mutation	SNP	ENST00000417570.1	37	CCDS56087.1	122	0.055860805860805864	59	0.11991869918699187	13	0.03591160220994475	3	0.005244755244755245	47	0.06200527704485488	t	12.58	1.982059	0.34942	0.14275	0.066579	ENSG00000187912	ENST00000547437;ENST00000397439;ENST00000417570	T;T;T	0.63255	-0.03;1.28;-0.03	3.42	-0.168	0.13343	.	2.549380	0.02249	N	0.066442	T	0.00440	0.0014	L	0.27053	0.805	0.19575	N	0.999962	B;B;B;B	0.21309	0.041;0.023;0.054;0.015	B;B;B;B	0.17722	0.019;0.01;0.014;0.011	T	0.08493	-1.0719	10	0.66056	D	0.02	-19.8414	2.8523	0.05561	0.1885:0.2354:0.0:0.5761	.	122;122;122;122	Q6ZS10-2;Q6ZS10-3;Q6ZS10;F8W1T8	.;.;CL17A_HUMAN;.	P	122;105;122	ENSP00000450065:L122P;ENSP00000380581:L105P;ENSP00000393719:L122P	ENSP00000341620:L122P	L	+	2	0	CLEC17A	14566574	0.484000	0.25964	0.013000	0.15412	0.011000	0.07611	1.094000	0.30951	-0.251000	0.09542	-0.560000	0.04181	CTG	T|0.943;C|0.057	0.057	strong		0.532	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403400.1	NM_207390	
ANLN	54443	hgsc.bcm.edu	37	7	36445855	36445855	+	Silent	SNP	A	A	C	rs386712160|rs61737563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:36445855A>C	ENST00000265748.2	+	4	774	c.553A>C	c.(553-555)Aga>Cga	p.R185R	ANLN_ENST00000396068.2_Silent_p.R185R	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	185	Nuclear localization.		R -> K (in dbSNP:rs197367). {ECO:0000269|PubMed:10931866, ECO:0000269|PubMed:16964243}.		hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						TTCCCCTCCCAGACCTCTGCT	0.468													A|||	238	0.047524	0.0431	0.0677	5008	,	,		18777	0.002		0.1064	False		,,,				2504	0.0256				p.R185R		Atlas-SNP	.											.	ANLN	101	.	0			c.A553C						PASS	.																																			SO:0001819	synonymous_variant	54443	exon4			CCTCCCAGACCTC	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"""Pleckstrin homology (PH) domain containing"""	14082	protein-coding gene	gene with protein product			"""anillin (Drosophila Scraps homolog), actin binding protein"", ""anillin, actin binding protein (scraps homolog, Drosophila)"""			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.553A>C	7.37:g.36445855A>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	37	CCDS5447.1																																																																																			A|0.929;C|0.071	0.071	strong		0.468	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685	
FCGBP	8857	hgsc.bcm.edu	37	19	40392631	40392631	+	Missense_Mutation	SNP	G	G	A	rs80068592	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40392631G>A	ENST00000221347.6	-	16	7880	c.7873C>T	c.(7873-7875)Ccc>Tcc	p.P2625S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2625	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGAGAGTCGGGCACCACCTCC	0.642													G|||	1353	0.270168	0.1808	0.4121	5008	,	,		18489	0.2093		0.3569	False		,,,				2504	0.2638				p.P2625S		Atlas-SNP	.											.	FCGBP	416	.	0			c.C7873T						PASS	.						14.0	17.0	16.0					19																	40392631		2165	4278	6443	SO:0001583	missense	8857	exon16			AGTCGGGCACCAC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.7873C>T	19.37:g.40392631G>A	ENSP00000221347:p.Pro2625Ser	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	717	176	0.245467	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	7.277	0.608327	0.14002	.	.	ENSG00000090920	ENST00000221347	T	0.18657	2.2	2.66	2.66	0.31614	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.27731	0.0682	M	0.71920	2.185	0.37706	P	0.07559199999999999	P	0.41131	0.739	P	0.48304	0.573	T	0.29761	-1.0001	8	0.02654	T	1	.	12.5273	0.56093	0.0:0.0:1.0:0.0	.	2625	Q9Y6R7	FCGBP_HUMAN	S	2625	ENSP00000221347:P2625S	ENSP00000221347:P2625S	P	-	1	0	FCGBP	45084471	0.034000	0.19679	0.110000	0.21437	0.008000	0.06430	0.899000	0.28417	1.495000	0.48549	0.298000	0.19748	CCC	G|0.772;A|0.228	0.228	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
MLC1	23209	hgsc.bcm.edu	37	22	50502526	50502526	+	Silent	SNP	A	A	G	rs11568187	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50502526A>G	ENST00000311597.5	-	11	1602	c.996T>C	c.(994-996)agT>agC	p.S332S	MLC1_ENST00000395876.2_Silent_p.S332S|MLC1_ENST00000431262.2_Silent_p.S302S|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000538737.1_Silent_p.S298S|MLC1_ENST00000535444.1_Silent_p.S253S|MLC1_ENST00000450140.2_Silent_p.S280S	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	332					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		GCAGCCTTGCACTGACCTTGA	0.677													g|||	657	0.13119	0.059	0.1758	5008	,	,		14057	0.0923		0.1312	False		,,,				2504	0.2372				p.S332S		Atlas-SNP	.											.	MLC1	48	.	0			c.T996C						PASS	.		,	326,4080	787.1+/-414.8	15,296,1892	51.0	47.0	48.0		996,996	0.8	0.0	22	dbSNP_120	48	1195,7403	754.8+/-407.5	91,1013,3195	no	coding-synonymous,coding-synonymous	MLC1	NM_015166.3,NM_139202.2	,	106,1309,5087	GG,GA,AA		13.8986,7.399,11.6964	,	332/378,332/378	50502526	1521,11483	2203	4299	6502	SO:0001819	synonymous_variant	23209	exon11			CCTTGCACTGACC	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.996T>C	22.37:g.50502526A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			A|0.894;G|0.106	0.106	strong		0.677	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
MGA	23269	hgsc.bcm.edu	37	15	42032383	42032383	+	Missense_Mutation	SNP	C	C	G	rs17677991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42032383C>G	ENST00000570161.1	+	13	4567	c.4567C>G	c.(4567-4569)Cca>Gca	p.P1523A	MGA_ENST00000389936.4_Missense_Mutation_p.P1523A|MGA_ENST00000219905.7_Missense_Mutation_p.P1523A|MGA_ENST00000545763.1_Missense_Mutation_p.P1523A|MGA_ENST00000566586.1_Missense_Mutation_p.P1523A			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GGCGTTTGTCCCAGCAAAACG	0.488													C|||	1509	0.301318	0.2141	0.4597	5008	,	,		17579	0.1875		0.3797	False		,,,				2504	0.3436				p.P1523A		Atlas-SNP	.											.	MGA	264	.	0			c.C4567G						PASS	.	C	ALA/PRO,ALA/PRO	871,2961		109,653,1154	55.0	53.0	54.0		4567,4567	4.2	1.0	15	dbSNP_123	54	2850,5406		486,1878,1764	yes	missense,missense	MGA	NM_001080541.2,NM_001164273.1	27,27	595,2531,2918	GG,GC,CC		34.5203,22.7296,30.7826	probably-damaging,probably-damaging	1523/2857,1523/3066	42032383	3721,8367	1916	4128	6044	SO:0001583	missense	23269	exon14			TTTGTCCCAGCAA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.4567C>G	15.37:g.42032383C>G	ENSP00000457035:p.Pro1523Ala	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	178	94	0.52809	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	661	0.30265567765567764	110	0.22357723577235772	161	0.4447513812154696	98	0.17132867132867133	292	0.38522427440633245	C	11.03	1.520149	0.27211	0.227296	0.345203	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.94828	-2.08;-2.09;-3.53	6.08	4.22	0.49857	.	0.216114	0.32459	N	0.006068	T	0.00012	0.0000	N	0.19112	0.55	0.33472	P	0.41374200000000005	P;P;B	0.51147	0.657;0.942;0.189	B;P;B	0.48304	0.138;0.573;0.058	T	0.01276	-1.1398	9	0.66056	D	0.02	.	8.768	0.34715	0.0:0.722:0.0:0.278	rs17677991;rs57914890;rs17677991	139;1523;1523	B4DVS1;F5H7K2;E7ENI0	.;.;.	A	1523	ENSP00000219905:P1523A;ENSP00000374586:P1523A;ENSP00000442467:P1523A	ENSP00000219905:P1523A	P	+	1	0	MGA	39819675	1.000000	0.71417	0.990000	0.47175	0.940000	0.58332	1.448000	0.35112	0.919000	0.36945	-0.218000	0.12543	CCA	C|0.698;G|0.302	0.302	strong		0.488	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
OR8D1	283159	hgsc.bcm.edu	37	11	124180082	124180082	+	Missense_Mutation	SNP	A	A	G	rs4936919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124180082A>G	ENST00000357821.2	-	1	651	c.581T>C	c.(580-582)cTc>cCc	p.L194P		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	194			L -> P (in dbSNP:rs4936919).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		AAGCTCATTGAGGTGTGTGTT	0.463													A|||	1435	0.286542	0.1543	0.3458	5008	,	,		21734	0.4206		0.4066	False		,,,				2504	0.1616				p.L194P		Atlas-SNP	.											.	OR8D1	53	.	0			c.T581C						PASS	.	A	PRO/LEU	876,3524		88,700,1412	58.0	47.0	50.0		581	1.9	0.1	11	dbSNP_111	50	3363,5235		670,2023,1606	yes	missense	OR8D1	NM_001002917.1	98	758,2723,3018	GG,GA,AA		39.1137,19.9091,32.6127	possibly-damaging	194/309	124180082	4239,8759	2200	4299	6499	SO:0001583	missense	283159	exon1			TCATTGAGGTGTG	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"""GPCR / Class A : Olfactory receptors"""	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.581T>C	11.37:g.124180082A>G	ENSP00000350474:p.Leu194Pro	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	37	CCDS31706.1	741	0.3392857142857143	65	0.13211382113821138	133	0.3674033149171271	245	0.42832167832167833	298	0.39313984168865435	a	12.30	1.897451	0.33535	0.199091	0.391137	ENSG00000196341	ENST00000357821	T	0.00262	8.4	4.29	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.243694	0.20189	U	0.097346	T	0.00012	0.0000	L	0.54908	1.71	0.54753	P	1.2000000000012001E-5	D	0.53619	0.961	P	0.59948	0.866	T	0.33675	-0.9859	9	0.87932	D	0	.	2.6159	0.04903	0.4092:0.0:0.2601:0.3307	rs4936919;rs52814445;rs58464091;rs4936919	194	Q8WZ84	OR8D1_HUMAN	P	194	ENSP00000350474:L194P	ENSP00000350474:L194P	L	-	2	0	OR8D1	123685292	0.000000	0.05858	0.084000	0.20598	0.001000	0.01503	0.080000	0.14802	0.208000	0.20626	-0.489000	0.04712	CTC	A|0.672;G|0.328	0.328	strong		0.463	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917	
SDK1	221935	hgsc.bcm.edu	37	7	4172006	4172006	+	Silent	SNP	C	C	T	rs13224870	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4172006C>T	ENST00000404826.2	+	28	4318	c.4179C>T	c.(4177-4179)tcC>tcT	p.S1393S	SDK1_ENST00000389531.3_Silent_p.S1393S	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1393	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GACTCACCTCCGTGCGGATAG	0.622													C|||	1226	0.244808	0.1067	0.3084	5008	,	,		17826	0.0992		0.3907	False		,,,				2504	0.3865				p.S1393S		Atlas-SNP	.											SDK1,NS,malignant_melanoma,+1,1	SDK1	361	1	0			c.C4179T						PASS	.	C		624,3782	262.5+/-264.9	43,538,1622	56.0	45.0	49.0		4179	-10.9	0.0	7	dbSNP_121	49	3494,5106	503.6+/-376.0	720,2054,1526	no	coding-synonymous	SDK1	NM_152744.3		763,2592,3148	TT,TC,CC		40.6279,14.1625,31.6623		1393/2214	4172006	4118,8888	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon28			CACCTCCGTGCGG	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4179C>T	7.37:g.4172006C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			C|0.720;T|0.280	0.280	strong		0.622	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
ITPR3	3710	hgsc.bcm.edu	37	6	33641379	33641379	+	Silent	SNP	T	T	C	rs1803831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33641379T>C	ENST00000374316.5	+	24	4000	c.2940T>C	c.(2938-2940)aaT>aaC	p.N980N	ITPR3_ENST00000605930.1_Silent_p.N980N			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	980					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TCATCCTCAATGTCCGCCTGG	0.557													T|||	2379	0.47504	0.3086	0.4813	5008	,	,		21094	0.5268		0.505	False		,,,				2504	0.6115				p.N980N		Atlas-SNP	.											.	ITPR3	409	.	0			c.T2940C						PASS	.	T		1442,2964	467.6+/-354.9	244,954,1005	282.0	242.0	256.0		2940	-10.4	0.3	6	dbSNP_89	256	4517,4083	594.2+/-393.3	1169,2179,952	no	coding-synonymous	ITPR3	NM_002224.3		1413,3133,1957	CC,CT,TT		47.4767,32.7281,45.8173		980/2672	33641379	5959,7047	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon23			CCTCAATGTCCGC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.2940T>C	6.37:g.33641379T>C		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	434	212	0.488479	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			A|0.000;C|0.461;T|0.538	0.461	strong		0.557	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
DHCR7	1717	hgsc.bcm.edu	37	11	71146577	71146577	+	Silent	SNP	G	G	A	rs909217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71146577G>A	ENST00000355527.3	-	9	1548	c.1272C>T	c.(1270-1272)ggC>ggT	p.G424G	DHCR7_ENST00000407721.2_Silent_p.G424G	NM_001163817.1|NM_001360.2	NP_001157289.1|NP_001351.2	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	424					blood vessel development (GO:0001568)|cell differentiation (GO:0030154)|cholesterol biosynthetic process (GO:0006695)|lung development (GO:0030324)|multicellular organism growth (GO:0035264)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|regulation of cholesterol biosynthetic process (GO:0045540)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear outer membrane (GO:0005640)	7-dehydrocholesterol reductase activity (GO:0047598)	p.G424G(1)		endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(1)|skin(1)	19						GCAGGTGGCCGCCGCCACAGG	0.672									Smith-Lemli-Opitz syndrome				G|||	1913	0.381989	0.2413	0.513	5008	,	,		15493	0.3839		0.6978	False		,,,				2504	0.1524				p.G424G		Atlas-SNP	.											DHCR7_ENST00000355527,NS,lymphoid_neoplasm,0,1	DHCR7	98	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1272T						PASS	.	G	,	1479,2915		273,933,991	23.0	26.0	25.0		1272,1272	-4.0	1.0	11	dbSNP_86	25	6337,2241		2352,1633,304	no	coding-synonymous,coding-synonymous	DHCR7	NM_001163817.1,NM_001360.2	,	2625,2566,1295	AA,AG,GG		26.125,33.6595,39.7471	,	424/476,424/476	71146577	7816,5156	2197	4289	6486	SO:0001819	synonymous_variant	1717	exon9	Familial Cancer Database	SLOS type I & II	GTGGCCGCCGCCA	AF034544	CCDS8200.1	11q13.4	2014-09-17	2004-02-13				1.3.1.21		2860	protein-coding gene	gene with protein product		602858	"""Smith-Lemli-Opitz syndrome"""	SLOS		9465114, 9634533	Standard	NM_001360		Approved		uc001oql.3	Q9UBM7		ENST00000355527.3:c.1272C>T	11.37:g.71146577G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	39	28	0.717949	NM_001163817	B2R6Z2|O60492|O60717	Silent	SNP	ENST00000355527.3	37	CCDS8200.1																																																																																			G|0.451;A|0.549	0.549	strong		0.672	DHCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394243.1	NM_001360	
CNTNAP5	129684	hgsc.bcm.edu	37	2	125281910	125281910	+	Missense_Mutation	SNP	C	C	T	rs17727261	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:125281910C>T	ENST00000431078.1	+	9	1719	c.1355C>T	c.(1354-1356)tCg>tTg	p.S452L		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	452	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		S -> L (in dbSNP:rs17727261).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CTGTGGCACTCGGTTAGCATC	0.522													C|||	90	0.0179712	0.0015	0.0187	5008	,	,		17605	0.001		0.0626	False		,,,				2504	0.0112				p.S452L		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.C1355T						PASS	.	C	LEU/SER	23,4135		0,23,2056	75.0	80.0	78.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1355	5.9	0.9	2	dbSNP_123	78	429,8005		13,403,3801	yes	missense	CNTNAP5	NM_130773.2	145	13,426,5857	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	5.0866,0.5532,3.5896	benign	452/1307	125281910	452,12140	2079	4217	6296	SO:0001583	missense	129684	exon9			GGCACTCGGTTAG	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1355C>T	2.37:g.125281910C>T	ENSP00000399013:p.Ser452Leu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	59	0.027014652014652016	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	48	0.0633245382585752	C	15.22	2.768382	0.49680	0.005532	0.050866	ENSG00000155052	ENST00000431078	T	0.79033	-1.23	5.95	5.95	0.96441	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.339680	0.21126	N	0.079740	T	0.34250	0.0891	M	0.66439	2.03	0.44337	D	0.997224	B	0.14805	0.011	B	0.11329	0.006	T	0.61584	-0.7033	10	0.54805	T	0.06	.	19.3736	0.94500	0.0:1.0:0.0:0.0	rs17727261;rs52806650;rs17727261	452	Q8WYK1	CNTP5_HUMAN	L	452	ENSP00000399013:S452L	ENSP00000399013:S452L	S	+	2	0	CNTNAP5	124998380	0.758000	0.28405	0.908000	0.35775	0.349000	0.29174	1.421000	0.34815	2.825000	0.97269	0.655000	0.94253	TCG	C|0.972;T|0.028	0.028	strong		0.522	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
LRIT3	345193	hgsc.bcm.edu	37	4	110791413	110791413	+	Missense_Mutation	SNP	C	C	T	rs2347132	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110791413C>T	ENST00000594814.1	+	4	1508	c.1508C>T	c.(1507-1509)aCg>aTg	p.T503M	LRIT3_ENST00000409621.2_Missense_Mutation_p.T320M|LRIT3_ENST00000379920.3_Missense_Mutation_p.T458M|LRIT3_ENST00000327908.3_Missense_Mutation_p.T320M	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	503	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> M (in dbSNP:rs2347132). {ECO:0000269|PubMed:15489334}.		regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		GTGACATTGACGTGGAATATG	0.463													C|||	1297	0.258986	0.27	0.3804	5008	,	,		22532	0.3224		0.1481	False		,,,				2504	0.2065				p.T503M		Atlas-SNP	.											.	LRIT3	107	.	0			c.C1508T						PASS	.	C	MET/THR	1072,3334	390.0+/-327.5	133,806,1264	155.0	141.0	146.0		1373	-10.1	0.0	4	dbSNP_100	146	1185,7415	241.3+/-271.7	100,985,3215	yes	missense	LRIT3	NM_198506.2	81	233,1791,4479	TT,TC,CC		13.7791,24.3305,17.3535	benign	458/635	110791413	2257,10749	2203	4300	6503	SO:0001583	missense	345193	exon4			CATTGACGTGGAA	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1508C>T	4.37:g.110791413C>T	ENSP00000469759:p.Thr503Met	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	521	0.23855311355311357	129	0.2621951219512195	117	0.32320441988950277	164	0.2867132867132867	111	0.14643799472295516	C	2.222	-0.378282	0.05000	0.243305	0.137791	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.33438	1.41;1.41;1.41	5.06	-10.1	0.00402	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.709224	0.14340	N	0.325797	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B;B	0.15141	0.007;0.012	B;B	0.10450	0.001;0.005	T	0.24905	-1.0147	9	0.36615	T	0.2	.	10.6999	0.45920	0.1566:0.5584:0.0:0.285	rs2347132;rs57546989;rs2347132	458;320	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	M	320;458;320	ENSP00000328222:T320M;ENSP00000369252:T458M;ENSP00000386734:T320M	ENSP00000328222:T320M	T	+	2	0	LRIT3	111010862	0.000000	0.05858	0.000000	0.03702	0.281000	0.26958	-0.356000	0.07661	-3.046000	0.00261	-1.876000	0.00548	ACG	C|0.787;N|0.001	.	strong		0.463	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
PABPN1L	390748	hgsc.bcm.edu	37	16	88932976	88932976	+	Silent	SNP	C	C	G	rs77252404	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88932976C>G	ENST00000419291.2	-	1	50	c.39G>C	c.(37-39)ccG>ccC	p.P13P	PABPN1L_ENST00000378358.4_Silent_p.P13P|PABPN1L_ENST00000427766.1_Silent_p.P13P|PABPN1L_ENST00000411789.2_Silent_p.P13P	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	13						cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						AGGCCTGAGTCGGGGGTGGGA	0.697													g|||	282	0.0563099	0.1566	0.0274	5008	,	,		17738	0.0198		0.0268	False		,,,				2504	0.0092				p.P13P		Atlas-SNP	.											.	PABPN1L	25	.	0			c.G39C						PASS	.	G		377,3275		23,331,1472	15.0	17.0	16.0		39	-1.4	0.0	16	dbSNP_132	16	176,7872		2,172,3850	no	coding-synonymous	PABPN1L	NM_001080487.2		25,503,5322	GG,GC,CC		2.1869,10.3231,4.7265		13/279	88932976	553,11147	1826	4024	5850	SO:0001819	synonymous_variant	390748	exon1			CTGAGTCGGGGGT		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"""RNA binding motif (RRM) containing"""	37237	protein-coding gene	gene with protein product	"""embryonic poly(A) binding protein 2"""					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.39G>C	16.37:g.88932976C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_001080487	A1L3B3|A2VDI2	Silent	SNP	ENST00000419291.2	37	CCDS45547.2																																																																																			C|0.957;G|0.043	0.043	strong		0.697	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	
FAT2	2196	hgsc.bcm.edu	37	5	150946773	150946773	+	Missense_Mutation	SNP	G	G	A	rs1432862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150946773G>A	ENST00000261800.5	-	1	1732	c.1720C>T	c.(1720-1722)Cgc>Tgc	p.R574C		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	574	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> C (in dbSNP:rs1432862).		epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGTCTTGGCGGATAGACCCT	0.448													G|||	2093	0.417931	0.4365	0.4524	5008	,	,		20289	0.3562		0.4901	False		,,,				2504	0.3579				p.R574C		Atlas-SNP	.											.	FAT2	465	.	0			c.C1720T						PASS	.	G	CYS/ARG	1936,2470	543.6+/-376.3	413,1110,680	73.0	77.0	76.0		1720	4.3	0.0	5	dbSNP_88	76	4501,4099	589.1+/-392.5	1184,2133,983	yes	missense	FAT2	NM_001447.2	180	1597,3243,1663	AA,AG,GG		47.6628,43.9401,49.4925	probably-damaging	574/4350	150946773	6437,6569	2203	4300	6503	SO:0001583	missense	2196	exon1			CTTGGCGGATAGA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.1720C>T	5.37:g.150946773G>A	ENSP00000261800:p.Arg574Cys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	167	55	0.329341	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	965	0.44184981684981683	234	0.47560975609756095	162	0.44751381215469616	201	0.3513986013986014	368	0.48548812664907653	G	12.72	2.022637	0.35701	0.439401	0.523372	ENSG00000086570	ENST00000261800	T	0.51071	0.72	5.22	4.33	0.51752	Cadherin (3);Cadherin-like (1);	0.788007	0.11570	N	0.550832	T	0.00012	0.0000	M	0.62723	1.935	0.24939	P	0.99186287	D	0.61697	0.99	P	0.51101	0.659	T	0.46952	-0.9154	9	0.66056	D	0.02	.	15.6599	0.77178	0.0:0.1377:0.8623:0.0	rs1432862;rs61018396;rs1432862	574	Q9NYQ8	FAT2_HUMAN	C	574	ENSP00000261800:R574C	ENSP00000261800:R574C	R	-	1	0	FAT2	150926966	1.000000	0.71417	0.027000	0.17364	0.064000	0.16182	6.638000	0.74309	1.148000	0.42385	0.655000	0.94253	CGC	G|0.528;A|0.472	0.472	strong		0.448	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
NBPF10	100132406	hgsc.bcm.edu	37	1	145368461	145368461	+	Missense_Mutation	SNP	A	A	C	rs12128680	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145368461A>C	ENST00000369339.3	+	17	2046	c.1793A>C	c.(1792-1794)gAa>gCa	p.E598A	NBPF10_ENST00000369338.1_Missense_Mutation_p.E596A|NBPF10_ENST00000342960.5_Missense_Mutation_p.E3480A			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	775	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GTGCTGATGGAAGTGGAAGAG	0.468																																					p.E3480A		Atlas-SNP	.											.	NBPF10	221	.	0			c.A10439C						PASS	.																																			SO:0001583	missense	100132406	exon84			TGATGGAAGTGGA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.1793A>C	1.37:g.145368461A>C	ENSP00000358345:p.Glu598Ala	Somatic	439	0	0		WXS	Illumina HiSeq	Phase_I	531	215	0.404896	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	6.133	0.392687	0.11638	.	.	ENSG00000163386	ENST00000369339;ENST00000369338;ENST00000342960	T;T	0.09817	2.94;2.94	0.732	-1.11	0.09840	.	.	.	.	.	T	0.04679	0.0127	M	0.83603	2.65	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.38178	-0.9673	9	0.66056	D	0.02	.	2.7049	0.05159	0.5769:0.0:0.0:0.4231	rs12128680;rs57717963;rs12128680	544	Q4VC10	.	A	600;596;3480	ENSP00000358344:E596A;ENSP00000345684:E3480A	ENSP00000345684:E3480A	E	+	2	0	NBPF10	144079818	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.155000	0.16362	-0.323000	0.08602	0.316000	0.21350	GAA	A|0.899;C|0.101	0.101	strong		0.468	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
C2orf70	339778	hgsc.bcm.edu	37	2	26799031	26799031	+	Silent	SNP	G	G	A	rs2272464	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:26799031G>A	ENST00000329615.3	+	2	367	c.336G>A	c.(334-336)acG>acA	p.T112T	C2orf70_ENST00000409392.1_Missense_Mutation_p.E100K	NM_001105519.1	NP_001098989.1	A6NJV1	CB070_HUMAN	chromosome 2 open reading frame 70	112						nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	13						CAGAGCTTACGAATTTCTACC	0.657													G|||	1802	0.359824	0.1785	0.232	5008	,	,		18685	0.623		0.336	False		,,,				2504	0.4489				p.T112T		Atlas-SNP	.											.	C2orf70	26	.	0			c.G336A						PASS	.	G		736,3246		71,594,1326	54.0	57.0	56.0		336	-9.6	0.0	2	dbSNP_100	56	2481,5851		350,1781,2035	no	coding-synonymous	C2orf70	NM_001105519.1		421,2375,3361	AA,AG,GG		29.7768,18.4832,26.1247		112/202	26799031	3217,9097	1991	4166	6157	SO:0001819	synonymous_variant	339778	exon2			GCTTACGAATTTC		CCDS42661.1	2p23.3	2011-05-09			ENSG00000173557	ENSG00000173557			27938	protein-coding gene	gene with protein product	"""hypothetical protein LOC339778"""						Standard	NM_001105519		Approved	LOC339778	uc010eyn.3	A6NJV1	OTTHUMG00000151994	ENST00000329615.3:c.336G>A	2.37:g.26799031G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001105519		Silent	SNP	ENST00000329615.3	37	CCDS42661.1	771|771	0.35302197802197804|0.35302197802197804	100|100	0.2032520325203252|0.2032520325203252	76|76	0.20994475138121546|0.20994475138121546	341|341	0.5961538461538461|0.5961538461538461	254|254	0.33509234828496043|0.33509234828496043	G|G	8.134|8.134	0.783761|0.783761	0.16189|0.16189	0.184832|0.184832	0.297768|0.297768	ENSG00000173557|ENSG00000173557	ENST00000409392|ENST00000453368	.|.	.|.	.|.	4.8|4.8	-9.61|-9.61	0.00550|0.00550	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.30621|0.30621	-0.9972|-0.9972	4|3	0.87932|.	D|.	0|.	0.6775|0.6775	1.4254|1.4254	0.02322|0.02322	0.1944:0.2379:0.3479:0.2198|0.1944:0.2379:0.3479:0.2198	rs2272464;rs57992066;rs2272464|rs2272464;rs57992066;rs2272464	.|.	.|.	.|.	K|Q	100|13	.|.	ENSP00000386615:E100K|.	E|R	+|+	1|2	0|0	C2orf70|C2orf70	26652535|26652535	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-3.581000|-3.581000	0.00424|0.00424	-3.293000|-3.293000	0.00194|0.00194	-1.621000|-1.621000	0.00791|0.00791	GAA|CGA	G|0.672;A|0.328	0.328	strong		0.657	C2orf70-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353258.1	NM_001105519	
KANK4	163782	hgsc.bcm.edu	37	1	62713246	62713246	+	Silent	SNP	G	G	A	rs10889315	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:62713246G>A	ENST00000371153.4	-	9	3159	c.2781C>T	c.(2779-2781)caC>caT	p.H927H	KANK4_ENST00000354381.3_Silent_p.H299H|KANK4_ENST00000371150.1_Silent_p.H283H|KANK4_ENST00000317477.4_Silent_p.H65H	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	927						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						AGGATCCATCGTGGTCCTGCA	0.627													G|||	1597	0.31889	0.3026	0.3444	5008	,	,		20100	0.1429		0.4195	False		,,,				2504	0.4008				p.H927H		Atlas-SNP	.											KANK4,NS,carcinoma,0,1	KANK4	135	1	0			c.C2781T						PASS	.	G		1464,2942	472.6+/-356.4	242,980,981	100.0	82.0	88.0		2781	-4.0	0.2	1	dbSNP_120	88	3620,4980	522.0+/-380.0	769,2082,1449	no	coding-synonymous	KANK4	NM_181712.4		1011,3062,2430	AA,AG,GG		42.093,33.2274,39.0897		927/996	62713246	5084,7922	2203	4300	6503	SO:0001819	synonymous_variant	163782	exon9			TCCATCGTGGTCC	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	27263	protein-coding gene	gene with protein product		614612	"""ankyrin repeat domain 38"""	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.2781C>T	1.37:g.62713246G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	121	45	0.371901	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	37	CCDS620.1																																																																																			G|0.637;A|0.363	0.363	strong		0.627	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
RECQL5	9400	hgsc.bcm.edu	37	17	73625430	73625430	+	Silent	SNP	G	G	A	rs4788902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73625430G>A	ENST00000317905.5	-	16	2232	c.2073C>T	c.(2071-2073)caC>caT	p.H691H	RECQL5_ENST00000423245.2_Silent_p.H664H|RECQL5_ENST00000443199.2_5'UTR	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	691	Interaction with RAD51.				chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			TCGGGGGCTCGTGCTCGCCTC	0.692								Other identified genes with known or suspected DNA repair function					G|||	2634	0.525958	0.1437	0.647	5008	,	,		13996	0.8085		0.6024	False		,,,				2504	0.5869				p.H691H		Atlas-SNP	.											.	RECQL5	77	.	0			c.C2073T						PASS	.	G		745,2893		111,523,1185	11.0	14.0	13.0		2073	-3.7	0.0	17	dbSNP_111	13	4795,3225		1491,1813,706	no	coding-synonymous	RECQL5	NM_004259.6		1602,2336,1891	AA,AG,GG		40.212,20.4783,47.521		691/992	73625430	5540,6118	1819	4010	5829	SO:0001819	synonymous_variant	9400	exon16			GGGCTCGTGCTCG	AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.2073C>T	17.37:g.73625430G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			G|0.424;A|0.576	0.576	strong		0.692	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
CAPG	822	hgsc.bcm.edu	37	2	85625222	85625222	+	Silent	SNP	T	T	G	rs6885	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85625222T>G	ENST00000409921.1	-	8	834	c.768A>C	c.(766-768)ccA>ccC	p.P256P	CAPG_ENST00000409724.1_Silent_p.P271P|CAPG_ENST00000483659.1_5'UTR|CAPG_ENST00000409670.1_Silent_p.P271P|CAPG_ENST00000263867.4_Silent_p.P271P			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						CAAGGGCAAATGGGCTGGAGT	0.557													G|||	1260	0.251597	0.4175	0.147	5008	,	,		19547	0.121		0.2336	False		,,,				2504	0.2546				p.P271P		Atlas-SNP	.											.	CAPG	32	.	0			c.A813C						PASS	.	G		1644,2762	659.6+/-400.6	319,1006,878	217.0	188.0	198.0		813	-2.2	1.0	2	dbSNP_52	198	2102,6498	716.7+/-406.1	272,1558,2470	no	coding-synonymous	CAPG	NM_001747.2		591,2564,3348	GG,GT,TT		24.4419,37.3128,28.8021		271/349	85625222	3746,9260	2203	4300	6503	SO:0001819	synonymous_variant	822	exon8			GGCAAATGGGCTG	M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"""macrophage capping protein"""	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.768A>C	2.37:g.85625222T>G		Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	359	182	0.506964	NM_001256139	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Silent	SNP	ENST00000409921.1	37	CCDS58715.1																																																																																			T|0.734;G|0.266	0.266	strong		0.557	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747	
ZAK	51776	hgsc.bcm.edu	37	2	174055646	174055646	+	Silent	SNP	T	T	C	rs35853276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:174055646T>C	ENST00000375213.3	+	6	517	c.439T>C	c.(439-441)Ttg>Ctg	p.L147L	MLTK_ENST00000431503.2_Silent_p.L46L|MLK7-AS1_ENST00000419609.1_RNA|MLTK_ENST00000409176.2_Silent_p.L147L|MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000480606.1_3'UTR|MLTK_ENST00000539448.1_Silent_p.L147L|MLTK_ENST00000338983.3_Silent_p.L147L	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		147	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										TGATGGAGTATTGAAGGTAGG	0.269													T|||	715	0.142772	0.3071	0.0821	5008	,	,		19235	0.0		0.1103	False		,,,				2504	0.1442				p.L147L		Atlas-SNP	.											.	ZAK	62	.	0			c.T439C						PASS	.	T	,	1068,3338	368.3+/-318.6	120,828,1255	67.0	76.0	73.0		439,439	-0.3	0.8	2	dbSNP_126	73	874,7720	195.1+/-240.3	49,776,3472	no	coding-synonymous,coding-synonymous	ZAK	NM_016653.2,NM_133646.2	,	169,1604,4727	CC,CT,TT		10.1699,24.2397,14.9385	,	147/801,147/456	174055646	1942,11058	2203	4297	6500	SO:0001819	synonymous_variant	0	exon6			GGAGTATTGAAGG																												ENST00000375213.3:c.439T>C	2.37:g.174055646T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_133646	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Silent	SNP	ENST00000375213.3	37	CCDS42777.1																																																																																			T|0.858;C|0.142	0.142	strong		0.269	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
RBM19	9904	hgsc.bcm.edu	37	12	114282496	114282496	+	Missense_Mutation	SNP	C	C	T	rs2075387	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:114282496C>T	ENST00000545145.2	-	23	2840	c.2762G>A	c.(2761-2763)cGg>cAg	p.R921Q	RBM19_ENST00000392561.3_Missense_Mutation_p.R921Q|RBM19_ENST00000261741.5_Missense_Mutation_p.R921Q	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	921			R -> Q (in dbSNP:rs2075387). {ECO:0000269|PubMed:11230166}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GGCCGTCTTCCGCCGCAGGGC	0.647													C|||	1100	0.219649	0.1815	0.2032	5008	,	,		17432	0.131		0.3002	False		,,,				2504	0.2914				p.R921Q		Atlas-SNP	.											.	RBM19	117	.	0			c.G2762A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	776,3630	286.9+/-279.0	78,620,1505	35.0	32.0	33.0		2762,2762,2762	5.1	1.0	12	dbSNP_96	33	2321,6279	356.9+/-330.5	326,1669,2305	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	43,43,43	404,2289,3810	TT,TC,CC		26.9884,17.6123,23.8121	possibly-damaging,possibly-damaging,possibly-damaging	921/961,921/961,921/961	114282496	3097,9909	2203	4300	6503	SO:0001583	missense	9904	exon23			GTCTTCCGCCGCA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.2762G>A	12.37:g.114282496C>T	ENSP00000442053:p.Arg921Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	486	0.22252747252747251	100	0.2032520325203252	74	0.20441988950276244	78	0.13636363636363635	234	0.3087071240105541	C	21.4	4.143675	0.77888	0.176123	0.269884	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05258	3.47;3.47;3.47	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.99999854926	D	0.69078	0.997	P	0.59595	0.86	T	0.43475	-0.9389	9	0.56958	D	0.05	-9.4086	18.1548	0.89687	0.0:1.0:0.0:0.0	rs2075387;rs60062169;rs2075387	921	Q9Y4C8	RBM19_HUMAN	Q	921	ENSP00000442053:R921Q;ENSP00000376344:R921Q;ENSP00000261741:R921Q	ENSP00000261741:R921Q	R	-	2	0	RBM19	112766879	1.000000	0.71417	0.999000	0.59377	0.194000	0.23727	4.408000	0.59761	2.368000	0.80403	0.561000	0.74099	CGG	C|0.781;T|0.219	0.219	strong		0.647	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
HLA-A	3105	hgsc.bcm.edu	37	6	29911149	29911149	+	Silent	SNP	C	C	T	rs1059506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29911149C>T	ENST00000396634.1	+	5	789	c.448C>T	c.(448-450)Ctg>Ttg	p.L150L	HLA-A_ENST00000376802.2_Silent_p.L150L|HLA-A_ENST00000376806.5_Silent_p.L150L|HLA-A_ENST00000376809.5_Silent_p.L150L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	150	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TTACATCGCCCTGAACGAGGA	0.642									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	783	0.15635	0.1891	0.1527	5008	,	,		13123	0.1438		0.1143	False		,,,				2504	0.1708				p.L150L		Atlas-SNP	.											.	HLA-A	89	.	0			c.C448T						PASS	.	C		546,2466		51,444,1011	46.0	32.0	37.0		448	2.9	1.0	6	dbSNP_86	37	616,4798		44,528,2135	no	coding-synonymous	HLA-A	NM_002116.7		95,972,3146	TT,TC,CC		11.3779,18.1275,13.7906		150/366	29911149	1162,7264	1506	2707	4213	SO:0001819	synonymous_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ATCGCCCTGAACG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.448C>T	6.37:g.29911149C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	358	220	0.614525	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.865;T|0.135	0.135	strong		0.642	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SAA2	6289	hgsc.bcm.edu	37	11	18267465	18267465	+	Missense_Mutation	SNP	T	T	G	rs138605229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18267465T>G	ENST00000526900.1	-	3	405	c.222A>C	c.(220-222)gaA>gaC	p.E74D	SAA2_ENST00000529528.1_Missense_Mutation_p.E74D|SAA2-SAA4_ENST00000524555.1_RNA|RNA5SP333_ENST00000363466.1_RNA|SAA2_ENST00000414546.2_Missense_Mutation_p.E74D|SAA2_ENST00000528349.1_Missense_Mutation_p.E74D|SAA2_ENST00000530400.1_Missense_Mutation_p.E74D|SAA2_ENST00000256733.4_Missense_Mutation_p.E74D			P0DJI9	SAA2_HUMAN	serum amyloid A2	74					acute-phase response (GO:0006953)	extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(1)	6						ACCTGATCACTTCTGCAGCCC	0.557													T|||	26	0.00519169	0.0053	0.0014	5008	,	,		25564	0.0		0.008	False		,,,				2504	0.0102				p.E74D		Atlas-SNP	.											.	SAA2	22	.	0			c.A222C						PASS	.	T	ASP/GLU,ASP/GLU,ASP/GLU	15,4383	22.3+/-47.3	0,15,2184	138.0	126.0	130.0		222,222,222	-0.2	0.0	11	dbSNP_134	130	50,8536	30.1+/-81.4	0,50,4243	no	missense,missense,missense	SAA2,SAA2-SAA4	NM_001127380.2,NM_001199744.1,NM_030754.4	45,45,45	0,65,6427	GG,GT,TT		0.5823,0.3411,0.5006	benign,benign,benign	74/84,74/209,74/123	18267465	65,12919	2199	4293	6492	SO:0001583	missense	6289	exon3			GATCACTTCTGCA	M26152	CCDS7833.1, CCDS44548.1	11p15.1-p14	2008-07-21			ENSG00000134339	ENSG00000134339			10514	protein-coding gene	gene with protein product		104751				7686132	Standard	NM_030754		Approved			P0DJI9	OTTHUMG00000166484	ENST00000526900.1:c.222A>C	11.37:g.18267465T>G	ENSP00000436126:p.Glu74Asp	Somatic	588	0	0		WXS	Illumina HiSeq	Phase_I	655	212	0.323664	NM_030754	G3XAK9|P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Missense_Mutation	SNP	ENST00000526900.1	37	CCDS7833.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821336	0.32237	0.003411	0.005823	ENSG00000134339	ENST00000414546;ENST00000530400;ENST00000528349;ENST00000256733;ENST00000529528;ENST00000526900	T;T;T;T;T;T	0.10763	2.84;2.84;2.84;2.84;2.84;2.84	5.09	-0.16	0.13375	.	0.647219	0.15120	N	0.279424	T	0.08802	0.0218	.	.	.	0.20563	N	0.999886	P;B	0.49358	0.923;0.452	P;B	0.46026	0.501;0.393	T	0.11665	-1.0578	9	0.87932	D	0	.	8.5429	0.33404	0.0:0.2971:0.0:0.7029	.	74;74	G3XAK9;E9PR14	.;.	D	74	ENSP00000416716:E74D;ENSP00000432370:E74D;ENSP00000435659:E74D;ENSP00000256733:E74D;ENSP00000437162:E74D;ENSP00000436126:E74D	ENSP00000256733:E74D	E	-	3	2	SAA2	18224041	0.832000	0.29368	0.031000	0.17742	0.228000	0.25075	0.681000	0.25320	-0.196000	0.10366	0.528000	0.53228	GAA	T|0.995;G|0.005	0.005	strong		0.557	SAA2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389983.1	NM_030754	
RNASE4	6038	hgsc.bcm.edu	37	14	21167576	21167576	+	Missense_Mutation	SNP	A	A	T	rs3748338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21167576A>T	ENST00000555835.1	+	2	722	c.46A>T	c.(46-48)Acc>Tcc	p.T16S	AL163636.6_ENST00000553909.1_3'UTR|RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000397995.2_Missense_Mutation_p.T16S|RNASE4_ENST00000304704.4_Missense_Mutation_p.T16S|RNASE4_ENST00000555597.1_Missense_Mutation_p.T16S	NM_002937.3	NP_002928.1	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4	16			T -> S (in dbSNP:rs3748338).		cellular response to starvation (GO:0009267)|mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		TTTGCTGCTGACCCTGCTGGG	0.562													A|||	639	0.127596	0.0068	0.1023	5008	,	,		19999	0.1935		0.1431	False		,,,				2504	0.2249				p.T16S	Esophageal Squamous(59;1059 1362 26290 51151)	Atlas-SNP	.											.	RNASE4	18	.	0			c.A46T						PASS	.	A	SER/THR,SER/THR	141,4265	95.7+/-134.4	3,135,2065	97.0	94.0	95.0		46,46	4.1	1.0	14	dbSNP_107	95	1256,7344	245.3+/-274.2	82,1092,3126	yes	missense,missense	RNASE4	NM_002937.3,NM_194431.1	58,58	85,1227,5191	TT,TA,AA		14.6047,3.2002,10.7412	possibly-damaging,possibly-damaging	16/148,16/148	21167576	1397,11609	2203	4300	6503	SO:0001583	missense	6038	exon2			CTGCTGACCCTGC	U36775	CCDS9555.1	14q11	2014-07-16			ENSG00000258818	ENSG00000258818		"""Ribonucleases, RNase A"""	10047	protein-coding gene	gene with protein product		601030				7501448	Standard	NM_002937		Approved		uc001vxy.4	P34096	OTTHUMG00000029575	ENST00000555835.1:c.46A>T	14.37:g.21167576A>T	ENSP00000452245:p.Thr16Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_002937		Missense_Mutation	SNP	ENST00000555835.1	37	CCDS9555.1	257	0.11767399267399267	4	0.008130081300813009	36	0.09944751381215469	109	0.19055944055944055	108	0.1424802110817942	A	19.15	3.772011	0.69992	0.032002	0.146047	ENSG00000258818;ENSG00000258818;ENSG00000258818;ENSG00000181784;ENSG00000181784;ENSG00000181784	ENST00000555835;ENST00000397995;ENST00000555597;ENST00000398001;ENST00000304704;ENST00000397999	T;T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37;-1.37	5.24	4.12	0.48240	Ribonuclease A, domain (1);	0.641420	0.15716	N	0.248145	T	0.00300	0.0009	L	0.46157	1.445	0.43835	P	0.0035809999999999453	D	0.54772	0.968	P	0.45856	0.495	T	0.32929	-0.9888	9	0.87932	D	0	-15.0045	6.9947	0.24777	0.9021:0.0:0.0979:0.0	rs3748338;rs17242797;rs52831469;rs3748338	16	P34096	RNAS4_HUMAN	S	16	ENSP00000452245:T16S;ENSP00000381081:T16S;ENSP00000451624:T16S;ENSP00000381087:T16S;ENSP00000307096:T16S;ENSP00000381085:T16S	ENSP00000307096:T16S	T	+	1	0	AL163636.2;RNASE4	20237416	0.998000	0.40836	0.999000	0.59377	0.879000	0.50718	0.755000	0.26405	2.285000	0.76669	0.533000	0.62120	ACC	A|0.887;N|0.000;T|0.113	0.113	strong		0.562	RNASE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073729.3		
HRNR	388697	hgsc.bcm.edu	37	1	152188118	152188118	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152188118C>T	ENST00000368801.2	-	3	6062	c.5987G>A	c.(5986-5988)cGc>cAc	p.R1996H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1996					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R1996L(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGTCCTGAGCGAGACTCTCG	0.567																																					p.R1996H		Atlas-SNP	.											HRNR,NS,carcinoma,-1,2	HRNR	403	2	1	Substitution - Missense(1)	large_intestine(1)	c.G5987A						scavenged	.						15.0	23.0	21.0					1																	152188118		1514	3278	4792	SO:0001583	missense	388697	exon3			CCTGAGCGAGACT	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5987G>A	1.37:g.152188118C>T	ENSP00000357791:p.Arg1996His	Somatic	493	0	0		WXS	Illumina HiSeq	Phase_I	2288	145	0.0633741	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	7.361	0.624908	0.14193	.	.	ENSG00000197915	ENST00000368801	T	0.02395	4.31	3.39	-2.43	0.06522	.	.	.	.	.	T	0.00552	0.0018	L	0.27053	0.805	0.09310	N	1	B	0.24576	0.106	B	0.10450	0.005	T	0.47598	-0.9105	9	0.33141	T	0.24	.	0.8288	0.01126	0.1527:0.2386:0.2994:0.3093	.	1996	Q86YZ3	HORN_HUMAN	H	1996	ENSP00000357791:R1996H	ENSP00000357791:R1996H	R	-	2	0	HRNR	150454742	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.278000	0.18753	-0.350000	0.08262	0.505000	0.49811	CGC	.	.	none		0.567	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998268	72998268	+	Silent	SNP	T	T	C	rs3744909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72998268T>C	ENST00000580243.1	+	2	1254	c.906T>C	c.(904-906)gaT>gaC	p.D302D	TSHZ1_ENST00000322038.5_Silent_p.D257D			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	302					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GGAAGGAGGATGCCCAGAAGG	0.552													C|||	1432	0.285942	0.1778	0.3732	5008	,	,		19407	0.1677		0.4085	False		,,,				2504	0.3661				p.D257D		Atlas-SNP	.											.	TSHZ1	104	.	0			c.T771C						PASS	.	C		911,3495	738.6+/-411.0	95,721,1387	140.0	113.0	122.0		771	-2.9	1.0	18	dbSNP_107	122	3455,5145	636.2+/-399.1	696,2063,1541	no	coding-synonymous	TSHZ1	NM_005786.4		791,2784,2928	CC,CT,TT		40.1744,20.6764,33.5691		257/1033	72998268	4366,8640	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GGAGGATGCCCAG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.906T>C	18.37:g.72998268T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	137	75	0.547445	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				T|0.676;C|0.324	0.324	strong		0.552	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
CCDC18	343099	hgsc.bcm.edu	37	1	93720070	93720070	+	Missense_Mutation	SNP	C	C	G	rs12030843	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:93720070C>G	ENST00000343253.7	+	24	3740	c.3238C>G	c.(3238-3240)Ctt>Gtt	p.L1080V	CCDC18_ENST00000557479.1_Missense_Mutation_p.L1199V|CCDC18_ENST00000401026.3_Missense_Mutation_p.L1081V|CCDC18_ENST00000338949.4_3'UTR|CCDC18_ENST00000334652.5_3'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	1080										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TAAAGAACAGCTTCGAGAAAA	0.279													C|||	1163	0.232228	0.1974	0.2392	5008	,	,		19962	0.3175		0.1511	False		,,,				2504	0.2699				p.L1081V		Atlas-SNP	.											.	CCDC18	93	.	0			c.C3241G						PASS	.	C	VAL/LEU	670,2966		61,548,1209	73.0	72.0	73.0		3241	4.2	1.0	1	dbSNP_120	73	1335,6811		128,1079,2866	yes	missense	CCDC18	NM_206886.3	32	189,1627,4075	GG,GC,CC		16.3884,18.4268,17.0175	probably-damaging	1081/1300	93720070	2005,9777	1818	4073	5891	SO:0001583	missense	343099	exon24			GAACAGCTTCGAG			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.3238C>G	1.37:g.93720070C>G	ENSP00000343377:p.Leu1080Val	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		467|467	0.21382783882783882|0.21382783882783882	91|91	0.18495934959349594|0.18495934959349594	84|84	0.23204419889502761|0.23204419889502761	172|172	0.3006993006993007|0.3006993006993007	120|120	0.158311345646438|0.158311345646438	C|C	15.69|15.69	2.909205|2.909205	0.52439|0.52439	0.184268|0.184268	0.163884|0.163884	ENSG00000122483|ENSG00000122483	ENST00000343253;ENST00000401026;ENST00000557479|ENST00000370276	T;T|.	0.78595|.	-1.19;-1.19|.	5.15|5.15	4.22|4.22	0.49857|0.49857	.|.	0.070956|.	0.56097|.	D|.	0.000040|.	T|T	0.48370|0.48370	0.1496|0.1496	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	P|P	0.9999999999999999|0.9999999999999999	P|.	0.35107|.	0.484|.	B|.	0.37267|.	0.245|.	T|T	0.49916|0.49916	-0.8888|-0.8888	9|4	0.39692|.	T|.	0.17|.	.|.	13.6901|13.6901	0.62539|0.62539	0.2993:0.7007:0.0:0.0|0.2993:0.7007:0.0:0.0	rs12030843;rs52792110;rs12030843|rs12030843;rs52792110;rs12030843	1199|.	G3V388|.	.|.	V|R	1080;1081;1199|1133	ENSP00000383808:L1081V;ENSP00000451099:L1199V|.	ENSP00000343377:L1080V|.	L|S	+|+	1|3	0|2	CCDC18|CCDC18	93492658|93492658	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	1.164000|1.164000	0.31810|0.31810	1.239000|1.239000	0.43787|0.43787	-0.410000|-0.410000	0.06199|0.06199	CTT|AGC	C|0.809;G|0.191	0.191	strong		0.279	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
ZNF500	26048	hgsc.bcm.edu	37	16	4802386	4802386	+	Silent	SNP	G	G	T	rs3747602	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4802386G>T	ENST00000219478.6	-	6	1733	c.1434C>A	c.(1432-1434)gcC>gcA	p.A478A	ZNF500_ENST00000591026.1_5'UTR|ZNF500_ENST00000545009.1_Intron|RP11-127I20.7_ENST00000588099.1_RNA			O60304	ZN500_HUMAN	zinc finger protein 500	478					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						ATCAGGCTTTGGCACCGGGGC	0.637													G|||	2574	0.513978	0.3646	0.5403	5008	,	,		16426	0.6607		0.6163	False		,,,				2504	0.4407				p.A478A		Atlas-SNP	.											.	ZNF500	45	.	0			c.C1434A						PASS	.	G		1872,2282		468,936,673	7.0	6.0	6.0		1434	2.6	0.0	16	dbSNP_107	6	5199,2945		1789,1621,662	no	coding-synonymous	ZNF500	NM_021646.1		2257,2557,1335	TT,TG,GG		36.1616,45.065,42.5028		478/481	4802386	7071,5227	2077	4072	6149	SO:0001819	synonymous_variant	26048	exon6			GGCTTTGGCACCG	AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23716	protein-coding gene	gene with protein product						9628581	Standard	XM_005255243		Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.1434C>A	16.37:g.4802386G>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Silent	SNP	ENST00000219478.6	37	CCDS32383.1																																																																																			G|0.445;T|0.555	0.555	strong		0.637	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507	
AIPL1	23746	hgsc.bcm.edu	37	17	6331803	6331803	+	Silent	SNP	T	T	C	rs8075035	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6331803T>C	ENST00000381129.3	-	3	380	c.300A>G	c.(298-300)ctA>ctG	p.L100L	AIPL1_ENST00000576776.1_Silent_p.L100L|AIPL1_ENST00000570466.1_Silent_p.L78L|AIPL1_ENST00000574506.1_Silent_p.L88L|AIPL1_ENST00000575265.1_Silent_p.L100L|AIPL1_ENST00000571740.1_Silent_p.L100L|AIPL1_ENST00000250087.5_Intron|AIPL1_ENST00000576307.1_Silent_p.L40L	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	100	PPIase FKBP-type.				negative regulation of apoptotic process (GO:0043066)|phototransduction, visible light (GO:0007603)|protein farnesylation (GO:0018343)|protein folding (GO:0006457)|regulation of cGMP metabolic process (GO:0030823)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)	farnesylated protein binding (GO:0001918)|unfolded protein binding (GO:0051082)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	12				COAD - Colon adenocarcinoma(228;0.141)		GGCTCCGGGATAGGATGGGGT	0.627													C|||	2884	0.575879	0.4569	0.6758	5008	,	,		19343	0.5367		0.6759	False		,,,				2504	0.6033				p.L100L		Atlas-SNP	.											.	AIPL1	34	.	0			c.A300G						PASS	.	C	,,	2203,2203	584.9+/-386.1	556,1091,556	75.0	62.0	67.0		,120,300	1.1	1.0	17	dbSNP_116	67	5669,2931	453.4+/-363.2	1859,1951,490	no	intron,coding-synonymous,coding-synonymous	AIPL1	NM_001033054.1,NM_001033055.1,NM_014336.3	,,	2415,3042,1046	CC,CT,TT		34.0814,50.0,39.4741	,,	,40/325,100/385	6331803	7872,5134	2203	4300	6503	SO:0001819	synonymous_variant	23746	exon3			CCGGGATAGGATG	AF148864	CCDS11075.1, CCDS32539.1, CCDS32540.1, CCDS67130.1, CCDS67131.1, CCDS67132.1, CCDS67133.1	17p13.1	2013-01-08	2001-11-29		ENSG00000129221	ENSG00000129221			359	protein-coding gene	gene with protein product		604392	"""aryl hydrocarbon receptor-interacting protein-like 1"""	LCA4		10615133, 14555765, 15365173	Standard	NM_001285402		Approved		uc002gcp.3	Q9NZN9	OTTHUMG00000102043	ENST00000381129.3:c.300A>G	17.37:g.6331803T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Silent	SNP	ENST00000381129.3	37	CCDS11075.1																																																																																			T|0.391;C|0.609	0.609	strong		0.627	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336	
HSPA6	3310	hgsc.bcm.edu	37	1	161495040	161495040	+	Missense_Mutation	SNP	C	C	T	rs63749092	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161495040C>T	ENST00000309758.4	+	1	1005	c.592C>T	c.(592-594)Ctc>Ttc	p.L198F	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	198			L -> F (in dbSNP:rs1079109). {ECO:0000269|Ref.2}.		ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCGCAACGTGCTCATTTTTGA	0.622													c|||	622	0.124201	0.0272	0.1268	5008	,	,		15815	0.2837		0.1183	False		,,,				2504	0.0951				p.L198F		Atlas-SNP	.											.	HSPA6	53	.	0			c.C592T						PASS	.	C	PHE/LEU	175,4231		3,169,2031	39.0	45.0	43.0		592	2.3	0.8	1	dbSNP_129	43	990,7610		57,876,3367	no	missense	HSPA6	NM_002155.3	22	60,1045,5398	TT,TC,CC		11.5116,3.9719,8.9574	probably-damaging	198/644	161495040	1165,11841	2203	4300	6503	SO:0001583	missense	3310	exon1			AACGTGCTCATTT		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.592C>T	1.37:g.161495040C>T	ENSP00000310219:p.Leu198Phe	Somatic	357	1	0.00280112		WXS	Illumina HiSeq	Phase_I	384	161	0.419271	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	307	0.14056776556776557	19	0.03861788617886179	39	0.10773480662983426	154	0.2692307692307692	95	0.12532981530343007	.	15.86	2.957350	0.53400	0.039719	0.115116	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.13538	2.58	3.19	2.27	0.28462	.	0.000000	0.34291	U	0.004084	T	0.34658	0.0905	H	0.97158	3.95	0.21984	P	0.999432756	D	0.89917	1.0	D	0.97110	1.0	T	0.43212	-0.9405	9	0.72032	D	0.01	-29.3593	7.5914	0.28023	0.0:0.8669:0.0:0.1331	rs63749092	198	P17066	HSP76_HUMAN	F	198;174	ENSP00000310219:L198F	ENSP00000310219:L198F	L	+	1	0	HSPA6	159761664	0.999000	0.42202	0.751000	0.31187	0.707000	0.40811	3.892000	0.56235	0.519000	0.28406	0.486000	0.48141	CTC	C|0.897;T|0.103	0.103	strong		0.622	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
IFI30	10437	hgsc.bcm.edu	37	19	18286008	18286008	+	Silent	SNP	G	G	C	rs200372	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18286008G>C	ENST00000407280.3	+	2	466	c.291G>C	c.(289-291)acG>acC	p.T97T	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	97					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)			endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						TCAATGTCACGCTGGTGCCCT	0.617													G|||	37	0.00738818	0.0265	0.0029	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.T97T		Atlas-SNP	.											IFI30,NS,carcinoma,+1,1	IFI30	12	1	0			c.G291C						PASS	.	G		103,4063		2,99,1982	38.0	38.0	38.0		291	-9.9	0.0	19	dbSNP_79	38	5,8409		0,5,4202	no	coding-synonymous	IFI30	NM_006332.3		2,104,6184	CC,CG,GG		0.0594,2.4724,0.8585		97/251	18286008	108,12472	2083	4207	6290	SO:0001819	synonymous_variant	10437	exon2			TGTCACGCTGGTG	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"""gamma-interferon-inducible lysosomal thiol reductase"", ""interferon gamma-inducible protein 30 preproprotein"""	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.291G>C	19.37:g.18286008G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Silent	SNP	ENST00000407280.3	37	CCDS46015.1																																																																																			G|0.994;C|0.006	0.006	strong		0.617	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332	
KLHL30	377007	hgsc.bcm.edu	37	2	239049540	239049540	+	Missense_Mutation	SNP	G	G	A	rs2241985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:239049540G>A	ENST00000409223.1	+	2	252	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	KLHL30_ENST00000305959.4_Missense_Mutation_p.G31S			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	49	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.			G -> S (in Ref. 4; AAI05697). {ECO:0000305}.						lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		ATGCCACCGCGGCCTCCTGGC	0.697													G|||	1935	0.386382	0.3812	0.4006	5008	,	,		17698	0.3938		0.3847	False		,,,				2504	0.3773				p.G49S		Atlas-SNP	.											.	KLHL30	79	.	0			c.G145A						PASS	.	G	SER/GLY	1662,2602		333,996,803	40.0	48.0	46.0		145	1.3	1.0	2	dbSNP_98	46	3261,5177		633,1995,1591	yes	missense	KLHL30	NM_198582.3	56	966,2991,2394	AA,AG,GG		38.6466,38.9775,38.7577	benign	49/579	239049540	4923,7779	2132	4219	6351	SO:0001583	missense	377007	exon2			CACCGCGGCCTCC		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.145G>A	2.37:g.239049540G>A	ENSP00000386389:p.Gly49Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	848	0.3882783882783883	194	0.3943089430894309	150	0.4143646408839779	213	0.3723776223776224	291	0.3839050131926121	G	6.300	0.423477	0.11928	0.389775	0.386466	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.66280	-0.2;-0.2	5.66	1.26	0.21427	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.378699	0.28958	N	0.013586	T	0.00012	0.0000	N	0.01529	-0.815	0.80722	P	0.0	B	0.23937	0.094	B	0.23018	0.043	T	0.42682	-0.9437	9	0.46703	T	0.11	.	7.8189	0.29276	0.485:0.0:0.515:0.0	rs2241985;rs2241985	49	Q0D2K2	KLH30_HUMAN	S	49;31	ENSP00000386389:G49S;ENSP00000302386:G31S	ENSP00000302386:G31S	G	+	1	0	KLHL30	238714279	0.319000	0.24607	0.963000	0.40424	0.927000	0.56198	0.962000	0.29280	0.329000	0.23460	-0.218000	0.12543	GGC	G|0.618;A|0.382	0.382	strong		0.697	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
SLC12A7	10723	hgsc.bcm.edu	37	5	1063998	1063998	+	Silent	SNP	G	G	A	rs7722287	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:1063998G>A	ENST00000264930.5	-	20	2743	c.2700C>T	c.(2698-2700)taC>taT	p.Y900Y	MIR4635_ENST00000583759.1_RNA	NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	900					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	TGCGCAAGTGGTACAAGAACA	0.637													G|||	1486	0.296725	0.0295	0.3588	5008	,	,		9752	0.3175		0.4523	False		,,,				2504	0.4325				p.Y900Y		Atlas-SNP	.											SLC12A7,NS,carcinoma,0,1	SLC12A7	97	1	0			c.C2700T						PASS	.	G		450,3954	214.5+/-233.7	19,412,1771	137.0	103.0	114.0		2700	3.4	1.0	5	dbSNP_116	114	4044,4556	557.1+/-387.0	935,2174,1191	no	coding-synonymous	SLC12A7	NM_006598.2		954,2586,2962	AA,AG,GG		47.0233,10.218,34.5586		900/1084	1063998	4494,8510	2202	4300	6502	SO:0001819	synonymous_variant	10723	exon20			CAAGTGGTACAAG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2700C>T	5.37:g.1063998G>A		Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	337	123	0.364985	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1	695	0.3182234432234432	20	0.04065040650406504	136	0.3756906077348066	180	0.3146853146853147	359	0.4736147757255937	G	6.481	0.456993	0.12283	0.10218	0.470233	ENSG00000113504	ENST00000513223	.	.	.	4.25	3.37	0.38596	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.49244	-0.8960	3	.	.	.	.	7.5063	0.27547	0.206:0.0:0.794:0.0	rs7722287;rs35783179;rs57920515;rs7722287	.	.	.	S	258	.	.	P	-	1	0	SLC12A7	1116998	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	2.387000	0.44389	0.773000	0.33404	0.305000	0.20034	CCA	G|0.675;A|0.325	0.325	strong		0.637	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
CSPG4	1464	hgsc.bcm.edu	37	15	75979782	75979782	+	Silent	SNP	G	G	T	rs8030131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75979782G>T	ENST00000308508.5	-	3	3716	c.3624C>A	c.(3622-3624)cgC>cgA	p.R1208R		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1208	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.			R -> E (in Ref. 1; CAA65529). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCATGGTGTCGCGGGGGCTGA	0.642													G|||	1925	0.384385	0.2716	0.5245	5008	,	,		20048	0.2292		0.5189	False		,,,				2504	0.4591				p.R1208R		Atlas-SNP	.											.	CSPG4	175	.	0			c.C3624A						PASS	.	G		1317,3075		195,927,1074	52.0	53.0	53.0		3624	-10.1	0.0	15	dbSNP_116	53	4650,3936		1272,2106,915	no	coding-synonymous	CSPG4	NM_001897.4		1467,3033,1989	TT,TG,GG		45.8421,29.9863,45.9778		1208/2323	75979782	5967,7011	2196	4293	6489	SO:0001819	synonymous_variant	1464	exon3			GGTGTCGCGGGGG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.3624C>A	15.37:g.75979782G>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			G|0.567;T|0.433	0.433	strong		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
IP6K3	117283	hgsc.bcm.edu	37	6	33690797	33690797	+	Silent	SNP	A	A	G	rs4711341|rs34332988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33690797A>G	ENST00000293756.4	-	6	1259	c.933T>C	c.(931-933)tcT>tcC	p.S311S	IP6K3_ENST00000451316.1_Silent_p.S311S	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	311					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						TCCTAATGACAGAGAGGAGGG	0.572													G|||	2664	0.531949	0.118	0.5865	5008	,	,		15977	0.8591		0.4761	False		,,,				2504	0.773				p.S311S		Atlas-SNP	.											.	IP6K3	52	.	0			c.T933C						PASS	.	G	,	898,3508		86,726,1391	52.0	57.0	56.0		933,933	-10.2	0.0	6	dbSNP_111	56	3750,4850		874,2002,1424	no	coding-synonymous,coding-synonymous	IP6K3	NM_001142883.1,NM_054111.4	,	960,2728,2815	GG,GA,AA		43.6047,20.3813,35.7374	,	311/411,311/411	33690797	4648,8358	2203	4300	6503	SO:0001819	synonymous_variant	117283	exon7			AATGACAGAGAGG	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"""inositol hexaphosphate kinase 3"""	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.933T>C	6.37:g.33690797A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	192	78	0.40625	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	37	CCDS34435.1																																																																																			A|0.615;G|0.385	0.385	strong		0.572	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
TBC1D2B	23102	hgsc.bcm.edu	37	15	78290635	78290635	+	Missense_Mutation	SNP	C	C	T	rs200408968		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78290635C>T	ENST00000300584.3	-	13	2758	c.2759G>A	c.(2758-2760)cGa>cAa	p.R920Q	TBC1D2B_ENST00000409931.3_Missense_Mutation_p.D903N|TBC1D2B_ENST00000492078.1_5'UTR	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	920							Rab GTPase activator activity (GO:0005097)	p.D903N(3)|p.R920Q(1)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						GTAGGCGCGTCGGTTCCGGAT	0.617																																					p.R920Q		Atlas-SNP	.											TBC1D2B_ENST00000300584,bladder,carcinoma,0,17	TBC1D2B	104	17	4	Substitution - Missense(4)	cervix(2)|upper_aerodigestive_tract(1)|ovary(1)	c.G2759A						scavenged	.						39.0	33.0	35.0					15																	78290635		2196	4291	6487	SO:0001583	missense	23102	exon13			GCGCGTCGGTTCC	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.2759G>A	15.37:g.78290635C>T	ENSP00000300584:p.Arg920Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	158	11	0.0696203	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	37	CCDS45314.1	88|88	0.040293040293040296|0.040293040293040296	2|2	0.0040650406504065045|0.0040650406504065045	10|10	0.027624309392265192|0.027624309392265192	8|8	0.013986013986013986|0.013986013986013986	68|68	0.08970976253298153|0.08970976253298153	c|c	22.6|22.6	4.311579|4.311579	0.81358|0.81358	.|.	.|.	ENSG00000167202|ENSG00000167202	ENST00000418039;ENST00000409931|ENST00000300584	T|T	0.11712|0.09445	2.75|2.98	4.48|4.48	4.48|4.48	0.54585|0.54585	.|.	0.787190|.	0.11177|.	N|.	0.591392|.	T|T	0.00608|0.00608	0.0020|0.0020	.|.	.|.	.|.	0.26703|0.26703	N|N	0.971136|0.971136	B|D	0.30193|0.57257	0.272|0.979	B|P	0.18561|0.51833	0.022|0.681	T|T	0.06807|0.06807	-1.0806|-1.0806	9|8	0.02654|0.23891	T|T	1|0.37	.|.	16.1645|16.1645	0.81745|0.81745	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	903|920	Q9UPU7-2|Q9UPU7	.|TBD2B_HUMAN	N|Q	802;903|920	ENSP00000387165:D903N|ENSP00000300584:R920Q	ENSP00000387165:D903N|ENSP00000300584:R920Q	D|R	-|-	1|2	0|0	TBC1D2B|TBC1D2B	76077690|76077690	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.855000|0.855000	0.48748|0.48748	6.002000|6.002000	0.70693|0.70693	2.033000|2.033000	0.60031|0.60031	0.479000|0.479000	0.44913|0.44913	GAC|CGA	C|0.960;T|0.040	0.040	strong		0.617	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	
PUS3	83480	hgsc.bcm.edu	37	11	125763746	125763746	+	Missense_Mutation	SNP	C	C	G	rs3088241	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:125763746C>G	ENST00000530811.1	-	3	1425	c.1380G>C	c.(1378-1380)gaG>gaC	p.E460D	PUS3_ENST00000227474.3_Missense_Mutation_p.E460D|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron|HYLS1_ENST00000425380.2_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	460			E -> D (in dbSNP:rs3088241). {ECO:0000269|PubMed:15489334}.		tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		AATTAGTATTCTCTTCCTCTA	0.413													C|||	2297	0.458666	0.3933	0.4236	5008	,	,		19356	0.5327		0.501	False		,,,				2504	0.4519				p.E460D		Atlas-SNP	.											.	PUS3	33	.	0			c.G1380C						PASS	.	C	,ASP/GLU,	1779,2623	526.5+/-371.9	355,1069,777	211.0	201.0	205.0		,1380,	-2.1	0.1	11	dbSNP_102	205	4289,4309	577.5+/-390.6	1071,2147,1081	yes	intron,missense,intron	PUS3,HYLS1	NM_001134793.1,NM_031307.3,NM_145014.2	,45,	1426,3216,1858	GG,GC,CC		49.8837,40.4134,46.6769	,possibly-damaging,	,460/482,	125763746	6068,6932	2201	4299	6500	SO:0001583	missense	83480	exon4			AGTATTCTCTTCC	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.1380G>C	11.37:g.125763746C>G	ENSP00000432386:p.Glu460Asp	Somatic	312	1	0.00320513		WXS	Illumina HiSeq	Phase_I	339	152	0.448378	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Missense_Mutation	SNP	ENST00000530811.1	37	CCDS8466.1	1056	0.4835164835164835	196	0.3983739837398374	154	0.425414364640884	322	0.5629370629370629	384	0.5065963060686016	C	8.796	0.931769	0.18131	0.404134	0.498837	ENSG00000110060	ENST00000227474;ENST00000530811	T;T	0.31247	1.5;1.5	4.92	-2.14	0.07123	.	0.667480	0.14995	N	0.286428	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	1.0000000000287557E-6	B	0.10296	0.003	B	0.08055	0.003	T	0.46062	-0.9218	9	0.20046	T	0.44	-10.5276	6.2703	0.20951	0.0:0.5046:0.1624:0.3331	rs3088241;rs17795488;rs17849865;rs17858239;rs3088241	460	Q9BZE2	PUS3_HUMAN	D	460	ENSP00000227474:E460D;ENSP00000432386:E460D	ENSP00000227474:E460D	E	-	3	2	PUS3	125268956	0.340000	0.24792	0.138000	0.22173	0.363000	0.29612	-0.041000	0.12084	-0.433000	0.07286	0.591000	0.81541	GAG	C|0.522;G|0.478	0.478	strong		0.413	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307	
PRUNE2	158471	hgsc.bcm.edu	37	9	79318921	79318921	+	Silent	SNP	A	A	G	rs620985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:79318921A>G	ENST00000376718.3	-	9	7731	c.7608T>C	c.(7606-7608)tgT>tgC	p.C2536C	PRUNE2_ENST00000428286.1_Silent_p.C2177C	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2536					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TCTTCTCTGTACATCTTTCTT	0.383													A|||	2149	0.429113	0.1936	0.634	5008	,	,		14795	0.3522		0.5865	False		,,,				2504	0.5194				p.C2536C		Atlas-SNP	.											.	PRUNE2	331	.	0			c.T7608C						PASS	.	A		849,2287		120,609,839	258.0	236.0	243.0		7608	-6.1	0.0	9	dbSNP_83	243	4322,2842		1305,1712,565	no	coding-synonymous	PRUNE2	NM_015225.2		1425,2321,1404	GG,GA,AA		39.6706,27.0727,49.7961		2536/3089	79318921	5171,5129	1568	3582	5150	SO:0001819	synonymous_variant	158471	exon9			CTCTGTACATCTT	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7608T>C	9.37:g.79318921A>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	239	104	0.435146	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	976	0.4468864468864469	103	0.20934959349593496	229	0.6325966850828729	210	0.36713286713286714	434	0.5725593667546174	A	0.224	-1.025963	0.02045	0.270727	0.603294	ENSG00000106772	ENST00000426088	.	.	.	6.08	-6.06	0.02165	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.36768	-0.9734	3	.	.	.	6.0858	9.8403	0.40996	0.361:0.4978:0.1413:0.0	rs620985;rs17784468;rs57892178;rs620985	.	.	.	H	1858	.	.	Y	-	1	0	PRUNE2	78508741	0.000000	0.05858	0.000000	0.03702	0.099000	0.18886	-1.646000	0.01998	-0.623000	0.05618	-0.177000	0.13119	TAC	A|0.565;G|0.435	0.435	strong		0.383	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
LRP3	4037	hgsc.bcm.edu	37	19	33698448	33698448	+	Silent	SNP	G	G	A	rs3745973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33698448G>A	ENST00000253193.7	+	7	2482	c.2280G>A	c.(2278-2280)gaG>gaA	p.E760E	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	760					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					CAATGCTGGAGGCCAGCGATG	0.657													G|||	407	0.08127	0.0038	0.1052	5008	,	,		13745	0.2024		0.0726	False		,,,				2504	0.0532				p.E760E		Atlas-SNP	.											.	LRP3	46	.	0			c.G2280A						PASS	.	G		76,4244		2,72,2086	15.0	17.0	16.0		2280	3.6	1.0	19	dbSNP_107	16	568,7864		18,532,3666	no	coding-synonymous	LRP3	NM_002333.3		20,604,5752	AA,AG,GG		6.7362,1.7593,5.0502		760/771	33698448	644,12108	2160	4216	6376	SO:0001819	synonymous_variant	4037	exon7			GCTGGAGGCCAGC	AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"""Low density lipoprotein receptors"""	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.2280G>A	19.37:g.33698448G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_002333	B3KQD6|B4DKF2	Silent	SNP	ENST00000253193.7	37	CCDS12430.1																																																																																			G|0.910;C|0.000;A|0.090	0.090	strong		0.657	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
CSAG1	158511	hgsc.bcm.edu	37	X	151908845	151908845	+	Nonsense_Mutation	SNP	C	C	G	rs1894360	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:151908845C>G	ENST00000370287.3	+	4	412	c.84C>G	c.(82-84)taC>taG	p.Y28*	CSAG1_ENST00000452779.2_Nonsense_Mutation_p.Y28*|CSAG1_ENST00000370291.2_Nonsense_Mutation_p.Y28*	NM_153478.1	NP_705611.1	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1	28			Y -> F (in dbSNP:rs1894359).	Y -> C (in Ref. 1; AF195880). {ECO:0000305}.						central_nervous_system(1)|kidney(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					GTAGACTGTACAGAGACACTG	0.537													.|||	377	0.0998675	0.0802	0.0533	3775	,	,		11961	0.0238		0.1531	False		,,,				2504	0.0573				p.Y28X		Atlas-SNP	.											.	CSAG1	27	.	0			c.C84G						PASS	.	G	stop/TYR,stop/TYR	322,3513		19,231,53,1382,518	231.0	209.0	217.0		84,84	0.8	0.0	X	dbSNP_92	217	1058,5670		80,555,343,1793,1529	no	stop-gained,stop-gained	CSAG1	NM_001102576.1,NM_153478.1	,	99,786,396,3175,2047	GG,GC,G,CC,C		15.7253,8.3963,13.0645	,	28/79,28/79	151908845	1380,9183	2203	4300	6503	SO:0001587	stop_gained	158511	exon4			ACTGTACAGAGAC	AF268419	CCDS76047.1	Xq28	2009-08-07			ENSG00000198930	ENSG00000198930			24294	protein-coding gene	gene with protein product	"""cancer/testis antigen family 24, member 1"""					12039054	Standard	XM_006724810		Approved	CSAGE, CT24.1	uc004fgf.3	Q6PB30	OTTHUMG00000022648	ENST00000370287.3:c.84C>G	X.37:g.151908845C>G	ENSP00000359310:p.Tyr28*	Somatic	1123	1	0.000890472		WXS	Illumina HiSeq	Phase_I	641	637	0.99376	NM_153478	A6NE22	Nonsense_Mutation	SNP	ENST00000370287.3	37	CCDS14711.1	146	0.08800482218203737	18	0.0375	16	0.04519774011299435	5	0.008896797153024912	67	0.09544159544159544	G	14.71	2.618155	0.46736	0.083963	0.157253	ENSG00000198930	ENST00000370287;ENST00000452779;ENST00000370291	.	.	.	0.837	0.837	0.18896	.	.	.	.	.	.	.	.	.	.	.	0.22666	P	0.99887022	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	.	.	.	rs1894360;rs52835846;rs60699427;rs1894360	.	.	.	X	28	.	ENSP00000359310:Y28X	Y	+	3	2	CSAG1	151659501	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-0.060000	0.11712	-0.097000	0.12307	-1.113000	0.02065	TAC	C|0.870;0|0.002	.	strong		0.537	CSAG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058760.2	NM_153479	
KCNN1	3780	hgsc.bcm.edu	37	19	18104350	18104350	+	Silent	SNP	G	G	A	rs376852061		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18104350G>A	ENST00000222249.9	+	10	1678	c.1359G>A	c.(1357-1359)acG>acA	p.T453T		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	453	Calmodulin-binding. {ECO:0000250}.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	AGGCTAACACGCTTACCGACC	0.662																																					p.T453T		Atlas-SNP	.											.	KCNN1	74	.	0			c.G1359A						PASS	.	G		0,4080		0,0,2040	46.0	51.0	49.0		1359	-9.0	0.1	19		49	1,8349		0,1,4174	no	coding-synonymous	KCNN1	NM_002248.3		0,1,6214	AA,AG,GG		0.012,0.0,0.0080		453/544	18104350	1,12429	2040	4175	6215	SO:0001819	synonymous_variant	3780	exon10			TAACACGCTTACC	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.1359G>A	19.37:g.18104350G>A		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	221	101	0.457014	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				.	.	weak		0.662	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
HK3	3101	hgsc.bcm.edu	37	5	176314639	176314639	+	Silent	SNP	G	G	A	rs6875296	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176314639G>A	ENST00000292432.5	-	11	1504	c.1413C>T	c.(1411-1413)gcC>gcT	p.A471A		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	471	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGGCAGCCACGGCAGTCACCA	0.652													G|||	1518	0.303115	0.0756	0.4294	5008	,	,		15488	0.3929		0.326	False		,,,				2504	0.4049				p.A471A		Atlas-SNP	.											HK3_ENST00000292432,NS,carcinoma,0,2	HK3	210	2	0			c.C1413T						scavenged	.	G		559,3847	239.9+/-250.9	34,491,1678	35.0	33.0	34.0		1413	-8.9	0.0	5	dbSNP_116	34	2929,5669	439.3+/-359.2	506,1917,1876	no	coding-synonymous	HK3	NM_002115.2		540,2408,3554	AA,AG,GG		34.0661,12.6872,26.8225		471/924	176314639	3488,9516	2203	4299	6502	SO:0001819	synonymous_variant	3101	exon11			AGCCACGGCAGTC		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1413C>T	5.37:g.176314639G>A		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	129	43	0.333333	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			G|0.724;A|0.276	0.276	strong		0.652	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
ODF3L1	161753	hgsc.bcm.edu	37	15	76017452	76017452	+	Missense_Mutation	SNP	C	C	T	rs55905564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:76017452C>T	ENST00000332145.2	+	2	345	c.122C>T	c.(121-123)cCg>cTg	p.P41L	DNM1P35_ENST00000501931.1_RNA	NM_175881.3	NP_787077.1	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	41			P -> L (in dbSNP:rs55905564).							kidney(1)|lung(1)	2						CTTACAGGTCCGGGGCCCGCC	0.597													C|||	693	0.138379	0.1104	0.1628	5008	,	,		18115	0.1032		0.2386	False		,,,				2504	0.092				p.P41L		Atlas-SNP	.											.	ODF3L1	10	.	0			c.C122T						PASS	.	C	LEU/PRO	560,3834		33,494,1670	56.0	50.0	52.0		122	5.3	0.8	15	dbSNP_129	52	2150,6438		287,1576,2431	yes	missense	ODF3L1	NM_175881.3	98	320,2070,4101	TT,TC,CC		25.0349,12.7447,20.8751	probably-damaging	41/275	76017452	2710,10272	2197	4294	6491	SO:0001583	missense	161753	exon2			CAGGTCCGGGGCC	BC039862	CCDS10285.1	15q23	2008-02-05			ENSG00000182950	ENSG00000182950			28735	protein-coding gene	gene with protein product							Standard	NM_175881		Approved	MGC48986	uc002bax.1	Q8IXM7	OTTHUMG00000142837	ENST00000332145.2:c.122C>T	15.37:g.76017452C>T	ENSP00000329584:p.Pro41Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_175881		Missense_Mutation	SNP	ENST00000332145.2	37	CCDS10285.1	363	0.1662087912087912	56	0.11382113821138211	63	0.17403314917127072	68	0.11888111888111888	176	0.23218997361477572	.	16.95	3.264521	0.59431	0.127447	0.250349	ENSG00000182950	ENST00000332145	T	0.62364	0.03	5.28	5.28	0.74379	.	0.000000	0.50627	D	0.000108	T	0.00073	0.0002	M	0.90814	3.15	0.09310	P	0.99999803192	D	0.89917	1.0	D	0.97110	1.0	T	0.01456	-1.1350	9	0.87932	D	0	-15.6431	14.3961	0.67013	0.0:1.0:0.0:0.0	rs55905564	41	Q8IXM7	OD3L1_HUMAN	L	41	ENSP00000329584:P41L	ENSP00000329584:P41L	P	+	2	0	ODF3L1	73804507	0.944000	0.32072	0.849000	0.33467	0.035000	0.12851	4.735000	0.62051	2.479000	0.83701	0.561000	0.74099	CCG	C|0.806;T|0.194	0.194	strong		0.597	ODF3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286473.1	NM_175881	
GBP3	2635	hgsc.bcm.edu	37	1	89479074	89479074	+	Missense_Mutation	SNP	C	C	T	rs4656078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89479074C>T	ENST00000370481.4	-	6	882	c.662G>A	c.(661-663)cGa>cAa	p.R221Q	GBP3_ENST00000475853.2_5'Flank	NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	254	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		GATACAGAGTCGGGGCAGATT	0.373													.|||	1672	0.333866	0.1793	0.2925	5008	,	,		18462	0.3075		0.4404	False		,,,				2504	0.4898				p.R221Q		Atlas-SNP	.											.	GBP3	53	.	0			c.G662A						PASS	.	C	GLN/ARG	1146,3258	371.7+/-320.1	142,862,1198	93.0	99.0	97.0		662	-0.5	0.5	1	dbSNP_111	97	3897,4703	528.3+/-381.3	871,2155,1274	yes	missense	GBP3	NM_018284.2	43	1013,3017,2472	TT,TC,CC		45.314,26.0218,38.7804	probably-damaging	221/596	89479074	5043,7961	2202	4300	6502	SO:0001583	missense	2635	exon6			CAGAGTCGGGGCA	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.662G>A	1.37:g.89479074C>T	ENSP00000359512:p.Arg221Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	705	0.3228021978021978	81	0.16463414634146342	124	0.3425414364640884	161	0.28146853146853146	339	0.4472295514511873	C	18.04	3.535117	0.64972	0.260218	0.45314	ENSG00000117226	ENST00000370481;ENST00000235878	D	0.84589	-1.87	3.85	-0.523	0.11924	Guanylate-binding protein, N-terminal (1);	0.391146	0.20230	N	0.096482	D	0.84808	0.5554	M	0.93375	3.41	0.51482	P	7.80000000000225E-5	D;D	0.69078	0.997;0.961	P;P	0.52217	0.693;0.498	T	0.80106	-0.1521	8	.	.	.	.	4.6468	0.12575	0.1512:0.5724:0.0:0.2764	rs4656078;rs4656078	87;221	F6X827;Q9H0R5	.;GBP3_HUMAN	Q	221	ENSP00000359512:R221Q	.	R	-	2	0	GBP3	89251662	0.307000	0.24500	0.490000	0.27465	0.898000	0.52572	2.143000	0.42187	-0.185000	0.10550	-0.290000	0.09829	CGA	C|0.661;T|0.339	0.339	strong		0.373	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
MEN1	4221	hgsc.bcm.edu	37	11	64572602	64572602	+	Silent	SNP	G	G	A	rs2071313	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64572602G>A	ENST00000337652.1	-	9	1772	c.1269C>T	c.(1267-1269)gaC>gaT	p.D423D	MEN1_ENST00000312049.6_Silent_p.D418D|MAP4K2_ENST00000294066.2_5'Flank|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000394376.1_Silent_p.D423D|MAP4K2_ENST00000377350.3_5'Flank|MEN1_ENST00000377316.2_Intron|MEN1_ENST00000394374.2_Silent_p.D423D|MEN1_ENST00000377313.1_Silent_p.D423D|MEN1_ENST00000478548.1_5'UTR|MEN1_ENST00000377321.1_Silent_p.D383D|MEN1_ENST00000443283.1_Silent_p.D423D|MEN1_ENST00000377326.3_Silent_p.D418D|MEN1_ENST00000315422.4_Silent_p.D418D	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	423			D -> H (in MEN1). {ECO:0000269|PubMed:15730416}.|D -> N (in MEN1). {ECO:0000269|PubMed:12050235, ECO:0000269|PubMed:12112656, ECO:0000269|PubMed:12652570, ECO:0000269|PubMed:9709921}.|Missing (in MEN1).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.L414_E425del(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						TGCAGATGCCGTCGTAGAATC	0.632			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated				G|||	1542	0.307907	0.0348	0.2997	5008	,	,		19274	0.372		0.4056	False		,,,				2504	0.5164				p.D423D	Esophageal Squamous(1;83 158 15500 18603 18803 29295)	Atlas-SNP	.	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	MEN1,NS,adenoma,-2,1	MEN1	442	1	1	Deletion - In frame(1)	parathyroid(1)	c.C1269T	GRCh37	CD005470|CD982777|CX066452	MEN1	D|X	rs2071313	PASS	.	G	,,,,,,	399,4003	196.4+/-220.7	19,361,1821	85.0	75.0	78.0		1269,1254,1269,1269,1269,1269,1269	-1.6	1.0	11	dbSNP_96	78	3552,5042	515.8+/-378.7	751,2050,1496	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MEN1	NM_000244.3,NM_130799.2,NM_130800.2,NM_130801.2,NM_130802.2,NM_130803.2,NM_130804.2	,,,,,,	770,2411,3317	AA,AG,GG		41.3312,9.0641,30.4017	,,,,,,	423/616,418/611,423/616,423/616,423/616,423/616,423/616	64572602	3951,9045	2201	4297	6498	SO:0001819	synonymous_variant	4221	exon9	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	GATGCCGTCGTAG	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1269C>T	11.37:g.64572602G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_130800	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000337652.1	37	CCDS8083.1																																																																																			G|0.698;A|0.302	0.302	strong		0.632	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1		
KMT2D	8085	hgsc.bcm.edu	37	12	49433883	49433883	+	Missense_Mutation	SNP	G	G	A	rs189888707	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49433883G>A	ENST00000301067.7	-	31	7669	c.7670C>T	c.(7669-7671)cCg>cTg	p.P2557L	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2557	Pro-rich.		P -> L (in dbSNP:rs189888707). {ECO:0000269|PubMed:21280141}.		chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										ATGGGGTGGCGGGAGACCAGG	0.607													G|||	43	0.00858626	0.0129	0.0086	5008	,	,		16848	0.0		0.005	False		,,,				2504	0.0153				p.P2557L		Atlas-SNP	.											MLL2_ENST00000301067,colon,carcinoma,0,2	MLL2	1173	2	0			c.C7670T						PASS	.	G	LEU/PRO	54,3794		0,54,1870	33.0	37.0	35.0		7670	4.4	1.0	12		35	58,8204		1,56,4074	yes	missense	MLL2	NM_003482.3	98	1,110,5944	AA,AG,GG		0.702,1.4033,0.9249	benign	2557/5538	49433883	112,11998	1924	4131	6055	SO:0001583	missense	8085	exon31			GGTGGCGGGAGAC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.7670C>T	12.37:g.49433883G>A	ENSP00000301067:p.Pro2557Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	171	76	0.444444	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	14	0.00641025641025641	6	0.012195121951219513	4	0.011049723756906077	0	0.0	4	0.005277044854881266	G	8.376	0.836499	0.16891	0.014033	0.00702	ENSG00000167548	ENST00000301067	T	0.80214	-1.35	5.3	4.42	0.53409	.	0.000000	0.37053	N	0.002277	T	0.61388	0.2343	N	0.19112	0.55	0.38713	D	0.953259	B	0.09022	0.002	B	0.06405	0.002	T	0.66106	-0.6006	10	0.87932	D	0	.	12.3413	0.55095	0.0828:0.0:0.9172:0.0	.	2557	O14686	MLL2_HUMAN	L	2557	ENSP00000301067:P2557L	ENSP00000301067:P2557L	P	-	2	0	MLL2	47720150	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	3.644000	0.54381	1.377000	0.46286	0.591000	0.81541	CCG	G|0.994;A|0.006	0.006	strong		0.607	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
KRT6A	3853	hgsc.bcm.edu	37	12	52886490	52886490	+	Silent	SNP	A	A	G	rs711317	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52886490A>G	ENST00000330722.6	-	1	551	c.483T>C	c.(481-483)gcT>gcC	p.A161A		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	161	Head.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.A161A(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CACGCTCCTCAGCCCGCACCC	0.597													A|||	2249	0.449081	0.1331	0.6023	5008	,	,		18611	0.6319		0.6044	False		,,,				2504	0.4192				p.A161A		Atlas-SNP	.											KRT6A,NS,carcinoma,0,1	KRT6A	89	1	1	Substitution - coding silent(1)	prostate(1)	c.T483C						PASS	.	A		868,3538	339.9+/-306.0	77,714,1412	169.0	155.0	160.0		483	-10.6	0.3	12	dbSNP_86	160	5019,3581	627.2+/-397.9	1467,2085,748	no	coding-synonymous	KRT6A	NM_005554.3		1544,2799,2160	GG,GA,AA		41.6395,19.7004,45.2637		161/565	52886490	5887,7119	2203	4300	6503	SO:0001819	synonymous_variant	3853	exon1			CTCCTCAGCCCGC	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.483T>C	12.37:g.52886490A>G		Somatic	479	1	0.00208768		WXS	Illumina HiSeq	Phase_I	458	457	0.997817	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																			A|0.452;G|0.547	0.547	strong		0.597	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
ATP10D	57205	hgsc.bcm.edu	37	4	47593283	47593283	+	Missense_Mutation	SNP	G	G	C	rs4145944	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:47593283G>C	ENST00000273859.3	+	23	4435	c.4166G>C	c.(4165-4167)aGt>aCt	p.S1389T		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1389			S -> T (in dbSNP:rs4145944). {ECO:0000269|PubMed:10819331}.		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						AAGTCAGCAAGTTCCTGTGCT	0.448													C|||	1888	0.376997	0.6899	0.4006	5008	,	,		19538	0.123		0.3638	False		,,,				2504	0.2127				p.S1389T		Atlas-SNP	.											.	ATP10D	168	.	0			c.G4166C						PASS	.	C	THR/SER	2708,1698	514.9+/-368.7	840,1028,335	148.0	146.0	147.0		4166	3.6	0.0	4	dbSNP_110	147	3009,5591	664.9+/-402.2	556,1897,1847	yes	missense	ATP10D	NM_020453.3	58	1396,2925,2182	CC,CG,GG		34.9884,38.5384,43.9566	benign	1389/1427	47593283	5717,7289	2203	4300	6503	SO:0001583	missense	57205	exon23			CAGCAAGTTCCTG	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.4166G>C	4.37:g.47593283G>C	ENSP00000273859:p.Ser1389Thr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	111	66	0.594595	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	888	0.4065934065934066	353	0.717479674796748	159	0.43922651933701656	87	0.1520979020979021	289	0.3812664907651715	C	0.369	-0.935039	0.02340	0.614616	0.349884	ENSG00000145246	ENST00000273859	T	0.37752	1.18	4.45	3.59	0.41128	.	1.477610	0.03813	N	0.266213	T	0.00012	0.0000	N	0.01109	-1.01	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40098	-0.9581	9	0.10902	T	0.67	-0.0353	6.374	0.21497	0.0:0.7135:0.1846:0.1019	rs4145944;rs56510786;rs4145944	1389	Q9P241	AT10D_HUMAN	T	1389	ENSP00000273859:S1389T	ENSP00000273859:S1389T	S	+	2	0	ATP10D	47288040	0.001000	0.12720	0.002000	0.10522	0.255000	0.26057	0.929000	0.28844	0.480000	0.27534	-0.499000	0.04595	AGT	G|0.592;C|0.408	0.408	strong		0.448	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
FAM186A	121006	hgsc.bcm.edu	37	12	50745822	50745822	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745822T>G	ENST00000327337.5	-	4	4792	c.4793A>C	c.(4792-4794)gAa>gCa	p.E1598A	FAM186A_ENST00000543111.1_Missense_Mutation_p.E1598A|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1598								p.E1598A(1)									GATCCCCAGTTCCTGCGCCTG	0.677																																					p.E1598A	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,6	FAM186A	181	6	1	Substitution - Missense(1)	endometrium(1)	c.A4793C						scavenged	.						6.0	6.0	6.0					12																	50745822		682	1559	2241	SO:0001583	missense	121006	exon4			CCCAGTTCCTGCG		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4793A>C	12.37:g.50745822T>G	ENSP00000329995:p.Glu1598Ala	Somatic	202	5	0.0247525		WXS	Illumina HiSeq	Phase_I	255	26	0.101961	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	t	0.013	-1.606964	0.00842	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.04119	3.7;3.7	4.05	-6.48	0.01896	.	.	.	.	.	T	0.01976	0.0062	N	0.03608	-0.345	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.04013	0.001;0.0	T	0.47573	-0.9107	9	0.05833	T	0.94	.	16.1776	0.81862	0.0:0.0:0.4015:0.5985	.	1598;1598	F5GYN0;A6NE01	.;F186A_HUMAN	A	1598	ENSP00000441337:E1598A;ENSP00000329995:E1598A	ENSP00000329995:E1598A	E	-	2	0	FAM186A	49032089	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.436000	0.00234	-1.527000	0.01758	-4.121000	0.00011	GAA	.	.	none		0.677	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
LRP1B	53353	hgsc.bcm.edu	37	2	141032088	141032088	+	Silent	SNP	C	C	T	rs1386356	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:141032088C>T	ENST00000389484.3	-	85	14018	c.13047G>A	c.(13045-13047)acG>acA	p.T4349T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4349	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTTCATAGCGCGTTGGACAGA	0.423										TSP Lung(27;0.18)			T|||	2435	0.486222	0.1558	0.5735	5008	,	,		15952	0.6508		0.665	False		,,,				2504	0.5174				p.T4349T	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G13047A						PASS	.	T		1129,3277	716.0+/-408.5	140,849,1214	178.0	143.0	155.0		13047	-2.2	1.0	2	dbSNP_88	155	5790,2810	443.8+/-360.5	1954,1882,464	no	coding-synonymous	LRP1B	NM_018557.2		2094,2731,1678	TT,TC,CC		32.6744,25.6241,46.8015		4349/4600	141032088	6919,6087	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon85			ATAGCGCGTTGGA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.13047G>A	2.37:g.141032088C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	183	89	0.486339	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1	1188	0.5439560439560439	92	0.18699186991869918	206	0.569060773480663	385	0.6730769230769231	505	0.6662269129287599	T	9.384	1.073697	0.20147	0.256241	0.673256	ENSG00000168702	ENST00000437977;ENST00000442974	.	.	.	5.36	-2.23	0.06930	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21553	P	0.999642195	.	.	.	.	.	.	T	0.40156	-0.9578	3	.	.	.	.	1.7664	0.03003	0.1132:0.2733:0.208:0.4055	rs1386356;rs3748866;rs1386356	.	.	.	H	581;81	.	.	R	-	2	0	LRP1B	140748558	0.956000	0.32656	0.993000	0.49108	0.991000	0.79684	0.285000	0.18883	-0.237000	0.09739	-0.254000	0.11334	CGC	C|0.462;T|0.538	0.538	strong		0.423	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
TUBGCP5	114791	hgsc.bcm.edu	37	15	22853808	22853808	+	Silent	SNP	C	C	T	rs142094970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:22853808C>T	ENST00000283645.4	+	12	1576	c.1446C>T	c.(1444-1446)caC>caT	p.H482H	TUBGCP5_ENST00000453949.2_Silent_p.H482H|TUBGCP5_ENST00000559846.1_3'UTR	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	482					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		GGATCGTGCACGGGCACCTGT	0.612													C|||	45	0.00898562	0.0008	0.0101	5008	,	,		14746	0.0		0.0129	False		,,,				2504	0.0245				p.H482H		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.C1446T						PASS	.	C	,	13,4393		0,13,2190	73.0	62.0	65.0		1446,1446	-10.8	0.0	15	dbSNP_134	65	179,8421		1,177,4122	no	coding-synonymous,coding-synonymous	TUBGCP5	NM_001102610.1,NM_052903.4	,	1,190,6312	TT,TC,CC		2.0814,0.2951,1.4762	,	482/1025,482/1025	22853808	192,12814	2203	4300	6503	SO:0001819	synonymous_variant	114791	exon12			CGTGCACGGGCAC	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"""gamma-tubulin complex component GCP5"""	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.1446C>T	15.37:g.22853808C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	102	63	0.617647	NM_052903	E9PB12|Q6IQ52|Q96PY8	Silent	SNP	ENST00000283645.4	37	CCDS10008.1																																																																																			C|0.988;T|0.012	0.012	strong		0.612	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903	
ATMIN	23300	hgsc.bcm.edu	37	16	81076821	81076821	+	Missense_Mutation	SNP	T	T	C	rs2278022	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81076821T>C	ENST00000299575.4	+	4	742	c.718T>C	c.(718-720)Tcc>Ccc	p.S240P	ATMIN_ENST00000564241.1_Missense_Mutation_p.S84P|ATMIN_ENST00000566488.1_Missense_Mutation_p.S84P|ATMIN_ENST00000539819.1_3'UTR	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	240	Required for formation of RAD51 foci.		S -> P (in dbSNP:rs2278022).		cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						CCAGAAGTTATCCAACAAGAC	0.368													T|||	515	0.102835	0.0499	0.1095	5008	,	,		21871	0.1974		0.0905	False		,,,				2504	0.0849				p.S240P		Atlas-SNP	.											.	ATMIN	50	.	0			c.T718C						PASS	.	T	PRO/SER	218,4186	130.2+/-166.9	6,206,1990	120.0	109.0	113.0		718	3.7	0.2	16	dbSNP_100	113	634,7966	164.2+/-216.6	23,588,3689	yes	missense	ATMIN	NM_015251.2	74	29,794,5679	CC,CT,TT		7.3721,4.95,6.5518	probably-damaging	240/824	81076821	852,12152	2202	4300	6502	SO:0001583	missense	23300	exon4			AAGTTATCCAACA	BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"""Zinc fingers, C2H2-type"""	29034	protein-coding gene	gene with protein product	"""ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein"", ""ATM INteracting protein"""	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.718T>C	16.37:g.81076821T>C	ENSP00000299575:p.Ser240Pro	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	147	64	0.435374	NM_015251	A8K4H8|Q68DC9	Missense_Mutation	SNP	ENST00000299575.4	37	CCDS32494.1	252	0.11538461538461539	26	0.052845528455284556	40	0.11049723756906077	112	0.1958041958041958	74	0.09762532981530343	T	8.993	0.978223	0.18812	0.0495	0.073721	ENSG00000166454	ENST00000299575;ENST00000539819	T	0.34072	1.38	5.94	3.72	0.42706	.	0.576832	0.20233	N	0.096450	T	0.00039	0.0001	M	0.70595	2.14	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.05257	-1.0896	9	0.54805	T	0.06	-10.0458	5.7863	0.18334	0.0:0.2145:0.1425:0.6431	rs2278022;rs52816318;rs59274599;rs2278022	240	O43313	ATMIN_HUMAN	P	240;11	ENSP00000299575:S240P	ENSP00000299575:S240P	S	+	1	0	ATMIN	79634322	0.975000	0.34042	0.223000	0.23860	0.065000	0.16274	0.897000	0.28390	0.522000	0.28464	0.459000	0.35465	TCC	T|0.911;C|0.089	0.089	strong		0.368	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251	
ATMIN	23300	hgsc.bcm.edu	37	16	81077204	81077204	+	Silent	SNP	T	T	A	rs16954513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81077204T>A	ENST00000299575.4	+	4	1125	c.1101T>A	c.(1099-1101)ccT>ccA	p.P367P	ATMIN_ENST00000564241.1_Silent_p.P211P|ATMIN_ENST00000566488.1_Silent_p.P211P|ATMIN_ENST00000539819.1_3'UTR	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	367	Required for formation of RAD51 foci.				cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						AGAGCCTACCTCTTTTCAAAA	0.463													T|||	274	0.0547125	0.1097	0.0447	5008	,	,		20369	0.001		0.0815	False		,,,				2504	0.0153				p.P367P		Atlas-SNP	.											.	ATMIN	50	.	0			c.T1101A						PASS	.	T		420,3984	197.7+/-221.8	19,382,1801	54.0	53.0	54.0		1101	2.2	0.9	16	dbSNP_123	54	574,8026	151.5+/-206.2	17,540,3743	no	coding-synonymous	ATMIN	NM_015251.2		36,922,5544	AA,AT,TT		6.6744,9.5368,7.6438		367/824	81077204	994,12010	2202	4300	6502	SO:0001819	synonymous_variant	23300	exon4			CCTACCTCTTTTC	BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"""Zinc fingers, C2H2-type"""	29034	protein-coding gene	gene with protein product	"""ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein"", ""ATM INteracting protein"""	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.1101T>A	16.37:g.81077204T>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	145	71	0.489655	NM_015251	A8K4H8|Q68DC9	Silent	SNP	ENST00000299575.4	37	CCDS32494.1																																																																																			T|0.929;A|0.071	0.071	strong		0.463	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251	
OR56A4	120793	hgsc.bcm.edu	37	11	6023818	6023818	+	Silent	SNP	G	G	A	rs10839221	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6023818G>A	ENST00000330728.4	-	1	606	c.561C>T	c.(559-561)taC>taT	p.Y187Y		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGATAGACGGGTATCTCAATG	0.493													.|||	812	0.162141	0.0582	0.1945	5008	,	,		22200	0.0794		0.2684	False		,,,				2504	0.2556				p.Y187Y		Atlas-SNP	.											.	OR56A4	66	.	0			c.C561T						PASS	.	G		477,3925	223.9+/-240.3	29,419,1753	65.0	58.0	60.0		561	-0.6	0.1	11	dbSNP_120	60	2565,6027	417.8+/-352.5	397,1771,2128	no	coding-synonymous	OR56A4	NM_001005179.2		426,2190,3881	AA,AG,GG		29.8534,10.836,23.4108		187/366	6023818	3042,9952	2201	4296	6497	SO:0001819	synonymous_variant	120793	exon1			AGACGGGTATCTC	BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"""GPCR / Class A : Olfactory receptors"""	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.561C>T	11.37:g.6023818G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_001005179	B9EH17	Silent	SNP	ENST00000330728.4	37	CCDS31404.1																																																																																			G|0.801;A|0.199	0.199	strong		0.493	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
CDR2L	30850	hgsc.bcm.edu	37	17	72999773	72999773	+	Silent	SNP	C	C	T	rs3744204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72999773C>T	ENST00000337231.5	+	5	1414	c.1002C>T	c.(1000-1002)caC>caT	p.H334H		NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	334												all_lung(278;0.226)					CCAGCCGGCACGCGGGCAACC	0.672													C|||	1306	0.260783	0.0991	0.4438	5008	,	,		17180	0.1925		0.3598	False		,,,				2504	0.318				p.H334H		Atlas-SNP	.											.	.	.	.	0			c.C1002T						PASS	.	C		517,3707		37,443,1632	13.0	13.0	13.0		1002	2.1	1.0	17	dbSNP_107	13	2341,5835		333,1675,2080	no	coding-synonymous	CDR2L	NM_014603.2		370,2118,3712	TT,TC,CC		28.6326,12.2396,23.0484		334/466	72999773	2858,9542	2112	4088	6200	SO:0001819	synonymous_variant	30850	exon5			CCGGCACGCGGGC		CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089			29999	protein-coding gene	gene with protein product	"""paraneoplastic antigen"""						Standard	NM_014603		Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.1002C>T	17.37:g.72999773C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_014603	B4DFA7|Q15175	Silent	SNP	ENST00000337231.5	37	CCDS11710.2																																																																																			C|0.748;T|0.252	0.252	strong		0.672	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603	
LAMTOR5	10542	hgsc.bcm.edu	37	1	110950439	110950439	+	5'Flank	SNP	C	C	T	rs6674775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:110950439C>T	ENST00000602318.1	-	0	0				LAMTOR5-AS1_ENST00000609709.1_RNA|LAMTOR5-AS1_ENST00000610148.1_RNA|LAMTOR5-AS1_ENST00000608602.1_RNA|LAMTOR5-AS1_ENST00000609512.1_RNA|LAMTOR5_ENST00000483260.1_5'Flank|LAMTOR5-AS1_ENST00000590826.1_RNA|LAMTOR5_ENST00000602858.1_5'Flank|LAMTOR5-AS1_ENST00000608486.1_RNA|LAMTOR5-AS1_ENST00000587691.1_RNA|LAMTOR5-AS1_ENST00000608499.1_RNA|LAMTOR5-AS1_ENST00000608253.1_RNA|LAMTOR5-AS1_ENST00000590413.1_RNA|LAMTOR5-AS1_ENST00000598454.1_RNA|LAMTOR5-AS1_ENST00000609244.1_RNA|LAMTOR5-AS1_ENST00000457535.1_RNA|LAMTOR5_ENST00000256644.4_Missense_Mutation_p.S17N|LAMTOR5-AS1_ENST00000608067.1_RNA|LAMTOR5_ENST00000474861.2_5'Flank			O43504	LTOR5_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5						cellular response to amino acid stimulus (GO:0071230)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)|response to virus (GO:0009615)|viral genome replication (GO:0019079)	cytosol (GO:0005829)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											CTGACGAAGGCTTGGGCTCCC	0.617													C|||	1820	0.363419	0.3056	0.379	5008	,	,		17756	0.2758		0.4453	False		,,,				2504	0.4366				p.S17N		Atlas-SNP	.											HBXIP,colon,carcinoma,0,1	.	.	1	0			c.G50A						PASS	.	C	ASN/SER	1534,2872	478.3+/-358.2	255,1024,924	43.0	39.0	41.0		50	-5.0	0.0	1	dbSNP_116	41	4245,4355	566.6+/-388.7	1020,2205,1075	yes	missense	HBXIP	NM_006402.2	46	1275,3229,1999	TT,TC,CC		49.3605,34.8162,44.4333	benign	17/174	110950439	5779,7227	2203	4300	6503	SO:0001631	upstream_gene_variant	10542	exon1			CGAAGGCTTGGGC	AF029890	CCDS824.1	1p12	2012-09-24	2012-09-24	2012-09-24	ENSG00000134248	ENSG00000134248			17955	protein-coding gene	gene with protein product	"""HBx-interacting protein"", ""hepatitis B virus x-interacting protein (9.6kD)"""	608521	"""hepatitis B virus x interacting protein"""	HBXIP		9499022, 22980980	Standard	NM_006402		Approved	XIP, MGC71071	uc001dzr.3	O43504	OTTHUMG00000011568		1.37:g.110950439C>T	Exception_encountered	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	120	71	0.591667	NM_006402	Q6IBD8	Missense_Mutation	SNP	ENST00000602318.1	37		813	0.37225274725274726	173	0.3516260162601626	146	0.40331491712707185	141	0.2465034965034965	353	0.4656992084432718	C	14.27	2.485686	0.44147	0.348162	0.493605	ENSG00000134248	ENST00000256644	.	.	.	2.48	-4.97	0.03029	.	.	.	.	.	T	0.05547	0.0146	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.27839	-1.0062	3	.	.	.	.	1.9189	0.03303	0.1984:0.2224:0.4274:0.1518	rs6674775;rs17627162;rs59054161;rs6674775	.	.	.	N	17	.	.	S	-	2	0	HBXIP	110751962	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.666000	0.05280	-1.854000	0.01163	0.563000	0.77884	AGC	C|0.604;T|0.396	0.396	strong		0.617	LAMTOR5-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467909.1	NM_006402	
FCGBP	8857	hgsc.bcm.edu	37	19	40368619	40368619	+	Silent	SNP	G	G	A	rs150027077	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40368619G>A	ENST00000221347.6	-	28	12736	c.12729C>T	c.(12727-12729)ggC>ggT	p.G4243G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4243	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCAGCTGCCGCCCCAGATGG	0.647																																					p.G4243G		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.C12729T						scavenged	.						12.0	15.0	14.0					19																	40368619		2182	4225	6407	SO:0001819	synonymous_variant	8857	exon28			GCTGCCGCCCCAG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12729C>T	19.37:g.40368619G>A		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	495	40	0.0808081	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.932;A|0.068	0.068	strong		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CEP68	23177	hgsc.bcm.edu	37	2	65298839	65298839	+	Silent	SNP	A	A	G	rs17849707	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:65298839A>G	ENST00000377990.2	+	3	812	c.609A>G	c.(607-609)acA>acG	p.T203T	CEP68_ENST00000497039.1_3'UTR|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000546106.1_Silent_p.T203T|CEP68_ENST00000260569.4_Silent_p.T203T|CEP68_ENST00000537589.1_5'UTR	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	203					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						CTTCCTCCACAGGCAGCAGTC	0.632													A|||	1239	0.247404	0.1475	0.2738	5008	,	,		19795	0.3304		0.2256	False		,,,				2504	0.3006				p.T203T		Atlas-SNP	.											.	CEP68	69	.	0			c.A609G						PASS	.	A		780,3626	314.1+/-293.5	70,640,1493	49.0	49.0	49.0		609	-12.0	0.0	2	dbSNP_123	49	2010,6590	350.0+/-327.7	251,1508,2541	no	coding-synonymous	CEP68	NM_015147.2		321,2148,4034	GG,GA,AA		23.3721,17.7031,21.4516		203/758	65298839	2790,10216	2203	4300	6503	SO:0001819	synonymous_variant	23177	exon3			CTCCACAGGCAGC	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.609A>G	2.37:g.65298839A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Silent	SNP	ENST00000377990.2	37	CCDS1880.2																																																																																			A|0.773;G|0.227	0.227	strong		0.632	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
ZC3H4	23211	hgsc.bcm.edu	37	19	47585517	47585517	+	Silent	SNP	G	G	C	rs7250850	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47585517G>C	ENST00000253048.5	-	10	1291	c.1254C>G	c.(1252-1254)ctC>ctG	p.L418L	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	418							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		GCTTCTTTGGGAGTTCGATGT	0.463													G|||	1876	0.374601	0.1006	0.5403	5008	,	,		21577	0.2758		0.6869	False		,,,				2504	0.408				p.L418L		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C1254G						PASS	.	G		954,2974		123,708,1133	175.0	156.0	162.0		1254	-3.1	1.0	19	dbSNP_116	162	5827,2503		2038,1751,376	no	coding-synonymous	ZC3H4	NM_015168.1		2161,2459,1509	CC,CG,GG		30.048,24.2872,44.681		418/1304	47585517	6781,5477	1964	4165	6129	SO:0001819	synonymous_variant	23211	exon10			CTTTGGGAGTTCG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1254C>G	19.37:g.47585517G>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	191	87	0.455497	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			G|0.552;C|0.448	0.448	strong		0.463	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
ZNF519	162655	hgsc.bcm.edu	37	18	14105016	14105016	+	Missense_Mutation	SNP	C	C	A	rs61609068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:14105016C>A	ENST00000590202.1	-	3	1675	c.1523G>T	c.(1522-1524)aGa>aTa	p.R508I	ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	508					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						AGTATGAATTCTCTGATGTTG	0.383													C|||	1463	0.292133	0.112	0.2622	5008	,	,		20730	0.6597		0.1958	False		,,,				2504	0.2771				p.R508I		Atlas-SNP	.											.	ZNF519	53	.	0			c.G1523T						PASS	.	C	ILE/ARG	573,3833	251.5+/-258.2	39,495,1669	80.0	84.0	83.0		1523	0.6	0.8	18	dbSNP_129	83	1882,6718	333.6+/-320.6	211,1460,2629	no	missense	ZNF519	NM_145287.3	97	250,1955,4298	AA,AC,CC		21.8837,13.005,18.8759	probably-damaging	508/541	14105016	2455,10551	2203	4300	6503	SO:0001583	missense	162655	exon3			TGAATTCTCTGAT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.1523G>T	18.37:g.14105016C>A	ENSP00000464872:p.Arg508Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	19	0.327586	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	670	0.3067765567765568	55	0.11178861788617886	86	0.23756906077348067	382	0.6678321678321678	147	0.19393139841688653	C	5.798	0.331605	0.10956	0.13005	0.218837	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.77313	2.365	0.28266	P	0.9246309	P	0.45396	0.857	B	0.39419	0.299	T	0.45101	-0.9284	7	0.33141	T	0.24	.	7.2226	0.25997	0.0:0.9999:0.0:1.0E-4	rs61609068;rs61730994	508	Q8TB69	ZN519_HUMAN	I	508	.	ENSP00000307908:R508I	R	-	2	0	ZNF519	14095016	0.000000	0.05858	0.791000	0.31998	0.513000	0.34164	0.368000	0.20399	0.661000	0.30985	0.089000	0.15464	AGA	C|0.781;A|0.219	0.219	strong		0.383	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
BRD8	10902	hgsc.bcm.edu	37	5	137475787	137475787	+	Silent	SNP	C	C	T	rs423258	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:137475787C>T	ENST00000254900.5	-	27	4055	c.3684G>A	c.(3682-3684)gtG>gtA	p.V1228V	NME5_ENST00000265191.2_5'Flank	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	1228					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)	p.V1228V(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTCCATCATCCACTGGGTTAG	0.433													C|||	1486	0.296725	0.0862	0.4035	5008	,	,		17057	0.3839		0.3091	False		,,,				2504	0.4029				p.V1228V		Atlas-SNP	.											BRD8,NS,carcinoma,0,1	BRD8	192	1	1	Substitution - coding silent(1)	stomach(1)	c.G3684A						PASS	.	C		653,3753	281.1+/-275.7	51,551,1601	157.0	149.0	152.0		3684	4.2	0.8	5	dbSNP_80	152	3061,5539	471.7+/-368.2	535,1991,1774	no	coding-synonymous	BRD8	NM_139199.1		586,2542,3375	TT,TC,CC		35.593,14.8207,28.5561		1228/1236	137475787	3714,9292	2203	4300	6503	SO:0001819	synonymous_variant	10902	exon27			ATCATCCACTGGG	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.3684G>A	5.37:g.137475787C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	190	120	0.631579	NM_139199	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Silent	SNP	ENST00000254900.5	37	CCDS4198.1																																																																																			C|0.714;T|0.286	0.286	strong		0.433	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696	
NOD2	64127	hgsc.bcm.edu	37	16	50733859	50733859	+	Silent	SNP	C	C	G	rs2067085	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50733859C>G	ENST00000300589.2	+	2	639	c.534C>G	c.(532-534)tcC>tcG	p.S178S	NOD2_ENST00000526417.2_3'UTR	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	178	CARD 2. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				TCACACCGTCCCAGAGGGTGA	0.537													C|||	1235	0.246605	0.2784	0.2954	5008	,	,		20716	0.0496		0.4264	False		,,,				2504	0.1871				p.S178S		Atlas-SNP	.											NOD2,NS,carcinoma,0,1	NOD2	118	1	0			c.C534G						PASS	.	C		1300,3096	440.8+/-346.1	196,908,1094	64.0	53.0	57.0		534	0.6	1.0	16	dbSNP_96	57	3520,5080	512.4+/-377.9	740,2040,1520	no	coding-synonymous	NOD2	NM_022162.1		936,2948,2614	GG,GC,CC		40.9302,29.5723,37.0883		178/1041	50733859	4820,8176	2198	4300	6498	SO:0001819	synonymous_variant	64127	exon2			ACCGTCCCAGAGG	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.534C>G	16.37:g.50733859C>G		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Silent	SNP	ENST00000300589.2	37	CCDS10746.1																																																																																			C|0.673;G|0.327	0.327	strong		0.537	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
GDPD5	81544	hgsc.bcm.edu	37	11	75152243	75152243	+	Missense_Mutation	SNP	C	C	T	rs571353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:75152243C>T	ENST00000336898.3	-	14	2275	c.1438G>A	c.(1438-1440)Gcc>Acc	p.A480T	GDPD5_ENST00000529721.1_Missense_Mutation_p.A480T|GDPD5_ENST00000533784.1_Missense_Mutation_p.A361T|GDPD5_ENST00000533805.1_Missense_Mutation_p.A235T|GDPD5_ENST00000376282.3_Missense_Mutation_p.A361T|GDPD5_ENST00000526177.1_Missense_Mutation_p.A342T|GDPD5_ENST00000443276.2_3'UTR	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	480	GP-PDE.		A -> T (in dbSNP:rs571353). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874}.		cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)	p.A480T(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						TGGGACAGGGCGTGGGAGTTG	0.642													t|||	3341	0.667133	0.4569	0.719	5008	,	,		18609	0.9236		0.7147	False		,,,				2504	0.6012				p.A480T		Atlas-SNP	.											GDPD5,NS,carcinoma,0,2	GDPD5	49	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1438A						PASS	.		THR/ALA	2246,2154	579.9+/-385.0	602,1042,556	68.0	49.0	55.0		1438	-0.1	0.0	11	dbSNP_83	55	6268,2318	385.5+/-341.5	2282,1704,307	yes	missense	GDPD5	NM_030792.6	58	2884,2746,863	TT,TC,CC		26.9974,48.9545,34.4371	benign	480/606	75152243	8514,4472	2200	4293	6493	SO:0001583	missense	81544	exon14			ACAGGGCGTGGGA	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.1438G>A	11.37:g.75152243C>T	ENSP00000337972:p.Ala480Thr	Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	254	239	0.940945	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Missense_Mutation	SNP	ENST00000336898.3	37	CCDS8238.1	1541	0.7055860805860806	217	0.4410569105691057	256	0.7071823204419889	527	0.9213286713286714	541	0.7137203166226913	t	6.751	0.507351	0.12883	0.510455	0.730026	ENSG00000158555	ENST00000526177;ENST00000533784;ENST00000529721;ENST00000336898;ENST00000533805;ENST00000376282;ENST00000534322	T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87	4.84	-0.0935	0.13649	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	1.037060	0.07548	N	0.914893	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.29731	-1.0002	9	0.16420	T	0.52	-7.1863	10.374	0.44071	0.0:0.5207:0.0:0.4793	rs571353;rs17856575;rs59030486;rs571353	361;480	Q8WTR4-2;Q8WTR4	.;GDPD5_HUMAN	T	342;361;480;480;235;361;64	ENSP00000434050:A342T;ENSP00000437049:A361T;ENSP00000433214:A480T;ENSP00000337972:A480T;ENSP00000435196:A235T;ENSP00000365459:A361T;ENSP00000435728:A64T	ENSP00000337972:A480T	A	-	1	0	GDPD5	74829891	0.000000	0.05858	0.014000	0.15608	0.731000	0.41821	-0.306000	0.08178	-0.362000	0.08113	-0.288000	0.09946	GCC	C|0.330;A|0.004	.	strong		0.642	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792	
MYPN	84665	hgsc.bcm.edu	37	10	69933921	69933921	+	Missense_Mutation	SNP	G	G	A	rs10997975	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:69933921G>A	ENST00000358913.5	+	11	2560	c.2072G>A	c.(2071-2073)aGc>aAc	p.S691N	MYPN_ENST00000354393.2_Missense_Mutation_p.S416N|MYPN_ENST00000540630.1_Missense_Mutation_p.S691N	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	691			S -> N (in dbSNP:rs10997975). {ECO:0000269|PubMed:11309420, ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						TTTCCTTTCAGCATGACTGTT	0.488													A|||	1682	0.335863	0.1762	0.4035	5008	,	,		17477	0.2649		0.4851	False		,,,				2504	0.4233				p.S691N		Atlas-SNP	.											.	MYPN	189	.	0			c.G2072A						PASS	.	A	ASN/SER	976,3430	733.0+/-410.4	109,758,1336	163.0	139.0	148.0		2072	3.2	0.4	10	dbSNP_120	148	4128,4472	589.8+/-392.6	1043,2042,1215	yes	missense	MYPN	NM_032578.2	46	1152,2800,2551	AA,AG,GG		48.0,22.1516,39.2434	benign	691/1321	69933921	5104,7902	2203	4300	6503	SO:0001583	missense	84665	exon11			CTTTCAGCATGAC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2072G>A	10.37:g.69933921G>A	ENSP00000351790:p.Ser691Asn	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	306	149	0.486928	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	783	0.3585164835164835	100	0.2032520325203252	153	0.42265193370165743	162	0.28321678321678323	368	0.48548812664907653	A	1.120	-0.655690	0.03480	0.221516	0.48	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.58797	0.31;0.42;0.4	5.51	3.21	0.36854	.	0.510690	0.22191	N	0.063361	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.46925	-0.9156	8	.	.	.	.	8.0938	0.30816	0.7773:0.0:0.2227:0.0	rs10997975;rs17458172;rs52815281;rs59577198;rs10997975	691;416;691	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	N	416;416;691;691	ENSP00000346369:S416N;ENSP00000351790:S691N;ENSP00000441668:S691N	.	S	+	2	0	MYPN	69603927	0.491000	0.26019	0.353000	0.25747	0.906000	0.53458	0.428000	0.21395	0.088000	0.17205	-0.254000	0.11334	AGC	A|0.370;G|0.630	0.370	strong		0.488	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
MUC4	4585	hgsc.bcm.edu	37	3	195512343	195512343	+	Silent	SNP	G	G	A	rs113457754		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195512343G>A	ENST00000463781.3	-	2	6567	c.6108C>T	c.(6106-6108)acC>acT	p.T2036T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2036T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T2036T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTATCGGTGACAGGAA	0.567																																					p.T2036T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	2	Substitution - coding silent(2)	stomach(2)	c.C6108T						PASS	.						29.0	25.0	26.0					3																	195512343		688	1575	2263	SO:0001819	synonymous_variant	4585	exon2			AGTATCGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6108C>T	3.37:g.195512343G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	422	121	0.28673	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.500;A|0.500	0.500	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KIAA1211	57482	hgsc.bcm.edu	37	4	57190356	57190356	+	Silent	SNP	G	G	A	rs7695701	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57190356G>A	ENST00000504228.1	+	8	3570	c.3465G>A	c.(3463-3465)agG>agA	p.R1155R	KIAA1211_ENST00000264229.6_Silent_p.R1155R|KIAA1211_ENST00000541073.1_Silent_p.R1148R			Q6ZU35	K1211_HUMAN	KIAA1211	1155								p.R1155R(1)		endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AAGAGAAGAGGCCCGAGACTG	0.567													G|||	1129	0.225439	0.0968	0.268	5008	,	,		20625	0.0704		0.4135	False		,,,				2504	0.3354				p.R1155R		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,2	KIAA1211	178	2	1	Substitution - coding silent(1)	prostate(1)	c.G3465A						PASS	.	G		555,3675		28,499,1588	59.0	66.0	63.0		3465	4.5	1.0	4	dbSNP_116	63	3519,4971		712,2095,1438	no	coding-synonymous	KIAA1211	NM_020722.1		740,2594,3026	AA,AG,GG		41.4488,13.1206,32.0283		1155/1234	57190356	4074,8646	2115	4245	6360	SO:0001819	synonymous_variant	57482	exon10			GAAGAGGCCCGAG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.3465G>A	4.37:g.57190356G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	291	137	0.47079	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			G|0.741;A|0.259	0.259	strong		0.567	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
ICE2	79664	hgsc.bcm.edu	37	15	60734697	60734697	+	Silent	SNP	A	A	G	rs1063100	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:60734697A>G	ENST00000261520.4	-	12	2577	c.2343T>C	c.(2341-2343)taT>taC	p.Y781Y	NARG2_ENST00000439632.1_Silent_p.Y644Y	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						CTTCAACTCCATAACAAGCTT	0.323													A|||	2978	0.594649	0.2534	0.6513	5008	,	,		18942	0.8244		0.5726	False		,,,				2504	0.8016				p.Y781Y		Atlas-SNP	.											.	NARG2	82	.	0			c.T2343C						PASS	.	A	,	1267,3139	430.4+/-342.5	187,893,1123	89.0	79.0	82.0		1932,2343	-7.4	0.9	15	dbSNP_86	82	4931,3667	621.5+/-397.2	1431,2069,799	no	coding-synonymous,coding-synonymous	NARG2	NM_001018089.1,NM_024611.4	,	1618,2962,1922	GG,GA,AA		42.6495,28.7562,47.6623	,	644/846,781/983	60734697	6198,6806	2203	4299	6502	SO:0001819	synonymous_variant	79664	exon12			AACTCCATAACAA																												ENST00000261520.4:c.2343T>C	15.37:g.60734697A>G		Somatic	480	0	0		WXS	Illumina HiSeq	Phase_I	494	489	0.989879	NM_024611		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																			.	.	weak		0.323	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1		
OR2B2	81697	hgsc.bcm.edu	37	6	27879200	27879200	+	Missense_Mutation	SNP	C	C	A	rs34788973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27879200C>A	ENST00000303324.2	-	1	974	c.898G>T	c.(898-900)Gcc>Tcc	p.A300S		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	300			A -> S (in dbSNP:rs34788973).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						CTTTTAAAGGCTTCCTTTACC	0.378													C|||	109	0.0217652	0.0106	0.0303	5008	,	,		16685	0.0		0.0736	False		,,,				2504	0.0				p.A300S		Atlas-SNP	.											.	OR2B2	54	.	0			c.G898T						PASS	.	C	SER/ALA	159,4247	106.0+/-144.5	4,151,2048	79.0	80.0	79.0		898	3.6	1.0	6	dbSNP_126	79	753,7847	179.9+/-228.9	35,683,3582	yes	missense	OR2B2	NM_033057.2	99	39,834,5630	AA,AC,CC		8.7558,3.6087,7.0121	possibly-damaging	300/358	27879200	912,12094	2203	4300	6503	SO:0001583	missense	81697	exon1			TAAAGGCTTCCTT	Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"""GPCR / Class A : Olfactory receptors"""	13966	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 9"""	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.898G>T	6.37:g.27879200C>A	ENSP00000304419:p.Ala300Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	146	55	0.376712	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	74	0.03388278388278388	6	0.012195121951219513	10	0.027624309392265192	0	0.0	58	0.07651715039577836	C	11.14	1.551573	0.27739	0.036087	0.087558	ENSG00000168131	ENST00000303324	T	0.44482	0.92	3.6	3.6	0.41247	.	0.000000	0.38959	U	0.001518	T	0.24967	0.0606	N	0.25060	0.705	0.52099	P	5.900000000003125E-5	D	0.54772	0.968	P	0.50405	0.64	T	0.13202	-1.0518	9	0.87932	D	0	.	11.0202	0.47713	0.0:1.0:0.0:0.0	rs34788973;rs61758134	300	Q9GZK3	OR2B2_HUMAN	S	300	ENSP00000304419:A300S	ENSP00000304419:A300S	A	-	1	0	OR2B2	27987179	0.165000	0.22948	0.998000	0.56505	0.577000	0.36160	0.875000	0.28079	2.293000	0.77203	0.313000	0.20887	GCC	C|0.943;A|0.057	0.057	strong		0.378	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
PPT2	9374	hgsc.bcm.edu	37	6	32122472	32122472	+	Missense_Mutation	SNP	C	C	A	rs3096696	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32122472C>A	ENST00000324816.6	+	2	669	c.101C>A	c.(100-102)gCg>gAg	p.A34E	PPT2_ENST00000375137.2_Missense_Mutation_p.A34E|PRRT1_ENST00000375150.2_5'Flank|PPT2_ENST00000493548.1_3'UTR|PPT2_ENST00000361568.2_Missense_Mutation_p.A40E|PPT2_ENST00000395523.1_Missense_Mutation_p.A34E|PRRT1_ENST00000211413.5_5'Flank|PPT2-EGFL8_ENST00000453656.2_3'UTR|PPT2-EGFL8_ENST00000422437.1_Missense_Mutation_p.A34E|PPT2_ENST00000375143.2_Missense_Mutation_p.A34E|PPT2_ENST00000445576.2_Missense_Mutation_p.A34E|PRRT1_ENST00000375152.2_5'Flank|PPT2_ENST00000437001.2_5'UTR			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	34			A -> E (in dbSNP:rs3096696). {ECO:0000269|PubMed:10051407, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14656967}.		cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						CCCCACCGCGCGTCCTACAAG	0.662													C|||	781	0.15595	0.2103	0.1023	5008	,	,		14262	0.0377		0.2018	False		,,,				2504	0.1953				p.A40E		Atlas-SNP	.											.	PPT2	19	.	0			c.C119A						PASS	.	C	GLU/ALA,GLU/ALA,GLU/ALA	574,2442		54,466,988	50.0	56.0	54.0		101,101,119	2.6	0.1	6	dbSNP_103	54	1143,4271		112,919,1676	yes	missense,missense,missense	PPT2	NM_001204103.1,NM_005155.6,NM_138717.2	107,107,107	166,1385,2664	AA,AC,CC		21.1119,19.0318,20.3677	benign,benign,benign	34/303,34/303,40/309	32122472	1717,6713	1508	2707	4215	SO:0001583	missense	9374	exon2			ACCGCGCGTCCTA	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.101C>A	6.37:g.32122472C>A	ENSP00000320528:p.Ala34Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Missense_Mutation	SNP	ENST00000324816.6	37	CCDS4742.1	312	0.14285714285714285	105	0.21341463414634146	33	0.09116022099447514	23	0.04020979020979021	151	0.19920844327176782	C	10.98	1.504887	0.26949	0.190318	0.211119	ENSG00000221988	ENST00000414204;ENST00000361568;ENST00000395523;ENST00000445576;ENST00000324816;ENST00000375137;ENST00000375143;ENST00000424499;ENST00000436118;ENST00000453656	D;D;D;D;D;D;D;D;T	0.94092	-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;1.42	4.63	2.61	0.31194	.	1.033790	0.07631	N	0.928533	T	0.68732	0.3033	N	0.14661	0.345	0.46458	P	9.460000000000024E-4	P;B;B	0.35226	0.491;0.209;0.116	B;B;B	0.31614	0.133;0.125;0.095	T	0.60367	-0.7277	9	0.02654	T	1	-2.8103	6.931	0.24442	0.0:0.6957:0.1926:0.1117	rs3096696;rs17208035;rs61155654	34;34;40	Q9UMR5-2;Q9UMR5;B0S872	.;PPT2_HUMAN;.	E	34;40;34;34;34;34;34;34;34;34	ENSP00000398847:A34E;ENSP00000354608:A40E;ENSP00000378894:A34E;ENSP00000412381:A34E;ENSP00000320528:A34E;ENSP00000364279:A34E;ENSP00000364285:A34E;ENSP00000409877:A34E;ENSP00000395456:A34E	ENSP00000320528:A34E	A	+	2	0	PPT2	32230450	0.006000	0.16342	0.052000	0.19188	0.733000	0.41908	0.937000	0.28951	1.107000	0.41642	0.484000	0.47621	GCG	C|0.825;A|0.175	0.175	strong		0.662	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717	
HEMGN	55363	hgsc.bcm.edu	37	9	100689693	100689693	+	Silent	SNP	A	A	G	rs1059003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100689693A>G	ENST00000259456.3	-	5	1571	c.1428T>C	c.(1426-1428)aaT>aaC	p.N476N		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	476					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				TATAGACATCATTTTCTGGAT	0.303													A|||	404	0.0806709	0.0242	0.1427	5008	,	,		16422	0.0089		0.1451	False		,,,				2504	0.1207				p.N476N		Atlas-SNP	.											.	HEMGN	55	.	0			c.T1428C						PASS	.	A	,	170,4236	113.3+/-151.4	5,160,2038	159.0	160.0	159.0		1428,1428	0.2	0.6	9	dbSNP_86	159	905,7693	201.4+/-244.9	57,791,3451	yes	coding-synonymous,coding-synonymous	HEMGN	NM_018437.3,NM_197978.1	,	62,951,5489	GG,GA,AA		10.5257,3.8584,8.2667	,	476/485,476/485	100689693	1075,11929	2203	4299	6502	SO:0001819	synonymous_variant	55363	exon4			GACATCATTTTCT	AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.1428T>C	9.37:g.100689693A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_197978	Q6XAR3|Q86XY5|Q9NPC0	Silent	SNP	ENST00000259456.3	37	CCDS6731.1																																																																																			A|0.923;G|0.077	0.077	strong		0.303	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978	
PI3	5266	hgsc.bcm.edu	37	20	43803613	43803613	+	Missense_Mutation	SNP	C	C	T	rs17333103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43803613C>T	ENST00000243924.3	+	1	97	c.50C>T	c.(49-51)aCg>aTg	p.T17M		NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived	17			T -> M (in dbSNP:rs17333103).		copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				ATCGCTGGGACGCTGGTTCTA	0.577													C|||	530	0.105831	0.1135	0.0879	5008	,	,		18324	0.0268		0.162	False		,,,				2504	0.1319				p.T17M		Atlas-SNP	.											PI3,caecum,carcinoma,0,2	PI3	21	2	0			c.C50T						PASS	.	C	MET/THR	554,3852	248.1+/-256.1	37,480,1686	178.0	134.0	149.0		50	-5.8	0.0	20	dbSNP_123	149	1508,7092	285.5+/-297.2	126,1256,2918	yes	missense	PI3	NM_002638.3	81	163,1736,4604	TT,TC,CC		17.5349,12.5738,15.8542	benign	17/118	43803613	2062,10944	2203	4300	6503	SO:0001583	missense	5266	exon1			CTGGGACGCTGGT	D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"""WAP four-disulfide core domain containing"""	8947	protein-coding gene	gene with protein product	"""skin-derived antileukoproteinase"", ""trappin-2"""	182257	"""protease inhibitor 3, skin-derived (SKALP)"""			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.50C>T	20.37:g.43803613C>T	ENSP00000243924:p.Thr17Met	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	141	75	0.531915	NM_002638	E1P618|Q6FG74	Missense_Mutation	SNP	ENST00000243924.3	37	CCDS13344.1	241	0.11034798534798534	62	0.12601626016260162	39	0.10773480662983426	16	0.027972027972027972	124	0.16358839050131926	C	5.411	0.261014	0.10239	0.125738	0.175349	ENSG00000124102	ENST00000243924	T	0.26660	1.72	3.9	-5.75	0.02384	.	2.011240	0.02672	N	0.108649	T	0.00039	0.0001	N	0.04508	-0.205	0.80722	P	0.0	B	0.23442	0.085	B	0.17722	0.019	T	0.18493	-1.0335	9	0.25751	T	0.34	.	5.7959	0.18387	0.1302:0.3719:0.0:0.4979	rs17333103;rs52824552;rs59862067;rs17333103	17	P19957	ELAF_HUMAN	M	17	ENSP00000243924:T17M	ENSP00000243924:T17M	T	+	2	0	PI3	43237027	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-2.102000	0.01343	-1.099000	0.03034	-1.166000	0.01754	ACG	C|0.864;T|0.136	0.136	strong		0.577	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638	
Unknown	0	hgsc.bcm.edu	37	11	124096122	124096122	+	IGR	SNP	G	G	A	rs7946182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124096122G>A								OR10D3 (39170 upstream) : OR8G1 (24300 downstream)																							CTCCGCATTCGCTCCACTGAG	0.498													g|||	2253	0.44988	0.612	0.3429	5008	,	,		20593	0.3155		0.338	False		,,,				2504	0.5603				p.R242H		Atlas-SNP	.											.	.	.	.	0			c.G725A						PASS	.	G	HIS/ARG	1784,2406		550,684,861	87.0	108.0	101.0		725	-3.8	0.0	11	dbSNP_116	101	2151,6399		431,1289,2555	no	missense	OR8G2	NM_001007249.1	29	981,1973,3416	AA,AG,GG		25.1579,42.5776,30.887	benign	242/305	124096122	3935,8805	2095	4275	6370	SO:0001628	intergenic_variant	26492	exon1			GCATTCGCTCCAC																													11.37:g.124096122G>A		Somatic	367	1	0.0027248		WXS	Illumina HiSeq	Phase_I	311	114	0.366559	NM_001007249		Missense_Mutation	SNP		37																																																																																				G|0.653;A|0.347	0.347	strong	0	0.498								
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709691	31709691	+	Missense_Mutation	SNP	G	G	A	rs2244485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:31709691G>A	ENST00000382835.2	-	1	321	c.296C>T	c.(295-297)gCg>gTg	p.A99V		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	99			A -> V (in dbSNP:rs2244485).			intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						TGATTGGCACGCTGTCCTTTC	0.502													G|||	1609	0.321286	0.1793	0.3473	5008	,	,		20460	0.2639		0.4503	False		,,,				2504	0.4213				p.A99V		Atlas-SNP	.											KRTAP27-1,NS,carcinoma,-1,1	KRTAP27-1	53	1	0			c.C296T						PASS	.	G	VAL/ALA	979,3427	367.8+/-318.4	108,763,1332	133.0	133.0	133.0		296	0.3	0.0	21	dbSNP_100	133	4174,4426	568.2+/-389.0	1012,2150,1138	yes	missense	KRTAP27-1	NM_001077711.1	64	1120,2913,2470	AA,AG,GG		48.5349,22.2197,39.6202	benign	99/208	31709691	5153,7853	2203	4300	6503	SO:0001583	missense	643812	exon1			TGGCACGCTGTCC	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"""Keratin associated proteins"""	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.296C>T	21.37:g.31709691G>A	ENSP00000372286:p.Ala99Val	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	227	92	0.405286	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	37	CCDS33532.1	674	0.3086080586080586	81	0.16463414634146342	127	0.35082872928176795	126	0.2202797202797203	340	0.44854881266490765	G	5.791	0.330292	0.10956	0.222197	0.485349	ENSG00000206107	ENST00000382835	T	0.03301	3.98	4.44	0.262	0.15597	.	2.953730	0.01681	N	0.026127	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P	0.40032	0.699	B	0.32677	0.15	T	0.44019	-0.9355	9	0.34782	T	0.22	2.1633	4.478	0.11753	0.2144:0.3548:0.4308:0.0	rs2244485;rs17593215;rs56539537;rs2244485	99	Q3LI81	KR271_HUMAN	V	99	ENSP00000372286:A99V	ENSP00000372286:A99V	A	-	2	0	KRTAP27-1	30631562	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.536000	0.23129	0.039000	0.15632	0.591000	0.81541	GCG	G|0.654;A|0.346	0.346	strong		0.502	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711	
OR51G2	81282	hgsc.bcm.edu	37	11	4936608	4936608	+	Missense_Mutation	SNP	C	C	G	rs12419598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4936608C>G	ENST00000322013.3	-	1	314	c.286G>C	c.(286-288)Gaa>Caa	p.E96Q	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	96			E -> Q (in dbSNP:rs12419598).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCTAATTTCTCGTGCTCCA	0.502													C|||	261	0.0521166	0.0053	0.072	5008	,	,		21521	0.002		0.1223	False		,,,				2504	0.0808				p.E96Q		Atlas-SNP	.											.	OR51G2	70	.	0			c.G286C						PASS	.	C	GLN/GLU	124,4278	90.2+/-128.9	1,122,2078	91.0	82.0	85.0		286	5.5	0.1	11	dbSNP_120	85	1034,7562	220.5+/-258.2	62,910,3326	yes	missense	OR51G2	NM_001005238.1	29	63,1032,5404	GG,GC,CC		12.0289,2.8169,8.9091	benign	96/315	4936608	1158,11840	2201	4298	6499	SO:0001583	missense	81282	exon1			TAATTTCTCGTGC	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"""GPCR / Class A : Olfactory receptors"""	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.286G>C	11.37:g.4936608C>G	ENSP00000322593:p.Glu96Gln	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_001005238	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	123	0.05631868131868132	5	0.01016260162601626	29	0.08011049723756906	1	0.0017482517482517483	88	0.11609498680738786	C	6.592	0.477565	0.12521	0.028169	0.120289	ENSG00000176893	ENST00000322013	T	0.00554	6.64	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.529639	0.17116	N	0.186427	T	0.00039	0.0001	M	0.67569	2.06	0.09310	N	1	B	0.32717	0.381	B	0.34301	0.179	T	0.48375	-0.9041	10	0.59425	D	0.04	.	18.052	0.89353	0.0:1.0:0.0:0.0	rs12419598;rs17252531	96	Q8NGK0	O51G2_HUMAN	Q	96	ENSP00000322593:E96Q	ENSP00000322593:E96Q	E	-	1	0	OR51G2	4893184	0.000000	0.05858	0.077000	0.20336	0.018000	0.09664	-0.312000	0.08113	2.847000	0.97988	0.655000	0.94253	GAA	C|0.921;G|0.079	0.079	strong		0.502	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238	
IL7R	3575	hgsc.bcm.edu	37	5	35874575	35874575	+	Missense_Mutation	SNP	C	C	T	rs6897932	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:35874575C>T	ENST00000303115.3	+	6	860	c.731C>T	c.(730-732)aCc>aTc	p.T244I	IL7R_ENST00000343305.4_Intron|IL7R_ENST00000506850.1_Intron	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	244			T -> I (in dbSNP:rs6897932). {ECO:0000269|PubMed:17660817, ECO:0000269|PubMed:9843216, ECO:0000269|Ref.5}.		B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)	p.T244_I245insPPVCSVT(2)|p.T244I(2)|p.T244>NECS(1)|p.T244>KKCTN(1)|p.L243_T244insMCP(1)|p.T244_I245insRPCG(1)|p.P240_T244>RFCPH(1)|p.T244_I245insCPT(1)|p.L243_T244insMPEQDCP(1)|p.T244_I245insLPCVY(1)|p.L243_T244>PIYRCVL(1)|p.L242_S246>PQGGC(1)|p.P240_S246>LKC(1)|p.L242_T243>CGIREI(1)|p.L243_T244>PCPL(1)|p.P240_S246>LQSC(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			ATCTTACTAACCATCAGCATT	0.443			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						C|||	864	0.172524	0.0658	0.183	5008	,	,		20099	0.1687		0.2714	False		,,,				2504	0.2117				p.T244I		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	IL7R,NS,carcinoma,-1,3	IL7R	200	3	18	Insertion - In frame(7)|Complex - insertion inframe(5)|Substitution - Missense(2)|Complex - deletion inframe(2)|Complex - compound substitution(2)	haematopoietic_and_lymphoid_tissue(17)|stomach(1)	c.C731T	GRCh37	CM074279	IL7R	M	rs6897932	PASS	.	C	ILE/THR	484,3922	227.5+/-242.7	28,428,1747	251.0	218.0	229.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	731	-2.5	0.0	5	dbSNP_116	229	2300,6300	386.4+/-341.8	296,1708,2296	yes	missense	IL7R	NM_002185.2	89	324,2136,4043	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	26.7442,10.985,21.4055	benign	244/460	35874575	2784,10222	2203	4300	6503	SO:0001583	missense	3575	exon6			TACTAACCATCAG	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.731C>T	5.37:g.35874575C>T	ENSP00000306157:p.Thr244Ile	Somatic	420	0	0		WXS	Illumina HiSeq	Phase_I	472	469	0.993644	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	417	0.19093406593406592	32	0.06504065040650407	72	0.19889502762430938	102	0.17832167832167833	211	0.2783641160949868	C	7.247	0.602421	0.13939	0.10985	0.267442	ENSG00000168685	ENST00000303115	D	0.96104	-3.91	5.97	-2.49	0.06403	.	1.508970	0.03292	N	0.187788	T	0.00039	0.0001	N	0.20766	0.605	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.55964	-0.8057	9	0.06757	T	0.87	-26.1859	7.3691	0.26792	0.0:0.3863:0.1198:0.4939	rs6897932;rs57894527;rs6897932	244	P16871	IL7RA_HUMAN	I	244	ENSP00000306157:T244I	ENSP00000306157:T244I	T	+	2	0	IL7R	35910332	0.000000	0.05858	0.000000	0.03702	0.889000	0.51656	-0.450000	0.06803	-0.378000	0.07918	0.655000	0.94253	ACC	C|0.810;T|0.190	0.190	strong		0.443	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
LAMA5	3911	hgsc.bcm.edu	37	20	60908964	60908964	+	Silent	SNP	G	G	A	rs13044266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60908964G>A	ENST00000252999.3	-	23	2937	c.2871C>T	c.(2869-2871)tgC>tgT	p.C957C	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	957	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CACAGTTGGCGCAGGTGGCCG	0.697													g|||	3613	0.721446	0.3109	0.7983	5008	,	,		8054	0.9365		0.9155	False		,,,				2504	0.8006				p.C957C		Atlas-SNP	.											LAMA5,caecum,carcinoma,0,1	LAMA5	268	1	0			c.C2871T						PASS	.			1795,2587		423,949,819	21.0	16.0	17.0		2871	-3.0	0.0	20	dbSNP_121	17	7831,687		3647,537,75	no	coding-synonymous	LAMA5	NM_005560.3		4070,1486,894	AA,AG,GG		8.0653,40.963,25.3798		957/3696	60908964	9626,3274	2191	4259	6450	SO:0001819	synonymous_variant	3911	exon23			GTTGGCGCAGGTG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.2871C>T	20.37:g.60908964G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.274;A|0.726	0.726	strong		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
FRMD1	79981	hgsc.bcm.edu	37	6	168463624	168463624	+	Missense_Mutation	SNP	G	G	A	rs902393	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:168463624G>A	ENST00000283309.6	-	7	884	c.820C>T	c.(820-822)Cgt>Tgt	p.R274C	FRMD1_ENST00000440994.2_Missense_Mutation_p.R206C|FRMD1_ENST00000537786.1_Missense_Mutation_p.R45C|FRMD1_ENST00000432403.1_5'UTR	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	274	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		R -> C (in dbSNP:rs902393).			cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		ACGGTGGGACGACCTTCCTTC	0.622													G|||	349	0.0696885	0.0779	0.0706	5008	,	,		16980	0.0506		0.0557	False		,,,				2504	0.092				p.R274C	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C820T						PASS	.	G	CYS/ARG,CYS/ARG	295,4111	160.7+/-193.0	8,279,1916	126.0	108.0	114.0		616,820	-1.9	0.0	6	dbSNP_86	114	618,7982	162.0+/-214.8	24,570,3706	yes	missense,missense	FRMD1	NM_001122841.1,NM_024919.3	180,180	32,849,5622	AA,AG,GG		7.186,6.6954,7.0198	probably-damaging,probably-damaging	206/482,274/550	168463624	913,12093	2203	4300	6503	SO:0001583	missense	79981	exon7			TGGGACGACCTTC		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.820C>T	6.37:g.168463624G>A	ENSP00000283309:p.Arg274Cys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	142	0.06501831501831502	38	0.07723577235772358	24	0.06629834254143646	31	0.05419580419580419	49	0.06464379947229551	G	7.963	0.747369	0.15710	0.066954	0.07186	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	D;D;T	0.83250	-1.7;-1.6;1.49	2.89	-1.93	0.07594	FERM domain (1);	0.301075	0.24922	U	0.034532	T	0.58509	0.2127	M	0.61703	1.905	0.80722	P	0.0	B;B;B;B	0.20459	0.045;0.004;0.006;0.02	B;B;B;B	0.21546	0.035;0.002;0.005;0.013	T	0.33471	-0.9867	9	0.54805	T	0.06	.	2.7246	0.05210	0.0898:0.27:0.3524:0.2878	rs902393;rs17219446;rs57716756;rs902393	186;274;206;146	B7Z8G9;Q8N878;Q8N878-2;Q5SZU5	.;FRMD1_HUMAN;.;.	C	274;206;45	ENSP00000283309:R274C;ENSP00000414115:R206C;ENSP00000440078:R45C	ENSP00000283309:R274C	R	-	1	0	FRMD1	168206473	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.007000	0.12810	-1.001000	0.03434	-0.657000	0.03884	CGT	G|0.932;A|0.068	0.068	strong		0.622	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
AUH	549	hgsc.bcm.edu	37	9	94087622	94087622	+	Silent	SNP	T	T	G	rs7874056	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:94087622T>G	ENST00000375731.4	-	4	506	c.483A>C	c.(481-483)atA>atC	p.I161I	AUH_ENST00000422391.2_Silent_p.I161I|AUH_ENST00000303617.5_Intron|AUH_ENST00000478465.1_5'UTR	NM_001698.2	NP_001689.1	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-CoA hydratase	161					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)|methylglutaconyl-CoA hydratase activity (GO:0004490)|mRNA 3'-UTR binding (GO:0003730)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						TCACTGCTCTTATTTTGGAGA	0.338													T|||	448	0.0894569	0.1853	0.085	5008	,	,		16022	0.0149		0.0964	False		,,,				2504	0.0327				p.I161I		Atlas-SNP	.											.	AUH	32	.	0			c.A483C						PASS	.	T		799,3607	321.3+/-297.0	74,651,1478	129.0	122.0	125.0		483	-4.1	0.8	9	dbSNP_116	125	903,7697	201.4+/-244.9	46,811,3443	no	coding-synonymous	AUH	NM_001698.2		120,1462,4921	GG,GT,TT		10.5,18.1344,13.0863		161/340	94087622	1702,11304	2203	4300	6503	SO:0001819	synonymous_variant	549	exon4			TGCTCTTATTTTG	X79888	CCDS6689.1	9q22	2014-09-17	2010-04-30		ENSG00000148090	ENSG00000148090			890	protein-coding gene	gene with protein product		600529	"""AU RNA-binding protein/enoyl-Coenzyme A hydratase"", ""AU RNA binding protein/enoyl-Coenzyme A hydratase"""			7892223	Standard	NM_001698		Approved		uc004arf.4	Q13825	OTTHUMG00000020207	ENST00000375731.4:c.483A>C	9.37:g.94087622T>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_001698	B1ALV7|B1ALV8|Q8WUE4	Silent	SNP	ENST00000375731.4	37	CCDS6689.1																																																																																			T|0.888;G|0.112	0.112	strong		0.338	AUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053032.1		
OR8H3	390152	hgsc.bcm.edu	37	11	55889895	55889895	+	Missense_Mutation	SNP	C	C	T	rs61751933	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:55889895C>T	ENST00000313472.3	+	1	47	c.47C>T	c.(46-48)aCg>aTg	p.T16M		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	16						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T16M(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TTCATCCTTACGGGACTGTCA	0.453													C|||	520	0.103834	0.0522	0.098	5008	,	,		19669	0.1429		0.1213	False		,,,				2504	0.1196				p.T16M		Atlas-SNP	.											OR8H3,NS,carcinoma,0,1	OR8H3	92	1	1	Substitution - Missense(1)	stomach(1)	c.C47T						scavenged	.	C	MET/THR	246,4156	143.1+/-178.2	7,232,1962	183.0	175.0	178.0		47	0.8	0.1	11	dbSNP_131	178	1007,7585	216.6+/-255.6	54,899,3343	yes	missense	OR8H3	NM_001005201.1	81	61,1131,5305	TT,TC,CC		11.7202,5.5884,9.6429	benign	16/313	55889895	1253,11741	2201	4296	6497	SO:0001583	missense	390152	exon1			TCCTTACGGGACT	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.47C>T	11.37:g.55889895C>T	ENSP00000323928:p.Thr16Met	Somatic	187	2	0.0106952		WXS	Illumina HiSeq	Phase_I	210	109	0.519048	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	255	0.11675824175824176	34	0.06910569105691057	33	0.09116022099447514	88	0.15384615384615385	100	0.13192612137203166	C	0.003	-2.579330	0.00129	0.055884	0.117202	ENSG00000181761	ENST00000313472	T	0.00421	7.46	3.43	0.837	0.18896	.	0.928117	0.09163	N	0.839876	T	0.00012	0.0000	N	0.01297	-0.9	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10382	-1.0632	9	0.36615	T	0.2	.	4.4628	0.11675	0.1467:0.1847:0.0:0.6686	rs61751933	16	Q8N146	OR8H3_HUMAN	M	16	ENSP00000323928:T16M	ENSP00000323928:T16M	T	+	2	0	OR8H3	55646471	0.000000	0.05858	0.086000	0.20670	0.074000	0.17049	-0.728000	0.04925	0.329000	0.23460	-1.252000	0.01501	ACG	C|0.900;T|0.100	0.100	strong		0.453	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
TNKS	8658	hgsc.bcm.edu	37	8	9605648	9605648	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:9605648G>A	ENST00000310430.6	+	18	2784	c.2758G>A	c.(2758-2760)Gcc>Acc	p.A920T	TNKS_ENST00000518281.1_Missense_Mutation_p.A683T	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	920					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)	p.A920T(1)		NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		GCAGCTGTGCGCCCTCCTCCT	0.507																																					p.A920T		Atlas-SNP	.											TNKS_ENST00000310430,NS,carcinoma,0,3	TNKS	198	3	1	Substitution - Missense(1)	kidney(1)	c.G2758A						PASS	.						93.0	88.0	90.0					8																	9605648		2203	4300	6503	SO:0001583	missense	8658	exon18			CTGTGCGCCCTCC	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.2758G>A	8.37:g.9605648G>A	ENSP00000311579:p.Ala920Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	113	16	0.141593	NM_003747	O95272|Q4G0F2	Missense_Mutation	SNP	ENST00000310430.6	37	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.288784	0.59976	.	.	ENSG00000173273	ENST00000310430;ENST00000518281	T;T	0.65549	-0.16;-0.16	5.88	5.88	0.94601	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.53948	0.1828	N	0.21194	0.64	0.80722	D	1	B	0.27791	0.189	B	0.29716	0.106	T	0.49123	-0.8972	10	0.41790	T	0.15	.	20.2381	0.98363	0.0:0.0:1.0:0.0	.	920	O95271	TNKS1_HUMAN	T	920;683	ENSP00000311579:A920T;ENSP00000429890:A683T	ENSP00000311579:A920T	A	+	1	0	TNKS	9643058	1.000000	0.71417	1.000000	0.80357	0.041000	0.13682	9.623000	0.98386	2.779000	0.95612	0.650000	0.86243	GCC	.	.	none		0.507	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	
REV3L	5980	hgsc.bcm.edu	37	6	111694124	111694124	+	Missense_Mutation	SNP	C	C	G	rs3218599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:111694124C>G	ENST00000358835.3	-	14	5888	c.5434G>C	c.(5434-5436)Gac>Cac	p.D1812H	REV3L_ENST00000368805.1_Missense_Mutation_p.D1812H|REV3L_ENST00000368802.3_Missense_Mutation_p.D1812H|REV3L_ENST00000435970.1_Missense_Mutation_p.D1734H			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1812			D -> H (in dbSNP:rs3218599). {ECO:0000269|Ref.5}.		DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TTGGCTGAGTCAAGAGACTGT	0.428								DNA polymerases (catalytic subunits)					C|||	46	0.0091853	0.0008	0.0245	5008	,	,		19961	0.0		0.0278	False		,,,				2504	0.0				p.D1812H		Atlas-SNP	.											.	REV3L	386	.	0			c.G5434C	GRCh37	CM065439	REV3L	M	rs3218599	PASS	.	C	HIS/ASP	23,4383	30.8+/-60.4	0,23,2180	149.0	136.0	140.0		5434	5.1	1.0	6	dbSNP_106	140	187,8413	84.2+/-146.7	6,175,4119	yes	missense	REV3L	NM_002912.3	81	6,198,6299	GG,GC,CC		2.1744,0.522,1.6146	benign	1812/3131	111694124	210,12796	2203	4300	6503	SO:0001583	missense	5980	exon13			CTGAGTCAAGAGA	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.5434G>C	6.37:g.111694124C>G	ENSP00000351697:p.Asp1812His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	54	0.62069	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	31	0.014194139194139194	0	0.0	7	0.019337016574585635	0	0.0	24	0.0316622691292876	C	10.13	1.266893	0.23136	0.00522	0.021744	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01685	4.79;4.79;4.79;4.69	5.93	5.06	0.68205	Ribonuclease H-like (1);	0.336140	0.29383	N	0.012319	T	0.00967	0.0032	L	0.56769	1.78	0.35663	D	0.812702	B	0.23735	0.09	B	0.20184	0.028	T	0.50039	-0.8874	10	0.21540	T	0.41	-0.47	10.7403	0.46149	0.0:0.7996:0.1321:0.0684	rs3218599;rs17539658;rs17686344;rs52831072;rs3218599	1812	O60673	DPOLZ_HUMAN	H	1812;1812;1812;1734	ENSP00000357792:D1812H;ENSP00000357795:D1812H;ENSP00000351697:D1812H;ENSP00000402003:D1734H	ENSP00000351697:D1812H	D	-	1	0	REV3L	111800817	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	3.495000	0.53280	1.484000	0.48361	0.655000	0.94253	GAC	C|0.985;G|0.015	0.015	strong		0.428	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
CEP120	153241	hgsc.bcm.edu	37	5	122685727	122685727	+	Missense_Mutation	SNP	C	C	G	rs1047437	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:122685727C>G	ENST00000306467.5	-	19	2941	c.2637G>C	c.(2635-2637)caG>caC	p.Q879H	CEP120_ENST00000306481.6_Missense_Mutation_p.Q853H|CEP120_ENST00000328236.5_Missense_Mutation_p.Q879H			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	879			Q -> H (in dbSNP:rs1047437).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						GTAGTCTCATCTGTTCCAATT	0.363													C|||	928	0.185304	0.118	0.2147	5008	,	,		17011	0.244		0.1581	False		,,,				2504	0.2229				p.Q879H		Atlas-SNP	.											.	CEP120	72	.	0			c.G2637C						PASS	.	C	HIS/GLN,HIS/GLN	591,3815	259.8+/-263.3	35,521,1647	130.0	125.0	126.0		2559,2637	2.6	1.0	5	dbSNP_86	126	1425,7173	273.5+/-290.7	118,1189,2992	yes	missense,missense	CEP120	NM_001166226.1,NM_153223.3	24,24	153,1710,4639	GG,GC,CC		16.5736,13.4135,15.5029	benign,benign	853/961,879/987	122685727	2016,10988	2203	4299	6502	SO:0001583	missense	153241	exon20			TCTCATCTGTTCC	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.2637G>C	5.37:g.122685727C>G	ENSP00000303058:p.Gln879His	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	389	164	0.421594	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	37	CCDS4134.2	406	0.1858974358974359	68	0.13821138211382114	71	0.19613259668508287	141	0.2465034965034965	126	0.1662269129287599	C	10.36	1.329111	0.24167	0.134135	0.165736	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481	T;T;T	0.22134	1.97;1.97;1.97	5.6	2.59	0.31030	.	0.269957	0.29806	U	0.011148	T	0.00012	0.0000	N	0.00801	-1.175	0.09310	P	0.9999999999997833	B	0.02656	0.0	B	0.04013	0.001	T	0.43065	-0.9414	9	0.23891	T	0.37	-5.1679	4.5832	0.12269	0.1132:0.4271:0.37:0.0896	rs1047437;rs3187444;rs52793214;rs1047437	879	Q8N960	CE120_HUMAN	H	879;879;853	ENSP00000303058:Q879H;ENSP00000327504:Q879H;ENSP00000307419:Q853H	ENSP00000303058:Q879H	Q	-	3	2	CEP120	122713626	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.127000	0.42035	1.371000	0.46172	0.563000	0.77884	CAG	C|0.836;G|0.164	0.164	strong		0.363	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
PLCG2	5336	hgsc.bcm.edu	37	16	81942134	81942134	+	Silent	SNP	G	G	A	rs372347274		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81942134G>A	ENST00000359376.3	+	17	1885	c.1671G>A	c.(1669-1671)aaG>aaA	p.K557K		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	557	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CGGGGGGCAAGGATGGCACCT	0.557																																					p.K557K		Atlas-SNP	.											.	PLCG2	276	.	0			c.G1671A						PASS	.	G		1,4091		0,1,2045	73.0	80.0	78.0		1671	2.9	1.0	16		78	13,8357		0,13,4172	no	coding-synonymous	PLCG2	NM_002661.3		0,14,6217	AA,AG,GG		0.1553,0.0244,0.1123		557/1266	81942134	14,12448	2046	4185	6231	SO:0001819	synonymous_variant	5336	exon17			GGGCAAGGATGGC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1671G>A	16.37:g.81942134G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	136	76	0.558824	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			.	.	weak		0.557	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
NRD1	4898	hgsc.bcm.edu	37	1	52290984	52290984	+	Silent	SNP	T	T	G	rs11205896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:52290984T>G	ENST00000354831.7	-	8	1404	c.1215A>C	c.(1213-1215)ggA>ggC	p.G405G	NRD1_ENST00000544028.1_Silent_p.G205G|NRD1_ENST00000539524.1_Silent_p.G273G|NRD1_ENST00000352171.7_Silent_p.G337G|NRD1_ENST00000485608.1_5'UTR	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	336					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						CCATAGGATGTCCAGGTCTAG	0.294													T|||	2496	0.498403	0.2496	0.6009	5008	,	,		18122	0.8313		0.5239	False		,,,				2504	0.3926				p.G405G		Atlas-SNP	.											.	NRD1	89	.	0			c.A1215C						PASS	.	T	,,	1286,3120	435.5+/-344.3	172,942,1089	62.0	62.0	62.0		1011,819,1215	4.3	1.0	1	dbSNP_120	62	4311,4289	576.1+/-390.3	1077,2157,1066	no	coding-synonymous,coding-synonymous,coding-synonymous	NRD1	NM_001101662.1,NM_001242361.1,NM_002525.2	,,	1249,3099,2155	GG,GT,TT		49.8721,29.1875,43.034	,,	337/1152,273/1088,405/1220	52290984	5597,7409	2203	4300	6503	SO:0001819	synonymous_variant	4898	exon8			AGGATGTCCAGGT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.1215A>C	1.37:g.52290984T>G		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	200	80	0.4	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	37	CCDS559.1																																																																																			T|0.532;G|0.468	0.468	strong		0.294	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
TMEM86B	255043	hgsc.bcm.edu	37	19	55738746	55738746	+	Silent	SNP	G	G	A	rs4374298	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55738746G>A	ENST00000327042.4	-	3	1006	c.484C>T	c.(484-486)Ctg>Ttg	p.L162L	AC010327.2_ENST00000598855.1_Silent_p.Q36Q	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	162					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CCGCGCCACAGCATGGCCATC	0.697													G|||	856	0.170927	0.205	0.2219	5008	,	,		16124	0.0764		0.1968	False		,,,				2504	0.1595				p.L162L		Atlas-SNP	.											.	TMEM86B	12	.	0			c.C484T						PASS	.	G		827,3545		76,675,1435	14.0	15.0	15.0		484	2.4	1.0	19	dbSNP_111	15	1676,6902		166,1344,2779	no	coding-synonymous	TMEM86B	NM_173804.4		242,2019,4214	AA,AG,GG		19.5384,18.9158,19.3282		162/227	55738746	2503,10447	2186	4289	6475	SO:0001819	synonymous_variant	255043	exon3			GCCACAGCATGGC	BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.484C>T	19.37:g.55738746G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	34	32	0.941176	NM_173804		Silent	SNP	ENST00000327042.4	37	CCDS12920.1																																																																																			G|0.828;A|0.172	0.172	strong		0.697	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804	
FAM186A	121006	hgsc.bcm.edu	37	12	50745785	50745785	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745785A>G	ENST00000327337.5	-	4	4829	c.4830T>C	c.(4828-4830)gcT>gcC	p.A1610A	FAM186A_ENST00000543111.1_Silent_p.A1610A|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1610								p.A1610A(1)									GGATCCCCTGAGCCTGCGCCT	0.672																																					p.A1610A	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - coding silent(1)	stomach(1)	c.T4830C						scavenged	.						11.0	11.0	11.0					12																	50745785		692	1589	2281	SO:0001819	synonymous_variant	121006	exon4			CCCCTGAGCCTGC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4830T>C	12.37:g.50745785A>G		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	253	75	0.296443	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			.	.	none		0.672	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
CCDC171	203238	hgsc.bcm.edu	37	9	15784560	15784560	+	Silent	SNP	A	A	G	rs55780067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:15784560A>G	ENST00000380701.3	+	21	3463	c.3135A>G	c.(3133-3135)gcA>gcG	p.A1045A	CCDC171_ENST00000297641.3_Silent_p.A1045A	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1045																	TAAATAATGCATTACTTCGGG	0.388													A|||	126	0.0251597	0.0008	0.0202	5008	,	,		18163	0.0		0.0557	False		,,,				2504	0.0562				p.A1045A		Atlas-SNP	.											.	.	.	.	0			c.A3135G						PASS	.	A		37,4369	41.6+/-74.8	0,37,2166	93.0	82.0	86.0		3135	-2.1	1.0	9	dbSNP_129	86	427,8173	132.3+/-190.0	11,405,3884	no	coding-synonymous	C9orf93	NM_173550.2		11,442,6050	GG,GA,AA		4.9651,0.8398,3.5676		1045/1327	15784560	464,12542	2203	4300	6503	SO:0001819	synonymous_variant	203238	exon21			TAATGCATTACTT	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3135A>G	9.37:g.15784560A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	104	37	0.355769	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Silent	SNP	ENST00000380701.3	37	CCDS6481.1	49	0.022435897435897436	0	0.0	9	0.024861878453038673	0	0.0	40	0.052770448548812667	A	9.759	1.169548	0.21621	0.008398	0.049651	ENSG00000164989	ENST00000449575;ENST00000432954	.	.	.	5.04	-2.06	0.07298	.	.	.	.	.	T	0.08758	0.0217	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.13255	-1.0516	4	.	.	.	-5.6568	2.304	0.04169	0.5751:0.1174:0.1948:0.1127	rs55780067;rs61745611	.	.	.	R	285;99	.	.	H	+	2	0	C9orf93	15774560	0.853000	0.29707	0.984000	0.44739	0.972000	0.66771	-0.078000	0.11375	-0.559000	0.06110	-0.266000	0.10368	CAT	A|0.966;G|0.034	0.034	strong		0.388	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
OR6N1	128372	hgsc.bcm.edu	37	1	158735892	158735892	+	Missense_Mutation	SNP	A	A	G	rs857827	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158735892A>G	ENST00000335094.2	-	1	600	c.581T>C	c.(580-582)aTa>aCa	p.I194T		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	194			I -> T (in dbSNP:rs857827). {ECO:0000269|PubMed:12213199}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					TAGGACATTTATAGACGTATC	0.473													A|||	3345	0.667931	0.7784	0.7839	5008	,	,		20865	0.6171		0.7217	False		,,,				2504	0.4335				p.I194T		Atlas-SNP	.											OR6N1,rectum,carcinoma,0,1	OR6N1	96	1	0			c.T581C						PASS	.	A	THR/ILE	3436,970	731.3+/-410.3	1329,778,96	105.0	111.0	109.0		581	3.7	0.8	1	dbSNP_86	109	6162,2438	697.1+/-404.9	2217,1728,355	yes	missense	OR6N1	NM_001005185.1	89	3546,2506,451	GG,GA,AA		28.3488,22.0154,26.2033	benign	194/313	158735892	9598,3408	2203	4300	6503	SO:0001583	missense	128372	exon1			ACATTTATAGACG	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.581T>C	1.37:g.158735892A>G	ENSP00000335535:p.Ile194Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	1561	0.7147435897435898	376	0.7642276422764228	286	0.7900552486187845	344	0.6013986013986014	555	0.7321899736147758	A	4.870	0.161768	0.09287	0.779846	0.716512	ENSG00000197403	ENST00000335094	T	0.00183	8.6	4.78	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.459103	0.18288	N	0.145796	T	0.00039	0.0001	L	0.27944	0.81	0.50632	P	1.1300000000002974E-4	B	0.06786	0.001	B	0.06405	0.002	T	0.13818	-1.0495	9	0.30078	T	0.28	-8.2149	4.054	0.09808	0.6369:0.1797:0.1834:0.0	rs857827;rs17698061;rs61135327;rs857827	194	Q8NGY5	OR6N1_HUMAN	T	194	ENSP00000335535:I194T	ENSP00000335535:I194T	I	-	2	0	OR6N1	157002516	0.000000	0.05858	0.805000	0.32314	0.908000	0.53690	0.391000	0.20784	0.836000	0.34901	0.533000	0.62120	ATA	A|0.287;G|0.713	0.713	strong		0.473	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
WEE1	7465	hgsc.bcm.edu	37	11	9607032	9607032	+	Silent	SNP	A	A	G	rs10770042	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:9607032A>G	ENST00000450114.2	+	8	1681	c.1428A>G	c.(1426-1428)gaA>gaG	p.E476E	WEE1_ENST00000299613.6_Silent_p.E262E	NM_003390.3	NP_003381.1	P30291	WEE1_HUMAN	WEE1 G2 checkpoint kinase	476	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|establishment of cell polarity (GO:0030010)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuron projection morphogenesis (GO:0048812)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	23				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		CACAAGTTGAAGAGGGCGATA	0.368													A|||	759	0.151558	0.1172	0.1787	5008	,	,		18585	0.1815		0.175	False		,,,				2504	0.1237				p.E476E		Atlas-SNP	.											.	WEE1	54	.	0			c.A1428G						PASS	.	A	,	550,3852	250.6+/-257.6	34,482,1685	202.0	196.0	198.0		786,1428	3.0	1.0	11	dbSNP_120	198	1283,7305	255.1+/-280.1	81,1121,3092	no	coding-synonymous,coding-synonymous	WEE1	NM_001143976.1,NM_003390.3	,	115,1603,4777	GG,GA,AA		14.9395,12.4943,14.1109	,	262/433,476/647	9607032	1833,11157	2201	4294	6495	SO:0001819	synonymous_variant	7465	exon8			AGTTGAAGAGGGC	X62048	CCDS7800.1, CCDS44536.1	11p15.4	2013-10-21	2013-10-21		ENSG00000166483	ENSG00000166483			12761	protein-coding gene	gene with protein product		193525	"""wee1+ (S. pombe) homolog"", ""WEE1 homolog (S. pombe)"""			1840647	Standard	NM_003390		Approved		uc001mhs.3	P30291	OTTHUMG00000165863	ENST00000450114.2:c.1428A>G	11.37:g.9607032A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_003390	B3KVE1|D3DQV0	Silent	SNP	ENST00000450114.2	37	CCDS7800.1																																																																																			A|0.852;G|0.148	0.148	strong		0.368	WEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386757.1	NM_003390	
ERLIN1	10613	hgsc.bcm.edu	37	10	101912064	101912064	+	Missense_Mutation	SNP	T	T	C	rs2862954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:101912064T>C	ENST00000421367.2	-	11	3578	c.871A>G	c.(871-873)Att>Gtt	p.I291V	ERLIN1_ENST00000407654.3_Missense_Mutation_p.I291V	NM_001100626.1|NM_006459.3	NP_001094096.1|NP_006450.2	O75477	ERLN1_HUMAN	ER lipid raft associated 1	289					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)							Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		TTAGAAGCAATGGCCTGGTAC	0.438													T|||	940	0.1877	0.0295	0.2997	5008	,	,		21899	0.0665		0.4811	False		,,,				2504	0.1452				p.I291V		Atlas-SNP	.											.	.	.	.	0			c.A871G						PASS	.	T	VAL/ILE,VAL/ILE	460,3946	220.7+/-238.1	29,402,1772	112.0	110.0	111.0		871,871	4.4	1.0	10	dbSNP_101	111	4044,4556	558.7+/-387.3	949,2146,1205	yes	missense,missense	ERLIN1	NM_001100626.1,NM_006459.3	29,29	978,2548,2977	CC,CT,TT		47.0233,10.4403,34.6302	benign,benign	291/349,291/349	101912064	4504,8502	2203	4300	6503	SO:0001583	missense	10613	exon11			AAGCAATGGCCTG	AF064093	CCDS7487.2	10q24.31	2014-03-03	2007-01-26	2007-01-26	ENSG00000107566	ENSG00000107566			16947	protein-coding gene	gene with protein product	"""Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9"""	611604	"""chromosome 10 open reading frame 69"", ""SPFH domain family, member 1"""	C10orf69, SPFH1		11118313, 16835267, 24482476	Standard	NM_006459		Approved	KE04, Erlin-1, SPG62	uc001kqo.4	O75477	OTTHUMG00000018900	ENST00000421367.2:c.871A>G	10.37:g.101912064T>C	ENSP00000410964:p.Ile291Val	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	249	249	1	NM_006459	B0QZ42|Q53HV0	Missense_Mutation	SNP	ENST00000421367.2	37	CCDS7487.2	540	0.24725274725274726	15	0.03048780487804878	135	0.3729281767955801	39	0.06818181818181818	351	0.4630606860158311	T	14.97	2.695080	0.48202	0.104403	0.470233	ENSG00000107566	ENST00000421367;ENST00000407654;ENST00000370410	T;T	0.66638	-0.22;-0.22	5.49	4.36	0.52297	.	0.175745	0.46442	U	0.000283	T	0.00012	0.0000	L	0.31157	0.91	0.09310	P	0.99999600384	B;B	0.13594	0.008;0.004	B;B	0.18263	0.021;0.015	T	0.41610	-0.9499	9	0.37606	T	0.19	-9.2173	9.7803	0.40645	0.0:0.0821:0.0:0.9179	rs2862954;rs17728805;rs59558087;rs2862954	289;291	O75477;D3DR65	ERLN1_HUMAN;.	V	291;291;207	ENSP00000410964:I291V;ENSP00000384900:I291V	ENSP00000359438:I207V	I	-	1	0	ERLIN1	101902054	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.751000	0.68720	1.037000	0.40024	0.459000	0.35465	ATT	A|0.005;C|0.270	0.270	strong		0.438	ERLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049840.2	NM_006459	
EYS	346007	hgsc.bcm.edu	37	6	66005970	66005970	+	Silent	SNP	G	G	A	rs9345601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:66005970G>A	ENST00000370621.3	-	12	2335	c.1809C>T	c.(1807-1809)gtC>gtT	p.V603V	EYS_ENST00000370616.2_Silent_p.V603V|EYS_ENST00000503581.1_Silent_p.V603V			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	603					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGTCAACATTGACAACACACA	0.383													G|||	2979	0.594848	0.2209	0.7161	5008	,	,		15118	0.8948		0.5915	False		,,,				2504	0.7086				p.V603V		Atlas-SNP	.											.	EYS	527	.	0			c.C1809T						PASS	.	G		416,968		70,276,346	112.0	86.0	94.0		1809	1.5	0.0	6	dbSNP_119	94	1855,1325		535,785,270	no	coding-synonymous	EYS	NM_001142800.1		605,1061,616	AA,AG,GG		41.6667,30.0578,49.759		603/3145	66005970	2271,2293	692	1590	2282	SO:0001819	synonymous_variant	346007	exon12			AACATTGACAACA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1809C>T	6.37:g.66005970G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				G|0.404;A|0.596	0.596	strong		0.383	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
HERC2	8924	hgsc.bcm.edu	37	15	28419566	28419566	+	Silent	SNP	T	T	C	rs201182375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28419566T>C	ENST00000261609.7	-	65	10140	c.10032A>G	c.(10030-10032)agA>agG	p.R3344R		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTAAAGGGTCTCTTGCAGTCT	0.488																																					p.R3344R		Atlas-SNP	.											.	HERC2	501	.	0			c.A10032G						PASS	.						30.0	28.0	29.0					15																	28419566		2203	4297	6500	SO:0001819	synonymous_variant	8924	exon65			AGGGTCTCTTGCA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.10032A>G	15.37:g.28419566T>C		Somatic	368	0	0		WXS	Illumina HiSeq	Phase_I	310	22	0.0709677	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			T|0.988;C|0.013	0.013	strong		0.488	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
FCGBP	8857	hgsc.bcm.edu	37	19	40376323	40376323	+	Missense_Mutation	SNP	A	A	G	rs377439998		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40376323A>G	ENST00000221347.6	-	25	11988	c.11981T>C	c.(11980-11982)gTc>gCc	p.V3994A	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3994	Cys-rich.					extracellular vesicular exosome (GO:0070062)		p.V3994A(3)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CTCATAGTAGACACCATTGTG	0.562																																					p.V3994A		Atlas-SNP	.											FCGBP,NS,carcinoma,0,3	FCGBP	416	3	3	Substitution - Missense(3)	endometrium(2)|upper_aerodigestive_tract(1)	c.T11981C						scavenged	.						65.0	59.0	61.0					19																	40376323		2199	4300	6499	SO:0001583	missense	8857	exon25			TAGTAGACACCAT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.11981T>C	19.37:g.40376323A>G	ENSP00000221347:p.Val3994Ala	Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	374	8	0.0213904	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	a	2.731	-0.264330	0.05754	.	.	ENSG00000090920	ENST00000221347	T	0.04360	3.64	3.4	-5.71	0.02413	von Willebrand factor, type C (1);	.	.	.	.	T	0.02418	0.0074	N	0.20483	0.58	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.49322	-0.8952	9	0.09590	T	0.72	.	7.1668	0.25695	0.2551:0.2893:0.4556:0.0	.	3994	Q9Y6R7	FCGBP_HUMAN	A	3994	ENSP00000221347:V3994A	ENSP00000221347:V3994A	V	-	2	0	FCGBP	45068163	0.000000	0.05858	0.034000	0.17996	0.099000	0.18886	1.012000	0.29924	-0.821000	0.04312	-0.850000	0.03035	GTC	.	.	weak		0.562	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ABL1	25	hgsc.bcm.edu	37	9	133755528	133755528	+	Silent	SNP	A	A	G	rs2227985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133755528A>G	ENST00000318560.5	+	9	1878	c.1497A>G	c.(1495-1497)gaA>gaG	p.E499E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	499					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	TGTTCCAGGAATCCAGTATCT	0.542			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								A|||	429	0.0856629	0.2057	0.0836	5008	,	,		18557	0.001		0.0696	False		,,,				2504	0.0286				p.E518E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.A1554G						PASS	.	A	,	757,3649	309.7+/-291.2	52,653,1498	106.0	106.0	106.0		1497,1554	-2.8	1.0	9	dbSNP_98	106	641,7959	164.3+/-216.7	27,587,3686	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	79,1240,5184	GG,GA,AA		7.4535,17.1811,10.7489	,	499/1131,518/1150	133755528	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	25	exon9			CCAGGAATCCAGT	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1497A>G	9.37:g.133755528A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.898;G|0.102	0.102	strong		0.542	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
MUC16	94025	hgsc.bcm.edu	37	19	9060572	9060572	+	Silent	SNP	G	G	A	rs56405542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9060572G>A	ENST00000397910.4	-	3	27077	c.26874C>T	c.(26872-26874)ggC>ggT	p.G8958G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8960	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCTCTGGGAGGCCTGGATAAG	0.468													g|||	1012	0.202077	0.0968	0.2824	5008	,	,		22043	0.3254		0.167	False		,,,				2504	0.1963				p.G8958G		Atlas-SNP	.											.	MUC16	4315	.	0			c.C26874T						PASS	.	G		413,3555		18,377,1589	200.0	186.0	191.0		26874	-3.2	0.0	19	dbSNP_129	191	1521,6807		137,1247,2780	yes	coding-synonymous	MUC16	NM_024690.2		155,1624,4369	AA,AG,GG		18.2637,10.4083,15.7287		8958/14508	9060572	1934,10362	1984	4164	6148	SO:0001819	synonymous_variant	94025	exon3			TGGGAGGCCTGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.26874C>T	19.37:g.9060572G>A		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	262	107	0.408397	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.788;A|0.212	0.212	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GABRA2	2555	hgsc.bcm.edu	37	4	46314593	46314593	+	Silent	SNP	T	T	C	rs279858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:46314593T>C	ENST00000510861.1	-	5	569	c.396A>G	c.(394-396)aaA>aaG	p.K132K	GABRA2_ENST00000515082.1_Silent_p.K132K|GABRA2_ENST00000356504.1_Silent_p.K132K|GABRA2_ENST00000507069.1_Silent_p.K132K|GABRA2_ENST00000540012.1_Silent_p.K77K|GABRA2_ENST00000514090.1_Silent_p.K132K|GABRA2_ENST00000381620.4_Silent_p.K132K			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	132					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CTACTGATTTTTTCCCATTGT	0.348													T|||	1818	0.363019	0.2262	0.4683	5008	,	,		14178	0.5327		0.4284	False		,,,				2504	0.2311				p.K132K		Atlas-SNP	.											GABRA2,NS,carcinoma,0,2	GABRA2	134	2	0			c.A396G						PASS	.	T	,	1158,3248	407.8+/-334.4	154,850,1199	115.0	117.0	116.0		396,396	-6.0	0.9	4	dbSNP_79	116	3752,4846	533.3+/-382.4	827,2098,1374	no	coding-synonymous,coding-synonymous	GABRA2	NM_000807.2,NM_001114175.1	,	981,2948,2573	CC,CT,TT		43.6381,26.2823,37.7576	,	132/452,132/452	46314593	4910,8094	2203	4299	6502	SO:0001819	synonymous_variant	2555	exon5			TGATTTTTTCCCA		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4076	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 2"""	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.396A>G	4.37:g.46314593T>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	225	108	0.48	NM_000807	A8K0U7|B7Z1H8|Q59G14	Silent	SNP	ENST00000510861.1	37	CCDS3471.1																																																																																			T|0.616;C|0.384	0.384	strong		0.348	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2		
NMD3	51068	hgsc.bcm.edu	37	3	160956548	160956548	+	Silent	SNP	A	A	G	rs11539155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:160956548A>G	ENST00000460469.1	+	8	1142	c.687A>G	c.(685-687)caA>caG	p.Q229Q	NMD3_ENST00000351193.2_Silent_p.Q229Q|NMD3_ENST00000472947.1_Silent_p.Q229Q			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	229					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			TGATCTCTCAAGATATCCATA	0.294													A|||	275	0.0549121	0.0061	0.0591	5008	,	,		17776	0.0516		0.0308	False		,,,				2504	0.1462				p.Q229Q		Atlas-SNP	.											.	NMD3	49	.	0			c.A687G						PASS	.	A		48,4354	48.2+/-83.0	1,46,2154	100.0	100.0	100.0		687	-3.4	1.0	3	dbSNP_120	100	298,8296	107.6+/-168.3	5,288,4004	no	coding-synonymous	NMD3	NM_015938.3		6,334,6158	GG,GA,AA		3.4675,1.0904,2.6624		229/504	160956548	346,12650	2201	4297	6498	SO:0001819	synonymous_variant	51068	exon9			CTCTCAAGATATC	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"""NMD3 homolog (S. cerevisiae)"""			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.687A>G	3.37:g.160956548A>G		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	305	124	0.406557	NM_015938	D3DNM7|Q9Y2Z6	Silent	SNP	ENST00000460469.1	37	CCDS3194.1																																																																																			A|0.972;G|0.028	0.028	strong		0.294	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938	
MTFP1	51537	hgsc.bcm.edu	37	22	30823196	30823196	+	Silent	SNP	T	T	C	rs5753130	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30823196T>C	ENST00000266263.5	+	3	584	c.234T>C	c.(232-234)acT>acC	p.T78T	RP4-539M6.19_ENST00000439838.1_Silent_p.T250T|MTFP1_ENST00000355143.4_Intron|MTFP1_ENST00000407550.3_Intron	NM_016498.4	NP_057582.2	Q9UDX5	MTFP1_HUMAN	mitochondrial fission process 1	78					apoptotic process (GO:0006915)|mitochondrial fission (GO:0000266)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(1)|lung(2)	4						CCAGGGTGACTGTGGCTGTGG	0.617													C|||	2901	0.579273	0.466	0.5821	5008	,	,		19189	0.6935		0.4553	False		,,,				2504	0.7403				p.T78T		Atlas-SNP	.											.	MTFP1	7	.	0			c.T234C						PASS	.	C	,	2111,2295	597.5+/-388.9	512,1087,604	112.0	105.0	107.0		,234	-9.8	0.2	22	dbSNP_114	107	3853,4747	607.5+/-395.2	840,2173,1287	no	intron,coding-synonymous	MTFP1	NM_001003704.2,NM_016498.4	,	1352,3260,1891	CC,CT,TT		44.8023,47.9119,45.8558	,	,78/167	30823196	5964,7042	2203	4300	6503	SO:0001819	synonymous_variant	51537	exon3			GGTGACTGTGGCT	AF151076	CCDS33634.1, CCDS33635.1	22q	2010-09-02			ENSG00000242114	ENSG00000242114			26945	protein-coding gene	gene with protein product		610235				15155745, 15985469	Standard	NM_016498		Approved	MTP18, HSPC242		Q9UDX5	OTTHUMG00000151057	ENST00000266263.5:c.234T>C	22.37:g.30823196T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	152	64	0.421053	NM_016498	A6NFQ5|Q9H3K1|Q9P0N6	Silent	SNP	ENST00000266263.5	37	CCDS33635.1																																																																																			T|0.514;C|0.486	0.486	strong		0.617	MTFP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321126.3	NM_016498	
NBPF3	84224	hgsc.bcm.edu	37	1	21806667	21806667	+	Missense_Mutation	SNP	C	C	G	rs12043777	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:21806667C>G	ENST00000318249.5	+	11	1682	c.1332C>G	c.(1330-1332)gaC>gaG	p.D444E	NBPF3_ENST00000342104.5_Missense_Mutation_p.D432E|NBPF3_ENST00000454000.2_Missense_Mutation_p.D374E|NBPF3_ENST00000318220.6_Missense_Mutation_p.D388E	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	444	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.		D -> E (in dbSNP:rs12043777). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.D444E(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ACAGAAGTGACTTTTACTCAT	0.453																																					p.S444S		Atlas-SNP	.											NBPF3,NS,carcinoma,0,2	NBPF3	55	2	1	Substitution - Missense(1)	prostate(1)	c.T1332G						scavenged	.	C	GLU/ASP	128,4248		35,58,2095	87.0	47.0	61.0		1332	-1.3	0.0	1	dbSNP_120	61	1540,6608		435,670,2969	no	missense	NBPF3	NM_032264.2	45	470,728,5064	GG,GC,CC		18.9003,2.925,13.3184	benign	444/634	21806667	1668,10856	2188	4074	6262	SO:0001583	missense	84224	exon11			AAGTGACTTTTAC	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.1332C>G	1.37:g.21806667C>G	ENSP00000316782:p.Asp444Glu	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	116	8	0.0689655	NM_032264	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Silent	SNP	ENST00000318249.5	37	CCDS216.1	705	0.3228021978021978	55	0.11178861788617886	140	0.3867403314917127	235	0.41083916083916083	275	0.3627968337730871	.	1.891	-0.455414	0.04540	0.02925	0.189003	ENSG00000142794	ENST00000454000;ENST00000318220;ENST00000318249;ENST00000342104;ENST00000434838	T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32	0.658	-1.32	0.09201	DUF1220 (2);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.24823	0.0;0.112	B;B	0.25140	0.001;0.058	T	0.45279	-0.9272	7	0.52906	T	0.07	.	.	.	.	rs56119644	432;444	Q9H094-3;Q9H094	.;NBPF3_HUMAN	E	374;388;444;432;388	ENSP00000415711:D374E;ENSP00000316739:D388E;ENSP00000316782:D444E;ENSP00000340336:D432E;ENSP00000391865:D388E	ENSP00000316739:D388E	D	+	3	2	NBPF3	21679254	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.088000	0.14979	-0.800000	0.04433	0.121000	0.15741	GAC	C|0.874;G|0.126	0.126	strong		0.453	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
DNAH9	1770	hgsc.bcm.edu	37	17	11835331	11835331	+	Splice_Site	SNP	G	G	A	rs17612861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11835331G>A	ENST00000262442.4	+	64	12174	c.12106G>A	c.(12106-12108)Gac>Aac	p.D4036N	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000608377.1_Splice_Site_p.D348N|DNAH9_ENST00000454412.2_Splice_Site_p.D3960N	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4036	AAA 6. {ECO:0000250}.		D -> N (in dbSNP:rs17612861).		cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CTCATTTCAGGACACTCTGGA	0.478													G|||	1052	0.210064	0.0363	0.2594	5008	,	,		20759	0.1806		0.341	False		,,,				2504	0.3057				p.D4036N		Atlas-SNP	.											.	DNAH9	695	.	0			c.G12106A						PASS	.	G	ASN/ASP,ASN/ASP	370,4036	187.1+/-213.8	22,326,1855	331.0	310.0	317.0		12106,1042	3.8	1.0	17	dbSNP_123	317	2876,5724	450.8+/-362.5	485,1906,1909	yes	missense-near-splice,missense-near-splice	DNAH9	NM_001372.3,NM_004662.2	23,23	507,2232,3764	AA,AG,GG		33.4419,8.3976,24.9577	benign,benign	4036/4487,348/799	11835331	3246,9760	2203	4300	6503	SO:0001630	splice_region_variant	1770	exon64			TTTCAGGACACTC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.12106-1G>A	17.37:g.11835331G>A		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	228	116	0.508772	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	495	0.22664835164835165	28	0.056910569105691054	103	0.2845303867403315	104	0.18181818181818182	260	0.34300791556728233	G	3.711	-0.059467	0.07317	0.083976	0.334419	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001	T;T;T	0.10382	2.88;4.57;2.88	4.82	3.83	0.44106	Dynein heavy chain (1);	0.174933	0.48286	D	0.000200	T	0.00012	0.0000	M	0.71036	2.16	0.09310	P	1.0	B	0.27823	0.19	B	0.37387	0.248	T	0.48502	-0.9030	8	.	.	.	.	13.4777	0.61318	0.0769:0.0:0.9231:0.0	rs17612861;rs17612861	4036	Q9NYC9	DYH9_HUMAN	N	4036;3960;2542;348	ENSP00000262442:D4036N;ENSP00000414874:D3960N;ENSP00000379323:D348N	.	D	+	1	0	DNAH9	11776056	1.000000	0.71417	1.000000	0.80357	0.509000	0.34042	5.387000	0.66243	2.477000	0.83638	0.563000	0.77884	GAC	G|0.766;A|0.233	0.233	strong		0.478	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	Missense_Mutation
BRCA1	672	hgsc.bcm.edu	37	17	41245466	41245466	+	Silent	SNP	G	G	A	rs1799949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41245466G>A	ENST00000357654.3	-	10	2200	c.2082C>T	c.(2080-2082)agC>agT	p.S694S	BRCA1_ENST00000354071.3_Silent_p.S694S|BRCA1_ENST00000309486.4_Silent_p.S398S|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000493795.1_Silent_p.S647S|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000346315.3_Silent_p.S694S|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000471181.2_Silent_p.S694S	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	694					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S694S(1)		NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GGAAAGTATCGCTGTCATGTC	0.408			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			G|||	1685	0.336462	0.2103	0.353	5008	,	,		20322	0.371		0.3002	False		,,,				2504	0.4969				p.S694S		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,NS,carcinoma,0,1	BRCA1	304	1	1	Substitution - coding silent(1)	stomach(1)	c.C2082T						PASS	.	G	,,,,	1055,3349	385.6+/-325.8	114,827,1261	116.0	104.0	108.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2082,1941,,,2082	0.6	0.0	17	dbSNP_89	108	2790,5810	442.1+/-360.0	443,1904,1953	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	,,,,	557,2731,3214	AA,AG,GG		32.4419,23.9555,29.5678	,,,,	694/1864,647/1817,,,694/1885	41245466	3845,9159	2202	4300	6502	SO:0001819	synonymous_variant	672	exon10	Familial Cancer Database		AGTATCGCTGTCA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.2082C>T	17.37:g.41245466G>A		Somatic	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	277	160	0.577617	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1																																																																																			G|0.697;A|0.303	0.303	strong		0.408	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
HOXB1	3211	hgsc.bcm.edu	37	17	46608030	46608030	+	Silent	SNP	G	G	A	rs12946855	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46608030G>A	ENST00000239174.6	-	1	329	c.237C>T	c.(235-237)tcC>tcT	p.S79S	HOXB1_ENST00000577092.1_Silent_p.S79S	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	79					anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCGAGGGCGCGGAGCTGGGGA	0.662													G|||	672	0.134185	0.1172	0.1225	5008	,	,		13599	0.0972		0.2048	False		,,,				2504	0.1309				p.S79S		Atlas-SNP	.											.	HOXB1	67	.	0			c.C237T						PASS	.	G		555,3849		34,487,1681	37.0	43.0	41.0		237	-8.7	0.4	17	dbSNP_121	41	1764,6832		179,1406,2713	no	coding-synonymous	HOXB1	NM_002144.3		213,1893,4394	AA,AG,GG		20.5212,12.6022,17.8385		79/302	46608030	2319,10681	2202	4298	6500	SO:0001819	synonymous_variant	3211	exon1			GGGCGCGGAGCTG		CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.237C>T	17.37:g.46608030G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	37	24	0.648649	NM_002144	Q4VB03	Silent	SNP	ENST00000239174.6	37	CCDS32675.1																																																																																			G|0.833;A|0.167	0.167	strong		0.662	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
XKR7	343702	hgsc.bcm.edu	37	20	30584710	30584710	+	Missense_Mutation	SNP	C	C	T	rs61750849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:30584710C>T	ENST00000562532.2	+	3	1364	c.1190C>T	c.(1189-1191)gCg>gTg	p.A397V		NM_001011718.1	NP_001011718.1	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related family, member 7	397						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GAGAACGCCGCGCTCACCGGC	0.597													C|||	357	0.0712859	0.1407	0.049	5008	,	,		16094	0.0179		0.0706	False		,,,				2504	0.0491				p.A397V		Atlas-SNP	.											XKR7,right_lower_lobe,carcinoma,-1,1	XKR7	62	1	0			c.C1190T						PASS	.	C	VAL/ALA	549,3857	247.5+/-255.7	26,497,1680	63.0	58.0	60.0		1190	3.2	0.1	20	dbSNP_129	60	698,7902	172.6+/-223.3	20,658,3622	yes	missense	XKR7	NM_001011718.1	64	46,1155,5302	TT,TC,CC		8.1163,12.4603,9.5879	benign	397/580	30584710	1247,11759	2203	4300	6503	SO:0001583	missense	343702	exon3			ACGCCGCGCTCAC	AY534245	CCDS33459.1	20q11.21	2014-07-16	2006-01-12		ENSG00000260903	ENSG00000260903			23062	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 7"", ""chromosome 20 open reading frame 159"""	C20orf159			Standard	NM_001011718		Approved	dJ310O13.4	uc002wxe.3	Q5GH72	OTTHUMG00000032198	ENST00000562532.2:c.1190C>T	20.37:g.30584710C>T	ENSP00000477059:p.Ala397Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_001011718	Q9NUG5	Missense_Mutation	SNP	ENST00000562532.2	37	CCDS33459.1	144	0.06593406593406594	60	0.12195121951219512	23	0.06353591160220995	9	0.015734265734265736	52	0.06860158311345646	C	12.30	1.897648	0.33535	0.124603	0.081163	ENSG00000101321	ENST00000217299	T	0.63744	-0.06	5.16	3.21	0.36854	.	0.059319	0.64402	D	0.000002	T	0.01870	0.0059	L	0.47078	1.49	0.20638	P	0.999874602	D	0.76494	0.999	D	0.66497	0.944	T	0.42999	-0.9418	9	0.12430	T	0.62	.	8.7001	0.34320	0.0:0.7636:0.0:0.2364	rs61750849	397	Q5GH72	XKR7_HUMAN	V	397	ENSP00000217299:A397V	ENSP00000217299:A397V	A	+	2	0	XKR7	30048371	0.377000	0.25106	0.072000	0.20136	0.111000	0.19643	1.068000	0.30629	0.565000	0.29255	-0.254000	0.11334	GCG	C|0.916;T|0.084	0.084	strong		0.597	XKR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078597.3	NM_001011718	
PSG9	5678	hgsc.bcm.edu	37	19	43763059	43763059	+	Missense_Mutation	SNP	C	C	T	rs12977717	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:43763059C>T	ENST00000270077.3	-	4	1034	c.938G>A	c.(937-939)cGg>cAg	p.R313Q	PSG9_ENST00000596730.1_Intron|PSG9_ENST00000291752.5_Intron|PSG9_ENST00000443718.3_Missense_Mutation_p.R220Q|PSG9_ENST00000593948.1_Intron|PSG9_ENST00000244293.7_Intron|PSG9_ENST00000418820.2_Missense_Mutation_p.R220Q	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	313	Ig-like C2-type 2.			R -> Q (in Ref. 9; AAH20759). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				ATATCGGTCCCGTATTTCACA	0.498													C|||	402	0.0802716	0.0113	0.1124	5008	,	,		16751	0.0		0.2177	False		,,,				2504	0.092				p.R313Q		Atlas-SNP	.											PSG9,trunk,malignant_melanoma,+1,1	PSG9	77	1	0			c.G938A						PASS	.	C	GLN/ARG	248,4030		51,146,1942	118.0	121.0	120.0		938	-2.5	0.0	19	dbSNP_121	120	1876,6692		307,1262,2715	no	missense	PSG9	NM_002784.3	43	358,1408,4657	TT,TC,CC		21.8954,5.7971,16.5343	benign	313/427	43763059	2124,10722	2139	4284	6423	SO:0001583	missense	5678	exon4			CGGTCCCGTATTT	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.938G>A	19.37:g.43763059C>T	ENSP00000270077:p.Arg313Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	37	CCDS12618.1	217	0.09935897435897435	5	0.01016260162601626	40	0.11049723756906077	2	0.0034965034965034965	170	0.22427440633245382	N	0.658	-0.806935	0.02819	0.057971	0.218954	ENSG00000183668	ENST00000270077;ENST00000443718;ENST00000435220	T;T	0.12672	2.66;2.66	1.39	-2.48	0.06423	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	P;B	0.37176	0.586;0.128	B;B	0.28784	0.094;0.055	T	0.43507	-0.9387	8	0.32370	T	0.25	.	4.6661	0.12666	0.0:0.416:0.0:0.584	rs12977717;rs17855485	220;313	E7EW65;Q00887	.;PSG9_HUMAN	Q	313;220;274	ENSP00000270077:R313Q;ENSP00000396753:R220Q	ENSP00000270077:R313Q	R	-	2	0	PSG9	48454899	0.001000	0.12720	0.000000	0.03702	0.016000	0.09150	-0.492000	0.06467	-0.676000	0.05238	0.194000	0.17425	CGG	C|0.865;T|0.135	0.135	strong		0.498	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
DDX51	317781	hgsc.bcm.edu	37	12	132626668	132626668	+	Missense_Mutation	SNP	T	T	C	rs17418886|rs1133690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:132626668T>C	ENST00000397333.3	-	5	922	c.884A>G	c.(883-885)cAg>cGg	p.Q295R	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	295	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		Q -> R (in dbSNP:rs1133690). {ECO:0000269|PubMed:15489334}.		rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		ACATACCTGCTGGGCCAGCTC	0.652													T|||	2716	0.542332	0.1989	0.6772	5008	,	,		18589	0.753		0.6958	False		,,,				2504	0.5358				p.Q295R		Atlas-SNP	.											.	DDX51	33	.	0			c.A884G						PASS	.	T	ARG/GLN	1293,2889		224,845,1022	54.0	64.0	61.0		884	4.7	1.0	12	dbSNP_86	61	5775,2653		2010,1755,449	yes	missense	DDX51	NM_175066.3	43	2234,2600,1471	CC,CT,TT		31.4784,30.9182,43.9492	possibly-damaging	295/667	132626668	7068,5542	2091	4214	6305	SO:0001583	missense	317781	exon5			ACCTGCTGGGCCA	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.884A>G	12.37:g.132626668T>C	ENSP00000380495:p.Gln295Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	1330	0.6089743589743589	119	0.241869918699187	247	0.6823204419889503	438	0.7657342657342657	526	0.6939313984168866	T	23.7	4.453070	0.84209	0.309182	0.685216	ENSG00000185163	ENST00000397333	T	0.15256	2.44	4.71	4.71	0.59529	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.27944	0.81	0.09310	P	0.99999826229	P	0.48230	0.907	P	0.55965	0.788	T	0.00475	-1.1717	9	0.54805	T	0.06	-25.2818	12.1532	0.54062	0.0:0.0:0.0:1.0	rs1133690;rs3195639;rs7958174;rs11556856;rs17846277;rs17859299;rs61243103;rs1133690	295	Q8N8A6	DDX51_HUMAN	R	295	ENSP00000380495:Q295R	ENSP00000380495:Q295R	Q	-	2	0	DDX51	131192621	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.419000	0.66435	1.756000	0.51951	0.402000	0.26972	CAG	T|0.404;C|0.596	0.596	strong		0.652	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
HLA-A	3105	hgsc.bcm.edu	37	6	29911225	29911225	+	Missense_Mutation	SNP	A	A	G	rs1059536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29911225A>G	ENST00000396634.1	+	5	865	c.524A>G	c.(523-525)cAt>cGt	p.H175R	HLA-A_ENST00000376802.2_Missense_Mutation_p.H175R|HLA-A_ENST00000376806.5_Missense_Mutation_p.H175R|HLA-A_ENST00000376809.5_Missense_Mutation_p.H175R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	175	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GAGGCGGCCCATGAGGCGGAG	0.642									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	1284	0.25639	0.4607	0.232	5008	,	,		12515	0.1617		0.165	False		,,,				2504	0.1892				p.H175R		Atlas-SNP	.											.	HLA-A	89	.	0			c.A524G						PASS	.						37.0	29.0	32.0					6																	29911225		1506	2704	4210	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGGCCCATGAGGC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.524A>G	6.37:g.29911225A>G	ENSP00000379873:p.His175Arg	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	386	261	0.676166	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	498|498	0.22802197802197802|0.22802197802197802	205|205	0.4166666666666667|0.4166666666666667	91|91	0.2513812154696133|0.2513812154696133	98|98	0.17132867132867133|0.17132867132867133	104|104	0.13720316622691292|0.13720316622691292	.|.	5.100|5.100	0.204103|0.204103	0.09704|0.09704	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802|ENST00000355767	T;T;T;T|.	0.00672|.	5.89;5.89;5.89;5.89|.	3.78|3.78	0.94|0.94	0.19513|0.19513	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);|.	49.238000|.	0.01015|.	U|.	0.003893|.	T|T	0.01627|0.01627	0.0052|0.0052	N|N	0.00057|0.00057	-2.355|-2.355	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B;B|.	0.09377|.	0.001;0.0;0.004;0.004;0.0;0.001|.	T|T	0.40590|0.40590	-0.9555|-0.9555	9|5	0.08179|0.87932	T|D	0.78|0	.|.	6.6995|6.6995	0.23217|0.23217	0.4174:0.0:0.5826:0.0|0.4174:0.0:0.5826:0.0	rs1059536;rs2975060;rs3173412;rs16896015;rs41540916|rs1059536;rs2975060;rs3173412;rs16896015;rs41540916	54;175;175;175;175;175|.	B4DVB9;P13746;Q5SRN7;Q5SRN5;P30455;P04439|.	.;1A11_HUMAN;.;.;1A36_HUMAN;1A03_HUMAN|.	R|V	175|150	ENSP00000379873:H175R;ENSP00000366002:H175R;ENSP00000366005:H175R;ENSP00000365998:H175R|.	ENSP00000365998:H175R|ENSP00000348012:M150V	H|M	+|+	2|1	0|0	HLA-A|HLA-A	30019204|30019204	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.538000|-0.538000	0.06120|0.06120	0.063000|0.063000	0.16370|0.16370	-1.697000|-1.697000	0.00723|0.00723	CAT|ATG	A|0.785;G|0.215	0.215	strong		0.642	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
TMEM2	23670	hgsc.bcm.edu	37	9	74332970	74332970	+	Missense_Mutation	SNP	G	G	A	rs25692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:74332970G>A	ENST00000377044.4	-	13	2832	c.2293C>T	c.(2293-2295)Ccc>Tcc	p.P765S	TMEM2_ENST00000377066.5_Missense_Mutation_p.P702S	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	765			P -> S (in dbSNP:rs25692).		multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GGTTTTTCGGGGTTTGCATCC	0.343													G|||	565	0.112819	0.0068	0.1138	5008	,	,		15906	0.1458		0.161	False		,,,				2504	0.1718				p.P765S		Atlas-SNP	.											.	TMEM2	112	.	0			c.C2293T						PASS	.	G	SER/PRO,SER/PRO	172,4234	112.9+/-151.0	2,168,2033	87.0	88.0	88.0		2104,2293	5.5	1.0	9	dbSNP_72	88	1418,7182	269.0+/-288.2	120,1178,3002	yes	missense,missense	TMEM2	NM_001135820.1,NM_013390.2	74,74	122,1346,5035	AA,AG,GG		16.4884,3.9038,12.2251	benign,benign	702/1321,765/1384	74332970	1590,11416	2203	4300	6503	SO:0001583	missense	23670	exon13			TTTCGGGGTTTGC		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.2293C>T	9.37:g.74332970G>A	ENSP00000366243:p.Pro765Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	258	0.11813186813186813	4	0.008130081300813009	46	0.1270718232044199	82	0.14335664335664336	126	0.1662269129287599	G	15.29	2.789688	0.50102	0.039038	0.164884	ENSG00000135048	ENST00000377044;ENST00000377066	T;T	0.56103	0.48;0.48	5.47	5.47	0.80525	Pectin lyase fold/virulence factor (1);	0.049302	0.85682	D	0.000000	T	0.00178	0.0005	L	0.52759	1.655	0.09310	P	1.0	B;P	0.36789	0.435;0.57	B;B	0.32211	0.141;0.142	T	0.02220	-1.1193	9	0.28530	T	0.3	.	19.3931	0.94592	0.0:0.0:1.0:0.0	rs25692;rs17475825;rs52794248;rs58515866;rs25692	765;702	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	S	765;702	ENSP00000366243:P765S;ENSP00000366266:P702S	ENSP00000366243:P765S	P	-	1	0	TMEM2	73522790	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.250000	0.78287	2.577000	0.86979	0.558000	0.71614	CCC	G|0.882;T|0.006	.	strong		0.343	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
SLC34A3	142680	hgsc.bcm.edu	37	9	140128085	140128085	+	Splice_Site	SNP	T	T	C	rs28407527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140128085T>C	ENST00000538474.1	+	8	981	c.757T>C	c.(757-759)Ttg>Ctg	p.L253L	SLC34A3_ENST00000361134.2_Splice_Site_p.L253L	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	253					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		TGGCCCCCAGTTGGACTCCGA	0.672													T|||	2282	0.455671	0.3994	0.5807	5008	,	,		12613	0.4673		0.4046	False		,,,				2504	0.4836				p.L253L		Atlas-SNP	.											.	SLC34A3	32	.	0			c.T757C						PASS	.	T	,,	1795,2611	525.1+/-371.5	367,1061,775	84.0	86.0	85.0		757,757,757	2.3	1.0	9	dbSNP_125	85	3585,5015	517.9+/-379.1	751,2083,1466	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SLC34A3	NM_001177316.1,NM_001177317.1,NM_080877.2	,,	1118,3144,2241	CC,CT,TT		41.686,40.7399,41.3655	,,	253/600,253/600,253/600	140128085	5380,7626	2203	4300	6503	SO:0001630	splice_region_variant	142680	exon8			CCCCAGTTGGACT	AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"""Solute carriers"""	20305	protein-coding gene	gene with protein product		609826	"""solute carrier family 34 (sodium phosphate), member 3"""			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.757-1T>C	9.37:g.140128085T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_001177317	A2BFA1	Silent	SNP	ENST00000538474.1	37	CCDS7038.1																																																																																			T|0.564;C|0.436	0.436	strong		0.672	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877	Silent
MUL1	79594	hgsc.bcm.edu	37	1	20827216	20827216	+	Silent	SNP	C	C	T	rs595980	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20827216C>T	ENST00000264198.3	-	4	1162	c.1026G>A	c.(1024-1026)gcG>gcA	p.A342A		NM_024544.2	NP_078820.2	Q969V5	MUL1_HUMAN	mitochondrial E3 ubiquitin protein ligase 1	342					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|cellular response to exogenous dsRNA (GO:0071360)|mitochondrial fission (GO:0000266)|mitochondrion localization (GO:0051646)|negative regulation of cell growth (GO:0030308)|negative regulation of chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of innate immune response (GO:0045824)|negative regulation of mitochondrial fusion (GO:0010637)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein sumoylation (GO:0033235)|protein stabilization (GO:0050821)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)	cytoplasm (GO:0005737)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(5)	11		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CCCGGGTGATCGCCTGTCTGC	0.557													C|||	357	0.0712859	0.0272	0.1023	5008	,	,		19030	0.001		0.1988	False		,,,				2504	0.0501				p.A342A		Atlas-SNP	.											MUL1,colon,carcinoma,-1,1	MUL1	34	1	0			c.G1026A						PASS	.	C		280,4126	154.4+/-187.8	12,256,1935	71.0	71.0	71.0		1026	-0.7	0.7	1	dbSNP_83	71	1750,6850	315.0+/-312.1	164,1422,2714	no	coding-synonymous	MUL1	NM_024544.2		176,1678,4649	TT,TC,CC		20.3488,6.355,15.6082		342/353	20827216	2030,10976	2203	4300	6503	SO:0001819	synonymous_variant	79594	exon4			GGTGATCGCCTGT	BC014010	CCDS208.1	1p36.12	2013-01-11	2010-09-17	2008-03-26	ENSG00000090432	ENSG00000090432		"""RING-type (C3HC4) zinc fingers"""	25762	protein-coding gene	gene with protein product	"""ring finger protein 218"", ""mitochondria-anchored protein ligase"", ""growth inhibition and death E3 ligase"", ""mitochondrial ubiquitin ligase activator of NFKB 1"""	612037	"""chromosome 1 open reading frame 166"""	C1orf166		18591963, 12761501, 18213395, 18207745	Standard	NM_024544		Approved	FLJ12875, MULAN, RNF218, MAPL, GIDE	uc001bdi.4	Q969V5	OTTHUMG00000002838	ENST00000264198.3:c.1026G>A	1.37:g.20827216C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	99	33	0.333333	NM_024544	B5M497|Q7Z431|Q9H9B5	Silent	SNP	ENST00000264198.3	37	CCDS208.1																																																																																			C|0.864;T|0.136	0.136	strong		0.557	MUL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007951.1	NM_024544	
ITGB1	3688	hgsc.bcm.edu	37	10	33200468	33200468	+	Silent	SNP	G	G	A	rs2298139	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:33200468G>A	ENST00000396033.2	-	13	1974	c.1839C>T	c.(1837-1839)tgC>tgT	p.C613C	ITGB1_ENST00000423113.1_Silent_p.C613C|ITGB1_ENST00000374956.4_Silent_p.C613C|ITGB1_ENST00000302278.3_Silent_p.C613C	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	613	Cysteine-rich tandem repeats.				axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	CACCACACTCGCAGATGCCCC	0.498													G|||	597	0.119209	0.0038	0.0836	5008	,	,		19108	0.1756		0.0736	False		,,,				2504	0.2894				p.C613C		Atlas-SNP	.											.	ITGB1	156	.	0			c.C1839T						PASS	.	G	,,	66,4340	61.7+/-98.7	1,64,2138	118.0	114.0	116.0		1839,1839,1839	-8.8	0.3	10	dbSNP_123	116	595,7999	156.6+/-210.4	29,537,3731	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB1	NM_002211.3,NM_033668.2,NM_133376.2	,,	30,601,5869	AA,AG,GG		6.9234,1.498,5.0846	,,	613/799,613/802,613/799	33200468	661,12339	2203	4297	6500	SO:0001819	synonymous_variant	3688	exon13			ACACTCGCAGATG	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"""CD molecules"", ""Integrins"""	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.1839C>T	10.37:g.33200468G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	168	77	0.458333	NM_002211	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Silent	SNP	ENST00000396033.2	37	CCDS7174.1																																																																																			G|0.803;A|0.197	0.197	strong		0.498	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211	
TEX14	56155	hgsc.bcm.edu	37	17	56676368	56676368	+	Missense_Mutation	SNP	T	T	C	rs389389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56676368T>C	ENST00000240361.8	-	14	2441	c.2356A>G	c.(2356-2358)Aat>Gat	p.N786D	TEX14_ENST00000349033.5_Missense_Mutation_p.N780D|TEX14_ENST00000389934.3_Missense_Mutation_p.N780D			Q8IWB6	TEX14_HUMAN	testis expressed 14	786					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTGTAGGCATTTGTAAACTCT	0.473													T|||	449	0.0896565	0.0356	0.1282	5008	,	,		20816	0.0		0.2286	False		,,,				2504	0.0849				p.N786D		Atlas-SNP	.											.	TEX14	343	.	0			c.A2356G						PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN	250,4156	144.2+/-179.2	10,230,1963	154.0	142.0	146.0		2356,2338,2338	-3.6	0.0	17	dbSNP_80	146	1851,6749	332.9+/-320.3	195,1461,2644	yes	missense,missense,missense	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	23,23,23	205,1691,4607	CC,CT,TT		21.5233,5.6741,16.1541	benign,benign,benign	786/1498,780/1452,780/1492	56676368	2101,10905	2203	4300	6503	SO:0001583	missense	56155	exon14			AGGCATTTGTAAA	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2356A>G	17.37:g.56676368T>C	ENSP00000240361:p.Asn786Asp	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	171	86	0.502924	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	240	0.10989010989010989	22	0.044715447154471545	57	0.1574585635359116	0	0.0	161	0.21240105540897097	T	8.000	0.755293	0.15846	0.056741	0.215233	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.78246	-1.16;-1.16;-1.13	5.63	-3.63	0.04529	.	0.669699	0.15016	N	0.285245	T	0.00073	0.0002	L	0.56769	1.78	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.003	T	0.04481	-1.0948	9	0.26408	T	0.33	-1.4549	7.0204	0.24910	0.0:0.3313:0.2115:0.4572	rs389389;rs389389	786;780;780	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	D	786;780;780	ENSP00000240361:N786D;ENSP00000374584:N780D;ENSP00000268910:N780D	ENSP00000240361:N786D	N	-	1	0	TEX14	54031367	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.600000	0.05693	-1.256000	0.02478	-1.139000	0.01908	AAT	T|0.866;C|0.134	0.134	strong		0.473	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
ZNF223	7766	hgsc.bcm.edu	37	19	44571154	44571154	+	Silent	SNP	T	T	C	rs4433920	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44571154T>C	ENST00000434772.3	+	5	1428	c.1173T>C	c.(1171-1173)caT>caC	p.H391H	ZNF223_ENST00000591793.1_Silent_p.H501H	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				ACTTGCACCATAGAGCCCACA	0.443													T|||	2075	0.414337	0.1498	0.3718	5008	,	,		19736	0.3006		0.6839	False		,,,				2504	0.6421				p.H391H		Atlas-SNP	.											.	ZNF223	61	.	0			c.T1173C						PASS	.	T		1037,3369	382.1+/-324.3	118,801,1284	92.0	86.0	88.0		1173	-0.1	0.0	19	dbSNP_111	88	5854,2746	680.3+/-403.6	1995,1864,441	no	coding-synonymous	ZNF223	NM_013361.4		2113,2665,1725	CC,CT,TT		31.9302,23.5361,47.0168		391/483	44571154	6891,6115	2203	4300	6503	SO:0001819	synonymous_variant	7766	exon5			GCACCATAGAGCC	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"""Zinc fingers, C2H2-type"", ""-"""	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.1173T>C	19.37:g.44571154T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Silent	SNP	ENST00000434772.3	37	CCDS12635.1																																																																																			T|0.490;C|0.510	0.510	strong		0.443	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2		
SPTB	6710	hgsc.bcm.edu	37	14	65260227	65260227	+	Silent	SNP	T	T	G	rs229591	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:65260227T>G	ENST00000389721.5	-	13	2186	c.2154A>C	c.(2152-2154)atA>atC	p.I718I	SPTB_ENST00000556626.1_Silent_p.I718I|SPTB_ENST00000542895.1_Silent_p.I718I|SPTB_ENST00000389720.3_Silent_p.I718I|SPTB_ENST00000389722.3_Silent_p.I718I	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	718					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		ACACCTCCTTTATGCGGGCCT	0.592													G|||	2255	0.45028	0.7201	0.3372	5008	,	,		19756	0.2004		0.3588	False		,,,				2504	0.5174				p.I718I		Atlas-SNP	.											.	SPTB	378	.	0			c.A2154C						PASS	.	G	,	2836,1570	489.6+/-361.5	916,1004,283	56.0	53.0	54.0		2154,2154	3.8	0.7	14	dbSNP_79	54	3147,5453	655.4+/-401.3	566,2015,1719	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1482,3019,2002	GG,GT,TT		36.593,35.6332,46.0018	,	718/2138,718/2329	65260227	5983,7023	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon13			CTCCTTTATGCGG		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.2154A>C	14.37:g.65260227T>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			T|0.558;G|0.442	0.442	strong		0.592	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
KIF23	9493	hgsc.bcm.edu	37	15	69728949	69728949	+	Silent	SNP	A	A	G	rs3825858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:69728949A>G	ENST00000260363.4	+	14	1560	c.1443A>G	c.(1441-1443)ccA>ccG	p.P481P	KIF23_ENST00000558585.1_Silent_p.P298P|KIF23_ENST00000537891.1_Silent_p.P298P|KIF23_ENST00000559279.1_Silent_p.P481P|KIF23_ENST00000395392.2_Silent_p.P481P|KIF23_ENST00000352331.4_Silent_p.P481P	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	481					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						CACCTTTGCCATCATGCGAAA	0.368													A|||	3841	0.766973	0.5386	0.8127	5008	,	,		15683	0.6776		0.9553	False		,,,				2504	0.9417				p.P481P		Atlas-SNP	.											.	KIF23	57	.	0			c.A1443G						PASS	.	A	,	2701,1697	652.3+/-399.4	815,1071,313	118.0	101.0	107.0		1443,1443	-11.3	0.0	15	dbSNP_107	107	8328,268	806.9+/-407.2	4036,256,6	no	coding-synonymous,coding-synonymous	KIF23	NM_004856.5,NM_138555.2	,	4851,1327,319	GG,GA,AA		3.1177,38.5857,15.1224	,	481/857,481/961	69728949	11029,1965	2199	4298	6497	SO:0001819	synonymous_variant	9493	exon14			TTTGCCATCATGC	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"""Kinesins"""	6392	protein-coding gene	gene with protein product		605064	"""kinesin-like 5 (mitotic kinesin-like protein 1)"""	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.1443A>G	15.37:g.69728949A>G		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_138555	Q8WVP0	Silent	SNP	ENST00000260363.4	37	CCDS32278.1																																																																																			A|0.184;G|0.816	0.816	strong		0.368	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
PRKD3	23683	hgsc.bcm.edu	37	2	37518045	37518045	+	Silent	SNP	G	G	C	rs10177176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:37518045G>C	ENST00000379066.1	-	4	1287	c.525C>G	c.(523-525)ctC>ctG	p.L175L	PRKD3_ENST00000234179.2_Silent_p.L175L			O94806	KPCD3_HUMAN	protein kinase D3	175					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				CCAATCCCCAGAGCATCTCAC	0.378													G|||	1535	0.30651	0.171	0.3343	5008	,	,		18877	0.4097		0.4274	False		,,,				2504	0.2393				p.L175L	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.C525G						PASS	.	G		834,3572	330.2+/-301.4	76,682,1445	159.0	153.0	155.0		525	0.1	1.0	2	dbSNP_119	155	3472,5128	509.6+/-377.3	719,2034,1547	no	coding-synonymous	PRKD3	NM_005813.3		795,2716,2992	CC,CG,GG		40.3721,18.9287,33.1078		175/891	37518045	4306,8700	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon3			TCCCCAGAGCATC	AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"""Pleckstrin homology (PH) domain containing"""	9408	protein-coding gene	gene with protein product		607077	"""protein kinase C, nu"""	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.525C>G	2.37:g.37518045G>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	150	66	0.44	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			G|0.650;C|0.350	0.350	strong		0.378	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
C3	718	hgsc.bcm.edu	37	19	6709848	6709848	+	Silent	SNP	C	C	T	rs2230204	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6709848C>T	ENST00000245907.6	-	14	1784	c.1692G>A	c.(1690-1692)gtG>gtA	p.V564V		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	564					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CGCTTTTTACCACCAGCTGTG	0.617													C|||	2180	0.435304	0.5477	0.3718	5008	,	,		11813	0.4613		0.2823	False		,,,				2504	0.4591				p.V564V		Atlas-SNP	.											.	C3	192	.	0			c.G1692A						PASS	.			2346,2060	601.5+/-389.7	625,1096,482	42.0	43.0	43.0		1692	3.0	1.0	19	dbSNP_98	43	2342,6258	387.0+/-342.0	303,1736,2261	no	coding-synonymous	C3	NM_000064.2		928,2832,2743	TT,TC,CC		27.2326,46.7544,36.0449		564/1664	6709848	4688,8318	2203	4300	6503	SO:0001819	synonymous_variant	718	exon14			TTTTACCACCAGC	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1692G>A	19.37:g.6709848C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																			C|0.634;N|0.001	.	strong		0.617	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
NUSAP1	51203	hgsc.bcm.edu	37	15	41672384	41672384	+	Silent	SNP	A	A	G	rs7168431	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41672384A>G	ENST00000559596.1	+	11	1413	c.1326A>G	c.(1324-1326)taA>taG	p.*442*	NUSAP1_ENST00000450318.1_Silent_p.*403*|NUSAP1_ENST00000260359.6_Silent_p.*427*|NUSAP1_ENST00000558123.1_3'UTR|NUSAP1_ENST00000414849.2_Silent_p.*441*|NUSAP1_ENST00000560747.1_Silent_p.*440*|NUSAP1_ENST00000560177.1_Silent_p.*441*|NUSAP1_ENST00000450592.2_Silent_p.*379*			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	0					establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		CTGAAGATTAATAATTTTTTA	0.373													A|||	579	0.115615	0.0091	0.1542	5008	,	,		19315	0.0079		0.2714	False		,,,				2504	0.183				p.X442X		Atlas-SNP	.											.	NUSAP1	32	.	0			c.A1326G						PASS	.	A	,,	186,3440		8,170,1635	71.0	80.0	77.0		1209,1326,1323	-1.1	0.0	15	dbSNP_116	77	2091,6035		252,1587,2224	no	coding-synonymous,coding-synonymous,coding-synonymous	NUSAP1	NM_001129897.1,NM_016359.4,NM_018454.7	,,	260,1757,3859	GG,GA,AA		25.7322,5.1296,19.3754	,,	403/403,442/442,441/441	41672384	2277,9475	1813	4063	5876	SO:0001819	synonymous_variant	51203	exon11			AGATTAATAATTT	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.1326A>G	15.37:g.41672384A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_016359	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Silent	SNP	ENST00000559596.1	37	CCDS45234.1																																																																																			A|0.876;G|0.124	0.124	strong		0.373	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359	
RTP4	64108	hgsc.bcm.edu	37	3	187088812	187088812	+	Missense_Mutation	SNP	C	C	T	rs3821812	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:187088812C>T	ENST00000259030.2	+	2	502	c.392C>T	c.(391-393)aCg>aTg	p.T131M		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	131				T -> M (in Ref. 1; AAT70683, 2; CAC14309 and 4; AAH13161). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		GGAAATGGCACGAGGAAGTCT	0.493													C|||	1925	0.384385	0.1399	0.4942	5008	,	,		21664	0.7351		0.3469	False		,,,				2504	0.3139				p.T131M		Atlas-SNP	.											.	RTP4	20	.	0			c.C392T						PASS	.	C	MET/THR	912,3494	348.5+/-309.9	94,724,1385	57.0	57.0	57.0		392	-7.4	0.0	3	dbSNP_107	57	3018,5582	466.6+/-366.8	525,1968,1807	yes	missense	RTP4	NM_022147.2	81	619,2692,3192	TT,TC,CC		35.093,20.699,30.2168	benign	131/247	187088812	3930,9076	2203	4300	6503	SO:0001583	missense	64108	exon2			ATGGCACGAGGAA	BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"""Receptor transporter proteins"""	23992	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 4"""	609350	"""receptor transporter protein 4"""			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.392C>T	3.37:g.187088812C>T	ENSP00000259030:p.Thr131Met	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_022147	Q9H4F3	Missense_Mutation	SNP	ENST00000259030.2	37	CCDS33910.1	887	0.40613553113553114	80	0.16260162601626016	154	0.425414364640884	393	0.6870629370629371	260	0.34300791556728233	C	1.751	-0.489207	0.04352	0.20699	0.35093	ENSG00000136514	ENST00000259030	T	0.22743	1.94	3.69	-7.38	0.01407	.	3.786760	0.00496	N	0.000148	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.28998	0.23	B	0.20767	0.031	T	0.34254	-0.9836	9	0.31617	T	0.26	4.8248	3.2926	0.06954	0.1014:0.3999:0.2046:0.2941	rs3821812;rs17779027;rs17856419;rs56552616;rs61531890;rs3821812	131	Q96DX8	RTP4_HUMAN	M	131	ENSP00000259030:T131M	ENSP00000259030:T131M	T	+	2	0	RTP4	188571506	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.461000	0.02366	-2.845000	0.00333	-1.834000	0.00590	ACG	C|0.657;N|0.000	.	strong		0.493	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
KRTAP11-1	337880	hgsc.bcm.edu	37	21	32253513	32253513	+	Missense_Mutation	SNP	A	A	T	rs9636845	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:32253513A>T	ENST00000332378.4	-	1	361	c.331T>A	c.(331-333)Tgt>Agt	p.C111S		NM_175858.2	NP_787054.1	Q8IUC1	KR111_HUMAN	keratin associated protein 11-1	111	4 X 10 AA approximate repeats.		C -> S (in dbSNP:rs9636845).			keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|pancreas(1)	18						AGGGGCTGACATCCACTAGAG	0.577													A|||	876	0.17492	0.0045	0.2032	5008	,	,		18222	0.4663		0.0885	False		,,,				2504	0.1738				p.C111S		Atlas-SNP	.											.	KRTAP11-1	46	.	0			c.T331A						PASS	.	A	SER/CYS	112,4294	86.8+/-125.4	0,112,2091	68.0	69.0	69.0		331	5.4	0.9	21	dbSNP_119	69	766,7834	183.5+/-231.7	27,712,3561	yes	missense	KRTAP11-1	NM_175858.2	112	27,824,5652	TT,TA,AA		8.907,2.542,6.7507	probably-damaging	111/164	32253513	878,12128	2203	4300	6503	SO:0001583	missense	337880	exon1			GCTGACATCCACT	AJ457065	CCDS13608.1	21q22.1	2003-03-11			ENSG00000182591	ENSG00000182591		"""Keratin associated proteins"""	18922	protein-coding gene	gene with protein product		600064				12359730	Standard	NM_175858		Approved	KAP11.1	uc002yov.3	Q8IUC1	OTTHUMG00000057773	ENST00000332378.4:c.331T>A	21.37:g.32253513A>T	ENSP00000330720:p.Cys111Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_175858	A1L4I8	Missense_Mutation	SNP	ENST00000332378.4	37	CCDS13608.1	396	0.1813186813186813	3	0.006097560975609756	74	0.20441988950276244	247	0.4318181818181818	72	0.09498680738786279	A	15.98	2.992318	0.54041	0.02542	0.08907	ENSG00000182591	ENST00000332378	T	0.04502	3.61	5.4	5.4	0.78164	.	0.333214	0.29059	N	0.013280	T	0.00012	0.0000	M	0.79258	2.445	0.23510	P	0.99752933	D	0.89917	1.0	D	0.91635	0.999	T	0.50939	-0.8768	9	0.51188	T	0.08	-6.3876	13.7235	0.62743	1.0:0.0:0.0:0.0	rs9636845;rs52829141;rs9636845	111	Q8IUC1	KR111_HUMAN	S	111	ENSP00000330720:C111S	ENSP00000330720:C111S	C	-	1	0	KRTAP11-1	31175384	0.998000	0.40836	0.915000	0.36163	0.372000	0.29890	4.106000	0.57804	2.197000	0.70478	0.529000	0.55759	TGT	A|0.892;T|0.108	0.108	strong		0.577	KRTAP11-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128225.1		
ADAM21	8747	hgsc.bcm.edu	37	14	70924294	70924294	+	Silent	SNP	C	C	T	rs112060847		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70924294C>T	ENST00000603540.1	+	2	336	c.78C>T	c.(76-78)tcC>tcT	p.S26S	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.S26S	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	26					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TGTCTATTTCCGGCTACTGTC	0.542																																					p.S26S		Atlas-SNP	.											ADAM21_ENST00000267499,NS,malignant_melanoma,+1,4	ADAM21	181	4	0			c.C78T						scavenged	.						101.0	110.0	107.0					14																	70924294		2203	4300	6503	SO:0001819	synonymous_variant	8747	exon2			TATTTCCGGCTAC	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.78C>T	14.37:g.70924294C>T		Somatic	270	4	0.0148148		WXS	Illumina HiSeq	Phase_I	186	14	0.0752688	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			C|0.779;T|0.221	0.221	strong		0.542	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
KLF17	128209	hgsc.bcm.edu	37	1	44595410	44595410	+	Missense_Mutation	SNP	A	A	G	rs2485652	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:44595410A>G	ENST00000372299.3	+	2	525	c.467A>G	c.(466-468)aAt>aGt	p.N156S	KLF17_ENST00000476802.1_Intron	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	156			N -> S (in dbSNP:rs2485652). {ECO:0000269|PubMed:15489334}.		gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					ATGCCCCCCAATGGGCTGCCA	0.562													A|||	1380	0.275559	0.0915	0.2594	5008	,	,		16923	0.4236		0.3966	False		,,,				2504	0.2587				p.N156S		Atlas-SNP	.											.	KLF17	92	.	0			c.A467G						PASS	.	A	SER/ASN	636,3770	270.4+/-269.6	47,542,1614	32.0	36.0	34.0		467	-9.3	0.0	1	dbSNP_100	34	3204,5396	473.2+/-368.5	593,2018,1689	yes	missense	KLF17	NM_173484.3	46	640,2560,3303	GG,GA,AA		37.2558,14.4349,29.5248	benign	156/390	44595410	3840,9166	2203	4300	6503	SO:0001583	missense	128209	exon2			CCCCCAATGGGCT	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.467A>G	1.37:g.44595410A>G	ENSP00000361373:p.Asn156Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	696	0.31868131868131866	49	0.09959349593495935	107	0.2955801104972376	252	0.4405594405594406	288	0.37994722955145116	A	0.027	-1.362961	0.01235	0.144349	0.372558	ENSG00000171872	ENST00000372299	T	0.07688	3.17	4.64	-9.27	0.00659	.	1.710450	0.03115	N	0.163023	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42310	-0.9459	9	0.05833	T	0.94	.	8.5854	0.33655	0.5506:0.1851:0.2643:0.0	rs2485652;rs17854589;rs56961994;rs2485652	156	Q5JT82	KLF17_HUMAN	S	156	ENSP00000361373:N156S	ENSP00000361373:N156S	N	+	2	0	KLF17	44367997	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.032000	0.01426	-2.352000	0.00616	-2.144000	0.00337	AAT	A|0.702;G|0.298	0.298	strong		0.562	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204433627	204433627	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204433627C>T	ENST00000367187.3	-	5	1696	c.1140G>A	c.(1138-1140)gtG>gtA	p.V380V	PIK3C2B_ENST00000424712.2_Silent_p.V380V	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	380	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			ACAACACAGTCACCTTCAGGT	0.547																																					p.V380V		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.G1140A						PASS	.						149.0	127.0	134.0					1																	204433627		2203	4300	6503	SO:0001819	synonymous_variant	5287	exon5			CACAGTCACCTTC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.1140G>A	1.37:g.204433627C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	197	21	0.106599	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			.	.	none		0.547	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
MUC20	200958	hgsc.bcm.edu	37	3	195452770	195452770	+	Silent	SNP	G	G	A	rs2550231		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195452770G>A	ENST00000447234.2	+	2	1422	c.1296G>A	c.(1294-1296)acG>acA	p.T432T	MUC20_ENST00000320736.6_Silent_p.T261T|MUC20_ENST00000436408.1_Silent_p.T432T|MUC20_ENST00000445522.2_Silent_p.T397T	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	432					activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		TAGAAACAACGACTTCCAGCA	0.557																																					p.T261T		Atlas-SNP	.											.	MUC20	84	.	0			c.G783A						PASS	.						26.0	22.0	23.0					3																	195452770		1913	4085	5998	SO:0001819	synonymous_variant	200958	exon3			AACAACGACTTCC	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1296G>A	3.37:g.195452770G>A		Somatic	667	1	0.00149925		WXS	Illumina HiSeq	Phase_I	663	265	0.399698	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Silent	SNP	ENST00000447234.2	37																																																																																				G|0.500;A|0.500	0.500	strong		0.557	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
MXD4	10608	hgsc.bcm.edu	37	4	2252845	2252845	+	Silent	SNP	C	C	T	rs2233042	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2252845C>T	ENST00000337190.2	-	5	751	c.438G>A	c.(436-438)acG>acA	p.T146T	MIR4800_ENST00000537353.2_RNA	NM_006454.2	NP_006445.1	Q14582	MAD4_HUMAN	MAX dimerization protein 4	146					negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|kidney(1)|lung(3)	6						CAGCAGAGCCCGTGCTATCTG	0.682													c|||	150	0.0299521	0.0076	0.0447	5008	,	,		17158	0.0317		0.0378	False		,,,				2504	0.0399				p.T146T		Atlas-SNP	.											MXD4,NS,carcinoma,0,2	MXD4	13	2	0			c.G438A						scavenged	.	T		81,4321		1,79,2121	20.0	20.0	20.0		438	-8.9	0.1	4	dbSNP_98	20	385,8211		8,369,3921	no	coding-synonymous	MXD4	NM_006454.2		9,448,6042	TT,TC,CC		4.4788,1.8401,3.5852		146/210	2252845	466,12532	2201	4298	6499	SO:0001819	synonymous_variant	10608	exon5			AGAGCCCGTGCTA		CCDS3361.1	4p16.3	2008-08-19			ENSG00000123933	ENSG00000123933		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	13906	protein-coding gene	gene with protein product						8521822	Standard	NM_006454		Approved	MAD4, MSTP149, MST149, bHLHc12	uc003geu.1	Q14582	OTTHUMG00000090243	ENST00000337190.2:c.438G>A	4.37:g.2252845C>T		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	158	79	0.5	NM_006454	A2A335|Q5TZX4	Silent	SNP	ENST00000337190.2	37	CCDS3361.1																																																																																			C|0.969;T|0.031	0.031	strong		0.682	MXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206519.1	NM_006454	
APOBR	55911	hgsc.bcm.edu	37	16	28508069	28508069	+	Silent	SNP	C	C	T	rs151174	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:28508069C>T	ENST00000431282.1	+	3	1690	c.1680C>T	c.(1678-1680)ggC>ggT	p.G560G	APOBR_ENST00000564831.1_Silent_p.G569G|CLN3_ENST00000569430.1_5'Flank|CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Silent_p.G560G			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	560	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						TGATGGGGGGCGCCCAGACCC	0.637													C|||	1194	0.238419	0.2156	0.4135	5008	,	,		17870	0.0933		0.3469	False		,,,				2504	0.183				p.G569G		Atlas-SNP	.											.	APOBR	89	.	0			c.C1707T						PASS	.	C		977,3027		149,679,1174	8.0	9.0	9.0		1680	-9.6	0.0	16	dbSNP_79	9	3211,5119		667,1877,1621	no	coding-synonymous	APOBR	NM_018690.3		816,2556,2795	TT,TC,CC		38.5474,24.4006,33.9549		560/1089	28508069	4188,8146	2002	4165	6167	SO:0001819	synonymous_variant	55911	exon2			GGGGGGCGCCCAG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1680C>T	16.37:g.28508069C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	203	102	0.502463	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				C|0.747;T|0.253	0.253	strong		0.637	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
MAST3	23031	hgsc.bcm.edu	37	19	18234441	18234441	+	Silent	SNP	C	C	T	rs740691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18234441C>T	ENST00000262811.6	+	7	522	c.522C>T	c.(520-522)caC>caT	p.H174H	MAST3_ENST00000608648.1_3'UTR	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	174							ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						TGATGAATCACGTGTACCGGG	0.582													T|||	2827	0.564497	0.4425	0.5331	5008	,	,		15958	0.6706		0.504	False		,,,				2504	0.7045				p.H174H		Atlas-SNP	.											.	MAST3	83	.	0			c.C522T						PASS	.	T		1885,2029		469,947,541	42.0	43.0	43.0		522	-9.4	0.0	19	dbSNP_86	43	4406,3866		1208,1990,938	no	coding-synonymous	MAST3	NM_015016.1		1677,2937,1479	TT,TC,CC		46.736,48.1604,48.3752		174/1310	18234441	6291,5895	1957	4136	6093	SO:0001819	synonymous_variant	23031	exon7			GAATCACGTGTAC	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.522C>T	19.37:g.18234441C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_015016	Q7LDZ8|Q9UPI0	Silent	SNP	ENST00000262811.6	37	CCDS46014.1																																																																																			C|0.468;N|0.000	.	strong		0.582	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150	
TTLL1	25809	hgsc.bcm.edu	37	22	43447891	43447891	+	Silent	SNP	C	C	T	rs9607998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43447891C>T	ENST00000266254.7	-	9	1134	c.894G>A	c.(892-894)ccG>ccA	p.P298P	AL022476.2_ENST00000443063.1_RNA|TTLL1_ENST00000331018.7_Intron	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	298	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		TGTTCATCACCGGCTGGAGAG	0.577													C|||	78	0.0155751	0.0068	0.0216	5008	,	,		21914	0.0		0.0497	False		,,,				2504	0.0041				p.P298P		Atlas-SNP	.											TTLL1,NS,carcinoma,-2,1	TTLL1	41	1	0			c.G894A						PASS	.	C		46,4360	48.2+/-83.0	3,40,2160	263.0	185.0	212.0		894	-3.7	1.0	22	dbSNP_119	212	419,8181	130.0+/-188.0	10,399,3891	no	coding-synonymous	TTLL1	NM_012263.4		13,439,6051	TT,TC,CC		4.8721,1.044,3.5753		298/424	43447891	465,12541	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon9			CATCACCGGCTGG	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.894G>A	22.37:g.43447891C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	123	82	0.666667	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	52	0.023809523809523808	6	0.012195121951219513	10	0.027624309392265192	0	0.0	36	0.047493403693931395	C	9.531	1.110796	0.20714	0.01044	0.048721	ENSG00000100271	ENST00000495814	.	.	.	5.97	-3.65	0.04502	.	.	.	.	.	T	0.07503	0.0189	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29941	-0.9995	4	.	.	.	.	0.9386	0.01351	0.3008:0.1773:0.3147:0.2072	rs9607998;rs52827145;rs9607998	.	.	.	Q	224	.	.	R	-	2	0	TTLL1	41777835	0.001000	0.12720	0.987000	0.45799	0.774000	0.43823	-1.617000	0.02051	-0.307000	0.08804	-0.126000	0.14955	CGG	C|0.971;T|0.029	0.029	strong		0.577	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	
FAAH	2166	hgsc.bcm.edu	37	1	46870761	46870761	+	Missense_Mutation	SNP	C	C	A	rs324420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46870761C>A	ENST00000243167.8	+	3	469	c.385C>A	c.(385-387)Cca>Aca	p.P129T	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	129			P -> T (polymorphism associated with susceptibility to drug abuse; the mutant enzyme is more sensitive to proteolytic degradation; displays reduced cellular expression probably due to a post- translational mechanism preceding productive folding; dbSNP:rs324420). {ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	GTCTCAGGCCCCAAGGCAGGG	0.582													C|||	1310	0.261581	0.3676	0.3516	5008	,	,		20101	0.1756		0.2107	False		,,,				2504	0.1953				p.P129T		Atlas-SNP	.											.	FAAH	36	.	0			c.C385A	GRCh37	CM023913	FAAH	M	rs324420	PASS	.	C	THR/PRO	1533,2873	485.7+/-360.4	274,985,944	79.0	72.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	385	3.1	0.4	1	dbSNP_79	74	1722,6878	313.8+/-311.5	172,1378,2750	yes	missense	FAAH	NM_001441.2	38	446,2363,3694	AA,AC,CC		20.0233,34.7935,25.0269	benign	129/580	46870761	3255,9751	2203	4300	6503	SO:0001583	missense	2166	exon3			CAGGCCCCAAGGC	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.385C>A	1.37:g.46870761C>A	ENSP00000243167:p.Pro129Thr	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	542	0.24816849816849818	180	0.36585365853658536	101	0.27900552486187846	100	0.17482517482517482	161	0.21240105540897097	C	3.886	-0.024929	0.07589	0.347935	0.200233	ENSG00000117480	ENST00000243167	T	0.53640	0.61	5.17	3.08	0.35506	Amidase signature domain (2);	0.475915	0.21894	N	0.067550	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.15719	0.014	B	0.17433	0.018	T	0.38929	-0.9638	9	0.18276	T	0.48	-12.2653	7.2179	0.25969	0.2941:0.6151:0.0:0.0908	rs324420;rs57947754;rs324420	129	O00519	FAAH1_HUMAN	T	129	ENSP00000243167:P129T	ENSP00000243167:P129T	P	+	1	0	FAAH	46643348	0.001000	0.12720	0.395000	0.26283	0.407000	0.30961	0.726000	0.25984	2.417000	0.82017	0.313000	0.20887	CCA	C|0.749;A|0.251	0.251	strong		0.582	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
DLG1	1739	hgsc.bcm.edu	37	3	196771554	196771554	+	Silent	SNP	T	T	C	rs35370245	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:196771554T>C	ENST00000419354.1	-	26	2941	c.2655A>G	c.(2653-2655)aaA>aaG	p.K885K	DLG1_ENST00000452595.1_Silent_p.K769K|DLG1_ENST00000314062.3_Silent_p.K834K|DLG1_ENST00000450955.1_Silent_p.K874K|DLG1_ENST00000392382.2_Silent_p.K852K|DLG1_ENST00000346964.2_Silent_p.K907K|DLG1_ENST00000443183.1_Silent_p.K781K|DLG1_ENST00000448528.2_Silent_p.K885K|DLG1_ENST00000422288.1_Silent_p.K834K|DLG1_ENST00000357674.4_Silent_p.K874K			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	885	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		CTATGATCTGTTTCACTTGGT	0.358													T|||	127	0.0253594	0.003	0.0303	5008	,	,		17651	0.001		0.0577	False		,,,				2504	0.044				p.K907K		Atlas-SNP	.											.	DLG1	120	.	0			c.A2721G						PASS	.	T	,,,,	57,4349	56.2+/-92.4	0,57,2146	164.0	154.0	158.0		2655,2619,2343,2307,2721	0.2	1.0	3	dbSNP_126	158	404,8196	129.0+/-187.1	9,386,3905	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLG1	NM_001098424.1,NM_001204386.1,NM_001204387.1,NM_001204388.1,NM_004087.2	,,,,	9,443,6051	CC,CT,TT		4.6977,1.2937,3.5445	,,,,	885/905,873/893,781/801,769/789,907/927	196771554	461,12545	2203	4300	6503	SO:0001819	synonymous_variant	1739	exon26			GATCTGTTTCACT	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.2655A>G	3.37:g.196771554T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	114	74	0.649123	NM_004087	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Silent	SNP	ENST00000419354.1	37	CCDS43194.1																																																																																			T|0.966;C|0.034	0.034	strong		0.358	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087	
OR2T34	127068	hgsc.bcm.edu	37	1	248737734	248737734	+	Missense_Mutation	SNP	G	G	A	rs139616012		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248737734G>A	ENST00000328782.2	-	1	346	c.325C>T	c.(325-327)Cac>Tac	p.H109Y		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGGGTCAGGTGGAAGAACATC	0.542																																					p.H109Y		Atlas-SNP	.											OR2T34,NS,carcinoma,0,4	OR2T34	72	4	0			c.C325T						scavenged	.						120.0	109.0	112.0					1																	248737734		2163	4276	6439	SO:0001583	missense	127068	exon1			TCAGGTGGAAGAA	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.325C>T	1.37:g.248737734G>A	ENSP00000330904:p.His109Tyr	Somatic	890	0	0		WXS	Illumina HiSeq	Phase_I	673	10	0.0148588	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	296	0.13553113553113552	69	0.1402439024390244	61	0.1685082872928177	71	0.12412587412587413	95	0.12532981530343007	.	0.011	-1.710055	0.00712	.	.	ENSG00000183310	ENST00000328782	T	0.01304	5.03	2.34	-0.481	0.12082	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00109	-2.105	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38908	-0.9639	8	0.02654	T	1	.	4.2299	0.10597	0.597:0.1723:0.2307:0.0	.	109	Q8NGX1	O2T34_HUMAN	Y	109	ENSP00000330904:H109Y	ENSP00000330904:H109Y	H	-	1	0	OR2T34	246804357	0.001000	0.12720	0.040000	0.18447	0.392000	0.30506	0.697000	0.25556	-0.366000	0.08064	-1.344000	0.01245	CAC	.	.	weak		0.542	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
EED	8726	hgsc.bcm.edu	37	11	85968623	85968623	+	Silent	SNP	C	C	T	rs974144	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:85968623C>T	ENST00000263360.6	+	6	1305	c.619C>T	c.(619-621)Ctg>Ttg	p.L207L	EED_ENST00000528180.1_Silent_p.L207L|EED_ENST00000327320.4_Silent_p.L207L|EED_ENST00000351625.6_Silent_p.L207L	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	207	Interaction with EZH2. {ECO:0000250}.|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K27 methylation (GO:0061087)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				AAATCTTCTCCTGTCAGTAAG	0.348													C|||	1476	0.294728	0.1203	0.2565	5008	,	,		18758	0.3135		0.4225	False		,,,				2504	0.407				p.L207L		Atlas-SNP	.											EED,NS,carcinoma,0,1	EED	50	1	0			c.C619T						PASS	.	C	,	788,3616	315.2+/-294.0	62,664,1476	89.0	81.0	83.0		619,619	1.3	1.0	11	dbSNP_86	83	3430,5168	503.1+/-375.8	694,2042,1563	no	coding-synonymous,coding-synonymous	EED	NM_003797.3,NM_152991.2	,	756,2706,3039	TT,TC,CC		39.893,17.8928,32.4412	,	207/442,207/401	85968623	4218,8784	2202	4299	6501	SO:0001819	synonymous_variant	8726	exon6			CTTCTCCTGTCAG	AF078933	CCDS8273.1, CCDS8274.1	11q14.2-q22.3	2013-01-10			ENSG00000074266	ENSG00000074266		"""WD repeat domain containing"""	3188	protein-coding gene	gene with protein product	"""WD protein associating with integrin cytoplasmic tails 1"""	605984				9765275, 9806832	Standard	NM_003797		Approved	WAIT-1, HEED	uc001pbp.3	O75530	OTTHUMG00000167209	ENST00000263360.6:c.619C>T	11.37:g.85968623C>T		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_003797	A8K7V5|O00149|Q6NTH2|Q7LDA5|Q7LDG8|Q86VV2|Q9UNY7	Silent	SNP	ENST00000263360.6	37	CCDS8273.1																																																																																			C|0.691;T|0.309	0.309	strong		0.348	EED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393733.1	NM_003797	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388379	1388379	+	Missense_Mutation	SNP	G	G	A	rs56109734	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388379G>A	ENST00000324803.4	+	1	3040	c.80G>A	c.(79-81)tGt>tAt	p.C27Y		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	27					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCCTGCTCATGTGCCCATGTG	0.637													N|||	602	0.120208	0.1301	0.1124	5008	,	,		16248	0.0208		0.1899	False		,,,				2504	0.1431				p.C27Y		Atlas-SNP	.											CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	0			c.G80A						scavenged	.						173.0	170.0	171.0					4																	1388379		2203	4300	6503	SO:0001583	missense	285464	exon1			GCTCATGTGCCCA	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.80G>A	4.37:g.1388379G>A	ENSP00000323978:p.Cys27Tyr	Somatic	270	9	0.0333333		WXS	Illumina HiSeq	Phase_I	234	71	0.303419	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	G	5.325	0.245358	0.10077	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.25579	1.79	0.824	-0.152	0.13407	.	.	.	.	.	T	0.09555	0.0235	N	0.08118	0	0.23673	N	0.997148	P	0.46912	0.886	B	0.38327	0.271	T	0.20571	-1.0271	9	0.22109	T	0.4	.	4.9218	0.13874	0.2545:0.0:0.7455:0.0	rs56109734	27	Q8N1N5	CRPAK_HUMAN	Y	27;20	ENSP00000323978:C27Y	ENSP00000323978:C27Y	C	+	2	0	CRIPAK	1378379	0.105000	0.21958	0.002000	0.10522	0.009000	0.06853	0.529000	0.23019	-0.063000	0.13065	0.420000	0.28162	TGT	G|0.996;A|0.004	0.004	strong		0.637	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
DDX60L	91351	hgsc.bcm.edu	37	4	169382991	169382991	+	Silent	SNP	C	C	A	rs17612630	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:169382991C>A	ENST00000511577.1	-	5	712	c.465G>T	c.(463-465)acG>acT	p.T155T	DDX60L_ENST00000260184.7_Silent_p.T155T|DDX60L_ENST00000505890.1_Silent_p.T155T			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	155							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TAAAAAGGTACGTTTGTAAAT	0.368													c|||	402	0.0802716	0.0098	0.0648	5008	,	,		19306	0.0109		0.1948	False		,,,				2504	0.1401				p.T155T		Atlas-SNP	.											DDX60L,caecum,carcinoma,-1,1	DDX60L	116	1	0			c.G465T						PASS	.	C		123,3577		4,115,1731	59.0	53.0	55.0		465	-5.2	0.0	4	dbSNP_123	55	1461,6719		128,1205,2757	no	coding-synonymous	DDX60L	NM_001012967.1		132,1320,4488	AA,AC,CC		17.8606,3.3243,13.3333		155/1707	169382991	1584,10296	1850	4090	5940	SO:0001819	synonymous_variant	91351	exon5			AAGGTACGTTTGT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.465G>T	4.37:g.169382991C>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.904;A|0.096	0.096	strong		0.368	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
RNASE3	6037	hgsc.bcm.edu	37	14	21360275	21360275	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21360275C>T	ENST00000304639.3	+	2	488	c.430C>T	c.(430-432)Cgg>Tgg	p.R144W		NM_002935.2	NP_002926.2	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3	144					antibacterial humoral response (GO:0019731)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)	9	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	CAGAGATCCACGGGATTCTCC	0.483																																					p.R144W		Atlas-SNP	.											RNASE3,right_upper_lobe,carcinoma,-1,1	RNASE3	24	1	0			c.C430T						scavenged	.						94.0	94.0	94.0					14																	21360275		2190	4300	6490	SO:0001583	missense	6037	exon2			GATCCACGGGATT	X55990	CCDS9560.1	14q11.2	2014-03-13	2010-05-07		ENSG00000169397	ENSG00000169397	3.1.27.-	"""Ribonucleases, RNase A"""	10046	protein-coding gene	gene with protein product	"""eosinophil cationic protein"""	131398		RNS3		1577491	Standard	NM_002935		Approved	ECP	uc001vyj.3	P12724	OTTHUMG00000029604	ENST00000304639.3:c.430C>T	14.37:g.21360275C>T	ENSP00000302324:p.Arg144Trp	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	146	3	0.0205479	NM_002935	Q4VBC1|Q8WTP7|Q8WZ62|Q9GZN9	Missense_Mutation	SNP	ENST00000304639.3	37	CCDS9560.1	.	.	.	.	.	.	.	.	.	.	c	11.91	1.778704	0.31502	.	.	ENSG00000169397	ENST00000304639	T	0.23754	1.89	2.38	-1.08	0.09936	Ribonuclease A, domain (4);	.	.	.	.	T	0.40040	0.1101	M	0.62723	1.935	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.20107	-1.0285	9	0.46703	T	0.11	.	5.5218	0.16938	0.2116:0.3725:0.4159:0.0	.	144	P12724	ECP_HUMAN	W	144	ENSP00000302324:R144W	ENSP00000302324:R144W	R	+	1	2	RNASE3	20430115	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.490000	0.06482	-0.243000	0.09653	0.537000	0.68136	CGG	.	.	none		0.483	RNASE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073795.2	NM_002935	
COL12A1	1303	hgsc.bcm.edu	37	6	75844458	75844458	+	Silent	SNP	C	C	T	rs77425231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:75844458C>T	ENST00000322507.8	-	32	5817	c.5508G>A	c.(5506-5508)acG>acA	p.T1836T	COL12A1_ENST00000416123.2_Silent_p.T1836T|COL12A1_ENST00000483888.2_Silent_p.T1836T|COL12A1_ENST00000345356.6_Silent_p.T672T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1836	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TGCCTCTTCCCGTCATCCGAC	0.463													C|||	21	0.00419329	0.0008	0.0029	5008	,	,		15447	0.001		0.0109	False		,,,				2504	0.0061				p.T1836T		Atlas-SNP	.											.	COL12A1	385	.	0			c.G5508A						PASS	.	C	,	10,3836		0,10,1913	124.0	121.0	122.0		5508,2016	-11.7	0.2	6	dbSNP_132	122	108,8154		1,106,4024	no	coding-synonymous,coding-synonymous	COL12A1	NM_004370.5,NM_080645.2	,	1,116,5937	TT,TC,CC		1.3072,0.26,0.9746	,	1836/3064,672/1900	75844458	118,11990	1923	4131	6054	SO:0001819	synonymous_variant	1303	exon32			TCTTCCCGTCATC	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.5508G>A	6.37:g.75844458C>T		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	266	109	0.409774	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1	13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	4.779	0.144796	0.09134	0.0026	0.013072	ENSG00000111799	ENST00000419671	.	.	.	5.87	-11.7	0.00046	.	.	.	.	.	T	0.13586	0.0329	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44498	-0.9324	4	.	.	.	.	1.0297	0.01535	0.2525:0.1443:0.1932:0.4101	.	.	.	.	R	571	.	.	G	-	1	0	COL12A1	75901178	0.000000	0.05858	0.205000	0.23548	0.828000	0.46876	-3.808000	0.00361	-2.770000	0.00365	-0.909000	0.02823	GGG	C|0.993;T|0.007	0.007	strong		0.463	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
IMPG1	3617	hgsc.bcm.edu	37	6	76633385	76633385	+	Missense_Mutation	SNP	C	C	T	rs3778005	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:76633385C>T	ENST00000369950.3	-	16	2471	c.2282G>A	c.(2281-2283)aGt>aAt	p.S761N	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				CTTTTTAACACTAGTTTTGTA	0.289													C|||	622	0.124201	0.0212	0.2262	5008	,	,		17448	0.0546		0.2634	False		,,,				2504	0.1196				p.S761N	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.G2282A						PASS	.	C	ASN/SER	267,4137	149.2+/-183.4	7,253,1942	133.0	120.0	125.0		2282	0.1	0.0	6	dbSNP_107	125	2239,6355	366.0+/-334.1	314,1611,2372	yes	missense	IMPG1	NM_001563.2	46	321,1864,4314	TT,TC,CC		26.0531,6.0627,19.2799	benign	761/798	76633385	2506,10492	2202	4297	6499	SO:0001583	missense	3617	exon16			TTAACACTAGTTT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.2282G>A	6.37:g.76633385C>T	ENSP00000358966:p.Ser761Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	115	35	0.304348	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	343	0.15705128205128205	12	0.024390243902439025	92	0.2541436464088398	31	0.05419580419580419	208	0.27440633245382584	C	0.005	-2.192799	0.00302	0.060627	0.260531	ENSG00000112706	ENST00000369950;ENST00000369952	T;T	0.20598	2.06;2.12	4.02	0.0666	0.14362	.	1.486350	0.04588	N	0.396120	T	0.03390	0.0098	N	0.19112	0.55	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.37979	-0.9682	9	0.22109	T	0.4	.	3.3272	0.07071	0.1838:0.514:0.0:0.3022	rs3778005;rs52805553;rs59953815;rs3778005	761	Q17R60	IMPG1_HUMAN	N	761;122	ENSP00000358966:S761N;ENSP00000358968:S122N	ENSP00000358966:S761N	S	-	2	0	IMPG1	76690105	0.000000	0.05858	0.001000	0.08648	0.103000	0.19146	0.064000	0.14437	-0.129000	0.11620	-0.157000	0.13467	AGT	C|0.832;T|0.168	0.168	strong		0.289	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592601	167592601	+	Missense_Mutation	SNP	G	G	A	rs200019718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167592601G>A	ENST00000366832.2	+	6	891	c.760G>A	c.(760-762)Gga>Aga	p.G254R		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	254										endometrium(1)|kidney(2)|lung(3)	6						GGCAGCAGCCGGAGTTGCTGG	0.577																																					p.G254R		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G760A						PASS	.																																			SO:0001583	missense	401285	exon6			GCAGCCGGAGTTG		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.760G>A	6.37:g.167592601G>A	ENSP00000355797:p.Gly254Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	113	21	0.185841	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	.	.	.	.	.	.	.	.	.	.	g	7.547	0.661865	0.14645	.	.	ENSG00000166984	ENST00000366832	T	0.41065	1.01	.	.	.	.	.	.	.	.	T	0.20981	0.0505	N	0.24115	0.695	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.13522	-1.0506	7	0.06891	T	0.86	.	.	.	.	.	254	B9ZVM9	TCP2L_HUMAN	R	254	ENSP00000355797:G254R	ENSP00000283507:G254R	G	+	1	0	TCP10L2	167512591	0.001000	0.12720	0.002000	0.10522	0.027000	0.11550	0.333000	0.19768	0.159000	0.19401	0.162000	0.16502	GGA	G|0.941;A|0.059	0.059	strong		0.577	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
SYT6	148281	hgsc.bcm.edu	37	1	114680310	114680310	+	Missense_Mutation	SNP	G	G	A	rs41274114	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:114680310G>A	ENST00000610222.1	-	3	1024	c.878C>T	c.(877-879)aCc>aTc	p.T293I	SYT6_ENST00000609117.1_Missense_Mutation_p.T208I|SYT6_ENST00000607941.1_Missense_Mutation_p.T208I|SYT6_ENST00000369547.1_Missense_Mutation_p.T208I|SYT6_ENST00000393296.1_Missense_Mutation_p.T293I			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	293	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCATCAAAGGTGGGGTTCAG	0.557													G|||	825	0.164736	0.2042	0.1902	5008	,	,		20755	0.0784		0.175	False		,,,				2504	0.1718				p.T208I		Atlas-SNP	.											.	SYT6	66	.	0			c.C623T						PASS	.	G	ILE/THR	876,3530	343.3+/-307.6	75,726,1402	121.0	114.0	116.0		623	5.4	1.0	1	dbSNP_127	116	1528,7072	287.3+/-298.2	133,1262,2905	yes	missense	SYT6	NM_205848.2	89	208,1988,4307	AA,AG,GG		17.7674,19.882,18.4838	possibly-damaging	208/426	114680310	2404,10602	2203	4300	6503	SO:0001583	missense	148281	exon3			TCAAAGGTGGGGT		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"""Synaptotagmins"""	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.878C>T	1.37:g.114680310G>A	ENSP00000476396:p.Thr293Ile	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	218	119	0.545872	NM_205848	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	37		371	0.16987179487179488	110	0.22357723577235772	73	0.20165745856353592	54	0.0944055944055944	134	0.17678100263852242	G	15.06	2.721352	0.48728	0.19882	0.177674	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.45	5.45	0.79879	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.050367	0.85682	D	0.000000	T	0.44138	0.1279	N	0.17723	0.515	0.09310	P	0.999999855013	B	0.17465	0.022	B	0.29353	0.101	T	0.36939	-0.9727	9	0.30854	T	0.27	.	19.29	0.94095	0.0:0.0:1.0:0.0	rs41274114;rs61080477;rs61730009	293	Q5T7P8	SYT6_HUMAN	I	208;293;208;293	ENSP00000358560:T208I;ENSP00000376974:T293I;ENSP00000358559:T208I;ENSP00000358558:T293I	ENSP00000358558:T293I	T	-	2	0	SYT6	114481833	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.813000	0.69201	2.567000	0.86603	0.650000	0.86243	ACC	G|0.820;A|0.180	0.180	strong		0.557	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848	
NOTCH1	4851	hgsc.bcm.edu	37	9	139407932	139407932	+	Silent	SNP	A	A	G	rs2229971|rs587778559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139407932A>G	ENST00000277541.6	-	14	2340	c.2265T>C	c.(2263-2265)aaT>aaC	p.N755N		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	755	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATTCACACTCATTGTTGTTGA	0.602			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2643	0.527756	0.6997	0.4784	5008	,	,		19531	0.7768		0.335	False		,,,				2504	0.272				p.N755N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	0			c.T2265C						PASS	.	G		2695,1683		864,967,358	109.0	123.0	118.0		2265	-2.3	0.0	9	dbSNP_98	118	2445,6109		358,1729,2190	no	coding-synonymous	NOTCH1	NM_017617.3		1222,2696,2548	GG,GA,AA		28.5831,38.4422,39.7464		755/2556	139407932	5140,7792	2189	4277	6466	SO:0001819	synonymous_variant	4851	exon14			ACACTCATTGTTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.2265T>C	9.37:g.139407932A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.484;G|0.516	0.516	strong		0.602	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
BCL2L13	23786	hgsc.bcm.edu	37	22	18209613	18209613	+	Silent	SNP	A	A	G	rs4488761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:18209613A>G	ENST00000317582.5	+	7	1118	c.771A>G	c.(769-771)tcA>tcG	p.S257S	BCL2L13_ENST00000543133.1_Silent_p.S95S|BCL2L13_ENST00000355028.3_3'UTR|BCL2L13_ENST00000485631.1_3'UTR|BCL2L13_ENST00000538149.1_Silent_p.S133S|BCL2L13_ENST00000337612.5_Silent_p.S95S|BCL2L13_ENST00000418951.2_3'UTR	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	257					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		TGTCACTGTCAGCTAGCCAGA	0.527													A|||	3335	0.665935	0.5764	0.6527	5008	,	,		20230	0.9325		0.5358	False		,,,				2504	0.6554				p.S281S		Atlas-SNP	.											.	BCL2L13	27	.	0			c.A843G						PASS	.	A		2644,1762	644.2+/-398.0	808,1028,367	67.0	54.0	58.0		771	-6.7	0.7	22	dbSNP_111	58	4541,4059	595.7+/-393.5	1208,2125,967	no	coding-synonymous	BCL2L13	NM_015367.2		2016,3153,1334	GG,GA,AA		47.1977,39.9909,44.7563		257/486	18209613	7185,5821	2203	4300	6503	SO:0001819	synonymous_variant	23786	exon6			ACTGTCAGCTAGC	AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.771A>G	22.37:g.18209613A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_001270726	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Silent	SNP	ENST00000317582.5	37	CCDS13746.1																																																																																			A|0.392;G|0.608	0.608	strong		0.527	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367	
MADCAM1	8174	hgsc.bcm.edu	37	19	501725	501725	+	Missense_Mutation	SNP	G	G	A	rs62130833		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:501725G>A	ENST00000215637.3	+	4	770	c.724G>A	c.(724-726)Gac>Aac	p.D242N	AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.D23N|MADCAM1_ENST00000382683.4_Intron	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	242	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.			D -> N (in Ref. 2; AAB02194 and 3; AAC51354). {ECO:0000305}.	aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGTCTCCCGACACCACCTC	0.682																																					p.D242N		Atlas-SNP	.											.	MADCAM1	29	.	0			c.G724A						PASS	.						26.0	42.0	36.0					19																	501725		2201	4299	6500	SO:0001583	missense	8174	exon4			TCTCCCGACACCA	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.724G>A	19.37:g.501725G>A	ENSP00000215637:p.Asp242Asn	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	252	134	0.531746	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	618	0.28296703296703296	75	0.1524390243902439	133	0.3674033149171271	184	0.32167832167832167	226	0.29815303430079154	g	7.171	0.587634	0.13812	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10288	2.89	3.55	-1.32	0.09201	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48670	-0.9015	8	0.22109	T	0.4	.	3.1363	0.06439	0.2817:0.0:0.3626:0.3557	rs62130833	242	Q13477	MADCA_HUMAN	N	266;258;250;242	ENSP00000215637:D242N	ENSP00000215637:D242N	D	+	1	0	MADCAM1	452725	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.632000	0.05489	-0.229000	0.09854	-0.378000	0.06908	GAC	G|0.717;A|0.283	0.283	strong		0.682	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
MYO1C	4641	hgsc.bcm.edu	37	17	1387472	1387472	+	Silent	SNP	C	C	T	rs11538156	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1387472C>T	ENST00000575158.1	-	2	272	c.96G>A	c.(94-96)ctG>ctA	p.L32L	MYO1C_ENST00000438665.2_Silent_p.L48L|MYO1C_ENST00000359786.5_Silent_p.L67L|MYO1C_ENST00000361007.2_Silent_p.L32L|MYO1C_ENST00000573198.1_5'Flank|MYO1C_ENST00000545534.2_Silent_p.L43L			Q12965	MYO1E_HUMAN	myosin IC	39	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ATCGCCGCCGCAGGTTCTCGA	0.627													C|||	332	0.0662939	0.0552	0.0562	5008	,	,		14022	0.0169		0.1322	False		,,,				2504	0.0716				p.L67L		Atlas-SNP	.											.	MYO1C	57	.	0			c.G201A						PASS	.	C	,,	333,4073	175.5+/-204.9	14,305,1884	49.0	46.0	47.0		201,144,96	2.5	1.0	17	dbSNP_120	47	1355,7245	264.3+/-285.5	106,1143,3051	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	120,1448,4935	TT,TC,CC		15.7558,7.5579,12.9786	,,	67/1064,48/1045,32/1029	1387472	1688,11318	2203	4300	6503	SO:0001819	synonymous_variant	4641	exon2			CCGCCGCAGGTTC	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"""Myosins / Myosin superfamily : Class I"""	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.96G>A	17.37:g.1387472C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			T|0.112;G|0.000;C|0.888	0.112	strong		0.627	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
NDST1	3340	hgsc.bcm.edu	37	5	149907533	149907533	+	Silent	SNP	T	T	G	rs2273235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:149907533T>G	ENST00000261797.6	+	3	1183	c.681T>G	c.(679-681)gtT>gtG	p.V227V	NDST1_ENST00000523767.1_Silent_p.V227V	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	227	Heparan sulfate N-deacetylase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACTGGACGGTTTTCCAGTCAA	0.627													G|||	1832	0.365815	0.2421	0.5	5008	,	,		20605	0.2788		0.4742	False		,,,				2504	0.4162				p.V227V		Atlas-SNP	.											.	NDST1	79	.	0			c.T681G						PASS	.	G		1312,3094	692.8+/-405.6	211,890,1102	51.0	44.0	46.0		681	2.0	1.0	5	dbSNP_100	46	4025,4575	594.8+/-393.4	971,2083,1246	no	coding-synonymous	NDST1	NM_001543.4		1182,2973,2348	GG,GT,TT		46.8023,29.7776,41.0349		227/883	149907533	5337,7669	2203	4300	6503	SO:0001819	synonymous_variant	3340	exon3			GACGGTTTTCCAG	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"""Sulfotransferases, membrane-bound"""	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.681T>G	5.37:g.149907533T>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	73	20	0.273973	NM_001543	Q96E57	Silent	SNP	ENST00000261797.6	37	CCDS34277.1																																																																																			T|0.626;G|0.374	0.374	strong		0.627	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
KCTD7	154881	hgsc.bcm.edu	37	7	66098384	66098384	+	Silent	SNP	G	G	A	rs3764904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:66098384G>A	ENST00000275532.3	+	2	451	c.267G>A	c.(265-267)acG>acA	p.T89T	KCTD7_ENST00000443322.1_Silent_p.T89T	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	89	BTB.				cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						ACATCCCCACGGACTCCGAGG	0.552													G|||	392	0.0782748	0.0053	0.0965	5008	,	,		17188	0.1101		0.1133	False		,,,				2504	0.0951				p.T89T		Atlas-SNP	.											.	KCTD7	26	.	0			c.G267A						PASS	.	G	,	120,4286	90.2+/-128.9	1,118,2084	120.0	89.0	100.0		267,267	-9.2	0.0	7	dbSNP_107	100	960,7640	210.4+/-251.3	54,852,3394	no	coding-synonymous,coding-synonymous	KCTD7	NM_001167961.2,NM_153033.4	,	55,970,5478	AA,AG,GG		11.1628,2.7236,8.3039	,	89/289,89/290	66098384	1080,11926	2203	4300	6503	SO:0001819	synonymous_variant	154881	exon2			CCCCACGGACTCC	AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"""potassium channel tetramerisation domain containing 7"""			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.267G>A	7.37:g.66098384G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_001167961	A4D2M4|Q8IVR0	Silent	SNP	ENST00000275532.3	37	CCDS5534.1																																																																																			G|0.906;A|0.094	0.094	strong		0.552	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033	
YDJC	150223	hgsc.bcm.edu	37	22	21984205	21984205	+	Silent	SNP	A	A	G	rs710177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21984205A>G	ENST00000292778.6	-	1	148	c.99T>C	c.(97-99)gcT>gcC	p.A33A	CCDC116_ENST00000607942.1_5'Flank|CCDC116_ENST00000292779.3_5'Flank|YDJC_ENST00000398873.3_Silent_p.A33A	NM_001017964.1	NP_001017964.1	A8MPS7	YDJC_HUMAN	YdjC homolog (bacterial)	33					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)					Colorectal(54;0.105)					CGCTGGTCACAGCCCCGGCCA	0.706													-|||	2301	0.459465	0.3926	0.4986	5008	,	,		13664	0.5109		0.3887	False		,,,				2504	0.5419				p.A33A		Atlas-SNP	.											YDJC,rectum,carcinoma,0,1	YDJC	8	1	0			c.T99C						PASS	.			1688,2672		342,1004,834	18.0	17.0	17.0		99	-8.9	0.0	22	dbSNP_86	17	3196,5354		640,1916,1719	no	coding-synonymous	YDJC	NM_001017964.1		982,2920,2553	GG,GA,AA		37.3801,38.7156,37.8311		33/324	21984205	4884,8026	2180	4275	6455	SO:0001819	synonymous_variant	150223	exon1			GGTCACAGCCCCG		CCDS33613.1	22q11.21	2008-02-26			ENSG00000161179	ENSG00000161179			27158	protein-coding gene	gene with protein product						18177738	Standard	XM_005261347		Approved		uc002zvb.2	A8MPS7	OTTHUMG00000150822	ENST00000292778.6:c.99T>C	22.37:g.21984205A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_001017964	Q2YDT4|Q4V9R7	Silent	SNP	ENST00000292778.6	37	CCDS33613.1																																																																																			A|0.605;G|0.395	0.395	strong		0.706	YDJC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320213.1		
GPR98	84059	hgsc.bcm.edu	37	5	90020923	90020923	+	Silent	SNP	T	T	G	rs16869042	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:90020923T>G	ENST00000405460.2	+	47	10023	c.9927T>G	c.(9925-9927)ccT>ccG	p.P3309P		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3309					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.P3309P(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TAGAAAATCCTAAAACTTGTG	0.269																																					p.P3309P		Atlas-SNP	.											GPR98,NS,carcinoma,0,2	GPR98	605	2	1	Substitution - coding silent(1)	stomach(1)	c.T9927G						PASS	.	T		772,2796		91,590,1103	29.0	29.0	29.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	9927	2.3	1.0	5	dbSNP_123	29	2676,5394		450,1776,1809	no	coding-synonymous	GPR98	NM_032119.3		541,2366,2912	GG,GT,TT		33.1599,21.6368,29.6271		3309/6307	90020923	3448,8190	1784	4035	5819	SO:0001819	synonymous_variant	84059	exon47			AAATCCTAAAACT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.9927T>G	5.37:g.90020923T>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	771	0.35302197802197804	110	0.22357723577235772	176	0.4861878453038674	245	0.42832167832167833	240	0.316622691292876	T	8.590	0.884356	0.17467	0.216368	0.331599	ENSG00000164199	ENST00000509621	.	.	.	5.15	2.33	0.28932	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999584104	.	.	.	.	.	.	T	0.48375	-0.9041	3	.	.	.	.	4.2044	0.10481	0.1927:0.1679:0.0:0.6393	rs16869042;rs16869042	.	.	.	R	875	.	.	L	+	2	0	GPR98	90056679	0.305000	0.24481	0.996000	0.52242	0.997000	0.91878	0.011000	0.13264	0.900000	0.36469	0.455000	0.32223	CTA	G|0.336;N|0.001	0.336	strong		0.269	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
CLCA1	1179	hgsc.bcm.edu	37	1	86959173	86959173	+	Missense_Mutation	SNP	T	T	C	rs2791494	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86959173T>C	ENST00000234701.3	+	11	1922	c.1571T>C	c.(1570-1572)aTg>aCg	p.M524T	CLCA1_ENST00000394711.1_Missense_Mutation_p.M524T			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	524			M -> T (in dbSNP:rs2791494). {ECO:0000269|PubMed:10437792, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9828122, ECO:0000269|Ref.5}.		calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		ACCTGGACAATGCAGCCTCCC	0.507													C|||	4255	0.849641	0.7753	0.8761	5008	,	,		18065	0.9058		0.8241	False		,,,				2504	0.8998				p.M524T		Atlas-SNP	.											.	CLCA1	109	.	0			c.T1571C						PASS	.	C	THR/MET	3393,1013	376.8+/-322.2	1291,811,101	172.0	138.0	149.0		1571	0.3	0.0	1	dbSNP_100	149	7034,1566	293.8+/-301.5	2882,1270,148	yes	missense	CLCA1	NM_001285.3	81	4173,2081,249	CC,CT,TT		18.2093,22.9914,19.8293	benign	524/915	86959173	10427,2579	2203	4300	6503	SO:0001583	missense	1179	exon10			GGACAATGCAGCC		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"""chloride channel, calcium activated, family member 1"", ""chloride channel regulator 1"""			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.1571T>C	1.37:g.86959173T>C	ENSP00000234701:p.Met524Thr	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	149	147	0.986577	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	37	CCDS709.1	1836	0.8406593406593407	379	0.7703252032520326	314	0.8674033149171271	523	0.9143356643356644	620	0.8179419525065963	C	0.004	-2.348343	0.00219	0.770086	0.817907	ENSG00000016490	ENST00000234701;ENST00000394711;ENST00000539889	T;T	0.27402	1.67;1.67	5.7	0.353	0.16058	Domain of unknown function DUF1973 (1);	1.031650	0.07687	N	0.938044	T	0.01835	0.0058	N	0.00621	-1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41270	-0.9518	9	0.08599	T	0.76	0.4671	5.3162	0.15856	0.4598:0.3463:0.0:0.1939	rs2791494;rs52789621;rs60548610;rs2791494	524	A8K7I4	CLCA1_HUMAN	T	524;524;237	ENSP00000234701:M524T;ENSP00000378200:M524T	ENSP00000234701:M524T	M	+	2	0	CLCA1	86731761	0.000000	0.05858	0.000000	0.03702	0.236000	0.25371	-0.146000	0.10250	-0.440000	0.07211	-0.226000	0.12346	ATG	T|0.169;C|0.831	0.831	strong		0.507	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	
OR6K3	391114	hgsc.bcm.edu	37	1	158687896	158687896	+	Missense_Mutation	SNP	C	C	T	rs857705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158687896C>T	ENST00000368146.1	-	1	57	c.58G>A	c.(58-60)Gga>Aga	p.G20R	OR6K3_ENST00000368145.1_Missense_Mutation_p.G4R			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	20			G -> R (in dbSNP:rs857705).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					GATTGGTTTCCGCTCTCCATA	0.388													c|||	1127	0.22504	0.2943	0.1614	5008	,	,		16757	0.1518		0.2227	False		,,,				2504	0.2546				p.G4R		Atlas-SNP	.											.	OR6K3	101	.	0			c.G10A						PASS	.	T	ARG/GLY	1248,3158	420.2+/-338.9	176,896,1131	48.0	47.0	48.0		10	-2.9	0.0	1	dbSNP_86	48	1756,6844	312.7+/-311.0	164,1428,2708	yes	missense	OR6K3	NM_001005327.2	125	340,2324,3839	TT,TC,CC		20.4186,28.325,23.097	benign	4/316	158687896	3004,10002	2203	4300	6503	SO:0001583	missense	391114	exon1			GGTTTCCGCTCTC	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.58G>A	1.37:g.158687896C>T	ENSP00000357128:p.Gly20Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_001005327	Q5VUV0|Q6IFR5	Missense_Mutation	SNP	ENST00000368146.1	37		463	0.211996336996337	145	0.29471544715447157	60	0.16574585635359115	81	0.14160839160839161	177	0.23350923482849603	c	4.440	0.081406	0.08533	0.28325	0.204186	ENSG00000203757	ENST00000368145;ENST00000368146	T;T	0.00484	7.08;7.08	3.89	-2.94	0.05581	.	.	.	.	.	T	0.00073	0.0002	N	0.25144	0.715	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.11060	-1.0603	8	0.17369	T	0.5	.	2.3035	0.04168	0.1216:0.3478:0.1196:0.411	rs857705;rs52837960;rs58065485;rs857705	20	Q8NGY3	OR6K3_HUMAN	R	4;20	ENSP00000357127:G4R;ENSP00000357128:G20R	ENSP00000357127:G4R	G	-	1	0	OR6K3	156954520	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.046000	0.03525	-0.465000	0.06953	-1.804000	0.00617	GGA	C|0.776;T|0.224	0.224	strong		0.388	OR6K3-201	KNOWN	basic	protein_coding	protein_coding			
WDFY4	57705	hgsc.bcm.edu	37	10	50022040	50022040	+	Silent	SNP	G	G	A	rs41283275	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50022040G>A	ENST00000325239.5	+	30	5280	c.5253G>A	c.(5251-5253)agG>agA	p.R1751R	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1751						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						TCCTGCAGAGGCACCACCAGG	0.582													G|||	749	0.149561	0.2322	0.1484	5008	,	,		19475	0.1022		0.1213	False		,,,				2504	0.1166				p.R1751R		Atlas-SNP	.											.	WDFY4	205	.	0			c.G5253A						PASS	.	G		318,1066		31,256,405	36.0	40.0	39.0		5253	-4.1	0.0	10	dbSNP_127	39	342,2840		19,304,1268	no	coding-synonymous	WDFY4	NM_020945.1		50,560,1673	AA,AG,GG		10.748,22.9769,14.4547		1751/3185	50022040	660,3906	692	1591	2283	SO:0001819	synonymous_variant	57705	exon31			GCAGAGGCACCAC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5253G>A	10.37:g.50022040G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	313	0.1433150183150183	105	0.21341463414634146	48	0.13259668508287292	68	0.11888111888111888	92	0.12137203166226913	G	5.144	0.212184	0.09757	0.229769	0.10748	ENSG00000128815	ENST00000312002;ENST00000374161	.	.	.	5.83	-4.12	0.03916	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.30698	P	0.750638	.	.	.	.	.	.	T	0.34104	-0.9842	3	.	.	.	.	2.7652	0.05318	0.5275:0.1495:0.21:0.1131	rs41283275;rs61838867	.	.	.	T	842;298	.	.	A	+	1	0	WDFY4	49692046	0.590000	0.26815	0.009000	0.14445	0.628000	0.37860	-0.339000	0.07832	-0.628000	0.05582	-0.964000	0.02622	GCA	G|0.855;A|0.145	0.145	strong		0.582	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
TBX15	6913	hgsc.bcm.edu	37	1	119469188	119469188	+	Missense_Mutation	SNP	G	G	T	rs10494217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:119469188G>T	ENST00000369429.3	-	3	475	c.466C>A	c.(466-468)Cat>Aat	p.H156N	TBX15_ENST00000207157.3_Missense_Mutation_p.H50N			Q96SF7	TBX15_HUMAN	T-box 15	156			H -> N (in dbSNP:rs10494217).		embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		TACTGCTGATGTGGATCTAGG	0.428													G|||	423	0.0844649	0.0076	0.1023	5008	,	,		19815	0.0655		0.165	False		,,,				2504	0.1125				p.H50N		Atlas-SNP	.											.	TBX15	95	.	0			c.C148A						PASS	.	G	ASN/HIS	151,4255	103.0+/-141.5	4,143,2056	170.0	140.0	150.0		148	6.1	1.0	1	dbSNP_119	150	1560,7040	291.7+/-300.5	146,1268,2886	yes	missense	TBX15	NM_152380.2	68	150,1411,4942	TT,TG,GG		18.1395,3.4271,13.1555	benign	50/497	119469188	1711,11295	2203	4300	6503	SO:0001583	missense	6913	exon3			GCTGATGTGGATC	AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"""T-boxes"""	11594	protein-coding gene	gene with protein product		604127	"""T-box 14"""	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.466C>A	1.37:g.119469188G>T	ENSP00000358437:p.His156Asn	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_152380	Q08E76|Q5JT54|Q5T9S7	Missense_Mutation	SNP	ENST00000369429.3	37		213	0.09752747252747253	4	0.008130081300813009	37	0.10220994475138122	43	0.07517482517482517	129	0.17018469656992086	G	15.39	2.819013	0.50633	0.034271	0.181395	ENSG00000092607	ENST00000207157;ENST00000369429	D;D	0.86956	-2.19;-2.19	6.06	6.06	0.98353	p53-like transcription factor, DNA-binding (1);	0.044485	0.85682	D	0.000000	T	0.77922	0.4203	N	0.11845	0.185	0.09310	P	0.9999999999531072	B	0.25105	0.118	B	0.39339	0.297	T	0.74074	-0.3782	9	0.34782	T	0.22	.	20.2501	0.98402	0.0:0.0:1.0:0.0	rs10494217;rs17185917;rs52794873;rs59613865;rs10494217	156	Q96SF7	TBX15_HUMAN	N	50;156	ENSP00000207157:H50N;ENSP00000358437:H156N	ENSP00000207157:H50N	H	-	1	0	TBX15	119270711	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.017000	0.88712	2.880000	0.98712	0.650000	0.86243	CAT	G|0.891;T|0.109	0.109	strong		0.428	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380	
RSPH4A	345895	hgsc.bcm.edu	37	6	116938232	116938232	+	Missense_Mutation	SNP	C	C	G	rs13213314	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116938232C>G	ENST00000229554.5	+	1	583	c.446C>G	c.(445-447)aCc>aGc	p.T149S	RSPH4A_ENST00000368581.4_Missense_Mutation_p.T149S|RSPH4A_ENST00000368580.4_Missense_Mutation_p.T149S	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	149			T -> S (in dbSNP:rs13213314).		axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						GAAGGAAACACCTTTCAACAG	0.453									Kartagener syndrome				C|||	186	0.0371406	0.0091	0.049	5008	,	,		21180	0.0		0.1292	False		,,,				2504	0.0102				p.T149S		Atlas-SNP	.											.	RSPH4A	54	.	0			c.C446G						PASS	.	C	SER/THR,SER/THR	118,4288	88.2+/-126.9	3,112,2088	127.0	126.0	126.0		446,446	2.8	0.0	6	dbSNP_121	126	1056,7544	223.1+/-260.0	58,940,3302	yes	missense,missense	RSPH4A	NM_001010892.2,NM_001161664.1	58,58	61,1052,5390	GG,GC,CC		12.2791,2.6782,9.0266	benign,benign	149/717,149/601	116938232	1174,11832	2203	4300	6503	SO:0001583	missense	345895	exon1	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GAAACACCTTTCA		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"""radial spokehead-like 3"""	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.446C>G	6.37:g.116938232C>G	ENSP00000229554:p.Thr149Ser	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	181	61	0.337017	NM_001161664	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	128	0.05860805860805861	9	0.018292682926829267	19	0.052486187845303865	0	0.0	100	0.13192612137203166	C	6.816	0.519696	0.13005	0.026782	0.122791	ENSG00000111834	ENST00000368581;ENST00000229554;ENST00000368580	T;T;T	0.64438	-0.1;1.54;1.51	5.53	2.84	0.33178	.	1.282210	0.05002	N	0.469321	T	0.23572	0.0570	L	0.27053	0.805	0.80722	P	0.0	B;B	0.11235	0.004;0.001	B;B	0.10450	0.005;0.002	T	0.06570	-1.0819	9	0.14656	T	0.56	0.5597	5.8791	0.18846	0.0:0.6759:0.1572:0.167	rs13213314;rs52838245;rs13213314	149;149	Q5TD94-3;Q5TD94	.;RSH4A_HUMAN	S	149	ENSP00000357570:T149S;ENSP00000229554:T149S;ENSP00000357569:T149S	ENSP00000229554:T149S	T	+	2	0	RSPH4A	117044925	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.850000	0.04317	0.465000	0.27167	-0.121000	0.15023	ACC	C|0.925;G|0.075	0.075	strong		0.453	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	
MMEL1	79258	hgsc.bcm.edu	37	1	2535672	2535672	+	Missense_Mutation	SNP	G	G	A	rs143132254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:2535672G>A	ENST00000378412.3	-	10	1026	c.865C>T	c.(865-867)Cgg>Tgg	p.R289W	MMEL1_ENST00000288709.6_Missense_Mutation_p.R280W|MMEL1_ENST00000502556.1_Intron			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	289						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		GCATCCTCCCGCAGCAACGTG	0.667																																					p.R289W		Atlas-SNP	.											.	MMEL1	64	.	0			c.C865T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	60.0	61.0	61.0		865	1.2	0.1	1	dbSNP_134	61	2,8598	2.2+/-6.3	0,2,4298	no	missense	MMEL1	NM_033467.3	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	289/780	2535672	2,13004	2203	4300	6503	SO:0001583	missense	79258	exon10			CCTCCCGCAGCAA	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"""membrane metallo-endopeptidase-like 2"""	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.865C>T	1.37:g.2535672G>A	ENSP00000367668:p.Arg289Trp	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	193	99	0.512953	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	37	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429289	0.43122	0.0	2.33E-4	ENSG00000142606	ENST00000288709;ENST00000378412	T;T	0.73897	-0.79;-0.79	4.43	1.16	0.20824	Peptidase M13 (1);	0.058612	0.64402	D	0.000002	D	0.84511	0.5488	M	0.80847	2.515	0.41175	D	0.986192	D	0.89917	1.0	D	0.97110	1.0	D	0.84034	0.0361	10	0.59425	D	0.04	-37.0008	12.2645	0.54670	0.0:0.0:0.5439:0.4561	.	289	Q495T6	MMEL1_HUMAN	W	280;289	ENSP00000288709:R280W;ENSP00000367668:R289W	ENSP00000288709:R280W	R	-	1	2	MMEL1	2525532	0.933000	0.31639	0.080000	0.20451	0.522000	0.34438	1.210000	0.32370	0.006000	0.14734	0.485000	0.47835	CGG	G|1.000;A|0.000	0.000	strong		0.667	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
KRT5	3852	hgsc.bcm.edu	37	12	52908872	52908872	+	Missense_Mutation	SNP	C	C	T	rs11549949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52908872C>T	ENST00000252242.4	-	9	2017	c.1627G>A	c.(1627-1629)Ggt>Agt	p.G543S		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	543	Ser-rich.|Tail.		G -> S (in dbSNP:rs11549949). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2455002}.		cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGCCCACCACCTAGgccgaca	0.677													C|||	645	0.128794	0.1793	0.1859	5008	,	,		12064	0.0387		0.1481	False		,,,				2504	0.093				p.G543S		Atlas-SNP	.											.	KRT5	88	.	0			c.G1627A						PASS	.	C	SER/GLY	766,3636	296.7+/-284.4	61,644,1496	34.0	35.0	35.0		1627	2.0	0.0	12	dbSNP_120	35	1200,7398	229.1+/-263.9	85,1030,3184	yes	missense	KRT5	NM_000424.3	56	146,1674,4680	TT,TC,CC		13.9567,17.4012,15.1231	benign	543/591	52908872	1966,11034	2201	4299	6500	SO:0001583	missense	3852	exon9			CACCACCTAGGCC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1627G>A	12.37:g.52908872C>T	ENSP00000252242:p.Gly543Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	37	CCDS8830.1	290	0.13278388278388278	103	0.20934959349593496	59	0.16298342541436464	20	0.03496503496503497	108	0.1424802110817942	c	4.125	0.021346	0.08006	0.174012	0.139567	ENSG00000186081	ENST00000252242;ENST00000456000	D	0.97455	-4.39	4.86	1.98	0.26296	.	.	.	.	.	T	0.00524	0.0017	N	0.14661	0.345	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.49234	-0.8961	8	0.08179	T	0.78	.	8.3579	0.32342	0.0:0.7466:0.0:0.2534	rs11549949;rs17855506;rs17855655;rs52824405;rs11549949	543	P13647	K2C5_HUMAN	S	543;508	ENSP00000252242:G543S	ENSP00000252242:G543S	G	-	1	0	KRT5	51195139	0.011000	0.17503	0.002000	0.10522	0.037000	0.13140	1.463000	0.35277	0.189000	0.20188	0.461000	0.40582	GGT	T|0.147;G|0.000;C|0.853;A|0.000	0.147	strong		0.677	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
RBM12B	389677	hgsc.bcm.edu	37	8	94746698	94746698	+	Silent	SNP	G	G	T	rs3133974	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:94746698G>T	ENST00000399300.2	-	3	2154	c.1941C>A	c.(1939-1941)ccC>ccA	p.P647P	RBM12B_ENST00000517700.1_Intron|RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	647							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			AGTCCTCCTCGGGGAGCTGCC	0.647													G|||	1332	0.265974	0.1755	0.232	5008	,	,		13293	0.3363		0.2843	False		,,,				2504	0.3211				p.P647P		Atlas-SNP	.											.	RBM12B	78	.	0			c.C1941A						PASS	.	G		702,3046		68,566,1240	86.0	89.0	88.0		1941	-8.2	0.0	8	dbSNP_103	88	2304,5910		329,1646,2132	no	coding-synonymous	RBM12B	NM_203390.2		397,2212,3372	TT,TG,GG		28.0497,18.73,25.1296		647/1002	94746698	3006,8956	1874	4107	5981	SO:0001819	synonymous_variant	389677	exon3			CTCCTCGGGGAGC		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1941C>A	8.37:g.94746698G>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	120	65	0.541667	NM_203390	A8MYB5	Silent	SNP	ENST00000399300.2	37	CCDS43755.1																																																																																			A|0.000;G|0.730;T|0.270	0.270	strong		0.647	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
BIN2	51411	hgsc.bcm.edu	37	12	51681903	51681903	+	Missense_Mutation	SNP	T	T	C	rs7954976	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51681903T>C	ENST00000267012.4	-	11	1646	c.1585A>G	c.(1585-1587)Aac>Gac	p.N529D	BIN2_ENST00000604560.1_Intron|BIN2_ENST00000544402.1_Missense_Mutation_p.N503D|BIN2_ENST00000452142.2_Missense_Mutation_p.N497D	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	529			N -> D (in dbSNP:rs7954976). {ECO:0000269|PubMed:10903846, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)			NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						TCCGAGGAGTTAGCTGAGATA	0.368													C|||	4179	0.834465	0.6029	0.8963	5008	,	,		20158	0.9296		0.8976	False		,,,				2504	0.9407				p.N529D		Atlas-SNP	.											.	BIN2	58	.	0			c.A1585G						PASS	.	C	ASP/ASN	2756,1650	506.4+/-366.4	874,1008,321	165.0	125.0	139.0		1585	1.8	0.0	12	dbSNP_116	139	7709,891	199.9+/-243.8	3461,787,52	yes	missense	BIN2	NM_016293.2	23	4335,1795,373	CC,CT,TT		10.3605,37.4489,19.5371	benign	529/566	51681903	10465,2541	2203	4300	6503	SO:0001583	missense	51411	exon11			AGGAGTTAGCTGA	AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.1585A>G	12.37:g.51681903T>C	ENSP00000267012:p.Asn529Asp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Missense_Mutation	SNP	ENST00000267012.4	37	CCDS8811.1	1836	0.8406593406593407	311	0.6321138211382114	314	0.8674033149171271	534	0.9335664335664335	677	0.8931398416886543	C	0.009	-1.825907	0.00589	0.625511	0.896395	ENSG00000110934	ENST00000452142;ENST00000267012;ENST00000544402	T;T;T	0.56444	0.46;0.5;0.47	3.01	1.8	0.24995	.	0.902450	0.09559	N	0.785896	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36625	-0.9740	9	0.02654	T	1	.	4.9528	0.14023	0.0:0.6352:0.0:0.3648	rs7954976;rs60054406;rs7954976	503;497;529	F5H0W4;Q9UBW5-2;Q9UBW5	.;.;BIN2_HUMAN	D	497;529;503	ENSP00000410217:N497D;ENSP00000267012:N529D;ENSP00000445874:N503D	ENSP00000267012:N529D	N	-	1	0	BIN2	49968170	0.100000	0.21855	0.000000	0.03702	0.002000	0.02628	0.262000	0.18460	0.154000	0.19237	-0.215000	0.12644	AAC	T|0.183;C|0.817	0.817	strong		0.368	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1		
CHPT1	56994	hgsc.bcm.edu	37	12	102108345	102108345	+	Missense_Mutation	SNP	T	T	C	rs3205421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:102108345T>C	ENST00000229266.3	+	3	720	c.485T>C	c.(484-486)tTc>tCc	p.F162S	CHPT1_ENST00000550385.1_3'UTR|CHPT1_ENST00000549872.1_Missense_Mutation_p.F162S	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	162			F -> S (in dbSNP:rs3205421). {ECO:0000269|PubMed:10893425}.		CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						TGGTTTTTTTTCTGCTCTTTT	0.353													T|||	1137	0.227037	0.0741	0.2738	5008	,	,		15511	0.3433		0.3022	False		,,,				2504	0.2035				p.F162S		Atlas-SNP	.											.	CHPT1	27	.	0			c.T485C						PASS	.	T	SER/PHE	495,3911	221.0+/-238.3	25,445,1733	160.0	148.0	152.0		485	6.1	1.0	12	dbSNP_105	152	2483,6117	393.6+/-344.4	351,1781,2168	yes	missense	CHPT1	NM_020244.2	155	376,2226,3901	CC,CT,TT		28.8721,11.2347,22.8971	possibly-damaging	162/407	102108345	2978,10028	2203	4300	6503	SO:0001583	missense	56994	exon3			TTTTTTTCTGCTC		CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"""phosphatidylcholine synthesizing enzyme"""					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.485T>C	12.37:g.102108345T>C	ENSP00000229266:p.Phe162Ser	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	271	124	0.457565	NM_020244	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Missense_Mutation	SNP	ENST00000229266.3	37	CCDS9086.1	570	0.260989010989011	40	0.08130081300813008	104	0.287292817679558	201	0.3513986013986014	225	0.29683377308707126	T	22.8	4.339740	0.81911	0.112347	0.288721	ENSG00000111666	ENST00000229266;ENST00000549872	T;T	0.40225	1.04;1.04	6.06	6.06	0.98353	.	0.089068	0.85682	D	0.000000	T	0.00012	0.0000	M	0.80982	2.52	0.21802	P	0.999532065	D;D	0.76494	0.997;0.999	D;D	0.79784	0.962;0.993	T	0.33675	-0.9859	9	0.56958	D	0.05	-0.3375	11.3701	0.49694	0.1353:0.0:0.0:0.8647	rs3205421;rs52798048;rs59280515;rs3205421	162;162	F8W1B3;Q8WUD6	.;CHPT1_HUMAN	S	162	ENSP00000229266:F162S;ENSP00000448766:F162S	ENSP00000229266:F162S	F	+	2	0	CHPT1	100632476	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.808000	0.69165	2.324000	0.78689	0.533000	0.62120	TTC	T|0.760;C|0.240	0.240	strong		0.353	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244	
OR3A1	4994	hgsc.bcm.edu	37	17	3195503	3195503	+	Missense_Mutation	SNP	C	C	T	rs703903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:3195503C>T	ENST00000323404.1	-	1	373	c.374G>A	c.(373-375)cGa>cAa	p.R125Q	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	125			R -> Q (in dbSNP:rs703903). {ECO:0000269|PubMed:10673334, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8004088, ECO:0000269|PubMed:8647456}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	20						GGCCAGGAATCGGTCATAGGC	0.592													.|||	2755	0.55012	0.2451	0.5447	5008	,	,		20550	0.9266		0.5427	False		,,,				2504	0.5859				p.R125Q	GBM(20;287 516 18743 28660 36594)	Atlas-SNP	.											.	OR3A1	46	.	0			c.G374A						PASS	.	C	GLN/ARG	1357,3049	440.6+/-346.1	189,979,1035	94.0	87.0	90.0		374	5.3	1.0	17	dbSNP_86	90	4620,3980	601.1+/-394.3	1237,2146,917	yes	missense	OR3A1	NM_002550.2	43	1426,3125,1952	TT,TC,CC		46.2791,30.7989,45.9557	probably-damaging	125/316	3195503	5977,7029	2203	4300	6503	SO:0001583	missense	4994	exon1			AGGAATCGGTCAT	X80391	CCDS11023.1	17p13.3	2012-08-09			ENSG00000180090	ENSG00000180090		"""GPCR / Class A : Olfactory receptors"""	8282	protein-coding gene	gene with protein product						8921386, 8647456	Standard	NM_002550		Approved	OLFRA03, OR40, OR17-40	uc002fvh.1	P47881	OTTHUMG00000090642	ENST00000323404.1:c.374G>A	17.37:g.3195503C>T	ENSP00000313803:p.Arg125Gln	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	338	173	0.511834	NM_002550	Q4VB06|Q6IFM4	Missense_Mutation	SNP	ENST00000323404.1	37	CCDS11023.1	1287	0.5892857142857143	125	0.2540650406504065	207	0.5718232044198895	548	0.958041958041958	407	0.5369393139841688	C	35	5.417656	0.96092	0.307989	0.537209	ENSG00000180090	ENST00000323404	T	0.76968	-1.06	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	D	0.000626	T	0.00012	0.0000	M	0.90977	3.165	0.21933	P	0.99946813	D	0.89917	1.0	D	0.71870	0.975	T	0.38436	-0.9661	9	0.87932	D	0	-14.5448	17.7101	0.88319	0.0:1.0:0.0:0.0	rs703903;rs61014652;rs703903	125	P47881	OR3A1_HUMAN	Q	125	ENSP00000313803:R125Q	ENSP00000313803:R125Q	R	-	2	0	OR3A1	3142253	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.592000	0.61027	2.753000	0.94483	0.650000	0.86243	CGA	A|0.000;C|0.493;T|0.507	0.507	strong		0.592	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2		
GPRC6A	222545	hgsc.bcm.edu	37	6	117130544	117130544	+	Missense_Mutation	SNP	A	A	C	rs28360548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:117130544A>C	ENST00000310357.3	-	2	452	c.431T>G	c.(430-432)aTa>aGa	p.I144R	GPRC6A_ENST00000368549.3_Missense_Mutation_p.I144R|GPRC6A_ENST00000530250.1_Missense_Mutation_p.I144R	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	144			I -> R (in dbSNP:rs28360548).		calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CCCAGAACCTATGACAGCCTT	0.433													A|||	939	0.1875	0.1657	0.17	5008	,	,		19939	0.0218		0.33	False		,,,				2504	0.2536				p.I144R		Atlas-SNP	.											.	GPRC6A	152	.	0			c.T431G						PASS	.	A	ARG/ILE	822,3584	325.9+/-299.3	86,650,1467	93.0	89.0	90.0		431	4.9	1.0	6	dbSNP_125	90	2897,5703	454.1+/-363.4	486,1925,1889	yes	missense	GPRC6A	NM_148963.2	97	572,2575,3356	CC,CA,AA		33.686,18.6564,28.5945	probably-damaging	144/927	117130544	3719,9287	2203	4300	6503	SO:0001583	missense	222545	exon2			GAACCTATGACAG	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.431T>G	6.37:g.117130544A>C	ENSP00000309493:p.Ile144Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	109	71	0.651376	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	402	0.18406593406593408	78	0.15853658536585366	66	0.18232044198895028	13	0.022727272727272728	245	0.3232189973614776	A	18.19	3.568339	0.65651	0.186564	0.33686	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.87179	-2.22;-2.22;-2.22	4.86	4.86	0.63082	Extracellular ligand-binding receptor (1);	0.063736	0.56097	D	0.000023	D	0.91828	0.7414	M	0.88775	2.98	0.27601	P	0.9489647999999999	D;D;D	0.69078	0.997;0.996;0.996	D;D;D	0.69479	0.949;0.931;0.964	D	0.93396	0.6756	9	0.87932	D	0	.	9.4609	0.38785	0.9097:0.0:0.0903:0.0	rs28360548	144;144;144	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	R	144	ENSP00000309493:I144R;ENSP00000357537:I144R;ENSP00000433465:I144R	ENSP00000309493:I144R	I	-	2	0	GPRC6A	117237237	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.904000	0.56325	2.047000	0.60756	0.477000	0.44152	ATA	A|0.747;C|0.253	0.253	strong		0.433	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
INADL	10207	hgsc.bcm.edu	37	1	62594593	62594593	+	Silent	SNP	C	C	T	rs2476194	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:62594593C>T	ENST00000371158.2	+	41	5361	c.5247C>T	c.(5245-5247)aaC>aaT	p.N1749N		NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1749	PDZ 10. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TGCTGAAGAACGCCTACGGGC	0.507													C|||	1657	0.330871	0.1362	0.4741	5008	,	,		17636	0.0754		0.5358	False		,,,				2504	0.545				p.N1749N		Atlas-SNP	.											.	INADL	179	.	0			c.C5247T						PASS	.	C		687,3329		74,539,1395	128.0	126.0	127.0		5247	-0.5	1.0	1	dbSNP_100	127	4591,3781		1237,2117,832	no	coding-synonymous	INADL	NM_176877.2		1311,2656,2227	TT,TC,CC		45.1624,17.1066,42.6057		1749/1802	62594593	5278,7110	2008	4186	6194	SO:0001819	synonymous_variant	10207	exon41			GAAGAACGCCTAC	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.5247C>T	1.37:g.62594593C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			C|0.648;T|0.352	0.352	strong		0.507	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
MYPN	84665	hgsc.bcm.edu	37	10	69926334	69926334	+	Missense_Mutation	SNP	C	C	G	rs10823148	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:69926334C>G	ENST00000358913.5	+	10	2372	c.1884C>G	c.(1882-1884)ttC>ttG	p.F628L	MYPN_ENST00000354393.2_Missense_Mutation_p.F353L|MYPN_ENST00000540630.1_Missense_Mutation_p.F628L	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	628			F -> L (in dbSNP:rs10823148). {ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CCGATTCTTTCCAGGAGAGGT	0.537													C|||	1585	0.316494	0.1104	0.4049	5008	,	,		16523	0.2163		0.5099	False		,,,				2504	0.4366				p.F628L		Atlas-SNP	.											.	MYPN	189	.	0			c.C1884G						PASS	.	C	LEU/PHE	768,3638	311.9+/-292.3	73,622,1508	71.0	66.0	68.0		1884	4.3	1.0	10	dbSNP_120	68	4382,4218	582.8+/-391.5	1167,2048,1085	yes	missense	MYPN	NM_032578.2	22	1240,2670,2593	GG,GC,CC		49.0465,17.4308,39.5971	benign	628/1321	69926334	5150,7856	2203	4300	6503	SO:0001583	missense	84665	exon10			TTCTTTCCAGGAG	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1884C>G	10.37:g.69926334C>G	ENSP00000351790:p.Phe628Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	736	0.336996336996337	64	0.13008130081300814	157	0.43370165745856354	128	0.22377622377622378	387	0.5105540897097626	C	0.738	-0.777515	0.02929	0.174308	0.509535	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.55588	0.51;0.57;0.55	5.29	4.3	0.51218	.	0.087877	0.49305	D	0.000149	T	0.00012	0.0000	N	0.22421	0.69	0.29149	P	0.878514	B;B;B	0.12013	0.005;0.002;0.001	B;B;B	0.13407	0.009;0.006;0.003	T	0.45071	-0.9286	8	.	.	.	.	7.6139	0.28145	0.129:0.6838:0.1132:0.0741	rs10823148;rs17457985;rs52812887;rs10823148	628;353;628	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	L	353;353;628;628	ENSP00000346369:F353L;ENSP00000351790:F628L;ENSP00000441668:F628L	.	F	+	3	2	MYPN	69596340	1.000000	0.71417	0.994000	0.49952	0.087000	0.18053	2.051000	0.41307	2.455000	0.83008	0.655000	0.94253	TTC	C|0.625;G|0.374	0.374	strong		0.537	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
MUC4	4585	hgsc.bcm.edu	37	3	195510910	195510910	+	Missense_Mutation	SNP	G	G	T	rs576459717		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195510910G>T	ENST00000463781.3	-	2	8000	c.7541C>A	c.(7540-7542)cCt>cAt	p.P2514H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2514H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTCGGTGACAGGTAGAGGGGT	0.562																																					p.P2514H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C7541A						scavenged	.						90.0	72.0	77.0					3																	195510910		661	1591	2252	SO:0001583	missense	4585	exon2			GTGACAGGTAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7541C>A	3.37:g.195510910G>T	ENSP00000417498:p.Pro2514His	Somatic	327	3	0.00917431		WXS	Illumina HiSeq	Phase_I	616	45	0.0730519	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.532	0.466443	0.12402	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.3;1.37	.	.	.	.	.	.	.	.	T	0.29524	0.0736	N	0.19112	0.55	0.20489	N	0.999893	D	0.54964	0.969	P	0.52710	0.707	T	0.18840	-1.0324	7	.	.	.	.	6.8646	0.24086	1.0E-4:0.0:0.9999:0.0	.	2514	E7ESK3	.	H	2514	ENSP00000417498:P2514H;ENSP00000420243:P2514H	.	P	-	2	0	MUC4	196995305	0.082000	0.21442	0.000000	0.03702	0.000000	0.00434	0.551000	0.23361	-0.000000	0.14550	0.000000	0.15137	CCT	.	.	none		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MSGN1	343930	hgsc.bcm.edu	37	2	17998025	17998025	+	Missense_Mutation	SNP	A	A	T	rs34069439	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:17998025A>T	ENST00000281047.3	+	1	263	c.240A>T	c.(238-240)gaA>gaT	p.E80D		NM_001105569.1	NP_001099039.1	A6NI15	MSGN1_HUMAN	mesogenin 1	80			E -> D (in dbSNP:rs34069439).		cell differentiation (GO:0030154)|segment specification (GO:0007379)|somitogenesis (GO:0001756)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGGGCAGCGAAGGCTGCAGTG	0.642													T|||	1612	0.321885	0.2814	0.3559	5008	,	,		14630	0.0268		0.5398	False		,,,				2504	0.4325				p.E80D	Melanoma(127;325 1712 14802 40657 49130)	Atlas-SNP	.											.	MSGN1	39	.	0			c.A240T						PASS	.	T	ASP/GLU	1369,2541		242,885,828	39.0	44.0	42.0		240	2.3	0.0	2	dbSNP_126	42	4812,3446		1425,1962,742	yes	missense	MSGN1	NM_001105569.1	45	1667,2847,1570	TT,TA,AA		41.7292,35.0128,49.2028	benign	80/194	17998025	6181,5987	1955	4129	6084	SO:0001583	missense	343930	exon1			CAGCGAAGGCTGC		CCDS42657.1	2p24.2	2007-07-23			ENSG00000151379	ENSG00000151379			14907	protein-coding gene	gene with protein product	"""paraxial mesogenin"""	612209				10837126	Standard	NM_001105569		Approved	pMesogenin1	uc010yjt.2	A6NI15	OTTHUMG00000159089	ENST00000281047.3:c.240A>T	2.37:g.17998025A>T	ENSP00000281047:p.Glu80Asp	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_001105569		Missense_Mutation	SNP	ENST00000281047.3	37	CCDS42657.1	720	0.32967032967032966	146	0.2967479674796748	148	0.4088397790055249	16	0.027972027972027972	410	0.5408970976253298	T	0.004	-2.296235	0.00245	0.350128	0.582708	ENSG00000151379	ENST00000281047	T	0.16324	2.35	4.75	2.33	0.28932	.	0.503112	0.16816	N	0.198368	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37430	-0.9706	9	0.11794	T	0.64	-4.0966	0.8901	0.01252	0.1587:0.1728:0.1656:0.5029	rs34069439;rs58519973	80	A6NI15	MSGN1_HUMAN	D	80	ENSP00000281047:E80D	ENSP00000281047:E80D	E	+	3	2	MSGN1	17861506	0.118000	0.22208	0.013000	0.15412	0.169000	0.22640	-0.049000	0.11924	0.087000	0.17167	-0.257000	0.10917	GAA	A|0.586;T|0.414	0.414	strong		0.642	MSGN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353253.1	XM_292850	
CLIP2	7461	hgsc.bcm.edu	37	7	73753250	73753250	+	Silent	SNP	T	T	C	rs539518	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73753250T>C	ENST00000395060.1	+	2	594	c.594T>C	c.(592-594)acT>acC	p.T198T	CLIP2_ENST00000223398.6_Silent_p.T198T|CLIP2_ENST00000361545.5_Silent_p.T198T			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	198						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						CCGTGAAGACTGGCAACGAGT	0.662													C|||	2712	0.541534	0.3464	0.5778	5008	,	,		14448	0.494		0.7584	False		,,,				2504	0.6053				p.T198T		Atlas-SNP	.											.	CLIP2	134	.	0			c.T594C						PASS	.	C	,	1728,2558		371,986,786	33.0	33.0	33.0		594,594	-8.8	0.7	7	dbSNP_83	33	6246,2146		2395,1456,345	no	coding-synonymous,coding-synonymous	CLIP2	NM_003388.4,NM_032421.2	,	2766,2442,1131	CC,CT,TT		25.572,40.3173,37.1036	,	198/1047,198/1012	73753250	7974,4704	2143	4196	6339	SO:0001819	synonymous_variant	7461	exon3			GAAGACTGGCAAC	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"""cytoplasmic linker 2"", ""Williams-Beuren syndrome chromosome region 3"""	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.594T>C	7.37:g.73753250T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_032421	O14527|O43611	Silent	SNP	ENST00000395060.1	37	CCDS5569.1																																																																																			T|0.406;C|0.594	0.594	strong		0.662	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388	
TRPM6	140803	hgsc.bcm.edu	37	9	77367203	77367203	+	Missense_Mutation	SNP	T	T	C	rs55679040	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:77367203T>C	ENST00000360774.1	-	29	5225	c.4988A>G	c.(4987-4989)cAg>cGg	p.Q1663R	TRPM6_ENST00000449912.2_Missense_Mutation_p.Q1658R|TRPM6_ENST00000376872.3_Missense_Mutation_p.Q614R|TRPM6_ENST00000451710.3_Missense_Mutation_p.Q1663R|TRPM6_ENST00000361255.3_Missense_Mutation_p.Q1658R|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.Q1663R	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1663			Q -> R (no effect on function or cell membrane localization; dbSNP:rs55679040). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23942199}.		calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						CTCTTGAGACTGCTTTAGGTA	0.338													T|||	14	0.00279553	0.0	0.0043	5008	,	,		17114	0.0		0.008	False		,,,				2504	0.0031				p.Q1663R		Atlas-SNP	.											.	TRPM6	377	.	0			c.A4988G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN	7,4395	14.3+/-33.2	0,7,2194	103.0	97.0	99.0		4973,4973,4988	3.5	0.9	9	dbSNP_129	99	90,8500	48.9+/-108.6	1,88,4206	yes	missense,missense,missense	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	43,43,43	1,95,6400	CC,CT,TT		1.0477,0.159,0.7466	possibly-damaging,possibly-damaging,possibly-damaging	1658/2018,1658/2018,1663/2023	77367203	97,12895	2201	4295	6496	SO:0001583	missense	140803	exon29			TGAGACTGCTTTA	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.4988A>G	9.37:g.77367203T>C	ENSP00000354006:p.Gln1663Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	T	18.23	3.577758	0.65878	0.00159	0.010477	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000449912;ENST00000361255;ENST00000376864	T;T;T;T;T;T	0.54866	0.65;0.65;0.61;0.65;0.65;0.55	5.84	3.53	0.40419	.	0.472549	0.22873	N	0.054606	T	0.52386	0.1731	M	0.66939	2.045	0.80722	D	1	D;P;P;P	0.57899	0.981;0.501;0.634;0.634	P;B;B;B	0.53593	0.73;0.107;0.215;0.215	T	0.58205	-0.7677	10	0.72032	D	0.01	.	10.0496	0.42208	0.0:0.1353:0.0:0.8647	rs55679040;rs61737749	614;1663;1658;1658	Q9BX84-5;Q9BX84;Q9BX84-3;Q9BX84-2	.;TRPM6_HUMAN;.;.	R	1663;1663;614;1658;1658;1663	ENSP00000354006:Q1663R;ENSP00000407341:Q1663R;ENSP00000366068:Q614R;ENSP00000396672:Q1658R;ENSP00000354962:Q1658R;ENSP00000366060:Q1663R	ENSP00000354006:Q1663R	Q	-	2	0	TRPM6	76557023	0.951000	0.32395	0.876000	0.34364	0.959000	0.62525	1.435000	0.34969	0.488000	0.27723	0.528000	0.53228	CAG	T|0.994;C|0.006	0.006	strong		0.338	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
TMEM170B	100113407	hgsc.bcm.edu	37	6	11538534	11538534	+	Silent	SNP	C	C	T	rs821443	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:11538534C>T	ENST00000379426.1	+	1	24	c.24C>T	c.(22-24)caC>caT	p.H8H	TMEM170B_ENST00000543875.1_Silent_p.H8H	NM_001100829.1	NP_001094299.1	Q5T4T1	T170B_HUMAN	transmembrane protein 170B	8						integral component of membrane (GO:0016021)				large_intestine(3)|lung(5)	8						GGGGCGACCACTCCATGATCA	0.741													C|||	1196	0.238818	0.0492	0.1571	5008	,	,		9205	0.2361		0.2813	False		,,,				2504	0.5123				p.H8H		Atlas-SNP	.											.	TMEM170B	9	.	0			c.C24T						PASS	.	C		279,3599		15,249,1675	19.0	25.0	23.0		24	3.9	1.0	6	dbSNP_86	23	2047,6137		282,1483,2327	no	coding-synonymous	TMEM170B	NM_001100829.1		297,1732,4002	TT,TC,CC		25.0122,7.1944,19.2837		8/133	11538534	2326,9736	1939	4092	6031	SO:0001819	synonymous_variant	100113407	exon1			CGACCACTCCATG		CCDS43425.1	6p24.1	2008-08-08			ENSG00000205269	ENSG00000205269			34244	protein-coding gene	gene with protein product							Standard	NM_001100829		Approved		uc010jpa.4	Q5T4T1	OTTHUMG00000014259	ENST00000379426.1:c.24C>T	6.37:g.11538534C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_001100829		Silent	SNP	ENST00000379426.1	37	CCDS43425.1																																																																																			C|0.787;T|0.213	0.213	strong		0.741	TMEM170B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000039862.1	NM_001100829	
GPRC6A	222545	hgsc.bcm.edu	37	6	117114290	117114290	+	Missense_Mutation	SNP	A	A	G	rs35937022	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:117114290A>G	ENST00000310357.3	-	6	1817	c.1796T>C	c.(1795-1797)aTt>aCt	p.I599T	GPRC6A_ENST00000368549.3_Missense_Mutation_p.I528T|GPRC6A_ENST00000530250.1_Missense_Mutation_p.I424T	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	599			I -> T (in dbSNP:rs35937022).		calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TAGGGAGAGAATCAGGAGTAG	0.433													A|||	661	0.131989	0.0136	0.1556	5008	,	,		19254	0.0218		0.3042	False		,,,				2504	0.2117				p.I599T		Atlas-SNP	.											.	GPRC6A	152	.	0			c.T1796C						PASS	.	A	THR/ILE	270,4136	151.4+/-185.3	22,226,1955	107.0	103.0	104.0		1796	2.4	1.0	6	dbSNP_126	104	2652,5948	427.6+/-355.6	408,1836,2056	yes	missense	GPRC6A	NM_148963.2	89	430,2062,4011	GG,GA,AA		30.8372,6.128,22.4666	benign	599/927	117114290	2922,10084	2203	4300	6503	SO:0001583	missense	222545	exon6			GAGAGAATCAGGA	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1796T>C	6.37:g.117114290A>G	ENSP00000309493:p.Ile599Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	304	0.1391941391941392	7	0.014227642276422764	59	0.16298342541436464	13	0.022727272727272728	225	0.29683377308707126	A	0.267	-0.995430	0.02145	0.06128	0.308372	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.90844	-2.51;-2.74;-2.73	5.17	2.37	0.29283	GPCR, family 3, C-terminal (1);	1.162580	0.06303	N	0.701252	T	0.59609	0.2206	N	0.08118	0	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.002	B;B;B	0.10450	0.002;0.005;0.001	T	0.44034	-0.9354	9	0.12430	T	0.62	.	4.4929	0.11822	0.2894:0.4026:0.308:0.0	rs35937022	528;424;599	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	T	599;528;424	ENSP00000309493:I599T;ENSP00000357537:I528T;ENSP00000433465:I424T	ENSP00000309493:I599T	I	-	2	0	GPRC6A	117220983	0.005000	0.15991	0.955000	0.39395	0.008000	0.06430	1.768000	0.38511	0.315000	0.23110	-1.182000	0.01712	ATT	A|0.803;G|0.197	0.197	strong		0.433	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
C6	729	hgsc.bcm.edu	37	5	41160293	41160293	+	Silent	SNP	A	A	G	rs62361567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:41160293A>G	ENST00000263413.3	-	11	1899	c.1635T>C	c.(1633-1635)agT>agC	p.S545S	C6_ENST00000337836.5_Silent_p.S545S|C6_ENST00000475349.1_5'Flank	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	545	EGF-like.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				CATAGGTGCCACTCTGACACA	0.468													A|||	56	0.0111821	0.0038	0.0187	5008	,	,		20151	0.0		0.0358	False		,,,				2504	0.002				p.S545S		Atlas-SNP	.											.	C6	197	.	0			c.T1635C						PASS	.	A	,	23,4383	31.7+/-61.6	0,23,2180	160.0	152.0	154.0		1635,1635	-12.1	0.0	5	dbSNP_129	154	299,8301	109.2+/-169.8	5,289,4006	no	coding-synonymous,coding-synonymous	C6	NM_000065.2,NM_001115131.1	,	5,312,6186	GG,GA,AA		3.4767,0.522,2.4758	,	545/935,545/935	41160293	322,12684	2203	4300	6503	SO:0001819	synonymous_variant	729	exon11			GGTGCCACTCTGA	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1635T>C	5.37:g.41160293A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	204	78	0.382353	NM_001115131		Silent	SNP	ENST00000263413.3	37	CCDS3936.1																																																																																			A|0.978;G|0.022	0.022	strong		0.468	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
ERCC6	2074	hgsc.bcm.edu	37	10	50740876	50740876	+	Silent	SNP	G	G	C	rs2228524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50740876G>C	ENST00000355832.5	-	2	213	c.135C>G	c.(133-135)ctC>ctG	p.L45L	PGBD3_ENST00000603152.1_Silent_p.L45L|ERCC6-PGBD3_ENST00000447839.2_Silent_p.L45L|ERCC6-PGBD3_ENST00000515869.1_Silent_p.L45L	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	45					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AACGAAAGGAGAGGTACTCCT	0.552								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	2959	0.590855	0.3336	0.6657	5008	,	,		19189	0.5079		0.7346	False		,,,				2504	0.8231				p.T45T		Atlas-SNP	.											.	ERCC6	162	.	0			c.G135G						PASS	.	C		1782,2624	643.7+/-397.9	374,1034,795	153.0	130.0	138.0		135	-1.4	0.0	10	dbSNP_98	138	6380,2220	377.4+/-338.5	2379,1622,299	no	coding-synonymous	ERCC6	NM_000124.2		2753,2656,1094	CC,CG,GG		25.814,40.4448,37.2443		45/1494	50740876	8162,4844	2203	4300	6503	SO:0001819	synonymous_variant	2074	exon2			AAAGGAGAGGTAC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.135C>G	10.37:g.50740876G>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			G|0.381;C|0.619	0.619	strong		0.552	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
VARS2	57176	hgsc.bcm.edu	37	6	30893728	30893728	+	Silent	SNP	C	C	T	rs1043483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30893728C>T	ENST00000321897.5	+	28	3665	c.3033C>T	c.(3031-3033)gaC>gaT	p.D1011D	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Silent_p.D871D|VARS2_ENST00000541562.1_Silent_p.D1041D|VARS2_ENST00000416670.2_Silent_p.D1011D			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	1011					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						AGCAGCTTGACAGCCTCACAG	0.607													T|||	3545	0.707867	0.4622	0.696	5008	,	,		18367	0.8671		0.7137	False		,,,				2504	0.8783				p.D1041D		Atlas-SNP	.											.	VARS2	60	.	0			c.C3123T						PASS	.	T	,,	1538,1480		397,744,368	71.0	69.0	70.0		2613,3123,3033	0.7	0.3	6	dbSNP_86	70	3971,1447		1447,1077,185	no	coding-synonymous,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	1844,1821,553	TT,TC,CC		26.7073,49.0391,34.6965	,,	871/924,1041/1094,1011/1064	30893728	5509,2927	1509	2709	4218	SO:0001819	synonymous_variant	57176	exon29			GCTTGACAGCCTC	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.3033C>T	6.37:g.30893728C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			C|0.324;T|0.676	0.676	strong		0.607	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
MAGED2	10916	hgsc.bcm.edu	37	X	54838077	54838077	+	Silent	SNP	C	C	T	rs2071932	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:54838077C>T	ENST00000375068.1	+	6	1214	c.981C>T	c.(979-981)tcC>tcT	p.S327S	MAGED2_ENST00000375062.4_Silent_p.S242S|MAGED2_ENST00000375053.2_Silent_p.S327S|MAGED2_ENST00000347546.4_Silent_p.S309S|MAGED2_ENST00000218439.4_Silent_p.S327S|MAGED2_ENST00000396224.1_Silent_p.S327S|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000375060.1_Silent_p.S242S|MAGED2_ENST00000375058.1_Silent_p.S327S			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	327	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					membrane (GO:0016020)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						CAGGCTATTCCTTGGAGAAGG	0.502													C|||	1622	0.429669	0.2943	0.2997	3775	,	,		16373	0.4494		0.2992	False		,,,				2504	0.2771				p.S327S		Atlas-SNP	.											.	MAGED2	74	.	0			c.C981T						PASS	.	C	,,	1381,2454		205,769,202,658,369	57.0	47.0	50.0		981,981,981	0.8	1.0	X	dbSNP_96	50	2273,4455		253,1099,668,1076,1204	no	coding-synonymous,coding-synonymous,coding-synonymous	MAGED2	NM_014599.4,NM_177433.1,NM_201222.1	,,	458,1868,870,1734,1573	TT,TC,T,CC,C		33.7842,36.0104,34.5924	,,	327/607,327/607,327/607	54838077	3654,6909	2203	4300	6503	SO:0001819	synonymous_variant	10916	exon6			CTATTCCTTGGAG	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated protein"", ""breast cancer associated gene 1"", ""melanoma-associated antigen D2"", ""hepatocellular carcinoma-associated protein HCA10"""	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.981C>T	X.37:g.54838077C>T		Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Silent	SNP	ENST00000375068.1	37	CCDS14362.1																																																																																			C|0.586;0|0.015	.	strong		0.502	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599	
C1orf106	55765	hgsc.bcm.edu	37	1	200881172	200881172	+	Silent	SNP	C	C	A	rs296521	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:200881172C>A	ENST00000367342.4	+	9	2006	c.1806C>A	c.(1804-1806)cgC>cgA	p.R602R	C1orf106_ENST00000413687.2_Silent_p.R517R|C1orf106_ENST00000465162.1_3'UTR	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	602										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						GGAGCACCCGCCCCCACTCAC	0.716													C|||	1632	0.325879	0.0923	0.5432	5008	,	,		13939	0.2688		0.5298	False		,,,				2504	0.3364				p.R616R		Atlas-SNP	.											.	C1orf106	59	.	0			c.C1848A						PASS	.						2.0	4.0	3.0					1																	200881172		1537	3096	4633	SO:0001819	synonymous_variant	55765	exon9			CACCCGCCCCCAC	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.1806C>A	1.37:g.200881172C>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	24	8	0.333333	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Silent	SNP	ENST00000367342.4	37																																																																																				C|0.250;A|0.750	0.750	weak		0.716	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50659598	50659598	+	Missense_Mutation	SNP	C	C	T	rs149231425	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50659598C>T	ENST00000248846.5	-	16	3294	c.3190G>A	c.(3190-3192)Ggg>Agg	p.G1064R	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Missense_Mutation_p.G1064R			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1064	9 X 27 AA tandem repeats.				G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACATTCTCCCCGACCCTGATG	0.607													C|||	66	0.0131789	0.0015	0.0259	5008	,	,		23347	0.0		0.0408	False		,,,				2504	0.0051				p.G1064R		Atlas-SNP	.											TUBGCP6,NS,carcinoma,0,1	TUBGCP6	132	1	0			c.G3190A						PASS	.	C	ARG/GLY	24,4382	31.7+/-61.6	0,24,2179	135.0	137.0	136.0		3190	3.1	0.9	22	dbSNP_134	136	240,8360	97.0+/-158.7	4,232,4064	no	missense	TUBGCP6	NM_020461.3	125	4,256,6243	TT,TC,CC		2.7907,0.5447,2.0298	probably-damaging	1064/1820	50659598	264,12742	2203	4300	6503	SO:0001583	missense	85378	exon16			TCTCCCCGACCCT	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.3190G>A	22.37:g.50659598C>T	ENSP00000248846:p.Gly1064Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	162	105	0.648148	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	36	0.016483516483516484	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	21	0.027704485488126648	C	18.10	3.549414	0.65311	0.005447	0.027907	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.20069	2.46;2.1	4.2	3.07	0.35406	.	0.000000	0.85682	D	0.000000	T	0.12603	0.0306	L	0.59436	1.845	0.50171	D	0.999851	D;P;D	0.89917	1.0;0.948;1.0	D;P;D	0.91635	0.999;0.597;0.999	T	0.01894	-1.1252	10	0.45353	T	0.12	.	13.7504	0.62904	0.0:0.8442:0.1558:0.0	.	1056;1064;1064	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	R	1064	ENSP00000248846:G1064R;ENSP00000397387:G1064R	ENSP00000248846:G1064R	G	-	1	0	TUBGCP6	49001725	0.730000	0.28100	0.882000	0.34594	0.145000	0.21501	3.255000	0.51484	2.283000	0.76528	0.655000	0.94253	GGG	C|0.981;T|0.019	0.019	strong		0.607	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
WDR19	57728	hgsc.bcm.edu	37	4	39216221	39216221	+	Splice_Site	SNP	C	C	T	rs2167494	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:39216221C>T	ENST00000399820.3	+	10	1045	c.891C>T	c.(889-891)tgC>tgT	p.C297C	WDR19_ENST00000506503.1_Splice_Site_p.C297C|WDR19_ENST00000288634.7_Splice_Site_p.C137C	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	297					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						TGTTTTTCAGCATTAAAATCC	0.269													C|||	1301	0.259784	0.2973	0.2406	5008	,	,		14844	0.1597		0.3231	False		,,,				2504	0.2607				p.C297C		Atlas-SNP	.											.	WDR19	96	.	0			c.C891T						PASS	.	C		1034,2546		162,710,918	42.0	40.0	41.0		891	2.9	1.0	4	dbSNP_96	41	2522,5596		376,1770,1913	yes	coding-synonymous-near-splice	WDR19	NM_025132.3		538,2480,2831	TT,TC,CC		31.0668,28.8827,30.3984		297/1343	39216221	3556,8142	1790	4059	5849	SO:0001630	splice_region_variant	57728	exon10			TTTCAGCATTAAA	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.891-1C>T	4.37:g.39216221C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	37	CCDS47042.1																																																																																			C|0.721;T|0.279	0.279	strong		0.269	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		Silent
SH3BP5	9467	hgsc.bcm.edu	37	3	15298590	15298590	+	Missense_Mutation	SNP	C	C	T	rs149397155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:15298590C>T	ENST00000383791.3	-	8	1140	c.920G>A	c.(919-921)tGt>tAt	p.C307Y	SH3BP5_ENST00000408919.3_Missense_Mutation_p.C150Y|SH3BP5-AS1_ENST00000436602.1_RNA|SH3BP5_ENST00000426925.1_Missense_Mutation_p.C150Y|SH3BP5-AS1_ENST00000413977.1_RNA|SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5_ENST00000253688.5_Missense_Mutation_p.C150Y	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	307	Ser-rich.				intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						AAAGTTGCTACAGCTGTCATC	0.527													C|||	2	0.000399361	0.0	0.0	5008	,	,		21362	0.0		0.002	False		,,,				2504	0.0				p.C307Y		Atlas-SNP	.											.	SH3BP5	32	.	0			c.G920A						PASS	.	C	TYR/CYS,TYR/CYS	1,4405	2.1+/-5.4	0,1,2202	92.0	83.0	86.0		449,920	5.7	1.0	3	dbSNP_134	86	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	SH3BP5	NM_001018009.2,NM_004844.3	194,194	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	possibly-damaging,possibly-damaging	150/299,307/456	15298590	14,12992	2203	4300	6503	SO:0001583	missense	9467	exon8			TTGCTACAGCTGT	AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"""SH3 binding protein"""	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.920G>A	3.37:g.15298590C>T	ENSP00000373301:p.Cys307Tyr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_004844	B3KQW6|Q5JWV9	Missense_Mutation	SNP	ENST00000383791.3	37	CCDS2625.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.041622	0.75732	2.27E-4	0.001512	ENSG00000131370	ENST00000383791;ENST00000426925;ENST00000253688;ENST00000408919	.	.	.	5.65	5.65	0.86999	.	0.307183	0.40554	N	0.001077	T	0.47544	0.1451	L	0.58101	1.795	0.53005	D	0.999962	P	0.48640	0.913	B	0.37601	0.254	T	0.53215	-0.8470	9	0.48119	T	0.1	-27.3345	14.2486	0.66004	0.1492:0.8508:0.0:0.0	.	307	O60239	3BP5_HUMAN	Y	307;150;150;150	.	ENSP00000253688:C150Y	C	-	2	0	SH3BP5	15273594	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	5.359000	0.66074	2.683000	0.91414	0.456000	0.33151	TGT	C|0.999;T|0.001	0.001	strong		0.527	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844	
BCAS3	54828	hgsc.bcm.edu	37	17	58786625	58786625	+	Missense_Mutation	SNP	A	A	G	rs2643103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:58786625A>G	ENST00000390652.5	+	5	291	c.260A>G	c.(259-261)aAt>aGt	p.N87S	BCAS3_ENST00000589222.1_Missense_Mutation_p.N87S|BCAS3_ENST00000407086.3_Missense_Mutation_p.N87S|BCAS3_ENST00000408905.3_Missense_Mutation_p.N87S|BCAS3_ENST00000588462.1_Missense_Mutation_p.N87S	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			AGTACTGGGAATGAACCGCCT	0.358													A|||	3750	0.748802	0.2118	0.9366	5008	,	,		19769	0.8958		0.993	False		,,,				2504	0.9387				p.N87S		Atlas-SNP	.											.	BCAS3	90	.	0			c.A260G						PASS	.	A	SER/ASN,SER/ASN	1500,2274		308,884,695	135.0	113.0	120.0		260,260	4.8	1.0	17	dbSNP_100	120	8175,57		4059,57,0	yes	missense,missense	BCAS3	NM_001099432.1,NM_017679.3	46,46	4367,941,695	GG,GA,AA		0.6924,39.7456,19.4153	benign,benign	87/929,87/914	58786625	9675,2331	1887	4116	6003	SO:0001583	missense	54828	exon5			CTGGGAATGAACC	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.260A>G	17.37:g.58786625A>G	ENSP00000375067:p.Asn87Ser	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	37	36	0.972973	NM_001099432		Missense_Mutation	SNP	ENST00000390652.5	37	CCDS45749.1	1714	0.7847985347985348	110	0.22357723577235772	342	0.9447513812154696	508	0.8881118881118881	754	0.9947229551451188	A	12.84	2.057270	0.36277	0.397456	0.993076	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000405070;ENST00000408905	T;T;T	0.05447	3.44;3.44;3.44	5.83	4.76	0.60689	.	0.190507	0.53938	N	0.000049	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	1.0	B;B;B	0.28291	0.206;0.007;0.012	B;B;B	0.24541	0.054;0.004;0.005	T	0.48186	-0.9057	9	0.06891	T	0.86	.	11.302	0.49311	0.9285:0.0:0.0715:0.0	rs2643103;rs52800243;rs61351013;rs2643103	87;87;87	Q9H6U6-7;Q9H6U6;Q9H6U6-2	.;BCAS3_HUMAN;.	S	87	ENSP00000375067:N87S;ENSP00000385323:N87S;ENSP00000386173:N87S	ENSP00000375067:N87S	N	+	2	0	BCAS3	56141407	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.655000	0.46707	1.040000	0.40099	0.482000	0.46254	AAT	A|0.222;G|0.778	0.778	strong		0.358	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	
SERPINB2	5055	hgsc.bcm.edu	37	18	61570470	61570470	+	Silent	SNP	T	T	G	rs6102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:61570470T>G	ENST00000299502.4	+	8	1259	c.1179T>G	c.(1177-1179)ccT>ccG	p.P393P	SERPINB2_ENST00000457692.1_Silent_p.P393P	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	393					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P393P(1)		NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	CAGATCATCCTTTTCTTTTTC	0.443													T|||	1091	0.217851	0.1747	0.2954	5008	,	,		19162	0.254		0.2058	False		,,,				2504	0.1963				p.P393P		Atlas-SNP	.											SERPINB2,NS,carcinoma,0,1	SERPINB2	63	1	1	Substitution - coding silent(1)	stomach(1)	c.T1179G						PASS	.	T	,	893,3513	345.1+/-308.4	79,735,1389	85.0	90.0	89.0		1179,1179	1.4	1.0	18	dbSNP_52	89	1755,6845	317.2+/-313.1	169,1417,2714	no	coding-synonymous,coding-synonymous	SERPINB2	NM_001143818.1,NM_002575.2	,	248,2152,4103	GG,GT,TT		20.407,20.2678,20.3598	,	393/416,393/416	61570470	2648,10358	2203	4300	6503	SO:0001819	synonymous_variant	5055	exon8			TCATCCTTTTCTT	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.1179T>G	18.37:g.61570470T>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	175	102	0.582857	NM_002575	Q96E96	Silent	SNP	ENST00000299502.4	37	CCDS11989.1																																																																																			T|0.779;G|0.221	0.221	strong		0.443	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
CERKL	375298	hgsc.bcm.edu	37	2	182521578	182521578	+	Silent	SNP	G	G	A	rs1473295	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:182521578G>A	ENST00000339098.5	-	1	155	c.156C>T	c.(154-156)ttC>ttT	p.F52F	CERKL_ENST00000410087.3_Silent_p.F52F|CERKL_ENST00000374969.2_Silent_p.F52F|CERKL_ENST00000479558.1_Intron|CERKL_ENST00000409440.3_Silent_p.F52F|CERKL_ENST00000374970.2_Silent_p.F52F			Q49MI3	CERKL_HUMAN	ceramide kinase-like	52					negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			TCCCGATCTCGAAGATGCCCC	0.716													G|||	2541	0.507388	0.1747	0.5216	5008	,	,		13568	0.7312		0.4433	False		,,,				2504	0.7822				p.F52F		Atlas-SNP	.											.	CERKL	138	.	0			c.C156T						PASS	.	G	,,,,	1077,3329		140,797,1266	28.0	34.0	32.0		156,156,156,156,156	1.5	1.0	2	dbSNP_88	32	4151,4447		1031,2089,1179	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CERKL	NM_001030311.2,NM_001030312.2,NM_001030313.2,NM_001160277.1,NM_201548.4	,,,,	1171,2886,2445	AA,AG,GG		48.2787,24.4439,40.203	,,,,	52/559,52/420,52/464,52/515,52/533	182521578	5228,7776	2203	4299	6502	SO:0001819	synonymous_variant	375298	exon1			GATCTCGAAGATG	BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"""retinitis pigmentosa 26 (autosomal recessive)"""	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.156C>T	2.37:g.182521578G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001160277	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Silent	SNP	ENST00000339098.5	37	CCDS42789.1																																																																																			G|0.565;A|0.435	0.435	strong		0.716	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1		
DNAH2	146754	hgsc.bcm.edu	37	17	7735063	7735063	+	Missense_Mutation	SNP	T	T	G	rs57985356	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7735063T>G	ENST00000572933.1	+	82	14156	c.12696T>G	c.(12694-12696)ttT>ttG	p.F4232L	DNAH2_ENST00000389173.2_Missense_Mutation_p.F4232L			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	4232					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				ATTGCATCTTTGATGCCCATG	0.498													T|||	755	0.150759	0.0045	0.268	5008	,	,		20127	0.2837		0.0626	False		,,,				2504	0.2188				p.F4232L		Atlas-SNP	.											.	DNAH2	498	.	0			c.T12696G						PASS	.	T	LEU/PHE	122,4284	89.7+/-128.4	3,116,2084	164.0	140.0	148.0		12696	4.3	1.0	17	dbSNP_129	148	728,7872	177.0+/-226.7	29,670,3601	yes	missense	DNAH2	NM_020877.2	22	32,786,5685	GG,GT,TT		8.4651,2.769,6.5354	benign	4232/4428	7735063	850,12156	2203	4300	6503	SO:0001583	missense	146754	exon81			CATCTTTGATGCC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.12696T>G	17.37:g.7735063T>G	ENSP00000458355:p.Phe4232Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	146	70	0.479452	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	262	0.11996336996336997	5	0.01016260162601626	76	0.20994475138121546	137	0.2395104895104895	44	0.05804749340369393	T	9.971	1.225367	0.22457	0.02769	0.084651	ENSG00000183914	ENST00000389173	T	0.07908	3.15	5.37	4.27	0.50696	Dynein heavy chain (1);	0.127433	0.53938	D	0.000041	T	0.00012	0.0000	L	0.28458	0.855	0.09310	P	1.0	B	0.10296	0.003	B	0.14023	0.01	T	0.47249	-0.9132	8	.	.	.	.	9.7193	0.40293	0.0:0.086:0.0:0.914	rs57985356;rs61747293	4232	Q9P225	DYH2_HUMAN	L	4232	ENSP00000373825:F4232L	.	F	+	3	2	DNAH2	7675788	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.018000	0.40991	1.038000	0.40049	0.533000	0.62120	TTT	T|0.921;G|0.079	0.079	strong		0.498	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
DNALI1	7802	hgsc.bcm.edu	37	1	38023316	38023316	+	Missense_Mutation	SNP	C	C	T	rs11749	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:38023316C>T	ENST00000296218.7	+	2	270	c.260C>T	c.(259-261)gCa>gTa	p.A87V	DNALI1_ENST00000541606.1_5'UTR	NM_003462.3	NP_003453.2	O14645	IDLC_HUMAN	dynein, axonemal, light intermediate chain 1	65					cellular component movement (GO:0006928)|metabolic process (GO:0008152)|single fertilization (GO:0007338)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|filopodium (GO:0030175)	microtubule motor activity (GO:0003777)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ACAAAGCAGGCAGAAGAAATC	0.537													C|||	1023	0.204273	0.0681	0.2046	5008	,	,		20615	0.3502		0.2535	False		,,,				2504	0.1871				p.A87V		Atlas-SNP	.											.	DNALI1	25	.	0			c.C260T						PASS	.	C	VAL/ALA	427,3979	208.8+/-229.8	19,389,1795	176.0	170.0	172.0		260	5.8	1.0	1	dbSNP_52	172	2211,6389	376.5+/-338.2	297,1617,2386	yes	missense	DNALI1	NM_003462.3	64	316,2006,4181	TT,TC,CC		25.7093,9.6913,20.2829	possibly-damaging	87/281	38023316	2638,10368	2203	4300	6503	SO:0001583	missense	7802	exon2			AGCAGGCAGAAGA	AF006386	CCDS420.1	1p35.1	2008-07-18	2006-09-04		ENSG00000163879	ENSG00000163879		"""Axonemal dyneins"""	14353	protein-coding gene	gene with protein product	"""inner dynein arm, homolog of clamydomonas"", ""dJ423B22.5 (axonemal dynein light chain (hp28))"""	602135	"""dynein, axonemal, light intermediate polypeptide 1"""			9284741	Standard	NM_003462		Approved	P28, hp28, dJ423B22.5	uc001cbj.3	O14645	OTTHUMG00000004222	ENST00000296218.7:c.260C>T	1.37:g.38023316C>T	ENSP00000296218:p.Ala87Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_003462	A8K387|B4DHN6|Q05BL9|Q5HYE2|Q5TGH0|Q7L0I5	Missense_Mutation	SNP	ENST00000296218.7	37	CCDS420.1	522	0.23901098901098902	34	0.06910569105691057	83	0.2292817679558011	216	0.3776223776223776	189	0.24934036939313983	C	22.9	4.346647	0.82022	0.096913	0.257093	ENSG00000163879	ENST00000296218	T	0.42513	0.97	5.76	5.76	0.90799	.	0.313134	0.38663	N	0.001610	T	0.00012	0.0000	N	0.12182	0.205	0.09310	P	1.0	P	0.41420	0.749	P	0.45753	0.492	T	0.47812	-0.9088	9	0.27082	T	0.32	-6.8937	17.4499	0.87589	0.0:1.0:0.0:0.0	rs11749;rs1047072;rs3170935;rs11540746;rs17350512;rs52811198;rs60888941;rs11540746	65	O14645	IDLC_HUMAN	V	87	ENSP00000296218:A87V	ENSP00000296218:A87V	A	+	2	0	DNALI1	37795903	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.974000	0.56852	2.725000	0.93324	0.591000	0.81541	GCA	C|0.786;G|0.000;N|0.000;T|0.213	0.213	strong		0.537	DNALI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012159.1	NM_003462	
DPCR1	135656	hgsc.bcm.edu	37	6	30916718	30916718	+	Silent	SNP	G	G	A	rs2247178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30916718G>A	ENST00000462446.1	+	2	505	c.477G>A	c.(475-477)acG>acA	p.T159T	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	159						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						AACATATAACGCCAGCACCCA	0.443													G|||	199	0.0397364	0.053	0.0159	5008	,	,		20278	0.0635		0.0149	False		,,,				2504	0.0399				p.T159T		Atlas-SNP	.											DPCR1_ENST00000462446,caecum,carcinoma,+1,2	DPCR1	99	2	0			c.G477A						PASS	.	G		54,1330		0,54,638	47.0	43.0	45.0		477	-4.3	0.0	6	dbSNP_100	45	40,3142		0,40,1551	no	coding-synonymous	DPCR1	NM_080870.3		0,94,2189	AA,AG,GG		1.2571,3.9017,2.0587		159/1394	30916718	94,4472	692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			TATAACGCCAGCA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.477G>A	6.37:g.30916718G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	37	CCDS4692.2																																																																																			G|0.972;A|0.028	0.028	strong		0.443	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
ZNF133	7692	hgsc.bcm.edu	37	20	18295730	18295730	+	Missense_Mutation	SNP	C	C	T	rs34099160	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:18295730C>T	ENST00000316358.4	+	4	332	c.235C>T	c.(235-237)Ctc>Ttc	p.L79F	ZNF133_ENST00000535822.1_5'UTR|ZNF133_ENST00000377671.3_Missense_Mutation_p.L78F|ZNF133_ENST00000401790.1_Missense_Mutation_p.L79F|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000538547.1_5'UTR|ZNF133_ENST00000396026.3_Missense_Mutation_p.L82F|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000402618.2_Missense_Mutation_p.L16F	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	79					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L78F(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						AGAGCCAGAGCTCTACCTCGA	0.527													C|||	611	0.122005	0.1551	0.1037	5008	,	,		20314	0.1409		0.0825	False		,,,				2504	0.1115				p.L78F		Atlas-SNP	.											ZNF133,NS,carcinoma,0,1	ZNF133	63	1	1	Substitution - Missense(1)	stomach(1)	c.C232T						PASS	.	C	PHE/LEU,PHE/LEU	659,3747	281.6+/-276.1	53,553,1597	90.0	85.0	86.0		232,232	1.8	0.0	20	dbSNP_126	86	681,7919	169.7+/-221.0	30,621,3649	yes	missense,missense	ZNF133	NM_001083330.1,NM_003434.4	22,22	83,1174,5246	TT,TC,CC		7.9186,14.9569,10.3029	probably-damaging,probably-damaging	78/654,78/654	18295730	1340,11666	2203	4300	6503	SO:0001583	missense	7692	exon4			CCAGAGCTCTACC	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.235C>T	20.37:g.18295730C>T	ENSP00000346090:p.Leu79Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Missense_Mutation	SNP	ENST00000316358.4	37		276	0.12637362637362637	94	0.1910569105691057	32	0.08839779005524862	87	0.1520979020979021	63	0.08311345646437995	C	2.553	-0.303546	0.05495	0.149569	0.079186	ENSG00000125846	ENST00000377671;ENST00000360010;ENST00000396026;ENST00000402618;ENST00000401790;ENST00000434018;ENST00000316358;ENST00000425686	T;T;T;T;T;T;T;T	0.08546	3.3;5.36;3.3;3.08;3.29;5.47;3.29;5.48	3.88	1.8	0.24995	.	0.851711	0.09860	N	0.746399	T	0.00012	0.0000	L	0.52573	1.65	0.53688	P	2.199999999996649E-5	B;B;B;B	0.20671	0.025;0.037;0.047;0.036	B;B;B;B	0.19666	0.011;0.011;0.017;0.026	T	0.30534	-0.9975	9	0.54805	T	0.06	-6.1499	5.9997	0.19513	0.2648:0.5487:0.1865:0.0	rs34099160	16;82;79;78	B4DIB8;B4DHU7;P52736;P52736-2	.;.;ZN133_HUMAN;.	F	78;93;82;16;79;79;79;79	ENSP00000366899:L78F;ENSP00000353105:L93F;ENSP00000400897:L82F;ENSP00000385279:L16F;ENSP00000383945:L79F;ENSP00000403835:L79F;ENSP00000346090:L79F;ENSP00000406638:L79F	ENSP00000346090:L79F	L	+	1	0	ZNF133	18243730	0.000000	0.05858	0.012000	0.15200	0.017000	0.09413	0.080000	0.14802	0.512000	0.28257	0.655000	0.94253	CTC	C|0.894;T|0.106	0.106	strong		0.527	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
PLCG2	5336	hgsc.bcm.edu	37	16	81929527	81929527	+	Silent	SNP	C	C	G	rs13333716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81929527C>G	ENST00000359376.3	+	13	1402	c.1188C>G	c.(1186-1188)acC>acG	p.T396T		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	396	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CCTTTGTTACCTCGAGGTCAG	0.547													C|||	224	0.0447284	0.0749	0.0403	5008	,	,		19718	0.002		0.0696	False		,,,				2504	0.0256				p.T396T		Atlas-SNP	.											.	PLCG2	276	.	0			c.C1188G						PASS	.	C		300,3886		11,278,1804	170.0	180.0	177.0		1188	3.0	1.0	16	dbSNP_121	177	619,7837		19,581,3628	no	coding-synonymous	PLCG2	NM_002661.3		30,859,5432	GG,GC,CC		7.3202,7.1667,7.2694		396/1266	81929527	919,11723	2093	4228	6321	SO:0001819	synonymous_variant	5336	exon13			TGTTACCTCGAGG		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1188C>G	16.37:g.81929527C>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			C|0.936;G|0.064	0.064	strong		0.547	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
UGT2B28	54490	hgsc.bcm.edu	37	4	70160277	70160277	+	Missense_Mutation	SNP	T	T	G	rs6843900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70160277T>G	ENST00000335568.5	+	6	1342	c.1340T>G	c.(1339-1341)aTa>aGa	p.I447R	UGT2B28_ENST00000511240.1_3'UTR	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	447			I -> R (in dbSNP:rs6843900). {ECO:0000269|PubMed:19054851}.		metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.I447R(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						AAATTATCAATAATTCAACAT	0.373													N|||	1888	0.376997	0.2678	0.4524	5008	,	,		13055	0.3819		0.4771	False		,,,				2504	0.363				p.I447R		Atlas-SNP	.											UGT2B28,NS,carcinoma,0,1	UGT2B28	101	1	1	Substitution - Missense(1)	stomach(1)	c.T1340G						PASS	.	G	,ARG/ILE	1389,2641		443,503,1069	39.0	46.0	44.0		,1340	2.2	0.0	4	dbSNP_116	44	4242,4208		1321,1600,1304	no	utr-3,missense	UGT2B28	NM_001207004.1,NM_053039.1	,97	1764,2103,2373	GG,GT,TT		49.7988,34.4665,45.1202	,benign	,447/530	70160277	5631,6849	2015	4225	6240	SO:0001583	missense	54490	exon6			TATCAATAATTCA	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1340T>G	4.37:g.70160277T>G	ENSP00000334276:p.Ile447Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	93	91	0.978495	NM_053039	B5BUM0|Q9BY62|Q9BY63	Missense_Mutation	SNP	ENST00000335568.5	37	CCDS3528.1	804	0.36813186813186816	101	0.20528455284552846	146	0.40331491712707185	198	0.34615384615384615	359	0.4736147757255937	-	0	-2.861548	0.00064	0.344665	0.502012	ENSG00000135226	ENST00000335568	T	0.60040	0.22	2.17	2.17	0.27698	.	0.310296	0.24102	N	0.041536	T	0.00012	0.0000	N	0.00504	-1.425	0.09310	P	0.999999892799	B	0.02656	0.0	B	0.01281	0.0	T	0.46148	-0.9212	9	0.02654	T	1	.	7.8253	0.29311	0.0:0.0:0.7495:0.2504	rs6843900;rs52813205	447	Q9BY64	UDB28_HUMAN	R	447	ENSP00000334276:I447R	ENSP00000334276:I447R	I	+	2	0	UGT2B28	70194866	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	0.223000	0.17719	0.254000	0.21573	-1.122000	0.02009	ATA	T|0.630;G|0.370	0.370	strong		0.373	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
GBP4	115361	hgsc.bcm.edu	37	1	89652094	89652094	+	Silent	SNP	G	G	A	rs1142887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89652094G>A	ENST00000355754.6	-	10	1726	c.1629C>T	c.(1627-1629)gcC>gcT	p.A543A	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	543						cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TCTCCATTTGGGCCATGTATT	0.483													G|||	1798	0.359026	0.1445	0.3141	5008	,	,		18373	0.3988		0.4881	False		,,,				2504	0.5072				p.A543A		Atlas-SNP	.											.	GBP4	89	.	0			c.C1629T						PASS	.	G		364,4038		116,132,1953	167.0	103.0	125.0		1629	-0.4	0.0	1	dbSNP_86	125	2588,5944		995,598,2673	no	coding-synonymous	GBP4	NM_052941.4		1111,730,4626	AA,AG,GG		30.3329,8.269,22.8236		543/641	89652094	2952,9982	2201	4266	6467	SO:0001819	synonymous_variant	115361	exon10			CATTTGGGCCATG	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1629C>T	1.37:g.89652094G>A		Somatic	459	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Silent	SNP	ENST00000355754.6	37	CCDS721.1																																																																																			G|0.527;A|0.473	0.473	strong		0.483	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
PRR23C	389152	hgsc.bcm.edu	37	3	138762707	138762707	+	Silent	SNP	C	C	G	rs7636403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:138762707C>G	ENST00000413199.1	-	1	1027	c.756G>C	c.(754-756)ccG>ccC	p.P252P	PRR23C_ENST00000502927.2_Silent_p.P252P|MRPS22_ENST00000495075.1_Intron	NM_001134657.1	NP_001128129.1	Q6ZRP0	PR23C_HUMAN	proline rich 23C	252	Pro-rich.									breast(2)|lung(7)|skin(2)	11						GGACCTTGCACGGAGGGCGCT	0.637													C|||	831	0.165935	0.1157	0.2637	5008	,	,		16338	0.2718		0.0835	False		,,,				2504	0.1401				p.P252P		Atlas-SNP	.											.	PRR23C	31	.	0			c.G756C						PASS	.	C		157,1227		7,143,542	23.0	25.0	24.0		756	-6.6	0.0	3	dbSNP_116	24	229,2953		16,197,1378	no	coding-synonymous	PRR23C	NM_001134657.1		23,340,1920	GG,GC,CC		7.1967,11.3439,8.4538		252/263	138762707	386,4180	692	1591	2283	SO:0001819	synonymous_variant	389152	exon1			CTTGCACGGAGGG		CCDS46924.1	3q22.3	2014-06-03				ENSG00000233701			37173	protein-coding gene	gene with protein product							Standard	NM_001134657		Approved	FLJ46210	uc011bmt.1	Q6ZRP0		ENST00000413199.1:c.756G>C	3.37:g.138762707C>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_001134657		Silent	SNP	ENST00000413199.1	37	CCDS46924.1																																																																																			C|0.849;G|0.151	0.151	strong		0.637	PRR23C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361502.1	NM_001134657	
FNDC7	163479	hgsc.bcm.edu	37	1	109268573	109268573	+	Missense_Mutation	SNP	T	T	C	rs4494160	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:109268573T>C	ENST00000370017.3	+	6	1335	c.1058T>C	c.(1057-1059)gTc>gCc	p.V353A	FNDC7_ENST00000271311.2_Missense_Mutation_p.V354A	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	353	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> A (in dbSNP:rs4494160). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		AGTGTTTTTGTCTATAACAAG	0.403													C|||	2969	0.592851	0.7958	0.5346	5008	,	,		18189	0.2341		0.7127	False		,,,				2504	0.6063				p.V353A		Atlas-SNP	.											.	FNDC7	113	.	0			c.T1058C						PASS	.	C	ALA/VAL	3481,925	352.6+/-311.8	1375,731,97	167.0	161.0	163.0		1058	6.1	1.0	1	dbSNP_111	163	6132,2468	406.4+/-348.8	2179,1774,347	yes	missense	FNDC7	NM_001144937.1	64	3554,2505,444	CC,CT,TT		28.6977,20.9941,26.088	benign	353/734	109268573	9613,3393	2203	4300	6503	SO:0001583	missense	163479	exon6			TTTTTGTCTATAA		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1058T>C	1.37:g.109268573T>C	ENSP00000359034:p.Val353Ala	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	37	CCDS44185.1	1271	0.581959706959707	383	0.7784552845528455	214	0.5911602209944752	133	0.23251748251748253	541	0.7137203166226913	C	9.867	1.197876	0.22037	0.790059	0.713023	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.18016	2.24;2.24	6.05	6.05	0.98169	Fibronectin, type III (3);	0.045897	0.85682	N	0.000000	T	0.01092	0.0036	N	0.00146	-1.995	0.47994	P	4.370000000000207E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40515	-0.9559	9	0.02654	T	1	-18.8069	15.6206	0.76802	0.0:0.9345:0.0:0.0655	rs4494160;rs17618805;rs52804563;rs57234410;rs4494160	354;353	Q5VTL7;E9PAZ5	FNDC7_HUMAN;.	A	353;354	ENSP00000359034:V353A;ENSP00000271311:V354A	ENSP00000271311:V354A	V	+	2	0	FNDC7	109070096	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.626000	0.67777	1.592000	0.50018	-0.119000	0.15052	GTC	T|0.350;C|0.650	0.650	strong		0.403	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833174	27833174	+	Silent	SNP	A	A	G	rs200981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27833174A>G	ENST00000357320.2	+	1	141	c.42A>G	c.(40-42)aaA>aaG	p.K14K		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	14						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						CTCGCGCCAAAGCCAAGACCC	0.627													G|||	614	0.122604	0.2005	0.1398	5008	,	,		15027	0.0655		0.0895	False		,,,				2504	0.0982				p.K14K		Atlas-SNP	.											.	HIST1H2AL	14	.	0			c.A42G						PASS	.	G		829,3577		78,673,1452	82.0	93.0	89.0		42	2.8	1.0	6	dbSNP_79	89	951,7649		53,845,3402	no	coding-synonymous	HIST1H2AL	NM_003511.2		131,1518,4854	GG,GA,AA		11.0581,18.8153,13.686		14/131	27833174	1780,11226	2203	4300	6503	SO:0001819	synonymous_variant	8332	exon1			CGCCAAAGCCAAG	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"""Histones / Replication-dependent"""	4730	protein-coding gene	gene with protein product		602793	"""H2A histone family, member I"", ""histone 1, H2al"""	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.42A>G	6.37:g.27833174A>G		Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	271	104	0.383764	NM_003511	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	CCDS4634.1																																																																																			.	.	weak		0.627	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511	
SNX5	27131	hgsc.bcm.edu	37	20	17950545	17950545	+	5'Flank	SNP	A	A	T	rs11551768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:17950545A>T	ENST00000377768.3	-	0	0				SNX5_ENST00000606557.1_5'Flank|SNX5_ENST00000486039.1_5'Flank|MGME1_ENST00000377704.4_Missense_Mutation_p.S15C|MGME1_ENST00000377710.5_Missense_Mutation_p.S15C|SNX5_ENST00000377759.4_5'Flank|SNX5_ENST00000481323.1_5'Flank|MGME1_ENST00000377709.1_Missense_Mutation_p.S15C|SNX5_ENST00000606602.1_5'Flank	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5						intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						GCAGCTCAGGAGTTCAAAGTT	0.408													A|||	427	0.0852636	0.0582	0.1066	5008	,	,		18875	0.0288		0.1362	False		,,,				2504	0.1125				p.S15C		Atlas-SNP	.											.	.	.	.	0			c.A43T						PASS	.	A	CYS/SER	313,4093	164.0+/-195.7	13,287,1903	59.0	60.0	60.0		43	-0.9	0.0	20	dbSNP_120	60	1129,7471	228.0+/-263.2	64,1001,3235	yes	missense	C20orf72	NM_052865.2	112	77,1288,5138	TT,TA,AA		13.1279,7.1039,11.0872	possibly-damaging	15/345	17950545	1442,11564	2203	4300	6503	SO:0001631	upstream_gene_variant	92667	exon2			CTCAGGAGTTCAA	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953		20.37:g.17950545A>T	Exception_encountered	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	49	0.569767	NM_052865	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	173	0.07921245421245421	25	0.0508130081300813	43	0.11878453038674033	17	0.02972027972027972	88	0.11609498680738786	A	11.12	1.544737	0.27563	0.071039	0.131279	ENSG00000125871	ENST00000377710;ENST00000377709;ENST00000377704	T;T;T	0.51325	0.79;0.74;0.71	5.67	-0.887	0.10587	.	1.937770	0.01666	N	0.025351	T	0.00608	0.0020	L	0.44542	1.39	0.09310	N	1	D	0.59357	0.985	P	0.46796	0.527	T	0.21075	-1.0256	10	0.62326	D	0.03	2.34	9.91	0.41399	0.2479:0.5412:0.0:0.2109	rs11551768;rs28970272	15	Q9BQP7	CT072_HUMAN	C	15	ENSP00000366939:S15C;ENSP00000366938:S15C;ENSP00000366933:S15C	ENSP00000366933:S15C	S	+	1	0	C20orf72	17898545	0.000000	0.05858	0.000000	0.03702	0.126000	0.20510	0.776000	0.26704	-0.475000	0.06852	-0.488000	0.04728	AGT	A|0.900;T|0.100	0.100	strong		0.408	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
C20orf203	284805	hgsc.bcm.edu	37	20	31238627	31238627	+	lincRNA	SNP	C	C	T	rs7272020	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:31238627C>T	ENST00000608990.1	-	0	764							Q8NBC4	CT203_HUMAN	chromosome 20 open reading frame 203							cytoplasm (GO:0005737)											TCCTCCTTCCCGCCCCACCGC	0.602													C|||	610	0.121805	0.0484	0.147	5008	,	,		11617	0.0		0.2714	False		,,,				2504	0.1748				p.A64A		Atlas-SNP	.											.	.	.	.	0			c.G192A						PASS	.																																					284805	exon3			CCTTCCCGCCCCA	AK091025		20q11.21	2013-12-06			ENSG00000198547	ENSG00000198547			26592	protein-coding gene	gene with protein product						20376170	Standard	NM_182584		Approved	FLJ33706	uc021wbx.1	Q8NBC4	OTTHUMG00000032224		20.37:g.31238627C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_182584	B8JHY2	Silent	SNP	ENST00000608990.1	37																																																																																				C|0.860;T|0.140	0.140	strong		0.602	C20orf203-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000078641.3	NM_182584	
QRFPR	84109	hgsc.bcm.edu	37	4	122301597	122301597	+	Missense_Mutation	SNP	A	A	C	rs34270076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:122301597A>C	ENST00000394427.2	-	1	617	c.206T>G	c.(205-207)gTg>gGg	p.V69G	QRFPR_ENST00000334383.5_Missense_Mutation_p.V69G	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	69					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						GCGGGTCACCACGTAGAACAC	0.612													A|||	38	0.00758786	0.0008	0.0187	5008	,	,		15547	0.0		0.0239	False		,,,				2504	0.0				p.V69G		Atlas-SNP	.											.	QRFPR	65	.	0			c.T206G						PASS	.						92.0	74.0	80.0					4																	122301597		2203	4300	6503	SO:0001583	missense	84109	exon1			GTCACCACGTAGA	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.206T>G	4.37:g.122301597A>C	ENSP00000377948:p.Val69Gly	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	180	93	0.516667	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	A	24.8	4.575947	0.86645	.	.	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.46451	0.87;0.87	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.053895	0.64402	D	0.000001	T	0.60143	0.2246	H	0.95679	3.705	0.80722	D	1	D;D;D	0.76494	0.986;0.999;0.999	P;D;D	0.74674	0.907;0.984;0.963	T	0.79184	-0.1908	10	0.87932	D	0	.	14.6829	0.69031	1.0:0.0:0.0:0.0	rs34270076	69;69;69	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	G	69	ENSP00000377948:V69G;ENSP00000335610:V69G	ENSP00000335610:V69G	V	-	2	0	QRFPR	122521047	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.979000	0.93455	1.930000	0.55929	0.383000	0.25322	GTG	A|0.987;C|0.013	0.013	strong		0.612	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
OR5A1	219982	hgsc.bcm.edu	37	11	59210761	59210761	+	Silent	SNP	C	C	G	rs11605572	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59210761C>G	ENST00000302030.2	+	1	145	c.120C>G	c.(118-120)acC>acG	p.T40T		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						TCTATCTTACCACCCTGGCCT	0.502													.|||	642	0.128195	0.0333	0.1326	5008	,	,		19888	0.1111		0.2525	False		,,,				2504	0.1431				p.T40T		Atlas-SNP	.											OR5A1,right_upper_lobe,carcinoma,+1,1	OR5A1	72	1	0			c.C120G						PASS	.	G		287,4115	799.4+/-415.5	12,263,1926	135.0	129.0	131.0		120	-2.2	0.0	11	dbSNP_120	131	2264,6326	707.1+/-405.6	283,1698,2314	no	coding-synonymous	OR5A1	NM_001004728.1		295,1961,4240	GG,GC,CC		26.3562,6.5198,19.6352		40/316	59210761	2551,10441	2201	4295	6496	SO:0001819	synonymous_variant	219982	exon1			TCTTACCACCCTG	AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"""GPCR / Class A : Olfactory receptors"""	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.120C>G	11.37:g.59210761C>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_001004728	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																			C|0.809;G|0.191	0.191	strong		0.502	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728	
ALPK2	115701	hgsc.bcm.edu	37	18	56203411	56203411	+	Silent	SNP	G	G	C	rs3809980	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56203411G>C	ENST00000361673.3	-	5	4221	c.4008C>G	c.(4006-4008)ccC>ccG	p.P1336P	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1336						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCAGGAGTCTGGGTTGGCTGA	0.498													g|||	3363	0.671526	0.4667	0.6772	5008	,	,		19728	0.7966		0.7674	False		,,,				2504	0.7168				p.P1336P		Atlas-SNP	.											.	ALPK2	487	.	0			c.C4008G						PASS	.			2278,2128	598.5+/-389.1	597,1084,522	76.0	76.0	76.0		4008	0.9	0.0	18	dbSNP_107	76	6608,1992	722.5+/-406.4	2550,1508,242	no	coding-synonymous	ALPK2	NM_052947.3		3147,2592,764	CC,CG,GG		23.1628,48.2978,31.6777		1336/2171	56203411	8886,4120	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			GAGTCTGGGTTGG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4008C>G	18.37:g.56203411G>C		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			G|0.303;C|0.697	0.697	strong		0.498	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
REV1	51455	hgsc.bcm.edu	37	2	100058870	100058870	+	Missense_Mutation	SNP	C	C	T	rs3087403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:100058870C>T	ENST00000258428.3	-	5	640	c.412G>A	c.(412-414)Gtg>Atg	p.V138M	REV1_ENST00000393445.3_Missense_Mutation_p.V138M|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	138			V -> M (in dbSNP:rs3087403).		DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCTTTCTGCACACTGGACTGC	0.453								Direct reversal of damage					.|||	1131	0.225839	0.2995	0.3415	5008	,	,		17072	0.0625		0.2833	False		,,,				2504	0.1534				p.V138M		Atlas-SNP	.											.	REV1	100	.	0			c.G412A						PASS	.	C	MET/VAL,MET/VAL	1246,3160	428.7+/-342.0	166,914,1123	138.0	122.0	127.0		412,412	1.8	0.0	2	dbSNP_102	127	2396,6204	397.5+/-345.8	310,1776,2214	yes	missense,missense	REV1	NM_001037872.1,NM_016316.2	21,21	476,2690,3337	TT,TC,CC		27.8605,28.2796,28.0025	benign,benign	138/1251,138/1252	100058870	3642,9364	2203	4300	6503	SO:0001583	missense	51455	exon5			TCTGCACACTGGA	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.412G>A	2.37:g.100058870C>T	ENSP00000258428:p.Val138Met	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	156	78	0.5	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	521	0.23855311355311357	151	0.30691056910569103	123	0.3397790055248619	31	0.05419580419580419	216	0.2849604221635884	C	12.34	1.908171	0.33721	0.282796	0.278605	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.28895	1.59;1.59	5.59	1.76	0.24704	.	0.501568	0.22005	N	0.065958	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B;B;B	0.19706	0.038;0.003;0.019	B;B;B	0.20577	0.03;0.01;0.029	T	0.31024	-0.9958	9	0.46703	T	0.11	.	6.6283	0.22843	0.0:0.6148:0.1185:0.2667	rs3087403;rs17713429;rs52807598;rs58647355;rs3087403	117;138;138	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	M	138	ENSP00000377091:V138M;ENSP00000258428:V138M	ENSP00000258428:V138M	V	-	1	0	REV1	99425302	0.005000	0.15991	0.004000	0.12327	0.997000	0.91878	1.136000	0.31467	0.052000	0.16007	0.655000	0.94253	GTG	C|0.747;T|0.253	0.253	strong		0.453	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
ADAM29	11086	hgsc.bcm.edu	37	4	175898988	175898988	+	Missense_Mutation	SNP	G	G	A	rs202055137	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175898988G>A	ENST00000359240.3	+	5	2982	c.2312G>A	c.(2311-2313)cGg>cAg	p.R771Q	ADAM29_ENST00000404450.4_Missense_Mutation_p.R771Q|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.R771Q|ADAM29_ENST00000445694.1_Missense_Mutation_p.R771Q	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	771	9 X 9 AA approximate repeats.			QPRVM -> HPQLT (in Ref. 1; AAF03777). {ECO:0000305}.	spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AGTCAACCTCGGGTGATGCCT	0.577													G|||	340	0.0678914	0.034	0.0663	5008	,	,		20151	0.0615		0.0964	False		,,,				2504	0.092				p.R771Q	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,NS,carcinoma,0,2	ADAM29	262	2	0			c.G2312A						PASS	.																																			SO:0001583	missense	11086	exon4			AACCTCGGGTGAT	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2312G>A	4.37:g.175898988G>A	ENSP00000352177:p.Arg771Gln	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	213	34	0.159624	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.708063	0.30322	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.01871	4.59;4.59;4.59;4.59	0.945	-0.164	0.13359	.	.	.	.	.	T	0.00875	0.0029	N	0.08118	0	0.09310	N	1	P	0.48834	0.916	B	0.22152	0.038	T	0.53279	-0.8461	8	.	.	.	.	6.4136	0.21704	0.0:0.3102:0.6898:0.0	.	771	Q9UKF5	ADA29_HUMAN	Q	771	ENSP00000352177:R771Q;ENSP00000414544:R771Q;ENSP00000384229:R771Q;ENSP00000423517:R771Q	.	R	+	2	0	ADAM29	176135563	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.587000	0.00902	-0.079000	0.12707	0.453000	0.30009	CGG	.	.	weak		0.577	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
DNMT3L	29947	hgsc.bcm.edu	37	21	45670770	45670770	+	Missense_Mutation	SNP	T	T	C	rs7354779	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45670770T>C	ENST00000418993.1	-	10	1315	c.832A>G	c.(832-834)Agg>Ggg	p.R278G	AP001059.5_ENST00000442785.1_RNA|DNMT3L_ENST00000270172.3_Missense_Mutation_p.R278G	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	278			R -> G (in dbSNP:rs7354779). {ECO:0000269|PubMed:15489334}.		chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		AAGAAGGGCCTGGGGCTGCCT	0.662													T|||	827	0.165136	0.233	0.1484	5008	,	,		11468	0.0595		0.2416	False		,,,				2504	0.1155				p.R278G		Atlas-SNP	.											.	DNMT3L	33	.	0			c.A832G						PASS	.	T	GLY/ARG,GLY/ARG	1051,3355	377.1+/-322.3	132,787,1284	56.0	50.0	52.0		832,832	0.1	0.0	21	dbSNP_116	52	2265,6335	377.7+/-338.6	340,1585,2375	yes	missense,missense	DNMT3L	NM_013369.2,NM_175867.1	125,125	472,2372,3659	CC,CT,TT		26.3372,23.8538,25.4959	possibly-damaging,possibly-damaging	278/388,278/387	45670770	3316,9690	2203	4300	6503	SO:0001583	missense	29947	exon10			AGGGCCTGGGGCT	AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"""cytosine-5-methyltransferase 3-like protein"", ""human cytosine-5-methyltransferase 3-like protein"""	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.832A>G	21.37:g.45670770T>C	ENSP00000412862:p.Arg278Gly	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	145	82	0.565517	NM_013369	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	393	0.17994505494505494	112	0.22764227642276422	61	0.1685082872928177	34	0.05944055944055944	186	0.24538258575197888	T	3.648	-0.072092	0.07228	0.238538	0.263372	ENSG00000142182	ENST00000270172;ENST00000418993;ENST00000431166	T;T;T	0.31769	1.48;1.48;1.48	3.32	0.124	0.14714	.	0.528199	0.17788	N	0.161977	T	0.00012	0.0000	L	0.56199	1.76	0.54753	P	1.8999999999991246E-5	P;P	0.35793	0.521;0.521	B;B	0.31442	0.13;0.13	T	0.21586	-1.0241	9	0.59425	D	0.04	-5.4523	9.4162	0.38523	0.0:0.0:0.4421:0.5579	rs7354779;rs17844951;rs17857691;rs52825641;rs56657657;rs7354779	278;278	Q9UJW3-2;Q9UJW3	.;DNM3L_HUMAN	G	278;278;263	ENSP00000270172:R278G;ENSP00000412862:R278G;ENSP00000400242:R263G	ENSP00000270172:R278G	R	-	1	2	DNMT3L	44495198	0.008000	0.16893	0.002000	0.10522	0.060000	0.15804	0.785000	0.26830	-0.117000	0.11872	-1.642000	0.00770	AGG	T|0.786;C|0.214	0.214	strong		0.662	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369	
ZNF880	400713	hgsc.bcm.edu	37	19	52887427	52887427	+	Missense_Mutation	SNP	A	A	C	rs8104808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52887427A>C	ENST00000422689.2	+	4	609	c.594A>C	c.(592-594)agA>agC	p.R198S		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	198					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						TGTCTTCAAGACTTGCTAACA	0.373													C|||	1900	0.379393	0.2428	0.379	5008	,	,		20891	0.3462		0.4205	False		,,,				2504	0.5562				p.R198S		Atlas-SNP	.											.	ZNF880	45	.	0			c.A594C						PASS	.	C	SER/ARG	394,990		53,288,351	51.0	50.0	50.0		594	-2.1	0.0	19	dbSNP_116	50	1214,1968		222,770,599	yes	missense	ZNF880	NM_001145434.1	110	275,1058,950	CC,CA,AA		38.1521,28.4682,35.2168	benign	198/578	52887427	1608,2958	692	1591	2283	SO:0001583	missense	400713	exon4			TTCAAGACTTGCT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.594A>C	19.37:g.52887427A>C	ENSP00000406318:p.Arg198Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	119	65	0.546219	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	746	0.3415750915750916	120	0.24390243902439024	138	0.3812154696132597	177	0.3094405594405594	311	0.4102902374670185	C	1.585	-0.530539	0.04112	0.284682	0.381521	ENSG00000221923	ENST00000422689	T	0.26660	1.72	1.84	-2.1	0.07210	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00408	-1.53	0.80722	P	0.0	B	0.18741	0.03	B	0.04013	0.001	T	0.42932	-0.9422	7	.	.	.	.	3.0674	0.06219	0.3498:0.3892:0.0:0.261	rs8104808;rs17736357;rs52798557;rs8104808	198	Q6PDB4	ZN880_HUMAN	S	198	ENSP00000406318:R198S	.	R	+	3	2	ZNF880	57579239	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.885000	0.01620	-0.814000	0.04352	-1.140000	0.01884	AGA	A|0.652;C|0.348	0.348	strong		0.373	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
MICA	100507436	hgsc.bcm.edu	37	6	31379115	31379115	+	Missense_Mutation	SNP	G	G	A	rs1131896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31379115G>A	ENST00000449934.2	+	3	646	c.592G>A	c.(592-594)Ggc>Agc	p.G198S	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TCTAGAATCCGGCGTAGTCCT	0.537													g|||	1730	0.345447	0.2852	0.3501	5008	,	,		20682	0.4216		0.2823	False		,,,				2504	0.41				p.G198S		Atlas-SNP	.											.	MICA	21	.	0			c.G592A						PASS	.	G	SER/GLY	379,1005		53,273,366	97.0	86.0	89.0		592	-2.8	0.0	6	dbSNP_86	89	805,2377		100,605,886	yes	missense	MICA	NM_001177519.1	56	153,878,1252	AA,AG,GG		25.2986,27.3844,25.9308	benign	198/333	31379115	1184,3382	692	1591	2283	SO:0001583	missense	100507436	exon3			GAATCCGGCGTAG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.592G>A	6.37:g.31379115G>A	ENSP00000413079:p.Gly198Ser	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	672	0.3076923076923077	143	0.29065040650406504	112	0.30939226519337015	228	0.3986013986013986	189	0.24934036939313983	N	6.785	0.513740	0.12944	0.273844	0.252986	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934	T	0.00995	5.46	1.41	-2.82	0.05787	.	3.067170	0.01197	N	0.007461	T	0.00412	0.0013	M	0.67625	2.065	0.80722	P	0.0	B;P	0.34837	0.435;0.472	B;B	0.28553	0.036;0.091	T	0.41161	-0.9524	9	0.62326	D	0.03	.	0.6695	0.00856	0.1927:0.1761:0.3847:0.2464	rs1131896;rs2523494;rs3819266;rs17884174;rs56738748;rs1131896	60;198	Q5SS58;Q96QC4	.;.	S	60;198;155;198	ENSP00000413079:G198S	ENSP00000365394:G198S	G	+	1	0	MICA	31487094	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.607000	0.05648	-1.451000	0.01933	-1.206000	0.01644	GGC	G|0.689;A|0.311	0.311	strong		0.537	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
TRMT1	55621	hgsc.bcm.edu	37	19	13220734	13220734	+	Silent	SNP	G	G	A	rs142446751		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:13220734G>A	ENST00000592062.1	-	10	1671	c.1101C>T	c.(1099-1101)agC>agT	p.S367S	TRMT1_ENST00000221504.8_Intron|TRMT1_ENST00000437766.1_Silent_p.S367S|TRMT1_ENST00000357720.4_Silent_p.S367S			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	367	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		CTCACCGGCCGCTGGGGACTC	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16571	0.0		0.0	False		,,,				2504	0.001				p.S367S		Atlas-SNP	.											.	TRMT1	31	.	0			c.C1101T						PASS	.	G	,,	0,4406		0,0,2203	58.0	66.0	64.0		1101,,1101	-8.5	0.0	19	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,coding-synonymous	TRMT1	NM_001136035.2,NM_001142554.1,NM_017722.3	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	367/660,,367/660	13220734	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55621	exon9			CCGGCCGCTGGGG	AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.1101C>T	19.37:g.13220734G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	60	21	0.35	NM_001136035	O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	CCDS12293.1																																																																																			G|1.000;A|0.000	0.000	weak		0.642	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722	
WSB2	55884	hgsc.bcm.edu	37	12	118473054	118473054	+	Silent	SNP	T	T	C	rs9788041	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:118473054T>C	ENST00000315436.3	-	7	1050	c.909A>G	c.(907-909)ccA>ccG	p.P303P	WSB2_ENST00000542304.1_Silent_p.P78P|WSB2_ENST00000535496.1_Silent_p.P305P|WSB2_ENST00000441406.2_Silent_p.P320P|WSB2_ENST00000544233.1_Silent_p.P93P|WSB2_ENST00000536738.1_5'Flank	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	303					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACAAGCCTTCTGGAGAGAAGC	0.527											OREG0022175	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1907	0.380791	0.2905	0.3674	5008	,	,		22520	0.5446		0.2366	False		,,,				2504	0.4918				p.P303P		Atlas-SNP	.											.	WSB2	32	.	0			c.A909G						PASS	.	C		1229,3177	706.5+/-407.4	173,883,1147	125.0	110.0	115.0		909	-11.6	0.0	12	dbSNP_119	115	2194,6406	711.5+/-405.8	284,1626,2390	no	coding-synonymous	WSB2	NM_018639.3		457,2509,3537	CC,CT,TT		25.5116,27.8938,26.3186		303/405	118473054	3423,9583	2203	4300	6503	SO:0001819	synonymous_variant	55884	exon7			GCCTTCTGGAGAG	AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"""WD repeat domain containing"""	19222	protein-coding gene	gene with protein product			"""WD repeat and SOCS box-containing 2"""			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.909A>G	12.37:g.118473054T>C		Somatic	93	0	0	1488	WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Silent	SNP	ENST00000315436.3	37	CCDS9186.1																																																																																			T|0.701;C|0.299	0.299	strong		0.527	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639	
POLR1E	64425	hgsc.bcm.edu	37	9	37493588	37493588	+	Silent	SNP	C	C	T	rs10758434	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37493588C>T	ENST00000377798.4	+	6	548	c.435C>T	c.(433-435)acC>acT	p.T145T	POLR1E_ENST00000442009.2_Silent_p.T75T|POLR1E_ENST00000377792.3_Silent_p.T207T	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		TTGGTACCACCAAACAGAAGC	0.468													C|||	1078	0.215256	0.1694	0.3112	5008	,	,		24276	0.244		0.2018	False		,,,				2504	0.1933				p.T145T	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.C435T						PASS	.	C		806,3600	321.0+/-296.9	71,664,1468	124.0	112.0	116.0		435	6.0	1.0	9	dbSNP_120	116	1872,6728	334.9+/-321.2	201,1470,2629	no	coding-synonymous	POLR1E	NM_022490.1		272,2134,4097	TT,TC,CC		21.7674,18.2932,20.5905		145/420	37493588	2678,10328	2203	4300	6503	SO:0001819	synonymous_variant	64425	exon6			TACCACCAAACAG	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.435C>T	9.37:g.37493588C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	56	0.589474	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000377798.4	37	CCDS6611.1																																																																																			C|0.796;T|0.204	0.204	strong		0.468	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
ZNF224	7767	hgsc.bcm.edu	37	19	44612014	44612014	+	Silent	SNP	A	A	T	rs3200505	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44612014A>T	ENST00000336976.6	+	6	1955	c.1701A>T	c.(1699-1701)ccA>ccT	p.P567P	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	567					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				GAGAAAAACCATTCAAATGTG	0.418													A|||	2932	0.585463	0.4085	0.5144	5008	,	,		20439	0.5367		0.8131	False		,,,				2504	0.6912				p.P567P		Atlas-SNP	.											.	ZNF224	70	.	0			c.A1701T						PASS	.	A		2010,2396	560.3+/-380.4	468,1074,661	96.0	92.0	93.0		1701	-2.7	0.1	19	dbSNP_105	93	7037,1559	744.9+/-407.2	2904,1229,165	no	coding-synonymous	ZNF224	NM_013398.2		3372,2303,826	TT,TA,AA		18.1363,45.6196,30.4184		567/708	44612014	9047,3955	2203	4298	6501	SO:0001819	synonymous_variant	7767	exon6			AAAACCATTCAAA	AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"""Zinc fingers, C2H2-type"", ""-"""	13017	protein-coding gene	gene with protein product		194555	"""zinc finger protein 255"", ""zinc finger protein 27"""	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1701A>T	19.37:g.44612014A>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Silent	SNP	ENST00000336976.6	37	CCDS33046.1																																																																																			A|0.314;T|0.686	0.686	strong		0.418	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398	
PADI2	11240	hgsc.bcm.edu	37	1	17402255	17402255	+	Silent	SNP	C	C	T	rs3818032	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17402255C>T	ENST00000375486.4	-	12	1437	c.1374G>A	c.(1372-1374)gcG>gcA	p.A458A	PADI2_ENST00000466151.1_5'UTR|PADI2_ENST00000444885.2_Silent_p.A342A	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	458					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GCTCCACGGGCGCCTGCACCT	0.592											OREG0013145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2634	0.525958	0.4834	0.5807	5008	,	,		18334	0.4028		0.6561	False		,,,				2504	0.5378				p.A458A		Atlas-SNP	.											.	PADI2	72	.	0			c.G1374A						PASS	.	C		2384,2022	612.8+/-392.0	643,1098,462	98.0	95.0	96.0		1374	-8.2	0.3	1	dbSNP_107	96	5616,2984	665.8+/-402.3	1841,1934,525	no	coding-synonymous	PADI2	NM_007365.2		2484,3032,987	TT,TC,CC		34.6977,45.892,38.4899		458/666	17402255	8000,5006	2203	4300	6503	SO:0001819	synonymous_variant	11240	exon12			CACGGGCGCCTGC	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1374G>A	1.37:g.17402255C>T		Somatic	175	0	0	717	WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	CCDS177.1																																																																																			C|0.399;T|0.601	0.601	strong		0.592	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
PFAS	5198	hgsc.bcm.edu	37	17	8166498	8166498	+	Silent	SNP	G	G	A	rs34778863	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8166498G>A	ENST00000314666.6	+	13	1615	c.1482G>A	c.(1480-1482)aaG>aaA	p.K494K	PFAS_ENST00000545834.1_Silent_p.K70K|PFAS_ENST00000585319.1_3'UTR	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	494					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	TGGAACAGAAGATGAACCGTG	0.572													G|||	76	0.0151757	0.0076	0.0317	5008	,	,		18258	0.0		0.0398	False		,,,				2504	0.0041				p.K494K		Atlas-SNP	.											.	PFAS	91	.	0			c.G1482A						PASS	.	G		55,4351	54.2+/-90.2	1,53,2149	138.0	137.0	138.0		1482	2.9	1.0	17	dbSNP_126	138	326,8274	114.4+/-174.4	6,314,3980	no	coding-synonymous	PFAS	NM_012393.2		7,367,6129	AA,AG,GG		3.7907,1.2483,2.9294		494/1339	8166498	381,12625	2203	4300	6503	SO:0001819	synonymous_variant	5198	exon13			ACAGAAGATGAAC	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.1482G>A	17.37:g.8166498G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_012393	A6H8V8	Silent	SNP	ENST00000314666.6	37	CCDS11136.1																																																																																			G|0.973;A|0.027	0.027	strong		0.572	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
R3HCC1	203069	hgsc.bcm.edu	37	8	23148978	23148978	+	Silent	SNP	G	G	T	rs2272760	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:23148978G>T	ENST00000411463.1	+	6	1077	c.1077G>T	c.(1075-1077)gtG>gtT	p.V359V	R3HCC1_ENST00000522012.1_3'UTR|R3HCC1_ENST00000265806.6_Silent_p.V132V|R3HCC1_ENST00000518454.1_Silent_p.V132V			Q9Y3T6	R3HC1_HUMAN	R3H domain and coiled-coil containing 1	359							nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			central_nervous_system(1)|skin(2)	3						TTGCCCACGTGGTAGAGATCT	0.537													G|||	629	0.125599	0.0295	0.2133	5008	,	,		21083	0.0536		0.2803	False		,,,				2504	0.1084				p.V132V		Atlas-SNP	.											.	R3HCC1	11	.	0			c.G396T						PASS	.	G		89,1295		6,77,609	127.0	114.0	118.0		396	5.9	1.0	8	dbSNP_100	118	884,2298		116,652,823	no	coding-synonymous	R3HCC1	NM_001136108.1		122,729,1432	TT,TG,GG		27.7813,6.4306,21.3097		132/254	23148978	973,3593	692	1591	2283	SO:0001819	synonymous_variant	203069	exon5			CCACGTGGTAGAG		CCDS47826.1	8p21.3	2012-05-23		2005-11-20	ENSG00000104679	ENSG00000104679			27329	protein-coding gene	gene with protein product						12477932	Standard	XM_005273427		Approved	DKFZp564N123	uc003xdf.3	Q9Y3T6	OTTHUMG00000163786	ENST00000411463.1:c.1077G>T	8.37:g.23148978G>T		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	124	122	0.983871	NM_001136108	B7ZLI1	Silent	SNP	ENST00000411463.1	37																																																																																				G|0.820;T|0.180	0.180	strong		0.537	R3HCC1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001136108	
ISM1	140862	hgsc.bcm.edu	37	20	13269248	13269248	+	Silent	SNP	C	C	T	rs3827705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:13269248C>T	ENST00000262487.4	+	4	711	c.705C>T	c.(703-705)aaC>aaT	p.N235N	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	235	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					extracellular region (GO:0005576)				NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						CCTGCGGGAACGGCAACCAGA	0.577													C|||	437	0.0872604	0.0514	0.049	5008	,	,		16402	0.1974		0.0477	False		,,,				2504	0.09				p.N235N		Atlas-SNP	.											.	ISM1	41	.	0			c.C705T						PASS	.	C		178,3918		4,170,1874	77.0	82.0	80.0		705	-11.7	0.4	20	dbSNP_107	80	343,8069		9,325,3872	no	coding-synonymous	ISM1	NM_080826.1		13,495,5746	TT,TC,CC		4.0775,4.3457,4.1653		235/465	13269248	521,11987	2048	4206	6254	SO:0001819	synonymous_variant	140862	exon4			CGGGAACGGCAAC	AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"""chromosome 20 open reading frame 82"", ""isthmin 1 homolog (zebrafish)"""	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.705C>T	20.37:g.13269248C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_080826	Q8WVH9	Silent	SNP	ENST00000262487.4	37	CCDS46579.1																																																																																			C|0.906;T|0.094	0.094	strong		0.577	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2		
TRIM46	80128	hgsc.bcm.edu	37	1	155148520	155148520	+	Missense_Mutation	SNP	G	G	A	rs80254867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:155148520G>A	ENST00000334634.4	+	3	482	c.482G>A	c.(481-483)cGc>cAc	p.R161H	KRTCAP2_ENST00000295682.4_5'Flank|TRIM46_ENST00000368383.3_Missense_Mutation_p.R161H|TRIM46_ENST00000543729.1_Missense_Mutation_p.R168H|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000392451.2_Missense_Mutation_p.R161H|TRIM46_ENST00000545012.1_Missense_Mutation_p.R35H|TRIM46_ENST00000368385.4_Missense_Mutation_p.R161H|KRTCAP2_ENST00000490672.1_5'Flank|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000368382.1_Missense_Mutation_p.R138H	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	161				R -> H (in Ref. 1; AAP51206 and 2; BAB15580). {ECO:0000305}.		intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GAGCGGTACCGCCAGAGTGTG	0.652													G|||	37	0.00738818	0.0008	0.0086	5008	,	,		15348	0.0		0.0239	False		,,,				2504	0.0061				p.R161H		Atlas-SNP	.											.	TRIM46	79	.	0			c.G482A						PASS	.	G	HIS/ARG	28,4378	35.2+/-66.4	0,28,2175	186.0	175.0	179.0		482	4.4	1.0	1	dbSNP_131	179	248,8352	97.7+/-159.3	3,242,4055	yes	missense	TRIM46	NM_025058.3	29	3,270,6230	AA,AG,GG		2.8837,0.6355,2.1221	probably-damaging	161/760	155148520	276,12730	2203	4300	6503	SO:0001583	missense	80128	exon3			GGTACCGCCAGAG		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19019	protein-coding gene	gene with protein product		600986	"""tripartite motif-containing 46"""				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.482G>A	1.37:g.155148520G>A	ENSP00000334657:p.Arg161His	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	252	139	0.551587	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	37	CCDS1097.1	29	0.013278388278388278	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	26	0.03430079155672823	G	21.5	4.162892	0.78226	0.006355	0.028837	ENSG00000163462	ENST00000543729;ENST00000430513;ENST00000368385;ENST00000545012;ENST00000392451;ENST00000368383;ENST00000368382;ENST00000334634	T;T;T;T;T;T;T	0.68331	0.72;0.46;-0.32;0.66;0.4;0.15;0.2	5.36	4.43	0.53597	Zinc finger, RING/FYVE/PHD-type (1);	0.114028	0.64402	D	0.000020	T	0.75155	0.3811	M	0.73962	2.25	0.35515	D	0.800933	D;D;P;D;D	0.89917	0.999;1.0;0.48;1.0;0.999	D;D;B;D;D	0.77557	0.976;0.99;0.055;0.99;0.977	T	0.80558	-0.1329	10	0.66056	D	0.02	.	14.0509	0.64736	0.0:0.1523:0.8477:0.0	.	148;161;138;161;161	F5H5Z2;Q5VT61;B1AVQ4;Q7Z4K8;Q7Z4K8-2	.;.;.;TRI46_HUMAN;.	H	168;148;161;35;161;161;138;161	ENSP00000442719:R168H;ENSP00000357369:R161H;ENSP00000440254:R35H;ENSP00000376245:R161H;ENSP00000357367:R161H;ENSP00000357366:R138H;ENSP00000334657:R161H	ENSP00000334657:R161H	R	+	2	0	TRIM46	153415144	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.067000	0.93955	1.351000	0.45789	0.655000	0.94253	CGC	G|0.985;A|0.015	0.015	strong		0.652	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058	
USP6NL	9712	hgsc.bcm.edu	37	10	11504687	11504687	+	Missense_Mutation	SNP	G	G	A	rs41291253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:11504687G>A	ENST00000609104.1	-	15	2634	c.2240C>T	c.(2239-2241)aCg>aTg	p.T747M	USP6NL_ENST00000379237.2_Missense_Mutation_p.T770M|USP6NL_ENST00000277575.5_Missense_Mutation_p.T764M	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	747					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						TTGTCCCTGCGTCTCAGGTCT	0.468													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		20911	0.0		0.004	False		,,,				2504	0.0				p.T764M		Atlas-SNP	.											.	USP6NL	57	.	0			c.C2291T						PASS	.	G	MET/THR,MET/THR	5,3907		0,5,1951	137.0	142.0	140.0		2291,2240	-1.2	0.0	10	dbSNP_127	140	35,8269		0,35,4117	yes	missense,missense	USP6NL	NM_001080491.2,NM_014688.2	81,81	0,40,6068	AA,AG,GG		0.4215,0.1278,0.3274	benign,benign	764/846,747/829	11504687	40,12176	1956	4152	6108	SO:0001583	missense	9712	exon14			CCCTGCGTCTCAG	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.2240C>T	10.37:g.11504687G>A	ENSP00000476462:p.Thr747Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	37	CCDS53492.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	3.027	-0.200380	0.06219	0.001278	0.004215	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.03889	3.77;3.77	6.17	-1.16	0.09678	.	1.547390	0.03119	N	0.163470	T	0.02888	0.0086	N	0.02802	-0.49	0.09310	N	1	B;B	0.18968	0.019;0.032	B;B	0.11329	0.002;0.006	T	0.44360	-0.9333	10	0.31617	T	0.26	.	11.551	0.50721	0.5617:0.0:0.4383:0.0	rs41291253	747;764	Q92738;Q92738-2	US6NL_HUMAN;.	M	747;764;747	ENSP00000277575:T764M;ENSP00000368539:T747M	ENSP00000277575:T764M	T	-	2	0	USP6NL	11544693	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.006000	0.12833	-0.047000	0.13423	-0.290000	0.09829	ACG	G|0.997;A|0.003	0.003	strong		0.468	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45479055	45479055	+	Silent	SNP	C	C	T	rs2838475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:45479055C>T	ENST00000291574.4	+	6	925	c.750C>T	c.(748-750)gaC>gaT	p.D250D	TRAPPC10_ENST00000380221.3_Silent_p.D250D	NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	250					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						ACGAACTGGACGCCCTCTTCT	0.507													C|||	275	0.0549121	0.0129	0.0576	5008	,	,		16057	0.0506		0.1093	False		,,,				2504	0.0583				p.D250D		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.C750T						PASS	.	C		113,4293	86.8+/-125.4	3,107,2093	72.0	59.0	63.0		750	1.0	1.0	21	dbSNP_100	63	905,7695	201.3+/-244.8	60,785,3455	no	coding-synonymous	TRAPPC10	NM_003274.4		63,892,5548	TT,TC,CC		10.5233,2.5647,7.8272		250/1260	45479055	1018,11988	2203	4300	6503	SO:0001819	synonymous_variant	7109	exon6			ACTGGACGCCCTC	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.750C>T	21.37:g.45479055C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																			C|0.929;T|0.071	0.071	strong		0.507	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
METTL5	29081	hgsc.bcm.edu	37	2	170678476	170678476	+	Silent	SNP	G	G	A	rs35417312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:170678476G>A	ENST00000260953.5	-	2	517	c.201C>T	c.(199-201)atC>atT	p.I67I	METTL5_ENST00000409837.1_Silent_p.I67I|METTL5_ENST00000409340.1_Intron|METTL5_ENST00000410097.1_Silent_p.I67I|METTL5_ENST00000392640.2_Silent_p.I67I|METTL5_ENST00000308099.3_Silent_p.I67I|METTL5_ENST00000409965.1_Silent_p.I67I	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5	67							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						TTGCAGTTCCGATGCTAAGTA	0.363													G|||	123	0.0245607	0.0227	0.0187	5008	,	,		19258	0.0179		0.0318	False		,,,				2504	0.0307				p.I67I		Atlas-SNP	.											.	METTL5	24	.	0			c.C201T						PASS	.	G		121,4285	90.2+/-128.9	1,119,2083	183.0	158.0	166.0		201	-1.8	1.0	2	dbSNP_126	166	329,8271	115.9+/-175.7	7,315,3978	no	coding-synonymous	METTL5	NM_014168.2		8,434,6061	AA,AG,GG		3.8256,2.7463,3.4599		67/210	170678476	450,12556	2203	4300	6503	SO:0001819	synonymous_variant	29081	exon2			AGTTCCGATGCTA	AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.201C>T	2.37:g.170678476G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_014168	D3DPC9|Q9NVX1	Silent	SNP	ENST00000260953.5	37	CCDS33320.1																																																																																			G|0.965;A|0.035	0.035	strong		0.363	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168	
C1orf141	400757	hgsc.bcm.edu	37	1	67561090	67561090	+	Missense_Mutation	SNP	T	T	C	rs72933970	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:67561090T>C	ENST00000371007.2	-	7	540	c.431A>G	c.(430-432)cAg>cGg	p.Q144R	C1orf141_ENST00000371006.1_Missense_Mutation_p.Q144R|C1orf141_ENST00000544837.1_Missense_Mutation_p.Q144R	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	144										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						ATCGTTCATCTGTGGAGATTT	0.363													C|||	582	0.116214	0.2617	0.085	5008	,	,		19959	0.0645		0.0507	False		,,,				2504	0.0624				p.Q144R		Atlas-SNP	.											.	C1orf141	58	.	0			c.A431G						PASS	.	C	ARG/GLN	926,3478		95,736,1371	43.0	41.0	42.0		431	-1.1	0.0	1	dbSNP_130	42	402,8194		10,382,3906	yes	missense	C1orf141	NM_001013674.1	43	105,1118,5277	CC,CT,TT		4.6766,21.0263,10.2154	possibly-damaging	144/401	67561090	1328,11672	2202	4298	6500	SO:0001583	missense	400757	exon7			TTCATCTGTGGAG	BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.431A>G	1.37:g.67561090T>C	ENSP00000360046:p.Gln144Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_001276351	Q0P5P5|Q5JVX5	Missense_Mutation	SNP	ENST00000371007.2	37	CCDS30745.1	223	0.1021062271062271	128	0.2601626016260163	19	0.052486187845303865	32	0.055944055944055944	44	0.05804749340369393	C	10.40	1.339284	0.24339	0.210263	0.046766	ENSG00000203963	ENST00000371007;ENST00000371006;ENST00000544837;ENST00000371005;ENST00000448166	T;T;T	0.28895	1.59;1.59;1.59	5.76	-1.07	0.09968	.	2.750990	0.01545	N	0.019435	T	0.05364	0.0142	N	0.24115	0.695	0.80722	P	0.0	P	0.38250	0.624	B	0.31337	0.128	T	0.10019	-1.0648	9	0.27082	T	0.32	2.7976	2.5553	0.04758	0.1112:0.1536:0.1509:0.5843	.	144	Q5JVX7	CA141_HUMAN	R	144;144;144;215;215	ENSP00000360046:Q144R;ENSP00000360045:Q144R;ENSP00000444018:Q144R	ENSP00000360044:Q215R	Q	-	2	0	C1orf141	67333678	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.005000	0.03674	-0.099000	0.12263	-1.286000	0.01371	CAG	T|0.903;C|0.097	0.097	strong		0.363	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674	
EPM2A	7957	hgsc.bcm.edu	37	6	146007332	146007332	+	Silent	SNP	C	C	T	rs35230590	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:146007332C>T	ENST00000367519.3	-	2	927	c.402G>A	c.(400-402)ggG>ggA	p.G134G	EPM2A_ENST00000496228.1_5'UTR	NM_005670.3	NP_005661.1	O95278	EPM2A_HUMAN	epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)	134					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|habituation (GO:0046959)|inositol phosphate dephosphorylation (GO:0046855)|nervous system development (GO:0007399)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polysome (GO:0005844)	carbohydrate phosphatase activity (GO:0019203)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|starch binding (GO:2001070)			kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	7		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		CATTGGTGTGCCCAGTGGCCT	0.418													C|||	611	0.122005	0.0008	0.3314	5008	,	,		17112	0.0089		0.2266	False		,,,				2504	0.1462				p.G134G		Atlas-SNP	.											.	EPM2A	21	.	0			c.G402A						PASS	.	C	,	204,4202	126.1+/-163.2	7,190,2006	175.0	150.0	159.0		402,402	3.8	1.0	6	dbSNP_126	159	2127,6473	367.5+/-334.7	256,1615,2429	no	coding-synonymous,coding-synonymous	EPM2A	NM_001018041.1,NM_005670.3	,	263,1805,4435	TT,TC,CC		24.7326,4.63,17.9225	,	134/318,134/332	146007332	2331,10675	2203	4300	6503	SO:0001819	synonymous_variant	7957	exon2			GGTGTGCCCAGTG	AF284580	CCDS5206.1	6q24	2011-06-09			ENSG00000112425	ENSG00000112425		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3413	protein-coding gene	gene with protein product		607566	"""epilepsy, progressive myoclonus type 2, Lafora disease (laforin)"""			9222970, 7485240	Standard	XM_006715564		Approved	LDE, LD	uc003qkw.3	B3EWF7	OTTHUMG00000015747	ENST00000367519.3:c.402G>A	6.37:g.146007332C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	156	62	0.397436	NM_005670	B3KMU5|B4DRZ2|O95483|Q5T3F5|Q6IS15|Q8IU96|Q8IX24|Q8IX25|Q9BS66|Q9UEN2	Silent	SNP	ENST00000367519.3	37	CCDS5206.1	309	0.14148351648351648	1	0.0020325203252032522	129	0.356353591160221	2	0.0034965034965034965	177	0.23350923482849603	C	9.721	1.159735	0.21454	0.0463	0.247326	ENSG00000112425	ENST00000450221;ENST00000435470	D;D	0.96554	-3.06;-4.05	5.6	3.81	0.43845	.	0.000000	0.85682	D	0.000000	D	0.95589	0.8566	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	D	0.95635	0.8693	6	0.66056	D	0.02	-32.4686	10.7796	0.46369	0.0:0.7916:0.0:0.2084	rs35230590;rs61748671	.	.	.	D	34;54	ENSP00000414900:G34D;ENSP00000405913:G54D	ENSP00000405913:G54D	G	-	2	0	EPM2A	146049025	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.678000	0.25277	1.357000	0.45904	0.491000	0.48974	GGC	C|0.823;T|0.177	0.177	strong		0.418	EPM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042564.1		
GGT1	2678	hgsc.bcm.edu	37	22	25023444	25023444	+	Missense_Mutation	SNP	G	G	T	rs201546887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:25023444G>T	ENST00000400382.1	+	12	1821	c.1066G>T	c.(1066-1068)Gcc>Tcc	p.A356S	GGT1_ENST00000403838.1_Missense_Mutation_p.A12S|GGT1_ENST00000404223.1_Missense_Mutation_p.A12S|GGT1_ENST00000248923.4_Missense_Mutation_p.A356S|GGT1_ENST00000404532.1_Missense_Mutation_p.A12S|GGT1_ENST00000404920.1_Missense_Mutation_p.A12S|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000406383.2_Missense_Mutation_p.A356S|GGT1_ENST00000401885.1_Missense_Mutation_p.A12S|GGT1_ENST00000400380.1_Missense_Mutation_p.A356S|GGT1_ENST00000400383.1_Missense_Mutation_p.A356S			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	356				A -> S (in Ref. 10; AAI28240). {ECO:0000305}.	arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.A356S(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	CCAGCTCCGGGCCCAGATCTC	0.652													g|||	27	0.00539137	0.0023	0.0058	5008	,	,		10309	0.0		0.0109	False		,,,				2504	0.0092				p.A356S		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	prostate(1)	c.G1066T						scavenged	.						45.0	46.0	45.0					22																	25023444		2201	4297	6498	SO:0001583	missense	2678	exon12			CTCCGGGCCCAGA	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1066G>T	22.37:g.25023444G>T	ENSP00000383232:p.Ala356Ser	Somatic	394	1	0.00253807		WXS	Illumina HiSeq	Phase_I	421	38	0.0902613	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	0.717	-0.784921	0.02907	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23	3.4	2.37	0.29283	.	0.683912	0.14246	N	0.331733	T	0.03695	0.0105	N	0.16066	0.365	0.21527	N	0.999659	B	0.02656	0.0	B	0.09377	0.004	T	0.45789	-0.9237	10	0.09084	T	0.74	-4.876	3.5096	0.07703	0.2536:0.2162:0.5302:0.0	.	356	P19440	GGT1_HUMAN	S	356;356;356;356;356;356;12;12;12;12;12	ENSP00000248923:A356S;ENSP00000393537:A356S;ENSP00000383232:A356S;ENSP00000383233:A356S;ENSP00000383231:A356S;ENSP00000385975:A356S;ENSP00000384381:A12S;ENSP00000385445:A12S;ENSP00000384820:A12S;ENSP00000385016:A12S;ENSP00000385001:A12S	ENSP00000248923:A356S	A	+	1	0	GGT1	23353444	0.490000	0.26012	0.009000	0.14445	0.418000	0.31294	1.292000	0.33342	0.762000	0.33152	0.298000	0.19748	GCC	.	.	weak		0.652	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
PDE3A	5139	hgsc.bcm.edu	37	12	20522252	20522252	+	Missense_Mutation	SNP	G	G	A	rs12305038	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:20522252G>A	ENST00000359062.3	+	1	74	c.34G>A	c.(34-36)Gac>Aac	p.D12N	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	12			D -> N (in dbSNP:rs12305038). {ECO:0000269|PubMed:8695850}.		blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	ACGAGTCAGGGACAAGCCCGT	0.726													G|||	1671	0.333666	0.5061	0.219	5008	,	,		10216	0.3056		0.3091	False		,,,				2504	0.2362				p.D12N		Atlas-SNP	.											PDE3A,NS,carcinoma,0,1	PDE3A	184	1	0			c.G34A						scavenged	.	G	ASN/ASP	1554,2186		396,762,712	4.0	7.0	6.0		34	3.9	0.0	12	dbSNP_120	6	1943,5269		352,1239,2015	yes	missense	PDE3A	NM_000921.4	23	748,2001,2727	AA,AG,GG		26.9412,41.5508,31.9302	possibly-damaging	12/1142	20522252	3497,7455	1870	3606	5476	SO:0001583	missense	5139	exon1			GTCAGGGACAAGC		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.34G>A	12.37:g.20522252G>A	ENSP00000351957:p.Asp12Asn	Somatic	20	1	0.05		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	726	0.3324175824175824	269	0.5467479674796748	81	0.22375690607734808	140	0.24475524475524477	236	0.3113456464379947	G	9.693	1.152350	0.21371	0.415508	0.269412	ENSG00000172572	ENST00000359062	T	0.62232	0.04	3.9	3.9	0.45041	.	4.361550	0.00166	N	0.000016	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.23058	0.079	B	0.20955	0.032	T	0.33059	-0.9883	9	0.33940	T	0.23	.	11.4979	0.50419	0.0:0.1835:0.8165:0.0	rs12305038;rs12305038	12	Q14432	PDE3A_HUMAN	N	12	ENSP00000351957:D12N	ENSP00000351957:D12N	D	+	1	0	PDE3A	20413519	0.164000	0.22935	0.032000	0.17829	0.460000	0.32559	3.310000	0.51911	1.999000	0.58509	0.484000	0.47621	GAC	G|0.663;A|0.337	0.337	strong		0.726	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
ZNF443	10224	hgsc.bcm.edu	37	19	12542772	12542772	+	Missense_Mutation	SNP	C	C	T	rs1134389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12542772C>T	ENST00000301547.5	-	4	411	c.214G>A	c.(214-216)Gtt>Att	p.V72I	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	72	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.			V -> I (in Ref. 1; BAA75543 and 3; AAH32753). {ECO:0000305}.	apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						TTACTTTCAACAAATCTCTCT	0.338													.|||	1308	0.261182	0.171	0.4207	5008	,	,		20498	0.1071		0.496	False		,,,				2504	0.1871				p.V72I		Atlas-SNP	.											.	ZNF443	63	.	0			c.G214A						PASS	.						51.0	43.0	46.0					19																	12542772		2201	4278	6479	SO:0001583	missense	10224	exon4			TTTCAACAAATCT	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.214G>A	19.37:g.12542772C>T	ENSP00000301547:p.Val72Ile	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	211	100	0.473934	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	678	0.31043956043956045	88	0.17886178861788618	157	0.43370165745856354	56	0.0979020979020979	377	0.4973614775725594	C	1.200	-0.632838	0.03584	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.07327	3.2	1.37	0.266	0.15617	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B	0.17852	0.024	B	0.22601	0.04	T	0.37979	-0.9682	8	0.21540	T	0.41	.	5.5758	0.17222	0.6931:0.3069:0.0:0.0	rs1134389;rs13382105	72	Q9Y2A4	ZN443_HUMAN	I	72	ENSP00000301547:V72I	ENSP00000301547:V72I	V	-	1	0	ZNF443	12403772	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.193000	0.09573	0.039000	0.15632	-0.534000	0.04291	GTT	T|1.000;|0.000	1.000	weak		0.338	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
OXA1L	5018	hgsc.bcm.edu	37	14	23235808	23235808	+	Silent	SNP	G	G	A	rs1957374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:23235808G>A	ENST00000285848.5	+	1	78	c.78G>A	c.(76-78)ctG>ctA	p.L26L	CTD-2555K7.2_ENST00000553792.1_RNA|OXA1L_ENST00000604262.1_5'Flank|CTD-2555K7.2_ENST00000554857.1_RNA|CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000412791.1_5'Flank|OXA1L_ENST00000358043.5_5'Flank	NM_005015.3	NP_005006.3	Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	0					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		CGCCTGATCTGCGGCTACAAT	0.522													G|||	1969	0.393171	0.0507	0.5965	5008	,	,		19117	0.6776		0.4662	False		,,,				2504	0.3436				p.L26L		Atlas-SNP	.											.	OXA1L	49	.	0			c.G78A						PASS	.	G		545,3861	246.8+/-255.3	32,481,1690	112.0	119.0	117.0		78	-3.8	0.0	14	dbSNP_92	117	3856,4744	542.3+/-384.2	860,2136,1304	no	coding-synonymous	OXA1L	NM_005015.3		892,2617,2994	AA,AG,GG		44.8372,12.3695,33.8382		26/496	23235808	4401,8605	2203	4300	6503	SO:0001819	synonymous_variant	5018	exon1			TGATCTGCGGCTA		CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000285848.5:c.78G>A	14.37:g.23235808G>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_005015	B4DPA2	Silent	SNP	ENST00000285848.5	37	CCDS9573.1																																																																																			G|0.629;A|0.371	0.371	strong		0.522	OXA1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071630.2	NM_005015	
CROCC	9696	hgsc.bcm.edu	37	1	17265416	17265416	+	Missense_Mutation	SNP	G	G	T	rs114323849	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17265416G>T	ENST00000375541.5	+	12	1456	c.1387G>T	c.(1387-1389)Gac>Tac	p.D463Y	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CGTCTTGTCAGACTCTGAGAG	0.697													g|||	82	0.0163738	0.0038	0.0303	5008	,	,		18158	0.0		0.0447	False		,,,				2504	0.0112				p.D463Y		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.G1387T						PASS	.	G	TYR/ASP	32,4368		0,32,2168	30.0	28.0	29.0		1387	5.4	0.1	1	dbSNP_132	29	353,8233		0,353,3940	yes	missense	CROCC	NM_014675.3	160	0,385,6108	TT,TG,GG		4.1113,0.7273,2.9647	probably-damaging	463/2018	17265416	385,12601	2200	4293	6493	SO:0001583	missense	9696	exon12			TTGTCAGACTCTG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1387G>T	1.37:g.17265416G>T	ENSP00000364691:p.Asp463Tyr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	125	51	0.408	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	39	0.017857142857142856	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	30	0.0395778364116095	G	10.41	1.343259	0.24339	0.007273	0.041113	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.13538	2.58	5.39	5.39	0.77823	.	.	.	.	.	T	0.08670	0.0215	L	0.53249	1.67	0.38482	D	0.947745	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.991;0.988;0.998	T	0.00263	-1.1866	9	0.59425	D	0.04	.	12.5136	0.56019	0.0813:0.0:0.9187:0.0	.	326;326;463	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	Y	463;344	ENSP00000364691:D463Y	ENSP00000364691:D463Y	D	+	1	0	CROCC	17138003	1.000000	0.71417	0.120000	0.21714	0.003000	0.03518	6.294000	0.72738	2.702000	0.92279	0.561000	0.74099	GAC	G|0.972;T|0.028	0.028	strong		0.697	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
SAMD9	54809	hgsc.bcm.edu	37	7	92734451	92734451	+	Silent	SNP	A	A	G	rs6965201	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:92734451A>G	ENST00000379958.2	-	3	1229	c.960T>C	c.(958-960)taT>taC	p.Y320Y		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	320						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TAATCTGGAAATAATCATATT	0.338													A|||	2610	0.521166	0.8359	0.4971	5008	,	,		19412	0.5188		0.2873	False		,,,				2504	0.3558				p.Y320Y		Atlas-SNP	.											.	SAMD9	239	.	0			c.T960C						PASS	.	A	,	3224,1182	707.0+/-407.4	1179,866,158	89.0	85.0	86.0		960,960	3.2	1.0	7	dbSNP_116	86	2470,6130	404.2+/-348.1	365,1740,2195	no	coding-synonymous,coding-synonymous	SAMD9	NM_001193307.1,NM_017654.3	,	1544,2606,2353	GG,GA,AA		28.7209,26.8271,43.7798	,	320/1590,320/1590	92734451	5694,7312	2203	4300	6503	SO:0001819	synonymous_variant	54809	exon2			CTGGAAATAATCA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.960T>C	7.37:g.92734451A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																			A|0.525;G|0.475	0.475	strong		0.338	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
FUT5	2527	hgsc.bcm.edu	37	19	5867154	5867154	+	Missense_Mutation	SNP	G	G	A	rs140776824	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:5867154G>A	ENST00000588525.1	-	2	670	c.583C>T	c.(583-585)Cca>Tca	p.P195S	FUT5_ENST00000252675.5_Missense_Mutation_p.P195S	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	195					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						TTGAGCGGTGGGTGGGCAGGC	0.662													G|||	104	0.0207668	0.0015	0.0259	5008	,	,		12928	0.0079		0.0656	False		,,,				2504	0.0102				p.P195S		Atlas-SNP	.											.	FUT5	29	.	0			c.C583T						PASS	.	G	SER/PRO	47,4169		1,45,2062	15.0	16.0	15.0		583	-4.3	0.0	19	dbSNP_134	15	585,7781		23,539,3621	no	missense	FUT5	NM_002034.2	74	24,584,5683	AA,AG,GG		6.9926,1.1148,5.023	benign	195/375	5867154	632,11950	2108	4183	6291	SO:0001583	missense	2527	exon2			GCGGTGGGTGGGC		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.583C>T	19.37:g.5867154G>A	ENSP00000466880:p.Pro195Ser	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	143	72	0.503497	NM_002034	A8K4X2	Missense_Mutation	SNP	ENST00000588525.1	37	CCDS12154.1	63	0.028846153846153848	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	51	0.06728232189973615	G	0.053	-1.243341	0.01481	0.011148	0.069926	ENSG00000130383	ENST00000252675	T	0.22743	1.94	2.17	-4.35	0.03656	.	1.868570	0.03005	U	0.148748	T	0.00815	0.0027	N	0.20685	0.6	0.09310	N	1	B	0.21225	0.053	B	0.29440	0.102	T	0.20773	-1.0265	10	0.08837	T	0.75	.	5.3404	0.15981	0.0:0.2057:0.4987:0.2956	.	195	Q11128	FUT5_HUMAN	S	195	ENSP00000252675:P195S	ENSP00000252675:P195S	P	-	1	0	FUT5	5818154	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.395000	0.02516	-1.422000	0.02004	-0.693000	0.03709	CCA	G|0.900;A|0.100	0.100	strong		0.662	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
PRIM1	5557	hgsc.bcm.edu	37	12	57133140	57133140	+	Silent	SNP	T	T	G	rs1131514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57133140T>G	ENST00000338193.6	-	10	1026	c.990A>C	c.(988-990)atA>atC	p.I330I		NM_000946.2	NP_000937.1	P49642	PRI1_HUMAN	primase, DNA, polypeptide 1 (49kDa)	330					DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			kidney(1)|lung(6)|prostate(1)	8						TAGGCACAGATATGCGACCTG	0.328													T|||	3043	0.607628	0.3343	0.6657	5008	,	,		18766	0.7401		0.6252	False		,,,				2504	0.7812				p.I330I		Atlas-SNP	.											PRIM1,NS,carcinoma,0,1	PRIM1	22	1	0			c.A990C						PASS	.	T		1591,2143		348,895,624	79.0	70.0	73.0		990	2.9	1.0	12	dbSNP_86	73	5095,3095		1594,1907,594	no	coding-synonymous	PRIM1	NM_000946.2		1942,2802,1218	GG,GT,TT		37.79,42.6085,43.9282		330/421	57133140	6686,5238	1867	4095	5962	SO:0001819	synonymous_variant	5557	exon10			CACAGATATGCGA	BC005266	CCDS44926.1	12q13.3	2007-06-19	2007-06-19			ENSG00000198056			9369	protein-coding gene	gene with protein product		176635				8530050	Standard	NM_000946		Approved		uc001smd.3	P49642	OTTHUMG00000170034	ENST00000338193.6:c.990A>C	12.37:g.57133140T>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_000946		Silent	SNP	ENST00000338193.6	37	CCDS44926.1																																																																																			T|0.243;G|0.376	0.376	strong		0.328	PRIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406956.1	NM_000946	
PINK1	65018	hgsc.bcm.edu	37	1	20971158	20971158	+	Missense_Mutation	SNP	A	A	T	rs139226733		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20971158A>T	ENST00000321556.4	+	4	1046	c.952A>T	c.(952-954)Atg>Ttg	p.M318L	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.		M -> L. {ECO:0000269|PubMed:15596610}.		activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GTTCCTCGTTATGAAGAAGTA	0.632													A|||	1	0.000199681	0.0	0.0	5008	,	,		18148	0.0		0.001	False		,,,				2504	0.0				p.M318L	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.A952T	GRCh37	CM053378	PINK1	M	rs139226733	PASS	.	A	LEU/MET	2,4404	4.2+/-10.8	0,2,2201	47.0	44.0	45.0		952	6.1	0.9	1	dbSNP_134	45	7,8593	4.3+/-15.6	0,7,4293	yes	missense	PINK1	NM_032409.2	15	0,9,6494	TT,TA,AA		0.0814,0.0454,0.0692	probably-damaging	318/582	20971158	9,12997	2203	4300	6503	SO:0001583	missense	65018	exon4			CTCGTTATGAAGA	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.952A>T	1.37:g.20971158A>T	ENSP00000364204:p.Met318Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	37	CCDS211.1	.	.	.	.	.	.	.	.	.	.	A	19.96	3.923054	0.73213	4.54E-4	8.14E-4	ENSG00000158828	ENST00000321556	T	0.75589	-0.95	6.07	6.07	0.98685	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.72120	0.3421	L	0.60845	1.875	0.80722	D	1	B	0.23650	0.089	B	0.26517	0.07	T	0.70749	-0.4787	10	0.72032	D	0.01	-15.4264	13.0206	0.58784	1.0:0.0:0.0:0.0	.	318	Q9BXM7	PINK1_HUMAN	L	318	ENSP00000364204:M318L	ENSP00000364204:M318L	M	+	1	0	PINK1	20843745	1.000000	0.71417	0.946000	0.38457	0.934000	0.57294	7.964000	0.87933	2.326000	0.78906	0.533000	0.62120	ATG	A|0.999;T|0.001	0.001	strong		0.632	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
PTPN6	5777	hgsc.bcm.edu	37	12	7064352	7064352	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7064352C>T	ENST00000318974.9	+	5	799	c.555C>T	c.(553-555)gaC>gaT	p.D185D	PTPN6_ENST00000447931.2_Silent_p.D146D|PTPN6_ENST00000456013.1_Silent_p.D185D|PTPN6_ENST00000399448.1_Silent_p.D187D	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	185	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|apoptotic process (GO:0006915)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell proliferation (GO:0008285)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein dephosphorylation (GO:0006470)|regulation of B cell differentiation (GO:0045577)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|type I interferon signaling pathway (GO:0060337)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D185D(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						AGACCTTCGACAGCCTCACGG	0.622																																					p.D187D		Atlas-SNP	.											PTPN6,NS,carcinoma,0,2	PTPN6	42	2	1	Substitution - coding silent(1)	prostate(1)	c.C561T						scavenged	.						116.0	124.0	121.0					12																	7064352		2000	4165	6165	SO:0001819	synonymous_variant	5777	exon5			CTTCGACAGCCTC		CCDS41744.1, CCDS44820.1, CCDS44821.1	12p13.31	2013-02-14			ENSG00000111679	ENSG00000111679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9658	protein-coding gene	gene with protein product		176883				1639416	Standard	NM_080548		Approved	HCP, HCPH, PTP-1C, SHP-1, SHP1	uc001qsa.1	P29350	OTTHUMG00000168518	ENST00000318974.9:c.555C>T	12.37:g.7064352C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	140	5	0.0357143	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Silent	SNP	ENST00000318974.9	37	CCDS44820.1																																																																																			.	.	none		0.622	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136287582	136287582	+	Missense_Mutation	SNP	C	C	T	rs34024143	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136287582C>T	ENST00000371929.3	+	1	463	c.19C>T	c.(19-21)Cgg>Tgg	p.R7W	ADAMTS13_ENST00000371911.3_Missense_Mutation_p.R7W|ADAMTS13_ENST00000485925.1_Intron|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.R7W|ADAMTS13_ENST00000356589.2_Missense_Mutation_p.R7W|ADAMTS13_ENST00000371916.1_Missense_Mutation_p.R7W	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	7			R -> W (does not affect protein secretion; dbSNP:rs34024143). {ECO:0000269|PubMed:11586351, ECO:0000269|Ref.6}.		cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GCGTCACCCCCGGGCAAGATG	0.632													C|||	264	0.0527157	0.0356	0.0735	5008	,	,		16616	0.006		0.1262	False		,,,				2504	0.0337				p.R7W		Atlas-SNP	.											ADAMTS13,colon,carcinoma,-2,1	ADAMTS13	113	1	0			c.C19T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	228,4178	136.5+/-172.5	3,222,1978	84.0	78.0	80.0		19,19,19	-6.6	0.0	9	dbSNP_126	80	1071,7529	225.5+/-261.6	66,939,3295	yes	missense,missense,missense	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	101,101,101	69,1161,5273	TT,TC,CC		12.4535,5.1748,9.9877	benign,benign,benign	7/1428,7/1341,7/1372	136287582	1299,11707	2203	4300	6503	SO:0001583	missense	11093	exon1			CACCCCCGGGCAA	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.19C>T	9.37:g.136287582C>T	ENSP00000360997:p.Arg7Trp	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_139026	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	153	0.07005494505494506	26	0.052845528455284556	26	0.0718232044198895	5	0.008741258741258742	96	0.1266490765171504	C	9.203	1.028867	0.19512	0.051748	0.124535	ENSG00000160323	ENST00000371929;ENST00000371916;ENST00000355699;ENST00000356589;ENST00000371911	T;T;T;T;D	0.85339	-0.13;-1.45;-0.17;-0.2;-1.97	3.35	-6.55	0.01854	.	.	.	.	.	T	0.01061	0.0035	N	0.04880	-0.145	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.11421	-1.0588	8	0.45353	T	0.12	.	1.1031	0.01688	0.1589:0.3274:0.1622:0.3515	rs34024143;rs36218241	7;7;7;7	Q76LX8;Q76LX8-3;Q76LX8-2;E7EV88	ATS13_HUMAN;.;.;.	W	7	ENSP00000360997:R7W;ENSP00000360984:R7W;ENSP00000347927:R7W;ENSP00000348997:R7W;ENSP00000360979:R7W	ENSP00000347927:R7W	R	+	1	2	ADAMTS13	135277403	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.569000	0.02142	-1.237000	0.02539	-1.311000	0.01308	CGG	C|0.905;T|0.095	0.095	strong		0.632	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
WSB1	26118	hgsc.bcm.edu	37	17	25639329	25639329	+	Silent	SNP	C	C	T	rs61761626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:25639329C>T	ENST00000262394.2	+	9	1516	c.1200C>T	c.(1198-1200)ccC>ccT	p.P400P	WSB1_ENST00000348811.2_Silent_p.P254P|RP11-173M1.8_ENST00000578929.1_lincRNA	NM_015626.8	NP_056441.6	Q9Y6I7	WSB1_HUMAN	WD repeat and SOCS box containing 1	400	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				lung(3)	3	all_cancers(1;2e-13)|all_epithelial(1;4.8e-15)|Lung NSC(42;0.00152)		BRCA - Breast invasive adenocarcinoma(3;0.0152)	UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		GAGTGATGCCCACCCAAGAAG	0.483													C|||	52	0.0103834	0.0008	0.0	5008	,	,		16318	0.003		0.005	False		,,,				2504	0.044				p.P400P		Atlas-SNP	.											WSB1,NS,carcinoma,+1,1	WSB1	29	1	0			c.C1200T						scavenged	.	C	,	9,4397	12.9+/-30.5	0,9,2194	279.0	265.0	270.0		1200,762	0.5	1.0	17	dbSNP_129	270	79,8521	46.7+/-105.8	0,79,4221	no	coding-synonymous,coding-synonymous	WSB1	NM_015626.8,NM_134265.2	,	0,88,6415	TT,TC,CC		0.9186,0.2043,0.6766	,	400/422,254/276	25639329	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	26118	exon9			GATGCCCACCCAA	AF069313	CCDS11220.1, CCDS11221.1	17q11.2	2013-01-09	2011-01-25		ENSG00000109046	ENSG00000109046		"""WD repeat domain containing"""	19221	protein-coding gene	gene with protein product		610091	"""WD repeat and SOCS box-containing 1"""			10354473, 12076535	Standard	XR_243778		Approved	DKFZp564A122, DKFZp564B0482, SWIP1	uc002gzd.1	Q9Y6I7	OTTHUMG00000132293	ENST00000262394.2:c.1200C>T	17.37:g.25639329C>T		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	154	64	0.415584	NM_015626	Q9NRB1|Q9UBH9|Q9UG25|Q9UNN6|Q9Y656	Silent	SNP	ENST00000262394.2	37	CCDS11220.1																																																																																			C|0.994;T|0.006	0.006	strong		0.483	WSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255391.4	NM_015626	
HECW1	23072	hgsc.bcm.edu	37	7	43540887	43540887	+	Silent	SNP	A	A	C	rs17339479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43540887A>C	ENST00000395891.2	+	21	4202	c.3597A>C	c.(3595-3597)cgA>cgC	p.R1199R	HECW1_ENST00000453890.1_Silent_p.R1165R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1199					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R1199R(2)|p.R1178R(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TCTCTCCCCGATGTTCACCCT	0.473													C|||	583	0.116414	0.0696	0.1499	5008	,	,		16872	0.0079		0.2068	False		,,,				2504	0.1748				p.R1199R		Atlas-SNP	.											HECW1_ENST00000395891,caecum,adenoma,+1,3	HECW1	540	3	3	Substitution - coding silent(3)	prostate(3)	c.A3597C						PASS	.	C		295,3569		6,283,1643	84.0	80.0	81.0		3597	1.7	1.0	7	dbSNP_123	81	1675,6575		184,1307,2634	no	coding-synonymous	HECW1	NM_015052.3		190,1590,4277	CC,CA,AA		20.303,7.6346,16.2622		1199/1607	43540887	1970,10144	1932	4125	6057	SO:0001819	synonymous_variant	23072	exon21			TCCCCGATGTTCA	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3597A>C	7.37:g.43540887A>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			A|0.838;C|0.162	0.162	strong		0.473	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
PIH1D1	55011	hgsc.bcm.edu	37	19	49949652	49949652	+	Missense_Mutation	SNP	G	G	A	rs7462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49949652G>A	ENST00000262265.5	-	9	1095	c.860C>T	c.(859-861)cCg>cTg	p.P287L	PIH1D1_ENST00000596049.1_Missense_Mutation_p.P287L|PIH1D1_ENST00000602226.1_5'UTR	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	287			P -> L (in dbSNP:rs7462). {ECO:0000269|PubMed:15489334}.		box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		AGAAGGCACCGGCAGAAGCGG	0.522													G|||	930	0.185703	0.2746	0.2032	5008	,	,		15967	0.005		0.3231	False		,,,				2504	0.0982				p.P287L		Atlas-SNP	.											.	PIH1D1	23	.	0			c.C860T						PASS	.	G	LEU/PRO	1114,3292	399.9+/-331.4	140,834,1229	60.0	59.0	59.0		860	2.2	0.0	19	dbSNP_52	59	2895,5705	453.9+/-363.3	479,1937,1884	yes	missense	PIH1D1	NM_017916.2	98	619,2771,3113	AA,AG,GG		33.6628,25.2837,30.8242	benign	287/291	49949652	4009,8997	2203	4300	6503	SO:0001583	missense	55011	exon9			GGCACCGGCAGAA	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.860C>T	19.37:g.49949652G>A	ENSP00000262265:p.Pro287Leu	Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	261	137	0.524904	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Missense_Mutation	SNP	ENST00000262265.5	37	CCDS12765.1	472	0.21611721611721613	148	0.3008130081300813	78	0.2154696132596685	3	0.005244755244755245	243	0.32058047493403696	G	4.396	0.073136	0.08485	0.252837	0.336628	ENSG00000104872	ENST00000262265	T	0.16457	2.34	3.32	2.25	0.28309	.	0.348457	0.26680	N	0.023057	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45190	-0.9278	9	0.51188	T	0.08	-1.7009	6.9777	0.24686	0.1285:0.0:0.8715:0.0	rs7462;rs1043253;rs3182784;rs17856032;rs52817842;rs60098984;rs7462	287	Q9NWS0	PIHD1_HUMAN	L	287	ENSP00000262265:P287L	ENSP00000262265:P287L	P	-	2	0	PIH1D1	54641464	0.052000	0.20516	0.022000	0.16811	0.207000	0.24258	1.153000	0.31676	0.954000	0.37851	0.655000	0.94253	CCG	G|0.723;A|0.277	0.277	strong		0.522	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916	
NLRP2	55655	hgsc.bcm.edu	37	19	55494157	55494157	+	Missense_Mutation	SNP	G	G	A	rs4306647	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55494157G>A	ENST00000543010.1	+	6	1234	c.1091G>A	c.(1090-1092)aGg>aAg	p.R364K	NLRP2_ENST00000427260.2_Missense_Mutation_p.R341K|NLRP2_ENST00000538819.1_Missense_Mutation_p.R340K|NLRP2_ENST00000263437.6_Missense_Mutation_p.R361K|NLRP2_ENST00000448584.2_Missense_Mutation_p.R364K|NLRP2_ENST00000339757.7_Missense_Mutation_p.R342K|NLRP2_ENST00000537859.1_Missense_Mutation_p.R342K|NLRP2_ENST00000391721.4_Missense_Mutation_p.R340K	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	364	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		R -> K (in dbSNP:rs4306647). {ECO:0000269|PubMed:11270363}.		positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GAGGAGGACAGGAGGGCCTAT	0.642													G|||	823	0.164337	0.1694	0.1527	5008	,	,		17832	0.2679		0.0527	False		,,,				2504	0.1738				p.R364K		Atlas-SNP	.											.	NLRP2	161	.	0			c.G1091A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	593,3813	250.0+/-257.2	30,533,1640	31.0	30.0	31.0		1091,1025,1022,1091	1.6	0.0	19	dbSNP_111	31	322,8278	111.2+/-171.5	3,316,3981	no	missense,missense,missense,missense	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	26,26,26,26	33,849,5621	AA,AG,GG		3.7442,13.4589,7.0352	benign,benign,benign,benign	364/1063,342/1041,341/1040,364/1063	55494157	915,12091	2203	4300	6503	SO:0001583	missense	55655	exon6			AGGACAGGAGGGC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.1091G>A	19.37:g.55494157G>A	ENSP00000445135:p.Arg364Lys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	314	0.14377289377289376	96	0.1951219512195122	41	0.1132596685082873	136	0.23776223776223776	41	0.05408970976253298	G	11.53	1.665435	0.29604	0.134589	0.037442	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	D;D;D;D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54;-1.54	1.64	1.64	0.23874	NACHT nucleoside triphosphatase (1);	0.266539	0.18301	N	0.145409	T	0.00039	0.0001	L	0.28344	0.845	0.47183	P	6.559999999999899E-4	B;B;B;B;B	0.32302	0.309;0.313;0.363;0.313;0.363	B;B;B;B;P	0.44647	0.272;0.209;0.313;0.209;0.456	T	0.04140	-1.0974	9	0.10111	T	0.7	.	9.3286	0.38008	0.0:0.0:1.0:0.0	rs4306647;rs4306647	341;342;361;340;364	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	K	364;340;342;364;342;341;340;361	ENSP00000445135:R364K;ENSP00000375601:R340K;ENSP00000344074:R342K;ENSP00000409370:R364K;ENSP00000440601:R342K;ENSP00000402474:R341K;ENSP00000441133:R340K;ENSP00000263437:R361K	ENSP00000263437:R361K	R	+	2	0	NLRP2	60185969	0.005000	0.15991	0.019000	0.16419	0.218000	0.24690	0.780000	0.26760	1.260000	0.44134	0.556000	0.70494	AGG	G|0.896;A|0.104	0.104	strong		0.642	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
CYP1A1	1543	hgsc.bcm.edu	37	15	75012987	75012987	+	Missense_Mutation	SNP	G	G	T	rs1799814	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75012987G>T	ENST00000379727.3	-	7	1580	c.1382C>A	c.(1381-1383)aCc>aAc	p.T461N	CYP1A1_ENST00000395049.4_Missense_Mutation_p.T432N|CYP1A1_ENST00000395048.2_Missense_Mutation_p.T461N|CYP1A1_ENST00000567032.1_Missense_Mutation_p.T461N			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	461			T -> N (in allele CYP1A1*4; dbSNP:rs1799814). {ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15643613, ECO:0000269|PubMed:8895751}.		9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)			autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	GCGGGCAATGGTCTCACCGAT	0.537									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				G|||	69	0.013778	0.003	0.0317	5008	,	,		22650	0.0		0.0338	False		,,,				2504	0.0092				p.T461N		Atlas-SNP	.											.	CYP1A1	60	.	0			c.C1382A	GRCh37	CM057662	CYP1A1	M	rs1799814	PASS	.	G	ASN/THR	41,4353	46.0+/-80.4	0,41,2156	131.0	120.0	124.0		1382	2.7	1.0	15	dbSNP_89	124	417,8175	131.0+/-188.9	9,399,3888	yes	missense	CYP1A1	NM_000499.3	65	9,440,6044	TT,TG,GG		4.8534,0.9331,3.5269	benign	461/513	75012987	458,12528	2197	4296	6493	SO:0001583	missense	1543	exon7	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	GCAATGGTCTCAC	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"""Cytochrome P450s"""	2595	protein-coding gene	gene with protein product		108330	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"""	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.1382C>A	15.37:g.75012987G>T	ENSP00000369050:p.Thr461Asn	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	118	45	0.381356	NM_000499	A4F3V9|A4F3W0|Q53G18	Missense_Mutation	SNP	ENST00000379727.3	37	CCDS10268.1	33	0.01510989010989011	0	0.0	15	0.04143646408839779	0	0.0	18	0.023746701846965697	G	10.11	1.259931	0.23051	0.009331	0.048534	ENSG00000140465	ENST00000379727;ENST00000395048;ENST00000395049;ENST00000268062	T;T;T	0.77620	-1.11;-1.11;-1.11	5.61	2.71	0.32032	.	0.444729	0.26435	N	0.024387	T	0.24967	0.0606	L	0.35288	1.05	0.30195	N	0.799163	B;B	0.15473	0.013;0.013	B;B	0.21151	0.033;0.033	T	0.48536	-0.9027	10	0.51188	T	0.08	.	7.0881	0.25270	0.1317:0.0:0.5531:0.3151	rs1799814;rs4134575;rs4986876;rs17861093;rs52803905;rs1799814	432;461	E7EMT5;P04798	.;CP1A1_HUMAN	N	461;461;432;433	ENSP00000369050:T461N;ENSP00000378488:T461N;ENSP00000378489:T432N	ENSP00000268062:T433N	T	-	2	0	CYP1A1	72800040	0.027000	0.19231	0.965000	0.40720	0.959000	0.62525	0.279000	0.18771	0.321000	0.23259	0.650000	0.86243	ACC	G|0.968;T|0.032	0.032	strong		0.537	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499	
PCDHA1	56147	hgsc.bcm.edu	37	5	140168151	140168151	+	Missense_Mutation	SNP	G	G	T	rs2240695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140168151G>T	ENST00000504120.2	+	1	2276	c.2276G>T	c.(2275-2277)tGc>tTc	p.C759F	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000378133.3_Missense_Mutation_p.C759F	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	759	5 X 4 AA repeats of P-X-X-P.		C -> F (in dbSNP:rs2240695).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAGGGTGTGCTCTAGCGAG	0.597													.|||	2625	0.524161	0.4758	0.5879	5008	,	,		15955	0.5317		0.5368	False		,,,				2504	0.5235				p.C759F		Atlas-SNP	.											.	PCDHA1	387	.	0			c.G2276T						PASS	.	G	PHE/CYS,PHE/CYS,	2172,2234	582.0+/-385.5	524,1124,555	43.0	40.0	41.0		2276,2276,	4.3	1.0	5	dbSNP_98	41	4540,4060	592.4+/-393.0	1193,2154,953	no	missense,missense,intron	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	205,205,	1717,3278,1508	TT,TG,GG		47.2093,49.2964,48.393	,,	759/951,759/808,	140168151	6712,6294	2203	4300	6503	SO:0001583	missense	56147	exon1			GGGTGTGCTCTAG	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.2276G>T	5.37:g.140168151G>T	ENSP00000420840:p.Cys759Phe	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	294	85	0.289116	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	1156	0.5293040293040293	249	0.5060975609756098	192	0.5303867403314917	311	0.5437062937062938	404	0.5329815303430079	g	10.36	1.328001	0.24080	0.492964	0.527907	ENSG00000204970	ENST00000504120;ENST00000378133	T;T	0.14640	2.49;2.49	4.34	4.34	0.51931	.	0.170635	0.27478	U	0.019194	T	0.00012	0.0000	M	0.91872	3.25	0.34095	P	0.338859	B;B	0.27140	0.122;0.169	B;B	0.26202	0.03;0.067	T	0.42565	-0.9444	9	0.72032	D	0.01	.	10.5955	0.45336	0.0908:0.0:0.9092:0.0	rs2240695;rs17844242;rs2240695	759;759	Q9Y5I3;Q9Y5I3-3	PCDA1_HUMAN;.	F	759	ENSP00000420840:C759F;ENSP00000367373:C759F	ENSP00000367373:C759F	C	+	2	0	PCDHA1	140148335	0.994000	0.37717	0.994000	0.49952	0.038000	0.13279	2.645000	0.46621	2.145000	0.66743	0.644000	0.83932	TGC	G|0.481;T|0.519	0.519	strong		0.597	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
GAS2L1	10634	hgsc.bcm.edu	37	22	29704125	29704125	+	Silent	SNP	C	C	T	rs11090564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29704125C>T	ENST00000406549.3	+	2	180	c.30C>T	c.(28-30)ggC>ggT	p.G10G	GAS2L1_ENST00000403764.1_Silent_p.G10G|GAS2L1_ENST00000341313.6_Silent_p.G10G|GAS2L1_ENST00000471961.1_Silent_p.G10G|GAS2L1_ENST00000407854.1_Silent_p.G10G|GAS2L1_ENST00000407647.2_Silent_p.G10G|GAS2L1_ENST00000360113.2_Silent_p.G10G	NM_001278730.1	NP_001265659.1	Q99501	GA2L1_HUMAN	growth arrest-specific 2 like 1	10					cell cycle arrest (GO:0007050)|cellular response to starvation (GO:0009267)|cellular response to thyroid hormone stimulus (GO:0097067)|microtubule bundle formation (GO:0001578)|negative regulation of cell growth (GO:0030308)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of gene expression (GO:0010629)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)|thyroid hormone receptor binding (GO:0046966)			endometrium(2)|lung(2)|prostate(1)	5						GCATCGCGGGCTCGGCGGCCA	0.662													C|||	1639	0.327276	0.1808	0.5159	5008	,	,		12397	0.2847		0.3588	False		,,,				2504	0.4029				p.G10G		Atlas-SNP	.											GAS2L1_ENST00000333679,NS,carcinoma,0,4	GAS2L1	54	4	0			c.C30T						PASS	.	C	,,	892,3496		106,680,1408	17.0	17.0	17.0		30,30,30	3.3	1.0	22	dbSNP_120	17	3271,5303		656,1959,1672	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS2L1	NM_006478.3,NM_152236.1,NM_152237.1	,,	762,2639,3080	TT,TC,CC		38.1502,20.3282,32.117	,,	10/682,10/682,10/338	29704125	4163,8799	2194	4287	6481	SO:0001819	synonymous_variant	10634	exon2			CGCGGGCTCGGCG	BC001782	CCDS63438.1, CCDS74840.1	22q12.2	2008-06-11			ENSG00000185340	ENSG00000185340			16955	protein-coding gene	gene with protein product		602128				8975699, 12584248, 1607387	Standard	NM_001278730		Approved	GAR22	uc003afc.1	Q99501	OTTHUMG00000151108	ENST00000406549.3:c.30C>T	22.37:g.29704125C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_152237	B5MCR7|Q53EN7|Q92640|Q9BUY9	Silent	SNP	ENST00000406549.3	37																																																																																				C|0.704;T|0.296	0.296	strong		0.662	GAS2L1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321365.1	NM_006478	
FBXW10	10517	hgsc.bcm.edu	37	17	18653188	18653188	+	Missense_Mutation	SNP	G	G	T	rs139431164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18653188G>T	ENST00000395665.4	+	3	1045	c.824G>T	c.(823-825)cGa>cTa	p.R275L	FBXW10_ENST00000301938.4_Missense_Mutation_p.R275L|FBXW10_ENST00000395667.1_Missense_Mutation_p.R275L|FBXW10_ENST00000308799.4_Missense_Mutation_p.R275L			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	275				R -> L (in Ref. 1; AAU43731 and 4; AAH28364). {ECO:0000305}.						NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						AGCAAATACCGAGACTTCATC	0.507													.|||	287	0.0573083	0.0333	0.0476	5008	,	,		20533	0.002		0.0865	False		,,,				2504	0.1237				p.R275L		Atlas-SNP	.											.	FBXW10	82	.	0			c.G824T						PASS	.	G	LEU/ARG	67,4337	53.6+/-89.4	2,63,2137	101.0	75.0	84.0		824	1.5	1.0	17	dbSNP_134	84	475,8083	119.4+/-178.7	21,433,3825	no	missense	FBXW10	NM_031456.3	102	23,496,5962	TT,TG,GG		5.5504,1.5213,4.1815	probably-damaging	275/1052	18653188	542,12420	2202	4279	6481	SO:0001583	missense	10517	exon3			AATACCGAGACTT	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.824G>T	17.37:g.18653188G>T	ENSP00000379025:p.Arg275Leu	Somatic	695	1	0.00143885		WXS	Illumina HiSeq	Phase_I	686	200	0.291545	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	102	0.046703296703296704	15	0.03048780487804878	28	0.07734806629834254	0	0.0	59	0.07783641160949868	G	15.96	2.986545	0.53934	0.015213	0.055504	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	2.49	1.49	0.22878	F-box domain, Skp2-like (1);	0.362610	0.15655	U	0.251206	T	0.03305	0.0096	M	0.67953	2.075	0.39647	P	0.029598000000000013	D;D;D;D	0.76494	0.995;0.999;0.997;0.999	P;D;P;D	0.72075	0.878;0.976;0.823;0.965	T	0.20174	-1.0283	9	0.52906	T	0.07	.	3.8614	0.08998	0.3383:0.0:0.6617:0.0	.	275;275;275;275	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	L	275	ENSP00000379026:R275L;ENSP00000310382:R275L;ENSP00000306937:R275L;ENSP00000379025:R275L	ENSP00000306937:R275L	R	+	2	0	FBXW10	18593913	0.013000	0.17824	0.990000	0.47175	0.992000	0.81027	1.457000	0.35212	1.393000	0.46605	0.405000	0.27470	CGA	T|1.000;|0.000	1.000	weak		0.507	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229702	87229702	+	Silent	SNP	A	A	G	rs4546639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:87229702A>G	ENST00000297524.3	-	3	1279	c.1176T>C	c.(1174-1176)taT>taC	p.Y392Y	SLC7A13_ENST00000520624.1_5'Flank|SLC7A13_ENST00000419776.2_Silent_p.Y383Y	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	392						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						ATTTTACCTTATAAGGTATAG	0.289													A|||	1014	0.202476	0.0688	0.1974	5008	,	,		17572	0.3383		0.1372	False		,,,				2504	0.3139				p.Y392Y		Atlas-SNP	.											.	SLC7A13	97	.	0			c.T1176C						PASS	.	A		394,3954		20,354,1800	21.0	23.0	22.0		1176	5.0	1.0	8	dbSNP_111	22	1098,7456		81,936,3260	no	coding-synonymous	SLC7A13	NM_138817.2		101,1290,5060	GG,GA,AA		12.8361,9.0616,11.5641		392/471	87229702	1492,11410	2174	4277	6451	SO:0001819	synonymous_variant	157724	exon3			TACCTTATAAGGT	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1176T>C	8.37:g.87229702A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	NM_138817	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	37	CCDS34917.1																																																																																			A|0.858;G|0.142	0.142	strong		0.289	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
LPPR3	79948	hgsc.bcm.edu	37	19	814680	814680	+	Intron	SNP	G	G	T	rs56944467	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:814680G>T	ENST00000520876.3	-	6	736				MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Silent_p.A223A	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN								integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										GGCAGTGAGGGGCCGGACTCA	0.662													G|||	676	0.134984	0.0764	0.2565	5008	,	,		14874	0.0208		0.1312	False		,,,				2504	0.2495				p.A223A		Atlas-SNP	.											.	.	.	.	0			c.C669A						PASS	.	G		359,4033	179.7+/-208.2	15,329,1852	54.0	50.0	51.0		669	0.9	0.0	19	dbSNP_129	51	1094,7502	225.7+/-261.6	62,970,3266	no	coding-synonymous	LPPR3	NM_024888.1		77,1299,5118	TT,TG,GG		12.7268,8.174,11.1872		223/747	814680	1453,11535	2196	4298	6494	SO:0001627	intron_variant	0	exon6			GTGAGGGGCCGGA																												ENST00000520876.3:c.657+11C>A	19.37:g.814680G>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	37	11	0.297297	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Silent	SNP	ENST00000520876.3	37	CCDS58636.1																																																																																			G|0.886;T|0.114	0.114	strong		0.662	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3		
HSPG2	3339	hgsc.bcm.edu	37	1	22201438	22201438	+	Silent	SNP	C	C	T	rs41307806	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22201438C>T	ENST00000374695.3	-	26	3439	c.3360G>A	c.(3358-3360)gcG>gcA	p.A1120A		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1120	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCACTTCCAGCGCGGGGTCCT	0.682													C|||	155	0.0309505	0.0038	0.0418	5008	,	,		16118	0.0		0.0954	False		,,,				2504	0.0256				p.A1120A		Atlas-SNP	.											HSPG2,NS,carcinoma,0,1	HSPG2	311	1	0			c.G3360A						PASS	.	C		78,4326	68.7+/-106.4	1,76,2125	42.0	38.0	39.0		3360	-10.5	0.1	1	dbSNP_127	39	675,7925	158.2+/-211.7	28,619,3653	no	coding-synonymous	HSPG2	NM_005529.5		29,695,5778	TT,TC,CC		7.8488,1.7711,5.7905		1120/4392	22201438	753,12251	2202	4300	6502	SO:0001819	synonymous_variant	3339	exon26			TTCCAGCGCGGGG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.3360G>A	1.37:g.22201438C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			C|0.950;T|0.050	0.050	strong		0.682	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
NRG1	3084	hgsc.bcm.edu	37	8	32611970	32611970	+	Missense_Mutation	SNP	G	G	T	rs74942016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:32611970G>T	ENST00000405005.3	+	8	781	c.781G>T	c.(781-783)Gtg>Ttg	p.V261L	NRG1_ENST00000523079.1_Missense_Mutation_p.V258L|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000519301.1_Missense_Mutation_p.V211L|NRG1_ENST00000539990.1_Missense_Mutation_p.V104L|NRG1_ENST00000287842.3_Missense_Mutation_p.V258L|NRG1_ENST00000287845.5_Missense_Mutation_p.V232L|NRG1_ENST00000356819.4_Missense_Mutation_p.V266L|NRG1_ENST00000338921.4_Missense_Mutation_p.V269L|NRG1_ENST00000521670.1_Missense_Mutation_p.V261L			Q02297	NRG1_HUMAN	neuregulin 1	261				V -> L (in Ref. 10; ABQ53540). {ECO:0000305}.	activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CATCATGTGTGTGGTGGCCTA	0.527													G|||	72	0.014377	0.0008	0.0259	5008	,	,		17487	0.0		0.0467	False		,,,				2504	0.0061				p.V266L		Atlas-SNP	.											.	NRG1	260	.	0			c.G796T	GRCh37	CM066934	NRG1	M	rs74942016	PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	47,4359	48.9+/-83.8	0,47,2156	226.0	165.0	186.0		682,319,733,631,772,772,796,772,781,781	5.6	1.0	8	dbSNP_131	186	405,8195	127.5+/-185.8	12,381,3907	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	NRG1	NM_001159995.1,NM_001159996.1,NM_001159999.1,NM_001160001.1,NM_001160004.1,NM_001160008.1,NM_013956.3,NM_013957.3,NM_013960.3,NM_013964.3	32,32,32,32,32,32,32,32,32,32	12,428,6063	TT,TG,GG		4.7093,1.0667,3.4753	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	228/608,107/309,245/625,211/591,258/460,258/421,266/646,258/638,261/463,261/641	32611970	452,12554	2203	4300	6503	SO:0001583	missense	3084	exon9			ATGTGTGTGGTGG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.781G>T	8.37:g.32611970G>T	ENSP00000384620:p.Val261Leu	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	188	69	0.367021	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	40	0.018315018315018316	0	0.0	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	35	5.558867	0.96514	0.010667	0.047093	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000522402;ENST00000519240;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;2.63;0.14	5.62	5.62	0.85841	Neuregulin 1-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.40932	0.1137	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;P;D;P;D;D	0.71674	0.979;0.998;0.995;0.979;0.983;0.995;0.599;0.962;0.946;0.979;0.994	D;D;D;P;D;D;B;P;P;P;D	0.85130	0.986;0.997;0.972;0.879;0.926;0.972;0.283;0.879;0.893;0.879;0.914	T	0.67722	-0.5597	10	0.72032	D	0.01	-36.9375	19.6569	0.95845	0.0:0.0:1.0:0.0	.	104;107;258;232;266;257;269;258;261;266;261	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	L	228;211;334;258;269;266;261;232;258;261;261;107;104;104	ENSP00000430053:V228L;ENSP00000429582:V211L;ENSP00000429067:V334L;ENSP00000430120:V258L;ENSP00000343395:V269L;ENSP00000349275:V266L;ENSP00000287840:V261L;ENSP00000287845:V232L;ENSP00000287842:V258L;ENSP00000384620:V261L;ENSP00000428828:V261L;ENSP00000430862:V107L;ENSP00000428411:V104L;ENSP00000439276:V104L	ENSP00000287840:V261L	V	+	1	0	NRG1	32731512	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.639000	0.89480	0.650000	0.86243	GTG	G|0.968;T|0.032	0.032	strong		0.527	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
ISL2	64843	hgsc.bcm.edu	37	15	76630717	76630717	+	Silent	SNP	C	C	T	rs62028361	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:76630717C>T	ENST00000290759.4	+	3	533	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L	RP11-685G9.2_ENST00000559539.1_RNA	NM_145805.1	NP_665804.1	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	125	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|peripheral nervous system neuron development (GO:0048935)|regulation of transcription, DNA-templated (GO:0006355)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord motor neuron cell fate specification (GO:0021520)|visceral motor neuron differentiation (GO:0021524)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6						CCGCCAGCTGCTGCCTGGGGA	0.726													C|||	265	0.0529153	0.0484	0.0418	5008	,	,		9628	0.0367		0.0954	False		,,,				2504	0.0399				p.L125L	GBM(97;953 1391 16164 31496 36951)	Atlas-SNP	.											.	ISL2	20	.	0			c.C373T						PASS	.	C		262,4084		11,240,1922	13.0	12.0	13.0		373	3.5	1.0	15	dbSNP_129	13	752,7766		42,668,3549	no	coding-synonymous	ISL2	NM_145805.1		53,908,5471	TT,TC,CC		8.8284,6.0285,7.8825		125/360	76630717	1014,11850	2173	4259	6432	SO:0001819	synonymous_variant	64843	exon3			CAGCTGCTGCCTG	AK001022	CCDS10290.1	15q24.3	2012-03-09	2007-07-13		ENSG00000159556	ENSG00000159556		"""Homeoboxes / LIM class"""	18524	protein-coding gene	gene with protein product		609481	"""ISL2 transcription factor, LIM/homeodomain, (islet-2)"""				Standard	NM_145805		Approved	FLJ10160	uc002bbw.1	Q96A47	OTTHUMG00000143723	ENST00000290759.4:c.373C>T	15.37:g.76630717C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	14	6	0.428571	NM_145805	B3KM37	Silent	SNP	ENST00000290759.4	37	CCDS10290.1																																																																																			C|0.925;T|0.075	0.075	strong		0.726	ISL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289779.1		
TREML4	285852	hgsc.bcm.edu	37	6	41196605	41196605	+	Missense_Mutation	SNP	T	T	C	rs9369265	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41196605T>C	ENST00000341495.2	+	2	321	c.217T>C	c.(217-219)Tgg>Cgg	p.W73R	TREML4_ENST00000448827.2_Missense_Mutation_p.W73R	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	73	Ig-like V-type.		W -> R (in dbSNP:rs9369265).			extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					CTCCAAGCCCTGGACAGCAGT	0.507													C|||	3458	0.690495	0.4228	0.8141	5008	,	,		18477	0.8383		0.7734	False		,,,				2504	0.727				p.W73R		Atlas-SNP	.											TREML4,NS,carcinoma,-1,1	TREML4	25	1	0			c.T217C						PASS	.	C	ARG/TRP	2156,2250		515,1126,562	83.0	77.0	79.0		217	-0.5	0.0	6	dbSNP_119	79	6800,1800		2686,1428,186	yes	missense	TREML4	NM_198153.2	101	3201,2554,748	CC,CT,TT		20.9302,48.9333,31.1395	benign	73/201	41196605	8956,4050	2203	4300	6503	SO:0001583	missense	285852	exon2			AAGCCCTGGACAG	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"""Immunoglobulin superfamily / V-set domain containing"""	30807	protein-coding gene	gene with protein product	"""TREM like transcript 4"""	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.217T>C	6.37:g.41196605T>C	ENSP00000342570:p.Trp73Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_198153	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	37	CCDS34446.1	1571	0.7193223443223443	207	0.42073170731707316	285	0.787292817679558	496	0.8671328671328671	583	0.7691292875989446	.	0.010	-1.792391	0.00623	0.489333	0.790698	ENSG00000188056	ENST00000341495;ENST00000445267;ENST00000448827	T;T	0.03860	3.78;3.78	4.06	-0.497	0.12023	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00271	0.0008	N	0.00335	-1.625	0.80722	P	0.0	B	0.12013	0.005	B	0.12156	0.007	T	0.39440	-0.9614	8	0.02654	T	1	-0.0212	3.9934	0.09548	0.1782:0.2621:0.0:0.5598	rs9369265;rs52824613;rs9369265	73	Q6UXN2	TRML4_HUMAN	R	73	ENSP00000342570:W73R;ENSP00000418078:W73R	ENSP00000342570:W73R	W	+	1	0	TREML4	41304583	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.954000	0.00326	-0.463000	0.06973	-0.880000	0.02959	TGG	T|0.307;C|0.693	0.693	strong		0.507	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
CINP	51550	hgsc.bcm.edu	37	14	102815042	102815042	+	Missense_Mutation	SNP	C	C	T	rs7011	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:102815042C>T	ENST00000216756.6	-	5	531	c.491G>A	c.(490-492)cGc>cAc	p.R164H	CINP_ENST00000541568.2_3'UTR|CINP_ENST00000536961.2_Missense_Mutation_p.R179H|CINP_ENST00000560326.1_5'Flank	NM_032630.2	NP_116019.1	Q9BW66	CINP_HUMAN	cyclin-dependent kinase 2 interacting protein	164			R -> H (in dbSNP:rs7011).		cell cycle (GO:0007049)|cell division (GO:0051301)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	nucleus (GO:0005634)				large_intestine(2)|lung(2)	4						GGCCACCGTGCGCTTCAGGAG	0.552													C|||	826	0.164936	0.0756	0.1643	5008	,	,		20078	0.1081		0.2654	False		,,,				2504	0.2413				p.R179H		Atlas-SNP	.											CINP,NS,carcinoma,-1,1	CINP	17	1	0			c.G536A						scavenged	.	C	HIS/ARG,,HIS/ARG	462,3944	220.7+/-238.1	35,392,1776	78.0	53.0	61.0		536,,491	2.8	0.7	14	dbSNP_52	61	2570,6030	417.0+/-352.3	371,1828,2101	yes	missense,utr-3,missense	CINP	NM_001177611.1,NM_001177612.1,NM_032630.2	29,,29	406,2220,3877	TT,TC,CC		29.8837,10.4857,23.3123	benign,,benign	179/228,,164/213	102815042	3032,9974	2203	4300	6503	SO:0001583	missense	51550	exon5			ACCGTGCGCTTCA	AK056112, AF228148, AF228149	CCDS9972.1	14q32.33	2010-02-17			ENSG00000100865	ENSG00000100865			23789	protein-coding gene	gene with protein product		613362				16082200	Standard	NM_032630		Approved	MGC849	uc021sea.1	Q9BW66		ENST00000216756.6:c.491G>A	14.37:g.102815042C>T	ENSP00000216756:p.Arg164His	Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	132	78	0.590909	NM_001177611	F5H7P3|F5H8A7|Q9NPF9	Missense_Mutation	SNP	ENST00000216756.6	37	CCDS9972.1	349	0.15979853479853479	37	0.07520325203252033	61	0.1685082872928177	52	0.09090909090909091	199	0.262532981530343	C	10.76	1.440241	0.25900	0.104857	0.298837	ENSG00000100865	ENST00000216756;ENST00000536961	T;T	0.53206	0.67;0.63	6.07	2.76	0.32466	.	0.355408	0.30101	N	0.010410	T	0.00012	0.0000	L	0.50919	1.6	0.09310	P	0.999999999841401	B	0.21309	0.054	B	0.09377	0.004	T	0.23940	-1.0174	9	0.30854	T	0.27	-2.3364	9.4492	0.38717	0.0:0.6095:0.0:0.3905	rs7011;rs17664746;rs52824323;rs59427525;rs7011	164	Q9BW66	CINP_HUMAN	H	164;179	ENSP00000216756:R164H;ENSP00000442057:R179H	ENSP00000216756:R164H	R	-	2	0	CINP	101884795	0.999000	0.42202	0.701000	0.30321	0.134000	0.20937	0.621000	0.24418	0.644000	0.30656	-0.140000	0.14226	CGC	C|0.795;N|0.000	.	strong		0.552	CINP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415055.1	NM_032630	
PREX2	80243	hgsc.bcm.edu	37	8	69009268	69009268	+	Silent	SNP	C	C	T	rs3812458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:69009268C>T	ENST00000288368.4	+	22	2662	c.2385C>T	c.(2383-2385)ttC>ttT	p.F795F	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	795					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TTGACAAATTCAACACTATGG	0.383													C|||	1333	0.266174	0.2731	0.2435	5008	,	,		17724	0.1885		0.2783	False		,,,				2504	0.3405				p.F795F		Atlas-SNP	.											.	PREX2	614	.	0			c.C2385T						PASS	.	C	,	1201,3205	419.3+/-338.6	169,863,1171	132.0	121.0	124.0		2385,2385	2.2	1.0	8	dbSNP_107	124	2270,6330	383.0+/-340.6	311,1648,2341	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	480,2511,3512	TT,TC,CC		26.3953,27.2583,26.6877	,	795/1607,795/980	69009268	3471,9535	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon22			CAAATTCAACACT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2385C>T	8.37:g.69009268C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	107	58	0.542056	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			C|0.740;T|0.260	0.260	strong		0.383	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
HSP90AB1	3326	hgsc.bcm.edu	37	6	44221299	44221299	+	Silent	SNP	C	C	T	rs143048794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44221299C>T	ENST00000371554.1	+	12	2353	c.2139C>T	c.(2137-2139)ggC>ggT	p.G713G	SLC35B2_ENST00000495706.1_5'Flank|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000371646.5_Silent_p.G713G|HSP90AB1_ENST00000353801.3_Silent_p.G713G			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	713					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)	p.G713G(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTCTCGAGGGCGATGAGGATG	0.498											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G713G		Atlas-SNP	.											HSP90AB1,NS,carcinoma,0,1	HSP90AB1	83	1	1	Substitution - coding silent(1)	lung(1)	c.C2139T						PASS	.						79.0	82.0	81.0					6																	44221299		2203	4300	6503	SO:0001819	synonymous_variant	3326	exon12			CGAGGGCGATGAG	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2139C>T	6.37:g.44221299C>T		Somatic	146	0	0	922	WXS	Illumina HiSeq	Phase_I	246	41	0.166667	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Silent	SNP	ENST00000371554.1	37	CCDS4909.1																																																																																			C|0.863;T|0.137	0.137	strong		0.498	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
UPF2	26019	hgsc.bcm.edu	37	10	12077085	12077085	+	Missense_Mutation	SNP	T	T	C	rs375002070		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:12077085T>C	ENST00000356352.2	-	1	811	c.338A>G	c.(337-339)cAa>cGa	p.Q113R	UPF2_ENST00000460569.1_5'UTR|UPF2_ENST00000357604.5_Missense_Mutation_p.Q113R|UPF2_ENST00000397053.2_Missense_Mutation_p.Q113R			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	113	Glu/Lys-rich.|Sufficient for interaction with UPF1.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				TTCTTCTTCTTGCTGACGTTT	0.378																																					p.Q113R		Atlas-SNP	.											.	UPF2	111	.	0			c.A338G						PASS	.	T	ARG/GLN,ARG/GLN	0,4406		0,0,2203	211.0	198.0	202.0		338,338	5.4	1.0	10		202	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	UPF2	NM_080599.1,NM_015542.2	43,43	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign,benign	113/1273,113/1273	12077085	2,13004	2203	4300	6503	SO:0001583	missense	26019	exon2			TCTTCTTGCTGAC	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"""smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.338A>G	10.37:g.12077085T>C	ENSP00000348708:p.Gln113Arg	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	170	82	0.482353	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	37	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.067554	0.36470	0.0	2.33E-4	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000379172;ENST00000397053;ENST00000313977	T;T;T	0.21734	1.99;1.99;1.99	5.44	5.44	0.79542	.	0.136504	0.50627	D	0.000115	T	0.07773	0.0195	N	0.02011	-0.69	0.28417	N	0.917902	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.23619	-1.0183	10	0.18710	T	0.47	.	9.9399	0.41574	0.0:0.077:0.0:0.923	.	83;113	Q9HAU5-2;Q9HAU5	.;RENT2_HUMAN	R	113;113;83;113;83	ENSP00000348708:Q113R;ENSP00000350221:Q113R;ENSP00000380244:Q113R	ENSP00000313617:Q83R	Q	-	2	0	UPF2	12117091	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.725000	0.54970	2.198000	0.70561	0.482000	0.46254	CAA	.	.	none		0.378	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1		
DPPA3	359787	hgsc.bcm.edu	37	12	7867847	7867847	+	Missense_Mutation	SNP	G	G	C	rs2024320	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7867847G>C	ENST00000345088.2	+	2	268	c.151G>C	c.(151-153)Gaa>Caa	p.E51Q		NM_199286.2	NP_954980.1	Q6W0C5	DPPA3_HUMAN	developmental pluripotency associated 3	51			E -> Q (in dbSNP:rs2024320).		chromatin modification (GO:0016568)|embryonic cleavage (GO:0040016)|negative regulation of DNA demethylation (GO:1901536)|protection of DNA demethylation of female pronucleus (GO:0044726)|regulation of genetic imprinting (GO:2000653)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)	8				Kidney(36;0.0887)		CGCTAGTAGCGAATCTGTTTC	0.463													G|||	1091	0.217851	0.1884	0.2349	5008	,	,		-128	0.1845		0.3121	False		,,,				2504	0.183				p.E51Q		Atlas-SNP	.											DPPA3,NS,carcinoma,0,1	DPPA3	26	1	0			c.G151C						scavenged	.	G	GLN/GLU	943,3463	357.6+/-314.0	99,745,1359	80.0	82.0	81.0		151	-4.9	0.0	12	dbSNP_94	81	2638,5962	421.6+/-353.8	417,1804,2079	no	missense	DPPA3	NM_199286.2	29	516,2549,3438	CC,CG,GG		30.6744,21.4026,27.5334	benign	51/160	7867847	3581,9425	2203	4300	6503	SO:0001583	missense	359787	exon2			AGTAGCGAATCTG	AY317075	CCDS8582.1	12p13.31	2012-10-02			ENSG00000187569	ENSG00000187569			19199	protein-coding gene	gene with protein product		608408					Standard	NM_199286		Approved	Stella	uc001qtf.3	Q6W0C5	OTTHUMG00000168434	ENST00000345088.2:c.151G>C	12.37:g.7867847G>C	ENSP00000339250:p.Glu51Gln	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	166	72	0.433735	NM_199286	Q0P5U3|Q6JZS6	Missense_Mutation	SNP	ENST00000345088.2	37	CCDS8582.1	535	0.24496336996336995	100	0.2032520325203252	88	0.2430939226519337	108	0.1888111888111888	239	0.3153034300791557	G	2.265	-0.368323	0.05069	0.214026	0.306744	ENSG00000187569	ENST00000345088	T	0.46063	0.88	2.48	-4.95	0.03048	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.28299	-1.0048	8	0.48119	T	0.1	0.0024	8.0509	0.30577	0.165:0.5213:0.3137:0.0	rs2024320;rs2024320	51	Q6W0C5	DPPA3_HUMAN	Q	51	ENSP00000339250:E51Q	ENSP00000339250:E51Q	E	+	1	0	DPPA3	7759114	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.670000	0.00844	-2.785000	0.00359	-1.250000	0.01514	GAA	G|0.700;C|0.300	0.300	strong		0.463	DPPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399718.1	NM_199286	
FAM186A	121006	hgsc.bcm.edu	37	12	50745703	50745703	+	Missense_Mutation	SNP	T	T	G	rs201307392		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745703T>G	ENST00000327337.5	-	4	4911	c.4912A>C	c.(4912-4914)Act>Cct	p.T1638P	FAM186A_ENST00000543111.1_Missense_Mutation_p.T1638P|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1638																	GGGGTGAGAGTGATCCCCTGA	0.637																																					p.T1638P	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,caecum,carcinoma,0,2	FAM186A	181	2	0			c.A4912C						scavenged	.						28.0	28.0	28.0					12																	50745703		692	1591	2283	SO:0001583	missense	121006	exon4			TGAGAGTGATCCC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4912A>C	12.37:g.50745703T>G	ENSP00000329995:p.Thr1638Pro	Somatic	174	3	0.0172414		WXS	Illumina HiSeq	Phase_I	218	32	0.146789	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	T	7.684	0.689691	0.14973	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.04862	3.54;3.54	4.23	-8.46	0.00942	.	.	.	.	.	T	0.02119	0.0066	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39901	-0.9591	9	0.20519	T	0.43	.	1.9715	0.03407	0.2999:0.0795:0.1553:0.4652	.	1638;1638	F5GYN0;A6NE01	.;F186A_HUMAN	P	1638	ENSP00000441337:T1638P;ENSP00000329995:T1638P	ENSP00000329995:T1638P	T	-	1	0	FAM186A	49031970	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-5.912000	0.00091	-3.131000	0.00236	-2.179000	0.00317	ACT	.	.	weak		0.637	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
SSH1	54434	hgsc.bcm.edu	37	12	109194652	109194652	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109194652C>G	ENST00000326495.5	-	12	1145	c.1052G>C	c.(1051-1053)gGc>gCc	p.G351A	SSH1_ENST00000326470.5_Missense_Mutation_p.G362A|SSH1_ENST00000360239.3_Missense_Mutation_p.G39A|SSH1_ENST00000551165.1_Missense_Mutation_p.G351A	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	351	Tyrosine-protein phosphatase.				actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGCAAATAAGCCAGGAAAAAA	0.348																																					p.G362A		Atlas-SNP	.											SSH1_ENST00000326470,NS,carcinoma,0,2	SSH1	144	2	0			c.G1085C						PASS	.						93.0	101.0	98.0					12																	109194652		2203	4300	6503	SO:0001583	missense	54434	exon11			AATAAGCCAGGAA	BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30579	protein-coding gene	gene with protein product		606778	"""slingshot homolog 1 (Drosophila)"""			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.1052G>C	12.37:g.109194652C>G	ENSP00000315713:p.Gly351Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	130	74	0.569231	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Missense_Mutation	SNP	ENST00000326495.5	37	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.811838	0.90707	.	.	ENSG00000084112	ENST00000360239;ENST00000326495;ENST00000551165;ENST00000326470	D;T;T;T	0.85556	-2.0;0.09;0.09;0.09	5.72	5.72	0.89469	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.90800	0.7111	L	0.50919	1.6	0.80722	D	1	B;P;B;D	0.76494	0.068;0.562;0.084;0.999	B;B;B;D	0.80764	0.077;0.239;0.125;0.994	D	0.89849	0.4008	10	0.51188	T	0.08	-49.7361	20.2626	0.98452	0.0:1.0:0.0:0.0	.	362;351;351;39	Q8WYL5-5;Q8WYL5-2;Q8WYL5;Q8WYL5-4	.;.;SSH1_HUMAN;.	A	39;351;351;362	ENSP00000353374:G39A;ENSP00000315713:G351A;ENSP00000448824:G351A;ENSP00000326107:G362A	ENSP00000326107:G362A	G	-	2	0	SSH1	107718781	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.818000	0.86416	2.873000	0.98535	0.563000	0.77884	GGC	.	.	none		0.348	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	
ZNF479	90827	hgsc.bcm.edu	37	7	57188718	57188718	+	Missense_Mutation	SNP	T	T	C	rs62464802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:57188718T>C	ENST00000331162.4	-	5	674	c.404A>G	c.(403-405)tAt>tGt	p.Y135C		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			GTGCACCTCATATTCACCCAC	0.328													.|||	1641	0.327676	0.115	0.379	5008	,	,		17489	0.5427		0.2913	False		,,,				2504	0.3947				p.Y135C		Atlas-SNP	.											.	ZNF479	193	.	0			c.A404G						PASS	.	C	CYS/TYR	550,3188		35,480,1354	124.0	113.0	117.0		404	-1.1	0.0	7	dbSNP_129	117	2751,5495		487,1777,1859	yes	missense	ZNF479	NM_033273.1	194	522,2257,3213	CC,CT,TT		33.3616,14.7138,27.5451	benign	135/525	57188718	3301,8683	1869	4123	5992	SO:0001583	missense	90827	exon5			ACCTCATATTCAC	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"""Zinc fingers, C2H2-type"", ""-"""	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.404A>G	7.37:g.57188718T>C	ENSP00000333776:p.Tyr135Cys	Somatic	435	0	0		WXS	Illumina HiSeq	Phase_I	447	214	0.478747	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	37	CCDS43590.1	722	0.3305860805860806	43	0.08739837398373984	115	0.31767955801104975	339	0.5926573426573427	225	0.29683377308707126	N	0	-2.671338	0.00104	0.147138	0.333616	ENSG00000185177	ENST00000331162	T	0.06449	3.3	1.6	-1.1	0.09872	.	.	.	.	.	T	0.00012	0.0000	N	0.00182	-1.905	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41016	-0.9532	8	0.02654	T	1	.	0.203	0.00147	0.2087:0.239:0.2071:0.3452	rs62464802	135	Q96JC4	ZN479_HUMAN	C	135	ENSP00000333776:Y135C	ENSP00000333776:Y135C	Y	-	2	0	ZNF479	57192660	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.701000	0.05075	-0.649000	0.05430	-0.498000	0.04607	TAT	T|0.680;C|0.320	0.320	strong		0.328	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202	
PDZD2	23037	hgsc.bcm.edu	37	5	32087808	32087808	+	Silent	SNP	G	G	C	rs3733720	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:32087808G>C	ENST00000438447.1	+	20	4642	c.4254G>C	c.(4252-4254)ggG>ggC	p.G1418G	PDZD2_ENST00000282493.3_Silent_p.G1418G			O15018	PDZD2_HUMAN	PDZ domain containing 2	1418					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCCCAGGGGGGAGTAGAGAGA	0.602													G|||	589	0.117612	0.0439	0.1441	5008	,	,		19185	0.2371		0.0755	False		,,,				2504	0.1186				p.G1418G		Atlas-SNP	.											.	PDZD2	306	.	0			c.G4254C						PASS	.																																			SO:0001819	synonymous_variant	23037	exon19			AGGGGGGAGTAGA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.4254G>C	5.37:g.32087808G>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	161	59	0.36646	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			G|0.891;C|0.109	0.109	strong		0.602	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
PCDHGB6	56100	hgsc.bcm.edu	37	5	140788107	140788107	+	Missense_Mutation	SNP	C	C	T	rs201370009		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140788107C>T	ENST00000520790.1	+	1	338	c.338C>T	c.(337-339)cCt>cTt	p.P113L	PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	113	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGAAAATCCTTTAAATATT	0.383													.|||	1	0.000199681	0.0	0.0	5008	,	,		17773	0.0		0.001	False		,,,				2504	0.0				p.P113L		Atlas-SNP	.											PCDHGB6,right_lower_lobe,carcinoma,0,1	PCDHGB6	120	1	0			c.C338T						PASS	.	C	,,,,,,,,,,,,,LEU/PRO,,LEU/PRO	1,3661		0,1,1830	156.0	162.0	160.0		,,,,,,,,,,,,,338,,338	5.4	1.0	5		160	14,8126		0,14,4056	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032100.1	,,,,,,,,,,,,,98,,98	0,15,5886	TT,TC,CC		0.172,0.0273,0.1271	,,,,,,,,,,,,,,,	,,,,,,,,,,,,,113/931,,113/821	140788107	15,11787	1831	4070	5901	SO:0001583	missense	56100	exon1			AAAATCCTTTAAA	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"""Cadherins / Protocadherins : Clustered"""	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.338C>T	5.37:g.140788107C>T	ENSP00000428603:p.Pro113Leu	Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	206	115	0.558252	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	c	18.01	3.528330	0.64860	2.73E-4	0.00172	ENSG00000253305	ENST00000520790	T	0.37235	1.21	5.38	5.38	0.77491	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.72391	0.3454	H	0.95574	3.69	0.58432	D	0.999998	D;D	0.71674	0.998;0.998	D;D	0.71414	0.973;0.969	T	0.81824	-0.0755	9	0.87932	D	0	.	19.1331	0.93415	0.0:1.0:0.0:0.0	.	113;113	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	L	113	ENSP00000428603:P113L	ENSP00000428603:P113L	P	+	2	0	PCDHGB6	140768291	1.000000	0.71417	0.995000	0.50966	0.378000	0.30076	7.779000	0.85648	2.517000	0.84864	0.467000	0.42956	CCT	C|0.994;T|0.006	0.006	strong		0.383	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
MCM10	55388	hgsc.bcm.edu	37	10	13239651	13239651	+	Missense_Mutation	SNP	A	A	G	rs2274110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:13239651A>G	ENST00000484800.2	+	15	2109	c.2006A>G	c.(2005-2007)aAa>aGa	p.K669R	MCM10_ENST00000378714.3_Missense_Mutation_p.K668R|MCM10_ENST00000378694.1_Missense_Mutation_p.K668R			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	669			K -> R (in dbSNP:rs2274110). {ECO:0000269|PubMed:15489334}.		cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.K669R(1)		central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						TTAAGGGCAAAAGGCCAGGTT	0.418													A|||	547	0.109225	0.0129	0.134	5008	,	,		16861	0.1002		0.1948	False		,,,				2504	0.1431				p.K669R		Atlas-SNP	.											MCM10,NS,carcinoma,0,1	MCM10	76	1	1	Substitution - Missense(1)	stomach(1)	c.A2006G						PASS	.	A	ARG/LYS,ARG/LYS	171,4235	112.1+/-150.2	4,163,2036	85.0	81.0	83.0		2003,2006	5.3	1.0	10	dbSNP_100	83	1605,6995	297.1+/-303.3	163,1279,2858	yes	missense,missense	MCM10	NM_018518.4,NM_182751.2	26,26	167,1442,4894	GG,GA,AA		18.6628,3.8811,13.6552	probably-damaging,probably-damaging	668/875,669/876	13239651	1776,11230	2203	4300	6503	SO:0001583	missense	55388	exon15			GGGCAAAAGGCCA	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.2006A>G	10.37:g.13239651A>G	ENSP00000418268:p.Lys669Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	260	0.11904761904761904	8	0.016260162601626018	56	0.15469613259668508	52	0.09090909090909091	144	0.18997361477572558	A	26.1	4.704765	0.88924	0.038811	0.186628	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.18810	2.2;2.2;2.19	5.33	5.33	0.75918	Replication factor Mcm10 (1);	0.042443	0.85682	D	0.000000	T	0.00073	0.0002	L	0.58969	1.84	0.09310	P	0.9999999831145	D;P;D	0.57571	0.98;0.947;0.957	P;P;P	0.59012	0.824;0.766;0.85	T	0.01252	-1.1405	9	0.40728	T	0.16	-4.2679	15.6241	0.76840	1.0:0.0:0.0:0.0	rs2274110;rs52802669;rs59009311;rs2274110	668;668;669	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	R	668;669;669;668	ENSP00000367986:K668R;ENSP00000418268:K669R;ENSP00000367966:K668R	ENSP00000354945:K669R	K	+	2	0	MCM10	13279657	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.021000	0.76425	2.145000	0.66743	0.533000	0.62120	AAA	A|0.880;G|0.120	0.120	strong		0.418	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
NRAP	4892	hgsc.bcm.edu	37	10	115381747	115381747	+	Missense_Mutation	SNP	G	G	A	rs868738	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115381747G>A	ENST00000359988.3	-	24	2894	c.2650C>T	c.(2650-2652)Cgc>Tgc	p.R884C	NRAP_ENST00000369360.3_Missense_Mutation_p.R857C|NRAP_ENST00000369358.4_Missense_Mutation_p.R892C|NRAP_ENST00000360478.3_Missense_Mutation_p.R849C	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.R884C(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TGAGCTTTGCGGGCATGCACG	0.537													G|||	1049	0.209465	0.0446	0.4409	5008	,	,		23149	0.1786		0.3211	False		,,,				2504	0.1851				p.R884C		Atlas-SNP	.											NRAP,colon,carcinoma,0,2	NRAP	208	2	1	Substitution - Missense(1)	stomach(1)	c.C2650T						PASS	.	G	CYS/ARG,CYS/ARG	455,3951	215.5+/-234.4	24,407,1772	265.0	199.0	221.0		2545,2650	5.1	1.0	10	dbSNP_86	221	2904,5696	455.2+/-363.7	500,1904,1896	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	180,180	524,2311,3668	AA,AG,GG		33.7674,10.3268,25.8265	probably-damaging,probably-damaging	849/1696,884/1731	115381747	3359,9647	2203	4300	6503	SO:0001583	missense	4892	exon24			CTTTGCGGGCATG		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2650C>T	10.37:g.115381747G>A	ENSP00000353078:p.Arg884Cys	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	286	136	0.475524	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	519	0.23763736263736263	30	0.06097560975609756	144	0.39779005524861877	98	0.17132867132867133	247	0.3258575197889182	G	21.7	4.187415	0.78789	0.103268	0.337674	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.99	5.08	0.68730	.	0.176401	0.50627	D	0.000110	T	0.00012	0.0000	L	0.27053	0.805	0.21740	P	0.99956126	D;D;D	0.59767	0.975;0.985;0.986	P;P;P	0.54815	0.582;0.761;0.582	T	0.44267	-0.9339	9	0.72032	D	0.01	.	8.3557	0.32329	0.0765:0.0:0.6729:0.2506	rs868738;rs17772691;rs52791341;rs59077407;rs868738	884;849;884	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	C	892;857;884;849	ENSP00000358365:R892C;ENSP00000358367:R857C;ENSP00000353078:R884C;ENSP00000353666:R849C	ENSP00000353078:R884C	R	-	1	0	NRAP	115371737	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	4.833000	0.62766	1.529000	0.49120	0.655000	0.94253	CGC	G|0.758;N|0.000	.	strong		0.537	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
OR10H1	26539	hgsc.bcm.edu	37	19	15918500	15918500	+	Silent	SNP	G	G	A	rs148327766	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15918500G>A	ENST00000334920.2	-	1	436	c.348C>T	c.(346-348)acC>acT	p.T116T		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						AGCCCATGACGGTGAGCAGGA	0.657													.|||	303	0.0605032	0.0257	0.0764	5008	,	,		21186	0.0625		0.0915	False		,,,				2504	0.0624				p.T116T		Atlas-SNP	.											.	OR10H1	59	.	0			c.C348T						PASS	.	A		153,4253		1,151,2051	36.0	33.0	34.0		348	-9.4	0.5	19	dbSNP_134	34	905,7681		58,789,3446	no	coding-synonymous	OR10H1	NM_013940.2		59,940,5497	AA,AG,GG		10.5404,3.4725,8.1435		116/319	15918500	1058,11934	2203	4293	6496	SO:0001819	synonymous_variant	26539	exon1			CATGACGGTGAGC	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.348C>T	19.37:g.15918500G>A		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	267	122	0.456929	NM_013940	Q6IFQ2|Q96R59	Silent	SNP	ENST00000334920.2	37	CCDS12335.1																																																																																			G|0.750;A|0.250	0.250	strong		0.657	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
UBASH3A	53347	hgsc.bcm.edu	37	21	43854985	43854985	+	Silent	SNP	A	A	C	rs17114925	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43854985A>C	ENST00000319294.6	+	10	1345	c.1314A>C	c.(1312-1314)ccA>ccC	p.P438P	UBASH3A_ENST00000398367.1_Silent_p.P400P|UBASH3A_ENST00000291535.6_Silent_p.P400P	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	438	Phosphatase-like.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						GCAGTCTGCCAAGACGGAGTC	0.438													C|||	1253	0.2502	0.4864	0.2017	5008	,	,		23312	0.2073		0.1262	False		,,,				2504	0.137				p.P438P		Atlas-SNP	.											.	UBASH3A	72	.	0			c.A1314C						PASS	.	C	,	1918,2488	624.6+/-394.4	424,1070,709	109.0	104.0	105.0		1200,1314	2.7	0.5	21	dbSNP_123	105	1259,7341	761.0+/-407.6	105,1049,3146	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	529,2119,3855	CC,CA,AA		14.6395,43.5315,24.4272	,	400/624,438/662	43854985	3177,9829	2203	4300	6503	SO:0001819	synonymous_variant	53347	exon10			TCTGCCAAGACGG	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.1314A>C	21.37:g.43854985A>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			A|0.750;C|0.250	0.250	strong		0.438	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
EHD2	30846	hgsc.bcm.edu	37	19	48244569	48244569	+	Silent	SNP	G	G	A	rs3745758	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48244569G>A	ENST00000263277.3	+	6	1763	c.1512G>A	c.(1510-1512)gaG>gaA	p.E504E	EHD2_ENST00000540884.1_3'UTR|EHD2_ENST00000538399.1_Silent_p.E368E	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	504	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.|EH. {ECO:0000255|PROSITE- ProRule:PRU00077}.				blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		TGGATGATGAGGAGTTCGCGC	0.672													G|||	2265	0.452276	0.1309	0.4885	5008	,	,		16609	0.5536		0.5497	False		,,,				2504	0.6564				p.E504E		Atlas-SNP	.											.	EHD2	59	.	0			c.G1512A						PASS	.	G		927,3479	344.1+/-307.9	111,705,1387	43.0	36.0	38.0		1512	3.9	1.0	19	dbSNP_107	38	4924,3676	607.3+/-395.2	1389,2146,765	no	coding-synonymous	EHD2	NM_014601.3		1500,2851,2152	AA,AG,GG		42.7442,21.0395,44.9869		504/544	48244569	5851,7155	2203	4300	6503	SO:0001819	synonymous_variant	30846	exon6			TGATGAGGAGTTC	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.1512G>A	19.37:g.48244569G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1																																																																																			G|0.559;A|0.441	0.441	strong		0.672	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
L3MBTL4	91133	hgsc.bcm.edu	37	18	5956238	5956238	+	Missense_Mutation	SNP	C	C	T	rs3737353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:5956238C>T	ENST00000284898.6	-	20	2053	c.1853G>A	c.(1852-1854)gGc>gAc	p.G618D	L3MBTL4_ENST00000317931.7_Missense_Mutation_p.G609D|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.G618D|RP11-793A3.1_ENST00000577704.1_RNA|L3MBTL4_ENST00000535782.1_Missense_Mutation_p.G422D	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	618			G -> D (in dbSNP:rs3737353). {ECO:0000269|PubMed:14702039}.		chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				GACTTCTTGGCCTGAGGCAAT	0.463													C|||	1927	0.384784	0.2927	0.2723	5008	,	,		20537	0.4742		0.3976	False		,,,				2504	0.4836				p.G618D	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											L3MBTL4,colon,carcinoma,0,1	L3MBTL4	87	1	0			c.G1853A						PASS	.	C	ASP/GLY	1114,2710		168,778,966	154.0	150.0	151.0		1853	2.8	0.0	18	dbSNP_107	151	3192,5078		658,1876,1601	yes	missense	L3MBTL4	NM_173464.3	94	826,2654,2567	TT,TC,CC		38.5973,29.1318,35.6044	possibly-damaging	618/624	5956238	4306,7788	1912	4135	6047	SO:0001583	missense	91133	exon20			TCTTGGCCTGAGG	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"""Sterile alpha motif (SAM) domain containing"""	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.1853G>A	18.37:g.5956238C>T	ENSP00000284898:p.Gly618Asp	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	127	71	0.559055	NM_173464	A8MTL8|Q8IXS3	Missense_Mutation	SNP	ENST00000284898.6	37	CCDS11839.2	831	0.3804945054945055	147	0.29878048780487804	103	0.2845303867403315	268	0.46853146853146854	313	0.4129287598944591	C	10.73	1.432921	0.25813	0.291318	0.385973	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000535782	T;T;T;T	0.16457	2.34;2.36;2.34;2.36	5.49	2.78	0.32641	.	0.425518	0.20187	N	0.097387	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.21225	0.053;0.049	B;B	0.23018	0.019;0.043	T	0.46062	-0.9218	9	0.39692	T	0.17	.	7.854	0.29472	0.0:0.741:0.0:0.259	rs3737353;rs58882188;rs3737353	618;609	Q8NA19;F8W9S8	LMBL4_HUMAN;.	D	618;609;618;422	ENSP00000382976:G618D;ENSP00000318543:G609D;ENSP00000284898:G618D;ENSP00000444774:G422D	ENSP00000284898:G618D	G	-	2	0	L3MBTL4	5946238	0.015000	0.18098	0.010000	0.14722	0.006000	0.05464	0.125000	0.15749	0.310000	0.22990	-0.880000	0.02959	GGC	C|0.627;T|0.373	0.373	strong		0.463	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464	
PDIA3	2923	hgsc.bcm.edu	37	15	44038899	44038899	+	Silent	SNP	C	C	T	rs2411284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:44038899C>T	ENST00000300289.5	+	1	310	c.162C>T	c.(160-162)gcC>gcT	p.A54A	CATSPER2P1_ENST00000381680.2_RNA|PDIA3_ENST00000538521.1_5'UTR|PDIA3_ENST00000469684.1_3'UTR	NM_005313.4	NP_005304.3	P30101	PDIA3_HUMAN	protein disulfide isomerase family A, member 3	54	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein N-linked glycosylation via asparagine (GO:0018279)|protein retention in ER lumen (GO:0006621)|proteolysis (GO:0006508)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|phospholipase C activity (GO:0004629)|poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(2)|skin(1)	17		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)		AGTTCTTCGCCCCCTGGTGAG	0.687													C|||	2750	0.549121	0.1755	0.7003	5008	,	,		13521	0.6944		0.7127	False		,,,				2504	0.6288				p.A54A		Atlas-SNP	.											PDIA3,NS,carcinoma,0,2	PDIA3	40	2	0			c.C162T						PASS	.	C		1361,2837		247,867,985	27.0	27.0	27.0		162	-1.5	1.0	15	dbSNP_100	27	6008,2282		2216,1576,353	no	coding-synonymous	PDIA3	NM_005313.4		2463,2443,1338	TT,TC,CC		27.5271,32.4202,40.9914		54/506	44038899	7369,5119	2099	4145	6244	SO:0001819	synonymous_variant	2923	exon1			CTTCGCCCCCTGG		CCDS10101.1	15q15	2009-11-20	2005-06-29	2005-03-03	ENSG00000167004	ENSG00000167004	5.3.4.1	"""Protein disulfide isomerases"""	4606	protein-coding gene	gene with protein product		602046	"""glucose regulated protein, 58kDa"", ""protein disulfide isomerase-associated 3"""	GRP58		8974399	Standard	NM_005313		Approved	P58, ERp61, ERp57, ERp60, GRP57, PI-PLC, HsT17083	uc001zsu.3	P30101	OTTHUMG00000044444	ENST00000300289.5:c.162C>T	15.37:g.44038899C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_005313	Q13453|Q14255|Q8IYF8|Q9UMU7	Silent	SNP	ENST00000300289.5	37	CCDS10101.1																																																																																			C|0.434;T|0.566	0.566	strong		0.687	PDIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103532.3	NM_005313	
ZGLP1	100125288	hgsc.bcm.edu	37	19	10416154	10416154	+	Silent	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10416154G>T	ENST00000403903.3	-	3	1808	c.610C>A	c.(610-612)Cgg>Agg	p.R204R	FDX1L_ENST00000541276.1_3'UTR|CTD-2369P2.10_ENST00000452032.2_3'UTR|ZGLP1_ENST00000403352.1_Silent_p.R120R	NM_001103167.1	NP_001096637.1	P0C6A0	ZGLP1_HUMAN	zinc finger, GATA-like protein 1	204					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|ovary(1)	6						GCACAGCGCCGGGGCTCTGAA	0.617																																					p.R204R		Atlas-SNP	.											ZGLP1_ENST00000403903,NS,carcinoma,+1,2	ZGLP1	18	2	0			c.C610A						scavenged	.						13.0	15.0	14.0					19																	10416154		1955	4137	6092	SO:0001819	synonymous_variant	100125288	exon3			AGCGCCGGGGCTC	AK096830	CCDS45959.1	19p13.2	2013-01-25			ENSG00000220201	ENSG00000220201		"""GATA zinc finger domain containing"""	37245	protein-coding gene	gene with protein product	"""GATA like protein 1"", ""GATA zinc finger domain containing 3"""	611639				16982049	Standard	NM_001103167		Approved	GLP1, GLP-1, GATAD3	uc002mnw.4	P0C6A0	OTTHUMG00000152114	ENST00000403903.3:c.610C>A	19.37:g.10416154G>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	2	0.0137931	NM_001103167		Silent	SNP	ENST00000403903.3	37	CCDS45959.1																																																																																			.	.	none		0.617	ZGLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325278.1	NM_001103167	
IMMT	10989	hgsc.bcm.edu	37	2	86400824	86400824	+	Missense_Mutation	SNP	G	G	A	rs1050301	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:86400824G>A	ENST00000410111.3	-	4	757	c.370C>T	c.(370-372)Cct>Tct	p.P124S	IMMT_ENST00000449247.2_Missense_Mutation_p.P124S|IMMT_ENST00000254636.5_Missense_Mutation_p.P37S|IMMT_ENST00000442664.2_Missense_Mutation_p.P124S|IMMT_ENST00000490238.1_5'Flank|IMMT_ENST00000409051.2_Missense_Mutation_p.P124S	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	124			P -> S (in dbSNP:rs6750289). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9168817}.		mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TGTGAGGCAGGCTGTTTAGAT	0.328													G|||	1649	0.329273	0.0219	0.4236	5008	,	,		16353	0.5069		0.3628	False		,,,				2504	0.4601				p.P124S		Atlas-SNP	.											IMMT,NS,carcinoma,0,1	IMMT	65	1	0			c.C370T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	331,3325		11,309,1508	144.0	120.0	127.0		370,370,370	3.4	1.0	2	dbSNP_86	127	2750,5406		456,1838,1784	no	missense,missense,missense	IMMT	NM_001100169.1,NM_001100170.1,NM_006839.2	74,74,74	467,2147,3292	AA,AG,GG		33.7175,9.0536,26.0836	possibly-damaging,possibly-damaging,possibly-damaging	124/758,124/748,124/759	86400824	3081,8731	1828	4078	5906	SO:0001583	missense	10989	exon4			AGGCAGGCTGTTT	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"""mitofilin"", ""mitochondrial inner membrane organizing system 2"""	600378	"""inner membrane protein, mitochondrial (mitofilin)"""			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.370C>T	2.37:g.86400824G>A	ENSP00000387262:p.Pro124Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	37	CCDS46355.1	725|725	0.33195970695970695|0.33195970695970695	6|6	0.012195121951219513|0.012195121951219513	151|151	0.4171270718232044|0.4171270718232044	286|286	0.5|0.5	282|282	0.3720316622691293|0.3720316622691293	G|G	18.35|18.35	3.604107|3.604107	0.66445|0.66445	0.090536|0.090536	0.337175|0.337175	ENSG00000132305|ENSG00000132305	ENST00000419070|ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715	.|T;T;T;T;T	.|0.30714	.|1.52;1.52;1.52;1.52;1.52	3.43|3.43	3.43|3.43	0.39272|0.39272	.|.	.|0.176656	.|0.51477	.|D	.|0.000090	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.71581|0.71581	2.175|2.175	0.09310|0.09310	P|P	0.9999999284871|0.9999999284871	.|P;P;P;B;B;P;B;P	.|0.52061	.|0.938;0.747;0.95;0.147;0.007;0.938;0.007;0.95	.|P;P;P;B;B;P;B;P	.|0.58266	.|0.747;0.679;0.836;0.153;0.065;0.747;0.065;0.836	T|T	0.48536|0.48536	-0.9027|-0.9027	4|9	.|0.14656	.|T	.|0.56	-9.876|-9.876	13.8948|13.8948	0.63764|0.63764	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs6750289;rs6750289|rs6750289;rs6750289	.|124;124;124;124;124;124;124;124	.|F5GZ32;B9A067;B4DKR1;Q05DN3;F8W9I1;Q16891-2;Q16891-3;Q16891	.|.;.;.;.;.;.;.;IMMT_HUMAN	V|S	21|37;124;124;124;124;124;124;124;124	.|ENSP00000254636:P37S;ENSP00000396899:P124S;ENSP00000387262:P124S;ENSP00000407788:P124S;ENSP00000387227:P124S	.|ENSP00000254636:P37S	A|P	-|-	2|1	0|0	IMMT|IMMT	86254335|86254335	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.063000|6.063000	0.71162|0.71162	1.836000|1.836000	0.53414|0.53414	0.561000|0.561000	0.74099|0.74099	GCC|CCT	T|0.038;G|0.593;C|0.070;N|0.001;A|0.299	0.299	strong		0.328	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
FAM218A	152756	hgsc.bcm.edu	37	4	165878335	165878335	+	Missense_Mutation	SNP	A	A	G	rs3733418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:165878335A>G	ENST00000513876.2	+	1	236	c.161A>G	c.(160-162)cAt>cGt	p.H54R	TRIM61_ENST00000329314.5_Intron	NM_153027.1	NP_694572.1	Q96MZ4	F218A_HUMAN	family with sequence similarity 218, member A	54			H -> R (in dbSNP:rs3733418).														GGCGGCCGCCATGGCAGTGTC	0.617													a|||	1395	0.278554	0.0598	0.1671	5008	,	,		16434	0.6488		0.16	False		,,,				2504	0.3937				p.H54R		Atlas-SNP	.											.	.	.	.	0			c.A161G						PASS	.		,ARG/HIS	348,4058		19,310,1874	25.0	23.0	24.0		,161	-1.1	0.0	4	dbSNP_107	24	1298,7302		104,1090,3106	yes	intron,missense	C4orf39,TRIM61	NM_001012414.2,NM_153027.1	,29	123,1400,4980	GG,GA,AA		15.093,7.8983,12.6557	,benign	,54/158	165878335	1646,11360	2203	4300	6503	SO:0001583	missense	152756	exon1			GCCGCCATGGCAG	AK056221	CCDS3807.1	4q32.3	2012-03-01	2012-03-01	2012-03-01	ENSG00000250486	ENSG00000250486			26466	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 39"""	C4orf39		12477932	Standard	NM_153027		Approved	FLJ31659	uc003iqx.1	Q96MZ4	OTTHUMG00000161252	ENST00000513876.2:c.161A>G	4.37:g.165878335A>G	ENSP00000427428:p.His54Arg	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	265	112	0.422642	NM_153027		Missense_Mutation	SNP	ENST00000513876.2	37	CCDS3807.1	540	0.24725274725274726	26	0.052845528455284556	64	0.17679558011049723	332	0.5804195804195804	118	0.15567282321899736	a	2.249	-0.371940	0.05034	0.078983	0.15093	ENSG00000250486	ENST00000513876	T	0.52526	0.66	0.543	-1.09	0.09904	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.20780	0.048	B	0.13407	0.009	T	0.43556	-0.9384	7	0.87932	D	0	.	.	.	.	rs3733418;rs57200258;rs3733418	54	Q96MZ4	CD039_HUMAN	R	54	ENSP00000427428:H54R	ENSP00000427428:H54R	H	+	2	0	C4orf39	166097785	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-1.703000	0.01900	-1.189000	0.02702	-1.465000	0.01017	CAT	A|0.813;G|0.187	0.187	strong		0.617	FAM218A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364308.1	NM_153027	
PSMB1	5689	hgsc.bcm.edu	37	6	170862300	170862300	+	Missense_Mutation	SNP	G	G	C	rs12717	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:170862300G>C	ENST00000262193.6	-	1	129	c.31C>G	c.(31-33)Cct>Gct	p.P11A	TBP_ENST00000540980.1_5'Flank|PSMB1_ENST00000462957.1_5'Flank|TBP_ENST00000230354.6_5'Flank|TBP_ENST00000392092.2_5'Flank	NM_002793.3	NP_002784.1	P20618	PSB1_HUMAN	proteasome (prosome, macropain) subunit, beta type, 1	11			P -> A (in dbSNP:rs12717). {ECO:0000269|PubMed:15489334}.		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	5		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)|Carfilzomib(DB08889)	TCTCTGCCAGGAGCCGAATAC	0.597													G|||	2254	0.45008	0.2708	0.3991	5008	,	,		17181	0.7728		0.4085	False		,,,				2504	0.4387				p.P11A		Atlas-SNP	.											.	PSMB1	12	.	0			c.C31G						PASS	.	G	ALA/PRO	1308,3098	433.1+/-343.5	184,940,1079	42.0	38.0	39.0		31	0.4	0.0	6	dbSNP_52	39	3350,5248	485.3+/-371.6	656,2038,1605	yes	missense	PSMB1	NM_002793.3	27	840,2978,2684	CC,CG,GG		38.9625,29.6868,35.8197	benign	11/242	170862300	4658,8346	2203	4299	6502	SO:0001583	missense	5689	exon1			TGCCAGGAGCCGA	D00761	CCDS34577.1	6q27	2008-02-05			ENSG00000008018	ENSG00000008018		"""Proteasome (prosome, macropain) subunits"""	9537	protein-coding gene	gene with protein product		602017				2025653	Standard	NM_002793		Approved	PMSB1, HC5	uc011ehe.2	P20618	OTTHUMG00000016087	ENST00000262193.6:c.31C>G	6.37:g.170862300G>C	ENSP00000262193:p.Pro11Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_002793	B5BU76|Q9BWA8	Missense_Mutation	SNP	ENST00000262193.6	37	CCDS34577.1	1049	0.4803113553113553	143	0.29065040650406504	152	0.4198895027624309	450	0.7867132867132867	304	0.40105540897097625	G	10.34	1.324311	0.24080	0.296868	0.389625	ENSG00000008018	ENST00000262193;ENST00000392093	T	0.24538	1.85	4.37	0.413	0.16401	.	1.016080	0.07851	N	0.964623	T	0.04227	0.0117	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42498	-0.9448	9	0.25751	T	0.34	0.0024	6.0254	0.19652	0.1757:0.2916:0.5328:0.0	rs12717;rs1049686;rs3189890;rs17354871;rs17655245;rs17849329;rs17860781;rs52804979;rs60717301;rs12717	11	P20618	PSB1_HUMAN	A	11;16	ENSP00000262193:P11A	ENSP00000262193:P11A	P	-	1	0	PSMB1	170704225	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	0.024000	0.13555	-0.128000	0.11641	0.563000	0.77884	CCT	G|0.580;C|0.420	0.420	strong		0.597	PSMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043278.2	NM_002793	
FCRL1	115350	hgsc.bcm.edu	37	1	157768000	157768000	+	Silent	SNP	G	G	C	rs3811024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:157768000G>C	ENST00000368176.3	-	8	1132	c.1065C>G	c.(1063-1065)acC>acG	p.T355T	FCRL1_ENST00000491942.1_Silent_p.T355T|FCRL1_ENST00000358292.3_Silent_p.T316T|FCRL1_ENST00000489998.1_5'UTR	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	355						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGTTGAGGTAGGTGAACTCTT	0.493													G|||	1158	0.23123	0.3434	0.2032	5008	,	,		20568	0.1855		0.2406	False		,,,				2504	0.137				p.T355T	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.C1065G						PASS	.	G	,,	1381,3025	456.3+/-351.3	216,949,1038	116.0	111.0	112.0		948,1065,1065	-0.7	0.0	1	dbSNP_107	112	2098,6502	362.6+/-332.8	252,1594,2454	no	coding-synonymous,coding-synonymous,coding-synonymous	FCRL1	NM_001159397.1,NM_001159398.1,NM_052938.4	,,	468,2543,3492	CC,CG,GG		24.3953,31.3436,26.7492	,,	316/367,355/429,355/430	157768000	3479,9527	2203	4300	6503	SO:0001819	synonymous_variant	115350	exon8			GAGGTAGGTGAAC	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.1065C>G	1.37:g.157768000G>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	180	84	0.466667	NM_001159398	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			G|0.747;C|0.253	0.253	strong		0.493	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	
ANKRD36	375248	hgsc.bcm.edu	37	2	97864333	97864333	+	Missense_Mutation	SNP	C	C	A	rs61218502|rs71329611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97864333C>A	ENST00000461153.2	+	44	2937	c.2693C>A	c.(2692-2694)gCc>gAc	p.A898D	ANKRD36_ENST00000420699.2_Missense_Mutation_p.A898D			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	898										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCTTCAAGTGCCGAGAAAGAT	0.303													.|||	2026	0.404553	0.2542	0.4957	5008	,	,		24678	0.2619		0.7972	False		,,,				2504	0.2863				p.A898D		Atlas-SNP	.											.	ANKRD36	170	.	0			c.C2693A						PASS	.						34.0	19.0	24.0					2																	97864333		691	1578	2269	SO:0001583	missense	375248	exon44			CAAGTGCCGAGAA	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.2693C>A	2.37:g.97864333C>A	ENSP00000419530:p.Ala898Asp	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.869581	0.00063	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000461694	T;T	0.78126	-1.15;-1.15	0.458	0.458	0.16670	.	.	.	.	.	T	0.42585	0.1209	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.21381	0.055;0.0	B;B	0.20767	0.031;0.0	T	0.35649	-0.9780	7	0.10636	T	0.68	.	.	.	.	rs61218502;rs62154821	898;314	A6QL64;F2Z332	AN36A_HUMAN;.	D	898;898;314;260	ENSP00000419530:A898D;ENSP00000391950:A898D	ENSP00000377149:A314D	A	+	2	0	ANKRD36	97228060	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.652000	0.05366	-0.681000	0.05204	-1.212000	0.01626	GCC	AT|1.000;|0.000	.	alt		0.303	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
C17orf74	201243	hgsc.bcm.edu	37	17	7329632	7329632	+	Missense_Mutation	SNP	T	T	G	rs13290	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7329632T>G	ENST00000333870.3	+	3	396	c.322T>G	c.(322-324)Tcc>Gcc	p.S108A	RP11-104H15.7_ENST00000575310.1_RNA|C17orf74_ENST00000574034.1_Intron	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	108			S -> A (in dbSNP:rs13290).			integral component of membrane (GO:0016021)				cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				CTCCTCTTTCTCCTGCCACCA	0.612													T|||	1728	0.345048	0.2837	0.3732	5008	,	,		15818	0.0427		0.5984	False		,,,				2504	0.4591				p.S108A		Atlas-SNP	.											.	C17orf74	56	.	0			c.T322G						PASS	.	T	ALA/SER	1500,2726		292,916,905	109.0	111.0	110.0		322	3.2	0.3	17	dbSNP_52	110	5402,3036		1729,1944,546	yes	missense	C17orf74	NM_175734.4	99	2021,2860,1451	GG,GT,TT		35.9801,35.4946,45.4991	possibly-damaging	108/502	7329632	6902,5762	2113	4219	6332	SO:0001583	missense	201243	exon3			TCTTTCTCCTGCC	BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.322T>G	17.37:g.7329632T>G	ENSP00000328061:p.Ser108Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	780	0.35714285714285715	151	0.30691056910569103	152	0.4198895027624309	19	0.033216783216783216	458	0.604221635883905	T	12.71	2.019575	0.35606	0.354946	0.640199	ENSG00000184560	ENST00000333870	T	0.35973	1.28	3.18	3.18	0.36537	.	0.000000	0.34802	N	0.003665	T	0.00012	0.0000	L	0.50333	1.59	0.24486	P	0.99432703	D	0.61697	0.99	D	0.72625	0.978	T	0.40572	-0.9556	9	0.49607	T	0.09	-8.748	8.1327	0.31037	0.0:0.0:0.0:1.0	rs13290;rs888259;rs3174745;rs3883243;rs59963573;rs13290	108	Q0P670	CQ074_HUMAN	A	108	ENSP00000328061:S108A	ENSP00000328061:S108A	S	+	1	0	C17orf74	7270356	0.011000	0.17503	0.329000	0.25429	0.047000	0.14425	0.457000	0.21875	1.683000	0.51011	0.402000	0.26972	TCC	T|0.588;G|0.412	0.412	strong		0.612	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734	
TECTA	7007	hgsc.bcm.edu	37	11	121038810	121038810	+	Silent	SNP	C	C	T	rs2155369	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:121038810C>T	ENST00000392793.1	+	19	5905	c.5634C>T	c.(5632-5634)agC>agT	p.S1878S	TECTA_ENST00000264037.2_Silent_p.S1878S			O75443	TECTA_HUMAN	tectorin alpha	1878	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		S -> R (in dbSNP:rs2155369).		cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GGATCGAAAGCGCCAACAACA	0.453													C|||	928	0.185304	0.0136	0.1571	5008	,	,		22018	0.3105		0.1402	False		,,,				2504	0.3548				p.S1878S		Atlas-SNP	.											TECTA,colon,carcinoma,+2,1	TECTA	329	1	0			c.C5634T						PASS	.	C		144,4262	100.7+/-139.4	7,130,2066	233.0	199.0	211.0		5634	-0.1	1.0	11	dbSNP_96	211	1141,7457	235.0+/-267.7	84,973,3242	no	coding-synonymous	TECTA	NM_005422.2		91,1103,5308	TT,TC,CC		13.2705,3.2683,9.8816		1878/2156	121038810	1285,11719	2203	4299	6502	SO:0001819	synonymous_variant	7007	exon18			CGAAAGCGCCAAC	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5634C>T	11.37:g.121038810C>T		Somatic	286	1	0.0034965		WXS	Illumina HiSeq	Phase_I	296	143	0.483108	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																			T|0.129;G|0.000;C|0.871	0.129	strong		0.453	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
LAMA5	3911	hgsc.bcm.edu	37	20	60893639	60893639	+	Silent	SNP	G	G	C	rs6089732	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:60893639G>C	ENST00000252999.3	-	53	7176	c.7110C>G	c.(7108-7110)acC>acG	p.T2370T		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2370	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCCGGTCGCGGGTTTGTGTGG	0.682													.|||	977	0.195088	0.0356	0.2478	5008	,	,		10169	0.373		0.2008	False		,,,				2504	0.184				p.T2370T		Atlas-SNP	.											LAMA5,caecum,carcinoma,0,1	LAMA5	268	1	0			c.C7110G						PASS	.			231,4125		8,215,1955	33.0	42.0	39.0		7110	0.6	0.0	20	dbSNP_114	39	1823,6719		186,1451,2634	no	coding-synonymous	LAMA5	NM_005560.3		194,1666,4589	CC,CG,GG		21.3416,5.303,15.9249		2370/3696	60893639	2054,10844	2178	4271	6449	SO:0001819	synonymous_variant	3911	exon53			GTCGCGGGTTTGT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7110C>G	20.37:g.60893639G>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.822;C|0.178	0.178	strong		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
ZNF772	400720	hgsc.bcm.edu	37	19	57985460	57985460	+	Missense_Mutation	SNP	T	T	A	rs2074059	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57985460T>A	ENST00000343280.4	-	5	912	c.652A>T	c.(652-654)Atg>Ttg	p.M218L	ZNF772_ENST00000601768.1_Intron|AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000427512.2_Missense_Mutation_p.M106L|ZNF772_ENST00000600175.1_Intron|ZNF772_ENST00000425074.3_3'UTR|ZNF772_ENST00000356584.3_Missense_Mutation_p.M177L|AC004076.9_ENST00000596831.1_Intron	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	218			M -> L (in dbSNP:rs2074059). {ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		GACATCTCCATTGATTGCACA	0.498													A|||	3388	0.676518	0.6127	0.7176	5008	,	,		20866	0.7014		0.6392	False		,,,				2504	0.7464				p.M218L	Melanoma(5;289 436 14293 15924 30817)	Atlas-SNP	.											.	ZNF772	42	.	0			c.A652T						PASS	.	A	LEU/MET,LEU/MET	2725,1681	507.3+/-366.6	849,1027,327	86.0	77.0	80.0		652,529	1.6	0.0	19	dbSNP_96	80	5448,3152	479.4+/-370.1	1680,2088,532	yes	missense,missense	ZNF772	NM_001024596.2,NM_001144068.1	15,15	2529,3115,859	AA,AT,TT		36.6512,38.1525,37.1598	benign,benign	218/490,177/449	57985460	8173,4833	2203	4300	6503	SO:0001583	missense	400720	exon5			TCTCCATTGATTG	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"""Zinc fingers, C2H2-type"", ""-"""	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.652A>T	19.37:g.57985460T>A	ENSP00000341165:p.Met218Leu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	198	87	0.439394	NM_001024596	A6NJK9|B4DH56|B4DYS0	Missense_Mutation	SNP	ENST00000343280.4	37	CCDS33133.1	1451	0.6643772893772893	302	0.6138211382113821	254	0.7016574585635359	411	0.7185314685314685	484	0.6385224274406333	A	9.582	1.123935	0.20959	0.618475	0.633488	ENSG00000197128	ENST00000343280;ENST00000427512;ENST00000319969;ENST00000356584;ENST00000291809	T;T;T	0.05382	3.58;3.45;3.54	3.79	1.63	0.23807	.	.	.	.	.	T	0.00012	0.0000	N	0.02158	-0.66	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.16719	-1.0393	8	0.66056	D	0.02	.	0.4889	0.00560	0.439:0.1827:0.2022:0.1761	rs2074059;rs59319118;rs2074059	106;177;218	Q68DY9-2;A6NJK9;Q68DY9	.;.;ZN772_HUMAN	L	218;106;164;177;143	ENSP00000341165:M218L;ENSP00000395967:M106L;ENSP00000348992:M177L	ENSP00000291809:M143L	M	-	1	0	ZNF772	62677272	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.073000	0.14640	-0.101000	0.12219	-0.496000	0.04628	ATG	T|0.353;A|0.647	0.647	strong		0.498	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
FAM66D	100132923	hgsc.bcm.edu	37	8	11991449	11991449	+	RNA	SNP	G	G	A	rs75826165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11991449G>A	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		GCATCTAGCCGAGAAGATGTG	0.478													G|||	1192	0.238019	0.0635	0.2089	5008	,	,		20967	0.498		0.2276	False		,,,				2504	0.2372				p.R24W		Atlas-SNP	.											.	.	.	.	0			c.C70T						PASS	.																																					392197	exon1			CTAGCCGAGAAGA			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11991449G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	7	4	0.571429	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				G|0.762;A|0.238	0.238	strong		0.478	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
CMYA5	202333	hgsc.bcm.edu	37	5	79032562	79032562	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:79032562A>G	ENST00000446378.2	+	2	8005	c.7974A>G	c.(7972-7974)gtA>gtG	p.V2658V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2658					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAAATCTAGTATTAGAAAAGT	0.408																																					p.V2658V		Atlas-SNP	.											CMYA5_ENST00000446378,lower_third,carcinoma,0,2	CMYA5	643	2	0			c.A7974G						scavenged	.						48.0	48.0	48.0					5																	79032562		1831	4091	5922	SO:0001819	synonymous_variant	202333	exon2			TCTAGTATTAGAA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7974A>G	5.37:g.79032562A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	168	3	0.0178571	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			.	.	none		0.408	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
CCNJL	79616	hgsc.bcm.edu	37	5	159682580	159682580	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:159682580C>T	ENST00000393977.3	-	6	1148	c.863G>A	c.(862-864)aGc>aAc	p.S288N	CCNJL_ENST00000519673.1_Missense_Mutation_p.S240N|CCNJL_ENST00000377503.2_5'UTR|CCNJL_ENST00000257536.7_Missense_Mutation_p.S240N|CCNJL_ENST00000541762.1_Missense_Mutation_p.S239N	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	288						nucleus (GO:0005634)				endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AATACACGTGCTGAGGTGCTC	0.552																																					p.S288N		Atlas-SNP	.											.	CCNJL	36	.	0			c.G863A						PASS	.						174.0	175.0	174.0					5																	159682580		1905	4140	6045	SO:0001583	missense	79616	exon6			CACGTGCTGAGGT	BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.863G>A	5.37:g.159682580C>T	ENSP00000377547:p.Ser288Asn	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	199	67	0.336683	NM_024565	Q6ZN43|Q9H7W8	Missense_Mutation	SNP	ENST00000393977.3	37	CCDS4350.2	.	.	.	.	.	.	.	.	.	.	C	8.336	0.827560	0.16749	.	.	ENSG00000135083	ENST00000393977;ENST00000257536;ENST00000519673;ENST00000541762	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.61	3.79	0.43588	Cyclin, C-terminal (1);Cyclin-like (3);	0.173358	0.51477	D	0.000099	T	0.09818	0.0241	N	0.20685	0.6	0.31077	N	0.712353	B;B;P	0.34724	0.014;0.099;0.465	B;B;B	0.30401	0.036;0.036;0.115	T	0.10965	-1.0607	10	0.19590	T	0.45	-12.2999	4.6847	0.12752	0.1373:0.4338:0.3483:0.0806	.	240;240;288	E7EN43;B4DZA8;Q8IV13	.;.;CCNJL_HUMAN	N	288;240;240;239	ENSP00000377547:S288N;ENSP00000257536:S240N;ENSP00000427960:S240N;ENSP00000446367:S239N	ENSP00000257536:S240N	S	-	2	0	CCNJL	159615158	1.000000	0.71417	0.976000	0.42696	0.446000	0.32137	2.239000	0.43079	1.334000	0.45468	0.655000	0.94253	AGC	.	.	none		0.552	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565	
PIGO	84720	hgsc.bcm.edu	37	9	35092480	35092480	+	Silent	SNP	T	T	G	rs35287398	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35092480T>G	ENST00000378617.3	-	7	1798	c.1404A>C	c.(1402-1404)gcA>gcC	p.A468A	PIGO_ENST00000492770.1_5'Flank|PIGO_ENST00000298004.5_Intron|PIGO_ENST00000341666.3_Silent_p.A468A|PIGO_ENST00000361778.2_Intron	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	468					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CCCACTGAGATGCCAGCAGGC	0.602													T|||	46	0.0091853	0.0053	0.0115	5008	,	,		18861	0.0		0.0169	False		,,,				2504	0.0143				p.A468A		Atlas-SNP	.											.	PIGO	86	.	0			c.A1404C						PASS	.	T	,,	25,4381	31.7+/-61.6	0,25,2178	86.0	86.0	86.0		,1404,	-2.0	0.7	9	dbSNP_126	86	127,8473	64.2+/-126.4	1,125,4174	no	intron,coding-synonymous,intron	PIGO	NM_001201484.1,NM_032634.3,NM_152850.3	,,	1,150,6352	GG,GT,TT		1.4767,0.5674,1.1687	,,	,468/1090,	35092480	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	84720	exon7			CTGAGATGCCAGC	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"""Phosphatidylinositol glycan anchor biosynthesis"""	23215	protein-coding gene	gene with protein product		614730	"""phosphatidylinositol glycan, class O"""			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.1404A>C	9.37:g.35092480T>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_032634	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Silent	SNP	ENST00000378617.3	37	CCDS6575.1																																																																																			T|0.990;G|0.010	0.010	strong		0.602	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634	
NLRP11	204801	hgsc.bcm.edu	37	19	56320663	56320663	+	Missense_Mutation	SNP	G	G	A	rs12461110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56320663G>A	ENST00000589093.1	-	3	1406	c.1313C>T	c.(1312-1314)cCg>cTg	p.P438L	NLRP11_ENST00000592953.1_Missense_Mutation_p.P339L|NLRP11_ENST00000443188.1_Missense_Mutation_p.P438L|NLRP11_ENST00000589824.2_Missense_Mutation_p.P438L|NLRP11_ENST00000360133.3_Missense_Mutation_p.P438L			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	438	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		P -> L (in dbSNP:rs12461110).				ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)	p.P438L(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AGTGTTGCTCGGCAAAAGAAT	0.458													G|||	1171	0.233826	0.0348	0.3415	5008	,	,		20530	0.2758		0.338	False		,,,				2504	0.2761				p.P438L		Atlas-SNP	.											NLRP11,NS,carcinoma,0,1	NLRP11	139	1	1	Substitution - Missense(1)	stomach(1)	c.C1313T						PASS	.	G	LEU/PRO	365,4041	186.0+/-213.0	13,339,1851	56.0	58.0	58.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1313	-4.4	0.0	19	dbSNP_120	58	2954,5646	460.2+/-365.1	536,1882,1882	yes	missense	NLRP11	NM_145007.3	98	549,2221,3733	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.3488,8.2842,25.519	possibly-damaging	438/1034	56320663	3319,9687	2203	4300	6503	SO:0001583	missense	204801	exon5			TTGCTCGGCAAAA	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.1313C>T	19.37:g.56320663G>A	ENSP00000466285:p.Pro438Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	533	0.24404761904761904	31	0.06300813008130081	124	0.3425414364640884	139	0.243006993006993	239	0.3153034300791557	G	8.650	0.897941	0.17686	0.082842	0.343488	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.74526	-0.85;-0.79	2.2	-4.4	0.03600	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;D	0.63880	0.947;0.993	B;P	0.51385	0.195;0.668	T	0.24693	-1.0153	8	0.51188	T	0.08	.	6.5746	0.22557	0.0:0.4019:0.1909:0.4072	rs12461110;rs17709352;rs52791389;rs56482655;rs59936961;rs12461110	438;438	P59045;P59045-2	NAL11_HUMAN;.	L	438	ENSP00000409898:P438L;ENSP00000353251:P438L	ENSP00000353251:P438L	P	-	2	0	NLRP11	61012475	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.428000	0.01025	-2.453000	0.00541	-0.868000	0.02995	CCG	G|0.761;A|0.239	0.239	strong		0.458	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
KIAA1377	57562	hgsc.bcm.edu	37	11	101832608	101832608	+	Missense_Mutation	SNP	T	T	C	rs11225090	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:101832608T>C	ENST00000263468.8	+	6	1112	c.842T>C	c.(841-843)aTt>aCt	p.I281T	KIAA1377_ENST00000537689.1_Missense_Mutation_p.I82T	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	281			I -> T (in dbSNP:rs11225090).							breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		CGGAATACCATTTCCCTCAAA	0.368													T|||	587	0.117212	0.025	0.1037	5008	,	,		17977	0.2679		0.0517	False		,,,				2504	0.1636				p.I281T		Atlas-SNP	.											.	KIAA1377	111	.	0			c.T842C						PASS	.	T	THR/ILE	112,4294	85.3+/-124.0	2,108,2093	73.0	70.0	71.0		842	2.0	0.0	11	dbSNP_120	71	334,8264	116.5+/-176.2	5,324,3970	yes	missense	KIAA1377	NM_020802.2	89	7,432,6063	CC,CT,TT		3.8846,2.542,3.4297	benign	281/1118	101832608	446,12558	2203	4299	6502	SO:0001583	missense	57562	exon6			ATACCATTTCCCT	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.842T>C	11.37:g.101832608T>C	ENSP00000263468:p.Ile281Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	245	0.11217948717948718	19	0.03861788617886179	37	0.10220994475138122	152	0.26573426573426573	37	0.048812664907651716	T	3.202	-0.163599	0.06502	0.02542	0.038846	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.07908	3.15;3.15	5.64	2.04	0.26737	.	1.366600	0.04626	N	0.402742	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.16802	0.019	B	0.12156	0.007	T	0.46400	-0.9194	9	0.37606	T	0.19	-0.003	5.2511	0.15522	0.0:0.2687:0.143:0.5883	rs11225090;rs52825191;rs58969642;rs11225090	281	Q9P2H0	K1377_HUMAN	T	281;82	ENSP00000263468:I281T;ENSP00000443184:I82T	ENSP00000263468:I281T	I	+	2	0	KIAA1377	101337818	0.003000	0.15002	0.005000	0.12908	0.367000	0.29736	0.899000	0.28417	0.097000	0.17492	-0.256000	0.11100	ATT	T|0.931;C|0.069	0.069	strong		0.368	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
UGT1A9	54600	hgsc.bcm.edu	37	2	234581002	234581002	+	Missense_Mutation	SNP	C	C	G	rs76167146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234581002C>G	ENST00000354728.4	+	1	504	c.422C>G	c.(421-423)tCt>tGt	p.S141C	UGT1A1_ENST00000609637.1_Missense_Mutation_p.S141C|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	141					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)			breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	AAGGAGAGTTCTTTTGATGCA	0.358																																					p.S141C		Atlas-SNP	.											UGT1A9,NS,carcinoma,0,1	UGT1A9	79	1	0			c.C422G						scavenged	.						125.0	125.0	125.0					2																	234581002		2203	4300	6503	SO:0001583	missense	54600	exon1			AGAGTTCTTTTGA	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"""UDP glucuronosyltransferases"""	12541	other	complex locus constituent		606434	"""UDP glycosyltransferase 1 family, polypeptide A9"""			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.422C>G	2.37:g.234581002C>G	ENSP00000346768:p.Ser141Cys	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	129	4	0.0310078	NM_021027	B8K285|P36509|Q9HAX0	Missense_Mutation	SNP	ENST00000354728.4	37	CCDS2505.1	.	.	.	.	.	.	.	.	.	.	C	5.531	0.282927	0.10458	.	.	ENSG00000241119	ENST00000354728	T	0.62639	0.01	3.41	3.41	0.39046	.	.	.	.	.	T	0.61375	0.2342	M	0.81942	2.565	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.12837	0.008;0.008	T	0.58036	-0.7707	9	0.66056	D	0.02	.	6.3779	0.21517	0.334:0.5079:0.1581:0.0	.	141;141	Q5DSZ5;O60656	.;UD19_HUMAN	C	141	ENSP00000346768:S141C	ENSP00000346768:S141C	S	+	2	0	UGT1A9	234245741	0.000000	0.05858	0.866000	0.34008	0.471000	0.32888	0.356000	0.20181	1.907000	0.55213	0.440000	0.28878	TCT	C|0.943;G|0.057	0.057	strong		0.358	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027	
MIIP	60672	hgsc.bcm.edu	37	1	12082461	12082461	+	Missense_Mutation	SNP	C	C	T	rs11588712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12082461C>T	ENST00000235332.4	+	3	593	c.424C>T	c.(424-426)Ccg>Tcg	p.P142S	MIIP_ENST00000436478.2_Missense_Mutation_p.P142S|Y_RNA_ENST00000365591.1_RNA|MIIP_ENST00000466860.1_3'UTR	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	142			P -> S (in dbSNP:rs11588712). {ECO:0000269|PubMed:15867349}.							autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						GGCACAGACCCCGAGGTCCAT	0.632													C|||	419	0.0836661	0.0242	0.0893	5008	,	,		19449	0.0675		0.159	False		,,,				2504	0.0992				p.P142S		Atlas-SNP	.											MIIP,NS,carcinoma,0,1	MIIP	34	1	0			c.C424T						PASS	.	C	SER/PRO	202,4200		5,192,2004	23.0	22.0	23.0		424	2.5	0.0	1	dbSNP_120	23	1295,7301		102,1091,3105	yes	missense	MIIP	NM_021933.3	74	107,1283,5109	TT,TC,CC		15.0651,4.5888,11.5172	benign	142/389	12082461	1497,11501	2201	4298	6499	SO:0001583	missense	60672	exon3			CAGACCCCGAGGT	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"""invasion inhibitory protein 45"""	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.424C>T	1.37:g.12082461C>T	ENSP00000235332:p.Pro142Ser	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	119	41	0.344538	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Missense_Mutation	SNP	ENST00000235332.4	37	CCDS143.1	173	0.07921245421245421	8	0.016260162601626018	25	0.06906077348066299	21	0.03671328671328671	119	0.15699208443271767	C	11.55	1.671371	0.29693	0.045888	0.150651	ENSG00000116691	ENST00000235332;ENST00000436478	T;T	0.18174	2.23;2.23	4.42	2.51	0.30379	.	2.687200	0.01449	N	0.015426	T	0.00073	0.0002	L	0.47716	1.5	0.80722	P	0.0	P	0.35272	0.493	B	0.36845	0.234	T	0.21586	-1.0241	9	0.19590	T	0.45	2.1469	5.7764	0.18281	0.1928:0.7043:0.0:0.103	rs11588712;rs17856240;rs52816027;rs11588712	142	Q5JXC2	MIIP_HUMAN	S	142	ENSP00000235332:P142S;ENSP00000392417:P142S	ENSP00000235332:P142S	P	+	1	0	MIIP	12005048	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.286000	0.18902	0.550000	0.28991	0.591000	0.81541	CCG	C|0.911;T|0.089	0.089	strong		0.632	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933	
GRM7	2917	hgsc.bcm.edu	37	3	7494417	7494417	+	Missense_Mutation	SNP	A	A	T	rs2229902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:7494417A>T	ENST00000357716.4	+	6	1572	c.1298A>T	c.(1297-1299)tAc>tTc	p.Y433F	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000403881.1_Missense_Mutation_p.Y433F|GRM7_ENST00000389336.4_Missense_Mutation_p.Y433F|GRM7_ENST00000402647.2_Missense_Mutation_p.Y433F|GRM7_ENST00000486284.1_Missense_Mutation_p.Y433F	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	433			Y -> F (in dbSNP:rs2229902). {ECO:0000269|PubMed:11163549}.		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TGTGCTGACTACCGGGGTGTC	0.483													A|||	788	0.157348	0.0272	0.2507	5008	,	,		17213	0.0744		0.4046	False		,,,				2504	0.0982				p.Y433F		Atlas-SNP	.											GRM7,NS,carcinoma,-1,1	GRM7	223	1	0			c.A1298T						PASS	.	A	PHE/TYR,PHE/TYR	431,3975	209.8+/-230.5	22,387,1794	87.0	74.0	78.0		1298,1298	3.4	1.0	3	dbSNP_98	78	3743,4857	533.1+/-382.3	830,2083,1387	yes	missense,missense	GRM7	NM_000844.3,NM_181874.2	22,22	852,2470,3181	TT,TA,AA		43.5233,9.7821,32.0929	benign,benign	433/916,433/923	7494417	4174,8832	2203	4300	6503	SO:0001583	missense	2917	exon6			CTGACTACCGGGG	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1298A>T	3.37:g.7494417A>T	ENSP00000350348:p.Tyr433Phe	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	37	CCDS43042.1	472	0.21611721611721613	18	0.036585365853658534	102	0.281767955801105	42	0.07342657342657342	310	0.40897097625329815	A	9.927	1.213739	0.22289	0.097821	0.435233	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492;ENST00000445087	D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	5.88	3.39	0.38822	Extracellular ligand-binding receptor (1);	0.405345	0.27956	N	0.017169	T	0.00012	0.0000	L	0.33245	0.995	0.30035	P	0.813151	B;P;B;B	0.35821	0.255;0.523;0.299;0.001	B;B;B;B	0.37015	0.109;0.239;0.175;0.008	T	0.34875	-0.9811	9	0.10111	T	0.7	.	6.5412	0.22380	0.5864:0.1417:0.0:0.272	rs2229902;rs2234977;rs17656320;rs52827757;rs2229902	433;188;433;433	Q14831-5;Q59G95;Q14831;Q14831-2	.;.;GRM7_HUMAN;.	F	433;433;433;433;433;433;433;90	ENSP00000350348:Y433F;ENSP00000417536:Y433F;ENSP00000373987:Y433F;ENSP00000385664:Y433F;ENSP00000384585:Y433F;ENSP00000395035:Y90F	ENSP00000350348:Y433F	Y	+	2	0	GRM7	7469417	0.817000	0.29147	0.994000	0.49952	0.996000	0.88848	2.335000	0.43929	0.414000	0.25790	0.533000	0.62120	TAC	A|0.712;T|0.288	0.288	strong		0.483	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
CACNA1H	8912	hgsc.bcm.edu	37	16	1273490	1273490	+	IGR	SNP	C	C	T	rs760357	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1273490C>T	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.V60M	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit						aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CACACGTGCACCCTCCGCAGG	0.721													c|||	588	0.117412	0.0182	0.1383	5008	,	,		13741	0.1647		0.1988	False		,,,				2504	0.1043				p.V60M		Atlas-SNP	.											.	TPSG1	19	.	0			c.G178A						PASS	.		MET/VAL	154,3954		6,142,1906	7.0	8.0	8.0		178	2.8	0.3	16	dbSNP_86	8	1509,6741		134,1241,2750	yes	missense	TPSG1	NM_012467.3	21	140,1383,4656	TT,TC,CC		18.2909,3.7488,13.4569	benign	60/322	1273490	1663,10695	2054	4125	6179	SO:0001628	intergenic_variant	25823	exon3			CGTGCACCCTCCG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180			16.37:g.1273490C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	15	11	0.733333	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	307	0.14056776556776557	9	0.018292682926829267	50	0.13812154696132597	93	0.16258741258741258	155	0.20448548812664907	c	6.505	0.461463	0.12342	0.037488	0.182909	ENSG00000116176	ENST00000234798	D	0.88586	-2.4	2.76	2.76	0.32466	.	.	.	.	.	T	0.00695	0.0023	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.05533	-1.0879	5	0.45353	T	0.12	.	11.6863	0.51487	0.0:1.0:0.0:0.0	rs760357	.	.	.	M	60	ENSP00000234798:V60M	ENSP00000234798:V60M	V	-	1	0	TPSG1	1213491	0.000000	0.05858	0.260000	0.24451	0.554000	0.35429	-1.007000	0.03667	1.471000	0.48121	0.486000	0.48141	GTG	C|0.860;T|0.140	0.140	strong		0.721	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
OBSCN	84033	hgsc.bcm.edu	37	1	228451826	228451826	+	Missense_Mutation	SNP	C	C	T	rs453140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228451826C>T	ENST00000422127.1	+	16	4639	c.4595C>T	c.(4594-4596)gCg>gTg	p.A1532V	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A1532V|OBSCN_ENST00000570156.2_Missense_Mutation_p.A1716V|OBSCN_ENST00000359599.6_Missense_Mutation_p.A188V|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1532	Ig-like 16.		A -> V (in dbSNP:rs453140). {ECO:0000269|PubMed:17344846}.		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GAGCCCAAGGCGGTGTTTGCC	0.667													C|||	1534	0.30631	0.2761	0.2983	5008	,	,		18890	0.4226		0.2823	False		,,,				2504	0.2577				p.A1716V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C5147T						PASS	.	C	VAL/ALA,VAL/ALA	1025,3213		112,801,1206	50.0	52.0	51.0		4595,4595	-1.6	0.0	1	dbSNP_80	51	2373,6073		356,1661,2206	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	64,64	468,2462,3412	TT,TC,CC		28.0961,24.1859,26.7897	benign,benign	1532/7969,1532/6621	228451826	3398,9286	2119	4223	6342	SO:0001583	missense	84033	exon18			CCAAGGCGGTGTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.4595C>T	1.37:g.228451826C>T	ENSP00000409493:p.Ala1532Val	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	333	192	0.576577	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	666	0.30494505494505497	127	0.258130081300813	96	0.26519337016574585	237	0.4143356643356643	206	0.2717678100263852	.	0.764	-0.768350	0.02974	0.241859	0.280961	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.04049	3.72;3.72;3.72	4.82	-1.6	0.08426	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.228930	0.05887	N	0.627575	T	0.00012	0.0000	N	0.01202	-0.96	0.58432	P	1.0000000000287557E-6	B;B	0.34313	0.002;0.448	B;B	0.16722	0.003;0.016	T	0.42916	-0.9423	9	0.19590	T	0.45	.	6.177	0.20449	0.1856:0.4888:0.0:0.3256	rs453140;rs61438529	1532;1532	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	V	1532;1532;188	ENSP00000284548:A1532V;ENSP00000409493:A1532V;ENSP00000352613:A188V	ENSP00000284548:A1532V	A	+	2	0	OBSCN	226518449	0.000000	0.05858	0.000000	0.03702	0.234000	0.25298	-2.744000	0.00796	-0.476000	0.06842	-0.469000	0.05056	GCG	C|0.696;T|0.304	0.304	strong		0.667	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
GSDMB	55876	hgsc.bcm.edu	37	17	38062196	38062196	+	Missense_Mutation	SNP	G	G	A	rs2305480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38062196G>A	ENST00000394179.1	-	8	1046	c.916C>T	c.(916-918)Cca>Tca	p.P306S	GSDMB_ENST00000360317.3_Missense_Mutation_p.P311S|GSDMB_ENST00000418519.1_Missense_Mutation_p.P311S|GSDMB_ENST00000520542.1_Missense_Mutation_p.P302S|GSDMB_ENST00000394175.2_Missense_Mutation_p.P289S|GSDMB_ENST00000309481.7_Missense_Mutation_p.P298S			Q8TAX9	GSDMB_HUMAN	gasdermin B	306			P -> S (in dbSNP:rs2305480). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.P289S(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						GGCTTGTCTGGGTCCTCCATG	0.537													G|||	1436	0.286741	0.1074	0.3357	5008	,	,		16886	0.2817		0.4662	False		,,,				2504	0.3149				p.P311S		Atlas-SNP	.											GSDMB,NS,carcinoma,0,1	GSDMB	87	1	1	Substitution - Missense(1)	stomach(1)	c.C931T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	647,3759	274.9+/-272.2	49,549,1605	70.0	69.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	892,931,904,865	0.5	0.0	17	dbSNP_100	69	3808,4792	535.7+/-382.9	832,2144,1324	yes	missense,missense,missense,missense	GSDMB	NM_001042471.1,NM_001165958.1,NM_001165959.1,NM_018530.2	74,74,74,74	881,2693,2929	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	44.2791,14.6845,34.2534	benign,benign,benign,benign	298/404,311/417,302/408,289/395	38062196	4455,8551	2203	4300	6503	SO:0001583	missense	55876	exon9			TGTCTGGGTCCTC	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"""gasdermin-like"""	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.916C>T	17.37:g.38062196G>A	ENSP00000377733:p.Pro306Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	167	163	0.976048	NM_001165958	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Missense_Mutation	SNP	ENST00000394179.1	37		718	0.32875457875457875	53	0.10772357723577236	126	0.34806629834254144	180	0.3146853146853147	359	0.4736147757255937	G	0.915	-0.717902	0.03182	0.146845	0.442791	ENSG00000073605	ENST00000360317;ENST00000394175;ENST00000309481;ENST00000520542;ENST00000418519;ENST00000394179	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	3.8	0.469	0.16741	.	0.282386	0.24991	N	0.034000	T	0.00012	0.0000	L	0.38531	1.155	0.80722	P	0.0	P;B;P;B;B	0.46395	0.877;0.336;0.636;0.336;0.336	P;B;B;B;B	0.51615	0.675;0.087;0.404;0.143;0.087	T	0.41662	-0.9496	9	0.14252	T	0.57	.	5.491	0.16777	0.4151:0.0:0.5849:0.0	rs2305480;rs17677099;rs17845769;rs17858729;rs58161295;rs2305480	302;311;306;298;289	B4DKK7;Q8TAX9-4;Q8TAX9;Q8TAX9-3;Q8TAX9-2	.;.;GSDMB_HUMAN;.;.	S	306;289;298;302;311;306	ENSP00000377729:P289S;ENSP00000312584:P298S;ENSP00000430157:P302S;ENSP00000415049:P311S;ENSP00000377733:P306S	ENSP00000312584:P298S	P	-	1	0	GSDMB	35315722	0.032000	0.19561	0.001000	0.08648	0.002000	0.02628	0.422000	0.21296	0.325000	0.23359	-0.466000	0.05196	CCA	G|0.674;A|0.326	0.326	strong		0.537	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	
SLC28A1	9154	hgsc.bcm.edu	37	15	85448875	85448875	+	Missense_Mutation	SNP	C	C	A	rs8187758	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85448875C>A	ENST00000286749.3	+	7	799	c.709C>A	c.(709-711)Cag>Aag	p.Q237K	SLC28A1_ENST00000537216.1_Missense_Mutation_p.Q237K|SLC28A1_ENST00000394573.1_Missense_Mutation_p.Q237K|SLC28A1_ENST00000538177.1_Missense_Mutation_p.Q237K|SLC28A1_ENST00000537624.1_Missense_Mutation_p.Q237K|SLC28A1_ENST00000537703.1_Missense_Mutation_p.Q159K			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	237			Q -> K (in dbSNP:rs8187758).		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GCTGGGCGAGCAGATCCGGGT	0.572													C|||	1505	0.300519	0.1573	0.3646	5008	,	,		16768	0.3075		0.2366	False		,,,				2504	0.5072				p.Q237K		Atlas-SNP	.											.	SLC28A1	118	.	0			c.C709A						PASS	.	C	LYS/GLN	752,3654	308.0+/-290.3	65,622,1516	139.0	112.0	121.0		709	4.0	1.0	15	dbSNP_123	121	1926,6672	341.8+/-324.2	210,1506,2583	yes	missense	SLC28A1	NM_004213.3	53	275,2128,4099	AA,AC,CC		22.4006,17.0676,20.5937	benign	237/650	85448875	2678,10326	2203	4299	6502	SO:0001583	missense	9154	exon8			GGCGAGCAGATCC	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.709C>A	15.37:g.85448875C>A	ENSP00000286749:p.Gln237Lys	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	549	0.25137362637362637	78	0.15853658536585366	125	0.3453038674033149	163	0.28496503496503495	183	0.24142480211081793	C	10.23	1.292038	0.23564	0.170676	0.224006	ENSG00000156222	ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573;ENST00000537703	T;T;T;T;T;T	0.13307	2.6;2.6;2.6;2.6;2.6;2.6	4.03	4.03	0.46877	Na dependent nucleoside transporter (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.46885	1.475	0.09310	P	0.99999771651	P;B;D;B;P	0.76494	0.927;0.094;0.999;0.115;0.927	P;B;D;B;P	0.91635	0.679;0.155;0.999;0.241;0.679	T	0.49370	-0.8947	9	0.22706	T	0.39	-5.2491	11.8824	0.52583	0.0:1.0:0.0:0.0	rs8187758;rs17222323;rs52791431;rs60871224;rs8187758	237;237;237;159;237	B7Z533;F5H560;B7Z3L6;B7Z3M4;O00337	.;.;.;.;S28A1_HUMAN	K	237;237;237;237;237;159	ENSP00000440546:Q237K;ENSP00000443752:Q237K;ENSP00000444700:Q237K;ENSP00000286749:Q237K;ENSP00000378074:Q237K;ENSP00000443764:Q159K	ENSP00000286749:Q237K	Q	+	1	0	SLC28A1	83249879	1.000000	0.71417	0.974000	0.42286	0.561000	0.35649	5.575000	0.67430	2.240000	0.73641	0.557000	0.71058	CAG	C|0.768;A|0.232	0.232	strong		0.572	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
ALKBH1	8846	hgsc.bcm.edu	37	14	78140355	78140355	+	Missense_Mutation	SNP	T	T	A	rs6494	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:78140355T>A	ENST00000216489.3	-	6	985	c.970A>T	c.(970-972)Atg>Ttg	p.M324L		NM_006020.2	NP_006011.2	Q13686	ALKB1_HUMAN	alkB, alkylation repair homolog 1 (E. coli)	324	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.		M -> L (in dbSNP:rs6494).		developmental growth (GO:0048589)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|in utero embryonic development (GO:0001701)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|oxidative demethylation (GO:0070989)|placenta development (GO:0001890)|RNA repair (GO:0042245)	mitochondrion (GO:0005739)|nuclear euchromatin (GO:0005719)	chemoattractant activity (GO:0042056)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)			endometrium(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CAGTCCTCCATAGAACAAGGC	0.552													T|||	594	0.11861	0.0613	0.1153	5008	,	,		18443	0.0456		0.2425	False		,,,				2504	0.1462				p.M324L		Atlas-SNP	.											.	ALKBH1	30	.	0			c.A970T						PASS	.	T	LEU/MET	403,4003	199.4+/-223.0	15,373,1815	70.0	66.0	67.0		970	-0.8	1.0	14	dbSNP_52	67	1873,6727	333.2+/-320.4	228,1417,2655	yes	missense	ALKBH1	NM_006020.2	15	243,1790,4470	AA,AT,TT		21.7791,9.1466,17.4996	benign	324/390	78140355	2276,10730	2203	4300	6503	SO:0001583	missense	8846	exon6			CCTCCATAGAACA	X91992	CCDS32127.1	14q24	2014-07-23	2006-02-09	2006-02-09	ENSG00000100601	ENSG00000100601		"""Alkylation repair homologs"""	17911	protein-coding gene	gene with protein product		605345	"""alkB, alkylation repair homolog (E. coli)"""	ALKBH		8600462	Standard	XM_005268165		Approved	hABH, alkB, ABH	uc001xuc.1	Q13686	OTTHUMG00000171542	ENST00000216489.3:c.970A>T	14.37:g.78140355T>A	ENSP00000216489:p.Met324Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	NM_006020	Q8TAU1|Q9ULA7	Missense_Mutation	SNP	ENST00000216489.3	37	CCDS32127.1	313	0.1433150183150183	40	0.08130081300813008	47	0.1298342541436464	34	0.05944055944055944	192	0.2532981530343008	T	11.42	1.632379	0.29068	0.091466	0.217791	ENSG00000100601	ENST00000216489	T	0.27890	1.64	5.95	-0.831	0.10789	Oxoglutarate/iron-dependent oxygenase (1);	0.961429	0.08699	N	0.906694	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41288	-0.9517	9	0.27082	T	0.32	-1.543	1.3631	0.02196	0.227:0.4227:0.1102:0.2401	rs6494;rs17795859;rs52802500;rs6494	324	Q13686	ALKB1_HUMAN	L	324	ENSP00000216489:M324L	ENSP00000216489:M324L	M	-	1	0	ALKBH1	77210108	0.000000	0.05858	0.970000	0.41538	0.831000	0.47069	0.058000	0.14301	-0.103000	0.12175	-0.904000	0.02843	ATG	T|0.823;A|0.177	0.177	strong		0.552	ALKBH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414037.1	NM_006020	
PELI3	246330	hgsc.bcm.edu	37	11	66240882	66240882	+	Silent	SNP	T	T	C	rs2277302	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66240882T>C	ENST00000320740.7	+	6	787	c.627T>C	c.(625-627)gaT>gaC	p.D209D	PELI3_ENST00000349459.6_Silent_p.D185D|CTD-3074O7.5_ENST00000602951.1_RNA|CTD-3074O7.5_ENST00000533502.1_RNA|PELI3_ENST00000524466.1_Silent_p.D209D|PELI3_ENST00000531856.1_Intron|CTD-3074O7.5_ENST00000527092.1_RNA	NM_001243136.1|NM_145065.2	NP_001230065.1|NP_659502.2	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	209					defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						CTGGCTTCGATGCCTCTAGCA	0.602													t|||	1327	0.264976	0.3623	0.1801	5008	,	,		19279	0.2877		0.2425	False		,,,				2504	0.1933				p.D209D		Atlas-SNP	.											.	PELI3	36	.	0			c.T627C						PASS	.	T	,	1435,2965	464.0+/-353.7	243,949,1008	57.0	44.0	48.0		555,627	-3.3	1.0	11	dbSNP_100	48	2015,6575	351.1+/-328.1	227,1561,2507	yes	coding-synonymous,coding-synonymous	PELI3	NM_001098510.1,NM_145065.2	,	470,2510,3515	CC,CT,TT		23.4575,32.6136,26.5589	,	185/446,209/470	66240882	3450,9540	2200	4295	6495	SO:0001819	synonymous_variant	246330	exon6			CTTCGATGCCTCT	AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516		"""Pellino homologs"""	30010	protein-coding gene	gene with protein product		609827	"""pellino homolog 3 (Drosophila)"""			12874243, 15917247	Standard	NM_145065		Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000320740.7:c.627T>C	11.37:g.66240882T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_145065	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	Silent	SNP	ENST00000320740.7	37	CCDS31615.1																																																																																			T|0.739;C|0.261	0.261	strong		0.602	PELI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393226.1	NM_145065	
SRMS	6725	hgsc.bcm.edu	37	20	62172219	62172219	+	Silent	SNP	G	G	A	rs6122130	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62172219G>A	ENST00000217188.1	-	8	1459	c.1419C>T	c.(1417-1419)ttC>ttT	p.F473F		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	473	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			GCAGCGTGGCGAAGGAGGGCC	0.706													G|||	1852	0.369808	0.0144	0.4784	5008	,	,		16735	0.9613		0.2157	False		,,,				2504	0.3221				p.F473F		Atlas-SNP	.											.	SRMS	48	.	0			c.C1419T						PASS	.	G		250,4154	141.9+/-177.2	6,238,1958	96.0	88.0	91.0		1419	0.6	0.0	20	dbSNP_114	91	1891,6709	335.0+/-321.2	213,1465,2622	no	coding-synonymous	SRMS	NM_080823.2		219,1703,4580	AA,AG,GG		21.9884,5.6767,16.4642		473/489	62172219	2141,10863	2202	4300	6502	SO:0001819	synonymous_variant	6725	exon8			CGTGGCGAAGGAG		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.1419C>T	20.37:g.62172219G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	78	27	0.346154	NM_080823		Silent	SNP	ENST00000217188.1	37	CCDS13525.1																																																																																			G|0.767;A|0.233	0.233	strong		0.706	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
CWF19L2	143884	hgsc.bcm.edu	37	11	107197640	107197640	+	Missense_Mutation	SNP	T	T	C	rs3758911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:107197640T>C	ENST00000282251.5	-	18	2708	c.2681A>G	c.(2680-2682)tAt>tGt	p.Y894C		NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	894			Y -> C (in dbSNP:rs3758911). {ECO:0000269|PubMed:15489334}.				catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		TACACCTCAATAGTTTTTACT	0.413													C|||	1283	0.25619	0.2095	0.2003	5008	,	,		18994	0.2927		0.3121	False		,,,				2504	0.2638				p.Y894C		Atlas-SNP	.											.	CWF19L2	135	.	0			c.A2681G						PASS	.	C	CYS/TYR	959,3443	733.1+/-410.4	108,743,1350	92.0	96.0	94.0		2681	2.0	0.0	11	dbSNP_107	94	2871,5725	672.2+/-402.9	491,1889,1918	yes	missense	CWF19L2	NM_152434.2	194	599,2632,3268	CC,CT,TT		33.3993,21.7856,29.4661	benign	894/895	107197640	3830,9168	2201	4298	6499	SO:0001583	missense	143884	exon18			CCTCAATAGTTTT	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.2681A>G	11.37:g.107197640T>C	ENSP00000282251:p.Tyr894Cys	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	583	0.26694139194139194	105	0.21341463414634146	85	0.23480662983425415	153	0.2674825174825175	240	0.316622691292876	C	13.95	2.390991	0.42410	0.217856	0.333993	ENSG00000152404	ENST00000282251	T	0.10960	2.82	4.94	2.01	0.26516	.	1.226040	0.05686	N	0.591429	T	0.00012	0.0000	N	0.00926	-1.1	0.47441	P	5.730000000000457E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.45760	-0.9239	9	0.62326	D	0.03	.	0.9374	0.01347	0.1549:0.3768:0.1508:0.3174	rs3758911;rs52805989;rs58247370;rs3758911	894	Q2TBE0	C19L2_HUMAN	C	894	ENSP00000282251:Y894C	ENSP00000282251:Y894C	Y	-	2	0	CWF19L2	106702850	0.999000	0.42202	0.004000	0.12327	0.046000	0.14306	1.008000	0.29872	0.026000	0.15269	-0.128000	0.14901	TAT	T|0.725;C|0.275	0.275	strong		0.413	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
CTNNAL1	8727	hgsc.bcm.edu	37	9	111727670	111727670	+	Missense_Mutation	SNP	C	C	G	rs7021366	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:111727670C>G	ENST00000325551.4	-	11	1665	c.1579G>C	c.(1579-1581)Gaa>Caa	p.E527Q	CTNNAL1_ENST00000374595.4_Missense_Mutation_p.E527Q|CTNNAL1_ENST00000325580.6_Missense_Mutation_p.E443Q|CTNNAL1_ENST00000374594.1_5'Flank	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	527			E -> Q (in dbSNP:rs7021366). {ECO:0000269|Ref.6}.		cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		CGTCTTCCTTCAAACACGTCA	0.333													C|||	991	0.197883	0.0166	0.3199	5008	,	,		17796	0.3155		0.2694	False		,,,				2504	0.1616				p.E527Q		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.G1579C						PASS	.	C	GLN/GLU	259,4147	146.5+/-181.1	16,227,1960	173.0	158.0	163.0		1579	5.9	1.0	9	dbSNP_116	163	2442,6158	404.1+/-348.0	334,1774,2192	yes	missense	CTNNAL1	NM_003798.2	29	350,2001,4152	GG,GC,CC		28.3953,5.8783,20.7673	benign	527/735	111727670	2701,10305	2203	4300	6503	SO:0001583	missense	8727	exon11			TTCCTTCAAACAC	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"""alpha-catulin"", ""alpha2-catulin"""	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.1579G>C	9.37:g.111727670C>G	ENSP00000320434:p.Glu527Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	37	CCDS6775.1	494	0.2261904761904762	13	0.026422764227642278	98	0.27071823204419887	182	0.3181818181818182	201	0.26517150395778366	C	13.82	2.352183	0.41700	0.058783	0.283953	ENSG00000119326	ENST00000374595;ENST00000325551;ENST00000325580	T;T;T	0.27720	1.67;1.8;1.65	5.91	5.91	0.95273	.	0.143577	0.64402	D	0.000006	T	0.00012	0.0000	L	0.32530	0.975	0.31394	P	0.677511	B;D;B;B;B	0.67145	0.19;0.996;0.19;0.011;0.19	B;D;B;B;B	0.63877	0.076;0.919;0.076;0.025;0.076	T	0.33292	-0.9874	9	0.17369	T	0.5	-16.4177	17.7923	0.88558	0.0:1.0:0.0:0.0	rs7021366;rs17802108;rs7021366	527;443;527;527;527	B2RBI4;Q9UBT7-3;B3KMX6;Q9UBT7-2;Q9UBT7	.;.;.;.;CTNL1_HUMAN	Q	527;527;443	ENSP00000363723:E527Q;ENSP00000320434:E527Q;ENSP00000323351:E443Q	ENSP00000320434:E527Q	E	-	1	0	CTNNAL1	110767491	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.063000	0.71162	2.793000	0.96121	0.655000	0.94253	GAA	C|0.786;G|0.214	0.214	strong		0.333	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798	
MUC4	4585	hgsc.bcm.edu	37	3	195508108	195508108	+	Missense_Mutation	SNP	G	G	A	rs374140595		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508108G>A	ENST00000463781.3	-	2	10802	c.10343C>T	c.(10342-10344)tCa>tTa	p.S3448L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3448L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTAGATGCTGAGGAAGTGCT	0.597																																					p.S3448L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C10343T						PASS	.						24.0	21.0	22.0					3																	195508108		680	1577	2257	SO:0001583	missense	4585	exon2			GATGCTGAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10343C>T	3.37:g.195508108G>A	ENSP00000417498:p.Ser3448Leu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	369	82	0.222222	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.150	0.395913	0.11638	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35421	1.31;1.42	0.743	-1.49	0.08718	.	.	.	.	.	T	0.33089	0.0851	N	0.19112	0.55	0.09310	N	1	P	0.52170	0.951	D	0.65443	0.935	T	0.20240	-1.0281	8	.	.	.	.	2.1531	0.03805	0.0:0.3256:0.3506:0.3237	.	3320	E7ESK3	.	L	3448	ENSP00000417498:S3448L;ENSP00000420243:S3448L	.	S	-	2	0	MUC4	196992887	0.051000	0.20477	0.010000	0.14722	0.010000	0.07245	0.898000	0.28404	0.088000	0.17205	0.089000	0.15464	TCA	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CCDC18	343099	hgsc.bcm.edu	37	1	93672688	93672688	+	Silent	SNP	C	C	T	rs2783499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:93672688C>T	ENST00000343253.7	+	9	1444	c.942C>T	c.(940-942)aaC>aaT	p.N314N	CCDC18_ENST00000401026.3_Silent_p.N314N|CCDC18_ENST00000557479.1_Silent_p.N432N|CCDC18_ENST00000338949.4_Silent_p.N113N|CCDC18_ENST00000334652.5_5'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	314										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AAAATAACAACGGAAAAGAAA	0.274													C|||	1163	0.232228	0.1974	0.2392	5008	,	,		16376	0.3175		0.1511	False		,,,				2504	0.2699				p.N314N		Atlas-SNP	.											.	CCDC18	93	.	0			c.C942T						PASS	.	C		664,2932		60,544,1194	37.0	32.0	33.0		942	0.9	1.0	1	dbSNP_100	33	1326,6790		128,1070,2860	no	coding-synonymous	CCDC18	NM_206886.3		188,1614,4054	TT,TC,CC		16.3381,18.465,16.9911		314/1300	93672688	1990,9722	1798	4058	5856	SO:0001819	synonymous_variant	343099	exon9			TAACAACGGAAAA			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.942C>T	1.37:g.93672688C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_206886	Q6ZU17	Silent	SNP	ENST00000343253.7	37		469	0.21474358974358973	91	0.18495934959349594	84	0.23204419889502761	174	0.3041958041958042	120	0.158311345646438	C	5.368	0.253238	0.10185	0.18465	0.163381	ENSG00000122483	ENST00000370276	.	.	.	5.83	0.948	0.19561	.	.	.	.	.	T	0.32194	0.0821	.	.	.	0.09310	P	0.999999999729022	.	.	.	.	.	.	T	0.11867	-1.0570	3	.	.	.	.	9.6036	0.39619	0.0:0.3783:0.0:0.6217	rs2783499;rs57879641;rs2783499	.	.	.	M	368	.	.	T	+	2	0	CCDC18	93445276	0.315000	0.24571	0.976000	0.42696	0.868000	0.49771	0.374000	0.20501	-0.076000	0.12775	-1.300000	0.01332	ACG	C|0.794;T|0.206	0.206	strong		0.274	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
HECW1	23072	hgsc.bcm.edu	37	7	43484310	43484310	+	Silent	SNP	T	T	C	rs73098706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43484310T>C	ENST00000395891.2	+	11	2144	c.1539T>C	c.(1537-1539)tcT>tcC	p.S513S	HECW1_ENST00000453890.1_Silent_p.S513S	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	513	Glu-rich.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GAGATGTGTCTACCCTGGAGC	0.632													T|||	1478	0.295128	0.2307	0.2839	5008	,	,		18387	0.1508		0.4155	False		,,,				2504	0.4151				p.S513S		Atlas-SNP	.											.	HECW1	540	.	0			c.T1539C						PASS	.	T		1038,3216		138,762,1227	26.0	33.0	31.0		1539	-5.1	0.0	7	dbSNP_130	31	3277,5169		673,1931,1619	no	coding-synonymous	HECW1	NM_015052.3		811,2693,2846	CC,CT,TT		38.7994,24.4006,33.9764		513/1607	43484310	4315,8385	2127	4223	6350	SO:0001819	synonymous_variant	23072	exon11			TGTGTCTACCCTG	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1539T>C	7.37:g.43484310T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			T|0.710;C|0.290	0.290	strong		0.632	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
ALPK2	115701	hgsc.bcm.edu	37	18	56203447	56203447	+	Silent	SNP	A	A	G	rs3809979	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56203447A>G	ENST00000361673.3	-	5	4185	c.3972T>C	c.(3970-3972)caT>caC	p.H1324H	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1324						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GACTTCTCCAATGTACACTGA	0.502													g|||	3364	0.671725	0.4675	0.6772	5008	,	,		18595	0.7966		0.7674	False		,,,				2504	0.7168				p.H1324H		Atlas-SNP	.											.	ALPK2	487	.	0			c.T3972C						PASS	.			2278,2128	578.7+/-384.7	597,1084,522	95.0	90.0	92.0		3972	-11.3	0.0	18	dbSNP_107	92	6608,1992	349.2+/-327.3	2550,1508,242	no	coding-synonymous	ALPK2	NM_052947.3		3147,2592,764	GG,GA,AA		23.1628,48.2978,31.6777		1324/2171	56203447	8886,4120	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			TCTCCAATGTACA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3972T>C	18.37:g.56203447A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			A|0.317;G|0.683	0.683	strong		0.502	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
SPNS3	201305	hgsc.bcm.edu	37	17	4351560	4351560	+	Silent	SNP	G	G	A	rs12450838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4351560G>A	ENST00000355530.2	+	6	1012	c.732G>A	c.(730-732)agG>agA	p.R244R	SPNS3_ENST00000333476.2_Silent_p.R117R|SPNS3_ENST00000576069.1_3'UTR	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	244					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						GAGGCTTCAGGAGCAGCTGGT	0.622													G|||	1251	0.2498	0.0794	0.4669	5008	,	,		18277	0.1151		0.3469	False		,,,				2504	0.365				p.R244R		Atlas-SNP	.											.	SPNS3	52	.	0			c.G732A						PASS	.	G		513,3893	231.4+/-245.2	30,453,1720	46.0	40.0	42.0		732	2.1	1.0	17	dbSNP_120	42	3190,5410	475.0+/-369.0	584,2022,1694	no	coding-synonymous	SPNS3	NM_182538.4		614,2475,3414	AA,AG,GG		37.093,11.6432,28.4715		244/513	4351560	3703,9303	2203	4300	6503	SO:0001819	synonymous_variant	201305	exon6			CTTCAGGAGCAGC		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.732G>A	17.37:g.4351560G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_182538	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																			G|0.750;A|0.250	0.250	strong		0.622	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
C19orf12	83636	hgsc.bcm.edu	37	19	30193721	30193721	+	Silent	SNP	G	G	A	rs10424582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:30193721G>A	ENST00000392278.2	-	3	483	c.357C>T	c.(355-357)acC>acT	p.T119T	C19orf12_ENST00000392276.1_Silent_p.T44T|C19orf12_ENST00000392275.1_5'UTR|C19orf12_ENST00000592153.1_Intron|C19orf12_ENST00000323670.9_Silent_p.T108T	NM_001031726.3	NP_001026896.2	Q9NSK7	CS012_HUMAN	chromosome 19 open reading frame 12	119					cell death (GO:0008219)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)						Ovarian(5;0.000567)|Breast(6;0.0203)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0435)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.183)			TGACCAGCGCGGTCAGCTGCA	0.622													G|||	3074	0.613818	0.7905	0.5216	5008	,	,		14590	0.3006		0.7565	False		,,,				2504	0.6166				p.T119T		Atlas-SNP	.											.	C19orf12	16	.	0			c.C357T						PASS	.	G	,	3382,1024	722.0+/-409.2	1304,774,125	49.0	49.0	49.0		357,324	-3.8	0.0	19	dbSNP_119	49	6399,2201	706.1+/-405.5	2389,1621,290	no	coding-synonymous,coding-synonymous	C19orf12	NM_001031726.2,NM_031448.3	,	3693,2395,415	AA,AG,GG		25.593,23.241,24.7962	,	119/153,108/142	30193721	9781,3225	2203	4300	6503	SO:0001819	synonymous_variant	83636	exon3			CAGCGCGGTCAGC	AK057185	CCDS12418.2, CCDS42542.1, CCDS59373.1, CCDS74325.1	19q13.11	2013-07-24			ENSG00000131943	ENSG00000131943			25443	protein-coding gene	gene with protein product	"""neurodegeneration with brain iron accumulation 4"""	614297	"""spastic paraplegia 43 (autosomal recessive)"""	SPG43		21981780, 23857908	Standard	NM_031448		Approved	MGC10922, DKFZP762D096, NBIA4	uc002nsj.3	Q9NSK7	OTTHUMG00000149838	ENST00000392278.2:c.357C>T	19.37:g.30193721G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_001031726	B3KQ16|Q0D2Q0|Q6P4C5|Q9BSL7	Silent	SNP	ENST00000392278.2	37	CCDS42542.1																																																																																			G|0.297;A|0.703	0.703	strong		0.622	C19orf12-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313509.2	NM_031448	
ZBED2	79413	hgsc.bcm.edu	37	3	111313031	111313031	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:111313031G>A	ENST00000317012.4	-	2	1026	c.18C>T	c.(16-18)gaC>gaT	p.D6D	CD96_ENST00000438817.2_Intron|CD96_ENST00000283285.5_Intron|CD96_ENST00000352690.4_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	6							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						CCTCTTCCTCGTCTTCCCGCC	0.428																																					p.D6D		Atlas-SNP	.											ZBED2,colon,carcinoma,-2,1	ZBED2	22	1	0			c.C18T						scavenged	.						209.0	179.0	190.0					3																	111313031		2203	4300	6503	SO:0001819	synonymous_variant	79413	exon2			TTCCTCGTCTTCC	BC003536	CCDS2960.2	3p13-q13.2	2013-05-03			ENSG00000177494	ENSG00000177494		"""Zinc fingers, BED-type"""	20710	protein-coding gene	gene with protein product		615246				23533661	Standard	NM_024508		Approved	MGC10796	uc003dxy.3	Q9BTP6	OTTHUMG00000074061	ENST00000317012.4:c.18C>T	3.37:g.111313031G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	296	4	0.0135135	NM_024508	D3DN62	Silent	SNP	ENST00000317012.4	37	CCDS2960.2																																																																																			.	.	none		0.428	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508	
OR2J2	26707	hgsc.bcm.edu	37	6	29141632	29141632	+	Missense_Mutation	SNP	T	T	C	rs3116855	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29141632T>C	ENST00000377167.2	+	1	322	c.220T>C	c.(220-222)Tac>Cac	p.Y74H		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	74			H -> Y (in allele 6M1-6*02 and allele 6M1-6*03; dbSNP:rs3116855). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						GGATCTCTGCTACACCACCAG	0.483													T|||	1585	0.316494	0.0408	0.4035	5008	,	,		18639	0.3512		0.5149	False		,,,				2504	0.3875				p.Y74H		Atlas-SNP	.											.	OR2J2	51	.	0			c.T220C						PASS	.	T	HIS/TYR	462,3530		39,384,1573	148.0	136.0	140.0		220	2.3	1.0	6	dbSNP_103	140	4139,4289		1028,2083,1103	no	missense	OR2J2	NM_030905.2	83	1067,2467,2676	CC,CT,TT		49.1101,11.5731,37.0451	benign	74/313	29141632	4601,7819	1996	4214	6210	SO:0001583	missense	26707	exon1			CTCTGCTACACCA		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.220T>C	6.37:g.29141632T>C	ENSP00000366372:p.Tyr74His	Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	383	215	0.561358	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	37	CCDS43434.1	778	0.35622710622710624	22	0.044715447154471545	150	0.4143646408839779	198	0.34615384615384615	408	0.5382585751978892	T	11.43	1.636528	0.29068	0.115731	0.491101	ENSG00000204700	ENST00000377167	T	0.01388	4.95	2.3	2.3	0.28687	.	.	.	.	.	T	0.02848	0.0085	M	0.87038	2.855	0.38904	P	0.04260799999999998	.	.	.	.	.	.	T	0.08700	-1.0709	6	0.72032	D	0.01	.	9.0762	0.36522	0.0:0.0:0.0:1.0	rs3116855;rs57471851	.	.	.	H	74	ENSP00000366372:Y74H	ENSP00000366372:Y74H	Y	+	1	0	OR2J2	29249611	0.028000	0.19301	1.000000	0.80357	0.423000	0.31445	2.328000	0.43867	1.039000	0.40074	0.172000	0.16884	TAC	T|0.593;C|0.407	0.407	strong		0.483	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2		
CLEC16A	23274	hgsc.bcm.edu	37	16	11097155	11097155	+	Silent	SNP	G	G	A	rs45464291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11097155G>A	ENST00000409790.1	+	11	1526	c.1296G>A	c.(1294-1296)gaG>gaA	p.E432E	CLEC16A_ENST00000409552.3_Intron	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A											breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CGAGTGGGGAGAGTGAAGGTG	0.617													G|||	4	0.000798722	0.0	0.0	5008	,	,		17429	0.0		0.004	False		,,,				2504	0.0				p.E432E		Atlas-SNP	.											.	CLEC16A	101	.	0			c.G1296A						PASS	.	G		5,4135		0,5,2065	76.0	87.0	83.0		1296	3.6	1.0	16	dbSNP_127	83	25,8389		0,25,4182	no	coding-synonymous	CLEC16A	NM_015226.2		0,30,6247	AA,AG,GG		0.2971,0.1208,0.239		432/1054	11097155	30,12524	2070	4207	6277	SO:0001819	synonymous_variant	23274	exon10			TGGGGAGAGTGAA	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1296G>A	16.37:g.11097155G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
DNAH5	1767	hgsc.bcm.edu	37	5	13864728	13864728	+	Silent	SNP	C	C	A	rs6554827	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13864728C>A	ENST00000265104.4	-	28	4478	c.4374G>T	c.(4372-4374)cgG>cgT	p.R1458R	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1458	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R1458R(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCTTCAAGGCCCGGGGAAGCT	0.478									Kartagener syndrome																												p.R1458R		Atlas-SNP	.											DNAH5,NS,carcinoma,0,1	DNAH5	868	1	1	Substitution - coding silent(1)	stomach(1)	c.G4374T						PASS	.	C		1386,3020	457.5+/-351.6	229,928,1046	59.0	60.0	60.0		4374	0.9	1.0	5	dbSNP_116	60	3807,4793	537.7+/-383.3	893,2021,1386	no	coding-synonymous	DNAH5	NM_001369.2		1122,2949,2432	AA,AC,CC		44.2674,31.4571,39.9277		1458/4625	13864728	5193,7813	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon28	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAAGGCCCGGGGA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.4374G>T	5.37:g.13864728C>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	181	107	0.59116	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			C|0.626;A|0.374	0.374	strong		0.478	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
SNF8	11267	hgsc.bcm.edu	37	17	47007963	47007963	+	Silent	SNP	C	C	T	rs2270576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:47007963C>T	ENST00000502492.1	-	8	1033	c.651G>A	c.(649-651)ctG>ctA	p.L217L	AC091133.1_ENST00000435491.1_RNA|SNF8_ENST00000514089.1_5'UTR|SNF8_ENST00000290330.3_Silent_p.L216L			Q96H20	SNF8_HUMAN	SNF8, ESCRT-II complex subunit	217					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|lung(1)	3						ACCCTTCCTTCAGCAGGTGTT	0.552													C|||	1169	0.233427	0.1959	0.4063	5008	,	,		17216	0.1746		0.2664	False		,,,				2504	0.1881				p.L217L		Atlas-SNP	.											.	SNF8	15	.	0			c.G651A						PASS	.	C		1016,3390	373.2+/-320.7	110,796,1297	43.0	41.0	41.0		651	1.5	1.0	17	dbSNP_100	41	2414,6186	395.4+/-345.0	334,1746,2220	no	coding-synonymous	SNF8	NM_007241.2		444,2542,3517	TT,TC,CC		28.0698,23.0595,26.3724		217/259	47007963	3430,9576	2203	4300	6503	SO:0001819	synonymous_variant	11267	exon8			TTCCTTCAGCAGG	AF156102	CCDS11541.1	17q21.32	2013-06-05	2013-06-05		ENSG00000159210	ENSG00000159210			17028	protein-coding gene	gene with protein product		610904	"""SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)"""			10419521, 15329733	Standard	NM_007241		Approved	EAP30, VPS22, Dot3	uc002ioj.3	Q96H20	OTTHUMG00000160569	ENST00000502492.1:c.651G>A	17.37:g.47007963C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_007241	Q8IXY3|Q9UN50	Silent	SNP	ENST00000502492.1	37	CCDS11541.1																																																																																			C|0.747;T|0.253	0.253	strong		0.552	SNF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361172.1	NM_007241	
CLIP4	79745	hgsc.bcm.edu	37	2	29383256	29383256	+	Missense_Mutation	SNP	G	G	T	rs3100246	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29383256G>T	ENST00000320081.5	+	12	1712	c.1457G>T	c.(1456-1458)cGc>cTc	p.R486L	CLIP4_ENST00000401617.2_Missense_Mutation_p.R379L|CLIP4_ENST00000401605.1_Missense_Mutation_p.R486L|CLIP4_ENST00000404424.1_Missense_Mutation_p.R486L	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	486			R -> L (in dbSNP:rs3100246).							endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					GGGGAACTCCGCCTCGGAGAG	0.488													G|||	255	0.0509185	0.0091	0.1023	5008	,	,		16976	0.001		0.1441	False		,,,				2504	0.0266				p.R486L		Atlas-SNP	.											.	CLIP4	69	.	0			c.G1457T						PASS	.	G	LEU/ARG	148,4258	101.2+/-139.8	2,144,2057	104.0	98.0	100.0		1457	-8.6	0.0	2	dbSNP_103	100	1277,7323	255.1+/-280.1	80,1117,3103	yes	missense	CLIP4	NM_024692.4	102	82,1261,5160	TT,TG,GG		14.8488,3.3591,10.9565	benign	486/706	29383256	1425,11581	2203	4300	6503	SO:0001583	missense	79745	exon12			AACTCCGCCTCGG	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.1457G>T	2.37:g.29383256G>T	ENSP00000327009:p.Arg486Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	137	55	0.40146	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Missense_Mutation	SNP	ENST00000320081.5	37	CCDS1770.1	145	0.06639194139194139	6	0.012195121951219513	41	0.1132596685082873	1	0.0017482517482517483	97	0.1279683377308707	G	14.12	2.440097	0.43326	0.033591	0.148488	ENSG00000115295	ENST00000401605;ENST00000401617;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000530644	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	6.16	-8.63	0.00878	Cytoskeleton-associated protein, Gly-rich domain (2);	0.978007	0.08466	N	0.941749	T	0.00496	0.0016	L	0.29908	0.895	0.09310	N	1	B	0.25007	0.116	B	0.22601	0.04	T	0.04140	-1.0974	10	0.33940	T	0.23	.	15.3941	0.74778	0.4545:0.0:0.5455:0.0	rs3100246;rs52833373;rs57545939;rs3100246	486	Q8N3C7	CLIP4_HUMAN	L	486;379;486;486;486;504;446	ENSP00000384242:R486L;ENSP00000385148:R379L;ENSP00000385594:R486L;ENSP00000327009:R486L	ENSP00000327009:R486L	R	+	2	0	CLIP4	29236760	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.044000	0.12023	-1.766000	0.01302	-0.355000	0.07637	CGC	G|0.905;T|0.095	0.095	strong		0.488	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
SZT2	23334	hgsc.bcm.edu	37	1	43906896	43906896	+	Silent	SNP	A	A	G	rs2027130	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:43906896A>G	ENST00000562955.1	+	52	7185	c.7185A>G	c.(7183-7185)gaA>gaG	p.E2395E	SZT2_ENST00000372442.1_Silent_p.E1553E	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2452					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						GTAAAACAGAATGTGGGGATT	0.547													A|||	983	0.196286	0.0885	0.3847	5008	,	,		19153	0.0823		0.4205	False		,,,				2504	0.0951				p.E2395E		Atlas-SNP	.											.	SZT2	383	.	0			c.A7185G						PASS	.	A		586,3820	254.6+/-260.1	40,506,1657	140.0	150.0	147.0		7185	3.1	1.0	1	dbSNP_94	147	3555,5045	515.1+/-378.5	756,2043,1501	no	coding-synonymous	SZT2	NM_015284.3		796,2549,3158	GG,GA,AA		41.3372,13.3,31.8392		2395/3376	43906896	4141,8865	2203	4300	6503	SO:0001819	synonymous_variant	23334	exon52			AACAGAATGTGGG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.7185A>G	1.37:g.43906896A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																			A|0.698;G|0.302	0.302	strong		0.547	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
MYH10	4628	hgsc.bcm.edu	37	17	8416901	8416901	+	Silent	SNP	C	C	T	rs11374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8416901C>T	ENST00000269243.4	-	21	2745	c.2607G>A	c.(2605-2607)acG>acA	p.T869T	MYH10_ENST00000396239.1_Silent_p.T890T|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000379980.4_Silent_p.T885T|MYH10_ENST00000360416.3_Silent_p.T900T	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	869					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.T869T(1)		breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CTTCCACCTTCGTCTGCTTCT	0.507													C|||	2120	0.423323	0.3835	0.4323	5008	,	,		18617	0.502		0.3519	False		,,,				2504	0.4632				p.T900T		Atlas-SNP	.											MYH10,NS,carcinoma,0,1	MYH10	148	1	1	Substitution - coding silent(1)	prostate(1)	c.G2700A						PASS	.	C		1685,2721	510.4+/-367.5	316,1053,834	188.0	146.0	160.0		2607	-10.2	0.2	17	dbSNP_52	160	3299,5301	494.0+/-373.7	626,2047,1627	no	coding-synonymous	MYH10	NM_005964.1		942,3100,2461	TT,TC,CC		38.3605,38.2433,38.3208		869/1977	8416901	4984,8022	2203	4300	6503	SO:0001819	synonymous_variant	4628	exon23			CACCTTCGTCTGC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2607G>A	17.37:g.8416901C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			A|0.000;C|0.606;G|0.000;T|0.394	0.394	strong		0.507	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
PIH1D1	55011	hgsc.bcm.edu	37	19	49954803	49954803	+	Missense_Mutation	SNP	C	C	T	rs2293013	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49954803C>T	ENST00000262265.5	-	1	264	c.29G>A	c.(28-30)gGg>gAg	p.G10E	PIH1D1_ENST00000596049.1_Missense_Mutation_p.G10E|ALDH16A1_ENST00000540132.1_5'Flank|ALDH16A1_ENST00000293350.4_5'Flank|ALDH16A1_ENST00000455361.2_5'Flank|ALDH16A1_ENST00000433981.2_5'Flank	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	10			G -> E (in dbSNP:rs2293013). {ECO:0000269|PubMed:14702039}.	MG -> LE (in Ref. 2; AAH01108). {ECO:0000305}.	box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		CTCGCTTAGCCCCATTCCCAG	0.617													c|||	3049	0.608826	0.6475	0.6124	5008	,	,		16180	0.4117		0.7535	False		,,,				2504	0.6084				p.G10E		Atlas-SNP	.											.	PIH1D1	23	.	0			c.G29A						PASS	.		GLU/GLY	2720,1686	653.6+/-399.6	855,1010,338	86.0	73.0	78.0		29	3.8	0.2	19	dbSNP_100	78	6586,2014	720.4+/-406.3	2511,1564,225	no	missense	PIH1D1	NM_017916.2	98	3366,2574,563	TT,TC,CC		23.4186,38.266,28.4484	benign	10/291	49954803	9306,3700	2203	4300	6503	SO:0001583	missense	55011	exon1			CTTAGCCCCATTC	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.29G>A	19.37:g.49954803C>T	ENSP00000262265:p.Gly10Glu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Missense_Mutation	SNP	ENST00000262265.5	37	CCDS12765.1	1326	0.6071428571428571	316	0.6422764227642277	229	0.6325966850828729	223	0.38986013986013984	558	0.7361477572559367	c	0.018	-1.474623	0.01044	0.61734	0.765814	ENSG00000104872	ENST00000262265	T	0.09817	2.94	4.87	3.85	0.44370	.	0.630766	0.16193	N	0.225304	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30679	-0.9970	9	0.02654	T	1	-12.6966	7.6469	0.28325	0.0:0.0962:0.0:0.9038	rs2293013;rs17855355;rs2293013	10	Q9NWS0	PIHD1_HUMAN	E	10	ENSP00000262265:G10E	ENSP00000262265:G10E	G	-	2	0	PIH1D1	54646615	0.940000	0.31905	0.225000	0.23894	0.079000	0.17450	1.388000	0.34442	0.976000	0.38417	-0.430000	0.05897	GGG	C|0.332;T|0.668	0.668	strong		0.617	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916	
PCDHGC5	56097	hgsc.bcm.edu	37	5	140870516	140870516	+	Missense_Mutation	SNP	A	A	G	rs2074912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140870516A>G	ENST00000252087.1	+	1	1709	c.1709A>G	c.(1708-1710)gAc>gGc	p.D570G	PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	570			D -> G (in dbSNP:rs2074912).		homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGGCCAGACTGGGAACAC	0.602													G|||	936	0.186901	0.1437	0.3545	5008	,	,		20886	0.129		0.2127	False		,,,				2504	0.1595				p.D570G		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.A1709G						PASS	.	G	,,,,,,,,,,,,,,,,,,,,GLY/ASP,,,,GLY/ASP	706,3700	757.9+/-412.8	58,590,1555	61.0	57.0	58.0		,,,,,,,,,,,,,,,,,,,,1709,,,,1709	5.4	0.1	5	dbSNP_96	58	1696,6904	736.3+/-407.0	156,1384,2760	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,intron,missense	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGC5,PCDHGC4,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_018928.2,NM_018929.2,NM_032088.1,NM_032092.1,NM_032403.1,NM_032407.1	,,,,,,,,,,,,,,,,,,,,94,,,,94	214,1974,4315	GG,GA,AA		19.7209,16.0236,18.4684	,,,,,,,,,,,,,,,,,,,,benign,,,,benign	,,,,,,,,,,,,,,,,,,,,570/945,,,,570/879	140870516	2402,10604	2203	4300	6503	SO:0001583	missense	56097	exon1			GGCCAGACTGGGA	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"""Cadherins / Protocadherins : Clustered"""	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.1709A>G	5.37:g.140870516A>G	ENSP00000252087:p.Asp570Gly	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_018929	Q9Y5C2	Missense_Mutation	SNP	ENST00000252087.1	37	CCDS4263.1	430	0.19688644688644688	70	0.14227642276422764	120	0.3314917127071823	77	0.1346153846153846	163	0.21503957783641162	G	0.787	-0.760117	0.03019	0.160236	0.197209	ENSG00000240764	ENST00000252087	T	0.48836	0.8	5.45	5.45	0.79879	Cadherin-like (1);	0.000000	0.64402	N	0.000019	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38023	-0.9680	9	0.16420	T	0.52	.	6.1051	0.20069	0.0738:0.1326:0.6568:0.1368	rs2074912;rs60363178;rs2074912	570;570	Q9Y5F6-2;Q9Y5F6	.;PCDGM_HUMAN	G	570	ENSP00000252087:D570G	ENSP00000252087:D570G	D	+	2	0	PCDHGC5	140850700	0.978000	0.34361	0.145000	0.22337	0.992000	0.81027	2.437000	0.44828	1.550000	0.49438	-0.119000	0.15052	GAC	A|0.821;G|0.179	0.179	strong		0.602	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929	
HELZ2	85441	hgsc.bcm.edu	37	20	62191321	62191321	+	Silent	SNP	A	A	G	rs3810477	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62191321A>G	ENST00000467148.1	-	18	7854	c.7785T>C	c.(7783-7785)aaT>aaC	p.N2595N	HELZ2_ENST00000427522.2_Silent_p.N2026N	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2595	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TGACAGCCACATTCACTTGGT	0.657													G|||	3053	0.609625	0.4652	0.5908	5008	,	,		13790	0.8502		0.5338	False		,,,				2504	0.6483				p.N2595N		Atlas-SNP	.											PRIC285,caecum,carcinoma,0,1	.	.	1	0			c.T7785C						PASS	.	G	,	2116,2288	593.1+/-387.9	513,1090,599	69.0	62.0	65.0		7785,6078	-3.0	1.0	20	dbSNP_107	65	4699,3901	544.4+/-384.6	1267,2165,868	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	1780,3255,1467	GG,GA,AA		45.3605,48.0472,47.593	,	2595/2650,2026/2081	62191321	6815,6189	2202	4300	6502	SO:0001819	synonymous_variant	85441	exon19			AGCCACATTCACT	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.7785T>C	20.37:g.62191321A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			A|0.441;G|0.559	0.559	strong		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
CAPN9	10753	hgsc.bcm.edu	37	1	230916260	230916260	+	Silent	SNP	C	C	T	rs28359687	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:230916260C>T	ENST00000271971.2	+	11	1400	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D	CAPN9_ENST00000366666.2_Silent_p.D366D|CAPN9_ENST00000354537.1_Silent_p.D403D|RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	429	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				CTGACAAAGACGAACACCTGA	0.517													C|||	540	0.107827	0.087	0.1297	5008	,	,		16813	0.0813		0.1481	False		,,,				2504	0.1063				p.D429D		Atlas-SNP	.											.	CAPN9	116	.	0			c.C1287T						PASS	.	C	,	424,3982	206.2+/-227.9	21,382,1800	84.0	82.0	83.0		1287,1209	-8.1	0.0	1	dbSNP_125	83	1327,7273	260.8+/-283.4	94,1139,3067	no	coding-synonymous,coding-synonymous	CAPN9	NM_006615.2,NM_016452.1	,	115,1521,4867	TT,TC,CC		15.4302,9.6232,13.463	,	429/691,403/665	230916260	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	10753	exon11			CAAAGACGAACAC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1287C>T	1.37:g.230916260C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_006615	B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	37	CCDS1586.1																																																																																			C|0.878;T|0.122	0.122	strong		0.517	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
TDG	6996	hgsc.bcm.edu	37	12	104376700	104376700	+	Missense_Mutation	SNP	A	A	C	rs61937630		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:104376700A>C	ENST00000392872.3	+	5	836	c.602A>C	c.(601-603)aAa>aCa	p.K201T	AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Missense_Mutation_p.K25Q|TDG_ENST00000266775.9_Missense_Mutation_p.K197T|TDG_ENST00000544861.1_Missense_Mutation_p.K58T	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	201					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)	p.K201T(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		CCCGGCAGCAAAGATCTCTCC	0.458								Base excision repair (BER), DNA glycosylases																													p.K201T		Atlas-SNP	.											TDG,extremity,malignant_melanoma,0,1	TDG	43	1	1	Substitution - Missense(1)	skin(1)	c.A602C						PASS	.						81.0	78.0	79.0					12																	104376700		2203	4300	6503	SO:0001583	missense	6996	exon5			GCAGCAAAGATCT	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.602A>C	12.37:g.104376700A>C	ENSP00000376611:p.Lys201Thr	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	296	23	0.0777027	NM_003211	Q8IUZ6|Q8IZM3	Missense_Mutation	SNP	ENST00000392872.3	37	CCDS9095.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.68|17.68	3.450099|3.450099	0.63290|0.63290	.|.	.|.	ENSG00000139372|ENSG00000139372	ENST00000542036|ENST00000392872;ENST00000266775;ENST00000544861;ENST00000537100	T|T;T;T;T	0.22539|0.45276	1.95|0.9;0.9;0.9;0.9	5.4|5.4	5.4|5.4	0.78164|0.78164	.|Uracil-DNA glycosylase-like (3);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.47116|0.47116	0.1428|0.1428	L|L	0.36672|0.36672	1.1|1.1	0.29181|0.29181	N|N	0.876493|0.876493	B|P;P	0.22346|0.42692	0.068|0.787;0.787	B|P;P	0.12837|0.52159	0.008|0.691;0.581	T|T	0.42699|0.42699	-0.9436|-0.9436	10|10	0.87932|0.31617	D|T	0|0.26	-25.7328|-25.7328	15.4266|15.4266	0.75055|0.75055	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs61937630|rs61937630	25|201;201	B4DI29|B2R848;Q13569	.|.;TDG_HUMAN	Q|T	25|201;197;58;194	ENSP00000439054:K25Q|ENSP00000376611:K201T;ENSP00000266775:K197T;ENSP00000445899:K58T;ENSP00000439825:K194T	ENSP00000439054:K25Q|ENSP00000266775:K197T	K|K	+|+	1|2	0|0	TDG|TDG	102900830|102900830	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.736000|0.736000	0.42039|0.42039	9.271000|9.271000	0.95698|0.95698	2.037000|2.037000	0.60232|0.60232	0.460000|0.460000	0.39030|0.39030	AAG|AAA	.	.	weak		0.458	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
COL12A1	1303	hgsc.bcm.edu	37	6	75797302	75797302	+	Missense_Mutation	SNP	C	C	T	rs970547	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:75797302C>T	ENST00000322507.8	-	65	9481	c.9172G>A	c.(9172-9174)Ggc>Agc	p.G3058S	COL12A1_ENST00000511023.1_5'Flank|COL12A1_ENST00000416123.2_Missense_Mutation_p.G2982S|COL12A1_ENST00000483888.2_Missense_Mutation_p.G3054S|COL12A1_ENST00000345356.6_Missense_Mutation_p.G1894S	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	3058	Nonhelical region (NC1).		G -> S (in dbSNP:rs970547). {ECO:0000269|PubMed:9143499}.		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.G3058S(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CCTGGATAGCCTTGCCCGTTG	0.512													C|||	3565	0.711861	0.6831	0.7738	5008	,	,		18205	0.6796		0.7744	False		,,,				2504	0.6759				p.G3058S		Atlas-SNP	.											COL12A1,NS,carcinoma,0,1	COL12A1	385	1	1	Substitution - Missense(1)	stomach(1)	c.G9172A	GRCh37	CM067364	COL12A1	M	rs970547	PASS	.	C	SER/GLY,SER/GLY	2515,1301		827,861,220	84.0	89.0	87.0		9172,5680	5.8	1.0	6	dbSNP_86	87	6486,1784		2532,1422,181	yes	missense,missense	COL12A1	NM_004370.5,NM_080645.2	56,56	3359,2283,401	TT,TC,CC		21.5719,34.0933,25.5254	probably-damaging,probably-damaging	3058/3064,1894/1900	75797302	9001,3085	1908	4135	6043	SO:0001583	missense	1303	exon65			GATAGCCTTGCCC	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.9172G>A	6.37:g.75797302C>T	ENSP00000325146:p.Gly3058Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	1577	0.7220695970695971	319	0.6483739837398373	287	0.7928176795580111	387	0.6765734265734266	584	0.7704485488126649	C	35	5.486790	0.96323	0.659067	0.784281	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D;D	0.89050	-2.11;-2.46;-2.16;-2.1;-2.08	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.92286	0.7553	L	0.52573	1.65	0.09310	P	0.99999322828	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.91945	0.5566	9	0.56958	D	0.05	.	19.5476	0.95305	0.0:1.0:0.0:0.0	rs970547;rs3818139;rs52836519;rs57305730;rs970547	1894;3058	Q99715-2;Q99715	.;COCA1_HUMAN	S	3058;696;2982;1894;2982;3054	ENSP00000325146:G3058S;ENSP00000399812:G696S;ENSP00000305147:G1894S;ENSP00000412864:G2982S;ENSP00000421216:G3054S	ENSP00000325146:G3058S	G	-	1	0	COL12A1	75854022	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.463000	0.80869	2.719000	0.93026	0.655000	0.94253	GGC	T|0.713;G|0.002	0.713	strong		0.512	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
OR2T34	127068	hgsc.bcm.edu	37	1	248737595	248737595	+	Missense_Mutation	SNP	A	A	G	rs150601708	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248737595A>G	ENST00000328782.2	-	1	485	c.464T>C	c.(463-465)gTt>gCt	p.V155A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V155A(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATTCCCAAAACCCAGCAGGC	0.522																																					p.V155A		Atlas-SNP	.											OR2T34,NS,carcinoma,0,2	OR2T34	72	2	1	Substitution - Missense(1)	ovary(1)	c.T464C						scavenged	.						17.0	23.0	21.0					1																	248737595		2143	4273	6416	SO:0001583	missense	127068	exon1			CCCAAAACCCAGC	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.464T>C	1.37:g.248737595A>G	ENSP00000330904:p.Val155Ala	Somatic	593	1	0.00168634		WXS	Illumina HiSeq	Phase_I	689	149	0.216255	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	602	0.27564102564102566	196	0.3983739837398374	85	0.23480662983425415	151	0.263986013986014	170	0.22427440633245382	.	5.973	0.363525	0.11296	.	.	ENSG00000183310	ENST00000328782	T	0.38722	1.12	2.34	0.992	0.19819	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B	0.15930	0.015	B	0.19666	0.026	T	0.47522	-0.9111	8	0.28530	T	0.3	.	6.4829	0.22073	0.7538:0.2461:0.0:0.0	.	155	Q8NGX1	O2T34_HUMAN	A	155	ENSP00000330904:V155A	ENSP00000330904:V155A	V	-	2	0	OR2T34	246804218	0.000000	0.05858	0.011000	0.14972	0.090000	0.18270	-0.276000	0.08514	0.953000	0.37825	0.319000	0.21371	GTT	A|0.500;G|0.500	0.500	weak		0.522	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
C12orf43	64897	hgsc.bcm.edu	37	12	121442199	121442199	+	Silent	SNP	T	T	A	rs3751151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121442199T>A	ENST00000288757.3	-	6	568	c.546A>T	c.(544-546)acA>acT	p.T182T	C12orf43_ENST00000536407.2_Intron|C12orf43_ENST00000537817.1_Silent_p.T183T|C12orf43_ENST00000539736.1_Silent_p.T172T|C12orf43_ENST00000366211.2_Silent_p.T141T|C12orf43_ENST00000445832.3_Silent_p.T152T	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	182										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTTCTCCACTGTTCCAGGGC	0.602													.|||	1295	0.258586	0.3101	0.196	5008	,	,		19038	0.2748		0.3241	False		,,,				2504	0.1493				p.T182T		Atlas-SNP	.											C12orf43,NS,adenoma,0,1	C12orf43	30	1	0			c.A546T						PASS	.	T		1398,3008	457.3+/-351.6	222,954,1027	120.0	136.0	131.0		546	-8.9	0.0	12	dbSNP_107	131	2693,5907	431.5+/-356.8	426,1841,2033	no	coding-synonymous	C12orf43	NM_022895.1		648,2795,3060	AA,AT,TT		31.314,31.7295,31.4547		182/263	121442199	4091,8915	2203	4300	6503	SO:0001819	synonymous_variant	64897	exon6			CTCCACTGTTCCA	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.546A>T	12.37:g.121442199T>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	160	160	1	NM_022895	Q53HF0|Q9H9Z7	Silent	SNP	ENST00000288757.3	37	CCDS9210.1	612	0.2802197802197802	158	0.32113821138211385	74	0.20441988950276244	135	0.23601398601398602	245	0.3232189973614776	T	5.337	0.247414	0.10130	0.317295	0.31314	ENSG00000157895	ENST00000546272	.	.	.	5.28	-8.94	0.00768	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.38845	-0.9642	3	.	.	.	12.9924	1.7231	0.02916	0.1567:0.269:0.3073:0.267	rs3751151;rs17845433;rs17858305;rs3751151	.	.	.	L	136	.	.	Q	-	2	0	C12orf43	119926582	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.286000	0.02788	-1.292000	0.02366	-1.715000	0.00711	CAG	T|0.704;A|0.296	0.296	strong		0.602	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
TEKT1	83659	hgsc.bcm.edu	37	17	6704121	6704121	+	Missense_Mutation	SNP	C	C	T	rs2271233	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:6704121C>T	ENST00000338694.2	-	7	1123	c.994G>A	c.(994-996)Gtc>Atc	p.V332I	TEKT1_ENST00000535086.1_Missense_Mutation_p.V186I	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	332			V -> I (in dbSNP:rs2271233).			cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				TATTGTGCGACATCACGACAC	0.562											OREG0024124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	255	0.0509185	0.0015	0.0403	5008	,	,		19687	0.0516		0.0746	False		,,,				2504	0.1002				p.V332I		Atlas-SNP	.											TEKT1,rectum,carcinoma,+2,1	TEKT1	49	1	0			c.G994A						scavenged	.	C	ILE/VAL	68,4338	61.7+/-98.7	1,66,2136	232.0	208.0	216.0		994	1.5	0.0	17	dbSNP_100	216	694,7906	172.2+/-222.9	30,634,3636	yes	missense	TEKT1	NM_053285.1	29	31,700,5772	TT,TC,CC		8.0698,1.5433,5.8588	benign	332/419	6704121	762,12244	2203	4300	6503	SO:0001583	missense	83659	exon7			GTGCGACATCACG		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.994G>A	17.37:g.6704121C>T	ENSP00000341346:p.Val332Ile	Somatic	171	1	0.00584795	636	WXS	Illumina HiSeq	Phase_I	194	88	0.453608	NM_053285	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	37	CCDS11083.1	88	0.040293040293040296	1	0.0020325203252032522	20	0.055248618784530384	8	0.013986013986013986	59	0.07783641160949868	C	10.03	1.239842	0.22711	0.015433	0.080698	ENSG00000167858	ENST00000338694;ENST00000535086	T;T	0.02472	4.28;4.28	5.85	1.46	0.22682	.	0.545369	0.19348	N	0.116471	T	0.00144	0.0004	L	0.27053	0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39542	-0.9609	9	0.35671	T	0.21	.	5.0249	0.14379	0.0:0.5096:0.1422:0.3482	rs2271233;rs17202721;rs52797408;rs60310395;rs2271233	332	Q969V4	TEKT1_HUMAN	I	332;186	ENSP00000341346:V332I;ENSP00000444142:V186I	ENSP00000341346:V332I	V	-	1	0	TEKT1	6644845	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.230000	0.09083	0.119000	0.18210	0.655000	0.94253	GTC	C|0.951;T|0.049	0.049	strong		0.562	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	
TBX4	9496	hgsc.bcm.edu	37	17	59560685	59560685	+	Silent	SNP	C	C	T	rs2270150	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59560685C>T	ENST00000240335.1	+	8	1491	c.1446C>T	c.(1444-1446)gtC>gtT	p.V482V	TBX4_ENST00000393853.4_Silent_p.V483V|TBX4_ENST00000589449.1_3'UTR	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	482					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						AGTCTCAGGTCCGAGAGCGGG	0.622													C|||	521	0.104034	0.1188	0.1052	5008	,	,		17375	0.0268		0.1402	False		,,,				2504	0.1258				p.V482V		Atlas-SNP	.											.	TBX4	69	.	0			c.C1446T						PASS	.	C		571,3835	255.2+/-260.5	45,481,1677	59.0	61.0	61.0		1446	4.3	1.0	17	dbSNP_100	61	1184,7416	240.7+/-271.3	92,1000,3208	no	coding-synonymous	TBX4	NM_018488.2		137,1481,4885	TT,TC,CC		13.7674,12.9596,13.4938		482/546	59560685	1755,11251	2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			TCAGGTCCGAGAG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1446C>T	17.37:g.59560685C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	149	55	0.369128	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			C|0.880;T|0.120	0.120	strong		0.622	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
IL1A	3552	hgsc.bcm.edu	37	2	113539246	113539246	+	Missense_Mutation	SNP	C	C	T	rs3783531	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113539246C>T	ENST00000263339.3	-	4	409	c.254G>A	c.(253-255)cGg>cAg	p.R85Q		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	85			R -> Q (in dbSNP:rs3783531). {ECO:0000269|Ref.10}.		apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|response to copper ion (GO:0046688)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	copper ion binding (GO:0005507)|cytokine activity (GO:0005125)			breast(2)|large_intestine(1)|lung(9)	12					Rilonacept(DB06372)	TAAACTCAACCGTCTCTTCTT	0.453													C|||	3	0.000599042	0.0	0.0014	5008	,	,		23078	0.0		0.002	False		,,,				2504	0.0				p.R85Q		Atlas-SNP	.											.	IL1A	19	.	0			c.G254A						PASS	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	230.0	211.0	217.0		254	4.9	0.1	2	dbSNP_107	217	23,8577	16.6+/-54.9	0,23,4277	yes	missense	IL1A	NM_000575.3	43	0,25,6478	TT,TC,CC		0.2674,0.0454,0.1922	probably-damaging	85/272	113539246	25,12981	2203	4300	6503	SO:0001583	missense	3552	exon4			CTCAACCGTCTCT	M28983	CCDS2101.1	2q14	2014-01-30			ENSG00000115008	ENSG00000115008		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5991	protein-coding gene	gene with protein product	"""preinterleukin 1 alpha"", ""hematopoietin-1"", ""pro-interleukin-1-alpha"""	147760		IL1		8188271, 2989698	Standard	NM_000575		Approved	IL1F1, IL-1A, IL1-ALPHA	uc002tig.3	P01583	OTTHUMG00000131315	ENST00000263339.3:c.254G>A	2.37:g.113539246C>T	ENSP00000263339:p.Arg85Gln	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	306	124	0.405229	NM_000575	Q53QF9|Q7RU02	Missense_Mutation	SNP	ENST00000263339.3	37	CCDS2101.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	19.02	3.745767	0.69418	4.54E-4	0.002674	ENSG00000115008	ENST00000263339	T	0.47177	0.85	5.78	4.88	0.63580	Interleukin-1 propeptide (1);	0.000000	0.52532	D	0.000061	T	0.66742	0.2820	M	0.80847	2.515	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.60672	-0.7217	10	0.27082	T	0.32	-17.4428	12.36	0.55197	0.1687:0.8313:0.0:0.0	rs3783531;rs3783531	85	P01583	IL1A_HUMAN	Q	85	ENSP00000263339:R85Q	ENSP00000263339:R85Q	R	-	2	0	IL1A	113255717	0.053000	0.20554	0.081000	0.20488	0.602000	0.36980	3.439000	0.52878	1.543000	0.49345	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.453	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575	
MICB	4277	hgsc.bcm.edu	37	6	31473957	31473957	+	Missense_Mutation	SNP	C	C	G	rs3134900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31473957C>G	ENST00000252229.6	+	3	442	c.363C>G	c.(361-363)atC>atG	p.I121M	MICB_ENST00000399150.3_Intron|MICB_ENST00000538442.1_Missense_Mutation_p.I89M	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						TCTGTGAGATCCATGAAGACA	0.562													c|||	385	0.076877	0.1188	0.0447	5008	,	,		17796	0.0685		0.0895	False		,,,				2504	0.0389				p.I121M		Atlas-SNP	.											MICB,NS,neuroblastoma,0,2	MICB	26	2	0			c.C363G						PASS	.	-	MET/ILE	479,3385		32,415,1485	28.0	30.0	30.0		363	1.4	0.0	6	dbSNP_103	30	975,7281		62,851,3215	no	missense	MICB	NM_005931.3	10	94,1266,4700	GG,GC,CC		11.8096,12.3965,11.9967	probably-damaging	121/384	31473957	1454,10666	1932	4128	6060	SO:0001583	missense	4277	exon3			TGAGATCCATGAA		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"""Immunoglobulin superfamily / C1-set domain containing"""	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.363C>G	6.37:g.31473957C>G	ENSP00000252229:p.Ile121Met	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	208	72	0.346154	NM_005931		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	162	0.07417582417582418	53	0.10772357723577236	14	0.03867403314917127	26	0.045454545454545456	69	0.09102902374670185	N	8.773	0.926504	0.18056	0.123965	0.118096	ENSG00000204516	ENST00000538442;ENST00000252229	T;T	0.00856	5.61;5.61	2.33	1.44	0.22558	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.455993	0.16197	U	0.225128	T	0.01421	0.0046	M	0.69823	2.125	0.80722	P	0.0	D;D	0.76494	0.991;0.999	D;D	0.87578	0.994;0.998	T	0.48917	-0.8992	9	0.59425	D	0.04	.	3.8543	0.08968	0.0:0.5964:0.2512:0.1524	rs3134900	89;121	F5H7Q8;Q29980	.;MICB_HUMAN	M	89;121	ENSP00000442345:I89M;ENSP00000252229:I121M	ENSP00000252229:I121M	I	+	3	3	MICB	31581936	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.976000	0.03786	0.543000	0.28864	-0.755000	0.03482	ATC	C|0.918;G|0.082	0.082	strong		0.562	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931	
CHDH	55349	hgsc.bcm.edu	37	3	53856653	53856653	+	Silent	SNP	C	C	T	rs2241808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:53856653C>T	ENST00000315251.6	-	4	1157	c.720G>A	c.(718-720)gcG>gcA	p.A240A		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	240					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	AGGCACAGGCCGCGCTCCACC	0.647													C|||	2217	0.442692	0.1581	0.4438	5008	,	,		19438	0.5655		0.5268	False		,,,				2504	0.6135				p.A240A		Atlas-SNP	.											CHDH,colon,carcinoma,-2,1	CHDH	34	1	0			c.G720A						PASS	.	C		986,3420	368.8+/-318.8	111,764,1328	74.0	62.0	66.0		720	-11.3	0.0	3	dbSNP_98	66	4716,3884	606.1+/-395.1	1280,2156,864	no	coding-synonymous	CHDH	NM_018397.4		1391,2920,2192	TT,TC,CC		45.1628,22.3786,43.8413		240/595	53856653	5702,7304	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon4			ACAGGCCGCGCTC	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.720G>A	3.37:g.53856653C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			C|0.555;T|0.444	0.444	strong		0.647	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
CHAC1	79094	hgsc.bcm.edu	37	15	41245676	41245676	+	Silent	SNP	G	G	A	rs11557249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41245676G>A	ENST00000446533.3	+	1	330	c.21G>A	c.(19-21)gaG>gaA	p.E7E	CHAC1_ENST00000444189.2_Silent_p.E7E|CHAC1_ENST00000487220.1_5'Flank	NM_001142776.1|NM_024111.3	NP_001136248.1|NP_077016.2	Q9BUX1	CHAC1_HUMAN	ChaC, cation transport regulator homolog 1 (E. coli)	7					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein processing (GO:0010955)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|trans-Golgi network (GO:0005802)	Notch binding (GO:0005112)			endometrium(1)|large_intestine(1)|skin(1)	3		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.66e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.163)		CTCAGCTGGAGCTACCGAGCG	0.701													G|||	1186	0.236821	0.1142	0.3112	5008	,	,		13088	0.2292		0.3907	False		,,,				2504	0.1994				p.E7E		Atlas-SNP	.											CHAC1_ENST00000446533,NS,carcinoma,0,1	CHAC1	25	1	0			c.G21A						PASS	.	G	,	204,1180		10,184,498	14.0	21.0	19.0		21,21	4.0	1.0	15	dbSNP_120	19	1266,1916		250,766,575	no	coding-synonymous,coding-synonymous	CHAC1	NM_001142776.1,NM_024111.3	,	260,950,1073	AA,AG,GG		39.7863,14.7399,32.1945	,	7/220,7/265	41245676	1470,3096	692	1591	2283	SO:0001819	synonymous_variant	79094	exon1			GCTGGAGCTACCG	BC019625	CCDS10070.2, CCDS45233.1	15q15.1	2013-09-12	2006-09-12		ENSG00000128965	ENSG00000128965			28680	protein-coding gene	gene with protein product	"""gamma-GCT acting on glutathione homolog 1"""	614587	"""ChaC, cation transport regulator-like 1 (E. coli)"""			23070364	Standard	NM_024111		Approved	MGC4504	uc001znh.2	Q9BUX1	OTTHUMG00000130208	ENST00000446533.3:c.21G>A	15.37:g.41245676G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_024111	Q0VIA0	Silent	SNP	ENST00000446533.3	37	CCDS10070.2																																																																																			G|0.742;A|0.258	0.258	strong		0.701	CHAC1-001	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252526.3	NM_024111	
CXorf65	158830	hgsc.bcm.edu	37	X	70324157	70324157	+	Silent	SNP	C	C	T	rs1130009	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:70324157C>T	ENST00000374251.5	-	5	465	c.417G>A	c.(415-417)gcG>gcA	p.A139A		NM_001025265.2	NP_001020436.1	A6NEN9	CX065_HUMAN	chromosome X open reading frame 65	139										breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)	10						CCGGGACACTCGCAGGGGGTT	0.507													C|||	422	0.111788	0.0197	0.1326	3775	,	,		13137	0.001		0.2555	False		,,,				2504	0.047				p.A139A		Atlas-SNP	.											.	CXorf65	23	.	0			c.G417A						PASS	.	C		243,3592		11,187,34,1434,537	82.0	64.0	70.0		417	2.1	0.0	X	dbSNP_86	70	2153,4575		236,1079,602,1113,1270	no	coding-synonymous	CXorf65	NM_001025265.2		247,1266,636,2547,1807	TT,TC,T,CC,C		32.0006,6.3364,22.6829		139/184	70324157	2396,8167	2203	4300	6503	SO:0001819	synonymous_variant	158830	exon5			GACACTCGCAGGG	BC144434	CCDS35324.1	Xq13.1	2009-03-06			ENSG00000204165	ENSG00000204165			33713	protein-coding gene	gene with protein product							Standard	NM_001025265		Approved		uc011mpo.2	A6NEN9	OTTHUMG00000021785	ENST00000374251.5:c.417G>A	X.37:g.70324157C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	77	74	0.961039	NM_001025265		Silent	SNP	ENST00000374251.5	37	CCDS35324.1																																																																																			0|0.002;T|0.182	0.182	strong		0.507	CXorf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057089.2	NM_001025265	
KRTAP15-1	254950	hgsc.bcm.edu	37	21	31812772	31812772	+	Missense_Mutation	SNP	C	C	A	rs2832873	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:31812772C>A	ENST00000334067.3	+	1	176	c.127C>A	c.(127-129)Ctg>Atg	p.L43M		NM_181623.1	NP_853654.1	Q3LI76	KR151_HUMAN	keratin associated protein 15-1	43			L -> M (in dbSNP:rs2832873). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			intermediate filament (GO:0005882)				kidney(1)|large_intestine(3)|lung(6)|skin(1)	11						TACCTGCCAACTGGGCTCCTC	0.488													C|||	2775	0.554113	0.6543	0.6427	5008	,	,		19927	0.2788		0.5736	False		,,,				2504	0.6196				p.L43M		Atlas-SNP	.											KRTAP15-1,rectum,carcinoma,-2,1	KRTAP15-1	35	1	0			c.C127A						PASS	.	C	MET/LEU	2839,1567	669.0+/-402.1	900,1039,264	85.0	85.0	85.0		127	0.8	1.0	21	dbSNP_100	85	5043,3557	630.1+/-398.3	1483,2077,740	yes	missense	KRTAP15-1	NM_181623.1	15	2383,3116,1004	AA,AC,CC		41.3605,35.5651,39.3972	possibly-damaging	43/138	31812772	7882,5124	2203	4300	6503	SO:0001583	missense	254950	exon1			TGCCAACTGGGCT	AP001708	CCDS13593.1	21q22.1	2008-05-21			ENSG00000186970	ENSG00000186970		"""Keratin associated proteins"""	18927	protein-coding gene	gene with protein product						12359730	Standard	NM_181623		Approved	KAP15.1	uc002yod.3	Q3LI76	OTTHUMG00000057784	ENST00000334067.3:c.127C>A	21.37:g.31812772C>A	ENSP00000334866:p.Leu43Met	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_181623	Q2M3F4	Missense_Mutation	SNP	ENST00000334067.3	37	CCDS13593.1	1153	0.5279304029304029	329	0.6686991869918699	234	0.6464088397790055	170	0.2972027972027972	420	0.554089709762533	C	12.58	1.980915	0.34942	0.644349	0.586395	ENSG00000186970	ENST00000334067	T	0.03635	3.86	4.79	0.826	0.18829	.	1.886810	0.02903	N	0.135621	T	0.00012	0.0000	M	0.76170	2.325	0.54753	P	1.399999999995849E-5	P	0.52842	0.956	P	0.49799	0.622	T	0.43925	-0.9361	9	0.59425	D	0.04	0.1574	3.5753	0.07932	0.1394:0.3289:0.4302:0.1015	rs2832873;rs17596869;rs52830193;rs57673787;rs2832873	43	Q3LI76	KR151_HUMAN	M	43	ENSP00000334866:L43M	ENSP00000334866:L43M	L	+	1	2	KRTAP15-1	30734643	0.917000	0.31117	0.961000	0.40146	0.252000	0.25951	0.037000	0.13840	0.140000	0.18849	0.655000	0.94253	CTG	C|0.432;A|0.568	0.568	strong		0.488	KRTAP15-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128236.1		
POLN	353497	hgsc.bcm.edu	37	4	2194946	2194946	+	Missense_Mutation	SNP	C	C	T	rs10011549	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2194946C>T	ENST00000511885.2	-	7	1359	c.1006G>A	c.(1006-1008)Ggc>Agc	p.G336S	POLN_ENST00000382865.1_Missense_Mutation_p.G336S|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	336			G -> S (in dbSNP:rs10011549). {ECO:0000269|Ref.3}.		double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			TTCCAACTGCCATCATTGCCA	0.358								DNA polymerases (catalytic subunits)					C|||	1656	0.330671	0.6029	0.2464	5008	,	,		17328	0.372		0.1243	False		,,,				2504	0.1922				p.G336S		Atlas-SNP	.											.	POLN	82	.	0			c.G1006A						PASS	.	C	SER/GLY	2357,2047	601.5+/-389.7	663,1031,508	83.0	90.0	88.0		1006	0.4	0.0	4	dbSNP_119	88	992,7608	212.8+/-253.0	60,872,3368	yes	missense	POLN	NM_181808.2	56	723,1903,3876	TT,TC,CC		11.5349,46.4805,25.7536	benign	336/901	2194946	3349,9655	2202	4300	6502	SO:0001583	missense	353497	exon5			AACTGCCATCATT	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.1006G>A	4.37:g.2194946C>T	ENSP00000435506:p.Gly336Ser	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	165	69	0.418182	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	37	CCDS3360.1	694	0.31776556776556775	299	0.6077235772357723	91	0.2513812154696133	209	0.36538461538461536	95	0.12532981530343007	C	3.265	-0.150292	0.06585	0.535195	0.115349	ENSG00000130997	ENST00000511885;ENST00000382865;ENST00000253313	T;T	0.04862	3.54;3.54	5.48	0.379	0.16213	.	1.209770	0.05508	N	0.559735	T	0.00012	0.0000	L	0.31294	0.92	0.80722	P	0.0	B;B	0.15719	0.014;0.006	B;B	0.13407	0.009;0.004	T	0.36601	-0.9741	9	0.15952	T	0.53	-0.5074	3.1464	0.06473	0.3199:0.4138:0.0:0.2663	rs10011549;rs52816412;rs58504233;rs10011549	336;336	E7ERY2;Q7Z5Q5	.;DPOLN_HUMAN	S	336;336;27	ENSP00000435506:G336S;ENSP00000372316:G336S	ENSP00000253313:G27S	G	-	1	0	POLN	2164744	0.000000	0.05858	0.005000	0.12908	0.048000	0.14542	-0.334000	0.07883	0.249000	0.21456	0.655000	0.94253	GGC	C|0.708;T|0.292	0.292	strong		0.358	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
FGD5	152273	hgsc.bcm.edu	37	3	14861665	14861665	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14861665T>C	ENST00000285046.5	+	1	1197	c.1087T>C	c.(1087-1089)Tct>Cct	p.S363P	FGD5_ENST00000543601.1_Missense_Mutation_p.S122P	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	363					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						CGAGAGCTGTTCTCCTCTTTC	0.532																																					p.S363P		Atlas-SNP	.											.	FGD5	248	.	0			c.T1087C						PASS	.						59.0	60.0	59.0					3																	14861665		1909	4138	6047	SO:0001583	missense	152273	exon1			AGCTGTTCTCCTC	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.1087T>C	3.37:g.14861665T>C	ENSP00000285046:p.Ser363Pro	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	149	6	0.0402685	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.401385	0.25291	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.76316	-1.01;-0.85	5.34	-3.2	0.05156	.	0.543869	0.16888	N	0.195436	T	0.53883	0.1824	N	0.20986	0.625	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.30475	-0.9977	10	0.38643	T	0.18	-0.7487	1.4964	0.02467	0.1367:0.2613:0.302:0.3	.	122;363	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	P	363;122	ENSP00000285046:S363P;ENSP00000445949:S122P	ENSP00000285046:S363P	S	+	1	0	FGD5	14836669	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.262000	0.08682	-0.905000	0.03871	-0.250000	0.11733	TCT	.	.	none		0.532	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
TCIRG1	10312	hgsc.bcm.edu	37	11	67810297	67810297	+	Silent	SNP	C	C	T	rs3808973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67810297C>T	ENST00000265686.3	+	4	492	c.384C>T	c.(382-384)caC>caT	p.H128H	TCIRG1_ENST00000532635.1_5'Flank	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	128					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						TGCAGCTCCACGCCGCCGTGC	0.711													C|||	260	0.0519169	0.0643	0.0331	5008	,	,		14610	0.0724		0.0378	False		,,,				2504	0.0419				p.H128H		Atlas-SNP	.											.	TCIRG1	40	.	0			c.C384T						PASS	.	C		156,3622		1,154,1734	4.0	6.0	5.0		384	0.4	0.1	11	dbSNP_107	5	202,7052		3,196,3428	no	coding-synonymous	TCIRG1	NM_006019.3		4,350,5162	TT,TC,CC		2.7847,4.1292,3.2451		128/831	67810297	358,10674	1889	3627	5516	SO:0001819	synonymous_variant	10312	exon4			GCTCCACGCCGCC	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"""ATPases / V-type"""	11647	protein-coding gene	gene with protein product	"""T-cell immune response cDNA 7"""	604592	"""T-cell, immune regulator 1"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"""			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.384C>T	11.37:g.67810297C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_006019	O75877|Q8WVC5	Silent	SNP	ENST00000265686.3	37	CCDS8177.1																																																																																			C|0.948;T|0.052	0.052	strong		0.711	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019	
IL22RA1	58985	hgsc.bcm.edu	37	1	24465113	24465113	+	Silent	SNP	C	C	T	rs10903022	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:24465113C>T	ENST00000270800.1	-	2	173	c.135G>A	c.(133-135)ccG>ccA	p.P45P		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	45	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		GGGTGCCCTCCGGCCCGCTGT	0.582													C|||	2357	0.470647	0.261	0.5231	5008	,	,		20665	0.7619		0.3628	False		,,,				2504	0.5276				p.P45P		Atlas-SNP	.											.	IL22RA1	62	.	0			c.G135A						PASS	.	C		1200,3206	418.3+/-338.2	167,866,1170	97.0	92.0	93.0		135	-5.4	0.0	1	dbSNP_120	93	3278,5322	490.9+/-373.0	635,2008,1657	no	coding-synonymous	IL22RA1	NM_021258.3		802,2874,2827	TT,TC,CC		38.1163,27.2356,34.4303		45/575	24465113	4478,8528	2203	4300	6503	SO:0001819	synonymous_variant	58985	exon2			GCCCTCCGGCCCG	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"""Interleukins and interleukin receptors"""	13700	protein-coding gene	gene with protein product		605457	"""interleukin 22 receptor"""	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.135G>A	1.37:g.24465113C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	156	154	0.987179	NM_021258	A8K839|B2R9Y9|Q9HB22	Silent	SNP	ENST00000270800.1	37	CCDS247.1																																																																																			C|0.607;N|0.000	.	strong		0.582	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
KLF17	128209	hgsc.bcm.edu	37	1	44595426	44595426	+	Silent	SNP	G	G	A	rs2429050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:44595426G>A	ENST00000372299.3	+	2	541	c.483G>A	c.(481-483)tcG>tcA	p.S161S	KLF17_ENST00000476802.1_Intron	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	161					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					TGCCAGTCTCGGCTTCCACTG	0.577													G|||	1378	0.27516	0.0915	0.2579	5008	,	,		17305	0.4236		0.3966	False		,,,				2504	0.2577				p.S161S		Atlas-SNP	.											.	KLF17	92	.	0			c.G483A						PASS	.	G		638,3768	270.1+/-269.4	49,540,1614	34.0	38.0	36.0		483	-2.0	0.0	1	dbSNP_100	36	3202,5396	475.0+/-369.0	589,2024,1686	no	coding-synonymous	KLF17	NM_173484.3		638,2564,3300	AA,AG,GG		37.2412,14.4803,29.5294		161/390	44595426	3840,9164	2203	4299	6502	SO:0001819	synonymous_variant	128209	exon2			AGTCTCGGCTTCC	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.483G>A	1.37:g.44595426G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_173484	Q86VQ7|Q8N805	Silent	SNP	ENST00000372299.3	37	CCDS508.1																																																																																			G|0.699;A|0.301	0.301	strong		0.577	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
MASP1	5648	hgsc.bcm.edu	37	3	186959295	186959295	+	Missense_Mutation	SNP	C	C	T	rs28945068	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186959295C>T	ENST00000337774.5	-	10	1666	c.1277G>A	c.(1276-1278)gGg>gAg	p.G426E	MASP1_ENST00000495249.1_Intron|MASP1_ENST00000392472.2_Missense_Mutation_p.G313E|MASP1_ENST00000296280.6_Missense_Mutation_p.G426E	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	426	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TAGGCTTCTCCCCAATACTTT	0.478													C|||	39	0.00778754	0.0023	0.0159	5008	,	,		19262	0.0		0.0239	False		,,,				2504	0.001				p.G426E		Atlas-SNP	.											MASP1_ENST00000296280,NS,carcinoma,+1,4	MASP1	240	4	0			c.G1277A						PASS	.	C	GLU/GLY,GLU/GLY	11,4395	19.1+/-41.9	0,11,2192	147.0	140.0	142.0		1277,1277	3.1	1.0	3	dbSNP_125	142	124,8476	63.9+/-126.0	0,124,4176	yes	missense,missense	MASP1	NM_001879.5,NM_139125.3	98,98	0,135,6368	TT,TC,CC		1.4419,0.2497,1.038	benign,benign	426/700,426/729	186959295	135,12871	2203	4300	6503	SO:0001583	missense	5648	exon10			CTTCTCCCCAATA	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"""Serine peptidases / Serine peptidases"""	6901	protein-coding gene	gene with protein product		600521	"""mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"""	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1277G>A	3.37:g.186959295C>T	ENSP00000336792:p.Gly426Glu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	71	0.489655	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Missense_Mutation	SNP	ENST00000337774.5	37	CCDS33907.1	19	0.0086996336996337	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	13	0.017150395778364115	C	0.020	-1.439930	0.01098	0.002497	0.014419	ENSG00000127241	ENST00000337774;ENST00000296280;ENST00000392472;ENST00000541896	T;D;D	0.82803	0.78;-1.64;-1.65	5.81	3.06	0.35304	Complement control module (2);Sushi/SCR/CCP (2);	0.143291	0.64402	N	0.000006	T	0.68118	0.2966	L	0.61218	1.895	0.80722	D	1	B;B;B	0.26577	0.075;0.012;0.153	B;B;B	0.34536	0.185;0.042;0.088	T	0.65825	-0.6074	10	0.23891	T	0.37	.	9.8477	0.41037	0.0:0.7792:0.0:0.2208	rs28945068	313;426;426	P48740-4;P48740-2;P48740	.;.;MASP1_HUMAN	E	426;426;313;313	ENSP00000336792:G426E;ENSP00000296280:G426E;ENSP00000376264:G313E	ENSP00000296280:G426E	G	-	2	0	MASP1	188441989	0.952000	0.32445	0.989000	0.46669	0.082000	0.17680	1.901000	0.39838	0.373000	0.24621	-0.768000	0.03414	GGG	C|0.989;T|0.011	0.011	strong		0.478	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879	
ANKK1	255239	hgsc.bcm.edu	37	11	113270015	113270015	+	Missense_Mutation	SNP	G	G	C	rs4938016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:113270015G>C	ENST00000303941.3	+	8	1418	c.1324G>C	c.(1324-1326)Ggc>Cgc	p.G442R		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	442			G -> R (in dbSNP:rs4938016). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TGGGGATGACGGCACTGCGCG	0.607													C|||	2751	0.549321	0.4259	0.6066	5008	,	,		19201	0.4663		0.6829	False		,,,				2504	0.6237				p.G442R		Atlas-SNP	.											ANKK1,NS,carcinoma,0,1	ANKK1	83	1	0			c.G1324C						PASS	.	C	ARG/GLY	2069,2201		535,999,601	22.0	26.0	25.0		1324	1.8	0.1	11	dbSNP_111	25	5896,2582		2077,1742,420	yes	missense	ANKK1	NM_178510.1	125	2612,2741,1021	CC,CG,GG		30.4553,48.4543,37.5196	benign	442/766	113270015	7965,4783	2135	4239	6374	SO:0001583	missense	255239	exon8			GATGACGGCACTG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.1324G>C	11.37:g.113270015G>C	ENSP00000306678:p.Gly442Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	1204	0.5512820512820513	214	0.4349593495934959	226	0.6243093922651933	256	0.44755244755244755	508	0.6701846965699209	C	0.137	-1.106843	0.01813	0.484543	0.695447	ENSG00000170209	ENST00000303941	T	0.15718	2.4	4.7	1.82	0.25136	Ankyrin repeat-containing domain (4);	0.114870	0.36591	N	0.002511	T	0.00012	0.0000	N	0.05158	-0.105	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28964	-1.0027	9	0.11182	T	0.66	-2.6625	2.025	0.03517	0.1365:0.5066:0.1326:0.2242	rs4938016;rs4938016	442	Q8NFD2	ANKK1_HUMAN	R	442	ENSP00000306678:G442R	ENSP00000306678:G442R	G	+	1	0	ANKK1	112775225	0.000000	0.05858	0.100000	0.21137	0.023000	0.10783	-0.708000	0.05035	-0.013000	0.14199	-0.365000	0.07479	GGC	C|0.560;G|0.440	0.560	strong		0.607	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
MUC4	4585	hgsc.bcm.edu	37	3	195506983	195506983	+	Missense_Mutation	SNP	G	G	A	rs541438739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506983G>A	ENST00000463781.3	-	2	11927	c.11468C>T	c.(11467-11469)aCc>aTc	p.T3823I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3823I	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3823I(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGAGGGGTGGTGTCACC	0.587													.|||	248	0.0495208	0.1399	0.0317	5008	,	,		9423	0.002		0.0358	False		,,,				2504	0.0031				p.T3823I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C11468T						scavenged	.						5.0	5.0	5.0					3																	195506983		440	1246	1686	SO:0001583	missense	4585	exon2			AGAGGGGTGGTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11468C>T	3.37:g.195506983G>A	ENSP00000417498:p.Thr3823Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	159	28	0.176101	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.889	0.533565	0.13188	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.55	.	.	.	.	.	.	.	.	T	0.13200	0.0320	N	0.14661	0.345	0.09310	N	1	P	0.47604	0.898	B	0.36885	0.235	T	0.15838	-1.0423	7	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3695	E7ESK3	.	I	3823	ENSP00000417498:T3823I;ENSP00000420243:T3823I	.	T	-	2	0	MUC4	196991762	0.000000	0.05858	0.110000	0.21437	0.111000	0.19643	-0.374000	0.07484	0.064000	0.16427	0.064000	0.15345	ACC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
C12orf71	728858	hgsc.bcm.edu	37	12	27234200	27234200	+	Silent	SNP	T	T	C	rs708165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:27234200T>C	ENST00000429849.2	-	2	747	c.717A>G	c.(715-717)aaA>aaG	p.K239K		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	239										endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						GATGGGGACTTTTGGTGGCAT	0.522													C|||	1003	0.20028	0.1316	0.2176	5008	,	,		19100	0.0357		0.4433	False		,,,				2504	0.2004				p.K239K		Atlas-SNP	.											.	C12orf71	20	.	0			c.A717G						PASS	.	C		744,3398		66,612,1393	89.0	87.0	88.0		717	0.2	0.0	12	dbSNP_86	88	3764,4680		843,2078,1301	no	coding-synonymous	C12orf71	NM_001080406.1		909,2690,2694	CC,CT,TT		44.576,17.9623,35.8176		239/270	27234200	4508,8078	2071	4222	6293	SO:0001819	synonymous_variant	728858	exon2			GGGACTTTTGGTG		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.717A>G	12.37:g.27234200T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001080406		Silent	SNP	ENST00000429849.2	37	CCDS44851.1																																																																																			T|0.739;C|0.261	0.261	strong		0.522	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
ZNF532	55205	hgsc.bcm.edu	37	18	56620910	56620910	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56620910C>T	ENST00000336078.4	+	8	3805	c.3029C>T	c.(3028-3030)cCt>cTt	p.P1010L	ZNF532_ENST00000591083.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000591230.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000589288.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000591808.1_Missense_Mutation_p.P1010L	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1010					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						TCTCCATCTCCTGTGAAAAAA	0.433																																					p.P1010L		Atlas-SNP	.											.	ZNF532	108	.	0			c.C3029T						PASS	.						77.0	77.0	77.0					18																	56620910		2203	4300	6503	SO:0001583	missense	55205	exon8			CATCTCCTGTGAA	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.3029C>T	18.37:g.56620910C>T	ENSP00000338217:p.Pro1010Leu	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	253	139	0.549407	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	37	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.102745	0.56183	.	.	ENSG00000074657	ENST00000336078	T	0.01705	4.68	5.23	5.23	0.72850	.	0.109437	0.64402	D	0.000006	T	0.03520	0.0101	M	0.63843	1.955	0.80722	D	1	B;B	0.17852	0.024;0.012	B;B	0.15052	0.012;0.009	T	0.51779	-0.8662	10	0.22706	T	0.39	-0.2311	18.7617	0.91855	0.0:1.0:0.0:0.0	.	1010;1010	B3KXW2;Q9HCE3	.;ZN532_HUMAN	L	1010	ENSP00000338217:P1010L	ENSP00000338217:P1010L	P	+	2	0	ZNF532	54771890	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.384000	0.66225	2.599000	0.87857	0.637000	0.83480	CCT	.	.	none		0.433	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
PGM1	5236	hgsc.bcm.edu	37	1	64114301	64114301	+	Missense_Mutation	SNP	T	T	C	rs11208257	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:64114301T>C	ENST00000371084.3	+	8	1471	c.1258T>C	c.(1258-1260)Tat>Cat	p.Y420H	PGM1_ENST00000371083.4_Missense_Mutation_p.Y438H|PGM1_ENST00000540265.1_Missense_Mutation_p.Y223H	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	420			Y -> H (in allele PGM1*1-, allele PGM1*2-, allele PGM1*3- and allele PGM1*7-; dbSNP:rs11208257). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7902567, ECO:0000269|PubMed:7902568, ECO:0000269|Ref.2}.		carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						TTGGCAAAAGTATGGCCGGAA	0.552													T|||	1131	0.225839	0.1967	0.3963	5008	,	,		19029	0.2083		0.2237	False		,,,				2504	0.1646				p.Y438H		Atlas-SNP	.											PGM1_ENST00000371083,NS,carcinoma,0,2	PGM1	75	2	0			c.T1312C						PASS	.	T	HIS/TYR,HIS/TYR,HIS/TYR	760,3646	311.9+/-292.3	69,622,1512	85.0	81.0	82.0		1312,667,1258	4.8	1.0	1	dbSNP_120	82	1583,7017	295.9+/-302.6	143,1297,2860	yes	missense,missense,missense	PGM1	NM_001172818.1,NM_001172819.1,NM_002633.2	83,83,83	212,1919,4372	CC,CT,TT		18.407,17.2492,18.0148	benign,benign,benign	438/581,223/366,420/563	64114301	2343,10663	2203	4300	6503	SO:0001583	missense	5236	exon8			CAAAAGTATGGCC	BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.1258T>C	1.37:g.64114301T>C	ENSP00000360125:p.Tyr420His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	72	52	0.722222	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	37	CCDS625.1	522	0.23901098901098902	105	0.21341463414634146	130	0.35911602209944754	116	0.20279720279720279	171	0.22559366754617413	T	16.10	3.027395	0.54683	0.172492	0.18407	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000540265;ENST00000371083	T;T;T	0.54675	0.56;0.56;0.56	5.9	4.77	0.60923	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (1);Alpha-D-phosphohexomutase, alpha/beta/alpha domain III (1);	0.182967	0.49305	D	0.000151	T	0.49372	0.1553	M	0.82132	2.575	0.27607	P	0.9487826	B;B	0.33494	0.414;0.031	B;B	0.41723	0.365;0.108	T	0.58301	-0.7660	9	0.66056	D	0.02	-40.626	13.2602	0.60101	0.0:0.0:0.1326:0.8674	rs11208257;rs11557106;rs58004593;rs11208257	438;420	P36871-2;P36871	.;PGM1_HUMAN	H	396;420;223;438	ENSP00000360125:Y420H;ENSP00000443449:Y223H;ENSP00000360124:Y438H	ENSP00000360124:Y438H	Y	+	1	0	PGM1	63886889	1.000000	0.71417	0.998000	0.56505	0.893000	0.52053	6.299000	0.72770	1.045000	0.40225	-0.313000	0.08912	TAT	T|0.809;C|0.191	0.191	strong		0.552	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633	
SIGLEC12	89858	hgsc.bcm.edu	37	19	52000151	52000151	+	Missense_Mutation	SNP	T	T	A	rs61743147	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52000151T>A	ENST00000291707.3	-	7	1637	c.1582A>T	c.(1582-1584)Agg>Tgg	p.R528W	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.R410W	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	528				R -> W (in Ref. 3; AAQ88507). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GCTGAGCCCCTGACAGCGTTT	0.577													N|||	111	0.0221645	0.003	0.0202	5008	,	,		19175	0.002		0.0457	False		,,,				2504	0.046				p.R528W		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1582T						PASS	.	T	TRP/ARG,TRP/ARG	33,4373		0,33,2170	181.0	132.0	148.0		1228,1582	-3.4	0.0	19	dbSNP_129	148	378,8222		9,360,3931	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	101,101	9,393,6101	AA,AT,TT		4.3953,0.749,3.1601	probably-damaging,probably-damaging	410/478,528/596	52000151	411,12595	2203	4300	6503	SO:0001583	missense	89858	exon7			AGCCCCTGACAGC	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1582A>T	19.37:g.52000151T>A	ENSP00000291707:p.Arg528Trp	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	182	76	0.417582	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	45	0.020604395604395604	1	0.0020325203252032522	9	0.024861878453038673	2	0.0034965034965034965	33	0.04353562005277045	.	11.46	1.646131	0.29246	0.00749	0.043953	ENSG00000254521	ENST00000291707	T	0.41065	1.01	1.7	-3.39	0.04868	.	.	.	.	.	T	0.15392	0.0371	L	0.54323	1.7	0.09310	N	1	D;B	0.56968	0.978;0.012	P;B	0.57911	0.829;0.009	T	0.19192	-1.0313	9	0.66056	D	0.02	.	3.1884	0.06609	0.1904:0.0:0.2826:0.527	rs61743147	528;410	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	W	528	ENSP00000291707:R528W	ENSP00000291707:R528W	R	-	1	2	SIGLEC12	56691963	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.558000	0.00923	-0.927000	0.03766	0.412000	0.27726	AGG	T|0.958;A|0.042	0.042	strong		0.577	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
ARSD	414	hgsc.bcm.edu	37	X	2836084	2836084	+	Silent	SNP	C	C	G	rs73632973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836084C>G	ENST00000381154.1	-	5	699	c.624G>C	c.(622-624)gcG>gcC	p.A208A	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	208					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GAATCCCCAGCGCCAGGAACT	0.657																																					p.A208A		Atlas-SNP	.											.	ARSD	47	.	0			c.G624C						PASS	.						16.0	19.0	18.0					X																	2836084		2199	4294	6493	SO:0001819	synonymous_variant	414	exon5			CCCCAGCGCCAGG	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.624G>C	X.37:g.2836084C>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			C|0.928;G|0.072	0.072	strong		0.657	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
SPAG16	79582	hgsc.bcm.edu	37	2	214160817	214160817	+	Missense_Mutation	SNP	G	G	A	rs61752198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:214160817G>A	ENST00000331683.5	+	2	261	c.166G>A	c.(166-168)Gac>Aac	p.D56N	SPAG16_ENST00000432529.2_Missense_Mutation_p.D56N|SPAG16_ENST00000447990.1_Missense_Mutation_p.D56N|SPAG16_ENST00000272898.7_Missense_Mutation_p.D56N|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000374309.3_Start_Codon_SNP_p.M1I|SPAG16_ENST00000413312.1_Intron	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	56					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		ATCTGAAGATGACTATGAATA	0.279													G|||	61	0.0121805	0.0053	0.0043	5008	,	,		15997	0.004		0.0159	False		,,,				2504	0.0317				p.D56N		Atlas-SNP	.											.	SPAG16	134	.	0			c.G166A						PASS	.	G	ASN/ASP,ASN/ASP	32,4372	37.6+/-69.7	0,32,2170	91.0	100.0	97.0		166,166	5.3	1.0	2	dbSNP_129	97	153,8431	72.9+/-135.5	2,149,4141	yes	missense,missense	SPAG16	NM_001025436.1,NM_024532.3	23,23	2,181,6311	AA,AG,GG		1.7824,0.7266,1.4244	benign,benign	56/184,56/632	214160817	185,12803	2202	4292	6494	SO:0001583	missense	79582	exon2			GAAGATGACTATG	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.166G>A	2.37:g.214160817G>A	ENSP00000332592:p.Asp56Asn	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	161	87	0.540373	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	23|23	0.010531135531135532|0.010531135531135532	6|6	0.012195121951219513|0.012195121951219513	2|2	0.0055248618784530384|0.0055248618784530384	2|2	0.0034965034965034965|0.0034965034965034965	13|13	0.017150395778364115|0.017150395778364115	G|G	11.78|11.78	1.742080|1.742080	0.30865|0.30865	0.007266|0.007266	0.017824|0.017824	ENSG00000144451|ENSG00000144451	ENST00000331683;ENST00000432529;ENST00000272898;ENST00000447990|ENST00000374309	T|T	0.60299|0.55588	0.2|0.51	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.175804|.	0.33419|.	N|.	0.004932|.	T|T	0.31670|0.31670	0.0804|0.0804	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	0.999998|0.999998	D;D;D|B	0.76494|0.25667	0.964;0.999;0.979|0.131	P;D;P|B	0.66979|0.22386	0.637;0.948;0.801|0.039	T|T	0.39396|0.39396	-0.9616|-0.9616	10|9	0.46703|0.87932	T|D	0.11|0	.|.	14.7325|14.7325	0.69393|0.69393	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs61752198|rs61752198	56;56;56|1	Q8N0X2;E7EWV3;Q8N0X2-4|B4DYB5	SPG16_HUMAN;.;.|.	N|I	56|1	ENSP00000332592:D56N|ENSP00000363428:M1I	ENSP00000272898:D56N|ENSP00000363428:M1I	D|M	+|+	1|3	0|0	SPAG16|SPAG16	213869062|213869062	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.795000|0.795000	0.44927|0.44927	5.541000|5.541000	0.67212|0.67212	2.597000|2.597000	0.87782|0.87782	0.585000|0.585000	0.79938|0.79938	GAC|ATG	G|0.985;A|0.015	0.015	strong		0.279	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
EMILIN2	84034	hgsc.bcm.edu	37	18	2885118	2885118	+	Silent	SNP	C	C	T	rs592120	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:2885118C>T	ENST00000254528.3	+	3	573	c.414C>T	c.(412-414)aaC>aaT	p.N138N		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	138					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GGCCTCGAAACAGCTTGAAGA	0.507													C|||	854	0.170527	0.1014	0.2406	5008	,	,		19637	0.0119		0.3668	False		,,,				2504	0.1759				p.N138N		Atlas-SNP	.											.	EMILIN2	97	.	0			c.C414T						PASS	.	C		659,3747	276.6+/-273.2	67,525,1611	60.0	61.0	61.0		414	2.7	0.0	18	dbSNP_83	61	3165,5435	478.8+/-370.0	578,2009,1713	no	coding-synonymous	EMILIN2	NM_032048.2		645,2534,3324	TT,TC,CC		36.8023,14.9569,29.4018		138/1054	2885118	3824,9182	2203	4300	6503	SO:0001819	synonymous_variant	84034	exon3			TCGAAACAGCTTG	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"""EMI domain containing"""	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.414C>T	18.37:g.2885118C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	37	CCDS11828.1																																																																																			C|0.763;T|0.237	0.237	strong		0.507	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048	
AGGF1	55109	hgsc.bcm.edu	37	5	76332463	76332463	+	Missense_Mutation	SNP	C	C	A	rs78273685		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:76332463C>A	ENST00000312916.7	+	4	981	c.599C>A	c.(598-600)gCg>gAg	p.A200E		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	200					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)	p.A200E(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		GCAGCAGAAGCGGCTGTATCA	0.398																																					p.A200E		Atlas-SNP	.											AGGF1,NS,carcinoma,0,1	AGGF1	71	1	1	Substitution - Missense(1)	prostate(1)	c.C599A						scavenged	.						80.0	80.0	80.0					5																	76332463		2203	4300	6503	SO:0001583	missense	55109	exon4			CAGAAGCGGCTGT	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.599C>A	5.37:g.76332463C>A	ENSP00000316109:p.Ala200Glu	Somatic	232	2	0.00862069		WXS	Illumina HiSeq	Phase_I	296	7	0.0236486	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.675227	0.47781	.	.	ENSG00000164252	ENST00000312916	D	0.85629	-2.01	5.09	5.09	0.68999	.	0.065026	0.64402	D	0.000007	D	0.84392	0.5462	L	0.41710	1.295	0.80722	D	1	D	0.52996	0.957	P	0.48921	0.595	D	0.83644	0.0152	9	.	.	.	-37.6142	18.4903	0.90844	0.0:1.0:0.0:0.0	.	200	Q8N302	AGGF1_HUMAN	E	200	ENSP00000316109:A200E	.	A	+	2	0	AGGF1	76368219	1.000000	0.71417	0.999000	0.59377	0.884000	0.51177	5.450000	0.66626	2.363000	0.80096	0.585000	0.79938	GCG	A|0.001;C|0.999	0.001	weak		0.398	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
ZNF701	55762	hgsc.bcm.edu	37	19	53085813	53085813	+	Silent	SNP	T	T	C	rs3745101	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53085813T>C	ENST00000540331.1	+	5	924	c.699T>C	c.(697-699)gcT>gcC	p.A233A	ZNF701_ENST00000391785.3_Silent_p.A167A|ZNF701_ENST00000301093.2_Silent_p.A233A|CTD-3099C6.7_ENST00000599222.1_RNA	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	233					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		TTGAGAAGGCTATCAACGATG	0.388													T|||	1451	0.289736	0.0522	0.2839	5008	,	,		21445	0.3681		0.3608	False		,,,				2504	0.4611				p.A233A	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											.	ZNF701	44	.	0			c.T699C						PASS	.	T	,	405,4001	201.8+/-224.7	17,371,1815	73.0	71.0	71.0		699,501	0.7	0.0	19	dbSNP_107	71	3369,5231	494.5+/-373.8	635,2099,1566	no	coding-synonymous,coding-synonymous	ZNF701	NM_001172655.1,NM_018260.2	,	652,2470,3381	CC,CT,TT		39.1744,9.192,29.0174	,	233/532,167/466	53085813	3774,9232	2203	4300	6503	SO:0001819	synonymous_variant	55762	exon5			GAAGGCTATCAAC	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"""Zinc fingers, C2H2-type"", ""-"""	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.699T>C	19.37:g.53085813T>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	160	68	0.425	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Silent	SNP	ENST00000540331.1	37	CCDS54311.1																																																																																			T|0.704;C|0.296	0.296	strong		0.388	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
DCUN1D2	55208	hgsc.bcm.edu	37	13	114112389	114112389	+	Silent	SNP	T	T	C	rs41286638	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:114112389T>C	ENST00000478244.1	-	7	1017	c.735A>G	c.(733-735)gaA>gaG	p.E245E	DCUN1D2_ENST00000332592.3_Silent_p.E112E	NM_001014283.1	NP_001014305.1	Q6PH85	DCNL2_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 2	245	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.							p.E245E(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(3)|stomach(1)	7	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.029)|GBM - Glioblastoma multiforme(44;0.234)			GCCGTGCATATTCTACAAAAT	0.428											OREG0022535	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	186	0.0371406	0.0015	0.0101	5008	,	,		19251	0.124		0.0288	False		,,,				2504	0.0235				p.E245E		Atlas-SNP	.											DCUN1D2,NS,carcinoma,0,1	DCUN1D2	17	1	1	Substitution - coding silent(1)	stomach(1)	c.A735G						PASS	.	T		24,4382	31.7+/-61.6	0,24,2179	210.0	218.0	215.0		735	-1.8	0.0	13	dbSNP_127	215	198,8402	86.6+/-149.0	8,182,4110	no	coding-synonymous	DCUN1D2	NM_001014283.1		8,206,6289	CC,CT,TT		2.3023,0.5447,1.7069		245/260	114112389	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	55208	exon7			TGCATATTCTACA	AK001566	CCDS32013.1	13q34	2013-06-10	2013-06-10	2005-10-04	ENSG00000150401	ENSG00000150401			20328	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 17"", ""DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)"""	C13orf17		15988528	Standard	XM_005268320		Approved	FLJ10704, FLJ20092	uc001vtr.1	Q6PH85	OTTHUMG00000017390	ENST00000478244.1:c.735A>G	13.37:g.114112389T>C		Somatic	63	0	0	1455	WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_001014283	Q5JSA5|Q5JSA6|Q5JSA7|Q9NVJ1|Q9NXR6	Silent	SNP	ENST00000478244.1	37	CCDS32013.1																																																																																			T|0.976;C|0.024	0.024	strong		0.428	DCUN1D2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045938.4	NM_018185	
SAGE1	55511	hgsc.bcm.edu	37	X	134986700	134986700	+	Silent	SNP	T	T	C	rs12014884	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:134986700T>C	ENST00000370709.3	+	3	285	c.285T>C	c.(283-285)aaT>aaC	p.N95N	SAGE1_ENST00000535938.1_Silent_p.N95N|SAGE1_ENST00000537770.1_Silent_p.N95N|SAGE1_ENST00000324447.3_Silent_p.N95N			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	95						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					TAGCTGATAATGTCTTGTCAA	0.423													N|||	610	0.161589	0.0673	0.1614	3775	,	,		15712	0.1002		0.2058	False		,,,				2504	0.1033				p.N95N		Atlas-SNP	.											.	SAGE1	160	.	0			c.T285C						PASS	.	C		557,3278		30,426,71,1176,500	167.0	132.0	144.0		285	1.4	0.0	X	dbSNP_120	144	1755,4973		188,924,455,1316,1417	no	coding-synonymous	SAGE1	NM_018666.2		218,1350,526,2492,1917	CC,CT,C,TT,T		26.085,14.5241,21.8877		95/905	134986700	2312,8251	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon4			TGATAATGTCTTG	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.285T>C	X.37:g.134986700T>C		Somatic	463	0	0		WXS	Illumina HiSeq	Phase_I	218	217	0.995413	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			T|0.806;C|0.194	0.194	strong		0.423	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50682865	50682865	+	Silent	SNP	G	G	A	rs5771270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50682865G>A	ENST00000248846.5	-	1	128	c.24C>T	c.(22-24)ttC>ttT	p.F8F	MAPK12_ENST00000497036.1_5'Flank|HDAC10_ENST00000498366.1_5'Flank|TUBGCP6_ENST00000439308.2_Silent_p.F8F			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	8					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACAGGTCGTCGAACAGCTGCG	0.657													G|||	1410	0.28155	0.0802	0.2478	5008	,	,		15545	0.3562		0.4026	False		,,,				2504	0.3763				p.F8F		Atlas-SNP	.											TUBGCP6,NS,carcinoma,0,1	TUBGCP6	132	1	0			c.C24T						scavenged	.	G		618,3788	242.8+/-252.7	54,510,1639	23.0	26.0	25.0		24	2.1	1.0	22	dbSNP_114	25	3344,5256	465.7+/-366.6	645,2054,1601	no	coding-synonymous	TUBGCP6	NM_020461.3		699,2564,3240	AA,AG,GG		38.8837,14.0263,30.4629		8/1820	50682865	3962,9044	2203	4300	6503	SO:0001819	synonymous_variant	85378	exon1			GTCGTCGAACAGC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.24C>T	22.37:g.50682865G>A		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			G|0.710;A|0.290	0.290	strong		0.657	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
SARDH	1757	hgsc.bcm.edu	37	9	136536679	136536679	+	Silent	SNP	G	G	A	rs129932	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136536679G>A	ENST00000371872.4	-	18	2561	c.2304C>T	c.(2302-2304)atC>atT	p.I768I	SARDH_ENST00000422262.2_Silent_p.I600I|SARDH_ENST00000439388.1_Silent_p.I768I|SARDH_ENST00000371868.1_Silent_p.I196I	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	768					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		TCAGGGAGTCGATGGCGCGGT	0.677													G|||	2921	0.583267	0.6483	0.5879	5008	,	,		16133	0.7569		0.4523	False		,,,				2504	0.4479				p.I768I		Atlas-SNP	.											.	SARDH	112	.	0			c.C2304T						PASS	.	G	,	2540,1858		742,1056,401	38.0	31.0	33.0		2304,2304	-0.1	1.0	9	dbSNP_78	33	3712,4876		793,2126,1375	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	1535,3182,1776	AA,AG,GG		43.2231,42.2465,48.1442	,	768/919,768/919	136536679	6252,6734	2199	4294	6493	SO:0001819	synonymous_variant	1757	exon18			GGAGTCGATGGCG		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.2304C>T	9.37:g.136536679G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	254	130	0.511811	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			G|0.464;A|0.536	0.536	strong		0.677	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
PZP	5858	hgsc.bcm.edu	37	12	9316773	9316773	+	Missense_Mutation	SNP	T	T	C	rs3213831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:9316773T>C	ENST00000261336.2	-	20	2598	c.2570A>G	c.(2569-2571)aAt>aGt	p.N857S	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Intron	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	857			N -> S (in dbSNP:rs3213831). {ECO:0000269|PubMed:1989698}.		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						TTGTCTCTCATTTCCACAGAT	0.483													T|||	2021	0.403554	0.3858	0.3646	5008	,	,		-128	0.4187		0.3966	False		,,,				2504	0.4468				p.N857S	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A2570G						PASS	.	T	SER/ASN	1840,2566	537.5+/-374.7	392,1056,755	189.0	173.0	179.0		2570	1.4	0.0	12	dbSNP_106	179	3696,4904	529.3+/-381.6	802,2092,1406	yes	missense	PZP	NM_002864.2	46	1194,3148,2161	CC,CT,TT		42.9767,41.7612,42.565	possibly-damaging	857/1483	9316773	5536,7470	2203	4300	6503	SO:0001583	missense	5858	exon20			CTCTCATTTCCAC	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2570A>G	12.37:g.9316773T>C	ENSP00000261336:p.Asn857Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	165	86	0.521212	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	856	0.39194139194139194	183	0.3719512195121951	137	0.3784530386740331	243	0.42482517482517484	293	0.3865435356200528	T	11.65	1.701569	0.30142	0.417612	0.429767	ENSG00000126838	ENST00000261336	T	0.33438	1.41	3.85	1.37	0.22104	.	0.205916	0.31531	N	0.007482	T	0.00012	0.0000	M	0.70595	2.14	0.34545	P	0.28933	P	0.51933	0.949	P	0.49332	0.607	T	0.43507	-0.9387	9	0.54805	T	0.06	.	6.336	0.21296	0.0:0.0886:0.1598:0.7516	rs3213831;rs52795442;rs57015394;rs3213831	857	P20742	PZP_HUMAN	S	857	ENSP00000261336:N857S	ENSP00000261336:N857S	N	-	2	0	PZP	9208040	0.647000	0.27304	0.005000	0.12908	0.707000	0.40811	2.556000	0.45862	0.156000	0.19299	0.383000	0.25322	AAT	T|0.582;C|0.418	0.418	strong		0.483	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
CYP1B1	1545	hgsc.bcm.edu	37	2	38298139	38298139	+	Missense_Mutation	SNP	T	T	C	rs1800440	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:38298139T>C	ENST00000260630.3	-	3	1759	c.1358A>G	c.(1357-1359)aAc>aGc	p.N453S	CYP1B1_ENST00000407341.1_Missense_Mutation_p.N453S|CYP1B1_ENST00000494864.1_5'UTR	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	453			N -> S (in allele CYP1B1*4; dbSNP:rs1800440). {ECO:0000269|PubMed:10655546, ECO:0000269|PubMed:11854439, ECO:0000269|PubMed:12036985, ECO:0000269|PubMed:12525557, ECO:0000269|PubMed:14635112, ECO:0000269|PubMed:15342693, ECO:0000269|PubMed:15475877, ECO:0000269|PubMed:16688110, ECO:0000269|PubMed:9823305, ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	CAGGTCCTTGTTGATGAGGCC	0.473													T|||	499	0.0996406	0.0068	0.1311	5008	,	,		20848	0.005		0.1958	False		,,,				2504	0.2014				p.N453S		Atlas-SNP	.											CYP1B1,colon,carcinoma,0,3	CYP1B1	39	3	0			c.A1358G	GRCh37	CM994676	CYP1B1	M	rs1800440	PASS	.	T	SER/ASN	147,4259	103.4+/-141.9	4,139,2060	82.0	77.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1358	5.9	0.9	2	dbSNP_89	78	1608,6992	298.6+/-304.0	143,1322,2835	yes	missense	CYP1B1	NM_000104.3	46	147,1461,4895	CC,CT,TT		18.6977,3.3364,13.4938	possibly-damaging	453/544	38298139	1755,11251	2203	4300	6503	SO:0001583	missense	1545	exon3			TCCTTGTTGATGA	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.1358A>G	2.37:g.38298139T>C	ENSP00000260630:p.Asn453Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	149	71	0.47651	NM_000104	Q5TZW8|Q93089|Q9H316	Missense_Mutation	SNP	ENST00000260630.3	37	CCDS1793.1	216	0.0989010989010989	3	0.006097560975609756	58	0.16022099447513813	4	0.006993006993006993	151	0.19920844327176782	T	18.56	3.651256	0.67472	0.033364	0.186977	ENSG00000138061	ENST00000260630;ENST00000407341	T;T	0.66638	-0.22;-0.22	5.95	5.95	0.96441	.	0.172254	0.64402	D	0.000008	T	0.00144	0.0004	L	0.55103	1.725	0.20403	P	0.9999085855	P	0.37466	0.596	B	0.39660	0.306	T	0.08411	-1.0723	9	0.59425	D	0.04	.	14.3758	0.66874	0.0:0.0:0.0:1.0	rs1800440;rs4134586;rs4986886;rs17405302;rs56879535;rs1800440	453	Q53TK1	.	S	453	ENSP00000260630:N453S;ENSP00000384972:N453S	ENSP00000260630:N453S	N	-	2	0	CYP1B1	38151643	1.000000	0.71417	0.934000	0.37439	0.897000	0.52465	6.035000	0.70940	2.279000	0.76181	0.533000	0.62120	AAC	T|0.882;C|0.118	0.118	strong		0.473	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
PRADC1	84279	hgsc.bcm.edu	37	2	73455600	73455600	+	Silent	SNP	C	C	T	rs11559241	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:73455600C>T	ENST00000258083.2	-	5	616	c.549G>A	c.(547-549)ccG>ccA	p.P183P	PRADC1_ENST00000480093.1_5'UTR	NM_032319.1	NP_115695.1	Q9BSG0	PADC1_HUMAN	protease-associated domain containing 1	183						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(1)|lung(2)	4						AGGTCCAGGGCGGTTGCAGCA	0.532													C|||	357	0.0712859	0.2262	0.0447	5008	,	,		18311	0.0		0.0268	False		,,,				2504	0.0				p.P183P		Atlas-SNP	.											.	PRADC1	15	.	0			c.G549A						PASS	.	C		823,3583	327.2+/-299.9	70,683,1450	78.0	69.0	72.0		549	-9.6	0.0	2	dbSNP_120	72	157,8443	74.5+/-137.1	0,157,4143	no	coding-synonymous	PRADC1	NM_032319.1		70,840,5593	TT,TC,CC		1.8256,18.6791,7.535		183/189	73455600	980,12026	2203	4300	6503	SO:0001819	synonymous_variant	84279	exon5			CCAGGGCGGTTGC	BC005069	CCDS1924.1	2p13.2	2012-10-31	2011-04-15	2011-04-15	ENSG00000135617	ENSG00000135617			16047	protein-coding gene	gene with protein product	"""protease-associated domain-containing glycoprotein 21 kDa"""		"""chromosome 2 open reading frame 7"""	C2orf7		15498570	Standard	NM_032319		Approved	MGC13004, PAP21, hPAP21	uc002siy.3	Q9BSG0	OTTHUMG00000129773	ENST00000258083.2:c.549G>A	2.37:g.73455600C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	167	73	0.437126	NM_032319	Q2Z1P2	Silent	SNP	ENST00000258083.2	37	CCDS1924.1																																																																																			C|0.922;T|0.078	0.078	strong		0.532	PRADC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251989.1	NM_032319	
UGT1A6	54578	hgsc.bcm.edu	37	2	234602191	234602191	+	Missense_Mutation	SNP	A	A	G	rs2070959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234602191A>G	ENST00000305139.6	+	1	680	c.541A>G	c.(541-543)Aca>Gca	p.T181A	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000406651.1_5'Flank|AC114812.8_ENST00000439336.1_RNA|UGT1A6_ENST00000373424.1_Intron|UGT1A10_ENST00000373445.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	181			T -> A (in allele UGT1A6*2; dbSNP:rs2070959). {ECO:0000269|PubMed:15284531, ECO:0000269|PubMed:19204906, ECO:0000269|PubMed:9429234, ECO:0000269|Ref.4}.		cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	CCTGGAGCATACATTCAGCAG	0.512													A|||	1390	0.277556	0.239	0.2233	5008	,	,		19575	0.1964		0.3101	False		,,,				2504	0.4182				p.T181A		Atlas-SNP	.											.	UGT1A6	63	.	0			c.A541G	GRCh37	CM057770|CP995124	UGT1A6	M|X	rs2070959	PASS	.	A	ALA/THR,,,,,	1110,3296	400.1+/-331.5	155,800,1248	158.0	148.0	152.0		541,,,,,	-9.4	0.0	2	dbSNP_96	152	2852,5748	448.5+/-361.8	480,1892,1928	yes	missense,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2,NM_205862.1	58,,,,,	635,2692,3176	GG,GA,AA		33.1628,25.1929,30.4629	,,,,,	181/533,,,,,	234602191	3962,9044	2203	4300	6503	SO:0001583	missense	54578	exon1			GAGCATACATTCA	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.541A>G	2.37:g.234602191A>G	ENSP00000303174:p.Thr181Ala	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	153	83	0.542484	NM_001072	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1	581	0.266025641025641	118	0.23983739837398374	96	0.26519337016574585	130	0.22727272727272727	237	0.31266490765171506	A	0.018	-1.475651	0.01035	0.251929	0.331628	ENSG00000167165	ENST00000441351;ENST00000305139	T;T	0.59224	0.28;0.28	5.31	-9.43	0.00607	.	.	.	.	.	T	0.00012	0.0000	N	0.05259	-0.085	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.22695	-1.0209	8	0.12766	T	0.61	.	11.5483	0.50706	0.6559:0.0:0.2517:0.0924	rs2070959;rs3903007;rs17683988;rs61246460;rs2070959	181	P19224	UD16_HUMAN	A	181	ENSP00000389637:T181A;ENSP00000303174:T181A	ENSP00000303174:T181A	T	+	1	0	UGT1A6	234266930	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.930000	0.03972	-1.892000	0.01108	-0.959000	0.02639	ACA	A|0.710;G|0.290	0.290	strong		0.512	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
B3GALT5	10317	hgsc.bcm.edu	37	21	41032740	41032740	+	Missense_Mutation	SNP	T	T	C	rs3746887	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:41032740T>C	ENST00000380620.4	+	5	846	c.254T>C	c.(253-255)aTg>aCg	p.M85T	B3GALT5_ENST00000343118.4_Missense_Mutation_p.M85T|B3GALT5_ENST00000380618.1_Missense_Mutation_p.M85T|AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000398714.2_Missense_Mutation_p.M85T			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	85			M -> T (in dbSNP:rs3746887). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				AAAGAGAGGATGGTGAAGGGA	0.602													C|||	3272	0.653355	0.3888	0.7233	5008	,	,		18301	0.6508		0.8151	False		,,,				2504	0.7975				p.M85T		Atlas-SNP	.											B3GALT5,NS,carcinoma,-1,2	B3GALT5	40	2	0			c.T254C						PASS	.	C	THR/MET,THR/MET,THR/MET,THR/MET,THR/MET	1943,2463	621.9+/-393.8	444,1055,704	60.0	55.0	57.0		254,254,254,254,254	-5.7	0.0	21	dbSNP_107	57	6967,1633	302.1+/-305.8	2821,1325,154	yes	missense,missense,missense,missense,missense	B3GALT5	NM_006057.1,NM_033170.1,NM_033171.1,NM_033172.1,NM_033173.1	81,81,81,81,81	3265,2380,858	CC,CT,TT		18.9884,44.099,31.4932	benign,benign,benign,benign,benign	85/311,85/311,85/311,85/311,85/311	41032740	8910,4096	2203	4300	6503	SO:0001583	missense	10317	exon3			AGAGGATGGTGAA	AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"""Beta 3-glycosyltransferases"""	920	protein-coding gene	gene with protein product	"""homolog of C. elegans Bt toxin resistance gene bre-5"", ""GlcNAc-beta-1,3-galactosyltransferase 5"""	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.254T>C	21.37:g.41032740T>C	ENSP00000369994:p.Met85Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_033170	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Missense_Mutation	SNP	ENST00000380620.4	37	CCDS13667.1	1435	0.657051282051282	188	0.3821138211382114	276	0.7624309392265194	350	0.6118881118881119	621	0.8192612137203166	C	1.715	-0.498176	0.04291	0.44099	0.810116	ENSG00000183778	ENST00000380620;ENST00000380618;ENST00000343118;ENST00000398714	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.89	-5.7	0.02421	.	3.016860	0.01379	N	0.012860	T	0.00012	0.0000	N	0.02120	-0.675	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.31916	-0.9926	9	0.13108	T	0.6	.	2.6827	0.05099	0.2372:0.3665:0.0821:0.3142	rs3746887;rs52801990;rs56746936;rs3746887	85	Q9Y2C3	B3GT5_HUMAN	T	85	ENSP00000369994:M85T;ENSP00000369992:M85T;ENSP00000343318:M85T;ENSP00000381699:M85T	ENSP00000343318:M85T	M	+	2	0	B3GALT5	39954610	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.510000	0.00447	-1.037000	0.03283	-0.960000	0.02634	ATG	T|0.335;C|0.665	0.665	strong		0.602	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170	
FAM170B	170370	hgsc.bcm.edu	37	10	50341954	50341954	+	Missense_Mutation	SNP	A	A	G	rs34110351	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50341954A>G	ENST00000311787.5	-	1	99	c.10T>C	c.(10-12)Tac>Cac	p.Y4H	FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA|FAM170B-AS1_ENST00000443389.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	4										central_nervous_system(1)|endometrium(1)|skin(1)	3						TCTGTGAAGTAGCATTTCATG	0.577													G|||	1228	0.245208	0.118	0.3444	5008	,	,		21931	0.3075		0.2684	False		,,,				2504	0.2587				p.Y4H		Atlas-SNP	.											.	FAM170B	20	.	0			c.T10C						PASS	.	G	HIS/TYR	223,1161		20,183,489	177.0	149.0	157.0		10	2.4	0.0	10	dbSNP_126	157	924,2258		149,626,816	yes	missense	FAM170B	NM_001164484.1	83	169,809,1305	GG,GA,AA		29.0383,16.1127,25.1205	benign	4/284	50341954	1147,3419	692	1591	2283	SO:0001583	missense	170370	exon1			TGAAGTAGCATTT		CCDS53536.1	10q11.23	2008-11-06	2008-06-12	2008-06-12	ENSG00000172538	ENSG00000172538			19736	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 73"""	C10orf73			Standard	NM_001164484		Approved	Em:AC084727.4	uc001jhj.3	A6NMN3	OTTHUMG00000018187	ENST00000311787.5:c.10T>C	10.37:g.50341954A>G	ENSP00000308292:p.Tyr4His	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	217	216	0.995392	NM_001164484	Q86WY6|Q8N6K8	Missense_Mutation	SNP	ENST00000311787.5	37	CCDS53536.1	526	0.24084249084249085	61	0.12398373983739837	117	0.32320441988950277	147	0.256993006993007	201	0.26517150395778366	G	0.014	-1.574567	0.00887	0.161127	0.290383	ENSG00000172538	ENST00000311787	T	0.26067	1.76	4.29	2.42	0.29668	.	1.076690	0.07150	N	0.848962	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44143	-0.9347	9	0.02654	T	1	-13.5173	6.5541	0.22450	0.3069:0.0:0.6931:0.0	rs34110351	4	A6NMN3	F170B_HUMAN	H	4	ENSP00000308292:Y4H	ENSP00000308292:Y4H	Y	-	1	0	FAM170B	50011960	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.772000	0.26647	0.201000	0.20466	-1.551000	0.00897	TAC	A|0.759;G|0.241	0.241	strong		0.577	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
NUDT8	254552	hgsc.bcm.edu	37	11	67395714	67395714	+	Silent	SNP	C	C	T	rs7124513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67395714C>T	ENST00000376693.2	-	4	423	c.414G>A	c.(412-414)gaG>gaA	p.E138E	RP11-655M14.13_ENST00000533311.1_lincRNA|NUDT8_ENST00000301490.4_3'UTR	NM_001243750.1	NP_001230679.1	Q8WV74	NUDT8_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 8	138	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(1)|lung(1)|prostate(1)|skin(1)	4						GTGCAAACACCTCATCTACCT	0.617													C|||	1166	0.232827	0.1815	0.4496	5008	,	,		20782	0.127		0.332	False		,,,				2504	0.1554				p.E138E		Atlas-SNP	.											.	NUDT8	12	.	0			c.G414A						PASS	.	C		340,1406		28,284,561	43.0	42.0	43.0			-1.5	1.0	11	dbSNP_116	43	1238,2732		203,832,950	no	utr-3	NUDT8	NM_181843.2		231,1116,1511	TT,TC,CC		31.1839,19.4731,27.6067			67395714	1578,4138	873	1985	2858	SO:0001819	synonymous_variant	254552	exon4			AAACACCTCATCT	AI743601	CCDS8174.1, CCDS58151.1	11q13.2	2008-07-21			ENSG00000167799	ENSG00000167799		"""Nudix motif containing"""	8055	protein-coding gene	gene with protein product						11415433	Standard	NM_181843		Approved	FLJ41567	uc001omo.2	Q8WV74	OTTHUMG00000167292	ENST00000376693.2:c.414G>A	11.37:g.67395714C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_001243750	Q6ZW59	Silent	SNP	ENST00000376693.2	37	CCDS58151.1																																																																																			C|0.746;T|0.254	0.254	strong		0.617	NUDT8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394036.1	NM_181843	
KIAA1429	25962	hgsc.bcm.edu	37	8	95541371	95541371	+	Silent	SNP	T	T	A	rs957446	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95541371T>A	ENST00000297591.5	-	7	882	c.807A>T	c.(805-807)cgA>cgT	p.R269R	KIAA1429_ENST00000437199.1_Silent_p.R269R|KIAA1429_ENST00000421249.2_Silent_p.R269R	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	269	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TGTCTACTGTTCGTCGATCAT	0.443													A|||	3516	0.702077	0.6558	0.7435	5008	,	,		20289	0.8056		0.5636	False		,,,				2504	0.771				p.R269R		Atlas-SNP	.											KIAA1429_ENST00000421249,NS,carcinoma,-1,4	KIAA1429	176	4	0			c.A807T						PASS	.	A	,	2774,1632	500.5+/-364.7	887,1000,316	459.0	350.0	387.0		807,807	-2.4	0.9	8	dbSNP_86	387	4755,3845	538.9+/-383.5	1303,2149,848	no	coding-synonymous,coding-synonymous	KIAA1429	NM_015496.4,NM_183009.2	,	2190,3149,1164	AA,AT,TT		44.7093,37.0404,42.1113	,	269/1813,269/1148	95541371	7529,5477	2203	4300	6503	SO:0001819	synonymous_variant	25962	exon7			TACTGTTCGTCGA	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.807A>T	8.37:g.95541371T>A		Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	239	110	0.460251	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			A|0.628;T|0.372	0.628	strong		0.443	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
UBE3C	9690	hgsc.bcm.edu	37	7	156974354	156974354	+	Silent	SNP	G	G	A	rs17646047	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:156974354G>A	ENST00000348165.5	+	7	1119	c.759G>A	c.(757-759)ccG>ccA	p.P253P	UBE3C_ENST00000389103.4_Silent_p.P210P	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	253					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		ACTCCTGTCCGGAAGGTGCGA	0.338													g|||	129	0.0257588	0.0038	0.0476	5008	,	,		18915	0.0069		0.0606	False		,,,				2504	0.0235				p.P253P		Atlas-SNP	.											.	UBE3C	124	.	0			c.G759A						PASS	.	A		58,4348	55.5+/-91.7	0,58,2145	74.0	77.0	76.0		759	-3.4	0.7	7	dbSNP_123	76	615,7985	159.8+/-213.0	25,565,3710	no	coding-synonymous	UBE3C	NM_014671.2		25,623,5855	AA,AG,GG		7.1512,1.3164,5.1745		253/1084	156974354	673,12333	2203	4300	6503	SO:0001819	synonymous_variant	9690	exon7			CTGTCCGGAAGGT	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.759G>A	7.37:g.156974354G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	111	45	0.405405	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Silent	SNP	ENST00000348165.5	37	CCDS34789.1																																																																																			G|0.953;A|0.047	0.047	strong		0.338	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671	
CTSH	1512	hgsc.bcm.edu	37	15	79237293	79237293	+	Missense_Mutation	SNP	C	C	T	rs2289702	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:79237293C>T	ENST00000220166.5	-	1	140	c.31G>A	c.(31-33)Ggg>Agg	p.G11R		NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	11			G -> R (in dbSNP:rs2289702).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						AGCCAGGCCCCGGCGCAGAGC	0.721													C|||	385	0.076877	0.0151	0.0533	5008	,	,		11873	0.0714		0.1054	False		,,,				2504	0.1534				p.G11R		Atlas-SNP	.											.	CTSH	23	.	0			c.G31A						PASS	.	C	ARG/GLY	103,3647		2,99,1774	7.0	8.0	8.0		31	3.1	0.5	15	dbSNP_100	8	663,6797		26,611,3093	no	missense	CTSH	NM_004390.3	125	28,710,4867	TT,TC,CC		8.8874,2.7467,6.8332		11/336	79237293	766,10444	1875	3730	5605	SO:0001583	missense	1512	exon1			AGGCCCCGGCGCA	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.31G>A	15.37:g.79237293C>T	ENSP00000220166:p.Gly11Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	178|178	0.0815018315018315|0.0815018315018315	28|28	0.056910569105691054|0.056910569105691054	21|21	0.058011049723756904|0.058011049723756904	44|44	0.07692307692307693|0.07692307692307693	85|85	0.11213720316622691|0.11213720316622691	C|C	7.291|7.291	0.610990|0.610990	0.14066|0.14066	0.027467|0.027467	0.088874|0.088874	ENSG00000103811|ENSG00000103811	ENST00000394758|ENST00000220166;ENST00000444399	.|T	.|0.72051	.|-0.62	3.12|3.12	3.12|3.12	0.35913|0.35913	.|.	.|131.017000	.|0.00531	.|U	.|0.000202	T|T	0.04679|0.04679	0.0127|0.0127	N|N	0.19112|0.19112	0.55|0.55	0.45330|0.45330	P|P	0.0016800000000000148|0.0016800000000000148	.|D	.|0.76494	.|0.999	.|D	.|0.65323	.|0.934	T|T	0.56263|0.56263	-0.8008|-0.8008	5|9	0.49607|0.27785	T|T	0.09|0.31	.|.	9.9555|9.9555	0.41663|0.41663	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2289702|rs2289702	.|11	.|E9PF73	.|.	T|R	11|11	.|ENSP00000220166:G11R	ENSP00000378240:A11T|ENSP00000220166:G11R	A|G	-|-	1|1	0|0	CTSH|CTSH	77024348|77024348	0.001000|0.001000	0.12720|0.12720	0.483000|0.483000	0.27378|0.27378	0.004000|0.004000	0.04260|0.04260	0.281000|0.281000	0.18810|0.18810	2.040000|2.040000	0.60383|0.60383	0.491000|0.491000	0.48974|0.48974	GCC|GGG	C|0.917;T|0.083	0.083	strong		0.721	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
RAI1	10743	hgsc.bcm.edu	37	17	17696755	17696755	+	Missense_Mutation	SNP	C	C	A	rs11649804	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17696755C>A	ENST00000353383.1	+	3	962	c.493C>A	c.(493-495)Ccc>Acc	p.P165T	RAI1_ENST00000261641.6_Missense_Mutation_p.P165T	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	165	Gln-rich.		P -> T (in dbSNP:rs11649804).		circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CGCCCAGGTGCCCTTTCGGAC	0.617													C|||	2823	0.563698	0.41	0.5058	5008	,	,		17268	0.8353		0.334	False		,,,				2504	0.7689				p.P165T		Atlas-SNP	.											RAI1,NS,carcinoma,0,1	RAI1	121	1	0			c.C493A						PASS	.	C	THR/PRO	1742,2664	516.5+/-369.2	339,1064,800	58.0	56.0	57.0		493	3.6	1.0	17	dbSNP_120	57	2643,5957	422.3+/-354.0	427,1789,2084	yes	missense	RAI1	NM_030665.3	38	766,2853,2884	AA,AC,CC		30.7326,39.537,33.7152	probably-damaging	165/1907	17696755	4385,8621	2203	4300	6503	SO:0001583	missense	10743	exon3			CAGGTGCCCTTTC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.493C>A	17.37:g.17696755C>A	ENSP00000323074:p.Pro165Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	58	0.58	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	37	CCDS11188.1	1094	0.5009157509157509	194	0.3943089430894309	165	0.4558011049723757	479	0.8374125874125874	256	0.33773087071240104	C	16.09	3.025501	0.54683	0.39537	0.307326	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.66995	-0.24;2.48;0.35	4.55	3.58	0.41010	.	0.101091	0.41938	D	0.000800	T	0.00012	0.0000	M	0.62723	1.935	0.34918	P	0.251845	D	0.89917	1.0	D	0.85130	0.997	T	0.31166	-0.9953	9	0.49607	T	0.09	.	11.7853	0.52039	0.0:0.913:0.0:0.087	rs11649804;rs57680432;rs11649804	165	Q7Z5J4	RAI1_HUMAN	T	165	ENSP00000323074:P165T;ENSP00000379120:P165T;ENSP00000261641:P165T	ENSP00000261641:P165T	P	+	1	0	RAI1	17637480	0.775000	0.28604	1.000000	0.80357	0.989000	0.77384	0.679000	0.25291	0.902000	0.36520	0.462000	0.41574	CCC	C|0.584;A|0.415	0.415	strong		0.617	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
PLEKHG4	25894	hgsc.bcm.edu	37	16	67318630	67318630	+	Silent	SNP	T	T	G	rs61738731	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:67318630T>G	ENST00000360461.5	+	12	4242	c.1707T>G	c.(1705-1707)gcT>gcG	p.A569A	PLEKHG4_ENST00000427155.2_Silent_p.A569A|PLEKHG4_ENST00000450733.1_Silent_p.A488A|PLEKHG4_ENST00000379344.3_Silent_p.A569A	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	569							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		TGACGTGGGCTGAGGAGGGGC	0.642													T|||	190	0.0379393	0.0507	0.0144	5008	,	,		17225	0.0		0.0308	False		,,,				2504	0.0838				p.A569A		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.T1707G						PASS	.	T	,,,,	160,4234		1,158,2038	21.0	23.0	22.0		1707,1707,1707,1464,1707	-2.8	1.0	16	dbSNP_129	22	281,8311		3,275,4018	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEKHG4	NM_001129727.1,NM_001129728.1,NM_001129729.1,NM_001129731.1,NM_015432.3	,,,,	4,433,6056	GG,GT,TT		3.2705,3.6413,3.396	,,,,	569/1192,569/1192,569/1192,488/1111,569/1192	67318630	441,12545	2197	4296	6493	SO:0001819	synonymous_variant	25894	exon13			GTGGGCTGAGGAG	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.1707T>G	16.37:g.67318630T>G		Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	239	104	0.435146	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Silent	SNP	ENST00000360461.5	37	CCDS32466.1																																																																																			T|0.970;G|0.030	0.030	strong		0.642	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
BTN3A2	11118	hgsc.bcm.edu	37	6	26368279	26368279	+	Splice_Site	SNP	G	G	A	rs71557335	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26368279G>A	ENST00000356386.2	+	2	183		c.e2+1		BTN3A2_ENST00000527422.1_Splice_Site|BTN3A2_ENST00000508906.2_Splice_Site|AL021917.1_ENST00000401160.1_RNA|BTN3A2_ENST00000396934.3_Intron|BTN3A2_ENST00000396948.1_Splice_Site|BTN3A2_ENST00000532994.1_Splice_Site|BTN3A2_ENST00000377708.2_Splice_Site	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2						interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						TTTGGCAGAGGTAAGATCTTC	0.428													G|||	409	0.0816693	0.0287	0.0403	5008	,	,		19572	0.0992		0.1123	False		,,,				2504	0.1329				.		Atlas-SNP	.											.	BTN3A2	44	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	11118	.			GCAGAGGTAAGAT	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.-6+1G>A	6.37:g.26368279G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	147	79	0.537415	.	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Splice_Site	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			G|0.927;A|0.073	0.073	strong		0.428	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		Intron
PCSK4	54760	hgsc.bcm.edu	37	19	1487981	1487981	+	Silent	SNP	C	C	T	rs151115553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1487981C>T	ENST00000300954.5	-	4	559	c.498G>A	c.(496-498)ccG>ccA	p.P166P	CTB-25B13.6_ENST00000585643.1_RNA|PCSK4_ENST00000587784.1_5'UTR	NM_017573.3	NP_060043.2			proprotein convertase subtilisin/kexin type 4											cervix(2)|endometrium(2)|kidney(1)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCAGAGGTCCGGGTGGTCCT	0.692													C|||	3	0.000599042	0.0	0.0014	5008	,	,		14584	0.0		0.002	False		,,,				2504	0.0				p.P166P		Atlas-SNP	.											.	PCSK4	44	.	0			c.G498A						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	71.0	71.0	71.0		498	-5.3	1.0	19	dbSNP_134	71	68,8532	40.3+/-97.0	0,68,4232	no	coding-synonymous	PCSK4	NM_017573.3		0,72,6431	TT,TC,CC		0.7907,0.0908,0.5536		166/756	1487981	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	54760	exon4			GAGGTCCGGGTGG	AK057235	CCDS12069.2	19p13.3	2008-02-05			ENSG00000115257	ENSG00000115257			8746	protein-coding gene	gene with protein product		600487				7782070	Standard	XM_005259586		Approved	PC4, SPC5, DKFZp434B217, MGC34749	uc002ltb.1	Q6UW60	OTTHUMG00000128541	ENST00000300954.5:c.498G>A	19.37:g.1487981C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_017573		Silent	SNP	ENST00000300954.5	37	CCDS12069.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	2.497	-0.316156	0.05422	9.08E-4	0.007907	ENSG00000115257	ENST00000441747	.	.	.	2.67	-5.34	0.02705	.	.	.	.	.	T	0.29491	0.0735	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.04373	-1.0956	7	0.54805	T	0.06	.	3.7736	0.08652	0.2281:0.3213:0.0:0.4506	.	8	B3KQ28	.	Q	8	.	ENSP00000402772:R8Q	R	-	2	0	PCSK4	1438981	0.000000	0.05858	0.987000	0.45799	0.937000	0.57800	-7.956000	0.00027	-0.883000	0.03982	-0.658000	0.03865	CGG	C|0.996;T|0.004	0.004	strong		0.692	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573	
CPPED1	55313	hgsc.bcm.edu	37	16	12758966	12758966	+	Missense_Mutation	SNP	T	T	C	rs1713480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:12758966T>C	ENST00000381774.4	-	4	962	c.722A>G	c.(721-723)aAa>aGa	p.K241R	CPPED1_ENST00000261660.4_Intron|CPPED1_ENST00000433677.2_Missense_Mutation_p.K99R	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	241	Catalytic.		K -> R (in dbSNP:rs1713480). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15991289, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:21269460}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						GAACACGACTTTGACACCTGC	0.502													T|||	3657	0.730232	0.6876	0.7305	5008	,	,		13475	0.5367		0.9453	False		,,,				2504	0.7658				p.K241R		Atlas-SNP	.											.	CPPED1	41	.	0			c.A722G						PASS	.	T	ARG/LYS,ARG/LYS	3019,945		1159,701,122	29.0	30.0	30.0		296,722	-0.7	0.3	16	dbSNP_89	30	7880,468		3720,440,14	yes	missense,missense	CPPED1	NM_001099455.1,NM_018340.2	26,26	4879,1141,136	CC,CT,TT		5.6061,23.8396,11.4766	benign,benign	99/173,241/315	12758966	10899,1413	1982	4174	6156	SO:0001583	missense	55313	exon4			ACGACTTTGACAC	AK022710	CCDS42119.1, CCDS42120.1	16p13.12	2014-02-12	2009-03-13		ENSG00000103381	ENSG00000103381			25632	protein-coding gene	gene with protein product	"""complete S transactivated protein 1"""	615603				12477932	Standard	NM_018340		Approved	CSTP1, FLJ11151	uc002dca.4	Q9BRF8	OTTHUMG00000167711	ENST00000381774.4:c.722A>G	16.37:g.12758966T>C	ENSP00000371193:p.Lys241Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	76	0.974359	NM_018340	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Missense_Mutation	SNP	ENST00000381774.4	37	CCDS42120.1	1672	0.7655677655677655	341	0.693089430894309	280	0.7734806629834254	329	0.5751748251748252	722	0.9525065963060686	T	10.46	1.356647	0.24598	0.761604	0.943939	ENSG00000103381	ENST00000381774;ENST00000433677	D;D	0.94376	-2.04;-3.41	5.87	-0.704	0.11256	Metallophosphoesterase domain (1);	0.198107	0.53938	N	0.000058	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	0.99999999897815	B;B	0.20459	0.045;0.006	B;B	0.17979	0.015;0.02	T	0.32719	-0.9896	9	0.20046	T	0.44	-4.6114	5.4337	0.16469	0.0:0.231:0.2674:0.5016	rs1713480;rs3791733;rs17850067;rs52826625;rs57117524;rs1713480	99;241	Q9BRF8-2;Q9BRF8	.;CPPED_HUMAN	R	241;99	ENSP00000371193:K241R;ENSP00000411127:K99R	ENSP00000371193:K241R	K	-	2	0	CPPED1	12666467	0.906000	0.30813	0.335000	0.25508	0.796000	0.44982	0.265000	0.18515	-0.307000	0.08804	-0.408000	0.06270	AAA	T|0.221;C|0.779	0.779	strong		0.502	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340	
POLR2B	5431	hgsc.bcm.edu	37	4	57876955	57876955	+	Silent	SNP	G	G	A	rs1718878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:57876955G>A	ENST00000381227.1	+	13	2003	c.1590G>A	c.(1588-1590)gcG>gcA	p.A530A	POLR2B_ENST00000441246.2_Silent_p.A523A|POLR2B_ENST00000431623.2_Silent_p.A455A|POLR2B_ENST00000314595.5_Silent_p.A530A|POLR2B_ENST00000510355.1_3'UTR			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	530					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					CCTTGATGGCGTATATTTCAG	0.353													A|||	1937	0.386781	0.4365	0.2954	5008	,	,		16271	0.2986		0.3469	False		,,,				2504	0.5164				p.A530A		Atlas-SNP	.											.	POLR2B	108	.	0			c.G1590A						PASS	.	A		1880,2526	624.5+/-394.3	400,1080,723	117.0	124.0	121.0		1590	2.0	1.0	4	dbSNP_89	121	2935,5661	666.9+/-402.4	487,1961,1850	no	coding-synonymous	POLR2B	NM_000938.1		887,3041,2573	AA,AG,GG		34.1438,42.6691,37.0328		530/1175	57876955	4815,8187	2203	4298	6501	SO:0001819	synonymous_variant	5431	exon12			GATGGCGTATATT		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1590G>A	4.37:g.57876955G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	242	241	0.995868	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			G|0.635;A|0.365	0.365	strong		0.353	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
MUC4	4585	hgsc.bcm.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	C	T	rs368695884	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506555C>T	ENST00000463781.3	-	2	12355	c.11896G>A	c.(11896-11898)Gcc>Acc	p.A3966T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3966T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3966T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACCTGTG	0.592													.|||	176	0.0351438	0.0083	0.0677	5008	,	,		7977	0.0119		0.0915	False		,,,				2504	0.0143				p.A3966T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.G11896A						scavenged	.						15.0	10.0	11.0					3																	195506555		666	1488	2154	SO:0001583	missense	4585	exon2			AGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11896G>A	3.37:g.195506555C>T	ENSP00000417498:p.Ala3966Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	12	0.210526	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.905	-0.721125	0.03182	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.48522	1.23;0.81	.	.	.	.	.	.	.	.	T	0.22551	0.0544	N	0.19112	0.55	0.09310	N	1	B	0.18741	0.03	B	0.06405	0.002	T	0.12915	-1.0529	7	.	.	.	-3.1782	2.1866	0.03888	0.0:0.3341:0.3337:0.3322	.	3838	E7ESK3	.	T	3966	ENSP00000417498:A3966T;ENSP00000420243:A3966T	.	A	-	1	0	MUC4	196991334	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.202000	0.09451	-2.037000	0.00920	-2.088000	0.00374	GCC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CDH23	64072	hgsc.bcm.edu	37	10	73537978	73537978	+	Silent	SNP	C	C	T	rs10762480	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:73537978C>T	ENST00000224721.6	+	39	5120	c.5115C>T	c.(5113-5115)taC>taT	p.Y1705Y		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1700	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						AGCTGGACTACGAGATCAGCC	0.602													C|||	898	0.179313	0.1755	0.1556	5008	,	,		20598	0.2004		0.2097	False		,,,				2504	0.1483				p.Y1700Y		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	0			c.C5100T						PASS	.	C		781,3459		70,641,1409	70.0	77.0	75.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5100	-5.9	0.9	10	dbSNP_120	75	1660,6786		168,1324,2731	no	coding-synonymous	CDH23	NM_022124.5		238,1965,4140	TT,TC,CC		19.6543,18.4198,19.2417		1700/3355	73537978	2441,10245	2120	4223	6343	SO:0001819	synonymous_variant	64072	exon38			GGACTACGAGATC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.5115C>T	10.37:g.73537978C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.824;T|0.176	0.176	strong		0.602	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
KIAA1755	85449	hgsc.bcm.edu	37	20	36859711	36859711	+	Silent	SNP	G	G	A	rs1205418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:36859711G>A	ENST00000279024.4	-	5	2035	c.1764C>T	c.(1762-1764)gcC>gcT	p.A588A		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	588										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GGGGCCGCCCGGCCCTGTCCC	0.632													G|||	1303	0.260184	0.2458	0.2219	5008	,	,		18278	0.2778		0.2833	False		,,,				2504	0.2648				p.A588A		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1764T						PASS	.	G		1203,3203	396.7+/-330.2	161,881,1161	39.0	38.0	38.0		1764	-9.9	0.0	20	dbSNP_87	38	2617,5983	395.5+/-345.1	424,1769,2107	no	coding-synonymous	KIAA1755	NM_001029864.1		585,2650,3268	AA,AG,GG		30.4302,27.3037,29.3711		588/1201	36859711	3820,9186	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon5			CCGCCCGGCCCTG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1764C>T	20.37:g.36859711G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	60	38	0.633333	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.703;A|0.297	0.297	strong		0.632	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
PIEZO1	9780	hgsc.bcm.edu	37	16	88788060	88788060	+	Silent	SNP	G	G	A	rs72811487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88788060G>A	ENST00000301015.9	-	38	5535	c.5289C>T	c.(5287-5289)taC>taT	p.Y1763Y	RP5-1142A6.9_ENST00000564984.1_RNA|PIEZO1_ENST00000327397.7_5'Flank	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1763					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						GCTTGTTCTCGTAGCGCCGCA	0.617													G|||	71	0.0141773	0.003	0.0159	5008	,	,		14075	0.0		0.0249	False		,,,				2504	0.0317				p.Y1763Y		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C5289T						PASS	.	G		8,1376		0,8,684	55.0	55.0	55.0		5289	-3.7	1.0	16	dbSNP_130	55	112,3060		2,108,1476	no	coding-synonymous	PIEZO1	NM_001142864.2		2,116,2160	AA,AG,GG		3.5309,0.578,2.6339		1763/2522	88788060	120,4436	692	1586	2278	SO:0001819	synonymous_variant	9780	exon38			GTTCTCGTAGCGC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.5289C>T	16.37:g.88788060G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	33	0.01510989010989011	6	0.012195121951219513	8	0.022099447513812154	0	0.0	19	0.025065963060686015	G	10.25	1.297104	0.23650	0.00578	0.035309	ENSG00000103335	ENST00000451779	.	.	.	4.82	-3.71	0.04424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.2539	12.989	0.58608	0.3197:0.0:0.6803:0.0	.	.	.	.	X	1709	.	.	R	-	1	2	FAM38A	87315561	0.580000	0.26733	0.952000	0.39060	0.989000	0.77384	-0.387000	0.07361	-0.899000	0.03901	0.448000	0.29417	CGA	G|0.985;A|0.015	0.015	strong		0.617	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
CTR9	9646	hgsc.bcm.edu	37	11	10786175	10786175	+	Silent	SNP	C	C	T	rs7118399	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:10786175C>T	ENST00000361367.2	+	12	1920	c.1494C>T	c.(1492-1494)acC>acT	p.T498T		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	498					cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)		p.T498T(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TTTCCGTTACCACGTCATATA	0.393													C|||	997	0.199081	0.1112	0.1542	5008	,	,		17362	0.2133		0.3052	False		,,,				2504	0.226				p.T498T		Atlas-SNP	.											CTR9,NS,carcinoma,0,1	CTR9	94	1	1	Substitution - coding silent(1)	stomach(1)	c.C1494T						PASS	.	C		613,3789	267.1+/-267.6	47,519,1635	92.0	81.0	85.0		1494	-4.3	0.8	11	dbSNP_116	85	2626,5962	424.0+/-354.5	404,1818,2072	no	coding-synonymous	CTR9	NM_014633.3		451,2337,3707	TT,TC,CC		30.5776,13.9255,24.9346		498/1174	10786175	3239,9751	2201	4294	6495	SO:0001819	synonymous_variant	9646	exon12			CGTTACCACGTCA	D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"""Tetratricopeptide (TTC) repeat domain containing"""	16850	protein-coding gene	gene with protein product		609366	"""SH2 domain binding protein 1 (tetratricopeptide repeat containing)"", ""Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"""	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.1494C>T	11.37:g.10786175C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	121	57	0.471074	NM_014633	D3DQV8|Q15015	Silent	SNP	ENST00000361367.2	37	CCDS7805.1																																																																																			C|0.772;T|0.228	0.228	strong		0.393	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633	
POM121L2	94026	hgsc.bcm.edu	37	6	27279805	27279805	+	Missense_Mutation	SNP	G	G	T	rs61736098	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27279805G>T	ENST00000444565.1	-	1	144	c.145C>A	c.(145-147)Cct>Act	p.P49T	POM121L2_ENST00000377451.2_Missense_Mutation_p.P49T	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	49										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						CGTGGGGCAGGGTGGGCGCGG	0.647													G|||	98	0.0195687	0.0257	0.0202	5008	,	,		14288	0.001		0.0298	False		,,,				2504	0.0194				p.P49T		Atlas-SNP	.											.	POM121L2	61	.	0			c.C145A						PASS	.	G	THR/PRO	34,1350		1,32,659	23.0	28.0	26.0		145	1.5	0.0	6	dbSNP_129	26	92,3090		1,90,1500	yes	missense	POM121L2	NM_033482.3	38	2,122,2159	TT,TG,GG		2.8913,2.4566,2.7595	probably-damaging	49/1036	27279805	126,4440	692	1591	2283	SO:0001583	missense	94026	exon1			GGGCAGGGTGGGC	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.145C>A	6.37:g.27279805G>T	ENSP00000392726:p.Pro49Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	43	0.019688644688644688	12	0.024390243902439025	9	0.024861878453038673	0	0.0	22	0.029023746701846966	G	10.26	1.300694	0.23650	0.024566	0.028913	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.19938	2.17;2.11	3.47	1.47	0.22746	.	0.255127	0.20727	N	0.086794	T	0.19127	0.0459	M	0.70595	2.14	0.09310	N	1	D	0.67145	0.996	P	0.60286	0.872	T	0.04481	-1.0948	10	0.72032	D	0.01	.	3.8726	0.09042	0.1546:0.2478:0.5975:0.0	.	49	C9J1I7	.	T	49	ENSP00000366671:P49T;ENSP00000392726:P49T	ENSP00000366671:P49T	P	-	1	0	POM121L2	27387784	0.796000	0.28864	0.049000	0.19019	0.006000	0.05464	0.538000	0.23160	0.375000	0.24679	0.561000	0.74099	CCT	G|0.979;T|0.021	0.021	strong		0.647	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
KRT32	3882	hgsc.bcm.edu	37	17	39619115	39619115	+	Missense_Mutation	SNP	G	G	A	rs2071563	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39619115G>A	ENST00000225899.3	-	6	1287	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	395	Coil 2.|Rod.		T -> M (in dbSNP:rs2071563).		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GCTCCGGTACGTGTTGATCTC	0.632													G|||	1847	0.36881	0.4259	0.402	5008	,	,		16423	0.3363		0.4245	False		,,,				2504	0.2444				p.T395M		Atlas-SNP	.											.	KRT32	57	.	0			c.C1184T						PASS	.	G	MET/THR	1809,2597	530.3+/-372.9	371,1067,765	72.0	73.0	72.0		1184	5.1	1.0	17	dbSNP_96	72	3226,5374	483.7+/-371.2	622,1982,1696	no	missense	KRT32	NM_002278.3	81	993,3049,2461	AA,AG,GG		37.5116,41.0576,38.7129	probably-damaging	395/449	39619115	5035,7971	2203	4300	6503	SO:0001583	missense	3882	exon6			CGGTACGTGTTGA	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.1184C>T	17.37:g.39619115G>A	ENSP00000225899:p.Thr395Met	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	869	0.39789377289377287	213	0.4329268292682927	125	0.3453038674033149	208	0.36363636363636365	323	0.4261213720316623	G	17.48	3.400513	0.62177	0.410576	0.375116	ENSG00000108759	ENST00000225899	D	0.91996	-2.95	5.07	5.07	0.68467	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.40554	N	0.001074	T	0.00012	0.0000	H	0.95114	3.625	0.31049	P	0.715462	D	0.89917	1.0	D	0.97110	1.0	T	0.00000	-1.5298	9	0.72032	D	0.01	.	17.8011	0.88587	0.0:0.0:1.0:0.0	rs2071563;rs52800623;rs58844466;rs2071563	395	Q14532	K1H2_HUMAN	M	395	ENSP00000225899:T395M	ENSP00000225899:T395M	T	-	2	0	KRT32	36872641	0.563000	0.26594	0.969000	0.41365	0.720000	0.41350	2.380000	0.44327	2.493000	0.84123	0.561000	0.74099	ACG	G|0.611;A|0.389	0.389	strong		0.632	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
OR4D6	219983	hgsc.bcm.edu	37	11	59225221	59225221	+	Missense_Mutation	SNP	T	T	C	rs1453541	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59225221T>C	ENST00000300127.2	+	1	811	c.788T>C	c.(787-789)aTg>aCg	p.M263T		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	263			M -> T (in dbSNP:rs1453541).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						CGGCCCTTCATGACGCTGCCC	0.527													C|||	1329	0.265375	0.3245	0.2695	5008	,	,		20460	0.1845		0.2972	False		,,,				2504	0.2331				p.M263T		Atlas-SNP	.											OR4D6,NS,carcinoma,-1,2	OR4D6	65	2	0			c.T788C						PASS	.	T	THR/MET	1469,2933	679.3+/-403.7	238,993,970	114.0	109.0	111.0		788	-2.7	0.0	11	dbSNP_88	111	2714,5876	681.6+/-403.7	417,1880,1998	yes	missense	OR4D6	NM_001004708.1	81	655,2873,2968	CC,CT,TT		31.5949,33.3712,32.1967	benign	263/315	59225221	4183,8809	2201	4295	6496	SO:0001583	missense	219983	exon1			CCTTCATGACGCT	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.788T>C	11.37:g.59225221T>C	ENSP00000300127:p.Met263Thr	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	201	91	0.452736	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	623	0.28525641025641024	159	0.3231707317073171	109	0.3011049723756906	119	0.20804195804195805	236	0.3113456464379947	C	0.001	-3.142940	0.00029	0.333712	0.315949	ENSG00000166884	ENST00000300127	T	0.00054	8.8	6.01	-2.74	0.05932	GPCR, rhodopsin-like superfamily (1);	0.805216	0.11028	N	0.607551	T	0.00012	0.0000	N	0.00055	-2.37	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37126	-0.9719	9	0.02654	T	1	-1.5571	4.6597	0.12636	0.0933:0.5045:0.0917:0.3105	rs1453541;rs17500443;rs59250564;rs1453541	263	Q8NGJ1	OR4D6_HUMAN	T	263	ENSP00000300127:M263T	ENSP00000300127:M263T	M	+	2	0	OR4D6	58981797	0.000000	0.05858	0.001000	0.08648	0.089000	0.18198	-0.221000	0.09202	-0.898000	0.03906	-1.990000	0.00449	ATG	T|0.689;C|0.311	0.311	strong		0.527	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
NEK5	341676	hgsc.bcm.edu	37	13	52667228	52667228	+	Silent	SNP	G	G	A	rs55715265	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:52667228G>A	ENST00000355568.4	-	13	1309	c.1170C>T	c.(1168-1170)taC>taT	p.Y390Y		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	390					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		TTTCCTGACCGTAATCCTCAA	0.363													g|||	155	0.0309505	0.0113	0.0231	5008	,	,		17266	0.0079		0.0358	False		,,,				2504	0.0818				p.Y390Y		Atlas-SNP	.											.	NEK5	189	.	0			c.C1170T						PASS	.	A		99,4307	79.9+/-118.3	0,99,2104	169.0	143.0	152.0		1170	-4.7	0.0	13	dbSNP_129	152	392,8208	126.7+/-185.1	9,374,3917	no	coding-synonymous	NEK5	NM_199289.1		9,473,6021	AA,AG,GG		4.5581,2.2469,3.7752		390/709	52667228	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	341676	exon13			CTGACCGTAATCC	BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)-related kinase 5"""			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.1170C>T	13.37:g.52667228G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	167	60	0.359281	NM_199289	Q5TAP5	Silent	SNP	ENST00000355568.4	37	CCDS31979.1																																																																																			G|0.967;A|0.033	0.033	strong		0.363	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289	
OR6T1	219874	hgsc.bcm.edu	37	11	123813940	123813940	+	Silent	SNP	G	G	C	rs7130003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:123813940G>C	ENST00000321252.2	-	1	640	c.606C>G	c.(604-606)ctC>ctG	p.L202L		NM_001005187.1	NP_001005187.1	Q8NGN1	OR6T1_HUMAN	olfactory receptor, family 6, subfamily T, member 1	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CCAACGTAGAGAGCATGAAAG	0.547													G|||	1318	0.263179	0.0582	0.3199	5008	,	,		12599	0.3839		0.3181	False		,,,				2504	0.319				p.L202L		Atlas-SNP	.											.	OR6T1	85	.	0			c.C606G						PASS	.	G		481,3923	226.9+/-242.2	32,417,1753	77.0	71.0	73.0		606	-2.7	0.0	11	dbSNP_116	73	2865,5733	451.5+/-362.7	459,1947,1893	no	coding-synonymous	OR6T1	NM_001005187.1		491,2364,3646	CC,CG,GG		33.3217,10.9219,25.7345		202/324	123813940	3346,9656	2202	4299	6501	SO:0001819	synonymous_variant	219874	exon1			CGTAGAGAGCATG	AB065759	CCDS31700.1	11q24.1	2012-08-09			ENSG00000181499	ENSG00000181499		"""GPCR / Class A : Olfactory receptors"""	14848	protein-coding gene	gene with protein product							Standard	NM_001005187		Approved		uc010sab.2	Q8NGN1	OTTHUMG00000165962	ENST00000321252.2:c.606C>G	11.37:g.123813940G>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_001005187	Q6IFE7	Silent	SNP	ENST00000321252.2	37	CCDS31700.1																																																																																			G|0.738;C|0.262	0.262	strong		0.547	OR6T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387264.1	NM_001005187	
KATNAL2	83473	hgsc.bcm.edu	37	18	44595647	44595647	+	Silent	SNP	C	C	T	rs56297904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:44595647C>T	ENST00000245121.5	+	9	860	c.666C>T	c.(664-666)ggC>ggT	p.G222G	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Silent_p.G294G	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						TGCTGTACGGCCCTCCAGGTA	0.478													C|||	32	0.00638978	0.0008	0.0086	5008	,	,		21037	0.0		0.0219	False		,,,				2504	0.0031				p.G222G		Atlas-SNP	.											.	KATNAL2	64	.	0			c.C666T						PASS	.	C		18,4388	25.3+/-52.1	0,18,2185	178.0	161.0	167.0		666	3.8	1.0	18	dbSNP_129	167	136,8464	68.0+/-130.5	0,136,4164	no	coding-synonymous	KATNAL2	NM_031303.2		0,154,6349	TT,TC,CC		1.5814,0.4085,1.1841		222/467	44595647	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	83473	exon9			GTACGGCCCTCCA	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"""ATPases / AAA-type"""	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.666C>T	18.37:g.44595647C>T		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	190	67	0.352632	NM_031303		Silent	SNP	ENST00000245121.5	37	CCDS32828.1																																																																																			C|0.988;T|0.012	0.012	strong		0.478	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303	
FAM169A	26049	hgsc.bcm.edu	37	5	74109840	74109840	+	Silent	SNP	G	G	A	rs76561443	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:74109840G>A	ENST00000389156.4	-	6	585	c.495C>T	c.(493-495)agC>agT	p.S165S	FAM169A_ENST00000510496.1_Intron|FAM169A_ENST00000380515.3_Missense_Mutation_p.A108V	NM_015566.2	NP_056381.1	Q9Y6X4	F169A_HUMAN	family with sequence similarity 169, member A	165						membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	27						AGGCACATATGCTTCCTGCAG	0.318													G|||	195	0.0389377	0.0968	0.0317	5008	,	,		15438	0.0129		0.0159	False		,,,				2504	0.0164				p.S165S		Atlas-SNP	.											.	FAM169A	61	.	0			c.C495T						PASS	.	G		307,3333		13,281,1526	91.0	89.0	89.0		495	1.4	0.9	5	dbSNP_131	89	174,7996		2,170,3913	no	coding-synonymous	FAM169A	NM_015566.1		15,451,5439	AA,AG,GG		2.1297,8.4341,4.0728		165/671	74109840	481,11329	1820	4085	5905	SO:0001819	synonymous_variant	26049	exon6			ACATATGCTTCCT		CCDS43330.1	5q13.3	2008-08-08			ENSG00000198780	ENSG00000198780			29138	protein-coding gene	gene with protein product		615769				10048485	Standard	NM_015566		Approved	KIAA0888	uc003kdm.4	Q9Y6X4	OTTHUMG00000162930	ENST00000389156.4:c.495C>T	5.37:g.74109840G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_015566	A8K1T9|Q6MZT0|Q9H989	Silent	SNP	ENST00000389156.4	37	CCDS43330.1	84	0.038461538461538464	51	0.10365853658536585	9	0.024861878453038673	11	0.019230769230769232	13	0.017150395778364115	G	2.290	-0.362684	0.05103	0.084341	0.021297	ENSG00000198780	ENST00000380515	.	.	.	5.28	1.37	0.22104	.	.	.	.	.	T	0.01421	0.0046	.	.	.	0.19945	N	0.999946	.	.	.	.	.	.	T	0.03354	-1.1045	5	0.87932	D	0	-1.4971	9.2093	0.37309	0.5233:0.0:0.4767:0.0	.	.	.	.	V	108	.	ENSP00000369886:A108V	A	-	2	0	FAM169A	74145596	0.503000	0.26115	0.863000	0.33907	0.916000	0.54674	0.688000	0.25422	-0.048000	0.13401	-0.137000	0.14449	GCA	G|0.968;A|0.032	0.032	strong		0.318	FAM169A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371092.2		
DNAH17	8632	hgsc.bcm.edu	37	17	76482432	76482432	+	Silent	SNP	A	A	G	rs691151	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76482432A>G	ENST00000585328.1	-	45	7084	c.6960T>C	c.(6958-6960)atT>atC	p.I2320I	DNAH17_ENST00000389840.5_Silent_p.I2311I|RP11-559N14.5_ENST00000585969.1_RNA|RP11-559N14.5_ENST00000588565.1_RNA|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2311					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			GCAGGTACAGAATCGTTTGGA	0.577													G|||	3277	0.654353	0.5719	0.768	5008	,	,		18396	0.5952		0.659	False		,,,				2504	0.7413				p.I2325I		Atlas-SNP	.											.	DNAH17	347	.	0			c.T6975C						PASS	.	G		2523,1829		729,1065,382	75.0	81.0	79.0		6975	1.0	0.8	17	dbSNP_83	79	5666,2876		1898,1870,503	no	coding-synonymous	DNAH17	NM_173628.3		2627,2935,885	GG,GA,AA		33.6689,42.0267,36.4898		2325/4463	76482432	8189,4705	2176	4271	6447	SO:0001819	synonymous_variant	8632	exon45			GTACAGAATCGTT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.6960T>C	17.37:g.76482432A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				A|0.343;G|0.657	0.657	strong		0.577	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
SMO	6608	hgsc.bcm.edu	37	7	128846328	128846328	+	Silent	SNP	G	G	C	rs2228617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128846328G>C	ENST00000249373.3	+	6	1444	c.1164G>C	c.(1162-1164)ggG>ggC	p.G388G		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	388					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	CTGTGAGTGGGATTTGTTTTG	0.597			Mis		skin basal cell								C|||	3787	0.75619	0.6687	0.7896	5008	,	,		19589	0.7718		0.8231	False		,,,				2504	0.7658				p.G388G		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.G1164C						PASS	.	C		3054,1352	451.8+/-349.8	1066,922,215	231.0	190.0	204.0		1164	5.3	1.0	7	dbSNP_98	204	7216,1384	269.4+/-288.4	3025,1166,109	no	coding-synonymous	SMO	NM_005631.4		4091,2088,324	CC,CG,GG		16.093,30.6854,21.0364		388/788	128846328	10270,2736	2203	4300	6503	SO:0001819	synonymous_variant	6608	exon6			GAGTGGGATTTGT	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.1164G>C	7.37:g.128846328G>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_005631	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																			G|0.216;C|0.784	0.784	strong		0.597	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
LCE1E	353135	hgsc.bcm.edu	37	1	152759950	152759950	+	Missense_Mutation	SNP	A	A	G	rs11205106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152759950A>G	ENST00000368770.3	+	2	228	c.175A>G	c.(175-177)Agc>Ggc	p.S59G	LCE1E_ENST00000368771.1_Missense_Mutation_p.S59G	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	59	Cys-rich.		S -> G (in dbSNP:rs11205106).		keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTGGGGGCAGCTGTGGCTC	0.662													G|||	2683	0.535743	0.7625	0.5058	5008	,	,		12821	0.4097		0.5	False		,,,				2504	0.4172				p.S59G		Atlas-SNP	.											.	LCE1E	26	.	0			c.A175G						PASS	.	G	GLY/SER	3099,1305		1096,907,199	39.0	48.0	45.0		175	0.3	1.0	1	dbSNP_120	45	4199,4397		1034,2131,1133	no	missense	LCE1E	NM_178353.1	56	2130,3038,1332	GG,GA,AA		48.8483,29.6322,43.8615	benign	59/119	152759950	7298,5702	2202	4298	6500	SO:0001583	missense	353135	exon2			GGGGGCAGCTGTG	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"""Late cornified envelopes"""	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.175A>G	1.37:g.152759950A>G	ENSP00000357759:p.Ser59Gly	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	258	254	0.984496	NM_178353	D3DV30	Missense_Mutation	SNP	ENST00000368770.3	37	CCDS1024.1	1116	0.510989010989011	347	0.7052845528455285	190	0.5248618784530387	229	0.40034965034965037	350	0.46174142480211083	G	8.154	0.788065	0.16258	0.703678	0.488483	ENSG00000186226	ENST00000368771;ENST00000368770	T;T	0.03663	3.85;3.85	3.03	0.345	0.16011	.	.	.	.	.	T	0.00496	0.0016	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	8	0.87932	D	0	.	4.4897	0.11808	0.1912:0.0:0.4028:0.406	rs11205106;rs59603833	59	Q5T753	LCE1E_HUMAN	G	59	ENSP00000357760:S59G;ENSP00000357759:S59G	ENSP00000357759:S59G	S	+	1	0	LCE1E	151026574	0.399000	0.25287	0.995000	0.50966	0.969000	0.65631	-0.000000	0.12993	-0.384000	0.07845	-1.983000	0.00453	AGC	A|0.454;G|0.546	0.546	strong		0.662	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353	
GALR3	8484	hgsc.bcm.edu	37	22	38219570	38219570	+	Missense_Mutation	SNP	C	C	G	rs78650836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38219570C>G	ENST00000249041.2	+	1	182	c.157C>G	c.(157-159)Cct>Gct	p.P53A		NM_003614.1	NP_003605.1	O60755	GALR3_HUMAN	galanin receptor 3	53					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|learning or memory (GO:0007611)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|peptide hormone binding (GO:0017046)			endometrium(1)|liver(2)|lung(1)	4	Melanoma(58;0.045)					CTGGCAGGAGCCTGGCAGCAC	0.632													C|||	5	0.000998403	0.0008	0.0029	5008	,	,		11722	0.0		0.001	False		,,,				2504	0.001				p.P53A		Atlas-SNP	.											.	GALR3	12	.	0			c.C157G						PASS	.	C	ALA/PRO	5,4401	9.9+/-24.2	0,5,2198	72.0	53.0	59.0		157	4.2	1.0	22	dbSNP_131	59	52,8548	33.3+/-86.6	0,52,4248	yes	missense	GALR3	NM_003614.1	27	0,57,6446	GG,GC,CC		0.6047,0.1135,0.4383	possibly-damaging	53/369	38219570	57,12949	2203	4300	6503	SO:0001583	missense	8484	exon1			CAGGAGCCTGGCA	AF073799	CCDS13958.1	22q113.1	2012-08-08			ENSG00000128310	ENSG00000128310		"""GPCR / Class A : Galanin receptors"""	4134	protein-coding gene	gene with protein product		603692				9722565, 9832121	Standard	NM_003614		Approved		uc003aub.1	O60755	OTTHUMG00000150658	ENST00000249041.2:c.157C>G	22.37:g.38219570C>G	ENSP00000249041:p.Pro53Ala	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	154	73	0.474026	NM_003614	Q53YJ4	Missense_Mutation	SNP	ENST00000249041.2	37	CCDS13958.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	11.45	1.643789	0.29246	0.001135	0.006047	ENSG00000128310	ENST00000249041	T	0.36878	1.23	5.25	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.253805	0.39274	N	0.001413	T	0.12860	0.0312	N	0.20610	0.595	0.25697	N	0.985627	B	0.25206	0.12	B	0.18871	0.023	T	0.12993	-1.0526	10	0.12766	T	0.61	.	6.6972	0.23205	0.2991:0.6141:0.0:0.0869	.	53	O60755	GALR3_HUMAN	A	53	ENSP00000249041:P53A	ENSP00000249041:P53A	P	+	1	0	GALR3	36549516	0.992000	0.36948	1.000000	0.80357	0.921000	0.55340	2.077000	0.41557	2.885000	0.99019	0.655000	0.94253	CCT	C|0.996;G|0.004	0.004	strong		0.632	GALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319452.1		
PKN1	5585	hgsc.bcm.edu	37	19	14581063	14581063	+	Silent	SNP	A	A	G	rs1042728	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14581063A>G	ENST00000242783.6	+	19	2547	c.2382A>G	c.(2380-2382)cgA>cgG	p.R794R	PKN1_ENST00000342216.4_Silent_p.R800R	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	794	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						CGTACACGCGAGCTGTGGACT	0.642													G|||	999	0.199481	0.4796	0.1542	5008	,	,		19432	0.1081		0.0825	False		,,,				2504	0.0675				p.R800R	NSCLC(185;2539 2965 10733 52867)	Atlas-SNP	.											.	PKN1	99	.	0			c.A2400G						PASS	.	G	,	1876,2530	625.9+/-394.6	399,1078,726	102.0	115.0	111.0		2382,2400	-5.1	0.0	19	dbSNP_86	111	596,8004	789.7+/-407.6	26,544,3730	no	coding-synonymous,coding-synonymous	PKN1	NM_002741.3,NM_213560.1	,	425,1622,4456	GG,GA,AA		6.9302,42.5783,19.0066	,	794/943,800/949	14581063	2472,10534	2203	4300	6503	SO:0001819	synonymous_variant	5585	exon19			CACGCGAGCTGTG	S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"""protein kinase C-like 1"""	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.2382A>G	19.37:g.14581063A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Silent	SNP	ENST00000242783.6	37	CCDS42513.1																																																																																			A|0.837;G|0.163	0.163	strong		0.642	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560	
SPRR1B	6699	hgsc.bcm.edu	37	1	153004848	153004848	+	Silent	SNP	T	T	C	rs3795381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:153004848T>C	ENST00000307098.4	+	2	92	c.27T>C	c.(25-27)ccT>ccC	p.P9P	SPRR1B_ENST00000392661.3_Silent_p.P9P	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	9	2 X 12 AA approximate repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGAAGCAGCCTTGCACCCCAC	0.552													C|||	2474	0.49401	0.4402	0.4251	5008	,	,		16307	0.5913		0.5099	False		,,,				2504	0.499				p.P9P		Atlas-SNP	.											.	SPRR1B	18	.	0			c.T27C						PASS	.	C		2068,2338	603.3+/-390.1	482,1104,617	144.0	140.0	141.0		27	2.1	1.0	1	dbSNP_107	141	4392,4208	568.8+/-389.1	1128,2136,1036	yes	coding-synonymous	SPRR1B	NM_003125.2		1610,3240,1653	CC,CT,TT		48.9302,46.936,49.6694		9/90	153004848	6460,6546	2203	4300	6503	SO:0001819	synonymous_variant	6699	exon2			GCAGCCTTGCACC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.27T>C	1.37:g.153004848T>C		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	339	195	0.575221	NM_003125	B2R5H7|P22529|P22530|Q5T524	Silent	SNP	ENST00000307098.4	37	CCDS30863.1																																																																																			T|0.497;C|0.503	0.503	strong		0.552	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
MYO16	23026	hgsc.bcm.edu	37	13	109518578	109518578	+	Silent	SNP	T	T	C	rs9559428	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:109518578T>C	ENST00000357550.2	+	11	1388	c.1347T>C	c.(1345-1347)atT>atC	p.I449I	MYO16_ENST00000251041.5_Silent_p.I449I|MYO16_ENST00000356711.2_Silent_p.I449I	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			AGCTTCCAATTTATTCTTCCA	0.308													T|||	320	0.0638978	0.025	0.072	5008	,	,		12976	0.0754		0.1282	False		,,,				2504	0.0327				p.I471I		Atlas-SNP	.											.	MYO16	285	.	0			c.T1413C						PASS	.	T	,	174,4232	114.6+/-152.6	7,160,2036	104.0	104.0	104.0		1413,1347	1.6	1.0	13	dbSNP_119	104	1093,7503	227.8+/-263.0	72,949,3277	no	coding-synonymous,coding-synonymous	MYO16	NM_001198950.1,NM_015011.1	,	79,1109,5313	CC,CT,TT		12.7152,3.9492,9.7447	,	471/1881,449/1859	109518578	1267,11735	2203	4298	6501	SO:0001819	synonymous_variant	23026	exon12			TCCAATTTATTCT		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.1347T>C	13.37:g.109518578T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	252	127	0.503968	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			T|0.907;C|0.093	0.093	strong		0.308	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
ALDH3B2	222	hgsc.bcm.edu	37	11	67433869	67433869	+	Missense_Mutation	SNP	C	C	T	rs1551888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67433869C>T	ENST00000349015.3	-	5	593	c.155G>A	c.(154-156)aGt>aAt	p.S52N	ALDH3B2_ENST00000531881.1_5'Flank|ALDH3B2_ENST00000530069.1_Missense_Mutation_p.S52N	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	52			S -> N (in dbSNP:rs1551888). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7484374, ECO:0000269|PubMed:8890755}.		alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						CACCACGCAACTCCCTGCAGG	0.667													t|||	4350	0.86861	0.7201	0.9193	5008	,	,		16274	0.9097		0.8877	False		,,,				2504	0.9714				p.S52N		Atlas-SNP	.											.	ALDH3B2	46	.	0			c.G155A						PASS	.	T	ASN/SER,ASN/SER	3307,1093		1244,819,137	24.0	24.0	24.0		155,155	4.2	0.9	11	dbSNP_88	24	7730,858		3476,778,40	yes	missense,missense	ALDH3B2	NM_000695.3,NM_001031615.1	46,46	4720,1597,177	TT,TC,CC		9.9907,24.8409,15.0216	benign,benign	52/386,52/386	67433869	11037,1951	2200	4294	6494	SO:0001583	missense	222	exon5			ACGCAACTCCCTG	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"""Aldehyde dehydrogenases"""	411	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 8"", ""acetaldehyde dehydrogenase 8"""	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.155G>A	11.37:g.67433869C>T	ENSP00000255084:p.Ser52Asn	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_001031615	Q53Y98|Q8NAL5|Q96IB2	Missense_Mutation	SNP	ENST00000349015.3	37	CCDS31622.1	1922	0.88003663003663	379	0.7703252032520326	328	0.9060773480662984	537	0.9388111888111889	678	0.8944591029023746	T	2.060	-0.415668	0.04766	0.751591	0.900093	ENSG00000132746	ENST00000530069;ENST00000349015;ENST00000525827;ENST00000528756	T;T;T;T	0.60040	0.22;0.22;0.22;0.22	4.2	4.2	0.49525	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00003	-3.465	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41610	-0.9499	9	0.02654	T	1	.	9.6594	0.39945	0.0:0.0854:0.0:0.9146	rs1551888;rs2228115;rs3191880;rs57578350;rs1551888	52	P48448	AL3B2_HUMAN	N	52	ENSP00000431595:S52N;ENSP00000255084:S52N;ENSP00000433718:S52N;ENSP00000433466:S52N	ENSP00000255084:S52N	S	-	2	0	ALDH3B2	67190445	1.000000	0.71417	0.934000	0.37439	0.528000	0.34623	4.871000	0.63042	0.761000	0.33130	-0.254000	0.11334	AGT	C|0.139;T|0.861	0.861	strong		0.667	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695	
CD109	135228	hgsc.bcm.edu	37	6	74521947	74521947	+	Missense_Mutation	SNP	C	C	T	rs2917862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:74521947C>T	ENST00000287097.5	+	29	3834	c.3722C>T	c.(3721-3723)aCg>aTg	p.T1241M	CD109_ENST00000422508.2_Missense_Mutation_p.T1164M|CD109_ENST00000437994.2_Missense_Mutation_p.T1224M			Q6YHK3	CD109_HUMAN	CD109 molecule	1241			T -> M (in dbSNP:rs2917862). {ECO:0000269|PubMed:11861284, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GTACAGCCAACGGCAGTTAAT	0.328													C|||	2045	0.408347	0.202	0.4669	5008	,	,		20547	0.4583		0.4901	False		,,,				2504	0.5102				p.T1241M		Atlas-SNP	.											.	CD109	170	.	0			c.C3722T						PASS	.	C	MET/THR,MET/THR,MET/THR	1141,3265	406.6+/-333.9	144,853,1206	149.0	141.0	144.0		3671,3491,3722	-2.0	0.0	6	dbSNP_101	144	4056,4544	558.9+/-387.3	977,2102,1221	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	81,81,81	1121,2955,2427	TT,TC,CC		47.1628,25.8965,39.9585	benign,benign,benign	1224/1429,1164/1369,1241/1446	74521947	5197,7809	2203	4300	6503	SO:0001583	missense	135228	exon29			AGCCAACGGCAGT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3722C>T	6.37:g.74521947C>T	ENSP00000287097:p.Thr1241Met	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	210	210	1	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	920	0.42124542124542125	112	0.22764227642276422	159	0.43922651933701656	265	0.4632867132867133	384	0.5065963060686016	C	4.096	0.015803	0.07959	0.258965	0.471628	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.25579	1.79;2.02;1.8	5.25	-1.95	0.07548	.	0.901547	0.09940	N	0.736070	T	0.10035	0.0246	L	0.50333	1.59	0.80722	P	0.0	B;P;P	0.43542	0.177;0.81;0.607	B;B;B	0.37550	0.03;0.253;0.107	T	0.19321	-1.0309	9	0.44086	T	0.13	.	12.6268	0.56634	0.0:0.2844:0.0:0.7156	rs2917862;rs58804669;rs2917862	1164;1224;1241	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	M	1224;1164;1241	ENSP00000388062:T1224M;ENSP00000404475:T1164M;ENSP00000287097:T1241M	ENSP00000287097:T1241M	T	+	2	0	CD109	74578668	0.000000	0.05858	0.001000	0.08648	0.536000	0.34869	-0.978000	0.03778	-0.333000	0.08476	-0.251000	0.11542	ACG	C|0.593;T|0.407	0.407	strong		0.328	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086407	46086407	+	Missense_Mutation	SNP	C	C	T	rs12481809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:46086407C>T	ENST00000360770.3	-	1	437	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	133	23 X 5 AA approximate repeats.					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						CTGCAGAGGACGCTGGTGCAG	0.622													C|||	731	0.145966	0.0946	0.1657	5008	,	,		19372	0.0923		0.2068	False		,,,				2504	0.1943				p.V133I		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.G397A						PASS	.	C	,ILE/VAL	403,3907		22,359,1774	54.0	60.0	58.0		,397	1.5	0.1	21	dbSNP_120	58	1732,6738		170,1392,2673	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,29	192,1751,4447	TT,TC,CC		20.4486,9.3503,16.7058	,benign	,133/147	46086407	2135,10645	2155	4235	6390	SO:0001583	missense	353323	exon1			AGAGGACGCTGGT	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.397G>A	21.37:g.46086407C>T	ENSP00000354001:p.Val133Ile	Somatic	368	0	0		WXS	Illumina HiSeq	Phase_I	386	185	0.479275	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	321	0.14697802197802198	45	0.09146341463414634	61	0.1685082872928177	56	0.0979020979020979	159	0.20976253298153033	c	2.766	-0.256710	0.05829	0.093503	0.204486	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.02656	4.21	3.62	1.54	0.23209	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.29936	0.262	B	0.23150	0.044	T	0.46762	-0.9168	8	0.24483	T	0.36	.	5.7725	0.18261	0.1361:0.2197:0.6442:0.0	rs12481809	133	P59991	KR122_HUMAN	I	133;83	ENSP00000354001:V133I	ENSP00000354001:V133I	V	-	1	0	KRTAP12-2	44910835	0.005000	0.15991	0.063000	0.19743	0.005000	0.04900	0.296000	0.19083	0.697000	0.31718	-0.502000	0.04539	GTC	C|0.844;T|0.156	0.156	strong		0.622	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
RYR1	6261	hgsc.bcm.edu	37	19	38990593	38990593	+	Silent	SNP	C	C	T	rs12973632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38990593C>T	ENST00000359596.3	+	45	7260	c.7260C>T	c.(7258-7260)caC>caT	p.H2420H	RYR1_ENST00000355481.4_Silent_p.H2420H|RYR1_ENST00000360985.3_Silent_p.H2420H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2420	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACCTGGGACACGCCATCATGT	0.637													C|||	117	0.0233626	0.0234	0.0375	5008	,	,		14309	0.001		0.0388	False		,,,				2504	0.0204				p.H2420H		Atlas-SNP	.											RYR1,NS,carcinoma,+2,1	RYR1	708	1	0			c.C7260T						PASS	.	C	,	92,4314	76.8+/-115.0	1,90,2112	145.0	108.0	120.0		7260,7260	-7.4	0.9	19	dbSNP_121	120	287,8313	106.2+/-167.1	6,275,4019	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	7,365,6131	TT,TC,CC		3.3372,2.0881,2.914	,	2420/5039,2420/5034	38990593	379,12627	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon45			GGGACACGCCATC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.7260C>T	19.37:g.38990593C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.969;T|0.031	0.031	strong		0.637	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
POTEF	728378	hgsc.bcm.edu	37	2	130872529	130872529	+	Silent	SNP	G	G	A	rs556671650	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130872529G>A	ENST00000409914.2	-	5	1134	c.735C>T	c.(733-735)taC>taT	p.Y245Y	POTEF_ENST00000361163.4_Silent_p.Y255Y|POTEF_ENST00000360967.5_Silent_p.Y245Y|POTEF_ENST00000357462.5_Silent_p.Y245Y	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	245					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TATAGATAGCGTAGTGCAGAG	0.383													.|||	220	0.0439297	0.0151	0.0504	5008	,	,		20686	0.1121		0.0338	False		,,,				2504	0.0184				p.Y245Y		Atlas-SNP	.											POTEF,NS,carcinoma,0,2	POTEF	140	2	0			c.C735T						scavenged	.																																			SO:0001819	synonymous_variant	728378	exon5			GATAGCGTAGTGC	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.735C>T	2.37:g.130872529G>A		Somatic	1370	2	0.00145985		WXS	Illumina HiSeq	Phase_I	1467	3	0.00204499	NM_001099771	A6NC34	Silent	SNP	ENST00000409914.2	37	CCDS46409.1																																																																																			.	.	none		0.383	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
MRPL20	55052	hgsc.bcm.edu	37	1	1342394	1342394	+	Silent	SNP	G	G	A	rs11548045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1342394G>A	ENST00000344843.7	-	2	188	c.93C>T	c.(91-93)ttC>ttT	p.F31F	RP4-758J18.13_ENST00000607307.1_lincRNA|MRPL20_ENST00000493287.1_5'Flank|RN7SL657P_ENST00000582431.1_RNA|MRPL20_ENST00000482352.1_Silent_p.F31F	NM_017971.3	NP_060441.2	Q9BYC9	RM20_HUMAN	mitochondrial ribosomal protein L20	31					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TCCTTCCCCGGAAGTGCTGGG	0.612													G|||	71	0.0141773	0.0061	0.0274	5008	,	,		12955	0.0		0.0417	False		,,,				2504	0.002				p.F31F		Atlas-SNP	.											.	MRPL20	13	.	0			c.C93T						PASS	.	G		20,4386	29.0+/-57.7	0,20,2183	122.0	142.0	136.0		93	2.0	1.0	1	dbSNP_120	136	250,8342	96.6+/-158.3	6,238,4052	no	coding-synonymous	MRPL20	NM_017971.3		6,258,6235	AA,AG,GG		2.9097,0.4539,2.0772		31/150	1342394	270,12728	2203	4296	6499	SO:0001819	synonymous_variant	55052	exon2			TCCCCGGAAGTGC	AB049644	CCDS26.1	1p36.3-p36.2	2012-09-13			ENSG00000242485	ENSG00000242485		"""Mitochondrial ribosomal proteins / large subunits"""	14478	protein-coding gene	gene with protein product		611833					Standard	NM_017971		Approved	FLJ10024	uc001afo.4	Q9BYC9	OTTHUMG00000002916	ENST00000344843.7:c.93C>T	1.37:g.1342394G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_017971	B2RE41|B7Z746	Silent	SNP	ENST00000344843.7	37	CCDS26.1																																																																																			G|0.978;A|0.022	0.022	strong		0.612	MRPL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008139.1	NM_017971	
GOLGA8A	23015	hgsc.bcm.edu	37	15	34673722	34673722	+	Missense_Mutation	SNP	C	C	T	rs347877		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:34673722C>T	ENST00000359187.4	-	16	1766	c.1702G>A	c.(1702-1704)Gtc>Atc	p.V568I	GOLGA8A_ENST00000432566.2_Missense_Mutation_p.V598I|MIR1233-1_ENST00000408722.1_RNA|GOLGA8A_ENST00000543376.1_Missense_Mutation_p.V425I|GOLGA8A_ENST00000360553.3_Missense_Mutation_p.V568I	NM_181077.3	NP_851422.1	A7E2F4	GOG8A_HUMAN	golgin A8 family, member A	596	Golgi-targeting domain. {ECO:0000250}.					Golgi apparatus (GO:0005794)|membrane (GO:0016020)							all_lung(180;2.78e-08)		all cancers(64;8.27e-19)|GBM - Glioblastoma multiforme(113;6.98e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		AGCTGCACGACTGGCTGTGCA	0.597																																					p.V568I		Atlas-SNP	.											.	GOLGA8A	8	.	0			c.G1702A						PASS	.						122.0	105.0	111.0					15																	34673722		2199	4296	6495	SO:0001583	missense	23015	exon16			GCACGACTGGCTG	BX648160	CCDS10038.1	15q14	2011-10-25	2010-02-12		ENSG00000175265	ENSG00000175265			31972	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 8A"""			10660574, 10677249	Standard	NM_181077		Approved	GM88, GOLGIN-67	uc001zii.3	A7E2F4	OTTHUMG00000129447	ENST00000359187.4:c.1702G>A	15.37:g.34673722C>T	ENSP00000352111:p.Val568Ile	Somatic	780	2	0.0025641		WXS	Illumina HiSeq	Phase_I	604	211	0.349338	NM_181077	A7MCY9|B7ZMK5|O94937|Q52M46|Q68DK6|Q9NZG8|Q9NZW0|Q9NZW3	Missense_Mutation	SNP	ENST00000359187.4	37	CCDS10038.1	1079	0.49404761904761907	121	0.2459349593495935	182	0.5027624309392266	345	0.6031468531468531	431	0.5686015831134564	c	0.011	-1.718415	0.00700	.	.	ENSG00000175265	ENST00000359187;ENST00000360553;ENST00000432566;ENST00000543376	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	0.514	0.514	0.17007	.	.	.	.	.	T	0.00012	0.0000	N	0.00045	-2.445	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.39563	-0.9608	7	0.02654	T	1	.	.	.	.	.	568;596	A7E2F4-3;A7E2F4	.;GOG8A_HUMAN	I	568;568;598;425	ENSP00000352111:V568I;ENSP00000353755:V568I;ENSP00000402791:V598I;ENSP00000438613:V425I	ENSP00000352111:V568I	V	-	1	0	GOLGA8A	32461014	1.000000	0.71417	0.003000	0.11579	0.001000	0.01503	1.839000	0.39220	-0.399000	0.07668	-0.903000	0.02851	GTC	C|0.511;T|0.489	0.489	strong		0.597	GOLGA8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251830.2	NM_181076	
ATAD5	79915	hgsc.bcm.edu	37	17	29187497	29187497	+	Silent	SNP	A	A	G	rs9896095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:29187497A>G	ENST00000321990.4	+	10	3381	c.3003A>G	c.(3001-3003)gtA>gtG	p.V1001V	CTD-2349P21.11_ENST00000580873.1_RNA|RNU6-298P_ENST00000390888.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1001					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				GGAAACTCGTAGAAGCAGAAA	0.353													G|||	864	0.172524	0.1762	0.1902	5008	,	,		16243	0.1359		0.1074	False		,,,				2504	0.2597				p.V1001V		Atlas-SNP	.											.	ATAD5	150	.	0			c.A3003G						PASS	.	G		730,3674	744.8+/-411.6	60,610,1532	66.0	66.0	66.0		3003	-3.3	0.0	17	dbSNP_119	66	902,7698	773.0+/-407.7	37,828,3435	no	coding-synonymous	ATAD5	NM_024857.3		97,1438,4967	GG,GA,AA		10.4884,16.5758,12.55		1001/1845	29187497	1632,11372	2202	4300	6502	SO:0001819	synonymous_variant	79915	exon10			ACTCGTAGAAGCA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3003A>G	17.37:g.29187497A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	184	184	1	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																			A|0.862;G|0.138	0.138	strong		0.353	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
MUC4	4585	hgsc.bcm.edu	37	3	195511364	195511364	+	Missense_Mutation	SNP	T	T	A	rs75187745		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195511364T>A	ENST00000463781.3	-	2	7546	c.7087A>T	c.(7087-7089)Aca>Tca	p.T2363S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2363S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGTCACCTGTGGATACTGAG	0.587																																					p.T2363S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.A7087T						PASS	.						23.0	21.0	21.0					3																	195511364		689	1583	2272	SO:0001583	missense	4585	exon2			CACCTGTGGATAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7087A>T	3.37:g.195511364T>A	ENSP00000417498:p.Thr2363Ser	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	393	33	0.0839695	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	T	5.115	0.206928	0.09704	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.49720	0.77;1.01	.	.	.	.	.	.	.	.	T	0.29321	0.0730	N	0.19112	0.55	0.09310	N	1	P	0.34587	0.458	B	0.39152	0.292	T	0.18272	-1.0342	7	.	.	.	.	2.7352	0.05238	0.0:0.3911:0.0:0.6089	.	2363	E7ESK3	.	S	2363	ENSP00000417498:T2363S;ENSP00000420243:T2363S	.	T	-	1	0	MUC4	196995759	0.007000	0.16637	0.008000	0.14137	0.111000	0.19643	-2.023000	0.01438	0.408000	0.25621	0.055000	0.15244	ACA	T|0.500;A|0.500	0.500	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DOCK9	23348	hgsc.bcm.edu	37	13	99575568	99575568	+	Silent	SNP	G	G	A	rs12428661	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:99575568G>A	ENST00000376460.1	-	5	554	c.474C>T	c.(472-474)gtC>gtT	p.V158V	DOCK9_ENST00000339416.2_Silent_p.V159V|DOCK9_ENST00000442173.1_Silent_p.V158V|DOCK9_ENST00000448493.2_Silent_p.V170V	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	159					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CATCTTTGTCGACCTCCTCGT	0.353													G|||	839	0.167532	0.0862	0.1729	5008	,	,		20251	0.2063		0.1899	False		,,,				2504	0.2106				p.V159V		Atlas-SNP	.											DOCK9_ENST00000448493,caecum,carcinoma,0,3	DOCK9	311	3	0			c.C477T						PASS	.	G	,,,	333,3457		13,307,1575	150.0	147.0	148.0		474,477,474,477	-7.9	0.3	13	dbSNP_120	148	1329,6901		104,1121,2890	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DOCK9	NM_001130048.1,NM_001130049.1,NM_001130050.1,NM_015296.2	,,,	117,1428,4465	AA,AG,GG		16.1482,8.7863,13.827	,,,	158/2069,159/1255,158/1254,159/2070	99575568	1662,10358	1895	4115	6010	SO:0001819	synonymous_variant	23348	exon5			TTTGTCGACCTCC	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.474C>T	13.37:g.99575568G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Silent	SNP	ENST00000376460.1	37	CCDS45062.1																																																																																			G|0.826;A|0.174	0.174	strong		0.353	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	
PELP1	27043	hgsc.bcm.edu	37	17	4576216	4576216	+	Silent	SNP	G	G	A	rs147763003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576216G>A	ENST00000574876.1	-	16	2087	c.2070C>T	c.(2068-2070)ccC>ccT	p.P690P	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Silent_p.P600P|PELP1_ENST00000301396.4_Silent_p.P834P|PELP1_ENST00000572293.1_Silent_p.P740P|PELP1_ENST00000436683.2_Silent_p.P543P			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	690	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GGCCTGCTGAGGGCATGGGGC	0.687													G|||	107	0.0213658	0.0045	0.0072	5008	,	,		12426	0.0079		0.0159	False		,,,				2504	0.0736				p.P690P		Atlas-SNP	.											.	PELP1	102	.	0			c.C2070T						PASS	.	G		11,3975		0,11,1982	34.0	40.0	38.0		2070	3.6	0.7	17	dbSNP_134	38	48,8244		0,48,4098	no	coding-synonymous	PELP1	NM_014389.2		0,59,6080	AA,AG,GG		0.5789,0.276,0.4805		690/1131	4576216	59,12219	1993	4146	6139	SO:0001819	synonymous_variant	27043	exon16			TGCTGAGGGCATG		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2070C>T	17.37:g.4576216G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	146	41	0.280822	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			G|0.995;A|0.005	0.005	strong		0.687	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
SYNE1	23345	hgsc.bcm.edu	37	6	152675854	152675854	+	Silent	SNP	A	A	G	rs9397102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152675854A>G	ENST00000367255.5	-	67	11467	c.10866T>C	c.(10864-10866)agT>agC	p.S3622S	SYNE1_ENST00000341594.5_Silent_p.S3593S|SYNE1_ENST00000423061.1_Intron|SYNE1_ENST00000448038.1_Intron|SYNE1_ENST00000265368.4_Silent_p.S3622S	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3622					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGGTCCTGGGACTAACTTTCT	0.423										HNSCC(10;0.0054)			A|||	2846	0.568291	0.5136	0.6196	5008	,	,		19686	0.6171		0.6014	False		,,,				2504	0.5215				p.S3622S		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T10866C						PASS	.	A	,	2285,2121	600.2+/-389.4	604,1077,522	262.0	229.0	240.0		,10866	-2.1	0.0	6	dbSNP_119	240	5274,3326	644.5+/-400.1	1645,1984,671	no	intron,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	2249,3061,1193	GG,GA,AA		38.6744,48.1389,41.8807	,	,3622/8798	152675854	7559,5447	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon67			CCTGGGACTAACT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.10866T>C	6.37:g.152675854A>G		Somatic	295	1	0.00338983		WXS	Illumina HiSeq	Phase_I	269	120	0.446097	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			A|0.411;G|0.589	0.589	strong		0.423	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
RARS	5917	hgsc.bcm.edu	37	5	167919825	167919825	+	Silent	SNP	G	G	A	rs2305728	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:167919825G>A	ENST00000231572.3	+	3	396	c.342G>A	c.(340-342)caG>caA	p.Q114Q	RARS_ENST00000538719.1_5'UTR	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	114					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		GGGACTATCAGTGTAATAGTG	0.388													G|||	372	0.0742812	0.0091	0.0908	5008	,	,		17943	0.0645		0.1799	False		,,,				2504	0.0521				p.Q114Q		Atlas-SNP	.											.	RARS	58	.	0			c.G342A						PASS	.	G		161,4245	108.6+/-147.0	2,157,2044	143.0	146.0	145.0		342	0.8	1.0	5	dbSNP_100	145	1626,6974	300.6+/-305.0	162,1302,2836	no	coding-synonymous	RARS	NM_002887.3		164,1459,4880	AA,AG,GG		18.907,3.6541,13.7398		114/661	167919825	1787,11219	2203	4300	6503	SO:0001819	synonymous_variant	5917	exon3			CTATCAGTGTAAT	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.342G>A	5.37:g.167919825G>A		Somatic	412	0	0		WXS	Illumina HiSeq	Phase_I	414	413	0.997585	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	37	CCDS4367.1																																																																																			G|0.881;A|0.119	0.119	strong		0.388	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
DOCK2	1794	hgsc.bcm.edu	37	5	169127097	169127097	+	Silent	SNP	C	C	A	rs2112703	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:169127097C>A	ENST00000256935.8	+	13	1292	c.1212C>A	c.(1210-1212)acC>acA	p.T404T		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	404					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGGACAGGACCACCGTGGTGG	0.567													C|||	609	0.121605	0.0363	0.0893	5008	,	,		17531	0.122		0.2048	False		,,,				2504	0.1738				p.T404T		Atlas-SNP	.											.	DOCK2	389	.	0			c.C1212A						PASS	.	C		323,4083	171.9+/-202.1	18,287,1898	160.0	146.0	151.0		1212	1.6	1.0	5	dbSNP_96	151	1783,6817	322.8+/-315.7	197,1389,2714	no	coding-synonymous	DOCK2	NM_004946.2		215,1676,4612	AA,AC,CC		20.7326,7.3309,16.1925		404/1831	169127097	2106,10900	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon13			CAGGACCACCGTG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.1212C>A	5.37:g.169127097C>A		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			C|0.852;A|0.148	0.148	strong		0.567	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
RNF168	165918	hgsc.bcm.edu	37	3	196199204	196199204	+	Missense_Mutation	SNP	G	G	T	rs3796129	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:196199204G>T	ENST00000318037.3	-	6	1796	c.1202C>A	c.(1201-1203)cCa>cAa	p.P401Q	CTD-2002J20.1_ENST00000610042.1_RNA	NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	401			P -> Q (in dbSNP:rs3796129). {ECO:0000269|PubMed:14702039}.		cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		AGAAAAGCATGGATCCTTGAC	0.393													G|||	2015	0.402356	0.2368	0.4798	5008	,	,		21262	0.1756		0.6044	False		,,,				2504	0.5971				p.P401Q		Atlas-SNP	.											.	RNF168	49	.	0			c.C1202A						PASS	.	G	GLN/PRO	1373,3033	453.2+/-350.3	224,925,1054	125.0	121.0	123.0		1202	4.3	0.0	3	dbSNP_107	123	5354,3246	649.6+/-400.6	1657,2040,603	yes	missense	RNF168	NM_152617.3	76	1881,2965,1657	TT,TG,GG		37.7442,31.1621,48.2777	benign	401/572	196199204	6727,6279	2203	4300	6503	SO:0001583	missense	165918	exon6			AAGCATGGATCCT	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"""RING-type (C3HC4) zinc fingers"""	26661	protein-coding gene	gene with protein product		612688	"""ring finger protein 168"""			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.1202C>A	3.37:g.196199204G>T	ENSP00000320898:p.Pro401Gln	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_152617	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	37	CCDS3317.1	875	0.40064102564102566	128	0.2601626016260163	181	0.5	106	0.1853146853146853	460	0.6068601583113457	G	8.256	0.810125	0.16537	0.311621	0.622558	ENSG00000163961	ENST00000318037	T	0.07567	3.18	6.08	4.29	0.51040	.	0.539087	0.18523	N	0.138717	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	P	0.43169	0.8	B	0.36030	0.216	T	0.16129	-1.0413	9	0.49607	T	0.09	-3.7596	8.5913	0.33688	0.2483:0.0:0.7517:0.0	rs3796129;rs52828201;rs57224299;rs3796129	401	Q8IYW5	RN168_HUMAN	Q	401	ENSP00000320898:P401Q	ENSP00000320898:P401Q	P	-	2	0	RNF168	197683601	0.041000	0.20044	0.005000	0.12908	0.118000	0.20060	2.318000	0.43779	1.586000	0.49944	0.591000	0.81541	CCA	G|0.546;T|0.454	0.454	strong		0.393	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617	
TFE3	7030	hgsc.bcm.edu	37	X	48888074	48888074	+	Silent	SNP	T	T	C	rs3027472|rs199492429	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:48888074T>C	ENST00000315869.7	-	10	1582	c.1323A>G	c.(1321-1323)gtA>gtG	p.V441V	TFE3_ENST00000487451.1_5'Flank	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	441					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GAGTGGGAGGTACTGGCAGGC	0.582			T	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""	"""papillary renal, alveolar soft part sarcoma, renal"""								T|||	873	0.231258	0.0204	0.2363	3775	,	,		11253	0.0546		0.4185	False		,,,				2504	0.2106				p.V441V		Atlas-SNP	.		Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	TFE3	93	.	0			c.A1323G						PASS	.	T		306,3528		12,230,52,1390,518	47.0	43.0	44.0		1323	-5.1	0.4	X	dbSNP_102	44	3549,3179		693,1178,985,557,887	no	coding-synonymous	TFE3	NM_006521.4		705,1408,1037,1947,1405	CC,CT,C,TT,T		47.2503,7.9812,36.4988		441/576	48888074	3855,6707	2202	4300	6502	SO:0001819	synonymous_variant	7030	exon10			GGGAGGTACTGGC	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"""Basic helix-loop-helix proteins"""	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.1323A>G	X.37:g.48888074T>C		Somatic	299	1	0.00334448		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_006521	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Silent	SNP	ENST00000315869.7	37	CCDS14315.3																																																																																			T|0.674;C|0.326	0.326	strong		0.582	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521	
GGT6	124975	hgsc.bcm.edu	37	17	4463699	4463699	+	Missense_Mutation	SNP	G	G	A	rs7216284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4463699G>A	ENST00000574154.1	-	1	414	c.118C>T	c.(118-120)Cgg>Tgg	p.R40W	GGT6_ENST00000301395.3_Missense_Mutation_p.R40W|GGT6_ENST00000573591.1_5'Flank|GGT6_ENST00000381550.3_Missense_Mutation_p.R40W			Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6	40			R -> W (in dbSNP:rs7216284). {ECO:0000269|PubMed:14702039}.		glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			endometrium(2)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TGGTGCCTCCGGGGGTTTAGA	0.627													A|||	893	0.178315	0.0363	0.1816	5008	,	,		16068	0.1577		0.2674	False		,,,				2504	0.2975				p.R40W		Atlas-SNP	.											.	GGT6	22	.	0			c.C118T						PASS	.	A	TRP/ARG,TRP/ARG	316,4090	797.7+/-415.4	15,286,1902	93.0	87.0	89.0		118,118	0.7	0.0	17	dbSNP_116	89	2321,6279	704.6+/-405.4	309,1703,2288	yes	missense,missense	GGT6	NM_001122890.1,NM_153338.2	101,101	324,1989,4190	AA,AG,GG		26.9884,7.172,20.2753	benign,benign	40/494,40/462	4463699	2637,10369	2203	4300	6503	SO:0001583	missense	124975	exon1			GCCTCCGGGGGTT	AK074646	CCDS11047.1, CCDS45582.1, CCDS73942.1	17p13.2	2014-08-12	2008-03-10		ENSG00000167741	ENSG00000167741		"""Gamma-glutamyltransferases"""	26891	protein-coding gene	gene with protein product		612341	"""gamma-glutamyltransferase 6 homolog (rat)"""			18357469	Standard	NM_001122890		Approved	FLJ90165	uc002fyd.4	Q6P531	OTTHUMG00000177827	ENST00000574154.1:c.118C>T	17.37:g.4463699G>A	ENSP00000458307:p.Arg40Trp	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_001122890	B4DUH4|Q8NCM0	Missense_Mutation	SNP	ENST00000574154.1	37	CCDS45582.1	393	0.17994505494505494	22	0.044715447154471545	69	0.19060773480662985	94	0.16433566433566432	208	0.27440633245382584	A	11.22	1.573159	0.28092	0.07172	0.269884	ENSG00000167741	ENST00000381550;ENST00000301395	T;T	0.26223	2.36;1.75	4.18	0.734	0.18294	.	0.790748	0.10779	N	0.635030	T	0.00012	0.0000	N	0.04880	-0.145	0.58432	P	5.000000000032756E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41395	-0.9511	9	0.52906	T	0.07	-0.6547	3.4582	0.07523	0.4348:0.0:0.3375:0.2277	rs7216284;rs52804472;rs57585258;rs7216284	40;40;40	B4DKN3;Q6P531;Q6P531-2	.;GGT6_HUMAN;.	W	40	ENSP00000370962:R40W;ENSP00000301395:R40W	ENSP00000301395:R40W	R	-	1	2	GGT6	4410448	0.000000	0.05858	0.048000	0.18961	0.397000	0.30659	-0.374000	0.07484	-0.149000	0.11215	-0.254000	0.11334	CGG	G|0.813;A|0.187	0.187	strong		0.627	GGT6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439122.1	NM_153338	
LRRC55	219527	hgsc.bcm.edu	37	11	56949691	56949691	+	Missense_Mutation	SNP	G	G	A	rs12364102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56949691G>A	ENST00000497933.1	+	1	471	c.324G>A	c.(322-324)atG>atA	p.M108I		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	78					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						ACCTGCCAATGGACACCCGAA	0.612													G|||	333	0.0664936	0.0144	0.0879	5008	,	,		18285	0.0714		0.1113	False		,,,				2504	0.0706				p.M108I		Atlas-SNP	.											.	LRRC55	52	.	0			c.G324A						PASS	.	G	ILE/MET	136,4266	97.1+/-135.8	2,132,2067	59.0	63.0	62.0		324	4.9	0.9	11	dbSNP_120	62	1052,7540	222.2+/-259.3	75,902,3319	yes	missense	LRRC55	NM_001005210.2	10	77,1034,5386	AA,AG,GG		12.2439,3.0895,9.1427	benign	108/342	56949691	1188,11806	2201	4296	6497	SO:0001583	missense	219527	exon1			GCCAATGGACACC		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.324G>A	11.37:g.56949691G>A	ENSP00000419542:p.Met108Ile	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_001005210	A7E2U7|B2RN81	Missense_Mutation	SNP	ENST00000497933.1	37	CCDS31539.1	162	0.07417582417582418	11	0.022357723577235773	35	0.09668508287292818	42	0.07342657342657342	74	0.09762532981530343	G	15.67	2.901736	0.52227	0.030895	0.122439	ENSG00000183908	ENST00000497933	T	0.41065	1.01	5.8	4.89	0.63831	Leucine-rich repeat-containing N-terminal (1);	0.575233	0.18019	N	0.154310	T	0.00271	0.0008	N	0.01668	-0.77	0.23386	P	0.99778324	B	0.09022	0.002	B	0.09377	0.004	T	0.04053	-1.0981	9	0.46703	T	0.11	.	13.5959	0.61988	0.0752:0.0:0.9248:0.0	rs12364102;rs52808242;rs56765576;rs12364102	78	Q6ZSA7	LRC55_HUMAN	I	108	ENSP00000419542:M108I	ENSP00000419542:M108I	M	+	3	0	LRRC55	56706267	1.000000	0.71417	0.894000	0.35097	0.759000	0.43091	4.049000	0.57397	1.455000	0.47813	0.655000	0.94253	ATG	G|0.920;A|0.080	0.080	strong		0.612	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
LY6G5B	58496	hgsc.bcm.edu	37	6	31639757	31639757	+	Missense_Mutation	SNP	G	G	A	rs805267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31639757G>A	ENST00000375864.4	+	3	1088	c.304G>A	c.(304-306)Gat>Aat	p.D102N	LY6G5B_ENST00000409525.1_Missense_Mutation_p.D47N|CSNK2B-LY6G5B-1181_ENST00000375880.2_3'UTR	NM_021221.2	NP_067044.2	Q8NDX9	LY65B_HUMAN	lymphocyte antigen 6 complex, locus G5B	102	UPAR/Ly6.		D -> N (in dbSNP:rs805267).			extracellular region (GO:0005576)				lung(4)	4						CTGTCAGTACGATTATTGCAA	0.557													G|||	596	0.11901	0.2239	0.085	5008	,	,		19450	0.1478		0.0348	False		,,,				2504	0.0583				p.D102N		Atlas-SNP	.											.	LY6G5B	8	.	0			c.G304A						PASS	.	G	ASN/ASP	590,2430		64,462,984	117.0	111.0	114.0		304	2.5	0.7	6	dbSNP_86	114	170,5246		2,166,2540	yes	missense	LY6G5B	NM_021221.2	23	66,628,3524	AA,AG,GG		3.1388,19.5364,9.009	probably-damaging	102/202	31639757	760,7676	1510	2708	4218	SO:0001583	missense	58496	exon3			CAGTACGATTATT	AF129756	CCDS34400.1	6p21.3	2008-08-01	2002-07-29	2002-08-01	ENSG00000240053	ENSG00000240053			13931	protein-coding gene	gene with protein product		610433	"""chromosome 6 open reading frame 19"""	C6orf19		8812450, 12079290, 17008713	Standard	NM_021221		Approved	G5b		Q8NDX9	OTTHUMG00000031227	ENST00000375864.4:c.304G>A	6.37:g.31639757G>A	ENSP00000365024:p.Asp102Asn	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	156	83	0.532051	NM_021221	B0UXB2|B0UZ65|B0UZP8|B7ZCA3|Q5SQ62|Q5SST3|Q9UKT0|Q9UMQ0	Missense_Mutation	SNP	ENST00000375864.4	37	CCDS34400.1	213	0.09752747252747253	98	0.1991869918699187	26	0.0718232044198895	66	0.11538461538461539	23	0.030343007915567283	G	11.92	1.783074	0.31593	0.195364	0.031388	ENSG00000240053	ENST00000409691;ENST00000375864;ENST00000409525	T;T	0.74106	-0.81;1.28	4.31	2.52	0.30459	.	.	.	.	.	T	0.40448	0.1117	L	0.32530	0.975	.	.	.	B	0.31989	0.35	B	0.23275	0.045	T	0.11155	-1.0599	8	0.56958	D	0.05	-6.6609	6.9429	0.24502	0.1957:0.0:0.8043:0.0	rs805267;rs6923420;rs60104204;rs805267	102	Q8NDX9	LY65B_HUMAN	N	99;102;47	ENSP00000365024:D102N;ENSP00000386365:D47N	ENSP00000365024:D102N	D	+	1	0	LY6G5B	31747736	0.686000	0.27661	0.727000	0.30756	0.596000	0.36781	0.748000	0.26305	0.579000	0.29504	0.462000	0.41574	GAT	G|0.905;A|0.095	0.095	strong		0.557	LY6G5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000124389.4		
SYCE1	93426	hgsc.bcm.edu	37	10	135368906	135368906	+	Silent	SNP	G	G	C	rs138177213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:135368906G>C	ENST00000343131.5	-	12	971	c.867C>G	c.(865-867)gtC>gtG	p.V289V	SPRN_ENST00000541506.1_Intron|SYCE1_ENST00000368517.3_Silent_p.V253V|SYCE1_ENST00000432597.2_Silent_p.V253V	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	289	Gln-rich.				synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		CTTGGGCAGGGACTTGCATTC	0.567													G|||	13	0.00259585	0.0	0.0014	5008	,	,		19664	0.0		0.005	False		,,,				2504	0.0072				p.V289V		Atlas-SNP	.											.	SYCE1	81	.	0			c.C867G						PASS	.	G	,,	4,4402	8.1+/-20.4	0,4,2199	133.0	117.0	122.0		867,867,759	0.0	0.0	10	dbSNP_134	122	51,8549	32.3+/-84.9	0,51,4249	no	coding-synonymous,coding-synonymous,coding-synonymous	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	,,	0,55,6448	CC,CG,GG		0.593,0.0908,0.4229	,,	289/319,289/352,253/283	135368906	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	93426	exon12			GGCAGGGACTTGC	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.867C>G	10.37:g.135368906G>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	155	74	0.477419	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Silent	SNP	ENST00000343131.5	37	CCDS44501.1																																																																																			G|0.997;C|0.003	0.003	strong		0.567	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
LAMP3	27074	hgsc.bcm.edu	37	3	182853670	182853670	+	Missense_Mutation	SNP	T	T	C	rs482912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:182853670T>C	ENST00000265598.3	-	5	1207	c.952A>G	c.(952-954)Att>Gtt	p.I318V	LAMP3_ENST00000466939.1_Missense_Mutation_p.I294V	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	318			I -> V (in dbSNP:rs482912). {ECO:0000269|PubMed:9721848, ECO:0000269|Ref.3}.		cell proliferation (GO:0008283)|immune system process (GO:0002376)	alveolar lamellar body membrane (GO:0097233)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			CCTTGGTAAATTGTCTCTGAA	0.522													T|||	2486	0.496406	0.2224	0.5029	5008	,	,		18728	0.4712		0.7247	False		,,,				2504	0.6534				p.I318V		Atlas-SNP	.											.	LAMP3	48	.	0			c.A952G						PASS	.	T	VAL/ILE	1327,3079	445.1+/-347.6	197,933,1073	201.0	197.0	199.0		952	-1.4	0.0	3	dbSNP_83	199	6366,2234	709.8+/-405.7	2366,1634,300	yes	missense	LAMP3	NM_014398.3	29	2563,2567,1373	CC,CT,TT		25.9767,30.118,40.8504	benign	318/417	182853670	7693,5313	2203	4300	6503	SO:0001583	missense	27074	exon5			GGTAAATTGTCTC	AB013924	CCDS3242.1	3q26.3-q27	2011-11-24			ENSG00000078081	ENSG00000078081		"""CD molecules"""	14582	protein-coding gene	gene with protein product		605883				9721848	Standard	NM_014398		Approved	LAMP, TSC403, DC-LAMP, DCLAMP, CD208	uc003flh.4	Q9UQV4	OTTHUMG00000158387	ENST00000265598.3:c.952A>G	3.37:g.182853670T>C	ENSP00000265598:p.Ile318Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_014398	D3DNS4|O94781|Q8NEC8	Missense_Mutation	SNP	ENST00000265598.3	37	CCDS3242.1	1151	0.527014652014652	135	0.27439024390243905	190	0.5248618784530387	285	0.4982517482517482	541	0.7137203166226913	T	0.129	-1.116168	0.01799	0.30118	0.740233	ENSG00000078081	ENST00000265598;ENST00000466939	T;T	0.33438	1.41;1.41	5.47	-1.37	0.09056	.	1.391350	0.04601	N	0.398459	T	0.00012	0.0000	N	0.01410	-0.885	0.29514	P	0.853963	B	0.02656	0.0	B	0.04013	0.001	T	0.38243	-0.9670	9	0.02654	T	1	0.4151	9.4867	0.38933	0.0:0.5767:0.0:0.4233	rs482912;rs3736552;rs17856962;rs57467289;rs482912	318	Q9UQV4	LAMP3_HUMAN	V	318;294	ENSP00000265598:I318V;ENSP00000418912:I294V	ENSP00000265598:I318V	I	-	1	0	LAMP3	184336364	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.439000	0.06897	-0.082000	0.12640	-0.274000	0.10170	ATT	T|0.458;C|0.542	0.542	strong		0.522	LAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350863.1		
CCDC168	643677	hgsc.bcm.edu	37	13	103384824	103384824	+	Missense_Mutation	SNP	G	G	A	rs9300756	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:103384824G>A	ENST00000322527.2	-	1	4335	c.4336C>T	c.(4336-4338)Cgt>Tgt	p.R1446C		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1446			R -> C (in dbSNP:rs9300756).														TGATCTTTACGTTTGGGAGAA	0.313													g|||	2938	0.586661	0.3654	0.6153	5008	,	,		19757	0.8442		0.6123	False		,,,				2504	0.5736				p.R6075C		Atlas-SNP	.											.	.	.	.	0			c.C18223T						PASS	.	G	CYS/ARG	562,822		118,326,248	137.0	100.0	111.0		18223	0.0	0.0	13	dbSNP_119	111	1908,1272		574,760,256	yes	missense	CCDC168	NM_001146197.1	180	692,1086,504	AA,AG,GG		40.0,40.6069,45.8808	benign	6075/7082	103384824	2470,2094	692	1590	2282	SO:0001583	missense	643677	exon4			CTTTACGTTTGGG		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.4336C>T	13.37:g.103384824G>A	ENSP00000320232:p.Arg1446Cys	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		1338	0.6126373626373627	186	0.3780487804878049	210	0.580110497237569	473	0.8269230769230769	469	0.6187335092348285	g	3.276	-0.148121	0.06627	0.406069	0.6	ENSG00000175820	ENST00000322527	T	0.03689	3.84	2.62	0.0102	0.14082	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02868	-1.1100	8	0.38643	T	0.18	.	4.9317	0.13921	0.7117:0.0:0.2883:0.0	rs9300756;rs52830042;rs59881186;rs9300756	1446	Q8NDH2	CC168_HUMAN	C	1446	ENSP00000320232:R1446C	ENSP00000320232:R1446C	R	-	1	0	CCDC168	102182825	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.080000	0.14802	0.010000	0.14839	-0.416000	0.06073	CGT	G|0.321;A|0.679	0.679	strong		0.313	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
HEATR2	54919	hgsc.bcm.edu	37	7	810219	810219	+	Missense_Mutation	SNP	T	T	C	rs4720951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:810219T>C	ENST00000297440.6	+	9	1915	c.1895T>C	c.(1894-1896)gTg>gCg	p.V632A	HEATR2_ENST00000403952.3_Missense_Mutation_p.V57A|HEATR2_ENST00000313147.5_Missense_Mutation_p.V632A	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	632			V -> A (in dbSNP:rs4720951).			cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		CTGTCCACCGTGCTGCTCAGA	0.682													T|||	1960	0.391374	0.3578	0.4395	5008	,	,		15713	0.3532		0.4632	False		,,,				2504	0.3681				p.V632A		Atlas-SNP	.											HEATR2,colon,carcinoma,-1,1	HEATR2	62	1	0			c.T1895C						PASS	.		ALA/VAL	1569,2837	489.2+/-361.4	285,999,919	75.0	61.0	66.0		1895	3.5	0.6	7	dbSNP_111	66	4049,4551	556.9+/-386.9	945,2159,1196	yes	missense	HEATR2	NM_017802.3	64	1230,3158,2115	CC,CT,TT		47.0814,35.6105,43.1954	benign	632/856	810219	5618,7388	2203	4300	6503	SO:0001583	missense	54919	exon9			CCACCGTGCTGCT	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.1895T>C	7.37:g.810219T>C	ENSP00000297440:p.Val632Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_017802	Q69YL1|Q96FI9|Q9NX75	Missense_Mutation	SNP	ENST00000297440.6	37	CCDS34580.1	915	0.41895604395604397	215	0.4369918699186992	157	0.43370165745856354	203	0.3548951048951049	340	0.44854881266490765	T	9.151	1.016258	0.19355	0.356105	0.470814	ENSG00000164818	ENST00000297440;ENST00000313147;ENST00000537862;ENST00000403952	T;T;T	0.67171	-0.25;-0.25;-0.25	4.7	3.55	0.40652	Armadillo-like helical (1);Armadillo-type fold (1);	0.733999	0.12874	N	0.432019	T	0.00012	0.0000	L	0.43152	1.355	0.39575	P	0.030664000000000025	B;B;B	0.15719	0.014;0.002;0.006	B;B;B	0.09377	0.003;0.003;0.004	T	0.37478	-0.9704	9	0.49607	T	0.09	-7.7725	9.7282	0.40344	0.0:0.0837:0.0:0.9163	rs4720951;rs11547678;rs17293410;rs4720951	632;57;378	Q86Y56;E9PGY2;F5H8D4	HEAT2_HUMAN;.;.	A	632;632;378;57	ENSP00000297440:V632A;ENSP00000321451:V632A;ENSP00000384884:V57A	ENSP00000297440:V632A	V	+	2	0	HEATR2	776745	0.999000	0.42202	0.590000	0.28732	0.025000	0.11179	3.805000	0.55575	0.662000	0.31006	0.533000	0.62120	GTG	T|0.578;C|0.422	0.422	strong		0.682	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802	
SEC23B	10483	hgsc.bcm.edu	37	20	18513350	18513350	+	Missense_Mutation	SNP	G	G	A	rs41309927	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:18513350G>A	ENST00000336714.3	+	11	1708	c.1276G>A	c.(1276-1278)Gta>Ata	p.V426I	SEC23B_ENST00000377465.1_Missense_Mutation_p.V426I|SEC23B_ENST00000262544.2_Missense_Mutation_p.V426I|SEC23B_ENST00000377475.3_Missense_Mutation_p.V426I	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	426			V -> I (in dbSNP:rs41309927). {ECO:0000269|PubMed:19561605}.		ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						TGGTCCATGCGTATCTCTGAA	0.458													G|||	83	0.0165735	0.0008	0.0231	5008	,	,		21921	0.0		0.0487	False		,,,				2504	0.0174				p.V426I		Atlas-SNP	.											.	SEC23B	70	.	0			c.G1276A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	39,4367	41.6+/-74.8	0,39,2164	141.0	134.0	136.0		1276,1222,1276,1276,1276	2.8	0.8	20	dbSNP_127	136	526,8074	146.8+/-202.3	13,500,3787	yes	missense,missense,missense,missense,missense	SEC23B	NM_001172745.1,NM_001172746.1,NM_006363.4,NM_032985.4,NM_032986.3	29,29,29,29,29	13,539,5951	AA,AG,GG		6.1163,0.8852,4.3441	benign,benign,benign,benign,benign	426/768,408/750,426/768,426/768,426/768	18513350	565,12441	2203	4300	6503	SO:0001583	missense	10483	exon11			CCATGCGTATCTC	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"""Sec23 (S. cerevisiae) homolog B"", ""congenital dyserythropoietic anemia, type II"""	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.1276G>A	20.37:g.18513350G>A	ENSP00000338844:p.Val426Ile	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	173	90	0.520231	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	37	CCDS13137.1	48	0.02197802197802198	0	0.0	8	0.022099447513812154	0	0.0	40	0.052770448548812667	G	12.02	1.812485	0.32053	0.008852	0.061163	ENSG00000101310	ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89	4.75	2.81	0.32909	Sec23/Sec24 beta-sandwich (1);	0.116916	0.56097	N	0.000021	T	0.11750	0.0286	N	0.17594	0.5	0.58432	D	0.999998	B;B	0.06786	0.001;0.0	B;B	0.08055	0.002;0.003	T	0.13335	-1.0513	10	0.25751	T	0.34	-12.3351	9.7549	0.40498	0.2344:0.0:0.7656:0.0	rs41309927;rs62216394	408;426	B4DJW8;Q15437	.;SC23B_HUMAN	I	426	ENSP00000338844:V426I;ENSP00000262544:V426I;ENSP00000366695:V426I;ENSP00000366685:V426I	ENSP00000262544:V426I	V	+	1	0	SEC23B	18461350	0.998000	0.40836	0.805000	0.32314	0.994000	0.84299	2.773000	0.47686	1.362000	0.46000	0.655000	0.94253	GTA	G|0.962;A|0.038	0.038	strong		0.458	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5		
OR13C2	392376	hgsc.bcm.edu	37	9	107367431	107367431	+	Missense_Mutation	SNP	A	A	T	rs1851716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107367431A>T	ENST00000542196.1	-	1	520	c.478T>A	c.(478-480)Tca>Aca	p.S160T		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	160			S -> T (in dbSNP:rs1851716).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						ACAAACACTGATTGTACTGCA	0.458																																					p.S160T		Atlas-SNP	.											.	OR13C2	46	.	0			c.T478A						PASS	.						108.0	150.0	136.0					9																	107367431		2201	4300	6501	SO:0001583	missense	392376	exon1			ACACTGATTGTAC		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.478T>A	9.37:g.107367431A>T	ENSP00000438815:p.Ser160Thr	Somatic	449	0	0		WXS	Illumina HiSeq	Phase_I	378	130	0.343915	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	710	0.3250915750915751	230	0.46747967479674796	73	0.20165745856353592	303	0.5297202797202797	104	0.13720316622691292	T	0.025	-1.379759	0.01204	.	.	ENSG00000257019	ENST00000542196	T	0.00017	9.09	3.72	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37955	N	0.001874	T	0.00012	0.0000	N	0.00230	-1.795	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.18999	-1.0319	9	0.02654	T	1	.	7.6109	0.28129	0.1903:0.0:0.0:0.8097	rs1851716;rs59641728	160	Q8NGS9	O13C2_HUMAN	T	160	ENSP00000438815:S160T	ENSP00000438815:S160T	S	-	1	0	OR13C2	106407252	0.000000	0.05858	0.008000	0.14137	0.470000	0.32858	0.065000	0.14466	0.509000	0.28195	-0.527000	0.04329	TCA	A|0.158;T|0.842	0.842	strong		0.458	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
MYLK3	91807	hgsc.bcm.edu	37	16	46773999	46773999	+	Missense_Mutation	SNP	C	C	A	rs28407821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:46773999C>A	ENST00000394809.4	-	2	653	c.538G>T	c.(538-540)Gtg>Ttg	p.V180L	MYLK3_ENST00000536476.1_5'UTR	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	180			V -> L (in dbSNP:rs28407821). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)	p.V180L(1)|p.V231L(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				TCAGACTGCACCCCACTGGTG	0.453													C|||	2334	0.466054	0.1203	0.464	5008	,	,		18437	0.5536		0.5984	False		,,,				2504	0.7086				p.V180L		Atlas-SNP	.											MYLK3,NS,carcinoma,0,2	MYLK3	82	2	2	Substitution - Missense(2)	stomach(2)	c.G538T						PASS	.	C	LEU/VAL	875,3531	341.5+/-306.7	99,677,1427	202.0	176.0	185.0		538	2.6	0.1	16	dbSNP_125	185	5060,3540	631.9+/-398.5	1498,2064,738	yes	missense	MYLK3	NM_182493.2	32	1597,2741,2165	AA,AC,CC		41.1628,19.8593,45.6328	possibly-damaging	180/820	46773999	5935,7071	2203	4300	6503	SO:0001583	missense	91807	exon2			ACTGCACCCCACT	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"""MLC kinase"""	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.538G>T	16.37:g.46773999C>A	ENSP00000378288:p.Val180Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	153	77	0.503268	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	1020	0.46703296703296704	56	0.11382113821138211	179	0.494475138121547	316	0.5524475524475524	469	0.6187335092348285	C	12.44	1.938748	0.34189	0.198593	0.588372	ENSG00000140795	ENST00000394809	T	0.72505	-0.66	5.58	2.57	0.30868	.	0.601209	0.12878	N	0.431687	T	0.00012	0.0000	L	0.40543	1.245	0.36580	P	0.12650499999999998	B	0.09022	0.002	B	0.04013	0.001	T	0.44922	-0.9296	9	0.31617	T	0.26	.	5.3239	0.15895	0.1413:0.5918:0.0:0.2669	rs28407821;rs59283497;rs28407821	180	Q32MK0	MYLK3_HUMAN	L	180	ENSP00000378288:V180L	ENSP00000378288:V180L	V	-	1	0	MYLK3	45331500	0.026000	0.19158	0.050000	0.19076	0.007000	0.05969	1.065000	0.30592	0.400000	0.25396	-0.158000	0.13435	GTG	C|0.544;A|0.456	0.456	strong		0.453	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493	
CHST10	9486	hgsc.bcm.edu	37	2	101010082	101010082	+	Silent	SNP	G	G	C	rs3748930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:101010082G>C	ENST00000264249.3	-	7	1081	c.696C>G	c.(694-696)acC>acG	p.T232T	CHST10_ENST00000409701.1_Silent_p.T232T|CHST10_ENST00000542617.1_Silent_p.T280T	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	232					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						GGATCCCCCGGGTCTCTGTCC	0.507													G|||	3034	0.605831	0.6263	0.5778	5008	,	,		18067	0.8065		0.499	False		,,,				2504	0.501				p.T232T		Atlas-SNP	.											.	CHST10	42	.	0			c.C696G						PASS	.	G		2762,1644	659.5+/-400.6	862,1038,303	194.0	188.0	190.0		696	5.1	1.0	2	dbSNP_107	190	4260,4340	576.1+/-390.3	1073,2114,1113	no	coding-synonymous	CHST10	NM_004854.4		1935,3152,1416	CC,CG,GG		49.5349,37.3128,46.0095		232/357	101010082	7022,5984	2203	4300	6503	SO:0001819	synonymous_variant	9486	exon7			CCCCCGGGTCTCT	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"""Sulfotransferases, membrane-bound"""	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.696C>G	2.37:g.101010082G>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_004854	Q53T18	Silent	SNP	ENST00000264249.3	37	CCDS2047.1																																																																																			G|0.426;C|0.574	0.574	strong		0.507	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854	
ELN	2006	hgsc.bcm.edu	37	7	73474825	73474825	+	Missense_Mutation	SNP	G	G	C	rs17855988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73474825G>C	ENST00000252034.7	+	25	2140	c.1741G>C	c.(1741-1743)Ggg>Cgg	p.G581R	ELN_ENST00000380575.4_Missense_Mutation_p.G552R|ELN_ENST00000380562.4_Missense_Mutation_p.G587R|ELN_ENST00000414324.1_Missense_Mutation_p.G557R|ELN_ENST00000320492.7_Missense_Mutation_p.G500R|ELN_ENST00000380584.4_Missense_Mutation_p.G533R|ELN_ENST00000429192.1_Missense_Mutation_p.G567R|ELN_ENST00000458204.1_Missense_Mutation_p.G571R|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000380576.5_Missense_Mutation_p.G562R|ELN_ENST00000357036.5_Missense_Mutation_p.G586R|ELN_ENST00000445912.1_Missense_Mutation_p.G581R|ELN_ENST00000358929.4_Missense_Mutation_p.G616R|ELN_ENST00000320399.6_Missense_Mutation_p.G581R|ELN_ENST00000380553.4_Missense_Mutation_p.G445R	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				TCCTGGCTTCGGGGCAGGTGC	0.622			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""						G|||	201	0.0401358	0.0023	0.0778	5008	,	,		18732	0.0		0.0915	False		,,,				2504	0.0532				p.G586R		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.G1756C						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	87,4319	74.1+/-112.3	2,83,2118	223.0	227.0	226.0		1741,1654,1699,1756,1684	3.5	0.7	7	dbSNP_123	226	856,7744	193.8+/-239.4	48,760,3492	yes	missense,missense,missense,missense,missense	ELN	NM_000501.2,NM_001081752.1,NM_001081753.1,NM_001081754.1,NM_001081755.1	125,125,125,125,125	50,843,5610	CC,CG,GG		9.9535,1.9746,7.2505	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	581/725,552/678,567/693,586/712,562/706	73474825	943,12063	2203	4300	6503	SO:0001583	missense	2006	exon25			GGCTTCGGGGCAG		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1741G>C	7.37:g.73474825G>C	ENSP00000252034:p.Gly581Arg	Somatic	628	0	0		WXS	Illumina HiSeq	Phase_I	643	279	0.433904	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	37	CCDS5562.2	103	0.04716117216117216	2	0.0040650406504065045	33	0.09116022099447514	0	0.0	68	0.08970976253298153	G	14.37	2.516071	0.44763	0.019746	0.099535	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000320492;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000442462;ENST00000380553;ENST00000380576;ENST00000320399	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.46451	1.2;1.25;0.97;1.3;1.15;1.24;1.22;1.15;1.22;1.18;1.18;1.2;1.16;0.87	3.46	3.46	0.39613	.	.	.	.	.	T	0.02304	0.0071	.	.	.	0.22996	P	0.99845179	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	T	0.20273	-1.0280	7	0.17369	T	0.5	2.9464	10.6615	0.45704	0.0:0.0:1.0:0.0	rs17855988	581;500;557;571;587;552;567;586;562;445;492;533;581	E7ENM0;G5E950;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;B3KRT8;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.;.	R	581;581;616;500;557;587;552;533;571;586;567;520;445;562;581	ENSP00000389857:G581R;ENSP00000252034:G581R;ENSP00000351807:G616R;ENSP00000315607:G500R;ENSP00000392575:G557R;ENSP00000369936:G587R;ENSP00000369949:G552R;ENSP00000369958:G533R;ENSP00000403162:G571R;ENSP00000349540:G586R;ENSP00000391129:G567R;ENSP00000369926:G445R;ENSP00000369950:G562R;ENSP00000313565:G581R	ENSP00000252034:G581R	G	+	1	0	ELN	73112761	0.999000	0.42202	0.725000	0.30721	0.761000	0.43186	4.713000	0.61895	1.953000	0.56701	0.555000	0.69702	GGG	G|0.931;C|0.069	0.069	strong		0.622	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
CEL	1056	hgsc.bcm.edu	37	9	135946483	135946483	+	Missense_Mutation	SNP	C	C	T	rs200231984		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135946483C>T	ENST00000372080.4	+	11	1619	c.1603C>T	c.(1603-1605)Cgg>Tgg	p.R535W	CEL_ENST00000351304.7_Missense_Mutation_p.R466W	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	532					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CTCCATGAAGCGGAGCCTGAG	0.622																																					p.R535W		Atlas-SNP	.											.	CEL	71	.	0			c.C1603T						PASS	.	C	TRP/ARG	2,3834		0,2,1916	30.0	35.0	33.0		1603	3.2	0.0	9		33	9,8191		0,9,4091	no	missense	CEL	NM_001807.3	101	0,11,6007	TT,TC,CC		0.1098,0.0521,0.0914	probably-damaging	535/757	135946483	11,12025	1918	4100	6018	SO:0001583	missense	1056	exon11			ATGAAGCGGAGCC	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1603C>T	9.37:g.135946483C>T	ENSP00000361151:p.Arg535Trp	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.003200	0.35320	5.21E-4	0.001098	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.71341	-0.39;-0.56	5.2	3.23	0.37069	Carboxylesterase, type B (1);	0.713375	0.14331	N	0.326364	T	0.75568	0.3867	L	0.56769	1.78	0.09310	N	1	D	0.71674	0.998	P	0.56563	0.801	T	0.64740	-0.6336	10	0.72032	D	0.01	.	9.357	0.38173	0.0:0.7253:0.1927:0.082	.	532	P19835	CEL_HUMAN	W	535;466;534	ENSP00000361151:R535W;ENSP00000342217:R466W	ENSP00000304021:R534W	R	+	1	2	CEL	134936304	0.941000	0.31946	0.013000	0.15412	0.045000	0.14185	0.437000	0.21543	0.461000	0.27071	0.478000	0.44815	CGG	C|0.999;T|0.001	0.001	weak		0.622	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
HJURP	55355	hgsc.bcm.edu	37	2	234750542	234750542	+	Missense_Mutation	SNP	G	G	C	rs3732215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234750542G>C	ENST00000411486.2	-	8	949	c.884C>G	c.(883-885)tCc>tGc	p.S295C	HJURP_ENST00000434039.1_5'UTR|HJURP_ENST00000441687.1_Missense_Mutation_p.S210C|HJURP_ENST00000432087.1_Missense_Mutation_p.S241C	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	295			S -> C (in dbSNP:rs3732215). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17823411, ECO:0000269|Ref.2}.		cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		CCTCCTCCTGGAGTTCCAGTT	0.498													G|||	1751	0.349641	0.1044	0.5202	5008	,	,		22098	0.374		0.5368	False		,,,				2504	0.3425				p.S295C		Atlas-SNP	.											HJURP,NS,haematopoietic_neoplasm,+1,4	HJURP	72	4	0			c.C884G						PASS	.	G	CYS/SER	729,3677	301.3+/-286.8	64,601,1538	115.0	106.0	110.0		884	-0.8	0.0	2	dbSNP_107	110	4570,4030	596.6+/-393.6	1213,2144,943	yes	missense	HJURP	NM_018410.3	112	1277,2745,2481	CC,CG,GG		46.8605,16.5456,40.7427	benign	295/749	234750542	5299,7707	2203	4300	6503	SO:0001583	missense	55355	exon8			CTCCTGGAGTTCC		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.884C>G	2.37:g.234750542G>C	ENSP00000414109:p.Ser295Cys	Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	204	204	1	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	890	0.4075091575091575	66	0.13414634146341464	182	0.5027624309392266	220	0.38461538461538464	422	0.5567282321899736	G	8.441	0.850749	0.17034	0.165456	0.531395	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924;ENST00000454020	T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73	4.25	-0.842	0.10748	Holliday junction recognition protein, HJURP (1);	1.365940	0.04523	N	0.384964	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.002;0.003;0.005	T	0.48222	-0.9054	9	0.48119	T	0.1	-0.6475	4.9717	0.14119	0.3174:0.3919:0.2907:0.0	rs3732215;rs17849558;rs52820320;rs3732215	210;241;295	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	C	295;241;210;210;254	ENSP00000414109:S295C;ENSP00000407208:S241C;ENSP00000401944:S210C;ENSP00000393253:S210C;ENSP00000414051:S254C	ENSP00000414109:S295C	S	-	2	0	HJURP	234415281	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	0.044000	0.13992	-0.172000	0.10779	-0.126000	0.14955	TCC	G|0.593;C|0.407	0.407	strong		0.498	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
IL11	3589	hgsc.bcm.edu	37	19	55879872	55879872	+	Silent	SNP	C	C	T	rs1126757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55879872C>T	ENST00000264563.2	-	3	308	c.246G>A	c.(244-246)gcG>gcA	p.A82A	IL11_ENST00000585513.1_Silent_p.A82A|IL11_ENST00000590625.1_Silent_p.A3A	NM_000641.3	NP_000632.1	P20809	IL11_HUMAN	interleukin 11	82					B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|fat cell differentiation (GO:0045444)|megakaryocyte differentiation (GO:0030219)|negative regulation of hormone secretion (GO:0046888)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|interleukin-11 receptor binding (GO:0005142)			large_intestine(1)|skin(1)	2	Breast(117;0.191)	Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CCAGTGCCCCCGCACTCATGG	0.652													C|||	1975	0.394369	0.0234	0.4452	5008	,	,		12524	0.7093		0.4722	False		,,,				2504	0.455				p.A82A		Atlas-SNP	.											.	IL11	16	.	0			c.G246A						PASS	.	C		420,3986	198.7+/-222.5	21,378,1804	49.0	50.0	49.0	http://www.ncbi.nlm.nih.gov/pubmed?term	246	-7.7	0.0	19	dbSNP_86	49	4037,4563	538.2+/-383.4	954,2129,1217	yes	coding-synonymous	IL11	NM_000641.2		975,2507,3021	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	46.9419,9.5325,34.2688		82/200	55879872	4457,8549	2203	4300	6503	SO:0001819	synonymous_variant	3589	exon3			TGCCCCCGCACTC	X58377	CCDS12923.1, CCDS59423.1	19q13.3-q13.4	2014-01-30			ENSG00000095752	ENSG00000095752		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5966	protein-coding gene	gene with protein product	"""adipogenesis inhibitory factor"", ""oprelvekin"""	147681				1386338	Standard	NM_001267718		Approved	IL-11, AGIF	uc002qks.2	P20809		ENST00000264563.2:c.246G>A	19.37:g.55879872C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	149	86	0.577181	NM_000641	B4DQV5|Q96EB4	Silent	SNP	ENST00000264563.2	37	CCDS12923.1																																																																																			C|0.636;T|0.364	0.364	strong		0.652	IL11-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453027.1	NM_000641	
FAM186A	121006	hgsc.bcm.edu	37	12	50745827	50745827	+	Silent	SNP	C	C	A	rs12317332		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745827C>A	ENST00000327337.5	-	4	4787	c.4788G>T	c.(4786-4788)gcG>gcT	p.A1596A	FAM186A_ENST00000543111.1_Silent_p.A1596A|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1596																	CCAGTTCCTGCGCCTGCTGAG	0.677																																					p.A1596A	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,caecum,carcinoma,0,1	FAM186A	181	1	0			c.G4788T						PASS	.						5.0	6.0	6.0					12																	50745827		680	1556	2236	SO:0001819	synonymous_variant	121006	exon4			TTCCTGCGCCTGC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4788G>T	12.37:g.50745827C>A		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	258	38	0.147287	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			.	.	weak		0.677	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
ZNF211	10520	hgsc.bcm.edu	37	19	58152817	58152817	+	Silent	SNP	G	G	C	rs11880050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58152817G>C	ENST00000347302.3	+	3	1142	c.963G>C	c.(961-963)tcG>tcC	p.S321S	ZNF211_ENST00000391703.3_Silent_p.S260S|ZNF211_ENST00000420680.1_Silent_p.S325S|ZNF211_ENST00000254182.7_Silent_p.S312S|ZNF211_ENST00000544273.1_Silent_p.S333S|ZNF211_ENST00000541801.1_Silent_p.S312S|ZNF211_ENST00000299871.5_Silent_p.S386S|ZNF211_ENST00000240731.4_Silent_p.S334S	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTGGGAAATCGTTTAGTCAGA	0.413													C|||	1072	0.214058	0.2352	0.1297	5008	,	,		21915	0.3214		0.159	False		,,,				2504	0.1912				p.S386S		Atlas-SNP	.											.	ZNF211	78	.	0			c.G1158C						PASS	.	C	,	980,3426	731.2+/-410.2	117,746,1340	72.0	73.0	73.0		1002,963	-4.2	0.0	19	dbSNP_120	73	1344,7256	755.7+/-407.5	97,1150,3053	no	coding-synonymous,coding-synonymous	ZNF211	NM_006385.3,NM_198855.2	,	214,1896,4393	CC,CG,GG		15.6279,22.2424,17.8687	,	334/578,321/565	58152817	2324,10682	2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			GAAATCGTTTAGT	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.963G>C	19.37:g.58152817G>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	37	CCDS12957.1	485	0.22206959706959706	135	0.27439024390243905	52	0.143646408839779	180	0.3146853146853147	118	0.15567282321899736	C	5.103	0.204570	0.09704	0.222424	0.156279	ENSG00000121417	ENST00000407202	.	.	.	3.21	-4.21	0.03812	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19575	P	0.9999641552	.	.	.	.	.	.	T	0.41305	-0.9516	3	.	.	.	.	1.3807	0.02230	0.2524:0.1475:0.1254:0.4747	rs11880050;rs11880050	.	.	.	L	325	.	.	V	+	1	0	ZNF211	62844629	0.000000	0.05858	0.012000	0.15200	0.866000	0.49608	-4.980000	0.00163	-0.850000	0.04152	-0.977000	0.02584	GTT	G|0.804;C|0.196	0.196	strong		0.413	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
OR11H4	390442	hgsc.bcm.edu	37	14	20711852	20711852	+	Missense_Mutation	SNP	C	C	G	rs17277270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20711852C>G	ENST00000315409.2	+	1	955	c.902C>G	c.(901-903)aCt>aGt	p.T301S		NM_001004479.1	NP_001004479.1	Q8NGC9	O11H4_HUMAN	olfactory receptor, family 11, subfamily H, member 4	301			T -> S (in dbSNP:rs17277270).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	29	all_cancers(95;0.000888)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0146)		CTGATCTATACTCTTCGTAAT	0.383													c|||	346	0.0690895	0.0234	0.0922	5008	,	,		21401	0.0208		0.166	False		,,,				2504	0.0644				p.T301S		Atlas-SNP	.											.	OR11H4	63	.	0			c.C902G						PASS	.	C	SER/THR	190,4216	120.0+/-157.7	3,184,2016	105.0	105.0	105.0		902	3.8	1.0	14	dbSNP_123	105	1350,7250	263.9+/-285.3	108,1134,3058	yes	missense	OR11H4	NM_001004479.1	58	111,1318,5074	GG,GC,CC		15.6977,4.3123,11.8407	benign	301/325	20711852	1540,11466	2203	4300	6503	SO:0001583	missense	390442	exon1			TCTATACTCTTCG		CCDS32034.1	14q11.2	2013-09-24			ENSG00000176198	ENSG00000176198		"""GPCR / Class A : Olfactory receptors"""	15347	protein-coding gene	gene with protein product							Standard	NM_001004479		Approved		uc010tld.2	Q8NGC9	OTTHUMG00000170852	ENST00000315409.2:c.902C>G	14.37:g.20711852C>G	ENSP00000318997:p.Thr301Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_001004479	B2RNQ4|Q6IF07	Missense_Mutation	SNP	ENST00000315409.2	37	CCDS32034.1	189	0.08653846153846154	17	0.034552845528455285	36	0.09944751381215469	8	0.013986013986013986	128	0.16886543535620052	c	2.561	-0.301898	0.05495	0.043123	0.156977	ENSG00000176198	ENST00000315409	T	0.36157	1.27	4.7	3.81	0.43845	.	0.093112	0.46758	N	0.000270	T	0.00039	0.0001	N	0.03253	-0.375	0.41546	P	0.011454999999999993	B	0.02656	0.0	B	0.04013	0.001	T	0.14980	-1.0453	9	0.02654	T	1	-9.5805	12.8336	0.57761	0.0:0.1661:0.8338:0.0	rs17277270;rs17277270	301	Q8NGC9	O11H4_HUMAN	S	301	ENSP00000318997:T301S	ENSP00000318997:T301S	T	+	2	0	OR11H4	19781692	0.981000	0.34729	1.000000	0.80357	0.970000	0.65996	2.055000	0.41345	1.207000	0.43291	-0.128000	0.14901	ACT	C|0.896;G|0.104	0.104	strong		0.383	OR11H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410678.1		
IDO2	169355	hgsc.bcm.edu	37	8	39862881	39862881	+	Missense_Mutation	SNP	C	C	T	rs10109853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:39862881C>T	ENST00000389060.4	+	8	703	c.703C>T	c.(703-705)Cgg>Tgg	p.R235W	IDO2_ENST00000502986.2_Missense_Mutation_p.R248W|IDO2_ENST00000343295.4_Intron			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	235			R -> W (reduced catalytic activity; dbSNP:rs10109853). {ECO:0000269|PubMed:17671174}.		cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						TGCAGGCATCCGGATCTTTCT	0.403													C|||	2094	0.418131	0.326	0.4582	5008	,	,		21276	0.2877		0.5139	False		,,,				2504	0.5501				p.R248W		Atlas-SNP	.											.	IDO2	78	.	0			c.C742T						PASS	.	C	TRP/ARG	1347,2425		249,849,788	184.0	158.0	166.0		742	6.0	1.0	8	dbSNP_119	166	4162,4062		1057,2048,1007	yes	missense	IDO2	NM_194294.2	101	1306,2897,1795	TT,TC,CC		49.392,35.7105,45.9236	probably-damaging	248/421	39862881	5509,6487	1886	4112	5998	SO:0001583	missense	169355	exon9			GGCATCCGGATCT	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.703C>T	8.37:g.39862881C>T	ENSP00000426447:p.Arg235Trp	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	232	100	0.431034	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		890	0.4075091575091575	170	0.34552845528455284	166	0.4585635359116022	156	0.2727272727272727	398	0.525065963060686	C	19.83	3.900616	0.72754	0.357105	0.50608	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.68331	-0.32;-0.32	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.95574	3.69	0.23589	P	0.9973499	D	0.89917	1.0	D	0.97110	1.0	T	0.47114	-0.9142	8	.	.	.	.	15.9341	0.79688	0.1353:0.8647:0.0:0.0	rs10109853;rs58007243;rs10109853	248	F5H5G0	.	W	248;235	ENSP00000443432:R248W;ENSP00000426447:R235W	.	R	+	1	2	IDO2	39982038	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.023000	0.49666	2.861000	0.98227	0.655000	0.94253	CGG	C|0.600;T|0.400	0.400	strong		0.403	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
PKD1L1	168507	hgsc.bcm.edu	37	7	47851578	47851578	+	Missense_Mutation	SNP	G	G	A	rs140456142		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:47851578G>A	ENST00000289672.2	-	50	7468	c.7418C>T	c.(7417-7419)tCt>tTt	p.S2473F	PKD1L1_ENST00000462350.1_5'Flank|C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2473					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GAAGTGCACAGACACAGCCCT	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		19929	0.0		0.0	False		,,,				2504	0.001				p.S2473F		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C7418T						PASS	.	G	,PHE/SER	2,4404		0,2,2201	79.0	64.0	69.0		,7418	4.6	0.8	7	dbSNP_134	69	10,8588		0,10,4289	yes	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,155	0,12,6490	AA,AG,GG		0.1163,0.0454,0.0923	,probably-damaging	,2473/2850	47851578	12,12992	2203	4299	6502	SO:0001583	missense	168507	exon50			TGCACAGACACAG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7418C>T	7.37:g.47851578G>A	ENSP00000289672:p.Ser2473Phe	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	8.910	0.958416	0.18507	4.54E-4	0.001163	ENSG00000158683	ENST00000289672	T	0.61742	0.08	5.49	4.55	0.56014	Polycystin cation channel, PKD1/PKD2 (1);	0.725348	0.12568	N	0.457613	T	0.34629	0.0904	N	0.10874	0.06	0.18873	N	0.999984	P	0.38922	0.651	B	0.39068	0.289	T	0.09357	-1.0678	10	0.09843	T	0.71	-19.6503	8.5081	0.33199	0.0:0.166:0.6623:0.1717	.	2473	Q8TDX9	PK1L1_HUMAN	F	2473	ENSP00000289672:S2473F	ENSP00000289672:S2473F	S	-	2	0	PKD1L1	47818103	0.001000	0.12720	0.800000	0.32199	0.787000	0.44495	0.791000	0.26915	2.573000	0.86826	0.453000	0.30009	TCT	G|0.999;A|0.001	0.001	strong		0.592	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
ZNF248	57209	hgsc.bcm.edu	37	10	38120642	38120642	+	Silent	SNP	C	C	T	rs1208731	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:38120642C>T	ENST00000395867.3	-	6	2191	c.1641G>A	c.(1639-1641)ccG>ccA	p.P547P	ZNF248_ENST00000357328.4_Silent_p.P547P|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000374648.3_Intron	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	547					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TACACTCATACGGCTTCTCCC	0.438													C|||	160	0.0319489	0.0023	0.0648	5008	,	,		18392	0.0		0.1034	False		,,,				2504	0.0082				p.P547P		Atlas-SNP	.											.	ZNF248	61	.	0			c.G1641A						PASS	.	C		80,4326	69.8+/-107.6	1,78,2124	125.0	113.0	117.0		1641	0.5	1.0	10	dbSNP_87	117	758,7842	181.6+/-230.3	32,694,3574	no	coding-synonymous	ZNF248	NM_021045.1		33,772,5698	TT,TC,CC		8.814,1.8157,6.4432		547/580	38120642	838,12168	2203	4300	6503	SO:0001819	synonymous_variant	57209	exon6			CTCATACGGCTTC	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1641G>A	10.37:g.38120642C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	127	50	0.393701	NM_001267597	Q8NDV8|Q9UMP3	Silent	SNP	ENST00000395867.3	37	CCDS7194.1																																																																																			C|0.936;T|0.064	0.064	strong		0.438	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
FBXO6	26270	hgsc.bcm.edu	37	1	11728894	11728894	+	Missense_Mutation	SNP	G	G	A	rs3125818	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11728894G>A	ENST00000376753.4	+	2	314	c.179G>A	c.(178-180)cGa>cAa	p.R60Q		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	60			R -> Q (in dbSNP:rs3125818).		DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		AAGTGCCTGCGAGAGGGCTTC	0.627													.|||	683	0.136382	0.0726	0.1758	5008	,	,		19109	0.1498		0.1173	False		,,,				2504	0.2004				p.R60Q	NSCLC(54;506 1562 46490 51389)	Atlas-SNP	.											FBXO6,NS,carcinoma,0,1	FBXO6	17	1	0			c.G179A						PASS	.	G	GLN/ARG	361,4045	187.1+/-213.8	10,341,1852	60.0	64.0	63.0		179	-3.5	0.0	1	dbSNP_103	63	975,7625	212.5+/-252.8	53,869,3378	no	missense	FBXO6	NM_018438.5	43	63,1210,5230	AA,AG,GG		11.3372,8.1934,10.2722	benign	60/294	11728894	1336,11670	2203	4300	6503	SO:0001583	missense	26270	exon2			GCCTGCGAGAGGG	AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"""F-boxes /  ""other"""""	13585	protein-coding gene	gene with protein product		605647	"""F-box only protein 6"""			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.179G>A	1.37:g.11728894G>A	ENSP00000365944:p.Arg60Gln	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	168	85	0.505952	NM_018438	B1AK42|B2RC88|Q9UKT3	Missense_Mutation	SNP	ENST00000376753.4	37	CCDS133.1	251|251	0.11492673992673992|0.11492673992673992	30|30	0.06097560975609756|0.06097560975609756	62|62	0.1712707182320442|0.1712707182320442	73|73	0.12762237762237763|0.12762237762237763	86|86	0.11345646437994723|0.11345646437994723	G|G	7.166|7.166	0.586706|0.586706	0.13749|0.13749	0.081934|0.081934	0.113372|0.113372	ENSG00000116663|ENSG00000116663	ENST00000449067|ENST00000376753	.|T	.|0.49139	.|0.79	5.15|5.15	-3.48|-3.48	0.04739|0.04739	.|F-box domain, Skp2-like (1);	.|0.120339	.|0.56097	.|N	.|0.000038	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.45470|0.45470	1.425|1.425	0.47511|0.47511	P|P	5.579999999999474E-4|5.579999999999474E-4	.|B	.|0.32128	.|0.357	.|B	.|0.29716	.|0.106	T|T	0.14008|0.14008	-1.0488|-1.0488	4|9	.|0.18276	.|T	.|0.48	-12.4923|-12.4923	5.8202|5.8202	0.18524|0.18524	0.1932:0.0:0.3929:0.4138|0.1932:0.0:0.3929:0.4138	rs3125818;rs9430593;rs52826022;rs3125818|rs3125818;rs9430593;rs52826022;rs3125818	.|60	.|Q9NRD1	.|FBX6_HUMAN	K|Q	48|60	.|ENSP00000365944:R60Q	.|ENSP00000365944:R60Q	E|R	+|+	1|2	0|0	FBXO6|FBXO6	11651481|11651481	0.007000|0.007000	0.16637|0.16637	0.002000|0.002000	0.10522|0.10522	0.042000|0.042000	0.13812|0.13812	-0.088000|-0.088000	0.11198|0.11198	-0.548000|-0.548000	0.06199|0.06199	-0.175000|-0.175000	0.13238|0.13238	GAG|CGA	.	.	weak		0.627	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438	
OBSCN	84033	hgsc.bcm.edu	37	1	228524961	228524961	+	Silent	SNP	C	C	A	rs3795808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228524961C>A	ENST00000422127.1	+	66	16721	c.16677C>A	c.(16675-16677)ccC>ccA	p.P5559P	OBSCN_ENST00000570156.2_Silent_p.P6516P|OBSCN_ENST00000366707.4_Silent_p.P3193P|OBSCN_ENST00000366709.4_Silent_p.P2678P|OBSCN_ENST00000284548.11_Silent_p.P5559P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5559					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGCAGGTGCCCGGAGGTGACA	0.632													T|||	1201	0.239816	0.0575	0.3458	5008	,	,		18520	0.25		0.4185	False		,,,				2504	0.2168				p.P6516P		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19548A						PASS	.	T	,	412,3738		29,354,1692	30.0	39.0	36.0		16677,16677	-4.5	0.8	1	dbSNP_107	36	3541,4839		761,2019,1410	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	790,2373,3102	AA,AC,CC		42.2554,9.9277,31.5483	,	5559/7969,5559/6621	228524961	3953,8577	2075	4190	6265	SO:0001819	synonymous_variant	84033	exon77			GGTGCCCGGAGGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.16677C>A	1.37:g.228524961C>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	181	92	0.508287	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			A|0.286;C|0.714;G|0.000	0.286	strong		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ATXN1	6310	hgsc.bcm.edu	37	6	16327906	16327906	+	Missense_Mutation	SNP	C	C	A	rs376233432		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:16327906C>A	ENST00000244769.4	-	8	1572	c.636G>T	c.(634-636)caG>caT	p.Q212H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q212H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	212	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgctgatgctgat	0.672																																					p.Q212H		Atlas-SNP	.											ATXN1,colon,carcinoma,0,3	ATXN1	117	3	0			c.G636T						scavenged	.						5.0	8.0	7.0					6																	16327906		1594	3492	5086	SO:0001583	missense	6310	exon7			CTGCTGCTGATGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.636G>T	6.37:g.16327906C>A	ENSP00000244769:p.Gln212His	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	105	4	0.0380952	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	5.858	0.342494	0.11069	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.57752	0.38;0.38	.	.	.	.	.	.	.	.	T	0.12689	0.0308	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.21552	-1.0242	5	0.49607	T	0.09	.	.	.	.	.	212	P54253	ATX1_HUMAN	H	212	ENSP00000244769:Q212H;ENSP00000416360:Q212H	ENSP00000244769:Q212H	Q	-	3	2	ATXN1	16435885	0.148000	0.22702	0.022000	0.16811	0.070000	0.16714	0.333000	0.19768	0.000000	0.14550	0.000000	0.15137	CAG	.	.	weak		0.672	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
MIDN	90007	hgsc.bcm.edu	37	19	1256998	1256998	+	Silent	SNP	C	C	T	rs9823	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1256998C>T	ENST00000591446.2	+	7	1543	c.1134C>T	c.(1132-1134)gaC>gaT	p.D378D	CIRBP_ENST00000588030.1_5'Flank|MIDN_ENST00000300952.2_Silent_p.D378D			Q504T8	MIDN_HUMAN	midnolin	378						cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTGCAGGGGACCGGCTTCGGC	0.632													c|||	1512	0.301917	0.0825	0.3444	5008	,	,		16413	0.4901		0.3479	False		,,,				2504	0.3272				p.D378D		Atlas-SNP	.											MIDN,NS,carcinoma,0,2	MIDN	34	2	0			c.C1134T						PASS	.	C		546,3856		34,478,1689	28.0	32.0	31.0		1134	2.4	1.0	19	dbSNP_52	31	2932,5652		500,1932,1860	no	coding-synonymous	MIDN	NM_177401.4		534,2410,3549	TT,TC,CC		34.1566,12.4035,26.7827		378/469	1256998	3478,9508	2201	4292	6493	SO:0001819	synonymous_variant	90007	exon8			AGGGGACCGGCTT	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.1134C>T	19.37:g.1256998C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_177401	Q96BW8	Silent	SNP	ENST00000591446.2	37	CCDS32864.1																																																																																			C|0.713;T|0.287	0.287	strong		0.632	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2		
ZNF573	126231	hgsc.bcm.edu	37	19	38230398	38230398	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38230398C>T	ENST00000590414.2	-	4	1014	c.993G>A	c.(991-993)gaG>gaA	p.E331E	ZNF573_ENST00000392138.1_Silent_p.E244E|ZNF573_ENST00000536220.1_Silent_p.E243E|ZNF573_ENST00000339503.4_Silent_p.E273E|ZNF573_ENST00000357309.3_Silent_p.E243E			Q86YE8	ZN573_HUMAN	zinc finger protein 573	331					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			ATTCTTTACACTCATATGGCT	0.403																																					p.E331E		Atlas-SNP	.											ZNF573,NS,carcinoma,-2,1	ZNF573	63	1	0			c.G993A						scavenged	.						78.0	75.0	76.0					19																	38230398		2203	4300	6503	SO:0001819	synonymous_variant	126231	exon5			TTTACACTCATAT	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"""Zinc fingers, C2H2-type"", ""-"""	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.993G>A	19.37:g.38230398C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	162	4	0.0246914	NM_001172690	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Silent	SNP	ENST00000590414.2	37	CCDS59381.1																																																																																			.	.	none		0.403	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360	
C2orf70	339778	hgsc.bcm.edu	37	2	26798893	26798893	+	Missense_Mutation	SNP	A	A	T	rs13002673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:26798893A>T	ENST00000329615.3	+	2	229	c.198A>T	c.(196-198)caA>caT	p.Q66H	C2orf70_ENST00000409392.1_Missense_Mutation_p.R54W	NM_001105519.1	NP_001098989.1	A6NJV1	CB070_HUMAN	chromosome 2 open reading frame 70	66			Q -> H (in dbSNP:rs13002673).			nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	13						CCTTCAGCCAAGGCGGCCATT	0.627													A|||	1675	0.334465	0.0953	0.2262	5008	,	,		18527	0.623		0.336	False		,,,				2504	0.4356				p.Q66H		Atlas-SNP	.											.	C2orf70	26	.	0			c.A198T						PASS	.	A	HIS/GLN	537,3657		41,455,1601	118.0	129.0	125.0		198	-1.1	0.0	2	dbSNP_121	125	2502,5954		350,1802,2076	yes	missense	C2orf70	NM_001105519.1	24	391,2257,3677	TT,TA,AA		29.5885,12.804,24.0237	benign	66/202	26798893	3039,9611	2097	4228	6325	SO:0001583	missense	339778	exon2			CAGCCAAGGCGGC		CCDS42661.1	2p23.3	2011-05-09			ENSG00000173557	ENSG00000173557			27938	protein-coding gene	gene with protein product	"""hypothetical protein LOC339778"""						Standard	NM_001105519		Approved	LOC339778	uc010eyn.3	A6NJV1	OTTHUMG00000151994	ENST00000329615.3:c.198A>T	2.37:g.26798893A>T	ENSP00000332875:p.Gln66His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_001105519		Missense_Mutation	SNP	ENST00000329615.3	37	CCDS42661.1	721|721	0.3301282051282051|0.3301282051282051	52|52	0.10569105691056911|0.10569105691056911	74|74	0.20441988950276244|0.20441988950276244	341|341	0.5961538461538461|0.5961538461538461	254|254	0.33509234828496043|0.33509234828496043	A|A	6.171|6.171	0.399809|0.399809	0.11696|0.11696	0.12804|0.12804	0.295885|0.295885	ENSG00000173557|ENSG00000173557	ENST00000329615|ENST00000409392	T|.	0.49139|.	0.79|.	4.43|4.43	-1.1|-1.1	0.09872|0.09872	.|.	1.741470|.	0.03300|.	N|.	0.188809|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	P|.	0.40731|.	0.728|.	B|.	0.36092|.	0.217|.	T|T	0.40136|0.40136	-0.9579|-0.9579	9|5	0.59425|0.87932	D|D	0.04|0	1.3311|1.3311	4.1823|4.1823	0.10381|0.10381	0.3399:0.3594:0.3007:0.0|0.3399:0.3594:0.3007:0.0	rs13002673;rs60890621;rs13002673|rs13002673;rs60890621;rs13002673	66|.	A6NJV1|.	CB070_HUMAN|.	H|W	66|54	ENSP00000332875:Q66H|.	ENSP00000332875:Q66H|ENSP00000386615:R54W	Q|R	+|+	3|1	2|2	C2orf70|C2orf70	26652397|26652397	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.252000|0.252000	0.25951|0.25951	-1.156000|-1.156000	0.03160|0.03160	-0.206000|-0.206000	0.10203|0.10203	0.379000|0.379000	0.24179|0.24179	CAA|AGG	A|0.675;T|0.325	0.325	strong		0.627	C2orf70-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353258.1	NM_001105519	
POTED	317754	hgsc.bcm.edu	37	21	15011886	15011886	+	Missense_Mutation	SNP	G	G	A	rs562875736	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:15011886G>A	ENST00000299443.5	+	10	1512	c.1460G>A	c.(1459-1461)gGa>gAa	p.G487E		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	487						plasma membrane (GO:0005886)		p.G487E(1)		central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						CAGAACACTGGAATATCACAA	0.323													g|||	225	0.0449281	0.1067	0.0101	5008	,	,		5566	0.0486		0.0189	False		,,,				2504	0.0092				p.G487E		Atlas-SNP	.											POTED,NS,carcinoma,0,1	POTED	57	1	1	Substitution - Missense(1)	prostate(1)	c.G1460A						scavenged	.						9.0	15.0	13.0					21																	15011886		951	3208	4159	SO:0001583	missense	317754	exon10			ACACTGGAATATC	AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	23822	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 1"""	607549	"""ankyrin repeat domain 21"", ""ANKRD26-like family B, member 3"""	ANKRD21, A26B3		12475935, 15276201, 16364570	Standard	NM_174981		Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.1460G>A	21.37:g.15011886G>A	ENSP00000299443:p.Gly487Glu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	374	4	0.0106952	NM_174981	C9JCF7	Missense_Mutation	SNP	ENST00000299443.5	37	CCDS13562.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.214319	0.00289	.	.	ENSG00000166351	ENST00000299443	T	0.23950	1.88	1.71	0.761	0.18448	.	.	.	.	.	T	0.11067	0.0270	L	0.40543	1.245	0.09310	N	1	P	0.41232	0.743	B	0.26693	0.072	T	0.20273	-1.0280	9	0.06099	T	0.92	.	4.2377	0.10634	0.2306:0.0:0.7694:0.0	.	487	Q86YR6	POTED_HUMAN	E	487	ENSP00000299443:G487E	ENSP00000299443:G487E	G	+	2	0	POTED	13933757	0.998000	0.40836	0.007000	0.13788	0.000000	0.00434	3.609000	0.54117	0.082000	0.17018	-0.489000	0.04712	GGA	.	.	none		0.323	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157660.1	NM_174981	
FOXE3	2301	hgsc.bcm.edu	37	1	47882497	47882497	+	Silent	SNP	C	C	T	rs34082359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:47882497C>T	ENST00000335071.2	+	1	754	c.510C>T	c.(508-510)gcC>gcT	p.A170A		NM_012186.2	NP_036318.1	Q13461	FOXE3_HUMAN	forkhead box E3	170					camera-type eye development (GO:0043010)|cell development (GO:0048468)|positive regulation of epithelial cell proliferation (GO:0050679)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|upper_aerodigestive_tract(1)	5				READ - Rectum adenocarcinoma(2;0.0908)		TCAAGCGCGCCGAGCTgcccg	0.776													c|||	1395	0.278554	0.2315	0.2378	5008	,	,		4975	0.2123		0.3569	False		,,,				2504	0.3589				p.A170A		Atlas-SNP	.											.	FOXE3	8	.	0			c.C510T						PASS	.			1084,3226		172,740,1243	8.0	9.0	9.0		510	-3.4	0.1	1	dbSNP_126	9	2914,5542		546,1822,1860	no	coding-synonymous	FOXE3	NM_012186.2		718,2562,3103	TT,TC,CC		34.4607,25.1508,31.3176		170/320	47882497	3998,8768	2155	4228	6383	SO:0001819	synonymous_variant	2301	exon1			GCGCGCCGAGCTG	AF275722	CCDS550.1	1p32	2008-02-05			ENSG00000186790	ENSG00000186790		"""Forkhead boxes"""	3808	protein-coding gene	gene with protein product		601094		FKHL12		8825632	Standard	NM_012186		Approved	FREAC8	uc001crk.3	Q13461	OTTHUMG00000007954	ENST00000335071.2:c.510C>T	1.37:g.47882497C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_012186	Q5SVY9|Q9NQV9	Silent	SNP	ENST00000335071.2	37	CCDS550.1																																																																																			C|0.710;T|0.290	0.290	strong		0.776	FOXE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021836.1	NM_012186	
ZNF529	57711	hgsc.bcm.edu	37	19	37038092	37038092	+	Silent	SNP	T	T	C	rs2278168	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:37038092T>C	ENST00000591340.1	-	5	1526	c.1368A>G	c.(1366-1368)ggA>ggG	p.G456G	ZNF529_ENST00000334116.7_Silent_p.G351G	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	Esophageal squamous(110;0.198)					TAAAGAACTTTCCACACTCCT	0.368													T|||	1127	0.22504	0.2791	0.1916	5008	,	,		21349	0.1756		0.2425	False		,,,				2504	0.2086				p.G456G		Atlas-SNP	.											.	ZNF529	82	.	0			c.A1368G						PASS	.	T	,,	1090,3220		133,824,1198	83.0	89.0	87.0		1368,1314,1368	-4.7	0.6	19	dbSNP_100	87	1854,6712		206,1442,2635	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF529	NM_001145649.1,NM_001145650.1,NM_020951.4	,,	339,2266,3833	CC,CT,TT		21.6437,25.29,22.8642	,,	456/564,438/546,456/564	37038092	2944,9932	2155	4283	6438	SO:0001819	synonymous_variant	57711	exon6			GAACTTTCCACAC	AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"""Zinc fingers, C2H2-type"", ""-"""	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.1368A>G	19.37:g.37038092T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Silent	SNP	ENST00000591340.1	37	CCDS54256.1																																																																																			T|0.774;C|0.226	0.226	strong		0.368	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951	
FAM98C	147965	hgsc.bcm.edu	37	19	38896204	38896204	+	Missense_Mutation	SNP	T	T	G	rs117354953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38896204T>G	ENST00000252530.5	+	6	698	c.679T>G	c.(679-681)Tgc>Ggc	p.C227G	FAM98C_ENST00000588262.1_Intron|FAM98C_ENST00000343358.7_Missense_Mutation_p.C201G	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	227										endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCAGTACCGCTGCCGCCGCTG	0.592													T|||	24	0.00479233	0.0008	0.0058	5008	,	,		16729	0.0		0.0169	False		,,,				2504	0.002				p.C227G		Atlas-SNP	.											FAM98C,NS,carcinoma,-1,1	FAM98C	39	1	0			c.T679G						PASS	.	T	GLY/CYS	12,4366		0,12,2177	52.0	59.0	57.0		679	4.0	1.0	19	dbSNP_132	57	127,8463		0,127,4168	yes	missense	FAM98C	NM_174905.3	159	0,139,6345	GG,GT,TT		1.4785,0.2741,1.0719	benign	227/350	38896204	139,12829	2189	4295	6484	SO:0001583	missense	147965	exon6			TACCGCTGCCGCC		CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.679T>G	19.37:g.38896204T>G	ENSP00000252530:p.Cys227Gly	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_174905	A6NMW3|Q66K45	Missense_Mutation	SNP	ENST00000252530.5	37	CCDS42562.1	19	0.0086996336996337	2	0.0040650406504065045	3	0.008287292817679558	1	0.0017482517482517483	13	0.017150395778364115	T	13.51	2.259355	0.39995	0.002741	0.014785	ENSG00000130244	ENST00000252530;ENST00000343358	T;T	0.45668	0.89;0.89	5.02	3.99	0.46301	.	0.548059	0.15348	N	0.267098	T	0.25457	0.0619	M	0.79926	2.475	0.44295	D	0.997163	P;B	0.47910	0.902;0.086	B;B	0.38225	0.268;0.056	T	0.13602	-1.0503	10	0.30854	T	0.27	-0.3593	8.8557	0.35227	0.0:0.0:0.1896:0.8104	.	201;227	Q17RN3-2;Q17RN3	.;FA98C_HUMAN	G	227;201	ENSP00000252530:C227G;ENSP00000340348:C201G	ENSP00000252530:C227G	C	+	1	0	FAM98C	43588044	0.998000	0.40836	0.969000	0.41365	0.832000	0.47134	2.019000	0.41001	0.738000	0.32606	0.456000	0.33151	TGC	T|0.989;G|0.011	0.011	strong		0.592	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905	
OR52H1	390067	hgsc.bcm.edu	37	11	5566051	5566051	+	Missense_Mutation	SNP	C	C	A	rs1995157	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5566051C>A	ENST00000322653.4	-	1	728	c.703G>T	c.(703-705)Ggc>Tgc	p.G235C	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	235			G -> C (in dbSNP:rs1995157).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGGGAAGGCCAAAGACAGCA	0.483													G|||	1910	0.38139	0.4493	0.513	5008	,	,		22664	0.0853		0.5775	False		,,,				2504	0.2996				p.G235C		Atlas-SNP	.											.	OR52H1	46	.	0			c.G703T						PASS	.	G	CYS/GLY	2028,2374		483,1062,656	114.0	101.0	105.0		703	5.4	1.0	11	dbSNP_92	105	5201,3393		1570,2061,666	yes	missense	OR52H1	NM_001005289.1	159	2053,3123,1322	AA,AC,CC		39.481,46.07,44.3752	benign	235/321	5566051	7229,5767	2201	4297	6498	SO:0001583	missense	390067	exon1			GAAGGCCAAAGAC	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.703G>T	11.37:g.5566051C>A	ENSP00000326259:p.Gly235Cys	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_001005289	B9EH26|Q6IF79	Missense_Mutation	SNP	ENST00000322653.4	37	CCDS31386.1	900	0.41208791208791207	216	0.43902439024390244	185	0.511049723756906	58	0.10139860139860139	441	0.5817941952506597	G	0.031	-1.333725	0.01298	0.4607	0.60519	ENSG00000181616	ENST00000322653	T	0.00123	8.7	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.845789	0.10273	N	0.694575	T	0.00012	0.0000	L	0.31476	0.935	0.80722	P	0.0	B	0.25904	0.137	B	0.25614	0.062	T	0.01488	-1.1342	9	0.48119	T	0.1	.	8.9214	0.35615	0.0:0.1407:0.5911:0.2682	rs1995157;rs52822388;rs61075426;rs1995157	235	Q8NGJ2	O52H1_HUMAN	C	235	ENSP00000326259:G235C	ENSP00000326259:G235C	G	-	1	0	OR52H1	5522627	0.000000	0.05858	0.975000	0.42487	0.291000	0.27294	0.044000	0.13992	1.277000	0.44412	-0.127000	0.14921	GGC	C|0.525;A|0.475	0.475	strong		0.483	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
NFKBIZ	64332	hgsc.bcm.edu	37	3	101576175	101576175	+	Silent	SNP	T	T	C	rs14134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:101576175T>C	ENST00000326172.5	+	11	2090	c.1975T>C	c.(1975-1977)Ttg>Ctg	p.L659L	NFKBIZ_ENST00000394054.2_Silent_p.L559L|NFKBIZ_ENST00000326151.5_Silent_p.L537L	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	659	Interaction with NFKB1/p50. {ECO:0000250}.				inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						TGCTGCCAGCTTGCAGTATCG	0.478													C|||	2676	0.534345	0.497	0.6772	5008	,	,		21394	0.4405		0.6282	False		,,,				2504	0.4836				p.L659L		Atlas-SNP	.											.	NFKBIZ	55	.	0			c.T1975C						PASS	.	C	,	2288,2118	577.4+/-384.4	609,1070,524	103.0	97.0	99.0		1675,1975	6.0	1.0	3	dbSNP_52	99	5408,3192	481.0+/-370.5	1662,2084,554	no	coding-synonymous,coding-synonymous	NFKBIZ	NM_001005474.2,NM_031419.3	,	2271,3154,1078	CC,CT,TT		37.1163,48.0708,40.8273	,	559/619,659/719	101576175	7696,5310	2203	4300	6503	SO:0001819	synonymous_variant	64332	exon11			GCCAGCTTGCAGT	AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"""Ankyrin repeat domain containing"""	29805	protein-coding gene	gene with protein product	"""IL-1 inducible nuclear ankyrin-repeat protein"""	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.1975T>C	3.37:g.101576175T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	158	87	0.550633	NM_031419	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Silent	SNP	ENST00000326172.5	37	CCDS2946.1																																																																																			T|0.427;C|0.573	0.573	strong		0.478	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419	
NLRP8	126205	hgsc.bcm.edu	37	19	56487603	56487603	+	Missense_Mutation	SNP	A	A	G	rs306481	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56487603A>G	ENST00000291971.3	+	8	2881	c.2810A>G	c.(2809-2811)aAg>aGg	p.K937R	NLRP8_ENST00000590542.1_Missense_Mutation_p.K918R	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	937			K -> R (in dbSNP:rs306481).		neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AATAGCCTGAAGGATGATGGG	0.463													A|||	2820	0.563099	0.4024	0.6037	5008	,	,		17430	0.6657		0.5537	False		,,,				2504	0.6554				p.K937R		Atlas-SNP	.											.	NLRP8	225	.	0			c.A2810G						PASS	.	A	ARG/LYS	1801,2605	529.8+/-372.8	357,1087,759	137.0	134.0	135.0		2810	-5.0	0.0	19	dbSNP_79	135	4778,3822	611.3+/-395.8	1314,2150,836	yes	missense	NLRP8	NM_176811.2	26	1671,3237,1595	GG,GA,AA		44.4419,40.8761,49.4157	benign	937/1049	56487603	6579,6427	2203	4300	6503	SO:0001583	missense	126205	exon8			GCCTGAAGGATGA	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2810A>G	19.37:g.56487603A>G	ENSP00000291971:p.Lys937Arg	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	238	238	1	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	1208	0.5531135531135531	200	0.4065040650406504	216	0.5966850828729282	370	0.6468531468531469	422	0.5567282321899736	A	0.018	-1.470150	0.01044	0.408761	0.555581	ENSG00000179709	ENST00000291971	T	0.63096	-0.02	2.94	-5.02	0.02982	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.16603	0.007;0.018	B;B	0.20577	0.018;0.03	T	0.41324	-0.9515	8	0.09590	T	0.72	.	2.5502	0.04747	0.2329:0.1605:0.4488:0.1578	rs306481;rs52827447;rs58300306;rs306481	918;937	Q86W28-2;Q86W28	.;NALP8_HUMAN	R	937	ENSP00000291971:K937R	ENSP00000291971:K937R	K	+	2	0	NLRP8	61179415	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.429000	0.06982	-1.533000	0.01745	-0.476000	0.04901	AAG	A|0.474;G|0.526	0.526	strong		0.463	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
IL3RA	3563	hgsc.bcm.edu	37	X	1497644	1497644	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:1497644G>C	ENST00000331035.4	+	10	1316	c.967G>C	c.(967-969)Gtg>Ctg	p.V323L	IL3RA_ENST00000381469.2_Missense_Mutation_p.V245L	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	323			V -> L (in dbSNP:rs17883366). {ECO:0000269|Ref.5}.		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)			lung(1)|skin(2)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	CTGTGTCTTCGTGATCTGCAG	0.592													g|||	525	0.104832	0.0378	0.1297	5008	,	,		16681	0.0694		0.2058	False		,,,				2504	0.1104				p.V323L		Atlas-SNP	.											.	IL3RA	49	.	0			c.G967C						PASS	.		LEU/VAL	293,4109		12,269,1920	130.0	106.0	114.0		967	-1.6	0.0	X	dbSNP_134	114	1580,7012		144,1292,2860	no	missense	IL3RA	NM_002183.2	32	156,1561,4780	CC,CG,GG		18.3892,6.6561,14.4143	benign	323/379	1497644	1873,11121	2201	4296	6497	SO:0001583	missense	3563	exon10			GTCTTCGTGATCT	M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"""Pseudoautosomal regions / PAR1"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.967G>C	X.37:g.1497644G>C	ENSP00000327890:p.Val323Leu	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	331	153	0.462236	NM_002183	A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Missense_Mutation	SNP	ENST00000331035.4	37	CCDS14113.1	283	0.1295787545787546	21	0.042682926829268296	54	0.14917127071823205	53	0.09265734265734266	155	0.20448548812664907	.	0	-2.808565	0.00074	0.066561	0.183892	ENSG00000185291	ENST00000331035;ENST00000381469	T;D	0.96522	1.74;-4.04	0.798	-1.6	0.08426	.	0.471891	0.15240	N	0.272951	T	0.00271	0.0008	N	0.00841	-1.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.51957	-0.8639	9	0.06757	T	0.87	.	.	.	.	.	244;323	P26951-2;P26951	.;IL3RA_HUMAN	L	323;245	ENSP00000327890:V323L;ENSP00000370878:V245L	ENSP00000327890:V323L	V	+	1	0	IL3RA	1457644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.991000	0.03728	-2.554000	0.00477	-2.540000	0.00180	GTG	G|0.868;C|0.132	0.132	strong		0.592	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3		
CEP89	84902	hgsc.bcm.edu	37	19	33414392	33414392	+	Silent	SNP	T	T	C	rs17599843	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33414392T>C	ENST00000305768.5	-	12	1309	c.1221A>G	c.(1219-1221)gaA>gaG	p.E407E		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	407					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CTTGGTGCAATTCTTCATTTT	0.373													T|||	38	0.00758786	0.0	0.0058	5008	,	,		18272	0.001		0.008	False		,,,				2504	0.0256				p.E407E		Atlas-SNP	.											.	CEP89	82	.	0			c.A1221G						PASS	.	T		12,4392	19.1+/-41.9	0,12,2190	250.0	221.0	231.0		1221	-2.9	0.0	19	dbSNP_123	231	70,8528	42.6+/-100.3	0,70,4229	no	coding-synonymous	CEP89	NM_032816.3		0,82,6419	CC,CT,TT		0.8141,0.2725,0.6307		407/784	33414392	82,12920	2202	4299	6501	SO:0001819	synonymous_variant	84902	exon12			GTGCAATTCTTCA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1221A>G	19.37:g.33414392T>C		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	216	97	0.449074	NM_032816	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																			T|0.995;C|0.005	0.005	strong		0.373	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
UGT2B28	54490	hgsc.bcm.edu	37	4	70156313	70156313	+	Missense_Mutation	SNP	T	T	A	rs4235127	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70156313T>A	ENST00000335568.5	+	5	1096	c.1094T>A	c.(1093-1095)cTt>cAt	p.L365H	UGT2B28_ENST00000511240.1_Intron	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	365			L -> H (in dbSNP:rs4235127). {ECO:0000269|PubMed:19054851}.		metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						ATCCTAGGTCTTCCAAAAACC	0.378													N|||	1875	0.374401	0.2549	0.4539	5008	,	,		4011	0.3829		0.4771	False		,,,				2504	0.365				p.L365H		Atlas-SNP	.											.	UGT2B28	101	.	0			c.T1094A						PASS	.	A	,HIS/LEU	1110,2894		339,432,1231	52.0	53.0	53.0		,1094	1.9	1.0	4	dbSNP_111	53	3771,4609		1200,1371,1619	no	intron,missense	UGT2B28	NM_001207004.1,NM_053039.1	,99	1539,1803,2850	AA,AT,TT		45.0,27.7223,39.4138	,benign	,365/530	70156313	4881,7503	2002	4190	6192	SO:0001583	missense	54490	exon5			TAGGTCTTCCAAA	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1094T>A	4.37:g.70156313T>A	ENSP00000334276:p.Leu365His	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_053039	B5BUM0|Q9BY62|Q9BY63	Missense_Mutation	SNP	ENST00000335568.5	37	CCDS3528.1	794	0.36355311355311354	100	0.2032520325203252	145	0.4005524861878453	196	0.34265734265734266	353	0.4656992084432718	-	0.003	-2.487047	0.00161	0.277223	0.45	ENSG00000135226	ENST00000335568	T	0.36157	1.27	1.85	1.85	0.25348	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00000	-4.25	0.09310	P	0.9999999999999958	B	0.02656	0.0	B	0.01281	0.0	T	0.47995	-0.9073	9	0.02654	T	1	.	5.249	0.15512	0.743:0.0:0.0:0.257	rs4235127	365	Q9BY64	UDB28_HUMAN	H	365	ENSP00000334276:L365H	ENSP00000334276:L365H	L	+	2	0	UGT2B28	70190902	1.000000	0.71417	0.986000	0.45419	0.081000	0.17604	6.037000	0.70956	0.007000	0.14760	-1.489000	0.00976	CTT	.	.	weak		0.378	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
AHSA1	10598	hgsc.bcm.edu	37	14	77926011	77926011	+	Silent	SNP	C	C	T	rs1061629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:77926011C>T	ENST00000216479.3	+	2	293	c.133C>T	c.(133-135)Ctg>Ttg	p.L45L	VIPAS39_ENST00000553888.1_5'Flank|VIPAS39_ENST00000448935.2_5'Flank|AHSA1_ENST00000555517.1_Silent_p.L45L|VIPAS39_ENST00000557658.1_5'Flank|AHSA1_ENST00000535854.2_Silent_p.L45L|VIPAS39_ENST00000556412.1_5'Flank|VIPAS39_ENST00000343765.2_5'Flank|VIPAS39_ENST00000556909.1_5'Flank|VIPAS39_ENST00000327028.4_5'Flank	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	45					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AACACTGTTCCTGGCAGTGCA	0.463													C|||	2376	0.474441	0.0688	0.5144	5008	,	,		23229	0.9236		0.4901	False		,,,				2504	0.5153				p.L45L		Atlas-SNP	.											.	AHSA1	24	.	0			c.C133T						PASS	.	C		643,3763	274.6+/-272.0	57,529,1617	184.0	159.0	168.0		133	3.7	1.0	14	dbSNP_86	168	4494,4106	593.0+/-393.1	1195,2104,1001	no	coding-synonymous	AHSA1	NM_012111.2		1252,2633,2618	TT,TC,CC		47.7442,14.5937,39.4972		45/339	77926011	5137,7869	2203	4300	6503	SO:0001819	synonymous_variant	10598	exon2			CTGTTCCTGGCAG	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"""chromosome 14 open reading frame 3"""	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.133C>T	14.37:g.77926011C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_012111	B2R9L2|B4DUR9|Q96IL6|Q9P060	Silent	SNP	ENST00000216479.3	37	CCDS9863.1																																																																																			C|0.563;T|0.437	0.437	strong		0.463	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111	
MPP3	4356	hgsc.bcm.edu	37	17	41891437	41891437	+	Silent	SNP	G	G	A	rs17742929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:41891437G>A	ENST00000398389.4	-	16	1362	c.1197C>T	c.(1195-1197)caC>caT	p.H399H	MPP3_ENST00000475450.1_5'UTR|MPP3_ENST00000398393.1_Silent_p.H424H	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	399	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		GCTTCAGCTCGTGCAGTCGGG	0.592													G|||	533	0.10643	0.025	0.1239	5008	,	,		18892	0.001		0.2505	False		,,,				2504	0.1646				p.H399H		Atlas-SNP	.											.	MPP3	42	.	0			c.C1197T						PASS	.	G		173,3755		4,165,1795	89.0	93.0	91.0		1197	-8.4	0.7	17	dbSNP_123	91	1791,6515		197,1397,2559	no	coding-synonymous	MPP3	NM_001932.4		201,1562,4354	AA,AG,GG		21.5627,4.4043,16.0536		399/586	41891437	1964,10270	1964	4153	6117	SO:0001819	synonymous_variant	4356	exon16			CAGCTCGTGCAGT		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 3"", ""discs, large (Drosophila) homolog 3"", ""membrane protein palmitoylated 3"""	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.1197C>T	17.37:g.41891437G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_001932	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Silent	SNP	ENST00000398389.4	37	CCDS42344.1																																																																																			G|0.872;A|0.128	0.128	strong		0.592	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932	
SVIL	6840	hgsc.bcm.edu	37	10	29759225	29759225	+	Silent	SNP	A	A	G	rs11007607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29759225A>G	ENST00000355867.4	-	32	6575	c.5823T>C	c.(5821-5823)gcT>gcC	p.A1941A	SVIL_ENST00000375398.2_Silent_p.A1941A|SVIL_ENST00000375400.3_Silent_p.A1515A|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000535393.1_Silent_p.A855A|PTCHD3P1_ENST00000455774.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1941					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.A1941A(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TCTTGTTCGCAGCGGTCCTTC	0.602													G|||	1238	0.247204	0.2814	0.2839	5008	,	,		19079	0.2391		0.2286	False		,,,				2504	0.2025				p.A1941A		Atlas-SNP	.											SVIL,NS,carcinoma,0,1	SVIL	226	1	1	Substitution - coding silent(1)	stomach(1)	c.T5823C						PASS	.	G	,	1185,3221	711.7+/-408.0	162,861,1180	180.0	147.0	158.0		4545,5823	-11.2	0.0	10	dbSNP_120	158	1819,6781	731.9+/-406.8	203,1413,2684	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	365,2274,3864	GG,GA,AA		21.1512,26.8951,23.097	,	1515/1789,1941/2215	29759225	3004,10002	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon32			GTTCGCAGCGGTC	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5823T>C	10.37:g.29759225A>G		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	200	95	0.475	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			A|0.769;G|0.231	0.231	strong		0.602	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
CFAP46	54777	hgsc.bcm.edu	37	10	134626293	134626293	+	Missense_Mutation	SNP	C	C	A	rs3750587	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134626293C>A	ENST00000368586.5	-	55	7597	c.7497G>T	c.(7495-7497)ttG>ttT	p.L2499F	TTC40_ENST00000263170.5_Missense_Mutation_p.L660F	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCTCACCTTGCAAGTTCATGG	0.607													C|||	187	0.0373403	0.0038	0.0288	5008	,	,		12831	0.0605		0.0586	False		,,,				2504	0.0429				p.L2499F		Atlas-SNP	.											.	TTC40	100	.	0			c.G7497T						PASS	.	C	PHE/LEU	56,4350	54.9+/-90.9	1,54,2148	85.0	83.0	84.0		2433	-5.8	0.1	10	dbSNP_107	84	531,8069	147.6+/-202.9	14,503,3783	yes	missense	C10orf92	NM_001200049.1	22	15,557,5931	AA,AC,CC		6.1744,1.271,4.5133	probably-damaging	811/1028	134626293	587,12419	2203	4300	6503	SO:0001583	missense	54777	exon55			ACCTTGCAAGTTC																												ENST00000368586.5:c.7497G>T	10.37:g.134626293C>A	ENSP00000357575:p.Leu2499Phe	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	39	23	0.589744	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	103	0.04716117216117216	6	0.012195121951219513	8	0.022099447513812154	44	0.07692307692307693	45	0.059366754617414245	C	10.52	1.371860	0.24857	0.01271	0.061744	ENSG00000171811	ENST00000435957;ENST00000368586;ENST00000263170	T;T	0.38401	1.14;1.14	4.13	-5.76	0.02376	.	0.115721	0.31648	N	0.007286	T	0.03305	0.0096	M	0.69823	2.125	0.19945	N	0.999946	D	0.76494	0.999	D	0.87578	0.998	T	0.06734	-1.0810	10	0.51188	T	0.08	.	3.5165	0.07727	0.1216:0.1935:0.1203:0.5646	rs3750587;rs52795792;rs3750587	660	Q8IYW2	CJ092_HUMAN	F	82;2499;660	ENSP00000357575:L2499F;ENSP00000263170:L660F	ENSP00000263170:L660F	L	-	3	2	C10orf93	134476283	0.023000	0.18921	0.054000	0.19295	0.255000	0.26057	-1.166000	0.03129	-1.295000	0.02357	-0.367000	0.07326	TTG	C|0.954;A|0.046	0.046	strong		0.607	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
SCML4	256380	hgsc.bcm.edu	37	6	108068003	108068003	+	Missense_Mutation	SNP	C	C	T	rs6934505	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:108068003C>T	ENST00000369020.3	-	4	622	c.377G>A	c.(376-378)cGg>cAg	p.R126Q	SCML4_ENST00000369022.2_Missense_Mutation_p.R68Q|SCML4_ENST00000479803.1_5'Flank|SCML4_ENST00000369021.3_Missense_Mutation_p.R97Q	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	126			R -> Q (in dbSNP:rs6934505). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CGCCGATGGCCGCTCGGGCCC	0.632													C|||	586	0.117013	0.0212	0.1427	5008	,	,		16476	0.0972		0.1938	False		,,,				2504	0.1697				p.R126Q		Atlas-SNP	.											.	SCML4	65	.	0			c.G377A						PASS	.	C	GLN/ARG	200,4206	122.5+/-159.9	3,194,2006	55.0	55.0	55.0		377	2.1	0.8	6	dbSNP_116	55	1524,7076	282.8+/-295.8	145,1234,2921	yes	missense	SCML4	NM_198081.3	43	148,1428,4927	TT,TC,CC		17.7209,4.5393,13.2554	probably-damaging	126/415	108068003	1724,11282	2203	4300	6503	SO:0001583	missense	256380	exon4			GATGGCCGCTCGG		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.377G>A	6.37:g.108068003C>T	ENSP00000358016:p.Arg126Gln	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	107	104	0.971963	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	245	0.11217948717948718	10	0.02032520325203252	53	0.1464088397790055	41	0.07167832167832168	141	0.18601583113456466	C	12.90	2.075751	0.36662	0.045393	0.177209	ENSG00000146285	ENST00000369022;ENST00000369020;ENST00000369021;ENST00000440927	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.88	2.14	0.27477	.	0.316704	0.36234	N	0.002711	T	0.19644	0.0472	M	0.77103	2.36	0.21652	P	0.999606207	B;B	0.34372	0.234;0.451	B;B	0.29524	0.087;0.103	T	0.11155	-1.0599	9	0.15952	T	0.53	.	10.2202	0.43192	0.0:0.7909:0.0:0.2091	rs6934505;rs60016463;rs6934505	126;97	Q8N228;Q8N228-3	SCML4_HUMAN;.	Q	68;126;97;97	ENSP00000358018:R68Q;ENSP00000358016:R126Q;ENSP00000358017:R97Q;ENSP00000404688:R97Q	ENSP00000358016:R126Q	R	-	2	0	SCML4	108174696	0.985000	0.35326	0.762000	0.31397	0.286000	0.27126	3.207000	0.51106	0.265000	0.21872	0.563000	0.77884	CGG	C|0.875;T|0.125	0.125	strong		0.632	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
SKAP1	8631	hgsc.bcm.edu	37	17	46266849	46266849	+	Silent	SNP	G	G	A	rs66753385	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:46266849G>A	ENST00000336915.6	-	5	363	c.294C>T	c.(292-294)atC>atT	p.I98I	RP11-456D7.1_ENST00000582246.1_RNA|SKAP1_ENST00000584924.1_Silent_p.I98I	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	98					positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						CTCCTTTTACGATGTCTTCCA	0.358													G|||	179	0.0357428	0.0129	0.0202	5008	,	,		21223	0.0556		0.0338	False		,,,				2504	0.0593				p.I98I		Atlas-SNP	.											.	SKAP1	41	.	0			c.C294T						PASS	.	G	,	69,4337	62.9+/-100.1	0,69,2134	157.0	133.0	141.0		294,294	0.0	0.0	17	dbSNP_130	141	323,8277	115.2+/-175.0	9,305,3986	no	coding-synonymous,coding-synonymous	SKAP1	NM_001075099.1,NM_003726.3	,	9,374,6120	AA,AG,GG		3.7558,1.566,3.014	,	98/359,98/360	46266849	392,12614	2203	4300	6503	SO:0001819	synonymous_variant	8631	exon5			TTTTACGATGTCT	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"""Pleckstrin homology (PH) domain containing"""	15605	protein-coding gene	gene with protein product		604969	"""src family associated phosphoprotein 1"""	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.294C>T	17.37:g.46266849G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	116	62	0.534483	NM_003726	D3DTV1|O15268	Silent	SNP	ENST00000336915.6	37	CCDS32674.1																																																																																			G|0.965;A|0.035	0.035	strong		0.358	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726	
COG1	9382	hgsc.bcm.edu	37	17	71197439	71197439	+	Silent	SNP	C	C	T	rs1551036	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:71197439C>T	ENST00000299886.4	+	7	1553	c.1473C>T	c.(1471-1473)agC>agT	p.S491S		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	491					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			CCTGGGTCAGCGTGGCAAACC	0.532													C|||	660	0.131789	0.0083	0.1225	5008	,	,		20222	0.1746		0.1958	False		,,,				2504	0.1953				p.S491S		Atlas-SNP	.											.	COG1	46	.	0			c.C1473T						PASS	.	C		172,4234	112.5+/-150.6	5,162,2036	139.0	129.0	132.0		1473	-2.5	0.0	17	dbSNP_88	132	1661,6939	304.5+/-307.0	178,1305,2817	no	coding-synonymous	COG1	NM_018714.2		183,1467,4853	TT,TC,CC		19.314,3.9038,14.0935		491/981	71197439	1833,11173	2203	4300	6503	SO:0001819	synonymous_variant	9382	exon7			GGTCAGCGTGGCA		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1473C>T	17.37:g.71197439C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_018714	Q9NPV9|Q9P2G6	Silent	SNP	ENST00000299886.4	37	CCDS11692.1																																																																																			C|0.867;N|0.001	.	strong		0.532	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
OGFOD1	55239	hgsc.bcm.edu	37	16	56500132	56500132	+	Missense_Mutation	SNP	C	C	T	rs34883368	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:56500132C>T	ENST00000566157.1	+	5	640	c.517C>T	c.(517-519)Ccc>Tcc	p.P173S	OGFOD1_ENST00000568397.1_Missense_Mutation_p.P173S	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	173	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.		P -> S (in dbSNP:rs34883368). {ECO:0000269|PubMed:14702039}.		cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	CCTGGTTCCTCCCTGGGACAG	0.512													C|||	391	0.0780751	0.0174	0.0403	5008	,	,		19730	0.1657		0.0268	False		,,,				2504	0.1493				p.P173S		Atlas-SNP	.											.	OGFOD1	31	.	0			c.C517T						PASS	.	C	SER/PRO	120,4276	89.7+/-128.4	0,120,2078	166.0	121.0	136.0		517	-2.5	1.0	16	dbSNP_126	136	334,8266	115.2+/-175.0	7,320,3973	yes	missense	OGFOD1	NM_018233.3	74	7,440,6051	TT,TC,CC		3.8837,2.7298,3.4934	benign	173/543	56500132	454,12542	2198	4300	6498	SO:0001583	missense	55239	exon5			GTTCCTCCCTGGG	BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"""TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"""	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.517C>T	16.37:g.56500132C>T	ENSP00000457258:p.Pro173Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Missense_Mutation	SNP	ENST00000566157.1	37	CCDS10761.2	124	0.056776556776556776	9	0.018292682926829267	13	0.03591160220994475	81	0.14160839160839161	21	0.027704485488126648	C	10.84	1.462916	0.26248	0.027298	0.038837	ENSG00000087263	ENST00000336111;ENST00000540727	.	.	.	5.64	-2.46	0.06461	Oxoglutarate/iron-dependent oxygenase (1);Prolyl 4-hydroxylase, alpha subunit (1);	0.471002	0.27424	N	0.019426	T	0.00328	0.0010	L	0.55017	1.72	0.26331	P	0.9775233	B	0.06786	0.001	B	0.19148	0.024	T	0.04165	-1.0972	8	0.36615	T	0.2	-12.196	6.6802	0.23115	0.0:0.5902:0.2102:0.1996	rs34883368	173	Q8N543	OGFD1_HUMAN	S	173;17	.	ENSP00000337196:P173S	P	+	1	0	OGFOD1	55057633	0.251000	0.23961	0.980000	0.43619	0.577000	0.36160	0.361000	0.20267	-0.337000	0.08426	-0.367000	0.07326	CCC	C|0.958;T|0.042	0.042	strong		0.512	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	
ZMYND12	84217	hgsc.bcm.edu	37	1	42898843	42898843	+	Missense_Mutation	SNP	A	A	G	rs1034268	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:42898843A>G	ENST00000372565.3	-	7	1215	c.946T>C	c.(946-948)Ttt>Ctt	p.F316L	ZMYND12_ENST00000475426.1_5'UTR|ZMYND12_ENST00000433602.2_Missense_Mutation_p.F206L	NM_032257.4	NP_115633.3	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12	316			F -> L (in dbSNP:rs1034268). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			intracellular (GO:0005622)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|skin(2)	17	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				AGGTAGTAAAACATGACCAGG	0.373													G|||	3252	0.649361	0.6021	0.5965	5008	,	,		20878	0.6508		0.662	False		,,,				2504	0.7362				p.F316L		Atlas-SNP	.											.	ZMYND12	35	.	0			c.T946C						PASS	.	G	LEU/PHE,LEU/PHE	2616,1790	527.6+/-372.2	782,1052,369	141.0	149.0	146.0		616,946	4.8	1.0	1	dbSNP_86	146	5785,2815	445.1+/-360.9	1920,1945,435	yes	missense,missense	ZMYND12	NM_001146192.1,NM_032257.4	22,22	2702,2997,804	GG,GA,AA		32.7326,40.6264,35.4067	benign,benign	206/256,316/366	42898843	8401,4605	2203	4300	6503	SO:0001583	missense	84217	exon7			AGTAAAACATGAC	AK057384	CCDS467.1	1p34.1	2008-02-05			ENSG00000066185	ENSG00000066185		"""Zinc fingers, MYND-type"""	21192	protein-coding gene	gene with protein product						11230166	Standard	NM_032257		Approved	DKFZp434N2435	uc001chj.3	Q9H0C1	OTTHUMG00000007333	ENST00000372565.3:c.946T>C	1.37:g.42898843A>G	ENSP00000361646:p.Phe316Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	105	65	0.619048	NM_032257	Q5VUS6|Q8TC87|Q96M51	Missense_Mutation	SNP	ENST00000372565.3	37	CCDS467.1	1386	0.6346153846153846	297	0.6036585365853658	238	0.6574585635359116	349	0.6101398601398601	502	0.662269129287599	G	6.418	0.445335	0.12164	0.593736	0.672674	ENSG00000066185	ENST00000372565;ENST00000433602	T;T	0.72615	-0.67;2.0	5.71	4.8	0.61643	Tetratricopeptide-like helical (1);	0.062950	0.64402	N	0.000005	T	0.00012	0.0000	N	0.00056	-2.365	0.58432	P	9.000000000036756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46830	-0.9163	9	0.02654	T	1	-2.9041	7.9922	0.30248	0.2477:0.0:0.7523:0.0	rs1034268;rs3748844;rs16829501;rs17845746;rs17858699;rs59210170;rs1034268	206;316	E9PFV0;Q9H0C1	.;ZMY12_HUMAN	L	316;206	ENSP00000361646:F316L;ENSP00000398340:F206L	ENSP00000361646:F316L	F	-	1	0	ZMYND12	42671430	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	1.876000	0.39588	0.776000	0.33473	-0.119000	0.15052	TTT	A|0.361;G|0.639	0.639	strong		0.373	ZMYND12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019170.1	NM_032257	
TTC28	23331	hgsc.bcm.edu	37	22	28501580	28501580	+	Silent	SNP	G	G	A	rs189318371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:28501580G>A	ENST00000397906.2	-	8	3135	c.2994C>T	c.(2992-2994)gaC>gaT	p.D998D		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	998					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						CACAGGCTGCGTCACTCTCCA	0.532													G|||	15	0.00299521	0.0	0.0029	5008	,	,		18507	0.0		0.002	False		,,,				2504	0.0112				p.D998D		Atlas-SNP	.											.	TTC28	84	.	0			c.C2994T						PASS	.	G		2,1382		0,2,690	94.0	85.0	88.0		2994	-11.6	0.0	22		88	31,3151		1,29,1561	no	coding-synonymous	TTC28	NM_001145418.1		1,31,2251	AA,AG,GG		0.9742,0.1445,0.7227		998/2482	28501580	33,4533	692	1591	2283	SO:0001819	synonymous_variant	23331	exon8			GGCTGCGTCACTC	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.2994C>T	22.37:g.28501580G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	232	129	0.556035	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			G|0.997;A|0.003	0.003	strong		0.532	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
CAPN1	823	hgsc.bcm.edu	37	11	64981522	64981522	+	IGR	SNP	C	C	A	rs11605576	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64981522C>A	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		CACACTGAGGCCTCCACCAAC	0.706													C|||	1438	0.287141	0.1324	0.4611	5008	,	,		13157	0.2629		0.3608	False		,,,				2504	0.3221				p.A60D		Atlas-SNP	.											SLC22A20,NS,carcinoma,0,2	SLC22A20	36	2	0			c.C179A						PASS	.	C	ASP/ALA	663,3141		59,545,1298	10.0	14.0	13.0		179	3.3	0.0	11	dbSNP_120	13	2755,5419		457,1841,1789	yes	missense	SLC22A20	NM_001004326.4	126	516,2386,3087	AA,AC,CC		33.7044,17.429,28.5356	benign	60/350	64981522	3418,8560	1902	4087	5989	SO:0001628	intergenic_variant	440044	exon1			CTGAGGCCTCCAC	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		11.37:g.64981522C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			C|0.706;A|0.294	0.294	strong		0.706	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
ALG8	79053	hgsc.bcm.edu	37	11	77825320	77825320	+	Missense_Mutation	SNP	T	T	C	rs665278	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:77825320T>C	ENST00000299626.5	-	6	736	c.665A>G	c.(664-666)aAt>aGt	p.N222S	ALG8_ENST00000376156.3_Missense_Mutation_p.N222S|ALG8_ENST00000532552.2_Intron	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	222			N -> S (in dbSNP:rs665278). {ECO:0000269|PubMed:11124703, ECO:0000269|PubMed:15235028}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)			NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			GCCTGGTTTATTTGCAGTGAA	0.383													T|||	733	0.146366	0.0439	0.2003	5008	,	,		20019	0.0942		0.2286	False		,,,				2504	0.2157				p.N222S		Atlas-SNP	.											.	ALG8	54	.	0			c.A665G						PASS	.	T	SER/ASN,SER/ASN	325,4075	170.1+/-200.6	7,311,1882	88.0	83.0	84.0		665,665	1.6	1.0	11	dbSNP_83	84	1967,6617	344.4+/-325.3	229,1509,2554	yes	missense,missense	ALG8	NM_001007027.2,NM_024079.4	46,46	236,1820,4436	CC,CT,TT		22.9147,7.3864,17.6525	benign,benign	222/468,222/527	77825320	2292,10692	2200	4292	6492	SO:0001583	missense	79053	exon6			GGTTTATTTGCAG	AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	608103	"""asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.665A>G	11.37:g.77825320T>C	ENSP00000299626:p.Asn222Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	85	32	0.376471	NM_024079	A6NDW6|O60860	Missense_Mutation	SNP	ENST00000299626.5	37	CCDS8258.1	332|332	0.152014652014652|0.152014652014652	22|22	0.044715447154471545|0.044715447154471545	77|77	0.212707182320442|0.212707182320442	58|58	0.10139860139860139|0.10139860139860139	175|175	0.23087071240105542|0.23087071240105542	T|T	2.710|2.710	-0.269072|-0.269072	0.05716|0.05716	0.073864|0.073864	0.229147|0.229147	ENSG00000159063|ENSG00000159063	ENST00000532306;ENST00000529139|ENST00000299626;ENST00000376156;ENST00000532440;ENST00000525755;ENST00000530454;ENST00000525870;ENST00000527099	.|D;D;D;D;D;D;D	.|0.83419	.|-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72	5.43|5.43	1.56|1.56	0.23342|0.23342	.|.	.|0.537635	.|0.21930	.|N	.|0.067028	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.33485|0.33485	1.01|1.01	0.35199|0.35199	P|P	0.225893|0.225893	.|B;B;B	.|0.06786	.|0.0;0.0;0.001	.|B;B;B	.|0.09377	.|0.004;0.002;0.004	T|T	0.03784|0.03784	-1.1004|-1.1004	4|9	.|0.06099	.|T	.|0.92	-2.1437|-2.1437	5.0202|5.0202	0.14358|0.14358	0.1276:0.2353:0.0:0.637|0.1276:0.2353:0.0:0.637	rs665278;rs3197648;rs52799833;rs56532042;rs57243244;rs665278|rs665278;rs3197648;rs52799833;rs56532042;rs57243244;rs665278	.|222;222;222	.|B3KQL8;Q9BVK2;A6NDW6	.|.;ALG8_HUMAN;.	V|S	96;67|222;222;40;171;223;134;134	.|ENSP00000299626:N222S;ENSP00000365326:N222S;ENSP00000433429:N40S;ENSP00000435467:N171S;ENSP00000434660:N223S;ENSP00000435417:N134S;ENSP00000436064:N134S	.|ENSP00000299626:N222S	I|N	-|-	1|2	0|0	ALG8|ALG8	77502968|77502968	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.989000|0.989000	0.77384|0.77384	0.541000|0.541000	0.23207|0.23207	0.064000|0.064000	0.16427|0.16427	0.383000|0.383000	0.25322|0.25322	ATA|AAT	T|0.842;C|0.158	0.158	strong		0.383	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079	
CEP104	9731	hgsc.bcm.edu	37	1	3761479	3761479	+	Silent	SNP	C	C	T	rs2275822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:3761479C>T	ENST00000378230.3	-	6	882	c.558G>A	c.(556-558)acG>acA	p.T186T	CEP104_ENST00000378223.3_Silent_p.T186T	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	186						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						ACCTGGCGTACGTTCCTTCTA	0.488													C|||	1750	0.349441	0.2345	0.4928	5008	,	,		16172	0.3383		0.4294	False		,,,				2504	0.3323				p.T186T		Atlas-SNP	.											.	CEP104	79	.	0			c.G558A						PASS	.	C		1160,3246	410.9+/-335.5	165,830,1208	113.0	97.0	102.0		558	-5.7	0.0	1	dbSNP_100	102	3739,4861	532.6+/-382.2	815,2109,1376	no	coding-synonymous	CEP104	NM_014704.3		980,2939,2584	TT,TC,CC		43.4767,26.3277,37.6672		186/926	3761479	4899,8107	2203	4300	6503	SO:0001819	synonymous_variant	9731	exon6			GGCGTACGTTCCT	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"""glycine, glutamate, thienylcyclohexylpiperidine binding protein"""		"""KIAA0562"""	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.558G>A	1.37:g.3761479C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Silent	SNP	ENST00000378230.3	37	CCDS30571.1																																																																																			C|0.630;T|0.370	0.370	strong		0.488	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704	
ZC3H3	23144	hgsc.bcm.edu	37	8	144620855	144620855	+	Missense_Mutation	SNP	C	C	A	rs4873802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144620855C>A	ENST00000262577.5	-	2	713	c.682G>T	c.(682-684)Gcg>Tcg	p.A228S		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	228			A -> S (in dbSNP:rs4873802).		mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			GGGAAGCTCGCCTTGACGGCA	0.667													C|||	748	0.149361	0.0348	0.2536	5008	,	,		16516	0.0804		0.1978	False		,,,				2504	0.2515				p.A228S		Atlas-SNP	.											.	ZC3H3	75	.	0			c.G682T						PASS	.	C	SER/ALA	281,4113	142.7+/-177.9	19,243,1935	30.0	26.0	27.0		682	0.5	0.0	8	dbSNP_111	27	1582,7010	275.3+/-291.7	146,1290,2860	yes	missense	ZC3H3	NM_015117.2	99	165,1533,4795	AA,AC,CC		18.4125,6.3951,14.3462	benign	228/949	144620855	1863,11123	2197	4296	6493	SO:0001583	missense	23144	exon2			AGCTCGCCTTGAC	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.682G>T	8.37:g.144620855C>A	ENSP00000262577:p.Ala228Ser	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	309	0.14148351648351648	14	0.028455284552845527	83	0.2292817679558011	53	0.09265734265734266	159	0.20976253298153033	C	3.323	-0.138368	0.06669	0.063951	0.184125	ENSG00000014164	ENST00000262577	T	0.03607	3.87	5.09	0.477	0.16784	.	1.374230	0.04843	N	0.440856	T	0.00012	0.0000	L	0.48362	1.52	0.80722	P	0.0	B	0.22346	0.068	B	0.13407	0.009	T	0.46911	-0.9157	9	0.07990	T	0.79	-0.0025	3.8282	0.08863	0.1438:0.4559:0.2563:0.1441	rs4873802;rs59350978;rs4873802	228	Q8IXZ2	ZC3H3_HUMAN	S	228	ENSP00000262577:A228S	ENSP00000262577:A228S	A	-	1	0	ZC3H3	144691998	0.045000	0.20229	0.011000	0.14972	0.004000	0.04260	-0.131000	0.10482	0.147000	0.19030	-0.150000	0.13652	GCG	C|0.858;A|0.142	0.142	strong		0.667	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
CECR5	27440	hgsc.bcm.edu	37	22	17640045	17640045	+	Missense_Mutation	SNP	G	G	A	rs7287672	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:17640045G>A	ENST00000336737.4	-	1	122	c.97C>T	c.(97-99)Cgc>Tgc	p.R33C	CECR5_ENST00000155674.5_Intron|CECR5-AS1_ENST00000431923.1_RNA|CECR5_ENST00000480451.1_5'UTR|CECR5_ENST00000399852.3_Missense_Mutation_p.R33C|CECR5-AS1_ENST00000329743.3_RNA	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	33						mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				TAGCACCTgcgggcggggcgg	0.791													G|||	1052	0.210064	0.3177	0.1844	5008	,	,		5516	0.0347		0.2803	False		,,,				2504	0.1912				p.R33C		Atlas-SNP	.											.	CECR5	46	.	0			c.C97T						PASS	.						2.0	2.0	2.0					22																	17640045		998	2399	3397	SO:0001583	missense	27440	exon1			ACCTGCGGGCGGG	AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.97C>T	22.37:g.17640045G>A	ENSP00000337358:p.Arg33Cys	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_033070	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Missense_Mutation	SNP	ENST00000336737.4	37	CCDS33595.1	471	0.21565934065934067	162	0.32926829268292684	85	0.23480662983425415	24	0.04195804195804196	200	0.2638522427440633	G	13.35	2.211993	0.39102	.	.	ENSG00000069998	ENST00000336737;ENST00000399852	T;T	0.28255	1.81;1.62	2.3	-1.53	0.08611	.	1.332850	0.05843	N	0.619692	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P	0.49559	0.925;0.833	B;B	0.37731	0.257;0.196	T	0.29336	-1.0015	9	0.66056	D	0.02	-2.3391	5.1552	0.15031	0.0:0.4811:0.3372:0.1817	rs7287672;rs11550529	33;33	A8MYZ9;Q9BXW7	.;CECR5_HUMAN	C	33	ENSP00000337358:R33C;ENSP00000382745:R33C	ENSP00000337358:R33C	R	-	1	0	CECR5	16020045	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.853000	0.04303	-0.249000	0.09569	0.561000	0.74099	CGC	G|0.785;A|0.215	0.215	strong		0.791	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829	
KRT25	147183	hgsc.bcm.edu	37	17	38910676	38910676	+	Missense_Mutation	SNP	G	G	C	rs146092638	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38910676G>C	ENST00000312150.4	-	2	534	c.474C>G	c.(472-474)atC>atG	p.I158M		NM_181534.3	NP_853512.1			keratin 25											endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(4)	16		Breast(137;0.00526)				TGGCATTATCGATCTGCAGAA	0.388																																					p.I158M		Atlas-SNP	.											.	KRT25	63	.	0			c.C474G						PASS	.	G	MET/ILE	0,4406		0,0,2203	137.0	130.0	133.0		474	-1.5	1.0	17	dbSNP_134	133	2,8598	2.2+/-6.3	0,2,4298	no	missense	KRT25	NM_181534.3	10	0,2,6501	CC,CG,GG		0.0233,0.0,0.0154	possibly-damaging	158/451	38910676	2,13004	2203	4300	6503	SO:0001583	missense	147183	exon2			ATTATCGATCTGC	AK129503	CCDS11373.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000204897	ENSG00000204897		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30839	protein-coding gene	gene with protein product			"""keratin 25A"""	KRT25A		16831889	Standard	NM_181534		Approved		uc002hve.3	Q7Z3Z0	OTTHUMG00000133373	ENST00000312150.4:c.474C>G	17.37:g.38910676G>C	ENSP00000310573:p.Ile158Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	145	56	0.386207	NM_181534		Missense_Mutation	SNP	ENST00000312150.4	37	CCDS11373.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305005	0.60305	0.0	2.33E-4	ENSG00000204897	ENST00000394042;ENST00000312150	D	0.89810	-2.57	5.73	-1.51	0.08664	Filament (1);	0.088817	0.49305	D	0.000153	D	0.92760	0.7698	M	0.84156	2.68	0.39210	D	0.963294	D	0.67145	0.996	D	0.66196	0.942	D	0.91638	0.5324	10	0.72032	D	0.01	.	11.8009	0.52126	0.6185:0.0:0.3815:0.0	.	158	Q7Z3Z0	K1C25_HUMAN	M	158	ENSP00000310573:I158M	ENSP00000310573:I158M	I	-	3	3	KRT25	36164202	0.036000	0.19791	0.972000	0.41901	0.900000	0.52787	-0.494000	0.06451	-0.516000	0.06470	-0.136000	0.14681	ATC	A|0.000;C|0.000;G|1.000	0.000	strong		0.388	KRT25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257218.1	NM_181534	
WAPAL	23063	hgsc.bcm.edu	37	10	88260252	88260252	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88260252C>A	ENST00000298767.5	-	3	1220	c.748G>T	c.(748-750)Gac>Tac	p.D250Y		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	250	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						AAAATACAGTCTTCTGATCTG	0.353																																					p.D250Y		Atlas-SNP	.											WAPAL,NS,carcinoma,0,1	WAPAL	81	1	0			c.G748T						scavenged	.						100.0	100.0	100.0					10																	88260252		2203	4300	6503	SO:0001583	missense	23063	exon3			TACAGTCTTCTGA	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"""friend of EBNA2"""	610754	"""KIAA0261"""	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.748G>T	10.37:g.88260252C>A	ENSP00000298767:p.Asp250Tyr	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	237	3	0.0126582	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	37	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.371473	0.42003	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.48836	0.8	5.78	5.78	0.91487	.	0.204155	0.41605	D	0.000857	T	0.53530	0.1802	L	0.36672	1.1	0.80722	D	1	P;P;D	0.54964	0.948;0.948;0.969	B;B;P	0.57620	0.446;0.446;0.824	T	0.54556	-0.8276	10	0.72032	D	0.01	.	13.2393	0.59987	0.0:0.9275:0.0:0.0725	.	250;250;293	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	Y	335;250;335	ENSP00000298767:D250Y	ENSP00000298767:D250Y	D	-	1	0	WAPAL	88250232	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.293000	0.51779	2.722000	0.93159	0.655000	0.94253	GAC	.	.	none		0.353	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045	
CACNA1H	8912	hgsc.bcm.edu	37	16	1268485	1268485	+	Silent	SNP	C	C	T	rs2738891	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1268485C>T	ENST00000348261.5	+	33	5969	c.5721C>T	c.(5719-5721)ggC>ggT	p.G1907G	CACNA1H_ENST00000358590.4_Silent_p.G1901G|CACNA1H_ENST00000565831.1_Silent_p.G1901G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1907					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	AGAGTCCGGGCGCCAGGGACG	0.692													C|||	449	0.0896565	0.0113	0.0605	5008	,	,		14302	0.0317		0.1133	False		,,,				2504	0.2515				p.G1907G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5721T						PASS	.	C	,	94,3926		0,94,1916	22.0	29.0	27.0		5703,5721	-3.0	0.0	16	dbSNP_100	27	969,7165		49,871,3147	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	49,965,5063	TT,TC,CC		11.913,2.3383,8.7461	,	1901/2348,1907/2354	1268485	1063,11091	2010	4067	6077	SO:0001819	synonymous_variant	8912	exon33			TCCGGGCGCCAGG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5721C>T	16.37:g.1268485C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	16	14	0.875	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.936;T|0.064	0.064	strong		0.692	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
DNAH7	56171	hgsc.bcm.edu	37	2	196749504	196749504	+	Silent	SNP	G	G	A	rs60214909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:196749504G>A	ENST00000312428.6	-	35	5668	c.5568C>T	c.(5566-5568)tcC>tcT	p.S1856S		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1856					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AAGCACCAACGGACCAGATCA	0.333													G|||	508	0.101438	0.177	0.0937	5008	,	,		20616	0.0		0.1292	False		,,,				2504	0.0808				p.S1856S		Atlas-SNP	.											.	DNAH7	512	.	0			c.C5568T						PASS	.	G		665,3019		53,559,1230	70.0	64.0	66.0		5568	-5.0	0.0	2	dbSNP_129	66	1088,7098		70,948,3075	no	coding-synonymous	DNAH7	NM_018897.2		123,1507,4305	AA,AG,GG		13.291,18.051,14.7683		1856/4025	196749504	1753,10117	1842	4093	5935	SO:0001819	synonymous_variant	56171	exon35			ACCAACGGACCAG	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.5568C>T	2.37:g.196749504G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			G|0.877;A|0.123	0.123	strong		0.333	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56735015	56735015	+	Silent	SNP	T	T	C	rs4801692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56735015T>C	ENST00000587340.1	-	5	1268	c.573A>G	c.(571-573)gcA>gcG	p.A191A	ZSCAN5A_ENST00000254165.3_Silent_p.A74A|ZSCAN5A_ENST00000587492.1_Silent_p.A45A|ZSCAN5A_ENST00000391713.1_Silent_p.A191A|ZSCAN5A_ENST00000592355.1_Silent_p.A191A			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	191					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TCCTGGACAATGCAGGGACCC	0.612													T|||	226	0.0451278	0.0946	0.0562	5008	,	,		17867	0.0		0.0457	False		,,,				2504	0.0164				p.A191A		Atlas-SNP	.											.	ZSCAN5A	118	.	0			c.A573G						PASS	.	T		451,3955	212.8+/-232.6	27,397,1779	49.0	45.0	47.0		573	-5.6	0.0	19	dbSNP_111	47	433,8167	131.2+/-189.0	9,415,3876	no	coding-synonymous	ZSCAN5A	NM_024303.1		36,812,5655	CC,CT,TT		5.0349,10.236,6.7969		191/497	56735015	884,12122	2203	4300	6503	SO:0001819	synonymous_variant	79149	exon3			GGACAATGCAGGG	AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"""-"", ""Zinc fingers, C2H2-type"""	23710	protein-coding gene	gene with protein product			"""zinc finger protein 495"", ""zinc finger and SCAN domain containing 5"""	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.573A>G	19.37:g.56735015T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_024303	B4DX98|Q49A73|Q53F04|Q8N7B3	Silent	SNP	ENST00000587340.1	37	CCDS12941.1																																																																																			T|0.937;C|0.063	0.063	strong		0.612	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303	
GNAT1	2779	hgsc.bcm.edu	37	3	50232262	50232262	+	Silent	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50232262G>T	ENST00000433068.1	+	8	983	c.927G>T	c.(925-927)cgG>cgT	p.R309R	GNAT1_ENST00000232461.3_Silent_p.R309R	NM_000172.3	NP_000163.2	P11488	GNAT1_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1	309					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell proliferation (GO:0008283)|cellular response to electrical stimulus (GO:0071257)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|phototransduction, visible light (GO:0007603)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to light intensity (GO:0009642)|response to light stimulus (GO:0009416)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	acyl binding (GO:0000035)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TCAACATGCGGCGCGACGTGA	0.577											OREG0015580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R309R		Atlas-SNP	.											.	GNAT1	39	.	0			c.G927T						PASS	.						91.0	73.0	79.0					3																	50232262		2203	4300	6503	SO:0001819	synonymous_variant	2779	exon8			CATGCGGCGCGAC		CCDS2812.1	3p21	2014-01-28			ENSG00000114349	ENSG00000114349			4393	protein-coding gene	gene with protein product		139330					Standard	NM_000172		Approved	CSNBAD3	uc003cyl.2	P11488	OTTHUMG00000156808	ENST00000433068.1:c.927G>T	3.37:g.50232262G>T		Somatic	95	0	0	968	WXS	Illumina HiSeq	Phase_I	87	31	0.356322	NM_144499	Q4VBN2	Silent	SNP	ENST00000433068.1	37	CCDS2812.1																																																																																			.	.	none		0.577	GNAT1-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345957.1	NM_000172	
SEC24B	10427	hgsc.bcm.edu	37	4	110384790	110384790	+	Silent	SNP	A	A	G	rs33911248	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110384790A>G	ENST00000265175.5	+	2	922	c.867A>G	c.(865-867)ccA>ccG	p.P289P	SEC24B_ENST00000399100.2_Silent_p.P289P|SEC24B_ENST00000504968.2_Silent_p.P320P	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	289					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		ACAACAACCCAACCATTACTG	0.413													A|||	355	0.0708866	0.1051	0.0591	5008	,	,		21905	0.0		0.0934	False		,,,				2504	0.0828				p.P289P		Atlas-SNP	.											SEC24B_ENST00000265175,rectum,carcinoma,+1,2	SEC24B	186	2	0			c.A867G						PASS	.	A	,	484,3528		30,424,1552	64.0	63.0	64.0		867,867	-3.8	0.0	4	dbSNP_126	64	892,7488		42,808,3340	no	coding-synonymous,coding-synonymous	SEC24B	NM_001042734.1,NM_006323.2	,	72,1232,4892	GG,GA,AA		10.6444,12.0638,11.1039	,	289/1234,289/1269	110384790	1376,11016	2006	4190	6196	SO:0001819	synonymous_variant	10427	exon2			CAACCCAACCATT	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.867A>G	4.37:g.110384790A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Silent	SNP	ENST00000265175.5	37	CCDS47124.1																																																																																			A|0.915;G|0.085	0.085	strong		0.413	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		
KAT6A	7994	hgsc.bcm.edu	37	8	41794934	41794934	+	Silent	SNP	C	C	T	rs13748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:41794934C>T	ENST00000396930.3	-	17	3735	c.3192G>A	c.(3190-3192)acG>acA	p.T1064T	KAT6A_ENST00000265713.2_Silent_p.T1064T|KAT6A_ENST00000406337.1_Silent_p.T1064T	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1064					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CGATCTCAAACGTGGGTTCTA	0.438													C|||	1049	0.209465	0.4849	0.1484	5008	,	,		18800	0.004		0.2704	False		,,,				2504	0.0297				p.T1064T		Atlas-SNP	.											.	.	.	.	0			c.G3192A						PASS	.	C	,,	1890,2516	543.4+/-376.3	417,1056,730	122.0	117.0	119.0		3192,3192,3192	-11.3	0.2	8	dbSNP_52	119	2019,6581	353.5+/-329.1	243,1533,2524	no	coding-synonymous,coding-synonymous,coding-synonymous	KAT6A	NM_001099412.1,NM_001099413.1,NM_006766.3	,,	660,2589,3254	TT,TC,CC		23.4767,42.8961,30.0554	,,	1064/2005,1064/2005,1064/2005	41794934	3909,9097	2203	4300	6503	SO:0001819	synonymous_variant	7994	exon17			CTCAAACGTGGGT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.3192G>A	8.37:g.41794934C>T		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	312	146	0.467949	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	37	CCDS6124.1																																																																																			C|0.720;T|0.280	0.280	strong		0.438	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
ANXA4	307	hgsc.bcm.edu	37	2	70033584	70033584	+	Missense_Mutation	SNP	C	C	T	rs2228203	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:70033584C>T	ENST00000394295.4	+	5	508	c.260C>T	c.(259-261)aCg>aTg	p.T87M	ANXA4_ENST00000409920.1_Intron|ANXA4_ENST00000536030.1_Missense_Mutation_p.T3M	NM_001153.3	NP_001144.1	P09525	ANXA4_HUMAN	annexin A4	85					epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						GGGATGATGACGCCCACGGTG	0.537													C|||	1005	0.200679	0.3169	0.17	5008	,	,		21921	0.1736		0.1958	False		,,,				2504	0.0982				p.T87M		Atlas-SNP	.											.	ANXA4	34	.	0			c.C260T						PASS	.	C	MET/THR	1367,3039	453.6+/-350.4	227,913,1063	207.0	145.0	166.0		260	-1.3	0.7	2	dbSNP_98	166	1628,6972	301.4+/-305.4	155,1318,2827	yes	missense	ANXA4	NM_001153.3	81	382,2231,3890	TT,TC,CC		18.9302,31.0259,23.0278	benign	87/322	70033584	2995,10011	2203	4300	6503	SO:0001583	missense	307	exon5			TGATGACGCCCAC	M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975		"""Annexins"""	542	protein-coding gene	gene with protein product		106491		ANX4		1346776	Standard	NM_001153		Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000394295.4:c.260C>T	2.37:g.70033584C>T	ENSP00000377833:p.Thr87Met	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	334	145	0.434132	NM_001153	B4DDF9|Q96F33|Q9BWK1	Missense_Mutation	SNP	ENST00000394295.4	37	CCDS1894.1	491	0.22481684981684982	162	0.32926829268292684	61	0.1685082872928177	112	0.1958041958041958	156	0.20580474934036938	C	0.114	-1.134746	0.01742	0.310259	0.189302	ENSG00000196975	ENST00000394295;ENST00000536030	T;T	0.11930	2.73;2.73	4.97	-1.3	0.09259	.	0.184470	0.56097	N	0.000028	T	0.00012	0.0000	N	0.05078	-0.115	0.30952	P	0.724574	B;B	0.20671	0.023;0.047	B;B	0.17098	0.004;0.017	T	0.49485	-0.8935	8	.	.	.	.	10.5802	0.45250	0.0:0.5408:0.0:0.4592	rs2228203;rs11549470;rs17355624;rs52832365;rs61061911;rs11549470	85;87	P09525;Q6LES2	ANXA4_HUMAN;.	M	87;3	ENSP00000377833:T87M;ENSP00000441931:T3M	.	T	+	2	0	ANXA4	69887088	0.129000	0.22400	0.707000	0.30419	0.004000	0.04260	0.043000	0.13971	-0.232000	0.09811	-1.056000	0.02311	ACG	C|0.770;A|0.001	.	strong		0.537	ANXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251848.2	NM_001153	
ZNF610	162963	hgsc.bcm.edu	37	19	52856955	52856955	+	Silent	SNP	C	C	T	rs1961205	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52856955C>T	ENST00000403906.3	+	4	540	c.84C>T	c.(82-84)gaC>gaT	p.D28D	ZNF610_ENST00000601151.1_Silent_p.D28D|ZNF610_ENST00000321287.8_Silent_p.D28D|ZNF610_ENST00000327920.8_Silent_p.D28D	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	28	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D28D(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		CATTCATGGACGTGGCCATCG	0.418													c|||	2073	0.413938	0.3903	0.3357	5008	,	,		17553	0.4504		0.3926	False		,,,				2504	0.4857				p.D28D		Atlas-SNP	.											ZNF610,NS,carcinoma,+1,2	ZNF610	84	2	1	Substitution - coding silent(1)	stomach(1)	c.C84T						PASS	.	T	,,,	1815,2591	533.0+/-373.6	373,1069,761	96.0	96.0	96.0		84,84,84,84	-2.9	0.6	19	dbSNP_92	96	3259,5341	489.0+/-372.5	619,2021,1660	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	,,,	992,3090,2421	TT,TC,CC		37.8953,41.1938,39.0128	,,,	28/463,28/463,28/420,28/463	52856955	5074,7932	2203	4300	6503	SO:0001819	synonymous_variant	162963	exon4			CATGGACGTGGCC	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.84C>T	19.37:g.52856955C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_001161427	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	37	CCDS12851.1																																																																																			C|0.610;T|0.390	0.390	strong		0.418	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
CIT	11113	hgsc.bcm.edu	37	12	120166407	120166407	+	Missense_Mutation	SNP	T	T	C	rs145731510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:120166407T>C	ENST00000261833.7	-	27	3417	c.3365A>G	c.(3364-3366)aAt>aGt	p.N1122S	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Missense_Mutation_p.N1164S	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1122	Interaction with Rho/Rac.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CTCCAGGTCATTGAGCTAGAC	0.443																																					p.N1164S		Atlas-SNP	.											.	CIT	535	.	0			c.A3491G						PASS	.	T	SER/ASN,SER/ASN	0,4406		0,0,2203	170.0	159.0	163.0		3491,3365	4.1	1.0	12	dbSNP_134	163	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	CIT	NM_001206999.1,NM_007174.2	46,46	0,14,6489	CC,CT,TT		0.1628,0.0,0.1076	probably-damaging,probably-damaging	1164/2070,1122/2028	120166407	14,12992	2203	4300	6503	SO:0001583	missense	11113	exon28			AGGTCATTGAGCT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3365A>G	12.37:g.120166407T>C	ENSP00000261833:p.Asn1122Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.39|13.39	2.222469|2.222469	0.39300|0.39300	0.0|0.0	0.001628|0.001628	ENSG00000122966|ENSG00000122966	ENST00000392520|ENST00000392521;ENST00000261833	.|T;T	.|0.63913	.|-0.03;-0.07	5.29|5.29	4.14|4.14	0.48551|0.48551	.|.	.|0.052340	.|0.85682	.|N	.|0.000000	T|T	0.53769|0.53769	0.1817|0.1817	N|N	0.17082|0.17082	0.46|0.46	0.45791|0.45791	D|D	0.998671|0.998671	.|D;B;B	.|0.62365	.|0.991;0.0;0.023	.|P;B;B	.|0.52343	.|0.696;0.002;0.032	T|T	0.50792|0.50792	-0.8786|-0.8786	5|10	.|0.32370	.|T	.|0.25	.|.	11.2234|11.2234	0.48869|0.48869	0.0:0.0724:0.0:0.9276|0.0:0.0724:0.0:0.9276	.|.	.|1164;1122;655	.|Q2M5E1;O14578;O14578-3	.|.;CTRO_HUMAN;.	V|S	750|1164;1122	.|ENSP00000376306:N1164S;ENSP00000261833:N1122S	.|ENSP00000261833:N1122S	M|N	-|-	1|2	0|0	CIT|CIT	118650790|118650790	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.105000|3.105000	0.50314|0.50314	0.959000|0.959000	0.37980|0.37980	0.533000|0.533000	0.62120|0.62120	ATG|AAT	T|0.999;C|0.001	0.001	strong		0.443	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
SELE	6401	hgsc.bcm.edu	37	1	169698643	169698643	+	Missense_Mutation	SNP	T	T	G	rs41272475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169698643T>G	ENST00000333360.7	-	6	1026	c.887A>C	c.(886-888)aAg>aCg	p.K296T	SELE_ENST00000367776.1_Missense_Mutation_p.K296T|SELE_ENST00000367780.4_Missense_Mutation_p.K234T|SELE_ENST00000367779.4_Missense_Mutation_p.K296T|SELE_ENST00000367782.4_Missense_Mutation_p.K296T|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367774.1_Missense_Mutation_p.K296T|SELE_ENST00000367777.1_Missense_Mutation_p.K296T|SELE_ENST00000367775.1_Missense_Mutation_p.K234T|SELE_ENST00000367781.4_Missense_Mutation_p.K296T	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	296	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	ACACGTTGGCTTCTCGTTGTC	0.463													T|||	6	0.00119808	0.0	0.0	5008	,	,		22358	0.0		0.006	False		,,,				2504	0.0				p.K296T		Atlas-SNP	.											.	SELE	84	.	0			c.A887C						PASS	.	T	THR/LYS	4,4402	8.1+/-20.4	0,4,2199	144.0	134.0	137.0		887	-6.9	0.0	1	dbSNP_127	137	33,8567	22.2+/-67.0	0,33,4267	yes	missense	SELE	NM_000450.2	78	0,37,6466	GG,GT,TT		0.3837,0.0908,0.2845	benign	296/611	169698643	37,12969	2203	4300	6503	SO:0001583	missense	6401	exon6			GTTGGCTTCTCGT	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"""CD molecules"""	10718	protein-coding gene	gene with protein product		131210	"""endothelial adhesion molecule 1"""	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.887A>C	1.37:g.169698643T>G	ENSP00000331736:p.Lys296Thr	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	190	79	0.415789	NM_000450	A2RRD6|P16111	Missense_Mutation	SNP	ENST00000333360.7	37	CCDS1283.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	2.610	-0.291098	0.05568	9.08E-4	0.003837	ENSG00000007908	ENST00000367781;ENST00000367782;ENST00000367780;ENST00000367779;ENST00000333360;ENST00000367777;ENST00000367775;ENST00000367776;ENST00000367774	T;T;T;T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.71	-6.86	0.01676	Complement control module (2);Sushi/SCR/CCP (3);	0.864791	0.09823	N	0.751202	T	0.16769	0.0403	L	0.27053	0.805	0.09310	N	1	B	0.27700	0.186	B	0.34093	0.175	T	0.25433	-1.0132	10	0.18710	T	0.47	-2.3072	0.7368	0.00967	0.2045:0.3013:0.1795:0.3146	rs41272475;rs62617134	296	P16581	LYAM2_HUMAN	T	296;296;234;296;296;296;234;296;296	ENSP00000356755:K296T;ENSP00000356756:K296T;ENSP00000356754:K234T;ENSP00000356753:K296T;ENSP00000331736:K296T;ENSP00000356751:K296T;ENSP00000356749:K234T;ENSP00000356750:K296T;ENSP00000356748:K296T	ENSP00000331736:K296T	K	-	2	0	SELE	167965267	0.000000	0.05858	0.048000	0.18961	0.195000	0.23768	-2.070000	0.01380	-1.060000	0.03189	-0.248000	0.11899	AAG	T|0.996;G|0.004	0.004	strong		0.463	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450	
ZNF618	114991	hgsc.bcm.edu	37	9	116764283	116764283	+	Silent	SNP	C	C	T	rs4978561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:116764283C>T	ENST00000374126.5	+	5	540	c.441C>T	c.(439-441)taC>taT	p.Y147Y	ZNF618_ENST00000288466.7_Silent_p.Y115Y			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	147					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						CAGGGTCTTACGAATGCGGAA	0.562													T|||	1654	0.330272	0.1293	0.2882	5008	,	,		21788	0.6022		0.3489	False		,,,				2504	0.3323				p.Y115Y		Atlas-SNP	.											.	ZNF618	184	.	0			c.C345T						PASS	.	T		611,3365		37,537,1414	131.0	134.0	133.0		345	-3.8	1.0	9	dbSNP_111	133	2760,5542		468,1824,1859	no	coding-synonymous	ZNF618	NM_133374.2		505,2361,3273	TT,TC,CC		33.245,15.3672,27.4556		115/862	116764283	3371,8907	1988	4151	6139	SO:0001819	synonymous_variant	114991	exon4			GTCTTACGAATGC	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.441C>T	9.37:g.116764283C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				C|0.645;T|0.355	0.355	strong		0.562	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835218	27835218	+	Silent	SNP	G	G	A	rs17763089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:27835218G>A	ENST00000331442.3	-	1	141	c.90C>T	c.(88-90)ggC>ggT	p.G30G		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	30					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CAGCGCCGGCGCCGGCAGCCT	0.617													G|||	103	0.0205671	0.0023	0.0389	5008	,	,		13957	0.0		0.0726	False		,,,				2504	0.0				p.G30G		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C90T						PASS	.	G		90,4302		2,86,2108	31.0	38.0	36.0		90	-5.1	0.0	6	dbSNP_123	36	768,7824		35,698,3563	no	coding-synonymous	HIST1H1B	NM_005322.2		37,784,5671	AA,AG,GG		8.9385,2.0492,6.6081		30/227	27835218	858,12126	2196	4296	6492	SO:0001819	synonymous_variant	3009	exon1			GCCGGCGCCGGCA	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.90C>T	6.37:g.27835218G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	178	79	0.44382	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			G|0.945;A|0.055	0.055	strong		0.617	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
C1orf192	257177	hgsc.bcm.edu	37	1	161335414	161335414	+	Missense_Mutation	SNP	G	G	A	rs141881555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161335414G>A	ENST00000367974.1	-	4	255	c.250C>T	c.(250-252)Cgt>Tgt	p.R84C	RP11-122G18.5_ENST00000437833.2_lincRNA	NM_001013625.2	NP_001013647.2	Q5VTH2	CA192_HUMAN	chromosome 1 open reading frame 192	84										endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10	all_cancers(52;4.64e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCAGTTGTACGGGAGGTCAGG	0.507													g|||	3	0.000599042	0.0	0.0	5008	,	,		16556	0.0		0.002	False		,,,				2504	0.001				p.R84C		Atlas-SNP	.											.	C1orf192	20	.	0			c.C250T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	142.0	150.0	148.0		250	3.5	0.9	1	dbSNP_134	148	15,8585	11.2+/-40.8	0,15,4285	yes	missense	C1orf192	NM_001013625.2	180	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	probably-damaging	84/178	161335414	15,12991	2203	4300	6503	SO:0001583	missense	257177	exon4			TTGTACGGGAGGT		CCDS30921.1	1q23.3	2014-02-21			ENSG00000188931	ENSG00000188931			32325	protein-coding gene	gene with protein product							Standard	NM_001013625		Approved	Flattop, Fltp	uc001gal.4	Q5VTH2	OTTHUMG00000034462	ENST00000367974.1:c.250C>T	1.37:g.161335414G>A	ENSP00000356951:p.Arg84Cys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	276	175	0.634058	NM_001013625		Missense_Mutation	SNP	ENST00000367974.1	37	CCDS30921.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	19.41	3.821832	0.71028	0.0	0.001744	ENSG00000188931	ENST00000367974	.	.	.	5.49	3.5	0.40072	.	0.074082	0.53938	N	0.000057	T	0.56877	0.2015	M	0.66939	2.045	0.36982	D	0.894331	D	0.89917	1.0	D	0.97110	1.0	T	0.62955	-0.6744	8	0.72032	D	0.01	-12.236	8.235	0.31620	0.0838:0.0:0.7599:0.1564	.	84	Q5VTH2	CA192_HUMAN	C	84	.	ENSP00000356951:R84C	R	-	1	0	C1orf192	159602038	1.000000	0.71417	0.902000	0.35471	0.983000	0.72400	3.636000	0.54317	1.456000	0.47831	0.655000	0.94253	CGT	G|0.999;A|0.001	0.001	strong		0.507	C1orf192-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083309.1	NM_001013625	
SLC25A29	123096	hgsc.bcm.edu	37	14	100759046	100759046	+	Silent	SNP	C	C	A	rs3825555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:100759046C>A	ENST00000359232.3	-	4	786	c.486G>T	c.(484-486)acG>acT	p.T162T	SLC25A29_ENST00000539621.1_Silent_p.T96T|SLC25A29_ENST00000556505.1_Silent_p.T96T|SLC25A29_ENST00000555927.1_Silent_p.T96T|RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000554912.1_Silent_p.T96T|AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000392908.3_3'UTR	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	162						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	acyl carnitine transmembrane transporter activity (GO:0015227)			NS(1)|endometrium(1)|ovary(1)	3		Melanoma(154;0.152)			L-Carnitine(DB00583)	CGAAGCTGGGCGTCTCACGCA	0.682													C|||	2656	0.530351	0.3865	0.6081	5008	,	,		13189	0.7083		0.5676	False		,,,				2504	0.4479				p.T162T		Atlas-SNP	.											SLC25A29,NS,carcinoma,0,1	SLC25A29	14	1	0			c.G486T						PASS	.	C		1913,2477		431,1051,713	29.0	19.0	22.0		486	1.1	1.0	14	dbSNP_107	22	4870,3718		1397,2076,821	no	coding-synonymous	SLC25A29	NM_001039355.1		1828,3127,1534	AA,AC,CC		43.293,43.5763,47.7346		162/304	100759046	6783,6195	2195	4294	6489	SO:0001819	synonymous_variant	123096	exon4			GCTGGGCGTCTCA	AK095532	CCDS32156.1	14q32.2	2013-05-22	2012-03-29	2004-01-21	ENSG00000197119	ENSG00000197119		"""Solute carriers"""	20116	protein-coding gene	gene with protein product		615064	"""chromosome 14 open reading frame 69"", ""solute carrier family 25, member 29"""	C14orf69			Standard	XM_005267343		Approved	FLJ38975	uc010twx.2	Q8N8R3	OTTHUMG00000171569	ENST00000359232.3:c.486G>T	14.37:g.100759046C>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	NM_001039355	A3KMR5|Q541V0	Silent	SNP	ENST00000359232.3	37	CCDS32156.1																																																																																			C|0.465;A|0.535	0.535	strong		0.682	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3		
BRINP2	57795	hgsc.bcm.edu	37	1	177245369	177245369	+	Missense_Mutation	SNP	C	C	T	rs145109858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177245369C>T	ENST00000361539.4	+	6	1123	c.811C>T	c.(811-813)Cgc>Tgc	p.R271C	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	271	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											TCTGCGTGAGCGCTTTGTAGC	0.562																																					p.R271C		Atlas-SNP	.											FAM5B,NS,carcinoma,0,3	FAM5B	191	3	0			c.C811T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	68.0	61.0	64.0		811	6.1	1.0	1	dbSNP_134	64	7,8593	5.7+/-21.5	0,7,4293	yes	missense	FAM5B	NM_021165.2	180	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	probably-damaging	271/784	177245369	8,12998	2203	4300	6503	SO:0001583	missense	57795	exon6			CGTGAGCGCTTTG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.811C>T	1.37:g.177245369C>T	ENSP00000354481:p.Arg271Cys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	224	126	0.5625	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939863	0.73557	2.27E-4	8.14E-4	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.15834	2.39	6.07	6.07	0.98685	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.85682	D	0.000000	T	0.38719	0.1051	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.993	D;P;P	0.67725	0.953;0.899;0.548	T	0.03453	-1.1035	10	0.87932	D	0	-25.4339	15.0142	0.71570	0.1424:0.8576:0.0:0.0	.	21;166;271	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	C	21;271	ENSP00000354481:R271C	ENSP00000354481:R271C	R	+	1	0	FAM5B	175511992	0.998000	0.40836	1.000000	0.80357	0.989000	0.77384	0.813000	0.27225	2.884000	0.98904	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	strong		0.562	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
NPC1	4864	hgsc.bcm.edu	37	18	21119777	21119777	+	Silent	SNP	G	G	A	rs1140458	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21119777G>A	ENST00000269228.5	-	18	3347	c.2793C>T	c.(2791-2793)aaC>aaT	p.N931N	NPC1_ENST00000412552.2_Silent_p.N613N|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	931					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GTACTGACTAGTTGTCCAGCT	0.527													G|||	2424	0.484026	0.3646	0.611	5008	,	,		18099	0.6111		0.4573	False		,,,				2504	0.4519				p.N931N		Atlas-SNP	.											NPC1,NS,carcinoma,0,1	NPC1	114	1	0			c.C2793T						PASS	.	G		1709,2697	513.7+/-368.4	311,1087,805	56.0	52.0	53.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2793	4.4	1.0	18	dbSNP_86	53	4040,4560	553.0+/-386.2	936,2168,1196	no	coding-synonymous	NPC1	NM_000271.4		1247,3255,2001	AA,AG,GG		46.9767,38.788,44.2027		931/1279	21119777	5749,7257	2203	4300	6503	SO:0001819	synonymous_variant	4864	exon18			TGACTAGTTGTCC	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2793C>T	18.37:g.21119777G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	117	41	0.350427	NM_000271	B4DET3|Q9P130	Silent	SNP	ENST00000269228.5	37	CCDS11878.1																																																																																			T|0.094;G|0.438;C|0.101;A|0.366	0.366	strong		0.527	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
FRG2B	441581	hgsc.bcm.edu	37	10	135438933	135438933	+	Silent	SNP	C	C	T	rs200793608		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:135438933C>T	ENST00000425520.1	-	4	559	c.507G>A	c.(505-507)ccG>ccA	p.P169P	FRG2B_ENST00000443774.1_Silent_p.P170P	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	169						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TTCGAATTGACGGTGTTTGGA	0.552																																					p.P169P		Atlas-SNP	.											FRG2B,colon,carcinoma,-1,1	FRG2B	47	1	0			c.G507A						scavenged	.						126.0	151.0	143.0					10																	135438933		2193	4291	6484	SO:0001819	synonymous_variant	441581	exon4			AATTGACGGTGTT	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.507G>A	10.37:g.135438933C>T		Somatic	494	5	0.0101215		WXS	Illumina HiSeq	Phase_I	580	12	0.0206897	NM_001080998	Q5VSQ1	Silent	SNP	ENST00000425520.1	37	CCDS44502.1																																																																																			C|0.996;T|0.004	0.004	weak		0.552	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
CDH17	1015	hgsc.bcm.edu	37	8	95158382	95158382	+	Silent	SNP	C	C	T	rs1131830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95158382C>T	ENST00000027335.3	-	15	2065	c.1941G>A	c.(1939-1941)ttG>ttA	p.L647L	CDH17_ENST00000441892.2_Silent_p.L433L|CDH17_ENST00000450165.2_Silent_p.L647L	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	647	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			ACACAGAGCTCAAGGAAGACC	0.443													C|||	2161	0.43151	0.2678	0.3761	5008	,	,		18107	0.5327		0.5457	False		,,,				2504	0.4703				p.L647L		Atlas-SNP	.											.	CDH17	119	.	0			c.G1941A						PASS	.	C	,	1319,3087	443.1+/-346.9	185,949,1069	85.0	78.0	81.0		1941,1941	5.9	0.1	8	dbSNP_86	81	4604,3996	599.3+/-394.1	1238,2128,934	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	1423,3077,2003	TT,TC,CC		46.4651,29.9365,45.5405	,	647/833,647/833	95158382	5923,7083	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon15			AGAGCTCAAGGAA	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1941G>A	8.37:g.95158382C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	170	68	0.4	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			T|0.375;G|0.108;C|0.432;A|0.085	0.375	strong		0.443	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
PRB2	653247	hgsc.bcm.edu	37	12	11546192	11546192	+	Missense_Mutation	SNP	G	G	A	rs10845349	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:11546192G>A	ENST00000389362.4	-	3	855	c.820C>T	c.(820-822)Cct>Tct	p.P274S	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	274	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].		S -> P (may abrogate glycosylation at N- 272; dbSNP:rs10845349). {ECO:0000269|PubMed:16541075, ECO:0000269|PubMed:8554050}.			extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGACCTTGAGGTTTGTTGCCT	0.607													g|||	1566	0.3127	0.0439	0.3588	5008	,	,		21147	0.376		0.5477	False		,,,				2504	0.3364				p.P274S		Atlas-SNP	.											PRB2_ENST00000389362,brain,glioma,0,8	PRB2	168	8	0			c.C820T						PASS	.		SER/PRO	575,3495		78,419,1538	60.0	83.0	75.0		820	0.1	0.0	12	dbSNP_120	75	5021,3209		1553,1915,647	no	missense	PRB2	NM_006248.3	74	1631,2334,2185	AA,AG,GG		38.9915,14.1278,45.4959	benign	274/417	11546192	5596,6704	2035	4115	6150	SO:0001583	missense	653247	exon3			CTTGAGGTTTGTT	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.820C>T	12.37:g.11546192G>A	ENSP00000374013:p.Pro274Ser	Somatic	361	1	0.00277008		WXS	Illumina HiSeq	Phase_I	419	315	0.75179	NM_006248	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	37	CCDS41757.2	528	0.24175824175824176	35	0.07113821138211382	93	0.2569060773480663	136	0.23776223776223776	264	0.3482849604221636	.	0.011	-1.731107	0.00687	0.141278	0.610085	ENSG00000121335	ENST00000389362	T	0.04015	3.73	1.23	0.0818	0.14426	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.11767	-1.0574	5	0.15066	T	0.55	.	4.2417	0.10650	0.2844:0.0:0.7156:0.0	rs10845349	.	.	.	S	274	ENSP00000374013:P274S	ENSP00000374013:P274S	P	-	1	0	PRB2	11437459	0.001000	0.12720	0.000000	0.03702	0.029000	0.11900	-0.952000	0.03881	-0.292000	0.08999	0.175000	0.17021	CCT	G|0.771;A|0.229	0.229	strong		0.607	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
FMNL2	114793	hgsc.bcm.edu	37	2	153468107	153468107	+	Silent	SNP	C	C	T	rs35776654	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:153468107C>T	ENST00000288670.9	+	11	1417	c.1050C>T	c.(1048-1050)gaC>gaT	p.D350D		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	350	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)		p.D350D(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						TAGGCCTGGACGAATACTTGG	0.393													C|||	260	0.0519169	0.0053	0.0576	5008	,	,		18613	0.0069		0.1392	False		,,,				2504	0.0675				p.D350D		Atlas-SNP	.											FMNL2,NS,carcinoma,0,1	FMNL2	75	1	1	Substitution - coding silent(1)	prostate(1)	c.C1050T						PASS	.	C		86,3704		0,86,1809	86.0	76.0	79.0		1050	-0.6	1.0	2	dbSNP_126	79	1167,7075		91,985,3045	no	coding-synonymous	FMNL2	NM_052905.3		91,1071,4854	TT,TC,CC		14.1592,2.2691,10.4139		350/1093	153468107	1253,10779	1895	4121	6016	SO:0001819	synonymous_variant	114793	exon11			CCTGGACGAATAC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1050C>T	2.37:g.153468107C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																			C|0.918;T|0.082	0.082	strong		0.393	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
LAD1	3898	hgsc.bcm.edu	37	1	201358304	201358304	+	Missense_Mutation	SNP	C	C	A	rs3738281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:201358304C>A	ENST00000391967.2	-	2	467	c.166G>T	c.(166-168)Gcc>Tcc	p.A56S	LAD1_ENST00000367313.3_Missense_Mutation_p.A70S	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	56			A -> S (in dbSNP:rs3738281).			basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						GAAGCAGAGGCCTGCCGGTCT	0.602													C|||	890	0.177716	0.357	0.0735	5008	,	,		18618	0.1081		0.0944	False		,,,				2504	0.1667				p.A56S		Atlas-SNP	.											.	LAD1	42	.	0			c.G166T						PASS	.	C	SER/ALA	1396,3010	457.6+/-351.7	217,962,1024	73.0	72.0	73.0		166	1.0	0.0	1	dbSNP_107	73	882,7718	198.5+/-242.8	48,786,3466	yes	missense	LAD1	NM_005558.3	99	265,1748,4490	AA,AC,CC		10.2558,31.6841,17.515	benign	56/518	201358304	2278,10728	2203	4300	6503	SO:0001583	missense	3898	exon2			CAGAGGCCTGCCG	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.166G>T	1.37:g.201358304C>A	ENSP00000375829:p.Ala56Ser	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	202	72	0.356436	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	37	CCDS1410.1	346	0.15842490842490842	181	0.3678861788617886	31	0.0856353591160221	56	0.0979020979020979	78	0.10290237467018469	C	0.120	-1.126198	0.01770	0.316841	0.102558	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.11604	2.77;2.76	5.17	0.998	0.19857	.	1.789730	0.04429	U	0.368840	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B;B	0.25563	0.038;0.129	B;B	0.27608	0.034;0.081	T	0.43637	-0.9379	9	0.07175	T	0.84	0.041	5.2288	0.15410	0.1438:0.6204:0.1457:0.0901	rs3738281;rs11539493;rs56846552;rs3738281	70;56	E9PDI4;O00515	.;LAD1_HUMAN	S	56;70	ENSP00000375829:A56S;ENSP00000356282:A70S	ENSP00000356282:A70S	A	-	1	0	LAD1	199624927	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.218000	0.02976	-0.080000	0.12685	-0.978000	0.02582	GCC	C|0.826;A|0.174	0.174	strong		0.602	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
ATXN3	4287	hgsc.bcm.edu	37	14	92537354	92537354	+	Missense_Mutation	SNP	C	C	G	rs12895357	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:92537354C>G	ENST00000532032.1	-	10	925	c.916G>C	c.(916-918)Ggg>Cgg	p.G306R	ATXN3_ENST00000545170.1_Missense_Mutation_p.G315R|ATXN3_ENST00000502250.1_Missense_Mutation_p.G127R|ATXN3_ENST00000429774.2_Missense_Mutation_p.G299R|ATXN3_ENST00000393287.5_Missense_Mutation_p.G306R|ATXN3_ENST00000503767.1_Missense_Mutation_p.G291R|ATXN3_ENST00000340660.6_Missense_Mutation_p.G251R|ATXN3_ENST00000554491.1_5'UTR			P54252	ATX3_HUMAN	ataxin 3	306			G -> QQQQQQQQQQQQR. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7874163, ECO:0000269|PubMed:9274833}.		actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G306R(1)		endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		GATAGGTCCCCctgctgctgc	0.443													C|||	1382	0.275958	0.1687	0.1844	5008	,	,		15680	0.4236		0.2724	False		,,,				2504	0.3374				p.G306R	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											ATXN3,NS,carcinoma,0,2	ATXN3	46	2	1	Substitution - Missense(1)	lung(1)	c.G916C						PASS	.	C	ARG/GLY,ARG/GLY,ALA/GLY,ALA/GLY,ALA/GLY,ALA/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ALA/GLY,ARG/GLY,ARG/GLY	496,3910		54,388,1761	97.0	75.0	82.0		871,763,233,278,113,431,553,379,706,68,916,751	0.2	0.0	14	dbSNP_121	82	1619,6981		285,1049,2966	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	ATXN3	NM_001127696.1,NM_001127697.2,NM_001164774.1,NM_001164776.1,NM_001164777.1,NM_001164778.1,NM_001164779.1,NM_001164780.1,NM_001164781.1,NM_001164782.1,NM_004993.5,NM_030660.4	125,125,60,60,60,60,125,125,125,60,125,125	339,1437,4727	GG,GC,CC		18.8256,11.2574,16.2617	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	291/347,255/311,78/89,93/104,38/49,144/155,185/241,127/183,236/292,23/34,306/362,251/307	92537354	2115,10891	2203	4300	6503	SO:0001583	missense	4287	exon10			GGTCCCCCTGCTG	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"""Ataxins"""	7106	protein-coding gene	gene with protein product		607047	"""Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"""	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.916G>C	14.37:g.92537354C>G	ENSP00000437157:p.Gly306Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	70	24	0.342857	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37		560	0.2564102564102564	88	0.17886178861788618	59	0.16298342541436464	238	0.4160839160839161	175	0.23087071240105542	C	9.580	1.123237	0.20959	0.112574	0.188256	ENSG00000066427	ENST00000545278;ENST00000539555;ENST00000537884;ENST00000545170;ENST00000447800;ENST00000359819;ENST00000393289;ENST00000429774;ENST00000539454;ENST00000393287;ENST00000502250;ENST00000503767;ENST00000340660;ENST00000532032;ENST00000555381;ENST00000557311;ENST00000554592;ENST00000554672;ENST00000553491;ENST00000556220	T;T;T;T;T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	4.78	0.191	0.15130	.	5.350120	0.00508	N	0.000162	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.08055	0.001;0.001;0.003;0.003;0.001	T	0.42430	-0.9452	8	0.35671	T	0.21	.	3.2489	0.06807	0.1547:0.5342:0.1949:0.1162	rs12895357	306;291;317;251;306	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	R	322;319;317;315;315;314;311;299;320;306;127;291;251;306;236;127;305;208;255;200	ENSP00000445618:G315R;ENSP00000389376:G299R;ENSP00000376965:G306R;ENSP00000425322:G127R;ENSP00000426697:G291R;ENSP00000339110:G251R;ENSP00000437157:G306R;ENSP00000451001:G236R;ENSP00000450642:G127R;ENSP00000451385:G305R;ENSP00000451417:G208R;ENSP00000451996:G255R;ENSP00000450641:G200R	ENSP00000339110:G251R	G	-	1	0	ATXN3	91607107	0.000000	0.05858	0.031000	0.17742	0.053000	0.15095	-1.306000	0.02735	0.441000	0.26529	0.454000	0.30748	GGG	C|0.783;G|0.217	0.217	strong		0.443	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
ZBTB46	140685	hgsc.bcm.edu	37	20	62378418	62378418	+	Silent	SNP	C	C	T	rs74552928	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62378418C>T	ENST00000245663.4	-	5	1785	c.1635G>A	c.(1633-1635)gcG>gcA	p.A545A	ZBTB46_ENST00000302995.2_Silent_p.A545A|ZBTB46_ENST00000395104.1_Silent_p.A545A|RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	545					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CCAGCTCCTCCGCCTCCCCTC	0.726													C|||	286	0.0571086	0.0038	0.0764	5008	,	,		9647	0.001		0.1044	False		,,,				2504	0.1247				p.A545A		Atlas-SNP	.											.	ZBTB46	72	.	0			c.G1635A						PASS	.	C		105,4299		0,105,2097	29.0	28.0	29.0		1635	0.3	1.0	20	dbSNP_131	29	930,7654		48,834,3410	no	coding-synonymous	ZBTB46	NM_025224.3		48,939,5507	TT,TC,CC		10.8341,2.3842,7.9689		545/590	62378418	1035,11953	2202	4292	6494	SO:0001819	synonymous_variant	140685	exon5			CTCCTCCGCCTCC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1635G>A	20.37:g.62378418C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.926;T|0.074	0.074	strong		0.726	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
PBXIP1	57326	hgsc.bcm.edu	37	1	154919080	154919080	+	Missense_Mutation	SNP	C	C	T	rs2061690	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154919080C>T	ENST00000368463.3	-	10	1141	c.1070G>A	c.(1069-1071)gGt>gAt	p.G357D	PBXIP1_ENST00000542459.1_Missense_Mutation_p.G202D|PBXIP1_ENST00000368465.1_Missense_Mutation_p.G328D|PBXIP1_ENST00000539880.1_Missense_Mutation_p.G184D|PBXIP1_ENST00000498553.1_5'Flank	NM_020524.2	NP_065385.2	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein 1	357			G -> D (in dbSNP:rs2061690). {ECO:0000269|PubMed:10825160, ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)	cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(6)|lung(13)|prostate(1)|urinary_tract(1)	24	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TGGGCCTCTACCCCCACTGAG	0.672													C|||	2584	0.515974	0.1498	0.6297	5008	,	,		16333	0.8958		0.4334	False		,,,				2504	0.6237				p.G357D		Atlas-SNP	.											.	PBXIP1	59	.	0			c.G1070A						PASS	.	C	ASP/GLY	893,3513	341.5+/-306.7	90,713,1400	51.0	47.0	48.0		1070	3.6	0.3	1	dbSNP_94	48	3740,4860	528.4+/-381.4	826,2088,1386	yes	missense	PBXIP1	NM_020524.2	94	916,2801,2786	TT,TC,CC		43.4884,20.2678,35.622	benign	357/732	154919080	4633,8373	2203	4300	6503	SO:0001583	missense	57326	exon10			CCTCTACCCCCAC	AF221521	CCDS1074.1	1q22	2008-02-05	2007-01-30		ENSG00000163346	ENSG00000163346			21199	protein-coding gene	gene with protein product			"""pre-B-cell leukemia transcription factor interacting protein 1"""			7505766, 10825160	Standard	NM_020524		Approved	HPIP	uc001ffr.3	Q96AQ6	OTTHUMG00000037369	ENST00000368463.3:c.1070G>A	1.37:g.154919080C>T	ENSP00000357448:p.Gly357Asp	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_020524	Q5T174|Q5T176|Q9H8X6|Q9HA02|Q9HD85	Missense_Mutation	SNP	ENST00000368463.3	37	CCDS1074.1	1134	0.5192307692307693	85	0.17276422764227642	211	0.5828729281767956	507	0.8863636363636364	331	0.4366754617414248	C	3.845	-0.032974	0.07543	0.202678	0.434884	ENSG00000163346	ENST00000368465;ENST00000368463;ENST00000351146;ENST00000539880;ENST00000543593;ENST00000542459	T;T;T;T	0.13196	2.61;2.65;2.69;2.67	4.49	3.57	0.40892	.	0.000000	0.36932	N	0.002324	T	0.03095	0.0091	L	0.36672	1.1	0.80722	P	0.0	B	0.23540	0.087	B	0.25759	0.063	T	0.38672	-0.9650	9	0.12766	T	0.61	-9.241	6.9331	0.24451	0.0:0.7945:0.0:0.2054	rs2061690;rs3753643;rs52834797;rs59260875;rs2061690	357	Q96AQ6	PBIP1_HUMAN	D	328;357;357;184;133;202	ENSP00000357450:G328D;ENSP00000357448:G357D;ENSP00000440142:G184D;ENSP00000438584:G202D	ENSP00000295523:G357D	G	-	2	0	PBXIP1	153185704	0.000000	0.05858	0.276000	0.24689	0.038000	0.13279	0.459000	0.21908	1.107000	0.41642	0.563000	0.77884	GGT	C|0.565;T|0.435	0.435	strong		0.672	PBXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090943.1	NM_020524	
THSD7A	221981	hgsc.bcm.edu	37	7	11521542	11521542	+	Silent	SNP	T	T	C	rs3735502	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:11521542T>C	ENST00000423059.4	-	7	2141	c.1890A>G	c.(1888-1890)ccA>ccG	p.P630P	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	630					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CTTTCGGGCATGGGGCATCAC	0.527										HNSCC(18;0.044)			C|||	926	0.184904	0.1188	0.183	5008	,	,		18109	0.1786		0.2505	False		,,,				2504	0.2147				p.P630P		Atlas-SNP	.											.	THSD7A	219	.	0			c.A1890G						PASS	.	C		481,3721		30,421,1650	99.0	99.0	99.0		1890	-12.3	0.0	7	dbSNP_107	99	2218,6240		319,1580,2330	no	coding-synonymous	THSD7A	NM_015204.2		349,2001,3980	CC,CT,TT		26.2237,11.4469,21.3191		630/1658	11521542	2699,9961	2101	4229	6330	SO:0001819	synonymous_variant	221981	exon7			CGGGCATGGGGCA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1890A>G	7.37:g.11521542T>C		Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	266	125	0.469925	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			T|0.800;C|0.200	0.200	strong		0.527	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
ANO3	63982	hgsc.bcm.edu	37	11	26656563	26656563	+	Silent	SNP	C	C	T	rs7946841	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:26656563C>T	ENST00000256737.3	+	20	2841	c.1989C>T	c.(1987-1989)ttC>ttT	p.F663F	ANO3_ENST00000525139.1_Silent_p.F647F|ANO3_ENST00000531568.1_Silent_p.F517F|ANO3_ENST00000537978.1_Silent_p.F647F	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	663					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						CTTACAGATTCGTAGGCCACC	0.433													C|||	1709	0.341254	0.2277	0.2507	5008	,	,		18554	0.3552		0.4165	False		,,,				2504	0.4673				p.F663F		Atlas-SNP	.											.	ANO3	145	.	0			c.C1989T						PASS	.	C		1032,3374	381.8+/-324.2	112,808,1283	134.0	121.0	125.0		1989	1.3	1.0	11	dbSNP_116	125	3589,5009	519.7+/-379.5	735,2119,1445	no	coding-synonymous	ANO3	NM_031418.2		847,2927,2728	TT,TC,CC		41.7423,23.4226,35.5352		663/982	26656563	4621,8383	2203	4299	6502	SO:0001819	synonymous_variant	63982	exon20			CAGATTCGTAGGC	AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	14004	protein-coding gene	gene with protein product	"""transmembrane protein 16C (eight membrane-spanning domains)"""	610110	"""chromosome 11 open reading frame 25"", ""transmembrane protein 16C"""	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1989C>T	11.37:g.26656563C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_031418	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																			C|0.652;T|0.348	0.348	strong		0.433	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418	
DPH1	1801	hgsc.bcm.edu	37	17	1939971	1939971	+	Silent	SNP	G	G	A	rs61753099	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1939971G>A	ENST00000263083.6	+	5	609	c.564G>A	c.(562-564)tcG>tcA	p.S188S	DPH1_ENST00000570477.1_Silent_p.S108S|DPH1_ENST00000576891.2_3'UTR	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	188					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						AGTTTGTGTCGACCTTGCAGG	0.617													G|||	186	0.0371406	0.0076	0.0634	5008	,	,		18339	0.001		0.0954	False		,,,				2504	0.0358				p.S188S		Atlas-SNP	.											.	DPH1	32	.	0			c.G564A						PASS	.	G		74,4100		2,70,2015	81.0	87.0	85.0		564	-5.8	1.0	17	dbSNP_129	85	737,7653		26,685,3484	no	coding-synonymous	DPH1	NM_001383.3		28,755,5499	AA,AG,GG		8.7843,1.7729,6.455		188/444	1939971	811,11753	2087	4195	6282	SO:0001819	synonymous_variant	1801	exon5			TGTGTCGACCTTG	S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"""ovarian tumor suppressor candidate 1"""	603527	"""diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)"", ""DPH-like 1 (S. cerevisiae)"", ""DPH1 homolog (S. cerevisiae)"""	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.564G>A	17.37:g.1939971G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	172	77	0.447674	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Silent	SNP	ENST00000263083.6	37	CCDS42228.1																																																																																			G|0.936;A|0.064	0.064	strong		0.617	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383	
ALKBH1	8846	hgsc.bcm.edu	37	14	78140329	78140329	+	Silent	SNP	G	G	A	rs6493	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:78140329G>A	ENST00000216489.3	-	6	1011	c.996C>T	c.(994-996)agC>agT	p.S332S		NM_006020.2	NP_006011.2	Q13686	ALKB1_HUMAN	alkB, alkylation repair homolog 1 (E. coli)	332	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				developmental growth (GO:0048589)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|in utero embryonic development (GO:0001701)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|oxidative demethylation (GO:0070989)|placenta development (GO:0001890)|RNA repair (GO:0042245)	mitochondrion (GO:0005739)|nuclear euchromatin (GO:0005719)	chemoattractant activity (GO:0042056)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)			endometrium(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		TCTTCAAGTAGCTGGCACACA	0.532													G|||	451	0.0900559	0.0575	0.0994	5008	,	,		17484	0.0169		0.1958	False		,,,				2504	0.0941				p.S332S		Atlas-SNP	.											.	ALKBH1	30	.	0			c.C996T						PASS	.	G		358,4048	183.6+/-211.2	12,334,1857	81.0	71.0	74.0		996	5.1	1.0	14	dbSNP_52	74	1405,7195	271.6+/-289.6	133,1139,3028	no	coding-synonymous	ALKBH1	NM_006020.2		145,1473,4885	AA,AG,GG		16.3372,8.1253,13.5553		332/390	78140329	1763,11243	2203	4300	6503	SO:0001819	synonymous_variant	8846	exon6			CAAGTAGCTGGCA	X91992	CCDS32127.1	14q24	2014-07-23	2006-02-09	2006-02-09	ENSG00000100601	ENSG00000100601		"""Alkylation repair homologs"""	17911	protein-coding gene	gene with protein product		605345	"""alkB, alkylation repair homolog (E. coli)"""	ALKBH		8600462	Standard	XM_005268165		Approved	hABH, alkB, ABH	uc001xuc.1	Q13686	OTTHUMG00000171542	ENST00000216489.3:c.996C>T	14.37:g.78140329G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	164	72	0.439024	NM_006020	Q8TAU1|Q9ULA7	Silent	SNP	ENST00000216489.3	37	CCDS32127.1																																																																																			G|0.869;A|0.131	0.131	strong		0.532	ALKBH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414037.1	NM_006020	
FBXO6	26270	hgsc.bcm.edu	37	1	11733846	11733846	+	Missense_Mutation	SNP	C	C	A	rs148957324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11733846C>A	ENST00000376753.4	+	6	955	c.820C>A	c.(820-822)Cag>Aag	p.Q274K		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	274					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		TCAGCCTGGGCAGAAGCATGG	0.607													C|||	10	0.00199681	0.0	0.0	5008	,	,		18989	0.0		0.0089	False		,,,				2504	0.001				p.Q274K	NSCLC(54;506 1562 46490 51389)	Atlas-SNP	.											.	FBXO6	17	.	0			c.C820A						PASS	.	C	LYS/GLN	11,4395	17.9+/-39.9	0,11,2192	79.0	77.0	78.0		820	-9.2	0.0	1	dbSNP_134	78	85,8515	48.9+/-108.6	1,83,4216	yes	missense	FBXO6	NM_018438.5	53	1,94,6408	AA,AC,CC		0.9884,0.2497,0.7381	benign	274/294	11733846	96,12910	2203	4300	6503	SO:0001583	missense	26270	exon6			CCTGGGCAGAAGC	AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"""F-boxes /  ""other"""""	13585	protein-coding gene	gene with protein product		605647	"""F-box only protein 6"""			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.820C>A	1.37:g.11733846C>A	ENSP00000365944:p.Gln274Lys	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	243	95	0.390947	NM_018438	B1AK42|B2RC88|Q9UKT3	Missense_Mutation	SNP	ENST00000376753.4	37	CCDS133.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	0.015	-1.552659	0.00918	0.002497	0.009884	ENSG00000116663	ENST00000376753	T	0.21734	1.99	4.63	-9.25	0.00666	.	6.681920	0.00166	N	0.000000	T	0.05868	0.0153	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15206	-1.0445	10	0.22109	T	0.4	.	11.0102	0.47659	0.1177:0.5049:0.3774:0.0	.	274	Q9NRD1	FBX6_HUMAN	K	274	ENSP00000365944:Q274K	ENSP00000365944:Q274K	Q	+	1	0	FBXO6	11656433	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.870000	0.04228	-2.568000	0.00469	-3.108000	0.00062	CAG	C|0.994;A|0.006	0.006	strong		0.607	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438	
PRAME	23532	hgsc.bcm.edu	37	22	22890752	22890752	+	Silent	SNP	A	A	G	rs17497512	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:22890752A>G	ENST00000398741.1	-	6	1573	c.1267T>C	c.(1267-1269)Ttg>Ctg	p.L423L	PRAME_ENST00000539862.1_Silent_p.L407L|PRAME_ENST00000398743.2_Silent_p.L423L|PRAME_ENST00000405655.3_Silent_p.L423L|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Silent_p.L407L|PRAME_ENST00000543184.1_Silent_p.L423L|PRAME_ENST00000402697.1_Silent_p.L423L	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	423	Mediates interaction with RARA.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		AGACTCTGCAAGGCAGATATG	0.552													G|||	353	0.0704872	0.031	0.1354	5008	,	,		19923	0.0308		0.1402	False		,,,				2504	0.047				p.L423L	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											PRAME,NS,carcinoma,+2,1	PRAME	78	1	0			c.T1267C						PASS	.	G	,,,,	240,4166	804.3+/-415.7	7,226,1970	96.0	90.0	92.0		1267,1267,1267,1267,1267	1.3	0.0	22	dbSNP_123	92	1305,7295	758.0+/-407.5	103,1099,3098	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRAME	NM_006115.3,NM_206953.1,NM_206954.1,NM_206955.1,NM_206956.1	,,,,	110,1325,5068	GG,GA,AA		15.1744,5.4471,11.8791	,,,,	423/510,423/510,423/510,423/510,423/510	22890752	1545,11461	2203	4300	6503	SO:0001819	synonymous_variant	23532	exon6			TCTGCAAGGCAGA	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.1267T>C	22.37:g.22890752A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_206954	B2R6Y7|O43481|Q8IXN8	Silent	SNP	ENST00000398741.1	37	CCDS13801.1																																																																																			A|0.896;G|0.104	0.104	strong		0.552	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
DISC1	27185	hgsc.bcm.edu	37	1	231830295	231830295	+	Missense_Mutation	SNP	G	G	A	rs3738401	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:231830295G>A	ENST00000602281.1	+	2	844	c.791G>A	c.(790-792)cGg>cAg	p.R264Q	DISC1_ENST00000539444.1_Missense_Mutation_p.R264Q|DISC1_ENST00000366636.4_Missense_Mutation_p.R264Q|DISC1_ENST00000439617.2_Missense_Mutation_p.R264Q|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000317586.4_Missense_Mutation_p.R264Q|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000535983.1_Missense_Mutation_p.R264Q|DISC1_ENST00000537876.1_Missense_Mutation_p.R264Q|DISC1_ENST00000366633.3_Missense_Mutation_p.R264Q	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	264	Interaction with MAP1A.		R -> Q (in dbSNP:rs3738401). {ECO:0000269|PubMed:10814723, ECO:0000269|PubMed:12573262, ECO:0000269|PubMed:9455484}.		canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				TGTCTCTCTCGGCCCTTCAGT	0.612													G|||	1163	0.232228	0.1172	0.3329	5008	,	,		19997	0.2173		0.339	False		,,,				2504	0.2219				p.R264Q		Atlas-SNP	.											DISC1_ENST00000366638,NS,carcinoma,+1,3	DISC1	207	3	0			c.G791A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG	648,3758	276.3+/-273.0	54,540,1609	46.0	52.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,791,,791	-9.9	0.0	1	dbSNP_107	50	2734,5866	434.7+/-357.8	426,1882,1992	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,intron,missense	DISC1	NM_001012957.1,NM_001012958.1,NM_001012959.1,NM_001164537.1,NM_001164538.1,NM_001164539.1,NM_001164540.1,NM_001164541.1,NM_001164542.1,NM_001164544.1,NM_001164545.1,NM_001164546.1,NM_001164547.1,NM_001164548.1,NM_001164549.1,NM_001164550.1,NM_001164551.1,NM_001164552.1,NM_001164553.1,NM_001164554.1,NM_001164555.1,NM_001164556.1,NM_018662.2	43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,,43	480,2422,3601	AA,AG,GG		31.7907,14.7072,26.0034	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,,benign	264/833,264/370,264/679,264/887,264/804,264/756,264/733,264/696,264/682,264/663,264/580,264/560,264/560,264/552,264/548,264/430,264/424,264/388,264/388,264/376,264/357,,264/855	231830295	3382,9624	2203	4300	6503	SO:0001583	missense	27185	exon2			TCTCTCGGCCCTT	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.791G>A	1.37:g.231830295G>A	ENSP00000473425:p.Arg264Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001164541	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	612	0.2802197802197802	68	0.13821138211382114	142	0.39226519337016574	147	0.256993006993007	255	0.33641160949868076	G	9.745	1.165955	0.21538	0.147072	0.317907	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000317586;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944;ENST00000366632	T;T;T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84	4.94	-9.87	0.00470	.	1.746570	0.02520	N	0.092507	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.27559	0.001;0.025;0.068;0.012;0.009;0.181;0.025;0.068;0.009;0.025;0.001;0.004;0.002;0.025;0.026;0.004;0.026;0.026;0.009;0.001	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.12156	0.001;0.007;0.007;0.007;0.004;0.007;0.007;0.007;0.004;0.007;0.0;0.004;0.001;0.007;0.004;0.002;0.004;0.004;0.004;0.0	T	0.32402	-0.9908	9	0.25751	T	0.34	4.3858	1.7516	0.02973	0.1374:0.1906:0.3457:0.3262	rs3738401;rs52831689;rs57749630;rs3738401	264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264;264	C4P094;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P091;C4P0D2;C4P0D3;C4P0B1;Q5T409;C4P0D0;Q9NRI5-2;Q9NRI5;Q9NRI5-3;Q9NRI5-4	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.;.	Q	264;264;264;264;264;264;264;264;264;264;264;264;115	ENSP00000403888:R264Q;ENSP00000320784:R264Q;ENSP00000355596:R264Q;ENSP00000443996:R264Q;ENSP00000440909:R264Q;ENSP00000355593:R264Q;ENSP00000440953:R264Q;ENSP00000295051:R264Q;ENSP00000441193:R264Q	ENSP00000295051:R264Q	R	+	2	0	DISC1	229896918	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.466000	0.02355	-3.304000	0.00192	-1.288000	0.01363	CGG	G|0.746;A|0.254	0.254	strong		0.612	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
ASB2	51676	hgsc.bcm.edu	37	14	94417586	94417586	+	Silent	SNP	G	G	A	rs4483793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94417586G>A	ENST00000315988.4	-	4	983	c.495C>T	c.(493-495)tgC>tgT	p.C165C	ASB2_ENST00000556337.1_Intron|ASB2_ENST00000555019.1_Silent_p.C213C|MIR4506_ENST00000584693.1_RNA	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	165					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		TCTTGCGCTCGCAGGCTGTGC	0.612													G|||	2905	0.580072	0.4107	0.487	5008	,	,		20056	0.7817		0.6541	False		,,,				2504	0.591				p.C213C		Atlas-SNP	.											ASB2,NS,carcinoma,-2,1	ASB2	71	1	0			c.C639T						PASS	.	G	,	2048,2358	563.5+/-381.2	458,1132,613	50.0	45.0	47.0		639,495	1.9	1.0	14	dbSNP_111	47	5573,3027	660.6+/-401.8	1808,1957,535	no	coding-synonymous,coding-synonymous	ASB2	NM_001202429.1,NM_016150.4	,	2266,3089,1148	AA,AG,GG		35.1977,46.4821,41.404	,	213/636,165/588	94417586	7621,5385	2203	4300	6503	SO:0001819	synonymous_variant	51676	exon6			GCGCTCGCAGGCT	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.495C>T	14.37:g.94417586G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	37	CCDS9915.1																																																																																			G|0.404;A|0.596	0.596	strong		0.612	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
OR8J1	219477	hgsc.bcm.edu	37	11	56128081	56128081	+	Missense_Mutation	SNP	A	A	G	rs10896290	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:56128081A>G	ENST00000303039.3	+	1	391	c.359A>G	c.(358-360)tAt>tGt	p.Y120C		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	120			Y -> C (in dbSNP:rs10896290). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:14983052, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					TTGATGGCCTATGACCGCTAT	0.488													A|||	1103	0.220248	0.2542	0.1873	5008	,	,		18213	0.1369		0.328	False		,,,				2504	0.1728				p.Y120C		Atlas-SNP	.											OR8J1,head_neck,carcinoma,0,1	OR8J1	87	1	0			c.A359G						PASS	.	A	CYS/TYR	1238,3164	425.5+/-340.8	183,872,1146	149.0	137.0	141.0		359	4.8	1.0	11	dbSNP_120	141	2939,5653	458.5+/-364.6	521,1897,1878	yes	missense	OR8J1	NM_001005205.2	194	704,2769,3024	GG,GA,AA		34.2062,28.1236,32.1456	benign	120/317	56128081	4177,8817	2201	4296	6497	SO:0001583	missense	219477	exon1			TGGCCTATGACCG	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.359A>G	11.37:g.56128081A>G	ENSP00000304060:p.Tyr120Cys	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	290	127	0.437931	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	37	CCDS31529.1	524	0.23992673992673993	112	0.22764227642276422	68	0.1878453038674033	88	0.15384615384615385	256	0.33773087071240104	A	12.19	1.863321	0.32884	0.281236	0.342062	ENSG00000172487	ENST00000303039	T	0.00490	7.03	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000031	T	0.00012	0.0000	M	0.91196	3.185	0.33499	P	0.41034099999999996	B	0.24651	0.108	B	0.29942	0.109	T	0.39014	-0.9634	9	0.72032	D	0.01	.	13.3744	0.60730	1.0:0.0:0.0:0.0	rs10896290;rs52824219;rs59409905;rs10896290	120	Q8NGP2	OR8J1_HUMAN	C	120	ENSP00000304060:Y120C	ENSP00000304060:Y120C	Y	+	2	0	OR8J1	55884657	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	3.624000	0.54231	1.910000	0.55303	0.523000	0.50628	TAT	A|0.712;G|0.288	0.288	strong		0.488	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76587202	76587202	+	Missense_Mutation	SNP	T	T	G	rs7202925	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:76587202T>G	ENST00000476707.1	+	21	3613	c.3474T>G	c.(3472-3474)gaT>gaG	p.D1158E	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.D1154E|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.D1106E|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.D1082E|RP11-58C22.1_ENST00000563764.1_5'Flank			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	1155	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)		p.D1082E(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						TGGACCAGGATACTGCACTGG	0.517													G|||	1504	0.300319	0.3449	0.196	5008	,	,		18787	0.2847		0.2773	False		,,,				2504	0.3538				p.D1082E		Atlas-SNP	.											CNTNAP4_ENST00000478060,NS,carcinoma,0,1	CNTNAP4	600	1	1	Substitution - Missense(1)	stomach(1)	c.T3246G						PASS	.	G	GLU/ASP,GLU/ASP	1309,2613		209,891,861	28.0	30.0	29.0		3464,3246	3.3	1.0	16	dbSNP_116	29	2328,6014		317,1694,2160	yes	missense,missense	CNTNAP4	NM_033401.3,NM_138994.3	45,45	526,2585,3021	GG,GT,TT		27.907,33.3758,29.6559	benign,benign	1155/1309,1082/1236	76587202	3637,8627	1961	4171	6132	SO:0001583	missense	85445	exon21			CCAGGATACTGCA	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.3474T>G	16.37:g.76587202T>G	ENSP00000417628:p.Asp1158Glu	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	191	99	0.518325	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		619	0.2834249084249084	162	0.32926829268292684	76	0.20994475138121546	168	0.2937062937062937	213	0.28100263852242746	G	1.370	-0.586320	0.03827	0.333758	0.27907	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.32	3.32	0.38043	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.41938	N	0.000790	T	0.00012	0.0000	.	.	.	0.58432	P	4.000000000004E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.002;0.001;0.004	T	0.35968	-0.9767	8	0.02654	T	1	.	10.8875	0.46976	0.0:0.1204:0.5057:0.374	rs7202925;rs60336736;rs7202925	1082;1158;1155	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	E	1154;1106;1082;1158	ENSP00000306893:D1154E;ENSP00000439733:D1106E;ENSP00000418741:D1082E;ENSP00000417628:D1158E	ENSP00000306893:D1154E	D	+	3	2	CNTNAP4	75144703	0.998000	0.40836	0.996000	0.52242	0.464000	0.32679	0.388000	0.20735	0.366000	0.24427	-0.121000	0.15023	GAT	T|0.706;G|0.294	0.294	strong		0.517	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
OR52D1	390066	hgsc.bcm.edu	37	11	5510688	5510688	+	Missense_Mutation	SNP	T	T	C	rs7101919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:5510688T>C	ENST00000322641.5	+	1	774	c.752T>C	c.(751-753)aTc>aCc	p.I251T	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	251			I -> T (in dbSNP:rs7101919).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTGGCATCATCCTGGTTTTC	0.498													T|||	773	0.154353	0.0567	0.2767	5008	,	,		22676	0.0397		0.3111	False		,,,				2504	0.1564				p.I251T		Atlas-SNP	.											.	OR52D1	66	.	0			c.T752C						PASS	.	T	THR/ILE	425,3977	204.8+/-226.9	27,371,1803	199.0	174.0	182.0		752	5.6	1.0	11	dbSNP_116	182	2767,5827	441.7+/-359.9	458,1851,1988	yes	missense	OR52D1	NM_001005163.2	89	485,2222,3791	CC,CT,TT		32.1969,9.6547,24.5614	probably-damaging	251/319	5510688	3192,9804	2201	4297	6498	SO:0001583	missense	390066	exon1			GCATCATCCTGGT	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"""GPCR / Class A : Olfactory receptors"""	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.752T>C	11.37:g.5510688T>C	ENSP00000326232:p.Ile251Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	90	0.967742	NM_001005163	B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	37	CCDS31384.1	402	0.18406593406593408	42	0.08536585365853659	96	0.26519337016574585	26	0.045454545454545456	238	0.31398416886543534	T	17.70	3.454892	0.63290	0.096547	0.321969	ENSG00000181609	ENST00000322641	T	0.00220	8.52	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	M	0.91920	3.255	0.23816	P	0.99676052	D	0.89917	1.0	D	0.77557	0.99	T	0.57335	-0.7829	9	0.87932	D	0	.	14.7227	0.69320	0.0:0.0:0.0:1.0	rs7101919;rs17370162;rs60009125;rs7101919	251	Q9H346	O52D1_HUMAN	T	251	ENSP00000326232:I251T	ENSP00000326232:I251T	I	+	2	0	OR52D1	5467264	0.268000	0.24133	0.964000	0.40570	0.480000	0.33159	2.095000	0.41729	2.343000	0.79666	0.533000	0.62120	ATC	C|0.204;N|0.000	0.204	strong		0.498	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163	
POGK	57645	hgsc.bcm.edu	37	1	166819117	166819117	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:166819117G>A	ENST00000367875.1	+	5	1661	c.1301G>A	c.(1300-1302)cGc>cAc	p.R434H	POGK_ENST00000367876.4_Missense_Mutation_p.R434H|POGK_ENST00000536514.1_Missense_Mutation_p.R349H|POGK_ENST00000537173.1_Missense_Mutation_p.R316H			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	434	DDE.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R434H(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	22						ATGGAAATTCGCTGCCACCGG	0.547																																					p.R434H	GBM(76;192 1530 30153 48742)	Atlas-SNP	.											POGK,NS,carcinoma,0,3	POGK	54	3	1	Substitution - Missense(1)	prostate(1)	c.G1301A						scavenged	.						82.0	79.0	80.0					1																	166819117		2203	4300	6503	SO:0001583	missense	57645	exon5			AAATTCGCTGCCA	AB040946	CCDS1254.1	1q23.2	2013-01-08			ENSG00000143157	ENSG00000143157		"""-"""	18800	protein-coding gene	gene with protein product	"""KRAB box domain containing 2"""						Standard	NM_017542		Approved	KIAA15131, LST003, BASS2, KRBOX2	uc001gdt.1	Q9P215	OTTHUMG00000034325	ENST00000367875.1:c.1301G>A	1.37:g.166819117G>A	ENSP00000356849:p.Arg434His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	2	0.025	NM_017542	Q5TIJ1|Q8TE07	Missense_Mutation	SNP	ENST00000367875.1	37	CCDS1254.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.130321	0.37630	.	.	ENSG00000143157	ENST00000537173;ENST00000536514;ENST00000367876;ENST00000367875	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.49	3.64	0.41730	.	0.000000	0.51477	D	0.000082	T	0.16300	0.0392	N	0.19112	0.55	0.34301	D	0.684366	P;P;B	0.52061	0.828;0.95;0.027	B;P;B	0.46237	0.27;0.508;0.013	T	0.03608	-1.1020	8	.	.	.	-21.2951	10.3339	0.43839	0.1587:0.0:0.8413:0.0	.	316;349;434	G3V1P0;B4DS22;Q9P215	.;.;POGK_HUMAN	H	316;349;434;434	ENSP00000442763:R316H;ENSP00000441187:R349H;ENSP00000356850:R434H;ENSP00000356849:R434H	.	R	+	2	0	POGK	165085741	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.738000	0.55067	0.891000	0.36235	-0.143000	0.13931	CGC	.	.	none		0.547	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542	
ASGR2	433	hgsc.bcm.edu	37	17	7004927	7004927	+	Silent	SNP	C	C	T	rs11653054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7004927C>T	ENST00000380952.2	-	9	1167	c.903G>A	c.(901-903)gaG>gaA	p.E301E	ASGR2_ENST00000446679.2_Silent_p.E282E|ASGR2_ENST00000254850.7_Silent_p.E277E|ASGR2_ENST00000355035.5_Silent_p.E301E	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	301	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	TCCGCCTTTTCTCACACACCC	0.602													C|||	44	0.00878594	0.0008	0.0101	5008	,	,		18902	0.001		0.0328	False		,,,				2504	0.002				p.E301E		Atlas-SNP	.											.	ASGR2	38	.	0			c.G903A						PASS	.	C	,,,,	28,4378	34.3+/-65.2	0,28,2175	89.0	76.0	81.0		903,888,903,831,846	3.8	1.0	17	dbSNP_120	81	266,8334	102.7+/-163.9	6,254,4040	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	,,,,	6,282,6215	TT,TC,CC		3.093,0.6355,2.2605	,,,,	301/312,296/307,301/312,277/288,282/293	7004927	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	433	exon9			CCTTTTCTCACAC	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.903G>A	17.37:g.7004927C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Silent	SNP	ENST00000380952.2	37	CCDS32544.1																																																																																			C|0.980;T|0.020	0.020	strong		0.602	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	
C10orf71	118461	hgsc.bcm.edu	37	10	50532588	50532588	+	Missense_Mutation	SNP	C	C	G	rs10857469	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:50532588C>G	ENST00000374144.3	+	3	2286	c.1998C>G	c.(1996-1998)caC>caG	p.H666Q	C10orf71_ENST00000323868.4_Missense_Mutation_p.H666Q			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	666			H -> Q (in dbSNP:rs10857469).							endometrium(1)	1						TGAAGACCCACCAGCTAGAGA	0.532													C|||	478	0.0954473	0.053	0.0663	5008	,	,		19595	0.122		0.1193	False		,,,				2504	0.1217				p.H666Q		Atlas-SNP	.											.	C10orf71	179	.	0			c.C1998G						PASS	.	C	GLN/HIS,GLN/HIS	190,3550		3,184,1683	36.0	39.0	38.0		1998,1998	-1.2	0.0	10	dbSNP_120	38	1085,7137		68,949,3094	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	24,24	71,1133,4777	GG,GC,CC		13.1963,5.0802,10.6588	benign,benign	666/1436,666/720	50532588	1275,10687	1870	4111	5981	SO:0001583	missense	118461	exon3			GACCCACCAGCTA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1998C>G	10.37:g.50532588C>G	ENSP00000363259:p.His666Gln	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	211	0.09661172161172162	32	0.06504065040650407	30	0.08287292817679558	60	0.1048951048951049	89	0.11741424802110818	C	11.54	1.669304	0.29604	0.050802	0.131963	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.14893	2.47;3.59	5.53	-1.24	0.09435	.	0.981567	0.08269	N	0.971860	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	B	0.10296	0.003	B	0.13407	0.009	T	0.44574	-0.9319	9	0.10636	T	0.68	.	6.3808	0.21533	0.0:0.3596:0.4084:0.232	rs10857469;rs59643639;rs10857469	666	Q711Q0-3	.	Q	666	ENSP00000318713:H666Q;ENSP00000363259:H666Q	ENSP00000318713:H666Q	H	+	3	2	C10orf71	50202594	0.000000	0.05858	0.000000	0.03702	0.648000	0.38561	-0.954000	0.03873	-0.536000	0.06298	0.591000	0.81541	CAC	C|0.906;G|0.094	0.094	strong		0.532	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
NDUFAB1	4706	hgsc.bcm.edu	37	16	23607504	23607504	+	Silent	SNP	G	G	C	rs466719	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23607504G>C	ENST00000570319.1	-	1	108	c.108C>G	c.(106-108)ctC>ctG	p.L36L	NDUFAB1_ENST00000007516.3_Silent_p.L36L			O14561	ACPM_HUMAN	NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa	36					cellular metabolic process (GO:0044237)|fatty acid biosynthetic process (GO:0006633)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein lipoylation (GO:0009249)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process (GO:0000036)|calcium ion binding (GO:0005509)|fatty acid binding (GO:0005504)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|large_intestine(1)|lung(1)	3				GBM - Glioblastoma multiforme(48;0.0339)		CCGCGGAGCAGAGAGCGGTGC	0.692													C|||	629	0.125599	0.202	0.062	5008	,	,		12669	0.1726		0.0736	False		,,,				2504	0.0726				p.L36L		Atlas-SNP	.											NDUFAB1,NS,carcinoma,0,1	NDUFAB1	8	1	0			c.C108G						PASS	.	C		733,3641		58,617,1512	14.0	18.0	17.0		108	1.7	0.0	16	dbSNP_80	17	600,7960		19,562,3699	no	coding-synonymous	NDUFAB1	NM_005003.2		77,1179,5211	CC,CG,GG		7.0093,16.7581,10.3062		36/157	23607504	1333,11601	2187	4280	6467	SO:0001819	synonymous_variant	4706	exon1			GGAGCAGAGAGCG	AF087660	CCDS10614.1	16p12.3	2011-07-04	2002-08-29		ENSG00000004779	ENSG00000004779		"""Mitochondrial respiratory chain complex / Complex I"""	7694	protein-coding gene	gene with protein product	"""acyl carrier protein, mitochondrial"", ""complex I SDAP subunit"""	603836	"""NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1 (8kD, SDAP)"""			9763677, 9878551	Standard	NM_005003		Approved	SDAP, FASN2A, ACP	uc002dlw.3	O14561	OTTHUMG00000096985	ENST00000570319.1:c.108C>G	16.37:g.23607504G>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_005003	B2R4M1|Q9UNV1	Silent	SNP	ENST00000570319.1	37	CCDS10614.1																																																																																			G|0.883;C|0.117	0.117	strong		0.692	NDUFAB1-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436917.1	NM_005003	
OVCH1	341350	hgsc.bcm.edu	37	12	29628016	29628016	+	Silent	SNP	G	G	A	rs2043623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:29628016G>A	ENST00000318184.5	-	14	1577	c.1578C>T	c.(1576-1578)gcC>gcT	p.A526A	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	526	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.A526A(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TGGTAAATCTGGCCTTGAAGC	0.348													A|||	2554	0.509984	0.6687	0.3934	5008	,	,		17713	0.3948		0.5517	False		,,,				2504	0.454				p.A526A		Atlas-SNP	.											OVCH1,NS,carcinoma,0,1	OVCH1	195	1	1	Substitution - coding silent(1)	stomach(1)	c.C1578T						PASS	.	A		2512,1186		858,796,195	61.0	56.0	57.0		1578	-2.0	0.0	12	dbSNP_94	57	4425,3753		1178,2069,842	no	coding-synonymous	OVCH1	NM_183378.2		2036,2865,1037	AA,AG,GG		45.8914,32.0714,41.5881		526/1135	29628016	6937,4939	1849	4089	5938	SO:0001819	synonymous_variant	341350	exon14			AAATCTGGCCTTG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1578C>T	12.37:g.29628016G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	188	73	0.388298	NM_183378		Silent	SNP	ENST00000318184.5	37																																																																																				G|0.461;A|0.539	0.539	strong		0.348	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
FAM209A	200232	hgsc.bcm.edu	37	20	55100054	55100054	+	Missense_Mutation	SNP	C	C	T	rs2019515		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55100054C>T	ENST00000371328.3	+	1	513	c.190C>T	c.(190-192)Ctt>Ttt	p.L64F	FAM209A_ENST00000481560.1_3'UTR|GCNT7_ENST00000243913.4_Intron	NM_001012971.3	NP_001012989.2	Q5JX71	F209A_HUMAN	family with sequence similarity 209, member A	64						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.L64I(1)									GCTCTGGCTTCTTTTTGTTGT	0.468																																					p.L64F		Atlas-SNP	.											C20orf106,caecum,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	large_intestine(1)	c.C190T						PASS	.						152.0	139.0	143.0					20																	55100054		2203	4300	6503	SO:0001583	missense	200232	exon1			TGGCTTCTTTTTG	AL109806	CCDS33493.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000124103	ENSG00000124103			16100	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 106"""	C20orf106			Standard	NM_001012971		Approved	dJ1153D9.3		Q5JX71	OTTHUMG00000032799	ENST00000371328.3:c.190C>T	20.37:g.55100054C>T	ENSP00000360379:p.Leu64Phe	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	311	35	0.11254	NM_001012971	Q05C43	Missense_Mutation	SNP	ENST00000371328.3	37	CCDS33493.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.470784	0.26423	.	.	ENSG00000124103	ENST00000371328	T	0.08896	3.04	5.51	-3.08	0.05347	.	1.580940	0.04026	N	0.300512	T	0.03739	0.0106	N	0.17474	0.49	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.34153	-0.9840	10	0.07482	T	0.82	0.1847	0.4716	0.00533	0.3755:0.2307:0.1287:0.2652	rs2019515	64	Q5JX71	CT106_HUMAN	F	64	ENSP00000360379:L64F	ENSP00000360379:L64F	L	+	1	0	C20orf106	54533461	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.316000	0.01123	-0.884000	0.03976	-0.516000	0.04426	CTT	C|1.000;T|0.000	0.000	weak		0.468	FAM209A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079815.2		
MUC16	94025	hgsc.bcm.edu	37	19	9049726	9049726	+	Silent	SNP	G	G	A	rs11670328	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9049726G>A	ENST00000397910.4	-	5	32108	c.31905C>T	c.(31903-31905)gaC>gaT	p.D10635D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10637	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGAGCTGACGTCTGCCCCAT	0.473													G|||	1247	0.249002	0.1558	0.2233	5008	,	,		20530	0.2351		0.337	False		,,,				2504	0.317				p.D10635D		Atlas-SNP	.											.	MUC16	4315	.	0			c.C31905T						PASS	.			701,3289		66,569,1360	119.0	109.0	112.0		31905	-2.0	0.0	19	dbSNP_120	112	2693,5643		421,1851,1896	no	coding-synonymous	MUC16	NM_024690.2		487,2420,3256	AA,AG,GG		32.3057,17.5689,27.5353		10635/14508	9049726	3394,8932	1995	4168	6163	SO:0001819	synonymous_variant	94025	exon5			GCTGACGTCTGCC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31905C>T	19.37:g.9049726G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	209	104	0.497608	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.737;A|0.263	0.263	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
INPP4B	8821	hgsc.bcm.edu	37	4	143324094	143324094	+	Silent	SNP	G	G	A	rs1982966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:143324094G>A	ENST00000513000.1	-	8	802	c.369C>T	c.(367-369)gaC>gaT	p.D123D	INPP4B_ENST00000508116.1_Silent_p.D123D|INPP4B_ENST00000509777.1_Silent_p.D123D|INPP4B_ENST00000308502.4_Silent_p.D123D|INPP4B_ENST00000262992.4_Silent_p.D123D|INPP4B_ENST00000506217.1_Silent_p.D123D	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	123	C2.				cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.D123D(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					TACTTACGGTGTCATGAGACT	0.363													G|||	1265	0.252596	0.0318	0.2378	5008	,	,		20821	0.2907		0.3489	False		,,,				2504	0.4233				p.D123D		Atlas-SNP	.											INPP4B,NS,carcinoma,0,1	INPP4B	132	1	1	Substitution - coding silent(1)	stomach(1)	c.C369T						PASS	.	G	,	374,4032	188.1+/-214.6	16,342,1845	164.0	129.0	141.0		369,369	2.8	1.0	4	dbSNP_92	141	2980,5620	462.6+/-365.7	489,2002,1809	no	coding-synonymous,coding-synonymous	INPP4B	NM_001101669.1,NM_003866.2	,	505,2344,3654	AA,AG,GG		34.6512,8.4884,25.7881	,	123/925,123/925	143324094	3354,9652	2203	4300	6503	SO:0001819	synonymous_variant	8821	exon8			TACGGTGTCATGA	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.369C>T	4.37:g.143324094G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	58	17	0.293103	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			G|0.743;A|0.257	0.257	strong		0.363	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	
NBPF7	343505	hgsc.bcm.edu	37	1	120384205	120384205	+	IGR	SNP	A	A	G	rs2994820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120384205A>G								REG4 (29922 upstream) : ADAM30 (51950 downstream)																							CCTGAGAGTGAACCAGGACTT	0.443													a|||	3130	0.625	0.3979	0.7118	5008	,	,		21939	0.4673		0.8121	False		,,,				2504	0.8405				p.V119V		Atlas-SNP	.											.	NBPF7	46	.	0			c.T357C						PASS	.	A		1996,2410	537.5+/-374.7	469,1058,676	124.0	137.0	133.0		357	-0.3	0.0	1	dbSNP_101	133	6796,1800	725.8+/-406.6	2695,1406,197	no	coding-synonymous	NBPF7	NM_001047980.1		3164,2464,873	GG,GA,AA		20.94,45.3019,32.3796		119/422	120384205	8792,4210	2203	4298	6501	SO:0001628	intergenic_variant	343505	exon3			AGAGTGAACCAGG																													1.37:g.120384205A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	161	57	0.354037	NM_001047980		Silent	SNP		37																																																																																				A|0.333;G|0.667	0.667	strong	0	0.443								
MUC4	4585	hgsc.bcm.edu	37	3	195512822	195512822	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195512822C>T	ENST00000463781.3	-	2	6088	c.5629G>A	c.(5629-5631)Gac>Aac	p.D1877N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1877N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGCGTCGGTGACAAGA	0.572																																					p.D1877N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,2	MUC4	1505	2	0			c.G5629A						scavenged	.						56.0	41.0	45.0					3																	195512822		691	1589	2280	SO:0001583	missense	4585	exon2			AAGCGTCGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5629G>A	3.37:g.195512822C>T	ENSP00000417498:p.Asp1877Asn	Somatic	301	9	0.0299003		WXS	Illumina HiSeq	Phase_I	583	17	0.0291595	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	10.08	1.251047	0.22880	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37235	1.21;1.23	0.423	-0.846	0.10734	.	0.558648	0.09230	U	0.830697	T	0.18509	0.0444	N	0.19112	0.55	0.09310	N	1	B	0.16802	0.019	B	0.08055	0.003	T	0.25537	-1.0129	9	.	.	.	.	3.7818	0.08683	0.0:0.3383:0.0:0.6617	.	1877	E7ESK3	.	N	1877	ENSP00000417498:D1877N;ENSP00000420243:D1877N	.	D	-	1	0	MUC4	196997217	0.001000	0.12720	0.003000	0.11579	0.093000	0.18481	-0.024000	0.12435	-0.400000	0.07656	0.089000	0.15464	GAC	.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PCDH12	51294	hgsc.bcm.edu	37	5	141337177	141337177	+	Missense_Mutation	SNP	G	G	C	rs138689340	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141337177G>C	ENST00000231484.3	-	1	1450	c.240C>G	c.(238-240)gaC>gaG	p.D80E	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	80	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCCTCAGAGTCCACCTGAA	0.637													G|||	28	0.00559105	0.0008	0.013	5008	,	,		17451	0.0		0.0149	False		,,,				2504	0.0031				p.D80E		Atlas-SNP	.											.	PCDH12	133	.	0			c.C240G						PASS	.	G	GLU/ASP	15,4391	22.3+/-47.3	0,15,2188	52.0	53.0	53.0		240	-1.3	0.0	5	dbSNP_134	53	145,8455	70.0+/-132.6	1,143,4156	yes	missense	PCDH12	NM_016580.2	45	1,158,6344	CC,CG,GG		1.686,0.3404,1.2302	benign	80/1185	141337177	160,12846	2203	4300	6503	SO:0001583	missense	51294	exon1			CTCAGAGTCCACC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.240C>G	5.37:g.141337177G>C	ENSP00000231484:p.Asp80Glu	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	198	125	0.631313	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	21	0.009615384615384616	3	0.006097560975609756	6	0.016574585635359115	0	0.0	12	0.0158311345646438	G	5.339	0.247807	0.10130	0.003404	0.01686	ENSG00000113555	ENST00000231484	T	0.27890	1.64	4.81	-1.34	0.09143	Cadherin, N-terminal (1);Cadherin (4);	0.577641	0.19689	N	0.108338	T	0.13841	0.0335	L	0.57130	1.785	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.20874	-1.0262	10	0.49607	T	0.09	.	9.9206	0.41462	0.5973:0.0:0.4027:0.0	.	80	Q9NPG4	PCD12_HUMAN	E	80	ENSP00000231484:D80E	ENSP00000231484:D80E	D	-	3	2	PCDH12	141317361	0.000000	0.05858	0.007000	0.13788	0.138000	0.21146	-1.159000	0.03150	-0.212000	0.10109	0.563000	0.77884	GAC	G|0.986;C|0.014	0.014	strong		0.637	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
POTEF	728378	hgsc.bcm.edu	37	2	130832185	130832185	+	Missense_Mutation	SNP	G	G	A	rs62165870	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130832185G>A	ENST00000409914.2	-	17	3259	c.2860C>T	c.(2860-2862)Cgg>Tgg	p.R954W	POTEF_ENST00000357462.5_Missense_Mutation_p.R954W	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	954	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						CAGCGGAACCGCTCGTTGCCG	0.592													.|||	2933	0.585663	0.6074	0.6282	5008	,	,		20867	0.506		0.5865	False		,,,				2504	0.6074				p.R954W		Atlas-SNP	.											POTEF,NS,carcinoma,0,1	POTEF	140	1	0			c.C2860T						scavenged	.						2.0	2.0	2.0					2																	130832185		669	1633	2302	SO:0001583	missense	728378	exon17			GGAACCGCTCGTT	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2860C>T	2.37:g.130832185G>A	ENSP00000386786:p.Arg954Trp	Somatic	216	5	0.0231481		WXS	Illumina HiSeq	Phase_I	260	49	0.188462	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	5.422	0.262972	0.10294	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.97303	-4.33;-4.33	.	.	.	.	.	.	.	.	D	0.97269	0.9107	H	0.99117	4.435	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	D	0.92402	0.5930	8	0.45353	T	0.12	.	2.8768	0.05634	3.0E-4:2.0E-4:0.5045:0.4949	.	954	A5A3E0	POTEF_HUMAN	W	954	ENSP00000350052:R954W;ENSP00000386786:R954W	ENSP00000350052:R954W	R	-	1	2	POTEF	130548655	1.000000	0.71417	0.097000	0.21041	0.098000	0.18820	0.992000	0.29667	0.119000	0.18210	0.121000	0.15741	CGG	.	.	weak		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
PCSK5	5125	hgsc.bcm.edu	37	9	78969059	78969059	+	Missense_Mutation	SNP	C	C	A	rs7036921	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:78969059C>A	ENST00000545128.1	+	36	5635	c.5097C>A	c.(5095-5097)gaC>gaA	p.D1699E		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1699	CRM (Cys-rich motif).				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						ACATGGACGACAGCCACTGCC	0.592													C|||	1162	0.232029	0.2579	0.1873	5008	,	,		18912	0.0863		0.2932	False		,,,				2504	0.316				p.D1699E		Atlas-SNP	.											PCSK5_ENST00000545128,NS,carcinoma,+1,1	PCSK5	329	1	0			c.C5097A						scavenged	.						17.0	15.0	16.0					9																	78969059		876	1991	2867	SO:0001583	missense	5125	exon36			GGACGACAGCCAC		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.5097C>A	9.37:g.78969059C>A	ENSP00000446280:p.Asp1699Glu	Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	236	107	0.45339	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	477	0.2184065934065934	135	0.27439024390243905	79	0.21823204419889503	50	0.08741258741258741	213	0.28100263852242746	C	3.362	-0.130284	0.06753	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.64438	-0.1;-0.1	5.82	0.0282	0.14158	.	0.322809	0.33457	N	0.004898	T	0.00012	0.0000	N	0.21240	0.645	0.46028	P	0.0011710000000000331	.	.	.	.	.	.	T	0.11203	-1.0597	7	0.05959	T	0.93	-21.1474	2.861	0.05586	0.2044:0.2208:0.4208:0.154	rs7036921;rs56654594;rs7036921	.	.	.	E	1699;1429;1399	ENSP00000446280:D1699E;ENSP00000411654:D1399E	ENSP00000365945:D1429E	D	+	3	2	PCSK5	78158879	0.000000	0.05858	0.148000	0.22405	0.115000	0.19883	-0.235000	0.09016	0.341000	0.23771	-0.304000	0.09214	GAC	C|0.769;A|0.231	0.231	strong		0.592	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TENM1	10178	hgsc.bcm.edu	37	X	123554646	123554646	+	Silent	SNP	T	T	C	rs12013090	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:123554646T>C	ENST00000371130.3	-	24	4539	c.4476A>G	c.(4474-4476)gcA>gcG	p.A1492A	TENM1_ENST00000422452.2_Silent_p.A1499A|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1492					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CTTTCATCTTTGCATCTTTGG	0.453													T|||	795	0.210596	0.2557	0.0591	3775	,	,		16029	0.0813		0.0865	False		,,,				2504	0.2526				p.A1499A		Atlas-SNP	.											.	.	.	.	0			c.A4497G						PASS	.	T	,,	1149,2686		156,668,169,808,402	106.0	93.0	98.0		4497,4494,4476	-3.0	1.0	X	dbSNP_120	98	870,5858		42,519,267,1867,1605	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	198,1187,436,2675,2007	CC,CT,C,TT,T		12.931,29.9609,19.1139	,,	1499/2733,1498/2732,1492/2726	123554646	2019,8544	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon25			CATCTTTGCATCT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.4476A>G	X.37:g.123554646T>C		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			T|0.812;C|0.188	0.188	strong		0.453	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
HRH4	59340	hgsc.bcm.edu	37	18	22056970	22056970	+	Missense_Mutation	SNP	A	A	G	rs11662595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:22056970A>G	ENST00000256906.4	+	3	717	c.617A>G	c.(616-618)cAt>cGt	p.H206R	HRH4_ENST00000426880.2_Missense_Mutation_p.H118R	NM_001160166.1|NM_021624.3	NP_001153638.1|NP_067637.2	Q9H3N8	HRH4_HUMAN	histamine receptor H4	206			H -> R (in dbSNP:rs11662595). {ECO:0000269|PubMed:10973974}.		inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of MAPK cascade (GO:0043408)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Amitriptyline(DB00321)|Amoxapine(DB00543)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Mianserin(DB06148)|Olanzapine(DB00334)	AAGCGTGATCATCTCAGTAGG	0.438													A|||	314	0.0626997	0.0197	0.1455	5008	,	,		20703	0.0347		0.0984	False		,,,				2504	0.0542				p.H206R		Atlas-SNP	.											.	HRH4	46	.	0			c.A617G						PASS	.	A	ARG/HIS,,ARG/HIS	139,4267	100.7+/-139.4	1,137,2065	155.0	146.0	149.0		353,,617	-4.7	0.0	18	dbSNP_120	149	851,7749	194.5+/-239.9	44,763,3493	yes	missense,utr-3,missense	HRH4	NM_001143828.1,NM_001160166.1,NM_021624.3	29,,29	45,900,5558	GG,GA,AA		9.8953,3.1548,7.6119	benign,,benign	118/303,,206/391	22056970	990,12016	2203	4300	6503	SO:0001583	missense	59340	exon3			GTGATCATCTCAG	AF312230	CCDS11887.1, CCDS45841.1	18q11.2	2012-08-08			ENSG00000134489	ENSG00000134489		"""GPCR / Class A : Histamine receptors"""	17383	protein-coding gene	gene with protein product		606792				11118334, 10973974	Standard	NM_021624		Approved	H4R, HH4R, AXOR35, GPCR105, GPRv53	uc002kvi.3	Q9H3N8	OTTHUMG00000131945	ENST00000256906.4:c.617A>G	18.37:g.22056970A>G	ENSP00000256906:p.His206Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	134	50	0.373134	NM_021624	B0YJ19|B2KJ48|Q4G0I6|Q9GZQ0	Missense_Mutation	SNP	ENST00000256906.4	37	CCDS11887.1	154	0.07051282051282051	7	0.014227642276422764	44	0.12154696132596685	28	0.04895104895104895	75	0.09894459102902374	A	9.686	1.150716	0.21371	0.031548	0.098953	ENSG00000134489	ENST00000256906;ENST00000426880	T;T	0.36878	1.23;1.23	5.5	-4.72	0.03269	GPCR, rhodopsin-like superfamily (1);	1.727610	0.02540	N	0.094577	T	0.00241	0.0007	N	0.13140	0.3	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.15983	-1.0418	9	0.02654	T	1	2.4326	6.0158	0.19603	0.3424:0.3375:0.3201:0.0	rs11662595;rs17203342;rs52816511;rs58861250;rs11662595	118;206	B2KJ48;Q9H3N8	.;HRH4_HUMAN	R	206;118	ENSP00000256906:H206R;ENSP00000402526:H118R	ENSP00000256906:H206R	H	+	2	0	HRH4	20310968	0.000000	0.05858	0.000000	0.03702	0.529000	0.34654	0.063000	0.14410	-0.779000	0.04560	0.459000	0.35465	CAT	A|0.927;G|0.073	0.073	strong		0.438	HRH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254904.1		
VSX2	338917	hgsc.bcm.edu	37	14	74711883	74711883	+	Silent	SNP	C	C	T	rs35435463	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:74711883C>T	ENST00000261980.2	+	3	561	c.471C>T	c.(469-471)tcC>tcT	p.S157S		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	157					cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		TCTTTACCTCCTACCAGCTAG	0.547													C|||	1302	0.259984	0.0628	0.4755	5008	,	,		14812	0.0754		0.5129	False		,,,				2504	0.3037				p.S157S		Atlas-SNP	.											.	VSX2	32	.	0			c.C471T						PASS	.	C		564,3842	252.4+/-258.8	37,490,1676	57.0	50.0	52.0		471	4.8	1.0	14	dbSNP_126	52	4487,4113	590.0+/-392.6	1192,2103,1005	no	coding-synonymous	VSX2	NM_182894.2		1229,2593,2681	TT,TC,CC		47.8256,12.8007,38.8359		157/362	74711883	5051,7955	2203	4300	6503	SO:0001819	synonymous_variant	338917	exon3			TACCTCCTACCAG	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"""Homeoboxes / PRD class"""	1975	protein-coding gene	gene with protein product		142993	"""C elegans ceh-10 homeo domain-containing homolog"", ""ceh-10 homeo domain containing homolog (C. elegans)"", ""ceh-10 homeodomain containing homolog (C. elegans)"""	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.471C>T	14.37:g.74711883C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	79	23	0.291139	NM_182894	A1A4X6	Silent	SNP	ENST00000261980.2	37	CCDS9827.1																																																																																			C|0.634;T|0.366	0.366	strong		0.547	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894	
UTP20	27340	hgsc.bcm.edu	37	12	101755809	101755809	+	Silent	SNP	T	T	C	rs12309241	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:101755809T>C	ENST00000261637.4	+	44	5935	c.5761T>C	c.(5761-5763)Ttg>Ctg	p.L1921L		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1921					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						GGTCGGAGATTTGGACTCTTG	0.398													T|||	1825	0.364417	0.6785	0.2089	5008	,	,		16463	0.5417		0.0229	False		,,,				2504	0.2188				p.L1921L		Atlas-SNP	.											.	UTP20	222	.	0			c.T5761C						PASS	.	T		2515,1891	629.9+/-395.4	726,1063,414	174.0	174.0	174.0		5761	2.4	1.0	12	dbSNP_120	174	216,8384	89.9+/-152.1	2,212,4086	no	coding-synonymous	UTP20	NM_014503.2		728,1275,4500	CC,CT,TT		2.5116,42.9187,20.998		1921/2786	101755809	2731,10275	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon44			GGAGATTTGGACT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.5761T>C	12.37:g.101755809T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			T|0.737;C|0.263	0.263	strong		0.398	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
ZNF189	7743	hgsc.bcm.edu	37	9	104171856	104171856	+	Silent	SNP	C	C	T	rs17772514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:104171856C>T	ENST00000339664.2	+	3	1935	c.1806C>T	c.(1804-1806)gaC>gaT	p.D602D	ZNF189_ENST00000259395.4_Silent_p.D560D|ZNF189_ENST00000374861.3_Silent_p.D588D	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	602					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				ATGAATGTGACGCTTGTGGTG	0.418													C|||	198	0.0395367	0.0023	0.0634	5008	,	,		21051	0.002		0.0785	False		,,,				2504	0.0716				p.D602D		Atlas-SNP	.											.	ZNF189	79	.	0			c.C1806T						PASS	.	C	,	62,4344	52.9+/-88.7	1,60,2142	77.0	82.0	80.0		1806,1680	0.6	1.0	9	dbSNP_123	80	689,7909	170.4+/-221.6	28,633,3638	no	coding-synonymous,coding-synonymous	ZNF189	NM_003452.2,NM_197977.1	,	29,693,5780	TT,TC,CC		8.0135,1.4072,5.7751	,	602/627,560/585	104171856	751,12253	2203	4299	6502	SO:0001819	synonymous_variant	7743	exon3			ATGTGACGCTTGT	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1806C>T	9.37:g.104171856C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	37	CCDS6754.1																																																																																			C|0.953;T|0.047	0.047	strong		0.418	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
SLC7A6OS	84138	hgsc.bcm.edu	37	16	68337948	68337948	+	Missense_Mutation	SNP	T	T	C	rs11548855	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:68337948T>C	ENST00000263997.6	-	3	677	c.659A>G	c.(658-660)tAc>tGc	p.Y220C		NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	220			Y -> C (in dbSNP:rs11548855).		hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		TTCTTGGCTGTAGGGCTGCAC	0.522													T|||	89	0.0177716	0.0023	0.0274	5008	,	,		18947	0.001		0.0567	False		,,,				2504	0.0092				p.Y220C		Atlas-SNP	.											.	SLC7A6OS	22	.	0			c.A659G						PASS	.	T	CYS/TYR	58,4338	55.5+/-91.7	0,58,2140	105.0	93.0	97.0		659	4.7	0.7	16	dbSNP_120	97	566,8034	153.6+/-207.9	16,534,3750	yes	missense	SLC7A6OS	NM_032178.2	194	16,592,5890	CC,CT,TT		6.5814,1.3194,4.8015	probably-damaging	220/310	68337948	624,12372	2198	4300	6498	SO:0001583	missense	84138	exon3			TGGCTGTAGGGCT		CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.659A>G	16.37:g.68337948T>C	ENSP00000263997:p.Tyr220Cys	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	201	87	0.432836	NM_032178	Q8TCZ3|Q9H8R8	Missense_Mutation	SNP	ENST00000263997.6	37	CCDS10865.1	60	0.027472527472527472	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	45	0.059366754617414245	T	19.49	3.837918	0.71373	0.013194	0.065814	ENSG00000103061	ENST00000263997	T	0.20463	2.07	5.79	4.68	0.58851	.	0.111684	0.64402	D	0.000006	T	0.03739	0.0106	L	0.58354	1.805	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.00069	-1.2138	10	0.46703	T	0.11	-15.2116	10.5	0.44800	0.1453:0.0:0.0:0.8547	rs11548855;rs11548855	220	Q96CW6	S7A6O_HUMAN	C	220	ENSP00000263997:Y220C	ENSP00000263997:Y220C	Y	-	2	0	SLC7A6OS	66895449	1.000000	0.71417	0.681000	0.30009	0.955000	0.61496	5.530000	0.67141	0.999000	0.39023	0.454000	0.30748	TAC	T|0.956;C|0.044	0.044	strong		0.522	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242198	81242198	+	RNA	SNP	G	G	A	rs7499011	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81242198G>A	ENST00000525539.1	-	0	657				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGTAGCTCCTGGCACTGGCCT	0.552													G|||	810	0.161741	0.0923	0.2349	5008	,	,		20582	0.003		0.3837	False		,,,				2504	0.1391				p.Q220X		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C658T						PASS	.	G	stop/GLN,stop/GLN	597,3607		50,497,1555	66.0	63.0	64.0		658,658	4.3	1.0	16	dbSNP_116	64	3074,5372		536,2002,1685	yes	stop-gained,stop-gained	PKD1L2	NM_001076780.1,NM_052892.3	,	586,2499,3240	AA,AG,GG		36.3959,14.2008,29.0198	,	220/992,220/2460	81242198	3671,8979	2102	4223	6325			114780	exon4			GCTCCTGGCACTG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242198G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Nonsense_Mutation	SNP	ENST00000525539.1	37		427	0.1955128205128205	39	0.07926829268292683	109	0.3011049723756906	1	0.0017482517482517483	278	0.36675461741424803	G	30	5.056326	0.93793	0.142008	0.363959	ENSG00000166473	ENST00000337114	.	.	.	4.31	4.31	0.51392	.	0.067881	0.64402	D	0.000017	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-12.5705	16.402	0.83643	0.0:0.0:1.0:0.0	rs7499011	.	.	.	X	220	.	ENSP00000337397:Q220X	Q	-	1	0	PKD1L2	79799699	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	7.373000	0.79623	1.957000	0.56846	0.313000	0.20887	CAG	G|0.742;A|0.258	0.258	strong		0.552	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
NFATC1	4772	hgsc.bcm.edu	37	18	77246406	77246406	+	Missense_Mutation	SNP	T	T	G	rs754093	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:77246406T>G	ENST00000427363.2	+	9	2251	c.2251T>G	c.(2251-2253)Tgt>Ggt	p.C751G	NFATC1_ENST00000397790.2_Missense_Mutation_p.C279G|NFATC1_ENST00000542384.1_Intron|NFATC1_ENST00000253506.5_Missense_Mutation_p.C751G|NFATC1_ENST00000586434.1_Intron|NFATC1_ENST00000318065.5_Missense_Mutation_p.C738G|NFATC1_ENST00000329101.4_Missense_Mutation_p.C738G|NFATC1_ENST00000545796.1_Missense_Mutation_p.C279G			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	751	Trans-activation domain B (TAD-B).		C -> G (in dbSNP:rs754093).		calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	CTTCCCGCCCTGTCCGCAGAG	0.677													t|||	1697	0.338858	0.1566	0.415	5008	,	,		12463	0.3542		0.4722	False		,,,				2504	0.3783				p.C751G	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											NFATC1,NS,carcinoma,0,1	NFATC1	105	1	0			c.T2251G						scavenged	.		GLY/CYS,GLY/CYS,GLY/CYS,GLY/CYS	808,3598	317.4+/-295.1	79,650,1474	87.0	97.0	94.0		2251,2212,835,2212	3.5	0.1	18	dbSNP_86	94	3984,4612	544.3+/-384.6	920,2144,1234	yes	missense,missense,missense,missense	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1	159,159,159,159	999,2794,2708	GG,GT,TT		46.3471,18.3386,36.8559	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	751/826,738/931,279/354,738/813	77246406	4792,8210	2203	4298	6501	SO:0001583	missense	4772	exon9			CCGCCCTGTCCGC	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.2251T>G	18.37:g.77246406T>G	ENSP00000389377:p.Cys751Gly	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_006162	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		820	0.37545787545787546	72	0.14634146341463414	171	0.4723756906077348	220	0.38461538461538464	357	0.470976253298153	t	9.583	1.124206	0.20959	0.183386	0.463471	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000397790;ENST00000329101;ENST00000545796;ENST00000427363;ENST00000397794	T;T;T;T	0.21031	2.03;2.03;2.03;2.03	4.66	3.49	0.39957	.	0.281920	0.40385	N	0.001103	T	0.00012	0.0000	L	0.55213	1.73	0.21782	P	0.999540869	P;B	0.46064	0.872;0.304	B;B	0.40285	0.325;0.115	T	0.47849	-0.9085	9	0.87932	D	0	-5.2307	9.6915	0.40131	0.0:0.0852:0.0:0.9148	rs754093;rs1660168;rs754093	751;738	O95644;B5B2M5	NFAC1_HUMAN;.	G	751;751;279;738;279;738;715	ENSP00000253506:C751G;ENSP00000380892:C279G;ENSP00000327850:C738G;ENSP00000439992:C279G	ENSP00000253506:C751G	C	+	1	0	NFATC1	75347394	1.000000	0.71417	0.064000	0.19789	0.101000	0.19017	4.802000	0.62539	0.745000	0.32763	0.520000	0.50463	TGT	T|0.641;G|0.359	0.359	strong		0.677	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
HAAO	23498	hgsc.bcm.edu	37	2	42994814	42994814	+	Missense_Mutation	SNP	C	C	G	rs34053133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:42994814C>G	ENST00000294973.6	-	9	758	c.703G>C	c.(703-705)Ggc>Cgc	p.G235R		NM_012205.2	NP_036337.2			3-hydroxyanthranilate 3,4-dioxygenase											breast(2)|cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(2)	11						ACCGAGGAGCCCTCCTGGAGA	0.627													.|||	16	0.00319489	0.0008	0.0101	5008	,	,		18963	0.0		0.008	False		,,,				2504	0.0				p.G235R		Atlas-SNP	.											.	HAAO	26	.	0			c.G703C						PASS	.		ARG/GLY	4,4388		0,4,2192	18.0	16.0	16.0		703	5.0	1.0	2	dbSNP_126	16	47,8519		0,47,4236	yes	missense	HAAO	NM_012205.2	125	0,51,6428	GG,GC,CC		0.5487,0.0911,0.3936	probably-damaging	235/287	42994814	51,12907	2196	4283	6479	SO:0001583	missense	23498	exon9			AGGAGCCCTCCTG	Z29481	CCDS33187.1	2p	2008-02-05			ENSG00000162882	ENSG00000162882	1.13.11.6		4796	protein-coding gene	gene with protein product		604521				7514594	Standard	NM_012205		Approved		uc002rst.4	P46952	OTTHUMG00000152348	ENST00000294973.6:c.703G>C	2.37:g.42994814C>G	ENSP00000294973:p.Gly235Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_012205		Missense_Mutation	SNP	ENST00000294973.6	37	CCDS33187.1	7	0.003205128205128205	0	0.0	4	0.011049723756906077	0	0.0	3	0.00395778364116095	c	16.44	3.123602	0.56613	9.11E-4	0.005487	ENSG00000162882	ENST00000294973	D	0.94092	-3.35	4.99	4.99	0.66335	Cupin, RmlC-type (1);	0.000000	0.85682	D	0.000000	D	0.92658	0.7667	M	0.77313	2.365	0.58432	D	0.999998	P	0.49961	0.93	P	0.49708	0.62	D	0.93260	0.6642	10	0.87932	D	0	.	13.7971	0.63177	0.0:1.0:0.0:0.0	rs34053133	235	P46952	3HAO_HUMAN	R	235	ENSP00000294973:G235R	ENSP00000294973:G235R	G	-	1	0	HAAO	42848318	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	1.780000	0.38634	2.331000	0.79229	0.550000	0.68814	GGC	C|0.996;G|0.004	0.004	strong		0.627	HAAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325948.2		
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105924731	105924731	+	Missense_Mutation	SNP	C	C	G	rs201941079		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:105924731C>G	ENST00000393359.2	-	2	454	c.28G>C	c.(28-30)Gtc>Ctc	p.V10L	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.V10L			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	10					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						ACAGCAGAGACAAGCGTAAAG	0.522																																					p.V10L	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.G28C						PASS	.	C	LEU/VAL,LEU/VAL	0,4406		0,0,2203	36.0	36.0	36.0		28,28	4.8	1.0	2		36	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	TGFBRAP1	NM_001142621.1,NM_004257.4	32,32	0,3,6500	GG,GC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	10/861,10/861	105924731	3,13003	2203	4300	6503	SO:0001583	missense	9392	exon2			CAGAGACAAGCGT	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.28G>C	2.37:g.105924731C>G	ENSP00000377027:p.Val10Leu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	37	CCDS2067.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	20.4	3.979858	0.74360	0.0	3.49E-4	ENSG00000135966	ENST00000393359;ENST00000258449	T;T	0.49139	0.79;0.79	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.44265	0.1285	M	0.67953	2.075	0.80722	D	1	B	0.31968	0.349	B	0.24848	0.056	T	0.42949	-0.9421	10	0.10377	T	0.69	-44.8777	18.4493	0.90697	0.0:1.0:0.0:0.0	.	10	Q8WUH2	TGFA1_HUMAN	L	10	ENSP00000377027:V10L;ENSP00000258449:V10L	ENSP00000258449:V10L	V	-	1	0	TGFBRAP1	105291163	1.000000	0.71417	0.981000	0.43875	0.983000	0.72400	5.892000	0.69790	2.654000	0.90174	0.655000	0.94253	GTC	C|0.999;G|0.001	0.001	strong		0.522	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
OR2A25	392138	hgsc.bcm.edu	37	7	143771557	143771557	+	Missense_Mutation	SNP	T	T	C	rs61731397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:143771557T>C	ENST00000408898.2	+	1	283	c.245T>C	c.(244-246)gTg>gCg	p.V82A		NM_001004488.1	NP_001004488.1	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A, member 25	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(16)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	24	Melanoma(164;0.0783)					CAGATGCTGGTGAACCTCCTG	0.552													.|||	746	0.148962	0.0318	0.3386	5008	,	,		20884	0.2877		0.0606	False		,,,				2504	0.1207				p.V82A		Atlas-SNP	.											.	OR2A25	66	.	0			c.T245C						PASS	.	T	ALA/VAL	140,4266	97.1+/-135.8	1,138,2064	79.0	83.0	82.0		245	0.9	0.7	7	dbSNP_129	82	445,8155	133.5+/-191.0	19,407,3874	yes	missense	OR2A25	NM_001004488.1	64	20,545,5938	CC,CT,TT		5.1744,3.1775,4.4979	benign	82/311	143771557	585,12421	2203	4300	6503	SO:0001583	missense	392138	exon1			TGCTGGTGAACCT		CCDS43669.1	7q35	2012-08-09		2004-03-10	ENSG00000221933	ENSG00000221933		"""GPCR / Class A : Olfactory receptors"""	19562	protein-coding gene	gene with protein product				OR2A25P, OR2A27			Standard	NM_001004488		Approved		uc011ktx.2	A4D2G3	OTTHUMG00000158013	ENST00000408898.2:c.245T>C	7.37:g.143771557T>C	ENSP00000386167:p.Val82Ala	Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	267	125	0.468165	NM_001004488	B2RNC9	Missense_Mutation	SNP	ENST00000408898.2	37	CCDS43669.1	340	0.15567765567765568	24	0.04878048780487805	100	0.27624309392265195	167	0.291958041958042	49	0.06464379947229551	T	5.560	0.288267	0.10513	0.031775	0.051744	ENSG00000221933	ENST00000408898	T	0.00388	7.59	4.88	0.922	0.19408	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.13145	0.007	B	0.14023	0.01	T	0.06162	-1.0842	8	0.11485	T	0.65	-1.4616	1.1088	0.01700	0.1502:0.1751:0.1554:0.5194	rs61731397	82	A4D2G3	O2A25_HUMAN	A	82	ENSP00000386167:V82A	ENSP00000386167:V82A	V	+	2	0	OR2A25	143402490	0.000000	0.05858	0.651000	0.29564	0.932000	0.56968	-0.634000	0.05477	0.315000	0.23110	0.460000	0.39030	GTG	T|0.882;C|0.118	0.118	strong		0.552	OR2A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350000.1		
ABCC6	368	hgsc.bcm.edu	37	16	16251599	16251599	+	Missense_Mutation	SNP	C	C	T	rs2238472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:16251599C>T	ENST00000205557.7	-	27	3832	c.3803G>A	c.(3802-3804)cGg>cAg	p.R1268Q		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1268	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> Q (associated with lower plasma triglycerides and higher plasma HDL cholesterol; dbSNP:rs2238472). {ECO:0000269|PubMed:10811882, ECO:0000269|PubMed:10913334, ECO:0000269|PubMed:11536079, ECO:0000269|PubMed:11776382, ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:18987736}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CCCAAAGTCCCGGAACTCGAT	0.622													C|||	908	0.18131	0.0673	0.2983	5008	,	,		18599	0.125		0.3012	False		,,,				2504	0.1871				p.R1268Q		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3803A	GRCh37	CM001044	ABCC6	M	rs2238472	PASS	.	C	GLN/ARG	473,3921	222.6+/-239.4	29,415,1753	52.0	45.0	48.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3803	2.0	0.6	16	dbSNP_98	48	2437,6163	401.1+/-347.0	345,1747,2208	yes	missense	ABCC6	NM_001171.5	43	374,2162,3961	TT,TC,CC		28.3372,10.7647,22.395	benign	1268/1504	16251599	2910,10084	2197	4300	6497	SO:0001583	missense	368	exon27			AAGTCCCGGAACT	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3803G>A	16.37:g.16251599C>T	ENSP00000205557:p.Arg1268Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	423	0.1936813186813187	41	0.08333333333333333	90	0.24861878453038674	68	0.11888111888111888	224	0.2955145118733509	c	11.76	1.734060	0.30684	0.107647	0.283372	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.90563	-2.69	5.09	2.01	0.26516	ABC transporter-like (1);	0.165125	0.27654	N	0.018411	T	0.00012	0.0000	N	0.17901	0.54	0.09310	P	0.9999999999913843	B	0.24576	0.106	B	0.12156	0.007	T	0.02639	-1.1130	9	0.25106	T	0.35	.	10.2379	0.43294	0.0:0.7787:0.0:0.2213	rs2238472;rs17289934;rs52824827;rs60072648;rs2238472	1268	O95255	MRP6_HUMAN	Q	1268;206	ENSP00000205557:R1268Q	ENSP00000205557:R1268Q	R	-	2	0	ABCC6	16159100	0.000000	0.05858	0.612000	0.29024	0.951000	0.60555	-0.326000	0.07965	0.191000	0.20236	0.530000	0.56133	CGG	C|0.810;T|0.190	0.190	strong		0.622	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
CROCC	9696	hgsc.bcm.edu	37	1	17275382	17275382	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17275382G>A	ENST00000375541.5	+	19	2866	c.2797G>A	c.(2797-2799)Gag>Aag	p.E933K	CROCC_ENST00000467938.1_Intron	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCTGGAAGCCGAGGGGCAGGC	0.662																																					p.E933K		Atlas-SNP	.											CROCC,NS,haematopoietic_neoplasm,0,1	CROCC	185	1	0			c.G2797A						PASS	.						22.0	27.0	25.0					1																	17275382		2169	4240	6409	SO:0001583	missense	9696	exon19			GAAGCCGAGGGGC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2797G>A	1.37:g.17275382G>A	ENSP00000364691:p.Glu933Lys	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	312	50	0.160256	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.992618	0.74703	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.24350	1.86	4.38	4.38	0.52667	.	.	.	.	.	T	0.21427	0.0516	L	0.41492	1.28	0.48040	D	0.999579	P;P	0.41748	0.761;0.641	B;B	0.35182	0.197;0.116	T	0.06445	-1.0826	9	0.51188	T	0.08	.	15.2441	0.73493	0.0:0.0:1.0:0.0	.	236;933	Q5TZA2-2;Q5TZA2	.;CROCC_HUMAN	K	933;814	ENSP00000364691:E933K	ENSP00000364691:E933K	E	+	1	0	CROCC	17147969	1.000000	0.71417	0.180000	0.23079	0.929000	0.56500	6.930000	0.75858	2.374000	0.81015	0.557000	0.71058	GAG	.	.	none		0.662	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
KLHL6	89857	hgsc.bcm.edu	37	3	183226114	183226114	+	Silent	SNP	G	G	T	rs73188786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183226114G>T	ENST00000341319.3	-	3	677	c.642C>A	c.(640-642)ccC>ccA	p.P214P		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	214	BACK.				B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			gagtgtccacgggcaggtcaa	0.502													G|||	313	0.0625	0.0083	0.0576	5008	,	,		21109	0.0069		0.1143	False		,,,				2504	0.1431				p.P214P		Atlas-SNP	.											.	KLHL6	100	.	0			c.C642A						PASS	.	G		102,4304	80.4+/-118.8	0,102,2101	77.0	68.0	71.0		642	-11.7	0.0	3	dbSNP_130	71	1047,7553	220.1+/-257.9	69,909,3322	no	coding-synonymous	KLHL6	NM_130446.2		69,1011,5423	TT,TG,GG		12.1744,2.315,8.8344		214/622	183226114	1149,11857	2203	4300	6503	SO:0001819	synonymous_variant	89857	exon3			GTCCACGGGCAGG	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.642C>A	3.37:g.183226114G>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	219	94	0.429224	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	37	CCDS3245.2																																																																																			G|0.917;T|0.083	0.083	strong		0.502	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
RADIL	55698	hgsc.bcm.edu	37	7	4845312	4845312	+	Silent	SNP	T	T	G	rs2306919	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:4845312T>G	ENST00000399583.3	-	10	2362	c.2175A>C	c.(2173-2175)gcA>gcC	p.A725A	RADIL_ENST00000538469.1_Silent_p.A485A|RADIL_ENST00000536091.1_3'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	725	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CTGGGCTCAGTGCGGGGAACG	0.667													G|||	1657	0.330871	0.708	0.183	5008	,	,		15966	0.0526		0.2117	False		,,,				2504	0.3354				p.A725A		Atlas-SNP	.											.	RADIL	110	.	0			c.A2175C						PASS	.	G		2327,1895		659,1009,443	21.0	28.0	26.0		2175	1.3	1.0	7	dbSNP_100	26	1660,6874		164,1332,2771	no	coding-synonymous	RADIL	NM_018059.4		823,2341,3214	GG,GT,TT		19.4516,44.8839,31.2559		725/1076	4845312	3987,8769	2111	4267	6378	SO:0001819	synonymous_variant	55698	exon10			GCTCAGTGCGGGG	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2175A>C	7.37:g.4845312T>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			T|0.748;G|0.252	0.252	strong		0.667	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
SERPIND1	3053	hgsc.bcm.edu	37	22	21134023	21134023	+	Silent	SNP	G	G	A	rs35646566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21134023G>A	ENST00000215727.5	+	2	706	c.423G>A	c.(421-423)ctG>ctA	p.L141L	PI4KA_ENST00000466162.1_Intron|PI4KA_ENST00000255882.6_Intron|PI4KA_ENST00000572273.1_Intron|SERPIND1_ENST00000406799.1_Silent_p.L141L	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	141					blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	ACCGAGTGCTGAAAGACCAGG	0.493													G|||	52	0.0103834	0.0	0.013	5008	,	,		20876	0.0		0.0268	False		,,,				2504	0.0164				p.L141L		Atlas-SNP	.											.	SERPIND1	92	.	0			c.G423A						PASS	.	G	,	25,4381	31.7+/-61.6	0,25,2178	96.0	81.0	86.0		423,	-0.4	0.2	22	dbSNP_126	86	242,8358	96.6+/-158.3	5,232,4063	no	coding-synonymous,intron	SERPIND1,PI4KA	NM_000185.3,NM_058004.3	,	5,257,6241	AA,AG,GG		2.814,0.5674,2.0529	,	141/500,	21134023	267,12739	2203	4300	6503	SO:0001819	synonymous_variant	3053	exon2			AGTGCTGAAAGAC	M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"""Serine (or cysteine) peptidase inhibitors"""	4838	protein-coding gene	gene with protein product	"""heparin cofactor II"""	142360	"""serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"""	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.423G>A	22.37:g.21134023G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	185	92	0.497297	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Silent	SNP	ENST00000215727.5	37	CCDS13783.1																																																																																			G|0.984;A|0.016	0.016	strong		0.493	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185	
LRIT3	345193	hgsc.bcm.edu	37	4	110791543	110791543	+	Silent	SNP	C	C	T	rs2347133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110791543C>T	ENST00000594814.1	+	4	1638	c.1638C>T	c.(1636-1638)ccC>ccT	p.P546P	LRIT3_ENST00000409621.2_Silent_p.P363P|LRIT3_ENST00000379920.3_Silent_p.P501P|LRIT3_ENST00000327908.3_Silent_p.P363P	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	546	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		GCTTGGAACCCGGTGGGCAAT	0.488													C|||	1246	0.248802	0.27	0.3804	5008	,	,		20723	0.2728		0.1481	False		,,,				2504	0.2055				p.P546P		Atlas-SNP	.											.	LRIT3	107	.	0			c.C1638T						PASS	.	C		1072,3334	389.3+/-327.3	133,806,1264	101.0	96.0	98.0		1503	-10.3	0.0	4	dbSNP_100	98	1186,7414	241.4+/-271.8	100,986,3214	no	coding-synonymous	LRIT3	NM_198506.2		233,1792,4478	TT,TC,CC		13.7907,24.3305,17.3612		501/635	110791543	2258,10748	2203	4300	6503	SO:0001819	synonymous_variant	345193	exon4			GGAACCCGGTGGG	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1638C>T	4.37:g.110791543C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	142	75	0.528169	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	37	CCDS3688.3																																																																																			C|0.804;T|0.196	0.196	strong		0.488	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
C5orf46	389336	hgsc.bcm.edu	37	5	147286054	147286054	+	Missense_Mutation	SNP	G	G	A	rs2250145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147286054G>A	ENST00000318315.4	-	1	11	c.11C>T	c.(10-12)tCa>tTa	p.S4L	C5orf46_ENST00000510432.1_5'Flank|C5orf46_ENST00000515291.1_Missense_Mutation_p.S4L	NM_206966.2	NP_996849.2	Q6UWT4	CE046_HUMAN	chromosome 5 open reading frame 46	4				S -> L (in Ref. 2; AAQ89019 and 4; AAH21680). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)				NS(1)|lung(1)|prostate(1)	3						GCGAAGTACTGAGACAGCCAT	0.448													G|||	2409	0.48103	0.1846	0.4741	5008	,	,		17666	0.619		0.6163	False		,,,				2504	0.6053				p.S4L		Atlas-SNP	.											.	C5orf46	8	.	0			c.C11T						PASS	.	G	LEU/SER	1001,3405	371.2+/-319.9	105,791,1307	99.0	86.0	91.0		11	4.9	1.0	5	dbSNP_100	91	5030,3570	627.6+/-398.0	1468,2094,738	yes	missense	C5orf46	NM_206966.2	145	1573,2885,2045	AA,AG,GG		41.5116,22.719,46.3709	probably-damaging	4/88	147286054	6031,6975	2203	4300	6503	SO:0001583	missense	389336	exon1			AGTACTGAGACAG		CCDS34267.1	5q33.1	2013-12-13			ENSG00000178776	ENSG00000178776			33768	protein-coding gene	gene with protein product	"""skin and saliva secreted protein 1"""						Standard	NM_206966		Approved	MGC23985, SSSP1	uc003lou.3	Q6UWT4	OTTHUMG00000163420	ENST00000318315.4:c.11C>T	5.37:g.147286054G>A	ENSP00000315370:p.Ser4Leu	Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	351	351	1	NM_206966	A8K038|Q8WU04	Missense_Mutation	SNP	ENST00000318315.4	37	CCDS34267.1	1105	0.5059523809523809	89	0.18089430894308944	184	0.5082872928176796	362	0.6328671328671329	470	0.6200527704485488	G	16.93	3.259231	0.59321	0.22719	0.584884	ENSG00000178776	ENST00000318315;ENST00000515291	T;T	0.57907	0.37;0.37	4.88	4.88	0.63580	.	0.000000	0.39407	N	0.001368	T	0.00012	0.0000	.	.	.	0.31861	P	0.6209629999999999	D	0.89917	1.0	D	0.87578	0.998	T	0.54057	-0.8350	7	.	.	.	-26.4373	13.7499	0.62901	0.0:0.0:1.0:0.0	rs2250145;rs17625621;rs17845658;rs17858593;rs56430324;rs59500495;rs2250145	4	Q6UWT4	CE046_HUMAN	L	4	ENSP00000315370:S4L;ENSP00000425984:S4L	.	S	-	2	0	C5orf46	147266247	0.999000	0.42202	0.999000	0.59377	0.824000	0.46624	4.186000	0.58337	2.721000	0.93114	0.655000	0.94253	TCA	G|0.523;A|0.477	0.477	strong		0.448	C5orf46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373314.1	NM_206966	
REXO4	57109	hgsc.bcm.edu	37	9	136279935	136279935	+	Missense_Mutation	SNP	C	C	T	rs6597630	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136279935C>T	ENST00000371942.3	-	2	621	c.422G>A	c.(421-423)aGg>aAg	p.R141K	REXO4_ENST00000371935.2_Missense_Mutation_p.G82R|ADAMTS13_ENST00000485925.1_Intron|REXO4_ENST00000478037.1_5'UTR	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	141			R -> K (in dbSNP:rs6597630).		regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		TACTGGCGCCCTCCTGTCCAT	0.542													T|||	449	0.0896565	0.2126	0.0519	5008	,	,		18683	0.0198		0.0855	False		,,,				2504	0.0266				p.R141K		Atlas-SNP	.											.	REXO4	27	.	0			c.G422A						PASS	.	T	LYS/ARG	824,3582	748.0+/-411.9	84,656,1463	147.0	118.0	128.0		422	-3.9	0.0	9	dbSNP_116	128	743,7857	785.5+/-407.6	37,669,3594	yes	missense	REXO4	NM_020385.2	26	121,1325,5057	TT,TC,CC		8.6395,18.7018,12.0483	benign	141/423	136279935	1567,11439	2203	4300	6503	SO:0001583	missense	57109	exon2			GGCGCCCTCCTGT	AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"""Xenopus prevents mitotic catatrophe 2 homolog"", ""XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"""	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.422G>A	9.37:g.136279935C>T	ENSP00000361010:p.Arg141Lys	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	209	102	0.488038	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Missense_Mutation	SNP	ENST00000371942.3	37	CCDS6969.1	198|198	0.09065934065934066|0.09065934065934066	98|98	0.1991869918699187|0.1991869918699187	21|21	0.058011049723756904|0.058011049723756904	12|12	0.02097902097902098|0.02097902097902098	67|67	0.08839050131926121|0.08839050131926121	T|T	1.245|1.245	-0.620319|-0.620319	0.03636|0.03636	0.187018|0.187018	0.086395|0.086395	ENSG00000148300|ENSG00000148300	ENST00000371935;ENST00000454825|ENST00000453165;ENST00000371942;ENST00000445916	.|T;T;T	.|0.19105	.|2.43;2.44;2.17	4.45|4.45	-3.93|-3.93	0.04143|0.04143	.|.	.|18.384800	.|0.00481	.|N	.|0.000133	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00179|0.00179	-1.91|-1.91	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.35525|0.35525	-0.9785|-0.9785	7|9	0.87932|0.02654	D|T	0|1	.|.	7.2986|7.2986	0.26408|0.26408	0.0:0.2359:0.483:0.2811|0.0:0.2359:0.483:0.2811	rs6597630|rs6597630	82|141	Q9GZR2-2|Q9GZR2	.|REXO4_HUMAN	R|K	82|126;141;48	.|ENSP00000403272:R126K;ENSP00000361010:R141K;ENSP00000391534:R48K	ENSP00000361003:G82R|ENSP00000361010:R141K	G|R	-|-	1|2	0|0	REXO4|REXO4	135269756|135269756	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.094000|-0.094000	0.11094|0.11094	-1.093000|-1.093000	0.03058|0.03058	-0.361000|-0.361000	0.07541|0.07541	GGG|AGG	C|0.889;T|0.111	0.111	strong		0.542	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1		
DNAJC30	84277	hgsc.bcm.edu	37	7	73097654	73097654	+	Missense_Mutation	SNP	C	C	T	rs1128349	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:73097654C>T	ENST00000395176.2	-	1	129	c.100G>A	c.(100-102)Gga>Aga	p.G34R	WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000464615.1_3'UTR|WBSCR22_ENST00000265758.2_5'Flank|WBSCR22_ENST00000423497.1_5'Flank	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	34			G -> R (in dbSNP:rs1128349). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(1)	4						GTCCTCGCTCCTAGGCCCAGG	0.627													C|||	1516	0.302716	0.1967	0.268	5008	,	,		13139	0.3204		0.4463	False		,,,				2504	0.3047				p.G34R		Atlas-SNP	.											.	DNAJC30	12	.	0			c.G100A						PASS	.	C	ARG/GLY	923,3461		122,679,1391	63.0	74.0	70.0		100	-1.8	0.0	7	dbSNP_86	70	3837,4737		888,2061,1338	yes	missense	DNAJC30	NM_032317.2	125	1010,2740,2729	TT,TC,CC		44.7516,21.0538,36.7341	benign	34/227	73097654	4760,8198	2192	4287	6479	SO:0001583	missense	84277	exon1			TCGCTCCTAGGCC	AF412025	CCDS5556.1	7q11.23	2011-09-02	2008-06-17	2008-06-17	ENSG00000176410	ENSG00000176410		"""Heat shock proteins / DNAJ (HSP40)"""	16410	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 18"""	WBSCR18		12073013	Standard	NM_032317		Approved		uc003tys.1	Q96LL9	OTTHUMG00000023290	ENST00000395176.2:c.100G>A	7.37:g.73097654C>T	ENSP00000378605:p.Gly34Arg	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_032317	Q9BSG8	Missense_Mutation	SNP	ENST00000395176.2	37	CCDS5556.1	753	0.3447802197802198	105	0.21341463414634146	108	0.2983425414364641	201	0.3513986013986014	339	0.4472295514511873	C	10.84	1.464115	0.26335	0.210538	0.447516	ENSG00000176410	ENST00000395176;ENST00000539255	T	0.57436	0.4	4.87	-1.84	0.07809	Heat shock protein DnaJ, N-terminal (1);	1.599000	0.03889	N	0.278387	T	0.00012	0.0000	N	0.04508	-0.205	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.37174	-0.9717	9	0.13470	T	0.59	-9.3373	1.673	0.02816	0.1192:0.267:0.339:0.2748	rs1128349;rs11541498;rs17553400;rs17845038;rs17857811;rs58147772;rs1128349	34	Q96LL9	DJC30_HUMAN	R	34;31	ENSP00000378605:G34R	ENSP00000378605:G34R	G	-	1	0	DNAJC30	72735590	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.498000	0.06420	-0.483000	0.06772	0.591000	0.81541	GGA	C|0.641;T|0.359	0.359	strong		0.627	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2		
SEC23IP	11196	hgsc.bcm.edu	37	10	121693246	121693246	+	Silent	SNP	A	A	G	rs34826964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:121693246A>G	ENST00000369075.3	+	18	3042	c.2970A>G	c.(2968-2970)acA>acG	p.T990T	SEC23IP_ENST00000543134.1_Silent_p.T779T|SEC23IP_ENST00000475542.1_3'UTR	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	990					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.T990T(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TTTATCGAACAATGAACATTA	0.313													A|||	584	0.116613	0.0023	0.0274	5008	,	,		19108	0.1984		0.0537	False		,,,				2504	0.3149				p.T990T		Atlas-SNP	.											SEC23IP,NS,carcinoma,0,1	SEC23IP	100	1	1	Substitution - coding silent(1)	stomach(1)	c.A2970G						PASS	.	A		38,4368	43.8+/-77.6	0,38,2165	79.0	73.0	75.0		2970	3.4	1.0	10	dbSNP_126	75	475,8125	138.7+/-195.5	9,457,3834	no	coding-synonymous	SEC23IP	NM_007190.3		9,495,5999	GG,GA,AA		5.5233,0.8625,3.9443		990/1001	121693246	513,12493	2203	4300	6503	SO:0001819	synonymous_variant	11196	exon18			TCGAACAATGAAC	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"""Sterile alpha motif (SAM) domain containing"""	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.2970A>G	10.37:g.121693246A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Silent	SNP	ENST00000369075.3	37	CCDS7618.1																																																																																			A|0.948;G|0.052	0.052	strong		0.313	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1		
PELI1	57162	hgsc.bcm.edu	37	2	64327592	64327592	+	Silent	SNP	T	T	C	rs329497	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:64327592T>C	ENST00000358912.4	-	4	685	c.243A>G	c.(241-243)ttA>ttG	p.L81L	PELI1_ENST00000466177.2_5'UTR	NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	81					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						GGGCCCGAGATAAAGTATATG	0.343													T|||	1754	0.35024	0.0688	0.3112	5008	,	,		15865	0.752		0.2992	False		,,,				2504	0.3967				p.L81L		Atlas-SNP	.											.	PELI1	34	.	0			c.A243G						PASS	.	T		535,3871	241.5+/-251.9	33,469,1701	168.0	148.0	155.0		243	0.1	1.0	2	dbSNP_79	155	2617,5983	424.1+/-354.6	403,1811,2086	no	coding-synonymous	PELI1	NM_020651.3		436,2280,3787	CC,CT,TT		30.4302,12.1425,24.235		81/419	64327592	3152,9854	2203	4300	6503	SO:0001819	synonymous_variant	57162	exon4			CCGAGATAAAGTA		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"""Pellino homologs"""	8827	protein-coding gene	gene with protein product		614797	"""pellino (Drosophila) homolog 1"", ""pellino homolog 1 (Drosophila)"""			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.243A>G	2.37:g.64327592T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_020651	Q96SM0|Q9GZY5|Q9HCX0	Silent	SNP	ENST00000358912.4	37	CCDS1876.1																																																																																			T|0.705;C|0.295	0.295	strong		0.343	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651	
HIBCH	26275	hgsc.bcm.edu	37	2	191184475	191184475	+	Start_Codon_SNP	SNP	A	A	G	rs291466	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:191184475A>G	ENST00000359678.5	-	1	296	c.2T>C	c.(1-3)aTg>aCg	p.M1T	HIBCH_ENST00000392332.3_Start_Codon_SNP_p.M1T	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	1					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			GCGCTGCCCCATCGCCAAACA	0.677													A|||	2162	0.431709	0.4349	0.3429	5008	,	,		14560	0.1567		0.5974	False		,,,				2504	0.6033				p.M1T		Atlas-SNP	.											.	HIBCH	28	.	0			c.T2C						PASS	.	A	THR/MET,THR/MET	2008,2398	541.9+/-375.9	470,1068,665	52.0	41.0	44.0		2,2	3.9	0.3	2	dbSNP_79	44	5170,3430	623.1+/-397.4	1540,2090,670	yes	missense,missense	HIBCH	NM_014362.3,NM_198047.2	81,81	2010,3158,1335	GG,GA,AA		39.8837,45.5742,44.8101	possibly-damaging,possibly-damaging	1/387,1/339	191184475	7178,5828	2203	4300	6503	SO:0001582	initiator_codon_variant	26275	exon1			TGCCCCATCGCCA	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"""3-hydroxyisobutyryl-Coenzyme A hydrolase"""			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.2T>C	2.37:g.191184475A>G	ENSP00000352706:p.Met1Thr	Somatic	372	0	0		WXS	Illumina HiSeq	Phase_I	394	207	0.525381	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	37	CCDS2304.1	877	0.4015567765567766	218	0.44308943089430897	135	0.3729281767955801	80	0.13986013986013987	444	0.5857519788918206	A	15.05	2.718971	0.48622	0.455742	0.601163	ENSG00000198130	ENST00000392332;ENST00000359678	T;T	0.56444	0.46;0.46	3.88	3.88	0.44766	.	0.089786	0.34156	U	0.004201	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999120968	B;B	0.22146	0.065;0.039	B;B	0.22601	0.04;0.018	T	0.45977	-0.9224	8	0.72032	D	0.01	-18.8562	9.3695	0.38246	1.0:0.0:0.0:0.0	rs291466;rs3749021;rs52816500;rs291466	1;1	Q6NVY1-2;Q6NVY1	.;HIBCH_HUMAN	T	1	ENSP00000376144:M1T;ENSP00000352706:M1T	ENSP00000352706:M1T	M	-	2	0	HIBCH	190892720	0.129000	0.22400	0.299000	0.25016	0.010000	0.07245	1.290000	0.33319	1.988000	0.58038	0.533000	0.62120	ATG	A|0.492;C|0.001	.	strong		0.677	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1		Missense_Mutation
SLC2A14	144195	hgsc.bcm.edu	37	12	7967076	7967076	+	Silent	SNP	A	A	G	rs10845983	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:7967076A>G	ENST00000543909.1	-	16	2158	c.1399T>C	c.(1399-1401)Ttg>Ctg	p.L467L	SLC2A14_ENST00000431042.2_Silent_p.L444L|SLC2A14_ENST00000535295.1_Silent_p.L358L|SLC2A14_ENST00000539924.1_Silent_p.L482L|SLC2A14_ENST00000396589.2_Silent_p.L467L|SLC2A14_ENST00000542505.1_Silent_p.L108L|SLC2A14_ENST00000340749.5_Silent_p.L444L|SLC2A14_ENST00000542546.1_Silent_p.L358L			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	467					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		GTAAAGGCCAAGAAGGTAATG	0.453													A|||	1049	0.209465	0.0204	0.3674	5008	,	,		-128	0.1181		0.338	False		,,,				2504	0.3149				p.L467L		Atlas-SNP	.											SLC2A14,NS,carcinoma,+2,1	SLC2A14	78	1	0			c.T1399C						scavenged	.	A		333,4073	173.0+/-202.9	18,297,1888	66.0	66.0	66.0		1399	2.4	0.2	12	dbSNP_120	66	2898,5702	449.7+/-362.2	459,1980,1861	no	coding-synonymous	SLC2A14	NM_153449.2		477,2277,3749	GG,GA,AA		33.6977,7.5579,24.8424		467/521	7967076	3231,9775	2203	4300	6503	SO:0001819	synonymous_variant	144195	exon12			AGGCCAAGAAGGT	AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"""Solute carriers"""	18301	protein-coding gene	gene with protein product		611039	"""solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"""	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1399T>C	12.37:g.7967076A>G		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1																																																																																			A|0.760;G|0.240	0.240	strong		0.453	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	
SIRPG	55423	hgsc.bcm.edu	37	20	1629906	1629906	+	Silent	SNP	C	C	T	rs6079967	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:1629906C>T	ENST00000303415.3	-	2	286	c.222G>A	c.(220-222)cgG>cgA	p.R74R	RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000344103.4_Silent_p.R74R|SIRPG_ENST00000216927.4_Silent_p.R74R|SIRPG_ENST00000381583.2_Silent_p.R74R|SIRPG_ENST00000381580.1_Silent_p.R41R	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	74	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R74R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						AGATTAATTCCCGGCCTGGTC	0.507													t|||	1761	0.351637	0.3064	0.5058	5008	,	,		19787	0.2708		0.4394	False		,,,				2504	0.2965				p.R74R		Atlas-SNP	.											SIRPG,right_upper_lobe,carcinoma,-1,2	SIRPG	61	2	1	Substitution - coding silent(1)	stomach(1)	c.G222A						PASS	.	T	,,	1457,2949		248,961,994	182.0	165.0	171.0		222,222,222	-0.1	0.0	20	dbSNP_114	171	3939,4661		906,2127,1267	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	1154,3088,2261	TT,TC,CC		45.8023,33.0685,41.4885	,,	74/277,74/388,74/171	1629906	5396,7610	2203	4300	6503	SO:0001819	synonymous_variant	55423	exon2			TAATTCCCGGCCT	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.222G>A	20.37:g.1629906C>T		Somatic	407	2	0.004914		WXS	Illumina HiSeq	Phase_I	446	446	1	NM_001039508	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			C|0.593;T|0.407	0.407	strong		0.507	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
L2HGDH	79944	hgsc.bcm.edu	37	14	50769717	50769717	+	Silent	SNP	G	G	A	rs2297995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50769717G>A	ENST00000267436.4	-	2	556	c.159C>T	c.(157-159)atC>atT	p.I53I	L2HGDH_ENST00000261699.4_Silent_p.I53I|L2HGDH_ENST00000556393.1_5'UTR|L2HGDH_ENST00000555423.1_Silent_p.I53I|L2HGDH_ENST00000555610.1_Silent_p.I53I|L2HGDH_ENST00000421284.3_Silent_p.I53I			Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase	53					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2-hydroxyglutarate dehydrogenase activity (GO:0047545)			kidney(1)|large_intestine(4)|lung(3)|ovary(2)	10	all_epithelial(31;0.000599)|Breast(41;0.0102)					CGCCACCAACGATGACTATAT	0.403													A|||	2988	0.596645	0.6407	0.5317	5008	,	,		19800	0.6468		0.5477	False		,,,				2504	0.5818				p.I53I		Atlas-SNP	.											.	L2HGDH	33	.	0			c.C159T						PASS	.	A		2695,1711	515.5+/-368.9	822,1051,330	93.0	94.0	94.0		159	0.3	0.1	14	dbSNP_100	94	4774,3826	540.2+/-383.8	1337,2100,863	no	coding-synonymous	L2HGDH	NM_024884.2		2159,3151,1193	AA,AG,GG		44.4884,38.8334,42.5727		53/464	50769717	7469,5537	2203	4300	6503	SO:0001819	synonymous_variant	79944	exon2			ACCAACGATGACT		CCDS9698.1	14q22.1	2006-04-28	2005-05-25	2005-05-25	ENSG00000087299	ENSG00000087299	1.1.99.2		20499	protein-coding gene	gene with protein product	"""2-hydroxyglutarate dehydrogenase"""	609584	"""chromosome 14 open reading frame 160"""	C14orf160		16005139	Standard	NM_024884		Approved	FLJ12618	uc001wxu.3	Q9H9P8	OTTHUMG00000140289	ENST00000267436.4:c.159C>T	14.37:g.50769717G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_024884	Q9BRR1	Silent	SNP	ENST00000267436.4	37	CCDS9698.1																																																																																			G|0.419;A|0.581	0.581	strong		0.403	L2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276870.2	NM_024884	
PCDH20	64881	hgsc.bcm.edu	37	13	61986314	61986314	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:61986314T>C	ENST00000409186.1	-	5	4023	c.1918A>G	c.(1918-1920)Atc>Gtc	p.I640V	PCDH20_ENST00000409204.4_Missense_Mutation_p.I640V			Q8N6Y1	PCD20_HUMAN	protocadherin 20	640	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		TCCTTGTTGATAAACCGAGGA	0.458																																					p.I640V		Atlas-SNP	.											PCDH20_ENST00000409186,NS,adenocarcinoma,+2,2	PCDH20	265	2	0			c.A1918G						scavenged	.						117.0	110.0	112.0					13																	61986314		2203	4300	6503	SO:0001583	missense	64881	exon2			TGTTGATAAACCG	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1918A>G	13.37:g.61986314T>C	ENSP00000386653:p.Ile640Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	149	2	0.0134228	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	T	10.77	1.444733	0.25987	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	T;T	0.01665	4.7;4.7	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000007	T	0.01627	0.0052	N	0.12182	0.205	0.50632	D	0.999886	B	0.27229	0.172	B	0.22152	0.038	T	0.68191	-0.5474	10	0.28530	T	0.3	.	16.3908	0.83537	0.0:0.0:0.0:1.0	.	640	A8K1K9	.	V	640;640;386	ENSP00000387250:I640V;ENSP00000386653:I640V	ENSP00000351500:I386V	I	-	1	0	PCDH20	60884315	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.219000	0.72231	2.269000	0.75478	0.455000	0.32223	ATC	.	.	none		0.458	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
NAB2	4665	hgsc.bcm.edu	37	12	57485291	57485291	+	Missense_Mutation	SNP	G	G	A	rs140433833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57485291G>A	ENST00000300131.3	+	2	845	c.467G>A	c.(466-468)cGc>cAc	p.R156H	NAB2_ENST00000357680.4_Missense_Mutation_p.R156H|NAB2_ENST00000342556.6_Missense_Mutation_p.R156H|NAB2_ENST00000554718.1_3'UTR	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	156					cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GGCAGTGCCCGCAGTTTTAGC	0.632													G|||	12	0.00239617	0.0076	0.0029	5008	,	,		16784	0.0		0.0	False		,,,				2504	0.0				p.R156H		Atlas-SNP	.											NAB2,NS,carcinoma,-1,1	NAB2	47	1	0			c.G467A						PASS	.	G	HIS/ARG	13,4393	21.2+/-45.6	0,13,2190	55.0	56.0	56.0		467	4.2	1.0	12	dbSNP_134	56	5,8595	5.0+/-18.6	0,5,4295	yes	missense	NAB2	NM_005967.3	29	0,18,6485	AA,AG,GG		0.0581,0.2951,0.1384	probably-damaging	156/526	57485291	18,12988	2203	4300	6503	SO:0001583	missense	4665	exon2			GTGCCCGCAGTTT	BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.467G>A	12.37:g.57485291G>A	ENSP00000300131:p.Arg156His	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	41	23	0.560976	NM_005967	B2RAK3|O76006|Q14797	Missense_Mutation	SNP	ENST00000300131.3	37	CCDS8930.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	16.63	3.176780	0.57692	0.002951	5.81E-4	ENSG00000166886	ENST00000300131;ENST00000342556;ENST00000357680	.	.	.	4.18	4.18	0.49190	.	0.433911	0.21867	N	0.067954	T	0.32315	0.0825	N	0.14661	0.345	0.49051	D	0.999745	D	0.59767	0.986	P	0.46299	0.511	T	0.35325	-0.9793	9	0.46703	T	0.11	-8.9058	14.0515	0.64739	0.0:0.0:1.0:0.0	.	156	Q15742	NAB2_HUMAN	H	156	.	ENSP00000300131:R156H	R	+	2	0	NAB2	55771558	0.991000	0.36638	0.997000	0.53966	0.957000	0.61999	1.829000	0.39121	2.156000	0.67533	0.462000	0.41574	CGC	G|0.997;A|0.003	0.003	strong		0.632	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967	
SETD1B	23067	hgsc.bcm.edu	37	12	122261456	122261456	+	Silent	SNP	G	G	A	rs3741593	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:122261456G>A	ENST00000604567.1	+	12	5039	c.4971G>A	c.(4969-4971)gcG>gcA	p.A1657A	SETD1B_ENST00000542440.1_Silent_p.A1614A|SETD1B_ENST00000267197.5_Silent_p.A1614A			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	1657	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						TGCCACCTGCGGGCTCGCCCG	0.647													G|||	1863	0.372005	0.0287	0.4798	5008	,	,		10853	0.5427		0.5199	False		,,,				2504	0.4315				p.A1614A		Atlas-SNP	.											.	SETD1B	105	.	0			c.G4842A						PASS	.	G		135,1249		5,125,562	35.0	39.0	38.0		4842	-9.1	0.0	12	dbSNP_107	38	1751,1431		497,757,337	no	coding-synonymous	SETD1B	NM_015048.1		502,882,899	AA,AG,GG		44.9717,9.7543,41.3053		1614/1924	122261456	1886,2680	692	1591	2283	SO:0001819	synonymous_variant	23067	exon12			ACCTGCGGGCTCG	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.4971G>A	12.37:g.122261456G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	43	30	0.697674	NM_015048	F6MFW1	Silent	SNP	ENST00000604567.1	37																																																																																				G|0.591;A|0.409	0.409	strong		0.647	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
TMEM86B	255043	hgsc.bcm.edu	37	19	55739605	55739605	+	Silent	SNP	C	C	T	rs4606850	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55739605C>T	ENST00000327042.4	-	2	774	c.252G>A	c.(250-252)tcG>tcA	p.S84S	AC010327.2_ENST00000598855.1_3'UTR	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	84					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CCCCCACAGCCGAGCACACAA	0.657													C|||	842	0.168131	0.1989	0.2205	5008	,	,		16486	0.0754		0.1968	False		,,,				2504	0.1554				p.S84S		Atlas-SNP	.											.	TMEM86B	12	.	0			c.G252A						PASS	.	C		816,3588		68,680,1454	29.0	30.0	30.0		252	-10.8	0.0	19	dbSNP_111	30	1723,6877		180,1363,2757	no	coding-synonymous	TMEM86B	NM_173804.4		248,2043,4211	TT,TC,CC		20.0349,18.5286,19.5248		84/227	55739605	2539,10465	2202	4300	6502	SO:0001819	synonymous_variant	255043	exon2			CACAGCCGAGCAC	BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.252G>A	19.37:g.55739605C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_173804		Silent	SNP	ENST00000327042.4	37	CCDS12920.1																																																																																			C|0.829;T|0.171	0.171	strong		0.657	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804	
COL20A1	57642	hgsc.bcm.edu	37	20	61951489	61951489	+	Silent	SNP	G	G	C	rs6089881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61951489G>C	ENST00000358894.6	+	24	3115	c.3015G>C	c.(3013-3015)gcG>gcC	p.A1005A	COL20A1_ENST00000326996.6_Silent_p.A1005A|COL20A1_ENST00000435874.1_Silent_p.A1012A|COL20A1_ENST00000422202.1_Silent_p.A1012A	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1005	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					CACCCGCTGCGGGCTTCGTCA	0.721													C|||	4426	0.883786	0.5946	0.964	5008	,	,		14034	0.996		0.997	False		,,,				2504	0.9857				p.A1005A		Atlas-SNP	.											.	COL20A1	137	.	0			c.G3015C						PASS	.	C		2650,1020		939,772,124	6.0	7.0	6.0		3015	-6.0	0.0	20	dbSNP_114	6	7917,37		3941,35,1	no	coding-synonymous	COL20A1	NM_020882.2		4880,807,125	CC,CG,GG		0.4652,27.7929,9.0933		1005/1285	61951489	10567,1057	1835	3977	5812	SO:0001819	synonymous_variant	57642	exon24			CGCTGCGGGCTTC	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.3015G>C	20.37:g.61951489G>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	37	CCDS46628.1																																																																																			G|0.094;C|0.906	0.906	strong		0.721	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
NLK	51701	hgsc.bcm.edu	37	17	26519204	26519204	+	Silent	SNP	C	C	T	rs3182380	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:26519204C>T	ENST00000407008.3	+	10	2212	c.1494C>T	c.(1492-1494)atC>atT	p.I498I		NM_016231.4	NP_057315.3	Q9UBE8	NLK_HUMAN	nemo-like kinase	498	Required for homodimerization and kinase activation and localization to the nucleus. {ECO:0000250}.|Required for interaction with TAB2. {ECO:0000250}.				intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of Wnt signaling pathway (GO:0030178)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|serine phosphorylation of STAT3 protein (GO:0033136)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|SH2 domain binding (GO:0042169)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(1)	14	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CTCTCTGCATCAACCCTCAGT	0.348													C|||	98	0.0195687	0.0023	0.0375	5008	,	,		20189	0.0		0.0616	False		,,,				2504	0.0072				p.I498I		Atlas-SNP	.											.	NLK	88	.	0			c.C1494T						PASS	.	C		61,4345	56.8+/-93.2	1,59,2143	108.0	105.0	106.0		1494	4.9	1.0	17	dbSNP_105	106	496,8104	140.8+/-197.2	18,460,3822	yes	coding-synonymous	NLK	NM_016231.4		19,519,5965	TT,TC,CC		5.7674,1.3845,4.2826		498/528	26519204	557,12449	2203	4300	6503	SO:0001819	synonymous_variant	51701	exon10			CTGCATCAACCCT	AF197898	CCDS11224.2	17q11.2	2005-12-22	2005-12-22		ENSG00000087095	ENSG00000087095			29858	protein-coding gene	gene with protein product		609476	"""nemo like kinase"""			9448268, 10863097	Standard	NM_016231		Approved		uc010crj.3	Q9UBE8	OTTHUMG00000132451	ENST00000407008.3:c.1494C>T	17.37:g.26519204C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_016231	B2RCX1|Q2PNI9|Q6P2A3	Silent	SNP	ENST00000407008.3	37	CCDS11224.2																																																																																			C|0.967;T|0.033	0.033	strong		0.348	NLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255607.3	NM_016231	
COL24A1	255631	hgsc.bcm.edu	37	1	86512536	86512536	+	Missense_Mutation	SNP	C	C	T	rs60891279	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86512536C>T	ENST00000370571.2	-	12	2288	c.1922G>A	c.(1921-1923)cGt>cAt	p.R641H	COL24A1_ENST00000436319.1_Missense_Mutation_p.R641H	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	641			R -> H (in dbSNP:rs60891279).		extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		cttctttccacggatcccagg	0.313													C|||	921	0.183906	0.1097	0.2651	5008	,	,		17486	0.2788		0.1322	False		,,,				2504	0.182				p.R641H		Atlas-SNP	.											COL24A1,NS,carcinoma,-1,1	COL24A1	202	1	0			c.G1922A						PASS	.	C	HIS/ARG	404,3202		20,364,1419	114.0	114.0	114.0		1922	4.2	1.0	1	dbSNP_129	114	1200,6924		77,1046,2939	yes	missense	COL24A1	NM_152890.5	29	97,1410,4358	TT,TC,CC		14.771,11.2035,13.6743	benign	641/1715	86512536	1604,10126	1803	4062	5865	SO:0001583	missense	255631	exon12			TTTCCACGGATCC	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.1922G>A	1.37:g.86512536C>T	ENSP00000359603:p.Arg641His	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	171	96	0.561404	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	402	0.18406593406593408	59	0.11991869918699187	84	0.23204419889502761	161	0.28146853146853146	98	0.12928759894459102	C	11.28	1.591078	0.28357	0.112035	0.14771	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.95035	-3.59;-3.59	4.22	4.22	0.49857	.	0.000000	0.38272	N	0.001752	D	0.86171	0.5869	L	0.38953	1.18	0.35679	P	0.18606299999999998	B;B	0.18013	0.025;0.004	B;B	0.13407	0.009;0.002	T	0.83293	-0.0032	9	0.41790	T	0.15	.	12.3912	0.55360	0.0:1.0:0.0:0.0	rs60891279	641;641	F8WDM8;Q17RW2	.;COOA1_HUMAN	H	641	ENSP00000359603:R641H;ENSP00000392531:R641H	ENSP00000359603:R641H	R	-	2	0	COL24A1	86285124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.707000	0.37888	2.616000	0.88540	0.655000	0.94253	CGT	C|0.832;T|0.168	0.168	strong		0.313	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
MLST8	64223	hgsc.bcm.edu	37	16	2257105	2257105	+	Silent	SNP	C	C	G	rs26862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2257105C>G	ENST00000569417.1	+	5	768	c.414C>G	c.(412-414)ccC>ccG	p.P138P	MLST8_ENST00000397124.1_Silent_p.P138P|MLST8_ENST00000561651.1_3'UTR|MLST8_ENST00000301725.7_Silent_p.P157P|MLST8_ENST00000382450.4_Silent_p.P137P|AC009065.3_ENST00000517149.1_RNA|MLST8_ENST00000301724.10_Silent_p.P138P|MLST8_ENST00000564088.1_Silent_p.P138P|MLST8_ENST00000565250.1_Silent_p.P138P	NM_022372.4	NP_071767.3	Q9BVC4	LST8_HUMAN	MTOR associated protein, LST8 homolog (S. cerevisiae)	138					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of TOR signaling (GO:0032008)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac GTPase activity (GO:0032314)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				large_intestine(3)|lung(2)|skin(1)	6						GCCTGCACCCCAACCAGGTGA	0.677													C|||	1919	0.383187	0.0333	0.464	5008	,	,		18109	0.5714		0.4891	False		,,,				2504	0.4959				p.P138P		Atlas-SNP	.											.	MLST8	60	.	0			c.C414G						PASS	.	C	,,,	406,3594		24,358,1618	56.0	62.0	60.0		414,414,411,414	3.7	1.0	16	dbSNP_76	60	4025,4271		1007,2011,1130	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MLST8	NM_001199173.1,NM_001199174.1,NM_001199175.1,NM_022372.4	,,,	1031,2369,2748	GG,GC,CC		48.5174,10.15,36.0361	,,,	138/327,138/327,137/326,138/327	2257105	4431,7865	2000	4148	6148	SO:0001819	synonymous_variant	64223	exon5			GCACCCCAACCAG		CCDS10462.2, CCDS58409.1	16p13.3	2013-01-09			ENSG00000167965	ENSG00000167965		"""WD repeat domain containing"""	24825	protein-coding gene	gene with protein product	"""G protein beta subunit like"""	612190				12477932	Standard	NM_022372		Approved	Lst8, Pop3, GBL, GbetaL	uc002cpc.3	Q9BVC4	OTTHUMG00000128827	ENST00000569417.1:c.414C>G	16.37:g.2257105C>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	NM_001199174	B3KMM4|B4DY00|D3DU88|Q5M800|Q86Y18|Q8WUI5|Q9HA66|Q9UJV6	Silent	SNP	ENST00000569417.1	37	CCDS10462.2																																																																																			C|0.581;G|0.419	0.419	strong		0.677	MLST8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250763.2	NM_022372	
DDX60L	91351	hgsc.bcm.edu	37	4	169369920	169369920	+	Missense_Mutation	SNP	C	C	T	rs12507582	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:169369920C>T	ENST00000511577.1	-	9	1254	c.1007G>A	c.(1006-1008)tGt>tAt	p.C336Y	DDX60L_ENST00000260184.7_Missense_Mutation_p.C336Y|DDX60L_ENST00000505890.1_Missense_Mutation_p.C336Y			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	336			C -> Y (in dbSNP:rs12507582).				ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		GAAATATTCACACCACTTGTT	0.323													C|||	1645	0.328474	0.0212	0.5159	5008	,	,		17749	0.619		0.3429	False		,,,				2504	0.2965				p.C336Y		Atlas-SNP	.											.	DDX60L	116	.	0			c.G1007A						PASS	.	C	TYR/CYS	264,3362		20,224,1569	44.0	40.0	41.0		1007	2.5	1.0	4	dbSNP_120	41	2690,5432		431,1828,1802	yes	missense	DDX60L	NM_001012967.1	194	451,2052,3371	TT,TC,CC		33.1199,7.2808,25.1447	probably-damaging	336/1707	169369920	2954,8794	1813	4061	5874	SO:0001583	missense	91351	exon9			TATTCACACCACT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.1007G>A	4.37:g.169369920C>T	ENSP00000422423:p.Cys336Tyr	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		808	0.36996336996337	13	0.026422764227642278	171	0.4723756906077348	369	0.6451048951048951	255	0.33641160949868076	C	13.99	2.402486	0.42613	0.072808	0.331199	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.26223	1.75;1.75;1.76;2.41	2.46	2.46	0.29980	.	0.000000	0.39759	U	0.001276	T	0.00012	0.0000	M	0.68317	2.08	0.41717	P	0.01051599999999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.40850	-0.9541	9	0.87932	D	0	.	9.9101	0.41399	0.0:1.0:0.0:0.0	rs12507582;rs52810781;rs12507582	336;336;336	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	Y	336;336;336;64	ENSP00000260184:C336Y;ENSP00000422423:C336Y;ENSP00000422202:C336Y;ENSP00000421026:C64Y	ENSP00000260184:C336Y	C	-	2	0	DDX60L	169606495	1.000000	0.71417	0.966000	0.40874	0.881000	0.50899	3.413000	0.52686	1.346000	0.45694	0.467000	0.42956	TGT	C|0.632;T|0.368	0.368	strong		0.323	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
DTX2	113878	hgsc.bcm.edu	37	7	76121509	76121509	+	Silent	SNP	C	C	T	rs148279131	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76121509C>T	ENST00000324432.5	+	6	1458	c.948C>T	c.(946-948)agC>agT	p.S316S	DTX2_ENST00000307569.8_Silent_p.S316S|DTX2_ENST00000413936.2_Silent_p.S316S|DTX2_ENST00000430490.2_Silent_p.S316S|DTX2_ENST00000446600.1_Silent_p.S225S|DTX2_ENST00000446820.2_Silent_p.S316S	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	316					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						GCCCAGGGAGCGTCCCTGCCA	0.632																																					p.S316S		Atlas-SNP	.											DTX2,NS,carcinoma,0,1	DTX2	64	1	0			c.C948T						scavenged	.						6.0	10.0	9.0					7																	76121509		1723	3883	5606	SO:0001819	synonymous_variant	113878	exon3			AGGGAGCGTCCCT		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.948C>T	7.37:g.76121509C>T		Somatic	612	1	0.00163399		WXS	Illumina HiSeq	Phase_I	653	84	0.128637	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			C|1.000;|0.000	.	weak		0.632	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
PTPLAD2	401494	hgsc.bcm.edu	37	9	21029330	21029330	+	Missense_Mutation	SNP	T	T	C	rs2298260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:21029330T>C	ENST00000495827.2	-	2	151	c.106A>G	c.(106-108)Aca>Gca	p.T36A	PTPLAD2_ENST00000513293.2_Missense_Mutation_p.T36A|PTPLAD2_ENST00000488436.1_5'Flank	NM_001010915.3	NP_001010915.2	Q5VWC8	HACD4_HUMAN	protein tyrosine phosphatase-like A domain containing 2	36			T -> A (in dbSNP:rs2298260).		fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)		GTCATATTTGTAAATATCCAA	0.313													T|||	1723	0.34405	0.2776	0.389	5008	,	,		19330	0.503		0.2883	False		,,,				2504	0.2955				p.T36A		Atlas-SNP	.											.	PTPLAD2	26	.	0			c.A106G						PASS	.	T	ALA/THR	945,2705		130,685,1010	90.0	90.0	90.0		106	4.1	1.0	9	dbSNP_100	90	2226,5926		304,1618,2154	yes	missense	PTPLAD2	NM_001010915.3	58	434,2303,3164	CC,CT,TT		27.3062,25.8904,26.8683	benign	36/233	21029330	3171,8631	1825	4076	5901	SO:0001583	missense	401494	exon2			TATTTGTAAATAT		CCDS43791.1	9p21.3	2008-02-05			ENSG00000188921	ENSG00000188921			20920	protein-coding gene	gene with protein product		615941					Standard	NM_001010915		Approved	Em:AL662879.1, OTTHUMG00000021016	uc010mir.1	Q5VWC8	OTTHUMG00000021016	ENST00000495827.2:c.106A>G	9.37:g.21029330T>C	ENSP00000419503:p.Thr36Ala	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	153	57	0.372549	NM_001010915	Q7Z385	Missense_Mutation	SNP	ENST00000495827.2	37	CCDS43791.1	745	0.3411172161172161	121	0.2459349593495935	130	0.35911602209944754	289	0.5052447552447552	205	0.2704485488126649	T	11.44	1.638463	0.29157	0.258904	0.273062	ENSG00000188921	ENST00000513293;ENST00000495827	T;T	0.21361	2.01;2.01	5.3	4.12	0.48240	.	0.122950	0.53938	N	0.000041	T	0.00012	0.0000	N	0.10733	0.035	0.29235	P	0.873013	B	0.10296	0.003	B	0.10450	0.005	T	0.43909	-0.9362	9	0.17369	T	0.5	-13.4153	10.7399	0.46147	0.0:0.0779:0.0:0.9221	rs2298260;rs57409575;rs2298260	36	Q5VWC8	HACD4_HUMAN	A	36	ENSP00000426475:T36A;ENSP00000419503:T36A	ENSP00000419503:T36A	T	-	1	0	PTPLAD2	21019330	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.608000	0.46308	0.913000	0.36797	0.533000	0.62120	ACA	T|0.655;C|0.345	0.345	strong		0.313	PTPLAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055434.3	NM_001010915	
LRWD1	222229	hgsc.bcm.edu	37	7	102105566	102105566	+	Silent	SNP	G	G	A	rs79978502	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:102105566G>A	ENST00000292616.5	+	1	191	c.39G>A	c.(37-39)ggG>ggA	p.G13G	ALKBH4_ENST00000292566.3_5'Flank|MIR5090_ENST00000582533.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	13					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						TGCAGCGCGGGCGCCCCAAGA	0.746													G|||	181	0.0361422	0.0446	0.0418	5008	,	,		12157	0.0		0.0716	False		,,,				2504	0.0215				p.G13G		Atlas-SNP	.											.	LRWD1	41	.	0			c.G39A						PASS	.	G		125,3713		0,125,1794	3.0	5.0	5.0		39	0.2	1.0	7	dbSNP_131	5	470,7478		12,446,3516	no	coding-synonymous	LRWD1	NM_152892.1		12,571,5310	AA,AG,GG		5.9134,3.2569,5.0484		13/648	102105566	595,11191	1919	3974	5893	SO:0001819	synonymous_variant	222229	exon1			GCGCGGGCGCCCC	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"""WD repeat domain containing"""	21769	protein-coding gene	gene with protein product	"""origin recognition complex associated"", ""centromere protein 33"""	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.39G>A	7.37:g.102105566G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1																																																																																			A|0.043;C|0.000;G|0.957	0.043	strong		0.746	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
COL4A2	1284	hgsc.bcm.edu	37	13	111098226	111098226	+	Silent	SNP	C	C	T	rs4103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:111098226C>T	ENST00000360467.5	+	17	1314	c.1008C>T	c.(1006-1008)ccC>ccT	p.P336P		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	336	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			CCCGGGGACCCAAGGTGAGCC	0.537													C|||	2418	0.482827	0.3714	0.464	5008	,	,		18286	0.5625		0.5139	False		,,,				2504	0.5327				p.P336P		Atlas-SNP	.											COL4A2,colon,carcinoma,0,1	COL4A2	178	1	0			c.C1008T						PASS	.	C		1538,2346		313,912,717	99.0	102.0	101.0		1008	0.9	0.9	13	dbSNP_36	101	4411,3849		1174,2063,893	no	coding-synonymous	COL4A2	NM_001846.2		1487,2975,1610	TT,TC,CC		46.5981,39.5984,48.9872		336/1713	111098226	5949,6195	1942	4130	6072	SO:0001819	synonymous_variant	1284	exon17			GGGACCCAAGGTG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1008C>T	13.37:g.111098226C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			C|0.496;T|0.504	0.504	strong		0.537	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
EXO1	9156	hgsc.bcm.edu	37	1	242035438	242035438	+	Missense_Mutation	SNP	G	G	A	rs4149965	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:242035438G>A	ENST00000366548.3	+	12	1965	c.1372G>A	c.(1372-1374)Gtg>Atg	p.V458M	EXO1_ENST00000518483.1_Missense_Mutation_p.V458M|EXO1_ENST00000348581.5_Missense_Mutation_p.V458M	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	458	Interaction with MLH1.		V -> M (in dbSNP:rs4149965). {ECO:0000269|Ref.5}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			CTTTTCTGAAGTGTTTGTGCC	0.373								Editing and processing nucleases					G|||	450	0.0898562	0.0061	0.1354	5008	,	,		15011	0.0		0.2505	False		,,,				2504	0.0982				p.V458M		Atlas-SNP	.											EXO1,caecum,carcinoma,0,2	EXO1	103	2	0			c.G1372A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	194,4212	122.9+/-160.3	8,178,2017	66.0	65.0	65.0		1372,1372,1372	-3.2	0.0	1	dbSNP_110	65	2075,6525	359.5+/-331.6	259,1557,2484	yes	missense,missense,missense	EXO1	NM_003686.4,NM_006027.4,NM_130398.3	21,21,21	267,1735,4501	AA,AG,GG		24.1279,4.4031,17.4458	benign,benign,benign	458/804,458/847,458/847	242035438	2269,10737	2203	4300	6503	SO:0001583	missense	9156	exon10			TCTGAAGTGTTTG	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1372G>A	1.37:g.242035438G>A	ENSP00000355506:p.Val458Met	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	265	117	0.441509	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	37	CCDS1620.1	257	0.11767399267399267	7	0.014227642276422764	59	0.16298342541436464	0	0.0	191	0.2519788918205805	G	0.150	-1.092237	0.01858	0.044031	0.241279	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.32988	1.43;1.43;1.43	5.3	-3.18	0.05186	.	1.150810	0.06104	N	0.665867	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.16166	0.016;0.003	B;B	0.08055	0.003;0.001	T	0.37337	-0.9710	9	0.31617	T	0.26	-12.247	0.5491	0.00659	0.3634:0.2096:0.2326:0.1943	rs4149965;rs17391648;rs52794763;rs59699975;rs4149965	458;458	Q9UQ84-4;Q9UQ84	.;EXO1_HUMAN	M	458	ENSP00000355506:V458M;ENSP00000311873:V458M;ENSP00000430251:V458M	ENSP00000311873:V458M	V	+	1	0	EXO1	240102061	0.013000	0.17824	0.020000	0.16555	0.207000	0.24258	0.025000	0.13577	-0.430000	0.07318	-0.355000	0.07637	GTG	G|0.851;A|0.149	0.149	strong		0.373	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
H1FNT	341567	hgsc.bcm.edu	37	12	48723324	48723324	+	Missense_Mutation	SNP	C	C	G	rs2732441	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:48723324C>G	ENST00000335017.1	+	1	562	c.250C>G	c.(250-252)Cga>Gga	p.R84G		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	84			R -> G (in a Japanese man; dbSNP:rs2732441). {ECO:0000269|PubMed:16533358}.		chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						GAAGGAGCTCCGAAACGCCGG	0.672													G|||	861	0.171925	0.0272	0.1859	5008	,	,		13258	0.0159		0.326	False		,,,				2504	0.3599				p.R84G		Atlas-SNP	.											H1FNT,NS,carcinoma,0,2	H1FNT	30	2	0			c.C250G						PASS	.	G	GLY/ARG	288,4114	782.4+/-414.6	13,262,1926	31.0	34.0	33.0		250	3.4	0.0	12	dbSNP_100	33	2894,5704	655.6+/-401.3	479,1936,1884	yes	missense	H1FNT	NM_181788.1	125	492,2198,3810	GG,GC,CC		33.659,6.5425,24.4769	benign	84/256	48723324	3182,9818	2201	4299	6500	SO:0001583	missense	341567	exon1			GAGCTCCGAAACG	AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"""Histones / Replication-independent"""	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.250C>G	12.37:g.48723324C>G	ENSP00000334805:p.Arg84Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_181788	Q147U8|Q5GKZ5|Q7Z694	Missense_Mutation	SNP	ENST00000335017.1	37	CCDS8762.1	344	0.1575091575091575	17	0.034552845528455285	76	0.20994475138121546	5	0.008741258741258742	246	0.3245382585751979	G	0.022	-1.418303	0.01136	0.065425	0.33659	ENSG00000187166	ENST00000335017	T	0.15139	2.45	5.39	3.44	0.39384	.	.	.	.	.	T	0.00012	0.0000	N	0.00321	-1.65	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46400	-0.9194	8	0.02654	T	1	-8.0021	8.9868	0.35999	0.0794:0.2792:0.6414:0.0	rs2732441;rs2732441	84	Q75WM6	H1FNT_HUMAN	G	84	ENSP00000334805:R84G	ENSP00000334805:R84G	R	+	1	2	H1FNT	47009591	0.634000	0.27190	0.017000	0.16124	0.415000	0.31203	1.831000	0.39141	0.669000	0.31146	-0.127000	0.14921	CGA	C|0.798;G|0.202	0.202	strong		0.672	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788	
ZNF626	199777	hgsc.bcm.edu	37	19	20808418	20808418	+	Missense_Mutation	SNP	G	G	C	rs8111015	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20808418G>C	ENST00000601440.1	-	4	411	c.265C>G	c.(265-267)Cag>Gag	p.Q89E	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	89			Q -> E (in dbSNP:rs8111015).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						TTCATGCTCTGCTCTGGCCAA	0.313													N|||	363	0.072484	0.2436	0.0259	5008	,	,		17032	0.0		0.0139	False		,,,				2504	0.0092				p.Q89E		Atlas-SNP	.											.	ZNF626	121	.	0			c.C265G						PASS	.	G	GLU/GLN	758,3578		90,578,1500	50.0	56.0	54.0		265	1.1	0.0	19	dbSNP_116	54	82,8474		3,76,4199	no	missense	ZNF626	NM_001076675.2	29	93,654,5699	CC,CG,GG		0.9584,17.4815,6.5157	benign	89/529	20808418	840,12052	2168	4278	6446	SO:0001583	missense	199777	exon4			TGCTCTGCTCTGG	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.265C>G	19.37:g.20808418G>C	ENSP00000469958:p.Gln89Glu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	140	0.0641025641025641	119	0.241869918699187	10	0.027624309392265192	0	0.0	11	0.014511873350923483	N	7.931	0.740652	0.15642	0.174815	0.009584	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	1.08	1.08	0.20341	.	.	.	.	.	T	0.00039	0.0001	M	0.91818	3.245	0.58432	P	1.999999999946489E-6	B	0.20780	0.048	B	0.29524	0.103	T	0.10474	-1.0628	7	0.37606	T	0.19	.	7.5639	0.27868	0.0:0.0:1.0:0.0	rs8111015;rs8111015	89	Q68DY1	ZN626_HUMAN	E	89;13;89	.	ENSP00000445201:Q89E	Q	-	1	0	ZNF626	20600258	0.000000	0.05858	0.014000	0.15608	0.369000	0.29798	-0.692000	0.05127	0.503000	0.28060	0.289000	0.19496	CAG	G|0.944;C|0.056	0.056	strong		0.313	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
TXK	7294	hgsc.bcm.edu	37	4	48091768	48091768	+	Splice_Site	SNP	G	G	A	rs17470585	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:48091768G>A	ENST00000264316.4	-	9	868	c.783C>T	c.(781-783)taC>taT	p.Y261Y	TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	261					activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						ACACTTTACCGTAGCTAAACC	0.463													G|||	98	0.0195687	0.034	0.0245	5008	,	,		18833	0.001		0.0308	False		,,,				2504	0.0041				p.Y261Y		Atlas-SNP	.											.	TXK	58	.	0			c.C783T						PASS	.	G		158,4248	108.2+/-146.6	2,154,2047	89.0	85.0	86.0		783	-3.6	1.0	4	dbSNP_123	86	227,8373	93.5+/-155.5	5,217,4078	yes	coding-synonymous-near-splice	TXK	NM_003328.2		7,371,6125	AA,AG,GG		2.6395,3.586,2.9602		261/528	48091768	385,12621	2203	4300	6503	SO:0001630	splice_region_variant	7294	exon9			TTTACCGTAGCTA	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"""SH2 domain containing"""	12434	protein-coding gene	gene with protein product		600058	"""PTK4 protein tyrosine kinase 4"""	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.784+1C>T	4.37:g.48091768G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	189	103	0.544974	NM_003328	Q14220	Silent	SNP	ENST00000264316.4	37	CCDS3480.1																																																																																			G|0.969;A|0.031	0.031	strong		0.463	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328	Silent
ZNF224	7767	hgsc.bcm.edu	37	19	44612005	44612005	+	Silent	SNP	A	A	G	rs3746321	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44612005A>G	ENST00000336976.6	+	6	1946	c.1692A>G	c.(1690-1692)ggA>ggG	p.G564G	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	564					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				TGCACAGTGGAGAAAAACCAT	0.423													A|||	2929	0.584864	0.4085	0.5144	5008	,	,		20394	0.5357		0.8131	False		,,,				2504	0.6892				p.G564G		Atlas-SNP	.											.	ZNF224	70	.	0			c.A1692G						PASS	.	A		2007,2399	560.2+/-380.4	468,1071,664	93.0	89.0	90.0		1692	1.9	0.6	19	dbSNP_107	90	7041,1559	744.9+/-407.2	2906,1229,165	no	coding-synonymous	ZNF224	NM_013398.2		3374,2300,829	GG,GA,AA		18.1279,45.5515,30.4321		564/708	44612005	9048,3958	2203	4300	6503	SO:0001819	synonymous_variant	7767	exon6			CAGTGGAGAAAAA	AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"""Zinc fingers, C2H2-type"", ""-"""	13017	protein-coding gene	gene with protein product		194555	"""zinc finger protein 255"", ""zinc finger protein 27"""	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1692A>G	19.37:g.44612005A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Silent	SNP	ENST00000336976.6	37	CCDS33046.1																																																																																			A|0.318;G|0.682	0.682	strong		0.423	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398	
SLC6A5	9152	hgsc.bcm.edu	37	11	20673867	20673867	+	Silent	SNP	G	G	A	rs2276433	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:20673867G>A	ENST00000525748.1	+	15	2376	c.2103G>A	c.(2101-2103)gaG>gaA	p.E701E	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	701					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	ACCAGTGGGAGCCCATGACCT	0.468													G|||	2395	0.478235	0.1543	0.5562	5008	,	,		16796	0.8234		0.4414	False		,,,				2504	0.5429				p.E701E		Atlas-SNP	.											.	SLC6A5	151	.	0			c.G2103A						PASS	.	G		816,3590	325.3+/-299.0	71,674,1458	224.0	197.0	206.0		2103	-2.2	1.0	11	dbSNP_100	206	3395,5205	502.8+/-375.8	681,2033,1586	no	coding-synonymous	SLC6A5	NM_004211.3		752,2707,3044	AA,AG,GG		39.4767,18.5202,32.3774		701/798	20673867	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	9152	exon15			GTGGGAGCCCATG	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.2103G>A	11.37:g.20673867G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			G|0.601;T|0.003	.	strong		0.468	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
TIAM2	26230	hgsc.bcm.edu	37	6	155561796	155561796	+	Missense_Mutation	SNP	C	C	T	rs11751128	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:155561796C>T	ENST00000461783.3	+	18	4574	c.3301C>T	c.(3301-3303)Cgc>Tgc	p.R1101C	TIAM2_ENST00000275246.7_Missense_Mutation_p.R26C|TIAM2_ENST00000528391.2_Missense_Mutation_p.R437C|TIAM2_ENST00000367174.2_Missense_Mutation_p.R477C|TIAM2_ENST00000360366.4_Missense_Mutation_p.R1125C|TIAM2_ENST00000318981.5_Missense_Mutation_p.R1101C|TIAM2_ENST00000456144.1_Missense_Mutation_p.R1101C|TIAM2_ENST00000456877.2_Missense_Mutation_p.R413C|TIAM2_ENST00000529824.2_Missense_Mutation_p.R1101C			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1101	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		R -> C (in dbSNP:rs11751128).		apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AGACCGCCTCCGCAAAGTCAT	0.552													C|||	467	0.0932508	0.0144	0.1455	5008	,	,		21462	0.003		0.2773	False		,,,				2504	0.0665				p.R1101C		Atlas-SNP	.											.	TIAM2	161	.	0			c.C3301T						PASS	.	C	CYS/ARG,CYS/ARG	257,4149	147.6+/-182.1	5,247,1951	54.0	52.0	52.0		76,3301	4.1	1.0	6	dbSNP_120	52	2487,6113	406.8+/-348.9	365,1757,2178	yes	missense,missense	TIAM2	NM_001010927.2,NM_012454.3	180,180	370,2004,4129	TT,TC,CC		28.9186,5.833,21.098	probably-damaging,probably-damaging	26/627,1101/1702	155561796	2744,10262	2203	4300	6503	SO:0001583	missense	26230	exon15			CGCCTCCGCAAAG		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.3301C>T	6.37:g.155561796C>T	ENSP00000437188:p.Arg1101Cys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	30	20	0.666667	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	283	0.1295787545787546	10	0.02032520325203252	60	0.16574585635359115	2	0.0034965034965034965	211	0.2783641160949868	C	21.9	4.217544	0.79352	0.05833	0.289186	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391;ENST00000275246;ENST00000462408	T;T;T;T;T;T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;1.93	5.09	4.13	0.48395	Dbl homology (DH) domain (3);	0.000000	0.85682	D	0.000000	T	0.79913	0.4528	M	0.89095	3.005	0.09310	P	0.99999826644	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.997	D	0.83883	0.0280	9	0.87932	D	0	.	12.0581	0.53546	0.2431:0.7569:0.0:0.0	rs11751128;rs56905056;rs11751128	437;1101;1125;1101	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	C	1101;1347;1101;1101;1101;477;1125;1101;413;437;26;39	ENSP00000437188:R1101C;ENSP00000434901:R1101C;ENSP00000407746:R1101C;ENSP00000327315:R1101C;ENSP00000356142:R477C;ENSP00000353528:R1125C;ENSP00000433348:R1101C;ENSP00000407183:R413C;ENSP00000435335:R437C;ENSP00000275246:R26C;ENSP00000431269:R39C	ENSP00000275246:R26C	R	+	1	0	TIAM2	155603488	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	2.889000	0.48601	2.362000	0.80069	0.491000	0.48974	CGC	C|0.825;T|0.175	0.175	strong		0.552	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
HK3	3101	hgsc.bcm.edu	37	5	176314459	176314459	+	Silent	SNP	G	G	A	rs2278492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176314459G>A	ENST00000292432.5	-	11	1684	c.1593C>T	c.(1591-1593)gaC>gaT	p.D531D		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	531	Catalytic.|Hexokinase type-1 2.			PD -> LT (in Ref. 4; AAC50422). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TACCGCTGCCGTCAGGGGTGG	0.672													A|||	1669	0.333267	0.1793	0.4452	5008	,	,		17657	0.3948		0.327	False		,,,				2504	0.4049				p.D531D		Atlas-SNP	.											.	HK3	210	.	0			c.C1593T						PASS	.	A		974,3432	716.2+/-408.6	109,756,1338	32.0	35.0	34.0		1593	-1.5	0.6	5	dbSNP_100	34	2941,5659	657.9+/-401.5	511,1919,1870	no	coding-synonymous	HK3	NM_002115.2		620,2675,3208	AA,AG,GG		34.1977,22.1062,30.1015		531/924	176314459	3915,9091	2203	4300	6503	SO:0001819	synonymous_variant	3101	exon11			GCTGCCGTCAGGG		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1593C>T	5.37:g.176314459G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	86	26	0.302326	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			G|0.694;A|0.306	0.306	strong		0.672	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855720	12855720	+	Missense_Mutation	SNP	C	C	T	rs113708906	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12855720C>T	ENST00000332296.7	+	4	1103	c.1000C>T	c.(1000-1002)Cgc>Tgc	p.R334C	PRAMEF1_ENST00000400814.3_Missense_Mutation_p.R89C	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	334					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGCTGTTCCGCATCAGTCT	0.502													.|||	133	0.0265575	0.0023	0.0432	5008	,	,		26201	0.0		0.0706	False		,,,				2504	0.0297				p.R334C		Atlas-SNP	.											.	PRAMEF1	78	.	0			c.C1000T						PASS	.	C	CYS/ARG	51,4355		0,51,2152	120.0	127.0	125.0		1000	-3.1	0.0	1	dbSNP_132	125	498,8098		14,470,3814	no	missense	PRAMEF1	NM_023013.2	180	14,521,5966	TT,TC,CC		5.7934,1.1575,4.2224	probably-damaging	334/475	12855720	549,12453	2203	4298	6501	SO:0001583	missense	65121	exon4			CTGTTCCGCATCA	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.1000C>T	1.37:g.12855720C>T	ENSP00000332134:p.Arg334Cys	Somatic	509	0	0		WXS	Illumina HiSeq	Phase_I	427	169	0.395785	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	79	0.036172161172161175	3	0.006097560975609756	21	0.058011049723756904	0	0.0	55	0.07255936675461741	.	0.930	-0.713009	0.03206	0.011575	0.057934	ENSG00000116721	ENST00000332296;ENST00000400814	T;T	0.00958	5.5;5.5	1.56	-3.12	0.05282	.	4.291190	0.00822	N	0.001584	T	0.00073	0.0002	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.49818	-0.8899	10	0.39692	T	0.17	.	0.279	0.00242	0.2345:0.1618:0.2912:0.3125	.	334	O95521	PRAM1_HUMAN	C	334;89	ENSP00000332134:R334C;ENSP00000383616:R89C	ENSP00000332134:R334C	R	+	1	0	PRAMEF1	12778307	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.615000	0.00414	-2.681000	0.00408	-0.974000	0.02594	CGC	C|0.986;T|0.014	0.014	weak		0.502	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
DNAH8	1769	hgsc.bcm.edu	37	6	38773293	38773293	+	Missense_Mutation	SNP	G	G	A	rs874808	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38773293G>A	ENST00000359357.3	+	21	2674	c.2420G>A	c.(2419-2421)gGa>gAa	p.G807E	DNAH8_ENST00000449981.2_Missense_Mutation_p.G1024E|DNAH8_ENST00000441566.1_Missense_Mutation_p.G807E			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	807			G -> E (in dbSNP:rs874808). {ECO:0000269|PubMed:12297094}.		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AGTGAAACAGGAGAGGGTGAA	0.303													A|||	2379	0.47504	0.3245	0.5821	5008	,	,		18684	0.6994		0.3817	False		,,,				2504	0.4673				p.G1024E		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G3071A						PASS	.	A	GLU/GLY	1492,2914	676.6+/-403.3	253,986,964	111.0	108.0	109.0		3071	4.2	1.0	6	dbSNP_86	109	3768,4832	614.7+/-396.3	837,2094,1369	yes	missense	DNAH8	NM_001206927.1	98	1090,3080,2333	AA,AG,GG		43.814,33.8629,40.4429	benign	1024/4708	38773293	5260,7746	2203	4300	6503	SO:0001583	missense	1769	exon23			AAACAGGAGAGGG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2420G>A	6.37:g.38773293G>A	ENSP00000352312:p.Gly807Glu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		1051	0.48122710622710624	164	0.3333333333333333	198	0.5469613259668509	397	0.6940559440559441	292	0.38522427440633245	A	1.874	-0.459527	0.04508	0.338629	0.43814	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.23348	1.96;1.94;1.91	5.45	4.22	0.49857	.	0.523157	0.20667	N	0.087901	T	0.03959	0.0111	N	0.22421	0.69	0.53005	P	3.399999999997849E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.35375	-0.9791	9	0.02654	T	1	.	7.0813	0.25234	0.7731:0.1467:0.0802:0.0	rs874808;rs1678683;rs17624464;rs52811411;rs57769299;rs874808	807	Q96JB1	DYH8_HUMAN	E	1012;1012;807;807	ENSP00000333363:G1012E;ENSP00000352312:G807E;ENSP00000402294:G807E	ENSP00000333363:G1012E	G	+	2	0	DNAH8	38881271	0.994000	0.37717	0.969000	0.41365	0.750000	0.42670	2.661000	0.46758	1.018000	0.39521	-0.254000	0.11334	GGA	G|0.502;A|0.498	0.498	strong		0.303	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
NES	10763	hgsc.bcm.edu	37	1	156640678	156640678	+	Missense_Mutation	SNP	G	G	A	rs2886443	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156640678G>A	ENST00000368223.3	-	4	3434	c.3302C>T	c.(3301-3303)cCg>cTg	p.P1101L		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1101	Tail.		P -> L (in dbSNP:rs2886443). {ECO:0000269|PubMed:1478958}.		brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCCCTGCCCCGGGCCTGGCTC	0.647													G|||	3116	0.622204	0.3858	0.67	5008	,	,		11968	0.8621		0.6481	False		,,,				2504	0.6339				p.P1101L		Atlas-SNP	.											NES,NS,carcinoma,0,1	NES	196	1	0			c.C3302T						PASS	.	G	LEU/PRO	1788,2592		377,1034,779	18.0	22.0	21.0		3302	-4.2	0.0	1	dbSNP_101	21	5445,3117		1815,1815,651	yes	missense	NES	NM_006617.1	98	2192,2849,1430	AA,AG,GG		36.405,40.8219,44.1122	probably-damaging	1101/1622	156640678	7233,5709	2190	4281	6471	SO:0001583	missense	10763	exon4			TGCCCCGGGCCTG	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3302C>T	1.37:g.156640678G>A	ENSP00000357206:p.Pro1101Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	170	81	0.476471	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	1421	0.6506410256410257	199	0.40447154471544716	242	0.6685082872928176	489	0.8548951048951049	491	0.6477572559366754	G	6.686	0.495244	0.12762	0.408219	0.63595	ENSG00000132688	ENST00000368223	D	0.84873	-1.91	4.16	-4.17	0.03857	.	1.304050	0.05885	N	0.627213	T	0.55305	0.1912	L	0.56769	1.78	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.32903	-0.9889	9	0.07030	T	0.85	.	4.0525	0.09801	0.2772:0.0:0.3442:0.3786	rs2886443;rs3748572;rs57956552;rs2886443	1101	P48681	NEST_HUMAN	L	1101	ENSP00000357206:P1101L	ENSP00000357206:P1101L	P	-	2	0	NES	154907302	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.984000	0.00320	-0.966000	0.03587	-1.141000	0.01876	CCG	G|0.356;A|0.644	0.644	strong		0.647	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
LGR6	59352	hgsc.bcm.edu	37	1	202287813	202287813	+	Silent	SNP	T	T	C	rs788793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202287813T>C	ENST00000367278.3	+	18	2471	c.2382T>C	c.(2380-2382)ttT>ttC	p.F794F	LGR6_ENST00000439764.2_Silent_p.F655F|LGR6_ENST00000255432.7_Silent_p.F742F	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	794					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						TCCTCAGCTTTGCCTCCATGC	0.652													C|||	3057	0.610423	0.3389	0.7233	5008	,	,		16498	0.7679		0.6392	False		,,,				2504	0.7055				p.F794F		Atlas-SNP	.											.	LGR6	102	.	0			c.T2382C						PASS	.	C	,,	1644,2762	659.1+/-400.5	301,1042,860	100.0	81.0	87.0		2382,1965,2226	-6.4	0.3	1	dbSNP_86	87	5260,3340	497.1+/-374.4	1601,2058,641	no	coding-synonymous,coding-synonymous,coding-synonymous	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	,,	1902,3100,1501	CC,CT,TT		38.8372,37.3128,46.9168	,,	794/968,655/829,742/916	202287813	6904,6102	2203	4300	6503	SO:0001819	synonymous_variant	59352	exon18			CAGCTTTGCCTCC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2382T>C	1.37:g.202287813T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	213	213	1	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																			T|0.445;C|0.555	0.555	strong		0.652	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
TCIRG1	10312	hgsc.bcm.edu	37	11	67809268	67809268	+	Missense_Mutation	SNP	C	C	T	rs36027301	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67809268C>T	ENST00000265686.3	+	3	274	c.166C>T	c.(166-168)Cgg>Tgg	p.R56W	TCIRG1_ENST00000532635.1_5'Flank	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	56			R -> W (in dbSNP:rs36027301).		ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						GGTTGATGTTCGGCGCTGTGA	0.602													C|||	85	0.0169728	0.0038	0.0216	5008	,	,		18487	0.0		0.0497	False		,,,				2504	0.0153				p.R56W		Atlas-SNP	.											.	TCIRG1	40	.	0			c.C166T						PASS	.	C	TRP/ARG	44,4356	44.6+/-78.6	0,44,2156	92.0	69.0	77.0		166	3.7	1.0	11	dbSNP_126	77	547,8039	146.6+/-202.2	23,501,3769	yes	missense	TCIRG1	NM_006019.3	101	23,545,5925	TT,TC,CC		6.3708,1.0,4.5511	probably-damaging	56/831	67809268	591,12395	2200	4293	6493	SO:0001583	missense	10312	exon3			GATGTTCGGCGCT	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"""ATPases / V-type"""	11647	protein-coding gene	gene with protein product	"""T-cell immune response cDNA 7"""	604592	"""T-cell, immune regulator 1"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"""			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.166C>T	11.37:g.67809268C>T	ENSP00000265686:p.Arg56Trp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_006019	O75877|Q8WVC5	Missense_Mutation	SNP	ENST00000265686.3	37	CCDS8177.1	49	0.022435897435897436	4	0.008130081300813009	5	0.013812154696132596	0	0.0	40	0.052770448548812667	C	21.7	4.193773	0.78902	0.01	0.063708	ENSG00000110719	ENST00000265686;ENST00000524598;ENST00000529657	D;D;D	0.88354	-2.37;-2.37;-2.37	3.72	3.72	0.42706	.	0.000000	0.85682	D	0.000000	T	0.77909	0.4201	H	0.94620	3.56	0.80722	D	1	D	0.76494	0.999	D	0.70016	0.967	D	0.84506	0.0619	10	0.87932	D	0	-46.7811	12.7234	0.57154	0.0:1.0:0.0:0.0	rs36027301;rs61749183;rs36027301	56	Q13488	VPP3_HUMAN	W	56;42;56	ENSP00000265686:R56W;ENSP00000432846:R42W;ENSP00000435023:R56W	ENSP00000265686:R56W	R	+	1	2	TCIRG1	67565844	0.989000	0.36119	0.980000	0.43619	0.920000	0.55202	4.169000	0.58223	2.090000	0.63153	0.462000	0.41574	CGG	C|0.964;T|0.036	0.036	strong		0.602	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019	
ANKRD36	375248	hgsc.bcm.edu	37	2	97909661	97909661	+	Silent	SNP	A	A	C	rs199689273		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97909661A>C	ENST00000461153.2	+	70	4708	c.4464A>C	c.(4462-4464)atA>atC	p.I1488I	ANKRD36_ENST00000357042.4_5'Flank|ANKRD36_ENST00000420699.2_Silent_p.I1488I			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1488										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						AGTTAAGAATAACAGAAGAGC	0.343																																					p.I1488I		Atlas-SNP	.											ANKRD36_ENST00000420699,right_lower_lobe,carcinoma,0,2	ANKRD36	170	2	0			c.A4464C						scavenged	.						138.0	92.0	106.0					2																	97909661		689	1589	2278	SO:0001819	synonymous_variant	375248	exon70			AAGAATAACAGAA	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.4464A>C	2.37:g.97909661A>C		Somatic	1832	0	0		WXS	Illumina HiSeq	Phase_I	1204	149	0.123754	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Silent	SNP	ENST00000461153.2	37	CCDS54379.1																																																																																			.	.	weak		0.343	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
ART1	417	hgsc.bcm.edu	37	11	3681519	3681519	+	Missense_Mutation	SNP	T	T	C	rs2280134	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:3681519T>C	ENST00000250693.1	+	3	871	c.770T>C	c.(769-771)cTg>cCg	p.L257P		NM_004314.2	NP_004305.2	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1	257			L -> P (in dbSNP:rs2280134). {ECO:0000269|PubMed:7947688}.		innate immune response (GO:0045087)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|skin(1)	8		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)		GCCAGCAGACTGGCCCAGGGC	0.612													C|||	2763	0.551717	0.4463	0.8141	5008	,	,		17458	0.2877		0.6998	False		,,,				2504	0.6278				p.L257P		Atlas-SNP	.											.	ART1	21	.	0			c.T770C						PASS	.	C	PRO/LEU	2095,2307	579.9+/-385.0	502,1091,608	44.0	48.0	47.0		770	4.0	0.8	11	dbSNP_100	47	5886,2710	416.1+/-352.0	2019,1848,431	yes	missense	ART1	NM_004314.2	98	2521,2939,1039	CC,CT,TT		31.5263,47.592,38.5982	benign	257/328	3681519	7981,5017	2201	4298	6499	SO:0001583	missense	417	exon3			GCAGACTGGCCCA	S74683	CCDS7744.1	11p15	2006-02-23			ENSG00000129744	ENSG00000129744		"""CD molecules"""	723	protein-coding gene	gene with protein product		601625				8812442	Standard	NM_004314		Approved	ART2, CD296	uc001lye.1	P52961	OTTHUMG00000011845	ENST00000250693.1:c.770T>C	11.37:g.3681519T>C	ENSP00000250693:p.Leu257Pro	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	33	32	0.969697	NM_004314	Q6NTD2|Q96KT9	Missense_Mutation	SNP	ENST00000250693.1	37	CCDS7744.1	1201	0.549908424908425	212	0.43089430894308944	273	0.7541436464088398	190	0.3321678321678322	526	0.6939313984168866	C	9.645	1.139928	0.21205	0.47592	0.684737	ENSG00000129744	ENST00000250693	T	0.07444	3.19	4.99	4.01	0.46588	.	0.815350	0.11276	N	0.580834	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22347	-1.0219	8	.	.	.	.	4.8122	0.13349	0.0:0.6311:0.1779:0.191	rs2280134;rs59555110;rs2280134	257	P52961	NAR1_HUMAN	P	257	ENSP00000250693:L257P	.	L	+	2	0	ART1	3638095	0.001000	0.12720	0.841000	0.33234	0.976000	0.68499	0.913000	0.28611	1.108000	0.41662	-0.213000	0.12676	CTG	T|0.426;C|0.574	0.574	strong		0.612	ART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032765.1	NM_004314	
CUL4A	8451	hgsc.bcm.edu	37	13	113897320	113897320	+	Silent	SNP	C	C	T	rs3764124	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:113897320C>T	ENST00000375440.4	+	11	1158	c.1074C>T	c.(1072-1074)gaC>gaT	p.D358D	CUL4A_ENST00000375441.3_Silent_p.D258D|CUL4A_ENST00000451881.1_Silent_p.D258D|CUL4A_ENST00000326335.4_Silent_p.D258D	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	358					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			CTGAGAAAGACAAAGACATGG	0.443													T|||	1307	0.260982	0.0439	0.3271	5008	,	,		17107	0.3383		0.2336	False		,,,				2504	0.456				p.D358D		Atlas-SNP	.											.	CUL4A	50	.	0			c.C1074T						PASS	.	T	,	340,4066	795.0+/-415.3	11,318,1874	166.0	135.0	146.0		1074,774	-9.6	0.3	13	dbSNP_107	146	1986,6614	722.9+/-406.4	246,1494,2560	no	coding-synonymous,coding-synonymous	CUL4A	NM_001008895.1,NM_003589.2	,	257,1812,4434	TT,TC,CC		23.093,7.7167,17.8841	,	358/760,258/660	113897320	2326,10680	2203	4300	6503	SO:0001819	synonymous_variant	8451	exon11			GAAAGACAAAGAC	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.1074C>T	13.37:g.113897320C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	151	149	0.986755	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Silent	SNP	ENST00000375440.4	37	CCDS41908.1																																																																																			C|0.794;T|0.206	0.206	strong		0.443	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589	
PRRC2A	7916	hgsc.bcm.edu	37	6	31604591	31604591	+	Missense_Mutation	SNP	C	C	T	rs10885	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31604591C>T	ENST00000376033.2	+	28	6250	c.6016C>T	c.(6016-6018)Ccc>Tcc	p.P2006S	PRRC2A_ENST00000376007.4_Missense_Mutation_p.P2006S	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	2006	3 X 50 AA type C repeats.		P -> S (in dbSNP:rs10885). {ECO:0000269|PubMed:14574404}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TGCCCCACCTCCCCTTTCTCT	0.622													C|||	668	0.133387	0.2126	0.0793	5008	,	,		15995	0.0714		0.1461	False		,,,				2504	0.1155				p.P2006S		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C6016T						PASS	.	C	SER/PRO,SER/PRO	590,2424		59,472,976	132.0	170.0	156.0		6016,6016	5.3	1.0	6	dbSNP_52	156	955,4459		93,769,1845	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	74,74	152,1241,2821	TT,TC,CC		17.6395,19.5753,18.3318	probably-damaging,probably-damaging	2006/2158,2006/2158	31604591	1545,6883	1507	2707	4214	SO:0001583	missense	7916	exon28			CCACCTCCCCTTT	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.6016C>T	6.37:g.31604591C>T	ENSP00000365201:p.Pro2006Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	286	0.13095238095238096	112	0.22764227642276422	30	0.08287292817679558	33	0.057692307692307696	111	0.14643799472295516	C	12.65	2.002477	0.35320	0.195753	0.176395	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01767	4.65;4.65	5.28	5.28	0.74379	.	0.000000	0.56097	D	0.000029	T	0.02156	0.0067	N	0.19112	0.55	0.26717	P	0.9708672	D	0.55172	0.97	P	0.57244	0.816	T	0.64266	-0.6448	9	0.87932	D	0	-9.7066	17.8506	0.88746	0.0:1.0:0.0:0.0	rs10885;rs1046121;rs3173341;rs3817660;rs17207260;rs17342597;rs17354298;rs10885	2006	P48634	PRC2A_HUMAN	S	1998;1987;2006;2006;1231	ENSP00000365175:P2006S;ENSP00000365201:P2006S	ENSP00000365175:P2006S	P	+	1	0	PRRC2A	31712570	0.553000	0.26513	0.968000	0.41197	0.994000	0.84299	3.080000	0.50112	2.747000	0.94245	0.643000	0.83706	CCC	C|0.836;T|0.164	0.164	strong		0.622	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
BFSP2	8419	hgsc.bcm.edu	37	3	133167363	133167363	+	Silent	SNP	G	G	A	rs2276737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:133167363G>A	ENST00000302334.2	+	3	692	c.603G>A	c.(601-603)gcG>gcA	p.A201A	BFSP2-AS1_ENST00000515542.1_RNA	NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	201	Rod.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						TTCGAAAGGCGGCAGAAGAGG	0.348													G|||	2186	0.436502	0.0968	0.3833	5008	,	,		21426	0.5853		0.5746	False		,,,				2504	0.638				p.A201A		Atlas-SNP	.											.	BFSP2	48	.	0			c.G603A						PASS	.	G		753,3653	302.7+/-287.5	69,615,1519	59.0	62.0	61.0		603	-2.0	0.9	3	dbSNP_100	61	5282,3318	643.3+/-399.9	1629,2024,647	no	coding-synonymous	BFSP2	NM_003571.2		1698,2639,2166	AA,AG,GG		38.5814,17.0903,46.4017		201/416	133167363	6035,6971	2203	4300	6503	SO:0001819	synonymous_variant	8419	exon3			AAAGGCGGCAGAA	U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.603G>A	3.37:g.133167363G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	98	95	0.969388	NM_003571	Q14D32|Q9HBW5	Silent	SNP	ENST00000302334.2	37	CCDS33859.1																																																																																			G|0.551;A|0.449	0.449	strong		0.348	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552016	32552016	+	Silent	SNP	C	C	A	rs17880973		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32552016C>A	ENST00000360004.5	-	2	345	c.240G>T	c.(238-240)acG>acT	p.T80T		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	80	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCCCCAGCTCCGTCACCGCCC	0.642										Multiple Myeloma(14;0.17)																											p.T80T		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G240T						PASS	.						37.0	40.0	39.0					6																	32552016		2195	4294	6489	SO:0001819	synonymous_variant	3123	exon2			CAGCTCCGTCACC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.240G>T	6.37:g.32552016C>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	107	22	0.205607	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			C|0.792;A|0.208	0.208	strong		0.642	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ZCWPW2	152098	hgsc.bcm.edu	37	3	28520417	28520417	+	Missense_Mutation	SNP	T	T	A	rs1563656	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:28520417T>A	ENST00000383768.2	+	5	793	c.605T>A	c.(604-606)cTa>cAa	p.L202Q	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.L202Q			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	202			L -> Q (in dbSNP:rs1563656).				zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						CTATCAAAACTACAAGGTGTA	0.303													A|||	2277	0.454673	0.323	0.4654	5008	,	,		12654	0.6171		0.4304	False		,,,				2504	0.4826				p.L202Q		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.T605A						PASS	.	A	GLN/LEU	1561,2845	664.3+/-401.3	279,1003,921	68.0	71.0	70.0		605	0.2	0.0	3	dbSNP_88	70	3658,4938	619.7+/-397.0	768,2122,1408	yes	missense	ZCWPW2	NM_001040432.1	113	1047,3125,2329	AA,AT,TT		42.5547,35.429,40.14	benign	202/357	28520417	5219,7783	2203	4298	6501	SO:0001583	missense	152098	exon4			CAAAACTACAAGG	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.605T>A	3.37:g.28520417T>A	ENSP00000373278:p.Leu202Gln	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_001040432		Missense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	1006	0.4606227106227106	173	0.3516260162601626	163	0.45027624309392267	343	0.5996503496503497	327	0.4313984168865435	A	0.016	-1.524785	0.00959	0.35429	0.425547	ENSG00000206559	ENST00000383768;ENST00000421010	T;T	0.33438	1.41;1.41	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39702	-0.9601	7	0.12430	T	0.62	2.2514	.	.	.	rs1563656;rs4493386;rs17357234;rs52813176;rs56536652;rs60931131;rs1563656	202	Q504Y3	ZCPW2_HUMAN	Q	202	ENSP00000373278:L202Q;ENSP00000412386:L202Q	ENSP00000373278:L202Q	L	+	2	0	ZCWPW2	28495421	0.002000	0.14202	0.004000	0.12327	0.092000	0.18411	-0.562000	0.05950	-0.843000	0.04189	-0.868000	0.02995	CTA	T|0.574;A|0.426	0.426	strong		0.303	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384	
SLC52A3	113278	hgsc.bcm.edu	37	20	746197	746197	+	Missense_Mutation	SNP	G	G	C	rs35655964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:746197G>C	ENST00000217254.7	-	2	463	c.222C>G	c.(220-222)atC>atG	p.I74M	SLC52A3_ENST00000381944.3_Missense_Mutation_p.I74M|SLC52A3_ENST00000473664.1_5'UTR	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	74			I -> M (in dbSNP:rs35655964).		cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										GGGTGAAGATGATGGGCACTT	0.617													G|||	154	0.0307508	0.0023	0.049	5008	,	,		19137	0.005		0.0825	False		,,,				2504	0.0297				p.I74M		Atlas-SNP	.											.	.	.	.	0			c.C222G						PASS	.	G	MET/ILE	83,4317		0,83,2117	52.0	43.0	46.0		222	2.7	0.9	20	dbSNP_126	46	820,7768		48,724,3522	yes	missense	C20orf54	NM_033409.3	10	48,807,5639	CC,CG,GG		9.5482,1.8864,6.9526	benign	74/470	746197	903,12085	2200	4294	6494	SO:0001583	missense	113278	exon2			GAAGATGATGGGC	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.222C>G	20.37:g.746197G>C	ENSP00000217254:p.Ile74Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	37	CCDS13007.1	88	0.040293040293040296	1	0.0020325203252032522	19	0.052486187845303865	4	0.006993006993006993	64	0.08443271767810026	G	18.06	3.539786	0.65085	0.018864	0.095482	ENSG00000101276	ENST00000217254;ENST00000381944	D;D	0.85629	-2.01;-2.01	5.79	2.69	0.31865	.	0.828599	0.11387	N	0.569168	T	0.12603	0.0306	L	0.28192	0.835	0.34973	D	0.75332	P;P	0.50272	0.933;0.89	P;P	0.54401	0.751;0.472	T	0.55566	-0.8121	10	0.30078	T	0.28	-17.6335	7.4317	0.27131	0.1468:0.2696:0.5835:0.0	rs35655964	74;74	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	M	74	ENSP00000217254:I74M;ENSP00000371370:I74M	ENSP00000217254:I74M	I	-	3	3	C20orf54	694197	0.990000	0.36364	0.873000	0.34254	0.935000	0.57460	0.228000	0.17814	0.334000	0.23590	0.655000	0.94253	ATC	G|0.942;C|0.058	0.058	strong		0.617	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
OBSCN	84033	hgsc.bcm.edu	37	1	228547901	228547901	+	Intron	SNP	C	C	T	rs12035900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228547901C>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000366709.4_Silent_p.D3555D|OBSCN_ENST00000284548.11_Silent_p.D6436D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AAGACGGAGACGCCTTTGTGA	0.637													C|||	1496	0.298722	0.1142	0.3112	5008	,	,		18726	0.2669		0.328	False		,,,				2504	0.5419				p.D6436D		Atlas-SNP	.											OBSCN_ENST00000284548,NS,carcinoma,0,1	OBSCN	2142	1	0			c.C19308T						PASS	.	C	,	699,3671		53,593,1539	51.0	63.0	59.0		,19308	-3.8	0.0	1	dbSNP_120	59	2582,5992		417,1748,2122	yes	intron,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	470,2341,3661	TT,TC,CC		30.1143,15.9954,25.3477	,	,6436/6621	228547901	3281,9663	2185	4287	6472	SO:0001627	intron_variant	84033	exon81			CGGAGACGCCTTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2376C>T	1.37:g.228547901C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.727;T|0.273	0.273	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MUC16	94025	hgsc.bcm.edu	37	19	9075969	9075969	+	Missense_Mutation	SNP	C	C	T	rs2591593	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9075969C>T	ENST00000397910.4	-	3	11680	c.11477G>A	c.(11476-11478)gGg>gAg	p.G3826E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3827	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.G3826E(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGCACCTGCCCTGGATGTGC	0.507													C|||	1243	0.248203	0.2005	0.2118	5008	,	,		21707	0.249		0.3121	False		,,,				2504	0.272				p.G3826E		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - Missense(2)	stomach(2)	c.G11477A						PASS	.	C	GLU/GLY	852,3266		98,656,1305	209.0	197.0	201.0		11477	-0.6	0.0	19	dbSNP_100	201	2423,5995		347,1729,2133	yes	missense	MUC16	NM_024690.2	98	445,2385,3438	TT,TC,CC		28.7836,20.6897,26.1248	possibly-damaging	3826/14508	9075969	3275,9261	2059	4209	6268	SO:0001583	missense	94025	exon3			ACCTGCCCTGGAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11477G>A	19.37:g.9075969C>T	ENSP00000381008:p.Gly3826Glu	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	246	115	0.46748	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	c	4.377	0.069544	0.08436	0.206897	0.287836	ENSG00000181143	ENST00000397910	T	0.03553	3.89	1.67	-0.571	0.11749	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	P	0.38370	0.628	B	0.28232	0.087	T	0.49753	-0.8906	8	0.87932	D	0	.	4.0285	0.09698	0.0:0.5788:0.0:0.4212	rs2591593;rs17418331;rs52808109;rs60034029;rs2591593	3826	B5ME49	.	E	3826	ENSP00000381008:G3826E	ENSP00000381008:G3826E	G	-	2	0	MUC16	8936969	0.000000	0.05858	0.001000	0.08648	0.179000	0.23085	-0.107000	0.10873	-0.095000	0.12351	0.205000	0.17691	GGG	C|0.750;T|0.250	0.250	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MUC4	4585	hgsc.bcm.edu	37	3	195515304	195515304	+	Silent	SNP	T	T	A	rs202019266		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515304T>A	ENST00000463781.3	-	2	3606	c.3147A>T	c.(3145-3147)gcA>gcT	p.A1049A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.A1049A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	479					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A1049A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CACCTGTGGATGCTGAGGAAA	0.562																																					p.A1049A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	kidney(1)|endometrium(1)	c.A3147T						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			TGTGGATGCTGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3147A>T	3.37:g.195515304T>A		Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	183	4	0.0218579	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HMBS	3145	hgsc.bcm.edu	37	11	118962230	118962230	+	Silent	SNP	G	G	T	rs1131488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118962230G>T	ENST00000278715.3	+	9	757	c.606G>T	c.(604-606)gtG>gtT	p.V202V	HMBS_ENST00000542729.1_Silent_p.V185V|HMBS_ENST00000544387.1_Silent_p.V202V|HMBS_ENST00000534956.1_Intron|HMBS_ENST00000537841.1_Silent_p.V185V|HMBS_ENST00000442944.2_Silent_p.V185V|HMBS_ENST00000392841.1_Silent_p.V185V|HMBS_ENST00000543090.1_Silent_p.V184V	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase	202			V -> L (in AIP). {ECO:0000269|PubMed:10657149}.		heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		ACAACCGGGTGGGGCAGGTAG	0.562													G|||	923	0.184305	0.1286	0.1931	5008	,	,		17883	0.1558		0.2952	False		,,,				2504	0.1687				p.V202V		Atlas-SNP	.											.	HMBS	27	.	0			c.G606T						PASS	.	G	,	516,3152		45,426,1363	30.0	24.0	26.0		606,555	2.0	1.0	11	dbSNP_86	26	1650,5172		199,1252,1960	no	coding-synonymous,coding-synonymous	HMBS	NM_000190.3,NM_001024382.1	,	244,1678,3323	TT,TG,GG		24.1865,14.0676,20.6482	,	202/362,185/345	118962230	2166,8324	1834	3411	5245	SO:0001819	synonymous_variant	3145	exon9			CCGGGTGGGGCAG	X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	"""uroporphyrinogen I synthase"", ""porphobilinogen deaminase"", ""porphyria, acute; Chester type"""	PBGD, UPS, PORC		8432552, 17298217	Standard	NM_001258208		Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.606G>T	11.37:g.118962230G>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_000190	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	Silent	SNP	ENST00000278715.3	37	CCDS8409.1																																																																																			G|0.792;T|0.208	0.208	strong		0.562	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399188.1	NM_000190	
PXK	54899	hgsc.bcm.edu	37	3	58395863	58395863	+	Missense_Mutation	SNP	A	A	G	rs56384862	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58395863A>G	ENST00000356151.2	+	16	1551	c.1442A>G	c.(1441-1443)aAg>aGg	p.K481R	PXK_ENST00000536660.1_Missense_Mutation_p.K344R|PXK_ENST00000479241.1_Missense_Mutation_p.K464R|PXK_ENST00000383716.3_Missense_Mutation_p.K448R|PXK_ENST00000383715.4_Missense_Mutation_p.K464R|PXK_ENST00000484288.1_Missense_Mutation_p.K481R|PXK_ENST00000463280.1_Missense_Mutation_p.K448R|PXK_ENST00000302779.5_Missense_Mutation_p.K464R	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		CATTCAGCGAAGTACAGCAAC	0.428													A|||	888	0.177316	0.1112	0.2767	5008	,	,		18559	0.001		0.3777	False		,,,				2504	0.1718				p.K481R		Atlas-SNP	.											PXK_ENST00000356151,NS,carcinoma,0,1	PXK	89	1	0			c.A1442G						PASS	.	A	ARG/LYS	580,3826	256.7+/-261.4	39,502,1662	88.0	82.0	84.0		1442	5.9	1.0	3	dbSNP_129	84	3205,5395	483.2+/-371.1	614,1977,1709	yes	missense	PXK	NM_017771.3	26	653,2479,3371	GG,GA,AA		37.2674,13.1639,29.102	benign	481/579	58395863	3785,9221	2203	4300	6503	SO:0001583	missense	54899	exon16			CAGCGAAGTACAG	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.1442A>G	3.37:g.58395863A>G	ENSP00000348472:p.Lys481Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_017771		Missense_Mutation	SNP	ENST00000356151.2	37	CCDS2889.1	445|445	0.20375457875457875|0.20375457875457875	65|65	0.13211382113821138|0.13211382113821138	107|107	0.2955801104972376|0.2955801104972376	0|0	0.0|0.0	273|273	0.36015831134564646|0.36015831134564646	A|A	14.95|14.95	2.689584|2.689584	0.48097|0.48097	0.131639|0.131639	0.372674|0.372674	ENSG00000168297|ENSG00000168297	ENST00000356151;ENST00000302779;ENST00000383716;ENST00000463280;ENST00000383715;ENST00000484288;ENST00000479241;ENST00000536660;ENST00000493474|ENST00000479134;ENST00000495557	T;T;T;T;T;T;T;T;T|.	0.57752|.	1.94;1.94;1.94;1.49;1.49;1.49;1.46;2.14;0.38|.	5.9|5.9	5.9|5.9	0.94986|0.94986	Protein kinase, catalytic domain (1);|.	0.291482|.	0.37623|.	N|.	0.002018|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.41236|0.41236	1.265|1.265	0.24800|0.24800	P|P	0.9927006|0.9927006	B;B;B;B;B|.	0.24618|.	0.107;0.001;0.001;0.003;0.0|.	B;B;B;B;B|.	0.18263|.	0.021;0.003;0.001;0.003;0.003|.	T|T	0.35649|0.35649	-0.9780|-0.9780	9|4	0.33141|.	T|.	0.24|.	-8.3281|-8.3281	14.9448|14.9448	0.71023|0.71023	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs56384862;rs62258125|rs56384862;rs62258125	448;448;481;464;481|.	E9PD56;Q7Z7A4-6;Q7Z7A4;Q7Z7A4-4;Q7Z7A4-2|.	.;.;PXK_HUMAN;.;.|.	R|G	481;464;448;448;464;481;464;344;17|236;53	ENSP00000348472:K481R;ENSP00000305045:K464R;ENSP00000373222:K448R;ENSP00000417903:K448R;ENSP00000373221:K464R;ENSP00000417915:K481R;ENSP00000419049:K464R;ENSP00000438356:K344R;ENSP00000418836:K17R|.	ENSP00000305045:K464R|.	K|S	+|+	2|1	0|0	PXK|PXK	58370903|58370903	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.963000|0.963000	0.63663|0.63663	4.760000|4.760000	0.62235|0.62235	2.268000|2.268000	0.75426|0.75426	0.519000|0.519000	0.50382|0.50382	AAG|AGT	A|0.717;G|0.283	0.283	strong		0.428	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771	
ALPL	249	hgsc.bcm.edu	37	1	21894735	21894735	+	Missense_Mutation	SNP	T	T	C	rs3200254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:21894735T>C	ENST00000374840.3	+	7	1037	c.787T>C	c.(787-789)Tac>Cac	p.Y263H	ALPL_ENST00000539907.1_Missense_Mutation_p.Y186H|ALPL_ENST00000374832.1_Missense_Mutation_p.Y263H|ALPL_ENST00000374830.1_5'Flank|ALPL_ENST00000540617.1_Missense_Mutation_p.Y208H|ALPL_ENST00000425315.2_Missense_Mutation_p.Y263H	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	263			Y -> H (common polymorphism; dbSNP:rs3200254). {ECO:0000269|PubMed:11855933, ECO:0000269|PubMed:1409720, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2928120, ECO:0000269|PubMed:9781036}.		cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	CAAACCGAGATACAAGGTAGC	0.557													C|||	1337	0.266973	0.2655	0.268	5008	,	,		18511	0.4534		0.1203	False		,,,				2504	0.227				p.Y263H		Atlas-SNP	.											.	ALPL	50	.	0			c.T787C	GRCh37	CM980072	ALPL	M	rs3200254	PASS	.	C	HIS/TYR,HIS/TYR,HIS/TYR	1109,3297	718.2+/-408.8	138,833,1232	71.0	64.0	67.0		787,622,556	1.9	0.9	1	dbSNP_105	67	956,7644	775.1+/-407.7	48,860,3392	yes	missense,missense,missense	ALPL	NM_000478.4,NM_001127501.2,NM_001177520.1	83,83,83	186,1693,4624	CC,CT,TT		11.1163,25.1702,15.8773	benign,benign,benign	263/525,208/470,186/448	21894735	2065,10941	2203	4300	6503	SO:0001583	missense	249	exon7			CCGAGATACAAGG	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.787T>C	1.37:g.21894735T>C	ENSP00000363973:p.Tyr263His	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	30	0.3125	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Missense_Mutation	SNP	ENST00000374840.3	37	CCDS217.1	609	0.27884615384615385	136	0.2764227642276423	94	0.2596685082872928	282	0.493006993006993	97	0.1279683377308707	C	0.016	-1.521911	0.00967	0.251702	0.111163	ENSG00000162551	ENST00000539907;ENST00000540617;ENST00000374840;ENST00000374832;ENST00000425315	D;D;D;D;D	0.96232	-3.95;-3.95;-3.95;-3.95;-3.95	3.97	1.91	0.25777	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.579699	0.19198	N	0.120256	T	0.00012	0.0000	N	0.11789	0.175	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.0;0.004;0.0	T	0.36672	-0.9738	9	0.13108	T	0.6	-6.9786	0.7701	0.01022	0.2758:0.3727:0.149:0.2026	rs3200254;rs3738099;rs17433800;rs52825308;rs59928547;rs3738099	186;211;263	B7Z387;B7Z1D1;P05186	.;.;PPBT_HUMAN	H	186;208;263;263;263	ENSP00000437674:Y186H;ENSP00000442672:Y208H;ENSP00000363973:Y263H;ENSP00000363965:Y263H;ENSP00000394765:Y263H	ENSP00000363965:Y263H	Y	+	1	0	ALPL	21767322	0.005000	0.15991	0.875000	0.34327	0.500000	0.33767	-0.042000	0.12063	0.462000	0.27095	-0.215000	0.12644	TAC	A|0.131;C|0.169	0.169	strong		0.557	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478	
DEFB129	140881	hgsc.bcm.edu	37	20	210061	210061	+	Silent	SNP	G	G	A	rs13045643	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:210061G>A	ENST00000246105.4	+	2	232	c.201G>A	c.(199-201)ctG>ctA	p.L67L		NM_080831.3	NP_543021.1	Q9H1M3	DB129_HUMAN	defensin, beta 129	67					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.L67L(1)		endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|stomach(1)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			AAAACTACCTGCAATATGGAA	0.348													G|||	1353	0.270168	0.0333	0.3761	5008	,	,		22149	0.2857		0.3907	False		,,,				2504	0.3753				p.L67L		Atlas-SNP	.											DEFB129,NS,carcinoma,0,1	DEFB129	24	1	1	Substitution - coding silent(1)	stomach(1)	c.G201A						scavenged	.	G		395,4011	198.7+/-222.5	15,365,1823	99.0	98.0	98.0		201	-4.3	0.0	20	dbSNP_121	98	3567,5033	518.7+/-379.3	737,2093,1470	yes	coding-synonymous	DEFB129	NM_080831.3		752,2458,3293	AA,AG,GG		41.4767,8.965,30.4629		67/184	210061	3962,9044	2203	4300	6503	SO:0001819	synonymous_variant	140881	exon2			CTACCTGCAATAT	AY358186	CCDS12992.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125903	ENSG00000125903		"""Defensins, beta"""	16218	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 87"""	C20orf87		11854508	Standard	NM_080831		Approved	bA530N10.3, DEFB-29	uc002wda.3	Q9H1M3	OTTHUMG00000031618	ENST00000246105.4:c.201G>A	20.37:g.210061G>A		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_080831	Q8NES7	Silent	SNP	ENST00000246105.4	37	CCDS12992.1																																																																																			G|0.710;A|0.289	0.289	strong		0.348	DEFB129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077430.2	NM_080831	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274235	39274235	+	Silent	SNP	G	G	A	rs11654403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39274235G>A	ENST00000391413.2	-	1	371	c.333C>T	c.(331-333)cgC>cgT	p.R111R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	111	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.R111R(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcagctggggcgacagcagc	0.652													g|||	1468	0.293131	0.2852	0.2522	5008	,	,		17468	0.1042		0.4235	False		,,,				2504	0.3937				p.R111R		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	1	Substitution - coding silent(1)	kidney(1)	c.C333T						scavenged	.						4.0	9.0	7.0					17																	39274235		652	1539	2191	SO:0001819	synonymous_variant	653240	exon1			GCTGGGGCGACAG	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.333C>T	17.37:g.39274235G>A		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	110	98	0.890909	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			G|0.724;A|0.276	0.276	strong		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
FAM198A	729085	hgsc.bcm.edu	37	3	43095101	43095101	+	Missense_Mutation	SNP	A	A	G	rs536119	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:43095101A>G	ENST00000430121.2	+	3	1474	c.1379A>G	c.(1378-1380)cAg>cGg	p.Q460R	KRBOX1_ENST00000443313.1_3'UTR	NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	460			Q -> R (in dbSNP:rs536119). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)				endometrium(1)	1						GAGAAATGCCAGAACCCAGCC	0.597													G|||	2710	0.541134	0.4644	0.6686	5008	,	,		16542	0.6696		0.5954	False		,,,				2504	0.3661				p.Q460R		Atlas-SNP	.											.	FAM198A	23	.	0			c.A1379G						PASS	.	G	ARG/GLN	625,759		142,341,209	32.0	43.0	40.0		1379	0.7	1.0	3	dbSNP_83	40	1929,1253		582,765,244	yes	missense	FAM198A	NM_001129908.2	43	724,1106,453	GG,GA,AA		39.3777,45.159,44.0648	benign	460/576	43095101	2554,2012	692	1591	2283	SO:0001583	missense	729085	exon3			AATGCCAGAACCC	AL117530	CCDS46808.1	3p22.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000144649	ENSG00000144649			24485	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 41"""	C3orf41			Standard	NM_001129908		Approved	DKFZP434B172	uc003cmp.4	Q9UFP1	OTTHUMG00000156449	ENST00000430121.2:c.1379A>G	3.37:g.43095101A>G	ENSP00000407301:p.Gln460Arg	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	147	80	0.544218	NM_001129908	B3KR48	Missense_Mutation	SNP	ENST00000430121.2	37	CCDS46808.1	1315	0.6021062271062271	252	0.5121951219512195	253	0.6988950276243094	373	0.6520979020979021	437	0.5765171503957783	G	3.612	-0.079297	0.07141	0.45159	0.606223	ENSG00000144649	ENST00000488863;ENST00000430121	T;T	0.27104	1.69;1.69	5.62	0.681	0.17986	.	0.564021	0.18201	N	0.148503	T	0.00012	0.0000	N	0.00054	-2.38	0.58432	P	9.99999999995449E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36237	-0.9756	9	0.02654	T	1	-20.7108	6.9169	0.24365	0.322:0.1098:0.5682:0.0	rs536119;rs17469537;rs58673217;rs536119	31;460	F5H4W4;Q9UFP1	.;F198A_HUMAN	R	31;460	ENSP00000439905:Q31R;ENSP00000407301:Q460R	ENSP00000273146:Q460R	Q	+	2	0	FAM198A	43070105	0.469000	0.25846	0.965000	0.40720	0.817000	0.46193	0.166000	0.16583	-0.417000	0.07461	-0.974000	0.02594	CAG	A|0.413;G|0.587	0.587	strong		0.597	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
HRNR	388697	hgsc.bcm.edu	37	1	152186837	152186837	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152186837C>T	ENST00000368801.2	-	3	7343	c.7268G>A	c.(7267-7269)cGa>cAa	p.R2423Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2423					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R2423Q(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACCCATGTCGGCCACGGCT	0.612																																					p.R2423Q		Atlas-SNP	.											HRNR,NS,carcinoma,0,4	HRNR	403	4	1	Substitution - Missense(1)	ovary(1)	c.G7268A						scavenged	.						1.0	1.0	1.0					1																	152186837		251	755	1006	SO:0001583	missense	388697	exon3			CCATGTCGGCCAC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7268G>A	1.37:g.152186837C>T	ENSP00000357791:p.Arg2423Gln	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	1140	88	0.077193	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	6.285	0.420671	0.11928	.	.	ENSG00000197915	ENST00000368801	T	0.02974	4.09	2.94	-5.88	0.02290	.	.	.	.	.	T	0.00328	0.0010	N	0.03115	-0.41	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.45293	-0.9271	9	0.10636	T	0.68	.	7.9897	0.30233	0.1213:0.2056:0.0:0.673	.	2423	Q86YZ3	HORN_HUMAN	Q	2423	ENSP00000357791:R2423Q	ENSP00000357791:R2423Q	R	-	2	0	HRNR	150453461	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.624000	0.02038	-2.325000	0.00638	-0.762000	0.03455	CGA	.	.	none		0.612	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
KCNB2	9312	hgsc.bcm.edu	37	8	73850203	73850203	+	Silent	SNP	G	G	A	rs11782118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:73850203G>A	ENST00000523207.1	+	3	3201	c.2613G>A	c.(2611-2613)gtG>gtA	p.V871V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	871					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	ACCATGCTGTGAGTGAAGTCA	0.483													G|||	1183	0.236222	0.1989	0.2767	5008	,	,		19028	0.0942		0.4314	False		,,,				2504	0.2035				p.V871V		Atlas-SNP	.											.	KCNB2	228	.	0			c.G2613A						PASS	.	G		1013,3393	376.3+/-322.0	111,791,1301	93.0	89.0	90.0		2613	2.7	0.6	8	dbSNP_120	90	3543,5057	516.7+/-378.9	723,2097,1480	no	coding-synonymous	KCNB2	NM_004770.2		834,2888,2781	AA,AG,GG		41.1977,22.9914,35.03		871/912	73850203	4556,8450	2203	4300	6503	SO:0001819	synonymous_variant	9312	exon3			TGCTGTGAGTGAA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.2613G>A	8.37:g.73850203G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																			G|0.686;A|0.314	0.314	strong		0.483	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
EFCAB13	124989	hgsc.bcm.edu	37	17	45425287	45425287	+	Nonsense_Mutation	SNP	C	C	T	rs71377306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45425287C>T	ENST00000331493.2	+	9	1042	c.631C>T	c.(631-633)Cga>Tga	p.R211*	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	211						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TTTAGAAATGCGACAGGCACT	0.299													C|||	459	0.0916534	0.0023	0.0331	5008	,	,		16292	0.2252		0.0835	False		,,,				2504	0.1247				p.R211X		Atlas-SNP	.											.	.	.	.	0			c.C631T						PASS	.	C	,stop/ARG	59,4347	58.7+/-95.3	1,57,2145	70.0	69.0	69.0		,631	2.4	0.9	17	dbSNP_130	69	458,8134	135.9+/-193.0	15,428,3853	yes	intron,stop-gained	C17orf57	NM_001195192.1,NM_152347.4	,	16,485,5998	TT,TC,CC		5.3305,1.3391,3.9775	,	,211/974	45425287	517,12481	2203	4296	6499	SO:0001587	stop_gained	124989	exon9			GAAATGCGACAGG	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.631C>T	17.37:g.45425287C>T	ENSP00000332111:p.Arg211*	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_152347	G3V128|Q49AG9	Nonsense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	193	0.08836996336996338	0	0.0	11	0.03038674033149171	114	0.1993006993006993	68	0.08970976253298153	C	37	6.586646	0.97684	0.013391	0.053305	ENSG00000178852	ENST00000331493	.	.	.	4.57	2.38	0.29361	.	0.000000	0.27826	N	0.017688	.	.	.	.	.	.	0.40293	P	0.021479000000000026	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.6487	8.9246	0.35632	0.4056:0.5944:0.0:0.0	.	.	.	.	X	211	.	ENSP00000332111:R211X	R	+	1	2	C17orf57	42780286	0.796000	0.28864	0.861000	0.33841	0.678000	0.39670	1.225000	0.32551	0.870000	0.35726	0.650000	0.86243	CGA	C|0.948;T|0.052	0.052	strong		0.299	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
ITGB6	3694	hgsc.bcm.edu	37	2	161029218	161029218	+	Silent	SNP	G	G	A	rs2305818	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:161029218G>A	ENST00000283249.2	-	6	1020	c.783C>T	c.(781-783)gaC>gaT	p.D261D	ITGB6_ENST00000409872.1_Silent_p.D261D|ITGB6_ENST00000409967.2_Silent_p.D261D|ITGB6_ENST00000485635.1_5'UTR|ITGB6_ENST00000428609.2_Silent_p.D219D	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	261	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						GGTGGAGGGAGTCATTCCGCC	0.453													G|||	1144	0.228435	0.0325	0.2594	5008	,	,		17071	0.3323		0.4225	False		,,,				2504	0.1646				p.D261D		Atlas-SNP	.											.	ITGB6	68	.	0			c.C783T						PASS	.	G		413,3993	200.8+/-224.0	14,385,1804	127.0	121.0	123.0		783	-5.1	0.8	2	dbSNP_100	123	3499,5101	512.2+/-377.9	740,2019,1541	no	coding-synonymous	ITGB6	NM_000888.3		754,2404,3345	AA,AG,GG		40.686,9.3736,30.0784		261/789	161029218	3912,9094	2203	4300	6503	SO:0001819	synonymous_variant	3694	exon6			GAGGGAGTCATTC		CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"""Integrins"""	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.783C>T	2.37:g.161029218G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Silent	SNP	ENST00000283249.2	37	CCDS2212.1																																																																																			G|0.727;A|0.273	0.273	strong		0.453	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888	
PLAT	5327	hgsc.bcm.edu	37	8	42036577	42036577	+	Silent	SNP	A	A	G	rs1136159	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:42036577A>G	ENST00000220809.4	-	13	1624	c.1368T>C	c.(1366-1368)tcT>tcC	p.S456S	PLAT_ENST00000352041.3_Silent_p.S410S|PLAT_ENST00000429089.2_Silent_p.S456S|PLAT_ENST00000519510.1_Silent_p.S393S|PLAT_ENST00000429710.2_Silent_p.S330S|PLAT_ENST00000270189.6_Missense_Mutation_p.L287P|PLAT_ENST00000524009.1_Silent_p.S367S	NM_000930.3	NP_000921.1	P00750	TPA_HUMAN	plasminogen activator, tissue	456	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|fibrinolysis (GO:0042730)|negative regulation of proteolysis (GO:0045861)|plasminogen activation (GO:0031639)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of ovulation (GO:0060279)|proteolysis (GO:0006508)|regulation of synaptic plasticity (GO:0048167)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|smooth muscle cell migration (GO:0014909)|synaptic transmission, glutamatergic (GO:0035249)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|synapse (GO:0045202)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|skin(1)|soft_tissue(1)|urinary_tract(1)	27	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Aminocaproic Acid(DB00513)|Ibuprofen(DB01050)|Iloprost(DB01088)|Urokinase(DB00013)	AATAGAAAGGAGACACTGAAA	0.408													A|||	516	0.103035	0.0151	0.0749	5008	,	,		19846	0.1885		0.1143	False		,,,				2504	0.1421				p.S456S		Atlas-SNP	.											.	PLAT	62	.	0			c.T1368C						PASS	.	A	,	136,4270	96.7+/-135.4	2,132,2069	52.0	52.0	52.0		1368,1230	4.0	1.0	8	dbSNP_86	52	1094,7506	222.2+/-259.3	68,958,3274	no	coding-synonymous,coding-synonymous	PLAT	NM_000930.3,NM_033011.2	,	70,1090,5343	GG,GA,AA		12.7209,3.0867,9.4572	,	456/563,410/517	42036577	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	5327	exon13			GAAAGGAGACACT		CCDS6126.1, CCDS6127.1	8p11.21	2012-10-02			ENSG00000104368	ENSG00000104368			9051	protein-coding gene	gene with protein product		173370					Standard	NM_033011		Approved		uc003xos.2	P00750	OTTHUMG00000164072	ENST00000220809.4:c.1368T>C	8.37:g.42036577A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_000930	A8K022|B2R8E8|Q15103|Q503B0|Q6PJA5|Q7Z7N2|Q86YK8|Q9BU99|Q9BZW1	Silent	SNP	ENST00000220809.4	37	CCDS6126.1	220	0.10073260073260074	11	0.022357723577235773	30	0.08287292817679558	93	0.16258741258741258	86	0.11345646437994723	A	11.00	1.511239	0.27036	0.030867	0.127209	ENSG00000104368	ENST00000270189	T	0.74947	-0.89	5.22	4.04	0.47022	.	.	.	.	.	T	0.00695	0.0023	.	.	.	0.20764	P	0.99985116	.	.	.	.	.	.	T	0.32534	-0.9903	5	0.41790	T	0.15	.	7.8996	0.29727	0.7212:0.1426:0.0:0.1362	rs1136159;rs2020924;rs2229412;rs3199378;rs11537822;rs17420641;rs56900864;rs1136159	.	.	.	P	287	ENSP00000270189:L287P	ENSP00000270189:L287P	L	-	2	0	PLAT	42155734	1.000000	0.71417	0.982000	0.44146	0.313000	0.28021	3.768000	0.55295	0.895000	0.36342	0.533000	0.62120	CTC	A|0.908;G|0.092	0.092	strong		0.408	PLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377100.1	NM_000930	
PI3	5266	hgsc.bcm.edu	37	20	43804522	43804522	+	Missense_Mutation	SNP	A	A	C	rs2664581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43804522A>C	ENST00000243924.3	+	2	147	c.100A>C	c.(100-102)Act>Cct	p.T34P		NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived	34	2 X tandem repeats of SVP-1 like motif.		T -> P (in dbSNP:rs2664581).		copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				AGGTCAAGACACTGTCAAAGG	0.453													A|||	537	0.107228	0.1127	0.0951	5008	,	,		21020	0.0268		0.167	False		,,,				2504	0.1299				p.T34P		Atlas-SNP	.											.	PI3	21	.	0			c.A100C						PASS	.	A	PRO/THR	560,3846	247.5+/-255.7	37,486,1680	106.0	98.0	101.0		100	-5.1	0.0	20	dbSNP_100	101	1581,7019	290.8+/-300.0	134,1313,2853	yes	missense	PI3	NM_002638.3	38	171,1799,4533	CC,CA,AA		18.3837,12.7099,16.4616	benign	34/118	43804522	2141,10865	2203	4300	6503	SO:0001583	missense	5266	exon2			CAAGACACTGTCA	D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"""WAP four-disulfide core domain containing"""	8947	protein-coding gene	gene with protein product	"""skin-derived antileukoproteinase"", ""trappin-2"""	182257	"""protease inhibitor 3, skin-derived (SKALP)"""			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.100A>C	20.37:g.43804522A>C	ENSP00000243924:p.Thr34Pro	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_002638	E1P618|Q6FG74	Missense_Mutation	SNP	ENST00000243924.3	37	CCDS13344.1	245	0.11217948717948718	62	0.12601626016260162	42	0.11602209944751381	16	0.027972027972027972	125	0.16490765171503957	A	7.273	0.607461	0.14002	0.127099	0.183837	ENSG00000124102	ENST00000243924	T	0.41065	1.01	3.6	-5.09	0.02920	.	1.319810	0.05350	N	0.531676	T	0.00039	0.0001	L	0.38175	1.15	0.80722	P	0.0	B	0.16603	0.018	B	0.15052	0.012	T	0.19418	-1.0306	9	0.09843	T	0.71	.	0.7426	0.00976	0.2732:0.1441:0.3241:0.2587	rs2664581;rs17333320;rs57162342;rs2664581	34	P19957	ELAF_HUMAN	P	34	ENSP00000243924:T34P	ENSP00000243924:T34P	T	+	1	0	PI3	43237936	0.000000	0.05858	0.000000	0.03702	0.392000	0.30506	-2.385000	0.01062	-1.163000	0.02793	0.533000	0.62120	ACT	A|0.862;C|0.138	0.138	strong		0.453	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638	
SLC37A3	84255	hgsc.bcm.edu	37	7	140080087	140080087	+	Missense_Mutation	SNP	C	C	G	rs62490396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:140080087C>G	ENST00000326232.9	-	3	396	c.193G>C	c.(193-195)Gtg>Ctg	p.V65L	SLC37A3_ENST00000461089.1_Intron|SLC37A3_ENST00000429996.2_Missense_Mutation_p.V65L|SLC37A3_ENST00000340308.3_Missense_Mutation_p.V65L|SLC37A3_ENST00000447932.2_Missense_Mutation_p.V65L	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	65				V -> L (in Ref. 1; BAC11231). {ECO:0000305}.	carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.V65L(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					CTTACCTCCACAGGCAGCTCA	0.463													C|||	1875	0.374401	0.2103	0.3602	5008	,	,		18303	0.4474		0.4592	False		,,,				2504	0.4438				p.V65L	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											SLC37A3,NS,carcinoma,0,1	SLC37A3	80	1	1	Substitution - Missense(1)	stomach(1)	c.G193C						PASS	.	C	LEU/VAL,LEU/VAL	1109,3297	399.2+/-331.1	139,831,1233	121.0	96.0	105.0		193,193	1.9	0.4	7	dbSNP_129	105	3941,4659	548.9+/-385.4	888,2165,1247	yes	missense,missense	SLC37A3	NM_032295.2,NM_207113.1	32,32	1027,2996,2480	GG,GC,CC		45.8256,25.1702,38.8282	benign,benign	65/444,65/495	140080087	5050,7956	2203	4300	6503	SO:0001583	missense	84255	exon3			CCTCCACAGGCAG	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.193G>C	7.37:g.140080087C>G	ENSP00000321498:p.Val65Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	846	0.3873626373626374	102	0.2073170731707317	140	0.3867403314917127	253	0.4423076923076923	351	0.4630606860158311	C	8.305	0.820809	0.16678	0.251702	0.458256	ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232;ENST00000429996;ENST00000539816;ENST00000469193	T;T;T;T;T	0.42131	2.3;2.58;2.59;0.98;1.0	4.93	1.88	0.25563	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.920160	0.02218	N	0.063802	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B	0.15473	0.0;0.002;0.013;0.002	B;B;B;B	0.13407	0.002;0.004;0.009;0.007	T	0.41502	-0.9505	9	0.20519	T	0.43	-23.4191	4.7566	0.13086	0.0:0.6204:0.1791:0.2005	rs62490396	65;65;65;65	F5H743;Q8NCC5-2;Q8NCC5-3;Q8NCC5	.;.;.;SPX3_HUMAN	L	65	ENSP00000343358:V65L;ENSP00000397481:V65L;ENSP00000321498:V65L;ENSP00000412208:V65L;ENSP00000419024:V65L	ENSP00000321498:V65L	V	-	1	0	SLC37A3	139726556	0.028000	0.19301	0.408000	0.26446	0.771000	0.43674	0.407000	0.21049	1.078000	0.41014	0.313000	0.20887	GTG	C|0.599;G|0.401	0.401	strong		0.463	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	
XYLT2	64132	hgsc.bcm.edu	37	17	48431032	48431032	+	Silent	SNP	G	G	A	rs739990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:48431032G>A	ENST00000017003.2	+	2	226	c.177G>A	c.(175-177)gaG>gaA	p.E59E	XYLT2_ENST00000507602.1_Silent_p.E59E	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	59					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					ACCCTGGCGAGGGTTCCAAGG	0.637													G|||	660	0.131789	0.0408	0.2795	5008	,	,		17426	0.0784		0.2147	False		,,,				2504	0.1196				p.E59E		Atlas-SNP	.											XYLT2,NS,carcinoma,0,1	XYLT2	51	1	0			c.G177A						PASS	.	G		317,4071		17,283,1894	16.0	14.0	15.0		177	2.1	1.0	17	dbSNP_86	15	1855,6721		205,1445,2638	no	coding-synonymous	XYLT2	NM_022167.2		222,1728,4532	AA,AG,GG		21.6301,7.2242,16.7541		59/866	48431032	2172,10792	2194	4288	6482	SO:0001819	synonymous_variant	64132	exon2			TGGCGAGGGTTCC	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.177G>A	17.37:g.48431032G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_022167	Q6UY41|Q86V00	Silent	SNP	ENST00000017003.2	37	CCDS11563.1																																																																																			G|0.851;A|0.149	0.149	strong		0.637	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
SVEP1	79987	hgsc.bcm.edu	37	9	113169619	113169619	+	Missense_Mutation	SNP	A	A	G	rs199899670	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:113169619A>G	ENST00000401783.2	-	38	8597	c.8261T>C	c.(8260-8262)tTa>tCa	p.L2754S	SVEP1_ENST00000374469.1_Missense_Mutation_p.L2731S|SVEP1_ENST00000297826.5_Missense_Mutation_p.L680S	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2754	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ACAAAGCCTTAAGTCAGAGCC	0.453													A|||	8	0.00159744	0.0	0.0	5008	,	,		22575	0.0		0.002	False		,,,				2504	0.0061				p.L2754S		Atlas-SNP	.											.	SVEP1	326	.	0			c.T8261C						PASS	.	A	SER/LEU	0,3978		0,0,1989	76.0	80.0	79.0		8261	1.0	0.0	9	dbSNP_132	79	12,8300		0,12,4144	yes	missense	SVEP1	NM_153366.3	145	0,12,6133	GG,GA,AA		0.1444,0.0,0.0976	benign	2754/3572	113169619	12,12278	1989	4156	6145	SO:0001583	missense	79987	exon38			AGCCTTAAGTCAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8261T>C	9.37:g.113169619A>G	ENSP00000384917:p.Leu2754Ser	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	260	121	0.465385	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0.008	-1.912475	0.00508	0.0	0.001444	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.63255	-0.03;-0.03;-0.03	5.87	0.967	0.19674	Complement control module (2);Sushi/SCR/CCP (3);	0.805314	0.12128	N	0.497090	T	0.28134	0.0694	N	0.04387	-0.21	0.09310	N	1	B	0.20164	0.042	B	0.25506	0.061	T	0.30679	-0.9970	10	0.06494	T	0.89	.	0.0954	0.00043	0.2867:0.1649:0.2327:0.3157	.	2754	Q4LDE5	SVEP1_HUMAN	S	2754;2731;680;426	ENSP00000384917:L2754S;ENSP00000363593:L2731S;ENSP00000297826:L680S	ENSP00000297826:L680S	L	-	2	0	SVEP1	112209440	0.073000	0.21202	0.001000	0.08648	0.119000	0.20118	2.094000	0.41719	1.062000	0.40625	0.477000	0.44152	TTA	A|0.998;G|0.002	0.002	strong		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SEC14L3	266629	hgsc.bcm.edu	37	22	30864610	30864610	+	Missense_Mutation	SNP	A	A	G	rs4820853	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30864610A>G	ENST00000215812.4	-	5	398	c.308T>C	c.(307-309)aTt>aCt	p.I103T	SEC14L3_ENST00000415957.2_Missense_Mutation_p.I44T|SEC14L3_ENST00000539629.1_Missense_Mutation_p.I44T|SEC14L3_ENST00000540910.1_Missense_Mutation_p.I26T|SEC14L3_ENST00000401751.1_Missense_Mutation_p.I44T|SEC14L3_ENST00000403066.1_Missense_Mutation_p.I44T|SEC14L3_ENST00000402286.1_Missense_Mutation_p.I26T	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	103	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		I -> T (in dbSNP:rs4820853). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	AAGTGGCCCAATGATGTCATA	0.547													A|||	2271	0.453474	0.4486	0.3501	5008	,	,		18827	0.4663		0.338	False		,,,				2504	0.6391				p.I103T	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											SEC14L3,NS,malignant_melanoma,-1,1	SEC14L3	46	1	0			c.T308C						PASS	.	A	THR/ILE	1798,2608	529.5+/-372.7	375,1048,780	189.0	151.0	164.0		308	4.6	1.0	22	dbSNP_111	164	2877,5723	451.1+/-362.6	470,1937,1893	yes	missense	SEC14L3	NM_174975.4	89	845,2985,2673	GG,GA,AA		33.4535,40.808,35.9449	benign	103/401	30864610	4675,8331	2203	4300	6503	SO:0001583	missense	266629	exon5			GGCCCAATGATGT	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.308T>C	22.37:g.30864610A>G	ENSP00000215812:p.Ile103Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	110	38	0.345455	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	904	0.4139194139194139	243	0.49390243902439024	149	0.4116022099447514	256	0.44755244755244755	256	0.33773087071240104	A	15.93	2.979447	0.53827	0.40808	0.334535	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99;-0.99;-0.99;-0.99	4.55	4.55	0.56014	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.175010	0.49305	D	0.000146	T	0.00012	0.0000	L	0.42581	1.335	0.09310	P	1.0	B;B	0.15930	0.015;0.001	B;B	0.32211	0.142;0.061	T	0.43556	-0.9384	9	0.48119	T	0.1	-8.023	13.8493	0.63487	1.0:0.0:0.0:0.0	rs4820853;rs52825334;rs58974618;rs4820853	26;103	E9PE57;Q9UDX4	.;S14L3_HUMAN	T	44;44;103;26;44;44;26	ENSP00000385941:I44T;ENSP00000401864:I44T;ENSP00000215812:I103T;ENSP00000385004:I26T;ENSP00000383896:I44T;ENSP00000444691:I44T;ENSP00000439752:I26T	ENSP00000215812:I103T	I	-	2	0	SEC14L3	29194610	1.000000	0.71417	0.978000	0.43139	0.974000	0.67602	7.394000	0.79862	1.810000	0.52873	0.519000	0.50382	ATT	A|0.608;G|0.392	0.392	strong		0.547	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
ARHGEF15	22899	hgsc.bcm.edu	37	17	8222455	8222455	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8222455C>T	ENST00000361926.3	+	13	2274	c.2164C>T	c.(2164-2166)Cga>Tga	p.R722*	ARHGEF15_ENST00000582060.1_3'UTR|AC135178.7_ENST00000458568.1_RNA|ARHGEF15_ENST00000421050.1_Nonsense_Mutation_p.R722*	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	722					negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						CCCCACCCACCGACTACTCCA	0.597																																					p.R722X		Atlas-SNP	.											ARHGEF15,NS,carcinoma,-1,1	ARHGEF15	97	1	0			c.C2164T						scavenged	.						74.0	85.0	81.0					17																	8222455		2203	4300	6503	SO:0001587	stop_gained	22899	exon13			ACCCACCGACTAC	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"""Rho guanine nucleotide exchange factors"""	15590	protein-coding gene	gene with protein product	"""Rho guanine exchange factor (GEF) 15"""	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.2164C>T	17.37:g.8222455C>T	ENSP00000355026:p.Arg722*	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	106	2	0.0188679	NM_025014	A8K6G1|Q8N449|Q9H8B4	Nonsense_Mutation	SNP	ENST00000361926.3	37	CCDS11139.1	.	.	.	.	.	.	.	.	.	.	c	37	6.528301	0.97637	.	.	ENSG00000198844	ENST00000361926;ENST00000455564;ENST00000421050	.	.	.	5.04	3.0	0.34707	.	0.120375	0.51477	D	0.000097	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-26.0899	5.7173	0.17968	0.2006:0.7002:0.0:0.0992	.	.	.	.	X	722;512;722	.	ENSP00000355026:R722X	R	+	1	2	ARHGEF15	8163180	0.999000	0.42202	1.000000	0.80357	0.972000	0.66771	0.656000	0.24948	0.670000	0.31165	0.561000	0.74099	CGA	.	.	none		0.597	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548545	32548545	+	Silent	SNP	G	G	A	rs201168487	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32548545G>A	ENST00000360004.5	-	4	846	c.741C>T	c.(739-741)ttC>ttT	p.F247F		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	247					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TGAAGTAGATGAACAGCCCGG	0.547										Multiple Myeloma(14;0.17)																											p.F247F		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C741T						PASS	.						86.0	100.0	95.0					6																	32548545		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon4			GTAGATGAACAGC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.741C>T	6.37:g.32548545G>A		Somatic	421	0	0		WXS	Illumina HiSeq	Phase_I	724	58	0.0801105	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.963;A|0.037	0.037	strong		0.547	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
MYT1L	23040	hgsc.bcm.edu	37	2	1946968	1946968	+	Silent	SNP	C	C	T	rs3748989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:1946968C>T	ENST00000399161.2	-	9	1038	c.291G>A	c.(289-291)gaG>gaA	p.E97E	MYT1L_ENST00000428368.2_Silent_p.E97E	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	97	Asp/Glu-rich.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		catccatgtcctcAGTCCCAT	0.567													C|||	829	0.165535	0.1437	0.1081	5008	,	,		17458	0.3442		0.0944	False		,,,				2504	0.1247				p.E97E		Atlas-SNP	.											.	MYT1L	241	.	0			c.G291A						PASS	.	C		518,3730		31,456,1637	103.0	103.0	103.0		291	-3.1	0.2	2	dbSNP_107	103	683,7683		28,627,3528	no	coding-synonymous	MYT1L	NM_015025.2		59,1083,5165	TT,TC,CC		8.164,12.194,9.5212		97/1185	1946968	1201,11413	2124	4183	6307	SO:0001819	synonymous_variant	23040	exon9			CATGTCCTCAGTC	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"""Zinc fingers, C2HC-type containing"""	7623	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 1"""	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.291G>A	2.37:g.1946968C>T		Somatic	383	1	0.00261097		WXS	Illumina HiSeq	Phase_I	392	167	0.42602	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																				C|0.830;T|0.170	0.170	strong		0.567	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152656	151152656	+	Silent	SNP	T	T	C	rs803411	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:151152656T>C	ENST00000358517.2	+	15	2620	c.2409T>C	c.(2407-2409)acT>acC	p.T803T	PLEKHG1_ENST00000367328.1_Silent_p.T803T			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	803							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		ATCAGGCCACTCCCGATCATG	0.512													C|||	3192	0.63738	0.6112	0.7205	5008	,	,		20279	0.5397		0.7107	False		,,,				2504	0.6391				p.T803T		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.T2409C						PASS	.	C		2851,1555	486.9+/-360.8	923,1005,275	116.0	113.0	114.0		2409	0.8	0.0	6	dbSNP_86	114	6184,2416	398.7+/-346.2	2239,1706,355	no	coding-synonymous	PLEKHG1	NM_001029884.1		3162,2711,630	CC,CT,TT		28.093,35.2928,30.5321		803/1386	151152656	9035,3971	2203	4300	6503	SO:0001819	synonymous_variant	57480	exon16			GGCCACTCCCGAT	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.2409T>C	6.37:g.151152656T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	126	124	0.984127	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																			T|0.326;C|0.674	0.674	strong		0.512	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
GBP4	115361	hgsc.bcm.edu	37	1	89652078	89652078	+	Missense_Mutation	SNP	A	A	T	rs608339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:89652078A>T	ENST00000355754.6	-	10	1742	c.1645T>A	c.(1645-1647)Ttg>Atg	p.L549M	GBP4_ENST00000471938.1_5'Flank	NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	549			L -> M (in dbSNP:rs608339).	LEE -> MER (in Ref. 1; AAL02054 and 3; BAC85144). {ECO:0000305}.		cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		TCCTCCTCCAACTTCTTCTCC	0.488													A|||	1800	0.359425	0.1445	0.3141	5008	,	,		18963	0.3988		0.4891	False		,,,				2504	0.5082				p.L549M		Atlas-SNP	.											.	GBP4	89	.	0			c.T1645A						PASS	.	A	MET/LEU	889,3517		121,647,1435	186.0	127.0	147.0		1645	-6.2	0.0	1	dbSNP_83	147	4032,4562		1093,1846,1358	yes	missense	GBP4	NM_052941.4	15	1214,2493,2793	TT,TA,AA		46.9165,20.177,37.8538	benign	549/641	89652078	4921,8079	2203	4297	6500	SO:0001583	missense	115361	exon10			CCTCCAACTTCTT	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1645T>A	1.37:g.89652078A>T	ENSP00000359490:p.Leu549Met	Somatic	444	1	0.00225225		WXS	Illumina HiSeq	Phase_I	130	128	0.984615	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	679	0.3108974358974359	43	0.08739837398373984	117	0.32320441988950277	188	0.32867132867132864	331	0.4366754617414248	A	0.182	-1.061175	0.01950	0.20177	0.469165	ENSG00000162654	ENST00000355754	T	0.02421	4.3	4.29	-6.25	0.02039	Guanylate-binding protein, C-terminal (3);	0.381500	0.29737	N	0.011330	T	0.00300	0.0009	N	0.03253	-0.375	0.53688	P	2.8999999999945736E-5	B	0.14805	0.011	B	0.25614	0.062	T	0.26916	-1.0089	9	0.02654	T	1	.	7.3538	0.26706	0.5342:0.0:0.1115:0.3542	rs608339;rs1142891;rs3180077;rs3206373;rs608339	549	Q96PP9	GBP4_HUMAN	M	549	ENSP00000359490:L549M	ENSP00000359490:L549M	L	-	1	2	GBP4	89424666	0.001000	0.12720	0.007000	0.13788	0.003000	0.03518	-0.767000	0.04720	-1.293000	0.02362	-1.750000	0.00680	TTG	A|0.658;T|0.342	0.342	strong		0.488	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
DNAH6	1768	hgsc.bcm.edu	37	2	84896628	84896628	+	Silent	SNP	G	G	A	rs17708884	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:84896628G>A	ENST00000237449.6	+	37	6308	c.6300G>A	c.(6298-6300)gtG>gtA	p.V2100V	DNAH6_ENST00000398278.2_Silent_p.V2100V|DNAH6_ENST00000389394.3_Silent_p.V2100V|DNAH6_ENST00000602588.1_Silent_p.V121V			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2100	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TAACTGGAGTGGGCAAGGTAG	0.423													G|||	313	0.0625	0.0113	0.1282	5008	,	,		19963	0.004		0.1312	False		,,,				2504	0.0746				p.V2100V		Atlas-SNP	.											DNAH6,colon,carcinoma,+1,1	DNAH6	194	1	0			c.G6300A						PASS	.	G		40,1344		0,40,652	94.0	80.0	84.0		6300	-5.0	1.0	2	dbSNP_123	84	449,2733		36,377,1178	no	coding-synonymous	DNAH6	NM_001370.1		36,417,1830	AA,AG,GG		14.1106,2.8902,10.7096		2100/4159	84896628	489,4077	692	1591	2283	SO:0001819	synonymous_variant	1768	exon38			TGGAGTGGGCAAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.6300G>A	2.37:g.84896628G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			G|0.926;A|0.074	0.074	strong		0.423	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
QSOX1	5768	hgsc.bcm.edu	37	1	180144485	180144485	+	Silent	SNP	G	G	A	rs10913939	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:180144485G>A	ENST00000367602.3	+	3	470	c.396G>A	c.(394-396)tcG>tcA	p.S132S	QSOX1_ENST00000367600.5_Silent_p.S132S			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	132	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						AGAACGGCTCGGGAGCAGTAT	0.542													G|||	493	0.0984425	0.0946	0.1066	5008	,	,		15983	0.003		0.1421	False		,,,				2504	0.1513				p.S132S		Atlas-SNP	.											.	QSOX1	79	.	0			c.G396A						PASS	.	G	,	539,3867	245.3+/-254.3	38,463,1702	137.0	119.0	125.0		396,396	-7.7	0.0	1	dbSNP_120	125	1367,7233	266.3+/-286.6	118,1131,3051	no	coding-synonymous,coding-synonymous	QSOX1	NM_001004128.2,NM_002826.4	,	156,1594,4753	AA,AG,GG		15.8953,12.2333,14.6548	,	132/605,132/748	180144485	1906,11100	2203	4300	6503	SO:0001819	synonymous_variant	5768	exon3			CGGCTCGGGAGCA	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.396G>A	1.37:g.180144485G>A		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	268	144	0.537313	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Silent	SNP	ENST00000367602.3	37	CCDS1337.1																																																																																			G|0.866;A|0.134	0.134	strong		0.542	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
MUC4	4585	hgsc.bcm.edu	37	3	195518330	195518330	+	Missense_Mutation	SNP	C	C	G	rs3107764	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195518330C>G	ENST00000463781.3	-	2	580	c.121G>C	c.(121-123)Gct>Cct	p.A41P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A41P	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	41			A -> P (in dbSNP:rs3107764). {ECO:0000269|PubMed:10920259, ECO:0000269|PubMed:12084055}.		cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGGGGCAGCAGTTTTACTT	0.443													N|||	2527	0.504593	0.2073	0.5245	5008	,	,		19636	0.756		0.6362	False		,,,				2504	0.498				p.A41P		Atlas-SNP	.											.	MUC4	1505	.	0			c.G121C						PASS	.		,,PRO/ALA	1106,2816		153,800,1008	283.0	248.0	259.0		,,121	-5.9	0.0	3	dbSNP_103	259	5188,3132		1628,1932,600	yes	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,27	1781,2732,1608	GG,GC,CC		37.6442,28.1999,48.5868	,,benign	,,41/5413	195518330	6294,5948	1961	4160	6121	SO:0001583	missense	4585	exon2			GGGCAGCAGTTTT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.121G>C	3.37:g.195518330C>G	ENSP00000417498:p.Ala41Pro	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	1187	0.5434981684981685	118	0.23983739837398374	186	0.5138121546961326	407	0.7115384615384616	476	0.6279683377308707	c	0.537	-0.855433	0.02630	0.281999	0.623558	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.48836	0.8;0.82	2.96	-5.93	0.02254	.	2.564240	0.02754	U	0.117775	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12630	0.006	B	0.04013	0.001	T	0.14008	-1.0488	9	0.08837	T	0.75	.	0.7436	0.00978	0.2132:0.2847:0.279:0.223	rs3107764;rs17364582;rs52820426;rs59213331;rs3107764	41	E7ESK3	.	P	41;41;15	ENSP00000417498:A41P;ENSP00000420243:A41P	ENSP00000376209:A15P	A	-	1	0	MUC4	197002725	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.803000	0.00759	-5.091000	0.00022	-2.315000	0.00254	GCT	C|0.453;G|0.546	0.546	strong		0.443	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
Unknown	0	hgsc.bcm.edu	37	11	124096247	124096247	+	IGR	SNP	G	G	A	rs2466613	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124096247G>A								OR10D3 (39295 upstream) : OR8G1 (24175 downstream)																							CATGGACCAGGGGAAAGTGTC	0.458																																					p.G284R		Atlas-SNP	.											.	.	.	.	0			c.G850A						PASS	.						72.0	72.0	72.0					11																	124096247		1971	4186	6157	SO:0001628	intergenic_variant	26492	exon1			GACCAGGGGAAAG																													11.37:g.124096247G>A		Somatic	522	0	0		WXS	Illumina HiSeq	Phase_I	341	131	0.384164	NM_001007249		Missense_Mutation	SNP		37																																																																																				G|0.495;A|0.505	0.505	strong	0	0.458								
MMRN2	79812	hgsc.bcm.edu	37	10	88717154	88717154	+	Missense_Mutation	SNP	C	C	T	rs3750823	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88717154C>T	ENST00000372027.5	-	1	466	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	SNCG_ENST00000372017.3_5'Flank|SNCG_ENST00000348795.4_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	49			G -> S (in dbSNP:rs3750823). {ECO:0000269|PubMed:11559704}.		angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.G49S(1)		breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						GGGTCCTTGCCGGTGTCCTCA	0.622													C|||	2121	0.423522	0.1899	0.4179	5008	,	,		17586	0.7113		0.4742	False		,,,				2504	0.3947				p.G49S		Atlas-SNP	.											MMRN2,NS,carcinoma,0,1	MMRN2	49	1	1	Substitution - Missense(1)	stomach(1)	c.G145A						PASS	.	C	SER/GLY	998,3408	372.0+/-320.2	122,754,1327	111.0	108.0	109.0		145	-5.3	0.0	10	dbSNP_107	109	4016,4584	555.5+/-386.7	923,2170,1207	yes	missense	MMRN2	NM_024756.2	56	1045,2924,2534	TT,TC,CC		46.6977,22.6509,38.5514	benign	49/950	88717154	5014,7992	2203	4300	6503	SO:0001583	missense	79812	exon1			CCTTGCCGGTGTC	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.145G>A	10.37:g.88717154C>T	ENSP00000361097:p.Gly49Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_024756	Q504V7|Q6P2N2	Missense_Mutation	SNP	ENST00000372027.5	37	CCDS7379.1	994	0.4551282051282051	94	0.1910569105691057	134	0.3701657458563536	408	0.7132867132867133	358	0.47229551451187335	C	3.925	-0.017394	0.07681	0.226509	0.466977	ENSG00000173269	ENST00000372027;ENST00000443699	T	0.13196	2.61	3.93	-5.26	0.02772	.	1.607910	0.03256	N	0.182630	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.35525	-0.9785	9	0.07482	T	0.82	-3.0939	6.0887	0.19983	0.0:0.4018:0.1377:0.4604	rs3750823;rs3750823	49	Q9H8L6	MMRN2_HUMAN	S	49	ENSP00000361097:G49S	ENSP00000361097:G49S	G	-	1	0	MMRN2	88707134	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-1.357000	0.02607	-0.985000	0.03503	-0.379000	0.06801	GGC	C|0.595;T|0.405	0.405	strong		0.622	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
SYMPK	8189	hgsc.bcm.edu	37	19	46352122	46352122	+	Silent	SNP	A	A	G	rs2303014	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46352122A>G	ENST00000245934.7	-	6	556	c.312T>C	c.(310-312)atT>atC	p.I104I		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	104	Interaction with HSF1.				cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		GCAGCAACTCAATGTCTCGCT	0.512													A|||	619	0.123602	0.031	0.2233	5008	,	,		24932	0.0952		0.1581	False		,,,				2504	0.1718				p.I104I		Atlas-SNP	.											SYMPK,colon,carcinoma,-2,1	SYMPK	104	1	0			c.T312C						PASS	.	A		237,4169	138.8+/-174.5	5,227,1971	144.0	124.0	131.0		312	-5.2	0.9	19	dbSNP_100	131	1270,7330	253.2+/-279.0	98,1074,3128	no	coding-synonymous	SYMPK	NM_004819.2		103,1301,5099	GG,GA,AA		14.7674,5.379,11.587		104/1275	46352122	1507,11499	2203	4300	6503	SO:0001819	synonymous_variant	8189	exon6			CAACTCAATGTCT	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.312T>C	19.37:g.46352122A>G		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	200	93	0.465	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			A|0.892;G|0.108	0.108	strong		0.512	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
CDH11	1009	hgsc.bcm.edu	37	16	65022234	65022234	+	Missense_Mutation	SNP	C	C	T	rs1130821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:65022234C>T	ENST00000268603.4	-	7	1440	c.825G>A	c.(823-825)atG>atA	p.M275I	CDH11_ENST00000394156.3_Missense_Mutation_p.M275I|CDH11_ENST00000566827.1_Missense_Mutation_p.M149I	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	275	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		M -> I (in dbSNP:rs1130821). {ECO:0000269|PubMed:8163513}.		adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CTGACACAGACATCTGGTATA	0.383			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			C|||	1088	0.217252	0.1014	0.3127	5008	,	,		20877	0.4216		0.1322	False		,,,				2504	0.183				p.M275I		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	CDH11	260	.	0			c.G825A						PASS	.	C	ILE/MET	469,3937	222.3+/-239.2	29,411,1763	153.0	141.0	145.0		825	5.8	1.0	16	dbSNP_86	145	1030,7570	219.4+/-257.5	61,908,3331	yes	missense	CDH11	NM_001797.2	10	90,1319,5094	TT,TC,CC		11.9767,10.6446,11.5254	probably-damaging	275/797	65022234	1499,11507	2203	4300	6503	SO:0001583	missense	1009	exon7			CACAGACATCTGG	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.825G>A	16.37:g.65022234C>T	ENSP00000268603:p.Met275Ile	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	198	100	0.50505	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	488	0.22344322344322345	64	0.13008130081300814	89	0.24585635359116023	230	0.4020979020979021	105	0.13852242744063326	C	29.0	4.964541	0.92791	0.106446	0.119767	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.01647	4.71;4.71	5.75	5.75	0.90469	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.17901	0.54	0.09310	P	0.9999999366822	P;B	0.50943	0.94;0.221	P;B	0.53649	0.731;0.209	T	0.67492	-0.5657	9	0.62326	D	0.03	.	18.9282	0.92553	0.0:1.0:0.0:0.0	rs1130821;rs3190128;rs4424934;rs17413248;rs52807906;rs57534627;rs4424934	275;275	P55287-2;P55287	.;CAD11_HUMAN	I	275;275;258	ENSP00000268603:M275I;ENSP00000377711:M275I	ENSP00000268603:M275I	M	-	3	0	CDH11	63579735	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.930000	0.56522	2.721000	0.93114	0.650000	0.86243	ATG	T|0.115;G|0.155;C|0.690;A|0.041	0.115	strong		0.383	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
F5	2153	hgsc.bcm.edu	37	1	169510475	169510475	+	Missense_Mutation	SNP	G	G	T	rs1046712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:169510475G>T	ENST00000367797.3	-	13	4054	c.3853C>A	c.(3853-3855)Ctt>Att	p.L1285I	F5_ENST00000367796.3_Missense_Mutation_p.L1290I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1285	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.		L -> I (in dbSNP:rs1046712). {ECO:0000269|PubMed:2827731, ECO:0000269|PubMed:8713778, ECO:0000269|Ref.3}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TCTAGAGAAAGGGTTGTATGG	0.522													G|||	825	0.164736	0.1611	0.1441	5008	,	,		20586	0.1131		0.1819	False		,,,				2504	0.2198				p.L1285I		Atlas-SNP	.											.	F5	301	.	0			c.C3853A						PASS	.	G	ILE/LEU	775,3631	313.8+/-293.3	79,617,1507	218.0	236.0	230.0		3853	-1.4	0.0	1	dbSNP_86	230	1502,7098	283.1+/-295.9	127,1248,2925	yes	missense	F5	NM_000130.4	5	206,1865,4432	TT,TG,GG		17.4651,17.5897,17.5073	benign	1285/2225	169510475	2277,10729	2203	4300	6503	SO:0001583	missense	2153	exon13			GAGAAAGGGTTGT	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.3853C>A	1.37:g.169510475G>T	ENSP00000356771:p.Leu1285Ile	Somatic	570	0	0		WXS	Illumina HiSeq	Phase_I	653	329	0.503828	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	322	0.14743589743589744	63	0.12804878048780488	53	0.1464088397790055	68	0.11888111888111888	138	0.1820580474934037	G	2.831	-0.242704	0.05906	0.175897	0.174651	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.37411	1.2;1.2	4.19	-1.42	0.08913	.	1.645520	0.02890	N	0.134092	T	0.07728	0.0194	L	0.35542	1.07	0.20307	N	0.999913	B	0.10296	0.003	B	0.06405	0.002	T	0.13072	-1.0523	9	0.21540	T	0.41	1.3999	0.7167	0.00933	0.1828:0.2731:0.2328:0.3113	rs1046712;rs9332606	1285	P12259	FA5_HUMAN	I	1285;1290	ENSP00000356771:L1285I;ENSP00000356770:L1290I	ENSP00000356770:L1290I	L	-	1	0	F5	167777099	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.152000	0.16302	-0.125000	0.11703	-1.513000	0.00942	CTT	G|0.827;T|0.173	0.173	strong		0.522	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
CPS1	1373	hgsc.bcm.edu	37	2	211540507	211540507	+	Missense_Mutation	SNP	C	C	A	rs1047891	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:211540507C>A	ENST00000233072.5	+	36	4413	c.4217C>A	c.(4216-4218)aCc>aAc	p.T1406N	CPS1_ENST00000430249.2_Missense_Mutation_p.T1412N|CPS1_ENST00000451903.2_Missense_Mutation_p.T955N	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1406			T -> N (associated with PHN susceptibility; 30-40% higher activity; also highly associated with hepatocellular carcinoma (HCC) progression; dbSNP:rs1047891). {ECO:0000269|PubMed:11407344, ECO:0000269|PubMed:12853138, ECO:0000269|PubMed:12955727, ECO:0000269|PubMed:1840546, ECO:0000269|PubMed:20520828, ECO:0000269|PubMed:21767969, ECO:0000269|PubMed:24237036}.		anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GTCCCTGCCACCCCAGTGGCA	0.443													C|||	1445	0.288538	0.3684	0.3429	5008	,	,		16610	0.1389		0.3012	False		,,,				2504	0.2832				p.T1412N		Atlas-SNP	.											.	CPS1	485	.	0			c.C4235A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR	1605,2801	497.2+/-363.8	305,995,903	68.0	68.0	68.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4235,2864,4217	5.2	1.0	2	dbSNP_86	68	2676,5924	428.0+/-355.8	422,1832,2046	yes	missense,missense,missense	CPS1	NM_001122633.2,NM_001122634.2,NM_001875.4	65,65,65	727,2827,2949	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	31.1163,36.4276,32.9156	benign,benign,benign	1412/1507,955/1050,1406/1501	211540507	4281,8725	2203	4300	6503	SO:0001583	missense	1373	exon37			CTGCCACCCCAGT	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.4217C>A	2.37:g.211540507C>A	ENSP00000233072:p.Thr1406Asn	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	586	0.2683150183150183	154	0.3130081300813008	122	0.3370165745856354	81	0.14160839160839161	229	0.3021108179419525	C	14.03	2.413514	0.42817	0.364276	0.311163	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.82984	-1.67;-1.67;-1.67	6.08	5.2	0.72013	Methylglyoxal synthase-like domain (4);	0.301714	0.35124	N	0.003423	T	0.00012	0.0000	L	0.48877	1.53	0.37459	P	0.08485100000000001	B;B	0.14012	0.009;0.009	B;B	0.19391	0.025;0.025	T	0.08371	-1.0725	9	0.32370	T	0.25	-11.1012	9.5512	0.39310	0.1496:0.7771:0.0:0.0732	rs1047891;rs2229587;rs3187890;rs7422339;rs52831019;rs7422339	1416;1406	Q59HF8;P31327	.;CPSM_HUMAN	N	1412;1414;1406;955	ENSP00000402608:T1412N;ENSP00000233072:T1406N;ENSP00000406136:T955N	ENSP00000233072:T1406N	T	+	2	0	CPS1	211248752	0.977000	0.34250	1.000000	0.80357	0.981000	0.71138	1.756000	0.38390	1.580000	0.49851	0.591000	0.81541	ACC	C|0.699;A|0.301	0.301	strong		0.443	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
RPGRIP1	57096	hgsc.bcm.edu	37	14	21770681	21770681	+	Silent	SNP	A	A	G	rs17792599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21770681A>G	ENST00000400017.2	+	4	525	c.525A>G	c.(523-525)ccA>ccG	p.P175P	RPGRIP1_ENST00000206660.6_Silent_p.P175P|RPGRIP1_ENST00000557771.1_Silent_p.P175P|RPGRIP1_ENST00000556336.1_Silent_p.P175P	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	175					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		CAGCCCCTCCATCGTTTAAGG	0.478													A|||	678	0.135383	0.1362	0.1527	5008	,	,		18254	0.0933		0.1889	False		,,,				2504	0.1104				p.P175P		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.A525G						PASS	.	A		476,3398		26,424,1487	51.0	51.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	525	-4.8	0.0	14	dbSNP_123	51	1565,6715		163,1239,2738	no	coding-synonymous	RPGRIP1	NM_020366.3		189,1663,4225	GG,GA,AA		18.901,12.287,16.7928		175/1287	21770681	2041,10113	1937	4140	6077	SO:0001819	synonymous_variant	57096	exon4			CCCTCCATCGTTT	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.525A>G	14.37:g.21770681A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	51	0.451327	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1																																																																																			A|0.857;G|0.142	0.142	strong		0.478	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
CTNNAL1	8727	hgsc.bcm.edu	37	9	111755008	111755008	+	Silent	SNP	C	C	T	rs2297581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:111755008C>T	ENST00000325551.4	-	3	509	c.423G>A	c.(421-423)gtG>gtA	p.V141V	CTNNAL1_ENST00000374595.4_Silent_p.V141V|CTNNAL1_ENST00000325580.6_Silent_p.V141V|RNA5-8SP3_ENST00000364357.1_RNA|CTNNAL1_ENST00000374593.4_Silent_p.V141V	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	141					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		CAGCCTTTATCACTCCTGTTT	0.378													C|||	993	0.198283	0.0166	0.3228	5008	,	,		21396	0.3145		0.2674	False		,,,				2504	0.1646				p.V141V		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.G423A						PASS	.	C		255,4151	145.4+/-180.2	16,223,1964	128.0	120.0	123.0		423	-7.3	0.9	9	dbSNP_100	123	2434,6166	402.8+/-347.6	333,1768,2199	no	coding-synonymous	CTNNAL1	NM_003798.2		349,1991,4163	TT,TC,CC		28.3023,5.7876,20.6751		141/735	111755008	2689,10317	2203	4300	6503	SO:0001819	synonymous_variant	8727	exon3			CTTTATCACTCCT	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"""alpha-catulin"", ""alpha2-catulin"""	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.423G>A	9.37:g.111755008C>T		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	264	112	0.424242	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Silent	SNP	ENST00000325551.4	37	CCDS6775.1																																																																																			C|0.775;A|0.002	.	strong		0.378	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798	
LANCL3	347404	hgsc.bcm.edu	37	X	37527659	37527659	+	Intron	SNP	T	T	C	rs28503960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:37527659T>C	ENST00000378619.3	+	4	1322				TM4SF2_ENST00000465127.1_Intron|LANCL3_ENST00000378621.3_Missense_Mutation_p.L381P	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)								catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						gaacatctgctgtataccaga	0.294													T|||	568	0.150464	0.1256	0.0994	3775	,	,		9346	0.0496		0.1123	False		,,,				2504	0.1738				p.L381P		Atlas-SNP	.											.	LANCL3	42	.	0			c.T1142C						PASS	.	T	,PRO/LEU	697,3136		55,490,97,1086,474	54.0	49.0	51.0		,1142	2.2	0.0	X	dbSNP_125	51	1168,5558		84,695,305,1648,1567	yes	intron,missense	LANCL3	NM_001170331.1,NM_198511.2	,98	139,1185,402,2734,2041	CC,CT,C,TT,T		17.3654,18.1842,17.6627	,benign	,381/389	37527659	1865,8694	2202	4299	6501	SO:0001627	intron_variant	347404	exon5			ATCTGCTGTATAC	AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.1103+917T>C	X.37:g.37527659T>C		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_198511	A6NHE3	Missense_Mutation	SNP	ENST00000378619.3	37	CCDS55398.1	214	0.1289933694996986	46	0.10222222222222223	20	0.060240963855421686	16	0.02877697841726619	63	0.08898305084745763	T	4.137	0.023659	0.08006	0.181842	0.173654	ENSG00000147036	ENST00000378621	.	.	.	2.17	2.17	0.27698	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.32968	0.392	B	0.27500	0.08	T	0.13872	-1.0493	6	0.30078	T	0.28	.	5.629	0.17499	0.0:0.0:0.0:1.0	rs28503960	381	Q6ZV70-2	.	P	381	.	ENSP00000367885:L381P	L	+	2	0	LANCL3	37412578	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.193000	0.17116	1.111000	0.41721	0.430000	0.28490	CTG	T|0.847;C|0.153	0.153	strong		0.294	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511	
ARHGAP21	57584	hgsc.bcm.edu	37	10	24908668	24908668	+	Missense_Mutation	SNP	T	T	C	rs142573508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:24908668T>C	ENST00000396432.2	-	9	2642	c.2156A>G	c.(2155-2157)cAa>cGa	p.Q719R	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.Q506R	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	718					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						TTCAGCCTCTTGTAAACTTAA	0.453													T|||	11	0.00219649	0.0	0.0	5008	,	,		19618	0.0		0.0	False		,,,				2504	0.0112				p.Q719R		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.A2156G						PASS	.	T	ARG/GLN	0,4406		0,0,2203	61.0	58.0	59.0		2156	-2.6	0.0	10	dbSNP_134	59	2,8598	2.2+/-6.3	0,2,4298	no	missense	ARHGAP21	NM_020824.3	43	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign	719/1959	24908668	2,13004	2203	4300	6503	SO:0001583	missense	57584	exon9			GCCTCTTGTAAAC	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.2156A>G	10.37:g.24908668T>C	ENSP00000379709:p.Gln719Arg	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	143	65	0.454545	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	T	4.856	0.159203	0.09236	0.0	2.33E-4	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.1	-2.62	0.06152	.	1.071100	0.07121	N	0.843866	T	0.24774	0.0601	L	0.31294	0.92	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.24190	-1.0167	10	0.16420	T	0.52	.	5.0428	0.14467	0.1188:0.0718:0.4868:0.3226	.	709;718	F8W9U9;Q5T5U3	.;RHG21_HUMAN	R	719;506;709;719;554	ENSP00000379709:Q719R;ENSP00000365604:Q506R;ENSP00000365592:Q709R;ENSP00000405018:Q719R	ENSP00000365604:Q506R	Q	-	2	0	ARHGAP21	24948674	0.004000	0.15560	0.043000	0.18650	0.866000	0.49608	0.189000	0.17037	-0.256000	0.09473	0.533000	0.62120	CAA	T|1.000;C|0.000	0.000	strong		0.453	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105363289	105363289	+	Silent	SNP	T	T	C	rs3740471	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:105363289T>C	ENST00000369774.4	-	15	1962	c.1686A>G	c.(1684-1686)gcA>gcG	p.A562A	SH3PXD2A_ENST00000540321.1_Silent_p.A429A|SH3PXD2A_ENST00000355946.2_Silent_p.A534A|SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000538130.1_Silent_p.A397A|SH3PXD2A_ENST00000427662.2_Intron			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	562					superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		CAAAGCCGAATGCAGGGATGT	0.677													T|||	679	0.135583	0.0643	0.1628	5008	,	,		15829	0.1548		0.1998	False		,,,				2504	0.1268				p.A534A		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.A1602G						PASS	.	T		389,4017	191.9+/-217.4	21,347,1835	42.0	46.0	45.0		1602	1.3	1.0	10	dbSNP_107	45	1922,6678	333.3+/-320.5	216,1490,2594	yes	coding-synonymous	SH3PXD2A	NM_014631.2		237,1837,4429	CC,CT,TT		22.3488,8.8289,17.7687		534/1106	105363289	2311,10695	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			GCCGAATGCAGGG	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.1686A>G	10.37:g.105363289T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		333	0.15247252747252749	22	0.044715447154471545	53	0.1464088397790055	98	0.17132867132867133	160	0.21108179419525067	T	0.325	-0.959357	0.02267	0.088289	0.223488	ENSG00000107957	ENST00000420222	.	.	.	5.47	1.31	0.21738	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999847	.	.	.	.	.	.	T	0.22521	-1.0214	3	.	.	.	-30.7092	2.7623	0.05310	0.1377:0.114:0.4585:0.2898	rs3740471;rs17738234;rs56448553;rs3740471	.	.	.	V	489	.	.	I	-	1	0	SH3PXD2A	105353279	1.000000	0.71417	0.994000	0.49952	0.225000	0.24961	1.815000	0.38981	0.211000	0.20683	-0.441000	0.05720	ATT	T|0.835;C|0.165	0.165	strong		0.677	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
MKI67	4288	hgsc.bcm.edu	37	10	129904286	129904286	+	Missense_Mutation	SNP	G	G	A	rs146273614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:129904286G>A	ENST00000368654.3	-	13	6193	c.5818C>T	c.(5818-5820)Cgg>Tgg	p.R1940W	MKI67_ENST00000368653.3_Missense_Mutation_p.R1580W	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1940	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GTTTGTGGCCGTCTCTTGCTG	0.493													G|||	15	0.00299521	0.0	0.0072	5008	,	,		18668	0.0		0.0089	False		,,,				2504	0.001				p.R1940W		Atlas-SNP	.											.	MKI67	363	.	0			c.C5818T						PASS	.	G	TRP/ARG,TRP/ARG	7,4399	14.3+/-33.2	0,7,2196	173.0	179.0	177.0		4738,5818	-8.8	0.0	10	dbSNP_134	177	78,8522	46.7+/-105.8	0,78,4222	no	missense,missense	MKI67	NM_001145966.1,NM_002417.4	101,101	0,85,6418	AA,AG,GG		0.907,0.1589,0.6535	benign,benign	1580/2897,1940/3257	129904286	85,12921	2203	4300	6503	SO:0001583	missense	4288	exon13			GTGGCCGTCTCTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.5818C>T	10.37:g.129904286G>A	ENSP00000357643:p.Arg1940Trp	Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	403	163	0.404467	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	9.208	1.030151	0.19512	0.001589	0.00907	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02446	4.29;4.29	4.42	-8.82	0.00810	.	.	.	.	.	T	0.01320	0.0043	L	0.35854	1.095	0.09310	N	1	B;B;B	0.30104	0.006;0.268;0.012	B;B;B	0.21360	0.005;0.034;0.005	T	0.26950	-1.0088	9	0.59425	D	0.04	.	4.3783	0.11281	0.1014:0.0852:0.3233:0.4901	.	1939;1580;1940	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	W	1940;1580;1939	ENSP00000357643:R1940W;ENSP00000357642:R1580W	ENSP00000357642:R1580W	R	-	1	2	MKI67	129794276	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.725000	0.01863	-2.749000	0.00375	-2.677000	0.00143	CGG	G|0.994;A|0.006	0.006	strong		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
LRCH1	23143	hgsc.bcm.edu	37	13	47279258	47279258	+	Missense_Mutation	SNP	G	G	T	rs11617392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:47279258G>T	ENST00000389798.3	+	12	1653	c.1456G>T	c.(1456-1458)Gca>Tca	p.A486S	LRCH1_ENST00000311191.6_Missense_Mutation_p.A486S|LRCH1_ENST00000389797.3_Missense_Mutation_p.A486S	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	486			A -> S (in dbSNP:rs11617392).							breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		TATGGGATCAGCAGAAGCCTT	0.294													G|||	39	0.00778754	0.0008	0.0072	5008	,	,		17206	0.0		0.0288	False		,,,				2504	0.0041				p.A486S		Atlas-SNP	.											.	LRCH1	104	.	0			c.G1456T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	26,4380	32.6+/-62.9	0,26,2177	112.0	124.0	120.0		1456,1456,1456	5.1	0.9	13	dbSNP_120	120	273,8327	102.5+/-163.7	4,265,4031	yes	missense,missense,missense	LRCH1	NM_001164211.1,NM_001164213.1,NM_015116.2	99,99,99	4,291,6208	TT,TG,GG		3.1744,0.5901,2.2989	benign,benign,benign	486/764,486/697,486/729	47279258	299,12707	2203	4300	6503	SO:0001583	missense	23143	exon12			GGATCAGCAGAAG	AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"""calponin homology (CH) domain containing 1"""	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.1456G>T	13.37:g.47279258G>T	ENSP00000374448:p.Ala486Ser	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	214	93	0.434579	NM_015116	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	ENST00000389798.3	37	CCDS31972.1	30	0.013736263736263736	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	25	0.032981530343007916	G	7.774	0.708144	0.15239	0.005901	0.031744	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.55052	0.54;0.59;0.59	5.95	5.1	0.69264	.	0.509560	0.21773	N	0.069329	T	0.24812	0.0602	M	0.67953	2.075	0.23186	N	0.998159	B;B;B;B	0.14805	0.0;0.011;0.001;0.011	B;B;B;B	0.17098	0.004;0.017;0.009;0.005	T	0.31806	-0.9930	10	0.09338	T	0.73	-1.0147	13.4916	0.61399	0.0:0.0:0.8433:0.1566	rs11617392;rs17281816;rs52819157;rs61459892;rs11617392	486;486;486;486	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	S	486	ENSP00000308493:A486S;ENSP00000374448:A486S;ENSP00000374447:A486S	ENSP00000308493:A486S	A	+	1	0	LRCH1	46177259	0.993000	0.37304	0.907000	0.35723	0.457000	0.32468	1.831000	0.39141	1.490000	0.48466	0.655000	0.94253	GCA	G|0.982;T|0.018	0.018	strong		0.294	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116	
MUC4	4585	hgsc.bcm.edu	37	3	195507999	195507999	+	Silent	SNP	A	A	T	rs200187145		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195507999A>T	ENST00000463781.3	-	2	10911	c.10452T>A	c.(10450-10452)ggT>ggA	p.G3484G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.G3484G	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGTGTGACCTGTAGATG	0.592																																					p.G3484G		Atlas-SNP	.											.	MUC4	1505	.	0			c.T10452A						PASS	.						28.0	25.0	26.0					3																	195507999		671	1576	2247	SO:0001819	synonymous_variant	4585	exon2			GGTGTGACCTGTA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10452T>A	3.37:g.195507999A>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	319	108	0.338558	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SSTR4	6754	hgsc.bcm.edu	37	20	23017082	23017082	+	Missense_Mutation	SNP	T	T	C	rs2567608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:23017082T>C	ENST00000255008.3	+	1	1026	c.962T>C	c.(961-963)tTc>tCc	p.F321S	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	321			F -> S (in dbSNP:rs2567608). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8483934, ECO:0000269|PubMed:8512564, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					TTCCGCCGATTCTTCCAGCGG	0.577													C|||	2602	0.519569	0.5303	0.4726	5008	,	,		18159	0.5466		0.4304	False		,,,				2504	0.6022				p.F321S	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,colon,carcinoma,0,1	SSTR4	83	1	0			c.T962C						PASS	.	C	SER/PHE	2237,2157	530.0+/-372.8	585,1067,545	73.0	79.0	77.0		962	3.7	0.2	20	dbSNP_100	77	3917,4683	587.0+/-392.1	925,2067,1308	yes	missense	SSTR4	NM_001052.2	155	1510,3134,1853	CC,CT,TT		45.5465,49.0897,47.3603	benign	321/389	23017082	6154,6840	2197	4300	6497	SO:0001583	missense	6754	exon1			GCCGATTCTTCCA		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.962T>C	20.37:g.23017082T>C	ENSP00000255008:p.Phe321Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	1113	0.5096153846153846	272	0.5528455284552846	177	0.4889502762430939	343	0.5996503496503497	321	0.4234828496042216	C	0.006	-2.097028	0.00360	0.509103	0.455465	ENSG00000132671	ENST00000255008	T	0.35973	1.28	3.65	3.65	0.41850	.	0.000000	0.64402	N	0.000016	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47195	-0.9136	9	0.02654	T	1	.	9.9983	0.41913	0.0:0.8974:0.0:0.1026	rs2567608;rs3746729;rs60934281;rs2567608	321	P31391	SSR4_HUMAN	S	321	ENSP00000255008:F321S	ENSP00000255008:F321S	F	+	2	0	SSTR4	22965082	0.010000	0.17322	0.154000	0.22540	0.215000	0.24574	1.591000	0.36665	0.739000	0.32628	-0.119000	0.15052	TTC	T|0.474;C|0.526	0.526	strong		0.577	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
ZNF880	400713	hgsc.bcm.edu	37	19	52887437	52887437	+	Missense_Mutation	SNP	A	A	C	rs8104812	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52887437A>C	ENST00000422689.2	+	4	619	c.604A>C	c.(604-606)Aat>Cat	p.N202H		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	202					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						ACTTGCTAACAATCAAGTAAT	0.373													C|||	1897	0.378794	0.2405	0.379	5008	,	,		20813	0.3462		0.4205	False		,,,				2504	0.5562				p.N202H		Atlas-SNP	.											.	ZNF880	45	.	0			c.A604C						PASS	.	C	HIS/ASN	392,992		53,286,353	47.0	46.0	46.0		604	0.7	0.0	19	dbSNP_116	46	1214,1968		222,770,599	yes	missense	ZNF880	NM_001145434.1	68	275,1056,952	CC,CA,AA		38.1521,28.3237,35.173	benign	202/578	52887437	1606,2960	692	1591	2283	SO:0001583	missense	400713	exon4			GCTAACAATCAAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.604A>C	19.37:g.52887437A>C	ENSP00000406318:p.Asn202His	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	745	0.3411172161172161	119	0.241869918699187	138	0.3812154696132597	177	0.3094405594405594	311	0.4102902374670185	C	0.005	-2.223193	0.00283	0.283237	0.381521	ENSG00000221923	ENST00000422689	T	0.12879	2.64	1.84	0.682	0.17992	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00005	-3.26	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41698	-0.9494	7	.	.	.	.	5.3499	0.16030	0.2302:0.5451:0.2247:0.0	rs8104812;rs17736363;rs8104812	202	Q6PDB4	ZN880_HUMAN	H	202	ENSP00000406318:N202H	.	N	+	1	0	ZNF880	57579249	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.069000	0.14552	-0.288000	0.09051	-1.160000	0.01791	AAT	A|0.655;C|0.345	0.345	strong		0.373	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ACP1	52	hgsc.bcm.edu	37	2	277003	277003	+	Missense_Mutation	SNP	A	A	G	rs79716074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:277003A>G	ENST00000272065.5	+	5	410	c.317A>G	c.(316-318)cAa>cGa	p.Q106R	ACP1_ENST00000484464.1_3'UTR|ACP1_ENST00000272067.6_Missense_Mutation_p.Q106R	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble	106			Q -> R (in allele ACP1*A; dbSNP:rs7576247). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	AAAAGTAATCAAGTTAAAACC	0.323													A|||	1323	0.264177	0.2065	0.2363	5008	,	,		18004	0.246		0.335	False		,,,				2504	0.3078				p.Q106R		Atlas-SNP	.											ACP1_ENST00000272067,NS,carcinoma,+1,4	ACP1	42	4	0			c.A317G						PASS	.	A	ARG/GLN,ARG/GLN	983,3417	336.0+/-304.2	107,769,1324	52.0	55.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	317,317	3.1	1.0	2	dbSNP_131	54	2959,5631	442.4+/-360.1	483,1993,1819	yes	missense,missense	ACP1	NM_004300.3,NM_007099.3	43,43	590,2762,3143	GG,GA,AA		34.447,22.3409,30.3464	benign,benign	106/159,106/159	277003	3942,9048	2200	4295	6495	SO:0001583	missense	52	exon5			GTAATCAAGTTAA	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"""Protein tyrosine phosphatases / Class II Cys-based PTPs"""	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.317A>G	2.37:g.277003A>G	ENSP00000272065:p.Gln106Arg	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	178	84	0.47191	NM_007099	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Missense_Mutation	SNP	ENST00000272065.5	37	CCDS1639.1	551	0.2522893772893773	87	0.17682926829268292	87	0.24033149171270718	126	0.2202797202797203	251	0.3311345646437995	A	11.29	1.595656	0.28445	0.223409	0.34447	ENSG00000143727	ENST00000272067;ENST00000272065	T;T	0.16457	2.34;2.34	5.48	3.09	0.35607	Phosphotyrosine protein phosphatase I superfamily (3);	0.404011	0.29624	N	0.011622	T	0.00012	0.0000	N	0.05414	-0.055	0.09310	P	0.9999999842883	B;B	0.10296	0.0;0.003	B;B	0.14578	0.003;0.011	T	0.49679	-0.8914	9	0.23302	T	0.38	-2.9532	6.7926	0.23707	0.7665:0.1527:0.0807:0.0	rs7576247;rs17357270;rs59972259	106;106	P24666-2;P24666	.;PPAC_HUMAN	R	106	ENSP00000272067:Q106R;ENSP00000272065:Q106R	ENSP00000272065:Q106R	Q	+	2	0	ACP1	267003	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.840000	0.48215	0.370000	0.24538	0.533000	0.62120	CAA	A|0.725;G|0.275	0.275	strong		0.323	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3		
MTRF1L	54516	hgsc.bcm.edu	37	6	153315695	153315695	+	Missense_Mutation	SNP	C	C	T	rs3192723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:153315695C>T	ENST00000367233.5	-	4	639	c.640G>A	c.(640-642)Gtc>Atc	p.V214I	MTRF1L_ENST00000367230.1_Missense_Mutation_p.V178I|MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367231.5_Missense_Mutation_p.V214I	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	214			V -> I (in dbSNP:rs3192723).			mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		CTAGTATGGACGCGGCCTTGC	0.507													C|||	1186	0.236821	0.2663	0.3026	5008	,	,		15054	0.1498		0.162	False		,,,				2504	0.317				p.V214I		Atlas-SNP	.											.	MTRF1L	21	.	0			c.G640A						PASS	.	C	ILE/VAL,ILE/VAL	1094,3312	393.1+/-328.7	134,826,1243	185.0	161.0	169.0		640,640	-0.0	1.0	6	dbSNP_105	169	1540,7060	290.1+/-299.6	149,1242,2909	no	missense,missense	MTRF1L	NM_001114184.1,NM_019041.5	29,29	283,2068,4152	TT,TC,CC		17.907,24.8298,20.2522	benign,benign	214/272,214/381	153315695	2634,10372	2203	4300	6503	SO:0001583	missense	54516	exon4			TATGGACGCGGCC	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.640G>A	6.37:g.153315695C>T	ENSP00000356202:p.Val214Ile	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	183	80	0.437158	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	37	CCDS5243.1	444	0.2032967032967033	138	0.2804878048780488	108	0.2983425414364641	76	0.13286713286713286	122	0.16094986807387862	C	4.256	0.046602	0.08243	0.248298	0.17907	ENSG00000112031	ENST00000367233;ENST00000367231;ENST00000367230;ENST00000414771;ENST00000448966	T;T;T;T;T	0.10668	2.85;2.85;2.85;2.85;2.85	5.18	-0.0148	0.13979	.	0.373796	0.34291	N	0.004098	T	0.00784	0.0026	N	0.02169	-0.655	0.46113	P	0.0011250000000000426	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.47420	-0.9119	9	0.02654	T	1	-2.1994	9.1054	0.36694	0.0:0.285:0.0:0.715	rs3192723;rs3799134;rs6942312;rs52828127;rs3192723	214;178;214	Q9UGC7-2;Q9UGC7-4;Q9UGC7	.;.;RF1ML_HUMAN	I	214;214;178;65;78	ENSP00000356202:V214I;ENSP00000356200:V214I;ENSP00000356199:V178I;ENSP00000414383:V65I;ENSP00000415113:V78I	ENSP00000356199:V178I	V	-	1	0	MTRF1L	153357388	1.000000	0.71417	0.979000	0.43373	0.903000	0.53119	1.945000	0.40273	-0.140000	0.11394	-0.324000	0.08512	GTC	C|0.800;T|0.200	0.200	strong		0.507	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197549	39197549	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39197549G>C	ENST00000306271.4	-	1	164	c.101C>G	c.(100-102)tCc>tGc	p.S34C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	34			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.S34C(6)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGGAGCTGGTCTC	0.612																																					p.S34C		Atlas-SNP	.											KRTAP1-1,NS,carcinoma,0,7	KRTAP1-1	23	7	6	Substitution - Missense(6)	kidney(4)|lung(1)|prostate(1)	c.C101G						scavenged	.						49.0	62.0	58.0					17																	39197549		2018	4199	6217	SO:0001583	missense	81851	exon1			TGGCAGGAGCTGG	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.101C>G	17.37:g.39197549G>C	ENSP00000305975:p.Ser34Cys	Somatic	113	2	0.0176991		WXS	Illumina HiSeq	Phase_I	253	58	0.229249	NM_030967	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	G	0.085	-1.176298	0.01646	.	.	ENSG00000188581	ENST00000306271	T	0.16196	2.36	3.91	1.65	0.23941	.	.	.	.	.	T	0.01835	0.0058	N	0.00010	-3.04	0.22552	N	0.998996	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	9	0.02654	T	1	.	7.8006	0.29172	0.1777:0.6415:0.1808:0.0	.	34	Q07627	KRA11_HUMAN	C	34	ENSP00000305975:S34C	ENSP00000305975:S34C	S	-	2	0	KRTAP1-1	36451075	1.000000	0.71417	0.987000	0.45799	0.816000	0.46133	1.227000	0.32576	0.919000	0.36945	-0.233000	0.12211	TCC	.	.	none		0.612	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
PCSK5	5125	hgsc.bcm.edu	37	9	78638797	78638797	+	Splice_Site	SNP	C	C	T	rs34417623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:78638797C>T	ENST00000545128.1	+	4	1093	c.555C>T	c.(553-555)taC>taT	p.Y185Y	PCSK5_ENST00000376767.3_Splice_Site_p.Y185Y|PCSK5_ENST00000376752.4_Splice_Site_p.Y185Y	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	185	Peptidase S8.				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						TGCAAAACTACGTGAGTGTAT	0.438													C|||	43	0.00858626	0.0174	0.0029	5008	,	,		19983	0.0		0.0129	False		,,,				2504	0.0051				p.Y185Y		Atlas-SNP	.											.	PCSK5	329	.	0			c.C555T						PASS	.	C	,	42,4364	46.0+/-80.4	1,40,2162	173.0	150.0	158.0		555,555	-11.3	0.3	9	dbSNP_126	158	110,8490	58.7+/-120.3	3,104,4193	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PCSK5	NM_001190482.1,NM_006200.3	,	4,144,6355	TT,TC,CC		1.2791,0.9532,1.1687	,	185/1861,185/914	78638797	152,12854	2203	4300	6503	SO:0001630	splice_region_variant	5125	exon4			AAACTACGTGAGT		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.555+1C>T	9.37:g.78638797C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			C|0.989;T|0.011	0.011	strong		0.438	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Silent
OR13C9	286362	hgsc.bcm.edu	37	9	107380414	107380414	+	Missense_Mutation	SNP	C	C	A	rs2900373	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107380414C>A	ENST00000259362.1	-	1	71	c.72G>T	c.(70-72)gaG>gaT	p.E24D		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	24			E -> D (in dbSNP:rs2900373).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AAAAGAGTAACTCAAGCCTTG	0.403													C|||	2138	0.426917	0.6142	0.2262	5008	,	,		18141	0.5754		0.1779	False		,,,				2504	0.4192				p.E24D		Atlas-SNP	.											.	OR13C9	42	.	0			c.G72T						PASS	.	C	ASP/GLU	2419,1987	617.9+/-393.1	668,1083,452	127.0	125.0	125.0		72	3.9	1.0	9	dbSNP_101	125	1664,6936	306.9+/-308.1	183,1298,2819	no	missense	OR13C9	NM_001001956.1	45	851,2381,3271	AA,AC,CC		19.3488,45.0976,31.3932	possibly-damaging	24/319	107380414	4083,8923	2203	4300	6503	SO:0001583	missense	286362	exon1			GAGTAACTCAAGC		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.72G>T	9.37:g.107380414C>A	ENSP00000259362:p.Glu24Asp	Somatic	342	1	0.00292398		WXS	Illumina HiSeq	Phase_I	375	185	0.493333	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	826	0.3782051282051282	284	0.5772357723577236	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	C	11.21	1.571963	0.28092	0.549024	0.193488	ENSG00000136839	ENST00000259362	T	0.01092	5.35	4.79	3.89	0.44902	.	0.134094	0.33753	N	0.004592	T	0.00012	0.0000	M	0.69358	2.11	0.58432	P	1.0000000000287557E-6	B	0.28971	0.229	B	0.25614	0.062	T	0.10941	-1.0608	9	0.87932	D	0	.	10.9252	0.47187	0.0:0.9082:0.0:0.0918	rs2900373;rs56843910;rs2900373	24	Q8NGT0	O13C9_HUMAN	D	24	ENSP00000259362:E24D	ENSP00000259362:E24D	E	-	3	2	OR13C9	106420235	0.557000	0.26546	0.982000	0.44146	0.622000	0.37654	1.318000	0.33643	1.236000	0.43740	0.573000	0.79308	GAG	A|0.365;C|0.635	0.365	strong		0.403	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
LAG3	3902	hgsc.bcm.edu	37	12	6884585	6884585	+	Missense_Mutation	SNP	A	A	T	rs149434241	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6884585A>T	ENST00000203629.2	+	5	1261	c.928A>T	c.(928-930)Act>Tct	p.T310S	LAG3_ENST00000441671.2_Missense_Mutation_p.T310S	NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	310	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CCTCCTGGTGACTGGAGACAA	0.627													A|||	10	0.00199681	0.0	0.0043	5008	,	,		17324	0.0		0.007	False		,,,				2504	0.0				p.T310S		Atlas-SNP	.											.	LAG3	35	.	0			c.A928T						PASS	.	A	SER/THR	5,4401	11.4+/-27.6	0,5,2198	96.0	88.0	91.0		928	-2.2	1.0	12	dbSNP_134	91	74,8526	44.5+/-102.8	1,72,4227	yes	missense	LAG3	NM_002286.5	58	1,77,6425	TT,TA,AA		0.8605,0.1135,0.6074	benign	310/526	6884585	79,12927	2203	4300	6503	SO:0001583	missense	3902	exon5			CTGGTGACTGGAG		CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.928A>T	12.37:g.6884585A>T	ENSP00000203629:p.Thr310Ser	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	216	102	0.472222	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	A	6.623	0.483348	0.12581	0.001135	0.008605	ENSG00000089692	ENST00000441671;ENST00000203629	T;T	0.11169	2.8;2.8	5.55	-2.19	0.07015	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.731904	0.12659	N	0.449835	T	0.03390	0.0098	L	0.34521	1.04	0.09310	N	0.999994	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.43782	-0.9370	10	0.08599	T	0.76	-1.8946	2.0189	0.03505	0.235:0.2239:0.4154:0.1257	.	310;310	P18627;Q7Z643	LAG3_HUMAN;.	S	310	ENSP00000413825:T310S;ENSP00000203629:T310S	ENSP00000203629:T310S	T	+	1	0	LAG3	6754846	0.105000	0.21958	0.992000	0.48379	0.722000	0.41435	-0.198000	0.09505	-0.199000	0.10317	-1.741000	0.00685	ACT	A|0.994;T|0.006	0.006	strong		0.627	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1		
USP36	57602	hgsc.bcm.edu	37	17	76799860	76799860	+	Missense_Mutation	SNP	T	T	C	rs3088040	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76799860T>C	ENST00000542802.3	-	16	2860	c.2417A>G	c.(2416-2418)cAg>cGg	p.Q806R	USP36_ENST00000312010.6_Missense_Mutation_p.Q806R|USP36_ENST00000449938.2_Intron			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	806			Q -> R (in dbSNP:rs3088040). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			AGAGGGGCTCTGGGGGGGCTC	0.632													C|||	2856	0.570288	0.6006	0.4914	5008	,	,		14096	0.6111		0.5477	False		,,,				2504	0.5665				p.Q806R		Atlas-SNP	.											.	USP36	243	.	0			c.A2417G						PASS	.	C	ARG/GLN	2477,1853		769,939,457	38.0	45.0	43.0		2417	-8.6	0.0	17	dbSNP_102	43	4634,3874		1343,1948,963	yes	missense	USP36	NM_025090.3	43	2112,2887,1420	CC,CT,TT		45.5336,42.7945,44.6098	benign	806/1124	76799860	7111,5727	2165	4254	6419	SO:0001583	missense	57602	exon16			GGGCTCTGGGGGG	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2417A>G	17.37:g.76799860T>C	ENSP00000441214:p.Gln806Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	37	CCDS32755.1	1253	0.5737179487179487	305	0.6199186991869918	165	0.4558011049723757	358	0.6258741258741258	425	0.5606860158311345	C	0.010	-1.783789	0.00628	0.572055	0.544664	ENSG00000055483	ENST00000312010;ENST00000542802	T;T	0.06294	3.32;3.32	5.42	-8.65	0.00870	.	2.568530	0.00751	N	0.001065	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.41805	-0.9488	9	0.14656	T	0.56	0.0129	2.75	0.05277	0.1748:0.389:0.1773:0.2589	rs3088040;rs3169894;rs52835644;rs3088040	806;806	Q9P275;Q9P275-2	UBP36_HUMAN;.	R	806	ENSP00000310590:Q806R;ENSP00000441214:Q806R	ENSP00000310590:Q806R	Q	-	2	0	USP36	74311455	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.813000	0.01725	-2.360000	0.00610	-2.031000	0.00424	CAG	T|0.442;C|0.558	0.558	strong		0.632	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
TPO	7173	hgsc.bcm.edu	37	2	1499899	1499899	+	Silent	SNP	C	C	T	rs732608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:1499899C>T	ENST00000345913.4	+	12	2236	c.2145C>T	c.(2143-2145)ccC>ccT	p.P715P	TPO_ENST00000337415.3_Silent_p.P715P|TPO_ENST00000382198.1_Silent_p.P542P|TPO_ENST00000349624.3_Silent_p.P542P|TPO_ENST00000346956.3_Silent_p.P715P|TPO_ENST00000329066.4_Silent_p.P715P|TPO_ENST00000382201.3_Silent_p.P658P|TPO_ENST00000497517.2_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	715					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GCAAATTCCCCGAAGACTTTG	0.557													C|||	2198	0.438898	0.4349	0.4265	5008	,	,		14667	0.4087		0.4016	False		,,,				2504	0.5225				p.P715P		Atlas-SNP	.											TPO,NS,malignant_melanoma,+2,2	TPO	224	2	0			c.C2145T						PASS	.	C	,,,,,	1945,2461	550.5+/-378.0	434,1077,692	63.0	62.0	63.0		2145,2145,1974,1974,2145,1626	-5.7	0.0	2	dbSNP_86	63	3427,5173	502.0+/-375.6	672,2083,1545	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	1106,3160,2237	TT,TC,CC		39.8488,44.1443,41.304	,,,,,	715/934,715/934,658/877,658/877,715/890,542/761	1499899	5372,7634	2203	4300	6503	SO:0001819	synonymous_variant	7173	exon12			ATTCCCCGAAGAC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2145C>T	2.37:g.1499899C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1	918	0.42032967032967034	224	0.45528455284552843	152	0.4198895027624309	248	0.43356643356643354	294	0.38786279683377306	C	0.025	-1.379854	0.01204	0.441443	0.398488	ENSG00000115705	ENST00000446278	T	0.72394	-0.65	4.59	-5.71	0.02413	.	0.097704	0.64402	D	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999898673	.	.	.	.	.	.	T	0.29971	-0.9994	6	0.87932	D	0	-33.1603	2.7509	0.05280	0.2787:0.1316:0.0891:0.5007	rs732608;rs1042584;rs3182053;rs17731931;rs732608	.	.	.	L	190	ENSP00000400033:P190L	ENSP00000400033:P190L	P	+	2	0	TPO	1478906	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-1.559000	0.02162	-1.146000	0.02854	-1.066000	0.02275	CCG	C|0.585;A|0.003	.	strong		0.557	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
SH3GL1	6455	hgsc.bcm.edu	37	19	4362691	4362691	+	Silent	SNP	G	G	C	rs243261	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4362691G>C	ENST00000269886.3	-	8	949	c.771C>G	c.(769-771)ccC>ccG	p.P257P	AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000417295.2_Silent_p.P209P|SH3GL1_ENST00000598564.1_Silent_p.P193P	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	257					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		CCCGGGGCTTGGGCTTATACT	0.652			T	MLL	AL								G|||	1961	0.391573	0.3434	0.4063	5008	,	,		17905	0.6042		0.2744	False		,,,				2504	0.3476				p.P257P	NSCLC(94;1152 2133 30346 33362)	Atlas-SNP	.		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	SH3GL1	52	.	0			c.C771G						PASS	.	G	,,	1506,2900		270,966,967	58.0	56.0	57.0		627,579,771	-0.3	1.0	19	dbSNP_79	57	2423,6177		333,1757,2210	no	coding-synonymous,coding-synonymous,coding-synonymous	SH3GL1	NM_001199943.1,NM_001199944.1,NM_003025.3	,,	603,2723,3177	CC,CG,GG		28.1744,34.1807,30.2091	,,	209/321,193/305,257/369	4362691	3929,9077	2203	4300	6503	SO:0001819	synonymous_variant	6455	exon8			GGGCTTGGGCTTA		CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"""extra 11-19 leukemia fusion"", ""fusion partner of MLL"", ""SH3-containing Grb-2-like 1 protein"", ""SH3-containing protein EEN"", ""SH3 domain GRB2-like 1"""	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.771C>G	19.37:g.4362691G>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	28	0.4	NM_003025	B4DRA1|E7EVZ4|M0QZV5|Q99668	Silent	SNP	ENST00000269886.3	37	CCDS32874.1																																																																																			G|0.684;C|0.316	0.316	strong		0.652	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025	
DNAH14	127602	hgsc.bcm.edu	37	1	225521101	225521101	+	Intron	SNP	G	G	C	rs41268715	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:225521101G>C	ENST00000445597.2	+	45	7485				DNAH14_ENST00000439375.2_Missense_Mutation_p.E3232Q|DNAH14_ENST00000430092.1_Missense_Mutation_p.E3232Q			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TTTAACACCAGAATTTCGCCA	0.338													G|||	133	0.0265575	0.003	0.0245	5008	,	,		14751	0.001		0.0547	False		,,,				2504	0.0573				p.E3232Q		Atlas-SNP	.											.	DNAH14	300	.	0			c.G9694C						PASS	.	G	GLN/GLU	10,1374		0,10,682	123.0	107.0	112.0		9694	4.7	1.0	1	dbSNP_127	112	161,3021		3,155,1433	yes	missense	DNAH14	NM_001373.1	29	3,165,2115	CC,CG,GG		5.0597,0.7225,3.7451	possibly-damaging	3232/4516	225521101	171,4395	692	1591	2283	SO:0001627	intron_variant	127602	exon64			ACACCAGAATTTC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.7486-3867G>C	1.37:g.225521101G>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		50	0.022893772893772892	3	0.006097560975609756	9	0.024861878453038673	0	0.0	38	0.05013192612137203	G	13.68	2.309067	0.40895	0.007225	0.050597	ENSG00000185842	ENST00000430092;ENST00000439375	T;T	0.74315	-0.83;-0.83	5.62	4.71	0.59529	.	0.258285	0.20213	N	0.096852	T	0.29158	0.0725	L	0.39020	1.185	0.80722	D	1	P	0.48016	0.904	P	0.48227	0.571	T	0.51204	-0.8735	10	0.10636	T	0.68	.	13.473	0.61292	0.0772:0.0:0.9228:0.0	rs41268715	3232	Q0VDD8-4	.	Q	3232	ENSP00000414402:E3232Q;ENSP00000392061:E3232Q	ENSP00000414402:E3232Q	E	+	1	0	DNAH14	223587724	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.510000	0.60455	1.370000	0.46153	0.603000	0.83216	GAA	G|0.968;C|0.032	0.032	strong		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
DENND5B	160518	hgsc.bcm.edu	37	12	31648826	31648826	+	Missense_Mutation	SNP	C	C	T	rs4930979	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:31648826C>T	ENST00000389082.5	-	2	419	c.155G>A	c.(154-156)aGa>aAa	p.R52K	DENND5B_ENST00000306833.6_Missense_Mutation_p.R87K|DENND5B_ENST00000545147.1_5'UTR|DENND5B_ENST00000354285.4_Missense_Mutation_p.R74K|DENND5B_ENST00000536562.1_Missense_Mutation_p.R87K	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	52	UDENN.		R -> K (in dbSNP:rs4930979). {ECO:0000269|PubMed:14702039}.		positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						GAATGTTCTTCTCAAAGGACT	0.333													C|||	1986	0.396565	0.084	0.6095	5008	,	,		16127	0.5734		0.4165	False		,,,				2504	0.4652				p.R52K		Atlas-SNP	.											.	DENND5B	114	.	0			c.G155A						PASS	.	C	LYS/ARG	458,3182		32,394,1394	113.0	101.0	105.0		155	3.7	1.0	12	dbSNP_111	105	3279,4887		678,1923,1482	yes	missense	DENND5B	NM_144973.3	26	710,2317,2876	TT,TC,CC		40.1543,12.5824,31.6534	benign	52/1275	31648826	3737,8069	1820	4083	5903	SO:0001583	missense	160518	exon2			GTTCTTCTCAAAG	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.155G>A	12.37:g.31648826C>T	ENSP00000373734:p.Arg52Lys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	908	0.4157509157509158	49	0.09959349593495935	206	0.569060773480663	334	0.583916083916084	319	0.420844327176781	C	13.73	2.323020	0.41096	0.125824	0.401543	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.28895	3.82;1.59;1.59;3.35;3.34	4.6	3.71	0.42584	uDENN (3);	0.133121	0.49916	N	0.000128	T	0.00012	0.0000	N	0.25380	0.74	0.21697	P	0.999584744	B;B;B	0.11235	0.004;0.002;0.003	B;B;B	0.20577	0.03;0.008;0.017	T	0.41734	-0.9492	9	0.31617	T	0.26	-3.6645	11.8628	0.52476	0.0:0.9123:0.0:0.0877	rs4930979;rs4930979	74;52;87	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	K	52;87;87;74;4	ENSP00000373734:R52K;ENSP00000306482:R87K;ENSP00000444889:R87K;ENSP00000346238:R74K;ENSP00000442938:R4K	ENSP00000306482:R87K	R	-	2	0	DENND5B	31540093	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.535000	0.36061	1.277000	0.44412	0.650000	0.86243	AGA	C|0.605;T|0.395	0.395	strong		0.333	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
REEP1	65055	hgsc.bcm.edu	37	2	86481835	86481835	+	Silent	SNP	C	C	T	rs2276625	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:86481835C>T	ENST00000165698.5	-	4	428	c.285G>A	c.(283-285)acG>acA	p.T95T	REEP1_ENST00000473407.1_5'UTR|REEP1_ENST00000540790.1_Silent_p.T74T|REEP1_ENST00000541910.1_Intron|REEP1_ENST00000538924.1_Silent_p.T102T|REEP1_ENST00000535845.1_Silent_p.T68T	NM_022912.2	NP_075063.1	Q9H902	REEP1_HUMAN	receptor accessory protein 1	95					cell death (GO:0008219)|endoplasmic reticulum tubular network organization (GO:0071786)|protein insertion into membrane (GO:0051205)|regulation of intracellular transport (GO:0032386)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	microtubule binding (GO:0008017)|olfactory receptor binding (GO:0031849)			breast(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	13						TTGAAGATAGCGTGGGATGTA	0.373													C|||	2147	0.428714	0.1815	0.6037	5008	,	,		19312	0.5962		0.4602	False		,,,				2504	0.4335				p.T102T		Atlas-SNP	.											.	REEP1	22	.	0			c.G306A						PASS	.	C	,,,	1032,3374	379.2+/-323.2	104,824,1275	96.0	93.0	94.0		306,204,,285	-10.8	0.1	2	dbSNP_100	94	3804,4796	537.9+/-383.3	856,2092,1352	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	REEP1	NM_001164730.1,NM_001164731.1,NM_001164732.1,NM_022912.2	,,,	960,2916,2627	TT,TC,CC		44.2326,23.4226,37.1828	,,,	102/209,68/175,,95/202	86481835	4836,8170	2203	4300	6503	SO:0001819	synonymous_variant	65055	exon4			AGATAGCGTGGGA	AK023172	CCDS1989.1, CCDS54372.1, CCDS54373.1, CCDS54374.1	2p11.2	2014-09-17	2006-02-07	2006-02-07	ENSG00000068615	ENSG00000068615		"""Receptor accessory proteins"""	25786	protein-coding gene	gene with protein product	"""receptor expression enhancing protein 1"""	609139	"""chromosome 2 open reading frame 23"""	C2orf23		16271481, 15550249	Standard	NM_022912		Approved	FLJ13110, SPG31	uc002srh.4	Q9H902	OTTHUMG00000130205	ENST00000165698.5:c.285G>A	2.37:g.86481835C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001164730	B7Z4D7|B7Z4F2|B7Z5R9|D6W5M2|Q53TI0	Silent	SNP	ENST00000165698.5	37	CCDS1989.1																																																																																			C|0.593;T|0.407	0.407	strong		0.373	REEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252523.2	NM_022912	
HES4	57801	hgsc.bcm.edu	37	1	934951	934951	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:934951T>C	ENST00000304952.6	-	3	384	c.247A>G	c.(247-249)Atg>Gtg	p.M83V	HES4_ENST00000428771.2_Missense_Mutation_p.M109V|HES4_ENST00000484667.2_Missense_Mutation_p.M51V|RP11-54O7.17_ENST00000606034.1_lincRNA			Q9HCC6	HES4_HUMAN	hes family bHLH transcription factor 4	83	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			lung(2)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;9.36e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.41e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00237)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CTCACGGTCATCTCCAGGATG	0.736																																					p.M109V		Atlas-SNP	.											.	HES4	9	.	0			c.A325G						PASS	.						13.0	17.0	15.0					1																	934951		2167	4263	6430	SO:0001583	missense	57801	exon2			CGGTCATCTCCAG	BC012351	CCDS5.1, CCDS44034.1	1p36	2013-10-17	2013-10-17		ENSG00000188290	ENSG00000188290		"""Basic helix-loop-helix proteins"""	24149	protein-coding gene	gene with protein product		608060	"""hairy and enhancer of split 4 (Drosophila)"""			11260262, 15254753	Standard	NM_021170		Approved	bHLHb42	uc001aci.2	Q9HCC6	OTTHUMG00000040758	ENST00000304952.6:c.247A>G	1.37:g.934951T>C	ENSP00000304595:p.Met83Val	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	50	32	0.64	NM_001142467	Q5SVA5	Missense_Mutation	SNP	ENST00000304952.6	37	CCDS5.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.756340	0.31137	.	.	ENSG00000188290	ENST00000428771;ENST00000304952;ENST00000484667	D;D;T	0.98090	-4.71;-4.71;1.1	3.29	2.15	0.27550	Helix-loop-helix DNA-binding (5);	0.176901	0.26820	U	0.022332	D	0.97932	0.9320	M	0.86178	2.8	0.43868	D	0.996478	P;P	0.46859	0.883;0.885	P;P	0.55222	0.771;0.688	D	0.96838	0.9616	10	0.56958	D	0.05	.	9.0774	0.36531	0.0:0.0:0.1982:0.8018	.	109;83	E9PB28;Q9HCC6	.;HES4_HUMAN	V	109;83;51	ENSP00000393198:M109V;ENSP00000304595:M83V;ENSP00000425085:M51V	ENSP00000304595:M83V	M	-	1	0	HES4	924814	1.000000	0.71417	0.980000	0.43619	0.960000	0.62799	2.653000	0.46691	0.366000	0.24427	0.334000	0.21626	ATG	.	.	none		0.736	HES4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097944.1	NM_021170	
DTX2	113878	hgsc.bcm.edu	37	7	76111835	76111835	+	Silent	SNP	G	G	A	rs4236506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76111835G>A	ENST00000324432.5	+	5	789	c.279G>A	c.(277-279)cgG>cgA	p.R93R	DTX2_ENST00000472426.1_3'UTR|DTX2_ENST00000307569.8_Silent_p.R93R|DTX2_ENST00000413936.2_Silent_p.R93R|DTX2_ENST00000430490.2_Silent_p.R93R|DTX2_ENST00000446600.1_Silent_p.R2R|DTX2_ENST00000446820.2_Silent_p.R93R	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	93	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						GCACCATGCGGGCTGTGCGGA	0.527													.|||	1130	0.225639	0.1256	0.2767	5008	,	,		19820	0.2302		0.2495	False		,,,				2504	0.2955				p.R93R		Atlas-SNP	.											DTX2,rectum,carcinoma,0,2	DTX2	64	2	0			c.G279A						PASS	.	G	,,,	640,3766		48,544,1611	83.0	87.0	85.0		279,279,279,279	1.0	1.0	7	dbSNP_111	85	1989,6611		241,1507,2552	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	289,2051,4163	AA,AG,GG		23.1279,14.5256,20.2137	,,,	93/623,93/623,93/576,93/623	76111835	2629,10377	2203	4300	6503	SO:0001819	synonymous_variant	113878	exon2			CATGCGGGCTGTG		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.279G>A	7.37:g.76111835G>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	243	114	0.469136	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			G|0.795;A|0.205	0.205	strong		0.527	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
SESN1	27244	hgsc.bcm.edu	37	6	109322554	109322554	+	Silent	SNP	C	C	T	rs12214121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:109322554C>T	ENST00000356644.7	-	3	400	c.306G>A	c.(304-306)caG>caA	p.Q102Q	SESN1_ENST00000302071.2_Silent_p.Q36Q|SESN1_ENST00000436639.2_Silent_p.Q161Q|RP11-787I22.3_ENST00000605885.1_RNA	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	102					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		GTAGATAGTGCTGAGTTTTTA	0.363													T|||	482	0.096246	0.0431	0.0735	5008	,	,		18104	0.0407		0.1352	False		,,,				2504	0.2014				p.Q161Q		Atlas-SNP	.											.	SESN1	29	.	0			c.G483A						PASS	.	T	,,	224,4182	804.7+/-415.8	6,212,1985	84.0	80.0	82.0		306,108,483	0.5	1.0	6	dbSNP_120	82	1005,7593	771.8+/-407.7	72,861,3366	no	coding-synonymous,coding-synonymous,coding-synonymous	SESN1	NM_001199933.1,NM_001199934.1,NM_014454.2	,,	78,1073,5351	TT,TC,CC		11.6888,5.084,9.4509	,,	102/493,36/427,161/552	109322554	1229,11775	2203	4299	6502	SO:0001819	synonymous_variant	27244	exon3			ATAGTGCTGAGTT	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.306G>A	6.37:g.109322554C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	140	50	0.357143	NM_014454	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Silent	SNP	ENST00000356644.7	37	CCDS56445.1																																																																																			C|0.915;T|0.085	0.085	strong		0.363	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454	
PRR34	55267	hgsc.bcm.edu	37	22	46447714	46447714	+	Missense_Mutation	SNP	T	T	C	rs59929908	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:46447714T>C	ENST00000396008.2	-	2	460	c.410A>G	c.(409-411)cAg>cGg	p.Q137R	RP6-109B7.3_ENST00000416202.1_RNA|C22orf26_ENST00000333761.1_Missense_Mutation_p.Q137R|RP6-109B7.5_ENST00000608644.1_RNA|RP6-109B7.3_ENST00000451166.1_RNA|FLJ27365_ENST00000381051.2_5'Flank			Q9NV39	PRR34_HUMAN		137			Q -> R (in dbSNP:rs59929908).										Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.0784)|LUAD - Lung adenocarcinoma(64;0.247)		agctcatacctgtaattccag	0.512													T|||	443	0.0884585	0.062	0.0908	5008	,	,		19210	0.1419		0.1004	False		,,,				2504	0.0552				p.Q137R		Atlas-SNP	.											.	C22orf26	1	.	0			c.A410G						PASS	.	T	ARG/GLN	135,1881		3,129,876	112.0	134.0	127.0		410	-0.3	0.0	22	dbSNP_129	127	432,3788		19,394,1697	yes	missense	C22orf26	NM_018280.2	43	22,523,2573	CC,CT,TT		10.237,6.6964,9.0924	possibly-damaging	137/139	46447714	567,5669	1008	2110	3118	SO:0001583	missense	55267	exon2			CATACCTGTAATT																												ENST00000396008.2:c.410A>G	22.37:g.46447714T>C	ENSP00000379329:p.Gln137Arg	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_018280	B0QZ24	Missense_Mutation	SNP	ENST00000396008.2	37	CCDS14071.1	224	0.10256410256410256	30	0.06097560975609756	40	0.11049723756906077	83	0.1451048951048951	71	0.09366754617414248	T	1.623	-0.521060	0.04171	0.066964	0.10237	ENSG00000182257	ENST00000396008;ENST00000333761	T;T	0.38560	1.13;1.13	0.772	-0.328	0.12690	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	P	0.42039	0.769	P	0.49332	0.607	T	0.09100	-1.0690	8	0.87932	D	0	.	2.7796	0.05357	0.0:0.3573:0.0:0.6427	rs59929908	137	Q9NV39	CV026_HUMAN	R	137	ENSP00000379329:Q137R;ENSP00000327764:Q137R	ENSP00000327764:Q137R	Q	-	2	0	C22orf26	44826378	.	.	0.003000	0.11579	0.024000	0.10985	.	.	-0.184000	0.10567	0.460000	0.39030	CAG	T|0.897;C|0.103	0.103	strong		0.512	C22orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317994.1		
SKA3	221150	hgsc.bcm.edu	37	13	21732060	21732060	+	Splice_Site	SNP	C	C	G	rs151054732		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:21732060C>G	ENST00000314759.5	-	7	1244		c.e7+1		SKA3_ENST00000400018.3_Splice_Site	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GGAAAAATAACCTGGAGAATA	0.313																																					.		Atlas-SNP	.											SKA3_ENST00000400018,NS,carcinoma,0,2	SKA3	76	2	0			c.1119+1G>C						PASS	.						52.0	57.0	55.0					13																	21732060		2203	4299	6502	SO:0001630	splice_region_variant	221150	exon8			AAATAACCTGGAG	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.1119+1G>C	13.37:g.21732060C>G		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	38	11	0.289474	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Splice_Site	SNP	ENST00000314759.5	37	CCDS31946.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.766754	0.49574	.	.	ENSG00000165480	ENST00000314759;ENST00000400018	.	.	.	5.69	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7465	0.40451	0.0:0.8389:0.0:0.1611	.	.	.	.	.	-1	.	.	.	-	.	.	SKA3	20630060	1.000000	0.71417	0.998000	0.56505	0.836000	0.47400	2.904000	0.48719	0.767000	0.33267	-0.229000	0.12294	.	.	.	weak		0.313	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	Intron
BFSP1	631	hgsc.bcm.edu	37	20	17475217	17475217	+	Silent	SNP	C	C	T	rs6136118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:17475217C>T	ENST00000377873.3	-	8	1539	c.1500G>A	c.(1498-1500)gcG>gcA	p.A500A	BFSP1_ENST00000544874.1_Silent_p.A361A|BFSP1_ENST00000536626.1_Silent_p.A361A|BFSP1_ENST00000377868.2_Silent_p.A375A	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	500	Tail.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						CAGAGTCTTCCGCAACAGAAA	0.552													C|||	1700	0.339457	0.3404	0.3069	5008	,	,		15488	0.4038		0.2435	False		,,,				2504	0.3937				p.A500A		Atlas-SNP	.											.	BFSP1	55	.	0			c.G1500A						PASS	.	C	,	1458,2948	472.8+/-356.5	251,956,996	64.0	56.0	58.0		1125,1500	0.3	0.2	20	dbSNP_114	58	2028,6572	353.6+/-329.2	246,1536,2518	no	coding-synonymous,coding-synonymous	BFSP1	NM_001161705.1,NM_001195.3	,	497,2492,3514	TT,TC,CC		23.5814,33.0912,26.803	,	375/541,500/666	17475217	3486,9520	2203	4300	6503	SO:0001819	synonymous_variant	631	exon8			GTCTTCCGCAACA	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.1500G>A	20.37:g.17475217C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	181	181	1	NM_001195	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Silent	SNP	ENST00000377873.3	37	CCDS13126.1																																																																																			C|0.697;T|0.303	0.303	strong		0.552	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73179672	73179672	+	Silent	SNP	C	C	T	rs3749645	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:73179672C>T	ENST00000426542.2	+	23	3038	c.3018C>T	c.(3016-3018)taC>taT	p.Y1006Y	ARHGEF28_ENST00000296794.6_Silent_p.Y1006Y|ARHGEF28_ENST00000513042.2_Silent_p.Y1006Y|ARHGEF28_ENST00000287898.5_Silent_p.Y1006Y|ARHGEF28_ENST00000512883.1_5'Flank|ARHGEF28_ENST00000296799.4_Silent_p.Y693Y|ARHGEF28_ENST00000545377.1_Silent_p.Y1006Y|ARHGEF28_ENST00000437974.1_Silent_p.Y1006Y			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1006	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										TTACAAAATACCCTGTCTTGG	0.383													C|||	868	0.173323	0.1747	0.098	5008	,	,		17907	0.2639		0.1133	False		,,,				2504	0.1933				p.Y1006Y		Atlas-SNP	.											.	.	.	.	0			c.C3018T						PASS	.	C	,	613,3081		54,505,1288	51.0	51.0	51.0		3018,3018	4.9	1.0	5	dbSNP_107	51	938,7206		63,812,3197	no	coding-synonymous,coding-synonymous	RGNEF	NM_001080479.2,NM_001177693.1	,	117,1317,4485	TT,TC,CC		11.5177,16.5945,13.1019	,	1006/1732,1006/1706	73179672	1551,10287	1847	4072	5919	SO:0001819	synonymous_variant	64283	exon24			AAAATACCCTGTC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.3018C>T	5.37:g.73179672C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			C|0.820;T|0.180	0.180	strong		0.383	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
SLC5A1	6523	hgsc.bcm.edu	37	22	32506104	32506104	+	Silent	SNP	G	G	A	rs33943816	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:32506104G>A	ENST00000266088.4	+	15	2149	c.1899G>A	c.(1897-1899)acG>acA	p.T633T	SLC5A1_ENST00000543737.1_Silent_p.T506T	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	633					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	TGAAGATGACGGACACCTCTG	0.502													G|||	167	0.0333466	0.0061	0.0418	5008	,	,		20474	0.0198		0.0577	False		,,,				2504	0.0532				p.T633T		Atlas-SNP	.											.	SLC5A1	80	.	0			c.G1899A						PASS	.	G		53,4353	53.6+/-89.4	0,53,2150	288.0	220.0	243.0		1899	-3.8	0.9	22	dbSNP_126	243	536,8064	149.7+/-204.7	20,496,3784	no	coding-synonymous	SLC5A1	NM_000343.3		20,549,5934	AA,AG,GG		6.2326,1.2029,4.5287		633/665	32506104	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	6523	exon15			GATGACGGACACC		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"""Solute carriers"""	11036	protein-coding gene	gene with protein product	"""sodium/glucose cotransporter 1"""	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.1899G>A	22.37:g.32506104G>A		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	248	116	0.467742	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Silent	SNP	ENST00000266088.4	37	CCDS13902.1																																																																																			G|0.956;A|0.044	0.044	strong		0.502	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	
GIMAP1	170575	hgsc.bcm.edu	37	7	150417677	150417677	+	Silent	SNP	G	G	A	rs4725358	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150417677G>A	ENST00000307194.5	+	3	725	c.585G>A	c.(583-585)cgG>cgA	p.R195R		NM_130759.3	NP_570115.1	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	195	AIG1-type G.				B cell differentiation (GO:0030183)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCACCGGCCGGGAGCAGGAAG	0.657													G|||	398	0.0794728	0.0522	0.1182	5008	,	,		14913	0.0298		0.1064	False		,,,				2504	0.1125				p.R195R		Atlas-SNP	.											GIMAP1,colon,carcinoma,+2,2	GIMAP1	61	2	0			c.G585A						PASS	.	G	,	234,4170	127.4+/-164.3	9,216,1977	24.0	30.0	28.0		,585	-3.9	0.0	7	dbSNP_111	28	858,7742	181.5+/-230.2	46,766,3488	no	intron,coding-synonymous	GIMAP1,GIMAP1-GIMAP5	NM_001199577.1,NM_130759.3	,	55,982,5465	AA,AG,GG		9.9767,5.3134,8.3974	,	,195/307	150417677	1092,11912	2202	4300	6502	SO:0001819	synonymous_variant	170575	exon3			CGGCCGGGAGCAG	AJ306287	CCDS5906.1	7q36.1	2014-04-04			ENSG00000213203	ENSG00000213203		"""GTPases, IMAP"""	23237	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 2"""	608084				15474311, 18701445	Standard	NM_130759		Approved	HIMAP1, IMAP38, IMAP1, IAN2		Q8WWP7	OTTHUMG00000157489	ENST00000307194.5:c.585G>A	7.37:g.150417677G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	53	0.630952	NM_130759	B2RCI3|Q8NAZ0	Silent	SNP	ENST00000307194.5	37	CCDS5906.1																																																																																			G|0.926;A|0.074	0.074	strong		0.657	GIMAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348951.2	NM_130759	
IFI16	3428	hgsc.bcm.edu	37	1	159002389	159002389	+	Missense_Mutation	SNP	T	T	A	rs1057028	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:159002389T>A	ENST00000295809.7	+	7	1492	c.1237T>A	c.(1237-1239)Tat>Aat	p.Y413N	IFI16_ENST00000368131.4_Missense_Mutation_p.Y413N|IFI16_ENST00000430894.2_Missense_Mutation_p.Y361N|IFI16_ENST00000359709.3_Missense_Mutation_p.Y357N|IFI16_ENST00000448393.2_Missense_Mutation_p.Y413N|IFI16_ENST00000368132.3_Missense_Mutation_p.Y413N|IFI16_ENST00000340979.6_Missense_Mutation_p.Y413N			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	413			Y -> N (in dbSNP:rs1057028). {ECO:0000269|PubMed:12894224, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					TCAGCTTCCATATCCTTCAGA	0.453													A|||	3159	0.630791	0.3207	0.8689	5008	,	,		17933	0.5873		0.838	False		,,,				2504	0.7127				p.Y413N		Atlas-SNP	.											.	IFI16	111	.	0			c.T1237A						PASS	.	A	ASN/TYR,ASN/TYR	1896,2510	628.4+/-395.1	414,1068,721	129.0	120.0	123.0		1069,1237	-4.3	0.0	1	dbSNP_86	123	7028,1572	293.4+/-301.3	2881,1266,153	yes	missense,missense	IFI16	NM_001206567.1,NM_005531.2	143,143	3295,2334,874	AA,AT,TT		18.2791,43.0322,31.3855	benign,benign	357/730,413/730	159002389	8924,4082	2203	4300	6503	SO:0001583	missense	3428	exon7			CTTCCATATCCTT	M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.1237T>A	1.37:g.159002389T>A	ENSP00000295809:p.Tyr413Asn	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	193	77	0.398964	NM_005531	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	ENST00000295809.7	37		1485|1485	0.679945054945055|0.679945054945055	149|149	0.30284552845528456|0.30284552845528456	314|314	0.8674033149171271|0.8674033149171271	379|379	0.6625874125874126|0.6625874125874126	643|643	0.8482849604221636|0.8482849604221636	A|A	0.135|0.135	-1.109001|-1.109001	0.01813|0.01813	0.430322|0.430322	0.817209|0.817209	ENSG00000163565|ENSG00000163565	ENST00000448393|ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894	.|T;T;T;T;T	.|0.04049	.|3.72;3.73;3.73;3.73;3.72	2.15|2.15	-4.3|-4.3	0.03710|0.03710	.|.	.|.	.|.	.|.	.|.	T|T	0.00328|0.00328	0.0010|0.0010	N|N	0.01352|0.01352	-0.895|-0.895	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.45338|0.45338	-0.9268|-0.9268	4|8	.|0.13853	.|T	.|0.58	.|.	0.1053|0.1053	0.00052|0.00052	0.2851:0.1582:0.2388:0.3179|0.2851:0.1582:0.2388:0.3179	rs1057028;rs2070269;rs3197639;rs17856526;rs56618598;rs60298181;rs1057028|rs1057028;rs2070269;rs3197639;rs17856526;rs56618598;rs60298181;rs1057028	.|361;413;413	.|E7EPR3;Q16666-3;Q16666-2	.|.;.;.	Q|N	233|413;413;413;413;361	.|ENSP00000295809:Y413N;ENSP00000342741:Y413N;ENSP00000357113:Y413N;ENSP00000357114:Y413N;ENSP00000394935:Y361N	.|ENSP00000295809:Y413N	H|Y	+|+	3|1	2|0	IFI16|IFI16	157269013|157269013	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-2.519000|-2.519000	0.00952|0.00952	-1.913000|-1.913000	0.01079|0.01079	-0.527000|-0.527000	0.04329|0.04329	CAT|TAT	T|0.329;A|0.671	0.671	strong		0.453	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531	
BLNK	29760	hgsc.bcm.edu	37	10	97990583	97990583	+	Silent	SNP	A	A	G	rs727852	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:97990583A>G	ENST00000224337.5	-	4	312	c.171T>C	c.(169-171)ccT>ccC	p.P57P	BLNK_ENST00000427367.2_Silent_p.P57P|BLNK_ENST00000371176.2_Silent_p.P57P|BLNK_ENST00000413476.2_Silent_p.P57P	NM_013314.3	NP_037446.1	Q8WV28	BLNK_HUMAN	B-cell linker	57					B cell differentiation (GO:0030183)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.P57P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(2)|stomach(1)	14		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		CTTCGTCAGCAGGGCTCTCTG	0.562													G|||	2310	0.461262	0.1551	0.6571	5008	,	,		19157	0.4514		0.7127	False		,,,				2504	0.4877				p.P57P		Atlas-SNP	.											BLNK,NS,carcinoma,0,1	BLNK	46	1	1	Substitution - coding silent(1)	stomach(1)	c.T171C						PASS	.	G	,	1074,3332	711.6+/-408.0	149,776,1278	49.0	37.0	41.0		171,171	-7.0	0.1	10	dbSNP_86	41	6186,2414	389.8+/-343.1	2207,1772,321	no	coding-synonymous,coding-synonymous	BLNK	NM_001114094.1,NM_013314.3	,	2356,2548,1599	GG,GA,AA		28.0698,24.3759,44.1796	,	57/434,57/457	97990583	7260,5746	2203	4300	6503	SO:0001819	synonymous_variant	29760	exon4			GTCAGCAGGGCTC	AF068180	CCDS7446.1, CCDS44464.1, CCDS58091.1, CCDS73171.1	10q23.2-q23.33	2014-09-17			ENSG00000095585	ENSG00000095585		"""SH2 domain containing"""	14211	protein-coding gene	gene with protein product	"""B-cell adapter containing a SH2 domain protein"", ""B-cell activation"", ""Src homology [SH2] domain-containing leukocyte protein of 65 kD"", ""B cell adaptor containing SH2 domain"""	604515				9697839, 10583958	Standard	NM_013314		Approved	SLP65, Ly57, SLP-65, BLNK-s, BASH, bca	uc001kls.4	Q8WV28	OTTHUMG00000018827	ENST00000224337.5:c.171T>C	10.37:g.97990583A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_001114094	O75498|O75499|Q2MD49	Silent	SNP	ENST00000224337.5	37	CCDS7446.1																																																																																			A|0.478;G|0.522	0.522	strong		0.562	BLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049593.1	NM_013314	
ZNF467	168544	hgsc.bcm.edu	37	7	149462642	149462642	+	Silent	SNP	G	G	T	rs61742446	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149462642G>T	ENST00000302017.3	-	5	1362	c.949C>A	c.(949-951)Cgg>Agg	p.R317R	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTTTGGTGCCGCACCAAGTGC	0.662													G|||	57	0.0113818	0.0008	0.0029	5008	,	,		13129	0.0		0.0239	False		,,,				2504	0.0307				p.R317R		Atlas-SNP	.											.	ZNF467	50	.	0			c.C949A						PASS	.	G		19,4377		1,17,2180	18.0	16.0	17.0		949	2.4	1.0	7	dbSNP_129	17	143,8443		2,139,4152	no	coding-synonymous	ZNF467	NM_207336.1		3,156,6332	TT,TG,GG		1.6655,0.4322,1.2479		317/596	149462642	162,12820	2198	4293	6491	SO:0001819	synonymous_variant	168544	exon5			GGTGCCGCACCAA	BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"""Zinc fingers, C2H2-type"""	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.949C>A	7.37:g.149462642G>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	79	0.724771	NM_207336		Silent	SNP	ENST00000302017.3	37	CCDS5899.1																																																																																			G|0.990;T|0.010	0.010	strong		0.662	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336	
GPR98	84059	hgsc.bcm.edu	37	5	89988504	89988504	+	Missense_Mutation	SNP	A	A	G	rs2366926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:89988504A>G	ENST00000405460.2	+	32	7130	c.7034A>G	c.(7033-7035)aAt>aGt	p.N2345S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2345			N -> S (in dbSNP:rs2366926). {ECO:0000269|PubMed:14740321}.		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.N2345S(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATTCCTGCCAATGATGATCCT	0.403													A|||	1614	0.322284	0.208	0.5029	5008	,	,		17570	0.375		0.3191	False		,,,				2504	0.2975				p.N2345S		Atlas-SNP	.											GPR98,NS,carcinoma,0,1	GPR98	605	1	1	Substitution - Missense(1)	stomach(1)	c.A7034G						PASS	.	A	SER/ASN	777,2955		90,597,1179	93.0	89.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7034	5.9	1.0	5	dbSNP_100	91	2701,5503		447,1807,1848	yes	missense	GPR98	NM_032119.3	46	537,2404,3027	GG,GA,AA		32.923,20.8199,29.1387	probably-damaging	2345/6307	89988504	3478,8458	1866	4102	5968	SO:0001583	missense	84059	exon32			CTGCCAATGATGA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.7034A>G	5.37:g.89988504A>G	ENSP00000384582:p.Asn2345Ser	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	224	224	1	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	763	0.34935897435897434	104	0.21138211382113822	174	0.48066298342541436	245	0.42832167832167833	240	0.316622691292876	A	24.1	4.498831	0.85069	0.208199	0.32923	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.31247	1.5	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.51914	1.62	0.09310	P	1.0	D	0.89917	1.0	D	0.85130	0.997	T	0.48514	-0.9029	9	0.87932	D	0	.	16.4237	0.83790	1.0:0.0:0.0:0.0	rs2366926;rs52814624;rs61626672;rs2366926	2345	Q8WXG9	GPR98_HUMAN	S	2345	ENSP00000384582:N2345S	ENSP00000296619:N2345S	N	+	2	0	GPR98	90024260	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.074000	0.93998	2.279000	0.76181	0.533000	0.62120	AAT	A|0.667;G|0.333	0.333	strong		0.403	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
PTX4	390667	hgsc.bcm.edu	37	16	1538363	1538363	+	Intron	SNP	C	C	A	rs1040499	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1538363C>A	ENST00000447419.2	-	2	167				PTX4_ENST00000293922.1_Missense_Mutation_p.G36C|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CCCGACAGGCCCACAGCACTC	0.652													A|||	2502	0.499601	0.7534	0.3242	5008	,	,		16625	0.5119		0.3897	False		,,,				2504	0.3814				p.G36C		Atlas-SNP	.											.	PTX4	46	.	0			c.G106T						PASS	.	A	CYS/GLY	2988,1410	458.8+/-352.1	998,992,209	63.0	61.0	62.0		106	-0.2	0.0	16	dbSNP_86	62	3259,5341	647.5+/-400.4	589,2081,1630	yes	missense	PTX4	NM_001013658.1	159	1587,3073,1839	AA,AC,CC		37.8953,32.06,48.0612	benign	36/474	1538363	6247,6751	2199	4300	6499	SO:0001627	intron_variant	390667	exon1			ACAGGCCCACAGC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.142-392G>T	16.37:g.1538363C>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	233	119	0.51073	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		1092	0.5	347	0.7052845528455285	117	0.32320441988950277	315	0.5506993006993007	313	0.4129287598944591	A	6.903	0.536146	0.13188	0.6794	0.378953	ENSG00000251692	ENST00000293922	T	0.08102	3.13	0.943	-0.196	0.13232	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11542	-1.0583	7	0.42905	T	0.14	.	2.4424	0.04498	0.2564:0.3221:0.4215:0.0	rs1040499;rs59677019;rs1040499	36	Q96A99-2	.	C	36	ENSP00000293922:G36C	ENSP00000293922:G36C	G	-	1	0	PTX4	1478364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.524000	0.06222	-0.511000	0.06514	-1.564000	0.00881	GGC	C|0.502;A|0.498	0.498	strong		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
BRAT1	221927	hgsc.bcm.edu	37	7	2582878	2582878	+	Missense_Mutation	SNP	T	T	C	rs151317339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2582878T>C	ENST00000340611.4	-	6	1139	c.883A>G	c.(883-885)Atg>Gtg	p.M295V	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	295					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						AGGGGTCCCATGTGGGTGGGA	0.647													T|||	3	0.000599042	0.0023	0.0	5008	,	,		14712	0.0		0.0	False		,,,				2504	0.0				p.M295V		Atlas-SNP	.											.	BRAT1	57	.	0			c.A883G						PASS	.	T	VAL/MET	1,4405	2.1+/-5.4	0,1,2202	58.0	61.0	60.0		883	4.0	0.0	7	dbSNP_134	60	5,8595	3.7+/-12.6	0,5,4295	yes	missense	BRAT1	NM_152743.3	21	0,6,6497	CC,CT,TT		0.0581,0.0227,0.0461	benign	295/822	2582878	6,13000	2203	4300	6503	SO:0001583	missense	221927	exon6			GTCCCATGTGGGT	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.883A>G	7.37:g.2582878T>C	ENSP00000339637:p.Met295Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	T	0.409	-0.914401	0.02415	2.27E-4	5.81E-4	ENSG00000106009	ENST00000340611	T	0.67698	-0.28	5.85	4.02	0.46733	Armadillo-type fold (1);	0.985177	0.08314	N	0.964822	T	0.43166	0.1235	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31916	-0.9926	10	0.19590	T	0.45	-0.4835	5.0952	0.14729	0.1497:0.6269:0.1447:0.0787	.	295	Q6PJG6	BRAT1_HUMAN	V	295	ENSP00000339637:M295V	ENSP00000339637:M295V	M	-	1	0	BRAT1	2549404	0.006000	0.16342	0.001000	0.08648	0.031000	0.12232	0.555000	0.23422	0.788000	0.33755	-0.146000	0.13790	ATG	T|1.000;C|0.000	0.000	strong		0.647	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
SPHKAP	80309	hgsc.bcm.edu	37	2	228884299	228884299	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228884299A>G	ENST00000392056.3	-	7	1317	c.1271T>C	c.(1270-1272)gTa>gCa	p.V424A	SPHKAP_ENST00000344657.5_Missense_Mutation_p.V424A	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	424						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		AGAACTTCCTACAGAAACACT	0.433																																					p.V424A		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,-1,2	SPHKAP	750	2	0			c.T1271C						scavenged	.						117.0	112.0	114.0					2																	228884299		2203	4300	6503	SO:0001583	missense	80309	exon7			CTTCCTACAGAAA		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.1271T>C	2.37:g.228884299A>G	ENSP00000375909:p.Val424Ala	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	173	2	0.0115607	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	A	8.327	0.825585	0.16749	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12465	2.68;2.68	5.76	-1.15	0.09709	.	0.859197	0.10483	N	0.669348	T	0.09291	0.0229	L	0.38838	1.175	0.09310	N	1	B;B	0.15141	0.001;0.012	B;B	0.15484	0.002;0.013	T	0.40194	-0.9576	10	0.22109	T	0.4	-0.4759	6.5499	0.22427	0.3776:0.2605:0.3619:0.0	.	424;424	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	A	424	ENSP00000375909:V424A;ENSP00000339886:V424A	ENSP00000339886:V424A	V	-	2	0	SPHKAP	228592543	0.000000	0.05858	0.318000	0.25279	0.795000	0.44927	0.171000	0.16685	-0.108000	0.12066	-0.331000	0.08364	GTA	.	.	none		0.433	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
KRT5	3852	hgsc.bcm.edu	37	12	52908917	52908917	+	Missense_Mutation	SNP	T	T	C	rs11549950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52908917T>C	ENST00000252242.4	-	9	1972	c.1582A>G	c.(1582-1584)Agc>Ggc	p.S528G		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	528	Ser-rich.|Tail.		S -> G (in dbSNP:rs11549950). {ECO:0000269|PubMed:15489334}.		cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		cttccactgctacctccggca	0.642													C|||	760	0.151757	0.2632	0.1916	5008	,	,		12764	0.0387		0.1481	False		,,,				2504	0.093				p.S528G		Atlas-SNP	.											.	KRT5	88	.	0			c.A1582G						PASS	.	C	GLY/SER	1049,3357	696.2+/-406.1	116,817,1270	33.0	32.0	33.0		1582	0.1	0.0	12	dbSNP_120	33	1202,7398	737.7+/-407.0	86,1030,3184	yes	missense	KRT5	NM_000424.3	56	202,1847,4454	CC,CT,TT		13.9767,23.8084,17.3074	benign	528/591	52908917	2251,10755	2203	4300	6503	SO:0001583	missense	3852	exon9			CACTGCTACCTCC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1582A>G	12.37:g.52908917T>C	ENSP00000252242:p.Ser528Gly	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	37	CCDS8830.1	319	0.14606227106227107	130	0.26422764227642276	61	0.1685082872928177	20	0.03496503496503497	108	0.1424802110817942	c	7.130	0.579777	0.13686	0.238084	0.139767	ENSG00000186081	ENST00000252242;ENST00000456000	D	0.83837	-1.77	5.35	0.0841	0.14436	.	0.509323	0.14654	N	0.306421	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03315	-1.1049	9	0.14252	T	0.57	.	12.3792	0.55297	0.0:0.5138:0.0:0.4862	rs11549950;rs17855505;rs17855654;rs52835152;rs56980853;rs11549950	528	P13647	K2C5_HUMAN	G	528;493	ENSP00000252242:S528G	ENSP00000252242:S528G	S	-	1	0	KRT5	51195184	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.710000	0.05024	-0.548000	0.06199	-1.799000	0.00621	AGC	T|0.835;C|0.165	0.165	strong		0.642	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
ANKRD36	375248	hgsc.bcm.edu	37	2	97864334	97864334	+	Silent	SNP	C	C	T	rs71329611|rs56835800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97864334C>T	ENST00000461153.2	+	44	2938	c.2694C>T	c.(2692-2694)gcC>gcT	p.A898A	ANKRD36_ENST00000420699.2_Silent_p.A898A			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	898										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						CTTCAAGTGCCGAGAAAGATT	0.308													.|||	2026	0.404553	0.2542	0.4957	5008	,	,		24722	0.2619		0.7972	False		,,,				2504	0.2863				p.A898A		Atlas-SNP	.											.	ANKRD36	170	.	0			c.C2694T						PASS	.						33.0	19.0	23.0					2																	97864334		691	1578	2269	SO:0001819	synonymous_variant	375248	exon44			AAGTGCCGAGAAA	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.2694C>T	2.37:g.97864334C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Silent	SNP	ENST00000461153.2	37	CCDS54379.1																																																																																			C|0.257;T|0.743	0.743	strong		0.308	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
FLNB	2317	hgsc.bcm.edu	37	3	58081888	58081888	+	Silent	SNP	T	T	C	rs1522384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58081888T>C	ENST00000295956.4	+	6	1092	c.927T>C	c.(925-927)agT>agC	p.S309S	FLNB_ENST00000490882.1_Silent_p.S309S|FLNB_ENST00000419752.2_Silent_p.S140S|FLNB_ENST00000493452.1_Silent_p.S140S|FLNB_ENST00000429972.2_Silent_p.S309S|FLNB_ENST00000348383.5_Silent_p.S309S|FLNB_ENST00000358537.3_Silent_p.S309S|FLNB_ENST00000357272.4_Silent_p.S309S	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	309					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCCCTGACAGTGACAAGAACA	0.552													C|||	3215	0.641973	0.5825	0.5821	5008	,	,		19936	0.9772		0.3668	False		,,,				2504	0.7025				p.S309S		Atlas-SNP	.											.	FLNB	430	.	0			c.T927C						PASS	.	C	,,,	2349,2057	566.4+/-381.9	621,1107,475	97.0	79.0	85.0		927,927,927,927	-2.9	0.3	3	dbSNP_88	85	2790,5810	677.4+/-403.4	463,1864,1973	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	1084,2971,2448	CC,CT,TT		32.4419,46.6863,39.5125	,,,	309/2634,309/2592,309/2579,309/2603	58081888	5139,7867	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon6			TGACAGTGACAAG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.927T>C	3.37:g.58081888T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			T|0.536;C|0.464	0.464	strong		0.552	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
TBC1D29	26083	hgsc.bcm.edu	37	17	28890301	28890301	+	Missense_Mutation	SNP	G	G	A	rs80145926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:28890301G>A	ENST00000580161.1	+	6	2808	c.311G>A	c.(310-312)aGc>aAc	p.S104N	TBC1D29_ENST00000579181.1_Missense_Mutation_p.S104N|TBC1D29_ENST00000584297.1_3'UTR|RP11-218M11.1_ENST00000563063.1_lincRNA			Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	104							Rab GTPase activator activity (GO:0005097)	p.S104N(1)		breast(1)|kidney(1)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Myeloproliferative disorder(56;0.0255)				TCAGAGAGCAGCAGAGGCCCC	0.587																																					p.S104N		Atlas-SNP	.											TBC1D29,NS,carcinoma,0,1	TBC1D29	19	1	1	Substitution - Missense(1)	prostate(1)	c.G311A						scavenged	.						48.0	45.0	46.0					17																	28890301		2203	4300	6503	SO:0001583	missense	26083	exon5			AGAGCAGCAGAGG	BC096718	CCDS32606.1	17q11.2	2014-09-04			ENSG00000266733	ENSG00000266733			24509	protein-coding gene	gene with protein product						12618308	Standard	XM_006721805		Approved	DKFZP434O047	uc002hfh.3	Q9UFV1	OTTHUMG00000178857	ENST00000580161.1:c.311G>A	17.37:g.28890301G>A	ENSP00000462799:p.Ser104Asn	Somatic	121	2	0.0165289		WXS	Illumina HiSeq	Phase_I	135	6	0.0444444	NM_015594		Missense_Mutation	SNP	ENST00000580161.1	37	CCDS32606.1	.	.	.	.	.	.	.	.	.	.	.	9.179	1.023040	0.19433	.	.	ENSG00000197689	ENST00000329040	.	.	.	.	.	.	.	.	.	.	.	T	0.22820	0.0551	N	0.08118	0	0.18873	N	0.999983	B	0.33000	0.393	B	0.42319	0.383	T	0.34850	-0.9812	7	0.72032	D	0.01	.	5.89	0.18904	8.0E-4:0.0:0.9992:0.0	.	104	Q9UFV1	TBC29_HUMAN	N	104	.	ENSP00000330052:S104N	S	+	2	0	TBC1D29	25914427	0.966000	0.33281	0.071000	0.20095	0.071000	0.16799	-0.367000	0.07553	0.107000	0.17824	0.109000	0.15622	AGC	G|0.928;A|0.072	0.072	strong		0.587	TBC1D29-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443632.1	NM_015594	
GP5	2814	hgsc.bcm.edu	37	3	194118565	194118565	+	Silent	SNP	C	C	T	rs71316299	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:194118565C>T	ENST00000401815.1	-	1	518	c.447G>A	c.(445-447)caG>caA	p.Q149Q	GP5_ENST00000323007.3_Silent_p.Q149Q			P40197	GPV_HUMAN	glycoprotein V (platelet)	149					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|negative regulation of platelet activation (GO:0010544)|platelet activation (GO:0030168)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(14)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	35	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)		GAGCGAGCTCCTGCAGGTTAA	0.483													C|||	104	0.0207668	0.0008	0.0187	5008	,	,		19650	0.0079		0.0437	False		,,,				2504	0.0389				p.Q149Q		Atlas-SNP	.											.	GP5	106	.	0			c.G447A						PASS	.	C		40,4366	42.3+/-75.8	1,38,2164	80.0	80.0	80.0		447	1.9	1.0	3	dbSNP_130	80	417,8183	129.5+/-187.6	13,391,3896	no	coding-synonymous	GP5	NM_004488.2		14,429,6060	TT,TC,CC		4.8488,0.9079,3.5138		149/561	194118565	457,12549	2203	4300	6503	SO:0001819	synonymous_variant	2814	exon2			GAGCTCCTGCAGG	L11238	CCDS3307.1	3q29	2008-02-01			ENSG00000178732	ENSG00000178732		"""CD molecules"""	4443	protein-coding gene	gene with protein product		173511				7690959	Standard	NM_004488		Approved	CD42d	uc003ftv.1	P40197	OTTHUMG00000150345	ENST00000401815.1:c.447G>A	3.37:g.194118565C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_004488	D1MER9	Silent	SNP	ENST00000401815.1	37	CCDS3307.1																																																																																			C|0.969;T|0.031	0.031	strong		0.483	GP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317710.1	NM_004488	
GSG1L	146395	hgsc.bcm.edu	37	16	27974487	27974487	+	Silent	SNP	T	T	C	rs2051743	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:27974487T>C	ENST00000447459.2	-	2	471	c.387A>G	c.(385-387)gcA>gcG	p.A129A	GSG1L_ENST00000380898.2_5'UTR|GSG1L_ENST00000395724.3_Silent_p.A129A	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	129					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						CTTTCTCCGATGCCGGGGCCA	0.542													C|||	2908	0.580671	0.4244	0.6787	5008	,	,		22024	0.754		0.5577	False		,,,				2504	0.5675				p.A129A		Atlas-SNP	.											.	GSG1L	82	.	0			c.A387G						PASS	.	C		1838,2154		432,974,590	73.0	79.0	77.0		387	-9.1	0.1	16	dbSNP_94	77	4833,3497		1441,1951,773	no	coding-synonymous	GSG1L	NM_001109763.1		1873,2925,1363	CC,CT,TT		41.9808,46.0421,45.8611		129/332	27974487	6671,5651	1996	4165	6161	SO:0001819	synonymous_variant	146395	exon2			CTCCGATGCCGGG	AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.387A>G	16.37:g.27974487T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_001109763	Q7Z6F8|Q8TB81	Silent	SNP	ENST00000447459.2	37	CCDS45450.1																																																																																			T|0.424;C|0.576	0.576	strong		0.542	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675	
MTMR9	66036	hgsc.bcm.edu	37	8	11162496	11162496	+	Silent	SNP	A	A	C	rs2164272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11162496A>C	ENST00000221086.3	+	4	1037	c.564A>C	c.(562-564)ctA>ctC	p.L188L	MTMR9_ENST00000526292.1_Silent_p.L103L	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	188	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		TCCCAGTACTAAGCTATTACC	0.463													A|||	2004	0.40016	0.1536	0.353	5008	,	,		21032	0.7063		0.3917	False		,,,				2504	0.4601				p.L188L		Atlas-SNP	.											.	MTMR9	58	.	0			c.A564C						PASS	.	A		881,3525	342.8+/-307.3	94,693,1416	123.0	104.0	110.0		564	-5.6	0.9	8	dbSNP_96	110	3482,5118	510.7+/-377.6	707,2068,1525	no	coding-synonymous	MTMR9	NM_015458.3		801,2761,2941	CC,CA,AA		40.4884,19.9955,33.5461		188/550	11162496	4363,8643	2203	4300	6503	SO:0001819	synonymous_variant	66036	exon4			AGTACTAAGCTAT	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	14596	protein-coding gene	gene with protein product		606260	"""myotubularin related protein 8"""	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.564A>C	8.37:g.11162496A>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Silent	SNP	ENST00000221086.3	37	CCDS5979.1																																																																																			A|0.640;C|0.360	0.360	strong		0.463	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458	
FKBP5	2289	hgsc.bcm.edu	37	6	35544942	35544942	+	Silent	SNP	G	G	A	rs34866878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:35544942G>A	ENST00000539068.1	-	10	1297	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	FKBP5_ENST00000536438.1_Silent_p.N365N|FKBP5_ENST00000540787.1_Silent_p.N186N|FKBP5_ENST00000357266.4_Silent_p.N365N	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	365					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						ACTCAAACTCGTTCATGAGCA	0.483													G|||	334	0.0666933	0.2239	0.0245	5008	,	,		18453	0.001		0.0179	False		,,,				2504	0.002				p.N365N		Atlas-SNP	.											.	FKBP5	64	.	0			c.C1095T						PASS	.	G	,,	815,3591	326.1+/-299.4	68,679,1456	161.0	154.0	156.0		1095,1095,1095	-3.6	0.8	6	dbSNP_126	156	225,8375	92.8+/-154.8	5,215,4080	no	coding-synonymous,coding-synonymous,coding-synonymous	FKBP5	NM_001145775.1,NM_001145776.1,NM_004117.3	,,	73,894,5536	AA,AG,GG		2.6163,18.4975,7.9963	,,	365/458,365/458,365/458	35544942	1040,11966	2203	4300	6503	SO:0001819	synonymous_variant	2289	exon11			AAACTCGTTCATG	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"""Tetratricopeptide (TTC) repeat domain containing"""	3721	protein-coding gene	gene with protein product		602623	"""FK506-binding protein 5"""			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.1095C>T	6.37:g.35544942G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	206	82	0.398058	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Silent	SNP	ENST00000539068.1	37	CCDS4808.1																																																																																			G|0.928;A|0.072	0.072	strong		0.483	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2		
TRIM66	9866	hgsc.bcm.edu	37	11	8671369	8671369	+	Silent	SNP	C	C	T	rs10840101	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8671369C>T	ENST00000299550.6	-	3	269	c.75G>A	c.(73-75)ctG>ctA	p.L25L	TRIM66_ENST00000531498.1_5'UTR|TRIM66_ENST00000402157.2_Silent_p.L25L	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	25						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						AAGAGCTGCACAGCCAGCGAT	0.562													C|||	742	0.148163	0.0076	0.2003	5008	,	,		19751	0.1329		0.2744	False		,,,				2504	0.1871				p.L25L		Atlas-SNP	.											.	TRIM66	45	.	0			c.G75A						PASS	.	C		70,1314		1,68,623	74.0	74.0	74.0		75	-0.9	1.0	11	dbSNP_120	74	954,2228		131,692,768	no	coding-synonymous	TRIM66	NM_014818.1		132,760,1391	TT,TC,CC		29.9811,5.0578,22.4266		25/1217	8671369	1024,3542	692	1591	2283	SO:0001819	synonymous_variant	9866	exon3			GCTGCACAGCCAG	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.75G>A	11.37:g.8671369C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_014818	Q9BQQ4	Silent	SNP	ENST00000299550.6	37																																																																																				C|0.817;T|0.183	0.183	strong		0.562	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
ATP13A2	23400	hgsc.bcm.edu	37	1	17314942	17314942	+	Silent	SNP	G	G	A	rs9435662	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17314942G>A	ENST00000326735.8	-	24	2670	c.2637C>T	c.(2635-2637)ggC>ggT	p.G879G	ATP13A2_ENST00000452699.1_Silent_p.G874G|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.G835G			Q9NQ11	AT132_HUMAN	ATPase type 13A2	879					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGTCATTGGCGCCGTCTCCGC	0.617													G|||	1696	0.338658	0.1369	0.4568	5008	,	,		14687	0.2599		0.508	False		,,,				2504	0.4346				p.G879G		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C2637T						PASS	.	G	,,	912,3494	352.3+/-311.7	101,710,1392	85.0	84.0	84.0		2622,2505,2637	-7.5	0.6	1	dbSNP_119	84	4491,4109	590.3+/-392.7	1154,2183,963	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	1255,2893,2355	AA,AG,GG		47.7791,20.699,41.5424	,,	874/1176,835/1159,879/1181	17314942	5403,7603	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon24			ATTGGCGCCGTCT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2637C>T	1.37:g.17314942G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			G|0.606;A|0.394	0.394	strong		0.617	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
HABP2	3026	hgsc.bcm.edu	37	10	115348046	115348046	+	Missense_Mutation	SNP	G	G	A	rs7080536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:115348046G>A	ENST00000351270.3	+	13	1697	c.1601G>A	c.(1600-1602)gGg>gAg	p.G534E	HABP2_ENST00000542051.1_Missense_Mutation_p.G508E	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	534	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		G -> E (in Marburg I polymorphism; impairs the pro-urokinase activating potency; could be a prominent risk predictor of carotid stenosis; dbSNP:rs7080536). {ECO:0000269|PubMed:12578864, ECO:0000269|Ref.3}.		cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	CTGGAGTGTGGGAAGAGGCCA	0.532													G|||	41	0.0081869	0.0	0.0144	5008	,	,		19083	0.0		0.0268	False		,,,				2504	0.0041				p.G534E		Atlas-SNP	.											.	HABP2	52	.	0			c.G1601A	GRCh37	CM032937	HABP2	M	rs7080536	PASS	.	G	GLU/GLY,GLU/GLY	29,4377	36.0+/-67.5	0,29,2174	94.0	90.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1523,1601	5.9	1.0	10	dbSNP_116	91	334,8266	115.7+/-175.5	5,324,3971	yes	missense,missense	HABP2	NM_001177660.1,NM_004132.3	98,98	5,353,6145	AA,AG,GG		3.8837,0.6582,2.791	probably-damaging,probably-damaging	508/535,534/561	115348046	363,12643	2203	4300	6503	SO:0001583	missense	3026	exon13			AGTGTGGGAAGAG		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.1601G>A	10.37:g.115348046G>A	ENSP00000277903:p.Gly534Glu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_004132	A8K467|B7Z8U5|F5H5M6|O00663	Missense_Mutation	SNP	ENST00000351270.3	37	CCDS7577.1	30	0.013736263736263736	0	0.0	8	0.022099447513812154	0	0.0	22	0.029023746701846966	G	20.4	3.989569	0.74589	0.006582	0.038837	ENSG00000148702	ENST00000542051;ENST00000351270	D;D	0.94330	-3.4;-3.4	5.93	5.93	0.95920	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.89812	0.6823	M	0.76433	2.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89697	0.3902	10	0.87932	D	0	.	20.3437	0.98782	0.0:0.0:1.0:0.0	rs7080536;rs52799969;rs7080536	534	Q14520	HABP2_HUMAN	E	508;534	ENSP00000443283:G508E;ENSP00000277903:G534E	ENSP00000277903:G534E	G	+	2	0	HABP2	115338036	1.000000	0.71417	1.000000	0.80357	0.100000	0.18952	7.569000	0.82380	2.815000	0.96918	0.561000	0.74099	GGG	G|0.979;A|0.021	0.021	strong		0.532	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37730456	37730456	+	Missense_Mutation	SNP	G	G	T	rs7341564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:37730456G>T	ENST00000330843.4	-	4	1876	c.1864C>A	c.(1864-1866)Cag>Aag	p.Q622K	RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	622			Q -> K (in dbSNP:rs7341564). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16920206}.		protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			GACTTGGCCTGGCCCCTGTCT	0.522													G|||	1490	0.297524	0.497	0.2666	5008	,	,		20691	0.12		0.3767	False		,,,				2504	0.1513				p.Q622K		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C1864A						PASS	.	G	LYS/GLN,	2018,2388	563.8+/-381.3	472,1074,657	101.0	94.0	96.0		1864,	3.0	0.0	8	dbSNP_116	96	3028,5572	466.3+/-366.7	517,1994,1789	yes	missense,intron	RAB11FIP1	NM_001002814.2,NM_025151.4	53,	989,3068,2446	TT,TG,GG		35.2093,45.8012,38.7975	benign,	622/1284,	37730456	5046,7960	2203	4300	6503	SO:0001583	missense	80223	exon4			TGGCCTGGCCCCT	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.1864C>A	8.37:g.37730456G>T	ENSP00000331342:p.Gln622Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	684	0.3131868131868132	251	0.5101626016260162	107	0.2955801104972376	58	0.10139860139860139	268	0.35356200527704484	G	13.08	2.131448	0.37630	0.458012	0.352093	ENSG00000156675	ENST00000330843	T	0.13307	2.6	5.8	2.95	0.34219	.	0.570331	0.15816	N	0.243228	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.30937	-0.9961	6	0.06757	T	0.87	-1.1565	11.2559	0.49054	0.0:0.4333:0.4399:0.1268	rs7341564;rs61018507;rs7341564	.	.	.	K	622	ENSP00000331342:Q622K	ENSP00000331342:Q622K	Q	-	1	0	RAB11FIP1	37849614	0.003000	0.15002	0.009000	0.14445	0.013000	0.08279	0.563000	0.23547	0.321000	0.23259	0.655000	0.94253	CAG	G|0.643;N|0.001	.	strong		0.522	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151	
GP2	2813	hgsc.bcm.edu	37	16	20328685	20328685	+	Silent	SNP	T	T	C	rs1129818	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20328685T>C	ENST00000381362.4	-	9	1351	c.1275A>G	c.(1273-1275)caA>caG	p.Q425Q	GP2_ENST00000302555.5_Silent_p.Q422Q|GP2_ENST00000381360.5_Silent_p.Q278Q|GP2_ENST00000341642.5_Silent_p.Q275Q|GP2_ENST00000573897.1_5'Flank	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	425	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						TGGAATCACGTTGATTTGAGC	0.483													T|||	1194	0.238419	0.0522	0.3012	5008	,	,		16717	0.1071		0.4364	False		,,,				2504	0.3773				p.Q425Q		Atlas-SNP	.											.	GP2	122	.	0			c.A1275G						PASS	.	T	,,,	557,3849	248.4+/-256.2	29,499,1675	86.0	69.0	75.0		1275,834,825,1266	-1.7	0.0	16	dbSNP_86	75	3778,4822	535.9+/-382.9	830,2118,1352	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GP2	NM_001007240.1,NM_001007241.1,NM_001007242.1,NM_001502.2	,,,	859,2617,3027	CC,CT,TT		43.9302,12.6419,33.3308	,,,	425/538,278/391,275/388,422/535	20328685	4335,8671	2203	4300	6503	SO:0001819	synonymous_variant	2813	exon9			ATCACGTTGATTT	U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.1275A>G	16.37:g.20328685T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001007240	A6NFM9|A6NJA8|Q13338|Q9UIF1	Silent	SNP	ENST00000381362.4	37	CCDS42128.1																																																																																			T|0.687;C|0.313	0.313	strong		0.483	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347053	140347053	+	Silent	SNP	C	C	T	rs155807	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140347053C>T	ENST00000289269.5	+	1	1234	c.702C>T	c.(700-702)atC>atT	p.I234I	PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	234	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGGGGGCATCCCAGCCCGCT	0.602													C|||	1777	0.354832	0.2239	0.3934	5008	,	,		21052	0.5456		0.332	False		,,,				2504	0.3313				p.I234I	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C702T						PASS	.	C	,,,,,,,,,,,,,,,,,,	1101,3305	394.0+/-329.1	144,813,1246	55.0	54.0	55.0		,702,,,,,,,,,,,,,,,,,702	3.0	1.0	5	dbSNP_79	55	2820,5780	441.0+/-359.7	446,1928,1926	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	590,2741,3172	TT,TC,CC		32.7907,24.9887,30.1476	,,,,,,,,,,,,,,,,,,	,234/1008,,,,,,,,,,,,,,,,,234/885	140347053	3921,9085	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			GGGCATCCCAGCC	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.702C>T	5.37:g.140347053C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	140	44	0.314286	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			C|0.679;T|0.321	0.321	strong		0.602	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
SYNPO2	171024	hgsc.bcm.edu	37	4	119947985	119947985	+	Missense_Mutation	SNP	G	G	C	rs12645298	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:119947985G>C	ENST00000429713.2	+	3	643	c.461G>C	c.(460-462)gGc>gCc	p.G154A	SYNPO2_ENST00000434046.2_Missense_Mutation_p.G154A|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.G154A	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	154			G -> A (in dbSNP:rs12645298). {ECO:0000269|PubMed:17974005}.			actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GACTGTGCAGGCAGCTTGAAA	0.552													G|||	1288	0.257188	0.0908	0.3876	5008	,	,		17925	0.4196		0.2256	False		,,,				2504	0.2546				p.G154A		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G461C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	538,3868	227.8+/-242.9	38,462,1703	38.0	41.0	40.0		461,461,461	1.3	0.0	4	dbSNP_120	40	2231,6369	360.3+/-331.9	291,1649,2360	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	60,60,60	329,2111,4063	CC,CG,GG		25.9419,12.2106,21.2902	possibly-damaging,possibly-damaging,possibly-damaging	154/1094,154/1110,154/1262	119947985	2769,10237	2203	4300	6503	SO:0001583	missense	171024	exon3			GTGCAGGCAGCTT	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.461G>C	4.37:g.119947985G>C	ENSP00000395143:p.Gly154Ala	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	116	50	0.431034	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	598|598	0.27380952380952384|0.27380952380952384	52|52	0.10569105691056911|0.10569105691056911	119|119	0.3287292817679558|0.3287292817679558	244|244	0.42657342657342656|0.42657342657342656	183|183	0.24142480211081793|0.24142480211081793	G|G	3.203|3.203	-0.163297|-0.163297	0.06502|0.06502	0.122106|0.122106	0.259419|0.259419	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.07908|.	3.15;3.18;3.17|.	4.98|4.98	1.33|1.33	0.21861|0.21861	.|.	0.862354|.	0.10111|.	N|.	0.714774|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.64997|0.64997	1.995|1.995	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	P;P;P;P|.	0.46784|.	0.884;0.873;0.805;0.805|.	B;B;B;B|.	0.33454|.	0.142;0.164;0.142;0.142|.	T|T	0.41627|0.41627	-0.9498|-0.9498	9|4	0.40728|.	T|.	0.16|.	-3.3096|-3.3096	8.3309|8.3309	0.32187|0.32187	0.4442:0.0:0.5558:0.0|0.4442:0.0:0.5558:0.0	rs12645298;rs52814983;rs12645298|rs12645298;rs52814983;rs12645298	154;154;154;154|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	A|S	154|105	ENSP00000306015:G154A;ENSP00000395143:G154A;ENSP00000390965:G154A|.	ENSP00000306015:G154A|.	G|R	+|+	2|3	0|2	SYNPO2|SYNPO2	120167433|120167433	0.006000|0.006000	0.16342|0.16342	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.548000|0.548000	0.23314|0.23314	0.032000|0.032000	0.15435|0.15435	-0.262000|-0.262000	0.10625|0.10625	GGC|AGG	G|0.768;C|0.232	0.232	strong		0.552	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
DXO	1797	hgsc.bcm.edu	37	6	31938451	31938451	+	Silent	SNP	T	T	C	rs35337578	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31938451T>C	ENST00000375349.3	-	4	1155	c.744A>G	c.(742-744)ccA>ccG	p.P248P	DXO_ENST00000337523.5_Silent_p.P248P|STK19_ENST00000375333.2_5'Flank|DXO_ENST00000375356.3_Silent_p.P248P|DXO_ENST00000478221.1_5'UTR|STK19_ENST00000375331.2_5'Flank			O77932	DXO_HUMAN	decapping exoribonuclease	248					metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										CATAGCAGGTTGGGGGCTGTG	0.612													C|||	600	0.119808	0.1725	0.0764	5008	,	,		17169	0.0347		0.0994	False		,,,				2504	0.1881				p.P248P		Atlas-SNP	.											.	DOM3Z	20	.	0			c.A744G						PASS	.	C		452,2568		34,384,1092	68.0	75.0	73.0		744	-7.2	0.0	6	dbSNP_126	73	497,4921		35,427,2247	no	coding-synonymous	DOM3Z	NM_005510.3		69,811,3339	CC,CT,TT		9.1731,14.9669,11.2467		248/397	31938451	949,7489	1510	2709	4219	SO:0001819	synonymous_variant	1797	exon4			GCAGGTTGGGGGC	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"""DOM-3 (C. elegans) homolog Z"", ""dom-3 homolog Z (C. elegans)"""	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.744A>G	6.37:g.31938451T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	127	79	0.622047	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Silent	SNP	ENST00000375349.3	37	CCDS4732.1	221	0.10119047619047619	95	0.19308943089430894	26	0.0718232044198895	22	0.038461538461538464	78	0.10290237467018469	C	3.700	-0.061674	0.07317	0.149669	0.091731	ENSG00000204348	ENST00000495340	.	.	.	4.46	-7.15	0.01521	.	.	.	.	.	T	0.03011	0.0089	.	.	.	0.09310	P	0.9999999999990461	.	.	.	.	.	.	T	0.28038	-1.0056	3	.	.	.	-17.4696	0.1015	0.00048	0.3164:0.1726:0.1974:0.3137	rs35337578	.	.	.	R	55	.	.	Q	-	2	0	DOM3Z	32046430	0.000000	0.05858	0.037000	0.18230	0.818000	0.46254	-2.978000	0.00664	-2.191000	0.00756	-2.364000	0.00238	CAA	T|0.893;C|0.107	0.107	strong		0.612	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3		
TMEM88B	643965	hgsc.bcm.edu	37	1	1361530	1361530	+	Missense_Mutation	SNP	C	C	T	rs144957058|rs560540562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1361530C>T	ENST00000378821.3	+	1	23	c.23C>T	c.(22-24)aCg>aTg	p.T8M		NM_001146685.1	NP_001140157.1	A6NKF7	TM88B_HUMAN	transmembrane protein 88B	8	Poly-Glu.					integral component of membrane (GO:0016021)											GGGAGGGAGACGGAGGAGGAG	0.697														141	0.028155	0.003	0.0202	5008	,	,		12389	0.001		0.0437	False		,,,				2504	0.0798				p.T8M		Atlas-SNP	.											.	.	.	.	0			c.C23T						PASS	.		MET/THR	12,1366		0,12,677	18.0	25.0	23.0		23	-1.9	0.0	1	dbSNP_134	23	184,2982		8,168,1407	yes	missense	TMEM88B	NM_001146685.1	81	8,180,2084	TT,TC,CC		5.8117,0.8708,4.3134	benign	8/164	1361530	196,4348	689	1583	2272	SO:0001583	missense	643965	exon1			GGGAGACGGAGGA		CCDS57964.1	1p36.33	2013-01-16			ENSG00000205116	ENSG00000205116			37099	protein-coding gene	gene with protein product							Standard	NM_001146685		Approved		uc010nyp.2	A6NKF7	OTTHUMG00000153395	ENST00000378821.3:c.23C>T	1.37:g.1361530C>T	ENSP00000455099:p.Thr8Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_001146685		Missense_Mutation	SNP	ENST00000378821.3	37	CCDS57964.1																																																																																			C|0.978;T|0.022	0.022	strong		0.697	TMEM88B-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331012.2	NM_001146685	
GP6	51206	hgsc.bcm.edu	37	19	55539094	55539094	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55539094G>A	ENST00000417454.1	-	4	489	c.462C>T	c.(460-462)taC>taT	p.Y154Y	CTC-550B14.6_ENST00000585492.1_RNA|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Silent_p.Y154Y|CTC-550B14.7_ENST00000586845.1_RNA|CTC-550B14.7_ENST00000586961.1_RNA|GP6_ENST00000310373.3_Silent_p.Y154Y	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	154	Ig-like C2-type 2.				blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		CGGGATTCTTGTAGGGCGCAG	0.587																																					p.Y154Y		Atlas-SNP	.											.	GP6	55	.	0			c.C462T						PASS	.						77.0	86.0	83.0					19																	55539094		1985	4171	6156	SO:0001819	synonymous_variant	51206	exon4			ATTCTTGTAGGGC	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.462C>T	19.37:g.55539094G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_016363	Q9HCN7|Q9UIF2	Silent	SNP	ENST00000417454.1	37	CCDS46184.1																																																																																			.	.	none		0.587	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
PMEL	6490	hgsc.bcm.edu	37	12	56348028	56348028	+	Silent	SNP	G	G	A	rs1052206	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56348028G>A	ENST00000548747.1	-	11	2618	c.1956C>T	c.(1954-1956)aaC>aaT	p.N652N	PMEL_ENST00000360714.4_Silent_p.N659N|PMEL_ENST00000449260.2_Silent_p.N659N|PMEL_ENST00000550447.1_Silent_p.N281N|PMEL_ENST00000536427.1_Silent_p.N617N|PMEL_ENST00000552882.1_Silent_p.N652N|PMEL_ENST00000539511.1_Silent_p.N566N|PMEL_ENST00000550464.1_Silent_p.N566N|PMEL_ENST00000548493.1_Silent_p.N652N			P40967	PMEL_HUMAN	premelanosome protein	652					melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGAGGGGGCTGTTCTCACCAA	0.522													G|||	3603	0.719449	0.5076	0.7522	5008	,	,		19637	0.7748		0.7932	False		,,,				2504	0.8497				p.N659N		Atlas-SNP	.											.	PMEL	60	.	0			c.C1977T						PASS	.	G	,,	2445,1961	620.2+/-393.5	697,1051,455	112.0	100.0	104.0		1698,1977,1956	2.8	0.8	12	dbSNP_86	104	6970,1630	741.9+/-407.2	2800,1370,130	no	coding-synonymous,coding-synonymous,coding-synonymous	PMEL	NM_001200053.1,NM_001200054.1,NM_006928.4	,,	3497,2421,585	AA,AG,GG		18.9535,44.5075,27.6103	,,	566/576,659/669,652/662	56348028	9415,3591	2203	4300	6503	SO:0001819	synonymous_variant	6490	exon11			GGGGCTGTTCTCA	AK092881	CCDS8897.1, CCDS55833.1, CCDS55834.1	12q13-q14	2010-12-17	2010-12-17	2010-12-17	ENSG00000185664	ENSG00000185664			10880	protein-coding gene	gene with protein product		155550	"""silver (mouse homolog) like"", ""silver homolog (mouse)"""	SIL, SILV		8739560	Standard	NM_001200053		Approved	D12S53E, SI, Pmel17, gp100	uc001siq.3	P40967		ENST00000548747.1:c.1956C>T	12.37:g.56348028G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001200054	B3KS57|B7Z6D7|Q12763|Q14448|Q14817|Q16565	Silent	SNP	ENST00000548747.1	37	CCDS8897.1																																																																																			G|0.272;A|0.728	0.728	strong		0.522	PMEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409626.1	NM_006928	
C11orf16	56673	hgsc.bcm.edu	37	11	8948680	8948680	+	Silent	SNP	A	A	T	rs3751065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8948680A>T	ENST00000326053.5	-	4	472	c.366T>A	c.(364-366)ccT>ccA	p.P122P	C11orf16_ENST00000525780.1_Silent_p.P122P|C11orf16_ENST00000528998.1_5'UTR	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	122										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		CTGCGACAAGAGGAGCCTCGA	0.517													A|||	2642	0.527556	0.2821	0.6772	5008	,	,		21267	0.7093		0.6044	False		,,,				2504	0.4867				p.P122P		Atlas-SNP	.											.	C11orf16	43	.	0			c.T366A						PASS	.	A		1468,2934	472.0+/-356.2	244,980,977	53.0	46.0	48.0		366	3.3	0.5	11	dbSNP_107	48	5219,3373	639.7+/-399.5	1580,2059,657	no	coding-synonymous	C11orf16	NM_020643.2		1824,3039,1634	TT,TA,AA		39.2574,33.3485,48.5378		122/468	8948680	6687,6307	2201	4296	6497	SO:0001819	synonymous_variant	56673	exon4			GACAAGAGGAGCC	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.366T>A	11.37:g.8948680A>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	NM_020643	Q53FB2|Q8N6Y9	Silent	SNP	ENST00000326053.5	37	CCDS7794.1																																																																																			A|0.472;T|0.528	0.528	strong		0.517	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388635	1388635	+	Silent	SNP	T	T	C	rs74518227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388635T>C	ENST00000324803.4	+	1	3296	c.336T>C	c.(334-336)tgT>tgC	p.C112C		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	112					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.C112C(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCCATGTGGAGTGCCCG	0.672													N|||	258	0.0515176	0.0348	0.0548	5008	,	,		16946	0.0069		0.0507	False		,,,				2504	0.1186				p.C112C		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,4	CRIPAK	185	4	1	Substitution - coding silent(1)	prostate(1)	c.T336C						PASS	.						189.0	145.0	160.0					4																	1388635		2203	4299	6502	SO:0001819	synonymous_variant	285464	exon1			CCCATGTGGAGTG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.336T>C	4.37:g.1388635T>C		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	133	83	0.62406	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.811	0.333996	0.11013	.	.	ENSG00000179979	ENST00000382944	.	.	.	0.948	-1.08	0.09936	.	.	.	.	.	T	0.21427	0.0516	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.27123	-1.0083	5	0.25106	T	0.35	.	4.049	0.09786	0.3111:0.0:0.0:0.6889	.	.	.	.	R	96	.	ENSP00000372402:W96R	W	+	1	0	CRIPAK	1378635	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-1.127000	0.03251	-0.202000	0.10268	0.102000	0.15555	TGG	T|0.937;C|0.063	0.063	strong		0.672	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
TBC1D26	353149	hgsc.bcm.edu	37	17	15644506	15644506	+	Missense_Mutation	SNP	C	C	T	rs11650318	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:15644506C>T	ENST00000437605.2	+	10	867	c.617C>T	c.(616-618)gCt>gTt	p.A206V	AC005324.6_ENST00000433873.1_RNA|AC005324.6_ENST00000580194.1_RNA|ZNF286A_ENST00000413242.2_3'UTR|AC005324.6_ENST00000434017.1_RNA	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	206	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		A -> V (in dbSNP:rs11650318). {ECO:0000269|PubMed:15489334}.				Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		GAGGAAGATGCTTTCTGGGCG	0.622													.|||	1235	0.246605	0.0817	0.2651	5008	,	,		21089	0.255		0.3946	False		,,,				2504	0.2955				p.A206V		Atlas-SNP	.											.	TBC1D26	16	.	0			c.C617T						PASS	.	C	VAL/ALA	577,3797	223.0+/-239.6	41,495,1651	91.0	98.0	96.0		617	0.7	0.0	17	dbSNP_120	96	3426,5150	489.3+/-372.6	665,2096,1527	yes	missense	TBC1D26	NM_178571.4	64	706,2591,3178	TT,TC,CC		39.9487,13.1916,30.9112	probably-damaging	206/251	15644506	4003,8947	2187	4288	6475	SO:0001583	missense	353149	exon10			AAGATGCTTTCTG		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.617C>T	17.37:g.15644506C>T	ENSP00000410111:p.Ala206Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_178571	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	37	CCDS42265.1																																																																																			C|0.723;T|0.277	0.277	strong		0.622	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571	
SEZ6L	23544	hgsc.bcm.edu	37	22	26688838	26688838	+	Silent	SNP	C	C	T	rs17304075	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26688838C>T	ENST00000248933.6	+	2	656	c.561C>T	c.(559-561)gaC>gaT	p.D187D	SEZ6L_ENST00000404234.3_Silent_p.D187D|SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000360929.3_Silent_p.D187D|SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000529632.2_Silent_p.D187D|SEZ6L_ENST00000343706.4_Silent_p.D187D			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	187					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TTTGGCTGGACCGAAAGGAGA	0.642													C|||	267	0.0533147	0.0083	0.0576	5008	,	,		17473	0.0		0.1362	False		,,,				2504	0.0808				p.D187D		Atlas-SNP	.											SEZ6L,NS,carcinoma,+2,1	SEZ6L	174	1	0			c.C561T						PASS	.	C	,,,,,	94,4312	75.7+/-113.9	1,92,2110	53.0	54.0	54.0		561,561,561,561,561,561	-6.2	0.0	22	dbSNP_123	54	1025,7575	213.6+/-253.5	53,919,3328	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	54,1011,5438	TT,TC,CC		11.9186,2.1335,8.6037	,,,,,	187/1024,187/1014,187/1012,187/950,187/949,187/1025	26688838	1119,11887	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon2			GCTGGACCGAAAG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.561C>T	22.37:g.26688838C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			C|0.919;T|0.081	0.081	strong		0.642	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
CCNT1	904	hgsc.bcm.edu	37	12	49086963	49086963	+	Silent	SNP	G	G	A	rs3741632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49086963G>A	ENST00000261900.3	-	9	2256	c.2034C>T	c.(2032-2034)ccC>ccT	p.P678P		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	678					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						CAAATGCAGTGGGCTGAGTGG	0.512													G|||	2975	0.59405	0.4463	0.5692	5008	,	,		17119	0.7768		0.5746	False		,,,				2504	0.6431				p.P678P		Atlas-SNP	.											.	CCNT1	55	.	0			c.C2034T						PASS	.	G		2008,2398	559.8+/-380.3	457,1094,652	147.0	137.0	140.0		2034	-0.2	1.0	12	dbSNP_107	140	5082,3518	632.4+/-398.6	1486,2110,704	no	coding-synonymous	CCNT1	NM_001240.2		1943,3204,1356	AA,AG,GG		40.907,45.5742,45.4867		678/727	49086963	7090,5916	2203	4300	6503	SO:0001819	synonymous_variant	904	exon9			TGCAGTGGGCTGA	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.2034C>T	12.37:g.49086963G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	216	216	1	NM_001240	A9XU13|E7EX76|O60581	Silent	SNP	ENST00000261900.3	37	CCDS8766.1																																																																																			G|0.434;A|0.566	0.566	strong		0.512	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240	
MUC2	4583	hgsc.bcm.edu	37	11	1092553	1092553	+	Missense_Mutation	SNP	A	A	C	rs570715417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1092553A>C	ENST00000441003.2	+	30	4399	c.4372A>C	c.(4372-4374)Ata>Cta	p.I1458L	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.I1459L|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4238	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CAGCCCTCCAATAAGcaccac	0.632													a|||	114	0.0227636	0.0189	0.0274	5008	,	,		16743	0.0188		0.0219	False		,,,				2504	0.0297				p.I1458L		Atlas-SNP	.											MUC2_ENST00000441003,extremity,malignant_melanoma,-1,2	MUC2	614	2	0			c.A4372C						scavenged	.						150.0	246.0	213.0					11																	1092553		1570	3013	4583	SO:0001583	missense	4583	exon30			CCTCCAATAAGCA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4372A>C	11.37:g.1092553A>C	ENSP00000415183:p.Ile1458Leu	Somatic	312	6	0.0192308		WXS	Illumina HiSeq	Phase_I	312	14	0.0448718	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	a	2.178	-0.388262	0.04932	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12255	2.73;2.7	1.61	-3.21	0.05140	.	46.913700	0.01168	N	0.006809	T	0.07413	0.0187	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20706	-1.0267	9	0.26408	T	0.33	.	1.1043	0.01690	0.3277:0.2218:0.3119:0.1387	.	1458	E7EUV1	.	L	1458;1459	ENSP00000415183:I1458L;ENSP00000351956:I1459L	ENSP00000351956:I1459L	I	+	1	0	MUC2	1082553	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.082000	0.14847	-1.929000	0.01057	0.000000	0.15137	ATA	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
PXK	54899	hgsc.bcm.edu	37	3	58382846	58382846	+	Silent	SNP	C	C	T	rs3191903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58382846C>T	ENST00000356151.2	+	10	1012	c.903C>T	c.(901-903)tgC>tgT	p.C301C	PXK_ENST00000536660.1_Silent_p.C164C|PXK_ENST00000479241.1_Silent_p.C284C|PXK_ENST00000383716.3_Silent_p.C268C|PXK_ENST00000383715.4_Silent_p.C284C|PXK_ENST00000484288.1_Silent_p.C301C|PXK_ENST00000463280.1_Silent_p.C268C|PXK_ENST00000302779.5_Silent_p.C284C	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		GGGACACTTGCCGGCTGCTGG	0.433													C|||	1005	0.200679	0.1959	0.2839	5008	,	,		18767	0.001		0.3777	False		,,,				2504	0.1718				p.C301C		Atlas-SNP	.											.	PXK	89	.	0			c.C903T						PASS	.	C		907,3499	350.8+/-311.0	89,729,1385	162.0	170.0	167.0		903	5.5	1.0	3	dbSNP_105	167	3210,5390	484.3+/-371.4	617,1976,1707	no	coding-synonymous	PXK	NM_017771.3		706,2705,3092	TT,TC,CC		37.3256,20.5856,31.6546		301/579	58382846	4117,8889	2203	4300	6503	SO:0001819	synonymous_variant	54899	exon10			CACTTGCCGGCTG	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.903C>T	3.37:g.58382846C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_017771		Silent	SNP	ENST00000356151.2	37	CCDS2889.1	493	0.22573260073260074	110	0.22357723577235772	110	0.30386740331491713	0	0.0	273	0.36015831134564646	C	10.37	1.332515	0.24167	0.205856	0.373256	ENSG00000168297	ENST00000479134	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.01452	-1.1351	3	.	.	.	-12.8138	19.5916	0.95514	0.0:1.0:0.0:0.0	rs3191903;rs17845192;rs17858004;rs17858288;rs3191903	.	.	.	V	56	.	.	A	+	2	0	PXK	58357886	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.606000	0.36826	2.861000	0.98227	0.655000	0.94253	GCC	C|0.701;T|0.299	0.299	strong		0.433	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771	
GNPTG	84572	hgsc.bcm.edu	37	16	1411894	1411894	+	Silent	SNP	G	G	A	rs76594024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1411894G>A	ENST00000204679.4	+	5	298	c.255G>A	c.(253-255)ccG>ccA	p.P85P	LA16c-316G12.2_ENST00000569831.1_RNA	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit	85	PRKCSH.				carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				AGTTCTGCCCGTTCCACAACG	0.657													G|||	11	0.00219649	0.0015	0.0029	5008	,	,		15450	0.0		0.007	False		,,,				2504	0.0				p.P85P		Atlas-SNP	.											.	GNPTG	18	.	0			c.G255A						PASS	.	G		23,4375	29.9+/-59.1	0,23,2176	58.0	53.0	54.0		255	-10.0	0.0	16	dbSNP_131	54	71,8529	42.6+/-100.3	0,71,4229	no	coding-synonymous	GNPTG	NM_032520.4		0,94,6405	AA,AG,GG		0.8256,0.523,0.7232		85/306	1411894	94,12904	2199	4300	6499	SO:0001819	synonymous_variant	84572	exon5			CTGCCCGTTCCAC	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"""GlcNAc-phosphotransferase gamma-subunit"""	607838	"""N-acetylglucosamine-1-phosphotransferase, gamma subunit"", ""chromosome 16 open reading frame 27"""	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835	ENST00000204679.4:c.255G>A	16.37:g.1411894G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_032520	B2R556|Q6XYD7|Q96L13	Silent	SNP	ENST00000204679.4	37	CCDS10436.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	0.346	-0.947731	0.02304	0.00523	0.008256	ENSG00000090581	ENST00000529110	.	.	.	5.0	-10.0	0.00425	.	.	.	.	.	T	0.31231	0.0790	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56288	-0.8004	4	.	.	.	-13.0868	2.9834	0.05961	0.31:0.094:0.4001:0.1959	.	.	.	.	I	108	.	.	V	+	1	0	GNPTG	1351895	0.000000	0.05858	0.027000	0.17364	0.670000	0.39368	-3.271000	0.00532	-4.717000	0.00035	-1.021000	0.02439	GTT	G|0.994;A|0.006	0.006	strong		0.657	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520	
MYH7B	57644	hgsc.bcm.edu	37	20	33586674	33586674	+	Silent	SNP	C	C	T	rs377482062		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:33586674C>T	ENST00000262873.7	+	33	4364	c.4272C>T	c.(4270-4272)taC>taT	p.Y1424Y		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1382						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGAGCAAGTACGAAGCAGATG	0.632																																					p.Y1424Y		Atlas-SNP	.											.	MYH7B	145	.	0			c.C4272T						PASS	.	C		3,4401	4.2+/-10.8	0,3,2199	26.0	30.0	28.0		4272	-6.0	0.8	20		28	0,8596		0,0,4298	no	coding-synonymous	MYH7B	NM_020884.3		0,3,6497	TT,TC,CC		0.0,0.0681,0.0231		1424/1984	33586674	3,12997	2202	4298	6500	SO:0001819	synonymous_variant	57644	exon35			CAAGTACGAAGCA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.4272C>T	20.37:g.33586674C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	121	50	0.413223	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			.	.	weak		0.632	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
BAD	572	hgsc.bcm.edu	37	11	64051823	64051823	+	Silent	SNP	C	C	T	rs34882006	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64051823C>T	ENST00000394532.3	-	1	288	c.18G>A	c.(16-18)gaG>gaA	p.E6E	GPR137_ENST00000539851.1_5'Flank|GPR137_ENST00000438980.2_5'Flank|GPR137_ENST00000411458.1_5'UTR|BAD_ENST00000394531.3_Silent_p.E6E|GPR137_ENST00000377702.4_5'Flank|GPR137_ENST00000313074.3_5'Flank|BAD_ENST00000309032.3_Silent_p.E6E|BAD_ENST00000544785.1_Silent_p.E6E	NM_004322.3	NP_004313.1	Q92934	BAD_HUMAN	BCL2-associated agonist of cell death	6					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ADP metabolic process (GO:0046031)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|ATP metabolic process (GO:0046034)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to chromate (GO:0071247)|cellular response to hypoxia (GO:0071456)|cellular response to lipid (GO:0071396)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose catabolic process (GO:0006007)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|pore complex assembly (GO:0046931)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of autophagy (GO:0010508)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane potential (GO:0010918)|positive regulation of neuron death (GO:1901216)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to amino acid (GO:0043200)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to oleic acid (GO:0034201)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|suppression by virus of host apoptotic process (GO:0019050)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|lipid binding (GO:0008289)|phospholipid binding (GO:0005543)|protein kinase binding (GO:0019901)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4						TCGGCTCAAACTCTGGGATCT	0.642													C|||	48	0.00958466	0.0015	0.0187	5008	,	,		18513	0.0		0.0308	False		,,,				2504	0.002				p.E6E		Atlas-SNP	.											.	BAD	8	.	0			c.G18A						PASS	.	C	,,	38,4364	43.1+/-76.7	0,38,2163	71.0	76.0	75.0		,18,18	4.8	1.0	11	dbSNP_126	75	350,8242	117.2+/-176.8	7,336,3953	no	utr-5,coding-synonymous,coding-synonymous	BAD,GPR137	NM_001170726.1,NM_004322.3,NM_032989.2	,,	7,374,6116	TT,TC,CC		4.0736,0.8632,2.986	,,	,6/169,6/169	64051823	388,12606	2201	4296	6497	SO:0001819	synonymous_variant	572	exon2			CTCAAACTCTGGG	AF021792	CCDS8065.1	11q13.1	2014-03-07	2008-08-19		ENSG00000002330	ENSG00000002330			936	protein-coding gene	gene with protein product		603167				8929532	Standard	NM_004322		Approved	BCL2L8, BBC2	uc001nzd.3	Q92934	OTTHUMG00000134302	ENST00000394532.3:c.18G>A	11.37:g.64051823C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_032989	O14803|Q6FH21	Silent	SNP	ENST00000394532.3	37	CCDS8065.1																																																																																			C|0.978;T|0.022	0.022	strong		0.642	BAD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259180.2	NM_032989	
MYH11	4629	hgsc.bcm.edu	37	16	15818141	15818141	+	Silent	SNP	A	A	C	rs587781059|rs2075511	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15818141A>C	ENST00000300036.5	-	31	4351	c.4242T>G	c.(4240-4242)gcT>gcG	p.A1414A	NDE1_ENST00000396354.1_3'UTR|AF001548.5_ENST00000574212.1_RNA|NDE1_ENST00000571896.1_3'UTR|NDE1_ENST00000342673.5_3'UTR|NDE1_ENST00000396355.1_3'UTR|MYH11_ENST00000576790.2_Silent_p.A1414A|MYH11_ENST00000452625.2_Silent_p.A1421A|MYH11_ENST00000396324.3_Silent_p.A1421A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1414					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GTTTATCATAAGCGGCCGCCT	0.537			T	CBFB	AML								A|||	2054	0.410144	0.2564	0.5317	5008	,	,		18915	0.3155		0.496	False		,,,				2504	0.5409				p.A1421A		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.T4263G						PASS	.	A	,,,,,	1354,3040	450.2+/-349.3	215,924,1058	85.0	79.0	81.0		4263,4263,,4242,,4242	1.7	1.0	16	dbSNP_96	81	4610,3990	600.0+/-394.1	1233,2144,923	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous,utr-3,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	1448,3068,1981	CC,CA,AA		46.3953,30.8147,45.8981	,,,,,	1421/1946,1421/1980,,1414/1973,,1414/1939	15818141	5964,7030	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon32			ATCATAAGCGGCC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.4242T>G	16.37:g.15818141A>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	171	77	0.450292	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			A|0.589;C|0.411	0.411	strong		0.537	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
USH2A	7399	hgsc.bcm.edu	37	1	216258213	216258213	+	Missense_Mutation	SNP	A	A	G	rs56222536	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:216258213A>G	ENST00000307340.3	-	25	5380	c.4994T>C	c.(4993-4995)aTc>aCc	p.I1665T	RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.I1665T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1665	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.		I -> T (in dbSNP:rs56222536). {ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACCTTTTTGGATTATCTCTGC	0.328										HNSCC(13;0.011)			A|||	314	0.0626997	0.003	0.0937	5008	,	,		16915	0.0248		0.163	False		,,,				2504	0.0573				p.I1665T		Atlas-SNP	.											.	USH2A	1168	.	0			c.T4994C						PASS	.	A	THR/ILE	124,4278	88.2+/-126.9	2,120,2079	62.0	65.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4994	2.6	0.3	1	dbSNP_129	64	1354,7246	258.8+/-282.3	113,1128,3059	yes	missense	USH2A	NM_206933.2	89	115,1248,5138	GG,GA,AA		15.7442,2.8169,11.3675	benign	1665/5203	216258213	1478,11524	2201	4300	6501	SO:0001583	missense	7399	exon25			TTTTGGATTATCT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4994T>C	1.37:g.216258213A>G	ENSP00000305941:p.Ile1665Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	176	0.08058608058608059	2	0.0040650406504065045	40	0.11049723756906077	13	0.022727272727272728	121	0.15963060686015831	A	10.62	1.400689	0.25291	0.028169	0.157442	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.79247	-1.25;-1.25	4.93	2.62	0.31277	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.479810	0.17138	N	0.185577	T	0.00552	0.0018	L	0.56769	1.78	0.47511	P	5.549999999999722E-4	B	0.13145	0.007	B	0.12837	0.008	T	0.14337	-1.0476	9	0.31617	T	0.26	.	4.44	0.11570	0.7008:0.0:0.1555:0.1437	rs56222536	1665	O75445	USH2A_HUMAN	T	1665	ENSP00000305941:I1665T;ENSP00000355910:I1665T	ENSP00000305941:I1665T	I	-	2	0	USH2A	214324836	0.854000	0.29725	0.299000	0.25016	0.951000	0.60555	0.932000	0.28884	0.261000	0.21753	-0.262000	0.10625	ATC	A|0.892;G|0.108	0.108	strong		0.328	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
ST6GAL1	6480	hgsc.bcm.edu	37	3	186760591	186760591	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760591T>A	ENST00000169298.3	+	4	774	c.100T>A	c.(100-102)Tac>Aac	p.Y34N	ST6GAL1_ENST00000457772.2_Intron|ST6GAL1_ENST00000448044.1_Missense_Mutation_p.Y34N	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	34					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		GAAAGGGAGTTACTATGATTC	0.438																																					p.Y34N		Atlas-SNP	.											.	ST6GAL1	36	.	0			c.T100A						PASS	.						132.0	134.0	134.0					3																	186760591		2203	4300	6503	SO:0001583	missense	6480	exon3			GGGAGTTACTATG	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.100T>A	3.37:g.186760591T>A	ENSP00000169298:p.Tyr34Asn	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	189	20	0.10582	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	37	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489702	0.26686	.	.	ENSG00000073849	ENST00000169298;ENST00000430309;ENST00000417392;ENST00000438590;ENST00000448408;ENST00000440338;ENST00000448044;ENST00000416235;ENST00000423451;ENST00000446170	T;T	0.24350	1.86;1.86	5.44	2.95	0.34219	.	0.288497	0.39020	N	0.001500	T	0.21347	0.0514	M	0.61703	1.905	0.80722	D	1	P	0.38582	0.638	B	0.34242	0.178	T	0.04440	-1.0951	10	0.15066	T	0.55	-39.6557	9.6725	0.40021	0.0:0.0:0.3568:0.6432	.	34	P15907	SIAT1_HUMAN	N	34	ENSP00000169298:Y34N;ENSP00000389337:Y34N	ENSP00000169298:Y34N	Y	+	1	0	ST6GAL1	188243285	1.000000	0.71417	0.826000	0.32828	0.613000	0.37349	1.659000	0.37387	0.410000	0.25675	0.459000	0.35465	TAC	.	.	none		0.438	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	
ACSBG2	81616	hgsc.bcm.edu	37	19	6183233	6183233	+	Silent	SNP	G	G	A	rs17851957	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:6183233G>A	ENST00000586696.1	+	10	1548	c.1272G>A	c.(1270-1272)gaG>gaA	p.E424E	ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000591403.1_Silent_p.E424E|ACSBG2_ENST00000252669.5_Silent_p.E424E|ACSBG2_ENST00000588304.1_Silent_p.E374E|ACSBG2_ENST00000588485.1_Silent_p.E237E			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	424					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGTTGAGTGAGAGCTCGGGAC	0.537													A|||	480	0.0958466	0.23	0.0331	5008	,	,		17293	0.0466		0.0338	False		,,,				2504	0.0736				p.E424E		Atlas-SNP	.											.	ACSBG2	83	.	0			c.G1272A						PASS	.	A		805,3601	750.2+/-412.1	76,653,1474	73.0	74.0	73.0		1272	-3.0	0.0	19	dbSNP_123	73	299,8301	805.9+/-407.3	3,293,4004	no	coding-synonymous	ACSBG2	NM_030924.3		79,946,5478	AA,AG,GG		3.4767,18.2705,8.4884		424/667	6183233	1104,11902	2203	4300	6503	SO:0001819	synonymous_variant	81616	exon10			GAGTGAGAGCTCG		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1272G>A	19.37:g.6183233G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Silent	SNP	ENST00000586696.1	37	CCDS12159.1																																																																																			G|0.919;A|0.081	0.081	strong		0.537	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
CCDC151	115948	hgsc.bcm.edu	37	19	11545690	11545690	+	Missense_Mutation	SNP	G	G	A	rs143295007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11545690G>A	ENST00000356392.4	-	1	235	c.148C>T	c.(148-150)Cca>Tca	p.P50S	PRKCSH_ENST00000591462.1_5'Flank|PRKCSH_ENST00000589838.1_5'Flank|CCDC151_ENST00000586836.1_Intron|PRKCSH_ENST00000412601.1_5'Flank|CCDC151_ENST00000591179.1_Missense_Mutation_p.P50S|PRKCSH_ENST00000592741.1_5'Flank|PRKCSH_ENST00000252455.2_5'Flank|PRKCSH_ENST00000587327.1_5'Flank|CCDC151_ENST00000545100.1_Intron	NM_145045.4	NP_659482.3	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	50										endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	12						GAACGGCCTGGGGTCCACGCC	0.597											OREG0025257	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	13	0.00259585	0.0008	0.0058	5008	,	,		18177	0.0		0.008	False		,,,				2504	0.0				p.P50S		Atlas-SNP	.											.	CCDC151	44	.	0			c.C148T						PASS	.	G	SER/PRO	3,3943		0,3,1970	68.0	73.0	72.0		148	-2.5	0.0	19	dbSNP_134	72	34,8254		1,32,4111	yes	missense	CCDC151	NM_145045.4	74	1,35,6081	AA,AG,GG		0.4102,0.076,0.3024	benign	50/596	11545690	37,12197	1973	4144	6117	SO:0001583	missense	115948	exon1			GGCCTGGGGTCCA		CCDS42501.1	19p13.2	2014-02-20				ENSG00000198003			28303	protein-coding gene	gene with protein product		615956				24067530	Standard	NM_145045		Approved	MGC20983	uc002mrs.3	A5D8V7		ENST00000356392.4:c.148C>T	19.37:g.11545690G>A	ENSP00000348757:p.Pro50Ser	Somatic	88	0	0	673	WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_145045	B4DXT0|Q96CG5	Missense_Mutation	SNP	ENST00000356392.4	37	CCDS42501.1	10	0.004578754578754579	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	10.12	1.263504	0.23136	7.6E-4	0.004102	ENSG00000198003	ENST00000356392;ENST00000543934	T	0.10192	2.9	4.54	-2.55	0.06288	.	0.428688	0.17419	N	0.174920	T	0.02727	0.0082	N	0.11560	0.145	0.18873	N	0.999989	B;B	0.12013	0.002;0.005	B;B	0.12837	0.008;0.003	T	0.45396	-0.9264	10	0.09338	T	0.73	-5.9352	9.2378	0.37477	0.1027:0.6325:0.2648:0.0	.	50;50	B3KPH7;A5D8V7	.;CC151_HUMAN	S	50;29	ENSP00000348757:P50S	ENSP00000348757:P50S	P	-	1	0	CCDC151	11406690	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.152000	0.10159	-0.084000	0.12595	0.655000	0.94253	CCA	G|0.997;A|0.003	0.003	strong		0.597	CCDC151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458800.1	NM_145045	
PCDHAC1	56135	hgsc.bcm.edu	37	5	140307746	140307746	+	Silent	SNP	C	C	G	rs155820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140307746C>G	ENST00000253807.2	+	1	1269	c.1269C>G	c.(1267-1269)ccC>ccG	p.P423P	PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHAC1_ENST00000409700.3_Silent_p.P423P|PCDHA8_ENST00000531613.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	423	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGCTCACCCCCACTTAGCA	0.507													c|||	1783	0.35603	0.23	0.3948	5008	,	,		19684	0.5476		0.333	False		,,,				2504	0.3252				p.P423P		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.C1269G						PASS	.	C	,,,,,,,,,,,,,,,,,	1120,3286	394.7+/-329.4	150,820,1233	73.0	73.0	73.0		1269,,,,,,,,,,,,,,,,,1269	1.8	0.4	5	dbSNP_79	73	2818,5782	437.7+/-358.7	448,1922,1930	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031882.2	,,,,,,,,,,,,,,,,,	598,2742,3163	GG,GC,CC		32.7674,25.4199,30.2783	,,,,,,,,,,,,,,,,,	423/964,,,,,,,,,,,,,,,,,423/819	140307746	3938,9068	2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			CTCACCCCCACTT	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1269C>G	5.37:g.140307746C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																			C|0.680;G|0.320	0.320	strong		0.507	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
KRT7	3855	hgsc.bcm.edu	37	12	52635360	52635360	+	Silent	SNP	G	G	A	rs999665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52635360G>A	ENST00000331817.5	+	5	981	c.798G>A	c.(796-798)gcG>gcA	p.A266A		NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	266	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.A266A(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	AGGTCAAGGCGCAGTATGAGG	0.602													G|||	2122	0.423722	0.3714	0.4366	5008	,	,		20705	0.3145		0.5378	False		,,,				2504	0.4806				p.A266A		Atlas-SNP	.											KRT7,NS,carcinoma,0,1	KRT7	48	1	1	Substitution - coding silent(1)	stomach(1)	c.G798A						PASS	.	G		1871,2535	540.8+/-375.6	387,1097,719	91.0	81.0	85.0		798	-0.1	0.7	12	dbSNP_86	85	4739,3861	608.7+/-395.4	1285,2169,846	no	coding-synonymous	KRT7	NM_005556.3		1672,3266,1565	AA,AG,GG		44.8953,42.4648,49.1773		266/470	52635360	6610,6396	2203	4300	6503	SO:0001819	synonymous_variant	3855	exon5			CAAGGCGCAGTAT		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.798G>A	12.37:g.52635360G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Silent	SNP	ENST00000331817.5	37	CCDS8822.1																																																																																			G|0.514;A|0.486	0.486	strong		0.602	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
SPTBN5	51332	hgsc.bcm.edu	37	15	42162467	42162467	+	Nonsense_Mutation	SNP	G	G	A	rs61750839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42162467G>A	ENST00000320955.6	-	31	5874	c.5647C>T	c.(5647-5649)Cga>Tga	p.R1883*		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1883					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		ACGAGTTCTCGCTCCAGCCCC	0.662													G|||	54	0.0107827	0.0	0.0101	5008	,	,		17221	0.0		0.0358	False		,,,				2504	0.0112				p.R1848X		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C5542T						PASS	.	G	stop/ARG	20,3888		0,20,1934	10.0	12.0	12.0		5542	0.3	0.1	15	dbSNP_129	12	277,7857		7,263,3797	yes	stop-gained	SPTBN5	NM_016642.2		7,283,5731	AA,AG,GG		3.4055,0.5118,2.4664		1848/3640	42162467	297,11745	1954	4067	6021	SO:0001587	stop_gained	51332	exon31			GTTCTCGCTCCAG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.5647C>T	15.37:g.42162467G>A	ENSP00000317790:p.Arg1883*	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	110	70	0.636364	NM_016642		Nonsense_Mutation	SNP	ENST00000320955.6	37		38	0.0173992673992674	0	0.0	6	0.016574585635359115	0	0.0	32	0.04221635883905013	.	44	10.798073	0.99469	0.005118	0.034055	ENSG00000137877	ENST00000320955	.	.	.	4.63	0.285	0.15705	.	0.608014	0.15586	N	0.254650	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.4729	0.11720	0.2652:0.0:0.5822:0.1526	.	.	.	.	X	1883	.	ENSP00000317790:R1883X	R	-	1	2	SPTBN5	39949759	0.002000	0.14202	0.057000	0.19452	0.159000	0.22180	0.862000	0.27899	0.057000	0.16193	0.655000	0.94253	CGA	G|0.982;A|0.018	0.018	strong		0.662	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
ADCY6	112	hgsc.bcm.edu	37	12	49177113	49177113	+	Silent	SNP	T	T	G	rs2453486	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49177113T>G	ENST00000307885.4	-	1	799	c.105A>C	c.(103-105)gcA>gcC	p.A35A	ADCY6_ENST00000550422.1_Silent_p.A35A|ADCY6_ENST00000357869.3_Silent_p.A35A	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	35					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						AGAAGCCACCTGCCCGAGTGC	0.662													T|||	1463	0.292133	0.2201	0.451	5008	,	,		17097	0.3492		0.33	False		,,,				2504	0.1789				p.A35A		Atlas-SNP	.											ADCY6,NS,carcinoma,0,1	ADCY6	81	1	0			c.A105C						scavenged	.	T	,	1107,3299	387.5+/-326.5	141,825,1237	35.0	34.0	34.0		105,105	0.0	0.0	12	dbSNP_100	34	2400,6200	380.5+/-339.7	332,1736,2232	no	coding-synonymous,coding-synonymous	ADCY6	NM_015270.3,NM_020983.2	,	473,2561,3469	GG,GT,TT		27.907,25.1248,26.9645	,	35/1169,35/1116	49177113	3507,9499	2203	4300	6503	SO:0001819	synonymous_variant	112	exon2			GCCACCTGCCCGA		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"""Adenylate cyclases"""	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.105A>C	12.37:g.49177113T>G		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_020983	Q9NR75|Q9UDB0	Silent	SNP	ENST00000307885.4	37	CCDS8767.1																																																																																			T|0.723;G|0.277	0.277	strong		0.662	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983	
CMKLR1	1240	hgsc.bcm.edu	37	12	108686549	108686549	+	Missense_Mutation	SNP	A	A	G	rs192034694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:108686549A>G	ENST00000312143.7	-	3	554	c.191T>C	c.(190-192)aTt>aCt	p.I64T	CMKLR1_ENST00000397688.2_Missense_Mutation_p.I62T|CMKLR1_ENST00000412676.1_Missense_Mutation_p.I64T|CMKLR1_ENST00000552995.1_Missense_Mutation_p.I62T|CMKLR1_ENST00000550402.1_Missense_Mutation_p.I64T	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	64					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						GAAGGTGGCAATGATGATCAC	0.517													A|||	11	0.00219649	0.0	0.0014	5008	,	,		23509	0.0		0.008	False		,,,				2504	0.002				p.I64T		Atlas-SNP	.											CMKLR1,NS,chondrosarcoma,0,1	CMKLR1	67	1	0			c.T191C						scavenged	.		THR/ILE,THR/ILE,THR/ILE,THR/ILE	5,4041		0,5,2018	120.0	118.0	119.0		191,191,191,185	5.0	0.6	12		119	65,8295		0,65,4115	yes	missense,missense,missense,missense	CMKLR1	NM_001142343.1,NM_001142344.1,NM_001142345.1,NM_004072.2	89,89,89,89	0,70,6133	GG,GA,AA		0.7775,0.1236,0.5642	probably-damaging,probably-damaging,probably-damaging,probably-damaging	64/374,64/374,64/374,62/372	108686549	70,12336	2023	4180	6203	SO:0001583	missense	1240	exon3			GTGGCAATGATGA	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.191T>C	12.37:g.108686549A>G	ENSP00000311733:p.Ile64Thr	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	183	101	0.551913	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Missense_Mutation	SNP	ENST00000312143.7	37	CCDS44965.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	a	19.71	3.878841	0.72294	0.001236	0.007775	ENSG00000174600	ENST00000312143;ENST00000412676;ENST00000397688;ENST00000552995;ENST00000550402;ENST00000550573;ENST00000549466	T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.418236	0.25741	N	0.028605	T	0.45438	0.1342	L	0.48362	1.52	0.47441	D	0.999421	D	0.60575	0.988	P	0.60286	0.872	T	0.53844	-0.8381	10	0.87932	D	0	.	13.5319	0.61627	1.0:0.0:0.0:0.0	.	64	Q99788	CML1_HUMAN	T	64;64;62;62;64;64;64	ENSP00000311733:I64T;ENSP00000401293:I64T;ENSP00000380803:I62T;ENSP00000447579:I62T;ENSP00000449716:I64T;ENSP00000448925:I64T;ENSP00000448362:I64T	ENSP00000311733:I64T	I	-	2	0	CMKLR1	107210679	1.000000	0.71417	0.646000	0.29493	0.969000	0.65631	9.291000	0.96070	1.886000	0.54624	0.387000	0.25754	ATT	A|0.996;G|0.004	0.004	strong		0.517	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1		
CLCA2	9635	hgsc.bcm.edu	37	1	86913265	86913265	+	Silent	SNP	C	C	T	rs2275001	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:86913265C>T	ENST00000370565.4	+	11	1950	c.1788C>T	c.(1786-1788)cgC>cgT	p.R596R		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	596					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TGACCTCTCGCGCCTCCAACT	0.493													C|||	1275	0.254593	0.0908	0.2032	5008	,	,		17596	0.3889		0.2634	False		,,,				2504	0.365				p.R596R	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C1788T						PASS	.	C		581,3825	256.7+/-261.4	40,501,1662	132.0	129.0	130.0		1788	-11.2	0.0	1	dbSNP_100	130	2352,6248	393.4+/-344.3	306,1740,2254	no	coding-synonymous	CLCA2	NM_006536.5		346,2241,3916	TT,TC,CC		27.3488,13.1866,22.5511		596/944	86913265	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon11			CTCTCGCGCCTCC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1788C>T	1.37:g.86913265C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	108	63	0.583333	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			C|0.765;T|0.235	0.235	strong		0.493	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
ARHGEF25	115557	hgsc.bcm.edu	37	12	58010163	58010163	+	Missense_Mutation	SNP	A	A	G	rs57224884|rs1564374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:58010163A>G	ENST00000286494.4	+	14	1977	c.1517A>G	c.(1516-1518)cAg>cGg	p.Q506R	ARHGEF25_ENST00000333972.7_Missense_Mutation_p.Q545R|AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000610219.1_RNA|AC025165.8_ENST00000356672.3_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	506			Q -> R (in dbSNP:rs1564374). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						GGAAGAATTCAGCTTGGAGAT	0.617													G|||	3156	0.630192	0.5197	0.6657	5008	,	,		16921	0.7222		0.5527	False		,,,				2504	0.7393				p.Q545R		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.A1634G						PASS	.	G	ARG/GLN,ARG/GLN	2353,2053		632,1089,482	74.0	73.0	73.0		1634,1517	3.7	0.4	12	dbSNP_88	73	4851,3749		1381,2089,830	yes	missense,missense	ARHGEF25	NM_001111270.1,NM_182947.2	43,43	2013,3178,1312	GG,GA,AA		43.593,46.5956,44.6102	benign,benign	545/620,506/581	58010163	7204,5802	2203	4300	6503	SO:0001583	missense	115557	exon15			GAATTCAGCTTGG		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"""Rho guanine nucleotide exchange factors"""	30275	protein-coding gene	gene with protein product	"""RAC/CDC42 exchange factor"""	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1517A>G	12.37:g.58010163A>G	ENSP00000286494:p.Gln506Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	37	CCDS8947.1	1398	0.6401098901098901	284	0.5772357723577236	222	0.6132596685082873	453	0.791958041958042	439	0.579155672823219	N	0.006	-2.114913	0.00349	0.534044	0.56407	ENSG00000240771	ENST00000333972;ENST00000286494	T;T	0.37411	1.23;1.2	4.56	3.66	0.41972	.	0.252152	0.21027	N	0.081419	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39961	-0.9588	9	0.02654	T	1	.	7.6461	0.28321	0.1977:0.0:0.8023:0.0	rs1564374;rs17856409;rs17857334;rs56537767;rs1564374	545;506	F8W7Z4;Q86VW2	.;ARHGP_HUMAN	R	545;506	ENSP00000335560:Q545R;ENSP00000286494:Q506R	ENSP00000286494:Q506R	Q	+	2	0	ARHGEF25	56296430	0.247000	0.23920	0.431000	0.26735	0.122000	0.20287	0.321000	0.19558	0.659000	0.30945	-0.128000	0.14901	CAG	A|0.402;G|0.598;T|0.000	0.598	strong		0.617	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483	
ARGFX	503582	hgsc.bcm.edu	37	3	121305071	121305071	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121305071G>T	ENST00000334384.3	+	4	582	c.572G>T	c.(571-573)tGg>tTg	p.W191L		NM_001012659.1	NP_001012677.1	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(114;0.152)		AATTGGGCATGGAACTCTACC	0.502																																					p.W191L		Atlas-SNP	.											ARGFX,caecum,carcinoma,+1,3	ARGFX	36	3	0			c.G572T						scavenged	.						163.0	157.0	159.0					3																	121305071		2203	4300	6503	SO:0001583	missense	503582	exon5			GGGCATGGAACTC		CCDS33834.1	3q13.33	2011-06-20			ENSG00000186103	ENSG00000186103		"""Homeoboxes / PRD class"""	30146	protein-coding gene	gene with protein product		611164					Standard	XM_005247505		Approved		uc003eef.3	A6NJG6	OTTHUMG00000159395	ENST00000334384.3:c.572G>T	3.37:g.121305071G>T	ENSP00000335578:p.Trp191Leu	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	213	4	0.0187793	NM_001012659		Missense_Mutation	SNP	ENST00000334384.3	37	CCDS33834.1	.	.	.	.	.	.	.	.	.	.	G	5.166	0.216234	0.09810	.	.	ENSG00000186103	ENST00000334384	D	0.88201	-2.35	3.47	-0.704	0.11256	.	1.475770	0.04510	N	0.382724	T	0.74718	0.3753	N	0.19112	0.55	0.09310	N	1	P	0.38922	0.651	B	0.27076	0.076	T	0.64495	-0.6394	10	0.11182	T	0.66	3.883	6.2755	0.20979	0.5772:0.0:0.4228:0.0	.	191	A6NJG6	ARGFX_HUMAN	L	191	ENSP00000335578:W191L	ENSP00000335578:W191L	W	+	2	0	ARGFX	122787761	0.001000	0.12720	0.000000	0.03702	0.018000	0.09664	0.230000	0.17852	-0.159000	0.11021	0.561000	0.74099	TGG	.	.	none		0.502	ARGFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355096.2	NM_001012659	
ANXA13	312	hgsc.bcm.edu	37	8	124710729	124710729	+	Missense_Mutation	SNP	C	C	T	rs2294013	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:124710729C>T	ENST00000419625.1	-	4	329	c.257G>A	c.(256-258)cGt>cAt	p.R86H	ANXA13_ENST00000262219.6_Missense_Mutation_p.R127H	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	86			R -> H (in dbSNP:rs2294013).		cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			CTCGCTGGGACGGTCCAGAAG	0.577													C|||	1172	0.234026	0.2118	0.2133	5008	,	,		19804	0.1935		0.34	False		,,,				2504	0.2117				p.R127H		Atlas-SNP	.											.	ANXA13	38	.	0			c.G380A						PASS	.	C	HIS/ARG,HIS/ARG	939,3467	357.1+/-313.8	107,725,1371	126.0	118.0	121.0		380,257	-0.2	0.0	8	dbSNP_100	121	2895,5705	454.3+/-363.5	502,1891,1907	yes	missense,missense	ANXA13	NM_001003954.1,NM_004306.2	29,29	609,2616,3278	TT,TC,CC		33.6628,21.3118,29.4787	benign,benign	127/358,86/317	124710729	3834,9172	2203	4300	6503	SO:0001583	missense	312	exon5			CTGGGACGGTCCA	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"""Annexins"""	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.257G>A	8.37:g.124710729C>T	ENSP00000390809:p.Arg86His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_001003954	Q9BQR5	Missense_Mutation	SNP	ENST00000419625.1	37	CCDS47917.1	534	0.2445054945054945	101	0.20528455284552846	90	0.24861878453038674	93	0.16258741258741258	250	0.32981530343007914	C	13.84	2.358382	0.41801	0.213118	0.336628	ENSG00000104537	ENST00000262219;ENST00000419625;ENST00000520519	T;T;T	0.22134	3.56;1.97;3.56	5.67	-0.199	0.13220	.	0.389731	0.31589	N	0.007400	T	0.00012	0.0000	L	0.40543	1.245	0.53688	P	2.8000000000028002E-5	B;B	0.17268	0.002;0.021	B;B	0.16722	0.003;0.016	T	0.42965	-0.9420	9	0.62326	D	0.03	.	6.8696	0.24113	0.1174:0.5038:0.0:0.3788	rs2294013;rs17341816;rs60830097;rs2294013	86;127	P27216;P27216-2	ANX13_HUMAN;.	H	127;86;57	ENSP00000262219:R127H;ENSP00000390809:R86H;ENSP00000429358:R57H	ENSP00000262219:R127H	R	-	2	0	ANXA13	124779910	0.003000	0.15002	0.005000	0.12908	0.981000	0.71138	0.044000	0.13992	0.030000	0.15379	0.561000	0.74099	CGT	C|0.733;T|0.267	0.267	strong		0.577	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	
SLC11A2	4891	hgsc.bcm.edu	37	12	51386066	51386066	+	Silent	SNP	A	A	G	rs1048230	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51386066A>G	ENST00000262051.7	-	13	1341	c.1254T>C	c.(1252-1254)atT>atC	p.I418I	SLC11A2_ENST00000545993.2_Silent_p.I414I|SLC11A2_ENST00000541174.2_Silent_p.I418I|SLC11A2_ENST00000547198.1_Silent_p.I418I|SLC11A2_ENST00000262052.5_Silent_p.I418I|SLC11A2_ENST00000394904.3_Silent_p.I447I|SLC11A2_ENST00000547688.1_Silent_p.I447I|SLC11A2_ENST00000546743.1_Silent_p.I339I	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	418					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						GGATGATGGCAATAGAGCGAG	0.473													A|||	691	0.137979	0.0484	0.1037	5008	,	,		21367	0.1151		0.1809	False		,,,				2504	0.2628				p.I447I		Atlas-SNP	.											.	SLC11A2	51	.	0			c.T1341C						PASS	.	A	,,,,,,	304,4102	166.9+/-198.0	9,286,1908	148.0	117.0	128.0		1254,1341,1254,1254,1254,1254,1242	3.0	1.0	12	dbSNP_86	128	1675,6925	308.4+/-308.9	164,1347,2789	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC11A2	NM_000617.2,NM_001174125.1,NM_001174126.1,NM_001174127.1,NM_001174128.1,NM_001174129.1,NM_001174130.1	,,,,,,	173,1633,4697	GG,GA,AA		19.4767,6.8997,15.2161	,,,,,,	418/562,447/591,418/569,418/569,418/562,418/562,414/558	51386066	1979,11027	2203	4300	6503	SO:0001819	synonymous_variant	4891	exon13			GATGGCAATAGAG	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1254T>C	12.37:g.51386066A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	57	0.581633	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Silent	SNP	ENST00000262051.7	37	CCDS53792.1																																																																																			A|0.856;G|0.144	0.144	strong		0.473	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
Unknown	0	hgsc.bcm.edu	37	11	124095414	124095414	+	IGR	SNP	C	C	G	rs10893172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:124095414C>G								OR10D3 (38462 upstream) : OR8G1 (25008 downstream)																							TTTCTTTCCTCCGTAGAAACT	0.468													-|||	2254	0.45008	0.6127	0.3429	5008	,	,		16626	0.3165		0.337	False		,,,				2504	0.5603				p.S6C		Atlas-SNP	.											.	.	.	.	0			c.C17G						PASS	.	C	CYS/SER	2055,1735		564,927,404	61.0	61.0	61.0		17	-2.5	0.0	11	dbSNP_120	61	2683,5565		446,1791,1887	yes	missense	OR8G2	NM_001007249.1	112	1010,2718,2291	GG,GC,CC		32.5291,45.7784,39.3587	possibly-damaging	6/305	124095414	4738,7300	1895	4124	6019	SO:0001628	intergenic_variant	26492	exon1			TTTCCTCCGTAGA																													11.37:g.124095414C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	64	0.64	NM_001007249		Missense_Mutation	SNP		37																																																																																				C|0.606;G|0.394	0.394	strong	0	0.468								
HELLS	3070	hgsc.bcm.edu	37	10	96313960	96313960	+	Silent	SNP	A	A	C	rs11188019	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96313960A>C	ENST00000348459.5	+	3	336	c.231A>C	c.(229-231)atA>atC	p.I77I	HELLS_ENST00000371332.4_Silent_p.I77I|HELLS_ENST00000394045.1_Silent_p.I77I|HELLS_ENST00000394044.1_Silent_p.I77I|HELLS_ENST00000394036.1_Silent_p.I77I|HELLS_ENST00000239026.6_Silent_p.I77I|HELLS_ENST00000462057.1_3'UTR	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		AAAGCAATATATACTCCAAAT	0.328													C|||	2657	0.530551	0.469	0.3228	5008	,	,		16049	0.746		0.4404	False		,,,				2504	0.6319				p.I77I		Atlas-SNP	.											.	HELLS	63	.	0			c.A231C						PASS	.	C		2107,2299	590.4+/-387.4	518,1071,614	73.0	81.0	78.0		231	1.3	1.0	10	dbSNP_120	78	3807,4793	609.2+/-395.5	809,2189,1302	no	coding-synonymous	HELLS	NM_018063.3		1327,3260,1916	CC,CA,AA		44.2674,47.8212,45.4713		77/839	96313960	5914,7092	2203	4300	6503	SO:0001819	synonymous_variant	3070	exon3			CAATATATACTCC	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"""SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6"", ""proliferation-associated SNF2-like protein"""	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.231A>C	10.37:g.96313960A>C		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	206	94	0.456311	NM_018063		Silent	SNP	ENST00000348459.5	37	CCDS7434.1																																																																																			A|0.531;C|0.469	0.469	strong		0.328	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063	
DMXL1	1657	hgsc.bcm.edu	37	5	118484804	118484804	+	Silent	SNP	G	G	A	rs7734532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:118484804G>A	ENST00000311085.8	+	18	3362	c.3282G>A	c.(3280-3282)gaG>gaA	p.E1094E	DMXL1_ENST00000539542.1_Silent_p.E1094E	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1094										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GGGTCCTTGAGCAGACAATTC	0.368													A|||	3096	0.618211	0.4584	0.6268	5008	,	,		22824	0.9524		0.4781	False		,,,				2504	0.6278				p.E1094E		Atlas-SNP	.											.	DMXL1	268	.	0			c.G3282A						PASS	.	A		2132,2272	598.2+/-389.0	529,1074,599	160.0	162.0	161.0		3282	0.6	1.0	5	dbSNP_116	161	4094,4506	591.9+/-392.9	998,2098,1204	no	coding-synonymous	DMXL1	NM_005509.4		1527,3172,1803	AA,AG,GG		47.6047,48.4105,47.8776		1094/3028	118484804	6226,6778	2202	4300	6502	SO:0001819	synonymous_variant	1657	exon18			CCTTGAGCAGACA	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.3282G>A	5.37:g.118484804G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	198	95	0.479798	NM_005509		Silent	SNP	ENST00000311085.8	37	CCDS4125.1																																																																																			G|0.471;A|0.529	0.529	strong		0.368	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
ALPK2	115701	hgsc.bcm.edu	37	18	56202768	56202768	+	Missense_Mutation	SNP	C	C	A	rs3809983	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56202768C>A	ENST00000361673.3	-	5	4864	c.4651G>T	c.(4651-4653)Gct>Tct	p.A1551S	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1551			A -> S (in dbSNP:rs3809983). {ECO:0000269|PubMed:17974005}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCAAGAGAAGCGTGAGTCATT	0.468													C|||	1660	0.33147	0.2118	0.3862	5008	,	,		20824	0.2381		0.5348	False		,,,				2504	0.3415				p.A1551S		Atlas-SNP	.											.	ALPK2	487	.	0			c.G4651T						PASS	.	C	SER/ALA	1145,3261	406.6+/-333.9	140,865,1198	114.0	109.0	110.0		4651	-0.1	0.0	18	dbSNP_107	110	4191,4409	568.8+/-389.1	1025,2141,1134	yes	missense	ALPK2	NM_052947.3	99	1165,3006,2332	AA,AC,CC		48.7326,25.9873,41.0272	benign	1551/2171	56202768	5336,7670	2203	4300	6503	SO:0001583	missense	115701	exon5			GAGAAGCGTGAGT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4651G>T	18.37:g.56202768C>A	ENSP00000354991:p.Ala1551Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	197	87	0.441624	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	834	0.38186813186813184	113	0.22967479674796748	165	0.4558011049723757	139	0.243006993006993	417	0.5501319261213721	C	13.02	2.113587	0.37339	0.259873	0.487326	ENSG00000198796	ENST00000361673	T	0.46819	0.86	5.71	-0.0922	0.13658	.	2.375810	0.01312	N	0.010641	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	P;B	0.37955	0.612;0.145	B;B	0.30401	0.115;0.055	T	0.46176	-0.9210	9	0.15952	T	0.53	-3.1963	0.4633	0.00520	0.1895:0.3075:0.1652:0.3378	rs3809983;rs17728545;rs52816616;rs60880749;rs3809983	1546;1551	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	S	1551	ENSP00000354991:A1551S	ENSP00000354991:A1551S	A	-	1	0	ALPK2	54353748	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.557000	0.05985	0.043000	0.15746	-0.137000	0.14449	GCT	C|0.609;N|0.000	.	strong		0.468	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
LRRC8A	56262	hgsc.bcm.edu	37	9	131670217	131670217	+	Silent	SNP	C	C	T	rs41275930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131670217C>T	ENST00000259324.5	+	3	1297	c.774C>T	c.(772-774)gaC>gaT	p.D258D	LRRC8A_ENST00000372600.4_Silent_p.D258D|LRRC8A_ENST00000372599.3_Silent_p.D258D	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	258					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						AGGAGGGGGACATTGTGTACC	0.547													C|||	76	0.0151757	0.0008	0.0115	5008	,	,		21421	0.0		0.0099	False		,,,				2504	0.0583				p.D258D		Atlas-SNP	.											.	LRRC8A	69	.	0			c.C774T						PASS	.	C	,,	9,4397	14.3+/-33.2	0,9,2194	200.0	172.0	182.0		774,774,774	2.3	1.0	9	dbSNP_127	182	127,8473	65.3+/-127.6	0,127,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	LRRC8A	NM_001127244.1,NM_001127245.1,NM_019594.3	,,	0,136,6367	TT,TC,CC		1.4767,0.2043,1.0457	,,	258/811,258/811,258/811	131670217	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	56262	exon3			GGGGGACATTGTG	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"""leucine rich repeat containing 8"""	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.774C>T	9.37:g.131670217C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	147	67	0.455782	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Silent	SNP	ENST00000259324.5	37	CCDS35155.1																																																																																			C|0.991;T|0.009	0.009	strong		0.547	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594	
NLRP12	91662	hgsc.bcm.edu	37	19	54307322	54307322	+	Silent	SNP	G	G	A	rs12460528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54307322G>A	ENST00000324134.6	-	6	2637	c.2469C>T	c.(2467-2469)ctC>ctT	p.L823L	NLRP12_ENST00000354278.3_Silent_p.L823L|NLRP12_ENST00000391772.1_Silent_p.L824L|NLRP12_ENST00000345770.5_Silent_p.L824L|NLRP12_ENST00000351894.4_Silent_p.L823L|NLRP12_ENST00000391773.1_Silent_p.L824L|NLRP12_ENST00000391775.3_Silent_p.L823L|NLRP12_ENST00000535162.1_Silent_p.L823L	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	823					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		GGTTGGTGCCGAGCACAGAAG	0.557													G|||	2137	0.426717	0.1346	0.5778	5008	,	,		15305	0.5675		0.5805	False		,,,				2504	0.411				p.N823N		Atlas-SNP	.											.	NLRP12	236	.	0			c.C2469T						PASS	.	G	,	949,3457		117,715,1371	79.0	71.0	74.0		318,2469	-0.2	0.0	19	dbSNP_120	74	5372,3228		1591,2190,519	no	coding-synonymous,coding-synonymous	NLRP12	NM_033297.2,NM_144687.2	,	1708,2905,1890	AA,AG,GG		37.5349,21.5388,48.6006	,	106/288,823/1062	54307322	6321,6685	2203	4300	6503	SO:0001819	synonymous_variant	91662	exon6			GGTGCCGAGCACA	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2469C>T	19.37:g.54307322G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	37	CCDS12864.1																																																																																			A|0.488;G|0.496;T|0.016	0.488	strong		0.557	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
TREML4	285852	hgsc.bcm.edu	37	6	41197857	41197857	+	Missense_Mutation	SNP	C	C	T	rs7769759	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:41197857C>T	ENST00000341495.2	+	4	607	c.503C>T	c.(502-504)aCc>aTc	p.T168I	TREML4_ENST00000448827.2_Missense_Mutation_p.T168I	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	168			T -> I (in dbSNP:rs7769759).			extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					GGCTCTGAGACCAGGTAGGTC	0.557													C|||	3459	0.690695	0.4228	0.8141	5008	,	,		20330	0.8393		0.7734	False		,,,				2504	0.727				p.T168I		Atlas-SNP	.											.	TREML4	25	.	0			c.C503T						PASS	.	C	ILE/THR	2155,2251		515,1125,563	96.0	89.0	92.0		503	-2.1	0.0	6	dbSNP_116	92	6802,1798		2687,1428,185	yes	missense	TREML4	NM_198153.2	89	3202,2553,748	TT,TC,CC		20.907,48.9106,31.1318	benign	168/201	41197857	8957,4049	2203	4300	6503	SO:0001583	missense	285852	exon4			CTGAGACCAGGTA	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"""Immunoglobulin superfamily / V-set domain containing"""	30807	protein-coding gene	gene with protein product	"""TREM like transcript 4"""	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.503C>T	6.37:g.41197857C>T	ENSP00000342570:p.Thr168Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_198153	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	37	CCDS34446.1	1573	0.7202380952380952	207	0.42073170731707316	286	0.7900552486187845	496	0.8671328671328671	584	0.7704485488126649	.	8.685	0.906053	0.17760	0.489106	0.79093	ENSG00000188056	ENST00000341495;ENST00000448827	T;T	0.06933	3.24;3.24	3.27	-2.09	0.07232	.	.	.	.	.	T	0.01124	0.0037	N	0.19112	0.55	0.80722	P	0.0	B	0.14012	0.009	B	0.08055	0.003	T	0.48115	-0.9063	8	0.27785	T	0.31	3.4912	1.6642	0.02798	0.3026:0.4196:0.1199:0.1579	rs7769759;rs59433071;rs7769759	168	Q6UXN2	TRML4_HUMAN	I	168	ENSP00000342570:T168I;ENSP00000418078:T168I	ENSP00000342570:T168I	T	+	2	0	TREML4	41305835	0.002000	0.14202	0.007000	0.13788	0.077000	0.17291	-0.289000	0.08365	-0.405000	0.07599	0.591000	0.81541	ACC	C|0.306;T|0.694	0.694	strong		0.557	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
ABL1	25	hgsc.bcm.edu	37	9	133760106	133760106	+	Missense_Mutation	SNP	C	C	T	rs2229071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760106C>T	ENST00000318560.5	+	11	2810	c.2429C>T	c.(2428-2430)cCg>cTg	p.P810L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	810	Pro-rich.		P -> L (in dbSNP:rs2229071). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GGCTCCAGCCCGCCCAACCTG	0.627			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	11	0.00219649	0.0	0.0072	5008	,	,		17189	0.0		0.004	False		,,,				2504	0.002				p.P829L		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2486T						PASS	.	C	LEU/PRO,LEU/PRO	6,4394		0,6,2194	16.0	20.0	18.0		2429,2486	4.8	0.9	9	dbSNP_98	18	80,8518		0,80,4219	yes	missense,missense	ABL1	NM_005157.4,NM_007313.2	98,98	0,86,6413	TT,TC,CC		0.9304,0.1364,0.6616	probably-damaging,probably-damaging	810/1131,829/1150	133760106	86,12912	2200	4299	6499	SO:0001583	missense	25	exon11			CCAGCCCGCCCAA	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2429C>T	9.37:g.133760106C>T	ENSP00000323315:p.Pro810Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	14.83	2.651718	0.47362	0.001364	0.009304	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.23950	1.88;1.88	5.69	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.25606	0.0623	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.04128	-1.0975	10	0.08837	T	0.75	.	13.6197	0.62130	0.0:0.9257:0.0:0.0743	rs2229071	810;847	P00519;Q59FK4	ABL1_HUMAN;.	L	625;829;810	ENSP00000361423:P829L;ENSP00000323315:P810L	ENSP00000323315:P810L	P	+	2	0	ABL1	132749927	1.000000	0.71417	0.922000	0.36590	0.138000	0.21146	7.563000	0.82314	1.410000	0.46936	0.561000	0.74099	CCG	C|0.995;T|0.005	0.005	strong		0.627	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
TCOF1	6949	hgsc.bcm.edu	37	5	149776232	149776232	+	Missense_Mutation	SNP	C	C	T	rs15251	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:149776232C>T	ENST00000504761.2	+	24	4169	c.4169C>T	c.(4168-4170)gCa>gTa	p.A1390V	TCOF1_ENST00000439160.2_Missense_Mutation_p.A1353V|TCOF1_ENST00000513346.1_Missense_Mutation_p.A1390V|TCOF1_ENST00000323668.7_Missense_Mutation_p.A1313V|TCOF1_ENST00000445265.2_Missense_Mutation_p.A1314V|TCOF1_ENST00000377797.3_Missense_Mutation_p.A1391V|TCOF1_ENST00000451292.1_Missense_Mutation_p.A1427V			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1390			A -> V (in dbSNP:rs15251). {ECO:0000269|PubMed:9042910}.		skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGGGGAAAGCAAAGAGAGAC	0.567													C|||	1122	0.224042	0.0567	0.2305	5008	,	,		16898	0.2044		0.2972	False		,,,				2504	0.3906				p.A1390V		Atlas-SNP	.											.	TCOF1	154	.	0			c.C4169T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	386,4020	178.7+/-207.4	18,350,1835	24.0	21.0	22.0		3938,4169,4058,3941,4055	2.6	0.1	5	dbSNP_52	22	2349,6251	360.0+/-331.8	313,1723,2264	yes	missense,missense,missense,missense,missense	TCOF1	NM_000356.3,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	64,64,64,64,64	331,2073,4099	TT,TC,CC		27.314,8.7608,21.0288	benign,benign,benign,benign,benign	1313/1412,1390/1489,1353/1452,1314/1413,1352/1451	149776232	2735,10271	2203	4300	6503	SO:0001583	missense	6949	exon24			GGAAAGCAAAGAG		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.4169C>T	5.37:g.149776232C>T	ENSP00000421655:p.Ala1390Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	111	71	0.63964	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	471	0.21565934065934067	29	0.05894308943089431	87	0.24033149171270718	125	0.21853146853146854	230	0.3034300791556728	C	15.44	2.833743	0.50951	0.087608	0.27314	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86	3.51	2.64	0.31445	.	1.294980	0.05705	N	0.594858	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;P;P;P;P	0.47409	0.557;0.557;0.557;0.895;0.557	B;B;B;P;B	0.44518	0.125;0.125;0.125;0.452;0.125	T	0.02766	-1.1113	9	0.52906	T	0.07	-0.0123	6.7651	0.23562	0.0:0.873:0.0:0.127	rs15251;rs3180828;rs17713229;rs58771965;rs15251	1353;1313;1352;1390;1314	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;TCOF_HUMAN;.	V	1427;1391;1314;1313;1353;1352;1390;1390	ENSP00000400939:A1427V;ENSP00000367028:A1391V;ENSP00000409944:A1314V;ENSP00000325223:A1313V;ENSP00000406888:A1353V;ENSP00000390717:A1352V;ENSP00000421655:A1390V;ENSP00000427484:A1390V	ENSP00000325223:A1313V	A	+	2	0	TCOF1	149756425	0.973000	0.33851	0.094000	0.20943	0.882000	0.50991	3.327000	0.52045	1.067000	0.40740	0.561000	0.74099	GCA	C|0.790;T|0.210	0.210	strong		0.567	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
OR1I1	126370	hgsc.bcm.edu	37	19	15198666	15198666	+	Missense_Mutation	SNP	T	T	A	rs144766527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198666T>A	ENST00000209540.2	+	1	876	c.790T>A	c.(790-792)Tcc>Acc	p.S264T		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						ACAGCCCACATCCCCCAGCTC	0.537													T|||	28	0.00559105	0.0008	0.0101	5008	,	,		22065	0.0		0.0189	False		,,,				2504	0.001				p.S264T		Atlas-SNP	.											OR1I1,NS,malignant_melanoma,-1,1	OR1I1	58	1	0			c.T790A						PASS	.	T	THR/SER	10,4396	17.9+/-39.9	0,10,2193	112.0	91.0	98.0		790	-0.9	0.0	19	dbSNP_134	98	132,8468	67.3+/-129.8	3,126,4171	yes	missense	OR1I1	NM_001004713.1	58	3,136,6364	AA,AT,TT		1.5349,0.227,1.0918	possibly-damaging	264/356	15198666	142,12864	2203	4300	6503	SO:0001583	missense	126370	exon1			CCCACATCCCCCA	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.790T>A	19.37:g.15198666T>A	ENSP00000209540:p.Ser264Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	132	54	0.409091	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	T	6.410	0.443810	0.12164	0.00227	0.015349	ENSG00000094661	ENST00000209540	T	0.00258	8.41	4.33	-0.906	0.10524	GPCR, rhodopsin-like superfamily (1);	0.721661	0.10719	U	0.641993	T	0.00073	0.0002	L	0.46567	1.45	0.09310	N	1	B	0.30914	0.3	B	0.28916	0.096	T	0.09796	-1.0658	10	0.30854	T	0.27	.	1.0468	0.01571	0.2892:0.0999:0.3283:0.2825	.	264	O60431	OR1I1_HUMAN	T	264	ENSP00000209540:S264T	ENSP00000209540:S264T	S	+	1	0	OR1I1	15059666	0.000000	0.05858	0.006000	0.13384	0.236000	0.25371	-0.466000	0.06672	-0.070000	0.12908	0.449000	0.29647	TCC	T|0.989;A|0.011	0.011	strong		0.537	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
NLRP10	338322	hgsc.bcm.edu	37	11	7982094	7982094	+	Silent	SNP	G	G	A	rs12363522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:7982094G>A	ENST00000328600.2	-	2	1226	c.1065C>T	c.(1063-1065)ggC>ggT	p.G355G		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	355	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCCAGCAAATGCCTGGAACCT	0.498													G|||	136	0.0271565	0.0083	0.0764	5008	,	,		20764	0.0		0.0596	False		,,,				2504	0.0123				p.G355G		Atlas-SNP	.											NLRP10,NS,carcinoma,-1,2	NLRP10	146	2	0			c.C1065T						PASS	.	G		53,4349	52.3+/-87.9	0,53,2148	86.0	72.0	77.0		1065	-4.6	0.2	11	dbSNP_120	77	517,8075	145.4+/-201.1	16,485,3795	no	coding-synonymous	NLRP10	NM_176821.3		16,538,5943	AA,AG,GG		6.0172,1.204,4.3866		355/656	7982094	570,12424	2201	4296	6497	SO:0001819	synonymous_variant	338322	exon2			GCAAATGCCTGGA	AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"""Nucleotide-binding domain and leucine rich repeat containing"""	21464	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"""	609662	"""NACHT, leucine rich repeat and PYD containing 10"""	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1065C>T	11.37:g.7982094G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_176821	Q2M3C4|Q6JGT0	Silent	SNP	ENST00000328600.2	37	CCDS7784.1																																																																																			G|0.958;A|0.042	0.042	strong		0.498	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821	
PER1	5187	hgsc.bcm.edu	37	17	8046664	8046664	+	Missense_Mutation	SNP	C	C	T	rs112474322	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:8046664C>T	ENST00000317276.4	-	19	3229	c.2992G>A	c.(2992-2994)Gct>Act	p.A998T	PER1_ENST00000581082.1_Missense_Mutation_p.A975T|PER1_ENST00000578089.1_5'Flank	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	998	Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GCAACAGCAGCCCCCTCAGCA	0.667			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					C|||	77	0.0153754	0.0272	0.0202	5008	,	,		11095	0.0		0.0239	False		,,,				2504	0.0031				p.A998T		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.G2992A						PASS	.	C	THR/ALA	108,4274		1,106,2084	22.0	25.0	24.0		2992	2.4	0.8	17	dbSNP_132	24	183,8393		2,179,4107	yes	missense	PER1	NM_002616.2	58	3,285,6191	TT,TC,CC		2.1339,2.4646,2.2457	benign	998/1291	8046664	291,12667	2191	4288	6479	SO:0001583	missense	5187	exon19			CAGCAGCCCCCTC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2992G>A	17.37:g.8046664C>T	ENSP00000314420:p.Ala998Thr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	100	39	0.39	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	41	0.018772893772893772	15	0.03048780487804878	8	0.022099447513812154	0	0.0	18	0.023746701846965697	C	8.261	0.811110	0.16537	0.024646	0.021339	ENSG00000179094	ENST00000317276	T	0.13657	2.57	5.47	2.39	0.29439	.	0.627738	0.17425	N	0.174672	T	0.01765	0.0056	N	0.08118	0	0.80722	D	1	B	0.16802	0.019	B	0.14023	0.01	T	0.36553	-0.9743	10	0.10111	T	0.7	3.0E-4	9.3049	0.37870	0.0:0.7602:0.0:0.2398	.	998	O15534	PER1_HUMAN	T	998	ENSP00000314420:A998T	ENSP00000314420:A998T	A	-	1	0	PER1	7987389	0.998000	0.40836	0.771000	0.31576	0.329000	0.28539	2.891000	0.48617	0.290000	0.22444	-0.373000	0.07131	GCT	C|0.980;T|0.020	0.020	strong		0.667	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
TFAP2B	7021	hgsc.bcm.edu	37	6	50791444	50791444	+	Missense_Mutation	SNP	G	G	C	rs139904414		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:50791444G>C	ENST00000393655.3	+	2	575	c.406G>C	c.(406-408)Gac>Cac	p.D136H	TFAP2B_ENST00000263046.4_Missense_Mutation_p.D145H|TFAP2B_ENST00000489228.1_3'UTR	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	136					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					CTCGGGCCTTGACCCCCGGAG	0.711																																					p.D136H	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											.	TFAP2B	91	.	0			c.G406C						PASS	.	G	HIS/ASP	0,4398		0,0,2199	13.0	16.0	15.0		406	5.6	0.9	6	dbSNP_134	15	1,8595		0,1,4297	no	missense	TFAP2B	NM_003221.3	81	0,1,6496	CC,CG,GG		0.0116,0.0,0.0077	possibly-damaging	136/461	50791444	1,12993	2199	4298	6497	SO:0001583	missense	7021	exon2			GGCCTTGACCCCC	X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"""			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.406G>C	6.37:g.50791444G>C	ENSP00000377265:p.Asp136His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	37	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	G	30	5.057098	0.93846	0.0	1.16E-4	ENSG00000008196	ENST00000393655;ENST00000344788;ENST00000263046	D;D;D	0.88201	-2.35;-2.35;-2.35	5.58	5.58	0.84498	.	0.145200	0.64402	D	0.000012	D	0.86264	0.5891	L	0.58428	1.81	0.80722	D	1	P	0.41041	0.736	B	0.41036	0.346	D	0.87780	0.2611	10	0.59425	D	0.04	-16.9265	19.5711	0.95419	0.0:0.0:1.0:0.0	.	136	Q92481	AP2B_HUMAN	H	136;134;145	ENSP00000377265:D136H;ENSP00000342252:D134H;ENSP00000263046:D145H	ENSP00000263046:D145H	D	+	1	0	TFAP2B	50899403	1.000000	0.71417	0.926000	0.36857	0.956000	0.61745	7.875000	0.87205	2.638000	0.89438	0.563000	0.77884	GAC	G|1.000;C|0.000	0.000	weak		0.711	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221	
BRCA2	675	hgsc.bcm.edu	37	13	32906729	32906729	+	Missense_Mutation	SNP	A	A	C	rs144848	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:32906729A>C	ENST00000380152.3	+	10	1347	c.1114A>C	c.(1114-1116)Aat>Cat	p.N372H	BRCA2_ENST00000544455.1_Missense_Mutation_p.N372H			P51587	BRCA2_HUMAN	breast cancer 2, early onset	372			H -> N (common polymorphism; associated with an increased risk of breast cancer and with an effect on prenatal viability with increased fitness of males and decreased fitness of females; dbSNP:rs144848). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:10978364, ECO:0000269|PubMed:11062481, ECO:0000269|PubMed:12552570, ECO:0000269|PubMed:15057823, ECO:0000269|PubMed:15172753, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:8665505, ECO:0000269|PubMed:8673091, ECO:0000269|Ref.3}.		brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.N372H(1)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AAATGTAGCAAATCAGAAGCC	0.373			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	1249	0.249401	0.084	0.2997	5008	,	,		17972	0.2847		0.2952	False		,,,				2504	0.3538				p.N372H	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	BRCA2_ENST00000544455,NS,carcinoma,0,1	BRCA2	812	1	1	Substitution - Missense(1)	stomach(1)	c.A1114C	GRCh37	CM002750	BRCA2	M	rs144848	PASS	.	A	HIS/ASN	558,3770		42,474,1648	167.0	186.0	180.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1114	0.4	0.0	13	dbSNP_83	180	2449,6117		345,1759,2179	yes	missense	BRCA2	NM_000059.3	68	387,2233,3827	CC,CA,AA		28.5898,12.8928,23.3209	benign	372/3419	32906729	3007,9887	2164	4283	6447	SO:0001583	missense	675	exon10	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	GTAGCAAATCAGA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.1114A>C	13.37:g.32906729A>C	ENSP00000369497:p.Asn372His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	525	0.2403846153846154	48	0.0975609756097561	113	0.31215469613259667	146	0.25524475524475526	218	0.287598944591029	A	6.228	0.410176	0.11812	0.128928	0.285898	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00717	5.79;5.79	5.6	0.396	0.16309	.	1.242150	0.05390	N	0.538920	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41448	-0.9508	6	0.46703	T	0.11	.	5.256	0.15548	0.4454:0.162:0.3926:0.0	rs144848;rs703222;rs766172;rs17593227;rs52835869;rs60042381;rs144848	.	.	.	H	372;372;370	ENSP00000369497:N372H;ENSP00000439902:N372H	ENSP00000369497:N372H	N	+	1	0	BRCA2	31804729	0.001000	0.12720	0.000000	0.03702	0.316000	0.28119	0.757000	0.26433	-0.147000	0.11254	-0.250000	0.11733	AAT	T|0.005;G|0.003	.	strong		0.373	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
PNPLA5	150379	hgsc.bcm.edu	37	22	44282307	44282307	+	Silent	SNP	G	G	A	rs739232	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:44282307G>A	ENST00000597664.1	-	6	954	c.825C>T	c.(823-825)gaC>gaT	p.D275D	PNPLA5_ENST00000593866.1_Silent_p.D161D|PNPLA5_ENST00000381198.2_Silent_p.D161D|PNPLA5_ENST00000216177.4_Silent_p.D275D			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	275					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CCCAGTTTCCGTCAGCCGGGG	0.572													A|||	2486	0.496406	0.2224	0.4568	5008	,	,		18935	0.9048		0.3748	False		,,,				2504	0.5992				p.D275D		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C825T						PASS	.	A	,	1099,3307	720.0+/-409.0	142,815,1246	85.0	77.0	80.0		483,825	-4.8	0.0	22	dbSNP_86	80	3208,5392	652.5+/-400.9	585,2038,1677	no	coding-synonymous,coding-synonymous	PNPLA5	NM_001177675.1,NM_138814.3	,	727,2853,2923	AA,AG,GG		37.3023,24.9433,33.1155	,	161/316,275/430	44282307	4307,8699	2203	4300	6503	SO:0001819	synonymous_variant	150379	exon6			GTTTCCGTCAGCC	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.825C>T	22.37:g.44282307G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	69	24	0.347826	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Silent	SNP	ENST00000597664.1	37																																																																																				G|0.598;A|0.402	0.402	strong		0.572	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
CCDC50	152137	hgsc.bcm.edu	37	3	191075902	191075902	+	Silent	SNP	C	C	T	rs11542549	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:191075902C>T	ENST00000392455.3	+	3	826	c.228C>T	c.(226-228)cgC>cgT	p.R76R	CCDC50_ENST00000392456.3_Silent_p.R76R	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	76						cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		TCCAGAAGCGCTACAAAGACC	0.552													C|||	1339	0.267372	0.2322	0.3156	5008	,	,		17820	0.2579		0.332	False		,,,				2504	0.2239				p.R76R		Atlas-SNP	.											.	CCDC50	39	.	0			c.C228T						PASS	.	C	,	1123,3283	398.3+/-330.8	143,837,1223	105.0	103.0	103.0		228,228	4.4	1.0	3	dbSNP_120	103	2734,5866	435.2+/-358.0	439,1856,2005	no	coding-synonymous,coding-synonymous	CCDC50	NM_174908.3,NM_178335.2	,	582,2693,3228	TT,TC,CC		31.7907,25.488,29.6555	,	76/307,76/483	191075902	3857,9149	2203	4300	6503	SO:0001819	synonymous_variant	152137	exon3			GAAGCGCTACAAA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.228C>T	3.37:g.191075902C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	142	82	0.577465	NM_174908	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																			C|0.584;A|0.042	.	strong		0.552	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
SLC6A7	6534	hgsc.bcm.edu	37	5	149583300	149583300	+	Silent	SNP	T	T	C	rs2240793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:149583300T>C	ENST00000230671.2	+	9	1529	c.1158T>C	c.(1156-1158)ttT>ttC	p.F386F	SLC6A7_ENST00000524041.1_Silent_p.F386F	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7	386					proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	TCTGGTCCTTTCTCTTCTTCT	0.602													C|||	3314	0.661741	0.6014	0.7695	5008	,	,		17091	0.502		0.7306	False		,,,				2504	0.7607				p.F386F		Atlas-SNP	.											.	SLC6A7	52	.	0			c.T1158C						PASS	.	C		2779,1627	500.1+/-364.6	870,1039,294	108.0	78.0	88.0		1158	3.0	1.0	5	dbSNP_98	88	6567,2033	353.9+/-329.3	2496,1575,229	no	coding-synonymous	SLC6A7	NM_014228.3		3366,2614,523	CC,CT,TT		23.6395,36.9269,28.1409		386/637	149583300	9346,3660	2203	4300	6503	SO:0001819	synonymous_variant	6534	exon9			GTCCTTTCTCTTC	S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"""Solute carriers"""	11054	protein-coding gene	gene with protein product	"""brain-specific L-proline transporter"", ""sodium-dependent proline transporter"""	606205	"""solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"""			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.1158T>C	5.37:g.149583300T>C		Somatic	277	1	0.00361011		WXS	Illumina HiSeq	Phase_I	276	276	1	NM_014228	Q0VG81|Q52LU6	Silent	SNP	ENST00000230671.2	37	CCDS4305.1																																																																																			T|0.321;C|0.679	0.679	strong		0.602	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252325.1	NM_014228	
EYA1	2138	hgsc.bcm.edu	37	8	72111599	72111599	+	Silent	SNP	A	A	G	rs10103397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:72111599A>G	ENST00000340726.3	-	18	2394	c.1755T>C	c.(1753-1755)caT>caC	p.H585H	EYA1_ENST00000388743.2_Silent_p.H584H|EYA1_ENST00000388740.3_Silent_p.H552H|EYA1_ENST00000303824.7_Silent_p.H579H|RP11-326E22.1_ENST00000521685.1_RNA|EYA1_ENST00000388742.4_Silent_p.H585H|EYA1_ENST00000388741.2_Silent_p.H551H|EYA1_ENST00000419131.1_Silent_p.H550H	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	585					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			GTTCCAAGGCATGGTGCAGGG	0.607													G|||	2387	0.476637	0.3623	0.464	5008	,	,		18146	0.7688		0.3101	False		,,,				2504	0.5102				p.H585H		Atlas-SNP	.											.	EYA1	108	.	0			c.T1755C						PASS	.	G	,,,	1532,2874	668.8+/-402.1	262,1008,933	88.0	65.0	73.0		1755,1755,1650,1656	-12.3	0.0	8	dbSNP_119	73	2625,5975	684.3+/-404.0	385,1855,2060	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EYA1	NM_000503.4,NM_172058.2,NM_172059.2,NM_172060.2	,,,	647,2863,2993	GG,GA,AA		30.5233,34.7708,31.9622	,,,	585/593,585/593,550/558,552/560	72111599	4157,8849	2203	4300	6503	SO:0001819	synonymous_variant	2138	exon18			CAAGGCATGGTGC	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3519	protein-coding gene	gene with protein product		601653	"""eyes absent (Drosophila) homolog 1"", ""eyes absent homolog 1 (Drosophila)"""	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1755T>C	8.37:g.72111599A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_000503	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	37	CCDS34906.1																																																																																			A|0.620;G|0.380	0.380	strong		0.607	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060	
OR4N2	390429	hgsc.bcm.edu	37	14	20295778	20295778	+	Silent	SNP	C	C	A	rs11621883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20295778C>A	ENST00000315947.1	+	1	171	c.171C>A	c.(169-171)gcC>gcA	p.A57A	OR4N2_ENST00000568211.1_Silent_p.A57A	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	57						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GGCTCACAGCCCCCCTCTATT	0.473													.|||	1054	0.210463	0.2769	0.1657	5008	,	,		26389	0.1161		0.2107	False		,,,				2504	0.2495				p.A57A		Atlas-SNP	.											.	OR4N2	125	.	0			c.C171A						PASS	.	C		106,4300		30,46,2127	178.0	214.0	202.0		171	-5.2	0.1	14	dbSNP_120	202	130,8466		39,52,4207	no	coding-synonymous	OR4N2	NM_001004723.1		69,98,6334	AA,AC,CC		1.5123,2.4058,1.8151		57/308	20295778	236,12766	2203	4298	6501	SO:0001819	synonymous_variant	390429	exon1			CACAGCCCCCCTC		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.171C>A	14.37:g.20295778C>A		Somatic	361	1	0.00277008		WXS	Illumina HiSeq	Phase_I	294	135	0.459184	NM_001004723	Q6IEY9|Q6IFA2	Silent	SNP	ENST00000315947.1	37	CCDS32022.1																																																																																			A|0.114;C|0.886;T|0.000	0.114	strong		0.473	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
PTPRZ1	5803	hgsc.bcm.edu	37	7	121513561	121513561	+	Missense_Mutation	SNP	T	T	G	rs740965	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:121513561T>G	ENST00000393386.2	+	1	419	c.8T>G	c.(7-9)aTc>aGc	p.I3S	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.I3S	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	3			I -> S (in dbSNP:rs740965).		axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GAAATGCGAATCCTAAAGCGT	0.567													T|||	815	0.16274	0.0136	0.2305	5008	,	,		13339	0.3026		0.1243	False		,,,				2504	0.2117				p.I3S		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T8G						PASS	.	T	SER/ILE,SER/ILE,SER/ILE	192,4214	121.3+/-158.8	3,186,2014	98.0	92.0	94.0		8,8,8	-2.7	0.0	7	dbSNP_86	94	1317,7283	260.9+/-283.5	104,1109,3087	yes	missense,missense,missense	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	142,142,142	107,1295,5101	GG,GT,TT		15.314,4.3577,11.6023	probably-damaging,probably-damaging,probably-damaging	3/1456,3/1449,3/2316	121513561	1509,11497	2203	4300	6503	SO:0001583	missense	5803	exon1			TGCGAATCCTAAA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.8T>G	7.37:g.121513561T>G	ENSP00000377047:p.Ile3Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	351	0.16071428571428573	11	0.022357723577235773	74	0.20441988950276244	179	0.3129370629370629	87	0.11477572559366754	T	12.81	2.049157	0.36181	0.043577	0.15314	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.52983	0.65;0.64	4.27	-2.66	0.06077	.	2.658710	0.02120	N	0.055569	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.17038	0.008;0.02	B;B	0.15052	0.005;0.012	T	0.32241	-0.9914	9	0.87932	D	0	.	4.6046	0.12371	0.1552:0.3918:0.0:0.453	rs740965;rs1050503;rs3190831;rs740965	3;3	C9JFM0;P23471	.;PTPRZ_HUMAN	S	3	ENSP00000377047:I3S;ENSP00000410000:I3S	ENSP00000377047:I3S	I	+	2	0	PTPRZ1	121300797	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.488000	0.22371	-0.449000	0.07117	-0.516000	0.04426	ATC	T|0.868;G|0.132	0.132	strong		0.567	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
DPP6	1804	hgsc.bcm.edu	37	7	154667643	154667643	+	Silent	SNP	G	G	A	rs2230064	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:154667643G>A	ENST00000377770.3	+	20	2052	c.1911G>A	c.(1909-1911)gtG>gtA	p.V637V	DPP6_ENST00000427557.1_Silent_p.V530V|DPP6_ENST00000404039.1_Silent_p.V573V|DPP6_ENST00000332007.3_Silent_p.V575V			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	637					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GCCAGAGTGTGGCTGAGAAGT	0.652													G|||	889	0.177516	0.1369	0.2133	5008	,	,		16015	0.0159		0.3459	False		,,,				2504	0.2004				p.V637V	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.G1911A						PASS	.	G	,,	694,3458		57,580,1439	28.0	34.0	32.0		1365,1284,1284	4.0	0.9	7	dbSNP_98	32	2941,5447		526,1889,1779	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	583,2469,3218	AA,AG,GG		35.062,16.7148,28.9872	,,	455/684,428/657,428/657	154667643	3635,8905	2076	4194	6270	SO:0001819	synonymous_variant	1804	exon20			GAGTGTGGCTGAG	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1911G>A	7.37:g.154667643G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	60	0.6	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				G|0.805;A|0.195	0.195	strong		0.652	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
TRAPPC11	60684	hgsc.bcm.edu	37	4	184615117	184615117	+	Missense_Mutation	SNP	A	A	C	rs62358032	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:184615117A>C	ENST00000334690.6	+	22	2636	c.2434A>C	c.(2434-2436)Aca>Cca	p.T812P	TRAPPC11_ENST00000512476.1_Missense_Mutation_p.T418P|TRAPPC11_ENST00000357207.4_Missense_Mutation_p.T812P	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	812				T -> P (in Ref. 1; CAD91169, 4; CAG38584 and 5; CAB66686). {ECO:0000305}.	vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											TCTTCATGGAACAGAACTGTG	0.408													A|||	220	0.0439297	0.0045	0.0375	5008	,	,		19922	0.0268		0.0944	False		,,,				2504	0.0675				p.T812P		Atlas-SNP	.											.	.	.	.	0			c.A2434C						PASS	.	A	PRO/THR,PRO/THR	100,4306	80.4+/-118.8	1,98,2104	118.0	116.0	117.0		2434,2434	-1.6	0.2	4	dbSNP_129	117	997,7603	214.5+/-254.1	66,865,3369	yes	missense,missense	C4orf41	NM_021942.4,NM_199053.1	38,38	67,963,5473	CC,CA,AA		11.593,2.2696,8.4346	benign,benign	812/1134,812/1087	184615117	1097,11909	2203	4300	6503	SO:0001583	missense	60684	exon22			CATGGAACAGAAC		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"""Trafficking protein particle complex"""	25751	protein-coding gene	gene with protein product	"""gryzun homolog (Drosophila)"", ""foie gras homolog (zebrafish)"""	614138	"""chromosome 4 open reading frame 41"""	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.2434A>C	4.37:g.184615117A>C	ENSP00000335371:p.Thr812Pro	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	187	99	0.529412	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Missense_Mutation	SNP	ENST00000334690.6	37	CCDS34112.1	124	0.056776556776556776	4	0.008130081300813009	21	0.058011049723756904	19	0.033216783216783216	80	0.10554089709762533	A	11.85	1.761997	0.31228	0.022696	0.11593	ENSG00000168538	ENST00000334690;ENST00000357207;ENST00000360109;ENST00000512476	.	.	.	5.78	-1.58	0.08479	.	0.406317	0.27185	N	0.020536	T	0.00440	0.0014	N	0.25647	0.755	0.44555	P	0.0024889999999999635	B;B;B;B	0.27316	0.175;0.055;0.0;0.045	B;B;B;B	0.35770	0.21;0.137;0.001;0.084	T	0.11842	-1.0571	8	0.28530	T	0.3	.	7.1561	0.25639	0.4422:0.0:0.438:0.1198	rs62358032	543;418;812;812	B3KR79;D6RHE5;Q7Z392;Q7Z392-3	.;.;TPC11_HUMAN;.	P	812;812;812;418	.	ENSP00000335371:T812P	T	+	1	0	C4orf41	184852111	0.004000	0.15560	0.155000	0.22561	0.802000	0.45316	0.463000	0.21972	-0.468000	0.06922	-0.336000	0.08194	ACA	A|0.924;C|0.076	0.076	strong		0.408	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
FKBP15	23307	hgsc.bcm.edu	37	9	115931692	115931692	+	Silent	SNP	A	A	G	rs3810909	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:115931692A>G	ENST00000238256.3	-	26	3414	c.3297T>C	c.(3295-3297)acT>acC	p.T1099T		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1099					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)		p.T1099T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CGGGGTCTGAAGTCAGGGACA	0.572													A|||	964	0.192492	0.2133	0.2767	5008	,	,		18055	0.1925		0.167	False		,,,				2504	0.1309				p.T1099T		Atlas-SNP	.											FKBP15_ENST00000238256,NS,carcinoma,0,1	FKBP15	128	1	1	Substitution - coding silent(1)	stomach(1)	c.T3297C						PASS	.	A		832,3038		97,638,1200	82.0	85.0	84.0		3297	-0.2	0.9	9	dbSNP_107	84	1506,6760		139,1228,2766	no	coding-synonymous	FKBP15	NM_015258.1		236,1866,3966	GG,GA,AA		18.2192,21.4987,19.265		1099/1220	115931692	2338,9798	1935	4133	6068	SO:0001819	synonymous_variant	23307	exon26			GTCTGAAGTCAGG	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.3297T>C	9.37:g.115931692A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	250	123	0.492	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			A|0.798;G|0.202	0.202	strong		0.572	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859879	144859879	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859879G>A	ENST00000369354.3	-	38	6394	c.6205C>T	c.(6205-6207)Cga>Tga	p.R2069*	PDE4DIP_ENST00000369359.4_Nonsense_Mutation_p.R2205*|PDE4DIP_ENST00000530740.1_Nonsense_Mutation_p.R2154*|PDE4DIP_ENST00000313382.9_Nonsense_Mutation_p.R1963*|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Nonsense_Mutation_p.R2069*|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2069					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGCTGCAGTCGCAGACAATTG	0.582			T	PDGFRB	MPD																																p.R2069X		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6205T						PASS	.						70.0	67.0	68.0					1																	144859879		2203	4298	6501	SO:0001587	stop_gained	9659	exon38			GCAGTCGCAGACA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6205C>T	1.37:g.144859879G>A	ENSP00000358360:p.Arg2069*	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	307	27	0.0879479	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Nonsense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	44	11.091583	0.99515	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	.	.	.	4.95	1.8	0.24995	.	.	.	.	.	.	.	.	.	.	.	0.39652	D	0.97048	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6096	0.28122	0.0839:0.0:0.6302:0.2859	.	.	.	.	X	1963;2069;2069;2154;2205	.	ENSP00000327209:R1963X	R	-	1	2	PDE4DIP	143571236	0.995000	0.38212	0.113000	0.21522	0.000000	0.00434	0.225000	0.17757	0.604000	0.29930	-0.911000	0.02809	CGA	.	.	none		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
LONP1	9361	hgsc.bcm.edu	37	19	5696146	5696146	+	Silent	SNP	G	G	A	rs3745624	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:5696146G>A	ENST00000360614.3	-	13	2089	c.1932C>T	c.(1930-1932)acC>acT	p.T644T	LONP1_ENST00000585374.1_Silent_p.T530T|LONP1_ENST00000593119.1_Silent_p.T580T|LONP1_ENST00000540670.2_Silent_p.T448T|LONP1_ENST00000590729.1_Silent_p.T514T	NM_004793.2	NP_004784.2			lon peptidase 1, mitochondrial											breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GCTCGGGGATGGTGTCCGTGA	0.677													G|||	997	0.199081	0.2655	0.2622	5008	,	,		14403	0.0913		0.2386	False		,,,				2504	0.135				p.V644V		Atlas-SNP	.											.	LONP1	66	.	0			c.G1932T						PASS	.	G		1122,3284	395.4+/-329.6	148,826,1229	62.0	56.0	58.0		1932	3.6	1.0	19	dbSNP_107	58	2041,6559	352.0+/-328.5	242,1557,2501	no	coding-synonymous	LONP1	NM_004793.2		390,2383,3730	AA,AG,GG		23.7326,25.4653,24.3195		644/960	5696146	3163,9843	2203	4300	6503	SO:0001819	synonymous_variant	9361	exon13			GGGGATGGTGTCC	U02389	CCDS12148.1, CCDS62507.1, CCDS62508.1	19p13.2	2014-01-28	2006-10-20	2006-10-20	ENSG00000196365	ENSG00000196365		"""ATPases / AAA-type"", ""Serine peptidases / Serine peptidases"""	9479	protein-coding gene	gene with protein product		605490	"""protease, serine, 15"""	PRSS15		8248235, 8119403	Standard	NM_004793		Approved	LonHS, hLON, PIM1	uc002mcx.4	P36776		ENST00000360614.3:c.1932C>T	19.37:g.5696146G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	51	16	0.313726	NM_004793		Silent	SNP	ENST00000360614.3	37	CCDS12148.1																																																																																			G|0.776;A|0.224	0.224	strong		0.677	LONP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451662.1	NM_004793	
SEMG2	6407	hgsc.bcm.edu	37	20	43850400	43850400	+	Missense_Mutation	SNP	C	C	A	rs2233896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43850400C>A	ENST00000372769.3	+	2	217	c.127C>A	c.(127-129)Caa>Aaa	p.Q43K		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	43			Q -> K (in dbSNP:rs2233896).		sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				TCCACATGGACAAAAGGGCCA	0.378													C|||	497	0.0992412	0.0885	0.0922	5008	,	,		20685	0.0317		0.161	False		,,,				2504	0.1247				p.Q43K		Atlas-SNP	.											SEMG2,caecum,carcinoma,0,1	SEMG2	92	1	0			c.C127A						scavenged	.	C	LYS/GLN	472,3934	218.7+/-236.7	29,414,1760	109.0	106.0	107.0		127	-3.8	0.0	20	dbSNP_98	107	1515,7085	282.7+/-295.7	122,1271,2907	yes	missense	SEMG2	NM_003008.2	53	151,1685,4667	AA,AC,CC		17.6163,10.7127,15.2776	benign	43/583	43850400	1987,11019	2203	4300	6503	SO:0001583	missense	6407	exon2			CATGGACAAAAGG		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.127C>A	20.37:g.43850400C>A	ENSP00000361855:p.Gln43Lys	Somatic	212	2	0.00943396		WXS	Illumina HiSeq	Phase_I	252	125	0.496032	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Missense_Mutation	SNP	ENST00000372769.3	37	CCDS13346.1	222	0.10164835164835165	42	0.08536585365853659	40	0.11049723756906077	20	0.03496503496503497	120	0.158311345646438	C	6.356	0.433764	0.12045	0.107127	0.176163	ENSG00000124157	ENST00000372769	T	0.06849	3.25	1.88	-3.76	0.04359	.	.	.	.	.	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	B;B	0.26935	0.164;0.164	B;B	0.32211	0.098;0.142	T	0.43130	-0.9410	8	0.30854	T	0.27	.	0.7148	0.00930	0.3117:0.3251:0.2058:0.1573	rs2233896;rs52807159;rs2233896	43;43	A8K6Z6;Q02383	.;SEMG2_HUMAN	K	43	ENSP00000361855:Q43K	ENSP00000361855:Q43K	Q	+	1	0	SEMG2	43283814	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.632000	0.02024	-1.111000	0.02988	-0.474000	0.04947	CAA	C|0.876;A|0.124	0.124	strong		0.378	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
TNIK	23043	hgsc.bcm.edu	37	3	170825920	170825920	+	Silent	SNP	G	G	A	rs2291900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:170825920G>A	ENST00000436636.2	-	20	2660	c.2316C>T	c.(2314-2316)ctC>ctT	p.L772L	TNIK_ENST00000357327.5_Silent_p.L743L|TNIK_ENST00000538048.1_Silent_p.L717L|TNIK_ENST00000369326.5_Silent_p.L743L|TNIK_ENST00000475336.1_Silent_p.L688L|TNIK_ENST00000341852.6_Silent_p.L688L|TNIK_ENST00000460047.1_Silent_p.L717L|TNIK_ENST00000488470.1_Silent_p.L717L|MIR569_ENST00000385228.1_RNA|TNIK_ENST00000470834.1_Silent_p.L743L|TNIK_ENST00000284483.8_Silent_p.L772L	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	772	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.L772L(1)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			GCTCATGGGGGAGCACAGGTG	0.488													G|||	987	0.197085	0.0787	0.2421	5008	,	,		18113	0.1885		0.2883	False		,,,				2504	0.2403				p.L772L		Atlas-SNP	.											TNIK_ENST00000436636,NS,carcinoma,0,3	TNIK	313	3	1	Substitution - coding silent(1)	stomach(1)	c.C2316T						PASS	.	G	,,,,,,,	391,3407		21,349,1529	51.0	54.0	53.0		2316,2229,2229,2151,2151,2064,2064,2316	4.7	1.0	3	dbSNP_100	53	2204,6048		314,1576,2236	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TNIK	NM_001161560.1,NM_001161561.1,NM_001161562.1,NM_001161563.1,NM_001161564.1,NM_001161565.1,NM_001161566.1,NM_015028.2	,,,,,,,	335,1925,3765	AA,AG,GG		26.7087,10.2949,21.5353	,,,,,,,	772/1353,743/1332,743/1324,717/1306,717/1298,688/1277,688/1269,772/1361	170825920	2595,9455	1899	4126	6025	SO:0001819	synonymous_variant	23043	exon20			ATGGGGGAGCACA	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2316C>T	3.37:g.170825920G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Silent	SNP	ENST00000436636.2	37	CCDS46956.1																																																																																			G|0.792;A|0.208	0.208	strong		0.488	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
APLF	200558	hgsc.bcm.edu	37	2	68729931	68729931	+	Silent	SNP	A	A	G	rs112136813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:68729931A>G	ENST00000303795.4	+	3	408	c.237A>G	c.(235-237)ctA>ctG	p.L79L		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	79	FHA-like.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AGCCAAATCTATGGTGCTATT	0.338													A|||	137	0.0273562	0.0038	0.0144	5008	,	,		16672	0.0357		0.0398	False		,,,				2504	0.047				p.L79L		Atlas-SNP	.											.	APLF	69	.	0			c.A237G						PASS	.	A		30,4376	36.8+/-68.6	0,30,2173	112.0	111.0	111.0		237	-5.0	0.0	2	dbSNP_132	111	334,8266	115.0+/-174.9	8,318,3974	no	coding-synonymous	APLF	NM_173545.2		8,348,6147	GG,GA,AA		3.8837,0.6809,2.7987		79/512	68729931	364,12642	2203	4300	6503	SO:0001819	synonymous_variant	200558	exon3			AAATCTATGGTGC	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.237A>G	2.37:g.68729931A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Silent	SNP	ENST00000303795.4	37	CCDS1888.1																																																																																			A|0.972;G|0.028	0.028	strong		0.338	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
SKA3	221150	hgsc.bcm.edu	37	13	21742311	21742311	+	Missense_Mutation	SNP	C	C	T	rs61950353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:21742311C>T	ENST00000314759.5	-	4	683	c.559G>A	c.(559-561)Gta>Ata	p.V187I	SKA3_ENST00000400018.3_Missense_Mutation_p.V187I	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	187					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GTTACAATTACGGGCTCTTCC	0.398																																					p.V187I		Atlas-SNP	.											.	SKA3	76	.	0			c.G559A						PASS	.	C	ILE/VAL,ILE/VAL	172,4234		0,172,2031	187.0	201.0	196.0		559,559	-11.5	0.0	13	dbSNP_129	196	1012,7588		0,1012,3288	yes	missense,missense	SKA3	NM_001166017.1,NM_145061.5	29,29	0,1184,5319	TT,TC,CC		11.7674,3.9038,9.1035	benign,benign	187/389,187/413	21742311	1184,11822	2203	4300	6503	SO:0001583	missense	221150	exon4			CAATTACGGGCTC	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.559G>A	13.37:g.21742311C>T	ENSP00000319417:p.Val187Ile	Somatic	479	1	0.00208768		WXS	Illumina HiSeq	Phase_I	813	268	0.329643	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	310	0.14194139194139194	15	0.03048780487804878	59	0.16298342541436464	128	0.22377622377622378	108	0.1424802110817942	C	11.24	1.580771	0.28180	0.039038	0.117674	ENSG00000165480	ENST00000314759;ENST00000400018	T;T	0.22743	1.95;1.94	5.88	-11.5	0.00074	.	1.396020	0.04148	N	0.320754	T	0.00012	0.0000	N	0.22421	0.69	0.09310	N	1	B;B	0.21753	0.06;0.001	B;B	0.08055	0.003;0.001	T	0.16988	-1.0384	10	0.27785	T	0.31	1.2613	19.3159	0.94213	0.0:0.5809:0.0:0.4191	rs61950353	187;187	Q8IX90-3;Q8IX90	.;SKA3_HUMAN	I	187	ENSP00000319417:V187I;ENSP00000382896:V187I	ENSP00000319417:V187I	V	-	1	0	SKA3	20640311	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.018000	0.00644	-2.167000	0.00779	-2.097000	0.00363	GTA	C|0.893;T|0.107	0.107	strong		0.398	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
FLII	2314	hgsc.bcm.edu	37	17	18148485	18148485	+	Silent	SNP	G	G	A	rs7498	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18148485G>A	ENST00000327031.4	-	30	4002	c.3777C>T	c.(3775-3777)caC>caT	p.H1259H	FLII_ENST00000545457.2_Silent_p.H1204H|FLII_ENST00000579294.1_Silent_p.H1248H|FLII_ENST00000578558.1_Missense_Mutation_p.T669M|FLII_ENST00000379450.4_Silent_p.H1173H	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1259					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					CGCTCCAGGCGTGGAAGCAGC	0.627													A|||	1280	0.255591	0.2882	0.2622	5008	,	,		18123	0.3204		0.2435	False		,,,				2504	0.1524				p.H1259H		Atlas-SNP	.											.	FLII	79	.	0			c.C3777T						PASS	.	A		1213,3193	699.9+/-406.5	168,877,1158	85.0	93.0	90.0		3777	-7.1	0.6	17	dbSNP_52	90	2167,6433	706.2+/-405.5	271,1625,2404	no	coding-synonymous	FLII	NM_002018.2		439,2502,3562	AA,AG,GG		25.1977,27.5306,25.988		1259/1270	18148485	3380,9626	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon30			CCAGGCGTGGAAG	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3777C>T	17.37:g.18148485G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			G|0.728;A|0.272	0.272	strong		0.627	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
RANBP2	5903	hgsc.bcm.edu	37	2	109382170	109382170	+	Silent	SNP	A	A	G	rs535428027		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:109382170A>G	ENST00000283195.6	+	20	5301	c.5175A>G	c.(5173-5175)gaA>gaG	p.E1725E		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1725					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E1725E(9)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CTAAGAAGGAAGGACAGTGGG	0.418													A|||	1	0.000199681	0.0	0.0014	5008	,	,		23860	0.0		0.0	False		,,,				2504	0.0				p.E1725E		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,6	RANBP2	488	6	9	Substitution - coding silent(9)	prostate(9)	c.A5175G						scavenged	.						182.0	173.0	176.0					2																	109382170		2203	4300	6503	SO:0001819	synonymous_variant	5903	exon20			GAAGGAAGGACAG	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.5175A>G	2.37:g.109382170A>G		Somatic	611	8	0.0130933		WXS	Illumina HiSeq	Phase_I	644	12	0.0186335	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																			.	.	none		0.418	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
ZNF407	55628	hgsc.bcm.edu	37	18	72776121	72776121	+	Silent	SNP	G	G	A	rs3744913	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:72776121G>A	ENST00000299687.5	+	8	6444	c.6444G>A	c.(6442-6444)acG>acA	p.T2148T		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TCATCGTGACGGAGGAGCTGG	0.657													G|||	3808	0.760383	0.4939	0.7896	5008	,	,		16655	0.9167		0.8857	False		,,,				2504	0.8098				p.T2148T		Atlas-SNP	.											.	ZNF407	231	.	0			c.G6444A						PASS	.	G		2530,1838		732,1066,386	28.0	34.0	32.0		6444	-8.9	0.9	18	dbSNP_107	32	7327,1249		3134,1059,95	no	coding-synonymous	ZNF407	NM_017757.2		3866,2125,481	AA,AG,GG		14.5639,42.0788,23.8489		2148/2249	72776121	9857,3087	2184	4288	6472	SO:0001819	synonymous_variant	55628	exon8			CGTGACGGAGGAG	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.6444G>A	18.37:g.72776121G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			G|0.221;A|0.779	0.779	strong		0.657	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
TMEM70	54968	hgsc.bcm.edu	37	8	74893821	74893821	+	Missense_Mutation	SNP	A	A	G	rs1053079	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:74893821A>G	ENST00000312184.5	+	3	821	c.748A>G	c.(748-750)Acc>Gcc	p.T250A	Y_RNA_ENST00000365350.1_RNA	NM_001040613.2|NM_017866.5	NP_001035703.1|NP_060336.3	Q9BUB7	TMM70_HUMAN	transmembrane protein 70	250			T -> A (in dbSNP:rs1053079). {ECO:0000269|PubMed:14702039}.		mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)				breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8	Breast(64;0.0311)		Epithelial(68;0.0186)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0564)			TATGGAAGAAACCAGTGAAGA	0.323													G|||	1297	0.258986	0.3971	0.3631	5008	,	,		20707	0.1478		0.169	False		,,,				2504	0.2055				p.T250A		Atlas-SNP	.											.	TMEM70	12	.	0			c.A748G						PASS	.	G	,ALA/THR	1569,2827	606.1+/-390.7	281,1007,910	45.0	50.0	48.0		,748	-2.3	0.0	8	dbSNP_86	48	1338,7260	737.6+/-407.0	108,1122,3069	yes	utr-3,missense	TMEM70	NM_001040613.2,NM_017866.5	,58	389,2129,3979	GG,GA,AA		15.5618,35.6915,22.3719	,benign	,250/261	74893821	2907,10087	2198	4299	6497	SO:0001583	missense	54968	exon3			GAAGAAACCAGTG	BC002748	CCDS6215.1, CCDS47876.1	8q21.11	2013-05-23				ENSG00000175606			26050	protein-coding gene	gene with protein product		612418				21945727, 22986587	Standard	NM_017866		Approved	FLJ20533	uc003yab.3	Q9BUB7		ENST00000312184.5:c.748A>G	8.37:g.74893821A>G	ENSP00000312599:p.Thr250Ala	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	NM_017866	E9PDY9|Q9NWY5	Missense_Mutation	SNP	ENST00000312184.5	37	CCDS6215.1	544	0.2490842490842491	219	0.4451219512195122	133	0.3674033149171271	81	0.14160839160839161	111	0.14643799472295516	G	0.005	-2.157845	0.00321	0.356915	0.155618	ENSG00000175606	ENST00000312184	T	0.35421	1.31	5.38	-2.28	0.06826	.	2.077890	0.01824	N	0.034274	T	0.00012	0.0000	N	0.00879	-1.12	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37820	-0.9689	9	0.08599	T	0.76	3.5746	3.4868	0.07622	0.3489:0.0799:0.421:0.1502	rs1053079;rs3193564;rs52822564;rs57446939;rs1053079	250	Q9BUB7	TMM70_HUMAN	A	250	ENSP00000312599:T250A	ENSP00000312599:T250A	T	+	1	0	TMEM70	75056375	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.704000	0.05058	-0.637000	0.05516	-3.968000	0.00014	ACC	A|0.767;G|0.233	0.233	strong		0.323	TMEM70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379028.1	NM_017866	
PKD1L1	168507	hgsc.bcm.edu	37	7	47879049	47879049	+	Missense_Mutation	SNP	G	G	A	rs76100363	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:47879049G>A	ENST00000289672.2	-	36	5814	c.5764C>T	c.(5764-5766)Cgg>Tgg	p.R1922W		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1922					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CCTACCTTCCGGAAGCCGAGT	0.642													G|||	816	0.162939	0.0174	0.2291	5008	,	,		16788	0.2321		0.2078	False		,,,				2504	0.1953				p.R1922W		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	0			c.C5764T						PASS	.	G	TRP/ARG	211,4195		3,205,1995	29.0	24.0	26.0		5764	-9.7	0.1	7	dbSNP_131	26	1513,7087		124,1265,2911	yes	missense	PKD1L1	NM_138295.3	101	127,1470,4906	AA,AG,GG		17.593,4.7889,13.2554	benign	1922/2850	47879049	1724,11282	2203	4300	6503	SO:0001583	missense	168507	exon36			CCTTCCGGAAGCC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5764C>T	7.37:g.47879049G>A	ENSP00000289672:p.Arg1922Trp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	155	81	0.522581	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	376	0.17216117216117216	11	0.022357723577235773	91	0.2513812154696133	120	0.2097902097902098	154	0.20316622691292877	G	6.846	0.525413	0.13066	0.047889	0.17593	ENSG00000158683	ENST00000289672	T	0.20738	2.05	4.87	-9.73	0.00512	.	1.518000	0.04159	N	0.322748	T	0.00012	0.0000	N	0.11064	0.09	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.28776	-1.0033	9	0.48119	T	0.1	0.0923	8.3591	0.32348	0.6412:0.0:0.1727:0.1862	.	1922	Q8TDX9	PK1L1_HUMAN	W	1922	ENSP00000289672:R1922W	ENSP00000289672:R1922W	R	-	1	2	PKD1L1	47845574	0.000000	0.05858	0.055000	0.19348	0.255000	0.26057	-2.918000	0.00695	-2.336000	0.00628	-0.749000	0.03505	CGG	G|0.859;A|0.141	0.141	strong		0.642	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
MYH6	4624	hgsc.bcm.edu	37	14	23869993	23869993	+	Silent	SNP	G	G	A	rs61731179	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:23869993G>A	ENST00000356287.3	-	12	1364	c.1335C>T	c.(1333-1335)aaC>aaT	p.N445N	MYH6_ENST00000405093.3_Silent_p.N445N			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	445	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CCAGGGTGGCGTTGATGCGCG	0.587													G|||	161	0.0321486	0.0023	0.0403	5008	,	,		21394	0.0		0.0755	False		,,,				2504	0.0552				p.N445N		Atlas-SNP	.											.	MYH6	274	.	0			c.C1335T						PASS	.	G		48,4358		0,48,2155	144.0	113.0	123.0		1335	-4.4	0.9	14	dbSNP_129	123	533,8067		17,499,3784	no	coding-synonymous	MYH6	NM_002471.3		17,547,5939	AA,AG,GG		6.1977,1.0894,4.4672		445/1940	23869993	581,12425	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon13			GGTGGCGTTGATG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.1335C>T	14.37:g.23869993G>A		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	348	162	0.465517	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			G|0.960;A|0.040	0.040	strong		0.587	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
IVD	3712	hgsc.bcm.edu	37	15	40705225	40705225	+	Silent	SNP	C	C	T	rs2229312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40705225C>T	ENST00000249760.2	+	7	1066	c.723C>T	c.(721-723)gaC>gaT	p.D241D	IVD_ENST00000487418.2_Silent_p.D244D|IVD_ENST00000479013.2_Silent_p.D214D	NM_002225.3	NP_002216.2	P26440	IVD_HUMAN	isovaleryl-CoA dehydrogenase	241					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	flavin adenine dinucleotide binding (GO:0050660)|isovaleryl-CoA dehydrogenase activity (GO:0008470)			kidney(1)|lung(5)|ovary(2)|prostate(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;1.52e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.65e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0808)	Flavin adenine dinucleotide(DB03147)	AGAAGCTGGACAAGCTGGGGA	0.527													C|||	396	0.0790735	0.0696	0.0821	5008	,	,		21832	0.0129		0.1421	False		,,,				2504	0.093				p.D244D	GBM(31;293 617 7486 32527 34655)	Atlas-SNP	.											.	IVD	29	.	0			c.C732T						PASS	.	C	,	367,4039	185.7+/-212.7	15,337,1851	97.0	92.0	94.0		642,732	5.7	1.0	15	dbSNP_98	94	1178,7422	240.3+/-271.1	81,1016,3203	no	coding-synonymous,coding-synonymous	IVD	NM_001159508.1,NM_002225.3	,	96,1353,5054	TT,TC,CC		13.6977,8.3296,11.8791	,	214/397,244/427	40705225	1545,11461	2203	4300	6503	SO:0001819	synonymous_variant	3712	exon7			GCTGGACAAGCTG	AF038317	CCDS10057.1, CCDS10057.2, CCDS53930.1	15q14-q15	2010-05-11	2010-05-11		ENSG00000128928	ENSG00000128928	1.3.99.10		6186	protein-coding gene	gene with protein product		607036	"""isovaleryl Coenzyme A dehydrogenase"", ""isovaleryl CoA dehydrogenase"""			2063866	Standard	NM_002225		Approved	ACAD2	uc001zls.3	P26440	OTTHUMG00000129984	ENST00000249760.2:c.723C>T	15.37:g.40705225C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_002225	B2RCV5|B3KVI7|J3KR54|Q53XZ9|Q96AF6	Silent	SNP	ENST00000249760.2	37		204	0.09340659340659341	36	0.07317073170731707	35	0.09668508287292818	5	0.008741258741258742	128	0.16886543535620052	C	8.979	0.974946	0.18736	0.083296	0.136977	ENSG00000128928	ENST00000473112	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.18366	-1.0339	3	.	.	.	.	7.4079	0.27001	0.0:0.7999:0.0:0.2001	rs2229312;rs34751404	.	.	.	I	161	.	.	T	+	2	0	IVD	38492517	0.996000	0.38824	1.000000	0.80357	0.993000	0.82548	0.420000	0.21263	2.673000	0.90976	0.591000	0.81541	ACA	C|0.887;T|0.113	0.113	strong		0.527	IVD-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
FAM186A	121006	hgsc.bcm.edu	37	12	50745779	50745779	+	Silent	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50745779C>A	ENST00000327337.5	-	4	4835	c.4836G>T	c.(4834-4836)ggG>ggT	p.G1612G	FAM186A_ENST00000543111.1_Silent_p.G1612G|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1612								p.G1612G(1)									TGAGAGGGATCCCCTGAGCCT	0.677																																					p.G1612G	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - coding silent(1)	stomach(1)	c.G4836T						PASS	.						14.0	14.0	14.0					12																	50745779		692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			AGGGATCCCCTGA		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4836G>T	12.37:g.50745779C>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	266	60	0.225564	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			.	.	none		0.677	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
ZNF45	7596	hgsc.bcm.edu	37	19	44418077	44418077	+	Missense_Mutation	SNP	C	C	T	rs407731	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:44418077C>T	ENST00000269973.5	-	10	2601	c.1511G>A	c.(1510-1512)aGg>aAg	p.R504K	RP11-15A1.2_ENST00000586247.1_RNA|ZNF45_ENST00000589703.1_Missense_Mutation_p.R504K	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	504			R -> K (in dbSNP:rs407731). {ECO:0000269|PubMed:15057824}.		gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						CTTACCACACCTCTCGCATTT	0.493													T|||	2630	0.52516	0.3336	0.6484	5008	,	,		20800	0.7996		0.5169	False		,,,				2504	0.4223				p.R504K		Atlas-SNP	.											.	ZNF45	51	.	0			c.G1511A						PASS	.	T	LYS/ARG	1581,2825	666.0+/-401.6	294,993,916	62.0	58.0	60.0		1511	2.6	1.0	19	dbSNP_80	60	4351,4249	573.4+/-389.9	1117,2117,1066	yes	missense	ZNF45	NM_003425.3	26	1411,3110,1982	TT,TC,CC		49.407,35.8829,45.6097	benign	504/683	44418077	5932,7074	2203	4300	6503	SO:0001583	missense	7596	exon10			CCACACCTCTCGC	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"""Zinc fingers, C2H2-type"", ""-"""	13111	protein-coding gene	gene with protein product		194554	"""zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)"", ""zinc finger protein 13"""	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.1511G>A	19.37:g.44418077C>T	ENSP00000269973:p.Arg504Lys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	1254|1254	0.5741758241758241|0.5741758241758241	187|187	0.3800813008130081|0.3800813008130081	208|208	0.574585635359116|0.574585635359116	470|470	0.8216783216783217|0.8216783216783217	389|389	0.5131926121372031|0.5131926121372031	T|T	5.190|5.190	0.220623|0.220623	0.09863|0.09863	0.358829|0.358829	0.50593|0.50593	ENSG00000124459|ENSG00000124459	ENST00000328762|ENST00000269973	.|T	.|0.07327	.|3.2	3.61|3.61	2.56|2.56	0.30785|0.30785	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.200214	.|0.24801	.|N	.|0.035499	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01679|0.01679	-0.765|-0.765	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.06338|0.06338	-1.0832|-1.0832	5|9	0.59425|0.46703	D|T	0.04|0.11	-11.4279|-11.4279	5.9628|5.9628	0.19308|0.19308	0.0:0.0945:0.1643:0.7412|0.0:0.0945:0.1643:0.7412	rs407731;rs17712947;rs407731|rs407731;rs17712947;rs407731	.|504	.|Q02386	.|ZNF45_HUMAN	S|K	504|504	.|ENSP00000269973:R504K	ENSP00000367176:G504S|ENSP00000269973:R504K	G|R	-|-	1|2	0|0	ZNF45|ZNF45	49109917|49109917	0.000000|0.000000	0.05858|0.05858	0.997000|0.997000	0.53966|0.53966	0.974000|0.974000	0.67602|0.67602	0.794000|0.794000	0.26958|0.26958	0.096000|0.096000	0.17463|0.17463	-0.556000|-0.556000	0.04195|0.04195	GGT|AGG	C|0.480;T|0.520	0.520	strong		0.493	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
MYH11	4629	hgsc.bcm.edu	37	16	15811062	15811062	+	Silent	SNP	C	C	T	rs587781066|rs1050162	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15811062C>T	ENST00000300036.5	-	38	5548	c.5439G>A	c.(5437-5439)aaG>aaA	p.K1813K	NDE1_ENST00000396354.1_Intron|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396355.1_Intron|MYH11_ENST00000576790.2_Silent_p.K1813K|MYH11_ENST00000452625.2_Silent_p.K1820K|MYH11_ENST00000396324.3_Silent_p.K1820K	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1813					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CGATGGTGGACTTGAACTTGG	0.622			T	CBFB	AML								C|||	1987	0.396765	0.2542	0.5029	5008	,	,		19368	0.3323		0.4841	False		,,,				2504	0.4908				p.K1820K		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	MYH11_ENST00000396324,NS,neuroblastoma,-1,2	MYH11	520	2	0			c.G5460A						scavenged	.	C	,,,,,	1339,3055	447.5+/-348.4	208,923,1066	123.0	103.0	110.0		5460,5460,,5439,,5439	3.4	1.0	16	dbSNP_86	110	4371,4229	582.5+/-391.4	1133,2105,1062	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	1341,3028,2128	TT,TC,CC		49.1744,30.4734,43.9434	,,,,,	1820/1946,1820/1980,,1813/1973,,1813/1939	15811062	5710,7284	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon39			GGTGGACTTGAAC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5439G>A	16.37:g.15811062C>T		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			C|0.596;T|0.404	0.404	strong		0.622	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
MLH1	4292	hgsc.bcm.edu	37	3	37089130	37089130	+	Missense_Mutation	SNP	A	A	G	rs587778949|rs35502531|rs35001569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37089130A>G	ENST00000231790.2	+	16	2068	c.1852A>G	c.(1852-1854)Aag>Gag	p.K618E	MLH1_ENST00000435176.1_Missense_Mutation_p.K520E|MLH1_ENST00000536378.1_Missense_Mutation_p.K377E|MLH1_ENST00000455445.2_Missense_Mutation_p.K377E|MLH1_ENST00000539477.1_Missense_Mutation_p.K377E|MLH1_ENST00000458205.2_Missense_Mutation_p.K377E	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	618	Interaction with EXO1.		K -> A (common polymorphism; requires 2 nucleotide substitutions; dbSNP:rs35502531). {ECO:0000269|PubMed:10598809, ECO:0000269|PubMed:10713887, ECO:0000269|PubMed:11726306, ECO:0000269|PubMed:11870161, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12373605, ECO:0000269|PubMed:16083711, ECO:0000269|PubMed:18033691, ECO:0000269|PubMed:9311737}.|K -> R (in colorectal cancer; dbSNP:rs63750449). {ECO:0000269|PubMed:14504054}.|K -> T (in HNPCC2; type II). {ECO:0000269|PubMed:10573010, ECO:0000269|PubMed:11839723, ECO:0000269|PubMed:12095971, ECO:0000269|PubMed:7757073, ECO:0000269|PubMed:8872463}.|Missing (in HNPCC2). {ECO:0000269|PubMed:16451135}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.K618del(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TCTGAAGAAGAAGGCTGAGAT	0.428		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	16	0.00319489	0.0008	0.0072	5008	,	,		20450	0.0		0.0099	False		,,,				2504	0.0				p.K618E		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,colon,carcinoma,-1,5	MLH1	226	5	2	Whole gene deletion(1)|Deletion - In frame(1)	ovary(1)|large_intestine(1)	c.A1852G	GRCh37	CD951778|CM973729|CM981294|CP035449|CX973308	MLH1	D|M|X	rs35001569	scavenged	.	A	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	9,4397	15.5+/-35.6	0,9,2194	158.0	161.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1852,1558,1129,1129	5.3	1.0	3	dbSNP_126	160	39,8561	16.6+/-54.9	0,39,4261	yes	missense,missense,missense,missense	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	56,56,56,56	0,48,6455	GG,GA,AA		0.4535,0.2043,0.3691	probably-damaging,probably-damaging,probably-damaging,probably-damaging	618/757,520/659,377/516,377/516	37089130	48,12958	2203	4300	6503	SO:0001583	missense	4292	exon16	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AAGAAGAAGGCTG	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.1852A>G	3.37:g.37089130A>G	ENSP00000231790:p.Lys618Glu	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	134	80	0.597015	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	9	0.004120879120879121	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	24.4	4.530975	0.85706	0.002043	0.004535	ENSG00000076242	ENST00000231790;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	D;D;D;D;D;D	0.94613	-3.47;-3.47;-3.47;-3.47;-3.47;-3.47	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.96583	0.8885	M	0.91406	3.205	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.993;0.999;0.993	D;P;D;P	0.64042	0.921;0.779;0.921;0.868	D	0.95740	0.8782	10	0.66056	D	0.02	-23.9591	15.372	0.74573	1.0:0.0:0.0:0.0	rs35001569	520;618;618;618	E9PCU2;B2R6K0;Q53GX1;P40692	.;.;.;MLH1_HUMAN	E	618;482;377;377;377;520;377	ENSP00000231790:K618E;ENSP00000402667:K377E;ENSP00000443665:K377E;ENSP00000398272:K377E;ENSP00000402564:K520E;ENSP00000444286:K377E	ENSP00000231790:K618E	K	+	1	0	MLH1	37064134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.070000	0.76763	2.044000	0.60594	0.477000	0.44152	AAG	.	.	alt		0.428	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4446217	4446217	+	Silent	SNP	C	C	T	rs138864176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4446217C>T	ENST00000254718.4	-	20	3189	c.2883G>A	c.(2881-2883)acG>acA	p.T961T	MYBBP1A_ENST00000381556.2_Silent_p.T961T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	961					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						CCTGCGGGCCCGTGGGCATGT	0.657													C|||	11	0.00219649	0.0	0.0029	5008	,	,		16836	0.0		0.0089	False		,,,				2504	0.0				p.T961T		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G2883A						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	38.0	43.0	42.0		2883,2883	-0.6	0.0	17	dbSNP_134	42	37,8563	24.6+/-71.5	0,37,4263	no	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	0,41,6462	TT,TC,CC		0.4302,0.0908,0.3152	,	961/1333,961/1329	4446217	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	10514	exon20			CGGGCCCGTGGGC	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.2883G>A	17.37:g.4446217C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
GMEB2	26205	hgsc.bcm.edu	37	20	62236148	62236148	+	Silent	SNP	T	T	C	rs6090471	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62236148T>C	ENST00000266068.1	-	2	655	c.177A>G	c.(175-177)gcA>gcG	p.A59A	GMEB2_ENST00000370069.1_Silent_p.A8A|GMEB2_ENST00000370077.1_Silent_p.A59A			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	59	Poly-Ala.				regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			CGGCAGCTGCTGCCGCTGCAT	0.592													C|||	3369	0.672724	0.5499	0.6844	5008	,	,		15286	0.6171		0.9165	False		,,,				2504	0.637				p.A59A		Atlas-SNP	.											.	GMEB2	44	.	0			c.A177G						PASS	.	C		2736,1670	492.4+/-362.4	858,1020,325	58.0	62.0	61.0		177	-10.0	0.0	20	dbSNP_114	61	7835,765	176.9+/-226.6	3565,705,30	no	coding-synonymous	GMEB2	NM_012384.3		4423,1725,355	CC,CT,TT		8.8953,37.9029,18.7221		59/531	62236148	10571,2435	2203	4300	6503	SO:0001819	synonymous_variant	26205	exon3			AGCTGCTGCCGCT	AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.177A>G	20.37:g.62236148T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_012384	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Silent	SNP	ENST00000266068.1	37	CCDS13528.1																																																																																			T|0.254;C|0.746	0.746	strong		0.592	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384	
WDR11	55717	hgsc.bcm.edu	37	10	122666320	122666320	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:122666320T>C	ENST00000263461.6	+	28	3716	c.3470T>C	c.(3469-3471)gTg>gCg	p.V1157A	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						GCCTTATTTGTGGAAGCTTGC	0.438																																					p.V1157A		Atlas-SNP	.											WDR11,NS,haematopoietic_neoplasm,+1,1	WDR11	95	1	0			c.T3470C						scavenged	.						224.0	202.0	210.0					10																	122666320		2203	4300	6503	SO:0001583	missense	55717	exon28			TATTTGTGGAAGC	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.3470T>C	10.37:g.122666320T>C	ENSP00000263461:p.Val1157Ala	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	256	3	0.0117188	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	37	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.911215	0.33721	.	.	ENSG00000120008	ENST00000263461	D	0.90197	-2.63	5.72	5.72	0.89469	.	0.258145	0.39615	N	0.001308	T	0.81828	0.4905	N	0.19112	0.55	0.36408	D	0.863562	B;B	0.20780	0.048;0.02	B;B	0.16289	0.015;0.015	T	0.79259	-0.1877	10	0.21540	T	0.41	-9.0414	10.3671	0.44030	0.0:0.0726:0.0:0.9274	.	1157;1157	Q9BZH6;B2RCJ6	WDR11_HUMAN;.	A	1157	ENSP00000263461:V1157A	ENSP00000263461:V1157A	V	+	2	0	WDR11	122656310	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	5.691000	0.68249	2.174000	0.68829	0.533000	0.62120	GTG	.	.	none		0.438	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
CMPK2	129607	hgsc.bcm.edu	37	2	6990020	6990020	+	Silent	SNP	C	C	T	rs10495545	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:6990020C>T	ENST00000256722.5	-	5	1310	c.1311G>A	c.(1309-1311)acG>acA	p.T437T	CMPK2_ENST00000458098.1_Intron|CMPK2_ENST00000478738.1_5'UTR	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	437					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGCTTAATACCGTCTGCAGGA	0.483													C|||	518	0.103435	0.0197	0.1023	5008	,	,		18490	0.2669		0.1153	False		,,,				2504	0.0368				p.T437T		Atlas-SNP	.											.	CMPK2	30	.	0			c.G1311A						PASS	.	C		120,3700		0,120,1790	113.0	113.0	113.0		1311	-3.6	0.0	2	dbSNP_119	113	897,7333		53,791,3271	no	coding-synonymous	CMPK2	NM_207315.2		53,911,5061	TT,TC,CC		10.8991,3.1414,8.4398		437/450	6990020	1017,11033	1910	4115	6025	SO:0001819	synonymous_variant	129607	exon5			TAATACCGTCTGC		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"""cytidylate kinase 2"""	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.1311G>A	2.37:g.6990020C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_207315	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Silent	SNP	ENST00000256722.5	37	CCDS42648.1																																																																																			C|0.876;N|0.001	.	strong		0.483	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315	
CEP57	9702	hgsc.bcm.edu	37	11	95564259	95564259	+	Missense_Mutation	SNP	A	A	G	rs644799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:95564259A>G	ENST00000325542.5	+	11	1580	c.1342A>G	c.(1342-1344)Aga>Gga	p.R448G	CEP57_ENST00000541150.1_Missense_Mutation_p.R439G|CEP57_ENST00000537677.1_Missense_Mutation_p.R421G|CEP57_ENST00000325486.5_Missense_Mutation_p.R422G	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	448	Mediates interaction with microtubules. {ECO:0000250}.		R -> G (in dbSNP:rs644799). {ECO:0000269|PubMed:12717444, ECO:0000269|PubMed:14702039}.		fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGATGAAGAAAGAAACAGCAG	0.373									Mosaic Variegated Aneuploidy Syndrome				G|||	1031	0.205871	0.0772	0.2363	5008	,	,		13719	0.253		0.3738	False		,,,				2504	0.137				p.R448G		Atlas-SNP	.											CEP57,colon,carcinoma,0,1	CEP57	40	1	0			c.A1342G						PASS	.	G	GLY/ARG	546,3856	765.6+/-413.4	34,478,1689	56.0	58.0	58.0		1342	4.9	1.0	11	dbSNP_83	58	3286,5310	636.7+/-399.1	602,2082,1614	yes	missense	CEP57	NM_014679.4	125	636,2560,3303	GG,GA,AA		38.2271,12.4035,29.4815	benign	448/501	95564259	3832,9166	2201	4298	6499	SO:0001583	missense	9702	exon11	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GAAGAAAGAAACA	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.1342A>G	11.37:g.95564259A>G	ENSP00000317902:p.Arg448Gly	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_014679	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	37	CCDS8304.1	590|590	0.27014652014652013|0.27014652014652013	44|44	0.08943089430894309|0.08943089430894309	102|102	0.281767955801105|0.281767955801105	163|163	0.28496503496503495|0.28496503496503495	281|281	0.370712401055409|0.370712401055409	G|G	4.527|4.527	0.097865|0.097865	0.08681|0.08681	0.124035|0.124035	0.382271|0.382271	ENSG00000166037|ENSG00000166037	ENST00000535224|ENST00000537677;ENST00000325542;ENST00000325486;ENST00000541150	.|T;T;T;T	.|0.30182	.|1.55;1.55;1.54;1.54	5.89|5.89	4.92|4.92	0.64577|0.64577	.|.	.|0.499946	.|0.20276	.|N	.|0.095553	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01219|0.01219	-0.95|-0.95	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.35251|0.35251	-0.9796|-0.9796	4|9	.|0.87932	.|D	.|0	-4.9723|-4.9723	6.4242|6.4242	0.21760|0.21760	0.1897:0.1507:0.6596:0.0|0.1897:0.1507:0.6596:0.0	rs644799;rs1150354;rs16922608;rs17228646;rs52796376;rs644799|rs644799;rs1150354;rs16922608;rs17228646;rs52796376;rs644799	.|439;422;448	.|F5H5F7;Q86XR8-2;Q86XR8	.|.;.;CEP57_HUMAN	R|G	237|421;448;422;439	.|ENSP00000441392:R421G;ENSP00000317902:R448G;ENSP00000317487:R422G;ENSP00000443436:R439G	.|ENSP00000317487:R422G	K|R	+|+	2|1	0|2	CEP57|CEP57	95203907|95203907	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.664000|0.664000	0.39144|0.39144	1.006000|1.006000	0.29847|0.29847	1.511000|1.511000	0.48818|0.48818	-0.226000|-0.226000	0.12346|0.12346	AAG|AGA	T|0.005;G|0.275;C|0.007;N|0.000;A|0.713	0.275	strong		0.373	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679	
MT-ATP8	4509	hgsc.bcm.edu	37	M	8448	8448	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrM:8448T>C	ENST00000361851.1	+	1	83	c.83T>C	c.(82-84)aTa>aCa	p.I28T	MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA			P03928	ATP8_HUMAN	mitochondrially encoded ATP synthase 8	28			M -> T. {ECO:0000269|PubMed:9461455}.		ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)										CCAACTAAAAATATTAAACAC	0.383																																					p.M28T		Atlas-SNP	.											.	.	.	.	0			c.T83C						PASS	.																																			SO:0001583	missense	0	exon1			TAAAAATATTAAA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000228253	ENSG00000228253		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7415	protein-coding gene	gene with protein product		516070	"""ATP synthase 8"""	MTATP8			Standard			Approved	ATP8, A6L		P03928		ENST00000361851.1:c.83T>C	M.37:g.8448T>C	ENSP00000355265:p.Ile28Thr	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	ENST00000361851	Q34771	Missense_Mutation	SNP	ENST00000361851.1	37																																																																																				.	.	none		0.383	MT-ATP8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024030	
C2CD3	26005	hgsc.bcm.edu	37	11	73785326	73785326	+	Silent	SNP	T	T	C	rs4453265	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:73785326T>C	ENST00000334126.7	-	24	5149	c.4923A>G	c.(4921-4923)gtA>gtG	p.V1641V	C2CD3_ENST00000313663.7_Silent_p.V1641V			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1641	C2 2.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TTGCTCTTTCTACTAGGATGC	0.532													T|||	2259	0.451078	0.4312	0.4798	5008	,	,		20957	0.4425		0.4692	False		,,,				2504	0.4479				p.V1641V		Atlas-SNP	.											.	C2CD3	288	.	0			c.A4923G						PASS	.	T		1833,2567	534.0+/-373.9	369,1095,736	106.0	89.0	95.0		4923	1.6	1.0	11	dbSNP_111	95	4033,4553	555.8+/-386.7	982,2069,1242	yes	coding-synonymous	C2CD3	NM_015531.4		1351,3164,1978	CC,CT,TT		46.9718,41.6591,45.1717		1641/1964	73785326	5866,7120	2200	4293	6493	SO:0001819	synonymous_variant	26005	exon24			TCTTTCTACTAGG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4923A>G	11.37:g.73785326T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	162	161	0.993827	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Silent	SNP	ENST00000334126.7	37																																																																																				T|0.543;C|0.457	0.457	strong		0.532	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
PRKRA	8575	hgsc.bcm.edu	37	2	179315757	179315757	+	Start_Codon_SNP	SNP	T	T	G	rs9406386	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179315757T>G	ENST00000325748.4	-	1	201	c.1A>C	c.(1-3)Atg>Ctg	p.M1L	PRKRA_ENST00000432031.2_5'Flank|DFNB59_ENST00000409117.3_5'Flank|PRKRA_ENST00000487082.1_5'Flank|PRKRA_ENST00000470200.1_Intron|PRKRA_ENST00000438687.3_5'UTR|DFNB59_ENST00000375129.4_5'Flank	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	1	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CTCTGGGACATGGCGAGAAGG	0.746																																					p.M1L	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											.	PRKRA	56	.	0			c.A1C						PASS	.						6.0	9.0	8.0					2																	179315757		1711	3612	5323	SO:0001582	initiator_codon_variant	8575	exon1			GGGACATGGCGAG	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.1A>C	2.37:g.179315757T>G	ENSP00000318176:p.Met1Leu	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Missense_Mutation	SNP	ENST00000325748.4	37	CCDS2279.1	354	0.1620879120879121	36	0.07317073170731707	85	0.23480662983425415	70	0.12237762237762238	163	0.21503957783641162	T	17.06	3.292620	0.59976	.	.	ENSG00000180228	ENST00000325748	T	0.70164	-0.46	4.45	3.29	0.37713	.	0.824018	0.10788	N	0.634052	T	0.00039	0.0001	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04635	-1.0937	9	0.87932	D	0	.	6.5676	0.22521	0.0:0.1104:0.0:0.8896	rs9406386	1	O75569	PRKRA_HUMAN	L	1	ENSP00000318176:M1L	ENSP00000318176:M1L	M	-	1	0	PRKRA	179024003	0.994000	0.37717	0.921000	0.36526	0.909000	0.53808	1.278000	0.33179	0.853000	0.35312	0.338000	0.21704	ATG	T|0.825;G|0.175	0.175	strong		0.746	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	Missense_Mutation
MTRF1L	54516	hgsc.bcm.edu	37	6	153316326	153316326	+	Silent	SNP	A	A	G	rs3734467	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:153316326A>G	ENST00000367233.5	-	3	467	c.468T>C	c.(466-468)taT>taC	p.Y156Y	MTRF1L_ENST00000367230.1_Intron|MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367231.5_Silent_p.Y156Y	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	156						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)	p.Y156Y(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		TAAATGCAGCATATTGCTGAT	0.348													A|||	735	0.146765	0.1475	0.1081	5008	,	,		16505	0.131		0.1083	False		,,,				2504	0.229				p.Y156Y		Atlas-SNP	.											MTRF1L,NS,carcinoma,0,1	MTRF1L	21	1	1	Substitution - coding silent(1)	stomach(1)	c.T468C						PASS	.	A	,	556,3850	231.4+/-245.2	37,482,1684	37.0	35.0	36.0		468,468	1.4	1.0	6	dbSNP_107	36	958,7634	205.9+/-248.2	61,836,3399	no	coding-synonymous,coding-synonymous	MTRF1L	NM_001114184.1,NM_019041.5	,	98,1318,5083	GG,GA,AA		11.1499,12.6192,11.6479	,	156/272,156/381	153316326	1514,11484	2203	4296	6499	SO:0001819	synonymous_variant	54516	exon3			TGCAGCATATTGC	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.468T>C	6.37:g.153316326A>G		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	306	150	0.490196	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Silent	SNP	ENST00000367233.5	37	CCDS5243.1																																																																																			A|0.888;G|0.112	0.112	strong		0.348	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041	
PLA2G2A	5320	hgsc.bcm.edu	37	1	20304962	20304962	+	Silent	SNP	C	C	G	rs2236771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20304962C>G	ENST00000375111.3	-	4	367	c.96G>C	c.(94-96)acG>acC	p.T32T	PLA2G2A_ENST00000496748.1_5'UTR|PLA2G2A_ENST00000400520.3_Silent_p.T32T	NM_000300.3|NM_001161727.1	NP_000291.1|NP_001155199.1	P14555	PA2GA_HUMAN	phospholipase A2, group IIA (platelets, synovial fluid)	32					defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of epithelial cell proliferation (GO:0050680)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidic acid metabolic process (GO:0046473)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|small molecule metabolic process (GO:0044281)|somatic stem cell maintenance (GO:0035019)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|phospholipase A2 activity (GO:0004623)|phospholipid binding (GO:0005543)			central_nervous_system(1)|lung(6)|prostate(1)|stomach(1)	9		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Diclofenac(DB00586)|Ginkgo biloba(DB01381)|Indomethacin(DB00328)|Suramin(DB04786)	CCTTTCCTGTCGTCAACTTGA	0.557													C|||	486	0.0970447	0.0053	0.1009	5008	,	,		19229	0.2282		0.0775	False		,,,				2504	0.1033				p.T32T		Atlas-SNP	.											.	PLA2G2A	14	.	0			c.G96C						PASS	.	C	,,,	81,4325	69.2+/-107.0	1,79,2123	81.0	79.0	80.0		96,96,96,96	-4.2	0.0	1	dbSNP_98	80	794,7806	185.5+/-233.2	42,710,3548	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLA2G2A	NM_000300.3,NM_001161727.1,NM_001161728.1,NM_001161729.1	,,,	43,789,5671	GG,GC,CC		9.2326,1.8384,6.7277	,,,	32/145,32/145,32/145,32/145	20304962	875,12131	2203	4300	6503	SO:0001819	synonymous_variant	5320	exon3			TCCTGTCGTCAAC	BC005919	CCDS201.1	1p35	2008-09-19			ENSG00000188257	ENSG00000188257	3.1.1.4		9031	protein-coding gene	gene with protein product		172411		PLA2B, PLA2L		8838795	Standard	NM_000300		Approved		uc010odb.2	P14555	OTTHUMG00000002699	ENST00000375111.3:c.96G>C	1.37:g.20304962C>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_001161729	A8K5I7|Q6DN24|Q6IBD9|Q9UCD2	Silent	SNP	ENST00000375111.3	37	CCDS201.1																																																																																			C|0.904;G|0.096	0.096	strong		0.557	PLA2G2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007675.1	NM_000300	
MAD2L1	4085	hgsc.bcm.edu	37	4	120981323	120981323	+	Missense_Mutation	SNP	T	T	C	rs61752608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:120981323T>C	ENST00000296509.6	-	5	907	c.568A>G	c.(568-570)Atc>Gtc	p.I190V		NM_002358.3	NP_002349.1	Q13257	MD2L1_HUMAN	MAD2 mitotic arrest deficient-like 1 (yeast)	190	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.			I -> V (in Ref. 11; AAH70283). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(2)|kidney(2)|large_intestine(2)|lung(3)	9						ACTTTGTGGATTGTAGTAGTA	0.378													T|||	15	0.00299521	0.0015	0.0058	5008	,	,		17896	0.0		0.006	False		,,,				2504	0.0031				p.I190V		Atlas-SNP	.											.	MAD2L1	17	.	0			c.A568G						PASS	.	T	VAL/ILE	8,4398	14.3+/-33.2	0,8,2195	119.0	116.0	117.0		568	3.9	1.0	4	dbSNP_129	117	49,8551	31.2+/-83.2	1,47,4252	no	missense	MAD2L1	NM_002358.3	29	1,55,6447	CC,CT,TT		0.5698,0.1816,0.4383	benign	190/206	120981323	57,12949	2203	4300	6503	SO:0001583	missense	4085	exon5			TGTGGATTGTAGT	U65410	CCDS3715.1	4q27	2013-01-17	2001-11-28		ENSG00000164109	ENSG00000164109			6763	protein-coding gene	gene with protein product		601467	"""MAD2 (mitotic arrest deficient, yeast, homolog)-like 1"""			8824189, 9345911	Standard	NM_002358		Approved	MAD2, HSMAD2	uc003idl.2	Q13257	OTTHUMG00000132967	ENST00000296509.6:c.568A>G	4.37:g.120981323T>C	ENSP00000296509:p.Ile190Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	NM_002358	Q53F56|Q548X9|Q6IRW7|Q8IZX3	Missense_Mutation	SNP	ENST00000296509.6	37	CCDS3715.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	12.85	2.062016	0.36373	0.001816	0.005698	ENSG00000164109	ENST00000296509	.	.	.	5.13	3.94	0.45596	DNA-binding HORMA (4);	0.000000	0.85682	D	0.000000	T	0.37210	0.0995	L	0.33753	1.03	0.80722	D	1	B	0.31274	0.317	B	0.34824	0.19	T	0.16453	-1.0402	9	0.21540	T	0.41	-14.1793	11.0557	0.47915	0.0:0.0739:0.0:0.9261	rs61752608	190	Q13257	MD2L1_HUMAN	V	190	.	ENSP00000296509:I190V	I	-	1	0	MAD2L1	121200771	1.000000	0.71417	0.974000	0.42286	0.993000	0.82548	5.799000	0.69101	0.888000	0.36160	0.482000	0.46254	ATC	T|0.997;C|0.003	0.003	strong		0.378	MAD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256525.2		
AMACR	23600	hgsc.bcm.edu	37	5	34004707	34004707	+	Missense_Mutation	SNP	C	C	T	rs10941112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:34004707C>T	ENST00000335606.6	-	3	612	c.524G>A	c.(523-525)gGc>gAc	p.G175D	AMACR_ENST00000382072.2_Intron|AMACR_ENST00000382068.3_Intron|AMACR_ENST00000514195.1_Intron|RP11-1084J3.4_ENST00000382079.3_Intron|AMACR_ENST00000502637.1_Missense_Mutation_p.G175D|AMACR_ENST00000426255.2_Missense_Mutation_p.G175D|AMACR_ENST00000441713.2_Intron|AMACR_ENST00000382085.3_Missense_Mutation_p.G175D|AMACR_ENST00000512079.1_Missense_Mutation_p.G175D	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	175			G -> D (in dbSNP:rs10941112). {ECO:0000269|PubMed:11060344, ECO:0000269|Ref.4}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						CTGACCCTTGCCAGTGCGTGT	0.458													C|||	1265	0.252596	0.0242	0.4006	5008	,	,		16552	0.3472		0.504	False		,,,				2504	0.1002				p.G175D		Atlas-SNP	.											.	AMACR	38	.	0			c.G524A						PASS	.	C	ASP/GLY,ASP/GLY,	483,3923	227.2+/-242.5	32,419,1752	151.0	133.0	139.0		524,524,	5.9	1.0	5	dbSNP_120	139	4514,4086	593.3+/-393.1	1170,2174,956	yes	missense,missense,intron	AMACR	NM_001167595.1,NM_014324.5,NM_203382.2	94,94,	1202,2593,2708	TT,TC,CC		47.5116,10.9623,38.4207	probably-damaging,probably-damaging,	175/395,175/383,	34004707	4997,8009	2203	4300	6503	SO:0001583	missense	23600	exon3			CCCTTGCCAGTGC	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.524G>A	5.37:g.34004707C>T	ENSP00000334424:p.Gly175Asp	Somatic	367	0	0		WXS	Illumina HiSeq	Phase_I	366	363	0.991803	NM_014324	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	768	0.3516483516483517	16	0.032520325203252036	160	0.4419889502762431	202	0.3531468531468531	390	0.5145118733509235	C	35	5.477865	0.96291	0.109623	0.524884	ENSG00000242110	ENST00000335606;ENST00000382085;ENST00000502637	T;T;T	0.72505	-0.66;-0.66;-0.66	5.92	5.92	0.95590	CoA-transferase family III domain (2);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.98786	4.33	0.09310	P	1.0	P;P;P	0.50066	0.915;0.931;0.931	P;P;P	0.56434	0.622;0.798;0.798	T	0.25950	-1.0117	9	0.56958	D	0.05	-21.7172	20.3206	0.98668	0.0:1.0:0.0:0.0	rs10941112;rs52822382;rs59795499;rs10941112	175;175;175	F8W9N1;D6RB81;Q9UHK6	.;.;AMACR_HUMAN	D	175	ENSP00000334424:G175D;ENSP00000371517:G175D;ENSP00000424351:G175D	ENSP00000334424:G175D	G	-	2	0	AMACR	34040464	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.414000	0.59802	2.809000	0.96659	0.655000	0.94253	GGC	C|0.655;T|0.345	0.345	strong		0.458	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324	
ZBED4	9889	hgsc.bcm.edu	37	22	50278642	50278642	+	Silent	SNP	C	C	T	rs910800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50278642C>T	ENST00000216268.5	+	2	1809	c.1332C>T	c.(1330-1332)ggC>ggT	p.G444G		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	444						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		TTGAATCTGGCGCCATCTTCC	0.557													C|||	3006	0.60024	0.174	0.8213	5008	,	,		19869	0.8244		0.7922	False		,,,				2504	0.591				p.G444G		Atlas-SNP	.											.	ZBED4	102	.	0			c.C1332T						PASS	.	C		1268,3138	431.8+/-343.0	191,886,1126	64.0	69.0	68.0		1332	-10.6	0.0	22	dbSNP_86	68	6766,1834	729.5+/-406.7	2662,1442,196	no	coding-synonymous	ZBED4	NM_014838.2		2853,2328,1322	TT,TC,CC		21.3256,28.7789,38.2285		444/1172	50278642	8034,4972	2203	4300	6503	SO:0001819	synonymous_variant	9889	exon2			ATCTGGCGCCATC	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.1332C>T	22.37:g.50278642C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	40	39	0.975	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			C|0.380;T|0.620	0.620	strong		0.557	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
ZFP28	140612	hgsc.bcm.edu	37	19	57065189	57065189	+	Silent	SNP	T	T	C	rs145011	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:57065189T>C	ENST00000301318.3	+	8	1106	c.1035T>C	c.(1033-1035)ttT>ttC	p.F345F	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	345					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F345F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		ACTATGTGTTTGGAAGGAAGC	0.388													T|||	1160	0.231629	0.0545	0.304	5008	,	,		18113	0.3294		0.2396	False		,,,				2504	0.3108				p.F345F	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											ZFP28,NS,carcinoma,0,1	ZFP28	99	1	1	Substitution - coding silent(1)	stomach(1)	c.T1035C						PASS	.	T		322,4084	170.5+/-200.9	9,304,1890	84.0	77.0	80.0		1035	3.7	1.0	19	dbSNP_80	80	2173,6427	372.1+/-336.5	298,1577,2425	no	coding-synonymous	ZFP28	NM_020828.1		307,1881,4315	CC,CT,TT		25.2674,7.3082,19.1835		345/869	57065189	2495,10511	2203	4300	6503	SO:0001819	synonymous_variant	140612	exon8			TGTGTTTGGAAGG		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"""Zinc fingers, C2H2-type"", ""-"""	17801	protein-coding gene	gene with protein product			"""zinc finger protein 28 homolog (mouse)"""				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1035T>C	19.37:g.57065189T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Silent	SNP	ENST00000301318.3	37	CCDS12946.1																																																																																			T|0.798;C|0.202	0.202	strong		0.388	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
TMEM176B	28959	hgsc.bcm.edu	37	7	150490238	150490238	+	Missense_Mutation	SNP	G	G	A	rs17256042	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150490238G>A	ENST00000447204.2	-	5	910	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W	TMEM176B_ENST00000434545.1_Missense_Mutation_p.R180W|TMEM176B_ENST00000450753.2_Missense_Mutation_p.R143W|TMEM176B_ENST00000326442.5_Missense_Mutation_p.R180W|TMEM176B_ENST00000492607.1_Missense_Mutation_p.R180W|TMEM176B_ENST00000429904.2_Missense_Mutation_p.R180W	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	180			R -> W (in dbSNP:rs17256042).		cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGACTTCGCCGCATCCATCTG	0.512													G|||	99	0.0197684	0.0076	0.0317	5008	,	,		21434	0.001		0.0577	False		,,,				2504	0.0082				p.R180W		Atlas-SNP	.											TMEM176B,NS,carcinoma,+1,2	TMEM176B	36	2	0			c.C538T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	44,4362	48.2+/-83.0	1,42,2160	150.0	125.0	133.0		538,538,427,538	-2.4	0.0	7	dbSNP_123	133	458,8142	137.1+/-194.1	13,432,3855	yes	missense,missense,missense,missense	TMEM176B	NM_001101311.1,NM_001101312.1,NM_001101314.1,NM_014020.3	101,101,101,101	14,474,6015	AA,AG,GG		5.3256,0.9986,3.8598	probably-damaging,probably-damaging,probably-damaging,probably-damaging	180/271,180/271,143/234,180/271	150490238	502,12504	2203	4300	6503	SO:0001583	missense	28959	exon5			TTCGCCGCATCCA	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.538C>T	7.37:g.150490238G>A	ENSP00000410269:p.Arg180Trp	Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	219	102	0.465753	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	60	0.027472527472527472	5	0.01016260162601626	14	0.03867403314917127	0	0.0	41	0.05408970976253298	G	11.90	1.776134	0.31411	0.009986	0.053256	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	T;T;T;T;T;T	0.02498	4.27;4.27;4.27;4.27;4.27;4.27	3.1	-2.36	0.06663	.	1.402630	0.04900	N	0.451178	T	0.00845	0.0028	L	0.57536	1.79	0.09310	N	1	D;D	0.60575	0.988;0.988	P;P	0.51266	0.664;0.541	T	0.22906	-1.0203	10	0.54805	T	0.06	1.2904	2.7714	0.05335	0.2776:0.0:0.331:0.3914	rs17256042;rs52810663;rs58586485;rs17256042	143;180	E9PAV4;Q3YBM2	.;T176B_HUMAN	W	180;180;180;180;180;143;180	ENSP00000419258:R180W;ENSP00000318409:R180W;ENSP00000410269:R180W;ENSP00000413531:R180W;ENSP00000397810:R180W;ENSP00000404831:R143W	ENSP00000318409:R180W	R	-	1	2	TMEM176B	150121171	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.341000	0.19909	-0.672000	0.05266	0.280000	0.19369	CGG	G|0.964;A|0.036	0.036	strong		0.512	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020	
HLA-A	3105	hgsc.bcm.edu	37	6	29912149	29912149	+	Silent	SNP	G	G	C	rs114818671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:29912149G>C	ENST00000396634.1	+	6	1211	c.870G>C	c.(868-870)ctG>ctC	p.L290L	HLA-A_ENST00000376802.2_Silent_p.L290L|HLA-A_ENST00000376806.5_Silent_p.L290L|HLA-A_ENST00000376809.5_Silent_p.L290L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	290	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ATGAGGGTCTGCCCAAGCCCC	0.602									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.L290L		Atlas-SNP	.											.	HLA-A	89	.	0			c.G870C						PASS	.						68.0	60.0	63.0					6																	29912149		1511	2709	4220	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGGTCTGCCCAAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.870G>C	6.37:g.29912149G>C		Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	477	134	0.280922	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.960;C|0.040	0.040	strong		0.602	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
FAM69B	138311	hgsc.bcm.edu	37	9	139617836	139617836	+	Silent	SNP	C	C	T	rs6874	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139617836C>T	ENST00000371692.4	+	5	1002	c.906C>T	c.(904-906)aaC>aaT	p.N302N	SNHG7_ENST00000362567.2_RNA|SNHG7_ENST00000436596.1_RNA|SNHG7_ENST00000414282.1_RNA|SNHG7_ENST00000447221.1_RNA|FAM69B_ENST00000371691.1_Silent_p.N215N|SNHG7_ENST00000416970.1_RNA	NM_152421.3	NP_689634.2	Q5VUD6	FA69B_HUMAN	family with sequence similarity 69, member B	302						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|large_intestine(2)|lung(1)|prostate(1)	8	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.03e-05)|Epithelial(140;0.00013)		CACTGGCCAACGTGGGCTACA	0.647													C|||	317	0.0632987	0.0424	0.0735	5008	,	,		17740	0.001		0.1193	False		,,,				2504	0.091				p.N302N		Atlas-SNP	.											.	FAM69B	22	.	0			c.C906T						PASS	.	C		247,4159	136.1+/-172.1	5,237,1961	44.0	46.0	45.0		906	1.8	1.0	9	dbSNP_52	45	1057,7543	213.5+/-253.4	69,919,3312	no	coding-synonymous	FAM69B	NM_152421.3		74,1156,5273	TT,TC,CC		12.2907,5.606,10.0261		302/432	139617836	1304,11702	2203	4300	6503	SO:0001819	synonymous_variant	138311	exon5			GGCCAACGTGGGC		CCDS7004.1	9q34.3	2012-08-03			ENSG00000165716	ENSG00000165716			28290	protein-coding gene	gene with protein product		614543				21334309	Standard	NM_152421		Approved	MGC20262, C9orf136	uc004cik.3	Q5VUD6	OTTHUMG00000020940	ENST00000371692.4:c.906C>T	9.37:g.139617836C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_152421	Q5VUD7|Q8N5N0|Q8WYU5	Silent	SNP	ENST00000371692.4	37	CCDS7004.1																																																																																			C|0.915;T|0.085	0.085	strong		0.647	FAM69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055102.1	NM_152421	
KHNYN	23351	hgsc.bcm.edu	37	14	24901992	24901992	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24901992C>T	ENST00000251343.5	+	4	1553	c.1414C>T	c.(1414-1416)Cgt>Tgt	p.R472C	KHNYN_ENST00000553935.1_Missense_Mutation_p.R472C|KHNYN_ENST00000554268.1_5'Flank|KHNYN_ENST00000556842.1_Missense_Mutation_p.R472C|CBLN3_ENST00000555436.1_5'Flank			O15037	KHNYN_HUMAN	KH and NYN domain containing	472							RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						CTTCTGGGACCGTGGTCACCG	0.582											OREG0022627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R472C		Atlas-SNP	.											KHNYN,NS,adenocarcinoma,0,1	KHNYN	46	1	0			c.C1414T						scavenged	.						162.0	135.0	144.0					14																	24901992		2203	4300	6503	SO:0001583	missense	23351	exon4			TGGGACCGTGGTC	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.1414C>T	14.37:g.24901992C>T	ENSP00000251343:p.Arg472Cys	Somatic	134	0	0	774	WXS	Illumina HiSeq	Phase_I	117	2	0.017094	NM_015299	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	37	CCDS32058.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.714689	0.68730	.	.	ENSG00000100441	ENST00000251343;ENST00000556842;ENST00000553935	T;T;T	0.55413	0.52;0.52;0.52	4.83	4.83	0.62350	Ribonuclease Zc3h12a-like (1);	0.063093	0.64402	D	0.000004	T	0.76521	0.3999	M	0.88105	2.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	T	0.81430	-0.0936	10	0.72032	D	0.01	.	15.4597	0.75346	0.0:1.0:0.0:0.0	.	513;472	D3DS77;O15037	.;KHNYN_HUMAN	C	472	ENSP00000251343:R472C;ENSP00000451106:R472C;ENSP00000450799:R472C	ENSP00000251343:R472C	R	+	1	0	KHNYN	23971832	0.987000	0.35691	1.000000	0.80357	0.995000	0.86356	1.876000	0.39588	2.495000	0.84180	0.462000	0.41574	CGT	.	.	none		0.582	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
TARSL2	123283	hgsc.bcm.edu	37	15	102264476	102264476	+	Missense_Mutation	SNP	C	C	A	rs1143136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:102264476C>A	ENST00000335968.3	-	1	331	c.115G>T	c.(115-117)Gcg>Tcg	p.A39S		NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	39					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CTGTAGGGCGCGTTCAGCTGC	0.746													C|||	963	0.192292	0.2897	0.2853	5008	,	,		9080	0.0099		0.2237	False		,,,				2504	0.1503				p.A39S		Atlas-SNP	.											.	TARSL2	63	.	0			c.G115T						PASS	.	C	SER/ALA	763,2699		89,585,1057	6.0	6.0	6.0		115	2.3	0.2	15	dbSNP_86	6	1417,5697		175,1067,2315	yes	missense	TARSL2	NM_152334.2	99	264,1652,3372	AA,AC,CC		19.9185,22.0393,20.6127	benign	39/803	102264476	2180,8396	1731	3557	5288	SO:0001583	missense	123283	exon1			AGGGCGCGTTCAG	AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.115G>T	15.37:g.102264476C>A	ENSP00000338093:p.Ala39Ser	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_152334	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	37	CCDS10394.1	442	0.20238095238095238	155	0.3150406504065041	103	0.2845303867403315	6	0.01048951048951049	178	0.23482849604221637	.	10.09	1.254065	0.22965	0.220393	0.199185	ENSG00000185418	ENST00000335968;ENST00000333018;ENST00000539112	.	.	.	3.28	2.33	0.28932	.	1.372480	0.04874	N	0.446500	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.27732	0.187	B	0.21151	0.033	T	0.18745	-1.0327	8	0.45353	T	0.12	-0.7096	7.7599	0.28946	0.2501:0.7499:0.0:0.0	rs1143136;rs58456433	39	A2RTX5	SYTC2_HUMAN	S	39	.	ENSP00000329291:A39S	A	-	1	0	TARSL2	100081999	0.256000	0.24012	0.208000	0.23602	0.288000	0.27193	0.678000	0.25277	0.708000	0.31955	0.298000	0.19748	GCG	C|0.794;A|0.206	0.206	strong		0.746	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334	
MAPK1IP1L	93487	hgsc.bcm.edu	37	14	55529860	55529860	+	Silent	SNP	A	A	G	rs17851309	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:55529860A>G	ENST00000395468.4	+	3	720	c.543A>G	c.(541-543)caA>caG	p.Q181Q		NM_144578.3	NP_653179.1	Q8NDC0	MISSL_HUMAN	mitogen-activated protein kinase 1 interacting protein 1-like	181	Pro-rich.									endometrium(2)|large_intestine(1)|lung(3)	6						CTCCTCCCCAAGCCCCTGGGG	0.612													A|||	199	0.0397364	0.0484	0.0346	5008	,	,		17398	0.0069		0.0398	False		,,,				2504	0.0654				p.Q181Q		Atlas-SNP	.											.	MAPK1IP1L	14	.	0			c.A543G						PASS	.	A		188,4218		8,172,2023	57.0	55.0	55.0		543	1.4	1.0	14	dbSNP_123	55	345,8255		10,325,3965	no	coding-synonymous	MAPK1IP1L	NM_144578.3		18,497,5988	GG,GA,AA		4.0116,4.2669,4.0981		181/246	55529860	533,12473	2203	4300	6503	SO:0001819	synonymous_variant	93487	exon3			TCCCCAAGCCCCT	AK025580	CCDS32085.1	14q22.1	2008-01-30	2008-01-30	2008-01-16		ENSG00000168175			19840	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 32"", ""mitogen activated protein kinase 1 interacting protein 1-like"""	C14orf32		12011110	Standard	NM_144578		Approved		uc001xbq.1	Q8NDC0		ENST00000395468.4:c.543A>G	14.37:g.55529860A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_144578	B2RDD8|Q96BG5	Silent	SNP	ENST00000395468.4	37	CCDS32085.1																																																																																			A|0.960;G|0.040	0.040	strong		0.612	MAPK1IP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411302.2	NM_144578	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128839526	128839526	+	Missense_Mutation	SNP	C	C	G	rs60847789	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:128839526C>G	ENST00000310343.9	-	22	5539	c.5540G>C	c.(5539-5541)aGc>aCc	p.S1847T	ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.S1498T|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.S1498T	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1847	Interaction with FYN.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						CGGCTGCGTGCTACCATGGCC	0.617													C|||	446	0.0890575	0.1581	0.0648	5008	,	,		17829	0.0506		0.1153	False		,,,				2504	0.0256				p.S1847T		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.G5540C						PASS	.	C	THR/SER,THR/SER	529,3873	240.6+/-251.3	35,459,1707	62.0	57.0	59.0		5540,4493	0.3	0.0	11	dbSNP_129	59	656,7938	166.1+/-218.1	30,596,3671	yes	missense,missense	ARHGAP32	NM_001142685.1,NM_014715.3	58,58	65,1055,5378	GG,GC,CC		7.6332,12.0173,9.1182	benign,benign	1847/2088,1498/1739	128839526	1185,11811	2201	4297	6498	SO:0001583	missense	9743	exon22			TGCGTGCTACCAT	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.5540G>C	11.37:g.128839526C>G	ENSP00000310561:p.Ser1847Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	37	CCDS44769.1	203	0.09294871794871795	66	0.13414634146341464	30	0.08287292817679558	26	0.045454545454545456	81	0.10686015831134564	C	3.494	-0.103292	0.06967	0.120173	0.076332	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.09073	3.02;3.02;3.02	6.07	0.314	0.15847	.	0.072599	0.64402	D	0.000019	T	0.00073	0.0002	L	0.29908	0.895	0.80722	P	0.0	B	0.19817	0.039	B	0.19148	0.024	T	0.29941	-0.9995	9	0.56958	D	0.05	.	9.7585	0.40517	0.0:0.29:0.0:0.71	rs60847789;rs61746235	1847	A7KAX9	RHG32_HUMAN	T	1847;1498;1498	ENSP00000310561:S1847T;ENSP00000376425:S1498T;ENSP00000432862:S1498T	ENSP00000310561:S1847T	S	-	2	0	ARHGAP32	128344736	0.861000	0.29849	0.018000	0.16275	0.009000	0.06853	1.338000	0.33873	-0.147000	0.11254	-0.136000	0.14681	AGC	C|0.902;G|0.098	0.098	strong		0.617	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
FAM92B	339145	hgsc.bcm.edu	37	16	85141661	85141661	+	Silent	SNP	G	G	A	rs17200833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:85141661G>A	ENST00000539556.1	-	3	455	c.300C>T	c.(298-300)taC>taT	p.Y100Y		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	100										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						TCTGTGCCCCGTAGAGCTTCA	0.652													G|||	352	0.0702875	0.0174	0.0836	5008	,	,		15220	0.002		0.1461	False		,,,				2504	0.1247				p.Y100Y		Atlas-SNP	.											.	FAM92B	29	.	0			c.C300T						PASS	.	G		193,4203	123.7+/-161.0	5,183,2010	98.0	95.0	96.0		300	-6.9	0.1	16	dbSNP_123	96	1384,7216	268.2+/-287.7	95,1194,3011	no	coding-synonymous	FAM92B	NM_198491.1		100,1377,5021	AA,AG,GG		16.093,4.3904,12.1345		100/305	85141661	1577,11419	2198	4300	6498	SO:0001819	synonymous_variant	339145	exon3			TGCCCCGTAGAGC		CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.300C>T	16.37:g.85141661G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_198491		Silent	SNP	ENST00000539556.1	37	CCDS32500.1																																																																																			G|0.904;A|0.096	0.096	strong		0.652	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491	
AQP12B	653437	hgsc.bcm.edu	37	2	241621869	241621869	+	Missense_Mutation	SNP	G	G	A	rs74882485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:241621869G>A	ENST00000407834.3	-	1	448	c.386C>T	c.(385-387)aCg>aTg	p.T129M		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	117						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		GCAGAGGCGCGTCAGGGTGCA	0.697																																					p.T129M		Atlas-SNP	.											AQP12B,rectum,carcinoma,0,2	AQP12B	33	2	0			c.C386T						scavenged	.						24.0	24.0	24.0					2																	241621869		2196	4279	6475	SO:0001583	missense	653437	exon1			AGGCGCGTCAGGG	BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.386C>T	2.37:g.241621869G>A	ENSP00000384894:p.Thr129Met	Somatic	96	2	0.0208333		WXS	Illumina HiSeq	Phase_I	27	9	0.333333	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	.	.	.	.	.	.	.	.	.	.	.	7.337	0.620131	0.14193	.	.	ENSG00000185176	ENST00000407834	T	0.15017	2.46	2.84	1.94	0.25998	.	0.293024	0.38492	N	0.001671	T	0.26810	0.0656	.	.	.	0.80722	P	0.0	D	0.71674	0.998	P	0.61592	0.891	T	0.30995	-0.9959	8	0.28530	T	0.3	-0.0254	8.3053	0.32038	0.1286:0.0:0.8714:0.0	.	129	A6NM10-2	.	M	129	ENSP00000384894:T129M	ENSP00000384894:T129M	T	-	2	0	AQP12B	241270542	0.997000	0.39634	0.002000	0.10522	0.132000	0.20833	5.268000	0.65536	0.748000	0.32831	0.473000	0.43528	ACG	G|0.972;A|0.028	0.028	strong		0.697	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
TPTE	7179	hgsc.bcm.edu	37	21	10910340	10910340	+	Silent	SNP	C	C	G	rs62211191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:10910340C>G	ENST00000361285.4	-	22	1745	c.1416G>C	c.(1414-1416)ctG>ctC	p.L472L	TPTE_ENST00000342420.5_Silent_p.L434L|TPTE_ENST00000298232.7_Silent_p.L454L|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	472	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CATCATCATACAGAGGTAGAC	0.348																																					p.L472L		Atlas-SNP	.											.	TPTE	513	.	0			c.G1416C						PASS	.						212.0	205.0	208.0					21																	10910340		2203	4300	6503	SO:0001819	synonymous_variant	7179	exon22			ATCATACAGAGGT	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1416G>C	21.37:g.10910340C>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	368	117	0.317935	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Silent	SNP	ENST00000361285.4	37	CCDS13560.2																																																																																			C|0.846;G|0.154	0.154	strong		0.348	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
ZNF80	7634	hgsc.bcm.edu	37	3	113955187	113955187	+	Nonsense_Mutation	SNP	A	A	C	rs3732781	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:113955187A>C	ENST00000482457.2	-	1	1238	c.735T>G	c.(733-735)taT>taG	p.Y245*	RP11-553L6.2_ENST00000493033.1_RNA|RP11-553L6.2_ENST00000481773.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				CAAGGCACTCATAAGGTTTCT	0.448													A|||	929	0.185503	0.025	0.2435	5008	,	,		19496	0.1567		0.2803	False		,,,				2504	0.2935				p.Y245X	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.T735G						PASS	.	A	stop/TYR	280,4126	155.2+/-188.4	9,262,1932	98.0	98.0	98.0		735	-2.2	0.0	3	dbSNP_107	98	2404,6196	399.7+/-346.5	321,1762,2217	yes	stop-gained	ZNF80	NM_007136.3		330,2024,4149	CC,CA,AA		27.9535,6.355,20.6366		245/274	113955187	2684,10322	2203	4300	6503	SO:0001587	stop_gained	7634	exon1			GCACTCATAAGGT	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"""Zinc fingers, C2H2-type"""	13155	protein-coding gene	gene with protein product		194553	"""zinc finger protein 80 (pT17)"""			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.735T>G	3.37:g.113955187A>C	ENSP00000417192:p.Tyr245*	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_007136	Q6NSW4|Q6NT14	Nonsense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	408	0.18681318681318682	20	0.04065040650406504	74	0.20441988950276244	96	0.16783216783216784	218	0.287598944591029	A	26.6	4.753196	0.89753	0.06355	0.279535	ENSG00000174255	ENST00000482457	.	.	.	3.14	-2.2	0.06994	.	.	.	.	.	.	.	.	.	.	.	0.24628	P	0.99363169	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.594	0.39563	0.6231:0.0:0.3769:0.0	rs3732781;rs17606507;rs52838282;rs60910931;rs3732781	.	.	.	X	245	.	ENSP00000309812:Y245X	Y	-	3	2	ZNF80	115437877	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.759000	0.04761	-0.899000	0.03901	-2.109000	0.00356	TAT	C|0.195;N|0.000	0.195	strong		0.448	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
QSER1	79832	hgsc.bcm.edu	37	11	32996805	32996805	+	Silent	SNP	C	C	T	rs11032076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:32996805C>T	ENST00000399302.2	+	12	5318	c.4983C>T	c.(4981-4983)gtC>gtT	p.V1661V	QSER1_ENST00000527788.1_Silent_p.V1422V	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1661										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					AGTTTGCTGTCGATCCAGAGA	0.308													c|||	295	0.0589058	0.0015	0.0994	5008	,	,		15385	0.005		0.1481	False		,,,				2504	0.0716				p.V1661V		Atlas-SNP	.											QSER1,caecum,carcinoma,0,1	QSER1	153	1	0			c.C4983T						PASS	.	T		98,3494		2,94,1700	97.0	92.0	93.0		4983	-2.5	1.0	11	dbSNP_120	93	1124,7000		72,980,3010	no	coding-synonymous	QSER1	NM_001076786.1		74,1074,4710	TT,TC,CC		13.8355,2.7283,10.4302		1661/1736	32996805	1222,10494	1796	4062	5858	SO:0001819	synonymous_variant	79832	exon12			TGCTGTCGATCCA	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.4983C>T	11.37:g.32996805C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_001076786	Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	37	CCDS41631.1	158	0.07234432234432235	1	0.0020325203252032522	44	0.12154696132596685	3	0.005244755244755245	110	0.14511873350923482	c	7.557	0.663876	0.14710	0.027283	0.138355	ENSG00000060749	ENST00000524678	.	.	.	5.67	-2.55	0.06288	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.21999	-1.0229	3	.	.	.	.	6.1626	0.20372	0.2699:0.3365:0.0:0.3936	rs11032076;rs17756863;rs61521589;rs11032076	.	.	.	L	682	.	.	S	+	2	0	QSER1	32953381	0.998000	0.40836	0.972000	0.41901	0.923000	0.55619	0.465000	0.22004	-0.725000	0.04901	-1.873000	0.00551	TCG	C|0.907;T|0.093	0.093	strong		0.308	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774	
ADAR	103	hgsc.bcm.edu	37	1	154561925	154561925	+	Silent	SNP	C	C	T	rs1127309	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154561925C>T	ENST00000368474.4	-	9	2881	c.2682G>A	c.(2680-2682)gtG>gtA	p.V894V	ADAR_ENST00000292205.5_Silent_p.V937V|ADAR_ENST00000368471.3_Silent_p.V599V	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	894	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		AATCTCCTTTCACACAGCGAT	0.438													C|||	1407	0.28095	0.2927	0.2133	5008	,	,		21281	0.3244		0.3221	False		,,,				2504	0.226				p.V894V		Atlas-SNP	.											.	ADAR	113	.	0			c.G2682A						PASS	.	C	,,,,	1357,3049	451.0+/-349.5	205,947,1051	90.0	81.0	84.0		1797,2682,1797,2604,2547	3.4	1.0	1	dbSNP_86	84	2519,6081	413.4+/-351.1	391,1737,2172	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADAR	NM_001025107.2,NM_001111.4,NM_001193495.1,NM_015840.3,NM_015841.3	,,,,	596,2684,3223	TT,TC,CC		29.2907,30.7989,29.8016	,,,,	599/932,894/1227,599/932,868/1201,849/1182	154561925	3876,9130	2203	4300	6503	SO:0001819	synonymous_variant	103	exon9			TCCTTTCACACAG	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.2682G>A	1.37:g.154561925C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	91	28	0.307692	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Silent	SNP	ENST00000368474.4	37	CCDS1071.1																																																																																			T|0.294;G|0.003;C|0.701;A|0.002	0.294	strong		0.438	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
SAA1	6288	hgsc.bcm.edu	37	11	18291321	18291321	+	Silent	SNP	T	T	C	rs12218	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:18291321T>C	ENST00000405158.2	+	4	472	c.288T>C	c.(286-288)gcT>gcC	p.A96A	SAA1_ENST00000532858.1_Silent_p.A96A|SAA1_ENST00000356524.4_Silent_p.A96A	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	96				ADQAAN -> SEATVK (in Ref. 9; AA sequence). {ECO:0000305}.	acute-phase response (GO:0006953)|innate immune response (GO:0045087)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of inflammatory response (GO:0050728)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of interleukin-1 secretion (GO:0050716)|regulation of protein secretion (GO:0050708)	endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)	p.A96A(1)		endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	ACTCGCTGGCTGATCAGGCTG	0.527													T|||	1490	0.297524	0.0303	0.4712	5008	,	,		18503	0.2748		0.4911	False		,,,				2504	0.3599				p.A96A		Atlas-SNP	.											SAA1,NS,carcinoma,0,1	SAA1	14	1	1	Substitution - coding silent(1)	stomach(1)	c.T288C						PASS	.	T	,,	511,3887	233.0+/-246.3	29,453,1717	114.0	97.0	103.0		288,288,288	-5.6	0.0	11	dbSNP_52	103	4273,4313	575.0+/-390.2	1069,2135,1089	no	coding-synonymous,coding-synonymous,coding-synonymous	SAA1	NM_000331.4,NM_001178006.1,NM_199161.3	,,	1098,2588,2806	CC,CT,TT		49.7671,11.6189,36.8453	,,	96/123,96/123,96/123	18291321	4784,8200	2199	4293	6492	SO:0001819	synonymous_variant	6288	exon4			GCTGGCTGATCAG	M10906	CCDS7835.1	11p15.1	2014-01-30			ENSG00000173432	ENSG00000173432		"""Endogenous ligands"""	10513	protein-coding gene	gene with protein product		104750		SAA		2595451, 9305847	Standard	NM_199161		Approved	PIG4, TP53I4	uc021qeo.1	P0DJI8	OTTHUMG00000166147	ENST00000405158.2:c.288T>C	11.37:g.18291321T>C		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	237	125	0.527426	NM_199161	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Silent	SNP	ENST00000405158.2	37	CCDS7835.1																																																																																			T|0.648;C|0.352	0.352	strong		0.527	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161	
SPNS3	201305	hgsc.bcm.edu	37	17	4356375	4356375	+	Missense_Mutation	SNP	G	G	T	rs11655342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4356375G>T	ENST00000355530.2	+	8	1268	c.988G>T	c.(988-990)Gcg>Tcg	p.A330S	SPNS3_ENST00000333476.2_Missense_Mutation_p.A203S|SPNS3_ENST00000576069.1_3'UTR	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	330			A -> S (in dbSNP:rs11655342). {ECO:0000269|PubMed:15489334}.		lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						GGCAGAAGCTGCGAGGAGGTA	0.602													G|||	1227	0.245008	0.0439	0.4582	5008	,	,		17966	0.1091		0.3459	False		,,,				2504	0.4018				p.A330S		Atlas-SNP	.											.	SPNS3	52	.	0			c.G988T						PASS	.	G	SER/ALA	391,4015	195.3+/-220.0	16,359,1828	113.0	106.0	109.0		988	-1.2	0.2	17	dbSNP_120	109	3079,5521	471.9+/-368.2	543,1993,1764	yes	missense	SPNS3	NM_182538.4	99	559,2352,3592	TT,TG,GG		35.8023,8.8743,26.68	benign	330/513	4356375	3470,9536	2203	4300	6503	SO:0001583	missense	201305	exon8			GAAGCTGCGAGGA		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.988G>T	17.37:g.4356375G>T	ENSP00000347721:p.Ala330Ser	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	37	CCDS11045.1	504	0.23076923076923078	29	0.05894308943089431	154	0.425414364640884	55	0.09615384615384616	266	0.35092348284960423	G	0.061	-1.224667	0.01530	0.088743	0.358023	ENSG00000182557	ENST00000355530;ENST00000333476	T;T	0.56444	0.46;0.46	4.68	-1.19	0.09585	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.404259	0.25238	N	0.032119	T	0.00012	0.0000	N	0.04994	-0.135	0.80722	P	0.0	B;B	0.13145	0.002;0.007	B;B	0.20955	0.009;0.032	T	0.35847	-0.9772	9	0.02654	T	1	-0.3757	8.7901	0.34845	0.0888:0.0:0.2077:0.7035	rs11655342;rs17845726;rs17858676;rs11655342	203;330	Q6ZMD2-2;Q6ZMD2	.;SPNS3_HUMAN	S	330;203	ENSP00000347721:A330S;ENSP00000333207:A203S	ENSP00000333207:A203S	A	+	1	0	SPNS3	4303124	0.004000	0.15560	0.179000	0.23059	0.456000	0.32438	0.283000	0.18846	-0.372000	0.07992	0.442000	0.29010	GCG	G|0.759;T|0.241	0.241	strong		0.602	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
NLRP1	22861	hgsc.bcm.edu	37	17	5462240	5462240	+	Silent	SNP	C	C	T	rs61753142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5462240C>T	ENST00000572272.1	-	4	1775	c.1776G>A	c.(1774-1776)agG>agA	p.R592R	NLRP1_ENST00000269280.4_Silent_p.R592R|NLRP1_ENST00000262467.5_Silent_p.R592R|NLRP1_ENST00000345221.3_Silent_p.R592R|NLRP1_ENST00000354411.3_Silent_p.R592R|NLRP1_ENST00000577119.1_Silent_p.R592R|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	592	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				ACCCATGCTTCCTGAGGTCAT	0.522													C|||	140	0.0279553	0.003	0.049	5008	,	,		20705	0.001		0.0855	False		,,,				2504	0.0153				p.R592R		Atlas-SNP	.											.	NLRP1	358	.	0			c.G1776A						PASS	.	C	,,,,	82,4324	68.1+/-105.8	1,80,2122	58.0	60.0	59.0		1776,1776,1776,1776,1776	-0.2	0.0	17	dbSNP_129	59	821,7779	188.9+/-235.7	37,747,3516	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	,,,,	38,827,5638	TT,TC,CC		9.5465,1.8611,6.9429	,,,,	592/1376,592/1430,592/1474,592/1444,592/1400	5462240	903,12103	2203	4300	6503	SO:0001819	synonymous_variant	22861	exon4			ATGCTTCCTGAGG	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.1776G>A	17.37:g.5462240C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Silent	SNP	ENST00000572272.1	37	CCDS42246.1																																																																																			C|0.937;T|0.063	0.063	strong		0.522	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035301	110035301	+	Silent	SNP	A	A	G	rs1026607	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:110035301A>G	ENST00000278590.3	+	6	1542	c.1491A>G	c.(1489-1491)acA>acG	p.T497T	ZC3H12C_ENST00000453089.2_Silent_p.T466T|ZC3H12C_ENST00000528673.1_Silent_p.T498T	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	497							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GCATAAGGACACAAGTCTACC	0.448													G|||	1222	0.24401	0.3041	0.2248	5008	,	,		23059	0.2004		0.2724	False		,,,				2504	0.1922				p.T497T		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A1491G						PASS	.	G		1098,2738		170,758,990	108.0	105.0	106.0		1491	-1.1	0.9	11	dbSNP_86	106	2086,6162		248,1590,2286	no	coding-synonymous	ZC3H12C	NM_033390.1		418,2348,3276	GG,GA,AA		25.291,28.6236,26.3489		497/884	110035301	3184,8900	1918	4124	6042	SO:0001819	synonymous_variant	85463	exon6			AAGGACACAAGTC		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1491A>G	11.37:g.110035301A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			A|0.729;G|0.271	0.271	strong		0.448	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
MOB3B	79817	hgsc.bcm.edu	37	9	27455135	27455135	+	Silent	SNP	G	G	A	rs34959338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:27455135G>A	ENST00000262244.5	-	2	838	c.414C>T	c.(412-414)tgC>tgT	p.C138C		NM_024761.4	NP_079037.3	Q86TA1	MOB3B_HUMAN	MOB kinase activator 3B	138							metal ion binding (GO:0046872)										ACTTACCCACGCATGTTGGAA	0.438													G|||	364	0.0726837	0.0537	0.0879	5008	,	,		20257	0.0		0.1879	False		,,,				2504	0.044				p.C138C		Atlas-SNP	.											.	.	.	.	0			c.C414T						PASS	.	G		301,4105	162.9+/-194.8	13,275,1915	95.0	88.0	90.0		414	-7.9	0.1	9	dbSNP_126	90	1603,6997	298.7+/-304.1	154,1295,2851	no	coding-synonymous	MOB3B	NM_024761.4		167,1570,4766	AA,AG,GG		18.6395,6.8316,14.6394		138/217	27455135	1904,11102	2203	4300	6503	SO:0001819	synonymous_variant	79817	exon2			ACCCACGCATGTT	AK023266	CCDS6520.1	9p21.1	2012-07-05	2011-09-28	2011-09-28	ENSG00000120162	ENSG00000120162		"""MOB kinase activators"""	23825	protein-coding gene	gene with protein product	"""monopolar spindle 1 binding, MOB1, domain containing"""		"""MOB1, Mps One Binder kinase activator-like 2B (yeast)"", ""chromosome 9 open reading frame 35"""	MOBKL2B, C9orf35		12477932	Standard	NM_024761		Approved	MOB1D, FLJ13204	uc003zqn.3	Q86TA1	OTTHUMG00000019717	ENST00000262244.5:c.414C>T	9.37:g.27455135G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_024761	Q8NEB4|Q9H8V4	Silent	SNP	ENST00000262244.5	37	CCDS6520.1																																																																																			G|0.872;A|0.128	0.128	strong		0.438	MOB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051974.2	NM_024761	
SOX21	11166	hgsc.bcm.edu	37	13	95364046	95364046	+	Silent	SNP	C	C	G	rs1060474	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:95364046C>G	ENST00000376945.2	-	1	343	c.258G>C	c.(256-258)ctG>ctC	p.L86L	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	86					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					CCTTCTTGAGCAGCGTCTTGG	0.692													c|||	1905	0.380391	0.267	0.428	5008	,	,		8078	0.4692		0.4692	False		,,,				2504	0.317				p.L86L		Atlas-SNP	.											.	SOX21	21	.	0			c.G258C						PASS	.	C		1334,3072	442.5+/-346.7	205,924,1074	67.0	60.0	62.0		258	3.0	1.0	13	dbSNP_86	62	3639,4961	522.1+/-380.0	760,2119,1421	no	coding-synonymous	SOX21	NM_007084.2		965,3043,2495	GG,GC,CC		42.314,30.2769,38.2362		86/277	95364046	4973,8033	2203	4300	6503	SO:0001819	synonymous_variant	11166	exon1			CTTGAGCAGCGTC	AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"""SRY (sex determining region Y)-boxes"""	11197	protein-coding gene	gene with protein product	"""SRY-box 21"""	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.258G>C	13.37:g.95364046C>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_007084	P35715|Q15504|Q5TBS1	Silent	SNP	ENST00000376945.2	37	CCDS9473.1																																																																																			C|0.605;G|0.395	0.395	strong		0.692	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084	
NPTX1	4884	hgsc.bcm.edu	37	17	78444679	78444679	+	Silent	SNP	T	T	C	rs28364735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:78444679T>C	ENST00000306773.4	-	5	1390	c.1233A>G	c.(1231-1233)gaA>gaG	p.E411E	NPTX1_ENST00000575212.1_5'Flank	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	411	Pentaxin.				axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			CGATGTGGGATTCAGCCCAGG	0.642													T|||	965	0.192692	0.0295	0.1657	5008	,	,		14102	0.3175		0.2684	False		,,,				2504	0.226				p.E411E		Atlas-SNP	.											.	NPTX1	28	.	0			c.A1233G						PASS	.	T		337,4069	177.3+/-206.3	11,315,1877	95.0	83.0	87.0		1233	3.6	0.8	17	dbSNP_125	87	2488,6112	408.9+/-349.7	342,1804,2154	no	coding-synonymous	NPTX1	NM_002522.3		353,2119,4031	CC,CT,TT		28.9302,7.6487,21.7207		411/433	78444679	2825,10181	2203	4300	6503	SO:0001819	synonymous_variant	4884	exon5			GTGGGATTCAGCC	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.1233A>G	17.37:g.78444679T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_002522	B3KXH3|Q5FWE6	Silent	SNP	ENST00000306773.4	37	CCDS32762.1																																																																																			T|0.780;C|0.220	0.220	strong		0.642	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1		
CCDC154	645811	hgsc.bcm.edu	37	16	1486462	1486462	+	Missense_Mutation	SNP	C	C	T	rs35583599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1486462C>T	ENST00000389176.3	-	13	1664	c.1498G>A	c.(1498-1500)Gcc>Acc	p.A500T	CCDC154_ENST00000409671.1_Missense_Mutation_p.A346T	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	500						endosome (GO:0005768)		p.A500T(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						TTGCCTTCGGCGGAAATCCTG	0.647													C|||	262	0.0523163	0.0265	0.0836	5008	,	,		18142	0.001		0.1123	False		,,,				2504	0.0562				p.A491T		Atlas-SNP	.											CCDC154,NS,lymphoid_neoplasm,0,1	CCDC154	27	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1471A						PASS	.	C	THR/ALA	55,1329		0,55,637	54.0	54.0	54.0		1471	0.3	0.0	16	dbSNP_126	54	385,2797		21,343,1227	yes	missense	CCDC154	NM_001143980.1	58	21,398,1864	TT,TC,CC		12.0993,3.974,9.6364	possibly-damaging	491/668	1486462	440,4126	692	1591	2283	SO:0001583	missense	645811	exon13			CTTCGGCGGAAAT			16p13.3	2012-12-13			ENSG00000197599	ENSG00000197599			34454	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 29"""	C16orf29			Standard	NM_001143980		Approved	LOC645811	uc010uve.2	A6NI56	OTTHUMG00000154097	ENST00000389176.3:c.1498G>A	16.37:g.1486462C>T	ENSP00000373828:p.Ala500Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	38	26	0.684211	NM_001143980	G9JV18	Missense_Mutation	SNP	ENST00000389176.3	37		134	0.06135531135531135	8	0.016260162601626018	34	0.09392265193370165	0	0.0	92	0.12137203166226913	C	7.896	0.733344	0.15574	0.03974	0.120993	ENSG00000197599	ENST00000409671;ENST00000389176	.	.	.	4.61	0.311	0.15831	.	0.705929	0.12364	N	0.475365	T	0.00178	0.0005	N	0.17082	0.46	0.80722	P	0.0	P	0.41420	0.749	B	0.32211	0.142	T	0.19095	-1.0316	8	0.27082	T	0.32	-4.5205	3.4262	0.07412	0.3577:0.4494:0.0:0.1929	rs35583599;rs61734650	500	A6NI56	CC154_HUMAN	T	346;500	.	ENSP00000373828:A500T	A	-	1	0	CCDC154	1426463	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.754000	0.04787	0.252000	0.21531	0.491000	0.48974	GCC	C|0.928;T|0.072	0.072	strong		0.647	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
ITPR3	3710	hgsc.bcm.edu	37	6	33636907	33636907	+	Silent	SNP	C	C	T	rs2077163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33636907C>T	ENST00000374316.5	+	19	3223	c.2163C>T	c.(2161-2163)caC>caT	p.H721H	ITPR3_ENST00000605930.1_Silent_p.H721H			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	721					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GCAACGCCCACGACGAGAATG	0.607													C|||	2458	0.490815	0.3707	0.4827	5008	,	,		17767	0.5238		0.504	False		,,,				2504	0.6115				p.H721H		Atlas-SNP	.											.	ITPR3	409	.	0			c.C2163T						PASS	.	C		1707,2699	513.1+/-368.2	332,1043,828	86.0	81.0	82.0		2163	1.7	1.0	6	dbSNP_96	82	4528,4072	594.4+/-393.3	1177,2174,949	no	coding-synonymous	ITPR3	NM_002224.3		1509,3217,1777	TT,TC,CC		47.3488,38.7426,47.9394		721/2672	33636907	6235,6771	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon18			CGCCCACGACGAG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.2163C>T	6.37:g.33636907C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	88	55	0.625	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.521;T|0.479	0.479	strong		0.607	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
FGFBP3	143282	hgsc.bcm.edu	37	10	93668110	93668110	+	Missense_Mutation	SNP	T	T	A	rs1107947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:93668110T>A	ENST00000311575.5	-	2	780	c.617A>T	c.(616-618)gAg>gTg	p.E206V	RP11-402D21.2_ENST00000610263.1_RNA	NM_152429.4	NP_689642.3	Q8TAT2	FGFP3_HUMAN	fibroblast growth factor binding protein 3	206			E -> V (in dbSNP:rs1107947). {ECO:0000269|PubMed:16303743}.		positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of vascular permeability (GO:0043117)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	fibroblast growth factor binding (GO:0017134)|heparin binding (GO:0008201)			large_intestine(1)|prostate(1)	2		Colorectal(252;0.162)				CCTCTTGCCCTCGTTGGTCTT	0.721													T|||	671	0.133986	0.1135	0.1657	5008	,	,		12827	0.0208		0.2505	False		,,,				2504	0.136				p.E206V		Atlas-SNP	.											.	FGFBP3	6	.	0			c.A617T						PASS	.	T	VAL/GLU	623,3783	268.0+/-268.2	48,527,1628	62.0	67.0	65.0		617	-3.7	0.0	10	dbSNP_86	65	2201,6399	373.7+/-337.1	283,1635,2382	yes	missense	FGFBP3	NM_152429.4	121	331,2162,4010	AA,AT,TT		25.593,14.1398,21.7131	benign	206/259	93668110	2824,10182	2203	4300	6503	SO:0001583	missense	143282	exon2			TTGCCCTCGTTGG	AK075410	CCDS7418.1	10q23.33	2006-12-14	2006-12-14	2006-12-14	ENSG00000174721	ENSG00000174721			23428	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 13"""	C10orf13			Standard	NM_152429		Approved	MGC39320	uc001khq.4	Q8TAT2	OTTHUMG00000018751	ENST00000311575.5:c.617A>T	10.37:g.93668110T>A	ENSP00000339067:p.Glu206Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_152429	B2RD68|Q8NBN0	Missense_Mutation	SNP	ENST00000311575.5	37	CCDS7418.1	332	0.152014652014652	68	0.13821138211382114	63	0.17403314917127072	11	0.019230769230769232	190	0.25065963060686014	T	11.08	1.534716	0.27475	0.141398	0.25593	ENSG00000174721	ENST00000311575	T	0.15372	2.43	3.98	-3.7	0.04437	.	8.943870	0.00604	N	0.000383	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.16722	0.016	T	0.39418	-0.9615	9	0.36615	T	0.2	0.0545	8.5613	0.33511	0.0:0.391:0.4381:0.1709	rs1107947;rs1107947	206	Q8TAT2	FGFP3_HUMAN	V	206	ENSP00000339067:E206V	ENSP00000339067:E206V	E	-	2	0	FGFBP3	93658090	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-2.098000	0.01347	-0.953000	0.03645	-0.414000	0.06135	GAG	T|0.805;A|0.195	0.195	strong		0.721	FGFBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049379.1	NM_152429	
DVL2	1856	hgsc.bcm.edu	37	17	7133162	7133162	+	Silent	SNP	G	G	A	rs222836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7133162G>A	ENST00000005340.5	-	5	903	c.621C>T	c.(619-621)agC>agT	p.S207S	DVL2_ENST00000574642.1_5'UTR|DVL2_ENST00000575458.1_Silent_p.S201S	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	207					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						AGTCCCCCAGGCTGGTACTCT	0.657													G|||	2264	0.452077	0.3018	0.451	5008	,	,		18255	0.4712		0.5109	False		,,,				2504	0.5757				p.S207S		Atlas-SNP	.											.	DVL2	49	.	0			c.C621T						PASS	.	G		1510,2896	479.2+/-358.4	248,1014,941	80.0	86.0	84.0		621	3.1	1.0	17	dbSNP_79	84	4449,4151	587.6+/-392.2	1154,2141,1005	no	coding-synonymous	DVL2	NM_004422.2		1402,3155,1946	AA,AG,GG		48.2674,34.2714,45.8173		207/737	7133162	5959,7047	2203	4300	6503	SO:0001819	synonymous_variant	1856	exon5			CCCCAGGCTGGTA	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.621C>T	17.37:g.7133162G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	28	0.373333	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	37	CCDS11091.1																																																																																			G|0.552;A|0.448	0.448	strong		0.657	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
SPRR3	6707	hgsc.bcm.edu	37	1	152975829	152975829	+	Silent	SNP	A	A	G	rs1970328|rs527966074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152975829A>G	ENST00000295367.4	+	2	375	c.333A>G	c.(331-333)gaA>gaG	p.E111E	SPRR3_ENST00000542696.1_Silent_p.E103E|SPRR3_ENST00000331860.3_Silent_p.E111E	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	111	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGTCCCTGAACCAGGCAGCA	0.562													-|||	2629	0.52496	0.5	0.4337	5008	,	,		19495	0.6319		0.5328	False		,,,				2504	0.5051				p.E111E		Atlas-SNP	.											.	SPRR3	45	.	0			c.A333G						PASS	.	G	,	2313,2093	572.9+/-383.4	595,1123,485	100.0	81.0	87.0		333,333	0.7	0.0	1	dbSNP_92	87	4673,3927	547.6+/-385.2	1279,2115,906	no	coding-synonymous,coding-synonymous	SPRR3	NM_001097589.1,NM_005416.2	,	1874,3238,1391	GG,GA,AA		45.6628,47.5034,46.2863	,	111/170,111/170	152975829	6986,6020	2203	4300	6503	SO:0001819	synonymous_variant	6707	exon2			CCCTGAACCAGGC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.333A>G	1.37:g.152975829A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	221	116	0.524887	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			A|0.462;G|0.538	0.538	strong		0.562	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
CKAP5	9793	hgsc.bcm.edu	37	11	46789135	46789135	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:46789135G>C	ENST00000529230.1	-	27	3447	c.3401C>G	c.(3400-3402)tCt>tGt	p.S1134C	CKAP5_ENST00000415402.1_Missense_Mutation_p.S1134C|CKAP5_ENST00000354558.3_Missense_Mutation_p.S1134C|CKAP5_ENST00000312055.5_Missense_Mutation_p.S1134C			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1134					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						CTTTGCTTTAGAGGATAATCC	0.328																																					p.S1134C	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.C3401G						PASS	.						128.0	131.0	130.0					11																	46789135		2201	4299	6500	SO:0001583	missense	9793	exon27			GCTTTAGAGGATA		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.3401C>G	11.37:g.46789135G>C	ENSP00000432768:p.Ser1134Cys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.568689	0.86439	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.52754	0.66;0.65;0.65;0.65	5.7	5.7	0.88788	Armadillo-type fold (1);	0.272597	0.42964	D	0.000632	T	0.68393	0.2996	M	0.63843	1.955	0.51767	D	0.999933	D;D;D	0.71674	0.996;0.998;0.98	D;D;P	0.79108	0.947;0.992;0.706	T	0.68887	-0.5290	10	0.66056	D	0.02	-10.0808	19.8276	0.96624	0.0:0.0:1.0:0.0	.	1134;1134;1134	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	C	1134	ENSP00000432768:S1134C;ENSP00000395302:S1134C;ENSP00000310227:S1134C;ENSP00000346566:S1134C	ENSP00000310227:S1134C	S	-	2	0	CKAP5	46745711	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.176000	0.77643	2.697000	0.92050	0.585000	0.79938	TCT	.	.	none		0.328	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756	
RXRG	6258	hgsc.bcm.edu	37	1	165377552	165377552	+	Silent	SNP	G	G	A	rs2134095	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:165377552G>A	ENST00000359842.5	-	8	1352	c.1050C>T	c.(1048-1050)gtC>gtT	p.V350V	RXRG_ENST00000470566.1_5'Flank	NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	350	Ligand-binding. {ECO:0000250}.				gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	GCTCAGTTAGGACTCTGTTAA	0.433													A|||	2398	0.478834	0.2284	0.6023	5008	,	,		19617	0.5079		0.671	False		,,,				2504	0.502				p.V350V		Atlas-SNP	.											.	RXRG	91	.	0			c.C1050T						PASS	.	A		1364,3042	690.9+/-405.3	214,936,1053	121.0	107.0	112.0		1050	-4.1	0.5	1	dbSNP_96	112	5847,2753	436.9+/-358.5	1990,1867,443	no	coding-synonymous	RXRG	NM_006917.4		2204,2803,1496	AA,AG,GG		32.0116,30.9578,44.5564		350/464	165377552	7211,5795	2203	4300	6503	SO:0001819	synonymous_variant	6258	exon8			AGTTAGGACTCTG	U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"""Nuclear hormone receptors"""	10479	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 3"""	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.1050C>T	1.37:g.165377552G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	193	87	0.450777	NM_006917	A6NIP1|Q6IBU7	Silent	SNP	ENST00000359842.5	37	CCDS1248.1																																																																																			G|0.486;A|0.514	0.514	strong		0.433	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917	
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1797050	1797050	+	Silent	SNP	C	C	T	rs2294613	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1797050C>T	ENST00000250894.4	+	6	922	c.765C>T	c.(763-765)tcC>tcT	p.S255S	MAPK8IP3_ENST00000568271.1_3'UTR|MAPK8IP3_ENST00000356010.5_Silent_p.S255S	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	255					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						ATGAAATGTCCGAGTCAGGCC	0.672													C|||	428	0.0854633	0.0893	0.0476	5008	,	,		13208	0.0843		0.0905	False		,,,				2504	0.1033				p.S255S		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.C765T						PASS	.	C	,	409,3881		25,359,1761	39.0	56.0	50.0		765,765	-5.3	1.0	16	dbSNP_100	50	798,7712		38,722,3495	no	coding-synonymous,coding-synonymous	MAPK8IP3	NM_001040439.1,NM_015133.3	,	63,1081,5256	TT,TC,CC		9.3772,9.5338,9.4297	,	255/1331,255/1337	1797050	1207,11593	2145	4255	6400	SO:0001819	synonymous_variant	23162	exon6			AATGTCCGAGTCA	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.765C>T	16.37:g.1797050C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	37	CCDS10442.2																																																																																			C|0.916;T|0.084	0.084	strong		0.672	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
PTPRN2	5799	hgsc.bcm.edu	37	7	157903538	157903538	+	Silent	SNP	A	A	G	rs1130501	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:157903538A>G	ENST00000389418.4	-	10	1635	c.1626T>C	c.(1624-1626)agT>agC	p.S542S	PTPRN2_ENST00000404321.2_Silent_p.S565S|PTPRN2_ENST00000409483.1_Silent_p.S504S|PTPRN2_ENST00000389416.4_Silent_p.S525S|PTPRN2_ENST00000389413.3_Intron	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	542					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CAGCGAACGCACTGCTGGGCA	0.672													G|||	1332	0.265974	0.2511	0.2637	5008	,	,		15804	0.1399		0.3777	False		,,,				2504	0.3027				p.S542S		Atlas-SNP	.											.	PTPRN2	243	.	0			c.T1626C						PASS	.		,,	1091,3271		135,821,1225	45.0	31.0	36.0		1626,1575,	2.8	0.0	7	dbSNP_107	36	3211,5367		603,2005,1681	no	coding-synonymous,coding-synonymous,intron	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	738,2826,2906	GG,GA,AA		37.433,25.0115,33.2457	,,	542/1016,525/999,	157903538	4302,8638	2181	4289	6470	SO:0001819	synonymous_variant	5799	exon10			GAACGCACTGCTG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1626T>C	7.37:g.157903538A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	20	0.253165	NM_002847	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			A|0.722;G|0.278	0.278	strong		0.672	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
CCDC50	152137	hgsc.bcm.edu	37	3	191097966	191097966	+	Missense_Mutation	SNP	T	T	C	rs293813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:191097966T>C	ENST00000392455.3	+	6	1065	c.467T>C	c.(466-468)aTg>aCg	p.M156T	CCDC50_ENST00000392456.3_Missense_Mutation_p.M332T	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	156			M -> T (in dbSNP:rs293813).			cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)	p.M332T(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		CCAAGAGTGATGAAAGAAGCT	0.353													C|||	3228	0.644569	0.854	0.5764	5008	,	,		14198	0.6865		0.495	False		,,,				2504	0.5204				p.M332T		Atlas-SNP	.											CCDC50,NS,carcinoma,0,1	CCDC50	39	1	1	Substitution - Missense(1)	stomach(1)	c.T995C						PASS	.	C	THR/MET,THR/MET	3482,924	351.8+/-311.4	1370,742,91	52.0	52.0	52.0		467,995	0.6	0.0	3	dbSNP_79	52	3965,4635	599.3+/-394.1	923,2119,1258	yes	missense,missense	CCDC50	NM_174908.3,NM_178335.2	81,81	2293,2861,1349	CC,CT,TT		46.1047,20.9714,42.7418	benign,benign	156/307,332/483	191097966	7447,5559	2203	4300	6503	SO:0001583	missense	152137	exon7			GAGTGATGAAAGA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.467T>C	3.37:g.191097966T>C	ENSP00000376249:p.Met156Thr	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	37	CCDS33913.1	1367	0.6259157509157509	411	0.8353658536585366	209	0.5773480662983426	371	0.6486013986013986	376	0.49604221635883905	C	2.262	-0.368957	0.05069	0.790286	0.461047	ENSG00000152492	ENST00000392455;ENST00000392456	T;T	0.28895	1.6;1.59	5.57	0.585	0.17428	.	1.051930	0.07306	N	0.874929	T	0.00012	0.0000	N	0.04746	-0.17	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27502	-1.0072	9	0.17369	T	0.5	.	8.5288	0.33321	0.0:0.4501:0.0:0.5499	rs293813;rs697908;rs1196016;rs11542548;rs17811313;rs52827949;rs293813	156;332	Q8IVM0;Q8IVM0-2	CCD50_HUMAN;.	T	156;332	ENSP00000376249:M156T;ENSP00000376250:M332T	ENSP00000376249:M156T	M	+	2	0	CCDC50	192580660	0.018000	0.18449	0.002000	0.10522	0.001000	0.01503	0.488000	0.22371	-0.118000	0.11851	-1.163000	0.01768	ATG	T|0.396;C|0.603	0.603	strong		0.353	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
OBSCN	84033	hgsc.bcm.edu	37	1	228492044	228492044	+	Intron	SNP	G	G	A	rs1150910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:228492044G>A	ENST00000422127.1	+	44	11703				OBSCN_ENST00000570156.2_Silent_p.E4681E|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000366707.4_Silent_p.E1371E|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000359599.6_3'UTR|OBSCN_ENST00000284548.11_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAAACCAGGAGGCCAGAGAAG	0.577													G|||	1849	0.369209	0.4221	0.4121	5008	,	,		20930	0.249		0.4861	False		,,,				2504	0.271				p.E4681E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G14043A						PASS	.	G	,	648,1104		120,408,348	141.0	124.0	129.0		,	2.0	0.9	1	dbSNP_87	129	1953,2029		483,987,521	no	intron,intron	OBSCN	NM_001098623.1,NM_052843.2	,	603,1395,869	AA,AG,GG		49.0457,36.9863,45.361	,	,	228492044	2601,3133	876	1991	2867	SO:0001627	intron_variant	84033	exon53			CCAGGAGGCCAGA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11660-2029G>A	1.37:g.228492044G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.636;A|0.364	0.364	strong		0.577	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SSC4D	136853	hgsc.bcm.edu	37	7	76029695	76029695	+	Missense_Mutation	SNP	C	C	T	rs4728712	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76029695C>T	ENST00000275560.3	-	4	730	c.383G>A	c.(382-384)cGc>cAc	p.R128H	ZP3_ENST00000336517.4_Intron	NM_080744.1	NP_542782.1														autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						TTCCTGCCCGCGGCACTCCAC	0.672													C|||	947	0.189097	0.0454	0.255	5008	,	,		14858	0.2421		0.2048	False		,,,				2504	0.2658				p.R128H		Atlas-SNP	.											SRCRB4D,colon,carcinoma,0,1	SRCRB4D	47	1	0			c.G383A						PASS	.	C	,HIS/ARG	377,4029		19,339,1845	27.0	28.0	28.0		,383	2.5	0.5	7	dbSNP_111	28	1751,6845		188,1375,2735	yes	intron,missense	ZP3,SRCRB4D	NM_007155.5,NM_080744.1	,29	207,1714,4580	TT,TC,CC		20.3699,8.5565,16.3667	,possibly-damaging	,128/576	76029695	2128,10874	2203	4298	6501	SO:0001583	missense	136853	exon4			TGCCCGCGGCACT																												ENST00000275560.3:c.383G>A	7.37:g.76029695C>T	ENSP00000275560:p.Arg128His	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	96	60	0.625	NM_080744		Missense_Mutation	SNP	ENST00000275560.3	37	CCDS5585.1	381	0.17445054945054944	22	0.044715447154471545	83	0.2292817679558011	119	0.20804195804195805	157	0.20712401055408972	C	13.93	2.385104	0.42308	0.085565	0.203699	ENSG00000146700	ENST00000275560	T	0.44482	0.92	5.45	2.55	0.30701	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.381167	0.27155	N	0.020663	T	0.00012	0.0000	L	0.35854	1.095	0.32285	P	0.567124	B	0.10296	0.003	B	0.09377	0.004	T	0.22730	-1.0208	9	0.17832	T	0.49	.	4.0754	0.09901	0.1716:0.5366:0.0:0.2918	rs4728712;rs10353882;rs4728712	128	Q8WTU2	SRB4D_HUMAN	H	128	ENSP00000275560:R128H	ENSP00000275560:R128H	R	-	2	0	SRCRB4D	75867631	0.000000	0.05858	0.452000	0.26994	0.995000	0.86356	-0.167000	0.09940	0.748000	0.32831	0.563000	0.77884	CGC	C|0.829;T|0.171	0.171	strong		0.672	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253001.3		
FARP1	10160	hgsc.bcm.edu	37	13	99100547	99100547	+	Silent	SNP	T	T	C	rs12261	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:99100547T>C	ENST00000319562.6	+	27	3379	c.3114T>C	c.(3112-3114)agT>agC	p.S1038S	FARP1_ENST00000595437.1_Silent_p.S1069S|FARP1_ENST00000376586.2_Silent_p.S1069S	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	1038					dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			ACGTGTTGAGTCACAAAGAGT	0.527											OREG0022475	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2516	0.502396	0.4637	0.438	5008	,	,		21272	0.5625		0.5905	False		,,,				2504	0.4479				p.S1038S		Atlas-SNP	.											.	FARP1	207	.	0			c.T3114C						PASS	.	C		2144,2262	597.3+/-388.8	524,1096,583	209.0	163.0	179.0		3114	1.2	0.9	13	dbSNP_52	179	4991,3609	521.6+/-379.9	1441,2109,750	no	coding-synonymous	FARP1	NM_005766.2		1965,3205,1333	CC,CT,TT		41.9651,48.6609,45.1407		1038/1046	99100547	7135,5871	2203	4300	6503	SO:0001819	synonymous_variant	10160	exon27			GTTGAGTCACAAA	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"""Rho guanine nucleotide exchange factors"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Pleckstrin homology (PH) domain containing"""	3591	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 75"""	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.3114T>C	13.37:g.99100547T>C		Somatic	272	1	0.00367647	1341	WXS	Illumina HiSeq	Phase_I	327	153	0.46789	NM_005766	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	37	CCDS9487.1																																																																																			T|0.458;C|0.542	0.542	strong		0.527	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	
MYO3B	140469	hgsc.bcm.edu	37	2	171260820	171260820	+	Silent	SNP	T	T	C	rs6751520	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:171260820T>C	ENST00000408978.4	+	20	2484	c.2341T>C	c.(2341-2343)Ttg>Ctg	p.L781L	MYO3B_ENST00000334231.6_Silent_p.L790L|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.L781L	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	781	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						CCGCCCGCTCTTGGACATGTT	0.502													T|||	3911	0.78095	0.6846	0.889	5008	,	,		18753	0.7321		0.8966	False		,,,				2504	0.7658				p.L781L		Atlas-SNP	.											.	MYO3B	320	.	0			c.T2341C						PASS	.	T	,,	2771,1043		1010,751,146	121.0	116.0	117.0		2341,2341,2341	-2.8	1.0	2	dbSNP_116	117	7408,826		3332,744,41	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	4342,1495,187	CC,CT,TT		10.0316,27.3466,15.5129	,,	781/1315,781/1276,781/1342	171260820	10179,1869	1907	4117	6024	SO:0001819	synonymous_variant	140469	exon20			CCGCTCTTGGACA		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2341T>C	2.37:g.171260820T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	113	112	0.99115	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																			T|0.196;C|0.804	0.804	strong		0.502	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
DLGAP2	9228	hgsc.bcm.edu	37	8	1616640	1616640	+	Silent	SNP	G	G	A	rs4565482	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:1616640G>A	ENST00000421627.2	+	6	1850	c.1716G>A	c.(1714-1716)ccG>ccA	p.P572P		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	651					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)		p.P616P(1)|p.P594P(1)		breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GGATGTCCCCGTGGCCCCAGG	0.672													G|||	367	0.0732827	0.0106	0.0951	5008	,	,		13887	0.003		0.1958	False		,,,				2504	0.089				p.P572P		Atlas-SNP	.											DLGAP2_ENST00000356067,NS,carcinoma,0,5	DLGAP2	292	5	2	Substitution - coding silent(2)	prostate(2)	c.G1716A						PASS	.	G		159,3979		1,157,1911	12.0	18.0	16.0		1716	-11.1	0.0	8	dbSNP_111	16	1716,6654		188,1340,2657	no	coding-synonymous	DLGAP2	NM_004745.3		189,1497,4568	AA,AG,GG		20.5018,3.8424,14.9904		572/976	1616640	1875,10633	2069	4185	6254	SO:0001819	synonymous_variant	9228	exon6			GTCCCCGTGGCCC	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1716G>A	8.37:g.1616640G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Silent	SNP	ENST00000421627.2	37	CCDS47760.1	193	0.08836996336996338	4	0.008130081300813009	46	0.1270718232044199	1	0.0017482517482517483	142	0.18733509234828497	G	3.107	-0.183454	0.06340	0.038424	0.205018	ENSG00000198010	ENST00000520901	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.99999280338	.	.	.	.	.	.	T	0.05937	-1.0855	3	.	.	.	-10.5133	11.1444	0.48422	0.4809:0.3504:0.1687:0.0	rs4565482	.	.	.	H	589	.	.	R	+	2	0	DLGAP2	1604047	0.000000	0.05858	0.010000	0.14722	0.388000	0.30384	-3.479000	0.00457	-2.726000	0.00386	-1.619000	0.00793	CGT	G|0.894;A|0.106	0.106	strong		0.672	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
OR13C8	138802	hgsc.bcm.edu	37	9	107331504	107331504	+	Missense_Mutation	SNP	C	C	A	rs7026705	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:107331504C>A	ENST00000335040.1	+	1	56	c.56C>A	c.(55-57)gCc>gAc	p.A19D		NM_001004483.1	NP_001004483.1	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C, member 8	19			A -> D (in dbSNP:rs7026705).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|skin(1)	25						GGGCTTTCTGCCCACCCAAAG	0.413													C|||	3233	0.645567	0.6475	0.5937	5008	,	,		19478	0.9464		0.4254	False		,,,				2504	0.5961				p.A19D		Atlas-SNP	.											.	OR13C8	77	.	0			c.C56A						PASS	.	C	ASP/ALA	2734,1672	658.2+/-400.4	856,1022,325	150.0	151.0	151.0		56	-1.6	0.9	9	dbSNP_116	151	3638,4962	524.4+/-380.5	800,2038,1462	yes	missense	OR13C8	NM_001004483.1	126	1656,3060,1787	AA,AC,CC		42.3023,37.9483,48.9928	benign	19/321	107331504	6372,6634	2203	4300	6503	SO:0001583	missense	138802	exon1			TTTCTGCCCACCC		CCDS35090.1	9q31.1	2013-09-24			ENSG00000186943	ENSG00000186943		"""GPCR / Class A : Olfactory receptors"""	15103	protein-coding gene	gene with protein product							Standard	NM_001004483		Approved		uc011lvo.2	Q8NGS7	OTTHUMG00000020409	ENST00000335040.1:c.56C>A	9.37:g.107331504C>A	ENSP00000334068:p.Ala19Asp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_001004483	Q5VVG0|Q96R44	Missense_Mutation	SNP	ENST00000335040.1	37	CCDS35090.1	1400	0.6410256410256411	317	0.6443089430894309	206	0.569060773480663	542	0.9475524475524476	335	0.4419525065963061	C	2.567	-0.300408	0.05532	0.620517	0.423023	ENSG00000186943	ENST00000335040	T	0.00433	7.43	4.97	-1.64	0.08318	.	0.513993	0.17887	N	0.158677	T	0.00012	0.0000	N	0.01202	-0.96	0.58432	P	9.99999999995449E-6	B	0.09022	0.002	B	0.08055	0.003	T	0.39099	-0.9630	9	0.02654	T	1	.	8.9508	0.35788	0.5703:0.3539:0.0:0.0758	rs7026705;rs52790597;rs57774899;rs7026705	19	Q8NGS7	O13C8_HUMAN	D	19	ENSP00000334068:A19D	ENSP00000334068:A19D	A	+	2	0	OR13C8	106371325	0.000000	0.05858	0.866000	0.34008	0.588000	0.36517	-1.544000	0.02192	-0.066000	0.12998	-0.169000	0.13324	GCC	C|0.434;A|0.566	0.566	strong		0.413	OR13C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053480.1		
C1orf186	440712	hgsc.bcm.edu	37	1	206239574	206239574	+	Silent	SNP	T	T	C	rs28391411	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206239574T>C	ENST00000331555.5	-	6	962	c.324A>G	c.(322-324)acA>acG	p.T108T		NM_001007544.1	NP_001007545.1	Q6ZWK4	CA186_HUMAN	chromosome 1 open reading frame 186	108						integral component of membrane (GO:0016021)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.0754)			CCACATCCTCTGTGGCCTTAG	0.458													t|||	1000	0.199681	0.4448	0.111	5008	,	,		20620	0.0744		0.0646	False		,,,				2504	0.1994				p.T108T		Atlas-SNP	.											.	C1orf186	26	.	0			c.A324G						PASS	.	C		1714,2692	510.9+/-367.7	363,988,852	63.0	56.0	58.0		324	2.9	0.0	1	dbSNP_125	58	768,7832	180.6+/-229.5	45,678,3577	no	coding-synonymous	C1orf186	NM_001007544.1		408,1666,4429	CC,CT,TT		8.9302,38.9015,19.0835		108/173	206239574	2482,10524	2203	4300	6503	SO:0001819	synonymous_variant	440712	exon6			ATCCTCTGTGGCC	AK122631	CCDS73014.1	1q32.1	2014-05-06			ENSG00000196533	ENSG00000263961			25341	protein-coding gene	gene with protein product							Standard	XM_005272738		Approved	FLJ16052	uc001hdt.2	Q6ZWK4	OTTHUMG00000184376	ENST00000331555.5:c.324A>G	1.37:g.206239574T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_001007544		Silent	SNP	ENST00000331555.5	37	CCDS30995.1																																																																																			T|0.811;C|0.189	0.189	strong		0.458	C1orf186-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088002.1	NM_001007544	
KLRC3	3823	hgsc.bcm.edu	37	12	10573094	10573094	+	Missense_Mutation	SNP	C	C	G	rs2682491	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10573094C>G	ENST00000396439.2	-	1	100	c.56G>C	c.(55-57)tGg>tCg	p.W19S	NKG2-E_ENST00000539033.1_Intron|KLRC3_ENST00000381904.2_Missense_Mutation_p.W19S|KLRC3_ENST00000381903.2_Missense_Mutation_p.W19S	NM_002261.2	NP_002252.2	Q07444	NKG2E_HUMAN	killer cell lectin-like receptor subfamily C, member 3	19			W -> P (in allele NKG2-E*01 and allele NKG2-E*03; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:10201920, ECO:0000269|PubMed:8276468, ECO:0000269|PubMed:9683661}.|W -> R (in allele NKG2-E*02; dbSNP:rs2682490). {ECO:0000269|PubMed:11751968, ECO:0000269|Ref.5}.		cellular defense response (GO:0006968)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						CCTTTGCTGCCACTTTGGGTC	0.433													c|||	2221	0.44349	0.2012	0.5576	5008	,	,		9481	0.5159		0.5785	False		,,,				2504	0.4765				p.W19S		Atlas-SNP	.											.	KLRC3	25	.	0			c.G56C						PASS	.						82.0	77.0	78.0					12																	10573094		2202	4284	6486	SO:0001583	missense	3823	exon1			TGCTGCCACTTTG	L14542	CCDS31744.1, CCDS41755.1	12p13	2008-08-05			ENSG00000205810	ENSG00000205810		"""Killer cell lectin-like receptors"""	6376	protein-coding gene	gene with protein product		602892				9598306	Standard	NM_002261		Approved	NKG2-E	uc001qyi.1	Q07444	OTTHUMG00000167149	ENST00000396439.2:c.56G>C	12.37:g.10573094C>G	ENSP00000379716:p.Trp19Ser	Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	226	149	0.659292	NM_007333	Q8WXA4|Q96RL0|Q9UP04	Missense_Mutation	SNP	ENST00000396439.2	37	CCDS41755.1	1006	0.4606227106227106	102	0.2073170731707317	191	0.5276243093922652	303	0.5297202797202797	410	0.5408970976253298	c	4.749	0.139191	0.09083	.	.	ENSG00000205810	ENST00000396439;ENST00000381904;ENST00000381903	T;T;T	0.04275	3.66;3.66;3.66	2.55	-0.201	0.13212	.	0.475912	0.19666	N	0.108869	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.34129	-0.9841	9	0.59425	D	0.04	.	4.5619	0.12165	0.0:0.4578:0.0:0.5422	rs2682491	19;19	Q07444-2;Q07444	.;NKG2E_HUMAN	S	19	ENSP00000379716:W19S;ENSP00000371329:W19S;ENSP00000371328:W19S	ENSP00000371328:W19S	W	-	2	0	KLRC3	10464361	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	1.111000	0.31159	-0.060000	0.13132	0.585000	0.79938	TGG	C|0.500;G|0.500	0.500	weak		0.433	KLRC3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393471.1	NM_002261	
ADAM29	11086	hgsc.bcm.edu	37	4	175899076	175899076	+	Silent	SNP	A	A	G	rs61744599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175899076A>G	ENST00000359240.3	+	5	3070	c.2400A>G	c.(2398-2400)acA>acG	p.T800T	ADAM29_ENST00000404450.4_Silent_p.T800T|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Silent_p.T800T|ADAM29_ENST00000445694.1_Silent_p.T800T	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	800	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CTCCTGTGACACCCTCCCAGA	0.562																																					p.T800T	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,NS,carcinoma,0,1	ADAM29	262	1	0			c.A2400G						scavenged	.	A	,,,	1,4405	2.1+/-5.4	0,1,2202	140.0	129.0	133.0		2400,2400,2400,2400	-1.5	0.0	4	dbSNP_129	133	0,8600		0,0,4300	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADAM29	NM_001130703.1,NM_001130704.1,NM_001130705.1,NM_014269.4	,,,	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	,,,	800/821,800/821,800/821,800/821	175899076	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11086	exon4			TGTGACACCCTCC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2400A>G	4.37:g.175899076A>G		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	208	66	0.317308	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	37	CCDS3823.1																																																																																			A|0.994;G|0.006	0.006	strong		0.562	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
TRIM64C	646754	hgsc.bcm.edu	37	11	49080565	49080565	+	Missense_Mutation	SNP	A	A	C	rs7932738	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49080565A>C	ENST00000530230.1	-	1	99	c.100T>G	c.(100-102)Ttt>Gtt	p.F34V		NM_001206631.1	NP_001193560.1	A6NLI5	TR64C_HUMAN	tripartite motif containing 64C	34						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.F34V(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						GGCCTGCAAAAGCTGTGCACA	0.517													A|||	904	0.180511	0.3185	0.1268	5008	,	,		17437	0.1607		0.1352	False		,,,				2504	0.0992				p.F34V		Atlas-SNP	.											TRIM64C,NS,carcinoma,0,1	TRIM64C	18	1	1	Substitution - Missense(1)	stomach(1)	c.T100G						PASS	.																																			SO:0001583	missense	646754	exon1			TGCAAAAGCTGTG		CCDS73287.1	11p11.12	2014-04-02	2011-01-25		ENSG00000214891	ENSG00000214891		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	37148	protein-coding gene	gene with protein product			"""tripartite motif-containing 64C"""				Standard	NM_001206631		Approved		uc021qiy.1	A6NLI5	OTTHUMG00000166752	ENST00000530230.1:c.100T>G	11.37:g.49080565A>C	ENSP00000431987:p.Phe34Val	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	327	169	0.51682	NM_001206631		Missense_Mutation	SNP	ENST00000530230.1	37		382	0.1749084249084249	142	0.2886178861788618	45	0.12430939226519337	90	0.15734265734265734	105	0.13852242744063326	A	14.70	2.612876	0.46631	.	.	ENSG00000214891	ENST00000530230	T	0.32753	1.44	1.55	1.55	0.23275	.	.	.	.	.	T	0.00012	0.0000	M	0.77103	2.36	0.44149	P	0.0030569999999999764	.	.	.	.	.	.	T	0.17048	-1.0382	6	0.66056	D	0.02	.	5.2593	0.15563	1.0:0.0:0.0:0.0	rs7932738;rs52833221;rs57539737;rs7932738	.	.	.	V	34	ENSP00000431987:F34V	ENSP00000431987:F34V	F	-	1	0	TRIM64C	49037141	1.000000	0.71417	0.054000	0.19295	0.026000	0.11368	4.322000	0.59215	0.994000	0.38892	0.155000	0.16302	TTT	A|0.844;C|0.156	0.156	strong		0.517	TRIM64C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391366.1		
ELTD1	64123	hgsc.bcm.edu	37	1	79357360	79357360	+	Missense_Mutation	SNP	G	G	C	rs2275902	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:79357360G>C	ENST00000370742.3	-	14	1922	c.1859C>G	c.(1858-1860)gCc>gGc	p.A620G		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	620			A -> G (in dbSNP:rs2275902). {ECO:0000269|Ref.1}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		AAGAGCGAGGGCTCCTCTTGC	0.463													G|||	1266	0.252796	0.2905	0.2046	5008	,	,		18525	0.2312		0.3091	False		,,,				2504	0.2004				p.A620G		Atlas-SNP	.											.	ELTD1	143	.	0			c.C1859G						PASS	.	G	GLY/ALA	1026,2914		138,750,1082	59.0	60.0	60.0		1859	5.6	1.0	1	dbSNP_100	60	2437,5847		343,1751,2048	yes	missense	ELTD1	NM_022159.3	60	481,2501,3130	CC,CG,GG		29.4182,26.0406,28.3295	probably-damaging	620/691	79357360	3463,8761	1970	4142	6112	SO:0001583	missense	64123	exon14			GCGAGGGCTCCTC	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1859C>G	1.37:g.79357360G>C	ENSP00000359778:p.Ala620Gly	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	573	0.2623626373626374	138	0.2804878048780488	82	0.2265193370165746	120	0.2097902097902098	233	0.3073878627968338	G	27.6	4.843199	0.91197	0.260406	0.294182	ENSG00000162618	ENST00000370742;ENST00000401034	T;T	0.49432	0.78;0.78	5.59	5.59	0.84812	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.69886	0.3161	M	0.86805	2.84	0.09310	P	0.999999999491564	D	0.76494	0.999	D	0.79108	0.992	T	0.73097	-0.4090	8	.	.	.	.	19.5833	0.95478	0.0:0.0:1.0:0.0	rs2275902;rs17403304;rs52818952;rs2275902	620	Q9HBW9	ELTD1_HUMAN	G	620;78	ENSP00000359778:A620G;ENSP00000383813:A78G	.	A	-	2	0	ELTD1	79129948	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.835000	0.99442	2.612000	0.88384	0.655000	0.94253	GCC	G|0.733;C|0.266	0.266	strong		0.463	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
ZBTB21	49854	hgsc.bcm.edu	37	21	43412705	43412705	+	Silent	SNP	A	A	G	rs61751943	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43412705A>G	ENST00000310826.5	-	3	1683	c.1500T>C	c.(1498-1500)aaT>aaC	p.N500N	ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398505.3_Silent_p.N500N|ZBTB21_ENST00000398499.1_Silent_p.N500N|ZBTB21_ENST00000398511.3_Silent_p.N500N	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	500					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										ACCCGTGCTCATTCACCTTTA	0.433													A|||	142	0.0283546	0.0023	0.0346	5008	,	,		19551	0.0		0.1034	False		,,,				2504	0.0112				p.N500N		Atlas-SNP	.											.	.	.	.	0			c.T1500C						PASS	.	A	,,	107,4299	83.9+/-122.4	1,105,2097	107.0	107.0	107.0		1500,1500,1500	-6.6	0.0	21	dbSNP_129	107	916,7684	204.0+/-246.8	52,812,3436	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF295	NM_001098402.1,NM_001098403.1,NM_020727.4	,,	53,917,5533	GG,GA,AA		10.6512,2.4285,7.8656	,,	500/1067,500/866,500/1067	43412705	1023,11983	2203	4300	6503	SO:0001819	synonymous_variant	49854	exon3			GTGCTCATTCACC	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.1500T>C	21.37:g.43412705A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Silent	SNP	ENST00000310826.5	37	CCDS13678.1																																																																																			A|0.931;G|0.069	0.069	strong		0.433	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
ZNF831	128611	hgsc.bcm.edu	37	20	57768607	57768607	+	Missense_Mutation	SNP	G	G	C	rs181984	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57768607G>C	ENST00000371030.2	+	1	2533	c.2533G>C	c.(2533-2535)Ggt>Cgt	p.G845R		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	845			G -> R (in dbSNP:rs181984).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					AGAGACCCCAGGTGGGCCCAC	0.642													.|||	674	0.134585	0.3086	0.062	5008	,	,		15690	0.1002		0.0398	False		,,,				2504	0.0838				p.G845R		Atlas-SNP	.											.	ZNF831	287	.	0			c.G2533C						PASS	.	G	ARG/GLY	1027,3009		110,807,1101	27.0	35.0	32.0		2533	-1.0	0.0	20	dbSNP_79	32	223,8167		2,219,3974	yes	missense	ZNF831	NM_178457.1	125	112,1026,5075	CC,CG,GG		2.6579,25.446,10.0596	probably-damaging	845/1678	57768607	1250,11176	2018	4195	6213	SO:0001583	missense	128611	exon1			ACCCCAGGTGGGC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2533G>C	20.37:g.57768607G>C	ENSP00000360069:p.Gly845Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	265	0.12133699633699634	148	0.3008130081300813	24	0.06629834254143646	65	0.11363636363636363	28	0.036939313984168866	G	14.64	2.596217	0.46318	0.25446	0.026579	ENSG00000124203	ENST00000371030	T	0.05382	3.45	4.77	-1.03	0.10102	.	0.366959	0.23377	N	0.048859	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.24882	0.113	B	0.23419	0.046	T	0.48833	-0.9000	9	0.41790	T	0.15	-11.8529	2.6697	0.05064	0.168:0.257:0.4441:0.1309	rs181984;rs181984	845	Q5JPB2	ZN831_HUMAN	R	845	ENSP00000360069:G845R	ENSP00000360069:G845R	G	+	1	0	ZNF831	57202002	0.038000	0.19896	0.000000	0.03702	0.000000	0.00434	0.668000	0.25127	0.178000	0.19917	-1.147000	0.01851	GGT	G|0.898;C|0.102	0.102	strong		0.642	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
LAMB3	3914	hgsc.bcm.edu	37	1	209796329	209796329	+	Missense_Mutation	SNP	T	T	A	rs12748250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:209796329T>A	ENST00000356082.4	-	17	2688	c.2554A>T	c.(2554-2556)Atg>Ttg	p.M852L	MIR4260_ENST00000583107.1_RNA|LAMB3_ENST00000367030.3_Missense_Mutation_p.M852L|LAMB3_ENST00000391911.1_Missense_Mutation_p.M852L	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	852	Domain I.		M -> L (in dbSNP:rs12748250). {ECO:0000269|Ref.6}.		brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCACTTACCATCTGCCTGGTC	0.632													T|||	513	0.102436	0.0439	0.0865	5008	,	,		15100	0.001		0.159	False		,,,				2504	0.2393				p.M852L		Atlas-SNP	.											.	LAMB3	136	.	0			c.A2554T						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	236,4168		4,228,1970	78.0	91.0	86.0		2554,2554,2554	5.2	1.0	1	dbSNP_121	86	1313,7283		104,1105,3089	yes	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	15,15,15	108,1333,5059	AA,AT,TT		15.2745,5.3588,11.9154	benign,benign,benign	852/1173,852/1173,852/1173	209796329	1549,11451	2202	4298	6500	SO:0001583	missense	3914	exon17			TTACCATCTGCCT	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.2554A>T	1.37:g.209796329T>A	ENSP00000348384:p.Met852Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	174	0.07967032967032966	20	0.04065040650406504	31	0.0856353591160221	1	0.0017482517482517483	122	0.16094986807387862	T	11.55	1.673222	0.29693	0.053588	0.152745	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.19394	2.15;2.15;2.15	5.21	5.21	0.72293	.	0.142994	0.64402	D	0.000011	T	0.00073	0.0002	M	0.61703	1.905	0.32625	P	0.522823	B	0.18610	0.029	B	0.17433	0.018	T	0.10064	-1.0646	9	0.28530	T	0.3	.	11.6693	0.51391	0.0:0.0:0.1479:0.8521	rs12748250;rs17388506	852	Q13751	LAMB3_HUMAN	L	852	ENSP00000375778:M852L;ENSP00000348384:M852L;ENSP00000355997:M852L	ENSP00000348384:M852L	M	-	1	0	LAMB3	207862952	1.000000	0.71417	1.000000	0.80357	0.600000	0.36913	1.767000	0.38501	1.992000	0.58205	0.374000	0.22700	ATG	T|0.890;A|0.110	0.110	strong		0.632	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
CHPF2	54480	hgsc.bcm.edu	37	7	150931268	150931268	+	Silent	SNP	C	C	G	rs2608293	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150931268C>G	ENST00000035307.2	+	1	1684	c.171C>G	c.(169-171)tcC>tcG	p.S57S	CHPF2_ENST00000495645.1_Silent_p.S49S	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	57					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						ATCCAGATTCCAGAGCTCGGC	0.587													G|||	2245	0.448283	0.3207	0.4207	5008	,	,		18057	0.7183		0.4493	False		,,,				2504	0.3609				p.S57S		Atlas-SNP	.											.	CHPF2	52	.	0			c.C171G						PASS	.	G		1500,2906	676.7+/-403.3	259,982,962	71.0	75.0	74.0		171	-3.7	0.0	7	dbSNP_100	74	3525,5075	632.4+/-398.6	709,2107,1484	no	coding-synonymous	CHPF2	NM_019015.1		968,3089,2446	GG,GC,CC		40.9884,34.0445,38.636		57/773	150931268	5025,7981	2203	4300	6503	SO:0001819	synonymous_variant	54480	exon1			AGATTCCAGAGCT	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.171C>G	7.37:g.150931268C>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Silent	SNP	ENST00000035307.2	37	CCDS34779.1																																																																																			C|0.584;G|0.416	0.416	strong		0.587	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
MUC6	4588	hgsc.bcm.edu	37	11	1018574	1018574	+	Silent	SNP	C	C	T	rs567109346		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1018574C>T	ENST00000421673.2	-	31	4277	c.4227G>A	c.(4225-4227)ccG>ccA	p.P1409P		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1409	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCGCCGTAGGCGGGGAGTGTG	0.582													c|||	1	0.000199681	0.0	0.0	5008	,	,		14981	0.0		0.0	False		,,,				2504	0.001				p.P1409P		Atlas-SNP	.											MUC6,NS,carcinoma,-1,1	MUC6	408	1	0			c.G4227A						scavenged	.						97.0	118.0	111.0					11																	1018574		1927	4129	6056	SO:0001819	synonymous_variant	4588	exon31			CGTAGGCGGGGAG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4227G>A	11.37:g.1018574C>T		Somatic	600	27	0.045		WXS	Illumina HiSeq	Phase_I	605	47	0.077686	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	none		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
CEP55	55165	hgsc.bcm.edu	37	10	95279506	95279506	+	Missense_Mutation	SNP	A	A	T	rs2293277	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:95279506A>T	ENST00000371485.3	+	8	1437	c.1133A>T	c.(1132-1134)cAt>cTt	p.H378L	CEP55_ENST00000496302.1_3'UTR	NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	378	Required for localization to the interphase centrosome and to the midbody during cytokinesis.		H -> L (in dbSNP:rs2293277). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.7}.		establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				CATCAATTGCATGTAATTCTT	0.393													A|||	2803	0.559704	0.2587	0.7118	5008	,	,		21114	0.5437		0.7525	False		,,,				2504	0.6769				p.H378L		Atlas-SNP	.											.	CEP55	35	.	0			c.A1133T						PASS	.	A	LEU/HIS,LEU/HIS	1443,2963	468.1+/-355.0	244,955,1004	109.0	96.0	100.0		1133,1133	5.8	1.0	10	dbSNP_100	100	6494,2106	716.3+/-406.1	2458,1578,264	yes	missense,missense	CEP55	NM_001127182.1,NM_018131.4	99,99	2702,2533,1268	TT,TA,AA		24.4884,32.7508,38.9743	possibly-damaging,possibly-damaging	378/465,378/465	95279506	7937,5069	2203	4300	6503	SO:0001583	missense	55165	exon8			AATTGCATGTAAT	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"""cancer/testis antigen 111"""	610000	"""chromosome 10 open reading frame 3"""	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.1133A>T	10.37:g.95279506A>T	ENSP00000360540:p.His378Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	37	CCDS7428.1	1260	0.5769230769230769	116	0.23577235772357724	258	0.712707182320442	319	0.5576923076923077	567	0.7480211081794196	A	19.55	3.848845	0.71603	0.327508	0.755116	ENSG00000138180	ENST00000371485;ENST00000358339	T	0.18502	2.21	5.79	5.79	0.91817	.	0.377447	0.32459	N	0.006065	T	0.00012	0.0000	L	0.50333	1.59	0.26975	P	0.9654839	P	0.35077	0.483	B	0.27887	0.084	T	0.04128	-1.0975	9	0.44086	T	0.13	-10.8855	14.6899	0.69076	1.0:0.0:0.0:0.0	rs2293277;rs17845193;rs17858005;rs2293277	378	Q53EZ4	CEP55_HUMAN	L	378	ENSP00000360540:H378L	ENSP00000351102:H378L	H	+	2	0	CEP55	95269496	1.000000	0.71417	0.992000	0.48379	0.925000	0.55904	6.083000	0.71326	2.208000	0.71279	0.459000	0.35465	CAT	A|0.421;T|0.579	0.579	strong		0.393	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
SLC25A40	55972	hgsc.bcm.edu	37	7	87476292	87476292	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:87476292A>G	ENST00000341119.5	-	8	949	c.603T>C	c.(601-603)ccT>ccC	p.P201P		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	201					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	17	Esophageal squamous(14;0.00202)					TAAGAACAGTAGGAGCCCAGC	0.393																																					p.P201P		Atlas-SNP	.											.	SLC25A40	32	.	0			c.T603C						PASS	.						99.0	106.0	104.0					7																	87476292		2203	4300	6503	SO:0001819	synonymous_variant	55972	exon8			AACAGTAGGAGCC	AF125531	CCDS5610.1	7q21.12	2013-05-22			ENSG00000075303	ENSG00000075303		"""Solute carriers"""	29680	protein-coding gene	gene with protein product		610821				16949250	Standard	NM_018843		Approved	MCFP	uc003uje.3	Q8TBP6	OTTHUMG00000131033	ENST00000341119.5:c.603T>C	7.37:g.87476292A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	74	4	0.0540541	NM_018843	A8K483|D6W5P6|Q53GB1|Q9UHR1	Silent	SNP	ENST00000341119.5	37	CCDS5610.1																																																																																			.	.	none		0.393	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843	
C9orf9	11092	hgsc.bcm.edu	37	9	135763816	135763816	+	Silent	SNP	C	C	T	rs2073869	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135763816C>T	ENST00000372136.3	+	4	934	c.487C>T	c.(487-489)Ctg>Ttg	p.L163L	C9orf9_ENST00000356311.5_Silent_p.L163L|C9orf9_ENST00000350499.6_Silent_p.L163L			Q96E40	CI009_HUMAN	chromosome 9 open reading frame 9	163						cytoplasmic microtubule (GO:0005881)		p.?(1)		cervix(1)|large_intestine(1)|lung(1)|prostate(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|GBM - Glioblastoma multiforme(294;4.84e-07)|Epithelial(140;1.28e-06)		GCGCAAGGTGCTGCAGCACGT	0.637													C|||	1016	0.202875	0.2035	0.1282	5008	,	,		16241	0.2659		0.1988	False		,,,				2504	0.1943				p.L163L		Atlas-SNP	.											.	C9orf9	10	.	1	Unknown(1)	bone(1)	c.C487T						PASS	.	C		892,3514	341.8+/-306.9	94,704,1405	53.0	42.0	46.0		487	-0.6	0.4	9	dbSNP_96	46	1454,7146	276.0+/-292.1	127,1200,2973	no	coding-synonymous	C9orf9	NM_018956.3		221,1904,4378	TT,TC,CC		16.907,20.2451,18.0378		163/169	135763816	2346,10660	2203	4300	6503	SO:0001819	synonymous_variant	11092	exon4			AAGGTGCTGCAGC		CCDS6955.1	9q34.13	2012-03-06			ENSG00000165698	ENSG00000165698			1367	protein-coding gene	gene with protein product							Standard	NM_018956		Approved		uc004cby.1	Q96E40	OTTHUMG00000020847	ENST00000372136.3:c.487C>T	9.37:g.135763816C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	240	110	0.458333	NM_018956	Q9UGQ0	Silent	SNP	ENST00000372136.3	37																																																																																				C|0.808;T|0.192	0.192	strong		0.637	C9orf9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000054806.1	NM_018956	
CRADD	8738	hgsc.bcm.edu	37	12	94243853	94243853	+	Silent	SNP	C	C	T	rs56944668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:94243853C>T	ENST00000542893.2	+	3	724	c.406C>T	c.(406-408)Ctg>Ttg	p.L136L	CRADD_ENST00000548330.1_3'UTR|CRADD_ENST00000548483.1_Intron|CRADD_ENST00000541813.1_Intron|CRADD_ENST00000332896.3_Silent_p.L136L			P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with death domain	136	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|positive regulation of apoptotic signaling pathway (GO:2001235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death domain binding (GO:0070513)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)	p.L136L(1)		endometrium(1)|large_intestine(5)|lung(1)|ovary(1)	8						GCCCATGGTGCTGTCTCTGGG	0.617													C|||	1138	0.227236	0.1059	0.1686	5008	,	,		17245	0.4911		0.1551	False		,,,				2504	0.2352				p.L136L		Atlas-SNP	.											CRADD,colon,carcinoma,0,1	CRADD	21	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C406T						scavenged	.	C		537,3869	245.3+/-254.3	31,475,1697	57.0	53.0	54.0		406	5.9	1.0	12	dbSNP_129	54	1357,7243	265.0+/-285.9	105,1147,3048	yes	coding-synonymous	CRADD	NM_003805.3		136,1622,4745	TT,TC,CC		15.7791,12.1879,14.5625		136/200	94243853	1894,11112	2203	4300	6503	SO:0001819	synonymous_variant	8738	exon3			ATGGTGCTGTCTC	U84388	CCDS9048.1	12q21.33-q23.1	2008-08-04				ENSG00000169372			2340	protein-coding gene	gene with protein product	"""RIP-associated ICH1/CED3-homologous protein with death domain"""	603454				8985253, 9044836	Standard	NM_003805		Approved	RAIDD	uc001tda.3	P78560		ENST00000542893.2:c.406C>T	12.37:g.94243853C>T		Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	126	69	0.547619	NM_003805	B7Z2Q5	Silent	SNP	ENST00000542893.2	37	CCDS9048.1																																																																																			C|0.825;T|0.175	0.175	strong		0.617	CRADD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408515.1	NM_003805	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28358335	28358335	+	Intron	SNP	G	G	C	rs1416918	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28358335G>C	ENST00000361028.1	-	4	1840				ZSCAN12_ENST00000396827.3_Intron			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						TAGGTACCACGTCTATTATGG	0.428													C|||	1935	0.386382	0.5582	0.3271	5008	,	,		21477	0.2996		0.2893	False		,,,				2504	0.3855				p.R578G		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.C1732G						PASS	.	C	GLY/ARG	644,740		147,350,195	291.0	256.0	267.0		1732	-0.5	0.1	6	dbSNP_88	267	1003,2179		161,681,749	yes	missense	ZSCAN12	NM_001163391.1	125	308,1031,944	CC,CG,GG		31.5211,46.5318,36.071		578/612	28358335	1647,2919	692	1591	2283	SO:0001627	intron_variant	9753	exon4			TACCACGTCTATT	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.1694+37C>G	6.37:g.28358335G>C		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	249	97	0.389558	NM_001163391	O43724	Missense_Mutation	SNP	ENST00000361028.1	37																																																																																				G|0.614;C|0.386	0.386	strong		0.428	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
MYL10	93408	hgsc.bcm.edu	37	7	101256833	101256833	+	Silent	SNP	T	T	C	rs2240389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:101256833T>C	ENST00000223167.4	-	8	780	c.603A>G	c.(601-603)gcA>gcG	p.A201A		NM_138403.4	NP_612412.2	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	201	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	12						CTGGGGGAAATGCTGCAAACA	0.562													C|||	1143	0.228235	0.3056	0.2695	5008	,	,		18535	0.1448		0.2565	False		,,,				2504	0.1513				p.A201A	Esophageal Squamous(24;575 709 17516 40384 51639)	Atlas-SNP	.											.	MYL10	32	.	0			c.A603G						PASS	.	C		1283,3123	700.3+/-406.6	176,931,1096	143.0	122.0	129.0		603	-9.6	0.1	7	dbSNP_98	129	2333,6267	704.1+/-405.4	317,1699,2284	no	coding-synonymous	MYL10	NM_138403.4		493,2630,3380	CC,CT,TT		27.1279,29.1194,27.8026		201/227	101256833	3616,9390	2203	4300	6503	SO:0001819	synonymous_variant	93408	exon8			GGGAAATGCTGCA	BC002778	CCDS34713.1	7q22.1	2013-01-10			ENSG00000106436	ENSG00000106436		"""Myosins / Light chain"", ""EF-hand domain containing"""	29825	protein-coding gene	gene with protein product						1628631	Standard	NM_138403		Approved	MGC3479, MYLC2PL, PLRLC	uc003uyr.3	Q9BUA6	OTTHUMG00000157137	ENST00000223167.4:c.603A>G	7.37:g.101256833T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	165	99	0.6	NM_138403		Silent	SNP	ENST00000223167.4	37	CCDS34713.1																																																																																			T|0.742;C|0.258	0.258	strong		0.562	MYL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347575.1	NM_138403	
DBI	1622	hgsc.bcm.edu	37	2	120125053	120125053	+	Intron	SNP	C	C	G	rs3731608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:120125053C>G	ENST00000355857.3	+	1	140				C2orf76_ENST00000409523.1_5'Flank|DBI_ENST00000535617.1_Nonsense_Mutation_p.Y28*|DBI_ENST00000311521.4_Intron|DBI_ENST00000409094.1_Intron|DBI_ENST00000460901.1_Intron|C2orf76_ENST00000498049.1_5'Flank|C2orf76_ENST00000334816.7_5'Flank|C2orf76_ENST00000409466.2_5'Flank|DBI_ENST00000393103.2_5'Flank|DBI_ENST00000542275.1_Nonsense_Mutation_p.Y47*|DBI_ENST00000535757.1_Intron|C2orf76_ENST00000409877.1_5'Flank	NM_001079862.1|NM_001178043.1	NP_001073331.1|NP_001171514.1	P07108	ACBP_HUMAN	diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein)						hair follicle development (GO:0001942)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|transport (GO:0006810)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear endoplasmic reticulum (GO:0097038)	benzodiazepine receptor binding (GO:0030156)|lipid binding (GO:0008289)|long-chain fatty acyl-CoA binding (GO:0036042)|protein dimerization activity (GO:0046983)			kidney(1)|lung(4)|skin(1)	6						AGGGGAAGTACGGGGCCGGCT	0.672													C|||	803	0.160343	0.121	0.1527	5008	,	,		13882	0.2173		0.1998	False		,,,				2504	0.1196				p.Y47X		Atlas-SNP	.											.	DBI	10	.	0			c.C141G						PASS	.																																			SO:0001627	intron_variant	1622	exon1			GAAGTACGGGGCC	L76366	CCDS2126.1, CCDS42740.1, CCDS42741.1, CCDS74568.1	2q12-q21	2010-10-20	2010-04-30		ENSG00000155368	ENSG00000155368			2690	protein-coding gene	gene with protein product	"""endozepine"""	125950	"""diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein)"""			1440058	Standard	NM_001079863		Approved	ACBP, ACBD1	uc021vnj.1	P07108	OTTHUMG00000131403	ENST00000355857.3:c.9+417C>G	2.37:g.120125053C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_001178017	B8ZWD2|B8ZWD6|B8ZWD7|P08869|Q4VWZ6|Q53SQ7|Q6IB48|Q9UCI8	Nonsense_Mutation	SNP	ENST00000355857.3	37	CCDS42740.1	393	0.17994505494505494	63	0.12804878048780488	54	0.14917127071823205	131	0.229020979020979	145	0.19129287598944592	C	13.58	2.279026	0.40294	.	.	ENSG00000155368	ENST00000535617;ENST00000542275	.	.	.	1.14	-2.27	0.06846	.	.	.	.	.	.	.	.	.	.	.	0.54753	P	1.4999999999987246E-5	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	0.1405	0.00083	0.2512:0.2516:0.2511:0.2461	rs3731608	.	.	.	X	28;47	.	ENSP00000442917:Y28X	Y	+	3	2	DBI	119841523	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.376000	0.07465	-1.267000	0.02443	0.313000	0.20887	TAC	C|0.819;G|0.181	0.181	strong		0.672	DBI-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330590.1	NM_020548	
MYH11	4629	hgsc.bcm.edu	37	16	15811023	15811023	+	Silent	SNP	C	C	T	rs587781067|rs1050163	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15811023C>T	ENST00000300036.5	-	38	5587	c.5478G>A	c.(5476-5478)ctG>ctA	p.L1826L	NDE1_ENST00000396354.1_Intron|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396355.1_Intron|MYH11_ENST00000576790.2_Silent_p.L1826L|MYH11_ENST00000452625.2_Silent_p.L1833L|MYH11_ENST00000396324.3_Silent_p.L1833L	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1826					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CCTGCTCCTCCAGCTGTGCAA	0.602			T	CBFB	AML								C|||	1984	0.396166	0.2549	0.5029	5008	,	,		20047	0.3313		0.4811	False		,,,				2504	0.4908				p.L1833L		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G5499A						PASS	.	C	,,,,,	1343,3051	448.3+/-348.6	209,925,1063	134.0	111.0	119.0		5499,5499,,5478,,5478	0.2	1.0	16	dbSNP_86	119	4361,4239	582.1+/-391.3	1128,2105,1067	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	1337,3030,2130	TT,TC,CC		49.2907,30.5644,43.8972	,,,,,	1833/1946,1833/1980,,1826/1973,,1826/1939	15811023	5704,7290	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon39			CTCCTCCAGCTGT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5478G>A	16.37:g.15811023C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			C|0.592;T|0.408	0.408	strong		0.602	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
AP3B1	8546	hgsc.bcm.edu	37	5	77473165	77473165	+	Silent	SNP	A	A	G	rs4532349	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:77473165A>G	ENST00000255194.6	-	9	1213	c.1038T>C	c.(1036-1038)aaT>aaC	p.N346N	AP3B1_ENST00000519295.1_Silent_p.N297N	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	346					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		TGACCTACCTATTGCTACGAA	0.328									Hermansky-Pudlak syndrome				A|||	715	0.142772	0.0968	0.3026	5008	,	,		17278	0.0724		0.1968	False		,,,				2504	0.1084				p.N346N		Atlas-SNP	.											AP3B1,colon,carcinoma,0,1	AP3B1	94	1	0			c.T1038C						PASS	.	A		529,3877	240.9+/-251.5	39,451,1713	96.0	92.0	94.0		1038	3.0	1.0	5	dbSNP_111	94	1905,6695	338.0+/-322.5	232,1441,2627	no	coding-synonymous	AP3B1	NM_003664.3		271,1892,4340	GG,GA,AA		22.1512,12.0064,18.7144		346/1095	77473165	2434,10572	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon9	Familial Cancer Database	HPS, HPS1-8	CTACCTATTGCTA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1038T>C	5.37:g.77473165A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.832;G|0.168	0.168	strong		0.328	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
LILRA4	23547	hgsc.bcm.edu	37	19	54849942	54849942	+	Missense_Mutation	SNP	G	G	A	rs534566751|rs2241384	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54849942G>A	ENST00000291759.4	-	3	136	c.80C>T	c.(79-81)cCc>cTc	p.P27L	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	27	Ig-like C2-type 1.		P -> L (in dbSNP:rs2241384).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		GATGGGTTTGGGTAGGTTTTC	0.597											OREG0003656	type=REGULATORY REGION|Gene=LILRA4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	A|||	990	0.197684	0.1566	0.2133	5008	,	,		18609	0.2679		0.169	False		,,,				2504	0.1994				p.P27L		Atlas-SNP	.											.	LILRA4	91	.	0			c.C80T						PASS	.	A	LEU/PRO	701,3705		51,599,1553	50.0	49.0	50.0		80	-1.0	0.0	19	dbSNP_98	50	1421,7179		127,1167,3006	yes	missense	LILRA4	NM_012276.3	98	178,1766,4559	AA,AG,GG		16.5233,15.9101,16.3155	benign	27/500	54849942	2122,10884	2203	4300	6503	SO:0001583	missense	23547	exon3			GGTTTGGGTAGGT	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.80C>T	19.37:g.54849942G>A	ENSP00000291759:p.Pro27Leu	Somatic	46	0	0	1003	WXS	Illumina HiSeq	Phase_I	40	24	0.6	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	420	0.19230769230769232	79	0.16056910569105692	76	0.20994475138121546	135	0.23601398601398602	130	0.17150395778364116	.	6.236	0.411693	0.11812	0.159101	0.165233	ENSG00000239961	ENST00000291759	T	0.13538	2.58	2.5	-1.05	0.10036	Immunoglobulin-like fold (1);	0.398226	0.21610	N	0.071815	T	0.00012	0.0000	M	0.80183	2.485	0.80722	P	0.0	B	0.20780	0.048	B	0.25759	0.063	T	0.18116	-1.0347	9	0.48119	T	0.1	.	4.7733	0.13166	0.2633:0.1811:0.5555:0.0	rs2241384;rs52794492;rs60249083;rs2241384	27	P59901	LIRA4_HUMAN	L	27	ENSP00000291759:P27L	ENSP00000291759:P27L	P	-	2	0	LILRA4	59541754	0.033000	0.19621	0.014000	0.15608	0.001000	0.01503	0.493000	0.22451	-0.466000	0.06943	-3.327000	0.00044	CCC	G|0.827;A|0.173	0.173	strong		0.597	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
CIITA	4261	hgsc.bcm.edu	37	16	11002904	11002904	+	Silent	SNP	G	G	A	rs2228238	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11002904G>A	ENST00000324288.8	+	12	2809	c.2676G>A	c.(2674-2676)acG>acA	p.T892T	CIITA_ENST00000381835.5_Silent_p.T308T|CIITA_ENST00000537380.1_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	892					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						TGAGCGACACGGTGGCGCTGT	0.602			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								A|||	3321	0.663139	0.472	0.5504	5008	,	,		20083	0.8671		0.7137	False		,,,				2504	0.7393				p.T892T		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.G2676A						PASS	.	A		2235,2159	568.3+/-382.3	553,1129,515	58.0	44.0	49.0		2676	-9.7	0.0	16	dbSNP_98	49	6012,2588	406.3+/-348.8	2117,1778,405	no	coding-synonymous	CIITA	NM_000246.3		2670,2907,920	AA,AG,GG		30.093,49.1352,36.5322		892/1131	11002904	8247,4747	2197	4300	6497	SO:0001819	synonymous_variant	4261	exon12			CGACACGGTGGCG	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2676G>A	16.37:g.11002904G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	143	74	0.517483	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			A|0.642;C|0.004	0.642	strong		0.602	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
B4GALNT4	338707	hgsc.bcm.edu	37	11	380395	380395	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:380395C>T	ENST00000329962.6	+	18	2819	c.2819C>T	c.(2818-2820)gCg>gTg	p.A940V		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	940					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGGCCTTCGCGCCCGTGGTC	0.687																																					p.A940V		Atlas-SNP	.											B4GALNT4,NS,carcinoma,+1,1	B4GALNT4	83	1	0			c.C2819T						scavenged	.						55.0	40.0	45.0					11																	380395		2202	4299	6501	SO:0001583	missense	338707	exon18			CCTTCGCGCCCGT	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2819C>T	11.37:g.380395C>T	ENSP00000328277:p.Ala940Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	52	3	0.0576923	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	c	25.9	4.682412	0.88542	.	.	ENSG00000182272	ENST00000329962	T	0.35236	1.32	3.81	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.67517	2.055	0.58432	D	0.99999	P	0.46512	0.879	P	0.45856	0.495	T	0.36432	-0.9748	10	0.20519	T	0.43	-32.7173	16.2551	0.82510	0.0:1.0:0.0:0.0	.	940	Q76KP1	B4GN4_HUMAN	V	940	ENSP00000328277:A940V	ENSP00000328277:A940V	A	+	2	0	B4GALNT4	370395	1.000000	0.71417	0.977000	0.42913	0.811000	0.45836	7.456000	0.80751	2.118000	0.64928	0.561000	0.74099	GCG	.	.	none		0.687	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
OTOL1	131149	hgsc.bcm.edu	37	3	161221705	161221705	+	Missense_Mutation	SNP	A	A	C	rs3921595	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:161221705A>C	ENST00000327928.4	+	4	1409	c.1409A>C	c.(1408-1410)gAg>gCg	p.E470A		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	470	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.		E -> A (in dbSNP:rs3921595).			collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						TTGTACCCAGAGGAAACTTCT	0.403													A|||	2467	0.492612	0.6475	0.4222	5008	,	,		15058	0.2708		0.4662	False		,,,				2504	0.589				p.E470A		Atlas-SNP	.											.	OTOL1	63	.	0			c.A1409C						PASS	.	A	ALA/GLU	2213,1465		661,891,287	39.0	37.0	38.0		1409	2.9	0.8	3	dbSNP_108	38	3848,4324		952,1944,1190	yes	missense	OTOL1	NM_001080440.1	107	1613,2835,1477	CC,CA,AA		47.0876,39.8314,48.8523	possibly-damaging	470/478	161221705	6061,5789	1839	4086	5925	SO:0001583	missense	131149	exon4			ACCCAGAGGAAAC		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1409A>C	3.37:g.161221705A>C	ENSP00000330808:p.Glu470Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	37	CCDS46948.1	936	0.42857142857142855	296	0.6016260162601627	160	0.4419889502762431	137	0.2395104895104895	343	0.4525065963060686	A	14.38	2.516747	0.44763	0.601686	0.470876	ENSG00000182447	ENST00000327928	D	0.90900	-2.75	5.27	2.86	0.33363	Tumour necrosis factor-like (1);Complement C1q protein (2);	0.110601	0.64402	D	0.000020	T	0.00012	0.0000	L	0.46157	1.445	0.37143	P	0.09820200000000001	D	0.57257	0.979	P	0.49999	0.628	T	0.44236	-0.9341	9	0.66056	D	0.02	.	8.76	0.34669	0.8423:0.0:0.1577:0.0	rs3921595;rs61139900;rs3921595	470	A6NHN0	OTOL1_HUMAN	A	470	ENSP00000330808:E470A	ENSP00000330808:E470A	E	+	2	0	OTOL1	162704399	1.000000	0.71417	0.771000	0.31576	0.810000	0.45777	5.600000	0.67599	0.323000	0.23307	0.456000	0.33151	GAG	A|0.541;C|0.459	0.459	strong		0.403	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549525	32549525	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549525C>G	ENST00000360004.5	-	3	566	c.461G>C	c.(460-462)gGc>gCc	p.G154A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	154	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TTCAATGCTGCCTGGATAGAA	0.542										Multiple Myeloma(14;0.17)																											p.G154A		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G461C						PASS	.						97.0	115.0	109.0					6																	32549525		1511	2709	4220	SO:0001583	missense	3123	exon3			ATGCTGCCTGGAT	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.461G>C	6.37:g.32549525C>G	ENSP00000353099:p.Gly154Ala	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	558	77	0.137993	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	13.63	2.293183	0.40594	.	.	ENSG00000196126	ENST00000360004	T	0.08370	3.1	3.87	3.87	0.44632	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.367213	0.29551	N	0.011839	T	0.03011	0.0089	L	0.33137	0.985	0.27655	N	0.947267	B	0.30605	0.287	B	0.33454	0.164	T	0.27806	-1.0063	10	0.87932	D	0	.	9.8873	0.41268	0.0:0.7906:0.2094:0.0	rs1059352;rs1059620;rs3200389	154	P01911	2B1F_HUMAN	A	154	ENSP00000353099:G154A	ENSP00000353099:G154A	G	-	2	0	HLA-DRB1	32657503	0.002000	0.14202	0.957000	0.39632	0.929000	0.56500	1.302000	0.33459	1.883000	0.54544	0.453000	0.30009	GGC	C|0.932;G|0.068	0.068	strong		0.542	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
RAG1	5896	hgsc.bcm.edu	37	11	36597313	36597313	+	Missense_Mutation	SNP	A	A	G	rs2227973	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:36597313A>G	ENST00000299440.5	+	2	2571	c.2459A>G	c.(2458-2460)aAg>aGg	p.K820R		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	820			K -> R (in dbSNP:rs2227973).		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GAAGTGTATAAGAATCCCAAT	0.458									Familial Hemophagocytic Lymphohistiocytosis				A|||	1292	0.257987	0.0847	0.2795	5008	,	,		20870	0.5665		0.1193	False		,,,				2504	0.3016				p.K820R	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A2459G	GRCh37	CM068079	RAG1	M	rs2227973	PASS	.	A	ARG/LYS	474,3930	220.4+/-237.8	25,424,1753	62.0	63.0	63.0		2459	2.6	0.4	11	dbSNP_98	63	981,7615	211.0+/-251.7	54,873,3371	yes	missense	RAG1	NM_000448.2	26	79,1297,5124	GG,GA,AA		11.4123,10.7629,11.1923	benign	820/1044	36597313	1455,11545	2202	4298	6500	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TGTATAAGAATCC	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.2459A>G	11.37:g.36597313A>G	ENSP00000299440:p.Lys820Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	37	CCDS7902.1	538	0.24633699633699635	33	0.06707317073170732	73	0.20165745856353592	340	0.5944055944055944	92	0.12137203166226913	A	12.48	1.949342	0.34377	0.107629	0.114123	ENSG00000166349	ENST00000534663;ENST00000299440	D;D	0.86562	-2.14;-2.14	6.13	2.58	0.30949	.	0.434403	0.26231	N	0.025575	T	0.00012	0.0000	L	0.58428	1.81	0.09310	P	0.9999999999147186	B	0.06786	0.001	B	0.11329	0.006	T	0.41805	-0.9488	9	0.87932	D	0	.	9.8233	0.40896	0.8084:0.0:0.1916:0.0	rs2227973;rs3829279;rs58239341;rs2227973	820	P15918	RAG1_HUMAN	R	820	ENSP00000434610:K820R;ENSP00000299440:K820R	ENSP00000299440:K820R	K	+	2	0	RAG1	36553889	1.000000	0.71417	0.393000	0.26258	0.992000	0.81027	2.867000	0.48428	0.204000	0.20548	0.524000	0.50904	AAG	A|0.820;G|0.180	0.180	strong		0.458	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
SLC5A10	125206	hgsc.bcm.edu	37	17	18855611	18855611	+	Silent	SNP	T	T	C	rs2076562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18855611T>C	ENST00000395645.3	+	1	111	c.93T>C	c.(91-93)aaT>aaC	p.N31N	SLC5A10_ENST00000395647.2_Silent_p.N31N|SLC5A10_ENST00000395643.2_Silent_p.N31N|AC090286.4_ENST00000354432.3_RNA|SLC5A10_ENST00000417251.2_Silent_p.N31N|SLC5A10_ENST00000395642.1_5'UTR|SLC5A10_ENST00000317977.6_Intron	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	31					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						TTGCTCTGAATGTGGCCGTGG	0.612													T|||	1865	0.372404	0.1687	0.513	5008	,	,		19904	0.2331		0.6173	False		,,,				2504	0.4397				p.N31N		Atlas-SNP	.											SLC5A10,NS,carcinoma,0,1	SLC5A10	55	1	0			c.T93C						scavenged	.	T	,	1042,3288		151,740,1274	121.0	127.0	125.0		93,93	-6.7	0.9	17	dbSNP_96	125	5247,3273		1605,2037,618	no	coding-synonymous,coding-synonymous	SLC5A10	NM_001042450.1,NM_152351.3	,	1756,2777,1892	CC,CT,TT		38.4155,24.0647,48.9416	,	31/597,31/613	18855611	6289,6561	2165	4260	6425	SO:0001819	synonymous_variant	125206	exon1			TCTGAATGTGGCC		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.93T>C	17.37:g.18855611T>C		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	203	75	0.369458	NM_001042450	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Silent	SNP	ENST00000395645.3	37	CCDS42275.1																																																																																			T|0.605;C|0.395	0.395	strong		0.612	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
MAMLD1	10046	hgsc.bcm.edu	37	X	149642019	149642019	+	Missense_Mutation	SNP	A	A	G	rs2073043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:149642019A>G	ENST00000370401.2	+	5	2295	c.1985A>G	c.(1984-1986)aAc>aGc	p.N662S	MAMLD1_ENST00000432680.2_Intron|MAMLD1_ENST00000426613.2_Missense_Mutation_p.N637S|MAMLD1_ENST00000262858.5_Missense_Mutation_p.N662S|MAMLD1_ENST00000455522.2_Intron			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	662			N -> S (in dbSNP:rs2073043). {ECO:0000269|PubMed:17086185}.		male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					CAACACGGGAACTCTTTCACT	0.463													A|||	246	0.0651656	0.0053	0.0807	3775	,	,		14820	0.0417		0.1113	False		,,,				2504	0.0297				p.N662S		Atlas-SNP	.											.	MAMLD1	263	.	0			c.A1985G						PASS	.	A	,SER/ASN,SER/ASN	115,3720		3,96,13,1533,558	168.0	136.0	147.0		,1910,1985	2.5	0.0	X	dbSNP_96	147	976,5752		43,616,274,1769,1598	yes	intron,missense,missense	MAMLD1	NM_001177465.1,NM_001177466.1,NM_005491.3	,46,46	46,712,287,3302,2156	GG,GA,G,AA,A		14.5065,2.9987,10.3285	,,	,637/750,662/775	149642019	1091,9472	2203	4300	6503	SO:0001583	missense	10046	exon4			ACGGGAACTCTTT	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1985A>G	X.37:g.149642019A>G	ENSP00000359428:p.Asn662Ser	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_005491	B2RCQ4|B4DG93|B9EGA5	Missense_Mutation	SNP	ENST00000370401.2	37	CCDS14693.2	154	0.09282700421940929	5	0.01020408163265306	27	0.08083832335329341	14	0.025362318840579712	54	0.07736389684813753	A	4.083	0.013370	0.07912	0.029987	0.145065	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000262858;ENST00000426613	T;T;T	0.61980	0.06;0.06;0.06	3.66	2.46	0.29980	.	0.458064	0.19938	N	0.102708	T	0.00328	0.0010	L	0.51422	1.61	0.80722	P	0.0	B;B	0.31817	0.218;0.341	B;B	0.25140	0.04;0.058	T	0.04178	-1.0971	9	0.25106	T	0.35	.	5.1898	0.15203	0.8643:0.0:0.1357:0.0	rs2073043;rs17318818;rs56676839;rs2073043	637;662	Q13495-4;Q13495	.;MAMD1_HUMAN	S	534;662;662;637	ENSP00000359428:N662S;ENSP00000262858:N662S;ENSP00000397438:N637S	ENSP00000262858:N662S	N	+	2	0	MAMLD1	149392677	0.151000	0.22747	0.002000	0.10522	0.119000	0.20118	0.452000	0.21795	0.580000	0.29522	0.451000	0.29950	AAC	A|0.889;0|0.027	.	strong		0.463	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491	
ADGB	79747	hgsc.bcm.edu	37	6	147136212	147136212	+	Missense_Mutation	SNP	A	A	T	rs1052444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:147136212A>T	ENST00000397944.3	+	36	4939	c.4863A>T	c.(4861-4863)gaA>gaT	p.E1621D	ADGB_ENST00000367493.3_3'UTR|ADGB_ENST00000367488.1_3'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	1621					oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						ACATCCGGGAAGAGTACAGAA	0.468													a|||	2025	0.404353	0.2375	0.4467	5008	,	,		14577	0.6895		0.3161	False		,,,				2504	0.3967				p.E1621D		Atlas-SNP	.											.	ADGB	93	.	0			c.A4863T						PASS	.	A	ASP/GLU	297,1085		27,243,421	16.0	17.0	16.0		4863	-1.3	0.7	6	dbSNP_86	16	1023,2159		183,657,751	no	missense	C6orf103	NM_024694.3	45	210,900,1172	TT,TA,AA		32.1496,21.4906,28.922	benign	1621/1668	147136212	1320,3244	691	1591	2282	SO:0001583	missense	79747	exon36			CCGGGAAGAGTAC	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.4863A>T	6.37:g.147136212A>T	ENSP00000381036:p.Glu1621Asp	Somatic	367	1	0.0027248		WXS	Illumina HiSeq	Phase_I	399	180	0.451128	NM_024694	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	37		928	0.4249084249084249	117	0.23780487804878048	155	0.4281767955801105	405	0.708041958041958	251	0.3311345646437995	a	14.56	2.571650	0.45798	0.214906	0.321496	ENSG00000118492	ENST00000397944;ENST00000367490	T;T	0.66460	0.42;-0.21	4.34	-1.29	0.09288	.	.	.	.	.	T	0.48960	0.1529	N	0.19112	0.55	0.47659	P	5.110000000000392E-4	D;B	0.76494	0.999;0.04	D;B	0.78314	0.991;0.012	T	0.38585	-0.9654	8	0.56958	D	0.05	-14.3004	4.7722	0.13162	0.4413:0.1738:0.3849:0.0	rs1052444;rs3192859;rs17414483;rs58569690	1621;566	Q8N7X0;Q8N7X0-2	CAN7L_HUMAN;.	D	1621;579	ENSP00000381036:E1621D;ENSP00000356460:E579D	ENSP00000356460:E579D	E	+	3	2	C6orf103	147177905	0.276000	0.24211	0.653000	0.29593	0.203000	0.24098	-0.565000	0.05929	-0.143000	0.11334	0.327000	0.21459	GAA	A|0.575;T|0.425	0.425	strong		0.468	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
PLG	5340	hgsc.bcm.edu	37	6	161139480	161139480	+	Silent	SNP	C	C	T	rs1130656	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:161139480C>T	ENST00000308192.9	+	8	1005	c.942C>T	c.(940-942)ttC>ttT	p.F314F		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	314	Kringle 3. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.F314F(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CAGAAAACTTCCCCTGCAAGT	0.493													T|||	1752	0.34984	0.2368	0.2824	5008	,	,		17527	0.4554		0.3897	False		,,,				2504	0.4008				p.F314F		Atlas-SNP	.											PLG,NS,carcinoma,0,1	PLG	150	1	1	Substitution - coding silent(1)	prostate(1)	c.C942T						PASS	.	T		1176,3230	711.8+/-408.0	161,854,1188	115.0	121.0	119.0		942	-7.0	0.9	6	dbSNP_86	119	3466,5134	634.2+/-398.8	711,2044,1545	no	coding-synonymous	PLG	NM_000301.3		872,2898,2733	TT,TC,CC		40.3023,26.6909,35.6912		314/811	161139480	4642,8364	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon8			AAACTTCCCCTGC	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.942C>T	6.37:g.161139480C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			C|0.636;T|0.364	0.364	strong		0.493	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
AGTR1	185	hgsc.bcm.edu	37	3	148459395	148459395	+	Silent	SNP	C	C	T	rs5182	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:148459395C>T	ENST00000497524.1	+	2	964	c.573C>T	c.(571-573)ctC>ctT	p.L191L	AGTR1_ENST00000461609.1_Silent_p.L191L|AGTR1_ENST00000475347.1_Silent_p.L191L|AGTR1_ENST00000404754.2_Silent_p.L191L|AGTR1_ENST00000418473.2_Silent_p.L191L|AGTR1_ENST00000349243.3_Silent_p.L191L|AGTR1_ENST00000402260.1_Silent_p.L191L|AGTR1_ENST00000474935.1_Silent_p.L191L|AGTR1_ENST00000542281.1_Silent_p.L191L	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	191					angiotensin-activated signaling pathway (GO:0038166)|calcium-mediated signaling (GO:0019722)|cell chemotaxis (GO:0060326)|G-protein coupled receptor signaling pathway (GO:0007186)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|phospholipase C-activating angiotensin-activated signaling pathway (GO:0086097)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of phospholipase A2 activity (GO:0032430)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|renin-angiotensin regulation of aldosterone production (GO:0002018)|Rho protein signal transduction (GO:0007266)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin type I receptor activity (GO:0001596)|angiotensin type II receptor activity (GO:0004945)|bradykinin receptor binding (GO:0031711)|protein heterodimerization activity (GO:0046982)			breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Azilsartan medoxomil(DB08822)|Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)	ATTCAACCCTCCCGATAGGGC	0.398													C|||	2294	0.458067	0.1566	0.585	5008	,	,		18816	0.6865		0.492	False		,,,				2504	0.5051				p.L226L		Atlas-SNP	.											.	AGTR1	63	.	0			c.C678T						PASS	.	C	,,,,	951,3455	339.7+/-305.9	97,757,1349	64.0	70.0	68.0		573,573,573,573,573	1.7	1.0	3	dbSNP_52	68	4011,4589	543.9+/-384.5	917,2177,1206	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AGTR1	NM_000685.4,NM_004835.3,NM_009585.3,NM_031850.2,NM_032049.2	,,,,	1014,2934,2555	TT,TC,CC		46.6395,21.5842,38.1516	,,,,	191/360,191/360,191/360,191/360,191/360	148459395	4962,8044	2203	4300	6503	SO:0001819	synonymous_variant	185	exon4			AACCCTCCCGATA	M87290	CCDS3137.1	3q24	2012-08-08	2002-02-20		ENSG00000144891	ENSG00000144891		"""GPCR / Class A : Angiotensin receptors"""	336	protein-coding gene	gene with protein product		106165	"""angiotensin receptor 1B"""	AGTR1B		1550596	Standard	NM_009585		Approved	AT1, AT2R1, AGTR1A, AT2R1A, HAT1R, AG2S, AT2R1B, AT1B	uc003ewh.4	P30556	OTTHUMG00000159503	ENST00000497524.1:c.573C>T	3.37:g.148459395C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	198	92	0.464646	NM_031850	Q13725|Q8TBK4	Silent	SNP	ENST00000497524.1	37	CCDS3137.1																																																																																			C|0.584;T|0.416	0.416	strong		0.398	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1		
UGT1A6	54578	hgsc.bcm.edu	37	2	234601965	234601965	+	Silent	SNP	A	A	G	rs1105880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234601965A>G	ENST00000305139.6	+	1	454	c.315A>G	c.(313-315)ctA>ctG	p.L105L	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000406651.1_5'Flank|AC114812.8_ENST00000439336.1_RNA|UGT1A6_ENST00000373424.1_Intron|UGT1A10_ENST00000373445.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	105					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	GATCATTCCTAACTGCTCCTC	0.448													G|||	1716	0.342652	0.3684	0.304	5008	,	,		21918	0.2242		0.333	False		,,,				2504	0.4673				p.L105L		Atlas-SNP	.											.	UGT1A6	63	.	0			c.A315G						PASS	.	G	,,,,,	1611,2795	663.2+/-401.2	308,995,900	91.0	82.0	85.0		315,,,,,	2.5	0.0	2	dbSNP_86	85	3078,5522	660.8+/-401.8	563,1952,1785	no	coding-synonymous,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2,NM_205862.1	,,,,,	871,2947,2685	GG,GA,AA		35.7907,36.5638,36.0526	,,,,,	105/533,,,,,	234601965	4689,8317	2203	4300	6503	SO:0001819	synonymous_variant	54578	exon1			ATTCCTAACTGCT	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.315A>G	2.37:g.234601965A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_001072	A6NKK6|B8K289|Q96TE7	Silent	SNP	ENST00000305139.6	37	CCDS2507.1																																																																																			A|0.659;G|0.341	0.341	strong		0.448	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
R3HCC1L	27291	hgsc.bcm.edu	37	10	99969568	99969568	+	Missense_Mutation	SNP	A	A	G	rs11189513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:99969568A>G	ENST00000298999.3	+	5	2000	c.1697A>G	c.(1696-1698)cAc>cGc	p.H566R	R3HCC1L_ENST00000370586.2_Intron|R3HCC1L_ENST00000314594.5_5'UTR|R3HCC1L_ENST00000370584.3_Missense_Mutation_p.H566R	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	566			H -> R (in dbSNP:rs11189513). {ECO:0000269|PubMed:14702039}.				nucleotide binding (GO:0000166)										GAAACTTCTCACACAGAGGGA	0.418													A|||	1445	0.288538	0.087	0.3761	5008	,	,		18965	0.3542		0.3062	False		,,,				2504	0.4131				p.H566R		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A1697G						PASS	.	A	ARG/HIS	559,3847	252.4+/-258.8	39,481,1683	147.0	146.0	146.0		1697	-2.0	0.0	10	dbSNP_120	146	2591,6009	420.1+/-353.3	393,1805,2102	yes	missense	C10orf28	NM_014472.4	29	432,2286,3785	GG,GA,AA		30.1279,12.6872,24.2196	benign	566/779	99969568	3150,9856	2203	4300	6503	SO:0001583	missense	27291	exon4			CTTCTCACACAGA	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1697A>G	10.37:g.99969568A>G	ENSP00000298999:p.His566Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_001256620	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	607	0.27793040293040294	55	0.11178861788617886	123	0.3397790055248619	188	0.32867132867132864	241	0.3179419525065963	A	0.452	-0.893451	0.02491	0.126872	0.301279	ENSG00000166024	ENST00000370584;ENST00000298999	T;T	0.06294	3.32;3.32	5.15	-1.98	0.07480	.	1.154960	0.06282	N	0.697645	T	0.00012	0.0000	L	0.41824	1.3	0.58432	P	1.0000000000287557E-6	B;B	0.14438	0.01;0.004	B;B	0.14023	0.01;0.01	T	0.48725	-0.9010	8	.	.	.	3.9448	6.6258	0.22828	0.2716:0.5357:0.1927:0.0	rs11189513;rs17451509;rs52798740;rs60579534;rs11189513	566;566	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	R	566	ENSP00000359616:H566R;ENSP00000298999:H566R	.	H	+	2	0	C10orf28	99959558	0.000000	0.05858	0.003000	0.11579	0.063000	0.16089	-0.007000	0.12810	-0.269000	0.09298	0.402000	0.26972	CAC	A|0.750;G|0.250	0.250	strong		0.418	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
SLC4A3	6508	hgsc.bcm.edu	37	2	220502367	220502367	+	Missense_Mutation	SNP	A	A	C	rs635311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220502367A>C	ENST00000358055.3	+	17	3112	c.2600A>C	c.(2599-2601)gAt>gCt	p.D867A	SLC4A3_ENST00000373762.3_Missense_Mutation_p.D894A|SLC4A3_ENST00000317151.3_Missense_Mutation_p.D867A|SLC4A3_ENST00000273063.6_Missense_Mutation_p.D894A|SLC4A3_ENST00000373760.2_Missense_Mutation_p.D867A			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	867	Membrane (anion exchange).		D -> A (in dbSNP:rs635311). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7923606, ECO:0000269|Ref.6}.		bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGGTCCCTGGATGCTGGTCTG	0.637													A|||	3393	0.677516	0.466	0.7925	5008	,	,		16266	0.8065		0.7624	False		,,,				2504	0.6616				p.D894A		Atlas-SNP	.											.	SLC4A3	144	.	0			c.A2681C						PASS	.	A	ALA/ASP,ALA/ASP	2222,2184	586.9+/-386.6	565,1092,546	40.0	39.0	39.0		2600,2681	-2.3	0.0	2	dbSNP_83	39	6574,2026	716.8+/-406.1	2523,1528,249	no	missense,missense	SLC4A3	NM_005070.3,NM_201574.2	126,126	3088,2620,795	CC,CA,AA		23.5581,49.5688,32.3697	benign,benign	867/1233,894/1260	220502367	8796,4210	2203	4300	6503	SO:0001583	missense	6508	exon17			CCCTGGATGCTGG		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"""Solute carriers"""	11029	protein-coding gene	gene with protein product	"""Anion exchanger 3, neuronal"""	106195	"""solute carrier family 4, anion exchanger, member 3"""			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2600A>C	2.37:g.220502367A>C	ENSP00000350756:p.Asp867Ala	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	196	87	0.443878	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	37	CCDS2445.1	1575	0.7211538461538461	223	0.4532520325203252	274	0.7569060773480663	483	0.8444055944055944	595	0.7849604221635884	A	9.570	1.120745	0.20877	0.504312	0.764419	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12	4.54	-2.34	0.06704	Bicarbonate transporter, C-terminal (1);	3.632590	0.00357	N	0.000023	T	0.00012	0.0000	N	0.02158	-0.66	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45731	-0.9241	9	0.38643	T	0.18	.	2.1114	0.03703	0.2608:0.428:0.1724:0.1388	rs635311;rs60492639;rs635311	571;867;894	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	A	867;867;894;894;867	ENSP00000350756:D867A;ENSP00000362865:D867A;ENSP00000273063:D894A;ENSP00000362867:D894A;ENSP00000314006:D867A	ENSP00000273063:D894A	D	+	2	0	SLC4A3	220210611	0.008000	0.16893	0.001000	0.08648	0.066000	0.16364	0.627000	0.24506	-0.231000	0.09825	0.451000	0.29950	GAT	A|0.312;C|0.688	0.688	strong		0.637	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070	
RSPO2	340419	hgsc.bcm.edu	37	8	108970367	108970367	+	Missense_Mutation	SNP	A	A	G	rs601558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:108970367A>G	ENST00000276659.5	-	5	1177	c.557T>C	c.(556-558)cTg>cCg	p.L186P	RSPO2_ENST00000378439.2_Missense_Mutation_p.L122P|RSPO2_ENST00000517781.1_Missense_Mutation_p.L122P|RSPO2_ENST00000517939.1_Missense_Mutation_p.L119P	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	186	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.		L -> P (in dbSNP:rs601558). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			GGTTGGACACAGTATTGTGTC	0.443													G|||	2455	0.490216	0.0764	0.598	5008	,	,		17575	0.6885		0.6551	False		,,,				2504	0.5992				p.L186P		Atlas-SNP	.											.	RSPO2	65	.	0			c.T557C						PASS	.	G	PRO/LEU	765,3641	755.1+/-412.5	63,639,1501	340.0	287.0	305.0		557	4.9	0.9	8	dbSNP_83	305	5385,3215	485.2+/-371.6	1684,2017,599	yes	missense	RSPO2	NM_178565.4	98	1747,2656,2100	GG,GA,AA		37.3837,17.3627,47.2859	benign	186/244	108970367	6150,6856	2203	4300	6503	SO:0001583	missense	340419	exon5			GGACACAGTATTG	AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"""Endogenous ligands"""	28583	protein-coding gene	gene with protein product		610575	"""R-spondin 2 homolog (Xenopus laevis)"""			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.557T>C	8.37:g.108970367A>G	ENSP00000276659:p.Leu186Pro	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	245	245	1	NM_178565	B3KVP0|Q4G0U4|Q8N6X6	Missense_Mutation	SNP	ENST00000276659.5	37	CCDS6307.1	1173	0.5370879120879121	57	0.11585365853658537	227	0.6270718232044199	393	0.6870629370629371	496	0.6543535620052771	G	11.67	1.706977	0.30232	0.173627	0.626163	ENSG00000147655	ENST00000517939;ENST00000517781;ENST00000378439;ENST00000276659;ENST00000521502	T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89;-0.89	5.83	4.95	0.65309	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00583	-1.355	0.23685	P	0.99711247	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40079	-0.9582	9	0.16896	T	0.51	-0.132	13.1397	0.59428	0.1317:0.0:0.8683:0.0	rs601558;rs859541;rs17318499;rs52821172;rs59391797;rs601558	186;122	Q6UXX9;Q6UXX9-3	RSPO2_HUMAN;.	P	119;122;122;186;119	ENSP00000428940:L119P;ENSP00000427937:L122P;ENSP00000367698:L122P;ENSP00000276659:L186P;ENSP00000428614:L119P	ENSP00000276659:L186P	L	-	2	0	RSPO2	109039543	1.000000	0.71417	0.876000	0.34364	0.935000	0.57460	4.621000	0.61233	1.487000	0.48415	-0.213000	0.12676	CTG	A|0.508;G|0.492	0.492	strong		0.443	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565	
ZNF479	90827	hgsc.bcm.edu	37	7	57188016	57188016	+	Missense_Mutation	SNP	A	A	G	rs78588121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:57188016A>G	ENST00000331162.4	-	5	1376	c.1106T>C	c.(1105-1107)aTg>aCg	p.M369T		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	369					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M369T(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			CCTATGTCTCATAAGGTTCGA	0.428													.|||	1611	0.321685	0.0915	0.379	5008	,	,		21876	0.5427		0.2913	False		,,,				2504	0.3957				p.M369T		Atlas-SNP	.											ZNF479,NS,carcinoma,0,1	ZNF479	193	1	1	Substitution - Missense(1)	stomach(1)	c.T1106C						PASS	.	G	THR/MET	542,3632		35,472,1580	44.0	45.0	45.0		1106	-0.4	0.0	7	dbSNP_130	45	2798,5670		493,1812,1929	no	missense	ZNF479	NM_033273.1	81	528,2284,3509	GG,GA,AA		33.042,12.9851,26.4199	benign	369/525	57188016	3340,9302	2087	4234	6321	SO:0001583	missense	90827	exon5			TGTCTCATAAGGT	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"""Zinc fingers, C2H2-type"", ""-"""	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.1106T>C	7.37:g.57188016A>G	ENSP00000333776:p.Met369Thr	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	297	123	0.414141	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	37	CCDS43590.1	728	0.3333333333333333	45	0.09146341463414634	116	0.32044198895027626	340	0.5944055944055944	227	0.2994722955145119	N	0.001	-3.605008	0.00007	0.129851	0.33042	ENSG00000185177	ENST00000331162	T	0.06768	3.26	0.946	-0.375	0.12509	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.03194	-0.395	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45862	-0.9232	8	0.02654	T	1	.	2.1961	0.03911	0.3833:0.0:0.3777:0.239	.	369	Q96JC4	ZN479_HUMAN	T	369	ENSP00000333776:M369T	ENSP00000333776:M369T	M	-	2	0	ZNF479	57191958	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.761000	0.01805	-2.973000	0.00285	-3.053000	0.00069	ATG	A|0.678;G|0.322	0.322	strong		0.428	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202	
PGR	5241	hgsc.bcm.edu	37	11	100922202	100922202	+	Silent	SNP	G	G	A	rs1042839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100922202G>A	ENST00000325455.5	-	5	3763	c.2310C>T	c.(2308-2310)caC>caT	p.H770H	PGR_ENST00000263463.5_Silent_p.H668H|PGR_ENST00000534013.1_Silent_p.H176H	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	770	Steroid-binding.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	GCCCACTGACGTGTTTGTAGG	0.348													G|||	352	0.0702875	0.0061	0.1354	5008	,	,		16564	0.0099		0.1789	False		,,,				2504	0.0613				p.H770H	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C2310T						PASS	.	G	,	131,4275	94.8+/-133.5	1,129,2073	127.0	123.0	124.0		2310,1818	-0.9	1.0	11	dbSNP_86	124	1407,7193	271.7+/-289.7	106,1195,2999	no	coding-synonymous,coding-synonymous	PGR	NM_000926.4,NM_001202474.1	,	107,1324,5072	AA,AG,GG		16.3605,2.9732,11.8253	,	770/934,606/770	100922202	1538,11468	2203	4300	6503	SO:0001819	synonymous_variant	5241	exon5			ACTGACGTGTTTG	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.2310C>T	11.37:g.100922202G>A		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	191	190	0.994764	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	37	CCDS8310.1																																																																																			G|0.892;A|0.108	0.108	strong		0.348	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
FAM167A	83648	hgsc.bcm.edu	37	8	11301733	11301733	+	Missense_Mutation	SNP	G	G	A	rs147319341	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11301733G>A	ENST00000528897.1	-	2	807	c.188C>T	c.(187-189)cCg>cTg	p.P63L	FAM167A_ENST00000534308.1_Missense_Mutation_p.P63L|FAM167A_ENST00000531564.1_5'Flank|FAM167A_ENST00000284486.4_Missense_Mutation_p.P63L			Q96KS9	F167A_HUMAN	family with sequence similarity 167, member A	63										breast(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)	9						CTCCGCAGCCGGCCTCGGGAA	0.697													G|||	122	0.024361	0.0015	0.0245	5008	,	,		12905	0.0089		0.0258	False		,,,				2504	0.0695				p.P63L		Atlas-SNP	.											.	FAM167A	21	.	0			c.C188T						PASS	.	G	LEU/PRO	22,4382		0,22,2180	27.0	33.0	31.0		188	4.0	0.0	8	dbSNP_134	31	262,8336		4,254,4041	yes	missense	FAM167A	NM_053279.2	98	4,276,6221	AA,AG,GG		3.0472,0.4995,2.1843	possibly-damaging	63/215	11301733	284,12718	2202	4299	6501	SO:0001583	missense	83648	exon2			GCAGCCGGCCTCG		CCDS5981.1	8p23-p22	2010-08-27	2008-06-11	2008-06-11	ENSG00000154319	ENSG00000154319			15549	protein-coding gene	gene with protein product		610085	"""chromosome 8 open reading frame 13"""	C8orf13			Standard	NM_053279		Approved		uc003wtw.2	Q96KS9	OTTHUMG00000129361	ENST00000528897.1:c.188C>T	8.37:g.11301733G>A	ENSP00000436655:p.Pro63Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_053279	A8K3T9|Q3SXY1|Q3SXY3|Q8N3M3|Q9NSR0	Missense_Mutation	SNP	ENST00000528897.1	37	CCDS5981.1	36	0.016483516483516484	0	0.0	12	0.03314917127071823	4	0.006993006993006993	20	0.026385224274406333	G	13.73	2.323004	0.41096	0.004995	0.030472	ENSG00000154319	ENST00000284486;ENST00000534308;ENST00000528897;ENST00000531804	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	4.89	4.02	0.46733	.	0.399666	0.25241	N	0.032095	T	0.02688	0.0081	L	0.54323	1.7	0.29089	N	0.882195	B	0.32731	0.382	B	0.25884	0.064	T	0.05386	-1.0888	10	0.40728	T	0.16	-0.4828	12.4819	0.55847	0.0807:0.0:0.9193:0.0	.	63	Q96KS9	F167A_HUMAN	L	63	ENSP00000284486:P63L;ENSP00000432232:P63L;ENSP00000436655:P63L;ENSP00000431951:P63L	ENSP00000284486:P63L	P	-	2	0	FAM167A	11339143	0.063000	0.20901	0.026000	0.17262	0.004000	0.04260	2.020000	0.41010	1.276000	0.44395	0.655000	0.94253	CCG	G|0.979;A|0.021	0.021	strong		0.697	FAM167A-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000383901.1		
DMXL2	23312	hgsc.bcm.edu	37	15	51914716	51914716	+	Silent	SNP	T	T	C	rs2278989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:51914716T>C	ENST00000251076.5	-	1	314	c.27A>G	c.(25-27)ggA>ggG	p.G9G	DMXL2_ENST00000449909.3_Silent_p.G9G|DMXL2_ENST00000543779.2_Silent_p.G9G	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	9						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		GGTTGACAGCTCCGGTGAGGA	0.677													C|||	2064	0.412141	0.3623	0.4856	5008	,	,		15610	0.3333		0.5169	False		,,,				2504	0.4008				p.G9G		Atlas-SNP	.											.	DMXL2	262	.	0			c.A27G						PASS	.	C	,,	1639,2727		326,987,870	29.0	25.0	26.0		27,27,27	2.1	1.0	15	dbSNP_100	26	4201,4327		1103,1995,1166	no	coding-synonymous,coding-synonymous,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	1429,2982,2036	CC,CT,TT		49.2613,37.5401,45.2924	,,	9/3038,9/2401,9/3037	51914716	5840,7054	2183	4264	6447	SO:0001819	synonymous_variant	23312	exon1			GACAGCTCCGGTG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.27A>G	15.37:g.51914716T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	202	91	0.450495	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			T|0.563;C|0.437	0.437	strong		0.677	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
KCNH5	27133	hgsc.bcm.edu	37	14	63174700	63174700	+	Silent	SNP	G	G	A	rs142813655		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63174700G>A	ENST00000322893.7	-	11	2761	c.2493C>T	c.(2491-2493)gtC>gtT	p.V831V	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	831					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CAGCTTTAGTGACATTATTCC	0.433																																					p.V831V		Atlas-SNP	.											.	KCNH5	320	.	0			c.C2493T						PASS	.	G	,	0,4406		0,0,2203	158.0	148.0	151.0		2493,	5.0	1.0	14	dbSNP_134	151	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,utr-3	KCNH5	NM_139318.3,NM_172375.1	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	831/989,	63174700	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	27133	exon11			TTTAGTGACATTA	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2493C>T	14.37:g.63174700G>A		Somatic	359	0	0		WXS	Illumina HiSeq	Phase_I	425	210	0.494118	NM_139318	C9JP98	Silent	SNP	ENST00000322893.7	37	CCDS9756.1																																																																																			G|1.000;A|0.000	0.000	weak		0.433	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
CELSR3	1951	hgsc.bcm.edu	37	3	48697654	48697654	+	Missense_Mutation	SNP	C	C	G	rs3821875	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:48697654C>G	ENST00000164024.4	-	1	2694	c.2414G>C	c.(2413-2415)aGc>aCc	p.S805T	CELSR3_ENST00000544264.1_Missense_Mutation_p.S805T	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	805	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> T (in dbSNP:rs3821875).		axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCCCTGGGTGCTGATGGCAAA	0.587													C|||	501	0.10004	0.1271	0.0793	5008	,	,		23362	0.1171		0.1193	False		,,,				2504	0.0409				p.S805T		Atlas-SNP	.											.	CELSR3	237	.	0			c.G2414C						PASS	.	C	THR/SER	589,3817	261.3+/-264.2	28,533,1642	96.0	89.0	91.0		2414	5.7	1.0	3	dbSNP_107	91	1014,7586	218.1+/-256.6	65,884,3351	yes	missense	CELSR3	NM_001407.2	58	93,1417,4993	GG,GC,CC		11.7907,13.3681,12.3251	possibly-damaging	805/3313	48697654	1603,11403	2203	4300	6503	SO:0001583	missense	1951	exon1			TGGGTGCTGATGG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.2414G>C	3.37:g.48697654C>G	ENSP00000164024:p.Ser805Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	37	CCDS2775.1	243	0.11126373626373626	67	0.13617886178861788	29	0.08011049723756906	57	0.09965034965034965	90	0.11873350923482849	C	10.15	1.270306	0.23221	0.133681	0.117907	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.02974	4.09;4.09	5.67	5.67	0.87782	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00039	0.0001	N	0.17838	0.53	0.09310	P	0.99999999688412	B;D	0.76494	0.384;0.999	B;D	0.83275	0.23;0.996	T	0.49818	-0.8899	8	0.02654	T	1	.	19.7607	0.96316	0.0:1.0:0.0:0.0	rs3821875;rs3821875	805;875	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	T	805	ENSP00000164024:S805T;ENSP00000445694:S805T	ENSP00000164024:S805T	S	-	2	0	CELSR3	48672658	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.885000	0.63142	2.686000	0.91538	0.561000	0.74099	AGC	C|0.877;G|0.123	0.123	strong		0.587	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
FAM170A	340069	hgsc.bcm.edu	37	5	118969960	118969960	+	Missense_Mutation	SNP	C	C	T	rs328694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:118969960C>T	ENST00000515256.1	+	3	689	c.517C>T	c.(517-519)Ccc>Tcc	p.P173S				A1A519	F170A_HUMAN	family with sequence similarity 170, member A	173			P -> S (in dbSNP:rs328694).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P173S(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	24						AGGTACTCCCCCCTCTGATGT	0.542													C|||	2221	0.44349	0.3495	0.3876	5008	,	,		21739	0.495		0.4453	False		,,,				2504	0.5552				p.P173S		Atlas-SNP	.											FAM170A,NS,carcinoma,0,1	FAM170A	47	1	1	Substitution - Missense(1)	prostate(1)	c.C517T						PASS	.	C	SER/PRO,SER/PRO	1354,2620		238,878,871	91.0	95.0	94.0		376,517	2.1	0.1	5	dbSNP_79	94	3719,4641		851,2017,1312	yes	missense,missense	FAM170A	NM_001163991.1,NM_182761.3	74,74	1089,2895,2183	TT,TC,CC		44.4856,34.0715,41.1302	probably-damaging,probably-damaging	126/283,173/330	118969960	5073,7261	1987	4180	6167	SO:0001583	missense	340069	exon3			ACTCCCCCCTCTG	AF427126	CCDS43353.1, CCDS54889.1	5q23.1	2008-06-12			ENSG00000164334	ENSG00000164334			27963	protein-coding gene	gene with protein product						12477932	Standard	NM_182761		Approved		uc003ksn.3	A1A519	OTTHUMG00000162946	ENST00000515256.1:c.517C>T	5.37:g.118969960C>T	ENSP00000422684:p.Pro173Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	166	68	0.409639	NM_182761	Q66LM8|Q7Z4V2|Q8IW94	Missense_Mutation	SNP	ENST00000515256.1	37		936	0.42857142857142855	172	0.34959349593495936	144	0.39779005524861877	299	0.5227272727272727	321	0.4234828496042216	C	10.32	1.318429	0.23994	0.340715	0.444856	ENSG00000164334	ENST00000296787;ENST00000515256	T	0.42131	0.98	4.89	2.11	0.27256	.	0.000000	0.64402	D	0.000013	T	0.00012	0.0000	M	0.67953	2.075	0.80722	P	0.0	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.47129	-0.9141	8	.	.	.	-10.0542	3.7305	0.08491	0.171:0.5741:0.165:0.0898	rs328694;rs52831294;rs60487150;rs328694	126;173	D6RIE9;A1A519	.;F170A_HUMAN	S	126;173	ENSP00000422684:P173S	.	P	+	1	0	FAM170A	118997859	0.002000	0.14202	0.077000	0.20336	0.131000	0.20780	0.813000	0.27225	0.357000	0.24183	-0.136000	0.14681	CCC	C|0.562;T|0.438	0.438	strong		0.542	FAM170A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371126.1	NM_182761	
FXYD4	53828	hgsc.bcm.edu	37	10	43869097	43869097	+	5'UTR	SNP	C	C	A	rs10899795	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43869097C>A	ENST00000476166.1	+	0	237				FXYD4_ENST00000480834.1_Intron	NM_173160.2	NP_775183.1	P59646	FXYD4_HUMAN	FXYD domain containing ion transport regulator 4						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)			NS(1)|large_intestine(1)|lung(3)	5						TGCCTCCTCTCGCTGACCAAT	0.612													A|||	1900	0.379393	0.5492	0.255	5008	,	,		16681	0.4256		0.2197	False		,,,				2504	0.3548				.	GBM(173;880 2047 13035 42390 49655)	Atlas-SNP	.											.	FXYD4	9	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	53828	.			TCCTCTCGCTGAC		CCDS7203.1	10q11.21	2008-02-01	2002-01-14		ENSG00000150201	ENSG00000150201			4028	protein-coding gene	gene with protein product			"""FXYD domain-containing ion transport regulator 4"""			10950925, 12763854	Standard	NM_001184963		Approved	CHIF	uc001jaq.1	P59646	OTTHUMG00000018027	ENST00000476166.1:c.-98C>A	10.37:g.43869097C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	30	12	0.4	.	Q6UWZ1|Q7Z4M5	Splice_Site	SNP	ENST00000476166.1	37	CCDS7203.1																																																																																			C|0.603;A|0.397	0.397	strong		0.612	FXYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047698.2	NM_173160	
PTX4	390667	hgsc.bcm.edu	37	16	1538433	1538433	+	Intron	SNP	A	A	G	rs2745102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1538433A>G	ENST00000447419.2	-	1	167				PTX4_ENST00000293922.1_Silent_p.P12P|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GACTGCCACAAGGTGGACCTG	0.667													A|||	1355	0.270567	0.1694	0.196	5008	,	,		16054	0.499		0.2445	False		,,,				2504	0.2515				p.P12P		Atlas-SNP	.											.	PTX4	46	.	0			c.T36C						PASS	.	A		715,3683	295.3+/-283.6	56,603,1540	71.0	61.0	64.0		36	-1.0	0.0	16	dbSNP_100	64	2185,6415	366.0+/-334.1	255,1675,2370	no	coding-synonymous	PTX4	NM_001013658.1		311,2278,3910	GG,GA,AA		25.407,16.2574,22.3111		12/474	1538433	2900,10098	2199	4300	6499	SO:0001627	intron_variant	390667	exon1			GCCACAAGGTGGA		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.141+336T>C	16.37:g.1538433A>G		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	231	109	0.471861	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				A|0.759;G|0.241	0.241	strong		0.667	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
GPR133	283383	hgsc.bcm.edu	37	12	131590404	131590404	+	Silent	SNP	G	G	A	rs4759544	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:131590404G>A	ENST00000261654.5	+	17	2440	c.1881G>A	c.(1879-1881)ccG>ccA	p.P627P	GPR133_ENST00000543617.1_Silent_p.P146P|GPR133_ENST00000376682.4_Silent_p.P313P|GPR133_ENST00000535015.1_Silent_p.P659P	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	627					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GCCTCGAGCCGGGCACGGTGA	0.617													G|||	1030	0.205671	0.028	0.1859	5008	,	,		20228	0.1935		0.2922	False		,,,				2504	0.3834				p.P627P		Atlas-SNP	.											.	GPR133	136	.	0			c.G1881A						PASS	.	G		328,4078	165.8+/-197.2	15,298,1890	113.0	75.0	88.0		1881	-2.0	1.0	12	dbSNP_111	88	2488,6112	393.7+/-344.5	382,1724,2194	no	coding-synonymous	GPR133	NM_198827.3		397,2022,4084	AA,AG,GG		28.9302,7.4444,21.6515		627/875	131590404	2816,10190	2203	4300	6503	SO:0001819	synonymous_variant	283383	exon17			CGAGCCGGGCACG	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.1881G>A	12.37:g.131590404G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Silent	SNP	ENST00000261654.5	37	CCDS9272.1																																																																																			G|0.798;A|0.202	0.202	strong		0.617	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
BLK	640	hgsc.bcm.edu	37	8	11414237	11414237	+	Silent	SNP	T	T	C	rs2306234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:11414237T>C	ENST00000259089.4	+	9	1435	c.843T>C	c.(841-843)ttT>ttC	p.F281F	RP11-148O21.3_ENST00000527922.1_RNA|RP11-148O21.2_ENST00000533322.1_RNA|BLK_ENST00000529894.1_Silent_p.F210F|RP11-148O21.4_ENST00000528629.1_RNA	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		CAGAAGCCTTTCTGGGTGAGG	0.542													C|||	4145	0.827676	0.7247	0.8991	5008	,	,		18235	0.9474		0.8489	False		,,,				2504	0.771				p.F281F		Atlas-SNP	.											.	BLK	78	.	0			c.T843C						PASS	.	C		3292,1114	400.1+/-331.5	1234,824,145	108.0	87.0	94.0		843	0.6	1.0	8	dbSNP_100	94	7275,1325	261.9+/-284.1	3077,1121,102	no	coding-synonymous	BLK	NM_001715.2		4311,1945,247	CC,CT,TT		15.407,25.2837,18.7529		281/506	11414237	10567,2439	2203	4300	6503	SO:0001819	synonymous_variant	640	exon9			AGCCTTTCTGGGT	BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"""SH2 domain containing"""	1057	protein-coding gene	gene with protein product		191305	"""B lymphoid tyrosine kinase"""			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.843T>C	8.37:g.11414237T>C		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_001715	Q16291|Q96IN1	Silent	SNP	ENST00000259089.4	37	CCDS5982.1																																																																																			T|0.171;C|0.829	0.829	strong		0.542	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1		
DNAH12	201625	hgsc.bcm.edu	37	3	57414434	57414434	+	Missense_Mutation	SNP	A	A	G	rs4462937	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:57414434A>G	ENST00000351747.2	-	34	5290	c.5110T>C	c.(5110-5112)Tat>Cat	p.Y1704H		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1704			Y -> H (in dbSNP:rs4462937).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						AGAGCTTGATATTCTGGTTCA	0.403													A|||	1502	0.29992	0.1218	0.3127	5008	,	,		19134	0.4187		0.2416	False		,,,				2504	0.4693				p.Y1704H		Atlas-SNP	.											.	DNAH12	182	.	0			c.T5110C						PASS	.	A	HIS/TYR	195,1189		14,167,511	125.0	106.0	112.0		5110	-1.9	0.0	3	dbSNP_111	112	759,2423		91,577,923	yes	missense	DNAH12	NM_178504.4	83	105,744,1434	GG,GA,AA		23.8529,14.0896,20.8936	benign	1704/3093	57414434	954,3612	692	1591	2283	SO:0001583	missense	201625	exon34			CTTGATATTCTGG	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.5110T>C	3.37:g.57414434A>G	ENSP00000295937:p.Tyr1704His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		594	0.27197802197802196	62	0.12601626016260162	111	0.30662983425414364	239	0.4178321678321678	182	0.24010554089709762	A	0.006	-2.027775	0.00410	0.140896	0.238529	ENSG00000174844	ENST00000351747;ENST00000495027	T;T	0.23147	1.92;1.92	5.76	-1.92	0.07618	.	.	.	.	.	T	0.00012	0.0000	N	0.00360	-1.595	0.51482	P	7.100000000004325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43940	-0.9360	8	0.02654	T	1	.	5.2318	0.15426	0.2915:0.0:0.4287:0.2798	rs4462937;rs4462937	1704	Q6ZR08	DYH12_HUMAN	H	1704;1727	ENSP00000295937:Y1704H;ENSP00000418137:Y1727H	ENSP00000295937:Y1704H	Y	-	1	0	DNAH12	57389474	0.015000	0.18098	0.001000	0.08648	0.016000	0.09150	0.114000	0.15520	-0.118000	0.11851	-0.789000	0.03336	TAT	A|0.728;G|0.272	0.272	strong		0.403	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
TSPYL4	23270	hgsc.bcm.edu	37	6	116574455	116574455	+	Silent	SNP	G	G	A	rs2232472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:116574455G>A	ENST00000420283.1	-	1	806	c.717C>T	c.(715-717)caC>caT	p.H239H	RP3-486I3.7_ENST00000448740.2_lincRNA|DSE_ENST00000540275.1_5'Flank	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	239					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(2)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.045)|OV - Ovarian serous cystadenocarcinoma(136;0.0666)|GBM - Glioblastoma multiforme(226;0.095)|Epithelial(106;0.125)		TGCGCTGCATGTGGAGCCTTC	0.527													G|||	1945	0.388379	0.0923	0.3804	5008	,	,		19788	0.6359		0.3648	False		,,,				2504	0.5634				p.H239H		Atlas-SNP	.											.	TSPYL4	18	.	0			c.C717T						PASS	.	G		453,3545		37,379,1583	34.0	35.0	35.0		717	-3.5	1.0	6	dbSNP_98	35	2966,5398		529,1908,1745	no	coding-synonymous	TSPYL4	NM_021648.4		566,2287,3328	AA,AG,GG		35.4615,11.3307,27.6573		239/415	116574455	3419,8943	1999	4182	6181	SO:0001819	synonymous_variant	23270	exon1			CTGCATGTGGAGC		CCDS5106.1	6q22.1	2010-05-12			ENSG00000187189	ENSG00000187189			21559	protein-coding gene	gene with protein product							Standard	NM_021648		Approved	dJ486I3.2, KIAA0721	uc003pwn.3	Q9UJ04	OTTHUMG00000015429	ENST00000420283.1:c.717C>T	6.37:g.116574455G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	59	0.621053	NM_021648	B4DYQ2|O94828|Q96GW8	Silent	SNP	ENST00000420283.1	37	CCDS5106.1																																																																																			G|0.630;A|0.370	0.370	strong		0.527	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2		
PRG4	10216	hgsc.bcm.edu	37	1	186281400	186281400	+	Missense_Mutation	SNP	C	C	T	rs12134934	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:186281400C>T	ENST00000445192.2	+	11	3932	c.3887C>T	c.(3886-3888)aCg>aTg	p.T1296M	RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367483.4_Missense_Mutation_p.T1255M|PRG4_ENST00000367485.4_Missense_Mutation_p.T1203M|TPR_ENST00000367478.4_3'UTR|PRG4_ENST00000367484.3_Missense_Mutation_p.T825M|PRG4_ENST00000367486.3_Missense_Mutation_p.T1253M	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1296			T -> M (in dbSNP:rs12134934). {ECO:0000269|Ref.1}.		cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TATGGAGAAACGACACAGGTT	0.443													C|||	153	0.0305511	0.0454	0.013	5008	,	,		15416	0.002		0.0388	False		,,,				2504	0.044				p.T1296M		Atlas-SNP	.											.	PRG4	259	.	0			c.C3887T						PASS	.	C	MET/THR,MET/THR,MET/THR,,MET/THR	203,4203	124.5+/-161.8	2,199,2002	131.0	128.0	129.0		3764,3608,3485,,3887	-1.6	0.0	1	dbSNP_120	129	388,8212	125.3+/-183.9	12,364,3924	yes	missense,missense,missense,utr-3,missense	TPR,PRG4	NM_001127708.1,NM_001127709.1,NM_001127710.1,NM_003292.2,NM_005807.3	81,81,81,,81	14,563,5926	TT,TC,CC		4.5116,4.6074,4.5441	probably-damaging,probably-damaging,probably-damaging,,probably-damaging	1255/1364,1203/1312,1162/1271,,1296/1405	186281400	591,12415	2203	4300	6503	SO:0001583	missense	10216	exon11			GAGAAACGACACA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3887C>T	1.37:g.186281400C>T	ENSP00000399679:p.Thr1296Met	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	68	0.031135531135531136	30	0.06097560975609756	4	0.011049723756906077	1	0.0017482517482517483	33	0.04353562005277045	C	10.40	1.339292	0.24339	0.046074	0.045116	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.05447	3.45;3.56;3.56;3.44;3.56	5.38	-1.59	0.08453	Hemopexin/matrixin (1);	0.526053	0.15728	N	0.247589	T	0.00815	0.0027	L	0.47716	1.5	0.09310	N	1	D;D;P;D	0.53312	0.959;0.959;0.931;0.959	P;P;B;P	0.48189	0.57;0.483;0.366;0.57	T	0.17198	-1.0377	10	0.72032	D	0.01	0.1886	9.3509	0.38138	0.0:0.4603:0.0:0.5397	rs12134934;rs52836796;rs58324543;rs12134934	1162;1203;1296;1255	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	M	1253;825;1255;1203;1296	ENSP00000356456:T1253M;ENSP00000356454:T825M;ENSP00000356453:T1255M;ENSP00000356455:T1203M;ENSP00000399679:T1296M	ENSP00000356453:T1255M	T	+	2	0	PRG4	184548023	0.000000	0.05858	0.000000	0.03702	0.960000	0.62799	-0.888000	0.04148	-0.516000	0.06470	0.585000	0.79938	ACG	C|0.958;T|0.042	0.042	strong		0.443	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
CHRNA4	1137	hgsc.bcm.edu	37	20	61981134	61981134	+	Silent	SNP	G	G	A	rs1044396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:61981134G>A	ENST00000370263.4	-	5	1850	c.1629C>T	c.(1627-1629)agC>agT	p.S543S	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	543					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TGACCGTGGCGCTCGGGGACA	0.687													G|||	1620	0.323482	0.0613	0.4899	5008	,	,		12618	0.2679		0.5288	False		,,,				2504	0.4059				p.S543S		Atlas-SNP	.											.	CHRNA4	98	.	0			c.C1629T						PASS	.	G		657,3745	270.4+/-269.6	57,543,1601	37.0	40.0	39.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1629	-3.1	0.0	20	dbSNP_86	39	4651,3947	582.1+/-391.3	1273,2105,921	no	coding-synonymous	CHRNA4	NM_000744.5		1330,2648,2522	AA,AG,GG		45.906,14.925,40.8308		543/628	61981134	5308,7692	2201	4299	6500	SO:0001819	synonymous_variant	1137	exon5			CGTGGCGCTCGGG		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1958	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 4 (neuronal)"""	118504	"""cholinergic receptor, nicotinic, alpha polypeptide 4"""	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1629C>T	20.37:g.61981134G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	40	23	0.575	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Silent	SNP	ENST00000370263.4	37	CCDS13517.1																																																																																			G|0.625;A|0.375	0.375	strong		0.687	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
C1orf53	388722	hgsc.bcm.edu	37	1	197874949	197874949	+	Silent	SNP	T	T	C	rs2270763	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197874949T>C	ENST00000367393.3	+	2	291	c.288T>C	c.(286-288)gaT>gaC	p.D96D	C1orf53_ENST00000542800.1_3'UTR	NM_001024594.2	NP_001019765.1	Q5VUE5	CA053_HUMAN	chromosome 1 open reading frame 53	96										endometrium(1)|lung(1)	2						ACTATGTGGATCCAGCTACTG	0.408													T|||	1801	0.359625	0.4123	0.3948	5008	,	,		18098	0.2619		0.3668	False		,,,				2504	0.3569				p.D96D		Atlas-SNP	.											.	C1orf53	18	.	0			c.T288C						PASS	.	T		1591,2363		339,913,725	160.0	151.0	154.0		288	-0.9	1.0	1	dbSNP_100	154	2921,5421		512,1897,1762	no	coding-synonymous	C1orf53	NM_001024594.2		851,2810,2487	CC,CT,TT		35.0156,40.2377,36.6949		96/146	197874949	4512,7784	1977	4171	6148	SO:0001819	synonymous_variant	388722	exon2			TGTGGATCCAGCT	BC038214	CCDS44290.1	1q31.3	2011-01-26			ENSG00000203724	ENSG00000203724			30003	protein-coding gene	gene with protein product						15897902	Standard	NM_001024594		Approved		uc001guh.3	Q5VUE5	OTTHUMG00000035659	ENST00000367393.3:c.288T>C	1.37:g.197874949T>C		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	268	141	0.526119	NM_001024594	A1L4N2|Q5VUE4	Silent	SNP	ENST00000367393.3	37	CCDS44290.1	735	0.33653846153846156	187	0.3800813008130081	151	0.4171270718232044	139	0.243006993006993	258	0.3403693931398417	T	8.716	0.913213	0.17907	0.402377	0.350156	ENSG00000203724	ENST00000436652	.	.	.	5.73	-0.891	0.10573	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999697	.	.	.	.	.	.	T	0.43376	-0.9395	3	.	.	.	-2.0025	11.3485	0.49575	0.0:0.4741:0.0:0.5259	rs2270763;rs61130784;rs2270763	.	.	.	P	33	.	.	S	+	1	0	C1orf53	196141572	0.993000	0.37304	0.968000	0.41197	0.989000	0.77384	0.140000	0.16056	-0.399000	0.07668	-0.290000	0.09829	TCC	T|0.659;C|0.341	0.341	strong		0.408	C1orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086555.1	NM_001024594	
HLA-C	3107	hgsc.bcm.edu	37	6	31238853	31238853	+	Missense_Mutation	SNP	C	C	T	rs17849598		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31238853C>T	ENST00000376228.5	-	3	630	c.616G>A	c.(616-618)Gca>Aca	p.A206T	HLA-C_ENST00000383329.3_Missense_Mutation_p.A206T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	206	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTGGTACCTGCGCGCTGCAGC	0.647																																					p.A206T		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	0			c.G616A						scavenged	.						47.0	42.0	44.0					6																	31238853		2202	4300	6502	SO:0001583	missense	3107	exon3			TACCTGCGCGCTG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.616G>A	6.37:g.31238853C>T	ENSP00000365402:p.Ala206Thr	Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	315	10	0.031746	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	9.192|9.192	1.026185|1.026185	0.19512|0.19512	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|T	0.00695|0.00235	5.84;5.83|8.48	2.55|2.55	-4.93|-4.93	0.03066|0.03066	MHC class I-like antigen recognition (1);|.	0.959209|.	0.08469|.	N|.	0.941313|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.25060|0.25060	0.705|0.705	0.21290|0.21290	N|N	0.999739|0.999739	B;B;B;B|.	0.21905|.	0.062;0.002;0.008;0.004|.	B;B;B;B|.	0.18263|.	0.021;0.005;0.005;0.007|.	T|T	0.18555|0.18555	-1.0333|-1.0333	10|7	0.30078|0.87932	T|D	0.28|0	.|.	6.1502|6.1502	0.20308|0.20308	0.1486:0.2084:0.0:0.643|0.1486:0.2084:0.0:0.643	rs17849598;rs17850340|rs17849598;rs17850340	206;206;206;206|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	T|H	206;206;206;243|205	ENSP00000365402:A206T;ENSP00000372819:A206T|ENSP00000400410:R205H	ENSP00000365402:A206T|ENSP00000400410:R205H	A|R	-|-	1|2	0|0	HLA-C|HLA-C	31346832|31346832	0.000000|0.000000	0.05858|0.05858	0.261000|0.261000	0.24466|0.24466	0.005000|0.005000	0.04900|0.04900	-0.679000|-0.679000	0.05203|0.05203	-1.431000|-1.431000	0.01982|0.01982	-0.704000|-0.704000	0.03662|0.03662	GCA|CGC	.	.	weak		0.647	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
RBM26	64062	hgsc.bcm.edu	37	13	79940811	79940811	+	Silent	SNP	T	T	C	rs7327603	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:79940811T>C	ENST00000438737.2	-	7	1532	c.1092A>G	c.(1090-1092)gtA>gtG	p.V364V	RBM26_ENST00000438724.1_Silent_p.V364V|RBM26_ENST00000267229.7_Silent_p.V364V|RBM26_ENST00000461008.1_5'UTR			Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	364	Pro-rich.				mRNA processing (GO:0006397)|negative regulation of phosphatase activity (GO:0010923)		metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		CTGGCGGTGGTACTGGGGGCC	0.512													C|||	2343	0.467851	0.5802	0.3732	5008	,	,		12979	0.2698		0.506	False		,,,				2504	0.5481				p.V364V		Atlas-SNP	.											.	RBM26	199	.	0			c.A1092G						PASS	.	C		2497,1909	534.7+/-374.0	706,1085,412	39.0	45.0	43.0		1092	3.7	1.0	13	dbSNP_116	43	4431,4169	565.6+/-388.5	1133,2165,1002	no	coding-synonymous	RBM26	NM_022118.3		1839,3250,1414	CC,CT,TT		48.4767,43.3273,46.7323		364/981	79940811	6928,6078	2203	4300	6503	SO:0001819	synonymous_variant	64062	exon7			CGGTGGTACTGGG	AF116667	CCDS9462.1, CCDS66566.1, CCDS73591.1	13q31.1	2014-06-13	2006-06-22	2006-06-22	ENSG00000139746	ENSG00000139746		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	20327	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 2"", ""protein phosphatase 1, regulatory 132"""		"""chromosome 13 open reading frame 10"""	C13orf10		11149944, 15741184	Standard	XM_005266497		Approved	PRO1777, SE70-2, FLJ20957, ZC3H17, ARRS2, PPP1R132	uc001vky.2	Q5T8P6	OTTHUMG00000017133	ENST00000438737.2:c.1092A>G	13.37:g.79940811T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_022118	B4DZE0|Q2NKM2|Q2NKQ2|Q5CZH8|Q5T8P5|Q5T8P8|Q5U5P5|Q5W0G7|Q8N3H5|Q96K92|Q96SZ3|Q9H2F8|Q9H7F9|Q9P1G7	Silent	SNP	ENST00000438737.2	37																																																																																				T|0.502;C|0.498	0.498	strong		0.512	RBM26-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045373.4	NM_022118	
FCRLA	84824	hgsc.bcm.edu	37	1	161683136	161683136	+	Missense_Mutation	SNP	G	G	A	rs11746	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161683136G>A	ENST00000236938.6	+	5	1339	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q	FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000367957.2_Missense_Mutation_p.R226Q|FCRLA_ENST00000294796.4_Missense_Mutation_p.R215Q|FCRLA_ENST00000309691.6_Missense_Mutation_p.R260Q|FCRLA_ENST00000367959.2_Missense_Mutation_p.R372Q|FCRLA_ENST00000540926.1_Missense_Mutation_p.R355Q|FCRLA_ENST00000540521.1_Missense_Mutation_p.R232Q|FCRLA_ENST00000367949.2_Missense_Mutation_p.R182Q|FCRLA_ENST00000546024.1_Missense_Mutation_p.R277Q|FCRLA_ENST00000350710.3_Missense_Mutation_p.R131Q|FCRLA_ENST00000367953.3_Missense_Mutation_p.R355Q|FCRLA_ENST00000349527.4_Missense_Mutation_p.R254Q|FCRLA_ENST00000367950.1_Missense_Mutation_p.R142Q	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	349					cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)		p.R349Q(1)		breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			TCTGGCCACCGGAAGCCTGGG	0.463													G|||	1488	0.297125	0.0469	0.3444	5008	,	,		18540	0.2371		0.5129	False		,,,				2504	0.4417				p.R372Q		Atlas-SNP	.											FCRLA,NS,carcinoma,0,1	FCRLA	101	1	1	Substitution - Missense(1)	stomach(1)	c.G1115A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	533,3873	241.5+/-251.9	40,453,1710	70.0	66.0	67.0		1115,830,695,392,677,545,1097	-3.4	0.0	1	dbSNP_52	67	4144,4456	564.3+/-388.3	985,2174,1141	yes	missense,missense,missense,missense,missense,missense,missense	FCRLA	NM_001184866.1,NM_001184867.1,NM_001184870.1,NM_001184871.1,NM_001184872.1,NM_001184873.1,NM_032738.3	43,43,43,43,43,43,43	1025,2627,2851	AA,AG,GG		48.186,12.0971,35.9603	benign,benign,benign,benign,benign,benign,benign	372/383,277/288,232/243,131/142,226/237,182/193,366/377	161683136	4677,8329	2203	4300	6503	SO:0001583	missense	84824	exon6			GCCACCGGAAGCC	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18504	protein-coding gene	gene with protein product		606891	"""Fc receptor-like and mucin-like 1"""	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.1097G>A	1.37:g.161683136G>A	ENSP00000236938:p.Arg366Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Missense_Mutation	SNP	ENST00000236938.6	37	CCDS30926.1	690	0.3159340659340659	27	0.054878048780487805	135	0.3729281767955801	148	0.25874125874125875	380	0.5013192612137203	G	6.278	0.419487	0.11928	0.120971	0.48186	ENSG00000132185	ENST00000236938;ENST00000367959;ENST00000546024;ENST00000540521;ENST00000367949;ENST00000350710;ENST00000540926;ENST00000367957;ENST00000349527;ENST00000309691;ENST00000294796;ENST00000367953;ENST00000367950	T;T;T;T;T;T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.23	-3.37	0.04898	.	0.909229	0.09180	N	0.837550	T	0.07188	0.0182	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B;B;B	0.25235	0.003;0.121;0.087;0.052;0.032;0.021;0.009	B;B;B;B;B;B;B	0.15870	0.001;0.01;0.014;0.004;0.005;0.004;0.006	T	0.25882	-1.0119	9	0.25751	T	0.34	.	7.078	0.25215	0.3066:0.0:0.4801:0.2133	rs11746;rs1105125;rs3202905;rs17413841;rs17850109;rs52825965;rs56459424;rs11746	131;182;232;226;277;372;366	F8W743;A6NL20;F5H720;Q5VXB1;G3V1J2;A6NC03;Q7L513-9	.;.;.;.;.;.;.	Q	366;372;277;232;182;131;355;226;254;260;215;355;142	ENSP00000236938:R366Q;ENSP00000356936:R372Q;ENSP00000439838:R277Q;ENSP00000442870:R232Q;ENSP00000356926:R182Q;ENSP00000344808:R131Q;ENSP00000446380:R355Q;ENSP00000356934:R226Q;ENSP00000294798:R254Q;ENSP00000309596:R260Q;ENSP00000294796:R215Q;ENSP00000356930:R355Q;ENSP00000356927:R142Q	ENSP00000236938:R366Q	R	+	2	0	FCRLA	159949760	0.000000	0.05858	0.003000	0.11579	0.223000	0.24884	-0.770000	0.04705	-0.846000	0.04174	-0.880000	0.02959	CGG	G|0.661;A|0.339	0.339	strong		0.463	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	
ARSD	414	hgsc.bcm.edu	37	X	2836047	2836047	+	Missense_Mutation	SNP	C	C	T	rs67359049		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2836047C>T	ENST00000381154.1	-	5	736	c.661G>A	c.(661-663)Ggt>Agt	p.G221S	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	221					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GAGAAGAAACCGCAGGTCTGG	0.652																																					p.G221S		Atlas-SNP	.											.	ARSD	47	.	0			c.G661A						PASS	.						17.0	22.0	20.0					X																	2836047		2202	4298	6500	SO:0001583	missense	414	exon5			AGAAACCGCAGGT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.661G>A	X.37:g.2836047C>T	ENSP00000370546:p.Gly221Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	102	0.06148282097649186	36	0.0782608695652174	20	0.055865921787709494	33	0.05871886120996441	55	0.07412398921832884	c	15.90	2.969913	0.53614	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.93659	-3.26	3.47	2.6	0.31112	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.64402	U	0.000004	T	0.64349	0.2590	M	0.80847	2.515	0.09310	N	1	D;D	0.76494	0.999;0.994	D;P	0.66351	0.943;0.812	T	0.73418	-0.3989	10	0.42905	T	0.14	.	7.3482	0.26676	0.0:0.7823:0.0:0.2177	.	221;221	E9PAW5;P51689	.;ARSD_HUMAN	S	221	ENSP00000370546:G221S	ENSP00000217890:G221S	G	-	1	0	ARSD	2846047	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.249000	0.08842	0.383000	0.24910	-0.454000	0.05498	GGT	C|0.938;T|0.062	0.062	strong		0.652	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13788886	13788886	+	Missense_Mutation	SNP	C	C	A	rs10513155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:13788886C>A	ENST00000265104.4	-	51	8690	c.8586G>T	c.(8584-8586)ttG>ttT	p.L2862F		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2862			L -> F (in dbSNP:rs10513155).		cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CACAATCCACCAAGAGTTTTT	0.408									Kartagener syndrome				C|||	1045	0.208666	0.1256	0.2608	5008	,	,		18751	0.2173		0.2744	False		,,,				2504	0.2076				p.L2862F		Atlas-SNP	.											.	DNAH5	868	.	0			c.G8586T						PASS	.	C	PHE/LEU	719,3687	298.4+/-285.3	60,599,1544	126.0	123.0	124.0		8586	4.0	0.9	5	dbSNP_119	124	2482,6118	409.1+/-349.7	351,1780,2169	yes	missense	DNAH5	NM_001369.2	22	411,2379,3713	AA,AC,CC		28.8605,16.3187,24.6117	benign	2862/4625	13788886	3201,9805	2203	4300	6503	SO:0001583	missense	1767	exon51	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATCCACCAAGAGT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8586G>T	5.37:g.13788886C>A	ENSP00000265104:p.Leu2862Phe	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	261	151	0.578544	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	485	0.22206959706959706	77	0.1565040650406504	80	0.22099447513812154	122	0.21328671328671328	206	0.2717678100263852	C	6.173	0.400141	0.11696	0.163187	0.288605	ENSG00000039139	ENST00000265104	T	0.25749	1.78	5.86	4.02	0.46733	.	0.766181	0.12748	N	0.442423	T	0.00012	0.0000	L	0.29908	0.895	0.39024	P	0.040198999999999985	B	0.02656	0.0	B	0.08055	0.003	T	0.42258	-0.9462	9	0.20046	T	0.44	.	5.5757	0.17222	0.1491:0.5932:0.0:0.2577	rs10513155;rs17205615;rs52829442;rs59857566;rs10513155	2862	Q8TE73	DYH5_HUMAN	F	2862	ENSP00000265104:L2862F	ENSP00000265104:L2862F	L	-	3	2	DNAH5	13841886	0.008000	0.16893	0.918000	0.36340	0.775000	0.43874	-0.096000	0.11059	0.745000	0.32763	0.655000	0.94253	TTG	C|0.765;A|0.235	0.235	strong		0.408	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
FCHO2	115548	hgsc.bcm.edu	37	5	72347223	72347223	+	Silent	SNP	A	A	G	rs7712838	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:72347223A>G	ENST00000430046.2	+	12	1103	c.987A>G	c.(985-987)acA>acG	p.T329T	FCHO2_ENST00000512348.1_Silent_p.T296T|FCHO2_ENST00000341845.6_Silent_p.T329T	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	329					clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		AACCAGAAACAAATCAGAATG	0.294													A|||	1513	0.302117	0.2897	0.1859	5008	,	,		16811	0.4782		0.3181	False		,,,				2504	0.2035				p.T329T		Atlas-SNP	.											.	FCHO2	96	.	0			c.A987G						PASS	.	A	,	914,2522		132,650,936	75.0	72.0	73.0		888,987	3.9	1.0	5	dbSNP_116	73	2096,5608		294,1508,2050	no	coding-synonymous,coding-synonymous	FCHO2	NM_001146032.1,NM_138782.2	,	426,2158,2986	GG,GA,AA		27.2066,26.6007,27.0197	,	296/778,329/811	72347223	3010,8130	1718	3852	5570	SO:0001819	synonymous_variant	115548	exon12			AGAAACAAATCAG	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.987A>G	5.37:g.72347223A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Silent	SNP	ENST00000430046.2	37	CCDS47230.1																																																																																			A|0.673;G|0.327	0.327	strong		0.294	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142	
WDR91	29062	hgsc.bcm.edu	37	7	134889141	134889141	+	Missense_Mutation	SNP	G	G	A	rs292592	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:134889141G>A	ENST00000354475.4	-	6	801	c.770C>T	c.(769-771)cCt>cTt	p.P257L	WDR91_ENST00000423565.1_Missense_Mutation_p.P222L|WDR91_ENST00000485942.1_5'UTR|AC009542.2_ENST00000595902.1_RNA|WDR91_ENST00000344400.5_Missense_Mutation_p.P257L	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	257			P -> L (in dbSNP:rs292592). {ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.8}.					p.P257L(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						GCCCACACGAGGTGACTGGGA	0.587													G|||	3281	0.655152	0.4955	0.804	5008	,	,		20206	0.6131		0.7087	False		,,,				2504	0.7536				p.P257L		Atlas-SNP	.											WDR91,NS,carcinoma,0,1	WDR91	82	1	1	Substitution - Missense(1)	lung(1)	c.C770T						PASS	.	G	LEU/PRO	2423,1983	617.7+/-393.0	672,1079,452	73.0	57.0	63.0		770	5.4	0.6	7	dbSNP_79	63	6223,2377	701.1+/-405.2	2262,1699,339	yes	missense	WDR91	NM_014149.3	98	2934,2778,791	AA,AG,GG		27.6395,45.0068,33.523	probably-damaging	257/748	134889141	8646,4360	2203	4300	6503	SO:0001583	missense	29062	exon6			ACACGAGGTGACT	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"""WD repeat domain containing"""	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.770C>T	7.37:g.134889141G>A	ENSP00000346466:p.Pro257Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	37	CCDS34758.1	1430	0.6547619047619048	259	0.5264227642276422	289	0.7983425414364641	339	0.5926573426573427	543	0.716358839050132	G	25.0	4.596691	0.86953	0.549932	0.723605	ENSG00000105875	ENST00000344400;ENST00000354475;ENST00000423565	T;T;T	0.66099	1.37;-0.19;0.39	5.4	5.4	0.78164	.	0.105818	0.64402	D	0.000002	T	0.00012	0.0000	L	0.32530	0.975	0.09310	P	0.9999939951	P	0.47677	0.899	B	0.41723	0.365	T	0.21449	-1.0245	9	0.21014	T	0.42	-4.9945	17.3703	0.87374	0.0:0.0:1.0:0.0	rs292592;rs1647888;rs10363224;rs11539106;rs17856532;rs52813949;rs59857001;rs292592	257	A4D1P6	WDR91_HUMAN	L	257;257;222	ENSP00000340877:P257L;ENSP00000346466:P257L;ENSP00000392555:P222L	ENSP00000340877:P257L	P	-	2	0	WDR91	134539681	1.000000	0.71417	0.636000	0.29352	0.954000	0.61252	6.474000	0.73578	2.548000	0.85928	0.655000	0.94253	CCT	G|0.349;A|0.651	0.651	strong		0.587	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149	
HIPK2	28996	hgsc.bcm.edu	37	7	139288937	139288937	+	Silent	SNP	C	C	T	rs34093649	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:139288937C>T	ENST00000406875.3	-	10	2239	c.2145G>A	c.(2143-2145)ctG>ctA	p.L715L	HIPK2_ENST00000428878.2_Silent_p.L688L|HIPK2_ENST00000342645.6_Silent_p.L715L	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	715	Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					CTGGGGGAAGCAGGATCTGCT	0.552													C|||	77	0.0153754	0.0234	0.0173	5008	,	,		19169	0.0089		0.0189	False		,,,				2504	0.0061				p.L715L		Atlas-SNP	.											.	HIPK2	192	.	0			c.G2145A						PASS	.	C	,	68,4176		1,66,2055	123.0	127.0	126.0		1014,1095	2.5	1.0	7	dbSNP_126	126	129,8329		0,129,4100	no	coding-synonymous,coding-synonymous	HIPK2	NM_001113239.2,NM_022740.4	,	1,195,6155	TT,TC,CC		1.5252,1.6023,1.5509	,	338/822,365/849	139288937	197,12505	2122	4229	6351	SO:0001819	synonymous_variant	28996	exon10			GGGAAGCAGGATC	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.2145G>A	7.37:g.139288937C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	37																																																																																				C|0.981;T|0.019	0.019	strong		0.552	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
GTPBP4	23560	hgsc.bcm.edu	37	10	1046712	1046712	+	Silent	SNP	G	G	A	rs2306409	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:1046712G>A	ENST00000360803.4	+	7	832	c.750G>A	c.(748-750)gcG>gcA	p.A250A	GTPBP4_ENST00000491635.1_3'UTR|GTPBP4_ENST00000538293.1_Silent_p.A134A|GTPBP4_ENST00000545048.1_Silent_p.A203A	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	250	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		TCCGTGCTGCGGTCCTGTATG	0.552													G|||	2655	0.530152	0.407	0.5447	5008	,	,		18185	0.6111		0.5199	False		,,,				2504	0.6135				p.A250A		Atlas-SNP	.											.	GTPBP4	57	.	0			c.G750A						PASS	.	G		1916,2490	547.5+/-377.3	421,1074,708	186.0	160.0	169.0		750	-12.1	0.0	10	dbSNP_100	169	4540,4060	595.6+/-393.5	1200,2140,960	no	coding-synonymous	GTPBP4	NM_012341.2		1621,3214,1668	AA,AG,GG		47.2093,43.4862,49.6386		250/635	1046712	6456,6550	2203	4300	6503	SO:0001819	synonymous_variant	23560	exon7			TGCTGCGGTCCTG	AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"""G protein-binding protein CRFG"", "" GTP-binding protein"""					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.750G>A	10.37:g.1046712G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	141	139	0.985816	NM_012341	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Silent	SNP	ENST00000360803.4	37	CCDS31132.1																																																																																			G|0.492;N|0.000	.	strong		0.552	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341	
MPDZ	8777	hgsc.bcm.edu	37	9	13150558	13150558	+	Missense_Mutation	SNP	A	A	C	rs188840960	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:13150558A>C	ENST00000319217.7	-	25	3829	c.3582T>G	c.(3580-3582)agT>agG	p.S1194R	MPDZ_ENST00000546205.1_Missense_Mutation_p.S1208R|MPDZ_ENST00000541718.1_Missense_Mutation_p.S1194R|MPDZ_ENST00000538841.1_Missense_Mutation_p.S86R|MPDZ_ENST00000447879.1_Missense_Mutation_p.S1194R|MPDZ_ENST00000536827.1_Missense_Mutation_p.S1194R|MPDZ_ENST00000381022.2_Missense_Mutation_p.S1194R|MPDZ_ENST00000381015.4_Missense_Mutation_p.S1194R	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1194	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TGCCAGCTGGACTATCTTCCA	0.433													A|||	7	0.00139776	0.0015	0.0	5008	,	,		12656	0.0		0.005	False		,,,				2504	0.0				p.S1194R		Atlas-SNP	.											.	MPDZ	324	.	0			c.T3582G						PASS	.	A	ARG/SER	5,3753		0,5,1874	162.0	161.0	161.0		3582	2.5	1.0	9		161	74,8146		0,74,4036	yes	missense	MPDZ	NM_003829.3	110	0,79,5910	CC,CA,AA		0.9002,0.133,0.6595	probably-damaging	1194/2042	13150558	79,11899	1879	4110	5989	SO:0001583	missense	8777	exon25			AGCTGGACTATCT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.3582T>G	9.37:g.13150558A>C	ENSP00000320006:p.Ser1194Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	141	75	0.531915	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	18.56	3.649452	0.67358	0.00133	0.009002	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205;ENST00000433359;ENST00000542239	T;T;T;T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.95	2.47	0.30058	.	0.000000	0.53938	D	0.000053	T	0.50667	0.1629	M	0.92169	3.28	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;1.0	T	0.60786	-0.7194	10	0.87932	D	0	.	7.4829	0.27415	0.7093:0.0:0.2907:0.0	.	1194;86;1194;1144;1194	B7ZMI4;B7ZB24;O75970-3;E7EPZ1;O75970-2	.;.;.;.;.	R	1194;1194;1194;200;86;1194;1194;1194;1144;1208;86;86	ENSP00000320006:S1194R;ENSP00000439807:S1194R;ENSP00000370410:S1194R;ENSP00000444230:S200R;ENSP00000444717:S86R;ENSP00000444151:S1194R;ENSP00000415208:S1194R;ENSP00000370403:S1194R;ENSP00000446358:S1208R;ENSP00000389705:S86R;ENSP00000443672:S86R	ENSP00000320006:S1194R	S	-	3	2	MPDZ	13140558	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	1.439000	0.35013	1.089000	0.41292	0.533000	0.62120	AGT	A|0.997;C|0.003	0.003	strong		0.433	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
COL3A1	1281	hgsc.bcm.edu	37	2	189864080	189864080	+	Missense_Mutation	SNP	G	G	A	rs1800255	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:189864080G>A	ENST00000304636.3	+	30	2262	c.2092G>A	c.(2092-2094)Gct>Act	p.A698T	COL3A1_ENST00000317840.5_Missense_Mutation_p.A698T	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	698	Triple-helical region.		A -> T (in dbSNP:rs1800255). {ECO:0000269|PubMed:18272325, ECO:0000269|PubMed:2235526}.		aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TAGAGGTGGAGCTGGTCCCCC	0.463													G|||	1094	0.21845	0.1051	0.2522	5008	,	,		15459	0.2331		0.2624	False		,,,				2504	0.2873				p.A698T		Atlas-SNP	.											.	COL3A1	292	.	0			c.G2092A	GRCh37	CM086593	COL3A1	M	rs1800255	PASS	.	G	THR/ALA	592,3814		40,512,1651	36.0	38.0	37.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2092	0.9	1.0	2	dbSNP_89	37	2190,6410		297,1596,2407	yes	missense	COL3A1	NM_000090.3	58	337,2108,4058	AA,AG,GG		25.4651,13.4362,21.3901	benign	698/1467	189864080	2782,10224	2203	4300	6503	SO:0001583	missense	1281	exon30			GGTGGAGCTGGTC	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2092G>A	2.37:g.189864080G>A	ENSP00000304408:p.Ala698Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	456	0.2087912087912088	39	0.07926829268292683	85	0.23480662983425415	139	0.243006993006993	193	0.2546174142480211	G	14.88	2.666284	0.47677	0.134362	0.254651	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.93488	-3.23;-3.22	4.96	0.873	0.19118	.	0.169588	0.27912	N	0.017354	T	0.00073	0.0002	N	0.16266	0.395	0.34524	P	0.291559	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	9	0.28530	T	0.3	.	1.7367	0.02943	0.2601:0.2137:0.4107:0.1155	rs1800255;rs3817316;rs17831227;rs52832986;rs1800255	698	P02461	CO3A1_HUMAN	T	698	ENSP00000304408:A698T;ENSP00000315243:A698T	ENSP00000304408:A698T	A	+	1	0	COL3A1	189572325	0.046000	0.20272	0.979000	0.43373	0.998000	0.95712	0.487000	0.22356	0.246000	0.21394	0.650000	0.86243	GCT	G|0.808;A|0.192	0.192	strong		0.463	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
MYO3A	53904	hgsc.bcm.edu	37	10	26357747	26357747	+	Silent	SNP	C	C	T	rs35379457|rs386742102	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:26357747C>T	ENST00000265944.5	+	12	1270	c.1104C>T	c.(1102-1104)taC>taT	p.Y368Y	MYO3A_ENST00000543632.1_Silent_p.Y368Y	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	368	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ATCAGATCTACGTCTATGTGG	0.368													T|||	1986	0.396565	0.3124	0.3516	5008	,	,		17370	0.2956		0.5616	False		,,,				2504	0.4765				p.Y368Y		Atlas-SNP	.											MYO3A,brain,glioma,0,3	MYO3A	371	3	0			c.C1104T						PASS	.	T		1479,2927		312,855,1036	140.0	123.0	129.0		1104	-4.0	0.5	10	dbSNP_126	129	4424,4176		1328,1768,1204	no	coding-synonymous	MYO3A	NM_017433.4		1640,2623,2240	TT,TC,CC		48.5581,33.5679,45.3867		368/1617	26357747	5903,7103	2203	4300	6503	SO:0001819	synonymous_variant	53904	exon12			GATCTACGTCTAT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1104C>T	10.37:g.26357747C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																			C|0.552;T|0.448	0.448	strong		0.368	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
GLDC	2731	hgsc.bcm.edu	37	9	6610326	6610326	+	Silent	SNP	C	C	T	rs35374927	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:6610326C>T	ENST00000321612.6	-	4	651	c.501G>A	c.(499-501)gaG>gaA	p.E167E		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	167					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	CCTGAGACACCTCAGGCTGGT	0.498													C|||	962	0.192093	0.1437	0.1902	5008	,	,		18973	0.0863		0.2753	False		,,,				2504	0.2822				p.E167E		Atlas-SNP	.											.	GLDC	118	.	0			c.G501A						PASS	.	C		640,3766	276.3+/-273.0	44,552,1607	63.0	52.0	56.0		501	1.5	1.0	9	dbSNP_126	56	2432,6168	402.3+/-347.4	351,1730,2219	no	coding-synonymous	GLDC	NM_000170.2		395,2282,3826	TT,TC,CC		28.2791,14.5256,23.6199		167/1021	6610326	3072,9934	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon4			AGACACCTCAGGC	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"""glycine cleavage system protein P"", ""glycine decarboxylase"""	238300	"""glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"""			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.501G>A	9.37:g.6610326C>T		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	150	79	0.526667	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			C|0.773;T|0.227	0.227	strong		0.498	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28366151	28366151	+	Missense_Mutation	SNP	A	A	G	rs2232423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28366151A>G	ENST00000361028.1	-	2	177	c.32T>C	c.(31-33)aTg>aCg	p.M11T	ZSCAN12_ENST00000396827.3_Missense_Mutation_p.M11T			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12	11					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						ATCCTGGTCCATGTGGGCCTG	0.468													A|||	116	0.0231629	0.0242	0.0216	5008	,	,		18098	0.0		0.0686	False		,,,				2504	0.0				p.M11T		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.T32C						PASS	.	A	THR/MET	58,1326		2,54,636	184.0	161.0	168.0		32	-0.9	0.0	6	dbSNP_98	168	306,2876		11,284,1296	yes	missense	ZSCAN12	NM_001163391.1	81	13,338,1932	GG,GA,AA		9.6166,4.1908,7.972	benign	11/612	28366151	364,4202	692	1591	2283	SO:0001583	missense	9753	exon2			TGGTCCATGTGGG	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.32T>C	6.37:g.28366151A>G	ENSP00000354305:p.Met11Thr	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	353	140	0.396601	NM_001163391	O43724	Missense_Mutation	SNP	ENST00000361028.1	37		76	0.0347985347985348	11	0.022357723577235773	8	0.022099447513812154	0	0.0	57	0.07519788918205805	A	3.426	-0.117064	0.06838	0.041908	0.096166	ENSG00000158691	ENST00000361028;ENST00000396827	T;T	0.06068	3.35;3.35	3.26	-0.902	0.10537	.	0.992491	0.08160	N	0.988573	T	0.00754	0.0025	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48896	-0.8994	10	0.27785	T	0.31	.	0.7463	0.00982	0.2025:0.1214:0.1994:0.4767	rs2232423;rs52816048;rs2232423	11;11	A8K187;O43309	.;ZSC12_HUMAN	T	11	ENSP00000354305:M11T;ENSP00000380039:M11T	ENSP00000354305:M11T	M	-	2	0	ZSCAN12	28474130	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.260000	0.02858	-0.281000	0.09141	-0.418000	0.06021	ATG	A|0.959;G|0.041	0.041	strong		0.468	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
BCKDK	10295	hgsc.bcm.edu	37	16	31121793	31121793	+	Silent	SNP	G	G	A	rs14235	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:31121793G>A	ENST00000394951.1	+	8	1238	c.615G>A	c.(613-615)acG>acA	p.T205T	BCKDK_ENST00000287507.3_Silent_p.T205T|BCKDK_ENST00000394950.3_Silent_p.T205T|AC135050.1_ENST00000517000.2_RNA|BCKDK_ENST00000219794.6_Silent_p.T205T			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	205	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|stomach(1)	2						TGTTGGCCACGCATCACCTGG	0.567													G|||	1799	0.359225	0.0893	0.3833	5008	,	,		18067	0.8849		0.3817	False		,,,				2504	0.1421				p.T205T		Atlas-SNP	.											BCKDK_ENST00000394951,rectum,carcinoma,0,2	BCKDK	52	2	0			c.G615A						PASS	.	G	,	592,3802	255.8+/-260.9	44,504,1649	62.0	63.0	63.0		615,615	-9.0	0.9	16	dbSNP_52	63	3344,5256	492.2+/-373.3	638,2068,1594	no	coding-synonymous,coding-synonymous	BCKDK	NM_001122957.1,NM_005881.2	,	682,2572,3243	AA,AG,GG		38.8837,13.4729,30.2909	,	205/366,205/413	31121793	3936,9058	2197	4300	6497	SO:0001819	synonymous_variant	10295	exon7			GGCCACGCATCAC	AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.615G>A	16.37:g.31121793G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	122	64	0.52459	NM_005881	A8MY43|Q6FGL4|Q96G95|Q96IN5	Silent	SNP	ENST00000394951.1	37	CCDS10705.1																																																																																			G|0.642;A|0.358	0.358	strong		0.567	BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881	
LARS	51520	hgsc.bcm.edu	37	5	145543972	145543972	+	Silent	SNP	G	G	A	rs3763373	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145543972G>A	ENST00000394434.2	-	6	661	c.495C>T	c.(493-495)ggC>ggT	p.G165G	LARS_ENST00000545646.1_Silent_p.G119G|LARS_ENST00000274562.9_Silent_p.G138G|LARS_ENST00000511505.1_5'UTR|LARS_ENST00000510191.1_Silent_p.G111G	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	165					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.G165G(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	CATCAGACAGGCCAAGGGATT	0.378													A|||	910	0.181709	0.0076	0.3775	5008	,	,		16692	0.1984		0.2525	False		,,,				2504	0.1881				p.G165G		Atlas-SNP	.											LARS,NS,carcinoma,0,1	LARS	100	1	1	Substitution - coding silent(1)	stomach(1)	c.C495T						scavenged	.	A		266,4140	802.1+/-415.6	12,242,1949	148.0	155.0	153.0		495	-5.0	0.3	5	dbSNP_107	153	2401,6199	699.8+/-405.1	352,1697,2251	no	coding-synonymous	LARS	NM_020117.9		364,1939,4200	AA,AG,GG		27.9186,6.0372,20.5059		165/1177	145543972	2667,10339	2203	4300	6503	SO:0001819	synonymous_variant	51520	exon6			AGACAGGCCAAGG	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.495C>T	5.37:g.145543972G>A		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	253	68	0.268775	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			G|0.801;A|0.199	0.199	strong		0.378	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
ERI2	112479	hgsc.bcm.edu	37	16	20811681	20811681	+	Silent	SNP	C	C	T	rs2301771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20811681C>T	ENST00000357967.4	-	6	546	c.504G>A	c.(502-504)aaG>aaA	p.K168K	ERI2_ENST00000563117.1_Silent_p.K75K|ERI2_ENST00000389345.5_Intron|ERI2_ENST00000569729.1_Silent_p.K168K|ERI2_ENST00000300005.3_Silent_p.K168K|ERI2_ENST00000564349.1_Silent_p.K75K	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	168	Exonuclease.						exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						TTAACAGCTGCTTTCTTTTAC	0.358													T|||	3154	0.629792	0.6452	0.6326	5008	,	,		15230	0.4435		0.7177	False		,,,				2504	0.7086				p.K168K		Atlas-SNP	.											ERI2_ENST00000357967,colon,carcinoma,-1,2	ERI2	50	2	0			c.G504A						scavenged	.	T	,	2917,1485	470.9+/-355.9	972,973,256	74.0	74.0	74.0		504,504	0.5	1.0	16	dbSNP_100	74	6267,2333	383.9+/-340.9	2282,1703,315	no	coding-synonymous,coding-synonymous	ERI2	NM_001142725.1,NM_080663.2	,	3254,2676,571	TT,TC,CC		27.1279,33.7347,29.3647	,	168/692,168/329	20811681	9184,3818	2201	4300	6501	SO:0001819	synonymous_variant	112479	exon6			CAGCTGCTTTCTT	BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678		"""Enhanced RNAi three prime mRNA exonucleases"""	30541	protein-coding gene	gene with protein product	"""enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans)"", ""exoribonuclease 2"", ""zinc finger, GRF-type containing 5"""		"""exonuclease domain containing 1"""	EXOD1		10819331	Standard	NM_080663		Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000357967.4:c.504G>A	16.37:g.20811681C>T		Somatic	276	2	0.00724638		WXS	Illumina HiSeq	Phase_I	252	110	0.436508	NM_080663	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Silent	SNP	ENST00000357967.4	37	CCDS45436.1																																																																																			C|0.331;T|0.669	0.669	strong		0.358	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663	
SVIL	6840	hgsc.bcm.edu	37	10	29754609	29754609	+	Silent	SNP	T	T	C	rs1057952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:29754609T>C	ENST00000355867.4	-	34	6800	c.6048A>G	c.(6046-6048)acA>acG	p.T2016T	SVIL_ENST00000375398.2_Silent_p.T2016T|SVIL_ENST00000375400.3_Silent_p.T1590T|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000535393.1_Silent_p.T930T|PTCHD3P1_ENST00000455774.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2016					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.T2016T(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ACACAAACTCTGTGGCTGCAA	0.557													C|||	2119	0.423123	0.3638	0.4323	5008	,	,		16072	0.5625		0.3817	False		,,,				2504	0.3957				p.T2016T		Atlas-SNP	.											SVIL,NS,carcinoma,0,1	SVIL	226	1	1	Substitution - coding silent(1)	stomach(1)	c.A6048G						PASS	.	C	,	1667,2739	647.6+/-398.6	316,1035,852	36.0	41.0	39.0		4770,6048	-9.4	0.0	10	dbSNP_86	39	2973,5627	656.6+/-401.4	531,1911,1858	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	847,2946,2710	CC,CT,TT		34.5698,37.8348,35.6758	,	1590/1789,2016/2215	29754609	4640,8366	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon34			AAACTCTGTGGCT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.6048A>G	10.37:g.29754609T>C		Somatic	403	0	0		WXS	Illumina HiSeq	Phase_I	390	203	0.520513	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			T|0.629;C|0.371	0.371	strong		0.557	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
C19orf40	91442	hgsc.bcm.edu	37	19	33467576	33467576	+	Silent	SNP	G	G	A	rs7258185	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33467576G>A	ENST00000588258.1	+	5	746	c.636G>A	c.(634-636)acG>acA	p.T212T	C19orf40_ENST00000590179.1_Silent_p.T117T|C19orf40_ENST00000590281.1_Silent_p.T212T|C19orf40_ENST00000589646.1_Silent_p.T117T	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	212	RuvA domain 2-like.				DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					CCTTCTTCACGCAGCCCAGGT	0.537								Direct reversal of damage			OREG0025408	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	1346	0.26877	0.3094	0.4366	5008	,	,		19432	0.1647		0.2157	False		,,,				2504	0.2566				p.T212T		Atlas-SNP	.											.	C19orf40	21	.	0			c.G636A						PASS	.	A		1337,3069	694.4+/-405.8	196,945,1062	83.0	75.0	78.0		636	-3.4	0.8	19	dbSNP_116	78	1979,6621	723.3+/-406.4	202,1575,2523	no	coding-synonymous	C19orf40	NM_152266.3		398,2520,3585	AA,AG,GG		23.0116,30.345,25.4959		212/216	33467576	3316,9690	2203	4300	6503	SO:0001819	synonymous_variant	91442	exon5			CTTCACGCAGCCC	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 24kDa"""	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.636G>A	19.37:g.33467576G>A		Somatic	87	0	0	840	WXS	Illumina HiSeq	Phase_I	112	44	0.392857	NM_152266	B3KY46|Q8WUJ7|Q96FX6	Silent	SNP	ENST00000588258.1	37	CCDS12426.1																																																																																			G|0.753;A|0.247	0.247	strong		0.537	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266	
FAM47E	100129583	hgsc.bcm.edu	37	4	77192868	77192868	+	Missense_Mutation	SNP	G	G	A	rs3733250	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:77192868G>A	ENST00000424749.2	+	5	823	c.817G>A	c.(817-819)Gag>Aag	p.E273K	FAM47E_ENST00000510197.1_Missense_Mutation_p.E175K|FAM47E_ENST00000339906.6_Missense_Mutation_p.E175K|FAM47E-STBD1_ENST00000539752.1_5'UTR|FAM47E_ENST00000515604.1_Missense_Mutation_p.E273K	NM_001136570.2	NP_001130042.1	Q6ZV65	FA47E_HUMAN	family with sequence similarity 47, member E	273				E -> K (in Ref. 1; BAC85998). {ECO:0000305}.													TAAACTGCAGGAGACAGAGTT	0.463													G|||	1603	0.320088	0.1717	0.428	5008	,	,		18148	0.3224		0.4076	False		,,,				2504	0.3517				p.E273K		Atlas-SNP	.											.	.	.	.	0			c.G817A						PASS	.	G	LYS/GLU	311,1073		38,235,419	103.0	87.0	92.0		817	0.5	0.0	4	dbSNP_107	92	1317,1865		273,771,547	yes	missense	FAM47E	NM_001136570.2	56	311,1006,966	AA,AG,GG		41.3891,22.4711,35.6548	benign	273/394	77192868	1628,2938	692	1591	2283	SO:0001583	missense	0	exon5			CTGCAGGAGACAG	AC034139, AK124936, CR591456, CR627383	CCDS47081.1, CCDS58907.1	4q21.1	2013-04-23			ENSG00000189157	ENSG00000189157			34343	protein-coding gene	gene with protein product	"""similar to genethonin 1"""						Standard	NM_001136570		Approved	FLJ42946, LOC100129583	uc003hjx.3	Q6ZV65	OTTHUMG00000185390	ENST00000424749.2:c.817G>A	4.37:g.77192868G>A	ENSP00000409423:p.Glu273Lys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	99	55	0.555556	NM_001242939	D6R8Y4	Missense_Mutation	SNP	ENST00000424749.2	37	CCDS47081.1	761	0.3484432234432234	109	0.22154471544715448	140	0.3867403314917127	197	0.34440559440559443	315	0.4155672823218997	G	12.22	1.873593	0.33069	0.224711	0.413891	ENSG00000189157	ENST00000510197;ENST00000339906;ENST00000515604;ENST00000509377;ENST00000424749;ENST00000514140	T;T;T;T	0.47869	0.83;0.83;1.39;1.42	4.74	0.488	0.16848	.	0.797101	0.10624	N	0.652981	T	0.00012	0.0000	M	0.62088	1.915	0.58432	P	9.000000000036756E-6	B;P;B;B;B	0.35656	0.11;0.514;0.154;0.015;0.041	B;B;B;B;B	0.29862	0.018;0.108;0.078;0.028;0.011	T	0.36792	-0.9733	9	0.54805	T	0.06	-1.7053	3.9358	0.09305	0.3515:0.1752:0.4734:0.0	rs3733250;rs17236563;rs52802996;rs56884110;rs3733250	120;273;273;273;175	D6RCS4;Q6ZV65-1;Q6ZV65;C9JTC9;Q6ZV65-2	.;.;FA47E_HUMAN;.;.	K	175;175;273;120;273;81	ENSP00000422262:E175K;ENSP00000340401:E175K;ENSP00000422067:E273K;ENSP00000409423:E273K	ENSP00000340401:E175K	E	+	1	0	FAM47E	77411892	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	0.138000	0.16016	-0.049000	0.13379	0.655000	0.94253	GAG	G|0.650;A|0.350	0.350	strong		0.463	FAM47E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362528.2	NM_001136570	
SCN10A	6336	hgsc.bcm.edu	37	3	38748833	38748833	+	Silent	SNP	T	T	C	rs6790627	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:38748833T>C	ENST00000449082.2	-	25	4322	c.4323A>G	c.(4321-4323)aaA>aaG	p.K1441K		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1441					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K1441K(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CATTGTAGTATTTCTTCTGCT	0.542													C|||	1214	0.242412	0.3578	0.2104	5008	,	,		19164	0.3115		0.1571	False		,,,				2504	0.1258				p.K1441K		Atlas-SNP	.											SCN10A,NS,carcinoma,0,1	SCN10A	359	1	1	Substitution - coding silent(1)	stomach(1)	c.A4323G						PASS	.	C		1500,2906	676.4+/-403.2	263,974,966	131.0	139.0	136.0		4323	1.7	1.0	3	dbSNP_116	136	1230,7370	762.2+/-407.6	75,1080,3145	no	coding-synonymous	SCN10A	NM_006514.2		338,2054,4111	CC,CT,TT		14.3023,34.0445,20.9903		1441/1957	38748833	2730,10276	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon25			GTAGTATTTCTTC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4323A>G	3.37:g.38748833T>C		Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	269	160	0.594796	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			T|0.796;C|0.204	0.204	strong		0.542	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
COL6A5	256076	hgsc.bcm.edu	37	3	130095179	130095179	+	Missense_Mutation	SNP	T	T	C	rs113396273	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:130095179T>C	ENST00000432398.2	+	3	661	c.167T>C	c.(166-168)aTg>aCg	p.M56T	COL6A5_ENST00000265379.6_Missense_Mutation_p.M56T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	56	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ATCAACAAAATGATCAACAGT	0.512													T|||	52	0.0103834	0.0008	0.0072	5008	,	,		18183	0.0		0.0219	False		,,,				2504	0.0245				p.M56T		Atlas-SNP	.											.	COL6A5	205	.	0			c.T167C	GRCh37	CM076120	COL6A5	M	rs113396273	PASS	.	T	THR/MET	9,1375		0,9,683	113.0	93.0	99.0		167	5.1	0.2	3	dbSNP_132	99	86,3096		1,84,1506	yes	missense	COL6A5	NM_153264.5	81	1,93,2189	CC,CT,TT		2.7027,0.6503,2.0806	benign	56/2527	130095179	95,4471	692	1591	2283	SO:0001583	missense	256076	exon3			ACAAAATGATCAA	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.167T>C	3.37:g.130095179T>C	ENSP00000390895:p.Met56Thr	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		25	0.011446886446886446	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	20	0.026385224274406333	T	3.317	-0.139498	0.06669	0.006503	0.027027	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.78003	-1.14;-1.14	5.14	5.14	0.70334	.	.	.	.	.	T	0.46210	0.1381	L	0.36672	1.1	0.09310	N	0.999999	B	0.17038	0.02	B	0.21708	0.036	T	0.54186	-0.8331	9	0.52906	T	0.07	.	9.402	0.38437	0.0:0.085:0.0:0.915	.	56	A8TX70-2	.	T	56	ENSP00000390895:M56T;ENSP00000265379:M56T	ENSP00000265379:M56T	M	+	2	0	COL6A5	131577869	0.728000	0.28080	0.184000	0.23157	0.108000	0.19459	3.906000	0.56340	2.064000	0.61679	0.455000	0.32223	ATG	T|0.989;C|0.011	0.011	strong		0.512	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
MUC4	4585	hgsc.bcm.edu	37	3	195508235	195508235	+	Missense_Mutation	SNP	T	T	C	rs201826718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508235T>C	ENST00000463781.3	-	2	10675	c.10216A>G	c.(10216-10218)Acc>Gcc	p.T3406A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3406A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGCATGGTGTCACCTGTG	0.587																																					p.T3406A		Atlas-SNP	.											.	MUC4	1505	.	0			c.A10216G						PASS	.						29.0	22.0	24.0					3																	195508235		686	1575	2261	SO:0001583	missense	4585	exon2			GCATGGTGTCACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10216A>G	3.37:g.195508235T>C	ENSP00000417498:p.Thr3406Ala	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	364	28	0.0769231	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	t	4.225	0.040596	0.08196	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.53	0.743	0.743	0.18347	.	.	.	.	.	T	0.10078	0.0247	N	0.08118	0	0.09310	N	1	P	0.37985	0.613	B	0.25140	0.058	T	0.17410	-1.0370	8	.	.	.	.	3.5009	0.07673	0.0:0.0:0.4186:0.5813	.	3278	E7ESK3	.	A	3406	ENSP00000417498:T3406A;ENSP00000420243:T3406A	.	T	-	1	0	MUC4	196993014	0.000000	0.05858	0.010000	0.14722	0.010000	0.07245	-1.539000	0.02202	0.077000	0.16863	0.076000	0.15429	ACC	T|0.006;C|0.994	0.994	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GPR142	350383	hgsc.bcm.edu	37	17	72366771	72366771	+	Missense_Mutation	SNP	T	T	C	rs138812881		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72366771T>C	ENST00000335666.4	+	3	518	c.470T>C	c.(469-471)gTc>gCc	p.V157A		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	157						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						GTGGCTGGCGTCATCCCTGTC	0.642													T|||	1	0.000199681	0.0	0.0	5008	,	,		14047	0.001		0.0	False		,,,				2504	0.0				p.V157A		Atlas-SNP	.											.	GPR142	74	.	0			c.T470C						PASS	.	T	ALA/VAL	0,4406		0,0,2203	100.0	84.0	90.0		470	3.7	0.0	17	dbSNP_134	90	16,8584	11.9+/-42.8	0,16,4284	yes	missense	GPR142	NM_181790.1	64	0,16,6487	CC,CT,TT		0.186,0.0,0.123	possibly-damaging	157/463	72366771	16,12990	2203	4300	6503	SO:0001583	missense	350383	exon3			CTGGCGTCATCCC	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"""GPCR / Class A : Orphans"""	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.470T>C	17.37:g.72366771T>C	ENSP00000335158:p.Val157Ala	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	187	91	0.486631	NM_181790	A4CYJ8|Q86SL3	Missense_Mutation	SNP	ENST00000335666.4	37	CCDS11698.1	.	.	.	.	.	.	.	.	.	.	T	13.53	2.264799	0.40095	0.0	0.00186	ENSG00000257008	ENST00000335666	T	0.38077	1.16	4.81	3.7	0.42460	.	0.301194	0.32473	N	0.006046	T	0.28001	0.0690	N	0.19112	0.55	0.09310	N	1	B;P	0.49447	0.039;0.924	B;P	0.47044	0.014;0.535	T	0.06041	-1.0849	10	0.48119	T	0.1	-15.9965	9.3696	0.38246	0.0:0.089:0.0:0.911	.	157;1119	Q7Z601;Q8NGB0	GP142_HUMAN;.	A	157	ENSP00000335158:V157A	ENSP00000335158:V157A	V	+	2	0	GPR142	69878366	0.272000	0.24172	0.002000	0.10522	0.911000	0.54048	2.875000	0.48491	0.908000	0.36671	0.397000	0.26171	GTC	T|0.999;C|0.001	0.001	strong		0.642	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790	
E2F7	144455	hgsc.bcm.edu	37	12	77419593	77419593	+	Silent	SNP	A	A	G	rs310830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:77419593A>G	ENST00000322886.7	-	12	2545	c.2310T>C	c.(2308-2310)tcT>tcC	p.S770S	E2F7_ENST00000416496.2_Intron	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	770					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						CACCAAGAGTAGAAGAAACCG	0.542													A|||	212	0.0423323	0.0045	0.0677	5008	,	,		17686	0.0		0.1402	False		,,,				2504	0.0184				p.S770S		Atlas-SNP	.											.	E2F7	201	.	0			c.T2310C						PASS	.	A		104,4302	79.9+/-118.3	2,100,2101	50.0	52.0	51.0		2310	-1.6	0.1	12	dbSNP_79	51	1051,7549	222.4+/-259.5	67,917,3316	no	coding-synonymous	E2F7	NM_203394.2		69,1017,5417	GG,GA,AA		12.2209,2.3604,8.8805		770/912	77419593	1155,11851	2203	4300	6503	SO:0001819	synonymous_variant	144455	exon12			AAGAGTAGAAGAA	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.2310T>C	12.37:g.77419593A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1																																																																																			A|0.919;G|0.081	0.081	strong		0.542	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151161018	151161018	+	Silent	SNP	A	A	G	rs17348890	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:151161018A>G	ENST00000358517.2	+	16	3355	c.3144A>G	c.(3142-3144)agA>agG	p.R1048R	PLEKHG1_ENST00000367328.1_Silent_p.R1048R			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1048							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		TTGTATTCAGAGAGTCTCCCT	0.478													A|||	638	0.127396	0.0348	0.2133	5008	,	,		18591	0.1071		0.1461	False		,,,				2504	0.1933				p.R1048R		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A3144G						PASS	.	A		256,4150	146.1+/-180.8	2,252,1949	78.0	81.0	80.0		3144	2.2	1.0	6	dbSNP_123	80	1406,7194	271.7+/-289.7	138,1130,3032	yes	coding-synonymous	PLEKHG1	NM_001029884.1		140,1382,4981	GG,GA,AA		16.3488,5.8103,12.7787		1048/1386	151161018	1662,11344	2203	4300	6503	SO:0001819	synonymous_variant	57480	exon17			ATTCAGAGAGTCT	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.3144A>G	6.37:g.151161018A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	155	82	0.529032	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																			A|0.883;G|0.117	0.117	strong		0.478	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
COLEC11	78989	hgsc.bcm.edu	37	2	3673648	3673648	+	Intron	SNP	G	G	A	rs10170348	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:3673648G>A	ENST00000349077.4	+	4	305				COLEC11_ENST00000382062.2_Intron|COLEC11_ENST00000404205.1_Intron|COLEC11_ENST00000403096.3_Intron|COLEC11_ENST00000402794.1_Intron|COLEC11_ENST00000418971.2_Intron|COLEC11_ENST00000236693.7_Silent_p.K53K|COLEC11_ENST00000402922.1_Intron|COLEC11_ENST00000487365.1_Intron	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11						developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		CCAAAAGGAAGTGCACCTCGT	0.453													G|||	597	0.119209	0.0129	0.0735	5008	,	,		21665	0.3115		0.1571	False		,,,				2504	0.0583				p.K53K		Atlas-SNP	.											.	COLEC11	93	.	0			c.G159A						PASS	.	G	,	164,4242	108.6+/-147.0	6,152,2045	193.0	189.0	191.0		,159	-2.2	0.0	2	dbSNP_119	191	1240,7360	249.2+/-276.5	95,1050,3155	no	intron,coding-synonymous	COLEC11	NM_024027.3,NM_199235.1	,	101,1202,5200	AA,AG,GG		14.4186,3.7222,10.795	,	,53/269	3673648	1404,11602	2203	4300	6503	SO:0001627	intron_variant	78989	exon4			AAGGAAGTGCACC	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"""Collectins"""	17213	protein-coding gene	gene with protein product	"""Collectin K1"""	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.203-11475G>A	2.37:g.3673648G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_199235	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Silent	SNP	ENST00000349077.4	37	CCDS1649.1																																																																																			G|0.878;A|0.122	0.122	strong		0.453	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027	
SULT2B1	6820	hgsc.bcm.edu	37	19	49079246	49079246	+	Silent	SNP	C	C	T	rs2544794	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49079246C>T	ENST00000201586.2	+	2	298	c.120C>T	c.(118-120)ccC>ccT	p.P40P	SULT2B1_ENST00000323090.4_Silent_p.P25P	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	40					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		TCCCCTTCCCCGTCGGCCTGT	0.587													C|||	652	0.130192	0.23	0.1023	5008	,	,		14059	0.003		0.1481	False		,,,				2504	0.1278				p.P40P		Atlas-SNP	.											.	SULT2B1	72	.	0			c.C120T						PASS	.	C	,	1010,3396	373.7+/-320.9	119,772,1312	150.0	117.0	128.0		75,120	-5.5	0.0	19	dbSNP_100	128	1396,7204	271.1+/-289.3	125,1146,3029	no	coding-synonymous,coding-synonymous	SULT2B1	NM_004605.2,NM_177973.1	,	244,1918,4341	TT,TC,CC		16.2326,22.9233,18.4992	,	25/351,40/366	49079246	2406,10600	2203	4300	6503	SO:0001819	synonymous_variant	6820	exon2			CTTCCCCGTCGGC	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.120C>T	19.37:g.49079246C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_177973	O00205|O75814	Silent	SNP	ENST00000201586.2	37	CCDS12723.1																																																																																			C|0.852;T|0.148	0.148	strong		0.587	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
MTHFR	4524	hgsc.bcm.edu	37	1	11863057	11863057	+	Silent	SNP	G	G	A	rs2066470	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11863057G>A	ENST00000376592.1	-	1	245	c.117C>T	c.(115-117)ccC>ccT	p.P39P	MTHFR_ENST00000376583.3_Silent_p.P80P|MTHFR_ENST00000376590.3_Silent_p.P39P|MTHFR_ENST00000376585.1_Silent_p.P80P			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	39					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	CATGCCGCTCGGGGTCCAGGC	0.592													G|||	509	0.101637	0.0719	0.0548	5008	,	,		18607	0.123		0.0984	False		,,,				2504	0.1564				p.P39P		Atlas-SNP	.											.	MTHFR	65	.	0			c.C117T						PASS	.	G		345,4061	180.1+/-208.5	15,315,1873	60.0	57.0	58.0		117	-11.3	0.0	1	dbSNP_94	58	822,7778	190.8+/-237.2	41,740,3519	no	coding-synonymous	MTHFR	NM_005957.4		56,1055,5392	AA,AG,GG		9.5581,7.8302,8.9728		39/657	11863057	1167,11839	2203	4300	6503	SO:0001819	synonymous_variant	4524	exon2			CCGCTCGGGGTCC	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.117C>T	1.37:g.11863057G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	124	42	0.33871	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Silent	SNP	ENST00000376592.1	37	CCDS137.1																																																																																			G|0.910;A|0.090	0.090	strong		0.592	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
DPP3	10072	hgsc.bcm.edu	37	11	66272237	66272237	+	Missense_Mutation	SNP	G	G	A	rs2305535	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66272237G>A	ENST00000360510.2	+	17	2098	c.2033G>A	c.(2032-2034)cGc>cAc	p.R678H	DPP3_ENST00000531863.1_Missense_Mutation_p.R698H|DPP3_ENST00000541961.1_Missense_Mutation_p.R678H|DPP3_ENST00000532677.1_Missense_Mutation_p.R697H|DPP3_ENST00000530165.1_Missense_Mutation_p.R648H|DPP3_ENST00000453114.1_Missense_Mutation_p.R678H			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	678			R -> H (in dbSNP:rs2305535). {ECO:0000269|PubMed:9425109, ECO:0000269|Ref.1}.		proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						CCCAACACTCGCCTTGAAGGT	0.567													G|||	1060	0.211661	0.1475	0.1614	5008	,	,		19222	0.3036		0.2396	False		,,,				2504	0.2106				p.R678H		Atlas-SNP	.											.	DPP3	61	.	0			c.G2033A						PASS	.	G	HIS/ARG,HIS/ARG	587,3813	260.1+/-263.5	34,519,1647	109.0	97.0	101.0		2033,2033	4.5	1.0	11	dbSNP_100	101	1981,6609	348.1+/-326.9	222,1537,2536	yes	missense,missense	DPP3	NM_005700.3,NM_130443.2	29,29	256,2056,4183	AA,AG,GG		23.0617,13.3409,19.7691	possibly-damaging,possibly-damaging	678/738,678/738	66272237	2568,10422	2200	4295	6495	SO:0001583	missense	10072	exon17			ACACTCGCCTTGA	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.2033G>A	11.37:g.66272237G>A	ENSP00000353701:p.Arg678His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_130443	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Missense_Mutation	SNP	ENST00000360510.2	37	CCDS8141.1	497	0.22756410256410256	60	0.12195121951219512	73	0.20165745856353592	170	0.2972027972027972	194	0.2559366754617414	G	9.045	0.990693	0.18966	0.133409	0.230617	ENSG00000254986	ENST00000531863;ENST00000532677;ENST00000360510;ENST00000453114;ENST00000541961;ENST00000530165;ENST00000543807;ENST00000347422	T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93	5.43	4.52	0.55395	.	0.391294	0.27691	N	0.018250	T	0.00012	0.0000	L	0.33485	1.01	0.49687	P	1.8499999999999073E-4	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.003	T	0.27806	-1.0063	9	0.02654	T	1	.	12.1029	0.53794	0.0836:0.0:0.9164:0.0	rs2305535;rs3185806;rs17581177;rs52825912;rs60940855;rs2305535	697;678	G3V1D3;Q9NY33	.;DPP3_HUMAN	H	698;697;678;678;678;648;576;258	ENSP00000432782:R698H;ENSP00000435284:R697H;ENSP00000353701:R678H;ENSP00000389943:R678H;ENSP00000440502:R678H;ENSP00000436941:R648H	ENSP00000309957:R258H	R	+	2	0	DPP3	66028813	0.996000	0.38824	0.996000	0.52242	0.979000	0.70002	2.248000	0.43160	1.350000	0.45770	0.549000	0.68633	CGC	G|0.793;A|0.207	0.207	strong		0.567	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2		
SMYD4	114826	hgsc.bcm.edu	37	17	1704296	1704296	+	Missense_Mutation	SNP	C	C	A	rs7224496	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1704296C>A	ENST00000305513.7	-	5	559	c.392G>T	c.(391-393)aGa>aTa	p.R131I		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	131			R -> I (in dbSNP:rs7224496). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						TGTCTGTGCTCTGTTAATGTC	0.433													C|||	1439	0.28734	0.2073	0.2594	5008	,	,		19093	0.2688		0.4851	False		,,,				2504	0.2311				p.R131I		Atlas-SNP	.											.	SMYD4	50	.	0			c.G392T						PASS	.	C	ILE/ARG	1001,3405	359.9+/-315.0	106,789,1308	132.0	134.0	133.0		392	4.0	0.9	17	dbSNP_116	133	4198,4402	558.9+/-387.3	1007,2184,1109	yes	missense	SMYD4	NM_052928.2	97	1113,2973,2417	AA,AC,CC		48.814,22.719,39.9739	possibly-damaging	131/805	1704296	5199,7807	2203	4300	6503	SO:0001583	missense	114826	exon5			TGTGCTCTGTTAA	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.392G>T	17.37:g.1704296C>A	ENSP00000304360:p.Arg131Ile	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	131	60	0.458015	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	741	0.3392857142857143	91	0.18495934959349594	109	0.3011049723756906	157	0.2744755244755245	384	0.5065963060686016	C	13.14	2.148721	0.37923	0.22719	0.48814	ENSG00000186532	ENST00000305513	T	0.18810	2.19	5.98	3.97	0.46021	Tetratricopeptide-like helical (1);	0.518027	0.24193	N	0.040700	T	0.00012	0.0000	M	0.86028	2.79	0.20403	P	0.9999024143	D	0.63880	0.993	D	0.68943	0.961	T	0.47302	-0.9128	9	0.35671	T	0.21	-5.7323	9.7875	0.40686	0.0:0.7882:0.0:0.2118	rs7224496;rs11549831;rs17846126;rs17859131;rs60531171;rs7224496	131	Q8IYR2	SMYD4_HUMAN	I	131	ENSP00000304360:R131I	ENSP00000304360:R131I	R	-	2	0	SMYD4	1651046	1.000000	0.71417	0.942000	0.38095	0.069000	0.16628	3.005000	0.49521	0.844000	0.35094	-0.157000	0.13467	AGA	C|0.642;A|0.358	0.358	strong		0.433	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
SYNJ1	8867	hgsc.bcm.edu	37	21	34059352	34059352	+	Missense_Mutation	SNP	T	T	C	rs2254562	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:34059352T>C	ENST00000322229.7	-	7	883	c.884A>G	c.(883-885)aAa>aGa	p.K295R	SYNJ1_ENST00000357345.3_Missense_Mutation_p.K295R|SYNJ1_ENST00000433931.2_Missense_Mutation_p.K334R|SYNJ1_ENST00000382491.3_Missense_Mutation_p.K295R|SYNJ1_ENST00000382499.2_Missense_Mutation_p.K334R			O43426	SYNJ1_HUMAN	synaptojanin 1	295	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.		K -> R (in dbSNP:rs2254562). {ECO:0000269|PubMed:9428629}.		cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TATTATTTGTTTACCATATAA	0.289													T|||	1523	0.304113	0.2988	0.2882	5008	,	,		16567	0.3284		0.2873	False		,,,				2504	0.3149				p.K334R		Atlas-SNP	.											.	SYNJ1	253	.	0			c.A1001G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	1307,3093	435.9+/-344.5	198,911,1091	100.0	96.0	98.0		1001,1001,884,884	5.8	1.0	21	dbSNP_100	98	2559,6031	414.9+/-351.6	365,1829,2101	yes	missense,missense,missense,missense	SYNJ1	NM_203446.2,NM_003895.3,NM_001160306.1,NM_001160302.1	26,26,26,26	563,2740,3192	CC,CT,TT		29.7905,29.7045,29.7614	benign,benign,benign,benign	334/1351,334/1613,295/1527,295/1296	34059352	3866,9124	2200	4295	6495	SO:0001583	missense	8867	exon8			ATTTGTTTACCAT	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.884A>G	21.37:g.34059352T>C	ENSP00000322234:p.Lys295Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_203446	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	639	0.2925824175824176	123	0.25	100	0.27624309392265195	193	0.3374125874125874	223	0.2941952506596306	T	32	5.106299	0.94292	0.297045	0.297905	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229;ENST00000429236	T;T;T;T;T;T	0.59083	0.29;0.29;0.29;0.29;0.29;0.29	5.85	5.85	0.93711	Synaptojanin, N-terminal (2);	0.143592	0.64402	D	0.000005	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	0.9999999116388	B;P;B;D	0.63046	0.425;0.835;0.261;0.992	B;P;B;P	0.58660	0.221;0.471;0.324;0.843	T	0.04203	-1.0969	9	0.62326	D	0.03	.	16.2392	0.82399	0.0:0.0:0.0:1.0	rs2254562;rs52814583;rs61140656;rs2254562	334;295;295;295	C9JFZ1;O43426-2;O43426;O43426-4	.;.;SYNJ1_HUMAN;.	R	295;295;334;334;295;295	ENSP00000371931:K295R;ENSP00000349903:K295R;ENSP00000371939:K334R;ENSP00000409667:K334R;ENSP00000322234:K295R;ENSP00000413649:K295R	ENSP00000322234:K295R	K	-	2	0	SYNJ1	32981223	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.888000	0.87302	2.239000	0.73571	0.383000	0.25322	AAA	T|0.699;C|0.301	0.301	strong		0.289	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
BRDT	676	hgsc.bcm.edu	37	1	92457843	92457843	+	Missense_Mutation	SNP	C	C	T	rs10747493	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:92457843C>T	ENST00000362005.3	+	15	2505	c.2087C>T	c.(2086-2088)cCg>cTg	p.P696L	BRDT_ENST00000370389.2_Missense_Mutation_p.P623L|BRDT_ENST00000394530.3_Missense_Mutation_p.P650L|BRDT_ENST00000399546.2_Missense_Mutation_p.P696L|BRDT_ENST00000402388.1_Missense_Mutation_p.P696L	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	696			P -> L (in dbSNP:rs10747493). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15647849, ECO:0000269|PubMed:9367677, ECO:0000269|Ref.5}.		cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		GAATGCATACCGCCTGAAGGA	0.294													T|||	3556	0.710064	0.5908	0.7738	5008	,	,		13823	0.6081		0.8429	False		,,,				2504	0.7945				p.P700L		Atlas-SNP	.											.	BRDT	133	.	0			c.C2099T						PASS	.	T	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	2765,1641	463.0+/-353.4	870,1025,308	28.0	30.0	29.0		2087,2099,1949,1949,1868,2087,2087	0.0	0.0	1	dbSNP_120	29	7347,1241	236.2+/-268.5	3142,1063,89	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	98,98,98,98,98,98,98	4012,2088,397	TT,TC,CC		14.4504,37.2447,22.1795	benign,benign,benign,benign,benign,benign,benign	696/948,700/952,650/902,650/902,623/875,696/948,696/948	92457843	10112,2882	2203	4294	6497	SO:0001583	missense	676	exon14			GCATACCGCCTGA	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.2087C>T	1.37:g.92457843C>T	ENSP00000354568:p.Pro696Leu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	1557	0.7129120879120879	310	0.6300813008130082	280	0.7734806629834254	328	0.5734265734265734	639	0.8430079155672823	T	0.017	-1.498000	0.01001	0.627553	0.855496	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000394530;ENST00000402388	T;T;T;T;T	0.06218	3.33;3.34;3.33;3.39;3.33	2.7	0.0309	0.14168	.	1.525420	0.04848	N	0.441804	T	0.00784	0.0026	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47302	-0.9128	9	0.40728	T	0.16	30.9298	2.4313	0.04472	0.4323:0.1373:0.0:0.4305	rs10747493;rs52795206;rs60238775;rs10747493	650;696	B7Z811;Q58F21	.;BRDT_HUMAN	L	696;623;696;650;696	ENSP00000354568:P696L;ENSP00000359416:P623L;ENSP00000387822:P696L;ENSP00000378038:P650L;ENSP00000384051:P696L	ENSP00000354568:P696L	P	+	2	0	BRDT	92230431	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.908000	0.04063	-0.347000	0.08299	-0.550000	0.04213	CCG	C|0.259;T|0.741	0.741	strong		0.294	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
PCNXL2	80003	hgsc.bcm.edu	37	1	233134086	233134086	+	Missense_Mutation	SNP	C	C	T	rs56231757	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:233134086C>T	ENST00000258229.9	-	32	5936	c.5702G>A	c.(5701-5703)aGt>aAt	p.S1901N	PCNXL2_ENST00000344698.2_Missense_Mutation_p.S553N	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1901			S -> N (in dbSNP:rs56231757). {ECO:0000269|PubMed:9455477}.			integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				GCTGCCACCACTCGGGGCATT	0.627													C|||	919	0.183506	0.2542	0.1657	5008	,	,		18270	0.12		0.2147	False		,,,				2504	0.1339				p.S1901N		Atlas-SNP	.											.	PCNXL2	204	.	0			c.G5702A						PASS	.	C	ASN/SER	1011,3043		106,799,1122	47.0	48.0	48.0		5702	3.8	0.0	1	dbSNP_129	48	1921,6477		222,1477,2500	yes	missense	PCNXL2	NM_014801.3	46	328,2276,3622	TT,TC,CC		22.8745,24.9383,23.5464	benign	1901/2138	233134086	2932,9520	2027	4199	6226	SO:0001583	missense	80003	exon32			CCACCACTCGGGG	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5702G>A	1.37:g.233134086C>T	ENSP00000258229:p.Ser1901Asn	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	434	0.1987179487179487	132	0.2682926829268293	67	0.1850828729281768	75	0.13111888111888112	160	0.21108179419525067	C	13.99	2.402301	0.42613	0.249383	0.228745	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.23754	1.89;3.06	5.71	3.82	0.43975	.	0.900119	0.09944	N	0.735589	T	0.00012	0.0000	L	0.31294	0.92	0.41241	P	0.01335900000000001	B;B	0.11235	0.0;0.004	B;B	0.09377	0.002;0.004	T	0.29027	-1.0025	9	0.44086	T	0.13	.	9.345	0.38102	0.0:0.7795:0.0:0.2205	rs56231757;rs61738804	1901;553	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	N	553;1901	ENSP00000340759:S553N;ENSP00000258229:S1901N	ENSP00000258229:S1901N	S	-	2	0	PCNXL2	231200709	0.003000	0.15002	0.009000	0.14445	0.119000	0.20118	1.895000	0.39778	0.757000	0.33036	0.563000	0.77884	AGT	C|0.789;T|0.211	0.211	strong		0.627	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
LIMA1	51474	hgsc.bcm.edu	37	12	50571221	50571221	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50571221C>T	ENST00000341247.4	-	11	2055	c.1906G>A	c.(1906-1908)Gtg>Atg	p.V636M	LIMA1_ENST00000394943.3_Missense_Mutation_p.V637M|LIMA1_ENST00000552491.1_Missense_Mutation_p.V333M|LIMA1_ENST00000552823.1_Missense_Mutation_p.V476M|LIMA1_ENST00000552909.1_Missense_Mutation_p.V475M|LIMA1_ENST00000547825.1_Missense_Mutation_p.V334M|LIMA1_ENST00000552783.1_Missense_Mutation_p.V477M	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	636					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GCATTTTCCACTTGTTTCCTT	0.463																																					p.V637M		Atlas-SNP	.											.	LIMA1	67	.	0			c.G1909A						PASS	.						284.0	292.0	289.0					12																	50571221		2203	4300	6503	SO:0001583	missense	51474	exon11			TTTCCACTTGTTT	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1906G>A	12.37:g.50571221C>T	ENSP00000340184:p.Val636Met	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	277	125	0.451264	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	6.055	0.378474	0.11466	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;T;D;T;T;T	0.84146	-1.07;-1.07;-1.39;-1.81;-1.07;-1.39;-1.39	5.31	1.23	0.21249	.	0.834586	0.11054	N	0.604718	T	0.65312	0.2679	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.14438	0.01;0.01;0.007	B;B;B	0.15052	0.002;0.002;0.012	T	0.52305	-0.8593	10	0.22109	T	0.4	.	7.9273	0.29883	0.0:0.4745:0.0:0.5255	.	646;636;475	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	M	333;334;476;637;636;477;475;555	ENSP00000448463:V333M;ENSP00000448706:V334M;ENSP00000450266:V476M;ENSP00000378400:V637M;ENSP00000340184:V636M;ENSP00000448779:V477M;ENSP00000450087:V475M	ENSP00000340184:V636M	V	-	1	0	LIMA1	48857488	0.000000	0.05858	0.036000	0.18154	0.640000	0.38277	0.484000	0.22308	0.399000	0.25367	0.650000	0.86243	GTG	.	.	none		0.463	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
ITSN2	50618	hgsc.bcm.edu	37	2	24426534	24426534	+	Silent	SNP	A	A	G	rs61754183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:24426534A>G	ENST00000355123.4	-	40	5498	c.5055T>C	c.(5053-5055)cgT>cgC	p.R1685R	ITSN2_ENST00000361999.3_Silent_p.R1658R|AC008073.9_ENST00000429717.1_RNA	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1685					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAGGTCAAAACGGACCCAGA	0.547													G|||	143	0.0285543	0.0424	0.0259	5008	,	,		16464	0.0069		0.0169	False		,,,				2504	0.046				p.R1685R		Atlas-SNP	.											.	ITSN2	224	.	0			c.T5055C						PASS	.	G	,	138,4268	813.3+/-416.1	1,136,2066	56.0	59.0	58.0		5055,4974	4.6	1.0	2	dbSNP_129	58	166,8434	810.6+/-407.1	5,156,4139	yes	coding-synonymous,coding-synonymous	ITSN2	NM_006277.2,NM_019595.3	,	6,292,6205	GG,GA,AA		1.9302,3.1321,2.3374	,	1685/1698,1658/1671	24426534	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	50618	exon40			GTCAAAACGGACC	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.5055T>C	2.37:g.24426534A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																			A|0.975;G|0.025	0.025	strong		0.547	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
ELOVL4	6785	hgsc.bcm.edu	37	6	80626375	80626375	+	Missense_Mutation	SNP	T	T	C	rs3812153	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:80626375T>C	ENST00000369816.4	-	6	1195	c.895A>G	c.(895-897)Atg>Gtg	p.M299V		NM_022726.3	NP_073563.1	Q9GZR5	ELOV4_HUMAN	ELOVL fatty acid elongase 4	299			M -> V (in dbSNP:rs3812153). {ECO:0000269|PubMed:11138005, ECO:0000269|PubMed:12592226}.		cellular lipid metabolic process (GO:0044255)|detection of visible light (GO:0009584)|fatty acid biosynthetic process (GO:0006633)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)	G-protein coupled photoreceptor activity (GO:0008020)|transferase activity (GO:0016740)			central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;1.83e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.011)		BRCA - Breast invasive adenocarcinoma(397;0.0168)	Alpha-Linolenic Acid(DB00132)	TTTTCTATCATGAGTTGTTTT	0.368													C|||	1210	0.241613	0.2458	0.1974	5008	,	,		17007	0.2282		0.1153	False		,,,				2504	0.411				p.M299V		Atlas-SNP	.											.	ELOVL4	46	.	0			c.A895G	GRCh37	CM052232	ELOVL4	M	rs3812153	PASS	.	C	VAL/MET	1008,3398	728.9+/-410.0	120,768,1315	102.0	91.0	95.0		895	5.6	0.4	6	dbSNP_107	95	939,7661	775.1+/-407.7	56,827,3417	yes	missense	ELOVL4	NM_022726.3	21	176,1595,4732	CC,CT,TT		10.9186,22.8779,14.97	benign	299/315	80626375	1947,11059	2203	4300	6503	SO:0001583	missense	6785	exon6			CTATCATGAGTTG	AF277094	CCDS4992.1	6q14	2013-01-08	2011-05-25		ENSG00000118402	ENSG00000118402			14415	protein-coding gene	gene with protein product	"""cancer/testis antigen 118"""	605512	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4"""	STGD2, STGD3		11138005	Standard	NM_022726		Approved	CT118	uc003pja.4	Q9GZR5	OTTHUMG00000015087	ENST00000369816.4:c.895A>G	6.37:g.80626375T>C	ENSP00000358831:p.Met299Val	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	270	171	0.633333	NM_022726	B2R6B5|Q5TCS2|Q86YJ1|Q9H139	Missense_Mutation	SNP	ENST00000369816.4	37	CCDS4992.1	406	0.1858974358974359	134	0.27235772357723576	75	0.20718232044198895	116	0.20279720279720279	81	0.10686015831134564	C	0.008	-1.901284	0.00517	0.228779	0.109186	ENSG00000118402	ENST00000369816	T	0.15834	2.39	5.61	5.61	0.85477	.	0.432752	0.24920	N	0.034550	T	0.03520	0.0101	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34453	-0.9828	9	0.25106	T	0.35	-4.8075	13.9098	0.63860	0.0:0.9272:0.0:0.0728	rs3812153;rs52819344;rs57220964;rs3812153	299	Q9GZR5	ELOV4_HUMAN	V	299	ENSP00000358831:M299V	ENSP00000358831:M299V	M	-	1	0	ELOVL4	80683094	0.878000	0.30173	0.426000	0.26672	0.034000	0.12701	1.850000	0.39328	1.388000	0.46506	-0.226000	0.12346	ATG	T|0.831;C|0.169	0.169	strong		0.368	ELOVL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041315.1		
PEAR1	375033	hgsc.bcm.edu	37	1	156883546	156883546	+	Missense_Mutation	SNP	A	A	G	rs12137505	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156883546A>G	ENST00000338302.3	+	22	2932	c.2707A>G	c.(2707-2709)Aat>Gat	p.N903D	PEAR1_ENST00000292357.7_Missense_Mutation_p.N903D			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	903	Pro-rich.		N -> D (in dbSNP:rs12137505).		recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCATTCTACAATAAAGGTAT	0.582													A|||	2259	0.451078	0.2557	0.5591	5008	,	,		17614	0.5913		0.3926	False		,,,				2504	0.5542				p.N903D		Atlas-SNP	.											.	PEAR1	118	.	0			c.A2707G						PASS	.	A	ASP/ASN	1133,3273	402.6+/-332.4	145,843,1215	52.0	54.0	53.0		2707	-3.9	0.0	1	dbSNP_120	53	3483,5117	508.4+/-377.0	719,2045,1536	yes	missense	PEAR1	NM_001080471.1	23	864,2888,2751	GG,GA,AA		40.5,25.7149,35.4913	benign	903/1038	156883546	4616,8390	2203	4300	6503	SO:0001583	missense	375033	exon21			TTCTACAATAAAG	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.2707A>G	1.37:g.156883546A>G	ENSP00000344465:p.Asn903Asp	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	168	103	0.613095	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	939	0.42994505494505497	139	0.28252032520325204	177	0.4889502762430939	317	0.5541958041958042	306	0.40369393139841686	A	7.885	0.731082	0.15507	0.257149	0.405	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.88354	-2.37;-2.37	5.49	-3.91	0.04168	.	1.037990	0.07657	N	0.932935	T	0.56834	0.2012	N	0.14661	0.345	0.80722	P	0.0	B	0.23937	0.094	B	0.16722	0.016	T	0.32428	-0.9907	9	0.24483	T	0.36	.	6.234	0.20752	0.3626:0.2625:0.3749:0.0	rs12137505;rs56635659;rs58160272;rs12137505	903	Q5VY43	PEAR1_HUMAN	D	903	ENSP00000344465:N903D;ENSP00000292357:N903D	ENSP00000292357:N903D	N	+	1	0	PEAR1	155150170	0.012000	0.17670	0.000000	0.03702	0.009000	0.06853	0.203000	0.17315	-0.553000	0.06158	-0.461000	0.05368	AAT	A|0.621;G|0.379	0.379	strong		0.582	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
OR4X2	119764	hgsc.bcm.edu	37	11	48266736	48266736	+	Nonsense_Mutation	SNP	C	C	G	rs7120775	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:48266736C>G	ENST00000302329.3	+	1	129	c.81C>G	c.(79-81)taC>taG	p.Y27*		NM_001004727.1	NP_001004727.1	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X, member 2	27						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y27*(1)		breast(1)|large_intestine(4)|lung(12)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	20						TGTTCTTGTACACAGCAATTG	0.453													C|||	875	0.17472	0.2882	0.1268	5008	,	,		23916	0.1627		0.1252	False		,,,				2504	0.1186				p.Y27X		Atlas-SNP	.											OR4X2,NS,carcinoma,0,1	OR4X2	65	1	1	Substitution - Nonsense(1)	stomach(1)	c.C81G						PASS	.	C	stop/TYR	1183,3219	414.8+/-337.0	169,845,1187	206.0	172.0	184.0		81	2.5	0.9	11	dbSNP_116	184	1137,7459	234.6+/-267.5	77,983,3238	yes	stop-gained	OR4X2	NM_001004727.1		246,1828,4425	GG,GC,CC		13.2271,26.8741,17.8489		27/304	48266736	2320,10678	2201	4298	6499	SO:0001587	stop_gained	119764	exon1			CTTGTACACAGCA	AB065847	CCDS31486.1	11p11.2	2012-08-09			ENSG00000172208	ENSG00000172208		"""GPCR / Class A : Olfactory receptors"""	15184	protein-coding gene	gene with protein product							Standard	NM_001004727		Approved		uc001ngs.1	Q8NGF9	OTTHUMG00000165302	ENST00000302329.3:c.81C>G	11.37:g.48266736C>G	ENSP00000307751:p.Tyr27*	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	248	119	0.479839	NM_001004727	B2RNK3|Q6IF73|Q96R63	Nonsense_Mutation	SNP	ENST00000302329.3	37	CCDS31486.1	364	0.16666666666666666	127	0.258130081300813	46	0.1270718232044199	93	0.16258741258741258	98	0.12928759894459102	C	18.54	3.645426	0.67358	0.268741	0.132271	ENSG00000172208	ENST00000302329	.	.	.	5.37	2.46	0.29980	.	0.000000	0.48767	D	0.000161	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.8228	0.23866	0.0:0.664:0.0:0.336	rs7120775;rs7120775	.	.	.	X	27	.	ENSP00000307751:Y27X	Y	+	3	2	OR4X2	48223312	0.000000	0.05858	0.914000	0.36105	0.969000	0.65631	-0.233000	0.09041	1.255000	0.44051	0.650000	0.86243	TAC	C|0.823;G|0.176;T|0.002	0.176	strong		0.453	OR4X2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383376.2	NM_001004727	
CFI	3426	hgsc.bcm.edu	37	4	110682723	110682723	+	Missense_Mutation	SNP	G	G	A	rs138346388	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110682723G>A	ENST00000394634.2	-	4	815	c.608C>T	c.(607-609)aCt>aTt	p.T203I	CFI_ENST00000394635.3_Missense_Mutation_p.T203I|CFI_ENST00000512148.1_Missense_Mutation_p.T203I	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	203	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		GTAACCCATAGTTCTTCTCTT	0.393													G|||	2	0.000399361	0.0	0.0029	5008	,	,		20003	0.0		0.0	False		,,,				2504	0.0				p.T203I		Atlas-SNP	.											.	CFI	59	.	0			c.C608T						PASS	.	G	ILE/THR	0,4406		0,0,2203	166.0	155.0	159.0		608	0.1	0.0	4	dbSNP_134	159	7,8593	5.7+/-21.5	0,7,4293	yes	missense	CFI	NM_000204.3	89	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	benign	203/584	110682723	7,12999	2203	4300	6503	SO:0001583	missense	3426	exon4			CCCATAGTTCTTC	J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"""Complement system"""	5394	protein-coding gene	gene with protein product	"""Konglutinogen-activating factor"", ""C3b-inactivator"""	217030	"""I factor (complement)"""	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.608C>T	4.37:g.110682723G>A	ENSP00000378130:p.Thr203Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_000204	O60442	Missense_Mutation	SNP	ENST00000394634.2	37	CCDS34049.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	8.946	0.967013	0.18659	0.0	8.14E-4	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000540104;ENST00000512148;ENST00000536228	T;T;T	0.36878	1.23;1.23;1.23	5.36	0.101	0.14517	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.803530	0.01919	N	0.040391	T	0.27489	0.0675	L	0.41236	1.265	0.09310	N	1	B;B;B	0.24721	0.03;0.11;0.063	B;B;B	0.19946	0.01;0.025;0.027	T	0.10405	-1.0631	10	0.37606	T	0.19	-0.3525	1.2864	0.02052	0.1647:0.3065:0.2732:0.2555	.	203;203;203	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	I	203;203;203;203;185	ENSP00000378131:T203I;ENSP00000378130:T203I;ENSP00000427438:T203I	ENSP00000378130:T203I	T	-	2	0	CFI	110902172	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	0.324000	0.19610	-0.031000	0.13781	-0.274000	0.10170	ACT	G|0.999;A|0.001	0.001	strong		0.393	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204	
IER2	9592	hgsc.bcm.edu	37	19	13264398	13264398	+	Missense_Mutation	SNP	C	C	T	rs1042164	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:13264398C>T	ENST00000588173.1	+	1	1610	c.398C>T	c.(397-399)gCt>gTt	p.A133V	CTC-250I14.6_ENST00000586483.1_RNA|IER2_ENST00000292433.3_Missense_Mutation_p.A133V|IER2_ENST00000587885.1_Missense_Mutation_p.A133V|CTC-250I14.6_ENST00000592882.1_RNA			Q9BTL4	IER2_HUMAN	immediate early response 2	133			A -> V (in dbSNP:rs1042164). {ECO:0000269|PubMed:2061303}.			cytoplasm (GO:0005737)				kidney(1)|lung(1)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			GGCGGGGACGCTGGACTGGTC	0.682											OREG0025291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	352	0.0702875	0.0159	0.1124	5008	,	,		13931	0.0129		0.175	False		,,,				2504	0.0654				p.A133V		Atlas-SNP	.											.	IER2	14	.	0			c.C398T						PASS	.	C	VAL/ALA	181,4157		4,173,1992	12.0	13.0	13.0		398	0.6	0.0	19	dbSNP_86	13	1425,7093		137,1151,2971	yes	missense	IER2	NM_004907.2	64	141,1324,4963	TT,TC,CC		16.7293,4.1724,12.4922	benign	133/224	13264398	1606,11250	2169	4259	6428	SO:0001583	missense	9592	exon2			GGGACGCTGGACT	M62831	CCDS12295.1	19p13.13	2008-02-05				ENSG00000160888			28871	protein-coding gene	gene with protein product						2061303	Standard	NM_004907		Approved	ETR101	uc002mwr.3	Q9BTL4		ENST00000588173.1:c.398C>T	19.37:g.13264398C>T	ENSP00000465617:p.Ala133Val	Somatic	23	0	0	686	WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_004907	Q03827|Q2TAZ2	Missense_Mutation	SNP	ENST00000588173.1	37	CCDS12295.1	212	0.09706959706959707	10	0.02032520325203252	50	0.13812154696132597	12	0.02097902097902098	140	0.18469656992084432	C	12.81	2.050513	0.36181	0.041724	0.167293	ENSG00000160888	ENST00000292433	T	0.10288	2.89	4.18	0.597	0.17504	.	0.350700	0.20201	N	0.097097	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.38243	-0.9670	9	0.48119	T	0.1	-0.4452	5.1108	0.14808	0.0:0.6165:0.1694:0.2141	rs1042164;rs57863418;rs1042164	133	Q9BTL4	IER2_HUMAN	V	133	ENSP00000292433:A133V	ENSP00000292433:A133V	A	+	2	0	IER2	13125398	0.013000	0.17824	0.001000	0.08648	0.564000	0.35744	1.510000	0.35790	-0.084000	0.12595	-0.379000	0.06801	GCT	C|0.921;T|0.079	0.079	strong		0.682	IER2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453033.1	NM_004907	
VWA5B2	90113	hgsc.bcm.edu	37	3	183951431	183951431	+	Missense_Mutation	SNP	C	C	T	rs902417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183951431C>T	ENST00000426955.2	+	4	698	c.598C>T	c.(598-600)Cct>Tct	p.P200S	VWA5B2_ENST00000273794.5_5'UTR|EIF2B5_ENST00000444495.1_Intron	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	211								p.P200S(1)		breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						GCTGGCTGCCCCTCGGGACGT	0.662													C|||	1088	0.217252	0.177	0.2075	5008	,	,		16546	0.2351		0.2485	False		,,,				2504	0.228				p.P200S		Atlas-SNP	.											VWA5B2,NS,carcinoma,0,1	VWA5B2	47	1	1	Substitution - Missense(1)	kidney(1)	c.C598T						scavenged	.	C	SER/PRO	241,1143		25,191,476	30.0	37.0	35.0		598	2.0	1.0	3	dbSNP_92	35	724,2458		83,558,950	yes	missense	VWA5B2	NM_138345.1	74	108,749,1426	TT,TC,CC		22.753,17.4133,21.1345	benign	200/1243	183951431	965,3601	692	1591	2283	SO:0001583	missense	90113	exon4			GCTGCCCCTCGGG		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.598C>T	3.37:g.183951431C>T	ENSP00000398688:p.Pro200Ser	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	188	98	0.521277	NM_138345	B9EGN7	Missense_Mutation	SNP	ENST00000426955.2	37	CCDS54686.1	444	0.2032967032967033	88	0.17886178861788618	74	0.20441988950276244	94	0.16433566433566432	188	0.24802110817941952	C	1.623	-0.521080	0.04171	0.174133	0.22753	ENSG00000145198	ENST00000426955	T	0.60424	0.19	3.84	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999633179	B;B	0.27823	0.19;0.004	B;B	0.29267	0.1;0.006	T	0.19160	-1.0314	8	0.33141	T	0.24	-0.1148	4.7979	0.13281	0.2103:0.6742:0.0:0.1154	rs902417;rs1687244;rs3882317;rs59041042;rs902417	200;211	B9EGN7;C9JW99	.;.	S	200	ENSP00000398688:P200S	ENSP00000398688:P200S	P	+	1	0	VWA5B2	185434125	0.999000	0.42202	0.982000	0.44146	0.641000	0.38312	1.678000	0.37586	0.384000	0.24942	0.462000	0.41574	CCT	C|0.788;T|0.212	0.212	strong		0.662	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
PEMT	10400	hgsc.bcm.edu	37	17	17409560	17409560	+	Missense_Mutation	SNP	C	C	T	rs7946	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17409560C>T	ENST00000395783.1	-	6	702	c.523G>A	c.(523-525)Gtg>Atg	p.V175M	RP11-524F11.1_ENST00000582325.1_RNA|PEMT_ENST00000484838.2_5'UTR|PEMT_ENST00000395781.2_Missense_Mutation_p.S222N|PEMT_ENST00000255389.5_Missense_Mutation_p.V212M|PEMT_ENST00000435340.2_Missense_Mutation_p.S201N|PEMT_ENST00000395782.1_Missense_Mutation_p.V175M	NM_007169.2	NP_009100.2	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	175			V -> M (in dbSNP:rs7946). {ECO:0000269|PubMed:11420179, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9989271, ECO:0000269|Ref.3, ECO:0000269|Ref.6, ECO:0000269|Ref.9}.		cell proliferation (GO:0008283)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	phosphatidyl-N-dimethylethanolamine N-methyltransferase activity (GO:0080101)|phosphatidyl-N-methylethanolamine N-methyltransferase activity (GO:0000773)|phosphatidylethanolamine N-methyltransferase activity (GO:0004608)	p.V212M(1)		endometrium(1)|kidney(1)|large_intestine(2)|prostate(3)	7				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		AGGAGAGCCACTATGTAGGTG	0.657													C|||	2126	0.424521	0.3222	0.5562	5008	,	,		18060	0.1716		0.7038	False		,,,				2504	0.4427				p.S222N		Atlas-SNP	.											PEMT,NS,carcinoma,0,1	PEMT	12	1	1	Substitution - Missense(1)	prostate(1)	c.G665A	GRCh37	CM054062	PEMT	M	rs7946	PASS	.	C	MET/VAL,MET/VAL,MET/VAL	1784,2608		350,1084,762	23.0	18.0	20.0		523,634,523	2.2	0.2	17	dbSNP_52	20	6195,2377		2269,1657,360	yes	missense,missense,missense	PEMT	NM_007169.2,NM_148172.1,NM_148173.1	21,21,21	2619,2741,1122	TT,TC,CC		27.7298,40.6193,38.4526	possibly-damaging,possibly-damaging,possibly-damaging	175/200,212/237,175/200	17409560	7979,4985	2196	4286	6482	SO:0001583	missense	10400	exon7			GAGCCACTATGTA	AF176806	CCDS11186.1, CCDS11187.1, CCDS58520.1	17p11.2	2008-02-05			ENSG00000133027	ENSG00000133027	2.1.1.17		8830	protein-coding gene	gene with protein product		602391				9989271, 17881348	Standard	NM_148173		Approved	PEMPT, PEMT2	uc002grl.4	Q9UBM1	OTTHUMG00000059290	ENST00000395783.1:c.523G>A	17.37:g.17409560C>T	ENSP00000379129:p.Val175Met	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	NM_001267552	A8MZ66|B4DY41|D3DXC3|Q6IAQ5|Q86VL3|Q9BW86|Q9UHY6|Q9Y6V9	Missense_Mutation	SNP	ENST00000395783.1	37	CCDS11187.1	1007|1007	0.4610805860805861|0.4610805860805861	155|155	0.3150406504065041|0.3150406504065041	214|214	0.5911602209944752|0.5911602209944752	103|103	0.18006993006993008|0.18006993006993008	535|535	0.7058047493403694|0.7058047493403694	C|C	0.226|0.226	-1.024667|-1.024667	0.02061|0.02061	0.406193|0.406193	0.722702|0.722702	ENSG00000133027|ENSG00000133027	ENST00000435340;ENST00000395781|ENST00000255389;ENST00000395783;ENST00000395782	T;T|T;T;T	0.26957|0.47177	1.7;1.74|0.85;0.85;0.85	4.24|4.24	2.16|2.16	0.27623|0.27623	.|.	.|0.458656	.|0.23247	.|N	.|0.050295	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	P|P	0.0|0.0	B|P;P	0.11235|0.52692	0.004|0.945;0.955	B|P;P	0.13407|0.48454	0.009|0.539;0.578	T|T	0.37314|0.37314	-0.9711|-0.9711	8|9	0.15066|0.46703	T|T	0.55|0.11	-10.5541|-10.5541	5.4807|5.4807	0.16721|0.16721	0.0:0.6385:0.1694:0.192|0.0:0.6385:0.1694:0.192	rs7946;rs1128207;rs1918248;rs3184881;rs11554364;rs57409990;rs7946|rs7946;rs1128207;rs1918248;rs3184881;rs11554364;rs57409990;rs7946	222|212;175	A8MZ66|Q9UBM1-2;Q9UBM1	.|.;PEMT_HUMAN	N|M	201;222|212;175;175	ENSP00000391288:S201N;ENSP00000379127:S222N|ENSP00000255389:V212M;ENSP00000379129:V175M;ENSP00000379128:V175M	ENSP00000379127:S222N|ENSP00000255389:V212M	S|V	-|-	2|1	0|0	PEMT|PEMT	17350285|17350285	0.001000|0.001000	0.12720|0.12720	0.231000|0.231000	0.23993|0.23993	0.114000|0.114000	0.19823|0.19823	-0.047000|-0.047000	0.11963|0.11963	0.380000|0.380000	0.24823|0.24823	0.484000|0.484000	0.47621|0.47621	AGT|GTG	C|0.580;T|0.420	0.420	strong		0.657	PEMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131657.1	NM_007169	
CELSR3	1951	hgsc.bcm.edu	37	3	48699519	48699519	+	Silent	SNP	C	C	T	rs3733086	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:48699519C>T	ENST00000164024.4	-	1	829	c.549G>A	c.(547-549)aaG>aaA	p.K183K	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Silent_p.K183K	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	183					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AGGACACCGGCTTGGGACCGT	0.647													C|||	499	0.0996406	0.1271	0.0793	5008	,	,		14171	0.1171		0.1173	False		,,,				2504	0.0409				p.K183K		Atlas-SNP	.											.	CELSR3	237	.	0			c.G549A						PASS	.	C		577,3823		26,525,1649	44.0	53.0	50.0		549	4.3	0.1	3	dbSNP_107	50	998,7596		60,878,3359	no	coding-synonymous	CELSR3	NM_001407.2		86,1403,5008	TT,TC,CC		11.6128,13.1136,12.121		183/3313	48699519	1575,11419	2200	4297	6497	SO:0001819	synonymous_variant	1951	exon1			CACCGGCTTGGGA	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.549G>A	3.37:g.48699519C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_001407	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																			C|0.885;T|0.115	0.115	strong		0.647	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
LGR6	59352	hgsc.bcm.edu	37	1	202288293	202288293	+	Silent	SNP	C	C	T	rs56234832	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202288293C>T	ENST00000367278.3	+	18	2951	c.2862C>T	c.(2860-2862)ggC>ggT	p.G954G	LGR6_ENST00000439764.2_Silent_p.G815G|LGR6_ENST00000255432.7_Silent_p.G902G	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	954	Poly-Gly.				G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						CAGGGGGTGGCGGCTTTCAGC	0.587													C|||	328	0.0654952	0.0136	0.1009	5008	,	,		18241	0.0466		0.1113	False		,,,				2504	0.0828				p.G954G		Atlas-SNP	.											.	LGR6	102	.	0			c.C2862T						PASS	.	C	,,	96,4310	77.8+/-116.1	3,90,2110	46.0	50.0	48.0		2862,2445,2706	-0.6	0.0	1	dbSNP_129	48	1126,7474	232.9+/-266.4	79,968,3253	no	coding-synonymous,coding-synonymous,coding-synonymous	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	,,	82,1058,5363	TT,TC,CC		13.093,2.1788,9.3957	,,	954/968,815/829,902/916	202288293	1222,11784	2203	4300	6503	SO:0001819	synonymous_variant	59352	exon18			GGGTGGCGGCTTT	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2862C>T	1.37:g.202288293C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	204	98	0.480392	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																			C|0.914;T|0.086	0.086	strong		0.587	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
CCL23	6368	hgsc.bcm.edu	37	17	34340284	34340284	+	Missense_Mutation	SNP	C	C	T	rs1003645	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34340284C>T	ENST00000591423.1	-	4	380	c.316G>A	c.(316-318)Gtg>Atg	p.V106M	CCL23_ENST00000293280.2_Missense_Mutation_p.V123M|RP11-104J23.1_ENST00000590192.1_RNA|RP11-104J23.1_ENST00000588294.1_RNA|RP11-104J23.2_ENST00000590149.1_lincRNA	NM_145898.1	NP_665905.1	P55773	CCL23_HUMAN	chemokine (C-C motif) ligand 23	106			V -> M (in dbSNP:rs1003645). {ECO:0000269|PubMed:10213461, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9104803, ECO:0000269|PubMed:9558365, ECO:0000269|Ref.1, ECO:0000269|Ref.6}.		cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|monocyte chemotaxis (GO:0002548)|negative regulation of C-C chemokine binding (GO:2001264)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)			large_intestine(2)|liver(1)|lung(2)|prostate(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGCATTCTCACGCAAACCTGA	0.498													T|||	2608	0.520767	0.1044	0.719	5008	,	,		18556	0.5744		0.8062	False		,,,				2504	0.5941				p.V123M		Atlas-SNP	.											.	CCL23	17	.	0			c.G367A						PASS	.	T	MET/VAL,MET/VAL	880,3526	743.2+/-411.4	95,690,1418	111.0	88.0	96.0		367,316	-0.2	0.0	17	dbSNP_89	96	7001,1599	297.7+/-303.5	2819,1363,118	yes	missense,missense	CCL23	NM_005064.3,NM_145898.1	21,21	2914,2053,1536	TT,TC,CC		18.593,19.9728,39.4049	benign,benign	123/138,106/121	34340284	7881,5125	2203	4300	6503	SO:0001583	missense	6368	exon4			TTCTCACGCAAAC	U58913	CCDS11305.1, CCDS59282.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000167236	ENSG00000274736		"""Chemokine ligands"", ""Endogenous ligands"""	10622	protein-coding gene	gene with protein product		602494	"""small inducible cytokine subfamily A (Cys-Cys), member 23"""	SCYA23		9104803, 10409433	Standard	XR_429910		Approved	Ckb-8, MPIF-1, MIP-3, CKb8	uc002hks.1	P55773	OTTHUMG00000188409	ENST00000591423.1:c.316G>A	17.37:g.34340284C>T	ENSP00000465954:p.Val106Met	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	134	57	0.425373	NM_005064	B7ZKQ3|O00174|O75950|Q52LD4	Missense_Mutation	SNP	ENST00000591423.1	37	CCDS59282.1	1268	0.5805860805860806	63	0.12804878048780488	267	0.7375690607734806	323	0.5646853146853147	615	0.8113456464379947	T	0.693	-0.793645	0.02862	0.199728	0.81407	ENSG00000167236	ENST00000293280	T	0.04194	3.68	3.71	-0.245	0.13027	Chemokine interleukin-8-like domain (3);	1.502520	0.04759	N	0.426020	T	0.00012	0.0000	N	0.01197	-0.965	0.80722	P	0.0	B;B	0.13145	0.007;0.002	B;B	0.16289	0.015;0.003	T	0.27839	-1.0062	9	0.02654	T	1	.	4.3408	0.11108	0.0:0.3091:0.17:0.5209	rs1003645;rs52818917;rs60170953;rs1003645	106;123	P55773;P55773-2	CCL23_HUMAN;.	M	123	ENSP00000293280:V123M	ENSP00000293280:V123M	V	-	1	0	CCL23	31364397	0.099000	0.21834	0.015000	0.15790	0.003000	0.03518	-0.206000	0.09398	-0.566000	0.06054	-0.443000	0.05667	GTG	C|0.421;T|0.579	0.579	strong		0.498	CCL23-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450228.1	NM_005064, NM_145898	
EFCAB7	84455	hgsc.bcm.edu	37	1	63997633	63997633	+	Silent	SNP	A	A	T	rs9804078	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:63997633A>T	ENST00000371088.4	+	3	576	c.330A>T	c.(328-330)tcA>tcT	p.S110S	RN7SL488P_ENST00000585186.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	110	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						TACTAAAATCATTTAAGCAAT	0.294													A|||	983	0.196286	0.2738	0.1715	5008	,	,		17546	0.1855		0.1441	False		,,,				2504	0.1738				p.S110S		Atlas-SNP	.											EFCAB7,colon,carcinoma,+1,1	EFCAB7	45	1	0			c.A330T						PASS	.	A		997,3409	346.2+/-308.9	114,769,1320	47.0	50.0	49.0		330	4.1	1.0	1	dbSNP_119	49	1324,7266	252.8+/-278.7	92,1140,3063	no	coding-synonymous	EFCAB7	NM_032437.2		206,1909,4383	TT,TA,AA		15.4133,22.6282,17.8593		110/630	63997633	2321,10675	2203	4295	6498	SO:0001819	synonymous_variant	84455	exon3			AAAATCATTTAAG	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.330A>T	1.37:g.63997633A>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_032437	Q658P0|Q96B95|Q96JM6	Silent	SNP	ENST00000371088.4	37	CCDS30737.1																																																																																			A|0.815;T|0.185	0.185	strong		0.294	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
C12orf42	374470	hgsc.bcm.edu	37	12	103696182	103696182	+	Missense_Mutation	SNP	T	T	G	rs79387839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:103696182T>G	ENST00000378113.2	-	6	1012	c.787A>C	c.(787-789)Agc>Cgc	p.S263R	C12orf42_ENST00000315192.8_Intron|C12orf42_ENST00000548048.1_Missense_Mutation_p.S196R|C12orf42_ENST00000548883.1_Missense_Mutation_p.S263R	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	263										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						AGGAGTCTGCTTTGGATGTCG	0.667													T|||	632	0.126198	0.0477	0.0965	5008	,	,		14553	0.1319		0.17	False		,,,				2504	0.2025				p.S263R		Atlas-SNP	.											.	C12orf42	50	.	0			c.A787C						PASS	.	T	ARG/SER,ARG/SER	299,3871		22,255,1808	54.0	63.0	60.0		787,787	-3.1	0.0	12	dbSNP_131	60	1342,7110		129,1084,3013	yes	missense,missense	C12orf42	NM_001099336.1,NM_198521.2	110,110	151,1339,4821	GG,GT,TT		15.8779,7.1703,13.0011	benign,benign	263/361,263/361	103696182	1641,10981	2085	4226	6311	SO:0001583	missense	374470	exon6			GTCTGCTTTGGAT	AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.787A>C	12.37:g.103696182T>G	ENSP00000367353:p.Ser263Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	112	62	0.553571	NM_001099336	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	37	CCDS44963.1	279	0.12774725274725274	29	0.05894308943089431	37	0.10220994475138122	85	0.1486013986013986	128	0.16886543535620052	T	10.34	1.324188	0.24080	0.071703	0.158779	ENSG00000179088	ENST00000548883;ENST00000548048;ENST00000378113	T;T;T	0.58652	0.32;0.32;0.32	4.42	-3.12	0.05282	.	0.699661	0.11917	N	0.517108	T	0.00073	0.0002	N	0.17082	0.46	0.80722	P	0.0	B	0.12013	0.005	B	0.10450	0.005	T	0.08576	-1.0715	9	0.42905	T	0.14	-2.9392	0.5073	0.00590	0.3601:0.2515:0.1297:0.2588	.	263	Q96LP6	CL042_HUMAN	R	263;196;263	ENSP00000447908:S263R;ENSP00000449362:S196R;ENSP00000367353:S263R	ENSP00000367353:S263R	S	-	1	0	C12orf42	102220312	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.094000	0.15107	-0.673000	0.05259	-1.288000	0.01363	AGC	T|0.864;G|0.136	0.136	strong		0.667	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521	
OR1F1	4992	hgsc.bcm.edu	37	16	3254972	3254972	+	Silent	SNP	T	T	C	rs2075851	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3254972T>C	ENST00000304646.2	+	1	726	c.726T>C	c.(724-726)ggT>ggC	p.G242G	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	242					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(7)	11						CCACCTGTGGTTCTCACCTGG	0.502													C|||	1954	0.390176	0.1203	0.5101	5008	,	,		22057	0.5685		0.4294	False		,,,				2504	0.4458				p.G242G		Atlas-SNP	.											.	OR1F1	36	.	0			c.T726C						PASS	.	C		824,3570	747.3+/-411.8	72,680,1445	207.0	188.0	194.0		726	-0.9	0.9	16	dbSNP_96	194	3762,4838	615.5+/-396.4	828,2106,1366	no	coding-synonymous	OR1F1	NM_012360.1		900,2786,2811	CC,CT,TT		43.7442,18.7528,35.2932		242/313	3254972	4586,8408	2197	4300	6497	SO:0001819	synonymous_variant	4992	exon1			CTGTGGTTCTCAC	Y14442	CCDS10496.1	16p13.3	2012-08-09			ENSG00000168124	ENSG00000168124		"""GPCR / Class A : Olfactory receptors"""	8194	protein-coding gene	gene with protein product		603232		OR1F4, OR1F6, OR1F7, OR1F8, OR1F9, OR1F5, OR1F10, OR1F13P		9288094, 9500546	Standard	NM_012360		Approved	Olfmf, OR16-36, OR16-37, OR16-88, OR16-89, OR16-90, OLFMF, OR3-145	uc010uwu.2	O43749	OTTHUMG00000133153	ENST00000304646.2:c.726T>C	16.37:g.3254972T>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	214	76	0.35514	NM_012360	O15246|Q6IFL5	Silent	SNP	ENST00000304646.2	37	CCDS10496.1																																																																																			T|0.618;C|0.382	0.382	strong		0.502	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1		
ERI2	112479	hgsc.bcm.edu	37	16	20810067	20810067	+	Missense_Mutation	SNP	T	T	C	rs3213646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:20810067T>C	ENST00000357967.4	-	9	1097	c.1055A>G	c.(1054-1056)tAt>tGt	p.Y352C	ERI2_ENST00000563117.1_Missense_Mutation_p.Y259C|ERI2_ENST00000389345.5_Missense_Mutation_p.Y87C|ERI2_ENST00000569729.1_Intron|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000564349.1_Missense_Mutation_p.Y259C	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	352				Y -> C (in Ref. 4; BAA96028). {ECO:0000305}.			exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						CTTTTGCATATAGATAGGTGA	0.383													T|||	1602	0.319888	0.0915	0.5014	5008	,	,		20635	0.1528		0.5805	False		,,,				2504	0.4039				p.Y352C		Atlas-SNP	.											.	ERI2	50	.	0			c.A1055G						PASS	.	T	CYS/TYR,	245,1139		18,209,465	105.0	90.0	95.0		1055,	-4.4	0.0	16	dbSNP_106	95	1820,1362		509,802,280	yes	missense,intron	ERI2	NM_001142725.1,NM_080663.2	194,	527,1011,745	CC,CT,TT		42.8033,17.7023,45.2256	benign,	352/692,	20810067	2065,2501	692	1591	2283	SO:0001583	missense	112479	exon9			TGCATATAGATAG	BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678		"""Enhanced RNAi three prime mRNA exonucleases"""	30541	protein-coding gene	gene with protein product	"""enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans)"", ""exoribonuclease 2"", ""zinc finger, GRF-type containing 5"""		"""exonuclease domain containing 1"""	EXOD1		10819331	Standard	NM_080663		Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000357967.4:c.1055A>G	16.37:g.20810067T>C	ENSP00000350651:p.Tyr352Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Missense_Mutation	SNP	ENST00000357967.4	37	CCDS45436.1	747	0.34203296703296704	54	0.10975609756097561	168	0.46408839779005523	88	0.15384615384615385	437	0.5765171503957783	T	7.807	0.714797	0.15306	0.177023	0.571967	ENSG00000196678	ENST00000357967;ENST00000389345	T;T	0.19105	2.21;2.17	4.94	-4.38	0.03622	.	2.213460	0.01814	N	0.033658	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46679	-0.9174	9	0.40728	T	0.16	1.6145	4.0005	0.09577	0.1145:0.2589:0.4658:0.1609	rs3213646;rs17690686;rs52837000;rs58027232;rs3213646	352	A8K979	ERI2_HUMAN	C	352;87	ENSP00000350651:Y352C;ENSP00000373996:Y87C	ENSP00000350651:Y352C	Y	-	2	0	ERI2	20717568	0.000000	0.05858	0.001000	0.08648	0.733000	0.41908	-0.080000	0.11339	-0.792000	0.04480	0.533000	0.62120	TAT	T|0.674;C|0.326	0.326	strong		0.383	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663	
ZNF354B	117608	hgsc.bcm.edu	37	5	178309735	178309735	+	Silent	SNP	A	A	C	rs148284462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178309735A>C	ENST00000322434.3	+	5	508	c.282A>C	c.(280-282)acA>acC	p.T94T	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	94					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTAAAATGACAAAGTCAACTC	0.373																																					p.T94T		Atlas-SNP	.											.	ZNF354B	67	.	0			c.A282C						PASS	.	A		0,4388		0,0,2194	60.0	61.0	61.0		282	2.3	1.0	5	dbSNP_134	61	3,8587		0,3,4292	no	coding-synonymous	ZNF354B	NM_058230.2		0,3,6486	CC,CA,AA		0.0349,0.0,0.0231		94/613	178309735	3,12975	2194	4295	6489	SO:0001819	synonymous_variant	117608	exon5			AATGACAAAGTCA	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.282A>C	5.37:g.178309735A>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_058230	A8K0V2|Q5U5Z4	Silent	SNP	ENST00000322434.3	37	CCDS4439.1																																																																																			A|0.999;C|0.001	0.001	strong		0.373	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
LIPG	9388	hgsc.bcm.edu	37	18	47093864	47093864	+	Missense_Mutation	SNP	C	C	T	rs2000813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:47093864C>T	ENST00000261292.4	+	3	610	c.332C>T	c.(331-333)aCa>aTa	p.T111I	LIPG_ENST00000577628.1_Missense_Mutation_p.T147I|LIPG_ENST00000580036.1_Missense_Mutation_p.T111I|LIPG_ENST00000427224.2_Missense_Mutation_p.T111I	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	111			T -> I (in dbSNP:rs2000813). {ECO:0000269|PubMed:12966036}.		cell proliferation (GO:0008283)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|regulation of lipoprotein metabolic process (GO:0050746)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)	extracellular space (GO:0005615)	heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phospholipase activity (GO:0004620)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(2)	18						GCCCTGCACACAAGAGAGAAA	0.493													C|||	1205	0.240615	0.0673	0.2277	5008	,	,		16337	0.3274		0.3022	False		,,,				2504	0.3313				p.T111I	Pancreas(126;280 1778 12814 26243 34948)	Atlas-SNP	.											.	LIPG	47	.	0			c.C332T	GRCh37	CM077882	LIPG	M	rs2000813	PASS	.	C	ILE/THR	473,3933	225.2+/-241.2	20,433,1750	88.0	75.0	79.0		332	-3.7	0.2	18	dbSNP_92	79	2506,6094	410.5+/-350.2	364,1778,2158	yes	missense	LIPG	NM_006033.2	89	384,2211,3908	TT,TC,CC		29.1395,10.7354,22.9048	benign	111/501	47093864	2979,10027	2203	4300	6503	SO:0001583	missense	9388	exon3			TGCACACAAGAGA	AF118767	CCDS11938.1	18q21.1	2006-04-22				ENSG00000101670			6623	protein-coding gene	gene with protein product		603684				10318835, 10192396	Standard	XM_005258390		Approved	EDL	uc002ldv.3	Q9Y5X9		ENST00000261292.4:c.332C>T	18.37:g.47093864C>T	ENSP00000261292:p.Thr111Ile	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Missense_Mutation	SNP	ENST00000261292.4	37	CCDS11938.1	532	0.24358974358974358	29	0.05894308943089431	101	0.27900552486187846	182	0.3181818181818182	220	0.29023746701846964	C	10.03	1.238711	0.22711	0.107354	0.291395	ENSG00000101670	ENST00000261292;ENST00000427224	D;D	0.90444	-2.67;-2.67	5.13	-3.65	0.04502	Lipase, N-terminal (1);	0.762883	0.13306	N	0.397833	T	0.00012	0.0000	N	0.12853	0.265	0.80722	P	0.0	B;B;B	0.12013	0.005;0.003;0.002	B;B;B	0.11329	0.006;0.006;0.004	T	0.07539	-1.0767	9	0.49607	T	0.09	-23.8984	5.0178	0.14345	0.372:0.2221:0.0:0.4059	rs2000813;rs3786250;rs52802490;rs56604138;rs58046713;rs2000813	111;111;111	B4DTR8;Q9Y5X9;Q9Y5X9-2	.;LIPE_HUMAN;.	I	111	ENSP00000261292:T111I;ENSP00000387978:T111I	ENSP00000261292:T111I	T	+	2	0	LIPG	45347862	0.013000	0.17824	0.170000	0.22879	0.332000	0.28634	0.406000	0.21032	-0.342000	0.08363	0.561000	0.74099	ACA	C|0.760;T|0.240	0.240	strong		0.493	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033	
NBPF10	100132406	hgsc.bcm.edu	37	1	145296403	145296403	+	Silent	SNP	C	C	T	rs4996269	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145296403C>T	ENST00000342960.5	+	3	360	c.325C>T	c.(325-327)Cta>Tta	p.L109L	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	109						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCTGACCCAGCTAAGGGAGAA	0.517																																					p.L109L		Atlas-SNP	.											NBPF10,NS,carcinoma,0,1	NBPF10	221	1	0			c.C325T						scavenged	.																																			SO:0001819	synonymous_variant	100132406	exon3			ACCCAGCTAAGGG	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.325C>T	1.37:g.145296403C>T		Somatic	269	4	0.0148699		WXS	Illumina HiSeq	Phase_I	178	8	0.0449438	NM_001039703	Q5RHC0|Q9NWN6	Silent	SNP	ENST00000342960.5	37	CCDS53355.1																																																																																			T|0.001;G|0.956	0.001	strong		0.517	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
NPHS1	4868	hgsc.bcm.edu	37	19	36342212	36342212	+	Missense_Mutation	SNP	C	C	T	rs3814995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36342212C>T	ENST00000378910.5	-	3	348	c.349G>A	c.(349-351)Gag>Aag	p.E117K	NPHS1_ENST00000591817.1_5'Flank|NPHS1_ENST00000353632.6_Missense_Mutation_p.E117K	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	117	Ig-like C2-type 1.		E -> K (in dbSNP:rs3814995). {ECO:0000269|PubMed:11317351, ECO:0000269|PubMed:19309778, ECO:0000269|PubMed:22009864, ECO:0000269|PubMed:9915943}.		cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGCCCCATCTCAGAGCGGCCG	0.637													C|||	1462	0.291933	0.056	0.3444	5008	,	,		17564	0.5982		0.3111	False		,,,				2504	0.2382				p.E117K		Atlas-SNP	.											.	NPHS1	165	.	0			c.G349A						PASS	.	C	LYS/GLU	405,4001	196.7+/-221.0	16,373,1814	33.0	34.0	34.0		349	5.9	0.7	19	dbSNP_107	34	2628,5972	418.3+/-352.7	402,1824,2074	yes	missense	NPHS1	NM_004646.3	56	418,2197,3888	TT,TC,CC		30.5581,9.192,23.32	possibly-damaging	117/1242	36342212	3033,9973	2203	4300	6503	SO:0001583	missense	4868	exon3			CCATCTCAGAGCG		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.349G>A	19.37:g.36342212C>T	ENSP00000368190:p.Glu117Lys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	738	0.33791208791208793	36	0.07317073170731707	101	0.27900552486187846	359	0.6276223776223776	242	0.31926121372031663	C	18.75	3.690627	0.68271	0.09192	0.305581	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.65916	-0.18;-0.18	5.92	5.92	0.95590	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);	0.059087	0.64402	D	0.000003	T	0.00012	0.0000	L	0.39514	1.22	0.09310	P	0.99999864835	D	0.76494	0.999	D	0.71414	0.973	T	0.28459	-1.0043	9	0.06236	T	0.91	-23.6864	17.8963	0.88890	0.0:1.0:0.0:0.0	rs3814995;rs3814995	117	O60500	NPHN_HUMAN	K	117	ENSP00000368190:E117K;ENSP00000343634:E117K	ENSP00000343634:E117K	E	-	1	0	NPHS1	41034052	0.978000	0.34361	0.706000	0.30403	0.004000	0.04260	2.555000	0.45854	2.828000	0.97474	0.650000	0.86243	GAG	C|0.735;T|0.265	0.265	strong		0.637	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
PTCHD2	57540	hgsc.bcm.edu	37	1	11579470	11579470	+	Missense_Mutation	SNP	G	G	A	rs2072994	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11579470G>A	ENST00000294484.6	+	8	2086	c.1948G>A	c.(1948-1950)Gct>Act	p.A650T	PTCHD2_ENST00000389575.3_Missense_Mutation_p.A650T	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	650			A -> T (in dbSNP:rs2072994). {ECO:0000269|PubMed:10718198}.		cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CGTGTTTGCCGCTCCCGAGCA	0.632													g|||	1802	0.359824	0.0545	0.6556	5008	,	,		18315	0.2698		0.6471	False		,,,				2504	0.3599				p.A650T		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G1948A						PASS	.		THR/ALA	566,3470		60,446,1512	133.0	146.0	141.0		1948	-5.8	0.0	1	dbSNP_96	141	5141,3209		1553,2035,587	yes	missense	PTCHD2	NM_020780.1	58	1613,2481,2099	AA,AG,GG		38.4311,14.0238,46.0762	benign	650/1393	11579470	5707,6679	2018	4175	6193	SO:0001583	missense	57540	exon8			TTTGCCGCTCCCG	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.1948G>A	1.37:g.11579470G>A	ENSP00000294484:p.Ala650Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	937	0.429029304029304	30	0.06097560975609756	243	0.6712707182320442	162	0.28321678321678323	502	0.662269129287599	g	0.242	-1.012886	0.02095	0.140238	0.615689	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.89123	-2.47;-2.47	5.31	-5.84	0.02318	.	0.834399	0.11066	N	0.603446	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.35351	-0.9792	9	0.19147	T	0.46	0.2018	8.0415	0.30523	0.608:0.0:0.2853:0.1067	rs2072994;rs17370621;rs2072994	650	Q9P2K9	PTHD2_HUMAN	T	650	ENSP00000294484:A650T;ENSP00000374226:A650T	ENSP00000294484:A650T	A	+	1	0	PTCHD2	11502057	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.647000	0.05397	-0.682000	0.05197	0.651000	0.88453	GCT	G|0.553;A|0.447	0.447	strong		0.632	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
SEMA3C	10512	hgsc.bcm.edu	37	7	80374438	80374438	+	Silent	SNP	T	T	C	rs1949972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:80374438T>C	ENST00000265361.3	-	18	2589	c.2028A>G	c.(2026-2028)ccA>ccG	p.P676P	SEMA3C_ENST00000544525.1_Silent_p.P694P|SEMA3C_ENST00000419255.2_Silent_p.P676P	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	676					axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CCCAGGTCCATGGGGACCATT	0.468													T|||	4227	0.84405	0.6921	0.8991	5008	,	,		18266	0.7698		0.9891	False		,,,				2504	0.9376				p.P676P		Atlas-SNP	.											.	SEMA3C	106	.	0			c.A2028G						PASS	.	T		3245,1161	713.8+/-408.3	1207,831,165	93.0	84.0	87.0		2028	-5.0	1.0	7	dbSNP_92	87	8518,82	815.6+/-407.0	4218,82,0	no	coding-synonymous	SEMA3C	NM_006379.3		5425,913,165	CC,CT,TT		0.9535,26.3504,9.5571		676/752	80374438	11763,1243	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon18			GGTCCATGGGGAC	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.2028A>G	7.37:g.80374438T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	237	237	1	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			T|0.123;C|0.877	0.877	strong		0.468	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
TEP1	7011	hgsc.bcm.edu	37	14	20863677	20863677	+	Silent	SNP	C	C	A	rs2228036	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:20863677C>A	ENST00000262715.5	-	12	1900	c.1860G>T	c.(1858-1860)cgG>cgT	p.R620R	TEP1_ENST00000556935.1_Silent_p.R512R	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	620	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TCATTGCCATCCGAAGCTGCT	0.502													C|||	983	0.196286	0.0893	0.2954	5008	,	,		20960	0.1379		0.3111	False		,,,				2504	0.2127				p.R620R		Atlas-SNP	.											.	TEP1	224	.	0			c.G1860T						PASS	.	C		577,3829	259.5+/-263.1	40,497,1666	144.0	119.0	128.0		1860	0.8	0.2	14	dbSNP_98	128	2846,5754	448.3+/-361.8	492,1862,1946	no	coding-synonymous	TEP1	NM_007110.4		532,2359,3612	AA,AC,CC		33.093,13.0958,26.3186		620/2628	20863677	3423,9583	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon12			TGCCATCCGAAGC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.1860G>T	14.37:g.20863677C>A		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	263	261	0.992395	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			C|0.753;A|0.247	0.247	strong		0.502	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
CPSF4L	642843	hgsc.bcm.edu	37	17	71248777	71248777	+	Silent	SNP	T	T	C	rs74909356	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:71248777T>C	ENST00000344935.4	-	5	550	c.489A>G	c.(487-489)caA>caG	p.Q163Q	CPSF4L_ENST00000397671.1_Silent_p.Q100Q	NM_001129885.1	NP_001123357.1	A6NMK7	CPS4L_HUMAN	cleavage and polyadenylation specific factor 4-like	163							metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|prostate(1)	2						ACTGAGCAAATTGGCACTTGG	0.493													T|||	8	0.00159744	0.0	0.0014	5008	,	,		21870	0.0		0.007	False		,,,				2504	0.0				p.Q163Q		Atlas-SNP	.											.	CPSF4L	8	.	0			c.A489G						PASS	.	T		0,1384		0,0,692	137.0	110.0	118.0		489	-3.6	0.2	17	dbSNP_132	118	10,3172		0,10,1581	no	coding-synonymous	CPSF4L	NM_001129885.1		0,10,2273	CC,CT,TT		0.3143,0.0,0.219		163/180	71248777	10,4556	692	1591	2283	SO:0001819	synonymous_variant	642843	exon5			AGCAAATTGGCAC		CCDS45768.1	17q25.1	2010-07-06			ENSG00000187959	ENSG00000187959			33632	protein-coding gene	gene with protein product							Standard	NM_001129885		Approved		uc010dfk.1	A6NMK7	OTTHUMG00000132640	ENST00000344935.4:c.489A>G	17.37:g.71248777T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	NM_001129885	A8MU95|B2RXI9	Silent	SNP	ENST00000344935.4	37	CCDS45768.1																																																																																			T|0.998;C|0.002	0.002	strong		0.493	CPSF4L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441896.1	NM_001129885	
BARD1	580	hgsc.bcm.edu	37	2	215674224	215674224	+	Missense_Mutation	SNP	G	G	A	rs1048108	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:215674224G>A	ENST00000260947.4	-	1	204	c.70C>T	c.(70-72)Ccc>Tcc	p.P24S	AC072062.1_ENST00000607412.1_RNA|BARD1_ENST00000449967.2_5'UTR|BARD1_ENST00000471787.1_5'UTR	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	24			P -> S (common polymorphism in Caucasians; less frequent in Africans; dbSNP:rs1048108). {ECO:0000269|PubMed:9425226}.		cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCCATGGCGGGCGCGGAACGA	0.687									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				G|||	1659	0.33127	0.1929	0.4006	5008	,	,		10138	0.3313		0.3946	False		,,,				2504	0.4039				p.P24S		Atlas-SNP	.											BARD1_ENST00000260947,NS,carcinoma,0,4	BARD1	138	4	0			c.C70T	GRCh37	CM076015	BARD1	M	rs1048108	PASS	.	G	SER/PRO	892,3252		114,664,1294	9.0	10.0	10.0		70	3.1	1.0	2	dbSNP_86	10	2859,5371		518,1823,1774	no	missense	BARD1	NM_000465.2	74	632,2487,3068	AA,AG,GG		34.7388,21.5251,30.3136	benign	24/778	215674224	3751,8623	2072	4115	6187	SO:0001583	missense	580	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGGCGGGCGCGGA		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.70C>T	2.37:g.215674224G>A	ENSP00000260947:p.Pro24Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	29	17	0.586207	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	757	0.3466117216117216	95	0.19308943089430894	152	0.4198895027624309	203	0.3548951048951049	307	0.4050131926121372	G	14.84	2.656841	0.47467	0.215251	0.347388	ENSG00000138376	ENST00000260947;ENST00000421162	T;D	0.85088	-0.72;-1.94	3.99	3.1	0.35709	.	0.095711	0.44902	D	0.000412	T	0.00012	0.0000	N	0.16478	0.41	0.09310	P	0.9999999999951874	B	0.09022	0.002	B	0.10450	0.005	T	0.15723	-1.0427	9	0.34782	T	0.22	-12.5199	5.3151	0.15850	0.1147:0.2331:0.6522:0.0	rs1048108;rs2070095;rs3188086;rs1048108	24	Q99728	BARD1_HUMAN	S	24	ENSP00000260947:P24S;ENSP00000392245:P24S	ENSP00000260947:P24S	P	-	1	0	BARD1	215382469	0.675000	0.27558	0.990000	0.47175	0.038000	0.13279	0.968000	0.29357	2.221000	0.72209	0.561000	0.74099	CCC	G|0.674;A|0.326	0.326	strong		0.687	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
CEP128	145508	hgsc.bcm.edu	37	14	81382845	81382845	+	Missense_Mutation	SNP	C	C	A	rs7160694	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:81382845C>A	ENST00000555265.1	-	3	422	c.47G>T	c.(46-48)cGa>cTa	p.R16L	CEP128_ENST00000216517.6_Missense_Mutation_p.R16L|CEP128_ENST00000281129.3_Missense_Mutation_p.R16L|CEP128_ENST00000327841.2_5'UTR			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	16			R -> L (in dbSNP:rs7160694).			centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TGGACTCAATCGGTCACGACA	0.418													C|||	172	0.034345	0.0045	0.036	5008	,	,		18212	0.0347		0.0726	False		,,,				2504	0.0337				p.R16L		Atlas-SNP	.											.	CEP128	146	.	0			c.G47T						PASS	.	C	LEU/ARG	54,4352	53.6+/-89.4	0,54,2149	148.0	130.0	136.0		47	2.9	0.1	14	dbSNP_116	136	586,8014	156.1+/-210.0	23,540,3737	yes	missense	CEP128	NM_152446.3	102	23,594,5886	AA,AC,CC		6.814,1.2256,4.9208	possibly-damaging	16/1095	81382845	640,12366	2203	4300	6503	SO:0001583	missense	145508	exon2			CTCAATCGGTCAC	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.47G>T	14.37:g.81382845C>A	ENSP00000451162:p.Arg16Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	83	0.038003663003663	5	0.01016260162601626	17	0.04696132596685083	13	0.022727272727272728	48	0.0633245382585752	C	8.469	0.857167	0.17106	0.012256	0.06814	ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619;ENST00000216517;ENST00000555529;ENST00000556042;ENST00000556981	T;T;T;T;T;T	0.54279	1.35;1.35;0.75;0.78;0.77;0.58	5.35	2.94	0.34122	.	0.709694	0.12339	N	0.477715	T	0.05135	0.0137	L	0.32530	0.975	0.19945	N	0.999948	P;P;P	0.38455	0.632;0.491;0.632	B;B;B	0.41202	0.35;0.275;0.275	T	0.02294	-1.1181	10	0.59425	D	0.04	.	10.4489	0.44509	0.0:0.8859:0.0:0.1141	rs7160694;rs17543093;rs52793377;rs57428333;rs7160694	16;16;16	G3V3F4;Q6ZU80-3;Q6ZU80	.;.;CE128_HUMAN	L	16	ENSP00000281129:R16L;ENSP00000451162:R16L;ENSP00000216517:R16L;ENSP00000451137:R16L;ENSP00000451214:R16L;ENSP00000451428:R16L	ENSP00000216517:R16L	R	-	2	0	CEP128	80452598	0.207000	0.23482	0.078000	0.20375	0.015000	0.08874	0.554000	0.23407	0.808000	0.34231	0.655000	0.94253	CGA	A|0.045;C|0.954;T|0.000	0.045	strong		0.418	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
LARS	51520	hgsc.bcm.edu	37	5	145508636	145508636	+	Missense_Mutation	SNP	T	T	C	rs61732383|rs35977062	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:145508636T>C	ENST00000394434.2	-	26	2840	c.2674A>G	c.(2674-2676)Aat>Gat	p.N892D	LARS_ENST00000545646.1_Missense_Mutation_p.N846D|LARS_ENST00000274562.9_Missense_Mutation_p.N865D|LARS_ENST00000510191.1_Missense_Mutation_p.N838D	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	892				N -> D (in Ref. 1; BAA95667). {ECO:0000305}.	gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.N892D(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	AAAACTTCATTAACAGGACCT	0.353													C|||	910	0.181709	0.0076	0.3775	5008	,	,		14471	0.1984		0.2525	False		,,,				2504	0.1881				p.N892D		Atlas-SNP	.											LARS,NS,carcinoma,0,1	LARS	100	1	1	Substitution - Missense(1)	stomach(1)	c.A2674G						PASS	.	C	ASP/ASN	257,4149	792.8+/-415.2	12,233,1958	69.0	79.0	76.0		2674	5.7	1.0	5	dbSNP_129	76	2373,6225	690.3+/-404.4	352,1669,2278	yes	missense	LARS	NM_020117.9	23	364,1902,4236	CC,CT,TT		27.5994,5.833,20.2245	benign	892/1177	145508636	2630,10374	2203	4299	6502	SO:0001583	missense	51520	exon26			CTTCATTAACAGG	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2674A>G	5.37:g.145508636T>C	ENSP00000377954:p.Asn892Asp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	ENST00000394434.2	37	CCDS34265.1	350	0.16025641025641027	8	0.016260162601626018	93	0.2569060773480663	94	0.16433566433566432	155	0.20448548812664907	C	7.868	0.727494	0.15439	0.05833	0.275994	ENSG00000133706	ENST00000394434;ENST00000545646;ENST00000540713;ENST00000510191;ENST00000274562	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	5.73	5.73	0.89815	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class I, anticodon-binding (1);Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00327	-1.64	0.38950	P	0.04167799999999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.41805	-0.9488	9	0.02654	T	1	-11.3151	15.0032	0.71489	0.0:0.932:0.0:0.068	.	865;846;892	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	D	892;846;201;838;865	ENSP00000377954:N892D;ENSP00000437791:N846D;ENSP00000426005:N838D;ENSP00000274562:N865D	ENSP00000274562:N865D	N	-	1	0	LARS	145488829	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	5.788000	0.69020	1.456000	0.47831	-0.119000	0.15052	AAT	T|0.808;C|0.192	0.192	strong		0.353	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
GFPT2	9945	hgsc.bcm.edu	37	5	179734200	179734200	+	Silent	SNP	A	A	G	rs73343449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:179734200A>G	ENST00000253778.8	-	16	1819	c.1650T>C	c.(1648-1650)taT>taC	p.Y550Y		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	550	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)	p.Y550Y(1)		breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	GGCAGGTGGCATAGTTGTAGC	0.647													g|||	1009	0.201478	0.1762	0.1297	5008	,	,		7779	0.2173		0.2535	False		,,,				2504	0.2168				p.Y550Y		Atlas-SNP	.											GFPT2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	GFPT2	74	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.T1650C						PASS	.			684,3212		69,546,1333	27.0	29.0	28.0		1650	-6.8	0.7	5	dbSNP_130	28	2056,6212		262,1532,2340	no	coding-synonymous	GFPT2	NM_005110.2		331,2078,3673	GG,GA,AA		24.867,17.5565,22.5255		550/683	179734200	2740,9424	1948	4134	6082	SO:0001819	synonymous_variant	9945	exon16			GGTGGCATAGTTG	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"""glutamine: fructose-6-phosphate aminotransferase 2"""	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.1650T>C	5.37:g.179734200A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	134	82	0.61194	NM_005110	Q53XM2|Q9BWS4	Silent	SNP	ENST00000253778.8	37	CCDS43411.1																																																																																			A|0.788;G|0.212	0.212	strong		0.647	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110	
AKNA	80709	hgsc.bcm.edu	37	9	117124731	117124731	+	Missense_Mutation	SNP	G	G	A	rs3748176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:117124731G>A	ENST00000307564.4	-	8	2032	c.1871C>T	c.(1870-1872)cCg>cTg	p.P624L	AKNA_ENST00000223791.3_Missense_Mutation_p.P84L|AKNA_ENST00000374075.5_Missense_Mutation_p.P543L|AKNA_ENST00000312033.3_Missense_Mutation_p.P624L|AKNA_ENST00000374088.3_Missense_Mutation_p.P624L	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	624			P -> L (in dbSNP:rs3748176). {ECO:0000269|PubMed:11853319, ECO:0000269|PubMed:14702039}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.P624L(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GCCGGCAAGCGGCTGGGCAGG	0.657													g|||	1924	0.384185	0.115	0.4798	5008	,	,		16480	0.3869		0.506	False		,,,				2504	0.5521				p.P624L		Atlas-SNP	.											AKNA,NS,carcinoma,0,1	AKNA	119	1	1	Substitution - Missense(1)	stomach(1)	c.C1871T						PASS	.		LEU/PRO	828,3578	320.2+/-296.5	83,662,1458	30.0	35.0	33.0		1871	-0.4	0.0	9	dbSNP_107	33	4570,4030	582.2+/-391.4	1195,2180,925	yes	missense	AKNA	NM_030767.4	98	1278,2842,2383	AA,AG,GG		46.8605,18.7926,41.5039	possibly-damaging	624/1440	117124731	5398,7608	2203	4300	6503	SO:0001583	missense	80709	exon8			GCAAGCGGCTGGG	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.1871C>T	9.37:g.117124731G>A	ENSP00000303769:p.Pro624Leu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	833	0.3814102564102564	55	0.11178861788617886	179	0.494475138121547	218	0.3811188811188811	381	0.5026385224274407	g	10.14	1.267287	0.23136	0.187926	0.531395	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000223791;ENST00000374075;ENST00000312033	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	4.7	-0.371	0.12525	.	0.691128	0.12739	N	0.443148	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	P;B	0.38110	0.618;0.072	B;B	0.31946	0.138;0.009	T	0.44847	-0.9301	9	0.07990	T	0.79	-4.3767	4.4668	0.11692	0.0:0.1894:0.3545:0.4561	rs3748176;rs3748176	624;543	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	L	624;465;624;84;543;624	ENSP00000303769:P624L;ENSP00000363201:P624L;ENSP00000223791:P84L;ENSP00000363188:P543L;ENSP00000309222:P624L	ENSP00000223791:P84L	P	-	2	0	AKNA	116164552	0.048000	0.20356	0.001000	0.08648	0.003000	0.03518	0.347000	0.20014	-0.219000	0.10003	-0.422000	0.05995	CCG	G|0.599;A|0.401	0.401	strong		0.657	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
SULT6B1	391365	hgsc.bcm.edu	37	2	37406644	37406644	+	Silent	SNP	A	A	G	rs10182091	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:37406644A>G	ENST00000535679.1	-	4	485	c.486T>C	c.(484-486)taT>taC	p.Y162Y	SULT6B1_ENST00000407963.1_Silent_p.Y124Y|SULT6B1_ENST00000260637.3_Silent_p.Y124Y|SULT6B1_ENST00000379149.2_Intron			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	162						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				CCCAAGAGCCATAGCTTGGAA	0.378													A|||	2128	0.42492	0.2322	0.4207	5008	,	,		19585	0.8006		0.2565	False		,,,				2504	0.4744				p.Y124Y		Atlas-SNP	.											.	SULT6B1	46	.	0			c.T372C						PASS	.	A		1101,3305	398.1+/-330.7	142,817,1244	160.0	150.0	154.0		372	-1.7	0.8	2	dbSNP_119	154	2157,6443	371.0+/-336.1	299,1559,2442	no	coding-synonymous	SULT6B1	NM_001032377.1		441,2376,3686	GG,GA,AA		25.0814,24.9887,25.05		124/266	37406644	3258,9748	2203	4300	6503	SO:0001819	synonymous_variant	391365	exon4			AGAGCCATAGCTT	AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"""Sulfotransferases, cytosolic"""	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.486T>C	2.37:g.37406644A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_001032377	B2RTS7	Silent	SNP	ENST00000535679.1	37																																																																																				A|0.697;G|0.303	0.303	strong		0.378	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377	
ZNF665	79788	hgsc.bcm.edu	37	19	53667804	53667804	+	Missense_Mutation	SNP	C	C	T	rs4801958	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:53667804C>T	ENST00000600412.1	-	2	1859	c.1744G>A	c.(1744-1746)Gtc>Atc	p.V582I	ZNF665_ENST00000396424.3_Missense_Mutation_p.V647I|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	582			V -> I (in dbSNP:rs4801958). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		CCAGTATGGACTGCCATATGG	0.388													T|||	2591	0.517372	0.1543	0.6499	5008	,	,		20489	0.6438		0.5974	False		,,,				2504	0.7014				p.V647I		Atlas-SNP	.											.	ZNF665	136	.	0			c.G1939A						PASS	.	T	ILE/VAL	1021,3377	686.7+/-404.7	127,767,1305	77.0	81.0	80.0		1939	2.7	0.0	19	dbSNP_111	80	5242,3358	487.8+/-372.2	1586,2070,644	yes	missense	ZNF665	NM_024733.3	29	1713,2837,1949	TT,TC,CC		39.0465,23.2151,48.1843	benign	647/679	53667804	6263,6735	2199	4300	6499	SO:0001583	missense	79788	exon4			TATGGACTGCCAT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1744G>A	19.37:g.53667804C>T	ENSP00000469154:p.Val582Ile	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	37		1113	0.5096153846153846	67	0.13617886178861788	218	0.6022099447513812	371	0.6486013986013986	457	0.6029023746701847	T	0.011	-1.692993	0.00731	0.232151	0.609535	ENSG00000197497	ENST00000396424	T	0.07688	3.17	2.67	2.67	0.31697	.	.	.	.	.	T	0.00012	0.0000	N	0.03304	-0.355	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.37776	-0.9691	8	0.02654	T	1	.	5.2111	0.15316	0.0:0.4054:0.0:0.5946	rs4801958;rs52820557;rs57753779;rs4801958	647	Q9H7R5-2	.	I	647	ENSP00000379702:V647I	ENSP00000379702:V647I	V	-	1	0	ZNF665	58359616	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.034000	0.12225	0.262000	0.21774	-0.408000	0.06270	GTC	C|0.514;T|0.486	0.486	strong		0.388	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
VAV3	10451	hgsc.bcm.edu	37	1	108185309	108185309	+	Missense_Mutation	SNP	G	G	A	rs12410676	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:108185309G>A	ENST00000370056.4	-	20	2120	c.1846C>T	c.(1846-1848)Cct>Tct	p.P616S	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000544443.1_Missense_Mutation_p.P20S|VAV3_ENST00000415432.2_Missense_Mutation_p.P56S|VAV3_ENST00000527011.1_Missense_Mutation_p.P616S	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	616	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.|Sufficient for interaction with ROS1.		P -> S (in dbSNP:rs12410676).		angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		AGCTGTAAAGGGGGTCCTTCA	0.478													G|||	711	0.141973	0.0439	0.1599	5008	,	,		17260	0.2073		0.1093	False		,,,				2504	0.228				p.P616S		Atlas-SNP	.											.	VAV3	176	.	0			c.C1846T						PASS	.	G	SER/PRO,SER/PRO	299,4107	163.3+/-195.1	16,267,1920	117.0	114.0	115.0		166,1846	3.8	0.4	1	dbSNP_120	115	1069,7531	226.1+/-261.9	68,933,3299	yes	missense,missense	VAV3	NM_001079874.1,NM_006113.4	74,74	84,1200,5219	AA,AG,GG		12.4302,6.7862,10.5182	benign,benign	56/288,616/848	108185309	1368,11638	2203	4300	6503	SO:0001583	missense	10451	exon20			GTAAAGGGGGTCC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1846C>T	1.37:g.108185309G>A	ENSP00000359073:p.Pro616Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	269	0.12316849816849818	19	0.03861788617886179	50	0.13812154696132597	122	0.21328671328671328	78	0.10290237467018469	G	0.012	-1.670431	0.00758	0.067862	0.124302	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000544443;ENST00000415432	T;T;T;T	0.28666	1.6;2.6;2.6;1.6	5.67	3.79	0.43588	Src homology-3 domain (3);Variant SH3 (1);	0.278574	0.41605	D	0.000851	T	0.09642	0.0237	L	0.37507	1.11	0.09310	P	0.9999999999981535	B;B;B;B	0.25955	0.005;0.006;0.018;0.138	B;B;B;B	0.24701	0.01;0.053;0.055;0.049	T	0.10800	-1.0614	9	0.35671	T	0.21	.	7.8404	0.29395	0.1411:0.1332:0.7257:0.0	rs12410676;rs17229675;rs52831754;rs57980445;rs12410676	616;20;616;56	E9PQ97;B7Z3Z5;Q9UKW4;Q9UKW4-3	.;.;VAV3_HUMAN;.	S	616;616;20;56	ENSP00000359073:P616S;ENSP00000432540:P616S;ENSP00000446404:P20S;ENSP00000394897:P56S	ENSP00000359073:P616S	P	-	1	0	VAV3	107986832	1.000000	0.71417	0.418000	0.26571	0.063000	0.16089	2.877000	0.48506	0.760000	0.33108	-0.228000	0.12330	CCT	G|0.884;A|0.116	0.116	strong		0.478	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526044	150526044	+	Missense_Mutation	SNP	G	G	C	rs41317515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:150526044G>C	ENST00000369038.2	+	4	778	c.577G>C	c.(577-579)Gct>Cct	p.A193P	ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.A193P|RP11-54A4.2_ENST00000442435.2_RNA|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.A193P|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.A193P			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	193			A -> P (in dbSNP:rs41317515). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			AGGGGAAGAGGCTATTCCGTC	0.607													C|||	2646	0.528355	0.6074	0.4337	5008	,	,		15288	0.5675		0.5338	False		,,,				2504	0.4427				p.A193P		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.G577C						PASS	.	C	PRO/ALA,PRO/ALA	2600,1806	530.3+/-372.9	787,1026,390	118.0	115.0	116.0		577,577	-4.6	0.0	1	dbSNP_127	116	4515,4085	561.1+/-387.7	1178,2159,963	yes	missense,missense	ADAMTSL4	NM_019032.4,NM_025008.3	27,27	1965,3185,1353	CC,CG,GG		47.5,40.9896,45.2945	benign,benign	193/1075,193/878	150526044	7115,5891	2203	4300	6503	SO:0001583	missense	54507	exon6			GAAGAGGCTATTC	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.577G>C	1.37:g.150526044G>C	ENSP00000358034:p.Ala193Pro	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	179	177	0.988827	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	1217	0.5572344322344323	295	0.5995934959349594	177	0.4889502762430939	319	0.5576923076923077	426	0.5620052770448549	C	0.516	-0.864147	0.02590	0.590104	0.525	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000369039;ENST00000369038	T;T;T;T	0.63255	0.05;-0.03;0.23;-0.03	3.65	-4.57	0.03421	.	.	.	.	.	T	0.12603	0.0306	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.11641	-1.0579	8	0.28530	T	0.3	.	3.1698	0.06549	0.1886:0.2054:0.4843:0.1217	rs41317515;rs59910312;rs61819441	193;193;193	F8WAD0;Q6UY14;Q6UY14-2	.;ATL4_HUMAN;.	P	193	ENSP00000358037:A193P;ENSP00000271643:A193P;ENSP00000358035:A193P;ENSP00000358034:A193P	ENSP00000271643:A193P	A	+	1	0	ADAMTSL4	148792668	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.494000	0.02296	-1.085000	0.03088	-1.087000	0.02190	GCT	G|0.456;C|0.544	0.544	strong		0.607	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
BMPER	168667	hgsc.bcm.edu	37	7	34009955	34009955	+	Silent	SNP	A	A	T	rs147600292	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:34009955A>T	ENST00000297161.2	+	6	791	c.417A>T	c.(415-417)acA>acT	p.T139T	BMPER_ENST00000426693.1_Silent_p.T139T	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	139	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GCGTTGTCACAGAGTCTGGGG	0.498													A|||	9	0.00179712	0.0015	0.0014	5008	,	,		19530	0.0		0.006	False		,,,				2504	0.0				p.T139T		Atlas-SNP	.											.	BMPER	131	.	0			c.A417T						PASS	.	A		10,4396	16.8+/-37.8	0,10,2193	235.0	198.0	211.0		417	-1.1	1.0	7	dbSNP_134	211	64,8536	39.8+/-96.3	0,64,4236	no	coding-synonymous	BMPER	NM_133468.3		0,74,6429	TT,TA,AA		0.7442,0.227,0.569		139/686	34009955	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon6			TGTCACAGAGTCT		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.417A>T	7.37:g.34009955A>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	242	111	0.458678	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	10.79	1.449114	0.26074	0.00227	0.007442	ENSG00000164619	ENST00000436222	.	.	.	5.75	-1.1	0.09872	.	.	.	.	.	T	0.47414	0.1444	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53927	-0.8369	5	0.87932	D	0	.	3.3583	0.07177	0.5251:0.2491:0.132:0.0939	.	.	.	.	L	106	.	ENSP00000399843:Q106L	Q	+	2	0	BMPER	33976480	0.376000	0.25098	0.996000	0.52242	0.772000	0.43724	-0.422000	0.07043	-0.145000	0.11294	-0.256000	0.11100	CAG	A|0.994;T|0.006	0.006	strong		0.498	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
CPN1	1369	hgsc.bcm.edu	37	10	101829514	101829514	+	Missense_Mutation	SNP	C	C	T	rs61751507	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:101829514C>T	ENST00000370418.3	-	3	784	c.533G>A	c.(532-534)gGc>gAc	p.G178D		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	178	Catalytic.		G -> D (in CPND; dbSNP:rs61751507). {ECO:0000269|PubMed:12560874}.		response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		GTGGTTGGGGCCTCCGTACTT	0.468													C|||	133	0.0265575	0.0023	0.0634	5008	,	,		15964	0.0248		0.0437	False		,,,				2504	0.0174				p.G178D		Atlas-SNP	.											.	CPN1	62	.	0			c.G533A	GRCh37	CM032216	CPN1	M	rs61751507	PASS	.		ASP/GLY	48,4358	49.6+/-84.7	0,48,2155	125.0	124.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	533	4.2	1.0	10	dbSNP_129	124	413,8187	129.0+/-187.1	9,395,3896	yes	missense	CPN1	NM_001308.2	94	9,443,6051	TT,TC,CC		4.8023,1.0894,3.5445	probably-damaging	178/459	101829514	461,12545	2203	4300	6503	SO:0001583	missense	1369	exon3			TTGGGGCCTCCGT	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.533G>A	10.37:g.101829514C>T	ENSP00000359446:p.Gly178Asp	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	202	105	0.519802	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	70	0.03205128205128205	1	0.0020325203252032522	22	0.06077348066298342	16	0.027972027972027972	31	0.040897097625329816	C	13.23	2.175745	0.38413	0.010894	0.048023	ENSG00000120054	ENST00000370418	T	0.13538	2.58	5.15	4.25	0.50352	Peptidase M14, carboxypeptidase A (2);	0.047712	0.85682	D	0.000000	T	0.03564	0.0102	M	0.67953	2.075	0.80722	D	1	P	0.45634	0.863	P	0.54924	0.764	T	0.00226	-1.1900	10	0.36615	T	0.2	-31.2132	16.1748	0.81844	0.0:0.8664:0.1336:0.0	rs61751507	178	P15169	CBPN_HUMAN	D	178	ENSP00000359446:G178D	ENSP00000359446:G178D	G	-	2	0	CPN1	101819504	1.000000	0.71417	0.997000	0.53966	0.011000	0.07611	6.045000	0.71020	1.316000	0.45131	-0.384000	0.06662	GGC	C|0.965;T|0.035	0.035	strong		0.468	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388553	1388553	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:1388553A>G	ENST00000324803.4	+	1	3214	c.254A>G	c.(253-255)cAc>cGc	p.H85R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	85					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGGAGTGCCCACCTGCTCACA	0.647																																					p.H85R		Atlas-SNP	.											CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	0			c.A254G						scavenged	.						276.0	239.0	251.0					4																	1388553		2203	4300	6503	SO:0001583	missense	285464	exon1			GTGCCCACCTGCT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.254A>G	4.37:g.1388553A>G	ENSP00000323978:p.His85Arg	Somatic	296	5	0.0168919		WXS	Illumina HiSeq	Phase_I	261	18	0.0689655	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	N	2.225	-0.377390	0.05000	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.22336	1.96	1.11	0.176	0.15049	.	.	.	.	.	T	0.08223	0.0205	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41734	-0.9492	9	0.11485	T	0.65	.	5.3685	0.16127	0.3874:0.0:0.6126:0.0	.	85	Q8N1N5	CRPAK_HUMAN	R	85;78	ENSP00000323978:H85R	ENSP00000323978:H85R	H	+	2	0	CRIPAK	1378553	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.861000	0.00726	-0.365000	0.08076	-1.123000	0.02005	CAC	.	.	none		0.647	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
MTHFS	10588	hgsc.bcm.edu	37	15	80189277	80189277	+	Silent	SNP	C	C	T	rs375170671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:80189277C>T	ENST00000258874.3	-	1	114	c.54G>A	c.(52-54)aaG>aaA	p.K18K	MTHFS_ENST00000559722.1_Intron|ST20-MTHFS_ENST00000479961.1_Intron|ST20-MTHFS_ENST00000494999.1_Intron	NM_006441.3	NP_006432.1	P49914	MTHFS_HUMAN	5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)	18					formate metabolic process (GO:0015942)|tetrahydrofolate metabolic process (GO:0046653)	cytoplasm (GO:0005737)	5-formyltetrahydrofolate cyclo-ligase activity (GO:0030272)|ATP binding (GO:0005524)|folic acid binding (GO:0005542)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|liver(1)	5				all cancers(203;0.00467)		GCAGACGCTGCTTCAGCTCTC	0.736													C|||	8	0.00159744	0.0	0.0029	5008	,	,		11491	0.0		0.004	False		,,,				2504	0.002				p.K18K		Atlas-SNP	.											.	MTHFS	11	.	0			c.G54A						PASS	.	C	,,	3,3811		0,3,1904	6.0	6.0	6.0		,,54	4.0	1.0	15		6	24,7530		0,24,3753	no	intron,intron,coding-synonymous	MTHFS,ST20-MTHFS	NM_001199758.1,NM_001199760.1,NM_006441.3	,,	0,27,5657	TT,TC,CC		0.3177,0.0787,0.2375	,,	,,18/204	80189277	27,11341	1907	3777	5684	SO:0001819	synonymous_variant	10588	exon1			ACGCTGCTTCAGC	L38928	CCDS10311.1	15q24.3	2014-05-15			ENSG00000136371	ENSG00000136371	6.3.3.2		7437	protein-coding gene	gene with protein product		604197				8522195	Standard	NM_006441		Approved	HsT19268	uc002bex.4	P49914	OTTHUMG00000144174	ENST00000258874.3:c.54G>A	15.37:g.80189277C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	19	15	0.789474	NM_006441	H3BQ75	Silent	SNP	ENST00000258874.3	37	CCDS10311.1																																																																																			.	.	weak		0.736	MTHFS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291374.2	NM_006441	
ASGR2	433	hgsc.bcm.edu	37	17	7012077	7012077	+	Splice_Site	SNP	C	C	T	rs2304979	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7012077C>T	ENST00000380952.2	-	3	519	c.255G>A	c.(253-255)ggG>ggA	p.G85G	ASGR2_ENST00000446679.2_Splice_Site_p.G66G|ASGR2_ENST00000254850.7_Intron|ASGR2_ENST00000355035.5_Splice_Site_p.G85G	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	85			G -> R (in dbSNP:rs2304978). {ECO:0000269|PubMed:1371982, ECO:0000269|PubMed:3863106, ECO:0000269|Ref.4}.		bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)	p.G85G(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	CCTGCTGGCCCCCGTGACCCT	0.632													C|||	1277	0.254992	0.0703	0.3689	5008	,	,		14724	0.2887		0.2724	False		,,,				2504	0.3712				p.G85G		Atlas-SNP	.											ASGR2,NS,carcinoma,-2,2	ASGR2	38	2	1	Substitution - coding silent(1)	stomach(1)	c.G255A						PASS	.	C	,,,,	474,3932	216.1+/-234.9	30,414,1759	68.0	60.0	63.0		255,,255,,198	-0.3	0.0	17	dbSNP_100	63	2427,6173	390.0+/-343.1	362,1703,2235	no	coding-synonymous-near-splice,intron,coding-synonymous-near-splice,intron,coding-synonymous-near-splice	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	,,,,	392,2117,3994	TT,TC,CC		28.2209,10.7581,22.3051	,,,,	85/312,,85/312,,66/293	7012077	2901,10105	2203	4300	6503	SO:0001630	splice_region_variant	433	exon3			CTGGCCCCCGTGA	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.256+1G>A	17.37:g.7012077C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	185	84	0.454054	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Silent	SNP	ENST00000380952.2	37	CCDS32544.1																																																																																			C|0.777;T|0.223	0.223	strong		0.632	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	Silent
MYO5C	55930	hgsc.bcm.edu	37	15	52534344	52534344	+	Silent	SNP	G	G	A	rs3751631	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:52534344G>A	ENST00000261839.7	-	20	2618	c.2457C>T	c.(2455-2457)cgC>cgT	p.R819R	MYO5C_ENST00000443683.2_Intron	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	819	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		CAAGATACCCGCGGCAGTGCT	0.498													G|||	1918	0.382987	0.1415	0.6167	5008	,	,		21504	0.0417		0.8171	False		,,,				2504	0.4489				p.R819R		Atlas-SNP	.											MYO5C,colon,carcinoma,0,1	MYO5C	162	1	0			c.C2457T						PASS	.	G		1127,2871		161,805,1033	264.0	266.0	266.0		2457	-10.3	0.0	15	dbSNP_107	266	6795,1557		2766,1263,147	no	coding-synonymous	MYO5C	NM_018728.3		2927,2068,1180	AA,AG,GG		18.6422,28.1891,35.8543		819/1743	52534344	7922,4428	1999	4176	6175	SO:0001819	synonymous_variant	55930	exon20			ATACCCGCGGCAG	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.2457C>T	15.37:g.52534344G>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	274	272	0.992701	NM_018728	Q6P1W8	Silent	SNP	ENST00000261839.7	37	CCDS42036.1																																																																																			G|0.534;A|0.466	0.466	strong		0.498	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
CAND2	23066	hgsc.bcm.edu	37	3	12857493	12857493	+	Missense_Mutation	SNP	C	C	T	rs2305397	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:12857493C>T	ENST00000456430.2	+	9	1468	c.1427C>T	c.(1426-1428)cCt>cTt	p.P476L	CAND2_ENST00000295989.5_Missense_Mutation_p.P383L	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	476			P -> L (in dbSNP:rs2305397).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GAGCATATGCCTGTGCTGGTA	0.627													C|||	1617	0.322883	0.3154	0.366	5008	,	,		19330	0.1766		0.5775	False		,,,				2504	0.1912				p.P476L	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,caecum,carcinoma,0,2	CAND2	138	2	0			c.C1427T						PASS	.	C	LEU/PRO,LEU/PRO	1410,2662		251,908,877	57.0	63.0	61.0		1427,1148	5.1	0.8	3	dbSNP_100	61	4400,3966		1144,2112,927	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	98,98	1395,3020,1804	TT,TC,CC		47.4062,34.6267,46.7117	benign,benign	476/1237,383/1120	12857493	5810,6628	2036	4183	6219	SO:0001583	missense	23066	exon9			ATATGCCTGTGCT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1427C>T	3.37:g.12857493C>T	ENSP00000387641:p.Pro476Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	203	110	0.541872	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	803	0.3676739926739927	162	0.32926829268292684	122	0.3370165745856354	88	0.15384615384615385	431	0.5686015831134564	C	12.11	1.841013	0.32513	0.346267	0.525938	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.11277	2.79;2.79	5.12	5.12	0.69794	Armadillo-like helical (1);Armadillo-type fold (1);	0.126888	0.53938	D	0.000055	T	0.00012	0.0000	M	0.69248	2.105	0.09310	P	1.0	B;B	0.25904	0.005;0.137	B;B	0.32533	0.009;0.147	T	0.45175	-0.9279	9	0.46703	T	0.11	-10.0664	16.0847	0.81038	0.0:1.0:0.0:0.0	rs2305397;rs17825005;rs52819689;rs59943117;rs2305397	476;383	O75155;O75155-2	CAND2_HUMAN;.	L	383;476	ENSP00000295989:P383L;ENSP00000387641:P476L	ENSP00000295989:P383L	P	+	2	0	CAND2	12832493	1.000000	0.71417	0.846000	0.33378	0.346000	0.29079	5.984000	0.70548	2.395000	0.81488	0.561000	0.74099	CCT	C|0.612;T|0.386	0.386	strong		0.627	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
TNS1	7145	hgsc.bcm.edu	37	2	218695102	218695102	+	Missense_Mutation	SNP	G	G	A	rs3796028	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:218695102G>A	ENST00000171887.4	-	21	3462	c.3010C>T	c.(3010-3012)Cgg>Tgg	p.R1004W	TNS1_ENST00000430930.1_Intron|TNS1_ENST00000419504.1_Missense_Mutation_p.R1004W	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1004			R -> W (in dbSNP:rs3796028).		cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGCTGGATCCGTCTTCTGGTA	0.567													G|||	1880	0.375399	0.32	0.4308	5008	,	,		19019	0.4276		0.3648	False		,,,				2504	0.3681				p.R1004W		Atlas-SNP	.											.	TNS1	251	.	0			c.C3010T						PASS	.	G	TRP/ARG	1375,3031	455.5+/-351.0	201,973,1029	84.0	73.0	77.0		3010	-1.2	1.0	2	dbSNP_107	77	2946,5654	457.3+/-364.3	501,1944,1855	yes	missense	TNS1	NM_022648.4	101	702,2917,2884	AA,AG,GG		34.2558,31.2074,33.2231	possibly-damaging	1004/1736	218695102	4321,8685	2203	4300	6503	SO:0001583	missense	7145	exon21			GGATCCGTCTTCT	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.3010C>T	2.37:g.218695102G>A	ENSP00000171887:p.Arg1004Trp	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	842	0.38553113553113555	175	0.3556910569105691	144	0.39779005524861877	256	0.44755244755244755	267	0.35224274406332456	G	3.509	-0.100132	0.07010	0.312074	0.342558	ENSG00000079308	ENST00000171887;ENST00000419504	D;D	0.91407	-2.84;-2.83	4.4	-1.23	0.09465	.	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999888189	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34725	-0.9817	9	0.59425	D	0.04	.	4.2296	0.10597	0.0938:0.2993:0.47:0.1369	rs3796028;rs17789579;rs3796028	1004;1004	Q9HBL0;E9PF55	TENS1_HUMAN;.	W	1004	ENSP00000171887:R1004W;ENSP00000408724:R1004W	ENSP00000171887:R1004W	R	-	1	2	TNS1	218403347	0.797000	0.28877	0.993000	0.49108	0.017000	0.09413	-0.422000	0.07043	-0.055000	0.13244	-2.034000	0.00421	CGG	G|0.646;A|0.354	0.354	strong		0.567	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
ZNF429	353088	hgsc.bcm.edu	37	19	21720803	21720803	+	Missense_Mutation	SNP	C	C	T	rs2562473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:21720803C>T	ENST00000358491.4	+	4	2156	c.1948C>T	c.(1948-1950)Cat>Tat	p.H650Y	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	650			H -> Y (in dbSNP:rs2562473).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						tgtggtggctcatgcctgtaa	0.488													t|||	819	0.163538	0.1778	0.1787	5008	,	,		14899	0.0754		0.2038	False		,,,				2504	0.183				p.H650Y		Atlas-SNP	.											ZNF429,NS,carcinoma,-2,2	ZNF429	338	2	0			c.C1948T						PASS	.	T	TYR/HIS	679,3211		55,569,1321	37.0	38.0	38.0		1948	-0.8	0.0	19	dbSNP_100	38	1600,6718		135,1330,2694	yes	missense	ZNF429	NM_001001415.2	83	190,1899,4015	TT,TC,CC		19.2354,17.455,18.6681	benign	650/675	21720803	2279,9929	1945	4159	6104	SO:0001583	missense	353088	exon4			GTGGCTCATGCCT	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1948C>T	19.37:g.21720803C>T	ENSP00000351280:p.His650Tyr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	37	CCDS42537.1	343	0.15705128205128205	83	0.16869918699186992	68	0.1878453038674033	35	0.06118881118881119	157	0.20712401055408972	.	0.004	-2.242206	0.00274	0.17455	0.192354	ENSG00000197013	ENST00000358491	T	0.51817	0.69	0.418	-0.836	0.10770	.	.	.	.	.	T	0.00039	0.0001	L	0.58428	1.81	0.58432	P	1.0000000000287557E-6	P	0.42456	0.78	B	0.32393	0.145	T	0.22730	-1.0208	8	0.02654	T	1	.	3.8318	0.08877	0.0:0.4162:0.0:0.5838	rs2562473	650	Q86V71	ZN429_HUMAN	Y	650	ENSP00000351280:H650Y	ENSP00000351280:H650Y	H	+	1	0	ZNF429	21512643	0.000000	0.05858	0.024000	0.17045	0.023000	0.10783	-1.171000	0.03115	-0.346000	0.08312	-0.346000	0.07831	CAT	C|0.842;T|0.158	0.158	strong		0.488	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	
DPM2	8818	hgsc.bcm.edu	37	9	130698043	130698043	+	Silent	SNP	A	A	G	rs6781	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:130698043A>G	ENST00000314392.8	-	4	876	c.213T>C	c.(211-213)taT>taC	p.Y71Y	RP11-203J24.8_ENST00000608805.1_RNA|RP11-203J24.8_ENST00000592240.1_RNA|RP11-203J24.8_ENST00000587978.1_RNA|RP11-203J24.8_ENST00000590283.1_RNA|RP11-203J24.8_ENST00000591408.1_RNA|RP11-203J24.8_ENST00000588890.1_RNA|RP11-203J24.8_ENST00000587355.1_RNA|RP11-203J24.8_ENST00000586374.1_RNA	NM_003863.3	NP_003854.1	O94777	DPM2_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 2, regulatory subunit	71					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|dolichol metabolic process (GO:0019348)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked mannosylation (GO:0035269)|regulation of protein stability (GO:0031647)	dolichol-phosphate-mannose synthase complex (GO:0033185)|endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of endoplasmic reticulum membrane (GO:0030176)|perinuclear region of cytoplasm (GO:0048471)	dolichyl-phosphate beta-D-mannosyltransferase activity (GO:0004582)|enzyme regulator activity (GO:0030234)			lung(1)	1						TCAGCATCACATAGGAGATGA	0.577													G|||	3661	0.73103	0.6498	0.8833	5008	,	,		21533	0.6498		0.8728	False		,,,				2504	0.6708				p.Y71Y		Atlas-SNP	.											.	DPM2	6	.	0			c.T213C						PASS	.	G		3001,1405	460.7+/-352.7	1024,953,226	130.0	109.0	116.0		213	-4.8	0.4	9	dbSNP_52	116	7478,1122	231.8+/-265.7	3262,954,84	no	coding-synonymous	DPM2	NM_003863.3		4286,1907,310	GG,GA,AA		13.0465,31.8883,19.4295		71/85	130698043	10479,2527	2203	4300	6503	SO:0001819	synonymous_variant	8818	exon4			CATCACATAGGAG	AB013361	CCDS6886.1	9q34.13	2013-02-26			ENSG00000136908	ENSG00000136908			3006	protein-coding gene	gene with protein product	"""DPM synthase complex subunit"""	603564				9724629	Standard	NM_003863		Approved	MGC21559, MGC111193	uc004bsv.2	O94777	OTTHUMG00000020725	ENST00000314392.8:c.213T>C	9.37:g.130698043A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_003863	Q5XKK9|Q6FGH3	Silent	SNP	ENST00000314392.8	37	CCDS6886.1																																																																																			A|0.231;G|0.769	0.769	strong		0.577	DPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054324.1	NM_003863	
FAM78A	286336	hgsc.bcm.edu	37	9	134136248	134136248	+	Silent	SNP	G	G	A	rs9966	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:134136248G>A	ENST00000372271.3	-	2	1180	c.813C>T	c.(811-813)taC>taT	p.Y271Y	FAM78A_ENST00000247295.4_5'UTR|FAM78A_ENST00000372269.3_Silent_p.Y268Y	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	271										NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		GCGGCTGCCCGTACTTGGGCC	0.582													G|||	434	0.0866613	0.0182	0.0951	5008	,	,		15398	0.0129		0.1879	False		,,,				2504	0.1452				p.Y271Y		Atlas-SNP	.											.	FAM78A	28	.	0			c.C813T						PASS	.	G		246,4160	135.7+/-171.8	9,228,1966	69.0	75.0	73.0		813	1.2	1.0	9	dbSNP_52	73	1859,6741	324.6+/-316.5	204,1451,2645	no	coding-synonymous	FAM78A	NM_033387.3		213,1679,4611	AA,AG,GG		21.6163,5.5833,16.1848		271/284	134136248	2105,10901	2203	4300	6503	SO:0001819	synonymous_variant	286336	exon2			CTGCCCGTACTTG	AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 59"""	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.813C>T	9.37:g.134136248G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_033387	Q86VQ9|Q9H7P4	Silent	SNP	ENST00000372271.3	37	CCDS6941.2																																																																																			G|0.872;A|0.128	0.128	strong		0.582	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387	
SEMA6D	80031	hgsc.bcm.edu	37	15	48056958	48056958	+	Silent	SNP	C	C	T	rs3743281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:48056958C>T	ENST00000316364.5	+	12	1660	c.1221C>T	c.(1219-1221)gcC>gcT	p.A407A	SEMA6D_ENST00000537942.1_Silent_p.A407A|SEMA6D_ENST00000355997.3_Silent_p.A407A|SEMA6D_ENST00000354744.4_Silent_p.A407A|SEMA6D_ENST00000389432.2_Silent_p.A407A|SEMA6D_ENST00000389428.3_Silent_p.A407A|SEMA6D_ENST00000536845.2_Silent_p.A407A|SEMA6D_ENST00000558014.1_Silent_p.A407A|SEMA6D_ENST00000358066.4_Silent_p.A407A|SEMA6D_ENST00000558816.1_Silent_p.A407A|SEMA6D_ENST00000389425.3_Silent_p.A407A|SEMA6D_ENST00000389433.2_Silent_p.A407A	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	407	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CACCCATTGCCGATGAGCCCT	0.502													C|||	945	0.188698	0.0431	0.2075	5008	,	,		21013	0.1746		0.2724	False		,,,				2504	0.3006				p.A407A		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C1221T						PASS	.	C	,,,,,,	305,4091	165.8+/-197.2	10,285,1903	78.0	74.0	75.0		1221,1221,1221,1221,1221,1221,1221	-4.9	0.4	15	dbSNP_107	75	2174,6420	370.8+/-336.0	268,1638,2391	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEMA6D	NM_001198999.1,NM_020858.1,NM_024966.2,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	,,,,,,	278,1923,4294	TT,TC,CC		25.2967,6.9381,19.0839	,,,,,,	407/1012,407/1012,407/477,407/999,407/1018,407/1074,407/598	48056958	2479,10511	2198	4297	6495	SO:0001819	synonymous_variant	80031	exon12			CATTGCCGATGAG	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1221C>T	15.37:g.48056958C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																			C|0.814;T|0.186	0.186	strong		0.502	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
ALPK1	80216	hgsc.bcm.edu	37	4	113353052	113353052	+	Silent	SNP	C	C	T	rs17044681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:113353052C>T	ENST00000458497.1	+	11	2628	c.2349C>T	c.(2347-2349)tcC>tcT	p.S783S	ALPK1_ENST00000177648.9_Silent_p.S783S|ALPK1_ENST00000504176.2_Silent_p.S705S	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	783							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CTAGTCCCTCCTGGGTTGACC	0.493													C|||	247	0.0493211	0.0197	0.0749	5008	,	,		19375	0.001		0.1501	False		,,,				2504	0.0174				p.S783S		Atlas-SNP	.											.	ALPK1	125	.	0			c.C2349T						PASS	.	C	,	173,4233	114.2+/-152.2	5,163,2035	56.0	55.0	55.0		2349,2349	-1.1	0.1	4	dbSNP_123	55	1189,7411	239.9+/-270.8	75,1039,3186	no	coding-synonymous,coding-synonymous	ALPK1	NM_001102406.1,NM_025144.3	,	80,1202,5221	TT,TC,CC		13.8256,3.9265,10.4721	,	783/1245,783/1245	113353052	1362,11644	2203	4300	6503	SO:0001819	synonymous_variant	80216	exon11			TCCCTCCTGGGTT	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2349C>T	4.37:g.113353052C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	42	24	0.571429	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	37	CCDS3697.1																																																																																			C|0.912;T|0.088	0.088	strong		0.493	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
FGD4	121512	hgsc.bcm.edu	37	12	32764184	32764184	+	Silent	SNP	G	G	A	rs10844253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32764184G>A	ENST00000427716.2	+	10	1729	c.1305G>A	c.(1303-1305)cgG>cgA	p.R435R	FGD4_ENST00000534526.2_Silent_p.R572R|FGD4_ENST00000531134.1_Silent_p.R520R|FGD4_ENST00000546442.1_Silent_p.R342R|FGD4_ENST00000381025.3_Silent_p.R187R|FGD4_ENST00000525053.1_Silent_p.R547R|FGD4_ENST00000266482.3_Silent_p.R187R	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	435	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					TAGCTGCTCGGAACACTTCAG	0.368													G|||	1328	0.265176	0.2027	0.2781	5008	,	,		18003	0.1657		0.3161	False		,,,				2504	0.3906				p.R435R		Atlas-SNP	.											FGD4,NS,carcinoma,+2,1	FGD4	86	1	0			c.G1305A						PASS	.	G		1049,3357	381.1+/-324.0	131,787,1285	95.0	98.0	97.0		1305	1.1	1.0	12	dbSNP_120	97	2691,5909	429.1+/-356.1	445,1801,2054	no	coding-synonymous	FGD4	NM_139241.2		576,2588,3339	AA,AG,GG		31.2907,23.8084,28.756		435/767	32764184	3740,9266	2203	4300	6503	SO:0001819	synonymous_variant	121512	exon10			TGCTCGGAACACT	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.1305G>A	12.37:g.32764184G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_139241	Q6ULS2|Q8TCP6	Silent	SNP	ENST00000427716.2	37	CCDS8727.1																																																																																			G|0.731;A|0.269	0.269	strong		0.368	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241	
SPTA1	6708	hgsc.bcm.edu	37	1	158584091	158584091	+	Missense_Mutation	SNP	A	A	G	rs952094	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158584091A>G	ENST00000368147.4	-	49	6974	c.6794T>C	c.(6793-6795)aTc>aCc	p.I2265T	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2265			I -> T (in dbSNP:rs952094).		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CACACCTTTGATGTCCCTGAA	0.333													G|||	2535	0.50619	0.4228	0.5202	5008	,	,		17099	0.6319		0.5636	False		,,,				2504	0.4202				p.I2265T		Atlas-SNP	.											.	SPTA1	720	.	0			c.T6794C						PASS	.	G	THR/ILE	1554,2056		323,908,574	67.0	65.0	65.0		6794	1.3	0.7	1	dbSNP_86	65	4396,3734		1214,1968,883	yes	missense	SPTA1	NM_003126.2	89	1537,2876,1457	GG,GA,AA		45.9287,43.0471,49.3186	benign	2265/2420	158584091	5950,5790	1805	4065	5870	SO:0001583	missense	6708	exon49			CCTTTGATGTCCC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6794T>C	1.37:g.158584091A>G	ENSP00000357129:p.Ile2265Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	1199	0.548992673992674	229	0.4654471544715447	188	0.5193370165745856	344	0.6013986013986014	438	0.5778364116094987	G	0.007	-1.972266	0.00457	0.430471	0.540713	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.49432	0.94;0.78	5.53	1.28	0.21552	EF-hand-like domain (1);	.	.	.	.	T	0.04998	0.0134	N	0.02247	-0.625	0.53688	P	2.8000000000028002E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.39761	-0.9598	8	0.02654	T	1	.	7.2407	0.26094	0.3063:0.1189:0.5748:0.0	rs952094;rs52828265;rs59527173;rs952094	2265	P02549	SPTA1_HUMAN	T	2265;2262	ENSP00000357130:I2265T;ENSP00000357129:I2262T	ENSP00000357129:I2262T	I	-	2	0	SPTA1	156850715	1.000000	0.71417	0.663000	0.29738	0.186000	0.23388	2.478000	0.45189	0.144000	0.18951	-0.724000	0.03597	ATC	A|0.461;G|0.539	0.539	strong		0.333	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20131115	20131115	+	Silent	SNP	C	C	T	rs9605069	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20131115C>T	ENST00000334554.7	+	10	2103	c.1962C>T	c.(1960-1962)aaC>aaT	p.N654N	ZDHHC8_ENST00000405930.3_Silent_p.N654N|ZDHHC8_ENST00000320602.7_Silent_p.N562N	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	654					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					CCAGCAGCAACGCCCCGGGGC	0.721													C|||	416	0.0830671	0.0045	0.1037	5008	,	,		14342	0.004		0.168	False		,,,				2504	0.1687				p.N654N		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.C1962T						PASS	.	C	,	132,4234		3,126,2054	18.0	19.0	19.0		1962,1962	0.9	0.8	22	dbSNP_119	19	1514,7072		129,1256,2908	no	coding-synonymous,coding-synonymous	ZDHHC8	NM_001185024.1,NM_013373.3	,	132,1382,4962	TT,TC,CC		17.6334,3.0234,12.7085	,	654/779,654/766	20131115	1646,11306	2183	4293	6476	SO:0001819	synonymous_variant	29801	exon10			CAGCAACGCCCCG	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1962C>T	22.37:g.20131115C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	8	6	0.75	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																			C|0.905;T|0.095	0.095	strong		0.721	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373	
HRNR	388697	hgsc.bcm.edu	37	1	152187551	152187551	+	Missense_Mutation	SNP	C	C	T	rs200451128		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:152187551C>T	ENST00000368801.2	-	3	6629	c.6554G>A	c.(6553-6555)cGc>cAc	p.R2185H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2185					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R2185H(2)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGTCGGCCGCGGCTAGGGGA	0.647																																					p.R2185H		Atlas-SNP	.											HRNR,colon,carcinoma,0,2	HRNR	403	2	2	Substitution - Missense(2)	large_intestine(2)	c.G6554A						scavenged	.						21.0	25.0	24.0					1																	152187551		2166	4278	6444	SO:0001583	missense	388697	exon3			CGGCCGCGGCTAG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6554G>A	1.37:g.152187551C>T	ENSP00000357791:p.Arg2185His	Somatic	247	5	0.0202429		WXS	Illumina HiSeq	Phase_I	501	7	0.0139721	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	5.811	0.334004	0.11013	.	.	ENSG00000197915	ENST00000368801	T	0.01599	4.74	3.24	-6.48	0.01896	.	.	.	.	.	T	0.00300	0.0009	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.48080	-0.9066	9	0.14252	T	0.57	.	1.9709	0.03406	0.1978:0.2038:0.3952:0.2031	.	2185	Q86YZ3	HORN_HUMAN	H	2185	ENSP00000357791:R2185H	ENSP00000357791:R2185H	R	-	2	0	HRNR	150454175	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.876000	0.00051	-2.560000	0.00474	-0.132000	0.14878	CGC	.	.	weak		0.647	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
HMHA1	23526	hgsc.bcm.edu	37	19	1068734	1068734	+	Silent	SNP	T	T	C	rs3764653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1068734T>C	ENST00000313093.2	+	2	643	c.412T>C	c.(412-414)Ttg>Ctg	p.L138L	HMHA1_ENST00000539243.2_Silent_p.L154L|HMHA1_ENST00000543365.1_5'Flank|HMHA1_ENST00000592335.1_5'Flank|HMHA1_ENST00000590214.1_Silent_p.L165L|HMHA1_ENST00000586866.1_Silent_p.L142L|HMHA1_ENST00000536472.1_Intron	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	138					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGTGTGTGTTGCGTGACGG	0.652													T|||	2027	0.404752	0.5265	0.3862	5008	,	,		16183	0.3611		0.3449	False		,,,				2504	0.3599				p.L154L		Atlas-SNP	.											.	HMHA1	78	.	0			c.T460C						PASS	.	T		2243,2157		578,1087,535	38.0	38.0	38.0		412	2.1	0.1	19	dbSNP_107	38	2998,5594		562,1874,1860	no	coding-synonymous	HMHA1	NM_012292.2		1140,2961,2395	CC,CT,TT		34.8929,49.0227,40.3402		138/1137	1068734	5241,7751	2200	4296	6496	SO:0001819	synonymous_variant	23526	exon2			TGTGTGTTGCGTG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.412T>C	19.37:g.1068734T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	201	73	0.363184	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			T|0.596;C|0.404	0.404	strong		0.652	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75981507	75981507	+	Silent	SNP	A	A	G	rs12900539	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:75981507A>G	ENST00000308508.5	-	3	1991	c.1899T>C	c.(1897-1899)ggT>ggC	p.G633G		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	633	Globular or compact configuration stabilized by disulfide bonds.|Interaction with COL5A1. {ECO:0000250}.|Interaction with COL6A2. {ECO:0000250}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCTGTGCAGGACCACCGCGGT	0.697													G|||	1870	0.373403	0.2716	0.4986	5008	,	,		16922	0.1865		0.5179	False		,,,				2504	0.4663				p.G633G		Atlas-SNP	.											.	CSPG4	175	.	0			c.T1899C						PASS	.	G		1293,3099		200,893,1103	22.0	23.0	23.0		1899	0.9	0.8	15	dbSNP_121	23	4587,3973		1292,2003,985	no	coding-synonymous	CSPG4	NM_001897.4		1492,2896,2088	GG,GA,AA		46.4136,29.4399,45.3984		633/2323	75981507	5880,7072	2196	4280	6476	SO:0001819	synonymous_variant	1464	exon3			TGCAGGACCACCG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1899T>C	15.37:g.75981507A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			A|0.591;G|0.409	0.409	strong		0.697	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
TERT	7015	hgsc.bcm.edu	37	5	1254594	1254594	+	Missense_Mutation	SNP	C	C	T	rs35719940	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:1254594C>T	ENST00000310581.5	-	15	3241	c.3184G>A	c.(3184-3186)Gcc>Acc	p.A1062T	TERT_ENST00000334602.6_Missense_Mutation_p.A999T|TERT_ENST00000296820.5_3'UTR	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1062	CTE.		A -> T (increased incidence in sporadic acute myeloid leukemia; dbSNP:rs35719940). {ECO:0000269|PubMed:15814878, ECO:0000269|PubMed:19147845, ECO:0000269|PubMed:19760749, ECO:0000269|Ref.7}.		DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	AGAGGGCCGGCGGCGCCCTTG	0.677									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis				c|||	26	0.00519169	0.0	0.0058	5008	,	,		15900	0.0		0.0219	False		,,,				2504	0.0				p.A1062T		Atlas-SNP	.											.	TERT	2594	.	0			c.G3184A						PASS	.	C	THR/ALA,THR/ALA	14,4152		0,14,2069	25.0	31.0	29.0		2995,3184	-8.6	0.0	5	dbSNP_126	29	186,8252		1,184,4034	yes	missense,missense	TERT	NM_001193376.1,NM_198253.2	58,58	1,198,6103	TT,TC,CC		2.2043,0.3361,1.5868	benign,benign	999/1070,1062/1133	1254594	200,12404	2083	4219	6302	SO:0001583	missense	7015	exon15	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GGCCGGCGGCGCC	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.3184G>A	5.37:g.1254594C>T	ENSP00000309572:p.Ala1062Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	37	CCDS3861.2	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	0	0.0	18	0.023746701846965697	c	10.86	1.469028	0.26335	0.003361	0.022043	ENSG00000164362	ENST00000310581;ENST00000334602	D;D	0.96396	-4.0;-3.89	4.28	-8.55	0.00908	.	1.569160	0.03262	N	0.183413	T	0.78349	0.4269	N	0.14661	0.345	0.09310	A	1.67216e-07	B;B	0.33022	0.394;0.336	B;B	0.22880	0.042;0.013	T	0.82281	-0.0535	9	0.09338	T	0.73	1.1101	5.3428	0.15992	0.1627:0.5321:0.0752:0.2299	rs35719940	999;1062	O14746-3;O14746	.;TERT_HUMAN	T	1062;999	ENSP00000309572:A1062T;ENSP00000334346:A999T	ENSP00000309572:A1062T	A	-	1	0	TERT	1307594	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	-2.306000	0.01133	-3.086000	0.00249	-0.516000	0.04426	GCC	C|0.990;T|0.010	0.010	strong		0.677	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2		
OR14C36	127066	hgsc.bcm.edu	37	1	248512498	248512498	+	Missense_Mutation	SNP	A	A	G	rs28448343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248512498A>G	ENST00000317861.1	+	1	422	c.422A>G	c.(421-423)cAg>cGg	p.Q141R		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	141			Q -> R (in dbSNP:rs28448343).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						ATCTGCATCCAGATGACACTG	0.522													a|||	1274	0.254393	0.0923	0.2594	5008	,	,		22483	0.4276		0.1938	False		,,,				2504	0.3538				p.Q141R		Atlas-SNP	.											OR14C36,rectum,carcinoma,+1,1	OR14C36	113	1	0			c.A422G						PASS	.	A	ARG/GLN	484,3922	225.2+/-241.2	28,428,1747	108.0	94.0	99.0		422	-1.4	0.0	1	dbSNP_125	99	1637,6963	303.4+/-306.4	154,1329,2817	yes	missense	OR14C36	NM_001001918.1	43	182,1757,4564	GG,GA,AA		19.0349,10.985,16.3079	probably-damaging	141/313	248512498	2121,10885	2203	4300	6503	SO:0001583	missense	127066	exon1			GCATCCAGATGAC	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"""GPCR / Class A : Olfactory receptors"""	15026	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BF, member 1"""	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.422A>G	1.37:g.248512498A>G	ENSP00000324534:p.Gln141Arg	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	184	84	0.456522	NM_001001918	Q6IEZ6	Missense_Mutation	SNP	ENST00000317861.1	37	CCDS31112.1	530	0.24267399267399267	61	0.12398373983739837	80	0.22099447513812154	232	0.40559440559440557	157	0.20712401055408972	A	10.28	1.305831	0.23736	0.10985	0.190349	ENSG00000177174	ENST00000317861	T	0.00091	8.74	4.05	-1.39	0.08997	GPCR, rhodopsin-like superfamily (1);	0.581781	0.14757	N	0.300211	T	0.00012	0.0000	L	0.42686	1.345	0.80722	P	0.0	D	0.60575	0.988	D	0.64877	0.93	T	0.11227	-1.0596	9	0.17832	T	0.49	.	1.3952	0.02259	0.4131:0.2239:0.2448:0.1182	rs28448343	141	Q8NHC7	O14CZ_HUMAN	R	141	ENSP00000324534:Q141R	ENSP00000324534:Q141R	Q	+	2	0	OR14C36	246579121	0.000000	0.05858	0.000000	0.03702	0.388000	0.30384	-1.082000	0.03400	-0.119000	0.11830	-0.560000	0.04181	CAG	A|0.811;G|0.189	0.189	strong		0.522	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918	
NKD1	85407	hgsc.bcm.edu	37	16	50667299	50667299	+	Silent	SNP	C	C	T	rs34100051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50667299C>T	ENST00000268459.3	+	10	1244	c.1020C>T	c.(1018-1020)gaC>gaT	p.D340D		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	340					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GCACCCAGGACGGGAGCAAGC	0.657													C|||	55	0.0109824	0.0015	0.0245	5008	,	,		13464	0.0		0.0278	False		,,,				2504	0.0082				p.D340D		Atlas-SNP	.											.	NKD1	43	.	0			c.C1020T						PASS	.	C		18,4378	24.3+/-50.5	0,18,2180	64.0	74.0	71.0		1020	-2.4	1.0	16	dbSNP_126	71	258,8342	100.8+/-162.1	2,254,4044	no	coding-synonymous	NKD1	NM_033119.4		2,272,6224	TT,TC,CC		3.0,0.4095,2.1237		340/471	50667299	276,12720	2198	4300	6498	SO:0001819	synonymous_variant	85407	exon10			CCAGGACGGGAGC	AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"""EF-hand domain containing"""	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.1020C>T	16.37:g.50667299C>T		Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	285	133	0.466667	NM_033119	B2RC39|Q8WZ08	Silent	SNP	ENST00000268459.3	37	CCDS10743.1																																																																																			C|0.981;T|0.019	0.019	strong		0.657	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1		
SALL4	57167	hgsc.bcm.edu	37	20	50407502	50407502	+	Missense_Mutation	SNP	A	A	C	rs6126344	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:50407502A>C	ENST00000217086.4	-	2	1631	c.1520T>G	c.(1519-1521)cTg>cGg	p.L507R	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	507			L -> R (in dbSNP:rs6126344). {ECO:0000269|PubMed:12395297}.		embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCCAGGCTGCAGGTCACCGGG	0.582													A|||	1797	0.358826	0.1218	0.3386	5008	,	,		18800	0.5962		0.335	False		,,,				2504	0.4734				p.L507R		Atlas-SNP	.											.	SALL4	168	.	0			c.T1520G						PASS	.	A	ARG/LEU	660,3746	275.4+/-272.5	47,566,1590	96.0	103.0	101.0		1520	1.9	1.0	20	dbSNP_114	101	2957,5643	453.1+/-363.1	519,1919,1862	yes	missense	SALL4	NM_020436.3	102	566,2485,3452	CC,CA,AA		34.3837,14.9796,27.8102	possibly-damaging	507/1054	50407502	3617,9389	2203	4300	6503	SO:0001583	missense	57167	exon2			GGCTGCAGGTCAC	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1520T>G	20.37:g.50407502A>C	ENSP00000217086:p.Leu507Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	765	0.35027472527472525	65	0.13211382113821138	130	0.35911602209944754	327	0.5716783216783217	243	0.32058047493403696	A	3.845	-0.033053	0.07543	0.149796	0.343837	ENSG00000101115	ENST00000217086	T	0.10382	2.88	5.34	1.9	0.25705	.	0.226097	0.22773	N	0.055811	T	0.00012	0.0000	M	0.61703	1.905	0.19775	P	0.9999563645	B	0.17852	0.024	B	0.10450	0.005	T	0.38564	-0.9655	9	0.10636	T	0.68	-2.9243	8.6398	0.33970	0.7793:0.0:0.2207:0.0	rs6126344	507	Q9UJQ4	SALL4_HUMAN	R	507	ENSP00000217086:L507R	ENSP00000217086:L507R	L	-	2	0	SALL4	49840909	0.998000	0.40836	0.979000	0.43373	0.486000	0.33341	2.155000	0.42301	0.343000	0.23821	-0.322000	0.08575	CTG	A|0.697;C|0.303	0.303	strong		0.582	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
PEX11A	8800	hgsc.bcm.edu	37	15	90226947	90226947	+	Silent	SNP	C	C	A	rs7169981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:90226947C>A	ENST00000300056.3	-	3	554	c.405G>T	c.(403-405)ctG>ctT	p.L135L	PEX11A_ENST00000561224.1_Intron|PEX11A_ENST00000561257.1_Silent_p.L104L|PEX11A_ENST00000559170.1_3'UTR|PEX11A_ENST00000557982.1_Intron	NM_001271573.1	NP_001258502.1	O75192	PX11A_HUMAN	peroxisomal biogenesis factor 11 alpha	135					brown fat cell differentiation (GO:0050873)|cellular lipid metabolic process (GO:0044255)|peroxisome fission (GO:0016559)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|regulation of peroxisome size (GO:0044375)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|lung(3)	7	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			GATCCCTGACCAGGCTCAGCA	0.502													C|||	2530	0.505192	0.5431	0.4914	5008	,	,		20987	0.2917		0.6958	False		,,,				2504	0.4877				p.L135L		Atlas-SNP	.											.	PEX11A	21	.	0			c.G405T						PASS	.	C		2561,1839	636.5+/-396.6	752,1057,391	151.0	148.0	149.0		405	1.3	1.0	15	dbSNP_116	149	6090,2508	694.3+/-404.7	2147,1796,356	no	coding-synonymous	PEX11A	NM_003847.1		2899,2853,747	AA,AC,CC		29.1696,41.7955,33.4436		135/248	90226947	8651,4347	2200	4299	6499	SO:0001819	synonymous_variant	8800	exon3			CCTGACCAGGCTC	AF093668	CCDS10354.1, CCDS61751.1	15q	2008-08-26	2008-08-26		ENSG00000166821	ENSG00000166821			8852	protein-coding gene	gene with protein product		603866	"""peroxisomal biogenesis factor 11A"""			9792670	Standard	NM_003847		Approved	PEX11-ALPHA, MGC119947, MGC138534	uc002boi.4	O75192	OTTHUMG00000149809	ENST00000300056.3:c.405G>T	15.37:g.90226947C>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	52	17	0.326923	NM_003847	B4DV88	Silent	SNP	ENST00000300056.3	37	CCDS10354.1																																																																																			C|0.398;A|0.602	0.602	strong		0.502	PEX11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313420.1	NM_003847	
TAS1R2	80834	hgsc.bcm.edu	37	1	19184077	19184077	+	Silent	SNP	A	A	G	rs68081213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:19184077A>G	ENST00000375371.3	-	2	252	c.231T>C	c.(229-231)ttT>ttC	p.F77F	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	77					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	CCTCCACCGCAAAGCGCATGG	0.547													-|||	1381	0.275759	0.3631	0.2853	5008	,	,		23250	0.1052		0.326	False		,,,				2504	0.2751				p.F77F		Atlas-SNP	.											.	TAS1R2	134	.	0			c.T231C						PASS	.			1451,2955		238,975,990	128.0	94.0	105.0		231	-2.2	1.0	1	dbSNP_130	105	2887,5713		471,1945,1884	no	coding-synonymous	TAS1R2	NM_152232.2		709,2920,2874	GG,GA,AA		33.5698,32.9324,33.3538		77/840	19184077	4338,8668	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon2			CACCGCAAAGCGC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.231T>C	1.37:g.19184077A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			A|0.684;G|0.316	0.316	strong		0.547	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
ALCAM	214	hgsc.bcm.edu	37	3	105266331	105266331	+	Silent	SNP	A	A	G	rs9855810	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:105266331A>G	ENST00000306107.5	+	11	1838	c.1338A>G	c.(1336-1338)caA>caG	p.Q446Q	ALCAM_ENST00000486979.2_Silent_p.Q395Q|ALCAM_ENST00000472644.2_Silent_p.Q446Q|ALCAM_ENST00000389927.4_Silent_p.Q168Q	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	446	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CAGCCATTCAATGGACAATTA	0.398													A|||	258	0.0515176	0.0091	0.049	5008	,	,		19951	0.0437		0.1074	False		,,,				2504	0.0613				p.Q446Q		Atlas-SNP	.											.	ALCAM	71	.	0			c.A1338G						PASS	.	A		125,4281	92.0+/-130.7	3,119,2081	103.0	99.0	101.0		1338	-0.6	1.0	3	dbSNP_119	101	1010,7588	215.5+/-254.8	67,876,3356	no	coding-synonymous	ALCAM	NM_001627.3		70,995,5437	GG,GA,AA		11.7469,2.837,8.7281		446/584	105266331	1135,11869	2203	4299	6502	SO:0001819	synonymous_variant	214	exon11			CATTCAATGGACA	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1338A>G	3.37:g.105266331A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	239	114	0.476987	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Silent	SNP	ENST00000306107.5	37	CCDS33810.1	133	0.060897435897435896	4	0.008130081300813009	23	0.06353591160220995	26	0.045454545454545456	80	0.10554089709762533	A	0.743	-0.775577	0.02951	0.02837	0.117469	ENSG00000170017	ENST00000465413	.	.	.	5.77	-0.614	0.11590	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.09310	P	0.9999999999986332	.	.	.	.	.	.	T	0.15407	-1.0438	3	.	.	.	-0.6385	1.9517	0.03368	0.3429:0.2099:0.3404:0.1068	rs9855810;rs17189333;rs56585623;rs9855810	.	.	.	V	207	.	.	M	+	1	0	ALCAM	106749021	0.999000	0.42202	0.995000	0.50966	0.182000	0.23217	0.379000	0.20585	-0.146000	0.11274	-1.039000	0.02377	ATG	A|0.924;G|0.076	0.076	strong		0.398	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
FAM83B	222584	hgsc.bcm.edu	37	6	54805889	54805889	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:54805889C>T	ENST00000306858.7	+	5	2236	c.2120C>T	c.(2119-2121)tCt>tTt	p.S707F	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	707								p.S707Y(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					CTGAAAAGTTCTAAAAGCATG	0.388																																					p.S707F		Atlas-SNP	.											FAM83B,rectum,carcinoma,0,1	FAM83B	186	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2120T						scavenged	.						90.0	92.0	91.0					6																	54805889		2203	4300	6503	SO:0001583	missense	222584	exon5			AAAGTTCTAAAAG	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2120C>T	6.37:g.54805889C>T	ENSP00000304078:p.Ser707Phe	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	109	2	0.0183486	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	8.661	0.900587	0.17686	.	.	ENSG00000168143	ENST00000306858	T	0.34472	1.36	5.55	2.78	0.32641	.	11.160900	0.00166	N	0.000000	T	0.22475	0.0542	L	0.53249	1.67	0.40031	D	0.975537	B	0.19200	0.034	B	0.17433	0.018	T	0.12630	-1.0540	10	0.72032	D	0.01	-12.6889	10.8617	0.46831	0.0:0.5604:0.3743:0.0654	.	707	Q5T0W9	FA83B_HUMAN	F	707	ENSP00000304078:S707F	ENSP00000304078:S707F	S	+	2	0	FAM83B	54913848	0.520000	0.26250	0.844000	0.33320	0.511000	0.34104	0.787000	0.26858	0.382000	0.24878	-0.150000	0.13652	TCT	.	.	none		0.388	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
SLIT3	6586	hgsc.bcm.edu	37	5	168233474	168233474	+	Silent	SNP	G	G	A	rs3797715	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:168233474G>A	ENST00000519560.1	-	9	1331	c.912C>T	c.(910-912)aaC>aaT	p.N304N	SLIT3_ENST00000332966.8_Silent_p.N304N|SLIT3_ENST00000404867.3_Silent_p.N304N	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	304	LRRNT 2.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCTCCGGCAAGTTGGCAGGAA	0.567													G|||	779	0.155551	0.0348	0.2032	5008	,	,		20482	0.2927		0.173	False		,,,				2504	0.1258				p.N304N	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C912T						PASS	.	G		283,4123	156.3+/-189.4	12,259,1932	87.0	79.0	82.0		912	3.6	0.9	5	dbSNP_107	82	1324,7276	258.7+/-282.2	107,1110,3083	no	coding-synonymous	SLIT3	NM_003062.2		119,1369,5015	AA,AG,GG		15.3953,6.4231,12.3558		304/1524	168233474	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	6586	exon9			CGGCAAGTTGGCA	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.912C>T	5.37:g.168233474G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	137	86	0.627737	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			G|0.859;A|0.141	0.141	strong		0.567	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
MYO7B	4648	hgsc.bcm.edu	37	2	128388790	128388790	+	Silent	SNP	G	G	A	rs13025791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:128388790G>A	ENST00000409816.2	+	35	4901	c.4869G>A	c.(4867-4869)gaG>gaA	p.E1623E	MYO7B_ENST00000389524.4_Silent_p.E1623E|MYO7B_ENST00000409090.1_Silent_p.E476E|MYO7B_ENST00000428314.1_Silent_p.E1623E			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1623	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GGGCTCCAGAGAAGGACATGG	0.657													G|||	842	0.168131	0.0499	0.1239	5008	,	,		15814	0.1349		0.2018	False		,,,				2504	0.3589				p.E1623E		Atlas-SNP	.											MYO7B_ENST00000428314,NS,carcinoma,0,2	MYO7B	359	2	0			c.G4869A						PASS	.	G		319,3965		11,297,1834	23.0	29.0	27.0		4869	0.1	1.0	2	dbSNP_121	27	1581,6879		132,1317,2781	no	coding-synonymous	MYO7B	NM_001080527.1		143,1614,4615	AA,AG,GG		18.6879,7.4463,14.909		1623/2117	128388790	1900,10844	2142	4230	6372	SO:0001819	synonymous_variant	4648	exon36			TCCAGAGAAGGAC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.4869G>A	2.37:g.128388790G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			G|0.852;A|0.148	0.148	strong		0.657	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
VWA5B2	90113	hgsc.bcm.edu	37	3	183953972	183953972	+	Silent	SNP	G	G	A	rs1709657	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:183953972G>A	ENST00000426955.2	+	8	1234	c.1134G>A	c.(1132-1134)ccG>ccA	p.P378P	VWA5B2_ENST00000273794.5_Silent_p.P159P|EIF2B5_ENST00000444495.1_Intron	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	389	VWFA.									breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						AGTCCCTCCCGCCCCAGACGC	0.627													G|||	998	0.199281	0.1369	0.1888	5008	,	,		17637	0.2351		0.2256	False		,,,				2504	0.227				p.P378P		Atlas-SNP	.											.	VWA5B2	47	.	0			c.G1134A						PASS	.	G		207,1177		17,173,502	78.0	72.0	74.0		1134	-7.7	0.0	3	dbSNP_89	74	660,2522		69,522,1000	yes	coding-synonymous	VWA5B2	NM_138345.1		86,695,1502	AA,AG,GG		20.7417,14.9566,18.9882		378/1243	183953972	867,3699	692	1591	2283	SO:0001819	synonymous_variant	90113	exon8			CCTCCCGCCCCAG		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.1134G>A	3.37:g.183953972G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	296	116	0.391892	NM_138345	B9EGN7	Silent	SNP	ENST00000426955.2	37	CCDS54686.1																																																																																			G|0.823;A|0.177	0.177	strong		0.627	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
MUC4	4585	hgsc.bcm.edu	37	3	195515413	195515413	+	Missense_Mutation	SNP	C	C	T	rs55868431	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195515413C>T	ENST00000463781.3	-	2	3497	c.3038G>A	c.(3037-3039)aGc>aAc	p.S1013N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1013N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGCTGGTGACAGG	0.572													.|||	808	0.161342	0.152	0.1124	5008	,	,		17298	0.2321		0.1352	False		,,,				2504	0.1626				p.S1013N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	4	Deletion - In frame(4)	stomach(4)	c.G3038A						scavenged	.						55.0	29.0	37.0					3																	195515413		688	1591	2279	SO:0001583	missense	4585	exon2			GAAGGGCTGGTGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3038G>A	3.37:g.195515413C>T	ENSP00000417498:p.Ser1013Asn	Somatic	598	68	0.113712		WXS	Illumina HiSeq	Phase_I	184	40	0.217391	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	4.515	0.095618	0.08681	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.42;1.41	0.814	-1.63	0.08345	.	.	.	.	.	T	0.14960	0.0361	N	0.19112	0.55	0.09310	N	1	B	0.17667	0.023	B	0.11329	0.006	T	0.15809	-1.0424	8	.	.	.	.	3.4557	0.07514	0.0:0.2084:0.4437:0.3479	rs55868431	1013	E7ESK3	.	N	1013	ENSP00000417498:S1013N;ENSP00000420243:S1013N	.	S	-	2	0	MUC4	196999808	.	.	0.000000	0.03702	0.010000	0.07245	.	.	-3.282000	0.00197	-2.088000	0.00374	AGC	C|0.963;T|0.037	0.037	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DUSP16	80824	hgsc.bcm.edu	37	12	12630669	12630669	+	Missense_Mutation	SNP	C	C	T	rs3809199|rs142947418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:12630669C>T	ENST00000228862.2	-	7	1727	c.1096G>A	c.(1096-1098)Gtg>Atg	p.V366M	DUSP16_ENST00000298573.4_3'UTR|DUSP16_ENST00000545864.1_5'Flank	NM_030640.2	NP_085143.1	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	366			V -> M (in dbSNP:rs3809199).		dephosphorylation (GO:0016311)|inactivation of MAPK activity (GO:0000188)|MAPK export from nucleus (GO:0045204)|MAPK phosphatase export from nucleus, leptomycin B sensitive (GO:0045209)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(7)|kidney(2)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(3)	26		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		GACGGCTgcacgctgggcacg	0.647													C|||	67	0.0133786	0.0015	0.0086	5008	,	,		16764	0.005		0.0288	False		,,,				2504	0.0256				p.V366M	Ovarian(158;443 1896 15437 36069 46477)	Atlas-SNP	.											.	DUSP16	64	.	0			c.G1096A						PASS	.						33.0	37.0	36.0					12																	12630669		2203	4300	6503	SO:0001583	missense	80824	exon7			GCTGCACGCTGGG	AB052156	CCDS8650.1	12p13	2011-06-09				ENSG00000111266		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	17909	protein-coding gene	gene with protein product	"""MAPK phosphatase-7"""	607175				11359773, 11489891, 15888437	Standard	NM_030640		Approved	MKP-7, KIAA1700, MKP7	uc001rao.2	Q9BY84		ENST00000228862.2:c.1096G>A	12.37:g.12630669C>T	ENSP00000228862:p.Val366Met	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	63	0.605769	NM_030640	Q547C7|Q96QS2|Q9C0G3	Missense_Mutation	SNP	ENST00000228862.2	37	CCDS8650.1	35	0.016025641025641024	2	0.0040650406504065045	4	0.011049723756906077	4	0.006993006993006993	25	0.032981530343007916	C	1.608	-0.524759	0.04141	.	.	ENSG00000111266	ENST00000228862	T	0.01887	4.58	4.62	-9.23	0.00672	.	9.299580	0.00669	U	0.000637	T	0.00440	0.0014	N	0.08118	0	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.09377	0.004;0.002	T	0.43376	-0.9395	10	0.44086	T	0.13	.	1.7558	0.02982	0.2481:0.086:0.3156:0.3502	rs3809199;rs3809199	366;366	Q9BY84;Q96N49	DUS16_HUMAN;.	M	366	ENSP00000228862:V366M	ENSP00000228862:V366M	V	-	1	0	DUSP16	12521936	0.985000	0.35326	0.000000	0.03702	0.018000	0.09664	0.194000	0.17135	-2.689000	0.00404	-1.254000	0.01491	GTG	C|0.982;T|0.018	0.018	strong		0.647	DUSP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400311.1	NM_030640	
AGAP6	414189	hgsc.bcm.edu	37	10	51748684	51748684	+	Missense_Mutation	SNP	G	G	A	rs61848260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:51748684G>A	ENST00000374056.4	+	1	607	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	AGAP6_ENST00000412531.3_Missense_Mutation_p.R70Q			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	70				R -> Q (in Ref. 2; BC131545). {ECO:0000305}.	regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						GTTCGTGACCGGGAGATGCCT	0.592													G|||	2505	0.5002	0.6067	0.5519	5008	,	,		18957	0.3899		0.4463	False		,,,				2504	0.4888				p.R70Q		Atlas-SNP	.											AGAP6,NS,carcinoma,0,1	AGAP6	53	1	0			c.G209A						PASS	.																																			SO:0001583	missense	414189	exon1			GTGACCGGGAGAT		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.209G>A	10.37:g.51748684G>A	ENSP00000363168:p.Arg70Gln	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_001077665		Missense_Mutation	SNP	ENST00000374056.4	37		.	.	.	.	.	.	.	.	.	.	G	4.840	0.156245	0.09236	.	.	ENSG00000204149	ENST00000374056;ENST00000412531	D;D	0.89196	-2.48;-2.48	1.2	1.2	0.21068	.	0.119796	0.56097	D	0.000023	T	0.76593	0.4009	N	0.20574	0.59	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.71314	-0.4630	9	0.40728	T	0.16	.	5.7611	0.18201	0.0:0.0:1.0:0.0	rs61848260	70	C9IYN2	.	Q	70	ENSP00000363168:R70Q;ENSP00000400972:R70Q	ENSP00000363168:R70Q	R	+	2	0	AGAP6	51418690	0.995000	0.38212	0.964000	0.40570	0.005000	0.04900	0.588000	0.23924	0.963000	0.38082	0.187000	0.17357	CGG	A|1.000;|0.000	1.000	weak		0.592	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
CECR1	51816	hgsc.bcm.edu	37	22	17690430	17690430	+	Silent	SNP	C	C	G	rs7289141	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:17690430C>G	ENST00000399839.1	-	2	408	c.138G>C	c.(136-138)ctG>ctC	p.L46L	CECR1_ENST00000262607.3_Silent_p.L46L|CECR1_ENST00000399837.2_Silent_p.L46L|CECR1_ENST00000449907.2_Silent_p.L4L	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	46	Dimerization.				adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.L46L(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				GCCGCCCCCCCAGCCGCATCA	0.532													C|||	917	0.183107	0.0734	0.1527	5008	,	,		16629	0.3214		0.1173	False		,,,				2504	0.2781				p.L46L		Atlas-SNP	.											CECR1,NS,carcinoma,0,1	CECR1	77	1	1	Substitution - coding silent(1)	stomach(1)	c.G138C						PASS	.	C		339,4067	171.2+/-201.5	19,301,1883	36.0	36.0	36.0		138	-8.9	0.0	22	dbSNP_116	36	964,7636	199.2+/-243.3	54,856,3390	no	coding-synonymous	CECR1	NM_017424.2		73,1157,5273	GG,GC,CC		11.2093,7.6941,10.0185		46/512	17690430	1303,11703	2203	4300	6503	SO:0001819	synonymous_variant	51816	exon1			CCCCCCCAGCCGC	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.138G>C	22.37:g.17690430C>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Silent	SNP	ENST00000399839.1	37	CCDS13742.1																																																																																			C|0.869;G|0.131	0.131	strong		0.532	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		
RHPN2	85415	hgsc.bcm.edu	37	19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84.0	83.0	83.0					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	52	2	0.0384615	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
WIPF3	644150	hgsc.bcm.edu	37	7	29923572	29923572	+	Silent	SNP	T	T	C	rs28439342	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:29923572T>C	ENST00000409290.1	+	4	462	c.462T>C	c.(460-462)aaT>aaC	p.N154N	WIPF3_ENST00000409123.1_Silent_p.N154N|WIPF3_ENST00000242140.5_Silent_p.N154N	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	154					cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						GGCTAGGCAATACCTCCGAGG	0.721													T|||	805	0.160743	0.2859	0.1081	5008	,	,		5568	0.0308		0.1769	False		,,,				2504	0.1462				p.N154N		Atlas-SNP	.											.	WIPF3	46	.	0			c.T462C						PASS	.	T		655,2473		59,537,968	3.0	4.0	4.0		462	-0.9	0.0	7	dbSNP_125	4	938,6434		63,812,2811	no	coding-synonymous	WIPF3	NM_001080529.2		122,1349,3779	CC,CT,TT		12.7238,20.9399,15.1714		154/484	29923572	1593,8907	1564	3686	5250	SO:0001819	synonymous_variant	644150	exon5			AGGCAATACCTCC	AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.462T>C	7.37:g.29923572T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001080529	B8ZZV2	Silent	SNP	ENST00000409290.1	37	CCDS56472.1																																																																																			T|0.850;C|0.150	0.150	strong		0.721	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
TMPO	7112	hgsc.bcm.edu	37	12	98927830	98927830	+	Intron	SNP	C	C	G	rs17459334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:98927830C>G	ENST00000556029.1	+	3	921				TMPO_ENST00000343315.5_Intron|TMPO_ENST00000266732.4_Missense_Mutation_p.Q599E|TMPO_ENST00000261210.5_Intron|TMPO_ENST00000393053.2_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						AGACATTAGTCAAGCTGCACA	0.468													C|||	295	0.0589058	0.003	0.0403	5008	,	,		22302	0.001		0.1093	False		,,,				2504	0.1554				p.Q599E		Atlas-SNP	.											TMPO_ENST00000266732,rectum,carcinoma,0,1	TMPO	111	1	0			c.C1795G						PASS	.	C	,,GLU/GLN	95,4311	77.3+/-115.6	2,91,2110	99.0	79.0	86.0		,,1795	6.0	1.0	12	dbSNP_123	86	830,7770	192.0+/-238.1	32,766,3502	yes	intron,intron,missense	TMPO	NM_001032283.2,NM_001032284.2,NM_003276.2	,,29	34,857,5612	GG,GC,CC		9.6512,2.1562,7.1121	,,possibly-damaging	,,599/695	98927830	925,12081	2203	4300	6503	SO:0001627	intron_variant	7112	exon4			ATTAGTCAAGCTG		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"""LEM domain containing 4"""	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.565+2214C>G	12.37:g.98927830C>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_003276	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	101	0.04624542124542125	1	0.0020325203252032522	19	0.052486187845303865	0	0.0	81	0.10686015831134564	C	14.20	2.463925	0.43736	0.021562	0.096512	ENSG00000120802	ENST00000266732	T	0.59772	0.24	5.96	5.96	0.96718	.	0.461649	0.22945	N	0.053734	T	0.01254	0.0041	N	0.24115	0.695	0.09310	P	1.0	P	0.49090	0.919	P	0.44447	0.45	T	0.10428	-1.0630	9	0.42905	T	0.14	.	15.9221	0.79583	0.0:1.0:0.0:0.0	rs17459334;rs52831524;rs17459334	599	P42166	LAP2A_HUMAN	E	599	ENSP00000266732:Q599E	ENSP00000266732:Q599E	Q	+	1	0	TMPO	97451961	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.147000	0.42226	2.832000	0.97577	0.655000	0.94253	CAA	C|0.934;G|0.066	0.066	strong		0.468	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276	
COL4A4	1286	hgsc.bcm.edu	37	2	228004877	228004877	+	Splice_Site	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228004877C>T	ENST00000396625.3	-	4	399	c.192G>A	c.(190-192)cgG>cgA	p.R64R	COL4A4_ENST00000329662.7_Splice_Site_p.R64R	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	64	7S domain.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CATCACTTACCCGAGACCCCT	0.393																																					p.R64R		Atlas-SNP	.											COL4A4,NS,lymphoid_neoplasm,-1,2	COL4A4	215	2	0			c.G192A						PASS	.						117.0	112.0	114.0					2																	228004877		1885	4096	5981	SO:0001630	splice_region_variant	1286	exon4			ACTTACCCGAGAC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.192+1G>A	2.37:g.228004877C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	142	81	0.570423	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			.	.	none		0.393	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	Silent
DGCR14	8220	hgsc.bcm.edu	37	22	19122665	19122665	+	Silent	SNP	C	C	T	rs2240111	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:19122665C>T	ENST00000252137.6	-	9	1102	c.1059G>A	c.(1057-1059)gaG>gaA	p.E353E		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	353					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					GACCCAGCCGCTCCCTGCGGC	0.647													C|||	832	0.166134	0.1203	0.1326	5008	,	,		15434	0.121		0.1869	False		,,,				2504	0.2771				p.E353E		Atlas-SNP	.											.	DGCR14	43	.	0			c.G1059A						PASS	.	C		513,3893	236.1+/-248.4	31,451,1721	68.0	61.0	64.0		1059	1.4	1.0	22	dbSNP_98	64	1729,6871	312.5+/-310.9	187,1355,2758	no	coding-synonymous	DGCR14	NM_022719.2		218,1806,4479	TT,TC,CC		20.1047,11.6432,17.2382		353/477	19122665	2242,10764	2203	4300	6503	SO:0001819	synonymous_variant	8220	exon9			CAGCCGCTCCCTG	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"""DiGeorge syndrome critical region gene 13"""	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.1059G>A	22.37:g.19122665C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_022719	Q49AH7|Q9BTZ4	Silent	SNP	ENST00000252137.6	37	CCDS13756.1																																																																																			C|0.835;A|0.001	.	strong		0.647	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2		
JAKMIP2	9832	hgsc.bcm.edu	37	5	147024509	147024509	+	Silent	SNP	C	C	T	rs2116765	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:147024509C>T	ENST00000265272.5	-	6	1454	c.987G>A	c.(985-987)agG>agA	p.R329R	JAKMIP2_ENST00000333010.6_Silent_p.R287R|JAKMIP2_ENST00000507386.1_Silent_p.R329R	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	329						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCACTTGTTCCTTTCCAGGA	0.458													C|||	1842	0.367812	0.5136	0.3631	5008	,	,		18363	0.4712		0.162	False		,,,				2504	0.2791				p.R329R		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.G987A						PASS	.	C		1914,2492	547.2+/-377.2	426,1062,715	195.0	191.0	193.0		987	5.5	1.0	5	dbSNP_96	193	1185,7415	241.3+/-271.7	80,1025,3195	no	coding-synonymous	JAKMIP2	NM_014790.3		506,2087,3910	TT,TC,CC		13.7791,43.4408,23.8275		329/811	147024509	3099,9907	2203	4300	6503	SO:0001819	synonymous_variant	9832	exon6			CTTGTTCCTTTCC	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.987G>A	5.37:g.147024509C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	205	132	0.643902	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																			C|0.698;T|0.302	0.302	strong		0.458	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
EML6	400954	hgsc.bcm.edu	37	2	55186394	55186394	+	Silent	SNP	A	A	C	rs17346629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:55186394A>C	ENST00000356458.6	+	33	5369	c.4849A>C	c.(4849-4851)Agg>Cgg	p.R1617R	EML6_ENST00000490828.1_3'UTR	NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	1617						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						CGGAAAAGAGAGGCCGTAAGC	0.507													C|||	2472	0.49361	0.1823	0.5865	5008	,	,		19086	0.6935		0.6928	False		,,,				2504	0.4376				p.R1617R		Atlas-SNP	.											.	EML6	85	.	0			c.A4849C						PASS	.	C		374,1010		53,268,371	52.0	50.0	51.0		4849	3.8	1.0	2	dbSNP_123	51	2276,906		815,646,130	no	coding-synonymous	EML6	NM_001039753.2		868,914,501	CC,CA,AA		28.4727,27.0231,41.9623		1617/1959	55186394	2650,1916	692	1591	2283	SO:0001819	synonymous_variant	400954	exon33			AAAGAGAGGCCGT		CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595		"""WD repeat domain containing"""	35412	protein-coding gene	gene with protein product							Standard	NM_001039753		Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.4849A>C	2.37:g.55186394A>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001039753	A8MUB5|B6ZDG7	Silent	SNP	ENST00000356458.6	37	CCDS46286.1																																																																																			A|0.447;C|0.553	0.553	strong		0.507	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324997.3	XM_001725002	
HNRNPM	4670	hgsc.bcm.edu	37	19	8553630	8553630	+	Silent	SNP	C	C	T	rs6992	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8553630C>T	ENST00000325495.4	+	16	2126	c.2085C>T	c.(2083-2085)ggC>ggT	p.G695G	HNRNPM_ENST00000602219.1_3'UTR|HNRNPM_ENST00000348943.3_Silent_p.G656G	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	695	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AGGGGTGTGGCGTGGTTAAGT	0.547													T|||	4387	0.875998	0.6225	0.9395	5008	,	,		16520	0.9802		0.9682	False		,,,				2504	0.9714				p.G695G		Atlas-SNP	.											.	HNRNPM	61	.	0			c.C2085T						PASS	.	T	,	2949,1457	470.9+/-355.9	988,973,242	135.0	117.0	123.0		2085,1968	2.0	1.0	19	dbSNP_52	123	8303,297	107.6+/-168.3	4008,287,5	no	coding-synonymous,coding-synonymous	HNRNPM	NM_005968.4,NM_031203.3	,	4996,1260,247	TT,TC,CC		3.4535,33.0685,13.4861	,	695/731,656/692	8553630	11252,1754	2203	4300	6503	SO:0001819	synonymous_variant	4670	exon16			GTGTGGCGTGGTT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"""RNA binding motif (RRM) containing"""	5046	protein-coding gene	gene with protein product	"""CEA receptor"""	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.2085C>T	19.37:g.8553630C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	163	162	0.993865	NM_005968	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Silent	SNP	ENST00000325495.4	37	CCDS12203.1																																																																																			C|0.122;T|0.878	0.878	strong		0.547	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		
UNC79	57578	hgsc.bcm.edu	37	14	93943998	93943998	+	Silent	SNP	G	G	A	rs61992606	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:93943998G>A	ENST00000393151.2	+	4	543	c.543G>A	c.(541-543)acG>acA	p.T181T	UNC79_ENST00000555664.1_Silent_p.T181T|UNC79_ENST00000256339.4_Silent_p.T4T|UNC79_ENST00000553484.1_Silent_p.T181T			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	181					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TGATATCAACGTTGGCTACCT	0.358													G|||	1867	0.372804	0.267	0.2421	5008	,	,		18127	0.6964		0.2883	False		,,,				2504	0.362				p.T4T		Atlas-SNP	.											.	UNC79	366	.	0			c.G12A						PASS	.	G		1214,3192	421.7+/-339.5	161,892,1150	270.0	225.0	240.0		12	-0.3	1.0	14	dbSNP_129	240	2640,5960	426.2+/-355.2	419,1802,2079	no	coding-synonymous	UNC79	NM_020818.3		580,2694,3229	AA,AG,GG		30.6977,27.5533,29.6325		4/2459	93943998	3854,9152	2203	4300	6503	SO:0001819	synonymous_variant	57578	exon4			ATCAACGTTGGCT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.543G>A	14.37:g.93943998G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	199	108	0.542714	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																				G|0.684;A|0.316	0.316	strong		0.358	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
TPR	7175	hgsc.bcm.edu	37	1	186301447	186301447	+	Silent	SNP	T	T	C	rs7526540	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:186301447T>C	ENST00000367478.4	-	38	5780	c.5484A>G	c.(5482-5484)ccA>ccG	p.P1828P		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1828	Sufficient and essential for mediating its nuclear import.				carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		GTGTACGCTTTGGCAAAGAAG	0.373			T	NTRK1	papillary thyroid								T|||	151	0.0301518	0.0446	0.013	5008	,	,		17549	0.001		0.0388	False		,,,				2504	0.044				p.P1828P		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A5484G						PASS	.	T		170,3568		1,168,1700	92.0	85.0	87.0		5484	-7.3	1.0	1	dbSNP_116	87	367,7811		11,345,3733	no	coding-synonymous	TPR	NM_003292.2		12,513,5433	CC,CT,TT		4.4876,4.5479,4.5065		1828/2364	186301447	537,11379	1869	4089	5958	SO:0001819	synonymous_variant	7175	exon38			ACGCTTTGGCAAA	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.5484A>G	1.37:g.186301447T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																			T|0.958;C|0.042	0.042	strong		0.373	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
OR10H1	26539	hgsc.bcm.edu	37	19	15918177	15918177	+	Missense_Mutation	SNP	G	G	T	rs62619246	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15918177G>T	ENST00000334920.2	-	1	759	c.671C>A	c.(670-672)gCc>gAc	p.A224D		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A224D(3)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						CAAGATGGCGGCCACGATGAA	0.582																																					p.A224D		Atlas-SNP	.											OR10H1,NS,carcinoma,0,3	OR10H1	59	3	3	Substitution - Missense(3)	kidney(3)	c.C671A						scavenged	.						79.0	66.0	70.0					19																	15918177		2202	4279	6481	SO:0001583	missense	26539	exon1			ATGGCGGCCACGA	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.671C>A	19.37:g.15918177G>T	ENSP00000335596:p.Ala224Asp	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	256	30	0.117188	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	121	0.0554029304029304	40	0.08130081300813008	15	0.04143646408839779	47	0.08216783216783216	19	0.025065963060686015	.	9.676	1.148119	0.21288	.	.	ENSG00000186723	ENST00000334920	T	0.38077	1.16	4.96	2.76	0.32466	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000141	T	0.05273	0.0140	M	0.82433	2.59	0.09310	N	1	D	0.53885	0.963	P	0.62649	0.905	T	0.04440	-1.0951	10	0.66056	D	0.02	.	5.0438	0.14473	0.1886:0.1747:0.6367:0.0	rs62619246	224	Q9Y4A9	O10H1_HUMAN	D	224	ENSP00000335596:A224D	ENSP00000335596:A224D	A	-	2	0	OR10H1	15779177	0.000000	0.05858	0.293000	0.24932	0.082000	0.17680	0.466000	0.22019	0.463000	0.27118	0.643000	0.83706	GCC	G|0.944;T|0.056	0.056	strong		0.582	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
FAM120AOS	158293	hgsc.bcm.edu	37	9	96209943	96209943	+	Missense_Mutation	SNP	T	T	C	rs10821128	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:96209943T>C	ENST00000375412.5	-	3	1603	c.721A>G	c.(721-723)Aag>Gag	p.K241E	FAM120AOS_ENST00000423591.1_Missense_Mutation_p.K59E|FAM120AOS_ENST00000479094.1_5'UTR	NM_198841.2	NP_942138.2	Q5T036	F120S_HUMAN	family with sequence similarity 120A opposite strand	241			K -> E (in dbSNP:rs10821128). {ECO:0000269|PubMed:14702039}.							kidney(1)|large_intestine(1)|lung(3)|skin(1)	6						GTGGTTTTCTTTGAGACTTTG	0.338													T|||	1138	0.227236	0.0363	0.3069	5008	,	,		20145	0.4117		0.3479	False		,,,				2504	0.1145				p.K241E		Atlas-SNP	.											.	FAM120AOS	13	.	0			c.A721G						PASS	.	-	GLU/LYS	403,4003	197.1+/-221.3	22,359,1822	224.0	207.0	213.0		721	-1.4	0.0	9	dbSNP_120	213	2898,5702	453.0+/-363.1	507,1884,1909	yes	missense	FAM120AOS	NM_198841.2	56	529,2243,3731	CC,CT,TT		33.6977,9.1466,25.3806	benign	241/257	96209943	3301,9705	2203	4300	6503	SO:0001583	missense	158293	exon3			TTTTCTTTGAGAC	AK056096	CCDS6705.1	9q22.32	2008-02-05	2006-07-04	2006-07-04	ENSG00000188938	ENSG00000188938			23389	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 10 opposite strand"""	C9orf10OS		14585507	Standard	NM_198841		Approved		uc004atu.4	Q5T036	OTTHUMG00000020251	ENST00000375412.5:c.721A>G	9.37:g.96209943T>C	ENSP00000364561:p.Lys241Glu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_198841	A6NN20	Missense_Mutation	SNP	ENST00000375412.5	37	CCDS6705.1	686	0.3141025641025641	26	0.052845528455284556	132	0.36464088397790057	257	0.4493006993006993	271	0.3575197889182058	T	2.509	-0.313505	0.05422	0.091466	0.336977	ENSG00000188938	ENST00000423591;ENST00000375412;ENST00000375409;ENST00000428378	T;T;T	0.57595	0.44;0.63;0.39	1.77	-1.41	0.08941	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43458	-0.9390	8	0.87932	D	0	.	5.3583	0.16073	0.0:0.5975:0.0:0.4025	rs10821128;rs10821128	241	Q5T036	F120S_HUMAN	E	59;241;58;58	ENSP00000414298:K59E;ENSP00000364561:K241E;ENSP00000416978:K58E	ENSP00000364558:K58E	K	-	1	0	FAM120AOS	95249764	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.584000	0.02114	-0.371000	0.08004	-0.280000	0.10049	AAG	T|0.734;C|0.266	0.266	strong		0.338	FAM120AOS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053154.1		
RFC1	5981	hgsc.bcm.edu	37	4	39302029	39302029	+	Silent	SNP	T	T	C	rs2066786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:39302029T>C	ENST00000381897.1	-	20	2677	c.2544A>G	c.(2542-2544)ccA>ccG	p.P848P	RNU6-32P_ENST00000383948.1_RNA|RFC1_ENST00000349703.2_Silent_p.P847P	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	848					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						CAACATCAAATGGGCCCTGAA	0.428													T|||	2330	0.465256	0.0552	0.6066	5008	,	,		20360	0.63		0.5477	False		,,,				2504	0.6646				p.P848P	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.A2544G						PASS	.	T	,	664,3742	276.6+/-273.2	59,546,1598	53.0	54.0	54.0		2544,2541	-5.6	0.9	4	dbSNP_94	54	4860,3740	616.4+/-396.5	1371,2118,811	no	coding-synonymous,coding-synonymous	RFC1	NM_001204747.1,NM_002913.4	,	1430,2664,2409	CC,CT,TT		43.4884,15.0704,42.4727	,	848/1149,847/1148	39302029	5524,7482	2203	4300	6503	SO:0001819	synonymous_variant	5981	exon20			ATCAAATGGGCCC	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.2544A>G	4.37:g.39302029T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_001204747	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	37	CCDS56329.1																																																																																			T|0.557;C|0.443	0.443	strong		0.428	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913	
U2AF2	11338	hgsc.bcm.edu	37	19	56181019	56181019	+	Silent	SNP	C	C	T	rs147666260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56181019C>T	ENST00000308924.4	+	11	1294	c.1254C>T	c.(1252-1254)ccC>ccT	p.P418P	U2AF2_ENST00000450554.2_Silent_p.P414P|CTD-2537I9.13_ENST00000592252.1_RNA|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000590551.1_Silent_p.P250P			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	418	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		TCGAGATCCCCCGGCCTGTGG	0.657													C|||	15	0.00299521	0.0	0.0101	5008	,	,		16186	0.0		0.008	False		,,,				2504	0.0				p.P418P		Atlas-SNP	.											.	U2AF2	62	.	0			c.C1254T						PASS	.	C	,	9,4397	15.5+/-35.6	0,9,2194	123.0	111.0	115.0		1242,1254	-0.6	1.0	19	dbSNP_134	115	87,8513	48.5+/-108.0	1,85,4214	no	coding-synonymous,coding-synonymous	U2AF2	NM_001012478.1,NM_007279.2	,	1,94,6408	TT,TC,CC		1.0116,0.2043,0.7381	,	414/472,418/476	56181019	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	11338	exon11			GATCCCCCGGCCT	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1254C>T	19.37:g.56181019C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	156	76	0.487179	NM_007279	Q96HC5	Silent	SNP	ENST00000308924.4	37	CCDS12933.1																																																																																			C|0.994;T|0.006	0.006	strong		0.657	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279	
CERS2	29956	hgsc.bcm.edu	37	1	150940625	150940625	+	Missense_Mutation	SNP	T	T	G	rs267738	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:150940625T>G	ENST00000271688.6	-	4	730	c.344A>C	c.(343-345)gAg>gCg	p.E115A	CERS2_ENST00000368954.5_Missense_Mutation_p.E115A|CERS2_ENST00000561294.1_Missense_Mutation_p.E106A|RP11-316M1.12_ENST00000561111.1_RNA|RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000345896.4_5'UTR	NM_181746.3	NP_859530.1	Q96G23	CERS2_HUMAN	ceramide synthase 2	115			E -> A (in dbSNP:rs267738).		ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GAACCAACGCTCTACCTGGCG	0.607													T|||	341	0.0680911	0.0061	0.0951	5008	,	,		16202	0.0258		0.1909	False		,,,				2504	0.0501				p.E115A		Atlas-SNP	.											LASS2,colon,carcinoma,0,1	.	.	1	0			c.A344C						PASS	.	T	ALA/GLU,ALA/GLU	176,4230	115.4+/-153.4	1,174,2028	67.0	73.0	71.0		344,344	4.9	1.0	1	dbSNP_79	71	1821,6779	325.8+/-317.1	200,1421,2679	yes	missense,missense	CERS2	NM_022075.4,NM_181746.3	107,107	201,1595,4707	GG,GT,TT		21.1744,3.9946,15.3545	probably-damaging,probably-damaging	115/381,115/381	150940625	1997,11009	2203	4300	6503	SO:0001583	missense	29956	exon4			CAACGCTCTACCT	AF189062	CCDS973.1	1q21.3	2012-09-20	2011-07-08	2011-07-08	ENSG00000143418	ENSG00000143418		"""Homeoboxes / CERS class"""	14076	protein-coding gene	gene with protein product		606920	"""longevity assurance (LAG1, S. cerevisiae) homolog 2"", ""LAG1 longevity assurance homolog 2 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 2"""	LASS2		11543633	Standard	NM_181746		Approved	SP260, FLJ10243	uc001evz.3	Q96G23	OTTHUMG00000035064	ENST00000271688.6:c.344A>C	1.37:g.150940625T>G	ENSP00000271688:p.Glu115Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_022075	D3DV06|Q5SZE5|Q9HD96|Q9NW79	Missense_Mutation	SNP	ENST00000271688.6	37	CCDS973.1	217	0.09935897435897435	4	0.008130081300813009	40	0.11049723756906077	19	0.033216783216783216	154	0.20316622691292877	T	32	5.158232	0.94686	0.039946	0.211744	ENSG00000143418	ENST00000368954;ENST00000271688;ENST00000368949;ENST00000361419;ENST00000421609;ENST00000457392	D;D;D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89;-3.89;-3.89	4.9	4.9	0.64082	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.115318	0.64402	D	0.000015	D	0.95915	0.8670	M	0.81942	2.565	0.09310	P	0.999999635895	P	0.45634	0.863	P	0.54590	0.756	D	0.95090	0.8221	9	0.30078	T	0.28	-19.5384	14.3739	0.66860	0.0:0.0:0.0:1.0	rs267738;rs556626;rs56588434;rs60175401;rs267738	115	Q96G23	CERS2_HUMAN	A	115;115;135;115;115;115	ENSP00000357950:E115A;ENSP00000271688:E115A;ENSP00000357945:E135A;ENSP00000355020:E115A;ENSP00000393239:E115A;ENSP00000394012:E115A	ENSP00000271688:E115A	E	-	2	0	CERS2	149207249	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.460000	0.80816	2.058000	0.61347	0.533000	0.62120	GAG	T|0.878;G|0.122	0.122	strong		0.607	CERS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084897.2	NM_022075	
PDPR	55066	hgsc.bcm.edu	37	16	70182375	70182375	+	Silent	SNP	T	T	C	rs62050977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:70182375T>C	ENST00000288050.4	+	17	2928	c.1971T>C	c.(1969-1971)agT>agC	p.S657S	PDPR_ENST00000568530.1_Silent_p.S657S|PDPR_ENST00000542659.1_Silent_p.S2S|PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000567046.1_Silent_p.S15S|PDPR_ENST00000398122.3_Silent_p.S557S	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	657					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		AGGAGATGAGTGTGGGCTATG	0.562																																					p.S657S		Atlas-SNP	.											.	PDPR	66	.	0			c.T1971C						PASS	.						80.0	76.0	77.0					16																	70182375		2108	4224	6332	SO:0001819	synonymous_variant	55066	exon17			GATGAGTGTGGGC		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1971T>C	16.37:g.70182375T>C		Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	446	87	0.195067	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Silent	SNP	ENST00000288050.4	37	CCDS45520.1																																																																																			T|0.715;C|0.286	0.286	strong		0.562	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49379182	49379182	+	Silent	SNP	G	G	C	rs386810065|rs527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49379182G>C	ENST00000200453.5	+	3	2246	c.1977G>C	c.(1975-1977)tcG>tcC	p.S659S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	659					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CTTCCCGCTCGTCTGCTGCTG	0.567													G|||	1786	0.356629	0.5764	0.2896	5008	,	,		16609	0.1984		0.2803	False		,,,				2504	0.3487				p.S659S		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1977C						PASS	.	G		2273,2133	583.2+/-385.8	569,1135,499	70.0	72.0	71.0		1977	-3.2	0.0	19	dbSNP_36	71	2469,6131	396.7+/-345.5	354,1761,2185	no	coding-synonymous	PPP1R15A	NM_014330.3		923,2896,2684	CC,CG,GG		28.7093,48.4113,36.4601		659/675	49379182	4742,8264	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon3			CCGCTCGTCTGCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1977G>C	19.37:g.49379182G>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	139	65	0.467626	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			G|0.646;C|0.354	0.354	strong		0.567	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
ZNF814	730051	hgsc.bcm.edu	37	19	58385954	58385954	+	Silent	SNP	T	T	C	rs74179449|rs10412929	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58385954T>C	ENST00000435989.2	-	3	1038	c.804A>G	c.(802-804)aaA>aaG	p.K268K	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	268					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K268K(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CACATTCATGTTTTTTTTCAG	0.373													.|||	1533	0.30611	0.2753	0.3818	5008	,	,		21372	0.4385		0.2833	False		,,,				2504	0.181				p.K268K		Atlas-SNP	.											ZNF814,NS,carcinoma,0,1	ZNF814	93	1	1	Substitution - coding silent(1)	kidney(1)	c.A804G						PASS	.	T		343,1041		40,263,389	45.0	38.0	40.0		804	-4.3	0.0	19	dbSNP_119	40	892,2290		121,650,820	no	coding-synonymous	ZNF814	NM_001144989.1		161,913,1209	CC,CT,TT		28.0327,24.7832,27.0477		268/856	58385954	1235,3331	692	1591	2283	SO:0001819	synonymous_variant	730051	exon3			TTCATGTTTTTTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.804A>G	19.37:g.58385954T>C		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	240	100	0.416667	NM_001144989	A6NF35	Silent	SNP	ENST00000435989.2	37	CCDS46212.1																																																																																			T|0.664;C|0.336	0.336	strong		0.373	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
SPTBN5	51332	hgsc.bcm.edu	37	15	42171655	42171655	+	Missense_Mutation	SNP	C	C	A	rs55637254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42171655C>A	ENST00000320955.6	-	16	3212	c.2985G>T	c.(2983-2985)caG>caT	p.Q995H		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	995					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TGTGTGCCAGCTGCACGGCCT	0.632													C|||	154	0.0307508	0.0	0.0519	5008	,	,		21533	0.0129		0.0368	False		,,,				2504	0.0695				p.Q960H		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G2880T						PASS	.	C	HIS/GLN	27,4009		0,27,1991	17.0	20.0	19.0		2880	2.7	0.6	15	dbSNP_129	19	305,8009		9,287,3861	yes	missense	SPTBN5	NM_016642.2	24	9,314,5852	AA,AC,CC		3.6685,0.669,2.6883	probably-damaging	960/3640	42171655	332,12018	2018	4157	6175	SO:0001583	missense	51332	exon16			TGCCAGCTGCACG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.2985G>T	15.37:g.42171655C>A	ENSP00000317790:p.Gln995His	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		54	0.024725274725274724	0	0.0	18	0.049723756906077346	8	0.013986013986013986	28	0.036939313984168866	.	10.88	1.476158	0.26511	0.00669	0.036685	ENSG00000137877	ENST00000320955	T	0.52526	0.66	4.85	2.71	0.32032	.	0.290697	0.27451	N	0.019319	T	0.07098	0.0180	L	0.48362	1.52	0.25668	N	0.985926	B	0.30068	0.267	B	0.27380	0.079	T	0.12116	-1.0560	10	0.62326	D	0.03	.	5.1509	0.15009	0.2544:0.5578:0.0:0.1878	rs55637254;rs61739353	995	Q9NRC6	SPTN5_HUMAN	H	995	ENSP00000317790:Q995H	ENSP00000317790:Q995H	Q	-	3	2	SPTBN5	39958947	0.997000	0.39634	0.577000	0.28562	0.079000	0.17450	0.462000	0.21956	1.024000	0.39682	0.313000	0.20887	CAG	C|0.973;A|0.027	0.027	strong		0.632	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
COL4A3BP	10087	hgsc.bcm.edu	37	5	74681773	74681773	+	Silent	SNP	T	T	C	rs698912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:74681773T>C	ENST00000405807.4	-	13	1792	c.1371A>G	c.(1369-1371)gaA>gaG	p.E457E	COL4A3BP_ENST00000380494.5_Silent_p.E585E|COL4A3BP_ENST00000508692.1_5'Flank|COL4A3BP_ENST00000261415.7_Silent_p.E431E	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	457	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)	p.E457E(1)		breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		AATTGCAGACTTCATGTCCTG	0.328													t|||	1451	0.289736	0.2655	0.1715	5008	,	,		15831	0.3313		0.2197	False		,,,				2504	0.4356				p.E585E		Atlas-SNP	.											COL4A3BP,NS,carcinoma,0,1	COL4A3BP	72	1	1	Substitution - coding silent(1)	stomach(1)	c.A1755G						PASS	.	T	,,	1142,3262	398.8+/-331.0	149,844,1209	65.0	58.0	61.0		1755,1371,1293	1.4	1.0	5	dbSNP_86	61	1805,6791	318.7+/-313.8	192,1421,2685	no	coding-synonymous,coding-synonymous,coding-synonymous	COL4A3BP	NM_001130105.1,NM_005713.2,NM_031361.2	,,	341,2265,3894	CC,CT,TT		20.9981,25.931,22.6692	,,	585/753,457/625,431/599	74681773	2947,10053	2202	4298	6500	SO:0001819	synonymous_variant	10087	exon14			GCAGACTTCATGT	AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"""StAR-related lipid transfer (START) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2205	protein-coding gene	gene with protein product	"""ceramide transporter"", ""StAR-related lipid transfer (START) domain containing 11"""	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1371A>G	5.37:g.74681773T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Silent	SNP	ENST00000405807.4	37	CCDS4028.1																																																																																			T|0.743;C|0.257	0.257	strong		0.328	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713	
BRDT	676	hgsc.bcm.edu	37	1	92428495	92428495	+	Missense_Mutation	SNP	C	C	A	rs10783071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:92428495C>A	ENST00000362005.3	+	3	602	c.184C>A	c.(184-186)Cag>Aag	p.Q62K	BRDT_ENST00000370389.2_Intron|BRDT_ENST00000394530.3_Missense_Mutation_p.Q62K|BRDT_ENST00000399546.2_Missense_Mutation_p.Q62K|BRDT_ENST00000402388.1_Missense_Mutation_p.Q62K	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	62	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.		Q -> K (in dbSNP:rs10783071). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15647849, ECO:0000269|PubMed:9367677, ECO:0000269|Ref.5}.		cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		TGTGAAACTACAGTTGCCTGT	0.323													A|||	3786	0.75599	0.6551	0.8415	5008	,	,		17393	0.6141		0.9235	False		,,,				2504	0.8057				p.Q62K		Atlas-SNP	.											.	BRDT	133	.	0			c.C184A						PASS	.	A	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,,LYS/GLN,LYS/GLN	3079,1327	441.4+/-346.4	1070,939,194	99.0	97.0	98.0		184,184,184,184,,184,184	2.2	0.0	1	dbSNP_120	98	8096,504	143.9+/-199.8	3815,466,19	yes	missense,missense,missense,missense,intron,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	53,53,53,53,,53,53	4885,1405,213	AA,AC,CC		5.8605,30.118,14.0781	benign,benign,benign,benign,,benign,benign	62/948,62/952,62/902,62/902,,62/948,62/948	92428495	11175,1831	2203	4300	6503	SO:0001583	missense	676	exon2			AAACTACAGTTGC	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.184C>A	1.37:g.92428495C>A	ENSP00000354568:p.Gln62Lys	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	1677	0.7678571428571429	334	0.6788617886178862	314	0.8674033149171271	331	0.5786713286713286	698	0.920844327176781	A	8.916	0.959908	0.18507	0.69882	0.941395	ENSG00000137948	ENST00000362005;ENST00000399546;ENST00000539070;ENST00000423434;ENST00000394530;ENST00000440509;ENST00000427104;ENST00000448194;ENST00000426141;ENST00000450792;ENST00000548992;ENST00000402388	T;T;T;T;T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;2.21;1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.83	2.25	0.28309	Bromodomain (5);Bromodomain, conserved site (1);	0.332965	0.28600	N	0.014770	T	0.04724	0.0128	N	0.12443	0.215	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41288	-0.9517	9	0.20046	T	0.44	-2.1317	6.7075	0.23258	0.6339:0.2402:0.1259:0.0	rs10783071;rs11558348;rs52809094;rs61132034;rs10783071	62	Q58F21	BRDT_HUMAN	K	62	ENSP00000354568:Q62K;ENSP00000387822:Q62K;ENSP00000396351:Q62K;ENSP00000378038:Q62K;ENSP00000416714:Q62K;ENSP00000400002:Q62K;ENSP00000410587:Q62K;ENSP00000404969:Q62K;ENSP00000414349:Q62K;ENSP00000447394:Q62K;ENSP00000384051:Q62K	ENSP00000354568:Q62K	Q	+	1	0	BRDT	92201083	0.034000	0.19679	0.001000	0.08648	0.938000	0.57974	1.070000	0.30653	-0.025000	0.13918	-0.270000	0.10280	CAG	C|0.189;A|0.811	0.811	strong		0.323	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
KNG1	3827	hgsc.bcm.edu	37	3	186443018	186443018	+	Missense_Mutation	SNP	T	T	C	rs1656922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186443018T>C	ENST00000265023.4	+	4	745	c.533T>C	c.(532-534)aTg>aCg	p.M178T	KNG1_ENST00000287611.2_Missense_Mutation_p.M178T|KNG1_ENST00000447445.1_Missense_Mutation_p.M178T|RP11-573D15.8_ENST00000599314.1_RNA	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	178	Cystatin kininogen-type 2. {ECO:0000255|PROSITE-ProRule:PRU00979}.		M -> T (in dbSNP:rs1656922). {ECO:0000269|Ref.4, ECO:0000269|Ref.5, ECO:0000269|Ref.7}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.M178T(2)		endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		TCCCTCTTCATGCTTAATGAA	0.388													C|||	2625	0.524161	0.615	0.611	5008	,	,		17628	0.3562		0.5368	False		,,,				2504	0.5				p.M178T		Atlas-SNP	.											KNG1_ENST00000265023,NS,carcinoma,0,2	KNG1	129	2	2	Substitution - Missense(2)	stomach(2)	c.T533C	GRCh37	CM065290	KNG1	M	rs1656922	PASS	.	C	THR/MET,THR/MET,THR/MET	2628,1778	525.4+/-371.6	764,1100,339	114.0	100.0	105.0		533,533,533	-0.4	0.0	3	dbSNP_89	105	4470,4130	564.5+/-388.3	1194,2082,1024	yes	missense,missense,missense	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	81,81,81	1958,3182,1363	CC,CT,TT		48.0233,40.3541,45.4252	benign,benign,benign	178/428,178/645,178/392	186443018	7098,5908	2203	4300	6503	SO:0001583	missense	3827	exon4			TCTTCATGCTTAA		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"""Endogenous ligands"""	6383	protein-coding gene	gene with protein product	"""alpha-2-thiol proteinase inhibitor"", ""bradykinin"""	612358	"""kininogen"""	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.533T>C	3.37:g.186443018T>C	ENSP00000265023:p.Met178Thr	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	163	95	0.582822	NM_000893	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	37	CCDS43183.1	1095	0.5013736263736264	285	0.5792682926829268	221	0.6104972375690608	187	0.3269230769230769	402	0.5303430079155673	C	0.032	-1.327636	0.01309	0.596459	0.519767	ENSG00000113889	ENST00000287611;ENST00000265023;ENST00000447445;ENST00000432028	T;T;T	0.25912	1.77;1.77;1.77	4.92	-0.388	0.12459	Proteinase inhibitor I25, cystatin (2);	1.307410	0.04874	N	0.446548	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44298	-0.9337	9	0.12430	T	0.62	-0.1833	0.9891	0.01453	0.16:0.3474:0.1386:0.354	rs1656922;rs52798648;rs59372667;rs1656922	178;178	P01042;P01042-2	KNG1_HUMAN;.	T	178;178;178;166	ENSP00000287611:M178T;ENSP00000265023:M178T;ENSP00000396025:M178T	ENSP00000265023:M178T	M	+	2	0	KNG1	187925712	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.072000	0.11486	-0.128000	0.11641	-1.983000	0.00453	ATG	T|0.473;C|0.527	0.527	strong		0.388	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
HELZ2	85441	hgsc.bcm.edu	37	20	62194030	62194030	+	Missense_Mutation	SNP	G	G	C	rs3810483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:62194030G>C	ENST00000467148.1	-	8	6214	c.6145C>G	c.(6145-6147)Cag>Gag	p.Q2049E	HELZ2_ENST00000427522.2_Missense_Mutation_p.Q1480E	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2049			Q -> E (in dbSNP:rs3810483). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:12189208, ECO:0000269|PubMed:16239304}.		cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCCCAGTCCTGCGTCTGCCCG	0.701													C|||	2688	0.536741	0.3638	0.4827	5008	,	,		13687	0.8482		0.4026	False		,,,				2504	0.6258				p.Q2049E		Atlas-SNP	.											.	.	.	.	0			c.C6145G						PASS	.	C	GLU/GLN,GLU/GLN	1578,2782		289,1000,891	12.0	13.0	13.0		6145,4438	4.1	0.0	20	dbSNP_107	13	3547,5009		773,2001,1504	yes	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	29,29	1062,3001,2395	CC,CG,GG		41.4563,36.1927,39.6795	benign,benign	2049/2650,1480/2081	62194030	5125,7791	2180	4278	6458	SO:0001583	missense	85441	exon9			AGTCCTGCGTCTG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6145C>G	20.37:g.62194030G>C	ENSP00000417401:p.Gln2049Glu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	1146	0.5247252747252747	171	0.3475609756097561	175	0.48342541436464087	487	0.8513986013986014	313	0.4129287598944591	C	0.006	-2.030290	0.00410	0.361927	0.414563	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.78595	-1.19;-1.09	4.11	4.11	0.48088	.	10.299900	0.00678	N	0.000666	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48536	-0.9027	9	0.02654	T	1	-2.6915	13.8267	0.63354	0.0:0.845:0.155:0.0	rs3810483;rs60034780;rs3810483	2049;1480	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	E	1480;2049	ENSP00000393257:Q1480E;ENSP00000417401:Q2049E	ENSP00000393257:Q1480E	Q	-	1	0	RP4-697K14.7	61664474	0.003000	0.15002	0.016000	0.15963	0.023000	0.10783	1.822000	0.39052	0.734000	0.32515	-0.647000	0.03941	CAG	G|0.544;C|0.456	0.456	strong		0.701	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
CARS	833	hgsc.bcm.edu	37	11	3028140	3028140	+	Silent	SNP	G	G	A	rs729662	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:3028140G>A	ENST00000397111.5	-	18	2114	c.1869C>T	c.(1867-1869)ccC>ccT	p.P623P	CARS_ENST00000380525.4_Silent_p.P706P|CARS_ENST00000401769.3_Silent_p.P636P|CARS_ENST00000278224.9_Silent_p.P623P|CARS_ENST00000470221.2_5'UTR|CARS_ENST00000397114.3_Silent_p.P613P			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	623					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)		CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	CCCCAAGCTCGGGCAGGATGT	0.587			T	ALK	ALCL								G|||	1757	0.350839	0.0303	0.4957	5008	,	,		20311	0.6627		0.2922	False		,,,				2504	0.4202				p.P706P	Ovarian(61;932 1157 5961 20446 52152)	Atlas-SNP	.		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	CARS	114	.	0			c.C2118T						PASS	.	G	,,,	333,4071	174.4+/-204.0	12,309,1881	177.0	169.0	172.0		2118,2118,1869,1869	-4.1	1.0	11	dbSNP_86	172	2504,6092	409.7+/-349.9	363,1778,2157	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CARS	NM_001014437.2,NM_001194997.1,NM_001751.5,NM_139273.3	,,,	375,2087,4038	AA,AG,GG		29.1298,7.5613,21.8231	,,,	706/832,706/810,623/749,623/727	3028140	2837,10163	2202	4298	6500	SO:0001819	synonymous_variant	833	exon19			AAGCTCGGGCAGG	AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	1493	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 1, cytoplasmic"""	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.1869C>T	11.37:g.3028140G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Silent	SNP	ENST00000397111.5	37	CCDS7742.1																																																																																			G|0.727;A|0.273	0.273	strong		0.587	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751	
VCAN	1462	hgsc.bcm.edu	37	5	82833391	82833391	+	Silent	SNP	A	A	G	rs16900528	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:82833391A>G	ENST00000265077.3	+	8	5134	c.4569A>G	c.(4567-4569)acA>acG	p.T1523T	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Silent_p.T536T|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1523	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AATCAGTCACAGAGAGAGATA	0.443													A|||	288	0.057508	0.0098	0.036	5008	,	,		21611	0.0685		0.0825	False		,,,				2504	0.1002				p.T1523T		Atlas-SNP	.											.	VCAN	498	.	0			c.A4569G						PASS	.	A	,,,	109,4297	84.8+/-123.5	0,109,2094	77.0	75.0	75.0		,1608,,4569	-3.3	0.0	5	dbSNP_123	75	697,7903	171.4+/-222.4	26,645,3629	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	26,754,5723	GG,GA,AA		8.1047,2.4739,6.1971	,,,	,536/2410,,1523/3397	82833391	806,12200	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			AGTCACAGAGAGA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4569A>G	5.37:g.82833391A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	24	0.347826	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			A|0.942;G|0.058	0.058	strong		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
MUC21	394263	hgsc.bcm.edu	37	6	30954709	30954709	+	Missense_Mutation	SNP	G	G	A	rs11756238	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:30954709G>A	ENST00000376296.3	+	2	998	c.757G>A	c.(757-759)Ggc>Agc	p.G253S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	253	28 X 15 AA approximate tandem repeats.|Ser-rich.		G -> S (in dbSNP:rs41288655). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G253S(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CAGTGGGGCCGGCACAGCCAC	0.637													A|||	193	0.0385383	0.0356	0.062	5008	,	,		20371	0.0208		0.0467	False		,,,				2504	0.0358				p.G253S		Atlas-SNP	.											MUC21,colon,carcinoma,-1,2	MUC21	98	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.G757A						scavenged	.						135.0	138.0	137.0					6																	30954709		2203	4300	6503	SO:0001583	missense	394263	exon2			GGGGCCGGCACAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.757G>A	6.37:g.30954709G>A	ENSP00000365473:p.Gly253Ser	Somatic	187	7	0.0374332		WXS	Illumina HiSeq	Phase_I	219	11	0.0502283	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	1.863	-0.462214	0.04508	.	.	ENSG00000204544	ENST00000376296	T	0.01265	5.08	4.3	1.82	0.25136	.	.	.	.	.	T	0.00210	0.0006	N	0.01576	-0.805	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.18366	-1.0339	8	.	.	.	.	7.3667	0.26776	0.6106:0.0:0.3894:0.0	rs41288655	253	Q5SSG8	MUC21_HUMAN	S	253	ENSP00000365473:G253S	.	G	+	1	0	MUC21	31062688	0.000000	0.05858	0.003000	0.11579	0.041000	0.13682	-0.706000	0.05047	-0.001000	0.14495	-0.490000	0.04691	GGC	G|0.989;A|0.011	0.011	strong		0.637	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
CNTLN	54875	hgsc.bcm.edu	37	9	17135115	17135115	+	Silent	SNP	C	C	T	rs41306071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:17135115C>T	ENST00000380647.3	+	1	136	c.52C>T	c.(52-54)Ctg>Ttg	p.L18L	CNTLN_ENST00000380641.4_Silent_p.L18L|CNTLN_ENST00000484374.1_3'UTR|CNTLN_ENST00000425824.1_Silent_p.L18L|CNTLN_ENST00000262360.5_Silent_p.L18L			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	18					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGCGCGACAGCTGGGCCCCAG	0.697													T|||	658	0.13139	0.0643	0.1484	5008	,	,		14867	0.1548		0.2396	False		,,,				2504	0.0746				p.L18L		Atlas-SNP	.											CNTLN,NS,carcinoma,0,1	CNTLN	128	1	0			c.C52T						PASS	.	T	,	385,3489		26,333,1578	10.0	14.0	13.0		52,52	2.1	0.0	9	dbSNP_127	13	2247,5975		317,1613,2181	no	coding-synonymous,coding-synonymous	CNTLN	NM_001114395.1,NM_017738.2	,	343,1946,3759	TT,TC,CC		27.3291,9.938,21.7593	,	18/392,18/1407	17135115	2632,9464	1937	4111	6048	SO:0001819	synonymous_variant	54875	exon1			CGACAGCTGGGCC	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.52C>T	9.37:g.17135115C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Silent	SNP	ENST00000380647.3	37	CCDS43789.1																																																																																			C|0.819;T|0.181	0.181	strong		0.697	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
KARS	3735	hgsc.bcm.edu	37	16	75675609	75675609	+	Silent	SNP	T	T	C	rs5030748	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:75675609T>C	ENST00000302445.3	-	2	114	c.75A>G	c.(73-75)agA>agG	p.R25R	KARS_ENST00000319410.5_Silent_p.R53R|KARS_ENST00000568378.1_Intron	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase	25					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	CTTTCAGGCGTCTCTTCAGCT	0.473													T|||	149	0.0297524	0.0053	0.0403	5008	,	,		21087	0.0		0.0964	False		,,,				2504	0.0174				p.R53R		Atlas-SNP	.											.	KARS	77	.	0			c.A159G						PASS	.	T	,	114,4282	85.8+/-124.5	1,112,2085	136.0	121.0	126.0		159,75	2.4	1.0	16	dbSNP_113	126	942,7658	206.8+/-248.7	60,822,3418	no	coding-synonymous,coding-synonymous	KARS	NM_001130089.1,NM_005548.2	,	61,934,5503	CC,CT,TT		10.9535,2.5933,8.1256	,	53/626,25/598	75675609	1056,11940	2198	4300	6498	SO:0001819	synonymous_variant	3735	exon3			CAGGCGTCTCTTC	AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"""Aminoacyl tRNA synthetases / Class II"""	6215	protein-coding gene	gene with protein product	"""lysine tRNA ligase"""	601421	"""deafness, autosomal recessive 89"""	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.75A>G	16.37:g.75675609T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_001130089	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Silent	SNP	ENST00000302445.3	37	CCDS10923.1																																																																																			T|0.933;C|0.067	0.067	strong		0.473	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548	
MMRN2	79812	hgsc.bcm.edu	37	10	88702390	88702390	+	Silent	SNP	G	G	A	rs10887673	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:88702390G>A	ENST00000372027.5	-	6	2472	c.2151C>T	c.(2149-2151)gcC>gcT	p.A717A	MMRN2_ENST00000488950.1_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	717					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						CCCCGGCCTCGGCCTCGCAGC	0.731													G|||	1013	0.202276	0.1142	0.2248	5008	,	,		10659	0.0645		0.3002	False		,,,				2504	0.3466				p.A717A		Atlas-SNP	.											.	MMRN2	49	.	0			c.C2151T						PASS	.	G		638,3764		58,522,1621	18.0	17.0	17.0		2151	2.0	0.2	10	dbSNP_120	17	2588,6006		384,1820,2093	no	coding-synonymous	MMRN2	NM_024756.2		442,2342,3714	AA,AG,GG		30.114,14.4934,24.823		717/950	88702390	3226,9770	2201	4297	6498	SO:0001819	synonymous_variant	79812	exon6			GGCCTCGGCCTCG	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.2151C>T	10.37:g.88702390G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	13	9	0.692308	NM_024756	Q504V7|Q6P2N2	Silent	SNP	ENST00000372027.5	37	CCDS7379.1																																																																																			A|0.213;C|0.000;G|0.787	0.213	strong		0.731	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
BCLAF1	9774	hgsc.bcm.edu	37	6	136599912	136599912	+	Missense_Mutation	SNP	G	G	T	rs200334350		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:136599912G>T	ENST00000531224.1	-	4	359	c.107C>A	c.(106-108)tCt>tAt	p.S36Y	BCLAF1_ENST00000527536.1_Missense_Mutation_p.S36Y|BCLAF1_ENST00000527759.1_Intron|BCLAF1_ENST00000530767.1_Missense_Mutation_p.S36Y|BCLAF1_ENST00000392348.2_Intron|BCLAF1_ENST00000353331.4_Intron	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	36					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACGAGACCTAGAACTAAAAAT	0.318																																					p.S36Y	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,head_neck,carcinoma,-1,1	BCLAF1	203	1	0			c.C107A						scavenged	.						23.0	24.0	24.0					6																	136599912		2199	4289	6488	SO:0001583	missense	9774	exon4			GACCTAGAACTAA	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.107C>A	6.37:g.136599912G>T	ENSP00000435210:p.Ser36Tyr	Somatic	29	1	0.0344828		WXS	Illumina HiSeq	Phase_I	20	2	0.1	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	G	5.506	0.278344	0.10403	.	.	ENSG00000029363	ENST00000531224;ENST00000527536;ENST00000530767;ENST00000529826	T;T;T;T	0.46819	1.23;1.07;0.86;0.93	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000004	T	0.63295	0.2499	M	0.61703	1.905	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.74348	0.983;0.983	T	0.64245	-0.6453	10	0.87932	D	0	-6.9024	20.1392	0.98050	0.0:0.0:1.0:0.0	.	36;36	Q9NYF8;Q9NYF8-4	BCLF1_HUMAN;.	Y	36	ENSP00000435210:S36Y;ENSP00000435441:S36Y;ENSP00000436501:S36Y;ENSP00000431734:S36Y	ENSP00000435441:S36Y	S	-	2	0	BCLAF1	136641605	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.159000	0.77483	2.765000	0.95021	0.557000	0.71058	TCT	.	.	weak		0.318	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
ITPR2	3709	hgsc.bcm.edu	37	12	26733062	26733062	+	Silent	SNP	T	T	C	rs2230375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:26733062T>C	ENST00000381340.3	-	33	4823	c.4407A>G	c.(4405-4407)aaA>aaG	p.K1469K		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1469					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TGTCTGCATGTTTCCTGTCTG	0.358													T|||	1001	0.19988	0.0885	0.2305	5008	,	,		18889	0.0764		0.3559	False		,,,				2504	0.2955				p.K1469K		Atlas-SNP	.											.	ITPR2	270	.	0			c.A4407G						PASS	.	T		466,3188		29,408,1390	164.0	146.0	151.0		4407	-8.6	0.4	12	dbSNP_98	151	2793,5383		484,1825,1779	no	coding-synonymous	ITPR2	NM_002223.2		513,2233,3169	CC,CT,TT		34.161,12.7531,27.5486		1469/2702	26733062	3259,8571	1827	4088	5915	SO:0001819	synonymous_variant	3709	exon33			TGCATGTTTCCTG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4407A>G	12.37:g.26733062T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.774;C|0.226	0.226	strong		0.358	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
CEP68	23177	hgsc.bcm.edu	37	2	65296798	65296798	+	Missense_Mutation	SNP	G	G	A	rs7572857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:65296798G>A	ENST00000377990.2	+	2	423	c.220G>A	c.(220-222)Ggc>Agc	p.G74S	RAB1A_ENST00000494188.1_5'Flank|CEP68_ENST00000546106.1_Missense_Mutation_p.G74S|CEP68_ENST00000260569.4_Missense_Mutation_p.G74S|CEP68_ENST00000537589.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	74			G -> S (in dbSNP:rs7572857). {ECO:0000269|PubMed:15489334}.		centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.G74S(1)		breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						TGACCCTGGCGGCCCCTCTAG	0.647													G|||	578	0.115415	0.0076	0.1239	5008	,	,		16521	0.0913		0.171	False		,,,				2504	0.2229				p.G74S		Atlas-SNP	.											CEP68,NS,carcinoma,0,1	CEP68	69	1	1	Substitution - Missense(1)	prostate(1)	c.G220A						scavenged	.	G	SER/GLY	170,4236	105.2+/-143.6	3,164,2036	33.0	38.0	36.0		220	-5.9	0.0	2	dbSNP_116	36	1514,7086	270.2+/-288.9	142,1230,2928	yes	missense	CEP68	NM_015147.2	56	145,1394,4964	AA,AG,GG		17.6047,3.8584,12.9479	benign	74/758	65296798	1684,11322	2203	4300	6503	SO:0001583	missense	23177	exon2			CCTGGCGGCCCCT	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.220G>A	2.37:g.65296798G>A	ENSP00000367229:p.Gly74Ser	Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	244	0.11172161172161173	2	0.0040650406504065045	53	0.1464088397790055	55	0.09615384615384616	134	0.17678100263852242	G	4.206	0.036901	0.08148	0.038584	0.176047	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.19105	2.17;2.17;2.17	3.83	-5.92	0.02261	.	0.556823	0.15431	N	0.262729	T	0.00012	0.0000	N	0.03608	-0.345	0.53005	P	4.0000000000040004E-5	B;B;B;B;B	0.21520	0.057;0.057;0.014;0.003;0.057	B;B;B;B;B	0.14578	0.007;0.004;0.004;0.003;0.011	T	0.32561	-0.9902	9	0.11794	T	0.64	.	4.7843	0.13217	0.5233:0.0:0.1875:0.2891	rs7572857;rs17849706;rs17849872;rs52812658;rs60638735;rs7572857	62;74;74;74;74	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	S	74;74;74;62	ENSP00000367229:G74S;ENSP00000438306:G74S;ENSP00000260569:G74S	ENSP00000260569:G74S	G	+	1	0	CEP68	65150302	0.000000	0.05858	0.003000	0.11579	0.077000	0.17291	-1.258000	0.02863	-1.411000	0.02032	-1.012000	0.02466	GGC	G|0.877;A|0.122	0.122	strong		0.647	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
ADAM29	11086	hgsc.bcm.edu	37	4	175899079	175899079	+	Silent	SNP	C	C	T	rs151310201	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175899079C>T	ENST00000359240.3	+	5	3073	c.2403C>T	c.(2401-2403)ccC>ccT	p.P801P	ADAM29_ENST00000404450.4_Silent_p.P801P|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Silent_p.P801P|ADAM29_ENST00000445694.1_Silent_p.P801P	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	801	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CTGTGACACCCTCCCAGAGGC	0.567																																					p.P801P	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,NS,carcinoma,0,1	ADAM29	262	1	0			c.C2403T						PASS	.						138.0	128.0	131.0					4																	175899079		2203	4300	6503	SO:0001819	synonymous_variant	11086	exon4			GACACCCTCCCAG	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2403C>T	4.37:g.175899079C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	204	64	0.313726	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	37	CCDS3823.1																																																																																			C|0.986;T|0.013	0.013	strong		0.567	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
TECTA	7007	hgsc.bcm.edu	37	11	120998942	120998942	+	Silent	SNP	C	C	T	rs10502247	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:120998942C>T	ENST00000392793.1	+	9	2527	c.2256C>T	c.(2254-2256)atC>atT	p.I752I	TECTA_ENST00000264037.2_Silent_p.I752I			O75443	TECTA_HUMAN	tectorin alpha	752	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		ACTTGGAAATCGACATCAACA	0.602													C|||	1554	0.310304	0.1475	0.2622	5008	,	,		18572	0.4355		0.3022	False		,,,				2504	0.4438				p.I752I		Atlas-SNP	.											.	TECTA	329	.	0			c.C2256T						PASS	.	C		865,3541	337.6+/-304.9	80,705,1418	74.0	77.0	76.0		2256	-1.1	1.0	11	dbSNP_119	76	2482,6116	405.6+/-348.5	357,1768,2174	no	coding-synonymous	TECTA	NM_005422.2		437,2473,3592	TT,TC,CC		28.8672,19.6323,25.7382		752/2156	120998942	3347,9657	2203	4299	6502	SO:0001819	synonymous_variant	7007	exon8			GGAAATCGACATC	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.2256C>T	11.37:g.120998942C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																			C|0.668;T|0.332	0.332	strong		0.602	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
STKLD1	169436	hgsc.bcm.edu	37	9	136268952	136268952	+	Splice_Site	SNP	G	G	T	rs33919837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:136268952G>T	ENST00000371957.3	+	15	1710	c.1603G>T	c.(1603-1605)Ggc>Tgc	p.G535C	C9orf96_ENST00000371955.1_Splice_Site_p.G68C	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		535							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GTCCCTGCTGGGTGAGCTGGG	0.677													G|||	162	0.0323482	0.0045	0.0403	5008	,	,		15964	0.0188		0.0825	False		,,,				2504	0.0266				p.G535C		Atlas-SNP	.											.	C9orf96	77	.	0			c.G1603T						PASS	.	G	CYS/GLY	76,4330	65.8+/-103.3	1,74,2128	32.0	35.0	34.0		1603	4.6	0.9	9	dbSNP_126	34	723,7877	172.7+/-223.4	36,651,3613	yes	missense-near-splice	C9orf96	NM_153710.3	159	37,725,5741	TT,TG,GG		8.407,1.7249,6.1433	probably-damaging	535/681	136268952	799,12207	2203	4300	6503	SO:0001630	splice_region_variant	169436	exon15			CTGCTGGGTGAGC																												ENST00000371957.3:c.1603+1G>T	9.37:g.136268952G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	53	33	0.622642	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	97	0.044413919413919416	3	0.006097560975609756	16	0.04419889502762431	12	0.02097902097902098	66	0.0870712401055409	G	17.20	3.329732	0.60743	0.017249	0.08407	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.51817	0.69;0.72	4.6	4.6	0.57074	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.06050	0.0157	L	0.61218	1.895	0.09310	P	0.99999999878625	D	0.89917	1.0	D	0.91635	0.999	T	0.52726	-0.8537	9	0.87932	D	0	-33.6075	12.7755	0.57445	0.0:0.0:1.0:0.0	rs33919837	535	Q8NE28	SGK71_HUMAN	C	535;68	ENSP00000361025:G535C;ENSP00000361023:G68C	ENSP00000361023:G68C	G	+	1	0	C9orf96	135258773	1.000000	0.71417	0.942000	0.38095	0.418000	0.31294	4.743000	0.62110	2.354000	0.79902	0.561000	0.74099	GGC	G|0.944;T|0.056	0.056	strong		0.677	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		Missense_Mutation
FRMD1	79981	hgsc.bcm.edu	37	6	168464402	168464402	+	Missense_Mutation	SNP	C	C	T	rs73028318	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:168464402C>T	ENST00000283309.6	-	6	747	c.683G>A	c.(682-684)cGg>cAg	p.R228Q	FRMD1_ENST00000440994.2_Missense_Mutation_p.R160Q|FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000537786.1_5'UTR	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	228	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		AGGCATGTGCCGGAGGATGTA	0.662													C|||	26	0.00519169	0.0	0.0014	5008	,	,		19172	0.0		0.0089	False		,,,				2504	0.0164				p.R228Q	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											FRMD1,colon,carcinoma,-1,2	FRMD1	52	2	0			c.G683A						scavenged	.	C	GLN/ARG,GLN/ARG	8,4398	12.9+/-30.5	0,8,2195	104.0	86.0	92.0		479,683	-0.5	0.0	6	dbSNP_130	92	78,8522	45.4+/-104.0	1,76,4223	yes	missense,missense	FRMD1	NM_001122841.1,NM_024919.3	43,43	1,84,6418	TT,TC,CC		0.907,0.1816,0.6612	possibly-damaging,possibly-damaging	160/482,228/550	168464402	86,12920	2203	4300	6503	SO:0001583	missense	79981	exon6			ATGTGCCGGAGGA		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.683G>A	6.37:g.168464402C>T	ENSP00000283309:p.Arg228Gln	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	194	72	0.371134	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	4.333	0.061111	0.08339	0.001816	0.00907	ENSG00000153303	ENST00000283309;ENST00000440994	T;T	0.76316	-1.01;-1.01	2.83	-0.459	0.12179	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.506221	0.18349	N	0.143925	T	0.39306	0.1073	L	0.27053	0.805	0.80722	D	1	P;B;B	0.35959	0.53;0.178;0.085	B;B;B	0.25405	0.06;0.037;0.022	T	0.19160	-1.0314	10	0.46703	T	0.11	.	6.3332	0.21282	0.0:0.2703:0.0:0.7297	.	140;228;160	B7Z8G9;Q8N878;Q8N878-2	.;FRMD1_HUMAN;.	Q	228;160	ENSP00000283309:R228Q;ENSP00000414115:R160Q	ENSP00000283309:R228Q	R	-	2	0	FRMD1	168207251	0.542000	0.26426	0.004000	0.12327	0.062000	0.15995	1.103000	0.31062	0.011000	0.14865	-1.872000	0.00552	CGG	C|0.995;T|0.005	0.005	strong		0.662	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
RXRG	6258	hgsc.bcm.edu	37	1	165389129	165389129	+	Silent	SNP	G	G	A	rs1128977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:165389129G>A	ENST00000359842.5	-	3	722	c.420C>T	c.(418-420)gcC>gcT	p.A140A	RXRG_ENST00000470566.1_5'UTR	NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	140					gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	CTCCACAGATGGCACAGATGT	0.527													G|||	1139	0.227436	0.0719	0.2637	5008	,	,		17790	0.122		0.3996	False		,,,				2504	0.3436				p.A140A		Atlas-SNP	.											.	RXRG	91	.	0			c.C420T						PASS	.	G		537,3869	242.5+/-252.5	33,471,1699	143.0	131.0	135.0		420	4.3	1.0	1	dbSNP_86	135	3324,5276	495.8+/-374.1	646,2032,1622	no	coding-synonymous	RXRG	NM_006917.4		679,2503,3321	AA,AG,GG		38.6512,12.1879,29.6863		140/464	165389129	3861,9145	2203	4300	6503	SO:0001819	synonymous_variant	6258	exon3			ACAGATGGCACAG	U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"""Nuclear hormone receptors"""	10479	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 3"""	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.420C>T	1.37:g.165389129G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_006917	A6NIP1|Q6IBU7	Silent	SNP	ENST00000359842.5	37	CCDS1248.1																																																																																			G|0.737;A|0.263	0.263	strong		0.527	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917	
ESRP1	54845	hgsc.bcm.edu	37	8	95655596	95655596	+	Silent	SNP	T	T	C	rs72676907	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:95655596T>C	ENST00000433389.2	+	3	517	c.327T>C	c.(325-327)gaT>gaC	p.D109D	ESRP1_ENST00000454170.2_Silent_p.D109D|ESRP1_ENST00000423620.2_Silent_p.D109D|ESRP1_ENST00000358397.5_Silent_p.D109D	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	109					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						TCTGTACTGATGGGCAGCTTC	0.468													T|||	323	0.0644968	0.0053	0.0735	5008	,	,		19201	0.002		0.1968	False		,,,				2504	0.0665				p.D109D		Atlas-SNP	.											.	ESRP1	148	.	0			c.T327C						PASS	.	T	,,,,	127,3771		4,119,1826	110.0	106.0	107.0		327,327,327,327,327	-2.6	0.9	8	dbSNP_130	107	1501,6773		135,1231,2771	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	139,1350,4597	CC,CT,TT		18.1412,3.2581,13.375	,,,,	109/678,109/609,109/660,109/605,109/682	95655596	1628,10544	1949	4137	6086	SO:0001819	synonymous_variant	54845	exon3			TACTGATGGGCAG	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.327T>C	8.37:g.95655596T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	186	79	0.424731	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1																																																																																			T|0.887;C|0.113	0.113	strong		0.468	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
GLB1	2720	hgsc.bcm.edu	37	3	33055688	33055688	+	Missense_Mutation	SNP	T	T	C	rs73826339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:33055688T>C	ENST00000399402.3	-	15	1635	c.1504A>G	c.(1504-1506)Agt>Ggt	p.S502G	GLB1_ENST00000307377.8_Missense_Mutation_p.S401G|GLB1_ENST00000445488.2_Missense_Mutation_p.S580G|GLB1_ENST00000497796.1_5'UTR|GLB1_ENST00000307363.5_Missense_Mutation_p.S532G	NM_001079811.1	NP_001073279	P16278	BGAL_HUMAN	galactosidase, beta 1	532					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)	beta-galactosidase activity (GO:0004565)|galactoside binding (GO:0016936)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	21		Melanoma(143;0.104)				TGGTGGCCACTGTCACGGTGT	0.567													T|||	175	0.0349441	0.0272	0.0648	5008	,	,		17930	0.0		0.0785	False		,,,				2504	0.0153				p.S532G		Atlas-SNP	.											.	GLB1	51	.	0			c.A1594G	GRCh37	CM074252	GLB1	M	rs73826339	PASS	.	T	GLY/SER,GLY/SER,GLY/SER	133,3891		2,129,1881	89.0	97.0	94.0		1594,1504,1201	-6.7	0.0	3	dbSNP_130	94	504,7804		12,480,3662	yes	missense,missense,missense	GLB1	NM_000404.2,NM_001079811.1,NM_001135602.1	56,56,56	14,609,5543	CC,CT,TT		6.0664,3.3052,5.1654	benign,benign,benign	532/678,502/648,401/547	33055688	637,11695	2012	4154	6166	SO:0001583	missense	2720	exon15			GGCCACTGTCACG	M22590	CCDS43061.1, CCDS43062.1, CCDS46785.1	3p22.3	2012-10-02			ENSG00000170266	ENSG00000170266	3.2.1.23		4298	protein-coding gene	gene with protein product		611458	"""elastin receptor 1, 67kDa"", ""elastin receptor 1 (67kD)"""	ELNR1		110522, 3143362	Standard	NM_000404		Approved	EBP	uc003cfi.1	P16278	OTTHUMG00000155781	ENST00000399402.3:c.1504A>G	3.37:g.33055688T>C	ENSP00000382333:p.Ser502Gly	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	209	65	0.311005	NM_000404	B2R7H8|B7Z6B0|P16279	Missense_Mutation	SNP	ENST00000399402.3	37	CCDS43062.1	98	0.04487179487179487	15	0.03048780487804878	24	0.06629834254143646	0	0.0	59	0.07783641160949868	T	8.306	0.821051	0.16678	0.033052	0.060664	ENSG00000170266	ENST00000399402;ENST00000307363;ENST00000445488;ENST00000307377	D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45	5.11	-6.69	0.01772	Galactose-binding domain-like (1);	1.718320	0.02308	N	0.071806	T	0.28267	0.0698	N	0.04959	-0.14	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.0;0.001;0.001	B;B;B;B	0.06405	0.002;0.0;0.002;0.001	T	0.69756	-0.5059	9	0.22706	T	0.39	3.9938	6.8315	0.23913	0.0:0.2033:0.3264:0.4703	.	532;401;532;580	Q53G40;E7EQ29;P16278;B7Z6Q5	.;.;BGAL_HUMAN;.	G	502;532;580;401	ENSP00000382333:S502G;ENSP00000306920:S532G;ENSP00000393377:S580G;ENSP00000305920:S401G	ENSP00000306920:S532G	S	-	1	0	GLB1	33030692	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.443000	0.06862	-1.223000	0.02584	-0.248000	0.11899	AGT	A|0.000;C|0.056;T|0.944	0.056	strong		0.567	GLB1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341570.2	NM_000404	
MUC16	94025	hgsc.bcm.edu	37	19	9076163	9076163	+	Silent	SNP	C	C	T	rs2547073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9076163C>T	ENST00000397910.4	-	3	11486	c.11283G>A	c.(11281-11283)caG>caA	p.Q3761Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3762	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAGTGAGTTCCTGGGGAGTTG	0.527													T|||	1243	0.248203	0.2005	0.2118	5008	,	,		21334	0.249		0.3121	False		,,,				2504	0.272				p.Q3761Q		Atlas-SNP	.											.	MUC16	4315	.	0			c.G11283A						PASS	.	T		849,3241		97,655,1293	123.0	123.0	123.0		11283	0.9	0.0	19	dbSNP_100	123	2418,5966		346,1726,2120	no	coding-synonymous	MUC16	NM_024690.2		443,2381,3413	TT,TC,CC		28.8406,20.7579,26.1905		3761/14508	9076163	3267,9207	2045	4192	6237	SO:0001819	synonymous_variant	94025	exon3			GAGTTCCTGGGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.11283G>A	19.37:g.9076163C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	228	108	0.473684	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.745;T|0.255	0.255	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GPR125	166647	hgsc.bcm.edu	37	4	22439914	22439914	+	Silent	SNP	A	A	C	rs6823735	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:22439914A>C	ENST00000334304.5	-	8	1319	c.1050T>G	c.(1048-1050)ccT>ccG	p.P350P	GPR125_ENST00000508133.1_Silent_p.P124P|GPR125_ENST00000502482.1_Silent_p.P350P|GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	350					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				CCCTCTCTGGAGGACAGTACT	0.443													A|||	2752	0.549521	0.2632	0.6427	5008	,	,		17272	0.6151		0.7515	False		,,,				2504	0.5951				p.P350P		Atlas-SNP	.											GPR125,colon,carcinoma,-1,2	GPR125	118	2	0			c.T1050G						PASS	.	A		1532,2874	486.2+/-360.5	248,1036,919	163.0	143.0	150.0		1050	-4.0	0.8	4	dbSNP_116	150	6324,2276	707.0+/-405.6	2335,1654,311	no	coding-synonymous	GPR125	NM_145290.2		2583,2690,1230	CC,CA,AA		26.4651,34.7708,39.5971		350/1322	22439914	7856,5150	2203	4300	6503	SO:0001819	synonymous_variant	166647	exon8			CTCTGGAGGACAG	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.1050T>G	4.37:g.22439914A>C		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	268	143	0.533582	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	37	CCDS33964.1																																																																																			A|0.388;C|0.612	0.612	strong		0.443	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3		
PCDHB7	56129	hgsc.bcm.edu	37	5	140554481	140554481	+	Missense_Mutation	SNP	G	G	T	rs1811237	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140554481G>T	ENST00000231137.3	+	1	2239	c.2065G>T	c.(2065-2067)Gtg>Ttg	p.V689L	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	689					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGTCTACCTGGTGGTGGCGTT	0.711													G|||	1672	0.333866	0.2504	0.3516	5008	,	,		22188	0.5278		0.2465	False		,,,				2504	0.3241				p.V689L		Atlas-SNP	.											PCDHB7,NS,carcinoma,0,1	PCDHB7	231	1	0			c.G2065T						PASS	.	G	LEU/VAL	958,3440		139,680,1380	63.0	100.0	87.0		2065	2.9	0.5	5	dbSNP_92	87	1772,6820		228,1316,2752	no	missense	PCDHB7	NM_018940.2	32	367,1996,4132	TT,TG,GG		20.6238,21.7826,21.0162	probably-damaging	689/794	140554481	2730,10260	2199	4296	6495	SO:0001583	missense	56129	exon1			TACCTGGTGGTGG	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2065G>T	5.37:g.140554481G>T	ENSP00000231137:p.Val689Leu	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	159	60	0.377358	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	704	0.32234432234432236	117	0.23780487804878048	106	0.292817679558011	301	0.5262237762237763	180	0.23746701846965698	G	21.8	4.203707	0.79127	0.217826	0.206238	ENSG00000113212	ENST00000231137	T	0.46819	0.86	3.77	2.86	0.33363	.	.	.	.	.	T	0.00012	0.0000	H	0.97682	4.055	0.32646	P	0.520018	D	0.76494	0.999	D	0.85130	0.997	T	0.45702	-0.9243	8	0.87932	D	0	.	7.7855	0.29089	0.2703:0.0:0.7297:0.0	rs62378900	689	Q9Y5E2	PCDB7_HUMAN	L	689	ENSP00000231137:V689L	ENSP00000231137:V689L	V	+	1	0	PCDHB7	140534665	1.000000	0.71417	0.546000	0.28166	0.957000	0.61999	1.707000	0.37888	1.808000	0.52836	0.449000	0.29647	GTG	G|0.758;T|0.242	0.242	strong		0.711	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204399064	204399064	+	Silent	SNP	G	G	A	rs2271420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204399064G>A	ENST00000367187.3	-	30	4939	c.4383C>T	c.(4381-4383)ccC>ccT	p.P1461P	PIK3C2B_ENST00000424712.2_Silent_p.P1433P|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1461	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CCACCTCAGGGGGTGCGTGGA	0.667													G|||	690	0.13778	0.2784	0.1037	5008	,	,		16736	0.0774		0.1113	False		,,,				2504	0.0613				p.P1461P		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C4383T						PASS	.	G		117,4289		49,19,2135	88.0	78.0	81.0		4383	1.9	1.0	1	dbSNP_100	81	33,8567		10,13,4277	no	coding-synonymous	PIK3C2B	NM_002646.3		59,32,6412	AA,AG,GG		0.3837,2.6555,1.1533		1461/1635	204399064	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon30			CTCAGGGGGTGCG	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4383C>T	1.37:g.204399064G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	54	15	0.277778	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			G|0.866;A|0.134	0.134	strong		0.667	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
